[vistrails] 01/06: 2.1.1 upstream
Alastair McKinstry
mckinstry at moszumanska.debian.org
Mon Jun 8 14:37:02 UTC 2015
This is an automated email from the git hooks/post-receive script.
mckinstry pushed a commit to branch master
in repository vistrails.
commit 395f559afbceba550813e58565b12f2fa2a81204
Author: Alastair McKinstry <mckinstry at debian.org>
Date: Mon Jun 8 14:03:01 2015 +0100
2.1.1 upstream
---
LICENSE | 27 +
README.md | 10 +
RELEASE | 2128 +
contrib/NumSciPy/Array.py | 250 +
contrib/NumSciPy/ArrayAccess.py | 342 +
contrib/NumSciPy/ArrayConvert.py | 151 +
contrib/NumSciPy/ArrayIO.py | 364 +
contrib/NumSciPy/ArrayInterpolate.py | 152 +
contrib/NumSciPy/ArrayOperations.py | 632 +
contrib/NumSciPy/ArrayPlot.py | 638 +
contrib/NumSciPy/ArrayUtilities.py | 254 +
contrib/NumSciPy/DSP.py | 369 +
contrib/NumSciPy/EnsembleOrdering.py | 297 +
contrib/NumSciPy/Filters.py | 185 +
contrib/NumSciPy/Imaging.py | 193 +
contrib/NumSciPy/Matrix.py | 107 +
contrib/NumSciPy/MatrixUtilities.py | 93 +
contrib/NumSciPy/Stockwell.py | 763 +
contrib/NumSciPy/__init__.py | 276 +
contrib/NumSciPy/smt.py | 40 +
contrib/ParaView/PVBase.py | 53 +
contrib/ParaView/__init__.py | 22 +
contrib/ParaView/configuration.py | 7 +
contrib/ParaView/contour.vt | Bin 0 -> 463580 bytes
contrib/ParaView/init.py | 185 +
contrib/ParaView/pv.vt | Bin 0 -> 30902 bytes
contrib/ParaView/pvcell.py | 83 +
contrib/ParaView/pvconfig.py | 89 +
contrib/SCIRun/__init__.py | 9001 ++
contrib/SCIRun/cm2viewcell.py | 285 +
contrib/SCIRun/renderbase.py | 10 +
contrib/SCIRun/viewercell.py | 289 +
contrib/SciPy/DSP.py | 150 +
contrib/SciPy/Filters.py | 118 +
contrib/SciPy/MatlabReader.py | 51 +
contrib/SciPy/Matrix.py | 121 +
contrib/SciPy/MatrixConvert.py | 150 +
contrib/SciPy/MatrixInfo.py | 45 +
contrib/SciPy/MatrixOperations.py | 139 +
contrib/SciPy/SciPy.py | 36 +
contrib/SciPy/__init__.py | 226 +
contrib/TetGenBridge/CreateTestSurf.py | 102 +
contrib/TetGenBridge/Makefile | 19 +
contrib/TetGenBridge/TetGen.py | 313 +
contrib/TetGenBridge/__init__.py | 90 +
contrib/TetGenBridge/pill.nodes | 150 +
contrib/TetGenBridge/pill.tri | 295 +
contrib/TetGenBridge/tetgen.i | 284 +
contrib/cdat/NOTES | 17 +
contrib/cdat/__init__.py | 10094 ++
contrib/cdat/cdat.sip | 36 +
contrib/cdat/cdat.vt | Bin 0 -> 2948 bytes
contrib/cdat/cdat_cell.py | 291 +
contrib/cdat/cdat_window.py | 2356 +
contrib/cdat/configure.py | 72 +
contrib/cdat/graphics_method_controller.py | 1624 +
contrib/cdat/gui_controller.py | 350 +
contrib/cdat/pyqtscripting.sbf | 3 +
contrib/cdat/quickplot.py | 50 +
contrib/cdat/scripts/cdat_domain.py | 289 +
contrib/cdat/scripts/cdatwindow_init_inc.py | 85 +
contrib/cdat/scripts/gen_init.py | 267 +
contrib/cdat/scripts/init_inc.py | 49 +
contrib/cdat/scripts/old_cdat_init.py | 447 +
contrib/cdat/scripts/parse_cdat_xml_file.py | 165 +
contrib/cdat/scripts/xml/canvas.xml | 2747 +
contrib/cdat/scripts/xml/cdms2.xml | 26 +
contrib/cdat/scripts/xml/cdmsFile.xml | 23 +
contrib/edu_utah_sci_cscheid_macet/MANIFEST | 1 +
contrib/edu_utah_sci_cscheid_macet/__init__.py | 125 +
contrib/edu_utah_sci_cscheid_metro/MANIFEST | 2 +
contrib/edu_utah_sci_cscheid_metro/__init__.py | 158 +
contrib/edu_utah_sci_cscheid_teem/__init__.py | 909 +
contrib/edu_utah_sci_cscheid_teem/examples.vt | Bin 0 -> 52295 bytes
.../edu_utah_sci_eranders_proteindatabank/PDB.py | 144 +
.../__init__.py | 68 +
contrib/edu_utah_sci_vgc_afront/MANIFEST | 1 +
contrib/edu_utah_sci_vgc_afront/__init__.py | 143 +
contrib/itk/FeatureExtractionFilters.py | 208 +
contrib/itk/GradientFilters.py | 84 +
contrib/itk/ITK.py | 166 +
contrib/itk/Image.py | 64 +
contrib/itk/ImageReader.py | 169 +
contrib/itk/IntensityFilters.py | 343 +
contrib/itk/NeighborhoodFilters.py | 210 +
contrib/itk/PixelType.py | 71 +
contrib/itk/SegmentationFilters.py | 319 +
contrib/itk/SelectionFilters.py | 231 +
contrib/itk/SmoothingFilters.py | 558 +
contrib/itk/ThresholdFilters.py | 110 +
contrib/itk/__init__.py | 179 +
contrib/itk/filter_generator.py | 170 +
contrib/itk/itk_test_example.py | 42 +
contrib/meshutils.py | 104 +
contrib/mobile/__init__.py | 365 +
contrib/pc3/__init__.py | 420 +
contrib/pc3/info/__init__.py | 1 +
contrib/pc3/info/ipaw/__init__.py | 1 +
contrib/pc3/info/ipaw/pc3/LoadAppLogic.py | 441 +
contrib/pc3/info/ipaw/pc3/LoadConstants.py | 19 +
contrib/pc3/info/ipaw/pc3/LoadSql.py | 147 +
contrib/pc3/info/ipaw/pc3/LoadWorkflow.py | 112 +
contrib/pc3/info/ipaw/pc3/__init__.py | 1 +
contrib/pc3/workflow.vt | Bin 0 -> 8944 bytes
contrib/pc3/workflow_ifs.vt | Bin 0 -> 23612 bytes
contrib/pc3/workflow_log.xml | 74 +
contrib/pc3/workflow_log_err.xml | 49 +
contrib/pc3/workflow_opm.xml | 1379 +
contrib/pc3/workflow_opm_err.xml | 756 +
contrib/pc3/workflow_reg.xml | 330 +
contrib/pc3/workflow_vt.xml | 1153 +
contrib/pc3/workflow_wf.xml | 169 +
contrib/poissonrecon.py | 101 +
contrib/provenance/__init__.py | 274 +
contrib/provenance2/__init__.py | 366 +
contrib/sahm/ColorBreaks.csv | 18 +
contrib/sahm/Images/BinMap.png | Bin 0 -> 2627 bytes
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contrib/sahm/Images/icons.pptx | Bin 0 -> 79659 bytes
contrib/sahm/SahmOutputViewer.py | 494 +
contrib/sahm/SahmSpatialOutputViewer.py | 483 +
contrib/sahm/SahmSpatialViewerCell.py | 89 +
contrib/sahm/SahmViewerCell.py | 72 +
contrib/sahm/SelectPredictorsLayers.py | 428 +
contrib/sahm/__init__.py | 14 +
contrib/sahm/enum_modules.py | 11 +
contrib/sahm/enum_widget.py | 44 +
contrib/sahm/init.py | 1788 +
contrib/sahm/layers.csv | 820 +
contrib/sahm/layers.exampledata.csv | 6 +
contrib/sahm/maxent.csv | 33 +
contrib/sahm/pySAHM/FieldDataQuery.py | 385 +
contrib/sahm/pySAHM/MDSBuilder.py | 473 +
contrib/sahm/pySAHM/MaxentRunner.py | 319 +
contrib/sahm/pySAHM/PARC.py | 776 +
contrib/sahm/pySAHM/RasterFormatConverter.py | 204 +
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.../sahm/pySAHM/Resources/R_Modules/AppendOut.r | 170 +
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.../sahm/pySAHM/Resources/R_Modules/EvalStats.r | 25 +
.../Resources/R_Modules/EvalStatsHelperFcts.r | 122 +
.../pySAHM/Resources/R_Modules/EvaluationStats.r | 436 +
.../pySAHM/Resources/R_Modules/FIT_BRT_pluggable.r | 2505 +
.../pySAHM/Resources/R_Modules/FIT_GLM_pluggable.r | 775 +
.../Resources/R_Modules/FIT_MARS_pluggable.r | 1697 +
.../pySAHM/Resources/R_Modules/FIT_RF_pluggable.r | 649 +
.../sahm/pySAHM/Resources/R_Modules/FunctionCall.r | 87 +
.../pySAHM/Resources/R_Modules/LoadRequiredCode.r | 16 +
.../sahm/pySAHM/Resources/R_Modules/PairsExplore.r | 435 +
.../pySAHM/Resources/R_Modules/PairsExplore2.r | 430 +
.../sahm/pySAHM/Resources/R_Modules/Pred.Surface.r | 54 +
.../sahm/pySAHM/Resources/R_Modules/PredictModel.r | 331 +
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.../pySAHM/Resources/R_Modules/TestTrainRocPlot.r | 372 +
.../pySAHM/Resources/R_Modules/TestTrainSplit.r | 188 +
.../Resources/R_Modules/Testing/CallPairsPlot.r | 114 +
.../pySAHM/Resources/R_Modules/Testing/Debugging.r | 173 +
.../pySAHM/Resources/R_Modules/Testing/Dickessel.r | 231 +
.../Resources/R_Modules/Testing/QuickDebug.r | 75 +
.../R_Modules/Testing/RunTestTrainSplit.r | 171 +
.../pySAHM/Resources/R_Modules/Testing/RunTests.r | 173 +
.../Resources/R_Modules/Testing/SyntheticData.r | 78 +
.../R_Modules/Testing/TestCountModelRuns.r | 186 +
.../Resources/R_Modules/Testing/TestFunction2.r | 23 +
.../R_Modules/Testing/TestModelRuns (2).r | 148 +
.../Resources/R_Modules/Testing/TestModelRuns.r | 174 +
.../R_Modules/Testing/TestingRandomForest.r | 17 +
.../pySAHM/Resources/R_Modules/Testing/unit.test.r | 49 +
.../sahm/pySAHM/Resources/R_Modules/check.libs.r | 16 +
contrib/sahm/pySAHM/Resources/R_Modules/make.auc.r | 136 +
.../sahm/pySAHM/Resources/R_Modules/modalDialog.R | 46 +
.../sahm/pySAHM/Resources/R_Modules/proc.tiff.r | 212 +
contrib/sahm/pySAHM/Resources/R_Modules/read.ma.r | 209 +
.../sahm/pySAHM/Resources/R_Modules/read.maNew.r | 224 +
.../pySAHM/Resources/R_Modules/tmp_ThrowsError.r | 1 +
contrib/sahm/pySAHM/__init__.py | 0
contrib/sahm/pySAHM/singlePARC.py | 71 +
contrib/sahm/pySAHM/singleRasterFormatConverter.py | 73 +
contrib/sahm/pySAHM/utilities.py | 261 +
contrib/sahm/utils.py | 481 +
contrib/sahm/widgets.py | 369 +
contrib/stem/__init__.py | 6 +
contrib/stem/code/STEM_Globals.R | 236 +
contrib/stem/code/STEM_Globals.R.bkup | 236 +
contrib/stem/code/STEM_ModelFitting.R | 201 +
contrib/stem/code/STEM_erd.srd.data.subsetting.R | 273 +
contrib/stem/code/STEM_st.matrix.cv.average.R | 95 +
contrib/stem/code/predict.eBird.ST.matrix.R | 200 +
contrib/stem/code/stem.library.A.R | 2088 +
contrib/stem/code/stem.library.B.R | 2124 +
contrib/stem/code/stem.library.ST.R | 2430 +
contrib/stem/current.vt | Bin 0 -> 83005 bytes
contrib/stem/init.py | 646 +
contrib/stem/mycurrent.vt | Bin 0 -> 2882381 bytes
contrib/stem/mycurrent2.vt | Bin 0 -> 964975 bytes
contrib/titan/__init__.py | 59 +
contrib/titan/base_module.py | 203 +
contrib/titan/class_tree.py | 268 +
contrib/titan/fix_classes.py | 51 +
contrib/titan/hasher.py | 36 +
contrib/titan/init.py | 1132 +
contrib/titan/inspectors.py | 232 +
contrib/titan/offscreen.py | 62 +
contrib/titan/tf_widget.py | 575 +
contrib/titan/vtk_parser.py | 528 +
contrib/titan/vtkcell.py | 1094 +
contrib/titan/vtkcell_rc.py | 793 +
contrib/titan/vtkhandler.py | 292 +
contrib/titan/vtkviewcell.py | 1032 +
contrib/trimesh2.py | 123 +
contrib/vtksnl/__init__.py | 53 +
contrib/vtksnl/base_module.py | 203 +
contrib/vtksnl/class_tree.py | 268 +
contrib/vtksnl/fix_classes.py | 51 +
contrib/vtksnl/hasher.py | 36 +
contrib/vtksnl/init.py | 1073 +
contrib/vtksnl/inspectors.py | 231 +
contrib/vtksnl/offscreen.py | 62 +
contrib/vtksnl/tf_widget.py | 575 +
contrib/vtksnl/vtk_parser.py | 514 +
contrib/vtksnl/vtkcell.py | 1094 +
contrib/vtksnl/vtkcell_rc.py | 793 +
contrib/vtksnl/vtkhandler.py | 291 +
contrib/vtksnl/vtkviewcell.py | 1032 +
data/1n25.pdb | 6334 +
data/carotid.vtk | 111734 ++++++++++++++++++
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data/gktbhL123.vtk | Bin 0 -> 864137 bytes
data/head.120.vtk | 91541 ++++++++++++++
data/pdb.pdb | 3025 +
data/spx.vtk | 31678 +++++
data/torus.vtk | 22046 ++++
data/vslice_circ1.bp | 102 +
doc/coding_conventions.txt | 149 +
doc/custom_constants.txt | 118 +
doc/dist/build_from_source_mac.txt | 62 +
doc/dist/build_from_source_windows.txt | 123 +
doc/dist/instructions.txt | 188 +
doc/dist/setup_build_system_mac.txt | 55 +
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doc/module_registry.txt | 14 +
doc/package_system.txt | 99 +
doc/parameter_exploration.txt | 57 +
doc/pep-0008.txt | 1009 +
doc/pep-0257.txt | 328 +
doc/signal_mess.txt | 49 +
doc/source_tree_overview.tex | 102 +
doc/usersguide/Makefile | 89 +
doc/usersguide/_static/mystyle.css | 5 +
doc/usersguide/analogies.rst | 142 +
doc/usersguide/batch.rst | 381 +
doc/usersguide/cfassistant.rst | 145 +
doc/usersguide/cltools.rst | 264 +
doc/usersguide/conf.py | 208 +
doc/usersguide/controlflow.rst | 593 +
doc/usersguide/controlflowdev.rst | 197 +
doc/usersguide/creating.rst | 331 +
doc/usersguide/database.rst | 176 +
doc/usersguide/developer.rst | 16 +
doc/usersguide/example.rst | 58 +
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doc/usersguide/example_itk.rst | 293 +
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vistrails/core/vistrail/abstraction.py | 198 +
vistrails/core/vistrail/action.py | 280 +
vistrails/core/vistrail/action_annotation.py | 144 +
vistrails/core/vistrail/annotation.py | 136 +
vistrails/core/vistrail/connection.py | 408 +
vistrails/core/vistrail/controller.py | 3891 +
vistrails/core/vistrail/group.py | 344 +
vistrails/core/vistrail/location.py | 199 +
vistrails/core/vistrail/module.py | 526 +
vistrails/core/vistrail/module_function.py | 300 +
vistrails/core/vistrail/module_param.py | 403 +
vistrails/core/vistrail/operation.py | 413 +
vistrails/core/vistrail/pipeline.py | 1698 +
vistrails/core/vistrail/plugin_data.py | 101 +
vistrails/core/vistrail/port.py | 303 +
vistrails/core/vistrail/port_spec.py | 522 +
vistrails/core/vistrail/port_spec_item.py | 219 +
vistrails/core/vistrail/tag.py | 121 +
vistrails/core/vistrail/vistrail.py | 1382 +
vistrails/core/vistrail/vistrailvariable.py | 135 +
vistrails/db/__init__.py | 45 +
vistrails/db/bin/README | 27 +
vistrails/db/bin/__init__.py | 36 +
vistrails/db/bin/auto_gen_objects.py | 417 +
vistrails/db/bin/generate.py | 382 +
vistrails/db/bin/parser.py | 130 +
vistrails/db/bin/sql_gen_objects.py | 242 +
vistrails/db/bin/templates/domain.py.mako | 504 +
vistrails/db/bin/templates/sql.py.mako | 306 +
vistrails/db/bin/templates/sql_delete.sql.mako | 42 +
vistrails/db/bin/templates/sql_schema.sql.mako | 77 +
vistrails/db/bin/templates/xml.py.mako | 228 +
vistrails/db/bin/templates/xml_schema.xsd.mako | 103 +
vistrails/db/bin/xml_gen_objects.py | 208 +
vistrails/db/domain/__init__.py | 35 +
vistrails/db/persistence/__init__.py | 35 +
vistrails/db/services/__init__.py | 36 +
vistrails/db/services/abstraction.py | 57 +
vistrails/db/services/action.py | 174 +
vistrails/db/services/action_chain.py | 128 +
vistrails/db/services/io.py | 1905 +
vistrails/db/services/locator.py | 1235 +
vistrails/db/services/log.py | 45 +
vistrails/db/services/opm.py | 780 +
vistrails/db/services/prov.py | 585 +
vistrails/db/services/query.py | 262 +
vistrails/db/services/registry.py | 48 +
vistrails/db/services/vistrail.py | 1354 +
vistrails/db/services/workflow.py | 42 +
vistrails/db/specs/all.xml | 3823 +
vistrails/db/tests/__init__.py | 35 +
vistrails/db/tests/setup_db_tables.py | 65 +
vistrails/db/tests/sql_to_xml.py | 69 +
vistrails/db/tests/xml_to_sql.py | 69 +
vistrails/db/versions/__init__.py | 165 +
vistrails/db/versions/v0_3_0/__init__.py | 36 +
vistrails/db/versions/v0_3_0/domain/__init__.py | 36 +
vistrails/db/versions/v0_3_0/domain/auto_gen.py | 876 +
.../db/versions/v0_3_0/persistence/__init__.py | 53 +
.../db/versions/v0_3_0/persistence/xml/__init__.py | 36 +
.../db/versions/v0_3_0/persistence/xml/auto_gen.py | 638 +
vistrails/db/versions/v0_3_0/persistence/xml/io.py | 95 +
.../db/versions/v0_3_0/persistence/xml/xml_dao.py | 77 +
.../db/versions/v0_3_0/schemas/xml/vistrail.xsd | 161 +
vistrails/db/versions/v0_3_0/specs/action.xml | 101 +
.../db/versions/v0_3_0/specs/addConnection.xml | 68 +
vistrails/db/versions/v0_3_0/specs/addModule.xml | 60 +
.../db/versions/v0_3_0/specs/addModulePort.xml | 56 +
.../db/versions/v0_3_0/specs/changeAnnotation.xml | 52 +
.../db/versions/v0_3_0/specs/changeParameter.xml | 72 +
.../db/versions/v0_3_0/specs/deleteAnnotation.xml | 48 +
.../db/versions/v0_3_0/specs/deleteConnection.xml | 44 +
.../db/versions/v0_3_0/specs/deleteFunction.xml | 48 +
.../db/versions/v0_3_0/specs/deleteModule.xml | 44 +
.../db/versions/v0_3_0/specs/deleteModulePort.xml | 52 +
vistrails/db/versions/v0_3_0/specs/moveModule.xml | 52 +
vistrails/db/versions/v0_3_0/specs/tag.xml | 48 +
vistrails/db/versions/v0_3_0/specs/vistrail.xml | 52 +
vistrails/db/versions/v0_3_1/__init__.py | 36 +
vistrails/db/versions/v0_3_1/domain/__init__.py | 35 +
.../db/versions/v0_3_1/persistence/__init__.py | 35 +
.../db/versions/v0_3_1/schemas/xml/vistrail.xsd | 161 +
vistrails/db/versions/v0_3_1/specs/action.xml | 101 +
.../db/versions/v0_3_1/specs/addConnection.xml | 68 +
vistrails/db/versions/v0_3_1/specs/addModule.xml | 60 +
.../db/versions/v0_3_1/specs/addModulePort.xml | 56 +
.../db/versions/v0_3_1/specs/changeAnnotation.xml | 52 +
.../db/versions/v0_3_1/specs/changeParameter.xml | 72 +
.../db/versions/v0_3_1/specs/deleteAnnotation.xml | 48 +
.../db/versions/v0_3_1/specs/deleteConnection.xml | 44 +
.../db/versions/v0_3_1/specs/deleteFunction.xml | 48 +
.../db/versions/v0_3_1/specs/deleteModule.xml | 44 +
.../db/versions/v0_3_1/specs/deleteModulePort.xml | 52 +
vistrails/db/versions/v0_3_1/specs/moveModule.xml | 52 +
vistrails/db/versions/v0_3_1/specs/tag.xml | 48 +
vistrails/db/versions/v0_3_1/specs/vistrail.xml | 52 +
vistrails/db/versions/v0_3_1/translate/__init__.py | 36 +
vistrails/db/versions/v0_3_1/translate/v0_3_0.py | 47 +
vistrails/db/versions/v0_5_0/__init__.py | 36 +
vistrails/db/versions/v0_5_0/domain/__init__.py | 38 +
vistrails/db/versions/v0_5_0/domain/auto_gen.py | 2696 +
vistrails/db/versions/v0_5_0/domain/id_scope.py | 65 +
vistrails/db/versions/v0_5_0/domain/vistrail.py | 43 +
vistrails/db/versions/v0_5_0/domain/workflow.py | 116 +
.../db/versions/v0_5_0/persistence/__init__.py | 55 +
.../db/versions/v0_5_0/persistence/sql/__init__.py | 36 +
.../db/versions/v0_5_0/persistence/sql/auto_gen.py | 2228 +
.../db/versions/v0_5_0/persistence/sql/sql_dao.py | 141 +
.../db/versions/v0_5_0/persistence/xml/__init__.py | 36 +
.../db/versions/v0_5_0/persistence/xml/auto_gen.py | 1266 +
vistrails/db/versions/v0_5_0/persistence/xml/io.py | 95 +
.../db/versions/v0_5_0/persistence/xml/xml_dao.py | 77 +
.../db/versions/v0_5_0/schemas/sql/vistrails.sql | 236 +
.../versions/v0_5_0/schemas/sql/vistrails_drop.sql | 38 +
vistrails/db/versions/v0_5_0/schemas/xml/log.xsd | 102 +
.../db/versions/v0_5_0/schemas/xml/vistrail.xsd | 213 +
.../db/versions/v0_5_0/schemas/xml/workflow.xsd | 131 +
vistrails/db/versions/v0_5_0/specs/action.xml | 104 +
vistrails/db/versions/v0_5_0/specs/add.xml | 107 +
vistrails/db/versions/v0_5_0/specs/annotation.xml | 89 +
vistrails/db/versions/v0_5_0/specs/change.xml | 112 +
vistrails/db/versions/v0_5_0/specs/connection.xml | 86 +
vistrails/db/versions/v0_5_0/specs/delete.xml | 77 +
vistrails/db/versions/v0_5_0/specs/execRec.xml | 81 +
vistrails/db/versions/v0_5_0/specs/function.xml | 83 +
vistrails/db/versions/v0_5_0/specs/location.xml | 80 +
vistrails/db/versions/v0_5_0/specs/log.xml | 60 +
vistrails/db/versions/v0_5_0/specs/machine.xml | 82 +
vistrails/db/versions/v0_5_0/specs/macro.xml | 72 +
vistrails/db/versions/v0_5_0/specs/module.xml | 95 +
vistrails/db/versions/v0_5_0/specs/other.xml | 79 +
vistrails/db/versions/v0_5_0/specs/parameter.xml | 94 +
vistrails/db/versions/v0_5_0/specs/port.xml | 90 +
vistrails/db/versions/v0_5_0/specs/portSpec.xml | 84 +
vistrails/db/versions/v0_5_0/specs/session.xml | 91 +
vistrails/db/versions/v0_5_0/specs/tag.xml | 61 +
vistrails/db/versions/v0_5_0/specs/vistrail.xml | 80 +
vistrails/db/versions/v0_5_0/specs/wfExec.xml | 86 +
vistrails/db/versions/v0_5_0/specs/workflow.xml | 74 +
vistrails/db/versions/v0_5_0/translate/__init__.py | 36 +
vistrails/db/versions/v0_5_0/translate/v0_3_1.py | 754 +
vistrails/db/versions/v0_6_0/__init__.py | 36 +
vistrails/db/versions/v0_6_0/domain/__init__.py | 38 +
vistrails/db/versions/v0_6_0/domain/auto_gen.py | 3284 +
vistrails/db/versions/v0_6_0/domain/id_scope.py | 65 +
vistrails/db/versions/v0_6_0/domain/vistrail.py | 43 +
vistrails/db/versions/v0_6_0/domain/workflow.py | 116 +
.../db/versions/v0_6_0/persistence/__init__.py | 55 +
.../db/versions/v0_6_0/persistence/sql/__init__.py | 36 +
.../db/versions/v0_6_0/persistence/sql/auto_gen.py | 4069 +
.../db/versions/v0_6_0/persistence/sql/sql_dao.py | 141 +
.../db/versions/v0_6_0/persistence/xml/__init__.py | 36 +
.../db/versions/v0_6_0/persistence/xml/auto_gen.py | 1749 +
vistrails/db/versions/v0_6_0/persistence/xml/io.py | 95 +
.../db/versions/v0_6_0/persistence/xml/xml_dao.py | 80 +
.../db/versions/v0_6_0/schemas/sql/vistrails.sql | 242 +
.../versions/v0_6_0/schemas/sql/vistrails_drop.sql | 37 +
.../db/versions/v0_6_0/schemas/xml/vistrail.xsd | 227 +
vistrails/db/versions/v0_6_0/specs/abstraction.xml | 65 +
.../db/versions/v0_6_0/specs/abstractionRef.xml | 78 +
vistrails/db/versions/v0_6_0/specs/action.xml | 100 +
vistrails/db/versions/v0_6_0/specs/add.xml | 110 +
vistrails/db/versions/v0_6_0/specs/annotation.xml | 93 +
vistrails/db/versions/v0_6_0/specs/change.xml | 115 +
vistrails/db/versions/v0_6_0/specs/connection.xml | 74 +
vistrails/db/versions/v0_6_0/specs/delete.xml | 77 +
vistrails/db/versions/v0_6_0/specs/function.xml | 83 +
vistrails/db/versions/v0_6_0/specs/location.xml | 80 +
vistrails/db/versions/v0_6_0/specs/log.xml | 62 +
vistrails/db/versions/v0_6_0/specs/machine.xml | 85 +
vistrails/db/versions/v0_6_0/specs/module.xml | 107 +
vistrails/db/versions/v0_6_0/specs/module_exec.xml | 86 +
vistrails/db/versions/v0_6_0/specs/other.xml | 79 +
vistrails/db/versions/v0_6_0/specs/parameter.xml | 94 +
vistrails/db/versions/v0_6_0/specs/port.xml | 90 +
vistrails/db/versions/v0_6_0/specs/portSpec.xml | 84 +
vistrails/db/versions/v0_6_0/specs/tag.xml | 71 +
vistrails/db/versions/v0_6_0/specs/vistrail.xml | 81 +
vistrails/db/versions/v0_6_0/specs/workflow.xml | 79 +
.../db/versions/v0_6_0/specs/workflow_exec.xml | 106 +
vistrails/db/versions/v0_6_0/translate/__init__.py | 36 +
vistrails/db/versions/v0_6_0/translate/v0_3_1.py | 716 +
vistrails/db/versions/v0_6_0/translate/v0_5_0.py | 121 +
vistrails/db/versions/v0_7_0/__init__.py | 36 +
vistrails/db/versions/v0_7_0/domain/__init__.py | 40 +
vistrails/db/versions/v0_7_0/domain/abstraction.py | 54 +
vistrails/db/versions/v0_7_0/domain/auto_gen.py | 4137 +
vistrails/db/versions/v0_7_0/domain/id_scope.py | 76 +
vistrails/db/versions/v0_7_0/domain/vistrail.py | 46 +
vistrails/db/versions/v0_7_0/domain/workflow.py | 122 +
.../db/versions/v0_7_0/persistence/__init__.py | 55 +
.../db/versions/v0_7_0/persistence/sql/__init__.py | 36 +
.../db/versions/v0_7_0/persistence/sql/auto_gen.py | 4104 +
.../db/versions/v0_7_0/persistence/sql/sql_dao.py | 141 +
.../db/versions/v0_7_0/persistence/xml/__init__.py | 36 +
.../db/versions/v0_7_0/persistence/xml/auto_gen.py | 1778 +
vistrails/db/versions/v0_7_0/persistence/xml/io.py | 95 +
.../db/versions/v0_7_0/persistence/xml/xml_dao.py | 80 +
.../db/versions/v0_7_0/schemas/sql/vistrails.sql | 246 +
.../versions/v0_7_0/schemas/sql/vistrails_drop.sql | 38 +
.../db/versions/v0_7_0/schemas/xml/vistrail.xsd | 234 +
vistrails/db/versions/v0_7_0/specs/abstraction.xml | 65 +
.../db/versions/v0_7_0/specs/abstractionRef.xml | 82 +
vistrails/db/versions/v0_7_0/specs/action.xml | 110 +
vistrails/db/versions/v0_7_0/specs/add.xml | 111 +
vistrails/db/versions/v0_7_0/specs/annotation.xml | 93 +
vistrails/db/versions/v0_7_0/specs/change.xml | 116 +
vistrails/db/versions/v0_7_0/specs/connection.xml | 74 +
vistrails/db/versions/v0_7_0/specs/delete.xml | 78 +
vistrails/db/versions/v0_7_0/specs/function.xml | 83 +
vistrails/db/versions/v0_7_0/specs/location.xml | 83 +
vistrails/db/versions/v0_7_0/specs/log.xml | 62 +
vistrails/db/versions/v0_7_0/specs/machine.xml | 85 +
vistrails/db/versions/v0_7_0/specs/module.xml | 112 +
vistrails/db/versions/v0_7_0/specs/module_exec.xml | 86 +
vistrails/db/versions/v0_7_0/specs/other.xml | 79 +
vistrails/db/versions/v0_7_0/specs/parameter.xml | 94 +
vistrails/db/versions/v0_7_0/specs/port.xml | 95 +
vistrails/db/versions/v0_7_0/specs/portSpec.xml | 84 +
vistrails/db/versions/v0_7_0/specs/tag.xml | 71 +
vistrails/db/versions/v0_7_0/specs/vistrail.xml | 81 +
vistrails/db/versions/v0_7_0/specs/workflow.xml | 79 +
.../db/versions/v0_7_0/specs/workflow_exec.xml | 106 +
vistrails/db/versions/v0_7_0/translate/__init__.py | 36 +
vistrails/db/versions/v0_7_0/translate/v0_6_0.py | 218 +
vistrails/db/versions/v0_8_0/__init__.py | 36 +
vistrails/db/versions/v0_8_0/domain/__init__.py | 40 +
vistrails/db/versions/v0_8_0/domain/abstraction.py | 54 +
vistrails/db/versions/v0_8_0/domain/auto_gen.py | 4209 +
vistrails/db/versions/v0_8_0/domain/id_scope.py | 76 +
vistrails/db/versions/v0_8_0/domain/vistrail.py | 48 +
vistrails/db/versions/v0_8_0/domain/workflow.py | 126 +
.../db/versions/v0_8_0/persistence/__init__.py | 92 +
.../db/versions/v0_8_0/persistence/sql/__init__.py | 36 +
.../db/versions/v0_8_0/persistence/sql/auto_gen.py | 2332 +
.../db/versions/v0_8_0/persistence/sql/sql_dao.py | 165 +
.../db/versions/v0_8_0/persistence/xml/__init__.py | 36 +
.../db/versions/v0_8_0/persistence/xml/auto_gen.py | 1531 +
.../db/versions/v0_8_0/persistence/xml/xml_dao.py | 80 +
.../db/versions/v0_8_0/schemas/sql/vistrails.sql | 249 +
.../versions/v0_8_0/schemas/sql/vistrails_drop.sql | 38 +
.../db/versions/v0_8_0/schemas/xml/vistrail.xsd | 237 +
vistrails/db/versions/v0_8_0/specs/abstraction.xml | 65 +
.../db/versions/v0_8_0/specs/abstractionRef.xml | 100 +
vistrails/db/versions/v0_8_0/specs/action.xml | 110 +
vistrails/db/versions/v0_8_0/specs/add.xml | 111 +
vistrails/db/versions/v0_8_0/specs/annotation.xml | 97 +
vistrails/db/versions/v0_8_0/specs/change.xml | 116 +
vistrails/db/versions/v0_8_0/specs/connection.xml | 74 +
vistrails/db/versions/v0_8_0/specs/delete.xml | 78 +
vistrails/db/versions/v0_8_0/specs/function.xml | 86 +
vistrails/db/versions/v0_8_0/specs/location.xml | 83 +
vistrails/db/versions/v0_8_0/specs/log.xml | 62 +
vistrails/db/versions/v0_8_0/specs/machine.xml | 85 +
vistrails/db/versions/v0_8_0/specs/module.xml | 107 +
vistrails/db/versions/v0_8_0/specs/module_exec.xml | 86 +
vistrails/db/versions/v0_8_0/specs/other.xml | 79 +
vistrails/db/versions/v0_8_0/specs/parameter.xml | 94 +
vistrails/db/versions/v0_8_0/specs/port.xml | 95 +
vistrails/db/versions/v0_8_0/specs/portSpec.xml | 84 +
vistrails/db/versions/v0_8_0/specs/tag.xml | 71 +
vistrails/db/versions/v0_8_0/specs/vistrail.xml | 85 +
vistrails/db/versions/v0_8_0/specs/workflow.xml | 80 +
.../db/versions/v0_8_0/specs/workflow_exec.xml | 106 +
vistrails/db/versions/v0_8_0/translate/__init__.py | 36 +
vistrails/db/versions/v0_8_0/translate/v0_7_0.py | 128 +
vistrails/db/versions/v0_8_1/__init__.py | 36 +
vistrails/db/versions/v0_8_1/domain/__init__.py | 35 +
.../db/versions/v0_8_1/persistence/__init__.py | 35 +
.../db/versions/v0_8_1/schemas/sql/vistrails.sql | 249 +
.../versions/v0_8_1/schemas/sql/vistrails.sql.bkp | 248 +
.../versions/v0_8_1/schemas/sql/vistrails_drop.sql | 38 +
.../db/versions/v0_8_1/schemas/xml/vistrail.xsd | 237 +
vistrails/db/versions/v0_8_1/specs/abstraction.xml | 65 +
.../db/versions/v0_8_1/specs/abstractionRef.xml | 100 +
vistrails/db/versions/v0_8_1/specs/action.xml | 110 +
vistrails/db/versions/v0_8_1/specs/add.xml | 111 +
vistrails/db/versions/v0_8_1/specs/annotation.xml | 97 +
vistrails/db/versions/v0_8_1/specs/change.xml | 116 +
vistrails/db/versions/v0_8_1/specs/connection.xml | 74 +
vistrails/db/versions/v0_8_1/specs/delete.xml | 78 +
vistrails/db/versions/v0_8_1/specs/function.xml | 86 +
vistrails/db/versions/v0_8_1/specs/location.xml | 83 +
vistrails/db/versions/v0_8_1/specs/log.xml | 62 +
vistrails/db/versions/v0_8_1/specs/machine.xml | 85 +
vistrails/db/versions/v0_8_1/specs/module.xml | 107 +
vistrails/db/versions/v0_8_1/specs/module_exec.xml | 86 +
vistrails/db/versions/v0_8_1/specs/other.xml | 79 +
vistrails/db/versions/v0_8_1/specs/parameter.xml | 94 +
vistrails/db/versions/v0_8_1/specs/port.xml | 95 +
vistrails/db/versions/v0_8_1/specs/portSpec.xml | 84 +
vistrails/db/versions/v0_8_1/specs/tag.xml | 71 +
vistrails/db/versions/v0_8_1/specs/vistrail.xml | 85 +
vistrails/db/versions/v0_8_1/specs/workflow.xml | 80 +
.../db/versions/v0_8_1/specs/workflow_exec.xml | 106 +
vistrails/db/versions/v0_8_1/translate/__init__.py | 36 +
vistrails/db/versions/v0_8_1/translate/v0_8_0.py | 84 +
vistrails/db/versions/v0_9_0/__init__.py | 36 +
vistrails/db/versions/v0_9_0/domain/__init__.py | 41 +
vistrails/db/versions/v0_9_0/domain/abstraction.py | 55 +
vistrails/db/versions/v0_9_0/domain/auto_gen.py | 4458 +
vistrails/db/versions/v0_9_0/domain/id_scope.py | 76 +
vistrails/db/versions/v0_9_0/domain/log.py | 55 +
vistrails/db/versions/v0_9_0/domain/vistrail.py | 64 +
vistrails/db/versions/v0_9_0/domain/workflow.py | 155 +
.../db/versions/v0_9_0/persistence/__init__.py | 98 +
.../db/versions/v0_9_0/persistence/sql/__init__.py | 36 +
.../db/versions/v0_9_0/persistence/sql/auto_gen.py | 2525 +
.../db/versions/v0_9_0/persistence/sql/sql_dao.py | 165 +
.../db/versions/v0_9_0/persistence/xml/__init__.py | 36 +
.../db/versions/v0_9_0/persistence/xml/auto_gen.py | 1584 +
.../db/versions/v0_9_0/persistence/xml/xml_dao.py | 80 +
.../db/versions/v0_9_0/schemas/sql/vistrails.sql | 281 +
.../versions/v0_9_0/schemas/sql/vistrails_drop.sql | 38 +
.../db/versions/v0_9_0/schemas/xml/vistrail.xsd | 238 +
vistrails/db/versions/v0_9_0/specs/abstraction.xml | 69 +
.../db/versions/v0_9_0/specs/abstractionRef.xml | 106 +
vistrails/db/versions/v0_9_0/specs/action.xml | 113 +
vistrails/db/versions/v0_9_0/specs/add.xml | 114 +
vistrails/db/versions/v0_9_0/specs/annotation.xml | 100 +
vistrails/db/versions/v0_9_0/specs/change.xml | 119 +
vistrails/db/versions/v0_9_0/specs/connection.xml | 77 +
vistrails/db/versions/v0_9_0/specs/delete.xml | 81 +
vistrails/db/versions/v0_9_0/specs/function.xml | 89 +
vistrails/db/versions/v0_9_0/specs/location.xml | 86 +
vistrails/db/versions/v0_9_0/specs/log.xml | 80 +
vistrails/db/versions/v0_9_0/specs/machine.xml | 90 +
vistrails/db/versions/v0_9_0/specs/module.xml | 115 +
vistrails/db/versions/v0_9_0/specs/module_exec.xml | 109 +
vistrails/db/versions/v0_9_0/specs/other.xml | 82 +
vistrails/db/versions/v0_9_0/specs/parameter.xml | 97 +
vistrails/db/versions/v0_9_0/specs/port.xml | 98 +
vistrails/db/versions/v0_9_0/specs/portSpec.xml | 87 +
vistrails/db/versions/v0_9_0/specs/tag.xml | 75 +
vistrails/db/versions/v0_9_0/specs/vistrail.xml | 89 +
vistrails/db/versions/v0_9_0/specs/workflow.xml | 98 +
.../db/versions/v0_9_0/specs/workflow_exec.xml | 109 +
vistrails/db/versions/v0_9_0/translate/__init__.py | 36 +
vistrails/db/versions/v0_9_0/translate/v0_8_1.py | 135 +
vistrails/db/versions/v0_9_1/__init__.py | 36 +
vistrails/db/versions/v0_9_1/domain/__init__.py | 41 +
vistrails/db/versions/v0_9_1/domain/abstraction.py | 55 +
vistrails/db/versions/v0_9_1/domain/auto_gen.py | 4809 +
vistrails/db/versions/v0_9_1/domain/id_scope.py | 85 +
vistrails/db/versions/v0_9_1/domain/log.py | 55 +
vistrails/db/versions/v0_9_1/domain/vistrail.py | 66 +
vistrails/db/versions/v0_9_1/domain/workflow.py | 158 +
.../db/versions/v0_9_1/persistence/__init__.py | 95 +
.../db/versions/v0_9_1/persistence/sql/__init__.py | 36 +
.../db/versions/v0_9_1/persistence/sql/auto_gen.py | 2693 +
.../db/versions/v0_9_1/persistence/sql/sql_dao.py | 165 +
.../db/versions/v0_9_1/persistence/xml/__init__.py | 36 +
.../db/versions/v0_9_1/persistence/xml/auto_gen.py | 1707 +
.../db/versions/v0_9_1/persistence/xml/xml_dao.py | 80 +
.../db/versions/v0_9_1/schemas/sql/vistrails.sql | 298 +
.../versions/v0_9_1/schemas/sql/vistrails_drop.sql | 38 +
.../db/versions/v0_9_1/schemas/xml/vistrail.xsd | 277 +
.../db/versions/v0_9_1/schemas/xml/vtlink.xsd | 52 +
vistrails/db/versions/v0_9_1/specs/abstraction.xml | 69 +
.../db/versions/v0_9_1/specs/abstractionRef.xml | 106 +
vistrails/db/versions/v0_9_1/specs/action.xml | 113 +
vistrails/db/versions/v0_9_1/specs/add.xml | 117 +
vistrails/db/versions/v0_9_1/specs/annotation.xml | 104 +
vistrails/db/versions/v0_9_1/specs/change.xml | 122 +
vistrails/db/versions/v0_9_1/specs/connection.xml | 77 +
vistrails/db/versions/v0_9_1/specs/delete.xml | 81 +
vistrails/db/versions/v0_9_1/specs/function.xml | 92 +
vistrails/db/versions/v0_9_1/specs/group.xml | 120 +
vistrails/db/versions/v0_9_1/specs/location.xml | 89 +
vistrails/db/versions/v0_9_1/specs/log.xml | 80 +
vistrails/db/versions/v0_9_1/specs/machine.xml | 90 +
vistrails/db/versions/v0_9_1/specs/module.xml | 120 +
vistrails/db/versions/v0_9_1/specs/module_exec.xml | 109 +
vistrails/db/versions/v0_9_1/specs/other.xml | 82 +
vistrails/db/versions/v0_9_1/specs/parameter.xml | 97 +
vistrails/db/versions/v0_9_1/specs/port.xml | 98 +
vistrails/db/versions/v0_9_1/specs/portSpec.xml | 87 +
vistrails/db/versions/v0_9_1/specs/tag.xml | 75 +
vistrails/db/versions/v0_9_1/specs/vistrail.xml | 89 +
vistrails/db/versions/v0_9_1/specs/workflow.xml | 113 +
.../db/versions/v0_9_1/specs/workflow_exec.xml | 109 +
vistrails/db/versions/v0_9_1/translate/__init__.py | 36 +
vistrails/db/versions/v0_9_1/translate/v0_9_0.py | 142 +
vistrails/db/versions/v0_9_2/__init__.py | 36 +
vistrails/db/versions/v0_9_2/domain/__init__.py | 35 +
.../db/versions/v0_9_2/persistence/__init__.py | 35 +
vistrails/db/versions/v0_9_2/translate/__init__.py | 36 +
vistrails/db/versions/v0_9_2/translate/v0_9_1.py | 48 +
vistrails/db/versions/v0_9_3/__init__.py | 36 +
vistrails/db/versions/v0_9_3/domain/__init__.py | 41 +
vistrails/db/versions/v0_9_3/domain/abstraction.py | 55 +
vistrails/db/versions/v0_9_3/domain/auto_gen.py | 6369 +
vistrails/db/versions/v0_9_3/domain/id_scope.py | 85 +
vistrails/db/versions/v0_9_3/domain/log.py | 68 +
vistrails/db/versions/v0_9_3/domain/vistrail.py | 127 +
vistrails/db/versions/v0_9_3/domain/workflow.py | 170 +
.../db/versions/v0_9_3/persistence/__init__.py | 204 +
.../db/versions/v0_9_3/persistence/sql/__init__.py | 36 +
.../db/versions/v0_9_3/persistence/sql/auto_gen.py | 2811 +
.../db/versions/v0_9_3/persistence/sql/sql_dao.py | 183 +
.../db/versions/v0_9_3/persistence/xml/__init__.py | 36 +
.../db/versions/v0_9_3/persistence/xml/auto_gen.py | 1774 +
.../db/versions/v0_9_3/persistence/xml/xml_dao.py | 80 +
.../db/versions/v0_9_3/schemas/sql/vistrails.sql | 311 +
.../versions/v0_9_3/schemas/sql/vistrails_drop.sql | 38 +
.../db/versions/v0_9_3/schemas/xml/vistrail.xsd | 285 +
vistrails/db/versions/v0_9_3/specs/all.xml | 1652 +
vistrails/db/versions/v0_9_3/translate/__init__.py | 36 +
vistrails/db/versions/v0_9_3/translate/v0_9_1.py | 86 +
vistrails/db/versions/v0_9_3/translate/v0_9_2.py | 155 +
vistrails/db/versions/v0_9_3/translate/v0_9_4.py | 113 +
vistrails/db/versions/v0_9_4/__init__.py | 36 +
vistrails/db/versions/v0_9_4/domain/__init__.py | 40 +
vistrails/db/versions/v0_9_4/domain/auto_gen.py | 5971 +
vistrails/db/versions/v0_9_4/domain/id_scope.py | 85 +
vistrails/db/versions/v0_9_4/domain/log.py | 69 +
vistrails/db/versions/v0_9_4/domain/vistrail.py | 127 +
vistrails/db/versions/v0_9_4/domain/workflow.py | 172 +
.../db/versions/v0_9_4/persistence/__init__.py | 204 +
.../db/versions/v0_9_4/persistence/sql/__init__.py | 36 +
.../db/versions/v0_9_4/persistence/sql/auto_gen.py | 2712 +
.../db/versions/v0_9_4/persistence/sql/sql_dao.py | 183 +
.../db/versions/v0_9_4/persistence/xml/__init__.py | 36 +
.../db/versions/v0_9_4/persistence/xml/auto_gen.py | 1703 +
.../db/versions/v0_9_4/persistence/xml/xml_dao.py | 80 +
.../db/versions/v0_9_4/schemas/sql/vistrails.sql | 305 +
.../versions/v0_9_4/schemas/sql/vistrails_drop.sql | 38 +
.../db/versions/v0_9_4/schemas/xml/vistrail.xsd | 276 +
vistrails/db/versions/v0_9_4/specs/all.xml | 1601 +
vistrails/db/versions/v0_9_4/translate/__init__.py | 36 +
vistrails/db/versions/v0_9_4/translate/v0_9_3.py | 117 +
vistrails/db/versions/v0_9_4/translate/v0_9_5.py | 87 +
vistrails/db/versions/v0_9_5/__init__.py | 36 +
vistrails/db/versions/v0_9_5/domain/__init__.py | 41 +
vistrails/db/versions/v0_9_5/domain/auto_gen.py | 7786 ++
vistrails/db/versions/v0_9_5/domain/id_scope.py | 85 +
vistrails/db/versions/v0_9_5/domain/log.py | 69 +
vistrails/db/versions/v0_9_5/domain/registry.py | 61 +
vistrails/db/versions/v0_9_5/domain/vistrail.py | 127 +
vistrails/db/versions/v0_9_5/domain/workflow.py | 172 +
.../db/versions/v0_9_5/persistence/__init__.py | 230 +
.../db/versions/v0_9_5/persistence/sql/__init__.py | 36 +
.../db/versions/v0_9_5/persistence/sql/auto_gen.py | 3340 +
.../db/versions/v0_9_5/persistence/sql/sql_dao.py | 183 +
.../db/versions/v0_9_5/persistence/xml/__init__.py | 36 +
.../db/versions/v0_9_5/persistence/xml/auto_gen.py | 2117 +
.../db/versions/v0_9_5/persistence/xml/xml_dao.py | 80 +
.../db/versions/v0_9_5/schemas/sql/vistrails.sql | 373 +
.../versions/v0_9_5/schemas/sql/vistrails_drop.sql | 40 +
.../db/versions/v0_9_5/schemas/xml/vistrail.xsd | 278 +
vistrails/db/versions/v0_9_5/specs/all.xml | 2017 +
vistrails/db/versions/v0_9_5/translate/__init__.py | 36 +
vistrails/db/versions/v0_9_5/translate/v0_9_4.py | 99 +
vistrails/db/versions/v0_9_5/translate/v1_0_0.py | 113 +
vistrails/db/versions/v1_0_0/__init__.py | 36 +
vistrails/db/versions/v1_0_0/domain/__init__.py | 41 +
vistrails/db/versions/v1_0_0/domain/auto_gen.py | 11387 ++
vistrails/db/versions/v1_0_0/domain/id_scope.py | 85 +
vistrails/db/versions/v1_0_0/domain/log.py | 72 +
vistrails/db/versions/v1_0_0/domain/registry.py | 63 +
vistrails/db/versions/v1_0_0/domain/vistrail.py | 127 +
vistrails/db/versions/v1_0_0/domain/workflow.py | 172 +
.../db/versions/v1_0_0/persistence/__init__.py | 248 +
.../db/versions/v1_0_0/persistence/sql/__init__.py | 36 +
.../db/versions/v1_0_0/persistence/sql/auto_gen.py | 3332 +
.../db/versions/v1_0_0/persistence/sql/sql_dao.py | 183 +
.../db/versions/v1_0_0/persistence/xml/__init__.py | 36 +
.../db/versions/v1_0_0/persistence/xml/auto_gen.py | 3833 +
.../db/versions/v1_0_0/persistence/xml/xml_dao.py | 80 +
.../db/versions/v1_0_0/schemas/sql/vistrails.sql | 372 +
.../versions/v1_0_0/schemas/sql/vistrails_drop.sql | 40 +
.../db/versions/v1_0_0/schemas/xml/vistrail.xsd | 278 +
vistrails/db/versions/v1_0_0/specs/all.xml | 2684 +
vistrails/db/versions/v1_0_0/translate/__init__.py | 36 +
vistrails/db/versions/v1_0_0/translate/v0_9_5.py | 95 +
vistrails/db/versions/v1_0_0/translate/v1_0_1.py | 65 +
vistrails/db/versions/v1_0_1/__init__.py | 36 +
vistrails/db/versions/v1_0_1/domain/__init__.py | 41 +
vistrails/db/versions/v1_0_1/domain/auto_gen.py | 11447 ++
vistrails/db/versions/v1_0_1/domain/id_scope.py | 85 +
vistrails/db/versions/v1_0_1/domain/log.py | 72 +
vistrails/db/versions/v1_0_1/domain/registry.py | 63 +
vistrails/db/versions/v1_0_1/domain/vistrail.py | 203 +
vistrails/db/versions/v1_0_1/domain/workflow.py | 172 +
.../db/versions/v1_0_1/persistence/__init__.py | 248 +
.../db/versions/v1_0_1/persistence/sql/__init__.py | 36 +
.../db/versions/v1_0_1/persistence/sql/auto_gen.py | 3344 +
.../db/versions/v1_0_1/persistence/sql/sql_dao.py | 183 +
.../db/versions/v1_0_1/persistence/xml/__init__.py | 36 +
.../db/versions/v1_0_1/persistence/xml/auto_gen.py | 3845 +
.../db/versions/v1_0_1/persistence/xml/xml_dao.py | 80 +
.../db/versions/v1_0_1/schemas/sql/vistrails.sql | 382 +
.../versions/v1_0_1/schemas/sql/vistrails_drop.sql | 42 +
.../db/versions/v1_0_1/schemas/xml/vistrail.xsd | 280 +
.../db/versions/v1_0_1/schemas/xml/vtlink.xsd | 55 +
vistrails/db/versions/v1_0_1/specs/all.xml | 2699 +
vistrails/db/versions/v1_0_1/translate/__init__.py | 36 +
vistrails/db/versions/v1_0_1/translate/v1_0_0.py | 80 +
vistrails/db/versions/v1_0_1/translate/v1_0_2.py | 193 +
vistrails/db/versions/v1_0_2/__init__.py | 36 +
vistrails/db/versions/v1_0_2/domain/__init__.py | 41 +
vistrails/db/versions/v1_0_2/domain/auto_gen.py | 11719 ++
vistrails/db/versions/v1_0_2/domain/id_scope.py | 85 +
vistrails/db/versions/v1_0_2/domain/log.py | 72 +
vistrails/db/versions/v1_0_2/domain/registry.py | 63 +
vistrails/db/versions/v1_0_2/domain/vistrail.py | 216 +
vistrails/db/versions/v1_0_2/domain/workflow.py | 172 +
.../db/versions/v1_0_2/persistence/__init__.py | 473 +
.../db/versions/v1_0_2/persistence/sql/__init__.py | 36 +
.../db/versions/v1_0_2/persistence/sql/auto_gen.py | 5804 +
.../db/versions/v1_0_2/persistence/sql/sql_dao.py | 259 +
.../db/versions/v1_0_2/persistence/xml/__init__.py | 36 +
.../db/versions/v1_0_2/persistence/xml/auto_gen.py | 3902 +
.../db/versions/v1_0_2/persistence/xml/xml_dao.py | 86 +
.../db/versions/v1_0_2/schemas/sql/vistrails.sql | 390 +
.../versions/v1_0_2/schemas/sql/vistrails_drop.sql | 42 +
vistrails/db/versions/v1_0_2/schemas/xml/log.xsd | 146 +
.../db/versions/v1_0_2/schemas/xml/vistrail.xsd | 287 +
.../db/versions/v1_0_2/schemas/xml/vtlink.xsd | 69 +
.../db/versions/v1_0_2/schemas/xml/workflow.xsd | 185 +
vistrails/db/versions/v1_0_2/specs/all.xml | 2746 +
vistrails/db/versions/v1_0_2/translate/__init__.py | 36 +
vistrails/db/versions/v1_0_2/translate/v1_0_1.py | 145 +
vistrails/db/versions/v1_0_2/translate/v1_0_3.py | 207 +
vistrails/db/versions/v1_0_3/__init__.py | 36 +
vistrails/db/versions/v1_0_3/domain/__init__.py | 41 +
vistrails/db/versions/v1_0_3/domain/auto_gen.py | 16928 +++
vistrails/db/versions/v1_0_3/domain/id_scope.py | 85 +
vistrails/db/versions/v1_0_3/domain/log.py | 72 +
vistrails/db/versions/v1_0_3/domain/registry.py | 63 +
vistrails/db/versions/v1_0_3/domain/vistrail.py | 220 +
vistrails/db/versions/v1_0_3/domain/workflow.py | 172 +
.../db/versions/v1_0_3/persistence/__init__.py | 472 +
.../db/versions/v1_0_3/persistence/sql/__init__.py | 36 +
.../db/versions/v1_0_3/persistence/sql/auto_gen.py | 7984 ++
.../db/versions/v1_0_3/persistence/sql/sql_dao.py | 259 +
.../db/versions/v1_0_3/persistence/xml/__init__.py | 36 +
.../db/versions/v1_0_3/persistence/xml/auto_gen.py | 5822 +
.../db/versions/v1_0_3/persistence/xml/xml_dao.py | 89 +
.../db/versions/v1_0_3/schemas/sql/vistrails.sql | 528 +
.../versions/v1_0_3/schemas/sql/vistrails_drop.sql | 42 +
vistrails/db/versions/v1_0_3/schemas/xml/log.xsd | 146 +
.../db/versions/v1_0_3/schemas/xml/vistrail.xsd | 347 +
.../db/versions/v1_0_3/schemas/xml/vtlink.xsd | 69 +
.../db/versions/v1_0_3/schemas/xml/workflow.xsd | 200 +
vistrails/db/versions/v1_0_3/specs/all.xml | 3823 +
vistrails/db/versions/v1_0_3/translate/__init__.py | 36 +
vistrails/db/versions/v1_0_3/translate/v1_0_2.py | 342 +
vistrails/gui/__init__.py | 35 +
vistrails/gui/application.py | 853 +
vistrails/gui/application_server.py | 2229 +
vistrails/gui/base_view.py | 114 +
vistrails/gui/bundles/__init__.py | 35 +
vistrails/gui/bundles/installbundle.py | 270 +
vistrails/gui/bundles/linux_debian_install.py | 255 +
vistrails/gui/bundles/linux_fedora_install.py | 198 +
vistrails/gui/bundles/utils.py | 150 +
vistrails/gui/collection/__init__.py | 36 +
vistrails/gui/collection/explorer.py | 758 +
vistrails/gui/collection/vis_log.py | 582 +
vistrails/gui/collection/workspace.py | 1631 +
vistrails/gui/common_widgets.py | 833 +
vistrails/gui/configuration.py | 979 +
vistrails/gui/controlflow_assist.py | 325 +
vistrails/gui/debug.py | 375 +
vistrails/gui/debugger.py | 247 +
vistrails/gui/extras/__init__.py | 35 +
vistrails/gui/extras/core/__init__.py | 36 +
vistrails/gui/extras/core/db/__init__.py | 36 +
vistrails/gui/extras/core/db/locator.py | 221 +
vistrails/gui/graphics_view.py | 850 +
vistrails/gui/job_monitor.py | 387 +
vistrails/gui/mashups/__init__.py | 36 +
vistrails/gui/mashups/alias_inspector.py | 759 +
vistrails/gui/mashups/alias_list.py | 352 +
vistrails/gui/mashups/alias_parameter_view.py | 389 +
vistrails/gui/mashups/controller.py | 87 +
vistrails/gui/mashups/mashup_app.py | 624 +
vistrails/gui/mashups/mashup_view.py | 401 +
vistrails/gui/mashups/mashups_inspector.py | 408 +
vistrails/gui/mashups/mashups_manager.py | 450 +
vistrails/gui/mashups/mashups_widgets.py | 387 +
vistrails/gui/merge_gui.py | 322 +
vistrails/gui/module_annotation.py | 295 +
vistrails/gui/module_configuration.py | 193 +
vistrails/gui/module_documentation.py | 113 +
vistrails/gui/module_info.py | 211 +
vistrails/gui/module_palette.py | 544 +
vistrails/gui/modules/__init__.py | 63 +
vistrails/gui/modules/constant_configuration.py | 775 +
vistrails/gui/modules/list_configuration.py | 132 +
vistrails/gui/modules/module_configure.py | 272 +
vistrails/gui/modules/paramexplore.py | 798 +
vistrails/gui/modules/python_source_configure.py | 244 +
vistrails/gui/modules/query_configuration.py | 146 +
vistrails/gui/modules/resources/__init__.py | 35 +
vistrails/gui/modules/resources/colorconfig_rc.py | 1850 +
vistrails/gui/modules/source_configure.py | 413 +
vistrails/gui/modules/string_configure.py | 154 +
vistrails/gui/modules/tuple_configuration.py | 578 +
vistrails/gui/open_db_window.py | 775 +
vistrails/gui/paramexplore/__init__.py | 36 +
vistrails/gui/paramexplore/param_view.py | 410 +
vistrails/gui/paramexplore/pe_inspector.py | 291 +
vistrails/gui/paramexplore/pe_pipeline.py | 131 +
vistrails/gui/paramexplore/pe_tab.py | 337 +
vistrails/gui/paramexplore/pe_table.py | 1015 +
vistrails/gui/paramexplore/pe_view.py | 135 +
vistrails/gui/paramexplore/virtual_cell.py | 673 +
vistrails/gui/pipeline_view.py | 3405 +
vistrails/gui/pipeline_view_select.py | 186 +
vistrails/gui/port_documentation.py | 89 +
vistrails/gui/ports_pane.py | 613 +
vistrails/gui/preferences.py | 696 +
vistrails/gui/publishing.py | 857 +
vistrails/gui/qt.py | 220 +
vistrails/gui/query_view.py | 595 +
vistrails/gui/repository.py | 766 +
vistrails/gui/requirements.py | 61 +
vistrails/gui/resources/__init__.py | 35 +
vistrails/gui/resources/images/alias.png | Bin 0 -> 3658 bytes
vistrails/gui/resources/images/analogy.png | Bin 0 -> 1596 bytes
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vistrails/gui/resources/images/automatch.png | Bin 0 -> 1538 bytes
vistrails/gui/resources/images/bookmarks.png | Bin 0 -> 3113 bytes
vistrails/gui/resources/images/camera.png | Bin 0 -> 1974 bytes
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vistrails/gui/resources/images/closeview.png | Bin 0 -> 406 bytes
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vistrails/gui/resources/images/console.png | Bin 0 -> 2136 bytes
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vistrails/gui/resources/images/up.png | Bin 0 -> 933 bytes
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vistrails/gui/resources/images/version_bg.png | Bin 0 -> 8065 bytes
vistrails/gui/resources/images/view-refresh.png | Bin 0 -> 2024 bytes
vistrails/gui/resources/images/view_fullscreen.png | Bin 0 -> 1911 bytes
vistrails/gui/resources/images/vistrails_icon.png | Bin 0 -> 15938 bytes
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.../gui/resources/images/vistrails_splash.png | Bin 0 -> 160717 bytes
vistrails/gui/resources/images/visual_query.png | Bin 0 -> 3189 bytes
vistrails/gui/resources/images/zoom.png | Bin 0 -> 2968 bytes
vistrails/gui/resources/images/zoom_arrow_icon.png | Bin 0 -> 1774 bytes
vistrails/gui/resources/images/zoom_icon.png | Bin 0 -> 4424 bytes
vistrails/gui/resources/macroicons.qrc | 17 +
vistrails/gui/resources/macroicons_rc.py | 1404 +
vistrails/gui/resources/vistrails-mime.xml | 11 +
vistrails/gui/shell.py | 965 +
vistrails/gui/theme.py | 750 +
vistrails/gui/utils.py | 243 +
vistrails/gui/variable_dropbox.py | 510 +
vistrails/gui/version_prop.py | 817 +
vistrails/gui/version_view.py | 1299 +
vistrails/gui/view_manager.py | 903 +
vistrails/gui/vis_diff.py | 1277 +
vistrails/gui/vistrail_controller.py | 1558 +
vistrails/gui/vistrail_variables.py | 65 +
vistrails/gui/vistrail_view.py | 1295 +
vistrails/gui/vistrails_palette.py | 122 +
vistrails/gui/vistrails_window.py | 2695 +
vistrails/index/__core.py | 143 +
vistrails/index/__init__.py | 35 +
vistrails/index/indexworkflow.py | 226 +
vistrails/index/spec_io.py | 137 +
vistrails/index/vistrailanalyzer.py | 116 +
vistrails/packages/CLTools/README | 73 +
vistrails/packages/CLTools/__init__.py | 41 +
vistrails/packages/CLTools/icons/document-new.png | Bin 0 -> 692 bytes
vistrails/packages/CLTools/icons/document-open.png | Bin 0 -> 919 bytes
.../packages/CLTools/icons/document-save-as.png | Bin 0 -> 1097 bytes
vistrails/packages/CLTools/icons/document-save.png | Bin 0 -> 1150 bytes
vistrails/packages/CLTools/icons/go-down.png | Bin 0 -> 874 bytes
vistrails/packages/CLTools/icons/go-up.png | Bin 0 -> 877 bytes
vistrails/packages/CLTools/icons/list-add.png | Bin 0 -> 386 bytes
vistrails/packages/CLTools/icons/list-remove.png | Bin 0 -> 252 bytes
vistrails/packages/CLTools/icons/view-refresh.png | Bin 0 -> 1364 bytes
vistrails/packages/CLTools/identifiers.py | 4 +
vistrails/packages/CLTools/init.py | 563 +
.../CLTools/test_files/intern_cltools_1.clt | 78 +
.../CLTools/test_files/intern_cltools_2.clt | 81 +
.../packages/CLTools/test_files/test_1.cltest | 2 +
.../packages/CLTools/test_files/test_script_1.py | 42 +
vistrails/packages/CLTools/wizard.py | 1163 +
vistrails/packages/HTTP/__init__.py | 46 +
vistrails/packages/HTTP/http_directory.py | 175 +
vistrails/packages/HTTP/init.py | 539 +
vistrails/packages/ImageMagick/__init__.py | 48 +
vistrails/packages/ImageMagick/init.py | 280 +
vistrails/packages/JobSubmission/__init__.py | 34 +
.../packages/JobSubmission/common_definitions.py | 51 +
vistrails/packages/JobSubmission/init.py | 315 +
vistrails/packages/JobSubmission/machine.py | 31 +
vistrails/packages/SUDSWebServices/__init__.py | 72 +
vistrails/packages/SUDSWebServices/init.py | 874 +
vistrails/packages/__init__.py | 36 +
vistrails/packages/analytics/__init__.py | 39 +
vistrails/packages/analytics/counts.vt | Bin 0 -> 14895 bytes
vistrails/packages/analytics/executedWorkflows.vt | Bin 0 -> 22837 bytes
vistrails/packages/analytics/init.py | 180 +
vistrails/packages/analytics/times.vt | Bin 0 -> 55862 bytes
vistrails/packages/controlflow/__init__.py | 39 +
vistrails/packages/controlflow/conditional.py | 119 +
vistrails/packages/controlflow/fold.py | 308 +
vistrails/packages/controlflow/init.py | 214 +
vistrails/packages/controlflow/looping.py | 241 +
vistrails/packages/controlflow/order.py | 62 +
vistrails/packages/controlflow/products.py | 135 +
vistrails/packages/controlflow/utils.py | 116 +
vistrails/packages/dialogs/__init__.py | 41 +
vistrails/packages/dialogs/init.py | 110 +
vistrails/packages/matplotlib/README | 94 +
vistrails/packages/matplotlib/__init__.py | 63 +
vistrails/packages/matplotlib/artists.py | 3800 +
.../packages/matplotlib/artists_template.py.mako | 170 +
vistrails/packages/matplotlib/bases.py | 291 +
vistrails/packages/matplotlib/diff.py | 354 +
vistrails/packages/matplotlib/figure_cell.py | 294 +
vistrails/packages/matplotlib/generate.py | 29 +
vistrails/packages/matplotlib/identifiers.py | 46 +
vistrails/packages/matplotlib/init.py | 269 +
vistrails/packages/matplotlib/mixins.py | 62 +
vistrails/packages/matplotlib/mpl_artists.xml | 1935 +
vistrails/packages/matplotlib/mpl_artists_diff.xml | 36 +
vistrails/packages/matplotlib/mpl_artists_raw.xml | 1935 +
vistrails/packages/matplotlib/mpl_plots.xml | 3277 +
vistrails/packages/matplotlib/mpl_plots_diff.xml | 1113 +
vistrails/packages/matplotlib/mpl_plots_raw.xml | 3154 +
vistrails/packages/matplotlib/object.py | 20 +
vistrails/packages/matplotlib/parse.py | 1001 +
vistrails/packages/matplotlib/plots.py | 5482 +
.../packages/matplotlib/plots_template.py.mako | 210 +
vistrails/packages/matplotlib/specs.py | 753 +
vistrails/packages/matplotlib/update.py | 78 +
vistrails/packages/matplotlib/widgets.py | 49 +
vistrails/packages/parallelflow/__init__.py | 3 +
vistrails/packages/parallelflow/api.py | 116 +
vistrails/packages/parallelflow/engine_manager.py | 491 +
vistrails/packages/parallelflow/init.py | 36 +
vistrails/packages/parallelflow/map.py | 581 +
vistrails/packages/persistence/__init__.py | 44 +
vistrails/packages/persistence/compute_hash.py | 82 +
vistrails/packages/persistence/db_utils.py | 171 +
vistrails/packages/persistence/find_files.py | 113 +
vistrails/packages/persistence/find_workflows.py | 132 +
vistrails/packages/persistence/identifiers.py | 40 +
vistrails/packages/persistence/init.py | 682 +
vistrails/packages/persistence/repo.py | 272 +
vistrails/packages/persistence/schema.sql | 37 +
vistrails/packages/persistence/widgets.py | 1184 +
vistrails/packages/pipelineEdit/__init__.py | 42 +
vistrails/packages/pipelineEdit/init.py | 153 +
vistrails/packages/pythonCalc/__init__.py | 47 +
vistrails/packages/pythonCalc/init.py | 127 +
vistrails/packages/pythonCalcQt/__init__.py | 51 +
vistrails/packages/pythonCalcQt/init.py | 139 +
vistrails/packages/qgis/__init__.py | 48 +
vistrails/packages/qgis/init.py | 172 +
vistrails/packages/rpy/README | 11 +
vistrails/packages/rpy/__init__.py | 39 +
vistrails/packages/rpy/init.py | 482 +
vistrails/packages/rpy/widgets.py | 46 +
vistrails/packages/spreadsheet/__init__.py | 39 +
vistrails/packages/spreadsheet/analogy_api.py | 133 +
vistrails/packages/spreadsheet/basic_widgets.py | 267 +
vistrails/packages/spreadsheet/cell_rc.py | 3259 +
vistrails/packages/spreadsheet/celltoolbar_rc.py | 677 +
vistrails/packages/spreadsheet/identifiers.py | 39 +
vistrails/packages/spreadsheet/init.py | 153 +
vistrails/packages/spreadsheet/spreadsheet_base.py | 316 +
vistrails/packages/spreadsheet/spreadsheet_cell.py | 1179 +
.../packages/spreadsheet/spreadsheet_config.py | 39 +
.../packages/spreadsheet/spreadsheet_controller.py | 129 +
.../packages/spreadsheet/spreadsheet_event.py | 97 +
.../packages/spreadsheet/spreadsheet_execute.py | 207 +
.../packages/spreadsheet/spreadsheet_helpers.py | 294 +
vistrails/packages/spreadsheet/spreadsheet_rc.py | 1872 +
.../packages/spreadsheet/spreadsheet_registry.py | 104 +
.../packages/spreadsheet/spreadsheet_sheet.py | 531 +
vistrails/packages/spreadsheet/spreadsheet_tab.py | 1203 +
.../spreadsheet/spreadsheet_tabcontroller.py | 822 +
.../packages/spreadsheet/spreadsheet_window.py | 668 +
vistrails/packages/spreadsheet/widgets/__init__.py | 36 +
.../spreadsheet/widgets/iebrowser/__init__.py | 59 +
.../spreadsheet/widgets/iebrowser/iecell.py | 110 +
.../spreadsheet/widgets/imageviewer/__init__.py | 58 +
.../spreadsheet/widgets/imageviewer/imageviewer.py | 371 +
.../widgets/imageviewer/imageviewer_rc.py | 557 +
.../spreadsheet/widgets/richtext/__init__.py | 66 +
.../spreadsheet/widgets/richtext/richtext.py | 143 +
.../packages/spreadsheet/widgets/svg/__init__.py | 61 +
vistrails/packages/spreadsheet/widgets/svg/svg.py | 194 +
.../spreadsheet/widgets/webview/__init__.py | 59 +
.../spreadsheet/widgets/webview/webview.py | 110 +
vistrails/packages/sql/__init__.py | 47 +
vistrails/packages/sql/init.py | 225 +
vistrails/packages/tabledata/__init__.py | 29 +
vistrails/packages/tabledata/common.py | 64 +
vistrails/packages/tabledata/convert/__init__.py | 6 +
.../packages/tabledata/convert/convert_dates.py | 580 +
vistrails/packages/tabledata/identifiers.py | 3 +
vistrails/packages/tabledata/init.py | 17 +
vistrails/packages/tabledata/read/__init__.py | 7 +
vistrails/packages/tabledata/read/read_csv.py | 241 +
vistrails/packages/tabledata/read/read_numpy.py | 136 +
vistrails/packages/tabledata/test_files/random.dat | Bin 0 -> 24 bytes
vistrails/packages/tabledata/test_files/random.npy | Bin 0 -> 104 bytes
vistrails/packages/tabledata/test_files/test.csv | 4 +
vistrails/packages/tabledata/viewer.py | 55 +
vistrails/packages/vtk/__init__.py | 61 +
vistrails/packages/vtk/base_module.py | 272 +
vistrails/packages/vtk/class_tree.py | 303 +
vistrails/packages/vtk/fix_classes.py | 67 +
vistrails/packages/vtk/hasher.py | 49 +
vistrails/packages/vtk/identifiers.py | 38 +
vistrails/packages/vtk/init.py | 1383 +
vistrails/packages/vtk/inspectors.py | 244 +
vistrails/packages/vtk/offscreen.py | 87 +
vistrails/packages/vtk/tf_widget.py | 736 +
vistrails/packages/vtk/vtk_parser.py | 548 +
vistrails/packages/vtk/vtkcell.py | 1146 +
vistrails/packages/vtk/vtkcell_rc.py | 198 +
vistrails/packages/vtk/vtkhandler.py | 220 +
vistrails/packages/vtk/vtkviewcell.py | 1045 +
vistrails/packages/vtlcreator/__init__.py | 41 +
vistrails/packages/vtlcreator/init.py | 176 +
vistrails/packages/webServices/__init__.py | 79 +
.../packages/webServices/enumeration_widget.py | 115 +
vistrails/packages/webServices/init.py | 1527 +
vistrails/run.py | 147 +
vistrails/stop_vistrails_server.py | 57 +
vistrails/tests/__init__.py | 50 +
vistrails/tests/resources/__init__.py | 36 +
vistrails/tests/resources/console_mode_test.py | 101 +
vistrails/tests/resources/dummy.xml | 164 +
vistrails/tests/resources/dummy_broken.xml | 165 +
vistrails/tests/resources/dummy_new.vt | Bin 0 -> 2673 bytes
vistrails/tests/resources/dummy_new.xml | 342 +
vistrails/tests/resources/dynamic_module_error.xml | 42 +
vistrails/tests/resources/empty_bookmarks.xml | 36 +
vistrails/tests/resources/import_pkg/__init__.py | 0
.../import_pkg/test_import_pkg/__init__.py | 8 +
.../resources/import_pkg/test_import_pkg/init.py | 1 +
.../import_pkg/test_import_pkg/module1.py | 2 +
.../import_pkg/test_import_pkg/module2.py | 2 +
.../tests/resources/import_targets/__init__.py | 5 +
vistrails/tests/resources/import_targets/test1.py | 7 +
vistrails/tests/resources/import_targets/test2.py | 0
vistrails/tests/resources/import_targets/test3.py | 0
vistrails/tests/resources/import_targets/test4.py | 0
vistrails/tests/resources/import_targets/test5.py | 0
vistrails/tests/resources/import_targets/test6.py | 0
vistrails/tests/resources/paramexp-1.0.2.vt | Bin 0 -> 115626 bytes
vistrails/tests/resources/paramexp-1.0.3.vt | Bin 0 -> 115266 bytes
vistrails/tests/resources/pythonsource.xml | 288 +
vistrails/tests/resources/spx_loop.vt | Bin 0 -> 45577 bytes
vistrails/tests/resources/terminator.vt | Bin 0 -> 36502 bytes
vistrails/tests/resources/test_abstraction.xml | 227 +
vistrails/tests/resources/test_alias.xml | 178 +
vistrails/tests/resources/test_archive.zip | Bin 0 -> 459 bytes
vistrails/tests/resources/test_change_vistrail.xml | 386 +
vistrails/tests/resources/test_ticket_73.xml | 46 +
vistrails/tests/resources/triangle_count.vt | Bin 0 -> 7418 bytes
vistrails/tests/resources/visvar-1.0.2.vt | Bin 0 -> 114074 bytes
vistrails/tests/resources/visvar-1.0.3.vt | Bin 0 -> 114055 bytes
vistrails/tests/resources/vtk.xml | 3840 +
.../resources/vtkfiles/vtk_quadric_writer_test.vtk | 9001 ++
vistrails/tests/run_on_mac.sh | 25 +
vistrails/tests/runtestsuite.py | 484 +
vistrails/tests/utils.py | 212 +
vistrails/vistrails_server.py | 77 +
1804 files changed, 822902 insertions(+)
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..ac86225
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,27 @@
+VisTrails is distributed under the "Modified BSD License".
+
+Copyright (C) 2011-2014, NYU-Poly.
+Copyright (C) 2006-2011, University of Utah.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ * Neither the name of the University of Utah nor the
+ names of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL COPYRIGHT HOLDER BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..339e3e5
--- /dev/null
+++ b/README.md
@@ -0,0 +1,10 @@
+Homepage: <http://www.vistrails.org>
+
+VisTrails is an open-source data analysis and visualization tool. It provides a comprehensive provenance infrastructure that maintains detailed history information about the steps followed and data derived in the course of an exploratory task: VisTrails maintains provenance of data products, of the computational processes that derive these products and their executions.
+
+For more information, take a look at the [documentation](http://www.vistrails.org/index.php/Documentation), the [users guide](http://www.vistrails.org/usersguide/v2.0/html/), or our [publications](http://www.vistrails.org/index.php/Publications,_Tutorials_and_Presentations).
+
+Binary releases are available on our [download](http://www.vistrails.org/index.php/Downloads) page. To report bugs, please use the github [issue](https://github.com/VisTrails/VisTrails/issues) tracker, after checking our [FAQ](http://www.vistrails.org/index.php/FAQ)
+ for known issues.
+
+Who we are: <http://www.vistrails.org/index.php/People>
diff --git a/RELEASE b/RELEASE
new file mode 100644
index 0000000..fa4f501
--- /dev/null
+++ b/RELEASE
@@ -0,0 +1,2128 @@
+RELEASE NOTES
+-------------
+Release Name: v2.1.1 build 90975fc00211 from v2.1 branch
+
+Bug fixes:
+ - Ticket 816: Saved vistrail doesn't appear in 'my vistrails' (784414a617d2)
+ - Ticket 814: Parameter Exploration Broken (13da70d0b35f)
+ - Ticket Fix font issue for OS X 10.9. (22c0f0cca937)
+ - Fixes early gui import in application_server (3b2f6186cea9)
+
+From Release: v2.1 build 179c82045907 from v2.1 branch
+
+Enhancements:
+ - Ticket 292: Add XSL support to RichTextCell (ae0126167aa8)
+ - Set file associations on Linux (579d702aaab9)
+
+Bug fixes:
+ - Ticket 610: Exporting to the database should update locator (e6c3203a2710)
+ - Ticket 809: Suspending module attached to more than one sink kills workflow execution (3b791e47c453)
+ - Save button is not disabled when file is saved (d0dc3525f334)
+ - Items in workspace were sometimes shown incorrectly (d0dc3525f334)
+ - Context Menus in workspace were missing (d0dc3525f334)
+ - Read only string widget had multi-line button (9117e5bb367e)
+ - Opening configuration window with unsaved changes fails (fa3c1335580f)
+ - Infinite loop when changing string in Mashup App (2ee81b444300)
+ - Ticket 802: Can't exit VisTrails (da5c18a8b550)
+ - Ticket 796: [JobSubmssion] Issue when resuming job from unsaved vistrail after quitting (cc3d342688fb)
+ - Temporary files for untitled locators did not work correctly (3d9df4ab5ea2)
+ - Autosave prompts when vistrail is already open (cfc06bbc1c2c)
+ - Added LinuxMint as a supported Ubuntu variant (145c4c3c16ec)
+ - Ticket 581: Latex extension: clicking on a figure on the PDF file (on acrobat) gives an error (f1a581b11929)
+ - Publishing widget did not show unsaved vistrails correctly (0a4f49d7b081)
+ - Ticket 712: Useful messages when loading abstractions (07745fca0e99)
+ - Ticket 670: Traceback in configuration window (073b57d3bfca)
+ - Ticket 709: Recursing on abstractions tracebacks (5b850844b735)
+ - Ticket 776: 'Open in New Window' feature (71147be4b5ef)
+ - Ticket 794: Exits with 'cannot connect to X server' when starting core application (3c94ccc0ac9a)
+ - Fixed DBLocator equality method (e6c3203a2710)
+ - Ticket 771: Export to DB hangs if schema is not present (c102cb8f72c8)
+ - Ticket 787: Mac color chooser locks keyboard (628fb3e773fc)
+ - Ticket 740: Double-clicking a workflow in the workspace collapses the tree (3775961debd4)
+ - Ticket 738: Double-clicking a workflow in the workspace does not select it in the history view (3775961debd4)
+ - Ticket 723: Changing view fails on Fedora (ee7b4652e845)
+ - Ticket 722: Pipeline validation doesn't check for invalid functions (47d9c6de3e45)
+ - Ticket 277: Don't always receive "enable package" dialog (802fd0de0a7e)
+ - Ticket 415: Version tree refresh after API calls (0a2f6a59d6a7)
+ - Ticket 730: help() not available warning in Mac 2.1 binary (a946e4da59c1)
+ - Ticket 683: Packages should honor -S flag (9e5b83351d2f)
+ - Ticket 649: Batch mode doesn't allow a vt without a version (b5b65892aa10)
+ - Ticket 611: Mashups relational support missing (6bf5b2b02e48)
+ - Ticket 759: QLineEdit.setPlaceholderText does not exist in Qt 4.6.3 (a57fbba44e6e)
+ - Added progress reporting to Map module (0666e24d35f5)
+ - Cannot abort execution while a vtkAlgorithm is running (6b86705c0e59)
+ - Debian install script was used on Fedora (4acca49bcf74)
+ - Ticket 751: Display history view when opening vistrail with tagged versions (f2b053cee1aa)
+ - Spreadsheet history file path was set incorrectly (1789513a3afd)
+ - Fixes slot bug in PyQt 4.7.3 (17230667d58e)
+
+From Release: v2.1 beta2 build 99faabb791a0 from v2.1 branch
+
+Bug fixes:
+ - Ticket #735: Windows dulwich install via pip fails (14d362a695df)
+ - Ticket #718: persistence can't handle directories (2a668a6e9881)
+ - Fix issue with persistent paths in Windows (2a668a6e9881)
+ - Ticket #728: Upgrading vistrail with disabled package (b28c85b718ac)
+ - Fix issue with subworkflows using disabled packages (b28c85b718ac)
+ - Fix issue with staging persistent directories (6cddde545965)
+ - Fixed module upgrades not working with dynamic packages (bf997c6bb0c6)
+ - Fix issue with transfer function widget (11213143752c)
+ - Rewrites error-prone code for GitRepo#add_commit() (c1d2f60cc10d)
+ - Persistence sets up a Git username if none is set (f37129976ba5)
+ - Fixes default values on optional Boolean ports (34365eb22800)
+ - Ticket #705: zip.exe not found in Windows binary (69a16e3c5b84)
+ - Ticket #700: Upgrades with package identifier changes fail (32f934bef698)
+ - Ticket #716: The new IPython console does not receive console output (96d65c1d0e80)
+ - Ticket #699: Base classes for parameter config widgets do not enforce defaults (6e1a5624b2ae)
+ - Fix BooleanWidget default handling (6e1a5624b2ae)
+ - Fixed tricky upgrade bug (1385b1d04f4b)
+ - Ticket #626: Passing parameters to single instance still opens second instance of VisTrails (334c743f3c33)
+ - Fix issue with package identifier changes and upgrades (32f934bef698)
+ - run.py/fix_paths was broken (16aeafb32399)
+ - Looping over a failing PythonSource caused logger to fail (2b5ff8105562)
+ - Fixes line-endings for TestUnzip (05a41335f050)
+ - Disables deleting from the persistence store (3c816e2734b8)
+ - Adds tests for type-checking, using PythonSources (3f0c602b003a)
+ - Disables type-checking for InputPort modules (4cdad5f113df)
+ - module_info now shows a module's id (0c504fe06615)
+ - Limits copy and paste in module_info (b99c674c8494)
+ - Detects cycles when computing pipeline signature (3a0fe0b5a880)
+ - Adds some more checks for persistent path type (846631436bd0)
+ - Raises a ModuleError if persisting an empty dir (d3d8b2193b5f)
+ - Makes type-checking optional (30659a8b6525)
+ - Fixes adding a directory to persistence (0c26c5b68ee6)
+ - While requires *or* ConditionPort or MaxIterations (bdcd04e3366c)
+ - Fixes a package_dependencies() crashing VisTrails (3263be2d2a52)
+ - Lets PythonSource use the default source (7684997bd888)
+ - PythonSource configuration dialog now uses default (3dff503ce8ce)
+ - Fixes StringWidget not showing default correctly (49d9dbd161f0)
+ - Restores read-only mode removed by previous merge (4bdf4705a669)
+ - Removes most of the persistence_exp package (90c70ee525e6)
+ - Fixes matplotlib not able to reuse cells (243ae02dd499)
+ - Makes UntitledLocator inherit CoreLocator (fc863650a893)
+ - Fixes looping modules (34d3029f3419)
+ - Minor changes to persistence code (96a605e0ca3f)
+ - Adds back PersistentPath#git_command() (295f9ade09cf)
+ - Fixes an issue with fix_dates() (3ad431172b47)
+ - More fixes to found_another_instance_running() (916cdeb23f6f)
+ - Makes fix_dates static in PersistentRefModel (56dec62ea2aa)
+ - Fixes persistence view (1bbb9bfb5f45)
+ - Adds tests for Unzip and UnzipDirectory (22c9d361b78b)
+ - Makes HTTPFile cacheable again (5bc3619d5cba)
+ - Fixes running the CLTools wizard standalone (77bf72286a8c)
+ - Fixes CLTools test on Windows releases (c503e4df5cf9)
+ - Fixes UnicodeDecodeErrors in DebugView (5ce4fd3515d7)
+ - Adds an UnzipDirectory module (634e6415a62e)
+ - Fixes Unzip code (10a2a3753185)
+ - Fixes runtestsuite.py ignoring *system* (b1210c5dc5c7)
+ - ImageMagick fixes (b0994f0e5684)
+ - Cleans disabled packages from cache (51a4cf021a31)
+ - Removes QPackagesWidget#erase_cache attribute (2919064fcce2)
+ - Don't expand the module palette on package load (890b6796e4a2)
+ - Re-enables type checking after all (ec6539366bbd)
+ - Fixes optional tabledata->spreadsheet dependency (511ab651ad93)
+ - Makes numpy arrays valid Lists (6425d8d7a286)
+ - Merge branch 'optimize-module' into 'master' (906a6edf8e73)
+ - Minor fixes to installers (ba9550bb44f2)
+ - Moves rgb2hsv and hsv2rgb out of paramexplore (f00a710f2424)
+ - PythonSource now sets unconnected output ports (75f4d085c57f)
+ - Adds a Delay port on the While module (07087da25339)
+ - Renames 'optimization.py' to 'looping.py' (b4b2183e3bab)
+ - Renames Optimize to While, inverts condition (0a07b43c7a2f)
+ - Adds state output/input ports (e6f57d0f4999)
+ - Adds the Optimize module to ControlFlow (ea4ebd43293c)
+ - ExecuteInOrder now uses the ControlFlow style (3d286c21a17d)
+ - Adds a Delay port on the While module (2b2648c08820)
+ - Makes log-related flags not fold-specific (954c984cca31)
+
+From Release: v2.1 beta build 16ae99d82468 from v2.1 branch
+
+Enhancements:
+
+ - Ticket #695: Parameter explorations should be migrated through upgrades if possible (29f072af3087)
+ - Start migrating parameter explorations through upgrades (29f072af3087)
+ - Ticket #690: PythonSource Port Type Completion Requires "Enter" (f19e8a6e222a)
+ - Display version id in version properties (6eb10d9e3bcf)
+ - Static mashup animations (d40c74b42abb)
+ - Animation support for Mashups (cc578f2009a7)
+ - pip should now work on all platforms where it is available (b90fdba57189)
+ - Added graphical sudo for OSX (b90fdba57189)
+ - Added IPython Console (57f54943a73d)
+ - Use PyQt API version 2 (5229204a2dce)
+ - Multi-line editor for String modules (ff7d78aa76e4)
+ - Progress Dialog for workflow execution (459f3d003393)
+ - Improve interaction between pipeline views and controller. (a3bcdf6cc7a2)
+ - Improve API (aa1dbcc5f34d)
+ - Add more robust tracking of untitled vistrails. (913ed56d9445)
+ - Add matplotlib upgrades and integrate new pkg with new identifier scehme. (79bcb5673781)
+ - Support package identifier changes. (f77b92758c07)
+ - Build up the API and refactor core application methods (de9cea46a623)
+ - More updates to matplotlib package (44dff52c4da2)
+ - Add port spec translation from schema 1.0.3 to 1.0.2 (616a1090bf4b)
+ - Incremental/Online Layout (80cb92674de6)
+ - Spreadsheet: "Find Version" and "Save Camera" now works for unsaved, closed, and "saved as" vistrails (24243fd207fc)
+ - DB support for Mashups (4e8da08d81b1)
+ - Support backward comaptibility for packages that have not been updated to use the "vistrails." prefix when importing. (6ca1d510a773)
+ - Updated persistence package to use dulwich, a pure python implementation of git (263b6f339e50)
+ - PROV document can now be exported using the command line (script) (5f0b04c049e5)
+ - Ticket #604: Add vistrail variable support to parameter exploration (04496edc9bfd)
+ - Added PROV entities for input and output data (ae52faaadfa9)
+ - Using Dublin Core metadata for PROV document (PROV exporter) (652099fe855d)
+ - New version of the PROV exporter (03a0a2785e89)
+ - First version of PROV exporter (9d32409c7118)
+ - Serializable mixin class for modules (895fab7db230)
+ - User does not need to create IPython controller manually anymore (ba7edbc30ca4)
+ - Added support for SSH IPython engines in parallel flow (1a56f69a18e6)
+ - IPython controller is stopped when closing VisTrails or disabling the package (704658297b0f)
+ - Ongoing work on the exporter for the PROV model (704658297b0f)
+ - IPython controller and engines are now started from VisTrails (4ec53425ca92)
+ - Added information about the machine from each IPython engine (8a361420a384)
+ - Map (parallel flow) can execute an outer subworkflow in IPython engines (949f9edb24df)
+ - First version of package 'parallel flow' (ac162d9e7ccb)
+ - Module / Group executions from the IPython engines are added to the provenance (518b3a4b1129)
+ - Added some modifications in the code to allow the execution of workflow in IPython engines (d89b7f9861ee)
+ - Forward error messages when connecting to other instance (0ad89de1cb2a)
+ - Add uniform method for building descriptor, port_spec strings (9633bb6c1365)
+ - Allow selected portions of the workflow to be relaid out (6f558cc3e697)
+ - Add option to nicely layout workflows automatically (15ff124c6652)
+ - runtestsuite now returns 0 for passed test runs (5d44f2879811)
+ - Ticket #606: Copy parameter explorations between workflows (b8a25bc9bac8)
+ - Updates to parameter explorations (696b83875d73)
+ - Ticket #603: Parameter Exploration from command line (d5f554fa40e0)
+ - Ticket #545: Make unset parameters accessible from the Parameter Exploration view (7b5cbe95bbf3)
+ - Ticket #547: Migrate parameter exploration persistence to schema and controller (7b5cbe95bbf3)
+ - Unset parameters can be used in parameter explorations (7b5cbe95bbf3)
+ - New schema for parameter explorations (7b5cbe95bbf3)
+ - Parameter explorations can be named (7b5cbe95bbf3)
+ - Parameter explorations are visible in the workspace (7b5cbe95bbf3)
+ - Parameter explorations can be accessed without the gui (7b5cbe95bbf3)
+ - Improve exception message for invalid port specification (c01407d42d7c)
+ - Improve error messages during package loading (2ea29738dd9b)
+ - API: VisTrailsAPI.execute() now accepts the same parameters in core VistrailController.execute_current_workflow() (012a7e828338)
+ - LaTex Extension: Added support for relative .vtl links in pdf and relative filenames in .vtl files (2329f7e6eb10)
+ - AutoConnect: when dragging a new module into a workflow, try to connect it (5d6475919bb3)
+ - Allow port_and_port_spec_match to match two port specs (e068f2a835e2)
+ - Ticket #555: Move package-specific missing package handlers (42131938cd0f)
+ - Support enumerations for parameters (571a24363dda)
+ - Add gui support for different port shapes (9f7e54780c7b)
+ - Show when ports are set by darkening the port (9f7e54780c7b)
+ - Add visual cues for the number of connections set/needed/allowed (9f7e54780c7b)
+ - Added port docstrings to the VTK package (49aa19ba2ce3)
+ - Updated port documentation (befd489265d2)
+ - Add schema support for max/min connections for ports (befd489265d2)
+ - Native schema for Vistrail Variables (201b489e1c26)
+ - Add load_package method to API (abbc89ef42dc)
+ - Add load_workflow method to api (5786189661b2)
+ - Automatically install PyQt4 on Fedora Linux (b11e69aafe2e)
+
+Bug fixes:
+ - Fixed spreadsheet capturing keys in other windows (aad252798fe6)
+ - Fix issues with completions in port tables (f19e8a6e222a)
+ - Ticket #692: Parameter exploration schema logic invalid (44a29f0422b8)
+ - Fix translation bugs between schema versions. (6643e4dd610d)
+ - Ticket #693: Issue with PortSpecItem ids (16413b49c806)
+ - Fix ids on PortSpecItems (16413b49c806)
+ - Ticket #691: Executing a parameter exploration without the spreadsheet fails (48ccd5a64f54)
+ - Ticket #689: Mashups preview broken (3ea331e01abc)
+ - Refactor get_pipeline_name calls and remove substring hacks (3d8a9c875288)
+ - Fix QChar issue with parameter exploration (e07da85567a6)
+ - Fixed invalid current_view causing setCurrentWidget to fail (c93061c00bcb)
+ - Job Monitor: Could not run more than one job job in the same vistrail (609f09df5ce4)
+ - Job Monitor: Could not delete job other than current pipeline (609f09df5ce4)
+ - Job Monitor: Job for current pipeline was not stored on shutdown (609f09df5ce4)
+ - Looping over a failing PythonSource caused logger to fail (3bdf9620dd00)
+ - Ticket #678: Relational DB support for schema v1.0.3 broken (d54eb24cba1f)
+ - Fix issues with PortSpecItem (d54eb24cba1f)
+ - Ticket #680: Package configuration broken (20ba5b110fae)
+ - Fix broken clipboard check for paste (a6d1cc7c840c)
+ - Use codepath when identifier is not enabled when warning for old style imports (6a7f4a99a0c7)
+ - Disabling a package did not select it in the Available Packages list (8f50dcf2d941)
+ - Fixed vistrails->crowdlabs in latex/example2.tex (a95605ef12ab)
+ - Module: controller was not set in default moduleInfo (7360a90e23cd)
+ - Ticket #675: save_from_gui() is broken (482624c80e2e)
+ - Fix issue with saving untitled vistrails (482624c80e2e)
+ - Fix typo in application's convert_version (1866ec46e5ec)
+ - Logging fails when Group executed by Map fails (fcb6d4b1b637)
+ - VisTrails Server: fixed generating a pdf from a vistrail tree (0a3d02e92b48)
+ - Ticket #668: Commit 6cf6920 broke API tests (76887e74224e)
+ - open_many_from_db should not be used with pre 1.0.2 schemas (e2b247f2c588)
+ - Updated latex example files to use crowdlabs instead of vistrails.org (0314ecf38606)
+ - Fixed generating an image of workflow graph from the command line (3f40090c5e12)
+ - Images in thumbnails are now sorted by cell location (498081d7cdc5)
+ - Errors in package dependencies method caused VisTrails to fail on startup (1adc3d25bf73)
+ - Fix issue with intermediate persistent files not being found in the store when a uuid is already assigned. (72c89f5aa6ca)
+ - Fix earlier noted issue with importing the registry in create_instance_of_type (78df1961b099)
+ - Fix some issues with Windows paths and locators. (2e2c35df7dcf)
+ - Ticket #662: VistrailController constructor does not set _current_full_graph (a3bcdf6cc7a2)
+ - Push controller constructor calls through set_vistrail (a3bcdf6cc7a2)
+ - Don't generate an error when a user attempts to drag a module into a non-pipeline view (f7abe1fd73b9)
+ - Ticket #664: Debug Message Fails with AssertionError (5008bf52a105)
+ - Ticket #661: Controller's current_version=-1 causes issues (c69b430e1701)
+ - Fix issue with inconsistencies when current_version=-1 (c69b430e1701)
+ - Ticket #590: Packages are not updated when userpackages dir is modified (88480456e2cf)
+ - Fixed bug in matplotlib cell resizing (bbe9a6078797)
+ - Vistrail Variable list was changing while being iterated over (99e60cf4dccf)
+ - Saving log to prevoius version failed (d56da92fa406)
+ - Fixed update_db script to work with master (04968e309d94)
+ - Allow reading different versions of subworkflows from DB (c5a33a0b8ead)
+ - Fixed loading wrong abstraction DB version (06a06be04889)
+ - Fixed trying to write empty workflow list to DB (06a06be04889)
+ - PipelineView: Execution exceptions were not caught which caused jobView to lock up execution (3b460bdb7c95)
+ - Mashups: controller_changed caused widget to be redrawn even when the controller did not change (801c3b8e58a8)
+ - Ticket #656: Control Flow Wizard is broken (95275d116c24)
+ - Fixed deleting mashup alias using Del/Backspace key (1d68ccf02f81)
+ - color picker widget gets orphaned in the alias inspector (1d68ccf02f81)
+ - Fixed bug on PROV exporter (f7675297ad23)
+ - Fix issue with Mac binary and the vistrails.py sys.path changes (09840f6c815b)
+ - Save log to xml action was not enabled in menu (dbc83ce34917)
+ - Ticket #641: PersistentInputFile not recognizing changes in the file contents (4f85d3d25ab9)
+ - Fix issue where file changes were not being recognized (4f85d3d25ab9)
+ - Ticket #639: Package details are not updated when a disabled package is selected in preferences panel (a251d6fe54a0)
+ - Execution of workflows in IPython engines (ba7edbc30ca4)
+ - Groups and Subworkflows can now have their execution log annotated (d89b7f9861ee)
+ - Ticket #635: Error translating from schema 1.0.2 to 1.0.3 (5fbdbe702dcb)
+ - Fix issue with whitespace between port spec items (816094bc7d64)
+ - Ticket #577: Publish window always shows grayed out snippet (fc9c5e5e11ce)
+ - Ticket #633: Automatic package download is not working on master (bce780145a5c)
+ - Ticket #626: Passing parameters to single instance still opens second instance of VisTrails (0ad89de1cb2a)
+ - CLTools: Modules were not reloaded after reloading scripts (283f8b57166b)
+ - CLTools: "env" option was not reset in wizard when loading other tool (283f8b57166b)
+ - Server mashup request need to use db user with write access (81c51908662c)
+ - MissingPackageVersion exceptions need to be tied to specific modules (5d13c3e8292b)
+ - Ticket #629: Issue with namespace (63a696d66c3b)
+ - Fixed issue with reloading packages with namespaces (63a696d66c3b)
+ - Allow only a single MissingPackage exception to be included in an InvalidPipeline container exception (a1401ec6afbb)
+ - Fixed typo with ghosted pen color (a0bdae3f8c4a)
+ - Ticket #627: Duplicate enable package messages (fb21c5c5e4b0)
+ - Fix errors in parameter exploration when viewing invalid pipelines (fb21c5c5e4b0)
+ - Do not emit errors from the query view when the selected version changes (9e1eb696ce67)
+ - Ticket #617: Hard import from the v1_0_0 schema in opm.py makes it fail with other schemas (1c7b21fab942)
+ - Fix OPM import (1c7b21fab942)
+ - Windows: Saving vistrail zip xml fails when zip.exe cannot be located (d80fbb746549)
+ - Ticket #624: unix /bin/ls check fails on fedora 17 (bcd044c4ff75)
+ - runtestsuite.py should not care about empty string arguments (f417c703c364)
+ - Fixed typo in parse/update for parameter types introduced in recent commit (133102abe14f)
+ - #623 (133102abe14f)
+ - Fixed issue with connecting tuple ports in the API (5eddcc1a9e47)
+ - Ticket #621: Hidden ports that are used in connections are not set to visible (e40295454a40)
+ - Fixed visibility of a connected port in ports panel (e40295454a40)
+ - Fixed issue when connecting modules (2811ba5d4ff3)
+ - Fixed documentation file of CLTools that was causing a failure when building the pdf version of the usersguide (a0c19535e7d6)
+ - Ticket #618: Open Workflow from DB missing in file menu (61619a425285)
+ - Ticket #614: test_abtraction_create fails in test suite (6885385a769d)
+ - Preferences sometimes tried to set up a removed package (5d44f2879811)
+ - SplashScreen was never deleted (5d44f2879811)
+ - Ticket #613: triangle_area.vt fails on the map operator (ad4b579121c2)
+ - Fix bug with obtaining port spec signature (ad4b579121c2)
+ - Ticket #612: User-defined parameter exploration editor is problematic (7512a2d05434)
+ - Fix issue with modified group signatures (b542543e1332)
+ - is_running_gui missing in VistrailsServerSingleton (557586218e5a)
+ - Fixed issue where OPM export could not resolve ports in parent modules (d084c5742ffb)
+ - SUDSWebServices did not handle empty configurations correctly (0cfe904c59f4)
+ - Ticket #583: CLTools: sometimes a module called CLTools is displayed (f2d755b24f53)
+ - Empty packages could not be reloaded (f2d755b24f53)
+ - PortSpecItem schema did not work on MySQL (b7556465275b)
+ - Parameter Explorations were not being converted correctly from 1.0.2 (b7556465275b)
+ - Parameter Explorations were not being loaded from database correctly (b7556465275b)
+ - Saving a Vistrail failed when package manager was not available (b7556465275b)
+ - Ticket #601: Connection port compatibility should be checked at a lower-level (f984fd5087c0)
+ - Check port compatibility at controller level (f984fd5087c0)
+ - Ticket #602: core api does not work in console (1d965a2cf952)
+ - Add missing methods to GUI application (1d965a2cf952)
+ - Ticket #599: Missing defaults cause exception when adding a function (a98e0a7962c8)
+ - Ticket #594: Defaulted booleans added twice (ef684f869d62)
+ - Fix duplicate boolean values when using defaults (ef684f869d62)
+ - Update color of cached modules correctly and reset colors on re-execute (48981ae5cfbe)
+ - Do not set module color back to active after it has been run (4f55071bb133)
+ - Ticket #591: User-decorated modules do not change color during execution (86fe5d0ad9a1)
+ - Module status brushes are checked first when setting the color of a module (86fe5d0ad9a1)
+ - Ticket #592: Dragging a Group module into a pipeline causes an invalid pipeline error (bb2f60099e4c)
+ - Guard against empty group modules (bb2f60099e4c)
+ - Spreadsheet package: Checking if the GUI is running before trying to initialize the package. (c9d20070140c)
+ - Catch exceptions when selecting invalid modules (3c3a6755adfa)
+ - Ticket #586: Selecting an invalid module raises exceptions (cb6c5b161c57)
+ - enabling/disabling package did not invalidate pipeline (1a280b63a745)
+ - Ticket #585: Failed reloading of a package does not invalidate modules (057f031ee4c3)
+ - Fixed issue where modules were not marked as invalid before validation (057f031ee4c3)
+ - Ticket #584: Enabling a package adds it to the enabled package list even if there are errors (11125174c7ff)
+ - Fix issues with package list in preferences (11125174c7ff)
+ - Unselect port on mouseReleaseEvent (56f2d9aedf37)
+ - SUDSWebServices: Offline Mode by storing WSDL in .vt file was not portable (eba546527401)
+ - SUDSWebServices: Typo in handle_missing_module caused packages with wrong names (eba546527401)
+ - Ticket #575: Vistrail variables panel has an overdraw problem (52c864c3ddb2)
+ - Ticket #576: Analogies are only displayed if we change the focus out of VisTrails to another application and back (8c023062c639)
+ - Ticket #539: Standard Module Configuration Widget asks to save when two ports are enabled (c9d5d03962b2)
+ - Configuration widgets will prompt to save only when the current module change, making it easier to copy text from another application (c9d5d03962b2)
+ - Ticket #569: Connected icon in Module Information does not disappear after removing connection (11e93fd142cb)
+ - Loading an image from workflow graph or a version tree was not working in the command line (2329f7e6eb10)
+ - Workflow results that used a VTKCell were consisting of a black screen when running in batch mode (49adb4fd6b5d)
+ - Ticket #487: isosurface script version of terminator.vt causes vistrails to crash (76de9f741635)
+ - Ticket #540: Vistrail is not always marked as changed when containing a vistrail variable (49cb21769a83)
+ - Ticket #563: Temporary connection does not appear second time you create the same connection (3bd812f9cd6c)
+ - Fix issue with temporary connection disappearing (3bd812f9cd6c)
+ - Ticket #546: Selecting a version selects the text box instead of the version ellipse (a19863118684)
+ - Ticket #550: Workspace state_changed is slow (bd734eb57838)
+ - Ticket #553: Suspended module does not execute on second run even when notcacheable (8eb9f8d11575)
+ - Parameter Exploration only worked on parameters from the Basic Modules package (75cca6574d0e)
+ - Fixed minor issue with PortSpec shape and docstring attrs (aebf4f84b052)
+ - Ticket #418: The database schema should use larger data types (75c7c6c89fdf)
+ - Bug in translation from 1.0.3 to 1.0.2 (75c7c6c89fdf)
+ - Fix issue with configure item grabbing mouse. (479a29491abc)
+ - Removed capitalized methods from ports in VTK (49aa19ba2ce3)
+ - Parameter Exploration: Changed call to update the progress bar to be thread safe (b9942f416fe1)
+ - Mediawiki extension: fixed undefined variable (d3d68b1c53ab)
+ - WorkflowExecution.completed were set to False in the vis_log, it should be an int. (50a2a68e177a)
+ - DBVistrail.hash*Annotation() fails when annotation values are ints (3d7f1b9cc078)
+ - Fixed path_to_figures and get_wf_graph_ calls in application_server (6df2c53cc880)
+ - Do not import VTKCell unless we have the spreadsheet (a8b7c8345ee9)
+ - HTTP Package now respects alternate dotVistrails setting (88b53249d96d)
+ - The create analogy button is too small (65be8388e906)
+ - "Show raw pipeline" and "construct from root" commands should switch to the pipeline view (dc2deb9ed6e0)
+ - Fix command_line argv dependency (5786189661b2)
+ - Mashups: slider and numericstepper widgets are only displayed for numeric aliases (3b8c4f954bce)
+ - Mashups: Validating Min Max and Step edit boxes so they accept only numbers (3b8c4f954bce)
+
+From release: v2.0.2 build 3813fdd2573b from v2.0 branch
+
+Enhancements:
+ - Added animation support to matplotlib/pylab (38fb971b6305)
+ - Job Monitor Improvements (af8f43039c94)
+ - Job Monitoring Tool View (3c43a8c5b3b7)
+ - Add support for customizing which packages are (not) reloaded (91e18f8749a0)
+ - Testing: Validate Workflows by comparing old and new thumbnails (401588f3bfdb)
+ - Added saving/loading SubWorkflows to/from the DB as part of a vistrail bundle (0704f03b2011)
+ - Ticket #628: Set the path to the vistrails tmp dir (f07b3223d16d)
+
+Bug fixes:
+ - Saving log to previous version failed (e66941c40e22)
+ - Opened vistrails were not selected (14415ac3c709)
+ - parallelflow: Do not deepcopy module dict (e66a6a3713ec)
+ - Fixed matplotlib spreadsheet cell resizing issue. (45f803f0763c)
+ - API: return result after execution (aec0ed019ac5)
+ - Job Monitor icons were set incorrectly (d5e332c4e410)
+ - Job Monitor did not delete job when vistrail was closed (d5e332c4e410)
+ - Workspace: Sometimes selecting an open vistrail does not select it (e1f57079d0fd)
+ - Ticket #651: Function remap upgrade operations performed in incorrect order (6aaa72017fa8)
+ - Fix ordering in function remap (6aaa72017fa8)
+ - Ticket #648: 'OutputPort' object has no attribute 'module_exec' (c9847fc14bb9)
+ - Ticket #647: ModuleSuspended does not work inside Groups (c9847fc14bb9)
+ - Ticket #645: Document py_import in dev guide (bf9a58708fa2)
+ - Ticket #646: Reloading packages fails in some cases (91e18f8749a0)
+ - Fix issues with package reloading (91e18f8749a0)
+ - Fixed broken mimetypes on Windows (9aa51dd35301)
+ - Ticket #643: cannot open workflow triangle_area.vt (67726aceba3b)
+ - Ticket #625: Improve crowdLabs upload interface (7389abac0902)
+ - Added DB version map 1.0.2->1.0.3 needed when downgrading the log (172301ad3858)
+ - Saving abstractions do DB was missing version translation (45ebc5afa303)
+ - Removed faulty import DBProvModel (6727b6ee2fe8)
+ - Ticket #619: Create Analogy does not work on spreadsheet (39df0813e11c)
+ - Fix issue with analogy api in the spreadsheet (39df0813e11c)
+ - Ticket #638: Re-execution of SubWorkflow is missing parameters (294574341168)
+ - Fix issue with subworkflow caching (294574341168)
+ - Ticket #634: Package Documentation says port sigstring can contain spaces (dfc9db1f4dc5)
+
+From Release: v2.0.1 build 5e35e2b83b90 from v2.0 branch
+
+Enhancements:
+ - ALPS package: Updated to version 2.1.1 (4741aa04a9d7)
+ - Support import of schema v1.0.3 (94bb430fa0f0)
+ - CLTools: Preview command line arguments and module ports (6c737e297a60)
+ - CLTools: Reload modules from the wizard (6c737e297a60)
+ - CLTools: Add env port using wizard (6c737e297a60)
+ - CLTools: Extended documentation (6c737e297a60)
+ - CLTools: Ability to specify fixed environment variables for modules (6ece9152e511)
+ - CLTools: Write changes in environment variables to execution log (6ece9152e511)
+ - Added server function for seeing and enabling/disabling packages (1b7ad7717b31)
+ - CLTools: Ability to set working directory (cbf02c561ccd)
+ - CLTools: New arg type inputoutput that enables files be used as both input and output (692e3ce05961)
+ - CLTools: You can now specify file endings for output files using the suffix option (692e3ce05961)
+ - Ticket #582: CLTools: should support other types (c3b49457c3a5)
+ - Added single instance check as a configuration option and a command line option (4032ca504171)
+ - Improved exception message for invalid port specification (431802313d43)
+ - Improved error messages during package loading (4175f8c09b4d)
+
+Bug fixes:
+ - Added the missing v1_0_3 directory for schema v1_0_3 support from master branch (916cf9162df8)
+ - FileHooks for DBVistrail types should be skipped (94bb430fa0f0)
+ - Check if package has been removed before setting package information (94bb430fa0f0)
+ - CLTools: Modules were not reloaded after reloading scripts (6c737e297a60)
+ - CLTools: "env" option was not reset in wizard when loading other tool (6c737e297a60)
+ - Server mashup request need to use db user with write access (af73f32d44c0)
+ - get_vt_graph_png was broken (af73f32d44c0)
+ - Ticket #617: Hard import from the v1_0_0 schema in opm.py makes it fail with other schemas (2fefff447711)
+ - Fix OPM import (2fefff447711)
+ - Windows: Saving vistrail zip xml fails when zip.exe cannot be located (32bd4aa03c3b)
+ - Ticket #624: unix /bin/ls check fails on fedora 17 (ee2cd7d1f6c3)
+ - Ticket #621: Hidden ports that are used in connections are not set to visible (4cb7b1758bac)
+ - Fixed visibility of a connected port in ports panel (4cb7b1758bac)
+ - Fixed documentation file of CLTools that was causing a failure when
+building the pdf version of the usersguide (3899208009dd)
+ - is_running_gui missing in VistrailsServerSingleton (272006002712)
+ - Ticket #618: Open Workflow from DB missing in file menu (8e413fc8f504)
+ - Ticket #614: test_abtraction_create fails in test suite (2315d8e92026)
+ - Ticket #583: CLTools: sometimes a module called CLTools is displayed (11107c05a73a)
+ - Empty packages could not be reloaded (11107c05a73a)
+ - Ticket #612: User-defined parameter exploration editor is problematic (deab533c7302)
+ - Fix issue with modified group signatures (cd8e2467903b)
+ - Ticket #464: VTK Package does not support VTK 5.10 release (65462fd17800)
+ - Fixed issue where OPM export could not resolve ports in parent modules (cdc1a53bf496)
+ - Fixed issue where modifying a defaulted parameter caused a second copy of the parameter to be added (d6924b42d821)
+ - Ticket #602: core api does not work in console (ac85e1935819)
+ - Add missing methods to GUI application (ac85e1935819)
+ - Ticket #594: Defaulted booleans added twice (e90af069e58a) (d6924b42d821)
+ - Fix duplicate boolean values when using defaults (e90af069e58a)
+ - Update color of cached modules correctly and reset colors on re-execute (421ef3182f7b)
+ - Do not set module color back to active after it has been run (1f6ea4ff45e3)
+ - Ticket #591: User-decorated modules do not change color during execution (c53334a5e412)
+ - Module status brushes are checked first when setting the color of a module (c53334a5e412)
+ - Ticket #592: Dragging a Group module into a pipeline causes an invalid pipeline error (cd8b62b219a6)
+ - Guard against empty group modules (cd8b62b219a6)
+ - Spreadsheet package: Checking if the GUI is running before trying to initialize the package. (a71954b1639a)
+ - Ticket #586: Selecting an invalid module raises exceptions (225f057294dd)
+ - Catch exceptions when selecting invalid modules (225f057294dd)
+ - enabling/disabling package did not invalidate pipeline (a363ed3f0151)
+ - Ticket #585: Failed reloading of a package does not invalidate modules (46a6204cbab4)
+ - Fixed issue where modules were not marked as invalid before validation (46a6204cbab4)
+ - Ticket #584: Enabling a package adds it to the enabled package list even if there are errors (0593aad10533)
+ - Fix issues with package list in preferences (0593aad10533)
+ - SUDSWebServices: Offline Mode by storing WSDL in .vt file was not portable (6fa03241e9c6)
+ - SUDSWebServices: Typo in handle_missing_module caused packages with wrong names (6fa03241e9c6)
+
+From Release: v2.0 build 240bcab5bbcd from v2.0 branch
+
+Enhancements:
+ - Ticket #424: SUDSWebServices should store the WSDL spec in the .vt file to enable upgrades (88f616a741de)
+ - Packages can store files in .vt zip files (88f616a741de)
+ - .vt files using SUDS Web Services can now be edited offline (88f616a741de)
+ - CLTools: package menu option for reloading all scripts (3c83b7101bc0)
+ - CLTools: added Open Wizard to package menu (1f19d0a7339a)
+ - Added CLToolsWizard.command file to Mac Binary (99adfd823a2d)
+ - Ticket #430: use of absolute file names can be problematic in vtl files (2b731d8d5043)
+ - LaTex Extension: Added support for relative .vtl links in pdf and relative filenames
+ in .vtl files (2b731d8d5043)
+ - Package requirement for the job submission package (77f3f1761f92)
+ - Ticket #519: Executions in Version View that fail should change to pipeline (cea08c6e25d9)
+ - Switch to pipeline view if an execution fails (cea08c6e25d9)
+ - Ticket #557: Password dialog (f9739db121c4)
+ - Ticket #559: Persistent modules do not work in groups (4ef2b8639b6d)
+ - Allow modules in subpipelines to be cached (4ef2b8639b6d)
+ - Added alps package to VisTrails 64-bit Windows Binary (519d862a63f5)
+
+Bug fixes:
+ - Ticket #575: Vistrail variables panel has an overdraw
+ problem (c4171c8aab63) (09815c35efb8) (7ca53292670a) (07fdeb8602a7) (45a4818a0b5c)
+ - Ticket #404: Overriding a port via add_*_port does not work (47e72744ede1)
+ - Ensure add_*_port can override ports in superclass port lists (47e72744ede1)
+ - Ticket #523: Default values for parameters not showing (e3f1b1a3253f)
+ - Add default support back in (e3f1b1a3253f)
+ - Fixed spelling in repository.py (6c2259e84214)
+ - SUDSWebServices: Wrong indentation caused vistrail save to fail (5497e50c727f)
+ - Ticket #576: Analogies are only displayed if we change the focus out of VisTrails to
+ another application and back (d782197a1cab)
+ - Fix issue with redrawing the tree after analogies (d782197a1cab)
+ - Running instance was not accepting parameters from another instance (63b58b8416d0)
+ - Ticket #464: VTK Package does not support VTK 5.10 release (3e3700900ad0)
+ - Ticket #445: mashup previews is not always shown in the main window (9111971ce8c6)
+ - Now persistent cache works after one execution (87e8ff129b88)
+ - Ticket #573: Opened vistrail fail when reloading dependent package (b1ff731d904a)
+ - SUDSWebServices: Failed Web Services could not be removed (b1ff731d904a)
+ - Execution button may hang when execution fails (b1ff731d904a)
+ - Ticket #571: Vistrail variables cannot be used in more than one workflow (02f2acee1727)
+ - Fix issue when setting a vistrail variable on multiple modules (02f2acee1727)
+ - Ticket #574: Cannot add variable to empty detached Vistrail Variables window (4ae4f3d9c582)
+ - Fixed issue with creating vistrail variables in an undocked panel (4ae4f3d9c582)
+ - Ticket #539: Standard Module Configuration Widget asks to save when two ports are
+ enabled (154525da1047)
+ - Ticket #521: Annoying PythonSource behavior (154525da1047)
+ - Configuration widgets will prompt to save only when the current
+ module change, making it easier to copy text from another application (154525da1047)
+ - QVistrailsWindow.get_current_view() was returning the wrong view sometimes (154525da1047)
+ - CLTools: IOErrors when executing process (d810075f00a6)
+ - Fix issue with analogies that also require upgrades (215ceae6ef1f)
+ - Fix typo (50da981b6938)
+ - Fix issue with remove vistrail variable modules and connections (c3183771c5ea)
+ - Ticket #569: Connected icon in Module Information does not disappear after removing
+ connection (9a68ec624c9d)
+ - Fix issue with connected indicator for ports (9a68ec624c9d)
+ - Eliminate duplicate warnings (f6020fa412bb)
+ - Use lil_matrix for analogies (f6020fa412bb)
+ - Modify logic of analogy usage to use current selected version (f6020fa412bb)
+ - Ticket #419: Analogies fail on new terminator.vt (83c7735b0d28)
+ - Change analogies to use a suitable default alpha value (83c7735b0d28)
+ - Ticket #567: CLTools has issues reading man pages on Mac OS X (cdb5368df6fc)
+ - Ticket #370: dataDirectory setting not used (73fe930b49ff)
+ - Loading an image from workflow graph or a version tree was not
+ working in the command line (2b731d8d5043)
+ - Workflow results that used a VTKCell were consisting of a black
+ screen when running in batch mode (80d55defb140)
+ - Ticket #551: Cannot access messages window when preferences window is open (cc8fa8e6ad8a)
+ - Ticket #487: isosurface script version of terminator.vt causes vistrails to
+ crash (02caf56e6c0e)
+ - Ticket #564: Invalid view warning (3b2062c17cb0)
+ - Ticket #552: No visual clue when ubuntu package finishes installing (2f78b1b1d749)
+ - Ticket #540: Vistrail is not always marked as changed when containing a vistrail
+ variable (7acddff31ff1)
+ - Ticket #566: QPixmap scaled error message (c6842a9fa320)
+ - Fixed QPixmap scaled issue (c6842a9fa320)
+ - Ticket #517: Undo menu item not working (a7b574defe31)
+ - Fix undo/redo in pipeline view (a7b574defe31)
+ - Fix issue with executions of untagged versions (36c1a73a46ae)
+ - Ticket #560: Workspace has very inefficient updates (51a4e7982bb7)
+ - Workspace: made loading mashups more efficient (51a4e7982bb7)
+ - Ticket #562: "Save as" replaces items from workspace (d8fa58ccd9c0)
+ - Ticket #560: Workspace has very inefficient updates (3dfac92ab688)
+ - Partial fix to make workspace more efficient (3dfac92ab688)
+ - Ticket #565: Version labels in query results are not gray (22e9920d1ea0)
+ - Fix colors in query results view (22e9920d1ea0)
+ - Ticket #504: The Query's refine option doesn't do anything (1fce254de2c5)
+ - Reenable refined version tree in the query view (1fce254de2c5)
+ - Ticket #532: Edit Package Abstraction Error (7c03b6999125)
+ - Fixed issue with error message for editing package subworkflows (7c03b6999125)
+ - Ticket #541: Crash when detaching ModuleInformation dockwidget on Mac (72c7afc3a95e)
+ - Fix crash on undocking module info palette on Mac OS X (72c7afc3a95e)
+ - Ticket #546: Selecting a version selects the text box instead of the version
+ ellipse (5a7df50dd899)
+ - Make version tree selection more intuitive (5a7df50dd899)
+ - Ticket #538: Pipeline Connection Drawing? (ed11bdfffa54)
+ - Fix connection drawing issue on Mac (ed11bdfffa54)
+ - Ticket #558: Group signatures cannot be based only on interface (4ef2b8639b6d)
+ - Fix issue with caching group modules (4ef2b8639b6d)
+ - Fix initial layout of matplotlib cells (3a8d5c7c3d62)
+ - Decreased level of debug message when removing elements from Thumbnails cache (18531d5fb280)
+ - Ticket #534: Mashups hang with auto-update on (1472b6ba7f32)
+ - Ticket #550: Workspace state_changed is slow (1ed823ecbb96) (b75607ea9271)
+ - Ticket #556: Path to zip.exe not set correctly (d0389bec6df6)
+ - Fix logic in identifier checks in package manager (1882ed36cd76)
+ - Ticket #554: Port labels not displayed (a9454abc238a)
+ - Add missing port labels to ports panel (a9454abc238a)
+ - Ticket #553: Suspended module does not execute on second run even when
+ notcacheable (3e22759385d3)
+ - Ticket #549: update_db.py script does not work (fb5ad0eb480a)
+ - Parameter Exploration only worked on parameters from the Basic Modules
+ package (99969b93ece2)
+ - Autoloading a SUDS Web Service no longer produce error messages (c079bd9c52db)
+ - Ticket #513: Add detachHistoryView back (08bec17e40e6)
+ - Ticket #543: Changes to persistence module configuration doesn't work (d03382c67e1d)
+ - Fix issue where reconfiguring persistent modules caused unexpected behavior. (d03382c67e1d)
+ - Show error message when trying to open a vistrail with a newer schema version (32f47804b6c7)
+ - db_log_filename was not unset correctly for db cache (8fccb74ecab3)
+ - Ticket #531: Export To Stable Version menu does not work (1b742a9f70cc)
+ - Export to DB did not work (1b742a9f70cc)
+ - Reloading a vistrail from the database gave it the name "None" (1b742a9f70cc)
+
+From Release: v2.0-beta build 716501f8b2fd from v2.0 branch
+
+Enhancements:
+ - Mashup View: Added float slider (b5d481049666)
+ - New module execution state suspended added (cb47d3fc66b7)
+
+Bug fixes:
+ - Parameter Exploration: Changed call to update the progress bar to be
+ thread safe (716501f8b2fd)
+ - Fixed bug in iceCream.vt example (929ddcaa504a)
+ - MySQLdb was not being shipped correctly in Mac binary (e50f1c91b3e8)
+ - Mashup View: integer slider did not set step size correctly (b5d481049666)
+ - Cached interpreter failed when handling wrong input type (b5d481049666)
+ - Mashup View: failure when handling errors in execution that does not use the spreadsheet (b5d481049666)
+ - Fixed qt.conf problem in installer script files on Windows. (a01fabd12456)
+ - Fixed arguments of get_wf_graph_png rpc call (7cc451bdb606)
+ - updateUpstream* failed when modules did not contain the suspended attribute (256f4b4dd8a5)
+ - Mediawiki extension: fixed undefined variable (334083cc69e1)
+ - WorkflowExecution.completed were set to False in the vis_log, it
+ should be an int. (cb47d3fc66b7)
+
+
+From Release: v2.0-beta build 10836452c19a from v2.0 branch
+
+Bug fixes:
+ - Fix issue with deleting modules and connections (10836452c19a)
+ - VTK package: fix problem when upgrading vtkCellArray.InsertNextCell input port (e29a873af4a1)
+ - Ticket #525: The create analogy button is too small (bf61e06b0a50)
+ - Ticket #526: "Show raw pipeline" and "construct from root" commands should switch to the pipeline view (3ada5972d872)
+
+From Release: v2.0-beta build b074d3a4eb44 from v2.0 branch
+
+Enhancements:
+ - Added VisTrails Server documentation (611f2082f98d)
+ - Add more functionality to core.api (26c775f0a7bb)
+ - Ticket #518: Need to fix VTK ports with no parameters (9a985c40f6a2)
+ - Add separate workflow and log xml schemas (04cb36cc5305)
+ - Added support to hardcode necessary packages on startup (834e28f7cfa4)
+ - CLTools: Added enviroment variable and default directory support (5a6e1b0daba3) (7c9a113040c2)
+ - Add operation ids to messages about illegal operations (087b235e32de)
+ - Remove most PyQt4/gui dependencies in core functionality (e6ada340cc15)
+ - Ticket #55: Spreadsheet should have more shortcut icons (5f4db41dc8f2) (127037be178f)
+ - Ticket #284: Capturing Module Errors (60c055eff8f5)
+ - Display module toolTip errors in module stack trace dialog (60c055eff8f5)
+ - Wizard for CLTools - gui for wrapper creation (a7a1db436fd0)
+ - Added support for html and mediawiki extensions to
+access a remote vistrails server (dd7456507ab4)
+
+Bug fixes:
+ - Mashups: editing an alias' values list had no effect (c485a7433dde)
+ - Mashups: slider and numericstepper widgets are only displayed for
+ numeric aliases (c485a7433dde)
+ - Mashups: Validating Min Max and Step edit boxes so they accept only
+ numbers (c485a7433dde)
+ - Accessing Module Annotate from context menu did not work (ac100b566d84)
+ - Fixed problem where unrequested vistrail temporary files were being created during test suite (445e2b68d9e6) (1a539cad8a9a)
+ - Fix issue with alternate .vistrails directory and its subdirectories (7d26c36ef77a)
+ - Fixed MissingRequirement path and ubuntu detection (11dd911b66a3)
+ - Ticket #528: Install bundle fails with the new core_no_gui changes (87f9e83772ea)
+ - Rendering version and workflow view in server failed because of new gui in 2.0 (e149aa955dd5)
+ - save_many_to_db failed when list of objects were empty (ed257eb2d523)
+ - Vistrail server need to initialize theme after core_no_gui changes (c4d2809d9a09)
+ - Fixed server mode after merge with core_no_gui (4c2cad40c30f)
+ - Ticket #522: remove_connection failure (cc038a500e3c)
+ - Fix for remove_connection issues (cc038a500e3c)
+ - Fixed issues with tabbing in the python editor (c046c86bf0af)
+ - Fixed issue with vtkInteractionHandler which was not updated when the Save/Revert changes were made to source widgets (8abbfb8a51e9)
+ - Allow zero-parameter functions to be set from ports panel (9a985c40f6a2)
+ - Fixed issue with forced versions on modules (4ae602caa09e)
+ - Fix issue with merging thumbnails (5bcaa7e75c6d)
+ - Fixed typo in core.application's register_notification (42c7ae6b0e25)
+ - Argument error caused gui/vistrail_controller test to fail (e447e02b37ca)
+ - CHEBI wsdl changed (a7f1ab43159d) (6e00beb17ce6)
+ - Removed matplotlib backend selection warning (23a6e3a89001)
+ - Dragging a version directly on a spreadsheet cell was not executing
+ the workflow (3395a01a2139) (66d49a064e59)
+ - Fixed unable to display jpeg images in the spreadsheet
+due to a wrong Qt plugins configuration (a6a1950024a7) (333456765278)
+ - Display more meaningful error when persistent inputs do not exist in a repository (1c905da96eb1)
+ - Fix issue in ModuleDescriptor.expand_descriptor_string (7b973b4a4aeb) (35f1feb4d853)
+ - Add icons to CLTools so that they not only work on X11 (a6a08bc1dd4e) (69110931c4e3)
+ - SourceConfigurationWidget silently fails when code contains
+ non-ascii characters (0c020878edf3) (768fc8ed4df5)
+ - MultiHeads configuration was not working on 2.0 (669957620bdc) (07e9672e6186)
+ - Ticket #513: Add detachHistoryView back (f238870a17fe) (38a3b95d1b5d)
+ - Added back detachHistoryView option (f238870a17fe) (38a3b95d1b5d)
+ - Removed configuration options that are only used in non-interactive mode
+ from Expert Configuration (bb0046fe6f49)
+ - Ticket #515: opening a specific version from the command line does
+ not work (20ab44a5a4ce) (468fe95d351f)
+ - Fixed opening a specific version from the command line (20ab44a5a4ce) (468fe95d351f)
+ - Ticket #512: Add how to create alias to users guide (83e49a3d487b)
+ (d56e02d30133) (a6249193e674) (f5b881191441)
+ - Ticket #421: db version import error handling (a6eb8ae65052) (6ac6c0abec6e)
+ - Detect between when a db version is missing and when it contains
+ an error (a6eb8ae65052) (6ac6c0abec6e)
+ - Ticket #391: Module colors in Visual Diff are wrong after upgrades (6b16033351a9) (c28166f2110b)
+ - diff view did not use correct brush for non-upgraded modules (6b16033351a9) (c28166f2110b)
+ - autosave feature caused "new file" action to fail (9b19a0fc5193) (6c49e4329b8a)
+ - Ticket #511: "export workflow as xml" adds extension as "..xml" (two dots) if
+ not explicitly specified (39d605e721e5) (fb2061eec506)
+ - get_save_file_locator_from_gui was adding two dots (39d605e721e5) (fb2061eec506)
+ - SpreadSheet: prompt the user to save unsaved vistrails before trying
+ to save a spreadsheet (d296dae6e508) (5e29113d0694)
+ - Ubuntu Unity did not restore menu bar after being closed (3d702340c1fa) (719ad4dd22b5)
+ - Param Exploration User-defined function did not work because of new python
+ editor interface (8354a9340944) (0f62ec4023c7)
+ - Ticket #510: The Spreadsheet can't open/save spreadsheets (9259d3b8d619) (ae73b7e48971)
+ - Ticket #194: Copy and paste duplicates aliases (7419092665c4) (27ee5e68a7e3)
+ - Ticket #480: Executions button doesn't work (c6a9a6ac15cf)
+ - Ticket #500: Double-clicking the Execute button causes VisTrails to Hang (e024a352c6ce)
+ - Double clicking execute button no longer hangs vistrails (e024a352c6ce)
+ - Ticket #508: Add port documentation back to ports panel (01f189a1a184)
+ - Ticket #505: Version notes are not always visible after an upgrade (d16b3c834c47)
+ - Issue correct version_selected signal after upgrades (d16b3c834c47)
+ - Ticket #502: change_selected_version causes key error in adjacency_list (25104a599816)
+ - Ticket #472: parameters in parameter exploration are reset if not executed (d07bcbd5104b)
+ - Parameter exploration with Color Constant was not working (b0e0da8cc61b)
+ - Ticket #462: Ungrab mouse error after editing subworkflow (2ffac0767f88)
+ - Ticket #432: Problem with labeling groups (2ffac0767f88)
+ - Allowing opening vistrail files that contain mashups. Mashups will be ignored (7d568fec386f)
+ - Ticket #454: Can't interact with TransferFunction widget using Qt 4.7.* (f897a8e68285)
+ - Fixed header placement in xml files that were causing tests to fail (a76060081c31)
+
+
+From Release: v2.0-alpha build c4e3600b6481 from v2.0 branch
+
+Enhancements:
+ - Wizard for CLTools - gui for wrapper creation (de5fbcd6144a)
+
+Bug fixes:
+ - Ticket #508: Add port documentation back to ports panel (d83b2637f5b5)
+ - Ticket #502: change_selected_version causes key error in adjacency_list (815d38ff608a)
+ - Ticket #472: parameters in parameter exploration are reset if not executed (829303e1efeb)
+ - Parameter exploration with Color Constant was not working
+ (ecfbedcd4406)
+
+From Release: v2.0-alpha build c4e3600b6481 from v2.0 branch
+
+Enhancements:
+ - Wizard for CLTools - gui for wrapper creation (de5fbcd6144a)
+
+Bug fixes:
+ - Ticket #508: Add port documentation back to ports panel (d83b2637f5b5)
+ - Ticket #502: change_selected_version causes key error in adjacency_list (815d38ff608a)
+ - Ticket #472: parameters in parameter exploration are reset if not executed (829303e1efeb)
+ - Parameter exploration with Color Constant was not working
+ (ecfbedcd4406)
+
+
+From Release: v2.0-alpha build 1b88c3949efd from v2.0 branch
+
+Enhancements:
+ - VisTrails now requires Python 2.7.*, Qt 4.7.*, sip 4.12.2 and PyQt4 4.8.4 to run
+ - Reworked VisTrails interface. Added Workspace palette where user's vistrails
+ are kept. Users can open multiple pipelines in different tabs that are
+ detachable.
+ - In addition to Pipeline, History, Query and Exploration Views, new views were
+ added, including Provenance and Mashup views. The Provenance view displays the
+ execution logs of a vistrail. The Mashup view allows creating simple
+ applications based on workflows by exposing only the relevant parameters.
+ See the VisTrails manual for detailed instructions.
+ - Merged the "Methods" and the "Set Methods" panel into an improved
+ "Module Information" Palette. Now port visibility, connectedness, and
+ parameters are shown in a single display. Thus, for module types without
+ special configuration widgets, there is no need for a separate configuration
+ window.
+ - CLTools - package for wrapping command line tools (3ac68958d3db)
+ - Expand search results to include all open vistrails (b2a069e38956)
+ - Opening exported mashups using Open menu will execute them automatically (48cefab0a019)
+ - Added support for exporting a mashup to a .vtl file. To export a mashup, just
+ click the "Export" button in the mashups inspector. Double-clicking the .vtl
+ file will execute the mashup in VisTrails (09203c1e12b8)
+ - Show parameters for invalid modules (7078566f7b89)
+ - Changed "Keep" button to "Tag" in the Mashups View (5ed3637c2d6f)
+ - Open subworkflow from module palette (c48a11df430f)
+ - Executions in provenance view are now given names based on the
+ "tagname + n" naming scheme (31a4a94cf967)
+ - Update executions in workspace when they are created (8b7b85229c64)
+ - Make pipeline current when selected in provenance explorer (49e93f5f789d)
+ - Remove gui dependencies for core.modules widgets (1b8487908620)
+ - Improved default query support (b9fed84af41a)
+ - Added color difference support for queries (b9fed84af41a)
+ - Mashups: made keeping the camera across updates as an option (1642d3573f62)
+ - Add extensible query support (0df170d3335d) (5d776c28b7e2)
+ - Workspace now updates Workflows and Mashups as they are created (429ceb313408)
+ - Expand Workflows/Mashups items by default (429ceb313408)
+ - Ticket #479: Dropdown boxes have white text (677a0b750762)
+ - Added support for html and mediawiki extensions to access a
+ remote vistrails server (2eba04217a99)
+ - Displaying mashups in workspace. Double-clicking a mashup will show
+ version tree, select corresponding version and execute the mashup. (3df2af8d8cb2)
+ - Added support for multiple PythonSource configuration windows. Read-only
+ windows can be detached from the main module onfiguration window. (372c0143f6b6)
+ - Remove workspace entry when selected file has been deleted (8bdd77c78fe2)
+ - Workspace can show workflows in a tree view (c715b4a84a38)
+ - Added a Control Flow Assistant (f05f014bc778)
+ - Added Vistrail Variables support, so that modules deriving from Constant can
+ be used to create re-usable variables (a83402e0c218)
+ - Added support for cross-vistrail diffs (c300063531e8)
+ - Perform visual diff from workspace by dragging pipelines together (dd83c3f08cea)
+ - Simplify visual diff and improve parameter changes display (65849c433682)
+ - Search results show up in workspace window (f3a763972866)
+ - Improve query handling (e4b0722b1d70)
+ - Added support for opening a vistrail in a separate window (f502431ae11b)
+ - Added Expand All and Collapse All buttons to Module Palette (264410835b7)
+ - Added annotations to WorkflowExec in v1.0.2 schema (0ade1076517b)
+ - Provenance browser now shows status icon in list (fc112c4c1079)
+ - Autosort module palette (de80a5b0fb1c)
+ - Added merge by dragging vistrail to vistrail (6bb73281842a)
+ - Executable paper editing (3a96ea787a82)
+ - PythonSource editor will now indent newline to previous line (e221d10351d1)
+ - Improved PythonEditor class using QScintilla2 (d737455457db)
+ - PythonSource editor will now indent newline to previous line (d1e5d63bd715)
+ - Enhanced query capabilities (0e5f60ce0d91)
+ - Added support for interpreter to execute a pipeline with an extra list
+ of parameter values. Updating VistrailController calls to also accept
+ the new list (db6e4611305)
+ - persistence package now hides file references instead of deleting them (ae3d19282ef4)
+ - Added versioning for SUDS Web Services using content hash (47279d4246bf)
+ - Improved PythonEditor class using QScintilla2 (5ed5953f57b9)
+ - ParaView package: Added ScalarBarWidgetRepresentation to Rendering
+ namespace in modules list. (7429a1be15cf)
+ - Add better provenance information for persistent entities (22964cfeb53b)
+ - New manager for persistent store (f0dafc611fd0)
+ - Improved efficiency of vtk workflow upgrades (3736cc9ef269)
+ - LaTex extension: Added an example for embedding local files (be50aeab59ca)
+ - Group SQL statements to enable faster DB communication (b520f1c847c8)
+ - ParaView package: Added server configuration window options to
+package configuration and loading initial values from there. Also added
+option to start paraview server when the package is initialized. (9023c13aa76b)
+ - Ticket #408: Allow opening multiple PythonSource Editors (73e72b8419a8)
+ - Ticket #411: Support temporary directories in the FilePool (7eb29d2ba0fb)
+ - Initial version of a GIS package that uses QGIS (4cd7cc6df8db)
+
+Bug fixes:
+ - VTK Package: Call to ResetCamera() in vtkRenderer was producing wrong
+ results (d5789e5a560b)
+ - Ticket #499: Issue with BaseView.layout (9dc74870fde7)
+ - Fix issue where 'layout' was an overloaded field name (9dc74870fde7)
+ - Ticket #494: Tuple configuration is confusing and causes configuration errors (30bc134d5cdb)
+ - Ticket #498: Need to update code to show parameters for invalid modules (8da733c07199)
+ - Enable showing invalid function and show parameters in separate fields (8da733c07199)
+ - Updated version of suds python library on both Windows and Mac binary.
+ - Ticket #488: configuring webservices breaks vistrails (090a45a95f19)
+ - Ticket #456: Cannot copy/paste in detached pipelines/vistrails (970ec4ecfb42)
+ - Ignoring action updates when the view does not have the actions (970ec4ecfb42)
+ - Make provenance view read-only (9774b9e2928e)
+ - .vtl files marked to be executed when opening were not executed (09203c1e12b8)
+ - Ticket #496: Showing/hiding module ports resets module position (c073ff4bf200)
+ - Keep module position when changing visibility of ports (c073ff4bf200)
+ - Ticket #488: configuring webservices breaks vistrails (b8a935d8bbae)
+ - Ticket #495: vtkCellArray won't allow multiple points through
+ InsertCellPoint (0dcbf136aeb8)
+ - Fixed issue with ports that may have multiple functions associated with
+ them (e.g. in the vtk package) (0dcbf136aeb8)
+ - Ticket 481: Optional Output Ports collapse to non-Optional ones (7463f214023b)
+ - Fixed the issue of being unable to activate windows under Mac OS X
+ Lion. (7463f214023b)
+ - Mashups: Fixed bug introduced when removing gui
+ dependencies for core.modules widgets (76a998022666)
+ - Ticket #492: Upgrade error: signatures differ (5a70996965f8)
+ - Add upgrade for PythonSource to fix issue with 'self' port (5a70996965f8)
+ - Fixed messages during upgrades so that upgrade info is not flagged as
+ a warning (8714561fed05)
+ - Mashups: creating aliases in mashup view was not updating the alias
+ table (770f755d089d)
+ - Ticket #491: Opening a .vtl will always create a new file (3a25858be1ac)
+ - Opening vtl files: igonring showSpreadsheetOnly if execute is false (3a25858be1ac)
+ - Starting VisTrails by double-clicking a vistrail file was
+ not zooming the current pipeline view (3a25858be1ac)
+ - Can now delete from workspace using backspace key (d3f7af2868b0)
+ - Remove vistrail from workspace if removed from disk (044a841b97e9)
+ - view.is_abstraction logic fixed (044a841b97e9)
+ - sql package was not using new gui.modules.source_configure (1714703fb145)
+ - Updated VTK, Persistence and Matplolib packages to use
+ gui.modules import (f953ce4d25e4)
+ - get_current_view bug caused double-clicking a vistrail to fail (00b264c0920b)
+ - Ticket #489: VisTrails 2.0 can't open .vtl files anymore (2d450422c25b)
+ - opening .vtl files fails (2d450422c25b)
+ - Ticket #460: Subworkflow port naming errors after editing (687becdff050)
+ - Fixed issue where subworkflow edits could result in one-to-many
+ port mappings. (687becdff050)
+ - Fixed issues with multiple versions of subworkflows appearing in the
+ module palette (186d5c06a788)
+ - Do not store subworkflows in "recent files" or "My Vistrails" (17aebdbd32fa)
+ - workspace.item_selected had invalid setSelected call (3effd7a1385b)
+ - Fixed 2 detach view bugs (3f5159f5b49f)
+ - Ticket #468: Diff tab should have all modes except pipeline
+ disabled (4f691ba6ed23) (139ec1d18b22)
+ - Fixed an issue when loading a vistrail that references different versions
+ of a subworkflow that share common ancestors (4b34089abb09)
+ - Ticket #486: query execution and parameter problems (323f12916d09)
+ (0262b0410051) (d9fbb412a9b5)
+ - Added ability to open workflows from query results (323f12916d09)
+ - Ticket #484: subworkflow save causes window to change (bc100442dfe4)
+ - Fixed issues with executing queries (0262b0410051)
+ - Fixed issue where numeric comparisons were being done as
+ string compares (d9fbb412a9b5)
+ - Fixed issue where substring queries were backward (d9fbb412a9b5)
+ - Fix an issue with copy/paste to query view (b9fed84af41a)
+ - Fix issue with package subworkflows and namespaces (87c7c61f1c9e)
+ - Ticket #476: numeric stepper has wrong default value, in some cases
+ (1642d3573f62) (a08e8dc0f9c2)
+ - Ticket #485: Random Mashups Window (917b1d8b83c5)
+ - Allow return to original query in interface (0df170d3335d)
+ - Allow parameters to be set in queries (0df170d3335d)
+ - Allow return to original query in interface (5d776c28b7e2)
+ - Allow parameters to be set in queries (5d776c28b7e2)
+ - Ticket #478: Mashups updating issues (e5913008d81c)
+ - Mashups: Display Widget section was not updated when
+ switching aliases (e5913008d81c)
+ - Mashups: Mashup inspector was not updated when switching
+ vistrails using the workspace in Mashups View (e5913008d81c)
+ - Mashups: Mashup Pipeline Palette was not being updated when
+ switching mashups using the Mashup List Panel (e5913008d81c)
+ - Ticket #483: Index error when recovering a vistrail (8589b301ba13)
+ - Fixed issues with upgraded subworkflows (9c4dfcbef423)
+ - Ticket #475: Changing the background color fails in Mashup mode (31670c3e66f2)
+ - Ticket #477: opening mashup from workspace doesn't show exposed
+ parameters (429ceb313408)
+ - Sometimes closing a vistrail while closing VisTrails fails (429ceb313408)
+ - Double clicking a vistrail in file browser fails because of
+ _first_view bug (263f1947cf2c)
+ - vtkhandler did not handle new PythonEditor correctly (aa3511259f10)
+ - Ticket #443: ports are not added through Module Configuration
+ and annoying confirmation (01ed7a6566b3)
+ - Ticket #473: Cannot execute from history view immediately after
+ opening vistrail (e0ba2e97d058)
+ - Ticket #472: parameters in parameter exploration are reset if
+ not executed (63c55f11f03d)
+ - Ticket #474: Error quitting when spreadsheet is visible (afe4512b1ca9)
+ (107b24e904ea)
+ - Ticket #470: copy doesn't copy to the correct cell (c44347501d5a)
+ - Fixed issue with cell locations in spreadsheet editing mode (c44347501d5a)
+ - Ticket #471: visual diff window is missing the create analogy
+ button (14a24ea42b15)
+ - Ticket #469: locate version in editing mode selects history but shows
+ pipeline (080a2dc8b820)
+ - Opening xml vistrail from workspace showed open file dialog (069db5448e8e)
+ - Module documentation in module palette not working (647613ad637e)
+ - Ticket #467: A file is changed when test suit is run (37e0ab607139)
+ - Ticket #466: history mode selected and pipeline view shows up after
+ merging 2 trees (e22fe0a4f8b0)
+ - Ticket #459: the explore tab draws upside down (542e2cda8845)
+ - Outdated inspector.annotated_modules value caused explorer tab to be
+ drawn upside down on Mac (542e2cda8845)
+ - Ticket #446: subworkflow editing only good for one save (2ab6a92c2084)
+ (85b50d980ab1)
+ - Fixes to subworkflow upgrades and save as (2ab6a92c2084)
+ - Changes to subworkflow identification (85b50d980ab1)
+ - Ticket #465: Open Recent menu does not contain saved vistrails (a484b18b3eed)
+ - Update recent files list also when vistrail is saved (a484b18b3eed)
+ - Ticket #463: Current version not selected on open (154e9b2e8eaa)
+ - Select latest version when opening a vistrail (154e9b2e8eaa)
+ - Ticket #462: Ungrab mouse error after editing subworkflow (6aaa6bd2b526)
+ - Ticket #432: Problem with labeling groups (6aaa6bd2b526)
+ - Ticket #461: Initial history view for first vistrail is not zoomed to
+ fit (b3d8909ac0ed)
+ - Fix zoom to fit for initial vistrail (b3d8909ac0ed)
+ - Ticket #434: Can't remove tags of versions that were
+ upgraded (v2.0) (47636de1ec66)
+ - Fix issue where raw pipeline and construct from root were not
+ working (47636de1ec66)
+ - Enabled Embed version by default when selecting Publish > To Paper (8bf5e737a2c2)
+ - Ticket #456: Cannot copy/paste in detached pipelines/vistrails (0cb6ef7650af)
+ - Fixed issues with spreadsheet editing for copies and analogies (d2d4bae51a6d)
+ - Enabled Edit Configuration and Show Documentation from a module's
+ context menu (00dcb21d22a6)
+ - File > Export > PDF was not working (fce8cc569c14)
+ - Ticket #455: Module Information Tab stretches unnaturally when package
+ has a long name (2d07662227fd)
+ - module information stretches unnaturally (2d07662227fd)
+ - Ticket #457: PythonSource ports are not updated when configuration window
+ is saved (f6e151300476)
+ - Ticket #456: Cannot copy/paste in detached pipelines/vistrails (f9470d9fa04a)
+ - Removed missing web service (028fc4e03c62)
+ - Fixed header placement in xml files that were causing tests to fail (4db41b9e2e75)
+ - Workspace fixes for saving empty vistrail and closing detached
+ vistrail (1f798a7a0c84)
+ - Ticket #454: Can't interact with TransferFunction widget using
+ Qt 4.7.* (ea7e21dc9e01)
+ - Ticket #453: Workspace indexing error in tree mode (f8b17ab82b9b)
+ - Skip workspace make_tree when no window exist (f8b17ab82b9b)
+ - Ticket #450: Indexing failures need to be more graceful (f76532828242)
+ - Better error handling when indexing workflow (f76532828242)
+ - Ticket #452: Visual Diff Parameter Changes not detected (65849c433682)
+ - If the clipboard contained utf-8 characters, VisTrails would raise
+ an error (d7cecf541ced)
+ - QPipelineScene.addModule were calling addItem twice (d77e833f431f)
+ - Dropping vistrails variable created error (8c0b0e921201)
+ - Fixed export/import menu options (8d68b5b56ff3)
+ - Fixed parameter exploration in v2.0 (8485390429b1)
+ - Parameter exploration was not saving color parameters when they
+were being interpolated (8485390429b1)
+ - Fixed 'Diff properities' label typo (8a88bd21895a)
+ - Removed close button from Vistrails Messages view (2581ea446bad)
+ - Ticket #441: vistrail browser is not being updated (d892cd18e5b8)
+ - Correctly update collection on load/save (d892cd18e5b8)
+ - Show project selector (d892cd18e5b8)
+ - Sort default project by name (d892cd18e5b8)
+ - Ticket #435: diff result is not properly sized/centered (96c4adaa2a1a)
+ - Show executions for the current session as well (fc112c4c1079)
+ - Workspace threw exception when closing vistrails (47ae1c3c4428)
+ - Fixed crash when running VisTrails 64-bit on Windows with more than 4GB
+ of RAM (71b4bfc41a6d)
+ - 2 bugfixes to the vistrail merge code (4f05a96bcc2c)
+ - open merged vistrail in new tab and other fixes (556804ba40c4)
+ - builder_window was stealing ctrl-z/ctrl-y from PythonSource (e221d10351d1)
+ - Made new PythonEditor use correct font (2579b6f662ca)
+ - removed self reference in static method in persistence package (12e57882a72b)
+ - open merged vistrail in new tab and other fixes (971228751494)
+ - Fix menubar issue on non-Mac platforms (9d5e66156935)
+ - persistence package did not show dates correctly (357f3a55aaf5)
+ - Spreadsheet package: Fixed a typo on the usage of issubclass() which prevented
+ subclassed sheets to be used by the spreadsheet (8bcd8ac86cd4)
+ - SUDSWebServices wsdl caching in Windows need to use pickle
+ protocol=0 (4ca71139f604)
+ - SUDSWebService wsdl hash did not use the correct wsdl string (4ca71139f604)
+ - Fix issue with caching and persistent files (f56f14061d3f)
+ - ParaView package: Fixed example pipeline where it should display
+ both a box and a sphere. (7429a1be15cf)
+ - VTK Package: Fixed bug when drawing TransferFunction widget (daaacfcedfca)
+ - Handle unnamed data when writing from manager (22964cfeb53b)
+ - Fixed infovis example (7d6a0dace8ca)
+ - Fixed NOAA Web services example. NOAA had changed the urls
+for their services (7d6a0dace8ca)
+ - Do not import MySQLdb directly in sql_dao (b1d1809c0d57)
+ - Ticket #420: VisTrails fails to install package dependencies on Ubuntu (35cd1cceeded)
+ - debug imports cause ubuntu package install to fail (35cd1cceeded)
+ - Ticket #416: The log is not copied when saving a vistrail from database to disk (1af107087fbe)
+ - Include log when copying vistrail from DB (1af107087fbe)
+ - LaTex extension: When generating LaTex command using the Embed panel,
+ make sure to enclose tag between {} so symbols are escaped. (be50aeab59ca)
+ - LaTex extension: Fixed problem when passing envrionment variables
+using \vistrailsenv{} (be50aeab59ca)
+ - Ticket #417: Database INSERT statements are not protected from overflowing (b520f1c847c8)
+ - Overflow checking for SQL datatypes (b520f1c847c8)
+ - Changed memory size to be computed in megabytes instead of bytes
+to avoid large numbers (4d21156d99f5)
+ - Ticket #414: Focus out event on Tag version edit box generates an unnecessary
+ vistrail change event (6dc3154542ba)
+ - Media wiki extension: casting returned version of a given tag to
+string before using it (6dc3154542ba)
+ - Ticket #412: Parameter exploration on File parameters fails (e54b74bb9412)
+ - Fix parameter explorations on File parameters (e54b74bb9412)
+ - Added ability to create temporary directories in the FilePool (7eb29d2ba0fb)
+ - LaTex extension: added support to work on Windows with MikTex (2bdfb94be496)
+ - LaTex extension: changed behavior of passing environment variables -
+passed variables will not replace existing ones, they will be inserted at the
+beginning (2bdfb94be496)
+ - Removed warning when copying thumbnails fail because the files are the
+same (2bdfb94be496)
+ - New log file was not being created on Windows when the version was
+upgraded (2bdfb94be496)
+ - Ticket #410: Encode VTK changes as upgrades (fa2e48cedf06)
+ - Attempt to implement VTK upgrades (fa2e48cedf06)
+ - Ticket #409: Problem in workflow upgrade (5d57b4ce54b3)
+ - Fix issue with upgrading modules with null functions (no parameters) (5d57b4ce54b3)
+ - Ticket #407: Aliases in a workflow disappear after upgrade (843603916a48)
+ - Preserve aliases during upgrades (843603916a48)
+ - Replaced more GUI code that would work only on recent versions of Qt/PyQt4 (7cfcb98320ee)
+ - Replaced code that would work only on recent versions of PyQt4 (e5ca41c3fab7)
+ - Enabled with_statement for python2.5 (3ec5bdd47c3e)
+
+
+From Release: v1.7 build 325bfe1b517d from v1.7 branch
+
+Enhancements:
+ - VisTrails is now distributed under the "Modified BSD License"
+ - VisTrails binaries are now shipped with python 2.7.1, Qt 4.7.2, sip 4.12.2,
+ PyQt4 4.8.4, vtk 5.6.1, numpy 1.5.1, scipy 0.9.0 and matplotlib 1.0.1.
+Bug fixes:
+ - Importing basic_modules.py leads to import loop (325bfe1b517d)
+ - VTK Package: Fixed bug when drawing TransferFunction widget (7722fc6727aa)
+
+From Release: v1.6.2 build af4a69ad566a from v1.6 branch
+
+Enhancements:
+ - Adding pdf version of Usersguide to binaries. (60cec4e6d858)
+ - Improved efficiency of vtk workflow upgrades (501a552cd722)
+ - LaTex extension: Added an example for embedding local files (f5976c82826f)
+
+Bug fixes:
+ - Fixed infovis example (bd810b67daaf)
+ - Fixed NOAA Web services example. NOAA had changed the urls
+for their services (bd810b67daaf)
+ - Added matplotlib mplot3d toolkit to Mac binary (5054da25e2e8)
+ - Ticket #410: Encode VTK changes as upgrades (aeaa56469120)
+ - Attempt to implement VTK upgrades (aeaa56469120)
+ - Ticket #420: VisTrails fails to install package dependencies on Ubuntu (5180336d429d)
+ - debug imports cause ubuntu package install to fail (5180336d429d)
+ - LaTex extension: When generating LaTex command using the Embed panel,
+ make sure to enclose tag between {} so symbols are escaped. (f5976c82826f)
+ - LaTex extension: Fixed problem when passing envrionment variables
+using \vistrailsenv{} (f5976c82826f)
+ - Changed memory size to be computed in megabytes instead of bytes
+to avoid large numbers (5f57a040c97c)
+ - Ticket #414: Focus out event on Tag version edit box generates an unnecessary vistrail change event (460836e2206e)
+ - Media wiki extension: casting returned version of a given tag to
+string before using it (460836e2206e)
+ - Ticket #412: Parameter exploration on File parameters fails (7630f10fb73c)
+ - Fix parameter explorations on File parameters (7630f10fb73c)
+ - LaTex extension: added support to work on Windows with MikTex (36322a953de2)
+ - LaTex extension: changed behavior of passing environment variables -
+passed variables will not replace existing ones, they will be inserted at the
+beginning (36322a953de2)
+ - Removed warning when copying thumbnails fail because the files are the
+same (36322a953de2)
+ - New log file was not being created on Windows when the version was
+upgraded (36322a953de2)
+ - Ticket #409: Problem in workflow upgrade (040f46c2f980)
+ - Fix issue with upgrading modules with null functions (no parameters) (040f46c2f980)
+ - Ticket #407: Aliases in a workflow disappear after upgrade (5575069d2727)
+ - Preserve aliases during upgrades (5575069d2727)
+ - Replaced more GUI code that would work only on recent versions of Qt/PyQt4 (2704aa1fe222)
+ - Replaced code that would work only on recent versions of PyQt4 (50ead740f6de)
+ - Enabled with_statement for python2.5 (bec2a6498965)
+
+
+From Release: v1.6.1 build ba9616b413d2 from v1.6 branch
+
+Bug fixes:
+ - Ticket #406: Builder Window menu inconsistencies (fd46220842bf)
+ - Added support for executing workflows even if VisTrails is already
+running (useful for Latex extension) (16c1d253a63a)
+ - Added single instance limitation per user/machine instead of per
+machine. Now multiple users logged to the same system can execute their
+version of VisTrails (16c1d253a63a)
+ - VisTrails was ignoring batch mode input parameters if already running
+ (16c1d253a63a)
+ - Latex and Wiki extensions: all options can now be set from the builder. (16c1d253a63a)
+ - Ticket #405: VisTrails is not downloading unavailable packages if they are present in the packages repository (77cadf0fb8a1)
+ - VisTrails batch mode: Separated generation of the workflow graph from execution of the workflow. Added support for generating the history tree graph (77cadf0fb8a1)
+ - When generating a workflow graph VisTrails would sometimes generate a line in the borders (77cadf0fb8a1)
+ - When testing a database connection with a password=None VisTrails would crash without catching the exception (77cadf0fb8a1)
+ - When opening a vistrail from a vtl, VisTrails was ignoring the version that should be open and always opening the most recent one (77cadf0fb8a1)
+ - Latex extension: added support for running vistrails locally (15255a96e4e0)
+ - Latex extension: added support for embedding workflow and/or
+including full tree when generating vtl requests (15255a96e4e0)
+ - Wiki extension: workflows were not being embedded in .vtl file (5348cad089ba)
+ - Added title to console and debugger toolbars (b2e3bda06f62)
+ - Better error handling for duplicate module identifiers in packages (579520227409) (d5df9421d0c1)
+ - Fixed an issue where the FilePool's local copy mechanism failed in Windows (7b398b211212) (254bce86348e)
+
+
+From Release: v1.6 build e9f97c5908ac from v1.6 branch
+
+Enhancements:
+ - Added prompt for password for database access in batch mode (06c4b63434a7)
+ - Please notice that the parameter separator in the command line changed again from
+ '&&' to '$&$' so it's consistent with the server version. (35ad76515a97)
+ - VisTrails now has "Check for Updates" option in Help drop-down (b80862d8a39f)
+ - Show port_spec.sigstring in PortMismatch error message for more
+ detailed debugging (c28dad738abc)
+ - Turn off popup messages if messages window is open (62aeb9371235)
+ - add/delete Web Services from module palette for SUDSWebServices package (2e381a4394ed)
+ - Package-level context menus in the module palette (2e381a4394ed)
+ - Add preference for migrating tags and notes on upgrades (41177e74e687)
+ - Add stack trace to exception details for unexpected exceptions during
+ change_selected_version (fd3840df3c6b)
+ - Added new class Chdir to prevent users from triggering side-effects by accident
+ when using os.chdir() (4aa722db61d1)
+ - Added Open Recent to File menu (it works for vistrails in the file system or in
+ the database. The maximum number of files in the list can be configured from Advanced
+ Preferences Tab (search for maxRecentVistrails) (4aa722db61d1)
+ - Configuration object now supports bound methods as subscribers (4aa722db61d1)
+ - Debug messages now have a "details" attribute (f2911a6a6000)
+ - Buttons for filtering VisTrails messages (ebc728d49db3)
+ - Colors of message types added to theme file (ebc728d49db3)
+ - Improved log messages in the server log to also indicate the instance of the server that
+ is logging the messages (762902e79b7a)
+ - Improved handling of log messages (037568dc5960)
+ - Changed all examples using relative paths to datasets to use HTTPFile (403205442fd7)
+ - Updated head.vt and terminator.vt example to use TransferFunction widget (403205442fd7)
+ - Maintain suffixes on persistent files and directories (e9b5e906e069)
+ - Improved debug messages (9dcd1a5a2ea8)
+ - Ticket #390: Add support to Latex extension to download workflows at compilation
+ time (90ef6cee20a9)
+ - Improved error handling in vistrails.packages (a44800a88083)
+ - Improved debugging messages for vistrails.gui (25b718347ef0)
+ - Improved error handling in vistrails.core (2e095f36dc90)
+ - Debug library updated (41e3778d507e)
+ - Web Services package is now deprecated. Showing a warning message when the WebServices
+ package is loaded. Message will be shown only once. (9996bba52dd1)
+ - Ticket #375: Add GUI support for synchronizing vistrails (4efb09fbe5bd)
+ - Merge 2 Vistrails from within VisTrails (4efb09fbe5bd)
+ - Detect changes to directories so the cache can be invalidated when they change (3058d55966f2)
+ - New Web Services package that uses SUDS library (0d1d3efb99da)
+ - Add pinch gesture support to graphics views (3d01e549f849)
+ - ParaView package: Converted to new VisTrails package format (65453bd92aa5)
+ - Updated php scripts to work with Latex extension's new features (2b53ad32a374)
+ - VisTrails server: added new function to return version tree as pdf (2b53ad32a374)
+ - Created a separate php file to store the server configuration (8d15fdbe8e1d)
+ - Added support for running crowdlabs and vistrails server on separate machines
+ (still testing) (064304a99993)
+ - Ticket #382: Improvements to Latex extension (3123297d6a1b)
+ - LaTex extension: VisTrails can now embed a workflow graph or a history tree in
+ LaTex pdf (3123297d6a1b)
+ - LaTex extension: Caching latex instructions and images for embedding images in case python
+ is not available (3123297d6a1b)
+ - Ticket #381: Split HTTPFile.compute() method to download the file in a separate
+ function (62d25dca3f3a)
+ - Add MplScatterplot and MplHistogram modules to pylab (4af6514c20d4)
+ - Ticket #295: Add Debug .command to Mac distribution (e835d69d8426)
+ - Added git executable to windows repository. It will be included in future windows
+ binaries for persistence package (8d9931bbbe04)
+ - Updated version of the rpy package (c895125216cb)
+ - Migrating new persistence package from persistence_exp to persistence (5b6418233dea)
+ - Added methods to expand shortcut string representations for module descriptors and port
+ specs (5b6418233dea)
+ - Added support for shortcuts to remap modules/ports for upgrades (5b6418233dea)
+ - Use List for controlflow now instead of ListOfSElements (74f30460d3fe)
+ - Highlight invalidate port specs (74f30460d3fe)
+ - Improved support for work with the filesystem. Added DirectorySink module,
+ changed FileSink module to use 'overwrite'
+ instead of 'overrideFile', added support for getting the contents of a
+ directory, created a new OutputPath constant with a save-style widget
+ to select the output path, replaces OutputName on the FileSink module.
+ Added updgrade code to translate old FileSink module to new version.
+ Changed version of basic_modules and abstraction to static string
+ '1.6'. (fb30dca8a15d)
+ - HTTPFile now supports proxies. (3799edddbb62)
+
+Bug fixes:
+ - Fix issue with console mode and unit tests (a4d544eec673)
+ - Ticket #361: Cannot configure output cell layout for cells in groups in parameter
+ explorations (5807414236ba)
+ - Enable all spreadsheet cells for parameter exploration, even if they are embedded in
+ groups or subworkflows (5807414236ba)
+ - Ticket #399: Exception thrown when loading parameter exploration tab with no existing
+ exploration (4366e52c39cf)
+ - Fixed exception when loading parameter exploration tab for a workflow with no saved
+ explorations (4366e52c39cf)
+ - Ticket #154: vistrails should check for a new version being available and tell the
+ user to download it (b80862d8a39f)
+ - Ticket #398: Failure opening vtl files (filename issue) (c52ba7adc5f8)
+ - Matplotlib package: if hide toolbar parameter is set after the source
+ and there isn't an extra line at the end, the MplPlot would fail (c52ba7adc5f8)
+ - Ticket #398: Failure opening vtl files (filename issue) (cdfa0c97493d)
+ - Added escaping to filename in unzip commandline call (cdfa0c97493d)
+ - Fixed issue where it was not possible to ungroup a subpipeline that had an InputPort
+ connected directly to an OutputPort (e1ea9b437507)
+ - Fixed problem where controlflow package would raise duplicate errors (4351b3f0102f)
+ - Fixed issue with groups and input values that evaluate to False (6fc007c0535d)
+ - Fixed ordering of PortMismatch parameters in ensure_port_specs (c28dad738abc)
+ - Fixed bug introduced on Windows platforms when changed os.chdir() calls by
+ core.utils.Chdir (0a2b8a0d50d8)
+ - Enable the Linux theme for 'Linux' system types (57dfb4a85e7a)
+ - added deletion of namespaces in module palette (2e381a4394ed)
+ - Add ability to migrate tags when upgrades are not delayed (9c49285269ca)
+ - Message filter colors does not show in linux (ee8906c91039)
+ - Ticket #397: Save execution log when in console mode (2dae96a8f004) (1afa51d895e9)
+ - Update version tree when adding delayed actions (d1dbf3005499)
+ - Subworkflows from packages that need upgrades are now moved to local.abstractions
+ in the registry and picked up for workflow upgrades (04476a172f61)
+ - Fixed issue with spreadsheet and grouped spreadsheet cells (fd3840df3c6b)
+ - Replaced svn command with git command to get current commit (if present) (4aa722db61d1)
+ - Flush delayed actions (including upgrades) to fix issues with delayed upgrades and
+ grouping upgraded workflows (79dd982e6cef)
+ - VisTrails Server: Applied fix to caching of history tree images when
+ generated as pdfs (fc0ab9f1626d)
+ - VisTrails Server: fixed problem in caching of history tree images (4862e1f7d18a)
+ - Ignoring mouse gestures when Qt version is < 4.6 (4862e1f7d18a)
+ - Ticket #394: VisTrails server is not detecting updates in vistrails loaded
+ from the database (762902e79b7a)
+ - Restoring extensions/http/run_vistrails.php to version before merge (762902e79b7a)
+ - VisTrails server was ignoring the build_always variable if it
+ found cached images (762902e79b7a)
+ - Using port to identify the instance of the server instead of virtual
+ display in script that starts vistrails server using Xvfb (762902e79b7a)
+ - Ticket #393: Latex extension doesn't handle workflow exec. errors properly (16f522c459c5)
+ - Latex extension: Making sure to convert line breaks into \MessageBreak
+ Latex commands before displaying error messages. (16f522c459c5)
+ - Forwarding force build to server so the server can also bypass
+ caching (47a1105664a0)
+ - Ticket #392: Refactor php extensions caching logic used for wf executions (3125e0eb8e81)
+ - Updated mediawiki extension to work with crowdlabs server (3125e0eb8e81)
+ - Added workaround for RotateFileHandler problem on Windows when some
+ packages start child processes during workflow execution (e5afc47797cb)
+ - Fixed issue where named intermediate persistent files/directories were not
+ reused correctly (df3deb58a18c)
+ - Fixed git hash retrieval for persisted directories (df3deb58a18c)
+ - Pasted text in VisTrails shell was being ignored (c48e67f02ae8)
+ - Giving focus to VisTrails shell when showing it (c48e67f02ae8)
+ - Added 'VisTrails messages' button and fixed 'VisTrails debugger' button (b401b2498c74)
+ - Don't mask AttributeErrors when materializing pipelines (b5c3650e5ca6)
+ - Add upgrade path for old InputPort and OutputPort modules (8abfff56592c)
+ - Fixed an issue with groups and upgrades (720d93c8e3be)
+ - VisTrails shell was not using fixed-width font (b521e096f879)
+ - Latex extension: delaying check for a valid url so we can include
+ cached images if there's no Internet connection (79296270cc86)
+ - Batch mode: On Windows, VisTrails was not executing workflows
+ when an absolute path to a vt file was given (81812ac04e85)
+ - Minor error fixes (45b53eef1c53)
+ - Ticket #386: Moving modules after an upgrade generates invalid actions with
+ delayed upgrades (ad9e029035f7)
+ - With delayed upgrades, moving modules after an upgrade now generates actions
+ in the correct order (ad9e029035f7)
+ - Ticket #385: Workflow instantiation fails when doing on-demand package loading (aff3408c7a51)
+ - Fix issue with on-demand package loading leaving workflows as invalid (aff3408c7a51)
+ - Casting DBLocator names to string as they can store None sometimes (9996bba52dd1)
+ - Ticket #384: Deleting version edits version tag if delete is canceled (cc05bc9e80e5)
+ - Don't delete tag text when attempting to prune (cc05bc9e80e5)
+ - Expanding port specs deals with differences between descriptor and port signatures (c5763a437606)
+ - UpgradeWorkflowError tries to trim None-value (93b3be3d2a50)
+ - Ticket #383: Unversioned modules are not upgraded (4b3fa72869f0)
+ - If a module has no version, force it to be upgraded (4b3fa72869f0)
+ - Ticket #302: Moved modules action generated when nothing changed (3e59defe4685)
+ - Fixed logic so moved modules are properly detected and positions updated. (3e59defe4685)
+ - ParaView package: Removed hardcoded path to pvserver and mpiexec
+and using configuration object for that (accessible through Menu
+Preferences -> Module Packages) (65453bd92aa5)
+ - ParaView package: Updated pv.vt example to work with current version
+of the package (65453bd92aa5)
+ - Fixed bug in some php scripts when only the tag is passed instead of
+a version number (2b53ad32a374)
+ - Updated all php scripts in extensions/http to work with
+the current version of crowdlabs vistrails server (only local
+setup currently supported) (8d15fdbe8e1d)
+ - Fixed bug where server method get_wf_graph_png would sometimes
+fail (064304a99993)
+ - Fixed bug where although DBLocators were being cached, the
+ connections were not (b07c22d9e93d)
+ - Ticket #359: When using VTKRenderOffscreen module VisTrails crashes (48e477f4c1d9)
+ - VTK Package doesnt work with VTK version 5.7.0 (ba5e0bdbbb16)
+ - Fixed issue with query-by-example where parameters couldn't be updated (741b1c0d7737)
+ - Error using breakpoint due to new stack trace (d4f31af05a05)
+ - LaTex extension: removed hardcoded url for downloading vt files
+upon clicking on the images in the generated pdf. It can now be set using
+the \vistrailsdownload in the latex file (3123297d6a1b)
+ - HTTP package was not handling exceptions correctly (62d25dca3f3a)
+ - Ticket #380: HTTPFile corrupts binary files on Windows (0a5ec2007878)
+ - Color Constant: Initializing Color widget with default white
+color using RGB constructor instead of QtCore.Qt.White. We assume the
+color is always a QColor object and sometimes a GlobalColor object
+was being found (8565a276a353)
+ - Persistence Package: Added code to find tar executable similar
+to the way the path to git is set up (4a2494c09ef4)
+ - Persistence Package: adapted use of tar command to work
+on Windows (430e29bcaf2e)
+ - Windows binary: Including the gnu version of tar instead
+of the one that comes with git (430e29bcaf2e)
+ - Set MplFigureCell to fill spreadsheet cell (4af6514c20d4)
+ - Ticket #302: Moved modules action generated when nothing changed (8f60ea9a4737)
+ - Dangling move actions are displayed immediately after switching versions (8f60ea9a4737)
+ - Ticket #331: ImportError when trying to import userpackages (bc27cdc4b171)
+ - "import userpackages" fixed by reordering init steps (bc27cdc4b171)
+ - Ticket #293: Shell copy & paste on Mac doesn't work (694c0a43fbda)
+ - Use git ls-files instead of cat-file to retrive hash so that we don't have issues with Windows reading from stdin (1b190225cce9)
+ - Persistence package: fixed problem where persistent files
+couldn't be found on Windows (df8a7c2ef7d1)
+ - Ticket #369: picture-in-picture setting is confused when a new vistrail is opened (7ea68b3e863f)
+ - Check PIP preference when opening vistrails (7ea68b3e863f)
+ - Allow semi-translation from abstractionRef to abstraction so
+old workflows (version <= 0.9.3) with subworkflows can be opened (50b9ce2b28fc)
+ - Spreadsheet: fixed 'RuntimeError: underlying C/C++ object has
+been deleted' problem during EventFilter on Windows (93884b6a47c0)
+ - VTK Package: Fixed rendering context problem when embedding VTKCell in VisMashup on Linux (93884b6a47c0)
+ - PathChooserToolButton was not emitting proper signals necessary for
+VisMashup (93884b6a47c0)
+ - Persistence package: Fixed load package error on Windows (4ee8f244fc79)
+ - Change persistence package to use correct identifier for gui widgets (9dd3ad8e0b08)
+ - Ticket #378: Workflow execution log contains duplicate entries (6d65daec6089)
+ - Fixed logging so that executions are not duplicated when saving more than once per session (6d65daec6089)
+ - Ticket #377: Exporting to OPM XML fails (3ee1cc842182)
+ - Fixed OPM output capability to work with latest object layout (3ee1cc842182)
+ - Update sql package to use List instead of ListOfElements (4b08dd9018db)
+ - Fix typo with get_package_by_name (74f30460d3fe)
+ - keep selected modules after scene redraw (bb5e4e6e1f45)
+ - Optional input ports now don't show up as output ports (bb5e4e6e1f45)
+ - Ticket #376: execute_cmdline broken (bbbcf19704b8)
+ - Fixed copyright year in background image from About box (bcd3346d8865)
+ - Web Services package: fixed bug in certain Complex Types (60128ff3a89a)
+ - Ticket #374: Web service package can't be reloaded (38976729a2a9)
+ - Fixed an issue with package reloading where modules imported using the "from" syntax were not added to the imported list (38976729a2a9)
+ - HTTPFile: Fixed error when parsing the date from the file's header. (3799edddbb62)
+
+From Release: v1.5.1 build 1863
+
+Enhancements:
+ - branching is now supported when uploading to web repositories (r1853)
+ - Added ParaView package (r1850)
+ - Added Titan package (r1847)
+Bug fixes:
+ - Ticket #368: Spreadsheet: export as single image does not work (r1861)
+ - Fixed bug where RichTextCell was not displayed when running on
+ server mode (r1857)
+ - Fixed bug with thumbnails and RichTextCell (r1856)
+ - Making sure to use only image files when generating thumbnails (r1856)
+ - Fixed web repository commit bug where updated vistrail files where not
+ successfully loaded into VisTrails after being downloaded (r1853)
+ - web repository vt id annotation is now being saved (r1853)
+ - web repository cookie is now nullified if the web repository url
+ changes (r1853)
+ - VisTrails Batch mode: Changing parameter separator from '&' to '&&' so
+ urls with query urls work (r1846)
+ - Added procedure to WIndows installer script to remove VC Redist files
+ left behind (r1846)
+ - log file names are now updated according to VisTrails version (r1845)
+ - Ticket #366: VTK overloaded ports from old vistrail files are not being shown in the GUI (r1842)
+ - Fix translation of head example from old version (r1842)
+ - Ticket #367: Different port signatures when upgrading a workflow (r1841)
+ - Translate old parameter type serialization to match port/portSpecs (r1841)
+ - Ticket #364: actionAnnotation breaks view->show all (r1840)
+ - Fix issue with annotations that have the same key/value pairs (r1840)
+ - Ticket #363: Enabling the Web services package on-the-fly is broken (r1839)
+ - Spreadsheet package: SingleCellSheetReference could not be used (r1839)
+ - On Mac, the eventFilter was not being removed when finalizing
+ Vistrails and sometimes delayed events could not be processed (r1839)
+ - ImageViewerCell: Disabling the zoom slider when playing
+ animation (r1838)
+ - Ticket #362: ImageViewerCell Animation Icons Are Not Displayed (r1837)
+ - repository_vt_id now represents the crowdlabs vistrail object id instead
+ of the vistrails db id (r1834)
+ - when merging a vistrail with one on the web repository, a check is made
+ to see if that vistrail still exists (r1834)
+
+From Release: v1.5 build 1832
+
+Enhancements:
+ - Upgraded libraries: VTK 5.6, Qt 4.6.3, python 2.6
+ - Adding extension files to release
+ - Add support for calling binaries in Mac bundles (r1813)
+ - New methods for cmdline execution (r1813)
+ - Better configuration for persistence package (r1813)
+ - Added scripts for manipulating the database (r1809)
+ - User may now designate permissions when uploading vistrail to web repository (r1806)
+ - More informative upload dialog that lists incompatibilities between
+ vistrail files and web repository, including PythonSource module checks (r1806)
+ - Merges with web repository now updates local vistrail version (r1806)
+ - Changed VisTrails version to 1.5 (r1805)
+ - Files produced by FileSync modules are publishable by default.
+ Use publishFile boolean to avoid publishing the files. (r1805)
+ - Server mode: added support for executing workflows and returning
+ results as pdf files (r1804)
+ - Latex Extension: added support for embedding pdf files. See README file
+ in extensions/latex for help (r1804)
+ - Ticket #317: Add support to the spreadsheet cells also generate PDF files (r1801)
+ - Spreasheet Package: Added global configuration for controlling
+ the file type (PNG or PDF) when dumping cells (console mode). This can be set
+in the Spreadsheet configuration panel or as a
+command line option (use --pdf or -p
+for dumping files in pdf). (r1801)
+ - Added support for merging vistrails on the server side (r1798)
+ - Added support to draw workflow graphs (as png and pdf) and
+history trees (as png) (r1798)
+ - VTK Package: Added the ability to use the Transfer Funtion widget to
+create color mappings (vtkColorTransferFunction) not necessarily in
+volume property. (r1796)
+ - Changed version of VTK Package to 0.9.2 (r1796)
+ - Added two new output ports to vtkScaledTransferFunction: vtkPiecewiseFunction and vtkColorTransferFunction (r1796)
+ - Handle upgrade and prune annotations during merge (r1792)
+ - Added gui code for the interactive vistrails merge (r1791)
+ - Interactive interface for merging two vistrails (r1789)
+ - Make actions immutable by moving mutable attributes to a higher level (r1786)
+ - Try to fix as many errors as possible in an upgrade, even if all cannot be fixed (r1777)
+ - Merging action annotations (r1771)
+ - Methods for hashing tags and annotations (r1769)
+ - Merging of vistrails files for crowdlabs. (r1762)
+ - Preferences for upgrades (r1761)
+ - Allow delaying persistence of upgrades until changes (r1761)
+ - PRELIMINARY upgrade support (r1755)
+ - view pipelines without having the packages (r1755)
+ - view invalid pipelines (r1755)
+ - improved pipeline validation (r1755)
+ - Add method to allow updates of a single port rather than all ports as updateUpstream provides (r1753)
+ - Dump non-ModuleError exceptions to the console (r1753)
+ - Improved string formating of nested InvalidPipeline exceptions (r1752)
+ - Allow QSearchBox to do non-incremental searching (r1751)
+ - Improved version selection handling (r1744)
+ - Server Mode: added support for multithreading (r1741)
+ - Decoupled the directory where the spreadsheet will dump cells from the configuration. spreadsheetDumpCells configuration is now deprecated. Now this setting can be configured in a per workflow fashion (r1741)
+ - Added support for extra information to be passed along workflow executions. The spreadsheet now uses this mechanism instead of a global configuration for dumping cells (r1741)
+ - inital version of a VisTrails R package using rpy2 (r1723)
+ - easier namespace designation using _modules (r1722)
+ - easier constant extensibility and customization (r1721)
+ - improved List module (r1721)
+ - new Dictionary module (r1721)
+ - new SourceConfigurationWidget to make creating source configuration widget easier (r1720)
+
+Bug fixes:
+ - Sometimes matplotlib plots were not refreshed in the spreadsheet (r1828)
+ - Fixed the flickering issues of VTKCell on Windows (r1825)
+ - Updated Web services code to work with HTTP package chages (r1824)
+ - Fixed Python Wrapping issue with VTK 5.7.0 (r1818)
+ - Minor UI fixes to web repository dialog (r1817)
+ - web repository dialog now links to correct vistrail id on the web repository (r1817)
+ - Upon upload to web repository, an repository identification annotation is added automatically (r1817)
+ - Fixes for merging vistrails in server mode. (r1816)
+ - low-level merge code now allows passthrough gui references
+instead of importing them (r1812)
+ - Fix issue where annotation ids weren't properly assigned (r1809)
+ - Merging thumbnails (r1808)
+ - Fixed issue where database was saving parent id/type pairs as NULL (r1807)
+ - Fixed issue where deleted annotations were not translated to previous version (r1807)
+ - Fixed issue where deleted annotations could not be mapped back to previous schemas (r1807)
+ - Fixed issue where annotations were not set with the correct db flags (r1807)
+ - Generating the pdf of the workflow in console mode was not
+working. (r1805)
+ - Fixed bug in script that starts VisTrails in server mode using Xvfb (r1804)
+ - Spreadsheet package: corrected paper size of generated pdfs (r1803)
+ - Fixed Vistrail merge casting bugs (r1802)
+ - Spreadsheet Package: Standard non-image type cells now correctly dump
+contents to file. (r1801)
+ - Vistrail merge did not copy thumbnails (r1800)
+ - Fix issue with reading and writing the boolean parameters during persistence configuration (r1799)
+ - Fix issue when writing metadata of managed files (r1799)
+ - Ticket #358: HTTPFile header-based caching is broken (r1797)
+ - HTTPFile.is_cacheable is now implemented, and is aware of server headers. (r1797)
+ - Ticket #353: Import workflow doesn't set id scope correctly (r1790)
+ - update id scope after importing a workflow (r1790)
+ - Fix for older log files that have incorrectly moduleExec elements (r1788)
+ - Checking whether XML element is not None before trying to evaluate it as text (r1787)
+ - Fixed port spec naming in new persistence package (r1783)
+ - Fixed issue where always creating a new reference didn't generate an id (r1783)
+ - When pruning a node, make sure that node is removed from the version tree display (r1782)
+ - Fixed issue with re-saving to the database with groups (r1781)
+ - Fixed issue with upgrading groups and database persistence (r1781)
+ - References to thumbnaisl were being shared across
+different vistrails (r1780)
+ - Existing thumbnails were not being replaced by new ones (r1780)
+ - Don't automatically switch to pruned upgrade nodes (r1779)
+ - Ticket #357: Error after saving as [Errno 2] (r1778)
+ - Fixed issue with trying to upgrade groups introduced by upgrading port specs (r1777)
+ - Fix issues where pipelines are not validated after certain actions like copy-paste (r1776)
+ - Merging of vistrails did not work (r1775)
+ - Band-aid for analogies to make analogies with groups or abstractions a bit more robust (r1774)
+ - Fix error with handle_invalid_pipeline and subworkflows (r1773)
+ - Fix bugs in displaying missing dependencies in preferences (r1772)
+ - Pass module information through group to contained modules (r1770)
+ - Fix issue with upgrading module functions for user-defined ports (r1768)
+ - Fix issue with upgrading modules that have user-added ports (r1767)
+ - Change call to fix missing modules to the correct method (r1767)
+ - Merging of vistrails files for crowdlabs. (r1766)
+ - Fix issue with analogies where obselete method was being called (r1764)
+ - Fixed issue where automatic upgrades fail because a port is said to not be found even though the port does exist (r1763)
+ - Fixed issue with upgrading groups (r1761)
+ - Ticket #356: Action copy doesn't remap previous id (r1757)
+ - Pass simplify argument through in create_action_from_ops (r1756)
+ - Fixed issue with versions_increasing computation (r1752)
+ - Ticket #354: Package reloading raises duplicate package error (r1750)
+ - Fix issue with renabling packages where a signal was issued twice (r1750)
+ - VisTrails Server: the vistrail version was not being included in the .vt file generated by the server (r1746)
+ - fixed ModuleRegistry.auto_add_subworkflow so that it accepts the correct (filename, dict) format. (r1745)
+ - Server mode: Added a global variables to store information for accessing the database (r1743)
+ - Fixed a bug in the RequestHandler.get_wf_vt_zip() function. (r1742)
+ - The notes field in the History View now only supports plain text (r1741)
+ - Fixed issue where module label changes were not recognized correctly and raised an exception (r1740)
+ - Don't require a Module to a be of type __builtin__.type to
+allow boost:python, etc. classes (r1739)
+ - Differentiate between init.py not existing and init.py having ImportErrors (r1719)
+ - Ticket #346: Module Parameter Types Serialized Incorrectly (r1718)
+ - Update module parameter type serialization when containing namespaces to match port specs and ports (r1718)
+
+From Release: v1.4.2 build 1716
+
+Enhancements:
+ - Ticket #290: Reload packages without restating VisTrails (r1714)
+ - Package reloading support should now be fully functional (r1714)
+ - Enabling access to a Web package repository. (r1712)
+ - Started adding support for Qt4.6.x (r1711)
+ - Package vtlcreator: Exposing the function to create the contents
+of a .vtl file as a static method, so it can be called from other
+packages (r1709)
+ - Added support for embedding workflows when using the Web extensions (r1709)
+ - VisTrails Server: Added support for creating a .vt file for a given
+vistrail/workflow on the DB so it can be embedded on a .vtl file (r1709)
+ - New module, RepoSync, has been added to the HTTP package, which enables data files to be synced with an online repository (crowdLabs) (r1708)
+ - Added basic online web repository (crowdLabs) user authentication dialog (r1707)
+ - Added ability to upload VisTrail files to online web repository (crowdLabs) (r1707)
+ - Improved package reloading support (r1703)
+ - Added helper methods, get_inputPort_modules and get_outputPort_modules, to get modules that connect to a given input port or output port (r1701)
+ - Added helper method, connections_to_module, that returns a list of all modules that connect into a given module (r1701)
+ - Ticket #290: Reload packages without restating VisTrails (r1697)
+ - Enable package reloading without the need to restart VisTrails. (r1697)
+ - SQL package also connects to a PostgreSQL database server (r1696)
+ - SQL package: added cacheResults parameter to SQLSource (r1696)
+ - SQL package also handles connection timeouts (r1696)
+
+Bug fixes:
+ - Package menu items (on the toolbar) are now properly removed when the package is disabled (r1714)
+ - Package lists can now be traversed with the keyboard (r1714)
+ - Fixed bug that when enabling a package dynamically sometimes VisTrails
+would say that it failed but if you just selected the version node again the
+pipeline would be loaded without problems (r1711)
+ - MAC and Qt4.6: VisTrails would fail to start when using MacBrushMetalStyle (r1711)
+ - Mac and Qt4.6: There was not text anti-aliasing in modules and version
+nodes (r1711)
+ - Qt4.6: Moving a module in the pipeline view would not move the
+connections attached to it (r1711)
+ - Qt4.6: Legend Window in Visual Diff would not properly display the
+colors (r1711)
+ - Fixed a bug with opening .vtl files that embedded workflows (r1709)
+ - Package vtlcreator: Fixed a bug that the version of the embedded
+vistrail was not being set (r1709)
+ - Fixed the Capitalization error in the VisTrails App Bundle name (r1709)
+ - Properly track all modules in the hierarchy of a module loaded by a package for correct packing reloading (r1706)
+ - Made reset query work immediately for the version search box (r1705)
+ - Stop creating empty actions (r1704)
+ - DBLocator: Removing object name from XML serialization.
+This was causing inconsistencies with caching locators because we don't
+know the name of the object before we load it (r1702)
+ - Ticket #345: db connection edit bug (r1700)
+ - DBLocator: Serializing also db connection user so current
+permissions are not overriden by the cached version (r1700)
+ - Ticket #344: Ungroup failing (r1699)
+ - Ensure correct modules after ungrouping (r1699)
+ - Ticket #342: Method responses return None in Web Services Package (r1698)
+ - Complex types were ignoring the new 'self' input port when
+unwrapping contents (r1698)
+ - Ticket #341: On Ubuntu, VisTrails doesn't try to install MySQLdb (if not present) when accessing the database (r1695)
+ - Move Vistrail import into load_vistrail method to avoid
+circular imports. (r1694)
+
+From Release: v1.4.1 build 1693
+
+Enhancements:
+ - Code cleanup: removed unnecessary imports in a few files (r1687)
+
+Bug fixes:
+ - Using VisTrails as a library: added more imports to
+ init_for_library.py file (r1687)
+ - In the pipeline view, if you changed a module (moving it, for
+ example) and deselected the current node in the PIP view, VisTrails
+ would throw an error (r1687)
+ - Ticket #338: The DB Connection Setup Dialog opens twice (r1686)
+ - Package Web Services: expanded simple types map to include all
+ simple types defined in http://www.w3.org/2001/XMLSchema (r1685)
+ - Ticket #337: Web Services package fails to load a wsdl (r1684)
+ - Web Services package: Expanded simple types map to include missing types (r1684)
+ - Upgraded ZSI library in the binary releases to use trunk r1495
+ - Ticket #336: VisTrails fails when opening files with an older schema (r1683)
+ - Fix upgrades when module's version does not exist. (r1683)
+
+
+From Release: v1.4 build 1682
+
+Enhancements:
+ - EXPERIMENTAL: Packages can handle workflow upgrade requests. Still very much
+work-in-progress. If you want to enable this, set 'automaticallyUpgradeWorkflows'
+to True in the Expert Configuration tab in the Preferences menu. (r1665)
+ - Module Packages tab in Preferences menu now shows package version. (r1665)
+ - Initial revision of a sql scripting package (r1664)
+ - Improve error messages when sql statements fail (r1660)
+ - Ticket #318: Add support for generating a .vtl file within a workflow (r1657)
+ - Allow persistence package to search for persistent entities
+in multiple stores (r1654)
+ - Added script that generates nightly source releases. (r1648)
+ - Better delete buttons on the parameters. (r1646)
+ - Add data provenance support for persistent files. (r1644)
+ - Removed "Tag" entry in the method palette (r1643)
+ - Ticket #276: Make method deletion more visible (r1642)
+ - Ticket #287: Allow parameters to be named (r1642)
+ - Ticket #291: Allow functions to be populated with default values (r1642)
+ - Can delete functions/methods by clicking the check box next to the name (r1642)
+ - Can define default values for parameters (r1642)
+ - Can define labels for parameters (r1642)
+ - Added script for (re)starting vistrails in server mode with Xvfb.
+ - Visual Diff now shows matches in white; modules shared by history are colored
+gray while modules shared by matching are colored white. (r1634)
+ - Added better default descriptions to version tree. (r1634)
+ - Enabled the 'SetInputArrayToProcess' method of vtkAlgorithm class to use
+for the InfoVis package. This port was disallowed earlier for some reason, so
+we have to watch if this will cause any issue. (r1632)
+ - Added support for storing logs and thumbnails on the database. (r1625)
+ - Add a new module that allows the user to control the order of execution of
+two sinks. (r1618)
+ - Use the module descriptor to do hashing instead of the module since the
+descriptor used may be a different version. (r1615)
+ - Fix so core and gui controllers both use the same change_selected_version
+logic. (r1614)
+ - Streamline error handling for workflow materialization. (r1614)
+ - Added Path and Directory constants and updated File constant
+along with configuration widgets. (r1611)
+ - Updated persistence package to support persistent directories
+and compression. (r1611)
+ - Initial version of a persistence package that aims to cache
+files across VisTrails sessions. (r1598)
+ - Adds support for viewing web documents in a WebViewCell using
+Qt's QWebView which is based on WebKit (r1596)
+ - Moved the controlflow package from packages to vistrails/packages. (r1588)
+ - Moved doc folder to root. (r1581)
+ - First version of source tree documentation. (r1580)
+ - Added the InfoVis example using the new VTKViewCell. (r1564)
+ - Enable more intuitive command-line interactions with
+pipelines (r1563)
+ - Added VTKViewCell for displaying vtkRenderView compatible with the current VTK trunk. Just connect vtkRenderView to VTKViewCell. First attempt, only tested on Linux. (r1562)
+
+Bug fixes:
+ - Ticket #334: Programmatic change_parameter problem (r1679)
+ - Add translation to new ids back after input/output remap. (r1663)
+ - Ticket #328: Backslashes in SQL Problem (r1662)
+ - Use prepared statements for the relational database
+persistence. (r1662)
+ - Ticket #330: Ungroup and save to db fails (r1661)
+ - Make sure that new objects are saved to the database. (r1661)
+ - Ticket #328: Backslashes in SQL Problem (r1660)
+ - Added prepared statement support for db version 1.0.1 (r1660)
+ - Ticket #329: Analogy port remap needs to check input/output remaps (r1659)
+ - Check the correct remap when changing ports. (r1659)
+ - Check for __init__.py in userpackages on startup. (r1656)
+ - Improve feedback for undo/redo (r1655)
+ - Ticket #327: Bug in exporting registry to DB (r1653)
+ - Removed global setting on package ids from sql spec. (r1653)
+ - Fixed exporting Log, Workflow and Registry to XML (r1652)
+ - Fixed exporting Log and Workflow to DB (r1652)
+ - tag "tag" was being ignored when "version" was empty in .vtl file (r1651)
+ - Copying DBLog objects was not working (r1650)
+ - DBVistrail.do_copy doesn't fail when log is None (r1649)
+ - Add copy methods to enhanced DBVistrail (r1645)
+ - Don't disable entire vistrails when they contain **unused**
+invalid port specs (r1641)
+ - Ticket #323: Subworkflows with version mismatches in underlying pipelines don't fail gracefully (r1640)
+ - Subworkflows that fail to load fail gracefully and print the
+exception (r1640)
+ - Ticket #321: Save As... doesn't save log (r1639)
+ - Save As and Export now save log data from files to files or
+files to db. (r1639)
+ - Ticket #259: Undo not available (r1636)
+ - Undo and redo are now available when the should be. (r1636)
+ - Execute Version Difference menu item is enabled at the correct
+times and functions correctly. (r1636)
+ - Ticket #326: Visual difference not considering namespace (r1634)
+ - Modules from different packages or namespaces no longer
+match (r1634)
+ - Groups try to match on their tag during heuristic
+matches (r1634)
+ - Ticket #325: DB version translation loses deleted entities (r1633)
+ - Translating to different database versions now transfers
+deleted entites from the old object to new object. (r1633)
+ - wiki vistrails tags containing "tag" attributes were not executed on the wiki (r1627)
+ - Ticket #320: Version Tree Display Inconsistent Across Serializations (r1617)
+ - Fix to make version tree layout consistent across
+serializations. (r1617)
+ - Ticket #319: Database copy/pastes saves not working correctly (r1616)
+ - Version updates now update the id scope to avoid strange
+errors when using VisTrails with an older database schema. (r1616)
+ - Copy and paste operations reset the id of a group's pipeline
+to None in order to allow the database to assign the correct
+id. (r1616)
+ - Unserialization now sets the unserialized object's is_new flag
+to True instead of allowing it to default to False. (r1616)
+ - Add version support into module signatures so that persistent
+files will be recomputed when upstream modules are updated. (r1615)
+ - Analogies now replace annotations of the same key and
+parameter values instead of adding new copies. (r1614)
+ - Bring unit tests up-to-date. (r1614)
+ - Ensure that debug messages are written in core controller. (r1614)
+ - Make code that adds parameters after executions work again. (r1614)
+ - core.system.executable_in_path now checks the correct error code from core.system.execute_cmdline() (r1613)
+ - Ticket #314: Visual Diff Broken when PythonSource loses/gains a connection (r1612)
+ - Fix issue with dynamic modules and the visual diff when ports
+have been re-typed. (r1612)
+ - Update documentation on create_action. (r1611)
+ - Ticket #311: Method palette doesn't obey port overloading (r1610)
+ - Ensure that ports are only displayed once in method palette
+and obey port overriding. (r1610)
+ - Ticket #309: Subworkflows crash on package version mismatch (r1607)
+ - Run ensure_modules, ensure_connection_specs on subworkflows
+during loading to try to avoid package version mismatch
+errors. (r1607)
+ - Ticket #308: Analogies fail on changed location (r1606)
+ - Fix bug with analogies where module's locations were added
+instead of changed causing problems when that module was
+deleted. (r1606)
+ - Fixed issue with deletes in sql persistence for versions 0.9.5
+and 1.0.0 (r1603)
+ - Ticket #307: Error messages when executing a workflow more than once (r1602)
+ - This fixes bug where error messages would be printed to the terminal when executing a pipeline with cached modules more than once (r1602)
+ - Fixed a typo in create_port, we don't need to call the vistrails_port
+object that was created. (r1601)
+ - Fixes some of the shell interaction methods. (r1600)
+ - Remove ternary operator for python 2.4 compatibility (r1599)
+ - Ticket #305: vistrails.sql script in schema v1.0.0 is broken (r1595)
+ - Fixed issues with versions 0.9.5 and 1.0.0 of the relational schema. (r1595)
+ - Ticket #304: VisTrails does not check if the connection to the database is still alive before performing an sql command (r1594)
+ - This fixes bug where the MySQL has gone away error would show up when connected to a database and VisTrails was not being used for a while (r1594)
+ - Ticket #303: Thumbnail error when saving a vistrail (r1593)
+ - Fixes bug that prevented a vistrail to be saved because of an error related with thumbnails. (r1593)
+ - Ticket #301: Double-clicking .vt and .vtl files does not cause them to be open by an already running VisTrails (Mac only) (r1592)
+ - Moving condition check to the right place so FileOpen events are captured correctly on a Mac (r1592)
+ - Ticket #299: Delete ops in analogies broken (r1591)
+ - Add some checks to make analogies better behaved. (r1591)
+ - Ticket #300: Null actions being added to the tree (r1590)
+ - Parameter selections don't generate null actions. (r1590)
+ - Ticket #297: MissingPort exception not raised (r1589)
+ - Fixes bug where user is never notified if a module on the
+registry is missing the requested port. (r1589)
+ - Updated VisTrails Server code in the trunk to be consistent with the server
+running in vistrails.sci.utah.edu (r1583)
+ - Fixed small bug that prevented load a vistrail from the database
+using the GUI. (r1582)
+ - Partial fix to deprecation messages. Not closing the ticket because it's
+not fixed on Windows. (r1576)
+ - Ticket #283: Fold Type Mismatch Error (r1575)
+ - Fix the type mismatch error message. (r1575)
+ - Update current list of ignored classes in vtk package. (r1573)
+ - Ticket #279: Analogies broken with namespaces (r1572)
+ - Use module's _get_module_descriptor call to get the descriptor to fix
+namespace issues with analogies. (r1572)
+ - Fixes a bug that shouldn't currently be exposed to an end-user.
+Specifically, the registry's udpate_id_scope method didn't add 1 to
+the begin id. (r1571)
+ - Fixed the pipeline execution mechanism in the spreadsheet that didn't work
+with the new interpreter interface. (r1567)
+
+From release v1.3 build 1561
+
+Bug Fixes:
+ - Fixed bug that was preventing files from being saved on Windows
+
+
+From release: v1.3 build 1559
+
+Changes:
+ - Schema upgrade. Current version: 1.0.0.
+ - Updated VTK libs to use 5.4.2 release
+ - Removes conditional expression constructs, so that code runs on Python < 2.5.
+ - Including Gridfields python module
+ - Using only application single instance behavior if Qt 4.4 or later is
+ available
+ - Added support for SubWorkflows (with no database support yet)
+ - Added a Control Flow Package (see user's guide to see how to use it) and
+ related example files
+ - Added support for basic package repository
+ - Introduced a major reorg of the registry and related classes. Specifically,
+ it adds serialization capabilities, and unifies the
+ core.modules.module_registry.PortSpec and
+ core.vistrail.port_spec.PortSpec classes. In addition, all configuration and
+ drawing is done using PortSpecs (not Ports). It also includes revisions to
+ the PythonSource, and Tuple configuration dialogs, and adds controller code
+ to better support resulting updates. You can serialize the registry via the
+ "File -> Export -> Registry To ..." menu items.
+ - Added support for "registry quickstart" which allows VisTrails to boot
+ significantly faster. It also further changes registry behavior to allow
+ VisTrails to function without having access to the actual python modules
+ behind the ModuleDescriptors. Everything can be done by tracing the
+ descriptor hierarchy instead of the mro, but we still use the mro when we
+ have it. Try the quickstart by starting VisTrails normally and selecting
+ "File -> Export -> Registry To XML..." and saving the resulting file.
+ Then restart VisTrails with the -q flag followed by the registry file:
+ (ie "./vistrails -q <registry_filename>")
+ - Use solid colors instead of textured backgrounds on graphics views,
+ since Qt (or pyqt) redraws much slower when these are enabled.
+ - Improved layout of modules in visual diff and analogy
+ - Added support for displaying thumbnails below the notes panel and/or as a
+ version node tooltip. See Thumbnails Preference tab for changing specific
+ options
+ - Improved menu File organization
+ - Added translate* methods for versions 0.9.3 and up, and updated code to use
+ them. This should ensure that xml vistrails, workflows, logs, and
+ registries, can be updated when schemas change. The idea is that you open a
+ vistrail, and if it is not in the current schema, it is translated to the
+ current schema, no matter if you're using an xml-based file or relational
+ database. When saving the vistrail, the db code will attempt to translate
+ the vistrail to the schema of the database (even if it is an older version)
+ before saving. For xml-based files, you may optionally specify to save the
+ file as an older version. Currently, you are only able to translate back
+ to 0.9.3 (See menu "File -> Export -> Stable Version").
+ - Added initial support for workflow debugging
+ - Added the progress functionality allowing modules to show their progress
+ during the compute() by calling self.logging.update_progress(self, progress).
+ - The VisTrails Console is now a dockable window. Also fixed a long-standing
+ bug that hitting enter when cursor is not at EOL will carry garbage to next
+ line. Fixed also a bug where if user types fast enough in the shell, the
+ input fails.
+ - Added support for constants to generate custom hashes. The main current
+ usecase is File constants, which hash against filename and last-modified
+ times. The biggest consequence is that pipelines that use File objects will
+ now be smarter when it comes to files that change upstream, reducing the
+ number of times one has to clear the cache.
+ - Improved the initialization of packages: if package fails during call to
+ initialize(), we report failure, disable the package, and continue
+ initialization. This allows startup process to continue. Also in preferences
+ pane, when package fails to load, we now display the error message;
+ previously, it just said "error". (There's still the problem of reporting
+ packages that load ok but fail to initialize)
+ - Changed view behavior so that the initial pipeline view upon opening a
+ vistrail is reset.
+ - Added support for importing workflows that have been saved as xml.
+ - Added a function to change parameters from the api along with a function to
+ find modules by name (and package/namespace if specified). Note that the
+ param_list in change_parameter requires a list of strings---the serialized
+ representations of the parameters!
+ - Updated the gen_vtk_examples scripts to create better pipeline
+ specifications.
+ - Added pc3 package for the Third Provenance Challenge.
+ - VTK package:
+ + Added support for Picking in a VisTrails cell. By default, the
+ vtkRenderWindow contains a picker. The 'p' key activates the pick test in
+ the render window. A new vtkPicker can be attached to the VTKCell to
+ modify the picking behavior according to the mechanism provided by VTK.
+ + All VTK Filters are registered to show their progress while executing
+ + Added support of InfoVis to VTKCell. Notice that the saving camera feature
+ does not working with InfoVis (because there are no direct SetCamera port
+ for InfoVis classes).
+ + Added support for changing the backgorund color of a vtkRenderer using
+ color widget
+ - Spreadsheet:
+ + Added exporting images and echo mode feature
+
+Bug Fixes:
+ - Fixed bug where queries with multiple sources would fail in query by example
+ - Spreadsheet:
+ + Jpg/gif/png images can be correctly displayed on the spreadsheet
+ + Fixed many interaction bugs
+ + temp files were not being correctly removed
+ - VTK state changes with statically overloaded parameters are now handled
+ correctly. Typical example is vtkTreeMapView::SetLayoutStrategy
+ - Fixes a bug where the configuration wouldn't be setup properly for a new
+ .vistrails directory.
+ - Fixed plot.vt example to work with matplotlib version >= 0.98.5.2
+ - Catch exceptions when writing file to raise dialog box if there is an error.
+ This fixes bug that nothing was being shown to the user in case of a bad
+ write (ie, file permissions insufficient).
+ - Fixed PythonSource syntax highlighter error and (yes!) there's a line number
+ for debugging now.
+ - Fixed startup "bug" when package with dependencies fails to load
+ - Copy/paste is relative to the current canvas
+ - Shipping the GPL License in the distributions
+ - ImageMagick package:
+ + Added CombineRGBA class, configuration object, and fixed GaussianBlur bug
+ + Removed requirement check that prevented the package from loading if
+ ImageMagick was not found in the path
+ - Bug fixes in Windows installer:
+ + Installer always creates desktop shortcut and uninstaller did not remove
+ all pyc files
+ - Other minor fixes
+
+From Release v1.2.1 build 1336
+Changes:
+ - Schema upgrade. Current version: 0.9.3. If you keep vt files in a database,
+ you have to upgrade the database as well
+ - VisTrails now requires Qt 4.4 or later to run
+ - Adopted application single instance behavior (only one version of the
+ VisTrails application can be executing).
+ - Added Interactive expansion and collapsing in the version tree: the three
+ lines on edges in the version tree that used to represent multple
+ versions has been replaced by a plus symbol. Clicking this symbol
+ expands the link to show all the versions in betweeen (though this may
+ change to only a limited number later). A minus sign appears on the
+ top of a list of untagged, non-branching, non-selected versions that
+ will collapse that list.
+ - Added descriptions to the version tree. They show up in place of
+ a tag if one hasn't been set, but with a thinner italicized font.
+ Double-clicking on the node allows it to be changed and turned into a tag.
+ Showing a description for each action that is now displayed in the
+ properties overlay. This description is still very simple (eg.,
+ Added module), though in the future it might make sense to save off
+ more detailed descriptions for each action in the db (eg., Added
+ vtkRenderer module)
+ - Added new items to the View Menu to show and hide branches and nodes
+ - Restored the "Clear Recent Searches" in the search box in the version
+ properties
+ - Added command line options to execute workflows and show only
+ the spreadsheet when opening
+ - Logging information is now stored in .vt file
+
+ Bug fixes:
+ - Copying and Pasting dynamic modules, such as PythonSource threw an error
+ - File version was not set correctly
+ - Fixed a bug in analogies that sometimes corrupted vistrails files.
+ - Fixed some bugs and annoying behavior with autosave. A dialog
+ now prompts the user if they want to load autosaved data. This
+ dialog appears when opening a file or starting up vistrails.
+ Autosave data no longer is loaded when the user creates a new
+ vistrail by pressing the new button.
+ - Dragging versions to the spreadsheet is working again
+ - Dragging a spreadsheet tab created a window that couldn't be closed
+ or put back. A floating sheet can be docked back by simply closing it or
+ dragging it back the spreadsheet tab bar (if exists) or just the window
+ itself.
+ - There was no obvious way to exit full screen mode in spreadsheet. The
+ fullscreen mode can be closed either by:
+ * Pressing 'ESC', 'Ctrl-F', 'F11' or 'Alt-Enter'
+ * Right click on the fullscreen mode and unselect 'Fullscreen'
+ - Border color of selected cells in the spreadsheet is now consistent
+
+From Release: v1.2 build 1263
+Changes:
+ - Version tags can be edited directly by double-clicking the tree nodes
+ - Added basic support for package management on Fedora Core through YUM
+ - Added compatibility with Qt4.4
+ - Added support for dynamic addition of modules in packages
+ - Pipeline, Query and History views are now reset with Ctrl+R
+ (Command+R, on a Mac) so that it does not interfere with version text
+ items
+ - Add a transparent overlay to the version viewer that shows the
+ selected version's properties. By default this is turned off, but
+ can be enabled under the view menu.
+ - Added standalone functions that help third-party applications that
+ need an API into VisTrails, located on vistrails/api directory.
+ - Improvements in the command-line for both non-interactive and interactive mode:
+ + Added support for executing more than one workflow at a time
+ + Included support for opening a vistrails from the database
+ Now a version (tag or id) can be specified in the command-line
+ together with the filename (or vistrails id when opening from the
+ database).
+ - Added support for opening special vistrails files (.vtl files) on
+ the web (wiki integration)
+ - WebServices package: added support for loading wsdl urls automatically
+ when opening a pipeline using them
+
+
+Bug fixes:
+ - Improved handling of faulty packages
+ - Vistrails having groups with annotations or functions did not open
+ correctly
+ - Query display didn't ghost module fill
+ - Query execution and reset didn't update pipeline view
+ - Connection line was drawn twice in query canvas
+ - Editing parameters in query mode was cumbersome because of
+ bad focus management
+ - Fixed database support to pipelines with groups
+ - Fixed "Add Database" dialog confusing behavior
+ - Fixed a long-standing bug on PythonCalc where ModuleError was
+ being called without the self parameter
+ - HTTP Package: slightly better error handling with malformed URLs
+ - Improved general GUI performance when changing versions, including
+ Undo/Redo
+ - Removed obsolete command-line options
+ - Refine in the search box was not working
+ - Spreadsheet: Saving a spreadsheet also included cleared cells.
+
+
+From release: v1.1 build 1143
+
+Changes:
+ - Added "Set Module Label" feature (through the configuration pop-up
+ menu of the GUI)
+ - Improved error messages
+ - Added vistrails files for many of the vtk examples
+ - Added support for packages to create menus in the builder window
+ (see spreadsheet package for an example)
+ - Modules and input ports can be automatically registered by
+ setting per-module _input_ports and _output_ports fields and
+ per-package _modules field (see teem package at www.vistrails.org)
+ - Removed graphviz dependency
+ - Ability to export workflow and history views to PDF
+ - In WevServices Package: Improved support to web services using
+ complex types
+ - Added a BooleanWidget, so Booleans are now given by a checkbox
+ - In VTK Package:
+ + Added Transfer Function Widget
+ + Added dataset inspectors, special vtk modules that allow users
+ to easily query bounds and scalar range of an object.
+ + Added support for vtkTIFFReader to allow volumetric (slice-based)
+ reads.
+ - Added support for grouping modules in pipelines
+ - Incorporated many optimizations in the code
+ - Added namespace support to packages
+
+Bug fixes:
+ - Fixed analogies
+ - Version tree was not refreshed when analogy was applied on the spreadsheet
+ - Fixed double drawing of module names and version node names on the mac
+ - Added support for running Visual Diff for pipelines with
+ PythonSources and other modules with a local registry that
+ have different input and output ports
+ - Changed the behavior of selecting new cell locations on the
+ spreadsheet when it is full (cycling vs. using always the first
+ cell)
+ - Fixed bug where options passed through the command line were
+ written to the startup.xml file
+
+
+From Release v1.0.1 build 1063
+Changes:
+ - In VTK Package: Exporters now take a VTKCell as input when exporting
+ the scene
+
+Bug fixes:
+ - Caching mechanism: VTK modules didn't take the connections into account
+ when deciding whether to cache or not. This is related with the error
+ message "function expects 1 argument, got 0 instead".
+ - Fixed Parameter Exploration bugs where parameter widgets did not update
+ correctly when changes are made to the pipeline.
+
+
+From Release 1.0 build 1024
+Changes:
+ - Added a preference option to enable/disable Brushed Metal Style on Mac
+
+Bug fixes:
+ - Opening/Saving a .vt file on a path with spaces was not working on Unix
+ systems
+ - Creating/Applying analogies on the spreadsheet
+ - Opening/Saving spreadsheets
+
+Release Name: v1.0 rev954
+
+Changes:
+ - Added module VTKRenderOffscreen to vtk package
+
+Bug fixes:
+ - Version tags couldn't be reused
+ - Some vtk writers couldn't be dragged to the pipeline canvas
+ - Vistrails crashed when trying to copy and paste something other than
+ a serialized pipeline
+ - Modules lose focus when dragging to the pipeline canvas
+ - Modules downstream of a error module were green (as if they were executed)
+ - Select All button on the spreadsheet was not working
+ - Creating a version from the spreadsheet didn't work
+ - Tags weren't deleted when pruning the tree
+ - Booleans weren't supported in parameter exploration
+ - Fixed double-clicking on a vt file when opening vistrails on Windows
+
+From Release rev921:
+
+Changes:
+ - Interface was improved and it is now more consistent
+ - General configuration and package management accessible through menu Edit->Preferences
+ - Using a more efficient file format (*.vt)
+ - Auto saving feature
+
diff --git a/contrib/NumSciPy/Array.py b/contrib/NumSciPy/Array.py
new file mode 100644
index 0000000..f9ef1a1
--- /dev/null
+++ b/contrib/NumSciPy/Array.py
@@ -0,0 +1,250 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+
+import numpy
+
+class ArrayModule(object):
+ my_namespace = 'numpy|array'
+
+class NDArray(Module, ArrayModule):
+ """ Container class for the numpy.ndarray class """
+ def __init__(self):
+ Module.__init__(self)
+ self.array = None
+ self.names = {}
+ self.general_name = None
+ self.domain = ''
+ self.range = ''
+
+ def get_shape(self):
+ return self.array.shape
+
+ # Array Operation
+ def reshape(self, shape):
+ self.array.shape = shape
+
+ # Array Access
+ def get_reals(self):
+ return self.array.real
+
+ # Array Access
+ def get_imaginary(self):
+ return self.array.imag
+
+ # Array Access
+ def get_max(self):
+ return self.array.max()
+
+ # Array Access
+ def get_mean(self, axis=None):
+ return self.array.mean(axis=axis)
+
+ # Array Access
+ def get_min(self):
+ return self.array.min()
+
+ # Array Operation
+ def cumulative_sum(self):
+ return self.array.cumsum()
+
+ # Array Access
+ def get_arg_min(self):
+ return self.array.argmin()
+
+ # Array Access
+ def get_arg_max(self):
+ return self.array.argmax()
+
+ # Array Access
+ def get_diagonal(self):
+ return self.array.diagonal()
+
+ # Array Naming
+ def get_name(self, row):
+ if self.names.has_key(row):
+ return self.names[row]
+ else:
+ return None
+
+ # Array Naming
+ def get_general_name(self):
+ return self.general_name
+
+ # Array Naming
+ def set_name(self, name, index=False):
+ self.general_name = name
+ for i in range(self.array.shape[0]):
+ if index:
+ self.names[i] = name + " " + str(i+1)
+ else:
+ self.names[i] = name + " " + str(i)
+
+ # Array Naming
+ def set_row_name(self, name, row):
+ self.names[row] = name
+
+ # Array Naming
+ def clear_names(self):
+ self.general_name = None
+ self.names = {}
+
+ # Array Naming
+ def get_domain_name(self):
+ return self.domain
+
+ # Array Naming
+ def get_range_name(self):
+ return self.range
+
+ # Array Naming
+ def set_domain_name(self, name):
+ self.domain = name
+
+ # Array Naming
+ def set_range_name(self, name):
+ self.range = name
+
+ # Array Naming
+ def clear_domain_name(self):
+ self.domain = ''
+
+ # Array Naming
+ def clear_range_name(self):
+ self.range = ''
+
+ # Array Operation
+ def sort_array(self, axis=-1, kind='quicksort', order=None):
+ return self.array.argsort(axis, kind, order)
+
+ # Array Access
+ def get_array_as_type(self, t):
+ return self.array.astype(t)
+
+ # Array Operation
+ def swap_bytes(self, view=False):
+ return self.array.byteswap(view)
+
+ # Array Access
+ def get_conjugate(self):
+ return self.array.conjugate().copy()
+
+ # Array Operation
+ def cumulative_product(self):
+ return self.array.cumprod()
+
+ # Array Convert
+ def dump_to_file(self, fn):
+ self.array.dump(fn)
+
+ # Array Convert
+ def dump_to_string(self):
+ return self.array.dumps()
+
+ # Array Operation
+ def fill_array(self, val=0.):
+ self.array.fill(val)
+
+ # Array Access
+ def get_flattened(self):
+ return self.array.flatten()
+
+ # Array Access
+ def get_field(self, dtype, offset):
+ return self.array.getfield(dtype, offset)
+
+ # Array Access
+ def get_item(self):
+ return self.array.item()
+
+ # Array Access
+ def get_mem_size(self):
+ return self.array.nbytes
+
+ # Array Access
+ def get_num_dims(self):
+ return self.array.ndim
+
+ # Array Access
+ def get_nonzero_indices(self):
+ return self.array.nonzero()
+
+ # Array Operation
+ def put(self, indices, values, mode):
+ self.array.put(indices, values, mode)
+
+ # Array Operation
+ def ravel(self):
+ return self.array.ravel()
+
+ # Array Operation
+ def resize(self, newshape, refcheck=True, order=False):
+ return numpy.resize(self.array, newshape, refcheck=refcheck, order=order)
+
+ # Array Operation
+ def round(self, precision=0, out=None):
+ return self.array.round(precision, out)
+
+ # Array Operation
+ def set_field(self, val, dtype, offset):
+ self.array.set_field(val, dtype, offset)
+
+ # Array Access
+ def get_num_elements(self):
+ return self.array.size
+
+ # Array Operation
+ def squeeze(self):
+ return self.array.squeeze()
+
+ # Array Operation
+ def get_standard_deviation(self, axis=None, dtype=None, out=None):
+ return self.array.std(axis, dtype, out)
+
+ # Array Operation
+ def get_sum(self):
+ return self.array.sum()
+
+ # Array Operation
+ def swap_axes(self, axis1, axis2):
+ return self.array.swapaxes(axis1, axis2)
+
+ # Array Convert
+ def tofile(self, file, sep, format="%s"):
+ self.array.tofile(file, sep, format)
+
+ # Array Convert
+ def tolist(self):
+ return self.array.tolist()
+
+ # Array Convert
+ def tostring(self, order='C'):
+ return self.array.tostring(order)
+
+ # Array Operation
+ def get_trace(self, offset, axis1, axis2, dtype=None, out=None):
+ return self.array.trace(offset, axis1, axis2, dtype, out)
+
+ # Array Access
+ def get_transpose(self):
+ return self.array.transpose()
+
+ # Array Operation
+ def get_variance(self, axis=None, dtype=None, out=None):
+ return self.array.var(axis, dtype, out)
+
+ # Helper function for assignment
+ def get_array(self):
+ return self.array
+
+ # Helper function for assignment
+ def set_array(self, a):
+ self.array = a
+
+ # Array Access
+ def get_row_range(self, start, to):
+ return self.array[start:to+1,:]
+
+ # Array Access
+ def get_col_range(self, start, to):
+ return self.array[:, start:to+1]
diff --git a/contrib/NumSciPy/ArrayAccess.py b/contrib/NumSciPy/ArrayAccess.py
new file mode 100644
index 0000000..70d9e29
--- /dev/null
+++ b/contrib/NumSciPy/ArrayAccess.py
@@ -0,0 +1,342 @@
+import core.modules
+from core.modules.vistrails_module import Module, ModuleError
+
+import numpy
+from Array import *
+
+class ArrayAccess(object):
+ my_namespace = "numpy|array|access"
+
+class GetShape(Module, ArrayAccess):
+ """ Get the size of each dimension of an N-dimensional array"""
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ sh = a.get_shape()
+ dims = len(sh)
+ for i in xrange(dims):
+ pname = "dim" + str(i)
+ self.setResult(pname, sh[i])
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Array Shape", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "dim0", (basic.Integer, 'Dim 0 Size'))
+ reg.add_output_port(cls, "dim1", (basic.Integer, 'Dim 1 Size'))
+ reg.add_output_port(cls, "dim2", (basic.Integer, 'Dim 2 Size'))
+ reg.add_output_port(cls, "dim3", (basic.Integer, 'Dim 3 Size'), True)
+ reg.add_output_port(cls, "dim4", (basic.Integer, 'Dim 4 Size'), True)
+ reg.add_output_port(cls, "dim5", (basic.Integer, 'Dim 5 Size'), True)
+ reg.add_output_port(cls, "dim6", (basic.Integer, 'Dim 6 Size'), True)
+ reg.add_output_port(cls, "dim7", (basic.Integer, 'Dim 7 Size'), True)
+
+class GetReals(Module, ArrayAccess):
+ """ Get the real component of a complex array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ b = a.get_reals()
+ out = NDArray()
+ out.set_array(b)
+ self.setResult("Real Component", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Reals", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Real Component", (NDArray, 'Real Components'))
+
+
+class GetImaginaries(Module, ArrayAccess):
+ """ Get the imaginary component of a complex array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ b = a.get_imaginary()
+ out = NDArray()
+ out.set_array(b)
+ self.setResult("Im Component", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Imaginaries", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Im Component", (NDArray, 'Imaginary Components'))
+
+class GetMax(Module, ArrayAccess):
+ """ Get the maximal value from an array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ self.setResult("Max", float(a.get_max()))
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Max", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Max", (basic.Float, 'Max Value'))
+
+class GetMean(Module, ArrayAccess):
+ """ Get the mean value of an array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ axis = self.forceGetInputFromPort("Axis")
+ out = NDArray()
+ out.set_array(numpy.array(a.get_mean(axis)))
+ self.setResult("Mean", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Mean", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Axis", (basic.Integer, 'Axis'), True)
+ reg.add_output_port(cls, "Mean", (NDArray, 'Mean Value'))
+
+class GetMin(Module, ArrayAccess):
+ """ Get the smallest value in an array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ self.setResult("Min", float(a.get_min()))
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Min", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Min", (basic.Float, 'Min Value'))
+
+class GetDiagonal(Module, ArrayAccess):
+ """ Get an array representing the values on the diagonal of the input array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ out = NDArray()
+ out.set_array(a.get_diagonal())
+ self.setResult("Diagonal", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Diagonal", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Diagonal", (NDArray, 'Diagonal Elements'))
+
+class GetArrayAsType(Module, ArrayAccess):
+ """ Cast the array to the given type """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ t = self.getInputFromPort("Type")
+ t.setValue("0")
+ out = NDArray()
+ out.set_array(a.get_array_as_type(type(t.value)))
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Cast Array", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Type", (basic.Constant, 'Cast To Type'))
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
+
+class GetConjugate(Module, ArrayAccess):
+ """ Get the complex conjugate of the input array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ out = NDArray()
+ out.set_array(a.get_conjugate())
+ self.setResult("Conjugate", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Conjugate", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Conjugate", (NDArray, 'Complex Conjugate'))
+
+class GetFlattenedArray(Module, ArrayAccess):
+ """ Get a flattened representation of the input array"""
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ out = NDArray()
+ out.set_array(a.get_flattened())
+ self.setResult("Flat Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Flattened Array", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Flat Array", (NDArray, 'Output Vector'))
+
+class GetField(Module, ArrayAccess):
+ """ Get a field from an array given the output datatype and offset into the array"""
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ dt = self.getInputFromPort("DType")
+ dt.setValue("0")
+ o = self.getInputFromPort("Offset")
+ out = NDArray()
+ out.set_array(a.get_field(type(dt.value), o))
+ self.setResult("Field", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Field", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "DType", (basic.Constant, 'Output Type'))
+ reg.add_input_port(cls, "Offset", (basic.Integer, 'Offset'))
+ reg.add_output_port(cls, "Field", (NDArray, 'Output Field'))
+
+class ToScalar(Module, ArrayAccess):
+ """ Return an array of size 1 to a scalar """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ self.setResult("Item", float(a.get_item()))
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="To Scalar", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Item", (basic.Float, 'Item'))
+
+class GetMemoryFootprint(Module, ArrayAccess):
+ """ Return the amount of system memory consumed by the array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ self.setResult("Size", int(a.get_mem_size()))
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Memory Size", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'InputArray'))
+ reg.add_output_port(cls, "Size", (basic.Integer, 'Memory Size'))
+
+class GetArrayRank(Module, ArrayAccess):
+ """ Get the rank of the array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ self.setResult("Rank", int(a.get_num_dims()))
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Array Rank", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Rank", (basic.Integer, 'Array Rank'))
+
+class GetNonZeroEntries(Module, ArrayAccess):
+ """ Get an array consisting of the indices to all non-zero entries of the input array."""
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ out = NDArray()
+ out.set_array(a.get_nonzero_indices())
+ self.setResult("Entries", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Non-Zero Entries", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Entreis", (NDArray, 'Output Array'))
+
+class GetArraySize(Module, ArrayAccess):
+ """ Get the number of entries in an array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ self.setResult("Size", a.get_num_elements())
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Array Size", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Size", (basic.Integer, 'Number of Elements'))
+
+class GetTranspose(Module, ArrayAccess):
+ """ Get the transpose of the array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ out = NDArray()
+ out.set_array(a.get_transpose())
+ self.setResult("Transpose", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Get Transpose", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Transpose", (NDArray, 'Transposed Array'))
+
+class GetRowRange(Module, ArrayAccess):
+ """ Get a set of rows from the input array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ s = self.getInputFromPort("Start")
+ e = self.getInputFromPort("End")
+ out = NDArray()
+ if self.forceGetInputFromPort("One Indexed"):
+ s = s-1
+ e = e-1
+
+ out.set_array(a.get_row_range(s, e))
+ new_index = 0
+ for i in range(s,e+1):
+ out.set_row_name(a.get_name(i), new_index)
+ new_index += 1
+
+ out.set_domain_name(a.get_domain_name())
+ out.set_range_name(a.get_range_name())
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Start", (basic.Integer, 'Start Index'))
+ reg.add_input_port(cls, "End", (basic.Integer, 'End Index'))
+ reg.add_input_port(cls, "One Indexed", (basic.Boolean, 'One Indexed'), True)
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+
+class GetRows(Module, ArrayAccess):
+ """ Get a set of rows from the input array defined by a list of indexes """
+ def compute(self):
+ l = self.forceGetInputFromPort("Index List")
+ if l == None:
+ l = self.forceGetInputListFromPort("Indexes")
+
+ if l == None or len(l) == 0:
+ raise ModuleError("No indexes provided")
+
+ l.sort()
+ inp = self.getInputFromPort("Array")
+ in_ar = inp.get_array()
+ out_ar = in_ar[l[0],::]
+ for i in range(1,len(l)):
+ out_ar = numpy.vstack((out_ar,in_ar[i,::]))
+
+ out = NDArray()
+ for i in range(out_ar.shape[0]):
+ out.set_row_name(inp.get_row_name(l[i]), i)
+
+ out.set_array(out_ar)
+ out_order = NDArray()
+ out_order.set_array(numpy.array(l))
+ self.setResult("Output Array", out)
+ self.setResult("Output Order", out_order)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Indexes", (basic.Integer, 'Index'))
+ reg.add_input_port(cls, "Index List", (basic.List, 'Index List'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+ reg.add_output_port(cls, "Output Order", (NDArray, 'Output Ordering'))
+
+class GetColumnRange(Module, ArrayAccess):
+ """ Get a set of columns from the input array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ s = self.getInputFromPort("Start")
+ e = self.getInputFromPort("End")
+ out = NDArray()
+ out.set_array(a.get_col_range(s, e-1))
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Start", (basic.Integer, 'Start Index'))
+ reg.add_input_port(cls, "End", (basic.Integer, 'End Index'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
diff --git a/contrib/NumSciPy/ArrayConvert.py b/contrib/NumSciPy/ArrayConvert.py
new file mode 100644
index 0000000..067c774
--- /dev/null
+++ b/contrib/NumSciPy/ArrayConvert.py
@@ -0,0 +1,151 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from scipy import sparse
+from Array import *
+from Matrix import *
+
+class ArrayConvertModule(object):
+ my_namespace = 'numpy|array|convert'
+
+class ArrayDumpToFile(ArrayConvertModule, Module):
+ """ Pickle the input array and dump it to the specified file. This
+ array can then be read in via pickle.load or numpy.load """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ fn = self.getInputFromPort("Filename")
+ a.dump_to_file(fn)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="ArrayToPickledFile", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+
+class ArrayDumpToString(ArrayConvertModule, Module):
+ """ Pickle the input array and dump it to a string. This array
+ can then be read in via pickle.loads or numpy.loads """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ self.setResult("Output String", a.dump_to_string())
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="ArrayToPickledString", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Output String", (basic.String, 'Output String'))
+
+class ArrayToFile(ArrayConvertModule, Module):
+ """ Write the data to a file. If a separator char is given, the file
+ will be written in ASCII with the given char acting as a delimiter. If
+ no separator is given, the file is written in Binary. The array
+ is always written in row-major format regardless of the order of the
+ input array. """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ fn = self.getInputFromPort("Filename")
+ sep = ""
+ if self.hasInputFromPort("Separator"):
+ sep = self.getInputFromPort("Separator")
+ a.tofile(fn, sep)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+ reg.add_input_port(cls, "Separator", (basic.String, 'Separator'), True)
+
+class ArrayToString(ArrayConvertModule, Module):
+ """ Convert the array to a Python string. The output string will
+ be represented in row-major form regardless of the ordering of the
+ input array. """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ self.setResult("Output String", a.tostring())
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Output String", (basic.String, 'Output String'))
+
+class ArrayToMatrix(ArrayConvertModule, Module):
+ """ Convert the input Numpy Array to a Scipy Matrix. The input array
+ must be no more than 2-dimensional """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ try:
+ mat = sparse.csc_matrix(a.get_array())
+ out_mat = Matrix()
+ out_mat.set_matrix(mat)
+ self.setResult("Output Matrix", out_mat)
+
+ except:
+ raise ModuleError("Could not convert input array to matrix")
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Output Matrix", (Matrix, 'Output Matrix'))
+
+class ArrayToVTKImageData(ArrayConvertModule, Module):
+ """ Convert the array to a vtImageData dataset. This works well for
+ arrays up to (and including) rank 3. Behavior is undefined for array of
+ rank > 3."""
+ def compute(self):
+ import vtk
+
+ a = self.getInputFromPort("Array")
+ sh = a.get_shape()
+
+ if len(sh) < 2:
+ sh = tuple([sh[0], 1, 0])
+ if len(sh) < 3:
+ sh = tuple([sh[0], sh[1], 0])
+
+ (num_sigs, num_times, num_freqs) = sh
+ num_pts = a.get_num_elements()
+ vtk_set = core.modules.module_registry.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkStructuredPoints').module()
+ vtk_set.vtkInstance = vtk.vtkImageData()
+ vtk_set.vtkInstance.SetDimensions(sh[0], sh[1], sh[2]+1)
+ vtk_set.vtkInstance.SetScalarTypeToFloat()
+ scalars = vtk.vtkFloatArray()
+
+ ar = a.get_array()
+ for ar_x in xrange(sh[0]):
+ for ar_y in xrange(sh[1]):
+ if sh[2] == 0:
+ val = ar[ar_x, ar_y]
+ vtk_set.vtkInstance.SetScalarComponentFromFloat(ar_x, ar_y, 0, 0, val)
+ else:
+
+ for ar_z in xrange(sh[2]):
+ val = ar[ar_x, ar_y, ar_z]
+ vtk_set.vtkInstance.SetScalarComponentFromFloat(ar_x, ar_y, ar_z, 0, val)
+
+ if self.hasInputFromPort("SpacingX"):
+ x = self.getInputFromPort("SpacingX")
+ else:
+ x = 1.0
+ if self.hasInputFromPort("SpacingY"):
+ y = self.getInputFromPort("SpacingY")
+ else:
+ y = 1.0
+ if self.hasInputFromPort("SpacingZ"):
+ z = self.getInputFromPort("SpacingZ")
+ else:
+ z = 1.0
+ vtk_set.vtkInstance.SetSpacing(x,y,z)
+
+ self.setResult("vtkImageData", vtk_set)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array Volume'))
+ reg.add_input_port(cls, "SpacingX", (basic.Float, 'X Spacing'))
+ reg.add_input_port(cls, "SpacingY", (basic.Float, 'Y Spacing'))
+ reg.add_input_port(cls, "SpacingZ", (basic.Float, 'Z Spacing'))
+ reg.add_output_port(cls, "vtkImageData", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkImageData').module))
diff --git a/contrib/NumSciPy/ArrayIO.py b/contrib/NumSciPy/ArrayIO.py
new file mode 100644
index 0000000..554162e
--- /dev/null
+++ b/contrib/NumSciPy/ArrayIO.py
@@ -0,0 +1,364 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+import numpy
+import scipy
+import scipy.io
+import pylab
+from Array import *
+from Matrix import *
+
+class ArrayIOModule(object):
+ my_namespace = 'numpy|io'
+
+class NrrdHelper(object):
+ def __init__(self):
+ self.type = {}
+ self.type['float32'] = 'f'
+ self.type['float'] = 'f'
+ self.type['float64'] = 'd'
+ self.type['double'] = 'd'
+ self.type['int'] = 'i'
+ self.type['int16'] = 'i'
+ self.type['long'] = 'l'
+ self.type['int32'] = 'l'
+ self.type['unsigned short'] = 's'
+ self.type['unsigned char'] = 'c'
+
+ self.nrrd_type = {}
+ self.nrrd_type['float'] = 'float'
+ self.nrrd_type['float32'] = 'float'
+ self.nrrd_type['float64'] = 'double'
+ self.nrrd_type['double'] = 'double'
+ self.nrrd_type['int64'] = 'long'
+ self.nrrd_type['long'] = 'long'
+ self.nrrd_type['int32'] = 'int'
+ self.nrrd_type['int16'] = 'short'
+ self.nrrd_type['int8'] = 'uchar'
+ self.nrrd_type['unsigned short'] = 'short'
+
+ self.little_endian = True
+
+ def num_bytes(self, dtype):
+ if self.type.has_key(dtype):
+ return self.type[dtype]
+ else:
+ print "Cannot find " + dtype + " in type library."
+ print "Assuming float32 for dtype"
+ return 'f'
+
+ def get_nrrd_type(self, data):
+ dt = data.dtype.name
+ if self.nrrd_type.has_key(dt):
+ return self.nrrd_type[dt]
+ else:
+ print "Cannot find " + dt + " in type library."
+ print "Assuming float32 for dtype"
+ return 'float'
+
+ def read_raw(self, fn, sizes, dtype, little_end=True):
+ try:
+ fid = open(fn, 'rb')
+ dt = self.num_bytes(dtype)
+ ndim = len(sizes)
+ num_el = 1
+ for i in xrange(ndim):
+ num_el *= sizes[i]
+
+ if little_end:
+ dt = '<'+dt
+ else:
+ dt = '>'+dt
+
+ data = numpy.fromfile(fn, dt)
+ fid.close()
+ data.shape = sizes
+ return data
+ except:
+ raise ModuleError("Could not read .raw file!")
+
+ def write_raw(self, fn, data):
+ try:
+ fid = open(fn, 'wb')
+ scipy.io.fwrite(fid, data.size, data)
+ fid.close()
+ except:
+ raise ModuleError("Could not write .raw file!")
+
+ def write_nhdr(self, fn, data):
+ import os
+ l = fn.split('/')
+ name = l[len(l)-1]
+ base = name.split('.')[0]
+ rawname = base + '.raw'
+ rawpath = fn.rstrip(name)
+ rawpath += rawname
+ self.write_raw(rawpath, data)
+ cmd = 'unu make -h -t '
+ cmd += self.get_nrrd_type(data) + ' '
+ cmd += '-e raw -i ' + rawname + ' -s '
+ sh = data.shape
+ ndims = len(sh)
+ for i in xrange(ndims):
+ cmd += str(sh[i]) + ' '
+
+ cmd += '-o ' + fn
+ try:
+ os.system(cmd)
+ except:
+ raise ModuleError("Could not write NHDR file. Please make sure the Teem and UNU utilities are on your path.")
+
+ def read_nhdr(self, fn):
+ import os.path
+ try:
+ fid = open(fn, 'r')
+ for line in fid:
+ if line.split(':')[0] == 'type':
+ self.dtype = line.split(':')[1].strip()
+ if line.split(':')[0] == 'dimension':
+ self.ndim = int(line.split(':')[1].strip())
+ if line.split(':')[0] == 'sizes':
+ s = line.split(':')[1].strip().split(' ')
+ self.sizes = []
+ for l in s:
+ self.sizes.append(int(l))
+ if line.split(':')[0] == 'endian':
+ if line.split(':')[1].strip() == 'little':
+ self.little_endian = True
+ else:
+ self.little_endian = False
+ if line.split(':')[0] == 'data file':
+ self.fn = line.split(':')[1].strip()
+ if line.split(':')[0] == 'encoding':
+ self.encoding = line.split(':')[1].strip()
+ fid.close()
+ except:
+ raise ModuleError("Could not read .nhdr file!")
+
+ if self.encoding == 'raw':
+ curpath = os.getcwd()
+ npath = os.path.dirname(fn)
+ os.chdir(npath)
+ data = self.read_raw(self.fn, self.sizes, self.dtype, little_end=self.little_endian)
+ os.chdir(curpath)
+ return data
+
+ raise ModuleError(".nhdr file contains file not in .raw format!")
+
+class ReadPNG(ArrayIOModule, Module):
+ """ Load a .png type image into a Numpy Array. """
+ def compute(self):
+ fn = self.getInputFromPort("Filename")
+ ar = pylab.imread(fn)
+ out = NDArray()
+ out.set_array(ar)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class WritePNG(ArrayIOModule, Module):
+ """ Write a .png type image from a Numpy Array. """
+ def compute(self):
+ fn = self.getInputFromPort("Filename")
+ ar = self.getInputFromPort("Image")
+ minv = self.forceGetInputFromPort("Min")
+ maxv = self.forceGetInputFromPort("Max")
+ if minv == None:
+ minv = 0
+ if maxv == None:
+ maxv = 255
+ da_ar = ar.get_array().squeeze()
+ im = scipy.misc.toimage(da_ar, cmin=minv, cmax=maxv).save(fn)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+ reg.add_input_port(cls, "Min", (basic.Integer, 'Min Value'))
+ reg.add_input_port(cls, "Max", (basic.Integer, 'Max Value'))
+ reg.add_input_port(cls, "Image", (NDArray, 'Image To Write'))
+
+class ReadRAW(ArrayIOModule, Module):
+ """ Load a .raw file into a Numpy Array. The .raw files are
+ assumed to be in the volvis format: http://www.volvis.org """
+ def __init__(self):
+ Module.__init__(self)
+ self.helper = NrrdHelper()
+
+ def compute(self):
+ fn = self.getInputFromPort("Filename")
+ sizes = self.getInputListFromPort("Sizes")
+ dtype = self.getInputFromPort("DataType")
+ ar = self.helper.read_raw(fn, sizes, dtype)
+ out = NDArray()
+ out.set_array(ar)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+ reg.add_input_port(cls, "Sizes", (basic.Integer, 'Dimension Sizes'))
+ reg.add_input_port(cls, "DataType", (basic.String, 'Datatype'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class WriteRAW(ArrayIOModule, Module):
+ """ Write a .raw file from a Numpy Array. """
+ def __init__(self):
+ Module.__init__(self)
+ self.helper = NrrdHeler()
+
+ def compute(self):
+ fn = self.getInputFromPort("Filename")
+ ar = self.getInputFromPort("Array").get_array()
+ self.helper.write_raw(fn,ar)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+
+class ReadNHDR(ArrayIOModule, Module):
+ """ Load a .nhdr/.raw pair into a Numpy Array. """
+ def __init__(self):
+ Module.__init__(self)
+ self.helper = NrrdHelper()
+
+ def compute(self):
+ fn = ''
+ if self.hasInputFromPort("File"):
+ fn = self.getInputFromPort("File").name
+ else:
+ fn = self.getInputFromPort("Filename")
+ ar = self.helper.read_nhdr(fn)
+ out = NDArray()
+ out.set_array(ar)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+ reg.add_input_port(cls, "File", (basic.File, 'File'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class WriteNHDR(ArrayIOModule, Module):
+ """ Write a .nhdr/.raw pair from a Numpy Array """
+ def __init__(self):
+ Module.__init__(self)
+ self.helper = NrrdHelper()
+
+ def compute(self):
+ fn = self.getInputFromPort("Filename")
+ ar = self.getInputFromPort("Array").get_array()
+ self.helper.write_nhdr(fn,ar)
+ self.setResult("Filename Out", fn)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Filename Out", (basic.String, 'Output Filename'))
+
+class ReadStatisticalSummary(ArrayIOModule, Module):
+ """
+ Documentation
+ """
+ def compute(self):
+ fn = ''
+ if self.hasInputFromPort("File"):
+ fn = self.getInputFromPort("File").name
+ else:
+ fn = self.getInputFromPort("Filename")
+
+ if self.forceGetInputFromPort("Allocate Aggregated Array"):
+ alloc_array = True
+ else:
+ alloc_array = False
+
+ fid = open(fn, 'r')
+ dims = fid.readline().strip().split()
+ n_pts = int(dims[0])
+ n_bins = int(dims[1])
+
+ min_ar = numpy.zeros(n_pts)
+ lq_ar = numpy.zeros(n_pts)
+ med_ar = numpy.zeros(n_pts)
+ hq_ar = numpy.zeros(n_pts)
+ max_ar = numpy.zeros(n_pts)
+ mode_ar = numpy.zeros((n_pts, 4))
+ hist_ar = numpy.zeros((n_pts, n_bins))
+ if alloc_array:
+ ag_ar = numpy.zeros((n_pts, 5+4+n_bins))
+ for i in xrange(n_pts):
+ l = fid.readline().strip().split()
+ min_ar[i] = float(l[0])
+ lq_ar[i] = float(l[1])
+ med_ar[i] = float(l[2])
+ hq_ar[i] = float(l[3])
+ max_ar[i] = float(l[4])
+ for j in xrange(4):
+ mode_ar[i, j] = float(l[5+j])
+
+ for b in xrange(n_bins):
+ hist_ar[i, b] = float(l[9+b])
+
+ if alloc_array:
+ vals = numpy.array(l).astype('float')
+ ag_ar[i,:] += vals
+
+ fid.close()
+
+ min_ar_out = NDArray()
+ min_ar_out.set_array(min_ar)
+ self.setResult("Min Array", min_ar_out)
+
+ lq_ar_out = NDArray()
+ lq_ar_out.set_array(lq_ar)
+ self.setResult("Lower Quartile Array", lq_ar_out)
+
+ med_ar_out = NDArray()
+ med_ar_out.set_array(med_ar)
+ self.setResult("Median Array", med_ar_out)
+
+ hq_ar_out = NDArray()
+ hq_ar_out.set_array(hq_ar)
+ self.setResult("Upper Quartile Array", hq_ar_out)
+
+ max_ar_out = NDArray()
+ max_ar_out.set_array(max_ar)
+ self.setResult("Max Array", max_ar_out)
+
+ mode_ar_out = NDArray()
+ mode_ar_out.set_array(mode_ar)
+ self.setResult("Mode Array", mode_ar_out)
+
+ hist_ar_out = NDArray()
+ hist_ar_out.set_array(hist_ar)
+ self.setResult("Histogram Array", hist_ar_out)
+
+ if alloc_array:
+ ag_ar_out = NDArray()
+ ag_ar_out.set_array(ag_ar)
+ self.setResult("Aggregated Array", ag_ar_out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+ reg.add_input_port(cls, "File", (basic.File, 'File'))
+ reg.add_input_port(cls, "Allocate Aggregated Array", (basic.Boolean, 'Allocate Extra Space for Aggregated Array'), True)
+ reg.add_output_port(cls, "Min Array", (NDArray, 'Minima Array'))
+ reg.add_output_port(cls, "Lower Quartile Array", (NDArray, 'Lower Quartile Array'))
+ reg.add_output_port(cls, "Median Array", (NDArray, 'Median Array'))
+ reg.add_output_port(cls, "Upper Quartile Array", (NDArray, 'Upper Quartile Array'))
+ reg.add_output_port(cls, "Max Array", (NDArray, 'Maxima Array'))
+ reg.add_output_port(cls, "Mode Array", (NDArray, 'Mode Array'))
+ reg.add_output_port(cls, "Histogram Array", (NDArray, 'Histogram Array'))
+ reg.add_output_port(cls, "Aggregated Array", (NDArray, 'Aggregated Array'), True)
diff --git a/contrib/NumSciPy/ArrayInterpolate.py b/contrib/NumSciPy/ArrayInterpolate.py
new file mode 100644
index 0000000..3200c31
--- /dev/null
+++ b/contrib/NumSciPy/ArrayInterpolate.py
@@ -0,0 +1,152 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+import scipy
+import scipy.interpolate
+import scipy.ndimage
+import vtk
+from Array import *
+from Matrix import *
+
+class ArrayInterpModule(object):
+ my_namespace = 'scipy|interpolation'
+
+class RBFInterpolate(ArrayInterpModule, Module):
+ """ Use radial basis function interpolation to project scalars from
+ one mesh to another. The input, Source, describes the x,y,z coordinates and
+ values of the points in the form: [[x,y,z,v]] The input, Destination,
+ describes the x,y,z coordinates of the points to project onto in the form
+ [[x,y,z]]. Additional (optional) inputs controll the basis function (basis),
+ the smoothing factor (smoothing) and the tuning parameter (epsilon). Not
+ all parameters are valid for all bases. The following defaults are applied:
+
+ basis = inverse multiquadric
+ smoothing = 0.0
+ epsilon = 1.0
+ """
+
+ def compute(self):
+ src = self.getInputFromPort("Source").get_array()
+ if src.shape[1] != 4:
+ raise ModuleError("Source array must be in the form [[x,y,z,v]]")
+
+ dest = self.getInputFromPort("Destination").get_array()
+ if dest.shape[1] != 3:
+ raise ModuleError("Destination array must be in the form [[x,y,z]]")
+
+ if self.hasInputFromPort("Basis"):
+ self.basis = self.getInputFromPort("Basis")
+ else:
+ self.basis = 'inverse multiquadric'
+
+ if self.hasInputFromPort("Smoothing"):
+ self.smooth = self.getInputFromPort("Smoothing")
+ else:
+ self.smooth = 0.0
+
+ if self.hasInputFromPort("Epsilon"):
+ self.eps = self.getInputFromPort("Epsilon")
+ else:
+ self.eps = 1.0
+
+ rbfi = scipy.interpolate.Rbf(src[:,0], src[:,1], src[:,2], src[:,3], function=self.basis, smooth=self.smooth, epsilon=self.eps)
+
+ val_ar = rbfi(dest[:,0], dest[:,1], dest[:,2])
+
+ out = NDArray()
+ out.set_array(val_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Source", (NDArray, 'Source Array'))
+ reg.add_input_port(cls, "Destination", (NDArray, 'Destination Array'))
+ reg.add_input_port(cls, "Basis", (basic.String, 'Basis Function'), True)
+ reg.add_input_port(cls, "Smoothing", (basic.Float, 'Smoothing Factor'), True)
+ reg.add_input_port(cls, "Epsilon", (basic.Float, 'Basis Epsilon'), True)
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Scalars'))
+
+class BSplineInterpolate(ArrayInterpModule, Module):
+ """
+ Find the B-Spline representation of an N-dimensional curve.
+ """
+
+ def compute(self):
+ in_ar = self.getInputFromPort("Input").get_array()
+ num_samp = self.forceGetInputFromPort("Interpolant Support")
+ if not num_samp:
+ num_samp = in_ar.shape[0]
+
+ smoothing = self.forceGetInputFromPort("Smoothing")
+ if not smoothing:
+ smoothing = 0.0
+
+ degree = self.forceGetInputFromPort("Degree")
+ if not degree:
+ degree = 3
+
+ (tckvec, u) = scipy.interpolate.splprep(in_ar, s=smoothing, k=degree, nest=-1)
+ (x,y,z) = splev(numpy.linspace(0.,1.,num_samp), tckvec)
+ out_ar = numpy.zeros((x.shape[0], 3))
+ out_ar[:,0] = x
+ out_ar[:,1] = y
+ out_ar[:,2] = z
+
+ out = NDArray()
+ out.set_array(out_ar)
+
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, 'Source Array'))
+ reg.add_input_port(cls, "Smoothing", (basic.Float, 'Smoothing Factor'), True)
+ reg.add_input_port(cls, "Interpolant Support", (basic.Integer, 'Output Samples'), True)
+ reg.add_input_port(cls, "Degree", (basic.Integer, 'Polynomial Degree'), True)
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Scalars'))
+
+class BSplineResample(ArrayInterpModule, Module):
+ """
+ Resample the input array using an order-n bspline
+ """
+ def compute(self):
+ in_ar = self.getInputFromPort("Input").get_array()
+ order = self.forceGetInputFromPort("Order")
+ if order == None:
+ order = 3
+ planes = self.forceGetInputFromPort("Planes")
+ ndim = in_ar.ndim
+ gridshape = self.getInputFromPort("New Shape").values
+
+ out_ar = None
+ if planes:
+ out_ar = []
+ for i in range(in_ar.shape[0]):
+ pl = in_ar[i].squeeze()
+ arshape = pl.shape
+ g = scipy.mgrid[tuple([slice(0, v1-1, complex(0,v2)) for (v1,v2) in zip(arshape, gridshape)])]
+ coords = numpy.array(list(g))
+ out_ar.append(scipy.ndimage.map_coordinates(pl, coords))
+
+ out_ar = numpy.array(out_ar)
+
+ else:
+ arshape = in_ar.shape
+ g = scipy.mgrid[tuple([slice(0, v1-1, complex(0,v2)) for (v1,v2) in zip(arshape, gridshape)])]
+ coords = numpy.array(list(g))
+ out_ar = scipy.ndimage.map_coordinates(in_ar, coords)
+
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, 'Source Array'))
+ reg.add_input_port(cls, "Order", (basic.Integer, 'Bspline Order'), True)
+ reg.add_input_port(cls, "New Shape", (basic.Tuple, 'New Array Shape'))
+ reg.add_input_port(cls, "Planes", (basic.Boolean, 'Apply to each plane'), True)
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Scalars'))
diff --git a/contrib/NumSciPy/ArrayOperations.py b/contrib/NumSciPy/ArrayOperations.py
new file mode 100644
index 0000000..d7cf0bc
--- /dev/null
+++ b/contrib/NumSciPy/ArrayOperations.py
@@ -0,0 +1,632 @@
+from core.modules.vistrails_module import Module, ModuleError
+from Array import *
+
+class ArrayOperationModule(object):
+ my_namespace = 'numpy|array|operations'
+
+
+class ArrayReshape(ArrayOperationModule, Module):
+ """ Reshape the input array. The dimension sizes are presented
+ and used to reshape the array. Please note that the total number
+ of elements in the array must remain the same before and after
+ reshaping. """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ dims = self.getInputFromPort("Dims")
+ newdims = []
+
+ for i in xrange(dims):
+ pname = "dim" + str(i)
+ newdims.append(self.getInputFromPort(pname))
+
+ try:
+ a.reshape(tuple(newdims))
+ except:
+ raise ModuleError("Could not assign new shape. Be sure the number of elements remains constant")
+
+ self.setResult("Array Output", a.copy())
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="ReshapeArray", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Dims", (basic.Integer, 'New Dimensionality'))
+ reg.add_input_port(cls, "dim0", (basic.Integer, 'Dimension Size'))
+ reg.add_input_port(cls, "dim1", (basic.Integer, 'Dimension Size'))
+ reg.add_input_port(cls, "dim2", (basic.Integer, 'Dimension Size'))
+ reg.add_input_port(cls, "dim3", (basic.Integer, 'Dimension Size'), True)
+ reg.add_input_port(cls, "dim4", (basic.Integer, 'Dimension Size'), True)
+ reg.add_input_port(cls, "dim5", (basic.Integer, 'Dimension Size'), True)
+ reg.add_input_port(cls, "dim6", (basic.Integer, 'Dimension Size'), True)
+ reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
+
+class ArrayCumulativeSum(ArrayOperationModule, Module):
+ """ Get the cumulative sum of a given array. This is returned as a
+ flattened array of the same size as the input where each element
+ of the array serves as the cumulative sum up until that point."""
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ b = a.cumulative_sum()
+ out = NDArray()
+ out.set_array(b)
+ self.setResult("Array Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
+
+class ArrayScalarMultiply(ArrayOperationModule, Module):
+ """ Multiply the input array with a given scalar """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ b = self.getInputFromPort("Scalar")
+ out = NDArray()
+ out.set_array(a.get_array() * b)
+ self.setResult("Array Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Scalar", (basic.Float, 'Input Scalar'))
+ reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
+
+class ArraySort(ArrayOperationModule, Module):
+ def __init__(self):
+ Module.__init__(self)
+ self.axis = -1
+ self.kind = 'quicksort'
+ self.order = None
+
+ """ Sort the input array. By default, a flattened representation
+ of the input array is used as input to a quicksort. Optional
+ inputs are the axis in which to sort on and the type of sort to
+ use.
+
+ Sorting algorithms supported:
+ quicksort - best average speed, unstable
+ mergesort - needs additional working memory, stable
+ heapsort - good worst-case performance, unstable
+ """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ if self.hasInputFromPort("Axis"):
+ self.axis = self.getInputFromPort("Axis")
+ if self.hasInputFromPort("Sort"):
+ self.kind = self.getInputFromPort("Sort")
+ if self.hasInputFromPort("Order"):
+ self.order = self.getInputFromPort("Order")
+
+ b = a.sort_array(axis=self.axis, kind=self.kind, order=self.order)
+ out = NDArray()
+ out.set_array(b.copy())
+ self.setResult("Sorted Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Axis", (basic.Integer, 'Axis to sort'), True)
+ reg.add_input_port(cls, "Sort", (basic.String, 'Sort Algorithm'), True)
+ reg.add_input_port(cls, "Order", (basic.Integer, 'Order'),True)
+ reg.add_output_port(cls, "Sorted Array", (NDArray, 'Sorted Array'))
+
+class ArrayCumulativeProduct(ArrayOperationModule, Module):
+ """ Get the cumulative product of a given array. This is returned as
+ a flattened array of the same size as the input where each element of
+ the array serves as the cumulative product up until that point"""
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ b = a.cumulative_product()
+ out = NDArray()
+ out.set_array(b)
+ self.setResult("Array Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
+
+class ArrayFill(ArrayOperationModule, Module):
+ """ Fill the input array with the given value. If no value is given
+ it is filled with 0.0"""
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ if self.hasInputFromPort("Value"):
+ val = self.getInputFromPort("Value")
+ else:
+ val = 0.
+
+ a.fill_array(val)
+ self.setResult("Array Output", a)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Fill Array", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Value", (basic.Float, 'Value'))
+ reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
+
+class ArrayResize(ArrayOperationModule, Module):
+ """ Resize the input array. Unlike the ArrayReshape module,
+ the number of elements of the array need not be conserved.
+ If the shape is larger than the input array size, repeated
+ copies of the input array will be copied to the resized version.
+ If the shape is smaller, the input array will be cropped appropriately.
+ """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ dims = self.getInputFromPort("Dims")
+ newdims = []
+
+ for i in xrange(dims):
+ pname = "dim" + str(i)
+ newdims.append(self.getInputFromPort(pname))
+
+ try:
+ t = tuple(newdims)
+ b = a.resize(t)
+ out = NDArray()
+ out.set_array(b.copy())
+ except:
+ raise ModuleError("Could not assign new shape.")
+
+ self.setResult("Array Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Dims", (basic.Integer, 'Output Dimensionality'))
+ reg.add_input_port(cls, "dim0", (basic.Integer, 'Dimension Size'))
+ reg.add_input_port(cls, "dim1", (basic.Integer, 'Dimension Size'))
+ reg.add_input_port(cls, "dim2", (basic.Integer, 'Dimension Size'))
+ reg.add_input_port(cls, "dim3", (basic.Integer, 'Dimension Size'), True)
+ reg.add_input_port(cls, "dim4", (basic.Integer, 'Dimension Size'), True)
+ reg.add_input_port(cls, "dim5", (basic.Integer, 'Dimension Size'), True)
+ reg.add_input_port(cls, "dim6", (basic.Integer, 'Dimension Size'), True)
+ reg.add_input_port(cls, "dim7", (basic.Integer, 'Dimension Size'), True)
+ reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
+
+class ArrayExtractRegion(ArrayOperationModule, Module):
+ """ Extract a region from array as specified by the
+ dimension and starting and ending indices """
+ def compute(self):
+ import operator
+ a = self.getInputFromPort("Array")
+ dims = self.getInputFromPort("Dims")
+ a_dims = len(a.get_shape())
+ if dims > a_dims:
+ raise ModuleError("Output Dimensionality larger than Input Dimensionality")
+
+ slices = []
+ for i in xrange(dims):
+ (start, stop) = self.getInputFromPort("dim"+str(i))
+ slices.append(slice(start, stop))
+
+ ar = operator.__getitem__(a.get_array(), tuple(slices))
+ out = NDArray()
+ out.set_array(ar)
+ self.setResult("Array Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ l = [basic.Integer, basic.Integer]
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Dims", (basic.Integer, 'Output Dimensionality'))
+ reg.add_input_port(cls, "dim0", l, True)
+ reg.add_input_port(cls, "dim1", l, True)
+ reg.add_input_port(cls, "dim2", l, True)
+ reg.add_input_port(cls, "dim3", l, True)
+ reg.add_input_port(cls, "dim4", l, True)
+ reg.add_input_port(cls, "dim5", l, True)
+ reg.add_input_port(cls, "dim6", l, True)
+ reg.add_input_port(cls, "dim7", l, True)
+ reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
+
+class ArrayRavel(ArrayOperationModule, Module):
+ """ Get a 1D array containing the elements of the input array"""
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ b = NDArray()
+ b.set_array(a.ravel().copy())
+ self.setResult("Array Output", b)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
+
+class ArrayRound(ArrayOperationModule, Module):
+ """ Round each element of the array to the given number of
+ decimal places. This defaults to 0 resulting in a rounding
+ to integers """
+ def __init__(self):
+ Module.__init__(self)
+ self.decimals = 0
+
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ if self.hasInputFromPort("Decimals"):
+ self.decimals = self.getInputFromPort("Decimals")
+
+ out = NDArray()
+ out.set_array(a.round(precision=self.decimals))
+ self.setResult("Array Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Decimals", (basic.Integer, 'Precision'))
+ reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
+
+class ArrayGetSigma(ArrayOperationModule, Module):
+ """ Return the standard deviation of elements in the array """
+ def __init__(self):
+ Module.__init__(self)
+ self.axis=None
+
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ if self.hasInputFromPort("Axis"):
+ self.axis = self.getInputFromPort("Axis")
+
+ out = NDArray()
+ out.set_array(a.get_standard_deviation(self.axis))
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="ArrayStandardDeviation", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Axis", (basic.Integer, 'Axis'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArraySum(ArrayOperationModule, Module):
+ """ Get the sum of all elements in the input array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ self.setResult("Array Sum", float(a.get_sum()))
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Array Sum", (basic.Float, 'Sum'))
+
+class ArrayElementMultiply(ArrayOperationModule, Module):
+ """ Perform an element-wise multiply on the elements of two arrays """
+ def compute(self):
+ a1 = self.getInputFromPort("Array1")
+ a2 = self.getInputFromPort("Array2")
+ out = NDArray()
+ out.set_array(a1.get_array() * a2.get_array())
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array1", (NDArray, 'Input Array 1'))
+ reg.add_input_port(cls, "Array2", (NDArray, 'Input Array 2'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArraySetElement(ArrayOperationModule, Module):
+ """ Set a set of array elements given arrays of values and indices
+
+ Please note that this module creates a copy of the input to operate
+ on to preserve the original array data. """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ if self.hasInputFromPort("Scalar Value"):
+ self.v = self.getInputFromPort("Scalar Value")
+ else:
+ self.v = self.getInputFromPort("Value Array")
+
+ if self.hasInputFromPort("Single Index"):
+ self.ind = self.getInputFromPort("Single Index")
+ else:
+ self.ind = self.getInputFromPort("Index Array")
+
+ out_a = a.copy()
+
+ out_a.put(self.ind, self.v)
+ out = NDArray()
+ out.set_array(out_a)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Scalar Value", (basic.Float, 'Value to Set'))
+ reg.add_input_port(cls, "Value Array", (NDArray, 'Values to Set'))
+ reg.add_input_port(cls, "Single Index", (basic.Integer, 'Index to Set'))
+ reg.add_input_port(cls, "Index Array", (NDArray, 'Indexes to Set'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArrayVariance(ArrayOperationModule, Module):
+ """ Calculate the variance of the elements of an array """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ if self.hasInputFromPort("Axis"):
+ self.setResult("Variance", float(a.get_variance(axis=self.getInputFromPort("Axis"))))
+ else:
+ self.setResult("Variance", float(a.get_variance()))
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Axis", (basic.Integer, 'Axis'))
+ reg.add_output_port(cls, "Variance", (basic.Float, 'Variance'))
+
+class ArrayTrace(ArrayOperationModule, Module):
+ """ Calculate the trace of the input array.
+
+ The input array must have at least rank 2. The trace is taken
+ on the diagonal given by the inputs Axis1 and Axis2 using the
+ given Offset. If these values are not supplied, they default to:
+
+ Axis1 = 0
+ Axis2 = 1
+ Offset = 0
+ """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ if self.hasInputFromPort("Axis1"):
+ self.axis1 = self.getInputFromPort("Axis1")
+ else:
+ self.axis1 = 0
+
+ if self.hasInputFromPort("Axis2"):
+ self.axis2 = self.getInputFromPort("Axis2")
+ else:
+ self.axis2 = 1
+
+ if self.hasInputFromPort("Offset"):
+ self.offset = self.getInputFromPort("Offset")
+ else:
+ self.offset = 0
+
+ self.setResult("Trace", float(a.get_trace(self.offset, self.axis1, self.axis2)))
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Axis1", (basic.Integer, 'Axis 1'))
+ reg.add_input_port(cls, "Axis2", (basic.Integer, 'Axis 2'))
+ reg.add_input_port(cls, "Offset", (basic.Integer, 'Offset'))
+ reg.add_output_port(cls, "Trace", (basic.Float, 'Array Trace'))
+
+class ArraySwapAxes(ArrayOperationModule, Module):
+ """ Create a new view of the input array with the
+ given axes swapped.
+ """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ a1 = self.getInputFromPort("Axis1")
+ a2 = self.getInputFromPort("Axis2")
+ out = NDArray()
+ out.set_array(a.swap_axes(a1, a2).copy())
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Axis1", (basic.Integer, 'Axis 1'))
+ reg.add_input_port(cls, "Axis2", (basic.Integer, 'Axis 2'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArraySqueeze(ArrayOperationModule, Module):
+ """ Eliminate all length-1 dimensions in the input array. """
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ out = NDArray()
+ out.set_array(a.get_array().squeeze().copy())
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArrayAdd(ArrayOperationModule, Module):
+ """ Add two arrays of the same size and shape """
+ def compute(self):
+ a1 = self.getInputFromPort("Array One").get_array()
+ a2 = self.getInputFromPort("Array Two").get_array()
+
+ if a1.shape != a2.shape:
+ raise ModuleError("Cannot add arrays with different shapes")
+
+ out = NDArray()
+ out.set_array(a1 + a2)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array One", (NDArray, 'Input Array 1'))
+ reg.add_input_port(cls, "Array Two", (NDArray, 'Input Array 2'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArrayScalarAdd(ArrayOperationModule, Module):
+ """ Add two arrays of the same size and shape """
+ def compute(self):
+ a1 = self.getInputFromPort("Array One").get_array()
+ s = self.getInputFromPort("Scalar")
+
+ out = NDArray()
+ out.set_array(a1 + s)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array One", (NDArray, 'Input Array 1'))
+ reg.add_input_port(cls, "Scalar", (basic.Float, 'Scalar'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArrayLog10(ArrayOperationModule, Module):
+ """ Take the base-10 log of each element in the input array """
+ def compute(self):
+ a = self.getInputFromPort("Array").get_array()
+ out = NDArray()
+ out.set_array(numpy.log10(a))
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArrayAtan2(ArrayOperationModule, Module):
+ """ Calculate the oriented arc-tangent of a vector stored as two arrays.
+ Reals: Real components of complex vectors
+ Imaginaries: Imaginary components of complex vectors
+ """
+ def compute(self):
+ r = self.getInputFromPort("Reals").get_array()
+ i = self.getInputFromPort("Imaginaries").get_array()
+ out = NDArray()
+ out.set_array(numpy.arctan2(r,i))
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Reals", (NDArray, 'Real Components'))
+ reg.add_input_port(cls, "Imaginaries", (NDArray, 'Imaginary Components'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArraySqrt(ArrayOperationModule, Module):
+ """ Calculate the element-wise square root of the input array """
+ def compute(self):
+ a = self.getInputFromPort("Input Array").get_array()
+ out = NDArray()
+ out.set_array(numpy.sqrt(a))
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input Array", (NDArray, 'Input Array'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArrayThreshold(ArrayOperationModule, Module):
+ """ Threshold the array keeping only the values above the scalar value, v. """
+ def compute(self):
+ in_ar = self.getInputFromPort("Input Array").get_array()
+ v = self.getInputFromPort("Value")
+ r = self.forceGetInputFromPort("Replacement")
+ if r == None:
+ r = 0.
+ out = NDArray()
+ out.set_array(numpy.where(in_ar > v, in_ar, r))
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Value", (basic.Float, 'Threshold Value'))
+ reg.add_input_port(cls, "Replacement", (basic.Float, 'Replacement Value'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArrayWindow(ArrayOperationModule, Module):
+ """ Threshold the array from both above and below, keeping only
+ the values within the window. """
+ def compute(self):
+ in_ar = self.getInputFromPort("Input Array").get_array()
+ lo = self.forceGetInputFromPort("Lower Bound")
+ hi = self.forceGetInputFromPort("Upper Bound")
+ r = self.forceGetInputFromPort("Replacement")
+ if r == None:
+ r = 0.
+ if lo == None:
+ lo = in_ar.min()
+ if hi == None:
+ hi = in_ar.max()
+
+ out = NDArray()
+ o = numpy.where(in_ar >= lo, in_ar, r)
+ o = numpy.where(o <= hi, o, r)
+ out.set_array(o)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Lower Bound", (basic.Float, 'Lower Threshold Value'))
+ reg.add_input_port(cls, "Upper Bound", (basic.Float, 'Upper Threshold Value'))
+ reg.add_input_port(cls, "Replacement", (basic.Float, 'Replacement Value'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArrayNormalize(ArrayOperationModule, Module):
+ """ Normalize the input array """
+ def compute(self):
+ in_ar = self.getInputFromPort("Input Array").get_array()
+ ar = numpy.zeros(in_ar.shape)
+ if self.forceGetInputFromPort("Planes"):
+ for i in range(in_ar.shape[0]):
+ p = in_ar[i] - in_ar[i].min()
+ ar[i] = p / p.max()
+ else:
+ ar = in_ar - in_ar.min()
+ ar = ar/ar.max()
+
+ out = NDArray()
+ out.set_array(ar)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "Planes", (basic.Boolean, 'Plane-wise normalization'), True)
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ArrayName(ArrayOperationModule, Module):
+ """ Assign a name or label to the entries of an array """
+ def compute(self):
+ in_ar = self.getInputFromPort("Input Array")
+ gen_name = self.forceGetInputFromPort("Name")
+ one_index = self.forceGetInputFromPort("One Indexed")
+ if gen_name:
+ in_ar.set_name(gen_name, index=one_index)
+
+ name_list = self.forceGetInputListFromPort("Row Name")
+ if name_list != None:
+ for (i,n) in name_list:
+ in_ar.set_row_name(n, i)
+
+ dname = self.forceGetInputFromPort("Domain Name")
+ if dname:
+ in_ar.set_domain_name(dname)
+
+ rname = self.forceGetInputFromPort("Range Name")
+ if rname:
+ in_ar.set_range_name(rname)
+
+ self.setResult("Output Array", in_ar)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input Array", (NDArray, 'Input Array'))
+ reg.add_input_port(cls, "One Indexed", (basic.Boolean, 'One Indexed'))
+ reg.add_input_port(cls, "Name", (basic.String, 'Array Name'))
+ reg.add_input_port(cls, "Row Name", [basic.Integer, basic.String], True)
+ reg.add_input_port(cls, "Domain Name", (basic.String, 'Domain Label'))
+ reg.add_input_port(cls, "Range Name", (basic.String, 'Range Label'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
diff --git a/contrib/NumSciPy/ArrayPlot.py b/contrib/NumSciPy/ArrayPlot.py
new file mode 100644
index 0000000..ef6e1ae
--- /dev/null
+++ b/contrib/NumSciPy/ArrayPlot.py
@@ -0,0 +1,638 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from core.modules.basic_modules import PythonSource
+from Array import *
+from Matrix import *
+
+import pylab
+import matplotlib
+import urllib
+import random
+
+class ArrayPlot(object):
+ namespace = 'numpy|array|plotting'
+ def get_label(self, ar, i):
+ lab = ar.get_name(i)
+ if lab == None:
+ return 'Array ' + str(i)
+ else:
+ return lab
+
+ def is_cacheable(self):
+ return False
+
+ def get_color(self, colors, i, randomcolor):
+ if randomcolor:
+ return (random.random(), random.random(), random.random())
+
+ if self.color_dict == None:
+ self.color_dict = {}
+ for (k,r,g,b) in colors:
+ self.color_dict[k] = (r,g,b)
+
+ if self.color_dict.has_key(i):
+ return self.color_dict[i]
+ else:
+ return None
+
+ def get_marker(self, markers, i):
+ if markers == None:
+ return None
+
+ if self.marker_dict == None:
+ self.marker_dict = {}
+ for (k,m) in markers:
+ self.marker_dict[k] = m
+
+ if self.marker_dict.has_key(i):
+ return self.marker_dict[i]
+ else:
+ return None
+
+ def get_alpha(self, alphas, i):
+ return None
+
+class ArrayImage(ArrayPlot, Module):
+ '''
+ Display the 2D input Data Array as a color-mapped image.
+ Independent control of the aspect ratio, colormap, presence of the
+ colorbar and presented axis values are provided through the
+ appropriate input ports: Aspect Ratio, Colormap, Colorbar,
+ Extents. To change the colormap being used, it must be one of the
+ pre-made maps provided by matplotlib.cm. Only 1 2D array can be
+ viewed at a time.
+ '''
+ def compute(self):
+ data = self.getInputFromPort("Data Array")
+ da_ar = data.get_array().squeeze()
+ if da_ar.ndim != 2:
+ raise ModuleError("Input Data Array must have dimension = 2")
+
+ aspect_ratio = self.forceGetInputFromPort("Aspect Ratio")
+ colormap = self.forceGetInputFromPort("Colormap")
+ colorbar = self.forceGetInputFromPort("Colorbar")
+ extents = self.forceGetInputFromPort("Extents")
+
+ # Quickly check the assigned colormap to make sure it's valid
+ if colormap == None:
+ colormap = "jet"
+ if not hasattr(pylab, colormap):
+ colormap = "jet"
+
+ bg_color = self.forceGetInputFromPort("Background")
+ array_x_t = self.forceGetInputFromPort("Use X Title")
+ array_y_t = self.forceGetInputFromPort("Use Y Title")
+
+ p_title = self.forceGetInputFromPort("Title")
+ x_label = self.forceGetInputFromPort("X Title")
+ y_label = self.forceGetInputFromPort("Y Title")
+
+ s = urllib.unquote(str(self.forceGetInputFromPort("source", '')))
+
+ s = 'from pylab import *\n' +\
+ 'from numpy import *\n' +\
+ 'import numpy\n'
+
+ if bg_color == None:
+ bg_color = 'w'
+
+ if type(bg_color) == type(''):
+ s += 'figure(facecolor=\'' + bg_color + '\')\n'
+ else:
+ s += 'figure(facecolor=' + str(bg_color) + ')\n'
+
+ s += 'imshow(da_ar, interpolation=\'bicubic\''
+ if aspect_ratio != None:
+ s += ', aspect=' + str(aspect_ratio)
+
+ if extents != None:
+ s += ', extent=['+str(extents[0])+','+str(extents[1])+','+str(extents[2])+','+str(extents[3])+']'
+ s += ')\n'
+
+ s += colormap + '()\n'
+
+ if colorbar:
+ s += 'colorbar()\n'
+
+ if array_x_t:
+ s += 'xlabel(\'' + data.get_domain_name() + '\')\n'
+ elif x_label:
+ s += 'xlabel(\'' + x_label + '\')\n'
+
+ if array_y_t:
+ s += 'ylabel(\'' + data.get_range_name() + '\')\n'
+ elif y_label:
+ s += 'ylabel(\'' + y_label + '\')\n'
+
+ if p_title:
+ s += 'title(\'' + p_title + '\')\n'
+
+ exec s
+ self.setResult('source', s)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.namespace)
+
+ @classmethod
+ def register_ports(cls, reg, basic):
+ reg.add_input_port(cls, "source", (basic.String, 'source'), True)
+ reg.add_input_port(cls, "Data Array", (NDArray, 'Array to Plot'))
+ reg.add_input_port(cls, "Aspect Ratio", (basic.Float, 'Aspect Ratio'))
+ reg.add_input_port(cls, "Colormap", (basic.String, 'Colormap'))
+ reg.add_input_port(cls, "Colorbar", (basic.Boolean, 'Show Colorbar'), True)
+ reg.add_input_port(cls, "Extents", [basic.Float, basic.Float, basic.Float, basic.Float], True)
+ reg.add_input_port(cls, "Background", [basic.Float, basic.Float, basic.Float], True)
+ reg.add_input_port(cls, "Use X Title", (basic.Boolean, 'Apply X-axis Label'))
+ reg.add_input_port(cls, "Use Y Title", (basic.Boolean, 'Apply Y-axis Label'))
+ reg.add_input_port(cls, "Title", (basic.String, 'Figure Title'))
+ reg.add_input_port(cls, "X Title", (basic.String, 'X-axis label'), True)
+ reg.add_input_port(cls, "Y Title", (basic.String, 'Y-axis label'), True)
+ reg.add_output_port(cls, "source", (basic.String, 'source'))
+
+class Histogram(ArrayPlot, Module):
+ '''
+ Plot a histogram of the data values. Multiple datasets can be
+ presented by providing multiple connections to the Data Array
+ port. These data are then differentiated by assigned colors and
+ labels. By default, 10 bins are used to histogram the data.
+ Additionally, recapturing the PDF of the data is possible by
+ enabling the Normalize option.
+ '''
+ def compute(self):
+ data = self.getInputListFromPort("Data Array")
+ self.label_dict = None
+ self.color_dict = None
+ use_legend = self.forceGetInputFromPort("Legend")
+ randomcolors = self.forceGetInputFromPort("Random Colors")
+ colors = self.forceGetInputListFromPort("Colors")
+ bg_color = self.forceGetInputFromPort("Background")
+ array_x_t = self.forceGetInputFromPort("Use X Title")
+ array_y_t = self.forceGetInputFromPort("Use Y Title")
+ p_title = self.forceGetInputFromPort("Title")
+ x_label = self.forceGetInputFromPort("X Title")
+ nbins = self.forceGetInputFromPort("Bins")
+ if nbins == None:
+ nbins = 10
+ normed = self.forceGetInputFromPort("Normalize")
+ if normed == None:
+ normed = False
+
+ s = urllib.unquote(str(self.forceGetInputFromPort("source", '')))
+ self.source = ''
+
+ s = 'from pylab import *\n' +\
+ 'from numpy import *\n' +\
+ 'import numpy\n'
+
+ if bg_color == None:
+ bg_color = 'w'
+
+ if type(bg_color) == type(''):
+ s += 'figure(facecolor=\'' + bg_color + '\')\n'
+ else:
+ s += 'figure(facecolor=' + str(bg_color) + ')\n'
+
+ data_list = []
+ for i in data:
+ data_list.append(i.get_array().squeeze())
+
+ da_ar = None
+ try:
+ da_ar = numpy.array(data_list)
+ except:
+ raise ModuleException("Not all Data Array inputs are the same size!")
+
+ for i in range(da_ar.shape[0]):
+ lab = self.get_label(data[i], i)
+ col = self.get_color(colors, i, randomcolors)
+
+ s += 'hist(da_ar['+str(i)+',:], bins=' + str(nbins)
+
+ if lab != None:
+ s += ', label=\'' + lab + '\''
+ if col != None:
+ s += ', facecolor=' + str(col)
+
+ s += ', normed='+str(normed)
+ s += ')\n'
+
+ if use_legend:
+ s += 'legend()\n'
+
+ if array_x_t:
+ s += 'xlabel(\'' + data[0].get_domain_name() + '\')\n'
+ elif x_label:
+ s += 'xlabel(\'' + x_label + '\')\n'
+
+ if array_y_t:
+ s += 'ylabel(\'Histogram Value\')\n'
+
+ if p_title:
+ s += 'title(\'' + p_title + '\')\n'
+
+ exec s
+ self.setResult("source", s)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.namespace)
+
+ @classmethod
+ def register_ports(cls, reg, basic):
+ reg.add_input_port(cls, "source", (basic.String, 'source'), True)
+ reg.add_input_port(cls, "Data Array", (NDArray, 'Data Array to Plot'))
+ reg.add_input_port(cls, "Legend", (basic.Boolean, 'Use Legend'), True)
+ reg.add_input_port(cls, "Random Colors", (basic.Boolean, 'Assign Random Colors'), True)
+ reg.add_input_port(cls, "Colors", [basic.Integer, basic.Float, basic.Float, basic.Float], True)
+ reg.add_input_port(cls, "Background", [basic.Float, basic.Float, basic.Float], True)
+ reg.add_input_port(cls, "Use X Title", (basic.Boolean, 'Apply X-axis Label'))
+ reg.add_input_port(cls, "Use Y Title", (basic.Boolean, 'Apply Y-axis Label'))
+ reg.add_input_port(cls, "Title", (basic.String, 'Figure Title'))
+ reg.add_input_port(cls, "X Title", (basic.String, 'X-axis label'), True)
+ reg.add_input_port(cls, "Bins", (basic.Integer, 'Number of Bins'))
+ reg.add_input_port(cls, "Normalize", (basic.Boolean, 'Normalize to PDF'), True)
+ reg.add_output_port(cls, "source", (basic.String, 'source'))
+
+class BarChart(ArrayPlot, Module):
+ '''
+ Create a bar chart of the input data. Different datasets can be
+ used simultaneously by connecting to the Data input port multiple
+ times. Each successive data connection will be rendered on top of
+ the previous dataset. This creates a stacked bar chart. Error
+ bars are drawn with the errors for each of the datasets connected
+ to the Error Bars input port.
+ '''
+ def get_ticks(self, num):
+ a = []
+ for i in range(num):
+ a.append('')
+
+ for i in self.tick_dict.keys():
+ a[i] = self.tick_dict[i]
+
+ return a
+
+ def compute(self):
+ data = self.getInputListFromPort("Data")
+ errs = self.forceGetInputListFromPort("Error Bars")
+ if len(errs) == 0:
+ errs = None
+
+ self.label_dict = None
+ self.color_dict = None
+ use_legend = self.forceGetInputFromPort("Legend")
+ randomcolors = self.forceGetInputFromPort("Random Colors")
+ colors = self.forceGetInputListFromPort("Colors")
+ bg_color = self.forceGetInputFromPort("Background")
+ array_x_t = self.forceGetInputFromPort("Use X Title")
+ array_y_t = self.forceGetInputFromPort("Use Y Title")
+ ticks = self.forceGetInputListFromPort("Bar Labels")
+ self.tick_dict = {}
+ for (k,v) in ticks:
+ self.tick_dict[k] = v
+ p_title = self.forceGetInputFromPort("Title")
+ x_label = self.forceGetInputFromPort("X Title")
+ y_label = self.forceGetInputFromPort("Y Title")
+
+ width = self.forceGetInputFromPort("Bar Width")
+ if width == None:
+ width = 0.5
+
+ if errs != None:
+ if len(data) != len(errs):
+ raise ModuleError("Number of data does not match number of error bar data")
+
+ s = urllib.unquote(str(self.forceGetInputFromPort("source", '')))
+ self.source = ''
+
+ s = 'from pylab import *\n' +\
+ 'from numpy import *\n' +\
+ 'import numpy\n'
+
+ if bg_color == None:
+ bg_color = 'w'
+
+ if type(bg_color) == type(''):
+ s += 'figure(facecolor=\'' + bg_color + '\')\n'
+ else:
+ s += 'figure(facecolor=' + str(bg_color) + ')\n'
+
+ numpts = None
+ ind = None
+ prev = None
+ ind = numpy.arange(data[0].get_array().flatten().shape[0])
+ t = self.get_ticks(data[0].get_array().flatten().shape[0])
+ ag_ar = numpy.zeros((len(data), data[0].get_array().flatten().shape[0]))
+ for i in range(len(data)):
+ da_ar = data[i].get_array().flatten()
+ ag_ar[i,:] = da_ar
+
+ er_ar = numpy.zeros((len(data), data[0].get_array().flatten().shape[0]))
+ if errs != None:
+ for i in range(len(data)):
+ er_ar[i,:] = errs[i].get_array().flatten()
+
+ for i in range(ag_ar.shape[0]):
+ s += 'bar(ind, ag_ar[' + str(i) + ',:], width'
+ lab = self.get_label(data[i], i)
+ col = self.get_color(colors, i, randomcolors)
+ if lab != None:
+ s += ', label=\'' + lab + '\''
+ if col != None:
+ s += ', color=' + str(col)
+
+ if errs != None:
+ s += ', yerr=er_ar[' + str(i) + ',:]'
+
+ if prev != None:
+ s += ', bottom=ag_ar[' + str(i-1) + ',:]'
+
+ s += ')\n'
+ prev = ag_ar[i]
+
+ if use_legend:
+ s += 'legend()\n'
+
+ if array_x_t:
+ s += 'xlabel(\'' + data[0].get_domain_name() + '\')\n'
+ elif x_label:
+ s += 'xlabel(\'' + x_label + '\')\n'
+
+ if array_y_t:
+ s += 'ylabel(\'' + data[0].get_range_name() + '\')\n'
+ elif y_label:
+ s += 'ylabel(\'' + y_label + '\')\n'
+
+ if p_title:
+ s += 'title(\'' + p_title + '\')\n'
+
+ s += 'xticks(ind + width/2., t)\n'
+ exec s
+ self.setResult("source", s)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.namespace)
+
+ @classmethod
+ def register_ports(cls, reg, basic):
+ reg.add_input_port(cls, "source", (basic.String, 'source'), True)
+ reg.add_input_port(cls, "Data", (NDArray, 'Data Array to Plot'))
+ reg.add_input_port(cls, "Error Bars", (NDArray, 'Error Array to Plot'))
+ reg.add_input_port(cls, "Legend", (basic.Boolean, 'Use Legend'), True)
+ reg.add_input_port(cls, "Random Colors", (basic.Boolean, 'Assign Random Colors'), True)
+ reg.add_input_port(cls, "Colors", [basic.Integer, basic.Float, basic.Float, basic.Float], True)
+ reg.add_input_port(cls, "Background", [basic.Float, basic.Float, basic.Float], True)
+ reg.add_input_port(cls, "Bar Labels", [basic.Integer, basic.String], True)
+ reg.add_input_port(cls, "Use X Title", (basic.Boolean, 'Apply X-axis Label'))
+ reg.add_input_port(cls, "Use Y Title", (basic.Boolean, 'Apply Y-axis Label'))
+ reg.add_input_port(cls, "X Title", (basic.String, 'X-axis label'), True)
+ reg.add_input_port(cls, "Y Title", (basic.String, 'Y-axis label'), True)
+ reg.add_input_port(cls, "Title", (basic.String, 'Figure Title'))
+ reg.add_input_port(cls, "Bar Width", (basic.Float, 'Bar Width'), True)
+ reg.add_output_port(cls, "source", (basic.String, 'source'))
+
+class ScatterPlot(ArrayPlot, Module):
+ '''
+ Create a scatter plot from X and Y positions defined by the X
+ Array and Y Array ports, respectively. Datasets can be added by
+ connecting multiple arrays to the appropriate input ports.
+ Symbols representing each dataset can be defined by using the
+ Markers input assigning a valid pylab symbol to a dataset.
+ '''
+ def compute(self):
+ xdata = self.getInputListFromPort("X Array")
+ ydata = self.getInputListFromPort("Y Array")
+ self.label_dict = None
+ use_legend = self.forceGetInputFromPort("Legend")
+ randomcolors = self.forceGetInputFromPort("Random Colors")
+ colors = self.forceGetInputListFromPort("Colors")
+ self.color_dict = None
+ bg_color = self.forceGetInputFromPort("Background")
+ markers = self.forceGetInputListFromPort("Markers")
+ self.marker_dict = None
+ ps = self.forceGetInputFromPort("Point Size")
+ array_x_t = self.forceGetInputFromPort("Use X Title")
+ array_y_t = self.forceGetInputFromPort("Use Y Title")
+
+ p_title = self.forceGetInputFromPort("Title")
+ x_label = self.forceGetInputFromPort("X Title")
+ y_label = self.forceGetInputFromPort("Y Title")
+
+ s = urllib.unquote(str(self.forceGetInputFromPort("source", '')))
+ self.source = ''
+
+ if len(xdata) != len(ydata):
+ raise ModuleError("Cannot create scatter plot for different number of X and Y datasets.")
+
+ s = 'from pylab import *\n' +\
+ 'from numpy import *\n' +\
+ 'import numpy\n'
+
+ if bg_color == None:
+ bg_color = 'w'
+
+ if type(bg_color) == type(''):
+ s += 'figure(facecolor=\'' + bg_color + '\')\n'
+ else:
+ s += 'figure(facecolor=' + str(bg_color) + ')\n'
+
+ xdata_ar = numpy.zeros((len(xdata), xdata[0].get_array().flatten().shape[0]))
+ ydata_ar = numpy.zeros((len(xdata), xdata[0].get_array().flatten().shape[0]))
+
+ for i in range(len(xdata)):
+ xd = xdata[i]
+ yd = ydata[i]
+ xdata_ar[i,:] = xd.get_array().flatten()
+ ydata_ar[i,:] = yd.get_array().flatten()
+
+ for i in range(len(xdata)):
+ xar = xdata[i]
+ yar = ydata[i]
+
+ lab = self.get_label(xar, i)
+ col = self.get_color(colors, i, randomcolors)
+ mar = self.get_marker(markers, i)
+
+ s += 'scatter(xdata_ar[' + str(i) +',:], ydata_ar[' + str(i) + ',:]'
+
+ if lab != None:
+ s += ', label=\'' + lab +'\''
+ if col != None:
+ s += ', color=' + str(col)
+ if mar != None:
+ s += ', marker=\'' + mar + '\''
+ if ps != None:
+ s += ', size=' + str(ps)
+ s += ')\n'
+
+ if use_legend:
+ s += 'legend()\n'
+
+ if array_x_t:
+ s += 'xlabel(\'' + xar.get_domain_name() + '\')\n'
+ elif x_label:
+ s += 'xlabel(\'' + x_label + '\')\n'
+
+ if array_y_t:
+ s += 'ylabel(\'' + yar.get_domain_name() + '\')\n'
+ elif y_label:
+ s += 'ylabel(\'' + y_label + '\')\n'
+
+ if p_title:
+ s += 'title(\'' + p_title + '\')\n'
+
+ print s
+ exec s
+ self.setResult("source", s)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.namespace)
+
+ @classmethod
+ def register_ports(cls, reg, basic):
+ reg.add_input_port(cls, "source", (basic.String, 'source'), True)
+ reg.add_input_port(cls, "X Array", (NDArray, 'X Array to Plot'))
+ reg.add_input_port(cls, "Y Array", (NDArray, 'Y Array to Plot'))
+ reg.add_input_port(cls, "Legend", (basic.Boolean, 'Use Legend'), True)
+ reg.add_input_port(cls, "Random Colors", (basic.Boolean, 'Assign Random Colors'), True)
+ reg.add_input_port(cls, "Colors", [basic.Integer, basic.Float, basic.Float, basic.Float], True)
+ reg.add_input_port(cls, "Background", [basic.Float, basic.Float, basic.Float], True)
+ reg.add_input_port(cls, "Markers", [basic.Integer, basic.String], True)
+ reg.add_input_port(cls, "Use X Title", (basic.Boolean, 'Apply X-axis Label'))
+ reg.add_input_port(cls, "Use Y Title", (basic.Boolean, 'Apply Y-axis Label'))
+ reg.add_input_port(cls, "X Title", (basic.String, 'X-axis label'), True)
+ reg.add_input_port(cls, "Y Title", (basic.String, 'Y-axis label'), True)
+ reg.add_input_port(cls, "Title", (basic.String, 'Figure Title'))
+ reg.add_input_port(cls, "Point Size", (basic.Float, 'Point Size'), True)
+ reg.add_output_port(cls, "source", (basic.String, 'source'))
+
+class LinePlot(ArrayPlot, Module):
+ '''
+ Create a standard line plot from a 1 or 2-dimensional Input Array.
+ If the Input Array is 2-dimensional, each row will be plotted as a
+ new line.
+ '''
+ def compute(self):
+ data = self.getInputFromPort("Input Array")
+ indexes = self.forceGetInputFromPort("Indexes")
+ self.label_dict = None
+ use_legend = self.forceGetInputFromPort("Legend")
+ randomcolors = self.forceGetInputFromPort("Random Colors")
+ colors = self.forceGetInputListFromPort("Colors")
+ self.color_dict = None
+ markers = self.forceGetInputListFromPort("Markers")
+ self.marker_dict = None
+ x_label = self.forceGetInputFromPort("X Title")
+ y_label = self.forceGetInputFromPort("Y Title")
+ p_title = self.forceGetInputFromPort("Title")
+ bg_color = self.forceGetInputFromPort("Background")
+
+ array_x_t = self.forceGetInputFromPort("Use X Title")
+ array_y_t = self.forceGetInputFromPort("Use Y Title")
+
+ s = urllib.unquote(str(self.forceGetInputFromPort("source", '')))
+ self.source = ''
+ da_ar = data.get_array()
+
+ if da_ar.ndim > 2:
+ raise ModuleError("Cannot plot data with dimensions > 2")
+
+ s = 'from pylab import *\n' +\
+ 'from numpy import *\n' +\
+ 'import numpy\n'
+
+ if bg_color == None:
+ bg_color = 'w'
+
+ if type(bg_color) == type(''):
+ s += 'figure(facecolor=\'' + bg_color + '\')\n'
+ else:
+ s += 'figure(facecolor=' + str(bg_color) + ')\n'
+
+ if da_ar.ndim == 1:
+ da_ar.shape = (1, da_ar.shape[0])
+
+ xar = self.forceGetInputFromPort("X Values")
+ sf = self.forceGetInputFromPort("Scaling Factor")
+ if sf == None:
+ sf = 1.
+
+ if xar == None:
+ start_i = None
+ end_i = None
+ if indexes == None:
+ start_i = 0
+ end_i = da_ar.shape[1]
+ else:
+ start_i = indexes[0]
+ end_i = indexes[1]
+
+ xar = numpy.arange(start_i, end_i)
+ xar = xar * sf
+ else:
+ xar = xar.get_array()
+
+ print da_ar.shape
+ print xar.shape
+ for i in range(da_ar.shape[0]):
+ lab = self.get_label(data, i)
+ col = self.get_color(colors, i, randomcolors)
+ mar = self.get_marker(markers, i)
+ if indexes == None:
+ s += 'plot(xar, da_ar[' + str(i) + ',:]'
+ else:
+ s += 'plot(xar, da_ar[' + str(i) + ',' + str(indexes[0]) + ':' + str(indexes[1]) + ']'
+
+ if lab != None:
+ s += ', label=\'' + lab +'\''
+ if col != None:
+ s += ', color=' + str(col)
+ if mar != None:
+ s += ', marker=\'' + mar + '\''
+ s += ')\n'
+
+ if use_legend:
+ s += 'legend()\n'
+
+ if array_x_t:
+ s += 'xlabel(\'' + data.get_domain_name() + '\')\n'
+ elif x_label:
+ s += 'xlabel(\'' + x_label + '\')\n'
+
+ if array_y_t:
+ s += 'ylabel(\'' + data.get_range_name() + '\')\n'
+ elif y_label:
+ s += 'ylabel(\'' + y_label + '\')\n'
+
+ if p_title:
+ s += 'title(\'' + p_title + '\')\n'
+
+ exec s
+ self.setResult("source", s)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.namespace)
+
+ @classmethod
+ def register_ports(cls, reg, basic):
+ reg.add_input_port(cls, "source", (basic.String, 'source'), True)
+ reg.add_input_port(cls, "Input Array", (NDArray, 'Array to Plot'))
+ reg.add_input_port(cls, "X Values", (NDArray, 'Domain Values'))
+ reg.add_input_port(cls, "Legend", (basic.Boolean, 'Use Legend'), True)
+ reg.add_input_port(cls, "Random Colors", (basic.Boolean, 'Assign Random Colors'), True)
+ reg.add_input_port(cls, "Colors", [basic.Integer, basic.Float, basic.Float, basic.Float], True)
+ reg.add_input_port(cls, "Markers", [basic.Integer, basic.String], True)
+ reg.add_input_port(cls, "Use X Title", (basic.Boolean, 'Apply X-axis Label'))
+ reg.add_input_port(cls, "Use Y Title", (basic.Boolean, 'Apply Y-axis Label'))
+ reg.add_input_port(cls, "X Title", (basic.String, 'X-axis label'), True)
+ reg.add_input_port(cls, "Y Title", (basic.String, 'Y-axis label'), True)
+ reg.add_input_port(cls, "Title", (basic.String, 'Figure Title'))
+ reg.add_input_port(cls, "Background", [basic.Float, basic.Float, basic.Float], True)
+ reg.add_input_port(cls, "Indexes", [basic.Integer, basic.Integer], True)
+ reg.add_input_port(cls, "Scaling Factor", (basic.Float, 'Scaling Factor'), True)
+ reg.add_output_port(cls, "source", (basic.String, 'source'))
diff --git a/contrib/NumSciPy/ArrayUtilities.py b/contrib/NumSciPy/ArrayUtilities.py
new file mode 100644
index 0000000..2f3ffa9
--- /dev/null
+++ b/contrib/NumSciPy/ArrayUtilities.py
@@ -0,0 +1,254 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from scipy import sparse
+import vtk
+from Array import *
+from Matrix import *
+
+class ArrayUtilModule(object):
+ my_namespace = 'numpy|array|utilities'
+
+class ArrayToVTKVectors(ArrayUtilModule, Module):
+ def compute(self):
+ v0 = self.forceGetInputFromPort("Array0")
+ v1 = self.forceGetInputFromPort("Array1")
+ v2 = self.forceGetInputFromPort("Array2")
+ ds = self.getInputFromPort("VTK Data")
+
+ v_name = self.forceGetInputFromPort("Vector Name")
+ if v_name == None:
+ v_name = 'vectors'
+
+ vsize = 0
+ if v0:
+ vsize += 1
+ v0 = v0.get_array().flatten()
+ if v1:
+ vsize += 1
+ v1 = v1.get_array().flatten()
+ if v2:
+ vsize += 1
+ v2 = v2.get_array().flatten()
+
+ np = ds.vtkInstance.GetNumberOfPoints()
+ pd = ds.vtkInstance.GetPointData()
+ vtk_ar = vtk.vtkDoubleArray()
+# vtk_ar.SetNumberOfValues(np)
+ vtk_ar.SetNumberOfComponents(3)
+ for i in range(np):
+ if vsize == 2:
+ vtk_ar.InsertNextTuple3(v0[i], v1[i], 0.)
+ elif vsize == 3:
+ vtk_ar.InsertNextTuple3(v0[i], v1[i], v2[i])
+
+ vtk_ar.SetName(v_name)
+ ds.vtkInstance.GetPointData().AddArray(vtk_ar)
+ ds.vtkInstance.GetPointData().SetVectors(vtk_ar)
+# ds.vtkInstance.GetPointData().SetActiveVectors(v_name)
+ self.setResult("Output", ds)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+
+ @classmethod
+ def register_ports(cls, reg, basic):
+ reg.add_input_port(cls, "Array0", (NDArray, 'Scalar Array'))
+ reg.add_input_port(cls, "Array1", (NDArray, 'Scalar Array'))
+ reg.add_input_port(cls, "Array2", (NDArray, 'Scalar Array'))
+ reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
+ reg.add_input_port(cls, "Vector Name", (basic.String, 'Scalar Name'), True)
+ reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
+
+class ArrayToTimeVaryingVTKVectors(ArrayUtilModule, Module):
+ def update_progress(self, cur, total):
+ t = float(cur) / float(total)
+ self.logging.update_progress(self, t)
+
+ def compute(self):
+ v0 = self.forceGetInputFromPort("Array0")
+ v1 = self.forceGetInputFromPort("Array1")
+ v2 = self.forceGetInputFromPort("Array2")
+ ds = self.getInputFromPort("VTK Data")
+
+ v_name = self.forceGetInputFromPort("Vector Name")
+ if v_name == None:
+ v_name = 'vectors'
+
+ vsize = 0
+ if v0:
+ vsize += 1
+ if v1:
+ vsize += 1
+ if v2:
+ vsize += 1
+
+ num_times = ds.vtkInstance.GetNumberOfTimeSteps()
+ for i in range(num_times):
+ self.update_progress(i, num_times)
+ np = ds.vtkInstance.GetTimeStep(i).GetNumberOfPoints()
+ pd = ds.vtkInstance.GetTimeStep(i).GetPointData()
+ vtk_ar = vtk.vtkDoubleArray()
+# vtk_ar.SetNumberOfValues(np)
+ vtk_ar.SetNumberOfComponents(3)
+ arx = v0.get_array().squeeze()
+ arx = arx[i,::].squeeze().flatten()
+ ary = v1.get_array().squeeze()
+ ary = ary[i,::].squeeze().flatten()
+ if vsize == 3:
+ arz = v2.get_array().squeeze()
+ arz = arz[i,::].squeeze().flatten()
+ for j in range(np):
+ if vsize == 2:
+ vtk_ar.InsertNextTuple3(arx[j], ary[j], 0.)
+ elif vsize == 3:
+ vtk_ar.InsertNextTuple3(arz[j], ary[j], arz[j])
+
+ vtk_ar.SetName(v_name)
+ ds.vtkInstance.GetTimeStep(i).GetPointData().AddArray(vtk_ar)
+ ds.vtkInstance.GetTimeStep(i).GetPointData().SetVectors(vtk_ar)
+# ds.vtkInstance.GetPointData().SetActiveVectors(v_name)
+ self.setResult("Output", ds)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+
+ @classmethod
+ def register_ports(cls, reg, basic):
+ reg.add_input_port(cls, "Array0", (NDArray, 'Scalar Array'))
+ reg.add_input_port(cls, "Array1", (NDArray, 'Scalar Array'))
+ reg.add_input_port(cls, "Array2", (NDArray, 'Scalar Array'))
+ reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
+ reg.add_input_port(cls, "Vector Name", (basic.String, 'Scalar Name'), True)
+ reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
+
+
+class ArrayToTimeVaryingVTKScalars(ArrayUtilModule, Module):
+ def update_progress(self, cur, total):
+ t = float(cur) / float(total)
+ self.logging.update_progress(self, t)
+
+ def compute(self):
+ ds = self.getInputFromPort("VTK Data")
+ ar = self.getInputFromPort("Scalars")
+ v_name = self.forceGetInputFromPort("Array Name")
+ if v_name == None:
+ v_name = 'scalars'
+ num_times = ds.vtkInstance.GetNumberOfTimeSteps()
+ ar_ = ar.get_array()
+ if ar_.shape[0] != num_times:
+ raise ModuleError("Cannot process array with num timesteps = " +
+ str(ar_.shape[0]) +
+ " and vtkdata with " +
+ str(num_times) + " timesteps")
+
+ for i in range(num_times):
+ self.update_progress(i, num_times)
+ s_ar = ar_[i,::].squeeze().flatten()
+ vtk_ar = vtk.vtkDoubleArray()
+ vtk_ar.SetNumberOfValues(s_ar.size)
+ vtk_ar.SetName(v_name)
+ for j in range(s_ar.size):
+ vtk_ar.InsertNextValue(s_ar[j])
+
+ ds.vtkInstance.GetTimeStep(i).GetPointData().AddArray(vtk_ar)
+ ds.vtkInstance.GetTimeStep(i).GetPointData().SetScalars(vtk_ar)
+
+ self.setResult("Output", ds)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+
+ @classmethod
+ def register_ports(cls, reg, basic):
+ reg.add_input_port(cls, "Scalars", (NDArray, 'Scalar Array'))
+ reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
+ reg.add_input_port(cls, "Array Name", (basic.String, 'Scalar Name'), True)
+ reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
+
+class ArrayToVTKScalars(ArrayUtilModule, Module):
+ """ Take a scalar array and consider it as an array of scalars
+ to assign to a VTK dataset. The number of elements in the
+ scalar array must be equivalent to the number of points in
+ the VTK dataset. Please note that this module adds a scalar
+ array to the input dataset and can be considered a mutating filter
+ because of this."""
+
+ def compute(self):
+ a = self.getInputFromPort("Array")
+ ds = self.getInputFromPort("VTK Data")
+ scalar_name = ''
+ if self.hasInputFromPort("Scalar Name"):
+ scalar_name = self.getInputFromPort("Scalar Name")
+ else:
+ scalar_name = 'scalars'
+
+ s_ar = a.get_array().flatten()
+ np = ds.vtkInstance.GetNumberOfPoints()
+# if s_ar.size != np:
+# raise ModuleError("Could not assign scalars to VTK dataset with different number of elements")
+
+ pd = ds.vtkInstance.GetPointData()
+ vtk_ar = vtk.vtkDoubleArray()
+ vtk_ar.SetNumberOfValues(np)
+ for i in xrange(np):
+ vtk_ar.SetValue(i, s_ar[i])
+
+ vtk_ar.SetName(scalar_name)
+ ds.vtkInstance.GetPointData().AddArray(vtk_ar)
+# ds.vtkinstance.GetPointData().SetActiveScalars(scalar_name)
+ ds.vtkInstance.GetPointData().SetScalars(vtk_ar)
+ self.setResult("Output", ds)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+
+ @classmethod
+ def register_ports(cls, reg, basic):
+ reg.add_input_port(cls, "Array", (NDArray, 'Scalar Array'))
+ reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
+ reg.add_input_port(cls, "Scalar Name", (basic.String, 'Scalar Name'), True)
+ reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
+
+class VTKDataSetToPointArray(ArrayUtilModule, Module):
+ """
+ Extract points and scalar values from a vtkDataSet. The
+ output will be of the form [[x,y,z,v]] with the v component
+ optionally added if the IncludeScalars flag is set.
+ """
+ def compute(self):
+ data = self.getInputFromPort("vtkDataSet").vtkInstance
+ flag = self.forceGetInputFromPort("IncludeScalars")
+
+ np = data.GetNumberOfPoints()
+ ndim = 3
+ if flag:
+ ndim = 4
+
+ out_ar = numpy.ones((np, ndim))
+ for i in xrange(np):
+ (out_ar[i,0], out_ar[i,1], out_ar[i,2]) = data.GetPoint(i)
+ if flag:
+ out_ar[i,3] = data.GetPointData().GetArray(0).GetTuple1(i)
+
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+
+ @classmethod
+ def register_ports(cls, reg, basic):
+ reg.add_input_port(cls, "vtkDataSet", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
+ reg.add_input_port(cls, "IncludeScalars", (basic.Boolean, 'Include Scalars in Output'), True)
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
+
+
+
+
diff --git a/contrib/NumSciPy/DSP.py b/contrib/NumSciPy/DSP.py
new file mode 100644
index 0000000..15b4dcb
--- /dev/null
+++ b/contrib/NumSciPy/DSP.py
@@ -0,0 +1,369 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from Matrix import *
+from Array import *
+import scipy
+import scipy.signal
+from scipy import fftpack
+import numpy
+
+class DSPModule(object):
+ my_namespace = 'scipy|signals'
+
+class SignalGenerator(DSPModule, Module):
+ my_namespace = 'scipy|signals|generator'
+
+ def compute(self):
+ samples = self.getInputFromPort("Samples")
+ periods = self.getInputFromPort("Periods")
+ freqs = self.getInputListFromPort("Frequencies")
+
+ ar = numpy.linspace(0., float(periods) * 2. * scipy.pi, periods * samples)
+ out_ar = numpy.zeros(periods * samples)
+
+ for f in freqs:
+ out_ar += scipy.sin(f * ar)
+
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Samples", (basic.Integer, "Sampling Rate"))
+ reg.add_input_port(cls, "Periods", (basic.Integer, "Signal Length"))
+ reg.add_input_port(cls, "Frequencies", (basic.Float, "Additive Frequency"))
+ reg.add_output_port(cls, "Output", (NDArray, "Output Signal"))
+
+class FFT(DSPModule, Module):
+ __doc__ = """ Calculate the discrete Fourier transform of the arbitrary
+ sequence presented on the Signal port. This is done using
+ SciPy's FFTPack module.\n\n"""
+ __doc__ += """From fftpack.fft:\n\t"""
+ __doc__ += fftpack.fft.__doc__
+
+ my_namespace = 'scipy|signals|fourier'
+
+ def compute(self):
+ sig_array = self.getInputFromPort("Signals")
+
+ # If there is no input on the samples port,
+ # use the number of samples in an array row for
+ # the number of fft points.
+ if self.hasInputFromPort("Samples"):
+ pts = self.getInputFromPort("Samples")
+
+ else:
+ try:
+ pts = sig_array.get_shape()[1]
+ except:
+ pts = sig_array.get_shape()[0]
+
+ sh = sig_array.get_shape()
+ if len(sh) < 2:
+ shp = (1, sh[0])
+ sig_array.reshape(shp)
+
+ (num_sigs, num_samps) = sig_array.get_shape()
+ phasors = fftpack.fft(sig_array.get_row_range(0,0), pts)
+ out_ar = phasors
+
+ for i in xrange(1,num_sigs):
+ phasors = fftpack.fft(sig_array.get_row_range(i,i), pts)
+ out_ar = numpy.vstack([out_ar, phasors])
+
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("FFT Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Array'))
+ reg.add_input_port(cls, "Samples", (basic.Integer, 'FFT Samples'))
+ reg.add_output_port(cls, "FFT Output", (NDArray, 'FFT Output'))
+
+class FFTN(DSPModule, Module):
+ __doc__ = """ Calculate the discrete Fourier transform of the arbitrary
+ sequence presented on the Signal port. This is done using
+ SciPy's FFTPack module.\n\n"""
+ __doc__ += """From fftpack.fftn:\n\t"""
+ __doc__ += fftpack.fftn.__doc__
+
+ my_namespace = 'scipy|signals|fourier'
+
+ def compute(self):
+ sig_array = self.getInputFromPort("Signals")
+ # If there is no input on the samples port,
+ # use the number of samples in an array row for
+ # the number of fft points.
+ if self.hasInputFromPort("Samples"):
+ pts = self.getInputFromPort("Samples")
+
+ else:
+ pts = sig_array.get_shape()[1]
+
+ sh = (sig_array.get_shape()[0], pts)
+
+ phasors = fftpack.fftn(sig_array.get_array(), shape=sh)
+ out = NDArray()
+ out.set_array(phasors)
+ self.setResult("FFT Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Array'))
+ reg.add_input_port(cls, "Samples", (basic.Integer, 'FFT Samples'))
+ reg.add_output_port(cls, "FFT Output", (NDArray, 'FFT Output'))
+
+class ShortTimeFourierTransform(DSPModule, Module):
+ """ Calculate the short time Fourier transform of the
+ sequence presented on the Signal port. This is done using
+ SciPy's FFTPack fft module in conjuction with an input window.
+ If a window is not specified, a Hamming window of the specified
+ size is used. """
+ my_namespace = 'scipy|signals|fourier'
+
+ def get_signal(self, sigs, window, offset, size):
+ win = scipy.zeros(sigs.shape[0])
+ win[offset:offset+size] = window
+ part = sigs * win
+ return part
+
+ def compute(self):
+ sigs = self.getInputFromPort("Signals")
+ sr = self.getInputFromPort("SamplingRate")
+
+ out_vol = None
+
+ if self.hasInputFromPort("Window"):
+ window = self.getInputFromPort("Window").get_array()
+ win_size = window.shape[0]
+ else:
+ win_size = self.getInputFromPort("Window Size")
+ window = scipy.signal.hamming(win_size)
+
+ if self.hasInputFromPort("Stride"):
+ stride = self.getInputFromPort("Stride")
+ else:
+ stride = int(win_size / 2)
+
+ sh = sigs.get_shape()
+ if len(sh) < 2:
+ shp = (1, sh[0])
+ sigs.reshape(shp)
+ (num_sigs, num_samps) = sigs.get_shape()
+
+ for i in xrange(num_sigs):
+ offset = 0
+ signal = sigs.get_array()[i]
+ # We need to do the first window here so that we
+ # can have something to call vstack on.
+ sig = self.get_signal(signal, window, offset, win_size)
+ im_array = fftpack.fft(sig)
+ offset += stride
+ while 1:
+ try:
+ sig = self.get_signal(signal, window, offset, win_size)
+ phasors = fftpack.fft(sig)
+ offset += stride
+ im_array = numpy.vstack([im_array, phasors.ravel()])
+ except:
+ break
+
+ # STFT of one signal is done. Clean up the output
+ (slices, freqs) = im_array.shape
+ ar = im_array[0:,0:sr*2]
+ ar = ar[0:,::-1]
+ if out_vol == None:
+ out_vol = ar
+ ovshape = out_vol.shape
+ out_vol.shape = 1, ovshape[0], ovshape[1]
+ else:
+ arshape = ar.shape
+ ar.shape = 1, arshape[0], arshape[1]
+ out_vol = numpy.vstack([out_vol, ar])
+
+ # All signals have been processed and are in the volume.
+ out = NDArray()
+ out.set_array(out_vol)
+ self.setResult("FFT Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Signals", (NDArray, 'Signal Array'))
+ reg.add_input_port(cls, "SamplingRate", (basic.Integer, 'Sampling Rate'))
+ reg.add_input_port(cls, "Window", (NDArray, 'Windowing Function'))
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_input_port(cls, "Stride", (basic.Integer, 'Stride'))
+ reg.add_output_port(cls, "FFT Output", (NDArray, 'FFT Output'))
+
+class SignalSmoothing(DSPModule, Module):
+ """
+ Documentation
+ """
+ def compute(self):
+ window = self.getInputFromPort("Window").get_array()
+ in_signal = self.getInputFromPort("Signal").get_array()
+
+ to_conv = window/window.sum() # Make sure the window is normalized
+ if in_signal.ndim > 1:
+ out_ar = numpy.zeros(in_signal.shape)
+ else:
+ out_ar = numpy.zeros(1,in_signal.shape[0])
+ in_signal.shape = (1, in_signal.shape[0])
+
+ for row in xrange(in_signal.shape[0]):
+ out_ar[row] = numpy.convolve(to_conv, in_signal[row], mode='same')
+
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Signal", (NDArray, "Input Signals"))
+ reg.add_input_port(cls, "Window", (NDArray, "Smoothing Filter"))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Smoothed Signals'))
+
+# class SingleTrialPhaseLocking(DSPModule, Module):
+# """
+# Documentation
+# """
+# def get_time_indexes(self, t0, time_window):
+# if time_window % 2:
+# # odd number of samples: t0 +/- (window-1)/2
+# tw = (time_window - 1) / 2
+# else:
+# tw = time_window / 2
+# return (t0 - tw, t0 + tw)
+
+# def calc_pli(self, f_n_ar, f_m_ar):
+# phasors = numpy.concatenate((f_n_ar, f_m_ar))
+# norm_c = numpy.sqrt(phasors.real*phasors.real + phasors.imag*phasors.imag)
+# phasors /= norm_c
+# mean_phasor = phasors.mean()
+# pli = numpy.sqrt(mean_phasor.real*mean_phasor.real + mean_phasor.imag*mean_phasor.imag)
+# return pli
+
+# def compute(self):
+# phasors = self.getInputFromPort("Phasor Array").get_array()
+# time_window = self.getInputFromPort("Time Window")
+# time_step = self.forceGetInputFromPort("Time Step")
+# if time_step == None:
+# time_step = 1
+
+# ndims = phasors.ndim
+# if ndims == 2:
+# phasors.shape = (1, phasors.shape[0], phasors.shape[1])
+# elif ndims == 1:
+# phasors.shape = (1, phasors.shape[0], 1)
+# else:
+# raise ModuleError("Cannot Process Phasor set of dimension " + str(ndims))
+
+# num_freqs = phasors[0].shape[0]
+# num_times = phasors[0].shape[1]
+# num_times /= time_step
+# out_ar = numpy.zeros((phasors.shape[0], num_freqs, num_freqs, num_times))
+# for channel in xrange(phasors.shape[0]):
+# tfr = phasors[channel,:,:].squeeze()
+# for f_m in xrange(tfr.shape[0]):
+# f_m_row = tfr[f_m,:]
+# for f_n in xrange(f_m+1, tfr.shape[0], 1):
+# f_n_row = tfr[f_n,:]
+# t0 = 0
+# tn = 0
+# (start_i, end_i) = self.get_time_indexes(t0, time_window)
+# while t0 < f_m_row.shape[0]:
+# f_m_range = f_m_row[max(0,start_i):min(end_i,f_m_row.shape[0]-1)]
+# f_n_range = f_n_row[max(0,start_i):min(end_i,f_n_row.shape[0]-1)]
+# pli = self.calc_pli(f_m_range, f_n_range)
+# out_ar[channel, f_m, f_n, tn] = pli
+# out_ar[channel, f_n, f_m, tn] = pli
+# out_ar[channel, f_m, f_m, tn] = 1.0
+# tn += 1
+# t0 += time_step
+# start_i += time_step
+# end_i += time_step
+
+# out = NDArray()
+# out.set_array(out_ar)
+# self.setResult("Output Array", out)
+
+# @classmethod
+# def register(cls, reg, basic):
+# reg.add_module(cls, namespace=cls.my_namespace)
+# reg.add_input_port(cls, "Phasor Array", (NDArray, 'Phasor Array'))
+# reg.add_input_port(cls, "Time Step", (basic.Integer, 'Stride in the Time Domain'))
+# reg.add_input_port(cls, "Time Window", (basic.Integer, 'Samples per Timeslice'))
+# reg.add_output_port(cls, "Output Array", (NDArray, 'Result set'))
+
+# class CalculatePhaseLocking(DSPModule, Module):
+# """
+# documentation
+# """
+# def Phi(self, p):
+# return scipy.arctan2(p.real, p.imag)
+
+# def compute(self):
+# phasors = self.getInputFromPort("Phasor Array").get_array()
+# if phasors.ndim != 3:
+# raise ModuleError("Cannot handle phasor array with less than 3 dimensions")
+
+# (trials, times, frequencies) = phasors.shape
+# lowestF = self.getInputFromPort("Lowest Freq")
+# # highestF = self.getInputFromPort("Highest Freq")
+
+# Phi = self.Phi(phasors)
+
+# gamma_ar = numpy.zeros((times, frequencies, frequencies))
+
+# for t in range(times):
+# n = lowestF
+# for fn_i in range(frequencies):
+# n += fn_i
+# fn = fn_i + lowestF
+# m = lowestF
+# for fm_i in range(fn_i, frequencies, 1):
+# m += fm_i
+# fm = fm_i + lowestF
+# DeltaPhi = (float((n+m)/(2*m))Phi[:,t,fm_i] - float((n+m)/(2*n))Phi[:,t,fn_i]) % (2. * scipy.pi)
+# Gamma = exp(complex(0.,DeltaPhi))
+# Gamma = Gamma.sum()
+# Gamma = numpy.sqrt(Gamma * Gamma.conjugate())
+# gamma_ar[t, fn_i, fm_i] = Gamma
+# gamma_ar[t, fm_i, fn_i] = Gamma
+# m += 1
+# n += 1
+
+# out = NDArray()
+# out.set_array(gamma_ar)
+# self.setResults("Gamma", out)
+
+# @classmethod
+# def register(cls, reg, basic):
+# reg.add_module(cls, namespace=cls.my_namespace)
+# reg.add_input_port(cls, "Phasor Array", (NDArray, 'Phasor Array'))
+# reg.add_input_port(cls, "Lowest Freq", (basic.Integer, 'Lowest Frequency Phasor'))
+# reg.add_output_port(cls, "Gamma", (NDArray, 'Phase Locking Volume'))
+
+
+# class DifferentialPhaseLocking(DSPModule, Module):
+# """
+# documentation
+# """
+# def compute(self):
+# phasors = self.getInputFromPort("Phasor Array").get_array()
+# if phasors.ndim != 2:
+# raise ModuleError("Cannot handle phasor array with more than 2 dimensions")
+
+# mag = phasors.real*phasors.real + phasors.imag*phasors.imag
+# mag = numpy.sqrt(mag)
+# normalized = phasors / mag
+
+
diff --git a/contrib/NumSciPy/EnsembleOrdering.py b/contrib/NumSciPy/EnsembleOrdering.py
new file mode 100644
index 0000000..0b46b5a
--- /dev/null
+++ b/contrib/NumSciPy/EnsembleOrdering.py
@@ -0,0 +1,297 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from Array import *
+import copy
+import scipy
+import numpy
+from scipy import fftpack
+import time
+
+class EnsembleModule(object):
+ my_namespace = 'scipy|signals|ensembles'
+
+class ComputeDistance(EnsembleModule, Module):
+ def compute(self):
+ vol = self.getInputFromPort("Signals").get_array()
+ num_im = vol.shape[0]
+
+ out_ar = numpy.zeros((num_im, num_im))
+ for i in range(num_im):
+ im_i = vol[i].squeeze().flatten()
+ for j in range(i+1, num_im, 1):
+ im_j = vol[j].squeeze().flatten()
+
+ d = (im_i - im_j)
+ d = d * d
+ d = numpy.sqrt(d.sum())
+
+ out_ar[i,j] = d
+ out_ar[j,i] = d
+
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Planes'))
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Distance Matrix'))
+
+class OrderByIndexes(EnsembleModule, Module):
+ """ Order the inputs using an array containing the
+ indexes they should appear in """
+ def compute(self):
+ vol = self.getInputFromPort("Signals")
+ inds = self.getInputFromPort("Indexes")
+
+ sh = vol.get_shape()
+ vol = vol.get_array()
+ inds = inds.get_array()
+ out_ar = [vol[inds[0]]]
+ for i in xrange(sh[0] - 1):
+ i += 1
+ try:
+ out_ar = numpy.vstack((out_ar, [vol[inds[i]]]))
+ except:
+ pass
+
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Set'))
+ reg.add_input_port(cls, "Indexes", (NDArray, 'Sorted Index Set'))
+ reg.add_output_port(cls, "Output", (NDArray, 'Sorted Signal Set'))
+
+class OrderByCorrelation(EnsembleModule, Module):
+ """ Order the inputs using the correlations between a given
+ input index and all other slices in the volume """
+ def append_slice(self, vol, sl):
+ vol = numpy.vstack((vol, [sl]))
+ return vol
+
+ def append_cor(self, cor, sl_cor):
+ cor.append(sl_cor)
+ return cor
+
+ def prepend_slice(self, vol, sl):
+ vol = numpy.vstack(([sl], vol))
+ return vol
+
+ def prepend_cor(self, cor, sl_cor):
+ cor.insert(0, sl_cor)
+ return cor
+
+ def find_max(self, a):
+ f = a.max()
+ sh = a.shape
+ b = a.flatten()
+ ind = b.argmax()
+ row = int(ind/sh[1])
+ col = ind - row * sh[1]
+ return (row, col, f)
+
+ def compute(self):
+ ts = time.time()
+ vol = self.getInputFromPort("Signals")
+ ind = self.getInputFromPort("Key Slice")
+ if self.hasInputFromPort("Normalize"):
+ self.normalize = self.getInputFromPort("Normalize")
+ else:
+ self.normalize = False
+
+ vol_ar = vol.get_array()
+ if self.normalize:
+ for i in range(vol_ar.shape[0]):
+ sl = vol_ar[i]
+ sl = sl - sl.min()
+ sl = sl / sl.max()
+ vol_ar[i] = sl
+
+ pos = self.forceGetInputFromPort("Key Position")
+
+ key_slice = vol_ar[ind]
+ (r,c) = key_slice.shape
+ key_fft = fftpack.fftn(key_slice)
+ key_sq = key_slice * key_slice
+ norm = key_sq.sum()
+ norm = numpy.sqrt(norm)
+
+ num_slices = vol.get_shape()[0]
+ num_elements = key_slice.size
+ cor = []
+ for i in xrange(num_slices):
+ cur_slice = vol_ar[i]
+ cur_sq = cur_slice * cur_slice
+ cur_norm = cur_sq.sum()
+ cur_norm = numpy.sqrt(cur_norm)
+
+ cur_fft = fftpack.fftn(cur_slice)
+ cur_fft = cur_fft.conjugate()
+
+ cur_max = cur_slice.max()
+ prod_slice = key_fft * cur_fft
+ prod_slice = prod_slice / (norm * cur_norm)
+ cor_slice = fftpack.ifftn(prod_slice)
+
+ (row,col,val) = self.find_max(cor_slice.real)
+
+ cor.append((val,i,row,col))
+
+ cor.sort(lambda x,y:cmp(y[0],x[0]))
+ vol = [key_slice]
+ key_slice_out = key_slice
+ out_cor_ar = []
+ if pos == None:
+ app = True
+ for i in range(len(cor)):
+ sl_cor = cor[i]
+ if sl_cor[1] == ind:
+ continue
+ sl = vol_ar[sl_cor[1]]
+ if app:
+ vol = self.append_slice(vol, sl)
+ out_cor_ar = self.append_cor(out_cor_ar, cor[i][0])
+ else:
+ vol = self.prepend_slice(vol, sl)
+ out_cor_ar = self.prepend_cor(out_cor_ar, cor[i][0])
+
+ app = (app != True)
+ else:
+ for i in range(len(cor)):
+ sl_cor = cor[i]
+ sl = vol_ar[sl_cor[1]]
+ vol = self.append_slice(vol, sl)
+ out_cor_ar = self.append_cor(out_cor_ar, cor[i][0])
+
+ elapsed = time.time() - ts
+# elapsed *= 1000000.
+ print "took: ", elapsed
+ out_vol = NDArray()
+
+ out_vol.set_array(vol/vol.max())
+ out_cor = NDArray()
+ out_cor_ar = numpy.array(out_cor_ar)
+ out_cor.set_array(out_cor_ar / out_cor_ar.max())
+
+ out_key = NDArray()
+ out_key.set_array(key_slice_out)
+ self.setResult("Output Key Slice", out_key)
+ self.setResult("Output Volume", out_vol)
+ self.setResult("Output Correlation", out_cor)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Volume'))
+ reg.add_input_port(cls, "Key Slice", (basic.Integer, 'Key Slice Index'))
+ reg.add_input_port(cls, "Normalize", (basic.Boolean, 'Normalize Slice Power'))
+ reg.add_input_port(cls, "Key Position", (basic.Integer, 'Key Slice Position'))
+ reg.add_output_port(cls, "Output Volume", (NDArray, 'Sorted Signal Volume'))
+ reg.add_output_port(cls, "Output Correlation", (NDArray, 'Sorted Correlation Array'))
+ reg.add_output_port(cls, "Output Key Slice", (NDArray, 'Key Slice'))
+
+class OrderByProgressiveCorrelation(EnsembleModule, Module):
+ def find_max(self, a):
+ f = a.max()
+ sh = a.shape
+ b = a.flatten()
+ ind = b.argmax()
+ row = int(ind/sh[1])
+ col = ind - row * sh[1]
+ return (row, col, f)
+
+ def correlate(self, plane, ref_im):
+ (r,c) = ref_im.shape
+ key_fft = fftpack.fftn(ref_im)
+ key_sq = ref_im * ref_im
+ norm = key_sq.sum()
+ norm = numpy.sqrt(norm)
+
+ cur_slice = plane
+ cur_sq = cur_slice * cur_slice
+ cur_norm = cur_sq.sum()
+ cur_norm = numpy.sqrt(cur_norm)
+
+ cur_fft = fftpack.fftn(cur_slice)
+ cur_fft = cur_fft.conjugate()
+
+ cur_max = cur_slice.max()
+ prod_slice = key_fft * cur_fft
+ prod_slice = prod_slice / (norm * cur_norm)
+ cor_slice = fftpack.ifftn(prod_slice)
+
+ (row,col,val) = self.find_max(cor_slice.real)
+
+ return val
+
+ def compute(self):
+ vol = self.getInputFromPort("Signals").get_array()
+ ind = self.getInputFromPort("Key Slice")
+ normalize = self.forceGetInputFromPort("Normalize")
+
+ if normalize:
+ for i in range(vol.shape[0]):
+ sl = vol[i]
+ sl = sl - sl.min()
+ sl = sl / sl.max()
+ vol[i] = sl
+
+ tmp_vol = copy.copy(vol)
+
+ key_slice = vol[ind]
+ vol_ind = numpy.arange(vol.shape[0]).tolist()
+
+ out_ar = numpy.zeros(vol.shape)
+ out_ar[0,:,:] = key_slice
+ tmp_vol[ind,:,:] = 0.0
+
+ tmp_size = 1
+ cors_out = [self.correlate(key_slice,key_slice)]
+ print "key cor = ", cors_out[0]
+ while tmp_size < tmp_vol.shape[0]:
+ ts = time.time()
+ cors = []
+ print "output size is currently: ", tmp_size,
+ for i in range(tmp_vol.shape[0]):
+ plane = tmp_vol[i]
+ if plane.min() == 0. and plane.max() == 0.:
+ continue
+
+ cor = self.correlate(plane,out_ar[tmp_size-1,:,:])
+ cors.append((cor,i))
+
+ cors.sort(lambda x,y:cmp(y[0],x[0]))
+ (max_cor,ind) = cors[0]
+ print "\tcor = ", max_cor, ind
+ cors_out.append(max_cor)
+ out_ar[tmp_size,:,:] = vol[ind]
+ tmp_vol[ind,:,:] = 0.
+ tmp_size += 1
+ elapsed = time.time() - ts
+# elapsed *= 1000000.
+ print "\tCorrelation took: ", elapsed
+
+ cor_ar = numpy.array(cors_out)
+ cor_ar /= cor_ar.max()
+ out = NDArray()
+ out.set_array(out_ar)
+ out_cor = NDArray()
+ out_cor.set_array(cor_ar)
+
+ self.setResult("Output Signals", out)
+ self.setResult("Output Correlations", out_cor)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Signals", (NDArray, 'Input Time Frequency Planes'))
+ reg.add_input_port(cls, "Key Slice", (basic.Integer, 'Key Slice'))
+ reg.add_input_port(cls, "Normalize", (basic.Boolean, 'Normalize each plane'), True)
+ reg.add_output_port(cls, "Output Signals", (NDArray, 'Output Time Frequency Planes'))
+ reg.add_output_port(cls, "Output Correlations", (NDArray, 'Output Correlations'))
diff --git a/contrib/NumSciPy/Filters.py b/contrib/NumSciPy/Filters.py
new file mode 100644
index 0000000..11b588b
--- /dev/null
+++ b/contrib/NumSciPy/Filters.py
@@ -0,0 +1,185 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from Array import *
+import scipy
+import scipy.signal
+from scipy import sparse, fftpack
+import numpy
+
+class WindowModule(object):
+ my_namespace = 'scipy|signals|windows'
+
+class HanningWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ out = NDArray()
+ out.set_array(scipy.signal.hanning(size))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class TriangularWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ out = NDArray()
+ out.set_array(scipy.signal.triang(size))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class BlackmanWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ out = NDArray()
+ out.set_array(scipy.signal.blackman(size))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class BlackmanHarrisWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ out = NDArray()
+ out.set_array(scipy.signal.blackmanharris(size))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class ParzenWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ out = NDArray()
+ out.set_array(scipy.signal.parzen(size))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class HammingWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ out = NDArray()
+ out.set_array(scipy.signal.hamming(size))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class KaiserWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ beta = self.getInputFromPort("Beta")
+ out = NDArray()
+ out.set_array(scipy.signal.kaiser(size, beta))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_input_port(cls, "Beta", (basic.Float, 'Beta'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class BartlettHannWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ out = NDArray()
+ out.set_array(scipy.signal.barthann(size))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class GaussianWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ sigma = self.getInputFromPort("Sigma")
+ out = NDArray()
+ out.set_array(scipy.signal.gaussian(size, sigma))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_input_port(cls, "Sigma", (basic.Float, 'Sigma'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class BoxcarWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ out = NDArray()
+ out.set_array(scipy.signal.boxcar(size))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class BohmanWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ out = NDArray()
+ out.set_array(scipy.signal.bohman(size))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class BartlettWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ out = NDArray()
+ out.set_array(scipy.signal.bartlett(size))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
+class NuttallBlackmanHarrisWindow(WindowModule, Module):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ out = NDArray()
+ out.set_array(scipy.signal.nuttall(size))
+ self.setResult("Window", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
+
diff --git a/contrib/NumSciPy/Imaging.py b/contrib/NumSciPy/Imaging.py
new file mode 100644
index 0000000..2297e08
--- /dev/null
+++ b/contrib/NumSciPy/Imaging.py
@@ -0,0 +1,193 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+import numpy
+import scipy
+import scipy.ndimage
+from Array import *
+from Matrix import *
+
+class ArrayImaging(object):
+ my_namespace = 'numpy|imaging'
+
+class ExtractRGBAChannel(ArrayImaging, Module):
+ """ Extract a single color channel from an array representing an
+ RGBA type image. This will return a 2D array with the single channel
+ specified as the scalar elements """
+ def compute(self):
+ im = self.getInputFromPort("Image").get_array()
+ chan = self.getInputFromPort("Channel")
+ ar = im[:,:,chan]
+ out = NDArray()
+ out.set_array(ar)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Image", (NDArray, 'Image Array'))
+ reg.add_input_port(cls, "Channel", (basic.Integer, 'Channel'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class GaussianGradientMagnitude(ArrayImaging, Module):
+ """ Calculate the Gradient Magnitude of an input NDArray using gaussian derivatives.
+ The standard-deviation of the Gaussian filter are given for each axis as a sequence
+ or as a single number, in which case the filter will be isotropic. """
+ def compute(self):
+ im = self.getInputFromPort("Image")
+ sigma = self.getInputListFromPort("Sigmas")
+ if len(sigma) <= 1:
+ sigma = sigma[0]
+ der = scipy.ndimage.gaussian_gradient_magnitude(im.get_array(), sigma)
+ out = NDArray()
+ out.set_array(der)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Image", (NDArray, 'Image Array'))
+ reg.add_input_port(cls, "Sigmas", (basic.Float, 'Standard Deviations'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class JointHistogram(ArrayImaging, Module):
+ """ Calculate the Joint Histogram of 2 inputs. The inputs can be of arbitrary dimension,
+ but must be equivalently sized. """
+ def compute(self):
+ in_x = self.getInputFromPort("Array One").get_array()
+ in_y = self.getInputFromPort("Array Two").get_array()
+ size_x = self.getInputFromPort("Bins X")
+ size_y = self.getInputFromPort("Bins Y")
+
+ take_log = True
+ if self.hasInputFromPort("Log10"):
+ take_log = self.getInputFromPort("Log10")
+
+ out_ar = numpy.zeros((size_x, size_y))
+ min_x = in_x.min()
+ max_x = in_x.max() - min_x
+ min_y = in_y.min()
+ max_y = in_y.max() - min_y
+
+ in_x = in_x.flatten()
+ in_y = in_y.flatten()
+
+ for i in xrange(in_x.size):
+ x_cor = int(((in_x[i] - min_x)/max_x) * (size_x - 1))
+ y_cor = int(((in_y[i] - min_y)/max_y) * (size_y - 1))
+
+ out_ar[x_cor,y_cor] += 1.0
+
+ if take_log:
+ out_ar = out_ar + 1.0
+ out_ar = scipy.log(out_ar)
+ out = NDArray()
+ out_ar = out_ar.transpose()
+ out_ar = out_ar[::-1]
+ out.set_array(out_ar)
+ self.setResult("Joint Histogram", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Array One", (NDArray, 'X Axis Input'))
+ reg.add_input_port(cls, "Array Two", (NDArray, 'Y Axis Input'))
+ reg.add_input_port(cls, "Log10", (basic.Boolean, 'Use Log of Histogram'), True)
+ reg.add_input_port(cls, "Bins X", (basic.Integer, 'Number of X Bins'))
+ reg.add_input_port(cls, "Bins Y", (basic.Integer, 'Number of Y Bins'))
+ reg.add_output_port(cls, "Joint Histogram", (NDArray, 'Joint Histogram'))
+
+class GaussianSmooth(ArrayImaging, Module):
+ """ Smooth the Input array with a multi-dimensional gaussian kernel.
+ The standard-deviation of the Gaussian filter are given for each axis as a sequence
+ or as a single number, in which case the filter will be isotropic. """
+ def compute(self):
+ im = self.getInputFromPort("Input Array")
+ sigma = self.getInputListFromPort("Sigmas")
+ if len(sigma) <= 1:
+ sigma = sigma[0]
+ der = scipy.ndimage.gaussian_filter(im.get_array(), sigma)
+ out = NDArray()
+ out.set_array(der)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input Array", (NDArray, 'Image Array'))
+ reg.add_input_port(cls, "Sigmas", (basic.Float, 'Standard Deviations'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class MedianFilter(ArrayImaging, Module):
+ """ Smooth the Input array with a multi-dimensional median filter. """
+ def compute(self):
+ im = self.getInputFromPort("Input Array")
+ k_size = self.getInputFromPort("Size")
+ der = scipy.ndimage.median_filter(im.get_array(), size=k_size)
+ out = NDArray()
+ out.set_array(der)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input Array", (NDArray, 'Image Array'))
+ reg.add_input_port(cls, "Size", (basic.Integer, 'Kernel Size'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
+
+class ImageDifference(ArrayImaging, Module):
+ """ Calculate the difference between two input images. """
+ def compute(self):
+ im = self.getInputFromPort("Input 1")
+ im2 = self.getInputFromPort("Input 2")
+
+ da_ar = im.get_array() - im2.get_array()
+ da_ar = numpy.abs(da_ar)
+
+ out = NDArray()
+ out.set_array(da_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input 1", (NDArray, 'Image Array'))
+ reg.add_input_port(cls, "Input 2", (NDArray, 'Image Array'))
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
+
+class ImageNormalize(ArrayImaging, Module):
+ """ Move the range of the image to [0,1] """
+ def compute(self):
+ im = self.getInputFromPort("Input")
+ im_max = im.get_array().max()
+ im_ar = im.get_array() / im_max
+
+ out = NDArray()
+ out.set_array(im_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, 'Image Array'))
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
+
+class SobelGradientMagnitude(ArrayImaging, Module):
+ """ Use n-dimensional sobel kernels to compute the gradient magnitude
+ of an image """
+ def compute(self):
+ im = self.getInputFromPort("Input").get_array()
+ mag = numpy.zeros(im.shape)
+ for i in xrange(im.ndim):
+ kern = scipy.ndimage.sobel(im, axis=i)
+ mag += kern*kern
+
+ out = NDArray()
+ out.set_array(numpy.sqrt(mag))
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, 'Image Array'))
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
diff --git a/contrib/NumSciPy/Matrix.py b/contrib/NumSciPy/Matrix.py
new file mode 100644
index 0000000..013d687
--- /dev/null
+++ b/contrib/NumSciPy/Matrix.py
@@ -0,0 +1,107 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+
+import scipy
+import numpy
+from scipy import sparse
+
+from Array import *
+
+class MatrixModule(object):
+ my_namespace = 'scipy|matrix'
+
+class MatrixOp(object):
+ my_namespace = 'scipy|matrix|operation'
+
+class Matrix(MatrixModule, Module):
+ """ Container class for the scipy.sparse.csc_matrix class """
+ def __init__(self):
+ Module.__init__(self)
+ self.matrix = None
+
+ def get_shape(self):
+ return self.matrix.shape
+
+ def get_conjugate(self):
+ return self.matrix.conjugate()
+
+ def get_column(self, colId):
+ return self.matrix.getcol(colId)
+
+ def get_row(self, rowId):
+ return self.matrix.getrow(rowId)
+
+ def set_diagonal(self, vals):
+ self.matrix.setdiag(vals)
+
+ def toarray(self):
+ return self.matrix.toarray()
+
+ def transpose(self):
+ return self.matrix.transpose()
+
+ def get_num_elements(self):
+ return self.matrix.getnnz()
+
+ def get_max_elements(self):
+ return self.matrix.nzmax
+
+ def get_reals(self):
+ return self.matrix._real()
+
+ def get_imaginaries(self):
+ return self.matrix._imag()
+
+ def get_matrix(self):
+ return self.matrix
+
+ def set_matrix(self, mat):
+ self.matrix = mat
+
+class MatrixMultiply(MatrixOp, Module):
+ """ Multiply two matrices together """
+ def compute(self):
+ a = self.getInputFromPort("Matrix1")
+ b = self.getInputFromPort("Matrix2")
+ out = Matrix()
+ out.set_matrix(a.get_matrix() * b.get_matrix())
+
+ self.setResult("Matrix Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Matrix1", (Matrix, 'Input Matrix 1'))
+ reg.add_input_port(cls, "Matrix2", (Matrix, 'Input Matrix 2'))
+ reg.add_output_port(cls, "Matrix Output", (Matrix, 'Output Matrix'))
+
+class MatrixConjugate(MatrixOp, Module):
+ """ Get the complex conjugate of the input matrix. """
+ def compute(self):
+ a = self.getInputFromPort("Matrix")
+ b = a.get_conjugate().copy()
+ out = Matrix()
+ out.set_matrix(b)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Matrix", (Matrix, 'Input Matrix'))
+ reg.add_output_port(cls, "Output", (Matrix, 'Output Matrix'))
+
+class MatrixToArray(MatrixOp, Module):
+ """ Convert a SciPy matrix to a Numpy Array """
+ def compute(self):
+ m = self.getInputFromPort("Matrix")
+ a = m.toarray()
+ out = NDArray()
+ out.set_array(a)
+ self.setResult("Output Array", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Matrix", (Matrix, 'Input Matrix'))
+ reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
diff --git a/contrib/NumSciPy/MatrixUtilities.py b/contrib/NumSciPy/MatrixUtilities.py
new file mode 100644
index 0000000..7729d9c
--- /dev/null
+++ b/contrib/NumSciPy/MatrixUtilities.py
@@ -0,0 +1,93 @@
+from core.modules.vistrails_module import Module, ModuleError
+from Matrix import *
+from Array import *
+import scipy
+from scipy import io, sparse
+
+
+class ArrayUtilityModule(object):
+ my_namespace = 'scipy|matrix|utilities|Matlab'
+
+class MatlabReader(ArrayUtilityModule, Module):
+ """ Read a Matlab .mat file into a SciPy matrix """
+ # Gather inputs here
+ def get_inputs(self):
+ if self.hasInputFromPort("Filename"):
+ self.fname = self.getInputFromPort("Filename")
+ else:
+ self.fname = self.getInputFromPort("File").name
+
+ # Set required members externally. This is just a helper function!
+ def set_member(self, name, val):
+ setattr(self, name, val)
+
+ # This is the work that the compute() method does
+ def process_compute(self):
+ m = io.loadmat(self.fname, None, 0)
+ vals = m.values()
+
+ for t in vals:
+ if type(t) == numpy.ndarray:
+ if t.dtype == 'object':
+ continue
+ mat = t
+
+ return (mat,)
+
+ # Take the returns from the processing and put them out on the outputs.
+ def set_outputs(self, results):
+ try:
+ out = Matrix()
+ out.set_matrix(sparse.csc_matrix(results[0]))
+
+ self.setResult("Matrix Output", out)
+ except:
+ pass
+
+ out_ar = NDArray()
+ out_ar.set_array(numpy.array(results[0]))
+ self.setResult("Array Output", out_ar)
+
+ # The compute method for vistrails compatibility
+ def compute(self):
+ self.get_inputs()
+ results = self.process_compute()
+ self.set_outputs(results)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+ reg.add_input_port(cls, "File", (basic.File, 'File'))
+ reg.add_output_port(cls, "Matrix Output", (Matrix, 'Matrix Output'))
+ reg.add_output_port(cls, "Array Output", (NDArray, 'Array Output'))
+
+class MatlabWriter(ArrayUtilityModule, Module):
+ """ Write a Matlab .mat file from a SciPy matrix """
+ def compute(self):
+ if self.hasInputFromPort("Filename"):
+ fname = self.getInputFromPort("Filename")
+ else:
+ fname = self.getInputFromPort("File").name
+
+ ar_list = self.getInputListFromPort("Arrays")
+ mat_list = self.getInputListFromPort("Matrices")
+ ar_dict = {}
+ for i in xrange(len(ar_list)):
+ ar_name = "array_" + str(i)
+ ar_dict[ar_name] = ar_list[i].get_array()
+
+ for i in xrange(len(mat_list)):
+ mat_name = "matrix_" + str(i)
+ ar_dict[mat_name] = mat_list[i].get_matrix()
+
+ io.savemat(fname, ar_dict)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+ reg.add_input_port(cls, "File", (basic.File, 'File'))
+ reg.add_input_port(cls, "Arrays", (NDArray, 'Arrays to Save'))
+ reg.add_input_port(cls, "Matrices", (Matrix, 'Matrices to Save'))
+
diff --git a/contrib/NumSciPy/Stockwell.py b/contrib/NumSciPy/Stockwell.py
new file mode 100644
index 0000000..336c735
--- /dev/null
+++ b/contrib/NumSciPy/Stockwell.py
@@ -0,0 +1,763 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from Matrix import *
+from Array import *
+from DSP import DSPModule
+import scipy
+import scipy.signal
+import scipy.fftpack
+import numpy
+import smt
+import st
+import time
+
+class StockwellModule(object):
+ my_namespace = 'scipy|signals|stockwell'
+# my_namespace = 'scipy|signals'
+
+class IsotropicScaleVolumes(StockwellModule, Module):
+ def compute(self):
+ vol = self.getInputFromPort("Input").get_array()
+ lof = self.getInputFromPort("Low Freq")
+ hif = self.getInputFromPort("Hi Freq")
+ max_vol = numpy.zeros(vol.shape)
+ grav_vol = numpy.zeros(vol.shape)
+
+ (slices,rows,cols) = vol.shape
+ for z in range(slices):
+ tr = time.time()
+ for y in range(rows):
+ ray = vol[z,y,:].squeeze()
+ t = st.st(ray, lof, hif)
+ for x in range(cols):
+ scales = t[:,x].squeeze()
+ scales = scales * scales.conjugate()
+
+ max_vol[x,y,z] = float(scales.argmax())
+
+ grav = 0.
+ for i in range(scales.shape[0]):
+ v = scales[i]
+ f = lof + i
+ grav += float(v) * float(f)
+
+ grav_vol[x,y,z] = grav
+
+ print "done z = ", z
+ print "took: ", (time.time() - tr) * 1000.
+
+ grav_vol = grav_vol - grav_vol.min()
+ grav_vol = grav_vol / grav_vol.max()
+ grav_vol = grav_vol * float(hif - lof)
+ grav_vol = grav_vol + lof
+ max_out = NDArray()
+ max_out.set_array(max_vol)
+ grav_out = NDArray()
+ grav_out.set_array(grav_vol)
+ self.setResult("Max Output", max_out)
+ self.setResult("Grav Output", grav_out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, "Input Signals"))
+ reg.add_input_port(cls, "Low Freq", (basic.Float, "Low Frequency"))
+ reg.add_input_port(cls, "Hi Freq", (basic.Float, "High Frequency"))
+ reg.add_output_port(cls, "Max Output", (NDArray, "Output Max TFR"))
+ reg.add_output_port(cls, "Grav Output", (NDArray, "Output Grav TFR"))
+
+
+class ScaleVolumes(StockwellModule, Module):
+ def compute(self):
+ vol = self.getInputFromPort("Input").get_array()
+ lof = self.getInputFromPort("Low Freq")
+ hif = self.getInputFromPort("Hi Freq")
+ sigma = self.forceGetInputFromPort("Sigma")
+ max_vol = numpy.zeros(vol.shape)
+ grav_vol = numpy.zeros(vol.shape)
+
+ (slices,rows,cols) = vol.shape
+ for z in range(slices):
+ t = time.time()
+ for y in range(rows):
+ for x in range(cols):
+ # grab our 3 rays
+ xray = vol[z,y,:].squeeze()
+ yray = vol[z,:,x].squeeze()
+ zray = vol[:,y,x].squeeze()
+
+ # Transform each ray
+ xt = st.st(xray,lof,hif)
+ yt = st.st(yray,lof,hif)
+ zt = st.st(zray,lof,hif)
+
+ # Grab the point at all valid scales
+ xpt = xt[:,x]
+ ypt = yt[:,y]
+ zpt = zt[:,z]
+
+ # Take the magnitude
+ xpt = xpt * xpt.conjugate()
+ ypt = ypt * ypt.conjugate()
+ zpt = zpt * zpt.conjugate()
+
+ scale_vec = xpt.real + ypt.real + zpt.real
+ if sigma:
+ scale_vec = scale_vec * scipy.signal.gaussian(scale_vec.shape[0], sigma)
+
+ scale = scale_vec.argmax()
+ max_vol[x,y,z] = scale
+
+# scale_vec =
+# scale_vec = scale_vec / scale_vec.sum()
+
+
+ grav = 0
+ for s in range(scale_vec.shape[0]):
+ v = scale_vec[s]
+ f = lof + s
+ grav += float(f) * float(v)
+
+# grav = grav / float(scale_vec.shape[0])
+
+ grav_vol[x,y,z] = grav
+
+ print "done z = ", z
+ print "took: ", (time.time() - t) * 1000.
+
+ grav_vol = grav_vol - grav_vol.min()
+ grav_vol = grav_vol / grav_vol.max()
+ grav_vol = grav_vol * float(hif - lof)
+ grav_vol = grav_vol + lof
+ max_out = NDArray()
+ max_out.set_array(max_vol)
+ grav_out = NDArray()
+ grav_out.set_array(grav_vol)
+ self.setResult("Max Output", max_out)
+ self.setResult("Grav Output", grav_out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, "Input Signals"))
+ reg.add_input_port(cls, "Low Freq", (basic.Float, "Low Frequency"))
+ reg.add_input_port(cls, "Hi Freq", (basic.Float, "High Frequency"))
+ reg.add_input_port(cls, "Sigma", (basic.Float, "Sigma"))
+ reg.add_output_port(cls, "Max Output", (NDArray, "Output Max TFR"))
+ reg.add_output_port(cls, "Grav Output", (NDArray, "Output Grav TFR"))
+
+
+class MaximalScaleVolume(StockwellModule, Module):
+ def compute(self):
+ vol = self.getInputFromPort("Input").get_array()
+ lof = self.getInputFromPort("Low Freq")
+ hif = self.getInputFromPort("Hi Freq")
+ sigma = self.forceGetInputFromPort("Sigma")
+ out_vol = numpy.zeros(vol.shape)
+
+ (slices,rows,cols) = vol.shape
+ for z in range(slices):
+ t = time.time()
+ for y in range(rows):
+ for x in range(cols):
+ # grab our 3 rays
+ xray = vol[z,y,:].squeeze()
+ yray = vol[z,:,x].squeeze()
+ zray = vol[:,y,x].squeeze()
+
+ # Transform each ray
+ xt = st.st(xray,lof,hif)
+ yt = st.st(yray,lof,hif)
+ zt = st.st(zray,lof,hif)
+
+ # Grab the point at all valid scales
+ xpt = xt[:,x]
+ ypt = yt[:,y]
+ zpt = zt[:,z]
+
+ # Take the magnitude
+ xpt = xpt * xpt.conjugate()
+ ypt = ypt * ypt.conjugate()
+ zpt = zpt * zpt.conjugate()
+
+ scale_vec = xpt.real + ypt.real + zpt.real
+ if sigma:
+ scale_vec = scale_vec * scipy.signal.gaussian(scale_vec.shape[0], sigma)
+
+ scale = scale_vec.argmax()
+ out_vol[x,y,z] = scale
+ print "done z = ", z
+ print "took: ", (time.time() - t) * 1000.
+
+ out = NDArray()
+ out.set_array(out_vol)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, "Input Signals"))
+ reg.add_input_port(cls, "Low Freq", (basic.Float, "Low Frequency"))
+ reg.add_input_port(cls, "Hi Freq", (basic.Float, "High Frequency"))
+ reg.add_input_port(cls, "Sigma", (basic.Float, "Sigma"))
+ reg.add_output_port(cls, "Output", (NDArray, "Output TFR"))
+
+
+class StockwellTransform(StockwellModule, Module):
+ def compute(self):
+ t = time.time()
+ signals = self.getInputFromPort("Signals").get_array()
+ lof = self.getInputFromPort("Low Freq")
+ hif = self.getInputFromPort("Hi Freq")
+ if len(signals.shape) == 1:
+ signals.shape = (1, signals.shape[0])
+
+ outl = []
+ for i in xrange(signals.shape[0]):
+ sig_ar = signals[i]
+ x = st.st(sig_ar, lof, hif)
+ outl.append(x)
+
+ out_ar = numpy.array(outl).squeeze()
+ print "c time = ", (time.time() - t) * 1000.
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Signals", (NDArray, "Input Signals"))
+ reg.add_input_port(cls, "Low Freq", (basic.Float, "Low Frequency"))
+ reg.add_input_port(cls, "Hi Freq", (basic.Float, "High Frequency"))
+ reg.add_output_port(cls, "Output", (NDArray, "Output TFR"))
+
+class PyStockwellTransform(StockwellModule, Module):
+
+ def get_gaussian(self, length, freq, factor=1.0):
+ g = numpy.arange(float(length))
+ g = g*g
+ g = scipy.exp(-2. * scipy.pi * scipy.pi * g / (float(freq)*float(freq)))
+ return g
+# return numpy.roll(g, length/2)#.astype(complex)
+
+ def compute(self):
+ t = time.time()
+ signal = self.getInputFromPort("Signal").get_array().squeeze()
+ print "signal.shape = ", signal.shape
+ f = scipy.fftpack.fft(signal)
+ print "got f made"
+ f = scipy.fftpack.hilbert(f)
+ print "got hilbert done"
+# f2 = numpy.concatenate((f,f))
+
+ lof = self.getInputFromPort("Low Freq")
+ hif = self.getInputFromPort("Hi Freq")
+
+ out_ar = numpy.zeros((hif-lof+1, signal.shape[0]))
+
+ start = 0
+ if lof == 0:
+ out_ar[0,:] = signal.mean()
+ start = 1
+
+ for k in range(start, hif-lof, 1):
+ g = self.get_gaussian(signal.shape[0], lof+k)
+ o = scipy.fftpack.ifft(numpy.roll(f,lof+k) * g) / float(signal.size)
+ out_ar[k,:] = o
+
+ print "time = ", (time.time() - t) * 1000.
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Signal", (NDArray, "Input Signal"))
+ reg.add_input_port(cls, "Low Freq", (basic.Integer, "Low Frequency"))
+ reg.add_input_port(cls, "Hi Freq", (basic.Integer, "High Frequency"))
+ reg.add_output_port(cls, "Output", (NDArray, "Output TFR"))
+
+class MultiTaperStockwellTransform(StockwellModule, Module):
+ def compute(self):
+ signals = self.getInputFromPort("Signals").get_array()
+ sr = self.getInputFromPort("Sample Rate")
+ lof = self.getInputFromPort("Low Freq")
+ hif = self.getInputFromPort("Hi Freq")
+
+ if len(signals.shape) == 1:
+ signals.shape = (1, signals.shape[0])
+
+ if self.hasInputFromPort("Bandwidth"):
+ self.k = smt.calcK(self.getInputFromPort("Bandwidth"),signals.shape[1], sr)
+ else:
+ self.k = self.getInputFromPort("K")
+
+ outl = []
+ for i in xrange(signals.shape[0]):
+ sig_ar = signals[i]
+ x = smt.mtst(self.k, smt.calc_tapers(self.k, signals.shape[1]), sig_ar, lof, hif)
+ outl.append(x)
+
+ out_ar = numpy.array(outl).squeeze()
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Array'))
+ reg.add_input_port(cls, "Sample Rate", (basic.Integer, 'Sample Rate'))
+ reg.add_input_port(cls, "K", (basic.Float, "K"))
+ reg.add_input_port(cls, "Bandwidth", (basic.Float, "Bandwidth"))
+ reg.add_input_port(cls, "Low Freq", (basic.Float, "Low Frequency"))
+ reg.add_input_port(cls, "Hi Freq", (basic.Float, "High Frequency"))
+ reg.add_output_port(cls, "Output", (NDArray, "Output TFR"))
+
+class FastStockwell3D(StockwellModule, Module):
+ """
+ Compute an approximation to the 3D Stockwell Transform.
+ The output is a 4D array with dimensions as follows:
+ output.shape = (voices, slices, rows, columns)
+ """
+ def compute(self):
+ in_ar = self.getInputFromPort("Input").get_array()
+ lo_f = self.getInputFromPort("Low Freq")
+ hi_f = self.getInputFromPort("High Freq")
+ num_f = hi_f - lo_f + 1
+
+ (slices, rows, cols) = in_ar.shape
+ out_ar = numpy.zeros((num_f, slices, rows, cols))
+ for s in range(slices):
+ for r in range(rows):
+ sig = in_ar[s,r,:]
+ t = st.st(sig,lo_f,hi_f)
+ t = t.conjugate() * t
+ t = t.real
+ for f in range(t.shape[0]):
+ out_ar[f,s,r,:] = t[f,:]
+
+ print "done dim 1"
+ for s in range(slices):
+ for c in range(cols):
+ sig = in_ar[s,:,c]
+ t = st.st(sig,lo_f,hi_f)
+ t = t.conjugate() * t
+ t = t.real
+ for f in range(t.shape[0]):
+ out_ar[f,s,:,c] += t[f,:]
+
+ print "done dim 2"
+ for r in range(rows):
+ for c in range(cols):
+ sig = in_ar[:,r,c]
+ t = st.st(sig,lo_f,hi_f)
+ t = t.conjugate() * t
+ t = t.real
+ for f in range(t.shape[0]):
+ out_ar[f,:,r,c] += t[f,:]
+
+ print "done dim 3"
+# out_ar = out_ar * out_ar.conjugate()
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, 'Input Volume'))
+ reg.add_input_port(cls, "Low Freq", (basic.Integer, 'Lowest Voice'))
+ reg.add_input_port(cls, "High Freq", (basic.Integer, 'Highest Voice'))
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Voice Volume'))
+
+class ScaleSpaceHistogram(StockwellModule, Module):
+ def compute(self):
+ signal = self.getInputFromPort("Input").get_array()
+ lof = self.getInputFromPort("Low Freq")
+ hif = self.getInputFromPort("High Freq")
+
+ num_pts = signal.size
+ min_s = signal.min()
+ max_s = signal.max()
+ d = max_s - min_s
+ print "Accumulating over " + str(num_pts) + " points"
+ histo = numpy.zeros((512,hif-lof+1))
+ print "Histo: ",histo.shape
+ dist = numpy.zeros(512)
+ for z in range(signal.shape[2]):
+ for y in range(signal.shape[1]):
+ for x in range(signal.shape[0]):
+ sigx = signal[z,y,:]
+ sigy = signal[z,:,x]
+ tx = st.st(sigx, lof, hif)
+ ty = st.st(sigy, lof, hif)
+ sigz = signal[:,y,z]
+ tz = st.st(sigz, lof, hif)
+ tz = tz[:,x].squeeze()
+ tz = tz * tz.conjugate()
+ tx = tx[:,z].squeeze()
+ ty = ty[:,y].squeeze()
+ tx = tx * tx.conjugate()
+ ty = ty * ty.conjugate()
+
+ ar = tx.real + ty.real + tz.real
+ ar = ar / ar.sum()
+# ar = ar.sum(axis=1)
+# print "ar: ", ar.shape
+# ar.shape = (ar.shape[0],1)
+ scalar = signal[z,y,x]
+ try:
+ bin = int((scalar - min_s) / d * 511.)
+# dist[bin] += 1
+# print bin, scalar, ar
+ sigma = self.forceGetInputFromPort("Sigma")
+ if sigma:
+ ar = scipy.signal.gaussian(ar.size, sigma) * ar
+ histo[bin,:] += ar
+ except:
+ print "Cannot assign to bin: " + str(bin) +", scalar: " +str(scalar)
+ print "location = ", x, y, z
+ raise ModuleError("Cannot assign to bin: " + str(bin) +", scalar: " +str(scalar))
+
+# print "done with y = ", y
+ print "done with z = ", z
+
+ out = NDArray()
+ out.set_array(histo)# / dist)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, 'Input Volume'))
+ reg.add_input_port(cls, "Sigma", (basic.Float, 'Sigma'))
+ reg.add_input_port(cls, "Low Freq", (basic.Integer, 'Lowest Voice'))
+ reg.add_input_port(cls, "High Freq", (basic.Integer, 'Highest Voice'))
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Voice Volume'))
+
+class PyScaleSpaceHistogram(StockwellModule, Module):
+ def get_gaussian(self, length, freq, factor=1.0):
+ g = numpy.arange(float(length))
+ g = g*g
+ g = scipy.exp(-2. * scipy.pi * scipy.pi * g / (float(freq)*float(freq)))
+ return g
+
+ def stockwell(self, ray, lof, hif):
+ ret = numpy.zeros((hif-lof,ray.shape[0]))
+# ray = scipy.fftpack.hilbert(ray)
+# ray = numpy.concatenate((ray,ray[::-1]))
+ start = 0
+ if lof == 0:
+ ret[0,:] = ray.mean()
+ start = 1
+
+ for k in range(start, hif-lof, 1):
+ g = self.get_gaussian(ray.shape[0], lof+k)
+ o = scipy.fftpack.ifft(numpy.roll(ray,lof+k) * g) / float(ray.size)
+ ret[k,:] = o
+
+ return ret
+
+ def compute(self):
+ signal = self.getInputFromPort("Input").get_array().squeeze()
+ print "signal.shape = ", signal.shape
+ lof = self.getInputFromPort("Low Freq")
+ hif = self.getInputFromPort("High Freq")
+
+ num_scalar_bins = self.getInputFromPort("Scalar Bins")
+
+ num_pts = signal.size
+ min_s = signal.min()
+ max_s = signal.max()
+ d = max_s - min_s
+ print "Accumulating over " + str(num_pts) + " points"
+ histo = numpy.zeros((num_scalar_bins,hif-lof))
+
+ f_sig = scipy.fftpack.fftn(signal)
+
+ for z in range(signal.shape[0]):
+ for y in range(signal.shape[1]):
+ for x in range(signal.shape[2]):
+ yray = f_sig[z,:,x].squeeze()
+ ty = self.stockwell(yray, lof, hif)
+ zray = f_sig[:,y,x].squeeze()
+ tz = self.stockwell(zray, lof, hif)
+ xray = f_sig[z,y,:].squeeze()
+ tx = self.stockwell(xray, lof, hif)
+
+ tx = tx[:,z].squeeze()
+ ty = ty[:,y].squeeze()
+ tz = tz[:,x].squeeze()
+
+ tx = tx * tx.conjugate()
+ ty = ty * ty.conjugate()
+ tz = tz * tz.conjugate()
+
+ ar = tx.real + ty.real + tz.real
+ ar = ar / ar.sum()
+
+
+ scalar = signal[z,y,x]
+ try:
+ bin = int((scalar - min_s) / d * float(num_scalar_bins-1.))
+# dist[bin] += 1
+# print bin, scalar, ar
+ sigma = self.forceGetInputFromPort("Sigma")
+ if sigma:
+ ar = scipy.signal.gaussian(ar.size, sigma) * ar
+ histo[bin,:] += ar
+ except:
+ print "Cannot assign to bin: " + str(bin) +", scalar: " +str(scalar)
+ print "location = ", x, y, z
+ raise ModuleError("Cannot assign to bin: " + str(bin) +", scalar: " +str(scalar))
+
+# print "done with y = ", y
+ print "done with z = ", z
+
+ out = NDArray()
+ out.set_array(histo)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, 'Input Volume'))
+ reg.add_input_port(cls, "Scalar Bins", (basic.Integer, 'Scalar Bins'))
+ reg.add_input_port(cls, "Sigma", (basic.Float, 'Sigma'))
+ reg.add_input_port(cls, "Low Freq", (basic.Integer, 'Lowest Voice'))
+ reg.add_input_port(cls, "High Freq", (basic.Integer, 'Highest Voice'))
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Voice Volume'))
+
+class PointBasedStockwell(StockwellModule, Module):
+ def compute(self):
+ signal = self.getInputFromPort("Input").get_array()
+ ptx = self.getInputFromPort("X")
+ pty = self.getInputFromPort("Y")
+ ptz = self.getInputFromPort("Z")
+
+ lof = self.getInputFromPort("Low Freq")
+ hif = self.getInputFromPort("High Freq")
+
+ sigx = signal[ptz,pty,:]
+ sigy = signal[ptz,:,ptx]
+ sigz = signal[:,pty,ptx]
+
+ tx = st.st(sigx, lof, hif)
+ ty = st.st(sigy, lof, hif)
+ tz = st.st(sigz, lof, hif)
+
+ tx = tx * tx.conjugate()
+ ty = ty * ty.conjugate()
+ tz = tz * tz.conjugate()
+
+ out_ar = tx.real + ty.real + tz.real
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, 'Input Volume'))
+ reg.add_input_port(cls, "X", (basic.Integer, 'X'))
+ reg.add_input_port(cls, "Y", (basic.Integer, 'Y'))
+ reg.add_input_port(cls, "Z", (basic.Integer, 'Z'))
+ reg.add_input_port(cls, "Low Freq", (basic.Integer, 'Lowest Voice'))
+ reg.add_input_port(cls, "High Freq", (basic.Integer, 'Highest Voice'))
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Voice Volume'))
+
+class Stockwell2D(StockwellModule, Module):
+ ''' Calculate the 3D Stockwell Transform '''
+ def g_window(self, l, w):
+ if w != 0.0:
+ sigma = l / (2 * pi * w)
+ else:
+ print 'w is zero!'
+ g = numpy.zeros(l)
+ iarr = numpy.arange(float(l))
+ ex = (iarr - l / 2) ** 2 / (2 * sigma ** 2)
+ wl = numpy.where(numpy.ravel(ex < 25))[0]
+ g = numpy.where(ex < 25., numpy.exp(-1.*ex), ex)
+# g = roll(g, -l / 2)
+ return g.astype(complex)
+
+ def get_gaussian(self, sx, sy, kx, ky, factor=1.0):
+ wrow = factor * (float(sx) / float(kx))
+ wcol = factor * (float(sy) / float(ky))
+ sig_row = 1. / (2. * scipy.pi * wrow)
+ sig_col = 1. / (2. * scipy.pi * wcol)
+ print "sigmas = ", sig_row, sig_col
+
+ grow = scipy.signal.gaussian(sx, sig_row)
+ gcol = scipy.signal.gaussian(sy, sig_col)
+
+ print "gaussians good?"
+ grow.shape = sx,1
+ gcol.shape = 1,sy
+
+ print "gaussians reshaped"
+ gwin = grow*gcol
+ print "2d formed..."
+ gwin = gwin.astype(complex)
+ print "gaussian formed"
+ return gwin
+
+ def compute(self):
+ in_ar = self.getInputFromPort("Input").get_array()
+ lof = self.getInputFromPort("Low Freq")
+ hif = self.getInputFromPort("High Freq")
+ (nx,ny) = in_ar.shape
+ nf = hif-lof
+ kx_len = nf
+ nyquist_x = nx/2 + 1
+ ky_len = nf
+ h = scipy.fftpack.fftn(in_ar)
+ h = scipy.fftpack.fftshift(h)
+ or_spe = h
+
+ print "allocating output", nf,kx_len,ky_len
+ # allocate output
+ try:
+ l = numpy.zeros((nf, nx, ny))
+ except:
+ raise ModuleError("Cannot allocate output array")
+ print "Output Allocated - ", l.shape
+
+ vf = 0
+ for ky in range(lof, hif, 1):
+ print "ky = ", ky
+ for kx in range(lof, hif, 1):
+ print "kx = ", kx
+ if kx >= nyquist_x:
+ kxwidth = nx - kx
+ else:
+ kxwidth = kx
+
+ print "kxwidth = ", kxwidth
+ gw = self.get_gaussian(nx,ny,kxwidth,ky)
+
+ b = h * gw
+ h = numpy.roll(h,-1,axis=0)
+ voice = scipy.fftpack.ifftn(scipy.fftpack.ifftshift(b))
+ print "voice shape = ", voice
+ t = voice * voice.conjugate()
+ print "t.min() = ", t.min()
+ print "t.max() = ", t.max()
+ l[vf,:,:] += t.real
+ h = or_spe
+ h = numpy.roll(h, -1, axis=1)
+ vf += 1
+
+ print l.shape
+ out = NDArray()
+ out.set_array(l)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input", (NDArray, 'Input Volume'))
+ reg.add_input_port(cls, "Low Freq", (basic.Integer, 'Lowest Voice'))
+ reg.add_input_port(cls, "High Freq", (basic.Integer, 'Highest Voice'))
+ reg.add_output_port(cls, "Output", (NDArray, 'Output Voice Volume'))
+
+class FrequencyPhaseLocking(StockwellModule, Module):
+ """
+ Compute the phase-locking index with respect to a single frequency. The algorithm
+ implemented is the realization of that outline in Sauseng et al. Cross-frequency phase
+ synchronization: A brain mechanism of memory matching and attention: NeuroImage - 2008
+
+ To summarize, the instantaneous phase of a signal at a given frequency and time is denoted
+ \Phi(f, t) = arctan(F_{Real}(x(t)), F_{Imaginary}(x(t)))
+
+ The generalized phase differences between two signal components with an m:n frequency relationship
+ is:
+
+ \frac{m+n}{2n}f_n = \frac{n+m}{2m}f_m
+
+ \Delta \Phi(f_n,f_m,t) = (\frac{n+m}{2m} \Phi(f_m, t) - \frac{m+n}{2n}f_n \Phi(f_n, t)) % 2 \pi
+
+ And the Phase Synchronization Index is defined as:
+
+ \hat{\Gamma}_\Phi(f_n,f_m,t) = \|\langle e^{j \Delta \Phi(f_n,f_m,t)} \rangle\|, j = \sqrt{-1}
+
+ """
+ def make_delta_phi(self, phase_ar):
+ (freqs,times) = phase_ar.shape
+ dphi_ar = numpy.zeros((times, freqs, freqs))
+ for t in range(times):
+ for fn in range(freqs):
+ f_n = float(fn) + float(self.lof)
+ for fm in range(fn+1,freqs,1):
+ f_m = float(fm) + float(self.lof)
+ n = 1.
+ m = f_n / f_m
+ phi_m = phase_ar[fm,t]
+ phi_n = phase_ar[fn,t]
+ dphi = (((n+m)/2.*m) * phi_m) - (((n+m)/2.*n) * phi_n)
+ dphi = dphi % (2. * numpy.pi)
+ dphi_ar[t,fn,fm] = dphi
+ dphi_ar[t,fm,fn] = dphi
+
+ # dphi_ar.shape = (sig_len, freq_range, freq_range)
+ return dphi_ar
+
+ def compute(self):
+ trial_ar = self.getInputFromPort("Single Trials").get_array()
+ print "trial_ar.shape = ", trial_ar.shape
+ self.lof = self.getInputFromPort("Low Freq")
+ self.hif = self.getInputFromPort("High Freq")
+ sensor_list = self.forceGetInputListFromPort("Sensors")
+
+ if len(trial_ar.shape) != 3:
+ raise ModuleError("Cannot process input with rank not 3")
+
+ (trials, sensors, sig_len) = trial_ar.shape
+ if sensor_list == None:
+ sensor_list = numpy.arange(sensors)
+ else:
+ sensor_list = numpy.array(sensor_list)
+
+ # Compute the TFR for a single sensor across all trials
+ freq_range = self.hif - self.lof
+ out_ar = numpy.zeros((sensor_list.shape[0], sig_len, freq_range+1, freq_range+1))
+ print "sensor list = ", sensor_list
+
+ # For each sensor to consider, extract the signal array
+ for i in range(sensor_list.shape[0]):
+ tmp_sig = trial_ar[:,sensor_list[i],:].squeeze()
+ # For each trial, extract the signal
+ for j in range(trials):
+ sig = tmp_sig[j,:].squeeze()
+ tfr = st.st(sig, self.lof, self.hif)
+
+ # Compute the phase for the Time-freq plane
+ p = numpy.arctan2(tfr.real, tfr.imag)
+
+ # the ordering of p is: (freqs,times) = p.shape
+ dphi_ar = numpy.array(0.-1.j*self.make_delta_phi(p.real))
+ dphi_ar = numpy.exp(dphi_ar)
+ out_ar[i,:,:,:] += dphi_ar
+
+ print "Trial " + str(j) + " done processing..."
+ print "out_ar done with all trials"
+ out_ar[i,:,:,:] /= float(trials)
+ out_ar[i,:,:,:] = out_ar[i,:,:,:] * out_ar[i,:,:,:].conjugate()
+ out_ar[i,:,:,:] = out_ar[i,:,:,:].real
+ print "min,max,mean = ", out_ar[i].min(), out_ar[i].max(), out_ar[i].mean()
+ out = NDArray()
+ out.set_array(out_ar)
+ self.setResult("Output", out)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Single Trials", (NDArray, "Input Single Trial Array"))
+ reg.add_input_port(cls, "Low Freq", (basic.Integer, "Low Frequency"))
+ reg.add_input_port(cls, "High Freq", (basic.Integer, "High Frequency"))
+ reg.add_input_port(cls, "Sensors", (basic.Integer, "Sensors"))
+ reg.add_output_port(cls, "Output", (NDArray, "Phase Locking Volume"))
diff --git a/contrib/NumSciPy/__init__.py b/contrib/NumSciPy/__init__.py
new file mode 100644
index 0000000..554b4b8
--- /dev/null
+++ b/contrib/NumSciPy/__init__.py
@@ -0,0 +1,276 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+import scipy
+import scipy.interpolate
+
+# Numpy package imports
+import Array
+import ArrayAccess
+import ArrayOperations
+import ArrayUtilities
+import ArrayConvert
+import ArrayIO
+import Imaging
+
+# Scipy package imports
+import Matrix
+import MatrixUtilities
+import DSP
+import Filters
+import EnsembleOrdering
+
+# NumSciPy plotting
+import ArrayPlot
+
+version = '0.4.0'
+name = 'Num-SciPy'
+identifier = 'edu.utah.sci.vistrails.numpyscipy'
+
+def initialize(*args, **keywords):
+ reg = core.modules.module_registry
+ basic = core.modules.basic_modules
+
+ clslst = []
+
+ #########################################################################################
+ # Numpy Registry
+ reg.add_module(Array.NDArray, name="Numpy Array", namespace=Array.NDArray.my_namespace)
+ reg.add_output_port(Array.NDArray, "self", (Array.NDArray, 'self'))
+ reg.add_module(Matrix.Matrix, name="Scipy Matrix", namespace=Matrix.Matrix.my_namespace)
+
+
+ #########################################################################################
+ # Array Access registry
+ accessclass = [ArrayAccess.GetShape,
+ ArrayAccess.GetReals,
+ ArrayAccess.GetImaginaries,
+ ArrayAccess.GetMax,
+ ArrayAccess.GetMean,
+ ArrayAccess.GetMin,
+ ArrayAccess.GetDiagonal,
+ ArrayAccess.GetArrayAsType,
+ ArrayAccess.GetConjugate,
+ ArrayAccess.GetFlattenedArray,
+ ArrayAccess.GetField,
+ ArrayAccess.ToScalar,
+ ArrayAccess.GetMemoryFootprint,
+ ArrayAccess.GetArrayRank,
+ ArrayAccess.GetNonZeroEntries,
+ ArrayAccess.GetArraySize,
+ ArrayAccess.GetTranspose,
+ ArrayAccess.GetRowRange,
+ ArrayAccess.GetColumnRange,
+ ArrayAccess.GetRows]
+
+ for cls in accessclass:
+ cls.register(reg, basic)
+
+
+ #########################################################################################
+ # Array Operations registry
+ opclasses = [ArrayOperations.ArrayReshape,
+ ArrayOperations.ArrayCumulativeSum,
+ ArrayOperations.ArraySort,
+ ArrayOperations.ArrayCumulativeProduct,
+ ArrayOperations.ArrayFill,
+ ArrayOperations.ArrayResize,
+ ArrayOperations.ArrayExtractRegion,
+ ArrayOperations.ArrayRavel,
+ ArrayOperations.ArrayRound,
+ ArrayOperations.ArrayGetSigma,
+ ArrayOperations.ArraySum,
+ ArrayOperations.ArrayElementMultiply,
+ ArrayOperations.ArraySetElement,
+ ArrayOperations.ArrayVariance,
+ ArrayOperations.ArrayTrace,
+ ArrayOperations.ArraySwapAxes,
+ ArrayOperations.ArraySqueeze,
+ ArrayOperations.ArrayScalarMultiply,
+ ArrayOperations.ArrayAdd,
+ ArrayOperations.ArrayScalarAdd,
+ ArrayOperations.ArrayLog10,
+ ArrayOperations.ArrayAtan2,
+ ArrayOperations.ArraySqrt,
+ ArrayOperations.ArrayThreshold,
+ ArrayOperations.ArrayWindow,
+ ArrayOperations.ArrayNormalize,
+ ArrayOperations.ArrayName]
+
+ for cls in opclasses:
+ cls.register(reg, basic)
+
+
+ #########################################################################################
+ # Array Convert registry
+ convertclasses = [ArrayConvert.ArrayDumpToFile,
+ ArrayConvert.ArrayDumpToString,
+ ArrayConvert.ArrayToFile,
+ ArrayConvert.ArrayToString,
+ ArrayConvert.ArrayToMatrix,
+ ArrayConvert.ArrayToVTKImageData]
+
+ for cls in convertclasses:
+ cls.register(reg, basic)
+
+ #########################################################################################
+ # Array IO registry
+ ioclasses = [ArrayIO.ReadRAW,
+ ArrayIO.ReadNHDR,
+ ArrayIO.WriteRAW,
+ ArrayIO.WriteNHDR,
+ ArrayIO.ReadStatisticalSummary]
+
+ try:
+ import pylab
+ ioclasses.append(ArrayIO.ReadPNG)
+ ioclasses.append(ArrayIO.WritePNG)
+ except:
+ pass
+
+ for cls in ioclasses:
+ cls.register(reg, basic)
+
+ #########################################################################################
+ # Array Imaging registry
+ ar_util = [ArrayUtilities.ArrayToVTKScalars,
+ ArrayUtilities.ArrayToTimeVaryingVTKScalars,
+ ArrayUtilities.ArrayToTimeVaryingVTKVectors,
+ ArrayUtilities.ArrayToVTKVectors,
+ ArrayUtilities.VTKDataSetToPointArray]
+
+ clslst.extend(ar_util)
+
+ for cls in ar_util:
+ cls.register(reg, basic)
+
+ #########################################################################################
+ # Array Imaging registry
+ imclasses = [Imaging.ExtractRGBAChannel,
+ Imaging.GaussianGradientMagnitude,
+ Imaging.JointHistogram,
+ Imaging.GaussianSmooth,
+ Imaging.MedianFilter,
+ Imaging.ImageDifference,
+ Imaging.ImageNormalize,
+ Imaging.SobelGradientMagnitude]
+
+ for cls in imclasses:
+ cls.register(reg, basic)
+
+ #########################################################################################
+ # Scipy Registry
+ matrixclasses = [Matrix.MatrixMultiply,
+ Matrix.MatrixConjugate,
+ Matrix.MatrixToArray]
+
+ for cls in matrixclasses:
+ cls.register(reg,basic)
+
+ #########################################################################################
+ # Scipy Matrix Utilities Registry
+ matrixutils = [MatrixUtilities.MatlabReader,
+ MatrixUtilities.MatlabWriter]
+
+ for cls in matrixutils:
+ cls.register(reg, basic)
+
+ #########################################################################################
+ # Scipy DSP Registry
+ dspclasses = [DSP.FFT,
+ DSP.FFTN,
+ DSP.SignalSmoothing,
+ DSP.ShortTimeFourierTransform,
+ DSP.SignalGenerator]
+# DSP.FrequencyPhaseLocking,
+# DSP.SingleTrialPhaseLocking
+
+ try:
+ import smt
+ import Stockwell
+ dspclasses.append(Stockwell.StockwellTransform)
+ dspclasses.append(Stockwell.MultiTaperStockwellTransform)
+ dspclasses.append(Stockwell.FastStockwell3D)
+ dspclasses.append(Stockwell.Stockwell2D)
+ dspclasses.append(Stockwell.PyStockwellTransform)
+ dspclasses.append(Stockwell.PointBasedStockwell)
+ dspclasses.append(Stockwell.ScaleSpaceHistogram)
+ dspclasses.append(Stockwell.PyScaleSpaceHistogram)
+ dspclasses.append(Stockwell.MaximalScaleVolume)
+ dspclasses.append(Stockwell.ScaleVolumes)
+ dspclasses.append(Stockwell.IsotropicScaleVolumes)
+ dspclasses.append(Stockwell.FrequencyPhaseLocking)
+ except:
+ pass
+
+ for cls in dspclasses:
+ cls.register(reg, basic)
+
+ #########################################################################################
+ # Scipy Interpolation Registry
+ interpclasses = []
+ try:
+ import ArrayInterpolate
+ interpclasses.append(ArrayInterpolate.RBFInterpolate)
+ interpclasses.append(ArrayInterpolate.BSplineInterpolate)
+ except:
+ pass
+
+ interpclasses.append(ArrayInterpolate.BSplineResample)
+ for cls in interpclasses:
+ cls.register(reg, basic)
+
+ #########################################################################################
+ # Scipy Windows Registry
+ winclasses = [Filters.HanningWindow,
+ Filters.TriangularWindow,
+ Filters.BlackmanWindow,
+ Filters.BlackmanHarrisWindow,
+ Filters.ParzenWindow,
+ Filters.HammingWindow,
+ Filters.KaiserWindow,
+ Filters.BartlettHannWindow,
+ Filters.GaussianWindow,
+ Filters.BoxcarWindow,
+ Filters.BohmanWindow,
+ Filters.BartlettWindow,
+ Filters.NuttallBlackmanHarrisWindow]
+
+ for cls in winclasses:
+ cls.register(reg, basic)
+
+ #########################################################################################
+ # Scipy Signal Ensembles Registry
+ ensembles = [EnsembleOrdering.OrderByIndexes,
+ EnsembleOrdering.OrderByCorrelation,
+ EnsembleOrdering.OrderByProgressiveCorrelation,
+ EnsembleOrdering.ComputeDistance]
+
+ for cls in ensembles:
+ cls.register(reg, basic)
+
+ #########################################################################################
+ # NumSciPy Plotting Registry
+ pl = [ArrayPlot.LinePlot,
+ ArrayPlot.ScatterPlot,
+ ArrayPlot.BarChart,
+ ArrayPlot.Histogram,
+ ArrayPlot.ArrayImage]
+
+ for cls in pl:
+ cls.register(reg, basic)
+
+ clslst.extend(pl)
+
+ #########################################################################################
+ # Register all ports.
+ for cls in clslst:
+ cls.register_ports(reg, basic)
+
+def package_dependencies():
+ import core.packagemanager
+ manager = core.packagemanager.get_package_manager()
+ if manager.has_package('edu.utah.sci.vistrails.vtk'):
+ return ['edu.utah.sci.vistrails.vtk']
+ else:
+ return []
diff --git a/contrib/NumSciPy/smt.py b/contrib/NumSciPy/smt.py
new file mode 100644
index 0000000..590f313
--- /dev/null
+++ b/contrib/NumSciPy/smt.py
@@ -0,0 +1,40 @@
+import sys
+import numpy as npy
+from sine import sine_taper
+from st import st
+from math import sqrt
+
+def calcK(bw, N, srate):
+ """Calculate K for a given bandwidth, length, and sampling rate.
+ bw = 2p * fr, where fr = srate / N (frequency resolution).
+ p specifies the half bandwidth in bins (fr units).
+ K = 2p - 1"""
+
+ K = int(bw * float(N) / srate + .5) - 1
+ if K < 1: K = 1
+ return K
+
+def calcbw(K, N, srate):
+ """Calculate the bandwidth given K."""
+
+ return float(K + 1) * srate / N
+
+# Precompute the tapers.
+
+def calc_tapers(K, N):
+ return map(lambda k, N = N: sine_taper(k, N), npy.arange(K))
+
+# Multitaper Stockwell transform.
+
+def mtst(K, tapers, x, lo, hi):
+ N = len(x)
+ K2 = float(K * K)
+ s = 0.
+ n = 0.
+ for k in range(K):
+ X = st(tapers[k] * x, lo, hi)
+ mu = 1. - k * k / K2
+ s += mu * abs(X)**2
+ n += mu
+ s *= N / n
+ return s
diff --git a/contrib/ParaView/PVBase.py b/contrib/ParaView/PVBase.py
new file mode 100644
index 0000000..315e4fc
--- /dev/null
+++ b/contrib/ParaView/PVBase.py
@@ -0,0 +1,53 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+
+from paraview import servermanager
+import paraview.simple as pv
+
+def extract_pv_instances(paramList):
+ newList = []
+ for param in paramList:
+ if hasattr(param, "pvInstance"):
+ newList.append(param.pvInstance)
+ else:
+ newList.append(param)
+ return newList
+
+class PVModule(Module):
+ def __init__(self):
+ Module.__init__(self)
+ self.pvInstance = None
+
+ def compute(self):
+ if self.pvInstance:
+ del self.pvInstance
+ pv.SetActiveSource(None)
+ if not self.pvInstance:
+ if hasattr(self, "pvFunction"):
+ self.pvInstance = self.pvFunction()
+ else:
+ self.pvInstance = getattr(pv, self.pvClass)()
+
+ # We need to set input before other properties
+ if self.inputPorts.has_key('Input'):
+ inp = extract_pv_instances(self.forceGetInputListFromPort('Input'))[0]
+ setattr(self.pvInstance, "Input", inp)
+
+ for (function, connector_list) in self.inputPorts.iteritems():
+ paramList = extract_pv_instances(self.forceGetInputListFromPort(function))
+ if function != 'Input':
+ if len(paramList) > 1:
+ setattr(self.pvInstance, function, paramList)
+ else:
+ setattr(self.pvInstance, function, paramList[0])
+
+ if hasattr(self.pvInstance, 'UpdatePipeline'):
+ self.pvInstance.UpdatePipeline()
+
+ self.setResult('Output', self)
+
+class _funcs_internals:
+ "Internal class."
+ rep_counter = 0
+
diff --git a/contrib/ParaView/__init__.py b/contrib/ParaView/__init__.py
new file mode 100644
index 0000000..06fc47d
--- /dev/null
+++ b/contrib/ParaView/__init__.py
@@ -0,0 +1,22 @@
+version = '0.0.1'
+name = 'ParaView'
+identifier = 'edu.utah.sci.eranders.ParaView'
+
+from configuration import configuration
+
+def package_dependencies():
+ import core.packagemanager
+ manager = core.packagemanager.get_package_manager()
+ if manager.has_package('edu.utah.sci.vistrails.spreadsheet'):
+ return ['edu.utah.sci.vistrails.spreadsheet']
+ else:
+ return []
+
+def package_requirements():
+ import core.requirements
+ if not core.requirements.python_module_exists('vtk'):
+ raise core.requirements.MissingRequirement('vtk')
+ if not core.requirements.python_module_exists('PyQt4'):
+ print 'PyQt4 is not available. There will be no interaction',
+ print 'between VTK and the spreadsheet.'
+ import vtk
\ No newline at end of file
diff --git a/contrib/ParaView/configuration.py b/contrib/ParaView/configuration.py
new file mode 100644
index 0000000..963f4e2
--- /dev/null
+++ b/contrib/ParaView/configuration.py
@@ -0,0 +1,7 @@
+from core.configuration import ConfigurationObject
+
+configuration = ConfigurationObject(pvserver_bin=(None, str),
+ mpiexec_bin=(None, str),
+ start_server=False,
+ num_proc=4,
+ port=11111)
\ No newline at end of file
diff --git a/contrib/ParaView/contour.vt b/contrib/ParaView/contour.vt
new file mode 100644
index 0000000..31f0811
Binary files /dev/null and b/contrib/ParaView/contour.vt differ
diff --git a/contrib/ParaView/init.py b/contrib/ParaView/init.py
new file mode 100644
index 0000000..d17d77d
--- /dev/null
+++ b/contrib/ParaView/init.py
@@ -0,0 +1,185 @@
+import paraview
+import paraview.simple
+import paraview.servermanager as sm
+import PVBase
+import core.modules
+import core.modules.module_registry
+from pvconfig import QPVConfigWindow
+from core.modules.vistrails_module import new_module, Module, ModuleError
+from core.modules.module_registry import (registry, add_module,
+ has_input_port,
+ add_input_port, add_output_port)
+from core.modules.source_configure import SourceConfigurationWidget
+from core.modules.python_source_configure import PythonEditor, PythonSourceConfigurationWidget
+from core.modules.basic_modules import PythonSource
+from configuration import configuration
+import urllib
+
+forbidden = ['AlltoN',
+ 'Balance',
+ 'CTHSurface',
+ 'SelectionSourceBase']
+
+
+class ProgrammableFilterConfigurationWidget(SourceConfigurationWidget):
+ def __init__(self, module, controller, parent=None):
+ SourceConfigurationWidget.__init__(self, module, controller,
+ PythonEditor, False, False, parent,
+ portName='Script', encode=False)
+
+class PVServerPythonSourceConfigurationWidget(SourceConfigurationWidget):
+ def __init__(self, module, controller, parent=None):
+ SourceConfigurationWidget.__init__(self, module, controller,
+ PythonEditor, True, False, parent,
+ portName='Script', encode=False)
+
+class PVServerPythonSource(PVBase.PVModule):
+
+ def compute(self):
+ if self.pvInstance:
+ del self.pvInstance
+ paraview.simple.SetActiveSource(None)
+ inputDefs = ''
+ for k in self.inputPorts:
+ if k=='Script':
+ continue
+ value = self.getInputFromPort(k)
+ if type(value)==str:
+ inputDefs += '%s = "%s"\n' % (k, value.replace('"', '\\"'))
+ elif type(value)==int:
+ inputDefs += '%s = %s\n' % (k, value)
+ prefix = """
+import paraview.servermanager as sm
+import paraview.vtk.dataset_adapter as DA
+proc = sm.vtkProcessModule.GetProcessModule()
+nPartitions = proc.GetNumberOfLocalPartitions()
+partitionId = proc.GetPartitionId()
+result = ''
+"""
+ source = self.forceGetInputFromPort('Script', '')
+ suffix = """
+if len(result)>0:
+ import vtk
+ dataImporter = vtk.vtkImageImport()
+ dataImporter.CopyImportVoidPointer(result, len(result))
+ dataImporter.SetDataScalarTypeToUnsignedChar()
+ dataImporter.SetNumberOfScalarComponents(1)
+ dataImporter.SetDataExtent(0, len(result)-1, 0, 0, 0, 0)
+ dataImporter.SetWholeExtent(0, len(result)-1, 0, 0, 0, 0)
+ dataImporter.Update()
+ self.GetOutputDataObject(0).DeepCopy(dataImporter.GetOutput())
+"""
+ self.pvInstance = paraview.simple.ProgrammableFilter()
+ self.pvInstance.OutputDataSetType = 'vtkImageData'
+ self.pvInstance.Script = inputDefs + prefix + source + suffix
+ self.pvInstance.UpdatePipeline()
+
+ self.setResult('Output', self)
+
+
+class PVClientFetch(PythonSource):
+
+ def compute(self):
+ prefix = """
+import paraview.servermanager as sm
+import paraview.vtk.dataset_adapter as DA
+proc = sm.vtkProcessModule.GetProcessModule()
+nPartitions = proc.GetNumberOfPartitions(sm.ActiveConnection.ID)
+module = self.getInputFromPort('ServerModule')
+results = []
+for i in xrange(nPartitions):
+ data = sm.Fetch(module.pvInstance, i)
+ if data==None or data.GetPointData().GetNumberOfArrays()==0:
+ continue
+ narray = DA.numpy_support.vtk_to_numpy(data.GetPointData().GetArray(0))
+ result = narray.tostring()
+ results.append(result)
+"""
+ s = urllib.unquote(str(self.forceGetInputFromPort('source', '')))
+ self.run_code(prefix + s, use_input=True, use_output=True)
+
+
+def add_paraview_module(name, proxy, module_type, ns, hide=False, pvFunction=None):
+
+ mod = new_module(module_type, name)
+ mod.pvSpace = ns.lower()
+ mod.pvClass = name
+ if pvFunction != None:
+ mod.pvFunction = pvFunction
+ if name=='ProgrammableFilter':
+ add_module(mod, name = name, namespace=ns, configureWidgetType=ProgrammableFilterConfigurationWidget)
+ else:
+ add_module(mod, name = name, namespace=ns)
+
+ for prop in proxy.ListProperties():
+ optional = False
+ if hide and prop != "Input":
+ optional = True
+ p = proxy.GetProperty(prop)
+ if isinstance(p, sm.ProxyProperty):
+ add_input_port(mod, prop, PVBase.PVModule, optional)
+ continue
+ if isinstance(p, sm.EnumerationProperty):
+ add_input_port(mod, prop, core.modules.basic_modules.String, optional)
+ continue
+ if isinstance(p, sm.VectorProperty):
+ params = []
+ typ = None
+ if p.IsA("vtkSMDoubleVectorProperty"):
+ typ = core.modules.basic_modules.Float
+ elif p.IsA("vtkSMIntVectorProperty"):
+ typ = core.modules.basic_modules.Integer
+ elif p.IsA("vtkSMStringVectorProperty"):
+ typ = core.modules.basic_modules.String
+ elif p.IsA("vtkSMIdTypeVectorProperty"):
+ typ = core.modules.basic_modules.Integer
+ nel = len(p)
+ if nel > 0:
+ for i in range(nel):
+ params.append(typ)
+ else:
+ params.append(typ)
+ add_input_port(mod, prop, params, optional)
+
+ add_output_port(mod, "Output", module_type)
+
+def initialize(*args, **keywords):
+ reg = core.modules.module_registry
+ basic = core.modules.basic_modules
+ add_module(PVBase.PVModule, namespace='base')
+ mod_dict = {}
+
+ mlist = [("Sources", sm.sources), ("Filters", sm.filters),
+ ("Animation", sm.animation), ("Writers", sm.writers)]
+ for ns, m in mlist:
+ dt = m.__dict__
+ for key in dt.keys():
+ if forbidden.__contains__(key):
+ continue
+ if key.__contains__('Base'):
+ continue
+ cl = dt[key]
+ if not isinstance(cl, str):
+ if paraview.simple._func_name_valid(key):
+ add_paraview_module(key, m.__dict__[key](no_update=True), PVBase.PVModule, ns)
+
+
+ add_paraview_module("GeometryRepresentation", sm.rendering.GeometryRepresentation(no_update=True), PVBase.PVModule, "Rendering", True, sm.rendering.GeometryRepresentation)
+ add_paraview_module("PVLookupTable", sm.rendering.PVLookupTable(no_update=True), PVBase.PVModule, "Rendering", False, sm.rendering.PVLookupTable)
+ add_paraview_module("ScalarBarWidgetRepresentation", sm.rendering.ScalarBarWidgetRepresentation(no_update=True), PVBase.PVModule, "Rendering", True, sm.rendering.ScalarBarWidgetRepresentation)
+ add_module(PVServerPythonSource, name = "PVServerPythonSource", configureWidgetType=PVServerPythonSourceConfigurationWidget)
+ add_input_port(PVServerPythonSource, "Script", (core.modules.basic_modules.String, ""), True)
+ add_output_port(PVServerPythonSource, "self", PVServerPythonSource)
+ add_module(PVClientFetch, name = "PVClientFetch", configureWidgetType=PythonSourceConfigurationWidget)
+ add_input_port(PVClientFetch, "ServerModule", (PVServerPythonSource, ""))
+ add_input_port(PVClientFetch, "source", (core.modules.basic_modules.String, ""))
+
+ import pvcell
+ pvcell.registerSelf()
+
+ global pvConfigWindow
+ pvConfigWindow = QPVConfigWindow(proc_num=configuration.num_proc,
+ port=configuration.port)
+ pvConfigWindow.show()
+ if configuration.start_server == True:
+ pvConfigWindow.togglePVServer()
\ No newline at end of file
diff --git a/contrib/ParaView/pv.vt b/contrib/ParaView/pv.vt
new file mode 100644
index 0000000..34d152b
Binary files /dev/null and b/contrib/ParaView/pv.vt differ
diff --git a/contrib/ParaView/pvcell.py b/contrib/ParaView/pvcell.py
new file mode 100644
index 0000000..3967630
--- /dev/null
+++ b/contrib/ParaView/pvcell.py
@@ -0,0 +1,83 @@
+from PyQt4 import QtCore
+from core.modules.module_registry import get_module_registry
+from packages.vtk.vtkcell import QVTKWidget
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from packages.spreadsheet.spreadsheet_cell import QCellWidget
+from PVBase import PVModule
+import paraview.simple as pvsp
+import paraview.pvfilters
+import vtk
+
+class PVCell(SpreadsheetCell):
+ def __init__(self):
+ SpreadsheetCell.__init__(self)
+ self.cellWidget = None
+
+ def compute(self):
+ """ compute() -> None
+ Dispatch the vtkRenderer to the actual rendering widget
+ """
+ proxies = self.forceGetInputListFromPort('Proxy')
+ self.cellWidget = self.displayAndWait(QParaViewWidget, (proxies,))
+
+class QParaViewWidget(QVTKWidget):
+
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ QVTKWidget.__init__(self, parent, f)
+ self.view = None
+
+ def updateContents(self, inputPorts):
+
+ if self.view==None:
+ self.view = pvsp.CreateRenderView()
+ renWin = self.view.GetRenderWindow()
+ self.SetRenderWindow(renWin)
+ iren = renWin.GetInteractor()
+ print type(iren)
+ iren.SetNonInteractiveRenderDelay(0)
+ iren.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
+
+ (representations, ) = inputPorts
+ self.view.Representations = []
+ for r in representations:
+ self.view.Representations.append(r.pvInstance)
+
+ self.view.ResetCamera()
+ self.view.StillRender()
+
+ QCellWidget.updateContents(self, inputPorts)
+
+ def saveToPNG(self, filename):
+ """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
+
+ Save the current widget contents to an image file. If
+ str==None, then it returns the vtkUnsignedCharArray containing
+ the PNG image. Otherwise, the filename is returned.
+
+ """
+ image = self.view.CaptureWindow(1)
+ image.UnRegister(None)
+
+ writer = vtk.vtkPNGWriter()
+ writer.SetInput(image)
+ if filename!=None:
+ writer.SetFileName(filename)
+ else:
+ writer.WriteToMemoryOn()
+ writer.Write()
+ if filename:
+ return filename
+ else:
+ return writer.GetResult()
+
+ def deleteLater(self):
+ QCellWidget.deleteLater(self)
+
+
+
+def registerSelf():
+ registry = get_module_registry()
+ registry.add_module(PVCell)
+ registry.add_input_port(PVCell, "Location", CellLocation)
+ registry.add_input_port(PVCell, "Proxy", PVModule)
+ registry.add_output_port(PVCell, "self", PVCell)
diff --git a/contrib/ParaView/pvconfig.py b/contrib/ParaView/pvconfig.py
new file mode 100644
index 0000000..2da11b7
--- /dev/null
+++ b/contrib/ParaView/pvconfig.py
@@ -0,0 +1,89 @@
+from PyQt4 import QtCore, QtGui
+import sys
+import paraview.simple as pv
+from configuration import configuration
+
+class QPVConfigWindow(QtGui.QWidget):
+
+ def __init__(self, proc_num=4, port=11111, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.setWindowTitle('ParaView Local Server')
+ vbox = QtGui.QVBoxLayout()
+ self.setLayout(vbox)
+
+ hbox = QtGui.QHBoxLayout()
+ vbox.addLayout(hbox)
+
+ hbox.addWidget(QtGui.QLabel('# Procs'))
+ self.procSpin = QtGui.QSpinBox()
+ self.procSpin.setRange(1, 1024*1024)
+ self.procSpin.setValue(proc_num)
+ hbox.addWidget(self.procSpin)
+
+ hbox.addWidget(QtGui.QLabel('Port'))
+ self.portSpin = QtGui.QSpinBox()
+ self.portSpin.setRange(0, 64*1024)
+ self.portSpin.setValue(port)
+ hbox.addWidget(self.portSpin)
+
+ hbox.addStretch()
+
+ self.cmdOut = QtGui.QTextEdit()
+ self.cmdOut.setReadOnly(True)
+ vbox.addWidget(self.cmdOut)
+
+ self.runButton = QtGui.QPushButton('Start')
+ vbox.addWidget(self.runButton)
+
+ self.pvProcess = QtCore.QProcess()
+ self.pvProcess.setProcessChannelMode(QtCore.QProcess.MergedChannels)
+ self.connect(self.pvProcess, QtCore.SIGNAL('readyReadStandardOutput()'), self.updateLogs)
+ self.connect(self.pvProcess, QtCore.SIGNAL('error()'), self.updateError)
+ self.connect(self.pvProcess, QtCore.SIGNAL('finished(int,QProcess::ExitStatus)'), self.pvServerFinished)
+
+ self.connect(self.runButton, QtCore.SIGNAL('clicked()'), self.togglePVServer)
+
+ def buildArguments(self):
+ #defaults
+ mpiexec_bin = '/usr/bin/mpiexec'
+ pvserver_bin = '/usr/local/bin/pvserver'
+
+ if configuration.check('mpiexec_bin'):
+ mpiexec_bin = configuration.mpiexec_bin
+ if configuration.check("pvserver_bin"):
+ pvserver_bin = configuration.pvserver_bin
+
+ return (mpiexec_bin, ['-n', str(self.procSpin.value()), pvserver_bin, '--server-port=%s' % self.portSpin.value()])
+
+ def sizeHint(self):
+ return QtCore.QSize(384, 512)
+
+ def togglePVServer(self):
+ if self.pvProcess.state()==QtCore.QProcess.NotRunning:
+ self.runButton.setEnabled(False)
+ self.cmdOut.append('Starting...\n')
+ self.pvProcess.start(*self.buildArguments())
+ self.pvProcess.waitForStarted()
+ if self.pvProcess.state()==QtCore.QProcess.Running:
+ self.runButton.setText('Stop')
+ pv.Connect('localhost', self.portSpin.value())
+ self.runButton.setEnabled(True)
+ else:
+ self.pvProcess.terminate()
+ self.pvProcess.waitForFinished()
+
+ def updateLogs(self):
+ self.cmdOut.append(QtCore.QString(self.pvProcess.readAllStandardOutput()))
+
+ def updateError(self, error):
+ self.cmdOut.append('ERROR %s\n' % error)
+
+ def pvServerFinished(self, exitCode, exitStatus):
+ self.cmdOut.append('Exited\n')
+ self.runButton.setText('Start')
+
+if __name__=='__main__':
+ app = QtGui.QApplication(sys.argv)
+ window = QPVConfigWindow()
+ window.show()
+ app.exec_()
diff --git a/contrib/SCIRun/__init__.py b/contrib/SCIRun/__init__.py
new file mode 100644
index 0000000..27cd2cb
--- /dev/null
+++ b/contrib/SCIRun/__init__.py
@@ -0,0 +1,9001 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+# This file was generated using vistrail_converter.py
+
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from core.modules.basic_modules import Constant
+import sr_py
+import os
+import time
+
+
+version = "0.9.1"
+identifier = "edu.utah.sci.vistrails.scirun"
+name = "SCIRun"
+
+class Time(Constant):
+ def compute(self):
+ pass
+
+class Converters(Constant):
+ def compute(self):
+ pass
+
+class Texture(Constant):
+ def compute(self):
+ pass
+
+class Visualization(Constant):
+ def compute(self):
+ pass
+
+class MiscField(Constant):
+ def compute(self):
+ pass
+
+class DataArrayMath(Constant):
+ def compute(self):
+ pass
+
+class Math(Constant):
+ def compute(self):
+ pass
+
+class ChangeMesh(Constant):
+ def compute(self):
+ pass
+
+class ChangeFieldData(Constant):
+ def compute(self):
+ pass
+
+class Geometry(Constant):
+ def compute(self):
+ pass
+
+class NewField(Constant):
+ def compute(self):
+ pass
+
+class ColorMap(Constant):
+ def compute(self):
+ pass
+
+class Field(Constant):
+ def compute(self):
+ pass
+
+class Nrrd(Constant):
+ def compute(self):
+ pass
+
+class Matrix(Constant):
+ def compute(self):
+ pass
+
+class ColorMap2(Constant):
+ def compute(self):
+ pass
+
+class Path(Constant):
+ def compute(self):
+ pass
+
+class String(Constant):
+ def compute(self):
+ pass
+
+class Bundle(Constant):
+ def compute(self):
+ pass
+
+class DataIO(Constant):
+ def compute(self):
+ pass
+
+class WriteBundle(DataIO) :
+ def compute(self) :
+ p = sr_py.WriteBundleAlg()
+ if self.hasInputFromPort('p_filetype') :
+ p.set_p_filetype(self.getInputFromPort('p_filetype'))
+ if self.hasInputFromPort('p_confirm') :
+ p.set_p_confirm(self.getInputFromPort('p_confirm'))
+ if self.hasInputFromPort('p_confirm_once') :
+ p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(bundle, Filename)
+
+class WritePath(DataIO) :
+ def compute(self) :
+ p = sr_py.WritePathAlg()
+ if self.hasInputFromPort('p_filetype') :
+ p.set_p_filetype(self.getInputFromPort('p_filetype'))
+ if self.hasInputFromPort('p_confirm') :
+ p.set_p_confirm(self.getInputFromPort('p_confirm'))
+ if self.hasInputFromPort('p_confirm_once') :
+ p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
+ Input_Data = 0
+ if self.hasInputFromPort('Input Data') :
+ Input_Data = self.getInputFromPort('Input Data')
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Input_Data, Filename)
+
+class WriteColorMap2D(DataIO) :
+ def compute(self) :
+ p = sr_py.WriteColorMap2DAlg()
+ if self.hasInputFromPort('p_filetype') :
+ p.set_p_filetype(self.getInputFromPort('p_filetype'))
+ if self.hasInputFromPort('p_confirm') :
+ p.set_p_confirm(self.getInputFromPort('p_confirm'))
+ if self.hasInputFromPort('p_confirm_once') :
+ p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
+ if self.hasInputFromPort('p_exporttype') :
+ p.set_p_exporttype(self.getInputFromPort('p_exporttype'))
+ Input_Data = 0
+ if self.hasInputFromPort('Input Data') :
+ Input_Data = self.getInputFromPort('Input Data')
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Input_Data, Filename)
+
+class ReadHDF5File(DataIO) :
+ def compute(self) :
+ p = sr_py.ReadHDF5FileAlg()
+ if self.hasInputFromPort('p_have_HDF5') :
+ p.set_p_have_HDF5(self.getInputFromPort('p_have_HDF5'))
+ if self.hasInputFromPort('p_power_app') :
+ p.set_p_power_app(self.getInputFromPort('p_power_app'))
+ if self.hasInputFromPort('p_datasets') :
+ p.set_p_datasets(self.getInputFromPort('p_datasets'))
+ if self.hasInputFromPort('p_dumpname') :
+ p.set_p_dumpname(self.getInputFromPort('p_dumpname'))
+ if self.hasInputFromPort('p_ports') :
+ p.set_p_ports(self.getInputFromPort('p_ports'))
+ if self.hasInputFromPort('p_ndims') :
+ p.set_p_ndims(self.getInputFromPort('p_ndims'))
+ if self.hasInputFromPort('p_mergeData') :
+ p.set_p_mergeData(self.getInputFromPort('p_mergeData'))
+ if self.hasInputFromPort('p_assumeSVT') :
+ p.set_p_assumeSVT(self.getInputFromPort('p_assumeSVT'))
+ if self.hasInputFromPort('p_animate') :
+ p.set_p_animate(self.getInputFromPort('p_animate'))
+ if self.hasInputFromPort('p_animate_tab') :
+ p.set_p_animate_tab(self.getInputFromPort('p_animate_tab'))
+ if self.hasInputFromPort('p_basic_tab') :
+ p.set_p_basic_tab(self.getInputFromPort('p_basic_tab'))
+ if self.hasInputFromPort('p_extended_tab') :
+ p.set_p_extended_tab(self.getInputFromPort('p_extended_tab'))
+ if self.hasInputFromPort('p_playmode_tab') :
+ p.set_p_playmode_tab(self.getInputFromPort('p_playmode_tab'))
+ if self.hasInputFromPort('p_selectable_min') :
+ p.set_p_selectable_min(self.getInputFromPort('p_selectable_min'))
+ if self.hasInputFromPort('p_selectable_max') :
+ p.set_p_selectable_max(self.getInputFromPort('p_selectable_max'))
+ if self.hasInputFromPort('p_selectable_inc') :
+ p.set_p_selectable_inc(self.getInputFromPort('p_selectable_inc'))
+ if self.hasInputFromPort('p_range_min') :
+ p.set_p_range_min(self.getInputFromPort('p_range_min'))
+ if self.hasInputFromPort('p_range_max') :
+ p.set_p_range_max(self.getInputFromPort('p_range_max'))
+ if self.hasInputFromPort('p_playmode') :
+ p.set_p_playmode(self.getInputFromPort('p_playmode'))
+ if self.hasInputFromPort('p_current') :
+ p.set_p_current(self.getInputFromPort('p_current'))
+ if self.hasInputFromPort('p_execmode') :
+ p.set_p_execmode(self.getInputFromPort('p_execmode'))
+ if self.hasInputFromPort('p_delay') :
+ p.set_p_delay(self.getInputFromPort('p_delay'))
+ if self.hasInputFromPort('p_inc_amount') :
+ p.set_p_inc_amount(self.getInputFromPort('p_inc_amount'))
+ if self.hasInputFromPort('p_update_type') :
+ p.set_p_update_type(self.getInputFromPort('p_update_type'))
+ if self.hasInputFromPort('p_have_group') :
+ p.set_p_have_group(self.getInputFromPort('p_have_group'))
+ if self.hasInputFromPort('p_have_attributes') :
+ p.set_p_have_attributes(self.getInputFromPort('p_have_attributes'))
+ if self.hasInputFromPort('p_have_datasets') :
+ p.set_p_have_datasets(self.getInputFromPort('p_have_datasets'))
+ if self.hasInputFromPort('p_continuous') :
+ p.set_p_continuous(self.getInputFromPort('p_continuous'))
+ if self.hasInputFromPort('p_selectionString') :
+ p.set_p_selectionString(self.getInputFromPort('p_selectionString'))
+ if self.hasInputFromPort('p_regexp') :
+ p.set_p_regexp(self.getInputFromPort('p_regexp'))
+ if self.hasInputFromPort('p_allow_selection') :
+ p.set_p_allow_selection(self.getInputFromPort('p_allow_selection'))
+ if self.hasInputFromPort('p_read_error') :
+ p.set_p_read_error(self.getInputFromPort('p_read_error'))
+ if self.hasInputFromPort('p_max_dims') :
+ p.set_p_max_dims(self.getInputFromPort('p_max_dims'))
+ if self.hasInputFromPort('p_0_dim') :
+ p.set_p_0_dim(self.getInputFromPort('p_0_dim'))
+ if self.hasInputFromPort('p_0_start') :
+ p.set_p_0_start(self.getInputFromPort('p_0_start'))
+ if self.hasInputFromPort('p_0_start2') :
+ p.set_p_0_start2(self.getInputFromPort('p_0_start2'))
+ if self.hasInputFromPort('p_0_count') :
+ p.set_p_0_count(self.getInputFromPort('p_0_count'))
+ if self.hasInputFromPort('p_0_count2') :
+ p.set_p_0_count2(self.getInputFromPort('p_0_count2'))
+ if self.hasInputFromPort('p_0_stride') :
+ p.set_p_0_stride(self.getInputFromPort('p_0_stride'))
+ if self.hasInputFromPort('p_0_stride2') :
+ p.set_p_0_stride2(self.getInputFromPort('p_0_stride2'))
+ if self.hasInputFromPort('p_1_dim') :
+ p.set_p_1_dim(self.getInputFromPort('p_1_dim'))
+ if self.hasInputFromPort('p_1_start') :
+ p.set_p_1_start(self.getInputFromPort('p_1_start'))
+ if self.hasInputFromPort('p_1_start2') :
+ p.set_p_1_start2(self.getInputFromPort('p_1_start2'))
+ if self.hasInputFromPort('p_1_count') :
+ p.set_p_1_count(self.getInputFromPort('p_1_count'))
+ if self.hasInputFromPort('p_1_count2') :
+ p.set_p_1_count2(self.getInputFromPort('p_1_count2'))
+ if self.hasInputFromPort('p_1_stride') :
+ p.set_p_1_stride(self.getInputFromPort('p_1_stride'))
+ if self.hasInputFromPort('p_1_stride2') :
+ p.set_p_1_stride2(self.getInputFromPort('p_1_stride2'))
+ if self.hasInputFromPort('p_2_dim') :
+ p.set_p_2_dim(self.getInputFromPort('p_2_dim'))
+ if self.hasInputFromPort('p_2_start') :
+ p.set_p_2_start(self.getInputFromPort('p_2_start'))
+ if self.hasInputFromPort('p_2_start2') :
+ p.set_p_2_start2(self.getInputFromPort('p_2_start2'))
+ if self.hasInputFromPort('p_2_count') :
+ p.set_p_2_count(self.getInputFromPort('p_2_count'))
+ if self.hasInputFromPort('p_2_count2') :
+ p.set_p_2_count2(self.getInputFromPort('p_2_count2'))
+ if self.hasInputFromPort('p_2_stride') :
+ p.set_p_2_stride(self.getInputFromPort('p_2_stride'))
+ if self.hasInputFromPort('p_2_stride2') :
+ p.set_p_2_stride2(self.getInputFromPort('p_2_stride2'))
+ if self.hasInputFromPort('p_3_dim') :
+ p.set_p_3_dim(self.getInputFromPort('p_3_dim'))
+ if self.hasInputFromPort('p_3_start') :
+ p.set_p_3_start(self.getInputFromPort('p_3_start'))
+ if self.hasInputFromPort('p_3_start2') :
+ p.set_p_3_start2(self.getInputFromPort('p_3_start2'))
+ if self.hasInputFromPort('p_3_count') :
+ p.set_p_3_count(self.getInputFromPort('p_3_count'))
+ if self.hasInputFromPort('p_3_count2') :
+ p.set_p_3_count2(self.getInputFromPort('p_3_count2'))
+ if self.hasInputFromPort('p_3_stride') :
+ p.set_p_3_stride(self.getInputFromPort('p_3_stride'))
+ if self.hasInputFromPort('p_3_stride2') :
+ p.set_p_3_stride2(self.getInputFromPort('p_3_stride2'))
+ if self.hasInputFromPort('p_4_dim') :
+ p.set_p_4_dim(self.getInputFromPort('p_4_dim'))
+ if self.hasInputFromPort('p_4_start') :
+ p.set_p_4_start(self.getInputFromPort('p_4_start'))
+ if self.hasInputFromPort('p_4_start2') :
+ p.set_p_4_start2(self.getInputFromPort('p_4_start2'))
+ if self.hasInputFromPort('p_4_count') :
+ p.set_p_4_count(self.getInputFromPort('p_4_count'))
+ if self.hasInputFromPort('p_4_count2') :
+ p.set_p_4_count2(self.getInputFromPort('p_4_count2'))
+ if self.hasInputFromPort('p_4_stride') :
+ p.set_p_4_stride(self.getInputFromPort('p_4_stride'))
+ if self.hasInputFromPort('p_4_stride2') :
+ p.set_p_4_stride2(self.getInputFromPort('p_4_stride2'))
+ if self.hasInputFromPort('p_5_dim') :
+ p.set_p_5_dim(self.getInputFromPort('p_5_dim'))
+ if self.hasInputFromPort('p_5_start') :
+ p.set_p_5_start(self.getInputFromPort('p_5_start'))
+ if self.hasInputFromPort('p_5_start2') :
+ p.set_p_5_start2(self.getInputFromPort('p_5_start2'))
+ if self.hasInputFromPort('p_5_count') :
+ p.set_p_5_count(self.getInputFromPort('p_5_count'))
+ if self.hasInputFromPort('p_5_count2') :
+ p.set_p_5_count2(self.getInputFromPort('p_5_count2'))
+ if self.hasInputFromPort('p_5_stride') :
+ p.set_p_5_stride(self.getInputFromPort('p_5_stride'))
+ if self.hasInputFromPort('p_5_stride2') :
+ p.set_p_5_stride2(self.getInputFromPort('p_5_stride2'))
+ Full_filename = ''
+ if self.hasInputFromPort('Full filename') :
+ Full_filename = self.getInputFromPort('Full filename')
+ Current_Index = 0
+ if self.hasInputFromPort('Current Index') :
+ Current_Index = self.getInputFromPort('Current Index')
+ results = p.execute(Full_filename, Current_Index)
+ self.setResult('Output 0 Nrrd', results[0])
+ self.setResult('Output 1 Nrrd', results[1])
+ self.setResult('Output 2 Nrrd', results[2])
+ self.setResult('Output 3 Nrrd', results[3])
+ self.setResult('Output 4 Nrrd', results[4])
+ self.setResult('Output 5 Nrrd', results[5])
+ self.setResult('Output 6 Nrrd', results[6])
+ self.setResult('Output 7 Nrrd', results[7])
+ self.setResult('Selected Index', results[8])
+
+class ReadField(DataIO) :
+ def compute(self) :
+ p = sr_py.ReadFieldAlg()
+ if self.hasInputFromPort('p_from_env') :
+ p.set_p_from_env(self.getInputFromPort('p_from_env'))
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Filename)
+ self.setResult('Output Data', results[0])
+ self.setResult('Filename', results[1])
+
+class WriteColorMap(DataIO) :
+ def compute(self) :
+ p = sr_py.WriteColorMapAlg()
+ if self.hasInputFromPort('p_filetype') :
+ p.set_p_filetype(self.getInputFromPort('p_filetype'))
+ if self.hasInputFromPort('p_confirm') :
+ p.set_p_confirm(self.getInputFromPort('p_confirm'))
+ if self.hasInputFromPort('p_confirm_once') :
+ p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
+ if self.hasInputFromPort('p_exporttype') :
+ p.set_p_exporttype(self.getInputFromPort('p_exporttype'))
+ Input_Data = 0
+ if self.hasInputFromPort('Input Data') :
+ Input_Data = self.getInputFromPort('Input Data')
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Input_Data, Filename)
+
+class ReadColorMap2D(DataIO) :
+ def compute(self) :
+ p = sr_py.ReadColorMap2DAlg()
+ if self.hasInputFromPort('p_from_env') :
+ p.set_p_from_env(self.getInputFromPort('p_from_env'))
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Filename)
+ self.setResult('Output Data', results[0])
+ self.setResult('Filename', results[1])
+
+class ReadString(DataIO) :
+ def compute(self) :
+ p = sr_py.ReadStringAlg()
+ if self.hasInputFromPort('p_from_env') :
+ p.set_p_from_env(self.getInputFromPort('p_from_env'))
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Filename)
+ self.setResult('Output Data', results[0])
+ self.setResult('Filename', results[1])
+
+class ReadColorMap(DataIO) :
+ def compute(self) :
+ p = sr_py.ReadColorMapAlg()
+ if self.hasInputFromPort('p_from_env') :
+ p.set_p_from_env(self.getInputFromPort('p_from_env'))
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Filename)
+ self.setResult('Output Data', results[0])
+ self.setResult('Filename', results[1])
+
+class ReadMatrix(DataIO) :
+ def compute(self) :
+ p = sr_py.ReadMatrixAlg()
+ if self.hasInputFromPort('p_from_env') :
+ p.set_p_from_env(self.getInputFromPort('p_from_env'))
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Filename)
+ self.setResult('Output Data', results[0])
+ self.setResult('Filename', results[1])
+
+class WriteString(DataIO) :
+ def compute(self) :
+ p = sr_py.WriteStringAlg()
+ if self.hasInputFromPort('p_filetype') :
+ p.set_p_filetype(self.getInputFromPort('p_filetype'))
+ if self.hasInputFromPort('p_confirm') :
+ p.set_p_confirm(self.getInputFromPort('p_confirm'))
+ if self.hasInputFromPort('p_confirm_once') :
+ p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
+ String = ''
+ if self.hasInputFromPort('String') :
+ String = self.getInputFromPort('String')
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(String, Filename)
+
+class ReadPath(DataIO) :
+ def compute(self) :
+ p = sr_py.ReadPathAlg()
+ if self.hasInputFromPort('p_from_env') :
+ p.set_p_from_env(self.getInputFromPort('p_from_env'))
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Filename)
+ self.setResult('Output Data', results[0])
+ self.setResult('Filename', results[1])
+
+class WriteField(DataIO) :
+ def compute(self) :
+ p = sr_py.WriteFieldAlg()
+ if self.hasInputFromPort('p_filetype') :
+ p.set_p_filetype(self.getInputFromPort('p_filetype'))
+ if self.hasInputFromPort('p_confirm') :
+ p.set_p_confirm(self.getInputFromPort('p_confirm'))
+ if self.hasInputFromPort('p_confirm_once') :
+ p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
+ if self.hasInputFromPort('p_exporttype') :
+ p.set_p_exporttype(self.getInputFromPort('p_exporttype'))
+ if self.hasInputFromPort('p_increment') :
+ p.set_p_increment(self.getInputFromPort('p_increment'))
+ if self.hasInputFromPort('p_current') :
+ p.set_p_current(self.getInputFromPort('p_current'))
+ Input_Data = 0
+ if self.hasInputFromPort('Input Data') :
+ Input_Data = self.getInputFromPort('Input Data')
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Input_Data, Filename)
+
+class ReadBundle(DataIO) :
+ def compute(self) :
+ p = sr_py.ReadBundleAlg()
+ if self.hasInputFromPort('p_from_env') :
+ p.set_p_from_env(self.getInputFromPort('p_from_env'))
+ if self.hasInputFromPort('p_types') :
+ p.set_p_types(self.getInputFromPort('p_types'))
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Filename)
+ self.setResult('bundle', results[0])
+ self.setResult('Filename', results[1])
+
+class StreamMatrixFromDisk(DataIO) :
+ def compute(self) :
+ p = sr_py.StreamMatrixFromDiskAlg()
+ if self.hasInputFromPort('p_row_or_col') :
+ p.set_p_row_or_col(self.getInputFromPort('p_row_or_col'))
+ if self.hasInputFromPort('p_slider_min') :
+ p.set_p_slider_min(self.getInputFromPort('p_slider_min'))
+ if self.hasInputFromPort('p_slider_max') :
+ p.set_p_slider_max(self.getInputFromPort('p_slider_max'))
+ if self.hasInputFromPort('p_range_min') :
+ p.set_p_range_min(self.getInputFromPort('p_range_min'))
+ if self.hasInputFromPort('p_range_max') :
+ p.set_p_range_max(self.getInputFromPort('p_range_max'))
+ if self.hasInputFromPort('p_playmode') :
+ p.set_p_playmode(self.getInputFromPort('p_playmode'))
+ if self.hasInputFromPort('p_current') :
+ p.set_p_current(self.getInputFromPort('p_current'))
+ if self.hasInputFromPort('p_execmode') :
+ p.set_p_execmode(self.getInputFromPort('p_execmode'))
+ if self.hasInputFromPort('p_delay') :
+ p.set_p_delay(self.getInputFromPort('p_delay'))
+ if self.hasInputFromPort('p_inc_amount') :
+ p.set_p_inc_amount(self.getInputFromPort('p_inc_amount'))
+ if self.hasInputFromPort('p_send_amount') :
+ p.set_p_send_amount(self.getInputFromPort('p_send_amount'))
+ Indices = 0
+ if self.hasInputFromPort('Indices') :
+ Indices = self.getInputFromPort('Indices')
+ Weights = 0
+ if self.hasInputFromPort('Weights') :
+ Weights = self.getInputFromPort('Weights')
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Indices, Weights, Filename)
+ self.setResult('DataVector', results[0])
+ self.setResult('Index', results[1])
+ self.setResult('Scaled Index', results[2])
+ self.setResult('Filename', results[3])
+
+class WriteMatrix(DataIO) :
+ def compute(self) :
+ p = sr_py.WriteMatrixAlg()
+ if self.hasInputFromPort('p_filetype') :
+ p.set_p_filetype(self.getInputFromPort('p_filetype'))
+ if self.hasInputFromPort('p_confirm') :
+ p.set_p_confirm(self.getInputFromPort('p_confirm'))
+ if self.hasInputFromPort('p_confirm_once') :
+ p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
+ if self.hasInputFromPort('p_exporttype') :
+ p.set_p_exporttype(self.getInputFromPort('p_exporttype'))
+ if self.hasInputFromPort('p_split') :
+ p.set_p_split(self.getInputFromPort('p_split'))
+ Input_Data = 0
+ if self.hasInputFromPort('Input Data') :
+ Input_Data = self.getInputFromPort('Input Data')
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Input_Data, Filename)
+
+class ReadNrrd(DataIO) :
+ def compute(self) :
+ p = sr_py.ReadNrrdAlg()
+ if self.hasInputFromPort('p_from_env') :
+ p.set_p_from_env(self.getInputFromPort('p_from_env'))
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Filename)
+ self.setResult('Output Data', results[0])
+ self.setResult('Filename', results[1])
+
+class JoinFields(NewField) :
+ def compute(self) :
+ p = sr_py.JoinFieldsAlg()
+ if self.hasInputFromPort('p_tolerance') :
+ p.set_p_tolerance(self.getInputFromPort('p_tolerance'))
+ if self.hasInputFromPort('p_force_nodemerge') :
+ p.set_p_force_nodemerge(self.getInputFromPort('p_force_nodemerge'))
+ if self.hasInputFromPort('p_force_pointcloud') :
+ p.set_p_force_pointcloud(self.getInputFromPort('p_force_pointcloud'))
+ if self.hasInputFromPort('p_matchval') :
+ p.set_p_matchval(self.getInputFromPort('p_matchval'))
+ if self.hasInputFromPort('p_meshonly') :
+ p.set_p_meshonly(self.getInputFromPort('p_meshonly'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('Output Field', results)
+
+class RefineMeshByIsovalue(NewField) :
+ def compute(self) :
+ p = sr_py.RefineMeshByIsovalueAlg()
+ if self.hasInputFromPort('p_isoval') :
+ p.set_p_isoval(self.getInputFromPort('p_isoval'))
+ if self.hasInputFromPort('p_lte') :
+ p.set_p_lte(self.getInputFromPort('p_lte'))
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ Optional_Isovalue = 0
+ if self.hasInputFromPort('Optional Isovalue') :
+ Optional_Isovalue = self.getInputFromPort('Optional Isovalue')
+ results = p.execute(Input, Optional_Isovalue)
+ self.setResult('Refined', results[0])
+ self.setResult('Mapping', results[1])
+
+class FairMesh(NewField) :
+ def compute(self) :
+ p = sr_py.FairMeshAlg()
+ if self.hasInputFromPort('p_iterations') :
+ p.set_p_iterations(self.getInputFromPort('p_iterations'))
+ if self.hasInputFromPort('p_method') :
+ p.set_p_method(self.getInputFromPort('p_method'))
+ Input_Mesh = 0
+ if self.hasInputFromPort('Input Mesh') :
+ Input_Mesh = self.getInputFromPort('Input Mesh')
+ results = p.execute(Input_Mesh)
+ self.setResult('Faired Mesh', results)
+
+class CreateStructHex(NewField) :
+ def compute(self) :
+ p = sr_py.CreateStructHexAlg()
+ if self.hasInputFromPort('p_sizex') :
+ p.set_p_sizex(self.getInputFromPort('p_sizex'))
+ if self.hasInputFromPort('p_sizey') :
+ p.set_p_sizey(self.getInputFromPort('p_sizey'))
+ if self.hasInputFromPort('p_sizez') :
+ p.set_p_sizez(self.getInputFromPort('p_sizez'))
+ if self.hasInputFromPort('p_padpercent') :
+ p.set_p_padpercent(self.getInputFromPort('p_padpercent'))
+ if self.hasInputFromPort('p_data_at') :
+ p.set_p_data_at(self.getInputFromPort('p_data_at'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Sample Field', results)
+
+class ClipLatVolByIndicesOrWidget(NewField) :
+ def compute(self) :
+ p = sr_py.ClipLatVolByIndicesOrWidgetAlg()
+ if self.hasInputFromPort('p_use_text_bbox') :
+ p.set_p_use_text_bbox(self.getInputFromPort('p_use_text_bbox'))
+ if self.hasInputFromPort('p_text_min_x') :
+ p.set_p_text_min_x(self.getInputFromPort('p_text_min_x'))
+ if self.hasInputFromPort('p_text_min_y') :
+ p.set_p_text_min_y(self.getInputFromPort('p_text_min_y'))
+ if self.hasInputFromPort('p_text_min_z') :
+ p.set_p_text_min_z(self.getInputFromPort('p_text_min_z'))
+ if self.hasInputFromPort('p_text_max_x') :
+ p.set_p_text_max_x(self.getInputFromPort('p_text_max_x'))
+ if self.hasInputFromPort('p_text_max_y') :
+ p.set_p_text_max_y(self.getInputFromPort('p_text_max_y'))
+ if self.hasInputFromPort('p_text_max_z') :
+ p.set_p_text_max_z(self.getInputFromPort('p_text_max_z'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Selection Widget', results[0])
+ self.setResult('Output Field', results[1])
+ self.setResult('MaskVector', results[2])
+
+class GetFieldBoundary(NewField) :
+ def compute(self) :
+ p = sr_py.GetFieldBoundaryAlg()
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('BoundaryField', results[0])
+ self.setResult('Mapping', results[1])
+
+class ConvertMatricesToMesh(NewField) :
+ def compute(self) :
+ p = sr_py.ConvertMatricesToMeshAlg()
+ if self.hasInputFromPort('p_fieldname') :
+ p.set_p_fieldname(self.getInputFromPort('p_fieldname'))
+ if self.hasInputFromPort('p_meshname') :
+ p.set_p_meshname(self.getInputFromPort('p_meshname'))
+ if self.hasInputFromPort('p_fieldbasetype') :
+ p.set_p_fieldbasetype(self.getInputFromPort('p_fieldbasetype'))
+ if self.hasInputFromPort('p_datatype') :
+ p.set_p_datatype(self.getInputFromPort('p_datatype'))
+ Mesh_Elements = 0
+ if self.hasInputFromPort('Mesh Elements') :
+ Mesh_Elements = self.getInputFromPort('Mesh Elements')
+ Mesh_Positions = 0
+ if self.hasInputFromPort('Mesh Positions') :
+ Mesh_Positions = self.getInputFromPort('Mesh Positions')
+ Mesh_Normals = 0
+ if self.hasInputFromPort('Mesh Normals') :
+ Mesh_Normals = self.getInputFromPort('Mesh Normals')
+ results = p.execute(Mesh_Elements, Mesh_Positions, Mesh_Normals)
+ self.setResult('Output Field', results)
+
+class ClipFieldToFieldOrWidget(NewField) :
+ def compute(self) :
+ p = sr_py.ClipFieldToFieldOrWidgetAlg()
+ if self.hasInputFromPort('p_clip_location') :
+ p.set_p_clip_location(self.getInputFromPort('p_clip_location'))
+ if self.hasInputFromPort('p_clipmode') :
+ p.set_p_clipmode(self.getInputFromPort('p_clipmode'))
+ if self.hasInputFromPort('p_autoexecute') :
+ p.set_p_autoexecute(self.getInputFromPort('p_autoexecute'))
+ if self.hasInputFromPort('p_autoinvert') :
+ p.set_p_autoinvert(self.getInputFromPort('p_autoinvert'))
+ if self.hasInputFromPort('p_execmode') :
+ p.set_p_execmode(self.getInputFromPort('p_execmode'))
+ if self.hasInputFromPort('p_center_x') :
+ p.set_p_center_x(self.getInputFromPort('p_center_x'))
+ if self.hasInputFromPort('p_center_y') :
+ p.set_p_center_y(self.getInputFromPort('p_center_y'))
+ if self.hasInputFromPort('p_center_z') :
+ p.set_p_center_z(self.getInputFromPort('p_center_z'))
+ if self.hasInputFromPort('p_right_x') :
+ p.set_p_right_x(self.getInputFromPort('p_right_x'))
+ if self.hasInputFromPort('p_right_y') :
+ p.set_p_right_y(self.getInputFromPort('p_right_y'))
+ if self.hasInputFromPort('p_right_z') :
+ p.set_p_right_z(self.getInputFromPort('p_right_z'))
+ if self.hasInputFromPort('p_down_x') :
+ p.set_p_down_x(self.getInputFromPort('p_down_x'))
+ if self.hasInputFromPort('p_down_y') :
+ p.set_p_down_y(self.getInputFromPort('p_down_y'))
+ if self.hasInputFromPort('p_down_z') :
+ p.set_p_down_z(self.getInputFromPort('p_down_z'))
+ if self.hasInputFromPort('p_in_x') :
+ p.set_p_in_x(self.getInputFromPort('p_in_x'))
+ if self.hasInputFromPort('p_in_y') :
+ p.set_p_in_y(self.getInputFromPort('p_in_y'))
+ if self.hasInputFromPort('p_in_z') :
+ p.set_p_in_z(self.getInputFromPort('p_in_z'))
+ if self.hasInputFromPort('p_scale') :
+ p.set_p_scale(self.getInputFromPort('p_scale'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ Clip_Field = 0
+ if self.hasInputFromPort('Clip Field') :
+ Clip_Field = self.getInputFromPort('Clip Field')
+ results = p.execute(Input_Field, Clip_Field)
+ self.setResult('Selection Widget', results[0])
+ self.setResult('Output Field', results[1])
+
+class RefineMeshByIsovalue2(NewField) :
+ def compute(self) :
+ p = sr_py.RefineMeshByIsovalue2Alg()
+ if self.hasInputFromPort('p_isoval') :
+ p.set_p_isoval(self.getInputFromPort('p_isoval'))
+ if self.hasInputFromPort('p_lte') :
+ p.set_p_lte(self.getInputFromPort('p_lte'))
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ Optional_Isovalue = 0
+ if self.hasInputFromPort('Optional Isovalue') :
+ Optional_Isovalue = self.getInputFromPort('Optional Isovalue')
+ results = p.execute(Input, Optional_Isovalue)
+ self.setResult('Refined', results[0])
+ self.setResult('Mapping', results[1])
+
+class CreateLatVol(NewField) :
+ def compute(self) :
+ p = sr_py.CreateLatVolAlg()
+ if self.hasInputFromPort('p_sizex') :
+ p.set_p_sizex(self.getInputFromPort('p_sizex'))
+ if self.hasInputFromPort('p_sizey') :
+ p.set_p_sizey(self.getInputFromPort('p_sizey'))
+ if self.hasInputFromPort('p_sizez') :
+ p.set_p_sizez(self.getInputFromPort('p_sizez'))
+ if self.hasInputFromPort('p_padpercent') :
+ p.set_p_padpercent(self.getInputFromPort('p_padpercent'))
+ if self.hasInputFromPort('p_data_at') :
+ p.set_p_data_at(self.getInputFromPort('p_data_at'))
+ if self.hasInputFromPort('p_element_size') :
+ p.set_p_element_size(self.getInputFromPort('p_element_size'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ LatVol_Size = 0
+ if self.hasInputFromPort('LatVol Size') :
+ LatVol_Size = self.getInputFromPort('LatVol Size')
+ results = p.execute(Input_Field, LatVol_Size)
+ self.setResult('Output Sample Field', results)
+
+class InterfaceWithCamal(NewField) :
+ def compute(self) :
+ p = sr_py.InterfaceWithCamalAlg()
+ TriSurf = 0
+ if self.hasInputFromPort('TriSurf') :
+ TriSurf = self.getInputFromPort('TriSurf')
+ results = p.execute(TriSurf)
+ self.setResult('TetVol', results)
+
+class ClipVolumeByIsovalue(NewField) :
+ def compute(self) :
+ p = sr_py.ClipVolumeByIsovalueAlg()
+ if self.hasInputFromPort('p_isoval_min') :
+ p.set_p_isoval_min(self.getInputFromPort('p_isoval_min'))
+ if self.hasInputFromPort('p_isoval_max') :
+ p.set_p_isoval_max(self.getInputFromPort('p_isoval_max'))
+ if self.hasInputFromPort('p_isoval') :
+ p.set_p_isoval(self.getInputFromPort('p_isoval'))
+ if self.hasInputFromPort('p_lte') :
+ p.set_p_lte(self.getInputFromPort('p_lte'))
+ if self.hasInputFromPort('p_update_type') :
+ p.set_p_update_type(self.getInputFromPort('p_update_type'))
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ Optional_Isovalue = 0
+ if self.hasInputFromPort('Optional Isovalue') :
+ Optional_Isovalue = self.getInputFromPort('Optional Isovalue')
+ results = p.execute(Input, Optional_Isovalue)
+ self.setResult('Clipped', results[0])
+ self.setResult('Mapping', results[1])
+
+class RefineMesh(NewField) :
+ def compute(self) :
+ p = sr_py.RefineMeshAlg()
+ if self.hasInputFromPort('p_select') :
+ p.set_p_select(self.getInputFromPort('p_select'))
+ if self.hasInputFromPort('p_method') :
+ p.set_p_method(self.getInputFromPort('p_method'))
+ if self.hasInputFromPort('p_isoval') :
+ p.set_p_isoval(self.getInputFromPort('p_isoval'))
+ Mesh = 0
+ if self.hasInputFromPort('Mesh') :
+ Mesh = self.getInputFromPort('Mesh')
+ Isovalue = 0
+ if self.hasInputFromPort('Isovalue') :
+ Isovalue = self.getInputFromPort('Isovalue')
+ results = p.execute(Mesh, Isovalue)
+ self.setResult('RefinedMesh', results[0])
+ self.setResult('Mapping', results[1])
+
+class MergeFields(NewField) :
+ def compute(self) :
+ p = sr_py.MergeFieldsAlg()
+ Container_Mesh = 0
+ if self.hasInputFromPort('Container Mesh') :
+ Container_Mesh = self.getInputFromPort('Container Mesh')
+ Insert_Field = 0
+ if self.hasInputFromPort('Insert Field') :
+ Insert_Field = self.getInputFromPort('Insert Field')
+ results = p.execute(Container_Mesh, Insert_Field)
+ self.setResult('Combined Field', results[0])
+ self.setResult('Extended Insert Field', results[1])
+ self.setResult('Combined To Extended Mapping', results[2])
+
+class GetCentroidsFromMesh(NewField) :
+ def compute(self) :
+ p = sr_py.GetCentroidsFromMeshAlg()
+ TetVolField = 0
+ if self.hasInputFromPort('TetVolField') :
+ TetVolField = self.getInputFromPort('TetVolField')
+ results = p.execute(TetVolField)
+ self.setResult('PointCloudField', results)
+
+class ExtractIsosurfaceByFunction(NewField) :
+ def compute(self) :
+ p = sr_py.ExtractIsosurfaceByFunctionAlg()
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ if self.hasInputFromPort('p_zero_checks') :
+ p.set_p_zero_checks(self.getInputFromPort('p_zero_checks'))
+ if self.hasInputFromPort('p_slice_value_min') :
+ p.set_p_slice_value_min(self.getInputFromPort('p_slice_value_min'))
+ if self.hasInputFromPort('p_slice_value_max') :
+ p.set_p_slice_value_max(self.getInputFromPort('p_slice_value_max'))
+ if self.hasInputFromPort('p_slice_value') :
+ p.set_p_slice_value(self.getInputFromPort('p_slice_value'))
+ if self.hasInputFromPort('p_slice_value_typed') :
+ p.set_p_slice_value_typed(self.getInputFromPort('p_slice_value_typed'))
+ if self.hasInputFromPort('p_slice_value_quantity') :
+ p.set_p_slice_value_quantity(self.getInputFromPort('p_slice_value_quantity'))
+ if self.hasInputFromPort('p_quantity_range') :
+ p.set_p_quantity_range(self.getInputFromPort('p_quantity_range'))
+ if self.hasInputFromPort('p_quantity_clusive') :
+ p.set_p_quantity_clusive(self.getInputFromPort('p_quantity_clusive'))
+ if self.hasInputFromPort('p_quantity_min') :
+ p.set_p_quantity_min(self.getInputFromPort('p_quantity_min'))
+ if self.hasInputFromPort('p_quantity_max') :
+ p.set_p_quantity_max(self.getInputFromPort('p_quantity_max'))
+ if self.hasInputFromPort('p_quantity_list') :
+ p.set_p_quantity_list(self.getInputFromPort('p_quantity_list'))
+ if self.hasInputFromPort('p_slice_value_list') :
+ p.set_p_slice_value_list(self.getInputFromPort('p_slice_value_list'))
+ if self.hasInputFromPort('p_matrix_list') :
+ p.set_p_matrix_list(self.getInputFromPort('p_matrix_list'))
+ if self.hasInputFromPort('p_algorithm') :
+ p.set_p_algorithm(self.getInputFromPort('p_algorithm'))
+ if self.hasInputFromPort('p_active_slice_value_selection_tab') :
+ p.set_p_active_slice_value_selection_tab(self.getInputFromPort('p_active_slice_value_selection_tab'))
+ if self.hasInputFromPort('p_active_tab') :
+ p.set_p_active_tab(self.getInputFromPort('p_active_tab'))
+ if self.hasInputFromPort('p_update_type') :
+ p.set_p_update_type(self.getInputFromPort('p_update_type'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ Optional_Slice_values = 0
+ if self.hasInputFromPort('Optional Slice values') :
+ Optional_Slice_values = self.getInputFromPort('Optional Slice values')
+ results = p.execute(Input_Field, Optional_Slice_values)
+ self.setResult('Output Field', results)
+
+class MergeTriSurfs(NewField) :
+ def compute(self) :
+ p = sr_py.MergeTriSurfsAlg()
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Field', results)
+
+class InterfaceWithTetGen(NewField) :
+ def compute(self) :
+ p = sr_py.InterfaceWithTetGenAlg()
+ if self.hasInputFromPort('p_switch') :
+ p.set_p_switch(self.getInputFromPort('p_switch'))
+ Main = 0
+ if self.hasInputFromPort('Main') :
+ Main = self.getInputFromPort('Main')
+ Points = 0
+ if self.hasInputFromPort('Points') :
+ Points = self.getInputFromPort('Points')
+ Region_Attribs = 0
+ if self.hasInputFromPort('Region Attribs') :
+ Region_Attribs = self.getInputFromPort('Region Attribs')
+ Regions = 0
+ if self.hasInputFromPort('Regions') :
+ Regions = self.getInputFromPort('Regions')
+ results = p.execute(Main, Points, Region_Attribs, Regions)
+ self.setResult('TetVol', results)
+
+class CreateImage(NewField) :
+ def compute(self) :
+ p = sr_py.CreateImageAlg()
+ if self.hasInputFromPort('p_sizex') :
+ p.set_p_sizex(self.getInputFromPort('p_sizex'))
+ if self.hasInputFromPort('p_sizey') :
+ p.set_p_sizey(self.getInputFromPort('p_sizey'))
+ if self.hasInputFromPort('p_sizez') :
+ p.set_p_sizez(self.getInputFromPort('p_sizez'))
+ if self.hasInputFromPort('p_z_value') :
+ p.set_p_z_value(self.getInputFromPort('p_z_value'))
+ if self.hasInputFromPort('p_auto_size') :
+ p.set_p_auto_size(self.getInputFromPort('p_auto_size'))
+ if self.hasInputFromPort('p_axis') :
+ p.set_p_axis(self.getInputFromPort('p_axis'))
+ if self.hasInputFromPort('p_padpercent') :
+ p.set_p_padpercent(self.getInputFromPort('p_padpercent'))
+ if self.hasInputFromPort('p_pos') :
+ p.set_p_pos(self.getInputFromPort('p_pos'))
+ if self.hasInputFromPort('p_data_at') :
+ p.set_p_data_at(self.getInputFromPort('p_data_at'))
+ if self.hasInputFromPort('p_update_type') :
+ p.set_p_update_type(self.getInputFromPort('p_update_type'))
+ if self.hasInputFromPort('p_corigin_x') :
+ p.set_p_corigin_x(self.getInputFromPort('p_corigin_x'))
+ if self.hasInputFromPort('p_corigin_y') :
+ p.set_p_corigin_y(self.getInputFromPort('p_corigin_y'))
+ if self.hasInputFromPort('p_corigin_z') :
+ p.set_p_corigin_z(self.getInputFromPort('p_corigin_z'))
+ if self.hasInputFromPort('p_cnormal_x') :
+ p.set_p_cnormal_x(self.getInputFromPort('p_cnormal_x'))
+ if self.hasInputFromPort('p_cnormal_y') :
+ p.set_p_cnormal_y(self.getInputFromPort('p_cnormal_y'))
+ if self.hasInputFromPort('p_cnormal_z') :
+ p.set_p_cnormal_z(self.getInputFromPort('p_cnormal_z'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Sample Field', results)
+
+class InsertHexVolSheetAlongSurface(NewField) :
+ def compute(self) :
+ p = sr_py.InsertHexVolSheetAlongSurfaceAlg()
+ if self.hasInputFromPort('p_side') :
+ p.set_p_side(self.getInputFromPort('p_side'))
+ if self.hasInputFromPort('p_addlayer') :
+ p.set_p_addlayer(self.getInputFromPort('p_addlayer'))
+ HexField = 0
+ if self.hasInputFromPort('HexField') :
+ HexField = self.getInputFromPort('HexField')
+ TriField = 0
+ if self.hasInputFromPort('TriField') :
+ TriField = self.getInputFromPort('TriField')
+ results = p.execute(HexField, TriField)
+ self.setResult('Side1Field', results[0])
+ self.setResult('Side2Field', results[1])
+
+class GenerateSinglePointProbeFromField(NewField) :
+ def compute(self) :
+ p = sr_py.GenerateSinglePointProbeFromFieldAlg()
+ if self.hasInputFromPort('p_main_frame') :
+ p.set_p_main_frame(self.getInputFromPort('p_main_frame'))
+ if self.hasInputFromPort('p_locx') :
+ p.set_p_locx(self.getInputFromPort('p_locx'))
+ if self.hasInputFromPort('p_locy') :
+ p.set_p_locy(self.getInputFromPort('p_locy'))
+ if self.hasInputFromPort('p_locz') :
+ p.set_p_locz(self.getInputFromPort('p_locz'))
+ if self.hasInputFromPort('p_value') :
+ p.set_p_value(self.getInputFromPort('p_value'))
+ if self.hasInputFromPort('p_node') :
+ p.set_p_node(self.getInputFromPort('p_node'))
+ if self.hasInputFromPort('p_edge') :
+ p.set_p_edge(self.getInputFromPort('p_edge'))
+ if self.hasInputFromPort('p_face') :
+ p.set_p_face(self.getInputFromPort('p_face'))
+ if self.hasInputFromPort('p_cell') :
+ p.set_p_cell(self.getInputFromPort('p_cell'))
+ if self.hasInputFromPort('p_show_value') :
+ p.set_p_show_value(self.getInputFromPort('p_show_value'))
+ if self.hasInputFromPort('p_show_node') :
+ p.set_p_show_node(self.getInputFromPort('p_show_node'))
+ if self.hasInputFromPort('p_show_edge') :
+ p.set_p_show_edge(self.getInputFromPort('p_show_edge'))
+ if self.hasInputFromPort('p_show_face') :
+ p.set_p_show_face(self.getInputFromPort('p_show_face'))
+ if self.hasInputFromPort('p_show_cell') :
+ p.set_p_show_cell(self.getInputFromPort('p_show_cell'))
+ if self.hasInputFromPort('p_probe_scale') :
+ p.set_p_probe_scale(self.getInputFromPort('p_probe_scale'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('GenerateSinglePointProbeFromField Widget', results[0])
+ self.setResult('GenerateSinglePointProbeFromField Point', results[1])
+ self.setResult('Element Index', results[2])
+
+class InterfaceWithCubit(NewField) :
+ def compute(self) :
+ p = sr_py.InterfaceWithCubitAlg()
+ if self.hasInputFromPort('p_cubitdir') :
+ p.set_p_cubitdir(self.getInputFromPort('p_cubitdir'))
+ if self.hasInputFromPort('p_ncdump') :
+ p.set_p_ncdump(self.getInputFromPort('p_ncdump'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ PointCloudField = 0
+ if self.hasInputFromPort('PointCloudField') :
+ PointCloudField = self.getInputFromPort('PointCloudField')
+ results = p.execute(Field, PointCloudField)
+ self.setResult('Field', results)
+
+class ClipFieldByFunction(NewField) :
+ def compute(self) :
+ p = sr_py.ClipFieldByFunctionAlg()
+ if self.hasInputFromPort('p_mode') :
+ p.set_p_mode(self.getInputFromPort('p_mode'))
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ Function = ''
+ if self.hasInputFromPort('Function') :
+ Function = self.getInputFromPort('Function')
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ results = p.execute(Function, Input)
+ self.setResult('Clipped', results[0])
+ self.setResult('Mapping', results[1])
+ self.setResult('MaskVector', results[2])
+
+class GetDomainBoundary(NewField) :
+ def compute(self) :
+ p = sr_py.GetDomainBoundaryAlg()
+ if self.hasInputFromPort('p_userange') :
+ p.set_p_userange(self.getInputFromPort('p_userange'))
+ if self.hasInputFromPort('p_minrange') :
+ p.set_p_minrange(self.getInputFromPort('p_minrange'))
+ if self.hasInputFromPort('p_maxrange') :
+ p.set_p_maxrange(self.getInputFromPort('p_maxrange'))
+ if self.hasInputFromPort('p_usevalue') :
+ p.set_p_usevalue(self.getInputFromPort('p_usevalue'))
+ if self.hasInputFromPort('p_value') :
+ p.set_p_value(self.getInputFromPort('p_value'))
+ if self.hasInputFromPort('p_includeouterboundary') :
+ p.set_p_includeouterboundary(self.getInputFromPort('p_includeouterboundary'))
+ if self.hasInputFromPort('p_innerboundaryonly') :
+ p.set_p_innerboundaryonly(self.getInputFromPort('p_innerboundaryonly'))
+ if self.hasInputFromPort('p_noinnerboundary') :
+ p.set_p_noinnerboundary(self.getInputFromPort('p_noinnerboundary'))
+ if self.hasInputFromPort('p_disconnect') :
+ p.set_p_disconnect(self.getInputFromPort('p_disconnect'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ MinValueValue = 0
+ if self.hasInputFromPort('MinValueValue') :
+ MinValueValue = self.getInputFromPort('MinValueValue')
+ MaxValue = 0
+ if self.hasInputFromPort('MaxValue') :
+ MaxValue = self.getInputFromPort('MaxValue')
+ results = p.execute(Field, MinValueValue, MaxValue)
+ self.setResult('Field', results)
+
+class CollectFields(NewField) :
+ def compute(self) :
+ p = sr_py.CollectFieldsAlg()
+ if self.hasInputFromPort('p_buffersize') :
+ p.set_p_buffersize(self.getInputFromPort('p_buffersize'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ BufferSize = 0
+ if self.hasInputFromPort('BufferSize') :
+ BufferSize = self.getInputFromPort('BufferSize')
+ results = p.execute(Field, BufferSize)
+ self.setResult('Fields', results)
+
+class GeneratePointSamplesFromField(NewField) :
+ def compute(self) :
+ p = sr_py.GeneratePointSamplesFromFieldAlg()
+ if self.hasInputFromPort('p_num_seeds') :
+ p.set_p_num_seeds(self.getInputFromPort('p_num_seeds'))
+ if self.hasInputFromPort('p_probe_scale') :
+ p.set_p_probe_scale(self.getInputFromPort('p_probe_scale'))
+ if self.hasInputFromPort('p_send') :
+ p.set_p_send(self.getInputFromPort('p_send'))
+ if self.hasInputFromPort('p_widget') :
+ p.set_p_widget(self.getInputFromPort('p_widget'))
+ if self.hasInputFromPort('p_red') :
+ p.set_p_red(self.getInputFromPort('p_red'))
+ if self.hasInputFromPort('p_green') :
+ p.set_p_green(self.getInputFromPort('p_green'))
+ if self.hasInputFromPort('p_blue') :
+ p.set_p_blue(self.getInputFromPort('p_blue'))
+ if self.hasInputFromPort('p_auto_execute') :
+ p.set_p_auto_execute(self.getInputFromPort('p_auto_execute'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('GeneratePointSamplesFromField Widget', results[0])
+ self.setResult('GeneratePointSamplesFromField Point', results[1])
+
+class GeneratePointSamplesFromFieldOrWidget(NewField) :
+ def compute(self) :
+ p = sr_py.GeneratePointSamplesFromFieldOrWidgetAlg()
+ if self.hasInputFromPort('p_wtype') :
+ p.set_p_wtype(self.getInputFromPort('p_wtype'))
+ if self.hasInputFromPort('p_endpoints') :
+ p.set_p_endpoints(self.getInputFromPort('p_endpoints'))
+ if self.hasInputFromPort('p_maxseeds') :
+ p.set_p_maxseeds(self.getInputFromPort('p_maxseeds'))
+ if self.hasInputFromPort('p_numseeds') :
+ p.set_p_numseeds(self.getInputFromPort('p_numseeds'))
+ if self.hasInputFromPort('p_rngseed') :
+ p.set_p_rngseed(self.getInputFromPort('p_rngseed'))
+ if self.hasInputFromPort('p_rnginc') :
+ p.set_p_rnginc(self.getInputFromPort('p_rnginc'))
+ if self.hasInputFromPort('p_clamp') :
+ p.set_p_clamp(self.getInputFromPort('p_clamp'))
+ if self.hasInputFromPort('p_autoexecute') :
+ p.set_p_autoexecute(self.getInputFromPort('p_autoexecute'))
+ if self.hasInputFromPort('p_dist') :
+ p.set_p_dist(self.getInputFromPort('p_dist'))
+ if self.hasInputFromPort('p_whichtab') :
+ p.set_p_whichtab(self.getInputFromPort('p_whichtab'))
+ Field_to_Sample = 0
+ if self.hasInputFromPort('Field to Sample') :
+ Field_to_Sample = self.getInputFromPort('Field to Sample')
+ results = p.execute(Field_to_Sample)
+ self.setResult('Samples', results[0])
+ self.setResult('Sampling Widget', results[1])
+
+class DecimateTriSurf(NewField) :
+ def compute(self) :
+ p = sr_py.DecimateTriSurfAlg()
+ TriSurf = 0
+ if self.hasInputFromPort('TriSurf') :
+ TriSurf = self.getInputFromPort('TriSurf')
+ results = p.execute(TriSurf)
+ self.setResult('Decimated', results)
+
+class GetSliceFromStructuredFieldByIndices(NewField) :
+ def compute(self) :
+ p = sr_py.GetSliceFromStructuredFieldByIndicesAlg()
+ if self.hasInputFromPort('p_axis') :
+ p.set_p_axis(self.getInputFromPort('p_axis'))
+ if self.hasInputFromPort('p_dims') :
+ p.set_p_dims(self.getInputFromPort('p_dims'))
+ if self.hasInputFromPort('p_dim_i') :
+ p.set_p_dim_i(self.getInputFromPort('p_dim_i'))
+ if self.hasInputFromPort('p_dim_j') :
+ p.set_p_dim_j(self.getInputFromPort('p_dim_j'))
+ if self.hasInputFromPort('p_dim_k') :
+ p.set_p_dim_k(self.getInputFromPort('p_dim_k'))
+ if self.hasInputFromPort('p_index_i') :
+ p.set_p_index_i(self.getInputFromPort('p_index_i'))
+ if self.hasInputFromPort('p_index_j') :
+ p.set_p_index_j(self.getInputFromPort('p_index_j'))
+ if self.hasInputFromPort('p_index_k') :
+ p.set_p_index_k(self.getInputFromPort('p_index_k'))
+ if self.hasInputFromPort('p_update_type') :
+ p.set_p_update_type(self.getInputFromPort('p_update_type'))
+ if self.hasInputFromPort('p_continuous') :
+ p.set_p_continuous(self.getInputFromPort('p_continuous'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ Input_Matrix = 0
+ if self.hasInputFromPort('Input Matrix') :
+ Input_Matrix = self.getInputFromPort('Input Matrix')
+ results = p.execute(Input_Field, Input_Matrix)
+ self.setResult('Output Field', results[0])
+ self.setResult('Output Matrix', results[1])
+
+class RemoveHexVolSheet(NewField) :
+ def compute(self) :
+ p = sr_py.RemoveHexVolSheetAlg()
+ if self.hasInputFromPort('p_edge_list') :
+ p.set_p_edge_list(self.getInputFromPort('p_edge_list'))
+ HexField = 0
+ if self.hasInputFromPort('HexField') :
+ HexField = self.getInputFromPort('HexField')
+ results = p.execute(HexField)
+ self.setResult('NewHexField', results[0])
+ self.setResult('ExtractedHexes', results[1])
+
+class SubsampleStructuredFieldByIndices(NewField) :
+ def compute(self) :
+ p = sr_py.SubsampleStructuredFieldByIndicesAlg()
+ if self.hasInputFromPort('p_power_app') :
+ p.set_p_power_app(self.getInputFromPort('p_power_app'))
+ if self.hasInputFromPort('p_wrap') :
+ p.set_p_wrap(self.getInputFromPort('p_wrap'))
+ if self.hasInputFromPort('p_dims') :
+ p.set_p_dims(self.getInputFromPort('p_dims'))
+ if self.hasInputFromPort('p_dim_i') :
+ p.set_p_dim_i(self.getInputFromPort('p_dim_i'))
+ if self.hasInputFromPort('p_dim_j') :
+ p.set_p_dim_j(self.getInputFromPort('p_dim_j'))
+ if self.hasInputFromPort('p_dim_k') :
+ p.set_p_dim_k(self.getInputFromPort('p_dim_k'))
+ if self.hasInputFromPort('p_start_i') :
+ p.set_p_start_i(self.getInputFromPort('p_start_i'))
+ if self.hasInputFromPort('p_start_j') :
+ p.set_p_start_j(self.getInputFromPort('p_start_j'))
+ if self.hasInputFromPort('p_start_k') :
+ p.set_p_start_k(self.getInputFromPort('p_start_k'))
+ if self.hasInputFromPort('p_stop_i') :
+ p.set_p_stop_i(self.getInputFromPort('p_stop_i'))
+ if self.hasInputFromPort('p_stop_j') :
+ p.set_p_stop_j(self.getInputFromPort('p_stop_j'))
+ if self.hasInputFromPort('p_stop_k') :
+ p.set_p_stop_k(self.getInputFromPort('p_stop_k'))
+ if self.hasInputFromPort('p_stride_i') :
+ p.set_p_stride_i(self.getInputFromPort('p_stride_i'))
+ if self.hasInputFromPort('p_stride_j') :
+ p.set_p_stride_j(self.getInputFromPort('p_stride_j'))
+ if self.hasInputFromPort('p_stride_k') :
+ p.set_p_stride_k(self.getInputFromPort('p_stride_k'))
+ if self.hasInputFromPort('p_wrap_i') :
+ p.set_p_wrap_i(self.getInputFromPort('p_wrap_i'))
+ if self.hasInputFromPort('p_wrap_j') :
+ p.set_p_wrap_j(self.getInputFromPort('p_wrap_j'))
+ if self.hasInputFromPort('p_wrap_k') :
+ p.set_p_wrap_k(self.getInputFromPort('p_wrap_k'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ Input_Matrix = 0
+ if self.hasInputFromPort('Input Matrix') :
+ Input_Matrix = self.getInputFromPort('Input Matrix')
+ results = p.execute(Input_Field, Input_Matrix)
+ self.setResult('Output Field', results[0])
+ self.setResult('Output Matrix', results[1])
+
+class GetAllSegmentationBoundaries(NewField) :
+ def compute(self) :
+ p = sr_py.GetAllSegmentationBoundariesAlg()
+ Segmentations = 0
+ if self.hasInputFromPort('Segmentations') :
+ Segmentations = self.getInputFromPort('Segmentations')
+ results = p.execute(Segmentations)
+ self.setResult('Boundaries', results)
+
+class ClipFieldWithSeed(NewField) :
+ def compute(self) :
+ p = sr_py.ClipFieldWithSeedAlg()
+ if self.hasInputFromPort('p_mode') :
+ p.set_p_mode(self.getInputFromPort('p_mode'))
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ Function = ''
+ if self.hasInputFromPort('Function') :
+ Function = self.getInputFromPort('Function')
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ Seeds = 0
+ if self.hasInputFromPort('Seeds') :
+ Seeds = self.getInputFromPort('Seeds')
+ results = p.execute(Function, Input, Seeds)
+ self.setResult('Clipped', results[0])
+ self.setResult('Mapping', results[1])
+ self.setResult('MaskVector', results[2])
+
+class SplitNodesByDomain(NewField) :
+ def compute(self) :
+ p = sr_py.SplitNodesByDomainAlg()
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('SplitField', results)
+
+class ApplyMappingMatrix(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.ApplyMappingMatrixAlg()
+ Source = 0
+ if self.hasInputFromPort('Source') :
+ Source = self.getInputFromPort('Source')
+ Destination = 0
+ if self.hasInputFromPort('Destination') :
+ Destination = self.getInputFromPort('Destination')
+ Mapping = 0
+ if self.hasInputFromPort('Mapping') :
+ Mapping = self.getInputFromPort('Mapping')
+ results = p.execute(Source, Destination, Mapping)
+ self.setResult('Output', results)
+
+class MaskLatVolWithTriSurf(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.MaskLatVolWithTriSurfAlg()
+ LatVolField = 0
+ if self.hasInputFromPort('LatVolField') :
+ LatVolField = self.getInputFromPort('LatVolField')
+ TriSurfField = 0
+ if self.hasInputFromPort('TriSurfField') :
+ TriSurfField = self.getInputFromPort('TriSurfField')
+ results = p.execute(LatVolField, TriSurfField)
+ self.setResult('LatVol Mask', results)
+
+class ConvertFieldBasis(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.ConvertFieldBasisAlg()
+ if self.hasInputFromPort('p_output_basis') :
+ p.set_p_output_basis(self.getInputFromPort('p_output_basis'))
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ results = p.execute(Input)
+ self.setResult('Output', results[0])
+ self.setResult('Mapping', results[1])
+
+class ReportMeshQualityMeasures(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.ReportMeshQualityMeasuresAlg()
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ results = p.execute(Input)
+ self.setResult('Checked', results)
+
+class SelectAndSetFieldData(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.SelectAndSetFieldDataAlg()
+ if self.hasInputFromPort('p_selection1') :
+ p.set_p_selection1(self.getInputFromPort('p_selection1'))
+ if self.hasInputFromPort('p_function1') :
+ p.set_p_function1(self.getInputFromPort('p_function1'))
+ if self.hasInputFromPort('p_selection2') :
+ p.set_p_selection2(self.getInputFromPort('p_selection2'))
+ if self.hasInputFromPort('p_function2') :
+ p.set_p_function2(self.getInputFromPort('p_function2'))
+ if self.hasInputFromPort('p_selection3') :
+ p.set_p_selection3(self.getInputFromPort('p_selection3'))
+ if self.hasInputFromPort('p_function3') :
+ p.set_p_function3(self.getInputFromPort('p_function3'))
+ if self.hasInputFromPort('p_selection4') :
+ p.set_p_selection4(self.getInputFromPort('p_selection4'))
+ if self.hasInputFromPort('p_function4') :
+ p.set_p_function4(self.getInputFromPort('p_function4'))
+ if self.hasInputFromPort('p_functiondef') :
+ p.set_p_functiondef(self.getInputFromPort('p_functiondef'))
+ if self.hasInputFromPort('p_format') :
+ p.set_p_format(self.getInputFromPort('p_format'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ Array = 0
+ if self.hasInputFromPort('Array') :
+ Array = self.getInputFromPort('Array')
+ results = p.execute(Field, Array)
+ self.setResult('Field', results)
+
+class CalculateFieldData3(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateFieldData3Alg()
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ if self.hasInputFromPort('p_format') :
+ p.set_p_format(self.getInputFromPort('p_format'))
+ Field1 = 0
+ if self.hasInputFromPort('Field1') :
+ Field1 = self.getInputFromPort('Field1')
+ Field2 = 0
+ if self.hasInputFromPort('Field2') :
+ Field2 = self.getInputFromPort('Field2')
+ Field3 = 0
+ if self.hasInputFromPort('Field3') :
+ Field3 = self.getInputFromPort('Field3')
+ Function = ''
+ if self.hasInputFromPort('Function') :
+ Function = self.getInputFromPort('Function')
+ Array = 0
+ if self.hasInputFromPort('Array') :
+ Array = self.getInputFromPort('Array')
+ results = p.execute(Field1, Field2, Field3, Function, Array)
+ self.setResult('Field', results)
+
+class SetFieldData(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.SetFieldDataAlg()
+ if self.hasInputFromPort('p_keepscalartype') :
+ p.set_p_keepscalartype(self.getInputFromPort('p_keepscalartype'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ Matrix_Data = 0
+ if self.hasInputFromPort('Matrix Data') :
+ Matrix_Data = self.getInputFromPort('Matrix Data')
+ Nrrd_Data = 0
+ if self.hasInputFromPort('Nrrd Data') :
+ Nrrd_Data = self.getInputFromPort('Nrrd Data')
+ results = p.execute(Field, Matrix_Data, Nrrd_Data)
+ self.setResult('Field', results)
+
+class SwapFieldDataWithMatrixEntries(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.SwapFieldDataWithMatrixEntriesAlg()
+ if self.hasInputFromPort('p_preserve_scalar_type') :
+ p.set_p_preserve_scalar_type(self.getInputFromPort('p_preserve_scalar_type'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ Input_Matrix = 0
+ if self.hasInputFromPort('Input Matrix') :
+ Input_Matrix = self.getInputFromPort('Input Matrix')
+ results = p.execute(Input_Field, Input_Matrix)
+ self.setResult('Output Field', results[0])
+ self.setResult('Output Matrix', results[1])
+
+class ConvertLatVolDataFromElemToNode(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.ConvertLatVolDataFromElemToNodeAlg()
+ Elem_Field = 0
+ if self.hasInputFromPort('Elem Field') :
+ Elem_Field = self.getInputFromPort('Elem Field')
+ results = p.execute(Elem_Field)
+ self.setResult('Node Field', results)
+
+class CalculateNodeNormals(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateNodeNormalsAlg()
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ Input_Point = 0
+ if self.hasInputFromPort('Input Point') :
+ Input_Point = self.getInputFromPort('Input Point')
+ results = p.execute(Input_Field, Input_Point)
+ self.setResult('Output Field', results)
+
+class CalculateVectorMagnitudes(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateVectorMagnitudesAlg()
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output CalculateVectorMagnitudes', results)
+
+class ConvertIndicesToFieldData(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.ConvertIndicesToFieldDataAlg()
+ if self.hasInputFromPort('p_outputtype') :
+ p.set_p_outputtype(self.getInputFromPort('p_outputtype'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ Data = 0
+ if self.hasInputFromPort('Data') :
+ Data = self.getInputFromPort('Data')
+ results = p.execute(Field, Data)
+ self.setResult('Field', results)
+
+class CalculateDistanceToFieldBoundary(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateDistanceToFieldBoundaryAlg()
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('DistanceField', results)
+
+class MapFieldDataFromSourceToDestination(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.MapFieldDataFromSourceToDestinationAlg()
+ if self.hasInputFromPort('p_interpolation_basis') :
+ p.set_p_interpolation_basis(self.getInputFromPort('p_interpolation_basis'))
+ if self.hasInputFromPort('p_map_source_to_single_dest') :
+ p.set_p_map_source_to_single_dest(self.getInputFromPort('p_map_source_to_single_dest'))
+ if self.hasInputFromPort('p_exhaustive_search') :
+ p.set_p_exhaustive_search(self.getInputFromPort('p_exhaustive_search'))
+ if self.hasInputFromPort('p_exhaustive_search_max_dist') :
+ p.set_p_exhaustive_search_max_dist(self.getInputFromPort('p_exhaustive_search_max_dist'))
+ if self.hasInputFromPort('p_np') :
+ p.set_p_np(self.getInputFromPort('p_np'))
+ Source = 0
+ if self.hasInputFromPort('Source') :
+ Source = self.getInputFromPort('Source')
+ Destination = 0
+ if self.hasInputFromPort('Destination') :
+ Destination = self.getInputFromPort('Destination')
+ results = p.execute(Source, Destination)
+ self.setResult('Remapped Destination', results)
+
+class SelectAndSetFieldData3(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.SelectAndSetFieldData3Alg()
+ if self.hasInputFromPort('p_selection1') :
+ p.set_p_selection1(self.getInputFromPort('p_selection1'))
+ if self.hasInputFromPort('p_function1') :
+ p.set_p_function1(self.getInputFromPort('p_function1'))
+ if self.hasInputFromPort('p_selection2') :
+ p.set_p_selection2(self.getInputFromPort('p_selection2'))
+ if self.hasInputFromPort('p_function2') :
+ p.set_p_function2(self.getInputFromPort('p_function2'))
+ if self.hasInputFromPort('p_selection3') :
+ p.set_p_selection3(self.getInputFromPort('p_selection3'))
+ if self.hasInputFromPort('p_function3') :
+ p.set_p_function3(self.getInputFromPort('p_function3'))
+ if self.hasInputFromPort('p_selection4') :
+ p.set_p_selection4(self.getInputFromPort('p_selection4'))
+ if self.hasInputFromPort('p_function4') :
+ p.set_p_function4(self.getInputFromPort('p_function4'))
+ if self.hasInputFromPort('p_functiondef') :
+ p.set_p_functiondef(self.getInputFromPort('p_functiondef'))
+ if self.hasInputFromPort('p_format') :
+ p.set_p_format(self.getInputFromPort('p_format'))
+ Field1 = 0
+ if self.hasInputFromPort('Field1') :
+ Field1 = self.getInputFromPort('Field1')
+ Field2 = 0
+ if self.hasInputFromPort('Field2') :
+ Field2 = self.getInputFromPort('Field2')
+ Field3 = 0
+ if self.hasInputFromPort('Field3') :
+ Field3 = self.getInputFromPort('Field3')
+ Array = 0
+ if self.hasInputFromPort('Array') :
+ Array = self.getInputFromPort('Array')
+ results = p.execute(Field1, Field2, Field3, Array)
+ self.setResult('Field', results)
+
+class CreateFieldData(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CreateFieldDataAlg()
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ if self.hasInputFromPort('p_format') :
+ p.set_p_format(self.getInputFromPort('p_format'))
+ if self.hasInputFromPort('p_basis') :
+ p.set_p_basis(self.getInputFromPort('p_basis'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ Function = ''
+ if self.hasInputFromPort('Function') :
+ Function = self.getInputFromPort('Function')
+ DataArray = 0
+ if self.hasInputFromPort('DataArray') :
+ DataArray = self.getInputFromPort('DataArray')
+ results = p.execute(Field, Function, DataArray)
+ self.setResult('Field', results)
+
+class ConvertLatVolDataFromNodeToElem(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.ConvertLatVolDataFromNodeToElemAlg()
+ Node_Field = 0
+ if self.hasInputFromPort('Node Field') :
+ Node_Field = self.getInputFromPort('Node Field')
+ results = p.execute(Node_Field)
+ self.setResult('Elem Field', results)
+
+class CalculateFieldDataCompiled(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateFieldDataCompiledAlg()
+ if self.hasInputFromPort('p_outputdatatype') :
+ p.set_p_outputdatatype(self.getInputFromPort('p_outputdatatype'))
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ if self.hasInputFromPort('p_cache') :
+ p.set_p_cache(self.getInputFromPort('p_cache'))
+ Function = ''
+ if self.hasInputFromPort('Function') :
+ Function = self.getInputFromPort('Function')
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Function, Input_Field)
+ self.setResult('Output Field', results)
+
+class MapFieldDataFromElemToNode(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.MapFieldDataFromElemToNodeAlg()
+ if self.hasInputFromPort('p_method') :
+ p.set_p_method(self.getInputFromPort('p_method'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('Field', results)
+
+class ApplyFilterToFieldData(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.ApplyFilterToFieldDataAlg()
+ if self.hasInputFromPort('p_method') :
+ p.set_p_method(self.getInputFromPort('p_method'))
+ if self.hasInputFromPort('p_ed_method') :
+ p.set_p_ed_method(self.getInputFromPort('p_ed_method'))
+ if self.hasInputFromPort('p_ed_iterations') :
+ p.set_p_ed_iterations(self.getInputFromPort('p_ed_iterations'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('Field', results)
+
+class GetFieldData(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.GetFieldDataAlg()
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('Data', results)
+
+class CalculateFieldData2(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateFieldData2Alg()
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ if self.hasInputFromPort('p_format') :
+ p.set_p_format(self.getInputFromPort('p_format'))
+ Field1 = 0
+ if self.hasInputFromPort('Field1') :
+ Field1 = self.getInputFromPort('Field1')
+ Field2 = 0
+ if self.hasInputFromPort('Field2') :
+ Field2 = self.getInputFromPort('Field2')
+ Function = ''
+ if self.hasInputFromPort('Function') :
+ Function = self.getInputFromPort('Function')
+ Array = 0
+ if self.hasInputFromPort('Array') :
+ Array = self.getInputFromPort('Array')
+ results = p.execute(Field1, Field2, Function, Array)
+ self.setResult('Field', results)
+
+class CalculateLatVolGradientsAtNodes(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateLatVolGradientsAtNodesAlg()
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Gradient', results)
+
+class CalculateGradients(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateGradientsAlg()
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output CalculateGradients', results)
+
+class CalculateSignedDistanceToField(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateSignedDistanceToFieldAlg()
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ ObjectField = 0
+ if self.hasInputFromPort('ObjectField') :
+ ObjectField = self.getInputFromPort('ObjectField')
+ results = p.execute(Field, ObjectField)
+ self.setResult('SignedDistanceField', results)
+
+class CalculateInsideWhichField(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateInsideWhichFieldAlg()
+ if self.hasInputFromPort('p_outputbasis') :
+ p.set_p_outputbasis(self.getInputFromPort('p_outputbasis'))
+ if self.hasInputFromPort('p_outputtype') :
+ p.set_p_outputtype(self.getInputFromPort('p_outputtype'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ Object = 0
+ if self.hasInputFromPort('Object') :
+ Object = self.getInputFromPort('Object')
+ results = p.execute(Field, Object)
+ self.setResult('Field', results)
+
+class MapFieldDataFromNodeToElem(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.MapFieldDataFromNodeToElemAlg()
+ if self.hasInputFromPort('p_method') :
+ p.set_p_method(self.getInputFromPort('p_method'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('Field', results)
+
+class ConvertFieldDataType(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.ConvertFieldDataTypeAlg()
+ if self.hasInputFromPort('p_outputdatatype') :
+ p.set_p_outputdatatype(self.getInputFromPort('p_outputdatatype'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Field', results)
+
+class CalculateIsInsideField(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateIsInsideFieldAlg()
+ if self.hasInputFromPort('p_outputtype') :
+ p.set_p_outputtype(self.getInputFromPort('p_outputtype'))
+ if self.hasInputFromPort('p_outval') :
+ p.set_p_outval(self.getInputFromPort('p_outval'))
+ if self.hasInputFromPort('p_inval') :
+ p.set_p_inval(self.getInputFromPort('p_inval'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ ObjectField = 0
+ if self.hasInputFromPort('ObjectField') :
+ ObjectField = self.getInputFromPort('ObjectField')
+ results = p.execute(Field, ObjectField)
+ self.setResult('Field', results)
+
+class CalculateFieldData(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateFieldDataAlg()
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ if self.hasInputFromPort('p_format') :
+ p.set_p_format(self.getInputFromPort('p_format'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ Function = ''
+ if self.hasInputFromPort('Function') :
+ Function = self.getInputFromPort('Function')
+ Array = 0
+ if self.hasInputFromPort('Array') :
+ Array = self.getInputFromPort('Array')
+ results = p.execute(Field, Function, Array)
+ self.setResult('Field', results)
+
+class CalculateDistanceToField(ChangeFieldData) :
+ def compute(self) :
+ p = sr_py.CalculateDistanceToFieldAlg()
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ ObjectField = 0
+ if self.hasInputFromPort('ObjectField') :
+ ObjectField = self.getInputFromPort('ObjectField')
+ results = p.execute(Field, ObjectField)
+ self.setResult('DistanceField', results)
+
+class TransformPlanarMesh(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.TransformPlanarMeshAlg()
+ if self.hasInputFromPort('p_axis') :
+ p.set_p_axis(self.getInputFromPort('p_axis'))
+ if self.hasInputFromPort('p_invert') :
+ p.set_p_invert(self.getInputFromPort('p_invert'))
+ if self.hasInputFromPort('p_trans_x') :
+ p.set_p_trans_x(self.getInputFromPort('p_trans_x'))
+ if self.hasInputFromPort('p_trans_y') :
+ p.set_p_trans_y(self.getInputFromPort('p_trans_y'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ Index_Matrix = 0
+ if self.hasInputFromPort('Index Matrix') :
+ Index_Matrix = self.getInputFromPort('Index Matrix')
+ results = p.execute(Input_Field, Index_Matrix)
+ self.setResult('Transformed Field', results)
+
+class ConvertMeshToUnstructuredMesh(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.ConvertMeshToUnstructuredMeshAlg()
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Field', results)
+
+class ConvertQuadSurfToTriSurf(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.ConvertQuadSurfToTriSurfAlg()
+ QuadSurf = 0
+ if self.hasInputFromPort('QuadSurf') :
+ QuadSurf = self.getInputFromPort('QuadSurf')
+ results = p.execute(QuadSurf)
+ self.setResult('TriSurf', results)
+
+class TransformMeshWithFunction(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.TransformMeshWithFunctionAlg()
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Field', results)
+
+class ConvertHexVolToTetVol(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.ConvertHexVolToTetVolAlg()
+ HexVol = 0
+ if self.hasInputFromPort('HexVol') :
+ HexVol = self.getInputFromPort('HexVol')
+ results = p.execute(HexVol)
+ self.setResult('TetVol', results)
+
+class ConvertMeshCoordinateSystem(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.ConvertMeshCoordinateSystemAlg()
+ if self.hasInputFromPort('p_oldsystem') :
+ p.set_p_oldsystem(self.getInputFromPort('p_oldsystem'))
+ if self.hasInputFromPort('p_newsystem') :
+ p.set_p_newsystem(self.getInputFromPort('p_newsystem'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Field', results)
+
+class ConvertMeshToPointCloud(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.ConvertMeshToPointCloudAlg()
+ if self.hasInputFromPort('p_datalocation') :
+ p.set_p_datalocation(self.getInputFromPort('p_datalocation'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('Field', results)
+
+class TransformMeshWithTransform(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.TransformMeshWithTransformAlg()
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ Transform_Matrix = 0
+ if self.hasInputFromPort('Transform Matrix') :
+ Transform_Matrix = self.getInputFromPort('Transform Matrix')
+ results = p.execute(Input_Field, Transform_Matrix)
+ self.setResult('Transformed Field', results)
+
+class ConvertRegularMeshToStructuredMesh(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.ConvertRegularMeshToStructuredMeshAlg()
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Field', results)
+
+class CalculateMeshNodes(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.CalculateMeshNodesAlg()
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ Function = ''
+ if self.hasInputFromPort('Function') :
+ Function = self.getInputFromPort('Function')
+ Array = 0
+ if self.hasInputFromPort('Array') :
+ Array = self.getInputFromPort('Array')
+ results = p.execute(Field, Function, Array)
+ self.setResult('Field', results)
+
+class SmoothMesh(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.SmoothMeshAlg()
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ IsoValue = 0
+ if self.hasInputFromPort('IsoValue') :
+ IsoValue = self.getInputFromPort('IsoValue')
+ results = p.execute(Input, IsoValue)
+ self.setResult('Smoothed', results)
+
+class EditMeshBoundingBox(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.EditMeshBoundingBoxAlg()
+ if self.hasInputFromPort('p_outputcenterx') :
+ p.set_p_outputcenterx(self.getInputFromPort('p_outputcenterx'))
+ if self.hasInputFromPort('p_outputcentery') :
+ p.set_p_outputcentery(self.getInputFromPort('p_outputcentery'))
+ if self.hasInputFromPort('p_outputcenterz') :
+ p.set_p_outputcenterz(self.getInputFromPort('p_outputcenterz'))
+ if self.hasInputFromPort('p_outputsizex') :
+ p.set_p_outputsizex(self.getInputFromPort('p_outputsizex'))
+ if self.hasInputFromPort('p_outputsizey') :
+ p.set_p_outputsizey(self.getInputFromPort('p_outputsizey'))
+ if self.hasInputFromPort('p_outputsizez') :
+ p.set_p_outputsizez(self.getInputFromPort('p_outputsizez'))
+ if self.hasInputFromPort('p_useoutputcenter') :
+ p.set_p_useoutputcenter(self.getInputFromPort('p_useoutputcenter'))
+ if self.hasInputFromPort('p_useoutputsize') :
+ p.set_p_useoutputsize(self.getInputFromPort('p_useoutputsize'))
+ if self.hasInputFromPort('p_box_scale') :
+ p.set_p_box_scale(self.getInputFromPort('p_box_scale'))
+ if self.hasInputFromPort('p_box_mode') :
+ p.set_p_box_mode(self.getInputFromPort('p_box_mode'))
+ if self.hasInputFromPort('p_box_real_scale') :
+ p.set_p_box_real_scale(self.getInputFromPort('p_box_real_scale'))
+ if self.hasInputFromPort('p_box_center_x') :
+ p.set_p_box_center_x(self.getInputFromPort('p_box_center_x'))
+ if self.hasInputFromPort('p_box_center_y') :
+ p.set_p_box_center_y(self.getInputFromPort('p_box_center_y'))
+ if self.hasInputFromPort('p_box_center_z') :
+ p.set_p_box_center_z(self.getInputFromPort('p_box_center_z'))
+ if self.hasInputFromPort('p_box_right_x') :
+ p.set_p_box_right_x(self.getInputFromPort('p_box_right_x'))
+ if self.hasInputFromPort('p_box_right_y') :
+ p.set_p_box_right_y(self.getInputFromPort('p_box_right_y'))
+ if self.hasInputFromPort('p_box_right_z') :
+ p.set_p_box_right_z(self.getInputFromPort('p_box_right_z'))
+ if self.hasInputFromPort('p_box_down_x') :
+ p.set_p_box_down_x(self.getInputFromPort('p_box_down_x'))
+ if self.hasInputFromPort('p_box_down_y') :
+ p.set_p_box_down_y(self.getInputFromPort('p_box_down_y'))
+ if self.hasInputFromPort('p_box_down_z') :
+ p.set_p_box_down_z(self.getInputFromPort('p_box_down_z'))
+ if self.hasInputFromPort('p_box_in_x') :
+ p.set_p_box_in_x(self.getInputFromPort('p_box_in_x'))
+ if self.hasInputFromPort('p_box_in_y') :
+ p.set_p_box_in_y(self.getInputFromPort('p_box_in_y'))
+ if self.hasInputFromPort('p_box_in_z') :
+ p.set_p_box_in_z(self.getInputFromPort('p_box_in_z'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Field', results[0])
+ self.setResult('Transformation Widget', results[1])
+ self.setResult('Transformation Matrix', results[2])
+
+class SwapNodeLocationsWithMatrixEntries(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.SwapNodeLocationsWithMatrixEntriesAlg()
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ Input_Matrix = 0
+ if self.hasInputFromPort('Input Matrix') :
+ Input_Matrix = self.getInputFromPort('Input Matrix')
+ results = p.execute(Input_Field, Input_Matrix)
+ self.setResult('Output Field', results[0])
+ self.setResult('Output Matrix', results[1])
+
+class MapFieldDataToNodeCoordinate(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.MapFieldDataToNodeCoordinateAlg()
+ if self.hasInputFromPort('p_coord') :
+ p.set_p_coord(self.getInputFromPort('p_coord'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Field', results)
+
+class ScaleFieldMeshAndData(ChangeMesh) :
+ def compute(self) :
+ p = sr_py.ScaleFieldMeshAndDataAlg()
+ if self.hasInputFromPort('p_datascale') :
+ p.set_p_datascale(self.getInputFromPort('p_datascale'))
+ if self.hasInputFromPort('p_geomscale') :
+ p.set_p_geomscale(self.getInputFromPort('p_geomscale'))
+ if self.hasInputFromPort('p_usegeomcenter') :
+ p.set_p_usegeomcenter(self.getInputFromPort('p_usegeomcenter'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ GeomScaleFactor = 0
+ if self.hasInputFromPort('GeomScaleFactor') :
+ GeomScaleFactor = self.getInputFromPort('GeomScaleFactor')
+ DataScaleFactor = 0
+ if self.hasInputFromPort('DataScaleFactor') :
+ DataScaleFactor = self.getInputFromPort('DataScaleFactor')
+ results = p.execute(Field, GeomScaleFactor, DataScaleFactor)
+ self.setResult('Field', results)
+
+class ReportColumnMatrixMisfit(Math) :
+ def compute(self) :
+ p = sr_py.ReportColumnMatrixMisfitAlg()
+ if self.hasInputFromPort('p_have_ui') :
+ p.set_p_have_ui(self.getInputFromPort('p_have_ui'))
+ if self.hasInputFromPort('p_methodTCL') :
+ p.set_p_methodTCL(self.getInputFromPort('p_methodTCL'))
+ if self.hasInputFromPort('p_pTCL') :
+ p.set_p_pTCL(self.getInputFromPort('p_pTCL'))
+ Vec1 = 0
+ if self.hasInputFromPort('Vec1') :
+ Vec1 = self.getInputFromPort('Vec1')
+ Vec2 = 0
+ if self.hasInputFromPort('Vec2') :
+ Vec2 = self.getInputFromPort('Vec2')
+ results = p.execute(Vec1, Vec2)
+ self.setResult('Error Out', results)
+
+class EvaluateLinAlgGeneral(Math) :
+ def compute(self) :
+ p = sr_py.EvaluateLinAlgGeneralAlg()
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ i1 = 0
+ if self.hasInputFromPort('i1') :
+ i1 = self.getInputFromPort('i1')
+ i2 = 0
+ if self.hasInputFromPort('i2') :
+ i2 = self.getInputFromPort('i2')
+ i3 = 0
+ if self.hasInputFromPort('i3') :
+ i3 = self.getInputFromPort('i3')
+ i4 = 0
+ if self.hasInputFromPort('i4') :
+ i4 = self.getInputFromPort('i4')
+ i5 = 0
+ if self.hasInputFromPort('i5') :
+ i5 = self.getInputFromPort('i5')
+ results = p.execute(i1, i2, i3, i4, i5)
+ self.setResult('o1', results[0])
+ self.setResult('o2', results[1])
+ self.setResult('o3', results[2])
+ self.setResult('o4', results[3])
+ self.setResult('o5', results[4])
+
+class AppendMatrix(Math) :
+ def compute(self) :
+ p = sr_py.AppendMatrixAlg()
+ if self.hasInputFromPort('p_row_or_column') :
+ p.set_p_row_or_column(self.getInputFromPort('p_row_or_column'))
+ BaseMatrix = 0
+ if self.hasInputFromPort('BaseMatrix') :
+ BaseMatrix = self.getInputFromPort('BaseMatrix')
+ AppendMatrix = 0
+ if self.hasInputFromPort('AppendMatrix') :
+ AppendMatrix = self.getInputFromPort('AppendMatrix')
+ results = p.execute(BaseMatrix, AppendMatrix)
+ self.setResult('Matrix', results)
+
+class EvaluateLinAlgBinary(Math) :
+ def compute(self) :
+ p = sr_py.EvaluateLinAlgBinaryAlg()
+ if self.hasInputFromPort('p_op') :
+ p.set_p_op(self.getInputFromPort('p_op'))
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ A = 0
+ if self.hasInputFromPort('A') :
+ A = self.getInputFromPort('A')
+ B = 0
+ if self.hasInputFromPort('B') :
+ B = self.getInputFromPort('B')
+ results = p.execute(A, B)
+ self.setResult('Output', results)
+
+class ConvertMaskVectorToMappingMatrix(Math) :
+ def compute(self) :
+ p = sr_py.ConvertMaskVectorToMappingMatrixAlg()
+ MaskVector = 0
+ if self.hasInputFromPort('MaskVector') :
+ MaskVector = self.getInputFromPort('MaskVector')
+ results = p.execute(MaskVector)
+ self.setResult('MappingMatrix', results)
+
+class SolveLinearSystem(Math) :
+ def compute(self) :
+ p = sr_py.SolveLinearSystemAlg()
+ if self.hasInputFromPort('p_target_error') :
+ p.set_p_target_error(self.getInputFromPort('p_target_error'))
+ if self.hasInputFromPort('p_flops') :
+ p.set_p_flops(self.getInputFromPort('p_flops'))
+ if self.hasInputFromPort('p_floprate') :
+ p.set_p_floprate(self.getInputFromPort('p_floprate'))
+ if self.hasInputFromPort('p_memrefs') :
+ p.set_p_memrefs(self.getInputFromPort('p_memrefs'))
+ if self.hasInputFromPort('p_memrate') :
+ p.set_p_memrate(self.getInputFromPort('p_memrate'))
+ if self.hasInputFromPort('p_orig_error') :
+ p.set_p_orig_error(self.getInputFromPort('p_orig_error'))
+ if self.hasInputFromPort('p_current_error') :
+ p.set_p_current_error(self.getInputFromPort('p_current_error'))
+ if self.hasInputFromPort('p_method') :
+ p.set_p_method(self.getInputFromPort('p_method'))
+ if self.hasInputFromPort('p_precond') :
+ p.set_p_precond(self.getInputFromPort('p_precond'))
+ if self.hasInputFromPort('p_iteration') :
+ p.set_p_iteration(self.getInputFromPort('p_iteration'))
+ if self.hasInputFromPort('p_maxiter') :
+ p.set_p_maxiter(self.getInputFromPort('p_maxiter'))
+ if self.hasInputFromPort('p_use_previous_soln') :
+ p.set_p_use_previous_soln(self.getInputFromPort('p_use_previous_soln'))
+ if self.hasInputFromPort('p_emit_partial') :
+ p.set_p_emit_partial(self.getInputFromPort('p_emit_partial'))
+ if self.hasInputFromPort('p_emit_iter') :
+ p.set_p_emit_iter(self.getInputFromPort('p_emit_iter'))
+ if self.hasInputFromPort('p_status') :
+ p.set_p_status(self.getInputFromPort('p_status'))
+ if self.hasInputFromPort('p_np') :
+ p.set_p_np(self.getInputFromPort('p_np'))
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ RHS = 0
+ if self.hasInputFromPort('RHS') :
+ RHS = self.getInputFromPort('RHS')
+ results = p.execute(Matrix, RHS)
+ self.setResult('Solution', results)
+
+class ReportMatrixColumnMeasure(Math) :
+ def compute(self) :
+ p = sr_py.ReportMatrixColumnMeasureAlg()
+ if self.hasInputFromPort('p_method') :
+ p.set_p_method(self.getInputFromPort('p_method'))
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(Matrix)
+ self.setResult('Vector', results)
+
+class SortMatrix(Math) :
+ def compute(self) :
+ p = sr_py.SortMatrixAlg()
+ if self.hasInputFromPort('p_row_or_col') :
+ p.set_p_row_or_col(self.getInputFromPort('p_row_or_col'))
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(Matrix)
+ self.setResult('Matrix', results)
+
+class CreateGeometricTransform(Math) :
+ def compute(self) :
+ p = sr_py.CreateGeometricTransformAlg()
+ if self.hasInputFromPort('p_rotate_x') :
+ p.set_p_rotate_x(self.getInputFromPort('p_rotate_x'))
+ if self.hasInputFromPort('p_rotate_y') :
+ p.set_p_rotate_y(self.getInputFromPort('p_rotate_y'))
+ if self.hasInputFromPort('p_rotate_z') :
+ p.set_p_rotate_z(self.getInputFromPort('p_rotate_z'))
+ if self.hasInputFromPort('p_rotate_theta') :
+ p.set_p_rotate_theta(self.getInputFromPort('p_rotate_theta'))
+ if self.hasInputFromPort('p_translate_x') :
+ p.set_p_translate_x(self.getInputFromPort('p_translate_x'))
+ if self.hasInputFromPort('p_translate_y') :
+ p.set_p_translate_y(self.getInputFromPort('p_translate_y'))
+ if self.hasInputFromPort('p_translate_z') :
+ p.set_p_translate_z(self.getInputFromPort('p_translate_z'))
+ if self.hasInputFromPort('p_scale_uniform') :
+ p.set_p_scale_uniform(self.getInputFromPort('p_scale_uniform'))
+ if self.hasInputFromPort('p_scale_x') :
+ p.set_p_scale_x(self.getInputFromPort('p_scale_x'))
+ if self.hasInputFromPort('p_scale_y') :
+ p.set_p_scale_y(self.getInputFromPort('p_scale_y'))
+ if self.hasInputFromPort('p_scale_z') :
+ p.set_p_scale_z(self.getInputFromPort('p_scale_z'))
+ if self.hasInputFromPort('p_shear_plane_a') :
+ p.set_p_shear_plane_a(self.getInputFromPort('p_shear_plane_a'))
+ if self.hasInputFromPort('p_shear_plane_b') :
+ p.set_p_shear_plane_b(self.getInputFromPort('p_shear_plane_b'))
+ if self.hasInputFromPort('p_shear_plane_c') :
+ p.set_p_shear_plane_c(self.getInputFromPort('p_shear_plane_c'))
+ if self.hasInputFromPort('p_widget_resizable') :
+ p.set_p_widget_resizable(self.getInputFromPort('p_widget_resizable'))
+ if self.hasInputFromPort('p_permute_x') :
+ p.set_p_permute_x(self.getInputFromPort('p_permute_x'))
+ if self.hasInputFromPort('p_permute_y') :
+ p.set_p_permute_y(self.getInputFromPort('p_permute_y'))
+ if self.hasInputFromPort('p_permute_z') :
+ p.set_p_permute_z(self.getInputFromPort('p_permute_z'))
+ if self.hasInputFromPort('p_pre_transform') :
+ p.set_p_pre_transform(self.getInputFromPort('p_pre_transform'))
+ if self.hasInputFromPort('p_which_transform') :
+ p.set_p_which_transform(self.getInputFromPort('p_which_transform'))
+ if self.hasInputFromPort('p_widget_scale') :
+ p.set_p_widget_scale(self.getInputFromPort('p_widget_scale'))
+ if self.hasInputFromPort('p_ignoring_widget_changes') :
+ p.set_p_ignoring_widget_changes(self.getInputFromPort('p_ignoring_widget_changes'))
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(Matrix)
+ self.setResult('Matrix', results[0])
+ self.setResult('Geometry', results[1])
+
+class ChooseMatrix(Math) :
+ def compute(self) :
+ p = sr_py.ChooseMatrixAlg()
+ if self.hasInputFromPort('p_use_first_valid') :
+ p.set_p_use_first_valid(self.getInputFromPort('p_use_first_valid'))
+ if self.hasInputFromPort('p_port_valid_index') :
+ p.set_p_port_valid_index(self.getInputFromPort('p_port_valid_index'))
+ if self.hasInputFromPort('p_port_selected_index') :
+ p.set_p_port_selected_index(self.getInputFromPort('p_port_selected_index'))
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(Matrix)
+ self.setResult('Matrix', results)
+
+class ConvertMappingMatrixToMaskVector(Math) :
+ def compute(self) :
+ p = sr_py.ConvertMappingMatrixToMaskVectorAlg()
+ MappingMatrix = 0
+ if self.hasInputFromPort('MappingMatrix') :
+ MappingMatrix = self.getInputFromPort('MappingMatrix')
+ results = p.execute(MappingMatrix)
+ self.setResult('MaskVector', results)
+
+class ResizeMatrix(Math) :
+ def compute(self) :
+ p = sr_py.ResizeMatrixAlg()
+ if self.hasInputFromPort('p_dim_m') :
+ p.set_p_dim_m(self.getInputFromPort('p_dim_m'))
+ if self.hasInputFromPort('p_dim_n') :
+ p.set_p_dim_n(self.getInputFromPort('p_dim_n'))
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ M = 0
+ if self.hasInputFromPort('M') :
+ M = self.getInputFromPort('M')
+ N = 0
+ if self.hasInputFromPort('N') :
+ N = self.getInputFromPort('N')
+ results = p.execute(Matrix, M, N)
+ self.setResult('Matrix', results)
+
+class CollectMatrices(Math) :
+ def compute(self) :
+ p = sr_py.CollectMatricesAlg()
+ if self.hasInputFromPort('p_append') :
+ p.set_p_append(self.getInputFromPort('p_append'))
+ if self.hasInputFromPort('p_row') :
+ p.set_p_row(self.getInputFromPort('p_row'))
+ if self.hasInputFromPort('p_front') :
+ p.set_p_front(self.getInputFromPort('p_front'))
+ Optional_BaseMatrix = 0
+ if self.hasInputFromPort('Optional BaseMatrix') :
+ Optional_BaseMatrix = self.getInputFromPort('Optional BaseMatrix')
+ SubMatrix = 0
+ if self.hasInputFromPort('SubMatrix') :
+ SubMatrix = self.getInputFromPort('SubMatrix')
+ results = p.execute(Optional_BaseMatrix, SubMatrix)
+ self.setResult('CompositeMatrix', results)
+
+class GetColumnOrRowFromMatrix(Math) :
+ def compute(self) :
+ p = sr_py.GetColumnOrRowFromMatrixAlg()
+ if self.hasInputFromPort('p_row_or_col') :
+ p.set_p_row_or_col(self.getInputFromPort('p_row_or_col'))
+ if self.hasInputFromPort('p_selectable_min') :
+ p.set_p_selectable_min(self.getInputFromPort('p_selectable_min'))
+ if self.hasInputFromPort('p_selectable_max') :
+ p.set_p_selectable_max(self.getInputFromPort('p_selectable_max'))
+ if self.hasInputFromPort('p_selectable_inc') :
+ p.set_p_selectable_inc(self.getInputFromPort('p_selectable_inc'))
+ if self.hasInputFromPort('p_selectable_units') :
+ p.set_p_selectable_units(self.getInputFromPort('p_selectable_units'))
+ if self.hasInputFromPort('p_range_min') :
+ p.set_p_range_min(self.getInputFromPort('p_range_min'))
+ if self.hasInputFromPort('p_range_max') :
+ p.set_p_range_max(self.getInputFromPort('p_range_max'))
+ if self.hasInputFromPort('p_playmode') :
+ p.set_p_playmode(self.getInputFromPort('p_playmode'))
+ if self.hasInputFromPort('p_current') :
+ p.set_p_current(self.getInputFromPort('p_current'))
+ if self.hasInputFromPort('p_execmode') :
+ p.set_p_execmode(self.getInputFromPort('p_execmode'))
+ if self.hasInputFromPort('p_delay') :
+ p.set_p_delay(self.getInputFromPort('p_delay'))
+ if self.hasInputFromPort('p_inc_amount') :
+ p.set_p_inc_amount(self.getInputFromPort('p_inc_amount'))
+ if self.hasInputFromPort('p_send_amount') :
+ p.set_p_send_amount(self.getInputFromPort('p_send_amount'))
+ if self.hasInputFromPort('p_data_series_done') :
+ p.set_p_data_series_done(self.getInputFromPort('p_data_series_done'))
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ Weight_Vector = 0
+ if self.hasInputFromPort('Weight Vector') :
+ Weight_Vector = self.getInputFromPort('Weight Vector')
+ Current_Index = 0
+ if self.hasInputFromPort('Current Index') :
+ Current_Index = self.getInputFromPort('Current Index')
+ results = p.execute(Matrix, Weight_Vector, Current_Index)
+ self.setResult('Vector', results[0])
+ self.setResult('Selected Index', results[1])
+
+class BuildNoiseColumnMatrix(Math) :
+ def compute(self) :
+ p = sr_py.BuildNoiseColumnMatrixAlg()
+ if self.hasInputFromPort('p_snr') :
+ p.set_p_snr(self.getInputFromPort('p_snr'))
+ Signal = 0
+ if self.hasInputFromPort('Signal') :
+ Signal = self.getInputFromPort('Signal')
+ results = p.execute(Signal)
+ self.setResult('Noise', results)
+
+class EvaluateLinAlgUnary(Math) :
+ def compute(self) :
+ p = sr_py.EvaluateLinAlgUnaryAlg()
+ if self.hasInputFromPort('p_op') :
+ p.set_p_op(self.getInputFromPort('p_op'))
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ results = p.execute(Input)
+ self.setResult('Output', results)
+
+class GetSubmatrix(Math) :
+ def compute(self) :
+ p = sr_py.GetSubmatrixAlg()
+ if self.hasInputFromPort('p_mincol') :
+ p.set_p_mincol(self.getInputFromPort('p_mincol'))
+ if self.hasInputFromPort('p_maxcol') :
+ p.set_p_maxcol(self.getInputFromPort('p_maxcol'))
+ if self.hasInputFromPort('p_minrow') :
+ p.set_p_minrow(self.getInputFromPort('p_minrow'))
+ if self.hasInputFromPort('p_maxrow') :
+ p.set_p_maxrow(self.getInputFromPort('p_maxrow'))
+ if self.hasInputFromPort('p_nrow') :
+ p.set_p_nrow(self.getInputFromPort('p_nrow'))
+ if self.hasInputFromPort('p_ncol') :
+ p.set_p_ncol(self.getInputFromPort('p_ncol'))
+ Input_Matrix = 0
+ if self.hasInputFromPort('Input Matrix') :
+ Input_Matrix = self.getInputFromPort('Input Matrix')
+ Optional_Range_Bounds = 0
+ if self.hasInputFromPort('Optional Range Bounds') :
+ Optional_Range_Bounds = self.getInputFromPort('Optional Range Bounds')
+ results = p.execute(Input_Matrix, Optional_Range_Bounds)
+ self.setResult('Output Matrix', results)
+
+class ReorderMatrixByReverseCuthillMcKee(Math) :
+ def compute(self) :
+ p = sr_py.ReorderMatrixByReverseCuthillMcKeeAlg()
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(Matrix)
+ self.setResult('Matrix', results[0])
+ self.setResult('Mapping', results[1])
+ self.setResult('InverseMapping', results[2])
+
+class CreateMatrix(Math) :
+ def compute(self) :
+ p = sr_py.CreateMatrixAlg()
+ if self.hasInputFromPort('p_rows') :
+ p.set_p_rows(self.getInputFromPort('p_rows'))
+ if self.hasInputFromPort('p_cols') :
+ p.set_p_cols(self.getInputFromPort('p_cols'))
+ if self.hasInputFromPort('p_data') :
+ p.set_p_data(self.getInputFromPort('p_data'))
+ if self.hasInputFromPort('p_clabel') :
+ p.set_p_clabel(self.getInputFromPort('p_clabel'))
+ if self.hasInputFromPort('p_rlabel') :
+ p.set_p_rlabel(self.getInputFromPort('p_rlabel'))
+ results = p.execute()
+ self.setResult('matrix', results)
+
+class SolveMinNormLeastSqSystem(Math) :
+ def compute(self) :
+ p = sr_py.SolveMinNormLeastSqSystemAlg()
+ BasisVec1 = 0
+ if self.hasInputFromPort('BasisVec1') :
+ BasisVec1 = self.getInputFromPort('BasisVec1')
+ BasisVec2 = 0
+ if self.hasInputFromPort('BasisVec2') :
+ BasisVec2 = self.getInputFromPort('BasisVec2')
+ BasisVec3 = 0
+ if self.hasInputFromPort('BasisVec3') :
+ BasisVec3 = self.getInputFromPort('BasisVec3')
+ TargetVec = 0
+ if self.hasInputFromPort('TargetVec') :
+ TargetVec = self.getInputFromPort('TargetVec')
+ results = p.execute(BasisVec1, BasisVec2, BasisVec3, TargetVec)
+ self.setResult('WeightVec(Col)', results[0])
+ self.setResult('ResultVec(Col)', results[1])
+
+class ConvertMatrixType(Math) :
+ def compute(self) :
+ p = sr_py.ConvertMatrixTypeAlg()
+ if self.hasInputFromPort('p_oldtype') :
+ p.set_p_oldtype(self.getInputFromPort('p_oldtype'))
+ if self.hasInputFromPort('p_newtype') :
+ p.set_p_newtype(self.getInputFromPort('p_newtype'))
+ if self.hasInputFromPort('p_nrow') :
+ p.set_p_nrow(self.getInputFromPort('p_nrow'))
+ if self.hasInputFromPort('p_ncol') :
+ p.set_p_ncol(self.getInputFromPort('p_ncol'))
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ results = p.execute(Input)
+ self.setResult('Output', results)
+
+class ReportMatrixRowMeasure(Math) :
+ def compute(self) :
+ p = sr_py.ReportMatrixRowMeasureAlg()
+ if self.hasInputFromPort('p_method') :
+ p.set_p_method(self.getInputFromPort('p_method'))
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(Matrix)
+ self.setResult('Vector', results)
+
+class ReorderMatrixByCuthillMcKee(Math) :
+ def compute(self) :
+ p = sr_py.ReorderMatrixByCuthillMcKeeAlg()
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(Matrix)
+ self.setResult('Matrix', results[0])
+ self.setResult('Mapping', results[1])
+ self.setResult('InverseMapping', results[2])
+
+class ReportMatrixInfo(Math) :
+ def compute(self) :
+ p = sr_py.ReportMatrixInfoAlg()
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ results = p.execute(Input)
+ self.setResult('NumRows', results[0])
+ self.setResult('NumCols', results[1])
+ self.setResult('NumElements', results[2])
+
+class RemoveZerosFromMatrix(Math) :
+ def compute(self) :
+ p = sr_py.RemoveZerosFromMatrixAlg()
+ if self.hasInputFromPort('p_row_or_col') :
+ p.set_p_row_or_col(self.getInputFromPort('p_row_or_col'))
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(Matrix)
+ self.setResult('Matrix', results)
+
+class RemoveZeroRowsAndColumns(Math) :
+ def compute(self) :
+ p = sr_py.RemoveZeroRowsAndColumnsAlg()
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(Matrix)
+ self.setResult('ReducedMatrix', results[0])
+ self.setResult('LeftMapping', results[1])
+ self.setResult('RightMapping', results[2])
+
+class CreateDataArray(DataArrayMath) :
+ def compute(self) :
+ p = sr_py.CreateDataArrayAlg()
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ if self.hasInputFromPort('p_format') :
+ p.set_p_format(self.getInputFromPort('p_format'))
+ Size = 0
+ if self.hasInputFromPort('Size') :
+ Size = self.getInputFromPort('Size')
+ Function = ''
+ if self.hasInputFromPort('Function') :
+ Function = self.getInputFromPort('Function')
+ Array = 0
+ if self.hasInputFromPort('Array') :
+ Array = self.getInputFromPort('Array')
+ results = p.execute(Size, Function, Array)
+ self.setResult('DataArray', results)
+
+class CreateDataArrayFromIndices(DataArrayMath) :
+ def compute(self) :
+ p = sr_py.CreateDataArrayFromIndicesAlg()
+ Indices = 0
+ if self.hasInputFromPort('Indices') :
+ Indices = self.getInputFromPort('Indices')
+ Template = 0
+ if self.hasInputFromPort('Template') :
+ Template = self.getInputFromPort('Template')
+ results = p.execute(Indices, Template)
+ self.setResult('DataArray', results)
+
+class ReportDataArrayInfo(DataArrayMath) :
+ def compute(self) :
+ p = sr_py.ReportDataArrayInfoAlg()
+ DataArray = 0
+ if self.hasInputFromPort('DataArray') :
+ DataArray = self.getInputFromPort('DataArray')
+ results = p.execute(DataArray)
+ self.setResult('NumElements', results)
+
+class CreateVectorArray(DataArrayMath) :
+ def compute(self) :
+ p = sr_py.CreateVectorArrayAlg()
+ X = 0
+ if self.hasInputFromPort('X') :
+ X = self.getInputFromPort('X')
+ Y = 0
+ if self.hasInputFromPort('Y') :
+ Y = self.getInputFromPort('Y')
+ Z = 0
+ if self.hasInputFromPort('Z') :
+ Z = self.getInputFromPort('Z')
+ results = p.execute(X, Y, Z)
+ self.setResult('Vector', results)
+
+class ReplicateDataArray(DataArrayMath) :
+ def compute(self) :
+ p = sr_py.ReplicateDataArrayAlg()
+ if self.hasInputFromPort('p_size') :
+ p.set_p_size(self.getInputFromPort('p_size'))
+ DataArray = 0
+ if self.hasInputFromPort('DataArray') :
+ DataArray = self.getInputFromPort('DataArray')
+ Size = 0
+ if self.hasInputFromPort('Size') :
+ Size = self.getInputFromPort('Size')
+ results = p.execute(DataArray, Size)
+ self.setResult('DataArray', results)
+
+class SplitVectorArrayInXYZ(DataArrayMath) :
+ def compute(self) :
+ p = sr_py.SplitVectorArrayInXYZAlg()
+ VectorArray = 0
+ if self.hasInputFromPort('VectorArray') :
+ VectorArray = self.getInputFromPort('VectorArray')
+ results = p.execute(VectorArray)
+ self.setResult('X', results[0])
+ self.setResult('Y', results[1])
+ self.setResult('Z', results[2])
+
+class DecomposeTensorArrayIntoEigenVectors(DataArrayMath) :
+ def compute(self) :
+ p = sr_py.DecomposeTensorArrayIntoEigenVectorsAlg()
+ TensorArray = 0
+ if self.hasInputFromPort('TensorArray') :
+ TensorArray = self.getInputFromPort('TensorArray')
+ results = p.execute(TensorArray)
+ self.setResult('EigenVector1', results[0])
+ self.setResult('EigenVector2', results[1])
+ self.setResult('EigenVector3', results[2])
+ self.setResult('EigenValue1', results[3])
+ self.setResult('EigenValue2', results[4])
+ self.setResult('EigenValue3', results[5])
+
+class CalculateDataArray(DataArrayMath) :
+ def compute(self) :
+ p = sr_py.CalculateDataArrayAlg()
+ if self.hasInputFromPort('p_function') :
+ p.set_p_function(self.getInputFromPort('p_function'))
+ if self.hasInputFromPort('p_format') :
+ p.set_p_format(self.getInputFromPort('p_format'))
+ DataArray = 0
+ if self.hasInputFromPort('DataArray') :
+ DataArray = self.getInputFromPort('DataArray')
+ Function = ''
+ if self.hasInputFromPort('Function') :
+ Function = self.getInputFromPort('Function')
+ Array = 0
+ if self.hasInputFromPort('Array') :
+ Array = self.getInputFromPort('Array')
+ results = p.execute(DataArray, Function, Array)
+ self.setResult('DataArray', results)
+
+class ReportDataArrayMeasure(DataArrayMath) :
+ def compute(self) :
+ p = sr_py.ReportDataArrayMeasureAlg()
+ if self.hasInputFromPort('p_measure') :
+ p.set_p_measure(self.getInputFromPort('p_measure'))
+ Array = 0
+ if self.hasInputFromPort('Array') :
+ Array = self.getInputFromPort('Array')
+ results = p.execute(Array)
+ self.setResult('Measure', results)
+
+class AppendDataArrays(DataArrayMath) :
+ def compute(self) :
+ p = sr_py.AppendDataArraysAlg()
+ Array = 0
+ if self.hasInputFromPort('Array') :
+ Array = self.getInputFromPort('Array')
+ results = p.execute(Array)
+ self.setResult('Array', results)
+
+class CreateTensorArray(DataArrayMath) :
+ def compute(self) :
+ p = sr_py.CreateTensorArrayAlg()
+ EigenVector1 = 0
+ if self.hasInputFromPort('EigenVector1') :
+ EigenVector1 = self.getInputFromPort('EigenVector1')
+ EigenVector2 = 0
+ if self.hasInputFromPort('EigenVector2') :
+ EigenVector2 = self.getInputFromPort('EigenVector2')
+ EigenValue1 = 0
+ if self.hasInputFromPort('EigenValue1') :
+ EigenValue1 = self.getInputFromPort('EigenValue1')
+ EigenValue2 = 0
+ if self.hasInputFromPort('EigenValue2') :
+ EigenValue2 = self.getInputFromPort('EigenValue2')
+ EigenValue3 = 0
+ if self.hasInputFromPort('EigenValue3') :
+ EigenValue3 = self.getInputFromPort('EigenValue3')
+ results = p.execute(EigenVector1, EigenVector2, EigenValue1, EigenValue2, EigenValue3)
+ self.setResult('TensorArray', results)
+
+class PrintMatrixIntoString(String) :
+ def compute(self) :
+ p = sr_py.PrintMatrixIntoStringAlg()
+ if self.hasInputFromPort('p_formatstring') :
+ p.set_p_formatstring(self.getInputFromPort('p_formatstring'))
+ Format = ''
+ if self.hasInputFromPort('Format') :
+ Format = self.getInputFromPort('Format')
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ results = p.execute(Format, Input)
+ self.setResult('Output', results)
+
+class GetFileName(String) :
+ def compute(self) :
+ p = sr_py.GetFileNameAlg()
+ if self.hasInputFromPort('p_filename_base') :
+ p.set_p_filename_base(self.getInputFromPort('p_filename_base'))
+ if self.hasInputFromPort('p_delay') :
+ p.set_p_delay(self.getInputFromPort('p_delay'))
+ if self.hasInputFromPort('p_pinned') :
+ p.set_p_pinned(self.getInputFromPort('p_pinned'))
+ results = p.execute()
+ self.setResult('Full Filename', results)
+
+class SplitFileName(String) :
+ def compute(self) :
+ p = sr_py.SplitFileNameAlg()
+ Filename = ''
+ if self.hasInputFromPort('Filename') :
+ Filename = self.getInputFromPort('Filename')
+ results = p.execute(Filename)
+ self.setResult('Pathname', results[0])
+ self.setResult('Filename Base', results[1])
+ self.setResult('Extension', results[2])
+ self.setResult('Filename', results[3])
+
+class PrintStringIntoString(String) :
+ def compute(self) :
+ p = sr_py.PrintStringIntoStringAlg()
+ if self.hasInputFromPort('p_formatstring') :
+ p.set_p_formatstring(self.getInputFromPort('p_formatstring'))
+ Format = ''
+ if self.hasInputFromPort('Format') :
+ Format = self.getInputFromPort('Format')
+ Input = ''
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ results = p.execute(Format, Input)
+ self.setResult('Output', results)
+
+class CreateString(String) :
+ def compute(self) :
+ p = sr_py.CreateStringAlg()
+ if self.hasInputFromPort('p_inputstring') :
+ p.set_p_inputstring(self.getInputFromPort('p_inputstring'))
+ results = p.execute()
+ self.setResult('Output', results)
+
+class ReportStringInfo(String) :
+ def compute(self) :
+ p = sr_py.ReportStringInfoAlg()
+ if self.hasInputFromPort('p_inputstring') :
+ p.set_p_inputstring(self.getInputFromPort('p_inputstring'))
+ Input = ''
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ results = p.execute(Input)
+
+class JoinStrings(String) :
+ def compute(self) :
+ p = sr_py.JoinStringsAlg()
+ input = ''
+ if self.hasInputFromPort('input') :
+ input = self.getInputFromPort('input')
+ results = p.execute(input)
+ self.setResult('Output', results)
+
+class GetNetworkFileName(String) :
+ def compute(self) :
+ p = sr_py.GetNetworkFileNameAlg()
+ results = p.execute()
+ self.setResult('String', results)
+
+class SetFieldProperty(MiscField) :
+ def compute(self) :
+ p = sr_py.SetFieldPropertyAlg()
+ if self.hasInputFromPort('p_num_entries') :
+ p.set_p_num_entries(self.getInputFromPort('p_num_entries'))
+ if self.hasInputFromPort('p_property') :
+ p.set_p_property(self.getInputFromPort('p_property'))
+ if self.hasInputFromPort('p_type') :
+ p.set_p_type(self.getInputFromPort('p_type'))
+ if self.hasInputFromPort('p_value') :
+ p.set_p_value(self.getInputFromPort('p_value'))
+ if self.hasInputFromPort('p_readonly') :
+ p.set_p_readonly(self.getInputFromPort('p_readonly'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('Field', results)
+
+class ReportScalarFieldStats(MiscField) :
+ def compute(self) :
+ p = sr_py.ReportScalarFieldStatsAlg()
+ if self.hasInputFromPort('p_min') :
+ p.set_p_min(self.getInputFromPort('p_min'))
+ if self.hasInputFromPort('p_max') :
+ p.set_p_max(self.getInputFromPort('p_max'))
+ if self.hasInputFromPort('p_mean') :
+ p.set_p_mean(self.getInputFromPort('p_mean'))
+ if self.hasInputFromPort('p_median') :
+ p.set_p_median(self.getInputFromPort('p_median'))
+ if self.hasInputFromPort('p_sigma') :
+ p.set_p_sigma(self.getInputFromPort('p_sigma'))
+ if self.hasInputFromPort('p_is_fixed') :
+ p.set_p_is_fixed(self.getInputFromPort('p_is_fixed'))
+ if self.hasInputFromPort('p_nbuckets') :
+ p.set_p_nbuckets(self.getInputFromPort('p_nbuckets'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+
+class SelectFieldROIWithBoxWidget(MiscField) :
+ def compute(self) :
+ p = sr_py.SelectFieldROIWithBoxWidgetAlg()
+ if self.hasInputFromPort('p_stampvalue') :
+ p.set_p_stampvalue(self.getInputFromPort('p_stampvalue'))
+ if self.hasInputFromPort('p_runmode') :
+ p.set_p_runmode(self.getInputFromPort('p_runmode'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Selection Widget', results[0])
+ self.setResult('Output Field', results[1])
+
+class BuildMatrixOfSurfaceNormals(MiscField) :
+ def compute(self) :
+ p = sr_py.BuildMatrixOfSurfaceNormalsAlg()
+ Surface_Field = 0
+ if self.hasInputFromPort('Surface Field') :
+ Surface_Field = self.getInputFromPort('Surface Field')
+ results = p.execute(Surface_Field)
+ self.setResult('Nodal Surface Normals', results)
+
+class ReportFieldInfo(MiscField) :
+ def compute(self) :
+ p = sr_py.ReportFieldInfoAlg()
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('NumNodes', results[0])
+ self.setResult('NumElements', results[1])
+ self.setResult('NumData', results[2])
+ self.setResult('DataMin', results[3])
+ self.setResult('DataMax', results[4])
+ self.setResult('FieldSize', results[5])
+ self.setResult('FieldCenter', results[6])
+ self.setResult('Dimensions', results[7])
+
+class ReportFieldGeometryMeasures(MiscField) :
+ def compute(self) :
+ p = sr_py.ReportFieldGeometryMeasuresAlg()
+ if self.hasInputFromPort('p_simplexString') :
+ p.set_p_simplexString(self.getInputFromPort('p_simplexString'))
+ if self.hasInputFromPort('p_xFlag') :
+ p.set_p_xFlag(self.getInputFromPort('p_xFlag'))
+ if self.hasInputFromPort('p_yFlag') :
+ p.set_p_yFlag(self.getInputFromPort('p_yFlag'))
+ if self.hasInputFromPort('p_zFlag') :
+ p.set_p_zFlag(self.getInputFromPort('p_zFlag'))
+ if self.hasInputFromPort('p_idxFlag') :
+ p.set_p_idxFlag(self.getInputFromPort('p_idxFlag'))
+ if self.hasInputFromPort('p_sizeFlag') :
+ p.set_p_sizeFlag(self.getInputFromPort('p_sizeFlag'))
+ if self.hasInputFromPort('p_normalsFlag') :
+ p.set_p_normalsFlag(self.getInputFromPort('p_normalsFlag'))
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Measures Matrix', results)
+
+class SetFieldOrMeshStringProperty(MiscField) :
+ def compute(self) :
+ p = sr_py.SetFieldOrMeshStringPropertyAlg()
+ if self.hasInputFromPort('p_prop') :
+ p.set_p_prop(self.getInputFromPort('p_prop'))
+ if self.hasInputFromPort('p_val') :
+ p.set_p_val(self.getInputFromPort('p_val'))
+ if self.hasInputFromPort('p_meshprop') :
+ p.set_p_meshprop(self.getInputFromPort('p_meshprop'))
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ results = p.execute(Input)
+ self.setResult('Output', results)
+
+class ManageFieldSeries(MiscField) :
+ def compute(self) :
+ p = sr_py.ManageFieldSeriesAlg()
+ if self.hasInputFromPort('p_num_ports') :
+ p.set_p_num_ports(self.getInputFromPort('p_num_ports'))
+ Input = 0
+ if self.hasInputFromPort('Input') :
+ Input = self.getInputFromPort('Input')
+ results = p.execute(Input)
+ self.setResult('Output 0', results[0])
+ self.setResult('Output 1', results[1])
+ self.setResult('Output 2', results[2])
+ self.setResult('Output 3', results[3])
+
+class ReportSearchGridInfo(MiscField) :
+ def compute(self) :
+ p = sr_py.ReportSearchGridInfoAlg()
+ Input_Field = 0
+ if self.hasInputFromPort('Input Field') :
+ Input_Field = self.getInputFromPort('Input Field')
+ results = p.execute(Input_Field)
+ self.setResult('Output Sample Field', results)
+
+class ChooseField(MiscField) :
+ def compute(self) :
+ p = sr_py.ChooseFieldAlg()
+ if self.hasInputFromPort('p_use_first_valid') :
+ p.set_p_use_first_valid(self.getInputFromPort('p_use_first_valid'))
+ if self.hasInputFromPort('p_port_valid_index') :
+ p.set_p_port_valid_index(self.getInputFromPort('p_port_valid_index'))
+ if self.hasInputFromPort('p_port_selected_index') :
+ p.set_p_port_selected_index(self.getInputFromPort('p_port_selected_index'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('Field', results)
+
+class BuildPointCloudToLatVolMappingMatrix(MiscField) :
+ def compute(self) :
+ p = sr_py.BuildPointCloudToLatVolMappingMatrixAlg()
+ if self.hasInputFromPort('p_epsilon') :
+ p.set_p_epsilon(self.getInputFromPort('p_epsilon'))
+ PointCloudField = 0
+ if self.hasInputFromPort('PointCloudField') :
+ PointCloudField = self.getInputFromPort('PointCloudField')
+ LatVolField = 0
+ if self.hasInputFromPort('LatVolField') :
+ LatVolField = self.getInputFromPort('LatVolField')
+ results = p.execute(PointCloudField, LatVolField)
+ self.setResult('MappingMatrix', results)
+
+class BuildMappingMatrix(MiscField) :
+ def compute(self) :
+ p = sr_py.BuildMappingMatrixAlg()
+ if self.hasInputFromPort('p_interpolation_basis') :
+ p.set_p_interpolation_basis(self.getInputFromPort('p_interpolation_basis'))
+ if self.hasInputFromPort('p_map_source_to_single_dest') :
+ p.set_p_map_source_to_single_dest(self.getInputFromPort('p_map_source_to_single_dest'))
+ if self.hasInputFromPort('p_exhaustive_search') :
+ p.set_p_exhaustive_search(self.getInputFromPort('p_exhaustive_search'))
+ if self.hasInputFromPort('p_exhaustive_search_max_dist') :
+ p.set_p_exhaustive_search_max_dist(self.getInputFromPort('p_exhaustive_search_max_dist'))
+ if self.hasInputFromPort('p_np') :
+ p.set_p_np(self.getInputFromPort('p_np'))
+ Source = 0
+ if self.hasInputFromPort('Source') :
+ Source = self.getInputFromPort('Source')
+ Destination = 0
+ if self.hasInputFromPort('Destination') :
+ Destination = self.getInputFromPort('Destination')
+ results = p.execute(Source, Destination)
+ self.setResult('Mapping', results)
+
+class CoregisterPointClouds(MiscField) :
+ def compute(self) :
+ p = sr_py.CoregisterPointCloudsAlg()
+ if self.hasInputFromPort('p_allowScale') :
+ p.set_p_allowScale(self.getInputFromPort('p_allowScale'))
+ if self.hasInputFromPort('p_allowRotate') :
+ p.set_p_allowRotate(self.getInputFromPort('p_allowRotate'))
+ if self.hasInputFromPort('p_allowTranslate') :
+ p.set_p_allowTranslate(self.getInputFromPort('p_allowTranslate'))
+ if self.hasInputFromPort('p_seed') :
+ p.set_p_seed(self.getInputFromPort('p_seed'))
+ if self.hasInputFromPort('p_iters') :
+ p.set_p_iters(self.getInputFromPort('p_iters'))
+ if self.hasInputFromPort('p_misfitTol') :
+ p.set_p_misfitTol(self.getInputFromPort('p_misfitTol'))
+ if self.hasInputFromPort('p_method') :
+ p.set_p_method(self.getInputFromPort('p_method'))
+ Fixed_PointCloudField = 0
+ if self.hasInputFromPort('Fixed PointCloudField') :
+ Fixed_PointCloudField = self.getInputFromPort('Fixed PointCloudField')
+ Mobile_PointCloudField = 0
+ if self.hasInputFromPort('Mobile PointCloudField') :
+ Mobile_PointCloudField = self.getInputFromPort('Mobile PointCloudField')
+ DistanceField_From_Fixed = 0
+ if self.hasInputFromPort('DistanceField From Fixed') :
+ DistanceField_From_Fixed = self.getInputFromPort('DistanceField From Fixed')
+ results = p.execute(Fixed_PointCloudField, Mobile_PointCloudField, DistanceField_From_Fixed)
+ self.setResult('Transform', results)
+
+class CollectPointClouds(MiscField) :
+ def compute(self) :
+ p = sr_py.CollectPointCloudsAlg()
+ if self.hasInputFromPort('p_num_fields') :
+ p.set_p_num_fields(self.getInputFromPort('p_num_fields'))
+ Point_Cloud = 0
+ if self.hasInputFromPort('Point Cloud') :
+ Point_Cloud = self.getInputFromPort('Point Cloud')
+ results = p.execute(Point_Cloud)
+ self.setResult('Curve', results)
+
+class GetColorMapsFromBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.GetColorMapsFromBundleAlg()
+ if self.hasInputFromPort('p_colormap1_name') :
+ p.set_p_colormap1_name(self.getInputFromPort('p_colormap1_name'))
+ if self.hasInputFromPort('p_colormap2_name') :
+ p.set_p_colormap2_name(self.getInputFromPort('p_colormap2_name'))
+ if self.hasInputFromPort('p_colormap3_name') :
+ p.set_p_colormap3_name(self.getInputFromPort('p_colormap3_name'))
+ if self.hasInputFromPort('p_colormap4_name') :
+ p.set_p_colormap4_name(self.getInputFromPort('p_colormap4_name'))
+ if self.hasInputFromPort('p_colormap5_name') :
+ p.set_p_colormap5_name(self.getInputFromPort('p_colormap5_name'))
+ if self.hasInputFromPort('p_colormap6_name') :
+ p.set_p_colormap6_name(self.getInputFromPort('p_colormap6_name'))
+ if self.hasInputFromPort('p_colormap_selection') :
+ p.set_p_colormap_selection(self.getInputFromPort('p_colormap_selection'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ results = p.execute(bundle)
+ self.setResult('bundle', results[0])
+ self.setResult('colormap1', results[1])
+ self.setResult('colormap2', results[2])
+ self.setResult('colormap3', results[3])
+ self.setResult('colormap4', results[4])
+ self.setResult('colormap5', results[5])
+ self.setResult('colormap6', results[6])
+
+class InsertFieldsIntoBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.InsertFieldsIntoBundleAlg()
+ if self.hasInputFromPort('p_field1_name') :
+ p.set_p_field1_name(self.getInputFromPort('p_field1_name'))
+ if self.hasInputFromPort('p_field2_name') :
+ p.set_p_field2_name(self.getInputFromPort('p_field2_name'))
+ if self.hasInputFromPort('p_field3_name') :
+ p.set_p_field3_name(self.getInputFromPort('p_field3_name'))
+ if self.hasInputFromPort('p_field4_name') :
+ p.set_p_field4_name(self.getInputFromPort('p_field4_name'))
+ if self.hasInputFromPort('p_field5_name') :
+ p.set_p_field5_name(self.getInputFromPort('p_field5_name'))
+ if self.hasInputFromPort('p_field6_name') :
+ p.set_p_field6_name(self.getInputFromPort('p_field6_name'))
+ if self.hasInputFromPort('p_replace1') :
+ p.set_p_replace1(self.getInputFromPort('p_replace1'))
+ if self.hasInputFromPort('p_replace2') :
+ p.set_p_replace2(self.getInputFromPort('p_replace2'))
+ if self.hasInputFromPort('p_replace3') :
+ p.set_p_replace3(self.getInputFromPort('p_replace3'))
+ if self.hasInputFromPort('p_replace4') :
+ p.set_p_replace4(self.getInputFromPort('p_replace4'))
+ if self.hasInputFromPort('p_replace5') :
+ p.set_p_replace5(self.getInputFromPort('p_replace5'))
+ if self.hasInputFromPort('p_replace6') :
+ p.set_p_replace6(self.getInputFromPort('p_replace6'))
+ if self.hasInputFromPort('p_bundlename') :
+ p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ field1 = 0
+ if self.hasInputFromPort('field1') :
+ field1 = self.getInputFromPort('field1')
+ field2 = 0
+ if self.hasInputFromPort('field2') :
+ field2 = self.getInputFromPort('field2')
+ field3 = 0
+ if self.hasInputFromPort('field3') :
+ field3 = self.getInputFromPort('field3')
+ field4 = 0
+ if self.hasInputFromPort('field4') :
+ field4 = self.getInputFromPort('field4')
+ field5 = 0
+ if self.hasInputFromPort('field5') :
+ field5 = self.getInputFromPort('field5')
+ field6 = 0
+ if self.hasInputFromPort('field6') :
+ field6 = self.getInputFromPort('field6')
+ results = p.execute(bundle, field1, field2, field3, field4, field5, field6)
+ self.setResult('bundle', results)
+
+class GetFieldsFromBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.GetFieldsFromBundleAlg()
+ if self.hasInputFromPort('p_field1_name') :
+ p.set_p_field1_name(self.getInputFromPort('p_field1_name'))
+ if self.hasInputFromPort('p_field2_name') :
+ p.set_p_field2_name(self.getInputFromPort('p_field2_name'))
+ if self.hasInputFromPort('p_field3_name') :
+ p.set_p_field3_name(self.getInputFromPort('p_field3_name'))
+ if self.hasInputFromPort('p_field4_name') :
+ p.set_p_field4_name(self.getInputFromPort('p_field4_name'))
+ if self.hasInputFromPort('p_field5_name') :
+ p.set_p_field5_name(self.getInputFromPort('p_field5_name'))
+ if self.hasInputFromPort('p_field6_name') :
+ p.set_p_field6_name(self.getInputFromPort('p_field6_name'))
+ if self.hasInputFromPort('p_field_selection') :
+ p.set_p_field_selection(self.getInputFromPort('p_field_selection'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ results = p.execute(bundle)
+ self.setResult('bundle', results[0])
+ self.setResult('field1', results[1])
+ self.setResult('field2', results[2])
+ self.setResult('field3', results[3])
+ self.setResult('field4', results[4])
+ self.setResult('field5', results[5])
+ self.setResult('field6', results[6])
+
+class InsertColorMap2sIntoBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.InsertColorMap2sIntoBundleAlg()
+ if self.hasInputFromPort('p_colormap21_name') :
+ p.set_p_colormap21_name(self.getInputFromPort('p_colormap21_name'))
+ if self.hasInputFromPort('p_colormap22_name') :
+ p.set_p_colormap22_name(self.getInputFromPort('p_colormap22_name'))
+ if self.hasInputFromPort('p_colormap23_name') :
+ p.set_p_colormap23_name(self.getInputFromPort('p_colormap23_name'))
+ if self.hasInputFromPort('p_colormap24_name') :
+ p.set_p_colormap24_name(self.getInputFromPort('p_colormap24_name'))
+ if self.hasInputFromPort('p_colormap25_name') :
+ p.set_p_colormap25_name(self.getInputFromPort('p_colormap25_name'))
+ if self.hasInputFromPort('p_colormap26_name') :
+ p.set_p_colormap26_name(self.getInputFromPort('p_colormap26_name'))
+ if self.hasInputFromPort('p_replace1') :
+ p.set_p_replace1(self.getInputFromPort('p_replace1'))
+ if self.hasInputFromPort('p_replace2') :
+ p.set_p_replace2(self.getInputFromPort('p_replace2'))
+ if self.hasInputFromPort('p_replace3') :
+ p.set_p_replace3(self.getInputFromPort('p_replace3'))
+ if self.hasInputFromPort('p_replace4') :
+ p.set_p_replace4(self.getInputFromPort('p_replace4'))
+ if self.hasInputFromPort('p_replace5') :
+ p.set_p_replace5(self.getInputFromPort('p_replace5'))
+ if self.hasInputFromPort('p_replace6') :
+ p.set_p_replace6(self.getInputFromPort('p_replace6'))
+ if self.hasInputFromPort('p_bundlename') :
+ p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ colormap21 = 0
+ if self.hasInputFromPort('colormap21') :
+ colormap21 = self.getInputFromPort('colormap21')
+ colormap22 = 0
+ if self.hasInputFromPort('colormap22') :
+ colormap22 = self.getInputFromPort('colormap22')
+ colormap23 = 0
+ if self.hasInputFromPort('colormap23') :
+ colormap23 = self.getInputFromPort('colormap23')
+ colormap24 = 0
+ if self.hasInputFromPort('colormap24') :
+ colormap24 = self.getInputFromPort('colormap24')
+ colormap25 = 0
+ if self.hasInputFromPort('colormap25') :
+ colormap25 = self.getInputFromPort('colormap25')
+ colormap26 = 0
+ if self.hasInputFromPort('colormap26') :
+ colormap26 = self.getInputFromPort('colormap26')
+ results = p.execute(bundle, colormap21, colormap22, colormap23, colormap24, colormap25, colormap26)
+ self.setResult('bundle', results)
+
+class GetBundlesFromBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.GetBundlesFromBundleAlg()
+ if self.hasInputFromPort('p_bundle1_name') :
+ p.set_p_bundle1_name(self.getInputFromPort('p_bundle1_name'))
+ if self.hasInputFromPort('p_bundle2_name') :
+ p.set_p_bundle2_name(self.getInputFromPort('p_bundle2_name'))
+ if self.hasInputFromPort('p_bundle3_name') :
+ p.set_p_bundle3_name(self.getInputFromPort('p_bundle3_name'))
+ if self.hasInputFromPort('p_bundle4_name') :
+ p.set_p_bundle4_name(self.getInputFromPort('p_bundle4_name'))
+ if self.hasInputFromPort('p_bundle5_name') :
+ p.set_p_bundle5_name(self.getInputFromPort('p_bundle5_name'))
+ if self.hasInputFromPort('p_bundle6_name') :
+ p.set_p_bundle6_name(self.getInputFromPort('p_bundle6_name'))
+ if self.hasInputFromPort('p_bundle_selection') :
+ p.set_p_bundle_selection(self.getInputFromPort('p_bundle_selection'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ results = p.execute(bundle)
+ self.setResult('bundle', results[0])
+ self.setResult('bundle1', results[1])
+ self.setResult('bundle2', results[2])
+ self.setResult('bundle3', results[3])
+ self.setResult('bundle4', results[4])
+ self.setResult('bundle5', results[5])
+ self.setResult('bundle6', results[6])
+
+class GetPathsFromBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.GetPathsFromBundleAlg()
+ if self.hasInputFromPort('p_path1_name') :
+ p.set_p_path1_name(self.getInputFromPort('p_path1_name'))
+ if self.hasInputFromPort('p_path2_name') :
+ p.set_p_path2_name(self.getInputFromPort('p_path2_name'))
+ if self.hasInputFromPort('p_path3_name') :
+ p.set_p_path3_name(self.getInputFromPort('p_path3_name'))
+ if self.hasInputFromPort('p_path4_name') :
+ p.set_p_path4_name(self.getInputFromPort('p_path4_name'))
+ if self.hasInputFromPort('p_path5_name') :
+ p.set_p_path5_name(self.getInputFromPort('p_path5_name'))
+ if self.hasInputFromPort('p_path6_name') :
+ p.set_p_path6_name(self.getInputFromPort('p_path6_name'))
+ if self.hasInputFromPort('p_path_selection') :
+ p.set_p_path_selection(self.getInputFromPort('p_path_selection'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ results = p.execute(bundle)
+ self.setResult('bundle', results[0])
+ self.setResult('path1', results[1])
+ self.setResult('path2', results[2])
+ self.setResult('path3', results[3])
+ self.setResult('path4', results[4])
+ self.setResult('path5', results[5])
+ self.setResult('path6', results[6])
+
+class InsertStringsIntoBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.InsertStringsIntoBundleAlg()
+ if self.hasInputFromPort('p_string1_name') :
+ p.set_p_string1_name(self.getInputFromPort('p_string1_name'))
+ if self.hasInputFromPort('p_string2_name') :
+ p.set_p_string2_name(self.getInputFromPort('p_string2_name'))
+ if self.hasInputFromPort('p_string3_name') :
+ p.set_p_string3_name(self.getInputFromPort('p_string3_name'))
+ if self.hasInputFromPort('p_string4_name') :
+ p.set_p_string4_name(self.getInputFromPort('p_string4_name'))
+ if self.hasInputFromPort('p_string5_name') :
+ p.set_p_string5_name(self.getInputFromPort('p_string5_name'))
+ if self.hasInputFromPort('p_string6_name') :
+ p.set_p_string6_name(self.getInputFromPort('p_string6_name'))
+ if self.hasInputFromPort('p_replace1') :
+ p.set_p_replace1(self.getInputFromPort('p_replace1'))
+ if self.hasInputFromPort('p_replace2') :
+ p.set_p_replace2(self.getInputFromPort('p_replace2'))
+ if self.hasInputFromPort('p_replace3') :
+ p.set_p_replace3(self.getInputFromPort('p_replace3'))
+ if self.hasInputFromPort('p_replace4') :
+ p.set_p_replace4(self.getInputFromPort('p_replace4'))
+ if self.hasInputFromPort('p_replace5') :
+ p.set_p_replace5(self.getInputFromPort('p_replace5'))
+ if self.hasInputFromPort('p_replace6') :
+ p.set_p_replace6(self.getInputFromPort('p_replace6'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ string1 = ''
+ if self.hasInputFromPort('string1') :
+ string1 = self.getInputFromPort('string1')
+ string2 = ''
+ if self.hasInputFromPort('string2') :
+ string2 = self.getInputFromPort('string2')
+ string3 = ''
+ if self.hasInputFromPort('string3') :
+ string3 = self.getInputFromPort('string3')
+ string4 = ''
+ if self.hasInputFromPort('string4') :
+ string4 = self.getInputFromPort('string4')
+ string5 = ''
+ if self.hasInputFromPort('string5') :
+ string5 = self.getInputFromPort('string5')
+ string6 = ''
+ if self.hasInputFromPort('string6') :
+ string6 = self.getInputFromPort('string6')
+ results = p.execute(bundle, string1, string2, string3, string4, string5, string6)
+ self.setResult('bundle', results)
+
+class GetNrrdsFromBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.GetNrrdsFromBundleAlg()
+ if self.hasInputFromPort('p_nrrd1_name') :
+ p.set_p_nrrd1_name(self.getInputFromPort('p_nrrd1_name'))
+ if self.hasInputFromPort('p_nrrd2_name') :
+ p.set_p_nrrd2_name(self.getInputFromPort('p_nrrd2_name'))
+ if self.hasInputFromPort('p_nrrd3_name') :
+ p.set_p_nrrd3_name(self.getInputFromPort('p_nrrd3_name'))
+ if self.hasInputFromPort('p_nrrd4_name') :
+ p.set_p_nrrd4_name(self.getInputFromPort('p_nrrd4_name'))
+ if self.hasInputFromPort('p_nrrd5_name') :
+ p.set_p_nrrd5_name(self.getInputFromPort('p_nrrd5_name'))
+ if self.hasInputFromPort('p_nrrd6_name') :
+ p.set_p_nrrd6_name(self.getInputFromPort('p_nrrd6_name'))
+ if self.hasInputFromPort('p_transposenrrd1') :
+ p.set_p_transposenrrd1(self.getInputFromPort('p_transposenrrd1'))
+ if self.hasInputFromPort('p_transposenrrd2') :
+ p.set_p_transposenrrd2(self.getInputFromPort('p_transposenrrd2'))
+ if self.hasInputFromPort('p_transposenrrd3') :
+ p.set_p_transposenrrd3(self.getInputFromPort('p_transposenrrd3'))
+ if self.hasInputFromPort('p_transposenrrd4') :
+ p.set_p_transposenrrd4(self.getInputFromPort('p_transposenrrd4'))
+ if self.hasInputFromPort('p_transposenrrd5') :
+ p.set_p_transposenrrd5(self.getInputFromPort('p_transposenrrd5'))
+ if self.hasInputFromPort('p_transposenrrd6') :
+ p.set_p_transposenrrd6(self.getInputFromPort('p_transposenrrd6'))
+ if self.hasInputFromPort('p_nrrd_selection') :
+ p.set_p_nrrd_selection(self.getInputFromPort('p_nrrd_selection'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ results = p.execute(bundle)
+ self.setResult('bundle', results[0])
+ self.setResult('nrrd1', results[1])
+ self.setResult('nrrd2', results[2])
+ self.setResult('nrrd3', results[3])
+ self.setResult('nrrd4', results[4])
+ self.setResult('nrrd5', results[5])
+ self.setResult('nrrd6', results[6])
+
+class GetMatricesFromBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.GetMatricesFromBundleAlg()
+ if self.hasInputFromPort('p_matrix1_name') :
+ p.set_p_matrix1_name(self.getInputFromPort('p_matrix1_name'))
+ if self.hasInputFromPort('p_matrix2_name') :
+ p.set_p_matrix2_name(self.getInputFromPort('p_matrix2_name'))
+ if self.hasInputFromPort('p_matrix3_name') :
+ p.set_p_matrix3_name(self.getInputFromPort('p_matrix3_name'))
+ if self.hasInputFromPort('p_matrix4_name') :
+ p.set_p_matrix4_name(self.getInputFromPort('p_matrix4_name'))
+ if self.hasInputFromPort('p_matrix5_name') :
+ p.set_p_matrix5_name(self.getInputFromPort('p_matrix5_name'))
+ if self.hasInputFromPort('p_matrix6_name') :
+ p.set_p_matrix6_name(self.getInputFromPort('p_matrix6_name'))
+ if self.hasInputFromPort('p_transposenrrd1') :
+ p.set_p_transposenrrd1(self.getInputFromPort('p_transposenrrd1'))
+ if self.hasInputFromPort('p_transposenrrd2') :
+ p.set_p_transposenrrd2(self.getInputFromPort('p_transposenrrd2'))
+ if self.hasInputFromPort('p_transposenrrd3') :
+ p.set_p_transposenrrd3(self.getInputFromPort('p_transposenrrd3'))
+ if self.hasInputFromPort('p_transposenrrd4') :
+ p.set_p_transposenrrd4(self.getInputFromPort('p_transposenrrd4'))
+ if self.hasInputFromPort('p_transposenrrd5') :
+ p.set_p_transposenrrd5(self.getInputFromPort('p_transposenrrd5'))
+ if self.hasInputFromPort('p_transposenrrd6') :
+ p.set_p_transposenrrd6(self.getInputFromPort('p_transposenrrd6'))
+ if self.hasInputFromPort('p_matrix_selection') :
+ p.set_p_matrix_selection(self.getInputFromPort('p_matrix_selection'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ results = p.execute(bundle)
+ self.setResult('bundle', results[0])
+ self.setResult('matrix1', results[1])
+ self.setResult('matrix2', results[2])
+ self.setResult('matrix3', results[3])
+ self.setResult('matrix4', results[4])
+ self.setResult('matrix5', results[5])
+ self.setResult('matrix6', results[6])
+
+class JoinBundles(Bundle) :
+ def compute(self) :
+ p = sr_py.JoinBundlesAlg()
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ results = p.execute(bundle)
+ self.setResult('bundle', results)
+
+class ReportBundleInfo(Bundle) :
+ def compute(self) :
+ p = sr_py.ReportBundleInfoAlg()
+ if self.hasInputFromPort('p_tclinfostring') :
+ p.set_p_tclinfostring(self.getInputFromPort('p_tclinfostring'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ results = p.execute(bundle)
+
+class InsertPathsIntoBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.InsertPathsIntoBundleAlg()
+ if self.hasInputFromPort('p_path1_name') :
+ p.set_p_path1_name(self.getInputFromPort('p_path1_name'))
+ if self.hasInputFromPort('p_path2_name') :
+ p.set_p_path2_name(self.getInputFromPort('p_path2_name'))
+ if self.hasInputFromPort('p_path3_name') :
+ p.set_p_path3_name(self.getInputFromPort('p_path3_name'))
+ if self.hasInputFromPort('p_path4_name') :
+ p.set_p_path4_name(self.getInputFromPort('p_path4_name'))
+ if self.hasInputFromPort('p_path5_name') :
+ p.set_p_path5_name(self.getInputFromPort('p_path5_name'))
+ if self.hasInputFromPort('p_path6_name') :
+ p.set_p_path6_name(self.getInputFromPort('p_path6_name'))
+ if self.hasInputFromPort('p_replace1') :
+ p.set_p_replace1(self.getInputFromPort('p_replace1'))
+ if self.hasInputFromPort('p_replace2') :
+ p.set_p_replace2(self.getInputFromPort('p_replace2'))
+ if self.hasInputFromPort('p_replace3') :
+ p.set_p_replace3(self.getInputFromPort('p_replace3'))
+ if self.hasInputFromPort('p_replace4') :
+ p.set_p_replace4(self.getInputFromPort('p_replace4'))
+ if self.hasInputFromPort('p_replace5') :
+ p.set_p_replace5(self.getInputFromPort('p_replace5'))
+ if self.hasInputFromPort('p_replace6') :
+ p.set_p_replace6(self.getInputFromPort('p_replace6'))
+ if self.hasInputFromPort('p_bundlename') :
+ p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ path1 = 0
+ if self.hasInputFromPort('path1') :
+ path1 = self.getInputFromPort('path1')
+ path2 = 0
+ if self.hasInputFromPort('path2') :
+ path2 = self.getInputFromPort('path2')
+ path3 = 0
+ if self.hasInputFromPort('path3') :
+ path3 = self.getInputFromPort('path3')
+ path4 = 0
+ if self.hasInputFromPort('path4') :
+ path4 = self.getInputFromPort('path4')
+ path5 = 0
+ if self.hasInputFromPort('path5') :
+ path5 = self.getInputFromPort('path5')
+ path6 = 0
+ if self.hasInputFromPort('path6') :
+ path6 = self.getInputFromPort('path6')
+ results = p.execute(bundle, path1, path2, path3, path4, path5, path6)
+ self.setResult('bundle', results)
+
+class GetColorMap2sFromBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.GetColorMap2sFromBundleAlg()
+ if self.hasInputFromPort('p_colormap21_name') :
+ p.set_p_colormap21_name(self.getInputFromPort('p_colormap21_name'))
+ if self.hasInputFromPort('p_colormap22_name') :
+ p.set_p_colormap22_name(self.getInputFromPort('p_colormap22_name'))
+ if self.hasInputFromPort('p_colormap23_name') :
+ p.set_p_colormap23_name(self.getInputFromPort('p_colormap23_name'))
+ if self.hasInputFromPort('p_colormap24_name') :
+ p.set_p_colormap24_name(self.getInputFromPort('p_colormap24_name'))
+ if self.hasInputFromPort('p_colormap25_name') :
+ p.set_p_colormap25_name(self.getInputFromPort('p_colormap25_name'))
+ if self.hasInputFromPort('p_colormap26_name') :
+ p.set_p_colormap26_name(self.getInputFromPort('p_colormap26_name'))
+ if self.hasInputFromPort('p_colormap2_selection') :
+ p.set_p_colormap2_selection(self.getInputFromPort('p_colormap2_selection'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ results = p.execute(bundle)
+ self.setResult('bundle', results[0])
+ self.setResult('colormap21', results[1])
+ self.setResult('colormap22', results[2])
+ self.setResult('colormap23', results[3])
+ self.setResult('colormap24', results[4])
+ self.setResult('colormap25', results[5])
+ self.setResult('colormap26', results[6])
+
+class InsertMatricesIntoBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.InsertMatricesIntoBundleAlg()
+ if self.hasInputFromPort('p_matrix1_name') :
+ p.set_p_matrix1_name(self.getInputFromPort('p_matrix1_name'))
+ if self.hasInputFromPort('p_matrix2_name') :
+ p.set_p_matrix2_name(self.getInputFromPort('p_matrix2_name'))
+ if self.hasInputFromPort('p_matrix3_name') :
+ p.set_p_matrix3_name(self.getInputFromPort('p_matrix3_name'))
+ if self.hasInputFromPort('p_matrix4_name') :
+ p.set_p_matrix4_name(self.getInputFromPort('p_matrix4_name'))
+ if self.hasInputFromPort('p_matrix5_name') :
+ p.set_p_matrix5_name(self.getInputFromPort('p_matrix5_name'))
+ if self.hasInputFromPort('p_matrix6_name') :
+ p.set_p_matrix6_name(self.getInputFromPort('p_matrix6_name'))
+ if self.hasInputFromPort('p_replace1') :
+ p.set_p_replace1(self.getInputFromPort('p_replace1'))
+ if self.hasInputFromPort('p_replace2') :
+ p.set_p_replace2(self.getInputFromPort('p_replace2'))
+ if self.hasInputFromPort('p_replace3') :
+ p.set_p_replace3(self.getInputFromPort('p_replace3'))
+ if self.hasInputFromPort('p_replace4') :
+ p.set_p_replace4(self.getInputFromPort('p_replace4'))
+ if self.hasInputFromPort('p_replace5') :
+ p.set_p_replace5(self.getInputFromPort('p_replace5'))
+ if self.hasInputFromPort('p_replace6') :
+ p.set_p_replace6(self.getInputFromPort('p_replace6'))
+ if self.hasInputFromPort('p_bundlename') :
+ p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ matrix1 = 0
+ if self.hasInputFromPort('matrix1') :
+ matrix1 = self.getInputFromPort('matrix1')
+ matrix2 = 0
+ if self.hasInputFromPort('matrix2') :
+ matrix2 = self.getInputFromPort('matrix2')
+ matrix3 = 0
+ if self.hasInputFromPort('matrix3') :
+ matrix3 = self.getInputFromPort('matrix3')
+ matrix4 = 0
+ if self.hasInputFromPort('matrix4') :
+ matrix4 = self.getInputFromPort('matrix4')
+ matrix5 = 0
+ if self.hasInputFromPort('matrix5') :
+ matrix5 = self.getInputFromPort('matrix5')
+ matrix6 = 0
+ if self.hasInputFromPort('matrix6') :
+ matrix6 = self.getInputFromPort('matrix6')
+ results = p.execute(bundle, matrix1, matrix2, matrix3, matrix4, matrix5, matrix6)
+ self.setResult('bundle', results)
+
+class InsertNrrdsIntoBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.InsertNrrdsIntoBundleAlg()
+ if self.hasInputFromPort('p_nrrd1_name') :
+ p.set_p_nrrd1_name(self.getInputFromPort('p_nrrd1_name'))
+ if self.hasInputFromPort('p_nrrd2_name') :
+ p.set_p_nrrd2_name(self.getInputFromPort('p_nrrd2_name'))
+ if self.hasInputFromPort('p_nrrd3_name') :
+ p.set_p_nrrd3_name(self.getInputFromPort('p_nrrd3_name'))
+ if self.hasInputFromPort('p_nrrd4_name') :
+ p.set_p_nrrd4_name(self.getInputFromPort('p_nrrd4_name'))
+ if self.hasInputFromPort('p_nrrd5_name') :
+ p.set_p_nrrd5_name(self.getInputFromPort('p_nrrd5_name'))
+ if self.hasInputFromPort('p_nrrd6_name') :
+ p.set_p_nrrd6_name(self.getInputFromPort('p_nrrd6_name'))
+ if self.hasInputFromPort('p_replace1') :
+ p.set_p_replace1(self.getInputFromPort('p_replace1'))
+ if self.hasInputFromPort('p_replace2') :
+ p.set_p_replace2(self.getInputFromPort('p_replace2'))
+ if self.hasInputFromPort('p_replace3') :
+ p.set_p_replace3(self.getInputFromPort('p_replace3'))
+ if self.hasInputFromPort('p_replace4') :
+ p.set_p_replace4(self.getInputFromPort('p_replace4'))
+ if self.hasInputFromPort('p_replace5') :
+ p.set_p_replace5(self.getInputFromPort('p_replace5'))
+ if self.hasInputFromPort('p_replace6') :
+ p.set_p_replace6(self.getInputFromPort('p_replace6'))
+ if self.hasInputFromPort('p_bundlename') :
+ p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ nrrd1 = 0
+ if self.hasInputFromPort('nrrd1') :
+ nrrd1 = self.getInputFromPort('nrrd1')
+ nrrd2 = 0
+ if self.hasInputFromPort('nrrd2') :
+ nrrd2 = self.getInputFromPort('nrrd2')
+ nrrd3 = 0
+ if self.hasInputFromPort('nrrd3') :
+ nrrd3 = self.getInputFromPort('nrrd3')
+ nrrd4 = 0
+ if self.hasInputFromPort('nrrd4') :
+ nrrd4 = self.getInputFromPort('nrrd4')
+ nrrd5 = 0
+ if self.hasInputFromPort('nrrd5') :
+ nrrd5 = self.getInputFromPort('nrrd5')
+ nrrd6 = 0
+ if self.hasInputFromPort('nrrd6') :
+ nrrd6 = self.getInputFromPort('nrrd6')
+ results = p.execute(bundle, nrrd1, nrrd2, nrrd3, nrrd4, nrrd5, nrrd6)
+ self.setResult('bundle', results)
+
+class InsertBundlesIntoBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.InsertBundlesIntoBundleAlg()
+ if self.hasInputFromPort('p_bundle1_name') :
+ p.set_p_bundle1_name(self.getInputFromPort('p_bundle1_name'))
+ if self.hasInputFromPort('p_bundle2_name') :
+ p.set_p_bundle2_name(self.getInputFromPort('p_bundle2_name'))
+ if self.hasInputFromPort('p_bundle3_name') :
+ p.set_p_bundle3_name(self.getInputFromPort('p_bundle3_name'))
+ if self.hasInputFromPort('p_bundle4_name') :
+ p.set_p_bundle4_name(self.getInputFromPort('p_bundle4_name'))
+ if self.hasInputFromPort('p_bundle5_name') :
+ p.set_p_bundle5_name(self.getInputFromPort('p_bundle5_name'))
+ if self.hasInputFromPort('p_bundle6_name') :
+ p.set_p_bundle6_name(self.getInputFromPort('p_bundle6_name'))
+ if self.hasInputFromPort('p_replace1') :
+ p.set_p_replace1(self.getInputFromPort('p_replace1'))
+ if self.hasInputFromPort('p_replace2') :
+ p.set_p_replace2(self.getInputFromPort('p_replace2'))
+ if self.hasInputFromPort('p_replace3') :
+ p.set_p_replace3(self.getInputFromPort('p_replace3'))
+ if self.hasInputFromPort('p_replace4') :
+ p.set_p_replace4(self.getInputFromPort('p_replace4'))
+ if self.hasInputFromPort('p_replace5') :
+ p.set_p_replace5(self.getInputFromPort('p_replace5'))
+ if self.hasInputFromPort('p_replace6') :
+ p.set_p_replace6(self.getInputFromPort('p_replace6'))
+ if self.hasInputFromPort('p_bundlename') :
+ p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ bundle1 = 0
+ if self.hasInputFromPort('bundle1') :
+ bundle1 = self.getInputFromPort('bundle1')
+ bundle2 = 0
+ if self.hasInputFromPort('bundle2') :
+ bundle2 = self.getInputFromPort('bundle2')
+ bundle3 = 0
+ if self.hasInputFromPort('bundle3') :
+ bundle3 = self.getInputFromPort('bundle3')
+ bundle4 = 0
+ if self.hasInputFromPort('bundle4') :
+ bundle4 = self.getInputFromPort('bundle4')
+ bundle5 = 0
+ if self.hasInputFromPort('bundle5') :
+ bundle5 = self.getInputFromPort('bundle5')
+ bundle6 = 0
+ if self.hasInputFromPort('bundle6') :
+ bundle6 = self.getInputFromPort('bundle6')
+ results = p.execute(bundle, bundle1, bundle2, bundle3, bundle4, bundle5, bundle6)
+ self.setResult('bundle', results)
+
+class GetStringsFromBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.GetStringsFromBundleAlg()
+ if self.hasInputFromPort('p_string1_name') :
+ p.set_p_string1_name(self.getInputFromPort('p_string1_name'))
+ if self.hasInputFromPort('p_string2_name') :
+ p.set_p_string2_name(self.getInputFromPort('p_string2_name'))
+ if self.hasInputFromPort('p_string3_name') :
+ p.set_p_string3_name(self.getInputFromPort('p_string3_name'))
+ if self.hasInputFromPort('p_string4_name') :
+ p.set_p_string4_name(self.getInputFromPort('p_string4_name'))
+ if self.hasInputFromPort('p_string5_name') :
+ p.set_p_string5_name(self.getInputFromPort('p_string5_name'))
+ if self.hasInputFromPort('p_string6_name') :
+ p.set_p_string6_name(self.getInputFromPort('p_string6_name'))
+ if self.hasInputFromPort('p_string_selection') :
+ p.set_p_string_selection(self.getInputFromPort('p_string_selection'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ results = p.execute(bundle)
+ self.setResult('bundle', results[0])
+ self.setResult('string1', results[1])
+ self.setResult('string2', results[2])
+ self.setResult('string3', results[3])
+ self.setResult('string4', results[4])
+ self.setResult('string5', results[5])
+ self.setResult('string6', results[6])
+
+class InsertColorMapsIntoBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.InsertColorMapsIntoBundleAlg()
+ if self.hasInputFromPort('p_colormap1_name') :
+ p.set_p_colormap1_name(self.getInputFromPort('p_colormap1_name'))
+ if self.hasInputFromPort('p_colormap2_name') :
+ p.set_p_colormap2_name(self.getInputFromPort('p_colormap2_name'))
+ if self.hasInputFromPort('p_colormap3_name') :
+ p.set_p_colormap3_name(self.getInputFromPort('p_colormap3_name'))
+ if self.hasInputFromPort('p_colormap4_name') :
+ p.set_p_colormap4_name(self.getInputFromPort('p_colormap4_name'))
+ if self.hasInputFromPort('p_colormap5_name') :
+ p.set_p_colormap5_name(self.getInputFromPort('p_colormap5_name'))
+ if self.hasInputFromPort('p_colormap6_name') :
+ p.set_p_colormap6_name(self.getInputFromPort('p_colormap6_name'))
+ if self.hasInputFromPort('p_replace1') :
+ p.set_p_replace1(self.getInputFromPort('p_replace1'))
+ if self.hasInputFromPort('p_replace2') :
+ p.set_p_replace2(self.getInputFromPort('p_replace2'))
+ if self.hasInputFromPort('p_replace3') :
+ p.set_p_replace3(self.getInputFromPort('p_replace3'))
+ if self.hasInputFromPort('p_replace4') :
+ p.set_p_replace4(self.getInputFromPort('p_replace4'))
+ if self.hasInputFromPort('p_replace5') :
+ p.set_p_replace5(self.getInputFromPort('p_replace5'))
+ if self.hasInputFromPort('p_replace6') :
+ p.set_p_replace6(self.getInputFromPort('p_replace6'))
+ if self.hasInputFromPort('p_bundlename') :
+ p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
+ bundle = 0
+ if self.hasInputFromPort('bundle') :
+ bundle = self.getInputFromPort('bundle')
+ colormap1 = 0
+ if self.hasInputFromPort('colormap1') :
+ colormap1 = self.getInputFromPort('colormap1')
+ colormap2 = 0
+ if self.hasInputFromPort('colormap2') :
+ colormap2 = self.getInputFromPort('colormap2')
+ colormap3 = 0
+ if self.hasInputFromPort('colormap3') :
+ colormap3 = self.getInputFromPort('colormap3')
+ colormap4 = 0
+ if self.hasInputFromPort('colormap4') :
+ colormap4 = self.getInputFromPort('colormap4')
+ colormap5 = 0
+ if self.hasInputFromPort('colormap5') :
+ colormap5 = self.getInputFromPort('colormap5')
+ colormap6 = 0
+ if self.hasInputFromPort('colormap6') :
+ colormap6 = self.getInputFromPort('colormap6')
+ results = p.execute(bundle, colormap1, colormap2, colormap3, colormap4, colormap5, colormap6)
+ self.setResult('bundle', results)
+
+class CreateParameterBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.CreateParameterBundleAlg()
+ if self.hasInputFromPort('p_data') :
+ p.set_p_data(self.getInputFromPort('p_data'))
+ if self.hasInputFromPort('p_new_field_count') :
+ p.set_p_new_field_count(self.getInputFromPort('p_new_field_count'))
+ if self.hasInputFromPort('p_update_all') :
+ p.set_p_update_all(self.getInputFromPort('p_update_all'))
+ results = p.execute()
+ self.setResult('ParameterList', results)
+
+class InsertEnvironmentIntoBundle(Bundle) :
+ def compute(self) :
+ p = sr_py.InsertEnvironmentIntoBundleAlg()
+ results = p.execute()
+ self.setResult('Environment', results)
+
+class ShowColorMap(Visualization) :
+ def compute(self) :
+ p = sr_py.ShowColorMapAlg()
+ if self.hasInputFromPort('p_length') :
+ p.set_p_length(self.getInputFromPort('p_length'))
+ if self.hasInputFromPort('p_side') :
+ p.set_p_side(self.getInputFromPort('p_side'))
+ if self.hasInputFromPort('p_numlabels') :
+ p.set_p_numlabels(self.getInputFromPort('p_numlabels'))
+ if self.hasInputFromPort('p_scale') :
+ p.set_p_scale(self.getInputFromPort('p_scale'))
+ if self.hasInputFromPort('p_numsigdigits') :
+ p.set_p_numsigdigits(self.getInputFromPort('p_numsigdigits'))
+ if self.hasInputFromPort('p_units') :
+ p.set_p_units(self.getInputFromPort('p_units'))
+ if self.hasInputFromPort('p_color_r') :
+ p.set_p_color_r(self.getInputFromPort('p_color_r'))
+ if self.hasInputFromPort('p_color_g') :
+ p.set_p_color_g(self.getInputFromPort('p_color_g'))
+ if self.hasInputFromPort('p_color_b') :
+ p.set_p_color_b(self.getInputFromPort('p_color_b'))
+ if self.hasInputFromPort('p_text_fontsize') :
+ p.set_p_text_fontsize(self.getInputFromPort('p_text_fontsize'))
+ if self.hasInputFromPort('p_extra_padding') :
+ p.set_p_extra_padding(self.getInputFromPort('p_extra_padding'))
+ ColorMap = 0
+ if self.hasInputFromPort('ColorMap') :
+ ColorMap = self.getInputFromPort('ColorMap')
+ results = p.execute(ColorMap)
+ self.setResult('Geometry', results)
+
+class CreateAndEditColorMap2D(Visualization) :
+ def compute(self) :
+ p = sr_py.CreateAndEditColorMap2DAlg()
+ if self.hasInputFromPort('p_histo') :
+ p.set_p_histo(self.getInputFromPort('p_histo'))
+ if self.hasInputFromPort('p_selected_widget') :
+ p.set_p_selected_widget(self.getInputFromPort('p_selected_widget'))
+ if self.hasInputFromPort('p_selected_object') :
+ p.set_p_selected_object(self.getInputFromPort('p_selected_object'))
+ if self.hasInputFromPort('p_num_entries') :
+ p.set_p_num_entries(self.getInputFromPort('p_num_entries'))
+ if self.hasInputFromPort('p_marker') :
+ p.set_p_marker(self.getInputFromPort('p_marker'))
+ if self.hasInputFromPort('p_cm2view_targ') :
+ p.set_p_cm2view_targ(self.getInputFromPort('p_cm2view_targ'))
+ if self.hasInputFromPort('p_id') :
+ p.set_p_id(self.getInputFromPort('p_id'))
+ Input_Colormap = 0
+ if self.hasInputFromPort('Input Colormap') :
+ Input_Colormap = self.getInputFromPort('Input Colormap')
+ Histogram = 0
+ if self.hasInputFromPort('Histogram') :
+ Histogram = self.getInputFromPort('Histogram')
+ results = p.execute(Input_Colormap, Histogram)
+ self.setResult('Output Colormap', results)
+
+class ShowField(Visualization) :
+ def compute(self) :
+ p = sr_py.ShowFieldAlg()
+ if self.hasInputFromPort('p_nodes_on') :
+ p.set_p_nodes_on(self.getInputFromPort('p_nodes_on'))
+ if self.hasInputFromPort('p_nodes_transparency') :
+ p.set_p_nodes_transparency(self.getInputFromPort('p_nodes_transparency'))
+ if self.hasInputFromPort('p_nodes_color_type') :
+ p.set_p_nodes_color_type(self.getInputFromPort('p_nodes_color_type'))
+ if self.hasInputFromPort('p_nodes_display_type') :
+ p.set_p_nodes_display_type(self.getInputFromPort('p_nodes_display_type'))
+ if self.hasInputFromPort('p_edges_on') :
+ p.set_p_edges_on(self.getInputFromPort('p_edges_on'))
+ if self.hasInputFromPort('p_edges_transparency') :
+ p.set_p_edges_transparency(self.getInputFromPort('p_edges_transparency'))
+ if self.hasInputFromPort('p_edges_color_type') :
+ p.set_p_edges_color_type(self.getInputFromPort('p_edges_color_type'))
+ if self.hasInputFromPort('p_edges_display_type') :
+ p.set_p_edges_display_type(self.getInputFromPort('p_edges_display_type'))
+ if self.hasInputFromPort('p_faces_on') :
+ p.set_p_faces_on(self.getInputFromPort('p_faces_on'))
+ if self.hasInputFromPort('p_faces_transparency') :
+ p.set_p_faces_transparency(self.getInputFromPort('p_faces_transparency'))
+ if self.hasInputFromPort('p_faces_color_type') :
+ p.set_p_faces_color_type(self.getInputFromPort('p_faces_color_type'))
+ if self.hasInputFromPort('p_faces_normals') :
+ p.set_p_faces_normals(self.getInputFromPort('p_faces_normals'))
+ if self.hasInputFromPort('p_faces_usetexture') :
+ p.set_p_faces_usetexture(self.getInputFromPort('p_faces_usetexture'))
+ if self.hasInputFromPort('p_text_on') :
+ p.set_p_text_on(self.getInputFromPort('p_text_on'))
+ if self.hasInputFromPort('p_text_color_type') :
+ p.set_p_text_color_type(self.getInputFromPort('p_text_color_type'))
+ if self.hasInputFromPort('p_text_color_r') :
+ p.set_p_text_color_r(self.getInputFromPort('p_text_color_r'))
+ if self.hasInputFromPort('p_text_color_g') :
+ p.set_p_text_color_g(self.getInputFromPort('p_text_color_g'))
+ if self.hasInputFromPort('p_text_color_b') :
+ p.set_p_text_color_b(self.getInputFromPort('p_text_color_b'))
+ if self.hasInputFromPort('p_text_backface_cull') :
+ p.set_p_text_backface_cull(self.getInputFromPort('p_text_backface_cull'))
+ if self.hasInputFromPort('p_text_always_visible') :
+ p.set_p_text_always_visible(self.getInputFromPort('p_text_always_visible'))
+ if self.hasInputFromPort('p_text_fontsize') :
+ p.set_p_text_fontsize(self.getInputFromPort('p_text_fontsize'))
+ if self.hasInputFromPort('p_text_precision') :
+ p.set_p_text_precision(self.getInputFromPort('p_text_precision'))
+ if self.hasInputFromPort('p_text_render_locations') :
+ p.set_p_text_render_locations(self.getInputFromPort('p_text_render_locations'))
+ if self.hasInputFromPort('p_text_show_data') :
+ p.set_p_text_show_data(self.getInputFromPort('p_text_show_data'))
+ if self.hasInputFromPort('p_text_show_nodes') :
+ p.set_p_text_show_nodes(self.getInputFromPort('p_text_show_nodes'))
+ if self.hasInputFromPort('p_text_show_edges') :
+ p.set_p_text_show_edges(self.getInputFromPort('p_text_show_edges'))
+ if self.hasInputFromPort('p_text_show_faces') :
+ p.set_p_text_show_faces(self.getInputFromPort('p_text_show_faces'))
+ if self.hasInputFromPort('p_text_show_cells') :
+ p.set_p_text_show_cells(self.getInputFromPort('p_text_show_cells'))
+ if self.hasInputFromPort('p_def_color_r') :
+ p.set_p_def_color_r(self.getInputFromPort('p_def_color_r'))
+ if self.hasInputFromPort('p_def_color_g') :
+ p.set_p_def_color_g(self.getInputFromPort('p_def_color_g'))
+ if self.hasInputFromPort('p_def_color_b') :
+ p.set_p_def_color_b(self.getInputFromPort('p_def_color_b'))
+ if self.hasInputFromPort('p_def_color_a') :
+ p.set_p_def_color_a(self.getInputFromPort('p_def_color_a'))
+ if self.hasInputFromPort('p_nodes_scale') :
+ p.set_p_nodes_scale(self.getInputFromPort('p_nodes_scale'))
+ if self.hasInputFromPort('p_nodes_scaleNV') :
+ p.set_p_nodes_scaleNV(self.getInputFromPort('p_nodes_scaleNV'))
+ if self.hasInputFromPort('p_edges_scale') :
+ p.set_p_edges_scale(self.getInputFromPort('p_edges_scale'))
+ if self.hasInputFromPort('p_edges_scaleNV') :
+ p.set_p_edges_scaleNV(self.getInputFromPort('p_edges_scaleNV'))
+ if self.hasInputFromPort('p_active_tab') :
+ p.set_p_active_tab(self.getInputFromPort('p_active_tab'))
+ if self.hasInputFromPort('p_interactive_mode') :
+ p.set_p_interactive_mode(self.getInputFromPort('p_interactive_mode'))
+ if self.hasInputFromPort('p_show_progress') :
+ p.set_p_show_progress(self.getInputFromPort('p_show_progress'))
+ if self.hasInputFromPort('p_field_name') :
+ p.set_p_field_name(self.getInputFromPort('p_field_name'))
+ if self.hasInputFromPort('p_field_name_override') :
+ p.set_p_field_name_override(self.getInputFromPort('p_field_name_override'))
+ if self.hasInputFromPort('p_nodes_resolution') :
+ p.set_p_nodes_resolution(self.getInputFromPort('p_nodes_resolution'))
+ if self.hasInputFromPort('p_edges_resolution') :
+ p.set_p_edges_resolution(self.getInputFromPort('p_edges_resolution'))
+ if self.hasInputFromPort('p_approx_div') :
+ p.set_p_approx_div(self.getInputFromPort('p_approx_div'))
+ if self.hasInputFromPort('p_use_default_size') :
+ p.set_p_use_default_size(self.getInputFromPort('p_use_default_size'))
+ Mesh = 0
+ if self.hasInputFromPort('Mesh') :
+ Mesh = self.getInputFromPort('Mesh')
+ ColorMap = 0
+ if self.hasInputFromPort('ColorMap') :
+ ColorMap = self.getInputFromPort('ColorMap')
+ results = p.execute(Mesh, ColorMap)
+ self.setResult('Scene Graph', results)
+
+class ExtractIsosurface(Visualization) :
+ def compute(self) :
+ p = sr_py.ExtractIsosurfaceAlg()
+ if self.hasInputFromPort('p_isoval_min') :
+ p.set_p_isoval_min(self.getInputFromPort('p_isoval_min'))
+ if self.hasInputFromPort('p_isoval_max') :
+ p.set_p_isoval_max(self.getInputFromPort('p_isoval_max'))
+ if self.hasInputFromPort('p_isoval') :
+ p.set_p_isoval(self.getInputFromPort('p_isoval'))
+ if self.hasInputFromPort('p_isoval_typed') :
+ p.set_p_isoval_typed(self.getInputFromPort('p_isoval_typed'))
+ if self.hasInputFromPort('p_isoval_quantity') :
+ p.set_p_isoval_quantity(self.getInputFromPort('p_isoval_quantity'))
+ if self.hasInputFromPort('p_quantity_range') :
+ p.set_p_quantity_range(self.getInputFromPort('p_quantity_range'))
+ if self.hasInputFromPort('p_quantity_clusive') :
+ p.set_p_quantity_clusive(self.getInputFromPort('p_quantity_clusive'))
+ if self.hasInputFromPort('p_quantity_min') :
+ p.set_p_quantity_min(self.getInputFromPort('p_quantity_min'))
+ if self.hasInputFromPort('p_quantity_max') :
+ p.set_p_quantity_max(self.getInputFromPort('p_quantity_max'))
+ if self.hasInputFromPort('p_quantity_list') :
+ p.set_p_quantity_list(self.getInputFromPort('p_quantity_list'))
+ if self.hasInputFromPort('p_isoval_list') :
+ p.set_p_isoval_list(self.getInputFromPort('p_isoval_list'))
+ if self.hasInputFromPort('p_matrix_list') :
+ p.set_p_matrix_list(self.getInputFromPort('p_matrix_list'))
+ if self.hasInputFromPort('p_algorithm') :
+ p.set_p_algorithm(self.getInputFromPort('p_algorithm'))
+ if self.hasInputFromPort('p_build_trisurf') :
+ p.set_p_build_trisurf(self.getInputFromPort('p_build_trisurf'))
+ if self.hasInputFromPort('p_build_geom') :
+ p.set_p_build_geom(self.getInputFromPort('p_build_geom'))
+ if self.hasInputFromPort('p_transparency') :
+ p.set_p_transparency(self.getInputFromPort('p_transparency'))
+ if self.hasInputFromPort('p_np') :
+ p.set_p_np(self.getInputFromPort('p_np'))
+ if self.hasInputFromPort('p_active_isoval_selection_tab') :
+ p.set_p_active_isoval_selection_tab(self.getInputFromPort('p_active_isoval_selection_tab'))
+ if self.hasInputFromPort('p_active_tab') :
+ p.set_p_active_tab(self.getInputFromPort('p_active_tab'))
+ if self.hasInputFromPort('p_update_type') :
+ p.set_p_update_type(self.getInputFromPort('p_update_type'))
+ if self.hasInputFromPort('p_color_r') :
+ p.set_p_color_r(self.getInputFromPort('p_color_r'))
+ if self.hasInputFromPort('p_color_g') :
+ p.set_p_color_g(self.getInputFromPort('p_color_g'))
+ if self.hasInputFromPort('p_color_b') :
+ p.set_p_color_b(self.getInputFromPort('p_color_b'))
+ if self.hasInputFromPort('p_color_a') :
+ p.set_p_color_a(self.getInputFromPort('p_color_a'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ Optional_Color_Map = 0
+ if self.hasInputFromPort('Optional Color Map') :
+ Optional_Color_Map = self.getInputFromPort('Optional Color Map')
+ Optional_Isovalues = 0
+ if self.hasInputFromPort('Optional Isovalues') :
+ Optional_Isovalues = self.getInputFromPort('Optional Isovalues')
+ results = p.execute(Field, Optional_Color_Map, Optional_Isovalues)
+ self.setResult('Surface', results[0])
+ self.setResult('Geometry', results[1])
+ self.setResult('Mapping', results[2])
+
+class CreateViewerAxes(Visualization) :
+ def compute(self) :
+ p = sr_py.CreateViewerAxesAlg()
+ if self.hasInputFromPort('p_precision') :
+ p.set_p_precision(self.getInputFromPort('p_precision'))
+ if self.hasInputFromPort('p_squash') :
+ p.set_p_squash(self.getInputFromPort('p_squash'))
+ if self.hasInputFromPort('p_valuerez') :
+ p.set_p_valuerez(self.getInputFromPort('p_valuerez'))
+ if self.hasInputFromPort('p_labelrez') :
+ p.set_p_labelrez(self.getInputFromPort('p_labelrez'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_absolute') :
+ p.set_p_Plane_01_0_Axis_absolute(self.getInputFromPort('p_Plane_01_0_Axis_absolute'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_divisions') :
+ p.set_p_Plane_01_0_Axis_divisions(self.getInputFromPort('p_Plane_01_0_Axis_divisions'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_offset') :
+ p.set_p_Plane_01_0_Axis_offset(self.getInputFromPort('p_Plane_01_0_Axis_offset'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_range_first') :
+ p.set_p_Plane_01_0_Axis_range_first(self.getInputFromPort('p_Plane_01_0_Axis_range_first'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_range_second') :
+ p.set_p_Plane_01_0_Axis_range_second(self.getInputFromPort('p_Plane_01_0_Axis_range_second'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_min_absolute') :
+ p.set_p_Plane_01_0_Axis_min_absolute(self.getInputFromPort('p_Plane_01_0_Axis_min_absolute'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_max_absolute') :
+ p.set_p_Plane_01_0_Axis_max_absolute(self.getInputFromPort('p_Plane_01_0_Axis_max_absolute'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_minplane') :
+ p.set_p_Plane_01_0_Axis_minplane(self.getInputFromPort('p_Plane_01_0_Axis_minplane'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_maxplane') :
+ p.set_p_Plane_01_0_Axis_maxplane(self.getInputFromPort('p_Plane_01_0_Axis_maxplane'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_lines') :
+ p.set_p_Plane_01_0_Axis_lines(self.getInputFromPort('p_Plane_01_0_Axis_lines'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_minticks') :
+ p.set_p_Plane_01_0_Axis_minticks(self.getInputFromPort('p_Plane_01_0_Axis_minticks'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_maxticks') :
+ p.set_p_Plane_01_0_Axis_maxticks(self.getInputFromPort('p_Plane_01_0_Axis_maxticks'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_minlabel') :
+ p.set_p_Plane_01_0_Axis_minlabel(self.getInputFromPort('p_Plane_01_0_Axis_minlabel'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_maxlabel') :
+ p.set_p_Plane_01_0_Axis_maxlabel(self.getInputFromPort('p_Plane_01_0_Axis_maxlabel'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_minvalue') :
+ p.set_p_Plane_01_0_Axis_minvalue(self.getInputFromPort('p_Plane_01_0_Axis_minvalue'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_maxvalue') :
+ p.set_p_Plane_01_0_Axis_maxvalue(self.getInputFromPort('p_Plane_01_0_Axis_maxvalue'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_width') :
+ p.set_p_Plane_01_0_Axis_width(self.getInputFromPort('p_Plane_01_0_Axis_width'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_tickangle') :
+ p.set_p_Plane_01_0_Axis_tickangle(self.getInputFromPort('p_Plane_01_0_Axis_tickangle'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_ticktilt') :
+ p.set_p_Plane_01_0_Axis_ticktilt(self.getInputFromPort('p_Plane_01_0_Axis_ticktilt'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_ticksize') :
+ p.set_p_Plane_01_0_Axis_ticksize(self.getInputFromPort('p_Plane_01_0_Axis_ticksize'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_labelangle') :
+ p.set_p_Plane_01_0_Axis_labelangle(self.getInputFromPort('p_Plane_01_0_Axis_labelangle'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_labelheight') :
+ p.set_p_Plane_01_0_Axis_labelheight(self.getInputFromPort('p_Plane_01_0_Axis_labelheight'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_valuesize') :
+ p.set_p_Plane_01_0_Axis_valuesize(self.getInputFromPort('p_Plane_01_0_Axis_valuesize'))
+ if self.hasInputFromPort('p_Plane_01_0_Axis_valuesquash') :
+ p.set_p_Plane_01_0_Axis_valuesquash(self.getInputFromPort('p_Plane_01_0_Axis_valuesquash'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_absolute') :
+ p.set_p_Plane_01_1_Axis_absolute(self.getInputFromPort('p_Plane_01_1_Axis_absolute'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_divisions') :
+ p.set_p_Plane_01_1_Axis_divisions(self.getInputFromPort('p_Plane_01_1_Axis_divisions'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_offset') :
+ p.set_p_Plane_01_1_Axis_offset(self.getInputFromPort('p_Plane_01_1_Axis_offset'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_range_first') :
+ p.set_p_Plane_01_1_Axis_range_first(self.getInputFromPort('p_Plane_01_1_Axis_range_first'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_range_second') :
+ p.set_p_Plane_01_1_Axis_range_second(self.getInputFromPort('p_Plane_01_1_Axis_range_second'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_min_absolute') :
+ p.set_p_Plane_01_1_Axis_min_absolute(self.getInputFromPort('p_Plane_01_1_Axis_min_absolute'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_max_absolute') :
+ p.set_p_Plane_01_1_Axis_max_absolute(self.getInputFromPort('p_Plane_01_1_Axis_max_absolute'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_minplane') :
+ p.set_p_Plane_01_1_Axis_minplane(self.getInputFromPort('p_Plane_01_1_Axis_minplane'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_maxplane') :
+ p.set_p_Plane_01_1_Axis_maxplane(self.getInputFromPort('p_Plane_01_1_Axis_maxplane'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_lines') :
+ p.set_p_Plane_01_1_Axis_lines(self.getInputFromPort('p_Plane_01_1_Axis_lines'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_minticks') :
+ p.set_p_Plane_01_1_Axis_minticks(self.getInputFromPort('p_Plane_01_1_Axis_minticks'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_maxticks') :
+ p.set_p_Plane_01_1_Axis_maxticks(self.getInputFromPort('p_Plane_01_1_Axis_maxticks'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_minlabel') :
+ p.set_p_Plane_01_1_Axis_minlabel(self.getInputFromPort('p_Plane_01_1_Axis_minlabel'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_maxlabel') :
+ p.set_p_Plane_01_1_Axis_maxlabel(self.getInputFromPort('p_Plane_01_1_Axis_maxlabel'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_minvalue') :
+ p.set_p_Plane_01_1_Axis_minvalue(self.getInputFromPort('p_Plane_01_1_Axis_minvalue'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_maxvalue') :
+ p.set_p_Plane_01_1_Axis_maxvalue(self.getInputFromPort('p_Plane_01_1_Axis_maxvalue'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_width') :
+ p.set_p_Plane_01_1_Axis_width(self.getInputFromPort('p_Plane_01_1_Axis_width'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_tickangle') :
+ p.set_p_Plane_01_1_Axis_tickangle(self.getInputFromPort('p_Plane_01_1_Axis_tickangle'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_ticktilt') :
+ p.set_p_Plane_01_1_Axis_ticktilt(self.getInputFromPort('p_Plane_01_1_Axis_ticktilt'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_ticksize') :
+ p.set_p_Plane_01_1_Axis_ticksize(self.getInputFromPort('p_Plane_01_1_Axis_ticksize'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_labelangle') :
+ p.set_p_Plane_01_1_Axis_labelangle(self.getInputFromPort('p_Plane_01_1_Axis_labelangle'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_labelheight') :
+ p.set_p_Plane_01_1_Axis_labelheight(self.getInputFromPort('p_Plane_01_1_Axis_labelheight'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_valuesize') :
+ p.set_p_Plane_01_1_Axis_valuesize(self.getInputFromPort('p_Plane_01_1_Axis_valuesize'))
+ if self.hasInputFromPort('p_Plane_01_1_Axis_valuesquash') :
+ p.set_p_Plane_01_1_Axis_valuesquash(self.getInputFromPort('p_Plane_01_1_Axis_valuesquash'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_absolute') :
+ p.set_p_Plane_02_0_Axis_absolute(self.getInputFromPort('p_Plane_02_0_Axis_absolute'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_divisions') :
+ p.set_p_Plane_02_0_Axis_divisions(self.getInputFromPort('p_Plane_02_0_Axis_divisions'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_offset') :
+ p.set_p_Plane_02_0_Axis_offset(self.getInputFromPort('p_Plane_02_0_Axis_offset'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_range_first') :
+ p.set_p_Plane_02_0_Axis_range_first(self.getInputFromPort('p_Plane_02_0_Axis_range_first'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_range_second') :
+ p.set_p_Plane_02_0_Axis_range_second(self.getInputFromPort('p_Plane_02_0_Axis_range_second'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_min_absolute') :
+ p.set_p_Plane_02_0_Axis_min_absolute(self.getInputFromPort('p_Plane_02_0_Axis_min_absolute'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_max_absolute') :
+ p.set_p_Plane_02_0_Axis_max_absolute(self.getInputFromPort('p_Plane_02_0_Axis_max_absolute'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_minplane') :
+ p.set_p_Plane_02_0_Axis_minplane(self.getInputFromPort('p_Plane_02_0_Axis_minplane'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_maxplane') :
+ p.set_p_Plane_02_0_Axis_maxplane(self.getInputFromPort('p_Plane_02_0_Axis_maxplane'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_lines') :
+ p.set_p_Plane_02_0_Axis_lines(self.getInputFromPort('p_Plane_02_0_Axis_lines'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_minticks') :
+ p.set_p_Plane_02_0_Axis_minticks(self.getInputFromPort('p_Plane_02_0_Axis_minticks'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_maxticks') :
+ p.set_p_Plane_02_0_Axis_maxticks(self.getInputFromPort('p_Plane_02_0_Axis_maxticks'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_minlabel') :
+ p.set_p_Plane_02_0_Axis_minlabel(self.getInputFromPort('p_Plane_02_0_Axis_minlabel'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_maxlabel') :
+ p.set_p_Plane_02_0_Axis_maxlabel(self.getInputFromPort('p_Plane_02_0_Axis_maxlabel'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_minvalue') :
+ p.set_p_Plane_02_0_Axis_minvalue(self.getInputFromPort('p_Plane_02_0_Axis_minvalue'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_maxvalue') :
+ p.set_p_Plane_02_0_Axis_maxvalue(self.getInputFromPort('p_Plane_02_0_Axis_maxvalue'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_width') :
+ p.set_p_Plane_02_0_Axis_width(self.getInputFromPort('p_Plane_02_0_Axis_width'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_tickangle') :
+ p.set_p_Plane_02_0_Axis_tickangle(self.getInputFromPort('p_Plane_02_0_Axis_tickangle'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_ticktilt') :
+ p.set_p_Plane_02_0_Axis_ticktilt(self.getInputFromPort('p_Plane_02_0_Axis_ticktilt'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_ticksize') :
+ p.set_p_Plane_02_0_Axis_ticksize(self.getInputFromPort('p_Plane_02_0_Axis_ticksize'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_labelangle') :
+ p.set_p_Plane_02_0_Axis_labelangle(self.getInputFromPort('p_Plane_02_0_Axis_labelangle'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_labelheight') :
+ p.set_p_Plane_02_0_Axis_labelheight(self.getInputFromPort('p_Plane_02_0_Axis_labelheight'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_valuesize') :
+ p.set_p_Plane_02_0_Axis_valuesize(self.getInputFromPort('p_Plane_02_0_Axis_valuesize'))
+ if self.hasInputFromPort('p_Plane_02_0_Axis_valuesquash') :
+ p.set_p_Plane_02_0_Axis_valuesquash(self.getInputFromPort('p_Plane_02_0_Axis_valuesquash'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_absolute') :
+ p.set_p_Plane_02_2_Axis_absolute(self.getInputFromPort('p_Plane_02_2_Axis_absolute'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_divisions') :
+ p.set_p_Plane_02_2_Axis_divisions(self.getInputFromPort('p_Plane_02_2_Axis_divisions'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_offset') :
+ p.set_p_Plane_02_2_Axis_offset(self.getInputFromPort('p_Plane_02_2_Axis_offset'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_range_first') :
+ p.set_p_Plane_02_2_Axis_range_first(self.getInputFromPort('p_Plane_02_2_Axis_range_first'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_range_second') :
+ p.set_p_Plane_02_2_Axis_range_second(self.getInputFromPort('p_Plane_02_2_Axis_range_second'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_min_absolute') :
+ p.set_p_Plane_02_2_Axis_min_absolute(self.getInputFromPort('p_Plane_02_2_Axis_min_absolute'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_max_absolute') :
+ p.set_p_Plane_02_2_Axis_max_absolute(self.getInputFromPort('p_Plane_02_2_Axis_max_absolute'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_minplane') :
+ p.set_p_Plane_02_2_Axis_minplane(self.getInputFromPort('p_Plane_02_2_Axis_minplane'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_maxplane') :
+ p.set_p_Plane_02_2_Axis_maxplane(self.getInputFromPort('p_Plane_02_2_Axis_maxplane'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_lines') :
+ p.set_p_Plane_02_2_Axis_lines(self.getInputFromPort('p_Plane_02_2_Axis_lines'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_minticks') :
+ p.set_p_Plane_02_2_Axis_minticks(self.getInputFromPort('p_Plane_02_2_Axis_minticks'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_maxticks') :
+ p.set_p_Plane_02_2_Axis_maxticks(self.getInputFromPort('p_Plane_02_2_Axis_maxticks'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_minlabel') :
+ p.set_p_Plane_02_2_Axis_minlabel(self.getInputFromPort('p_Plane_02_2_Axis_minlabel'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_maxlabel') :
+ p.set_p_Plane_02_2_Axis_maxlabel(self.getInputFromPort('p_Plane_02_2_Axis_maxlabel'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_minvalue') :
+ p.set_p_Plane_02_2_Axis_minvalue(self.getInputFromPort('p_Plane_02_2_Axis_minvalue'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_maxvalue') :
+ p.set_p_Plane_02_2_Axis_maxvalue(self.getInputFromPort('p_Plane_02_2_Axis_maxvalue'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_width') :
+ p.set_p_Plane_02_2_Axis_width(self.getInputFromPort('p_Plane_02_2_Axis_width'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_tickangle') :
+ p.set_p_Plane_02_2_Axis_tickangle(self.getInputFromPort('p_Plane_02_2_Axis_tickangle'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_ticktilt') :
+ p.set_p_Plane_02_2_Axis_ticktilt(self.getInputFromPort('p_Plane_02_2_Axis_ticktilt'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_ticksize') :
+ p.set_p_Plane_02_2_Axis_ticksize(self.getInputFromPort('p_Plane_02_2_Axis_ticksize'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_labelangle') :
+ p.set_p_Plane_02_2_Axis_labelangle(self.getInputFromPort('p_Plane_02_2_Axis_labelangle'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_labelheight') :
+ p.set_p_Plane_02_2_Axis_labelheight(self.getInputFromPort('p_Plane_02_2_Axis_labelheight'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_valuesize') :
+ p.set_p_Plane_02_2_Axis_valuesize(self.getInputFromPort('p_Plane_02_2_Axis_valuesize'))
+ if self.hasInputFromPort('p_Plane_02_2_Axis_valuesquash') :
+ p.set_p_Plane_02_2_Axis_valuesquash(self.getInputFromPort('p_Plane_02_2_Axis_valuesquash'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_absolute') :
+ p.set_p_Plane_12_1_Axis_absolute(self.getInputFromPort('p_Plane_12_1_Axis_absolute'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_divisions') :
+ p.set_p_Plane_12_1_Axis_divisions(self.getInputFromPort('p_Plane_12_1_Axis_divisions'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_offset') :
+ p.set_p_Plane_12_1_Axis_offset(self.getInputFromPort('p_Plane_12_1_Axis_offset'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_range_first') :
+ p.set_p_Plane_12_1_Axis_range_first(self.getInputFromPort('p_Plane_12_1_Axis_range_first'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_range_second') :
+ p.set_p_Plane_12_1_Axis_range_second(self.getInputFromPort('p_Plane_12_1_Axis_range_second'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_min_absolute') :
+ p.set_p_Plane_12_1_Axis_min_absolute(self.getInputFromPort('p_Plane_12_1_Axis_min_absolute'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_max_absolute') :
+ p.set_p_Plane_12_1_Axis_max_absolute(self.getInputFromPort('p_Plane_12_1_Axis_max_absolute'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_minplane') :
+ p.set_p_Plane_12_1_Axis_minplane(self.getInputFromPort('p_Plane_12_1_Axis_minplane'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_maxplane') :
+ p.set_p_Plane_12_1_Axis_maxplane(self.getInputFromPort('p_Plane_12_1_Axis_maxplane'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_lines') :
+ p.set_p_Plane_12_1_Axis_lines(self.getInputFromPort('p_Plane_12_1_Axis_lines'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_minticks') :
+ p.set_p_Plane_12_1_Axis_minticks(self.getInputFromPort('p_Plane_12_1_Axis_minticks'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_maxticks') :
+ p.set_p_Plane_12_1_Axis_maxticks(self.getInputFromPort('p_Plane_12_1_Axis_maxticks'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_minlabel') :
+ p.set_p_Plane_12_1_Axis_minlabel(self.getInputFromPort('p_Plane_12_1_Axis_minlabel'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_maxlabel') :
+ p.set_p_Plane_12_1_Axis_maxlabel(self.getInputFromPort('p_Plane_12_1_Axis_maxlabel'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_minvalue') :
+ p.set_p_Plane_12_1_Axis_minvalue(self.getInputFromPort('p_Plane_12_1_Axis_minvalue'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_maxvalue') :
+ p.set_p_Plane_12_1_Axis_maxvalue(self.getInputFromPort('p_Plane_12_1_Axis_maxvalue'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_width') :
+ p.set_p_Plane_12_1_Axis_width(self.getInputFromPort('p_Plane_12_1_Axis_width'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_tickangle') :
+ p.set_p_Plane_12_1_Axis_tickangle(self.getInputFromPort('p_Plane_12_1_Axis_tickangle'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_ticktilt') :
+ p.set_p_Plane_12_1_Axis_ticktilt(self.getInputFromPort('p_Plane_12_1_Axis_ticktilt'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_ticksize') :
+ p.set_p_Plane_12_1_Axis_ticksize(self.getInputFromPort('p_Plane_12_1_Axis_ticksize'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_labelangle') :
+ p.set_p_Plane_12_1_Axis_labelangle(self.getInputFromPort('p_Plane_12_1_Axis_labelangle'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_labelheight') :
+ p.set_p_Plane_12_1_Axis_labelheight(self.getInputFromPort('p_Plane_12_1_Axis_labelheight'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_valuesize') :
+ p.set_p_Plane_12_1_Axis_valuesize(self.getInputFromPort('p_Plane_12_1_Axis_valuesize'))
+ if self.hasInputFromPort('p_Plane_12_1_Axis_valuesquash') :
+ p.set_p_Plane_12_1_Axis_valuesquash(self.getInputFromPort('p_Plane_12_1_Axis_valuesquash'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_absolute') :
+ p.set_p_Plane_12_2_Axis_absolute(self.getInputFromPort('p_Plane_12_2_Axis_absolute'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_divisions') :
+ p.set_p_Plane_12_2_Axis_divisions(self.getInputFromPort('p_Plane_12_2_Axis_divisions'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_offset') :
+ p.set_p_Plane_12_2_Axis_offset(self.getInputFromPort('p_Plane_12_2_Axis_offset'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_range_first') :
+ p.set_p_Plane_12_2_Axis_range_first(self.getInputFromPort('p_Plane_12_2_Axis_range_first'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_range_second') :
+ p.set_p_Plane_12_2_Axis_range_second(self.getInputFromPort('p_Plane_12_2_Axis_range_second'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_min_absolute') :
+ p.set_p_Plane_12_2_Axis_min_absolute(self.getInputFromPort('p_Plane_12_2_Axis_min_absolute'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_max_absolute') :
+ p.set_p_Plane_12_2_Axis_max_absolute(self.getInputFromPort('p_Plane_12_2_Axis_max_absolute'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_minplane') :
+ p.set_p_Plane_12_2_Axis_minplane(self.getInputFromPort('p_Plane_12_2_Axis_minplane'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_maxplane') :
+ p.set_p_Plane_12_2_Axis_maxplane(self.getInputFromPort('p_Plane_12_2_Axis_maxplane'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_lines') :
+ p.set_p_Plane_12_2_Axis_lines(self.getInputFromPort('p_Plane_12_2_Axis_lines'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_minticks') :
+ p.set_p_Plane_12_2_Axis_minticks(self.getInputFromPort('p_Plane_12_2_Axis_minticks'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_maxticks') :
+ p.set_p_Plane_12_2_Axis_maxticks(self.getInputFromPort('p_Plane_12_2_Axis_maxticks'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_minlabel') :
+ p.set_p_Plane_12_2_Axis_minlabel(self.getInputFromPort('p_Plane_12_2_Axis_minlabel'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_maxlabel') :
+ p.set_p_Plane_12_2_Axis_maxlabel(self.getInputFromPort('p_Plane_12_2_Axis_maxlabel'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_minvalue') :
+ p.set_p_Plane_12_2_Axis_minvalue(self.getInputFromPort('p_Plane_12_2_Axis_minvalue'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_maxvalue') :
+ p.set_p_Plane_12_2_Axis_maxvalue(self.getInputFromPort('p_Plane_12_2_Axis_maxvalue'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_width') :
+ p.set_p_Plane_12_2_Axis_width(self.getInputFromPort('p_Plane_12_2_Axis_width'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_tickangle') :
+ p.set_p_Plane_12_2_Axis_tickangle(self.getInputFromPort('p_Plane_12_2_Axis_tickangle'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_ticktilt') :
+ p.set_p_Plane_12_2_Axis_ticktilt(self.getInputFromPort('p_Plane_12_2_Axis_ticktilt'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_ticksize') :
+ p.set_p_Plane_12_2_Axis_ticksize(self.getInputFromPort('p_Plane_12_2_Axis_ticksize'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_labelangle') :
+ p.set_p_Plane_12_2_Axis_labelangle(self.getInputFromPort('p_Plane_12_2_Axis_labelangle'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_labelheight') :
+ p.set_p_Plane_12_2_Axis_labelheight(self.getInputFromPort('p_Plane_12_2_Axis_labelheight'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_valuesize') :
+ p.set_p_Plane_12_2_Axis_valuesize(self.getInputFromPort('p_Plane_12_2_Axis_valuesize'))
+ if self.hasInputFromPort('p_Plane_12_2_Axis_valuesquash') :
+ p.set_p_Plane_12_2_Axis_valuesquash(self.getInputFromPort('p_Plane_12_2_Axis_valuesquash'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('Axes', results)
+
+class RescaleColorMap(Visualization) :
+ def compute(self) :
+ p = sr_py.RescaleColorMapAlg()
+ if self.hasInputFromPort('p_main_frame') :
+ p.set_p_main_frame(self.getInputFromPort('p_main_frame'))
+ if self.hasInputFromPort('p_isFixed') :
+ p.set_p_isFixed(self.getInputFromPort('p_isFixed'))
+ if self.hasInputFromPort('p_min') :
+ p.set_p_min(self.getInputFromPort('p_min'))
+ if self.hasInputFromPort('p_max') :
+ p.set_p_max(self.getInputFromPort('p_max'))
+ if self.hasInputFromPort('p_makeSymmetric') :
+ p.set_p_makeSymmetric(self.getInputFromPort('p_makeSymmetric'))
+ ColorMap = 0
+ if self.hasInputFromPort('ColorMap') :
+ ColorMap = self.getInputFromPort('ColorMap')
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(ColorMap, Field)
+ self.setResult('ColorMap', results)
+
+class ConvertNrrdsToTexture(Visualization) :
+ def compute(self) :
+ p = sr_py.ConvertNrrdsToTextureAlg()
+ if self.hasInputFromPort('p_vmin') :
+ p.set_p_vmin(self.getInputFromPort('p_vmin'))
+ if self.hasInputFromPort('p_vmax') :
+ p.set_p_vmax(self.getInputFromPort('p_vmax'))
+ if self.hasInputFromPort('p_gmin') :
+ p.set_p_gmin(self.getInputFromPort('p_gmin'))
+ if self.hasInputFromPort('p_gmax') :
+ p.set_p_gmax(self.getInputFromPort('p_gmax'))
+ if self.hasInputFromPort('p_mmin') :
+ p.set_p_mmin(self.getInputFromPort('p_mmin'))
+ if self.hasInputFromPort('p_mmax') :
+ p.set_p_mmax(self.getInputFromPort('p_mmax'))
+ if self.hasInputFromPort('p_is_fixed') :
+ p.set_p_is_fixed(self.getInputFromPort('p_is_fixed'))
+ if self.hasInputFromPort('p_card_mem') :
+ p.set_p_card_mem(self.getInputFromPort('p_card_mem'))
+ if self.hasInputFromPort('p_card_mem_auto') :
+ p.set_p_card_mem_auto(self.getInputFromPort('p_card_mem_auto'))
+ if self.hasInputFromPort('p_is_uchar') :
+ p.set_p_is_uchar(self.getInputFromPort('p_is_uchar'))
+ if self.hasInputFromPort('p_histogram') :
+ p.set_p_histogram(self.getInputFromPort('p_histogram'))
+ if self.hasInputFromPort('p_gamma') :
+ p.set_p_gamma(self.getInputFromPort('p_gamma'))
+ Value_Nrrd = 0
+ if self.hasInputFromPort('Value Nrrd') :
+ Value_Nrrd = self.getInputFromPort('Value Nrrd')
+ Gradient_Magnitude_Nrrd = 0
+ if self.hasInputFromPort('Gradient Magnitude Nrrd') :
+ Gradient_Magnitude_Nrrd = self.getInputFromPort('Gradient Magnitude Nrrd')
+ results = p.execute(Value_Nrrd, Gradient_Magnitude_Nrrd)
+ self.setResult('Texture', results[0])
+ self.setResult('JointHistoGram', results[1])
+
+class ChooseColorMap(Visualization) :
+ def compute(self) :
+ p = sr_py.ChooseColorMapAlg()
+ if self.hasInputFromPort('p_use_first_valid') :
+ p.set_p_use_first_valid(self.getInputFromPort('p_use_first_valid'))
+ if self.hasInputFromPort('p_port_valid_index') :
+ p.set_p_port_valid_index(self.getInputFromPort('p_port_valid_index'))
+ if self.hasInputFromPort('p_port_selected_index') :
+ p.set_p_port_selected_index(self.getInputFromPort('p_port_selected_index'))
+ ColorMap = 0
+ if self.hasInputFromPort('ColorMap') :
+ ColorMap = self.getInputFromPort('ColorMap')
+ results = p.execute(ColorMap)
+ self.setResult('ColorMap', results)
+
+class CreateLightForViewer(Visualization) :
+ def compute(self) :
+ p = sr_py.CreateLightForViewerAlg()
+ if self.hasInputFromPort('p_control_pos_saved') :
+ p.set_p_control_pos_saved(self.getInputFromPort('p_control_pos_saved'))
+ if self.hasInputFromPort('p_control_x') :
+ p.set_p_control_x(self.getInputFromPort('p_control_x'))
+ if self.hasInputFromPort('p_control_y') :
+ p.set_p_control_y(self.getInputFromPort('p_control_y'))
+ if self.hasInputFromPort('p_control_z') :
+ p.set_p_control_z(self.getInputFromPort('p_control_z'))
+ if self.hasInputFromPort('p_at_x') :
+ p.set_p_at_x(self.getInputFromPort('p_at_x'))
+ if self.hasInputFromPort('p_at_y') :
+ p.set_p_at_y(self.getInputFromPort('p_at_y'))
+ if self.hasInputFromPort('p_at_z') :
+ p.set_p_at_z(self.getInputFromPort('p_at_z'))
+ if self.hasInputFromPort('p_type') :
+ p.set_p_type(self.getInputFromPort('p_type'))
+ if self.hasInputFromPort('p_on') :
+ p.set_p_on(self.getInputFromPort('p_on'))
+ results = p.execute()
+ self.setResult('Geometry', results)
+
+class ShowTextureVolume(Visualization) :
+ def compute(self) :
+ p = sr_py.ShowTextureVolumeAlg()
+ if self.hasInputFromPort('p_sampling_rate_hi') :
+ p.set_p_sampling_rate_hi(self.getInputFromPort('p_sampling_rate_hi'))
+ if self.hasInputFromPort('p_sampling_rate_lo') :
+ p.set_p_sampling_rate_lo(self.getInputFromPort('p_sampling_rate_lo'))
+ if self.hasInputFromPort('p_gradient_min') :
+ p.set_p_gradient_min(self.getInputFromPort('p_gradient_min'))
+ if self.hasInputFromPort('p_gradient_max') :
+ p.set_p_gradient_max(self.getInputFromPort('p_gradient_max'))
+ if self.hasInputFromPort('p_adaptive') :
+ p.set_p_adaptive(self.getInputFromPort('p_adaptive'))
+ if self.hasInputFromPort('p_cmap_size') :
+ p.set_p_cmap_size(self.getInputFromPort('p_cmap_size'))
+ if self.hasInputFromPort('p_sw_raster') :
+ p.set_p_sw_raster(self.getInputFromPort('p_sw_raster'))
+ if self.hasInputFromPort('p_render_style') :
+ p.set_p_render_style(self.getInputFromPort('p_render_style'))
+ if self.hasInputFromPort('p_alpha_scale') :
+ p.set_p_alpha_scale(self.getInputFromPort('p_alpha_scale'))
+ if self.hasInputFromPort('p_interp_mode') :
+ p.set_p_interp_mode(self.getInputFromPort('p_interp_mode'))
+ if self.hasInputFromPort('p_shading') :
+ p.set_p_shading(self.getInputFromPort('p_shading'))
+ if self.hasInputFromPort('p_ambient') :
+ p.set_p_ambient(self.getInputFromPort('p_ambient'))
+ if self.hasInputFromPort('p_diffuse') :
+ p.set_p_diffuse(self.getInputFromPort('p_diffuse'))
+ if self.hasInputFromPort('p_specular') :
+ p.set_p_specular(self.getInputFromPort('p_specular'))
+ if self.hasInputFromPort('p_shine') :
+ p.set_p_shine(self.getInputFromPort('p_shine'))
+ if self.hasInputFromPort('p_light') :
+ p.set_p_light(self.getInputFromPort('p_light'))
+ if self.hasInputFromPort('p_blend_res') :
+ p.set_p_blend_res(self.getInputFromPort('p_blend_res'))
+ if self.hasInputFromPort('p_multi_level') :
+ p.set_p_multi_level(self.getInputFromPort('p_multi_level'))
+ if self.hasInputFromPort('p_use_stencil') :
+ p.set_p_use_stencil(self.getInputFromPort('p_use_stencil'))
+ if self.hasInputFromPort('p_invert_opacity') :
+ p.set_p_invert_opacity(self.getInputFromPort('p_invert_opacity'))
+ if self.hasInputFromPort('p_num_clipping_planes') :
+ p.set_p_num_clipping_planes(self.getInputFromPort('p_num_clipping_planes'))
+ if self.hasInputFromPort('p_show_clipping_widgets') :
+ p.set_p_show_clipping_widgets(self.getInputFromPort('p_show_clipping_widgets'))
+ if self.hasInputFromPort('p_level_on') :
+ p.set_p_level_on(self.getInputFromPort('p_level_on'))
+ if self.hasInputFromPort('p_level_vals') :
+ p.set_p_level_vals(self.getInputFromPort('p_level_vals'))
+ if self.hasInputFromPort('p_id') :
+ p.set_p_id(self.getInputFromPort('p_id'))
+ Texture = 0
+ if self.hasInputFromPort('Texture') :
+ Texture = self.getInputFromPort('Texture')
+ ColorMap = 0
+ if self.hasInputFromPort('ColorMap') :
+ ColorMap = self.getInputFromPort('ColorMap')
+ ColorMap2 = 0
+ if self.hasInputFromPort('ColorMap2') :
+ ColorMap2 = self.getInputFromPort('ColorMap2')
+ results = p.execute(Texture, ColorMap, ColorMap2)
+ self.setResult('Geometry', results[0])
+ self.setResult('ColorMap', results[1])
+
+class ShowFieldGlyphs(Visualization) :
+ def compute(self) :
+ p = sr_py.ShowFieldGlyphsAlg()
+ if self.hasInputFromPort('p_scalars_has_data') :
+ p.set_p_scalars_has_data(self.getInputFromPort('p_scalars_has_data'))
+ if self.hasInputFromPort('p_scalars_on') :
+ p.set_p_scalars_on(self.getInputFromPort('p_scalars_on'))
+ if self.hasInputFromPort('p_scalars_display_type') :
+ p.set_p_scalars_display_type(self.getInputFromPort('p_scalars_display_type'))
+ if self.hasInputFromPort('p_scalars_transparency') :
+ p.set_p_scalars_transparency(self.getInputFromPort('p_scalars_transparency'))
+ if self.hasInputFromPort('p_scalars_normalize') :
+ p.set_p_scalars_normalize(self.getInputFromPort('p_scalars_normalize'))
+ if self.hasInputFromPort('p_scalars_color_type') :
+ p.set_p_scalars_color_type(self.getInputFromPort('p_scalars_color_type'))
+ if self.hasInputFromPort('p_scalars_resolution') :
+ p.set_p_scalars_resolution(self.getInputFromPort('p_scalars_resolution'))
+ if self.hasInputFromPort('p_vectors_has_data') :
+ p.set_p_vectors_has_data(self.getInputFromPort('p_vectors_has_data'))
+ if self.hasInputFromPort('p_vectors_on') :
+ p.set_p_vectors_on(self.getInputFromPort('p_vectors_on'))
+ if self.hasInputFromPort('p_vectors_display_type') :
+ p.set_p_vectors_display_type(self.getInputFromPort('p_vectors_display_type'))
+ if self.hasInputFromPort('p_vectors_transparency') :
+ p.set_p_vectors_transparency(self.getInputFromPort('p_vectors_transparency'))
+ if self.hasInputFromPort('p_vectors_normalize') :
+ p.set_p_vectors_normalize(self.getInputFromPort('p_vectors_normalize'))
+ if self.hasInputFromPort('p_vectors_bidirectional') :
+ p.set_p_vectors_bidirectional(self.getInputFromPort('p_vectors_bidirectional'))
+ if self.hasInputFromPort('p_vectors_color_type') :
+ p.set_p_vectors_color_type(self.getInputFromPort('p_vectors_color_type'))
+ if self.hasInputFromPort('p_vectors_resolution') :
+ p.set_p_vectors_resolution(self.getInputFromPort('p_vectors_resolution'))
+ if self.hasInputFromPort('p_tensors_has_data') :
+ p.set_p_tensors_has_data(self.getInputFromPort('p_tensors_has_data'))
+ if self.hasInputFromPort('p_tensors_on') :
+ p.set_p_tensors_on(self.getInputFromPort('p_tensors_on'))
+ if self.hasInputFromPort('p_tensors_display_type') :
+ p.set_p_tensors_display_type(self.getInputFromPort('p_tensors_display_type'))
+ if self.hasInputFromPort('p_tensors_transparency') :
+ p.set_p_tensors_transparency(self.getInputFromPort('p_tensors_transparency'))
+ if self.hasInputFromPort('p_tensors_normalize') :
+ p.set_p_tensors_normalize(self.getInputFromPort('p_tensors_normalize'))
+ if self.hasInputFromPort('p_tensors_color_type') :
+ p.set_p_tensors_color_type(self.getInputFromPort('p_tensors_color_type'))
+ if self.hasInputFromPort('p_tensors_resolution') :
+ p.set_p_tensors_resolution(self.getInputFromPort('p_tensors_resolution'))
+ if self.hasInputFromPort('p_tensors_emphasis') :
+ p.set_p_tensors_emphasis(self.getInputFromPort('p_tensors_emphasis'))
+ if self.hasInputFromPort('p_secondary_has_data') :
+ p.set_p_secondary_has_data(self.getInputFromPort('p_secondary_has_data'))
+ if self.hasInputFromPort('p_secondary_on') :
+ p.set_p_secondary_on(self.getInputFromPort('p_secondary_on'))
+ if self.hasInputFromPort('p_secondary_display_type') :
+ p.set_p_secondary_display_type(self.getInputFromPort('p_secondary_display_type'))
+ if self.hasInputFromPort('p_secondary_color_type') :
+ p.set_p_secondary_color_type(self.getInputFromPort('p_secondary_color_type'))
+ if self.hasInputFromPort('p_secondary_alpha') :
+ p.set_p_secondary_alpha(self.getInputFromPort('p_secondary_alpha'))
+ if self.hasInputFromPort('p_secondary_value') :
+ p.set_p_secondary_value(self.getInputFromPort('p_secondary_value'))
+ if self.hasInputFromPort('p_tertiary_has_data') :
+ p.set_p_tertiary_has_data(self.getInputFromPort('p_tertiary_has_data'))
+ if self.hasInputFromPort('p_tertiary_on') :
+ p.set_p_tertiary_on(self.getInputFromPort('p_tertiary_on'))
+ if self.hasInputFromPort('p_tertiary_display_type') :
+ p.set_p_tertiary_display_type(self.getInputFromPort('p_tertiary_display_type'))
+ if self.hasInputFromPort('p_tertiary_color_type') :
+ p.set_p_tertiary_color_type(self.getInputFromPort('p_tertiary_color_type'))
+ if self.hasInputFromPort('p_tertiary_alpha') :
+ p.set_p_tertiary_alpha(self.getInputFromPort('p_tertiary_alpha'))
+ if self.hasInputFromPort('p_tertiary_value') :
+ p.set_p_tertiary_value(self.getInputFromPort('p_tertiary_value'))
+ if self.hasInputFromPort('p_text_on') :
+ p.set_p_text_on(self.getInputFromPort('p_text_on'))
+ if self.hasInputFromPort('p_text_color_type') :
+ p.set_p_text_color_type(self.getInputFromPort('p_text_color_type'))
+ if self.hasInputFromPort('p_text_color_r') :
+ p.set_p_text_color_r(self.getInputFromPort('p_text_color_r'))
+ if self.hasInputFromPort('p_text_color_g') :
+ p.set_p_text_color_g(self.getInputFromPort('p_text_color_g'))
+ if self.hasInputFromPort('p_text_color_b') :
+ p.set_p_text_color_b(self.getInputFromPort('p_text_color_b'))
+ if self.hasInputFromPort('p_text_backface_cull') :
+ p.set_p_text_backface_cull(self.getInputFromPort('p_text_backface_cull'))
+ if self.hasInputFromPort('p_text_always_visible') :
+ p.set_p_text_always_visible(self.getInputFromPort('p_text_always_visible'))
+ if self.hasInputFromPort('p_text_fontsize') :
+ p.set_p_text_fontsize(self.getInputFromPort('p_text_fontsize'))
+ if self.hasInputFromPort('p_text_precision') :
+ p.set_p_text_precision(self.getInputFromPort('p_text_precision'))
+ if self.hasInputFromPort('p_text_render_locations') :
+ p.set_p_text_render_locations(self.getInputFromPort('p_text_render_locations'))
+ if self.hasInputFromPort('p_text_show_data') :
+ p.set_p_text_show_data(self.getInputFromPort('p_text_show_data'))
+ if self.hasInputFromPort('p_text_show_nodes') :
+ p.set_p_text_show_nodes(self.getInputFromPort('p_text_show_nodes'))
+ if self.hasInputFromPort('p_text_show_edges') :
+ p.set_p_text_show_edges(self.getInputFromPort('p_text_show_edges'))
+ if self.hasInputFromPort('p_text_show_faces') :
+ p.set_p_text_show_faces(self.getInputFromPort('p_text_show_faces'))
+ if self.hasInputFromPort('p_text_show_cells') :
+ p.set_p_text_show_cells(self.getInputFromPort('p_text_show_cells'))
+ if self.hasInputFromPort('p_def_color_r') :
+ p.set_p_def_color_r(self.getInputFromPort('p_def_color_r'))
+ if self.hasInputFromPort('p_def_color_g') :
+ p.set_p_def_color_g(self.getInputFromPort('p_def_color_g'))
+ if self.hasInputFromPort('p_def_color_b') :
+ p.set_p_def_color_b(self.getInputFromPort('p_def_color_b'))
+ if self.hasInputFromPort('p_def_color_a') :
+ p.set_p_def_color_a(self.getInputFromPort('p_def_color_a'))
+ if self.hasInputFromPort('p_active_tab') :
+ p.set_p_active_tab(self.getInputFromPort('p_active_tab'))
+ if self.hasInputFromPort('p_interactive_mode') :
+ p.set_p_interactive_mode(self.getInputFromPort('p_interactive_mode'))
+ if self.hasInputFromPort('p_show_progress') :
+ p.set_p_show_progress(self.getInputFromPort('p_show_progress'))
+ if self.hasInputFromPort('p_field_name') :
+ p.set_p_field_name(self.getInputFromPort('p_field_name'))
+ if self.hasInputFromPort('p_field_name_override') :
+ p.set_p_field_name_override(self.getInputFromPort('p_field_name_override'))
+ if self.hasInputFromPort('p_approx_div') :
+ p.set_p_approx_div(self.getInputFromPort('p_approx_div'))
+ if self.hasInputFromPort('p_use_default_size') :
+ p.set_p_use_default_size(self.getInputFromPort('p_use_default_size'))
+ Primary_Data = 0
+ if self.hasInputFromPort('Primary Data') :
+ Primary_Data = self.getInputFromPort('Primary Data')
+ Primary_ColorMap = 0
+ if self.hasInputFromPort('Primary ColorMap') :
+ Primary_ColorMap = self.getInputFromPort('Primary ColorMap')
+ Secondary_Data = 0
+ if self.hasInputFromPort('Secondary Data') :
+ Secondary_Data = self.getInputFromPort('Secondary Data')
+ Secondary_ColorMap = 0
+ if self.hasInputFromPort('Secondary ColorMap') :
+ Secondary_ColorMap = self.getInputFromPort('Secondary ColorMap')
+ Tertiary_Data = 0
+ if self.hasInputFromPort('Tertiary Data') :
+ Tertiary_Data = self.getInputFromPort('Tertiary Data')
+ Tertiary_ColorMap = 0
+ if self.hasInputFromPort('Tertiary ColorMap') :
+ Tertiary_ColorMap = self.getInputFromPort('Tertiary ColorMap')
+ results = p.execute(Primary_Data, Primary_ColorMap, Secondary_Data, Secondary_ColorMap, Tertiary_Data, Tertiary_ColorMap)
+ self.setResult('Scene Graph', results)
+
+class GenerateStreamLines(Visualization) :
+ def compute(self) :
+ p = sr_py.GenerateStreamLinesAlg()
+ if self.hasInputFromPort('p_stepsize') :
+ p.set_p_stepsize(self.getInputFromPort('p_stepsize'))
+ if self.hasInputFromPort('p_tolerance') :
+ p.set_p_tolerance(self.getInputFromPort('p_tolerance'))
+ if self.hasInputFromPort('p_maxsteps') :
+ p.set_p_maxsteps(self.getInputFromPort('p_maxsteps'))
+ if self.hasInputFromPort('p_direction') :
+ p.set_p_direction(self.getInputFromPort('p_direction'))
+ if self.hasInputFromPort('p_value') :
+ p.set_p_value(self.getInputFromPort('p_value'))
+ if self.hasInputFromPort('p_remove_colinear_pts') :
+ p.set_p_remove_colinear_pts(self.getInputFromPort('p_remove_colinear_pts'))
+ if self.hasInputFromPort('p_method') :
+ p.set_p_method(self.getInputFromPort('p_method'))
+ if self.hasInputFromPort('p_nthreads') :
+ p.set_p_nthreads(self.getInputFromPort('p_nthreads'))
+ if self.hasInputFromPort('p_auto_parameterize') :
+ p.set_p_auto_parameterize(self.getInputFromPort('p_auto_parameterize'))
+ Vector_Field = 0
+ if self.hasInputFromPort('Vector Field') :
+ Vector_Field = self.getInputFromPort('Vector Field')
+ Seed_Points = 0
+ if self.hasInputFromPort('Seed Points') :
+ Seed_Points = self.getInputFromPort('Seed Points')
+ results = p.execute(Vector_Field, Seed_Points)
+ self.setResult('Streamlines', results)
+
+class GenerateStreamLinesWithPlacementHeuristic(Visualization) :
+ def compute(self) :
+ p = sr_py.GenerateStreamLinesWithPlacementHeuristicAlg()
+ if self.hasInputFromPort('p_numsl') :
+ p.set_p_numsl(self.getInputFromPort('p_numsl'))
+ if self.hasInputFromPort('p_numpts') :
+ p.set_p_numpts(self.getInputFromPort('p_numpts'))
+ if self.hasInputFromPort('p_minper') :
+ p.set_p_minper(self.getInputFromPort('p_minper'))
+ if self.hasInputFromPort('p_maxper') :
+ p.set_p_maxper(self.getInputFromPort('p_maxper'))
+ if self.hasInputFromPort('p_ming') :
+ p.set_p_ming(self.getInputFromPort('p_ming'))
+ if self.hasInputFromPort('p_maxg') :
+ p.set_p_maxg(self.getInputFromPort('p_maxg'))
+ if self.hasInputFromPort('p_numsamples') :
+ p.set_p_numsamples(self.getInputFromPort('p_numsamples'))
+ if self.hasInputFromPort('p_method') :
+ p.set_p_method(self.getInputFromPort('p_method'))
+ if self.hasInputFromPort('p_stepsize') :
+ p.set_p_stepsize(self.getInputFromPort('p_stepsize'))
+ if self.hasInputFromPort('p_stepout') :
+ p.set_p_stepout(self.getInputFromPort('p_stepout'))
+ if self.hasInputFromPort('p_maxsteps') :
+ p.set_p_maxsteps(self.getInputFromPort('p_maxsteps'))
+ if self.hasInputFromPort('p_minmag') :
+ p.set_p_minmag(self.getInputFromPort('p_minmag'))
+ if self.hasInputFromPort('p_direction') :
+ p.set_p_direction(self.getInputFromPort('p_direction'))
+ Source = 0
+ if self.hasInputFromPort('Source') :
+ Source = self.getInputFromPort('Source')
+ Weighting = 0
+ if self.hasInputFromPort('Weighting') :
+ Weighting = self.getInputFromPort('Weighting')
+ Flow = 0
+ if self.hasInputFromPort('Flow') :
+ Flow = self.getInputFromPort('Flow')
+ Compare = 0
+ if self.hasInputFromPort('Compare') :
+ Compare = self.getInputFromPort('Compare')
+ Seed_points = 0
+ if self.hasInputFromPort('Seed points') :
+ Seed_points = self.getInputFromPort('Seed points')
+ results = p.execute(Source, Weighting, Flow, Compare, Seed_points)
+ self.setResult('Streamlines', results[0])
+ self.setResult('Render', results[1])
+
+class ShowString(Visualization) :
+ def compute(self) :
+ p = sr_py.ShowStringAlg()
+ if self.hasInputFromPort('p_bbox') :
+ p.set_p_bbox(self.getInputFromPort('p_bbox'))
+ if self.hasInputFromPort('p_size') :
+ p.set_p_size(self.getInputFromPort('p_size'))
+ if self.hasInputFromPort('p_location_x') :
+ p.set_p_location_x(self.getInputFromPort('p_location_x'))
+ if self.hasInputFromPort('p_location_y') :
+ p.set_p_location_y(self.getInputFromPort('p_location_y'))
+ if self.hasInputFromPort('p_color_r') :
+ p.set_p_color_r(self.getInputFromPort('p_color_r'))
+ if self.hasInputFromPort('p_color_g') :
+ p.set_p_color_g(self.getInputFromPort('p_color_g'))
+ if self.hasInputFromPort('p_color_b') :
+ p.set_p_color_b(self.getInputFromPort('p_color_b'))
+ Format_String = ''
+ if self.hasInputFromPort('Format String') :
+ Format_String = self.getInputFromPort('Format String')
+ results = p.execute(Format_String)
+ self.setResult('Title', results)
+
+class CreateAndEditColorMap(Visualization) :
+ def compute(self) :
+ p = sr_py.CreateAndEditColorMapAlg()
+ if self.hasInputFromPort('p_rgbhsv') :
+ p.set_p_rgbhsv(self.getInputFromPort('p_rgbhsv'))
+ if self.hasInputFromPort('p_rgb_points') :
+ p.set_p_rgb_points(self.getInputFromPort('p_rgb_points'))
+ if self.hasInputFromPort('p_alpha_points') :
+ p.set_p_alpha_points(self.getInputFromPort('p_alpha_points'))
+ if self.hasInputFromPort('p_resolution') :
+ p.set_p_resolution(self.getInputFromPort('p_resolution'))
+ ColorMap = 0
+ if self.hasInputFromPort('ColorMap') :
+ ColorMap = self.getInputFromPort('ColorMap')
+ results = p.execute(ColorMap)
+ self.setResult('ColorMap', results[0])
+ self.setResult('Geometry', results[1])
+
+class ShowMeshBoundingBox(Visualization) :
+ def compute(self) :
+ p = sr_py.ShowMeshBoundingBoxAlg()
+ if self.hasInputFromPort('p_sizex') :
+ p.set_p_sizex(self.getInputFromPort('p_sizex'))
+ if self.hasInputFromPort('p_sizey') :
+ p.set_p_sizey(self.getInputFromPort('p_sizey'))
+ if self.hasInputFromPort('p_sizez') :
+ p.set_p_sizez(self.getInputFromPort('p_sizez'))
+ Field = 0
+ if self.hasInputFromPort('Field') :
+ Field = self.getInputFromPort('Field')
+ results = p.execute(Field)
+ self.setResult('Scene Graph', results)
+
+class CreateStandardColorMaps(Visualization) :
+ def compute(self) :
+ p = sr_py.CreateStandardColorMapsAlg()
+ if self.hasInputFromPort('p_mapName') :
+ p.set_p_mapName(self.getInputFromPort('p_mapName'))
+ if self.hasInputFromPort('p_gamma') :
+ p.set_p_gamma(self.getInputFromPort('p_gamma'))
+ if self.hasInputFromPort('p_resolution') :
+ p.set_p_resolution(self.getInputFromPort('p_resolution'))
+ if self.hasInputFromPort('p_reverse') :
+ p.set_p_reverse(self.getInputFromPort('p_reverse'))
+ if self.hasInputFromPort('p_faux') :
+ p.set_p_faux(self.getInputFromPort('p_faux'))
+ if self.hasInputFromPort('p_positionList') :
+ p.set_p_positionList(self.getInputFromPort('p_positionList'))
+ if self.hasInputFromPort('p_nodeList') :
+ p.set_p_nodeList(self.getInputFromPort('p_nodeList'))
+ if self.hasInputFromPort('p_width') :
+ p.set_p_width(self.getInputFromPort('p_width'))
+ if self.hasInputFromPort('p_height') :
+ p.set_p_height(self.getInputFromPort('p_height'))
+ results = p.execute()
+ self.setResult('ColorMap', results)
+
+class ShowTextureSlices(Visualization) :
+ def compute(self) :
+ p = sr_py.ShowTextureSlicesAlg()
+ if self.hasInputFromPort('p_control_pos_saved') :
+ p.set_p_control_pos_saved(self.getInputFromPort('p_control_pos_saved'))
+ if self.hasInputFromPort('p_drawX') :
+ p.set_p_drawX(self.getInputFromPort('p_drawX'))
+ if self.hasInputFromPort('p_drawY') :
+ p.set_p_drawY(self.getInputFromPort('p_drawY'))
+ if self.hasInputFromPort('p_drawZ') :
+ p.set_p_drawZ(self.getInputFromPort('p_drawZ'))
+ if self.hasInputFromPort('p_drawView') :
+ p.set_p_drawView(self.getInputFromPort('p_drawView'))
+ if self.hasInputFromPort('p_interp_mode') :
+ p.set_p_interp_mode(self.getInputFromPort('p_interp_mode'))
+ if self.hasInputFromPort('p_draw_phi_0') :
+ p.set_p_draw_phi_0(self.getInputFromPort('p_draw_phi_0'))
+ if self.hasInputFromPort('p_draw_phi_1') :
+ p.set_p_draw_phi_1(self.getInputFromPort('p_draw_phi_1'))
+ if self.hasInputFromPort('p_phi_0') :
+ p.set_p_phi_0(self.getInputFromPort('p_phi_0'))
+ if self.hasInputFromPort('p_phi_1') :
+ p.set_p_phi_1(self.getInputFromPort('p_phi_1'))
+ if self.hasInputFromPort('p_multi_level') :
+ p.set_p_multi_level(self.getInputFromPort('p_multi_level'))
+ if self.hasInputFromPort('p_color_changed') :
+ p.set_p_color_changed(self.getInputFromPort('p_color_changed'))
+ if self.hasInputFromPort('p_colors') :
+ p.set_p_colors(self.getInputFromPort('p_colors'))
+ if self.hasInputFromPort('p_level_on') :
+ p.set_p_level_on(self.getInputFromPort('p_level_on'))
+ if self.hasInputFromPort('p_outline_levels') :
+ p.set_p_outline_levels(self.getInputFromPort('p_outline_levels'))
+ if self.hasInputFromPort('p_use_stencil') :
+ p.set_p_use_stencil(self.getInputFromPort('p_use_stencil'))
+ Texture = 0
+ if self.hasInputFromPort('Texture') :
+ Texture = self.getInputFromPort('Texture')
+ ColorMap = 0
+ if self.hasInputFromPort('ColorMap') :
+ ColorMap = self.getInputFromPort('ColorMap')
+ ColorMap2 = 0
+ if self.hasInputFromPort('ColorMap2') :
+ ColorMap2 = self.getInputFromPort('ColorMap2')
+ results = p.execute(Texture, ColorMap, ColorMap2)
+ self.setResult('Geometry', results[0])
+ self.setResult('ColorMap', results[1])
+
+class ShowMatrix(Visualization) :
+ def compute(self) :
+ p = sr_py.ShowMatrixAlg()
+ if self.hasInputFromPort('p_xpos') :
+ p.set_p_xpos(self.getInputFromPort('p_xpos'))
+ if self.hasInputFromPort('p_ypos') :
+ p.set_p_ypos(self.getInputFromPort('p_ypos'))
+ if self.hasInputFromPort('p_xscale') :
+ p.set_p_xscale(self.getInputFromPort('p_xscale'))
+ if self.hasInputFromPort('p_yscale') :
+ p.set_p_yscale(self.getInputFromPort('p_yscale'))
+ if self.hasInputFromPort('p_3d_mode') :
+ p.set_p_3d_mode(self.getInputFromPort('p_3d_mode'))
+ if self.hasInputFromPort('p_gmode') :
+ p.set_p_gmode(self.getInputFromPort('p_gmode'))
+ if self.hasInputFromPort('p_showtext') :
+ p.set_p_showtext(self.getInputFromPort('p_showtext'))
+ if self.hasInputFromPort('p_row_begin') :
+ p.set_p_row_begin(self.getInputFromPort('p_row_begin'))
+ if self.hasInputFromPort('p_rows') :
+ p.set_p_rows(self.getInputFromPort('p_rows'))
+ if self.hasInputFromPort('p_col_begin') :
+ p.set_p_col_begin(self.getInputFromPort('p_col_begin'))
+ if self.hasInputFromPort('p_cols') :
+ p.set_p_cols(self.getInputFromPort('p_cols'))
+ if self.hasInputFromPort('p_colormapmode') :
+ p.set_p_colormapmode(self.getInputFromPort('p_colormapmode'))
+ ColorMap = 0
+ if self.hasInputFromPort('ColorMap') :
+ ColorMap = self.getInputFromPort('ColorMap')
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(ColorMap, Matrix)
+ self.setResult('Geometry', results)
+
+class CreateViewerClockIcon(Visualization) :
+ def compute(self) :
+ p = sr_py.CreateViewerClockIconAlg()
+ if self.hasInputFromPort('p_type') :
+ p.set_p_type(self.getInputFromPort('p_type'))
+ if self.hasInputFromPort('p_bbox') :
+ p.set_p_bbox(self.getInputFromPort('p_bbox'))
+ if self.hasInputFromPort('p_format') :
+ p.set_p_format(self.getInputFromPort('p_format'))
+ if self.hasInputFromPort('p_min') :
+ p.set_p_min(self.getInputFromPort('p_min'))
+ if self.hasInputFromPort('p_max') :
+ p.set_p_max(self.getInputFromPort('p_max'))
+ if self.hasInputFromPort('p_current') :
+ p.set_p_current(self.getInputFromPort('p_current'))
+ if self.hasInputFromPort('p_size') :
+ p.set_p_size(self.getInputFromPort('p_size'))
+ if self.hasInputFromPort('p_location_x') :
+ p.set_p_location_x(self.getInputFromPort('p_location_x'))
+ if self.hasInputFromPort('p_location_y') :
+ p.set_p_location_y(self.getInputFromPort('p_location_y'))
+ if self.hasInputFromPort('p_color_r') :
+ p.set_p_color_r(self.getInputFromPort('p_color_r'))
+ if self.hasInputFromPort('p_color_g') :
+ p.set_p_color_g(self.getInputFromPort('p_color_g'))
+ if self.hasInputFromPort('p_color_b') :
+ p.set_p_color_b(self.getInputFromPort('p_color_b'))
+ Time_Matrix = 0
+ if self.hasInputFromPort('Time Matrix') :
+ Time_Matrix = self.getInputFromPort('Time Matrix')
+ Time_Nrrd = 0
+ if self.hasInputFromPort('Time Nrrd') :
+ Time_Nrrd = self.getInputFromPort('Time Nrrd')
+ results = p.execute(Time_Matrix, Time_Nrrd)
+ self.setResult('Clock', results)
+
+class ConvertFieldsToTexture(Visualization) :
+ def compute(self) :
+ p = sr_py.ConvertFieldsToTextureAlg()
+ if self.hasInputFromPort('p_vmin') :
+ p.set_p_vmin(self.getInputFromPort('p_vmin'))
+ if self.hasInputFromPort('p_vmax') :
+ p.set_p_vmax(self.getInputFromPort('p_vmax'))
+ if self.hasInputFromPort('p_gmin') :
+ p.set_p_gmin(self.getInputFromPort('p_gmin'))
+ if self.hasInputFromPort('p_gmax') :
+ p.set_p_gmax(self.getInputFromPort('p_gmax'))
+ if self.hasInputFromPort('p_is_fixed') :
+ p.set_p_is_fixed(self.getInputFromPort('p_is_fixed'))
+ if self.hasInputFromPort('p_card_mem') :
+ p.set_p_card_mem(self.getInputFromPort('p_card_mem'))
+ if self.hasInputFromPort('p_card_mem_auto') :
+ p.set_p_card_mem_auto(self.getInputFromPort('p_card_mem_auto'))
+ if self.hasInputFromPort('p_histogram') :
+ p.set_p_histogram(self.getInputFromPort('p_histogram'))
+ if self.hasInputFromPort('p_gamma') :
+ p.set_p_gamma(self.getInputFromPort('p_gamma'))
+ Value_Field = 0
+ if self.hasInputFromPort('Value Field') :
+ Value_Field = self.getInputFromPort('Value Field')
+ Gradient_Magnitude_Field = 0
+ if self.hasInputFromPort('Gradient Magnitude Field') :
+ Gradient_Magnitude_Field = self.getInputFromPort('Gradient Magnitude Field')
+ results = p.execute(Value_Field, Gradient_Magnitude_Field)
+ self.setResult('Texture', results[0])
+ self.setResult('JointHistoGram', results[1])
+
+class ColorMap2DSemantics(Visualization) :
+ def compute(self) :
+ p = sr_py.ColorMap2DSemanticsAlg()
+ Input_Colormap = 0
+ if self.hasInputFromPort('Input Colormap') :
+ Input_Colormap = self.getInputFromPort('Input Colormap')
+ results = p.execute(Input_Colormap)
+ self.setResult('Output Colormap', results)
+
+class ConvertMatrixToString(Converters) :
+ def compute(self) :
+ p = sr_py.ConvertMatrixToStringAlg()
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(Matrix)
+ self.setResult('String', results)
+
+class ConvertMatrixToField(Converters) :
+ def compute(self) :
+ p = sr_py.ConvertMatrixToFieldAlg()
+ if self.hasInputFromPort('p_datalocation') :
+ p.set_p_datalocation(self.getInputFromPort('p_datalocation'))
+ Matrix = 0
+ if self.hasInputFromPort('Matrix') :
+ Matrix = self.getInputFromPort('Matrix')
+ results = p.execute(Matrix)
+ self.setResult('Field', results)
+
+class TimeControls(Time) :
+ def compute(self) :
+ p = sr_py.TimeControlsAlg()
+ if self.hasInputFromPort('p_execmode') :
+ p.set_p_execmode(self.getInputFromPort('p_execmode'))
+ if self.hasInputFromPort('p_scale_factor') :
+ p.set_p_scale_factor(self.getInputFromPort('p_scale_factor'))
+ results = p.execute()
+ self.setResult('time', results)
+
+
+def initialize(*args, **keywords):
+
+ env = []
+ for k in os.environ.keys() :
+ estr = "%s=%s" % (k, os.environ[k])
+ env.append(estr)
+ sr_py.init_sr_py(env)
+
+ reg = core.modules.module_registry
+
+ reg.add_module(Time, abstract=True)
+ reg.add_module(Converters, abstract=True)
+ reg.add_module(Texture, abstract=True)
+ reg.add_module(Visualization, abstract=True)
+ reg.add_module(MiscField, abstract=True)
+ reg.add_module(DataArrayMath, abstract=True)
+ reg.add_module(Math, abstract=True)
+ reg.add_module(ChangeMesh, abstract=True)
+ reg.add_module(ChangeFieldData, abstract=True)
+ reg.add_module(Geometry, abstract=True)
+ reg.add_module(NewField, abstract=True)
+ reg.add_module(ColorMap, abstract=True)
+ reg.add_module(Field, abstract=True)
+ reg.add_module(Nrrd, abstract=True)
+ reg.add_module(Matrix, abstract=True)
+ reg.add_module(ColorMap2, abstract=True)
+ reg.add_module(Path, abstract=True)
+ reg.add_module(String, abstract=True)
+ reg.add_module(Bundle, abstract=True)
+ reg.add_module(DataIO, abstract=True)
+ reg.add_module(WriteBundle)
+ reg.add_input_port(WriteBundle, 'p_filetype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteBundle, 'p_confirm',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteBundle, 'p_confirm_once',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_input_port(WriteBundle, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(WritePath)
+ reg.add_input_port(WritePath, 'p_filetype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WritePath, 'p_confirm',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WritePath, 'p_confirm_once',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WritePath, 'Input Data',
+ (Path, "Path"))
+ reg.add_input_port(WritePath, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(WriteColorMap2D)
+ reg.add_input_port(WriteColorMap2D, 'p_filetype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteColorMap2D, 'p_confirm',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteColorMap2D, 'p_confirm_once',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteColorMap2D, 'p_exporttype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteColorMap2D, 'Input Data',
+ (ColorMap2, "ColorMap2"))
+ reg.add_input_port(WriteColorMap2D, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(ReadHDF5File)
+ reg.add_input_port(ReadHDF5File, 'p_have_HDF5',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_power_app',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_datasets',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_dumpname',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_ports',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_ndims',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_mergeData',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_assumeSVT',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_animate',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_animate_tab',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_basic_tab',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_extended_tab',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_playmode_tab',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_selectable_min',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_selectable_max',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_selectable_inc',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_range_min',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_range_max',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_playmode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_current',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_execmode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_delay',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_inc_amount',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_update_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_have_group',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_have_attributes',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_have_datasets',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_continuous',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_selectionString',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_regexp',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_allow_selection',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_read_error',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_max_dims',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_0_dim',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_0_start',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_0_start2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_0_count',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_0_count2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_0_stride',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_0_stride2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_1_dim',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_1_start',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_1_start2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_1_count',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_1_count2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_1_stride',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_1_stride2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_2_dim',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_2_start',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_2_start2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_2_count',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_2_count2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_2_stride',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_2_stride2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_3_dim',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_3_start',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_3_start2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_3_count',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_3_count2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_3_stride',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_3_stride2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_4_dim',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_4_start',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_4_start2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_4_count',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_4_count2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_4_stride',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_4_stride2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_5_dim',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_5_start',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_5_start2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_5_count',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_5_count2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_5_stride',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'p_5_stride2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadHDF5File, 'Full filename',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(ReadHDF5File, 'Current Index',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReadHDF5File, 'Output 0 Nrrd',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(ReadHDF5File, 'Output 1 Nrrd',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(ReadHDF5File, 'Output 2 Nrrd',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(ReadHDF5File, 'Output 3 Nrrd',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(ReadHDF5File, 'Output 4 Nrrd',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(ReadHDF5File, 'Output 5 Nrrd',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(ReadHDF5File, 'Output 6 Nrrd',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(ReadHDF5File, 'Output 7 Nrrd',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(ReadHDF5File, 'Selected Index',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReadField)
+ reg.add_input_port(ReadField, 'p_from_env',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadField, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(ReadField, 'Output Data',
+ (Field, "Field"))
+ reg.add_output_port(ReadField, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(WriteColorMap)
+ reg.add_input_port(WriteColorMap, 'p_filetype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteColorMap, 'p_confirm',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteColorMap, 'p_confirm_once',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteColorMap, 'p_exporttype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteColorMap, 'Input Data',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(WriteColorMap, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(ReadColorMap2D)
+ reg.add_input_port(ReadColorMap2D, 'p_from_env',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadColorMap2D, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(ReadColorMap2D, 'Output Data',
+ (ColorMap2, "ColorMap2"))
+ reg.add_output_port(ReadColorMap2D, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(ReadString)
+ reg.add_input_port(ReadString, 'p_from_env',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadString, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(ReadString, 'Output Data',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(ReadString, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(ReadColorMap)
+ reg.add_input_port(ReadColorMap, 'p_from_env',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadColorMap, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(ReadColorMap, 'Output Data',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(ReadColorMap, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(ReadMatrix)
+ reg.add_input_port(ReadMatrix, 'p_from_env',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadMatrix, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(ReadMatrix, 'Output Data',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReadMatrix, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(WriteString)
+ reg.add_input_port(WriteString, 'p_filetype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteString, 'p_confirm',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteString, 'p_confirm_once',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteString, 'String',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(WriteString, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(ReadPath)
+ reg.add_input_port(ReadPath, 'p_from_env',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadPath, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(ReadPath, 'Output Data',
+ (Path, "Path"))
+ reg.add_output_port(ReadPath, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(WriteField)
+ reg.add_input_port(WriteField, 'p_filetype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteField, 'p_confirm',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteField, 'p_confirm_once',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteField, 'p_exporttype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteField, 'p_increment',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(WriteField, 'p_current',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(WriteField, 'Input Data',
+ (Field, "Field"))
+ reg.add_input_port(WriteField, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(ReadBundle)
+ reg.add_input_port(ReadBundle, 'p_from_env',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadBundle, 'p_types',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadBundle, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(ReadBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(ReadBundle, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(StreamMatrixFromDisk)
+ reg.add_input_port(StreamMatrixFromDisk, 'p_row_or_col',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(StreamMatrixFromDisk, 'p_slider_min',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(StreamMatrixFromDisk, 'p_slider_max',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(StreamMatrixFromDisk, 'p_range_min',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(StreamMatrixFromDisk, 'p_range_max',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(StreamMatrixFromDisk, 'p_playmode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(StreamMatrixFromDisk, 'p_current',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(StreamMatrixFromDisk, 'p_execmode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(StreamMatrixFromDisk, 'p_delay',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(StreamMatrixFromDisk, 'p_inc_amount',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(StreamMatrixFromDisk, 'p_send_amount',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(StreamMatrixFromDisk, 'Indices',
+ (Matrix, "Matrix"))
+ reg.add_input_port(StreamMatrixFromDisk, 'Weights',
+ (Matrix, "Matrix"))
+ reg.add_input_port(StreamMatrixFromDisk, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(StreamMatrixFromDisk, 'DataVector',
+ (Matrix, "Matrix"))
+ reg.add_output_port(StreamMatrixFromDisk, 'Index',
+ (Matrix, "Matrix"))
+ reg.add_output_port(StreamMatrixFromDisk, 'Scaled Index',
+ (Matrix, "Matrix"))
+ reg.add_output_port(StreamMatrixFromDisk, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(WriteMatrix)
+ reg.add_input_port(WriteMatrix, 'p_filetype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteMatrix, 'p_confirm',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteMatrix, 'p_confirm_once',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteMatrix, 'p_exporttype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(WriteMatrix, 'p_split',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(WriteMatrix, 'Input Data',
+ (Matrix, "Matrix"))
+ reg.add_input_port(WriteMatrix, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(ReadNrrd)
+ reg.add_input_port(ReadNrrd, 'p_from_env',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReadNrrd, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(ReadNrrd, 'Output Data',
+ (Field, "Field"))
+ reg.add_output_port(ReadNrrd, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(JoinFields)
+ reg.add_input_port(JoinFields, 'p_tolerance',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(JoinFields, 'p_force_nodemerge',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(JoinFields, 'p_force_pointcloud',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(JoinFields, 'p_matchval',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(JoinFields, 'p_meshonly',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(JoinFields, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(JoinFields, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(RefineMeshByIsovalue)
+ reg.add_input_port(RefineMeshByIsovalue, 'p_isoval',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(RefineMeshByIsovalue, 'p_lte',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(RefineMeshByIsovalue, 'Input',
+ (Field, "Field"))
+ reg.add_input_port(RefineMeshByIsovalue, 'Optional Isovalue',
+ (Matrix, "Matrix"))
+ reg.add_output_port(RefineMeshByIsovalue, 'Refined',
+ (Field, "Field"))
+ reg.add_output_port(RefineMeshByIsovalue, 'Mapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(FairMesh)
+ reg.add_input_port(FairMesh, 'p_iterations',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(FairMesh, 'p_method',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(FairMesh, 'Input Mesh',
+ (Field, "Field"))
+ reg.add_output_port(FairMesh, 'Faired Mesh',
+ (Field, "Field"))
+
+ reg.add_module(CreateStructHex)
+ reg.add_input_port(CreateStructHex, 'p_sizex',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateStructHex, 'p_sizey',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateStructHex, 'p_sizez',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateStructHex, 'p_padpercent',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateStructHex, 'p_data_at',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateStructHex, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(CreateStructHex, 'Output Sample Field',
+ (Field, "Field"))
+
+ reg.add_module(ClipLatVolByIndicesOrWidget)
+ reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_use_text_bbox',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_min_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_min_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_min_z',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_max_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_max_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_max_z',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipLatVolByIndicesOrWidget, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(ClipLatVolByIndicesOrWidget, 'Selection Widget',
+ (Geometry, "Geometry"))
+ reg.add_output_port(ClipLatVolByIndicesOrWidget, 'Output Field',
+ (Field, "Field"))
+ reg.add_output_port(ClipLatVolByIndicesOrWidget, 'MaskVector',
+ (Nrrd, "Nrrd"))
+
+ reg.add_module(GetFieldBoundary)
+ reg.add_input_port(GetFieldBoundary, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(GetFieldBoundary, 'BoundaryField',
+ (Field, "Field"))
+ reg.add_output_port(GetFieldBoundary, 'Mapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ConvertMatricesToMesh)
+ reg.add_input_port(ConvertMatricesToMesh, 'p_fieldname',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertMatricesToMesh, 'p_meshname',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertMatricesToMesh, 'p_fieldbasetype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertMatricesToMesh, 'p_datatype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertMatricesToMesh, 'Mesh Elements',
+ (Matrix, "Matrix"))
+ reg.add_input_port(ConvertMatricesToMesh, 'Mesh Positions',
+ (Matrix, "Matrix"))
+ reg.add_input_port(ConvertMatricesToMesh, 'Mesh Normals',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ConvertMatricesToMesh, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(ClipFieldToFieldOrWidget)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_clip_location',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_clipmode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_autoexecute',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_autoinvert',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_execmode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_center_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_center_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_center_z',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_right_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_right_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_right_z',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_down_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_down_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_down_z',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_in_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_in_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_in_z',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'p_scale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'Input Field',
+ (Field, "Field"))
+ reg.add_input_port(ClipFieldToFieldOrWidget, 'Clip Field',
+ (Field, "Field"))
+ reg.add_output_port(ClipFieldToFieldOrWidget, 'Selection Widget',
+ (Geometry, "Geometry"))
+ reg.add_output_port(ClipFieldToFieldOrWidget, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(RefineMeshByIsovalue2)
+ reg.add_input_port(RefineMeshByIsovalue2, 'p_isoval',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(RefineMeshByIsovalue2, 'p_lte',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(RefineMeshByIsovalue2, 'Input',
+ (Field, "Field"))
+ reg.add_input_port(RefineMeshByIsovalue2, 'Optional Isovalue',
+ (Matrix, "Matrix"))
+ reg.add_output_port(RefineMeshByIsovalue2, 'Refined',
+ (Field, "Field"))
+ reg.add_output_port(RefineMeshByIsovalue2, 'Mapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CreateLatVol)
+ reg.add_input_port(CreateLatVol, 'p_sizex',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateLatVol, 'p_sizey',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateLatVol, 'p_sizez',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateLatVol, 'p_padpercent',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateLatVol, 'p_data_at',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateLatVol, 'p_element_size',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateLatVol, 'Input Field',
+ (Field, "Field"))
+ reg.add_input_port(CreateLatVol, 'LatVol Size',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CreateLatVol, 'Output Sample Field',
+ (Field, "Field"))
+
+ reg.add_module(InterfaceWithCamal)
+ reg.add_input_port(InterfaceWithCamal, 'TriSurf',
+ (Field, "Field"))
+ reg.add_output_port(InterfaceWithCamal, 'TetVol',
+ (Field, "Field"))
+
+ reg.add_module(ClipVolumeByIsovalue)
+ reg.add_input_port(ClipVolumeByIsovalue, 'p_isoval_min',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipVolumeByIsovalue, 'p_isoval_max',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipVolumeByIsovalue, 'p_isoval',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ClipVolumeByIsovalue, 'p_lte',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ClipVolumeByIsovalue, 'p_update_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ClipVolumeByIsovalue, 'Input',
+ (Field, "Field"))
+ reg.add_input_port(ClipVolumeByIsovalue, 'Optional Isovalue',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ClipVolumeByIsovalue, 'Clipped',
+ (Field, "Field"))
+ reg.add_output_port(ClipVolumeByIsovalue, 'Mapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(RefineMesh)
+ reg.add_input_port(RefineMesh, 'p_select',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(RefineMesh, 'p_method',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(RefineMesh, 'p_isoval',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(RefineMesh, 'Mesh',
+ (Field, "Field"))
+ reg.add_input_port(RefineMesh, 'Isovalue',
+ (Matrix, "Matrix"))
+ reg.add_output_port(RefineMesh, 'RefinedMesh',
+ (Field, "Field"))
+ reg.add_output_port(RefineMesh, 'Mapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(MergeFields)
+ reg.add_input_port(MergeFields, 'Container Mesh',
+ (Field, "Field"))
+ reg.add_input_port(MergeFields, 'Insert Field',
+ (Field, "Field"))
+ reg.add_output_port(MergeFields, 'Combined Field',
+ (Field, "Field"))
+ reg.add_output_port(MergeFields, 'Extended Insert Field',
+ (Field, "Field"))
+ reg.add_output_port(MergeFields, 'Combined To Extended Mapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(GetCentroidsFromMesh)
+ reg.add_input_port(GetCentroidsFromMesh, 'TetVolField',
+ (Field, "Field"))
+ reg.add_output_port(GetCentroidsFromMesh, 'PointCloudField',
+ (Field, "Field"))
+
+ reg.add_module(ExtractIsosurfaceByFunction)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_zero_checks',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value_min',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value_max',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value_typed',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value_quantity',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_quantity_range',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_quantity_clusive',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_quantity_min',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_quantity_max',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_quantity_list',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value_list',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_matrix_list',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_algorithm',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_active_slice_value_selection_tab',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_active_tab',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'p_update_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'Input Field',
+ (Field, "Field"))
+ reg.add_input_port(ExtractIsosurfaceByFunction, 'Optional Slice values',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ExtractIsosurfaceByFunction, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(MergeTriSurfs)
+ reg.add_input_port(MergeTriSurfs, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(MergeTriSurfs, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(InterfaceWithTetGen)
+ reg.add_input_port(InterfaceWithTetGen, 'p_switch',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InterfaceWithTetGen, 'Main',
+ (Field, "Field"))
+ reg.add_input_port(InterfaceWithTetGen, 'Points',
+ (Field, "Field"))
+ reg.add_input_port(InterfaceWithTetGen, 'Region Attribs',
+ (Field, "Field"))
+ reg.add_input_port(InterfaceWithTetGen, 'Regions',
+ (Field, "Field"))
+ reg.add_output_port(InterfaceWithTetGen, 'TetVol',
+ (Field, "Field"))
+
+ reg.add_module(CreateImage)
+ reg.add_input_port(CreateImage, 'p_sizex',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_sizey',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_sizez',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_z_value',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_auto_size',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_axis',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_padpercent',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_pos',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_data_at',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_update_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_corigin_x',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_corigin_y',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_corigin_z',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_cnormal_x',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_cnormal_y',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateImage, 'p_cnormal_z',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateImage, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(CreateImage, 'Output Sample Field',
+ (Field, "Field"))
+
+ reg.add_module(InsertHexVolSheetAlongSurface)
+ reg.add_input_port(InsertHexVolSheetAlongSurface, 'p_side',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertHexVolSheetAlongSurface, 'p_addlayer',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertHexVolSheetAlongSurface, 'HexField',
+ (Field, "Field"))
+ reg.add_input_port(InsertHexVolSheetAlongSurface, 'TriField',
+ (Field, "Field"))
+ reg.add_output_port(InsertHexVolSheetAlongSurface, 'Side1Field',
+ (Field, "Field"))
+ reg.add_output_port(InsertHexVolSheetAlongSurface, 'Side2Field',
+ (Field, "Field"))
+
+ reg.add_module(GenerateSinglePointProbeFromField)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_main_frame',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_locx',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_locy',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_locz',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_value',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_node',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_edge',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_face',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_cell',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_show_value',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_show_node',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_show_edge',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_show_face',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_show_cell',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'p_probe_scale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateSinglePointProbeFromField, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(GenerateSinglePointProbeFromField, 'GenerateSinglePointProbeFromField Widget',
+ (Geometry, "Geometry"))
+ reg.add_output_port(GenerateSinglePointProbeFromField, 'GenerateSinglePointProbeFromField Point',
+ (Field, "Field"))
+ reg.add_output_port(GenerateSinglePointProbeFromField, 'Element Index',
+ (Matrix, "Matrix"))
+
+ reg.add_module(InterfaceWithCubit)
+ reg.add_input_port(InterfaceWithCubit, 'p_cubitdir',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InterfaceWithCubit, 'p_ncdump',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InterfaceWithCubit, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(InterfaceWithCubit, 'PointCloudField',
+ (Field, "Field"))
+ reg.add_output_port(InterfaceWithCubit, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(ClipFieldByFunction)
+ reg.add_input_port(ClipFieldByFunction, 'p_mode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ClipFieldByFunction, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ClipFieldByFunction, 'Function',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(ClipFieldByFunction, 'Input',
+ (Field, "Field"))
+ reg.add_output_port(ClipFieldByFunction, 'Clipped',
+ (Field, "Field"))
+ reg.add_output_port(ClipFieldByFunction, 'Mapping',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ClipFieldByFunction, 'MaskVector',
+ (Nrrd, "Nrrd"))
+
+ reg.add_module(GetDomainBoundary)
+ reg.add_input_port(GetDomainBoundary, 'p_userange',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetDomainBoundary, 'p_minrange',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GetDomainBoundary, 'p_maxrange',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GetDomainBoundary, 'p_usevalue',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetDomainBoundary, 'p_value',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GetDomainBoundary, 'p_includeouterboundary',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetDomainBoundary, 'p_innerboundaryonly',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetDomainBoundary, 'p_noinnerboundary',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetDomainBoundary, 'p_disconnect',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetDomainBoundary, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(GetDomainBoundary, 'MinValueValue',
+ (Matrix, "Matrix"))
+ reg.add_input_port(GetDomainBoundary, 'MaxValue',
+ (Matrix, "Matrix"))
+ reg.add_output_port(GetDomainBoundary, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(CollectFields)
+ reg.add_input_port(CollectFields, 'p_buffersize',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CollectFields, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(CollectFields, 'BufferSize',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CollectFields, 'Fields',
+ (Field, "Field"))
+
+ reg.add_module(GeneratePointSamplesFromField)
+ reg.add_input_port(GeneratePointSamplesFromField, 'p_num_seeds',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromField, 'p_probe_scale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromField, 'p_send',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromField, 'p_widget',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromField, 'p_red',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromField, 'p_green',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromField, 'p_blue',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromField, 'p_auto_execute',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromField, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(GeneratePointSamplesFromField, 'GeneratePointSamplesFromField Widget',
+ (Geometry, "Geometry"))
+ reg.add_output_port(GeneratePointSamplesFromField, 'GeneratePointSamplesFromField Point',
+ (Field, "Field"))
+
+ reg.add_module(GeneratePointSamplesFromFieldOrWidget)
+ reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_wtype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_endpoints',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_maxseeds',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_numseeds',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_rngseed',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_rnginc',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_clamp',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_autoexecute',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_dist',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_whichtab',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'Field to Sample',
+ (Field, "Field"))
+ reg.add_output_port(GeneratePointSamplesFromFieldOrWidget, 'Samples',
+ (Field, "Field"))
+ reg.add_output_port(GeneratePointSamplesFromFieldOrWidget, 'Sampling Widget',
+ (Geometry, "Geometry"))
+
+ reg.add_module(DecimateTriSurf)
+ reg.add_input_port(DecimateTriSurf, 'TriSurf',
+ (Field, "Field"))
+ reg.add_output_port(DecimateTriSurf, 'Decimated',
+ (Field, "Field"))
+
+ reg.add_module(GetSliceFromStructuredFieldByIndices)
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_axis',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_dims',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_dim_i',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_dim_j',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_dim_k',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_index_i',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_index_j',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_index_k',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_update_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_continuous',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'Input Field',
+ (Field, "Field"))
+ reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'Input Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(GetSliceFromStructuredFieldByIndices, 'Output Field',
+ (Field, "Field"))
+ reg.add_output_port(GetSliceFromStructuredFieldByIndices, 'Output Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(RemoveHexVolSheet)
+ reg.add_input_port(RemoveHexVolSheet, 'p_edge_list',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(RemoveHexVolSheet, 'HexField',
+ (Field, "Field"))
+ reg.add_output_port(RemoveHexVolSheet, 'NewHexField',
+ (Field, "Field"))
+ reg.add_output_port(RemoveHexVolSheet, 'ExtractedHexes',
+ (Field, "Field"))
+
+ reg.add_module(SubsampleStructuredFieldByIndices)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_power_app',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_wrap',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_dims',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_dim_i',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_dim_j',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_dim_k',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_start_i',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_start_j',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_start_k',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stop_i',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stop_j',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stop_k',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stride_i',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stride_j',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stride_k',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_wrap_i',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_wrap_j',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_wrap_k',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'Input Field',
+ (Field, "Field"))
+ reg.add_input_port(SubsampleStructuredFieldByIndices, 'Input Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SubsampleStructuredFieldByIndices, 'Output Field',
+ (Field, "Field"))
+ reg.add_output_port(SubsampleStructuredFieldByIndices, 'Output Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(GetAllSegmentationBoundaries)
+ reg.add_input_port(GetAllSegmentationBoundaries, 'Segmentations',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(GetAllSegmentationBoundaries, 'Boundaries',
+ (Field, "Field"))
+
+ reg.add_module(ClipFieldWithSeed)
+ reg.add_input_port(ClipFieldWithSeed, 'p_mode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ClipFieldWithSeed, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ClipFieldWithSeed, 'Function',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(ClipFieldWithSeed, 'Input',
+ (Field, "Field"))
+ reg.add_input_port(ClipFieldWithSeed, 'Seeds',
+ (Field, "Field"))
+ reg.add_output_port(ClipFieldWithSeed, 'Clipped',
+ (Field, "Field"))
+ reg.add_output_port(ClipFieldWithSeed, 'Mapping',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ClipFieldWithSeed, 'MaskVector',
+ (Nrrd, "Nrrd"))
+
+ reg.add_module(SplitNodesByDomain)
+ reg.add_input_port(SplitNodesByDomain, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(SplitNodesByDomain, 'SplitField',
+ (Field, "Field"))
+
+ reg.add_module(ApplyMappingMatrix)
+ reg.add_input_port(ApplyMappingMatrix, 'Source',
+ (Field, "Field"))
+ reg.add_input_port(ApplyMappingMatrix, 'Destination',
+ (Field, "Field"))
+ reg.add_input_port(ApplyMappingMatrix, 'Mapping',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ApplyMappingMatrix, 'Output',
+ (Field, "Field"))
+
+ reg.add_module(MaskLatVolWithTriSurf)
+ reg.add_input_port(MaskLatVolWithTriSurf, 'LatVolField',
+ (Field, "Field"))
+ reg.add_input_port(MaskLatVolWithTriSurf, 'TriSurfField',
+ (Field, "Field"))
+ reg.add_output_port(MaskLatVolWithTriSurf, 'LatVol Mask',
+ (Field, "Field"))
+
+ reg.add_module(ConvertFieldBasis)
+ reg.add_input_port(ConvertFieldBasis, 'p_output_basis',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertFieldBasis, 'Input',
+ (Field, "Field"))
+ reg.add_output_port(ConvertFieldBasis, 'Output',
+ (Field, "Field"))
+ reg.add_output_port(ConvertFieldBasis, 'Mapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReportMeshQualityMeasures)
+ reg.add_input_port(ReportMeshQualityMeasures, 'Input',
+ (Field, "Field"))
+ reg.add_output_port(ReportMeshQualityMeasures, 'Checked',
+ (Nrrd, "Nrrd"))
+
+ reg.add_module(SelectAndSetFieldData)
+ reg.add_input_port(SelectAndSetFieldData, 'p_selection1',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData, 'p_function1',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData, 'p_selection2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData, 'p_function2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData, 'p_selection3',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData, 'p_function3',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData, 'p_selection4',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData, 'p_function4',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData, 'p_functiondef',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData, 'p_format',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(SelectAndSetFieldData, 'Array',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SelectAndSetFieldData, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(CalculateFieldData3)
+ reg.add_input_port(CalculateFieldData3, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateFieldData3, 'p_format',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateFieldData3, 'Field1',
+ (Field, "Field"))
+ reg.add_input_port(CalculateFieldData3, 'Field2',
+ (Field, "Field"))
+ reg.add_input_port(CalculateFieldData3, 'Field3',
+ (Field, "Field"))
+ reg.add_input_port(CalculateFieldData3, 'Function',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(CalculateFieldData3, 'Array',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CalculateFieldData3, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(SetFieldData)
+ reg.add_input_port(SetFieldData, 'p_keepscalartype',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SetFieldData, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(SetFieldData, 'Matrix Data',
+ (Matrix, "Matrix"))
+ reg.add_input_port(SetFieldData, 'Nrrd Data',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(SetFieldData, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(SwapFieldDataWithMatrixEntries)
+ reg.add_input_port(SwapFieldDataWithMatrixEntries, 'p_preserve_scalar_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SwapFieldDataWithMatrixEntries, 'Input Field',
+ (Field, "Field"))
+ reg.add_input_port(SwapFieldDataWithMatrixEntries, 'Input Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SwapFieldDataWithMatrixEntries, 'Output Field',
+ (Field, "Field"))
+ reg.add_output_port(SwapFieldDataWithMatrixEntries, 'Output Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ConvertLatVolDataFromElemToNode)
+ reg.add_input_port(ConvertLatVolDataFromElemToNode, 'Elem Field',
+ (Field, "Field"))
+ reg.add_output_port(ConvertLatVolDataFromElemToNode, 'Node Field',
+ (Field, "Field"))
+
+ reg.add_module(CalculateNodeNormals)
+ reg.add_input_port(CalculateNodeNormals, 'Input Field',
+ (Field, "Field"))
+ reg.add_input_port(CalculateNodeNormals, 'Input Point',
+ (Field, "Field"))
+ reg.add_output_port(CalculateNodeNormals, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(CalculateVectorMagnitudes)
+ reg.add_input_port(CalculateVectorMagnitudes, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(CalculateVectorMagnitudes, 'Output CalculateVectorMagnitudes',
+ (Field, "Field"))
+
+ reg.add_module(ConvertIndicesToFieldData)
+ reg.add_input_port(ConvertIndicesToFieldData, 'p_outputtype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertIndicesToFieldData, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(ConvertIndicesToFieldData, 'Data',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ConvertIndicesToFieldData, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(CalculateDistanceToFieldBoundary)
+ reg.add_input_port(CalculateDistanceToFieldBoundary, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(CalculateDistanceToFieldBoundary, 'DistanceField',
+ (Field, "Field"))
+
+ reg.add_module(MapFieldDataFromSourceToDestination)
+ reg.add_input_port(MapFieldDataFromSourceToDestination, 'p_interpolation_basis',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(MapFieldDataFromSourceToDestination, 'p_map_source_to_single_dest',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(MapFieldDataFromSourceToDestination, 'p_exhaustive_search',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(MapFieldDataFromSourceToDestination, 'p_exhaustive_search_max_dist',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(MapFieldDataFromSourceToDestination, 'p_np',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(MapFieldDataFromSourceToDestination, 'Source',
+ (Field, "Field"))
+ reg.add_input_port(MapFieldDataFromSourceToDestination, 'Destination',
+ (Field, "Field"))
+ reg.add_output_port(MapFieldDataFromSourceToDestination, 'Remapped Destination',
+ (Field, "Field"))
+
+ reg.add_module(SelectAndSetFieldData3)
+ reg.add_input_port(SelectAndSetFieldData3, 'p_selection1',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData3, 'p_function1',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData3, 'p_selection2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData3, 'p_function2',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData3, 'p_selection3',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData3, 'p_function3',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData3, 'p_selection4',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData3, 'p_function4',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData3, 'p_functiondef',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData3, 'p_format',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SelectAndSetFieldData3, 'Field1',
+ (Field, "Field"))
+ reg.add_input_port(SelectAndSetFieldData3, 'Field2',
+ (Field, "Field"))
+ reg.add_input_port(SelectAndSetFieldData3, 'Field3',
+ (Field, "Field"))
+ reg.add_input_port(SelectAndSetFieldData3, 'Array',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SelectAndSetFieldData3, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(CreateFieldData)
+ reg.add_input_port(CreateFieldData, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateFieldData, 'p_format',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateFieldData, 'p_basis',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateFieldData, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(CreateFieldData, 'Function',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(CreateFieldData, 'DataArray',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CreateFieldData, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(ConvertLatVolDataFromNodeToElem)
+ reg.add_input_port(ConvertLatVolDataFromNodeToElem, 'Node Field',
+ (Field, "Field"))
+ reg.add_output_port(ConvertLatVolDataFromNodeToElem, 'Elem Field',
+ (Field, "Field"))
+
+ reg.add_module(CalculateFieldDataCompiled)
+ reg.add_input_port(CalculateFieldDataCompiled, 'p_outputdatatype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateFieldDataCompiled, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateFieldDataCompiled, 'p_cache',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CalculateFieldDataCompiled, 'Function',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(CalculateFieldDataCompiled, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(CalculateFieldDataCompiled, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(MapFieldDataFromElemToNode)
+ reg.add_input_port(MapFieldDataFromElemToNode, 'p_method',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(MapFieldDataFromElemToNode, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(MapFieldDataFromElemToNode, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(ApplyFilterToFieldData)
+ reg.add_input_port(ApplyFilterToFieldData, 'p_method',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ApplyFilterToFieldData, 'p_ed_method',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ApplyFilterToFieldData, 'p_ed_iterations',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ApplyFilterToFieldData, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(ApplyFilterToFieldData, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(GetFieldData)
+ reg.add_input_port(GetFieldData, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(GetFieldData, 'Data',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CalculateFieldData2)
+ reg.add_input_port(CalculateFieldData2, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateFieldData2, 'p_format',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateFieldData2, 'Field1',
+ (Field, "Field"))
+ reg.add_input_port(CalculateFieldData2, 'Field2',
+ (Field, "Field"))
+ reg.add_input_port(CalculateFieldData2, 'Function',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(CalculateFieldData2, 'Array',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CalculateFieldData2, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(CalculateLatVolGradientsAtNodes)
+ reg.add_input_port(CalculateLatVolGradientsAtNodes, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(CalculateLatVolGradientsAtNodes, 'Output Gradient',
+ (Field, "Field"))
+
+ reg.add_module(CalculateGradients)
+ reg.add_input_port(CalculateGradients, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(CalculateGradients, 'Output CalculateGradients',
+ (Field, "Field"))
+
+ reg.add_module(CalculateSignedDistanceToField)
+ reg.add_input_port(CalculateSignedDistanceToField, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(CalculateSignedDistanceToField, 'ObjectField',
+ (Field, "Field"))
+ reg.add_output_port(CalculateSignedDistanceToField, 'SignedDistanceField',
+ (Field, "Field"))
+
+ reg.add_module(CalculateInsideWhichField)
+ reg.add_input_port(CalculateInsideWhichField, 'p_outputbasis',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateInsideWhichField, 'p_outputtype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateInsideWhichField, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(CalculateInsideWhichField, 'Object',
+ (Field, "Field"))
+ reg.add_output_port(CalculateInsideWhichField, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(MapFieldDataFromNodeToElem)
+ reg.add_input_port(MapFieldDataFromNodeToElem, 'p_method',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(MapFieldDataFromNodeToElem, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(MapFieldDataFromNodeToElem, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(ConvertFieldDataType)
+ reg.add_input_port(ConvertFieldDataType, 'p_outputdatatype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertFieldDataType, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(ConvertFieldDataType, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(CalculateIsInsideField)
+ reg.add_input_port(CalculateIsInsideField, 'p_outputtype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateIsInsideField, 'p_outval',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CalculateIsInsideField, 'p_inval',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CalculateIsInsideField, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(CalculateIsInsideField, 'ObjectField',
+ (Field, "Field"))
+ reg.add_output_port(CalculateIsInsideField, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(CalculateFieldData)
+ reg.add_input_port(CalculateFieldData, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateFieldData, 'p_format',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateFieldData, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(CalculateFieldData, 'Function',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(CalculateFieldData, 'Array',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CalculateFieldData, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(CalculateDistanceToField)
+ reg.add_input_port(CalculateDistanceToField, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(CalculateDistanceToField, 'ObjectField',
+ (Field, "Field"))
+ reg.add_output_port(CalculateDistanceToField, 'DistanceField',
+ (Field, "Field"))
+
+ reg.add_module(TransformPlanarMesh)
+ reg.add_input_port(TransformPlanarMesh, 'p_axis',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(TransformPlanarMesh, 'p_invert',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(TransformPlanarMesh, 'p_trans_x',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(TransformPlanarMesh, 'p_trans_y',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(TransformPlanarMesh, 'Input Field',
+ (Field, "Field"))
+ reg.add_input_port(TransformPlanarMesh, 'Index Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(TransformPlanarMesh, 'Transformed Field',
+ (Field, "Field"))
+
+ reg.add_module(ConvertMeshToUnstructuredMesh)
+ reg.add_input_port(ConvertMeshToUnstructuredMesh, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(ConvertMeshToUnstructuredMesh, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(ConvertQuadSurfToTriSurf)
+ reg.add_input_port(ConvertQuadSurfToTriSurf, 'QuadSurf',
+ (Field, "Field"))
+ reg.add_output_port(ConvertQuadSurfToTriSurf, 'TriSurf',
+ (Field, "Field"))
+
+ reg.add_module(TransformMeshWithFunction)
+ reg.add_input_port(TransformMeshWithFunction, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(TransformMeshWithFunction, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(TransformMeshWithFunction, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(ConvertHexVolToTetVol)
+ reg.add_input_port(ConvertHexVolToTetVol, 'HexVol',
+ (Field, "Field"))
+ reg.add_output_port(ConvertHexVolToTetVol, 'TetVol',
+ (Field, "Field"))
+
+ reg.add_module(ConvertMeshCoordinateSystem)
+ reg.add_input_port(ConvertMeshCoordinateSystem, 'p_oldsystem',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertMeshCoordinateSystem, 'p_newsystem',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertMeshCoordinateSystem, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(ConvertMeshCoordinateSystem, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(ConvertMeshToPointCloud)
+ reg.add_input_port(ConvertMeshToPointCloud, 'p_datalocation',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ConvertMeshToPointCloud, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(ConvertMeshToPointCloud, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(TransformMeshWithTransform)
+ reg.add_input_port(TransformMeshWithTransform, 'Input Field',
+ (Field, "Field"))
+ reg.add_input_port(TransformMeshWithTransform, 'Transform Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(TransformMeshWithTransform, 'Transformed Field',
+ (Field, "Field"))
+
+ reg.add_module(ConvertRegularMeshToStructuredMesh)
+ reg.add_input_port(ConvertRegularMeshToStructuredMesh, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(ConvertRegularMeshToStructuredMesh, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(CalculateMeshNodes)
+ reg.add_input_port(CalculateMeshNodes, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateMeshNodes, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(CalculateMeshNodes, 'Function',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(CalculateMeshNodes, 'Array',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CalculateMeshNodes, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(SmoothMesh)
+ reg.add_input_port(SmoothMesh, 'Input',
+ (Field, "Field"))
+ reg.add_input_port(SmoothMesh, 'IsoValue',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SmoothMesh, 'Smoothed',
+ (Field, "Field"))
+
+ reg.add_module(EditMeshBoundingBox)
+ reg.add_input_port(EditMeshBoundingBox, 'p_outputcenterx',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_outputcentery',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_outputcenterz',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_outputsizex',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_outputsizey',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_outputsizez',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_useoutputcenter',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_useoutputsize',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_scale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_mode',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_real_scale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_center_x',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_center_y',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_center_z',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_right_x',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_right_y',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_right_z',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_down_x',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_down_y',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_down_z',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_in_x',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_in_y',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'p_box_in_z',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EditMeshBoundingBox, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(EditMeshBoundingBox, 'Output Field',
+ (Field, "Field"))
+ reg.add_output_port(EditMeshBoundingBox, 'Transformation Widget',
+ (Geometry, "Geometry"))
+ reg.add_output_port(EditMeshBoundingBox, 'Transformation Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(SwapNodeLocationsWithMatrixEntries)
+ reg.add_input_port(SwapNodeLocationsWithMatrixEntries, 'Input Field',
+ (Field, "Field"))
+ reg.add_input_port(SwapNodeLocationsWithMatrixEntries, 'Input Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SwapNodeLocationsWithMatrixEntries, 'Output Field',
+ (Field, "Field"))
+ reg.add_output_port(SwapNodeLocationsWithMatrixEntries, 'Output Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(MapFieldDataToNodeCoordinate)
+ reg.add_input_port(MapFieldDataToNodeCoordinate, 'p_coord',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(MapFieldDataToNodeCoordinate, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(MapFieldDataToNodeCoordinate, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(ScaleFieldMeshAndData)
+ reg.add_input_port(ScaleFieldMeshAndData, 'p_datascale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ScaleFieldMeshAndData, 'p_geomscale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ScaleFieldMeshAndData, 'p_usegeomcenter',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ScaleFieldMeshAndData, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(ScaleFieldMeshAndData, 'GeomScaleFactor',
+ (Matrix, "Matrix"))
+ reg.add_input_port(ScaleFieldMeshAndData, 'DataScaleFactor',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ScaleFieldMeshAndData, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(ReportColumnMatrixMisfit)
+ reg.add_input_port(ReportColumnMatrixMisfit, 'p_have_ui',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReportColumnMatrixMisfit, 'p_methodTCL',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReportColumnMatrixMisfit, 'p_pTCL',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReportColumnMatrixMisfit, 'Vec1',
+ (Matrix, "Matrix"))
+ reg.add_input_port(ReportColumnMatrixMisfit, 'Vec2',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportColumnMatrixMisfit, 'Error Out',
+ (Matrix, "Matrix"))
+
+ reg.add_module(EvaluateLinAlgGeneral)
+ reg.add_input_port(EvaluateLinAlgGeneral, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EvaluateLinAlgGeneral, 'i1',
+ (Matrix, "Matrix"))
+ reg.add_input_port(EvaluateLinAlgGeneral, 'i2',
+ (Matrix, "Matrix"))
+ reg.add_input_port(EvaluateLinAlgGeneral, 'i3',
+ (Matrix, "Matrix"))
+ reg.add_input_port(EvaluateLinAlgGeneral, 'i4',
+ (Matrix, "Matrix"))
+ reg.add_input_port(EvaluateLinAlgGeneral, 'i5',
+ (Matrix, "Matrix"))
+ reg.add_output_port(EvaluateLinAlgGeneral, 'o1',
+ (Matrix, "Matrix"))
+ reg.add_output_port(EvaluateLinAlgGeneral, 'o2',
+ (Matrix, "Matrix"))
+ reg.add_output_port(EvaluateLinAlgGeneral, 'o3',
+ (Matrix, "Matrix"))
+ reg.add_output_port(EvaluateLinAlgGeneral, 'o4',
+ (Matrix, "Matrix"))
+ reg.add_output_port(EvaluateLinAlgGeneral, 'o5',
+ (Matrix, "Matrix"))
+
+ reg.add_module(AppendMatrix)
+ reg.add_input_port(AppendMatrix, 'p_row_or_column',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(AppendMatrix, 'BaseMatrix',
+ (Matrix, "Matrix"))
+ reg.add_input_port(AppendMatrix, 'AppendMatrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(AppendMatrix, 'Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(EvaluateLinAlgBinary)
+ reg.add_input_port(EvaluateLinAlgBinary, 'p_op',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EvaluateLinAlgBinary, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EvaluateLinAlgBinary, 'A',
+ (Matrix, "Matrix"))
+ reg.add_input_port(EvaluateLinAlgBinary, 'B',
+ (Matrix, "Matrix"))
+ reg.add_output_port(EvaluateLinAlgBinary, 'Output',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ConvertMaskVectorToMappingMatrix)
+ reg.add_input_port(ConvertMaskVectorToMappingMatrix, 'MaskVector',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(ConvertMaskVectorToMappingMatrix, 'MappingMatrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(SolveLinearSystem)
+ reg.add_input_port(SolveLinearSystem, 'p_target_error',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_flops',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_floprate',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_memrefs',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_memrate',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_orig_error',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_current_error',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_method',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_precond',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_iteration',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_maxiter',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_use_previous_soln',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_emit_partial',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_emit_iter',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_status',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'p_np',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SolveLinearSystem, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_input_port(SolveLinearSystem, 'RHS',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SolveLinearSystem, 'Solution',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReportMatrixColumnMeasure)
+ reg.add_input_port(ReportMatrixColumnMeasure, 'p_method',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReportMatrixColumnMeasure, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportMatrixColumnMeasure, 'Vector',
+ (Matrix, "Matrix"))
+
+ reg.add_module(SortMatrix)
+ reg.add_input_port(SortMatrix, 'p_row_or_col',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SortMatrix, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SortMatrix, 'Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CreateGeometricTransform)
+ reg.add_input_port(CreateGeometricTransform, 'p_rotate_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_rotate_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_rotate_z',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_rotate_theta',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_translate_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_translate_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_translate_z',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_scale_uniform',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_scale_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_scale_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_scale_z',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_shear_plane_a',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_shear_plane_b',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_shear_plane_c',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_widget_resizable',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_permute_x',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_permute_y',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_permute_z',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_pre_transform',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_which_transform',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_widget_scale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'p_ignoring_widget_changes',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateGeometricTransform, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CreateGeometricTransform, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CreateGeometricTransform, 'Geometry',
+ (Geometry, "Geometry"))
+
+ reg.add_module(ChooseMatrix)
+ reg.add_input_port(ChooseMatrix, 'p_use_first_valid',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ChooseMatrix, 'p_port_valid_index',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ChooseMatrix, 'p_port_selected_index',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ChooseMatrix, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ChooseMatrix, 'Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ConvertMappingMatrixToMaskVector)
+ reg.add_input_port(ConvertMappingMatrixToMaskVector, 'MappingMatrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ConvertMappingMatrixToMaskVector, 'MaskVector',
+ (Nrrd, "Nrrd"))
+
+ reg.add_module(ResizeMatrix)
+ reg.add_input_port(ResizeMatrix, 'p_dim_m',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ResizeMatrix, 'p_dim_n',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ResizeMatrix, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_input_port(ResizeMatrix, 'M',
+ (Matrix, "Matrix"))
+ reg.add_input_port(ResizeMatrix, 'N',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ResizeMatrix, 'Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CollectMatrices)
+ reg.add_input_port(CollectMatrices, 'p_append',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CollectMatrices, 'p_row',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CollectMatrices, 'p_front',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CollectMatrices, 'Optional BaseMatrix',
+ (Matrix, "Matrix"))
+ reg.add_input_port(CollectMatrices, 'SubMatrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CollectMatrices, 'CompositeMatrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(GetColumnOrRowFromMatrix)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_row_or_col',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_selectable_min',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_selectable_max',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_selectable_inc',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_selectable_units',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_range_min',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_range_max',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_playmode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_current',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_execmode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_delay',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_inc_amount',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_send_amount',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'p_data_series_done',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'Weight Vector',
+ (Matrix, "Matrix"))
+ reg.add_input_port(GetColumnOrRowFromMatrix, 'Current Index',
+ (Matrix, "Matrix"))
+ reg.add_output_port(GetColumnOrRowFromMatrix, 'Vector',
+ (Matrix, "Matrix"))
+ reg.add_output_port(GetColumnOrRowFromMatrix, 'Selected Index',
+ (Matrix, "Matrix"))
+
+ reg.add_module(BuildNoiseColumnMatrix)
+ reg.add_input_port(BuildNoiseColumnMatrix, 'p_snr',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(BuildNoiseColumnMatrix, 'Signal',
+ (Matrix, "Matrix"))
+ reg.add_output_port(BuildNoiseColumnMatrix, 'Noise',
+ (Matrix, "Matrix"))
+
+ reg.add_module(EvaluateLinAlgUnary)
+ reg.add_input_port(EvaluateLinAlgUnary, 'p_op',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EvaluateLinAlgUnary, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(EvaluateLinAlgUnary, 'Input',
+ (Matrix, "Matrix"))
+ reg.add_output_port(EvaluateLinAlgUnary, 'Output',
+ (Matrix, "Matrix"))
+
+ reg.add_module(GetSubmatrix)
+ reg.add_input_port(GetSubmatrix, 'p_mincol',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetSubmatrix, 'p_maxcol',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetSubmatrix, 'p_minrow',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetSubmatrix, 'p_maxrow',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetSubmatrix, 'p_nrow',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetSubmatrix, 'p_ncol',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetSubmatrix, 'Input Matrix',
+ (Matrix, "Matrix"))
+ reg.add_input_port(GetSubmatrix, 'Optional Range Bounds',
+ (Matrix, "Matrix"))
+ reg.add_output_port(GetSubmatrix, 'Output Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReorderMatrixByReverseCuthillMcKee)
+ reg.add_input_port(ReorderMatrixByReverseCuthillMcKee, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReorderMatrixByReverseCuthillMcKee, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReorderMatrixByReverseCuthillMcKee, 'Mapping',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReorderMatrixByReverseCuthillMcKee, 'InverseMapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CreateMatrix)
+ reg.add_input_port(CreateMatrix, 'p_rows',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateMatrix, 'p_cols',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateMatrix, 'p_data',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateMatrix, 'p_clabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateMatrix, 'p_rlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_output_port(CreateMatrix, 'matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(SolveMinNormLeastSqSystem)
+ reg.add_input_port(SolveMinNormLeastSqSystem, 'BasisVec1',
+ (Matrix, "Matrix"))
+ reg.add_input_port(SolveMinNormLeastSqSystem, 'BasisVec2',
+ (Matrix, "Matrix"))
+ reg.add_input_port(SolveMinNormLeastSqSystem, 'BasisVec3',
+ (Matrix, "Matrix"))
+ reg.add_input_port(SolveMinNormLeastSqSystem, 'TargetVec',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SolveMinNormLeastSqSystem, 'WeightVec(Col)',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SolveMinNormLeastSqSystem, 'ResultVec(Col)',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ConvertMatrixType)
+ reg.add_input_port(ConvertMatrixType, 'p_oldtype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertMatrixType, 'p_newtype',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertMatrixType, 'p_nrow',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertMatrixType, 'p_ncol',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertMatrixType, 'Input',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ConvertMatrixType, 'Output',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReportMatrixRowMeasure)
+ reg.add_input_port(ReportMatrixRowMeasure, 'p_method',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReportMatrixRowMeasure, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportMatrixRowMeasure, 'Vector',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReorderMatrixByCuthillMcKee)
+ reg.add_input_port(ReorderMatrixByCuthillMcKee, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReorderMatrixByCuthillMcKee, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReorderMatrixByCuthillMcKee, 'Mapping',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReorderMatrixByCuthillMcKee, 'InverseMapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReportMatrixInfo)
+ reg.add_input_port(ReportMatrixInfo, 'Input',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportMatrixInfo, 'NumRows',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportMatrixInfo, 'NumCols',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportMatrixInfo, 'NumElements',
+ (Matrix, "Matrix"))
+
+ reg.add_module(RemoveZerosFromMatrix)
+ reg.add_input_port(RemoveZerosFromMatrix, 'p_row_or_col',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(RemoveZerosFromMatrix, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(RemoveZerosFromMatrix, 'Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(RemoveZeroRowsAndColumns)
+ reg.add_input_port(RemoveZeroRowsAndColumns, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(RemoveZeroRowsAndColumns, 'ReducedMatrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(RemoveZeroRowsAndColumns, 'LeftMapping',
+ (Matrix, "Matrix"))
+ reg.add_output_port(RemoveZeroRowsAndColumns, 'RightMapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CreateDataArray)
+ reg.add_input_port(CreateDataArray, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateDataArray, 'p_format',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateDataArray, 'Size',
+ (Matrix, "Matrix"))
+ reg.add_input_port(CreateDataArray, 'Function',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(CreateDataArray, 'Array',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CreateDataArray, 'DataArray',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CreateDataArrayFromIndices)
+ reg.add_input_port(CreateDataArrayFromIndices, 'Indices',
+ (Matrix, "Matrix"))
+ reg.add_input_port(CreateDataArrayFromIndices, 'Template',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CreateDataArrayFromIndices, 'DataArray',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReportDataArrayInfo)
+ reg.add_input_port(ReportDataArrayInfo, 'DataArray',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportDataArrayInfo, 'NumElements',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CreateVectorArray)
+ reg.add_input_port(CreateVectorArray, 'X',
+ (Matrix, "Matrix"))
+ reg.add_input_port(CreateVectorArray, 'Y',
+ (Matrix, "Matrix"))
+ reg.add_input_port(CreateVectorArray, 'Z',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CreateVectorArray, 'Vector',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReplicateDataArray)
+ reg.add_input_port(ReplicateDataArray, 'p_size',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReplicateDataArray, 'DataArray',
+ (Matrix, "Matrix"))
+ reg.add_input_port(ReplicateDataArray, 'Size',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReplicateDataArray, 'DataArray',
+ (Matrix, "Matrix"))
+
+ reg.add_module(SplitVectorArrayInXYZ)
+ reg.add_input_port(SplitVectorArrayInXYZ, 'VectorArray',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SplitVectorArrayInXYZ, 'X',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SplitVectorArrayInXYZ, 'Y',
+ (Matrix, "Matrix"))
+ reg.add_output_port(SplitVectorArrayInXYZ, 'Z',
+ (Matrix, "Matrix"))
+
+ reg.add_module(DecomposeTensorArrayIntoEigenVectors)
+ reg.add_input_port(DecomposeTensorArrayIntoEigenVectors, 'TensorArray',
+ (Matrix, "Matrix"))
+ reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenVector1',
+ (Matrix, "Matrix"))
+ reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenVector2',
+ (Matrix, "Matrix"))
+ reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenVector3',
+ (Matrix, "Matrix"))
+ reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenValue1',
+ (Matrix, "Matrix"))
+ reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenValue2',
+ (Matrix, "Matrix"))
+ reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenValue3',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CalculateDataArray)
+ reg.add_input_port(CalculateDataArray, 'p_function',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateDataArray, 'p_format',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CalculateDataArray, 'DataArray',
+ (Matrix, "Matrix"))
+ reg.add_input_port(CalculateDataArray, 'Function',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(CalculateDataArray, 'Array',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CalculateDataArray, 'DataArray',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReportDataArrayMeasure)
+ reg.add_input_port(ReportDataArrayMeasure, 'p_measure',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReportDataArrayMeasure, 'Array',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportDataArrayMeasure, 'Measure',
+ (Matrix, "Matrix"))
+
+ reg.add_module(AppendDataArrays)
+ reg.add_input_port(AppendDataArrays, 'Array',
+ (Matrix, "Matrix"))
+ reg.add_output_port(AppendDataArrays, 'Array',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CreateTensorArray)
+ reg.add_input_port(CreateTensorArray, 'EigenVector1',
+ (Matrix, "Matrix"))
+ reg.add_input_port(CreateTensorArray, 'EigenVector2',
+ (Matrix, "Matrix"))
+ reg.add_input_port(CreateTensorArray, 'EigenValue1',
+ (Matrix, "Matrix"))
+ reg.add_input_port(CreateTensorArray, 'EigenValue2',
+ (Matrix, "Matrix"))
+ reg.add_input_port(CreateTensorArray, 'EigenValue3',
+ (Matrix, "Matrix"))
+ reg.add_output_port(CreateTensorArray, 'TensorArray',
+ (Matrix, "Matrix"))
+
+ reg.add_module(PrintMatrixIntoString)
+ reg.add_input_port(PrintMatrixIntoString, 'p_formatstring',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(PrintMatrixIntoString, 'Format',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(PrintMatrixIntoString, 'Input',
+ (Matrix, "Matrix"))
+ reg.add_output_port(PrintMatrixIntoString, 'Output',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(GetFileName)
+ reg.add_input_port(GetFileName, 'p_filename_base',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetFileName, 'p_delay',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetFileName, 'p_pinned',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_output_port(GetFileName, 'Full Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(SplitFileName)
+ reg.add_input_port(SplitFileName, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(SplitFileName, 'Pathname',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(SplitFileName, 'Filename Base',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(SplitFileName, 'Extension',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(SplitFileName, 'Filename',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(PrintStringIntoString)
+ reg.add_input_port(PrintStringIntoString, 'p_formatstring',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(PrintStringIntoString, 'Format',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(PrintStringIntoString, 'Input',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(PrintStringIntoString, 'Output',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(CreateString)
+ reg.add_input_port(CreateString, 'p_inputstring',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_output_port(CreateString, 'Output',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(ReportStringInfo)
+ reg.add_input_port(ReportStringInfo, 'p_inputstring',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReportStringInfo, 'Input',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(JoinStrings)
+ reg.add_input_port(JoinStrings, 'input',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(JoinStrings, 'Output',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(GetNetworkFileName)
+ reg.add_output_port(GetNetworkFileName, 'String',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(SetFieldProperty)
+ reg.add_input_port(SetFieldProperty, 'p_num_entries',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SetFieldProperty, 'p_property',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SetFieldProperty, 'p_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SetFieldProperty, 'p_value',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SetFieldProperty, 'p_readonly',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SetFieldProperty, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(SetFieldProperty, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(ReportScalarFieldStats)
+ reg.add_input_port(ReportScalarFieldStats, 'p_min',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ReportScalarFieldStats, 'p_max',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ReportScalarFieldStats, 'p_mean',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ReportScalarFieldStats, 'p_median',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ReportScalarFieldStats, 'p_sigma',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ReportScalarFieldStats, 'p_is_fixed',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReportScalarFieldStats, 'p_nbuckets',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReportScalarFieldStats, 'Input Field',
+ (Field, "Field"))
+
+ reg.add_module(SelectFieldROIWithBoxWidget)
+ reg.add_input_port(SelectFieldROIWithBoxWidget, 'p_stampvalue',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SelectFieldROIWithBoxWidget, 'p_runmode',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SelectFieldROIWithBoxWidget, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(SelectFieldROIWithBoxWidget, 'Selection Widget',
+ (Geometry, "Geometry"))
+ reg.add_output_port(SelectFieldROIWithBoxWidget, 'Output Field',
+ (Field, "Field"))
+
+ reg.add_module(BuildMatrixOfSurfaceNormals)
+ reg.add_input_port(BuildMatrixOfSurfaceNormals, 'Surface Field',
+ (Field, "Field"))
+ reg.add_output_port(BuildMatrixOfSurfaceNormals, 'Nodal Surface Normals',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReportFieldInfo)
+ reg.add_input_port(ReportFieldInfo, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(ReportFieldInfo, 'NumNodes',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportFieldInfo, 'NumElements',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportFieldInfo, 'NumData',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportFieldInfo, 'DataMin',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportFieldInfo, 'DataMax',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportFieldInfo, 'FieldSize',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportFieldInfo, 'FieldCenter',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ReportFieldInfo, 'Dimensions',
+ (Matrix, "Matrix"))
+
+ reg.add_module(ReportFieldGeometryMeasures)
+ reg.add_input_port(ReportFieldGeometryMeasures, 'p_simplexString',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReportFieldGeometryMeasures, 'p_xFlag',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReportFieldGeometryMeasures, 'p_yFlag',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReportFieldGeometryMeasures, 'p_zFlag',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReportFieldGeometryMeasures, 'p_idxFlag',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReportFieldGeometryMeasures, 'p_sizeFlag',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReportFieldGeometryMeasures, 'p_normalsFlag',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ReportFieldGeometryMeasures, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(ReportFieldGeometryMeasures, 'Output Measures Matrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(SetFieldOrMeshStringProperty)
+ reg.add_input_port(SetFieldOrMeshStringProperty, 'p_prop',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SetFieldOrMeshStringProperty, 'p_val',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(SetFieldOrMeshStringProperty, 'p_meshprop',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(SetFieldOrMeshStringProperty, 'Input',
+ (Field, "Field"))
+ reg.add_output_port(SetFieldOrMeshStringProperty, 'Output',
+ (Field, "Field"))
+
+ reg.add_module(ManageFieldSeries)
+ reg.add_input_port(ManageFieldSeries, 'p_num_ports',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ManageFieldSeries, 'Input',
+ (Field, "Field"))
+ reg.add_output_port(ManageFieldSeries, 'Output 0',
+ (Field, "Field"))
+ reg.add_output_port(ManageFieldSeries, 'Output 1',
+ (Field, "Field"))
+ reg.add_output_port(ManageFieldSeries, 'Output 2',
+ (Field, "Field"))
+ reg.add_output_port(ManageFieldSeries, 'Output 3',
+ (Field, "Field"))
+
+ reg.add_module(ReportSearchGridInfo)
+ reg.add_input_port(ReportSearchGridInfo, 'Input Field',
+ (Field, "Field"))
+ reg.add_output_port(ReportSearchGridInfo, 'Output Sample Field',
+ (Field, "Field"))
+
+ reg.add_module(ChooseField)
+ reg.add_input_port(ChooseField, 'p_use_first_valid',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ChooseField, 'p_port_valid_index',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ChooseField, 'p_port_selected_index',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ChooseField, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(ChooseField, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(BuildPointCloudToLatVolMappingMatrix)
+ reg.add_input_port(BuildPointCloudToLatVolMappingMatrix, 'p_epsilon',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(BuildPointCloudToLatVolMappingMatrix, 'PointCloudField',
+ (Field, "Field"))
+ reg.add_input_port(BuildPointCloudToLatVolMappingMatrix, 'LatVolField',
+ (Field, "Field"))
+ reg.add_output_port(BuildPointCloudToLatVolMappingMatrix, 'MappingMatrix',
+ (Matrix, "Matrix"))
+
+ reg.add_module(BuildMappingMatrix)
+ reg.add_input_port(BuildMappingMatrix, 'p_interpolation_basis',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(BuildMappingMatrix, 'p_map_source_to_single_dest',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(BuildMappingMatrix, 'p_exhaustive_search',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(BuildMappingMatrix, 'p_exhaustive_search_max_dist',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(BuildMappingMatrix, 'p_np',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(BuildMappingMatrix, 'Source',
+ (Field, "Field"))
+ reg.add_input_port(BuildMappingMatrix, 'Destination',
+ (Field, "Field"))
+ reg.add_output_port(BuildMappingMatrix, 'Mapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CoregisterPointClouds)
+ reg.add_input_port(CoregisterPointClouds, 'p_allowScale',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CoregisterPointClouds, 'p_allowRotate',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CoregisterPointClouds, 'p_allowTranslate',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CoregisterPointClouds, 'p_seed',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CoregisterPointClouds, 'p_iters',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CoregisterPointClouds, 'p_misfitTol',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CoregisterPointClouds, 'p_method',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CoregisterPointClouds, 'Fixed PointCloudField',
+ (Field, "Field"))
+ reg.add_input_port(CoregisterPointClouds, 'Mobile PointCloudField',
+ (Field, "Field"))
+ reg.add_input_port(CoregisterPointClouds, 'DistanceField From Fixed',
+ (Field, "Field"))
+ reg.add_output_port(CoregisterPointClouds, 'Transform',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CollectPointClouds)
+ reg.add_input_port(CollectPointClouds, 'p_num_fields',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CollectPointClouds, 'Point Cloud',
+ (Field, "Field"))
+ reg.add_output_port(CollectPointClouds, 'Curve',
+ (Field, "Field"))
+
+ reg.add_module(GetColorMapsFromBundle)
+ reg.add_input_port(GetColorMapsFromBundle, 'p_colormap1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMapsFromBundle, 'p_colormap2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMapsFromBundle, 'p_colormap3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMapsFromBundle, 'p_colormap4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMapsFromBundle, 'p_colormap5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMapsFromBundle, 'p_colormap6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMapsFromBundle, 'p_colormap_selection',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMapsFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetColorMapsFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetColorMapsFromBundle, 'colormap1',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(GetColorMapsFromBundle, 'colormap2',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(GetColorMapsFromBundle, 'colormap3',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(GetColorMapsFromBundle, 'colormap4',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(GetColorMapsFromBundle, 'colormap5',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(GetColorMapsFromBundle, 'colormap6',
+ (ColorMap, "ColorMap"))
+
+ reg.add_module(InsertFieldsIntoBundle)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_field1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_field2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_field3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_field4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_field5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_field6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_replace1',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_replace2',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_replace3',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_replace4',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_replace5',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_replace6',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'p_bundlename',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertFieldsIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertFieldsIntoBundle, 'field1',
+ (Field, "Field"))
+ reg.add_input_port(InsertFieldsIntoBundle, 'field2',
+ (Field, "Field"))
+ reg.add_input_port(InsertFieldsIntoBundle, 'field3',
+ (Field, "Field"))
+ reg.add_input_port(InsertFieldsIntoBundle, 'field4',
+ (Field, "Field"))
+ reg.add_input_port(InsertFieldsIntoBundle, 'field5',
+ (Field, "Field"))
+ reg.add_input_port(InsertFieldsIntoBundle, 'field6',
+ (Field, "Field"))
+ reg.add_output_port(InsertFieldsIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+
+ reg.add_module(GetFieldsFromBundle)
+ reg.add_input_port(GetFieldsFromBundle, 'p_field1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetFieldsFromBundle, 'p_field2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetFieldsFromBundle, 'p_field3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetFieldsFromBundle, 'p_field4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetFieldsFromBundle, 'p_field5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetFieldsFromBundle, 'p_field6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetFieldsFromBundle, 'p_field_selection',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetFieldsFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetFieldsFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetFieldsFromBundle, 'field1',
+ (Field, "Field"))
+ reg.add_output_port(GetFieldsFromBundle, 'field2',
+ (Field, "Field"))
+ reg.add_output_port(GetFieldsFromBundle, 'field3',
+ (Field, "Field"))
+ reg.add_output_port(GetFieldsFromBundle, 'field4',
+ (Field, "Field"))
+ reg.add_output_port(GetFieldsFromBundle, 'field5',
+ (Field, "Field"))
+ reg.add_output_port(GetFieldsFromBundle, 'field6',
+ (Field, "Field"))
+
+ reg.add_module(InsertColorMap2sIntoBundle)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap21_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap22_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap23_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap24_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap25_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap26_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace1',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace2',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace3',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace4',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace5',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace6',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'p_bundlename',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap21',
+ (ColorMap2, "ColorMap2"))
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap22',
+ (ColorMap2, "ColorMap2"))
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap23',
+ (ColorMap2, "ColorMap2"))
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap24',
+ (ColorMap2, "ColorMap2"))
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap25',
+ (ColorMap2, "ColorMap2"))
+ reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap26',
+ (ColorMap2, "ColorMap2"))
+ reg.add_output_port(InsertColorMap2sIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+
+ reg.add_module(GetBundlesFromBundle)
+ reg.add_input_port(GetBundlesFromBundle, 'p_bundle1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetBundlesFromBundle, 'p_bundle2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetBundlesFromBundle, 'p_bundle3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetBundlesFromBundle, 'p_bundle4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetBundlesFromBundle, 'p_bundle5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetBundlesFromBundle, 'p_bundle6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetBundlesFromBundle, 'p_bundle_selection',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetBundlesFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetBundlesFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetBundlesFromBundle, 'bundle1',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetBundlesFromBundle, 'bundle2',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetBundlesFromBundle, 'bundle3',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetBundlesFromBundle, 'bundle4',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetBundlesFromBundle, 'bundle5',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetBundlesFromBundle, 'bundle6',
+ (Bundle, "Bundle"))
+
+ reg.add_module(GetPathsFromBundle)
+ reg.add_input_port(GetPathsFromBundle, 'p_path1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetPathsFromBundle, 'p_path2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetPathsFromBundle, 'p_path3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetPathsFromBundle, 'p_path4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetPathsFromBundle, 'p_path5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetPathsFromBundle, 'p_path6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetPathsFromBundle, 'p_path_selection',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetPathsFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetPathsFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetPathsFromBundle, 'path1',
+ (Path, "Path"))
+ reg.add_output_port(GetPathsFromBundle, 'path2',
+ (Path, "Path"))
+ reg.add_output_port(GetPathsFromBundle, 'path3',
+ (Path, "Path"))
+ reg.add_output_port(GetPathsFromBundle, 'path4',
+ (Path, "Path"))
+ reg.add_output_port(GetPathsFromBundle, 'path5',
+ (Path, "Path"))
+ reg.add_output_port(GetPathsFromBundle, 'path6',
+ (Path, "Path"))
+
+ reg.add_module(InsertStringsIntoBundle)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_string1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_string2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_string3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_string4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_string5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_string6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_replace1',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_replace2',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_replace3',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_replace4',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_replace5',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'p_replace6',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertStringsIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertStringsIntoBundle, 'string1',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(InsertStringsIntoBundle, 'string2',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(InsertStringsIntoBundle, 'string3',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(InsertStringsIntoBundle, 'string4',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(InsertStringsIntoBundle, 'string5',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_input_port(InsertStringsIntoBundle, 'string6',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(InsertStringsIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+
+ reg.add_module(GetNrrdsFromBundle)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd1',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd2',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd3',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd4',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd5',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd6',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd_selection',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetNrrdsFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetNrrdsFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetNrrdsFromBundle, 'nrrd1',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(GetNrrdsFromBundle, 'nrrd2',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(GetNrrdsFromBundle, 'nrrd3',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(GetNrrdsFromBundle, 'nrrd4',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(GetNrrdsFromBundle, 'nrrd5',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(GetNrrdsFromBundle, 'nrrd6',
+ (Nrrd, "Nrrd"))
+
+ reg.add_module(GetMatricesFromBundle)
+ reg.add_input_port(GetMatricesFromBundle, 'p_matrix1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_matrix2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_matrix3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_matrix4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_matrix5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_matrix6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd1',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd2',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd3',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd4',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd5',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd6',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'p_matrix_selection',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetMatricesFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetMatricesFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetMatricesFromBundle, 'matrix1',
+ (Matrix, "Matrix"))
+ reg.add_output_port(GetMatricesFromBundle, 'matrix2',
+ (Matrix, "Matrix"))
+ reg.add_output_port(GetMatricesFromBundle, 'matrix3',
+ (Matrix, "Matrix"))
+ reg.add_output_port(GetMatricesFromBundle, 'matrix4',
+ (Matrix, "Matrix"))
+ reg.add_output_port(GetMatricesFromBundle, 'matrix5',
+ (Matrix, "Matrix"))
+ reg.add_output_port(GetMatricesFromBundle, 'matrix6',
+ (Matrix, "Matrix"))
+
+ reg.add_module(JoinBundles)
+ reg.add_input_port(JoinBundles, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(JoinBundles, 'bundle',
+ (Bundle, "Bundle"))
+
+ reg.add_module(ReportBundleInfo)
+ reg.add_input_port(ReportBundleInfo, 'p_tclinfostring',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ReportBundleInfo, 'bundle',
+ (Bundle, "Bundle"))
+
+ reg.add_module(InsertPathsIntoBundle)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_path1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_path2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_path3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_path4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_path5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_path6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_replace1',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_replace2',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_replace3',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_replace4',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_replace5',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_replace6',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'p_bundlename',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertPathsIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertPathsIntoBundle, 'path1',
+ (Path, "Path"))
+ reg.add_input_port(InsertPathsIntoBundle, 'path2',
+ (Path, "Path"))
+ reg.add_input_port(InsertPathsIntoBundle, 'path3',
+ (Path, "Path"))
+ reg.add_input_port(InsertPathsIntoBundle, 'path4',
+ (Path, "Path"))
+ reg.add_input_port(InsertPathsIntoBundle, 'path5',
+ (Path, "Path"))
+ reg.add_input_port(InsertPathsIntoBundle, 'path6',
+ (Path, "Path"))
+ reg.add_output_port(InsertPathsIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+
+ reg.add_module(GetColorMap2sFromBundle)
+ reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap21_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap22_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap23_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap24_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap25_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap26_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap2_selection',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetColorMap2sFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetColorMap2sFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetColorMap2sFromBundle, 'colormap21',
+ (ColorMap2, "ColorMap2"))
+ reg.add_output_port(GetColorMap2sFromBundle, 'colormap22',
+ (ColorMap2, "ColorMap2"))
+ reg.add_output_port(GetColorMap2sFromBundle, 'colormap23',
+ (ColorMap2, "ColorMap2"))
+ reg.add_output_port(GetColorMap2sFromBundle, 'colormap24',
+ (ColorMap2, "ColorMap2"))
+ reg.add_output_port(GetColorMap2sFromBundle, 'colormap25',
+ (ColorMap2, "ColorMap2"))
+ reg.add_output_port(GetColorMap2sFromBundle, 'colormap26',
+ (ColorMap2, "ColorMap2"))
+
+ reg.add_module(InsertMatricesIntoBundle)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_replace1',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_replace2',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_replace3',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_replace4',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_replace5',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_replace6',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'p_bundlename',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertMatricesIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertMatricesIntoBundle, 'matrix1',
+ (Matrix, "Matrix"))
+ reg.add_input_port(InsertMatricesIntoBundle, 'matrix2',
+ (Matrix, "Matrix"))
+ reg.add_input_port(InsertMatricesIntoBundle, 'matrix3',
+ (Matrix, "Matrix"))
+ reg.add_input_port(InsertMatricesIntoBundle, 'matrix4',
+ (Matrix, "Matrix"))
+ reg.add_input_port(InsertMatricesIntoBundle, 'matrix5',
+ (Matrix, "Matrix"))
+ reg.add_input_port(InsertMatricesIntoBundle, 'matrix6',
+ (Matrix, "Matrix"))
+ reg.add_output_port(InsertMatricesIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+
+ reg.add_module(InsertNrrdsIntoBundle)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace1',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace2',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace3',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace4',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace5',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace6',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'p_bundlename',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertNrrdsIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd1',
+ (Nrrd, "Nrrd"))
+ reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd2',
+ (Nrrd, "Nrrd"))
+ reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd3',
+ (Nrrd, "Nrrd"))
+ reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd4',
+ (Nrrd, "Nrrd"))
+ reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd5',
+ (Nrrd, "Nrrd"))
+ reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd6',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(InsertNrrdsIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+
+ reg.add_module(InsertBundlesIntoBundle)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_replace1',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_replace2',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_replace3',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_replace4',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_replace5',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_replace6',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'p_bundlename',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertBundlesIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertBundlesIntoBundle, 'bundle1',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertBundlesIntoBundle, 'bundle2',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertBundlesIntoBundle, 'bundle3',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertBundlesIntoBundle, 'bundle4',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertBundlesIntoBundle, 'bundle5',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertBundlesIntoBundle, 'bundle6',
+ (Bundle, "Bundle"))
+ reg.add_output_port(InsertBundlesIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+
+ reg.add_module(GetStringsFromBundle)
+ reg.add_input_port(GetStringsFromBundle, 'p_string1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetStringsFromBundle, 'p_string2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetStringsFromBundle, 'p_string3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetStringsFromBundle, 'p_string4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetStringsFromBundle, 'p_string5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetStringsFromBundle, 'p_string6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetStringsFromBundle, 'p_string_selection',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(GetStringsFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetStringsFromBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_output_port(GetStringsFromBundle, 'string1',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(GetStringsFromBundle, 'string2',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(GetStringsFromBundle, 'string3',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(GetStringsFromBundle, 'string4',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(GetStringsFromBundle, 'string5',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(GetStringsFromBundle, 'string6',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(InsertColorMapsIntoBundle)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap1_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap2_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap3_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap4_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap5_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap6_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace1',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace2',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace3',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace4',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace5',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace6',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'p_bundlename',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(InsertColorMapsIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+ reg.add_input_port(InsertColorMapsIntoBundle, 'colormap1',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(InsertColorMapsIntoBundle, 'colormap2',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(InsertColorMapsIntoBundle, 'colormap3',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(InsertColorMapsIntoBundle, 'colormap4',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(InsertColorMapsIntoBundle, 'colormap5',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(InsertColorMapsIntoBundle, 'colormap6',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(InsertColorMapsIntoBundle, 'bundle',
+ (Bundle, "Bundle"))
+
+ reg.add_module(CreateParameterBundle)
+ reg.add_input_port(CreateParameterBundle, 'p_data',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateParameterBundle, 'p_new_field_count',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateParameterBundle, 'p_update_all',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_output_port(CreateParameterBundle, 'ParameterList',
+ (Bundle, "Bundle"))
+
+ reg.add_module(InsertEnvironmentIntoBundle)
+ reg.add_output_port(InsertEnvironmentIntoBundle, 'Environment',
+ (Bundle, "Bundle"))
+
+ reg.add_module(ShowColorMap)
+ reg.add_input_port(ShowColorMap, 'p_length',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowColorMap, 'p_side',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowColorMap, 'p_numlabels',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowColorMap, 'p_scale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowColorMap, 'p_numsigdigits',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowColorMap, 'p_units',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowColorMap, 'p_color_r',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowColorMap, 'p_color_g',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowColorMap, 'p_color_b',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowColorMap, 'p_text_fontsize',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowColorMap, 'p_extra_padding',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowColorMap, 'ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(ShowColorMap, 'Geometry',
+ (Geometry, "Geometry"))
+
+ reg.add_module(CreateAndEditColorMap2D)
+ reg.add_input_port(CreateAndEditColorMap2D, 'p_histo',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateAndEditColorMap2D, 'p_selected_widget',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateAndEditColorMap2D, 'p_selected_object',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateAndEditColorMap2D, 'p_num_entries',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateAndEditColorMap2D, 'p_marker',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateAndEditColorMap2D, 'p_cm2view_targ',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateAndEditColorMap2D, 'p_id',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateAndEditColorMap2D, 'Input Colormap',
+ (ColorMap2, "ColorMap2"))
+ reg.add_input_port(CreateAndEditColorMap2D, 'Histogram',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(CreateAndEditColorMap2D, 'Output Colormap',
+ (ColorMap2, "ColorMap2"))
+
+ reg.add_module(ShowField)
+ reg.add_input_port(ShowField, 'p_nodes_on',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_nodes_transparency',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_nodes_color_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_nodes_display_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_edges_on',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_edges_transparency',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_edges_color_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_edges_display_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_faces_on',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_faces_transparency',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_faces_color_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_faces_normals',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_faces_usetexture',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_on',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_color_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_color_r',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_color_g',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_color_b',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_backface_cull',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_always_visible',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_fontsize',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_precision',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_render_locations',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_show_data',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_show_nodes',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_show_edges',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_show_faces',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_text_show_cells',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_def_color_r',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_def_color_g',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_def_color_b',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_def_color_a',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_nodes_scale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_nodes_scaleNV',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_edges_scale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_edges_scaleNV',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_active_tab',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_interactive_mode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_show_progress',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_field_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_field_name_override',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_nodes_resolution',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_edges_resolution',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_approx_div',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'p_use_default_size',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowField, 'Mesh',
+ (Field, "Field"))
+ reg.add_input_port(ShowField, 'ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(ShowField, 'Scene Graph',
+ (Geometry, "Geometry"))
+
+ reg.add_module(ExtractIsosurface)
+ reg.add_input_port(ExtractIsosurface, 'p_isoval_min',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_isoval_max',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_isoval',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_isoval_typed',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_isoval_quantity',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_quantity_range',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_quantity_clusive',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_quantity_min',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_quantity_max',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_quantity_list',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_isoval_list',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_matrix_list',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_algorithm',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_build_trisurf',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_build_geom',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_transparency',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_np',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_active_isoval_selection_tab',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_active_tab',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_update_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_color_r',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_color_g',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_color_b',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'p_color_a',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ExtractIsosurface, 'Field',
+ (Field, "Field"))
+ reg.add_input_port(ExtractIsosurface, 'Optional Color Map',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(ExtractIsosurface, 'Optional Isovalues',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ExtractIsosurface, 'Surface',
+ (Field, "Field"))
+ reg.add_output_port(ExtractIsosurface, 'Geometry',
+ (Geometry, "Geometry"))
+ reg.add_output_port(ExtractIsosurface, 'Mapping',
+ (Matrix, "Matrix"))
+
+ reg.add_module(CreateViewerAxes)
+ reg.add_input_port(CreateViewerAxes, 'p_precision',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_squash',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_valuerez',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_labelrez',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_divisions',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_offset',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_range_first',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_range_second',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_min_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_max_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_minplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_maxplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_lines',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_minticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_maxticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_minlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_maxlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_minvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_maxvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_width',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_tickangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_ticktilt',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_ticksize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_labelangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_labelheight',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_valuesize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_valuesquash',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_divisions',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_offset',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_range_first',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_range_second',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_min_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_max_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_minplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_maxplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_lines',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_minticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_maxticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_minlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_maxlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_minvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_maxvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_width',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_tickangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_ticktilt',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_ticksize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_labelangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_labelheight',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_valuesize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_valuesquash',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_divisions',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_offset',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_range_first',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_range_second',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_min_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_max_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_minplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_maxplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_lines',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_minticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_maxticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_minlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_maxlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_minvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_maxvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_width',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_tickangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_ticktilt',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_ticksize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_labelangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_labelheight',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_valuesize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_valuesquash',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_divisions',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_offset',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_range_first',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_range_second',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_min_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_max_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_minplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_maxplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_lines',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_minticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_maxticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_minlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_maxlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_minvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_maxvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_width',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_tickangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_ticktilt',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_ticksize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_labelangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_labelheight',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_valuesize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_valuesquash',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_divisions',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_offset',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_range_first',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_range_second',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_min_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_max_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_minplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_maxplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_lines',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_minticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_maxticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_minlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_maxlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_minvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_maxvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_width',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_tickangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_ticktilt',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_ticksize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_labelangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_labelheight',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_valuesize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_valuesquash',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_divisions',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_offset',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_range_first',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_range_second',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_min_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_max_absolute',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_minplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_maxplane',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_lines',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_minticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_maxticks',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_minlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_maxlabel',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_minvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_maxvalue',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_width',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_tickangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_ticktilt',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_ticksize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_labelangle',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_labelheight',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_valuesize',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_valuesquash',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerAxes, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(CreateViewerAxes, 'Axes',
+ (Geometry, "Geometry"))
+
+ reg.add_module(RescaleColorMap)
+ reg.add_input_port(RescaleColorMap, 'p_main_frame',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(RescaleColorMap, 'p_isFixed',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(RescaleColorMap, 'p_min',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(RescaleColorMap, 'p_max',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(RescaleColorMap, 'p_makeSymmetric',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(RescaleColorMap, 'ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(RescaleColorMap, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(RescaleColorMap, 'ColorMap',
+ (ColorMap, "ColorMap"))
+
+ reg.add_module(ConvertNrrdsToTexture)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_vmin',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_vmax',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_gmin',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_gmax',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_mmin',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_mmax',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_is_fixed',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_card_mem',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_card_mem_auto',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_is_uchar',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_histogram',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'p_gamma',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertNrrdsToTexture, 'Value Nrrd',
+ (Nrrd, "Nrrd"))
+ reg.add_input_port(ConvertNrrdsToTexture, 'Gradient Magnitude Nrrd',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(ConvertNrrdsToTexture, 'Texture',
+ (Texture, "Texture"))
+ reg.add_output_port(ConvertNrrdsToTexture, 'JointHistoGram',
+ (Nrrd, "Nrrd"))
+
+ reg.add_module(ChooseColorMap)
+ reg.add_input_port(ChooseColorMap, 'p_use_first_valid',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ChooseColorMap, 'p_port_valid_index',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ChooseColorMap, 'p_port_selected_index',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ChooseColorMap, 'ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(ChooseColorMap, 'ColorMap',
+ (ColorMap, "ColorMap"))
+
+ reg.add_module(CreateLightForViewer)
+ reg.add_input_port(CreateLightForViewer, 'p_control_pos_saved',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateLightForViewer, 'p_control_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateLightForViewer, 'p_control_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateLightForViewer, 'p_control_z',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateLightForViewer, 'p_at_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateLightForViewer, 'p_at_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateLightForViewer, 'p_at_z',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateLightForViewer, 'p_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateLightForViewer, 'p_on',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_output_port(CreateLightForViewer, 'Geometry',
+ (Geometry, "Geometry"))
+
+ reg.add_module(ShowTextureVolume)
+ reg.add_input_port(ShowTextureVolume, 'p_sampling_rate_hi',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_sampling_rate_lo',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_gradient_min',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_gradient_max',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_adaptive',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_cmap_size',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_sw_raster',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_render_style',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_alpha_scale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_interp_mode',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_shading',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_ambient',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_diffuse',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_specular',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_shine',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_light',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_blend_res',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_multi_level',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_use_stencil',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_invert_opacity',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_num_clipping_planes',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_show_clipping_widgets',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_level_on',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_level_vals',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'p_id',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowTextureVolume, 'Texture',
+ (Texture, "Texture"))
+ reg.add_input_port(ShowTextureVolume, 'ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(ShowTextureVolume, 'ColorMap2',
+ (ColorMap2, "ColorMap2"))
+ reg.add_output_port(ShowTextureVolume, 'Geometry',
+ (Geometry, "Geometry"))
+ reg.add_output_port(ShowTextureVolume, 'ColorMap',
+ (ColorMap, "ColorMap"))
+
+ reg.add_module(ShowFieldGlyphs)
+ reg.add_input_port(ShowFieldGlyphs, 'p_scalars_has_data',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_scalars_on',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_scalars_display_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_scalars_transparency',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_scalars_normalize',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_scalars_color_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_scalars_resolution',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_vectors_has_data',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_vectors_on',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_vectors_display_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_vectors_transparency',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_vectors_normalize',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_vectors_bidirectional',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_vectors_color_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_vectors_resolution',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tensors_has_data',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tensors_on',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tensors_display_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tensors_transparency',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tensors_normalize',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tensors_color_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tensors_resolution',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tensors_emphasis',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_secondary_has_data',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_secondary_on',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_secondary_display_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_secondary_color_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_secondary_alpha',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_secondary_value',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_has_data',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_on',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_display_type',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_color_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_alpha',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_value',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_on',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_color_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_color_r',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_color_g',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_color_b',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_backface_cull',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_always_visible',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_fontsize',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_precision',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_render_locations',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_show_data',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_show_nodes',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_show_edges',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_show_faces',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_text_show_cells',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_def_color_r',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_def_color_g',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_def_color_b',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_def_color_a',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_active_tab',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_interactive_mode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_show_progress',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_field_name',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_field_name_override',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_approx_div',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'p_use_default_size',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowFieldGlyphs, 'Primary Data',
+ (Field, "Field"))
+ reg.add_input_port(ShowFieldGlyphs, 'Primary ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(ShowFieldGlyphs, 'Secondary Data',
+ (Field, "Field"))
+ reg.add_input_port(ShowFieldGlyphs, 'Secondary ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(ShowFieldGlyphs, 'Tertiary Data',
+ (Field, "Field"))
+ reg.add_input_port(ShowFieldGlyphs, 'Tertiary ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(ShowFieldGlyphs, 'Scene Graph',
+ (Geometry, "Geometry"))
+
+ reg.add_module(GenerateStreamLines)
+ reg.add_input_port(GenerateStreamLines, 'p_stepsize',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateStreamLines, 'p_tolerance',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateStreamLines, 'p_maxsteps',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLines, 'p_direction',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLines, 'p_value',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLines, 'p_remove_colinear_pts',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLines, 'p_method',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLines, 'p_nthreads',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLines, 'p_auto_parameterize',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLines, 'Vector Field',
+ (Field, "Field"))
+ reg.add_input_port(GenerateStreamLines, 'Seed Points',
+ (Field, "Field"))
+ reg.add_output_port(GenerateStreamLines, 'Streamlines',
+ (Field, "Field"))
+
+ reg.add_module(GenerateStreamLinesWithPlacementHeuristic)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_numsl',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_numpts',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_minper',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_maxper',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_ming',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_maxg',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_numsamples',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_method',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_stepsize',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_stepout',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_maxsteps',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_minmag',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_direction',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'Source',
+ (Field, "Field"))
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'Weighting',
+ (Field, "Field"))
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'Flow',
+ (Field, "Field"))
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'Compare',
+ (Field, "Field"))
+ reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'Seed points',
+ (Field, "Field"))
+ reg.add_output_port(GenerateStreamLinesWithPlacementHeuristic, 'Streamlines',
+ (Field, "Field"))
+ reg.add_output_port(GenerateStreamLinesWithPlacementHeuristic, 'Render',
+ (Field, "Field"))
+
+ reg.add_module(ShowString)
+ reg.add_input_port(ShowString, 'p_bbox',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowString, 'p_size',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowString, 'p_location_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowString, 'p_location_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowString, 'p_color_r',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowString, 'p_color_g',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowString, 'p_color_b',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowString, 'Format String',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.add_output_port(ShowString, 'Title',
+ (Geometry, "Geometry"))
+
+ reg.add_module(CreateAndEditColorMap)
+ reg.add_input_port(CreateAndEditColorMap, 'p_rgbhsv',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateAndEditColorMap, 'p_rgb_points',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateAndEditColorMap, 'p_alpha_points',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateAndEditColorMap, 'p_resolution',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateAndEditColorMap, 'ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(CreateAndEditColorMap, 'ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_output_port(CreateAndEditColorMap, 'Geometry',
+ (Geometry, "Geometry"))
+
+ reg.add_module(ShowMeshBoundingBox)
+ reg.add_input_port(ShowMeshBoundingBox, 'p_sizex',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowMeshBoundingBox, 'p_sizey',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowMeshBoundingBox, 'p_sizez',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowMeshBoundingBox, 'Field',
+ (Field, "Field"))
+ reg.add_output_port(ShowMeshBoundingBox, 'Scene Graph',
+ (Geometry, "Geometry"))
+
+ reg.add_module(CreateStandardColorMaps)
+ reg.add_input_port(CreateStandardColorMaps, 'p_mapName',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateStandardColorMaps, 'p_gamma',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateStandardColorMaps, 'p_resolution',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateStandardColorMaps, 'p_reverse',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateStandardColorMaps, 'p_faux',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateStandardColorMaps, 'p_positionList',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateStandardColorMaps, 'p_nodeList',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateStandardColorMaps, 'p_width',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateStandardColorMaps, 'p_height',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_output_port(CreateStandardColorMaps, 'ColorMap',
+ (ColorMap, "ColorMap"))
+
+ reg.add_module(ShowTextureSlices)
+ reg.add_input_port(ShowTextureSlices, 'p_control_pos_saved',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_drawX',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_drawY',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_drawZ',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_drawView',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_interp_mode',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_draw_phi_0',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_draw_phi_1',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_phi_0',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_phi_1',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_multi_level',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_color_changed',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_colors',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_level_on',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_outline_levels',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'p_use_stencil',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowTextureSlices, 'Texture',
+ (Texture, "Texture"))
+ reg.add_input_port(ShowTextureSlices, 'ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(ShowTextureSlices, 'ColorMap2',
+ (ColorMap2, "ColorMap2"))
+ reg.add_output_port(ShowTextureSlices, 'Geometry',
+ (Geometry, "Geometry"))
+ reg.add_output_port(ShowTextureSlices, 'ColorMap',
+ (ColorMap, "ColorMap"))
+
+ reg.add_module(ShowMatrix)
+ reg.add_input_port(ShowMatrix, 'p_xpos',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'p_ypos',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'p_xscale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'p_yscale',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'p_3d_mode',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'p_gmode',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'p_showtext',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'p_row_begin',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'p_rows',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'p_col_begin',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'p_cols',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'p_colormapmode',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ShowMatrix, 'ColorMap',
+ (ColorMap, "ColorMap"))
+ reg.add_input_port(ShowMatrix, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ShowMatrix, 'Geometry',
+ (Geometry, "Geometry"))
+
+ reg.add_module(CreateViewerClockIcon)
+ reg.add_input_port(CreateViewerClockIcon, 'p_type',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'p_bbox',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'p_format',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'p_min',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'p_max',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'p_current',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'p_size',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'p_location_x',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'p_location_y',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'p_color_r',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'p_color_g',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'p_color_b',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(CreateViewerClockIcon, 'Time Matrix',
+ (Matrix, "Matrix"))
+ reg.add_input_port(CreateViewerClockIcon, 'Time Nrrd',
+ (Nrrd, "Nrrd"))
+ reg.add_output_port(CreateViewerClockIcon, 'Clock',
+ (Geometry, "Geometry"))
+
+ reg.add_module(ConvertFieldsToTexture)
+ reg.add_input_port(ConvertFieldsToTexture, 'p_vmin',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertFieldsToTexture, 'p_vmax',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertFieldsToTexture, 'p_gmin',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertFieldsToTexture, 'p_gmax',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertFieldsToTexture, 'p_is_fixed',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ConvertFieldsToTexture, 'p_card_mem',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ConvertFieldsToTexture, 'p_card_mem_auto',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ConvertFieldsToTexture, 'p_histogram',
+ (core.modules.basic_modules.Integer, 'tip'), True)
+ reg.add_input_port(ConvertFieldsToTexture, 'p_gamma',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_input_port(ConvertFieldsToTexture, 'Value Field',
+ (Field, "Field"))
+ reg.add_input_port(ConvertFieldsToTexture, 'Gradient Magnitude Field',
+ (Field, "Field"))
+ reg.add_output_port(ConvertFieldsToTexture, 'Texture',
+ (Texture, "Texture"))
+ reg.add_output_port(ConvertFieldsToTexture, 'JointHistoGram',
+ (Nrrd, "Nrrd"))
+
+ reg.add_module(ColorMap2DSemantics)
+ reg.add_input_port(ColorMap2DSemantics, 'Input Colormap',
+ (ColorMap2, "ColorMap2"))
+ reg.add_output_port(ColorMap2DSemantics, 'Output Colormap',
+ (ColorMap2, "ColorMap2"))
+
+ reg.add_module(ConvertMatrixToString)
+ reg.add_input_port(ConvertMatrixToString, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ConvertMatrixToString, 'String',
+ (core.modules.basic_modules.String, 'tip'))
+
+ reg.add_module(ConvertMatrixToField)
+ reg.add_input_port(ConvertMatrixToField, 'p_datalocation',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(ConvertMatrixToField, 'Matrix',
+ (Matrix, "Matrix"))
+ reg.add_output_port(ConvertMatrixToField, 'Field',
+ (Field, "Field"))
+
+ reg.add_module(TimeControls)
+ reg.add_input_port(TimeControls, 'p_execmode',
+ (core.modules.basic_modules.String, 'tip'), True)
+ reg.add_input_port(TimeControls, 'p_scale_factor',
+ (core.modules.basic_modules.Float, 'tip'), True)
+ reg.add_output_port(TimeControls, 'time',
+ (Time, "Time"))
+
+
+
+ import viewercell
+ viewercell.registerSelf()
+ import cm2viewcell
+ cm2viewcell.registerSelf()
+
+
+def package_dependencies():
+ return ['edu.utah.sci.vistrails.spreadsheet']
+
+
+def finalize():
+ sr_py.terminate()
+ time.sleep(.5)
diff --git a/contrib/SCIRun/cm2viewcell.py b/contrib/SCIRun/cm2viewcell.py
new file mode 100644
index 0000000..7c19e29
--- /dev/null
+++ b/contrib/SCIRun/cm2viewcell.py
@@ -0,0 +1,285 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+from PyQt4 import QtCore, QtGui, QtOpenGL
+import sip
+from core import system
+from core.modules.module_registry import registry
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+import gc
+from gui.qt import qt_super
+from core.vistrail.action import Action
+from core.vistrail.port import Port
+from core.vistrail import module
+from core.vistrail import connection
+from core.vistrail.module_function import ModuleFunction
+from core.vistrail.module_param import ModuleParam
+from core.modules.vistrails_module import Module, ModuleError
+import db.services.action
+import copy
+import sr_py
+import time
+import uuid
+from renderbase import Render
+
+################################################################################
+class CM2ViewCell(Render):
+ """
+ CM2ViewCell is a VisTrails Module that can display SCIRun Viewer.
+
+ """
+ def compute(self):
+ """ compute() -> None
+ Dispatch the SCIRun scene graph to the Viewer
+ """
+ sg = self.forceGetInputListFromPort('ColorMap2')
+ self.display(QCM2ViewWidget, (sg))
+
+
+
+class QCM2ViewWidget(QtOpenGL.QGLWidget) :
+ """
+ QCM2ViewWidget is the actual rendering widget that can display
+ a SCIRun scene graph inside a Qt QWidget
+
+ """
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QCM2ViewWidget(parent: QWidget, f: WindowFlags) -> QCM2ViewWidget
+ Initialize QCM2ViewWidget.
+ context
+
+ """
+ QtOpenGL.QGLWidget.__init__(self, parent)
+
+ self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
+ self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
+ self.setMouseTracking(True)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding))
+
+
+
+ self.sci_context = sr_py.CallbackOpenGLContext()
+ self.sci_context.set_pymake_current_func(self.make_current)
+ self.sci_context.set_pyswap_func(self.swap)
+ self.sci_context.set_pywidth_func(self.get_width)
+ self.sci_context.set_pyheight_func(self.get_height)
+ self.sci_context.set_pyrelease_func(self.release)
+ unique_id = uuid.uuid4()
+ self._id = "sr_viewer_%s" % str(unique_id)
+ #print self._id
+ self.full_speed = False
+ self.timer = QtCore.QTimer()
+ self.connect(self.timer,
+ QtCore.SIGNAL("timeout()"), self.updateGL)
+
+ def make_current(self) :
+ if self.isValid() :
+ self.makeCurrent()
+ return 1
+ return 0
+
+ def swap(self) :
+ if self.isValid() :
+ self.swapBuffers()
+ return 1
+ return 0
+
+ def get_width(self) :
+ if self.isValid() :
+ w = self.width()
+ return w
+ return 0
+
+ def get_height(self) :
+ if self.isValid() :
+ h = self.height()
+ return h
+ return 0
+
+ def release(self) :
+ #self.doneCurrent()
+ pass
+
+ def pointer_event(self, e, event) :
+ e.set_x(event.x())
+ e.set_y(event.y())
+
+ mask = e.get_modifiers()
+ mask = self.get_sr_py_modifier_mask(event, mask)
+ e.set_modifiers(mask)
+
+ state = e.get_pointer_state()
+ state, n = self.get_sr_py_pointer_modifier_mask(event, state)
+ e.set_pointer_state(state)
+ sr_py.add_pointer_event(e, self._id)
+
+ def get_sr_py_modifier_mask(self, event, mask) :
+ if event.modifiers() & QtCore.Qt.ShiftModifier :
+ mask |= sr_py.EventModifiers.SHIFT_E
+ if event.modifiers() & QtCore.Qt.ControlModifier :
+ mask |= sr_py.EventModifiers.CONTROL_E
+ if event.modifiers() & QtCore.Qt.AltModifier :
+ mask |= sr_py.EventModifiers.ALT_E
+ if event.modifiers() & QtCore.Qt.MetaModifier :
+ mask |= sr_py.EventModifiers.M1_E
+ return mask
+
+ def get_sr_py_pointer_modifier_mask(self, event, mask) :
+ n = 0
+
+ if event.buttons() & QtCore.Qt.LeftButton :
+ mask |= sr_py.PointerEvent.BUTTON_1_E
+ n = 1
+ if event.buttons() & QtCore.Qt.MidButton :
+ mask |= sr_py.PointerEvent.BUTTON_2_E
+ n = 2
+ if event.buttons() & QtCore.Qt.RightButton :
+ mask |= sr_py.PointerEvent.BUTTON_3_E
+ n = 3
+ return mask, n
+
+ def initializeGL(self):
+ # create the viewer
+ self.vid = sr_py.create_cm2view(self.sci_context, self._id)
+ #start the timer
+ #self.timer.start(33)
+
+## def paintGL(self):
+## #self.doneCurrent()
+## pass
+
+ def glDraw(self):
+ sr_py.update_cm2view(self.vid);
+
+ if self.timer.isActive() and not self.full_speed :
+ self.full_speed = True
+ self.timer.start(55)
+
+ if not self.timer.isActive() :
+ self.timer.start(1000)
+
+
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Echo mouse event to SCIRun event system.
+
+ """
+ e = sr_py.PointerEvent()
+ e.set_pointer_state(sr_py.PointerEvent.BUTTON_PRESS_E)
+ self.pointer_event(e, event)
+
+ def mouseReleaseEvent(self, event):
+ """ mouseReleaseEvent(e: QEvent) -> None
+ Echo mouse event to SCIRun event system.
+
+ """
+ e = sr_py.PointerEvent()
+ #e.set_time(long(event.time))
+ e.set_pointer_state(sr_py.PointerEvent.BUTTON_RELEASE_E)
+ self.pointer_event(e, event)
+
+ def mouseMoveEvent(self, event):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Echo mouse event to SCIRun event system.
+
+ """
+ e = sr_py.PointerEvent()
+ #e.set_time(long(event.time))
+ e.set_pointer_state(sr_py.PointerEvent.MOTION_E)
+ self.pointer_event(e, event)
+
+ def enterEvent(self,e):
+ """ enterEvent(e: QEvent) -> None
+
+ """
+
+ def leaveEvent(self,e):
+ """ leaveEvent(e: QEvent) -> None
+
+ """
+
+
+ def keyPressEvent(self, event):
+ """ keyPressEvent(e: QKeyEvent) -> None
+ Echo the key event to the SCIRun event system.
+
+ """
+
+ ascii_key = None
+ if event.text().length()>0:
+ ascii_key = event.text().toLatin1()[0]
+ else:
+ ascii_key = chr(0)
+
+ #for now use native...
+ keysym = event.nativeVirtualKey()
+ e = sr_py.KeyEvent()
+ #e.set_time(long(event.time))
+ # translate qt modifiers to sci modifiers
+ mask = e.get_modifiers()
+ e.set_modifiers(self.get_sr_py_modifier_mask(event, mask))
+ e.set_keyval(keysym)
+ e.set_key_string(ascii_key)
+ e.set_key_state(sr_py.KeyEvent.KEY_PRESS_E)
+ sr_py.add_key_event(e, self._id)
+
+
+ def keyReleaseEvent(self,e):
+ """ keyReleaseEvent(e: QKeyEvent) -> None
+
+ """
+ #print "keyReleaseEvent"
+
+ def wheelEvent(self,e):
+ """ wheelEvent(e: QWheelEvent) -> None
+ Zoom in/out while scrolling the mouse
+
+ """
+ print "wheelEvent"
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple)
+ Connects the input scene graph to this viewer
+
+ """
+
+## p = inputPorts[0]
+## for i in p:
+## if i != 0 :
+## sr_py.send_scene(i, self._id);
+
+def registerSelf():
+ """ registerSelf() -> None
+ Registry module with the registry
+ """
+ identifier = "edu.utah.sci.vistrails.scirun"
+# registry.add_module(Render, abstract=True)
+ registry.add_module(CM2ViewCell)
+ registry.add_input_port(CM2ViewCell, "Location", CellLocation)
+ registry.add_input_port(CM2ViewCell, "Scene Graph",
+ registry.get_module_by_name(identifier,
+ 'Geometry'),
+ 'Scene Graph')
+
diff --git a/contrib/SCIRun/renderbase.py b/contrib/SCIRun/renderbase.py
new file mode 100644
index 0000000..a4363f0
--- /dev/null
+++ b/contrib/SCIRun/renderbase.py
@@ -0,0 +1,10 @@
+from core import system
+from core.modules.module_registry import registry
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+
+class Render(SpreadsheetCell):
+ def compute(self):
+ pass
+
+def registerRender():
+ registry.add_module(Render, abstract=True)
diff --git a/contrib/SCIRun/viewercell.py b/contrib/SCIRun/viewercell.py
new file mode 100644
index 0000000..0c4053b
--- /dev/null
+++ b/contrib/SCIRun/viewercell.py
@@ -0,0 +1,289 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+from PyQt4 import QtCore, QtGui, QtOpenGL
+import sip
+from core import system
+from core.modules.module_registry import registry
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+import gc
+from gui.qt import qt_super
+from core.vistrail.action import Action
+from core.vistrail.port import Port
+from core.vistrail import module
+from core.vistrail import connection
+from core.vistrail.module_function import ModuleFunction
+from core.vistrail.module_param import ModuleParam
+from core.modules.vistrails_module import Module, ModuleError
+import db.services.action
+import copy
+import sr_py
+import time
+import uuid
+from renderbase import Render, registerRender
+
+
+################################################################################
+class ViewerCell(Render):
+ """
+ ViewerCell is a VisTrails Module that can display SCIRun Viewer.
+
+ """
+ def compute(self):
+ """ compute() -> None
+ Dispatch the SCIRun scene graph to the Viewer
+ """
+ sg = self.forceGetInputListFromPort('Scene Graph')
+ self.display(QViewerWidget, (sg))
+
+
+
+class QViewerWidget(QtOpenGL.QGLWidget) :
+ """
+ QViewerWidget is the actual rendering widget that can display
+ a SCIRun scene graph inside a Qt QWidget
+
+ """
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QViewerWidget(parent: QWidget, f: WindowFlags) -> QViewerWidget
+ Initialize QViewerWidget.
+ context
+
+ """
+ QtOpenGL.QGLWidget.__init__(self, parent)
+
+ self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
+ self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
+ self.setMouseTracking(True)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding))
+
+
+
+ self.sci_context = sr_py.CallbackOpenGLContext()
+ self.sci_context.set_pymake_current_func(self.make_current)
+ self.sci_context.set_pyswap_func(self.swap)
+ self.sci_context.set_pywidth_func(self.get_width)
+ self.sci_context.set_pyheight_func(self.get_height)
+ self.sci_context.set_pyrelease_func(self.release)
+ unique_id = uuid.uuid4()
+ self._id = "sr_viewer_%s" % str(unique_id)
+ #print self._id
+ self.full_speed = False
+ self.timer = QtCore.QTimer()
+ self.connect(self.timer,
+ QtCore.SIGNAL("timeout()"), self.updateGL)
+
+ def make_current(self) :
+ if self.isValid() :
+ self.makeCurrent()
+ return 1
+ return 0
+
+ def swap(self) :
+ if self.isValid() :
+ self.swapBuffers()
+ return 1
+ return 0
+
+ def get_width(self) :
+ if self.isValid() :
+ w = self.width()
+ return w
+ return 0
+
+ def get_height(self) :
+ if self.isValid() :
+ h = self.height()
+ return h
+ return 0
+
+ def release(self) :
+ #self.doneCurrent()
+ pass
+
+ def pointer_event(self, e, event) :
+ e.set_x(event.x())
+ e.set_y(event.y())
+
+ mask = e.get_modifiers()
+ mask = self.get_sr_py_modifier_mask(event, mask)
+ e.set_modifiers(mask)
+
+ state = e.get_pointer_state()
+ state, n = self.get_sr_py_pointer_modifier_mask(event, state)
+ e.set_pointer_state(state)
+ sr_py.add_pointer_event(e, self._id)
+
+ def get_sr_py_modifier_mask(self, event, mask) :
+ if event.modifiers() & QtCore.Qt.ShiftModifier :
+ mask |= sr_py.EventModifiers.SHIFT_E
+ if event.modifiers() & QtCore.Qt.ControlModifier :
+ mask |= sr_py.EventModifiers.CONTROL_E
+ if event.modifiers() & QtCore.Qt.AltModifier :
+ mask |= sr_py.EventModifiers.ALT_E
+ if event.modifiers() & QtCore.Qt.MetaModifier :
+ mask |= sr_py.EventModifiers.M1_E
+ return mask
+
+ def get_sr_py_pointer_modifier_mask(self, event, mask) :
+ n = 0
+
+ if event.buttons() & QtCore.Qt.LeftButton :
+ mask |= sr_py.PointerEvent.BUTTON_1_E
+ n = 1
+ if event.buttons() & QtCore.Qt.MidButton :
+ mask |= sr_py.PointerEvent.BUTTON_2_E
+ n = 2
+ if event.buttons() & QtCore.Qt.RightButton :
+ mask |= sr_py.PointerEvent.BUTTON_3_E
+ n = 3
+ return mask, n
+
+ def initializeGL(self):
+ # create the viewer
+ self.vid = sr_py.create_viewer(self.sci_context, self._id)
+ #start the timer
+ #self.timer.start(33)
+
+## def paintGL(self):
+## #self.doneCurrent()
+## pass
+
+ def glDraw(self):
+ sr_py.update_viewer(self.vid);
+
+ if self.timer.isActive() and not self.full_speed :
+ self.full_speed = True
+ self.timer.start(55)
+
+ if not self.timer.isActive() :
+ self.timer.start(1000)
+
+
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Echo mouse event to SCIRun event system.
+
+ """
+ e = sr_py.PointerEvent()
+ e.set_pointer_state(sr_py.PointerEvent.BUTTON_PRESS_E)
+ self.pointer_event(e, event)
+
+ def mouseReleaseEvent(self, event):
+ """ mouseReleaseEvent(e: QEvent) -> None
+ Echo mouse event to SCIRun event system.
+
+ """
+ e = sr_py.PointerEvent()
+ #e.set_time(long(event.time))
+ e.set_pointer_state(sr_py.PointerEvent.BUTTON_RELEASE_E)
+ self.pointer_event(e, event)
+
+ def mouseMoveEvent(self, event):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Echo mouse event to SCIRun event system.
+
+ """
+ e = sr_py.PointerEvent()
+ #e.set_time(long(event.time))
+ e.set_pointer_state(sr_py.PointerEvent.MOTION_E)
+ self.pointer_event(e, event)
+
+ def enterEvent(self,e):
+ """ enterEvent(e: QEvent) -> None
+
+ """
+
+ def leaveEvent(self,e):
+ """ leaveEvent(e: QEvent) -> None
+
+ """
+
+
+ def keyPressEvent(self, event):
+ """ keyPressEvent(e: QKeyEvent) -> None
+ Echo the key event to the SCIRun event system.
+
+ """
+
+ ascii_key = None
+ if event.text().length()>0:
+ ascii_key = event.text().toLatin1()[0]
+ else:
+ ascii_key = chr(0)
+
+ #for now use native...
+ keysym = event.nativeVirtualKey()
+ e = sr_py.KeyEvent()
+ #e.set_time(long(event.time))
+ # translate qt modifiers to sci modifiers
+ mask = e.get_modifiers()
+ e.set_modifiers(self.get_sr_py_modifier_mask(event, mask))
+ e.set_keyval(keysym)
+ e.set_key_string(ascii_key)
+ e.set_key_state(sr_py.KeyEvent.KEY_PRESS_E)
+ sr_py.add_key_event(e, self._id)
+
+
+ def keyReleaseEvent(self,e):
+ """ keyReleaseEvent(e: QKeyEvent) -> None
+
+ """
+ #print "keyReleaseEvent"
+
+ def wheelEvent(self,e):
+ """ wheelEvent(e: QWheelEvent) -> None
+ Zoom in/out while scrolling the mouse
+
+ """
+ print "wheelEvent"
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple)
+ Connects the input scene graph to this viewer
+
+ """
+ for p in inputPorts :
+ try:
+ for i in p:
+ if i != 0 :
+ print i
+ sr_py.send_scene(i, self._id);
+ except:
+ if p != 0 :
+ sr_py.send_scene(p, self._id);
+def registerSelf():
+ """ registerSelf() -> None
+ Registry module with the registry
+ """
+ identifier = "edu.utah.sci.vistrails.scirun"
+ registerRender()
+ registry.add_module(ViewerCell)
+ registry.add_input_port(ViewerCell, "Location", CellLocation)
+ registry.add_input_port(ViewerCell, "Scene Graph",
+ registry.get_module_by_name(identifier,
+ 'Geometry'),
+ 'Scene Graph')
+
diff --git a/contrib/SciPy/DSP.py b/contrib/SciPy/DSP.py
new file mode 100644
index 0000000..7cf5c69
--- /dev/null
+++ b/contrib/SciPy/DSP.py
@@ -0,0 +1,150 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from SciPy import SciPy
+from Matrix import *
+import scipy
+from scipy import sparse, fftpack
+import numpy
+
+#################################################################
+
+class DSP(SciPy):
+ def compute(self):
+ pass
+
+class FFT(DSP):
+ def compute(self):
+ mat = self.getInputFromPort("Signals")
+ pts = self.getInputFromPort("FFT Samples")
+
+ phasors = fftpack.fft(mat.matrix.data, pts)
+ outmat = sparse.csc_matrix(phasors)
+ out = SparseMatrix()
+ out.matrix = outmat
+ self.setResult("FFT Output", out)
+
+class FFT2(DSP):
+ def compute(self):
+ mat = self.getInputFromPort("Signals")
+
+ phasors = fftpack.fftn(mat.matrix.data)
+ outmat = sparse.csc_matrix(phasors)
+ out = SparseMatrix()
+ out.matrix = outmat
+ self.setResult("FFT Output", out)
+
+class WindowedFourierTransform(DSP):
+ def compute(self):
+ mat = self.getInputFromPort("Signal")
+
+ sr = self.getInputFromPort("Sampling Rate")
+ if self.hasInputFromPort("Window Size"):
+ window = self.getInputFromPort("Window Size")
+ else:
+ window = sr
+
+ if self.hasInputFromPort("Stride"):
+ stride = self.getInputFromPort("Stride")
+ else:
+ stride = int(sr / 2)
+
+
+ signal_array = mat.matrix.toarray().ravel()
+
+ # We now have a 1-D array that we can have good indexing into
+ pad = signal_array[0:int(window/2)]
+ signal_array = numpy.concatenate((pad,signal_array))
+ win_low = 0
+ win_hi = window - 1
+ phasors = fftpack.fft(signal_array[win_low:win_hi])
+ out_array = phasors.ravel()
+
+ win_low += stride
+ win_hi += stride
+
+ while win_hi < signal_array.shape[0]:
+ phasors = fftpack.fft(signal_array[win_low:win_hi])
+ win_low += stride
+ win_hi += stride
+ out_array = numpy.vstack([out_array, phasors.ravel()])
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(out_array)
+ self.setResult("FFT Output", out)
+
+class ShortTimeFourierTransform(DSP):
+ def get_signal(self, sigs, window, offset, size):
+ win = scipy.zeros(sigs.shape[0]).ravel()
+ win[offset:offset+size] = window.ravel()
+ part = sigs * win
+ return part
+
+ def compute(self):
+ mat = self.getInputFromPort("Signal")
+ sr = self.getInputFromPort("Sampling Rate")
+
+ if self.hasInputFromPort("Window"):
+ window = self.getInputFromPort("Window").matrix.toarray()
+ win_size = window.shape[1]
+ else:
+ win_size = self.getInputFromPort("WindowSize")
+ window = scipy.signal.hamming(win_size)
+
+ if self.hasInputFromPort("Stride"):
+ stride = self.getInputFromPort("Stride")
+ else:
+ stride = int(win_size / 2)
+
+ signal_array = mat.matrix.transpose().toarray().ravel()
+
+ samples = signal_array.shape[0]
+
+ offset = 0
+ sig = self.get_signal(signal_array, window, offset, win_size)
+ phasors = fftpack.fft(sig).ravel()
+ out_array = phasors
+ offset += stride
+
+ i = 1
+ while 1:
+ try:
+ sig = self.get_signal(signal_array, window, offset, win_size)
+ phasors = fftpack.fft(sig)
+ offset += stride
+ out_array = numpy.vstack([out_array, phasors.ravel()])
+ i += 1
+ except:
+ break
+
+ (slices, freqs) = out_array.shape
+ ar = out_array[0:,0:sr*2]
+ ar = ar[0:,::-1]
+
+ out = SparseMatrix()
+ sigout = SparseMatrix()
+ sigout.matrix = sparse.csc_matrix(signal_array)
+ out.matrix = sparse.csc_matrix(ar)
+ self.setResult("Signal Output", sigout)
+ self.setResult("FFT Output", out)
diff --git a/contrib/SciPy/Filters.py b/contrib/SciPy/Filters.py
new file mode 100644
index 0000000..9ddb308
--- /dev/null
+++ b/contrib/SciPy/Filters.py
@@ -0,0 +1,118 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from SciPy import SciPy
+from Matrix import *
+import scipy
+import scipy.signal
+from scipy import sparse, fftpack
+import numpy
+
+class DSPFilters(SciPy):
+ def compute(self):
+ pass
+
+class HanningWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.hanning(size))
+ self.setResult("Window", out)
+
+class TriangularWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.triang(size))
+ self.setResult("Window", out)
+
+class BlackmanWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.blackman(size))
+ self.setResult("Window", out)
+
+class BlackmanHarrisWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.blackmanharris(size))
+ self.setResult("Window", out)
+
+class ParzenWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.parzen(size))
+ self.setResult("Window", out)
+
+class HammingWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.hamming(size))
+ self.setResult("Window", out)
+
+class KaiserWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ beta = self.getInputFromPort("Beta")
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.kaiser(size, beta))
+ self.setResult("Window", out)
+
+class BartlettHannWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.barthann(size))
+ self.setResult("Window", out)
+
+class GaussianWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+ sigma = self.getInputFromPort("Sigma")
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.gaussian(size, sigma))
+ self.setResult("Window", out)
+
+class BoxcarWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.boxcar(size))
+ self.setResult("Window", out)
+
+class BohmanWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.bohman(size))
+ self.setResult("Window", out)
+
+class BartlettWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.bartlett(size))
+ self.setResult("Window", out)
+
+class NuttallBlackmanHarrisWindow(DSPFilters):
+ def compute(self):
+ size = self.getInputFromPort("Window Size")
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.signal.nuttall(size))
+ self.setResult("Window", out)
+
diff --git a/contrib/SciPy/MatlabReader.py b/contrib/SciPy/MatlabReader.py
new file mode 100644
index 0000000..38e2ced
--- /dev/null
+++ b/contrib/SciPy/MatlabReader.py
@@ -0,0 +1,51 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from SciPy import SciPy
+from Matrix import *
+from scipy import io, sparse
+import numpy
+
+#######################################################################
+
+class MatlabReader(SciPy):
+
+ def compute(self):
+ if self.hasInputFromPort("Filename"):
+ fname = self.getInputFromPort("Filename")
+ else:
+ fname = self.getInputFromPort("File").name
+ self.readFileAsCSC(fname)
+
+ def readFileAsCSC(self, filename):
+ m = io.loadmat(filename, None, 0)
+ vals = m.values()
+ for t in vals:
+ if type(t) == numpy.ndarray:
+ mat = t
+
+ cscmat = sparse.csr_matrix(mat)
+ self.matrix = SparseMatrix()
+ self.matrix.matrix = cscmat
+ self.setResult("sparseoutput", self.matrix)
diff --git a/contrib/SciPy/Matrix.py b/contrib/SciPy/Matrix.py
new file mode 100644
index 0000000..9c4d9f4
--- /dev/null
+++ b/contrib/SciPy/Matrix.py
@@ -0,0 +1,121 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from SciPy import SciPy
+
+from numpy import allclose, arange, eye, linalg, ones
+from scipy import linsolve, sparse
+
+#######################################################################
+class Matrix(SciPy):
+
+ def setSize(self, size):
+ pass
+
+ def setMatrix(self, m):
+ self.matrix = m
+
+ def numElements(self):
+ return self.matrix.getnnz()
+
+ def maxNumElements(self):
+ return self.matrix.nzmax
+
+ def rows(self):
+ return self.matrix.shape[0]
+
+ def cols(self):
+ return self.matrix.shape[1]
+
+ def Reals(self):
+ out = SparseMatrix()
+ tmp = self.matrix.copy()
+ out.matrix = tmp._real()
+ return out
+
+ def Imaginaries(self):
+ out = SparseMatrix()
+ tmp = self.matrix.copy()
+ out.matrix = tmp._imag()
+ return out
+
+ def Conjugate(self):
+ out = SparseMatrix()
+ out.matrix = self.matrix.conjugate().copy()
+ return out
+
+ def GetRow(self, i):
+ return self.matrix.getrow(i)
+
+ def GetCol(self, i):
+ return self.matrix.getcol(i)
+
+class SparseMatrix(Matrix):
+
+ def setSize(self, size):
+ self.matrix = sparse.csc_matrix((size, size))
+ self.matrix.setdiag(ones(size))
+
+class DenseMatrix(Matrix):
+
+ def setSize(self, size):
+ self.matrix = sparse.csc_matrix((size, size))
+ self.matrix.setdiag(ones(size))
+ self.matrix.todense()
+
+
+class DOKMatrix(Matrix):
+
+ def setSize(self, size):
+ self.matrix = sparse.dok_matrix((size, size))
+ self.matrix.setdiag(ones(size))
+
+class COOMatrix(Matrix):
+
+ def __init__(self, mat):
+ self.matrix=mat
+
+ def setSize(self, size):
+ self.matrix = sparse.coo_matrix((size, size))
+ self.matrix.setdiag(ones(size))
+
+class CSRMatrix(Matrix):
+
+ def __init__(self, mat):
+ self.matrix=mat
+
+ def setSize(self, size):
+ self.matrix = sparse.csr_matrix((size, size))
+ self.matrix.setdiag(ones(size))
+
+class LILMatrix(Matrix):
+
+ def __init__(self, mat):
+ self.matrix=mat
+
+ def setSize(self, size):
+ self.matrix = sparse.lil_matrix((size, size))
+ self.matrix.setdiag(ones(size))
+
+#######################################################################
diff --git a/contrib/SciPy/MatrixConvert.py b/contrib/SciPy/MatrixConvert.py
new file mode 100644
index 0000000..bacc865
--- /dev/null
+++ b/contrib/SciPy/MatrixConvert.py
@@ -0,0 +1,150 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from SciPy import SciPy
+from Matrix import Matrix, COOMatrix, SparseMatrix, CSRMatrix
+from scipy import sparse
+import numpy, scipy
+
+class MatrixConvert(SciPy):
+
+ def compute(self):
+ m = self.getInputFromPort("InputMatrix")
+ to = self.getInputFromPort("OutputType")
+
+ to = to.upper()
+ if to == 'Dense':
+ self.matrix = DenseMatrix(m.matrix.todense())
+ self.setResult("SparseOutput", self.matrix)
+ else:
+ self.matrix = SparseMatrix(m.matrix.tocsc())
+ self.setResult("SparseOutput", self.matrix)
+
+class vtkDataSetToMatrix(SciPy):
+ ''' In some cases, particularly in terms of user-defined VTK Filters, the
+ output of the filter is a vtk datatype representing '''
+
+ def from_unstructured_grid(self, vtkalgout):
+ import vtk
+ prod = vtkalgout.vtkInstance.GetProducer()
+ prod.Update()
+ grid = prod.GetOutput()
+ pt_set = grid.GetPoints()
+ scalars = grid.GetPointData().GetScalars()
+
+ ''' Points in vtk are always 3D... so we must assume this. '''
+ self.matrix_ = SparseMatrix()
+ self.matrix_.matrix = sparse.csc_matrix((grid.GetNumberOfPoints(), 3))
+
+ i = 0
+ while i < grid.GetNumberOfPoints():
+ (x,y,z) = pt_set.GetPoint(i)
+ self.matrix_.matrix[i,0] = x
+ self.matrix_.matrix[i,1] = y
+ self.matrix_.matrix[i,2] = z
+ print x, y, z
+ i += 1
+
+
+ def compute(self):
+ if self.hasInputFromPort("vtkUnstructuredGrid"):
+ self.from_unstructured_grid(self.getInputFromPort("vtkUnstructuredGrid"))
+ else:
+ pass
+
+ self.setResult("Output Matrix", self.matrix_)
+
+class PhaseHistogramToVTKPoints(SciPy):
+
+ def form_point_set(self, histo, point_set):
+ (slices, numbins) = histo.shape
+ phases = numpy.arange(numbins)
+ phases = phases * (360. / numbins)
+ phases += phases[1] / 2.
+ phi_step = phases[0]
+
+ for time in xrange(slices):
+ z = float(time)
+ for bin in xrange(numbins):
+ r = histo[time,bin]
+ theta = phi_step * (bin+1)
+ theta *= (scipy.pi / 180.)
+ x = r*scipy.cos(theta)
+ y = r*scipy.sin(theta)
+ point_set.InsertNextPoint(x, y, z)
+
+ for bin in xrange(numbins):
+ curbin = bin
+ lastbin = bin-1
+ if lastbin < 0:
+ lastbin = numbins-1
+
+ r = (histo[time,bin] - histo[time,lastbin]) / 2.
+ theta = curbin * 360. / numbins
+ x = r*scipy.cos(theta)
+ y = r*scipy.sin(theta)
+ point_set.InsertNextPoint(x, y, z)
+
+
+ def compute(self):
+ import vtk
+
+ phasors = self.getInputFromPort("FFT Input")
+ numbins = self.getInputFromPort("Num Bins")
+ phasor_matrix = phasors.matrix.toarray()
+ (timeslices,phases) = phasor_matrix.shape
+
+ point_set = vtk.vtkPoints()
+
+ histo = numpy.zeros((timeslices, numbins))
+
+ for time in xrange(timeslices):
+ phase_slice = phasor_matrix[time,:]
+ reals = phase_slice.real
+ imaginary = phase_slice.imag
+ phases = scipy.arctan2(imaginary, reals)
+ phases = phases * (180. / scipy.pi)
+ bins = phases % numbins
+ for b in bins:
+ histo[time,b] += 1
+
+ self.form_point_set(histo, point_set)
+
+ pointdata = vtk.vtkUnstructuredGrid()
+ pointdata.SetPoints(point_set)
+
+ self.surf_filter = vtk.vtkSurfaceReconstructionFilter()
+
+ self.surf_filter.SetInput(0,pointdata)
+# self.surf_filter.Update()
+ reg = core.modules.module_registry
+ vtk_set = reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkAlgorithmOutput').module()
+ vtk_set.vtkInstance = self.surf_filter.GetOutputPort()
+
+ histo_mat = SparseMatrix()
+ histo_mat.matrix = sparse.csc_matrix(histo)
+
+ self.setResult("Num Slices", timeslices)
+ self.setResult("Phase Histogram", histo_mat)
+ self.setResult("Phase Geometry", vtk_set)
diff --git a/contrib/SciPy/MatrixInfo.py b/contrib/SciPy/MatrixInfo.py
new file mode 100644
index 0000000..223e40c
--- /dev/null
+++ b/contrib/SciPy/MatrixInfo.py
@@ -0,0 +1,45 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import core.modules
+from core.modules.vistrails_module import Module, ModuleError
+from SciPy import SciPy
+from Matrix import Matrix
+
+class MatrixInfo(SciPy):
+
+ def getString(self, m):
+ numrows = m.rows()
+ numcols = m.cols()
+ numel = m.numElements()
+ maxel = m.maxNumElements()
+
+ out = "Matrix Info:\n\tNumber of Rows: " + str(numrows) + \
+ "\n\tNumber of Columns: " + str(numcols) + \
+ "\n\tNumber of Elements: " + str(numel) + \
+ "\n\tMaximum Number of Elements for compressed matrix: " + \
+ str(maxel)
+
+ return out
+
+ def compute(self):
+ m = self.getInputFromPort("InputMatrix")
+ self.setResult("output", self.getString(m))
diff --git a/contrib/SciPy/MatrixOperations.py b/contrib/SciPy/MatrixOperations.py
new file mode 100644
index 0000000..e18aebe
--- /dev/null
+++ b/contrib/SciPy/MatrixOperations.py
@@ -0,0 +1,139 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import core.modules
+import core.modules.module_registry
+
+from core.modules.vistrails_module import Module, ModuleError
+from SciPy import SciPy
+from Matrix import *
+import math
+import scipy
+
+class MatrixOperation(SciPy):
+ def compute(self):
+ pass
+
+class GetReals(MatrixOperation):
+ def compute(self):
+ m = self.getInputFromPort("InputMatrix")
+ self.setResult("OutputMatrix", m.Reals())
+
+class GetImaginaries(MatrixOperation):
+ def compute(self):
+ m = self.getInputFromPort("InputMatrix")
+ self.setResult("OutputMatrix", m.Imaginaries())
+
+class Conjugate(MatrixOperation):
+ def compute(self):
+ m = self.getInputFromPort("InputMatrix")
+ self.setResult("OutputMatrix", m.Conjugate())
+
+class GetRow(MatrixOperation):
+ def compute(self):
+ m = self.getInputFromPort("InputMatrix")
+ c = self.getInputFromPort("RowIndex")
+ row = m.GetRow(c)
+ mat = SparseMatrix()
+ mat.matrix = row
+ self.setResult("OutputMatrix", mat)
+
+class GetCol(MatrixOperation):
+ def compute(self):
+ m = self.getInputFromPort("InputMatrix")
+ c = self.getInputFromPort("ColIndex")
+ col = m.GetCol(c)
+ mat = SparseMatrix()
+ mat.matrix = col
+ self.setResult("OutputMatrix", mat)
+
+class MatrixMultiply(MatrixOperation):
+ def compute(self):
+ a = self.getInputFromPort("InputMatrix1")
+ b = self.getInputFromPort("InputMatrix2")
+ c = a.matrix * b.matrix
+ out = SparseMatrix()
+ out.matrix = c
+ return out
+
+class ScalarMultiply(MatrixOperation):
+ def compute(self):
+ m = self.getInputFromPort("InputMatrix")
+ s = self.getInputFromPort("Scalar")
+ m.matrix = m.matrix * s
+ self.setResult("OutputMatrix", m)
+
+class ElementMultiply(MatrixOperation):
+ def compute(self):
+ from numpy import array
+ a = self.getInputFromPort("InputMatrix1")
+ b = self.getInputFromPort("InputMatrix2")
+ if a.matrix.shape != b.matrix.shape:
+ raise ModuleError(self, 'Mismatching input dimensions!')
+ c = SparseMatrix()
+ c.matrix = sparse.csc_matrix(array(a.matrix.toarray())*array(b.matrix.toarray()))
+ self.setResult("OutputMatrix", c)
+
+class Transpose(MatrixOperation):
+ def compute(self):
+ m = self.getInputFromPort("InputMatrix")
+ m.matrix = m.matrix.transpose()
+ self.setResult("OutputMatrix", m)
+
+class PrintMatrix(Matrix):
+ def compute(self):
+ m = self.getInputFromPort("InputMatrix")
+ s = m.matrix.__str__()
+ self.setResult("Output", s)
+
+class GetColumnRange(Matrix):
+ def compute(self):
+ m = self.getInputFromPort("InputMatrix")
+ start = self.getInputFromPort("StartIndex")
+ end = self.getInputFromPort("EndIndex")
+ size = end - start
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix((m.matrix.shape[0], size))
+
+ i = 0
+ j = 0
+ while j < m.matrix.shape[0]:
+ while i < size:
+ val = m.matrix[j,start+i]
+ out.matrix[j,i] = val
+ i = i + 1
+ j = j + 1
+
+ self.setResult("Output", out)
+
+class ATan2(MatrixOperation):
+ def compute(self):
+ if self.hasInputFromPort("InputMatrix"):
+ m = self.getInputFromPort("InputMatrix")
+ r = m.Reals().matrix
+ im = m.Imaginaries().matrix
+ else:
+ r = self.getInputFromPort("RealMatrix").matrix
+ im = self.getInputFromPort("ImaginaryMatrix").matrix
+
+ out = SparseMatrix()
+ out.matrix = sparse.csc_matrix(scipy.arctan2(im.toarray(),r.toarray()))
+ self.setResult("Output", out)
diff --git a/contrib/SciPy/SciPy.py b/contrib/SciPy/SciPy.py
new file mode 100644
index 0000000..6ab54ea
--- /dev/null
+++ b/contrib/SciPy/SciPy.py
@@ -0,0 +1,36 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+
+################################################################################
+
+class SciPy(Module):
+ def compute(self):
+ pass
+# def __init__(self):
+# Module.__init__(self)
+
+ # The compute method is passed on as this is functioning only as a base class.
+
+################################################################################
diff --git a/contrib/SciPy/__init__.py b/contrib/SciPy/__init__.py
new file mode 100644
index 0000000..ba18208
--- /dev/null
+++ b/contrib/SciPy/__init__.py
@@ -0,0 +1,226 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from SciPy import SciPy
+from Matrix import *
+from MatlabReader import MatlabReader
+from MatrixInfo import MatrixInfo
+from MatrixConvert import *
+from MatrixOperations import *
+from DSP import *
+from Filters import *
+import core.modules.basic_modules
+
+version = '0.9.0'
+name = 'SciPy'
+identifier = 'edu.utah.sci.vistrails.scipy'
+
+##############################################################################
+
+from scipy import sparse
+
+def initialize(*args, **keywords):
+ reg = core.modules.module_registry.get_module_registry()
+ basic = core.modules.basic_modules
+
+ reg.add_module(SciPy)
+ reg.add_module(Matrix)
+ reg.add_module(MatrixOperation)
+ reg.add_module(DSP)
+ reg.add_module(DSPFilters, name="DSP Window Filters")
+
+ reg.add_module(SparseMatrix)
+ reg.add_input_port(SparseMatrix, "size", (basic.Integer, 'Matrix Size'))
+ reg.add_output_port(SparseMatrix, "output", (SparseMatrix, 'Output Matrix'))
+
+ reg.add_module(HanningWindow)
+ reg.add_input_port(HanningWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(HanningWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(TriangularWindow)
+ reg.add_input_port(TriangularWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(TriangularWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(BlackmanWindow)
+ reg.add_input_port(BlackmanWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(BlackmanWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(BlackmanHarrisWindow)
+ reg.add_input_port(BlackmanHarrisWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(BlackmanHarrisWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(ParzenWindow)
+ reg.add_input_port(ParzenWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(ParzenWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(HammingWindow)
+ reg.add_input_port(HammingWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(HammingWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(KaiserWindow)
+ reg.add_input_port(KaiserWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_input_port(KaiserWindow, "Beta", (basic.Float, 'Beta'))
+ reg.add_output_port(KaiserWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(BartlettHannWindow)
+ reg.add_input_port(BartlettHannWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(BartlettHannWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(GaussianWindow)
+ reg.add_input_port(GaussianWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_input_port(GaussianWindow, "Sigma", (basic.Integer, 'Sigma (Std. Deviation)'))
+ reg.add_output_port(GaussianWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(BoxcarWindow)
+ reg.add_input_port(BoxcarWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(BoxcarWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(BohmanWindow)
+ reg.add_input_port(BohmanWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(BohmanWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(BartlettWindow)
+ reg.add_input_port(BartlettWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(BartlettWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(NuttallBlackmanHarrisWindow)
+ reg.add_input_port(NuttallBlackmanHarrisWindow, "Window Size", (basic.Integer, 'Window Size'))
+ reg.add_output_port(NuttallBlackmanHarrisWindow, "Window", (SparseMatrix, 'Window'))
+
+ reg.add_module(PrintMatrix)
+ reg.add_input_port(PrintMatrix, "InputMatrix", (Matrix, 'Matrix'))
+ reg.add_output_port(PrintMatrix, "Output", (basic.String, 'Output String'))
+
+ reg.add_module(MatrixConvert)
+ reg.add_input_port(MatrixConvert, "InputMatrix", (Matrix, 'Matrix'))
+ reg.add_input_port(MatrixConvert, "OutputType", (basic.String, 'Output Type'))
+ reg.add_output_port(MatrixConvert, "SparseOutput", (SparseMatrix, 'Output Sparse Matrix'))
+# reg.add_output_port(MatrixConvert, "COOOutput", (COOMatrix, 'Output COO Matrix'))
+# reg.add_output_port(MatrixConvert, "CSCOutput", (CSCMatrix, 'Output CSC Matrix'))
+
+ reg.add_module(MatlabReader)
+ reg.add_input_port(MatlabReader, "Filename", (basic.String, 'Filename'))
+ reg.add_output_port(MatlabReader, "sparseoutput", (SparseMatrix, 'Output Sparse Matrix'))
+ reg.add_input_port(MatlabReader, "File", (basic.File, 'File'))
+
+ reg.add_module(MatrixInfo)
+ reg.add_input_port(MatrixInfo, "InputMatrix", (Matrix, 'Matrix'))
+ reg.add_output_port(MatrixInfo, "output", (basic.String, 'Output String'))
+
+ reg.add_module(GetReals)
+ reg.add_input_port(GetReals, "InputMatrix", (SparseMatrix, 'Input Matrix'))
+ reg.add_output_port(GetReals, "OutputMatrix", (SparseMatrix, 'Result'))
+
+ reg.add_module(GetImaginaries)
+ reg.add_input_port(GetImaginaries, "InputMatrix", (SparseMatrix, 'Input Matrix'))
+ reg.add_output_port(GetImaginaries, "OutputMatrix", (SparseMatrix, 'Result'))
+
+ reg.add_module(Conjugate)
+ reg.add_input_port(Conjugate, "InputMatrix", (SparseMatrix, 'Input Matrix'))
+ reg.add_output_port(Conjugate, "OutputMatrix", (SparseMatrix, 'Result'))
+
+ reg.add_module(GetRow)
+ reg.add_input_port(GetRow, "InputMatrix", (Matrix, 'Input Matrix'))
+ reg.add_input_port(GetRow, "RowIndex", (basic.Integer, 'Row Index'))
+ reg.add_output_port(GetRow, "OutputMatrix", (SparseMatrix, 'Result'))
+
+ reg.add_module(GetCol)
+ reg.add_input_port(GetCol, "InputMatrix", (Matrix, 'Input Matrix'))
+ reg.add_input_port(GetCol, "ColIndex", (basic.Integer, 'Col Index'))
+ reg.add_output_port(GetCol, "OutputMatrix", (SparseMatrix, 'Result'))
+
+ reg.add_module(GetColumnRange)
+ reg.add_input_port(GetColumnRange, "InputMatrix", (SparseMatrix, 'Input Matrix'))
+ reg.add_input_port(GetColumnRange, "StartIndex", (basic.Integer, 'Start Index'))
+ reg.add_input_port(GetColumnRange, "EndIndex", (basic.Integer, 'End Index'))
+ reg.add_output_port(GetColumnRange, "Output", (SparseMatrix, 'Result'))
+
+ reg.add_module(ScalarMultiply)
+ reg.add_input_port(ScalarMultiply, "InputMatrix", (Matrix, 'Input Matrix'))
+ reg.add_input_port(ScalarMultiply, "Scalar", (basic.Float, 'Scalar'))
+ reg.add_output_port(ScalarMultiply, "OutputMatrix", (SparseMatrix, 'Result'))
+
+ reg.add_module(Transpose)
+ reg.add_input_port(Transpose, "InputMatrix", (Matrix, 'Input Matrix'))
+ reg.add_output_port(Transpose, "OutputMatrix", (Matrix, 'Output Matrix'))
+
+ reg.add_module(MatrixMultiply)
+ reg.add_input_port(MatrixMultiply, "InputMatrix1", (Matrix, 'Input Matrix 1'))
+ reg.add_input_port(MatrixMultiply, "InputMatrix2", (Matrix, 'Input Matrix 2'))
+ reg.add_output_port(MatrixMultiply, "OutputMatrix", (Matrix, 'Output Matrix'))
+
+ reg.add_module(ElementMultiply)
+ reg.add_input_port(ElementMultiply, "InputMatrix1", (Matrix, 'Input Matrix 1'))
+ reg.add_input_port(ElementMultiply, "InputMatrix2", (Matrix, 'Input Matrix 2'))
+ reg.add_output_port(ElementMultiply, "OutputMatrix", (SparseMatrix, 'Output Matrix'))
+
+ reg.add_module(ATan2)
+ reg.add_input_port(ATan2, "InputMatrix", (SparseMatrix, 'Complex Matrix'))
+ reg.add_input_port(ATan2, "RealMatrix", (SparseMatrix, 'Real Matrix'), True)
+ reg.add_input_port(ATan2, "ImaginaryMatrix", (SparseMatrix, 'Imaginary Matrix'), True)
+ reg.add_output_port(ATan2, "Output", (SparseMatrix, 'Output Matrix'))
+
+ reg.add_module(FFT)
+ reg.add_input_port(FFT, "Signals", (Matrix, 'Input Signal Matrix'))
+ reg.add_input_port(FFT, "FFT Samples", (basic.Integer, 'FFT Samples'))
+ reg.add_output_port(FFT, "FFT Output", (SparseMatrix, 'FFT Output'))
+
+ reg.add_module(FFT2)
+ reg.add_input_port(FFT2, "Signals", (Matrix, 'Input Signal Matrix'))
+ reg.add_output_port(FFT2, "FFT Output", (SparseMatrix, 'FFT Output'))
+
+ reg.add_module(WindowedFourierTransform)
+ reg.add_input_port(WindowedFourierTransform, "Signal", (Matrix, 'Input Signal'))
+ reg.add_input_port(WindowedFourierTransform, "Sampling Rate", (basic.Integer, 'Sampling Rate'))
+ reg.add_input_port(WindowedFourierTransform, "Window Size", (basic.Integer, 'Window Size'), True)
+ reg.add_input_port(WindowedFourierTransform, "Stride", (basic.Integer, 'Window Stride'), True)
+ reg.add_output_port(WindowedFourierTransform, "FFT Output", (SparseMatrix, 'FFT Output'))
+
+ reg.add_module(ShortTimeFourierTransform)
+ reg.add_input_port(ShortTimeFourierTransform, "Signal", (Matrix, 'Input Signal'))
+ reg.add_input_port(ShortTimeFourierTransform, "Sampling Rate", (basic.Integer, 'Sampling Rate'))
+ reg.add_input_port(ShortTimeFourierTransform, "Stride", (basic.Integer, 'Window Stride'))
+ reg.add_input_port(ShortTimeFourierTransform, "Window", (Matrix, 'Window Function'), True)
+ reg.add_input_port(ShortTimeFourierTransform, "WindowSize", (basic.Integer, 'Window Size'))
+ reg.add_output_port(ShortTimeFourierTransform, "FFT Output", (SparseMatrix, 'FFT Output'))
+ reg.add_output_port(ShortTimeFourierTransform, "Signal Output", (SparseMatrix, 'Signal Output'), True)
+
+ reg.add_module(vtkDataSetToMatrix)
+ reg.add_input_port(vtkDataSetToMatrix, "vtkUnstructuredGrid", (reg.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkAlgorithmOutput').module, 'Input Unstructured Grid'))
+ reg.add_output_port(vtkDataSetToMatrix, "Output Matrix", (SparseMatrix, 'Output Matrix'))
+
+ reg.add_module(PhaseHistogramToVTKPoints)
+ reg.add_input_port(PhaseHistogramToVTKPoints, "FFT Input", (SparseMatrix, 'FFT Input'))
+ reg.add_input_port(PhaseHistogramToVTKPoints, "Num Bins", (basic.Integer, 'Number of Phase Bins'))
+ reg.add_output_port(PhaseHistogramToVTKPoints, "Num Slices", (basic.Integer, 'Number of Histogram Timeslices'), True)
+ reg.add_output_port(PhaseHistogramToVTKPoints, "Phase Histogram", (SparseMatrix, 'Phase Histogram'), True)
+ reg.add_output_port(PhaseHistogramToVTKPoints, "Phase Geometry", (reg.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkAlgorithmOutput').module, 'Phase Geometry Connection'))
+
+def package_dependencies():
+ import core.packagemanager
+ manager = core.packagemanager.get_package_manager()
+ if manager.has_package('edu.utah.sci.vistrails.vtk'):
+ return ['edu.utah.sci.vistrails.vtk']
+ else:
+ return []
diff --git a/contrib/TetGenBridge/CreateTestSurf.py b/contrib/TetGenBridge/CreateTestSurf.py
new file mode 100644
index 0000000..6a5f356
--- /dev/null
+++ b/contrib/TetGenBridge/CreateTestSurf.py
@@ -0,0 +1,102 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+import packages.TetGenBridge
+import TetGen
+import re
+import os
+
+# TetGen output on this mesh. -pqAz
+## Statistics:
+
+## Input points: 149
+## Input facets: 294
+## Input holes: 0
+## Input regions: 0
+
+## Mesh points: 2184
+## Mesh tetrahedra: 7462
+## Mesh faces: 16726
+## Mesh subfaces: 3604
+## Mesh subsegments: 2037
+
+nodes_exp = re.compile('([\d\-\.]+)\s+([\d\-\.]+)\s+([\d\-\.]+)')
+def getTestNodes() :
+ nodes = []
+ p = "%spackages%sTetGenBridge%s" % (os.sep, os.sep, os.sep)
+ f = open('%s%spill.nodes' % (os.getcwd(), p))
+ for l in f.readlines() :
+ mo = nodes_exp.match(l)
+ if mo != None :
+ nodes.append((float(mo.group(1)), float(mo.group(2)),
+ float(mo.group(3))))
+ return nodes
+
+tris_exp = re.compile('(\d+)\s+(\d+)\s+(\d+)')
+def getTestTris() :
+ tris = []
+ p = "%spackages%sTetGenBridge%s" % (os.sep, os.sep, os.sep)
+ f = open('%s%spill.tri' % (os.getcwd(), p))
+ for l in f.readlines() :
+ mo = tris_exp.match(l)
+ if mo != None :
+ tris.append((int(mo.group(1)), int(mo.group(2)),
+ int(mo.group(3))))
+ return tris
+
+def addSurfaceInfo(tgio, marker = 0) :
+
+ #iterate over nodes and add the points.
+ nodes = getTestNodes()
+ sz = len(nodes)
+ tgio.pointlist = TetGen.allocate_array(sz * 3)
+ tgio.numberofpoints = sz
+ idx = 0
+ for n in nodes :
+ TetGen.set_val(tgio.pointlist, idx * 3, n[0])
+ TetGen.set_val(tgio.pointlist, idx * 3 + 1, n[1])
+ TetGen.set_val(tgio.pointlist, idx * 3 + 2, n[2])
+ idx = idx + 1
+
+ #iterate over faces and add the facets.
+ tris = getTestTris()
+ fsz = len(tris)
+ tgio.facetlist = TetGen.allocate_facet_array(fsz)
+ tgio.numberoffacets = fsz;
+ idx = 0
+ for t in tris :
+ TetGen.add_tri(tgio.facetlist, idx, t[0], t[1], t[2])
+ idx = idx + 1
+
+class CreateTestSurf(Module):
+ def compute(self):
+ out = packages.TetGenBridge.tetgenio_wrapper()
+ addSurfaceInfo(out.data, 0)
+ self.setResult("tgio out", out)
+
+def initialize(reg):
+ reg.add_module(CreateTestSurf)
+ reg.add_output_port(CreateTestSurf, "tgio out",
+ (packages.TetGenBridge.tetgenio_wrapper,
+ 'output test surface'))
diff --git a/contrib/TetGenBridge/Makefile b/contrib/TetGenBridge/Makefile
new file mode 100644
index 0000000..6ed25f4
--- /dev/null
+++ b/contrib/TetGenBridge/Makefile
@@ -0,0 +1,19 @@
+SRCS := tetgen_wrap.cc
+
+INCLUDES := -I/usr/include/python2.4 -I/scratch/mjc/tetgen-dev
+
+CC := g++
+CXXFLAGS := -fPIC
+LIBS := -lpython2.4 -ltet
+
+%.o :: %.cc
+ $(CC) $(CXXFLAGS) -c -o $@ $(INCLUDES) $<
+
+
+_TetGen.so: tetgen_wrap.o
+ $(CC) $(CXXFLAGS) -shared -o _TetGen.so tetgen_wrap.o $(INCLUDES) -L . $(LIBS)
+
+tetgen_wrap.cc:tetgen.i
+ swig -v -o tetgen_wrap.cc $(INCLUDES) -python -c++ tetgen.i
+
+
diff --git a/contrib/TetGenBridge/TetGen.py b/contrib/TetGenBridge/TetGen.py
new file mode 100644
index 0000000..8794b17
--- /dev/null
+++ b/contrib/TetGenBridge/TetGen.py
@@ -0,0 +1,313 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+# This file was created automatically by SWIG 1.3.27.
+# Don't modify this file, modify the SWIG interface instead.
+
+import _TetGen
+
+# This file is compatible with both classic and new-style classes.
+def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
+ if (name == "this"):
+ if isinstance(value, class_type):
+ self.__dict__[name] = value.this
+ if hasattr(value,"thisown"): self.__dict__["thisown"] = value.thisown
+ del value.thisown
+ return
+ method = class_type.__swig_setmethods__.get(name,None)
+ if method: return method(self,value)
+ if (not static) or hasattr(self,name) or (name == "thisown"):
+ self.__dict__[name] = value
+ else:
+ raise AttributeError("You cannot add attributes to %s" % self)
+
+def _swig_setattr(self,class_type,name,value):
+ return _swig_setattr_nondynamic(self,class_type,name,value,0)
+
+def _swig_getattr(self,class_type,name):
+ method = class_type.__swig_getmethods__.get(name,None)
+ if method: return method(self)
+ raise AttributeError,name
+
+import types
+try:
+ _object = types.ObjectType
+ _newclass = 1
+except AttributeError:
+ class _object : pass
+ _newclass = 0
+del types
+
+
+class tetgenio(_object):
+ __swig_setmethods__ = {}
+ __setattr__ = lambda self, name, value: _swig_setattr(self, tetgenio, name, value)
+ __swig_getmethods__ = {}
+ __getattr__ = lambda self, name: _swig_getattr(self, tetgenio, name)
+ def __repr__(self):
+ return "<%s.%s; proxy of C++ tetgenio instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
+ FILENAMESIZE = _TetGen.tetgenio_FILENAMESIZE
+ INPUTLINESIZE = _TetGen.tetgenio_INPUTLINESIZE
+ __swig_getmethods__["init"] = lambda x: _TetGen.tetgenio_init
+ if _newclass:init = staticmethod(_TetGen.tetgenio_init)
+ __swig_setmethods__["firstnumber"] = _TetGen.tetgenio_firstnumber_set
+ __swig_getmethods__["firstnumber"] = _TetGen.tetgenio_firstnumber_get
+ if _newclass:firstnumber = property(_TetGen.tetgenio_firstnumber_get, _TetGen.tetgenio_firstnumber_set)
+ __swig_setmethods__["mesh_dim"] = _TetGen.tetgenio_mesh_dim_set
+ __swig_getmethods__["mesh_dim"] = _TetGen.tetgenio_mesh_dim_get
+ if _newclass:mesh_dim = property(_TetGen.tetgenio_mesh_dim_get, _TetGen.tetgenio_mesh_dim_set)
+ __swig_setmethods__["pointlist"] = _TetGen.tetgenio_pointlist_set
+ __swig_getmethods__["pointlist"] = _TetGen.tetgenio_pointlist_get
+ if _newclass:pointlist = property(_TetGen.tetgenio_pointlist_get, _TetGen.tetgenio_pointlist_set)
+ __swig_setmethods__["pointattributelist"] = _TetGen.tetgenio_pointattributelist_set
+ __swig_getmethods__["pointattributelist"] = _TetGen.tetgenio_pointattributelist_get
+ if _newclass:pointattributelist = property(_TetGen.tetgenio_pointattributelist_get, _TetGen.tetgenio_pointattributelist_set)
+ __swig_setmethods__["addpointlist"] = _TetGen.tetgenio_addpointlist_set
+ __swig_getmethods__["addpointlist"] = _TetGen.tetgenio_addpointlist_get
+ if _newclass:addpointlist = property(_TetGen.tetgenio_addpointlist_get, _TetGen.tetgenio_addpointlist_set)
+ __swig_setmethods__["addpointattributelist"] = _TetGen.tetgenio_addpointattributelist_set
+ __swig_getmethods__["addpointattributelist"] = _TetGen.tetgenio_addpointattributelist_get
+ if _newclass:addpointattributelist = property(_TetGen.tetgenio_addpointattributelist_get, _TetGen.tetgenio_addpointattributelist_set)
+ __swig_setmethods__["pointmarkerlist"] = _TetGen.tetgenio_pointmarkerlist_set
+ __swig_getmethods__["pointmarkerlist"] = _TetGen.tetgenio_pointmarkerlist_get
+ if _newclass:pointmarkerlist = property(_TetGen.tetgenio_pointmarkerlist_get, _TetGen.tetgenio_pointmarkerlist_set)
+ __swig_setmethods__["numberofpoints"] = _TetGen.tetgenio_numberofpoints_set
+ __swig_getmethods__["numberofpoints"] = _TetGen.tetgenio_numberofpoints_get
+ if _newclass:numberofpoints = property(_TetGen.tetgenio_numberofpoints_get, _TetGen.tetgenio_numberofpoints_set)
+ __swig_setmethods__["numberofpointattributes"] = _TetGen.tetgenio_numberofpointattributes_set
+ __swig_getmethods__["numberofpointattributes"] = _TetGen.tetgenio_numberofpointattributes_get
+ if _newclass:numberofpointattributes = property(_TetGen.tetgenio_numberofpointattributes_get, _TetGen.tetgenio_numberofpointattributes_set)
+ __swig_setmethods__["numberofaddpoints"] = _TetGen.tetgenio_numberofaddpoints_set
+ __swig_getmethods__["numberofaddpoints"] = _TetGen.tetgenio_numberofaddpoints_get
+ if _newclass:numberofaddpoints = property(_TetGen.tetgenio_numberofaddpoints_get, _TetGen.tetgenio_numberofaddpoints_set)
+ __swig_setmethods__["tetrahedronlist"] = _TetGen.tetgenio_tetrahedronlist_set
+ __swig_getmethods__["tetrahedronlist"] = _TetGen.tetgenio_tetrahedronlist_get
+ if _newclass:tetrahedronlist = property(_TetGen.tetgenio_tetrahedronlist_get, _TetGen.tetgenio_tetrahedronlist_set)
+ __swig_setmethods__["tetrahedronattributelist"] = _TetGen.tetgenio_tetrahedronattributelist_set
+ __swig_getmethods__["tetrahedronattributelist"] = _TetGen.tetgenio_tetrahedronattributelist_get
+ if _newclass:tetrahedronattributelist = property(_TetGen.tetgenio_tetrahedronattributelist_get, _TetGen.tetgenio_tetrahedronattributelist_set)
+ __swig_setmethods__["tetrahedronvolumelist"] = _TetGen.tetgenio_tetrahedronvolumelist_set
+ __swig_getmethods__["tetrahedronvolumelist"] = _TetGen.tetgenio_tetrahedronvolumelist_get
+ if _newclass:tetrahedronvolumelist = property(_TetGen.tetgenio_tetrahedronvolumelist_get, _TetGen.tetgenio_tetrahedronvolumelist_set)
+ __swig_setmethods__["neighborlist"] = _TetGen.tetgenio_neighborlist_set
+ __swig_getmethods__["neighborlist"] = _TetGen.tetgenio_neighborlist_get
+ if _newclass:neighborlist = property(_TetGen.tetgenio_neighborlist_get, _TetGen.tetgenio_neighborlist_set)
+ __swig_setmethods__["numberoftetrahedra"] = _TetGen.tetgenio_numberoftetrahedra_set
+ __swig_getmethods__["numberoftetrahedra"] = _TetGen.tetgenio_numberoftetrahedra_get
+ if _newclass:numberoftetrahedra = property(_TetGen.tetgenio_numberoftetrahedra_get, _TetGen.tetgenio_numberoftetrahedra_set)
+ __swig_setmethods__["numberofcorners"] = _TetGen.tetgenio_numberofcorners_set
+ __swig_getmethods__["numberofcorners"] = _TetGen.tetgenio_numberofcorners_get
+ if _newclass:numberofcorners = property(_TetGen.tetgenio_numberofcorners_get, _TetGen.tetgenio_numberofcorners_set)
+ __swig_setmethods__["numberoftetrahedronattributes"] = _TetGen.tetgenio_numberoftetrahedronattributes_set
+ __swig_getmethods__["numberoftetrahedronattributes"] = _TetGen.tetgenio_numberoftetrahedronattributes_get
+ if _newclass:numberoftetrahedronattributes = property(_TetGen.tetgenio_numberoftetrahedronattributes_get, _TetGen.tetgenio_numberoftetrahedronattributes_set)
+ __swig_setmethods__["facetlist"] = _TetGen.tetgenio_facetlist_set
+ __swig_getmethods__["facetlist"] = _TetGen.tetgenio_facetlist_get
+ if _newclass:facetlist = property(_TetGen.tetgenio_facetlist_get, _TetGen.tetgenio_facetlist_set)
+ __swig_setmethods__["facetmarkerlist"] = _TetGen.tetgenio_facetmarkerlist_set
+ __swig_getmethods__["facetmarkerlist"] = _TetGen.tetgenio_facetmarkerlist_get
+ if _newclass:facetmarkerlist = property(_TetGen.tetgenio_facetmarkerlist_get, _TetGen.tetgenio_facetmarkerlist_set)
+ __swig_setmethods__["numberoffacets"] = _TetGen.tetgenio_numberoffacets_set
+ __swig_getmethods__["numberoffacets"] = _TetGen.tetgenio_numberoffacets_get
+ if _newclass:numberoffacets = property(_TetGen.tetgenio_numberoffacets_get, _TetGen.tetgenio_numberoffacets_set)
+ __swig_setmethods__["holelist"] = _TetGen.tetgenio_holelist_set
+ __swig_getmethods__["holelist"] = _TetGen.tetgenio_holelist_get
+ if _newclass:holelist = property(_TetGen.tetgenio_holelist_get, _TetGen.tetgenio_holelist_set)
+ __swig_setmethods__["numberofholes"] = _TetGen.tetgenio_numberofholes_set
+ __swig_getmethods__["numberofholes"] = _TetGen.tetgenio_numberofholes_get
+ if _newclass:numberofholes = property(_TetGen.tetgenio_numberofholes_get, _TetGen.tetgenio_numberofholes_set)
+ __swig_setmethods__["regionlist"] = _TetGen.tetgenio_regionlist_set
+ __swig_getmethods__["regionlist"] = _TetGen.tetgenio_regionlist_get
+ if _newclass:regionlist = property(_TetGen.tetgenio_regionlist_get, _TetGen.tetgenio_regionlist_set)
+ __swig_setmethods__["numberofregions"] = _TetGen.tetgenio_numberofregions_set
+ __swig_getmethods__["numberofregions"] = _TetGen.tetgenio_numberofregions_get
+ if _newclass:numberofregions = property(_TetGen.tetgenio_numberofregions_get, _TetGen.tetgenio_numberofregions_set)
+ __swig_setmethods__["facetconstraintlist"] = _TetGen.tetgenio_facetconstraintlist_set
+ __swig_getmethods__["facetconstraintlist"] = _TetGen.tetgenio_facetconstraintlist_get
+ if _newclass:facetconstraintlist = property(_TetGen.tetgenio_facetconstraintlist_get, _TetGen.tetgenio_facetconstraintlist_set)
+ __swig_setmethods__["numberoffacetconstraints"] = _TetGen.tetgenio_numberoffacetconstraints_set
+ __swig_getmethods__["numberoffacetconstraints"] = _TetGen.tetgenio_numberoffacetconstraints_get
+ if _newclass:numberoffacetconstraints = property(_TetGen.tetgenio_numberoffacetconstraints_get, _TetGen.tetgenio_numberoffacetconstraints_set)
+ __swig_setmethods__["segmentconstraintlist"] = _TetGen.tetgenio_segmentconstraintlist_set
+ __swig_getmethods__["segmentconstraintlist"] = _TetGen.tetgenio_segmentconstraintlist_get
+ if _newclass:segmentconstraintlist = property(_TetGen.tetgenio_segmentconstraintlist_get, _TetGen.tetgenio_segmentconstraintlist_set)
+ __swig_setmethods__["numberofsegmentconstraints"] = _TetGen.tetgenio_numberofsegmentconstraints_set
+ __swig_getmethods__["numberofsegmentconstraints"] = _TetGen.tetgenio_numberofsegmentconstraints_get
+ if _newclass:numberofsegmentconstraints = property(_TetGen.tetgenio_numberofsegmentconstraints_get, _TetGen.tetgenio_numberofsegmentconstraints_set)
+ __swig_setmethods__["nodeconstraintlist"] = _TetGen.tetgenio_nodeconstraintlist_set
+ __swig_getmethods__["nodeconstraintlist"] = _TetGen.tetgenio_nodeconstraintlist_get
+ if _newclass:nodeconstraintlist = property(_TetGen.tetgenio_nodeconstraintlist_get, _TetGen.tetgenio_nodeconstraintlist_set)
+ __swig_setmethods__["numberofnodeconstraints"] = _TetGen.tetgenio_numberofnodeconstraints_set
+ __swig_getmethods__["numberofnodeconstraints"] = _TetGen.tetgenio_numberofnodeconstraints_get
+ if _newclass:numberofnodeconstraints = property(_TetGen.tetgenio_numberofnodeconstraints_get, _TetGen.tetgenio_numberofnodeconstraints_set)
+ __swig_setmethods__["pbcgrouplist"] = _TetGen.tetgenio_pbcgrouplist_set
+ __swig_getmethods__["pbcgrouplist"] = _TetGen.tetgenio_pbcgrouplist_get
+ if _newclass:pbcgrouplist = property(_TetGen.tetgenio_pbcgrouplist_get, _TetGen.tetgenio_pbcgrouplist_set)
+ __swig_setmethods__["numberofpbcgroups"] = _TetGen.tetgenio_numberofpbcgroups_set
+ __swig_getmethods__["numberofpbcgroups"] = _TetGen.tetgenio_numberofpbcgroups_get
+ if _newclass:numberofpbcgroups = property(_TetGen.tetgenio_numberofpbcgroups_get, _TetGen.tetgenio_numberofpbcgroups_set)
+ __swig_setmethods__["trifacelist"] = _TetGen.tetgenio_trifacelist_set
+ __swig_getmethods__["trifacelist"] = _TetGen.tetgenio_trifacelist_get
+ if _newclass:trifacelist = property(_TetGen.tetgenio_trifacelist_get, _TetGen.tetgenio_trifacelist_set)
+ __swig_setmethods__["adjtetlist"] = _TetGen.tetgenio_adjtetlist_set
+ __swig_getmethods__["adjtetlist"] = _TetGen.tetgenio_adjtetlist_get
+ if _newclass:adjtetlist = property(_TetGen.tetgenio_adjtetlist_get, _TetGen.tetgenio_adjtetlist_set)
+ __swig_setmethods__["trifacemarkerlist"] = _TetGen.tetgenio_trifacemarkerlist_set
+ __swig_getmethods__["trifacemarkerlist"] = _TetGen.tetgenio_trifacemarkerlist_get
+ if _newclass:trifacemarkerlist = property(_TetGen.tetgenio_trifacemarkerlist_get, _TetGen.tetgenio_trifacemarkerlist_set)
+ __swig_setmethods__["numberoftrifaces"] = _TetGen.tetgenio_numberoftrifaces_set
+ __swig_getmethods__["numberoftrifaces"] = _TetGen.tetgenio_numberoftrifaces_get
+ if _newclass:numberoftrifaces = property(_TetGen.tetgenio_numberoftrifaces_get, _TetGen.tetgenio_numberoftrifaces_set)
+ __swig_setmethods__["edgelist"] = _TetGen.tetgenio_edgelist_set
+ __swig_getmethods__["edgelist"] = _TetGen.tetgenio_edgelist_get
+ if _newclass:edgelist = property(_TetGen.tetgenio_edgelist_get, _TetGen.tetgenio_edgelist_set)
+ __swig_setmethods__["edgemarkerlist"] = _TetGen.tetgenio_edgemarkerlist_set
+ __swig_getmethods__["edgemarkerlist"] = _TetGen.tetgenio_edgemarkerlist_get
+ if _newclass:edgemarkerlist = property(_TetGen.tetgenio_edgemarkerlist_get, _TetGen.tetgenio_edgemarkerlist_set)
+ __swig_setmethods__["numberofedges"] = _TetGen.tetgenio_numberofedges_set
+ __swig_getmethods__["numberofedges"] = _TetGen.tetgenio_numberofedges_get
+ if _newclass:numberofedges = property(_TetGen.tetgenio_numberofedges_get, _TetGen.tetgenio_numberofedges_set)
+ def initialize(*args): return _TetGen.tetgenio_initialize(*args)
+ def deinitialize(*args): return _TetGen.tetgenio_deinitialize(*args)
+ def load_node_call(*args): return _TetGen.tetgenio_load_node_call(*args)
+ def load_node(*args): return _TetGen.tetgenio_load_node(*args)
+ def load_addnodes(*args): return _TetGen.tetgenio_load_addnodes(*args)
+ def load_pbc(*args): return _TetGen.tetgenio_load_pbc(*args)
+ def load_var(*args): return _TetGen.tetgenio_load_var(*args)
+ def load_mtr(*args): return _TetGen.tetgenio_load_mtr(*args)
+ def load_poly(*args): return _TetGen.tetgenio_load_poly(*args)
+ def load_off(*args): return _TetGen.tetgenio_load_off(*args)
+ def load_ply(*args): return _TetGen.tetgenio_load_ply(*args)
+ def load_stl(*args): return _TetGen.tetgenio_load_stl(*args)
+ def load_medit(*args): return _TetGen.tetgenio_load_medit(*args)
+ def load_plc(*args): return _TetGen.tetgenio_load_plc(*args)
+ def load_tetmesh(*args): return _TetGen.tetgenio_load_tetmesh(*args)
+ def save_nodes(*args): return _TetGen.tetgenio_save_nodes(*args)
+ def save_elements(*args): return _TetGen.tetgenio_save_elements(*args)
+ def save_faces(*args): return _TetGen.tetgenio_save_faces(*args)
+ def save_edges(*args): return _TetGen.tetgenio_save_edges(*args)
+ def save_neighbors(*args): return _TetGen.tetgenio_save_neighbors(*args)
+ def save_poly(*args): return _TetGen.tetgenio_save_poly(*args)
+ def readline(*args): return _TetGen.tetgenio_readline(*args)
+ def findnextfield(*args): return _TetGen.tetgenio_findnextfield(*args)
+ def readnumberline(*args): return _TetGen.tetgenio_readnumberline(*args)
+ def findnextnumber(*args): return _TetGen.tetgenio_findnextnumber(*args)
+ def __init__(self, *args):
+ _swig_setattr(self, tetgenio, 'this', _TetGen.new_tetgenio(*args))
+ _swig_setattr(self, tetgenio, 'thisown', 1)
+ def __del__(self, destroy=_TetGen.delete_tetgenio):
+ try:
+ if self.thisown: destroy(self)
+ except: pass
+
+
+class tetgenioPtr(tetgenio):
+ def __init__(self, this):
+ _swig_setattr(self, tetgenio, 'this', this)
+ if not hasattr(self,"thisown"): _swig_setattr(self, tetgenio, 'thisown', 0)
+ self.__class__ = tetgenio
+_TetGen.tetgenio_swigregister(tetgenioPtr)
+
+tetgenio_init = _TetGen.tetgenio_init
+
+class polygon(_object):
+ __swig_setmethods__ = {}
+ __setattr__ = lambda self, name, value: _swig_setattr(self, polygon, name, value)
+ __swig_getmethods__ = {}
+ __getattr__ = lambda self, name: _swig_getattr(self, polygon, name)
+ def __repr__(self):
+ return "<%s.%s; proxy of C++ tetgenio::polygon instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
+ def __init__(self, *args):
+ _swig_setattr(self, polygon, 'this', _TetGen.new_polygon(*args))
+ _swig_setattr(self, polygon, 'thisown', 1)
+ def __del__(self, destroy=_TetGen.delete_polygon):
+ try:
+ if self.thisown: destroy(self)
+ except: pass
+
+
+class polygonPtr(polygon):
+ def __init__(self, this):
+ _swig_setattr(self, polygon, 'this', this)
+ if not hasattr(self,"thisown"): _swig_setattr(self, polygon, 'thisown', 0)
+ self.__class__ = polygon
+_TetGen.polygon_swigregister(polygonPtr)
+
+class facet(_object):
+ __swig_setmethods__ = {}
+ __setattr__ = lambda self, name, value: _swig_setattr(self, facet, name, value)
+ __swig_getmethods__ = {}
+ __getattr__ = lambda self, name: _swig_getattr(self, facet, name)
+ def __repr__(self):
+ return "<%s.%s; proxy of C++ tetgenio::facet instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
+ def __init__(self, *args):
+ _swig_setattr(self, facet, 'this', _TetGen.new_facet(*args))
+ _swig_setattr(self, facet, 'thisown', 1)
+ def __del__(self, destroy=_TetGen.delete_facet):
+ try:
+ if self.thisown: destroy(self)
+ except: pass
+
+
+class facetPtr(facet):
+ def __init__(self, this):
+ _swig_setattr(self, facet, 'this', this)
+ if not hasattr(self,"thisown"): _swig_setattr(self, facet, 'thisown', 0)
+ self.__class__ = facet
+_TetGen.facet_swigregister(facetPtr)
+
+class pbcgroup(_object):
+ __swig_setmethods__ = {}
+ __setattr__ = lambda self, name, value: _swig_setattr(self, pbcgroup, name, value)
+ __swig_getmethods__ = {}
+ __getattr__ = lambda self, name: _swig_getattr(self, pbcgroup, name)
+ def __repr__(self):
+ return "<%s.%s; proxy of C++ tetgenio::pbcgroup instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
+ def __init__(self, *args):
+ _swig_setattr(self, pbcgroup, 'this', _TetGen.new_pbcgroup(*args))
+ _swig_setattr(self, pbcgroup, 'thisown', 1)
+ def __del__(self, destroy=_TetGen.delete_pbcgroup):
+ try:
+ if self.thisown: destroy(self)
+ except: pass
+
+
+class pbcgroupPtr(pbcgroup):
+ def __init__(self, this):
+ _swig_setattr(self, pbcgroup, 'this', this)
+ if not hasattr(self,"thisown"): _swig_setattr(self, pbcgroup, 'thisown', 0)
+ self.__class__ = pbcgroup
+_TetGen.pbcgroup_swigregister(pbcgroupPtr)
+
+
+tetrahedralize = _TetGen.tetrahedralize
+
+allocate_array = _TetGen.allocate_array
+
+set_val = _TetGen.set_val
+
+get_val = _TetGen.get_val
+
+allocate_facet_array = _TetGen.allocate_facet_array
+
+add_tri = _TetGen.add_tri
+
+
diff --git a/contrib/TetGenBridge/__init__.py b/contrib/TetGenBridge/__init__.py
new file mode 100644
index 0000000..e9abd51
--- /dev/null
+++ b/contrib/TetGenBridge/__init__.py
@@ -0,0 +1,90 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+"""The TetGenBridge package wraps the TetGen library, exposing the tetrahedralize function as well as the input/output classes."""
+
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+import TetGen
+import CreateTestSurf
+
+identifier = 'edu.utah.sci.vistrails.tetget'
+version = '0.9.0'
+name = 'tetgen'
+
+
+# The port that wraps a tetgenio class.
+class tetgenio_wrapper(Module):
+ def __init__(self) :
+ self.data = TetGen.tetgenio()
+
+
+class tetrahedralize(Module):
+ """tetrahedralize corresponds to the TetGen function of the same name"""
+
+
+ def __init__(self):
+ Module.__init__(self)
+
+
+ def compute(self):
+ switches = None
+ if self.hasInputFromPort("switches") :
+ switches = self.getInputFromPort("switches")
+ print switches
+ if self.hasInputFromPort("tgio in") :
+ tgio_in = self.getInputFromPort("tgio in").data
+
+ print "input has %d nodes!" % tgio_in.numberofpoints
+ tgio_in.save_nodes("/tmp/tgIN.vt")
+ tgio_in.save_poly("/tmp/tgIN.vt")
+ out = tetgenio_wrapper()
+ TetGen.tetrahedralize(switches, tgio_in, out.data)
+ print "Done making tets"
+
+ self.setResult("tgio out", out)
+
+
+
+
+def initialize(*args, **keywords):
+ reg = core.modules.module_registry
+
+ #calls the lib with function of the same name.
+ reg.add_module(tetrahedralize)
+
+ # command line switches that tell tetrahedralize what to do.
+ reg.add_input_port(tetrahedralize, "switches",
+ (core.modules.basic_modules.String, 'tetgen options'))
+ # input mesh information.
+ reg.add_input_port(tetrahedralize, "tgio in",
+ (tetgenio_wrapper, 'input data'))
+ # output mesh information.
+ reg.add_output_port(tetrahedralize, "tgio out",
+ (tetgenio_wrapper, 'output data'))
+
+ #holds the tetgenio class, and acts as a port.
+ reg.add_module(tetgenio_wrapper)
+
+ # get support and testing modules registered.
+ CreateTestSurf.initialize(reg)
+
diff --git a/contrib/TetGenBridge/pill.nodes b/contrib/TetGenBridge/pill.nodes
new file mode 100644
index 0000000..c5f5a68
--- /dev/null
+++ b/contrib/TetGenBridge/pill.nodes
@@ -0,0 +1,150 @@
+149
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+-0.112491 -2.852496 1.096028
+-0.056638 -2.866179 0.515760
+-0.503132 -2.472678 0.886320
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diff --git a/contrib/TetGenBridge/pill.tri b/contrib/TetGenBridge/pill.tri
new file mode 100644
index 0000000..ebd3206
--- /dev/null
+++ b/contrib/TetGenBridge/pill.tri
@@ -0,0 +1,295 @@
+294
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diff --git a/contrib/TetGenBridge/tetgen.i b/contrib/TetGenBridge/tetgen.i
new file mode 100644
index 0000000..72da66a
--- /dev/null
+++ b/contrib/TetGenBridge/tetgen.i
@@ -0,0 +1,284 @@
+%module TetGen
+%{
+#include <tetgen.h>
+%}
+
+class tetgenio {
+
+ public:
+
+ // Maximum number of characters in a file name (including the null).
+ enum {FILENAMESIZE = 1024};
+
+ // Maxi. numbers of chars in a line read from a file (incl. the null).
+ enum {INPUTLINESIZE = 1024};
+
+ // The polygon data structure. A "polygon" is a planar polygon. It can
+ // be arbitrary shaped (convex or non-convex) and bounded by non-
+ // crossing segments, i.e., the number of vertices it has indictes the
+ // same number of edges.
+ // 'vertexlist' is a list of vertex indices (integers), its length is
+ // indicated by 'numberofvertices'. The vertex indices are odered in
+ // either counterclockwise or clockwise way.
+
+ class polygon;
+
+ static void init(polygon* p) {
+ p->vertexlist = (int *) NULL;
+ p->numberofvertices = 0;
+ }
+
+ // The facet data structure. A "facet" is a planar facet. It is used
+ // to represent a planar straight line graph (PSLG) in two dimension.
+ // A PSLG contains a list of polygons. It also may conatin holes in it,
+ // indicated by a list of hole points (their coordinates).
+ class facet;
+
+ static void init(facet* f) {
+ f->polygonlist = (polygon *) NULL;
+ f->numberofpolygons = 0;
+ f->holelist = (REAL *) NULL;
+ f->numberofholes = 0;
+ }
+
+ // The periodic boundary condition group data structure. A "pbcgroup"
+ // contains the definition of a pbc and the list of pbc point pairs.
+ // 'fmark1' and 'fmark2' are the facetmarkers of the two pbc facets f1
+ // and f2, respectively. 'transmat' is the transformation matrix which
+ // maps a point in f1 into f2. An array of pbc point pairs are saved
+ // in 'pointpairlist'. The first point pair is at indices [0] and [1],
+ // followed by remaining pairs. Two integers per pair.
+ class pbcgroup;
+ public:
+
+ // Items are numbered starting from 'firstnumber' (0 or 1), default is 0.
+ int firstnumber;
+
+ // Dimension of the mesh (2 or 3), default is 3.
+ int mesh_dim;
+
+ // `pointlist': An array of point coordinates. The first point's x
+ // coordinate is at index [0] and its y coordinate at index [1], its
+ // z coordinate is at index [2], followed by the coordinates of the
+ // remaining points. Each point occupies three REALs.
+ // `pointattributelist': An array of point attributes. Each point's
+ // attributes occupy `numberofpointattributes' REALs.
+ // 'addpointlist': An array of additional point coordinates.
+ // 'addpointattributelist': An array of attributes for addition points.
+ // `pointmarkerlist': An array of point markers; one int per point.
+ REAL *pointlist;
+ REAL *pointattributelist;
+ REAL *addpointlist;
+ REAL *addpointattributelist;
+ int *pointmarkerlist;
+ int numberofpoints;
+ int numberofpointattributes;
+ int numberofaddpoints;
+
+ // `elementlist': An array of element (triangle or tetrahedron) corners.
+ // The first element's first corner is at index [0], followed by its
+ // other corners in counterclockwise order, followed by any other
+ // nodes if the element represents a nonlinear element. Each element
+ // occupies `numberofcorners' ints.
+ // `elementattributelist': An array of element attributes. Each
+ // element's attributes occupy `numberofelementattributes' REALs.
+ // `elementconstraintlist': An array of constraints, i.e. triangle's
+ // area or tetrahedron's volume; one REAL per element. Input only.
+ // `neighborlist': An array of element neighbors; 3 or 4 ints per
+ // element. Output only.
+ int *tetrahedronlist;
+ REAL *tetrahedronattributelist;
+ REAL *tetrahedronvolumelist;
+ int *neighborlist;
+ int numberoftetrahedra;
+ int numberofcorners;
+ int numberoftetrahedronattributes;
+
+ // `facetlist': An array of facets. Each entry is a structure of facet.
+ // `facetmarkerlist': An array of facet markers; one int per facet.
+ facet *facetlist;
+ int *facetmarkerlist;
+ int numberoffacets;
+
+ // `holelist': An array of holes. The first hole's x, y and z
+ // coordinates are at indices [0], [1] and [2], followed by the
+ // remaining holes. Three REALs per hole.
+ REAL *holelist;
+ int numberofholes;
+
+ // `regionlist': An array of regional attributes and volume constraints.
+ // The first constraint's x, y and z coordinates are at indices [0],
+ // [1] and [2], followed by the regional attribute at index [3], foll-
+ // owed by the maximum volume at index [4]. Five REALs per constraint.
+ // Note that each regional attribute is used only if you select the `A'
+ // switch, and each volume constraint is used only if you select the
+ // `a' switch (with no number following).
+ REAL *regionlist;
+ int numberofregions;
+
+ // `facetconstraintlist': An array of facet maximal area constraints.
+ // Two REALs per constraint. The first one is the facet marker (cast
+ // it to int), the second is its maximum area bound.
+ // Note the 'facetconstraintlist' is used only for the 'q' switch.
+ REAL *facetconstraintlist;
+ int numberoffacetconstraints;
+
+ // `segmentconstraintlist': An array of segment max. length constraints.
+ // Three REALs per constraint. The first two are the indices (pointing
+ // into 'pointlist') of the endpoints of the segment, the third is its
+ // maximum length bound.
+ // Note the 'segmentconstraintlist' is used only for the 'q' switch.
+ REAL *segmentconstraintlist;
+ int numberofsegmentconstraints;
+
+ // `nodeconstraintlist': An array of segment length constraints. Two
+ // REALs per constraint. The first one is the index (pointing into
+ // 'pointlist') of the node, the second is its edge length bound.
+ // Note the 'nodeconstraintlist' is used only for the 'q' switch.
+ REAL *nodeconstraintlist;
+ int numberofnodeconstraints;
+
+ // 'pbcgrouplist': An array of periodic boundary condition groups.
+ pbcgroup *pbcgrouplist;
+ int numberofpbcgroups;
+
+ // `trifacelist': An array of triangular face endpoints. The first
+ // face's endpoints are at indices [0], [1] and [2], followed by the
+ // remaining faces. Three ints per face.
+ // `adjtetlist': An array of adjacent tetrahedra to the faces of
+ // trifacelist. Each face has at most two adjacent tets, the first
+ // face's adjacent tets are at [0], [1]. Two ints per face. A '-1'
+ // indicates outside (no adj. tet). This list is output when '-n'
+ // switch is used.
+ // `trifacemarkerlist': An array of face markers; one int per face.
+ int *trifacelist;
+ int *adjtetlist;
+ int *trifacemarkerlist;
+ int numberoftrifaces;
+
+ // `edgelist': An array of edge endpoints. The first edge's endpoints
+ // are at indices [0] and [1], followed by the remaining edges. Two
+ // ints per edge.
+ // `edgemarkerlist': An array of edge markers; one int per edge.
+ int *edgelist;
+ int *edgemarkerlist;
+ int numberofedges;
+
+ public:
+
+ // Initialize routine.
+ void initialize();
+ void deinitialize();
+
+ // Input & output routines.
+ bool load_node_call(FILE* infile, int markers, char* nodefilename);
+ bool load_node(char* filename);
+ bool load_addnodes(char* filename);
+ bool load_pbc(char* filename);
+ bool load_var(char* filename);
+ bool load_mtr(char* filename);
+ bool load_poly(char* filename);
+ bool load_off(char* filename);
+ bool load_ply(char* filename);
+ bool load_stl(char* filename);
+ bool load_medit(char* filename);
+ bool load_plc(char* filename, int object);
+ bool load_tetmesh(char* filename);
+ void save_nodes(char* filename);
+ void save_elements(char* filename);
+ void save_faces(char* filename);
+ void save_edges(char* filename);
+ void save_neighbors(char* filename);
+ void save_poly(char* filename);
+
+ // Read line and parse string functions.
+ char *readline(char* string, FILE* infile, int *linenumber);
+ char *findnextfield(char* string);
+ char *readnumberline(char* string, FILE* infile, char* infilename);
+ char *findnextnumber(char* string);
+
+ // Constructor and destructor.
+ tetgenio() {initialize();}
+ ~tetgenio() {deinitialize();}
+};
+
+%rename(polygon) tetgenio::polygon;
+%rename(facet) tetgenio::facet;
+%rename(pbcgroup) tetgenio::pbcgroup;
+
+class tetgenio::polygon {
+ int *vertexlist;
+ int numberofvertices;
+};
+
+class tetgenio::facet {
+ polygon *polygonlist;
+ int numberofpolygons;
+ REAL *holelist;
+ int numberofholes;
+};
+
+class tetgenio::pbcgroup {
+ int fmark1, fmark2;
+ REAL transmat[4][4];
+ int numberofpointpairs;
+ int *pointpairlist;
+};
+
+
+void tetrahedralize(char *switches, tetgenio &in, tetgenio &out);
+
+
+// additional interface for data loading.
+REAL* allocate_array(unsigned int sz);
+void set_val(REAL*arr, unsigned int idx, float val);
+float get_val(REAL*arr, unsigned int idx);
+tetgenio::facet* allocate_facet_array(unsigned int sz);
+void add_tri(tetgenio::facet*arr, int fidx, int nidx0, int nidx1, int nidx2);
+
+%{
+#include <iostream>
+using namespace std;
+
+REAL* allocate_array(unsigned int sz)
+{
+ return new REAL[sz];
+}
+
+void set_val(REAL*arr, unsigned int idx, float val)
+{
+ arr[idx] = val;
+}
+float get_val(REAL*arr, unsigned int idx)
+{
+ return arr[idx];
+}
+
+tetgenio::facet* allocate_facet_array(unsigned int sz)
+{
+ return new tetgenio::facet[sz];
+}
+
+void add_tri(tetgenio::facet*arr, int fidx, int nidx0, int nidx1, int nidx2)
+{
+ tetgenio::facet *f = &arr[fidx];
+ f->numberofpolygons = 1;
+ f->polygonlist = new tetgenio::polygon[f->numberofpolygons];
+ f->numberofholes = 0;
+ f->holelist = 0;
+ tetgenio::polygon *p = &f->polygonlist[0];
+ p->numberofvertices = 3;
+ p->vertexlist = new int[p->numberofvertices];
+ p->vertexlist[0] = nidx0;
+ p->vertexlist[1] = nidx1;
+ p->vertexlist[2] = nidx2;
+}
+
+
+
+void tetrahedralize(char* switches, tetgenio &in, tetgenio &out)
+{
+ tetrahedralize(switches, &in, &out);
+}
+
+%}
\ No newline at end of file
diff --git a/contrib/cdat/NOTES b/contrib/cdat/NOTES
new file mode 100644
index 0000000..8a27f3b
--- /dev/null
+++ b/contrib/cdat/NOTES
@@ -0,0 +1,17 @@
+Issues:
+
+When the user closes vistrails or uses command + q to quit, the close event
+doesn't seem to be passed to vcdat so we won't execute functionality that we
+want to run before we close vcdat. Right now the only thing we want to do
+when we quit is to kill the process that is running the editor to view the
+teaching commands if it exists.
+
+Any operation that relies on data from a defined variable such as 'altered
+weighted average' doesn't work because the vistrails module must have access
+to all of the defined variables to execute these commands and it doesn't have
+that yet.
+
+Clicking on the plot will show the tooltip but the tooltip will disappear very
+fast. Right now there is a hardcoded wait(1) so the tooltip shows up for
+1 second, otherwise the tooltip usually doesn't appear.
+
diff --git a/contrib/cdat/__init__.py b/contrib/cdat/__init__.py
new file mode 100644
index 0000000..e99857e
--- /dev/null
+++ b/contrib/cdat/__init__.py
@@ -0,0 +1,10094 @@
+############################################################################
+##
+## Copyright (C) 2006-2008 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+""" Do not edit this file!
+
+File automatically generated by scripts/gen_init.py
+Change History:
+version : description
+ 0.2 : Integrated quickplot module that displays the CDAT plot
+ widget inside the spreadsheet
+ 0.1 : First automatically generated package based on xml descriptions
+
+"""
+from PyQt4 import QtCore, QtGui
+import sip
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import (Module, NotCacheable,
+ ModuleError, new_module)
+from core.bundles import py_import
+import os, sys, re
+
+#cdat specific packages
+vcs = py_import('vcs',{})
+cdms2 = py_import('cdms2', {})
+cdutil = py_import('cdutil', {})
+import MV2
+import genutil
+
+#local python modules
+from cdat_window import QCDATWindow
+from cdat_cell import QCDATWidget, CDATCell, Variable, GraphicsMethod, Quickplot
+#from quickplot import quickplot
+from packages.spreadsheet.basic_widgets import CellLocation
+from packages.spreadsheet.basic_widgets import SpreadsheetCell
+
+version = "0.2"
+identifier = "edu.utah.sci.vistrails.cdat"
+name = "CDAT"
+
+vt_type_dict = {}
+def get_late_type(type):
+ return vt_type_dict[type]
+
+Canvas = new_module(Module,'Canvas')
+Dp = new_module(Module,'Dp')
+vt_type_dict['vcs.displayplot.Dp'] = Dp
+Gfb = new_module(Module,'Gfb')
+vt_type_dict['vcs.boxfill.Gfb'] = Gfb
+Gfi = new_module(Module,'Gfi')
+vt_type_dict['vcs.isofill.Gfi'] = Gfi
+Gi = new_module(Module,'Gi')
+vt_type_dict['vcs.isoline.Gi'] = Gi
+Gfo = new_module(Module,'Gfo')
+vt_type_dict['vcs.outfill.Gfo'] = Gfo
+Go = new_module(Module,'Go')
+vt_type_dict['vcs.outline.Go'] = Go
+GSp = new_module(Module,'GSp')
+vt_type_dict['vcs.scatter.GSp'] = GSp
+GXY = new_module(Module,'GXY')
+vt_type_dict['vcs.xvsy.GXY'] = GXY
+GXy = new_module(Module,'GXy')
+vt_type_dict['vcs.xyvsy.GXy'] = GXy
+GYx = new_module(Module,'GYx')
+vt_type_dict['vcs.yxvsx.GYx'] = GYx
+CdmsFile = new_module(Module,'CdmsFile')
+vt_type_dict['cdms2.dataset.CdmsFile'] = CdmsFile
+TransientVariable = new_module(Module,'TransientVariable')
+vt_type_dict['cdms2.tvariable.TransientVariable'] = TransientVariable
+
+
+class boxfill(SpreadsheetCell,NotCacheable):
+ """
+ Function: boxfill # Generate a boxfill plot
+
+ Description of Function:
+ Generate a boxfill plot given the data, boxfill graphics method, and
+ template. If no boxfill class object is given, then the 'default' boxfill
+ graphics method is used. Similarly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('boxfill') # Show all the existing boxfill graphics methods
+ box=a.getboxfill('quick') # Create instance of 'quick'
+ a.boxfill(array,box) # Plot array using specified box and default
+ # template
+ templt=a.gettemplate('AMIP') # Create an instance of template 'AMIP'
+ a.clear() # Clear VCS canvas
+ a.boxfill(array,box,template) # Plot array using specified box and template
+ a.boxfill(box,array,template) # Plot array using specified box and template
+ a.boxfill(template,array,box) # Plot array using specified box and template
+ a.boxfill(template,array,box) # Plot array using specified box and template
+ a.boxfill(array,'AMIP','quick') # Use 'AMIP' template and 'quick' boxfill
+ a.boxfill('AMIP',array,'quick') # Use 'AMIP' template and 'quick' boxfill
+ a.boxfill('AMIP','quick',array) # Use 'AMIP' template and 'quick' boxfill
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End boxfill Description ################################################
+######################################### #################################################
+###################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ print 'got canvas'
+ print canvas
+ else:
+ print 'no canvas'
+ canvas = vcs.init()
+
+ # Build the argument list
+ args = []
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ args.append(slab)
+ # slab is a required port
+ if slab is None:
+ raise ModuleError(self, "'slab' is a mandatory port")
+
+ template = None
+ if self.hasInputFromPort('template'):
+ template = self.getInputFromPort('template')
+ args.append(template)
+ # template is a required port
+ if template is None:
+ raise ModuleError(self, "'template' is a mandatory port")
+
+ args.append('Boxfill')
+
+ gm_name = None
+ if self.hasInputFromPort('gm_name'):
+ gm_name = self.getInputFromPort('gm_name')
+ args.append(gm_name)
+ # gm_name is a required port
+ if gm_name is None:
+ raise ModuleError(self, "'template' is a mandatory port")
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ # force images to be created in the background
+ # kwargs['bg'] = 1
+
+ # TODO
+
+ #res = canvas.boxfill(*args,**kwargs)
+ #res = canvas.plot(slab, 'ASD', 'Boxfill', 'ASD')
+
+ #plotArgs = (graphics_method, 'ASD', dataset)
+ inputPorts = (canvas, args, kwargs)
+ self.displayAndWait(QCDATWidget, inputPorts)
+
+ # self.setResult('display', res)
+ self.setResult('canvas',canvas)
+
+class createboxfill(Module):
+ """
+ Function: createboxfill # Construct a new boxfill graphics method
+
+ Description of Function:
+ Create a new boxfill graphics method given the the name and the existing
+ boxfill graphics method to copy the attributes from. If no existing
+ boxfill graphics method name is given, then the default boxfill graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('boxfill')
+ box=a.createboxfill('example1',)
+ a.show('boxfill')
+ box=a.createboxfill('example2','quick')
+ a.show('boxfill')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createboxfill Description ################################################
+######################################### #################################################
+#########################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ new_GM_name = None
+ if self.hasInputFromPort('new_GM_name'):
+ new_GM_name = self.getInputFromPort('new_GM_name')
+ args.append(new_GM_name)
+
+ source_GM_name = None
+ if self.hasInputFromPort('source_GM_name'):
+ source_GM_name = self.getInputFromPort('source_GM_name')
+ args.append(source_GM_name)
+
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ self.setResult('slab_0_out', slab)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ gm = canvas.createboxfill(*args,**kwargs)
+ self.setResult('boxfill', gm)
+ self.setResult('canvas', canvas)
+
+class createisofill(Module):
+ """
+ Function: createisofill # Construct a new isofill graphics method
+
+ Description of Function:
+ Create a new isofill graphics method given the the name and the existing
+ isofill graphics method to copy the attributes from. If no existing
+ isofill graphics method name is given, then the default isofill graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('isofill')
+ iso=a.createisofill('example1',)
+ a.show('isofill')
+ iso=a.createisofill('example2','quick')
+ a.show('isofill')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createisofill Description ################################################
+######################################### #################################################
+#########################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ new_GM_name = None
+ if self.hasInputFromPort('new_GM_name'):
+ new_GM_name = self.getInputFromPort('new_GM_name')
+ args.append(new_GM_name)
+
+ source_GM_name = None
+ if self.hasInputFromPort('source_GM_name'):
+ source_GM_name = self.getInputFromPort('source_GM_name')
+ args.append(source_GM_name)
+
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ self.setResult('slab_0_out', slab)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ #kwargs['bg'] = 1
+ res = canvas.createisofill(*args,**kwargs)
+ self.setResult('isofill',res)
+ self.setResult('canvas',canvas)
+
+class createisoline(Module):
+ """
+ Function: createisoline # Construct a new isoline graphics method
+
+ Description of Function:
+ Create a new isoline graphics method given the the name and the existing
+ isoline graphics method to copy the attributes from. If no existing
+ isoline graphics method name is given, then the default isoline graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+
+ a=vcs.init()
+ a.show('isoline')
+ iso=a.createisoline('example1',)
+ a.show('isoline')
+ iso=a.createisoline('example2','quick')
+ a.show('isoline')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createisoline Description ################################################
+######################################### #################################################
+#########################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ new_GM_name = None
+ if self.hasInputFromPort('new_GM_name'):
+ new_GM_name = self.getInputFromPort('new_GM_name')
+ args.append(new_GM_name)
+ source_GM_name = None
+
+ if self.hasInputFromPort('source_GM_name'):
+ source_GM_name = self.getInputFromPort('source_GM_name')
+ args.append(source_GM_name)
+
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ self.setResult('slab_0_out', slab)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ #kwargs['bg'] = 1
+ res = canvas.createisoline(*args,**kwargs)
+ self.setResult('isoline',res)
+ self.setResult('canvas',canvas)
+
+class createoutfill(Module):
+ """
+ Function: createoutfill # Construct a new outfill graphics method
+
+ Description of Function:
+ Create a new outfill graphics method given the the name and the existing
+ outfill graphics method to copy the attributes from. If no existing
+ outfill graphics method name is given, then the default outfill graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+
+ a=vcs.init()
+ a.show('outfill')
+ out=a.createoutfill('example1',)
+ a.show('outfill')
+ out=a.createoutfill('example2','quick')
+ a.show('outfill')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createoutfill Description ################################################
+######################################### #################################################
+#########################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+
+ args = []
+ new_GM_name = None
+ if self.hasInputFromPort('new_GM_name'):
+ new_GM_name = self.getInputFromPort('new_GM_name')
+ args.append(new_GM_name)
+
+ source_GM_name = None
+ if self.hasInputFromPort('source_GM_name'):
+ source_GM_name = self.getInputFromPort('source_GM_name')
+ args.append(source_GM_name)
+
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ self.setResult('slab_0_out', slab)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ #kwargs['bg'] = 1
+ res = canvas.createoutfill(*args,**kwargs)
+ self.setResult('outfill',res)
+ self.setResult('canvas',canvas)
+
+class createoutline(Module):
+ """
+ Function: createoutline # Construct a new outline graphics method
+
+ Description of Function:
+ Create a new outline graphics method given the the name and the existing
+ outline graphics method to copy the attributes from. If no existing
+ outline graphics method name is given, then the default outline graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+
+ a=vcs.init()
+ a.show('outline')
+ out=a.createoutline('example1',)
+ a.show('outline')
+ out=a.createoutline('example2','quick')
+ a.show('outline')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createoutline Description ################################################
+######################################### #################################################
+#########################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ new_GM_name = None
+ if self.hasInputFromPort('new_GM_name'):
+ new_GM_name = self.getInputFromPort('new_GM_name')
+ args.append(new_GM_name)
+ source_GM_name = None
+
+ if self.hasInputFromPort('source_GM_name'):
+ source_GM_name = self.getInputFromPort('source_GM_name')
+ args.append(source_GM_name)
+
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ self.setResult('slab_0_out', slab)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ #kwargs['bg'] = 1
+ res = canvas.createoutline(*args,**kwargs)
+ self.setResult('outline',res)
+ self.setResult('canvas',canvas)
+
+class createscatter(Module):
+ """
+ Function: createscatter # Construct a new scatter graphics method
+
+ Description of Function:
+ Create a new scatter graphics method given the the name and the existing
+ scatter graphics method to copy the attributes from. If no existing
+ scatter graphics method name is given, then the default scatter graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('scatter')
+ sct=a.createscatter('example1',)
+ a.show('scatter')
+ sct=a.createscatter('example2','quick')
+ a.show('scatter')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createscatter Description ################################################
+######################################### #################################################
+#########################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ new_GM_name = None
+ if self.hasInputFromPort('new_GM_name'):
+ new_GM_name = self.getInputFromPort('new_GM_name')
+ args.append(new_GM_name)
+
+ source_GM_name = None
+ if self.hasInputFromPort('source_GM_name'):
+ source_GM_name = self.getInputFromPort('source_GM_name')
+ args.append(source_GM_name)
+
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ self.setResult('slab_0_out', slab)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ #kwargs['bg'] = 1
+ res = canvas.createscatter(*args,**kwargs)
+ self.setResult('scatter',res)
+ self.setResult('canvas',canvas)
+
+class createxvsy(Module):
+ """
+ Function: createxvsy # Construct a new XvsY graphics method
+
+ Description of Function:
+ Create a new XvsY graphics method given the the name and the existing
+ XvsY graphics method to copy the attributes from. If no existing
+ XvsY graphics method name is given, then the default XvsY graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('xvsy')
+ xy=a.createxvsy('example1',)
+ a.show('xvsy')
+ xy=a.createxvsy('example2','quick')
+ a.show('xvsy')
+
+######################################################################################################################
+########################################### ###############################################
+########################################## End createxvsy Description ################################################
+######################################### #################################################
+######################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ new_GM_name = None
+ if self.hasInputFromPort('new_GM_name'):
+ new_GM_name = self.getInputFromPort('new_GM_name')
+ args.append(new_GM_name)
+ source_GM_name = None
+
+ if self.hasInputFromPort('source_GM_name'):
+ source_GM_name = self.getInputFromPort('source_GM_name')
+ args.append(source_GM_name)
+
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ self.setResult('slab_0_out', slab)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ #kwargs['bg'] = 1
+ res = canvas.createxvsy(*args,**kwargs)
+ self.setResult('xvsy',res)
+ self.setResult('canvas',canvas)
+
+class createxyvsy(Module):
+ """
+ Function: createxyvsy # Construct a new Xyvsy graphics method
+
+ Description of Function:
+ Create a new Xyvsy graphics method given the the name and the existing
+ Xyvsy graphics method to copy the attributes from. If no existing
+ Xyvsy graphics method name is given, then the default Xyvsy graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+
+ a=vcs.init()
+ a.show('xyvsy')
+ xyy=a.createxyvsy('example1',)
+ a.show('xyvsy')
+ xyy=a.createxyvsy('example2','quick')
+ a.show('xyvsy')
+
+#######################################################################################################################
+########################################### ###############################################
+########################################## End createxyvsy Description ################################################
+######################################### #################################################
+#######################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ new_GM_name = None
+ if self.hasInputFromPort('new_GM_name'):
+ new_GM_name = self.getInputFromPort('new_GM_name')
+ args.append(new_GM_name)
+ source_GM_name = None
+
+ if self.hasInputFromPort('source_GM_name'):
+ source_GM_name = self.getInputFromPort('source_GM_name')
+ args.append(source_GM_name)
+
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ self.setResult('slab_0_out', slab)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ #kwargs['bg'] = 1
+ res = canvas.createxyvsy(*args,**kwargs)
+ self.setResult('xyvsy',res)
+ self.setResult('canvas',canvas)
+
+class createyxvsx(Module):
+ """
+ Function: createyxvsx # Construct a new Yxvsx graphics method
+
+ Description of Function:
+ Create a new Yxvsx graphics method given the the name and the existing
+ Yxvsx graphics method to copy the attributes from. If no existing
+ Yxvsx graphics method name is given, then the default Yxvsx graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+
+ a=vcs.init()
+ a.show('yxvsx')
+ yxx=a.createyxvsx('example1',)
+ a.show('yxvsx')
+ yxx=a.createyxvsx('example2','quick')
+ a.show('yxvsx')
+
+#######################################################################################################################
+########################################### ###############################################
+########################################## End createyxvsx Description ################################################
+######################################### #################################################
+#######################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ new_GM_name = None
+ if self.hasInputFromPort('new_GM_name'):
+ new_GM_name = self.getInputFromPort('new_GM_name')
+ args.append(new_GM_name)
+ source_GM_name = None
+
+ if self.hasInputFromPort('source_GM_name'):
+ source_GM_name = self.getInputFromPort('source_GM_name')
+ args.append(source_GM_name)
+
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ self.setResult('slab_0_out', slab)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ #kwargs['bg'] = 1
+
+ res = canvas.createyxvsx(*args,**kwargs)
+ self.setResult('yxvsx',res)
+ self.setResult('canvas',canvas)
+
+class getboxfill(Module):
+ """
+ Function: getboxfill # Construct a new boxfill graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ boxfill class object from an existing VCS boxfill graphics method. If
+ no boxfill name is given, then boxfill 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createboxfill function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('boxfill') # Show all the existing boxfill graphics methods
+ box=a.getboxfill() # box instance of 'default' boxfill graphics
+ # method
+ box2=a.getboxfill('quick') # box2 instance of existing 'quick' boxfill
+ # graphics method
+######################################################################################################################
+########################################### ###############################################
+########################################## End getboxfill Description ################################################
+######################################### #################################################
+######################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+
+ GM_name = None
+ if self.hasInputFromPort('GM_name'):
+ GM_name = self.getInputFromPort('GM_name')
+ args.append(GM_name)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ res = canvas.getboxfill(*args)
+ self.setResult('boxfill',res)
+ self.setResult('canvas',canvas)
+
+class getisofill(Module):
+ """
+ Function: getisofill Construct a new isofill graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ isofill class object from an existing VCS isofill graphics method. If
+ no isofill name is given, then isofill 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createisofill function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('isofill') # Show all the existing isofill graphics methods
+ iso=a.getisofill() # iso instance of 'default' isofill graphics
+ # method
+ iso2=a.getisofill('quick') # iso2 instance of existing 'quick' isofill
+ # graphics method
+######################################################################################################################
+########################################### ###############################################
+########################################## End getisofill Description ################################################
+######################################### #################################################
+######################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ GM_name = None
+ if self.hasInputFromPort('GM_name'):
+ GM_name = self.getInputFromPort('GM_name')
+ args.append(GM_name)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ res = canvas.getisofill(*args)
+
+ self.setResult('isofill',res)
+ self.setResult('canvas',canvas)
+
+class getisoline(Module):
+ """
+ Function: getisoline # Construct a new isoline graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ isoline class object from an existing VCS isoline graphics method. If
+ no isoline name is given, then isoline 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createisoline function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('isoline') # Show all the existing isoline graphics methods
+ iso=a.getisoline() # iso instance of 'default' isoline graphics
+ # method
+ iso2=a.getisoline('quick') # iso2 instance of existing 'quick' isoline
+ # graphics method
+######################################################################################################################
+########################################### ###############################################
+########################################## End getisoline Description ################################################
+######################################### #################################################
+######################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ GM_name = None
+ if self.hasInputFromPort('GM_name'):
+ GM_name = self.getInputFromPort('GM_name')
+ args.append(GM_name)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ res = canvas.getisoline(*args)
+ self.setResult('isoline',res)
+ self.setResult('canvas',canvas)
+
+class getoutfill(Module):
+ """
+ Function: getoutfill # Construct a new outfill graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ outfill class object from an existing VCS outfill graphics method. If
+ no outfill name is given, then outfill 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createoutfill function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('outfill') # Show all the existing outfill graphics methods
+ out=a.getoutfill() # out instance of 'default' outfill graphics
+ # method
+ out2=a.getoutfill('quick') # out2 instance of existing 'quick' outfill
+ # graphics method
+
+######################################################################################################################
+########################################### ###############################################
+########################################## End getoutfill Description ################################################
+######################################### #################################################
+######################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ GM_name = None
+ if self.hasInputFromPort('GM_name'):
+ GM_name = self.getInputFromPort('GM_name')
+ args.append(GM_name)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ res = canvas.getoutfill(*args,**kwargs)
+ self.setResult('outfill',res)
+ self.setResult('canvas',canvas)
+
+class getoutline(Module):
+ """
+ Function: getoutline # Construct a new outline graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ outline class object from an existing VCS outline graphics method. If
+ no outline name is given, then outline 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createoutline function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('outline') # Show all the existing outline graphics methods
+ out=a.getoutline() # out instance of 'default' outline graphics
+ # method
+ out2=a.getoutline('quick') # out2 instance of existing 'quick' outline
+ # graphics method
+
+######################################################################################################################
+########################################### ###############################################
+########################################## End getoutline Description ################################################
+######################################### #################################################
+######################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ GM_name = None
+ if self.hasInputFromPort('GM_name'):
+ GM_name = self.getInputFromPort('GM_name')
+ args.append(GM_name)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ res = canvas.getoutline(*args)
+ self.setResult('outline',res)
+ self.setResult('canvas',canvas)
+
+class getscatter(Module):
+ """
+ Function: getscatter # Construct a new scatter graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ scatter class object from an existing VCS scatter graphics method. If
+ no scatter name is given, then scatter 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createscatter function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('scatter') # Show all the existing scatter graphics methods
+ sct=a.getscatter() # sct instance of 'default' scatter graphics
+ # method
+ sct2=a.getscatter('quick') # sct2 instance of existing 'quick' scatter
+ # graphics method
+
+######################################################################################################################
+########################################### ###############################################
+########################################## End getscatter Description ################################################
+######################################### #################################################
+######################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ GM_name = None
+ if self.hasInputFromPort('GM_name'):
+ GM_name = self.getInputFromPort('GM_name')
+ args.append(GM_name)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ res = canvas.getscatter(*args)
+ self.setResult('scatter',res)
+ self.setResult('canvas',canvas)
+
+class getxvsy(Module):
+ """
+ Function: getxvsy # Construct a new XvsY graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ XvsY class object from an existing VCS XvsY graphics method. If
+ no XvsY name is given, then XvsY 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createxvsy function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('xvsy') # Show all the existing XvsY graphics methods
+ xy=a.getxvsy() # xy instance of 'default' XvsY graphics
+ # method
+ xy2=a.getxvsy('quick') # xy2 instance of existing 'quick' XvsY
+ # graphics method
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End getxvsy Description ################################################
+######################################### #################################################
+###################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ GM_name = None
+ if self.hasInputFromPort('GM_name'):
+ GM_name = self.getInputFromPort('GM_name')
+ args.append(GM_name)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ res = canvas.getxvsy(*args)
+ self.setResult('xvsy',res)
+ self.setResult('canvas',canvas)
+
+class getxyvsy(Module):
+ """
+ Function: getxyvsy # Construct a new Xyvsy graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ Xyvsy class object from an existing VCS Xyvsy graphics method. If
+ no Xyvsy name is given, then Xyvsy 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createxyvsy function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('xyvsy') # Show all the existing Xyvsy graphics methods
+ xyy=a.getxyvsy() # xyy instance of 'default' Xyvsy graphics
+ # method
+ xyy2=a.getxyvsy('quick') # xyy2 instance of existing 'quick' Xyvsy
+ # graphics method
+####################################################################################################################
+########################################### ###############################################
+########################################## End getxyvsy Description ################################################
+######################################### #################################################
+####################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ GM_name = None
+ if self.hasInputFromPort('GM_name'):
+ GM_name = self.getInputFromPort('GM_name')
+ args.append(GM_name)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ res = canvas.getxyvsy(*args)
+ self.setResult('xyvsy',res)
+ self.setResult('canvas',canvas)
+
+class getyxvsx(Module):
+ """
+ Function: getyxvsx # Construct a new Yxvsx graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ Yxvsx class object from an existing VCS Yxvsx graphics method. If
+ no Yxvsx name is given, then Yxvsx 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createyxvsx function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('yxvsx') # Show all the existing Yxvsx graphics methods
+ yxx=a.getyxvsx() # yxx instance of 'default' Yxvsx graphics
+ # method
+ yxx2=a.getyxvsx('quick') # yxx2 instance of existing 'quick' Yxvsx
+ # graphics method
+####################################################################################################################
+########################################### ###############################################
+########################################## End getyxvsx Description ################################################
+######################################### #################################################
+####################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ GM_name = None
+ if self.hasInputFromPort('GM_name'):
+ GM_name = self.getInputFromPort('GM_name')
+ args.append(GM_name)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ res = canvas.getyxvsx(*args,**kwargs)
+ self.setResult('yxvsx',res)
+ self.setResult('canvas',canvas)
+
+class isofill(Module,NotCacheable):
+ """
+ Function: isofill # Generate an isofill plot
+
+ Description of Function:
+ Generate a isofill plot given the data, isofill graphics method, and
+ template. If no isofill class object is given, then the 'default' isofill
+ graphics method is used. Similarly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('isofill') # Show all the existing isofill graphics methods
+ iso=a.getisofill('quick') # Create instance of 'quick'
+ a.isofill(array,iso) # Plot array using specified iso and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.isofill(array,iso,template) # Plot array using specified iso and template
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End isofill Description ################################################
+######################################### #################################################
+###################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+
+ args = []
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ args.append(slab)
+
+ template = None
+ if self.hasInputFromPort('template'):
+ template = self.getInputFromPort('template')
+ args.append(template)
+ # template is a required port
+ if template is None:
+ raise ModuleError(self, "'template' is a mandatory port")
+
+ args.append('Isofill')
+
+ gm_name = None
+ if self.hasInputFromPort('gm_name'):
+ gm_name = self.getInputFromPort('gm_name')
+ args.append(gm_name)
+ # gm_name is a required port
+ if gm_name is None:
+ raise ModuleError(self, "'template' is a mandatory port")
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ kwargs['bg'] = 1
+ res = canvas.isofill(*args,**kwargs)
+ self.setResult('display',res)
+ self.setResult('canvas',canvas)
+
+class isoline(Module,NotCacheable):
+ """
+ Function: isoline # Generate an isoline plot
+
+ Description of Function:
+ Generate a isoline plot given the data, isoline graphics method, and
+ template. If no isoline class object is given, then the 'default' isoline
+ graphics method is used. Similarly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('isoline') # Show all the existing isoline graphics methods
+ iso=a.getisoline('quick') # Create instance of 'quick'
+ a.isoline(array,iso) # Plot array using specified iso and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.isoline(array,iso,template) # Plot array using specified iso and template
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End isoline Description ################################################
+######################################### #################################################
+###################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+
+ args = []
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ args.append(slab)
+
+ template = None
+ if self.hasInputFromPort('template'):
+ template = self.getInputFromPort('template')
+ args.append(template)
+ # template is a required port
+ if template is None:
+ raise ModuleError(self, "'template' is a mandatory port")
+
+ args.append('Isoline')
+
+ gm_name = None
+ if self.hasInputFromPort('gm_name'):
+ gm_name = self.getInputFromPort('gm_name')
+ args.append(gm_name)
+ # gm_name is a required port
+ if gm_name is None:
+ raise ModuleError(self, "'template' is a mandatory port")
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ kwargs['bg'] = 1
+ res = canvas.isoline(*args,**kwargs)
+ self.setResult('display',res)
+ self.setResult('canvas',canvas)
+
+class outfill(Module):
+ """
+ Function: outfill # Generate an outfill plot
+
+ Description of Function:
+ Generate a outfill plot given the data, outfill graphics method, and
+ template. If no outfill class object is given, then the 'default' outfill
+ graphics method is used. Simerly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('outfill') # Show all the existing outfill graphics methods
+ out=a.getoutfill('quick') # Create instance of 'quick'
+ a.outfill(array,out) # Plot array using specified out and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.outfill(array,out,template) # Plot array using specified out and template
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End outfill Description ################################################
+######################################### #################################################
+###################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+
+ args = []
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ args.append(slab)
+
+ template = None
+ if self.hasInputFromPort('template'):
+ template = self.getInputFromPort('template')
+ args.append(template)
+ # template is a required port
+ if template is None:
+ raise ModuleError(self, "'template' is a mandatory port")
+
+ args.append('Outfill')
+
+ gm_name = None
+ if self.hasInputFromPort('gm_name'):
+ gm_name = self.getInputFromPort('gm_name')
+ args.append(gm_name)
+ # gm_name is a required port
+ if gm_name is None:
+ raise ModuleError(self, "'template' is a mandatory port")
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ kwargs['bg'] = 1
+ res = canvas.outfill(*args,**kwargs)
+ self.setResult('display',res)
+ self.setResult('canvas',canvas)
+
+class outline(Module):
+ """
+ Function: outline # Generate an outline plot
+
+ Description of Function:
+ Generate a outline plot given the data, outline graphics method, and
+ template. If no outline class object is given, then the 'default' outline
+ graphics method is used. Simerly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('outline') # Show all the existing outline graphics methods
+ out=a.getoutline('quick') # Create instance of 'quick'
+ a.outline(array,out) # Plot array using specified out and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.outline(array,out,template) # Plot array using specified out and template
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End outline Description ################################################
+######################################### #################################################
+###################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ args.append(slab)
+
+ template = None
+ if self.hasInputFromPort('template'):
+ template = self.getInputFromPort('template')
+ args.append(template)
+ # template is a required port
+ if template is None:
+ raise ModuleError(self, "'template' is a mandatory port")
+
+ args.append('Outline')
+
+ gm_name = None
+ if self.hasInputFromPort('gm_name'):
+ gm_name = self.getInputFromPort('gm_name')
+ args.append(gm_name)
+ # gm_name is a required port
+ if gm_name is None:
+ raise ModuleError(self, "'template' is a mandatory port")
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ kwargs['bg'] = 1
+ res = canvas.outline(*args,**kwargs)
+ self.setResult('display',res)
+ self.setResult('canvas',canvas)
+
+class plot(SpreadsheetCell,NotCacheable):
+ """
+ Function: plot
+
+ Description of plot:
+ Plot an array(s) of data given a template and graphics method. The VCS template is
+ used to define where the data and variable attributes will be displayed on the VCS
+ Canvas. The VCS graphics method is used to define how the array(s) will be shown
+ on the VCS Canvas.
+
+ The form of the call is:
+ plot(array1=None, array2=None, template_name=None, graphics_method=None,
+ graphics_name=None, [key=value [, key=value [, ...]]])
+
+ where array1 and array2 are NumPy arrays.
+
+ Plot keywords:
+ ratio [default is none]
+ None: let the self.ratio attribute decide
+ 0,'off': overwritte self.ratio and do nothing about the ratio
+ 'auto': computes an automatic ratio
+ '3',3: y dim will be 3 times bigger than x dim (restricted to original tempalte.data area
+ Adding a 't' at the end of the ratio, makes the tickmarks and boxes move along.
+
+ Variable attribute keys:
+ comment1 = string #Comment plotted above file_comment
+ comment2 = string #Comment plotted above comment1
+ comment3 = string #Comment plotted above comment2
+ comment4 = string #Comment plotted above comment4
+ file_comment = string #Comment (defaults to file.comment)
+ hms = string (hh:mm:ss) #Hour, minute, second
+ long_name = string #Descriptive variable name
+ name = string #Variable name (defaults to var.id)
+ time = cdtime #instance (relative or absolute),
+ cdtime, reltime or abstime value
+ units = string #Variable units
+ ymd = string (yy/mm/dd) #Year, month, day
+
+ Dimension attribute keys (dimension length=n):
+ [x|y|z|t|w]array = NumPy array of length n # x or y Dimension values
+ [x|y|z|t|w]array = NumPy array of length n # x or y Dimension values
+ [x|y]bounds = NumPy array of shape (n,2) # x or y Dimension boundaries
+ [x|y|z|t|w]name = string # x or y Dimension name
+ [x|y|z|t|w]units = string # x or y Dimension units
+ [x|y]weights = NumPy array of length n # x or y Dimension weights (used to
+ calculate area-weighted mean)
+
+ CDMS object:
+ [x|y|z|t|w]axis = CDMS axis object # x or y Axis
+ grid = CDMS grid object # Grid object (e.g. grid=var.getGrid()
+ variable = CDMS variable object # Variable object
+
+ Other:
+ [x|y]rev = 0|1 # if ==1, reverse the direction of the x
+ or y axis
+ continents = 0,1,2,3,4,5,6,7,8,9,10,11 # if >=1, plot continental outlines
+ (default: plot if xaxis is
+ longitude, yaxis is latitude -or-
+ xname is 'longitude' and yname is
+ 'latitude'
+ # The continents-type values are integers
+ # ranging from 0 to 11, where:
+ # 0 signifies "No Continents"
+ # 1 signifies "Fine Continents"
+ # 2 signifies "Coarse Continents"
+ # 3 signifies "United States"
+ # 4 signifies "Political Borders"
+ # 5 signifies "Rivers"
+
+ # Values 6 through 11 signify the line type
+ # defined by the files data_continent_other7
+ # through data_continent_other12.
+
+ Graphics Output in Background Mode:
+ bg = 0|1 # if ==1, create images in the background
+ (Don't display the VCS Canvas)
+
+ Note:
+ More specific attributes take precedence over general attributes. In particular,
+ specifie attributes override variable object attributes, dimension attributes and
+ arrays override axis objects, which override grid objects, which override variable
+ objects.
+
+ For example, if both 'file_comment' and 'variable' keywords are specified, the value of
+ 'file_comment' is used instead of the file comment in the parent of variable. Similarly,
+ if both 'xaxis' and 'grid' keywords are specified, the value of 'xaxis' takes precedence
+ over the x-axis of grid.
+
+ Example of Use:
+ x=vcs.init() # x is an instance of the VCS class object (constructor)
+ x.plot(array) # this call will use default settings for template and boxfill
+ x.plot(array, 'AMIP', 'isofill','AMIP_psl') # this is specifying the template and
+ graphics method
+ t=x.gettemplate('AMIP') # get a predefined the template 'AMIP'
+ vec=x.getvector('quick') # get a predefined the vector graphics method 'quick'
+ x.plot(array1, array2, t, vec) # plot the data as a vector using the 'AMIP' template
+ x.clear() # clear the VCS Canvas of all plots
+ box=x.createboxfill('new') # create boxfill graphics method 'new'
+ x.plot(box,t,array) # plot array data using box 'new' and template 't'
+
+###############################################################################################################
+########################################### ##############################################
+########################################## End plot Description ###############################################
+######################################### ################################################
+###############################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+
+ # Build up the argument list
+ args = []
+ slab2 = None
+ if self.hasInputFromPort('slab2_0'):
+ slab2 = self.getInputFromPort('slab2_0')
+ args.append(slab2)
+ slab1 = None
+ if self.hasInputFromPort('slab1_0'):
+ slab1 = self.getInputFromPort('slab1_0')
+ args.append(slab1)
+ template = None
+ if self.hasInputFromPort('template'):
+ template = self.getInputFromPort('template')
+ args.append(template)
+ plot_type = None
+ if self.hasInputFromPort('plot_type'):
+ plot_type = self.getInputFromPort('plot_type')
+ args.append(plot_type)
+ gm_name = None
+ if self.hasInputFromPort('gm_name'):
+ gm_name = self.getInputFromPort('gm_name')
+ args.append(gm_name)
+
+ # slab1 is a required port
+ if slab1 is None:
+ raise ModuleError(self, "'slab1' is a mandatory port")
+ # template is a required port
+ if template is None:
+ raise ModuleError(self, "'template' is a mandatory port")
+ # plot_type is a required port
+ if plot_type is None:
+ raise ModuleError(self, "'plot_type' is a mandatory port")
+ # gm_name is a required port
+ if gm_name is None:
+ raise ModuleError(self, "'gm_name' is a mandatory port")
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+
+ # Set the cell row / col
+ self.location = CellLocation()
+ if self.hasInputFromPort('row'):
+ self.location.row = self.getInputFromPort('row')
+ if self.hasInputFromPort('col'):
+ self.location.col = self.getInputFromPort('col')
+
+ # Plot into the cell
+ inputPorts = (canvas, args, kwargs)
+ self.displayAndWait(QCDATWidget, inputPorts)
+
+ self.setResult('canvas',canvas)
+
+class scatter(Module):
+ """
+ Function: scatter # Generate a scatter plot
+
+ Description of Function:
+ Generate a scatter plot given the data, scatter graphics method, and
+ template. If no scatter class object is given, then the 'default' scatter
+ graphics method is used. Similarly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('scatter') # Show all the existing scatter graphics methods
+ sct=a.getscatter('quick') # Create instance of 'quick'
+ a.scatter(array,sct) # Plot array using specified sct and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.scatter(array,sct,template) # Plot array using specified sct and template
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End scatter Description ################################################
+######################################### #################################################
+###################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ slab2 = None
+ if self.hasInputFromPort('slab2_0'):
+ slab2 = self.getInputFromPort('slab2_0')
+ args.append(slab2)
+ slab1 = None
+ if self.hasInputFromPort('slab1_0'):
+ slab1 = self.getInputFromPort('slab1_0')
+ args.append(slab1)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ kwargs['bg'] = 1
+ res = canvas.scatter(*args,**kwargs)
+ self.setResult('display',res)
+ self.setResult('canvas',canvas)
+
+class xvsy(Module):
+ """
+ Function: xvsy # Generate a XvsY plot
+
+ Description of Function:
+ Generate a XvsY plot given the data, XvsY graphics method, and
+ template. If no XvsY class object is given, then the 'default' XvsY
+ graphics method is used. Similarly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('xvsy') # Show all the existing XvsY graphics methods
+ xy=a.getxvsy('quick') # Create instance of 'quick'
+ a.xvsy(array,xy) # Plot array using specified xy and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.xvsy(array,xy,template) # Plot array using specified xy and template
+
+#################################################################################################################
+########################################### ###############################################
+########################################## End xvsy Description ################################################
+######################################### #################################################
+#################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ slab2 = None
+ if self.hasInputFromPort('slab2_0'):
+ slab2 = self.getInputFromPort('slab2_0')
+ args.append(slab2)
+ slab1 = None
+ if self.hasInputFromPort('slab1_0'):
+ slab1 = self.getInputFromPort('slab1_0')
+ args.append(slab1)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('yaxisconvert'):
+ kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ kwargs['bg'] = 1
+ res = canvas.xvsy(*args,**kwargs)
+ self.setResult('display',res)
+ self.setResult('canvas',canvas)
+
+class xyvsy(Module):
+ """
+ Function: xyvsy # Generate a Xyvsy plot
+
+ Description of Function:
+ Generate a Xyvsy plot given the data, Xyvsy graphics method, and
+ template. If no Xyvsy class object is given, then the 'default' Xyvsy
+ graphics method is used. Simerly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('xyvsy') # Show all the existing Xyvsy graphics methods
+ xyy=a.getxyvsy('quick') # Create instance of 'quick'
+ a.xyvsy(array,xyy) # Plot array using specified xyy and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.xyvsy(array,xyy,template) # Plot array using specified xyy and template
+
+#################################################################################################################
+########################################### ###############################################
+########################################## End xyvsy Description ################################################
+######################################### #################################################
+#################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ args.append(slab)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ kwargs['bg'] = 1
+ res = canvas.xyvsy(*args,**kwargs)
+ self.setResult('display',res)
+ self.setResult('canvas',canvas)
+
+class yxvsx(Module):
+ """
+ Function: yxvsx # Generate a Yxvsx plot
+
+ Description of Function:
+ Generate a Yxvsx plot given the data, Yxvsx graphics method, and
+ template. If no Yxvsx class object is given, then the 'default' Yxvsx
+ graphics method is used. Simerly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('yxvsx') # Show all the existing Yxvsx graphics methods
+ yxx=a.getyxvsx('quick') # Create instance of 'quick'
+ a.yxvsx(array,yxx) # Plot array using specified yxx and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.yxvsx(array,yxx,template) # Plot array using specified yxx and template
+
+#################################################################################################################
+########################################### ###############################################
+########################################## End yxvsx Description ################################################
+######################################### #################################################
+#################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ slab = None
+ if self.hasInputFromPort('slab_0'):
+ slab = self.getInputFromPort('slab_0')
+ args.append(slab)
+
+ # build up the keyword arguments from the optional inputs.
+ kwargs = {}
+ if self.hasInputFromPort('datawc_timeunits'):
+ kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
+ if self.hasInputFromPort('long_name'):
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('projection_0'):
+ kwargs['projection'] = self.getInputFromPort('projection_0')
+ if self.hasInputFromPort('xticlabels2_0'):
+ kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
+ if self.hasInputFromPort('xarray_0'):
+ kwargs['xarray'] = self.getInputFromPort('xarray_0')
+ if self.hasInputFromPort('yweights_0'):
+ kwargs['yweights'] = self.getInputFromPort('yweights_0')
+ if self.hasInputFromPort('xweights_0'):
+ kwargs['xweights'] = self.getInputFromPort('xweights_0')
+ if self.hasInputFromPort('warray_0'):
+ kwargs['warray'] = self.getInputFromPort('warray_0')
+ if self.hasInputFromPort('tunits'):
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('ymtics1_0'):
+ kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
+ if self.hasInputFromPort('ymtics2_0'):
+ kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
+ if self.hasInputFromPort('datawc_x1'):
+ kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
+ if self.hasInputFromPort('datawc_x2'):
+ kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+ if self.hasInputFromPort('xmtics1_0'):
+ kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
+ if self.hasInputFromPort('xmtics2_0'):
+ kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
+ if self.hasInputFromPort('xbounds_0'):
+ kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
+ if self.hasInputFromPort('ybounds_0'):
+ kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
+ if self.hasInputFromPort('datawc_y2'):
+ kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
+ if self.hasInputFromPort('wname'):
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('file_comment'):
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('datawc_calendar'):
+ kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
+ if self.hasInputFromPort('wunits'):
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xrev'):
+ kwargs['xrev'] = self.getInputFromPort('xrev')
+ if self.hasInputFromPort('ymd'):
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+ if self.hasInputFromPort('yarray_0'):
+ kwargs['yarray'] = self.getInputFromPort('yarray_0')
+ if self.hasInputFromPort('units'):
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('yunits'):
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zarray_0'):
+ kwargs['zarray'] = self.getInputFromPort('zarray_0')
+ if self.hasInputFromPort('xname'):
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('tarray_0'):
+ kwargs['tarray'] = self.getInputFromPort('tarray_0')
+ if self.hasInputFromPort('bg_0'):
+ kwargs['bg'] = self.getInputFromPort('bg_0')
+ elif self.hasInputFromPort('bg_1'):
+ kwargs['bg'] = self.getInputFromPort('bg_1')
+ if self.hasInputFromPort('xaxisconvert'):
+ kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
+ if self.hasInputFromPort('zname'):
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('hms'):
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('tname'):
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('yname'):
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('ratio_0'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_0')
+ elif self.hasInputFromPort('ratio_1'):
+ kwargs['ratio'] = self.getInputFromPort('ratio_1')
+ if self.hasInputFromPort('datawc_y1'):
+ kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
+ if self.hasInputFromPort('xunits'):
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('name'):
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('yticlabels1_0'):
+ kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
+ if self.hasInputFromPort('yticlabels2_0'):
+ kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
+ if self.hasInputFromPort('comment1'):
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('zunits'):
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('comment3'):
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment2'):
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('xticlabels1_0'):
+ kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
+ if self.hasInputFromPort('comment4'):
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('yrev'):
+ kwargs['yrev'] = self.getInputFromPort('yrev')
+ #force images to be created in the background
+ kwargs['bg'] = 1
+ res = canvas.yxvsx(*args,**kwargs)
+ self.setResult('display',res)
+ self.setResult('canvas',canvas)
+
+class png(Module,NotCacheable):
+ """
+ Function: png
+
+ Description of Function:
+ Png output is another form of raster graphics.
+
+ Example of Use:
+ a=vcs.init()
+ a.plot(array)
+ a.png('example') # Overwrite a png file
+ a.png('example', width=11.5, height= 8.5) # US Legal
+ a.png('example', width=21, height=29.7, units='cm') # A4
+#################################################################################################################
+########################################### ###############################################
+########################################## End png Description ################################################
+######################################### #################################################
+#################################################################################################################
+
+ """
+ def compute(self):
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ canvas = vcs.init()
+ args = []
+ file = None
+ if self.hasInputFromPort('file'):
+ file = self.getInputFromPort('file')
+ args.append(file)
+
+ # file is a required port
+ if file is None:
+ raise ModuleError(self, "'file' is a mandatory port")
+ width = None
+ if self.hasInputFromPort('width'):
+ width = self.getInputFromPort('width')
+ args.append(width)
+ height = None
+ if self.hasInputFromPort('height'):
+ height = self.getInputFromPort('height')
+ args.append(height)
+ units = None
+ if self.hasInputFromPort('units'):
+ units = self.getInputFromPort('units')
+ args.append(units)
+ ofile = core.modules.basic_modules.File()
+ ofile.name = file
+ canvas.png(*args)
+ self.setResult('file',ofile)
+
+class open(Module):
+ """
+ Function: open # Open an existing dataset
+
+Description of Function:
+ 'uri' is a Uniform Resource Identifier, referring to a cdunif file, XML file,
+ or LDAP URL of a catalog dataset entry.
+ 'mode' is 'r', 'r+', 'a', or 'w'
+###################################################################################################################
+########################################### ###############################################
+########################################## End open Description ################################################
+######################################### #################################################
+###################################################################################################################
+
+ """
+ def compute(self):
+ args = []
+ uri = None
+ if self.hasInputFromPort('uri'):
+ uri = self.getInputFromPort('uri')
+ args.append(uri)
+
+ # uri is a required port
+ if uri is None:
+ raise ModuleError(self, "'uri' is a mandatory port")
+ mode = None
+ if self.hasInputFromPort('mode'):
+ mode = self.getInputFromPort('mode')
+ args.append(mode)
+ template = None
+ if self.hasInputFromPort('template'):
+ template = self.getInputFromPort('template')
+ args.append(template)
+ dods = None
+ if self.hasInputFromPort('dods'):
+ dods = self.getInputFromPort('dods')
+ args.append(dods)
+ res = cdms2.open(*args)
+ self.setResult('dataset',res)
+
+class __call__(Module):
+ """
+ Function: __call__ # Call a variable object with the given id
+
+Description of Function:
+ Call a variable object with the given id
+ Exception if not found.
+ Call the variable with the other arguments.
+###################################################################################################################
+########################################### ###############################################
+########################################## End _call_ Description ################################################
+######################################### #################################################
+###################################################################################################################
+
+ """
+ def compute(self):
+ # Check ports
+ if not self.hasInputFromPort('cdmsfile'):
+ raise ModuleError(self, "'cdmsfile' is mandatory.")
+ if not self.hasInputFromPort('type'):
+ raise ModuleError(self, "'type' is mandatory.")
+ if not self.hasInputFromPort('id'):
+ raise ModuleError(self, "'id' is mandatory.")
+ if not self.hasInputFromPort('axes'):
+ raise ModuleError(self, "'axes' is mandatory.")
+ if not self.hasInputFromPort('axesOperations'):
+ raise ModuleError(self, "'axesOperations' is mandatory.")
+
+ # Get input from ports
+ cdmsfile = self.getInputFromPort('cdmsfile')
+ varType = self.getInputFromPort('type')
+ id = self.getInputFromPort('id')
+ axes = self.getInputFromPort('axes')
+ axesOperations = self.getInputFromPort('axesOperations')
+
+ # Get the variable
+ if (varType == 'variable'):
+ var = cdmsfile.__call__(id)
+ elif (varType == 'axis'):
+ varID = self.getAxisID(id)
+ axis = getattr(cdmsfile, 'axes')[varID]
+ var = MV2.array(axis)
+ var.setAxis(0, axis)
+ elif (varType == 'weighted-axis'):
+ varID, axisID = self.getVarAndAxisID(id)
+ var = cdmsfile.__call__(varID)
+ var = genutil.getAxisWeightByName(var, axisID)
+ var.id = varID +'_' + axisID + '_weight'
+ else:
+ var = None
+
+ # Get the updated variable
+ if axes is not None and var is not None:
+ try:
+ kwargs = eval(axes)
+ var = var(**kwargs)
+ except:
+ raise ModuleError(self, "Invalid 'axes' specification", axes)
+
+ # Apply axes ops to the variable
+ var = self.applyAxesOperations(var, axesOperations)
+
+ self.setResult('variable', var)
+
+ def applyAxesOperations(self, var, axesOperations):
+ """ Apply kwargs / axis operations to update the dataset """
+ try:
+ axesOperations = eval(axesOperations)
+ except:
+ raise TypeError("Invalid string 'axesOperations'")
+
+ for axis in list(axesOperations):
+ if axesOperations[axis] == 'sum':
+ var = cdutil.averager(var, axis="(%s)" % axis, weight='equal',
+ action='sum')
+ elif axesOperations[axis] == 'avg':
+ var = cdutil.averager(var, axis="(%s)" % axis, weight='equal')
+ elif axesOperations[axis] == 'wgt':
+ var = cdutil.averager(var, axis="(%s)" % axis)
+ elif axesOperations[axis] == 'gtm':
+ var = genutil.statistics.geometricmean(var, axis="(%s)" % axis)
+ elif axesOperations[axis] == 'std':
+ var = genutil.statistics.std(var, axis="(%s)" % axis)
+
+ return var
+
+ def getVarAndAxisID(self, varID):
+ """ get the varID and axisID from a string with format
+ varID_axisID_weight """
+
+ match = re.compile('(.+)(_)(.+)(_)(weight)').match(varID)
+ if match:
+ return (match.group(1), match.group(3))
+
+ return None
+
+ def getAxisID(self, varID):
+ """ get the axisID from a string with format varID_axisID_axis """
+
+ match = re.compile('(.+)(_)(.+)(_)(axis)').match(varID)
+ if match:
+ return match.group(3)
+
+ return varID
+
+def initialize(*args, **keywords):
+ reg = core.modules.module_registry.get_module_registry()
+
+ reg.add_module(Canvas,namespace='vcs|Canvas')
+ reg.add_module(GSp,namespace='vcs|scatter')
+ reg.add_module(CdmsFile,namespace='cdms2|dataset')
+ reg.add_module(TransientVariable,namespace='cdms2|tvariable')
+ reg.add_module(GXy,namespace='vcs|xyvsy')
+ reg.add_module(Go,namespace='vcs|outline')
+ reg.add_module(Gfi,namespace='vcs|isofill')
+ reg.add_module(Dp,namespace='vcs|displayplot')
+ reg.add_module(Gfb,namespace='vcs|boxfill')
+ reg.add_module(GYx,namespace='vcs|yxvsx')
+ reg.add_module(GXY,namespace='vcs|xvsy')
+ reg.add_module(Gi,namespace='vcs|isoline')
+ reg.add_module(Gfo,namespace='vcs|outfill')
+
+
+ ##########################################################################
+ # included from cdatwindow_init_inc.py
+ #display = sip.unwrapinstance(QtGui.QX11Info.display())
+ #vcs._vcs.setdisplay(display)
+
+ #cdat GUI modules
+ global cdatWindow
+ cdatWindow = QCDATWindow()
+ cdatWindow.show()
+
+
+ reg.add_module(CDATCell,namespace='cdat')
+ reg.add_input_port(CDATCell, 'slab1',
+ (TransientVariable, "variable to be plotted"))
+ reg.add_input_port(CDATCell, 'slab2',
+ (TransientVariable, "variable to be plotted"))
+ reg.add_input_port(CDATCell, 'plotType',
+ (core.modules.basic_modules.String, "Plot type"))
+ reg.add_input_port(CDATCell, 'template',
+ (core.modules.basic_modules.String, "template name"))
+ reg.add_input_port(CDATCell, 'gmName',
+ (core.modules.basic_modules.String, "graphics method name"))
+ reg.add_input_port(CDATCell, 'canvas',
+ (Canvas, "Canvas object"))
+ reg.add_input_port(CDATCell, 'col',
+ (core.modules.basic_modules.Integer, "Cell Col"))
+ reg.add_input_port(CDATCell, 'row',
+ (core.modules.basic_modules.Integer, "Cell Row"))
+ reg.add_input_port(CDATCell, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_output_port(CDATCell, 'canvas',
+ (Canvas, ""), True)
+
+ reg.add_module(Variable, namespace='cdat')
+ reg.add_module(Quickplot, namespace='cdat')
+ reg.add_input_port(Variable, 'id',
+ (core.modules.basic_modules.String,
+ ""))
+ reg.add_input_port(Variable, 'type',
+ (core.modules.basic_modules.String,
+ "variable, axis, or weighted-axis"))
+ reg.add_input_port(Variable, 'inputVariable',
+ (core.modules.basic_modules.List,
+ ""))
+ reg.add_output_port(Variable, 'variable',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ ""))
+ reg.add_input_port(Variable, 'axes',
+ (core.modules.basic_modules.String, "Axes of variables"))
+ reg.add_input_port(Variable, 'axesOperations',
+ (core.modules.basic_modules.String, "Axes Operations"))
+ reg.add_input_port(Variable, 'cdmsfile',
+ (CdmsFile, "cdmsfile"))
+
+ reg.add_module(GraphicsMethod, namespace='cdat')
+ reg.add_input_port(GraphicsMethod, 'gmName',
+ (core.modules.basic_modules.String,
+ "Get the graphics method object of the given name."))
+ reg.add_input_port(GraphicsMethod, 'plotType',
+ (core.modules.basic_modules.String, "Plot type"))
+ reg.add_input_port(GraphicsMethod, 'slab1',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "slab1"))
+ reg.add_input_port(GraphicsMethod, 'slab2',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "slab2"))
+ reg.add_input_port(GraphicsMethod, 'color_1',
+ (core.modules.basic_modules.Integer, "color_1"), True)
+ reg.add_input_port(GraphicsMethod, 'color_2',
+ (core.modules.basic_modules.Integer, "color_2"), True)
+ reg.add_input_port(GraphicsMethod, 'level_1',
+ (core.modules.basic_modules.Float, "level_1"), True)
+ reg.add_input_port(GraphicsMethod, 'level_2',
+ (core.modules.basic_modules.Float, "level_2"), True)
+ reg.add_output_port(GraphicsMethod, 'slab1',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "slab1"))
+ reg.add_output_port(GraphicsMethod, 'slab2',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "slab2"))
+ reg.add_output_port(GraphicsMethod, 'canvas', (Canvas, "Canvas object"))
+
+ # end of cdatwindow_init_inc.py
+ ##########################################################################
+
+
+ #Module boxfill
+ reg.add_module(boxfill,namespace='vcs|Canvas')
+ reg.add_input_port(boxfill, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(boxfill, 'template',
+ (core.modules.basic_modules.String,
+ "Name of the template"))
+ reg.add_input_port(boxfill, 'gm_name',
+ (core.modules.basic_modules.String,
+ "Name of the graphics method"))
+ reg.add_input_port(boxfill, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(boxfill, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(boxfill, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(boxfill, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(boxfill, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(boxfill, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(boxfill, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(boxfill, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(boxfill, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(boxfill, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(boxfill, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(boxfill, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(boxfill, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(boxfill, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(boxfill, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(boxfill, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(boxfill, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(boxfill, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(boxfill, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(boxfill, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(boxfill, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(boxfill, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(boxfill, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(boxfill, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(boxfill, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(boxfill, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(boxfill, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(boxfill, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(boxfill, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(boxfill, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(boxfill, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(boxfill, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(boxfill, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(boxfill, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(boxfill, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(boxfill, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(boxfill, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(boxfill, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(boxfill, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(boxfill, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(boxfill, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(boxfill, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(boxfill, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(boxfill, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(boxfill, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(boxfill, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(boxfill, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(boxfill, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(boxfill, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(boxfill, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(boxfill, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(boxfill, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(boxfill, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(boxfill, 'display',
+ (get_late_type('vcs.displayplot.Dp'),
+ "no default"))
+
+ #Module createboxfill
+ reg.add_module(createboxfill,namespace='vcs|Canvas')
+ reg.add_input_port(createboxfill, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_output_port(createboxfill, 'slab_0_out',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(createboxfill, 'new_GM_name',
+ (core.modules.basic_modules.String,
+ "name of the new graphics method object. If no name is given, then one will be created for use."))
+ reg.add_input_port(createboxfill, 'source_GM_name',
+ (core.modules.basic_modules.String,
+ "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
+ reg.add_input_port(createboxfill, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(createboxfill, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(createboxfill, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(createboxfill, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(createboxfill, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(createboxfill, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createboxfill, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createboxfill, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(createboxfill, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(createboxfill, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createboxfill, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createboxfill, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(createboxfill, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(createboxfill, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(createboxfill, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createboxfill, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createboxfill, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(createboxfill, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(createboxfill, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(createboxfill, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(createboxfill, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(createboxfill, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(createboxfill, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(createboxfill, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(createboxfill, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(createboxfill, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(createboxfill, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(createboxfill, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(createboxfill, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(createboxfill, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(createboxfill, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(createboxfill, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(createboxfill, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(createboxfill, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createboxfill, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(createboxfill, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(createboxfill, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(createboxfill, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(createboxfill, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createboxfill, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createboxfill, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(createboxfill, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createboxfill, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(createboxfill, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(createboxfill, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(createboxfill, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(createboxfill, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(createboxfill, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(createboxfill, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(createboxfill, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(createboxfill, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(createboxfill, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(createboxfill, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(createboxfill, 'boxfill',
+ (get_late_type('vcs.boxfill.Gfb'),
+ "no default"))
+
+ #Module createisofill
+ reg.add_module(createisofill,namespace='vcs|Canvas')
+ reg.add_input_port(createisofill, 'new_GM_name',
+ (core.modules.basic_modules.String,
+ "name of the new graphics method object. If no name is given, then one will be created for use."))
+ reg.add_input_port(createisofill, 'source_GM_name',
+ (core.modules.basic_modules.String,
+ "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
+ reg.add_input_port(createisofill, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_output_port(createisofill, 'slab_0_out',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(createisofill, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(createisofill, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(createisofill, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(createisofill, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(createisofill, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(createisofill, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createisofill, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createisofill, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(createisofill, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(createisofill, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createisofill, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createisofill, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(createisofill, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(createisofill, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(createisofill, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createisofill, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createisofill, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(createisofill, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(createisofill, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(createisofill, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(createisofill, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(createisofill, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(createisofill, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(createisofill, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(createisofill, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(createisofill, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(createisofill, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(createisofill, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(createisofill, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(createisofill, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(createisofill, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(createisofill, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(createisofill, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(createisofill, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createisofill, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(createisofill, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(createisofill, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(createisofill, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(createisofill, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createisofill, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createisofill, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(createisofill, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createisofill, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(createisofill, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(createisofill, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(createisofill, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(createisofill, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(createisofill, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(createisofill, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(createisofill, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(createisofill, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(createisofill, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(createisofill, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(createisofill, 'isofill',
+ (get_late_type('vcs.isofill.Gfi'),
+ "no default"))
+
+ #Module createisoline
+ reg.add_module(createisoline,namespace='vcs|Canvas')
+ reg.add_input_port(createisoline, 'new_GM_name',
+ (core.modules.basic_modules.String,
+ "name of the new graphics method object. If no name is given, then one will be created for use."))
+ reg.add_input_port(createisoline, 'source_GM_name',
+ (core.modules.basic_modules.String,
+ "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
+ reg.add_input_port(createisoline, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_output_port(createisoline, 'slab_0_out',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(createisoline, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(createisoline, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(createisoline, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(createisoline, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(createisoline, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(createisoline, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createisoline, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createisoline, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(createisoline, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(createisoline, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createisoline, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createisoline, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(createisoline, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(createisoline, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(createisoline, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createisoline, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createisoline, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(createisoline, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(createisoline, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(createisoline, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(createisoline, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(createisoline, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(createisoline, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(createisoline, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(createisoline, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(createisoline, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(createisoline, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(createisoline, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(createisoline, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(createisoline, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(createisoline, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(createisoline, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(createisoline, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(createisoline, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createisoline, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(createisoline, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(createisoline, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(createisoline, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(createisoline, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createisoline, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createisoline, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(createisoline, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createisoline, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(createisoline, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(createisoline, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(createisoline, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(createisoline, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(createisoline, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(createisoline, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(createisoline, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(createisoline, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(createisoline, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(createisoline, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(createisoline, 'isoline',
+ (get_late_type('vcs.isoline.Gi'),
+ "no default"))
+
+ #Module createoutfill
+ reg.add_module(createoutfill,namespace='vcs|Canvas')
+ reg.add_input_port(createoutfill, 'new_GM_name',
+ (core.modules.basic_modules.String,
+ "name of the new graphics method object. If no name is given, then one will be created for use."))
+ reg.add_input_port(createoutfill, 'source_GM_name',
+ (core.modules.basic_modules.String,
+ "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
+ reg.add_input_port(createoutfill, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_output_port(createoutfill, 'slab_0_out',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(createoutfill, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(createoutfill, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(createoutfill, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(createoutfill, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(createoutfill, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(createoutfill, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createoutfill, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createoutfill, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(createoutfill, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(createoutfill, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createoutfill, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createoutfill, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(createoutfill, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(createoutfill, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(createoutfill, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createoutfill, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createoutfill, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(createoutfill, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(createoutfill, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(createoutfill, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(createoutfill, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(createoutfill, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(createoutfill, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(createoutfill, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(createoutfill, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(createoutfill, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(createoutfill, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(createoutfill, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(createoutfill, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(createoutfill, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(createoutfill, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(createoutfill, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(createoutfill, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(createoutfill, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createoutfill, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(createoutfill, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(createoutfill, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(createoutfill, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(createoutfill, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createoutfill, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createoutfill, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(createoutfill, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createoutfill, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(createoutfill, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(createoutfill, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(createoutfill, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(createoutfill, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(createoutfill, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(createoutfill, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(createoutfill, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(createoutfill, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(createoutfill, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(createoutfill, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(createoutfill, 'outfill',
+ (get_late_type('vcs.outfill.Gfo'),
+ "no default"))
+
+ #Module createoutline
+ reg.add_module(createoutline,namespace='vcs|Canvas')
+ reg.add_input_port(createoutline, 'new_GM_name',
+ (core.modules.basic_modules.String,
+ "name of the new graphics method object. If no name is given, then one will be created for use."))
+ reg.add_input_port(createoutline, 'source_GM_name',
+ (core.modules.basic_modules.String,
+ "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
+ reg.add_input_port(createoutline, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_output_port(createoutline, 'slab_0_out',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(createoutline, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(createoutline, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(createoutline, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(createoutline, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(createoutline, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(createoutline, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createoutline, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createoutline, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(createoutline, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(createoutline, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createoutline, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createoutline, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(createoutline, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(createoutline, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(createoutline, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createoutline, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createoutline, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(createoutline, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(createoutline, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(createoutline, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(createoutline, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(createoutline, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(createoutline, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(createoutline, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(createoutline, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(createoutline, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(createoutline, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(createoutline, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(createoutline, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(createoutline, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(createoutline, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(createoutline, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(createoutline, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(createoutline, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createoutline, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(createoutline, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(createoutline, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(createoutline, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(createoutline, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createoutline, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createoutline, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(createoutline, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createoutline, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(createoutline, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(createoutline, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(createoutline, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(createoutline, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(createoutline, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(createoutline, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(createoutline, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(createoutline, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(createoutline, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(createoutline, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(createoutline, 'outline',
+ (get_late_type('vcs.outline.Go'),
+ "no default"))
+
+ #Module createscatter
+ reg.add_module(createscatter,namespace='vcs|Canvas')
+ reg.add_input_port(createscatter, 'new_GM_name',
+ (core.modules.basic_modules.String,
+ "name of the new graphics method object. If no name is given, then one will be created for use."))
+ reg.add_input_port(createscatter, 'source_GM_name',
+ (core.modules.basic_modules.String,
+ "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
+ reg.add_input_port(createscatter, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_output_port(createscatter, 'slab_0_out',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(createscatter, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(createscatter, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(createscatter, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(createscatter, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(createscatter, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(createscatter, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createscatter, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createscatter, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(createscatter, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(createscatter, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createscatter, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createscatter, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(createscatter, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(createscatter, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(createscatter, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createscatter, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createscatter, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(createscatter, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(createscatter, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(createscatter, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(createscatter, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(createscatter, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(createscatter, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(createscatter, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(createscatter, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(createscatter, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(createscatter, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(createscatter, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(createscatter, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(createscatter, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(createscatter, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(createscatter, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(createscatter, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(createscatter, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createscatter, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(createscatter, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(createscatter, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(createscatter, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(createscatter, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createscatter, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createscatter, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(createscatter, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createscatter, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(createscatter, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(createscatter, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(createscatter, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(createscatter, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(createscatter, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(createscatter, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(createscatter, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(createscatter, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(createscatter, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(createscatter, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(createscatter, 'scatter',
+ (get_late_type('vcs.scatter.GSp'),
+ "no default"))
+
+ #Module createxvsy
+ reg.add_module(createxvsy,namespace='vcs|Canvas')
+ reg.add_input_port(createxvsy, 'new_GM_name',
+ (core.modules.basic_modules.String,
+ "name of the new graphics method object. If no name is given, then one will be created for use."))
+ reg.add_input_port(createxvsy, 'source_GM_name',
+ (core.modules.basic_modules.String,
+ "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
+ reg.add_input_port(createxvsy, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_output_port(createxvsy, 'slab_0_out',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(createxvsy, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(createxvsy, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(createxvsy, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(createxvsy, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(createxvsy, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(createxvsy, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createxvsy, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createxvsy, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(createxvsy, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(createxvsy, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createxvsy, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createxvsy, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(createxvsy, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(createxvsy, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(createxvsy, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createxvsy, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createxvsy, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(createxvsy, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(createxvsy, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(createxvsy, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(createxvsy, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(createxvsy, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(createxvsy, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(createxvsy, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(createxvsy, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(createxvsy, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(createxvsy, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(createxvsy, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(createxvsy, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(createxvsy, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(createxvsy, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(createxvsy, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(createxvsy, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(createxvsy, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createxvsy, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(createxvsy, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(createxvsy, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(createxvsy, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(createxvsy, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createxvsy, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createxvsy, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(createxvsy, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createxvsy, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(createxvsy, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(createxvsy, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(createxvsy, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(createxvsy, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(createxvsy, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(createxvsy, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(createxvsy, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(createxvsy, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(createxvsy, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(createxvsy, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(createxvsy, 'xvsy',
+ (get_late_type('vcs.xvsy.GXY'),
+ "no default"))
+
+ #Module createxyvsy
+ reg.add_module(createxyvsy,namespace='vcs|Canvas')
+ reg.add_input_port(createxyvsy, 'new_GM_name',
+ (core.modules.basic_modules.String,
+ "name of the new graphics method object. If no name is given, then one will be created for use."))
+ reg.add_input_port(createxyvsy, 'source_GM_name',
+ (core.modules.basic_modules.String,
+ "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
+ reg.add_input_port(createxyvsy, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_output_port(createxyvsy, 'slab_0_out',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(createxyvsy, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(createxyvsy, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(createxyvsy, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(createxyvsy, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(createxyvsy, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(createxyvsy, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createxyvsy, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createxyvsy, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(createxyvsy, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(createxyvsy, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createxyvsy, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createxyvsy, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(createxyvsy, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(createxyvsy, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(createxyvsy, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createxyvsy, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createxyvsy, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(createxyvsy, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(createxyvsy, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(createxyvsy, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(createxyvsy, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(createxyvsy, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(createxyvsy, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(createxyvsy, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(createxyvsy, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(createxyvsy, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(createxyvsy, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(createxyvsy, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(createxyvsy, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(createxyvsy, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(createxyvsy, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(createxyvsy, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(createxyvsy, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(createxyvsy, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createxyvsy, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(createxyvsy, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(createxyvsy, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(createxyvsy, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(createxyvsy, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createxyvsy, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createxyvsy, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(createxyvsy, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createxyvsy, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(createxyvsy, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(createxyvsy, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(createxyvsy, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(createxyvsy, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(createxyvsy, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(createxyvsy, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(createxyvsy, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(createxyvsy, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(createxyvsy, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(createxyvsy, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(createxyvsy, 'xyvsy',
+ (get_late_type('vcs.xyvsy.GXy'),
+ "no default"))
+
+ #Module createyxvsx
+ reg.add_module(createyxvsx,namespace='vcs|Canvas')
+ reg.add_input_port(createyxvsx, 'new_GM_name',
+ (core.modules.basic_modules.String,
+ "name of the new graphics method object. If no name is given, then one will be created for use."))
+ reg.add_input_port(createyxvsx, 'source_GM_name',
+ (core.modules.basic_modules.String,
+ "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
+ reg.add_input_port(createyxvsx, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_output_port(createyxvsx, 'slab_0_out',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(createyxvsx, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(createyxvsx, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(createyxvsx, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(createyxvsx, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(createyxvsx, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(createyxvsx, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createyxvsx, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(createyxvsx, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(createyxvsx, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(createyxvsx, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createyxvsx, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createyxvsx, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(createyxvsx, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(createyxvsx, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(createyxvsx, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(createyxvsx, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(createyxvsx, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(createyxvsx, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(createyxvsx, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(createyxvsx, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(createyxvsx, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(createyxvsx, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(createyxvsx, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(createyxvsx, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(createyxvsx, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(createyxvsx, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(createyxvsx, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(createyxvsx, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(createyxvsx, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(createyxvsx, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(createyxvsx, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(createyxvsx, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(createyxvsx, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(createyxvsx, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createyxvsx, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(createyxvsx, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(createyxvsx, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(createyxvsx, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(createyxvsx, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createyxvsx, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(createyxvsx, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(createyxvsx, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(createyxvsx, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(createyxvsx, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(createyxvsx, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(createyxvsx, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(createyxvsx, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(createyxvsx, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(createyxvsx, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(createyxvsx, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(createyxvsx, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(createyxvsx, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(createyxvsx, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(createyxvsx, 'yxvsx',
+ (get_late_type('vcs.yxvsx.GYx'),
+ "no default"))
+
+ #Module getboxfill
+ reg.add_module(getboxfill,namespace='vcs|Canvas')
+ reg.add_input_port(getboxfill, 'GM_name',
+ (core.modules.basic_modules.String,
+ "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
+ reg.add_input_port(getboxfill, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(getboxfill, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(getboxfill, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(getboxfill, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(getboxfill, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(getboxfill, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getboxfill, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getboxfill, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(getboxfill, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(getboxfill, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getboxfill, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getboxfill, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(getboxfill, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(getboxfill, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(getboxfill, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getboxfill, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getboxfill, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(getboxfill, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(getboxfill, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(getboxfill, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(getboxfill, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(getboxfill, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(getboxfill, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(getboxfill, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(getboxfill, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(getboxfill, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(getboxfill, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(getboxfill, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(getboxfill, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(getboxfill, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(getboxfill, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(getboxfill, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(getboxfill, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(getboxfill, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getboxfill, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(getboxfill, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(getboxfill, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(getboxfill, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(getboxfill, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getboxfill, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getboxfill, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(getboxfill, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getboxfill, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(getboxfill, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(getboxfill, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(getboxfill, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(getboxfill, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(getboxfill, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(getboxfill, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(getboxfill, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(getboxfill, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(getboxfill, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(getboxfill, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(getboxfill, 'boxfill',
+ (get_late_type('vcs.boxfill.Gfb'),
+ "no default"))
+
+ #Module getisofill
+ reg.add_module(getisofill,namespace='vcs|Canvas')
+ reg.add_input_port(getisofill, 'GM_name',
+ (core.modules.basic_modules.String,
+ "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
+ reg.add_input_port(getisofill, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(getisofill, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(getisofill, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(getisofill, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(getisofill, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(getisofill, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getisofill, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getisofill, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(getisofill, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(getisofill, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getisofill, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getisofill, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(getisofill, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(getisofill, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(getisofill, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getisofill, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getisofill, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(getisofill, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(getisofill, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(getisofill, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(getisofill, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(getisofill, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(getisofill, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(getisofill, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(getisofill, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(getisofill, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(getisofill, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(getisofill, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(getisofill, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(getisofill, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(getisofill, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(getisofill, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(getisofill, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(getisofill, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getisofill, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(getisofill, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(getisofill, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(getisofill, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(getisofill, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getisofill, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getisofill, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(getisofill, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getisofill, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(getisofill, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(getisofill, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(getisofill, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(getisofill, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(getisofill, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(getisofill, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(getisofill, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(getisofill, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(getisofill, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(getisofill, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(getisofill, 'isofill',
+ (get_late_type('vcs.isofill.Gfi'),
+ "no default"))
+
+ #Module getisoline
+ reg.add_module(getisoline,namespace='vcs|Canvas')
+ reg.add_input_port(getisoline, 'GM_name',
+ (core.modules.basic_modules.String,
+ "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
+ reg.add_input_port(getisoline, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(getisoline, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(getisoline, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(getisoline, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(getisoline, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(getisoline, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getisoline, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getisoline, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(getisoline, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(getisoline, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getisoline, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getisoline, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(getisoline, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(getisoline, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(getisoline, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getisoline, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getisoline, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(getisoline, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(getisoline, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(getisoline, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(getisoline, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(getisoline, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(getisoline, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(getisoline, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(getisoline, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(getisoline, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(getisoline, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(getisoline, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(getisoline, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(getisoline, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(getisoline, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(getisoline, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(getisoline, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(getisoline, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getisoline, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(getisoline, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(getisoline, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(getisoline, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(getisoline, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getisoline, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getisoline, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(getisoline, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getisoline, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(getisoline, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(getisoline, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(getisoline, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(getisoline, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(getisoline, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(getisoline, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(getisoline, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(getisoline, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(getisoline, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(getisoline, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(getisoline, 'isoline',
+ (get_late_type('vcs.isoline.Gi'),
+ "no default"))
+
+ #Module getoutfill
+ reg.add_module(getoutfill,namespace='vcs|Canvas')
+ reg.add_input_port(getoutfill, 'GM_name',
+ (core.modules.basic_modules.String,
+ "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
+ reg.add_input_port(getoutfill, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(getoutfill, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(getoutfill, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(getoutfill, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(getoutfill, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(getoutfill, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getoutfill, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getoutfill, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(getoutfill, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(getoutfill, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getoutfill, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getoutfill, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(getoutfill, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(getoutfill, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(getoutfill, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getoutfill, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getoutfill, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(getoutfill, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(getoutfill, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(getoutfill, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(getoutfill, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(getoutfill, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(getoutfill, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(getoutfill, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(getoutfill, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(getoutfill, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(getoutfill, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(getoutfill, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(getoutfill, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(getoutfill, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(getoutfill, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(getoutfill, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(getoutfill, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(getoutfill, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getoutfill, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(getoutfill, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(getoutfill, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(getoutfill, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(getoutfill, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getoutfill, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getoutfill, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(getoutfill, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getoutfill, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(getoutfill, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(getoutfill, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(getoutfill, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(getoutfill, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(getoutfill, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(getoutfill, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(getoutfill, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(getoutfill, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(getoutfill, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(getoutfill, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(getoutfill, 'outfill',
+ (get_late_type('vcs.outfill.Gfo'),
+ "no default"))
+
+ #Module getoutline
+ reg.add_module(getoutline,namespace='vcs|Canvas')
+ reg.add_input_port(getoutline, 'GM_name',
+ (core.modules.basic_modules.String,
+ "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
+ reg.add_input_port(getoutline, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(getoutline, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(getoutline, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(getoutline, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(getoutline, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(getoutline, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getoutline, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getoutline, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(getoutline, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(getoutline, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getoutline, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getoutline, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(getoutline, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(getoutline, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(getoutline, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getoutline, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getoutline, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(getoutline, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(getoutline, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(getoutline, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(getoutline, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(getoutline, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(getoutline, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(getoutline, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(getoutline, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(getoutline, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(getoutline, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(getoutline, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(getoutline, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(getoutline, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(getoutline, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(getoutline, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(getoutline, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(getoutline, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getoutline, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(getoutline, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(getoutline, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(getoutline, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(getoutline, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getoutline, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getoutline, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(getoutline, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getoutline, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(getoutline, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(getoutline, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(getoutline, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(getoutline, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(getoutline, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(getoutline, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(getoutline, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(getoutline, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(getoutline, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(getoutline, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(getoutline, 'outline',
+ (get_late_type('vcs.outline.Go'),
+ "no default"))
+
+ #Module getscatter
+ reg.add_module(getscatter,namespace='vcs|Canvas')
+ reg.add_input_port(getscatter, 'GM_name',
+ (core.modules.basic_modules.String,
+ "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
+ reg.add_input_port(getscatter, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(getscatter, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(getscatter, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(getscatter, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(getscatter, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(getscatter, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getscatter, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getscatter, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(getscatter, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(getscatter, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getscatter, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getscatter, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(getscatter, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(getscatter, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(getscatter, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getscatter, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getscatter, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(getscatter, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(getscatter, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(getscatter, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(getscatter, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(getscatter, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(getscatter, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(getscatter, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(getscatter, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(getscatter, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(getscatter, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(getscatter, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(getscatter, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(getscatter, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(getscatter, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(getscatter, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(getscatter, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(getscatter, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getscatter, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(getscatter, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(getscatter, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(getscatter, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(getscatter, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getscatter, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getscatter, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(getscatter, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getscatter, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(getscatter, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(getscatter, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(getscatter, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(getscatter, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(getscatter, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(getscatter, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(getscatter, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(getscatter, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(getscatter, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(getscatter, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(getscatter, 'scatter',
+ (get_late_type('vcs.scatter.GSp'),
+ "no default"))
+
+ #Module getxvsy
+ reg.add_module(getxvsy,namespace='vcs|Canvas')
+ reg.add_input_port(getxvsy, 'GM_name',
+ (core.modules.basic_modules.String,
+ "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
+ reg.add_input_port(getxvsy, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(getxvsy, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(getxvsy, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(getxvsy, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(getxvsy, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(getxvsy, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getxvsy, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getxvsy, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(getxvsy, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(getxvsy, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getxvsy, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getxvsy, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(getxvsy, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(getxvsy, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(getxvsy, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getxvsy, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getxvsy, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(getxvsy, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(getxvsy, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(getxvsy, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(getxvsy, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(getxvsy, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(getxvsy, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(getxvsy, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(getxvsy, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(getxvsy, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(getxvsy, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(getxvsy, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(getxvsy, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(getxvsy, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(getxvsy, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(getxvsy, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(getxvsy, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(getxvsy, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getxvsy, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(getxvsy, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(getxvsy, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(getxvsy, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(getxvsy, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getxvsy, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getxvsy, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(getxvsy, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getxvsy, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(getxvsy, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(getxvsy, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(getxvsy, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(getxvsy, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(getxvsy, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(getxvsy, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(getxvsy, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(getxvsy, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(getxvsy, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(getxvsy, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(getxvsy, 'xvsy',
+ (get_late_type('vcs.xvsy.GXY'),
+ "no default"))
+
+ #Module getxyvsy
+ reg.add_module(getxyvsy,namespace='vcs|Canvas')
+ reg.add_input_port(getxyvsy, 'GM_name',
+ (core.modules.basic_modules.String,
+ "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
+ reg.add_input_port(getxyvsy, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(getxyvsy, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(getxyvsy, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(getxyvsy, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(getxyvsy, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(getxyvsy, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getxyvsy, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getxyvsy, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(getxyvsy, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(getxyvsy, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getxyvsy, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getxyvsy, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(getxyvsy, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(getxyvsy, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(getxyvsy, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getxyvsy, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getxyvsy, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(getxyvsy, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(getxyvsy, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(getxyvsy, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(getxyvsy, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(getxyvsy, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(getxyvsy, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(getxyvsy, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(getxyvsy, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(getxyvsy, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(getxyvsy, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(getxyvsy, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(getxyvsy, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(getxyvsy, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(getxyvsy, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(getxyvsy, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(getxyvsy, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(getxyvsy, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getxyvsy, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(getxyvsy, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(getxyvsy, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(getxyvsy, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(getxyvsy, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getxyvsy, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getxyvsy, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(getxyvsy, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getxyvsy, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(getxyvsy, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(getxyvsy, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(getxyvsy, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(getxyvsy, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(getxyvsy, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(getxyvsy, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(getxyvsy, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(getxyvsy, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(getxyvsy, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(getxyvsy, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(getxyvsy, 'xyvsy',
+ (get_late_type('vcs.xyvsy.GXy'),
+ "no default"))
+
+ #Module getyxvsx
+ reg.add_module(getyxvsx,namespace='vcs|Canvas')
+ reg.add_input_port(getyxvsx, 'GM_name',
+ (core.modules.basic_modules.String,
+ "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
+ reg.add_input_port(getyxvsx, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(getyxvsx, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(getyxvsx, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(getyxvsx, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(getyxvsx, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(getyxvsx, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getyxvsx, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(getyxvsx, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(getyxvsx, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(getyxvsx, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getyxvsx, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getyxvsx, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(getyxvsx, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(getyxvsx, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(getyxvsx, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(getyxvsx, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(getyxvsx, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(getyxvsx, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(getyxvsx, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(getyxvsx, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(getyxvsx, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(getyxvsx, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(getyxvsx, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(getyxvsx, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(getyxvsx, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(getyxvsx, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(getyxvsx, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(getyxvsx, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(getyxvsx, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(getyxvsx, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(getyxvsx, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(getyxvsx, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(getyxvsx, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(getyxvsx, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getyxvsx, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(getyxvsx, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(getyxvsx, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(getyxvsx, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(getyxvsx, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getyxvsx, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(getyxvsx, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(getyxvsx, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(getyxvsx, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(getyxvsx, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(getyxvsx, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(getyxvsx, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(getyxvsx, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(getyxvsx, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(getyxvsx, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(getyxvsx, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(getyxvsx, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(getyxvsx, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(getyxvsx, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(getyxvsx, 'yxvsx',
+ (get_late_type('vcs.yxvsx.GYx'),
+ "no default"))
+
+ #Module isofill
+ reg.add_module(isofill,namespace='vcs|Canvas')
+ reg.add_input_port(isofill, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(isofill, 'template',
+ (core.modules.basic_modules.String,
+ "Name of the template"))
+ reg.add_input_port(isofill, 'gm_name',
+ (core.modules.basic_modules.String,
+ "Name of the graphics method"))
+ reg.add_input_port(isofill, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(isofill, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(isofill, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(isofill, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(isofill, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(isofill, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(isofill, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(isofill, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(isofill, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(isofill, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(isofill, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(isofill, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(isofill, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(isofill, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(isofill, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(isofill, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(isofill, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(isofill, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(isofill, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(isofill, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(isofill, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(isofill, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(isofill, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(isofill, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(isofill, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(isofill, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(isofill, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(isofill, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(isofill, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(isofill, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(isofill, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(isofill, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(isofill, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(isofill, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(isofill, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(isofill, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(isofill, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(isofill, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(isofill, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(isofill, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(isofill, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(isofill, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(isofill, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(isofill, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(isofill, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(isofill, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(isofill, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(isofill, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(isofill, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(isofill, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(isofill, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(isofill, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(isofill, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(isofill, 'display',
+ (get_late_type('vcs.displayplot.Dp'),
+ "no default"))
+
+ #Module isoline
+ reg.add_module(isoline,namespace='vcs|Canvas')
+ reg.add_input_port(isoline, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(isoline, 'template',
+ (core.modules.basic_modules.String,
+ "Name of the template"))
+ reg.add_input_port(isoline, 'gm_name',
+ (core.modules.basic_modules.String,
+ "Name of the graphics method"))
+ reg.add_input_port(isoline, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(isoline, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(isoline, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(isoline, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(isoline, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(isoline, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(isoline, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(isoline, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(isoline, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(isoline, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(isoline, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(isoline, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(isoline, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(isoline, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(isoline, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(isoline, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(isoline, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(isoline, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(isoline, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(isoline, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(isoline, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(isoline, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(isoline, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(isoline, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(isoline, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(isoline, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(isoline, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(isoline, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(isoline, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(isoline, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(isoline, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(isoline, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(isoline, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(isoline, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(isoline, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(isoline, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(isoline, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(isoline, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(isoline, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(isoline, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(isoline, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(isoline, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(isoline, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(isoline, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(isoline, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(isoline, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(isoline, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(isoline, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(isoline, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(isoline, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(isoline, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(isoline, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(isoline, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(isoline, 'display',
+ (get_late_type('vcs.displayplot.Dp'),
+ "no default"))
+
+ #Module outfill
+ reg.add_module(outfill,namespace='vcs|Canvas')
+ reg.add_input_port(outfill, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(outfill, 'template',
+ (core.modules.basic_modules.String,
+ "Name of the template"))
+ reg.add_input_port(outfill, 'gm_name',
+ (core.modules.basic_modules.String,
+ "Name of the graphics method"))
+ reg.add_input_port(outfill, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(outfill, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(outfill, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(outfill, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(outfill, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(outfill, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(outfill, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(outfill, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(outfill, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(outfill, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(outfill, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(outfill, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(outfill, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(outfill, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(outfill, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(outfill, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(outfill, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(outfill, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(outfill, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(outfill, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(outfill, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(outfill, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(outfill, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(outfill, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(outfill, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(outfill, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(outfill, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(outfill, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(outfill, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(outfill, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(outfill, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(outfill, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(outfill, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(outfill, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(outfill, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(outfill, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(outfill, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(outfill, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(outfill, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(outfill, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(outfill, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(outfill, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(outfill, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(outfill, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(outfill, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(outfill, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(outfill, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(outfill, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(outfill, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(outfill, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(outfill, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(outfill, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(outfill, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(outfill, 'display',
+ (get_late_type('vcs.displayplot.Dp'),
+ "no default"))
+
+ #Module outline
+ reg.add_module(outline,namespace='vcs|Canvas')
+ reg.add_input_port(outline, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 2D, last 2 dimensions will be plotted"))
+ reg.add_input_port(outline, 'template',
+ (core.modules.basic_modules.String,
+ "Name of the template"))
+ reg.add_input_port(outline, 'gm_name',
+ (core.modules.basic_modules.String,
+ "Name of the graphics method"))
+ reg.add_input_port(outline, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(outline, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(outline, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(outline, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(outline, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(outline, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(outline, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(outline, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(outline, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(outline, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(outline, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(outline, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(outline, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(outline, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(outline, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(outline, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(outline, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(outline, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(outline, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(outline, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(outline, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(outline, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(outline, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(outline, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(outline, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(outline, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(outline, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(outline, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(outline, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(outline, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(outline, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(outline, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(outline, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(outline, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(outline, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(outline, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(outline, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(outline, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(outline, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(outline, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(outline, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(outline, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(outline, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(outline, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(outline, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(outline, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(outline, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(outline, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(outline, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(outline, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(outline, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(outline, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(outline, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(outline, 'display',
+ (get_late_type('vcs.displayplot.Dp'),
+ "no default"))
+
+ #Module plot
+ reg.add_module(plot,namespace='vcs|Canvas')
+ reg.add_input_port(plot, 'row',
+ (core.modules.basic_modules.Integer, "Cell Row"))
+ reg.add_input_port(plot, 'col',
+ (core.modules.basic_modules.Integer, "Cell Col"))
+ reg.add_input_port(plot, 'template',
+ (core.modules.basic_modules.String,
+ "Name of the template"))
+ reg.add_input_port(plot, 'gm_name',
+ (core.modules.basic_modules.String,
+ "Name of the graphics method"))
+ reg.add_input_port(plot, 'plot_type',
+ (core.modules.basic_modules.String,
+ "Type of plot - boxfill, isoline, etc"))
+ reg.add_input_port(plot, 'slab2_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 1D, last dimension will be plotted"))
+ reg.add_input_port(plot, 'slab1_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 1D, last dimension will be plotted"))
+
+ reg.add_input_port(plot, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(plot, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(plot, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(plot, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(plot, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(plot, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(plot, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(plot, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(plot, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(plot, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(plot, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(plot, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(plot, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(plot, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(plot, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(plot, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(plot, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(plot, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(plot, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(plot, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(plot, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(plot, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(plot, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(plot, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(plot, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(plot, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(plot, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(plot, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(plot, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(plot, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(plot, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(plot, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(plot, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(plot, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(plot, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(plot, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(plot, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(plot, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(plot, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(plot, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(plot, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(plot, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(plot, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(plot, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(plot, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(plot, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(plot, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(plot, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(plot, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(plot, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(plot, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(plot, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(plot, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(plot, 'display',
+ (get_late_type('vcs.displayplot.Dp'),
+ "no default"))
+
+ #Module scatter
+ reg.add_module(scatter,namespace='vcs|Canvas')
+ reg.add_input_port(scatter, 'template',
+ (core.modules.basic_modules.String,
+ "Name of the template"))
+ reg.add_input_port(scatter, 'gm_name',
+ (core.modules.basic_modules.String,
+ "Name of the graphics method"))
+ reg.add_input_port(scatter, 'slab2_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 1D, last dimension will be plotted"))
+ reg.add_input_port(scatter, 'slab1_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 1D, last dimension will be plotted"))
+ reg.add_input_port(scatter, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(scatter, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(scatter, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(scatter, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(scatter, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(scatter, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(scatter, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(scatter, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(scatter, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(scatter, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(scatter, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(scatter, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(scatter, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(scatter, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(scatter, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(scatter, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(scatter, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(scatter, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(scatter, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(scatter, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(scatter, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(scatter, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(scatter, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(scatter, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(scatter, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(scatter, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(scatter, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(scatter, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(scatter, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(scatter, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(scatter, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(scatter, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(scatter, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(scatter, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(scatter, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(scatter, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(scatter, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(scatter, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(scatter, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(scatter, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(scatter, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(scatter, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(scatter, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(scatter, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(scatter, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(scatter, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(scatter, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(scatter, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(scatter, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(scatter, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(scatter, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(scatter, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(scatter, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(scatter, 'display',
+ (get_late_type('vcs.displayplot.Dp'),
+ "no default"))
+
+ #Module xvsy
+ reg.add_module(xvsy,namespace='vcs|Canvas')
+ reg.add_input_port(xvsy, 'template',
+ (core.modules.basic_modules.String,
+ "Name of the template"))
+ reg.add_input_port(xvsy, 'gm_name',
+ (core.modules.basic_modules.String,
+ "Name of the graphics method"))
+ reg.add_input_port(xvsy, 'slab2_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 1D, last dimension will be plotted"))
+ reg.add_input_port(xvsy, 'slab1_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 1D, last dimension will be plotted"))
+ reg.add_input_port(xvsy, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(xvsy, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(xvsy, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(xvsy, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(xvsy, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(xvsy, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(xvsy, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(xvsy, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(xvsy, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(xvsy, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(xvsy, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(xvsy, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(xvsy, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(xvsy, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(xvsy, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(xvsy, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(xvsy, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(xvsy, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(xvsy, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(xvsy, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(xvsy, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(xvsy, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(xvsy, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(xvsy, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(xvsy, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(xvsy, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(xvsy, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(xvsy, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(xvsy, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(xvsy, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(xvsy, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(xvsy, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(xvsy, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(xvsy, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(xvsy, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(xvsy, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(xvsy, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(xvsy, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(xvsy, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(xvsy, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(xvsy, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(xvsy, 'yaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(xvsy, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(xvsy, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(xvsy, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(xvsy, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(xvsy, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(xvsy, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(xvsy, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(xvsy, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(xvsy, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(xvsy, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(xvsy, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(xvsy, 'display',
+ (get_late_type('vcs.displayplot.Dp'),
+ "no default"))
+
+ #Module xyvsy
+ reg.add_module(xyvsy,namespace='vcs|Canvas')
+ reg.add_input_port(xyvsy, 'template',
+ (core.modules.basic_modules.String,
+ "Name of the template"))
+ reg.add_input_port(xyvsy, 'gm_name',
+ (core.modules.basic_modules.String,
+ "Name of the graphics method"))
+ reg.add_input_port(xyvsy, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 1D, last dimension will be plotted"))
+ reg.add_input_port(xyvsy, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(xyvsy, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(xyvsy, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(xyvsy, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(xyvsy, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(xyvsy, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(xyvsy, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(xyvsy, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(xyvsy, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(xyvsy, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(xyvsy, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(xyvsy, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(xyvsy, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(xyvsy, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(xyvsy, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(xyvsy, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(xyvsy, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(xyvsy, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(xyvsy, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(xyvsy, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(xyvsy, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(xyvsy, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(xyvsy, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(xyvsy, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(xyvsy, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(xyvsy, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(xyvsy, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(xyvsy, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(xyvsy, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(xyvsy, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(xyvsy, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(xyvsy, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(xyvsy, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(xyvsy, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(xyvsy, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(xyvsy, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(xyvsy, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(xyvsy, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(xyvsy, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(xyvsy, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(xyvsy, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(xyvsy, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(xyvsy, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(xyvsy, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(xyvsy, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(xyvsy, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(xyvsy, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(xyvsy, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(xyvsy, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(xyvsy, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(xyvsy, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(xyvsy, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(xyvsy, 'display',
+ (get_late_type('vcs.displayplot.Dp'),
+ "no default"))
+
+ #Module yxvsx
+ reg.add_module(yxvsx,namespace='vcs|Canvas')
+ reg.add_input_port(yxvsx, 'template',
+ (core.modules.basic_modules.String,
+ "Name of the template"))
+ reg.add_input_port(yxvsx, 'gm_name',
+ (core.modules.basic_modules.String,
+ "Name of the graphics method"))
+ reg.add_input_port(yxvsx, 'slab_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Data at least 1D, last dimension will be plotted"))
+ reg.add_input_port(yxvsx, 'datawc_timeunits',
+ (core.modules.basic_modules.String,
+ "units to use when disaplaying time dimension auto tick"), True)
+ reg.add_input_port(yxvsx, 'long_name',
+ (core.modules.basic_modules.String,
+ "replaces long_name on plot"), True)
+ reg.add_input_port(yxvsx, 'projection_0',
+ (core.modules.basic_modules.String,
+ "projection to use, name or object"), True)
+ reg.add_input_port(yxvsx, 'xticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of x axis"), True)
+ reg.add_input_port(yxvsx, 'xarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis"), True)
+ reg.add_input_port(yxvsx, 'yweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(yxvsx, 'xweights_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "replace xaxis weights used for computing mean"), True)
+ reg.add_input_port(yxvsx, 'warray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of w axis, only if var has more than 4D"), True)
+ reg.add_input_port(yxvsx, 'tunits',
+ (core.modules.basic_modules.String,
+ "replace taxis units on plot (if exists)"), True)
+ reg.add_input_port(yxvsx, 'ymtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(yxvsx, 'ymtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(yxvsx, 'datawc_x1',
+ (core.modules.basic_modules.Float,
+ "first value of xaxis on plot"), True)
+ reg.add_input_port(yxvsx, 'datawc_x2',
+ (core.modules.basic_modules.Float,
+ "second value of xaxis on plot"), True)
+ reg.add_input_port(yxvsx, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+ reg.add_input_port(yxvsx, 'xmtics1_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
+ reg.add_input_port(yxvsx, 'xmtics2_0',
+ (core.modules.basic_modules.String,
+ "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
+ reg.add_input_port(yxvsx, 'xbounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of x axis bounds values"), True)
+ reg.add_input_port(yxvsx, 'ybounds_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis bounds values (if exist)"), True)
+ reg.add_input_port(yxvsx, 'datawc_y2',
+ (core.modules.basic_modules.Float,
+ "second value of yaxis on plot"), True)
+ reg.add_input_port(yxvsx, 'wname',
+ (core.modules.basic_modules.String,
+ "replace waxis name on plot (if exists)"), True)
+ reg.add_input_port(yxvsx, 'file_comment',
+ (core.modules.basic_modules.String,
+ "replaces file_comment on plot"), True)
+ reg.add_input_port(yxvsx, 'datawc_calendar',
+ (core.modules.basic_modules.Integer,
+ "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
+ reg.add_input_port(yxvsx, 'wunits',
+ (core.modules.basic_modules.String,
+ "replace waxis units on plot (if exists)"), True)
+ reg.add_input_port(yxvsx, 'xrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse x axis"), True)
+ reg.add_input_port(yxvsx, 'ymd',
+ (core.modules.basic_modules.String,
+ "replaces year/month/day on plot"), True)
+ reg.add_input_port(yxvsx, 'yarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of y axis, only if var has more than 1D"), True)
+ reg.add_input_port(yxvsx, 'units',
+ (core.modules.basic_modules.String,
+ "replaces units value on plot"), True)
+ reg.add_input_port(yxvsx, 'yunits',
+ (core.modules.basic_modules.String,
+ "replace yaxis units on plot (if exists)"), True)
+ reg.add_input_port(yxvsx, 'zarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of z axis, only if var has more than 2D"), True)
+ reg.add_input_port(yxvsx, 'xname',
+ (core.modules.basic_modules.String,
+ "replace xaxis name on plot"), True)
+ reg.add_input_port(yxvsx, 'tarray_0',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "Values to use instead of t axis, only if var has more than 3D"), True)
+ reg.add_input_port(yxvsx, 'bg_0',
+ (core.modules.basic_modules.Boolean,
+ "plots in background mode"), True)
+ reg.add_input_port(yxvsx, 'bg_1',
+ (core.modules.basic_modules.Integer,
+ "plots in background mode"), True)
+ reg.add_input_port(yxvsx, 'xaxisconvert',
+ (core.modules.basic_modules.String,
+ "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
+ reg.add_input_port(yxvsx, 'zname',
+ (core.modules.basic_modules.String,
+ "replace zaxis name on plot (if exists)"), True)
+ reg.add_input_port(yxvsx, 'hms',
+ (core.modules.basic_modules.String,
+ "replaces hh/mm/ss on plot"), True)
+ reg.add_input_port(yxvsx, 'tname',
+ (core.modules.basic_modules.String,
+ "replace taxis name on plot (if exists)"), True)
+ reg.add_input_port(yxvsx, 'yname',
+ (core.modules.basic_modules.String,
+ "replace yaxis name on plot (if exists)"), True)
+ reg.add_input_port(yxvsx, 'ratio_0',
+ (core.modules.basic_modules.Integer,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(yxvsx, 'ratio_1',
+ (core.modules.basic_modules.String,
+ "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
+ reg.add_input_port(yxvsx, 'datawc_y1',
+ (core.modules.basic_modules.Float,
+ "first value of yaxis on plot"), True)
+ reg.add_input_port(yxvsx, 'xunits',
+ (core.modules.basic_modules.String,
+ "replace xaxis units on plot"), True)
+ reg.add_input_port(yxvsx, 'name',
+ (core.modules.basic_modules.String,
+ "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
+ reg.add_input_port(yxvsx, 'yticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of y axis"), True)
+ reg.add_input_port(yxvsx, 'yticlabels2_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 2nd side of y axis"), True)
+ reg.add_input_port(yxvsx, 'comment1',
+ (core.modules.basic_modules.String,
+ "replaces comment1 on plot"), True)
+ reg.add_input_port(yxvsx, 'zunits',
+ (core.modules.basic_modules.String,
+ "replace zaxis units on plot (if exists)"), True)
+ reg.add_input_port(yxvsx, 'comment3',
+ (core.modules.basic_modules.String,
+ "replaces comment3 on plot"), True)
+ reg.add_input_port(yxvsx, 'comment2',
+ (core.modules.basic_modules.String,
+ "replaces comment2 on plot"), True)
+ reg.add_input_port(yxvsx, 'xticlabels1_0',
+ (core.modules.basic_modules.String,
+ "values for labels on 1st side of x axis"), True)
+ reg.add_input_port(yxvsx, 'comment4',
+ (core.modules.basic_modules.String,
+ "replaces comment4 on plot"), True)
+ reg.add_input_port(yxvsx, 'yrev',
+ (core.modules.basic_modules.Boolean,
+ "reverse y axis, only if slab has more than 1D"), True)
+ reg.add_output_port(yxvsx, 'display',
+ (get_late_type('vcs.displayplot.Dp'),
+ "no default"))
+
+ #Module png
+ reg.add_module(png,namespace='vcs|Canvas')
+ reg.add_input_port(png, 'file',
+ (core.modules.basic_modules.String,
+ ""))
+ reg.add_input_port(png, 'width',
+ (core.modules.basic_modules.Float,
+ ""))
+ reg.add_input_port(png, 'height',
+ (core.modules.basic_modules.Float,
+ ""))
+ reg.add_input_port(png, 'units',
+ (core.modules.basic_modules.String,
+ ""))
+ reg.add_output_port(png, 'file',
+ (core.modules.basic_modules.File,
+ "File output"))
+
+ #extra input ports not available in the xml file
+ reg.add_input_port(boxfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(createboxfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(createisofill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(createisoline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(createoutfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(createoutline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(createscatter, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(createxvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(createxyvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(createyxvsx, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(getboxfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(getisofill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(getisoline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(getoutfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(getoutline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(getscatter, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(getxvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(getxyvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(getyxvsx, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(isofill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(isoline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(outfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(outline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(plot, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(scatter, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(xvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(xyvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(yxvsx, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_input_port(png, 'canvas',
+ (Canvas,
+ "Canvas object"))
+
+ #extra output ports not available in the xml file
+ reg.add_output_port(boxfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(createboxfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(createisofill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(createisoline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(createoutfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(createoutline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(createscatter, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(createxvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(createxyvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(createyxvsx, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(getboxfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(getisofill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(getisoline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(getoutfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(getoutline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(getscatter, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(getxvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(getxyvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(getyxvsx, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(isofill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(isoline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(outfill, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(outline, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(plot, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(scatter, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(xvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(xyvsy, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(yxvsx, 'canvas',
+ (Canvas,
+ "Canvas object"))
+ reg.add_output_port(png, 'canvas',
+ (Canvas,
+ "Canvas object"))
+
+ #Module open
+ reg.add_module(open,namespace='cdms2')
+ reg.add_input_port(open, 'uri',
+ (core.modules.basic_modules.String,
+ ""))
+ reg.add_input_port(open, 'mode',
+ (core.modules.basic_modules.String,
+ ""))
+ reg.add_input_port(open, 'template',
+ (core.modules.basic_modules.String,
+ ""))
+ reg.add_input_port(open, 'dods',
+ (core.modules.basic_modules.Integer,
+ ""))
+ reg.add_output_port(open, 'dataset',
+ (get_late_type('cdms2.dataset.CdmsFile'),
+ ""))
+
+ #Module __call__
+ reg.add_module(__call__,namespace='cdms2|dataset')
+ reg.add_input_port(__call__, 'id',
+ (core.modules.basic_modules.String,
+ ""))
+ reg.add_input_port(__call__, 'type',
+ (core.modules.basic_modules.String,
+ "variable, axis, or weighted-axis"))
+ reg.add_output_port(__call__, 'variable',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ ""))
+
+ #extra input ports not available in the xml file
+ reg.add_input_port(__call__, 'axes',
+ (core.modules.basic_modules.String, "Axes of variables"))
+ reg.add_input_port(__call__, 'axesOperations',
+ (core.modules.basic_modules.String, "Axes Operations"))
+ reg.add_input_port(__call__, 'cdmsfile',
+ (CdmsFile, "cdmsfile"))
+
+def package_dependencies():
+ return []
+
+def package_requirements():
+ import core.requirements
+ if not core.requirements.python_module_exists('vcs'):
+ raise core.requirements.MissingRequirements('vcs')
+ if not core.requirements.python_module_exists('cdms2'):
+ raise core.requirements.MissingRequirements('cdms2')
+ if not core.requirements.python_module_exists('cdutil'):
+ raise core.requirements.MissingRequirements('cdutil')
+ import vcs, cdms2, cdutil
+
+
diff --git a/contrib/cdat/cdat.sip b/contrib/cdat/cdat.sip
new file mode 100644
index 0000000..f36d87f
--- /dev/null
+++ b/contrib/cdat/cdat.sip
@@ -0,0 +1,36 @@
+%Module coreappwrap 0
+
+%Import QtGui/QtGuimod.sip
+
+class MainWindow : QMainWindow {
+%TypeHeaderCode
+#include <Qt/mainwindow.h>
+%End
+
+public:
+ void paintEvent(QPaintEvent *);
+ virtual bool event(QEvent *);
+ void setupCairo();
+ void unsetupCairo();
+
+public slots:
+ void actionTriggered(QAction*);
+};
+
+class VCSQtManager {
+
+%TypeHeaderCode
+#include <Qt/qti.h>
+%End
+
+public:
+ static bool isCreated();
+ static MainWindow* window(int id);
+ static void sendEvent(int index, QEvent::Type eventType);
+
+public slots:
+
+signals:
+
+};
+
diff --git a/contrib/cdat/cdat.vt b/contrib/cdat/cdat.vt
new file mode 100644
index 0000000..c375fec
Binary files /dev/null and b/contrib/cdat/cdat.vt differ
diff --git a/contrib/cdat/cdat_cell.py b/contrib/cdat/cdat_cell.py
new file mode 100644
index 0000000..24fbd54
--- /dev/null
+++ b/contrib/cdat/cdat_cell.py
@@ -0,0 +1,291 @@
+from PyQt4 import QtCore, QtGui
+from core.modules.vistrails_module import Module, ModuleError, NotCacheable
+from core.modules.basic_modules import Constant
+from packages.spreadsheet.spreadsheet_controller import spreadsheetController
+from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from packages.spreadsheet.spreadsheet_event import DisplayCellEvent
+#from cdatwrap.coreappwrap import VCSQtManager
+import vcs
+import genutil
+import cdutil
+import time
+import api
+import re
+import MV2
+
+""" This file contains all of the classes related to the Vistrails Modules (the
+boxes). Eventually Variable and GraphicsMethod should be replaced by generating
+the proper graphics method, cdms2, MV2, etc... modules """
+
+# Index into the VCSQtManager window array so we can communicate with the
+# C++ Qt windows which the plots show up in. If this number is no longer
+# consistent with the number of C++ Qt windows due to adding or removing
+# vcs.init() calls, then when you plot, it will plot into a
+# separate window instead of in the cell and may crash.
+windowIndex = 1
+
+class Variable(Module):
+ """ Get the updated transient variable """
+
+ def compute(self):
+ # *** IMPORTANT ***
+ # Once someone figures out how to pass the tvariable object, to this
+ # module none of the computation in this method is necessary
+
+ # Check ports
+ if not self.hasInputFromPort('cdmsfile'):
+ raise ModuleError(self, "'cdmsfile' is mandatory.")
+ if not self.hasInputFromPort('id'):
+ raise ModuleError(self, "'id' is mandatory.")
+
+ # Get input from ports
+ cdmsfile = self.getInputFromPort('cdmsfile')
+ id = self.getInputFromPort('id')
+ axes = self.forceGetInputFromPort('axes') # None if no input
+ axesOperations = self.forceGetInputFromPort('axesOperations') # None if no input
+
+ # Get the variable
+ varType = self.getVarType(id, cdmsfile)
+ if (varType == 'variable'):
+ var = cdmsfile.__call__(id)
+ elif (varType == 'axis'):
+ varID = self.getAxisID(id)
+ axis = getattr(cdmsfile, 'axes')[varID]
+ var = MV2.array(axis)
+ var.setAxis(0, axis)
+ elif (varType == 'weighted-axis'):
+ varID, axisID = self.getVarAndAxisID(id)
+ var = cdmsfile.__call__(varID)
+ var = genutil.getAxisWeightByName(var, axisID)
+ var.id = varID +'_' + axisID + '_weight'
+ else:
+ var = None
+
+ # Eval the variable with the axes
+ if axes is not None and var is not None:
+ try:
+ kwargs = eval(axes)
+ var = var(**kwargs)
+ except:
+ raise ModuleError(self, "Invalid 'axes' specification", axes)
+
+ # Apply axes ops to the variable
+ if axesOperations is not None:
+ var = self.applyAxesOperations(var, axesOperations)
+
+ self.setResult('variable', var)
+
+ def applyAxesOperations(self, var, axesOperations):
+ """ Apply axes operations to update the slab """
+ try:
+ axesOperations = eval(axesOperations)
+ except:
+ raise TypeError("Invalid string 'axesOperations'")
+
+ for axis in list(axesOperations):
+ if axesOperations[axis] == 'sum':
+ var = cdutil.averager(var, axis="(%s)" % axis, weight='equal',
+ action='sum')
+ elif axesOperations[axis] == 'avg':
+ var = cdutil.averager(var, axis="(%s)" % axis, weight='equal')
+ elif axesOperations[axis] == 'wgt':
+ var = cdutil.averager(var, axis="(%s)" % axis)
+ elif axesOperations[axis] == 'gtm':
+ var = genutil.statistics.geometricmean(var, axis="(%s)" % axis)
+ elif axesOperations[axis] == 'std':
+ var = genutil.statistics.std(var, axis="(%s)" % axis)
+
+ return var
+
+ def getVarType(self, varID, file):
+ if varID in list(getattr(file, 'variables')):
+ return 'variable'
+ elif varID in list(getattr(file, 'axes')):
+ return 'axis'
+ elif re.compile('(.+)(_)(.+)(_)axis').match(varID):
+ return 'axis'
+ elif re.compile('(.+)(_)(.+)(_)weight').match(varID):
+ return 'weighted-axis'
+
+ def getVarAndAxisID(self, varID):
+ """ Get the varID and axisID from a string with format:
+ varID_axisID_weight """
+
+ match = re.compile('(.+)(_)(.+)(_)(weight)').match(varID)
+ if match:
+ return (match.group(1), match.group(3))
+
+ return None
+
+ def getAxisID(self, varID):
+ """ Get the axisID from a string with format: varID_axisID_axis """
+
+ match = re.compile('(.+)(_)(.+)(_)(axis)').match(varID)
+ if match:
+ return match.group(3)
+
+ return varID
+
+class Quickplot(Variable):
+ """ Quickplot is identical to Variable except we will only have a single
+ quickplot module in a pipeline. """
+
+ def foo(self):
+ return
+
+class GraphicsMethod(Module, NotCacheable):
+ """ GraphicsMethod initializes the vcs canvas and gets the graphics method
+ and modify it's attributes """
+
+ def compute(self):
+ # Check required input ports
+ if not self.hasInputFromPort('gmName'):
+ return
+ if not self.hasInputFromPort('plotType'):
+ return
+ if not self.hasInputFromPort('slab1'):
+ return
+
+ # Get required input
+ gmName = self.getInputFromPort('gmName')
+ plotType = self.getInputFromPort('plotType')
+
+ # GraphicsMethod doesn't need slab1/slab2 as input. It can be passed
+ # directly to CDATCell but I pass it to graphics method so it looks
+ # nicer in the pipeline.
+ slab1 = self.getInputFromPort('slab1')
+ if self.hasInputFromPort('slab2'):
+ self.setResult('slab2', self.getInputFromPort('slab2'))
+
+ # Initialize the canvas and get the graphics method
+ canvas = vcs.init()
+ gm = canvas.get_gm(plotType.lower(), gmName)
+
+ # Modify the graphics method's attributes
+ if self.hasInputFromPort('color_1'):
+ gm.color_1 = self.getInputFromPort('color_1')
+ if self.hasInputFromPort('color_2'):
+ gm.color_2 = self.getInputFromPort('color_2')
+ if self.hasInputFromPort('level_1'):
+ gm.level_1 = self.getInputFromPort('level_1')
+ if self.hasInputFromPort('level_2'):
+ gm.level_2 = self.getInputFromPort('level_2')
+ # TODO: more gm attributes ...
+
+ # Add canvas / slab to output Ports
+ self.setResult('slab1', slab1)
+ self.setResult('canvas', canvas)
+
+class CDATCell(SpreadsheetCell, NotCacheable):
+ def __init__(self):
+ SpreadsheetCell.__init__(self)
+ self.cellWidget = None
+
+ def compute(self):
+ """ compute() -> None
+ Dispatch the vtkRenderer to the actual rendering widget
+ """
+ # Check required input ports
+ if self.hasInputFromPort('canvas'):
+ canvas = self.getInputFromPort('canvas')
+ else:
+ self.cellWidget = self.displayAndWait(QCDATWidget, (None,))
+ self.setResult('canvas', self.cellWidget.canvas)
+ return
+ self.setResult('canvas', canvas)
+ if not self.hasInputFromPort('gmName'):
+ return
+ if not self.hasInputFromPort('plotType'):
+ return
+ if not self.hasInputFromPort('slab1'):
+ return
+ if not self.hasInputFromPort('template'):
+ return
+
+ # Build up the argument list
+ args = []
+ slab1 = self.getInputFromPort('slab1')
+ args.append(self.getInputFromPort('slab1'))
+ if self.hasInputFromPort('slab2'):
+ args.append(self.getInputFromPort('slab2'))
+ args.append(self.getInputFromPort('template'))
+ args.append(self.getInputFromPort('plotType'))
+ args.append(self.getInputFromPort('gmName'))
+
+ # Build up plot keyword args ...
+ kwargs = {}
+ if self.hasInputFromPort('continents'):
+ kwargs['continents'] = self.getInputFromPort('continents')
+
+ # Set the cell row / col
+ self.location = CellLocation()
+ if self.hasInputFromPort('row'):
+ self.location.row = self.getInputFromPort('row')
+ if self.hasInputFromPort('col'):
+ self.location.col = self.getInputFromPort('col')
+
+ # Plot into the cell
+ inputPorts = (canvas, args, kwargs)
+ self.displayAndWait(QCDATWidget, inputPorts)
+
+class QCDATWidget(QCellWidget):
+ """ QCDATWidget is the spreadsheet cell widget where the plots are displayed.
+ The widget interacts with the underlying C++, VCSQtManager through SIP.
+ This enables QCDATWidget to get a reference to the Qt MainWindow that the
+ plot will be displayed in and send signals (events) to that window widget.
+ """
+
+ def __init__(self, parent=None):
+ QCellWidget.__init__(self, parent)
+ self.window = None
+ self.canvas = None
+ self.windowIndex = self.getWindowIndex() #index to get QT Window from VCSQtManager
+
+ def getWindowIndex(self):
+ """ Return the index into the VCSQtManager's array of Qt Windows which
+ plots will be displayed in.
+ """
+ global windowIndex
+
+ windowIndex += 1
+ maxWindows = 8
+ if windowIndex > maxWindows:
+ windowIndex = 1
+ return windowIndex
+
+ def updateContents(self, inputPorts):
+ """ Get the vcs canvas, setup the cell's layout, and plot """
+ spreadsheetWindow = spreadsheetController.findSpreadsheetWindow()
+ spreadsheetWindow.setUpdatesEnabled(False)
+
+ # Set the canvas
+ self.canvas = inputPorts[0]
+ if self.canvas is None:
+ self.canvas = vcs.init()
+ self.canvas.clear()
+
+ # Place the mainwindow that the plot will be displayed in, into this
+ # cell widget's layout
+ self.window = VCSQtManager.window(self.windowIndex)
+ layout = QtGui.QVBoxLayout()
+ layout.addWidget(self.window)
+ self.setLayout(layout)
+
+ # Plot
+ if len(inputPorts) > 2:
+ args = inputPorts[1]
+ kwargs = inputPorts[2]
+ self.canvas.plot(*args, **kwargs)
+
+ spreadsheetWindow.setUpdatesEnabled(True)
+
+ def deleteLater(self):
+ """ deleteLater() -> None
+ Make sure to free render window resource when
+ deallocating. Overriding PyQt deleteLater to free up
+ resources
+ """
+ self.canvas = None
+ QCellWidget.deleteLater(self)
+
diff --git a/contrib/cdat/cdat_window.py b/contrib/cdat/cdat_window.py
new file mode 100644
index 0000000..03ade10
--- /dev/null
+++ b/contrib/cdat/cdat_window.py
@@ -0,0 +1,2356 @@
+from PyQt4 import QtCore, QtGui
+from cdat_cell import QCDATWidget
+from gui_controller import *
+from graphics_method_controller import QGraphicsMethodAttributeWindow
+import cdutil
+import genutil
+import cdms2
+import MV2
+import os
+import re
+import api
+import vcs
+
+class QCDATWindow(QtGui.QWidget):
+ """ Main class for VCDAT Window. Contains a menu widget, file widget,
+ defined variable widget, and variable widget """
+
+ def __init__(self, parent=None):
+ """ Instantiate the child widgets of the main VCDAT window and setup
+ the overall layout """
+ QtGui.QWidget.__init__(self, parent)
+
+ self.setWindowTitle('The Visual Climate Data Analysis Tools - (VCDAT)')
+ layout = QtGui.QVBoxLayout()
+ self.setLayout(layout)
+
+ # Init Menu Widget
+ self.menuWidget = QMenuWidget(self)
+
+ # Init File Widget
+ vsplitter = QtGui.QSplitter(QtCore.Qt.Vertical)
+ fileWidget = QLabeledWidgetContainer(QCDATFileWidget(),
+ 'FILE VARIABLES')
+ vsplitter.addWidget(fileWidget)
+
+ # Init Defined Variables Widget
+ definedVar = QLabeledWidgetContainer(QDefinedVariable(),
+ 'DEFINED VARIABLES')
+ vsplitter.addWidget(definedVar)
+ hsplitter = QtGui.QSplitter(QtCore.Qt.Horizontal)
+ hsplitter.addWidget(vsplitter)
+
+ # Init Var Plotting Widget
+ varView = QLabeledWidgetContainer(QVariableView(),
+ 'PLOTTING')
+ hsplitter.addWidget(varView)
+ hsplitter.setStretchFactor(1, 1)
+ layout.addWidget(hsplitter)
+
+ # Init guiController
+ guiController = GuiController(fileWidget.getWidget(),
+ definedVar.getWidget(),
+ varView.getWidget())
+ guiController.initTeachingCommands()
+ self.guiController = guiController # So guicontroller doesn't get garbage collected
+
+ # Connect signals between self & GuiController
+ self.connect(self, QtCore.SIGNAL('setRecordCommands'),
+ guiController.setRecordCommands)
+ self.connect(self, QtCore.SIGNAL('viewTeachingCommands'),
+ guiController.viewTeachingCommands)
+ self.connect(self, QtCore.SIGNAL('closeTeachingCommands'),
+ guiController.closeTeachingCommands)
+
+ # Connect Signals between QVariableView & QDefinedVariable
+ varView.connect(definedVar.getWidget(), QtCore.SIGNAL('selectDefinedVariableEvent'),
+ varView.getWidget().selectDefinedVariableEvent)
+ varView.connect(definedVar.getWidget(), QtCore.SIGNAL('setupDefinedVariableAxes'),
+ varView.getWidget().setupDefinedVariableAxes)
+ definedVar.connect(varView.getWidget(), QtCore.SIGNAL('plotPressed'),
+ definedVar.getWidget().defineQuickplot)
+ definedVar.connect(varView.getWidget(), QtCore.SIGNAL('defineVariable'),
+ definedVar.getWidget().defineVariable)
+
+ # Connect Signals between QFileWidget & QVariableView
+ varView.connect(fileWidget.getWidget(), QtCore.SIGNAL('variableChanged'),
+ varView.getWidget().setupDefinedVariableAxes)
+ varView.connect(fileWidget.getWidget(), QtCore.SIGNAL('defineVariableEvent'),
+ varView.getWidget().defineVariableEvent)
+
+ def closeEvent(self, event):
+ # TODO
+ # closeEvent() isn't called vistrails is closed,
+ # perhaps because the event isn't propagated by vistrails? Therefore,
+ # any functionality we want to execute when vistrails exits is not done
+ # unless the user specifically closes this gui.
+
+ self.emit(QtCore.SIGNAL('closeTeachingCommands'))
+
+ def sizeHint(self):
+ return QtCore.QSize(1024, 600)
+
+class QFileDialogWidget(QtGui.QFileDialog):
+
+ def __init__(self, parent=None):
+ QtGui.QFileDialog.__init__(self, parent, QtCore.Qt.Widget)
+ self.setModal(False)
+ self.setSizeGripEnabled(False)
+ self.setFileMode(QtGui.QFileDialog.ExistingFile)
+ self.setLabelText(QtGui.QFileDialog.LookIn, 'Directory')
+ self.setSidebarUrls([QtCore.QUrl('file://')])
+
+ gridLayout = self.findChild(QtGui.QGridLayout, 'gridLayout')
+ if gridLayout:
+ gridLayout.setMargin(0)
+ gridLayout.setVerticalSpacing(0)
+ gridLayout.setColumnStretch(1, 1)
+ hBoxLayout = gridLayout.itemAtPosition(0, 1).layout()
+ if hBoxLayout:
+ hBoxLayout.setSpacing(0)
+
+ # Hide the Back and Forward button
+ backButton = self.findChild(QtGui.QToolButton, 'backButton')
+ if backButton: backButton.hide()
+ forwardButton = self.findChild(QtGui.QToolButton, 'forwardButton')
+ if forwardButton: forwardButton.hide()
+
+ # Hide the File Name indicators
+ fileNameLabel = self.findChild(QtGui.QLabel, 'fileNameLabel')
+ if fileNameLabel: fileNameLabel.hide()
+ fileNameEdit = self.findChild(QtGui.QLineEdit, 'fileNameEdit')
+ if fileNameEdit: fileNameEdit.hide()
+
+ # Hide the File Type indicators
+ fileTypeLabel = self.findChild(QtGui.QLabel, 'fileTypeLabel')
+ if fileTypeLabel: fileTypeLabel.hide()
+ fileTypeCombo = self.findChild(QtGui.QComboBox, 'fileTypeCombo')
+ if fileTypeCombo: fileTypeCombo.hide()
+
+ # Hide the dialog buttons
+ buttonBox = self.findChild(QtGui.QDialogButtonBox, 'buttonBox')
+ buttonBox.hide()
+
+ # Adjust the sidebar width
+ splitter = self.findChild(QtGui.QSplitter, 'splitter')
+ splitter.setSizes([0, 1])
+
+ # Simplify the Details view to List View
+ stackedWidget = splitter.widget(1).findChild(QtGui.QStackedWidget, 'stackedWidget')
+ listView = stackedWidget.widget(0).findChild(QtGui.QListView, 'listView')
+ listView.setAlternatingRowColors(True)
+ listView.setWrapping(False)
+ self.setViewMode(QtGui.QFileDialog.List)
+
+ def done(self, result):
+ pass
+
+ def sizeHint(self):
+ return QtCore.QSize(384, 150)
+
+class QCDATFileWidget(QtGui.QWidget):
+ """ QCDATFileWidget contains a line-edit to enter the file name and a file
+ selection button. It also has a combo box to choose variables once a file
+ is specified. """
+
+ FILTER = "CDAT data (*.cdms *.ctl *.dic *.hdf *.nc *.xml)"
+
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+
+ self.cdmsFile = None
+
+ # Start the layout
+ layout = QtGui.QVBoxLayout()
+ self.setLayout(layout)
+ layout.setMargin(0)
+
+ self.fileDialog = QFileDialogWidget()
+ self.fileDialog.setNameFilter(QCDATFileWidget.FILTER)
+ layout.addWidget(self.fileDialog)
+
+ # A shared layout of the bottom half
+ vbox = QtGui.QVBoxLayout()
+ vbox.setMargin(0)
+ vbox.setSpacing(0)
+ layout.addLayout(vbox)
+ self.fileVarLayout = vbox
+
+ # Create the bottom horizontal indicator
+ hbox = QtGui.QHBoxLayout()
+
+ self.drawerButton = QtGui.QToolButton()
+ self.drawerButton.setArrowType(QtCore.Qt.UpArrow)
+ self.drawerButton.setAutoRaise(True)
+ self.drawerButton.setIconSize(QtCore.QSize(8, 8))
+ hbox.addWidget(self.drawerButton)
+
+ hline = QtGui.QFrame()
+ hline.setFrameStyle(QtGui.QFrame.HLine | QtGui.QFrame.Sunken)
+ hbox.addWidget(hline)
+
+ self.connect(self.drawerButton, QtCore.SIGNAL('clicked(bool)'),
+ self.toggleFileDialog)
+
+ vbox.addLayout(hbox)
+
+ # Create the file name box
+ grid = QtGui.QGridLayout()
+ grid.setHorizontalSpacing(10)
+ vbox.addLayout(grid)
+
+ # First line: File
+ fileNameLabel = QtGui.QLabel('File')
+ grid.addWidget(fileNameLabel)
+
+ hbox = QtGui.QHBoxLayout()
+ hbox.setSpacing(6)
+ self.fileNameEdit = QtGui.QLineEdit()
+ self.fileNameEdit.setToolTip('Enter file name or click on button on the right to select a file')
+ hbox.addWidget(self.fileNameEdit, 1)
+
+ self.fileSelectButton = QtGui.QToolButton()
+ self.fileSelectButton.setText('...')
+ self.fileSelectButton.setToolTip('View and select files')
+ hbox.addWidget(self.fileSelectButton)
+
+ grid.addLayout(hbox, 0, 1)
+
+ # Second line: Var
+ varNameLabel = QtGui.QLabel('Variable')
+ grid.addWidget(varNameLabel, 1, 0)
+
+ hbox = QtGui.QHBoxLayout()
+ hbox.setSpacing(6)
+
+ # Init combo box
+ self.varCombo = QtGui.QComboBox()
+ self.varCombo.setToolTip('View and select variables in file')
+ self.varCombo.setMinimumContentsLength(10)
+ comboPalette = self.varCombo.view().palette()
+ comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
+ comboPalette.setColor(QtGui.QPalette.Highlight, QtCore.Qt.blue)
+ self.varCombo.view().setPalette(comboPalette)
+
+ hbox.addWidget(self.varCombo, 1)
+
+ self.defineVarButton = QtGui.QPushButton('&Define')
+ self.defineVarButton.setToolTip('Define variable into memory')
+ hbox.addWidget(self.defineVarButton)
+
+ grid.addLayout(hbox, 1, 1)
+
+ # Connect signals
+ self.connect(self.fileDialog, QtCore.SIGNAL('filesSelected(const QStringList&)'),
+ self.filesSelected)
+ self.connect(self.fileNameEdit, QtCore.SIGNAL('returnPressed()'),
+ self.updateCDMSFile)
+ self.connect(self.fileSelectButton, QtCore.SIGNAL('clicked(bool)'),
+ self.openSelectFileDialog)
+ self.connect(self.varCombo, QtCore.SIGNAL('currentIndexChanged(const QString&)'),
+ self.variableChanged)
+ self.connect(self.defineVarButton, QtCore.SIGNAL('clicked(bool)'),
+ self.defineVariablePressed)
+
+ # Init the widget with its file dialog hidden
+ self.fileDialog.hide()
+ self.setFileName('')
+ self.varCombo.setCurrentIndex(1)
+
+ def updateSizeConstraints(self):
+ isDialogVisible = self.fileDialog.isVisible()
+ if isDialogVisible:
+ self.drawerButton.setArrowType(QtCore.Qt.UpArrow)
+ self.setMaximumHeight(16777215)
+ else:
+ self.drawerButton.setArrowType(QtCore.Qt.DownArrow)
+ self.setMaximumHeight(self.fileVarLayout.contentsRect().height())
+ self.fileSelectButton.setVisible(not isDialogVisible)
+
+ def toggleFileDialog(self, ignored=False):
+ self.fileDialog.setVisible(not self.fileDialog.isVisible())
+ self.updateSizeConstraints()
+
+ def showEvent(self, e):
+ self.updateSizeConstraints()
+ self.variableChanged(self.varCombo.currentText())
+
+ def setFileName(self, fn):
+ self.fileNameEdit.setText(fn)
+ self.updateCDMSFile()
+
+ def updateCDMSFile(self):
+ fn = str(self.fileNameEdit.text())
+ fi = QtCore.QFileInfo(fn)
+ if fi.exists():
+ self.fileDialog.setDirectory(fi.dir())
+ self.cdmsFile = cdms2.open(fn)
+ self.recordOpenFileTeachingCommand(fn)
+ # Create and update the open module
+ self.emit(QtCore.SIGNAL('createModule'), open_name)
+ self.emit(QtCore.SIGNAL('updateModule'), open_name, 'uri', fn)
+ else:
+ self.cdmsFile = None
+ self.updateVariableList()
+
+ def recordOpenFileTeachingCommand(self, file):
+ openFileComment = '\n# Open CDMS File\n'
+ varName = 'fid2'
+ command = "%s = cdms2.open('%s')\n" %(varName, file)
+
+ self.emit(QtCore.SIGNAL('recordTeachingCommand'), openFileComment)
+ self.emit(QtCore.SIGNAL('recordTeachingCommand'), command)
+
+ def filesSelected(self, files):
+ if files.count()>0:
+ self.setFileName(files[0])
+
+ def updateVariableList(self):
+ self.varCombo.clear()
+ if self.cdmsFile!=None:
+ # Add Variables sorted based on their dimensions
+ curDim = -1
+ for (dim, varId) in sorted([(len(var.listdimnames()), var.id)
+ for var in self.cdmsFile.variables.itervalues()]):
+ if dim!=curDim:
+ curDim = dim
+ count = self.varCombo.count()
+ self.varCombo.insertSeparator(count)
+ self.varCombo.model().item(count, 0).setText('%dD VARIABLES' % dim)
+ var = self.cdmsFile.variables[varId]
+ varName = var.id + ' ' + str(var.shape) + ' ['
+
+ if hasattr(var, 'long_name'):
+ varName += var.long_name
+ if hasattr(var, 'units') and var.units!='':
+ if varName[-1]!='[': varName += ' '
+ varName += var.units
+ varName += ']'
+ self.varCombo.addItem(varName, QtCore.QVariant(QtCore.QStringList(['variables', var.id])))
+
+ # Add Axis List
+ count = self.varCombo.count()
+ self.varCombo.insertSeparator(count)
+ self.varCombo.model().item(count, 0).setText('AXIS LIST')
+ for axis in self.cdmsFile.axes.itervalues():
+ axisName = axis.id + " (" + str(len(axis)) + ") - [" + axis.units + ": (" + str(axis[0]) + ", " + str(axis[-1]) + ")]"
+ self.varCombo.addItem(axisName, QtCore.QVariant(QtCore.QStringList(['axes', axis.id])))
+
+ # By default, not selecting anything
+ self.varCombo.setCurrentIndex(-1)
+
+ def openSelectFileDialog(self):
+ file = QtGui.QFileDialog.getOpenFileName(self, 'Open CDAT data file...',
+ self.fileDialog.directory().absolutePath(),
+ QCDATFileWidget.FILTER + ';;All files (*.*)')
+ if not file.isNull():
+ self.setFileName(file)
+
+ def variableChanged(self, varName):
+ if varName == '':
+ return
+
+ self.defineVarButton.setEnabled(not varName.isNull()) # Enable define button
+
+ # Send signal to setup axisList in 'quickplot' tab
+ self.emit(QtCore.SIGNAL('variableChanged'), self.getCDMSFile(),
+ self.getCDMSVariable(), 'quickplot')
+
+ def defineVariablePressed(self):
+ self.emit(QtCore.SIGNAL('defineVariableEvent'))
+
+ def getCDMSFile(self):
+ return self.cdmsFile
+
+ def getCDMSVariable(self):
+ if not self.cdmsFile is None:
+ data = self.varCombo.itemData(self.varCombo.currentIndex()).toStringList()
+ if data.count() > 0:
+ if data[0] == 'variables':
+ return getattr(self.cdmsFile, str(data[0]))[str(data[1])]
+ elif data[0] == 'axes':
+ axis = getattr(self.cdmsFile, str(data[0]))[str(data[1])]
+ var = MV2.array(axis)
+ var.setAxis(0, axis)
+ var.id = axis.id
+ return var
+ return None
+
+class QLabeledWidgetContainer(QtGui.QWidget):
+ """ Container widget for the 3 main widgets: QVariableView, QCDATFileWidget,
+ and QDefinedVariable """
+
+ def __init__(self, widget, label='', parent=None):
+ QtGui.QWidget.__init__(self, parent)
+
+ vbox = QtGui.QVBoxLayout()
+ vbox.setMargin(0)
+
+ self.label = QtGui.QLabel(label)
+ self.label.setAutoFillBackground(True)
+ self.label.setAlignment(QtCore.Qt.AlignCenter)
+ self.label.setFrameStyle(QtGui.QFrame.Panel | QtGui.QFrame.Raised)
+ vbox.addWidget(self.label, 0)
+
+ if widget!=None:
+ self.widget = widget
+ else:
+ self.widget = QtGui.QWidget()
+ vbox.addWidget(self.widget, 1)
+
+ self.setLayout(vbox)
+
+ def getWidget(self):
+ return self.widget
+
+ def event(self, e):
+ if e.type()==76: #QtCore.QEvent.LayoutRequest:
+ self.setMaximumHeight(min(self.label.height()+self.layout().spacing()+
+ self.widget.maximumHeight(), 16777215))
+ return False
+
+class QDefinedVariable(QtGui.QWidget):
+ """ QDefinedVariable contains a list of the user defined variables and allows the
+ user to apply functions on defined variables """
+
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.warningWidget = QDefVarWarningBox(self) # Popup box to warn var is already defined
+ self.quickplotItem = None
+ self.numVarsSelected = 0
+
+ # Create Layout
+ vbox = QtGui.QVBoxLayout()
+ vbox.setMargin(0)
+ self.setLayout(vbox)
+
+ # Create Toolbar and add it to the layout
+ self.createToolbar()
+ vbox.addWidget(self.toolBar)
+
+ # Create List for defined variables and add it to the layout
+ self.varList = QtGui.QListWidget()
+ self.varList.setAlternatingRowColors(True)
+ self.varList.setSelectionMode(QtGui.QAbstractItemView.MultiSelection)
+ vbox.addWidget(self.varList)
+
+ # Connect Signals
+ self.connect(self.varList, QtCore.SIGNAL('clicked(const QModelIndex&)'),
+ self.selectVariableFromListEvent)
+ self.connect(self.warningWidget, QtCore.SIGNAL('newVarID'),
+ self.addVariable)
+
+ def defineQuickplot(self, file, var):
+ """ When a user plots a variable that isn't explicitly defined a signal
+ is emitted and this function is called to define the variable under
+ the name 'quickplot'. Replace the 'quickplot' variable if it
+ already exists
+ """
+ if self.quickplotItem is None:
+ self.quickplotItem = QDefinedVariableItem(file, var, 'quickplot')
+ self.varList.addItem(self.quickplotItem)
+ else:
+ self.quickplotItem.setVariable(var)
+ self.quickplotItem.setFile(file)
+
+ def defineVariable(self, file, var, axesArgString):
+ """ Check if a variable with the same name has already been defined.
+ If so, warn user and prompt for a new variable name. Otherwise,
+ add the variable to the ListWidget
+ """
+ if self.isVariableDefined(var.id):
+ self.warningWidget.showWarning(var.id, file, var, axesArgString)
+ else:
+ self.addVariable(var.id, file, var, axesArgString)
+
+ def addVariable(self, varName, file, var, axesArgString):
+ """ Add variable into dict / list & emit signal to create
+ a tab for the variable
+ """
+ # If the variable is defined, replace existing variable, else create a new variable
+ if self.isVariableDefined(varName):
+ item = self.getItem(varName)
+ item.setVariable(var)
+ item.setFile(file)
+ else:
+ item = QDefinedVariableItem(file, var, varName)
+ self.varList.addItem(item)
+
+ # Recording define variable teaching command
+ self.recordDefineVariableTeachingCommand(varName, var.id, file, axesArgString)
+
+ # emit signal to QVariableView to create a new axisList / tab
+ self.emit(QtCore.SIGNAL('setupDefinedVariableAxes'), file, var, varName)
+
+ def selectVariableFromListEvent(self, modelIndex):
+ """ Update the number next to the selected defined variable and
+ send a signal to QVariableView to display the selected variable
+ """
+ item = self.varList.item(modelIndex.row())
+ selectedItems = self.varList.selectedItems()
+
+ # If the item is unselected then change the selection str back to '--'
+ # and decrement all the numbers of the other selected vars that are
+ # less than the number of the item that was unselected
+ if item not in selectedItems:
+ unselectedNum = item.getSelectNum()
+ item.updateVariableString(None)
+ self.numVarsSelected -= 1
+
+ for item in selectedItems:
+ num = item.getSelectNum()
+ if num > unselectedNum:
+ item.updateVariableString(item.getSelectNum() - 1)
+ # If item is selected, change the selection str to a number
+ else:
+ self.numVarsSelected += 1
+ item.updateVariableString(self.numVarsSelected)
+
+ # Send signal of all selected vars to qvariableview and bring up the
+ # most recently selected variable's tab
+ var = item.getVariable()
+ cdmsFile = item.getFile()
+ selectedVars = [item.getVariable() for item in selectedItems]
+ tabName = item.getVarName()
+
+ if item.isQuickplotItem():
+ self.emit(QtCore.SIGNAL('selectDefinedVariableEvent'), 'quickplot',
+ cdmsFile, selectedVars)
+ else:
+ self.emit(QtCore.SIGNAL('selectDefinedVariableEvent'), tabName,
+ cdmsFile, selectedVars)
+
+ def isVariableDefined(self, varID):
+ """ Return true if a variable with the given id is defined (this does
+ not include 'quickplot' """
+
+ for i in range(self.varList.count()):
+ item = self.varList.item(i)
+ if varID == item.getVariable().id and not item.isQuickplotItem():
+ return True
+ return False
+
+ def getItem(self, varID):
+ """ Return the item with the defined variable with name = varID """
+ for i in range(self.varList.count()):
+ listItem = self.varList.item(i)
+ if varID == listItem.getVariable().id:
+ return listItem
+ return None
+
+ def recordDefineVariableTeachingCommand(self, name, varName, file, axesArgString):
+ if varName in list(getattr(file, 'variables')):
+ fileID = "fid2"
+ command = '\n# Get new slab\n'
+ command += "%s = %s('%s', %s)\n" %(name, fileID, varName, axesArgString)
+
+ self.emit(QtCore.SIGNAL('recordTeachingCommand'), command)
+
+ def createToolbar(self):
+ ICONPATH = os.path.join(cdms2.__path__[0], '..', '..', '..', '..', 'bin')
+
+ # Create options bar
+ self.toolBar = QtGui.QToolBar()
+ self.toolBar.setIconSize(QtCore.QSize(16, 16))
+ actionInfo = [
+ ('edit_20.gif', 'Edit (in memory) selected defined variable.'),
+ ('save_20.gif', 'Save selected defined variable to a netCDF file.'),
+ ('info_20.gif', 'Display selected defined variable information.'),
+ ('editdelete_20.gif', 'Move selected defined variable(s) to trashcan for disposal.'),
+ ('recycle_20.gif', 'Move [ALL] defined variables to trashcan for disposal.'),
+ ('log_20.gif', 'Logged information about the defined variables.'),
+ ('trashcan_empty_20.gif', 'Defined variable items that can be disposed of permanetly or restored.'),
+ ]
+
+ for info in actionInfo:
+ icon = QtGui.QIcon(os.path.join(ICONPATH, info[0]))
+ action = self.toolBar.addAction(icon, '')
+ action.setStatusTip(info[1])
+ action.setToolTip(info[1])
+ self.toolBar.addSeparator()
+
+ self.opButton = QtGui.QToolButton()
+ self.opButton.setText('Ops')
+
+ # Create Operations Menu
+ menu = QtGui.QMenu(self)
+ grid = QtGui.QGridLayout()
+ grid.setMargin(0)
+ grid.setSpacing(0)
+ menu.setLayout(grid)
+ opDefs =[
+ ['Add a number or two (or more)\nselected Defined Variables.\n(Can be used as "or")','add.gif','add'],
+ ['Subtract a number or two (or more)\nselected Defined Variables.','subtract.gif','subtract'],
+ ['Multiply a number or two (or more)\nselected Defined Variables.\n(Can be used as "and")','multiply.gif','multiply'],
+ ['Divide a number or two (or more)\nselected Defined Variables.','divide.gif','divide'],
+ ['"Grows" variable 1 and variable 2 so that they end up having the same dimensions\n(order of variable 1 plus any extra dims)','grower.gif','grower'],
+ ['Spatially regrid the first selected Defined Variable\nto the second selected Defined Variable.','regrid.gif','regrid'],
+ ['Mask variable 2 where variable 1 is "true".','mask.gif','mask'],
+ ['Get variable mask','getmask.gif','getmask'],
+ ['Return true where variable 1 is less than variable 2 (or number)','less.gif','less'],
+ ['Return true where variable 1 is greater than variable 2 (or number)','greater.gif','greater'],
+ ['Return true where variable 1 is equal than variable 2 (or number)','equal.gif','equal'],
+ ['Return not of variable','not.gif','not'],
+ ['Compute the standard deviation\n(over first axis)','std.gif','std'],
+ ['Power (i.e., x ** y) of the most recently\nselected two Defined Variables, where\nx = variable 1 and y = variable 2 or float number.','power.gif','power'],
+ ['Exp (i.e., e ** x) of the most recently\nselected Defined Variable.','exp.gif','exp'],
+ ['Log (i.e., natural log) of the most recently\nselected Defined Variable.','mlog.gif','log'],
+ ['Base10 (i.e., 10 ** x) of the most recently\nselected Defined Variable.','base10.gif','base10'],
+ ['Log10 (i.e., log base 10) of the most\nrecently selected Defined Variable. ','mlog10.gif','log10'],
+ ['Inverse (i.e., 1/x) of the most recently\nselected Defined Variable.','inverse.gif','inverse'],
+ ['Abs (i.e., absolute value of x) of the most\nrecently selected Defined Variable.','fabs.gif','fabs'],
+ ['Sine (i.e., sin) of the most recently\nselected Defined Variable.','sin.gif','sin'],
+ ['Hyperbolic sine (i.e., sinh) of the most recently\nselected Defined Variable.','sinh.gif','sinh'],
+ ['Cosine (i.e., cos) of the most recently\nselected Defined Variable.','cos.gif', 'cos'],
+ ['Hyperbolic cosine (i.e., cosh) of the most recently\nselected Defined Variable.','cosh.gif','cosh'],
+ ['Tangent (i.e., tan) of the most recently\nselected Defined Variable.','tan.gif','tan'],
+ ['Hyperbolic tangent (i.e., tanh) of the most recently\nselected Defined Variable.','tanh.gif','tanh'],
+ ]
+ self.opActions = []
+ for i in xrange(len(opDefs)):
+ action = QtGui.QAction(QtGui.QIcon(os.path.join(ICONPATH, opDefs[i][1])), opDefs[i][2], menu)
+ action.setStatusTip(opDefs[i][0])
+ action.setToolTip(opDefs[i][0])
+ self.opActions.append(action)
+ b = QtGui.QToolButton()
+ b.setDefaultAction(action)
+ grid.addWidget(b, i/2, i%2)
+
+ self.opButton.setMenu(menu)
+ self.opButton.setPopupMode(QtGui.QToolButton.InstantPopup)
+ self.connect(self.opButton, QtCore.SIGNAL('clicked(bool)'), self.opButton.showMenu)
+
+ self.toolBar.addWidget(self.opButton)
+
+class QDefinedVariableItem(QtGui.QListWidgetItem):
+ """ Item to be stored by QDefinedVariable's list widget """
+
+ def __init__(self, cdmsFile, variable, varName, parent=None):
+ QtGui.QListWidgetItem.__init__(self, parent)
+ self.varName = varName # This is also the tabname
+ self.cdmsFile = cdmsFile
+ self.variable = variable
+
+ self.updateVariableString()
+
+ def getVariable(self):
+ return self.variable
+
+ def getVarName(self):
+ return self.varName
+
+ def getFile(self):
+ return self.cdmsFile
+
+ def getSelectNum(self):
+ return self.selectNum
+
+ def isQuickplotItem(self):
+ return self.varName == 'quickplot'
+
+ def updateVariableString(self, num=None):
+ """ updateVariableString(num: int)
+
+ Update the variable string that is shown to the user in the list.
+ format = '-- variableName (shape)', where num is the selection number
+ """
+ if num is None:
+ self.selectNum = -1
+ numString = '-- '
+ elif 0 < num < 10:
+ self.selectNum = num
+ numString = "-%s " % num
+ else:
+ self.selectNum = num
+ numString = "%s " % num
+
+ varString = numString + self.varName + ' ' + str(self.variable.shape)
+ self.setData(0, QtCore.QVariant(QtCore.QString(varString)))
+
+ def setFile(self, cdmsFile):
+ self.cdmsFile = cdmsFile
+
+ def setVariable(self, variable):
+ """ Set the variable and update the variable string that is shown to the
+ user in the list
+ """
+ self.variable = variable
+ self.updateVariableString()
+
+class QDefVarWarningBox(QtGui.QDialog):
+ """ Popup box to warn a user that a variable with same name is already
+ defined. Contains a line edit to allow a user to enter a new variable
+ name or to replace the existing defined variable """
+
+ def __init__(self, parent=None):
+ QtGui.QDialog.__init__(self, parent)
+ self.varID = None
+
+ # Init layout
+ vbox = QtGui.QVBoxLayout()
+ hbox = QtGui.QHBoxLayout()
+ hbox.setDirection(QtGui.QBoxLayout.RightToLeft)
+ vbox.setSpacing(10)
+
+ # Add LineEdit
+ self.text = QtGui.QLabel()
+ self.lineEdit = QtGui.QLineEdit()
+
+ # Add OK / Cancel Buttons
+ okButton = QtGui.QPushButton('OK')
+ cancelButton = QtGui.QPushButton('Cancel')
+ hbox.addWidget(cancelButton)
+ hbox.addWidget(okButton)
+
+ vbox.addWidget(self.text)
+ vbox.addWidget(self.lineEdit)
+ vbox.addLayout(hbox)
+ self.setLayout(vbox)
+
+ # Connect Signals
+ self.connect(okButton, QtCore.SIGNAL('pressed()'), self.okPressedEvent)
+ self.connect(cancelButton, QtCore.SIGNAL('pressed()'), self.close)
+ self.connect(self.lineEdit, QtCore.SIGNAL('returnPressed()'), self.okPressedEvent)
+
+ def showWarning(self, varID, file, var, axesArgString):
+ """ Show warning message and prompt user for a new variable name. Or use
+ the same var name to replace the existing defined variable """
+
+ self.varID = varID
+ self.file = file
+ self.var = var
+ self.axesArgString = axesArgString
+
+ message = "'%s' has already been defined. Enter a new variable name \n or press 'OK' to replace '%s'" %(varID, varID)
+ self.text.setText(message)
+ self.lineEdit.setText(varID)
+
+ self.open()
+
+ def okPressedEvent(self):
+ self.varID = self.lineEdit.text() # get the user entered variable name
+ self.close()
+
+ # Emit signal to QDefinedVar to indicate it's ok to add the variable to defined list
+ self.emit(QtCore.SIGNAL('newVarID'),
+ self.varID, self.file, self.var, self.axesArgString)
+
+class QSliderCombo(QtGui.QWidget):
+ """ Widget containing min slider, max slider, min label, max label, and a
+ corresponding combo box. The comboBox, labels, sliders must always be in
+ sync with each other """
+
+ def __init__(self, axis, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.isTime = axis.isTime()
+ self.indexMode = False
+ self.startIndex = 0
+
+ # Init Layout
+ hbox = QtGui.QHBoxLayout()
+ vbox = QtGui.QVBoxLayout()
+ vbox.setSpacing(0)
+ vbox.setMargin(0)
+ self.setLayout(hbox)
+
+ # Init combo box
+ self.axisCombo = QAxisComboWidget()
+ hbox.addWidget(self.axisCombo)
+
+ # Init sliders
+ hbox.addLayout(vbox)
+ self.topSlider = QtGui.QSlider(QtCore.Qt.Horizontal)
+ self.bottomSlider = QtGui.QSlider(QtCore.Qt.Horizontal)
+ vbox.addWidget(self.topSlider)
+ vbox.addWidget(self.bottomSlider)
+
+ # Init axis slider value labels
+ self.bottomLabel = QtGui.QLabel('To', self)
+ self.topLabel = QtGui.QLabel('From', self)
+ hbox = QtGui.QHBoxLayout()
+ hbox.addWidget(self.topLabel)
+ hbox.addWidget(self.bottomLabel)
+ vbox.addLayout(hbox)
+
+ # Initialize the sliders' and comboBox's values
+ self.initAxisValues(axis)
+ self.setSlidersMinMax()
+ self.topSlider.setValue(self.minIndex)
+ self.bottomSlider.setValue(self.maxIndex)
+ self.axisCombo.initValues(self.axisValues)
+
+ # Connect Signals
+ self.connect(self.topSlider, QtCore.SIGNAL('valueChanged (int)'),
+ self.updateMin)
+ self.connect(self.bottomSlider, QtCore.SIGNAL('valueChanged (int)'),
+ self.updateMax)
+ self.connect(self.axisCombo,
+ QtCore.SIGNAL('axisComboMinValueChanged (int)'),
+ self.updateTopSlider)
+ self.connect(self.axisCombo,
+ QtCore.SIGNAL('axisComboMaxValueChanged (int)'),
+ self.updateBottomSlider)
+
+ def initAxisValues(self, axis):
+ """ Initialize list containing the axis values and set the top slider /
+ combobox value to be the min value and the bottom slider / combobox
+ value to be the max value"""
+
+ if (axis != None):
+ if self.isTime:
+ self.axisValues = [repr(t.tocomponent())
+ for t in axis.asRelativeTime()]
+ else:
+ self.axisValues = axis.getValue()
+ else:
+ raise TypeError("Error: axis is not defined")
+
+ self.axisIndices = range(len(self.axisValues))
+ self.updateMin(0)
+ self.updateMax(len(self.axisValues) - 1)
+
+ def setStartIndex(self, index):
+ self.startIndex = index
+
+ def setIndexMode(self, mode):
+ """ Set the indexMode to True or False. If indexMode is True the widget
+ will display indices. If indexMode is False the widget will display
+ actual values """
+ self.indexMode = mode
+
+ def setSlidersMinMax(self):
+ self.topSlider.setMinimum(self.minIndex)
+ self.bottomSlider.setMinimum(self.minIndex)
+ self.topSlider.setMaximum(self.maxIndex)
+ self.bottomSlider.setMaximum(self.maxIndex)
+
+ def updateMin(self, minIndex=None):
+ """ Set min value, update the slider label and the comboBox line edit
+ to show the new min value"""
+
+ if not minIndex is None:
+ self.minIndex = minIndex
+
+ if (self.indexMode == True):
+ minValue = self.minIndex + self.startIndex
+ else:
+ minValue = self.axisValues[self.minIndex]
+
+ self.topLabel.setText(str(minValue))
+ self.axisCombo.setMinValue(minValue)
+
+ def updateMax(self, maxIndex=None):
+ """ Set max value, update the slider label and the comboBox line edit
+ to show the new max value"""
+
+ if not maxIndex is None:
+ self.maxIndex = maxIndex
+
+ if (self.indexMode == True):
+ maxValue = self.maxIndex + self.startIndex
+ else:
+ maxValue = self.axisValues[self.maxIndex]
+
+ self.bottomLabel.setText(str(maxValue))
+ self.axisCombo.setMaxValue(maxValue)
+
+ def updateTopSlider(self, index):
+ self.minIndex = index
+ self.topSlider.setValue(index)
+
+ def updateBottomSlider(self, index):
+ self.maxIndex = index
+ self.bottomSlider.setValue(index)
+
+ def replaceComboBoxValues(self, values):
+ self.axisCombo.replaceComboBoxValues(values)
+
+ def getAxisIndices(self):
+ return self.axisIndices
+
+ def getAxisValues(self):
+ return self.axisValues
+
+ def getCurrentValues(self):
+ return (self.axisValues[self.minIndex], self.axisValues[self.maxIndex])
+
+ def getCurrentValuesAsStr(self):
+ if self.isTime:
+ return "('%s', '%s')" % (self.axisValues[self.minIndex],
+ self.axisValues[self.maxIndex])
+ else:
+ return "(%s, %s)" % (self.axisValues[self.minIndex],
+ self.axisValues[self.maxIndex])
+
+ def numValues(self):
+ return len(self.axisValues)
+
+ def getIndex(self):
+ return (self.minIndex, self.maxIndex)
+
+class QAxis(QtGui.QWidget):
+ """ Axis widget containing: a button + popup-menu for modifying an axis, combobox
+ and sliders for setting axis values, and a function def button + popup-menu """
+
+ def __init__(self, axis, axisName, axisIndex, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.myParent = parent
+ self.axis = axis
+ self.axisName = axisName # Axis name including the label
+ self.axisIndex = axisIndex
+
+ hbox = QtGui.QHBoxLayout()
+ hbox.setSpacing(0)
+ hbox.setMargin(0)
+ self.sliderCombo = QSliderCombo(axis, self)
+ hbox.addWidget(self.sliderCombo)
+ self.setLayout(hbox)
+
+ # These buttons aren't added to the layout here, instead they are added
+ # in QAxisList which has a grid layout so they can line up properly
+ self.axisOperationsButton = self.createAxisOperationsButtonAndMenu()
+ self.axisButton = self.createAxisButtonAndMenu()
+
+ # Connect signals such that when the value of the axis slider is changed,
+ # a signal will be emitted to update the value in the corresponding
+ # Vistrails 'Variable' or 'Quickplot' box.
+ self.connect(self.sliderCombo.topSlider,
+ QtCore.SIGNAL('valueChanged (int)'),
+ parent.setVistrailsVariableAxes)
+ self.connect(self.sliderCombo.bottomSlider,
+ QtCore.SIGNAL('valueChanged (int)'),
+ parent.setVistrailsVariableAxes)
+
+ def createAxisOperationsButtonAndMenu(self):
+ """ Initialize the button to the right of the axis sliders and it's menu
+ with operations: def, sum, avg, wgt, gtm, awt, std
+ """
+ button = QtGui.QToolButton()
+ menu = QtGui.QMenu(self)
+
+ opDefs = ['def default axis points',
+ 'sum summation of selected axis points',
+ 'avg average of selected axis points',
+ 'wgt weighted average of selected axis points',
+ 'awt altered weighted average of selected axis points',
+ 'gtm geometrical mean of selected axis points',
+ 'std standard deviation of selected axis points',]
+
+ for op in opDefs:
+ action = menu.addAction(op)
+ self.connect(action, QtCore.SIGNAL('triggered ()'),
+ self.selectAxesOperationEvent)
+
+ button.setText(' def ')
+ button.setMenu(menu)
+ button.setPopupMode(QtGui.QToolButton.InstantPopup)
+
+ # Connect Signals
+ self.connect(button, QtCore.SIGNAL('clicked(bool)'),
+ button.showMenu)
+
+ return button
+
+ def selectAxesOperationEvent(self):
+ """ Event handler for when a user selects an operation from the
+ axes operations popup menu (located to right of the sliders):
+ sum, avg, awt, gtm, etc ...
+ """
+ # Get the operation selected by getting the text of who sent the signal
+ op = self.sender().text()[:3] # def, sum, avg, wgt, awt, gtm, or std
+
+ # If the operation is 'awt' ask the user for an alternate weight var
+ if op == 'awt':
+ definedVars = self.myParent.getParent().getDefinedVars()
+ QReplaceAxisWeightsDialog(definedVars, self).show()
+ return
+
+ # Set button text to what the user selected
+ self.axisOperationsButton.setText(" %s " % op)
+
+ # Update the vistrails 'Variable' module's axesOperations input
+ axesOperations = self.myParent.getAxesOperations()
+ varWidget = self.myParent.getParent()
+ varWidget.emit(QtCore.SIGNAL('updateModule'),
+ self.myParent.currentTabName(), 'axesOperations',
+ str(axesOperations))
+
+ def createAxisButtonAndMenu(self):
+ """ createAxisButtonAndMenu(axesNames: list)
+
+ Initialize the button to the left of the sliders / combo box and
+ it's menu which currently has options: index, raw, get axis values,
+ get axis weight values, replace axis values, re-order dimensions.
+ """
+ axisMenu = QtGui.QMenu(self)
+ menuVbox = QtGui.QVBoxLayout()
+ axisMenu.setLayout(menuVbox)
+
+
+ # Add index options to the menu
+ indexAction = axisMenu.addAction(self.axis.id + '_index')
+ indexAction.setCheckable(True)
+
+ # Add raw index option if this dimension is time
+ if self.axis.isTime():
+ rawIndexAction = axisMenu.addAction(self.axis.id + '_raw')
+ rawIndexAction.setCheckable(True)
+
+ axisMenu.addSeparator()
+
+ # Add axis value options to the menu
+ axisOptions = ['Get Axis Values', 'Get Axis Weight Values',
+ 'Replace Axis Values']
+ getAxisValuesAction = axisMenu.addAction(axisOptions[0])
+ getAxisWeightValuesAction = axisMenu.addAction(axisOptions[1])
+ replaceAxisValuesAction = axisMenu.addAction(axisOptions[2])
+
+ # Add 're-order dimensions' option to menu
+ axisMenu.addSeparator()
+ reorderAxesMenu = axisMenu.addMenu('Re-Order Dimensions')
+ axesNames = self.myParent.getAxesNames()
+ for axisID in axesNames:
+ reorderAction = reorderAxesMenu.addAction(axisID)
+ self.connect(reorderAction, QtCore.SIGNAL('triggered()'),
+ self.reorderAxesEvent)
+
+ # Create axis button
+ axisButton = QtGui.QToolButton()
+ axisButton.setMenu(axisMenu)
+ axisButton.setPopupMode(QtGui.QToolButton.InstantPopup)
+
+ # Connect signals emitted by the axis button menu
+ axisButton.connect(axisButton, QtCore.SIGNAL('clicked(bool)'),
+ axisButton.showMenu)
+ self.connect(indexAction, QtCore.SIGNAL('toggled (bool)'),
+ self.setIndexModeEvent)
+ self.connect(getAxisValuesAction, QtCore.SIGNAL('triggered ()'),
+ self.getAxisValuesEvent)
+ self.connect(replaceAxisValuesAction, QtCore.SIGNAL('triggered ()'),
+ self.getReplacementAxisValuesEvent)
+ self.connect(getAxisWeightValuesAction, QtCore.SIGNAL('triggered ()'),
+ self.getAxisWeightValuesEvent)
+
+ if self.axis.isTime():
+ self.connect(rawIndexAction, QtCore.SIGNAL('toggled (bool)'),
+ self.setRawIndexModeEvent)
+ # Dont allow _raw and _index to be checked simultaneously
+ self.connect(rawIndexAction, QtCore.SIGNAL('toggled (bool)'),
+ lambda : indexAction.setChecked(False))
+ self.connect(indexAction, QtCore.SIGNAL('toggled (bool)'),
+ lambda : rawIndexAction.setChecked(False))
+
+ return axisButton
+
+ def reorderAxesEvent(self):
+ """ reorderAxesEvent is called when the user selects 're-order
+ dimensions from the axis button. Swap this axis with the selected axis
+ and update the vistrails' Variable module's 'axes' input
+ """
+ axisB = self.sender().text()
+ self.myParent.swapAxes(self.axisName, axisB)
+ self.myParent.setVistrailsVariableAxes()
+
+ def getReplacementAxisValuesEvent(self):
+ """ getReplacementAxisValuesEvent is called when the user selects
+ 'Replace Axis Values' Show a dialog box which asks the user to select
+ a defined variable for replacement axis values
+ """
+ definedVars = self.myParent.getParent().getDefinedVars()
+ QReplaceAxisValuesDialog(definedVars, self).show()
+
+ def replaceAxisValues(self, newValuesVar):
+ """ replaceAxisValues(newValuesVar: tvariable)
+
+ replaceAxisValues is called after the user selects 'Replace Axis Values'
+ and selects a replacement variable from the popup dialog. This method
+ replaces the axis' values with 'newValuesVar'
+ """
+ # TODO doesn't work
+ var = self.myParent.getVar()
+ axis = var.getAxis(self.axisIndex)
+ axis[:] = newValuesVar.astype(axis[:].dtype.char).filled()
+ axis.setBounds(None)
+ self.myParent.setVar(var)
+
+ # Generate teaching command string
+ # TODO
+
+ def getAxisWeightValuesEvent(self):
+ """ getAxisWeightValuesEvent is called when the user selects 'Get Axis
+ Weight Values' from the axis button menu. This method will create and
+ define a new variable / tab with the axis' weight values
+ """
+ var = self.myParent.getVar()
+ axisVar = genutil.getAxisWeightByName(var, self.axis.id)
+ axisVar.id = var.id +'_' + self.axis.id + '_weight'
+
+ # Generate teaching command string
+ fileID = 'fid2'
+ teachingCommand = "\n## Getting axis %s\n" % self.axis.id
+ teachingCommand += "%s = genutil.getAxisWeightByName(%s[\"%s\"], \"%s\")\n" % (axisVar.id, fileID, var.id, self.axis.id)
+ teachingCommand += "%s.id = \"%s\"\n" % (axisVar.id, axisVar.id)
+
+ # Record teaching commands associate 'get axis weight values' and
+ # define a new variable/tab with only the axis' weight values
+ self.myParent.defineVarAxis(axisVar, teachingCommand)
+
+ def getAxisValuesEvent(self):
+ """ getAxisValuesEvent is called when the user selects 'Get Axis
+ Values' from the axis button menu. This method will create and
+ define a new variable / tab with the axis' values
+ """
+ varID = self.myParent.getVar().id
+ axisVar = MV2.array(self.axis)
+ axisVar.setAxis(0, self.axis)
+ axisVar.id = varID +'_' + self.axis.id + '_axis'
+
+ # Generate teaching command string
+ fileID = 'fid2'
+ teachingCommand = "\n## Getting axis %s\n" % self.axis.id
+ teachingCommand += "%s = MV2.array(%s[\"%s\"].getAxisList(axes = \"%s\")[0][:])\n" % (axisVar.id, fileID, varID, self.axis.id)
+ teachingCommand += "%s.setAxis(0, %s[\"%s\"].getAxisList(axes = \"%s\")[0])\n" % (axisVar.id, fileID, varID, self.axis.id)
+ teachingCommand += "%s.id = \"%s\"\n" % (axisVar.id, axisVar.id)
+
+ # Record teaching commands associate 'get axis values' and
+ # define a new variable/tab with only the axis' values
+ self.myParent.defineVarAxis(axisVar, teachingCommand)
+
+ def setIndexModeEvent(self, indexMode):
+ """ setIndexModeEvent(indexMode: bool)
+
+ If indexMode is True then set the combobox and
+ slider values to be indices. If indexMode is False then set the
+ combobox and slider values to be the actual axis values.
+ """
+ axisIndices = self.sliderCombo.getAxisIndices()
+ axisValues = self.sliderCombo.getAxisValues()
+
+ self.sliderCombo.setIndexMode(indexMode)
+ if (indexMode == True):
+ self.sliderCombo.setStartIndex(0)
+ self.sliderCombo.replaceComboBoxValues(axisIndices)
+ else:
+ self.sliderCombo.replaceComboBoxValues(axisValues)
+
+ self.sliderCombo.updateMax()
+ self.sliderCombo.updateMin()
+
+ def setRawIndexModeEvent(self, rawIndexMode):
+ """ setRawIndexModeEvent(rawIndexMode: bool)
+
+ If rawIndexMode is True then set the combobox and
+ slider values to be indices since january 1st 1979.
+ otherwise set the combobox and slider values to be the actual axis
+ values.
+ """
+ self.sliderCombo.setIndexMode(rawIndexMode)
+ axisValues = self.sliderCombo.getAxisValues()
+ axisIndices = self.sliderCombo.getAxisIndices()
+
+ if (rawIndexMode == True):
+ # Calculate months since jan 1st, 1979
+ firstTimeEntry = axisValues[0]
+ match = re.compile('(\d\d\d\d)(-)(.+)(-)(.*)').match(firstTimeEntry)
+
+ if match is None:
+ raise NameError("Invalid time string: %s" % firstTimeEntry)
+
+ year = int(match.group(1))
+ month = int(match.group(3))
+ monthsSince1979 = 12 * (year - 1979) + (month - 1)
+ self.sliderCombo.setStartIndex(monthsSince1979)
+
+ # Add months since jan 1979 to indices
+ rawIndices = map(lambda x: x + monthsSince1979, axisIndices)
+ self.sliderCombo.replaceComboBoxValues(rawIndices)
+ else:
+ self.sliderCombo.replaceComboBoxValues(axisValues)
+
+ self.sliderCombo.updateMax()
+ self.sliderCombo.updateMin()
+
+ def sumAxisPoints(self, var):
+ """ Update the variable by applying the sum operation to the given
+ axis. Note this function is called only when a variable is defined.
+ """
+ varID = var.id
+ var = cdutil.averager(var, axis="(%s)" % self.axis.id, weight='equal',
+ action='sum')
+ var.id = varID
+ return var
+
+ def avgAxisPoints(self, var):
+ """ Update the variable by applying the avg operation to the given
+ axis.
+ """
+ varID = var.id
+ var = cdutil.averager(var, axis="(%s)" % self.axis.id, weight='equal')
+ var.id = varID
+ return var
+
+ def weightedAvgAxisPoints(self, var):
+ """ Update the variable by applying the weighted avg operation to the
+ the given axis.
+ """
+ varID = var.id
+ var = cdutil.averager(var, axis="(%s)" % self.axis.id)
+ var.id = varID
+ return var
+
+ def geoMeanAxisPoints(self, var):
+ """ Update the variable by applying the geometrical mean operation to
+ the given axis.
+ """
+ varID = var.id
+ var = genutil.statistics.geometricmean(var, axis="(%s)" % self.axis.id)
+ var.id = varID
+ return var
+
+ def stdAxisPoints(self, var):
+ """ Update the variable by applying the standard deviation operation to
+ the given axis.
+ """
+ varID = var.id
+ var = genutil.statistics.std(var, axis="(%s)" % self.axis.id)
+ var.id = varID
+ return var
+
+ def alteredWeightedAvgAxisPoints(self, var):
+ """ Update the variable by applying the altered weighted avg operation
+ to the given axis.
+ """
+ varID = var.id
+ var = cdutil.averager(var, axis="(%s)" % self.axis.id,
+ weight=self.alteredWeightsVar.filled())
+ var.id = varID
+ return var
+
+ def setAlteredWeights(self, var):
+ self.alteredWeightsVar = var
+ self.axisOperationsButton.setText(' awt ')
+
+ def setAxisButtonText(self, name):
+ self.axisButton.setText(name + ' ')
+
+ def getCurrentValues(self):
+ return self.sliderCombo.getCurrentValues()
+
+ def getCurrentValuesAsStr(self):
+ return self.sliderCombo.getCurrentValuesAsStr()
+
+ def numValues(self):
+ return self.sliderCombo.numValues()
+
+ def getIndexes(self):
+ return self.sliderCombo.getIndexes()
+
+ def getID(self):
+ return self.axis.id
+
+ def getAxisOperationsButton(self):
+ return self.axisOperationsButton
+
+ def getAxisButton(self):
+ return self.axisButton
+
+ def getAlteredWeightsVar(self):
+ return self.alteredWeightsVar
+
+class QAxisComboWidget(QtGui.QComboBox):
+ """ Specialized ComboBox widget for Axis Values listing / selecting the
+ axis' values. """
+
+ def __init__(self, parent=None):
+ QtGui.QComboBox.__init__(self, parent)
+ self.setMin = False
+ self.stride = 1 # TODO : Changing the stride does nothing as of now
+ self.minValue = 0
+ self.maxValue = 0
+
+ self.setMouseTracking(True)
+ self.setEditable(True)
+ self.setMinimumContentsLength(10)
+ self.setCurrentIndex(1)
+ self.setMaxVisibleItems(10)
+ self.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToMinimumContentsLengthWithIcon)
+
+ # Set highlighted text color to gray instead of default white
+ comboPalette = self.view().palette()
+ comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.darkGray)
+ self.view().setPalette(comboPalette)
+
+ # Connect Signals
+ self.connect(self, QtCore.SIGNAL('currentIndexChanged(const QString&)'),
+ self.valueChangedEvent)
+
+ def initValues(self, axisValues):
+ """ initValues(axisValues: list)
+
+ Initialize the values in the combo box from a list of axis values.
+ """
+ for axisValue in axisValues:
+ self.addItem(str(axisValue),
+ QtCore.QVariant(QtCore.QStringList(['variables', str(axisValue)])))
+
+ self.minValue = axisValues[0]
+ self.maxValue = axisValues[-1]
+ self.setLineEditText() # Set lineedit text to be valueA : valueB by stride
+
+ def replaceComboBoxValues(self, axisValues):
+ """ replaceComboBoxValues(axisValues: list)
+
+ Replace the values in the comboBox with new values: raw indices, indices
+ or actual values.
+ """
+ for i in range(len(axisValues)):
+ data = QtCore.QVariant(QtCore.QStringList(['variables', str(axisValues[i])]))
+ self.setItemData(i, data)
+ self.setItemText(i, str(axisValues[i]))
+
+ self.minValue = axisValues[0]
+ self.maxValue = axisValues[-1]
+ self.setLineEditText()
+
+ def setMinValue(self, minValue):
+ self.minValue = minValue
+ self.setLineEditText()
+
+ def setMaxValue(self, maxValue):
+ self.maxValue = maxValue
+ self.setLineEditText()
+
+ def setLineEditText(self):
+ """ Set the comboBox's lineEdit to show: minValue : maxValue by stride
+ """
+ self.setEditText(str(self.minValue) + " : " + str(self.maxValue) + " by "
+ + str(self.stride))
+ self.lineEdit().setCursorPosition(0)
+
+ def valueChangedEvent(self, axisValue):
+ """ valueChangedEvent(axisValue: str)
+
+ Event handler for when a user changes a combobox value by selecting a
+ value or entering a value into the line edit. Update the corresponding
+ slider / label with the same value
+ """
+ index = self.findData(QtCore.QVariant(QtCore.QStringList(['variables', str(axisValue)])))
+
+ # If user entered a value into the lineEdit.
+ if index == -1:
+ self.updateValueFromLineEditText(axisValue)
+ return
+
+ # If user selected a value from the combo box.
+ # Selecting values from the combo box will alternate between setting the
+ # min and max values & emit a signal to update corresponding slider
+ if (self.setMin == True):
+ self.setMin = False
+ self.minValue = axisValue
+ self.emit(QtCore.SIGNAL('axisComboMinValueChanged (int)'), self.currentIndex())
+ else:
+ self.setMin = True
+ self.maxValue = axisValue
+ self.emit(QtCore.SIGNAL('axisComboMaxValueChanged (int)'), self.currentIndex())
+
+ self.setLineEditText()
+
+ def updateValueFromLineEditText(self, axisValue):
+ """ updateValueFromLineEditText(axisValue: str)
+
+ Check if the user entered a valid string in the line edit and if the
+ values exist. If it is valid & the values exist, set the values in the
+ corresponding slidingAxisWidget so the combobox and sliders match.
+ """
+ # The lineEdit text must have format "ValueA : ValueB by Stride"
+ pattern = re.compile("(.*)\s:\s(.*)\sby\s(\w*)")
+ result = pattern.match(axisValue)
+
+ # If invalid string format, do nothing
+ if (result == None):
+ return
+
+ # Set stride if it is a valid digit
+ # Stride functionality not implemented yet
+ if (str(result.group(3)).isdigit() == True):
+ self.stride = result.group(3)
+
+ minValue = result.group(1)
+ maxValue = result.group(2)
+ minIndex = self.findData(QtCore.QVariant(QtCore.QStringList(['variables', str(minValue)])))
+ maxIndex = self.findData(QtCore.QVariant(QtCore.QStringList(['variables', str(maxValue)])))
+
+ # If min or max values are not in the list of values do nothing
+ if (minIndex == -1 or maxIndex == -1):
+ return
+
+ # LineEdit string is valid, emit signal to update the corresponding axis sliders
+ self.emit(QtCore.SIGNAL('axisComboMinValueChanged (int)'), minIndex)
+ self.emit(QtCore.SIGNAL('axisComboMaxValueChanged (int)'), maxIndex)
+
+class QAxisList(QtGui.QWidget):
+ """ Widget containing a list of axis widgets for the selected variable """
+
+ def __init__(self, file=None, var=[], parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.axisWidgets = [] # List of QAxis widgets
+ self.axesNames = [] # List of axis names (including labels)
+ self.axisOrder = [] # List of ints to specify axes ordering
+ self.file = file # cdms file associated with the variable
+ self.var = var # variable associated with the axes
+ self.axisList = None # list of axes from the variable
+ self.myParent = parent
+
+ # Init & set the layout
+ vbox = QtGui.QVBoxLayout()
+ self.gridLayout = QtGui.QGridLayout()
+ self.gridLayout.setMargin(0)
+ self.gridLayout.setSpacing(0)
+ vbox.addLayout(self.gridLayout)
+ vbox.addStretch()
+ vbox.setSpacing(0)
+ vbox.setMargin(5)
+ self.setLayout(vbox)
+
+ def clear(self):
+ """ Remove the QAxis widgets, empty axisWidgets and axesNames lists from
+ the grid layout
+ """
+ self.gridLayout.setRowStretch(self.gridLayout.rowCount()-1, 0)
+ for i in reversed(range(self.gridLayout.count())):
+ item = self.gridLayout.itemAt(i)
+ axis = item.widget()
+ if axis:
+ self.gridLayout.removeWidget(axis)
+ axis.hide()
+ axis.deleteLater()
+ else:
+ self.gridLayout.removeItem(item)
+
+ self.axisWidgets = []
+ self.axesNames = []
+
+ def setupVariableAxes(self):
+ """ Iterate through the variable's axes and create and initialize an Axis
+ object for each axis.
+ """
+ if self.var is None:
+ return
+
+ if (self.axisList is None):
+ self.axisList = self.var.getAxisList()
+ self.axisOrder = range(len(self.axisList))
+
+ self.clear()
+ self.setAxesNames()
+
+ # Iterate through the variables axes & init each axis widget
+ axisIndex = 0
+ for axis, axisName in zip(self.axisList, self.axesNames):
+ # Create the axis widget
+ axisWidget = QAxis(axis, axisName, axisIndex, self)
+ axisWidget.setAxisButtonText(axisName)
+ self.axisWidgets.append(axisWidget)
+
+ # Setup the layout for each axis
+ row = self.gridLayout.rowCount()
+ self.gridLayout.addWidget(axisWidget.getAxisButton(), row, 0)
+ self.gridLayout.addWidget(axisWidget, row, 1)
+ self.gridLayout.addWidget(axisWidget.getAxisOperationsButton(), row, 2)
+
+ # Create separator line between each axis widget
+ vline = QtGui.QFrame()
+ vline.setFrameStyle(QtGui.QFrame.HLine | QtGui.QFrame.Sunken)
+ self.gridLayout.addWidget(vline, row+1, 0, 1,
+ self.gridLayout.columnCount())
+
+ axisIndex += 1
+
+ self.gridLayout.setRowStretch(self.gridLayout.rowCount(), 1)
+
+ def defineVarAxis(self, var, teachingCommand):
+ self.myParent.defineVarAxis(var, teachingCommand)
+
+ def swapAxes(self, axisA, axisB):
+ """ swapAxes(axisA: QAxis, axisB: QAxis)
+
+ swap the axis widgets: axisA and axisB
+ """
+ if (axisA == axisB):
+ return
+
+ if axisA in self.axesNames and axisB in self.axesNames:
+ i = self.axesNames.index(axisA)
+ j = self.axesNames.index(axisB)
+ self.axisList[i], self.axisList[j] = self.axisList[j], self.axisList[i]
+ self.axisOrder[i], self.axisOrder[j] = self.axisOrder[j], self.axisOrder[i]
+ self.setupVariableAxes()
+
+ def execAxesOperations(self, var):
+ """ Return the updated variable by doing the 'sum', 'avg', 'wgt', 'awt',
+ 'gtm' and 'std' operations.
+ """
+ for axis in self.axisWidgets:
+ op = str(axis.getAxisOperationsButton().text()).strip()
+ if op == 'sum':
+ var = axis.sumAxisPoints(var)
+ elif op == 'avg':
+ var = axis.avgAxisPoints(var)
+ elif op == 'wgt':
+ var = axis.weightedAvgAxisPoints(var)
+ elif op == 'gtm':
+ var = axis.geoMeanAxisPoints(var)
+ elif op == 'std':
+ var = axis.stdAxisPoints(var)
+ elif op == 'awt':
+ var = axis.alteredWeightedAvgAxisPoints(var)
+ return var
+
+ # * At this point in fixing up the code
+
+ def getAxesOperationsTeachingCommands(self, varID):
+ """ Create and return the teaching commands for the axes operations:
+ def, sum, avg, wgt, awt, gtm, std
+ """
+ commands = ""
+ for axis in self.axisWidgets:
+ axisID = axis.getID()
+ op = str(axis.getAxisOperationsButton().text()).strip()
+
+ if op == 'sum':
+ commands += "%s=cdutil.averager(%s, axis='(%s)', weight='equal', action='sum')\n" % (varID, varID, axisID)
+ commands += "%s.id = '%s'\n" % (varID, varID)
+ elif op == 'avg':
+ commands += "%s=cdutil.averager(%s, axis='(%s)', weight='equal')\n" % (varID, varID, axisID)
+ commands += "%s.id = '%s'\n" % (varID, varID)
+ elif op == 'wgt':
+ commands += "%s=cdutil.averager(%s, axis='(%s)')\n" % (varID, varID, axisID)
+ commands += "%s.id = '%s'\n" % (varID, varID)
+ elif op == 'awt':
+ alteredWeightsID = axis.getAlteredWeightsVar().id
+ commands += "%s=cdutil.averager(%s, axis='(%s)', weight=%s.filled())" % (varID, varID, axisID, alteredWeightsID)
+ commands += "\n# Currently, VCDAT cannot record the altered average weight command."
+ elif op == 'gtm':
+ commands += "%s=genutil.statistics.geometricmean(%s, axis='(%s)')\n" % (varID, varID, axisID)
+ commands += "%s.id = '%s'\n" % (varID, varID)
+ elif op == 'std':
+ commands += "%s=genutil.statistics.std(%s, axis='(%s)')\n" % (varID, varID, axisID)
+ commands += "%s.id = '%s'\n" % (varID, varID)
+ return commands
+
+ def getAxesOperations(self):
+ """ Return a dict where keys are axis names, and values are the
+ operation to be done on the axis such as: def, sum, avg, etc ... """
+
+ axisOpsDict = {}
+ for axis in self.axisWidgets:
+ op = str(axis.getAxisOperationsButton().text()).strip()
+ axisOpsDict[axis.getID()] = op
+
+ return axisOpsDict
+
+ def getAxesNames(self):
+ return self.axesNames
+
+ def getAxisWidgets(self):
+ return self.axisWidgets
+
+ def getFile(self):
+ return self.file
+
+ def getFileID(self):
+ return self.file.id
+
+ def getVar(self):
+ return self.var
+
+ def getVarID(self):
+ return self.var.id
+
+ def getParent(self):
+ return self.myParent
+
+ def getAxesOrderString(self):
+ """ Return a string with the axes' order """
+
+ order = list(self.axisOrder)
+ return ''.join(map(str, order))
+
+ def setAxesNames(self):
+ """ Generate a list with the axis label + axis name and store it in
+ self.axesNames """
+
+ labels = ['T', 'Z', 'Y', 'X'] + [chr(ord('S')-i) for i in xrange(18)]
+ if (len(self.axisList) >= 4):
+ i = 0
+ else:
+ i = 4 - len(self.axisList)
+
+ for axis in self.axisList:
+ self.axesNames.append(labels[i] + ' - ' + axis.id)
+ i += 1
+
+ def setFile(self, cdmsFile):
+ self.file = cdmsFile
+
+ def setVar(self, var):
+ self.var = var
+
+ def currentTabName(self):
+ return self.myParent.currentTabName()
+
+ def setVistrailsVariableAxes(self):
+ """ Vistrails: Update the vistrails Variable modules 'axes' input. This
+ method is called whenever the sliders values are changed.
+ """
+ axesKwargs = {}
+ # Add the each axes' args for example: latitude: (-90, 90)
+ for axisWidget in self.axisWidgets:
+ axesKwargs[axisWidget.axis.id] = axisWidget.getCurrentValues()
+ # Add other args
+ axesKwargs['squeeze'] = 0
+ axesKwargs['order'] = self.getAxesOrderString()
+
+ self.myParent.emit(QtCore.SIGNAL('updateModule'),
+ self.myParent.currentTabName(), 'axes', str(axesKwargs))
+
+class QVariableView(QtGui.QWidget):
+ """ Main widget containing plotting related information / options. Contains
+ a tab widget with a tab for each defined variable, plotting options widget,
+ and variable information widget """
+
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.selectedVars = []
+
+ # Init layout
+ vbox = QtGui.QVBoxLayout()
+ vbox.setMargin(0)
+ self.setLayout(vbox)
+
+ self.plotOptions = QPlotOptionsWidget(self)
+ self.tabWidget = QAxisListTabWidget(self)
+
+ # Init variable information widget
+ self.varInfoWidget = QtGui.QTextEdit()
+ self.varInfoWidget.setText('')
+ self.varInfoWidget.setReadOnly(True)
+
+ # Create splitter for tabWidget and variable information text
+ vsplitter = QtGui.QSplitter(QtCore.Qt.Vertical)
+ vsplitter.addWidget(self.tabWidget)
+ vsplitter.addWidget(self.varInfoWidget)
+ vsplitter.setStretchFactor(1,1)
+ vsplitter.setSizes([300, 100])
+
+ vbox.addWidget(self.plotOptions)
+ vbox.addWidget(vsplitter)
+
+ def getUpdatedVar(self):
+ """ Return a new tvariable object with the updated information from
+ evaluating the var with the current user selected args / options
+ """
+ axisList = self.tabWidget.currentWidget()
+ kwargs = self.generateKwArgs()
+ updatedVar = axisList.getVar()(**kwargs)
+
+ # Get the variable after carrying out the: def, sum, avg... operations
+ updatedVar = axisList.execAxesOperations(updatedVar)
+
+ return updatedVar
+
+ def generateKwArgs(self, axisList=None):
+ """ Generate and return the variable axes keyword arguments """
+ if axisList is None:
+ axisList = self.tabWidget.currentWidget()
+
+ kwargs = {}
+ for axisWidget in axisList.getAxisWidgets():
+ kwargs[axisWidget.axis.id] = axisWidget.getCurrentValues()
+
+ # Generate additional args
+ kwargs['squeeze'] = 0
+ kwargs['order'] = axisList.getAxesOrderString()
+
+ return kwargs
+
+ def generateKwargsAsString(self):
+ """ Generate and return the variable axes keyword arguments as a string
+ that is formatted to be used in teaching commands
+ """
+ args = ""
+ axisList = self.tabWidget.currentWidget()
+
+ for axisWidget in axisList.getAxisWidgets():
+ args += "%s = %s, " % (axisWidget.axis.id,
+ axisWidget.getCurrentValuesAsStr())
+
+ # Generate additional args
+ args += 'squeeze = 0'
+ args += ", order = '%s' " % axisList.getAxesOrderString()
+ return args
+
+ def updateVarInfo(self, axisList):
+ """ Update the text box with the variable's information """
+ if axisList is None:
+ return
+
+ var = axisList.getVar()
+ varInfo = ''
+ for line in var.listall():
+ varInfo += line + '\n'
+ self.varInfoWidget.setText(varInfo)
+
+ def setupDefinedVariableAxes(self, cdmsFile, var, tabName):
+ """ Create a new axis list and tab with the specified tab name and setup
+ the axis list. Initialize the vistrails Variable module associated with
+ the tab and variable.
+ """
+ if var is None:
+ return
+
+ # Create and setup the axislist
+ axisList = QAxisList(cdmsFile, var, self)
+ axisList.setupVariableAxes()
+ self.updateVarInfo(axisList)
+ self.tabWidget.createNewTab(axisList, tabName)
+
+ # Create the vistrails variable module if it doesn't exist, and update
+ # the modules input ports' values
+ if tabName == 'quickplot':
+ self.emit(QtCore.SIGNAL('createModule'), quickplot_name,
+ quickplot_name.lower())
+ else:
+ self.emit(QtCore.SIGNAL('createModule'), variable_name, tabName)
+ self.emit(QtCore.SIGNAL('updateModule'), tabName, 'id',
+ var.id)
+ self.emit(QtCore.SIGNAL('updateModule'), tabName, 'axes',
+ str(self.generateKwArgs()))
+ self.emit(QtCore.SIGNAL('updateModule'),
+ tabName, 'axesOperations',
+ str(axisList.getAxesOperations()))
+
+ def defineVarAxis(self, var, teachingCommand):
+ """ Create a new tab/axisList, store it in defined var list, and record
+ the associated teaching commands. This method is called when the user
+ clicks on the axisButton -> 'Get Axis Values' """
+
+ cdmsFile = self.tabWidget.currentWidget().getFile()
+ axisList = QAxisList(cdmsFile, var, self)
+ axisList.setupVariableAxes()
+ argString = self.generateKwargsAsString()
+
+ self.emit(QtCore.SIGNAL('recordTeachingCommand'), teachingCommand)
+ self.emit(QtCore.SIGNAL('defineVariable'), cdmsFile, var, argString)
+
+ def defineVariableEvent(self):
+ """ Get a copy of the updated var and file and pass it to the Defined
+ Variables widget """
+ if self.tabWidget.currentWidget() is None:
+ return
+
+ cdmsFile = self.tabWidget.currentWidget().getFile()
+ var = self.getUpdatedVar()
+ argString = self.generateKwargsAsString()
+
+ self.emit(QtCore.SIGNAL('defineVariable'), cdmsFile, var, argString)
+
+ def selectDefinedVariableEvent(self, tabName, cdmsFile, selectedVars):
+ """ Save the list of selected variables and show the selected variable,
+ variables are sorted in least recently selected to most recently selected
+ """
+ if selectedVars != []:
+ self.selectedVars = selectedVars
+ self.tabWidget.selectAndUpdateDefinedVarTab(tabName, cdmsFile, selectedVars[-1])
+
+ def plot(self):
+ """ Create the graphics method and cdatcell modules. Update the input
+ port values and setup connections. Then plot.
+ """
+ if self.tabWidget.count() == 0:
+ return
+
+ # Error if not enough slabs
+ plotType = str(self.plotOptions.getPlotType())
+ if len(self.selectedVars) < 2 and self.requiresTwoSlabs(plotType):
+ self.showError('Error Message to User', 'Vector, Scatter, Meshfill or XvsY plots \nmust have two data variables. The data \nvariables must be selected in the \n"Defined Variables" window.')
+ return
+
+ # Create & Update the graphics method / CDATCell vistrails modules
+ # *** IMPORTANT ***
+ # Everytime plot is pressed, this will create a new Graphics Method and
+ # CDATCell Module. Instead it should ONLY create a new graphics method
+ # and CDATCell module if the variable isn't already connected to an
+ # existing Graphics Method / CDATCell module. This results in plots
+ # being plotted multiple times.
+ axisList = self.tabWidget.currentWidget()
+ self.emit(QtCore.SIGNAL('createModule'), gm_name)
+ self.emit(QtCore.SIGNAL('createModule'), cdatcell_name)
+ self.setVistrailsGraphicsMethod()
+ self.setVistrailsCDATCell()
+
+ # Get the names of the 2 slabs so we can connect their modules in vistrails
+ if self.requiresTwoSlabs(plotType):
+ var1 = self.selectedVars[-1].id
+ var2 = self.selectedVars[-2].id
+ else:
+ var1 = self.currentTabName()
+ var2 = None
+
+ # Emit signal to GuiController to connect ports and plot
+ self.emit(QtCore.SIGNAL('plot'), var1, var2)
+
+ # If a quickplot is plotted, define current variable under 'quickplot'
+ if (self.currentTabName() == 'quickplot'):
+ var = self.getUpdatedVar()
+ self.emit(QtCore.SIGNAL('plotPressed'), axisList.getFile(), var)
+
+ # Record plot teaching commands
+ self.recordPlotTeachingCommand()
+
+ def recordPlotTeachingCommand(self):
+ axisList = self.tabWidget.currentWidget()
+ tabName = self.tabWidget.currentTabName()
+ argString = self.generateKwargsAsString()
+ var = axisList.getVar()
+ fileID = "fid2"
+
+ slabCommand = ''
+ if tabName == 'quickplot':
+ slabCommand += '\n# Get new slab\n'
+ slabCommand += "%s = %s('%s', %s)\n" %(tabName, fileID, var.id, argString)
+
+ slabCommand += '\n# Get new slab\n'
+ slabCommand += "%s = %s(%s)\n" %(tabName, tabName, argString)
+
+ slabCommand += axisList.getAxesOperationsTeachingCommands(tabName)
+
+ canvasNum = 0 # Change the canvas # with respect to the cell?
+ clearCommand = '\n# Clear the VCS Canvas\n'
+ clearCommand += "vcs_canvas_list[%d].clear()\n" % canvasNum
+
+ plotID = "vcs_display"
+ plotType = str(self.plotOptions.getPlotType())
+ template = self.getTemplateName(plotType)
+ gm = self.getGraphicsMethodName(plotType)
+ plotArgs = "%s, '%s', '%s', '%s'" % (tabName, template, plotType, gm)
+
+ if self.plotOptions.getContinentType() is not None:
+ plotArgs += ", continents = %d" % self.plotOptions.getContinentType()
+
+ plotCommand = '\n# Plot slab\n'
+ plotCommand += "%s = vcs_canvas_list[%d].plot(%s)\n" %(plotID, canvasNum, plotArgs)
+
+ command = slabCommand + clearCommand + plotCommand
+ self.emit(QtCore.SIGNAL('recordTeachingCommand'), command)
+
+ def requiresTwoSlabs(self, plotType):
+ """ Returns true if the plot requires 2 slabs """
+ multiVarPlots = ['Vector', 'Scatter', 'XvsY']
+ return plotType in multiVarPlots
+
+ def getDefinedVars(self):
+ """ Get a list of all of the defined tabnames / variables """
+ numTabs = self.tabWidget.count()
+ varList = []
+
+ for i in range(numTabs):
+ var = self.tabWidget.widget(i).getVar()
+ name = self.tabWidget.tabText(i)
+ varList.append([name, var])
+
+ return varList
+
+ def getAxisList(self, var):
+ for i in range(self.tabWidget.count()):
+ if self.tabWidget.widget(i).getVar() is var:
+ return self.tabWidget.widget(i)
+
+ return None
+
+ def getTemplateName(self, plotType):
+ """ Return the template given the plotType. This is currently hardcoded
+ but should change based on the user? """
+
+ # TODO ?
+ return self.getGraphicsMethodName(plotType)
+
+ def getGraphicsMethodName(self, plotType):
+ """ Return the graphics method given the plotType. This is currently
+ hardcoded but should change based on the user? """
+
+ # TODO ?
+ hasASD = ['Boxfill', 'Isofill', 'Isoline', 'Scatter', 'Taylordiagram']
+ hasquick = ['Vector']
+ hasASD1 = ['Xyvsy', 'Yxvsx']
+
+ if plotType in hasASD:
+ return 'ASD'
+ if plotType in hasquick:
+ return 'quick'
+ if plotType in hasASD1:
+ return 'ASD1'
+ return 'default'
+
+ def setVistrailsCDATCell(self):
+ """ Vistrails: Update the vistrails' CDAT Cell modules' input ports: """
+
+ visInput = []
+ plotType = str(self.plotOptions.getPlotType())
+
+ visInput.append(('plotType', plotType))
+ visInput.append(('row', str(self.plotOptions.getRow())))
+ visInput.append(('col', str(self.plotOptions.getCol())))
+ visInput.append(('gmName', self.getGraphicsMethodName(plotType)))
+ visInput.append(('template', self.getTemplateName(plotType)))
+
+ if self.plotOptions.getContinentType() is not None:
+ visInput.append(('continents', self.plotOptions.getContinentType())) # TODO
+
+ self.emit(QtCore.SIGNAL('updateModuleOps'), cdatcell_name, visInput)
+
+ def setVistrailsGraphicsMethod(self):
+ """ Vistrails: Update the vistrails' Graphics Method modules' boxfill
+ input ports. Only set the plotType and graphics method (gm) name.
+ Setting the input for gm attributes should be handled by the gm
+ controller (graphics_method_controller.py)
+ """
+ visInput = [] # List of tuples where each tuple = (inputPortName, value)
+ plotType = str(self.plotOptions.getPlotType())
+
+ visInput.append(('plotType', plotType))
+ visInput.append(('gmName', self.getGraphicsMethodName(plotType)))
+ self.emit(QtCore.SIGNAL('updateModuleOps'), gm_name, visInput)
+
+ def showError(self, title, text):
+ """ Show an error message in a simple popup message box. Currently there
+ is no error icon. """
+
+ errorWidget = QtGui.QMessageBox(self)
+ errorWidget.setWindowTitle(title)
+ errorWidget.setText(text)
+ errorWidget.show()
+
+ def currentTabName(self):
+ return self.tabWidget.currentTabName()
+
+class QSelectVarDialog(QtGui.QDialog):
+ """ Popup box that allows user to selected a defined variable to replace an
+ axis """
+
+ def __init__(self, definedVars, parent):
+ QtGui.QDialog.__init__(self, parent)
+ self.selectedVariable = None
+ self.currentListIndex = None
+ self.definedVars = definedVars
+ self.myParent = parent
+
+ vbox = QtGui.QVBoxLayout()
+ hbox = QtGui.QHBoxLayout()
+ self.setLayout(vbox)
+
+ vbox.addWidget(QtGui.QLabel("Defined Variables:"))
+
+ # Add List of defined vars
+ self.varList = QtGui.QListWidget()
+ self.varList.setAlternatingRowColors(True)
+ vbox.addWidget(self.varList)
+
+ # Initialize the list of defined vars
+ # self.definedVars = parent.getDefinedVars()
+ for name, var in self.definedVars:
+ label = name + ' ' + str(var.shape)
+ item = QtGui.QListWidgetItem()
+ item.setData(0, QtCore.QVariant(QtCore.QString(label)))
+ self.varList.addItem(item)
+
+ # Add OK / Cancel Buttons
+ okButton = QtGui.QPushButton('OK')
+ cancelButton = QtGui.QPushButton('Cancel')
+ hbox.addWidget(okButton)
+ hbox.addWidget(cancelButton)
+ vbox.addLayout(hbox)
+
+ # Connect Signals
+ self.connect(self.varList, QtCore.SIGNAL('clicked(const QModelIndex&)'),
+ self.selectVariableFromListEvent)
+ self.connect(okButton, QtCore.SIGNAL('pressed()'),
+ self.selectDefinedVariableEvent)
+ self.connect(cancelButton, QtCore.SIGNAL('pressed()'), self.close)
+
+ def selectVariableFromListEvent(self, modelIndex):
+ self.currentListIndex = modelIndex
+
+ def varIsValid(self, var):
+ """ Return true if the var has 1 dimension and it has the same # of
+ values as the one it is replacing
+ """
+ if len(var.getAxisList()) != 1:
+ return False
+ if self.myParent.numValues() != self.myParent.numValues():
+ return False
+ return True
+
+ def showError(self):
+ errorMsg = "Invalid shape or size. Axis requiers a 1D \narray that matches in size."
+ errorMessageBox = QtGui.QMessageBox(self)
+ errorMessageBox.setWindowTitle("Error")
+ errorMessageBox.setText(errorMsg)
+ errorMessageBox.show()
+ # TODO need an icon for the message box
+
+ def selectDefinedVariableEvent(self):
+ # Implement in child
+ return
+
+class QReplaceAxisValuesDialog(QSelectVarDialog):
+ """ Popup box that prompts user to select a variable to replace the current
+ axis values """
+
+ def __init__(self, definedVars, parent):
+ QSelectVarDialog.__init__(self, definedVars, parent)
+ self.setWindowTitle("Replace Axis Values")
+
+ def selectDefinedVariableEvent(self):
+ # Do nothing if no variable is selected
+ if self.currentListIndex is None:
+ return
+
+ name, var = self.definedVars[self.currentListIndex.row()]
+ if self.varIsValid(var):
+ self.myParent.replaceAxisValues(var)
+ self.close()
+ else:
+ self.showError()
+
+class QReplaceAxisWeightsDialog(QSelectVarDialog):
+ """ Popup box that prompts user to select a variable to replace the current
+ axis weight values """
+
+ def __init__(self, definedVars, parent):
+ QSelectVarDialog.__init__(self, definedVars, parent)
+ self.setWindowTitle("Replace Dimension Weights")
+
+ def selectDefinedVariableEvent(self):
+ # Do nothing if no variable is selected
+ if self.currentListIndex is None:
+ return
+
+ name, var = self.definedVars[self.currentListIndex.row()]
+ if self.varIsValid(var):
+ self.myParent.setAlteredWeights(var)
+ self.close()
+ else:
+ self.showError()
+
+class QPlotOptionsWidget(QtGui.QWidget):
+ """ Widget containing plot options: plot button, plot type combobox, cell
+ col and row selection combo box, and an options button """
+
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.myParent = parent
+ self.cellRow = -1 # if row/col = -1, then automatically plot in an open cell
+ self.cellCol = -1
+ hbox = QtGui.QHBoxLayout()
+
+ # Add plot button
+ self.plotButton = QtGui.QPushButton('&Plot')
+ hbox.addWidget(self.plotButton)
+
+ # Add plot type combo box
+ self.plotTypeCombo = QtGui.QComboBox()
+ comboPalette = self.plotTypeCombo.view().palette()
+ comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
+ comboPalette.setColor(QtGui.QPalette.Highlight, QtCore.Qt.blue)
+ self.plotTypeCombo.view().setPalette(comboPalette)
+
+ plotTypes = ['Boxfill', 'Isofill', 'Isoline', 'Meshfill', 'Outfill',
+ 'Outline', 'Scatter', 'Taylordiagram', 'Vector', 'XvsY',
+ 'Xyvsy', 'Yxvsx','Ext']
+ self.plotTypeCombo.addItems(plotTypes)
+ hbox.addWidget(self.plotTypeCombo)
+
+ # Add cell row / col combo boxes
+ rowLabel = QtGui.QLabel('Row')
+ colLabel = QtGui.QLabel('Col')
+ self.cellRowCombo = QtGui.QComboBox()
+ self.cellColCombo = QtGui.QComboBox()
+
+ comboPalette = self.cellRowCombo.view().palette()
+ comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
+ comboPalette.setColor(QtGui.QPalette.Highlight, QtCore.Qt.blue)
+ self.cellRowCombo.view().setPalette(comboPalette)
+
+ comboPalette = self.cellColCombo.view().palette()
+ comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
+ self.cellColCombo.view().setPalette(comboPalette)
+
+ self.cellRowCombo.addItem('Auto')
+ self.cellColCombo.addItem('Auto')
+
+ for i in range(1, 9):
+ self.cellRowCombo.addItems(str(i))
+ self.cellColCombo.addItems(str(i))
+
+ hbox.addWidget(rowLabel)
+ hbox.addWidget(self.cellRowCombo)
+ hbox.addWidget(colLabel)
+ hbox.addWidget(self.cellColCombo)
+
+ # Create the options menu
+ optionsMenu = QtGui.QMenu(self)
+ menuVbox = QtGui.QVBoxLayout()
+ menuVbox.setMargin(2)
+ optionsMenu.setLayout(menuVbox)
+
+ # Create the Continents Types Menu
+ self.continentTypesMenu = QCheckMenu()
+ self.continentTypesMenu.setTitle('Continent Types')
+ optionsMenu.addMenu(self.continentTypesMenu)
+ self.continentTypes = [('Auto Continents', None),
+ ('No Continents', 0),
+ ('Coarse Continents', 2),
+ ('Fine Continents', 1),
+ ('United States Continents', 3),
+ ('Political Boundary Continents', 4),
+ ('Rivers Continents', 5),
+ ('User1 Continents', 6),
+ ('User2 Continents', 7),
+ ('User3 Continents', 8),
+ ('User4 Continents', 9),
+ ('User5 Continents', 10),
+ ('User6 Continents', 11)]
+
+ for continentType in self.continentTypes:
+ self.continentTypesMenu.addCheckableAction(continentType[0])
+ self.continentTypesMenu.setDefaultAction('Auto Continents')
+
+ # Create graphic method attribute option / editor
+ canvas = vcs.init()
+ self.graphicsMethodController = QGraphicsMethodAttributeWindow(canvas, self)
+ graphicMethodAction = optionsMenu.addAction('Se&t Graphics Method Attributes')
+
+ # Create Colormap option / widget
+ colorMapAction = optionsMenu.addAction("&Colormap Editor")
+ self.colorDialog = QtGui.QColorDialog(self)
+ self.connect(colorMapAction, QtCore.SIGNAL('triggered ()'),
+ self.colorDialog.open)
+
+ # Create the options button
+ self.optionButton = QtGui.QToolButton()
+ self.optionButton.setText(' Options ')
+ self.optionButton.setMenu(optionsMenu)
+ self.optionButton.setPopupMode(QtGui.QToolButton.InstantPopup)
+
+ hbox.addWidget(self.optionButton)
+ hbox.addStretch()
+ self.setLayout(hbox)
+
+ # Connect Signals
+ self.connect(self.plotButton, QtCore.SIGNAL('clicked(bool)'),
+ parent.plot)
+ self.connect(self.optionButton, QtCore.SIGNAL('clicked(bool)'),
+ self.optionButton.showMenu)
+ self.connect(graphicMethodAction, QtCore.SIGNAL('triggered ()'),
+ self.graphicsMethodController.show)
+
+ def getRow(self):
+ if self.cellRowCombo.currentText() == 'Auto':
+ return -1
+ return int(self.cellRowCombo.currentText()) - 1
+
+ def getCol(self):
+ if self.cellColCombo.currentText() == 'Auto':
+ return -1
+ return int(self.cellColCombo.currentText()) - 1
+
+ def getPlotType(self):
+ return self.plotTypeCombo.currentText()
+
+ def getContinentType(self):
+ """ Returns None or a number from 0-11 corresponding to the option
+ selected in the continents menu """
+
+ selectedText = self.continentTypesMenu.getCheckedText()
+ for text, continentType in self.continentTypes:
+ if text == selectedText:
+ return continentType
+
+ return None
+
+ def getGraphicsMethodController(self):
+ return self.graphicsMethodController
+
+ def getParent(self):
+ return self.myParent
+
+class QCheckMenu(QtGui.QMenu):
+ """ Menu where only a single 'checkable' action can be checked at a time """
+
+ def __init__(self, parent=None):
+ QtGui.QMenu.__init__(self, parent)
+ self.defaultAction = None
+ self.currentAction = None
+ self.handleCheckEvent = False
+ self.actions = {}
+
+ def addCheckableAction(self, actionText):
+ action = self.addAction(actionText)
+ action.setCheckable(True)
+ self.actions[actionText] = action
+ self.connect(action, QtCore.SIGNAL('toggled (bool)'), self.checkEvent)
+
+ def setDefaultAction(self, actionText):
+ if actionText in list(self.actions):
+ self.currentAction = self.defaultAction = self.actions[actionText]
+ self.defaultAction.setChecked(True)
+
+ def getCheckedText(self):
+ return self.currentAction.text()
+
+ def checkEvent(self, isChecked):
+ """ Force the menu to have only 1 item checked. If an action is
+ unchecked, check the default item """
+
+ # handleCheckEvent prevents infinite recursion because this method also
+ # generates checkEvents
+ if self.handleCheckEvent == False:
+ self.handleCheckEvent = True
+ return
+
+ if isChecked == True:
+ self.handleCheckEvent = False
+ self.currentAction.setChecked(False)
+ self.currentAction = self.sender()
+ elif isChecked == False and not self.defaultAction is None:
+ self.handleCheckEvent = False
+ self.defaultAction.setChecked(True)
+
+class QAxisListTabWidget(QtGui.QTabWidget):
+ """ TabWidget where each tab contains a QAxisList """
+
+ def __init__(self, parent=None):
+ QtGui.QTabWidget.__init__(self, parent)
+ self.myParent = parent
+
+ self.connect(self, QtCore.SIGNAL('currentChanged(int)'),
+ self.tabChangeEvent)
+
+ def createNewTab(self, axisList, tabName):
+ """ Create a new tab given the axisList widget and tab name. If a
+ tab with the same name exists already, replace it. Set the current tab
+ to the newly created tab """
+
+ if (self.tabExists(tabName)):
+ self.removeTab(self.getTabIndexFromName(tabName))
+
+ if tabName == 'quickplot':
+ self.insertTab(0, axisList, tabName) # quickplot is always first tab
+ else:
+ self.addTab(axisList, tabName)
+
+ self.setTabTip(tabName)
+ self.setCurrentIndex(self.getTabIndexFromName(tabName))
+
+ def setupQuickplotTab(self, axisList):
+ """ Create a new quickplot tab if one doesn't exist otherwise replace
+ the existing quickplot tab """
+
+ tabName = 'quickplot'
+ if (self.tabExists(tabName) == True):
+ index = self.getTabIndexFromName(tabName)
+ self.removeTab(index)
+
+ self.insertTab(0, axisList, tabName)
+ self.setTabTip(tabName)
+ self.setCurrentIndex(0)
+
+ def setTabTip(self, tabName):
+ if self.tabExists(tabName):
+ index = self.getTabIndexFromName(tabName)
+ toolTip = "'%s' axisList tab widget" % tabName
+ self.setTabToolTip(index, toolTip)
+
+ def tabChangeEvent(self, tabIndex):
+ """ Event handler for when a tab is changed. Update the variable info
+ text box.
+ """
+ axisList = self.widget(tabIndex)
+ self.myParent.updateVarInfo(axisList)
+
+ def selectAndUpdateDefinedVarTab(self, tabName, cdmsFile, var):
+ """ This function selects a tab given the tabName and then updates the
+ tab's axisList using the passed var's values
+ """
+ if (not self.tabExists(tabName)):
+ raise NameError("Error: tab '%s' was not found" % tabName)
+
+ tabIndex = self.getTabIndexFromName(tabName)
+ self.setCurrentIndex(tabIndex)
+
+ if (tabName == 'quickplot'):
+ axisList = QAxisList(cdmsFile, var, self)
+ self.setupQuickplotTab(axisList)
+ axisList.setupVariableAxes()
+ else:
+ axisList = self.currentWidget()
+ axisList.setupVariableAxes()
+
+ self.emit(QtCore.SIGNAL('updateVarInfo'), axisList)
+
+ def tabExists(self, name):
+ """ Returns True if a tab with the given name exists """
+ numTabs = self.count()
+ for i in range(numTabs):
+ if (name == self.tabText(i)):
+ return True
+ return False
+
+ def getTabIndexFromName(self, name):
+ numTabs = self.count()
+ for i in range(numTabs):
+ if (name == self.tabText(i)):
+ return i
+ return None
+
+ def currentTabName(self):
+ currentTab = self.currentIndex()
+ return str(self.tabText(currentTab))
+
+class QMenuWidget(QtGui.QMenuBar):
+ def __init__(self, parent=None):
+ QtGui.QMenuBar.__init__(self, parent)
+ self.myParent = parent
+
+ self.file = self.addMenu('&File')
+ self.pref = self.addMenu('&Preferences')
+ self.tools = self.addMenu('&Tools')
+ self.pcmdiTools = self.addMenu('&PCMDITools')
+ self.help = self.addMenu('&Help')
+ self.initToolsMenu()
+
+ def initToolsMenu(self):
+ recordTeachingAction = self.tools.addAction('Record Commands')
+ recordTeachingAction.setCheckable(True)
+ recordTeachingAction.setChecked(True)
+
+ viewTeachingAction = self.tools.addAction('View Teaching Commands')
+ closeTeachingAction = self.tools.addAction('Close Teaching Commands')
+
+ self.connect(viewTeachingAction, QtCore.SIGNAL('triggered ()'),
+ self.viewTeachingCommands)
+ self.connect(closeTeachingAction, QtCore.SIGNAL('triggered ()'),
+ self.closeTeachingCommands)
+ self.connect(recordTeachingAction, QtCore.SIGNAL('toggled (bool)'),
+ self.setRecordCommands)
+
+ def setRecordCommands(self, checked):
+ self.myParent.emit(QtCore.SIGNAL('setRecordCommands'), checked)
+
+ def viewTeachingCommands(self):
+ self.myParent.emit(QtCore.SIGNAL('viewTeachingCommands'))
+
+ def closeTeachingCommands(self):
+ self.myParent.emit(QtCore.SIGNAL('closeTeachingCommands'))
+
diff --git a/contrib/cdat/configure.py b/contrib/cdat/configure.py
new file mode 100644
index 0000000..e36b245
--- /dev/null
+++ b/contrib/cdat/configure.py
@@ -0,0 +1,72 @@
+import os
+import sipconfig
+from PyQt4 import pyqtconfig
+
+
+from distutils import sysconfig
+
+vcs_so = '%s/vcs/_vcs.so' % sysconfig.get_python_lib()
+vcs_inc = '%s/vcs/Include' % sysconfig.get_python_lib()
+
+## vcs_so = '/Users/hvo/src/uvcdat/cdatBuild/lib/python2.7/site-packages/vcs/_vcs.so'
+## vcs_inc = '/Users/hvo/src/uvcdat/cdat/Packages/vcs/Include'
+
+
+# The name of the SIP build file generated by SIP and used by the build
+# system.
+build_file = "pyqtscripting.sbf"
+
+# Get the PyQt configuration information.
+config = pyqtconfig.Configuration()
+
+# Get the extra SIP flags needed by the imported qt module. Note that
+# this normally only includes those flags (-x and -t) that relate to SIP's
+# versioning system.
+qt_sip_flags = config.pyqt_sip_flags
+
+os.system("rm -rf cdatwrap")
+os.mkdir("cdatwrap")
+os.system("touch cdatwrap/__init__.py")
+
+# Run SIP to generate the code. Note that we tell SIP where to find the qt
+# module's specification files using the -I flag.
+os.system(" ".join([ \
+ config.sip_bin, \
+ "-c", "cdatwrap", \
+ "-b", build_file, \
+ "-I", config.pyqt_sip_dir, \
+ qt_sip_flags, \
+ "cdat.sip" \
+]))
+
+# Create the Makefile. The QtModuleMakefile class provided by the
+# pyqtconfig module takes care of all the extra preprocessor, compiler and
+# linker flags needed by the Qt library.
+makefile = pyqtconfig.QtGuiModuleMakefile(
+ dir="cdatwrap",
+ configuration=config,
+ build_file='../' + build_file
+)
+
+# Add the library we are wrapping. The name doesn't include any platform
+# specific prefixes or extensions (e.g. the "lib" prefix on UNIX, or the
+# ".dll" extension on Windows).
+#makefile.extra_libs = ["vcs"]
+import cdat_info
+makefile.CFLAGS.append("-I%s/include" % cdat_info.externals)
+makefile.CFLAGS.append("-I%s" % vcs_inc)
+makefile.CFLAGS.append("-I%s/.." % sysconfig.get_python_inc())
+
+makefile.CXXFLAGS.append("-I%s/include" % cdat_info.externals)
+makefile.CXXFLAGS.append("-I%s" % vcs_inc)
+makefile.CXXFLAGS.append("-I%s/.." % sysconfig.get_python_inc())
+
+cwd = os.getcwd()
+makefile.LFLAGS.append("-Wl,-rpath,%s/cdatwrap" % cwd)
+
+# Generate the Makefile itself.
+makefile.generate()
+os.chdir("cdatwrap")
+os.system("make clean")
+os.system("MACOSX_DEPLOYMENT_TARGET=10.6 make -j")
+os.system("make install")
diff --git a/contrib/cdat/graphics_method_controller.py b/contrib/cdat/graphics_method_controller.py
new file mode 100644
index 0000000..1d1ff10
--- /dev/null
+++ b/contrib/cdat/graphics_method_controller.py
@@ -0,0 +1,1624 @@
+import types
+from PyQt4 import QtCore, QtGui
+from gui_controller import gm_name
+
+indentSpacing = 10
+
+class QGraphicsMethodAttributeWindow(QtGui.QMainWindow):
+
+ def __init__(self, canvas=None, parent=None):
+ QtGui.QMainWindow.__init__(self, parent)
+ initialWidth = 480
+ initialHeight = 640
+ self.resize(initialWidth, initialHeight)
+ self.setWindowTitle('Graphics Methods Attrtibute Settings')
+ self.parent = parent
+
+ # Create tab widgets
+ self.tabWidget = QtGui.QTabWidget()
+ if canvas is not None:
+ self.boxfillEditor = QBoxfillEditor(gm=canvas.getboxfill('ASD'))
+ self.continentsEditor = QContinentsEditor(gm=canvas.getcontinents('ASD'))
+ self.meshfillEditor = QMeshfillEditor(gm=canvas.getmeshfill())
+ self.outfillEditor = QOutfillEditor(gm=canvas.getoutfill())
+ self.scatterEditor = QScatterEditor(gm=canvas.getscatter('ASD'))
+ self.taylorEditor = QTaylorDiagramEditor(gm=canvas.gettaylordiagram('ASD'))
+ self.vectorEditor = QVectorEditor(gm=canvas.getvector())
+ else:
+ self.boxfillEditor = QBoxfillEditor()
+ self.continentsEditor = QContinentsEditor()
+ self.meshfillEditor = QMeshfillEditor()
+ self.outfillEditor = QOutfillEditor()
+ self.scatterEditor = QScatterEditor()
+ self.taylorEditor = QTaylorDiagramEditor()
+ self.vectorEditor = QVectorEditor()
+
+ self.contourEditor = QContourEditor()
+ self.oneDimEditor = Q1DPlotEditor()
+ self.outlineEditor = QOutlineEditor()
+
+ # Add tabs
+ self.tabWidget.addTab(self.boxfillEditor, 'Boxfill')
+ self.tabWidget.addTab(self.continentsEditor, 'Continents')
+ self.tabWidget.addTab(self.contourEditor, 'Contour')
+ self.tabWidget.addTab(self.meshfillEditor, 'Meshfill')
+ self.tabWidget.addTab(self.oneDimEditor, '1D Plot')
+ self.tabWidget.addTab(self.outfillEditor, 'Outfill')
+ self.tabWidget.addTab(self.outlineEditor, 'Outline')
+ self.tabWidget.addTab(self.scatterEditor, 'Scatter')
+ self.tabWidget.addTab(self.taylorEditor, 'Taylor Diagram')
+ self.tabWidget.addTab(self.vectorEditor, 'Vector')
+ self.setToolTips()
+
+ # Add preview, reset, apply, cancel buttons
+ previewButton = self.getButton('Preview')
+ resetButton = self.getButton('Reset')
+ applyButton = self.getButton('Apply')
+ cancelButton = self.getButton('Cancel')
+
+ hbox = QtGui.QHBoxLayout()
+ hbox.addWidget(previewButton)
+ hbox.addWidget(resetButton)
+ hbox.addWidget(applyButton)
+ hbox.addWidget(cancelButton)
+
+ # Setup the layout
+ vbox = QtGui.QVBoxLayout()
+ vbox.addWidget(self.tabWidget)
+ vbox.addLayout(hbox)
+ wrapperWidget = QtGui.QWidget()
+ wrapperWidget.setLayout(vbox)
+ self.setCentralWidget(wrapperWidget)
+
+ # Connect Signals
+ self.connect(cancelButton, QtCore.SIGNAL('pressed()'), self.close)
+ self.connect(resetButton, QtCore.SIGNAL('pressed()'), self.resetPressedEvent)
+ self.connect(applyButton, QtCore.SIGNAL('pressed()'), self.applyPressedEvent)
+ self.connect(previewButton, QtCore.SIGNAL('pressed()'), self.previewPressedEvent)
+
+ def resetPressedEvent(self):
+ self.boxfillEditor.initValues()
+ self.continentsEditor.initValues()
+ self.meshfillEditor.initValues()
+ self.outfillEditor.initValues()
+ self.scatterEditor.initValues()
+ self.taylorEditor.initValues()
+ self.vectorEditor.initValues()
+
+ self.contourEditor.initValues()
+ self.oneDimEditor.initValues()
+ self.outlineEditor.initValues()
+
+ def applyPressedEvent(self):
+ self.boxfillEditor.setVistrailsGraphicsMethod(self.parent.getParent())
+
+ # TODO
+ # self.continentsEditor.setVistrailsGraphicsMethod()
+ # self.meshfillEditor.setVistrailsGraphicsMethod()
+ # self.outfillEditor.setVistrailsGraphicsMethod()
+ # self.scatterEditor.setVistrailsGraphicsMethod()
+ # self.taylorEditor.setVistrailsGraphicsMethod()
+ # self.vectorEditor.setVistrailsGraphicsMethod()
+ # self.contourEditor.setVistrailsGraphicsMethod()
+ # self.oneDimEditor.setVistrailsGraphicsMethod()
+ # self.outlineEditor.setVistrailsGraphicsMethod()
+
+ def previewPressedEvent(self):
+ return # TODO
+
+ def setToolTips(self):
+ self.tabWidget.setTabToolTip(0, 'The Boxfill graphics method displays a two-dimensional data\narray by surrounding each data value with a colored grid box.')
+ self.tabWidget.setTabToolTip(1, "The Continents graphics method draws a predefined,\ngeneric set of continental outlines in a longitude\nby latitude space. (To draw continental outlines,\nno external data set is required.)")
+ self.tabWidget.setTabToolTip(2, "This Contour notebook tab represent both the Isofill\nand Isoline graphics methods. The Isofill graphics\nmethod fills the area between selected isolevels\n(levels of constant value) of a two-dimensional\narray; the manner of filling the area is determined\nby the named fill area attributes. The Isoline\ngraphics method draws lines of constant value at\nspecified levels to graphically represent the values\nof a two-dimensional array; labels also c [...]
+ self.tabWidget.setTabToolTip(3, "The Meshfill graphics method draws data on irregular grid (or 'mesh')at specified levels to graphically represent\nthe values of a one-dimensional array;\nUnless the irregular grid is supported by cdms2, a mesh array must be passed as well")
+ self.tabWidget.setTabToolTip(4, "This 1D Plot notebook tab represent the XvsY, Xyvsy,\nand Yxvsx graphics methods. The XvsY graphics method\ndisplays a line plot from two 1D data arrays, that\nis X(t) and Y(t), where t represents the 1D\ncoordinate values. The Xyvsy graphics method displays\na line plot from a 1D data array, that is X(y),\nwhere y represents the 1D coordinate values. The\nYxvsx graphics method displays a line plot from\na 1D data array, that is Y(x), where y repr [...]
+ self.tabWidget.setTabToolTip(5, "The Outfill graphics method fills a set of integer\nvalues in any data array. Its primary purpose is\nto display continents by filling their area as\ndefined by a surface type array that indicates land,\nocean, and sea-ice points. ")
+ self.tabWidget.setTabToolTip(6, "The Outline graphics method outlines a set of integer\nvalues in any data array. Its primary purpose is\nto display continental outlines as defined by a\nsurface type array that indicates land, ocean, and\nsea-ice points.")
+ self.tabWidget.setTabToolTip(7, "The Scatter graphics method displays a scatter plot\nof two 4-dimensional data arrays, e.g. A(x,y,z,t)\nand B(x,y,z,t). ")
+ self.tabWidget.setTabToolTip(8, "The Taylor diagram graphics method provides a statistical\nsummary of pattern correspondence. A single point on\nthe diagram indicates how similar two patterns are in\nterms of their correlation, root-mean-square (RMS)\ndifference, and the ratio of their variances. The\nstandard deviation of a pattern is proportional to the\nradial distance. The correlation is given by the cosine\nof the azimuthal angle. The RMS difference is proportional\nto th [...]
+ self.tabWidget.setTabToolTip(9, "The Vector graphics method displays a vector plot\nof a 2D vector field. Vectors are located at the\ncoordinate locations and point in the direction of\nthe data vector field. Vector magnitudes are the\nproduct of data vector field lengths and a scaling\nfactor. ")
+
+ def getButton(self, text):
+ button = QtGui.QToolButton()
+ button.setText(text)
+ return button
+
+class QVectorEditor(QtGui.QScrollArea):
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+
+ frame = QFramedWidget()
+ self.lineType = frame.addLabeledComboBox('Vector Line Type:',
+ ['solid', 'dash', 'dot','dash-dot', 'long-dash'])
+ self.colorIndex = frame.addLabeledSpinBox('Vector Line Color Index',
+ 0, 255)
+ self.scale = frame.addLabeledDoubleSpinBox('Vector Scale', -1e20, 1e20, .1)
+ self.alignment = frame.addLabeledComboBox('Vector Alignment:',
+ ['head', 'center', 'tail'])
+ self.headType = frame.addLabeledComboBox('Vector Head Type:',
+ ['arrows', 'barbs', 'solidarrows'])
+ self.reference = frame.addLabeledDoubleSpinBox('Vector reference', -1e20, 1e20, .1)
+
+ vbox.addWidget(frame)
+
+ # Init values & set tool tips
+ self.initValues()
+ self.lineType.setToolTip("Select the vector line type.")
+ self.colorIndex.setToolTip("Select the vector color index.")
+ self.scale.setToolTip("Select the vector scale factor.")
+ self.alignment.setToolTip("Set the vector alignment.")
+ self.headType.setToolTip("Set the vector head type.")
+ self.reference.setToolTip("Set the vector reference. Note: if the value is 1e+20,\nthen VCS will determine the vector reference.")
+
+ # Set up the scrollbar
+ widgetWrapper = QtGui.QWidget()
+ widgetWrapper.setLayout(vbox)
+ widgetWrapper.setMinimumWidth(580)
+ self.setWidget(widgetWrapper)
+
+ def initValues(self):
+ # TODO: don't init w/ hardcoded values?
+ self.colorIndex.setValue(241)
+ self.scale.setValue(1)
+ self.alignment.setCurrentIndex(1)
+ self.headType.setCurrentIndex(0)
+ self.reference.setValue(1e20)
+
+class QTaylorDiagramEditor(QtGui.QScrollArea):
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+
+ tabWidget = QtGui.QTabWidget()
+ interfaceTab = QTaylorInterfaceTab()
+ tickAndLabelTab = QTaylorTicksLabels()
+ markersTab = QTaylorMarkers()
+ tabWidget.addTab(interfaceTab, 'Interface')
+ tabWidget.addTab(markersTab, 'Markers')
+ tabWidget.addTab(tickAndLabelTab, 'Ticks and Labels')
+ vbox.addWidget(tabWidget)
+
+ # Set up the scrollbar / widget size
+ widgetWrapper = QtGui.QWidget()
+ widgetWrapper.resize(670, 520)
+ widgetWrapper.setLayout(vbox)
+ self.setWidget(widgetWrapper)
+
+ def initValues(self):
+ interfaceTab.initValues()
+ markersTab.initValues()
+ tickAndLabelTab.initValues()
+
+class QTaylorMarkers(QtGui.QScrollArea):
+ """ Tabbed Widget for Taylor -> Markers """
+
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ self.row = 1
+ self.grid = QtGui.QGridLayout()
+ self.markerList = []
+ vbox = QtGui.QVBoxLayout()
+
+ # Create Column Labels
+ self.grid.addWidget(QtGui.QLabel(''), 0, 0)
+ self.grid.addWidget(QtGui.QLabel('#'), 0, 1)
+ self.grid.addWidget(QtGui.QLabel('Active'), 0, 2)
+ self.grid.addWidget(QtGui.QLabel('Symbol'), 0, 3)
+ self.grid.addWidget(QtGui.QLabel('Color'), 0, 4)
+ self.grid.addWidget(QtGui.QLabel('Size'), 0, 5)
+ self.grid.addWidget(QtGui.QLabel('Id'), 0, 6)
+ self.grid.addWidget(QtGui.QLabel('Id Size'), 0, 7)
+ self.grid.addWidget(QtGui.QLabel('+X'), 0, 8)
+ self.grid.addWidget(QtGui.QLabel('+Y'), 0, 9)
+ self.grid.addWidget(QtGui.QLabel('Id Color'), 0, 10)
+ self.grid.addWidget(QtGui.QLabel('Id Font'), 0, 11)
+ self.grid.addWidget(QtGui.QLabel('Line'), 0, 12)
+ self.grid.addWidget(QtGui.QLabel('Type'), 0, 13)
+ self.grid.addWidget(QtGui.QLabel('Size'), 0, 14)
+ self.grid.addWidget(QtGui.QLabel('Color'), 0, 15)
+
+ vbox.addLayout(self.grid)
+
+ # Create Buttons
+ hbox = QtGui.QHBoxLayout()
+ addButton = self.createButton('Add')
+ delButton = self.createButton('Delete')
+ insertButton = self.createButton('Insert')
+ hbox.addWidget(addButton)
+ hbox.addWidget(delButton)
+ hbox.addWidget(insertButton)
+ vbox.addLayout(hbox)
+ vbox.setAlignment(self.grid, QtCore.Qt.AlignTop)
+ vbox.setAlignment(hbox, QtCore.Qt.AlignBottom)
+
+ # Set up the scrollbar
+ widgetWrapper = QtGui.QWidget()
+ widgetWrapper.resize(1200, 440)
+ widgetWrapper.setLayout(vbox)
+ self.setWidget(widgetWrapper)
+
+ # Connect Signals
+ self.connect(addButton, QtCore.SIGNAL('pressed()'), self.addMarker)
+ self.connect(delButton, QtCore.SIGNAL('pressed()'), self.removeSelectedMarkers)
+ self.connect(insertButton, QtCore.SIGNAL('pressed()'), self.insertMarkers)
+
+ def initValues(self):
+ # Delete all markers
+ # TODO
+ return
+
+ def removeMarker(self, marker):
+ widgets = marker.getWidgets()
+ for key in list(widgets):
+ self.grid.removeWidget(widgets[key])
+ widgets[key].hide()
+
+ self.row -= 1
+
+ def removeSelectedMarkers(self):
+ """ Delete all of the selected markers from the grid layout"""
+
+ removeList = []
+ for marker in self.markerList:
+ if marker.isSelected():
+ self.removeMarker(marker)
+ removeList.append(marker)
+
+ # Update each subsequent marker's entry number, and position in the grid
+ for i in range(self.markerList.index(marker) + 1, len(self.markerList)):
+ row = int(self.markerList[i].getEntryNumber())
+ self.markerList[i].setEntryNumber(row - 1)
+ self.moveMarkerRow(row, row-1)
+
+ for marker in removeList:
+ if marker.isSelected():
+ self.markerList.remove(marker)
+
+ def moveMarkerRow(self, row, newRow):
+ """ Move a marker grid item at row to newRow """
+ numCols = 16
+ for col in range(numCols):
+ if self.grid.itemAtPosition(row, col) is not None:
+ widget = self.grid.itemAtPosition(row, col).widget()
+ self.grid.removeWidget(widget)
+ self.grid.addWidget(widget, newRow, col, QtCore.Qt.AlignTop)
+
+ def insertMarkers(self):
+ """ For each marker that is selected, create and insert a new marker before it """
+ selectedMarkerList = []
+ for marker in self.markerList:
+ if marker.isSelected():
+ selectedMarkerList.append(marker)
+ # Update the selected and each subsequent marker's entry number, and position in the grid
+ for i in range(self.markerList.index(marker), len(self.markerList)):
+ row = int(self.markerList[i].getEntryNumber())
+ self.markerList[i].setEntryNumber(row + 1)
+ self.moveMarkerRow(row, row + 1)
+
+ # Insert the new markers in the correct positions
+ for marker in selectedMarkerList:
+ index = self.markerList.index(marker)
+ newMarker = QMarkerEditorEntry(self.grid, index + 1)
+ self.markerList.insert(index, newMarker)
+ self.row += 1
+
+ def addMarker(self):
+ self.markerList.append(QMarkerEditorEntry(self.grid, self.row))
+ self.row += 1
+
+ def createButton(self, text):
+ button = QtGui.QToolButton()
+ button.setText(text)
+ return button
+
+class QMarkerEditorEntry(QtGui.QWidget):
+ def __init__(self, grid, row, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.widgets = {}
+
+ symbolList = ["dot", "plus", "star", "circle", "cross", "diamond", "triangle_up", "triangle_down", "triangle_left", "triangle_right", "square", "diamond_fill", "triangle_up_fill", "triangle_down_fill", "triangle_left_fill", "triangle_right_fill", "square_fill"]
+ lineList = ['None', 'Tail', 'Head', 'Line']
+ typeList = ['solid', 'dash', 'dot', 'dash-dot', 'long-dash']
+
+ self.widgets['selectedBox'] = QtGui.QCheckBox()
+ self.widgets['entryNumber'] = QtGui.QLabel(str(row))
+ self.widgets['activeBox'] = QtGui.QCheckBox()
+ self.widgets['symbolCombo'] = self.createCombo(symbolList)
+ self.widgets['colorCombo1'] = self.createCombo(['TODO'])
+ self.widgets['size'] = QtGui.QLineEdit()
+ self.widgets['id'] = QtGui.QLineEdit()
+ self.widgets['idSize'] = QtGui.QLineEdit()
+ self.widgets['x'] = QtGui.QLineEdit()
+ self.widgets['y'] = QtGui.QLineEdit()
+ self.widgets['idColorCombo'] = self.createCombo(['TODO'])
+ self.widgets['idFontCombo'] = self.createCombo(map(str, range(1,10)))
+ self.widgets['lineCombo'] = self.createCombo(lineList)
+ self.widgets['typeCombo'] = self.createCombo(typeList)
+ self.widgets['size2'] = QtGui.QLineEdit()
+ self.widgets['colorCombo2'] = self.createCombo(['TODO'])
+
+ grid.addWidget(self.widgets['selectedBox'], row, 0, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['entryNumber'], row, 1, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['activeBox'], row, 2, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['symbolCombo'], row, 3, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['colorCombo1'], row, 4, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['size'], row, 5, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['id'], row, 6, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['idSize'], row, 7, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['x'], row, 8, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['y'], row, 9, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['idColorCombo'], row, 10, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['idFontCombo'], row, 11, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['lineCombo'], row, 12, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['typeCombo'], row, 13, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['size2'], row, 14, QtCore.Qt.AlignTop)
+ grid.addWidget(self.widgets['colorCombo2'], row, 15, QtCore.Qt.AlignTop)
+
+ # TODO initialize the values
+
+ def getWidgets(self):
+ return self.widgets
+
+ def getColor2(self):
+ return self.widgets['colorCombo2'].currentText()
+
+ def getSize2(self):
+ return self.widgets['size2'].currentText()
+
+ def getType(self):
+ return self.widgets['typeCombo'].currentText()
+
+ def getLine(self):
+ return self.widgets['lineCombo'].currentText()
+
+ def getIdFont(self):
+ return self.widgets['idFontCombo'].currentText()
+
+ def getIdColor(self):
+ return self.widgets['idColorCombo'].currentText()
+
+ def getSize(self):
+ return self.widgets['size'].currentText()
+
+ def getID(self):
+ return self.widgets['id'].currentText()
+
+ def getIdSize(self):
+ return self.widgets['idSize'].currentText()
+
+ def getX(self):
+ return self.widgets['x'].currentText()
+
+ def gety(self):
+ return self.widgets['y'].currentText()
+
+ def getColor(self):
+ return self.widgets['colorCombo1'].currentText()
+
+ def getSymbol(self):
+ return self.widgets['symbolCombo'].currentText()
+
+ def getEntryNumber(self):
+ return int(self.widgets['entryNumber'].text())
+
+ def setEntryNumber(self, num):
+ self.widgets['entryNumber'].setText(str(num))
+
+ def isActive(self):
+ return self.widgets['activeBox'].isChecked()
+
+ def isSelected(self):
+ return self.widgets['selectedBox'].isChecked()
+
+ def createCombo(self, entries):
+ comboBox = QtGui.QComboBox()
+ comboBox.setMaximumWidth(120)
+ comboPalette = comboBox.view().palette()
+ comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
+ comboPalette.setColor(QtGui.QPalette.Highlight, QtCore.Qt.blue)
+ comboBox.view().setPalette(comboPalette)
+
+ for entry in entries:
+ comboBox.addItem(entry)
+
+ return comboBox
+
+class QTaylorTicksLabels(QtGui.QScrollArea):
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+
+ vbox = QtGui.QVBoxLayout()
+ xFrame = QFramedWidget('X axis')
+ self.xlabels = xFrame.addLabeledLineEdit('Labels:')
+ self.xticks = xFrame.addLabeledLineEdit('Ticks:')
+ vbox.addWidget(xFrame)
+
+ yFrame = QFramedWidget('Y axis')
+ self.ylabels = yFrame.addLabeledLineEdit('Labels:')
+ self.yticks = yFrame.addLabeledLineEdit('Ticks:')
+ vbox.addWidget(yFrame)
+
+ corArcFrame = QFramedWidget('Correlation arc')
+ self.corLabels = corArcFrame.addLabeledLineEdit('Labels:')
+ self.corTicks = corArcFrame.addLabeledLineEdit('Ticks:')
+ vbox.addWidget(corArcFrame)
+
+ # Init line edits
+ self.initValues()
+
+ # Set up the scrollbar
+ wrapperWidget = QtGui.QWidget()
+ wrapperWidget.setLayout(vbox)
+ wrapperWidget.setMinimumWidth(580)
+ self.setWidget(wrapperWidget)
+
+ def initValues(self):
+ self.xlabels.setText('*')
+ self.xticks.setText('*')
+ self.ylabels.setText('*')
+ self.yticks.setText('*')
+ self.corLabels.setText('*')
+ self.corTicks.setText('*')
+
+class QTaylorInterfaceTab(QtGui.QScrollArea):
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+
+ # General Aspect
+ genFrame = QFramedWidget('General Aspect')
+ self.detailSlider = genFrame.addLabeledSlider('Detail:', newRow=False)
+ self.maxValue = genFrame.addLabeledLineEdit('Maximum Value:')
+ self.quadran = genFrame.addRadioFrame('Quadran', ['1', '2'])
+ self.refValue = genFrame.addLabeledLineEdit('Reference Value:')
+ vbox.addWidget(genFrame)
+
+ # Skill
+ skillFrame = QFramedWidget('Skill')
+ self.skillValues = skillFrame.addLabeledLineEdit('Skill Values:')
+ self.skillLineColor = skillFrame.addLabeledComboBox('Skill Lines Color:',
+ ['TODO'])
+ self.drawLabels = skillFrame.addCheckBox('Draw Skill Contour Labels')
+ self.skillCoefficients = skillFrame.addLabeledLineEdit('Skill Coefficients:')
+ vbox.addWidget(skillFrame)
+
+ # Arrows
+ arrowFrame = QFramedWidget('Arrows')
+ self.lengthSlider = arrowFrame.addLabeledSlider('Length:', newRow=False)
+ self.angleSlider = arrowFrame.addLabeledSlider('Angle:')
+ self.baseSlider = arrowFrame.addLabeledSlider('Base:')
+ # TODO - Create a widget to draw the arrow
+
+ vbox.addWidget(arrowFrame)
+ vbox.setAlignment(arrowFrame, QtCore.Qt.AlignTop)
+
+ # Set up the scrollbar
+ wrapperWidget = QtGui.QWidget()
+ wrapperWidget.setLayout(vbox)
+ wrapperWidget.setMinimumWidth(580)
+ self.setWidget(wrapperWidget)
+
+ # Init Values
+ self.initValues()
+
+ # Connect Signals
+ self.connect(self.lengthSlider, QtCore.SIGNAL('valueChanged(int)'), self.lengthChangedEvent)
+ self.connect(self.angleSlider, QtCore.SIGNAL('valueChanged(int)'), self.angleChangedEvent)
+ self.connect(self.baseSlider, QtCore.SIGNAL('valueChanged(int)'), self.baseChangedEvent)
+
+ def initValues(self):
+ # TODO Init w/ non hardcoded values?
+
+ # General Aspect
+ self.detailSlider.setTickPosition(QtGui.QSlider.TicksBelow)
+ self.detailSlider.setMinimum(0)
+ self.detailSlider.setMaximum(100)
+ self.detailSlider.setSingleStep(5)
+ self.detailSlider.setTickInterval(10)
+
+ self.maxValue.setText('None')
+ self.refValue.setText('1.0')
+ self.quadran.setChecked('1')
+
+ # Arrows
+ self.lengthSlider.setTickPosition(QtGui.QSlider.TicksBelow)
+ self.angleSlider.setTickPosition(QtGui.QSlider.TicksBelow)
+ self.baseSlider.setTickPosition(QtGui.QSlider.TicksBelow)
+
+ def lengthChangedEvent(self, int):
+ return # TODO
+
+ def angleChangedEvent(self, int):
+ return # TODO
+
+ def baseChangedEvent(self, int):
+ return # TODO
+
+class QScatterEditor(QtGui.QScrollArea):
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+
+ # Create Widgets
+ frame = QFramedWidget()
+ markerTypes = ["dot", "plus", "star", "circle", "cross", "diamond", "triangle_up",
+ "triangle_down", "triangle_left", "triangle_right", "square",
+ "diamond_fill", "triangle_up_fill", "triangle_down_fill",
+ "triangle_left_fill", "triangle_right_fill", "square_fill"]
+ self.markerType = frame.addLabeledComboBox('Scatter Marker Type:',
+ markerTypes, indent=False)
+ self.colorIndex = frame.addLabeledSpinBox('Scatter Marker Color Index',
+ 0, 255, indent=False)
+ self.markerSize = frame.addLabeledSpinBox('Scatter Marker Size',
+ 1, 300, indent=False)
+
+ self.initValues()
+
+ # Set toolTips
+ self.markerType.setToolTip("Select the scatter marker type. ")
+ self.colorIndex.setToolTip("Select the scatter marker color index. ")
+ self.markerSize.setToolTip("Select the scatter marker size. ")
+
+ vbox.addWidget(frame)
+ vbox.setAlignment(frame, QtCore.Qt.AlignTop)
+
+ # Set up the scrollbar
+ widgetWrapper = QtGui.QWidget()
+ widgetWrapper.setMinimumWidth(580)
+ widgetWrapper.setLayout(vbox)
+ self.setWidget(widgetWrapper)
+
+ def initValues(self):
+ # TODO: init w/ non-hardcoded values?
+ self.colorIndex.setValue(241)
+ self.markerSize.setValue(3)
+
+class QOutlineEditor(QtGui.QScrollArea):
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+
+ # Create Widgets
+ frame = QFramedWidget()
+ self.lineType = frame.addLabeledComboBox('Outfill Fill Area Style:',
+ ['solid', 'dash', 'dot', 'dash-dot', 'long-dash'],
+ indent=False)
+ self.lineColorIndex = frame.addLabeledSpinBox('Outfill Line Color Index:',
+ 0, 255, indent=False)
+ self.indexValues = frame.addLabeledLineEdit('Outfill Index Values:',
+ indent=False)
+
+ # Init Values - TODO: init w/ non-hardcoded values?
+ self.lineColorIndex.setValue(241)
+ self.indexValues.setText('1')
+
+ # Set tool tips
+ self.lineType.setToolTip("Select the outline line type. ")
+ self.lineColorIndex.setToolTip("Enter the line color index value. There can only\nbe one color index value (ranging from 0 to 255).\nIf an error in the color index value occurs, then the\ndefault color value index (i.e., 241) will be used.")
+ self.indexValues.setToolTip("Outlines are drawn to enclose the specified values\nin the data array. As few as one, or\nas many as\nten values, can be specified:\noutline=([n1,[n2,[n3,...[n10]...]]]).")
+
+ vbox.addWidget(frame)
+ vbox.setAlignment(frame, QtCore.Qt.AlignTop)
+
+ # Set up the scrollbar
+ widgetWrapper = QtGui.QWidget()
+ widgetWrapper.setMinimumWidth(580)
+ widgetWrapper.setLayout(vbox)
+ self.setWidget(widgetWrapper)
+
+class QOutfillEditor(QtGui.QScrollArea):
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+
+ # Create Widgets
+ frame = QFramedWidget()
+ self.fillArea = frame.addLabeledComboBox('Outfill Fill Area Style:',
+ ['Solid', 'Hatch', 'Pattern', 'Hallow'],
+ indent=False)
+ self.fillAreaIndex = frame.addLabeledSpinBox('Outfill Fill Area Index:',
+ 1, 20, indent=False)
+ self.fillColorIndex = frame.addLabeledSpinBox('Outfill Fill Area Color Index:',
+ 0, 255, indent=False)
+ self.indexValues = frame.addLabeledLineEdit('Outfill Index Values:',
+ indent=False)
+ vbox.addWidget(frame)
+ vbox.setAlignment(frame, QtCore.Qt.AlignTop)
+
+ self.initValues()
+
+ # Set ToolTips
+ self.fillArea.setToolTip("Select the outfill fill area style type. ")
+ self.fillAreaIndex.setToolTip("Select the outfill fill area index value. ")
+ self.fillColorIndex.setToolTip("Enter the fillarea color index value. There can only\nbe one color index value (ranging from 0 to 255).\nIf an error in the color index value occurs, then the\ndefault color value index (i.e., 241) will be used.")
+ self.indexValues.setToolTip("Outlines are filled to enclose the selected values\nthat appear in the data array. As few as one, or\nas many as ten values, can be specified:\noutline=([n1,[n2,[n3,...[n10]...]]]).")
+
+ # Set up the scrollbar
+ widgetWrapper = QtGui.QWidget()
+ widgetWrapper.setMinimumWidth(580)
+ widgetWrapper.setLayout(vbox)
+ self.setWidget(widgetWrapper)
+
+ def initValues(self):
+ # TODO - init w/ non hardcoded values?
+ self.fillAreaIndex.setValue(1)
+ self.fillColorIndex.setValue(241)
+ self.indexValues.setText('1')
+
+class Q1DPlotEditor(QtGui.QScrollArea):
+
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+
+ frame = QFramedWidget()
+ frame.addWidget(QtGui.QLabel('Define up to 15 values:'), QtCore.Qt.AlignTop)
+ self.lineTypes = frame.addLabeledLineEdit('Line Types: ')
+ self.lineColors = frame.addLabeledLineEdit('Line Colors: ')
+ self.lineWidths = frame.addLabeledLineEdit('Line Widths: ')
+ self.markerTypes = frame.addLabeledLineEdit('Marker Types: ')
+ self.markerColors = frame.addLabeledLineEdit('Marker Colors: ')
+ self.markerSizes = frame.addLabeledLineEdit('Marker Sizes: ')
+
+ self.initValues()
+ self.lineTypes.setToolTip("Set the line types. The line values can either be\n('solid', 'dash', 'dot', 'dash-dot', 'long-dash')\nor (0, 1, 2, 3, 4) or None")
+ self.lineColors.setToolTip("Set the line colors. The line color attribute\n values must be integers ranging from 0 to 255.\n(e.g., 16, 32, 48, 64) ")
+ self.lineWidths.setToolTip("Set the line width. The line width is an integer\nor float value in the range (1 to 100)")
+ self.markerTypes.setToolTip("Set the marker types. The marker values can either\nbe (None, 'dot', 'plus', 'star', 'circle', 'cross', 'diamond',\n'triangle_up', 'triangle_down', 'triangle_left',\n'triangle_right', 'square', 'diamond_fill',\n'triangle_up_fill', 'triangle_down_fill',\n'triangle_left_fill', 'triangle_right_fill',\n'square_fill') or (0, 1, 2, 3, 4, 5, 6, 7, 8, 9,\n10, 11, 12, 13, 14, 15, 16, 17) or None. ")
+ self.markerColors.setToolTip("Set the marker colors. The marker color attribute\nvalues must be integers ranging from 0 to 255.")
+ self.markerSizes.setToolTip("Set the marker sizes. The marker size attribute\nvalues must be integers or floats ranging from\n1 to 300. " )
+
+ vbox.addWidget(frame)
+ vbox.setAlignment(frame, QtCore.Qt.AlignTop)
+
+ # Set up the scrollbar
+ widgetWrapper = QtGui.QWidget()
+ widgetWrapper.setMinimumWidth(580)
+ widgetWrapper.setLayout(vbox)
+ self.setWidget(widgetWrapper)
+
+ def initValues(self):
+ # TODO ?
+ self.lineTypes.setText('None')
+ self.lineColors.setText('None')
+ self.lineWidths.setText('None')
+ self.markerTypes.setText('None')
+ self.markerColors.setText('None')
+ self.markerSizes.setText('None')
+
+class QMeshfillEditor(QtGui.QScrollArea):
+
+ def __init__(self, parent=None, gm=None):
+ QtGui.QWidget.__init__(self, parent)
+
+ if type(gm) in [types.ListType, types.TupleType, types.NoneType]:
+ self.gm = gm
+ else:
+ self.gm=[gm,]
+
+ vbox = QtGui.QVBoxLayout()
+
+ # General Settings
+ genSettings = QFramedWidget('General Settings')
+ self.missing = genSettings.addLabeledLineEdit('Missing:')
+ self.xWrap = genSettings.addLabeledLineEdit('X Wrap:')
+ self.yWrap = genSettings.addLabeledLineEdit('Y Wrap:', newRow = False)
+ self.genLegend = genSettings.addLabeledLineEdit('Legend Labels')
+ self.showMesh = genSettings.addRadioFrame('Show Mesh:', ['No', 'Yes'])
+ self.ext1 = genSettings.addRadioFrame('Ext 1:', ['No', 'Yes'], newRow=False)
+ self.ext2 = genSettings.addRadioFrame('Ext 2:', ['No', 'Yes'], newRow=False)
+ vbox.addWidget(genSettings)
+
+ # Custom Settings
+ custSettings = QFramedWidget('Custom Settings')
+ custSettings.addLabel('Define iso level range values')
+ self.incZero = custSettings.addRadioFrame('Include Zero:', ['Off', 'On'],
+ newRow=False)
+ self.ranges = custSettings.addLabeledLineEdit('Ranges:')
+ self.colors = custSettings.addLabeledLineEdit('Colors:')
+ self.lineTypes = custSettings.addLabeledLineEdit('Line Types:')
+ self.lineWidths = custSettings.addLabeledLineEdit('Line Widths:')
+ self.orientation = custSettings.addLabeledLineEdit('Orientation:')
+ self.arrowScale = custSettings.addLabeledLineEdit('Contour Arrows Scale:')
+ self.arrowSpacing = custSettings.addLabeledLineEdit('Contour Arrows Spacing:')
+ self.arrowAngle = custSettings.addLabeledLineEdit('Contour Arrows Angle:')
+ self.custLegend = custSettings.addLabeledLineEdit('Legend Labels:')
+ self.isolineLabels = custSettings.addRadioFrame('Isoline Labels:',
+ ['Off', 'On'])
+ custSettings.newRow()
+ custSettings.addLabel('Define iso level parameters:')
+ self.spacing = custSettings.addRadioFrame('Spacing:',
+ ['Linear', 'Log'],
+ newRow=False)
+ self.minVal = custSettings.addLabeledLineEdit('Minimum Value:')
+ self.maxVal = custSettings.addLabeledLineEdit('Maximum Value:')
+ self.nIntervals = custSettings.addLabeledSpinBox('Number of Intervals:',
+ 2, 223)
+ self.smallestExpLabel, self.smallestExp = custSettings.addLabelAndLineEdit('Smallest Exponent for Negative Values:')
+ self.numNegDecLabel, self.numNegDec = custSettings.addLabelAndLineEdit('Number of Negative Decades:')
+ genRangesButton = custSettings.addButton('Generate Ranges')
+ clearButton = custSettings.addButton('Clear All', newRow=False)
+ vbox.addWidget(custSettings)
+
+ # Init values / tool tips
+ self.initValues()
+ self.setToolTips()
+
+ # Set up the scrollbar
+ widgetWrapper = QtGui.QWidget()
+ widgetWrapper.setLayout(vbox)
+ self.setWidget(widgetWrapper)
+
+ # Connect Signals
+ self.connect(clearButton, QtCore.SIGNAL('pressed()'),
+ custSettings.clearAllLineEdits)
+ self.connect(self.spacing.getButton('Linear'),
+ QtCore.SIGNAL('pressed()'),
+ lambda : self.setEnabledLogLineEdits(False))
+ self.connect(self.spacing.getButton('Log'),
+ QtCore.SIGNAL('pressed()'),
+ lambda : self.setEnabledLogLineEdits(True))
+ self.connect(genRangesButton, QtCore.SIGNAL('pressed()'),
+ self.generateRanges)
+
+ def initValues(self):
+ # TODO : init missing, x wrap, y wrap, legend labels
+
+ self.showMesh.setChecked('No')
+ self.ext1.setChecked('No')
+ self.ext2.setChecked('No')
+ self.incZero.setChecked('Off')
+ self.spacing.setChecked('Linear')
+ self.setEnabledLogLineEdits(False)
+
+ def generateRanges(self):
+ try:
+ minValue = float(self.minVal.text())
+ maxValue = float(self.maxVal.text())
+ numIntervals = int(self.nIntervals.text())
+ except:
+ QSimpleMessageBox('Values must be a number', self).show()
+ return
+
+ if numIntervals < 2 or numIntervals > 223:
+ QSimpleMessageBox("The 'number of intervals' value must be between 2 and 223.",
+ self).show()
+ return
+
+ colors = []
+ values = []
+ value = minValue
+ color = 16
+
+ # Generate ranges and colors (Linear)
+ if self.spacing.isChecked('Linear'):
+ delta = float((maxValue - minValue) / numIntervals)
+ d = int(222 / (numIntervals - 1))
+
+ for a in range(numIntervals + 1):
+ if color <= 238:
+ colors.append(color)
+ values.append(value)
+ color += d
+ value += delta
+ # Generate ranges (Log)
+ else:
+ A = float(self.minVal.text())
+ B = float(self.maxVal.text())
+ C = float(self.nIntervals.text())
+ try:
+ D = float(self.smallestExp.text())
+ except:
+ D = 0
+ try:
+ E = float(self.numNegDec.text())
+ except:
+ E = 0
+
+ if C > 0:
+ if E > 0: # Generate negative contours
+ for i in range(int(E * C), 0, -1):
+ values.append(round_number(-10.0 ** (D+(i-1)/C)))
+ if B > 0: # Generate positive contours
+ for i in range(1, int((B * C) + 1)):
+ values.append(round_number(10.0 ** (A+(i-1)/C)))
+ else:
+ QSimpleMessageBox("The 'Levels per Decade' must be a positive number.").show()
+
+ # Gen colors (Log)
+ numIntervals = len(values) - 1
+ d = int(222 / (numIntervals - 1))
+ for a in range(numIntervals):
+ colors.append(16 + a * d)
+
+ if self.incZero.isChecked('On'):
+ values.insert(0, 0.0)
+
+ self.ranges.setText(str(values))
+ self.colors.setText(str(colors))
+
+ def setEnabledLogLineEdits(self, enable):
+ """ Disable or Enable the 'Num neg decades' and 'smallest exp for neg
+ values' lineEdits """
+ self.smallestExp.setEnabled(enable)
+ self.numNegDec.setEnabled(enable)
+ self.smallestExpLabel.setEnabled(enable)
+ self.numNegDecLabel.setEnabled(enable)
+
+ if enable == True:
+ self.smallestExp.setToolTip("Smallest exponent for negative values")
+ self.numNegDec.setToolTip("Number of negative decades.")
+ else:
+ self.smallestExp.setToolTip("Disabled. Not in use for linear spacing.")
+ self.numNegDec.setToolTip("Disabled. Not in use for linear spacing.")
+
+ def setToolTips(self):
+ # General Setting Tips
+ self.missing.setToolTip("Set the missing color index value. The colormap\nranges from 0 to 255, enter the desired color index value 0\nthrough 255.")
+ self.xWrap.setToolTip("Set the wrapping along X axis, 0 means no wrapping")
+ self.yWrap.setToolTip("Set the wrapping along Y axis, 0 means no wrapping")
+ self.genLegend.setToolTip("Specify the desired legend labels.\nFor example:\nNone -- Allow VCS to generate legend labels\n( ), or [ ], or { } -- No legend labels\n[ 0, 10, 20 ] or { 0:'0', 10:'10', 20:'20' }\n[ 0, 10 ] or { 0:'text', 10:'more text' }")
+
+ # Custom Setting Tips
+ self.ranges.setToolTip("The iso level range values. (e.g., 10, 20, 30, 40, 50).")
+ self.colors.setToolTip("The iso level color index values. The index colors range\nfrom 0 to 255. For example:\n Use explicit indices: 16, 32, 48, 64, 80;\n Use two values to generate index range: 16, 32")
+ self.lineTypes.setToolTip("The line type for the isolines. (e.g., 4, 1, 3, 2, 0).")
+ self.lineWidths.setToolTip("The width values for the isolines. (e.g., 1, 3, 5, 2, 7).")
+ self.orientation.setToolTip("Drawing orientation arrows:\n none (0)\n clokwise (1)\n clockwise where y axis is positive (2)\n clockwise where x axis is positive(3)\n Negative values indicate counter-clockwise.")
+ self.arrowScale.setToolTip("Scale factor for arrows length")
+ self.arrowSpacing.setToolTip("Spacing factor for arrows")
+ self.arrowAngle.setToolTip("Angle of Arrows heads")
+ self.isolineLabels.setToolTip("Toggle 'Isoline Labels' on or off.")
+ self.custLegend.setToolTip("Specify the desired legend labels.\nFor example:\nNone -- Allow VCS to generate legend labels\n( ), or [ ], or { } -- No legend labels\n[ 0, 10, 20 ] or { 0:'0', 10:'10', 20:'20' }\n[ 0, 10 ] or { 0:'text', 10:'more text' }")
+ self.minVal.setToolTip("The minimum contour level.")
+ self.maxVal.setToolTip("The maximum contour level.")
+ self.nIntervals.setToolTip("The number of intervals between each contour level. Maximum number range [2 to 223].")
+ self.smallestExp.setToolTip("Disabled. Not in use for linear spacing.")
+ self.numNegDec.setToolTip("Disabled. Not in use for linear spacing.")
+
+class QContourEditor(QtGui.QScrollArea):
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+
+ #### TODO gm stuff
+
+ frame = QFramedWidget()
+
+ frame.addWidget(QtGui.QLabel('Define iso level range values:'))
+ self.includeZeroButtonGroup = frame.addRadioFrame('Include Zero:',
+ ['Off', 'On'],
+ newRow=False)
+ self.ranges = frame.addLabeledLineEdit('Ranges:')
+ self.colors = frame.addLabeledLineEdit('Colors:')
+ self.lineTypes = frame.addLabeledLineEdit('Line Types:', )
+ self.lineWidths = frame.addLabeledLineEdit('Line Widths:')
+ self.orientation = frame.addLabeledLineEdit('Orientation:')
+ self.arrowScale = frame.addLabeledLineEdit('Contour Arrows Scale:')
+ self.arrowSpacing = frame.addLabeledLineEdit('Contour Arrows Spacing:')
+ self.angle = frame.addLabeledLineEdit('Contour Arrows Angle:')
+ self.labelButtonGroup = frame.addRadioFrame('Isoline Labels:',
+ ['Off', 'On'])
+ self.legendLabels = frame.addLabeledLineEdit('Legend Labels')
+ frame.newRow()
+ frame.addWidget(QtGui.QLabel('Define iso level parameters:'))
+ self.spacingButtonGroup = frame.addRadioFrame('Spacing:',
+ ['Linear', 'Log'],
+ newRow=False)
+ self.minVal = frame.addLabeledLineEdit('Minimum Value:')
+ self.maxVal = frame.addLabeledLineEdit('Maximum Value:')
+ self.nIntervals = frame.addLabeledSpinBox('Number of Intervals:',
+ 2, 223,)
+ self.smallestExpLabel, self.smallestExp = frame.addLabelAndLineEdit('Smallest Exponent for Negative Values:')
+ self.numNegDecLabel, self.numNegDec = frame.addLabelAndLineEdit('Number of Negative Decades:')
+ genRangesButton = frame.addButton('Generate Ranges')
+ clearButton = frame.addButton('Clear All', newRow=False)
+
+ vbox.addWidget(frame)
+ self.frame = frame
+
+ # Init values / tool tips
+ self.initValues()
+ self.setToolTips()
+
+ # Set up the scrollbar
+ widgetWrapper = QtGui.QWidget()
+ widgetWrapper.setLayout(vbox)
+ widgetWrapper.setMinimumWidth(630)
+ self.setWidget(widgetWrapper)
+
+ # Connect Signals
+ self.connect(clearButton, QtCore.SIGNAL('pressed()'),
+ self.frame.clearAllLineEdits)
+ self.connect(genRangesButton, QtCore.SIGNAL('pressed()'),
+ self.generateRanges)
+ self.connect(self.spacingButtonGroup.getButton('Linear'),
+ QtCore.SIGNAL('pressed()'),
+ lambda : self.setEnabledLogLineEdits(False))
+ self.connect(self.spacingButtonGroup.getButton('Log'),
+ QtCore.SIGNAL('pressed()'),
+ lambda : self.setEnabledLogLineEdits(True))
+
+ def initValues(self):
+ self.includeZeroButtonGroup.setChecked('Off')
+ self.spacingButtonGroup.setChecked('Linear')
+ self.setEnabledLogLineEdits(False)
+
+ self.minVal.setText('1.0')
+ self.maxVal.setText('2.0')
+ self.nIntervals.setValue(2)
+
+ def generateRanges(self):
+ try:
+ minValue = float(self.minVal.text())
+ maxValue = float(self.maxVal.text())
+ numIntervals = int(self.nIntervals.text())
+ except:
+ QSimpleMessageBox('Values must be a number', self).show()
+ return
+
+ if numIntervals < 2 or numIntervals > 223:
+ QSimpleMessageBox("The 'number of intervals' value must be between 2 and 223.",
+ self).show()
+ return
+
+ colors = []
+ values = []
+ value = minValue
+ color = 16
+
+ # Generate ranges and colors (Linear)
+ if self.spacingButtonGroup.isChecked('Linear'):
+ delta = float((maxValue - minValue) / numIntervals)
+ d = int(222 / (numIntervals - 1))
+
+ for a in range(numIntervals + 1):
+ if color <= 238:
+ colors.append(color)
+ values.append(value)
+ color += d
+ value += delta
+ # Generate ranges (Log)
+ else:
+ A = float(self.minVal.text())
+ B = float(self.maxVal.text())
+ C = float(self.nIntervals.text())
+ try:
+ D = float(self.smallestExp.text())
+ except:
+ D = 0
+ try:
+ E = float(self.numNegDec.text())
+ except:
+ E = 0
+
+ if C > 0:
+ if E > 0: # Generate negative contours
+ for i in range(int(E * C), 0, -1):
+ values.append(round_number(-10.0 ** (D+(i-1)/C)))
+ if B > 0: # Generate positive contours
+ for i in range(1, int((B * C) + 1)):
+ values.append(round_number(10.0 ** (A+(i-1)/C)))
+ else:
+ QSimpleMessageBox("The 'Levels per Decade' must be a positive number.").show()
+
+ # Gen colors (Log)
+ numIntervals = len(values) - 1
+ d = int(222 / (numIntervals - 1))
+ for a in range(numIntervals):
+ colors.append(16 + a * d)
+
+ if self.includeZeroButtonGroup.isChecked('On'):
+ values.insert(0, 0.0)
+
+ self.ranges.setText(str(values))
+ self.colors.setText(str(colors))
+
+ def setEnabledLogLineEdits(self, enable):
+ """ Disable or Enable the 'Num neg decades' and 'smallest exp for neg
+ values' lineEdits """
+ self.smallestExp.setEnabled(enable)
+ self.numNegDec.setEnabled(enable)
+ self.smallestExpLabel.setEnabled(enable)
+ self.numNegDecLabel.setEnabled(enable)
+
+ if enable == True:
+ self.smallestExp.setToolTip("Smallest exponent for negative values")
+ self.numNegDec.setToolTip("Number of negative decades.")
+ else:
+ self.smallestExp.setToolTip("Disabled. Not in use for linear spacing.")
+ self.numNegDec.setToolTip("Disabled. Not in use for linear spacing.")
+
+ def setToolTips(self):
+ self.ranges.setToolTip("The iso level range values. (e.g., 10, 20, 30, 40, 50).")
+ self.colors.setToolTip("The iso level color index values. The index colors range\nfrom 0 to 255. For example:\n Use explicit indices: 16, 32, 48, 64, 80;\n Use two values to generate index range: 16, 32")
+ self.lineTypes.setToolTip("The line type for the isolines. (e.g., 4, 1, 3, 2, 0).")
+ self.lineWidths.setToolTip("The width values for the isolines. (e.g., 1, 3, 5, 2, 7).")
+ self.orientation.setToolTip("Drawing orientation arrows:\n none (0)\n clokwise (1)\n clockwise where y axis is positive (2)\n clockwise where x axis is positive(3)\n Negative values indicate counter-clockwise.")
+ self.arrowScale.setToolTip("Scale factor for arrows length")
+ self.arrowSpacing.setToolTip("Spacing factor for arrows")
+ self.angle.setToolTip("Angle of Arrows heads")
+ self.labelButtonGroup.setToolTip("Toggle 'Isoline Labels' on or off.")
+ self.legendLabels.setToolTip("Specify the desired legend labels.\nFor example:\nNone -- Allow VCS to generate legend labels\n( ), or [ ], or { } -- No legend labels\n[ 0, 10, 20 ] or { 0:'0', 10:'10', 20:'20' }\n[ 0, 10 ] or { 0:'text', 10:'more text' }")
+ self.minVal.setToolTip("The minimum contour level.")
+ self.maxVal.setToolTip("The maximum contour level.")
+ self.nIntervals.setToolTip("The number of intervals between each contour level. Maximum number range [2 to 223].")
+ self.smallestExp.setToolTip("Disabled. Not in use for linear spacing.")
+ self.numNegDec.setToolTip("Disabled. Not in use for linear spacing.")
+
+class QContinentsEditor(QtGui.QScrollArea):
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+ frame = QFramedWidget()
+
+ self.lineTypeComboBox = frame.addLabeledComboBox('Continents Line Type:',
+ ['solid', 'dash', 'dot', 'dash-dot', 'long-dash'])
+ self.lineColorIndex = frame.addLabeledSpinBox('Continents Line Color Index:',
+ 0, 255)
+ self.lineWidth = frame.addLabeledSpinBox('Continents Line Width:', 1, 300)
+ self.typeIndex = frame.addLabeledSpinBox('Continents Type Index:', -1, 11)
+ vbox.addWidget(frame)
+
+ # Init values / tool tips
+ self.initValues()
+ self.setToolTips()
+
+ # Set up the scrollbar
+ widgetWrapper = QtGui.QWidget()
+ widgetWrapper.setMinimumWidth(580)
+ widgetWrapper.setLayout(vbox)
+ self.setWidget(widgetWrapper)
+
+ def initValues(self):
+ self.lineColorIndex.setValue(0)
+ self.lineWidth.setValue(1)
+ self.typeIndex.setValue(-1)
+
+ def setToolTips(self):
+ self.lineTypeComboBox.setToolTip('Select the continents line type.')
+ self.lineColorIndex.setToolTip('Select the continents color index.')
+ self.lineWidth.setToolTip('Set the continents line width.')
+ self.typeIndex.setToolTip("Select the continents type index.Where\n-1 = 'Auto Continents';\n0 = 'No Continents';\n1 = 'Fine Continents';\n2 = 'Coarse Continents';\n3 = 'United States Continents';\n4 = 'Political Borders Continents';\n5 = 'Rivers Continents';\n6 - 11 = 'User defined Continents'")
+
+ def getLineType(self):
+ return self.lineTypeComboBox.currentText()
+
+ def getTypeIndex(self):
+ try:
+ return int(self.typeIndex.text())
+ except:
+ return None
+
+ def getLineWidth(self):
+ try:
+ return int(self.lineWidth.text())
+ except:
+ return None
+
+ def getLineColorIndex(self):
+ try:
+ return int(self.lineColorIndex.text())
+ except:
+ return None
+
+class QBoxfillEditor(QtGui.QScrollArea):
+
+ def __init__(self, parent=None, gm=None):
+ QtGui.QScrollArea.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+
+ if type(gm) in [types.ListType, types.TupleType, types.NoneType]:
+ self.gm = gm
+ elif type(gm) is not None:
+ self.gm=[gm,]
+
+ # 'define boxfill attributes + boxfill type radio buttons'
+ hbox1 = QtGui.QHBoxLayout()
+ hbox1.addWidget(QtGui.QLabel('Define boxfill attribute values'))
+
+ self.boxfillTypeButtonGroup = QRadioButtonFrame('Boxfill type:')
+ self.boxfillTypeButtonGroup.addButtonList(['linear', 'log10', 'custom'])
+ hbox1.addWidget(self.boxfillTypeButtonGroup)
+
+ vbox.addLayout(hbox1)
+
+ # General Settings
+ generalSettings = QFramedWidget('General Settings')
+ self.missingLineEdit = generalSettings.addLabeledLineEdit('Missing:')
+ self.ext1ButtonGroup = generalSettings.addRadioFrame('Ext1:',
+ ['No', 'Yes'],
+ newRow = False)
+ self.ext2ButtonGroup = generalSettings.addRadioFrame('Ext2:',
+ ['No', 'Yes'],
+ newRow = False)
+ self.legendLineEdit = generalSettings.addLabeledLineEdit('Legend Labels:')
+ vbox.addWidget(generalSettings)
+
+ # Linear & Log Settings
+ linLogSettings = QFramedWidget('Linear and Log Settings')
+
+ self.level1LineEdit = linLogSettings.addLabeledLineEdit('Level 1:')
+ self.level2LineEdit = linLogSettings.addLabeledLineEdit('Level 2:',
+ newRow = False)
+ self.color1LineEdit = linLogSettings.addLabeledLineEdit('Color 1:')
+ self.color2LineEdit = linLogSettings.addLabeledLineEdit('Color 2:',
+ newRow = False)
+ vbox.addWidget(linLogSettings)
+
+ # Custom Settings
+ customSettings = QFramedWidget('Custom Settings')
+
+ customSettings.addWidget(QtGui.QLabel('Define iso level range values:'))
+ self.includeZeroButtonGroup = customSettings.addRadioFrame('Include Zero:',
+ ['Off', 'On'],
+ newRow=False)
+ self.rangeLineEdit = customSettings.addLabeledLineEdit('Ranges:')
+ self.colorsLineEdit = customSettings.addLabeledLineEdit('Colors:')
+
+ customSettings.newRow()
+ customSettings.addWidget(QtGui.QLabel('Define iso level parameters:'))
+ self.spacingButtonGroup = customSettings.addRadioFrame('spacing:',
+ ['Linear', 'Log'],
+ newRow=False)
+
+ self.minValLineEdit = customSettings.addLabeledLineEdit('Minimum Value:')
+ self.maxValLineEdit = customSettings.addLabeledLineEdit('Maximum Value:')
+ self.nIntervals = customSettings.addLabeledSpinBox('Number of Intervals:',
+ 2, 223)
+ self.smallestExpLabel, self.expLineEdit = customSettings.addLabelAndLineEdit('Smallest Exponent for Negative Values:')
+ self.numNegDecLabel, self.negDecadesLineEdit = customSettings.addLabelAndLineEdit('Number of Negative Decades:')
+ genRangesButton = customSettings.addButton('Generate Ranges')
+ clearButton = customSettings.addButton('Clear All', newRow=False)
+ vbox.addWidget(customSettings)
+
+ # Init values
+ self.initValues()
+ self.setToolTips()
+
+ # Set up the scrollbar
+ widgetWrapper = QtGui.QWidget()
+ widgetWrapper.setLayout(vbox)
+ self.setWidget(widgetWrapper)
+
+ # Connect Signals
+ self.connect(clearButton, QtCore.SIGNAL('pressed()'), self.clearCustomSettings)
+ self.connect(genRangesButton, QtCore.SIGNAL('pressed()'), self.generateRanges)
+ self.connect(self.spacingButtonGroup.getButton('Linear'),
+ QtCore.SIGNAL('pressed()'),
+ lambda : self.setEnabledLogLineEdits(False))
+ self.connect(self.spacingButtonGroup.getButton('Log'),
+ QtCore.SIGNAL('pressed()'),
+ lambda : self.setEnabledLogLineEdits(True))
+
+ def initValues(self):
+ if self.gm is None:
+ return
+
+ # Init Line Edit Text
+ self.missingLineEdit.setText(str(self.gm[0].missing))
+ self.legendLineEdit.setText('None')
+ self.level1LineEdit.setText(str(self.gm[0].level_1))
+ self.level2LineEdit.setText(str(self.gm[0].level_2))
+ self.color1LineEdit.setText(str(self.gm[0].color_1))
+ self.color2LineEdit.setText(str(self.gm[0].color_2))
+ self.rangeLineEdit.setText(str(self.gm[0].levels))
+ self.colorsLineEdit.setText('None')
+ self.minValLineEdit.setText('')
+ self.maxValLineEdit.setText('')
+ self.expLineEdit.setText('')
+ self.negDecadesLineEdit.setText('')
+ self.nIntervals.setValue(2)
+ self.setEnabledLogLineEdits(False)
+
+ # Init selected radio buttons
+ self.boxfillTypeButtonGroup.setChecked('linear')
+ self.ext1ButtonGroup.setChecked('No')
+ self.ext2ButtonGroup.setChecked('No')
+ self.includeZeroButtonGroup.setChecked('Off')
+ self.spacingButtonGroup.setChecked('Linear')
+
+ def generateRanges(self):
+ try:
+ minValue = float(self.minValLineEdit.text())
+ maxValue = float(self.maxValLineEdit.text())
+ numIntervals = int(self.nIntervals.text())
+ except:
+ QSimpleMessageBox('Values must be a number', self).show()
+ return
+
+ if numIntervals < 2 or numIntervals > 223:
+ QSimpleMessageBox("The 'number of intervals' value must be between 2 and 223.",
+ self).show()
+ return
+
+ colors = []
+ values = []
+ value = minValue
+ color = 16
+
+ # Generate ranges and colors (Linear)
+ if self.spacingButtonGroup.isChecked('Linear'):
+ delta = float((maxValue - minValue) / numIntervals)
+ d = int(222 / (numIntervals - 1))
+
+ for a in range(numIntervals + 1):
+ if color <= 238:
+ colors.append(color)
+ values.append(value)
+ color += d
+ value += delta
+ # Generate ranges (Log)
+ else:
+ A = float(self.minValLineEdit.text())
+ B = float(self.maxValLineEdit.text())
+ C = float(self.nIntervals.text())
+
+ try:
+ D = float(self.expLineEdit.text())
+ except:
+ D = 0
+ try:
+ E = float(self.negDecadesLineEdit.text())
+ except:
+ E = 0
+
+ if C > 0:
+ if E > 0: # Generate negative contours
+ for i in range(int(E * C), 0, -1):
+ values.append(round_number(-10.0 ** (D+(i-1)/C)))
+ if B > 0: # Generate positive contours
+ for i in range(1, int((B * C) + 1)):
+ values.append(round_number(10.0 ** (A+(i-1)/C)))
+ else:
+ QSimpleMessageBox("The 'Levels per Decade' must be a positive number.").show()
+
+ # Gen colors (Log)
+ numIntervals = len(values) - 1
+ d = int(222 / (numIntervals - 1))
+ for a in range(numIntervals):
+ colors.append(16 + a * d)
+
+ if self.includeZeroButtonGroup.isChecked('On'):
+ values.insert(0, 0.0)
+
+ self.rangeLineEdit.setText(str(values))
+
+ self.colorsLineEdit.setText(str(colors))
+
+ def setEnabledLogLineEdits(self, enable):
+ """ Disable or Enable the 'Num neg decades' and 'smallest exp for neg
+ values' lineEdits """
+ self.expLineEdit.setEnabled(enable)
+ self.negDecadesLineEdit.setEnabled(enable)
+ self.smallestExpLabel.setEnabled(enable)
+ self.numNegDecLabel.setEnabled(enable)
+
+ if enable == True:
+ self.expLineEdit.setToolTip("Smallest exponent for negative values")
+ self.negDecadesLineEdit.setToolTip("Number of negative decades.")
+ else:
+ self.expLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
+ self.negDecadesLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
+
+ def setToolTips(self):
+ self.missingLineEdit.setToolTip("Set the missing color index value. The colormap\nranges from 0 to 255, enter the desired color index value 0\nthrough 255.")
+ self.legendLineEdit.setToolTip("Specify the desired legend labels.\nFor example:\n None -- Allow VCS to generate legend labels\n(), or [ ], or { } -- No legend labels\n [0, 10, 20] or { 0:'0', 10:'10', 20:'20' }\n[ 0, 10 ] or { 0:'text', 10:'more text'}")
+ self.level1LineEdit.setToolTip("The minimum data value. If level 1 is set to '1e+20',\nthen VCS will select the level.")
+ self.level2LineEdit.setToolTip("The maximum data value. If level 2 is set to '1e+20',\nthen VCS will select the level.")
+ self.color1LineEdit.setToolTip("The minimum color range index value. The colormap\nranges from 0 to 255, but only color indices 0\nthrough 239 can be changed.")
+ self.color2LineEdit.setToolTip("The maximum color range index value. The colormap\nranges from 0 to 255, but only color indices 0\nthrough 239 can be changed.")
+ self.rangeLineEdit.setToolTip("The iso level range values. (e.g., 10, 20, 30, 40, 50).")
+ self.colorsLineEdit.setToolTip("The iso level color index values. The index colors range\nfrom 0 to 255. For example:\n Use explicit indices: 16, 32, 48, 64, 80;\n Use two values to generate index range: 16, 32")
+ self.minValLineEdit.setToolTip("The minimum contour level.")
+ self.maxValLineEdit.setToolTip("The maximum contour level.")
+ self.nIntervals.setToolTip("The number of intervals between each contour level. Maximum number range [2 to 223].")
+ self.expLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
+ self.negDecadesLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
+
+ def clearCustomSettings(self):
+ self.rangeLineEdit.setText('')
+ self.colorsLineEdit.setText('')
+ self.minValLineEdit.setText('')
+ self.maxValLineEdit.setText('')
+ self.nIntervals.setValue(2)
+ self.expLineEdit.setText('')
+ self.negDecadesLineEdit.setText('')
+
+ def linearButtonPressEvent(self):
+ """ Disable the 'Num neg decades' and 'smallest exp for neg values'
+ lineEdits """
+
+ self.expLineEdit.setReadOnly(True)
+ self.negDecadesLineEdit.setReadOnly(True)
+ self.expLineEdit.setText('')
+ self.negDecadesLineEdit.setText('')
+ self.expLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
+ self.negDecadesLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
+
+ def logButtonPressEvent(self):
+ """ Enable the 'Num neg decades' and 'smallest exp for neg values'
+ lineEdits """
+
+ self.expLineEdit.setReadOnly(False)
+ self.negDecadesLineEdit.setReadOnly(False)
+ self.expLineEdit.setText('')
+ self.negDecadesLineEdit.setText('')
+ self.expLineEdit.setToolTip("Smallest exponent for negative values")
+ self.negDecadesLineEdit.setToolTip("Number of negative decades.")
+
+ def setVistrailsGraphicsMethod(self, varViewWidget):
+ """ Vistrails: Update the vistrails' Graphics Method modules' boxfill
+ input ports """
+
+ # Generate a list of tuples where each tuple is: (Input Port Name, value)
+ # and update the vistrails' graphics method input ports
+ visInput = []
+ visInput.append(('color_1', self.getValue(self.color1LineEdit, int)))
+ visInput.append(('color_2', self.getValue(self.color2LineEdit, int)))
+ visInput.append(('level_1', self.getValue(self.level1LineEdit, float)))
+ visInput.append(('level_2', self.getValue(self.level2LineEdit, float)))
+
+ varViewWidget.emit(QtCore.SIGNAL('createModule'), gm_name)
+ varViewWidget.emit(QtCore.SIGNAL('updateModuleOps'), gm_name, visInput)
+
+ def getValue(self, lineEdit, convertType, default=None):
+ try:
+ return convertType(lineEdit.text())
+ except:
+ return default
+
+class QSimpleMessageBox(QtGui.QMessageBox):
+
+ def __init__(self, text, parent):
+ QtGui.QMessageBox.__init__(self, parent)
+ self.setText(text)
+
+class QFramedWidget(QtGui.QFrame):
+
+ def __init__(self, titleText=None, parent=None):
+ QtGui.QFrame.__init__(self, parent)
+ self.setFrameStyle(QtGui.QFrame.Raised)
+ self.setFrameShape(QtGui.QFrame.Box)
+ self.lineEditList = []
+ self.vbox = QtGui.QVBoxLayout()
+ self.setLayout(self.vbox)
+ self.indent = 10
+
+ if titleText is not None:
+ title = QtGui.QLabel(titleText)
+ title.setFont(QtGui.QFont("Times", 14, QtGui.QFont.Bold))
+ self.vbox.addWidget(title)
+
+ self.newRow()
+
+ def setSpacing(self, spacing):
+ self.vbox.setSpacing(spacing)
+
+ def newRow(self):
+ self.hbox = QtGui.QHBoxLayout()
+ self.vbox.addLayout(self.hbox)
+
+ def addCheckBox(self, text, indent=True, newRow=True):
+ if newRow == True:
+ self.newRow()
+ if indent == True:
+ self.hbox.addSpacing(indentSpacing)
+
+ checkbox = QtGui.QCheckBox(text)
+ self.addWidget(checkbox)
+ return checkbox
+
+ def addLabeledComboBox(self, text, comboStringList, indent=True, newRow=True):
+ if newRow == True:
+ self.newRow()
+ if indent == True:
+ self.hbox.addSpacing(indentSpacing)
+
+ # Init combo box & set text to white on blue
+ comboBox = QtGui.QComboBox()
+ comboPalette = comboBox.view().palette()
+ comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
+ comboPalette.setColor(QtGui.QPalette.Highlight, QtCore.Qt.blue)
+ comboBox.view().setPalette(comboPalette)
+
+ for string in comboStringList:
+ comboBox.addItem(string)
+
+ self.addLabel(text)
+ self.addWidget(comboBox)
+ return comboBox
+
+ def addLabeledSpinBox(self, text, minValue=None, maxValue=None,
+ indent=True, newRow=True):
+ if newRow == True:
+ self.newRow()
+ if indent == True:
+ self.hbox.addSpacing(indentSpacing)
+
+ spinbox = QtGui.QSpinBox()
+ if maxValue is not None:
+ spinbox.setMaximum(maxValue)
+ if minValue is not None:
+ spinbox.setMinimum(minValue)
+ self.addWidget(QtGui.QLabel(text))
+ self.addWidget(spinbox)
+
+ return spinbox
+
+ def addLabeledDoubleSpinBox(self, text, minValue=None, maxValue=None,
+ step=None, indent=True, newRow=True):
+ if newRow == True:
+ self.newRow()
+ if indent == True:
+ self.hbox.addSpacing(indentSpacing)
+
+ spinbox = QtGui.QDoubleSpinBox()
+ if maxValue is not None:
+ spinbox.setMaximum(maxValue)
+ if minValue is not None:
+ spinbox.setMinimum(minValue)
+ if step is not None:
+ spinbox.setSingleStep(step)
+
+ self.addWidget(QtGui.QLabel(text))
+ self.addWidget(spinbox)
+ return spinbox
+
+ def addButton(self, text, newRow=True):
+ if newRow == True:
+ self.newRow()
+
+ button = QtGui.QToolButton()
+ button.setText(text)
+ self.addWidget(button)
+ return button
+
+ def addRadioFrame(self, text, buttonList, newRow=True):
+ if newRow == True:
+ self.newRow()
+
+ buttonGroup = QRadioButtonFrame(text, buttonList)
+ self.addWidget(buttonGroup)
+ return buttonGroup
+
+ def clearAllLineEdits(self):
+ for lineEdit in self.lineEditList:
+ lineEdit.setText('')
+
+ def addLabeledLineEdit(self, text, indent=True, newRow=True, align=None):
+ if newRow == True:
+ self.newRow()
+ if indent == True:
+ self.hbox.addSpacing(indentSpacing)
+
+ lineEdit = QtGui.QLineEdit()
+ self.lineEditList.append(lineEdit)
+ self.addWidget(QtGui.QLabel(text))
+ self.addWidget(lineEdit, align)
+
+ if align is not None:
+ self.vbox.setAlignment(self.hbox, align)
+
+ return lineEdit
+
+ def addLabelAndLineEdit(self, text, indent=True, newRow=True):
+ if newRow == True:
+ self.newRow()
+ if indent == True:
+ self.hbox.addSpacing(indentSpacing)
+
+ lineEdit = QtGui.QLineEdit()
+ self.lineEditList.append(lineEdit)
+ label = QtGui.QLabel(text)
+
+ self.addWidget(label)
+ self.addWidget(lineEdit)
+ return label, lineEdit
+
+ def addWidget(self, widget, align=None):
+ if align is None:
+ self.hbox.addWidget(widget)
+ else:
+ self.hbox.addWidget(widget, alignment=align)
+
+ def addLabel(self, text):
+ label = QtGui.QLabel(text)
+ self.addWidget(label)
+ return label
+
+ def addSlider(self):
+ slider = QtGui.QSlider(QtCore.Qt.Horizontal)
+ self.addWidget(slider)
+ return slider
+
+ def addLabeledSlider(self, text, newRow=True):
+ if newRow == True:
+ self.newRow()
+
+ labeledSlider = QLabeledSlider(text)
+ self.addWidget(labeledSlider)
+ return labeledSlider.getSlider()
+
+class QLabeledSlider(QtGui.QWidget):
+ def __init__(self, text, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout()
+ vbox.setSpacing(10)
+ self.setLayout(vbox)
+ self.text = text
+ self.label = QtGui.QLabel(text)
+ self.slider = QtGui.QSlider(QtCore.Qt.Horizontal)
+
+ vbox.addWidget(self.label)
+ vbox.addWidget(self.slider)
+
+ self.connect(self.slider, QtCore.SIGNAL('valueChanged(int)'),
+ self.updateLabel)
+
+ def getSlider(self):
+ return self.slider
+
+ def updateLabel(self, value):
+ self.label.setText("%s %d" %(self.text, value))
+
+class QRadioButtonFrame(QtGui.QFrame):
+ """ Framed widget containing a label and list of radiobuttons """
+ def __init__(self, labelText=None, buttonList=None, parent=None):
+ QtGui.QFrame.__init__(self, parent)
+ self.setFrameStyle(QtGui.QFrame.Raised)
+ self.setFrameShape(QtGui.QFrame.Box)
+
+ self.hbox = QtGui.QHBoxLayout()
+ self.setLayout(self.hbox)
+ self.buttonGroup = QtGui.QButtonGroup()
+ self.buttons = {}
+
+ if labelText is not None:
+ self.addLabel(QtGui.QLabel(labelText))
+ if buttonList is not None:
+ self.addButtonList(buttonList)
+
+ def addLabel(self, label):
+ self.hbox.addWidget(label)
+
+ def addButton(self, button):
+ self.buttonGroup.addButton(button)
+ self.hbox.addWidget(button)
+ self.buttons[str(button.text())] = button
+
+ def setChecked(self, buttonText):
+ if buttonText in list(self.buttons):
+ self.buttons[buttonText].setChecked(True)
+
+ def isChecked(self, buttonText):
+ if buttonText in list(self.buttons):
+ return self.buttons[buttonText].isChecked()
+
+ return False
+
+ def getButton(self, buttonText):
+ if buttonText in list(self.buttons):
+ return self.buttons[buttonText]
+
+ return None
+
+ def addButtonList(self, buttonList):
+ """ Create and add buttons from a list of strings """
+ for buttonText in buttonList:
+ button = QtGui.QRadioButton(buttonText)
+ self.buttons[buttonText] = button
+ self.addButton(button)
+
+def round_number( N ):
+ import numpy
+ P = 10.0 ** ( numpy.floor(numpy.log10(abs(N) ) ) )
+ return( sign(N) * int( abs(N)/P + 0.5) * P )
+
+def sign ( N ):
+ if (N < 0): return -1
+ else: return 1
+
+
diff --git a/contrib/cdat/gui_controller.py b/contrib/cdat/gui_controller.py
new file mode 100644
index 0000000..c6a9546
--- /dev/null
+++ b/contrib/cdat/gui_controller.py
@@ -0,0 +1,350 @@
+import core.modules.module_registry
+import core.modules.vistrails_module
+from logging import debug, warn
+from core.vistrail.connection import Connection
+from core.vistrail.port import Port
+from PyQt4 import QtGui, QtCore
+import api
+import vcs
+import os
+
+cdat_id = "edu.utah.sci.vistrails.cdat"
+
+# Module names
+# Note: open_name, quickplot_name, etc... are used in cdat_window.py
+# and graphics_method_controller.py
+open_name = 'open'
+quickplot_name = 'Quickplot'
+variable_name = 'Variable'
+cdatcell_name = 'CDATCell'
+gm_name = 'GraphicsMethod'
+
+# Port names
+
+
+# Module Namespaces
+namespace = {}
+namespace[open_name] = 'cdms2'
+namespace[quickplot_name] = 'cdat'
+namespace[variable_name] = 'cdat'
+namespace[cdatcell_name] = 'cdat'
+namespace[gm_name] = 'cdat'
+
+# MAJOR TODO: Support for multiple workflows
+
+class Workflow():
+ """ A Workflow contains a dict of modules belonging to the workflow. Workflow
+ manages the updating of its modules connections / values """
+
+ def __init__(self):
+ """ Workflow contains a dictionary of modules in the workflow.
+ * Key - if module is a variable then the key is the name of the variable
+ otherwise the key is the name of the module. ***** IMPORTANT *****
+ * Value - module object
+ """
+ self.modules = {}
+ self.variableNames = [] # Names of the variables in this workflow
+ self.filename = None # Name of the cdms file associated with this workflow
+
+ def moduleExists(self, key):
+ return key in list(self.modules)
+
+ def addModule(self, name, module, isVariable=False):
+ self.modules[name] = module
+
+ # If the module is a variable save the name and connect the variable
+ # module to the open module
+ if isVariable:
+ self.variableNames.append(name)
+ self.connectPorts(self.modules[open_name], 'dataset', module,
+ 'cdmsfile')
+
+ def updatePorts(self, var1, var2):
+ """ updatePorts(var1: str, var2: str)
+
+ updatePorts connects the output ports of Variable modules with vars
+ var1 and var2 to the input ports of Graphics Method and then connects
+ the output of Graphics Method to the input of CDATCell.
+ """
+ m_open = self.modules[open_name]
+ m_variable1 = self.modules[var1]
+ m_gm = self.modules[gm_name]
+ m_cdatcell = self.modules[cdatcell_name]
+
+ # Connect the variable module being plotted to the graphics method
+ # module and store the connection
+ self.connectPorts(m_variable1, 'variable', m_gm, 'slab1')
+
+ # Connect graphics method module & cdatcell module
+ self.connectPorts(m_gm, 'canvas', m_cdatcell, 'canvas')
+ self.connectPorts(m_gm, 'slab1', m_cdatcell, 'slab1')
+
+ # Connect the second variable module (if given) to graphics method
+ # and Graphics Method to CDATCell
+ if var2 is not None:
+ m_var2 = self.modules[var2]
+ self.connectPorts(m_var2, 'variable', m_gm, 'slab2')
+ self.connectPorts(m_gm, 'slab2', m_cdatcell, 'slab2')
+
+ def connectPorts(self, moduleA, outputPortName, moduleB, inputPortName):
+ """ connectPorts(moduleA: Module, outputPortName: str, moduleB: Module,
+ inputPortName: str) -> Connection
+
+ connectPorts connects moduleA's outputPort to moduleB's inputPort.
+ """
+ reg = api.get_module_registry()
+ in_port = moduleA.get_port_spec(outputPortName, 'output')
+ out_port = moduleB.get_port_spec(inputPortName, 'input')
+
+ return api.add_connection(moduleA.id, outputPortName, moduleB.id,
+ inputPortName)
+
+ def updateModule(self, name, portName, value):
+ """ updateModule(name: str, portName: str, value: *)
+
+ updateModule updates the vistrail module given the module name, input
+ port name, and value
+ """
+ if name not in list(self.modules):
+ return
+
+ # Set the filename associated w/ this workflow
+ if name == open_name:
+ self.filename = value
+
+ module = self.modules[name]
+ api.get_current_controller().update_function(module, portName, [value])
+
+ def updateModuleOps(self, name, args):
+ """ updateModule(name: str, args: list)
+
+ updateModule updates the vistrail module given the module name and a
+ list of tuples where each tuple = (input port name, value)
+ """
+ if name not in list(self.modules):
+ return
+
+ module = self.modules[name]
+ for portName, value in args:
+ api.get_current_controller().update_function(module, portName,
+ [value])
+
+class GuiController(QtCore.QObject):
+ """ GuiController calls vistrails functions and handles recording and
+ displaying teaching commands.
+
+ The two most important functions that GuiController provides are:
+ 'createModule' and 'updateModule'. 'createModule' creates a new box.
+ 'updateModule' updates the input of a box. Widgets interact with
+ GuiController by sending signals (which is why GuiController inherits
+ from QObject).
+ """
+
+ def __init__(self, fileWidget, defVarWidget, varWidget):
+ """ __init__(fileWidget: QCDATFileWidget, defVarWidget:QDefinedVariable,
+ varWidget: QVariableView)
+ """
+ QtCore.QObject.__init__(self)
+ self.teachingCommands = ''
+ self.editorPid = 0
+ self.recordCommands = True
+
+ self.workflows = [] # List of workflows
+
+ # X coordinates of open, variable, and plot related modules
+ self.openX = -300
+ self.variableX = -300
+ self.plotX = -320
+
+ self.m_open = None
+ self.m_variable = None
+ self.m_graphics_method = None
+ self.m_cdat_cell = None
+
+ # Connect the 3 main widgets to the primary GuiController
+ # functionality. If a childwidget of the 3 main widgets wants to
+ # send signals to GuiController, then it must send it through one of the
+ # main widgets to try to keep things less messy
+ self.connect(fileWidget, QtCore.SIGNAL('createModule'),
+ self.createModule)
+ self.connect(fileWidget, QtCore.SIGNAL('updateModule'),
+ self.updateModule)
+ self.connect(fileWidget, QtCore.SIGNAL('recordTeachingCommand'),
+ self.recordTeachingCommand)
+
+ self.connect(defVarWidget, QtCore.SIGNAL('createModule'),
+ self.createModule)
+ self.connect(defVarWidget, QtCore.SIGNAL('updateModule'),
+ self.updateModule)
+ self.connect(defVarWidget, QtCore.SIGNAL('recordTeachingCommand'),
+ self.recordTeachingCommand)
+
+ self.connect(varWidget, QtCore.SIGNAL('recordTeachingCommand'),
+ self.recordTeachingCommand)
+ self.connect(varWidget, QtCore.SIGNAL('createModule'),
+ self.createModule)
+ self.connect(varWidget, QtCore.SIGNAL('updateModule'),
+ self.updateModule)
+ self.connect(varWidget, QtCore.SIGNAL('updateModuleOps'),
+ self.updateModuleOps)
+ self.connect(varWidget, QtCore.SIGNAL('plot'),
+ self.plot)
+
+ def createNewWorkflow(self):
+ """ createnewWorkflow(filename: str)
+
+ createNewWorkflow is called when the user selects a new file. It makes
+ a new workflow and appends it to the workflow list.
+ """
+ if self.workflows == []:
+ api.get_current_controller().change_selected_version(0)
+
+ self.currentWorkflow = Workflow()
+ self.workflows.append(self.currentWorkflow)
+
+ def getCoordinates(self, name):
+ """ getCoordinates(name: str) -> x: int, y: int
+
+ Return the x, y coordinate of where to place the new module given the
+ name.
+ """
+ if name == open_name:
+ self.openX += 100
+ return self.openX, 170
+ elif name == variable_name or name == quickplot_name:
+ self.variableX += 120
+ return self.variableX, 70
+ elif name == gm_name:
+ self.plotX += 160
+ return self.plotX, -70
+ elif name == cdatcell_name:
+ return self.plotX, -170
+
+ def createModule(self, name, key=None):
+ """ createModule(name: str, key: str)
+
+ createModule creates a new module given the name and adds it to the
+ current workflow. If key is specified, use the key instead of the name
+ as the key into the workflow's module dictionary.
+
+ Note: For Variable modules I pass key = variabe name (the tabName)
+ """
+ # If module is the 'open' module, create a new workflow
+ if name == open_name:
+ self.createNewWorkflow()
+
+ # If module is 'quickplot' module, and it already exists, do nothing
+ if name == quickplot_name:
+ if self.currentWorkflow.moduleExists(quickplot_name.lower()):
+ return
+
+ # Create & add the module
+ x, y = self.getCoordinates(name)
+ module = api.add_module(x, y, cdat_id, name, namespace[name])
+
+ if key is not None:
+ self.currentWorkflow.addModule(key, module, isVariable=True)
+ else:
+ self.currentWorkflow.addModule(name, module)
+
+ def updateModule(self, name, portName, value):
+ """ updateModule(name: str, portName: str, value: *)
+
+ updateModule updates the vistrail module given the module name, input
+ port name, and value
+ """
+ self.currentWorkflow.updateModule(name, portName, value)
+
+ def updateModuleOps(self, name, args):
+ """ updateModule(name: str, args: list)
+
+ updateModule updates the vistrail module given the module name and a
+ list of tuples where each tuple = (input port name, value)
+ """
+ self.currentWorkflow.updateModuleOps(name, args)
+
+ def plot(self, var1, var2):
+ """ Connect / disconnect the necessary ports and exec workflow -> plot
+ into the cell
+ """
+ self.currentWorkflow.updatePorts(var1, var2)
+ api.get_current_controller().execute_current_workflow()
+
+ def initTeachingCommands(self):
+ """ The initial teaching commands still have 4 canvases like the old
+ vcdat. This allows you to run the teaching commands independently
+ of vistrails' spreadsheets.
+ """
+ self.teachingCommands += 'import cdms2, vcs, cdutil, genutil, os, sys\n'
+ self.teachingCommands += 'import MV2\n'
+
+ self.teachingCommands += '\n# Initialize the four VCS Canvases by creating\n'
+ self.teachingCommands += '# a list to hold the 4 VCS Canvas\n'
+ self.teachingCommands += 'vcs_canvas_list = []\n'
+
+ self.teachingCommands += '\n# Loop (from 0 to 3) to create VCS Canvas 1, 2, 3, and 4\n'
+ self.teachingCommands += 'for i in range(4):\n'
+ self.teachingCommands += ' vcs_canvas_list.append(vcs.init())\n'
+
+ self.teachingCommands += '\n# Set the Command Line VCS Canvas hooks\n'
+ self.teachingCommands += 'vcs_hook1 = vcs_canvas_list[0]\n'
+ self.teachingCommands += 'vcs_hook2 = vcs_canvas_list[1]\n'
+ self.teachingCommands += 'vcs_hook3 = vcs_canvas_list[2]\n'
+ self.teachingCommands += 'vcs_hook4 = vcs_canvas_list[3]\n'
+
+ self.writeTeachingCommands()
+
+ def recordTeachingCommand(self, command):
+ if (self.recordCommands == True):
+ self.teachingCommands += command
+ self.writeTeachingCommands()
+
+ def setRecordCommands(self, recordCommands):
+ self.recordCommands = recordCommands
+
+ def writeTeachingCommands(self):
+ try:
+ fn = '%s/PCMDI_GRAPHICS' % os.environ['HOME']
+ except:
+ print "Could not find the $HOME directory. Set your environment variable 'HOME'"
+ print "to your home directory. (e.g., 'setenv HOME /home/user')."
+ sys.exit()
+
+ # Create PCMDI_GRAPHICS directory if it does not exist
+ if (os.access(fn, os.X_OK) == 0):
+ try:
+ os.mkdir(fn)
+ except:
+ print 'Do not have write permission for home directory. Must have write permissions.'
+ sys.exit()
+
+ # Write teaching commands to vcdat_recording_script_file.py
+ self.teachingScript = fn + '/vcdat_recording_script_file.py'
+ file = open(self.teachingScript, 'w')
+ file.write(self.teachingCommands)
+ file.flush()
+
+ def viewTeachingCommands(self):
+ """ Open the teaching commands script in a child process """
+ self.editorPid = os.fork()
+
+ if (self.editorPid == 0):
+ editor = 'idle'
+
+ # If idle editor is found, view teaching commands with idle
+ for path in os.environ["PATH"].split(os.pathsep):
+ file = os.path.join(path, editor)
+ if (os.path.exists(file)):
+ args = (editor, self.teachingScript)
+ os.execvp(editor, args)
+ return
+
+ # If idle editor is not found, use default editor
+ secondaryEditor = os.environ['EDITOR']
+ args = (secondaryEditor, self.teachingScript)
+ os.execvp(secondaryEditor, args)
+
+ def closeTeachingCommands(self):
+ if (self.editorPid != 0):
+ os.kill(self.editorPid, 9)
+ self.editorPid = 0
diff --git a/contrib/cdat/pyqtscripting.sbf b/contrib/cdat/pyqtscripting.sbf
new file mode 100644
index 0000000..ccee4f3
--- /dev/null
+++ b/contrib/cdat/pyqtscripting.sbf
@@ -0,0 +1,3 @@
+target = coreappwrap
+sources = sipcoreappwrapcmodule.cpp sipcoreappwrapVCSQtManager.cpp sipcoreappwrapMainWindow.cpp
+headers = sipAPIcoreappwrap.h
diff --git a/contrib/cdat/quickplot.py b/contrib/cdat/quickplot.py
new file mode 100644
index 0000000..f38e54a
--- /dev/null
+++ b/contrib/cdat/quickplot.py
@@ -0,0 +1,50 @@
+from cdat_cell import QCDATWidget, CDATCell
+from core.modules.vistrails_module import (Module, ModuleError, NotCacheable)
+from packages.spreadsheet.spreadsheet_controller import spreadsheetController
+from packages.spreadsheet.spreadsheet_event import DisplayCellEvent
+from PyQt4 import QtCore, QtGui
+
+class quickplot(Module, NotCacheable):
+ """hackiness to push a cdat plot to our spreadsheet.
+ needs: QCDATWidget ref
+ cdms2.open()d dataset
+ blah this is out of date variable name"""
+
+ def compute(self):
+ args = []
+ if not self.hasInputFromPort('dataset'):
+ raise ModuleError(self, "'dataset' is mandatory.")
+ if not self.hasInputFromPort('plot'):
+ raise ModuleError(self, "'plot' is mandatory.")
+
+ dataset = self.getInputFromPort('dataset')
+ plotType = self.getInputFromPort('plot')
+ axes = self.forceGetInputFromPort('axes')
+ inCanvas = self.forceGetInputFromPort('canvas')
+
+ if axes!=None:
+ try:
+ kwargs = eval(axes)
+ except:
+ raise ModuleError(self, "Invalid 'axes' specification", axes)
+ dataset = dataset(**kwargs)
+
+ outCanvas = None
+ if inCanvas!=None:
+ inCanvas.plot(dataset, 'ASD', plotType)
+ outCanvas = inCanvas
+ else:
+ ev = DisplayCellEvent()
+ ev.vistrail = {'locator': None, 'version': -1, 'actions': []}
+ ev.cellType = QCDATWidget
+ ev.inputPorts = (dataset, 'ASD', plotType)
+
+ QtCore.QCoreApplication.processEvents()
+ spreadsheetWindow = spreadsheetController.findSpreadsheetWindow()
+
+ cdatWidget = spreadsheetWindow.displayCellEvent(ev)
+ if cdatWidget!=None:
+ outCanvas = cdatWidget.canvas
+
+ self.setResult('dataset', dataset)
+ self.setResult('canvas', outCanvas)
diff --git a/contrib/cdat/scripts/cdat_domain.py b/contrib/cdat/scripts/cdat_domain.py
new file mode 100755
index 0000000..1c29e44
--- /dev/null
+++ b/contrib/cdat/scripts/cdat_domain.py
@@ -0,0 +1,289 @@
+#!/usr/bin/env python
+############################################################################
+##
+## Copyright (C) 2006-2008 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+def convert_to_vt_type(t):
+ vt_type_dict = {'str':'core.modules.basic_modules.String',
+ 'float': 'core.modules.basic_modules.Float',
+ 'int':'core.modules.basic_modules.Integer',
+ 'bool':'core.modules.basic_modules.Boolean',
+ #'numpy.ndarray':'reg.get_module_by_name("edu.utah.sci.vistrails.numpyscipy", "Numpy Array", namespace="numpy|array")',
+ }
+ if vt_type_dict.has_key(t):
+ return vt_type_dict[t]
+ else:
+ print "Type %s not found!" % t
+ return None
+
+do_not_cache_me = ['png','plot','isofill','isoline','boxfill']
+class CDATModule:
+ _extra_modules = []
+ _extra_vistrails_modules = {}
+ def __init__(self, author=None, language=None, type=None, url=None,
+ codepath=None, version=None, actions=None):
+ self._author = author
+ self._language = language
+ self._type = type
+ self._url = url
+ self._codepath = codepath
+ self._version = version
+ self._actions = actions
+ (self._namespace, self._name) = self.split(codepath)
+
+ @staticmethod
+ def split(codepath):
+ dot = codepath.rfind('.')
+ if dot != -1:
+ name = codepath[dot+1:]
+ data = codepath[:dot]
+ namespace = data.replace('.','|')
+ else:
+ name = codepath
+ namespace = codepath
+ return (namespace,name)
+
+ def write_extra_module_definition(self, lines, name):
+ lines.append("%s = new_module(Module,'%s')\n"%(name,name))
+
+ @staticmethod
+ def write_extra_module_definitions_init(lines):
+ lines.append("vt_type_dict = {}\n")
+ lines.append("def get_late_type(type):\n")
+ lines.append(" return vt_type_dict[type]\n\n")
+
+ @staticmethod
+ def write_extra_module_definitions(lines):
+ for t in CDATModule._extra_modules:
+ namespace,name = CDATModule.split(t)
+ lines.append("%s = new_module(Module,'%s')\n"%(name,name))
+ lines.append("vt_type_dict['%s'] = %s\n"%(t,name))
+ CDATModule._extra_vistrails_modules[name] = namespace
+ lines.append("\n\n")
+
+ @staticmethod
+ def register_extra_vistrails_modules(lines, ident=''):
+ for (name,namespace) in CDATModule._extra_vistrails_modules.iteritems():
+ lines.append(ident + " reg.add_module(%s,namespace='%s')\n"%(name,
+ namespace))
+
+ def register_extra_vistrails_module(self, lines, name, ident=''):
+ lines.append(ident + " reg.add_module(%s,namespace='%s')\n"%(name,
+ self._namespace))
+
+ def write_module_definitions(self, lines):
+ for a in self._actions:
+ a.write_module_definition(lines)
+
+ def register_vistrails_modules(self, lines):
+ for a in self._actions:
+ a.register_itself(lines,self._namespace)
+
+ def build_vistrails_modules_dict(self):
+ for a in self._actions:
+ types = a.check_output_types()
+ for t in types:
+ if t not in CDATModule._extra_modules:
+ CDATModule._extra_modules.append(t)
+
+ def add_extra_input_port_to_all_modules(self, lines, port_name, port_type,
+ doc, optional = False):
+ lines.append("\n #extra input ports not available in the xml file\n")
+ for a in self._actions:
+ a.register_extra_input_port(port_name, port_type, lines, doc,
+ optional)
+
+ def add_extra_output_port_to_all_modules(self, lines, port_name, port_type,
+ doc, optional = False):
+ lines.append("\n #extra output ports not available in the xml file\n")
+ for a in self._actions:
+ a.register_extra_output_port(port_name, port_type, lines, doc,
+ optional)
+class CDATAction:
+ def __init__(self, name=None, type=None, options=None, inputs=None,
+ outputs=None, doc=None):
+ self._name = name
+ self._type = type
+ self._options = options
+ self._inputs = inputs
+ self._outputs = outputs
+ self._doc = doc
+
+ def write_module_definition(self, lines, ident='', compute_method=None):
+ def write_compute_method(self,lines, ident):
+ lines.append(ident + "def compute(self):\n")
+ lines.append(ident + " if self.hasInputFromPort('canvas'):\n")
+ lines.append(ident + " canvas = self.getInputFromPort('canvas')\n")
+ lines.append(ident + " else:\n")
+ lines.append(ident + " canvas = vcs.init()\n")
+ lines.append(ident + " args = []\n")
+ for inp in self._inputs:
+ lines.append(ident + " %s = None\n"%inp._name)
+ for inst in inp._valid_instances:
+ if inp._valid_instances.index(inst) == 0:
+ lines.append(ident + " if self.hasInputFromPort('%s'):\n" % inst)
+ lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
+ lines.append(ident + " args.append(%s)\n"%inp._name)
+ else:
+ lines.append(ident + " elif self.hasInputFromPort('%s'):\n" % inst)
+ lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
+ lines.append(ident + " args.append(%s)\n"%inp._name)
+ if inp._required:
+ lines.append("\n"+ ident +" # %s is a required port\n" % inp._name)
+ lines.append(ident + " if %s == None:\n" % inp._name)
+ lines.append(ident + " raise ModuleError(self, \"'%s' is a mandatory port\")\n" % inp._name)
+
+ lines.append("\n"+ident +" # build up the keyword arguments from the optional inputs.\n")
+ lines.append(ident +" kwargs = {}\n")
+
+ for opt in self._options:
+ for inst in opt._valid_instances:
+ if opt._valid_instances.index(inst) == 0:
+ lines.append(ident +" if self.hasInputFromPort('%s'):\n" % inst)
+ lines.append(ident +" kwargs['%s'] = self.getInputFromPort('%s')\n" % (opt._name, inst))
+ else:
+ lines.append(ident +" elif self.hasInputFromPort('%s'):\n" % inst)
+ lines.append(ident +" kwargs['%s'] = self.getInputFromPort('%s')\n" % (opt._name, inst))
+
+ lines.append(ident + " #force images to be created in the background\n")
+ lines.append(ident + " kwargs['bg'] = 1\n")
+ lines.append(ident + " res = canvas.%s(*args,**kwargs)\n"%self._name)
+ lines.append(ident + " self.setResult('%s',res)\n"%(self._outputs[0]._name))
+ lines.append(ident + " self.setResult('canvas',canvas)\n")
+ lines.append("\n")
+ if self._name in do_not_cache_me:
+ lines.append(ident + "class %s(Module,NotCacheable):\n" % self._name)
+ else:
+ lines.append(ident + "class %s(Module):\n" % self._name)
+ lines.append(ident + ' """%s\n'%self._doc)
+ lines.append(ident + ' """\n')
+ if not compute_method:
+ write_compute_method(self,lines,ident=" ")
+ else:
+ lines.extend(compute_method)
+
+ def register_itself(self,lines, namespace):
+ lines.append("\n #Module %s\n" % self._name)
+ lines.append(" reg.add_module(%s,namespace='%s')\n" % (self._name,namespace))
+ for inp in self._inputs:
+ inp.write_input_ports(self._name, lines)
+ for opt in self._options:
+ opt.write_input_ports(self._name, lines, True, force=False)
+ for out in self._outputs:
+ out.write_output_ports(self._name, lines, force=True)
+
+ def check_output_types(self):
+ types = []
+ for out in self._outputs:
+ if out._instance[0] not in types:
+ types.append(out._instance[0])
+ return types
+
+ def register_extra_input_port(self, port_name, port_type, lines, doc,
+ optional=False):
+ self._write_port('input', port_name, port_type, lines, doc, optional)
+
+ def register_extra_output_port(self, port_name, port_type, lines, doc,
+ optional=False):
+ self._write_port('output', port_name, port_type, lines, doc, optional)
+
+ #private methods
+ def _write_port(self, io_type, port_name, port_type,
+ lines, doc, optional=False):
+ lines.append(" reg.add_%s_port(%s, '%s', \n" % (io_type,
+ self._name,
+ port_name))
+ lines.append(" ")
+ lines.append("(%s,\n" % port_type)
+ lines.append(" ")
+ if not optional:
+ lines.append("\"%s\"))\n" % doc)
+ else:
+ lines.append("\"%s\"), True)\n" % doc)
+
+class CDATItem:
+ def __init__(self, tag=None, doc=None, instance=None, required=False):
+ self._name = tag
+ self._doc = doc
+ self._instance = [i.strip(" \t\n") for i in instance.split('/')]
+ self._valid_instances = []
+ if required == None:
+ self._required = False
+ else:
+ self._required = required
+
+ def write_input_ports(self, module_name, lines, optional=False, force=False):
+ self._write_ports('input',module_name, lines, optional, force)
+
+ def write_output_ports(self, module_name, lines, optional=False, force=False):
+ self._write_ports('output',module_name, lines, optional, force)
+
+ def _write_ports(self, port_type, module_name, lines, optional=False,
+ force=False):
+ if len(self._instance) == 1:
+ type = convert_to_vt_type(self._instance[0])
+ if type == None and self._instance[0] in CDATModule._extra_modules:
+ force = True
+ if force and type == None:
+ type = "get_late_type('%s')"%self._instance[0]
+ if type != None:
+ self._valid_instances.append(self._name)
+ lines.append(" reg.add_%s_port(%s, '%s', \n" % (port_type,
+ module_name,
+ self._name))
+ lines.append(" ")
+ lines.append("(%s,\n" % type)
+ lines.append(" ")
+ if not optional:
+ lines.append("\"%s\"))\n" % self._doc)
+ else:
+ lines.append("\"%s\"), True)\n" % self._doc)
+ else:
+ count = 0
+ for i in xrange(len(self._instance)):
+ type = convert_to_vt_type(self._instance[i])
+ new_force = force
+ if type == None and self._instance[i] in CDATModule._extra_modules:
+ new_force = True
+ if new_force and type == None:
+ type = "get_late_type('%s')"%self._instance[i]
+ if type != None:
+ name = "%s_%s"%(self._name,count)
+ self._valid_instances.append(name)
+ count += 1
+ lines.append(" reg.add_input_port(%s, '%s', \n" % (module_name,
+ name))
+ lines.append(" ")
+ lines.append("(%s,\n" % type)
+ lines.append(" ")
+ if not optional:
+ lines.append("\"%s\"))\n" % self._doc)
+ else:
+ lines.append("\"%s\"), True)\n" % self._doc)
+
+class CDATOption(CDATItem):
+ def __init__(self, tag=None, default=None, doc=None, instance=None):
+ CDATItem.__init__(self, tag, doc, instance, False)
+ self._default = default
+
+class CDATPort(CDATItem):
+ def __init__(self, tag=None, doc=None, instance=None, position=None, required=False):
+ CDATItem.__init__(self, tag, doc, instance, required)
+ self._position = position
\ No newline at end of file
diff --git a/contrib/cdat/scripts/cdatwindow_init_inc.py b/contrib/cdat/scripts/cdatwindow_init_inc.py
new file mode 100644
index 0000000..0122627
--- /dev/null
+++ b/contrib/cdat/scripts/cdatwindow_init_inc.py
@@ -0,0 +1,85 @@
+
+ ##########################################################################
+ # included from cdatwindow_init_inc.py
+ #display = sip.unwrapinstance(QtGui.QX11Info.display())
+ #vcs._vcs.setdisplay(display)
+
+ #cdat GUI modules
+ global cdatWindow
+ cdatWindow = QCDATWindow()
+ cdatWindow.show()
+
+ reg.add_module(CDATCell,namespace='cdat')
+ reg.add_input_port(CDATCell, 'slab1',
+ (TransientVariable, "variable to be plotted"))
+ reg.add_input_port(CDATCell, 'slab2',
+ (TransientVariable, "variable to be plotted"))
+ reg.add_input_port(CDATCell, 'plotType',
+ (core.modules.basic_modules.String, "Plot type"))
+ reg.add_input_port(CDATCell, 'template',
+ (core.modules.basic_modules.String, "template name"))
+ reg.add_input_port(CDATCell, 'gmName',
+ (core.modules.basic_modules.String, "graphics method name"))
+ reg.add_input_port(CDATCell, 'canvas',
+ (Canvas, "Canvas object"))
+ reg.add_input_port(CDATCell, 'col',
+ (core.modules.basic_modules.Integer, "Cell Col"))
+ reg.add_input_port(CDATCell, 'row',
+ (core.modules.basic_modules.Integer, "Cell Row"))
+ reg.add_input_port(CDATCell, 'continents',
+ (core.modules.basic_modules.Integer,
+ "continents type number"), True)
+
+ reg.add_module(Variable, namespace='cdat')
+ reg.add_module(Quickplot, namespace='cdat')
+ reg.add_input_port(Variable, 'id',
+ (core.modules.basic_modules.String,
+ ""))
+ reg.add_input_port(Variable, 'type',
+ (core.modules.basic_modules.String,
+ "variable, axis, or weighted-axis"))
+ reg.add_input_port(Variable, 'inputVariable',
+ (core.modules.basic_modules.List,
+ ""))
+ reg.add_output_port(Variable, 'variable',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ ""))
+ reg.add_input_port(Variable, 'axes',
+ (core.modules.basic_modules.String, "Axes of variables"))
+ reg.add_input_port(Variable, 'axesOperations',
+ (core.modules.basic_modules.String, "Axes Operations"))
+ reg.add_input_port(Variable, 'cdmsfile',
+ (CdmsFile, "cdmsfile"))
+
+ reg.add_module(GraphicsMethod, namespace='cdat')
+ reg.add_input_port(GraphicsMethod, 'gmName',
+ (core.modules.basic_modules.String,
+ "Get the graphics method object of the given name."))
+ reg.add_input_port(GraphicsMethod, 'plotType',
+ (core.modules.basic_modules.String, "Plot type"))
+ reg.add_input_port(GraphicsMethod, 'slab1',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "slab1"))
+ reg.add_input_port(GraphicsMethod, 'slab2',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "slab2"))
+ reg.add_input_port(GraphicsMethod, 'color_1',
+ (core.modules.basic_modules.Integer, "color_1"), True)
+ reg.add_input_port(GraphicsMethod, 'color_2',
+ (core.modules.basic_modules.Integer, "color_2"), True)
+ reg.add_input_port(GraphicsMethod, 'level_1',
+ (core.modules.basic_modules.Float, "level_1"), True)
+ reg.add_input_port(GraphicsMethod, 'level_2',
+ (core.modules.basic_modules.Float, "level_2"), True)
+ reg.add_output_port(GraphicsMethod, 'slab1',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "slab1"))
+ reg.add_output_port(GraphicsMethod, 'slab2',
+ (get_late_type('cdms2.tvariable.TransientVariable'),
+ "slab2"))
+ reg.add_output_port(GraphicsMethod, 'canvas', (Canvas, "Canvas object"))
+
+ # end of cdatwindow_init_inc.py
+ ##########################################################################
+
+
diff --git a/contrib/cdat/scripts/gen_init.py b/contrib/cdat/scripts/gen_init.py
new file mode 100755
index 0000000..c622bbe
--- /dev/null
+++ b/contrib/cdat/scripts/gen_init.py
@@ -0,0 +1,267 @@
+############################################################################
+##
+## Copyright (C) 2006-2008 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+import os, sys
+sys.path.append('../../../vistrails')
+from parse_cdat_xml_file import parse_cdat_xml_file
+from cdat_domain import CDATModule
+
+
+
+#cdat package identifiers
+cp_version = '0.2'
+cp_identifier = 'edu.utah.sci.vistrails.cdat'
+cp_name = 'CDAT'
+
+def write_init(output_file, classes_lines, init_lines):
+ """write_init(output_file: str, classes_lines: list, init_lines: list)
+ -> None
+ Writes the necessary contents for the package init file"""
+
+ # cdat dependencies
+ init_lines.append("\n\n")
+ init_lines.append("def package_dependencies():\n")
+ #init_lines.append(" return ['edu.utah.sci.vistrails.numpyscipy']\n")
+ init_lines.append(" return []\n")
+ init_lines.append("\n\n")
+ init_lines.append("def package_requirements():\n")
+ init_lines.append(" import core.requirements\n")
+ init_lines.append(" if not core.requirements.python_module_exists('vcs'):\n")
+ init_lines.append(" raise core.requirements.MissingRequirements('vcs')\n")
+ init_lines.append(" if not core.requirements.python_module_exists('cdms2'):\n")
+ init_lines.append(" raise core.requirements.MissingRequirements('cdms2')\n")
+ init_lines.append(" if not core.requirements.python_module_exists('cdutil'):\n")
+ init_lines.append(" raise core.requirements.MissingRequirements('cdutil')\n")
+ init_lines.append(" import vcs, cdms2, cdutil\n")
+ init_lines.append("\n\n")
+
+ header = open("init_inc.py").readlines()
+ header.append("\n\n")
+ header.append('version = "' + cp_version + '"\n')
+ header.append('identifier = "' + cp_identifier + '"\n')
+ header.append('name = "' + cp_name + '"\n\n')
+
+ outfile = open(output_file, "w")
+ outfile.writelines(header)
+ outfile.writelines(classes_lines)
+ outfile.writelines(init_lines)
+ outfile.close()
+
+def parse_files(input_files):
+ modules = []
+ for f in input_files:
+ modules.append(parse_cdat_xml_file(f))
+ return modules
+
+def add_canvas_ports_to_canvas_modules(canvas, lines):
+ canvas.add_extra_input_port_to_all_modules(lines,
+ port_name='canvas',
+ port_type='Canvas',
+ doc='Canvas object',
+ optional=False
+ )
+ canvas.add_extra_output_port_to_all_modules(lines,
+ port_name='canvas',
+ port_type='Canvas',
+ doc='Canvas object',
+ optional=False
+ )
+
+def add_canvas_module(canvas,init_lines,class_lines):
+ canvas.write_extra_module_definition(class_lines,'Canvas')
+ canvas.register_extra_vistrails_module(init_lines,'Canvas')
+
+def get_image_compute_method(action, ident=''):
+ lines = []
+ lines.append(ident + "def compute(self):\n")
+ lines.append(ident + " if self.hasInputFromPort('canvas'):\n")
+ lines.append(ident + " canvas = self.getInputFromPort('canvas')\n")
+ lines.append(ident + " else:\n")
+ lines.append(ident + " canvas = vcs.init()\n")
+ lines.append(ident + " args = []\n")
+ for inp in action._inputs:
+ lines.append(ident + " %s = None\n"%inp._name)
+ for inst in inp._valid_instances:
+ if inp._valid_instances.index(inst) == 0:
+ lines.append(ident + " if self.hasInputFromPort('%s'):\n" % inst)
+ lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
+ lines.append(ident + " args.append(%s)\n"%inp._name)
+ else:
+ lines.append(ident + " elif self.hasInputFromPort('%s'):\n" % inst)
+ lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
+ lines.append(ident + " args.append(%s)\n"%inp._name)
+ if inp._required:
+ lines.append("\n"+ ident +" # %s is a required port\n" % inp._name)
+ lines.append(ident + " if %s is None:\n" % inp._name)
+ lines.append(ident + " raise ModuleError(self, \"'%s' is a mandatory port\")\n" % inp._name)
+
+ lines.append(ident + " ofile = core.modules.basic_modules.File()\n")
+ lines.append(ident + " ofile.name = %s\n"%action._inputs[0]._name)
+
+ lines.append(ident + " canvas.%s(*args)\n"%action._name)
+ lines.append(ident + " self.setResult('file',ofile)\n")
+ lines.append("\n")
+ return lines
+
+def get_cdms2_compute_method(action, ident=''):
+ lines = []
+ lines.append(ident + "def compute(self):\n")
+ lines.append(ident + " args = []\n")
+ for inp in action._inputs:
+ lines.append(ident + " %s = None\n"%inp._name)
+ for inst in inp._valid_instances:
+ if inp._valid_instances.index(inst) == 0:
+ lines.append(ident + " if self.hasInputFromPort('%s'):\n" % inst)
+ lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
+ lines.append(ident + " args.append(%s)\n"%inp._name)
+ else:
+ lines.append(ident + " elif self.hasInputFromPort('%s'):\n" % inst)
+ lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
+ lines.append(ident + " args.append(%s)\n"%inp._name)
+ if inp._required:
+ lines.append("\n"+ ident +" # %s is a required port\n" % inp._name)
+ lines.append(ident + " if %s is None:\n" % inp._name)
+ lines.append(ident + " raise ModuleError(self, \"'%s' is a mandatory port\")\n" % inp._name)
+
+ lines.append(ident + " res = cdms2.%s(*args)\n"%action._name)
+ lines.append(ident + " self.setResult('%s',res)\n"%action._outputs[0]._name)
+ lines.append("\n")
+ return lines
+
+def get_CdmsFile_compute_method(action, ident=''):
+ lines = []
+ lines.append(ident + "def compute(self):\n")
+ lines.append(ident + " self.checkInputPort('cdmsfile')\n")
+ lines.append(ident + " cdmsfile = self.getInputFromPort('cdmsfile')\n")
+ lines.append(ident + " args = []\n")
+ for inp in action._inputs:
+ lines.append(ident + " %s = None\n"%inp._name)
+ for inst in inp._valid_instances:
+ if inp._valid_instances.index(inst) == 0:
+ lines.append(ident + " if self.hasInputFromPort('%s'):\n" % inst)
+ lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
+ lines.append(ident + " args.append(%s)\n"%inp._name)
+ else:
+ lines.append(ident + " elif self.hasInputFromPort('%s'):\n" % inst)
+ lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
+ lines.append(ident + " args.append(%s)\n"%inp._name)
+ if inp._required:
+ lines.append("\n"+ ident +" # %s is a required port\n" % inp._name)
+ lines.append(ident + " if %s is None:\n" % inp._name)
+ lines.append(ident + " raise ModuleError(self, \"'%s' is a mandatory port\")\n" % inp._name)
+
+ lines.append(ident + " res = cdmsfile.%s(*args)\n"%action._name)
+ lines.append(ident + " self.setResult('%s',res)\n"%action._outputs[0]._name)
+ lines.append("\n")
+ return lines
+
+if __name__ == '__main__':
+ # usage:
+ args = sys.argv
+ if len(args) > 2:
+ root_dir = args[1]
+ output_file = args[2]
+ else:
+ print "Usage: %s root_dir output_file" % args[0]
+ sys.exit(0)
+
+ xmlfiles = []
+ input_files = os.walk(root_dir)
+ for (d, tree, files) in input_files:
+ for f in files:
+ if os.path.isfile(os.path.join(d,f)) and f.endswith(".xml"):
+ xmlfiles.append(os.path.join(d,f))
+
+ modules = parse_files(xmlfiles)
+
+ extra_init_lines = []
+ init_lines = []
+ extra_init_lines.append("\ndef initialize(*args, **keywords):\n")
+ extra_init_lines.append(" reg = core.modules.module_registry.get_module_registry()\n\n")
+
+ class_lines = []
+ extra_class_lines = []
+
+ print "%s xml file(s) found."% len(modules)
+
+ CDATModule.write_extra_module_definitions_init(extra_class_lines)
+
+ for m in modules:
+ print "codepath: %s has %s Vistrails Modules."%(m._codepath, len(m._actions))
+ m.build_vistrails_modules_dict()
+
+ for m in modules:
+ m.register_vistrails_modules(init_lines)
+ if m._codepath == 'vcs.Canvas.Canvas':
+ for a in m._actions:
+ if a._name == 'png':
+ a.write_module_definition(class_lines,
+ ident='',
+ compute_method=get_image_compute_method(a,ident=" "))
+ a.register_extra_output_port('file',
+ 'core.modules.basic_modules.File',
+ init_lines,
+ "File output",
+ False)
+ else:
+ a.write_module_definition(class_lines)
+
+ add_canvas_ports_to_canvas_modules(m,init_lines)
+ add_canvas_module(m,extra_init_lines, extra_class_lines)
+
+ elif m._codepath == "cdms2.dataset.CdmsFile":
+ for a in m._actions:
+ if a._name == "__call__":
+ a.write_module_definition(class_lines,
+ ident='',
+ compute_method=get_CdmsFile_compute_method(a,
+ ident=" "))
+ else:
+ a.write_module_definition(class_lines)
+
+ m.add_extra_input_port_to_all_modules(init_lines,
+ port_name='cdmsfile',
+ port_type='CdmsFile',
+ doc='cdmsfile',
+ optional=False
+ )
+ elif m._codepath == 'cdms2':
+ for a in m._actions:
+ if a._name == "open":
+ a.write_module_definition(class_lines,
+ ident='',
+ compute_method=get_cdms2_compute_method(a,
+ ident=" "))
+ else:
+ a.write_module_definition(class_lines)
+ else:
+ m.write_module_definitions(class_lines)
+
+ CDATModule.write_extra_module_definitions(extra_class_lines)
+ CDATModule.register_extra_vistrails_modules(extra_init_lines)
+
+ cdatwindow_init_lines = open("cdatwindow_init_inc.py").readlines()
+ extra_init_lines.extend(cdatwindow_init_lines)
+
+ extra_init_lines.extend(init_lines)
+ extra_class_lines.extend(class_lines)
+ write_init(output_file, extra_class_lines, extra_init_lines)
\ No newline at end of file
diff --git a/contrib/cdat/scripts/init_inc.py b/contrib/cdat/scripts/init_inc.py
new file mode 100644
index 0000000..b4b7d89
--- /dev/null
+++ b/contrib/cdat/scripts/init_inc.py
@@ -0,0 +1,49 @@
+############################################################################
+##
+## Copyright (C) 2006-2008 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+""" Do not edit this file!
+
+File automatically generated by scripts/gen_init.py
+Change History:
+version : description
+ 0.2 : Integrated quickplot module that displays the CDAT plot
+ widget inside the spreadsheet
+ 0.1 : First automatically generated package based on xml descriptions
+
+"""
+from PyQt4 import QtCore, QtGui
+import sip
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import (Module, NotCacheable,
+ ModuleError, new_module)
+from core.bundles import py_import
+import os, sys
+
+#cdat specific packages
+vcs = py_import('vcs',{})
+cdms2 = py_import('cdms2', {})
+cdutil = py_import('cdutil', {})
+
+#local python modules
+from cdat_window import QCDATWindow
+from cdat_cell import QCDATWidget
+from quickplot import quickplot
\ No newline at end of file
diff --git a/contrib/cdat/scripts/old_cdat_init.py b/contrib/cdat/scripts/old_cdat_init.py
new file mode 100644
index 0000000..39f6cef
--- /dev/null
+++ b/contrib/cdat/scripts/old_cdat_init.py
@@ -0,0 +1,447 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+import vcs, cdms, cdutil
+import inspect
+import os, sys
+
+class cdms_dataarray(Module) :
+ def __init__(self, arr) :
+ self.arr = arr
+
+class cdms_dataset(Module) :
+ def __init__(self, dataset) :
+ self.dataset = dataset
+ def slice(self, id, kwargs) :
+ dummy = []
+ return self.dataset(id, *dummy, **kwargs)
+
+class cdms_get_data(Module) :
+ def compute(self) :
+ if not self.hasInputFromPort('id') :
+ print "Error: must have id input"
+ return
+
+ if not self.hasInputFromPort('dataset') :
+ print "Error: must have dataset input"
+ return
+ id = self.getInputFromPort('id')
+ dataset = self.getInputFromPort('dataset')
+ kwargs = {}
+
+ if (self.hasInputFromPort('arg_key_1') and
+ self.hasInputFromPort('arg_val_1')) :
+
+ k = self.getInputFromPort('arg_key_1')
+ t = self.getInputFromPort('arg_val_1')
+ kwargs[k] = t
+
+
+ if (self.hasInputFromPort('arg_key_2') and
+ self.hasInputFromPort('arg_val_2')) :
+
+ k = self.getInputFromPort('arg_key_2')
+ t = self.getInputFromPort('arg_val_2')
+ kwargs[k] = t
+
+
+ if (self.hasInputFromPort('arg_key_3') and
+ self.hasInputFromPort('arg_val_3')) :
+
+ k = self.getInputFromPort('arg_key_3')
+ t = self.getInputFromPort('arg_val_3')
+ kwargs[k] = t
+
+ dummy = []
+ arr = dataset.slice(id, kwargs)
+ darr = cdms_dataarray(arr)
+ self.setResult("cdms_dataarray", darr)
+
+class cdms_open(Module) :
+ def compute(self) :
+ args = inspect.getargspec(cdms.open)
+ def_args = args[3]
+ uri = None
+ mode = def_args[0]
+ template = def_args[1]
+ dods = def_args[2]
+
+ if not self.hasInputFromPort('uri') :
+ print "Error: must have uri input"
+ return
+
+ if self.hasInputFromPort('uri') :
+ inuri = self.getInputFromPort('uri')
+ uri = os.path.join(sys.prefix, inuri)
+ if self.hasInputFromPort('mode') :
+ mode = self.getInputFromPort('mode')
+ if self.hasInputFromPort('template') :
+ template = self.getInputFromPort('template')
+ if self.hasInputFromPort('dods') :
+ dods = self.getInputFromPort('dods')
+
+ # output the cdmsfile object.
+ cdmsfile = cdms.open(uri,mode,template,dods)
+ output = cdms_dataset(cdmsfile)
+ self.setResult("cdms_dataset", output)
+
+# just wrap whatever so it can be sent downstream
+class generic_port(Module) :
+ def __init__(self, data) :
+ self.data = data
+
+class vcs_canvas(Module) :
+ def __init__(self) :
+ Module.__init__(self)
+ self.canvas = None
+
+ def compute(self):
+ if self.canvas == None :
+ print "calling vcs.init()"
+ self.canvas = vcs.init()
+ self.setResult("vcs_canvas", self)
+
+
+class vcs_canvas_getboxfill(Module) :
+ def compute(self) :
+ if not self.hasInputFromPort('canvas') :
+ print "ERROR: Must have canvas input port"
+ return
+
+ bname = None
+ if self.hasInputFromPort('boxfill name') :
+ bname = self.getInputFromPort('boxfill name')
+ vcs_c = self.getInputFromPort('canvas')
+
+ if bname == None :
+ bfm = vcs_c.canvas.getboxfill()
+ else :
+ bfm = vcs_c.canvas.getboxfill(bname)
+
+ out = generic_port(bfm)
+ self.setResult("boxfill graphics method", out)
+
+class vcs_canvas_gettemplate(Module) :
+ def compute(self) :
+ if not self.hasInputFromPort('canvas') :
+ print "ERROR: Must have canvas input port"
+ return
+
+ tname = None
+ if self.hasInputFromPort('template name') :
+ tname = self.getInputFromPort('template name')
+ vcs_c = self.getInputFromPort('canvas')
+
+ if tname == None :
+ t = vcs_c.canvas.gettemplate()
+ else :
+ t = vcs_c.canvas.gettemplate(tname)
+
+ out = generic_port(t)
+ self.setResult("template", out)
+
+class vcs_canvas_plot(Module) :
+ def compute(self) :
+
+ canvas = self.getInputFromPort('vcs_canvas').canvas
+ data1 = self.getInputFromPort('array1').arr
+ data2 = None
+ if self.hasInputFromPort('array2') :
+ data2 = self.getInputFromPort('array2').arr
+
+ gm = self.getInputFromPort('graphics_method').data
+ t = self.getInputFromPort('template_name').data
+
+
+ # build up the kewword arguments from the optional inputs.
+ kwargs = {}
+ kwargs['bg'] = 1
+ if self.hasInputFromPort('ratio') :
+ kwargs['ratio'] = self.getInputFromPort('ratio')
+
+ #variable attribute keys
+ if self.hasInputFromPort('comment1') :
+ kwargs['comment1'] = self.getInputFromPort('comment1')
+ if self.hasInputFromPort('comment2') :
+ kwargs['comment2'] = self.getInputFromPort('comment2')
+ if self.hasInputFromPort('comment3') :
+ kwargs['comment3'] = self.getInputFromPort('comment3')
+ if self.hasInputFromPort('comment4') :
+ kwargs['comment4'] = self.getInputFromPort('comment4')
+ if self.hasInputFromPort('file_comment') :
+ kwargs['file_comment'] = self.getInputFromPort('file_comment')
+ if self.hasInputFromPort('hms') :
+ kwargs['hms'] = self.getInputFromPort('hms')
+ if self.hasInputFromPort('long_name') :
+ kwargs['long_name'] = self.getInputFromPort('long_name')
+ if self.hasInputFromPort('name') :
+ kwargs['name'] = self.getInputFromPort('name')
+ if self.hasInputFromPort('time') :
+ kwargs['time'] = self.getInputFromPort('time')
+ if self.hasInputFromPort('units') :
+ kwargs['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('ymd') :
+ kwargs['ymd'] = self.getInputFromPort('ymd')
+
+ # dimension attribute keys
+ if self.hasInputFromPort('xarray1') :
+ kwargs['xarray1'] = self.getInputFromPort('xarray1')
+ if self.hasInputFromPort('yarray1') :
+ kwargs['yarray1'] = self.getInputFromPort('yarray1')
+ if self.hasInputFromPort('zarray1') :
+ kwargs['zarray1'] = self.getInputFromPort('zarray1')
+ if self.hasInputFromPort('tarray1') :
+ kwargs['tarray1'] = self.getInputFromPort('tarray1')
+ if self.hasInputFromPort('warray1') :
+ kwargs['warray1'] = self.getInputFromPort('warray1')
+ if self.hasInputFromPort('xarray2') :
+ kwargs['xarray2'] = self.getInputFromPort('xarray2')
+ if self.hasInputFromPort('yarray2') :
+ kwargs['yarray2'] = self.getInputFromPort('yarray2')
+ if self.hasInputFromPort('zarray2') :
+ kwargs['zarray2'] = self.getInputFromPort('zarray2')
+ if self.hasInputFromPort('tarray2') :
+ kwargs['tarray2'] = self.getInputFromPort('tarray2')
+ if self.hasInputFromPort('warray2') :
+ kwargs['warray2'] = self.getInputFromPort('warray2')
+ if self.hasInputFromPort('xbounds') :
+ kwargs['xbounds'] = self.getInputFromPort('xbounds')
+ if self.hasInputFromPort('ybounds') :
+ kwargs['ybounds'] = self.getInputFromPort('ybounds')
+ if self.hasInputFromPort('xname') :
+ kwargs['xname'] = self.getInputFromPort('xname')
+ if self.hasInputFromPort('yname') :
+ kwargs['yname'] = self.getInputFromPort('yname')
+ if self.hasInputFromPort('zname') :
+ kwargs['zname'] = self.getInputFromPort('zname')
+ if self.hasInputFromPort('tname') :
+ kwargs['tname'] = self.getInputFromPort('tname')
+ if self.hasInputFromPort('wname') :
+ kwargs['wname'] = self.getInputFromPort('wname')
+ if self.hasInputFromPort('xunits') :
+ kwargs['xunits'] = self.getInputFromPort('xunits')
+ if self.hasInputFromPort('yunits') :
+ kwargs['yunits'] = self.getInputFromPort('yunits')
+ if self.hasInputFromPort('zunits') :
+ kwargs['zunits'] = self.getInputFromPort('zunits')
+ if self.hasInputFromPort('tunits') :
+ kwargs['tunits'] = self.getInputFromPort('tunits')
+ if self.hasInputFromPort('wunits') :
+ kwargs['wunits'] = self.getInputFromPort('wunits')
+ if self.hasInputFromPort('xweights') :
+ kwargs['xweights'] = self.getInputFromPort('xweights')
+ if self.hasInputFromPort('yweights') :
+ kwargs['yweights'] = self.getInputFromPort('yweights')
+
+ if data2 == None :
+ canvas.plot(data1, gm, t, **kwargs)
+ else :
+ canvas.plot(data1, data2, gm, t, **kwargs)
+ o = self.interpreter.filePool.create_file(suffix='.cdat.gif')
+ canvas.gif(o.name)
+ self.setResult("image", o)
+
+
+def initialize(*args, **keywords):
+ reg = core.modules.module_registry
+
+
+ reg.addModule(cdms_open)
+ reg.addInputPort(cdms_open, 'dods',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.addInputPort(cdms_open, 'template',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.addInputPort(cdms_open, 'mode',
+ (core.modules.basic_modules.String, 'tip'))
+ reg.addInputPort(cdms_open, 'uri',
+ (core.modules.basic_modules.String, 'tip'))
+
+ # output dataset.
+ reg.addOutputPort(cdms_open, "cdms_dataset",
+ (cdms_dataset, 'cdms.dataset'))
+ #holds the tetgenio class, and acts as a port.
+ reg.addModule(cdms_dataset)
+
+ reg.addModule(cdms_get_data)
+ reg.addInputPort(cdms_get_data, 'dataset',
+ (cdms_dataset, 'dataset'))
+ reg.addInputPort(cdms_get_data, 'id',
+ (core.modules.basic_modules.String, 'dataset id'))
+
+ reg.addInputPort(cdms_get_data, 'arg_key_1',
+ (core.modules.basic_modules.String, 'argument 1 key'))
+ reg.addInputPort(cdms_get_data, 'arg_val_1',
+ ([core.modules.basic_modules.Float,
+ core.modules.basic_modules.Float]))
+
+ reg.addInputPort(cdms_get_data, 'arg_key_2',
+ (core.modules.basic_modules.String, 'argument 2 key'))
+ reg.addInputPort(cdms_get_data, 'arg_val_2',
+ ([core.modules.basic_modules.Float,
+ core.modules.basic_modules.Float]))
+
+ reg.addInputPort(cdms_get_data, 'arg_key_3',
+ (core.modules.basic_modules.String, 'argument 3 key'))
+ reg.addInputPort(cdms_get_data, 'arg_val_3',
+ ([core.modules.basic_modules.Float,
+ core.modules.basic_modules.Float]))
+ # output data array.
+ reg.addOutputPort(cdms_get_data, "cdms_dataarray",
+ (cdms_dataarray, 'data'))
+
+
+ # port for passing data arrays
+ reg.addModule(cdms_dataarray)
+ # port for passing anything
+ reg.addModule(generic_port)
+ #canvas module
+ reg.addModule(vcs_canvas)
+ reg.addOutputPort(vcs_canvas, "vcs_canvas",
+ (vcs_canvas, 'the canvas'))
+
+ #canvas module methods...
+ reg.addModule(vcs_canvas_getboxfill)
+ reg.addInputPort(vcs_canvas_getboxfill, 'canvas',
+ (vcs_canvas, 'the canvas'))
+ reg.addInputPort(vcs_canvas_getboxfill, 'boxfill name',
+ (core.modules.basic_modules.String, 'boxfill method name'))
+
+ reg.addOutputPort(vcs_canvas_getboxfill, "boxfill graphics method",
+ (generic_port, 'graphics method'))
+
+ reg.addModule(vcs_canvas_gettemplate)
+ reg.addInputPort(vcs_canvas_gettemplate, 'canvas',
+ (vcs_canvas, 'the canvas'))
+ reg.addInputPort(vcs_canvas_gettemplate, 'template name',
+ (core.modules.basic_modules.String, 'template name'))
+
+ reg.addOutputPort(vcs_canvas_gettemplate, "template",
+ (generic_port, 'template'))
+
+
+ reg.addModule(vcs_canvas_plot)
+ reg.addInputPort(vcs_canvas_plot, 'vcs_canvas',
+ vcs_canvas)
+ reg.addInputPort(vcs_canvas_plot, 'array1',
+ cdms_dataarray)
+ reg.addInputPort(vcs_canvas_plot, 'array2',
+ cdms_dataarray)
+ reg.addInputPort(vcs_canvas_plot, 'template_name',
+ generic_port)
+ reg.addInputPort(vcs_canvas_plot, 'graphics_method',
+ generic_port)
+ reg.addInputPort(vcs_canvas_plot, 'graphics_name',
+ generic_port)
+
+ # keyword args
+ reg.addInputPort(vcs_canvas_plot, 'ratio',
+ core.modules.basic_modules.String, True)
+
+ # Variable attribute keys
+ reg.addInputPort(vcs_canvas_plot, 'comment1',
+ core.modules.basic_modules.String, True)
+
+ reg.addInputPort(vcs_canvas_plot, 'comment2',
+ core.modules.basic_modules.String, True)
+
+ reg.addInputPort(vcs_canvas_plot, 'comment3',
+ core.modules.basic_modules.String, True)
+
+ reg.addInputPort(vcs_canvas_plot, 'comment4',
+ core.modules.basic_modules.String, True)
+
+ reg.addInputPort(vcs_canvas_plot, 'file_comment',
+ core.modules.basic_modules.String, True)
+
+ reg.addInputPort(vcs_canvas_plot, 'hms',
+ core.modules.basic_modules.String, True)
+
+ reg.addInputPort(vcs_canvas_plot, 'long_name',
+ core.modules.basic_modules.String, True)
+
+ reg.addInputPort(vcs_canvas_plot, 'name',
+ core.modules.basic_modules.String, True)
+
+ reg.addInputPort(vcs_canvas_plot, 'time',
+ core.modules.basic_modules.String, True)
+
+ reg.addInputPort(vcs_canvas_plot, 'units',
+ core.modules.basic_modules.String, True)
+
+ reg.addInputPort(vcs_canvas_plot, 'ymd',
+ core.modules.basic_modules.String, True)
+
+ # Dimension attribuge keys
+ reg.addInputPort(vcs_canvas_plot, 'xarray1',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'yarray1',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'zarray1',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'tarray1',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'warray1',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'xarray2',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'yarray2',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'zarray2',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'tarray2',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'warray2',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'xbounds',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'ybounds',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'xname',
+ core.modules.basic_modules.String, True)
+ reg.addInputPort(vcs_canvas_plot, 'yname',
+ core.modules.basic_modules.String, True)
+ reg.addInputPort(vcs_canvas_plot, 'zname',
+ core.modules.basic_modules.String, True)
+ reg.addInputPort(vcs_canvas_plot, 'tname',
+ core.modules.basic_modules.String, True)
+ reg.addInputPort(vcs_canvas_plot, 'wname',
+ core.modules.basic_modules.String, True)
+ reg.addInputPort(vcs_canvas_plot, 'xunits',
+ core.modules.basic_modules.String, True)
+ reg.addInputPort(vcs_canvas_plot, 'yunits',
+ core.modules.basic_modules.String, True)
+ reg.addInputPort(vcs_canvas_plot, 'zunits',
+ core.modules.basic_modules.String, True)
+ reg.addInputPort(vcs_canvas_plot, 'tunits',
+ core.modules.basic_modules.String, True)
+ reg.addInputPort(vcs_canvas_plot, 'wunits',
+ core.modules.basic_modules.String, True)
+ reg.addInputPort(vcs_canvas_plot, 'xweights',
+ cdms_dataarray, True)
+ reg.addInputPort(vcs_canvas_plot, 'yweights',
+ cdms_dataarray, True)
+
+ reg.addOutputPort(vcs_canvas_plot, "image",
+ (core.modules.basic_modules.File, 'rendered image'))
diff --git a/contrib/cdat/scripts/parse_cdat_xml_file.py b/contrib/cdat/scripts/parse_cdat_xml_file.py
new file mode 100755
index 0000000..6a6ffe5
--- /dev/null
+++ b/contrib/cdat/scripts/parse_cdat_xml_file.py
@@ -0,0 +1,165 @@
+#!/usr/bin/env python
+############################################################################
+##
+## Copyright (C) 2006-2008 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+from core.system import get_elementtree_library
+ElementTree = get_elementtree_library()
+from cdat_domain import CDATAction, CDATModule, CDATOption, CDATPort
+
+class XMLNode:
+ def __init__(self):
+ pass
+
+ def has_attribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def get_attribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ @staticmethod
+ def convert_from_str(value, type):
+ def bool_conv(x):
+ s = str(x).upper()
+ if s == 'TRUE':
+ return True
+ if s == 'FALSE':
+ return False
+
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'bool':
+ return bool_conv(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+class CDATOptionNode(XMLNode):
+ @staticmethod
+ def from_xml(node):
+ tag = node.tag
+ data = node.get('default', None)
+ default = CDATOptionNode.convert_from_str(data, 'str')
+ data = node.get('doc', None)
+ doc = CDATOptionNode.convert_from_str(data, 'str')
+ data = node.get('instance', None)
+ instance = CDATOptionNode.convert_from_str(data, 'str')
+ return CDATOption(tag=tag, default=default,doc=doc,instance=instance)
+
+class CDATPortNode(XMLNode):
+ """Represents Input or Output nodes"""
+ @staticmethod
+ def from_xml(node):
+ tag = node.tag
+ data = node.get('doc', None)
+ doc = CDATPortNode.convert_from_str(data, 'str')
+ data = node.get('instance', None)
+ instance = CDATPortNode.convert_from_str(data, 'str')
+ data = node.get('position', None)
+ position = CDATPortNode.convert_from_str(data, 'int')
+ data = node.get('required', None)
+ required = CDATPortNode.convert_from_str(data, 'bool')
+ return CDATPort(tag=tag, doc=doc, instance=instance,
+ position=position, required=required)
+
+class CDATActionNode(XMLNode):
+ @staticmethod
+ def from_xml(node):
+ data = node.get('name', None)
+ name = CDATActionNode.convert_from_str(data,'str')
+ data = node.get('type', None)
+ type = CDATActionNode.convert_from_str(data,'str')
+
+ options = []
+ inputs = []
+ outputs = []
+
+ #read children
+ for child in node.getchildren():
+ if child.tag == 'options':
+ for optnode in child.getchildren():
+ option = CDATOptionNode.from_xml(optnode)
+ options.append(option)
+ elif child.tag == 'input':
+ for inode in child.getchildren():
+ port = CDATPortNode.from_xml(inode)
+ inputs.insert(port._position,port)
+ elif child.tag == 'output':
+ for onode in child.getchildren():
+ port = CDATPortNode.from_xml(onode)
+ outputs.insert(port._position,port)
+ elif child.tag == 'doc':
+ doc = child.text
+ return CDATAction(name=name, type=type, options=options, inputs=inputs,
+ outputs=outputs, doc=doc)
+
+class CDATModuleNode(XMLNode):
+ @staticmethod
+ def from_xml(node):
+ data = node.get('author',None)
+ author = CDATModuleNode.convert_from_str(data,'str')
+ data = node.get('programminglanguage', None)
+ language = CDATModuleNode.convert_from_str(data,'str')
+ data = node.get('type', None)
+ type = CDATModuleNode.convert_from_str(data, 'str')
+ data = node.get('url', None)
+ url = CDATModuleNode.convert_from_str(data, 'str')
+ data = node.get('version', None)
+ version = CDATModuleNode.convert_from_str(data, 'str')
+ data = node.get('codepath', None)
+ codepath = CDATModuleNode.convert_from_str(data, 'str')
+
+ actions = []
+ #read actions
+ for child in node.getchildren():
+ if child.tag == 'action':
+ action = CDATActionNode.from_xml(child)
+ actions.append(action)
+
+ return CDATModule(author=author,
+ language=language,
+ type=type,
+ url=url,
+ codepath=codepath,
+ version=version,
+ actions=actions)
+
+def parse_cdat_xml_file(filename):
+ """ parse_cdat_xml_file(filename:str) -> CDATDiagnostic
+ """
+ tree = ElementTree.parse(filename)
+ module = CDATModuleNode.from_xml(tree.getroot())
+ return module
\ No newline at end of file
diff --git a/contrib/cdat/scripts/xml/canvas.xml b/contrib/cdat/scripts/xml/canvas.xml
new file mode 100644
index 0000000..5d99a75
--- /dev/null
+++ b/contrib/cdat/scripts/xml/canvas.xml
@@ -0,0 +1,2747 @@
+<diagnostic author="PCMDI's software team" programminglanguage="Python" type="class" url="http://cdat.sf.net" version="5.0.0.alpha7" codepath="vcs.Canvas.Canvas">
+ <action name="boxfill" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <slab doc="Data at least 2D, last 2 dimensions will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0" required="True"/>
+ </input>
+ <output>
+ <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
+ </output>
+ <doc>
+ Function: boxfill # Generate a boxfill plot
+
+ Description of Function:
+ Generate a boxfill plot given the data, boxfill graphics method, and
+ template. If no boxfill class object is given, then the 'default' boxfill
+ graphics method is used. Similarly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('boxfill') # Show all the existing boxfill graphics methods
+ box=a.getboxfill('quick') # Create instance of 'quick'
+ a.boxfill(array,box) # Plot array using specified box and default
+ # template
+ templt=a.gettemplate('AMIP') # Create an instance of template 'AMIP'
+ a.clear() # Clear VCS canvas
+ a.boxfill(array,box,template) # Plot array using specified box and template
+ a.boxfill(box,array,template) # Plot array using specified box and template
+ a.boxfill(template,array,box) # Plot array using specified box and template
+ a.boxfill(template,array,box) # Plot array using specified box and template
+ a.boxfill(array,'AMIP','quick') # Use 'AMIP' template and 'quick' boxfill
+ a.boxfill('AMIP',array,'quick') # Use 'AMIP' template and 'quick' boxfill
+ a.boxfill('AMIP','quick',array) # Use 'AMIP' template and 'quick' boxfill
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End boxfill Description ################################################
+######################################### #################################################
+###################################################################################################################
+ </doc>
+ </action>
+ <action name="createboxfill" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
+ <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <boxfill doc="no default" instance="vcs.boxfill.Gfb" position="0"/>
+ </output>
+ <doc>
+ Function: createboxfill # Construct a new boxfill graphics method
+
+ Description of Function:
+ Create a new boxfill graphics method given the the name and the existing
+ boxfill graphics method to copy the attributes from. If no existing
+ boxfill graphics method name is given, then the default boxfill graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('boxfill')
+ box=a.createboxfill('example1',)
+ a.show('boxfill')
+ box=a.createboxfill('example2','quick')
+ a.show('boxfill')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createboxfill Description ################################################
+######################################### #################################################
+#########################################################################################################################
+ </doc>
+ </action>
+ <action name="createisofill" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
+ <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False" />
+ </input>
+ <output>
+ <isofill doc="no default" instance="vcs.isofill.Gfi" position="0"/>
+ </output>
+ <doc>
+ Function: createisofill # Construct a new isofill graphics method
+
+ Description of Function:
+ Create a new isofill graphics method given the the name and the existing
+ isofill graphics method to copy the attributes from. If no existing
+ isofill graphics method name is given, then the default isofill graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('isofill')
+ iso=a.createisofill('example1',)
+ a.show('isofill')
+ iso=a.createisofill('example2','quick')
+ a.show('isofill')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createisofill Description ################################################
+######################################### #################################################
+#########################################################################################################################
+ </doc>
+ </action>
+ <action name="createisoline" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
+ <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <isoline doc="no default" instance="vcs.isoline.Gi" position="0"/>
+ </output>
+ <doc>
+ Function: createisoline # Construct a new isoline graphics method
+
+ Description of Function:
+ Create a new isoline graphics method given the the name and the existing
+ isoline graphics method to copy the attributes from. If no existing
+ isoline graphics method name is given, then the default isoline graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+
+ a=vcs.init()
+ a.show('isoline')
+ iso=a.createisoline('example1',)
+ a.show('isoline')
+ iso=a.createisoline('example2','quick')
+ a.show('isoline')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createisoline Description ################################################
+######################################### #################################################
+#########################################################################################################################
+ </doc>
+ </action>
+ <action name="createoutfill" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
+ <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <outfill doc="no default" instance="vcs.outfill.Gfo" position="0"/>
+ </output>
+ <doc>
+ Function: createoutfill # Construct a new outfill graphics method
+
+ Description of Function:
+ Create a new outfill graphics method given the the name and the existing
+ outfill graphics method to copy the attributes from. If no existing
+ outfill graphics method name is given, then the default outfill graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+
+ a=vcs.init()
+ a.show('outfill')
+ out=a.createoutfill('example1',)
+ a.show('outfill')
+ out=a.createoutfill('example2','quick')
+ a.show('outfill')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createoutfill Description ################################################
+######################################### #################################################
+#########################################################################################################################
+ </doc>
+ </action>
+ <action name="createoutline" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
+ <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <outline doc="no default" instance="vcs.outline.Go" position="0"/>
+ </output>
+ <doc>
+ Function: createoutline # Construct a new outline graphics method
+
+ Description of Function:
+ Create a new outline graphics method given the the name and the existing
+ outline graphics method to copy the attributes from. If no existing
+ outline graphics method name is given, then the default outline graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+
+ a=vcs.init()
+ a.show('outline')
+ out=a.createoutline('example1',)
+ a.show('outline')
+ out=a.createoutline('example2','quick')
+ a.show('outline')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createoutline Description ################################################
+######################################### #################################################
+#########################################################################################################################
+ </doc>
+ </action>
+ <action name="createscatter" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
+ <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <scatter doc="no default" instance="vcs.scatter.GSp" position="0"/>
+ </output>
+ <doc>
+ Function: createscatter # Construct a new scatter graphics method
+
+ Description of Function:
+ Create a new scatter graphics method given the the name and the existing
+ scatter graphics method to copy the attributes from. If no existing
+ scatter graphics method name is given, then the default scatter graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('scatter')
+ sct=a.createscatter('example1',)
+ a.show('scatter')
+ sct=a.createscatter('example2','quick')
+ a.show('scatter')
+
+#########################################################################################################################
+########################################### ###############################################
+########################################## End createscatter Description ################################################
+######################################### #################################################
+#########################################################################################################################
+ </doc>
+ </action>
+ <action name="createxvsy" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
+ <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <xvsy doc="no default" instance="vcs.xvsy.GXY" position="0"/>
+ </output>
+ <doc>
+ Function: createxvsy # Construct a new XvsY graphics method
+
+ Description of Function:
+ Create a new XvsY graphics method given the the name and the existing
+ XvsY graphics method to copy the attributes from. If no existing
+ XvsY graphics method name is given, then the default XvsY graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('xvsy')
+ xy=a.createxvsy('example1',)
+ a.show('xvsy')
+ xy=a.createxvsy('example2','quick')
+ a.show('xvsy')
+
+######################################################################################################################
+########################################### ###############################################
+########################################## End createxvsy Description ################################################
+######################################### #################################################
+######################################################################################################################
+ </doc>
+ </action>
+ <action name="createxyvsy" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
+ <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <xyvsy doc="no default" instance="vcs.xyvsy.GXy" position="0"/>
+ </output>
+ <doc>
+ Function: createxyvsy # Construct a new Xyvsy graphics method
+
+ Description of Function:
+ Create a new Xyvsy graphics method given the the name and the existing
+ Xyvsy graphics method to copy the attributes from. If no existing
+ Xyvsy graphics method name is given, then the default Xyvsy graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+
+ a=vcs.init()
+ a.show('xyvsy')
+ xyy=a.createxyvsy('example1',)
+ a.show('xyvsy')
+ xyy=a.createxyvsy('example2','quick')
+ a.show('xyvsy')
+
+#######################################################################################################################
+########################################### ###############################################
+########################################## End createxyvsy Description ################################################
+######################################### #################################################
+#######################################################################################################################
+ </doc>
+ </action>
+ <action name="createyxvsx" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
+ <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <yxvsx doc="no default" instance="vcs.yxvsx.GYx" position="0"/>
+ </output>
+ <doc>
+ Function: createyxvsx # Construct a new Yxvsx graphics method
+
+ Description of Function:
+ Create a new Yxvsx graphics method given the the name and the existing
+ Yxvsx graphics method to copy the attributes from. If no existing
+ Yxvsx graphics method name is given, then the default Yxvsx graphics
+ method will be used as the graphics method to which the attributes will
+ be copied from.
+
+ If the name provided already exists, then a error will be returned. Graphics
+ method names must be unique.
+
+ Example of Use:
+
+ a=vcs.init()
+ a.show('yxvsx')
+ yxx=a.createyxvsx('example1',)
+ a.show('yxvsx')
+ yxx=a.createyxvsx('example2','quick')
+ a.show('yxvsx')
+
+#######################################################################################################################
+########################################### ###############################################
+########################################## End createyxvsx Description ################################################
+######################################### #################################################
+#######################################################################################################################
+ </doc>
+ </action>
+ <action name="getboxfill" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <boxfill doc="no default" instance="vcs.boxfill.Gfb" position="0"/>
+ </output>
+ <doc>
+ Function: getboxfill # Construct a new boxfill graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ boxfill class object from an existing VCS boxfill graphics method. If
+ no boxfill name is given, then boxfill 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createboxfill function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('boxfill') # Show all the existing boxfill graphics methods
+ box=a.getboxfill() # box instance of 'default' boxfill graphics
+ # method
+ box2=a.getboxfill('quick') # box2 instance of existing 'quick' boxfill
+ # graphics method
+######################################################################################################################
+########################################### ###############################################
+########################################## End getboxfill Description ################################################
+######################################### #################################################
+######################################################################################################################
+ </doc>
+ </action>
+ <action name="getisofill" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <isofill doc="no default" instance="vcs.isofill.Gfi" position="0"/>
+ </output>
+ <doc>
+ Function: getisofill Construct a new isofill graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ isofill class object from an existing VCS isofill graphics method. If
+ no isofill name is given, then isofill 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createisofill function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('isofill') # Show all the existing isofill graphics methods
+ iso=a.getisofill() # iso instance of 'default' isofill graphics
+ # method
+ iso2=a.getisofill('quick') # iso2 instance of existing 'quick' isofill
+ # graphics method
+######################################################################################################################
+########################################### ###############################################
+########################################## End getisofill Description ################################################
+######################################### #################################################
+######################################################################################################################
+ </doc>
+ </action>
+ <action name="getisoline" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <isoline doc="no default" instance="vcs.isoline.Gi" position="0"/>
+ </output>
+ <doc>
+ Function: getisoline # Construct a new isoline graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ isoline class object from an existing VCS isoline graphics method. If
+ no isoline name is given, then isoline 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createisoline function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('isoline') # Show all the existing isoline graphics methods
+ iso=a.getisoline() # iso instance of 'default' isoline graphics
+ # method
+ iso2=a.getisoline('quick') # iso2 instance of existing 'quick' isoline
+ # graphics method
+######################################################################################################################
+########################################### ###############################################
+########################################## End getisoline Description ################################################
+######################################### #################################################
+######################################################################################################################
+ </doc>
+ </action>
+ <action name="getoutfill" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <outfill doc="no default" instance="vcs.outfill.Gfo" position="0"/>
+ </output>
+ <doc>
+ Function: getoutfill # Construct a new outfill graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ outfill class object from an existing VCS outfill graphics method. If
+ no outfill name is given, then outfill 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createoutfill function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('outfill') # Show all the existing outfill graphics methods
+ out=a.getoutfill() # out instance of 'default' outfill graphics
+ # method
+ out2=a.getoutfill('quick') # out2 instance of existing 'quick' outfill
+ # graphics method
+
+######################################################################################################################
+########################################### ###############################################
+########################################## End getoutfill Description ################################################
+######################################### #################################################
+######################################################################################################################
+ </doc>
+ </action>
+ <action name="getoutline" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0" required="False"/>
+ </input>
+ <output>
+ <outline doc="no default" instance="vcs.outline.Go" position="0"/>
+ </output>
+ <doc>
+ Function: getoutline # Construct a new outline graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ outline class object from an existing VCS outline graphics method. If
+ no outline name is given, then outline 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createoutline function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('outline') # Show all the existing outline graphics methods
+ out=a.getoutline() # out instance of 'default' outline graphics
+ # method
+ out2=a.getoutline('quick') # out2 instance of existing 'quick' outline
+ # graphics method
+
+######################################################################################################################
+########################################### ###############################################
+########################################## End getoutline Description ################################################
+######################################### #################################################
+######################################################################################################################
+ </doc>
+ </action>
+ <action name="getscatter" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0"/>
+ </input>
+ <output>
+ <scatter doc="no default" instance="vcs.scatter.GSp" position="0"/>
+ </output>
+ <doc>
+ Function: getscatter # Construct a new scatter graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ scatter class object from an existing VCS scatter graphics method. If
+ no scatter name is given, then scatter 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createscatter function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('scatter') # Show all the existing scatter graphics methods
+ sct=a.getscatter() # sct instance of 'default' scatter graphics
+ # method
+ sct2=a.getscatter('quick') # sct2 instance of existing 'quick' scatter
+ # graphics method
+
+######################################################################################################################
+########################################### ###############################################
+########################################## End getscatter Description ################################################
+######################################### #################################################
+######################################################################################################################
+ </doc>
+ </action>
+ <action name="getxvsy" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0"/>
+ </input>
+ <output>
+ <xvsy doc="no default" instance="vcs.xvsy.GXY" position="0"/>
+ </output>
+ <doc>
+ Function: getxvsy # Construct a new XvsY graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ XvsY class object from an existing VCS XvsY graphics method. If
+ no XvsY name is given, then XvsY 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createxvsy function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('xvsy') # Show all the existing XvsY graphics methods
+ xy=a.getxvsy() # xy instance of 'default' XvsY graphics
+ # method
+ xy2=a.getxvsy('quick') # xy2 instance of existing 'quick' XvsY
+ # graphics method
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End getxvsy Description ################################################
+######################################### #################################################
+###################################################################################################################
+ </doc>
+ </action>
+ <action name="getxyvsy" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0"/>
+ </input>
+ <output>
+ <xyvsy doc="no default" instance="vcs.xyvsy.GXy" position="0"/>
+ </output>
+ <doc>
+ Function: getxyvsy # Construct a new Xyvsy graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ Xyvsy class object from an existing VCS Xyvsy graphics method. If
+ no Xyvsy name is given, then Xyvsy 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createxyvsy function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('xyvsy') # Show all the existing Xyvsy graphics methods
+ xyy=a.getxyvsy() # xyy instance of 'default' Xyvsy graphics
+ # method
+ xyy2=a.getxyvsy('quick') # xyy2 instance of existing 'quick' Xyvsy
+ # graphics method
+####################################################################################################################
+########################################### ###############################################
+########################################## End getxyvsy Description ################################################
+######################################### #################################################
+####################################################################################################################
+ </doc>
+ </action>
+ <action name="getyxvsx" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0"/>
+ </input>
+ <output>
+ <yxvsx doc="no default" instance="vcs.yxvsx.GYx" position="0"/>
+ </output>
+ <doc>
+ Function: getyxvsx # Construct a new Yxvsx graphics method
+
+ Description of Function:
+ VCS contains a list of graphics methods. This function will create a
+ Yxvsx class object from an existing VCS Yxvsx graphics method. If
+ no Yxvsx name is given, then Yxvsx 'default' will be used.
+
+ Note, VCS does not allow the modification of `default' attribute
+ sets. However, a `default' attribute set that has been copied under a
+ different name can be modified. (See the createyxvsx function.)
+
+ Example of Use:
+ a=vcs.init()
+ a.show('yxvsx') # Show all the existing Yxvsx graphics methods
+ yxx=a.getyxvsx() # yxx instance of 'default' Yxvsx graphics
+ # method
+ yxx2=a.getyxvsx('quick') # yxx2 instance of existing 'quick' Yxvsx
+ # graphics method
+####################################################################################################################
+########################################### ###############################################
+########################################## End getyxvsx Description ################################################
+######################################### #################################################
+####################################################################################################################
+ </doc>
+ </action>
+ <action name="isofill" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <slab doc="Data at least 2D, last 2 dimensions will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
+ </input>
+ <output>
+ <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
+ </output>
+ <doc>
+ Function: isofill # Generate an isofill plot
+
+ Description of Function:
+ Generate a isofill plot given the data, isofill graphics method, and
+ template. If no isofill class object is given, then the 'default' isofill
+ graphics method is used. Similarly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('isofill') # Show all the existing isofill graphics methods
+ iso=a.getisofill('quick') # Create instance of 'quick'
+ a.isofill(array,iso) # Plot array using specified iso and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.isofill(array,iso,template) # Plot array using specified iso and template
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End isofill Description ################################################
+######################################### #################################################
+###################################################################################################################
+ </doc>
+ </action>
+ <action name="isoline" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <slab doc="Data at least 2D, last 2 dimensions will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
+ </input>
+ <output>
+ <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
+ </output>
+ <doc>
+ Function: isoline # Generate an isoline plot
+
+ Description of Function:
+ Generate a isoline plot given the data, isoline graphics method, and
+ template. If no isoline class object is given, then the 'default' isoline
+ graphics method is used. Similarly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('isoline') # Show all the existing isoline graphics methods
+ iso=a.getisoline('quick') # Create instance of 'quick'
+ a.isoline(array,iso) # Plot array using specified iso and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.isoline(array,iso,template) # Plot array using specified iso and template
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End isoline Description ################################################
+######################################### #################################################
+###################################################################################################################
+ </doc>
+ </action>
+ <action name="outfill" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <slab doc="Data at least 2D, last 2 dimensions will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
+ </input>
+ <output>
+ <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
+ </output>
+ <doc>
+ Function: outfill # Generate an outfill plot
+
+ Description of Function:
+ Generate a outfill plot given the data, outfill graphics method, and
+ template. If no outfill class object is given, then the 'default' outfill
+ graphics method is used. Simerly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('outfill') # Show all the existing outfill graphics methods
+ out=a.getoutfill('quick') # Create instance of 'quick'
+ a.outfill(array,out) # Plot array using specified out and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.outfill(array,out,template) # Plot array using specified out and template
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End outfill Description ################################################
+######################################### #################################################
+###################################################################################################################
+ </doc>
+ </action>
+ <action name="outline" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <slab doc="Data at least 2D, last 2 dimensions will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
+ </input>
+ <output>
+ <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
+ </output>
+ <doc>
+ Function: outline # Generate an outline plot
+
+ Description of Function:
+ Generate a outline plot given the data, outline graphics method, and
+ template. If no outline class object is given, then the 'default' outline
+ graphics method is used. Simerly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('outline') # Show all the existing outline graphics methods
+ out=a.getoutline('quick') # Create instance of 'quick'
+ a.outline(array,out) # Plot array using specified out and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.outline(array,out,template) # Plot array using specified out and template
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End outline Description ################################################
+######################################### #################################################
+###################################################################################################################
+ </doc>
+ </action>
+ <action name="plot" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <slab1 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0" required="True"/>
+ <slab2 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0" required="False"/>
+ </input>
+ <output>
+ <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
+ </output>
+ <doc>
+ Function: plot
+
+ Description of plot:
+ Plot an array(s) of data given a template and graphics method. The VCS template is
+ used to define where the data and variable attributes will be displayed on the VCS
+ Canvas. The VCS graphics method is used to define how the array(s) will be shown
+ on the VCS Canvas.
+
+ The form of the call is:
+ plot(array1=None, array2=None, template_name=None, graphics_method=None,
+ graphics_name=None, [key=value [, key=value [, ...]]])
+
+ where array1 and array2 are NumPy arrays.
+
+ Plot keywords:
+ ratio [default is none]
+ None: let the self.ratio attribute decide
+ 0,'off': overwritte self.ratio and do nothing about the ratio
+ 'auto': computes an automatic ratio
+ '3',3: y dim will be 3 times bigger than x dim (restricted to original tempalte.data area
+ Adding a 't' at the end of the ratio, makes the tickmarks and boxes move along.
+
+ Variable attribute keys:
+ comment1 = string #Comment plotted above file_comment
+ comment2 = string #Comment plotted above comment1
+ comment3 = string #Comment plotted above comment2
+ comment4 = string #Comment plotted above comment4
+ file_comment = string #Comment (defaults to file.comment)
+ hms = string (hh:mm:ss) #Hour, minute, second
+ long_name = string #Descriptive variable name
+ name = string #Variable name (defaults to var.id)
+ time = cdtime #instance (relative or absolute),
+ cdtime, reltime or abstime value
+ units = string #Variable units
+ ymd = string (yy/mm/dd) #Year, month, day
+
+ Dimension attribute keys (dimension length=n):
+ [x|y|z|t|w]array = NumPy array of length n # x or y Dimension values
+ [x|y|z|t|w]array = NumPy array of length n # x or y Dimension values
+ [x|y]bounds = NumPy array of shape (n,2) # x or y Dimension boundaries
+ [x|y|z|t|w]name = string # x or y Dimension name
+ [x|y|z|t|w]units = string # x or y Dimension units
+ [x|y]weights = NumPy array of length n # x or y Dimension weights (used to
+ calculate area-weighted mean)
+
+ CDMS object:
+ [x|y|z|t|w]axis = CDMS axis object # x or y Axis
+ grid = CDMS grid object # Grid object (e.g. grid=var.getGrid()
+ variable = CDMS variable object # Variable object
+
+ Other:
+ [x|y]rev = 0|1 # if ==1, reverse the direction of the x
+ or y axis
+ continents = 0,1,2,3,4,5,6,7,8,9,10,11 # if >=1, plot continental outlines
+ (default: plot if xaxis is
+ longitude, yaxis is latitude -or-
+ xname is 'longitude' and yname is
+ 'latitude'
+ # The continents-type values are integers
+ # ranging from 0 to 11, where:
+ # 0 signifies "No Continents"
+ # 1 signifies "Fine Continents"
+ # 2 signifies "Coarse Continents"
+ # 3 signifies "United States"
+ # 4 signifies "Political Borders"
+ # 5 signifies "Rivers"
+
+ # Values 6 through 11 signify the line type
+ # defined by the files data_continent_other7
+ # through data_continent_other12.
+
+ Graphics Output in Background Mode:
+ bg = 0|1 # if ==1, create images in the background
+ (Don't display the VCS Canvas)
+
+ Note:
+ More specific attributes take precedence over general attributes. In particular,
+ specifie attributes override variable object attributes, dimension attributes and
+ arrays override axis objects, which override grid objects, which override variable
+ objects.
+
+ For example, if both 'file_comment' and 'variable' keywords are specified, the value of
+ 'file_comment' is used instead of the file comment in the parent of variable. Similarly,
+ if both 'xaxis' and 'grid' keywords are specified, the value of 'xaxis' takes precedence
+ over the x-axis of grid.
+
+ Example of Use:
+ x=vcs.init() # x is an instance of the VCS class object (constructor)
+ x.plot(array) # this call will use default settings for template and boxfill
+ x.plot(array, 'AMIP', 'isofill','AMIP_psl') # this is specifying the template and
+ graphics method
+ t=x.gettemplate('AMIP') # get a predefined the template 'AMIP'
+ vec=x.getvector('quick') # get a predefined the vector graphics method 'quick'
+ x.plot(array1, array2, t, vec) # plot the data as a vector using the 'AMIP' template
+ x.clear() # clear the VCS Canvas of all plots
+ box=x.createboxfill('new') # create boxfill graphics method 'new'
+ x.plot(box,t,array) # plot array data using box 'new' and template 't'
+
+###############################################################################################################
+########################################### ##############################################
+########################################## End plot Description ###############################################
+######################################### ################################################
+###############################################################################################################
+ </doc>
+ </action>
+ <action name="scatter" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <slab1 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
+ <slab2 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
+ </input>
+ <output>
+ <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
+ </output>
+ <doc>
+ Function: scatter # Generate a scatter plot
+
+ Description of Function:
+ Generate a scatter plot given the data, scatter graphics method, and
+ template. If no scatter class object is given, then the 'default' scatter
+ graphics method is used. Similarly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('scatter') # Show all the existing scatter graphics methods
+ sct=a.getscatter('quick') # Create instance of 'quick'
+ a.scatter(array,sct) # Plot array using specified sct and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.scatter(array,sct,template) # Plot array using specified sct and template
+
+###################################################################################################################
+########################################### ###############################################
+########################################## End scatter Description ################################################
+######################################### #################################################
+###################################################################################################################
+ </doc>
+ </action>
+ <action name="xvsy" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <slab1 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
+ <slab2 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
+ </input>
+ <output>
+ <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
+ </output>
+ <doc>
+ Function: xvsy # Generate a XvsY plot
+
+ Description of Function:
+ Generate a XvsY plot given the data, XvsY graphics method, and
+ template. If no XvsY class object is given, then the 'default' XvsY
+ graphics method is used. Similarly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('xvsy') # Show all the existing XvsY graphics methods
+ xy=a.getxvsy('quick') # Create instance of 'quick'
+ a.xvsy(array,xy) # Plot array using specified xy and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.xvsy(array,xy,template) # Plot array using specified xy and template
+
+#################################################################################################################
+########################################### ###############################################
+########################################## End xvsy Description ################################################
+######################################### #################################################
+#################################################################################################################
+ </doc>
+ </action>
+ <action name="xyvsy" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <slab doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
+ </input>
+ <output>
+ <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
+ </output>
+ <doc>
+ Function: xyvsy # Generate a Xyvsy plot
+
+ Description of Function:
+ Generate a Xyvsy plot given the data, Xyvsy graphics method, and
+ template. If no Xyvsy class object is given, then the 'default' Xyvsy
+ graphics method is used. Simerly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('xyvsy') # Show all the existing Xyvsy graphics methods
+ xyy=a.getxyvsy('quick') # Create instance of 'quick'
+ a.xyvsy(array,xyy) # Plot array using specified xyy and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.xyvsy(array,xyy,template) # Plot array using specified xyy and template
+
+#################################################################################################################
+########################################### ###############################################
+########################################## End xyvsy Description ################################################
+######################################### #################################################
+#################################################################################################################
+ </doc>
+ </action>
+ <action name="yxvsx" type="function">
+ <options>
+ <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
+ <long_name doc="replaces long_name on plot" instance="str"/>
+ <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
+ <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
+ <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
+ <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
+ <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
+ <continents doc="continents type number" instance="int"/>
+ <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
+ <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
+ <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
+ <wname doc="replace waxis name on plot (if exists)" instance="str"/>
+ <file_comment doc="replaces file_comment on plot" instance="str"/>
+ <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
+ <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
+ <xrev doc="reverse x axis" instance="bool"/>
+ <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
+ <ymd doc="replaces year/month/day on plot" instance="str"/>
+ <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <units doc="replaces units value on plot" instance="str"/>
+ <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
+ <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <xname doc="replace xaxis name on plot" instance="str"/>
+ <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
+ <bg doc="plots in background mode" instance="bool/int"/>
+ <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
+ <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
+ <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
+ <hms doc="replaces hh/mm/ss on plot" instance="str"/>
+ <tname doc="replace taxis name on plot (if exists)" instance="str"/>
+ <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
+ <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
+ <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
+ <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
+ <xunits doc="replace xaxis units on plot" instance="str"/>
+ <name doc="replaces variable name on plot
+time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
+ <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
+ <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
+ <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
+ <comment1 doc="replaces comment1 on plot" instance="str"/>
+ <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
+ <comment3 doc="replaces comment3 on plot" instance="str"/>
+ <comment2 doc="replaces comment2 on plot" instance="str"/>
+ <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
+ <comment4 doc="replaces comment4 on plot" instance="str"/>
+ <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
+ <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
+ </options>
+ <input>
+ <slab doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
+ </input>
+ <output>
+ <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
+ </output>
+ <doc>
+ Function: yxvsx # Generate a Yxvsx plot
+
+ Description of Function:
+ Generate a Yxvsx plot given the data, Yxvsx graphics method, and
+ template. If no Yxvsx class object is given, then the 'default' Yxvsx
+ graphics method is used. Simerly, if no template class object is given,
+ then the 'default' template is used.
+
+ Example of Use:
+ a=vcs.init()
+ a.show('yxvsx') # Show all the existing Yxvsx graphics methods
+ yxx=a.getyxvsx('quick') # Create instance of 'quick'
+ a.yxvsx(array,yxx) # Plot array using specified yxx and default
+ # template
+ a.clear() # Clear VCS canvas
+ a.yxvsx(array,yxx,template) # Plot array using specified yxx and template
+
+#################################################################################################################
+########################################### ###############################################
+########################################## End yxvsx Description ################################################
+######################################### #################################################
+#################################################################################################################
+ </doc>
+ </action>
+ <action name="png" type="function">
+ <input>
+ <file doc="" instance="str" position="0" required="True"/>
+ <width doc="" instance="float" position="1" required="False"/>
+ <height doc="" instance="float" position="2" required="False"/>
+ <units doc="" instance="str" position="3" required="False"/>
+ </input>
+ <doc>
+ Function: png
+
+ Description of Function:
+ Png output is another form of raster graphics.
+
+ Example of Use:
+ a=vcs.init()
+ a.plot(array)
+ a.png('example') # Overwrite a png file
+ a.png('example', width=11.5, height= 8.5) # US Legal
+ a.png('example', width=21, height=29.7, units='cm') # A4
+#################################################################################################################
+########################################### ###############################################
+########################################## End png Description ################################################
+######################################### #################################################
+#################################################################################################################
+ </doc>
+ </action>
+</diagnostic>
diff --git a/contrib/cdat/scripts/xml/cdms2.xml b/contrib/cdat/scripts/xml/cdms2.xml
new file mode 100644
index 0000000..1d384fc
--- /dev/null
+++ b/contrib/cdat/scripts/xml/cdms2.xml
@@ -0,0 +1,26 @@
+<diagnostic author="PCMDI's software team" programminglanguage="Python" type="class" url="http://cdat.sf.net" version="5.0.0.alpha7" codepath="cdms2">
+ <action name="open" type="function">
+ <input>
+ <uri doc="" instance="str" position="0" required="True"/>
+ <mode doc="" instance="str" position="1" required="False"/>
+ <template doc="" instance="str" position="2" required="False"/>
+ <dods doc="" instance="int" position="3" required="False"/>
+ </input>
+ <output>
+ <dataset doc="" instance="cdms2.dataset.CdmsFile" position="0"/>
+ </output>
+ <doc>
+ Function: open # Open an existing dataset
+
+Description of Function:
+ 'uri' is a Uniform Resource Identifier, referring to a cdunif file, XML file,
+ or LDAP URL of a catalog dataset entry.
+ 'mode' is 'r', 'r+', 'a', or 'w'
+###################################################################################################################
+########################################### ###############################################
+########################################## End open Description ################################################
+######################################### #################################################
+###################################################################################################################
+ </doc>
+</action>
+</diagnostic>
\ No newline at end of file
diff --git a/contrib/cdat/scripts/xml/cdmsFile.xml b/contrib/cdat/scripts/xml/cdmsFile.xml
new file mode 100644
index 0000000..fe2727a
--- /dev/null
+++ b/contrib/cdat/scripts/xml/cdmsFile.xml
@@ -0,0 +1,23 @@
+<diagnostic author="PCMDI's software team" programminglanguage="Python" type="class" url="http://cdat.sf.net" version="5.0.0.alpha7" codepath="cdms2.dataset.CdmsFile">
+ <action name="__call__" type="function">
+ <input>
+ <id doc="" instance="str" position="0" required="True"/>
+ </input>
+ <output>
+ <variable doc="" instance="cdms2.tvariable.TransientVariable" position="0"/>
+ </output>
+ <doc>
+ Function: __call__ # Call a variable object with the given id
+
+Description of Function:
+ Call a variable object with the given id
+ Exception if not found.
+ Call the variable with the other arguments.
+###################################################################################################################
+########################################### ###############################################
+########################################## End _call_ Description ################################################
+######################################### #################################################
+###################################################################################################################
+ </doc>
+</action>
+</diagnostic>
\ No newline at end of file
diff --git a/contrib/edu_utah_sci_cscheid_macet/MANIFEST b/contrib/edu_utah_sci_cscheid_macet/MANIFEST
new file mode 100644
index 0000000..61b0205
--- /dev/null
+++ b/contrib/edu_utah_sci_cscheid_macet/MANIFEST
@@ -0,0 +1 @@
+F __init__.py
diff --git a/contrib/edu_utah_sci_cscheid_macet/__init__.py b/contrib/edu_utah_sci_cscheid_macet/__init__.py
new file mode 100644
index 0000000..6a86374
--- /dev/null
+++ b/contrib/edu_utah_sci_cscheid_macet/__init__.py
@@ -0,0 +1,125 @@
+# VisTrails Macet package
+
+# Macet is an isosurface triangle mesh generator that consistently
+# generates good-triangle quality.
+
+# Macet is described in
+
+# Carlos Dietrich, Joao Comba, Luciana Nedel, Carlos Scheidegger, John
+# Schreiner, Claudio Silva. Edge Transformations for Improving Mesh
+# Quality of Marching Cubes. 2007, submitted.
+
+# This package was created by Carlos Eduardo Scheidegger, 2007
+# cscheid at sci.utah.edu. This is GPL v2 or later, your choice.
+
+##############################################################################
+
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from core.system import list2cmdline
+
+# This accomodates two different VisTrails versions: the released one,
+# and the one in development
+
+
+try:
+ from core.configuration import ConfigurationObject
+ global configuration
+ configuration = ConfigurationObject(executable_path=(None, str))
+ old_vistrails = False
+except ImportError:
+ old_vistrails = True
+
+import os
+
+identifier = 'edu.utah.sci.cscheid.macet'
+version = '0.1.0'
+name = 'Macet'
+
+##############################################################################
+
+def get_path():
+ global _macet_path
+ if old_vistrails:
+ return _macet_path
+ if configuration.has('executable_path'):
+ p = configuration.executable_path + '/'
+ else:
+ p = ''
+ p += 'macet'
+ return p
+
+class Macet(Module):
+
+ def compute(self):
+ self.checkInputPort('input_file')
+ self.checkInputPort('iso_value')
+
+ input_file = self.getInputFromPort('input_file')
+ output_file = self.interpreter.filePool.create_file(suffix='.off')
+
+ iso_value = self.getInputFromPort('iso_value')
+
+ values = [get_path(), input_file.name,
+ str(iso_value), output_file.name, '-isCombined']
+ cmdline = list2cmdline(values)
+ print cmdline
+ result = os.system(cmdline)
+ if result != 0:
+ raise ModuleError(self, 'Execution failed')
+
+ self.setResult('output_file', output_file)
+
+class MarchingCubes(Module):
+
+ def compute(self):
+ self.checkInputPort('input_file')
+ self.checkInputPort('iso_value')
+
+ input_file = self.getInputFromPort('input_file')
+ output_file = self.interpreter.filePool.create_file(suffix='.off')
+
+ iso_value = self.getInputFromPort('iso_value')
+
+ values = [get_path(), input_file.name,
+ str(iso_value), output_file.name]
+ cmdline = list2cmdline(values)
+ print cmdline
+ result = os.system(cmdline)
+ if result != 0:
+ raise ModuleError(self, 'Execution failed')
+
+ self.setResult('output_file', output_file)
+
+##############################################################################
+
+def initialize(executable_path=None):
+
+ if old_vistrails:
+ global _macet_path
+ if executable_path:
+ _macet_path = executable_path + '/macet'
+ else:
+ _macet_path = 'macet'
+
+ reg = core.modules.module_registry
+
+ reg.add_module(Macet)
+
+ reg.add_input_port(Macet, 'input_file',
+ core.modules.basic_modules.File)
+ reg.add_input_port(Macet, 'iso_value',
+ core.modules.basic_modules.Float)
+ reg.add_output_port(Macet, 'output_file',
+ core.modules.basic_modules.File)
+
+ reg.add_module(MarchingCubes)
+
+ reg.add_input_port(MarchingCubes, 'input_file',
+ core.modules.basic_modules.File)
+ reg.add_input_port(MarchingCubes, 'iso_value',
+ core.modules.basic_modules.Float)
+ reg.add_output_port(MarchingCubes, 'output_file',
+ core.modules.basic_modules.File)
+
diff --git a/contrib/edu_utah_sci_cscheid_metro/MANIFEST b/contrib/edu_utah_sci_cscheid_metro/MANIFEST
new file mode 100644
index 0000000..4273023
--- /dev/null
+++ b/contrib/edu_utah_sci_cscheid_metro/MANIFEST
@@ -0,0 +1,2 @@
+F __init__.py
+
diff --git a/contrib/edu_utah_sci_cscheid_metro/__init__.py b/contrib/edu_utah_sci_cscheid_metro/__init__.py
new file mode 100644
index 0000000..bf3b9a6
--- /dev/null
+++ b/contrib/edu_utah_sci_cscheid_metro/__init__.py
@@ -0,0 +1,158 @@
+# VisTrails package for metro support
+# Copyright Carlos Eduardo Scheidegger, 2007
+# Get metro at http://vcg.sourceforge.net/
+
+# License: GPLv2 or later
+
+# ChangeLog:
+
+# 2007-03-13 Carlos Scheidegger <cscheid at juggernaut>
+# * First release
+##############################################################################
+
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+import core.bundles
+from core.system import list2cmdline
+import core.requirements
+import os
+import re
+
+try:
+ from core.configuration import ConfigurationObject
+ global configuration
+ configuration = ConfigurationObject(executable_path=(None, str))
+ old_vistrails = False
+except ImportError:
+ old_vistrails = True
+
+identifier = 'edu.utah.sci.cscheid.metro'
+version = '0.1'
+name = 'metro'
+
+################################################################################
+
+def get_path():
+ global _metro_path
+ if old_vistrails:
+ return _metro_path
+ if configuration.has('executable_path'):
+ p = configuration.executable_path + '/'
+ else:
+ p = ''
+ p += 'metro'
+ return p
+
+class Metro(Module):
+
+ def __init__(self):
+ Module.__init__(self)
+ self.need_error_meshes = False
+ self.need_histograms = False
+
+ def is_cacheable(self):
+ return self.need_error_meshes and self.need_histograms
+
+ def compute(self):
+ self.checkInputPort('mesh1')
+ self.checkInputPort('mesh2')
+ f1 = self.getInputFromPort('mesh1')
+ f2 = self.getInputFromPort('mesh2')
+
+ make_file = self.interpreter.filePool.create_file
+
+ metro_output = make_file(suffix='.txt')
+
+ values = [get_path(), f1.name, f2.name, '-q']
+
+ need_error_meshes = False
+ if (self.outputPorts.has_key('error_mesh_1') or
+ self.outputPorts.has_key('error_mesh_2')):
+ need_error_meshes = True
+ error_mesh_output = (make_file(suffix='.ply'),
+ make_file(suffix='.ply'))
+ values.append('-c')
+ values.append(error_mesh_output[0].name)
+ values.append(error_mesh_output[1].name)
+
+ need_histograms = False
+ if (self.outputPorts.has_key('error_hist_1') or
+ self.outputPorts.has_key('error_hist_2')):
+ need_histograms = True
+ error_hist_output = (make_file(suffix='.csv'),
+ make_file(suffix='.csv'))
+ values.append('-h')
+ values.append(error_hist_output[0].name)
+ values.append(error_hist_output[1].name)
+
+ values.append('>')
+ values.append(metro_output.name)
+
+ cmdline = list2cmdline(values)
+
+# cmdline = ('%s ' * len(values)) % tuple(values)
+# cmdline += '> '
+# cmdline += metro_output.name
+ print cmdline
+
+ result = os.system(cmdline)
+ if result != 0:
+ raise ModuleError(self, "Execution failed")
+ l = [x for x in file(metro_output.name).readlines()
+ if x.startswith('Hausdorff')][0]
+ regexp = re.compile(r'Hausdorff distance: ([0123456789.]+) \(([0123456789.]+) wrt bounding box diagonal\)')
+ results = regexp.match(l).groups()
+
+ if need_error_meshes:
+ self.setResult('error_mesh_1', error_mesh_output[0])
+ self.setResult('error_mesh_2', error_mesh_output[1])
+
+ if need_histograms:
+ self.setResult('error_hist_1', error_hist_output[0])
+ self.setResult('error_hist_2', error_hist_output[1])
+
+ self.need_error_meshes = need_error_meshes
+ self.need_histograms = need_histograms
+
+ self.setResult('hausdorff_error', float(results[0]))
+ self.setResult('normalized_hausdorff_error', float(results[1]))
+
+################################################################################
+
+def initialize(executable_path=None):
+ if old_vistrails:
+ global _metro_path
+ if (core.requirements.executable_file_exists('metro') or
+ core.bundles.install({'linux-ubuntu': 'vcg-metro'})):
+ _metro_path = 'metro'
+ elif executable_path:
+ _metro_path = executable_path + '/metro'
+ print "Will assume metro is in ",executable_path
+ else:
+ raise core.requirements.MissingRequirement("VCG's Metro")
+ else:
+ if (not core.requirements.executable_file_exists('metro') and
+ not core.bundles.install({'linux-ubuntu': 'vcg-metro'})):
+ raise core.requirements.MissingRequirement("VCG's Metro")
+
+ reg = core.modules.module_registry
+
+ reg.add_module(Metro)
+ reg.add_input_port(Metro, 'mesh1',
+ core.modules.basic_modules.File)
+ reg.add_input_port(Metro, 'mesh2',
+ core.modules.basic_modules.File)
+
+ reg.add_output_port(Metro, 'hausdorff_error',
+ core.modules.basic_modules.Float)
+ reg.add_output_port(Metro, 'normalized_hausdorff_error',
+ core.modules.basic_modules.Float)
+ reg.add_output_port(Metro, 'error_mesh_1',
+ core.modules.basic_modules.File)
+ reg.add_output_port(Metro, 'error_mesh_2',
+ core.modules.basic_modules.File)
+ reg.add_output_port(Metro, 'error_hist_1',
+ core.modules.basic_modules.File)
+ reg.add_output_port(Metro, 'error_hist_2',
+ core.modules.basic_modules.File)
diff --git a/contrib/edu_utah_sci_cscheid_teem/__init__.py b/contrib/edu_utah_sci_cscheid_teem/__init__.py
new file mode 100644
index 0000000..1be4c00
--- /dev/null
+++ b/contrib/edu_utah_sci_cscheid_teem/__init__.py
@@ -0,0 +1,909 @@
+"""Teem package for VisTrails.
+"""
+
+##############################################################################
+# Changes
+#
+# 20081002: Added UnuSlice
+
+import core.modules
+import core.modules.module_registry
+import core.modules.basic_modules as basic
+from core.modules.vistrails_module import Module, ModuleError, \
+ new_module, IncompleteImplementation
+
+import os
+import subprocess
+
+_teemPath = None
+_teemLimnTestPath = None
+_teemTenTestPath = None
+
+identifier = 'edu.utah.sci.cscheid.teem'
+version = '0.2'
+name = 'teem'
+
+###############################################################################
+
+FileType = [(basic.File, '')]
+FloatType = [(basic.Float, '')]
+IntegerType = [(basic.Integer, '')]
+StringType = [(basic.String, '')]
+Vec3Type = [(basic.Float, 'x'),
+ (basic.Float, 'y'),
+ (basic.Float, 'z')]
+
+class Teem(Module):
+
+ def run_at_path(self, cmdline, path):
+ cmdline = path + cmdline
+ print cmdline
+ result = os.system(cmdline)
+ if result != 0:
+ raise ModuleError(self, '"%s" failed' % cmdline)
+
+ def run_path(self, *cmds):
+ cmdline = " ".join([str(cmd) for cmd in cmds])
+ self.run_at_path(cmdline, '')
+
+ def run_teem(self, *cmds):
+ cmdline = " ".join([str(cmd) for cmd in cmds])
+ self.run_at_path(cmdline, _teemPath)
+
+ def run_limn_test(self, *cmds):
+ cmdline = " ".join([str(cmd) for cmd in cmds])
+ self.run_at_path(cmdline, _teemLimnTestPath)
+
+ def run_ten_test(self, *cmds):
+ cmdline = " ".join([str(cmd) for cmd in cmds])
+ self.run_at_path(cmdline, _teemTenTestPath)
+
+ def opt_command_line_val(self, option_name, port_name):
+ if self.hasInputFromPort(port_name):
+ return [option_name, self.getInputFromPort(port_name)]
+ else:
+ return []
+
+ def opt_command_line_vec(self, option_name, port_name):
+ if self.hasInputFromPort(port_name):
+ t = self.getInputFromPort(port_name)
+ return [option_name] + list(t)
+ else:
+ return []
+
+ def opt_command_line_file(self, option_name, port_name):
+ if self.hasInputFromPort(port_name):
+ t = self.getInputFromPort(port_name)
+ return [option_name, t.name]
+ else:
+ return []
+
+ def opt_command_line_noopt(self, option_name, port_name):
+ if self.hasInputFromPort(port_name):
+ return [option_name]
+ else:
+ return []
+
+ ##########################################################################
+ # Default compute for (hopefully) most classes
+
+ _opt_dict = {'v': opt_command_line_val,
+ 'V': opt_command_line_vec,
+ 'f': opt_command_line_file,
+ 'n': opt_command_line_noopt}
+
+ def process_command_line_input(self):
+ cmdline = [self._cmdline_base]
+ for (opt_type, port_name, option_name) in self._cmdline_inputs:
+ call = self._opt_dict[opt_type]
+ cmdline += call(self, option_name=option_name,
+ port_name=port_name)
+ return cmdline
+
+ def process_command_line_output(self):
+ (port_name, opt_name, format) = self._cmdline_output
+ if callable(format):
+ format = format(self)
+ output_file = self.interpreter.filePool.create_file(suffix='.'+format)
+ self.setResult(port_name, output_file)
+ return [opt_name, output_file.name]
+
+ def compute(self):
+ cmdline_input = self.process_command_line_input()
+ cmdline_output = self.process_command_line_output()
+ self._cmdline_callable(*(cmdline_input + cmdline_output))
+
+class Emap(Teem):
+
+ def compute(self):
+ cmdline = ['emap']
+ cmdline += self.opt_command_line_vec(port_name='from',
+ option_name='-fr')
+ cmdline += self.opt_command_line_vec(port_name='ambient',
+ option_name='-amb')
+ cmdline += self.opt_command_line_vec(port_name='up',
+ option_name='-up')
+ cmdline += self.opt_command_line_noopt(port_name='right_hand',
+ option_name='-rh')
+ self.checkInputPort('input_file')
+ cmdline += self.opt_command_line_file(port_name='input_file',
+ option_name='-i')
+
+ output_file = self.interpreter.filePool.create_file(suffix='.nrrd')
+ cmdline += ['-o', output_file.name]
+
+ self.run_teem(*cmdline)
+
+ self.setResult("output_file", output_file)
+
+ _input_ports = [('right_hand', []),
+ ('input_file', [(basic.File, 'the lights input file')]),
+ ('from', Vec3Type),
+ ('ambient', Vec3Type),
+ ('up', Vec3Type)]
+ _output_ports = [('output_file', [(basic.File, 'the resulting nrrd')])]
+
+class Soid(Teem):
+
+ def compute(self):
+ cmdline = ['soid']
+ cmdline += self.opt_command_line_val(port_name='resolution',
+ option_name='-res')
+ cmdline += self.opt_command_line_val(port_name='radius',
+ option_name='-r')
+ cmdline += self.opt_command_line_vec(port_name='scalings',
+ option_name='-sc')
+ cmdline += self.opt_command_line_noopt(port_name='sphere',
+ option_name='-sphere')
+
+ if self.hasInputFromPort('AB'):
+ cmdline += self.opt_command_line_vec(port_name='AB',
+ option_name='-AB')
+ elif self.hasInputFromPort('A') and self.hasInputFromPort('B'):
+ cmdline += ['-AB',
+ self.getInputFromPort('A'),
+ self.getInputFromPort('B')]
+
+ output_file = self.interpreter.filePool.create_file(suffix='.nrrd')
+ cmdline += ['-o', output_file.name]
+
+ self.run_limn_test(*cmdline)
+ self.setResult("output_file", output_file)
+
+ _input_ports = [('resolution', [(basic.Float, 'The ellipsoid resolution')]),
+ ('radius', [(basic.Float, 'The radius')]),
+ ('sphere', []),
+ ('scalings', Vec3Type),
+ ('AB', [(basic.Float, 'A exponent'),
+ (basic.Float, 'B exponent')]),
+ ('A', [(basic.Float, 'A exponent')]),
+ ('B', [(basic.Float, 'B exponent')]),
+ ]
+ _output_ports = [('output_file', [(basic.File, 'the resulting OFF file')])]
+
+
+class OffToEps(Teem):
+
+ def compute(self):
+ cmdline = ['off2eps']
+ cmdline += self.opt_command_line_vec(port_name='from_point',
+ option_name='-fr')
+ cmdline += self.opt_command_line_vec(port_name='u_range',
+ option_name='-ur')
+ cmdline += self.opt_command_line_vec(port_name='v_range',
+ option_name='-vr')
+ cmdline += self.opt_command_line_vec(port_name='edge_widths',
+ option_name='-wd')
+ cmdline += self.opt_command_line_file(port_name='environment_map',
+ option_name='-e')
+ cmdline += self.opt_command_line_noopt(port_name='orthogonal',
+ option_name='-or')
+ cmdline += self.opt_command_line_noopt(port_name='right_hand',
+ option_name='-rh')
+ cmdline += self.opt_command_line_noopt(port_name='concave',
+ option_name='-concave')
+ cmdline += self.opt_command_line_noopt(port_name='no_background',
+ option_name='-nobg')
+ cmdline += self.opt_command_line_val(port_name='world_to_points_scale',
+ option_name='-ws')
+
+
+ self.checkInputPort('input_file')
+ input_file = self.getInputFromPort('input_file')
+ cmdline += ['-i', input_file.name]
+
+ output_file = self.interpreter.filePool.create_file(suffix='.eps')
+ cmdline += ['-o', output_file.name]
+
+ self.run_limn_test(*cmdline)
+ self.setResult("output_file", output_file)
+
+
+ _input_ports = [
+ ("right_hand", []),
+ ("input_file", [(basic.File, 'the input OFF file')]),
+ ("environment_map", [(basic.File, 'the nrrd storing the environment map')]),
+ ("from_point", [(basic.Float, '')] * 3),
+ ("u_range", [(basic.Float, '')] * 2),
+ ("v_range", [(basic.Float, '')] * 2),
+ ("edge_widths", [(basic.Float, '')] * 5),
+ ("orthogonal", []),
+ ("no_background", []),
+ ("concave", []),
+ ("world_to_points_scale", [(basic.Float, '')]),
+ ]
+
+ _output_ports = [
+ ("output_file", [(basic.File, '')]),
+ ]
+
+class EpsToPpm(Teem):
+
+ def compute(self):
+ cmdline = ['eps2ppm']
+ self.checkInputPort('input_file')
+ self.checkInputPort('resolution')
+ cmdline += [self.getInputFromPort('input_file').name]
+ cmdline += [self.getInputFromPort('resolution')]
+ cmdline += ['>']
+ output_file = self.interpreter.filePool.create_file(suffix='.ppm')
+ cmdline += [output_file.name]
+ self.run_path(*cmdline)
+ self.setResult("output_file", output_file)
+
+ _input_ports = [
+ ("input_file", [(basic.File, 'the input EPS')]),
+ ("resolution", [(basic.Float, 'the resolution to rasterize the EPS')]),
+ ]
+
+ _output_ports = [
+ ("output_file", [(basic.File, 'the resulting PPM file')]),
+ ]
+
+class Unu(Teem):
+
+ def do_output(self):
+ if self.hasInputFromPort('format'):
+ suffix = '.'+self.getInputFromPort('format')
+ else:
+ suffix = '.nrrd'
+ output_file = self.interpreter.filePool.create_file(suffix=suffix)
+ return (['-o', output_file.name], output_file)
+
+ def do_input(self):
+ self.checkInputPort('input_file')
+ return ['-i', self.getInputFromPort('input_file').name]
+
+ _input_ports = [
+ ("format", [(basic.String, 'file format for output')]),
+ ]
+ _output_ports = [
+ ("output_file", [(basic.File, 'the output file')]),
+ ]
+
+class UnuSave(Unu):
+
+ def compute(self):
+ cmdline = ['unu save']
+ cmdline += self.do_input()
+ (ocmd, output_file) = self.do_output()
+ self.setResult("output_file", output_file)
+ self.setResult("output_name", output_file.name)
+ cmdline += ocmd
+ cmdline += self.opt_command_line_val(port_name='output_format', option_name='-f')
+ self.run_teem(*cmdline)
+
+ _input_ports = [
+ ("input_file", [(basic.File, 'Input File')]),
+ ("output_format", [(basic.String, 'Output Format')]),
+ ]
+ _output_ports = [
+ ("output_name", [(basic.String, 'Output Filename')]),
+ ]
+
+class UnuSwap(Unu):
+
+ def compute(self):
+ cmdline = ['unu swap']
+ cmdline += self.do_input()
+ (ocmd, output_file) = self.do_output()
+ self.setResult("output_file", output_file)
+ v1, v2 = self.getInputFromPort('axes')
+ cmdline += ['-a', str(v1), str(v2)]
+ cmdline += ocmd
+ self.run_teem(*cmdline)
+
+ _input_ports = [
+ ("input_file", [(basic.File, 'Input File')]),
+ ("axes", [(basic.Integer, '')]*2),
+ ]
+
+class UnuProject(Unu):
+
+ def compute(self):
+ cmdline = ['unu project']
+ cmdline += self.do_input()
+ (ocmd, output_file) = self.do_output()
+ self.setResult("output_file", output_file)
+ cmdline += ocmd
+ cmdline += self.opt_command_line_val(port_name='axis',
+ option_name='-a')
+ cmdline += self.opt_command_line_val(port_name='measure',
+ option_name='-m')
+ self.run_teem(*cmdline)
+
+ _input_ports = [
+ ("input_file", [(basic.File, 'the input file')]),
+ ("measure", [(basic.String, 'the measure to use')]),
+ ("axis", (basic.Integer, 'the axis to project')),
+ ]
+
+class UnuMinmax(Teem):
+
+ def do_input(self):
+ self.checkInputPort('input_file')
+ return [self.getInputFromPort('input_file').name]
+
+ def compute(self):
+ cmdline = ['unu minmax']
+ cmdline += self.do_input()
+ if self.hasInputFromPort('blind8'):
+ cmdline += '-blind8 true'
+ output_file = self.interpreter.filePool.create_file()
+ # FIXME use popen*
+ cmdline += ['>%s'%output_file.name]
+ self.run_teem(*cmdline)
+ f = file(output_file.name)
+ try:
+ mn = float(f.readline().split()[-1])
+ mx = float(f.readline().split()[-1])
+ except:
+ raise ModuleError(self, 'Could not read result')
+ self.setResult('range', (mn, mx))
+
+ _input_ports = [('input_file', [(basic.File, 'the input file')]),
+ ('blind8', [])]
+ _output_ports = [('range', [(basic.Float,'')] * 2)]
+
+class UnuReshape(Unu):
+
+ def compute(self):
+ cmdline = ['unu reshape']
+ cmdline += self.do_input()
+ cmdline += self.opt_command_line_val(port_name='axes',
+ option_name='-s')
+ (ocmd, output_file) = self.do_output()
+ self.setResult("output_file", output_file)
+ cmdline += ocmd
+ self.run_teem(*cmdline)
+
+ _input_ports = [
+ ("input_file", [(basic.File, 'the input file')]),
+ ("axes", [(basic.String, 'axes to split')]),
+ ]
+
+
+class UnuResample(Unu):
+
+ def compute(self):
+ cmdline = ['unu resample']
+ cmdline += self.do_input()
+ (ocmd, output_file) = self.do_output()
+ cmdline += ocmd
+ self.setResult("output_file", output_file)
+ cmdline += self.opt_command_line_val(port_name='sampling_spec',
+ option_name='-s')
+ cmdline += self.opt_command_line_val(port_name='centering',
+ option_name='-c')
+ cmdline += self.opt_command_line_val(port_name='kernel',
+ option_name='-k')
+ self.run_teem(*cmdline)
+
+ _input_ports = [
+ ("input_file", [(basic.File, 'the input file')]),
+ ("sampling_spec", [(basic.String, 'the sampling spec')]),
+ ("centering", [(basic.String, 'centering (node/cell)')]),
+ ("kernel", [(basic.String, 'the resampling kernel')]),
+ ]
+
+class UnuJoin(Unu):
+
+ def do_input(self):
+ self.checkInputPort('input_list')
+ return ['-i'] + [x.name
+ for x in self.getInputFromPort('input_list')]
+
+ def compute(self):
+ cmdline = ['unu join']
+ cmdline += self.do_input()
+ cmdline += self.opt_command_line_val(port_name='axis',
+ option_name='-a')
+ (ocmd, output_file) = self.do_output()
+ cmdline += ocmd
+ self.setResult("output_file", output_file)
+ self.run_teem(*cmdline)
+
+ _input_ports = [
+ ("input_list", [(basic.List, 'list of input files')]),
+ ("axis", [(basic.Integer, 'the axis to join')]),
+ ]
+
+class UnuQuantize(Unu):
+
+ def do_input(self):
+ current = Unu.do_input(self)
+ self.checkInputPort('bits')
+ return current + ['-b', self.getInputFromPort('bits')]
+
+ def compute(self):
+ cmdline = ['unu quantize']
+ cmdline += self.do_input()
+ cmdline += self.opt_command_line_val(port_name='min',
+ option_name='-min')
+ cmdline += self.opt_command_line_val(port_name='max',
+ option_name='-max')
+ (ocmd, output_file) = self.do_output()
+ cmdline += ocmd
+ self.setResult("output_file", output_file)
+ self.run_teem(*cmdline)
+
+ _input_ports = [
+ ("input_file", [(basic.File, 'the input file')]),
+ ('bits', [(basic.Integer, 'bits to quantize down to')]),
+ ('min', [(basic.Float, 'min value')]),
+ ('max', [(basic.Float, 'max value')]),
+ ]
+
+class Unu1op(Unu):
+
+ def do_input(self):
+ r = []
+ if self.hasInputFromPort('in1_file'):
+ r += ['-i', self.getInputFromPort('in1_file').name]
+ return r
+
+ def is_cacheable(self):
+ return not self.getInputFromPort('op') in ['rand', 'nrand']
+
+ def compute(self):
+ allowed_ops = ['-', 'r', 'sin',
+ 'cos', 'tan', 'asin', 'acos', 'atan',
+ 'exp', 'log', 'log10', 'log1p', 'log2', 'sqrt'
+ 'cbrt', 'ceil', 'floor', 'erf', 'rup',
+ 'abs', 'sgn', 'exists', 'rand', 'nrand',
+ 'if', '0', '1']
+ self.checkInputPort('op')
+ if not self.getInputFromPort('op') in allowed_ops:
+ raise ModuleError(self, ("Operation %s is not allowed." %
+ self.getInputFromPort('op')))
+ cmdline = ['unu 1op']
+ cmdline += [self.getInputFromPort('op')]
+ cmdline += self.do_input()
+ (ocmd, output_file) = self.do_output()
+ cmdline += ocmd
+ self.setResult('output_file', output_file)
+ self.run_teem(*cmdline)
+
+ _input_ports = [
+ ("in1_file", [(basic.File, 'input file 1')]),
+ ("op", [(basic.String, 'the operation')]),
+ ]
+
+class Unu2op(Unu):
+
+ def do_input(self):
+ r = []
+ if self.hasInputFromPort('in1_file'):
+ r += [self.getInputFromPort('in1_file').name]
+ elif self.hasInputFromPort('in1_value'):
+ r += [self.getInputFromPort('in1_value')]
+ else:
+ raise ModuleError(self, "Needs either in1_file or in1_value")
+ if self.hasInputFromPort('in2_file'):
+ r += [self.getInputFromPort('in2_file').name]
+ elif self.hasInputFromPort('in2_value'):
+ r += [self.getInputFromPort('in2_value')]
+ else:
+ raise ModuleError(self, "Needs either in2_file or in2_value")
+ return r
+
+ def compute(self):
+ allowed_ops = ['+', '-', 'x', '/',
+ '^', 'pow', 'spow', '%', 'fmod', 'atan2',
+ 'min', 'max', 'lt', 'lte', 'gt', 'gte'
+ 'eq', 'neq', 'comp', 'if', 'exists']
+ self.checkInputPort('op')
+ if not self.getInputFromPort('op') in allowed_ops:
+ raise ModuleError(self, ("Operation %s is not allowed." %
+ self.getInputFromPort('op')))
+ cmdline = ['unu 2op']
+ cmdline += [self.getInputFromPort('op')]
+ cmdline += self.do_input()
+ (ocmd, output_file) = self.do_output()
+ cmdline += ocmd
+ self.setResult('output_file', output_file)
+ self.run_teem(*cmdline)
+
+ _input_ports = [
+ ("in1_file", [(basic.File, 'input file 1')]),
+ ("in1_value", [(basic.String, 'input value 1')]),
+ ("in2_file", [(basic.File, 'input file 2')]),
+ ("in2_value", [(basic.String, 'input value 2')]),
+ ("op", [(basic.String, 'the operation')]),
+ ]
+
+
+class Unu3op(Unu):
+
+ def do_input(self):
+ r = []
+ if self.hasInputFromPort('in1_file'):
+ r += [self.getInputFromPort('in1_file').name]
+ elif self.hasInputFromPort('in1_value'):
+ r += [self.getInputFromPort('in1_value')]
+ else:
+ raise ModuleError(self, "Needs either in1_file or in1_value")
+ if self.hasInputFromPort('in2_file'):
+ r += [self.getInputFromPort('in2_file').name]
+ elif self.hasInputFromPort('in2_value'):
+ r += [self.getInputFromPort('in2_value')]
+ else:
+ raise ModuleError(self, "Needs either in2_file or in2_value")
+ if self.hasInputFromPort('in3_file'):
+ r += [self.getInputFromPort('in3_file').name]
+ elif self.hasInputFromPort('in3_value'):
+ r += [self.getInputFromPort('in3_value')]
+ else:
+ raise ModuleError(self, "Needs either in3_file or in3_value")
+ return r
+
+ def compute(self):
+ allowed_ops = ['+', 'x',
+ 'min', 'max',
+ 'clamp', 'ifelse',
+ 'lerp', 'exists',
+ 'in_op', 'in_cl']
+ self.checkInputPort('op')
+ if not self.getInputFromPort('op') in allowed_ops:
+ raise ModuleError(self, ("Operation %s is not allowed." %
+ self.getInputFromPort('op')))
+ cmdline = ['unu 3op']
+ cmdline += [self.getInputFromPort('op')]
+ cmdline += self.do_input()
+ (ocmd, output_file) = self.do_output()
+ cmdline += ocmd
+ self.setResult('output_file', output_file)
+ self.run_teem(*cmdline)
+
+ _input_ports = [
+ ("in1_file", [(basic.File, 'input file 1')]),
+ ("in1_value", [(basic.String, 'input value 1')]),
+ ("in2_file", [(basic.File, 'input file 2')]),
+ ("in2_value", [(basic.String, 'input value 2')]),
+ ("in3_file", [(basic.File, 'input file 3')]),
+ ("in3_value", [(basic.String, 'input value 3')]),
+ ("op", [(basic.String, 'the operation')]),
+ ]
+
+class Teem_TT(Teem):
+ _cmdline_base = 'tt'
+ _cmdline_inputs = [('v', 'num_samples', '-n'),
+ ('V', 'location', '-p'),
+ ('v', 'max_ca', '-ca'),
+ ('n', 'right_triangle', '-r'),
+ ('n', 'whole', '-w'),
+ ('v', 'westin_metric', '-v'),
+ ('v', 'hack', '-hack')]
+ _cmdline_output = ('output_file', '-o', '.nrrd')
+ _cmdline_callable = Teem.run_ten_test
+
+ _input_ports = [
+ ("num_samples", [(basic.String, 'number of samples')]),
+ ("location", Vec3Type),
+ ("max_ca", [(basic.Float, 'max CA')]),
+ ("westin_metric", [(basic.Float, 'Metric to use')]),
+ ("hack", [(basic.Float, '"this is a hack"')]),
+ ("right_triangle", []),
+ ("whole", []),
+ ]
+ _output_ports = [
+ ("output_file", [(basic.File, "the output file")]),
+ ]
+
+class Tend_norm(Teem):
+ _cmdline_base = 'tend norm'
+ _cmdline_inputs = [('V', 'weights', '-w'),
+ ('v', 'amount', '-a'),
+ ('v', 'target', '-t'),
+ ('f', 'input_file', '-i')]
+ _cmdline_output = ('output_file', '-o', 'nrrd')
+ _cmdline_callable = Teem.run_teem
+
+ _input_ports = [
+ ("weights", Vec3Type),
+ ("amount", [(basic.Float, "amount of normalization")]),
+ ("target", [(basic.Float, "target size post normalization")]),
+ ("input_file", [(basic.File, "input DT volume")]),
+ ]
+
+ _output_ports = [
+ ("output_file", [(basic.File, "output file")]),
+ ]
+
+class Tend_glyph(Teem):
+ _cmdline_base = 'tend glyph'
+ _cmdline_inputs = [('v', 'sat', '-sat'),
+ ('f', 'emap', '-emap'),
+ ('f', 'input_file', '-i'),
+ ('V', 'from_point', '-fr'),
+ ('V', 'up', '-up'),
+ ('v', 'psc', '-psc'),
+ ('V', 'u_range', '-ur'),
+ ('V', 'v_range', '-vr'),
+ ('n', 'orthogonal', '-or'),
+ ('v', 'atr', '-atr'),
+ ('n', 'no_background', '-nobg'),
+ ('n', 'right_hand', '-rh'),
+ ('v', 'glyph_shape', '-g'),
+ ('v', 'glyph_size', '-gsc'),
+ ('v', 'glyph_resolution', '-gr'),
+ ('V', 'widths', '-wd')]
+ _cmdline_output = ('output_file', '-o', 'eps')
+ _cmdline_callable = Teem.run_teem
+
+ _input_ports = [
+ ("sat", [(basic.Float, "max saturation")]),
+ ("from_point", [(basic.Float, '')] * 3),
+ ("up", [(basic.Float, '')] * 3),
+ ("psc", [(basic.Float, 'ps scale')]),
+ ("u_range", [(basic.Float, '')] * 2),
+ ("v_range", [(basic.Float, '')] * 2),
+ ("orthogonal", []),
+ ("atr", [(basic.Float, 'anisotropy threshold')]),
+ ("emap", [(basic.File, 'environment map nrrd')]),
+ ("input_file", [(basic.File, 'the input file')]),
+ ("no_background", []),
+ ("glyph_shape", [(basic.String, 'glyph shape')]),
+ ("glyph_size", [(basic.Float, 'glyph size in world space')]),
+ ("glyph_resolution", [(basic.Integer, 'glyph resolution of polygonization')]),
+ ("widths", [(basic.Float, '')] * 3),
+ ("right_hand", []),
+ ]
+ _output_ports = [
+ ("output_file", [(basic.File, 'output EPS file')])
+ ]
+
+class UnuSlice(Unu):
+
+ def do_input(self):
+ r = []
+ self.checkInputPort('in_file')
+ self.checkInputPort('axis')
+ self.checkInputPort('position')
+ r += ['-i', self.getInputFromPort('in_file').name]
+ r += ['-a', str(self.getInputFromPort('axis'))]
+ r += ['-p', str(self.getInputFromPort('position'))]
+ return r
+
+ def compute(self):
+ cmdline = ['unu slice']
+ cmdline += self.do_input()
+ (ocmd, output_file) = self.do_output()
+ cmdline += ocmd
+ self.setResult('output_file', output_file)
+ self.run_teem(*cmdline)
+
+ _input_ports = [
+ ('in_file', basic.File),
+ ('axis', basic.Integer),
+ ('position', basic.Integer),
+ ]
+
+
+###############################################################################
+
+class TeemScaledTransferFunction(Teem):
+ _input_ports = [('range', [(basic.Float, '')] * 2),
+ ('steps', [basic.Integer])]
+ _output_ports = [('nrrd', [(basic.File, 'the output TF')])]
+
+ def compute(self):
+ ramp = self.interpreter.filePool.create_file(suffix='.txt')
+ tf_vals = self.interpreter.filePool.create_file(suffix='.txt')
+ output = self.interpreter.filePool.create_file(suffix='.nrrd')
+ steps = self.getInputFromPort('steps')
+ rng = self.getInputFromPort('range')
+ self.run_teem('echo "0 1"',
+ '| unu reshape -s 1 2',
+ '| unu resample -s = %d -k tent -c node' % steps,
+ '| unu save -f text -o %s' % ramp.name)
+ tf_file = file(tf_vals.name, 'w')
+ tf = self.getInputFromPort('transfer_function')
+ for (scalar, op, (r, g, b)) in tf._pts:
+ tf_file.write('%f %f %f %f %f\n' % (scalar, r, g, b, op))
+# tf_file.write('%f %f\n' % (scalar, op))
+ tf_file.close()
+ self.run_teem('cat %s' % tf_vals.name,
+ '| unu reshape -s 5 %d' % len(tf._pts),
+ '| unu imap -i %s -r -m -' % ramp.name,
+ '| unu reshape -s 4 %d' % steps,
+ '| unu axinfo -a 0 -l "RGBA"',
+ '| unu axinfo -a 1 -l "gage(scalar:v)" -mm %f %f -o %s' % (rng[0],
+ rng[1],
+ output.name))
+ self.setResult('nrrd', output)
+
+##############################################################################
+
+class Miter(Teem):
+
+ _input_ports = [
+ # Input data
+ ('input_file', FileType),
+ ('transfer_function', FileType),
+ # Camera
+ ('from_point', Vec3Type),
+ ('at_point', Vec3Type),
+ ('up_vec', Vec3Type),
+ ('right_handed', []),
+ ('relative_to_at_point', []),
+ ('near_dist', FloatType),
+ ('far_dist', FloatType),
+ ('image_plane_dist', FloatType),
+ ('urange', FloatType * 2),
+ ('vrange', FloatType * 2),
+ ('image_size', IntegerType * 2),
+ # Lighting
+ ('light_pos', Vec3Type),
+ ('ambient_light', FloatType * 3),
+ ('phong_components', FloatType * 3),
+ ('shininess', FloatType),
+ ('value_kernel', StringType),
+ ('d_kernel', StringType),
+ ('dd_kernel', StringType),
+ ('step_size', FloatType),
+ ('ref_step_size', FloatType),
+ ('thread_count', IntegerType),
+ ('opacity_termination', FloatType),
+ ]
+
+ _output_ports = [('output_file', FileType)]
+
+ def compute(self):
+ cmdline = ['miter']
+ self.checkInputPort('input_file')
+ self.checkInputPort('transfer_function')
+ cmdline += self.opt_command_line_file('-i', 'input_file')
+ f = self.interpreter.filePool.create_file(suffix='.nrrd')
+ cmdline += ['-o', f.name]
+ cmdline += self.opt_command_line_vec('-fr', 'from_point')
+ cmdline += self.opt_command_line_vec('-at', 'at_point')
+ cmdline += self.opt_command_line_vec('-up', 'up_vec')
+ cmdline += self.opt_command_line_noopt('-rh', 'right_handed')
+ cmdline += self.opt_command_line_noopt('-ar', 'relative_to_at_point')
+ cmdline += self.opt_command_line_val('-dn', 'near_dist')
+ cmdline += self.opt_command_line_val('-di', 'image_plane_dist')
+ cmdline += self.opt_command_line_val('-df', 'far_dist')
+ cmdline += self.opt_command_line_vec('-ur', 'urange')
+ cmdline += self.opt_command_line_vec('-vr', 'vrange')
+ cmdline += self.opt_command_line_vec('-is', 'image_size')
+ cmdline += self.opt_command_line_vec('-ld', 'light_pos')
+ cmdline += self.opt_command_line_vec('-am', 'ambient_light')
+ cmdline += self.opt_command_line_vec('-ads', 'phong_components')
+ cmdline += self.opt_command_line_val('-sp', 'shininess')
+ cmdline += self.opt_command_line_val('-k00', 'value_kernel')
+ cmdline += self.opt_command_line_val('-k11', 'd_kernel')
+ cmdline += self.opt_command_line_val('-k22', 'dd_kernel')
+ cmdline += self.opt_command_line_val('-step', 'step_size')
+ cmdline += self.opt_command_line_val('-ref', 'ref_step_size')
+ cmdline += self.opt_command_line_val('-nt', 'thread_count')
+ cmdline += self.opt_command_line_val('-n1', 'opacity_termination')
+ cmdline += self.opt_command_line_file('-txf', 'transfer_function')
+ self.setResult('output_file', f)
+ self.run_teem(*cmdline)
+
+###############################################################################
+
+class OverRGB(Teem):
+
+ _input_ports = [
+ ('input_file', FileType),
+ ('contrast', FloatType),
+ ('component_fixed_point', FloatType),
+ ('gamma', FloatType),
+ ('background', Vec3Type),
+ ('background_image', FileType),]
+
+ _output_ports = [
+ ('output_image', FileType),
+ ]
+
+ def compute(self):
+ cmdline = ['overrgb']
+ self.checkInputPort('input_file')
+ cmdline += self.opt_command_line_file('-i', 'input_file')
+ f = self.interpreter.filePool.create_file(suffix='.png')
+ cmdline += ['-o', f.name]
+ self.setResult('output_image', f)
+ cmdline += self.opt_command_line_val('-c', 'contrast')
+ cmdline += self.opt_command_line_val('-cfp', 'component_fixed_point')
+ cmdline += self.opt_command_line_val('-g', 'gamma')
+ cmdline += self.opt_command_line_vec('-b', 'background')
+ cmdline += self.opt_command_line_file('-bi', 'background_image')
+ self.run_teem(*cmdline)
+
+###############################################################################
+
+_modules = [Teem, Emap, Soid, Miter, OverRGB,
+ OffToEps,
+ EpsToPpm,
+ Unu,
+ UnuMinmax,
+ UnuSave,
+ UnuSwap,
+ UnuProject,
+ UnuReshape,
+ UnuResample,
+ UnuJoin,
+ UnuQuantize,
+ Unu1op,
+ Unu2op,
+ Unu3op,
+ UnuSlice,
+ Teem_TT,
+ Tend_norm,
+ Tend_glyph]
+
+##############################################################################
+
+def package_dependencies():
+ import core.packagemanager
+ manager = core.packagemanager.get_package_manager()
+ if manager.has_package('edu.utah.sci.vistrails.vtk'):
+ return ['edu.utah.sci.vistrails.vtk']
+ else:
+ return []
+
+###############################################################################
+
+def initialize(path=None, limnTestPath=None, tenTestPath=None,
+ *args, **keywords):
+ global _teemPath
+ if not path:
+ print "path not specified or incorrect: Will assume teem is on path"
+ _teemPath = ""
+ else:
+ print "will use teem from ", path
+ _teemPath = path + '/'
+
+ global _teemLimnTestPath
+ if not limnTestPath:
+ print "limnTestPath not specified or incorrect: Will not install",
+ print "limnTest modules"
+ _teemLimnTestPath = ""
+ else:
+ print "will use limnTest tools from ", limnTestPath
+ _teemLimnTestPath = limnTestPath + '/'
+
+ global _teemTenTestPath
+ if not tenTestPath:
+ print "tenTestPath not specified or incorrect: Will not install",
+ print "tenTestPath modules"
+ _teemTenTestPath = ""
+ else:
+ print "will use tenTest tools from ", tenTestPath
+ _teemTenTestPath = tenTestPath + '/'
+
+ reg = core.modules.module_registry.registry
+
+ # Register the TF widget interaction modules if they're available
+ if reg.has_module('edu.utah.sci.vistrails.vtk',
+ 'TransferFunction'):
+ # Update the auto-add _modules list
+ _modules.append(TeemScaledTransferFunction)
+ TF = reg.get_descriptor_by_name('edu.utah.sci.vistrails.vtk',
+ 'TransferFunction').module
+ # Update the input ports for TeemScaledTransferFunction now that we
+ # know TF is present
+ TeemScaledTransferFunction._input_ports.append(('transfer_function', [(TF,
+ "the transfer function")]))
diff --git a/contrib/edu_utah_sci_cscheid_teem/examples.vt b/contrib/edu_utah_sci_cscheid_teem/examples.vt
new file mode 100644
index 0000000..a79507f
Binary files /dev/null and b/contrib/edu_utah_sci_cscheid_teem/examples.vt differ
diff --git a/contrib/edu_utah_sci_eranders_proteindatabank/PDB.py b/contrib/edu_utah_sci_eranders_proteindatabank/PDB.py
new file mode 100644
index 0000000..39e4e92
--- /dev/null
+++ b/contrib/edu_utah_sci_eranders_proteindatabank/PDB.py
@@ -0,0 +1,144 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+
+class ProteinDataBank(Module):
+ pass
+
+class Protein(ProteinDataBank):
+
+ def __init__(self):
+ ProteinDataBank.__init__(self)
+ self.atoms = {}
+ self.sequence = {}
+ self.hatoms = {}
+ self.author = ''
+ self.title = ''
+
+ def compute(self):
+ pass
+
+ def getAtomOfType(self, type):
+ if self.atoms.has_key(type):
+ return self.atoms[type]
+ else:
+ return 0
+
+ def getHetAtomOfType(self, type):
+ if self.hatoms.has_key(type):
+ return self.hatoms[type]
+ else:
+ return 0
+
+ def getSequence(self, seqID):
+ if self.sequence.has_key(seqID):
+ return self.sequence[seqID].__str__()
+ else:
+ k = self.sequence.keys().__str__()
+ str = 'Invalid Sequence ID ' + k
+
+class PDBParser(ProteinDataBank):
+
+ ############################################################################
+ # line parsers
+
+ def is_continuation(self, line):
+ try:
+ int(line[0])
+ return True
+ except:
+ return False
+
+ def parse_ATOM(self, line, protein):
+ type = line[-1]
+ if protein.atoms.has_key(type):
+ protein.atoms[type] = protein.atoms[type] + 1
+ else:
+ protein.atoms[type] = 1
+
+ def parse_SEQRES(self, line, protein):
+ els = len(line)
+ seqID = line[2]
+ if not protein.sequence.has_key(seqID):
+ protein.sequence[seqID] = []
+
+ s = protein.sequence[seqID]
+
+ i = 4
+ while i < len(line):
+ s.append(line[i])
+ i = i + 1
+
+ protein.sequence[seqID] = s
+
+ def parse_HETATM(self, line, protein):
+ type = line[-1]
+ if protein.hatoms.has_key(type):
+ protein.hatoms[type] = protein.hatoms[type] + 1
+ else:
+ protein.hatoms[type] = 1
+
+ def parse_AUTHOR(self, line, protein):
+ if self.is_continuation(line):
+ protein.author += ' ' + ' '.join(line[1:])
+ else:
+ protein.author = ' '.join(line)
+
+ def parse_TITLE(self, line, protein):
+ if self.is_continuation(line):
+ protein.title += ' ' + ' '.join(line[1:])
+ else:
+ protein.title = ' '.join(line)
+
+ def parse_HEADER(self, line, protein):
+ protein.pdb_name = line[-1]
+ protein.date = line[-2]
+ protein.short_title = ' '.join(line[:-2])
+
+ ############################################################################
+
+ def compute(self):
+ f = self.getInputFromPort("File")
+
+ p = Protein()
+
+ for l in file(f.name):
+ l = l.strip()
+ toks = l.split()
+ if hasattr(self, 'parse_' + toks[0]):
+ getattr(self, 'parse_' + toks[0])(toks[1:], p)
+
+ self.setResult("Protein", p)
+
+class GetAtoms(ProteinDataBank):
+ def compute(self):
+ prot = self.getInputFromPort("Protein")
+ aType = self.getInputFromPort("Atom Type")
+ self.setResult("NumAtoms", prot.getAtomOfType(aType))
+
+class GetHetAtoms(ProteinDataBank):
+ def compute(self):
+ prot = self.getInputFromPort("Protein")
+ aType = self.getInputFromPort("Atom Type")
+ self.setResult("NumAtoms", prot.getHetAtomOfType(aType))
+
+class GetSequence(ProteinDataBank):
+ def compute(self):
+ prot = self.getInputFromPort("Protein")
+ sID = self.getInputFromPort("SequenceID")
+ self.setResult("Sequence", prot.getSequence(sID))
+
+class GetTitle(ProteinDataBank):
+ def compute(self):
+ prot = self.getInputFromPort("Protein")
+ self.setResult("Title", prot.title)
+
+class GetAuthor(ProteinDataBank):
+ def compute(self):
+ prot = self.getInputFromPort("Protein")
+ self.setResult("Title", prot.author)
+
+class GetPDBName(ProteinDataBank):
+ def compute(self):
+ prot = self.getInputFromPort("Protein")
+ self.setResult("name", prot.pdb_name)
diff --git a/contrib/edu_utah_sci_eranders_proteindatabank/__init__.py b/contrib/edu_utah_sci_eranders_proteindatabank/__init__.py
new file mode 100644
index 0000000..7c18d70
--- /dev/null
+++ b/contrib/edu_utah_sci_eranders_proteindatabank/__init__.py
@@ -0,0 +1,68 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+
+from PDB import *
+
+identifier = 'edu.utah.sci.eranders.proteindatabank'
+version = '0.1.0'
+name = 'Protein Data Bank'
+
+def initialize(*args, **keywords):
+ reg = core.modules.module_registry
+ basic = core.modules.basic_modules
+
+ reg.add_module(ProteinDataBank, abstract=True)
+ reg.add_module(Protein, abstract=True)
+
+ reg.add_module(PDBParser)
+ reg.add_input_port(PDBParser, "File", (basic.File, 'File'))
+ reg.add_output_port(PDBParser, "Protein", (Protein, 'Protein'))
+
+ reg.add_module(GetAtoms)
+ reg.add_input_port(GetAtoms, "Protein", (Protein, 'Protein'))
+ reg.add_input_port(GetAtoms, "Atom Type", (basic.String, 'AtomType'))
+ reg.add_output_port(GetAtoms, "NumAtoms", (basic.Integer, 'NumAtoms'))
+
+ reg.add_module(GetHetAtoms)
+ reg.add_input_port(GetHetAtoms, "Protein", (Protein, 'Protein'))
+ reg.add_input_port(GetHetAtoms, "Atom Type", (basic.String, 'AtomType'))
+ reg.add_output_port(GetHetAtoms, "NumAtoms", (basic.Integer, 'NumAtoms'))
+
+ reg.add_module(GetSequence)
+ reg.add_input_port(GetSequence, "Protein", (Protein, 'Protein'))
+ reg.add_input_port(GetSequence, "SequenceID", (basic.String, 'SequenceID'))
+ reg.add_output_port(GetSequence, "Sequence", (basic.String, 'Sequence'))
+
+ reg.add_module(GetTitle)
+ reg.add_input_port(GetTitle, "Protein", (Protein, 'Protein'))
+ reg.add_output_port(GetTitle, "Title", (basic.String, 'Title'))
+
+ reg.add_module(GetAuthor)
+ reg.add_input_port(GetAuthor, "Protein", (Protein, 'Protein'))
+ reg.add_output_port(GetAuthor, "Author", (basic.String, 'Author'))
+
+ reg.add_module(GetPDBName)
+ reg.add_input_port(GetPDBName, "Protein", (Protein, 'Protein'))
+ reg.add_output_port(GetPDBName, "Name", (basic.String, 'Name'))
diff --git a/contrib/edu_utah_sci_vgc_afront/MANIFEST b/contrib/edu_utah_sci_vgc_afront/MANIFEST
new file mode 100644
index 0000000..61b0205
--- /dev/null
+++ b/contrib/edu_utah_sci_vgc_afront/MANIFEST
@@ -0,0 +1 @@
+F __init__.py
diff --git a/contrib/edu_utah_sci_vgc_afront/__init__.py b/contrib/edu_utah_sci_vgc_afront/__init__.py
new file mode 100644
index 0000000..7a71995
--- /dev/null
+++ b/contrib/edu_utah_sci_vgc_afront/__init__.py
@@ -0,0 +1,143 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+"""The package afront defines three modules, Afront, AfrontIso and
+MeshQualityHistogram. These run the meshing code described in
+
+Schreiner et al, Vis 2006
+Schreiner et al, Eurographics 2006
+Scheidegger et al, SGP 2005
+
+"""
+
+from core.configuration import ConfigurationObject
+from core.modules.vistrails_module import Module, ModuleError
+from core.system import list2cmdline
+import core.bundles
+import core.modules.basic_modules
+import core.modules.module_registry
+import core.requirements
+import os
+
+configuration = ConfigurationObject(path=(None, str),
+ debug=False)
+version = '0.1.0'
+identifier = 'edu.utah.sci.vgc.afront'
+name = 'Afront'
+
+################################################################################
+
+class AfrontRun(object):
+
+ def run(self, args):
+ cmd = ['afront', '-nogui'] + args
+ cmdline = list2cmdline(cmd)
+ print cmdline
+ os.system(cmdline)
+# if result != 0:
+# raise ModuleError(self, "Execution failed")
+
+
+class Afront(Module, AfrontRun):
+
+ def compute(self):
+ o = self.interpreter.filePool.create_file(suffix='.m')
+ args = []
+ if not self.hasInputFromPort("file"):
+ raise ModuleError(self, "Needs input file")
+ args.append(self.getInputFromPort("file").name)
+ if self.hasInputFromPort("rho"):
+ args.append("-rho")
+ args.append(str(self.getInputFromPort("rho")))
+ if self.hasInputFromPort("eta"):
+ args.append("-reduction")
+ args.append(str(self.getInputFromPort("eta")))
+ args.append("-outname")
+ args.append(o.name)
+ args.append("-tri")
+ self.run(args)
+ self.setResult("output", o)
+
+
+class MeshQualityHistogram(Module, AfrontRun):
+
+ def compute(self):
+ o = self.interpreter.filePool.create_file(suffix='.csv')
+ args = []
+ self.checkInputPort("file")
+ args.append(self.getInputFromPort("file").name)
+ args.append('-histname')
+ args.append(o.name)
+ args.append('-histogram')
+ self.run(args)
+ self.setResult("output", o)
+
+class AfrontIso(Afront):
+
+ def compute(self):
+ o = self.interpreter.filePool.create_file(suffix='.m')
+ args = []
+ if not self.hasInputFromPort("file"):
+ raise ModuleError(self, "Needs input file")
+ args.append(self.getInputFromPort("file").name)
+ if self.hasInputFromPort("rho"):
+ args.append("-rho")
+ args.append(str(self.getInputFromPort("rho")))
+ if self.hasInputFromPort("eta"):
+ args.append("-eta")
+ args.append(str(self.getInputFromPort("eta")))
+ self.checkInputPort("iso")
+ args.append("-outname")
+ args.append(o.name)
+ args.append("-tri")
+ args.append(str(self.getInputFromPort("iso")))
+ self.run(args)
+ self.setResult("output", o)
+
+
+################################################################################
+
+def initialize():
+
+ print "Afront VisTrails package"
+ print "------------------------"
+ print "Testing afront presence..."
+
+# if (not core.requirements.executable_file_exists('afront') and
+# not core.bundles.install({'linux-ubuntu': 'afront'})):
+# raise core.requirements.MissingRequirement("Afront")
+
+ print "Ok, found afront"
+ __version__ = 0.1
+
+ reg = core.modules.module_registry
+ reg.add_module(Afront)
+ reg.add_input_port(Afront, "rho", (core.modules.basic_modules.Float, 'rho'))
+ reg.add_input_port(Afront, "eta", (core.modules.basic_modules.Float, 'eta'))
+ reg.add_input_port(Afront, "file", (core.modules.basic_modules.File, 'the file to process'))
+ reg.add_output_port(Afront, "output", (core.modules.basic_modules.File, 'the result'))
+
+ reg.add_module(MeshQualityHistogram)
+ reg.add_input_port(MeshQualityHistogram, "file", core.modules.basic_modules.File)
+ reg.add_output_port(MeshQualityHistogram, "output", core.modules.basic_modules.File)
+
+ reg.add_module(AfrontIso)
+ reg.add_input_port(AfrontIso, "iso", (core.modules.basic_modules.Float, 'iso'))
diff --git a/contrib/itk/FeatureExtractionFilters.py b/contrib/itk/FeatureExtractionFilters.py
new file mode 100644
index 0000000..6cb8cc7
--- /dev/null
+++ b/contrib/itk/FeatureExtractionFilters.py
@@ -0,0 +1,208 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import itk
+import core.modules
+from core.modules.vistrails_module import Module, ModuleError
+
+from ITK import *
+from Image import Image
+
+class GradientMagnitudeRecursiveGaussianImageFilter(Module):
+ my_namespace = "Filter|Feature"
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ sigma_ = self.getInputFromPort("Sigma")
+
+ self.filter_ = itk.GradientMagnitudeRecursiveGaussianImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.SetSigma(sigma_)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Gradient Magnitude Recursive Gaussian Image Filter", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Sigma", (basic.Float, 'Sigma'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+#TODO this filter doesn't produce any results
+class DanielssonDistanceMapImageFilter(Module):
+ my_namespace = 'Filter|Feature'
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ squared_distance = self.getInputFromPort("Squared Distance")
+
+ image_spaceing = self.getInputFromPort("Image Spaceing")
+
+ self.filter_ = itk.DanielssonDistanceMapImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.SetSquaredDistance(squared_distance)
+ self.filter_.SetUseImageSpacing(image_spaceing)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="DanielssonDistance Map Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+ reg.add_input_port(cls, "Squared Distance", (basic.Float, 'Squared Distance'))
+ reg.add_input_port(cls, "Image Spaceing", (basic.Float, 'Image Spaceing'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+class SobelEdgeDetectionImageFilter(Module):
+ my_namespace = 'Filter|Feature'
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ self.filter_ = itk.SobelEdgeDetectionImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Sobel Edge Detection Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
diff --git a/contrib/itk/GradientFilters.py b/contrib/itk/GradientFilters.py
new file mode 100644
index 0000000..931d4e5
--- /dev/null
+++ b/contrib/itk/GradientFilters.py
@@ -0,0 +1,84 @@
+#############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import itk
+import core.modules
+from core.modules.vistrails_module import Module, ModuleError
+
+from ITK import *
+from Image import Image
+
+class GradientMagnitudeImageFilter(Module):
+ my_namespace = 'Filter|Gradient'
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ self.filter_ = itk.GradientMagnitudeImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Gradient Magnitude Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
diff --git a/contrib/itk/ITK.py b/contrib/itk/ITK.py
new file mode 100644
index 0000000..2834326
--- /dev/null
+++ b/contrib/itk/ITK.py
@@ -0,0 +1,166 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import core.modules
+from core.modules.vistrails_module import Module, ModuleError
+
+import itk
+
+class ITK(object):
+ my_namespace="itk"
+
+class PixelType(Module, ITK):
+ my_namespace = "disregard"
+
+ def compute(self):
+ pass
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Pixel Type", namespace=cls.my_namespace)
+
+class Filter(Module, ITK):
+ my_namespace="disregard"
+
+ def compute(self):
+ pass
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Filter", namespace=cls.my_namespace)
+
+
+class Index2D(Module, ITK):
+ my_namespace = "index"
+
+ def compute(self):
+ self.ind_ = itk.Index[2]()
+ self.x_ = self.getInputFromPort("X Index")
+ self.y_ = self.getInputFromPort("Y Index")
+
+ self.ind_.SetElement(0,self.x_)
+ self.ind_.SetElement(1,self.y_)
+
+ self.setResult("Index", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Index2D", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "X Index", (basic.Integer, 'X Index'))
+ reg.add_input_port(cls, "Y Index", (basic.Integer, 'Y Index'))
+
+ reg.add_output_port(cls, "Index", (Index2D, 'Index'))
+
+class Index3D(Module, ITK):
+ my_namespace = "index"
+ def compute(self):
+ self.ind_ = itk.Index[3]()
+ self.x_ = self.getInputFromPort("X Index")
+ self.y_ = self.getInputFromPort("Y Index")
+ self.z_ = self.getInputFromPort("Z Index")
+
+ self.ind_.SetElement(0,self.x_)
+ self.ind_.SetElement(1,self.y_)
+ self.ind_.SetElement(2,self.z_)
+
+ self.setResult("Index", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Index3D", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "X Index", (basic.Integer, 'X Index'))
+ reg.add_input_port(cls, "Y Index", (basic.Integer, 'Y Index'))
+ reg.add_input_port(cls, "Z Index", (basic.Integer, 'Z Index'))
+
+ reg.add_output_port(cls, "Index", (Index3D, 'Index'))
+
+class Size(Module, ITK):
+ my_namespace = "size"
+ def compute(self):
+ dim = self.getInputFromPort("Dimension")
+ self.size_ = itk.Size[dim]()
+ self.x = self.getInputFromPort("Element 1")
+ self.y = self.getInputFromPort("Element 2")
+ if dim > 2:
+ self.z = self.getInputFromPort("Element 3")
+
+ self.size_.SetElement(0,self.x)
+ self.size_.SetElement(1,self.y)
+
+ if dim > 2:
+ self.size_.SetElement(2,self.z)
+
+ self.setResult("Size",self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Size", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
+ reg.add_input_port(cls, "Element 1", (basic.Integer, 'Element 1'))
+ reg.add_input_port(cls, "Element 2", (basic.Integer, 'Element 2'))
+ reg.add_input_port(cls, "Element 3", (basic.Integer, 'Element 3'))
+
+ reg.add_output_port(cls, "Size", (Size, 'Size'))
+
+class Region(Module, ITK):
+ my_namespace = "region"
+ def compute(self):
+ dim = self.getInputFromPort("Dimension")
+ self.region_ = itk.ImageRegion[dim]()
+ self.region_.SetSize(self.getInputFromPort("Size").size_)
+ if dim > 2:
+ self.region_.SetIndex(self.getInputFromPort("Input 3D Index").ind_)
+ else:
+ self.region_.SetIndex(self.getInputFromPort("Input 2D Index").ind_)
+
+ self.setResult("Region", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Region", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
+ reg.add_input_port(cls, "Size", (Size, 'Size'))
+ reg.add_input_port(cls, "Input 2D Index", (Index2D, 'Input 2D Index'))
+ reg.add_input_port(cls, "Input 3D Index", (Index3D, 'Input 3D Index'), True)
+
+ reg.add_output_port(cls, "Region", (Region, 'Region'))
+
+class Kernel(Module, ITK):
+ my_namespace = "kernel"
+ def compute(self):
+ dim = self.getInputFromPort("Dimension")
+ radius = self.getInputFromPort("Radius")
+ self.kernel = itk.strel(dim,radius)
+
+ self.setResult("Kernel", self.kernel)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Kernel", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
+ reg.add_input_port(cls, "Radius", (basic.Integer, 'Radius'))
+
+ reg.add_output_port(cls, "Kernel", (Kernel, 'Kernel'))
diff --git a/contrib/itk/Image.py b/contrib/itk/Image.py
new file mode 100644
index 0000000..c4facc4
--- /dev/null
+++ b/contrib/itk/Image.py
@@ -0,0 +1,64 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import itk
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from ITK import *
+from PixelType import *
+
+class Image(Module, ITK):
+ my_namespace="disregard"
+
+ def getPixelType(self):
+ return self._type
+
+ def getDim(self):
+ return self.dim
+
+ def getImg(self):
+ return self.inIm
+
+ def setImg(self, img):
+ self.inIm = img
+
+ def setDim(self, dim):
+ self.dim = dim
+
+ def setPixelType(self, pt):
+ self._type = pt
+
+ def compute(self):
+ self.inIm = self.getInputFromPort("Image")
+ self.dim = self.getInputFromPort("Dimension")
+ self._type = self.getInputFromPort("Pixel Type")
+
+ self.setResult("Output Image", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Image", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
+ reg.add_input_port(cls, "Image", (Image, 'Image'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
diff --git a/contrib/itk/ImageReader.py b/contrib/itk/ImageReader.py
new file mode 100644
index 0000000..c186ff7
--- /dev/null
+++ b/contrib/itk/ImageReader.py
@@ -0,0 +1,169 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import itk
+import core.modules
+
+from ITK import *
+from Image import Image
+
+class ImageReader(Module):
+ my_namespace = "ImageReader"
+ def compute(self):
+ dim = self.getInputFromPort("Dimension")
+ outPixelType = self.getInputFromPort("Pixel Type")
+ fn = self.getInputFromPort("Filename")
+ self.reader = itk.ImageFileReader[itk.Image[outPixelType._type, dim]].New()
+ self.reader.SetFileName(fn)
+ self.reader.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.reader.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ self.setResult("Image", outIm)
+ self.setResult("Reader", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="ImageReader", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
+ reg.add_input_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
+
+ reg.add_output_port(cls, "Image", (Image, 'Image'))
+ reg.add_output_port(cls, "Reader", (ImageReader, 'Reader'))
+
+class ImageToFile(Module):
+ my_namespace = "ImageReader"
+ def compute(self):
+ im = self.getInputFromPort("Image")
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")._type
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ suf = self.getInputFromPort("Suffix")
+ f = self.createOutputFile(suf)
+ writeType = itk.Image[inPixelType._type, dim]
+ writer = itk.ImageFileWriter[writeType].New(im.getImg(), FileName=f.name)
+ writer.Update()
+ self.setResult("File", f)
+
+ def createOutputFile(self, s):
+ return self.interpreter.filePool.create_file(suffix=s)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="ImageToFile", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Suffix", (basic.String, 'Suffix'))
+ reg.add_input_port(cls, "Pixel Type", (PixelType, 'Pixel Type'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Image", (Image, 'Image'))
+
+ reg.add_output_port(cls, "File", (basic.File, 'File'))
+
+class GDCMReader(Module):
+ my_namespace = "ImageReader"
+ def compute(self):
+ dir = self.getInputFromPort("Directory")
+ dim = self.getInputFromPort("Dimension")
+ self.dicomNames_ = itk.GDCMSeriesFileNames.New()
+
+ self.dicomNames_.SetDirectory(dir)
+ self.dicomNames_.SetUseSeriesDetails(True)
+ self.dicomNames_.SetRecursive(True)
+ self.dicomNames_.LoadSequencesOn()
+
+ self.iType_ = itk.Image[itk.US,dim]
+ self.reader_ = itk.ImageSeriesReader[self.iType_].New()
+ self.reader_.SetFileNames(self.dicomNames_.GetInputFileNames())
+ self.io_ = itk.GDCMImageIO.New()
+ self.reader_.SetImageIO(self.io_.GetPointer())
+ self.reader_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.reader_.GetOutput())
+ outIm.setPixelType(itk.US)
+ outIm.setDim(dim)
+
+ self.setResult("Image Series", outIm)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="GDCMReader", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Directory", (basic.String, 'Directory'))
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
+ reg.add_output_port(cls, "Image Series", (Image, 'Image Series'))
+
+class DICOMReader(Module):
+ my_namespace = "ImageReader"
+ def compute(self):
+ dir = self.getInputFromPort("Directory")
+ dim = self.getInputFromPort("Dimension")
+ self.dicomNames_ = itk.DICOMSeriesFileNames.New()
+
+ self.dicomNames_.SetFileNameSortingOrderToSortByImagePositionPatient()
+ self.dicomNames_.SetDirectory(dir)
+
+ self.iType_ = itk.Image[itk.US,dim]
+ self.reader_ = itk.ImageSeriesReader[self.iType_].New()
+ self.reader_.SetFileNames(self.dicomNames_.GetFileNames(False))
+ self.reader_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.reader_.GetOutput())
+ outIm.setPixelType(itk.US)
+ outIm.setDim(dim)
+
+ self.setResult("Image Series", outIm)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="DICOMReader", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Directory", (basic.String, 'Directory'))
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
+ reg.add_output_port(cls, "Image Series", (Image, 'Image Series'))
+
+class ITKImageToVTKData(Module):
+ my_namespace = "ImageReader"
+ def compute(self):
+ dim = self.getInputFromPort("Dimension")
+ pType = self.getInputFromPort("Input PixelType")
+ iType = itk.Image[itk.pType,dim]
+ self.vtkExport_ = itk.VTKImageExport[iType].New()
+ im = self.getInputFromPort("Input Image")
+ self.vtkExport_.SetInput(im)
+ self.vtkExport_.Update()
+ self.setResult("VTK Output", self.vtkExport_.GetOutput())
+
+ #TODO add register method
diff --git a/contrib/itk/IntensityFilters.py b/contrib/itk/IntensityFilters.py
new file mode 100644
index 0000000..987dfa9
--- /dev/null
+++ b/contrib/itk/IntensityFilters.py
@@ -0,0 +1,343 @@
+#############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import itk
+import core.modules
+from core.modules.vistrails_module import Module, ModuleError
+
+from ITK import *
+from Image import Image
+
+class RescaleIntensityImageFilter(Module):
+ my_namespace = "Filter|Intensity"
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ minimum = self.getInputFromPort("Minimum")
+ maximum = self.getInputFromPort("Maximum")
+
+ self.filter_ = itk.RescaleIntensityImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.SetOutputMaximum(maximum)
+ self.filter_.SetOutputMinimum(minimum)
+
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Rescale Intensity Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Minimum", (basic.Integer, 'Minimum'))
+ reg.add_input_port(cls, "Maximum", (basic.Integer, 'Maximum'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+class SigmoidImageFilter(Module):
+ my_namespace = "Filter|Intensity"
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ #default values are those that are recommended
+ if self.hasInputFromPort("Minimum"):
+ min = self.getInputFromPort("Minimum")
+ else:
+ min = 10
+
+ if self.hasInputFromPort("Maximum"):
+ max = self.getInputFromPort("Maximum")
+ else:
+ max = 240
+
+ if self.hasInputFromPort("Alpha"):
+ alpha = self.getInputFromPort("Alpha")
+ else:
+ alpha = 10
+
+ if self.hasInputFromPort("Beta"):
+ beta = self.getInputFromPort("Beta")
+ else:
+ beta = 170
+
+ self.filter_ = itk.SigmoidImageFilter[inImgType,outImgType].New(im.getImg())
+ self.filter_.SetOutputMinimum(min)
+ self.filter_.SetOutputMaximum(max)
+ self.filter_.SetAlpha(alpha)
+ self.filter_.SetBeta(beta)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Sigmoid Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Minimum", (basic.Integer, 'Minimum'), True)
+ reg.add_input_port(cls, "Maximum", (basic.Integer, 'Maximum'), True)
+ reg.add_input_port(cls, "Alpha", (basic.Float, 'Alpha'), True)
+ reg.add_input_port(cls, "Beta", (basic.Float, 'Beta'), True)
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Output Filter'),True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+class ThresholdImageFilter(Module):
+ my_namespace = "Filter|Intensity"
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #setup filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ up = self.getInputFromPort("Upper Value")
+ lo = self.getInputFromPort("Lower Value")
+
+ self.filter_ = itk.ThresholdImageFilter[inImgType].New(im.getImg())
+
+ self.filter_.SetUpper(up)
+ self.filter_.SetLower(lo)
+# self.filter_.ThresholdAbove(up)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(inPixelType)
+ outIm.setDim(dim)
+
+ self.setResult("Output Image", outIm)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Threshold Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Upper Value", (basic.Integer, 'Upper Value'))
+ reg.add_input_port(cls, "Lower Value", (basic.Integer, 'Lower Value'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+
+class ShiftScaleImageFilter(Module):
+ my_namespace = "Filter|Intensity"
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ shift_value = self.getInputFromPort("Shift Value")
+
+ scale_value = self.getInputFromPort("Scale Value")
+
+ self.filter_ = itk.ShiftScaleImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.SetShift(shift_value)
+ self.filter_.SetScale(scale_value)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Shift Scale Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+ reg.add_input_port(cls, "Shift Value", (basic.Float, 'Shift Value'))
+ reg.add_input_port(cls, "Scale Value", (basic.Integer, 'Scale Value'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+class NormalizeImageFilter(Module):
+ my_namespace = 'Filter|Intensity'
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ self.filter_ = itk.NormalizeImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Normalize Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
diff --git a/contrib/itk/NeighborhoodFilters.py b/contrib/itk/NeighborhoodFilters.py
new file mode 100644
index 0000000..0dbcaf2
--- /dev/null
+++ b/contrib/itk/NeighborhoodFilters.py
@@ -0,0 +1,210 @@
+#############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+import itk
+import core.modules
+from core.modules.vistrails_module import Module, ModuleError
+
+from ITK import *
+from Image import Image
+
+class MeanImageFilter(Module):
+ my_namespace = 'Filter|Neighborhood'
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ self.filter_ = itk.MeanImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Mean Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+
+class MedianImageFilter(Module):
+ my_namespace = 'Filter|Neighborhood'
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ self.filter_ = itk.MedianImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Median Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+#TODO does this filter even modify the image?
+class BinaryErodeImageFilter(Module):
+ my_namespace = 'Filter|Neighborhood'
+
+ def compute(self):
+ print "comput"
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ kernel = self.getInputFromPort("Kernel")
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ erode_value = self.getInputFromPort("Erode Value")
+
+ self.filter_ = itk.BinaryErodeImageFilter[inImgType, outImgType, kernel].New(im.getImg())
+ self.filter_.SetKernel(kernel)
+ self.filter_.SetErodeValue(erode_value)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Binary Erode Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Kernel", (Kernel, 'Kernel'))
+
+ reg.add_input_port(cls, "Erode Value", (basic.Integer, 'Erode Value'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
diff --git a/contrib/itk/PixelType.py b/contrib/itk/PixelType.py
new file mode 100644
index 0000000..2f2beb4
--- /dev/null
+++ b/contrib/itk/PixelType.py
@@ -0,0 +1,71 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import itk
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+
+from ITK import PixelType
+
+class PixelTypeFloat(Module):
+ my_namespace = "pixeltype"
+ def compute(self):
+ self._type = itk.F
+ self.setResult("Pixel Type", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Pixel Type Float", namespace=cls.my_namespace)
+ reg.add_output_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
+
+class PixelTypeUnsignedChar(Module):
+ my_namespace = "pixeltype"
+ def compute(self):
+ self._type = itk.UC
+ self.setResult("Pixel Type", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Pixel Type Unsigned Char", namespace=cls.my_namespace)
+ reg.add_output_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
+
+class PixelTypeUnsignedShort(Module):
+ my_namespace = "pixeltype"
+ def compute(self):
+ self._type = itk.US
+ self.setResult("Pixel Type", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Pixel Type Unsigned Short", namespace=cls.my_namespace)
+ reg.add_output_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
+
+class PixelTypeRGB(Module):
+ my_namespace = "pixeltype"
+ def compute(self):
+ self._type = itk.RGBPixel[itk.US]
+ self.setResult("Pixel Type", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Pixel Type RGB", namespace=cls.my_namespace)
+ reg.add_output_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
diff --git a/contrib/itk/SegmentationFilters.py b/contrib/itk/SegmentationFilters.py
new file mode 100644
index 0000000..77c5ad7
--- /dev/null
+++ b/contrib/itk/SegmentationFilters.py
@@ -0,0 +1,319 @@
+#############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import itk
+import core.modules
+from core.modules.vistrails_module import Module, ModuleError
+
+from ITK import *
+from Image import Image
+
+class IsolatedWatershedImageFilter(Module):
+ my_namespace="Filter|Segmentation"
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ self.filter_ = itk.IsolatedWatershedImageFilter[inImgType, outImgType].New(im.getImg())
+
+ if self.hasInputFromPort("Seed1"):
+ self.filter_.SetSeed1(self.getInputFromPort("Seed1").ind_)
+
+ if self.hasInputFromPort("Seed2"):
+ self.filter_.SetSeed2(self.getInputFromPort("Seed2").ind_)
+
+ if self.hasInputFromPort("ReplaceValue1"):
+ self.filter_.SetReplaceValue1(self.getInputFromPort("ReplaceValue1"))
+
+ if self.hasInputFromPort("ReplaceValue2"):
+ self.filter_.SetReplaceValue2(self.getInputFromPort("ReplaceValue2"))
+
+ if self.hasInputFromPort("Threshold"):
+ self.filter_.SetThreshold(self.getInputFromPort("Threshold"))
+
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ self.setResult("Output Image", outIm)
+ self.setResult("Output PixelType", outPixelType)
+ self.setResult("Filter", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Isolated Watershed Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Seed1", (Index2D, 'Seed 1 Location'))
+
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
+ reg.add_input_port(cls, "Threshold", (basic.Float, 'Threshold'), True)
+ reg.add_input_port(cls, "Seed2", (Index2D, 'Seed 2 Location'))
+ reg.add_input_port(cls, "ReplaceValue1", (basic.Float, 'Replacement Value 1'), True);
+ reg.add_input_port(cls, "ReplaceValue2", (basic.Float, 'Replacement Value 2'), True);
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
+
+class ConnectedThresholdImageFilter(Module):
+ my_namespace="Filter|Segmentation"
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ if self.hasInputFromPort("Seed2D"):
+ seed = self.getInputFromPort("Seed2D")
+ else:
+ seed = self.getInputFromPort("Seed3D")
+
+ replace = self.getInputFromPort("Replace Value")
+ t_lower = self.getInputFromPort("Lower Value")
+ t_upper = self.getInputFromPort("Upper Value")
+
+ #setup filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ self.filter_ = itk.ConnectedThresholdImageFilter[inImgType,outImgType].New(im.getImg())
+
+ self.filter_.SetSeed(seed.ind_)
+ self.filter_.SetReplaceValue(replace)
+ self.filter_.SetLower(t_lower)
+ self.filter_.SetUpper(t_upper)
+
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ self.setResult("Output Image", outIm)
+ self.setResult("Output PixelType", outPixelType)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Connected Threshold Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Seed2D", (Index2D, 'Seed Point'))
+ reg.add_input_port(cls, "Seed3D", (Index3D, 'Seed Point'))
+ reg.add_input_port(cls, "Replace Value", (basic.Float, 'Replacement Value'))
+ reg.add_input_port(cls, "Upper Value", (basic.Float, 'Upper Threshold Value'))
+ reg.add_input_port(cls, "Lower Value", (basic.Float, 'Lower Threshold Value'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
+
+class ConfidenceConnectedImageFilter(Module):
+ my_namespace="Filter|Segmentation"
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ if self.hasInputFromPort("Seed2D"):
+ seed = self.getInputFromPort("Seed2D")
+ else:
+ seed = self.getInputFromPort("Seed3D")
+
+ replace = self.getInputFromPort("Replace Value")
+ multiplier = self.getInputFromPort("Multiplier")
+ iterations = self.getInputFromPort("Iterations")
+ radius = self.getInputFromPort("Neighborhood Radius")
+
+ #setup filter
+ inImgType = itk.Image[inPixelType._type,dim]
+ outImgType = itk.Image[outPixelType._type,dim]
+
+ self.filter_ = itk.ConfidenceConnectedImageFilter[inImgType,outImgType].New(im.getImg())
+
+ self.filter_.SetReplaceValue(replace)
+ self.filter_.SetMultiplier(multiplier)
+ self.filter_.SetNumberOfIterations(iterations)
+ self.filter_.SetInitialNeighborhoodRadius(radius)
+
+ self.filter_.SetSeed(seed.ind_)
+
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ self.setResult("Output Image", outIm)
+ self.setResult("Output PixelType", outPixelType)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Confidence Connected Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Seed2D", (Index2D, 'Seed Point'))
+ reg.add_input_port(cls, "Seed3D", (Index3D, 'Seed Point'))
+ reg.add_input_port(cls, "Replace Value", (basic.Float, 'Replacement Value'))
+ reg.add_input_port(cls, "Multiplier", (basic.Float, 'Multiplier'))
+ reg.add_input_port(cls, "Iterations", (basic.Float, 'Iterations'))
+ reg.add_input_port(cls, "Neighborhood Radius", (basic.Float, 'Neighborhood Radius'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
+
+class IsolatedConnectedImageFilter(Module):
+ my_namespace="Filter|Segmentation"
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ seed1 = self.getInputFromPort("Seed1")
+ seed2 = self.getInputFromPort("Seed2")
+
+ replace = self.getInputFromPort("Replace Value")
+ t_lower = self.getInputFromPort("Lower Value")
+ t_upper = self.getInputFromPort("Upper Value")
+
+ inImgType = itk.Image[inPixelType._type,dim]
+ outImgType = itk.Image[outPixelType._type,dim]
+
+ self.filter_ = itk.IsolatedConnectedImageFilter[inImgType,outImgType].New(im.getImg())
+
+ self.filter_.SetReplaceValue(replace)
+ self.filter_.SetLower(t_lower)
+ self.filter_.SetUpperValueLimit(t_upper)
+ self.filter_.SetSeed1(seed1.ind_)
+ self.filter_.SetSeed2(seed2.ind_)
+
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ self.setResult("Output Image", outIm)
+ self.setResult("Output PixelType", outPixelType)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Isolated Connected Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Seed1", (Index2D, 'Seed Point'))
+ reg.add_input_port(cls, "Seed2", (Index2D, 'Seed Point'))
+ reg.add_input_port(cls, "Replace Value", (basic.Integer, 'Replacement Value'))
+ reg.add_input_port(cls, "Upper Value", (basic.Integer, 'Upper Threshold Value'))
+ reg.add_input_port(cls, "Lower Value", (basic.Integer, 'Lower Threshold Value'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
diff --git a/contrib/itk/SelectionFilters.py b/contrib/itk/SelectionFilters.py
new file mode 100644
index 0000000..61b5302
--- /dev/null
+++ b/contrib/itk/SelectionFilters.py
@@ -0,0 +1,231 @@
+#############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import itk
+import core.modules
+from core.modules.vistrails_module import Module, ModuleError
+from ITK import *
+from Image import Image
+
+class RegionOfInterestImageFilter(Module):
+ my_namespace="Filter|Selection"
+
+ def setStart(self, start):
+ if start == 2:
+ self.index = self.getInputFromPort("Input 2D Index").ind_
+ else:
+ self.index = self.getInputFromPort("Input 3D Index").ind_
+
+ self.region_.SetIndex(self.index)
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Input Dimension"):
+ dim = self.getInputFromPort("Input Dimension")
+ else:
+ dim = im.getDim()
+
+ if self.hasInputFromPort("Output Dimension"):
+ outDim = self.getInputFromPort("Output Dimension")
+ else:
+ outDim = dim
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, outDim]
+
+ self.filter_ = itk.RegionOfInterestImageFilter[inImgType, outImgType].New()
+
+ #TODO this is not correct, needs fixing
+ if self.hasInputFromPort("Input Region"):
+ self.region_ = self.getInputFromPort("Input Region").region_
+ else:
+ self.region_ = itk.ImageRegion[indim]()
+ self.setStart(indim)
+ self.region_.SetSize(self.getInputFromPort("Region Size").size_)
+
+ self.filter_.SetRegionOfInterest(self.region_)
+ self.filter_.SetInput(im.getImg())
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(outDim)
+
+ self.setResult("Output Image", outIm)
+ self.setResult("Output PixelType", outPixelType)
+ self.setResult("Output Dimension", outDim)
+ self.setResult("Filter", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Region of Interest Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Output Dimension", (basic.Integer, 'Dimension'),True)
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Input Region", (Region, 'Input Region'))
+ reg.add_input_port(cls, "Region Size", (Size, 'Region Size'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_output_port(cls, "Output Dimension", (basic.Integer, 'Dimension'),True)
+
+class CastImageFilter(Module):
+ my_namespace="Filter|Selection"
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for in dimension
+ if self.hasInputFromPort("Input Dimension"):
+ dim = self.getInputFromPort("Input Dimension")
+ else:
+ dim = im.getDim()
+
+ #check for out dimension
+ if self.hasInputFromPort("Output Dimension"):
+ outDim = self.getInputFromPort("Output Dimension")
+ else:
+ outDim = dim
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, outDim]
+
+ self.filter_ = itk.CastImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(outDim)
+
+ self.setResult("Output Image", outIm)
+ self.setResult("Output PixelType", outPixelType)
+ self.setResult("Output Dimension", outDim)
+ self.setResult("Filter", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Cast Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Input Dimension'),True)
+ reg.add_input_port(cls, "Output Dimension", (basic.Integer, 'Output Dimension'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'),True)
+ reg.add_output_port(cls, "Output Dimension", (basic.Integer, 'Output Dimension'),True)
+
+
+class ExtractImageFilter(Module):
+ my_namespace="Filter|Selection"
+ def compute(self):
+ #TODO should this be Input Volume?
+ im = self.getInputFromPort("Input Volume")
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #set outPixelType
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #check for out dimension
+ if self.hasInputFromPort("Output Dimension"):
+ outDim = self.getInputFromPort("Output Dimension")
+ else:
+ outDim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, outDim]
+
+ self.filter_ = itk.ExtractImageFilter[inImgType,outImgType].New(im.getImg())
+
+ region = self.getInputFromPort("Extraction Region")
+ self.filter_.SetExtractionRegion(region.region_)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(outDim)
+
+ self.setResult("Output Image", outIm)
+ self.setResult("Output PixelType", outPixelType)
+ self.setResult("Dimension", outDim)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Extract Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Volume", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Input Dimension'),True)
+ reg.add_input_port(cls, "Output Dimension", (basic.Integer, 'Output Dimension'),True)
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Extraction Region", (Region, 'Extraction Region'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_output_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
diff --git a/contrib/itk/SmoothingFilters.py b/contrib/itk/SmoothingFilters.py
new file mode 100644
index 0000000..dd9e764
--- /dev/null
+++ b/contrib/itk/SmoothingFilters.py
@@ -0,0 +1,558 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import itk
+import core.modules
+from core.modules.vistrails_module import Module, ModuleError
+from ITK import *
+from Image import Image
+
+class CurvatureAnisotropicDiffusionFilter(Module):
+ my_namespace="Filter|Smoothing"
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+
+ try:
+ self.filter_ = itk.CurvatureAnisotropicDiffusionImageFilter[inImgType, inImgType].New(im.getImg())
+ except:
+ raise ModuleError(self, "Filter requires a decimal PixelType")
+
+ #default values are recommended
+ if self.hasInputFromPort("Iterations"):
+ iterations = self.getInputFromPort("Iterations")
+ else:
+ iterations = 5
+
+ if self.hasInputFromPort("TimeStep"):
+ timestep = self.getInputFromPort("TimeStep")
+ else:
+ if dim == 2:
+ timestep = 0.125
+ else:
+ timestep = 0.0625
+
+ if self.hasInputFromPort("Conductance"):
+ conductance = self.getInputFromPort("Conductance")
+ else:
+ conductance = 3.0
+
+ self.filter_.SetNumberOfIterations(iterations)
+ self.filter_.SetTimeStep(timestep)
+ self.filter_.SetConductanceParameter(conductance)
+
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(inPixelType)
+ outIm.setDim(dim)
+
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Curvature Anisotropic Diffusion Filter", namespace=cls.my_namespace)
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Input Dimension'),True)
+ reg.add_input_port(cls, "Input PixelType Float", (PixelType, 'Input PixelType Float'),True)
+ reg.add_input_port(cls, "Iterations", (basic.Integer, 'Iterations'), True)
+ reg.add_input_port(cls, "TimeStep", (basic.Float, 'TimeStep'), True)
+ reg.add_input_port(cls, "Conductance", (basic.Float, 'Conductance'), True)
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+
+
+class RecursiveGaussianImageFilter(Module):
+ my_namespace="Filter|Smoothing"
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ outdim = dim
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ self.filter_ = itk.RecursiveGaussianImageFilter[inImgType, outImgType].New(im.getImg())
+
+ sigma = self.getInputFromPort("Sigma")
+ self.filter_.SetSigma(sigma)
+
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ self.setResult("Output Image", outIm)
+ self.setResult("Output PixelType", outPixelType)
+ self.setResult("Output Dimension", outdim)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Recursive Gaussian Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Input Dimension'),True)
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Sigma", (basic.Float, 'Sigma'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Output Dimension", (basic.Integer, 'Output Dimension'),True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+class CurvatureFlowImageFilter(Module):
+ my_namespace="Filter|Smoothing"
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+
+ try:
+ self.filter_ = itk.CurvatureFlowImageFilter[inImgType, inImgType].New(im.getImg())
+ except:
+ raise ModuleError(self, "Filter requires a decimal PixelType")
+
+ #default values recommended
+ if self.hasInputFromPort("TimeStep"):
+ self.ts = self.getInputFromPort("TimeStep")
+ else:
+ self.ts = 0.125
+
+ if self.hasInputFromPort("Iterations"):
+ self.iterations = self.getInputFromPort("Iterations")
+ else:
+ self.iterations = 5
+
+ self.filter_.SetTimeStep(self.ts)
+ self.filter_.SetNumberOfIterations(self.iterations)
+
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(inPixelType)
+ outIm.setDim(dim)
+
+ self.setResult("Output Image", outIm)
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Curvature Flow Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Input Dimension'),True)
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "TimeStep", (basic.Float, 'TimeStep'), True)
+ reg.add_input_port(cls, "Iterations", (basic.Integer, 'Iterations'), True)
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+
+class DiscreteGaussianImageFilter(Module):
+ my_namespace = 'Filter|Smoothing'
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ gaussian_variance = self.getInputFromPort("Gaussian Variance")
+
+ max_kernel_width = self.getInputFromPort("Max Kernel Width")
+
+ try:
+ self.filter_ = itk.DiscreteGaussianImageFilter[inImgType, outImgType].New(im.getImg())
+ except:
+ raise ModuleError(self, "Requires Signed PixelType")
+
+ self.filter_.SetVariance(gaussian_variance)
+ self.filter_.SetMaximumKernelWidth(max_kernel_width)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Discrete Gaussian Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+ reg.add_input_port(cls, "Gaussian Variance", (basic.Float, 'Gaussian Variance'))
+ reg.add_input_port(cls, "Max Kernel Width", (basic.Integer, 'Max Kernel Width'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+class BinomialBlurImageFilter(Module):
+ my_namespace = 'Filter|Smoothing'
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ repetitions = self.getInputFromPort("Repetitions")
+
+ self.filter_ = itk.BinomialBlurImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.SetRepetitions(repetitions)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="BinomialBlur Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+ reg.add_input_port(cls, "Repetitions", (basic.Integer, 'Repetitions'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+class GradientAnisotropicDiffusionImageFilter(Module):
+ my_namespace = 'Filter|Smoothing'
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ timestep = self.getInputFromPort("Timestep")
+
+ conductance = self.getInputFromPort("Conductance")
+
+ iterations = self.getInputFromPort("Iterations")
+
+ try:
+ self.filter_ = itk.GradientAnisotropicDiffusionImageFilter[inImgType, outImgType].New(im.getImg())
+ except:
+ raise ModuleError(self, "Requires Decimal PixelType")
+
+ self.filter_.SetTimeStep(timestep)
+ self.filter_.SetConductanceParameter(conductance)
+ self.filter_.SetNumberOfIterations(iterations)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Gradient Anisotropic Diffusion Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+ reg.add_input_port(cls, "Timestep", (basic.Float, 'Timestep'))
+ reg.add_input_port(cls, "Conductance", (basic.Float, 'Conductance'))
+ reg.add_input_port(cls, "Iterations", (basic.Integer, 'Iterations'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+
+class MinMaxCurvatureFlowImageFilter(Module):
+ my_namespace = 'Filter|Smoothing'
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ timestep = self.getInputFromPort("Timestep")
+
+ radius = self.getInputFromPort("Radius")
+
+ iterations = self.getInputFromPort("Iterations")
+
+ self.filter_ = itk.MinMaxCurvatureFlowImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.SetTimeStep(timestep)
+ self.filter_.SetStencilRadius(radius)
+ self.filter_.SetNumberOfIterations(iterations)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="MinMax Curvature Flow Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+ reg.add_input_port(cls, "Timestep", (basic.Float, 'Timestep'))
+ reg.add_input_port(cls, "Radius", (basic.Float, 'Radius'))
+ reg.add_input_port(cls, "Iterations", (basic.Integer, 'Iterations'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
+class BilateralImageFilter(Module):
+ my_namespace = 'Filter|Smoothing'
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ range_sigma = self.getInputFromPort("Range Sigma")
+
+ domain_sigma = self.getInputFromPort("Domain Sigma")
+
+ self.filter_ = itk.BilateralImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.SetRangeSigma(range_sigma)
+ self.filter_.SetDomainSigma(domain_sigma)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="Bilateral Image Filter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+ reg.add_input_port(cls, "Range Sigma", (basic.Float, 'Range Sigma'))
+ reg.add_input_port(cls, "Domain Sigma", (basic.Float, 'Domain Sigma'))
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
diff --git a/contrib/itk/ThresholdFilters.py b/contrib/itk/ThresholdFilters.py
new file mode 100644
index 0000000..bab496a
--- /dev/null
+++ b/contrib/itk/ThresholdFilters.py
@@ -0,0 +1,110 @@
+#############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+import itk
+import core.modules
+from core.modules.vistrails_module import Module, ModuleError
+
+from ITK import *
+from Image import Image
+
+class BinaryThresholdImageFilter(Module):
+ my_namespace = "Filter|Threshold"
+
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+
+ if self.hasInputFromPort("Upper Threshold"):
+ upper_threshold = self.getInputFromPort("Upper Threshold")
+ else:
+ upper_threshold = 255
+
+ lower_threshold = self.getInputFromPort("Lower Threshold")
+
+ if self.hasInputFromPort("Outside Value"):
+ outside_value = self.getInputFromPort("Outside Value")
+ else:
+ outside_value = 0
+
+ if self.hasInputFromPort("Inside Value"):
+ inside_value = self.getInputFromPort("Inside Value")
+ else:
+ inside_value = 255
+
+ self.filter_ = itk.BinaryThresholdImageFilter[inImgType, outImgType].New(im.getImg())
+ self.filter_.SetUpperThreshold(upper_threshold)
+ self.filter_.SetLowerThreshold(lower_threshold)
+ self.filter_.SetOutsideValue(outside_value)
+ self.filter_.SetInsideValue(inside_value)
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+
+
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="BinaryThresholdImageFilter", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+
+ reg.add_input_port(cls, "Upper Threshold", (basic.Integer, 'Upper Threshold'),True)
+ reg.add_input_port(cls, "Lower Threshold", (basic.Integer, 'Lower Threshold'))
+ reg.add_input_port(cls, "Outside Value", (basic.Integer, 'Outside Value'),True)
+ reg.add_input_port(cls, "Inside Value", (basic.Integer, 'Inside Value'),True)
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+
diff --git a/contrib/itk/__init__.py b/contrib/itk/__init__.py
new file mode 100644
index 0000000..65c2952
--- /dev/null
+++ b/contrib/itk/__init__.py
@@ -0,0 +1,179 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+# ITK package for VisTrails
+############################################################################
+
+"""ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. www.itk.org
+
+For info on installing itk and python-itk on ubuntu see: http://paulnovo.org/node/2
+
+For info on generating wrapper modules for more itk filters see itk/filter_generator.py"""
+
+version = '0.2'
+identifier = 'edu.utah.sci.vistrails.itk'
+name = 'ITK'
+
+import core.bundles.utils
+import core.requirements
+from core.modules.vistrails_module import Module, ModuleError
+
+# Ugly, but Carlos doesnt know any better
+if core.bundles.utils.guess_system() == 'linux-ubuntu':
+ import sys
+ sys.path.append('/usr/local/lib/VisTrailsITK')
+
+try:
+ from core.bundles import py_import
+ itk = py_import('itk', {'linux-ubuntu': 'vistrails-itk'})
+except ImportError:
+ raise core.requirements.MissingRequirement("ITK and WrapITK")
+
+import core.modules
+import core.modules.module_registry
+
+# ITK Package imports
+from PixelType import *
+from FeatureExtractionFilters import *
+from ITK import *
+from Image import Image
+from IntensityFilters import *
+from SegmentationFilters import *
+from SelectionFilters import *
+from SmoothingFilters import *
+from ThresholdFilters import *
+from GradientFilters import *
+from NeighborhoodFilters import *
+from ImageReader import *
+
+def initialize(*args, **keywords):
+ reg = core.modules.module_registry
+ basic = core.modules.basic_modules
+
+########################################################################################
+# Misc.
+ Index2D.register(reg,basic)
+ Index3D.register(reg,basic)
+ Size.register(reg,basic)
+ Region.register(reg,basic)
+ PixelType.register(reg,basic)
+ Filter.register(reg,basic)
+ Kernel.register(reg,basic)
+
+ Image.register(reg,basic)
+
+########################################################################################
+# Pixel Types
+ pixeltypes = [PixelTypeFloat,
+ PixelTypeUnsignedChar,
+ PixelTypeUnsignedShort,
+ PixelTypeRGB]
+
+ for cls in pixeltypes:
+ cls.register(reg,basic)
+
+
+########################################################################################
+# Feature Extraction Filters
+ featurefilters = [GradientMagnitudeRecursiveGaussianImageFilter,
+ DanielssonDistanceMapImageFilter,
+ SobelEdgeDetectionImageFilter]
+
+ for cls in featurefilters:
+ cls.register(reg,basic)
+
+########################################################################################
+# Intensity Filters
+ intensityfilters = [RescaleIntensityImageFilter,
+ SigmoidImageFilter,
+ ThresholdImageFilter,
+ ShiftScaleImageFilter,
+ NormalizeImageFilter]
+
+ for cls in intensityfilters:
+ cls.register(reg,basic)
+
+########################################################################################
+# Segmentation Filters
+ segmentationfilters = [IsolatedWatershedImageFilter,
+ ConnectedThresholdImageFilter,
+ ConfidenceConnectedImageFilter,
+ IsolatedConnectedImageFilter]
+
+ for cls in segmentationfilters:
+ cls.register(reg,basic)
+
+########################################################################################
+# Selection Filters
+ selectionfilters = [RegionOfInterestImageFilter,
+ CastImageFilter,
+ ExtractImageFilter]
+
+ for cls in selectionfilters:
+ cls.register(reg,basic)
+
+########################################################################################
+# Smoothing Filters
+ smoothingfilters = [CurvatureAnisotropicDiffusionFilter,
+ RecursiveGaussianImageFilter,
+ DiscreteGaussianImageFilter,
+ GradientAnisotropicDiffusionImageFilter,
+ MinMaxCurvatureFlowImageFilter,
+ BinomialBlurImageFilter,
+ BilateralImageFilter,
+ CurvatureFlowImageFilter]
+
+ for cls in smoothingfilters:
+ cls.register(reg,basic)
+
+########################################################################################
+# Threshold Filters
+ thresholdfilters = [BinaryThresholdImageFilter]
+
+ for cls in thresholdfilters:
+ cls.register(reg,basic)
+
+########################################################################################
+# Gradient Filters
+ gradientfilters = [GradientMagnitudeImageFilter]
+
+ for cls in gradientfilters:
+ cls.register(reg,basic)
+
+########################################################################################
+# Neighborhood Filters
+ neighborhoodfilters = [MeanImageFilter,
+ MedianImageFilter,
+ BinaryErodeImageFilter]
+
+ for cls in neighborhoodfilters:
+ cls.register(reg,basic)
+
+########################################################################################
+# Image Reader
+ imagereader = [ImageReader,
+ ImageToFile,
+ GDCMReader,
+ DICOMReader]
+
+
+ for cls in imagereader:
+ cls.register(reg,basic)
diff --git a/contrib/itk/filter_generator.py b/contrib/itk/filter_generator.py
new file mode 100644
index 0000000..352cd6a
--- /dev/null
+++ b/contrib/itk/filter_generator.py
@@ -0,0 +1,170 @@
+# This is a rough code generation tool that works to generate code used to wrap itk functions for Vistrails
+# In order to use this one must:
+# -set generation variables
+# -run script
+# -paste output into desired *Filters.py file
+# -add new filter name to __init__.py file
+#
+#NOTE: some filters require special calls, params, etc. that are not generated with this code
+# for example, many filters only accept decimal PixelTypes meaning that the
+# filter initialization should be wrapped in a try/except raising a ModuleError
+#
+# For example filter implementation, check out:
+# http://math.nist.gov/mcsd/savg/software/filters/
+# http://voxel.jouy.inra.fr/darcs/contrib-itk/WrapITK/Python/Tests/
+
+##########################################################
+#String Manipulation Methods
+##########################################################
+def AddSpaces(word):
+ output = ""
+ for char in word:
+ if char.isupper() and word.index(char)!=0:
+ output += " %s"%char
+ else:
+ output += char
+ return output
+
+def SplitCap(word):
+ temp = word.split("_")
+ output = ""
+ for elem in temp:
+ output += "%s "%elem.capitalize()
+ return output.strip()
+
+##########################################################
+#SETUP generation variables
+##########################################################
+#filter_name should be equal to itk.filter_name
+filter_name = "BinaryErodeImageFilter"
+
+#designate namespace
+namespace = "Filter|Neighborhood"
+
+#some filters require kernel inputs, usually they don't though
+has_kernel = True
+
+#usage: {variable name:[variable type, default value, itk filter set method]}
+#NOTE: you must look up the itk filter set method (dir(itk.filter_name))
+filter_values = {"level":["basic.Float",None, "SetSquaredDistance"],
+ "lower_threshold":["basic.Float",None, "SetUseImageSpacing"]}
+
+##########################################################
+#code generation
+##########################################################
+out_class = """class %s(Module):
+ my_namespace = '%s'"""%(filter_name, namespace)
+
+compute = """
+ def compute(self):
+ im = self.getInputFromPort("Input Image")
+
+ #check for input PixelType
+ if self.hasInputFromPort("Input PixelType"):
+ inPixelType = self.getInputFromPort("Input PixelType")
+ else:
+ inPixelType = im.getPixelType()
+
+ #check for output PixelType
+ if self.hasInputFromPort("Output PixelType"):
+ outPixelType = self.getInputFromPort("Output PixelType")
+ else:
+ outPixelType = inPixelType
+
+ #check for dimension
+ if self.hasInputFromPort("Dimension"):
+ dim = self.getInputFromPort("Dimension")
+ else:
+ dim = im.getDim()
+ """
+if has_kernel:
+ compute += """
+ kernel = self.getInputFromPort("Kernel")
+ """
+
+compute += """
+ #set up filter
+ inImgType = itk.Image[inPixelType._type, dim]
+ outImgType = itk.Image[outPixelType._type, dim]
+"""
+for param in filter_values:
+ #check if default value is set
+ if type(filter_values[param][1]).__name__ != "NoneType":
+ compute += """
+ if self.hasInputFromPort("%s"):
+ %s = self.getInputFromPort("%s")
+ else:
+ %s = %d\n"""%(SplitCap(param), param, SplitCap(param), param, filter_values[param][1])
+ else:
+ compute += """
+ %s = self.getInputFromPort("%s")\n"""%(param, SplitCap(param))
+
+if has_kernel:
+ compute += """
+ self.filter_ = itk.%s[inImgType, outImgType, kernel].New(im.getImg())
+ self.filter_.SetKernel(kernel)"""%filter_name
+
+else:
+ compute += """
+ self.filter_ = itk.%s[inImgType, outImgType].New(im.getImg())"""%filter_name
+
+#set filter values
+for param in filter_values:
+ compute += """
+ self.filter_.%s(%s)"""%(filter_values[param][2], param)
+
+compute += """
+ self.filter_.Update()
+
+ #setup output image
+ outIm = Image()
+ outIm.setImg(self.filter_.GetOutput())
+ outIm.setPixelType(outPixelType)
+ outIm.setDim(dim)
+
+ #set results
+ self.setResult("Output Image", outIm)
+ self.setResult("Filter", self)
+ self.setResult("Output PixelType", outPixelType)
+"""
+register = """
+ @classmethod
+ def register(cls, reg, basic):
+ reg.add_module(cls, name="%s", namespace=cls.my_namespace)
+
+ reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
+ reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
+ reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+ reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
+"""%AddSpaces(filter_name)
+if has_kernel:
+ register += """
+ reg.add_input_port(cls, "Kernel", (Kernel, 'Kernel'))
+ """
+
+for param in filter_values:
+ #check if default value is set
+ if type(filter_values[param][1]).__name__ != "NoneType":
+ register += """
+ reg.add_input_port(cls, "%s", (%s, '%s'),True)"""%(SplitCap(param),\
+ filter_values[param][0],\
+ SplitCap(param))
+ else:
+ register += """
+ reg.add_input_port(cls, "%s", (%s, '%s'))"""%(SplitCap(param),\
+ filter_values[param][0],\
+ SplitCap(param))
+
+register += """
+
+ reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
+ reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
+ reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
+"""
+
+##########################################################
+#Output
+##########################################################
+print out_class
+print compute
+print register
diff --git a/contrib/itk/itk_test_example.py b/contrib/itk/itk_test_example.py
new file mode 100644
index 0000000..4786ae7
--- /dev/null
+++ b/contrib/itk/itk_test_example.py
@@ -0,0 +1,42 @@
+#example code to be pasted into a python terminal to test itk filters
+#generally used to instaniate filters inorder lookup variable set methods
+
+import itk
+#image setup
+dim = 2
+pixeltype = itk.UC
+kernel = itk.stle(dim, 5)
+filename = "/home/mates/Desktop/brains.jpg"
+reader = itk.ImageFileReader[itk.Image[pixeltype, dim]].New()
+reader.SetFileName(filename)
+reader.Update()
+
+im = reader.GetOutput()
+inImg = itk.Image[pixeltype, dim]
+outImg = inImg
+
+size_ = itk.Size[dim]()
+size_.SetElement(0,150)
+size_.SetElement(1,150)
+region_ = itk.ImageRegion[dim]()
+region_.SetSize(size_)
+
+#filter
+filt = itk.IsolatedConnectedImageFilter[inImg, outImg].New(im)
+filt.SetReplaceValue(120)
+filt.SetLower(155)
+filt.SetUpperValueLimit(235)
+filt.SetSeed1([120,120])
+filt.SetSeed2([140,140])
+filt.Update()
+
+filt2 = itk.ConnectedThresholdImageFilter[itk.Image[pixeltype, dim], itk.Image[pixeltype, dim]].New(im)
+filt2.SetSeed([100,100])
+filt2.SetReplaceValue(100)
+filt2.SetLower(150)
+filt2.SetUpper(250)
+filt2.Update()
+
+#write to file
+writer = itk.ImageFileWriter[itk.Image[pixeltype, dim]].New(filt.GetOutput(), FileName="/home/mates/Desktop/output.jpg")
+writer.Update()
diff --git a/contrib/meshutils.py b/contrib/meshutils.py
new file mode 100644
index 0000000..af0f8f1
--- /dev/null
+++ b/contrib/meshutils.py
@@ -0,0 +1,104 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+import core.bundles
+import core.requirements
+import os
+import re
+
+identifier = 'edu.utah.sci.cscheid.meshutils'
+version = '0.1'
+name = 'Mesh utility'
+
+class MeshArea(Module):
+
+ def compute(self):
+ self.checkInputPort('input_file')
+ f1 = self.getInputFromPort('input_file')
+ text_output = self.interpreter.filePool.create_file()
+
+ cmdline = []
+ cmdline.append(meshareapath)
+ cmdline.append(f1.name)
+ cmdline.append('>' + text_output.name)
+ cmdline = ('%s ' * len(cmdline)) % tuple(cmdline)
+ print cmdline
+ result = os.system(cmdline)
+ if result != 0:
+ raise ModuleError(self, "execution failed")
+ try:
+ l = file(text_output.name).readlines()[-1]
+ v = float(l)
+ except:
+ raise ModuleError(self, "Expected a float, got '%s'" % l)
+ self.setResult('area', v)
+
+class MeshChoose(Module):
+
+ def guess_input_format(self, input_file_name):
+ i = input_file_name.rfind('.')
+ if i == -1:
+ return None
+ else:
+ return input_file_name[i:]
+
+ def compute(self):
+ self.checkInputPort('input_file_1')
+ self.checkInputPort('input_file_2')
+
+ input_file_1 = self.getInputFromPort('input_file_1')
+ input_file_2 = self.getInputFromPort('input_file_2')
+
+ if self.hasInputFromPort('output_format'):
+ output_suffix = self.getInputFromPort('output_format')
+ else:
+ output_suffix = self.guess_input_format(input_file_2.name)
+
+ output_file = self.interpreter.filePool.create_file(output_suffix)
+
+ cmdline = [meshchoosepath,
+ input_file_1.name,
+ input_file_2.name,
+ output_file.name]
+ cmdline = ('%s ' * len(cmdline)) % tuple(cmdline)
+ print cmdline
+ result = os.system(cmdline)
+ if result != 0:
+ raise ModuleError(self, "execution failed")
+ self.setResult('output_file', output_file)
+
+def setpath(prefix):
+ global meshareapath
+ meshareapath = prefix + 'mesh_area'
+ global meshchoosepath
+ meshchoosepath = prefix + 'mesh_choose'
+
+def initialize(meshutilspath=None):
+ global _mesh_utils_path
+ if not meshutilspath:
+ print "Assuming mesh_utils are on path"
+ setpath('')
+ else:
+ print "Assuming mesh_utils are in '%s/'" % meshutilspath
+ setpath(meshutilspath+'/')
+ reg = core.modules.module_registry
+ reg.add_module(MeshArea)
+ reg.add_input_port(MeshArea, 'input_file',
+ core.modules.basic_modules.File)
+ reg.add_output_port(MeshArea, 'area',
+ core.modules.basic_modules.Float)
+
+ reg.add_module(MeshChoose)
+ reg.add_input_port(MeshChoose, 'input_file_1',
+ core.modules.basic_modules.File)
+ reg.add_input_port(MeshChoose, 'input_file_2',
+ core.modules.basic_modules.File)
+ reg.add_input_port(MeshChoose, 'output_format',
+ core.modules.basic_modules.String)
+
+ reg.add_output_port(MeshChoose, 'output_file',
+ core.modules.basic_modules.File)
+
+
+
+
diff --git a/contrib/mobile/__init__.py b/contrib/mobile/__init__.py
new file mode 100644
index 0000000..4d191e2
--- /dev/null
+++ b/contrib/mobile/__init__.py
@@ -0,0 +1,365 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+"""This package provides interaction with mobile devices.
+It contains modules to represent a geolocation, to get an image and a sound memo.
+Executing on a desktop will do nothing for now.
+
+"""
+import base64
+from datetime import datetime
+
+from core.configuration import ConfigurationObject
+from core.modules.vistrails_module import Module, ModuleError
+from core.modules.basic_modules import Constant, Float, File, String
+from core.system import get_elementtree_library
+
+from time import strptime
+from datetime import datetime
+
+ElementTree = get_elementtree_library()
+
+name = "Mobile"
+identifier = "edu.utah.sci.vistrails.mobile"
+version = '0.0.1'
+
+class LocationCoordinate2D(Constant):
+ """A structure that contains a geographical coordinate using the
+ WGS 84 reference frame."""
+ def __init__(self):
+ Constant.__init__(self)
+ self.latitude = None
+ self.longitude = None
+ LocationCoordinate2D.default_value = self
+
+ @staticmethod
+ def from_xml_string(xml_string):
+ node = ElementTree.fromstring(xml_string)
+ if node.tag != 'coordinate':
+ return None
+ #read attributes
+ data = node.get('latitude', None)
+ lati = float(data)
+
+ data = node.get('longitude', None)
+ longi = float(data)
+
+ coord = LocationCoordinate2D()
+ coord.latitude = lati
+ coord.longitude = longi
+ return coord
+
+ @staticmethod
+ def to_xml_string(x):
+ node = ElementTree.Element('coordinate')
+ node.set('latitude', str(x.latitude))
+ node.set('longitude', str(x.longitude))
+ return ElementTree.tostring(node)
+
+ @staticmethod
+ def translate_to_python(x):
+ result = LocationCoordinate2D.from_xml_string(x)
+ result.setResult("value", result)
+ return result
+
+ @staticmethod
+ def translate_to_string(x):
+ return LocationCoordinate2D.to_xml_string(x)
+
+ def compute(self):
+ if self.hasInputFromPort("value"):
+ data = self.getInputFromPort("value")
+ self.latitude = data.latitude
+ self.longitude = data.longitude
+
+ if self.latitude is None or self.longitude is None:
+ self.checkInputPort("latitude")
+ self.checkInputPort("longitude")
+ self.latitude = self.getInputFromPort("latitude")
+ self.longitude = self.getInputFromPort("longitude")
+ self.setResult("value", self)
+ self.setResult("value_as_string", self.translate_to_string(self))
+
+ @classmethod
+ def provide_input_port_documentation(cls, port_name):
+ if port_name == "latitude":
+ return """The latitude in degrees.
+Positive values indicate latitudes north of the equator.
+Negative values indicate latitudes south of the equator."""
+ elif port_name == "longitude":
+ return """The longitude in degrees.
+Measurements are relative to the zero meridian with positive values extending
+east of the meridian and negative values extending west of the meridian."""
+
+LocationCoordinate2D._input_ports = [('value', LocationCoordinate2D),
+ ('latitude', Float, True),
+ ('longitude', Float, True)]
+
+LocationCoordinate2D._output_ports = [('value', LocationCoordinate2D)]
+
+class Location(Constant):
+ """This class represents the geographical coordinates and altitude of the
+ device's location along with values indicating the accuracy of the
+ measurements and when those measurements were made. In devices with a GPS,
+ this class also reports information about the speed and heading in which
+ the device is moving."""
+ def __init__(self):
+ Constant.__init__(self)
+ self.coordinate = None
+ self.altitude = None
+ self.horizontal_accuracy = None
+ self.vertical_accuracy = None
+ self.timestamp = None
+ self.speed = None
+ self.course = None
+ Location.default_value = self
+
+ @staticmethod
+ def from_xml_string(xml_string):
+ node = ElementTree.fromstring(xml_string)
+ if node.tag != 'location':
+ return None
+ #read attributes
+ data = node.get('altitude', None)
+ alti = float(data)
+
+ data = node.get('horizontalAccuracy', None)
+ hAcc = float(data)
+
+ data = node.get('verticalAccuracy', None)
+ vAcc = float(data)
+
+ data = node.get('timestamp', None)
+ timestamp = datetime(*strptime(data, '%Y-%m-%d %H:%M:%S')[0:6])
+
+ data = node.get('speed', None)
+ speed = float(data)
+
+ data = node.get('course', None)
+ course = float(data)
+
+ coord = None
+ for child in node.getchildren():
+ if child.tag == "coordinate":
+ text = ElementTree.tostring(child)
+ coord = LocationCoordinate2D.from_xml_string(text)
+
+ loc = Location()
+ loc.coordinate = coord
+ loc.altitude = alti
+ loc.horizontal_accuracy = hAcc
+ loc.vertical_accuracy = vAcc
+ loc.timestamp = timestamp
+ loc.speed = speed
+ loc.course = course
+
+ return loc
+
+ @staticmethod
+ def to_xml_string(x):
+ node = ElementTree.Element('location')
+ node.set('altitude', str(x.altitude))
+ node.set('horizontalAccuracy',str(x.horizontal_accuracy))
+ node.set('verticalAccuracy',str(x.vertical_accuracy))
+ node.set('timestamp', x.timestamp.strftime('%Y-%m-%d %H:%M:%S'))
+ node.set('speed', str(x.speed))
+ node.set('course', str(x.course))
+
+ child_str = LocationCoordinate2D.to_xml_string(x.coordinate)
+ child = ElementTree.fromstring(child_str)
+ node.append(child)
+
+ return ElementTree.tostring(node)
+
+ @staticmethod
+ def translate_to_python(x):
+ result = Location.from_xml_string(x)
+ result.setResult("value", result)
+ return result
+
+ @staticmethod
+ def translate_to_string(x):
+ return Location.to_xml_string(x)
+
+ def compute(self):
+ if self.hasInputFromPort("value"):
+ data = self.getInputFromPort("value")
+ self.coordinate = data.coordinate
+ self.altitude = data.altitude
+ self.horizontal_accuracy = data.horizontal_accuracy
+ self.vertical_accuracy = data.vertical_accuracy
+ self.timestamp = data.timestamp
+ self.speed = data.speed
+ self.course = data.course
+
+ if self.coordinate is None or self.altitude is None:
+ self.checkInputPort("coordinate")
+ self.checkInputPort("altitude")
+ self.coordinate = self.getInputFromPort("coordinate")
+ self.altitude = self.getInputFromPort("altitude")
+
+ #check optional ports
+ if self.hasInputFromPort("horizontalAccuracy"):
+ self.horizontal_accuracy = \
+ self.getInputFromPort("horizontalAccuracy")
+
+ if self.hasInputFromPort("verticalAccuracy"):
+ self.vertical_accuracy = \
+ self.getInputFromPort("verticalAccuracy")
+
+ if self.hasInputFromPort("timestamp"):
+ data = self.getInputFromPort("timestamp")
+ self.timestamp = \
+ datetime(*strptime(data, '%Y-%m-%d %H:%M:%S')[0:6])
+ if self.hasInputFromPort("speed"):
+ self.speed = self.getInputFromPort("speed")
+
+ if self.hasInputFromPort("course"):
+ self.course = self.getInputFromPort("course")
+
+ self.setResult("value", self)
+ self.setResult("value_as_string", self.translate_to_string(self))
+
+ @classmethod
+ def provide_input_port_documentation(cls, port_name):
+ if port_name == "coordinate":
+ return """The geographical coordinate information
+(latitude and longitude)."""
+ elif port_name == "altitude":
+ return """The altitude in meters.
+Positive values indicate altitudes above sea level.
+Negative values indicate altitudes below sea level."""
+ elif port_name == "horizontalAccuracy":
+ return """The radius of uncertainty for the location,
+measured in meters.
+The coordinate's latitude and longitude identify the center of the circle and
+this value indicates the radius of that circle. A negative value indicates
+that the coordinate's latitude and longitude are invalid."""
+ elif port_name == "verticalAccuracy":
+ return """The accuracy of the altitude value in meters.
+The value in the altitude port could be plus or minus the value indicated
+by this port. A negative value indicates that the altitude value is invalid.
+
+Determining the vertical accuracy requires a device with GPS capabilities.
+Thus, on some earlier iPhone OS-based devices, this property always contains a
+negative value."""
+ elif port_name == "timestamp":
+ return """The time at which this location was determined.
+Format: '%Y-%m-%d %H:%M:%S' """
+ elif port_name == "speed":
+ return """The instantaneous speed of the device in meters per second.
+This value reflects the instantaneous speed of the device in the direction of
+its current heading. A negative value indicates an invalid speed.
+Because the actual speed can change many times between the delivery of
+subsequent location events, you should use this property for informational
+purposes only."""
+ elif port_name == "course":
+ return """The direction in which the device is travelling.
+Course values are measured in degrees starting at due north and continuing
+clockwise around the compass. Thus, north is 0 degrees, east is 90 degrees,
+south is 180 degrees, and so on. Course values may not be available on all
+devices. A negative value indicates that the direction is invalid."""
+
+Location._input_ports = [('value', Location),
+ ('coordinate', LocationCoordinate2D, True),
+ ('altitude', Float, True),
+ ('horizontalAccuracy', Float, True),
+ ('verticalAccuracy', Float, True),
+ ('timestamp', String, True),
+ ('speed', Float, True),
+ ('course', Float, True)]
+
+Location._output_ports = [('value', Location)]
+
+class B64EncodedContents(Constant):
+ def __init__(self):
+ Constant.__init__(self)
+ self.contents = None
+ B64EncodedContents.default_value = self
+
+ @staticmethod
+ def translate_to_python(x):
+ result = B64EncodedContents()
+ result.contents = str(x)
+ result.setResult("value", result)
+ return result
+
+ @staticmethod
+ def translate_to_string(x):
+ return x.contents
+
+ def compute(self):
+ if self.hasInputFromPort("value"):
+ data = self.getInputFromPort("value")
+ self.contents = data.contents
+
+ if self.contents is None:
+ if self.hasInputFromPort("file"):
+ file_ = self.getInputFromPort("file")
+ c = open(file_.name)
+ self.contents = base64.b64encode(c.read())
+
+ self.setResult("value", self)
+ self.setResult("value_as_string", self.translate_to_string(self))
+
+B64EncodedContents._input_ports = [('value', B64EncodedContents),
+ ('contents', String, True),
+ ('file', File, True)]
+
+B64EncodedContents._output_ports = [('value', B64EncodedContents)]
+
+class Image(B64EncodedContents):
+ def __init__(self):
+ B64EncodedContents.__init__(self)
+ Image.default_value = self
+
+ @staticmethod
+ def translate_to_python(x):
+ result = Image()
+ result.contents = str(x)
+ result.setResult("value", result)
+ return result
+
+Image._input_ports = [('value', Image)]
+
+Image._output_ports = [('value', Image)]
+
+class Audio(B64EncodedContents):
+ def __init__(self):
+ B64EncodedContents.__init__(self)
+ Audio.default_value = self
+
+ @staticmethod
+ def translate_to_python(x):
+ result = Audio()
+ result.contents = str(x)
+ result.setResult("value", result)
+ return result
+
+Audio._input_ports = [('value', Audio)]
+
+Audio._output_ports = [('value', Audio)]
+
+_modules = [LocationCoordinate2D,
+ Location,
+ B64EncodedContents,
+ Image,
+ Audio]
diff --git a/contrib/pc3/__init__.py b/contrib/pc3/__init__.py
new file mode 100644
index 0000000..cad7b78
--- /dev/null
+++ b/contrib/pc3/__init__.py
@@ -0,0 +1,420 @@
+from core.modules.basic_modules import String, Boolean, File, Integer
+from core.modules.module_registry import get_module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from core.upgradeworkflow import UpgradeWorkflowHandler
+
+from info.ipaw.pc3.LoadAppLogic import LoadAppLogic
+
+import os
+
+name = "Provenance Challenge 3"
+identifier = "edu.utah.sci.dakoop.pc3"
+version = '1.0.1'
+
+# class Module(object):
+# pass
+
+# class String(Module):
+# pass
+
+# class Boolean(Module):
+# pass
+
+# class Integer(Module):
+# pass
+
+class Collection(Module):
+ def __init__(self, lst, klass=None):
+ Module.__init__(self)
+ self.lst = lst
+ self.klass = klass
+
+ def compute(self):
+ self.lst = self.forceGetInputListFromPort('elements')
+ self.setResult('collection', self.list)
+
+ _input_ports = [('elements', Module)]
+ _output_ports = []
+ # _output_ports = [('self', Collection)]
+Collection._output_ports.append(('self', Collection))
+
+class CSVFileEntry(Module):
+ def __init__(self, file_entry=None):
+ Module.__init__(self)
+ if file_entry is not None:
+ self.file_entry = file_entry
+ else:
+ self.file_entry = LoadAppLogic.CSVFileEntry()
+
+ def compute(self):
+ self.checkInputPort('filePath')
+ self.checkInputPort('headerPath')
+ self.checkInputPort('rowCount')
+ self.checkInputPort('targetTable')
+ self.checkInputPort('checksum')
+ self.checkInputPort('columnNames')
+ self.file_entry.FilePath = self.getInputFromPort('filePath')
+ self.file_entry.HeaderPath = self.getInputFromPort('headerPath')
+ self.file_entry.RowCount = self.getInputFromPort('rowCount')
+ self.file_entry.TargetTable = self.getInputFromPort('targetTable')
+ self.file_entry.Checksum = self.getInputFromPort('checksum')
+ self.file_entry.ColumnNames = self.getInputFromPort('columnNames').lst
+ self.setResult('self', self)
+
+ _input_ports = [('filePath', String),
+ ('headerPath', String),
+ ('rowCount', Integer),
+ ('targetTable', String),
+ ('checksum', String),
+ ('columnNames', Collection)]
+ _output_ports = []
+ # _output_ports = [('self', CSVFileEntry)]
+CSVFileEntry._output_ports.append(('self', CSVFileEntry))
+
+class DatabaseEntry(Module):
+ def __init__(self, db_entry=None):
+ Module.__init__(self)
+ if db_entry is not None:
+ self.db_entry = db_entry
+ else:
+ self.db_entry = LoadAppLogic.DatabaseEntry()
+
+ def compute(self):
+ self.checkInputPort('dbGuid')
+ self.checkInputPort('dbName')
+ self.checkInputPort('connectionString')
+ self.db_entry.DBGuid = self.getInputFromPort('dbGuid')
+ self.db_entry.DBName = self.getInputFromPort('dbName')
+ self.db_entry.ConnectionString = \
+ self.getInputFromPort('connectionString')
+ self.setResult('self', self)
+
+ _input_ports = [('dbGuid', String),
+ ('dbName', String),
+ ('connectionString', String)]
+ _output_ports = []
+ # _output_ports = [('self', DatabaseEntry)]
+DatabaseEntry._output_ports.append(('self', DatabaseEntry))
+
+class IsCSVReadyFileExists(Module):
+ def compute(self):
+ self.checkInputPort('csvRootPath')
+ path = self.getInputFromPort('csvRootPath')
+ res = LoadAppLogic.IsCSVReadyFileExists(path)
+ self.setResult('fileExists', res)
+
+ _input_ports = [('csvRootPath', String)]
+ _output_ports = [('fileExists', Boolean)]
+
+class ReadCSVReadyFile(Module):
+ def compute(self):
+ self.checkInputPort('csvRootPath')
+ path = self.getInputFromPort('csvRootPath')
+ self.annotate({'used_files':
+ str([os.path.join(path, "csv_ready.csv")])})
+ csv_files = LoadAppLogic.ReadCSVReadyFile(path)
+ # wrapped_res = Collection([CSVFileEntry(e) for e in res], CSVFileEntry)
+ list_of_elts = [CSVFileEntry(f) for f in csv_files]
+ for elt in list_of_elts:
+ elt.upToDate = True
+ self.setResult('csvFiles', list_of_elts)
+
+ _input_ports = [('csvRootPath', String)]
+ # _output_ports = [('csvFiles', [Collection, CSVFileEntry])]
+ _output_ports = [('csvFiles',
+ '(edu.utah.sci.vistrails.basic:List)')]
+
+class IsMatchCSVFileTables(Module):
+ def compute(self):
+ self.checkInputPort('csvFiles')
+ csv_files = self.getInputFromPort('csvFiles')
+ res = LoadAppLogic.IsMatchCSVFileTables([f.file_entry
+ for f in csv_files])
+ self.setResult('tablesMatch', res)
+
+ # _input_ports = [('csvFiles', [Collection, CSVFileEntry])]
+ _input_ports = [('csvFiles',
+ '(edu.utah.sci.vistrails.basic:List)')]
+ _output_ports = [('tablesMatch', Boolean)]
+
+class IsExistsCSVFile(Module):
+ def compute(self):
+ self.checkInputPort('csvFile')
+ csv_file = self.getInputFromPort('csvFile')
+ res = LoadAppLogic.IsExistsCSVFile(csv_file.file_entry)
+ self.setResult('fileExists', res)
+
+ _input_ports = [('csvFile', CSVFileEntry)]
+ _output_ports = [('fileExists', Boolean)]
+
+class ReadCSVFileColumnNames(Module):
+ def compute(self):
+ self.checkInputPort('csvFile')
+ csv_file = self.getInputFromPort('csvFile')
+ self.annotate({'used_files':
+ str([csv_file.file_entry.HeaderPath])})
+ res = LoadAppLogic.ReadCSVFileColumnNames(csv_file.file_entry)
+ self.setResult('csvFile', CSVFileEntry(res))
+
+ _input_ports = [('csvFile', CSVFileEntry)]
+ _output_ports = [('csvFile', CSVFileEntry)]
+
+class IsMatchCSVFileColumnNames(Module):
+ def compute(self):
+ self.checkInputPort('csvFile')
+ csv_file = self.getInputFromPort('csvFile')
+ res = LoadAppLogic.IsMatchCSVFileColumnNames(csv_file.file_entry)
+ self.setResult('columnsMatch', res)
+
+ _input_ports = [('csvFile', CSVFileEntry)]
+ _output_ports = [('columnsMatch', Boolean)]
+
+class CreateEmptyLoadDB(Module):
+ def compute(self):
+ self.checkInputPort('jobID')
+ job_id = self.getInputFromPort('jobID')
+ res = LoadAppLogic.CreateEmptyLoadDB(job_id)
+ self.setResult('dbEntry', DatabaseEntry(res))
+
+ _input_ports = [('jobID', String)]
+ _output_ports = [('dbEntry', DatabaseEntry)]
+
+class LoadCSVFileIntoTable(Module):
+ def compute(self):
+ self.checkInputPort('csvFile')
+ self.checkInputPort('dbEntry')
+ csv_file = self.getInputFromPort('csvFile')
+ db_entry = self.getInputFromPort('dbEntry')
+ self.annotate({'used_files':
+ str([csv_file.file_entry.FilePath]),
+ 'generated_tables':
+ str([(db_entry.db_entry.ConnectionString,
+ db_entry.db_entry.DBName,
+ csv_file.file_entry.TargetTable)])})
+ res = LoadAppLogic.LoadCSVFileIntoTable(db_entry.db_entry,
+ csv_file.file_entry)
+ self.setResult('success', res)
+
+ _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
+ _output_ports = [('success', Boolean)]
+
+class UpdateComputedColumns(Module):
+ def compute(self):
+ self.checkInputPort('csvFile')
+ self.checkInputPort('dbEntry')
+ csv_file = self.getInputFromPort('csvFile')
+ db_entry = self.getInputFromPort('dbEntry')
+ if csv_file.file_entry.TargetTable.upper() == 'P2DETECTION':
+ self.annotate({'used_tables':
+ str([(db_entry.db_entry.ConnectionString,
+ db_entry.db_entry.DBName,
+ csv_file.file_entry.TargetTable)])})
+ res = LoadAppLogic.UpdateComputedColumns(db_entry.db_entry,
+ csv_file.file_entry)
+ self.setResult('success', res)
+
+ _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
+ _output_ports = [('success', Boolean)]
+
+class IsMatchTableRowCount(Module):
+ def compute(self):
+ self.checkInputPort('csvFile')
+ self.checkInputPort('dbEntry')
+ csv_file = self.getInputFromPort('csvFile')
+ db_entry = self.getInputFromPort('dbEntry')
+ self.annotate({'used_tables':
+ str([(db_entry.db_entry.ConnectionString,
+ db_entry.db_entry.DBName,
+ csv_file.file_entry.TargetTable)])})
+ res = LoadAppLogic.IsMatchTableRowCount(db_entry.db_entry,
+ csv_file.file_entry)
+ self.setResult('countsMatch', res)
+
+ _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
+ _output_ports = [('countsMatch', Boolean)]
+
+class IsMatchTableColumnRanges(Module):
+ def compute(self):
+ self.checkInputPort('csvFile')
+ self.checkInputPort('dbEntry')
+ csv_file = self.getInputFromPort('csvFile')
+ db_entry = self.getInputFromPort('dbEntry')
+ if csv_file.file_entry.TargetTable.upper() == 'P2DETECTION':
+ self.annotate({'used_tables':
+ str([(db_entry.db_entry.ConnectionString,
+ db_entry.db_entry.DBName,
+ csv_file.file_entry.TargetTable)])})
+ res = LoadAppLogic.IsMatchTableColumnRanges(db_entry.db_entry,
+ csv_file.file_entry)
+ self.setResult('rangesMatch', res)
+
+ _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
+ _output_ports = [('rangesMatch', Boolean)]
+
+class CompactDatabase(Module):
+ def compute(self):
+ self.checkInputPort('dbEntry')
+ db_entry = self.getInputFromPort('dbEntry')
+ self.annotate({'used_tables':
+ str([(db_entry.db_entry.ConnectionString,
+ db_entry.db_entry.DBName,
+ "P2Detection"),
+ (db_entry.db_entry.ConnectionString,
+ db_entry.db_entry.DBName,
+ "P2FrameMeta"),
+ (db_entry.db_entry.ConnectionString,
+ db_entry.db_entry.DBName,
+ "P2ImageMeta")])})
+ LoadAppLogic.CompactDatabase(db_entry.db_entry)
+ self.setResult('dbEntry', db_entry)
+
+
+ _input_ports = [('dbEntry', DatabaseEntry)]
+ _output_ports = [('dbEntry', DatabaseEntry)]
+
+class GetCSVFiles(Module):
+ def compute(self):
+ self.checkInputPort('csvRootPath')
+ path = self.getInputFromPort('csvRootPath')
+ if not LoadAppLogic.IsCSVReadyFileExists(path):
+ raise ModuleError(self, "IsCSVReadyFileExists failed")
+ self.annotate({'used_files':
+ str([os.path.join(path, "csv_ready.csv")])})
+ csv_files = LoadAppLogic.ReadCSVReadyFile(path)
+ if not LoadAppLogic.IsMatchCSVFileTables(csv_files):
+ raise ModuleError(self, "IsMatchCSVFileTables failed")
+# getter = get_module_registry().get_descriptor_by_name
+# descriptor = getter('edu.utah.sci.vistrails.basic',
+# 'List')
+# list_of_elts = descriptor.module()
+# list_of_elts.value = [CSVFileEntry(f) for f in csv_files]
+# self.setResult('csvFiles', list_of_elts)
+ list_of_elts = [CSVFileEntry(f) for f in csv_files]
+ for elt in list_of_elts:
+ elt.upToDate = True
+ print 'list_of_elts:', list_of_elts
+ self.setResult('csvFiles', list_of_elts)
+# wrapped_res = Collection([CSVFileEntry(f) for f in csv_files],
+# CSVFileEntry)
+# self.setResult('csvFiles', wrapped_res)
+
+ _input_ports = [('csvRootPath', String)]
+ _output_ports = [('csvFiles',
+ '(edu.utah.sci.vistrails.basic:List)')]
+ # _output_ports = [('csvFiles', [Collection, CSVFileEntry])]
+
+class ReadCSVFile(Module):
+ def compute(self):
+ self.checkInputPort('csvFile')
+ csv_file = self.getInputFromPort('csvFile')
+ if not LoadAppLogic.IsExistsCSVFile(csv_file.file_entry):
+ raise ModuleError(self, "IsExistsCSVFile failed")
+ self.annotate({'used_files':
+ str([csv_file.file_entry.HeaderPath])})
+ csv_file.file_entry = \
+ LoadAppLogic.ReadCSVFileColumnNames(csv_file.file_entry)
+ if not LoadAppLogic.IsMatchCSVFileColumnNames(csv_file.file_entry):
+ raise ModuleError(self, "IsMatchCSVFileColumnNames failed")
+ self.setResult('csvFile', csv_file)
+
+ _input_ports = [('csvFile', CSVFileEntry)]
+ _output_ports = [('csvFile', CSVFileEntry)]
+
+class LoadCSVFileIntoDB(Module):
+ def compute(self):
+ self.checkInputPort('csvFile')
+ self.checkInputPort('dbEntry')
+ csv_file = self.getInputFromPort('csvFile')
+ print 'csv_file:', csv_file
+ db_entry = self.getInputFromPort('dbEntry')
+ self.annotate({'used_files':
+ str([csv_file.file_entry.FilePath])})
+ self.annotate({'generated_tables':
+ str([(db_entry.db_entry.ConnectionString,
+ db_entry.db_entry.DBName,
+ csv_file.file_entry.TargetTable)])})
+ if not LoadAppLogic.LoadCSVFileIntoTable(db_entry.db_entry,
+ csv_file.file_entry):
+ raise ModuleError(self, "LoadCSVFileIntoTable failed")
+ self.setResult('dbEntry', db_entry)
+
+ _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
+ _output_ports = [('dbEntry', DatabaseEntry)]
+
+class ComputeColumns(Module):
+ def compute(self):
+ self.checkInputPort('csvFile')
+ self.checkInputPort('dbEntry')
+ csv_file = self.getInputFromPort('csvFile')
+ db_entry = self.getInputFromPort('dbEntry')
+ self.annotate({'used_tables':
+ str([(db_entry.db_entry.ConnectionString,
+ db_entry.db_entry.DBName,
+ csv_file.file_entry.TargetTable)])})
+ if not LoadAppLogic.UpdateComputedColumns(db_entry.db_entry,
+ csv_file.file_entry):
+ raise ModuleError(self, "UpdateComputedColumns failed")
+ if not LoadAppLogic.IsMatchTableRowCount(db_entry.db_entry,
+ csv_file.file_entry):
+ raise ModuleError(self, "IsMatchTableRowCount failed")
+ if not LoadAppLogic.IsMatchTableColumnRanges(db_entry.db_entry,
+ csv_file.file_entry):
+ raise ModuleError(self, "IsMatchTableColumnRanges failed")
+ self.setResult('dbEntry', db_entry)
+
+ _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
+ _output_ports = [('dbEntry', DatabaseEntry)]
+
+class DetectionsHistogram(Module):
+ def compute(self):
+ self.checkInputPort('dbEntry')
+ db_entry = self.getInputFromPort('dbEntry')
+ high_quality = False
+ if self.hasInputFromPort('highQuality'):
+ high_quality = self.getInputFromPort('highQuality')
+ self.annotate({'used_tables':
+ str([(db_entry.db_entry.ConnectionString,
+ db_entry.db_entry.DBName,
+ "P2Detection")])})
+ histogram = LoadAppLogic.DetectionsHistogram(db_entry.db_entry,
+ high_quality)
+ self.setResult('histogram', histogram)
+
+ _input_ports = [('dbEntry', DatabaseEntry), ('highQuality', Boolean, True)]
+ _output_ports = [('histogram',
+ '(edu.utah.sci.vistrails.basic:List)')]
+
+_modules = [Collection,
+ CSVFileEntry,
+ DatabaseEntry,
+ IsCSVReadyFileExists,
+ ReadCSVReadyFile,
+ IsMatchCSVFileTables,
+ IsExistsCSVFile,
+ ReadCSVFileColumnNames,
+ IsMatchCSVFileColumnNames,
+ CreateEmptyLoadDB,
+ LoadCSVFileIntoTable,
+ UpdateComputedColumns,
+ IsMatchTableRowCount,
+ IsMatchTableColumnRanges,
+ CompactDatabase,
+ GetCSVFiles,
+ ReadCSVFile,
+ LoadCSVFileIntoDB,
+ ComputeColumns,
+ DetectionsHistogram,
+ ]
+
+def package_dependencies():
+ return ['edu.utah.sci.vistrails.control_flow']
+
+def handle_module_upgrade_request(controller, module_id, pipeline):
+ module_remap = {'ReadCSVReadyFile': [(None, '1.0.1', None, {})],
+ 'IsMatchCSVFileTables': [(None, '1.0.1', None, {})],
+ 'GetCSVFiles': [(None, '1.0.1', None, {})],
+ 'DetectionsHistogram': [(None, '1.0.1', None, {})],
+ }
+
+ return UpgradeWorkflowHandler.remap_module(controller, module_id, pipeline,
+ module_remap)
diff --git a/contrib/pc3/info/__init__.py b/contrib/pc3/info/__init__.py
new file mode 100644
index 0000000..2ae2839
--- /dev/null
+++ b/contrib/pc3/info/__init__.py
@@ -0,0 +1 @@
+pass
diff --git a/contrib/pc3/info/ipaw/__init__.py b/contrib/pc3/info/ipaw/__init__.py
new file mode 100644
index 0000000..2ae2839
--- /dev/null
+++ b/contrib/pc3/info/ipaw/__init__.py
@@ -0,0 +1 @@
+pass
diff --git a/contrib/pc3/info/ipaw/pc3/LoadAppLogic.py b/contrib/pc3/info/ipaw/pc3/LoadAppLogic.py
new file mode 100644
index 0000000..a85a563
--- /dev/null
+++ b/contrib/pc3/info/ipaw/pc3/LoadAppLogic.py
@@ -0,0 +1,441 @@
+import MySQLdb
+import os
+import uuid
+
+from LoadConstants import LoadConstants
+from LoadSql import LoadSql
+
+class LoadAppLogic(object):
+
+ #region Database Constants
+ SQL_SERVER = "localhost"
+ SQL_USER = "ipaw"
+ SQL_PASSWORD = "pc3_load-2009"
+ #endregion
+
+ #region Helper data structures
+ class CSVFileEntry(object):
+ def __init__(self):
+ self.FilePath = None
+ self.HeaderPath = None
+ self.RowCount = None
+ self.TargetTable = None
+ self.Checksum = None
+ self.ColumnNames = []
+
+ class DatabaseEntry(object):
+ def __init__(self):
+ self.DBGuid = None
+ self.DBName = None
+ self.ConnectionString = None
+ #endregion
+
+ #region Pre-Load Sanity Checks
+
+ @staticmethod
+ def IsCSVReadyFileExists(CSVRootPath):
+ """<summary>
+ Checks if the CSV Ready File exists in the given rooth path to the
+ CSV Batch
+ </summary>
+ <param name="CSVRootPath">Path to the root directory for the batch
+ </param>
+ <returns>true if the csv_ready.csv file exists in the CSVRoothPath.
+ False otherwise.</returns>
+ """
+
+ # 1. Check if parent directory exists.
+ if not os.path.exists(CSVRootPath):
+ return False
+
+ # 2. Check if CSV Ready file exists. We assume a static name for the ready file.
+ CSVReadyFilePath = os.path.join(CSVRootPath, "csv_ready.csv")
+ return os.path.exists(CSVReadyFilePath)
+
+ @staticmethod
+ def ReadCSVReadyFile(CSVRootPath):
+ """<summary>
+
+ </summary>
+ <param name="CSVRootPath"></param>
+ <returns></returns>
+ """
+
+ # 1. Initialize output list of file entries
+ CSVFileEntryList = []
+
+ # 2. Open input stream to read from CSV Ready File
+ CSVReadyFilePath = os.path.join(CSVRootPath, "csv_ready.csv")
+ ReadyFileStream = open(CSVReadyFilePath);
+
+ # 3. Read each line in CSV Ready file and split the lines into
+ # individual columns separated by commas
+ for ReadyFileLine in ReadyFileStream:
+
+ # 3.a. Expect each line in the CSV ready file to be of the format:
+ # <FileName>,<NumRows>,<TargetTable>,<MD5Checksum>
+ ReadyFileLineTokens = ReadyFileLine.split(',')
+
+ # 3.b. Create an empty FileEntry and populate it with the columns
+ FilePath = os.path.join(CSVRootPath,
+ ReadyFileLineTokens[0].strip())
+
+ # CSVFileEntry FileEntry = new CSVFileEntry();
+ FileEntry = LoadAppLogic.CSVFileEntry()
+ FileEntry.FilePath = FilePath
+ FileEntry.HeaderPath = FilePath + ".hdr"
+ FileEntry.RowCount = int(ReadyFileLineTokens[1].strip())
+ FileEntry.TargetTable = ReadyFileLineTokens[2].strip()
+ FileEntry.Checksum = ReadyFileLineTokens[3].strip()
+
+ # 3.c. Add file entry to output list
+ CSVFileEntryList.append(FileEntry);
+
+ # 4. Close input stream and return output file entry list
+ ReadyFileStream.close();
+
+ return CSVFileEntryList;
+
+ @staticmethod
+ def IsMatchCSVFileTables(FileEntries):
+ """<summary>
+ Check if the correct list of files/table names are present in this batch
+ </summary>
+ <param name="FileEntries"></param>
+ <returns></returns>
+ """
+
+ # check if the file count and the expected number of tables match
+ if (len(LoadConstants.EXPECTED_TABLES) != len(FileEntries)):
+ return false;
+
+ # for each expected table name, check if it is present
+ # in the list of file entries
+ for TableName in LoadConstants.EXPECTED_TABLES:
+ TableExists = False
+ for FileEntry in FileEntries:
+ if TableName == FileEntry.TargetTable:
+ TableExists = True
+ break
+
+ # if the table name did not exist in list of CSV files,
+ # this check fails.
+ if not TableExists:
+ return False
+
+ return True
+
+ @staticmethod
+ def IsExistsCSVFile(FileEntry):
+ """<summary>
+ Test if a CSV File defined in the CSV Ready list actually exists on disk.
+ </summary>
+ <param name="FileEntry">FileEntry for CSVFile to test</param>
+ <returns>True if the FilePath in the given FileEntry exists on disk. False otherwise.</returns>
+ """
+ if not os.path.exists(FileEntry.FilePath):
+ return False
+
+ return os.path.exists(FileEntry.HeaderPath)
+
+ @staticmethod
+ def ReadCSVFileColumnNames (FileEntry):
+ """<summary>
+
+ </summary>
+ <param name="FileEntry"></param>
+ <param name="FileEntry"></param>
+ <returns></returns>
+ """
+
+ # 2. Read the header line of the CSV File.
+ CSVFileReader = open(FileEntry.HeaderPath)
+ HeaderRow = CSVFileReader.readline()
+
+ # 3. Extract the comma-separated columns names of the CSV File from its header line.
+ # Strip empty spaces around column names.
+ ColumnNames = HeaderRow.split(',')
+ FileEntry.ColumnNames = []
+ for ColumnName in ColumnNames:
+ FileEntry.ColumnNames.append(ColumnName.strip())
+
+ CSVFileReader.close()
+
+ return FileEntry
+
+ @staticmethod
+ def IsMatchCSVFileColumnNames(FileEntry):
+ """<summary>
+ Checks if the correct list of column headers is present for the CSV file
+ to match the table
+ </summary>
+ <param name="FileEntry">FileEntry for CSV File whose column headers to test</param>
+ <returns>True if the column headers present in the CSV File are the same as the
+ expected table columns. False otherwise.</returns>
+ """
+
+ # determine expected columns
+ ExpectedColumns = None
+
+ ExpectedColumnsLookup = {"P2DETECTION": \
+ LoadConstants.EXPECTED_DETECTION_COLS,
+ "P2FRAMEMETA": \
+ LoadConstants.EXPECTED_FRAME_META_COLS,
+ "P2IMAGEMETA": \
+ LoadConstants.EXPECTED_IMAGE_META_COLS,
+ }
+ if FileEntry.TargetTable.upper() in ExpectedColumnsLookup:
+ ExpectedColumns = \
+ ExpectedColumnsLookup[FileEntry.TargetTable.upper()]
+ else:
+ return False
+
+ # test if the expected and present column name counts are the same
+ if len(ExpectedColumns) != len(FileEntry.ColumnNames):
+ return False
+
+ # test of all expected names exist in the columns present
+ for ColumnName in ExpectedColumns:
+ if ColumnName not in FileEntry.ColumnNames:
+ return False
+
+ # all columns match
+ return True;
+ #endregion
+
+ #region Loading Section
+ @staticmethod
+ def CreateEmptyLoadDB(JobID):
+ """<summary>
+
+ </summary>
+ <param name="JobID"></param>
+ <returns></returns>
+ """
+
+ # initialize database entry for storing database properties
+ DBEntry = LoadAppLogic.DatabaseEntry()
+ DBEntry.DBName = JobID + "_LoadDB"
+ DBEntry.DBGuid = str(uuid.uuid4())
+ DBEntry.ConnectionString = {'host': LoadAppLogic.SQL_SERVER,
+ 'user': LoadAppLogic.SQL_USER,
+ 'passwd': LoadAppLogic.SQL_PASSWORD,
+ }
+
+ # initialize Sql Connection String to sql server
+ SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
+
+ # Create empty database instance
+ SqlCur = SqlConn.cursor()
+ SqlCur.execute("CREATE DATABASE " + DBEntry.DBName)
+ DBEntry.ConnectionString['db'] = DBEntry.DBName
+
+ # update Sql Connection String to new create tables
+ SqlCur = SqlConn.cursor()
+ SqlCur.execute("use %s" % DBEntry.DBName)
+ SqlCur.execute(LoadSql.CREATE_DETECTION_TABLE)
+ SqlCur.execute(LoadSql.CREATE_FRAME_META_TABLE)
+ SqlCur.execute(LoadSql.CREATE_IMAGE_META_TABLE)
+ SqlCur.close()
+ SqlConn.close()
+
+ return DBEntry
+
+ # derby bulk load: SYSCS_UTIL.SYSCS_IMPORT_TABLE
+ @staticmethod
+ def LoadCSVFileIntoTable(DBEntry, FileEntry):
+ """<summary>
+ Loads a CSV File into an existing table using Sql BULK INSERT command
+ </summary>
+ <param name="DBEntry">Database into which to load the CSV file</param>
+ <param name="FileEntry">File to be bulk loaded into database table</param>
+ <returns>True if the bulk load ran without exceptions. False otherwise.</returns>
+ """
+ try:
+ # connect to database instance
+ SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
+ SqlCur = SqlConn.cursor()
+ # execute bulk insert command
+ SqlCur.execute(("LOAD DATA INFILE %%s INTO TABLE %s "
+ "FIELDS TERMINATED BY ','") % \
+ FileEntry.TargetTable,
+ (FileEntry.FilePath,))
+ SqlCur.close()
+ SqlConn.close()
+ except Exception, e:
+ # print e
+ # bulk insert failed
+ SqlCur.close()
+ SqlConn.close()
+ return False
+ # bulk insert success
+ return True
+
+ @staticmethod
+ def UpdateComputedColumns(DBEntry, FileEntry):
+ """<summary>
+
+ </summary>
+ <param name="DBEntry"></param>
+ <param name="FileEntry"></param>
+ """
+
+ def P2Detection(SqlCur):
+ # Update ZoneID
+ SqlCur.execute('UPDATE P2Detection '
+ 'SET zoneID = (`dec`+(90.0))/(0.0083333)')
+ # Update cx
+ SqlCur.execute('UPDATE P2Detection '
+ 'SET cx = (COS(RADIANS(`dec`))*COS(RADIANS(ra)))')
+ # Update cy
+ SqlCur.execute('UPDATE P2Detection '
+ 'SET cy = COS(RADIANS(`dec`))*SIN(RADIANS(ra))')
+ # Update cz
+ SqlCur.execute('UPDATE P2Detection '
+ 'SET cz = (SIN(RADIANS(`dec`)))')
+
+ def P2FrameMeta(SqlCur):
+ # No columns to be updated for FrameMeta
+ pass
+
+ def P2ImageMeta(SqlCur):
+ # No columns to be updated for ImageMeta
+ pass
+
+ TargetTableLookup = {"P2DETECTION": P2Detection,
+ "P2FRAMEMETA": P2FrameMeta,
+ "P2IMAGEMETA": P2ImageMeta,
+ }
+
+ try:
+ # connect to database instance
+ SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
+ SqlCur = SqlConn.cursor()
+ if FileEntry.TargetTable.upper() in TargetTableLookup:
+ TargetTableLookup[FileEntry.TargetTable.upper()](SqlCur)
+ else:
+ # none of the table types matches...invalid
+ SqlCur.close()
+ SqlConn.close()
+ return False
+
+ except Exception, e:
+ print e
+ # update column failed
+ SqlCur.close()
+ SqlConn.close()
+ return False
+ # update column success
+ return True
+
+ #endregion
+
+ #region Post-Load Checks
+ @staticmethod
+ def IsMatchTableRowCount(DBEntry, FileEntry):
+ """<summary>
+
+ </summary>
+ <param name="DBEntry"></param>
+ <param name="FileEntry"></param>
+ <returns></returns>
+ """
+
+ # does the number of rows expected match the number of rows loaded
+ SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
+ SqlCur = SqlConn.cursor()
+ # execute row count command
+ SqlCur.execute("SELECT COUNT(*) FROM %s" % FileEntry.TargetTable)
+ RowCount = SqlCur.fetchone()[0]
+ SqlCur.close()
+ SqlConn.close()
+ # check if row count matches expected row count
+ return RowCount == FileEntry.RowCount
+
+ @staticmethod
+ def IsMatchTableColumnRanges(DBEntry, FileEntry):
+ """<summary>
+
+ </summary>
+ <param name="DBEntry"></param>
+ <param name="FileEntry"></param>
+ <returns></returns>
+ """
+
+ # determine expected column ranges
+ ExpectedColumnRanges = None
+ ExpectedColumnRangesLookup = \
+ {"P2DETECTION": LoadConstants.EXPECTED_DETECTION_COL_RANGES,
+ "P2FRAMEMETA": [],
+ "P2IMAGEMETA": [],
+ }
+ if FileEntry.TargetTable.upper() in ExpectedColumnRangesLookup:
+ ExpectedColumnRanges = \
+ ExpectedColumnRangesLookup[FileEntry.TargetTable.upper()]
+ else:
+ # none of the table types matches...invalid
+ return False
+
+ # connect to database instance
+ SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
+ SqlCur = SqlConn.cursor()
+
+ # For each column in available list, test if rows in table fall
+ # outside expected range
+ for Column in ExpectedColumnRanges:
+ # build SQL command for error count
+ SqlCur.execute("SELECT COUNT(*) FROM %s "
+ "WHERE (%s < %s OR %s > %s) AND %s != -999" % \
+ (FileEntry.TargetTable, Column.ColumnName,
+ Column.MinValue, Column.ColumnName,
+ Column.MaxValue, Column.ColumnName))
+
+ ErrorCount = SqlCur.fetchone()[0]
+ if ErrorCount > 0:
+ print "ERROR COUNT", ErrorCount
+ SqlCur.close()
+ SqlConn.close()
+ return False
+
+ SqlCur.close()
+ SqlConn.close()
+
+ return True # no range errors found
+
+ @staticmethod
+ def CompactDatabase(DBEntry):
+ """<summary>
+
+ </summary>
+ <param name="DBEntry"></param>
+ """
+
+ # Shrink database instance
+ SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
+ SqlCur = SqlConn.cursor()
+
+ SqlCur.execute("SHOW TABLES")
+ SqlTables = SqlCur.fetchall()
+ for SqlTable in SqlTables:
+ SqlCur.execute("OPTIMIZE TABLE %s" % SqlTable)
+ SqlCur.close()
+ SqlConn.close()
+
+ #endregion
+
+ #region Histogram
+ @staticmethod
+ def DetectionsHistogram(DBEntry, HighQuality=False):
+ SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
+ SqlCur = SqlConn.cursor()
+ if HighQuality:
+ where_clause = "WHERE raErr < 0.1 and decErr < 0.05 "
+ else:
+ where_clause = ""
+
+ SqlCur.execute("SELECT ceiling(zoneId/10) as zoneGroup, "
+ "count(*) as detectionCount FROM P2Detection "
+ "%s"
+ "GROUP BY ceiling(zoneId/10) "
+ "ORDER BY ceiling(zoneId/10)" % where_clause)
+ return SqlCur.fetchall()
diff --git a/contrib/pc3/info/ipaw/pc3/LoadConstants.py b/contrib/pc3/info/ipaw/pc3/LoadConstants.py
new file mode 100644
index 0000000..f9b2928
--- /dev/null
+++ b/contrib/pc3/info/ipaw/pc3/LoadConstants.py
@@ -0,0 +1,19 @@
+
+
+
+class LoadConstants(object):
+ EXPECTED_TABLES = ["P2Detection", "P2FrameMeta", "P2ImageMeta"]
+ EXPECTED_DETECTION_COLS = ["objID", "detectID", "ippObjID", "ippDetectID", "filterID", "imageID", "obsTime", "xPos", "yPos", "xPosErr", "yPosErr", "instFlux", "instFluxErr", "psfWidMajor", "psfWidMinor", "psfTheta", "psfLikelihood", "psfCf", "infoFlag", "htmID", "zoneID", "assocDate", "modNum", "ra", "dec", "raErr", "decErr", "cx", "cy", "cz", "peakFlux", "calMag", "calMagErr", "calFlux", "calFluxErr", "calColor", "calColorErr", "sky", "skyErr", "sgSep", "dataRelease"]
+ EXPECTED_FRAME_META_COLS = ["frameID", "surveyID", "filterID", "cameraID", "telescopeID", "analysisVer", "p1Recip", "p2Recip", "p3Recip", "nP2Images", "astroScat", "photoScat", "nAstRef", "nPhoRef", "expStart", "expTime", "airmass", "raBore", "decBore"]
+ EXPECTED_IMAGE_META_COLS = ["imageID", "frameID", "ccdID", "photoCalID", "filterID", "bias", "biasScat", "sky", "skyScat", "nDetect", "magSat", "completMag", "astroScat", "photoScat", "nAstRef", "nPhoRef", "nx", "ny", "psfFwhm", "psfModelID", "psfSigMajor", "psfSigMinor", "psfTheta", "psfExtra1", "psfExtra2", "apResid", "dapResid", "detectorID", "qaFlags", "detrend1", "detrend2", "detrend3", "detrend4", "detrend5", "detrend6", "detrend7", "detrend8", "photoZero", "photoColor", "proje [...]
+
+ class ColumnRange(object):
+ def __init__(self, ColumnName_, MinValue_, MaxValue_):
+ self.ColumnName = ColumnName_
+ self.MinValue = MinValue_
+ self.MaxValue = MaxValue_
+
+ EXPECTED_DETECTION_COL_RANGES = [ColumnRange("ra", "0", "360"),
+ ColumnRange("\"dec\"", "-90", "90"),
+ ColumnRange("raErr", "-2000", "9"),
+ ColumnRange("decErr", "0", "9"),]
diff --git a/contrib/pc3/info/ipaw/pc3/LoadSql.py b/contrib/pc3/info/ipaw/pc3/LoadSql.py
new file mode 100644
index 0000000..7b16093
--- /dev/null
+++ b/contrib/pc3/info/ipaw/pc3/LoadSql.py
@@ -0,0 +1,147 @@
+class LoadSql(object):
+
+ CREATE_DETECTION_TABLE = \
+ """
+CREATE TABLE P2Detection(
+ `objID` bigint NOT NULL,
+ detectID bigint NOT NULL,
+ ippObjID bigint NOT NULL,
+ ippDetectID bigint NOT NULL,
+ filterID smallint NOT NULL,
+ imageID bigint NOT NULL,
+ obsTime float NOT NULL DEFAULT -999,
+ xPos real NOT NULL DEFAULT -999,
+ yPos real NOT NULL DEFAULT -999,
+ xPosErr real NOT NULL DEFAULT -999,
+ yPosErr real NOT NULL DEFAULT -999,
+ instFlux real NOT NULL DEFAULT -999,
+ instFluxErr real NOT NULL DEFAULT -999,
+ psfWidMajor real NOT NULL DEFAULT -999,
+ psfWidMinor real NOT NULL DEFAULT -999,
+ psfTheta real NOT NULL DEFAULT -999,
+ psfLikelihood real NOT NULL DEFAULT -999,
+ psfCf real NOT NULL DEFAULT -999,
+ infoFlag int NOT NULL DEFAULT -999,
+ htmID float NOT NULL DEFAULT -999,
+ zoneID float NOT NULL DEFAULT -999,
+ assocDate date NOT NULL DEFAULT '28881231',
+ modNum smallint NOT NULL DEFAULT 0,
+ ra float NOT NULL,
+ `dec` float NOT NULL,
+ raErr real NOT NULL DEFAULT 0,
+ decErr real NOT NULL DEFAULT 0,
+ cx float NOT NULL DEFAULT -999,
+ cy float NOT NULL DEFAULT -999,
+ cz float NOT NULL DEFAULT -999,
+ peakFlux real NOT NULL DEFAULT -999,
+ calMag real NOT NULL DEFAULT -999,
+ calMagErr real NOT NULL DEFAULT -999,
+ calFlux real NOT NULL DEFAULT -999,
+ calFluxErr real NOT NULL DEFAULT -999,
+ calColor real NOT NULL DEFAULT -999,
+ calColorErr real NOT NULL DEFAULT -999,
+ sky real NOT NULL DEFAULT -999,
+ skyErr real NOT NULL DEFAULT -999,
+ sgSep real NOT NULL DEFAULT -999,
+ dataRelease smallint NOT NULL,
+ CONSTRAINT PK_P2Detection_objID_detectID PRIMARY KEY
+(
+ `objID`,
+ detectID
+))
+"""
+
+ CREATE_FRAME_META_TABLE = \
+ """
+CREATE TABLE P2FrameMeta(
+ frameID int NOT NULL PRIMARY KEY,
+ surveyID smallint NOT NULL,
+ filterID smallint NOT NULL,
+ cameraID smallint NOT NULL,
+ telescopeID smallint NOT NULL,
+ analysisVer smallint NOT NULL,
+ p1Recip smallint NOT NULL DEFAULT -999,
+ p2Recip smallint NOT NULL DEFAULT -999,
+ p3Recip smallint NOT NULL DEFAULT -999,
+ nP2Images smallint NOT NULL DEFAULT -999,
+ astroScat real NOT NULL DEFAULT -999,
+ photoScat real NOT NULL DEFAULT -999,
+ nAstRef int NOT NULL DEFAULT -999,
+ nPhoRef int NOT NULL DEFAULT -999,
+ expStart float NOT NULL DEFAULT -999,
+ expTime real NOT NULL DEFAULT -999,
+ airmass real NOT NULL DEFAULT -999,
+ raBore float NOT NULL DEFAULT -999,
+ decBore float NOT NULL DEFAULT -999
+)
+"""
+
+ CREATE_IMAGE_META_TABLE = \
+ """
+CREATE TABLE P2ImageMeta(
+ imageID bigint NOT NULL PRIMARY KEY,
+ frameID int NOT NULL,
+ ccdID smallint NOT NULL,
+ photoCalID int NOT NULL,
+ filterID smallint NOT NULL,
+ bias real NOT NULL DEFAULT -999,
+ biasScat real NOT NULL DEFAULT -999,
+ sky real NOT NULL DEFAULT -999,
+ skyScat real NOT NULL DEFAULT -999,
+ nDetect int NOT NULL DEFAULT -999,
+ magSat real NOT NULL DEFAULT -999,
+ completMag real NOT NULL DEFAULT -999,
+ astroScat real NOT NULL DEFAULT -999,
+ photoScat real NOT NULL DEFAULT -999,
+ nAstRef int NOT NULL DEFAULT -999,
+ nPhoRef int NOT NULL DEFAULT -999,
+ nx smallint NOT NULL DEFAULT -999,
+ ny smallint NOT NULL DEFAULT -999,
+ psfFwhm real NOT NULL DEFAULT -999,
+ psfModelID int NOT NULL DEFAULT -999,
+ psfSigMajor real NOT NULL DEFAULT -999,
+ psfSigMinor real NOT NULL DEFAULT -999,
+ psfTheta real NOT NULL DEFAULT -999,
+ psfExtra1 real NOT NULL DEFAULT -999,
+ psfExtra2 real NOT NULL DEFAULT -999,
+ apResid real NOT NULL DEFAULT -999,
+ dapResid real NOT NULL DEFAULT -999,
+ detectorID smallint NOT NULL DEFAULT -999,
+ qaFlags int NOT NULL DEFAULT -999,
+ detrend1 bigint NOT NULL DEFAULT -999,
+ detrend2 bigint NOT NULL DEFAULT -999,
+ detrend3 bigint NOT NULL DEFAULT -999,
+ detrend4 bigint NOT NULL DEFAULT -999,
+ detrend5 bigint NOT NULL DEFAULT -999,
+ detrend6 bigint NOT NULL DEFAULT -999,
+ detrend7 bigint NOT NULL DEFAULT -999,
+ detrend8 bigint NOT NULL DEFAULT -999,
+ photoZero real NOT NULL DEFAULT -999,
+ photoColor real NOT NULL DEFAULT -999,
+ projection1 varchar(8000) NOT NULL DEFAULT '-999',
+ projection2 varchar(8000) NOT NULL DEFAULT '-999',
+ crval1 float NOT NULL DEFAULT -999,
+ crval2 float NOT NULL DEFAULT -999,
+ crpix1 float NOT NULL DEFAULT -999,
+ crpix2 float NOT NULL DEFAULT -999,
+ pc001001 float NOT NULL DEFAULT -999,
+ pc001002 float NOT NULL DEFAULT -999,
+ pc002001 float NOT NULL DEFAULT -999,
+ pc002002 float NOT NULL DEFAULT -999,
+ polyOrder int NOT NULL DEFAULT -999,
+ pca1x3y0 float NOT NULL DEFAULT -999,
+ pca1x2y1 float NOT NULL DEFAULT -999,
+ pca1x1y2 float NOT NULL DEFAULT -999,
+ pca1x0y3 float NOT NULL DEFAULT -999,
+ pca1x2y0 float NOT NULL DEFAULT -999,
+ pca1x1y1 float NOT NULL DEFAULT -999,
+ pca1x0y2 float NOT NULL DEFAULT -999,
+ pca2x3y0 float NOT NULL DEFAULT -999,
+ pca2x2y1 float NOT NULL DEFAULT -999,
+ pca2x1y2 float NOT NULL DEFAULT -999,
+ pca2x0y3 float NOT NULL DEFAULT -999,
+ pca2x2y0 float NOT NULL DEFAULT -999,
+ pca2x1y1 float NOT NULL DEFAULT -999,
+ pca2x0y2 float NOT NULL DEFAULT -999
+)
+"""
diff --git a/contrib/pc3/info/ipaw/pc3/LoadWorkflow.py b/contrib/pc3/info/ipaw/pc3/LoadWorkflow.py
new file mode 100644
index 0000000..97a71cb
--- /dev/null
+++ b/contrib/pc3/info/ipaw/pc3/LoadWorkflow.py
@@ -0,0 +1,112 @@
+from LoadAppLogic import LoadAppLogic
+
+class LoadWorkflow(object):
+ @staticmethod
+ def run(args):
+ JobID, CSVRootPath = args[1:3]
+
+
+ # /////////////////////////////////////
+ # ////// Batch Initialization //////
+ # /////////////////////////////////////
+
+ # 1. IsCSVReadyFileExists
+ IsCSVReadyFileExistsOutput = \
+ LoadAppLogic.IsCSVReadyFileExists(CSVRootPath)
+
+ # 2. Control Flow: Decision
+ if not IsCSVReadyFileExistsOutput:
+ raise Exception("IsCSVReadyFileExists failed")
+
+
+ # 3. ReadCSVReadyFile
+ ReadCSVReadyFileOutput = LoadAppLogic.ReadCSVReadyFile(CSVRootPath)
+
+
+ # 4. IsMatchCSVFileTables
+ IsMatchCSVFileTablesOutput = \
+ LoadAppLogic.IsMatchCSVFileTables(ReadCSVReadyFileOutput)
+ # 5. Control Flow: Decision
+ if not IsMatchCSVFileTablesOutput:
+ raise Exception("IsMatchCSVFileTables failed")
+
+
+ # 6. CreateEmptyLoadDB
+ CreateEmptyLoadDBOutput = LoadAppLogic.CreateEmptyLoadDB(JobID)
+
+
+ # 7. Control Flow: Loop. ForEach LoadAppLogic.CSVFileEntry
+ # in ReadCSVReadyFileOutput Do...
+ for FileEntry in ReadCSVReadyFileOutput:
+
+ # /////////////////////////////////////
+ # ////// Pre Load Validation //////
+ # /////////////////////////////////////
+ # 7.a. IsExistsCSVFile
+ IsExistsCSVFileOutput = LoadAppLogic.IsExistsCSVFile(FileEntry)
+ # 7.b. Control Flow: Decision
+ if not IsExistsCSVFileOutput:
+ raise Exception("IsExistsCSVFile failed")
+
+
+ # 7.c. ReadCSVFileColumnNames
+ ReadCSVFileColumnNamesOutput = \
+ LoadAppLogic.ReadCSVFileColumnNames(FileEntry)
+
+
+ # 7.d. IsMatchCSVFileColumnNames
+ IsMatchCSVFileColumnNamesOutput = \
+ LoadAppLogic.IsMatchCSVFileColumnNames(ReadCSVFileColumnNamesOutput)
+ # 7.e. Control Flow: Decision
+ if not IsMatchCSVFileColumnNamesOutput:
+ raise Exception("IsMatchCSVFileColumnNames failed")
+
+
+ # /////////////////////////////////////
+ # ////// Load File //////
+ # /////////////////////////////////////
+ # 7.f. LoadCSVFileIntoTable
+ IsLoadedCSVFileIntoTableOutput = \
+ LoadAppLogic.LoadCSVFileIntoTable(CreateEmptyLoadDBOutput,
+ ReadCSVFileColumnNamesOutput)
+ # 7.g. Control Flow: Decision
+ if not IsLoadedCSVFileIntoTableOutput:
+ raise Exception("LoadCSVFileIntoTable failed")
+
+
+ # 7.h. UpdateComputedColumns
+ IsUpdatedComputedColumnsOutput = \
+ LoadAppLogic.UpdateComputedColumns(CreateEmptyLoadDBOutput,
+ ReadCSVFileColumnNamesOutput)
+ # 7.i. Control Flow: Decision
+ if not IsUpdatedComputedColumnsOutput:
+ raise Exception("UpdateComputedColumns failed")
+
+
+ # /////////////////////////////////////
+ # ////// PostLoad Validation //////
+ # /////////////////////////////////////
+ # 7.j. IsMatchTableRowCount
+ IsMatchTableRowCountOutput = \
+ LoadAppLogic.IsMatchTableRowCount(CreateEmptyLoadDBOutput,
+ ReadCSVFileColumnNamesOutput)
+ # 7.k. Control Flow: Decision
+ if not IsMatchTableRowCountOutput:
+ raise Exception("IsMatchTableRowCount failed")
+
+
+ # 7.l. IsMatchTableColumnRanges
+ IsMatchTableColumnRangesOutput = \
+ LoadAppLogic.IsMatchTableColumnRanges(CreateEmptyLoadDBOutput,
+ ReadCSVFileColumnNamesOutput)
+ # 7.m. Control Flow: Decision
+ if not IsMatchTableColumnRangesOutput:
+ raise Exception("IsMatchTableColumnRanges failed")
+
+
+ # 8. CompactDatabase
+ LoadAppLogic.CompactDatabase(CreateEmptyLoadDBOutput)
+
+if __name__ == '__main__':
+ import sys
+ LoadWorkflow.run(sys.argv)
diff --git a/contrib/pc3/info/ipaw/pc3/__init__.py b/contrib/pc3/info/ipaw/pc3/__init__.py
new file mode 100644
index 0000000..2ae2839
--- /dev/null
+++ b/contrib/pc3/info/ipaw/pc3/__init__.py
@@ -0,0 +1 @@
+pass
diff --git a/contrib/pc3/workflow.vt b/contrib/pc3/workflow.vt
new file mode 100644
index 0000000..f363513
Binary files /dev/null and b/contrib/pc3/workflow.vt differ
diff --git a/contrib/pc3/workflow_ifs.vt b/contrib/pc3/workflow_ifs.vt
new file mode 100644
index 0000000..d4a0609
Binary files /dev/null and b/contrib/pc3/workflow_ifs.vt differ
diff --git a/contrib/pc3/workflow_log.xml b/contrib/pc3/workflow_log.xml
new file mode 100644
index 0000000..7f3459e
--- /dev/null
+++ b/contrib/pc3/workflow_log.xml
@@ -0,0 +1,74 @@
+<log id="" name="" version="1.0.0" vistrail_id="" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/log.xsd">
+ <workflowExec completed="1" id="1" ip="155.98.20.78" name="" parentId="" parentType="vistrail" parentVersion="121" session="9" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:46" user="koop" vtVersion="1.2">
+ <moduleExec cached="0" completed="1" error="" id="1" machine_id="1" moduleId="12" moduleName="String" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="2" machine_id="1" moduleId="13" moduleName="ConcatenateString" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="3" machine_id="1" moduleId="2" moduleName="GetCSVFiles" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="1" key="used_files" value="['/vistrails/pc3/SampleData/J062945/csv_ready.csv']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="4" machine_id="1" moduleId="4" moduleName="CreateEmptyLoadDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="5" machine_id="1" moduleId="8" moduleName="Map" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
+ <loopExec completed="1" error="" id="6" iteration="0" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="7" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
+ <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ </groupExec>
+ </loopExec>
+ <loopExec completed="1" error="" id="14" iteration="1" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="15" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <moduleExec cached="0" completed="1" error="" id="16" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="17" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="18" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="6" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="19" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="7" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv']" />
+ <annotation id="8" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="20" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="9" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="21" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ </groupExec>
+ </loopExec>
+ <loopExec completed="1" error="" id="22" iteration="2" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
+ <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="23" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
+ <moduleExec cached="0" completed="1" error="" id="24" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="25" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="26" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="10" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2Detection.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="27" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:47" tsStart="2009-05-14 16:51:46">
+ <annotation id="11" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2Detection.csv']" />
+ <annotation id="12" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="28" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:47">
+ <annotation id="13" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="29" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48" />
+ </groupExec>
+ </loopExec>
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="30" machine_id="1" moduleId="26" moduleName="If" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48" />
+ <moduleExec cached="0" completed="1" error="" id="31" machine_id="1" moduleId="21" moduleName="CompactDatabase" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48">
+ <annotation id="14" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection'), ({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMet [...]
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="32" machine_id="1" moduleId="28" moduleName="DetectionsHistogram" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49">
+ <annotation id="15" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="33" machine_id="1" moduleId="29" moduleName="MplPlot" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
+ <moduleExec cached="0" completed="1" error="" id="34" machine_id="1" moduleId="30" moduleName="MplFigure" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
+ <moduleExec cached="0" completed="1" error="" id="35" machine_id="1" moduleId="31" moduleName="MplFigureCell" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
+ </workflowExec>
+ <machine architecture="32" id="1" name="vgc-g5c.sci.utah.edu" os="Darwin" processor="powerpc" ram="4294967296" />
+</log>
diff --git a/contrib/pc3/workflow_log_err.xml b/contrib/pc3/workflow_log_err.xml
new file mode 100644
index 0000000..b2e24c1
--- /dev/null
+++ b/contrib/pc3/workflow_log_err.xml
@@ -0,0 +1,49 @@
+<log id="" name="" version="1.0.0" vistrail_id="" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/log.xsd">
+ <workflowExec completed="-1" id="1" ip="155.98.20.78" name="" parentId="" parentType="vistrail" parentVersion="121" session="9" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" user="koop" vtVersion="1.2">
+ <moduleExec cached="0" completed="1" error="" id="1" machine_id="1" moduleId="12" moduleName="String" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="2" machine_id="1" moduleId="13" moduleName="ConcatenateString" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="3" machine_id="1" moduleId="2" moduleName="GetCSVFiles" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="1" key="used_files" value="['/vistrails/pc3/SampleData/J062945/csv_ready.csv']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="4" machine_id="1" moduleId="4" moduleName="CreateEmptyLoadDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="-1" error="Error inside map: Error(s) inside group:
+ComputeColumns: IsMatchTableRowCount failed" id="5" machine_id="1" moduleId="8" moduleName="Map" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <loopExec completed="1" error="" id="6" iteration="0" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="7" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
+ <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ </groupExec>
+ </loopExec>
+ <loopExec completed="-1" error="Error(s) inside group:
+ComputeColumns: IsMatchTableRowCount failed" id="14" iteration="1" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <groupExec cached="0" completed="-1" error="Error(s) inside group:
+ComputeColumns: IsMatchTableRowCount failed" groupName="Group" groupType="Group" id="15" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <moduleExec cached="0" completed="1" error="" id="16" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="17" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="18" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="6" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="19" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="7" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv']" />
+ <annotation id="8" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="-1" error="IsMatchTableRowCount failed" id="20" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="9" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
+ </moduleExec>
+ </groupExec>
+ </loopExec>
+ </moduleExec>
+ </workflowExec>
+ <machine architecture="32" id="1" name="vgc-g5c.sci.utah.edu" os="Darwin" processor="powerpc" ram="4294967296" />
+</log>
diff --git a/contrib/pc3/workflow_opm.xml b/contrib/pc3/workflow_opm.xml
new file mode 100644
index 0000000..968e4b4
--- /dev/null
+++ b/contrib/pc3/workflow_opm.xml
@@ -0,0 +1,1379 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<opmGraph xmlns="http://openprovenance.org/model/v1.01.a">
+ <accounts>
+ <account id="acct0">
+ <value>0</value>
+ </account>
+ <account id="acct1">
+ <value>1</value>
+ </account>
+ <account id="acct2">
+ <value>2</value>
+ </account>
+ <overlaps>
+ <account id="acct0" />
+ <account id="acct1" />
+ </overlaps>
+ <overlaps>
+ <account id="acct0" />
+ <account id="acct2" />
+ </overlaps>
+ <overlaps>
+ <account id="acct1" />
+ <account id="acct2" />
+ </overlaps>
+ </accounts>
+ <processes>
+ <process id="p0">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="1" machine_id="1" moduleId="12" moduleName="String" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p1">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="2" machine_id="1" moduleId="13" moduleName="ConcatenateString" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p2">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="3" machine_id="1" moduleId="2" moduleName="GetCSVFiles" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="1" key="used_files" value="['/vistrails/pc3/SampleData/J062945/csv_ready.csv']" />
+ </moduleExec>
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p3">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="4" machine_id="1" moduleId="4" moduleName="CreateEmptyLoadDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p4">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="5" machine_id="1" moduleId="8" moduleName="Map" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
+ <loopExec completed="1" error="" id="6" iteration="0" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="7" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
+ <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ </groupExec>
+ </loopExec>
+ <loopExec completed="1" error="" id="14" iteration="1" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="15" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <moduleExec cached="0" completed="1" error="" id="16" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="17" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="18" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="6" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="19" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="7" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv']" />
+ <annotation id="8" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="20" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="9" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="21" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ </groupExec>
+ </loopExec>
+ <loopExec completed="1" error="" id="22" iteration="2" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
+ <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="23" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
+ <moduleExec cached="0" completed="1" error="" id="24" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="25" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="26" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="10" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2Detection.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="27" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:47" tsStart="2009-05-14 16:51:46">
+ <annotation id="11" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2Detection.csv']" />
+ <annotation id="12" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="28" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:47">
+ <annotation id="13" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="29" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48" />
+ </groupExec>
+ </loopExec>
+ </moduleExec>
+ </value>
+ <account id="acct0" />
+ </process>
+ <process id="p5">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="30" machine_id="1" moduleId="26" moduleName="If" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48" />
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p6">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="31" machine_id="1" moduleId="21" moduleName="CompactDatabase" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48">
+ <annotation id="14" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection'), ({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Fram [...]
+ </moduleExec>
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p7">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="32" machine_id="1" moduleId="28" moduleName="DetectionsHistogram" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49">
+ <annotation id="15" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
+ </moduleExec>
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p8">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="33" machine_id="1" moduleId="29" moduleName="MplPlot" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p9">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="34" machine_id="1" moduleId="30" moduleName="MplFigure" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p10">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="35" machine_id="1" moduleId="31" moduleName="MplFigureCell" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p11">
+ <value>
+ <moduleExec cached="" completed="1" error="" id="-1" machine_id="" moduleId="-1" moduleName="Split" tsEnd="" tsStart="" />
+ </value>
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p12">
+ <value>
+ <moduleExec cached="" completed="1" error="" id="-1" machine_id="" moduleId="-1" moduleName="Join" tsEnd="" tsStart="" />
+ </value>
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p13">
+ <value>
+ <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="7" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
+ <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ </groupExec>
+ </value>
+ <account id="acct1" />
+ </process>
+ <process id="p14">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ </value>
+ <account id="acct2" />
+ </process>
+ <process id="p15">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ </value>
+ <account id="acct2" />
+ </process>
+ <process id="p16">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
+ </moduleExec>
+ </value>
+ <account id="acct2" />
+ </process>
+ <process id="p17">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
+ <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ </value>
+ <account id="acct2" />
+ </process>
+ <process id="p18">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ </value>
+ <account id="acct2" />
+ </process>
+ <process id="p19">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ </value>
+ <account id="acct2" />
+ </process>
+ <process id="p20">
+ <value>
+ <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="15" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <moduleExec cached="0" completed="1" error="" id="16" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="17" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
+ <moduleExec cached="0" completed="1" error="" id="18" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="6" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="19" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="7" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv']" />
+ <annotation id="8" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="20" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
+ <annotation id="9" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
+ </moduleExec>
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+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p1" />
+ <role value="in" />
+ <cause id="a2" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p1" />
+ <role value="in" />
+ <cause id="a1" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a3" />
+ <role value="out" />
+ <cause id="p1" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p2" />
+ <role value="in" />
+ <cause id="a4" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p2" />
+ <role value="in" />
+ <cause id="a3" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a5" />
+ <role value="out" />
+ <cause id="p2" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p3" />
+ <role value="in" />
+ <cause id="a1" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a6" />
+ <role value="out" />
+ <cause id="p3" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p4" />
+ <role value="in" />
+ <cause id="a5" />
+ <account id="acct0" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a7" />
+ <role value="out" />
+ <cause id="p4" />
+ <account id="acct0" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p11" />
+ <role value="in" />
+ <cause id="a5" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a8" />
+ <role value="out" />
+ <cause id="p11" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p12" />
+ <role value="in" />
+ <cause id="a9" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p13" />
+ <role value="in" />
+ <cause id="a8" />
+ <account id="acct1" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a9" />
+ <role value="out" />
+ <cause id="p13" />
+ <account id="acct1" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p13" />
+ <role value="in" />
+ <cause id="a6" />
+ <account id="acct1" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a10" />
+ <role value="out" />
+ <cause id="p14" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p14" />
+ <role value="in" />
+ <cause id="a6" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a11" />
+ <role value="out" />
+ <cause id="p15" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p15" />
+ <role value="in" />
+ <cause id="a8" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p16" />
+ <role value="in" />
+ <cause id="a12" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p16" />
+ <role value="in" />
+ <cause id="a11" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a13" />
+ <role value="out" />
+ <cause id="p16" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p17" />
+ <role value="in" />
+ <cause id="a14" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a15" />
+ <role value="out" />
+ <cause id="p17" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p17" />
+ <role value="in" />
+ <cause id="a10" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p17" />
+ <role value="in" />
+ <cause id="a13" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a16" />
+ <role value="out" />
+ <cause id="p17" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p18" />
+ <role value="in" />
+ <cause id="a15" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p18" />
+ <role value="in" />
+ <cause id="a16" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p18" />
+ <role value="in" />
+ <cause id="a13" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a17" />
+ <role value="out" />
+ <cause id="p18" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p19" />
+ <role value="in" />
+ <cause id="a17" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a9" />
+ <role value="out" />
+ <cause id="p19" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <wasGeneratedBy>
+ <effect id="a18" />
+ <role value="out" />
+ <cause id="p11" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p12" />
+ <role value="in" />
+ <cause id="a19" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p20" />
+ <role value="in" />
+ <cause id="a18" />
+ <account id="acct1" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a19" />
+ <role value="out" />
+ <cause id="p20" />
+ <account id="acct1" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p20" />
+ <role value="in" />
+ <cause id="a6" />
+ <account id="acct1" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a20" />
+ <role value="out" />
+ <cause id="p21" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p21" />
+ <role value="in" />
+ <cause id="a6" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a21" />
+ <role value="out" />
+ <cause id="p22" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p22" />
+ <role value="in" />
+ <cause id="a18" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p23" />
+ <role value="in" />
+ <cause id="a22" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p23" />
+ <role value="in" />
+ <cause id="a21" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a23" />
+ <role value="out" />
+ <cause id="p23" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p24" />
+ <role value="in" />
+ <cause id="a24" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a25" />
+ <role value="out" />
+ <cause id="p24" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p24" />
+ <role value="in" />
+ <cause id="a20" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p24" />
+ <role value="in" />
+ <cause id="a23" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a26" />
+ <role value="out" />
+ <cause id="p24" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p25" />
+ <role value="in" />
+ <cause id="a25" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p25" />
+ <role value="in" />
+ <cause id="a26" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p25" />
+ <role value="in" />
+ <cause id="a23" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a27" />
+ <role value="out" />
+ <cause id="p25" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p26" />
+ <role value="in" />
+ <cause id="a27" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a19" />
+ <role value="out" />
+ <cause id="p26" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <wasGeneratedBy>
+ <effect id="a28" />
+ <role value="out" />
+ <cause id="p11" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p12" />
+ <role value="in" />
+ <cause id="a29" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p27" />
+ <role value="in" />
+ <cause id="a28" />
+ <account id="acct1" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a29" />
+ <role value="out" />
+ <cause id="p27" />
+ <account id="acct1" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p27" />
+ <role value="in" />
+ <cause id="a6" />
+ <account id="acct1" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a30" />
+ <role value="out" />
+ <cause id="p28" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p28" />
+ <role value="in" />
+ <cause id="a6" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a31" />
+ <role value="out" />
+ <cause id="p29" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p29" />
+ <role value="in" />
+ <cause id="a28" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p30" />
+ <role value="in" />
+ <cause id="a32" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p30" />
+ <role value="in" />
+ <cause id="a31" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a33" />
+ <role value="out" />
+ <cause id="p30" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p31" />
+ <role value="in" />
+ <cause id="a34" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a35" />
+ <role value="out" />
+ <cause id="p31" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p31" />
+ <role value="in" />
+ <cause id="a30" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p31" />
+ <role value="in" />
+ <cause id="a33" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a36" />
+ <role value="out" />
+ <cause id="p31" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p32" />
+ <role value="in" />
+ <cause id="a35" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p32" />
+ <role value="in" />
+ <cause id="a36" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p32" />
+ <role value="in" />
+ <cause id="a33" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a37" />
+ <role value="out" />
+ <cause id="p32" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p33" />
+ <role value="in" />
+ <cause id="a37" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a29" />
+ <role value="out" />
+ <cause id="p33" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <wasGeneratedBy>
+ <effect id="a7" />
+ <role value="out" />
+ <cause id="p12" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p5" />
+ <role value="in" />
+ <cause id="a7" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <wasTriggeredBy>
+ <effect id="p6" />
+ <role value="control" />
+ <cause id="p5" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasTriggeredBy>
+ <used>
+ <effect id="p6" />
+ <role value="in" />
+ <cause id="a35" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p6" />
+ <role value="in" />
+ <cause id="a15" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p6" />
+ <role value="in" />
+ <cause id="a25" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p6" />
+ <role value="in" />
+ <cause id="a6" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a38" />
+ <role value="out" />
+ <cause id="p6" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p7" />
+ <role value="in" />
+ <cause id="a35" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p7" />
+ <role value="in" />
+ <cause id="a39" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p7" />
+ <role value="in" />
+ <cause id="a38" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a40" />
+ <role value="out" />
+ <cause id="p7" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p8" />
+ <role value="in" />
+ <cause id="a41" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p8" />
+ <role value="in" />
+ <cause id="a40" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a42" />
+ <role value="out" />
+ <cause id="p8" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p9" />
+ <role value="in" />
+ <cause id="a42" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a43" />
+ <role value="out" />
+ <cause id="p9" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p10" />
+ <role value="in" />
+ <cause id="a43" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ </causalDependencies>
+</opmGraph>
diff --git a/contrib/pc3/workflow_opm_err.xml b/contrib/pc3/workflow_opm_err.xml
new file mode 100644
index 0000000..008bbdc
--- /dev/null
+++ b/contrib/pc3/workflow_opm_err.xml
@@ -0,0 +1,756 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<opmGraph xmlns="http://openprovenance.org/model/v1.01.a">
+ <accounts>
+ <account id="acct0">
+ <value>0</value>
+ </account>
+ <account id="acct1">
+ <value>1</value>
+ </account>
+ <account id="acct2">
+ <value>2</value>
+ </account>
+ <overlaps>
+ <account id="acct0" />
+ <account id="acct1" />
+ </overlaps>
+ <overlaps>
+ <account id="acct0" />
+ <account id="acct2" />
+ </overlaps>
+ <overlaps>
+ <account id="acct1" />
+ <account id="acct2" />
+ </overlaps>
+ </accounts>
+ <processes>
+ <process id="p0">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="1" machine_id="1" moduleId="12" moduleName="String" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p1">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="2" machine_id="1" moduleId="13" moduleName="ConcatenateString" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p2">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="3" machine_id="1" moduleId="2" moduleName="GetCSVFiles" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="1" key="used_files" value="['/vistrails/pc3/SampleData/J062945/csv_ready.csv']" />
+ </moduleExec>
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p3">
+ <value>
+ <moduleExec cached="0" completed="1" error="" id="4" machine_id="1" moduleId="4" moduleName="CreateEmptyLoadDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ </value>
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </process>
+ <process id="p4">
+ <value>
+ <moduleExec cached="0" completed="-1" error="Error inside map: Error(s) inside group: ComputeColumns: IsMatchTableRowCount failed" id="5" machine_id="1" moduleId="8" moduleName="Map" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <loopExec completed="1" error="" id="6" iteration="0" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="7" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
+ <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ </groupExec>
+ </loopExec>
+ <loopExec completed="-1" error="Error(s) inside group: ComputeColumns: IsMatchTableRowCount failed" id="14" iteration="1" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <groupExec cached="0" completed="-1" error="Error(s) inside group: ComputeColumns: IsMatchTableRowCount failed" groupName="Group" groupType="Group" id="15" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <moduleExec cached="0" completed="1" error="" id="16" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="17" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="18" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="6" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="19" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="7" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv']" />
+ <annotation id="8" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="-1" error="IsMatchTableRowCount failed" id="20" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="9" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
+ </moduleExec>
+ </groupExec>
+ </loopExec>
+ </moduleExec>
+ </value>
+ <account id="acct0" />
+ </process>
+ <process id="p5">
+ <value>
+ <moduleExec cached="" completed="1" error="" id="-1" machine_id="" moduleId="-1" moduleName="Split" tsEnd="" tsStart="" />
+ </value>
+ <account id="acct1" />
+ <account id="acct2" />
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+ <process id="p6">
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+ <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="7" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
+ <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ </groupExec>
+ </value>
+ <account id="acct1" />
+ </process>
+ <process id="p7">
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+ <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ </value>
+ <account id="acct2" />
+ </process>
+ <process id="p8">
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+ <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ </value>
+ <account id="acct2" />
+ </process>
+ <process id="p9">
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+ <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
+ </moduleExec>
+ </value>
+ <account id="acct2" />
+ </process>
+ <process id="p10">
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+ <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
+ <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ </value>
+ <account id="acct2" />
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+ <process id="p11">
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+ <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
+ </moduleExec>
+ </value>
+ <account id="acct2" />
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+ <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ </value>
+ <account id="acct2" />
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+ <process id="p13">
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+ <groupExec cached="0" completed="-1" error="Error(s) inside group: ComputeColumns: IsMatchTableRowCount failed" groupName="Group" groupType="Group" id="15" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <moduleExec cached="0" completed="1" error="" id="16" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="17" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
+ <moduleExec cached="0" completed="1" error="" id="18" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="6" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv.hdr']" />
+ </moduleExec>
+ <moduleExec cached="0" completed="1" error="" id="19" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="7" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv']" />
+ <annotation id="8" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
+ </moduleExec>
+ <moduleExec cached="0" completed="-1" error="IsMatchTableRowCount failed" id="20" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
+ <annotation id="9" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
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+ <account id="acct1" />
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+ <moduleExec cached="0" completed="1" error="" id="16" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
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+ <account id="acct2" />
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+ <account id="acct2" />
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+ <annotation id="6" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv.hdr']" />
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+ <annotation id="7" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv']" />
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+ </moduleExec>
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+ <annotation id="9" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
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+ <wasGeneratedBy>
+ <effect id="a6" />
+ <role value="out" />
+ <cause id="p3" />
+ <account id="acct0" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p4" />
+ <role value="in" />
+ <cause id="a5" />
+ <account id="acct0" />
+ </used>
+ <used>
+ <effect id="p5" />
+ <role value="in" />
+ <cause id="a5" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a7" />
+ <role value="out" />
+ <cause id="p5" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p6" />
+ <role value="in" />
+ <cause id="a7" />
+ <account id="acct1" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a8" />
+ <role value="out" />
+ <cause id="p6" />
+ <account id="acct1" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p6" />
+ <role value="in" />
+ <cause id="a6" />
+ <account id="acct1" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a9" />
+ <role value="out" />
+ <cause id="p7" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p7" />
+ <role value="in" />
+ <cause id="a6" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a10" />
+ <role value="out" />
+ <cause id="p8" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p8" />
+ <role value="in" />
+ <cause id="a7" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p9" />
+ <role value="in" />
+ <cause id="a11" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p9" />
+ <role value="in" />
+ <cause id="a10" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a12" />
+ <role value="out" />
+ <cause id="p9" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p10" />
+ <role value="in" />
+ <cause id="a13" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a14" />
+ <role value="out" />
+ <cause id="p10" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p10" />
+ <role value="in" />
+ <cause id="a9" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p10" />
+ <role value="in" />
+ <cause id="a12" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a15" />
+ <role value="out" />
+ <cause id="p10" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p11" />
+ <role value="in" />
+ <cause id="a14" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p11" />
+ <role value="in" />
+ <cause id="a15" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p11" />
+ <role value="in" />
+ <cause id="a12" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a16" />
+ <role value="out" />
+ <cause id="p11" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p12" />
+ <role value="in" />
+ <cause id="a16" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a8" />
+ <role value="out" />
+ <cause id="p12" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <wasGeneratedBy>
+ <effect id="a17" />
+ <role value="out" />
+ <cause id="p5" />
+ <account id="acct1" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p13" />
+ <role value="in" />
+ <cause id="a17" />
+ <account id="acct1" />
+ </used>
+ <used>
+ <effect id="p13" />
+ <role value="in" />
+ <cause id="a6" />
+ <account id="acct1" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a18" />
+ <role value="out" />
+ <cause id="p14" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p14" />
+ <role value="in" />
+ <cause id="a6" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a19" />
+ <role value="out" />
+ <cause id="p15" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p15" />
+ <role value="in" />
+ <cause id="a17" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p16" />
+ <role value="in" />
+ <cause id="a20" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p16" />
+ <role value="in" />
+ <cause id="a19" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a21" />
+ <role value="out" />
+ <cause id="p16" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p17" />
+ <role value="in" />
+ <cause id="a22" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a23" />
+ <role value="out" />
+ <cause id="p17" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p17" />
+ <role value="in" />
+ <cause id="a18" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p17" />
+ <role value="in" />
+ <cause id="a21" />
+ <account id="acct2" />
+ </used>
+ <wasGeneratedBy>
+ <effect id="a24" />
+ <role value="out" />
+ <cause id="p17" />
+ <account id="acct2" />
+ </wasGeneratedBy>
+ <used>
+ <effect id="p18" />
+ <role value="in" />
+ <cause id="a23" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p18" />
+ <role value="in" />
+ <cause id="a24" />
+ <account id="acct2" />
+ </used>
+ <used>
+ <effect id="p18" />
+ <role value="in" />
+ <cause id="a21" />
+ <account id="acct2" />
+ </used>
+ </causalDependencies>
+</opmGraph>
diff --git a/contrib/pc3/workflow_reg.xml b/contrib/pc3/workflow_reg.xml
new file mode 100644
index 0000000..a1cba59
--- /dev/null
+++ b/contrib/pc3/workflow_reg.xml
@@ -0,0 +1,330 @@
+<registry id="" rootDescriptorId="0" version="1.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/registry.xsd">
+ <package codepath="basic_modules" description="basic_modules defines basic VisTrails Modules that are used in most
+pipelines." id="0" identifier="edu.utah.sci.vistrails.basic" loadConfiguration="1" name="Basic Modules" version="1.2">
+ <moduleDescriptor baseDescriptorId="-1" id="0" name="Module" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="0" name="self" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="1" name="Constant" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="9" name="value_as_string" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="1" id="2" name="Boolean" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="1" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
+ <portSpec id="2" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="1" id="3" name="Float" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="3" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Float)" sortKey="-1" type="input" />
+ <portSpec id="4" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Float)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="1" id="4" name="Integer" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="5" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
+ <portSpec id="6" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="1" id="5" name="String" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="7" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="8" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="1" id="6" name="File" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="10" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
+ <portSpec id="11" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="output" />
+ <portSpec id="12" name="name" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="13" name="self" optional="1" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="output" />
+ <portSpec id="14" name="create_file" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
+ <portSpec id="15" name="local_filename" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="7" name="FileSink" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="16" name="file" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
+ <portSpec id="17" name="outputName" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="18" name="overrideFile" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="1" id="8" name="Color" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="19" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Color)" sortKey="-1" type="input" />
+ <portSpec id="20" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Color)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="9" name="StandardOutput" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="21" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="10" name="Tuple" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="22" name="self" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Tuple)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="11" name="TestTuple" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="23" name="tuple" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Integer,edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="12" name="Untuple" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="24" name="tuple" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Tuple)" sortKey="-1" type="input" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="13" name="ConcatenateString" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="25" name="str1" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="26" name="str2" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="27" name="str3" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="28" name="str4" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="29" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="14" name="List" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="30" name="head" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
+ <portSpec id="31" name="tail" optional="0" sigstring="(edu.utah.sci.vistrails.basic:List)" sortKey="-1" type="input" />
+ <portSpec id="32" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:List)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="15" name="Null" namespace="" package="edu.utah.sci.vistrails.basic" version="" />
+ <moduleDescriptor baseDescriptorId="0" id="16" name="PythonSource" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="33" name="source" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="34" name="self" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="17" name="SmartSource" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="35" name="source" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="18" name="Unzip" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="36" name="archive_file" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
+ <portSpec id="37" name="filename_in_archive" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="38" name="file" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="19" name="Variant" namespace="" package="edu.utah.sci.vistrails.basic" version="" />
+ <moduleDescriptor baseDescriptorId="0" id="20" name="InputPort" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="39" name="name" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="40" name="optional" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
+ <portSpec id="41" name="spec" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="42" name="old_name" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="43" name="ExternalPipe" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Variant)" sortKey="-1" type="input" />
+ <portSpec id="44" name="InternalPipe" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Variant)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="21" name="OutputPort" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="45" name="name" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="46" name="optional" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
+ <portSpec id="47" name="spec" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="48" name="InternalPipe" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Variant)" sortKey="-1" type="input" />
+ <portSpec id="49" name="ExternalPipe" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Variant)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="22" name="Group" namespace="" package="edu.utah.sci.vistrails.basic" version="">
+ <portSpec id="50" name="self" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Group)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="22" id="23" name="SubWorkflow" namespace="" package="edu.utah.sci.vistrails.basic" version="" />
+ </package>
+ <package codepath="pythonCalc" description="This package implements a very simple VisTrails module called
+PythonCalc. This is intended as a simple example that can be referred
+to by users to create their own packages and modules later.
+
+If you're interested in developing new modules for VisTrails, you
+should also consult the documentation in the User's Guide and in
+core/modules/vistrails_module.py.
+" id="1" identifier="edu.utah.sci.vistrails.pythoncalc" loadConfiguration="1" name="PythonCalc" version="0.9.0">
+ <moduleDescriptor baseDescriptorId="0" id="24" name="PythonCalc" namespace="" package="edu.utah.sci.vistrails.pythoncalc" version="">
+ <portSpec id="51" name="value1" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Float)" sortKey="-1" type="input" />
+ <portSpec id="52" name="value2" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Float)" sortKey="-1" type="input" />
+ <portSpec id="53" name="op" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="54" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Float)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ </package>
+ <package codepath="spreadsheet" description="No description available" id="2" identifier="edu.utah.sci.vistrails.spreadsheet" loadConfiguration="1" name="VisTrails Spreadsheet" version="0.9.0">
+ <moduleDescriptor baseDescriptorId="0" id="25" name="SheetReference" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
+ <portSpec id="55" name="MinRowCount" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
+ <portSpec id="56" name="MinColumnCount" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
+ <portSpec id="57" name="SheetName" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="58" name="self" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:SheetReference)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="26" name="CellLocation" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
+ <portSpec id="59" name="ColumnRowAddress" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="60" name="Row" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
+ <portSpec id="61" name="Column" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
+ <portSpec id="62" name="SheetReference" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:SheetReference)" sortKey="-1" type="input" />
+ <portSpec id="63" name="self" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:CellLocation)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="27" name="SpreadsheetCell" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
+ <portSpec id="64" name="Location" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:CellLocation)" sortKey="-1" type="input" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="25" id="28" name="SingleCellSheetReference" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
+ <portSpec id="65" name="SheetName" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="66" name="self" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:SingleCellSheetReference)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="27" id="29" name="ImageViewerCell" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
+ <portSpec id="67" name="Location" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:CellLocation)" sortKey="-1" type="input" />
+ <portSpec id="68" name="File" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="27" id="30" name="RichTextCell" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
+ <portSpec id="69" name="Location" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:CellLocation)" sortKey="-1" type="input" />
+ <portSpec id="70" name="File" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="27" id="31" name="SVGCell" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
+ <portSpec id="71" name="Location" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:CellLocation)" sortKey="-1" type="input" />
+ <portSpec id="72" name="File" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="32" name="SVGSplitter" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
+ <portSpec id="73" name="File" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
+ </moduleDescriptor>
+ </package>
+ <package codepath="controlflow" description="No description available" id="6" identifier="edu.utah.sci.vistrails.control_flow" loadConfiguration="1" name="Control Flow" version="0.1">
+ <moduleDescriptor baseDescriptorId="1" id="33" name="ListOfElements" namespace="" package="edu.utah.sci.vistrails.control_flow" version="">
+ <portSpec id="74" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
+ <portSpec id="75" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="34" name="Fold" namespace="" package="edu.utah.sci.vistrails.control_flow" version="">
+ <portSpec id="76" name="FunctionPort" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
+ <portSpec id="77" name="InputList" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
+ <portSpec id="78" name="InputPort" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
+ <portSpec id="79" name="OutputPort" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="80" name="Result" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Variant)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="34" id="35" name="Map" namespace="" package="edu.utah.sci.vistrails.control_flow" version="" />
+ <moduleDescriptor baseDescriptorId="34" id="36" name="Filter" namespace="" package="edu.utah.sci.vistrails.control_flow" version="" />
+ <moduleDescriptor baseDescriptorId="34" id="37" name="AreaFilter" namespace="" package="edu.utah.sci.vistrails.control_flow" version="" />
+ <moduleDescriptor baseDescriptorId="34" id="38" name="SimilarityFilter" namespace="" package="edu.utah.sci.vistrails.control_flow" version="" />
+ <moduleDescriptor baseDescriptorId="0" id="39" name="If" namespace="" package="edu.utah.sci.vistrails.control_flow" version="">
+ <portSpec id="81" name="Condition" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
+ <portSpec id="82" name="TruePort" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
+ <portSpec id="83" name="FalsePort" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
+ <portSpec id="84" name="TrueOutputPorts" optional="1" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
+ <portSpec id="85" name="FalseOutputPorts" optional="1" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
+ <portSpec id="86" name="Result" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Variant)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="40" name="Dot" namespace="" package="edu.utah.sci.vistrails.control_flow" version="">
+ <portSpec id="87" name="List_1" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
+ <portSpec id="88" name="List_2" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
+ <portSpec id="89" name="CombineTuple" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
+ <portSpec id="90" name="Result" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="41" name="Cross" namespace="" package="edu.utah.sci.vistrails.control_flow" version="">
+ <portSpec id="91" name="List_1" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
+ <portSpec id="92" name="List_2" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
+ <portSpec id="93" name="CombineTuple" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
+ <portSpec id="94" name="Result" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ </package>
+ <package codepath="HTTP" description="HTTP provides packages for HTTP-based file fetching. This provides
+a location-independent way of referring to files. This package uses a
+local cache of the files, inside the per-user VisTrails
+directory. This way, files that haven't been changed do not need
+downloading. The check is performed efficiently using the HTTP GET
+headers.
+" id="4" identifier="edu.utah.sci.vistrails.http" loadConfiguration="1" name="HTTP" version="0.9.0">
+ <moduleDescriptor baseDescriptorId="0" id="42" name="HTTP" namespace="" package="edu.utah.sci.vistrails.http" version="" />
+ <moduleDescriptor baseDescriptorId="42" id="43" name="HTTPFile" namespace="" package="edu.utah.sci.vistrails.http" version="">
+ <portSpec id="95" name="url" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="96" name="file" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="output" />
+ <portSpec id="97" name="local_filename" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ </package>
+ <package codepath="pylab" description="Matplotlib package for VisTrails.
+
+This package wrap Matplotlib to provide a plotting tool for
+VisTrails. We are going to use the 'Qt4Agg' backend of the library.
+
+" id="5" identifier="edu.utah.sci.vistrails.matplotlib" loadConfiguration="1" name="matplotlib" version="0.9.0">
+ <moduleDescriptor baseDescriptorId="16" id="44" name="MplPlot" namespace="" package="edu.utah.sci.vistrails.matplotlib" version="">
+ <portSpec id="98" name="source" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="45" name="MplFigureManager" namespace="" package="edu.utah.sci.vistrails.matplotlib" version="" />
+ <moduleDescriptor baseDescriptorId="0" id="46" name="MplFigure" namespace="" package="edu.utah.sci.vistrails.matplotlib" version="">
+ <portSpec id="99" name="Script" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="100" name="FigureManager" optional="0" sigstring="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" sortKey="-1" type="output" />
+ <portSpec id="101" name="File" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="27" id="47" name="MplFigureCell" namespace="" package="edu.utah.sci.vistrails.matplotlib" version="">
+ <portSpec id="102" name="FigureManager" optional="0" sigstring="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" sortKey="-1" type="input" />
+ </moduleDescriptor>
+ </package>
+ <package codepath="dialogs" description="dialogs provides modules for user-based interaction on execution.
+Users can then enter file names, numbers, strings, etc." id="3" identifier="edu.utah.sci.vistrails.dialogs" loadConfiguration="1" name="Dialogs" version="0.9.0">
+ <moduleDescriptor baseDescriptorId="0" id="48" name="Dialog" namespace="" package="edu.utah.sci.vistrails.dialogs" version="" />
+ <moduleDescriptor baseDescriptorId="48" id="49" name="TextDialog" namespace="" package="edu.utah.sci.vistrails.dialogs" version="">
+ <portSpec id="103" name="title" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="104" name="label" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="105" name="default" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="106" name="result" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ </package>
+ <package codepath="pc3" description="No description available" id="7" identifier="edu.utah.sci.dakoop.pc3" loadConfiguration="1" name="Provenance Challenge 3" version="1.0.0">
+ <moduleDescriptor baseDescriptorId="0" id="50" name="ReadCSVReadyFile" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="107" name="csvRootPath" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="108" name="csvFiles" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="51" name="IsMatchTableRowCount" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="109" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
+ <portSpec id="110" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
+ <portSpec id="111" name="countsMatch" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="52" name="LoadCSVFileIntoDB" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="112" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
+ <portSpec id="113" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
+ <portSpec id="114" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="53" name="IsMatchCSVFileColumnNames" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="115" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
+ <portSpec id="116" name="columnsMatch" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="54" name="ComputeColumns" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="117" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
+ <portSpec id="118" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
+ <portSpec id="119" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="55" name="ReadCSVFile" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="120" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
+ <portSpec id="121" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="56" name="LoadCSVFileIntoTable" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="122" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
+ <portSpec id="123" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
+ <portSpec id="124" name="success" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="57" name="IsMatchTableColumnRanges" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="125" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
+ <portSpec id="126" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
+ <portSpec id="127" name="rangesMatch" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="58" name="DetectionsHistogram" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="128" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
+ <portSpec id="129" name="highQuality" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
+ <portSpec id="130" name="histogram" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="59" name="Collection" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="131" name="elements" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
+ <portSpec id="132" name="self" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:Collection)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="60" name="CompactDatabase" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="133" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
+ <portSpec id="134" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="61" name="IsMatchCSVFileTables" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="135" name="csvFiles" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
+ <portSpec id="136" name="tablesMatch" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="62" name="ReadCSVFileColumnNames" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="137" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
+ <portSpec id="138" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="63" name="CreateEmptyLoadDB" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="139" name="jobID" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="140" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="64" name="GetCSVFiles" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="141" name="csvRootPath" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="142" name="csvFiles" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="65" name="IsExistsCSVFile" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="143" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
+ <portSpec id="144" name="fileExists" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="66" name="DatabaseEntry" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="145" name="dbGuid" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="146" name="dbName" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="147" name="connectionString" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="148" name="self" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="67" name="UpdateComputedColumns" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="149" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
+ <portSpec id="150" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
+ <portSpec id="151" name="success" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="68" name="CSVFileEntry" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="152" name="filePath" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="153" name="headerPath" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="154" name="rowCount" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
+ <portSpec id="155" name="targetTable" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="156" name="checksum" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="157" name="columnNames" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:Collection)" sortKey="-1" type="input" />
+ <portSpec id="158" name="self" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ <moduleDescriptor baseDescriptorId="0" id="69" name="IsCSVReadyFileExists" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
+ <portSpec id="159" name="csvRootPath" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
+ <portSpec id="160" name="fileExists" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
+ </moduleDescriptor>
+ </package>
+ <package codepath="subworkflows" description="No description available" id="8" identifier="local.abstractions" loadConfiguration="1" name="My SubWorkflows" version="1.2" />
+</registry>
diff --git a/contrib/pc3/workflow_vt.xml b/contrib/pc3/workflow_vt.xml
new file mode 100644
index 0000000..ce68b5f
--- /dev/null
+++ b/contrib/pc3/workflow_vt.xml
@@ -0,0 +1,1153 @@
+<vistrail id="" name="" version="0.9.5" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/vistrail.xsd">
+ <action date="2009-04-07 16:02:43" id="1" prevId="0" prune="" session="0" user="koop">
+ <add id="0" objectId="0" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="0" name="DatabaseEntry" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
+ </add>
+ <add id="1" objectId="0" parentObjId="0" parentObjType="module" what="location">
+ <location id="0" x="-162.420168067" y="79.5966386555" />
+ </add>
+ </action>
+ <action date="2009-04-07 16:02:45" id="2" prevId="1" prune="" session="0" user="koop">
+ <add id="2" objectId="1" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="1" name="LoadCSVFileIntoDB" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
+ </add>
+ <add id="3" objectId="1" parentObjId="1" parentObjType="module" what="location">
+ <location id="1" x="-104.336134454" y="-118.319327731" />
+ </add>
+ </action>
+ <action date="2009-04-07 16:04:24" id="3" prevId="2" prune="" session="0" user="koop">
+ <delete id="4" objectId="0" parentObjId="0" parentObjType="module" what="location" />
+ <delete id="5" objectId="0" parentObjId="" parentObjType="" what="module" />
+ <delete id="6" objectId="1" parentObjId="1" parentObjType="module" what="location" />
+ <delete id="7" objectId="1" parentObjId="" parentObjType="" what="module" />
+ </action>
+ <action date="2009-04-07 16:04:27" id="4" prevId="3" prune="" session="0" user="koop">
+ <add id="8" objectId="2" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="2" name="GetCSVFiles" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
+ </add>
+ <add id="9" objectId="2" parentObjId="2" parentObjType="module" what="location">
+ <location id="2" x="-84.974789916" y="105.411764706" />
+ </add>
+ </action>
+ <action date="2009-04-07 16:04:58" id="5" prevId="4" prune="" session="0" user="koop">
+ <change id="10" newObjId="3" oldObjId="2" parentObjId="2" parentObjType="module" what="location">
+ <location id="3" x="-20.4369747899" y="129.075630252" />
+ </change>
+ </action>
+ <action date="2009-04-07 16:04:58" id="6" prevId="5" prune="" session="0" user="koop">
+ <add id="11" objectId="3" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="3" name="ComputeColumns" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
+ </add>
+ <add id="12" objectId="4" parentObjId="3" parentObjType="module" what="location">
+ <location id="4" x="50.5546218487" y="-62.3865546218" />
+ </add>
+ </action>
+ <action date="2009-04-07 16:05:01" id="7" prevId="6" prune="" session="0" user="koop">
+ <add id="13" objectId="4" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="4" name="CreateEmptyLoadDB" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
+ </add>
+ <add id="14" objectId="5" parentObjId="4" parentObjType="module" what="location">
+ <location id="5" x="-236.638655462" y="118.319327731" />
+ </add>
+ </action>
+ <action date="2009-04-07 16:05:06" id="8" prevId="7" prune="" session="0" user="koop">
+ <add id="15" objectId="5" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="5" name="LoadCSVFileIntoDB" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
+ </add>
+ <add id="16" objectId="6" parentObjId="5" parentObjType="module" what="location">
+ <location id="6" x="-157.042016807" y="8.60504201681" />
+ </add>
+ </action>
+ <action date="2009-04-07 16:05:10" id="9" prevId="8" prune="" session="0" user="koop">
+ <add id="17" objectId="0" parentObjId="" parentObjType="" what="connection">
+ <connection id="0" />
+ </add>
+ <add id="18" objectId="0" parentObjId="0" parentObjType="connection" what="port">
+ <port id="0" moduleId="4" moduleName="CreateEmptyLoadDB" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
+ </add>
+ <add id="19" objectId="1" parentObjId="0" parentObjType="connection" what="port">
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+ </change>
+ </action>
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+ <add id="308" objectId="72" parentObjId="36" parentObjType="connection" what="port">
+ <port id="72" moduleId="30" moduleName="MplFigure" name="FigureManager" signature="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" type="source" />
+ </add>
+ <add id="309" objectId="73" parentObjId="36" parentObjType="connection" what="port">
+ <port id="73" moduleId="31" moduleName="MplFigureCell" name="FigureManager" signature="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" type="destination" />
+ </add>
+ </action>
+ <action date="2009-04-10 13:41:42" id="110" prevId="109" prune="" session="6" user="koop">
+ <add id="310" objectId="37" parentObjId="" parentObjType="" what="connection">
+ <connection id="37" />
+ </add>
+ <add id="311" objectId="74" parentObjId="37" parentObjType="connection" what="port">
+ <port id="74" moduleId="29" moduleName="MplPlot" name="source" signature="(edu.utah.sci.vistrails.basic:String)" type="source" />
+ </add>
+ <add id="312" objectId="75" parentObjId="37" parentObjType="connection" what="port">
+ <port id="75" moduleId="30" moduleName="MplFigure" name="Script" signature="(edu.utah.sci.vistrails.basic:String)" type="destination" />
+ </add>
+ </action>
+ <action date="2009-04-10 13:45:54" id="111" prevId="110" prune="" session="6" user="koop">
+ <add id="313" objectId="0" parentObjId="29" parentObjType="module" what="portSpec">
+ <portSpec id="0" name="histogramData" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="0" type="input" />
+ </add>
+ <add id="314" objectId="6" parentObjId="29" parentObjType="module" what="function">
+ <function id="6" name="source" pos="0" />
+ </add>
+ <add id="315" objectId="14" parentObjId="6" parentObjType="function" what="parameter">
+ <parameter alias="" id="14" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="x%20%3D%20%5Ba%5B1%5D%20for%20a%20in%20histogramData%5D%0Abins%20%3D%20%5Ba%5B0%5D%20for%20a%20in%20histogramData%5D%0A%0Ahist%28x%2C%20bins%29%0A" />
+ </add>
+ </action>
+ <action date="2009-04-10 13:45:58" id="112" prevId="111" prune="" session="6" user="koop">
+ <add id="316" objectId="38" parentObjId="" parentObjType="" what="connection">
+ <connection id="38" />
+ </add>
+ <add id="317" objectId="76" parentObjId="38" parentObjType="connection" what="port">
+ <port id="76" moduleId="28" moduleName="DetectionsHistogram" name="histogram" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="source" />
+ </add>
+ <add id="318" objectId="77" parentObjId="38" parentObjType="connection" what="port">
+ <port id="77" moduleId="29" moduleName="MplPlot" name="histogramData" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="destination" />
+ </add>
+ </action>
+ <action date="2009-04-10 14:02:37" id="113" prevId="112" prune="" session="7" user="koop">
+ <change id="319" newObjId="15" oldObjId="14" parentObjId="6" parentObjType="function" what="parameter">
+ <parameter alias="" id="15" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="x%20%3D%20%5Ba%5B1%5D%20for%20a%20in%20histogramData%5D%0Abins%20%3D%20%5Ba%5B0%5D%20for%20a%20in%20histogramData%5D%0A%0Abar%28x%2C%20bins%29%0A" />
+ </change>
+ </action>
+ <action date="2009-04-10 14:03:17" id="114" prevId="113" prune="" session="7" user="koop">
+ <change id="320" newObjId="16" oldObjId="15" parentObjId="6" parentObjType="function" what="parameter">
+ <parameter alias="" id="16" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="x%20%3D%20%5Ba%5B1%5D%20for%20a%20in%20histogramData%5D%0Abins%20%3D%20%5Ba%5B0%5D%20for%20a%20in%20histogramData%5D%0A%0Abar%28bins%2C%20x%29%0A" />
+ </change>
+ </action>
+ <action date="2009-04-10 14:03:32" id="115" prevId="114" prune="" session="7" user="koop">
+ <change id="321" newObjId="17" oldObjId="10" parentObjId="4" parentObjType="function" what="parameter">
+ <parameter alias="" id="17" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="J062945" />
+ </change>
+ </action>
+ <action date="2009-04-10 14:04:46" id="116" prevId="115" prune="" session="7" user="koop">
+ <add id="322" objectId="7" parentObjId="28" parentObjType="module" what="function">
+ <function id="7" name="highQuality" pos="0" />
+ </add>
+ <add id="323" objectId="18" parentObjId="7" parentObjType="function" what="parameter">
+ <parameter alias="" id="18" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Boolean" val="" />
+ </add>
+ </action>
+ <action date="2009-04-10 14:04:47" id="117" prevId="116" prune="" session="7" user="koop">
+ <change id="324" newObjId="19" oldObjId="18" parentObjId="7" parentObjType="function" what="parameter">
+ <parameter alias="" id="19" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Boolean" val="True" />
+ </change>
+ </action>
+ <action date="2009-04-10 14:06:31" id="118" prevId="117" prune="" session="8" user="koop" />
+ <action date="2009-04-10 14:06:32" id="119" prevId="118" prune="" session="8" user="koop">
+ <change id="325" newObjId="20" oldObjId="19" parentObjId="7" parentObjType="function" what="parameter">
+ <parameter alias="" id="20" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Boolean" val="False" />
+ </change>
+ </action>
+ <action date="2009-04-10 14:08:48" id="120" prevId="119" prune="" session="8" user="koop">
+ <change id="326" newObjId="21" oldObjId="20" parentObjId="7" parentObjType="function" what="parameter">
+ <parameter alias="" id="21" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Boolean" val="True" />
+ </change>
+ </action>
+ <action date="2009-04-10 14:09:20" id="121" prevId="120" prune="" session="8" user="koop" />
+ <tag id="46" name="Working Map" />
+ <tag id="60" name="SingleString" />
+ <tag id="85" name="Moved Compact" />
+ <tag id="99" name="Compact Outside" />
+ <tag id="103" name="Fixed False Branch" />
+ <tag id="119" name="Histogram" />
+ <tag id="120" name="High Quality Histogram" />
+</vistrail>
diff --git a/contrib/pc3/workflow_wf.xml b/contrib/pc3/workflow_wf.xml
new file mode 100644
index 0000000..756df00
--- /dev/null
+++ b/contrib/pc3/workflow_wf.xml
@@ -0,0 +1,169 @@
+<workflow id="0" name="untitled" version="1.0.0" vistrail_id="" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/workflow.xsd">
+ <connection id="32">
+ <port id="64" moduleId="8" moduleName="Map" name="Result" signature="(edu.utah.sci.vistrails.basic:Variant)" type="source" />
+ <port id="65" moduleId="26" moduleName="If" name="Condition" signature="(edu.utah.sci.vistrails.basic:Boolean)" type="destination" />
+ </connection>
+ <connection id="33">
+ <port id="66" moduleId="4" moduleName="CreateEmptyLoadDB" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
+ <port id="67" moduleId="21" moduleName="CompactDatabase" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="destination" />
+ </connection>
+ <connection id="34">
+ <port id="68" moduleId="27" moduleName="Module" name="self" signature="(edu.utah.sci.vistrails.basic:Module)" type="source" />
+ <port id="69" moduleId="26" moduleName="If" name="FalsePort" signature="(edu.utah.sci.vistrails.basic:Module)" type="destination" />
+ </connection>
+ <connection id="35">
+ <port id="70" moduleId="21" moduleName="CompactDatabase" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
+ <port id="71" moduleId="28" moduleName="DetectionsHistogram" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="destination" />
+ </connection>
+ <connection id="36">
+ <port id="72" moduleId="30" moduleName="MplFigure" name="FigureManager" signature="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" type="source" />
+ <port id="73" moduleId="31" moduleName="MplFigureCell" name="FigureManager" signature="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" type="destination" />
+ </connection>
+ <connection id="37">
+ <port id="74" moduleId="29" moduleName="MplPlot" name="source" signature="(edu.utah.sci.vistrails.basic:String)" type="source" />
+ <port id="75" moduleId="30" moduleName="MplFigure" name="Script" signature="(edu.utah.sci.vistrails.basic:String)" type="destination" />
+ </connection>
+ <connection id="6">
+ <port id="12" moduleId="2" moduleName="GetCSVFiles" name="csvFiles" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="source" />
+ <port id="13" moduleId="8" moduleName="Map" name="InputList" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="destination" />
+ </connection>
+ <connection id="38">
+ <port id="76" moduleId="28" moduleName="DetectionsHistogram" name="histogram" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="source" />
+ <port id="77" moduleId="29" moduleName="MplPlot" name="histogramData" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="destination" />
+ </connection>
+ <connection id="11">
+ <port id="22" moduleId="12" moduleName="String" name="value" signature="(edu.utah.sci.vistrails.basic:String)" type="source" />
+ <port id="23" moduleId="4" moduleName="CreateEmptyLoadDB" name="jobID" signature="(edu.utah.sci.vistrails.basic:String)" type="destination" />
+ </connection>
+ <connection id="12">
+ <port id="24" moduleId="12" moduleName="String" name="value" signature="(edu.utah.sci.vistrails.basic:String)" type="source" />
+ <port id="25" moduleId="13" moduleName="ConcatenateString" name="str2" signature="(edu.utah.sci.vistrails.basic:String)" type="destination" />
+ </connection>
+ <connection id="13">
+ <port id="26" moduleId="13" moduleName="ConcatenateString" name="value" signature="(edu.utah.sci.vistrails.basic:String)" type="source" />
+ <port id="27" moduleId="2" moduleName="GetCSVFiles" name="csvRootPath" signature="(edu.utah.sci.vistrails.basic:String)" type="destination" />
+ </connection>
+ <connection id="26">
+ <port id="52" moduleId="4" moduleName="CreateEmptyLoadDB" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
+ <port id="53" moduleId="25" moduleName="Group" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="destination" />
+ </connection>
+ <connection id="27">
+ <port id="54" moduleId="25" moduleName="Group" name="self" signature="(edu.utah.sci.vistrails.basic:Group)" type="source" />
+ <port id="55" moduleId="8" moduleName="Map" name="FunctionPort" signature="(edu.utah.sci.vistrails.basic:Module)" type="destination" />
+ </connection>
+ <connection id="31">
+ <port id="62" moduleId="21" moduleName="CompactDatabase" name="self" signature="(edu.utah.sci.vistrails.basic:Module)" type="source" />
+ <port id="63" moduleId="26" moduleName="If" name="TruePort" signature="(edu.utah.sci.vistrails.basic:Module)" type="destination" />
+ </connection>
+ <module cache="1" id="2" name="GetCSVFiles" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
+ <location id="21" x="338.293817527" y="-164.978391356" />
+ </module>
+ <module cache="1" id="4" name="CreateEmptyLoadDB" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
+ <location id="58" x="-38.9585627535" y="15.0773161002" />
+ </module>
+ <module cache="1" id="8" name="Map" namespace="" package="edu.utah.sci.vistrails.control_flow" tag="" version="0.1">
+ <location id="20" x="114.016806723" y="-292.571428571" />
+ <function id="2" name="InputPort" pos="0">
+ <parameter alias="" id="6" name="<no description>" pos="0" type="edu.utah.sci.vistrails.control_flow:ListOfElements" val="['csvFile']" />
+ </function>
+ <function id="3" name="OutputPort" pos="1">
+ <parameter alias="" id="13" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="dbEntry" />
+ </function>
+ </module>
+ <module cache="1" id="12" name="String" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
+ <location id="37" x="150.588235294" y="152.739495798" />
+ <function id="4" name="value" pos="0">
+ <parameter alias="" id="17" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="J062945" />
+ </function>
+ </module>
+ <module cache="1" id="13" name="ConcatenateString" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
+ <location id="36" x="271.058823529" y="52.7058823529" />
+ <function id="5" name="str1" pos="0">
+ <parameter alias="" id="12" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="/vistrails/pc3/SampleData/" />
+ </function>
+ </module>
+ <module cache="1" id="21" name="CompactDatabase" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
+ <location id="68" x="360.902962881" y="-460.065238478" />
+ </module>
+ <group cache="1" id="25" name="Group" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="">
+ <workflow id="" name="untitled" version="" vistrail_id="">
+ <connection id="1">
+ <port id="1" moduleId="1" moduleName="ComputeColumns" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="destination" />
+ <port id="2" moduleId="2" moduleName="LoadCSVFileIntoDB" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
+ </connection>
+ <connection id="2">
+ <port id="3" moduleId="2" moduleName="LoadCSVFileIntoDB" name="csvFile" signature="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" type="destination" />
+ <port id="4" moduleId="3" moduleName="ReadCSVFile" name="csvFile" signature="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" type="source" />
+ </connection>
+ <connection id="3">
+ <port id="5" moduleId="1" moduleName="ComputeColumns" name="csvFile" signature="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" type="destination" />
+ <port id="6" moduleId="3" moduleName="ReadCSVFile" name="csvFile" signature="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" type="source" />
+ </connection>
+ <connection id="4">
+ <port id="7" moduleId="4" moduleName="InputPort" name="InternalPipe" signature="(edu.utah.sci.vistrails.basic:Variant)" type="source" />
+ <port id="8" moduleId="3" moduleName="ReadCSVFile" name="csvFile" signature="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" type="destination" />
+ </connection>
+ <connection id="5">
+ <port id="9" moduleId="5" moduleName="InputPort" name="InternalPipe" signature="(edu.utah.sci.vistrails.basic:Variant)" type="source" />
+ <port id="10" moduleId="2" moduleName="LoadCSVFileIntoDB" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="destination" />
+ </connection>
+ <connection id="6">
+ <port id="11" moduleId="1" moduleName="ComputeColumns" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
+ <port id="12" moduleId="6" moduleName="OutputPort" name="InternalPipe" signature="(edu.utah.sci.vistrails.basic:Variant)" type="destination" />
+ </connection>
+ <module cache="1" id="1" name="ComputeColumns" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
+ <location id="1" x="66.7948593185" y="-134.829855648" />
+ </module>
+ <module cache="1" id="2" name="LoadCSVFileIntoDB" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
+ <location id="2" x="57.1141870494" y="-46.6281749756" />
+ </module>
+ <module cache="1" id="3" name="ReadCSVFile" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
+ <location id="3" x="-134.767894144" y="65.4297450412" />
+ </module>
+ <module cache="1" id="4" name="InputPort" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
+ <location id="4" x="-206.697188695" y="178.15512489" />
+ <function id="1" name="name" pos="0">
+ <parameter alias="" id="1" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="csvFile" />
+ </function>
+ </module>
+ <module cache="1" id="5" name="InputPort" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
+ <location id="5" x="56.8852296284" y="150.149492943" />
+ <function id="2" name="name" pos="0">
+ <parameter alias="" id="2" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="dbEntry" />
+ </function>
+ </module>
+ <module cache="1" id="6" name="OutputPort" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
+ <location id="6" x="160.670806843" y="-212.276332251" />
+ <function id="3" name="name" pos="0">
+ <parameter alias="" id="3" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="dbEntry" />
+ </function>
+ </module>
+ </workflow>
+ <location id="60" x="17.2473255251" y="-163.32861386" />
+ </group>
+ <module cache="1" id="26" name="If" namespace="" package="edu.utah.sci.vistrails.control_flow" tag="" version="0.1">
+ <location id="69" x="176.22882839" y="-382.689881848" />
+ </module>
+ <module cache="1" id="27" name="Module" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
+ <location id="71" x="201.936522474" y="-468.673570816" />
+ </module>
+ <module cache="1" id="28" name="DetectionsHistogram" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
+ <location id="72" x="429.549610616" y="-595.581197698" />
+ <function id="7" name="highQuality" pos="0">
+ <parameter alias="" id="21" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Boolean" val="True" />
+ </function>
+ </module>
+ <module cache="1" id="29" name="MplPlot" namespace="" package="edu.utah.sci.vistrails.matplotlib" tag="" version="0.9.0">
+ <location id="73" x="549.285584018" y="-710.147790766" />
+ <function id="6" name="source" pos="0">
+ <parameter alias="" id="16" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="x%20%3D%20%5Ba%5B1%5D%20for%20a%20in%20histogramData%5D%0Abins%20%3D%20%5Ba%5B0%5D%20for%20a%20in%20histogramData%5D%0A%0Abar%28bins%2C%20x%29%0A" />
+ </function>
+ <portSpec id="0" name="histogramData" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="0" type="input" />
+ </module>
+ <module cache="1" id="30" name="MplFigure" namespace="" package="edu.utah.sci.vistrails.matplotlib" tag="" version="0.9.0">
+ <location id="74" x="572.826394762" y="-823.928376027" />
+ </module>
+ <module cache="1" id="31" name="MplFigureCell" namespace="" package="edu.utah.sci.vistrails.matplotlib" tag="" version="0.9.0">
+ <location id="75" x="590.482002819" y="-937.708961288" />
+ </module>
+</workflow>
diff --git a/contrib/poissonrecon.py b/contrib/poissonrecon.py
new file mode 100644
index 0000000..5039182
--- /dev/null
+++ b/contrib/poissonrecon.py
@@ -0,0 +1,101 @@
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+import core.bundles
+import core.requirements
+import os
+import re
+
+from core.configuration import ConfigurationObject
+
+configuration = ConfigurationObject(executable_path=(None, str))
+
+identifier = 'edu.utah.sci.cscheid.poissonrecon'
+version = '0.1'
+name = 'Poisson Surface Reconstruction'
+
+##############################################################################
+
+class PoissonRecon(Module):
+
+ def __init__(self):
+ Module.__init__(self)
+
+ def compute(self):
+ self.checkInputPort('pts')
+ f1 = self.getInputFromPort('mesh1')
+
+ make_file = self.interpreter.filePool.create_file
+
+ metro_output = make_file(suffix='.ply')
+
+ values = ['', f1.name, f2.name, '-q']
+
+ need_error_meshes = False
+ if (self.outputPorts.has_key('error_mesh_1') or
+ self.outputPorts.has_key('error_mesh_2')):
+ need_error_meshes = True
+ error_mesh_output = (make_file(suffix='.ply'),
+ make_file(suffix='.ply'))
+ values.append('-c')
+ values.append(error_mesh_output[0].name)
+ values.append(error_mesh_output[1].name)
+
+ need_histograms = False
+ if (self.outputPorts.has_key('error_hist_1') or
+ self.outputPorts.has_key('error_hist_2')):
+ need_histograms = True
+ error_hist_output = (make_file(suffix='.csv'),
+ make_file(suffix='.csv'))
+ values.append('-h')
+ values.append(error_hist_output[0].name)
+ values.append(error_hist_output[1].name)
+
+ print values
+ print ('%s ' * len(values))
+ cmdline = ('%s ' * len(values)) % tuple(values)
+ cmdline += '> '
+ cmdline += metro_output.name
+ print cmdline
+
+ result = os.system(cmdline)
+ if result != 0:
+ raise ModuleError(self, "Execution failed")
+ l = [x for x in file(metro_output.name).readlines()
+ if x.startswith('Hausdorff')][0]
+ regexp = re.compile(r'Hausdorff distance: ([0123456789.]+) \(([0123456789.]+) wrt bounding box diagonal\)')
+ results = regexp.match(l).groups()
+
+ if need_error_meshes:
+ self.setResult('error_mesh_1', error_mesh_output[0])
+ self.setResult('error_mesh_2', error_mesh_output[1])
+
+ if need_histograms:
+ self.setResult('error_hist_1', error_hist_output[0])
+ self.setResult('error_hist_2', error_hist_output[1])
+
+ self.need_error_meshes = need_error_meshes
+ self.need_histograms = need_histograms
+
+ self.setResult('hausdorff_error', float(results[0]))
+ self.setResult('normalized_hausdorff_error', float(results[1]))
+
+##############################################################################
+
+def initialize():
+ if not core.requirements.executable_file_exists('PoissonRecon'):
+ raise core.requirements.MissingRequirement("PoissonRecon")
+
+ reg = core.modules.module_registry
+
+ reg.add_module(PoissonRecon)
+ reg.add_input_port(PoissonRecon, 'pts',
+ core.modules.basic_modules.File)
+ reg.add_input_port(PoissonRecon, 'binary',
+ core.modules.basic_modules.Boolean)
+ reg.add_input_port(PoissonRecon, 'depth',
+ core.modules.basic_modules.Integer)
+
+ reg.add_output_port(PoissonRecon, 'output',
+ core.modules.basic_modules.File)
+
diff --git a/contrib/provenance/__init__.py b/contrib/provenance/__init__.py
new file mode 100644
index 0000000..cadc047
--- /dev/null
+++ b/contrib/provenance/__init__.py
@@ -0,0 +1,274 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+"""This package defines a set of methods that perform the command-line
+tools necesary for the task designed for the first Provenance Challenge:
+
+http://twiki.ipaw.info
+
+This VisTrails package requires three software packages to be installed:
+
+AIR - Automated Image Registration: http://bishopw.loni.ucla.edu/AIR5/
+FSL - http://www.fmrib.ox.ac.uk/fsl/
+netpbm - http://netpbm.sourceforge.net/
+
+"""
+
+from core.modules.vistrails_module import Module, ModuleError, new_module
+import core.modules
+import core.modules.basic_modules
+import core.modules.module_registry
+import core.utils
+from core.system import list2cmdline
+import os
+import os.path
+import stat
+import subprocess
+
+version = '0.9.0'
+name = 'Provenance Challenge'
+identifier = 'edu.utah.sci.vistrails.provenance'
+################################################################################
+
+global_airpath = ""
+global_fslpath = ""
+global_netpbmpath = ""
+
+class ProvenanceChallenge(Module):
+ """ProvenanceChallenge is the base Module for all Modules in the provenance
+package. It simply define helper methods for subclasses."""
+
+ __quiet = True
+ __programsQuiet = True
+
+ def air_cmd_line(self, cmd, *params):
+ """Runs a command-line command for the AIR tools."""
+ return list2cmdline([global_airpath + cmd] + list(params))
+
+ def fsl_cmd_line(self, cmd, *params):
+ """Runs a command-line command for the FSL tools."""
+ return ('FSLOUTPUTTYPE=NIFTI_GZ ' +
+ list2cmdline([global_fslpath + cmd] + list(params)))
+
+ def run(self, cmd):
+ if not self.__quiet:
+ print cmd
+ if self.__programsQuiet:
+ cmd = '(' + cmd + ') 2>&1 >/dev/null'
+ r = os.system(cmd)
+ if r != 0:
+ raise ModuleError(self, "system call failed: '%s'" % cmd)
+
+
+class AIRHeaderFile(core.modules.basic_modules.File):
+ """AIRHeaderFile subclasses File to annotate the execution with header
+file information for later querying."""
+
+ def get_header_annotations(self):
+ """Returns the header information for the file using the AIR scanheader
+tool."""
+ process = subprocess.Popen(global_airpath + 'scanheader ' + self.name,
+ shell=True,
+ stdout=subprocess.PIPE)
+ if process.wait() != 0:
+ raise ModuleError(self, "Could not open header file " + self.name)
+
+ result = {}
+ lines = core.utils.no_interrupt(process.stdout.readlines)
+ for l in lines:
+ l = l[:-1]
+ if not l:
+ continue
+ entries = l.split('=')
+ if len(entries) != 2:
+ raise ModuleError(self,
+ "Error parsing line '%s' of header %s" %
+ (l[:-1], self.name))
+ result[entries[0]] = entries[1]
+ return result
+
+ def compute(self):
+ core.modules.basic_modules.File.compute(self)
+ d = self.get_header_annotations()
+ self.annotate(d)
+
+
+class AlignWarp(ProvenanceChallenge):
+ """AlignWarp executes the AIR warping tool on the input."""
+
+ def compute(self):
+ image = self.getInputFromPort("image")
+ ref = self.getInputFromPort("reference")
+ model = self.getInputFromPort("model")
+ o = self.interpreter.filePool.create_file(suffix='.warp')
+ cmd = self.air_cmd_line('align_warp',
+ image.name,
+ ref.name,
+ o.name,
+ '-m',
+ str(model),
+ '-q')
+ self.run(cmd)
+ self.setResult("output", o)
+
+
+class Reslice(ProvenanceChallenge):
+ """AlignWarp executes the AIR reslicing tool on the input."""
+
+ def compute(self):
+ warp = self.getInputFromPort("warp")
+ o = self.interpreter.filePool.create_file()
+ cmd = self.air_cmd_line('reslice',
+ warp.name,
+ o.name)
+ self.run(cmd)
+ self.setResult("output", o)
+
+
+class SoftMean(ProvenanceChallenge):
+ """SoftMean executes the AIR softmean averaging tool on the input."""
+
+ def compute(self):
+ imageList = self.getInputFromPort("imageList")
+ o = self.interpreter.filePool.create_file(suffix='.hdr')
+ cmd = self.air_cmd_line('softmean',
+ o.name,
+ 'y',
+ 'null',
+ *[f.name for f in imageList])
+ self.run(cmd)
+ self.setResult('output', o)
+
+
+class Slicer(ProvenanceChallenge):
+ """Slicer executes the FSL slicer tool on the input."""
+
+ def compute(self):
+ cmd = ['slicer']
+ i = self.getInputFromPort("input")
+ cmd.append(i.name)
+ if self.hasInputFromPort("slice_x"):
+ cmd.append('-x')
+ cmd.append(str(self.getInputFromPort("slice_x")))
+ elif self.hasInputFromPort("slice_y"):
+ cmd.append('-y')
+ cmd.append(str(self.getInputFromPort("slice_y")))
+ elif self.hasInputFromPort("slice_z"):
+ cmd.append('-z')
+ cmd.append(str(self.getInputFromPort("slice_z")))
+ o = self.interpreter.filePool.create_file(suffix='.pgm')
+ cmd.append(o.name)
+ self.run(self.fsl_cmd_line(*cmd))
+ self.setResult('output', o)
+
+
+class PGMToPPM(ProvenanceChallenge):
+ """PGMToPPM executes the netpbm pgmtoppm tool on the input."""
+
+ def compute(self):
+ cmd = ['pgmtoppm', 'white']
+ i = self.getInputFromPort("input")
+ cmd.append(i.name)
+ o = self.interpreter.filePool.create_file(suffix='.ppm')
+ cmd.append(' >')
+ cmd.append(o.name)
+ self.run(list2cmdline(cmd))
+ self.setResult('output', o)
+
+
+class PNMToJpeg(ProvenanceChallenge):
+ """PGMToPPM executes the netpbm pnmtojpeg tool on the input."""
+
+ def compute(self):
+ cmd = ['pnmtojpeg']
+ i = self.getInputFromPort("input")
+ cmd.append(i.name)
+ o = self.interpreter.filePool.create_file(suffix='.jpg')
+ cmd.append(' >')
+ cmd.append(o.name)
+ self.run(list2cmdline(cmd))
+ self.setResult('output', o)
+
+################################################################################
+
+def checkProgram(fileName):
+ return os.path.isfile(fileName) and os.stat(fileName) & 005
+
+def initialize(airpath=None, fslpath=None, netpbmpath=None, *args, **kwargs):
+ print "Initializing Provenance Challenge Package"
+
+ if not airpath:
+ print "airpath not specified or incorrect: Will assume AIR tools are on the path"
+ else:
+ print "Will use AIR tools from ", airpath
+ global global_airpath
+ global_airpath = airpath + '/'
+
+ if not fslpath:
+ print "fslpath not specified or incorrect: Will assume fsl tools are on the path"
+ else:
+ print "Will use FSL tools from ", fslpath
+ global global_fslpath
+ global_fslpath = fslpath + '/'
+
+ if not netpbmpath:
+ print "netpbmpath not specified or incorrect: Will assume netpbm tools are on the path"
+ else:
+ print "Will use netpbm tools from ", netpbmpath
+ global global_netpbmpath
+ global_netpbmpath = netpbmpath + '/'
+
+ reg = core.modules.module_registry
+ basic = core.modules.basic_modules
+ reg.add_module(ProvenanceChallenge)
+
+ reg.add_module(AlignWarp)
+ reg.add_input_port(AlignWarp, "image", (basic.File, 'the image file to be deformed'))
+ reg.add_input_port(AlignWarp, "image_header", (basic.File, 'the header of the image to be deformed'))
+ reg.add_input_port(AlignWarp, "reference", (basic.File, 'the reference image'))
+ reg.add_input_port(AlignWarp, "reference_header", (basic.File, 'the header of the reference image'))
+ reg.add_input_port(AlignWarp, "model", (basic.Integer, 'the deformation model'))
+ reg.add_output_port(AlignWarp, "output", (basic.File, 'the output deformation'))
+
+ reg.add_module(Reslice)
+ reg.add_input_port(Reslice, "warp", (basic.File, 'the warping to be resliced'))
+ reg.add_output_port(Reslice, "output", (basic.File, 'the new slice'))
+
+ reg.add_module(SoftMean)
+ reg.add_input_port(SoftMean, "imageList", (basic.List, 'image files'))
+ reg.add_output_port(SoftMean, "output", (basic.File, 'average image'))
+
+ reg.add_module(Slicer)
+ reg.add_input_port(Slicer, "input", (basic.File, 'the input file to be sliced'))
+ reg.add_input_port(Slicer, "slice_x", (basic.Float, 'sagittal slice with given value'))
+ reg.add_input_port(Slicer, "slice_y", (basic.Float, 'coronal slice with given value'))
+ reg.add_input_port(Slicer, "slice_z", (basic.Float, 'axial slice with given value'))
+ reg.add_output_port(Slicer, "output", (basic.File, 'slice output'))
+
+ reg.add_module(PGMToPPM)
+ reg.add_input_port(PGMToPPM, "input", (basic.File, "input"))
+ reg.add_output_port(PGMToPPM, "output", (basic.File, "output"))
+
+ reg.add_module(PNMToJpeg)
+ reg.add_input_port(PNMToJpeg, "input", (basic.File, "input"))
+ reg.add_output_port(PNMToJpeg, "output", (basic.File, "output"))
+
+ reg.add_module(AIRHeaderFile)
diff --git a/contrib/provenance2/__init__.py b/contrib/provenance2/__init__.py
new file mode 100644
index 0000000..7347b39
--- /dev/null
+++ b/contrib/provenance2/__init__.py
@@ -0,0 +1,366 @@
+############################################################################
+##
+## Copyright (C) 2006-2007 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+"""This package defines a set of methods that perform the command-line
+tools necesary for the task designed for the first Provenance Challenge:
+
+http://twiki.ipaw.info
+
+This VisTrails package requires three software packages to be installed:
+
+AIR - Automated Image Registration: http://bishopw.loni.ucla.edu/AIR5/
+FSL - http://www.fmrib.ox.ac.uk/fsl/
+netpbm - http://netpbm.sourceforge.net/
+
+"""
+
+from core.modules.vistrails_module import Module, ModuleError, new_module
+import core.modules
+import core.modules.basic_modules
+import core.modules.module_registry
+import core.utils
+import os
+import os.path
+import stat
+import subprocess
+import glob
+
+version = '0.9.0'
+name = 'Provenance Challenge'
+identifier = 'edu.utah.sci.vistrails.provenance2'
+
+################################################################################
+
+global_airpath = ""
+global_fslpath = ""
+global_netpbmpath = ""
+
+class ProvenanceChallenge(Module):
+ """ProvenanceChallenge is the base Module for all Modules in the provenance
+package. It simply define helper methods for subclasses."""
+
+ __quiet = True
+ __programsQuiet = True
+
+ def air_cmd_line(self, cmd, *params):
+ """Runs a command-line command for the AIR tools."""
+ return list2cmdline([global_airpath + cmd] + list(params))
+
+ def fsl_cmd_line(self, cmd, *params):
+ """Runs a command-line command for the FSL tools."""
+ return ('FSLOUTPUTTYPE=NIFTI_GZ ' +
+ list2cmdline([global_fslpath + cmd] + list(params)))
+
+ def netpbm_cmd_line(self, cmd, *params):
+ """Runs a command-line command for the netpbm tools."""
+ return list2cmdline([global_netpbmpath + cmd] + list(params))
+
+ def run(self, cmd):
+ if not self.__quiet:
+ print cmd
+ if self.__programsQuiet:
+ cmd = '(' + cmd + ') 2>&1 >/dev/null'
+ r = os.system(cmd)
+ if r != 0:
+ raise ModuleError(self, "system call failed: '%s'" % cmd)
+
+
+class AIRHeaderFile(core.modules.basic_modules.File):
+ """AIRHeaderFile subclasses File to annotate the execution with header
+file information for later querying."""
+
+ def get_header_annotations(self):
+ """Returns the header information for the file using the AIR scanheader
+tool."""
+ process = subprocess.Popen(global_airpath + 'scanheader ' + self.name,
+ shell=True,
+ stdout=subprocess.PIPE)
+
+ waitCode = 0
+ try:
+ waitCode = process.wait()
+ except OSError:
+ pass
+ if waitCode != 0:
+ raise ModuleError(self, "Could not open header file " + self.name)
+
+ result = {}
+ lines = core.utils.no_interrupt(process.stdout.readlines)
+ for l in lines:
+ l = l[:-1]
+ if not l:
+ continue
+ entries = l.split('=')
+ if len(entries) != 2:
+ raise ModuleError(self,
+ "Error parsing line '%s' of header %s" %
+ (l[:-1], self.name))
+ result[entries[0]] = entries[1]
+ return result
+
+ def compute(self):
+ core.modules.basic_modules.File.compute(self)
+ d = self.get_header_annotations()
+ self.annotate(d)
+
+
+class AlignWarp(ProvenanceChallenge):
+ """AlignWarp executes the AIR warping tool on the input."""
+
+ def compute(self):
+ image = self.getInputFromPort("image")
+ ref = self.getInputFromPort("reference")
+ model = self.getInputFromPort("model")
+ o = self.interpreter.filePool.create_file(suffix='.warp')
+ cmd = self.air_cmd_line('align_warp',
+ image.baseName,
+ ref.baseName,
+ o.name,
+ '-m',
+ model,
+ '-q')
+ self.run(cmd)
+ self.setResult("output", o)
+
+
+class Reslice(ProvenanceChallenge):
+ """AlignWarp executes the AIR reslicing tool on the input."""
+
+ def compute(self):
+ warp = self.getInputFromPort("warp")
+ o = self.interpreter.filePool.create_file()
+ cmd = self.air_cmd_line('reslice',
+ warp.name,
+ o.name)
+ self.run(cmd)
+ ofs = FileSet()
+ ofs.baseName = o.name
+ self.setResult("output", ofs)
+
+
+class SoftMean(ProvenanceChallenge):
+ """SoftMean executes the AIR softmean averaging tool on the input."""
+
+ def compute(self):
+ imageList = self.getInputFromPort("imageList")
+ o = self.interpreter.filePool.create_file()
+ cmd = self.air_cmd_line('softmean',
+ o.name,
+ 'y',
+ 'null',
+ *[f.baseName for f in imageList])
+ self.run(cmd)
+ ofs = FileSet()
+ ofs.baseName = o.name
+ self.setResult('output', ofs)
+
+class Slicer(ProvenanceChallenge):
+ """Slicer executes the FSL slicer tool on the input."""
+
+ def compute(self):
+ cmd = ['slicer']
+ i = self.getInputFromPort("input")
+ cmd.append(i.baseName)
+ if self.hasInputFromPort("slice_x"):
+ cmd.append('-x')
+ cmd.append(str(self.getInputFromPort("slice_x")))
+ elif self.hasInputFromPort("slice_y"):
+ cmd.append('-y')
+ cmd.append(str(self.getInputFromPort("slice_y")))
+ elif self.hasInputFromPort("slice_z"):
+ cmd.append('-z')
+ cmd.append(str(self.getInputFromPort("slice_z")))
+ o = self.interpreter.filePool.create_file(suffix='.pgm')
+ cmd.append(o.name)
+ self.run(self.fsl_cmd_line(*cmd))
+ self.setResult('output', o)
+
+
+class PGMToPPM(ProvenanceChallenge):
+ """PGMToPPM executes the netpbm pgmtoppm tool on the input."""
+
+ def compute(self):
+ cmd = ['pgmtoppm white']
+ i = self.getInputFromPort("input")
+ cmd.append(i.name)
+ o = self.interpreter.filePool.create_file(suffix='.ppm')
+ cmd.append(' >')
+ cmd.append(o.name)
+ self.run(self.netpbm_cmd_line(*cmd))
+ self.setResult('output', o)
+
+
+class PNMToJpeg(ProvenanceChallenge):
+ """PGMToPPM executes the netpbm pnmtojpeg tool on the input."""
+
+ def compute(self):
+ cmd = ['pnmtojpeg']
+ i = self.getInputFromPort("input")
+ cmd.append(i.name)
+ o = self.interpreter.filePool.create_file(suffix='.jpg')
+ cmd.append(' >')
+ cmd.append(o.name)
+ self.run(self.netpbm_cmd_line(*cmd))
+ self.setResult('output', o)
+
+class FileSet(ProvenanceChallenge):
+ """FileSet stores a set of files related by a common filename base."""
+
+ def compute(self):
+ self.checkInputPort("baseName")
+ n = self.getInputFromPort("baseName")
+ if self.hasInputFromPort("file_hdr") and \
+ self.hasInputFromPort("file_img"):
+ n1 = self.getInputFromPort("file_hdr").name
+ n2 = self.getInputFromPort("file_img").name
+ if n1.endswith('.hdr'):
+ n1base = n1.rsplit('.hdr',1)[0]
+ else:
+ n1base = n1
+ if n2.endswith('.img'):
+ n2base = n2.rsplit('.img',1)[0]
+ else:
+ n2base = n2
+ if n1base != n2base:
+ o = self.interpreter.filePool.create_file()
+ o1 = o.name + '.hdr'
+ o2 = o.name + '.img'
+ try:
+ core.system.link_or_copy(n1, o1)
+ except OSError, e:
+ msg = "error creating tmp file '%s'" % o1
+ raise ModuleError(self, msg)
+ try:
+ core.system.link_or_copy(n2, o2)
+ except OSError, e:
+ msg = "error creating tmp file '%s'" % o2
+ raise ModuleError(self, msg)
+ else:
+ self.baseName = n1base
+ else:
+ self.baseName = n
+ self.setResult("local_basename", self.baseName)
+
+class FileSetSink(ProvenanceChallenge):
+ """FileSetSink is a module that takes a file set and writes them
+ in a user-specified location in the file system."""
+
+ def compute(self):
+ self.checkInputPort("fileSet")
+ self.checkInputPort("outputBaseName")
+ v1 = self.getInputFromPort("fileSet")
+ v2 = self.getInputFromPort("outputBaseName")
+ filenames = glob.glob('%s.*' % v1.baseName)
+ for filename in filenames:
+ try:
+ outFilename = filename.replace(v1.baseName, v2, 1)
+ core.system.link_or_copy(filename, outFilename)
+ except OSError, e:
+ if (self.hasInputFromPort("overrideFile") and
+ self.getInputFromPort("overrideFile")):
+ try:
+ os.unlink(outFilename)
+ core.system.link_or_copy(filename, outFilename)
+ except OSError, e:
+ msg = "(override true) Could not create file '%s'" % \
+ outFilename
+ raise ModuleError(self, msg)
+ else:
+ msg = "Could not create file '%s': %s" % (outFilename, e)
+ raise ModuleError(self, msg)
+
+################################################################################
+
+def checkProgram(fileName):
+ return os.path.isfile(fileName) and os.stat(fileName) & 005
+
+def initialize(airpath=None, fslpath=None, netpbmpath=None, *args, **kwargs):
+ print "Initializing Provenance Challenge Package"
+
+ if not airpath:
+ print "airpath not specified or incorrect: Will assume AIR tools are on the path"
+ else:
+ print "Will use AIR tools from ", airpath
+ global global_airpath
+ global_airpath = airpath + '/'
+
+ if not fslpath:
+ print "fslpath not specified or incorrect: Will assume fsl tools are on the path"
+ else:
+ print "Will use FSL tools from ", fslpath
+ global global_fslpath
+ global_fslpath = fslpath + '/'
+
+ if not netpbmpath:
+ print "netpbmpath not specified or incorrect: Will assume netpbm tools are on the path"
+ else:
+ print "Will use netpbm tools from ", netpbmpath
+ global global_netpbmpath
+ global_netpbmpath = netpbmpath + '/'
+
+ reg = core.modules.module_registry
+ basic = core.modules.basic_modules
+ reg.add_module(ProvenanceChallenge)
+
+ reg.add_module(AlignWarp)
+ reg.add_input_port(AlignWarp, "image", (FileSet, 'the image file to be deformed'))
+# reg.add_input_port(AlignWarp, "image_header", (basic.File, 'the header of the image to be deformed'))
+ reg.add_input_port(AlignWarp, "reference", (FileSet, 'the reference image'))
+# reg.add_input_port(AlignWarp, "reference_header", (basic.File, 'the header of the reference image'))
+ reg.add_input_port(AlignWarp, "model", (basic.Integer, 'the deformation model'))
+ reg.add_output_port(AlignWarp, "output", (basic.File, 'the output deformation'))
+
+ reg.add_module(Reslice)
+ reg.add_input_port(Reslice, "warp", (basic.File, 'the warping to be resliced'))
+ reg.add_output_port(Reslice, "output", (FileSet, 'the new slice'))
+
+ reg.add_module(SoftMean)
+ reg.add_input_port(SoftMean, "imageList", (basic.List, 'image files'))
+ reg.add_output_port(SoftMean, "output", (FileSet, 'average image'))
+
+ reg.add_module(Slicer)
+ reg.add_input_port(Slicer, "input", (FileSet, 'the input file to be sliced'))
+ reg.add_input_port(Slicer, "slice_x", (basic.Float, 'sagittal slice with given value'))
+ reg.add_input_port(Slicer, "slice_y", (basic.Float, 'coronal slice with given value'))
+ reg.add_input_port(Slicer, "slice_z", (basic.Float, 'axial slice with given value'))
+ reg.add_output_port(Slicer, "output", (basic.File, 'slice output'))
+
+ reg.add_module(PGMToPPM)
+ reg.add_input_port(PGMToPPM, "input", (basic.File, "input"))
+ reg.add_output_port(PGMToPPM, "output", (basic.File, "output"))
+
+ reg.add_module(PNMToJpeg)
+ reg.add_input_port(PNMToJpeg, "input", (basic.File, "input"))
+ reg.add_output_port(PNMToJpeg, "output", (basic.File, "output"))
+
+ reg.add_module(AIRHeaderFile)
+
+ reg.add_module(FileSet)
+ reg.add_input_port(FileSet, "file_hdr", basic.File)
+ reg.add_input_port(FileSet, "file_img", basic.File)
+ reg.add_input_port(FileSet, "baseName", basic.String)
+ reg.add_output_port(FileSet, "self", FileSet)
+ reg.add_output_port(FileSet, "local_basename", basic.String)
+
+ reg.add_module(FileSetSink)
+ reg.add_input_port(FileSetSink, "fileSet", FileSet)
+ reg.add_input_port(FileSetSink, "outputBaseName", basic.String)
+ reg.add_input_port(FileSetSink, "overrideFile", basic.Boolean)
diff --git a/contrib/sahm/ColorBreaks.csv b/contrib/sahm/ColorBreaks.csv
new file mode 100644
index 0000000..ac8f0a2
--- /dev/null
+++ b/contrib/sahm/ColorBreaks.csv
@@ -0,0 +1,18 @@
+layer,StartBreak,r,g,b
+prob_map,0,0,0,255
+prob_map,0.25,85,255,255
+prob_map,0.5,0,255,0
+prob_map,0.75,255,255,0
+prob_map,1,255,0,0
+res_map,-1,0,0,255
+res_map,-0.00000001,85,255,255
+res_map,0.00000001,255,255,0
+res_map,1,255,0,0
+bin_map,0,0,0,0
+bin_map,0.499999999,0,0,0
+bin_map,0.5000001,255,255,255
+bin_map,1,255,255,255
+mes_map,-100,0,0,255
+mes_map,-0.00000001,85,255,255
+mes_map,0.00000001,255,255,0
+mes_map,100,255,0,0
diff --git a/contrib/sahm/Images/BinMap.png b/contrib/sahm/Images/BinMap.png
new file mode 100644
index 0000000..64c8c96
Binary files /dev/null and b/contrib/sahm/Images/BinMap.png differ
diff --git a/contrib/sahm/Images/BlackPoints.png b/contrib/sahm/Images/BlackPoints.png
new file mode 100644
index 0000000..590c048
Binary files /dev/null and b/contrib/sahm/Images/BlackPoints.png differ
diff --git a/contrib/sahm/Images/GreenPoints.png b/contrib/sahm/Images/GreenPoints.png
new file mode 100644
index 0000000..127f0a4
Binary files /dev/null and b/contrib/sahm/Images/GreenPoints.png differ
diff --git a/contrib/sahm/Images/MesMap.png b/contrib/sahm/Images/MesMap.png
new file mode 100644
index 0000000..180857a
Binary files /dev/null and b/contrib/sahm/Images/MesMap.png differ
diff --git a/contrib/sahm/Images/ModMap.png b/contrib/sahm/Images/ModMap.png
new file mode 100644
index 0000000..e3f057e
Binary files /dev/null and b/contrib/sahm/Images/ModMap.png differ
diff --git a/contrib/sahm/Images/ProbMap.png b/contrib/sahm/Images/ProbMap.png
new file mode 100644
index 0000000..cb56001
Binary files /dev/null and b/contrib/sahm/Images/ProbMap.png differ
diff --git a/contrib/sahm/Images/RedPoints.png b/contrib/sahm/Images/RedPoints.png
new file mode 100644
index 0000000..ef4b8d5
Binary files /dev/null and b/contrib/sahm/Images/RedPoints.png differ
diff --git a/contrib/sahm/Images/ResMap.png b/contrib/sahm/Images/ResMap.png
new file mode 100644
index 0000000..37b24bf
Binary files /dev/null and b/contrib/sahm/Images/ResMap.png differ
diff --git a/contrib/sahm/Images/icons.pptx b/contrib/sahm/Images/icons.pptx
new file mode 100644
index 0000000..fa9e1d0
Binary files /dev/null and b/contrib/sahm/Images/icons.pptx differ
diff --git a/contrib/sahm/SahmOutputViewer.py b/contrib/sahm/SahmOutputViewer.py
new file mode 100644
index 0000000..4f21f01
--- /dev/null
+++ b/contrib/sahm/SahmOutputViewer.py
@@ -0,0 +1,494 @@
+################################################################################
+# ImageViewer widgets/toolbar implementation
+################################################################################
+from PyQt4 import QtCore, QtGui, QAxContainer
+from core.modules.vistrails_module import Module
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+from packages.spreadsheet.spreadsheet_controller import spreadsheetController
+from SahmViewerCell import Ui_Frame
+#import imageviewer_rc
+import os
+################################################################################
+
+class SAHMModelOutputViewerCell(SpreadsheetCell):
+ """
+ SAHMModelOutputViewerCell displays the various non-spatial
+ outputs from a SAHM Model run
+ """
+ _input_ports = [("row", "(edu.utah.sci.vistrails.basic:Integer)"),
+ ("column", "(edu.utah.sci.vistrails.basic:Integer)"),
+ ('ModelWorkspace', '(edu.utah.sci.vistrails.basic:File)')]
+
+ def compute(self):
+ """ compute() -> None
+ Dispatch the display event to the spreadsheet with images and labels
+
+ """
+ if self.hasInputFromPort("ModelWorkspace"):
+ window = spreadsheetController.findSpreadsheetWindow()
+ model_workspace = self.getInputFromPort("ModelWorkspace").name
+ model_dir_full = os.path.normcase(os.path.split(model_workspace)[0])
+ model_dir = os.path.split(model_dir_full)[1]
+ model_name = model_dir[:model_dir.index('output')]
+
+# prob_map_path = os.path.join(model_dir_full, model_name + '_prob_map.jpeg')
+# prob_map = window.file_pool.make_local_copy(prob_map_path)
+
+ auc_graph_path = os.path.join(model_dir_full, model_name + '_auc_plot.jpg')
+ auc_graph = window.file_pool.make_local_copy(auc_graph_path)
+
+ text_output_path = os.path.join(model_dir_full, model_name + '_output.txt')
+ text_output = window.file_pool.make_local_copy(text_output_path)
+
+ response_path = os.path.join(model_dir_full, model_name + '_response_curves.pdf')
+ response_curves = window.file_pool.make_local_copy(response_path)
+
+ model_label = model_dir.capitalize().replace('output', 'Output')
+
+
+ if self.hasInputFromPort("row"):
+ if not self.location:
+ self.location = CellLocation()
+ self.location.row = self.getInputFromPort('row') - 1
+
+ if self.hasInputFromPort("column"):
+ if not self.location:
+ self.location = CellLocation()
+ self.location.col = self.getInputFromPort('column') - 1
+
+ else:
+ fileValue = None
+ self.cellWidget = self.displayAndWait(SAHMOutputViewerCellWidget, (auc_graph,
+ text_output,
+ response_curves,
+ model_label))
+
+class SAHMOutputViewerCellWidget(QCellWidget):
+ """
+ SAHMOutputViewerCellWidget is the widget that will display the various
+ non spatial outputs from a model run
+ """
+ def __init__(self, parent=None):
+ QCellWidget.__init__(self, parent)
+
+ centralLayout = QtGui.QVBoxLayout()
+ self.setLayout(centralLayout)
+ centralLayout.setMargin(0)
+ centralLayout.setSpacing(0)
+
+
+# self.setAnimationEnabled(True)
+
+ self.Frame = QtGui.QFrame()
+ self.ui = Ui_Frame()
+ self.ui.setupUi(self.Frame)
+
+# #add scenes to our graphicViews
+# self.gs_prob_map = QtGui.QGraphicsScene()
+# self.ui.gv_prob_map.setScene(self.gs_prob_map)
+# self.gs_prob_map.wheelEvent = self.wheel_event_prob
+
+ self.gs_auc_graph = QtGui.QGraphicsScene()
+ self.ui.gv_auc.setScene(self.gs_auc_graph)
+ self.gs_auc_graph.wheelEvent = self.wheel_event_auc
+
+ #add in ie browsers for the text and response
+ self.text_browser = QAxContainer.QAxWidget(self)
+ self.text_browser.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.text_browser.setControl("{8856F961-340A-11D0-A96B-00C04FD705A2}")
+ self.ui.text_output_layout.addWidget(self.text_browser)
+ self.text_urlSrc = None
+
+ self.response_browser = QAxContainer.QAxWidget(self)
+ self.response_browser.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.response_browser.setControl("{8856F961-340A-11D0-A96B-00C04FD705A2}")
+ self.ui.response_curves_layout.addWidget(self.response_browser)
+ self.response_urlSrc = None
+
+
+ self.layout().addWidget(self.Frame)
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple) -> None
+ Update the widget contents based on the input data
+
+ """
+ (auc_graph, text_output, response_curves, model_label) = inputPorts
+
+ self.images = {}
+# if prob_map:
+# #Value = (full image, sized image, scene, view, max_height)
+# pixmap = QtGui.QPixmap(prob_map.name)
+# max_size = self.getMaxSize(self.ui.gv_prob_map)
+# scaled_pixmap = pixmap.scaled(max_size, max_size,
+# QtCore.Qt.KeepAspectRatio,
+# QtCore.Qt.FastTransformation)
+#
+# self.images['prob_map'] = [pixmap,
+# scaled_pixmap,
+# self.gs_prob_map,
+# self.ui.gv_prob_map,
+# max_size]
+
+ if auc_graph:
+ pixmap = QtGui.QPixmap(auc_graph.name)
+ max_size = self.getMaxSize(self.ui.gv_auc)
+ scaled_pixmap = pixmap.scaled(max_size, max_size,
+ QtCore.Qt.KeepAspectRatio,
+ QtCore.Qt.SmoothTransformation)
+
+ self.images['auc_graph'] = [pixmap,
+ scaled_pixmap,
+ self.gs_auc_graph,
+ self.ui.gv_auc,
+ max_size]
+
+
+
+ self.text_urlSrc = QtCore.QUrl.fromLocalFile(text_output.name)
+ if self.text_urlSrc!=None:
+ self.text_browser.dynamicCall('Navigate(const QString&)', self.text_urlSrc.toString())
+ else:
+ self.text_browser.dynamicCall('Navigate(const QString&)', QtCore.QString('about:blank'))
+
+ self.response_urlSrc = QtCore.QUrl.fromLocalFile(response_curves.name)
+ if self.response_urlSrc!=None:
+ self.response_browser.dynamicCall('Navigate(const QString&)', self.response_urlSrc.toString())
+ else:
+ self.response_browser.dynamicCall('Navigate(const QString&)', QtCore.QString('about:blank'))
+
+ self.view_current()
+
+ #QCellWidget.updateContents(self, inputPorts)
+
+ def getMaxSize(self, view):
+ return self.Frame.size().width() - 10
+# if view.size().width() <= view.size().height():
+# return view.size().width() * 0.95
+# else:
+# return view.size().height() * 0.95
+
+ def view_current(self):
+ for k,v in self.images.iteritems():
+ size_img = v[1].size()
+ wth, hgt = QtCore.QSize.width(size_img), QtCore.QSize.height(size_img)
+ v[2].clear()
+ v[2].setSceneRect(0, 0, wth, hgt)
+ v[2].addPixmap(v[1])
+ QtCore.QCoreApplication.processEvents()
+
+ def wheel_event_prob(self, event):
+ self.wheel_event(event, 'prob_map', QtCore.Qt.FastTransformation)
+
+ def wheel_event_auc(self, event):
+ self.wheel_event(event, 'auc_graph', QtCore.Qt.SmoothTransformation)
+
+ def wheel_event (self, event, id, transform):
+ numDegrees = event.delta() / 8
+ numSteps = numDegrees / 15.0
+ self.zoom(numSteps, self.images[id], transform)
+ event.accept()
+
+ def zoom(self, step, images, transform):
+ zoom_step = 0.06
+ images[2].clear()
+ w = images[1].size().width()
+ h = images[1].size().height()
+ w, h = w * (1 + zoom_step*step), h * (1 + zoom_step*step)
+ images[1] = images[0].scaled(w, h,
+ QtCore.Qt.KeepAspectRatio,
+ transform)
+ self.view_current()
+
+ def saveToPNG(self, filename):
+ """ saveToPNG(filename: str) -> bool
+ Save the current widget contents to an image file
+
+ """
+
+ pixmap = QtGui.QPixmap(self.Frame.size())
+ painter = QtGui.QPainter(pixmap)
+ self.Frame.render(painter)
+ painter.end()
+
+ if pixmap and (not pixmap.isNull()):
+ return pixmap.save(filename)
+ return False
+
+ def saveToPDF(self, filename):
+ """ saveToPDF(filename: str) -> bool
+ Save the current widget contents to a pdf file
+
+ """
+ printer = QtGui.QPrinter()
+
+ printer.setOutputFormat(QtGui.QPrinter.PdfFormat)
+ printer.setOutputFileName(filename)
+ painter = QtGui.QPainter()
+ painter.begin(printer)
+ rect = painter.viewport()
+ pixmap = self.label.pixmap()
+ size = pixmap.size()
+ size.scale(rect.size(), QtCore.Qt.KeepAspectRatio)
+ painter.setViewport(rect.x(), rect.y(), size.width(), size.height())
+ painter.setWindow(pixmap.rect())
+ painter.drawPixmap(0, 0, pixmap)
+ painter.end()
+#
+# def resizeEvent(self, e):
+# if self.originalPix!=None:
+# self.label.setPixmap(self.originalPix.scaled(self.label.size(),
+# QtCore.Qt.KeepAspectRatio,
+# QtCore.Qt.SmoothTransformation))
+#
+
+class ImageViewerFitToCellAction(QtGui.QAction):
+ """
+ ImageViewerFitToCellAction is the action to stretch the image to
+ fit inside a cell
+
+ """
+ def __init__(self, parent=None):
+ """ ImageViewerFitToCellAction(parent: QWidget)
+ -> ImageViewerFitToCellAction
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/fittocell.png"),
+ "&Fit To Cell",
+ parent)
+ self.setStatusTip("Scale image content to fit cell frame")
+ self.setCheckable(True)
+ self.setChecked(True)
+
+ def toggledSlot(self, checked):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is toggled
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ cellWidget.label.setScaledContents(checked)
+ self.toolBar.slider.updateStatus((self.toolBar.sheet,
+ self.toolBar.row,
+ self.toolBar.col,
+ cellWidget))
+
+ def updateStatus(self, info):
+ """ updateStatus(info: tuple) -> None
+ Updates the status of the button based on the input info
+
+ """
+ (sheet, row, col, cellWidget) = info
+ self.setChecked(cellWidget.label.hasScaledContents())
+
+class ImageViewerSaveAction(QtGui.QAction):
+ """
+ ImageViewerSaveAction is the action to save the image to file
+
+ """
+ def __init__(self, parent=None):
+ """ ImageViewerSaveAction(parent: QWidget) -> ImageViewerSaveAction
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/save.png"),
+ "&Save image as...",
+ parent)
+ self.setStatusTip("Save image to file")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ if not cellWidget.label.pixmap() or cellWidget.label.pixmap().isNull():
+ return
+ fn = QtGui.QFileDialog.getSaveFileName(None, "Save image as...",
+ "screenshot.png",
+ "Images (*.png);;PDF files (*.pdf)")
+ if not fn:
+ return
+ if fn.endsWith(QtCore.QString("png"), QtCore.Qt.CaseInsensitive):
+ cellWidget.label.pixmap().toImage().save(fn, "png")
+ elif fn.endsWith(QtCore.QString("pdf"), QtCore.Qt.CaseInsensitive):
+ cellWidget.saveToPDF(str(fn))
+
+#class testButton(QtGui.QAction):
+# def __init__(self, parent=None):
+# """ ImageViewerRotateAction(parent: QWidget)
+# -> ImageViewerRotateAction
+# Setup the image, status tip, etc. of the action
+#
+# """
+# QtGui.QAction.__init__(self,
+# QtGui.QIcon(":/images/grass_split_line.png"),
+# "&Do Something...",
+# parent)
+# self.setStatusTip("We'll do something with this soon")
+# self.rotationMatrix = QtGui.QMatrix(0,1,-1,0,0,0)
+#
+#class ModelLabel(QtGui.QLabel):
+# def __init__(self, parent=None):
+# """A lable to indicate which model the output pertains to
+# """
+# self.text = QtCore.QString("testing")
+#
+#class ImageViewerZoomSlider(QtGui.QSlider):
+# """
+# ImageViewerZoomSlider is a slider that allows user to zoom in and
+# out by dragging it
+# """
+# def __init__(self, parent=None):
+# """ ImageViewerZoomSlider(parent: QWidget) -> ImageViewerZoomSlider
+# Setup the ranges, status tip, etc. of the slider
+#
+# """
+# QtGui.QSlider.__init__(self, QtCore.Qt.Horizontal, parent)
+# self.setRange(100, 600)
+# self.setValue(100)
+# self.setTracking(True)
+# self.setStatusTip("Zoom in the image")
+# self.connect(self, QtCore.SIGNAL("valueChanged(int)"), self.updateZoom)
+# self.connect(self, QtCore.SIGNAL("needUpdateStatus"), self.updateStatus)
+# self.setSizePolicy(QtGui.QSizePolicy.Preferred,
+# QtGui.QSizePolicy.Expanding)
+#
+# def updateZoom(self, value):
+# """ updateZoom(value: int) -> None
+# Update the image when the slider value changed
+#
+# """
+# if self.toolBar:
+# cellWidget = self.toolBar.getSnappedWidget()
+# if not cellWidget.label.hasScaledContents():
+# newWidth = cellWidget.originalPix.width()*value/100
+# pixmap = cellWidget.originalPix.scaledToWidth(newWidth)
+# cellWidget.label.setPixmap(pixmap)
+#
+# def updateStatus(self, info):
+# """ updateStatus(info: tuple) -> None
+# Updates the status of the button based on the input info
+#
+# """
+# (sheet, row, col, cellWidget) = info
+# if cellWidget:
+# if (not cellWidget.label.hasScaledContents() and
+# not cellWidget._playing):
+# self.setEnabled(True)
+# originalWidth = cellWidget.originalPix.width()
+# self.setValue(cellWidget.label.pixmap().width()*100/originalWidth)
+# else:
+# self.setEnabled(False)
+# self.setValue(100)
+#
+#class ImageViewerZoomLabel(QtGui.QLabel):
+# """
+# ImageViewerZoomLabel is the label sitting next to the ImageViewerZoomSlider
+#
+# """
+# def __init__(self, parent=None):
+# """ ImageViewerZoomSlider(parent: QWidget) -> None
+# Setup the label with a status tip
+#
+# """
+# QtGui.QLabel.__init__(self, "100%", parent)
+# self.setStatusTip("Zoom in the image")
+#
+# def updateValue(self, value):
+# """ updateValue(value: int)
+# Updates the label with the new percentage value
+# """
+# self.setText(str(value)+"%")
+#
+#class ImageViewerRotateAction(QtGui.QAction):
+# """
+# ImageViewerRotateAction is the action to rotate the image
+#
+# """
+# def __init__(self, parent=None):
+# """ ImageViewerRotateAction(parent: QWidget)
+# -> ImageViewerRotateAction
+# Setup the image, status tip, etc. of the action
+#
+# """
+# QtGui.QAction.__init__(self,
+# QtGui.QIcon(":/images/rotate.png"),
+# "&Rotate CW...",
+# parent)
+# self.setStatusTip("Rotate 90 degrees CW")
+# self.rotationMatrix = QtGui.QMatrix(0,1,-1,0,0,0)
+#
+# def triggeredSlot(self, checked=False):
+# """ toggledSlot(checked: boolean) -> None
+# Execute the action when the button is clicked
+#
+# """
+# cellWidget = self.toolBar.getSnappedWidget()
+# if not cellWidget.label.pixmap() or cellWidget.label.pixmap().isNull():
+# return
+# cellWidget.originalPix = cellWidget.originalPix.transformed(
+# self.rotationMatrix)
+# cellWidget.label.setPixmap(cellWidget.label.pixmap().transformed(
+# self.rotationMatrix))
+#
+#class ImageViewerFlipAction(QtGui.QAction):
+# """
+# ImageViewerFlipAction is the action to flip the image
+#
+# """
+# def __init__(self, parent=None):
+# """ ImageViewerFlipAction(parent: QWidget) -> ImageViewerFlipAction
+# Setup the image, status tip, etc. of the action
+#
+# """
+# QtGui.QAction.__init__(self,
+# QtGui.QIcon(":/images/flip.png"),
+# "&Flip Horizontal...",
+# parent)
+# self.setStatusTip("Flip the image horizontally")
+# self.flipMatrix = QtGui.QMatrix(-1,0,0,1,0,0)
+#
+# def triggeredSlot(self, checked=False):
+# """ toggledSlot(checked: boolean) -> None
+# Execute the action when the button is clicked
+#
+# """
+# cellWidget = self.toolBar.getSnappedWidget()
+# label = cellWidget.label
+# if not label.pixmap() or label.pixmap().isNull():
+# return
+# cellWidget.originalPix = cellWidget.originalPix.transformed(
+# self.flipMatrix)
+# label.setPixmap(label.pixmap().transformed(self.flipMatrix))
+#
+#class ImageViewerToolBar(QCellToolBar):
+# """
+# ImageViewerToolBar derives from CellToolBar to give the ImageViewerCellWidget
+# a customizable toolbar
+#
+# """
+# def createToolBar(self):
+# """ createToolBar() -> None
+# This will get call initiallly to add customizable widgets
+#
+# """
+# global SAHMModelOutputViewerCell
+#
+## self.appendAction(QtCore.QString(SAHMModelOutputViewerCell.model_label))
+# self.appendAction(testButton(self))
+# self.appendAction(ImageViewerFitToCellAction(self))
+# self.appendAction(ImageViewerSaveAction(self))
+# self.appendAction(ImageViewerRotateAction(self))
+# self.appendAction(ImageViewerFlipAction(self))
+# self.slider = ImageViewerZoomSlider(self)
+# label = ImageViewerZoomLabel(self)
+# self.connect(self.slider,
+# QtCore.SIGNAL("valueChanged(int)"),
+# label.updateValue)
+# self.appendWidget(self.slider)
+# self.appendWidget(label)
+# self.addAnimationButtons()
\ No newline at end of file
diff --git a/contrib/sahm/SahmSpatialOutputViewer.py b/contrib/sahm/SahmSpatialOutputViewer.py
new file mode 100644
index 0000000..c5f2696
--- /dev/null
+++ b/contrib/sahm/SahmSpatialOutputViewer.py
@@ -0,0 +1,483 @@
+################################################################################
+# ImageViewer widgets/toolbar implementation
+################################################################################
+from PyQt4 import QtCore, QtGui, QAxContainer
+from core.modules.vistrails_module import Module
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+from packages.spreadsheet.spreadsheet_controller import spreadsheetController
+from SahmSpatialViewerCell import Ui_Frame
+#import imageviewer_rc
+import os
+
+import csv
+
+from packages.sahm.pySAHM.utilities import mds_to_shape
+from utils import getrasterminmax
+################################################################################
+
+def setQGIS(qgis):
+ globals()["qgis"] = qgis
+
+class SAHMSpatialOutputViewerCell(SpreadsheetCell):
+ """
+ SAHMModelOutputViewerCell displays the various output from a SAHM Model run
+
+ """
+ _input_ports = [("row", "(edu.utah.sci.vistrails.basic:Integer)"),
+ ("column", "(edu.utah.sci.vistrails.basic:Integer)"),
+ ('model_workspace', '(edu.utah.sci.vistrails.basic:File)')]
+
+ def __init__(self):
+ SpreadsheetCell.__init__(self)
+
+# globals()["qgis"] = qgis
+
+ def compute(self):
+ inputs = {}
+ inputs["model_workspace"] = self.forceGetInputFromPort('model_workspace').name
+ inputs["model_dir"] = os.path.split(inputs["model_workspace"])[0]
+
+ inputs["prob_map"] = os.path.join(inputs["model_dir"],
+ self.find_file(inputs["model_dir"], "_prob_map.tif"))
+ inputs["bin_map"] = os.path.join(inputs["model_dir"],
+ self.find_file(inputs["model_dir"], "_bin_map.tif"))
+ inputs["res_map"] = os.path.join(inputs["model_dir"],
+ self.find_file(inputs["model_dir"], "_resid_map.tif"))
+ try:
+ inputs["mes_map"] = os.path.join(inputs["model_dir"],
+ self.find_file(inputs["model_dir"], "_mess_map.tif"))
+ except:
+ inputs["mes_map"] = ""
+
+ try:
+ inputs["mod_map"] = os.path.join(inputs["model_dir"],
+ self.find_file(inputs["model_dir"], "_MoD_map.tif"))
+ except:
+ inputs["mod_map"] = ""
+
+ mds = self.find_mds(inputs["model_dir"])
+ shaperoot = self.gen_points_shp(mds)
+ inputs["pres_points"] = shaperoot + "_pres.shp"
+ inputs["abs_points"] = shaperoot + "_abs.shp"
+ inputs["backs_points"] = shaperoot + "_backs.shp"
+
+ inputs["model_tag"] = os.path.split(inputs["model_dir"])[1]
+
+ if self.hasInputFromPort("row"):
+ if not self.location:
+ self.location = CellLocation()
+ self.location.row = self.getInputFromPort('row') - 1
+
+ if self.hasInputFromPort("column"):
+ if not self.location:
+ self.location = CellLocation()
+ self.location.col = self.getInputFromPort('column') - 1
+
+ self.displayAndWait(SAHMSpatialOutputViewerCellWidget,
+ inputs)
+
+
+ def find_file(self, model_dir, suffix):
+ return [file_name for file_name in os.listdir(model_dir)
+ if file_name.endswith(suffix)][0]
+
+ def find_mds(self, model_dir):
+ model_text = os.path.join(model_dir,
+ self.find_file(model_dir, "_output.txt"))
+
+ f = open(model_text, 'rb')
+ lines = f.read().splitlines()
+
+ # grab the line after "Data:"
+ result = [lines[i + 1] for i in range(len(lines))
+ if lines[i].startswith("Data:")][0].strip()
+
+ if os.path.exists(result):
+ return result
+ else:
+ raise RuntimeError('Valid input MDS file not found in Model text output.')
+
+ def gen_points_shp(self, mds):
+ """I couldn't figure out how to use a render on a shapefile
+ instead I split the shapefile into three separate files for each
+ class.
+ This split only occurs once per mds though.
+ """
+ parentfolder, filename = os.path.split(mds)
+ filenoext = os.path.splitext(filename)[0]
+ shpfolder = os.path.join(parentfolder, "PointShapefiles")
+
+ if not os.path.exists(shpfolder):
+ os.mkdir(shpfolder)
+ fileroot = os.path.join(shpfolder, filenoext)
+
+ pregenerated = True
+ for type in ["_pres", "_abs", "_backs"]:
+ shape_file = fileroot + type + ".shp"
+ if not os.path.exists(shape_file):
+ pregenerated = False
+
+ if not pregenerated:
+ mds_to_shape(mds, shpfolder)
+
+ return fileroot
+
+
+class SAHMSpatialOutputViewerCellWidget(QCellWidget):
+ """
+
+ """
+ def __init__(self, parent=None):
+ """ QGISCellWidget(parent: QWidget) -> QGISCellWidget
+ Initialize the widget with its central layout
+
+ """
+ QCellWidget.__init__(self, parent)
+
+ centralLayout = QtGui.QVBoxLayout()
+ self.setLayout(centralLayout)
+ centralLayout.setMargin(0)
+ centralLayout.setSpacing(0)
+
+# self.setAnimationEnabled(True)
+
+ self.Frame = QtGui.QFrame()
+ self.ui = Ui_Frame()
+ self.ui.setupUi(self.Frame)
+
+ self.toolBarType = SAHMSpatialViewerToolBar
+ self.controlBarType = SAHMSpatialViewerToolBar
+
+ self.layout().addWidget(self.Frame)
+
+
+ def updateContents(self, inputs):
+ """ updateContents(inputs: dictionary) -> None
+ Update the widget contents based on the input data
+ """
+
+ self.canvas = qgis.gui.QgsMapCanvas()
+ self.canvas.show()
+
+ self.ui.legend_label.setText(QtCore.QString(inputs["model_tag"]))
+
+ self.toolPan = qgis.gui.QgsMapToolPan(self.canvas)
+
+ self.canvas.setMapTool(self.toolPan)
+ self.canvas.setWheelAction(2)
+ self.canvas.setCanvasColor(QtCore.Qt.white)
+ self.canvas.enableAntiAliasing(True)
+
+ self.all_layers = {}
+ self.add_raster(inputs["prob_map"], "prob_map")
+ self.add_raster(inputs["bin_map"], "bin_map")
+ self.add_raster(inputs["res_map"], "res_map")
+ self.add_raster(inputs["mes_map"], "mes_map")
+ self.add_raster(inputs["mod_map"], "mod_map")
+
+ self.add_vector(inputs['pres_points'], "pres_points", '255,0,0')
+ self.add_vector(inputs['abs_points'], "abs_points", '0,255,0')
+ self.add_vector(inputs['backs_points'], "backs_points", '0,0,0')
+
+ self.canvas.setExtent(self.all_layers["prob_map"].layer().extent())
+ self.canvas.setLayerSet([self.all_layers["pres_points"],
+ self.all_layers["abs_points"],
+ self.all_layers["prob_map"]])
+
+ self.ui.map_frame.layout().addWidget(self.canvas)
+ legend = self.create_legend_ramp("prob_map", None, (0, 1), 6)
+
+ self.ui.legend.layout().addWidget(legend)
+ # Update the new figure canvas
+ self.update()
+
+ def dumpToFile(self, filename):
+ pass
+
+ def saveToPDF(self, filename):
+ pass
+
+ def add_raster(self, path, tag):
+ if os.path.exists(path):
+ fileInfo = QtCore.QFileInfo(path)
+ baseName = fileInfo.baseName()
+ raster = qgis.core.QgsRasterLayer(path, baseName)
+
+ if tag=="res_map":
+ min_max = getrasterminmax(path)
+ else:
+ min_max = None
+
+ self.set_color_ramp(tag, raster)
+ qgis.core.QgsMapLayerRegistry.instance().addMapLayer(raster)
+ self.all_layers[tag] = qgis.gui.QgsMapCanvasLayer(raster)
+ else:
+ print "The file " + path + " could not be found on the file system."
+ print " tag will not be enabled"
+
+ def set_color_ramp(self, layer_type, raster, min_max=None):
+ QgsColorRampShader = qgis.core.QgsColorRampShader
+
+
+ if layer_type == "mod_map":
+ #raster.setDrawingStyle(qgis.core.QgsRasterLayer.PalettedColor)
+ raster.setDrawingStyle(qgis.core.QgsRasterLayer.SingleBandPseudoColor)
+ raster.setColorShadingAlgorithm(qgis.core.QgsRasterLayer.PseudoColorShader)
+
+ #raster.setColorShadingAlgorithm(qgis.core.QgsRasterLayer.ColorRampShader)
+# raster.setDrawingStyle(qgis.core.QgsRasterLayer.SingleBandGray)
+ return None
+ else:
+ raster.setDrawingStyle(qgis.core.QgsRasterLayer.SingleBandPseudoColor)
+
+ csv_file = os.path.abspath(os.path.join(os.path.dirname(__file__), "ColorBreaks.csv"))
+ csvfile = open(csv_file, "r")
+ reader = csv.reader(csvfile)
+ header = reader.next() #skip the header
+
+ color_ramp_items = []
+ for row in reader:
+ if row[0] == layer_type:
+ r, g, b = [int(val) for val in row[2:5]]
+ cur_color = QtGui.QColor(r, g, b)
+ cur_val = float(row[1])
+ color_item = QgsColorRampShader.ColorRampItem(cur_val, cur_color)
+ color_ramp_items.append(color_item)
+
+ raster.setColorShadingAlgorithm(qgis.core.QgsRasterLayer.ColorRampShader)
+ fcn = raster.rasterShader().rasterShaderFunction()
+ fcn.setColorRampType(QgsColorRampShader.INTERPOLATED)
+ fcn.setColorRampItemList(color_ramp_items)
+
+ if hasattr(raster, "setCacheImage"): raster.setCacheImage(None)
+ raster.triggerRepaint()
+
+ qgis.core.QgsMapLayerRegistry.instance().addMapLayer(raster)
+
+ csvfile.close()
+
+ return None
+
+ def create_legend_ramp(self, layer_type, raster, min_max, num_tags):
+ legend = QtGui.QFrame()
+ legend.setObjectName(QtCore.QString.fromUtf8("legend"))
+ mainlayout = QtGui.QVBoxLayout(legend)
+ mainlayout.setSpacing(0)
+ mainlayout.setMargin(0)
+
+ frame_colorbar = QtGui.QFrame(legend)
+ frame_colorbar.setObjectName(QtCore.QString.fromUtf8("frame_colorbar"))
+ layout_colorbar = QtGui.QHBoxLayout(frame_colorbar)
+ layout_colorbar.setSpacing(0)
+ layout_colorbar.setContentsMargins(-1, 2, -1, 0)
+
+ frame_ticks = QtGui.QFrame(legend)
+ frame_ticks.setFrameShape(QtGui.QFrame.StyledPanel)
+ frame_ticks.setFrameShadow(QtGui.QFrame.Raised)
+ frame_ticks.setObjectName(QtCore.QString.fromUtf8("frame_ticks"))
+ layout_ticks = QtGui.QHBoxLayout(frame_ticks)
+ layout_ticks.setSpacing(0)
+ layout_ticks.setContentsMargins(-1, 0, -1, 0)
+
+ frame_labels = QtGui.QFrame(legend)
+ frame_labels.setObjectName(QtCore.QString.fromUtf8("frame_labels"))
+ layout_labels = QtGui.QHBoxLayout(frame_labels)
+ layout_labels.setSpacing(0)
+ layout_labels.setContentsMargins(4, 0, 4, 0)
+
+ csv_file = os.path.abspath(os.path.join(os.path.dirname(__file__), "ColorBreaks.csv"))
+ csvfile = open(csv_file, "r")
+ reader = csv.reader(csvfile)
+ header = reader.next() #skip the header
+
+ color_ramp_items = []
+ prev_color = None
+ for row in reader:
+ if row[0] == layer_type:
+ cur_color = ", ".join(row[2:5])
+
+ if prev_color:
+ color_label = QtGui.QLabel(frame_colorbar)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.MinimumExpanding)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(color_label.sizePolicy().hasHeightForWidth())
+ color_label.setSizePolicy(sizePolicy)
+ color_label.setMinimumSize(QtCore.QSize(0, 4))
+ stylesheet = "background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba("
+ stylesheet += prev_color
+ stylesheet += ", 255), stop:1 rgba("
+ stylesheet += cur_color
+ stylesheet += ", 255));"
+ color_label.setStyleSheet(QtCore.QString.fromUtf8(stylesheet))
+ color_label.setText(QtCore.QString.fromUtf8(""))
+ layout_colorbar.addWidget(color_label)
+
+ prev_color = cur_color
+
+ min = min_max[0]
+ max = min_max[1]
+ step = float(max - min) / num_tags
+ curStep = min
+
+ while curStep <= max:
+ line = QtGui.QFrame(frame_ticks)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(line.sizePolicy().hasHeightForWidth())
+ line.setSizePolicy(sizePolicy)
+ line.setMinimumSize(QtCore.QSize(0, 4))
+ line.setSizeIncrement(QtCore.QSize(0, 0))
+ line.setFrameShadow(QtGui.QFrame.Plain)
+ line.setFrameShape(QtGui.QFrame.VLine)
+ line.setFrameShadow(QtGui.QFrame.Sunken)
+ line.setObjectName(QtCore.QString.fromUtf8("line"))
+ layout_ticks.addWidget(line)
+ spacerItem = QtGui.QSpacerItem(133, 2, QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
+ layout_ticks.addItem(spacerItem)
+
+ lbl = QtGui.QLabel(frame_labels)
+ lbl.setMinimumSize(QtCore.QSize(0, 10))
+ txt = "%.1f" %curStep
+ lbl.setText(QtCore.QString.fromUtf8(txt))
+ lbl.setAlignment(QtCore.Qt.AlignCenter)
+ #lbl.setObjectName(QtCore.QString.fromUtf8("lbl"))
+ layout_labels.addWidget(lbl)
+ spacerItem2 = QtGui.QSpacerItem(5, 5, QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
+ layout_labels.addItem(spacerItem2)
+
+ curStep += step
+
+ layout_ticks.removeItem(spacerItem)
+ layout_labels.removeItem(spacerItem2)
+
+ mainlayout.addWidget(frame_colorbar)
+ mainlayout.addWidget(frame_ticks)
+ mainlayout.addWidget(frame_labels)
+ return legend
+
+
+ def add_vector(self, path, tag, strcolor):
+ fileInfo = QtCore.QFileInfo(path)
+ baseName = fileInfo.baseName()
+ points_layer = qgis.core.QgsVectorLayer(path, baseName, "ogr")
+
+ props = {'color':strcolor, 'radius':'3' }
+ s = qgis.core.QgsMarkerSymbolV2.createSimple(props)
+
+ points_layer.setRendererV2( qgis.core.QgsSingleSymbolRendererV2( s ) )
+
+ qgis.core.QgsMapLayerRegistry.instance().addMapLayer(points_layer)
+ self.all_layers[tag] = qgis.gui.QgsMapCanvasLayer(points_layer)
+
+#
+#def update_displayed_layers(cellWidget):
+# pass
+#
+#
+## [qgis.gui.QgsMapCanvasLayer(layer) for layer in layers]
+
+# layer = cellWidget.cur_layers[layer]
+# layers = cellWidget.canvas.layers()
+#
+# if visible:
+# layers.insert(0, layer.layer())
+# else:
+# layers.remove(layer.layer())
+#
+# cellWidget.canvas.setLayerSet(layerset)
+# cellWidget.canvas.repaint()
+
+
+class ViewLayerAction(QtGui.QAction):
+ def __init__(self, action_dict, parent=None):
+ icon = os.path.abspath(os.path.join(
+ os.path.dirname(__file__), "Images", action_dict["icon"]))
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(icon),
+ action_dict["label"],
+ parent)
+ self.setCheckable(True)
+ self.setChecked(action_dict["checked"])
+ self.tag = action_dict["tag"]
+ self.group = action_dict["group"]
+
+ def triggeredSlot(self, checked=False):
+# cellWidget = self.toolBar.getSnappedWidget()
+ self.toggleOthers()
+ self.displayLayer()
+
+ def toggleOthers(self):
+ for action in self.toolBar.actions():
+ if "group" in dir(action) and \
+ action.group == self.group and \
+ action.tag <> self.tag:
+ action.setChecked(False)
+
+ def displayLayer(self):
+ cellWidget = self.toolBar.getSnappedWidget()
+
+ all_layers = cellWidget.all_layers
+ layerset = []
+ for action in self.toolBar.actions():
+ if action.isChecked() and all_layers.has_key(action.tag):
+ layer = all_layers[action.tag]
+ layerset.append(qgis.gui.QgsMapCanvasLayer(layer))
+
+ cellWidget.canvas.setLayerSet(layerset)
+ cellWidget.canvas.repaint()
+
+
+class SAHMSpatialViewerToolBar(QCellToolBar):
+ """
+ The toolbar that allows users to toggle layers on and off
+ in the widget
+
+ """
+ def createToolBar(self):
+ """ createToolBar() -> None
+ This will get call initiallly to add customizable widgets
+
+ """
+ sw = self.getSnappedWidget()
+
+ actions = [{"tag":"pres_points", "icon":"RedPoints.png",
+ "checked":True, "label":"Display presence points",
+ "group":"pres_points"},
+ {"tag":"abs_points", "icon":"GreenPoints.png",
+ "checked":True, "label":"Display absence points",
+ "group":"abs_points"},
+ {"tag":"backs_points", "icon":"BlackPoints.png",
+ "checked":False, "label":"Display background points",
+ "group":"backs_points"},
+ {"tag":"prob_map", "icon":"ProbMap.png",
+ "checked":True, "label":"Display probability map",
+ "group":"Grids"},
+ {"tag":"bin_map", "icon":"BinMap.png",
+ "checked":False, "label":"Display binary map",
+ "group":"Grids"},
+ {"tag":"res_map", "icon":"ResMap.png",
+ "checked":False, "label":"Display residuals map",
+ "group":"Grids"},
+ {"tag":"mes_map", "icon":"MesMap.png",
+ "checked":False, "label":"Display Multivariate Environmental Similarity Surface (Mess) map",
+ "group":"Grids"},
+ {"tag":"mod_map", "icon":"ModMap.png",
+ "checked":False, "label":"Display Most Dissimilar Variable (MoD) map",
+ "group":"Grids"}]
+
+
+ for action_dict in actions:
+ self.appendAction(ViewLayerAction(action_dict, self))
+
+ def updateToolBar(self):
+ QCellToolBar.updateToolBar(self)
+ sw = self.getSnappedWidget()
+ for action in self.actions():
+ if type(action) == ViewLayerAction:
+ #disenable all action refering to data we don't have
+ action.setEnabled(action.tag in sw.all_layers)
+
+
\ No newline at end of file
diff --git a/contrib/sahm/SahmSpatialViewerCell.py b/contrib/sahm/SahmSpatialViewerCell.py
new file mode 100644
index 0000000..0f5db47
--- /dev/null
+++ b/contrib/sahm/SahmSpatialViewerCell.py
@@ -0,0 +1,89 @@
+# -*- coding: utf-8 -*-
+
+# Form implementation generated from reading ui file 'I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\SahmSpatialViewerCell.ui'
+#
+# Created: Tue Oct 11 16:20:25 2011
+# by: PyQt4 UI code generator 4.8.5
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore, QtGui
+
+try:
+ _fromUtf8 = QtCore.QString.fromUtf8
+except AttributeError:
+ _fromUtf8 = lambda s: s
+
+class Ui_Frame(object):
+ def setupUi(self, Frame):
+ Frame.setObjectName(_fromUtf8("Frame"))
+ Frame.resize(734, 706)
+ Frame.setWindowTitle(QtGui.QApplication.translate("Frame", "Frame", None, QtGui.QApplication.UnicodeUTF8))
+ Frame.setFrameShape(QtGui.QFrame.StyledPanel)
+ Frame.setFrameShadow(QtGui.QFrame.Plain)
+ self.gridLayout = QtGui.QGridLayout(Frame)
+ self.gridLayout.setMargin(0)
+ self.gridLayout.setSpacing(0)
+ self.gridLayout.setObjectName(_fromUtf8("gridLayout"))
+ self.splitter = QtGui.QSplitter(Frame)
+ self.splitter.setOrientation(QtCore.Qt.Vertical)
+ self.splitter.setObjectName(_fromUtf8("splitter"))
+ self.legend_frame_2 = QtGui.QFrame(self.splitter)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Preferred)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.legend_frame_2.sizePolicy().hasHeightForWidth())
+ self.legend_frame_2.setSizePolicy(sizePolicy)
+ self.legend_frame_2.setMinimumSize(QtCore.QSize(0, 0))
+ self.legend_frame_2.setBaseSize(QtCore.QSize(0, 0))
+ self.legend_frame_2.setFrameShape(QtGui.QFrame.StyledPanel)
+ self.legend_frame_2.setFrameShadow(QtGui.QFrame.Sunken)
+ self.legend_frame_2.setObjectName(_fromUtf8("legend_frame_2"))
+ self.horizontalLayout_2 = QtGui.QHBoxLayout(self.legend_frame_2)
+ self.horizontalLayout_2.setSpacing(5)
+ self.horizontalLayout_2.setContentsMargins(9, 0, 0, 0)
+ self.horizontalLayout_2.setObjectName(_fromUtf8("horizontalLayout_2"))
+ self.legend_label = QtGui.QLabel(self.legend_frame_2)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Minimum)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.legend_label.sizePolicy().hasHeightForWidth())
+ self.legend_label.setSizePolicy(sizePolicy)
+ self.legend_label.setText(QtGui.QApplication.translate("Frame", "TextLabel", None, QtGui.QApplication.UnicodeUTF8))
+ self.legend_label.setObjectName(_fromUtf8("legend_label"))
+ self.horizontalLayout_2.addWidget(self.legend_label)
+ self.legend = QtGui.QFrame(self.legend_frame_2)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.legend.sizePolicy().hasHeightForWidth())
+ self.legend.setSizePolicy(sizePolicy)
+ self.legend.setFrameShape(QtGui.QFrame.NoFrame)
+ self.legend.setFrameShadow(QtGui.QFrame.Plain)
+ self.legend.setLineWidth(0)
+ self.legend.setObjectName(_fromUtf8("legend"))
+ self.legend_layout = QtGui.QHBoxLayout(self.legend)
+ self.legend_layout.setMargin(0)
+ self.legend_layout.setObjectName(_fromUtf8("legend_layout"))
+ self.horizontalLayout_2.addWidget(self.legend)
+ self.map_frame = QtGui.QFrame(self.splitter)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Expanding)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(1)
+ sizePolicy.setHeightForWidth(self.map_frame.sizePolicy().hasHeightForWidth())
+ self.map_frame.setSizePolicy(sizePolicy)
+ self.map_frame.setFrameShape(QtGui.QFrame.StyledPanel)
+ self.map_frame.setFrameShadow(QtGui.QFrame.Sunken)
+ self.map_frame.setObjectName(_fromUtf8("map_frame"))
+ self.horizontalLayout = QtGui.QHBoxLayout(self.map_frame)
+ self.horizontalLayout.setSpacing(0)
+ self.horizontalLayout.setMargin(0)
+ self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
+ self.gridLayout.addWidget(self.splitter, 0, 0, 1, 1)
+
+ self.retranslateUi(Frame)
+ QtCore.QMetaObject.connectSlotsByName(Frame)
+
+ def retranslateUi(self, Frame):
+ pass
+
diff --git a/contrib/sahm/SahmViewerCell.py b/contrib/sahm/SahmViewerCell.py
new file mode 100644
index 0000000..af0be39
--- /dev/null
+++ b/contrib/sahm/SahmViewerCell.py
@@ -0,0 +1,72 @@
+# -*- coding: utf-8 -*-
+
+# Form implementation generated from reading ui file 'SahmViewerCell.ui'
+#
+# Created: Thu Sep 29 18:41:54 2011
+# by: PyQt4 UI code generator 4.8.5
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore, QtGui
+
+try:
+ _fromUtf8 = QtCore.QString.fromUtf8
+except AttributeError:
+ _fromUtf8 = lambda s: s
+
+class Ui_Frame(object):
+ def setupUi(self, Frame):
+ Frame.setObjectName(_fromUtf8("Frame"))
+ Frame.resize(546, 402)
+ Frame.setWindowTitle(QtGui.QApplication.translate("Frame", "Frame", None, QtGui.QApplication.UnicodeUTF8))
+ Frame.setFrameShape(QtGui.QFrame.StyledPanel)
+ Frame.setFrameShadow(QtGui.QFrame.Raised)
+ self.horizontalLayout = QtGui.QHBoxLayout(Frame)
+ self.horizontalLayout.setSpacing(0)
+ self.horizontalLayout.setMargin(0)
+ self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
+ self.tabWidget = QtGui.QTabWidget(Frame)
+ self.tabWidget.setEnabled(True)
+ self.tabWidget.setTabPosition(QtGui.QTabWidget.North)
+ self.tabWidget.setObjectName(_fromUtf8("tabWidget"))
+ self.text_output = QtGui.QWidget()
+ self.text_output.setObjectName(_fromUtf8("text_output"))
+ self.text_output_layout = QtGui.QHBoxLayout(self.text_output)
+ self.text_output_layout.setSpacing(0)
+ self.text_output_layout.setMargin(0)
+ self.text_output_layout.setObjectName(_fromUtf8("text_output_layout"))
+ self.tabWidget.addTab(self.text_output, _fromUtf8(""))
+ self.tabWidget.setTabToolTip(self.tabWidget.indexOf(self.text_output), QtGui.QApplication.translate("Frame", "Textual model output ", None, QtGui.QApplication.UnicodeUTF8))
+ self.response_curves = QtGui.QWidget()
+ self.response_curves.setObjectName(_fromUtf8("response_curves"))
+ self.response_curves_layout = QtGui.QHBoxLayout(self.response_curves)
+ self.response_curves_layout.setSpacing(0)
+ self.response_curves_layout.setMargin(0)
+ self.response_curves_layout.setObjectName(_fromUtf8("response_curves_layout"))
+ self.tabWidget.addTab(self.response_curves, _fromUtf8(""))
+ self.tabWidget.setTabToolTip(self.tabWidget.indexOf(self.response_curves), QtGui.QApplication.translate("Frame", "Response curves", None, QtGui.QApplication.UnicodeUTF8))
+ self.auc = QtGui.QWidget()
+ self.auc.setObjectName(_fromUtf8("auc"))
+ self.horizontalLayout_4 = QtGui.QHBoxLayout(self.auc)
+ self.horizontalLayout_4.setSpacing(0)
+ self.horizontalLayout_4.setMargin(0)
+ self.horizontalLayout_4.setObjectName(_fromUtf8("horizontalLayout_4"))
+ self.gv_auc = QtGui.QGraphicsView(self.auc)
+ self.gv_auc.setDragMode(QtGui.QGraphicsView.ScrollHandDrag)
+ self.gv_auc.setTransformationAnchor(QtGui.QGraphicsView.AnchorUnderMouse)
+ self.gv_auc.setResizeAnchor(QtGui.QGraphicsView.AnchorUnderMouse)
+ self.gv_auc.setObjectName(_fromUtf8("gv_auc"))
+ self.horizontalLayout_4.addWidget(self.gv_auc)
+ self.tabWidget.addTab(self.auc, _fromUtf8(""))
+ self.tabWidget.setTabToolTip(self.tabWidget.indexOf(self.auc), QtGui.QApplication.translate("Frame", "Area under the curve (AUC)", None, QtGui.QApplication.UnicodeUTF8))
+ self.horizontalLayout.addWidget(self.tabWidget)
+
+ self.retranslateUi(Frame)
+ self.tabWidget.setCurrentIndex(2)
+ QtCore.QMetaObject.connectSlotsByName(Frame)
+
+ def retranslateUi(self, Frame):
+ self.tabWidget.setTabText(self.tabWidget.indexOf(self.text_output), QtGui.QApplication.translate("Frame", "Model Results", None, QtGui.QApplication.UnicodeUTF8))
+ self.tabWidget.setTabText(self.tabWidget.indexOf(self.response_curves), QtGui.QApplication.translate("Frame", "Response", None, QtGui.QApplication.UnicodeUTF8))
+ self.tabWidget.setTabText(self.tabWidget.indexOf(self.auc), QtGui.QApplication.translate("Frame", "AUC", None, QtGui.QApplication.UnicodeUTF8))
+
diff --git a/contrib/sahm/SelectPredictorsLayers.py b/contrib/sahm/SelectPredictorsLayers.py
new file mode 100644
index 0000000..1815c27
--- /dev/null
+++ b/contrib/sahm/SelectPredictorsLayers.py
@@ -0,0 +1,428 @@
+'''
+Created on Sep 17, 2010
+
+ at author: talbertc
+'''
+from core.modules.vistrails_module import Module
+from PyQt4 import QtCore, QtGui
+import csv
+import utils
+from utils import writetolog
+import shutil
+import os
+from core.system import execute_cmdline
+import subprocess
+
+try:
+ _fromUtf8 = QtCore.QString.fromUtf8
+except AttributeError:
+ _fromUtf8 = lambda s: s
+
+class SelectListDialog(QtGui.QDialog):
+
+ def __init__(self, inputMDS, outputMDS, displayJPEG, rPath, parent=None):
+ #print inputMDS, outputMDS, rPath, modelsPath
+ self.rPath = rPath
+
+ self.selection_name = os.path.split(outputMDS)[1]
+ self.selection_name = os.path.splitext(self.selection_name)[0]
+ self.selection_name = self.selection_name.split('_')[-1]
+
+ self.displayJPEG = displayJPEG
+
+ QtGui.QDialog.__init__(self, parent)
+
+ self.inputMDS = inputMDS
+ self.outputMDS = outputMDS
+ self.outputDir = os.path.split(outputMDS)[0]
+
+ layout = QtGui.QVBoxLayout()
+ self.setWindowFlags(QtCore.Qt.Window)
+ ##begin autogenerated code from QtDesigner
+ #
+
+ self.horizontalLayout_4 = QtGui.QHBoxLayout()
+ self.horizontalLayout_4.setSpacing(5)
+ self.horizontalLayout_4.setMargin(5)
+ self.horizontalLayout_4.setObjectName(_fromUtf8("horizontalLayout_4"))
+ self.verticalLayout_3 = QtGui.QVBoxLayout()
+ self.verticalLayout_3.setObjectName(_fromUtf8("verticalLayout_3"))
+ self.splitter = QtGui.QSplitter()
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.splitter.sizePolicy().hasHeightForWidth())
+ self.splitter.setSizePolicy(sizePolicy)
+ self.splitter.setMinimumSize(QtCore.QSize(0, 0))
+ self.splitter.setFrameShape(QtGui.QFrame.Box)
+ self.splitter.setFrameShadow(QtGui.QFrame.Plain)
+ self.splitter.setLineWidth(1)
+ self.splitter.setOrientation(QtCore.Qt.Horizontal)
+ self.splitter.setHandleWidth(10)
+ self.splitter.setObjectName(_fromUtf8("splitter"))
+ self.widget = QtGui.QWidget(self.splitter)
+ self.widget.setObjectName(_fromUtf8("widget"))
+ self.verticalLayout = QtGui.QVBoxLayout(self.widget)
+ self.verticalLayout.setSpacing(4)
+ self.verticalLayout.setSizeConstraint(QtGui.QLayout.SetDefaultConstraint)
+ self.verticalLayout.setContentsMargins(6, 6, 3, 3)
+ self.verticalLayout.setObjectName(_fromUtf8("verticalLayout"))
+ self.label_2 = QtGui.QLabel(self.widget)
+ self.label_2.setObjectName(_fromUtf8("label_2"))
+ self.verticalLayout.addWidget(self.label_2)
+ self.treeview = QtGui.QTreeWidget(self.widget)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Ignored, QtGui.QSizePolicy.Expanding)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.treeview.sizePolicy().hasHeightForWidth())
+ self.treeview.setSizePolicy(sizePolicy)
+ self.treeview.setMinimumSize(QtCore.QSize(75, 0))
+ self.treeview.setMaximumSize(QtCore.QSize(16777215, 16777215))
+ self.treeview.setSizeIncrement(QtCore.QSize(100, 0))
+ self.treeview.setBaseSize(QtCore.QSize(0, 0))
+ self.treeview.setObjectName(_fromUtf8("treeview"))
+ self.verticalLayout.addWidget(self.treeview)
+ self.horizontalLayout_3 = QtGui.QHBoxLayout()
+ self.horizontalLayout_3.setSizeConstraint(QtGui.QLayout.SetDefaultConstraint)
+ self.horizontalLayout_3.setObjectName(_fromUtf8("horizontalLayout_3"))
+ self.btnRunR = QtGui.QPushButton(self.widget)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.btnRunR.sizePolicy().hasHeightForWidth())
+ self.btnRunR.setSizePolicy(sizePolicy)
+ self.btnRunR.setObjectName(_fromUtf8("btnRunR"))
+ self.horizontalLayout_3.addWidget(self.btnRunR)
+ spacerItem = QtGui.QSpacerItem(10, 0, QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
+ self.horizontalLayout_3.addItem(spacerItem)
+ self.label = QtGui.QLabel(self.widget)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Preferred)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.label.sizePolicy().hasHeightForWidth())
+ self.label.setSizePolicy(sizePolicy)
+ self.label.setObjectName(_fromUtf8("label"))
+ self.horizontalLayout_3.addWidget(self.label)
+ self.lineEdit = QtGui.QLineEdit(self.widget)
+ self.lineEdit.setText(_fromUtf8("0.7"))
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.lineEdit.sizePolicy().hasHeightForWidth())
+ self.lineEdit.setSizePolicy(sizePolicy)
+ self.lineEdit.setMaximumSize(QtCore.QSize(75, 16777215))
+ self.lineEdit.setObjectName(_fromUtf8("lineEdit"))
+ self.horizontalLayout_3.addWidget(self.lineEdit)
+
+ self.chkPresence = QtGui.QCheckBox(self.widget)
+ self.chkPresence.setChecked(True)
+ self.chkPresence.setText(_fromUtf8("Include presence/count points"))
+ self.chkPresence.setObjectName(_fromUtf8("chkPresence"))
+ self.verticalLayout.addWidget(self.chkPresence)
+ self.chkAbsence = QtGui.QCheckBox(self.widget)
+ self.chkAbsence.setChecked(True)
+ self.chkAbsence.setText(_fromUtf8("Include absence points"))
+ self.chkAbsence.setObjectName(_fromUtf8("chkAbsence"))
+ self.verticalLayout.addWidget(self.chkAbsence)
+ self.chkBackground = QtGui.QCheckBox(self.widget)
+ self.chkBackground.setChecked(True)
+ self.chkBackground.setText(_fromUtf8("Include background points"))
+ self.chkBackground.setObjectName(_fromUtf8("chkBackground"))
+ self.verticalLayout.addWidget(self.chkBackground)
+
+ self.verticalLayout.addLayout(self.horizontalLayout_3)
+
+ self.scene = QtGui.QGraphicsScene()
+ self.view = QtGui.QGraphicsView(self.scene)
+ #self.view = customGraphicsView(self.scene)
+ self.view.setDragMode(QtGui.QGraphicsView.ScrollHandDrag)
+
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
+ sizePolicy.setHorizontalStretch(4)
+ sizePolicy.setVerticalStretch(0)
+ #sizePolicy.setHeightForWidth(self.view.sizePolicy().hasHeightForWidth())
+ self.view.setSizePolicy(sizePolicy)
+ self.view.setResizeAnchor(QtGui.QGraphicsView.AnchorUnderMouse)
+ self.view.setObjectName(_fromUtf8("view"))
+
+ self.splitter.addWidget(self.view)
+
+ self.verticalLayout_3.addWidget(self.splitter)
+ self.horizontalLayout = QtGui.QHBoxLayout()
+ self.horizontalLayout.setContentsMargins(-1, 3, -1, 3)
+ self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
+ self.btnOK = QtGui.QPushButton()
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.btnOK.sizePolicy().hasHeightForWidth())
+ self.btnOK.setSizePolicy(sizePolicy)
+ self.btnOK.setBaseSize(QtCore.QSize(100, 0))
+ self.btnOK.setToolTip(_fromUtf8(""))
+ self.btnOK.setObjectName(_fromUtf8("btnOK"))
+ self.horizontalLayout.addWidget(self.btnOK)
+ self.btnCancel = QtGui.QPushButton()
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.btnCancel.sizePolicy().hasHeightForWidth())
+ self.btnCancel.setSizePolicy(sizePolicy)
+ self.btnCancel.setBaseSize(QtCore.QSize(100, 0))
+ self.btnCancel.setObjectName(_fromUtf8("btnCancel"))
+ self.horizontalLayout.addWidget(self.btnCancel)
+ self.verticalLayout_3.addLayout(self.horizontalLayout)
+ self.horizontalLayout_4.addLayout(self.verticalLayout_3)
+
+ self.setWindowTitle(_fromUtf8("Covariate Coorelation viewer"))
+ self.label_2.setText(_fromUtf8("Covariates"))
+ self.btnRunR.setText(_fromUtf8("Update"))
+ self.label.setText(_fromUtf8("Threshold"))
+ self.btnOK.setText(_fromUtf8("OK"))
+ self.btnCancel.setText(_fromUtf8("Cancel"))
+ self.resize(1100, 800)
+ self.view.resize(800, 750)
+
+ ##End autogenerated code from QtDesigner
+
+ layout.addLayout(self.horizontalLayout_4)
+
+ self.btnCancel.setShortcut('Esc')
+ self.connect(self.btnOK, QtCore.SIGNAL('clicked(bool)'),
+ self.okTriggered)
+ self.connect(self.btnCancel, QtCore.SIGNAL('clicked(bool)'),
+ self.cancel)
+ self.connect(self.btnRunR, QtCore.SIGNAL('clicked(bool)'),
+ self.updateROutput)
+# self.connect(self.view, QtCore.SIGNAL('resize()'),
+# self.resize)
+
+ self.scene.wheelEvent = self.wheel_event
+# self.resizeEvent = self.resize_event
+ #code to populate the treeview with the contents of our MDS
+ self.PopulateTreeview()
+
+ self.setLayout(layout)
+ self.repaint()
+ #utils.breakpoint()
+ #code to add in pictureviewer stuff
+ outputPic = self.runR(self.inputMDS)
+# self.setup_view()
+ self.load_picture(outputPic)
+
+ def okTriggered(self):
+ self.SaveMDSFromTreeview()
+ self.done(0)
+
+ def cancel(self):
+ self.done(1)
+ #raise Exception
+# shutil.copyfile(self.inputMDS, self.outputMDS)
+
+
+ def PopulateTreeview(self):
+ ''' Reads in the input MDS and populates the treeview widget
+ with the items in covariate columns.
+ Sets the check state to be the same as the 0/1 include flag.
+ '''
+ writetolog(" PopulateTreeview inputMDS = " + self.inputMDS, False, False)
+ self.treeview.setColumnCount(1)
+ #If an outputMDS already exists then the user has run this module before.
+ #We need to pull and apply their previous selections from that output file
+
+
+
+ csvfile = open(self.inputMDS, "r")
+ #print "MDS", self.inputMDS
+ reader = csv.reader(csvfile)
+ header = reader.next() #store the header
+ header2 = reader.next() #the 2nd line of the mds with use/don't use
+ header3 = reader.next() #the 3rd line of the mds with the path
+
+ self.responseCol = header[2]
+
+ headerList = []
+ n = 0
+ for i in range(0, len(header)):
+ headerList.append([header[i], header2[i], header3[i]])
+
+ #headerList.sort()
+ for item in headerList[3:]:
+ child_item = QtGui.QTreeWidgetItem([item[0],])
+ child_item.setFlags(QtCore.Qt.ItemIsUserCheckable |
+ QtCore.Qt.ItemIsEnabled)
+ checked = True
+ if int(item[1]) == 0:
+ checked = False
+
+ if not checked:
+ child_item.setCheckState(0, QtCore.Qt.Unchecked)
+ else:
+ child_item.setCheckState(0, QtCore.Qt.Checked)
+
+ self.treeview.addTopLevelItem(child_item)
+ #self.tree_items[file] = child_item
+ n += 1
+ csvfile.close()
+ #update the tree view label to show how many covariates there are
+ self.label_2.setText(_fromUtf8("Covariates (n=" + str(n) + ")"))
+
+ def SaveMDSFromTreeview(self):
+ #updates the second header line on the input MDS file
+ #to reflect the checked items in the tree view
+ #and saves the results to the output MDS.
+
+ reader = csv.reader(open(self.inputMDS, "r"))
+ header = reader.next() #store the header
+ header2 = reader.next() #the 2nd line of the mds with use/don't use
+ header3 = reader.next() #the 3rd line of the mds with the path
+
+ headerList = []
+ for i in range(0, len(header)):
+ headerList.append([header[i], header2[i], header3[i]])
+
+ outHeader2 = header2[:2] + [self.selection_name]
+
+ treeviewIter = QtGui.QTreeWidgetItemIterator(self.treeview)
+ while treeviewIter.value():
+ if treeviewIter.value().checkState(0) == QtCore.Qt.Checked:
+ outHeader2.append("1")
+ else:
+ outHeader2.append ("0")
+ treeviewIter += 1
+
+
+ oFile = open(self.outputMDS, 'wb')
+ writer = csv.writer(oFile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
+ writer.writerow(header)
+ writer.writerow(outHeader2)
+ writer.writerow(header3)
+ for row in reader:
+ writer.writerow(row)
+ oFile.close
+
+ def updateROutput(self):
+ self.SaveMDSFromTreeview()
+ outputPic = self.runR(self.outputMDS)
+ self.load_picture(outputPic)
+
+ def runR(self, MDSfile):
+#
+# program = os.path.join(self.rPath, "i386", "Rterm.exe")
+# script = os.path.join(utils.getModelsPath(), "PairsExplore.r")
+
+ args = "i=" + '"' + MDSfile + '"' + " o=" + '"' + self.displayJPEG + '"' + " m=" + str(self.lineEdit.text())
+ args += " rc=" + self.responseCol
+
+ if self.chkPresence.checkState() == QtCore.Qt.Checked:
+ args += " pres=TRUE"
+ else:
+ args += " pres=FALSE"
+ if self.chkAbsence.checkState() == QtCore.Qt.Checked:
+ args += " absn=TRUE"
+ else:
+ args += " absn=FALSE"
+ if self.chkBackground.checkState() == QtCore.Qt.Checked:
+ args += " bgd=TRUE"
+ else:
+ args += " bgd=FALSE"
+
+# command = program + " --vanilla -f " + script + " --args " + args
+# writetolog(" " + command, False, False)
+ if os.path.exists(os.path.join(self.outputDir, "Predictor_Correlation.jpg")):
+ os.remove(os.path.join(self.outputDir, "Predictor_Correlation.jpg"))
+
+ utils.runRScript('PairsExplore.r', args)
+
+# p = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
+#
+# writetolog(" Calculating covariate correlation in r R ")
+
+# ret = p.communicate()
+# if ret[1]:
+# msg = "An error was encountered in the R script for this module. The R error message is below - \n"
+# msg += ret[1]
+# writetolog(msg)
+# raise Exception, msg
+# else:
+# writetolog(" Finished in R. ")
+# del(ret)
+
+ if os.path.exists(os.path.join(self.displayJPEG)):
+ return os.path.join(self.displayJPEG)
+ else:
+ writetolog("Missing output from R processing: " + self.displayJPEG)
+ raise Exception, "Missing output from R processing"
+
+ def load_picture(self, strPicture):
+ #utils.breakpoint()
+ self.l_pix = QtGui.QPixmap(strPicture)
+ if self.view.size().width() <= self.view.size().height():
+ self.max_vsize = self.view.size().width() * 0.95
+ else:
+ self.max_vsize = self.view.size().height() * 0.95
+
+ self.c_view = self.l_pix.scaled(self.max_vsize, self.max_vsize,
+ QtCore.Qt.KeepAspectRatio,
+ QtCore.Qt.SmoothTransformation)
+ self.view_current()
+
+ def view_current(self):
+ #print "view_current"
+ size_img = self.c_view.size()
+ wth, hgt = QtCore.QSize.width(size_img), QtCore.QSize.height(size_img)
+ self.scene.clear()
+ self.scene.setSceneRect(0, 0, wth, hgt)
+ self.scene.addPixmap(self.c_view)
+ QtCore.QCoreApplication.processEvents()
+
+# def load_current(self, filePath):
+# print "load_current"
+# self.l_pix = QtGui.QPixmap(filePath)
+# self.c_view = self.l_pix.scaled(self.max_vsize, self.max_vsize,
+# QtCore.Qt.KeepAspectRatio,
+# QtCore.Qt.FastTransformation)
+# #change the previous line with QtCore.Qt.SmoothTransformation eventually
+# self.view_current()
+
+ def wheel_event (self, event):
+ numDegrees = event.delta() / 8
+ numSteps = numDegrees / 15.0
+ self.zoom(numSteps)
+ event.accept()
+
+ def zoom(self, step):
+ zoom_step = 0.06
+ self.scene.clear()
+ w = self.c_view.size().width()
+ h = self.c_view.size().height()
+ w, h = w * (1 + zoom_step*step), h * (1 + zoom_step*step)
+ self.c_view = self.l_pix.scaled(w, h,
+ QtCore.Qt.KeepAspectRatio,
+ QtCore.Qt.SmoothTransformation)
+ self.view_current()
+
+ def closeEvent(self, event):
+ self.cancel()
+
+ def resizeEvent(self, event):
+ self.load_picture(self.displayJPEG)
+
+# def resize_event(self, event):
+# utils.breakpoint()
+# origsize = self.c_view.size()
+# size = event.size()
+# w = size.width()
+# h = size.height()
+# self.c_view = self.l_pix.scaled(origsize.width(), origsize.height(),
+# QtCore.Qt.KeepAspectRatio,
+# QtCore.Qt.SmoothTransformation)
+# self.view_current()
+
+
+#class customGraphicsView(QtGui.QGraphicsView):
+#
+# def __init__(self, parent=None):
+# QtGui.QGraphicsView.__init__(self, parent)
+#
+# def resizeEvent(self, evt=None):
+# self.emit(QtCore.SIGNAL("resize()"))
diff --git a/contrib/sahm/__init__.py b/contrib/sahm/__init__.py
new file mode 100644
index 0000000..7a0d593
--- /dev/null
+++ b/contrib/sahm/__init__.py
@@ -0,0 +1,14 @@
+from core.configuration import ConfigurationObject
+
+name = "SAHM"
+identifier = "gov.usgs.sahm"
+version = '0.0.5'
+
+configuration = \
+ ConfigurationObject(output_dir= r'C:\temp\SAHM_workspace',
+ r_path = r'..\\Central_R\R-2.12.1\bin',
+ gdal_path = r'..\\Central_GDAL',
+ maxent_path = r'..\\Central_Maxent',
+ qgis_path = r'..\\Central_QGIS',
+ projection_layers_path = r'I:\WorldClim_Future_Climate\RenamedBILs', #This only applies to instances running in the FORT Infrastructure
+ verbose = 'True')
diff --git a/contrib/sahm/enum_modules.py b/contrib/sahm/enum_modules.py
new file mode 100644
index 0000000..142c0e8
--- /dev/null
+++ b/contrib/sahm/enum_modules.py
@@ -0,0 +1,11 @@
+from core.modules.basic_modules import String
+from enum_widget import build_enum_widget
+
+class MyEnum(String):
+ _input_ports = [('value', '(gov.usgs.sahm:MyEnum:DataInput)')]
+ _widget_class = build_enum_widget('MyEnumWidget',
+ ['abc', 'def', 'ghi'])
+
+ @staticmethod
+ def get_widget_class():
+ return MyEnum._widget_class
diff --git a/contrib/sahm/enum_widget.py b/contrib/sahm/enum_widget.py
new file mode 100644
index 0000000..3a61264
--- /dev/null
+++ b/contrib/sahm/enum_widget.py
@@ -0,0 +1,44 @@
+from PyQt4 import QtCore, QtGui
+from core.modules.constant_configuration import ConstantWidgetMixin
+
+class EnumWidget(QtGui.QComboBox, ConstantWidgetMixin):
+ param_values = []
+ def __init__(self, param, parent=None):
+ """__init__(param: core.vistrail.module_param.ModuleParam,
+ parent: QWidget)
+
+ """
+ contents = param.strValue
+ contentType = param.type
+ QtGui.QComboBox.__init__(self, parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ # want to look up in registry based on parameter type
+
+ self.addItem('')
+ for val in self.param_values:
+ self.addItem(val)
+
+ curIdx = self.findText(contents)
+ if curIdx != -1:
+ self.setCurrentIndex(curIdx)
+ self._contentType = contentType
+ self.connect(self,
+ QtCore.SIGNAL('currentIndexChanged(int)'),
+ self.update_parent)
+
+ def contents(self):
+ curIdx = self.currentIndex()
+ if curIdx == -1:
+ print '*** ""'
+ return ''
+ print '*** "%s"' % str(self.itemText(curIdx))
+ return str(self.itemText(curIdx))
+
+ def setContents(self, strValue, silent=True):
+ curIdx = self.findText(contents)
+ self.setCurrentIndex(curIdx)
+ if not silent:
+ self.update_parent()
+
+def build_enum_widget(name, param_values):
+ return type(name, (EnumWidget,), {'param_values': param_values})
diff --git a/contrib/sahm/init.py b/contrib/sahm/init.py
new file mode 100644
index 0000000..6e12900
--- /dev/null
+++ b/contrib/sahm/init.py
@@ -0,0 +1,1788 @@
+#test from marian
+import csv
+from datetime import datetime
+import glob
+import itertools
+import os
+import shutil
+import sys
+import subprocess
+import traceback
+
+from core.modules.vistrails_module import Module, ModuleError, ModuleConnector
+from core.modules.basic_modules import File, Directory, Path, new_constant, Constant
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+#from packages.persistence.init import PersistentPath, PersistentFile, PersistentDir
+
+from core.modules.basic_modules import List
+from core.modules.basic_modules import String
+
+from PyQt4 import QtCore, QtGui
+
+from widgets import get_predictor_widget, get_predictor_config
+from enum_widget import build_enum_widget
+
+from SelectPredictorsLayers import SelectListDialog
+
+import utils
+#import our python SAHM Processing files
+import packages.sahm.pySAHM.FieldDataQuery as FDQ
+import packages.sahm.pySAHM.MDSBuilder as MDSB
+import packages.sahm.pySAHM.PARC as parc
+import packages.sahm.pySAHM.RasterFormatConverter as RFC
+import packages.sahm.pySAHM.MaxentRunner as MaxentRunner
+from SahmOutputViewer import SAHMModelOutputViewerCell
+from SahmSpatialOutputViewer import SAHMSpatialOutputViewerCell
+
+from utils import writetolog
+from pySAHM.utilities import TrappedError
+
+from SahmSpatialOutputViewer import setQGIS
+
+identifier = 'gov.usgs.sahm'
+
+def menu_items():
+ """ Add a menu item which allows users to specify their session directory
+ """
+ def change_session_folder():
+ global session_dir
+
+ path = str(QtGui.QFileDialog.getExistingDirectory(None,
+ 'Browse to new session folder -'))
+ session_dir = path
+ utils.setrootdir(path)
+
+ writetolog("*" * 79 + "\n" + "*" * 79)
+ writetolog(" output directory: " + session_dir)
+ writetolog("*" * 79 + "\n" + "*" * 79)
+
+ lst = []
+ lst.append(("Change session folder", change_session_folder))
+ return(lst)
+
+
+
+
+def expand_ports(port_list):
+ new_port_list = []
+ for port in port_list:
+ port_spec = port[1]
+ if type(port_spec) == str: # or unicode...
+ if port_spec.startswith('('):
+ port_spec = port_spec[1:]
+ if port_spec.endswith(')'):
+ port_spec = port_spec[:-1]
+ new_spec_list = []
+ for spec in port_spec.split(','):
+ spec = spec.strip()
+ parts = spec.split(':', 1)
+# print 'parts:', parts
+ namespace = None
+ if len(parts) > 1:
+ mod_parts = parts[1].rsplit('|', 1)
+ if len(mod_parts) > 1:
+ namespace, module_name = mod_parts
+ else:
+ module_name = parts[1]
+ if len(parts[0].split('.')) == 1:
+ id_str = 'edu.utah.sci.vistrails.' + parts[0]
+ else:
+ id_str = parts[0]
+ else:
+ mod_parts = spec.rsplit('|', 1)
+ if len(mod_parts) > 1:
+ namespace, module_name = mod_parts
+ else:
+ module_name = spec
+ id_str = identifier
+ if namespace:
+ new_spec_list.append(id_str + ':' + module_name + ':' + \
+ namespace)
+ else:
+ new_spec_list.append(id_str + ':' + module_name)
+ port_spec = '(' + ','.join(new_spec_list) + ')'
+ new_port_list.append((port[0], port_spec) + port[2:])
+# print new_port_list
+ return new_port_list
+
+class FieldData(Path):
+ '''
+ Field Data
+
+ The FieldData module allows a user to add presence/absence points or count data recorded across a
+ landscape for the phenomenon being modeled (e.g., plant sightings, evidence of animal presence, etc.).
+ The input data for this module must be in the form of a .csv file that follows one of two formats:
+
+ Format 1
+ A .csv file with the following column headings, in order: "X," "Y," and "responseBinary".
+ In this case, the "X" field should be populated with the horizontal (longitudinal) positional
+ data for a sample point. The "Y" field should be populated with the vertical (latitudinal) data
+ for a sample point. These values must be in the same coordinate system/units as the template
+ layer used in the workflow. The column "responseBinary" should be populated with either a '0'
+ (indicating absence at the point) or a '1' (indicating presence at the point).
+
+ Format 2
+ A .csv file with the following column headings, in order: "X," "Y," and "responseCount".
+ In this case, the "X" field should be populated with the horizontal (longitudinal) positional
+ data for a sample point. The "Y" field should be populated with the vertical (latitudinal) data
+ for a sample point. These values must be in the same coordinate system/units as the template
+ layer used in the workflow. The column "responseCount" should be populated with either a '-9999'
+ (indicating that the point is a background point) or a numerical value (either '0' or a positive integer)
+ indicating the number of incidences of the phenomenon recorded at that point.
+ '''
+# _input_ports = [('csvFile', '(edu.utah.sci.vistrails.basic:File)')]
+ _output_ports = [('value', '(gov.usgs.sahm:FieldData:DataInput)'),
+ ('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
+
+
+
+class AggregationMethod(String):
+ '''
+ This module is a required class for other modules and scripts within the
+ SAHM package. It is not intended for direct use or incorporation into
+ the VisTrails workflow by the user.
+ '''
+ _input_ports = [('value', '(gov.usgs.sahm:AggregationMethod:Other)')]
+ _output_ports = [('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
+ _widget_class = build_enum_widget('AggregationMethod',
+ ['Mean', 'Max', 'Min', 'Majority', 'None'])
+
+ @staticmethod
+ def get_widget_class():
+ return AggregationMethod._widget_class
+
+class ResampleMethod(String):
+ '''
+ This module is a required class for other modules and scripts within the
+ SAHM package. It is not intended for direct use or incorporation into
+ the VisTrails workflow by the user.
+ '''
+ _input_ports = [('value', '(gov.usgs.sahm:ResampleMethod:Other)')]
+ _output_ports = [('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
+ _widget_class = build_enum_widget('ResampleMethod',
+ ['NearestNeighbor', 'Bilinear', 'Cubic', 'CubicSpline', 'Lanczos'])
+
+ @staticmethod
+ def get_widget_class():
+ return ResampleMethod._widget_class
+
+class Predictor(Constant):
+ '''
+ Predictor
+
+ The Predictor module allows a user to select a single raster layer for consideration in the
+ modeled analysis. Four parameters must be specified by the user:
+
+ 1. Aggregation Method: The aggregation method to be used in the event that the raster layer
+ must be up-scaled to match the template layer (e.g., generalizing a 10 m input layer to a
+ 100 m output layer). Care should be taken to ensure that the aggregation method that
+ best preserves the integrity of the data is used.
+
+ 2. Resample Method: The resample method employed to interpolate new cell values when
+ transforming the raster layer to the coordinate space or cell size of the template layer,
+ if necessary.
+
+ 3. Categorical (Boolean): Checking this box indicates that the data contained in the raster
+ layer is categorical (e.g. landcover categories). Leaving this box unchecked indicates that
+ the data contained in the raster is continuous (e.g., a DEM layer). This distinction is important
+ in determining an appropriate resampling method.
+
+ 4. File Path: The location of the raster predictor file, which a user can specify by navigating to the
+ file's location on their file system. When a user is selecting an ESRI grid raster, the user should navigate
+ to the 'hdr.adf' file contained within the grid folder.
+
+ '''
+ _input_ports = [('categorical', '(edu.utah.sci.vistrails.basic:Boolean)'),
+ ('ResampleMethod', '(gov.usgs.sahm:ResampleMethod:Other)', {'defaults':str(['Bilinear'])}),
+ ('AggregationMethod', '(gov.usgs.sahm:AggregationMethod:Other)', {'defaults':str(['Mean'])}),
+ ('file', '(edu.utah.sci.vistrails.basic:Path)')]
+ _output_ports = [('value', '(gov.usgs.sahm:Predictor:DataInput)'),
+ ('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
+
+ def compute(self):
+ if (self.hasInputFromPort("ResampleMethod")):
+ resampleMethod = self.getInputFromPort("ResampleMethod")
+ if resampleMethod.lower() not in ['nearestneighbor', 'bilinear', 'cubic', 'cubicspline', 'lanczos']:
+ raise ModuleError(self,
+ "Resample Method not one of 'nearestneighbor', 'bilinear', 'cubic', 'cubicspline', or 'lanczos'")
+ else:
+ resampleMethod = 'Bilinear'
+
+ if (self.hasInputFromPort("AggregationMethod")):
+ aggregationMethod = self.getInputFromPort("AggregationMethod")
+ if self.getInputFromPort("AggregationMethod").lower() not in ['mean', 'max', 'min', 'majority', 'none']:
+ raise ModuleError(self, "No Aggregation Method specified")
+ else:
+ aggregationMethod = "Mean"
+
+ if (self.hasInputFromPort("categorical")):
+ if self.getInputFromPort("categorical") == True:
+ categorical = '1'
+ else:
+ categorical = '0'
+ else:
+ categorical = '0'
+
+ if (self.hasInputFromPort("file")):
+ inFile = utils.getRasterName(self.getInputFromPort("file").name)
+ else:
+ raise ModuleError(self, "No input file specified")
+ self.setResult('value', (inFile, categorical, resampleMethod, aggregationMethod))
+
+class PredictorList(Constant):
+ '''
+ This module is a required class for other modules and scripts within the
+ SAHM package. It is not intended for direct use or incorporation into
+ the VisTrails workflow by the user.
+ '''
+ _input_ports = expand_ports([('value', 'Other|PredictorList'),
+ ('addPredictor', 'DataInput|Predictor')])
+ _output_ports = expand_ports([('value', 'Other|PredictorList')])
+
+ @staticmethod
+ def translate_to_string(v):
+ return str(v)
+
+ @staticmethod
+ def translate_to_python(v):
+ v_list = eval(v)
+ return v_list
+
+ @staticmethod
+ def validate(x):
+ return type(x) == list
+
+ def compute(self):
+ p_list = self.forceGetInputListFromPort("addPredictor")
+ v = self.forceGetInputFromPort("value", [])
+
+ b = self.validate(v)
+ if not b:
+ raise ModuleError(self, "Internal Error: Constant failed validation")
+ if len(v) > 0 and type(v[0]) == tuple:
+ f_list = [utils.create_file_module(v_elt[1]) for v_elt in v]
+ else:
+ f_list = v
+ p_list += f_list
+ #self.setResult("value", p_list)
+ self.setResult("value", v)
+
+class PredictorListFile(Module):
+ '''
+ Predictor List File
+
+ The PredictorListFile module allows a user to load a .csv file containing a list
+ of rasters for consideration in the modeled analysis. The .csv file should contain
+ a header row and four columns containing the following information, in order, for
+ each raster input.
+
+ Column 1: The full file path to the input raster layer.
+
+ Column 2: A binary value indicating whether the input layer is categorical or not.
+ A value of "0" indicates that an input raster is non-categorical data (continuous),
+ while a value of "1" indicates that an input raster is categorical data.
+
+ Column 3: The resampling method employed to interpolate new cell values when
+ transforming the raster layer to the coordinate space or cell size of the template
+ layer, if necessary. The resampling type should be specified using one of the following
+ values: "nearestneighbor," "bilinear," "cubic," or "lanczos."
+
+ Column 4: The aggregation method to be used in the event that the raster layer
+ must be up-scaled to match the template layer (e.g., generalizing a 10 m input layer to a
+ 100 m output layer). Care should be taken to ensure that the aggregation method that
+ best preserves the integrity of the data is used. The aggregation should be specified
+ using one of the following values: "Min," "Mean," "Max," "Majority," or "None."
+
+ In formatting the list of predictor files, the titles assigned to each of the columns
+ are unimportant as the module retrieves the information based on the order of the
+ values in the .csv file (the ordering of the information and the permissible values
+ in the file however, are strictly enforced). The module also anticipates a header row
+ and will ignore the first row in the .csv file.
+
+ '''
+ _input_ports = expand_ports([('csvFileList', '(edu.utah.sci.vistrails.basic:File)'),
+ ('addPredictor', 'DataInput|Predictor')])
+ _output_ports = expand_ports([('RastersWithPARCInfoCSV', '(gov.usgs.sahm:RastersWithPARCInfoCSV:Other)')])
+
+ #copies the input predictor list csv to our working directory
+ #and appends any additionally added predictors
+
+ @staticmethod
+ def translate_to_string(v):
+ return str(v)
+
+ @staticmethod
+ def translate_to_python(v):
+ v_list = eval(v)
+ return v_list
+
+ @staticmethod
+ def validate(x):
+ return type(x) == list
+
+ def compute(self):
+ if not (self.hasInputFromPort("csvFileList") or
+ self.hasInputFromPort("addPredictor")):
+ raise ModuleError(self, "No inputs or CSV file provided")
+
+ output_fname = utils.mknextfile(prefix='PredictorList_', suffix='.csv')
+ if (self.hasInputFromPort("csvFileList") and
+ os.path.exists(self.getInputFromPort("csvFileList").name)):
+ shutil.copy(self.getInputFromPort("csvFileList").name,
+ output_fname)
+ csv_writer = csv.writer(open(output_fname, 'ab'))
+ else:
+ #create an empty file to start with.
+ csv_writer = csv.writer(open(output_fname, 'wb'))
+ csv_writer.writerow(["file", "Resampling", "Aggregation"])
+
+ if self.hasInputFromPort("addPredictor"):
+ p_list = self.forceGetInputListFromPort("addPredictor")
+ for p in p_list:
+ if p.hasInputFromPort('resampleMethod'):
+ resMethod = p.getInputFromPort('resampleMethod')
+ else:
+ resMethod = "NearestNeighbor"
+ if p.hasInputFromPort('aggregationMethod'):
+ aggMethod = p.getInputFromPort('aggregationMethod')
+ else:
+ aggMethod = "Mean"
+ csv_writer.writerow([os.path.normpath(p.name), resMethod, aggMethod])
+
+ del csv_writer
+
+ output_file = utils.create_file_module(output_fname)
+ self.setResult('RastersWithPARCInfoCSV', output_file)
+
+class TemplateLayer(Path):
+ '''
+ Template Layer
+
+ The TemplateLayer is a raster data layer with a defined coordinate system, a known cell size,
+ and an extent that defines the study area. This raster layer serves as the template for all
+ the other inputs in the analysis. All additional raster layers used in the analysis will be
+ resampled and reprojected as needed to match the template, snapped to the template, and
+ clipped to have an extent that matches the template. Users should ensure that any additional
+ layers considered in the analysis have coverage within the extent of the template layer.
+
+ The TemplateLayer is a required input for the PARC module.
+
+ '''
+# _input_ports = [('FilePath', '(edu.utah.sci.vistrails.basic:File)')]
+ _output_ports = [('value', '(gov.usgs.sahm:TemplateLayer:DataInput)'),
+ ('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
+# def compute(self):
+# output_file = create_file_module(self.forceGetInputFromPort('FilePath', []))
+# self.setResult('value', output_file)
+
+#class SingleInputPredictor(Predictor):
+# pass
+#
+#class SpatialDef(Module):
+# _output_ports = [('spatialDef', '(gov.usgs.sahm:SpatialDef:DataInput)')]
+
+class MergedDataSet(File):
+ '''
+ This module is a required class for other modules and scripts within the
+ SAHM package. It is not intended for direct use or incorporation into
+ the VisTrails workflow by the user.
+ '''
+ _input_ports = expand_ports([('mdsFile', '(edu.utah.sci.vistrails.basic:File)')])
+ _output_ports = expand_ports([('value', '(gov.usgs.sahm:MergedDataSet:Other)')])
+
+ pass
+
+class RastersWithPARCInfoCSV(File):
+ '''
+ This module is a required class for other modules and scripts within the
+ SAHM package. It is not intended for direct use or incorporation into
+ the VisTrails workflow by the user.
+ '''
+ _input_ports = expand_ports([('mdsFile', '(edu.utah.sci.vistrails.basic:File)')])
+ _output_ports = expand_ports([('value', '(gov.usgs.sahm:MergedDataSet:Other)')])
+
+ pass
+# def compute(self, is_input=None):
+# PersistentPath.compute(self, is_input, 'blob')
+
+class ApplyModel(Module):
+ '''
+ Apply Model
+
+ The ApplyModel module allows the user to apply a model developed using a
+ particular package within the workflow and generate output probability and binary
+ maps. The process of creating an output probability map and binary map based on
+ a particular model can be time-consuming, depending on the input data. By
+ existing as a stand-alone process in the workflow, the ApplyModel module allows
+ a user to investigate the performance metrics for a particular model (such as
+ the ROC curve or the AUC) before dedicating the processing time needed to generate
+ the output maps. In most cases, a user will "fine tune" a model by exploring the
+ performance metrics of different model iterations before applying the model and
+ generating the actual maps as a final step.
+
+ The ApplyModel module also provides the user with the option of projecting the results
+ of a model developed from one set of environmental predictors onto a new modeled space
+ containing that same set of environmental predictors but representing data captured at
+ a different temporal or spatial location. For example, a user could generate a model
+ predicting habitat suitability using recorded presence points and certain environmental
+ predictors such as elevation, landcover, and proximity to water in one geographic
+ location. Based on the training from this information, the modeled results could be
+ generated for (or "projected to") a new location based on the range of values seen in
+ elevation, landcover, and proximity to water in the second geographic area. Similarly,
+ modeling predicted results through time is also possible. A model trained using field
+ data and a set of predictor layers representative of one time period could be projected
+ onto the same geographical area using a new set of layers corresponding to the same
+ predictors but representing data from a different time period (e.g., different climate
+ data).
+
+ The ApplyModel module accepts two inputs from the user:
+
+ 1. Model Workspace: The model workspace field accepts as an input a modeling
+ package element (complete with all required parameters) from upstream in the workflow.
+ The inputs and specifications provided in the dialogue fields of the model will be applied
+ and used to generate the output maps. A user should populate the model workspace field by
+ connecting a model element to the appropriate input port of the ApplyModel module in the
+ visual display of the model workflow.
+
+ 2. Projection Target: The projection target is an optional parameter that allows a user to
+ apply a model to a particular geographic area and or set of predictors (other than those
+ used to train the model) and create output maps within the spatial extent of the projection
+ target layers. This input field should be populated by connecting either the output of the
+ ProjectionLayers module or a separate MDSBuilder element to the appropriate input port of
+ the ApplyModel module.
+
+ '''
+
+ _input_ports = [('projectionTarget', '(gov.usgs.sahm:MergedDataSet:Other)'),
+ ('modelWorkspace', '(edu.utah.sci.vistrails.basic:File)'),
+ ('makeBinMap', '(edu.utah.sci.vistrails.basic:Boolean)'),
+ ('makeProbabilityMap', '(edu.utah.sci.vistrails.basic:Boolean)'),]
+ _output_ports = [('BinaryMap', '(edu.utah.sci.vistrails.basic:File)'),
+ ('ProbabilityMap', '(edu.utah.sci.vistrails.basic:File)')]
+
+
+
+ def compute(self):
+
+ workspace = self.forceGetInputFromPort('modelWorkspace').name
+ output_dname = utils.mknextdir(prefix='AppliedModel_')
+ if self.hasInputFromPort('projectionTarget'):
+ mdsFile = self.forceGetInputFromPort('projectionTarget').name
+ args = "ws=" + '"' + workspace + '"' + " c=" + '"' + mdsFile + '"' + " o=" + '"' + output_dname + '"'
+ else:
+ args = "ws=" + '"' + workspace + '"' + " o=" + '"' + output_dname + '"'
+
+ if self.hasInputFromPort('makeBinMap'):
+ makeBinMap = self.forceGetInputFromPort('makeBinMap')
+ args += ' mbt=' + str(makeBinMap).upper()
+ else:
+ args += ' mbt=TRUE'
+
+ if self.hasInputFromPort('makeProbabilityMap'):
+ makeProbabilityMap = self.forceGetInputFromPort('makeProbabilityMap')
+ args += ' mpt=' + str(makeProbabilityMap).upper()
+ else:
+ args += ' mpt=TRUE'
+
+
+ utils.runRScript('PredictModel.r', args, self)
+
+ input_fname = os.path.join(output_dname, "prob_map.tif")
+ output_fname = os.path.join(output_dname, 'prob_map.jpeg')
+ if os.path.exists(input_fname):
+ utils.tif_to_color_jpeg(input_fname, output_fname, color_breaks_csv)
+ output_file1 = utils.create_file_module(output_fname)
+ self.setResult('ProbabilityMap', output_file1)
+ else:
+ msg = "Expected output from ApplyModel was not found."
+ msg += "\nThis likely indicates problems with the inputs to the R module."
+ writetolog(msg, False, True)
+ raise ModuleError(self, msg)
+
+ if os.path.exists(os.path.join(output_dname, "bin_map.tif")):
+ outFileName = os.path.join(output_dname, "bin_map.tif")
+ output_file2 = utils.create_file_module(outFileName)
+ self.setResult('BinaryMap', output_file2)
+
+class Model(Module):
+ '''
+ This module is a required class for other modules and scripts within the
+ SAHM package. It is not intended for direct use or incorporation into
+ the VisTrails workflow by the user.
+ '''
+ _input_ports = [('mdsFile', '(gov.usgs.sahm:MergedDataSet:Other)'),
+ ('makeBinMap', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['True']), 'optional':False}),
+ ('makeProbabilityMap', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['True']), 'optional':False}),
+ ('makeMESMap', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['False']), 'optional':False}),
+ ('ThresholdOptimizationMethod', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['2']), 'optional':False})
+ ]
+ _output_ports = [('modelWorkspace', '(edu.utah.sci.vistrails.basic:File)'),
+ ('BinaryMap', '(edu.utah.sci.vistrails.basic:File)'),
+ ('ProbabilityMap', '(edu.utah.sci.vistrails.basic:File)'),
+ ('AUC_plot', '(edu.utah.sci.vistrails.basic:File)'),
+ ('ResponseCurves', '(edu.utah.sci.vistrails.basic:File)'),
+ ('Text_Output', '(edu.utah.sci.vistrails.basic:File)')]
+
+ def compute(self):
+ global color_breaks_csv
+
+ ModelOutput = {"FIT_BRT_pluggable.r":"brt",
+ "FIT_GLM_pluggable.r":"glm",
+ "FIT_RF_pluggable.r":"rf",
+ "FIT_MARS_pluggable.r":"mars"}
+ ModelAbbrev = ModelOutput[self.name]
+
+ output_dname = utils.mknextdir(prefix=ModelAbbrev + 'output_')
+ argsDict = utils.map_ports(self, self.port_map)
+ mdsFile = self.forceGetInputFromPort('mdsFile').name
+
+ args = ''
+ for k, v in argsDict.iteritems():
+ if k == 'c':
+ args += ' ' + '='.join([str(k),'"' + str(v) + '"'])
+ else:
+ args += ' ' + '='.join([str(k),str(v)])
+ args += " o=" + '"' + output_dname + '"'
+ args += " rc=" + utils.MDSresponseCol(mdsFile)
+# if self.hasInputFromPort('makeBinMap'):
+# makeBinMap = self.forceGetInputFromPort('makeBinMap')
+# args += ' mbt=' + str(makeBinMap).upper()
+# else:
+# makeBinMap = True
+# args += ' mbt=TRUE'
+#
+# if self.hasInputFromPort('makeProbabilityMap'):
+# makeProbabilityMap = self.forceGetInputFromPort('makeProbabilityMap')
+# args += ' mpt=' + str(makeProbabilityMap).upper()
+# else:
+# makeProbabilityMap = True
+# args += ' mpt=TRUE'
+#
+# if self.hasInputFromPort('seed'):
+# args += ' seed=' + str(self.forceGetInputFromPort('seed'))
+#
+# if self.hasInputFromPort('someParam'):
+# x = self.forceGetInputFromPort('someParam')
+# if x > 1:
+# msg = "Expected output from " + ModelAbbrev + " was not found."
+# msg += "\nThis likely indicates problems with the inputs to the R module."
+# writetolog(msg, False, True)
+# args += " abr=" + x
+
+ utils.runRScript(self.name, args, self)
+# utils.runRScript('FIT_BRT_pluggableErrorMessage.r', args, self)
+
+ input_fname = os.path.join(output_dname, ModelAbbrev + "_prob_map.tif")
+ output_fname = os.path.join(output_dname, ModelAbbrev + "_prob_map.jpeg")
+ if os.path.exists(input_fname):
+# utils.tif_to_color_jpeg(input_fname, output_fname, color_breaks_csv)
+# output_file4 = utils.create_file_module(output_fname)
+ self.setResult('ProbabilityMap', input_fname)
+ elif (argsDict.has_key('mpt') and argsDict['mpt'] == True) or \
+ not argsDict.has_key('mpt'):
+ msg = "Expected output from " + ModelAbbrev + " was not found."
+ msg += "\nThis might indicate problems with the inputs to the R module."
+ msg += "\nCheck the console output for additional R warnings "
+ writetolog(msg, False, True)
+ raise ModuleError(self, msg)
+
+ if (argsDict.has_key('mbt') and argsDict['mbt'] == True) or \
+ not argsDict.has_key('mbt'):
+ outFileName = os.path.join(output_dname, ModelAbbrev + "_bin_map.tif")
+ output_file1 = utils.create_file_module(outFileName)
+ self.setResult('BinaryMap', output_file1)
+
+ outFileName = os.path.join(output_dname, ModelAbbrev + "_output.txt")
+ output_file2 = utils.create_file_module(outFileName)
+ self.setResult('Text_Output', output_file2)
+
+ outFileName = os.path.join(output_dname, ModelAbbrev + "_auc_plot.jpg")
+# print "out auc: ", outFileName
+ output_file3 = utils.create_file_module(outFileName)
+ self.setResult('AUC_plot', output_file3)
+
+ outFileName = os.path.join(output_dname, ModelAbbrev + "_response_curves.pdf")
+ output_file5 = utils.create_file_module(outFileName)
+ self.setResult('ResponseCurves', output_file5)
+
+ outFileName = os.path.join(output_dname, "modelWorkspace")
+# print "out auc: ", outFileName
+ output_file6 = utils.create_file_module(outFileName)
+ self.setResult('modelWorkspace', output_file6)
+
+ writetolog("Finished " + ModelAbbrev + " builder\n", True, True)
+
+class GLM(Model):
+ _input_ports = list(Model._input_ports)
+ _input_ports.extend([('ModelFamily', '(edu.utah.sci.vistrails.basic:String)', {'defaults':str(['binomial']), 'optional':True}),
+ ('SimplificationMethod', '(edu.utah.sci.vistrails.basic:String)', {'defaults':str(['AIC']), 'optional':True}),
+ ])
+ def __init__(self):
+ global models_path
+ Model.__init__(self)
+ self.name = 'FIT_GLM_pluggable.r'
+ self.port_map = {'mdsFile':('c', None, True),#These ports are for all Models
+ 'makeProbabilityMap':('mpt', utils.R_boolean, False),
+ 'makeBinMap':('mbt', utils.R_boolean, False),
+ 'makeMESMap':('mes', utils.R_boolean, False),
+ 'ThresholdOptimizationMethod':('om', None, False),
+ 'ModelFamily':('mf', None, False), #This is a GLM specific port
+ 'SimplificationMethod':('sm', None, False) #This is a GLM specific port
+ }
+
+class RandomForest(Model):
+ _input_ports = list(Model._input_ports)
+ _input_ports.extend([('MTRY', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['1']), 'optional':True}),
+ ])
+ def __init__(self):
+ global models_path
+ Model.__init__(self)
+ self.name = 'FIT_RF_pluggable.r'
+ self.port_map = {'mdsFile':('c', None, True),#These ports are for all Models
+ 'makeProbabilityMap':('mpt', utils.R_boolean, False),
+ 'makeBinMap':('mbt', utils.R_boolean, False),
+ 'makeMESMap':('mes', utils.R_boolean, False),
+ 'ThresholdOptimizationMethod':('om', None, False),
+ 'MTRY': ('mtry', None, False) #This is a Random Forest specific port
+ }
+
+class MARS(Model):
+ _input_ports = list(Model._input_ports)
+ _input_ports.extend([('MarsDegree', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['1']), 'optional':True}),
+ ('MarsPenalty', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['2']), 'optional':True}),
+ ])
+ def __init__(self):
+ global models_path
+ Model.__init__(self)
+ self.name = 'FIT_MARS_pluggable.r'
+ self.port_map = {'mdsFile':('c', None, True),#These ports are for all Models
+ 'makeProbabilityMap':('mpt', utils.R_boolean, False),
+ 'makeBinMap':('mbt', utils.R_boolean, False),
+ 'makeMESMap':('mes', utils.R_boolean, False),
+ 'ThresholdOptimizationMethod':('om', None, False),
+ 'MarsDegree':('deg', None, False), #This is a MARS specific port
+ 'MarsPenalty':('pen', None, False), #This is a MARS specific port
+ }
+
+class BoostedRegressionTree(Model):
+ _input_ports = list(Model._input_ports)
+ _input_ports.extend([('Seed', '(edu.utah.sci.vistrails.basic:Integer)', True),
+ ('TreeComplexity', '(edu.utah.sci.vistrails.basic:Integer)', True),
+ ('NumberOfTrees', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['10000']), 'optional':True}),
+ ('BagFraction', '(edu.utah.sci.vistrails.basic:Float)', {'defaults':str(['0.5']), 'optional':True}),
+ ('NumberOfFolds', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['3']), 'optional':True}),
+ ('Alpha', '(edu.utah.sci.vistrails.basic:Float)', {'defaults':str(['1']), 'optional':True}),
+ ('PrevalenceStratify', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['True']), 'optional':True}),
+ ('ToleranceMethod', '(edu.utah.sci.vistrails.basic:String)', {'defaults':str(['auto']), 'optional':True}),
+ ('Tolerance', '(edu.utah.sci.vistrails.basic:Float)', {'defaults':str(['0.001']), 'optional':True})
+ ])
+ def __init__(self):
+ global models_path
+ Model.__init__(self)
+ self.name = 'FIT_BRT_pluggable.r'
+ self.port_map = {'mdsFile':('c', None, True),#These ports are for all Models
+ 'makeProbabilityMap':('mpt', utils.R_boolean, False),
+ 'makeBinMap':('mbt', utils.R_boolean, False),
+ 'makeMESMap':('mes', utils.R_boolean, False),
+ 'ThresholdOptimizationMethod':('om', None, False),
+ 'Seed':('seed', None, False), #This is a BRT specific port
+ 'TreeComplexity':('tc', None, False), #This is a BRT specific port
+ 'NumberOfTrees':('nf', None, False), #This is a BRT specific port
+ 'BagFraction':('bf', None, False), #This is a BRT specific port
+ 'NumberOfFolds':('nf', None, False), #This is a BRT specific port
+ 'Alpha':('alp', None, False), #This is a BRT specific port
+ 'PrevalenceStratify':('ps', None, False), #This is a BRT specific port
+ 'ToleranceMethod':('tolm', None, False), #This is a BRT specific port
+ 'Tolerance':('tol', None, False) #This is a BRT specific port
+ }
+
+class MDSBuilder(Module):
+ '''
+ MDS Builder
+
+ The Merged Data Set (MDS) Builder module is a utility that extracts the values of each predictor
+ layer to the point locations included in the field data set. The module produces a .csv file that
+ contains the x and y locations of the sample points and a column indicating whether each point
+ represents a presence recording, an absence recording, a presence count, or a background point.
+ Following these first three columns, each environmental predictor layer is appended as a column
+ with row entries representing the value present in the raster layer at each field sample point.
+ There are a total of three header rows in the output .csv of the MDSBuilder. The first row contains
+ the columns "x," "y," "ResponseBinary" or "ResponseCount," and the names of each of the raster
+ predictor files that were passed to the MDS Builder. The second row contains a binary value
+ indicating whether the column should be included when the model is finally applied; these values
+ are later modified during the Covariate Correlation and Selection process that takes place downstream
+ in the workflow. The final header row contains the full path on the file system to each of the raster
+ predictor files.
+
+ The MDSBuilder accepts four inputs from the user:
+
+ 1. Rasters with PARC Info .csv File: The raster layers listed in this file will have their values
+ extracted to the points in the field data .csv file. This parameter should be supplied by connecting
+ the output of a PARC module within the workflow to the MDSBuilder module. (In order to properly
+ extract the values of each predictor layer to the field data points, all the layers must have matching
+ coordinate systems and cell sizes; outputs from the PARC module will have had the prerequisite processing).
+
+ 2. Background Point Count: This is an optional value that applies only to workflows that employ the
+ Maxent modeling package. The dialogue box provides the option of specifying a number of background points
+ to be randomly scattered throughout the study area (the extent of the template layer) to capture a more
+ complete sample of the range of values present for each predictor layer. These points will be added to
+ the field data .csv file with a value of "-999" denoting them as background points.
+
+ 3. Background Probability Surface: This is an optional parameter that applies only to workflows that
+ employ the Maxent modeling package. In some analyses, it may be appropriate to spatially limit background
+ points to a particular subset of the study area (e.g., islands within a study area polygon, particular
+ regions within a study area polygon, or a region determined by the known bias present in the field data).
+ Specifying a background probability surface raster allows a user to control where random points will be
+ scattered within the extent of the study area. The raster layer specified by a user should have the same
+ projection and extent as the template layer and contain values ranging from 0 to 100. These values represent
+ the probability that a randomly generated point will be retained should it fall within a particular cell.
+ That is, randomly generated points will not be generated in any part of the probability grid with a value
+ of "0" while all points falling in an area with a value of "100" will be retained. A point falling in an
+ area with a value of "50" will be kept as a background point 50% of the time.
+
+ 4. Field Data: The field data input corresponds to a .csv file containing presence/absence points or count
+ data recorded across a landscape for the phenomenon being modeled (e.g., plant sightings, evidence of
+ animal presence, etc.). This input file must be in a particular format, and in most cases, a user should
+ populate this field by connecting a FieldData element to the MDSBuilder in the visual display within VisTrails.
+ Please see the documention for the FieldData module for more details.
+
+ '''
+
+# _input_ports = expand_ports([('RastersWithPARCInfoCSV', '(gov.usgs.sahm:RastersWithPARCInfoCSV:Other)'),
+# ('fieldData', '(gov.usgs.sahm:FieldData:DataInput)'),
+# ('backgroundPointCount', '(edu.utah.sci.vistrails.basic:Integer)'),
+# ('backgroundProbSurf', '(edu.utah.sci.vistrails.basic:File)')]
+# )
+# _input_ports = expand_ports([('RastersWithPARCInfoCSV', '(edu.utah.sci.vistrails.persistence:PersistentFile)'),
+# ('fieldData', '(gov.usgs.sahm:FieldData:DataInput)'),
+# ('backgroundPointCount', '(edu.utah.sci.vistrails.basic:Integer)'),
+# ('backgroundProbSurf', '(edu.utah.sci.vistrails.basic:File)')]
+# )
+ _input_ports = expand_ports([('RastersWithPARCInfoCSV', '(edu.utah.sci.vistrails.basic:File)'),
+ ('fieldData', '(gov.usgs.sahm:FieldData:DataInput)'),
+ ('backgroundPointCount', '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('backgroundProbSurf', '(edu.utah.sci.vistrails.basic:File)')]
+ )
+
+ _output_ports = expand_ports([('mdsFile', '(gov.usgs.sahm:MergedDataSet:Other)')])
+
+ def compute(self):
+ port_map = {'fieldData': ('fieldData', None, True),
+ 'backgroundPointCount': ('pointcount', None, False),
+ 'backgroundProbSurf': ('probsurf', None, False),}
+
+ MDSParams = utils.map_ports(self, port_map)
+ MDSParams['outputMDS'] = utils.mknextfile(prefix='MergedDataset_', suffix='.csv')
+
+ #allow multiple CSV of inputs to be provided.
+ #if more than one then combine into a single CSV before sending to MDSBuilder
+ inputs_csvs = self.forceGetInputListFromPort('RastersWithPARCInfoCSV')
+ if len(inputs_csvs) == 0:
+ raise ModuleError(self, "Must supply at least one 'RastersWithPARCInfoCSV'/nThis is the output from the PARC module")
+ if len(inputs_csvs) > 1:
+ inputs_csv = utils.mknextfile(prefix='CombinedPARCFiles_', suffix='.csv')
+ inputs_names = [f.name for f in inputs_csvs]
+ utils.merge_inputs_csvs(inputs_names, inputs_csv)
+ else:
+ inputs_csv = inputs_csvs[0].name
+ MDSParams['inputsCSV'] = inputs_csv
+
+ #inputsCSV = utils.path_port(self, 'RastersWithPARCInfoCSV')
+
+ ourMDSBuilder = MDSB.MDSBuilder()
+ utils.PySAHM_instance_params(ourMDSBuilder, MDSParams)
+
+ writetolog(" inputsCSV=" + ourMDSBuilder.inputsCSV, False, False)
+ writetolog(" fieldData=" + ourMDSBuilder.fieldData, False, False)
+ writetolog(" outputMDS=" + ourMDSBuilder.outputMDS, False, False)
+
+ try:
+ ourMDSBuilder.run()
+ except TrappedError as e:
+ raise ModuleError(self, e.message)
+ except:
+ utils.informative_untrapped_error(self, "MDSBuilder")
+
+ output_file = utils.create_file_module(ourMDSBuilder.outputMDS)
+
+ self.setResult('mdsFile', output_file)
+
+class FieldDataAggregateAndWeight(Module):
+ '''
+ Documentation to be updated when module finalized.
+ '''
+ _input_ports = expand_ports([('templateLayer', '(gov.usgs.sahm:TemplateLayer:DataInput)'),
+ ('fieldData', '(gov.usgs.sahm:FieldData:DataInput)'),
+ ('aggregateRows', 'basic:Boolean'),
+ ('aggregateRowsByYear', 'basic:Boolean')])
+ _output_ports = expand_ports([('fieldData', '(gov.usgs.sahm:FieldData:DataInput)')])
+
+ def compute(self):
+ writetolog("\nRunning FieldDataQuery", True)
+ port_map = {'templateLayer': ('template', None, True),
+ 'fieldData': ('csv', None, True),
+ 'aggregateRowsByYear': ('aggRows', None, False),
+ 'addKDE': ('addKDE', None, False),}
+
+ KDEParams = utils.map_ports(self, port_map)
+ output_fname = utils.mknextfile(prefix='FDQ_', suffix='.csv')
+ writetolog(" output_fname=" + output_fname, True, False)
+ KDEParams['output'] = output_fname
+
+ output_fname = utils.mknextfile(prefix='FDQ_', suffix='.csv')
+ writetolog(" output_fname=" + output_fname, True, False)
+
+ ourFDQ = FDQ.FieldDataQuery()
+ utils.PySAHM_instance_params(ourFDQ, KDEParams)
+
+ ourFDQ.processCSV()
+
+ output_file = utils.create_file_module(output_fname)
+ writetolog("Finished running FieldDataQuery", True)
+ self.setResult('fieldData', output_file)
+
+class PARC(Module):
+ '''
+ PARC
+
+ The Projection, Aggregation, Resampling, and Clipping (PARC) module is a powerful
+ utility that automates the preparation steps required for using raster layers in
+ most geospatial modeling packages. In order to successfully consider multiple
+ environmental predictors in raster format, each layer must have coincident cells
+ (pixels) of the same size, have the same coordinate system (and projection, if
+ applicable), and the same geographic extent. The PARC module ensures that all of
+ these conditions are met for the input layers by transforming and or reprojecting
+ each raster to match the coordinate system of the template layer. This process
+ usually involves aggregation (necessary when an input raster layer must be up-scaled
+ to match the template layer-- e.g., generalizing a 10 m input layer to a 100 m output
+ layer), and or resampling (necessary for interpolating new cell values when transforming
+ the raster layer to the coordinate space or cell size of the template layer). Lastly,
+ each raster predictor layer is clipped to match the extent of the template layer.
+
+ The settings used during these processing steps follow a particular set of decision rules
+ designed to preserve the integrity of data as much as possible. However, it is important
+ for a user to understand how these processing steps may modify the data inputs. For
+ additional information about the PARC module, please see the extended help and
+ documentation for the SAHM package.
+
+ The PARC module accepts four kinds of inputs:
+
+ 1. Predictor List: A user should not have to populate this field. This field is populated
+ when a selection is made from the pre-loaded .csv file of raster predictor layer inputs
+ (specified during the SAHM install) and connected to the PARC module in the visual display.
+
+ 2. .csv File List: The .csv file list corresponds to the Predictor List File element and
+ allows a user to load a .csv file containing a list of rasters for consideration in the
+ modeled analysis. For additional information, please see the documentation for the Predictor
+ List File element.
+
+ 3. Predictor: The predictor input allows a user to select a single raster predictor layer
+ to be considered in the analysis. It is recommended that a user add this input as a separate
+ element in the visual display (and then link it to the PARC module) so that the aggregation
+ and resampling settings can be established. The PARC module can accept multiple predictor
+ elements. For additional information, please see the documentation for the Predictor element.
+
+ 4. Template Layer: The template layer is a raster data layer with a defined coordinate system,
+ a known cell size, and an extent that defines the study area. This raster layer serves as the
+ template for all the other inputs in the analysis. All additional raster layers used in the
+ analysis will be resampled and reprojected as needed to match the template, snapped to the
+ template, and clipped to have an extent that matches the template. Users should ensure that
+ any additional layers considered in the analysis have coverage within the extent of the
+ template layer. The template layer is a required input for the PARC module.
+
+ '''
+
+ #configuration = []
+ _input_ports = [('predictor', "(gov.usgs.sahm:Predictor:DataInput)"),
+ ('PredictorList', '(gov.usgs.sahm:PredictorList:Other)'),
+ ('RastersWithPARCInfoCSV', '(gov.usgs.sahm:RastersWithPARCInfoCSV:Other)'),
+ ('templateLayer', '(gov.usgs.sahm:TemplateLayer:DataInput)'),
+ ('multipleCores', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['True']), 'optional':True})]
+
+# _output_ports = [('RastersWithPARCInfoCSV', '(gov.usgs.sahm:RastersWithPARCInfoCSV:Other)')]
+# _output_ports = [('RastersWithPARCInfoCSV', '(edu.utah.sci.vistrails.persistence:PersistentFile)')]
+ _output_ports = [('RastersWithPARCInfoCSV', '(edu.utah.sci.vistrails.basic:File)')]
+
+ def compute(self):
+ #writetolog("\nRunning PARC", True)
+
+ ourPARC = parc.PARC()
+ output_dname = utils.mknextdir(prefix='PARC_')
+
+ if configuration.verbose:
+ ourPARC.verbose = True
+ ourPARC.logger = utils.getLogger()
+
+ ourPARC.out_dir = output_dname
+
+ if self.hasInputFromPort("multipleCores"):
+ if self.getInputFromPort("multipleCores"):
+ ourPARC.multicores = "True"
+
+ workingCSV = utils.mknextfile(prefix='tmpFilesToPARC_', suffix='.csv')
+ outputCSV = utils.mknextfile(prefix='PARCOutput_', suffix='.csv')
+
+ #append additional inputs to the existing CSV if one was supplied
+ #otherwise start a new CSV
+ if self.hasInputFromPort("RastersWithPARCInfoCSV"):
+ inputCSV = self.forceGetInputFromPort("RastersWithPARCInfoCSV").name
+ shutil.copy(inputCSV, workingCSV)
+ f = open(workingCSV, "ab")
+ csvWriter = csv.writer(f)
+ else:
+ f = open(workingCSV, "wb")
+ csvWriter = csv.writer(f)
+ csvWriter.writerow(["FilePath", "Categorical", "Resampling", "Aggregation"])
+
+ if self.hasInputFromPort("PredictorList"):
+ predictor_lists = self.forceGetInputListFromPort('PredictorList')
+ for predictor_list in predictor_lists:
+ for predictor in predictor_list:
+ csvWriter.writerow(list(predictor))
+
+ if self.hasInputFromPort("predictor"):
+ predictor_list = self.forceGetInputListFromPort('predictor')
+ for predictor in predictor_list:
+ csvWriter.writerow(list(predictor))
+ f.close()
+ del csvWriter
+ ourPARC.inputs_CSV = workingCSV
+ ourPARC.template = self.forceGetInputFromPort('templateLayer').name
+ writetolog(' template layer = ' + self.forceGetInputFromPort('templateLayer').name)
+ writetolog(" output_dname=" + output_dname, False, False)
+ writetolog(" workingCSV=" + workingCSV, False, False)
+ try:
+ ourPARC.parcFiles()
+ except TrappedError as e:
+ writetolog(e.message)
+ raise ModuleError(self, e.message)
+ except:
+ utils.informative_untrapped_error(self, "PARC")
+
+ #delete our temp working file
+ os.remove(workingCSV)
+
+ predictorsDir = utils.create_dir_module(output_dname)
+ outputCSV = os.path.join(output_dname, "PARC_Files.csv")
+ output_file = utils.create_file_module(outputCSV)
+
+
+ writetolog("Finished running PARC", True)
+ self.setResult('RastersWithPARCInfoCSV', output_file)
+
+
+class RasterFormatConverter(Module):
+ '''
+ Raster Format Converter
+
+ The RasterFormatConverter module allows a user to easily convert .tif raster layers
+ into a different raster format for use and display in other software packages. The
+ module accepts as an input either a list of rasters in a Merged Dataset File (MDS)
+ or the location of a directory containing multiple raster files. All outputs will be
+ sent to a folder named "ConvertedRasters" (followed by an underscore and a number
+ corresponding to the run sequence of the module) within the user's current VisTrail
+ session folder.
+
+ Three parameters can be specified by the user:
+
+ 1. Format: The format corresponds to the desired raster output format. The following
+ output file formats are supported: Arc/Info ASCII Grid, ESRI BIL, ERDAS Imagine, and JPEG.
+
+ To specify the desired output, users should enter the values shown below.
+ For an ASCII (.asc) output, enter: "asc"
+ For an ESRI BIL output, enter: "bil"
+ For an Erdas Imagine (.img) output, enter: "img"
+ For a JPEG (.jpg) output, enter: "jpg"
+
+ If no value is entered by the user, the module will default to an ASCII (.asc) output
+ format.
+
+ 2. Input Directory: The input directory allows a user to point to an entire folder as
+ an input to the RasterFormatConverter. The contents of the specified folder will be
+ checked for raster files and all the raster files contained within the directory will
+ be converted to the format specified in the "Format" dialogue box. The module will
+ identify and convert files of the following raster types: .bil, .img, .tif, .jpg, and .asc.
+
+ 3. Input Merged Dataset (MDS): The input merged dataset allows a user to specify a .csv
+ file created in the VisTrails workflow (containing a list of .tif raster files) as an
+ input to the raster converter. All of the files listed in the MDS will be converted to
+ the raster format specified in the "Format" dialogue box.
+
+ '''
+
+ #configuration = []
+ _input_ports = [("inputMDS", "(gov.usgs.sahm:MergedDataSet:Other)"),
+ ('inputDir', '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('format', '(edu.utah.sci.vistrails.basic:String)'),
+ ('multipleCores', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['True']), 'optional':True})]
+
+ _output_ports = [('outputDir', '(edu.utah.sci.vistrails.basic:Directory)')]
+
+ def compute(self):
+ writetolog("\nRunning TiffConverter", True)
+ ourRFC = RFC.FormatConverter()
+ if self.hasInputFromPort('inputMDS'):
+ ourRFC.MDSFile = self.forceGetInputFromPort('inputMDS').name
+ elif self.hasInputFromPort('inputDir'):
+ ourRFC.inputDir = self.forceGetInputFromPort('inputDir').name
+
+ if self.hasInputFromPort('format'):
+ format = self.forceGetInputFromPort('format')
+ if format == '':
+ format = 'asc'
+ ourRFC.format = format
+
+ if self.hasInputFromPort("multipleCores"):
+ if self.getInputFromPort("multipleCores"):
+ ourRFC.multicores = "True"
+
+ ourRFC.outputDir = utils.mknextdir(prefix='ConvertedRasters_')
+ if configuration.verbose:
+ ourRFC.verbose = True
+ ourRFC.logger = utils.getLogger()
+ writetolog(" output directory = " + ourRFC.outputDir, False, False)
+
+ try:
+ ourRFC.run()
+ except TrappedError as e:
+ raise ModuleError(self, e.message)
+ except:
+ utils.informative_untrapped_error(self, "RasterFormatConverter")
+
+
+ outputDir = utils.create_dir_module(ourRFC.outputDir)
+ self.setResult('outputDir', outputDir)
+ writetolog("\nFinished running TiffConverter", True)
+
+class TestTrainingSplit(Module):
+ '''
+ Test Training Split
+
+ The TestTrainingSplit module provides the opportunity to establish specific settings
+ for how field data will be used in the modeling process. Three parameters can be set
+ by the user:
+
+ 1. Ratio of Presence/Absence Points:
+ This field is populated with a number corresponding to the desired proportion of
+ presence and absence points to be used in the analysis. If populated, this entry should
+ be a number greater than zero. (A value of '1' will result in an equal number of both
+ presence and absence points being used, a value of '2' indicates that twice as many
+ presence points will be used, a value of 0.5 indicates that twice as many absence points
+ will be used, etc.). All field data points with a value equal to or greater than 1 are
+ interpreted as presence points. Although the original field data is unmodified, this
+ option will reduce the sample size as the merged dataset containing sample points will
+ have points deleted from it to achieve the specified ratio. A warning will be generated
+ if more than 50% of either the presence or absence points will be deleted based on the
+ ratio specified by the user. Background points are ignored by this module (they are read
+ in and written out, but not assigned to either the test or training split).
+
+ When left empty, this field will default to 'null' and the model will use the existing
+ presence/absence ratio present in the field data.
+
+ 2. Input Merged Data Set (MDS):
+ This is the input data set consisting of locational data for each sample point, the
+ values of each predictor variable at those points, and if established, a field denoting
+ the weight that will be assigned to each point in modeling. This input is usually provided
+ by the upstream steps that precede the Test Training Split module. Any value entered here
+ (e.g., specifying another existing MDS on the file system) will override the input
+ specified by a model connection in the visual display.
+
+ 3. Training Proportion:
+ This is the proportion of the sample points that will be used to train the model, relative
+ to the total number of points. Entered values should be greater than 0 but less than 1.
+ For example, a value of '0.9' will result in 90% of the sample points being used to train
+ the model, with 10% of the sample being held out to test the model's performance. Choosing
+ an appropriate training proportion can depend on various factors, such as the total number
+ of sample points available.
+
+ '''
+
+ _input_ports = [("inputMDS", "(gov.usgs.sahm:MergedDataSet:Other)"),
+ ('trainingProportion', '(edu.utah.sci.vistrails.basic:Float)',
+ {'defaults':str(['0.7'])}),
+ ('RatioPresAbs', '(edu.utah.sci.vistrails.basic:Float)')]
+ _output_ports = [("outputMDS", "(gov.usgs.sahm:MergedDataSet:Other)")]
+
+ def compute(self):
+ if self.hasInputFromPort('trainingProportion'):
+ print 'real input'
+ writetolog("\nGenerating Test Training split ", True)
+ inputMDS = utils.dir_path_value(self.forceGetInputFromPort('inputMDS', []))
+ outputMDS = utils.mknextfile(prefix='TestTrainingSplit_', suffix='.csv')
+
+ global models_path
+
+ args = "i=" + '"' + inputMDS + '"' + " o=" + '"' + outputMDS + '"'
+ args += " rc=" + utils.MDSresponseCol(inputMDS)
+ if (self.hasInputFromPort("trainingProportion")):
+ try:
+ trainingProportion = float(self.getInputFromPort("trainingProportion"))
+ if trainingProportion <= 0 or trainingProportion > 1:
+ raise ModuleError(self, "Train Proportion (trainProp) must be a number between 0 and 1 excluding 0")
+ args += " p=" + str(trainingProportion)
+ except:
+ raise ModuleError(self, "Train Proportion (trainProp) must be a number between 0 and 1 excluding 0")
+ if (self.hasInputFromPort("RatioPresAbs")):
+ try:
+ RatioPresAbs = float(self.getInputFromPort("RatioPresAbs"))
+ if RatioPresAbs <= 0:
+ raise ModuleError(self, "The ratio of presence to absence (RatioPresAbs) must be a number greater than 0")
+ args += " m=" + str(trainingProportion)
+ except:
+ raise ModuleError(self, "The ratio of presence to absence (RatioPresAbs) must be a number greater than 0")
+
+ utils.runRScript("TestTrainSplit.r", args, self)
+
+ output = os.path.join(outputMDS)
+ if os.path.exists(output):
+ output_file = utils.create_file_module(output)
+ writetolog("Finished Test Training split ", True)
+ else:
+ msg = "Problem encountered generating Test Training split. Expected output file not found."
+ writetolog(msg, False)
+ raise ModuleError(self, msg)
+ self.setResult("outputMDS", output_file)
+
+class CovariateCorrelationAndSelection(Module):
+ '''
+ Covariate Correlation And Selection
+
+ The CovariateCorrelationAndSelection view provides a breakpoint in the modeling workflow
+ for the user to assess how well each variable explains the distribution of the sampled
+ data points and to remove any variables that may exhibit high correlation with others.
+
+ The display shows the 10 most correlated variables of those selected. These variables
+ are displayed on the diagonal and their respective graphical display and correlation with
+ other variables can be found by locating the row/column intersection between each (above
+ and below the diagonal). The column heading over each variable displays the number of
+ other variables with which the environmental predictor is correlated. The user defined
+ "Threshold" option allows a user to specify the degree of correlation required between
+ two variables for them to be counted in this tally.
+
+ A user is provided with the opportunity to select a new set of the environmental predictor
+ variables and "Update" the Covariate Correlation screen to investigate the relationships
+ among the new variables selected. The options are provided to include or exclude the
+ presence/count points, the absence points (when applicable), and the background points in
+ this correlation test. Variables with a high degree of correlation with other variables
+ should generally be unchecked in their respective radio buttons, and will be excluded from
+ subsequent analysis steps in the model workflow.
+
+ Multiple iterations can be run at this screen, allowing the user to investigate the
+ relationships among the environmental predictor variables and choose the most appropriate
+ set to be used in the subsequent modeling. When the desired set of variables has been chosen,
+ the "OK" button is selected and processing will resume in the VisTrails workflow.
+
+ '''
+ kwargs = {}
+ kwargs['defaults'] = str(['initial'])
+ _input_ports = [("inputMDS", "(gov.usgs.sahm:MergedDataSet:Other)"),
+ ('selectionName', '(edu.utah.sci.vistrails.basic:String)', kwargs),
+ ('ShowGUI', '(edu.utah.sci.vistrails.basic:Boolean)')]
+ _output_ports = [("outputMDS", "(gov.usgs.sahm:MergedDataSet:Other)")]
+
+ def compute(self):
+ writetolog("\nOpening Select Predictors Layers widget", True)
+ inputMDS = utils.dir_path_value(self.forceGetInputFromPort('inputMDS'))
+ selectionName = self.forceGetInputFromPort('selectionName', 'initial')
+# outputMDS = utils.mknextfile(prefix='SelectPredictorsLayers_' + selectionName + "_", suffix='.csv')
+# displayJPEG = utils.mknextfile(prefix='PredictorCorrelation_' + selectionName + "_", suffix='.jpg')
+ global session_dir
+ outputMDS = os.path.join(session_dir, "CovariateCorrelationOutputMDS_" + selectionName + ".csv")
+ displayJPEG = os.path.join(session_dir, "CovariateCorrelationDisplay.jpg")
+ writetolog(" inputMDS = " + inputMDS, False, False)
+ writetolog(" displayJPEG = " + displayJPEG, False, False)
+ writetolog(" outputMDS = " + outputMDS, False, False)
+
+ if os.path.exists(outputMDS):
+ utils.applyMDS_selection(outputMDS, inputMDS)
+ os.remove(outputMDS)
+
+ self.callDisplayMDS(inputMDS, outputMDS, displayJPEG)
+
+ output_file = utils.create_file_module(outputMDS)
+ writetolog("Finished Select Predictors Layers widget", True)
+ self.setResult("outputMDS", output_file)
+
+ def callDisplayMDS(self, inputMDS, outputMDS, displayJPEG):
+ dialog = SelectListDialog(inputMDS, outputMDS, displayJPEG, configuration.r_path)
+ #dialog.setWindowFlags(QtCore.Qt.WindowMaximizeButtonHint)
+# print " ... finished with dialog "
+ retVal = dialog.exec_()
+ #outputPredictorList = dialog.outputList
+ if retVal == 1:
+ raise ModuleError(self, "Cancel or Close selected (not OK) workflow halted.")
+
+
+class ProjectionLayers(Module):
+ '''
+ Projection Layers
+
+ Note: as of June 2011, this module offers some functionality that is only available
+ to users running the SAHM package within the USGS Fort Collins Science Center (FORT).
+
+ The ProjectionLayers module provides the option to prepare a separate set of predictor
+ layers so that the results of a model developed from one set of environmental predictors
+ can be projected onto a new modeled space. This second set of environmental predictors
+ (corresponding to the "projection target") most often contains the same environmental
+ predictors but represents data captured at a different temporal or spatial location. For
+ example, a user could generate a model predicting habitat suitability using recorded
+ presence points and certain environmental predictors such as elevation, landcover, and
+ proximity to water in one geographic location. Based on the training from this information,
+ the modeled results could be generated for (or "projected to") a new location based on the
+ range of values seen in elevation, landcover, and proximity to water in the second geographic
+ area. Similarly, modeling predicted results through time is also possible. A model trained
+ using field data and a set of predictor layers representative of one time period could be
+ projected onto the same geographical area using a new set of predictor layers corresponding
+ to the same predictors but representing data from a different time period (e.g., different
+ climate data).
+
+ The output of this module is subsequently used as the projection target in the ApplyModel module.
+
+ (As part of the process of preparing the layers for modeling, the ProjectionLayers module runs
+ the PARC module internally on the inputs. Outputs from the ProjectionLayers module will possess
+ matching coordinate systems, cell sizes, and extents and do not need to be run through PARC
+ before being used downstream in the workflow.)
+
+ Six parameters can be set by the user:
+
+ 1. Directory Crosswalk CSV: This is a .csv file containing two columns designating
+ the layers that should be swapped out in the projected model. The first column
+ contains a list of the full paths to the predictor layers used to develop the original
+ model that will be replaced in the projection process. The second column contains the
+ full paths to the new predictor layers that will substitute the respective layers used
+ in the original model. Each original layer in the first column should be paired with
+ its replacement in the second column (e.g., Column 1 = C:\ModelLayers\Precipitation1980.tif,
+ Column 2 = C:\ModelLayers\Precipitation2000.tif). In the case of any file used to develop
+ the first model that is not expressly listed in the Directory Crosswalk CSV with a
+ replacement, the original file will be used in the new model projection. The module
+ anticipates a header row in this .csv file (thus, the first row of data will be ignored).
+
+ 2. File List CSV: This is a .csv file containing the list of predictor files used to
+ develop the first model. Effectively, this file will be updated based on the information
+ provided in the directory crosswalk .csv and used as the input to the training process
+ for the projected model. The output of the PARC module from the first model iteration
+ should be used as the input to this parameter.
+
+ 3. Model (available only to users at the FORT): This parameter allows VisTrail users
+ running the SAHM package on site at the USGS Science Center in Fort Collins (FORT) to
+ specify one of three models to use for the projected model run ("CCCMA," "CSIRO,"
+ or "hadcm3").
+
+ 4. Scenario (available only to users at the FORT): This parameter allows VisTrail
+ users running the SAHM package on site at the USGS Science Center in Fort Collins
+ FORT) to specify one of two scenarios for the projected model run ("A2a" or "B2b").
+
+ 5. Template: This parameter allows a user to specify the new template layer to be used
+ in the projected model run. The template layer is a raster data layer with a defined
+ coordinate system, a known cell size, and an extent that defines the (new) study area.
+ This raster layer serves as the template for all the other inputs in the analysis. All
+ additional raster layers used in the analysis will be resampled and reprojected as
+ needed to match the template, snapped to the template, and clipped to have an extent
+ that matches the template. Users should ensure that all the layers used for the projected
+ analysis have coverage within the extent of the template layer.
+
+ 6. Year (available only to users at the FORT): This parameter allows VisTrail users
+ running the SAHM package on site at the USGS Science Center in Fort Collins (FORT)
+ to specify one of three years to use for the projected model run ("2020," "2050," or "2080").
+
+ '''
+ _input_ports = [('RastersWithPARCInfoCSV', '(gov.usgs.sahm:RastersWithPARCInfoCSV:Other)'),
+ ('templateLayer', '(gov.usgs.sahm:TemplateLayer:DataInput)'),
+ ('model', '(edu.utah.sci.vistrails.basic:String)'),
+ ('scenario', '(edu.utah.sci.vistrails.basic:String)'),
+ ('year', '(edu.utah.sci.vistrails.basic:String)'),
+ ('directoryCrosswalkCSV', '(edu.utah.sci.vistrails.basic:File)')
+ ]
+ _output_ports = [("MDS", "(gov.usgs.sahm:MergedDataSet:Other)")]
+
+ def compute(self):
+ models = ['CCCMA', 'CSIRO', 'hadcm3']
+ scenarioss = ['A2a', 'B2b']
+ years = ['2020', '2050', '2080']
+
+ writetolog("\nRunning make Projection Layers", True)
+
+ inputCSV = self.forceGetInputFromPort('RastersWithPARCInfoCSV').name
+
+ if self.hasInputFromPort('templateLayer'):
+ template = self.forceGetInputFromPort('templateLayer').name
+ else:
+ template = '' #we'll get a template below
+
+ fromto = []
+ climargs = {}
+
+ for input in ['model', 'scenario', 'year']:
+ if self.hasInputFromPort(input):
+ climargs[input] = self.forceGetInputFromPort(input)
+ if climargs <> {} and climargs.keys() <> ['model', 'scenario', 'year']:
+ #they did not add in one of each, Not going to fly
+ raise ModuleError(self, "All of model, scenario, and year must be supplied if any are used.")
+ elif climargs <> {} and climargs.keys <> ['model', 'scenario', 'year']:
+ #they specified a alt climate scenario add this to our list to search for
+ fromto.append([r'K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio',
+ os.path.join('I:\WorldClim_Future_Climate\RenamedBILs',
+ climargs['model'], climargs['scenario'], climargs['year'])])
+
+ if self.hasInputFromPort('directoryCrosswalkCSV'):
+ crosswalkCSV = csv.reader(open(self.forceGetInputFromPort('directoryCrosswalkCSV'), 'r'))
+ header = crosswalkCSV
+ for row in crosswalkCSV:
+ fromto.append(row[0], row[1])
+ del crosswalkCSV
+
+ #write out the outputs to an empty MDS file (just the header is needed to PARC the outputs)
+
+
+ inCSV = csv.reader(open(inputCSV, 'r'))
+ inCSV.next() #skip header
+ workingCSV = utils.mknextfile(prefix='tmpFilesToPARC_', suffix='.csv')
+ tmpCSV = csv.writer(open(workingCSV, 'wb'))
+ tmpCSV.writerow(["FilePath", "Categorical", "Resampling", "Aggregation"])
+ outHeader1 = ['x', 'y', 'response']
+ outHeader2 = ['', '', '']
+ outHeader3 = ['', '', '']
+
+ output_dname = utils.mknextdir(prefix='ProjectionLayers_')
+
+ for row in inCSV:
+ if template == '':
+ template = row[0]
+ fileShortName = utils.getShortName(row[0])
+ if row[1] == 1:
+ outHeader1.append(fileShortName + '_categorical')
+ else:
+ outHeader1.append(fileShortName)
+ outHeader2.append('1')
+ outHeader3.append(os.path.join(output_dname, fileShortName + '.tif'))
+
+ origFile = row[4]
+ newOrigFile = origFile
+ for lookup in fromto:
+ if lookup[0] in origFile:
+ newOrigFile = origFile.replace(lookup[0], lookup[1])
+ tmpCSV.writerow([newOrigFile,] + row[1:4])
+ del tmpCSV
+
+ #PARC the files here
+ ourPARC = parc.PARC()
+
+
+ if configuration.verbose:
+ ourPARC.verbose = True
+ writetolog(" output_dname=" + output_dname, False, False)
+ ourPARC.outDir = output_dname
+ ourPARC.inputsCSV = workingCSV
+ ourPARC.template = template
+
+ try:
+ ourPARC.parcFiles()
+ except TrappedError as e:
+ raise ModuleError(self, e.message)
+ except :
+ utils.informative_untrapped_error(self, "PARC")
+
+ #loop through our workingCSV and format it into an MDS header
+
+ #outputMDS = utils.mknextfile(prefix='ProjectionLayersMDS_', suffix = '.csv')
+ outputMDS = os.path.join(output_dname, 'ProjectionLayersMDS.csv')
+ outCSV = csv.writer(open(outputMDS, 'wb'))
+ outCSV.writerow(outHeader1)
+ outCSV.writerow(outHeader2)
+ outCSV.writerow(outHeader3)
+
+ output_file = utils.create_file_module(outputMDS)
+ self.setResult("MDS", output_file)
+ writetolog("Finished Select Projection Layers widget", True)
+
+#class ClimateModel(String):
+# _input_ports = [('value', '(gov.usgs.sahm:ClimateModel:Other)')]
+# _output_ports = [('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
+# _widget_class = build_enum_widget('ClimateModel',
+# ['CCCMA', 'CSIRO', 'hadcm3'])
+#
+# @staticmethod
+# def get_widget_class():
+# return ClimateModel._widget_class
+#
+#class ClimateScenario(String):
+# _input_ports = [('value', '(gov.usgs.sahm:ClimateScenario:Other)')]
+# _output_ports = [('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
+# _widget_class = build_enum_widget('ClimateScenario',
+# ['A2a', 'B2b'])
+#
+# @staticmethod
+# def get_widget_class():
+# return ClimateScenario._widget_class
+#
+#class ClimateYear(String):
+# _input_ports = [('value', '(gov.usgs.sahm:ClimateYear:Other)')]
+# _output_ports = [('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
+# _widget_class = build_enum_widget('ClimateYear',
+# ['2020', '2050', '2080'])
+#
+# @staticmethod
+# def get_widget_class():
+# return ClimateYear._widget_class
+
+class MAXENT(Module):
+
+ _output_ports = [("lambdas", "(edu.utah.sci.vistrails.basic:File)"),
+ ("report", "(edu.utah.sci.vistrails.basic:File)"),
+ ("roc", "(edu.utah.sci.vistrails.basic:File)")]
+
+ def compute(self):
+ global maxent_path
+
+ ourMaxent = MaxentRunner.MAXENTRunner()
+ ourMaxent.outputDir = utils.mknextdir(prefix='maxentFiles_')
+
+ ourMaxent.inputMDS = self.forceGetInputFromPort('inputMDS').name
+
+ ourMaxent.maxentpath = maxent_path
+
+ MaxentArgsCSV = utils.mknextfile(prefix='MaxentArgs', suffix='.csv')
+ argWriter = csv.writer(open(MaxentArgsCSV, 'wb'))
+ argWriter.writerow(['parameter','value'])
+ for port in self._input_ports:
+ #print port
+ if port[0] <> 'inputMDS' and port[0] <> 'projectionlayers':
+ if self.hasInputFromPort(port[0]):
+ port_val = self.getInputFromPort(port[0])
+ if port[1] == "(edu.utah.sci.vistrails.basic:Boolean)":
+ port_val = str(port_val).lower()
+ elif (port[1] == "(edu.utah.sci.vistrails.basic:Path)" or \
+ port[1] == "(edu.utah.sci.vistrails.basic:File)"):
+ port_val = port_val.name
+ argWriter.writerow([port[0], port_val])
+ else:
+ #print " has no input "
+ kwargs = port[2]
+ #print kwargs
+ try:
+ if port[1] == "(edu.utah.sci.vistrails.basic:Boolean)":
+ default = kwargs['defaults'][2:-2].lower()
+ else:
+ default = kwargs['defaults'][2:-2]
+ #args[port[0]] = default
+ argWriter.writerow([port[0], default])
+ except KeyError:
+ pass
+ if self.hasInputFromPort('projectionlayers'):
+ value = self.forceGetInputListFromPort('projectionlayers')
+ projlayers = ','.join([path.name for path in value])
+ argWriter.writerow(['projectionlayers', projlayers])
+
+ del argWriter
+ ourMaxent.argsCSV = MaxentArgsCSV
+ ourMaxent.logger = utils.getLogger()
+ try:
+ ourMaxent.run()
+ except TrappedError as e:
+ raise ModuleError(self, e.message)
+ except:
+ utils.informative_untrapped_error(self, "Maxent")
+
+ #set outputs
+ lambdasfile = os.path.join(ourMaxent.outputDir, ourMaxent.args["species_name"] + ".lambdas")
+ output_file = utils.create_file_module(lambdasfile)
+ self.setResult("lambdas", output_file)
+
+
+ rocfile = os.path.join(ourMaxent.outputDir, 'plots', ourMaxent.args["species_name"] + "_roc.png")
+ output_file = utils.create_file_module(rocfile)
+ self.setResult("roc", output_file)
+
+ htmlfile = os.path.join(ourMaxent.outputDir, ourMaxent.args["species_name"] + ".html")
+ print htmlfile
+ output_file = utils.create_file_module(htmlfile)
+ self.setResult("report", output_file)
+
+ writetolog("Finished Maxent widget", True)
+
+def load_max_ent_params():
+ maxent_fname = os.path.join(os.path.dirname(__file__), 'maxent.csv')
+ csv_reader = csv.reader(open(maxent_fname, 'rU'))
+ # pass on header
+ csv_reader.next()
+ input_ports = []
+
+ input_ports.append(('inputMDS', '(gov.usgs.sahm:MergedDataSet:Other)'))
+
+ docs = {}
+ basic_pkg = 'edu.utah.sci.vistrails.basic'
+ p_type_map = {'file/directory': 'Path',
+ 'double': 'Float'}
+ for row in csv_reader:
+ [name, flag, p_type, default, doc, notes] = row
+ name = name.strip()
+ p_type = p_type.strip()
+ if p_type in p_type_map:
+ p_type = p_type_map[str(p_type)]
+ else:
+ p_type = str(p_type).capitalize()
+ kwargs = {}
+ default = default.strip()
+ if default:
+ if p_type == 'Boolean':
+ default = default.capitalize()
+ kwargs['defaults'] = str([default])
+ if p_type == 'Boolean':
+ kwargs['optional'] = True
+ input_ports.append((name, '(' + basic_pkg + ':' + p_type + ')', kwargs))
+ # FIXME set documentation
+ #print 'port:', (name, '(' + basic_pkg + ':' + p_type + ')', kwargs)
+ docs[name] = doc
+
+
+ #print 'MAXENT:', input_ports
+ MAXENT._input_ports = input_ports
+ MAXENT._port_docs = docs
+
+ def provide_input_port_documentation(cls, port_name):
+ return cls._port_docs[port_name]
+ MAXENT.provide_input_port_documentation = \
+ classmethod(provide_input_port_documentation)
+
+
+#class ModelOutputCell(SpreadsheetCell):
+# _input_ports = [("row", "(edu.utah.sci.vistrails.basic:Integer)"),
+# ("column", "(edu.utah.sci.vistrails.basic:Integer)"),
+# ('ProbabilityMap', '(edu.utah.sci.vistrails.basic:File)')]
+#
+# def __init__(self):
+# SpreadsheetCell.__init__(self)
+# self.cellWidget = None
+#
+# def compute(self):
+# renderView = self.forceGetInputFromPort('SetRenderView')
+# if renderView==None:
+# raise ModuleError(self, 'A vtkRenderView input is required.')
+# self.cellWidget = self.displayAndWait(QVTKViewWidget, (renderView,))
+
+#class SAHMViewWidget(QCellWidget):
+# def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+# QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
+#
+
+#class RasterLayer(Module):
+# _input_ports = [('file', '(edu.utah.sci.vistrails.basic:File)'),
+# ('name', '(edu.utah.sci.vistrails.basic:String)')]
+# _output_ports = [('self', '(gov.usgs.sahm:RasterLayer:DataInput)')]
+#
+# def __init__(self):
+# Module.__init__(self)
+# self.qgis_obj = None
+#
+# def compute(self):
+# fname = self.getInputFromPort('file').name
+# if self.hasInputFromPort('name'):
+# name = self.getInputFromPort('name')
+# else:
+# name = os.path.splitext(os.path.basename(fname))[0]
+# self.qgis_obj = qgis.core.QgsRasterLayer(fname, name)
+# self.setResult('self', self)
+#
+#class VectorLayer(Module):
+# _input_ports = [('file', '(edu.utah.sci.vistrails.basic:File)'),
+# ('name', '(edu.utah.sci.vistrails.basic:String)')]
+# _output_ports = [('self', '(gov.usgs.sahm:VectorLayer:DataInput)')]
+#
+# def __init__(self):
+# Module.__init__(self)
+# self.qgis_obj = None
+#
+# def compute(self):
+# fname = self.getInputFromPort('file').name
+# if self.hasInputFromPort('name'):
+# name = self.getInputFromPort('name')
+# else:
+# name = os.path.splitext(os.path.basename(fname))[0]
+# self.qgis_obj = qgis.core.QgsVectorLayer(fname, name, "ogr")
+# self.setResult('self', self)
+
+
+
+def initialize():
+ global maxent_path, color_breaks_csv
+ global session_dir
+ utils.config = configuration
+
+ r_path = os.path.abspath(configuration.r_path)
+ maxent_path = os.path.abspath(configuration.maxent_path)
+
+
+ #I was previously setting the following environmental variables and path additions
+ #so that each user wouldn't have to do this on their individual machines.
+ #I was running into problems with imports occuring before this initialize routine so
+ #I moved the setting of these to an external .net application that sets these before
+ #starting up VisTrails.py.
+
+ #This should also make this package easier to port to other systems as this stuff would
+ #only work on a windows instance.
+ #the current dependencies are:
+ #an installation of GDAL and Proj.4
+ # this includes the GDAL_DATA and PROJ_LIB directories as environmental variables
+ #GDAL bindings for python in the python path.
+ #QGIS built for the version of Python, QT, PyQt, and SIP used by VisTrails.
+ # This one was a painful bear on Windows.
+ #All of the DLLs required by the above QGIS build must be on the path.
+ #In my case these were in a folder in the OSGeoW installation that QGIS was built
+ #off of.
+ #And finally QGIS bindings for python in the python path.
+
+
+ import qgis.core
+ import qgis.gui
+ globals()["qgis"] = qgis
+ setQGIS(qgis)
+
+ qgis_prefix = os.path.join(configuration.qgis_path, "qgis1.7.0")
+ qgis.core.QgsApplication.setPrefixPath(qgis_prefix, True)
+ qgis.core.QgsApplication.initQgis()
+
+
+ session_dir = utils.createrootdir(configuration.output_dir)
+ utils.createLogger(session_dir, configuration.output_dir)
+ #log_file = Utilities.createsessionlog(session_dir, configuration.verbose)
+
+ color_breaks_csv = os.path.abspath(os.path.join(os.path.dirname(__file__), "ColorBreaks.csv"))
+
+ load_max_ent_params()
+
+ global layers_csv_fname
+
+ writetolog("*" * 79)
+ writetolog("Initializing:", True, True)
+ writetolog(" Locations of dependencies")
+# writetolog(" Layers CSV = " + os.path.join(os.path.dirname(__file__), 'layers.csv'))
+ writetolog(" Layers CSV = " + layers_csv_fname)
+ writetolog(" R path = " + r_path)
+ writetolog(" GDAL folder = " + os.path.abspath(configuration.gdal_path))
+ writetolog(" Must contain subfolders proj, gdal-data, GDAL")
+ writetolog(" Maxent folder = " + maxent_path)
+ writetolog(" QGIS folder = " + os.path.abspath(configuration.qgis_path))
+ writetolog(" Must contain subfolders qgis1.7.0, OSGeo4W")
+ writetolog(" ")
+ writetolog("*" * 79)
+
+ writetolog("*" * 79)
+ writetolog(" output directory: " + session_dir)
+ writetolog("*" * 79)
+ writetolog("*" * 79)
+
+def finalize():
+ pass
+ #utils.cleantemps()#No longer used
+
+def generate_namespaces(modules):
+ module_list = []
+ for namespace, m_list in modules.iteritems():
+ for module in m_list:
+ m_dict = {'namespace': namespace}
+ if type(module) == tuple:
+ m_dict.update(module[1])
+ module_list.append((module[0], m_dict))
+ #print 'm_dict:', m_dict
+ else:
+ module_list.append((module, m_dict))
+ return module_list
+
+def build_available_trees():
+ trees = {}
+ global layers_csv_fname
+ layers_csv_fname = os.path.join(os.path.dirname(__file__), 'layers.csv')
+ csv_reader = csv.reader(open(layers_csv_fname, 'rU'))
+ csv_reader.next()
+ first_file = csv_reader.next()[0]
+
+ #if the first file in the layers file does not exist assume that none
+ #of them do and use the exampledata version
+ if not os.path.exists(first_file):
+ print (("!" * 30) + " WARNING " + ("!" * 30) + "\n")*3
+ print "The first grid in your layers CSV could not be found."
+ print "Defaulting to the example data csv."
+ print "fix/set paths in file " + layers_csv_fname + " to enable this functionality."
+ print "See documentation for more information on setting up the layers.csv\n"
+ print (("!" * 30) + " WARNING " + ("!" * 30) + "\n")*3
+ layers_csv_fname = os.path.join(os.path.dirname(__file__), 'layers.exampledata.csv')
+
+ csv_reader = csv.reader(open(layers_csv_fname, 'rU'))
+ # pass on header
+ csv_reader.next()
+ for row in csv_reader:
+ if row[2] not in trees:
+ trees[row[2]] = {}
+ available_dict = trees[row[2]]
+# if 'Daymet' not in available_dict:
+# available_dict['Daymet'] = []
+# available_dict['Daymet'].append((row[0], row[1], row[3]))
+ if row[3] not in available_dict:
+ available_dict[row[3]] = []
+ available_dict[row[3]].append((row[0], row[1], row[4]))
+
+ return trees
+
+def build_predictor_modules():
+ available_trees = build_available_trees()
+ modules = []
+ for name, tree in available_trees.iteritems():
+ name_arr = name.strip().split()
+ class_base = ''.join(n.capitalize() for n in name_arr)
+ widget_class = get_predictor_widget(class_base, tree)
+ config_class = get_predictor_config(class_base, tree)
+ class_name = class_base + "Predictors"
+ def get_widget_method(w_class):
+ @staticmethod
+ def get_widget_class():
+ return w_class
+ return get_widget_class
+ module = type(class_name, (PredictorList,),
+ {'get_widget_class': get_widget_method(widget_class),
+ '_input_ports': \
+ [('value',
+ '(gov.usgs.sahm:%s:DataInput)' % class_name, True)]})
+
+ modules.append((module, {'configureWidgetType': config_class}))
+ for module in modules:
+ module[0]._output_ports.append(('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True))
+
+ return modules
+
+
+
+
+_modules = generate_namespaces({'DataInput': [
+ Predictor,
+ PredictorListFile,
+ FieldData,
+ TemplateLayer] + \
+ build_predictor_modules(),
+ 'Tools': [FieldDataAggregateAndWeight,
+ MDSBuilder,
+ PARC,
+ RasterFormatConverter,
+ ProjectionLayers,
+ TestTrainingSplit,
+ CovariateCorrelationAndSelection,
+ ApplyModel],
+ 'Models': [GLM,
+ RandomForest,
+ MARS,
+ MAXENT,
+ BoostedRegressionTree],
+ 'Other': [(Model, {'abstract': True}),
+ (ResampleMethod, {'abstract': True}),
+ (AggregationMethod, {'abstract': True}),
+ (PredictorList, {'abstract': True}),
+ (MergedDataSet, {'abstract': True}),
+ (RastersWithPARCInfoCSV, {'abstract': True})],
+ 'Output': [SAHMModelOutputViewerCell,
+ SAHMSpatialOutputViewerCell,
+ ]
+# ClimateModel,
+# ClimateScenario,
+# ClimateYear
+
+ })
\ No newline at end of file
diff --git a/contrib/sahm/layers.csv b/contrib/sahm/layers.csv
new file mode 100644
index 0000000..dcf138b
--- /dev/null
+++ b/contrib/sahm/layers.csv
@@ -0,0 +1,820 @@
+FileName,LayerName,Group,Source,Categorical
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_1.tif,Annual mean temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_2.tif,Mean diurnal range,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_3.tif,Isothermality,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_4.tif,Temperature seasonality,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_5.tif,Max. temperature of warmest month,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_6.tif,Min. temperature of coldest month,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_7.tif,Temperature annual range,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_8.tif,Mean temperature of wettest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_9.tif,Mean temperature of driest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_10.tif,Mean temperature of warmest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_11.tif,Mean temperature of coldest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_12.tif,Annual precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_13.tif,Precipitation of wettest month,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_14.tif,Precipitation of driest month,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_15.tif,Precipitation seasonality,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_16.tif,Precipitation of wettest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_17.tif,Precipitation of driest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_18.tif,Precipitiation of warmest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_19.tif,Precipitation of coldest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax1.tif,Average Jan. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax2.tif,Average Feb. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax3.tif,Average March Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax4.tif,Average April Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax5.tif,Average May Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax6.tif,Average June Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax7.tif,Average July Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax8.tif,Average Aug. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax9.tif,Average Sept. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax10.tif,Average Oct. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax11.tif,Average Nov. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax12.tif,Average Dec. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean1.tif,Average Jan. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean2.tif,Average Feb. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean3.tif,Average March Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean4.tif,Average April Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean5.tif,Average May Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean6.tif,Average June Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean7.tif,Average July Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean8.tif,Average Aug. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean9.tif,Average Sept. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean10.tif,Average Oct. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean11.tif,Average Nov. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean12.tif,Average Dec. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin1.tif,Average Jan. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin2.tif,Average Feb. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin3.tif,Average March Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin4.tif,Average April Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin5.tif,Average May Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin6.tif,Average June Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin7.tif,Average July Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin8.tif,Average Aug. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin9.tif,Average Sept. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin10.tif,Average Oct. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin11.tif,Average Nov. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin12.tif,Average Dec. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt1.tif,Average Jan. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt2.tif,Average Feb. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt3.tif,Average March Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt4.tif,Average April Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt5.tif,Average May Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt6.tif,Average June Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt7.tif,Average July Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt8.tif,Average Aug. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt9.tif,Average Sept. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt10.tif,Average Oct. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt11.tif,Average Nov. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt12.tif,Average Dec. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_1,Average Jan. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_2,Average Feb. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_3,Average March Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_4,Average April Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_5,Average May Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_6,Average June Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_7,Average July Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_8,Average Aug. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_9,Average Sept. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_10,Average Oct. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_11,Average Nov. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_12,Average Dec. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_1,Average Jan. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_2,Average Feb. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_3,Average March Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_4,Average April Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_5,Average May Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_6,Average June Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_7,Average July Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_8,Average Aug. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_9,Average Sept. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_10,Average Oct. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_11,Average Nov. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_12,Average Dec. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_1,Average Jan. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_2,Average Feb. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_3,Average March Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_4,Average April Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_5,Average May Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_6,Average June Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_7,Average July Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_8,Average Aug. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_9,Average Sept. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_10,Average Oct. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_11,Average Nov. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_12,Average Dec. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_1,Average Jan. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_2,Average Feb. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_3,Average March Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_4,Average April Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_5,Average May Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_6,Average June Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_7,Average July Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_8,Average Aug. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_9,Average Sept. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_10,Average Oct. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_11,Average Nov. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_12,Average Dec. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_1,Annual mean temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_2,Mean diurnal range,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_3,Isothermality,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_4,Temperature seasonality,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_5,Max. temperature of warmest month,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_6,Min. temperature of coldest month,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_7,Temperature annual range,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_8,Mean temperature of wettest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_9,Mean temperature of driest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_10,Mean temperature of warmest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_11,Mean temperature of coldest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_12,Annual precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_13,Precipitation of wettest month,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_14,Precipitation of driest month,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_15,Precipitation seasonality,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_16,Precipitation of wettest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_17,Precipitation of driest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_18,Precipitiation of warmest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_19,Precipitation of coldest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_01.img,Average Jan. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_02.img,Average Feb. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_03.img,Average March Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_04.img,Average April Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_05.img,Average May Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_06.img,Average June Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_07.img,Average July Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_08.img,Average Aug. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_09.img,Average Sept. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_10.img,Average Oct. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_11.img,Average Nov. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_12.img,Average Dec. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_01.img,Average Jan. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_02.img,Average Feb. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_03.img,Average March Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_04.img,Average April Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_05.img,Average May Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_06.img,Average June Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_07.img,Average July Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_08.img,Average Aug. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_09.img,Average Sept. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_10.img,Average Oct. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_11.img,Average Nov. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_12.img,Average Dec. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_01.img,Average Jan. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_02.img,Average Feb. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_03.img,Average March Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_04.img,Average April Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_05.img,Average May Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_06.img,Average June Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_07.img,Average July Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_08.img,Average Aug. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_09.img,Average Sept. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_10.img,Average Oct. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_11.img,Average Nov. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_12.img,Average Dec. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_01_1971_2000.img,Annual mean temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_02_1971_2000.img,Mean diurnal range,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_03_1971_2000.img,Isothermality,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_04_1971_2000.img,Temperature seasonality,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_05_1971_2000.img,Max. temperature of warmest month,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_06_1971_2000.img,Min. temperature of coldest month,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_07_1971_2000.img,Temperature annual range,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_08_1971_2000.img,Mean temperature of wettest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_09_1971_2000.img,Mean temperature of driest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_10_1971_2000.img,Mean temperature of warmest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_11_1971_2000.img,Mean temperature of coldest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_12_1971_2000.img,Annual precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_13_1971_2000.img,Precipitation of wettest month,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_14_1971_2000.img,Precipitation of driest month,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_15_1971_2000.img,Precipitation seasonality,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_16_1971_2000.img,Precipitation of wettest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_17_1971_2000.img,Precipitation of driest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_18_1971_2000.img,Precipitiation of warmest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_19_1971_2000.img,Precipitation of coldest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.NA.2001.bare.tif,VCF Bare Landcover,Remote Sensing,MODIS / GLCF North America (2001) .5 km,N
+K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.NA.2001.herbaceous.tif,VCF Herbaceous Landcover,Remote Sensing,MODIS / GLCF North America (2001) .5 km,N
+K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.NA.2001.tree.tif,VCF Tree Landcover,Remote Sensing,MODIS / GLCF North America (2001) .5 km,N
+K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.SA.2001.bare.tif,VCF Bare Landcover,Remote Sensing,MODIS / GLCF South America (2001) .5 km,N
+K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.SA.2001.herbaceous.tif,VCF Herbaceous Landcover,Remote Sensing,MODIS / GLCF South America (2001) .5 km,N
+K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.SA.2001.tree.tif,VCF Tree Landcover,Remote Sensing,MODIS / GLCF South America (2001) .5 km,N
+K:\GIS_LIBRARY\Elevation\EDNA\dem\dem,DEM,Elevation / Topography,"EDNA Continental US, 30 m.",N
+K:\GIS_LIBRARY\Elevation\EDNA\aspect\aspect,DEM Derivative: Aspect,Elevation / Topography,"EDNA Continental US, 30 m.",N
+K:\GIS_LIBRARY\Elevation\EDNA\slopedeg\slopedeg,DEM Derivative: Slope in Degrees,Elevation / Topography,"EDNA Continental US, 30 m.",N
+K:\GIS_LIBRARY\Elevation\EDNA\facc\facc,DEM Derivative: Flow Accumulation,Hydrology,"EDNA Continental US, 30 m.",N
+K:\GIS_LIBRARY\Elevation\EDNA\fdir\fdir,DEM Derivative: Flow Direction,Hydrology,"EDNA Continental US, 30 m.",N
+K:\GIS_LIBRARY\Elevation\EDNA\cti\cti,DEM Derivative: CTI/Steady State Wetness,Hydrology,"EDNA Continental US, 30 m.",N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2000.tif,amplitudes1_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2001.tif,amplitudes1_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2002.tif,amplitudes1_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2003.tif,amplitudes1_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2004.tif,amplitudes1_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2005.tif,amplitudes1_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2006.tif,amplitudes1_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2007.tif,amplitudes1_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2008.tif,amplitudes1_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2009.tif,amplitudes1_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_Average.tif,amplitudes1_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2000.tif,amplitudes2_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2001.tif,amplitudes2_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2002.tif,amplitudes2_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2003.tif,amplitudes2_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2004.tif,amplitudes2_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2005.tif,amplitudes2_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2006.tif,amplitudes2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2007.tif,amplitudes2_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2008.tif,amplitudes2_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2009.tif,amplitudes2_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_Average.tif,amplitudes2_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2000.tif,annualMaximumValue_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2001.tif,annualMaximumValue_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2002.tif,annualMaximumValue_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2003.tif,annualMaximumValue_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2004.tif,annualMaximumValue_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2005.tif,annualMaximumValue_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2006.tif,annualMaximumValue_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2007.tif,annualMaximumValue_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2008.tif,annualMaximumValue_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2009.tif,annualMaximumValue_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_Average.tif,annualMaximumValue_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2000.tif,annualMeanValue_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2001.tif,annualMeanValue_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2002.tif,annualMeanValue_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2003.tif,annualMeanValue_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2004.tif,annualMeanValue_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2005.tif,annualMeanValue_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2006.tif,annualMeanValue_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2007.tif,annualMeanValue_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2008.tif,annualMeanValue_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2009.tif,annualMeanValue_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_Average.tif,annualMeanValue_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2000.tif,annualMinimumValue_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2001.tif,annualMinimumValue_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2002.tif,annualMinimumValue_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2003.tif,annualMinimumValue_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2004.tif,annualMinimumValue_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2005.tif,annualMinimumValue_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2006.tif,annualMinimumValue_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2007.tif,annualMinimumValue_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2008.tif,annualMinimumValue_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2009.tif,annualMinimumValue_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_Average.tif,annualMinimumValue_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2000.tif,baselevels1_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2001.tif,baselevels1_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2002.tif,baselevels1_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2003.tif,baselevels1_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2004.tif,baselevels1_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2005.tif,baselevels1_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2006.tif,baselevels1_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2007.tif,baselevels1_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2008.tif,baselevels1_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2009.tif,baselevels1_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_Average.tif,baselevels1_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2000.tif,baselevels2_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2001.tif,baselevels2_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2002.tif,baselevels2_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2003.tif,baselevels2_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2004.tif,baselevels2_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2005.tif,baselevels2_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2006.tif,baselevels2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2007.tif,baselevels2_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2008.tif,baselevels2_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2009.tif,baselevels2_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_Average.tif,baselevels2_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2000.tif,browndownrates1_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2001.tif,browndownrates1_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2002.tif,browndownrates1_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2003.tif,browndownrates1_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2004.tif,browndownrates1_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2005.tif,browndownrates1_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2006.tif,browndownrates1_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2007.tif,browndownrates1_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2008.tif,browndownrates1_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2009.tif,browndownrates1_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_Average.tif,browndownrates1_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2000.tif,browndownrates2_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2001.tif,browndownrates2_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2002.tif,browndownrates2_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2003.tif,browndownrates2_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2004.tif,browndownrates2_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2005.tif,browndownrates2_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2006.tif,browndownrates2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2007.tif,browndownrates2_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2008.tif,browndownrates2_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2009.tif,browndownrates2_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_Average.tif,browndownrates2_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2000.tif,browndowns1_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2001.tif,browndowns1_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2002.tif,browndowns1_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2003.tif,browndowns1_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2004.tif,browndowns1_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2005.tif,browndowns1_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2006.tif,browndowns1_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2007.tif,browndowns1_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2008.tif,browndowns1_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2009.tif,browndowns1_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_Average.tif,browndowns1_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2000.tif,browndowns2_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2001.tif,browndowns2_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2002.tif,browndowns2_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2003.tif,browndowns2_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2004.tif,browndowns2_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2005.tif,browndowns2_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2006.tif,browndowns2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2007.tif,browndowns2_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2008.tif,browndowns2_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2009.tif,browndowns2_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_Average.tif,browndowns2_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2000.tif,greenuprates1_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2001.tif,greenuprates1_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2002.tif,greenuprates1_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2003.tif,greenuprates1_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2004.tif,greenuprates1_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2005.tif,greenuprates1_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2006.tif,greenuprates1_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2007.tif,greenuprates1_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2008.tif,greenuprates1_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2009.tif,greenuprates1_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_Average.tif,greenuprates1_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2000.tif,greenuprates2_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2001.tif,greenuprates2_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2002.tif,greenuprates2_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2003.tif,greenuprates2_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2004.tif,greenuprates2_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2005.tif,greenuprates2_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2006.tif,greenuprates2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2007.tif,greenuprates2_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2008.tif,greenuprates2_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2009.tif,greenuprates2_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_Average.tif,greenuprates2_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2000.tif,greenups1_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2001.tif,greenups1_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2002.tif,greenups1_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2003.tif,greenups1_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2004.tif,greenups1_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2005.tif,greenups1_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2006.tif,greenups1_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2007.tif,greenups1_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2008.tif,greenups1_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2009.tif,greenups1_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_Average.tif,greenups1_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2000.tif,greenups2_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2001.tif,greenups2_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2002.tif,greenups2_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2003.tif,greenups2_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2004.tif,greenups2_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2005.tif,greenups2_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2006.tif,greenups2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2007.tif,greenups2_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2008.tif,greenups2_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2009.tif,greenups2_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_Average.tif,greenups2_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2000.tif,landcover_2000,MODIS Phenology,NDVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2001.tif,landcover_2001,MODIS Phenology,NDVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2002.tif,landcover_2002,MODIS Phenology,NDVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2003.tif,landcover_2003,MODIS Phenology,NDVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2004.tif,landcover_2004,MODIS Phenology,NDVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2005.tif,landcover_2005,MODIS Phenology,NDVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2006.tif,landcover_2006,MODIS Phenology,NDVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2007.tif,landcover_2007,MODIS Phenology,NDVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2008.tif,landcover_2008,MODIS Phenology,NDVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2009.tif,landcover_2009,MODIS Phenology,NDVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_Average.tif,landcover_Average,MODIS Phenology,NDVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2000.tif,largeintegrals1_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2001.tif,largeintegrals1_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2002.tif,largeintegrals1_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2003.tif,largeintegrals1_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2004.tif,largeintegrals1_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2005.tif,largeintegrals1_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2006.tif,largeintegrals1_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2007.tif,largeintegrals1_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2008.tif,largeintegrals1_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2009.tif,largeintegrals1_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_Average.tif,largeintegrals1_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2000.tif,largeintegrals2_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2001.tif,largeintegrals2_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2002.tif,largeintegrals2_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2003.tif,largeintegrals2_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2004.tif,largeintegrals2_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2005.tif,largeintegrals2_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2006.tif,largeintegrals2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2007.tif,largeintegrals2_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2008.tif,largeintegrals2_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2009.tif,largeintegrals2_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_Average.tif,largeintegrals2_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2000.tif,maxpeakvalues1_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2001.tif,maxpeakvalues1_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2002.tif,maxpeakvalues1_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2003.tif,maxpeakvalues1_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2004.tif,maxpeakvalues1_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2005.tif,maxpeakvalues1_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2006.tif,maxpeakvalues1_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2007.tif,maxpeakvalues1_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2008.tif,maxpeakvalues1_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2009.tif,maxpeakvalues1_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_Average.tif,maxpeakvalues1_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2000.tif,maxpeakvalues2_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2001.tif,maxpeakvalues2_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2002.tif,maxpeakvalues2_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2003.tif,maxpeakvalues2_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2004.tif,maxpeakvalues2_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2005.tif,maxpeakvalues2_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2006.tif,maxpeakvalues2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2007.tif,maxpeakvalues2_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2008.tif,maxpeakvalues2_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2009.tif,maxpeakvalues2_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_Average.tif,maxpeakvalues2_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2000.tif,peakdates1_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2001.tif,peakdates1_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2002.tif,peakdates1_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2003.tif,peakdates1_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2004.tif,peakdates1_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2005.tif,peakdates1_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2006.tif,peakdates1_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2007.tif,peakdates1_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2008.tif,peakdates1_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2009.tif,peakdates1_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_Average.tif,peakdates1_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2000.tif,peakdates2_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2001.tif,peakdates2_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2002.tif,peakdates2_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2003.tif,peakdates2_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2004.tif,peakdates2_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2005.tif,peakdates2_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2006.tif,peakdates2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2007.tif,peakdates2_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2008.tif,peakdates2_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2009.tif,peakdates2_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_Average.tif,peakdates2_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2000.tif,qualityFlag_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2001.tif,qualityFlag_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2002.tif,qualityFlag_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2003.tif,qualityFlag_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2004.tif,qualityFlag_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2005.tif,qualityFlag_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2006.tif,qualityFlag_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2007.tif,qualityFlag_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2008.tif,qualityFlag_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2009.tif,qualityFlag_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_Average.tif,qualityFlag_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2000.tif,RMSE_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2001.tif,RMSE_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2002.tif,RMSE_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2003.tif,RMSE_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2004.tif,RMSE_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2005.tif,RMSE_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2006.tif,RMSE_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2007.tif,RMSE_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2008.tif,RMSE_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2009.tif,RMSE_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_Average.tif,RMSE_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2000.tif,seasonlengths1_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2001.tif,seasonlengths1_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2002.tif,seasonlengths1_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2003.tif,seasonlengths1_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2004.tif,seasonlengths1_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2005.tif,seasonlengths1_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2006.tif,seasonlengths1_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2007.tif,seasonlengths1_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2008.tif,seasonlengths1_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2009.tif,seasonlengths1_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_Average.tif,seasonlengths1_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2000.tif,seasonlengths2_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2001.tif,seasonlengths2_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2002.tif,seasonlengths2_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2003.tif,seasonlengths2_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2004.tif,seasonlengths2_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2005.tif,seasonlengths2_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2006.tif,seasonlengths2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2006.tif,seasonlengths2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2007.tif,seasonlengths2_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2008.tif,seasonlengths2_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2009.tif,seasonlengths2_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_Average.tif,seasonlengths2_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2000.tif,smallintegrals1_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2001.tif,smallintegrals1_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2002.tif,smallintegrals1_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2003.tif,smallintegrals1_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2004.tif,smallintegrals1_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2005.tif,smallintegrals1_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2006.tif,smallintegrals1_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2007.tif,smallintegrals1_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2008.tif,smallintegrals1_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2009.tif,smallintegrals1_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_Average.tif,smallintegrals1_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2000.tif,smallintegrals2_2000,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2001.tif,smallintegrals2_2001,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2002.tif,smallintegrals2_2002,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2003.tif,smallintegrals2_2003,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2004.tif,smallintegrals2_2004,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2005.tif,smallintegrals2_2005,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2006.tif,smallintegrals2_2006,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2007.tif,smallintegrals2_2007,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2008.tif,smallintegrals2_2008,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2009.tif,smallintegrals2_2009,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_Average.tif,smallintegrals2_Average,MODIS Phenology,NDVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2000.tif,amplitudes1_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2001.tif,amplitudes1_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2002.tif,amplitudes1_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2003.tif,amplitudes1_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2004.tif,amplitudes1_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2005.tif,amplitudes1_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2006.tif,amplitudes1_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2007.tif,amplitudes1_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2008.tif,amplitudes1_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2009.tif,amplitudes1_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_Average.tif,amplitudes1_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2000.tif,amplitudes2_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2001.tif,amplitudes2_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2002.tif,amplitudes2_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2003.tif,amplitudes2_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2004.tif,amplitudes2_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2005.tif,amplitudes2_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2006.tif,amplitudes2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2007.tif,amplitudes2_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2008.tif,amplitudes2_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2009.tif,amplitudes2_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_Average.tif,amplitudes2_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2000.tif,annualMaximumValue_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2001.tif,annualMaximumValue_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2002.tif,annualMaximumValue_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2003.tif,annualMaximumValue_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2004.tif,annualMaximumValue_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2005.tif,annualMaximumValue_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2006.tif,annualMaximumValue_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2007.tif,annualMaximumValue_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2008.tif,annualMaximumValue_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2009.tif,annualMaximumValue_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_Average.tif,annualMaximumValue_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2000.tif,annualMeanValue_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2001.tif,annualMeanValue_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2002.tif,annualMeanValue_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2003.tif,annualMeanValue_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2004.tif,annualMeanValue_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2005.tif,annualMeanValue_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2006.tif,annualMeanValue_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2007.tif,annualMeanValue_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2008.tif,annualMeanValue_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2009.tif,annualMeanValue_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_Average.tif,annualMeanValue_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2000.tif,annualMinimumValue_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2001.tif,annualMinimumValue_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2002.tif,annualMinimumValue_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2003.tif,annualMinimumValue_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2004.tif,annualMinimumValue_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2005.tif,annualMinimumValue_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2006.tif,annualMinimumValue_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2007.tif,annualMinimumValue_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2008.tif,annualMinimumValue_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2009.tif,annualMinimumValue_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_Average.tif,annualMinimumValue_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2000.tif,baselevels1_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2001.tif,baselevels1_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2002.tif,baselevels1_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2003.tif,baselevels1_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2004.tif,baselevels1_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2005.tif,baselevels1_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2006.tif,baselevels1_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2007.tif,baselevels1_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2008.tif,baselevels1_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2009.tif,baselevels1_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_Average.tif,baselevels1_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2000.tif,baselevels2_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2001.tif,baselevels2_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2002.tif,baselevels2_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2003.tif,baselevels2_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2004.tif,baselevels2_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2005.tif,baselevels2_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2006.tif,baselevels2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2007.tif,baselevels2_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2008.tif,baselevels2_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2009.tif,baselevels2_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_Average.tif,baselevels2_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2000.tif,browndownrates1_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2001.tif,browndownrates1_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2002.tif,browndownrates1_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2003.tif,browndownrates1_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2004.tif,browndownrates1_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2005.tif,browndownrates1_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2006.tif,browndownrates1_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2007.tif,browndownrates1_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2008.tif,browndownrates1_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2009.tif,browndownrates1_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_Average.tif,browndownrates1_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2000.tif,browndownrates2_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2001.tif,browndownrates2_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2002.tif,browndownrates2_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2003.tif,browndownrates2_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2004.tif,browndownrates2_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2005.tif,browndownrates2_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2006.tif,browndownrates2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2007.tif,browndownrates2_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2008.tif,browndownrates2_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2009.tif,browndownrates2_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_Average.tif,browndownrates2_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2000.tif,browndowns1_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2001.tif,browndowns1_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2002.tif,browndowns1_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2003.tif,browndowns1_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2004.tif,browndowns1_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2005.tif,browndowns1_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2006.tif,browndowns1_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2007.tif,browndowns1_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2008.tif,browndowns1_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2009.tif,browndowns1_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_Average.tif,browndowns1_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2000.tif,browndowns2_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2001.tif,browndowns2_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2002.tif,browndowns2_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2003.tif,browndowns2_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2004.tif,browndowns2_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2005.tif,browndowns2_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2006.tif,browndowns2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2007.tif,browndowns2_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2008.tif,browndowns2_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2009.tif,browndowns2_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_Average.tif,browndowns2_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2000.tif,greenuprates1_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2001.tif,greenuprates1_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2002.tif,greenuprates1_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2003.tif,greenuprates1_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2004.tif,greenuprates1_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2005.tif,greenuprates1_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2006.tif,greenuprates1_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2007.tif,greenuprates1_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2008.tif,greenuprates1_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2009.tif,greenuprates1_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_Average.tif,greenuprates1_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2000.tif,greenuprates2_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2001.tif,greenuprates2_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2002.tif,greenuprates2_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2003.tif,greenuprates2_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2004.tif,greenuprates2_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2005.tif,greenuprates2_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2006.tif,greenuprates2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2007.tif,greenuprates2_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2008.tif,greenuprates2_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2009.tif,greenuprates2_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_Average.tif,greenuprates2_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2000.tif,greenups1_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2001.tif,greenups1_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2002.tif,greenups1_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2003.tif,greenups1_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2004.tif,greenups1_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2005.tif,greenups1_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2006.tif,greenups1_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2007.tif,greenups1_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2008.tif,greenups1_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2009.tif,greenups1_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_Average.tif,greenups1_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2000.tif,greenups2_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2001.tif,greenups2_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2002.tif,greenups2_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2003.tif,greenups2_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2004.tif,greenups2_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2005.tif,greenups2_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2006.tif,greenups2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2007.tif,greenups2_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2008.tif,greenups2_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2009.tif,greenups2_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_Average.tif,greenups2_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2000.tif,landcover_2000,MODIS Phenology,EVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2001.tif,landcover_2001,MODIS Phenology,EVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2002.tif,landcover_2002,MODIS Phenology,EVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2003.tif,landcover_2003,MODIS Phenology,EVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2004.tif,landcover_2004,MODIS Phenology,EVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2005.tif,landcover_2005,MODIS Phenology,EVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2006.tif,landcover_2006,MODIS Phenology,EVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2007.tif,landcover_2007,MODIS Phenology,EVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2008.tif,landcover_2008,MODIS Phenology,EVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2009.tif,landcover_2009,MODIS Phenology,EVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_Average.tif,landcover_Average,MODIS Phenology,EVI (230 m),Y
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2000.tif,largeintegrals1_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2001.tif,largeintegrals1_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2002.tif,largeintegrals1_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2003.tif,largeintegrals1_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2004.tif,largeintegrals1_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2005.tif,largeintegrals1_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2006.tif,largeintegrals1_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2007.tif,largeintegrals1_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2008.tif,largeintegrals1_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2009.tif,largeintegrals1_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_Average.tif,largeintegrals1_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2000.tif,largeintegrals2_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2001.tif,largeintegrals2_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2002.tif,largeintegrals2_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2003.tif,largeintegrals2_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2004.tif,largeintegrals2_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2005.tif,largeintegrals2_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2006.tif,largeintegrals2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2007.tif,largeintegrals2_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2008.tif,largeintegrals2_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2009.tif,largeintegrals2_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_Average.tif,largeintegrals2_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2000.tif,maxpeakvalues1_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2001.tif,maxpeakvalues1_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2002.tif,maxpeakvalues1_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2003.tif,maxpeakvalues1_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2004.tif,maxpeakvalues1_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2005.tif,maxpeakvalues1_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2006.tif,maxpeakvalues1_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2007.tif,maxpeakvalues1_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2008.tif,maxpeakvalues1_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2009.tif,maxpeakvalues1_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_Average.tif,maxpeakvalues1_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2000.tif,maxpeakvalues2_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2001.tif,maxpeakvalues2_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2002.tif,maxpeakvalues2_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2003.tif,maxpeakvalues2_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2004.tif,maxpeakvalues2_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2005.tif,maxpeakvalues2_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2006.tif,maxpeakvalues2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2007.tif,maxpeakvalues2_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2008.tif,maxpeakvalues2_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2009.tif,maxpeakvalues2_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_Average.tif,maxpeakvalues2_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2000.tif,peakdates1_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2001.tif,peakdates1_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2002.tif,peakdates1_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2003.tif,peakdates1_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2004.tif,peakdates1_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2005.tif,peakdates1_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2006.tif,peakdates1_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2007.tif,peakdates1_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2008.tif,peakdates1_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2009.tif,peakdates1_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_Average.tif,peakdates1_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2000.tif,peakdates2_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2001.tif,peakdates2_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2002.tif,peakdates2_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2003.tif,peakdates2_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2004.tif,peakdates2_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2005.tif,peakdates2_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2006.tif,peakdates2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2007.tif,peakdates2_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2008.tif,peakdates2_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2009.tif,peakdates2_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_Average.tif,peakdates2_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2000.tif,qualityFlag_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2001.tif,qualityFlag_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2002.tif,qualityFlag_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2003.tif,qualityFlag_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2004.tif,qualityFlag_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2005.tif,qualityFlag_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2006.tif,qualityFlag_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2007.tif,qualityFlag_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2008.tif,qualityFlag_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2009.tif,qualityFlag_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_Average.tif,qualityFlag_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2000.tif,RMSE_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2001.tif,RMSE_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2002.tif,RMSE_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2003.tif,RMSE_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2004.tif,RMSE_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2005.tif,RMSE_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2006.tif,RMSE_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2007.tif,RMSE_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2008.tif,RMSE_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2009.tif,RMSE_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_Average.tif,RMSE_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2000.tif,seasonlengths1_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2001.tif,seasonlengths1_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2002.tif,seasonlengths1_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2003.tif,seasonlengths1_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2004.tif,seasonlengths1_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2005.tif,seasonlengths1_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2006.tif,seasonlengths1_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2007.tif,seasonlengths1_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2008.tif,seasonlengths1_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2009.tif,seasonlengths1_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_Average.tif,seasonlengths1_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2000.tif,seasonlengths2_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2001.tif,seasonlengths2_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2002.tif,seasonlengths2_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2003.tif,seasonlengths2_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2004.tif,seasonlengths2_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2005.tif,seasonlengths2_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2006.tif,seasonlengths2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2006.tif,seasonlengths2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2007.tif,seasonlengths2_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2008.tif,seasonlengths2_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2009.tif,seasonlengths2_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_Average.tif,seasonlengths2_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2000.tif,smallintegrals1_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2001.tif,smallintegrals1_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2002.tif,smallintegrals1_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2003.tif,smallintegrals1_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2004.tif,smallintegrals1_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2005.tif,smallintegrals1_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2006.tif,smallintegrals1_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2007.tif,smallintegrals1_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2008.tif,smallintegrals1_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2009.tif,smallintegrals1_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_Average.tif,smallintegrals1_Average,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2000.tif,smallintegrals2_2000,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2001.tif,smallintegrals2_2001,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2002.tif,smallintegrals2_2002,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2003.tif,smallintegrals2_2003,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2004.tif,smallintegrals2_2004,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2005.tif,smallintegrals2_2005,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2006.tif,smallintegrals2_2006,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2007.tif,smallintegrals2_2007,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2008.tif,smallintegrals2_2008,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2009.tif,smallintegrals2_2009,MODIS Phenology,EVI (230 m),N
+\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_Average.tif,smallintegrals2_Average,MODIS Phenology,EVI (230 m),N
diff --git a/contrib/sahm/layers.exampledata.csv b/contrib/sahm/layers.exampledata.csv
new file mode 100644
index 0000000..f93f24c
--- /dev/null
+++ b/contrib/sahm/layers.exampledata.csv
@@ -0,0 +1,6 @@
+FileName,LayerName,Group,Source,Categorical
+..\examples\SAHM_example\PredictorLayers\Climate\DAYMET_WGS84\bio_1_wgs84.tif,Annual mean temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
+..\examples\SAHM_example\PredictorLayers\Climate\DAYMET_WGS84\bio_2_wgs84.tif,Mean diurnal range,Climate,"Daymet (1980-1997) Normals, 1km.",N
+..\examples\SAHM_example\PredictorLayers\Climate\PRISM\ppt_1971_2000_011.img,Average Jan. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
+..\examples\SAHM_example\PredictorLayers\NLCD\nlcd01_11.tif,NLCD Landcover,Remote Sensing,NLCD,Y
+..\examples\SAHM_example\PredictorLayers\Elevation\dem.tif,30m EDNA Elevation resampled to 90m,Elevation / Topography,"EDNA, NED",N
diff --git a/contrib/sahm/maxent.csv b/contrib/sahm/maxent.csv
new file mode 100644
index 0000000..f9c2c8d
--- /dev/null
+++ b/contrib/sahm/maxent.csv
@@ -0,0 +1,33 @@
+Flag ,Abbrv ,Type ,Default ,Meaning ,VisTrailsNotes
+projectionlayers ,j ,file/directory ,,"Location of an alternate set of environmental variables. Maxent models will be projected onto these variables.
Can be a .csv file (in SWD format) or a directory containing one file per variable.
Multiple projection files/directories can be separated by commas. ",
+randomtestpoints ,X ,integer ,0,"Percentage of presence localities to be randomly set aside as test points, used to compute AUC, omission etc. ","If the MDS input is from the test training split the will not be used, but instead this file will be generated from the input MDS Split column where it equals 'test'"
+betamultiplier ,b ,double ,1,Multiply all automatic regularization parameters by this number. A higher number gives a more spread-out distribution. ,
+maximumbackground ,MB ,integer ,10000,"If the number of background points / grid cells is larger than this number, then this number of cells is chosen randomly for background points ",
+testsamplesfile ,T ,file ,,"Use the presence localities in this file to compute statistics (AUC, omission etc.)
The file can contain different localities for different species.
It takes precedence over the random test percentage. ",
+replicates ,,integer ,1,"Number of replicate runs to do when cross-validating, bootstrapping or doing sampling with replacement runs ",If we supply the testsamples file or generate one from our testtraining split data can this also supplied? I think not.
+replicatetype ,,string ,subsample,"If replicates > 1, do multiple runs of this type:
Crossvalidate: samples divided into replicates folds; each fold in turn used for test data.
Bootstrap: replicate sample sets chosen by sampling with replacement.
Subsample: replicate sample sets chosen by removing random test percentage without replacement to be used for evaluation.
(Options)",same as above
+writebackgroundpredictions ,,boolean ,false ,Write .csv file with predictions at background points ,
+linear ,l ,boolean ,true ,Allow linear features to be used ,
+quadratic ,q ,boolean ,true ,Allow quadratic features to be used ,
+product ,p ,boolean ,true ,Allow product features to be used ,
+threshold ,,boolean ,true ,Allow threshold features to be used ,
+hinge ,h ,boolean ,true ,Allow hinge features to be used ,
+writeplotdata ,,boolean ,false ,"Write output files containing the data used to make response curves, for import into external plotting software ",
+fadebyclamping ,,boolean ,false ,"Reduce prediction at each point in projections by the difference between
clamped and non-clamped output at that point ",
+extrapolate ,,boolean ,true ,Predict to regions of environmental space outside the limits encountered during training ,
+autofeature ,A ,boolean ,true ,"Automatically select which feature classes to use, based on number of training samples ",
+doclamp ,,boolean ,true ,Apply clamping when projecting ,
+maximumiterations ,m ,integer ,500,Stop training after this many iterations of the optimization algorithm ,
+convergencethreshold ,c ,double ,1.00E-05,Stop training when the drop in log loss per iteration drops below this number ,
+beta_threshold ,,double ,-1,Regularization parameter to be applied to all threshold features; negative value enables automatic setting ,
+beta_categorical ,,double ,-1,Regularization parameter to be applied to all categorical features; negative value enables automatic setting ,
+beta_lqp ,,double ,-1,"Regularization parameter to be applied to all linear, quadratic and product features; negative value enables automatic setting ",
+beta_hinge ,,double ,-1,Regularization parameter to be applied to all hinge features; negative value enables automatic setting ,
+applythresholdrule ,,string ,,"Apply a threshold rule, generating a binary output grid in addition to the regular prediction grid. Options:
������ Fixed cumulative value 1
������ Fixed cumulative value 5
������ Fixed cumulative value 10
������ Minimum training presence
������ 10 percentile training presence
������ Equal training sensitivity and specificity
������ Maximum training sensitivity plus specificity
",
+prefixes,,boolean ,false ,,
+species_name,,string ,species,Used only by VisTrails to set the species name,
+responsecurves,p ,boolean ,true ,Create graphs showing how predicted relative probability of occurrence depends on the value of each environmental variable,
+jackknife,,boolean ,true ,Do jackknife to measure variable importance,
+writeclampgrid,,boolean ,false ,Do not create clamping grids when projecting,
+writemess,,boolean ,false ,Do not do MESS analysis when projecting,
+outputgrids,,boolean ,false ,Only create the summary grids when doing multiple iterations,
diff --git a/contrib/sahm/pySAHM/FieldDataQuery.py b/contrib/sahm/pySAHM/FieldDataQuery.py
new file mode 100644
index 0000000..6565ca7
--- /dev/null
+++ b/contrib/sahm/pySAHM/FieldDataQuery.py
@@ -0,0 +1,385 @@
+'''
+Created on Dec 29, 2010
+
+This module was created to
+
+ at author: talbertc
+'''
+
+import sys, os
+import math
+import csv
+
+from osgeo import gdalconst
+from osgeo import gdal
+from osgeo import osr
+from math import floor
+
+from optparse import OptionParser
+
+import utilities
+
+def main(argv):
+ usageStmt = "usage: options: -t --template -f --fieldData -a --aggPixel -y --aggYears -o --output"
+ desc = "Aggregates sample points by pixel and/or year."
+
+ parser = OptionParser(usage=usageStmt, description=desc)
+ parser.add_option("-t", "--template",
+ dest="template",
+ help="The template grid in Tif, ESRI grid, or ASC format")
+ parser.add_option("-f", "--fieldData",
+ dest="csv",
+ help="The CSV of field data")
+ parser.add_option("-o", "--output",
+ dest="output",
+ help="The output CSV file with appended frequency and numPresence")
+ parser.add_option("-p", "--aggregate",
+ dest="bAgg",
+ default=True,
+ action="store_true",
+ help="Flag to aggregate by pixel in the template")
+ parser.add_option("-y", "--aggregateYears",
+ dest="bAggYears",
+ default=False,
+ action="store_true",
+ help="Flag to aggregate by years in the template")
+ parser.add_option("-v", "--verbose",
+ dest="verbose",
+ default=False,
+ action="store_true",
+ help="the verbose flag causes diagnostic output to print")
+
+ (options, args) = parser.parse_args(argv)
+
+ ourFDQ = FieldDataQuery()
+ ourFDQ.template = options.template
+ ourFDQ.csv = options.csv
+ ourFDQ.output = options.output
+ ourFDQ.AggByPixel = options.bAgg
+ ourFDQ.AggByYear = options.bAggYears
+ ourFDQ.verbose = options.verbose
+ ourFDQ.processCSV()
+
+class FieldDataQuery(object):
+
+ def __init__(self):
+ #instance level variables
+ self.csv = None
+ self.template = None
+ self.output = None
+ self.templateParams = {}
+ self.AggByYear = False
+ self.AggByPixel = True
+ self.verbose = False
+ self.countdata = False
+ self.logger = None
+
+ def validateArgs(self):
+ """
+ Make sure the user sent us some stuff we can work with
+ """
+
+ # Validate template image.
+ if self.template is None:
+ raise Exception, "template raster not provided (-t command line argument missing)"
+
+ if not os.path.exists(self.template):
+ raise Exception, "Template file, " + self.template + ", does not exist on file system"
+
+ self.templateParams = self.getRasterParams(self.template)
+ if len(self.templateParams["Error"]) <> 0:
+ print ("There was a problem with the provided template: \n " +
+ " " + "\n ".join(self.templateParams["Error"]))
+ raise Exception, ("There was a problem with the provided template: \n " +
+ " " + "\n ".join(self.templateParams["Error"]))
+
+ # Ensure the template has square pixels.
+ if abs(abs(self.templateParams["xScale"]) - abs(self.templateParams["yScale"])) > 1e-6:
+ print "The template raster must have square pixels."
+ print "x pixel scale = " + str(xScale)
+ print "y pixel scale = " + str(yScale)
+ raise Exception, "template image must have square pixels."
+
+ #Validate the CSV
+ if self.csv is None:
+ raise Exception, "No csv provided"
+
+ if not os.path.exists(self.csv):
+ raise Exception, "CSV file, " + self.csv + ", does not exist on file system"
+
+ #make sure the directory the mds file is going into exists:
+ outDir = os.path.split(self.output)[0]
+ if not os.path.exists(outDir):
+ raise RuntimeError, "The directory of the supplied MDS output file path, " + self.output +", does not appear to exist on the filesystem"
+
+ if self.logger is None:
+ self.logger = utilities.logger(outDir, self.verbose)
+ self.writetolog = self.logger.writetolog
+
+ def getRasterParams(self, rasterFile):
+ """
+ Extracts a series of bits of information from a passed raster
+ All values are stored in a dictionary which is returned.
+ If errors are encountered along the way the error messages will
+ be returned as a list in the Error element.
+ """
+ try:
+ #initialize our params dictionary to have None for all parma
+ params = {}
+ allRasterParams = ["Error", "xScale", "yScale", "width", "height",
+ "ulx", "uly", "lrx", "lry", "Wkt",
+ "tUlx", "tUly", "tLrx", "tLry",
+ "srs", "gt", "prj", "NoData", "PixelType"]
+
+ for param in allRasterParams:
+ params[param] = None
+ params["Error"] = []
+
+ # Get the PARC parameters from the rasterFile.
+ dataset = gdal.Open(rasterFile, gdalconst.GA_ReadOnly)
+ if dataset is None:
+ params["Error"].append("Unable to open file")
+ #print "Unable to open " + rasterFile
+ #raise Exception, "Unable to open specifed file " + rasterFile
+
+
+ xform = dataset.GetGeoTransform()
+ params["xScale"] = xform[1]
+ params["yScale"] = xform[5]
+
+ params["width"] = dataset.RasterXSize
+ params["height"] = dataset.RasterYSize
+
+ params["ulx"] = xform[0]
+ params["uly"] = xform[3]
+ params["lrx"] = params["ulx"] + params["width"] * params["xScale"]
+ params["lry"] = params["uly"] + params["height"] * params["yScale"]
+
+
+ except:
+ #print "We ran into problems extracting raster parameters from " + rasterFile
+ params["Error"].append("Some untrapped error was encountered")
+ finally:
+ del dataset
+ return params
+
+ def processCSV(self):
+
+ self.validateArgs()
+ if self.verbose:
+ self.writetolog("Starting on Field Data Query for " + os.path.split(self.csv)[1])
+ self.writetolog(" using template " + os.path.split(self.template)[1])
+
+ templatename = os.path.split(self.template)[1]
+ if templatename == 'hdr.adf':
+ templatename = os.path.split(os.path.split(self.template)[0])[1]
+
+
+ csvfile = open(self.csv, "r")
+ #dialect = csv.Sniffer().sniff(csvfile.read(1024))
+ reader = csv.reader(csvfile)
+ usedPixels = {}
+ header = reader.next()
+ if header[2].lower() == 'responsecount':
+ self.countdata = True
+
+ #Commented this out because it is causing an error
+ #to be thrown by the java, uncomment out when the
+ #java has been replaced
+ header.append("frequency")
+ header.append("numPresence")
+ header.append("pixelColumn")
+ header.append("pixelRow")
+ header.append(os.path.abspath(self.template))
+ header.append(os.path.abspath(self.csv))
+
+ #loop through each row (observation) and
+ #if that particular pixel hasn't been encountered before
+ #add it to a dictionary containing a key of the pixel X,Y
+ #and values of each row encountered for that pixel
+ #if pixel
+ lineCount = linesInFile(self.csv)
+ extraPoints = []
+ pointCount = 0
+ pcntDone = 0
+ for row in reader:
+ if self.pointInTemplate(row[0], row[1]):
+ pixelColumn = int(floor((float(row[0]) - self.templateParams["ulx"])
+ / self.templateParams["xScale"]))
+ pixelRow = int(floor((float(row[1]) - self.templateParams["uly"])
+ / self.templateParams["yScale"]))
+ pixel = "".join(["X:",str(pixelColumn),":Y:",str(pixelRow)])
+ #if verbose == True:
+ if not pixel in usedPixels:
+ usedPixels[pixel] = [row]
+ #usedPixels[pixel] = usedPixels[pixel].append(row)
+ else:
+ curVal = usedPixels[pixel]
+ curVal.append(row)
+ usedPixels[pixel] = curVal
+ else:
+ extraPoints.append([row[0], row[1], row[2]])
+ pointCount += 1
+ if self.verbose:
+ if float(pointCount)/lineCount > float(pcntDone)/100:
+ pcntDone += 10
+ if self.verbose:
+ print str(pcntDone) + "...",
+
+ #Open up and write to an output file
+ oFile = open(self.output, 'wb')
+ fOut = csv.writer(oFile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
+ fOut.writerow(header)
+
+ #Add each used pixel to the output file
+ for k in usedPixels:
+ v = usedPixels[k]
+ outputLine = v[0]
+
+ pixelColumn = int(k.rsplit(':')[1])
+ pixelRow = int(k.rsplit(':')[3])
+ outPixelX = (self.templateParams["ulx"] + (self.templateParams["xScale"] * pixelColumn) +
+ self.templateParams["xScale"]/2)
+ outPixelY = (self.templateParams["uly"] + (self.templateParams["yScale"] * pixelRow) +
+ self.templateParams["yScale"]/2)
+ frequency = len(v)
+
+ #loop though the 'points' in each pixel
+ #for count data the value is the sum of the 'points'
+ # if there were any 'hits' not equal to 0
+ # otherwise if there were any absences the value is 0
+ # what's left is background points
+ #for presense/absense data
+ # The value is 1 if there were any 1s in our points
+ # Or 0 if there were any zeros (absenses)
+ # Otherwise it's a background pixel.
+ total = 0
+ numAbsense = 0
+ for i in range (frequency):
+ if int(float(v[i][2])) > 0:
+ total += int(float(v[i][2]))
+ if int(float(v[i][2])) == 0:
+ numAbsense += 1
+
+ outputLine[0] = outPixelX
+ outputLine[1] = outPixelY
+
+ if self.countdata and total > 0:
+ outputLine[2] = total
+ elif total > 0:
+ outputLine[2] = 1
+ elif numAbsense > 0:
+ outputLine[2] = 0
+ else:
+ outputLine[2] = -9999
+
+ outputLine.append(frequency)
+ outputLine.append(total)
+ outputLine.append(pixelColumn)
+ outputLine.append(pixelRow)
+
+
+ fOut.writerow(outputLine)
+ oFile.close
+ if self.verbose:
+ self.writetolog("Done\nFinished creating field data query output.\n")
+ if len(extraPoints) > 0:
+ self.writetolog (" WARNING: " + str(len(extraPoints)) + " points" +
+ " out of " + str(pointCount) + " total points in the " +
+ "original CSV were outside the template extent and WERE NOT " +
+ "INCLUDED IN THE FDQ OUTPUT.")
+ else:
+ pass
+
+ def pointInTemplate(self, x, y):
+ if (float(x) >= self.templateParams["ulx"] and
+ float(x) <= self.templateParams["lrx"] and
+ float(y) >= self.templateParams["lry"] and
+ float(y) <= self.templateParams["uly"]):
+ return True
+ else:
+ return False
+
+def linesInFile(filename):
+ f = open(filename)
+ lines = 0
+ buf_size = 1024 * 1024
+ read_f = f.read # loop optimization
+
+ buf = read_f(buf_size)
+ while buf:
+ lines += buf.count('\n')
+ buf = read_f(buf_size)
+
+ return lines
+#def getTemplateParams(template, verbose):
+# # Get the PARC parameters from the template.
+# dataset = gdal.Open(template, gdalconst.GA_ReadOnly)
+#
+# if dataset is None:
+# print "Unable to open " + template
+# raise RuntimeError
+# xform = dataset.GetGeoTransform()
+# xScale = xform[1]
+# yScale = xform[5]
+# # Ensure the template has square pixels.
+# if abs(math.fabs(xScale) - math.fabs(yScale)) > 1e-6:
+# print "The template image must have square pixels."
+# print "x pixel scale = " + str(math.fabs(xScale))
+# print "y pixel scale = " + str(math.fabs(yScale))
+# raise RuntimeError
+# width = dataset.RasterXSize
+# height = dataset.RasterYSize
+# ulx = xform[0]
+# uly = xform[3]
+# lrx = ulx + width * xScale
+# lry = uly + height * yScale
+# if verbose == True:
+# print "upper left = (" + str(ulx) + ", " + str(uly) + ")"
+# print "lower right = (" + str(lrx) + ", " + str(lry) + ")"
+# # Store the extent in geographic coordinates.
+# tEPSG = getEPSG(dataset)
+# if int(tEPSG) == 4326:
+# tGeoUlX = ulx
+# tGeoUlY = uly
+# tGeoLrX = lrx
+# tGeoLrY = lry
+# else:
+# tGeoUlX, tGeoUlY, tGeoLrX, tGeoLrY = getExtentInGeog(ulx, uly, lrx, lry, tEPSG)
+# return ulx, uly, lrx, lry, getEPSG(dataset), xScale, yScale
+#
+#def getEPSG(dataset):
+# #Returns code for the projection/datum used in the layer
+# wkt = dataset.GetProjection()
+# s_srs = osr.SpatialReference(wkt)
+# s_srs.AutoIdentifyEPSG()
+# epsg = s_srs.GetAuthorityCode("PROJCS")
+# if epsg == None:
+# epsg = s_srs.GetAuthorityCode("GEOGCS")
+# if epsg == None:
+# print "Unable to extract the EPSG code from the image."
+# raise RuntimeError
+# return epsg
+#
+#def getExtentInGeog(ulx, uly, lrx, lry, EPSG):
+#
+# s_srs = osr.SpatialReference()
+# s_srs.ImportFromEPSG(int(EPSG))
+#
+# t_srs = osr.SpatialReference()
+# t_srs.ImportFromEPSG(4326)
+#
+# coordXform = osr.CoordinateTransformation(s_srs, t_srs)
+#
+# result = coordXform.TransformPoint(ulx, uly)
+# gulx = result[0]
+# guly = result[1]
+#
+# result = coordXform.TransformPoint(lrx, lry)
+# glrx = result[0]
+# glry = result[1]
+#
+# return gulx, guly, glrx, glry
+
+if __name__ == '__main__':
+ main(sys.argv)
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/MDSBuilder.py b/contrib/sahm/pySAHM/MDSBuilder.py
new file mode 100644
index 0000000..7bf9739
--- /dev/null
+++ b/contrib/sahm/pySAHM/MDSBuilder.py
@@ -0,0 +1,473 @@
+'''
+Created on Jan 31, 2011
+
+This module creates a Merged Data Set (MDS)
+from an input CSV and directory
+or list of rasters. The MDS consists of three
+header lines 1st is a x, y, ResponseBinary,
+{other info fields}, then a list of raster covariates.
+The next header line contains ones and zeros for each of the
+raster covariates and indicates if the covariate is to be
+used in subsequent analyses. The last header line contains
+the full network path the raster dataset for that covariate.
+After the header lines comes the data which is the
+covariate values pulled from the raster cell
+with those coordinates.
+
+ at author: talbertc
+
+'''
+
+import sys
+import csv
+import os
+import time
+import random
+import shutil
+
+from osgeo import gdalconst
+from osgeo import gdal
+
+from optparse import OptionParser
+import utilities
+#from Utilities import self.writetolog
+
+class MDSBuilder(object):
+ '''Takes a csv with animal location x,y and attributes each with the values
+ extracted from each of the grids (covariates) indicated in the supplied
+ csv list of files
+ '''
+ def __init__(self):
+ #instance level variables
+ self.verbose = False
+ self.inputsCSV = ''
+ self.inputs = []
+ self.fieldData = ''
+ self.outputMDS = ''
+ self.probsurf = ''
+ self.pointcount = 0
+ self.NDFlag = -9999
+ self.deleteTmp = False
+ self.logger = None
+
+ def validateArgs(self):
+ #check our CSV file for expectations
+ if not os.path.exists(self.fieldData):
+ raise RuntimeError, "Could not find CSV file of fieldData provided. Please check input file: " + str(self.fieldData)
+
+ if not os.path.exists(self.inputsCSV):
+ raise RuntimeError, "Could not find CSV file of inputs provided. Please check input file: " + str(self.inputsCSV)
+
+ #check the input CSV file of inputs
+ reader = csv.reader(open(self.inputsCSV, 'r'))
+ header = reader.next()
+ missingfiles = []
+ for row in reader:
+ if not self.isRaster(row[0]):
+ missingfiles.append(row[0])
+ if not len(missingfiles) ==0:
+ msg = "One or more of the files in the input covariate list CSV could not be identified as rasters by GDAL."
+ msg += "\n ".join(missingfiles)
+ raise RuntimeError, msg
+
+ if self.probsurf <> '':
+ if not self.isRaster(self.probsurf):
+ raise RuntimeError, "The supplied probability surface, " + self.probsurf + ", does not appear to be a valid raster."
+
+ try:
+ self.pointcount = int(self.pointcount)
+ except:
+ raise RuntimeError, "The supplied point count parameter, " + self.pointcount +", does not appear to be an integer"
+
+ #make sure the directory the mds file is going into exists:
+ outDir = os.path.split(self.outputMDS)[0]
+ if not os.path.exists(outDir):
+ raise RuntimeError, "The directory of the supplied MDS output file path, " + self.outputMDS +", does not appear to exist on the filesystem"
+
+ if self.logger is None:
+ self.logger = utilities.logger(outDir, self.verbose)
+ self.writetolog = self.logger.writetolog
+
+ def run(self):
+ '''
+ This routine loops through a set of rasters and creates an MDS file
+ '''
+
+ self.validateArgs()
+ self.writetolog('\nRunning MDSBuilder', True, True)
+ # start timing
+ startTime = time.time()
+ gdal.UseExceptions()
+ gdal.AllRegister()
+
+ self.constructEmptyMDS()
+
+ if self.pointcount <> 0:
+ self.addBackgroundPoints()
+
+ outputRows = self.readInPoints()
+
+ #loop though each of the supplied rasters and add the
+ #extracted values to
+ for input in self.inputs:
+ inputND = self.getND(input)
+ rasterDS = gdal.Open(input, gdalconst.GA_ReadOnly)
+ # get image size
+ rows = rasterDS.RasterYSize
+ cols = rasterDS.RasterXSize
+ band = rasterDS.GetRasterBand(1)
+ # get georeference info
+ transform = rasterDS.GetGeoTransform()
+ xOrigin = transform[0]
+ yOrigin = transform[3]
+ pixelWidth = transform[1]
+ pixelHeight = transform[5]
+
+ if self.verbose:
+ self.writetolog(" Extracting raster values for " + input)
+ print " ",
+
+ pcntDone = 0
+ i = 1
+ badpoints = []
+ for row in outputRows:
+ x = float(row[0])
+ y = float(row[1])
+ # compute pixel offset
+ xOffset = int((x - xOrigin) / pixelWidth)
+ yOffset = int((y - yOrigin) / pixelHeight)
+# try:
+ if xOffset < 0 or yOffset < 0:
+ if row[:3] not in badpoints:
+ badpoints.append(row[:3])
+ row.append(str(self.NDFlag))
+ else:
+ try:
+ data = band.ReadAsArray(xOffset, yOffset, 1, 1)
+ value = data[0,0]
+ if value <> inputND:
+ row.append(value)
+ else:
+ row.append(str(self.NDFlag))
+ except:
+ badpoints.append(row[:3])
+ row.append(str(self.NDFlag))
+
+ if self.verbose:
+ if i/float(len(outputRows)) > float(pcntDone)/100:
+ pcntDone += 10
+ print str(pcntDone) + "...",
+ i += 1
+ if self.verbose:
+ self.writetolog(" Done")
+ if len(badpoints) > 0:
+ msg = "\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+ msg += "\n!!!!!!!!!!!!!!!!!!!!!WARNING!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n"
+ msg += str(len(badpoints)) + " point fell outside the Covariate coverage."
+ msg += "\nThese points were assigned the NoData value of -9999 for all covariates and will"
+ msg += "not be included in subsequent models.\n These points are:"
+ for badpoint in badpoints:
+ msg += " x:" + str(row[0]) + " Y: " + str(row[1]) + " response: " + str(row[2])
+ self.writetolog(msg)
+
+
+ outputMDS = csv.writer(open(self.outputMDS, 'ab'))
+ thrownOut = 0
+ kept = 0
+ for row in outputRows:
+ #remove this if when Marian handles the ND
+ if not str(self.NDFlag) in row[3:]:
+ outputMDS.writerow(row)
+ kept += 1
+ else:
+ outputMDS.writerow(row)
+ thrownOut += 1
+ if thrownOut > 0:
+ msg = "\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+ msg += "\n!!!!!!!!!!!!!!!!!!!!!WARNING!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n"
+ msg += str(thrownOut) + " points had 'nodata' in at least one of the covariates."
+ msg += "\nThese points will not be considered in subsequent Models."
+ msg += "\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+ msg += "\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+ self.writetolog(msg)
+ del outputMDS
+
+ #convert the mds csv to a shapefile
+ output_shp = self.outputMDS.replace(".csv", ".mds")
+ utilities.mds_to_shape(self.outputMDS, output_shp)
+
+ # figure out how long the script took to run
+ endTime = time.time()
+
+ if self.deleteTmp:
+ #if this flag is trud the field data we're working with is
+ # a temporary copy which we created so that we could add
+ # background points. Delete it to clean up our working file.
+ os.remove(self.fieldData)
+
+ if self.verbose:
+ self.writetolog('Finished running MDSBuilder', True, True)
+ self.writetolog(' The process took ' + str(endTime - startTime) + ' seconds')
+
+ def constructEmptyMDS(self):
+ '''Creates the triple header line format of our output file.
+ Also parses the inputs file to append the '_categorical' flag
+ to the covariate names of all categorical inputs.
+ '''
+
+ field_data_CSV = csv.reader(open(self.fieldData, "r"))
+ orig_header = field_data_CSV.next()
+ full_header = ["x", "y"]
+ if orig_header[2].lower not in ["responsebinary", "responsecount"]:
+ #inputs not conforming to our expected format will be assumed
+ #to be binary data
+ full_header.append("responseBinary")
+ else:
+ full_header.append(orig_header[2])
+
+ inputs_CSV = csv.reader(open(self.inputsCSV, "r"))
+ inputs_header = inputs_CSV.next()
+ self.inputs = []
+
+ #each row contains a covariate raster layer
+ #item 0 is the full path to the file
+ #item 1 is 0/1 indicating categorical
+ #Construct our output header by extracting each individual
+ #file (raster) name and appending '_categorical' if the flag is 1
+ rasters = {}
+ for row in inputs_CSV:
+ temp_raster = row[0]
+# self.inputs.append(temp_raster)
+ raster_shortname = os.path.split(temp_raster)[1]
+ raster_shortname = os.path.splitext(raster_shortname)[0]
+ if len(row) > 1 and row[1] == '1':
+ raster_shortname += "_categorical"
+ rasters[raster_shortname] = temp_raster
+
+ keys = rasters.keys()
+ keys.sort(key=lambda s: s.lower())
+ keys.sort(key=lambda s: s.lower())
+ for key in keys:
+ self.inputs.append(rasters[key])
+ full_header.append(key)
+
+ #Open up and write to an output file
+ oFile = open(self.outputMDS, 'wb')
+ fOut = csv.writer(oFile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
+
+ #Format and write out our three header lines
+ # the original template, fieldData, and parc folder are
+ # stored in spots 1,2,3 in the second header line
+ if len(orig_header) > 7 and os.path.exists(orig_header[7]):
+ #The input is an output from Field data query
+ original_field_data = orig_header[7]
+ field_data_template = orig_header[8]
+ else:
+ #The input is a raw field data file
+ original_field_data = self.fieldData
+ field_data_template = "NA"
+
+ if len(inputs_header) > 5:
+ parc_template = inputs_header[5]
+ parc_workspace = inputs_header[6]
+ else:
+ parc_template = "Unknown"
+ parc_workspace = "Unknown"
+
+ secondRow = [original_field_data, field_data_template, ""] + ["1" for elem in self.inputs]
+ thirdRow = [parc_template, parc_workspace, ""] + self.inputs
+ fOut.writerow(full_header)
+ fOut.writerow(secondRow)
+ fOut.writerow(thirdRow)
+ oFile.close()
+ del fOut
+
+ def readInPoints(self):
+ '''Loop through each row in our field data and add the X, Y, response
+ to our in memory list of rows to write to our output MDS file
+ '''
+ fieldDataCSV = csv.reader(open(self.fieldData, "r"))
+ origHeader = fieldDataCSV.next()
+ points = []
+ for row in fieldDataCSV:
+ points.append(row[:3])
+
+ del fieldDataCSV
+ return points
+
+ def addBackgroundPoints(self):
+ '''Add pointcount number of points to the supplied field data
+ If a probability surface was provided the distribution will
+ follow this otherwise it will be uniform within the extent of the first of our inputs.
+ No more than one per pixel is used.
+ '''
+ #First we'll create a temp copy of the Field Data to work with.
+ shutil.copy(self.fieldData, self.fieldData + ".tmp.csv")
+ self.fieldData = self.fieldData + ".tmp.csv"
+ self.deleteTmp = True
+
+ if self.probsurf <> '':
+ rasterDS = gdal.Open(self.probsurf, gdalconst.GA_ReadOnly)
+ useProbSurf = True
+ else:
+ print self.inputs[0]
+ rasterDS = gdal.Open(self.inputs[0], gdalconst.GA_ReadOnly)
+ useProbSurf = False
+
+ # get image size
+ rows = rasterDS.RasterYSize
+ cols = rasterDS.RasterXSize
+ band = rasterDS.GetRasterBand(1)
+ # get georeference info
+ transform = rasterDS.GetGeoTransform()
+ xOrigin = transform[0]
+ yOrigin = transform[3]
+ pixelWidth = transform[1]
+ pixelHeight = transform[5]
+ xRange = [xOrigin, xOrigin * pixelWidth * cols]
+ yRange = [yOrigin, yOrigin * pixelHeight * rows]
+
+ #Open up and write to an output file
+ oFile = open(self.fieldData, 'ab')
+ fOut = csv.writer(oFile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
+
+
+ if self.verbose:
+ self.writetolog(' Starting generation of ' + str(self.pointcount) + ' random background points, ')
+ if self.probsurf <> '':
+ self.writetolog(' using ' + self.probsurf + ' as the probability surface.')
+ print " Percent Done: ",
+
+ foundPoints = 0 # The running count of how many we've found
+ pcntDone = 0 #for status bar
+ while foundPoints < self.pointcount: #loop until we find enough
+ x = random.randint(0, cols - 1)
+ y = random.randint(0, rows - 1)
+ #print x, y
+ tmpPixel = [x, y, -9999] # a random pixel in the entire image
+ if useProbSurf:
+ # if they supplied a probability surface ignore the random pixel
+ # if a random number between 1 and 100 is > the probability surface value
+ pixelProb = int(band.ReadAsArray(tmpPixel[0], tmpPixel[1], 1, 1)[0,0])
+ #pixelProb is the extracted probability from the probability surface
+ rand = random.randint(1,100)
+ #rand is a uniform random integer between 1 and 100 inclusive
+ if rand > pixelProb:
+ continue
+ #don't record this pixel in our output file
+ #because our rand number was lower (or equal) than that pixel's probability
+
+ #convert our outValues for row, col to coordinates
+ tmpPixel[0] = xOrigin + tmpPixel[0] * pixelWidth
+ tmpPixel[1] = yOrigin + tmpPixel[1] * pixelHeight
+
+ fOut.writerow(tmpPixel)
+ foundPoints += 1
+ if self.verbose:
+ if float(foundPoints)/self.pointcount > float(pcntDone)/100:
+ pcntDone += 10
+ print str(pcntDone) + "...",
+ print "Done!\n"
+ oFile.close()
+ del fOut
+
+ def getRasters(self, directory):
+ #the list of rasters in the given directory
+ rasters = []
+ dirList = os.listdir(directory)
+ for file in [elem for elem in dirList if elem[-4:].lower() == ".tif"]:
+ if isRaster(os.path.join(directory, file)):
+ rasters.append(os.path.join(directory, file))
+ for file in [elem for elem in dirList if elem[-4:].lower() == ".asc"]:
+ if isRaster(os.path.join(directory,file)):
+ rasters.append(os.path.join(directory, file))
+ for folder in [name for name in dirList if os.path.isdir(os.path.join(directory, name)) ]:
+ if isRaster(os.path.join(directory, folder)):
+ rasters.append(os.path.join(directory, folder))
+
+ return rasters
+
+ def isRaster(self, filePath):
+ '''Verifies that a pased file and path is recognized by
+ GDAL as a raster file.
+ '''
+ try:
+ dataset = gdal.Open(filePath, gdalconst.GA_ReadOnly)
+ if dataset is None:
+ return False
+ else:
+ return True
+ del dataset
+ except:
+ return False
+
+ def getND(self, raster):
+ dataset = gdal.Open(raster, gdalconst.GA_ReadOnly)
+ ND = dataset.GetRasterBand(1).GetNoDataValue()
+ if ND is None:
+ if dataset.GetRasterBand(1).DataType == 1:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of 255"
+ return 255
+ elif dataset.GetRasterBand(1).DataType == 2:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of 65536"
+ return 65536
+ elif dataset.GetRasterBand(1).DataType == 3:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of 32767"
+ return 32767
+ elif dataset.GetRasterBand(1).DataType == 4:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of 2147483647"
+ return 2147483647
+ elif dataset.GetRasterBand(1).DataType == 5:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of 2147483647"
+ return 2147483647
+ elif dataset.GetRasterBand(1).DataType == 6:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of -3.40282346639e+038"
+ return -3.40282346639e+038
+ else:
+ return None
+ else:
+ return ND
+
+def main(argv):
+
+ usageStmt = "usage: options: -f --fieldData -i --inCSV -o --output -pc --pointcount -ps --probsurf"
+ desc = "Creates a merged dataset file (mds) from a csv of field points and rasters located in a csv listing one raster per line. Optionally this module adds a number of background points to the output."
+ parser = OptionParser(usage=usageStmt, description=desc)
+
+ parser.add_option("-v",
+ dest="verbose",
+ default=False,
+ action="store_true",
+ help="the verbose flag causes diagnostic output to print")
+ parser.add_option("-f", "--fieldData",
+ dest="fieldData",
+ help="The input CSV of field data points")
+ parser.add_option("-i", "--inCSV",
+ dest="inputsCSV",
+ help="The input CSV containing a list of our inputs, one per line.")
+ parser.add_option("-o", "--output",
+ dest="outputMDS",
+ help="Output MDS file to save to.")
+ parser.add_option("-p", "--probsurf",
+ dest="probsurf",
+ default='',
+ help="Probability surface to use for generation of background points (optional)")
+ parser.add_option("-c", "--pointcount",
+ dest="pointcount",
+ default=0,
+ help="Number of random background points to add(optional)")
+
+ (options, args) = parser.parse_args(argv)
+
+ ourMDS = MDSBuilder()
+ ourMDS.verbose = options.verbose
+ ourMDS.fieldData = options.fieldData
+ ourMDS.inputsCSV = options.inputsCSV
+ ourMDS.probsurf = options.probsurf
+ ourMDS.pointcount = options.pointcount
+ ourMDS.outputMDS = options.outputMDS
+ ourMDS.run()
+
+
+if __name__ == '__main__':
+ sys.exit(main(sys.argv))
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/MaxentRunner.py b/contrib/sahm/pySAHM/MaxentRunner.py
new file mode 100644
index 0000000..fa8b762
--- /dev/null
+++ b/contrib/sahm/pySAHM/MaxentRunner.py
@@ -0,0 +1,319 @@
+'''
+Created on Sep 17, 2010
+
+ at author: talbertc
+'''
+
+import time
+import os, sys
+import csv
+import itertools
+import traceback
+
+import subprocess
+
+from optparse import OptionParser
+
+#from core.modules.vistrails_module import Module, ModuleError, ModuleConnector
+#from core.system import execute_cmdline
+
+
+
+import utilities
+#from packages.sahm.pySAHM.Utilites import self.writetolog
+
+from osgeo import gdalconst
+from osgeo import gdal
+from osgeo import osr
+
+class MAXENTRunner(object):
+
+ def __init__(self):
+ self.verbose = False
+ self.maxentpath = ''
+ self.inputMDS = ''
+ self.projectionlayers = ''
+ self.testCSV = ''
+ self.trainingCSV = ''
+ self.backgroundCSV = ''
+ self.outputDir = ''
+ self.categoricals = []
+ self.argsCSV = ''
+ self.logger = None
+
+ def run(self):
+ self.loadArgs()
+ self.args['outputdirectory'] = self.outputDir
+
+# if self.projectionlayers <> '':
+# #A command line input overrides an input in the args csv
+# self.args['projectionlayers'] = self.projectionlayers
+#
+ self.validateInputs()
+
+ if self.inputMDS <> '':
+ self.prepInputs()
+ else:
+ raise Exception, "No MDS supplied."
+
+ if not self.args.has_key('projectionlayers'):
+ self.args['projectionlayers'] = ''
+
+ if self.trainingCSV <> '':
+ self.args['samplesfile'] = self.trainingCSV
+ else:
+ raise Exception, "No Samples file supplied"
+
+ if self.testCSV <> '':
+ self.args['testsamplesfile'] = self.testCSV
+
+ if self.backgroundCSV <> '':
+ self.args['environmentallayers'] = self.backgroundCSV
+
+
+ self.args['autorun'] = 'true'
+ #self.args['outputgrids'] = 'false'
+
+ if ' ' in self.args['species_name']:
+ self.args['species_name'] = self.args['species_name'].replace(' ', '_')
+
+ strargs = ['='.join((str(k),str(v))) for k,v in self.args.iteritems() if k <> "species_name"]
+ for categorical in self.categoricals:
+ strargs += ['togglelayertype=' + categorical.replace('_categorical', '')]
+ #strargs = ' '.join(strargs)
+ #print strargs
+
+ if not self.maxentpath.endswith('.jar'):
+ jar = os.path.join(self.maxentpath, 'maxent.jar')
+ else:
+ jar = self.maxentpath
+
+ self.run_cmd_line_jar(jar, strargs)
+
+
+ def run_cmd_line_jar(self, jar_name, args):
+ #arg_items = list(itertools.chain(*args.items()))
+ #arg_items = ['='.join((str(k),str(v))) for k,v in args.iteritems()]
+
+ cmd = ' '.join(['java', '-mx512m', '-jar', jar_name] + args)
+
+ self.writetolog(' running: ' + cmd, True, False)
+ #res = execute_cmdline(['java', '-jar', jar_name] + args, output)
+ p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+ self.writetolog(' Finished running: ', True, False)
+
+
+ ret = p.communicate()
+ self.writetolog(' Maxent strOut: ' + str(ret[0]))
+ if ret[1] is not None:
+ msg = "An error was encountered running the Maxent jar file. The error message is below - \n"
+ msg += ret[1]
+ writetolog(msg)
+ raise RuntimeError , msg
+ del ret
+
+ def loadArgs(self):
+ argsReader = csv.reader(open(self.argsCSV, 'r'))
+ header = argsReader.next()
+ self.args = {}
+ for row in argsReader:
+ self.args[row[0]] = row[1]
+
+ def validateInputs(self):
+ if not os.path.exists(self.argsCSV):
+ raise RuntimeError(self, 'Input argsFile, ' + self.argsCSV + ', could not be found on file system')
+
+ if not os.path.exists(self.inputMDS):
+ raise RuntimeError(self, 'Input MDS, ' + self.inputMDS + ', could not be found on file system')
+
+ if not self.args.has_key('projectionlayers'):
+ self.args['projectionlayers'] = ''
+
+ if self.args['projectionlayers'] <> '':
+ dirs = self.args['projectionlayers'].split(',')
+ for dir in dirs:
+ if not os.path.isdir(dir):
+ raise RuntimeError(self, "Input 'projectionlayers' must be a directory")
+
+ if not utilities.isMDSFile(self.inputMDS):
+ raise RuntimeError(self, 'Input MDS, ' + self.inputMDS + ', does not appear to be formated as an MDS file.')
+
+ if not os.path.exists(self.outputDir):
+ raise RuntimeError(self, 'Output directory, ' + self.outputDir + ', could not be found on file system')
+
+ if self.logger is None:
+ self.logger = utilities.logger(outDir, self.verbose)
+ self.writetolog = self.logger.writetolog
+
+ def prepInputs(self):
+ '''parses out input MDS file into the 1 to 3 SWD files that Maxent requires.
+ '''
+
+ #Create the outputs in our outputdirectory
+ self.testCSV = os.path.join(self.outputDir, 'testSamples.csv')
+ self.trainingCSV = os.path.join(self.outputDir, 'trainingSamples.csv')
+ self.backgroundCSV = os.path.join(self.outputDir, 'backgroundPoints.csv')
+
+ testWriter = csv.writer(open(self.testCSV, 'wb'))
+ trainingWriter = csv.writer(open(self.trainingCSV, 'wb'))
+ backgroundWriter = csv.writer(open(self.backgroundCSV, 'wb'))
+
+ #Read through the MDS and pull the headers
+ MDSreader = csv.reader(open(self.inputMDS, 'r'))
+ header1 = MDSreader.next()
+ header2 = MDSreader.next()
+ header3 = MDSreader.next()
+
+ self.pullCategoricals(header1)
+
+ #The split column indicates that this file has been run through the
+ #test training split and testing data should be writen to the test file.
+ splitcol = None
+ try:
+ splitcol = header1.index('Split')
+ deleteTest = False
+ except ValueError:
+ self.writetolog(" The supplied MDS does not have a 'Split' column defaulting to having Maxent apply test/training split.")
+ deleteTest = True
+
+ covariateIndexes = self.usedIndexes(header1, header2)
+ covariateNames = self.usedValues(header1, covariateIndexes)
+ covariateNamesClean = [name.replace('_categorical', '') for name in covariateNames]
+ usedCovariateFiles = self.usedValues(header3, covariateIndexes)
+
+ self.writetolog(' Used covariates:' + ", ".join(covariateNames), False, False)
+
+ testWriter.writerow(['full_name', 'x', 'y'] + covariateNamesClean)
+ trainingWriter.writerow(['full_name', 'x', 'y'] + covariateNamesClean)
+ backgroundWriter.writerow(['full_name', 'x', 'y'] + covariateNamesClean)
+
+ #loop through the rows sending each row to the appropriate file
+ hasBackground = False
+ for row in MDSreader:
+ if row[2] == '-9999':
+ hasBackground = True
+ vals = self.usedValues(row, covariateIndexes)
+ backgroundWriter.writerow([''] + row[:2] + vals)
+ elif splitcol is None and row[2] <> 0:
+ vals = self.usedValues(row, covariateIndexes)
+ trainingWriter.writerow([self.args['species_name']] + row[:2] + vals)
+ elif (row[splitcol] == 'test' and row[2] <> 0) or \
+ self.testCSV == '':
+ vals = self.usedValues(row, covariateIndexes)
+ testWriter.writerow([self.args['species_name']] + row[:2] + vals)
+ elif row[splitcol] == 'train' and row[2] <> 0:
+ vals = self.usedValues(row, covariateIndexes)
+ trainingWriter.writerow([self.args['species_name']] + row[:2] + vals)
+ #any absense points (row[2] == 0) will be ignored for maxent
+
+ if not hasBackground:
+ msg = " No background points were detected in the input file."
+ msg += "\n This implementation of Maxent does not have access to prepared ASCII environmental layers"
+ msg += " from which to extract values. Background points must be supplied in the MDS file."
+ self.writetolog(msg)
+ raise RuntimeError(msg)
+
+ #del our writers
+ try:
+ del testWriter
+ if deleteTest:
+ os.remove(self.testCSV)
+ self.testCSV = ''
+ del backgroundWriter
+ if not hasBackground:
+ os.remove(self.backgroundCSV)
+ self.backgroundCSV = ''
+ del trainingWriter
+ except:
+ print ' '.join([str(i) for i in sys.exc_info()[:2]])
+ pass
+
+ #First we have to figure out what they passed us
+ #either a directory, a SWD file, or a csv with a list of files
+
+ if self.args['projectionlayers'] <> '':
+ pass
+ else:
+ self.args['outputgrids'] = 'false'
+
+ def usedIndexes(self, header1, header2):
+ covariateIndexes = []
+ for i in range(len(header1)):
+ if header2[i] == '1' and header1[i] <> 'Split':
+ covariateIndexes.append(i)
+ return covariateIndexes
+
+ def usedValues(self, values, indexes):
+ usedvals = []
+ for i in indexes:
+ usedvals.append(values[i])
+ return usedvals
+
+ def pullCategoricals(self, headerline):
+ for item in headerline:
+ if item.endswith('_categorical'):
+ self.categoricals.append(item)
+
+
+ def isSWD(self, file):
+ '''Checks the format of a file to see if it is in the
+ Maxent samples with data (SWD) format.
+ '''
+ if os.path.exists(file):
+ reader = csv.reader(open(file, 'r'))
+ header = reader.next()
+ if header[0].lower() in ['species', 'full_name', 'fullname']:
+ return True
+
+ return False
+
+
+def main(argv):
+ '''Process our command line args and initiate a Maxent run
+ '''
+ usageStmt = "usage: -m --MDSFile -a --argsCSV -o --outputDir"
+ desc = "Formats and prepares input for running the Maxent Jar in a SAHM workflow"
+
+ parser = OptionParser(usage=usageStmt, description=desc)
+ parser.add_option("-m", "--MDSFile",
+ dest="MDSFile",
+ help="The MDS file with our sample data.")
+# parser.add_option("-p", "--projectionData",
+# dest="projectionData",
+# help="An optional CSV with a projection file for each of our environemnetal layers.")
+ parser.add_option("-a", "--argsCSV",
+ dest="argsCSV",
+ help="A CSV with each Maxent argument name and it's value on separate lines.")
+ parser.add_option("-e", "--maxentExecutable",
+ dest="maxentExecutable",
+ help="The full path to the maxent executable jar file.")
+ parser.add_option("-o", "--outputDir",
+ dest="outputDir",
+ help="The directory to save output files.")
+ parser.add_option("-v", "--verbose",
+ dest="verbose",
+ default=False,
+ action="store_true",
+ help="the verbose flag causes diagnostic output to print")
+
+ (options, args) = parser.parse_args(argv)
+
+ ourMaxent = MAXENTRunner()
+ ourMaxent.verbose = options.verbose
+ ourMaxent.maxentpath = options.maxentExecutable
+ ourMaxent.inputMDS = options.MDSFile
+ ourMaxent.outputDir = options.outputDir
+ ourMaxent.argsCSV = options.argsCSV
+ ourMaxent.projectionDataFile = options.projectionData
+
+ utilities.createsessionlog(options.outputDir, options.verbose)
+ ourMaxent.run()
+
+if __name__ == "__main__":
+ sys.exit(main(sys.argv[1:]))
+
+
+
+
+
+
diff --git a/contrib/sahm/pySAHM/PARC.py b/contrib/sahm/pySAHM/PARC.py
new file mode 100644
index 0000000..3417301
--- /dev/null
+++ b/contrib/sahm/pySAHM/PARC.py
@@ -0,0 +1,776 @@
+#!/usr/bin/python
+
+import glob
+import math
+import os
+import shutil
+import struct
+import sys
+import csv
+import Queue
+import thread
+import subprocess
+
+from optparse import OptionParser
+
+from osgeo import gdalconst
+from osgeo import gdal
+from osgeo import osr
+
+
+from numpy import *
+import numpy as np
+
+import utilities
+
+def main(args_in):
+ """
+ Process commandline Arguments,
+ Create an instance of PARC with the Variables,
+ Kick off the parkFiles function of our PARC instance
+ """
+ # Process command-line args.
+ usageStmt = "usage: %prog [options] <template image> <input dir or list of input files>"
+ desc = "This application projects, aggregates, resamples, and clips imagery."
+
+ parser = OptionParser(usage=usageStmt, description=desc)
+ parser.add_option("-l", dest="listMethodFlag", default=False, action="store_true", help="print the names of all known aggregation methods")
+ parser.add_option("-o", dest="out_dir", default="./", help="directory in which to put processed images, defaults to current directory")
+ parser.add_option("-v", dest="verbose", default=False, action="store_true", help="the verbose flag causes diagnostic output to print")
+ parser.add_option("-t", dest="templateRaster", help="The template raster used for projection, origin, cell size and extent")
+ parser.add_option("-i", dest="inputs_CSV", help="The CSV containing the list of files to process. Format is 'FilePath, Categorical, Resampling, Aggreagtion")
+ parser.add_option("-m", dest="multicore", default=True, help="'True', 'False' indicating whether to use multiple cores or not")
+ (options, args) = parser.parse_args(args_in)
+
+ ourPARC = PARC()
+ ourPARC.verbose = options.verbose
+ ourPARC.template = options.templateRaster
+ ourPARC.out_dir = options.out_dir
+ ourPARC.inputs_CSV = options.inputs_CSV
+ ourPARC.multicores = options.multicore
+ ourPARC.parcFiles()
+
+class PARC:
+ '''
+ PARC: Project, Aggregate, Resample, Clip
+ The workflow on this beast is as follows:
+ For each dataset
+ Step 1: RePrject the source raster into a tmp raster using
+ the projection info from the template and the method if
+ supplied or the default of nearest if not.
+ At this stage the tmp output will have a cell size about
+ the same as the input. We just use the default for this
+ setting.
+ Step 2: Aggregate the tmpRaster to have the same origin,
+ cell size and extent as our template.
+ '''
+
+ def __init__(self):
+ #instance level variables
+ self.verbose = False
+ self.template = ""
+ self.template_params = {}
+ self.out_dir = ""
+ self.inputs_CSV = ''
+ self.inputs = []
+ self.agg_methods = ['Min', 'Mean', 'Max', 'Majority']
+ self.resample_methods = ['NearestNeighbor', 'Bilinear', 'Cubic', 'CubicSpline', 'Lanczos']
+ self.logger = None
+ self.multicores = 'False'
+ self.module = None
+
+ def parcFiles(self):
+ '''
+ 1: Parse the inputs_CSV into our inputs list
+ 2: Make sure all of our instance variables are good and proper
+ 3: Loop through the list of sourceImages and PARC each one.
+ 4: The outputs will be stored in the output directory
+ 5: Additionally an output CSV will be produced that lists the
+ inputs, parameters used, and outputs
+ '''
+
+ self.logger.writetolog("Starting PARC", True, True)
+ self.validateArgs()
+ self.logger.writetolog(" Arguments validated successfully", True, True)
+ if self.multicores.lower() in ['true', 'yes', 't', 'y', '1']:
+ self.processFilesMC()
+ else:
+ self.processFiles()
+
+ self.logger.writetolog("Finished PARC", True, True)
+
+ def processFiles(self):
+ # Clip and reproject each source image.
+ for image in self.inputs:
+ # Ensure source is different from template.
+ #if not os.path.samefile(template, image):
+ inPath, inFileName = os.path.split(image[0])
+ outFile, ext = os.path.splitext(inFileName)
+ outFile = os.path.join(self.out_dir, outFile + ".tif")
+
+ # os.path.samefile(image, outFile):
+ if os.path.exists(outFile) and \
+ os.path.abspath(image[0]) == os.path.abspath(outFile):
+
+ baseName, extension = os.path.splitext(outFile)
+ outFile = baseName + "-PARC.tif"
+
+ if os.path.abspath(self.template) != os.path.abspath(image[0]):
+ self.parcFile(image, outFile)
+ elif os.path.abspath(self.template) == os.path.abspath(image[0]):
+ shutil.copyfile(self.template, outFile)
+
+
+
+ def processFilesMC(self):
+ '''This function has the same functionality as parcFiles
+ with the addition of utilizing multiple cores to do the processing.
+ '''
+ results= Queue.Queue()
+ process_count= 0
+
+ for image in self.inputs:
+ # Ensure source is different from template.
+ #if not os.path.samefile(template, image):
+ inPath, inFileName = os.path.split(image[0])
+ outFile, ext = os.path.splitext(inFileName)
+ outFile = os.path.join(self.out_dir, outFile + ".tif")
+
+ # os.path.samefile(image, outFile):
+ if os.path.exists(outFile) and \
+ os.path.abspath(image[0]) == os.path.abspath(outFile):
+
+ baseName, extension = os.path.splitext(outFile)
+ outFile = baseName + "-PARC.tif"
+
+ if os.path.abspath(self.template) != os.path.abspath(image[0]):
+ image_short_name = os.path.split(image[0])[1]
+ args = '-s ' + '"' + os.path.abspath(image[0]) + '"'
+ args += ' -c ' + '"' + image[1] + '"'
+ args += ' -d ' + os.path.abspath(outFile)
+ args += ' -t ' + os.path.abspath(self.template)
+ args += ' -r ' + image[2]
+ args += ' -a ' + image[3]
+
+ execDir = os.path.split(__file__)[0]
+ executable = os.path.join(execDir, 'singlePARC.py')
+
+ pyEx = sys.executable
+ command = ' '.join([pyEx, executable, args])
+ self.logger.writetolog(command, False, False)
+ proc = subprocess.Popen( command )
+ thread.start_new_thread(utilities.process_waiter,
+ (proc, image_short_name, results))
+ process_count+= 1
+
+ while process_count > 0:
+ description, rc= results.get()
+
+ if rc == 0:
+ if self.verbose:
+ msg = " " + description + " finished successfully: " + \
+ str(len(self.inputs) - process_count + 1) + " done out of " \
+ + str(len(self.inputs))
+ self.logger.writetolog(msg, True, True)
+ else:
+ self.logger.writetolog("There was a problem with: " + description , True, True)
+ process_count-= 1
+
+
+
+ self.logger.writetolog("Finished PARC", True, True)
+
+ def parcFile(self, source, dest):
+ """
+ Processes a single file
+ """
+ gdal.UseExceptions()
+
+ shortName = os.path.split(os.path.splitext(source[0])[0])[1]
+ self.logger.writetolog(" Starting processing of " + source[0])
+ sourceParams = self.getRasterParams(source[0])
+
+ gdalType = None
+ if source[2].lower() == "nearestneighbor":
+ gdalType = gdalconst.GRA_NearestNeighbour
+ if source[2].lower() == "bilinear":
+ gdalType = gdalconst.GRA_Bilinear
+ if source[2].lower() == "cubic":
+ gdalType = gdalconst.GRA_Cubic
+ if source[2].lower() == "cubicspline":
+ gdalType = gdalconst.GRA_CubicSpline
+ if source[2].lower() == "lanczos":
+ gdalType = gdalconst.GRA_Lanczos
+ if gdalType == None:
+ self.logger.writetolog(" Specified resampling method (" + source[2] + ") not one of 'NearestNeighbor', 'Bilinear', 'Cubic', 'CubicSpline', or 'Lanczos'. Defaulting to 'NearestNeighbor'")
+ gdalType = gdalconst.GRA_NearestNeighbour
+
+ #Open dgal dataset of the source to pull some values from
+ srcDs = gdal.Open(source[0])
+
+ cellRatio = self.getTemplateSRSCellSize(sourceParams)/self.template_params["xScale"]
+ msg = " ratio of source cell size to template cell size = " + str(cellRatio)
+ msg += " template cell size = " + str(self.template_params["xScale"])
+ msg += " " + shortName + " cell size = " + str(self.getTemplateSRSCellSize(sourceParams))
+ self.writetolog(msg)
+
+ if cellRatio > 0.5:
+ #The source cell size is close enough to our template cell size,
+ #or smaller so
+ #that all we need to do is reproject and resample.
+ self.logger.writetolog(" cell ratio > .5: reprojecting and resampling to template parameters only")
+ self.reprojectRaster(srcDs, sourceParams, self.template_params, dest,
+ gdalType, shortName, self.template_params["xScale"])
+ else:
+ #Our Target cell size is much bigger than our source we need to do
+ #some aggregation to make things work.
+ msg = ' cell ratio <= .5: reprojecting and resampling to template parameters'
+ msg += ' then aggregating the reprojected raster to match template parameters'
+ self.writetolog(msg)
+
+ targetCellSize, numSourcePerTarget = self.getAggregateTargetCellSize(sourceParams)
+ tmpOutput = os.path.join(os.path.dirname(dest), "tmp_" + os.path.basename(dest))
+
+ self.reprojectRaster(srcDs, sourceParams, self.template_params,
+ tmpOutput, gdalType, shortName, targetCellSize)
+ self.writetolog(" Starting on Aggregating: " + shortName)
+
+ tmpOutput2 = os.path.splitext(tmpOutput)[0] + ".tif"
+ self.Aggregate(tmpOutput2, dest,
+ sourceParams, self.template_params,
+ source[3], numSourcePerTarget)
+
+ try:
+ os.remove(tmpOutput2)
+ except WindowsError:
+ pass
+
+
+ def getTemplateSRSCellSize(self, sourceParams):
+ """
+ Calculate what size our source image pixels would be in the template SRS
+ """
+ #first convert our template origin into the source srs
+ tOriginX, tOriginY = self.transformPoint(self.template_params["west"], self.template_params["north"],
+ self.template_params["srs"], sourceParams["srs"])
+ #next add the source xScale to the converted origin x and convert that back to template srs
+ tOriginX1 = self.transformPoint (tOriginX + sourceParams["xScale"], tOriginY,
+ sourceParams["srs"], self.template_params["srs"])[0]
+
+
+# templateCellXCorner1 = (self.template_params["west"], self.template_params["north"],
+# self.template_params["srs"], sourceParams["srs"])[0]
+#
+# targetCellXCorner1 = (sourceParams["west"], sourceParams["north"],
+# sourceParams["srs"], self.template_params["srs"])[0]
+# targetCellXCorner2 = self.transformPoint(sourceParams["west"] + sourceParams["xScale"],
+# sourceParams["north"], sourceParams["srs"], self.template_params["srs"])[0]
+ templateSRSCellSize = abs(abs(tOriginX1) - abs(self.template_params["west"]))
+ return templateSRSCellSize
+
+ def getAggregateTargetCellSize(self, sourceParams):
+ """
+ This function determines the appropriate cell size to
+ reproject/resample our source raster into before
+ aggregating.
+ This size is the cell size that results in a template
+ cell containing a whole number of cells which are as
+ close as possible to the cell dimension that would
+ result if you reprojected the source cells into the
+ target srs without changing cell size.
+ """
+ #first determine what cell size we are going to use for the initial reproject/resample
+ #step 1: Determine the native cell size in the template coordinate system.
+ templateSRSCellSize = self.getTemplateSRSCellSize(sourceParams)
+ #step 2: round this up or down to an even fraction of the template cell size
+ # for example source = 30, target = 250 resampledSource = 250/round(250/30)
+ sourcePixelsPerTarget = round(self.template_params["xScale"]/templateSRSCellSize)
+ nearestWholeCellSize = (self.template_params["xScale"] /
+ sourcePixelsPerTarget)
+ return nearestWholeCellSize, sourcePixelsPerTarget
+
+
+ def Aggregate(self, inFile, outFile, sourceParams, templateParams, method=None, numSourcePerTarget=10):
+ sourceDs = gdal.Open(inFile, gdalconst.GA_ReadOnly)
+ sourceBand = sourceDs.GetRasterBand(1)
+
+ tmpOutput = os.path.splitext(outFile)[0] + ".tif"
+ tmpOutDataset = self.generateOutputDS(sourceParams, templateParams, tmpOutput)
+ outBand = tmpOutDataset.GetRasterBand(1)
+
+ rows = int(sourceParams["height"])
+ cols = int(sourceParams["width"])
+
+ row = 0
+ col = 0
+
+
+ pcntDone = 0.0
+ if self.verbose:
+ print " % Done: 0.0",
+
+ while row < templateParams["width"]:
+ while col < templateParams["height"]:
+ sourceRow = row * numSourcePerTarget
+ sourceCol = col * numSourcePerTarget
+
+ #kernel = self.getKernel(sourceRow, sourceCol, numSourcePerTarget, sourceDs)
+ kernel = sourceDs.GetRasterBand(1).ReadAsArray(int(sourceRow),
+ int(sourceCol),
+ int(numSourcePerTarget),
+ int(numSourcePerTarget))
+ #convert kernel values of our nodata to nan
+ ndMask = ma.masked_array(kernel, mask=(kernel==sourceParams["NoData"]))
+ #print kernel
+ if method == "Min":
+ ans = ndMask.min()
+ elif method == "Max":
+ ans = ndMask.max()
+ elif method == "Majority":
+# ndMask = ndMask.flatten()
+ uniques = np.unique(ndMask)
+ curMajority = -3.40282346639e+038
+ for val in uniques:
+ numOccurances = (array(ndMask)==val).sum()
+ if numOccurances > curMajority:
+ ans = val
+ curMajority = numOccurances
+
+# histogram = np.histogram(ndMask, uniques)
+# ans = histogram[1][histogram[0].argmax()]
+ else:
+ ans = ndMask.mean()
+
+# print ndMask
+# print ans
+ #special case real ugly
+ if ans < 0 and sourceParams["signedByte"]:
+ ans = ans + 255
+
+ ansArray = empty([1, 1])
+ if type(ans) == ma.core.MaskedArray:
+ ansArray[0, 0] = sourceParams["NoData"]
+ else:
+ ansArray[0, 0] = ans
+
+ outBand.WriteArray(ansArray, row, col)
+
+ col += 1
+
+ row += 1
+ col = 0
+ if self.verbose:
+ if float(row)/templateParams["width"] > float(pcntDone)/100:
+ pcntDone += 2.5
+ if int(pcntDone) % 10 == 0:
+ print str(pcntDone),
+ else:
+ print ".",
+ if self.verbose:
+ print "Done"
+# if self.verbose:
+# print "Done\nSaving to ASCII format"
+#
+# driver = gdal.GetDriverByName("AAIGrid")
+# driver.Register()
+#
+# dst_ds = driver.CreateCopy(outFile, tmpOutDataset, 0)
+# if self.verbose:
+# print " Finished Saving ", self.shortName
+
+ dst_ds = None
+ tmpOutDataset=None
+
+ def getRasterParams(self, rasterFile):
+ """
+ Extracts properties from a passed raster
+ All values are stored in a dictionary which is returned.
+ If errors are encountered along the way the error messages will
+ be returned as a list in the 'Error' element.
+ """
+ try:
+ #initialize our params dictionary to have None for all parma
+ params = {}
+ allRasterParams = ["Error", "xScale", "yScale", "width", "height",
+ "east", "north", "west", "south",
+ "tEast", "tNorth", "tWest", "tSouth",
+ "gEast", "gNorth", "gWest", "gSouth",
+ "Wkt", "srs", "gt", "prj", "NoData", "PixelType", "file_name"]
+
+ for param in allRasterParams:
+ params[param] = None
+ params["Error"] = []
+ params["file_name"] = rasterFile
+
+
+ # Get the PARC parameters from the rasterFile.
+ dataset = gdal.Open(rasterFile, gdalconst.GA_ReadOnly)
+ if dataset is None:
+ params["Error"].append("Unable to open file")
+ return params
+
+ #print "Unable to open " + rasterFile
+ #raise Exception, "Unable to open specifed file " + rasterFile
+
+
+ xform = dataset.GetGeoTransform()
+ params["xScale"] = xform[1]
+ params["yScale"] = xform[5]
+
+ params["width"] = dataset.RasterXSize
+ params["height"] = dataset.RasterYSize
+
+ params["west"] = xform[0]
+ params["north"] = xform[3]
+ params["east"] = params["west"] + params["width"] * params["xScale"]
+ params["south"] = params["north"] + params["height"] * params["yScale"]
+
+ try:
+ wkt = dataset.GetProjection()
+ params["gt"] = dataset.GetGeoTransform()
+ params["prj"] = dataset.GetProjectionRef()
+ params["srs"] = osr.SpatialReference(wkt)
+ if wkt == '':
+ params["Error"].append("Undefined projection")
+ else:
+
+ if rasterFile == self.template:
+ params["tWest"], params["tNorth"] = params["west"], params["north"]
+ params["tEast"], params["tSouth"] = params["east"], params["south"]
+ elif params["srs"].ExportToWkt() == self.template_params["srs"].ExportToWkt():
+ params["tWest"], params["tNorth"] = params["west"], params["north"]
+ params["tEast"], params["tSouth"] = params["east"], params["south"]
+ else:
+ try:
+ params["tWest"], params["tNorth"] = self.transformPoint(params["west"], params["north"], params["srs"], self.template_params["srs"])
+ params["tEast"], params["tSouth"] = self.transformPoint(params["east"], params["south"], params["srs"], self.template_params["srs"])
+ except:
+ params["Error"].append("Could not transform extent coordinates to template spatial reference")
+ #params["Error"] = "We ran into problems converting projected coordinates to template for " + rasterFile
+ try:
+ geographic = osr.SpatialReference()
+ geographic.ImportFromEPSG(4326)
+ params["gWest"], params["gNorth"] = self.transformPoint(params["west"], params["north"], params["srs"], geographic)
+ params["gEast"], params["gSouth"] = self.transformPoint(params["east"], params["south"], params["srs"], geographic)
+ except:
+ pass
+
+ except:
+ #print "We ran into problems getting the projection information for " + rasterFile
+ params["Error"].append("Undefined problems extracting the projection information")
+
+ try:
+ params["signedByte"] = dataset.GetRasterBand(1).GetMetadata('IMAGE_STRUCTURE')['PIXELTYPE'] == 'SIGNEDBYTE'
+ except KeyError:
+ params["signedByte"] = False
+
+ params["NoData"] = dataset.GetRasterBand(1).GetNoDataValue()
+ if params["NoData"] == None:
+ if dataset.GetRasterBand(1).DataType == 1:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of 255"
+ params["NoData"] = 255
+ elif dataset.GetRasterBand(1).DataType == 2:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of 65536"
+ params["NoData"] = 65536
+ elif dataset.GetRasterBand(1).DataType == 3:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of 32767"
+ params["NoData"] = 32767
+ elif dataset.GetRasterBand(1).DataType == 4:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of 2147483647"
+ params["NoData"] = 2147483647
+ elif dataset.GetRasterBand(1).DataType == 5:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of 2147483647"
+ params["NoData"] = 2147483647
+ elif dataset.GetRasterBand(1).DataType == 6:
+ print "Warning: Could not extract NoData value. Using assumed nodata value of -3.40282346639e+038"
+ params["NoData"] = -3.40282346639e+038
+ else:
+ params["Error"].append("Could not identify nodata value")
+ params["PixelType"] = dataset.GetRasterBand(1).DataType
+ if params["PixelType"] == None:
+ params["Error"].append("Could not identify pixel type (bit depth)")
+
+ except:
+ #print "We ran into problems extracting raster parameters from " + rasterFile
+ params["Error"].append("Some untrapped error was encountered")
+ finally:
+ del dataset
+ return params
+
+ def transformPoint(self, x, y, from_srs, to_srs):
+ """
+ Transforms a point from one srs to another
+ """
+ coordXform = osr.CoordinateTransformation(from_srs, to_srs)
+ yRound = round(y, 4)
+ xRound = round(x, 4)
+
+ result = coordXform.TransformPoint(xRound, yRound)
+
+ gx = result[0]
+ gy = result[1]
+
+ return gx, gy
+
+ def ImageCoversTemplate(self, sourceParams):
+ """
+ Checks to see if the template images
+ falls completely inside the source raster
+
+ it does this by generating a list of 16 coordinate
+ pairs equally distributed across the template,
+ including the four absolute corners.
+ These points are in the CRS of the image.
+ If all of these points have a valid data or nodata
+ value in the image, then the image covers the template.
+ (in nearly every case anyway)
+ """
+
+ n = 5
+ xOffset = (self.template_params["east"] - self.template_params["west"]) / (n) - \
+ ((self.template_params["east"] - self.template_params["west"]) / self.template_params["width"] / 1000)
+ yOffset = (self.template_params["north"] - self.template_params["south"]) / (n) - \
+ ((self.template_params["north"] - self.template_params["south"]) / self.template_params["height"] / 1000)
+ curX = self.template_params["west"]
+ curY = self.template_params["north"]
+ testPoints =[]
+
+ for x in range(n + 1):
+ for y in range(n + 1):
+ testPoints.append(self.transformPoint(curX, curY, self.template_params["srs"],
+ sourceParams["srs"]))
+ curY -= yOffset
+
+ curX += xOffset
+ curY = self.template_params["north"]
+
+ rasterDS = gdal.Open(sourceParams["file_name"], gdalconst.GA_ReadOnly)
+ band = rasterDS.GetRasterBand(1)
+ badPoint = False
+ for point in testPoints:
+ try:
+ xOffset = int((point[0] - sourceParams["west"]) / sourceParams["xScale"])
+ yOffset = int((point[1] - sourceParams["north"]) / sourceParams["yScale"])
+ data = band.ReadAsArray(xOffset, yOffset, 1, 1)
+ value = data[0,0]
+ except:
+ badPoint = True
+
+ #if valid values were returned from each of our points then
+ #the template falls entirely within the Source image.
+ if badPoint:
+ return False
+ else:
+ return True
+
+
+ def validateArgs(self):
+ """
+ Make sure the user sent us some stuff we can work with
+ """
+
+ if not os.path.exists(self.out_dir):
+ raise utilities.TrappedError("Specified Output directory " + self.out_dir + " not found on file system")
+
+ if not os.path.isdir(self.out_dir):
+ raise utilities.TrappedError("Specified Output directory " + self.out_dir + " is not a directory")
+
+ if self.logger is None:
+ self.logger = utilities.logger(self.out_dir, self.verbose)
+ self.writetolog = self.logger.writetolog
+
+ # Validate template image.
+ if self.template is None:
+ raise utilities.TrappedError("template raster not provided.")
+
+ if not os.path.exists(self.template):
+ raise utilities.TrappedError("Template file, " + self.template + ", does not exist on file system")
+
+ self.template_params = self.getRasterParams(self.template)
+ if len(self.template_params["Error"]) <> 0:
+ raise utilities.TrappedError("There was a problem with the provided template: \n " +
+ " " + "\n ".join(self.template_params["Error"]))
+
+ # Ensure the template has square pixels.
+ if abs(abs(self.template_params["xScale"]) - abs(self.template_params["yScale"])) > 1e-6:
+ raise utilities.TrappedError("template image must have square pixels." +
+ "/n x pixel scale = " + str(xScale) +
+ "/n y pixel scale = " + str(yScale))
+
+
+ #Validate input rasters
+ if not os.path.exists(self.inputs_CSV):
+ raise utilities.TrappedError("Inputs CSV, " + self.inputs_CSV + ", does not exist on file system.")
+
+ inputsCSV = csv.reader(open(self.inputs_CSV, 'r'))
+ header = inputsCSV.next()
+ strInputFileErrors = ""
+
+ outputCSV = os.path.join(self.out_dir, "PARC_Files.csv")
+ output = csv.writer(open(outputCSV, "wb"))
+ output.writerow(["PARCOutputFile", "Categorical", "Resampling", "Aggregation", "OriginalFile", os.path.abspath(self.template), os.path.abspath(self.out_dir)])
+
+ for row in inputsCSV:
+ inputFile = row[0]
+ sourceParams = self.getRasterParams(inputFile)
+ if len(sourceParams["Error"]) > 0:
+ strInputFileErrors += (" " + os.path.split(inputFile)[1] + " had the following errors:\n" +
+ " " + "\n ".join(sourceParams["Error"])) + "\n"
+ else:
+ pass
+ if not self.ImageCoversTemplate(sourceParams):
+ strInputFileErrors += ("\n Some part of the template image falls outside of " + os.path.split(inputFile)[1])
+ strInputFileErrors += "\n template upper left = (" + str(self.template_params["gWest"]) + ", " + str(self.template_params["gNorth"]) + ")"
+ strInputFileErrors += "\n template lower right = (" + str(self.template_params["gEast"]) + ", " + str(self.template_params["gSouth"]) + ")"
+ strInputFileErrors += "\n image upper left = (" + str(sourceParams["gWest"]) + ", " + str(sourceParams["gNorth"]) + ")"
+ strInputFileErrors += "\n image lower right = (" + str(sourceParams["gEast"]) + ", " + str(sourceParams["gSouth"]) + ")"
+# strInputFileErrors += "\n points are given in projected coordinates."
+# strInputFileErrors += "\n template upper left = (" + str(self.template_params["tWest"]) + ", " + str(self.template_params["tNorth"]) + ")"
+# strInputFileErrors += "\n template lower right = (" + str(self.template_params["tEast"]) + ", " + str(self.template_params["tSouth"]) + ")"
+# strInputFileErrors += "\n image upper left = (" + str(sourceParams["tWest"]) + ", " + str(sourceParams["tNorth"]) + ")"
+# strInputFileErrors += "\n image lower right = (" + str(sourceParams["tEast"]) + ", " + str(sourceParams["tSouth"]) + ")"
+# strInputFileErrors += "\n Note: points are given in the template coordinates." + "\n"
+#
+ if len(row) < 2 or not row[1] in ['0', '1']:
+ self.writetolog(" " + os.path.split(inputFile)[1] + " categorical either missing or not 0 or 1:\n Defaulting to 0 (continuous)")
+ if len(row) < 2:
+ row.append('0')
+ else:
+ row[1] = '0'
+
+ if len(row) < 3 or not row[2].lower() in [item.lower() for item in self.resample_methods]:
+ self.writetolog(" " + os.path.split(inputFile)[1] + " resample method either missing or not one of " +
+ ", ".join(self.resample_methods) + "\n Defaulting to 'Bilinear'")
+
+ if row[1] == '0':
+ default = 'Bilinear'
+ else:
+ default = 'NearestNeighbor'
+ if len(row) < 3:
+ row.append(default)
+ else:
+ row[2] = default
+
+ if len(row) < 4 or not row[3].lower() in [item.lower() for item in self.agg_methods]:
+ self.writetolog(" " + os.path.split(inputFile)[1] + " aggregation method either missing or not one of " +
+ ", ".join(self.agg_methods) + "\n Defaulting to 'Mean'")
+ if row[1] == '0':
+ default = 'Mean'
+ else:
+ default = 'Majority'
+ if len(row) < 4:
+ row.append(default)
+ else:
+ row[3] = default
+
+ self.inputs.append(row)
+ #also write the output row, reconfigured to our output file
+ fileName = self.getShortName(row[0])
+ fileName = os.path.abspath(os.path.join(self.out_dir, fileName + ".tif"))
+ outputrow = [fileName] + row[1:4] + [os.path.abspath(row[0]), os.path.abspath(self.out_dir)]
+ output.writerow(outputrow)
+ del output
+
+ if strInputFileErrors <> "":
+ self.writetolog(strInputFileErrors)
+ raise utilities.TrappedError("There was one or more problems with your input rasters: \n" + strInputFileErrors)
+
+ def reprojectRaster(self, srcDs, sourceParams, templateParams,
+ destFile, resamplingType, shortName='', outputCellSize = None):
+ """
+ Reprojects a raster to match the template_params
+ if outputCellSize is not provided defaults to the template cellSize
+ """
+# driver = gdal.GetDriverByName("AAIGrid")
+# driver.Register()
+
+ tmpOutput = os.path.splitext(destFile)[0] + ".tif"
+
+ tmpOutDataset = self.generateOutputDS(sourceParams, templateParams, tmpOutput, outputCellSize)
+
+ self.writetolog(" Starting intermediate reprojection of: " + shortName)
+
+ err = gdal.ReprojectImage(srcDs, tmpOutDataset, sourceParams["srs"].ExportToWkt(),
+ templateParams["srs"].ExportToWkt(), resamplingType)
+
+# dst_ds = driver.CreateCopy(destFile, tmpOutDataset, 0)
+ self.writetolog(" Finished reprojection " + shortName)
+ dst_ds = None
+ tmpOutDataset = None
+
+ def generateOutputDS(self, sourceParams, templateParams,
+ tmpOutput, outputCellSize = None):
+ """
+ Creates an output dataset (tiff format) that
+ has the nodata value of the sourceParams but
+ all other attributes from the template_params
+ This output is saved to tmpOutput.
+
+ The optional cell size will override the cell size
+ specified in the template_params
+ """
+ tifDriver = gdal.GetDriverByName("GTiff")
+
+ if outputCellSize == None:
+ width = templateParams["width"]
+ height = templateParams["height"]
+ else:
+ width = templateParams["width"] * int(templateParams["xScale"]/outputCellSize)
+ height = templateParams["height"] * int(templateParams["xScale"]/outputCellSize)
+
+ if sourceParams["signedByte"]:
+ tmpOutDataset = tifDriver.Create(tmpOutput,
+ width,
+ height,
+ 1, sourceParams["PixelType"], ["PIXELTYPE=SIGNEDBYTE"])
+ else:
+ tmpOutDataset = tifDriver.Create(tmpOutput,
+ width,
+ height,
+ 1, sourceParams["PixelType"])
+
+
+ if outputCellSize == None:
+ outputCellSize = templateParams["xScale"]
+ gtList = list(templateParams["gt"])
+ if templateParams["xScale"] < 0:
+ gtList[1] = -1 * outputCellSize
+ else:
+ gtList[1] = outputCellSize
+ if templateParams["yScale"] < 0:
+ gtList[5] = -1 * outputCellSize
+ else:
+ gtList[5] = outputCellSize
+ gt = tuple(gtList)
+
+ tmpOutDataset.SetGeoTransform(gt)
+ tmpOutDataset.SetProjection(templateParams["prj"])
+ tmpOutDataset.GetRasterBand(1).SetNoDataValue(sourceParams["NoData"])
+ if sourceParams["signedByte"]:
+ #tmpOutDataset.GetRasterBand(1).SetMetadataItem('PIXELTYPE', "SIGNEDBYTE")
+ tmpOutDataset.GetRasterBand(1).PixelType = "SIGNEDBYTE"
+ tmpOutDataset.GetRasterBand(1).SetMetadata({'PIXELTYPE': 'SIGNEDBYTE'}, 'IMAGE_STRUCTURE')
+
+# if self.verbose:
+# print tmpOutput
+# print "noDataValue = ", tmpOutDataset.GetRasterBand(1).GetNoDataValue()
+# print "Pixel type = ", gdal.GetDataTypeName(tmpOutDataset.GetRasterBand(1).DataType)
+ return tmpOutDataset
+
+ def getShortName(self, fullPathName):
+ if fullPathName.endswith('hdr.adf'):
+ shortname = os.path.split(fullPathName)[0]
+ shortname = os.path.split(shortname)[1]
+ else:
+ shortname = os.path.split(fullPathName)[1]
+ shortname = os.path.splitext(shortname)[0]
+ return shortname
+
+if __name__ == "__main__":
+ sys.exit(main(sys.argv[1:]))
+# try:
+## PARC().testing()
+# sys.exit(PARC().main(sys.argv[1:]))
+# except Exception as e:
+# print e
+# sys.exit(1)
diff --git a/contrib/sahm/pySAHM/RasterFormatConverter.py b/contrib/sahm/pySAHM/RasterFormatConverter.py
new file mode 100644
index 0000000..9004bd7
--- /dev/null
+++ b/contrib/sahm/pySAHM/RasterFormatConverter.py
@@ -0,0 +1,204 @@
+#!/usr/bin/python
+'''Takes an MDS file and converts all of the tiff files into
+ascii format in a supplied directory
+The optional parameter format can be used to specify other
+conversion types.
+'''
+import sys
+import csv
+import os
+import time
+import random
+import shutil
+
+import Queue
+import thread
+import subprocess
+
+from osgeo import gdalconst
+from osgeo import gdal
+
+from optparse import OptionParser
+
+import utilities
+from utilities import isMDSFile
+
+class FormatConverter(object):
+ def __init__(self):
+ #instance level variables
+ self.verbose = False
+ self.MDSFile = ''
+ self.inputDir = ''
+ self.outputDir = ''
+ self.format = 'asc'
+ self.logger = None
+ self.multicore = True
+ self.driverExt = {'asc':'AAIGrid', 'bil':'EHdr', 'img':'HFA', 'jpg':'JPEG'}
+
+ def run(self):
+ self.validateArgs()
+ if self.MDSFile <> '':
+ usedTifs = self.extractFileNames()
+ else:
+ usedTifs = self.fileNamesFromFolder()
+ #self.writetolog(' Converting: ' + ','.join(usedTifs))
+ if self.multicore:
+ self.convertEnvironmentalLayers_mc(usedTifs, self.outputDir, self.format)
+ else:
+ self.convertEnvironmentalLayers(usedTifs, self.outputDir, self.format)
+
+ def validateArgs(self):
+ argProblem = ""
+
+ if self.logger is None:
+ self.logger = utilities.logger(outDir, self.verbose)
+ self.writetolog = self.logger.writetolog
+
+ if os.path.isdir(self.inputDir):
+ pass
+ elif os.path.exists(self.MDSFile):
+ if not isMDSFile(self.MDSFile):
+ argProblem += "The supplied MDS file, " + self.MDSFile + ", does not appear to be in the appropriate format."
+ else:
+ argProblem += "Neither an input Directory or MDS File was supplied."
+
+ if not os.path.isdir(self.outputDir):
+ try:
+ os.mkdir(self.outputDir)
+ except:
+ argProblem += 'The supplied output directory, ' + self.outputDir + ", does not exist and could not be created."
+ if not self.format.lower() in self.driverExt.keys():
+ argProblem += "The supplied format must be one of " + ", ".join(self.driverExt.keys())
+
+ if argProblem:
+ raise utilities.TrappedError("There was a problem with one or more of the inputs to RasterFormatConverter")
+
+ def extractFileNames(self):
+ #Read through the MDS and pull the headers
+ MDSreader = csv.reader(open(self.MDSFile, 'r'))
+ header1 = MDSreader.next()
+ header2 = MDSreader.next()
+ header3 = MDSreader.next()
+
+ usedTifs = []
+ for i in range(3, len(header1)):
+ if header2[i] == '1' and header1[i] <> 'Split':
+ usedTifs.append(header3[i])
+ return usedTifs
+
+ def fileNamesFromFolder(self):
+ usedRasters = []
+ items = os.listdir(self.inputDir)
+ for item in items:
+# print item
+ fullPath = os.path.join(self.inputDir, item)
+ try:
+ if os.path.isdir(fullPath) or \
+ os.path.splitext(item)[1].lower() in \
+ ['.bil', '.img', '.tif', '.jpg', '.bmp', '.asc']:
+ inds = None
+ inds = gdal.Open(fullPath, gdalconst.GA_ReadOnly)
+ if inds is not None:
+ usedRasters.append(fullPath)
+ except:
+ pass
+ return usedRasters
+
+ def convertEnvironmentalLayers(self, files, outputFolder, type):
+
+ i = 1
+ for f in files:
+ f_name = os.path.splitext(os.path.split(f)[1])[0]
+ self.writetolog(' Starting on ' + f_name)
+ outputfile = os.path.join(outputFolder, f_name + '.' + type)
+ self.convertFormat(f, outputfile, self.driverExt[type])
+ if self.verbose:
+ self.writetolog(' Finished converting ' + f_name + ' ' + str(i) + ' out of ' + str(len(files)) + ' finished.')
+ i += 1
+
+ def convertEnvironmentalLayers_mc(self, files, outputFolder, type):
+ '''This function has the same functionality as convertEnvironmentalLayers
+ with the addition of utilizing multiple cores to do the processing.
+ '''
+ results = Queue.Queue()
+ process_count= 0
+
+ i = 1
+ for f in files:
+ f_name = os.path.splitext(os.path.split(f)[1])[0]
+ args = '-i ' + '"' + f + '"'
+ args += ' -o ' + '"' + outputFolder + '"'
+ args += ' -f ' + type
+# if self.verbose:
+# args += " -v"
+
+ execDir = os.path.split(__file__)[0]
+ executable = os.path.join(execDir, 'singleRasterFormatConverter.py')
+
+ pyEx = sys.executable
+ command = ' '.join([pyEx, executable, args])
+ self.logger.writetolog(command, False, False)
+ proc = subprocess.Popen( command )
+ thread.start_new_thread(utilities.process_waiter,
+ (proc, f_name, results))
+ process_count+= 1
+
+ while process_count > 0:
+ description, rc= results.get()
+
+ if rc == 0:
+ if self.verbose:
+ msg = " " + description + " finished successfully: " + \
+ str(len(files) - process_count + 1) + " done out of " \
+ + str(len(files))
+ self.logger.writetolog(msg, True, True)
+ else:
+ self.logger.writetolog("There was a problem with: " + description , True, True)
+ process_count-= 1
+
+
+ def convertFormat(self, file, outfile, driver):
+ inds = gdal.Open(file, gdalconst.GA_ReadOnly)
+
+ #ascii = "AAIGrid"
+ #bil = "EHdr"
+ Driver = gdal.GetDriverByName(driver)
+ Driver.CreateCopy(outfile, inds, 0)
+
+def main(argv):
+ usageStmt = "usage: options: -m --MDSFile -o --outputDir -f --format -v --verbose"
+ desc = "Converts all of the tif files specified in an MDS to ASCII format (or optionally other formats)"
+ parser = OptionParser(usage=usageStmt, description=desc)
+
+ parser.add_option("-v",
+ dest="verbose",
+ default=False,
+ action="store_true",
+ help="the verbose flag causes diagnostic output to print.")
+ parser.add_option("-m", "--MDSFile",
+ dest="MDSFile",
+ help="The input MDS used to determine tif inputs.")
+ parser.add_option("-o", "--outputDir",
+ dest="outputDir",
+ help="Output directory to save files in.")
+ parser.add_option("-f", "--format",
+ dest="format",
+ default='asc',
+ help="The format to convert into. 'bil', 'img', 'tif', 'jpg', 'bmp', 'asc'")
+ parser.add_option("-s", dest="multicore",
+ default=True,
+ action="store_true",
+ help="the use single-core flag causes each iteration to run on the same thread.")
+
+ (options, args) = parser.parse_args(argv)
+
+ ourFC = FormatConverter()
+ ourFC.verbose = options.verbose
+ ourFC.MDSFile = options.MDSFile
+ ourFC.outputDir = options.outputDir
+ ourFC.format = options.format
+ ourFC.multicore = options.multicore
+ ourFC.run()
+
+if __name__ == "__main__":
+ sys.exit(main(sys.argv[1:]))
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/Docs/SAHM User Help.docx b/contrib/sahm/pySAHM/Resources/Docs/SAHM User Help.docx
new file mode 100644
index 0000000..db2a430
Binary files /dev/null and b/contrib/sahm/pySAHM/Resources/Docs/SAHM User Help.docx differ
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/AppendOut.r b/contrib/sahm/pySAHM/Resources/R_Modules/AppendOut.r
new file mode 100644
index 0000000..2c2d8ee
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/AppendOut.r
@@ -0,0 +1,170 @@
+AppendOut<-function(compile.out,Header,x,out,test.split,parent){
+ Header.Length<-nrow(Header)
+ Parm.Len<-nrow(x)
+ if(file.access(compile.out,mode=0)==-1){ #if very first time through little to do
+ #A more complex than necessary way of writing a csv with several header lines
+ write.table(Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=",")
+ if(!is.null(out$dat$ma$ma.test))
+ write.table(cbind("","Train Split"),file=compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=",")
+ write.table(x,file=compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=",")
+ } else { #this else (not the first time through) goes to the very end of the function
+ input<-read.table(compile.out,fill=TRUE,sep=",")
+ Orig.Header<-input[1:Header.Length,]
+
+ if(!is.null(out$dat$ma$ma.test)){ #if there is a test train split this if lasts until after plotting
+ Train.x<-input[(Header.Length+2):(Header.Length+Parm.Len+1),]
+ Orig.Train<-input[(Header.Length+1),]
+
+ if(nrow(input)>15){ #if there is a test split in input (not in very first loop)
+ Test.x<-input[(Header.Length+Parm.Len+4):nrow(input),]
+ Orig.Test<-input[(Header.Length+Parm.Len+2):(Header.Length+Parm.Len+3),]
+ if(test.split){ # if we're hitting this on a test and not a train
+ Test.x[,ncol(Test.x)]<-x[,2]
+ class(Orig.Test[,ncol(Orig.Test)])="character"
+ Orig.Test[1,ncol(Orig.Test)]<-""
+ Orig.Test[2,ncol(Orig.Test)]<-"Test Split"
+ } else{
+ Orig.Header<-cbind(Orig.Header,Header[,2])
+ Train.x<-cbind(Train.x,x[,2])
+ Orig.Train<-cbind(Orig.Train,"Train Split")
+ }
+ } else{
+ Orig.Test=rbind(c("",""),cbind("","Test Split"))
+ Test.x=x
+ }
+
+ temp<-try(write.table(Orig.Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
+
+ while(class(temp)=="try-error"){
+ modalDialog("","Please Close the AppendedOutput.exe\ so that R can write to it then press ok to continue ","")
+ temp<-try(write.table(Orig.Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
+ }
+ try(write.table(Orig.Train,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
+ try(write.table(Train.x,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
+ try(write.table(Orig.Test,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
+ try(write.table(Test.x,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
+ if(ncol(Train.x)==ncol(Test.x) & ncol(Test.x)>2){
+
+ jpeg(file=paste(parent,"AcrossModelPerformTestTrain.jpg",sep="//"),width=1000,height=1000,pointsize=13)
+ par(mfrow=c(nrow(Train.x),1),mar=c(.2, 5, .6, 2),cex=1.1,oma=c(5, 0, 3, 0))
+ temp<-Train.x[,2:ncol(Train.x)]
+ temp<-matrix(data=as.numeric(as.matrix(temp,nrow=Par.Len)),nrow=Parm.Len,ncol=(ncol(Train.x)-1))
+ temp1<-temp
+ temp[2,]<-temp[2,]/100
+ temp[3,]<-temp[3,]/100
+ temp2<-Test.x[,2:ncol(Test.x)]
+ temp2<-matrix(data=as.numeric(as.matrix(temp2,nrow=Par.Len)),nrow=Parm.Len,ncol=(ncol(Test.x)-1))
+ temp2[2,]<-temp2[2,]/100
+ temp2[3,]<-temp2[3,]/100
+ ss<-seq(from=1,to=(ncol(Train.x)-1),by=1)
+ x.labs<-sub(" ","\n",Train.x[,1])
+ x.labs<-sub("Percent","Proportion",x.labs)
+ colors.test=c("chocolate3","gold1","darkolivegreen2","steelblue1","brown3")
+ colors.train=c("chocolate4","gold3","darkolivegreen4","steelblue4","brown4")
+ #Plot 1.
+ plot(c(0,(ncol(Test.x)+2)),c(0,1.1),type="n",xaxt="n",
+ xlab=paste("Corresponding Column in ",ifelse(!is.null(out$dat$ma$ma.test),"AppendedOutputTestTrain.csv","AppendedOutput.csv"),sep=""),
+ ylab=x.labs[1])
+ grid(nx=10)
+ legend(ncol(Test.x),y=.75,legend=c("Test","Train"),fill=c(colors.test[1],colors.train[1]))
+ rect(xleft=ss-.4,ybottom=0,xright=ss,ytop=temp[1,],col=colors.train[1],lwd=2)
+ rect(xleft=ss,ybottom=0,xright=(ss+.4),ytop=pmax(0,temp2[1,]),col=colors.test[1],lwd=2)
+ text((which(temp1[1,]==max(temp1[1,],na.rm=TRUE),arr.ind=TRUE)-.25),
+ max(temp1[1,],na.rm=TRUE)+.05,labels=as.character(round(max(temp1[1,]),digits=2)),cex=.8)
+ text((which(temp2[1,]==max(temp2[1,],na.rm=TRUE),arr.ind=TRUE)+.25),
+ max(temp2[1,],na.rm=TRUE)+.05,labels=as.character(round(max(temp2[1,]),digits=2)),cex=.8)
+ par(mar=c(.2, 5, .6, 2))
+ #Middle Plots.
+ for(i in 2:(nrow(Train.x)-1)){
+ plot(c(0,(ncol(Test.x)+2)),c(0,1.1),type="n",xaxt="n",
+ ylab=x.labs[i])
+ grid(nx=10)
+ rect(xleft=ss-.4,ybottom=0,xright=ss,ytop=temp[i,],col=colors.train[i],lwd=2)
+ rect(xleft=ss,ybottom=0,xright=(ss+.4),ytop=pmax(0,temp2[i,]),col=colors.test[i],lwd=2)
+ legend(ncol(Test.x),y=.75,legend=c("Test","Train"),fill=c(colors.test[i],colors.train[i]))
+ text((which(temp[i,]==max(temp[i,],na.rm=TRUE),arr.ind=TRUE)-.25),
+ max(temp[i,],na.rm=TRUE)+.05,labels=as.character(round(max(temp[i,]),digits=2)),cex=.8)
+ text((which(temp2[i,]==max(temp2[i,],na.rm=TRUE),arr.ind=TRUE)+.25),
+ max(temp2[i,],na.rm=TRUE)+.05,labels=as.character(round(max(temp2[i,]),digits=2)),cex=.8)
+ par(mar=c(.3, 5, .4, 2))
+ }
+ par(mar=c(2, 5, .4, 2))
+ #Last Plot.
+ i=nrow(Train.x)
+ plot(c(0,(ncol(Test.x)+2)),c(0,1.1),type="n",xaxt="n",
+ xlab="n",
+ ylab=x.labs[i])
+ grid(nx=10)
+ rect(xleft=ss-.4,ybottom=0,xright=ss,ytop=temp[i,],col=colors.train[i],lwd=2)
+ rect(xleft=ss,ybottom=0,xright=(ss+.4),ytop=pmax(0,temp2[i,]),col=colors.test[i],lwd=2)
+ legend(ncol(Test.x),y=.75,legend=c("Test","Train"),fill=c(colors.test[i],colors.train[i]))
+ text((which(temp1[i,]==max(temp1[i,],na.rm=TRUE),arr.ind=TRUE)-.25),
+ max(temp1[i,],na.rm=TRUE)+.05,labels=as.character(round(max(temp1[i,]),digits=2)),cex=.8)
+ text((which(temp2[i,]==max(temp2[i,],na.rm=TRUE),arr.ind=TRUE)+.25),
+ max(temp2[i,],na.rm=TRUE)+.05,labels=as.character(round(max(temp2[i,]),digits=2)),cex=.8)
+ #Outer margin labels
+ for(i in 2:ncol(Orig.Header)) mtext(Orig.Header[1,i],line=-12,at=(i-1),las=2)
+ mtext("Evaluation Metrics Performance Across Model Runs",outer=TRUE,side=3,cex=1.3)
+ mtext(paste("Folder Name where model is found in ",
+ ifelse(!is.null(out$dat$ma$ma.test),"AppendedOutputTestTrain.csv","AppendedOutput.csv"),sep=""),side=1,outer=TRUE,line=3)
+ dev.off()
+ }
+ } else{
+
+ Orig.x<-input[(Header.Length+1):nrow(input),]
+ temp<-try(write.table(cbind(Orig.Header,Header[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
+ while(class(temp)=="try-error"){
+ modalDialog("","Please Close the AppendedOutput.exe\ so that R can write to it then press ok to continue ","")
+ temp<-try(write.table(cbind(Orig.Header,Header[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
+ }
+ if(ncol(Orig.x)>2){
+
+ jpeg(file=paste(parent,"AcrossModelPerform.jpg",sep="//"),width=1000,height=1000,pointsize=13)
+ par(mfrow=c(5,1),mar=c(.2, 5, .6, 2),cex=1.1,oma=c(5, 0, 3, 0))
+ temp<-Orig.x[,2:ncol(Orig.x)]
+ temp<-matrix(data=as.numeric(as.matrix(temp,nrow=Par.Len)),nrow=Parm.Len,ncol=(ncol(Orig.x)-1))
+ temp1<-temp
+ temp[2,]<-temp[2,]/100
+ temp[3,]<-temp[3,]/100
+ ss<-seq(from=1,to=(ncol(Orig.x)-1),by=1)
+ x.labs<-sub(" ","\n",Orig.x[,1])
+ x.labs<-sub("Percent","Proportion",x.labs)
+ colors.train=c("chocolate4","gold3","darkolivegreen4","steelblue4","brown4")
+ #Plot 1.
+ plot(c(0,(ncol(Orig.x))),c(0,1.1),type="n",xaxt="n",ylab=x.labs[1])
+ grid(nx=10)
+ rect(xleft=ss-.3,ybottom=0,xright=ss+.3,ytop=temp[1,],col=colors.train[1],lwd=2)
+ text((which(temp1[1,]==max(temp1[1,],na.rm=TRUE),arr.ind=TRUE)),
+ max(temp1[1,],na.rm=TRUE)+.06,labels=as.character(round(max(temp1[1,]),digits=2)),cex=.8)
+ par(mar=c(.2, 5, .6, 2))
+ #Plot 2-4.
+ for(i in 2:(nrow(x)-1)){
+ plot(c(0,(ncol(Orig.x))),c(0,1.1),type="n",xaxt="n",
+ ylab=x.labs[i])
+ grid(nx=10)
+ rect(xleft=ss-.3,ybottom=0,xright=ss+.3,ytop=temp[i,],col=colors.train[i],lwd=2)
+ text((which(temp[i,]==max(temp[i,],na.rm=TRUE),arr.ind=TRUE)),
+ max(temp[i,],na.rm=TRUE)+.06,labels=as.character(round(max(temp[i,]),digits=2)),cex=.8)
+ par(mar=c(.3, 5, .4, 2))
+ }
+ par(mar=c(2, 5, .4, 2))
+ #Plot 5.
+ i=nrow(x)
+ plot(c(0,(ncol(Orig.x))),c(0,1.1),type="n",xaxt="n",
+ ylab=x.labs[i])
+ grid(nx=10)
+ rect(xleft=ss-.3,ybottom=0,xright=ss+.3,ytop=temp[i,],col=colors.train[i],lwd=2)
+ text((which(temp[i,]==max(temp[i,],na.rm=TRUE),arr.ind=TRUE)),
+ max(temp[i,],na.rm=TRUE)+.06,labels=as.character(round(max(temp[i,]),digits=2)),cex=.8)
+ #Outer margin labels
+ for(i in 2:ncol(Orig.Header)) mtext(Orig.Header[1,i],line=-12,at=(i-1),las=2)
+ mtext("Evaluation Metrics Performance Across Model Runs",outer=TRUE,side=3,cex=1.3)
+ mtext(paste("Folder Name where model is found in ",
+ ifelse(!is.null(out$dat$ma$ma.test),"AppendedOutputTestTrain.csv","AppendedOutput.csv"),sep=""),side=1,outer=TRUE,line=3)
+ dev.off()
+ }
+
+ try(write.table(cbind(Orig.x,x[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
+ }}
+ }
+
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/CompileOutput.r b/contrib/sahm/pySAHM/Resources/R_Modules/CompileOutput.r
new file mode 100644
index 0000000..82b38d9
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/CompileOutput.r
@@ -0,0 +1,12 @@
+Compile.Output<-function(out){
+last.dir<-strsplit(out$input$output.dir,split="/")
+length(last.dir[[1]])
+parent<-sub(paste("/",last.dir[[1]][length(last.dir[[1]])],sep=""),"",out$input$output.dir)
+
+txt0 <- paste("Generalized Liinear Results\n",out$input$run.time,"\n\n","Data:\n\t ",ma.name,"\n\t ","n(pres)=",
+ out$dat$ma$n.pres[2],"\n\t n(abs)=",out$dat$ma$n.abs[2],"\n\t number of covariates considered=",(length(names(out$dat$ma$ma))-1),
+ "\n\n","Settings:\n","\n\t model family=",out$input$model.family,
+ "\n\n","Results:\n\t ","number covariates in final model=",length(out$dat$ma$used.covs),
+ "\n\t pct deviance explained on train data =",round(out$mods$auc.output$pct.dev.exp,1),"%\n",
+ "\n\t total time for model fitting=",round((unclass(Sys.time())-t0)/60,2),"min\n",sep="")
+}
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/CrossValidationSplit.r b/contrib/sahm/pySAHM/Resources/R_Modules/CrossValidationSplit.r
new file mode 100644
index 0000000..a87e425
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/CrossValidationSplit.r
@@ -0,0 +1,99 @@
+CrossValidationSplit<-function(input.file,output.file,response.col="ResponseBinary",n.folds=10,stratify=FALSE){
+
+#Description:
+#this code takes as input an mds file with the first line being the predictor or
+#response name, the second line an indicator of predictors to include and the
+#third line being paths where tif files can be found. An output file and a
+#response column must also be specified. Given a number of folds, a new
+#column is created indicating which fold each observation will be assigned to
+#if a Split Column is also found (test/train split) then only the train portion
+#will be assigned a fold. Optional stratification by response is also available
+#Background points are ignored
+#by this module (they are read in, written out, but not assigned to cv folds.
+#Output is written to a csv that can be used by the
+#SAHM R modules.
+
+#Written by Marian Talbert 9/29/2011
+
+ if(n.folds<=1 | n.folds%%1!=0) stop("n.folds must be an integer greater than 1")
+ browser()
+
+ #Read input data and remove any columns to be excluded
+ dat.in<-read.csv(input.file,header=FALSE,as.is=TRUE)
+ dat<-as.data.frame(dat.in[4:dim(dat.in)[1],])
+ names(dat)<-dat.in[1,]
+
+ response<-dat[,match(tolower(response.col),tolower(names(dat)))]
+
+ if(sum(as.numeric(response)==0)==0 && !is.null(stratify)) stop("The ratio of presence to absence cannot be set with only presence data")
+
+ #Ignoring background data that might be present in the mds
+
+ bg.dat<-dat[response==-9999,]
+
+ if(dim(bg.dat)[1]!=0){
+ dat<-dat[-c(which(response==-9999,arr.ind=TRUE)),]
+ dat.in<-dat.in[-c(which(response==-9999,arr.ind=TRUE)+3),]
+ response<-response[-c(which(response==-9999,arr.ind=TRUE))]
+ bg.dat$TrainSplit=""
+ }
+
+ #this splits the training set
+ split.mask<-dat[,match(tolower("split"),tolower(names(dat)))]=="train"
+ index<-seq(1:nrow(dat))[split.mask]
+ if(stratify==TRUE){
+ dat[,ncol(dat)+1]<-NA
+ for(i in 1:names(table(response))){
+ index.i<-index[response[split.mask]==names(table(response))[i]]
+ index.i<-index.i[order(runif(length(index.i)))]
+ dat[index.i,ncol(dat)]<-c(rep(seq(1:n.folds),each=floor(length(index.i)/n.folds)),sample(seq(1:n.folds),size=length(index.i)%%n.folds,replace=FALSE))
+ }
+ } else{
+ index<-index[order(runif(length(index)))]
+ dat[index,ncol(dat)+1]<-c(rep(seq(1:n.folds),each=floor(length(index)/n.folds)),sample(seq(1:n.folds),size=length(index)%%n.folds,replace=FALSE))
+ }
+
+ #inserting data must be done in 3 steps because dat.in isn't a proper dataframe in that
+ #not all elements in a column are of the same type
+ dat.in<-dat.in[c(1:3,rownames(dat)),] #removing rows that weren't selected for the test train split
+ dat.in[4:(dim(dat.in)[1]),(dim(dat.in)[2]+1)]<-dat$TrainSplit
+ dat.in[c(1,3),(dim(dat.in)[2])]<-c("Split","")
+ dat.in[2,(dim(dat.in)[2])]<-1
+
+ if(dim(bg.dat)[1]!=0) {
+ names(bg.dat)<-names(dat.in)
+ dat.in<-rbind(dat.in,bg.dat)}
+
+ #write output files for R modules
+ write.table(dat.in,file=output.file,row.names=FALSE,col.names=FALSE,sep=",",quote=FALSE)
+
+
+ }
+
+
+ #Reading in command line arguments
+ Args <- commandArgs(T)
+ print(Args)
+ #assign default values
+
+ responseCol <- "responseBinary"
+ trainProp=.7
+ RatioPresAbs=NULL
+ #replace the defaults with passed values
+ for (arg in Args) {
+ argSplit <- strsplit(arg, "=")
+ argSplit[[1]][1]
+ argSplit[[1]][2]
+ if(argSplit[[1]][1]=="p") trainProp <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="m") RatioPresAbs <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="o") output.file <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="i") infil <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
+ }
+
+ RatioResAbs<-as.numeric(RatioPresAbs)
+ trainProp<-as.numeric(trainProp)
+
+ #Run the Test training split with these parameters
+ CrossValidationSplit(input.file=infil,output.file=output.file,response.col=responseCol,
+ trainProp=trainProp,RatioPresAbs=RatioPresAbs)
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/EvalStats.r b/contrib/sahm/pySAHM/Resources/R_Modules/EvalStats.r
new file mode 100644
index 0000000..6d566d5
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/EvalStats.r
@@ -0,0 +1,25 @@
+EvaluationStats<-function(out,thresh,train,train.pred,opt.methods=opt.methods){
+ response<-out$dat$ma$ma.test[,1]
+
+ if(out$input$model.source.file=="rf.r") {pred<-tweak.p(as.vector(predict(out$mods$final.mod,newdata=out$dat$ma$ma.test[,-1],type="prob")[,2]))
+ modelname="Random Forest"
+ }
+
+ if(out$input$model.source.file=="mars.r") {pred<-mars.predict(out$mods$final.mod,out$dat$ma$ma.test)$prediction[,1]
+ modelname="MARS"
+ }
+
+ if(out$input$model.source.file=="glm.r") {pred=glm.predict(out$mods$final.mod,out$dat$ma$ma.test)
+ modelname="GLM"
+ }
+
+ if(out$input$model.source.file=="brt.r") {pred=predict.gbm(out$mods$final.mod,out$dat$ma$ma.test,out$mods$final.mod$target.trees,type="response")
+ modelname="BRT"
+ }
+
+ auc.output<-make.auc.plot.jpg(out$dat$ma$ma.test,pred=pred,plotname=paste(out$dat$bname,"_auc_plot.jpg",sep=""),
+ modelname=modelname,test.split=TRUE,thresh=thresh,train=train,train.pred,opt.methods=opt.methods,weight=out$dat$ma$test.weights,out=out)
+
+ out$mods$auc.output<-auc.output
+
+}
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/EvalStatsHelperFcts.r b/contrib/sahm/pySAHM/Resources/R_Modules/EvalStatsHelperFcts.r
new file mode 100644
index 0000000..7fb65fd
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/EvalStatsHelperFcts.r
@@ -0,0 +1,122 @@
+"calibration" <-
+ function(obs, preds, family = "binomial")
+ {
+ #
+ # j elith/j leathwick 17th March 2005
+ # calculates calibration statistics for either binomial or count data
+ # but the family argument must be specified for the latter
+ # a conditional test for the latter will catch most failures to specify
+ # the family
+ #
+
+ if (family == "bernoulli") family <- "binomial"
+ pred.range <- max(preds) - min(preds)
+ if(pred.range > 1.2 & family == "binomial") {
+ print(paste("range of response variable is ", round(pred.range, 2)), sep = "", quote = F)
+ print("check family specification", quote = F)
+ return()
+ }
+ if(family == "binomial") {
+ pred <- preds + 1e-005
+ pred[pred >= 1] <- 0.99999
+ mod <- glm(obs ~ log((pred)/(1 - (pred))), family = binomial)
+ lp <- log((pred)/(1 - (pred)))
+ a0b1 <- glm(obs ~ offset(lp) - 1, family = binomial)
+ miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
+ ab1 <- glm(obs ~ offset(lp), family = binomial)
+ miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
+ miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
+ }
+ if(family == "poisson") {
+ mod <- glm(obs ~ log(preds), family = poisson)
+ lp <- log(preds)
+ a0b1 <- glm(obs ~ offset(lp) - 1, family = poisson)
+ miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
+ ab1 <- glm(obs ~ offset(lp), family = poisson)
+ miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
+ miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
+ }
+ calibration.result <- c(mod$coef, miller1, miller2, miller3)
+ names(calibration.result) <- c("intercept", "slope", "testa0b1", "testa0|b1", "testb1|a")
+ return(calibration.result)
+}
+
+"calc.dev" <-
+ function(obs.values, fitted.values, weights = rep(1,length(obs.values)), family="binomial", calc.mean = TRUE)
+ {
+ # j. leathwick/j. elith
+ #
+ # version 2.1 - 5th Sept 2005
+ #
+ # function to calculate deviance given two vectors of raw and fitted values
+ # requires a family argument which is set to binomial by default
+ #
+ #
+
+ if (length(obs.values) != length(fitted.values))
+ stop("observations and predictions must be of equal length")
+
+ y_i <- obs.values
+
+ u_i <- fitted.values
+
+ if (family == "binomial" | family == "bernoulli") {
+
+ deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
+ deviance <- -2 * sum(deviance.contribs * weights)
+
+ }
+
+ if (family == "poisson" | family == "Poisson") {
+
+ deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
+ deviance <- 2 * sum(deviance.contribs * weights)
+
+ }
+
+ if (family == "laplace") {
+ deviance <- sum(abs(y_i - u_i))
+ }
+
+ if (family == "gaussian") {
+ deviance <- sum((y_i - u_i) * (y_i - u_i))
+ }
+
+
+
+ if (calc.mean) deviance <- deviance/length(obs.values)
+ dev=list(deviance=deviance,dev.cont=deviance.contribs)
+ return(dev)
+
+}
+
+beachcolours<-function (heightrange, sealevel = 0, monochrome = FALSE, ncolours = if (monochrome) 16 else 64)
+{
+#this function was robbed from the spatstat library internals
+ if (monochrome)
+ return(grey(seq(0, 1, length = ncolours)))
+ stopifnot(is.numeric(heightrange) && length(heightrange) ==
+ 2)
+ stopifnot(all(is.finite(heightrange)))
+ depths <- heightrange[1]
+ peaks <- heightrange[2]
+ dv <- diff(heightrange)/(ncolours - 1)
+ epsilon <- dv/2
+ lowtide <- max(sealevel - epsilon, depths)
+ hightide <- min(sealevel + epsilon, peaks)
+ countbetween <- function(a, b, delta) {
+ max(0, round((b - a)/delta))
+ }
+ nsea <- countbetween(depths, lowtide, dv)
+ nbeach <- countbetween(lowtide, hightide, dv)
+ nland <- countbetween(hightide, peaks, dv)
+ colours <- character(0)
+ if (nsea > 0)
+ colours <- rev(rainbow(nsea, start = 3/6, end = 4/6))
+ if (nbeach > 0)
+ colours <- c(colours, rev(rainbow(nbeach, start = 3/12,
+ end = 5/12)))
+ if (nland > 0)
+ colours <- c(colours, rev(rainbow(nland, start = 0, end = 1/6)))
+ return(colours)
+}
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/EvaluationStats.r b/contrib/sahm/pySAHM/Resources/R_Modules/EvaluationStats.r
new file mode 100644
index 0000000..ca62d3d
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/EvaluationStats.r
@@ -0,0 +1,436 @@
+make.auc.plot.jpg<-function(ma.reduced,pred,plotname,modelname,test.split=FALSE,thresh=NULL,train=NULL,train.pred=NULL,opt.methods=2,weight,out){
+
+ if(is.null(weight)) weight=rep(1,times=dim(ma.reduced)[1])
+ auc.data <- data.frame(ID=1:nrow(ma.reduced),pres.abs=ma.reduced[,1],pred=pred)
+ p.bar <- sum(auc.data$pres.abs * weight) / sum(weight)
+ n.pres <- sum(auc.data$pres.abs)
+ n.abs <- nrow(auc.data)-n.pres
+
+ null.dev<-calc.dev(auc.data$pres.abs, rep(p.bar,times=length(auc.data$pres.abs)), weight, family="binomial")$deviance*nrow(ma.reduced)
+ dev.fit<-calc.dev(auc.data$pres.abs, pred, weight, family="binomial")$deviance*nrow(ma.reduced)
+ dev.exp <- null.dev - dev.fit
+ pct.dev.exp <- dev.exp/null.dev*100
+ correlation<-cor(auc.data$pres.abs,pred)
+
+ if(is.null(thresh)){
+ thresh <- as.numeric(optimal.thresholds(auc.data,opt.methods=opt.methods))[2]}
+ auc.fit <- auc(auc.data,st.dev=T)
+ if(test.split==TRUE){
+
+ jpeg(file=plotname)
+ d<-data.frame(ID=1:nrow(train),pres.abs=train[,1],pred=train.pred)
+ thresh<- as.numeric(optimal.thresholds(d,opt.methods=opt.methods))[2]
+ TestTrainRocPlot(DATA=d,opt.thresholds=thresh,add.legend=FALSE,lwd=2)
+ TestTrainRocPlot(auc.data,model.names=modelname,opt.thresholds=thresh,add.roc=TRUE,line.type=2,color="red",add.legend=FALSE)
+ legend(x=.66,y=.2,c("Training Split","Testing Split"),lty=2,col=c("black","red"),lwd=2)
+ graphics.off()} else {
+ jpeg(file=plotname)
+ TestTrainRocPlot(auc.data,model.names=modelname,opt.thresholds=thresh)
+ graphics.off()
+
+ }
+
+ cmx <- cmx(auc.data,threshold=thresh)
+ PCC <- pcc(cmx,st.dev=F)*100
+ SENS <- sensitivity(cmx,st.dev=F)
+ SPEC <- specificity(cmx,st.dev=F)
+ KAPPA <- Kappa(cmx,st.dev=F)
+ TSS <- SENS+SPEC-1
+ response<-ma.reduced$response
+
+ capture.output(cat("\n\n============================================================",
+ "\n\nEvaluation Statistics"),file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
+ if(!is.null(out$dat$ma$ma.test))
+ capture.output(cat(" applied to",ifelse(!test.split,"train","test"), "split:\n",sep=" "),
+ file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
+ capture.output(cat( "\n",
+ "\n\t Correlation Coefficient : ",cor.test(pred,response)$estimate,
+ "\n\t NULL Deviance : ",null.dev,
+ "\n\t Fit Deviance : ",dev.fit,
+ "\n\t Explained Deviance : ",dev.exp,
+ "\n\t Percent Deviance Explained : ",pct.dev.exp,
+ file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE))
+
+ capture.output(cat(
+ "\n\n Threshold Methods based on", switch(opt.methods,
+ "1"=".5 threshold",
+ "2"="Sens=Spec",
+ "3"="maximize (sensitivity+specificity)/2",
+ "4"="maximize Kappa",
+ "5"="maximize percent correctly classified",
+ "6"="predicted prevalence=observed prevalence",
+ "7"="threshold=observed prevalence",
+ "8"="mean predicted probability",
+ "9"="minimize distance between ROC plot and (0,1)",
+ ),
+ "\n\t Threshold : ",
+ thresh,
+ "\n\n\t Confusion Matrix: \n\n"),
+ print.table(cmx),
+ cat("\n\t AUC : ",auc.fit[1,1],
+ "\n\t Percent Correctly Classified : ",PCC,
+ "\n\t Sensitivity : ",SENS,
+ "\n\t Specificity : ",SPEC,
+ "\n\t Kappa : ",KAPPA,
+ "\n\t True Skill Statistic : ",TSS,"\n"),
+ file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
+
+ last.dir<-strsplit(out$input$output.dir,split="\\\\")
+ parent<-sub(paste("\\\\",last.dir[[1]][length(last.dir[[1]])],sep=""),"",out$input$output.dir)
+
+ if(!is.null(out$dat$ma$ma.test)) compile.out<-paste(parent,"AppendedOutputTestTrain.csv",sep="/")
+ else compile.out<-paste(parent,"AppendedOutput.csv",sep="/")
+
+ x=data.frame(cbind(c("Correlation Coefficient","Percent Deviance Explained","Percent Correctly Classified","Sensitivity","Specificity"),
+ c(as.vector(cor.test(pred,response)$estimate),pct.dev.exp,PCC,SENS,SPEC)))
+
+
+ Header<-cbind(c("","Original Field Data","Field Data Template","PARC Output Folder","PARC Template","Covariate Selection Name",""),
+ c(last.dir[[1]][length(last.dir[[1]])],
+ out$dat$ma$input$OrigFieldData,out$dat$ma$input$FieldDataTemp,out$dat$ma$input$ParcOutputFolder,
+ out$dat$ma$input$ParcTemplate,ifelse(length(out$dat$ma$input$CovSelectName)==0,"NONE",out$dat$ma$input$CovSelectName),""))
+ Header.Length<-nrow(Header)
+ Parm.Len<-nrow(x)
+
+ #Very first time through
+ if(file.access(compile.out,mode=0)==-1){
+ #A more complex than necessary way of writing a csv with several header lines
+ write.table(Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=",")
+ if(!is.null(out$dat$ma$ma.test))
+ write.table(cbind("","Train Split"),file=compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=",")
+ write.table(x,file=compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=",")
+ } else {
+ input<-read.table(compile.out,fill=TRUE,sep=",")
+ Orig.Header<-input[1:Header.Length,]
+
+ if(!is.null(out$dat$ma$ma.test)){
+ Train.x<-input[(Header.Length+2):(Header.Length+Parm.Len+1),]
+ Orig.Train<-input[(Header.Length+1),]
+
+ if(nrow(input)>15){
+ Test.x<-input[(Header.Length+Parm.Len+4):nrow(input),]
+ Orig.Test<-input[(Header.Length+Parm.Len+2):(Header.Length+Parm.Len+3),]
+ if(test.split){
+ Test.x[,ncol(Test.x)]<-x[,2]
+ class(Orig.Test[,ncol(Orig.Test)])="character"
+ Orig.Test[1,ncol(Orig.Test)]<-""
+ Orig.Test[2,ncol(Orig.Test)]<-"Test Split"
+ } else{
+ Orig.Header<-cbind(Orig.Header,Header[,2])
+ Train.x<-cbind(Train.x,x[,2])
+ Orig.Train<-cbind(Orig.Train,"Train Split")
+ }
+ } else{
+ Orig.Test=rbind(c("",""),cbind("","Test Split"))
+ Test.x=x
+ }
+
+ temp<-try(write.table(Orig.Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
+
+ while(class(temp)=="try-error"){
+ modalDialog("","Please Close the AppendedOutput.exe\ so that R can write to it then press ok to continue ","")
+ temp<-try(write.table(Orig.Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
+ }
+
+ try(write.table(Orig.Train,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
+ try(write.table(Train.x,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
+ try(write.table(Orig.Test,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
+ try(write.table(Test.x,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
+ } else{
+
+ Orig.x<-input[(Header.Length+1):nrow(input),]
+ temp<-try(write.table(cbind(Orig.Header,Header[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
+ while(class(temp)=="try-error"){
+ modalDialog("","Please Close the AppendedOutput.exe\ so that R can write to it then press ok to continue ","")
+ temp<-try(write.table(cbind(Orig.Header,Header[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
+ }
+
+
+ try(write.table(cbind(Orig.x,x[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
+ }}
+
+ return(list(thresh=thresh,cmx=cmx,null.dev=null.dev,dev.fit=dev.fit,dev.exp=dev.exp,pct.dev.exp=pct.dev.exp,auc=auc.fit[1,1],auc.sd=auc.fit[1,2],
+ plotname=plotname,pcc=PCC,sens=SENS,spec=SPEC,kappa=KAPPA,tss=TSS,correlation=correlation))
+}
+
+
+make.poisson.jpg<-function(ma.reduced,pred,plotname,modelname,test.split=FALSE,thresh=NULL,train=NULL,train.pred=NULL,weight,train.weight=NULL,out){
+
+ pois.data <- data.frame(ID=1:nrow(ma.reduced),pres.abs=ma.reduced[,1],pred=pred)
+ p.bar <- sum(pois.data$pres.abs * weight) / sum(weight)
+ n.pres <- sum(pois.data$pres.abs>=1)
+ n.abs <- nrow(pois.data)-n.pres
+
+ #takes into account potential weights but not offset
+
+ null.dev<-calc.dev(pois.data$pres.abs, rep(p.bar,times=length(pois.data$pres.abs)), weight, family="poisson")$deviance*nrow(ma.reduced)
+ dev.fit<-calc.dev(pois.data$pres.abs, pred, weight, family="poisson")$deviance*nrow(ma.reduced)
+ dev.exp <- null.dev - dev.fit
+ pct.dev.exp <- dev.exp/null.dev*100 #this is the pseudo R^2 using definition in the course notes
+ correlation<-cor(pois.data$pres.abs,pred)
+ #calibration(pois.data$pres.abs,pred,family="poisson") gbm hasn't implimented this for poisson though elith and leathwich use it, I can't find much
+ prediction.error<-sum((pois.data$pres.abs-pred)^2)
+
+ ## ADD Weights and offset?
+ #function (y, mu, wt)
+ #2 * wt * (y * log(ifelse(y == 0, 1, y/mu)) - (y - mu))
+
+ if(test.split==TRUE){
+ if(is.null(train.weight)) train.weight=rep(1,times=nrow(train))
+ null.dev.train<-calc.dev(train$response, rep(mean(train$response),times=nrow(train)), train.weight, family="poisson")$deviance*nrow(train)
+ dev.fit.train<-calc.dev(train$response, train.pred, train.weight, family="poisson")$deviance*nrow(train)
+ dev.exp.train <- null.dev.train - dev.fit.train
+ pct.dev.exp.train <- dev.exp.train/null.dev.train*100
+ correlation.train<-cor(train$response,train.pred)
+
+ jpeg(file=plotname)
+ dev.contrib<-calc.dev(pois.data$pres.abs, pred, weight, family="poisson")$dev.cont
+ par(mfrow=c(3,2))
+ z<-sign(pred-pois.data$pres.abs)*dev.contrib
+ z.range<-max(z)-min(z)
+ z.lim<-c((min(z)-.1*z.range),(max(z)+.1*z.range))
+ breaks<-quantile(z, probs = seq(0, .95,length=25))
+ a<-outer(z,breaks,"<")
+ res.mag<-apply(a,1,sum)
+ plot(out$dat$ma$test.xy,col=beachcolours(heightrange=c(min(res.mag),max(res.mag)),sealevel=mean(res.mag),ncolours=length(table(res.mag)))[res.mag],cex=4,pch=19)
+ x<-out$dat$ma$test.xy[,1]
+ y<-out$dat$ma$test.xy[,2]
+ a<-loess(z~x*y)
+ x.lim<-rep(seq(from=min(out$dat$ma$test.xy[,1]),to=max(out$dat$ma$test.xy[,1]),length=100),each=100)
+ y.lim<-rep(seq(from=min(out$dat$ma$test.xy[,2]),to=max(out$dat$ma$test.xy[,2]),length=100),times=100)
+ z<-predict(a,newdata=cbind("x"=x.lim,"y"=y.lim))
+ z[z>z.lim[2]]<-NA
+ z[z<z.lim[1]]<-NA
+ breaks<-quantile(na.omit(z), probs = seq(0, .95,length=25))
+ a<-outer(z,breaks,"<")
+ res.mag<-apply(a,1,sum)
+ z<-matrix(data=z,ncol=100,nrow=100,byrow=TRUE)
+ res.mag<-matrix(data=res.mag,ncol=100,nrow=100,byrow=TRUE)
+ image(x=seq(from=min(x.lim),to=max(x.lim),length=100),y=seq(from=min(y.lim),to=max(y.lim),length=100),
+ z=res.mag,
+ col=beachcolours(heightrange=c(min(na.omit(res.mag)),max(na.omit(res.mag))),sealevel=mean(na.omit(res.mag)),
+ ncolours=length(table(na.omit(res.mag)))),xlab="Latitude",ylab="Longitude",
+ main="Smoothed deviance residuals over space")
+
+ points(out$dat$ma$train.xy,pch=19,cex=1)
+ #plot(unique(x.lim),apply(z,2,sum))
+ #plot(unique(y.lim),apply(z,1,sum))
+
+ mod.resids<-residuals(out$mods$final.mod,type="deviance")
+ plot(pred,(pois.data$pres.abs-pred),xlab="Predicted Values",ylab="Residuals",main="Residuals vs Fitted")
+ panel.smooth(pred,(pois.data$pres.abs-pred))
+ plot(pred,sqrt(2*dev.contrib),ylab="sqrt(Std.deviance residuals)",xlab="Predicted Values",main="Scale Location")
+ panel.smooth(pred,sqrt(2*dev.contrib))
+ qqnorm((sqrt(2*dev.contrib)-mean(sqrt(2*dev.contrib))),ylab="Std.Deviance residuals")
+ abline(0,1)
+
+ graphics.off()
+ return(list(null.dev=null.dev,dev.fit=dev.fit,dev.exp=dev.exp,pct.dev.exp=pct.dev.exp,correlation=correlation,
+ null.dev.train=null.dev.train,dev.fit.train=dev.fit.train,dev.exp.train=dev.exp.train,pct.dev.exp.train=pct.dev.exp.train,correlation.train=correlation.train))
+
+ }else{
+ jpeg(file=plotname)
+
+ dev.contrib<-calc.dev(pois.data$pres.abs, pred, weight, family="poisson")$dev.cont
+ par(mfrow=c(3,2))
+
+ dev.contrib<-calc.dev(pois.data$pres.abs, pred, weight, family="poisson")$dev.cont
+ z<-sign(pred-pois.data$pres.abs)*dev.contrib
+ breaks<-quantile(z, probs = seq(0, .95,length=25))
+ a<-outer(z,breaks,"<")
+ res.mag<-apply(a,1,sum)
+ plot(out$dat$ma$train.xy,col=heat.colors(24)[res.mag],cex=4,pch=19)
+ x<-out$dat$ma$train.xy[,1]
+ y<-out$dat$ma$train.xy[,2]
+ a<-loess(z~x*y)
+ x.lim<-rep(seq(from=min(out$dat$ma$train.xy[,1]),to=max(out$dat$ma$train.xy[,1]),length=100),each=100)
+ y.lim<-rep(seq(from=min(out$dat$ma$train.xy[,2]),to=max(out$dat$ma$train.xy[,2]),length=100),times=100)
+ z<-predict(a,newdata=cbind("x"=x.lim,"y"=y.lim))
+ breaks<-quantile(z, probs = seq(0, .95,length=25))
+ a<-outer(z,breaks,"<")
+ res.mag<-apply(a,1,sum)
+ z<-matrix(data=z,ncol=100,nrow=100,byrow=TRUE)
+ res.mag<-matrix(data=res.mag,ncol=100,nrow=100,byrow=TRUE)
+
+ image(x=seq(from=min(x.lim),to=max(x.lim),length=100),y=seq(from=min(y.lim),to=max(y.lim),length=100),
+ z=res.mag,
+ col=beachcolours(heightrange=c(min(res.mag),max(res.mag)),sealevel=mean(res.mag),ncolours=length(table(res.mag))),xlab="Latitude",ylab="Longitude",
+ main="Smoothed deviance residuals over space")
+ points(out$dat$ma$train.xy,pch=19)
+ #plot(unique(x.lim),apply(z,2,sum))
+ #plot(unique(y.lim),apply(z,1,sum))
+
+ mod.resids<-residuals(out$mods$final.mod,type="deviance")
+ plot(pred,(pois.data$pres.abs-pred),xlab="Predicted Values",ylab="Residuals",main="Residuals vs Fitted")
+ panel.smooth(pred,(pois.data$pres.abs-pred))
+ plot(pred,sqrt(2*dev.contrib),ylab="sqrt(Std.deviance residuals)",xlab="Predicted Values",main="Scale Location")
+ panel.smooth(pred,sqrt(2*dev.contrib))
+ qqnorm((sqrt(2*dev.contrib)-mean(sqrt(2*dev.contrib))),ylab="Std.Deviance residuals")
+ abline(0,1)
+
+ graphics.off()
+
+ capture.output(cat("\n\nEvaluation Statistics applied to test split:\n",
+ "\n\t Correlation Coefficient : ",cor.test(pred,response)$estimate,
+ "\n\t NULL Deviance : ",auc.output$null.dev,
+ "\n\t Fit Deviance : ",auc.output$dev.fit,
+ "\n\t Explained Deviance : ",auc.output$dev.exp,
+ "\n\t Percent Deviance Explained : ",auc.output$pct.dev.exp,
+ file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE))
+
+ return(list(null.dev=null.dev,dev.fit=dev.fit,dev.exp=dev.exp,pct.dev.exp=pct.dev.exp,correlation=correlation))
+ }
+}
+
+##############################################################################
+EvaluationStats<-function(out,thresh,train,train.pred,opt.methods=opt.methods){
+ response<-out$dat$ma$ma.test[,1]
+
+ if(out$input$model.source.file=="rf.r") {pred<-tweak.p(as.vector(predict(out$mods$final.mod,newdata=out$dat$ma$ma.test[,-1],type="prob")[,2]))
+ modelname="Random Forest"
+ }
+
+ if(out$input$model.source.file=="mars.r") {pred<-mars.predict(out$mods$final.mod,out$dat$ma$ma.test)$prediction[,1]
+ modelname="MARS"
+ }
+
+ if(out$input$model.source.file=="glm.r") {pred=glm.predict(out$mods$final.mod,out$dat$ma$ma.test)
+ modelname="GLM"
+ }
+
+ if(out$input$model.source.file=="brt.r") {pred=predict.gbm(out$mods$final.mod,out$dat$ma$ma.test,out$mods$final.mod$target.trees,type="response")
+ modelname="BRT"
+ }
+
+ ifelse(out$input$model.family!="poisson",
+ auc.output<-make.auc.plot.jpg(out$dat$ma$ma.test,pred=pred,plotname=paste(out$dat$bname,"_auc_plot.jpg",sep=""),
+ modelname=modelname,test.split=TRUE,thresh=thresh,train=train,train.pred,opt.methods=opt.methods,weight=out$dat$ma$test.weights,out=out),
+ auc.output<-make.poisson.jpg(out$dat$ma$ma.test,pred=pred,plotname=paste(out$dat$bname,"_auc_plot.jpg",sep=""),
+ modelname=modelname,test.split=TRUE,thresh=thresh,train=train,train.pred,weight=out$dat$ma$test.weights,out=out))
+
+ out$mods$auc.output<-auc.output
+
+}
+
+"calibration" <-
+ function(obs, preds, family = "binomial")
+ {
+ #
+ # j elith/j leathwick 17th March 2005
+ # calculates calibration statistics for either binomial or count data
+ # but the family argument must be specified for the latter
+ # a conditional test for the latter will catch most failures to specify
+ # the family
+ #
+
+ if (family == "bernoulli") family <- "binomial"
+ pred.range <- max(preds) - min(preds)
+ if(pred.range > 1.2 & family == "binomial") {
+ print(paste("range of response variable is ", round(pred.range, 2)), sep = "", quote = F)
+ print("check family specification", quote = F)
+ return()
+ }
+ if(family == "binomial") {
+ pred <- preds + 1e-005
+ pred[pred >= 1] <- 0.99999
+ mod <- glm(obs ~ log((pred)/(1 - (pred))), family = binomial)
+ lp <- log((pred)/(1 - (pred)))
+ a0b1 <- glm(obs ~ offset(lp) - 1, family = binomial)
+ miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
+ ab1 <- glm(obs ~ offset(lp), family = binomial)
+ miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
+ miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
+ }
+ if(family == "poisson") {
+ mod <- glm(obs ~ log(preds), family = poisson)
+ lp <- log(preds)
+ a0b1 <- glm(obs ~ offset(lp) - 1, family = poisson)
+ miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
+ ab1 <- glm(obs ~ offset(lp), family = poisson)
+ miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
+ miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
+ }
+ calibration.result <- c(mod$coef, miller1, miller2, miller3)
+ names(calibration.result) <- c("intercept", "slope", "testa0b1", "testa0|b1", "testb1|a")
+ return(calibration.result)
+}
+
+"calc.dev" <-
+ function(obs.values, fitted.values, weights = rep(1,length(obs.values)), family="binomial", calc.mean = TRUE)
+ {
+ # j. leathwick/j. elith
+ #
+ # version 2.1 - 5th Sept 2005
+ #
+ # function to calculate deviance given two vectors of raw and fitted values
+ # requires a family argument which is set to binomial by default
+ #
+ #
+
+ if (length(obs.values) != length(fitted.values))
+ stop("observations and predictions must be of equal length")
+
+ y_i <- obs.values
+
+ u_i <- fitted.values
+
+ if (family == "binomial" | family == "bernoulli") {
+
+ deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
+ deviance <- -2 * sum(deviance.contribs * weights)
+
+ }
+
+ if (family == "poisson" | family == "Poisson") {
+
+ deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
+ deviance <- 2 * sum(deviance.contribs * weights)
+
+ }
+
+ if (family == "laplace") {
+ deviance <- sum(abs(y_i - u_i))
+ }
+
+ if (family == "gaussian") {
+ deviance <- sum((y_i - u_i) * (y_i - u_i))
+ }
+
+
+
+ if (calc.mean) deviance <- deviance/length(obs.values)
+ dev=list(deviance=deviance,dev.cont=deviance.contribs)
+ return(dev)
+
+}
+
+beachcolours<-function (heightrange, sealevel = 0, monochrome = FALSE, ncolours = if (monochrome) 16 else 64)
+{
+#this function was robbed from the spatstat library internals
+ if (monochrome)
+ return(grey(seq(0, 1, length = ncolours)))
+ stopifnot(is.numeric(heightrange) && length(heightrange) ==
+ 2)
+ stopifnot(all(is.finite(heightrange)))
+ depths <- heightrange[1]
+ peaks <- heightrange[2]
+ dv <- diff(heightrange)/(ncolours - 1)
+ epsilon <- dv/2
+ lowtide <- max(sealevel - epsilon, depths)
+ hightide <- min(sealevel + epsilon, peaks)
+ countbetween <- function(a, b, delta) {
+ max(0, round((b - a)/delta))
+ }
+ nsea <- countbetween(depths, lowtide, dv)
+ nbeach <- countbetween(lowtide, hightide, dv)
+ nland <- countbetween(hightide, peaks, dv)
+ colours <- character(0)
+ if (nsea > 0)
+ colours <- rev(rainbow(nsea, start = 3/6, end = 4/6))
+ if (nbeach > 0)
+ colours <- c(colours, rev(rainbow(nbeach, start = 3/12,
+ end = 5/12)))
+ if (nland > 0)
+ colours <- c(colours, rev(rainbow(nland, start = 0, end = 1/6)))
+ return(colours)
+}
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_BRT_pluggable.r b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_BRT_pluggable.r
new file mode 100644
index 0000000..f336475
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_BRT_pluggable.r
@@ -0,0 +1,2505 @@
+# A set of "pluggable" R functions for automated model fitting of boosted regression trees models to presence/absence data #
+#
+# Modified 12-2-09 to: remove categorical covariates from consideration if they only contain one level
+# ID factor variables based on "categorical" prefix and look for tifs in subdir
+# Give progress reports
+# write large output tif files in blocks to alleviate memory issues
+# various bug fixes
+#
+# Modified 3-4-09 to use a list object for passing of arguements and data
+#
+# Modified in early 2009 to incorporate new tools and methods as described in
+# Elith et al, 2008. The new algorithm:
+# 1. Subsets the data to a maximum of 500 used and 500 available to pick settings and
+# perform model selection.
+# 2. Fits a models using a range of learning rates to find a rate which produces an optimal number of ~1000 trees.
+# 3.
+# Modified 12-30-08 to use directories that don't end with a forward slash
+#
+# Modified 8-19-08 to include the creation of a image info table.
+# Modified 8-8-8 to modularize the model array input, and to include and xml output summary.
+# also added "debug.mode" to make debugging easier on my end.
+# Modified on 6-30-08 to avoid writing to directories other the 'output.dir' spec'd in the
+# command line arguements. If this arguement is not defined, output may still be written
+# to the input directories.
+# Modified on 6-27-08 to take in additional arguements for a file directory (containing
+# the .tif files used for prediction) and an output directory. Command line args are now
+# (note: ma=model array): 1. ma.name, 2. cov.list.name, 3. factor.list.name, 4. ma.dir,
+# 5. tif.dir, 6. output.dir. Also note that directories need to use forward slashes and end
+# with a forward slash.
+# modified on 6-24-08 to be 'pluggable'. The last 20 lines of code interpret command line
+# arguements and run the glm model.
+# modified on 6-23-08 to handle factor variables.
+# modified on 6-18-08 to remove MARS code.
+# modified on 6-18-08 to include new function to return covariate names from a model.
+# modified on 5/15/08 to fit both Logistic and MARS models
+
+
+# Libraries required to run this program #
+# PresenceAbsence - for ROC plots
+# XML - for XML i/o
+# rgdal - for geotiff i/o
+# gbm
+# gbmplus - not on CRAN, see elith et al or contact me.
+# survival - used by gbm library
+# splines - used by gbm library
+# lattice - used by gbm library
+# sp - used by rdgal library
+options(error=NULL)
+
+fit.brt.fct <- function(ma.name,tif.dir=NULL,output.dir=NULL,response.col="^response.binary",make.p.tif=T,make.binary.tif=T,
+ simp.method="cross-validation",debug.mode=F,responseCurveForm="jpg",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
+ learning.rate = NULL, bag.fraction = 0.5,
+ prev.stratify = TRUE, model.family = "bernoulli",max.trees = 10000,tolerance.method = "auto",
+ tolerance = 0.001,seed=NULL,opt.methods=2,save.model=TRUE,UnitTest=FALSE,MESS=FALSE){
+
+# Possibly to add later
+# offset = NULL, fold.vector = NULL, var.monotone = rep(0,length(gbm.x))
+
+# offset = NULL, # allows an offset to be specified
+# fold.vector = NULL, # allows a fold vector to be read in for CV with offsets,
+# tree.complexity = 1, # sets the complexity of individual trees
+# learning.rate = 0.01, # sets the weight applied to inidivudal trees
+# bag.fraction = 0.75, # sets the proportion of observations used in selecting variables
+# site.weights = rep(1, nrow(dat)), # allows varying weighting for sites
+# var.monotone = rep(0, length(gbm.x)), # restricts responses to individual predictors to monotone
+# n.folds = 10, # number of folds
+# prev.stratify = TRUE, # prevalence stratify the folds - only for p/a data
+# family = "bernoulli", # family - bernoulli (=binomial), poisson, laplace or gaussian
+# n.trees = 50, # number of initial trees to fit
+# step.size = n.trees, # numbers of trees to add at each cycle
+# max.trees = 10000, # max number of trees to fit before stopping
+# tolerance.method = "auto", # method to use in deciding to stop - "fixed" or "auto"
+# tolerance = 0.001, # tolerance value to use - if method == fixed is absolute,
+# seed=NULL # sets a seed for the algorithm, any inegeger is acceptable
+# opt.methods=2 # sets the method used for threshold optimization used in the
+# # the evaluation statistics module
+# save.model=FALSE # whether the model will be used to later produce tifs
+
+ # This function fits a boosted regression tree model to presence-absence data.
+ # written by Alan Swanson, Jan-March 2009
+ # uses code modified from that published in Elith et al 2008
+ # Maintained and edited by Marian Talbert September 2010-
+ #
+ # Arguements.
+ # ma.name: is the name of a .csv file with a model array. full path must be included unless it is in the current
+ # R working directory #
+ # tif.dir: is the directory containing geotiffs for each covariate. only required if geotiffs output of the
+ # response surface is requested # # cov.list.name: is the name of a text file with the names of covariates to be included in models (one per line).
+ # output.dir: is the directory that output files will be stored in. if not given, files will go to the current working directory.
+ # response.col: column number of the model array containing a binary 0/1 response. all other columns will be considered explanatory variables.
+ # make.p.tif: T if a geotiff of the response surface is desired.
+ # make.binary.tif: T if a geotiff of the response surface is desired.
+ # simp.method: model simplification method. valid methods include: "cross-validation", "rel-inf", and "none". "cross-validation" uses the
+ # methods of Elith et al, 2008 for removing covariates that don't contribute to the model. "rel-inf" simply removes covariates that contribute
+ # less than 1%. cross-validation is very slow - it can add up to 10min to a run.
+ # debug.mode: if T, output is directed to the console during the run. also, a pdf is generated which contains response curve plots and perspective plots
+ # showing the effects of interactions deemed important. if F, output is diverted to a text file and the console is kept clear
+ # except for final output of an xml file. in either case, a set of standard output files are created in the output directory.
+ # tc: tree-complexity for brt fits. if specified, this sets the tree-complexity of the final model fit. A lower tree-complexity will be used for
+ # model selection steps. if not set, this will be estimated loosely following the guidelines given by Elith et al, 2008.
+ #
+
+ # Value:
+ # returns nothing but generates a number of output files in the directory
+ # "output.dir" named above. These output files consist of:
+ #
+ # brt_output.txt: a text file with fairly detailed results of the final model.
+ # brt_output.xml: an xml-formatted text file with results from the final model.
+ # brt_response_curves.xml: an xml-formatted text file with response curves for
+ # each covariate in the final model.
+ # brt_prob_map.tif: a geotiff of the response surface
+ # brt_bin_map.tif: a geotiff of the binary response surface. threhold is based on the roc curve at the point where sensitivity=specificity.
+ # brt_log.txt: a file containing text output diverted from the console when debug.mode=F
+ # brt_auc_plot.jpg: a jpg file of a ROC plot.
+ # brt_response_curves.pdf: an pdf file with response curves for
+ # each covariate in the final model and perspective plots showing the effect of interactions deemed significant.
+ # only produced when debug.mode=T
+ #
+ # when debug.mode is true, these filenames will include a number in them so that they will not overwrite preexisting files. eg brt_1_output.txt.
+ #
+ times <- as.data.frame(matrix(NA,nrow=8,ncol=1,dimnames=list(c("start","read data","model tuning","model fit",
+ "model summary","response curves","tif output","done"),c("time"))))
+ times[1,1] <- unclass(Sys.time())
+ t0 <- unclass(Sys.time())
+
+ #simp.method <- match.arg(simp.method)
+ out <- list(
+ input=list(ma.name=ma.name,
+ tif.dir=tif.dir,
+ output.dir=output.dir,
+ response.col=response.col,
+ make.p.tif=make.p.tif,
+ make.binary.tif=make.binary.tif,
+ tc=tc,
+ save.model=save.model,
+ learning.rate=learning.rate,
+ n.folds=n.folds,
+ bag.fraction=bag.fraction,
+ prev.stratify=prev.stratify,
+ model.family=model.family,
+ max.trees=max.trees,
+ tolerance.method=tolerance.method,
+ tolerance=tolerance,
+ simp.method=simp.method,
+ alpha=alpha,
+ model.type="boosted regression tree",
+ model.source.file=script.name,
+ model.fitting.subset=c(n.pres=500,n.abs=500),
+ run.time=paste(c(format(Sys.time(),"%Y-%m-%d"),format(Sys.time(),"%H:%M:%S")),collapse="T"),
+ sig.test="relative influence",
+ MESS=MESS),
+ dat = list(missing.libs=NULL,
+ output.dir=list(dname=NULL,exist=F,readable=F,writable=F),
+ tif.dir=list(dname=NULL,exist=F,readable=F,writable=F),
+ tif.ind=NULL,
+ tif.names=NULL,
+ bname=NULL,
+ bad.factor.covs=NULL, # factorchange
+ ma=list( status=c(exists=F,readable=F),
+ dims=c(NA,NA),
+ n.pres=c(all=NA,complete=NA,subset=NA,test=NA),
+ n.abs=c(all=NA,complete=NA,subset=NA,test=NA),
+ ratio=NA,
+ resp.name=NULL,
+ factor.levels=NA,
+ used.covs=NULL,
+ ma=NULL,
+ train.weights=NULL,
+ test.weights=NULL,
+ train.xy=NULL,
+ test.xy=NULL,
+ ma.subset=NULL,
+ weight.subset=NULL),
+ ma.test=NULL),
+ mods=list(parms=list(n.target.trees=1000,tc.full=tc,tc.sub=tc),
+ lr.mod=NULL,
+ simp.mod=NULL,
+ final.mod=NULL,
+ r.curves=NULL,
+ tif.output=list(prob=NULL,bin=NULL),
+ auc.output=NULL,
+ interactions=NULL,
+ summary=NULL),
+ time=list(strt=unclass(Sys.time()),end=NULL),
+ error.mssg=list(NULL),
+ ec=0
+ )
+ if(!is.null(seed)) set.seed(seed)
+ # load libaries #
+
+ out <- check.libs(list("PresenceAbsence","rgdal","XML","sp","survival","lattice","raster","tcltk2","foreign","ade4","gbm"),out)
+
+ # exit program now if there are missing libraries #
+ if(!is.null(out$error.mssg[[1]])){
+ cat(saveXML(brt.to.xml(out),indent=T),'\n')
+ return()
+ }
+
+ if(is.na(match(simp.method,c("cross-validation","rel-inf","none")))){
+ out$ec <- out$ec+1
+ out$error.mssg[[out$ec]] <- "ERROR: arguement simp.method must be either cross-validation, rel-inf, or none"
+ cat(saveXML(brt.to.xml(out),indent=T),'\n')
+ return()
+ }
+
+ #if(simplify.brt==T) out$input$simp.method<-"cross-validation" else out$input$simp.method<-">1% rel. influence"
+
+ # check output dir #
+ out$dat$output.dir <- check.dir(output.dir)
+ if(out$dat$output.dir$writable==F) {out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: output directory",output.dir,"is not writable")
+ out$dat$output.dir$dname <- getwd()
+ }
+
+ # generate a filename for output #
+ if(debug.mode==T){
+ outfile <- paste(bname<-paste(out$dat$output.dir$dname,"/brt_",n<-1,sep=""),"_output.txt",sep="")
+ while(file.access(outfile)==0) outfile<-paste(bname<-paste(out$dat$output.dir$dname,"/brt_",n<-n+1,sep=""),"_output.txt",sep="")
+ capture.output(cat("temp"),file=outfile) # reserve the new basename #
+ } else bname <- paste(out$dat$output.dir$dname,"/brt",sep="")
+ out$dat$bname <- bname
+
+ # sink console output to log file #
+ if(!debug.mode) {sink(logname <- paste(bname,"_log.txt",sep=""));on.exit(sink)} else logname<-NULL
+ options(warn=1)
+
+ # check tif dir #
+ if(!is.null(tif.dir)){
+ out$dat$tif.dir <- check.dir(tif.dir)
+ if(out$dat$tif.dir$readable==F & (out$input$make.binary.tif | out$input$make.p.tif)) {
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: tif directory",tif.dir,"is not readable")
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ cat(saveXML(brt.to.xml(out),indent=T),'\n')
+ return()
+ }
+ }
+
+ # find .tif files in tif dir #
+
+ if(out$dat$tif.dir$readable) out$dat$tif.names <- list.files(out$dat$tif.dir$dname,pattern=".tif",recursive=T)
+
+ # check for model array #
+ out$input$ma.name <- check.dir(out$input$ma.name)$dname
+ out <- read.ma(out)
+ if(UnitTest==1) return(out)
+ # exit program now if there are errors in the input data #
+ if(!is.null(out$error.mssg[[1]])){
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ cat(saveXML(brt.to.xml(out),indent=T),'\n')
+ return()
+ }
+
+ cat("\nbegin processing of model array:",out$input$ma.name,"\n")
+ cat("\nfile basename set to:",out$dat$bname,"\n")
+ if(debug.mode) assign("out",out,envir=.GlobalEnv)
+ if(!debug.mode) {sink();cat("Progress:20%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("20%\n")} ### print time
+ ##############################################################################################################
+ # Begin model fitting #
+ ##############################################################################################################
+
+ # estimate optimal learning rate and tc # o
+
+ if(out$input$model.family=="binomial") out$input$model.family="bernoulli"
+ out <-est.lr(out)
+ if(debug.mode) assign("out",out,envir=.GlobalEnv)
+
+ # exit program now if lr estimation fails #
+ if(!is.null(out$error.mssg[[1]])){
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ cat(saveXML(brt.to.xml(out),indent=T),'\n')
+ return()}
+
+ cat("\nfinished with learning rate estimation, lr=",out$mods$lr.mod$lr0,", t=",round(out$mods$lr.mod$t.elapsed,2),"sec\n")
+ cat("\nfor final fit, lr=",out$mods$lr.mod$lr,"and tc=",out$mods$parms$tc.full,"\n");flush.console()
+ if(!debug.mode) {sink();cat("Progress:30%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("30%\n")}
+
+ if(out$input$simp.method=="cross-validation"){
+ # remove variables with <1% relative influence and re-fit model
+ print(debug.mode)
+ t1 <- unclass(Sys.time())
+ if(length(out$mods$lr.mod$good.cols)<=1) stop("BRT must have at least two independent variables")
+ m0 <- gbm.step.fast(dat=out$dat$ma$ma.subset,gbm.x=out$mods$lr.mod $good.cols,gbm.y=1,family=out$input$model.family,
+ n.trees = c(300,600,800,1000,1200,1500,1800),step.size=out$input$step.size,max.trees=out$input$max.trees,
+ tolerance.method=out$input$tolerance.method,tolerance=out$input$tolerance, n.folds=out$input$n.folds,tree.complexity=out$mods$parms$tc.sub,
+ learning.rate=out$mods$lr.mod$lr0,bag.fraction=out$input$bag.fraction,site.weights=out$dat$ma$weight.subset,autostop=T,debug.mode=F,silent=!debug.mode,
+ plot.main=F,superfast=F)
+ if(debug.mode) assign("m0",m0,envir=.GlobalEnv)
+
+ t1b <- unclass(Sys.time())
+ if(!debug.mode) {sink();cat("Progress:40%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("40%\n")}
+ cat("\nfinished with trimmed model fitting, n.trees=",m0$target.trees,", t=",round(t1b-t1,2),"sec\n");flush.console()
+ cat("\nbeginning model simplification - very slow...\n");flush.console()
+ out$mods$simp.mod <- gbm.simplify(m0,n.folds=out$input$n.folds,plot=F,verbose=F,alpha=out$input$alpha) # this step is very slow #
+ if(debug.mode) assign("out",out,envir=.GlobalEnv)
+
+ out$mods$simp.mod$good.cols <- out$mods$simp.mod$pred.list[[length(out$mods$simp.mod$pred.list)]]
+ out$mods$simp.mod$good.vars <- names(out$dat$ma$ma)[out$mods$simp.mod$good.cols]
+ cat("\nfinished with model simplification, t=",round((unclass(Sys.time())-t1b)/60,2),"min\n");flush.console()
+ if(!debug.mode) {sink();cat("Progress:50%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("50%\n")}
+ }
+
+ # fit final model #
+ t2 <- unclass(Sys.time())
+
+ if(out$mods$lr.mod$lr==0) out$mods$lr.mod$lr<-out$mods$lr.mod$lr0
+ out$mods$final.mod <- gbm.step.fast(dat=out$dat$ma$ma,gbm.x=out$mods$simp.mod$good.cols,gbm.y = 1,family=out$input$model.family,
+ n.trees = c(300,600,700,800,900,1000,1200,1500,1800,2200,2600,3000,3500,4000,4500,5000),n.folds=out$input$n.folds,
+ tree.complexity=out$mods$parms$tc.full,learning.rate=out$mods$lr.mod$lr,bag.fraction=out$input$bag.fraction,site.weights=out$dat$ma$train.weights,
+ autostop=T,debug.mode=F,silent=!debug.mode,plot.main=F,superfast=F)
+
+
+
+ assign("out",out,envir=.GlobalEnv)
+
+ t3 <- unclass(Sys.time())
+ cat("\nfinished with final model fitting, n.trees=",out$mods$final.mod$target.trees,", t=",round(t3-t2,2),"sec\n\n\n");flush.console()
+ if(!debug.mode) {sink();cat("Progress:60%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("60%\n")}
+
+ ##############################################################################################################
+ # Begin model output #
+ ##############################################################################################################
+
+ # Store .jpg ROC plot #
+
+ # Generate and store text summary #
+ y <- gbm.interactions(out$mods$final.mod)
+ if(debug.mode) assign("out",out,envir=.GlobalEnv)
+ if(class(y)!="try-error"){
+ int <- y$rank.list;
+ int<-int[int$p<.05,]
+ int <- int[order(int$p),]
+ int$p <- round(int$p,4)
+ names(int) <- c("v1","name1","v2","name2","int.size","p-value")
+ row.names(int)<-NULL
+ if(nrow(int)>0) out$mods$interactions <- int else out$mods$interactions <- NULL
+ } else {
+ out$ec <-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: problem assessing interactions:",y)
+ }
+
+ model.summary <- summary(out$mods$final.mod,plotit=F)
+ if(class(model.summary)=="try-error"){
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: can't generate summary of final model:",model.summary)
+ cat(saveXML(brt.to.xml(out),indent=T),'\n')
+ return()
+ } else {
+ out$mods$summary <- model.summary
+ }
+ if(debug.mode) assign("out",out,envir=.GlobalEnv)
+
+
+
+ if(!is.null(out$dat$bad.factor.cols)){
+ capture.output(cat("\nWarning: the following categorical response variables were removed from consideration\n",
+ "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n"),
+ file=paste(bname,"_output.txt",sep=""),append=T)
+ cat("\nWarning: the following categorical response variables were removed from consideration\n",
+ "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n\n")
+ }
+
+
+ txt0 <- paste("\nBoosted Regression Tree Modeling Results\n",out$input$run.time,"\n\n",
+ "Data:\n",ma.name,"\n",
+ "\n\tn(pres)=",out$dat$ma$n.pres[2],
+ "\n\tn(abs)=",out$dat$ma$n.abs[2],
+ "\n\tn covariates considered=",length(out$dat$ma$used.covs),
+ "\n\n","Settings:\n",
+ "\n\ttree complexity=",out$mods$parms$tc.full,
+ "\n\tlearning rate=",round(out$mods$lr.mod$lr,4),
+ "\n\tn(trees)=",out$mods$final.mod$target.trees,
+ "\n\tmodel simplification=",out$input$simp.method,
+ "\n\tn folds=",out$input$n.folds,
+ "\n\tn covariates in final model=",nrow(out$mods$final.mod$contributions),
+ "\n\ttotal time for model fitting=",round((unclass(Sys.time())-t0)/60,2),"min\n",sep="")
+ txt1 <- "\nRelative influence of predictors in final model:\n\n"
+ txt2 <- "\nImportant interactions in final model:\n\n"
+
+ capture.output(cat(txt0),cat(txt1),print(out$mods$final.mod$contributions),cat(txt2),print(out$mods$interactions,row.names=F),file=paste(bname,"_output.txt",sep=""))
+ cat(txt0);cat(txt1);print(out$mods$final.mod$contributions);cat(txt2);print(out$mods$interactions,row.names=F)
+
+ if(out$input$model.family=="bernoulli"){
+ auc.output <- make.auc.plot.jpg(out$dat$ma$ma,pred=predict.gbm(out$mods$final.mod,out$dat$ma$ma,
+ out$mods$final.mod$target.trees,type="response"),plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="BRT",opt.methods=opt.methods,
+ weight=out$dat$ma$train.weights,out=out)
+
+ out$mods$auc.output<-auc.output
+ }
+ if(out$input$model.family=="poisson"){
+ auc.output <- make.poisson.jpg(out$dat$ma$ma,pred=predict.gbm(out$mods$final.mod,out$dat$ma$ma,
+ out$mods$final.mod$target.trees,type="response"),plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="BRT",
+ weight=out$dat$ma$train.weights,out=out)
+
+ out$mods$auc.output<-auc.output
+ }
+
+ if(!debug.mode) {sink();cat("Progress:70%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("70%\n")}
+
+ # Response curves #
+ if(is.null(responseCurveForm)){
+ responseCurveForm<-0}
+
+ if(debug.mode | responseCurveForm=="pdf"){
+ nvar <- nrow(out$mods$final.mod$contributions)
+ pcol <- min(ceiling(sqrt(nvar)),4)
+ prow <- min(ceiling(nvar/pcol),3)
+
+ pdf(paste(bname,"_response_curves.pdf",sep=""),width=11,height=8.5,onefile=T)
+ par(oma=c(2,2,4,2))
+ r.curves <- try(gbm.plot(out$mods$final.mod,plotit=T,plot.layout=c(prow,pcol)))
+ if(class(r.curves)!="try-error") {out$mods$r.curves <- r.curves
+ mtext(paste("BRT response curves for",basename(ma.name)),outer=T,side=3,cex=1.3)}
+ par(mfrow=c(1,1))
+ #for(i in 1:min(nrow(int),2)) gbm.perspec(fit,int$var1.index[i],int$var2.index[i])
+ if(!is.null(out$mods$interactions)){
+ for(i in 1:nrow(out$mods$interactions)) {gbm.perspec(out$mods$final.mod,out$mods$interactions$v1[i],out$mods$interactions$v2[i])
+ mtext(paste("BRT interaction plots for",basename(ma.name)),outer=T,side=3,cex=1.5) }
+ }
+ graphics.off()
+ } else {
+ r.curves <- try(gbm.plot(out$mods$final.mod,plotit=F))
+ if(class(r.curves)!="try-error") {out$mods$r.curves <- r.curves
+ } else {
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: problem fitting response curves",r.curves)
+ }
+ }
+ t4 <- unclass(Sys.time())
+ cat("\nfinished with final model summarization, t=",round(t4-t3,2),"sec\n");flush.console()
+ if(!debug.mode) {sink();cat("Progress:80%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("80%\n")}
+
+ assign("out",out,envir=.GlobalEnv)
+ # Make .tif of predictions #
+
+ save.image(paste(output.dir,"modelWorkspace",sep="\\"))
+ if(out$input$make.p.tif==T | out$input$make.binary.tif==T){
+ cat("\nproducing prediction maps...","\n","\n");flush.console()
+ mssg <- proc.tiff(model=out$mods$final.mod,vnames=as.character(out$mods$final.mod$contributions$var),
+ tif.dir=out$dat$tif.dir$dname,filenames=out$dat$tif.ind,pred.fct=brt.predict,factor.levels=out$dat$ma$factor.levels,make.binary.tif=make.binary.tif,
+ thresh=out$mods$auc.output$thresh,make.p.tif=make.p.tif,outfile.p=paste(out$dat$bname,"_prob_map.tif",sep=""),
+ outfile.bin=paste(out$dat$bname,"_bin_map.tif",sep=""),tsize=50.0,NAval=-3000,logname=logname,out=out) #"brt.prob.map.tif"
+
+ if(class(mssg)=="try-error" | mssg!=0){
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("Error producing prediction maps:",mssg)
+ cat(saveXML(brt.to.xml(out),indent=T),'\n')
+ return()
+ } else {
+ if(make.p.tif) out$mods$tif.output$prob <- paste(out$dat$bname,"_prob_map.tif",sep="")
+ if(make.binary.tif) out$mods$tif.output$bin <- paste(out$dat$bname,"_bin_map.tif",sep="")
+ t5 <- unclass(Sys.time())
+ cat("\nfinished with prediction maps, t=",round(t5-t4,2),"sec\n");flush.console()
+ }
+ }
+ if(!debug.mode) {sink();cat("Progress:90%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("90%\n")} ### print time
+
+ # Evaluation Statistics on Test Data#
+
+ if(!is.null(out$dat$ma$ma.test)) Eval.Stat<-EvaluationStats(out,thresh=auc.output$thresh,train=out$dat$ma$ma,train.pred=predict.gbm(out$mods$final.mod,out$dat$ma$ma,
+ out$mods$final.mod$target.trees,type="response"),opt.methods)
+
+
+
+ # Write summaries to xml #
+ if(debug.mode) assign("out",out,envir=.GlobalEnv)
+ doc <- brt.to.xml(out)
+
+ cat(paste("\ntotal time=",round((unclass(Sys.time())-t0)/60,2),"min\n\n\n",sep=""))
+ if(!debug.mode) {
+ sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))
+ cat("Progress:100%\n");flush.console() ### print time
+
+ cat(saveXML(doc,indent=T),'\n')
+ }
+ capture.output(cat(saveXML(doc,indent=T)),file=paste(out$dat$bname,"_output.xml",sep=""))
+ if(debug.mode) assign("fit",out$mods$final.mod,envir=.GlobalEnv)
+ invisible(out)
+}
+
+brt.predict <- function(model,x) {
+ # retrieve key items from the global environment #
+ # make predictions from complete data only #
+ #y <- rep(NA,nrow(x))
+ #y[complete.cases(x)] <- predict.gbm(model, x[complete.cases(x),],model$target.trees,type="response")
+
+ # make predictions from full data #
+ y <- predict.gbm(model,x,model$target.trees,type="response")
+ # encode missing values as -1.
+ a<-complete.cases(x)
+ y[!(a)]<- NaN
+
+ # return predictions.
+ return(y)
+ }
+
+
+
+
+logit <- function(x) 1/(1+exp(-x))
+
+file_path_as_absolute <- function (x){
+ if (!file.exists(epath <- path.expand(x)))
+ stop(gettextf("file '%s' does not exist", x), domain = NA)
+ cwd <- getwd()
+ on.exit(setwd(cwd))
+ if (file_test("-d", epath)) {
+ setwd(epath)
+ getwd()
+ }
+ else {
+ setwd(dirname(epath))
+ file.path(getwd(), basename(epath))
+ }
+}
+#file_path_as_absolute(".")
+
+brt.to.xml <- function(out){
+ require(XML)
+ schema.http="http://www.w3.org/2001/XMLSchema-instance"
+ schema.fname="file:/Users/isfs2/Desktop/Source/2008-04-09/src/gov/nasa/gsfc/quickmap/ModelBuilder/modelRun_output_v2.xsd"
+ xml.out <- newXMLDoc()
+ mr <- newXMLNode("modelRunOutput",doc=xml.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))#,parent=xml.out
+ sm <- newXMLNode("singleModel",parent=mr)
+ bg <- newXMLNode("background",parent=sm)
+ newXMLNode("mdsName",out$input$ma.name,parent=bg)
+ newXMLNode("runDate",out$input$run.time,parent=bg)
+ lc <- newXMLNode("layersConsidered",parent=bg)#, parent = xml.out)
+ kids <- lapply(paste(out$dat$tif.dir$dname,"/",out$dat$ma$used.covs,".tif",sep=""),function(x) newXMLNode("layer", x))
+ addChildren(lc, kids)
+ mo <- newXMLNode("modelOutput",parent=sm)
+ newXMLNode("modelType",out$input$model.type,parent=mo)
+ newXMLNode("modelSourceFile",out$input$model.source.file,parent=mo)
+ newXMLNode("devianceExplained",out$mods$auc.output$pct_dev_exp,parent=mo,attrs=list(type="percentage"))
+ if(!is.null(out$mods$summary)){
+ newXMLNode("nativeOutput",paste(out$dat$bname,"_output.txt",sep=""),parent=mo)
+ } else {
+ newXMLNode("nativeOutput",NULL,parent=mo)
+ }
+ newXMLNode("binaryOutputFile",out$mods$tif.output[[2]],parent=mo)
+ newXMLNode("probOutputFile",out$mods$tif.output[[1]],parent=mo)
+ newXMLNode("auc",out$mods$auc.output$auc,parent=mo)
+ newXMLNode("rocGraphic",out$mods$auc.output$plotname,parent=mo)
+ newXMLNode("rocThresh",out$mods$auc.output$thresh,parent=mo)
+ newXMLNode("modelDeviance",out$mods$auc.output$dev_fit,parent=mo)
+ newXMLNode("nullDeviance",out$mods$auc.output$null_dev,parent=mo)
+ if(is.null(out$mods$r.curves)) rc.name <- NULL else rc.name <- paste(out$dat$bname,"_response_curves.xml",sep="")
+ newXMLNode("responsePlotsFile",rc.name,parent=mo)
+ newXMLNode("significanceDescription",out$input$sig.test,parent=mo)
+ mfp <- newXMLNode("modelFitParmas",parent=mo)
+ newXMLNode("treeComplexity",out$input$tc,parent=mfp)
+ newXMLNode("bagFraction",out$input$bag.fraction,parent=mfp)
+ newXMLNode("simpMethod",out$input$simp.method,parent=mfp)
+ newXMLNode("alpha",out$input$alpha,parent=mfp)
+
+ sv <- newXMLNode("significantVariables",parent=mo)
+ if(!is.null(out$mods$summary)) {
+ t.table <- data.frame(significanceMeasurement=out$mods$summary$rel.inf,row.names=out$mods$summary$var)
+ if(!is.null(out$mods$interactions)){
+ int1 <- int2 <- out$mods$interactions
+ int2$name1 <- int1$name2
+ int2$name2 <- int1$name1
+ int <- rbind(int1,int2)
+ }
+
+ for(i in 1:nrow(t.table)){
+ x <- newXMLNode("sigVar",parent=sv)
+ newXMLNode(name="name", row.names(t.table)[i],parent=x)
+ kids <- lapply(1:ncol(t.table),function(j) newXMLNode(name=names(t.table)[j], t.table[i,j]))
+ addChildren(x, kids)
+ if(!is.null(out$mods$interactions)){
+ ints <- c(1:nrow(int))[int$name1 %in% row.names(t.table)[i]]
+ if(length(ints)>0){
+ kids <- lapply(ints,function(j) newXMLNode(name="sigInteraction",attrs=list(name=as.character(int$name2)[j],size=int$int.size[j],p=int$"p-value"[j])))
+ addChildren(x,kids)
+ }
+
+ }
+ }
+ }
+
+ if(!is.null(out$mods$r.curves)){
+ r.curves <- out$mods$r.curves
+ factor.levels <- out$dat$ma$factor.levels
+ rc.out <- newXMLDoc()
+ root <- newXMLNode("responseCurves",doc=rc.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))
+ for(i in 1:length(r.curves$names)){
+ if(!is.na(f.index<-match(r.curves$names[i],names(factor.levels)))){
+ vartype <- "factor"} else vartype="continuous"
+ x <- newXMLNode("responseCurve",attrs=list(covariate=r.curves$names[i],type=vartype),parent=root)
+ kids <- lapply(1:length(r.curves$preds[[i]]),function(j){
+ newXMLNode(name="responsePt",parent=x,.children=list(
+ newXMLNode(name="explanatory",as.character(r.curves$preds[[i]])[j]),
+ newXMLNode(name="response",r.curves$resp[[i]][j])))})
+ addChildren(x, kids)
+ }
+ saveXML(rc.out,rc.name,indent=T)
+
+ }
+ if(!is.null(out$error.mssg[[1]])) {
+ kids <- lapply(out$error.mssg,function(j) newXMLNode(name="error",j))
+ addChildren(mo,kids)
+ }
+ return(xml.out)
+ }
+
+
+get.cov.names <- function(model){
+ return(attr(terms(formula(model)),"term.labels"))
+ }
+
+
+
+est.lr <- function(out){
+ # this function estimates optimal number of trees at a variety of learning rates #
+ # the learning rate that produces closest to 1000 trees is selected #
+ # in addition, variables with >1% influence are identified by column number in
+ # the original dataframe
+ # written by AKS early 2009
+ suppressMessages(require(gbm))
+
+ t0 <- unclass(Sys.time())
+
+ # set tree complexity for full-data run #
+ a<-2.69; b<-0.0012174
+ if(is.null(out$mods$parms$tc.full)) out$mods$parms$tc.full<-min(round(a+b*out$dat$ma$dims[1]),15) # this gives 3 for n=250
+ if(is.null(out$mods$parms$tc.sub)){
+ n <- out$dat$ma$n.abs[3]+out$dat$ma$n.pres[3] # this gives 3 for n=250
+ if(is.na(n)) (n=length(out$dat$ma$weight.subset))
+ out$mods$parms$tc.sub <- round(a+b*n)
+ }
+
+ cat("\n");cat("tree complexity set to",out$mods$parms$tc.sub,"\n")
+
+ n.trees <- c(100,200,400,800,900,1000,1100,1200,1500,1800,2400)
+ lrs <- c(.1,.06,.05,.04,.03,.02,.01,.005,.0025,.001,.0005,.0001)
+ lr.out <- data.frame(lrs=lrs,max.trees=0)
+ dat <- out$dat$ma$ma.subset
+ gbm.y <- 1
+ gbm.x <- 2:ncol(dat)
+
+ max.trees <- 0
+ i=1
+
+ while(max.trees<800 & i<=nrow(lr.out)){
+
+ tryCatch(gbm.fit <- gbm.step.fast(dat=dat,
+ gbm.x = gbm.x,
+ gbm.y = gbm.y,
+ family = out$input$model.family,
+ n.trees = n.trees,
+ n.folds=out$input$n.folds,
+ tree.complexity = out$mods$parms$tc.sub,
+ learning.rate = lrs[i],
+ bag.fraction = out$input$bag.fraction,
+ site.weights=out$dat$ma$weight.subset,
+ autostop=T,verbose=F,silent=T,plot.main=F),error=function(ex){cat("Error: learning rate estimation failed.\n");
+ print(ex);
+ stop();})
+
+ if(class(gbm.fit)=="try-error"){
+ out$ec <- out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: learning rate estimation failed:",gbm.fit)
+ return(out)
+ }
+ lr.out$max.trees[i] <- max.trees <- gbm.fit$target.trees
+ assign(paste("gbm.fit",i,sep="_"),gbm.fit)
+ cat("lr =",lrs[i]," optimal n trees =",max.trees,"\n");flush.console()
+ i<-i+1 #ifelse(max.trees<=200,i+2,i+1)
+ }
+ # pick lr that gives closest to 1000 trees #
+
+ lr.out$i <- 1:nrow(lr.out)
+ lr.out <- lr.out[lr.out$max.trees!=0,]
+ ab<-coef(lm(max.trees~log(lrs),data=lr.out))
+ tt <- out$dat$ma$ratio*800
+ lr.full <- round(as.numeric(exp((tt-ab[1])/ab[2])),4)
+ lr <- round(as.numeric(exp((1000-ab[1])/ab[2])),6)
+ lr.out$abs <- abs(lr.out$max.trees-1000)
+ lr.out$d.lr <- abs(lr.out$lrs-lr)
+ lr.out <- lr.out[order(lr.out$abs,lr.out$d.lr),]
+ lr0 <- lr.out$lrs[1]
+ i <- lr.out$i[1]
+ gbm.fit <- get(paste("gbm.fit",i,sep="_"))
+ gbm.fit$gbm.call$dataframe <- as.character(substitute(dat))
+ good.vars <- summary(gbm.fit,plotit=F)
+ good.vars <- good.vars$var[good.vars$rel.inf>ifelse(out$input$simp.method!="none",1,0)]
+ good.cols <- c(1:ncol(dat))[names(dat) %in% good.vars]
+ out$mods$simp.mod <- list(good.cols=good.cols,good.vars=good.vars)
+ out$mods$lr.mod <- list(tc=out$mods$parms$tc.sub,lr=lr.full,lr0=lr0,lr.out=lr.out,ab=ab,gbm.fit=gbm.fit,good.cols=good.cols,t.elapsed=c(unclass(Sys.time())-t0))
+ if(!is.null(out$input$learning.rate)) {out$mods$lr.mod$lr0=out$input$learning.rate
+ out$mods$lr.mod$lr=out$input$learning.rate
+ }
+ return(out)
+ }
+
+
+check.dir <- function(dname){
+ if(is.null(dname)) dname <- getwd()
+ dname <- gsub("[\\]","/",dname)
+ end.char <- substr(dname,nchar(dname),nchar(dname))
+ if(end.char == "/") dname <- substr(dname,1,nchar(dname)-1)
+ exist <- suppressWarnings(as.numeric(file.access(dname,mode=0))==0) # -1 if bad, 0 if ok #
+ if(exist) dname <- file_path_as_absolute(dname)
+ readable <- suppressWarnings(as.numeric(file.access(dname,mode=4))==0) # -1 if bad, 0 if ok #
+ writable <- suppressWarnings(as.numeric(file.access(dname,mode=2))==0) # -1 if bad, 0 if ok #
+ return(list(dname=dname,exist=exist,readable=readable,writable=writable))
+ }
+
+
+
+get.image.info <- function(image.names){
+ # this function creates a data.frame with summary image info for a set of images #
+ require(rgdal)
+ n.images <- length(image.names)
+
+ full.names <- image.names
+ out <- data.frame(image=full.names,available=rep(F,n.images),size=rep(NA,n.images),
+ type=factor(rep("unk",n.images),levels=c("asc","envi","tif","unk")))
+ out$type[grep(".tif",image.names)]<-"tif"
+ out$type[grep(".asc",image.names)]<-"asc"
+ for(i in 1:n.images){
+ if(out$type[i]=="tif"){
+ x <-try(GDAL.open(full.names[1],read.only=T))
+ suppressMessages(try(GDAL.close(x)))
+ if(class(x)!="try-error") out$available[i]<-T
+ x<-try(file.info(full.names[i]))
+ } else {
+ x<-try(file.info(full.names[i]))
+ if(!is.na(x$size)) out$available[i]<-T
+ }
+ if(out$available[i]==T){
+ out$size[i]<-x$size
+ if(out$type[i]=="unk"){
+ # if extension not known, look for envi .hdr file in same directory #
+ if(file.access(paste(file_path_sans_ext(full.names[i]),".hdr",sep=""))==0)
+ out$type[i]<-"envi"
+ }
+ }
+ }
+ return(out)
+}
+
+gbm.step.fast <- function(
+ dat, # the input dataframe
+ gbm.x, # the predictors
+ gbm.y, # and response
+ offset = NULL, # allows an offset to be specified
+ fold.vector = NULL, # allows a fold vector to be read in for CV with offsets,
+ tree.complexity = 1, # sets the complexity of individual trees
+ learning.rate = 0.01, # sets the weight applied to inidivudal trees
+ bag.fraction = 0.75, # sets the proportion of observations used in selecting variables
+ site.weights = rep(1, nrow(dat)), # allows varying weighting for sites
+ var.monotone = rep(0, length(gbm.x)), # restricts responses to individual predictors to monotone
+ n.folds = 10, # number of folds
+ prev.stratify = TRUE, # prevalence stratify the folds - only for p/a data
+ family = "bernoulli", # family - bernoulli (=binomial), poisson, laplace or gaussian
+ n.trees = 50, # number of initial trees to fit
+ step.size = n.trees, # numbers of trees to add at each cycle
+ max.trees = 10000, # max number of trees to fit before stopping
+ tolerance.method = "auto", # method to use in deciding to stop - "fixed" or "auto"
+ tolerance = 0.001, # tolerance value to use - if method == fixed is absolute,
+ # if auto is multiplier * total mean deviance
+ keep.data = FALSE, # keep raw data in final model
+ plot.main = TRUE, # plot hold-out deviance curve
+ plot.folds = FALSE, # plot the individual folds as well
+ verbose = TRUE, # control amount of screen reporting
+ silent = FALSE, # to allow running with no output for simplifying model)
+ keep.fold.models = FALSE, # keep the fold models from cross valiation
+ keep.fold.vector = FALSE, # allows the vector defining fold membership to be kept
+ keep.fold.fit = FALSE, # allows the predicted values for observations from CV to be kept
+ autostop = FALSE, # setting autostop to T causes the tree fitting while loop to terminate
+ # if the cv.loss value increases twice in a row (AKS).
+
+ superfast=FALSE, # controls whether or not to compute final model when optimal n.trees differs from 1000 (AKS)
+ ...) # allows for any additional plotting parameters
+{
+#
+# j. leathwick/j. elith - 19th September 2005
+#
+# version 2.9
+#
+# function to assess optimal no of boosting trees using k-fold cross validation
+#
+# implements the cross-validation procedure described on page 215 of
+# Hastie T, Tibshirani R, Friedman JH (2001) The Elements of Statistical Learning:
+# Data Mining, Inference, and Prediction Springer-Verlag, New York.
+#
+# divides the data into 10 subsets, with stratification by prevalence if required for pa data
+# then fits a gbm model of increasing complexity along the sequence from n.trees to n.trees + (n.steps * step.size)
+# calculating the residual deviance at each step along the way
+# after each fold processed, calculates the average holdout residual deviance and its standard error
+# then identifies the optimal number of trees as that at which the holdout deviance is minimised
+# and fits a model with this number of trees, returning it as a gbm model along with additional information
+# from the cv selection process
+#
+# updated 13/6/05 to accommodate weighting of sites
+#
+# updated 19/8/05 to increment all folds simultaneously, allowing the stopping rule
+# for the maxinum number of trees to be fitted to be imposed by the data,
+# rather than being fixed in advance
+#
+# updated 29/8/05 to return cv test statistics, and deviance as mean
+# time for analysis also returned via unclass(Sys.time())
+#
+# updated 5/9/05 to use external function calc.deviance
+# and to return cv test stats via predictions formed from fold models
+# with n.trees = target.trees
+#
+# updated 15/5/06 to calculate variance of fitted and predicted values across folds
+# these can be expected to approximate the variance of fitted values
+# as would be estimated for example by bootstrapping
+# as these will underestimate the true variance
+# they are corrected by multiplying by (n-1)2/n
+# where n is the number of folds
+#
+# updated 25/3/07 tp allow varying of bag fraction
+#
+# requires gbm library from Cran
+# requires roc and calibration scripts of J Elith
+# requires calc.deviance script of J Elith/J Leathwick
+#
+# updated 1/2/09 by aks:
+# now takes a vector arguement for n.trees: if n.trees is given as a (should be montonically
+# increasing) vector, then models with those # of trees are fit. if n.trees is a single number,
+# then the program works as default
+# there is also a provision for stopping the fitting of successive models IF the cv.loss.value increases
+# over two successive steps.
+
+ require(gbm)
+
+ if (silent) verbose <- FALSE
+
+# initiate timing call
+
+ z1 <- unclass(Sys.time())
+
+# setup input data and assign to position one
+
+ dataframe.name <- deparse(substitute(dat)) # get the dataframe name
+
+ dat <- eval(dat)
+ x.data <- eval(dat[, gbm.x]) #form the temporary datasets
+ names(x.data) <- names(dat)[gbm.x]
+ y.data <- eval(dat[, gbm.y])
+ sp.name <- names(dat)[gbm.y]
+ if (family == "bernoulli") prevalence <- mean(y.data)
+
+ assign("x.data", x.data, env = globalenv()) #and assign them for later use
+ assign("y.data", y.data, env = globalenv())
+
+ offset.name <- deparse(substitute(offset)) # get the dataframe name
+ offset = eval(offset)
+ #print(summary(offset))
+
+ n.cases <- nrow(dat)
+ n.preds <- length(gbm.x)
+
+ if (!silent) {
+ cat("\n","\n");cat("GBM STEP - version 2.9","\n","\n") #AKS
+ cat("Performing cross-validation optimization of a boosted regression tree model \n")#AKS
+ cat("for",sp.name,"with dataframe",dataframe.name,"and using a family of",family,"\n\n")
+ cat("Using",n.cases,"observations and",n.preds,"predictors \n\n")
+ flush.console() #AKS
+ }
+
+# set up the selector variable either with or without prevalence stratification
+
+ if (is.null(fold.vector)) {
+
+ if (prev.stratify & family == "bernoulli") {
+ presence.mask <- dat[,gbm.y] == 1
+ absence.mask <- dat[,gbm.y] == 0
+ n.pres <- sum(presence.mask)
+ n.abs <- sum(absence.mask)
+
+# create a vector of randomised numbers and feed into presences
+ selector <- rep(0,n.cases)
+ temp <- rep(seq(1, n.folds, by = 1), length = n.pres)
+ temp <- temp[order(runif(n.pres, 1, 100))]
+ selector[presence.mask] <- temp
+
+# and then do the same for absences
+ temp <- rep(seq(1, n.folds, by = 1), length = n.abs)
+ temp <- temp[order(runif(n.abs, 1, 100))]
+ selector[absence.mask] <- temp
+ }
+
+ else { #otherwise make them random with respect to presence/absence
+ selector <- rep(seq(1, n.folds, by = 1), length = n.cases)
+ selector <- selector[order(runif(n.cases, 1, 100))]
+ }
+ }
+ else {
+ if (length(fold.vector) != n.cases) stop("supplied fold vector is of wrong length")
+ cat("loading user-supplied fold vector \n\n")
+ selector <- eval(fold.vector)
+ }
+
+# set up the storage space for results
+
+ pred.values <- rep(0, n.cases)
+
+ cv.loss.matrix <- matrix(0, nrow = n.folds, ncol = 1)
+ training.loss.matrix <- matrix(0, nrow = n.folds, ncol = 1)
+ trees.fitted <- n.trees[1]
+
+ model.list <- list(paste("model",c(1:n.folds),sep="")) # dummy list for the tree models
+
+# set up the initial call to gbm
+
+ if (is.null(offset)) { #AKS (n.trees arg)
+ gbm.call <- paste("gbm(y.subset~.,data=x.subset,n.trees=n.trees[1],interaction.depth=tree.complexity,shrinkage=learning.rate,bag.fraction=bag.fraction,weights=weight.subset,distribution=as.character(family),var.monotone=var.monotone,verbose=FALSE)",sep="")
+ }
+ else { #AKS (n.trees arg)
+ gbm.call <- paste("gbm(y.subset~.+offset(offset.subset),data=x.subset,n.trees=n.trees[1],interaction.depth=tree.complexity,shrinkage=learning.rate,bag.fraction=bag.fraction,weights=weight.subset,distribution=as.character(family),var.monotone=var.monotone,verbose=FALSE)",sep="")
+ }
+
+
+ n.fitted <- n.trees[1] # AKS
+
+# calculate the total deviance
+
+ y_i <- y.data
+
+ u_i <- sum(y.data * site.weights) / sum(site.weights)
+ u_i <- rep(u_i,length(y_i))
+
+ total.deviance <- calc.deviance(y_i, u_i, weights = site.weights, family = family, calc.mean = FALSE)
+
+ mean.total.deviance <- total.deviance/n.cases
+
+ tolerance.test <- tolerance
+
+ if (tolerance.method == "auto") {
+ tolerance.test <- mean.total.deviance * tolerance
+ }
+
+# now step through the folds setting up the initial call
+
+ if (!silent){
+
+ cat("creating",n.folds,"initial models of",n.trees,"trees","\n")
+
+ if (prev.stratify & family == "bernoulli") {cat("\n");cat("folds are stratified by prevalence","\n","\n")#AKS
+ } else {cat("\n","folds are unstratified","\n","\n")}
+
+ cat ("total mean deviance = ",round(mean.total.deviance,4),"\n","\n")
+
+ cat("tolerance is fixed at ",round(tolerance.test,4),"\n","\n")
+ flush.console()#AKS
+
+ if (tolerance.method != "fixed" & tolerance.method != "auto") {
+ cat("invalid argument for tolerance method - should be auto or fixed","\n")
+ return()}
+ }
+
+ if (verbose) cat("fitting initial model...","\n");flush.console()#AKS
+
+ for (i in 1:n.folds) {
+
+ model.mask <- selector != i #used to fit model on majority of data
+ pred.mask <- selector == i #used to identify the with-held subset
+
+ y.subset <- y.data[model.mask]
+ x.subset <- x.data[model.mask,]
+ weight.subset <- site.weights[model.mask]
+
+ if (!is.null(offset)) {
+ offset.subset <- offset[model.mask]
+ }
+ else {
+ offset.subset <- NULL
+ }
+
+ model.list[[i]] <- eval(parse(text = gbm.call))
+
+ fitted.values <- model.list[[i]]$fit #predict.gbm(model.list[[i]], x.subset, type = "response", n.trees = n.trees)
+ if (!is.null(offset)) fitted.values <- fitted.values + offset[model.mask]
+ if (family == "bernoulli") fitted.values <- exp(fitted.values)/(1 + exp(fitted.values))
+ if (family == "poisson") fitted.values <- exp(fitted.values)
+
+ pred.values[pred.mask] <- predict.gbm(model.list[[i]], x.data[pred.mask, ], n.trees = n.trees[1])
+ if (!is.null(offset)) pred.values[pred.mask] <- pred.values[pred.mask] + offset[pred.mask]
+ if (family == "bernoulli") pred.values[pred.mask] <- exp(pred.values[pred.mask])/(1 + exp(pred.values[pred.mask]))
+ if (family == "poisson") pred.values[pred.mask] <- exp(pred.values[pred.mask])
+
+# calc training deviance
+
+ y_i <- y.subset
+ u_i <- fitted.values
+ weight.fitted <- site.weights[model.mask]
+ training.loss.matrix[i,1] <- calc.deviance(y_i, u_i, weight.fitted, family = family)
+
+# calc holdout deviance
+
+ y_i <- y.data[pred.mask]
+ u_i <- pred.values[pred.mask]
+ weight.preds <- site.weights[pred.mask]
+ cv.loss.matrix[i,1] <- calc.deviance(y_i, u_i, weight.preds, family = family)
+
+ } # end of first loop
+
+# now process until the change in mean deviance is =< tolerance or max.trees is exceeded
+
+ delta.deviance <- 1
+
+ cv.loss.values <- apply(cv.loss.matrix,2,mean)
+ if (verbose) cat("ntrees resid. dev.","\n")#AKS
+ if (verbose) cat(n.fitted," ",round(cv.loss.values,4),"\n","\n")
+
+ if (!silent) cat("")
+ if (!silent) cat("now adding trees...","\n");flush.console()#AKS
+
+ j <- 1
+ k <- 2 #AKS
+ stop.loop <- F #AKS
+ if(length(n.trees>1)) max.trees <- n.trees[length(n.trees)] #AKS
+
+ while (delta.deviance > tolerance.test & n.fitted < max.trees & stop.loop==F) { # beginning of inner loop
+
+ # add a new column to the results matrice..
+
+ training.loss.matrix <- cbind(training.loss.matrix,rep(0,n.folds))
+ cv.loss.matrix <- cbind(cv.loss.matrix,rep(0,n.folds))
+
+ if(length(n.trees>1)){ #AKS
+ n.fitted <- n.trees[k] #AKS
+ step.size <- n.trees[k]-n.trees[k-1]
+ k <- k+1 #AKS
+ } else { #AKS
+ n.fitted <- n.fitted + step.size
+ } #AKS
+
+ trees.fitted <- c(trees.fitted,n.fitted)
+
+ j <- j + 1
+
+ for (i in 1:n.folds) {
+
+ model.mask <- selector != i #used to fit model on majority of data
+ pred.mask <- selector == i #used to identify the with-held subset
+
+ y.subset <- y.data[model.mask]
+ x.subset <- x.data[model.mask,]
+ weight.subset <- site.weights[model.mask]
+ if (!is.null(offset)) {
+ offset.subset <- offset[model.mask]
+ }
+
+ model.list[[i]] <- gbm.more(model.list[[i]], weights = weight.subset, step.size)
+
+ fitted.values <- model.list[[i]]$fit # predict.gbm(model.list[[i]],x.subset, type = "response", n.trees = n.fitted)
+ if (!is.null(offset)) fitted.values <- fitted.values + offset[model.mask]
+ if (family == "bernoulli") fitted.values <- exp(fitted.values)/(1 + exp(fitted.values))
+ if (family == "poisson") fitted.values <- exp(fitted.values)
+
+ pred.values[pred.mask] <- predict.gbm(model.list[[i]], x.data[pred.mask, ], n.trees = n.fitted)
+ if (!is.null(offset)) pred.values[pred.mask] <- pred.values[pred.mask] + offset[pred.mask]
+ if (family == "bernoulli") pred.values[pred.mask] <- exp(pred.values[pred.mask])/(1 + exp(pred.values[pred.mask]))
+ if (family == "poisson") pred.values[pred.mask] <- exp(pred.values[pred.mask])
+
+ # calculate training deviance
+
+ y_i <- y.subset
+ u_i <- fitted.values
+ weight.fitted <- site.weights[model.mask]
+ training.loss.matrix[i,j] <- calc.deviance(y_i, u_i, weight.fitted, family = family)
+
+ # calc holdout deviance
+
+ u_i <- pred.values[pred.mask]
+ y_i <- y.data[pred.mask]
+ weight.preds <- site.weights[pred.mask]
+ cv.loss.matrix[i,j] <- calc.deviance(y_i, u_i, weight.preds, family = family)
+
+ } # end of inner loop
+
+ cv.loss.values <- apply(cv.loss.matrix,2,mean)
+
+ if (j < 5 & autostop==F) { #AKS
+ if (cv.loss.values[j] > cv.loss.values[j-1]) {
+ if (!silent) cat("restart model with a smaller learning rate or smaller step size...")
+ return()
+ }
+ }
+
+ if (j >= 20) { #calculate stopping rule value
+ test1 <- mean(cv.loss.values[(j-9):j])
+ test2 <- mean(cv.loss.values[(j-19):(j-9)])
+ delta.deviance <- test2 - test1
+ }
+
+ if (verbose) cat(n.fitted," ",round(cv.loss.values[j],4),"\n");flush.console()#AKS
+ if(autostop==T & j>2){ # this if statement added by AKS
+ if((cv.loss.values[j]>cv.loss.values[j-1])){# & (cv.loss.values[j-1]>cv.loss.values[j-2])){ # if deviance increases twice in a row
+ stop.loop=T#n.fitted <- max.trees # by setting n.fitted to max.trees, the while loop will terminate.
+ }
+ }
+
+
+
+ } # end of while loop
+
+# now begin process of calculating optimal number of trees
+
+ training.loss.values <- apply(training.loss.matrix,2,mean)
+
+ cv.loss.ses <- rep(0,length(cv.loss.values))
+ cv.loss.ses <- sqrt(apply(cv.loss.matrix,2,var)) / sqrt(n.folds)
+
+# find the target holdout deviance
+
+ y.bar <- min(cv.loss.values)
+
+# plot out the resulting curve of holdout deviance
+
+ if (plot.main) {
+
+ y.min <- min(cv.loss.values - cv.loss.ses) #je added multiplier 10/8/05
+ y.max <- max(cv.loss.values + cv.loss.ses) #je added multiplier 10/8/05 }
+
+ if (plot.folds) {
+ y.min <- min(cv.loss.matrix)
+ y.max <- max(cv.loss.matrix) }
+
+ plot(trees.fitted, cv.loss.values, type = 'l', ylab = "holdout deviance",
+ xlab = "no. of trees", ylim = c(y.min,y.max), ...)
+ abline(h = y.bar, col = 2)
+
+ lines(trees.fitted, cv.loss.values + cv.loss.ses, lty=2)
+ lines(trees.fitted, cv.loss.values - cv.loss.ses, lty=2)
+
+ if (plot.folds) {
+ for (i in 1:n.folds) {
+ lines(trees.fitted, cv.loss.matrix[i,],lty = 3)
+ }
+ }
+ }
+
+# identify the optimal number of trees
+
+ target.trees <- trees.fitted[match(TRUE,cv.loss.values == y.bar)]
+ #cat("\n");cat("optimal n trees =",target.trees,"\n") #AKS
+
+ if(plot.main) {
+ abline(v = target.trees, col=3)
+ title(paste(sp.name,", d - ",tree.complexity,", lr - ",learning.rate, sep=""))
+ }
+
+# skip additional details on final model unless target.trees is close to 1000 (AKS)#
+if(abs(target.trees-1000) >= 600 & superfast==T){ # AKS
+ return(list(target.trees=target.trees)) # AKS
+ } else { # AKS
+
+
+# estimate the cv deviance and test statistics
+# includes estimates of the standard error of the fitted values added 2nd may 2005
+
+ cv.deviance.stats <- rep(0, n.folds)
+ cv.roc.stats <- rep(0, n.folds)
+ cv.cor.stats <- rep(0, n.folds)
+ cv.calibration.stats <- matrix(0, ncol=5, nrow = n.folds)
+ if (family == "bernoulli") threshold.stats <- rep(0, n.folds)
+
+ fitted.matrix <- matrix(NA, nrow = n.cases, ncol = n.folds) #used to calculate se's
+ fold.fit <- rep(0,n.cases)
+
+ for (i in 1:n.folds) {
+
+ pred.mask <- selector == i #used to identify the with-held subset
+ model.mask <- selector != i #used to fit model on majority of data
+
+ fits <- predict.gbm(model.list[[i]], x.data[model.mask, ], n.trees = target.trees)
+ if (!is.null(offset)) fits <- fits + offset[model.mask]
+ if (family == "bernoulli") fits <- exp(fits)/(1 + exp(fits))
+ if (family == "poisson") fits <- exp(fits)
+ fitted.matrix[model.mask,i] <- fits
+
+ fits <- predict.gbm(model.list[[i]], x.data[pred.mask, ], n.trees = target.trees)
+ if (!is.null(offset)) fits <- fits + offset[pred.mask]
+ fold.fit[pred.mask] <- fits # store the linear predictor values
+ if (family == "bernoulli") fits <- exp(fits)/(1 + exp(fits))
+ if (family == "poisson") fits <- exp(fits)
+ fitted.matrix[pred.mask,i] <- fits
+
+ y_i <- y.data[pred.mask]
+ u_i <- fitted.matrix[pred.mask,i] #pred.values[pred.mask] ####
+ weight.preds <- site.weights[pred.mask]
+
+ cv.deviance.stats[i] <- calc.deviance(y_i, u_i, weight.preds, family = family)
+
+ cv.cor.stats[i] <- cor(y_i,u_i)
+
+ if (family == "bernoulli") {
+ cv.roc.stats[i] <- roc(y_i,u_i)
+ cv.calibration.stats[i,] <- calibration(y_i,u_i,"binomial")
+ threshold.stats[i] <- approx(ppoints(u_i), sort(u_i,decreasing = T), prevalence)$y
+ }
+
+ if (family == "poisson") {
+ cv.calibration.stats[i,] <- calibration(y_i,u_i,"poisson")
+ }
+ }
+
+ fitted.vars <- apply(fitted.matrix,1, var, na.rm = TRUE)
+
+ #now calculate the mean and se's for the folds
+
+ cv.dev <- mean(cv.deviance.stats, na.rm = TRUE)
+ cv.dev.se <- sqrt(var(cv.deviance.stats)) / sqrt(n.folds)
+
+ cv.cor <- mean(cv.cor.stats, na.rm = TRUE)
+ cv.cor.se <- sqrt(var(cv.cor.stats, use = "complete.obs")) / sqrt(n.folds)
+
+ cv.roc <- 0.0
+ cv.roc.se <- 0.0
+
+ if (family == "bernoulli") {
+ cv.roc <- mean(cv.roc.stats,na.rm=TRUE)
+ cv.roc.se <- sqrt(var(cv.roc.stats, use = "complete.obs")) / sqrt(n.folds)
+ cv.threshold <- mean(threshold.stats, na.rm = T)
+ cv.threshold.se <- sqrt(var(threshold.stats, use = "complete.obs")) / sqrt(n.folds)
+ }
+
+ cv.calibration <- 0.0
+ cv.calibration.se <- 0.0
+
+ if (family == "poisson" | family == "bernoulli") {
+ cv.calibration <- apply(cv.calibration.stats,2,mean)
+ cv.calibration.se <- apply(cv.calibration.stats,2,var)
+ cv.calibration.se <- sqrt(cv.calibration.se) / sqrt(n.folds) }
+
+ #fit the final model
+
+ if (is.null(offset)) {
+ gbm.call <- paste("gbm(y.data~.,data=x.data,n.trees=target.trees,interaction.depth=tree.complexity,shrinkage=learning.rate,bag.fraction=bag.fraction,weights=site.weights,distribution=as.character(family),var.monotone=var.monotone,verbose=FALSE)",sep="")
+ }
+ else {
+ gbm.call <- paste("gbm(y.data~.+ offset(offset),data=x.data,n.trees=target.trees,interaction.depth=tree.complexity,shrinkage=learning.rate,bag.fraction=bag.fraction,weights=site.weights,distribution=as.character(family),var.monotone=var.monotone,verbose=FALSE)",sep="")
+ }
+
+ if (!silent) cat("fitting final gbm model with a fixed number of ",target.trees," trees for ",sp.name,"\n")
+
+ gbm.object <- eval(parse(text = gbm.call)) # AKS
+
+ best.trees <- target.trees
+
+#extract fitted values and summary table
+
+ gbm.summary <- summary(gbm.object,n.trees = target.trees, plotit = FALSE)
+
+ fits <- predict.gbm(gbm.object,x.data,n.trees = target.trees)
+ if (!is.null(offset)) fits <- fits + offset
+ if (family == "bernoulli") fits <- exp(fits)/(1 + exp(fits))
+ if (family == "poisson") fits <- exp(fits)
+ fitted.values <- fits
+
+ y_i <- y.data
+ u_i <- fitted.values
+ resid.deviance <- calc.deviance(y_i, u_i, weights = site.weights, family = family, calc.mean = FALSE)
+
+ self.cor <- cor(y_i,u_i)
+ self.calibration <- 0.0
+ self.roc <- 0.0
+
+ if (family == "bernoulli") { #do this manually as we need the residuals
+ deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
+ residuals <- sqrt(abs(deviance.contribs * 2))
+ residuals <- ifelse((y_i - u_i) < 0, 0 - residuals, residuals)
+ self.roc <- roc(y_i,u_i)
+ self.calibration <- calibration(y_i,u_i,"binomial")
+ }
+
+ if (family == "poisson") { #do this manually as we need the residuals
+ deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
+ residuals <- sqrt(abs(deviance.contribs * 2))
+ residuals <- ifelse((y_i - u_i) < 0, 0 - residuals, residuals)
+ self.calibration <- calibration(y_i,u_i,"poisson")
+ }
+
+ if (family == "gaussian" | family == "laplace") {
+ residuals <- y_i - u_i
+ }
+
+ mean.resid.deviance <- resid.deviance/n.cases
+
+ z2 <- unclass(Sys.time())
+ elapsed.time.minutes <- round((z2 - z1)/ 60,2) # calculate the total elapsed time
+
+ if (verbose) {
+ cat("\n")
+ cat("mean total deviance =", round(mean.total.deviance,3),"\n")
+ cat("mean residual deviance =", round(mean.resid.deviance,3),"\n","\n")
+ cat("estimated cv deviance =", round(cv.dev,3),"; se =",
+ round(cv.dev.se,3),"\n","\n")
+ cat("training data correlation =",round(self.cor,3),"\n")
+ cat("cv correlation = ",round(cv.cor,3),"; se =",round(cv.cor.se,3),"\n","\n")
+ if (family == "bernoulli") {
+ cat("training data ROC score =",round(self.roc,3),"\n")
+ cat("cv ROC score =",round(cv.roc,3),"; se =",round(cv.roc.se,3),"\n","\n")
+ }
+ cat("elapsed time - ",round(elapsed.time.minutes,2),"minutes","\n")
+ }
+
+ if (n.fitted == max.trees & !silent) {
+ cat("\n"," warning ","\n","\n")
+ cat("maximum tree limit reached - results may not be optimal","\n")
+ cat(" - refit with faster learning rate or increase maximum number of trees","\n")
+
+
+ }
+
+ # now assemble data to be returned
+
+ gbm.detail <- list(dataframe = dataframe.name, gbm.x = gbm.x, predictor.names = names(x.data),
+ gbm.y = gbm.y, response.name = sp.name, offset = offset.name, family = family, tree.complexity = tree.complexity,
+ learning.rate = learning.rate, bag.fraction = bag.fraction, cv.folds = n.folds,
+ prev.stratification = prev.stratify, max.fitted = n.fitted, n.trees = target.trees,
+ best.trees = target.trees, train.fraction = 1.0, tolerance.method = tolerance.method,
+ tolerance = tolerance, var.monotone = var.monotone, date = date(),
+ elapsed.time.minutes = elapsed.time.minutes)
+
+ training.stats <- list(null = total.deviance, mean.null = mean.total.deviance,
+ resid = resid.deviance, mean.resid = mean.resid.deviance, correlation = self.cor,
+ discrimination = self.roc, calibration = self.calibration)
+
+ cv.stats <- list(deviance.mean = cv.dev, deviance.se = cv.dev.se,
+ correlation.mean = cv.cor, correlation.se = cv.cor.se,
+ discrimination.mean = cv.roc, discrimination.se = cv.roc.se,
+ calibration.mean = cv.calibration, calibration.se = cv.calibration.se)
+
+ if (family == "bernoulli") {
+ cv.stats$cv.threshold <- cv.threshold
+ cv.stats$cv.threshold.se <- cv.threshold.se
+ }
+
+ rm(x.data,y.data, envir = globalenv()) # finally, clean up the temporary dataframes
+
+ # and assemble results for return
+
+ gbm.object$gbm.call <- gbm.detail
+ gbm.object$fitted <- fitted.values
+ gbm.object$fitted.vars <- fitted.vars
+ gbm.object$residuals <- residuals
+ gbm.object$contributions <- gbm.summary
+ gbm.object$self.statistics <- training.stats
+ gbm.object$cv.statistics <- cv.stats
+ gbm.object$weights <- site.weights
+ gbm.object$trees.fitted <- trees.fitted
+ gbm.object$training.loss.values <- training.loss.values
+ gbm.object$cv.values <- cv.loss.values
+ gbm.object$cv.loss.ses <- cv.loss.ses
+ gbm.object$cv.loss.matrix <- cv.loss.matrix
+ gbm.object$cv.roc.matrix <- cv.roc.stats
+ gbm.object$target.trees <- target.trees
+
+ if (keep.fold.models) gbm.object$fold.models <- model.list
+ else gbm.object$fold.models <- NULL
+
+ if (keep.fold.vector) gbm.object$fold.vector <- selector
+ else gbm.object$fold.vector <- NULL
+
+ if (keep.fold.fit) gbm.object$fold.fit <- fold.fit
+ else gbm.object$fold.fit <- NULL
+
+ return(gbm.object)
+ } #end if statement
+}
+
+"gbm.plot" <-
+function(gbm.object, # a gbm object - could be one from gbm.step
+ variable.no = 0, # the var to plot - if zero then plots all
+ nt = gbm.object$n.trees, # how many trees to use
+ smooth = FALSE, # should we add a smoothed version of the fitted function
+ rug = T, # plot a rug of deciles
+ n.plots = length(pred.names), # plot the first n most important preds
+ common.scale = T, # use a common scale on the y axis
+ write.title = T, # plot a title above the plot
+ y.label = "fitted function", # the default y-axis label
+ x.label = NULL, # the default x-axis label
+ show.contrib = T, # show the contribution on the x axis
+ plot.layout = c(3,4), # define the default layout for graphs on the page
+ rug.side = 3, # which axis for rug plot? default (3) is top; bottom=1
+ rug.lwd = 1, # line width for rug plots
+ rug.tick = 0.03, # tick length for rug plots
+ plotit=T, # AKS
+ prob.scale=T, # AKS
+ ... # other arguments to pass to the plotting
+ # useful options include cex.axis, cex.lab, etc.
+ )
+{
+# function to plot gbm response variables, with the option
+# of adding a smooth representation of the response if requested
+# additional options in this version allow for plotting on a common scale
+# note too that fitted functions are now centered by subtracting their mean
+#
+# version 2.9
+#
+# j. leathwick/j. elith - March 2007
+#
+
+require(gbm)
+
+
+gbm.call <- gbm.object$gbm.call
+gbm.x <- gbm.call$gbm.x
+pred.names <- gbm.call$predictor.names
+out.names <- rep("",length(pred.names))
+response.name <- gbm.call$response.name
+dataframe.name <- gbm.call$dataframe
+data <- eval.parent(parse(text = dataframe.name))
+
+max.plots <- plot.layout[1] * plot.layout[2]
+plot.count <- 0
+n.pages <- 1
+
+if (length(variable.no) > 1) {stop("only one response variable can be plotted at a time")}
+
+if (variable.no > 0) { #we are plotting all vars in rank order of contribution
+ n.plots <- 1
+ }
+
+max.vars <- length(gbm.object$contributions$var)
+if (n.plots > max.vars) {
+ n.plots <- max.vars
+ cat("warning - reducing no of plotted predictors to maximum available (",max.vars,")\n",sep="")
+ }
+
+predictors <- list(rep(NA,n.plots)) # matrix(0,ncol=n.plots,nrow=100)
+responses <- list(rep(NA,n.plots)) # matrix(0,ncol=n.plots,nrow=100)
+
+for (j in c(1:n.plots)) { #cycle through the first time and get the range of the functions
+ if (n.plots == 1) {
+ k <- variable.no
+ }
+ else k <- match(gbm.object$contributions$var[j],pred.names)
+
+ if (is.null(x.label)) var.name <- gbm.call$predictor.names[k]
+ else var.name <- x.label
+
+ pred.data <- data[,gbm.call$gbm.x[k]]
+ out.names[j] <- names(data)[gbm.call$gbm.x[k]]
+
+ response.matrix <- plot.gbm(gbm.object, i.var = k, n.trees = nt, return.grid = TRUE,...)
+
+ predictors[[j]] <- response.matrix[,1]
+ if (is.factor(data[,gbm.call$gbm.x[k]])) {
+ predictors[[j]] <- factor(predictors[[j]],levels = levels(data[,gbm.call$gbm.x[k]]))
+ }
+ responses[[j]] <- response.matrix[,2] - mean(response.matrix[,2])
+ if(prob.scale) responses[[j]] <- logit(responses[[j]])
+
+ if(j == 1) {
+ ymin = min(responses[[j]])
+ ymax = max(responses[[j]])
+ }
+ else {
+ ymin = min(ymin,min(responses[[j]]))
+ ymax = max(ymax,max(responses[[j]]))
+ }
+ }
+
+# now do the actual plots
+ if(plotit==T){
+ for (j in c(1:n.plots)) {
+
+ if (plot.count == max.plots) {
+ plot.count = 0
+ n.pages <- n.pages + 1
+ }
+
+ if (plot.count == 0) {
+ #windows(width = 11, height = 8) #aks
+ par(mfrow = plot.layout)
+ }
+
+ plot.count <- plot.count + 1
+
+ if (n.plots == 1) {
+ k <- match(pred.names[variable.no],gbm.object$contributions$var)
+ if (show.contrib) {
+ x.label <- paste(var.name," (",round(gbm.object$contributions[k,2],1),"%)",sep="")
+ }
+ }
+ else {
+ k <- match(gbm.object$contributions$var[j],pred.names)
+ var.name <- gbm.call$predictor.names[k]
+ if (show.contrib) {
+ x.label <- paste(var.name," (",round(gbm.object$contributions[j,2],1),"%)",sep="")
+ }
+ else x.label <- var.name
+ }
+
+ if (common.scale) {
+ plot(predictors[[j]],responses[[j]],ylim=c(ymin,ymax), type='l',
+ xlab = x.label, ylab = y.label, ...)
+ }
+ else {
+ plot(predictors[[j]],responses[[j]], type='l',
+ xlab = x.label, ylab = y.label, ...)
+ }
+ if (smooth & is.vector(predictors[[j]])) {
+ temp.lo <- loess(responses[[j]] ~ predictors[[j]], span = 0.3)
+ lines(predictors[[j]],fitted(temp.lo), lty = 2, col = 2)
+ }
+ if (plot.count == 1) {
+ if (write.title) {
+ title(paste(response.name," - page ",n.pages,sep=""))
+ }
+ if (rug & is.vector(data[,gbm.call$gbm.x[k]])) {
+ rug(quantile(data[,gbm.call$gbm.x[k]], probs = seq(0, 1, 0.1), na.rm = TRUE), side = rug.side, lwd = rug.lwd, ticksize = rug.tick)
+ }
+ }
+ else {
+ if (write.title & j == 1) {
+ title(response.name)
+ }
+ if (rug & is.vector(data[,gbm.call$gbm.x[k]])) {
+ rug(quantile(data[,gbm.call$gbm.x[k]], probs = seq(0, 1, 0.1), na.rm = TRUE), side = rug.side, lwd = rug.lwd, ticksize = rug.tick)
+ }
+ }
+ }
+ }
+ return(invisible(list(names=out.names,preds=predictors,resp=responses)))
+}
+
+
+"gbm.perspec" <-
+function(gbm.object,
+ x = 1, # the first variable to be plotted
+ y = 2, # the second variable to be plotted
+ pred.means = NULL, # allows specification of values for other variables
+ x.label = NULL, # allows manual specification of the x label
+ x.range = NULL, # manual range specification for the x variable
+ y.label = NULL, # and y label
+ y.range = NULL, # and the y
+ z.range = NULL, # allows control of the vertical axis
+ ticktype = "detailed",# specifiy detailed types - otherwise "simple"
+ theta = 55, # rotation
+ phi=40, # and elevation
+ smooth = "none", # controls smoothing of the predicted surface
+ mask = FALSE, # controls masking using a sample intensity model
+ perspective = TRUE, # controls whether a contour or perspective plot is drawn
+ verbose=F, # AKS
+ ...) # allows the passing of additional arguments to plotting routine
+ # useful options include shade, ltheta, lphi for controlling illumination
+ # and cex for controlling text size - cex.axis and cex.lab have no effect
+{
+#
+# gbm.perspec version 2.9 April 2007
+# J Leathwick/J Elith
+#
+# takes a gbm boosted regression tree object produced by gbm.step and
+# plots a perspective plot showing predicted values for two predictors
+# as specified by number using x and y
+# values for all other variables are set at their mean by default
+# but values can be specified by giving a list consisting of the variable name
+# and its desired value, e.g., c(name1 = 12.2, name2 = 57.6)
+
+ require(gbm)
+
+
+#get the boosting model details
+
+ gbm.call <- gbm.object$gbm.call
+ gbm.x <- gbm.call$gbm.x
+ n.preds <- length(gbm.x)
+ gbm.y <- gbm.call$gbm.y
+ pred.names <- gbm.call$predictor.names
+ family = gbm.call$family
+
+ x.name <- gbm.call$predictor.names[x]
+
+ if (is.null(x.label)) {
+ x.label <- gbm.call$predictor.names[x]}
+
+ y.name <- gbm.call$predictor.names[y]
+
+ if (is.null(y.label)) {
+ y.label <- gbm.call$predictor.names[y]}
+
+ data <- eval.parent(parse(text=gbm.call$dataframe))[,gbm.x] #AKS
+ n.trees <- gbm.call$best.trees
+
+ if (is.null(x.range)) {
+ if(!is.factor(data[,x]))
+ x.var <- seq(min(data[,x],na.rm=T),max(data[,x],na.rm=T),length = 50)
+ else x.var<- sort(unique(as.numeric(levels(data[,x]))))
+ }
+ else {x.var <- seq(x.range[1],x.range[2],length = 50)}
+
+ if (is.null(y.range)) {
+ if(!is.factor(data[,y]))
+ y.var <- seq(min(data[,y],na.rm=T),max(data[,y],na.rm=T),length = 50)
+ else y.var<- sort(unique(as.numeric(levels(data[,y]))))
+ }
+ else {y.var <- seq(y.range[1],y.range[2],length = 50)}
+
+ pred.frame <- expand.grid(list(x.var,y.var))
+ names(pred.frame) <- c(x.name,y.name)
+
+ j <- 3
+ for (i in 1:n.preds) {
+ if (i != x & i != y) {
+ if (is.vector(data[,i])) {
+ m <- match(pred.names[i],names(pred.means))
+ if (is.na(m)) {
+ pred.frame[,j] <- mean(data[,i],na.rm=T)
+ }
+ else pred.frame[,j] <- pred.means[m]
+ }
+ if (is.factor(data[,i])) {
+ m <- match(pred.names[i],names(pred.means))
+ temp.table <- table(data[,i])
+ if (is.na(m)) {
+ pred.frame[,j] <- rep(names(temp.table)[2],2500)
+ }
+ else pred.frame[,j] <- pred.means[m]
+ pred.frame[,j] <- factor(pred.frame[,j],levels=names(temp.table))
+ }
+ names(pred.frame)[j] <- pred.names[i]
+ j <- j + 1
+ }
+ }
+#
+# form the prediction
+#
+ prediction <- predict.gbm(gbm.object,pred.frame,n.trees = n.trees, type="response")
+
+# model smooth if required
+
+ if (smooth == "model") {
+ require(splines)
+ pred.glm <- glm(prediction ~ ns(pred.frame[,1], df = 8) * ns(pred.frame[,2], df = 8), data=pred.frame,family=poisson)
+ prediction <- fitted(pred.glm)
+ }
+
+# report the maximum value and set up realistic ranges for z
+
+ max.pred <- max(prediction)
+ min.pred<-min(prediction)
+ if(verbose) cat("maximum value = ",round(max.pred,2),"\n") #AKS
+
+ if (is.null(z.range)) {
+ if (family == "bernoulli") {
+ z.range <- c(min.pred,max.pred)
+ }
+ else if (family == "poisson") {
+ z.range <- c(0,max.pred * 1.1)
+ }
+ else {
+ z.min <- min(data[,y],na.rm=T)
+ z.max <- max(data[,y],na.rm=T)
+ z.delta <- z.max - z.min
+ z.range <- c(z.min - (1.1 * z.delta), z.max + (1.1 * z.delta))
+ }
+ }
+# form the matrix
+
+ pred.matrix <- matrix(prediction,ncol=length(y.var),nrow=length(x.var))
+
+# kernel smooth if required
+
+ if (smooth == "average") { #apply a 3 x 3 smoothing average
+ pred.matrix.smooth <- pred.matrix
+ for (i in 2:(length(x.var)-1)) {
+ for (j in 2:(length(y.var)-1)) {
+ pred.matrix.smooth[i,j] <- mean(pred.matrix[c((i-1):(i+1)),c((j-1):(j+1))])
+ }
+ }
+ pred.matrix <- pred.matrix.smooth
+ }
+
+# mask out values inside hyper-rectangle but outside of sample space
+
+ if (mask) {
+ mask.trees <- mask.object$gbm.call$best.trees
+ point.prob <- predict.gbm(mask.object[[1]],pred.frame, n.trees = mask.trees, type="response")
+ point.prob <- matrix(point.prob,ncol=50,nrow=50)
+ pred.matrix[point.prob < 0.5] <- 0.0
+ }
+#
+# and finally plot the result
+
+ if (!perspective) {
+ image(x = x.var, y = y.var, z = pred.matrix, zlim = z.range)
+ }
+ else {
+ persp(x=x.var, y=y.var, z=pred.matrix, zlim= z.range, # input vars
+ xlab = x.label, ylab = y.label, zlab = "fitted value", # labels
+ theta=theta, phi=phi, r = sqrt(10), d = 3, # viewing pars
+ ticktype = ticktype, mgp = c(4,1,0), ...) #
+ }
+}
+
+"calibration" <-
+function(obs, preds, family = "binomial")
+{
+#
+# j elith/j leathwick 17th March 2005
+# calculates calibration statistics for either binomial or count data
+# but the family argument must be specified for the latter
+# a conditional test for the latter will catch most failures to specify
+# the family
+#
+
+if (family == "bernoulli") family <- "binomial"
+pred.range <- max(preds) - min(preds)
+if(pred.range > 1.2 & family == "binomial") {
+print(paste("range of response variable is ", round(pred.range, 2)), sep = "", quote = F)
+print("check family specification", quote = F)
+return()
+}
+if(family == "binomial") {
+pred <- preds + 1e-005
+pred[pred >= 1] <- 0.99999
+mod <- glm(obs ~ log((pred)/(1 - (pred))), family = binomial)
+lp <- log((pred)/(1 - (pred)))
+a0b1 <- glm(obs ~ offset(lp) - 1, family = binomial)
+miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
+ab1 <- glm(obs ~ offset(lp), family = binomial)
+miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
+miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
+}
+if(family == "poisson") {
+mod <- glm(obs ~ log(preds), family = poisson)
+lp <- log(preds)
+a0b1 <- glm(obs ~ offset(lp) - 1, family = poisson)
+miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
+ab1 <- glm(obs ~ offset(lp), family = poisson)
+miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
+miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
+}
+calibration.result <- c(mod$coef, miller1, miller2, miller3)
+names(calibration.result) <- c("intercept", "slope", "testa0b1", "testa0|b1", "testb1|a")
+return(calibration.result)
+}
+
+"roc" <-
+function (obsdat, preddat)
+{
+# code adapted from Ferrier, Pearce and Watson's code, by J.Elith
+#
+# see:
+# Hanley, J.A. & McNeil, B.J. (1982) The meaning and use of the area
+# under a Receiver Operating Characteristic (ROC) curve.
+# Radiology, 143, 29-36
+#
+# Pearce, J. & Ferrier, S. (2000) Evaluating the predictive performance
+# of habitat models developed using logistic regression.
+# Ecological Modelling, 133, 225-245.
+# this is the non-parametric calculation for area under the ROC curve,
+# using the fact that a MannWhitney U statistic is closely related to
+# the area
+#
+ if (length(obsdat) != length(preddat))
+ stop("obs and preds must be equal lengths")
+ n.x <- length(obsdat[obsdat == 0])
+ n.y <- length(obsdat[obsdat == 1])
+ xy <- c(preddat[obsdat == 0], preddat[obsdat == 1])
+ rnk <- rank(xy)
+ wilc <- ((n.x * n.y) + ((n.x * (n.x + 1))/2) - sum(rnk[1:n.x]))/(n.x *
+ n.y)
+ return(round(wilc, 4))
+}
+
+"calc.deviance" <-
+function(obs.values, fitted.values, weights = rep(1,length(obs.values)), family="binomial", calc.mean = TRUE)
+{
+# j. leathwick/j. elith
+#
+# version 2.1 - 5th Sept 2005
+#
+# function to calculate deviance given two vectors of raw and fitted values
+# requires a family argument which is set to binomial by default
+#
+#
+
+if (length(obs.values) != length(fitted.values))
+ stop("observations and predictions must be of equal length")
+
+y_i <- obs.values
+
+u_i <- fitted.values
+
+if (family == "binomial" | family == "bernoulli") {
+
+ deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
+ deviance <- -2 * sum(deviance.contribs * weights)
+
+}
+
+if (family == "poisson" | family == "Poisson") {
+
+ deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
+ deviance <- 2 * sum(deviance.contribs * weights)
+
+}
+
+if (family == "laplace") {
+ deviance <- sum(abs(y_i - u_i))
+ }
+
+if (family == "gaussian") {
+ deviance <- sum((y_i - u_i) * (y_i - u_i))
+ }
+
+
+
+if (calc.mean) deviance <- deviance/length(obs.values)
+
+return(deviance)
+
+}
+
+"gbm.interactions" <-
+function(gbm.object,
+ use.weights = FALSE, # use weights for samples
+ mask.object) # a gbm object describing sample intensity
+{
+#
+# gbm.interactions version 2.9
+#
+# j. leathwick, j. elith - May 2007
+#
+# functions assesses the magnitude of 2nd order interaction effects
+# in gbm models fitted with interaction depths greater than 1
+# this is achieved by:
+# 1. forming predictions on the linear scale for each predictor pair;
+# 2. fitting a linear model that relates these predictions to the predictor
+# pair, with the the predictors fitted as factors;
+# 3. calculating the mean value of the residuals, the magnitude of which
+# increases with the strength of any interaction effect;
+# 4. results are stored in an array;
+# 5. finally, the n most important interactions are identified,
+# where n is 25% of the number of interaction pairs;
+
+ require(gbm)
+
+ gbm.call <- gbm.object$gbm.call
+ n.trees <- gbm.call$best.trees
+ depth <- gbm.call$interaction.depth
+ gbm.x <- gbm.call$gbm.x
+ n.preds <- length(gbm.x)
+ pred.names <- gbm.object$gbm.call$predictor.names
+ cross.tab <- matrix(0,ncol=n.preds,nrow=n.preds)
+ dimnames(cross.tab) <- list(pred.names,pred.names)
+ int.p.table <- matrix(NA,ncol=n.preds,nrow=n.preds,dimnames=list(pred.names,pred.names))#AKS
+
+ if (use.weights) mask.trees <- mask.object$gbm.call$best.trees
+
+ #cat("gbm.interactions - version 2.9 \n") #aks
+ #cat("Cross tabulating interactions for gbm model with ",n.preds," predictors","\n",sep="") #aks
+
+ data <- eval.parent(parse(text=gbm.call$dataframe),n=1)[,gbm.x] #aks
+
+ for (i in 1:(n.preds - 1)) { # step through the predictor set
+ x.fac<-F
+ if (is.vector(data[,i])) { # create a sequence through the range
+ x.var <- seq(min(data[,i],na.rm=T),max(data[,i],na.rm=T),length = 20)
+ x2 <- as.vector(tapply(x.var,rep(1:10,rep(2,10)),mean))
+ } else { # otherwise set up simple factor variable
+ x.var <- factor(names(table(data[,i])),levels = levels(data[,i]))
+ x.fac<-T
+ }
+ x.length <- length(x.var)
+
+ #cat(i,"\n") #aks
+
+ for (j in (i+1):n.preds) { #create vector or factor data for second variable
+ y.fac<-F
+ if (is.vector(data[,j])) {
+ y.var <- seq(min(data[,j],na.rm=T),max(data[,j],na.rm=T),length = 20)
+ y2 <- as.vector(tapply(y.var,rep(1:10,rep(2,10)),mean))
+
+ } else {
+ y.var <- factor(names(table(data[,j])),levels = levels(data[,j]))
+ y.fac<-T
+ }
+ y.length <- length(y.var)
+
+# and now make a temporary data frame
+
+ pred.frame <- expand.grid(list(x.var,y.var))
+ names(pred.frame) <- c(pred.names[i],pred.names[j])
+
+ n <- 3 # and add the balance of the variables to it
+
+ for (k in 1:n.preds) {
+ if (k != i & k != j) {
+ if (is.vector(data[,k])) { # either with the mean
+ pred.frame[,n] <- mean(data[,k],na.rm=T)
+ } else { # or the most common factor level
+ temp.table <- sort(table(data[,k]),decreasing = TRUE)
+ pred.frame[,n] <- rep(names(temp.table)[1],x.length * y.length)
+ pred.frame[,n] <- as.factor(pred.frame[,n])
+ }
+ names(pred.frame)[n] <- pred.names[k]
+ n <- n + 1
+ }
+ }
+#
+# form the prediction
+#
+ prediction <- predict.gbm(gbm.object,pred.frame,n.trees = n.trees, type="link")
+
+ if (use.weights) {
+ point.prob <- predict.gbm(mask.object[[1]],pred.frame, n.trees = mask.trees, type="response")
+ interaction.test.model <- lm(prediction ~ as.factor(pred.frame[,1]) + as.factor(pred.frame[,2]),
+ weights = point.prob)
+ }
+
+ else {
+
+ interaction.test.model <- lm(prediction ~ as.factor(pred.frame[,1]) + as.factor(pred.frame[,2]))
+ }
+ #cat("\n",i,names(data)[i],x.length,length(unique(data[,i]))," ",
+ # j,names(data)[j],y.length,length(unique(data[,j])),dim(pred.frame));flush.console()
+ #print(summary(data[,i]));print(summary(data[,j]))
+ # check significance of interaction term in model that pools every 4 grid points #
+ pred.frame<<-pred.frame
+
+ if(x.fac==F | y.fac==F){ # case where at least one cov is not a factor
+ if(x.fac==T) {x3 <- pred.frame[,1]
+ } else { x3 <- rep(rep(x2,rep(2,10)),y.length) }
+ if(y.fac==T) {y3 <- pred.frame[,1]
+ } else { y3 <- rep(y2,rep(x.length*2,length(y2)))}
+ int.p.table[i,j] <- anova(lm(prediction~as.factor(x3)*as.factor(y3)))[3,5] #aks
+ }
+
+
+ interaction.flag <- round(mean(resid(interaction.test.model)^2)*1000,2)
+
+ cross.tab[i,j] <- interaction.flag
+ } # end of j loop
+ } # end of i loop
+
+# create an index of the values in descending order
+
+ search.index <- ((n.preds^2) + 1) - rank(cross.tab, ties.method = "first")
+
+ n.important <- max(2,round(0.1 * ((n.preds^2)/2),0))
+ var1.names <- rep(" ",n.important)
+ var1.index <- rep(0,n.important)
+ var2.names <- rep(" ",n.important)
+ var2.index <- rep(0,n.important)
+ int.size <- rep(0,n.important)
+ int.p <- rep(NA,n.important) #aks
+
+ for (i in 1:n.important) {
+
+ index.match <- match(i,search.index)
+
+ j <- trunc(index.match/n.preds) + 1
+ var1.index[i] <- j
+ var1.names[i] <- pred.names[j]
+
+ k <- index.match%%n.preds
+ if (k > 0) { #only do this if k > 0 - otherwise we have all zeros from here on
+ var2.index[i] <- k
+ var2.names[i] <- pred.names[k]
+
+ int.size[i] <- cross.tab[k,j]
+ int.p[i] <- int.p.table[k,j] #aks
+ }
+
+ }
+ rank.list <- data.frame(var1.index,var1.names,var2.index,var2.names,int.size,p=int.p)
+ rank.list <- rank.list[complete.cases(rank.list),]
+ return(list(rank.list = rank.list, interactions = cross.tab, gbm.call = gbm.object$gbm.call))
+}
+
+"gbm.simplify" <-
+function(gbm.object, # a gbm object describing sample intensity
+ n.folds = 10, # number of times to repeat the analysis
+ n.drops = "auto", # can be automatic or an integer specifying the number of drops to check
+ alpha = 1, # controls stopping when n.drops = "auto"
+ prev.stratify = TRUE, # use prevalence stratification in selecting evaluation data
+ eval.data = NULL, # an independent evaluation data set - leave here for now
+ plot = TRUE, # plot results
+ verbose=F) # to suppress text output.
+{
+# function to simplify a brt model fitted using gbm.step
+#
+# version 2.9 - J. Leathwick/J. Elith - June 2007
+#
+# starts with an inital cross-validated model as produced by gbm.step
+# and then assesses the potential to remove predictors using k-fold cv
+# does this for each fold, removing the lowest contributing predictor,
+# and repeating this process for a set number of steps
+# after the removal of each predictor, the change in predictive deviance
+# is computed relative to that obtained when using all predictors
+# it returns a list containing the mean change in deviance and its se
+# as a function of the number of variables removed
+# having completed the cross validation, it then identifies the sequence
+# of variable to remove when using the full data set, testing this
+# up to the number of steps used in the cross-validation phase of the analysis
+# with results reported to the screen - it then returns
+# a table containing the order in which variables are to be removed
+# and a list of vectors, each of which specifies the predictor col numbers
+# in the original dataframe - the latter can be used as an argument to gbm.step
+# e.g., gbm.step(data = data, gbm.x = simplify.object$pred.list[[4]]...
+# would implement a new analysis with the original predictor set, minus its
+# four lowest contributing predictors
+#
+
+require(gbm)
+
+# first get the original analysis details..
+
+ gbm.call <- gbm.object$gbm.call
+ data <- eval.parent(parse(text=gbm.call$dataframe))
+ n.cases <- nrow(data)
+ gbm.x <- gbm.call$gbm.x
+ gbm.y <- gbm.call$gbm.y
+ family <- gbm.call$family
+ lr <- gbm.call$learning.rate
+ tc <- gbm.call$tree.complexity
+ start.preds <- length(gbm.x)
+ max.drops <- start.preds - 2
+ response.name <- gbm.call$response.name
+ predictor.names <- gbm.call$predictor.names
+ n.trees <- gbm.call$best.trees
+ pred.list <- list(initial = gbm.x)
+ weights <- gbm.object$weights
+
+ if (n.drops == "auto") auto.stop <- TRUE
+
+ else auto.stop <- FALSE
+
+# take a copy of the original data and starting predictors
+
+ orig.data <- data
+ orig.gbm.x <- gbm.x
+ verbose=TRUE
+# if (!is.null(eval.data)) independent.test <- TRUE
+# else independent.test <- FALSE
+
+# extract original performance statistics...
+
+ original.deviance <- round(gbm.object$cv.statistics$deviance.mean,4)
+ original.deviance.se <- round(gbm.object$cv.statistics$deviance.se,4)
+
+ if(verbose){ #aks
+ cat("\n");cat("gbm.simplify - version 2.9","\n\n")#AKS
+ cat("simplifying gbm.step model for ",response.name," with ",start.preds," predictors",sep="")
+ cat(" and ",n.cases," observations \n",sep="")
+ cat("original deviance = ",original.deviance,"(",original.deviance.se,")\n\n",sep="")
+ }
+
+# check that n.drops is less than n.preds - 2 and update if required
+
+ if (auto.stop) {
+ if(verbose) cat("variable removal will proceed until average change exceeds the original se\n\n") #aks
+ n.drops <- 1 } else{
+ if (n.drops > start.preds - 2) {
+ if(verbose) cat("value of n.drops (",n.drops,") is greater than permitted","\n", #aks
+ "resetting value to ",start.preds - 2,"\n\n",sep="")
+ n.drops <- start.preds - 2
+ } else {
+ if(verbose) cat("a fixed number of",n.drops,"drops will be tested\n\n") #aks
+ }
+ }
+ flush.console()#AKS
+
+
+# set up storage for results
+
+ dev.results <- matrix(0, nrow = n.drops, ncol = n.folds)
+ dimnames(dev.results) <- list(paste("drop.",1:n.drops,sep=""),
+ paste("rep.",1:n.folds,sep=""))
+
+ drop.count <- matrix(NA, nrow = start.preds, ncol = n.folds)
+ dimnames(drop.count) <- list(predictor.names,paste("rep.",1:n.folds,sep=""))
+
+ original.deviances <- rep(0,n.folds)
+
+ model.list <- list(paste("model",c(1:n.folds),sep="")) # dummy list for the tree models
+
+# create gbm.fixed function call
+
+ gbm.call.string <- paste("gbm.fixed(data=train.data,gbm.x=gbm.new.x,gbm.y=gbm.y,",sep="")
+ gbm.call.string <- paste(gbm.call.string,"family=family,learning.rate=lr,tree.complexity=tc,",sep="")
+ gbm.call.string <- paste(gbm.call.string,"n.trees = ",n.trees,", site.weights = weights.subset,verbose=FALSE)",sep="")
+
+# now set up the fold structure
+
+ if (prev.stratify & family == "bernoulli") {
+ presence.mask <- data[,gbm.y] == 1
+ absence.mask <- data[,gbm.y] == 0
+ n.pres <- sum(presence.mask)
+ n.abs <- sum(absence.mask)
+
+# create a vector of randomised numbers and feed into presences
+ selector <- rep(0,n.cases)
+ temp <- rep(seq(1, n.folds, by = 1), length = n.pres)
+ temp <- temp[order(runif(n.pres, 1, 100))]
+ selector[presence.mask] <- temp
+
+# and then do the same for absences
+ temp <- rep(seq(1, n.folds, by = 1), length = n.abs)
+ temp <- temp[order(runif(n.abs, 1, 100))]
+ selector[absence.mask] <- temp
+ }
+
+ else { #otherwise make them random with respect to presence/absence
+ selector <- rep(seq(1, n.folds, by = 1), length = n.cases)
+ selector <- selector[order(runif(n.cases, 1, 100))]
+ }
+
+# now start by creating the intial models for each fold
+
+ if(verbose) cat("creating initial models");flush.console()#AKS
+
+ gbm.new.x <- orig.gbm.x
+
+ for (i in 1:n.folds) {
+
+# create the training and prediction folds
+
+ train.data <- orig.data[selector!=i,]
+ weights.subset <- weights[selector != i]
+ eval.data <- orig.data[selector==i,]
+
+ model.list[[i]] <- eval(parse(text=gbm.call.string)) # create a fixed size object
+
+# now make predictions to the withheld fold
+
+ u_i <- eval.data[,gbm.y]
+ y_i <- predict.gbm(model.list[[i]], eval.data, n.trees, "response")
+
+ original.deviances[i] <- round(calc.deviance(u_i,y_i, family = family, calc.mean = TRUE),4)
+ if(verbose) cat(".");flush.console()#AKS
+ } # end of creating initial models
+ if(verbose) {cat("\n");cat("done \n\n")} #aks
+ n.steps <- 1
+
+ while (n.steps <= n.drops & n.steps <= max.drops) {
+
+ if(verbose) cat("dropping predictor",n.steps,"\n");flush.console()#AKS
+
+ for (i in 1:n.folds) {
+
+# get the right data
+
+ train.data <- orig.data[selector!=i,]
+ eval.data <- orig.data[selector==i,]
+ weights.subset <- weights[selector != i]
+
+# get the current model details
+
+ gbm.x <- model.list[[i]]$gbm.call$gbm.x
+ n.preds <- length(gbm.x)
+ these.pred.names <- model.list[[i]]$gbm.call$predictor.names
+ contributions <- model.list[[i]]$contributions
+
+# get the index number in pred.names of the last variable in the contribution table
+
+ last.variable <- match(as.character(contributions[n.preds,1]),these.pred.names)
+ gbm.new.x <- gbm.x[-last.variable]
+
+# and keep a record of what has been dropped
+
+ last.variable <- match(as.character(contributions[n.preds,1]),predictor.names)
+ drop.count[last.variable,i] <- n.steps
+
+ model.list[[i]] <- eval(parse(text=gbm.call.string)) # create a fixed size object
+
+ u_i <- eval.data[,gbm.y]
+ y_i <- predict.gbm(model.list[[i]],eval.data,n.trees,"response")
+
+ deviance <- round(calc.deviance(u_i,y_i, family = family, calc.mean = TRUE),4)
+
+# calculate difference between intial and new model by subtracting new from old because we want to minimise deviance
+
+ dev.results[n.steps,i] <- round(deviance - original.deviances[i] ,4)
+
+ }
+
+ if (auto.stop){ # check to see if delta mean is less than original deviance error estimate
+
+ delta.mean <- mean(dev.results[n.steps,])
+
+ if (delta.mean < (alpha * original.deviance.se)) {
+ n.drops <- n.drops + 1
+ dev.results <- rbind(dev.results, rep(0,n.folds))
+ }
+ }
+ n.steps <- n.steps + 1
+ }
+
+# now label the deviance matrix
+
+ dimnames(dev.results) <- list(paste("drop.",1:n.drops,sep=""),
+ paste("rep.",1:n.folds,sep=""))
+
+# calculate mean changes in deviance and their se
+
+ mean.delta <- apply(dev.results,1,mean)
+ se.delta <- sqrt(apply(dev.results,1,var))/sqrt(n.folds)
+
+###########################
+
+ if (plot) {
+ y.max <- 1.5 * max(mean.delta + se.delta)
+ y.min <- 1.5 * min(mean.delta - se.delta)
+ plot(seq(0,n.drops),c(0,mean.delta),xlab="variables removed",
+ ylab = "change in predictive deviance",type='l',ylim=c(y.min,y.max))
+ lines(seq(0,n.drops),c(0,mean.delta) + c(0,se.delta),lty = 2)
+ lines(seq(0,n.drops),c(0,mean.delta) - c(0,se.delta),lty = 2)
+ abline(h = 0 , lty = 2, col = 3)
+ min.y <- min(c(0,mean.delta))
+ min.pos <- match(min.y,c(0,mean.delta)) - 1 # subtract one because now zero base
+ abline(v = min.pos, lty = 3, col = 2)
+ abline(h = original.deviance.se, lty = 2, col = 2)
+ title(paste("RFE deviance - ",response.name," - folds = ",n.folds,sep=""))
+ }
+
+# and do a final backwards drop sequence from the original model
+
+ if(verbose) cat("\nnow processing final dropping of variables with full data \n\n") #aks
+
+ gbm.call.string <- paste("gbm.fixed(data=orig.data,gbm.x=gbm.new.x,gbm.y=gbm.y,",sep="")
+ gbm.call.string <- paste(gbm.call.string,"family=family,learning.rate=lr,tree.complexity=tc,",sep="")
+ gbm.call.string <- paste(gbm.call.string,"n.trees = ",n.trees,", site.weights = weights,verbose=FALSE)",sep="")
+
+ n.steps <- n.steps - 1 #decrement by one to reverse last increment in prev loop
+
+ final.model <- gbm.object # restore the original model and data
+ train.data <- orig.data
+
+# and set up storage
+
+ final.drops <- matrix(NA, nrow = start.preds, ncol = 1)
+ dimnames(final.drops) <- list(predictor.names,"step")
+
+ for (i in 1:n.steps) {
+
+# get the current model details
+
+ gbm.x <- final.model$gbm.call$gbm.x
+ n.preds <- length(gbm.x)
+ these.pred.names <- final.model$gbm.call$predictor.names
+ contributions <- final.model$contributions
+
+ if(verbose) cat(i,"-",as.character(contributions[n.preds,1]),"\n");flush.console()#AKS
+
+# get the index number in pred.names of the last variable in the contribution table
+
+ last.variable <- match(as.character(contributions[n.preds,1]),these.pred.names)
+ gbm.new.x <- gbm.x[-last.variable]
+
+# and keep a record of what has been dropped
+
+ last.variable <- match(as.character(contributions[n.preds,1]),predictor.names)
+ final.drops[last.variable] <- i
+
+ final.model <- eval(parse(text=gbm.call.string)) # create a fixed size object
+
+ }
+
+#and then the corresponding numbers
+
+ removal.list <- dimnames(final.drops)[[1]]
+ removal.list <- removal.list[order(final.drops)]
+ removal.list <- removal.list[1:n.drops]
+
+ removal.numbers <- rep(0,n.steps)
+
+# construct predictor lists to faciliate final model fitting
+
+ for (i in 1:n.steps) {
+ removal.numbers[i] <- match(removal.list[i],predictor.names)
+ pred.list[[i]] <- orig.gbm.x[0-removal.numbers[1:i]]
+ names(pred.list)[i] <- paste("preds.",i,sep="")
+ }
+
+ deviance.summary <- data.frame(mean = round(mean.delta,4), se = round(se.delta,4))
+
+ final.drops <- data.frame("preds" = dimnames(final.drops)[[1]][order(final.drops)],
+ "order" = final.drops[order(final.drops)])
+
+ return(list(deviance.summary = deviance.summary,
+ deviance.matrix = dev.results, drop.count = drop.count,
+ final.drops = final.drops, pred.list = pred.list,
+ gbm.call = gbm.call))
+
+}
+
+"gbm.fixed" <-
+function (data, # the input dataframe
+ gbm.x, # indices of the predictors in the input dataframe
+ gbm.y, # index of the response in the input dataframe
+ tree.complexity = 1, # the tree depth - sometimes referred to as interaction depth
+ site.weights = rep(1, nrow(data)), # by default set equal
+ verbose = TRUE, # to control reporting
+ learning.rate = 0.001, # controls speed of the gradient descent
+ n.trees = 2000, # default number of trees
+ train.fraction = 1,
+ bag.fraction = 0.5, # varies random sample size for each new tree
+ family = "bernoulli", # can be any of bernoulli, poisson, gaussian, laplace - note quotes
+ keep.data = FALSE, # keep original data
+ var.monotone = rep(0, length(gbm.x)) # constrain to positive (1) or negative monontone (-1)
+ )
+{
+#
+# j leathwick, j elith - 6th May 2007
+#
+# version 2.9 - developed in R 2.0
+#
+# calculates a gradient boosting (gbm)object with a fixed number of trees
+# with the number of trees identified using gbm.step or some other procedure
+#
+# mostly used as a utility function, e.g., when being called by gbm.simplify
+#
+# takes as input a dataset and args selecting x and y variables, learning rate and tree complexity
+#
+# updated 13/6/05 to accommodate weighting of sites when calculating total and residual deviance
+#
+# updated 10/8/05 to correct how site.weights are returned
+#
+# requires gbm
+#
+#
+ require(gbm)
+
+# setup input data and assign to position one
+
+ dataframe.name <- deparse(substitute(data)) # get the dataframe name
+
+ if(length(gbm.x)<=1) stop("Only one predictor remains in backward selection\nplease select more predictors")
+ x.data <- eval(data[, gbm.x]) #form the temporary datasets
+ names(x.data) <- names(data)[gbm.x]
+ y.data <- eval(data[, gbm.y])
+ sp.name <- names(data)[gbm.y]
+
+
+ assign("x.data", x.data, pos = 1) #and assign them for later use
+ assign("y.data", y.data, pos = 1)
+
+#fit the gbm model
+
+ z1 <- unclass(Sys.time())
+
+ gbm.call <- paste("gbm(y.data ~ .,n.trees = n.trees, data=x.data, verbose = F, interaction.depth = tree.complexity,
+ weights = site.weights, shrinkage = learning.rate, distribution = as.character(family),
+ var.monotone = var.monotone, bag.fraction = bag.fraction, keep.data = keep.data)", sep="")
+
+ if (verbose) {
+ print(paste("fitting gbm model with a fixed number of ",n.trees," trees for ",sp.name,sep=""),quote=FALSE) }
+
+ gbm.object <- eval(parse(text = gbm.call))
+
+ best.trees <- n.trees
+
+#extract fitted values and summary table
+
+ fitted.values <- predict.gbm(gbm.object,x.data,n.trees = n.trees,type="response")
+ gbm.summary <- summary(gbm.object,n.trees = n.trees, plotit = FALSE)
+
+ y_i <- y.data
+ u_i <- fitted.values
+
+ if (family == "poisson") {
+ deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
+ resid.deviance <- 2 * sum(deviance.contribs * site.weights)
+ residuals <- sqrt(abs(deviance.contribs * 2))
+ residuals <- ifelse((y_i - u_i) < 0, 0 - residuals, residuals)
+
+ u_i <- sum(y.data * site.weights) / sum(site.weights)
+ deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
+ total.deviance <- 2 * sum(deviance.contribs * site.weights)
+ }
+
+ if (family == "bernoulli") {
+ deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
+ resid.deviance <- -2 * sum(deviance.contribs * site.weights)
+ residuals <- sqrt(abs(deviance.contribs * 2))
+ residuals <- ifelse((y_i - u_i) < 0, 0 - residuals, residuals)
+
+ u_i <- sum(y.data * site.weights) / sum(site.weights)
+ deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
+ total.deviance <- -2 * sum(deviance.contribs * site.weights)
+ }
+
+ if (family == "laplace") {
+ resid.deviance <- sum(abs(y_i - u_i))
+ residuals <- y_i - u_i
+ u_i <- mean(y.data)
+ total.deviance <- sum(abs(y_i - u_i))
+ }
+
+ if (family == "gaussian") {
+ resid.deviance <- sum((y_i - u_i) * (y_i - u_i))
+ residuals <- y_i - u_i
+ u_i <- mean(y.data)
+ total.deviance <- sum((y_i - u_i) * (y_i - u_i))
+ }
+
+ if (verbose) {
+ print(paste("total deviance = ",round(total.deviance,2),sep=""),quote=F)
+ print(paste("residual deviance = ",round(resid.deviance,2),sep=""),quote=F)}
+
+# now assemble data to be returned
+
+ z2 <- unclass(Sys.time())
+ elapsed.time.minutes <- round((z2 - z1)/ 60,2) #calculate the total elapsed time
+
+ gbm.detail <- list(dataframe = dataframe.name, gbm.x = gbm.x, predictor.names = names(x.data),
+ gbm.y = gbm.y, reponse.name = names(y.data), family = family, tree.complexity = tree.complexity,
+ learning.rate = learning.rate, bag.fraction = bag.fraction, cv.folds = 0, n.trees = n.trees, best.trees = best.trees,
+ train.fraction = train.fraction, var.monotone = var.monotone, date = date(), elapsed.time.minutes = elapsed.time.minutes)
+
+ gbm.object$gbm.call <- gbm.detail
+ gbm.object$fitted <- fitted.values
+ gbm.object$residuals <- residuals
+ gbm.object$contributions <- gbm.summary
+ gbm.object$self.statistics <- list(null.deviance = total.deviance, resid.deviance = resid.deviance)
+ gbm.object$weights <- site.weights
+
+ rm(x.data,y.data, pos=1) #finally, clean up the temporary dataframes
+
+ return(gbm.object)
+}
+
+
+make.p.tif=T
+make.binary.tif=T
+
+tc=NULL
+n.folds=3
+alpha=1
+
+learning.rate = NULL
+bag.fraction = 0.5
+prev.stratify = TRUE
+max.trees = 10000
+tolerance.method = "auto"
+tolerance = 0.001
+seed=NULL
+opt.methods=2
+save.model=TRUE
+MESS=FALSE
+# Interpret command line argurments #
+# Make Function Call #
+Args <- commandArgs(trailingOnly=FALSE)
+
+ for (i in 1:length(Args)){
+ if(Args[i]=="-f") ScriptPath<-Args[i+1]
+ }
+
+ for (arg in Args) {
+ argSplit <- strsplit(arg, "=")
+ argSplit[[1]][1]
+ argSplit[[1]][2]
+ if(argSplit[[1]][1]=="c") csv <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="o") output <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mpt") make.p.tif <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mbt") make.binary.tif <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="tc") tc <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="nf") n.folds <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="alp") alpha <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="lr") learning.rate <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="bf") bag.fraction <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="ps") prev.stratify <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mt") max.trees <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="om") opt.methods <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="seed") seed <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="savm") save.model <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="tolm") tolerance.method <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="tol") tolerance <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mes") MESS <- argSplit[[1]][2]
+
+ }
+ print(csv)
+ print(output)
+ print(responseCol)
+
+ScriptPath<-dirname(ScriptPath)
+source(paste(ScriptPath,"LoadRequiredCode.r",sep="\\"))
+
+
+alpha<-as.numeric(alpha)
+make.p.tif<-as.logical(make.p.tif)
+make.binary.tif<-as.logical(make.binary.tif)
+prev.stratify<-as.logical(prev.stratify)
+save.model<-make.p.tif | make.binary.tif
+opt.methods<-as.numeric(opt.methods)
+MESS<-as.logical(MESS)
+
+ fit.brt.fct(ma.name=csv,
+ tif.dir=NULL,
+ output.dir=output,
+ response.col=responseCol,
+ make.p.tif=make.p.tif,make.binary.tif=make.binary.tif,
+ simp.method="cross-validation",debug.mode=F,responseCurveForm="pdf",tc=tc,n.folds=n.folds,alpha=alpha,script.name="brt.r",
+ learning.rate =learning.rate, bag.fraction = bag.fraction,prev.stratify = prev.stratify,max.trees = max.trees,seed=seed,
+ save.model=save.model,opt.methods=opt.methods,MESS=MESS)
+
+
+
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_GLM_pluggable.r b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_GLM_pluggable.r
new file mode 100644
index 0000000..a472b6d
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_GLM_pluggable.r
@@ -0,0 +1,775 @@
+# A set of "pluggable" R functions for automated model fitting of glm models to presence/absence data #
+#
+# Modified 12-2-09 to: remove categorical covariates from consideration if they only contain one level
+# ID factor variables based on "categorical" prefix and look for tifs in subdir
+# Give progress reports
+# write large output tif files in blocks to alleviate memory issues
+# various bug fixes
+#
+#
+# Modified 3-4-09 to use a list object for passing of arguements and data
+#
+
+
+# Libraries required to run this program #
+# PresenceAbsence - for ROC plots
+# XML - for XML i/o
+# rgdal - for geotiff i/o
+# sp - used by rdgal library
+# raster for geotiff o
+options(error=NULL)
+
+fit.glm.fct <- function(ma.name,tif.dir=NULL,output.dir=NULL,response.col="^response.binary",make.p.tif=T,make.binary.tif=T,
+ simp.method="AIC",responseCurveForm=NULL,debug.mode=F,model.family="binomial",script.name="glm.r",opt.methods=2,save.model=TRUE,UnitTest=FALSE,MESS=FALSE){
+ # This function fits a stepwise GLM model to presence-absence data.
+ # written by Alan Swanson, 2008-2009
+ ## Maintained and edited by Marian Talbert September 2010-
+ # Arguements.
+ # ma.name: is the name of a .csv file with a model array. full path must be included unless it is in the current
+ # R working directory #
+ # tif.dir: is the directory containing geotiffs for each covariate. only required if geotiffs output of the
+ # response surface is requested # # cov.list.name: is the name of a text file with the names of covariates to be included in models (one per line).
+ # output.dir: is the directory that output files will be stored in. if not given, files will go to the current working directory.
+ # response.col: column number of the model array containing a binary 0/1 response. all other columns will be considered explanatory variables.
+ # make.p.tif: T if a geotiff of the response surface is desired.
+ # make.binary.tif: T if a geotiff of the response surface is desired.
+ # simp.method: model simplification method. valid methods include: "AIC" and "BIC".
+ # debug.mode: if T, output is directed to the console during the run. also, a pdf is generated which contains response curve plots and perspective plots
+ # showing the effects of interactions deemed important. if F, output is diverted to a text file and the console is kept clear
+ # except for final output of an xml file. in either case, a set of standard output files are created in the output directory.
+ #
+
+ # Value:
+ # returns nothing but generates a number of output files in the directory
+ # "output.dir" named above. These output files consist of:
+ #
+ # glm_output.txt: a text file with fairly detailed results of the final model.
+ # glm_output.xml: an xml-formatted text file with results from the final model.
+ # glm_response_curves.xml: an xml-formatted text file with response curves for
+ # each covariate in the final model.
+ # glm_prob_map.tif: a geotiff of the response surface
+ # glm_bin_map.tif: a geotiff of the binary response surface. threhold is based on the roc curve at the point where sensitivity=specificity.
+ # glm_log.txt: a file containing text output diverted from the console when debug.mode=F
+ # glm_auc_plot.jpg: a jpg file of a ROC plot.
+ # glm_response_curves.pdf: an pdf file with response curves for
+ # each covariate in the final model and perspective plots showing the effect of interactions deemed significant.
+ # only produced when debug.mode=T
+ # seed=NULL # sets a seed for the algorithm, any inegeger is acceptable
+ # opt.methods=2 # sets the method used for threshold optimization used in the
+ # # the evaluation statistics module
+ # save.model=FALSE # whether the model will be used to later produce tifs
+ #
+ # when debug.mode is true, these filenames will include a number in them so that they will not overwrite preexisting files. eg brt_1_output.txt.
+ #
+ times <- as.data.frame(matrix(NA,nrow=7,ncol=1,dimnames=list(c("start","read data","model fit",
+ "model summary","response curves","tif output","done"),c("time"))))
+ times[1,1] <- unclass(Sys.time())
+ t0 <- unclass(Sys.time())
+ #simp.method <- match.arg(simp.method)
+ out <- list(
+ input=list(ma.name=ma.name,
+ tif.dir=tif.dir,
+ output.dir=output.dir,
+ response.col=response.col,
+ make.p.tif=make.p.tif,
+ model.family=model.family,
+ make.binary.tif=make.binary.tif,
+ simp.method=simp.method,
+ model.type="stepwise glm",
+ model.source.file=script.name,
+ model.fitting.subset=NULL,
+ save.model=save.model,
+ run.time=paste(c(format(Sys.time(),"%Y-%m-%d"),format(Sys.time(),"%H:%M:%S")),collapse="T"),
+ sig.test="t-test p-value",
+ MESS=MESS),
+ dat = list(missing.libs=NULL,
+ output.dir=list(dname=NULL,exist=F,readable=F,writable=F),
+ tif.dir=list(dname=NULL,exist=F,readable=F,writable=F),
+ tiff.ind=NULL,
+ tif.names=NULL,
+ bname=NULL,
+ bad.factor.covs=NULL, # factorchange
+ ma=list( status=c(exists=F,readable=F),
+ dims=c(NA,NA),
+ resp.name=NULL,
+ factor.levels=NA,
+ used.covs=NULL,
+ ma=NULL,
+ train.weights=NULL,
+ test.weights=NULL,
+ train.xy=NULL,
+ test.xy=NULL,
+ ma.subset=NULL
+ ),
+ ma.test=NULL),
+ mods=list(final.mod=NULL,
+ r.curves=NULL,
+ tif.output=list(prob=NULL,bin=NULL),
+ auc.output=NULL,
+ interactions=NULL, # not used #
+ summary=NULL),
+ time=list(strt=unclass(Sys.time()),end=NULL),
+ error.mssg=list(NULL),
+ ec=0 # error count #
+ )
+ # load libaries #
+ out <- check.libs(list("PresenceAbsence","rgdal","XML","sp","survival","tools","raster","tcltk2","foreign","ade4"),out)
+
+ # exit program now if there are missing libraries #
+ if(!is.null(out$error.mssg[[1]])){
+ cat(saveXML(glm.to.xml(out),indent=T),'\n')
+ return()
+ }
+
+ if(is.na(match(simp.method,c("AIC","BIC")))){
+ return()
+ }
+
+ # check output dir #
+
+ out$dat$output.dir <- check.dir(output.dir)
+ if(out$dat$output.dir$writable==F) {out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: output directory",output.dir,"is not writable")
+ out$dat$output.dir$dname <- getwd()
+ }
+
+ # generate a filename for output #
+ if(debug.mode==T){ #paste(bname,"_summary.txt",sep="")
+ outfile <- paste(bname<-paste(out$dat$output.dir$dname,"/glm_",n<-1,sep=""),"_output.txt",sep="")
+ while(file.access(outfile)==0) outfile<-paste(bname<-paste(out$dat$output.dir$dname,"/glm_",n<-n+1,sep=""),"_output.txt",sep="")
+ capture.output(cat("temp"),file=outfile) # reserve the new basename #
+ } else bname <- paste(out$dat$output.dir$dname,"/glm",sep="")
+ out$dat$bname <- bname
+
+ # sink console output to log file #
+ if(!debug.mode) {sink(logname <- paste(bname,"_log.txt",sep=""));on.exit(sink)} else logname<-NULL
+ options(warn=1)
+
+ # check tif dir #
+ if(!is.null(tif.dir)){
+ out$dat$tif.dir <- check.dir(tif.dir)
+ if(out$dat$tif.dir$readable==F & (out$input$make.binary.tif | out$input$make.p.tif)) {
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: tif directory",tif.dir,"is not readable")
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ cat(saveXML(brt.to.xml(out),indent=T),'\n')
+ return()
+ }
+ }
+
+
+ # find .tif files in tif dir #
+
+ if(out$dat$tif.dir$readable) out$dat$tif.names <- list.files(out$dat$tif.dir$dname,pattern=".tif",recursive=T)
+
+ # check for model array #
+ out$input$ma.name <- check.dir(out$input$ma.name)$dname
+ if(UnitTest!=FALSE) options(warn=2)
+ out <- read.ma(out)
+ if(UnitTest==1) return(out)
+
+ if(!is.null(out$error.mssg[[1]])){
+ if(!debug.mode) {sink();on.exit();unlink(logname)}
+ cat(saveXML(glm.to.xml(out),indent=T),'\n')
+ return()
+ }
+ #allowing site weights
+
+ times[2,1] <- unclass(Sys.time())
+ if(!debug.mode) {sink();cat("Progress:20%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("20%\n")} ### print time
+ cat("\nbegin processing of model array:",out$input$ma.name,"\n")
+ cat("\nfile basename set to:",out$dat$bname,"\n")
+ if(debug.mode) assign("out",out,envir=.GlobalEnv)
+
+
+
+
+ ##############################################################################################################
+ # Begin model fitting #
+ ##############################################################################################################
+
+ # Fit null GLM and run stepwise, then print results #
+ cat("\n","Fitting stepwise GLM","\n")
+ flush.console()
+ penalty <- if(out$input$simp.method=="AIC") 2 else log(nrow(out$dat$ma$ma))
+ scope.glm <- list(lower=as.formula(paste(out$dat$ma$resp.name,"~1")),
+ upper=as.formula(paste(out$dat$ma$resp.name,"~",paste(out$dat$ma$used.covs,collapse='+'))))
+
+ mymodel.glm.step <- step(glm(as.formula(paste(out$dat$ma$resp.name,"~1")),family=out$input$model.family,data=out$dat$ma$ma,weights=out$dat$ma$train.weights,na.action="na.exclude"),
+ direction='both',scope=scope.glm,trace=0,k=penalty)
+
+ out$mods$final.mod <- mymodel.glm.step
+
+ out$dat$ma$used.covs <- attr(terms(formula(out$mods$final.mod)),"term.labels")
+ #assign("out",out,envir=.GlobalEnv)
+ t3 <- unclass(Sys.time())
+ cat("\n","Finished with stepwise GLM","\n")
+ cat("Summary of Model:","\n")
+ print(out$mods$summary <- summary(mymodel.glm.step))
+ if(!is.null(out$dat$bad.factor.cols)){
+ cat("\nWarning: the following categorical response variables were removed from consideration\n",
+ "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n\n")
+ }
+ flush.console()
+
+ flush.console()
+ times[3,1] <- unclass(Sys.time())
+ if(!debug.mode) {sink();cat("Progress:40%\n");flush.console();sink(logname,append=T)} else cat("40%\n")
+
+ #r<-residuals(out$mods$final.mod, "deviance")
+
+ if(length(coef(out$mods$final.mod))==1) stop("Null model was selected. \nEvaluation metrics and plots will not be produced")
+
+ ##############################################################################################################
+ # Begin model output #
+ ##############################################################################################################
+
+ # Store .jpg ROC plot #
+ txt0 <- paste("Generalized Linear Results\n",out$input$run.time,"\n\n","Data:\n\t ",ma.name,"\n\t ","n(pres)=",
+ out$dat$ma$n.pres[2],"\n\t n(abs)=",out$dat$ma$n.abs[2],"\n\t number of covariates considered=",(length(names(out$dat$ma$ma))-1),
+ "\n\n","Settings:\n","\n\t model family=",out$input$model.family,
+ "\n\n","Results:\n\t ","number covariates in final model=",length(out$dat$ma$used.covs),
+ "\n\t total time for model fitting=",round((unclass(Sys.time())-t0)/60,2),"min\n",sep="")
+
+ capture.output(cat(txt0),file=paste(bname,"_output.txt",sep=""))
+
+ capture.output(out$mods$summary,file=paste(bname,"_output.txt",sep=""),append=TRUE)
+ if(!is.null(out$dat$bad.factor.cols)){
+ capture.output(cat("\nWarning: the following categorical response variables were removed from consideration\n",
+ "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n"),
+ file=paste(bname,"_output.txt",sep=""),append=T)
+ }
+
+
+ auc.output <- make.auc.plot.jpg(out$dat$ma$ma,pred=predict(mymodel.glm.step,type='response'),plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="GLM",opt.methods=opt.methods,
+ weight=out$dat$ma$train.weights,out=out)
+
+ out$mods$auc.output<-auc.output
+
+ # if(out$input$model.family=="poisson"){
+ # auc.output <- make.poisson.jpg(out$dat$ma$ma,pred=predict(mymodel.glm.step,type='response'),
+ # plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="BRT",
+ # weight=out$dat$ma$train.weights,out=out)
+
+ # out$mods$auc.output<-auc.output
+ # }
+
+ # out$mods$auc.output<-auc.output
+
+
+
+
+ times[4,1] <- unclass(Sys.time())
+ if(!debug.mode) {sink();cat("Progress:70%\n");flush.console();sink(logname,append=T)} else cat("70%\n")
+
+ # Response curves #
+
+if(is.null(responseCurveForm)){
+responseCurveForm<-0}
+
+if(debug.mode | responseCurveForm=="pdf"){
+ nvar <- length(coef(out$mods$final.mod))-1
+ pcol <- min(ceiling(sqrt(nvar)),4)
+ prow <- min(ceiling(nvar/pcol),3)
+
+ pdf(paste(bname,"_response_curves.pdf",sep=""),width=11,height=8.5,onefile=T)
+ par(oma=c(2,2,4,2),mfrow=c(prow,pcol))
+ r.curves <-my.termplot(out$mods$final.mod,plot.it=T)
+ mtext(paste("GLM response curves for",basename(ma.name)),outer=T,side=3,cex=1.3)
+ par(mfrow=c(1,1))
+ graphics.off()
+ } else r.curves<-try(my.termplot(out$mods$final.mod,plot.it=F))
+
+
+ if(class(r.curves)!="try-error") {
+ out$mods$r.curves <- r.curves
+ } else {
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: problem fitting response curves",r.curves)
+ }
+
+
+ t4 <- unclass(Sys.time())
+ cat("\nfinished with final model summarization, t=",round(t4-t3,2),"sec\n");flush.console()
+ times[5,1] <- unclass(Sys.time())
+ if(!debug.mode) {sink();cat("Progress:80%\n");flush.console();sink(logname,append=T)} else cat("80%\n")
+
+
+ ##############################################################################################################
+ # Make .tif of predictions #
+ ##############################################################################################################
+ out$mods$final.mod$contributions$var<-attr(terms(formula(out$mods$final.mod)),"term.labels")
+ assign("out",out,envir=.GlobalEnv)
+
+ save.image(paste(output.dir,"modelWorkspace",sep="\\"))
+ if(out$input$make.p.tif==T | out$input$make.binary.tif==T){
+ if((n.var <- length(coef(out$mods$final.mod)))<2){
+ mssg <- "Error producing geotiff output: null model selected by stepwise procedure - pointless to make maps"
+ class(mssg)<-"try-error"
+ } else {
+ cat("\nproducing prediction maps...","\n","\n");flush.console()
+ mssg <- proc.tiff(model=out$mods$final.mod,vnames=attr(terms(formula(out$mods$final.mod)),"term.labels"),
+ tif.dir=out$dat$tif.dir$dname,filenames=out$dat$tif.ind,pred.fct=glm.predict,factor.levels=out$dat$ma$factor.levels,make.binary.tif=make.binary.tif,
+ thresh=out$mods$auc.output$thresh,make.p.tif=make.p.tif,outfile.p=paste(out$dat$bname,"_prob_map.tif",sep=""),
+ outfile.bin=paste(out$dat$bname,"_bin_map.tif",sep=""),tsize=50,NAval=-3000,fnames=out$dat$tif.names,logname=logname,out=out) #"brt.prob.map.tif"
+ }
+ # model=out$mods$final.mod;vnames=attr(terms(formula(out$mods$final.mod)),"term.labels");
+# tif.dir=out$dat$tif.dir$dname;pred.fct=glm.predict;factor.levels=out$dat$ma$factor.levels;make.binary.tif=make.binary.tif;
+# thresh=out$mods$auc.output$thresh;make.p.tif=make.p.tif;outfile.p=paste(out$dat$bname,"_prob_map.tif",sep="");
+# outfile.bin=paste(out$dat$bname,"_bin_map.tif",sep="");tsize=50;NAval=-3000;fnames=out$dat$tif.names
+ if(class(mssg)=="try-error"){
+ if(!debug.mode) {sink();on.exit();unlink(logname)}
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("Error producing prediction maps:",mssg)
+ cat(saveXML(glm.to.xml(out),indent=T),'\n')
+ return()
+ } else {
+ if(make.p.tif) out$mods$tif.output$prob <- paste(out$dat$bname,"_prob_map.tif",sep="")
+ if(make.binary.tif) out$mods$tif.output$bin <- paste(out$dat$bname,"_bin_map.tif",sep="")
+ t5 <- unclass(Sys.time())
+ cat("\nfinished with prediction maps, t=",round(t5-t4,2),"sec\n");flush.console()
+ }
+ }
+ times[6,1] <- unclass(Sys.time())
+ if(!debug.mode) {sink();cat("Progress:90%\n");flush.console();sink(logname,append=T)} else cat("90%\n")
+
+ # Evaluation Statistics on Test Data#
+
+ if(!is.null(out$dat$ma$ma.test)) Eval.Stat<-EvaluationStats(out,thresh=auc.output$thresh,train=out$dat$ma$ma,
+ train.pred=predict(mymodel.glm.step,type="response"),opt.methods)
+
+
+ # Write summaries to xml #
+ assign("out",out,envir=.GlobalEnv)
+ doc <- glm.to.xml(out)
+
+ #cat(paste("\ntotal time=",round((unclass(Sys.time())-t0)/60,2),"min\n\n\n",sep=""))
+ if(!debug.mode) {
+ sink();on.exit();unlink(logname)
+ cat("Progress:100%\n");flush.console()
+ cat(saveXML(doc,indent=T),'\n')
+ flush.console()
+ } else {cat("100%\n")}
+ capture.output(cat(saveXML(doc,indent=T)),file=paste(out$dat$bname,"_output.xml",sep=""))
+ assign("fit",out$mods$final.mod,envir=.GlobalEnv)
+ times[7,1] <- unclass(Sys.time())
+
+ times$net <- times$time - times$time[1]
+ times$pct <- round(times$net/times$net[7]*100,2)
+ times$process <- c(0,times$time[-1]-times$time[-7])
+ times$ppcnt <- round(times$process/times$net[7]*100,2)
+ write.csv(times,paste(bname,"times.csv",sep="_"))
+ invisible(out)
+}
+
+glm.predict <- function(model,x) {
+ # retrieve key items from the global environment #
+ # make predictionss.
+
+ y <- as.vector(predict(model,x,type="response"))
+
+ # encode missing values as -1.
+ y[is.na(y)]<- NaN
+
+ # return predictions.
+ return(y)
+ }
+
+logit <- function(x) 1/(1+exp(-x))
+
+
+file_path_as_absolute <- function (x){
+ if (!file.exists(epath <- path.expand(x)))
+ stop(gettextf("file '%s' does not exist", x), domain = NA)
+ cwd <- getwd()
+ on.exit(setwd(cwd))
+ if (file_test("-d", epath)) {
+ setwd(epath)
+ getwd()
+ }
+ else {
+ setwd(dirname(epath))
+ file.path(getwd(), basename(epath))
+ }
+}
+#file_path_as_absolute(".")
+
+glm.to.xml <- function(out){
+ require(XML)
+ schema.http="http://www.w3.org/2001/XMLSchema-instance"
+ schema.fname="file:/Users/isfs2/Desktop/Source/2008-04-09/src/gov/nasa/gsfc/quickmap/ModelBuilder/modelRun_output_v2.xsd"
+ xml.out <- newXMLDoc()
+ mr <- newXMLNode("modelRunOutput",doc=xml.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))#,parent=xml.out
+ sm <- newXMLNode("singleModel",parent=mr)
+ bg <- newXMLNode("background",parent=sm)
+ newXMLNode("mdsName",out$input$ma.name,parent=bg)
+ newXMLNode("runDate",out$input$run.time,parent=bg)
+ lc <- newXMLNode("layersConsidered",parent=bg)#, parent = xml.out)
+ kids <- lapply(paste(out$dat$tif.dir$dname,"/",out$dat$tif.names,sep=""),function(x) newXMLNode("layer", x))
+ addChildren(lc, kids)
+ mo <- newXMLNode("modelOutput",parent=sm)
+ newXMLNode("modelType",out$input$model.type,parent=mo)
+ newXMLNode("modelSourceFile",out$input$model.source.file,parent=mo)
+ newXMLNode("devianceExplained",out$mods$auc.output$pct_dev_exp,parent=mo,attrs=list(type="percentage"))
+ newXMLNode("nativeOutput",paste(out$dat$bname,"_output.txt",sep=""),parent=mo)
+ newXMLNode("binaryOutputFile",out$mods$tif.output[[2]],parent=mo)
+ newXMLNode("probOutputFile",out$mods$tif.output[[1]],parent=mo)
+ newXMLNode("auc",out$mods$auc.output$auc,parent=mo)
+ newXMLNode("rocGraphic",out$mods$auc.output$plotname,parent=mo)
+ newXMLNode("rocThresh",out$mods$auc.output$thresh,parent=mo)
+ newXMLNode("modelDeviance",out$mods$auc.output$dev_fit,parent=mo)
+ newXMLNode("nullDeviance",out$mods$auc.output$null_dev,parent=mo)
+ if(is.null(out$mods$r.curves)) rc.name <- NULL else rc.name <- paste(out$dat$bname,"_response_curves.xml",sep="")
+ newXMLNode("responsePlotsFile",rc.name,parent=mo)
+ newXMLNode("significanceDescription",out$input$sig.test,parent=mo)
+ mfp <- newXMLNode("modelFitParmas",parent=mo)
+ newXMLNode("simpMethod",out$input$model.type,parent=mfp)
+ newXMLNode("simpCriteria",out$input$simp.method,parent=mfp)
+
+ sv <- newXMLNode("significantVariables",parent=mo)
+ if(!is.null(out$mods$summary)) {
+ t.table <- out$mods$summary$coefficients
+ t.table <- t.table[order(t.table[,4]),]
+ dimnames(t.table)[[2]] <- c("coefficient","standardError","testStatistic","significanceMeasurement")
+ t.table <- as.data.frame(t.table)
+ for(i in 1:nrow(t.table)){
+ x <- newXMLNode("sigVar",parent=sv)
+ newXMLNode(name="name", row.names(t.table)[i],parent=x)
+ kids <- lapply(1:ncol(t.table),function(j) newXMLNode(name=names(t.table)[j], t.table[i,j]))
+ addChildren(x, kids)
+ }
+ }
+
+ if(!is.null(out$mods$r.curves)){
+ r.curves <- out$mods$r.curves
+ factor.levels <- out$dat$ma$factor.levels
+ rc.out <- newXMLDoc()
+ root <- newXMLNode("responseCurves",doc=rc.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))
+ for(i in 1:length(r.curves$names)){
+ if(!is.na(f.index<-match(r.curves$names[i],names(factor.levels)))){
+ vartype <- "factor"} else vartype="continuous"
+ x <- newXMLNode("responseCurve",attrs=list(covariate=r.curves$names[i],type=vartype),parent=root)
+ kids <- lapply(1:length(r.curves$preds[[i]]),function(j){
+ newXMLNode(name="responsePt",parent=x,.children=list(
+ newXMLNode(name="explanatory",as.character(r.curves$preds[[i]])[j]),
+ newXMLNode(name="response",r.curves$resp[[i]][j])))})
+ addChildren(x,kids)
+ }
+ saveXML(rc.out,rc.name,indent=T)
+
+ } else { rc.name<-NULL }
+ if(!is.null(out$error.mssg[[1]])) {
+ kids <- lapply(out$error.mssg,function(j) newXMLNode(name="error",j))
+ addChildren(mo,kids)
+ }
+ return(xml.out)
+ }
+
+
+get.cov.names <- function(model){
+ return(attr(terms(formula(model)),"term.labels"))
+ }
+
+
+check.dir <- function(dname){
+ if(is.null(dname)) dname <- getwd()
+ dname <- gsub("[\\]","/",dname)
+ end.char <- substr(dname,nchar(dname),nchar(dname))
+ if(end.char == "/") dname <- substr(dname,1,nchar(dname)-1)
+ exist <- suppressWarnings(as.numeric(file.access(dname,mode=0))==0) # -1 if bad, 0 if ok #
+ if(exist) dname <- file_path_as_absolute(dname)
+ readable <- suppressWarnings(as.numeric(file.access(dname,mode=4))==0) # -1 if bad, 0 if ok #
+ writable <- suppressWarnings(as.numeric(file.access(dname,mode=2))==0) # -1 if bad, 0 if ok #
+ return(list(dname=dname,exist=exist,readable=readable,writable=writable))
+ }
+
+
+get.image.info <- function(image.names){
+ # this function creates a data.frame with summary image info for a set of images #
+ require(rgdal)
+ require(tools)
+ n.images <- length(image.names)
+
+ full.names <- image.names
+ out <- data.frame(image=full.names,available=rep(F,n.images),size=rep(NA,n.images),
+ type=factor(rep("unk",n.images),levels=c("asc","envi","tif","unk")))
+ out$type[grep(".tif",image.names)]<-"tif"
+ out$type[grep(".asc",image.names)]<-"asc"
+ for(i in 1:n.images){
+ if(out$type[i]=="tif"){
+ x <-try(GDAL.open(full.names[1],read.only=T))
+ suppressMessages(try(GDAL.close(x)))
+ if(class(x)!="try-error") out$available[i]<-T
+ x<-try(file.info(full.names[i]))
+ } else {
+ x<-try(file.info(full.names[i]))
+ if(!is.na(x$size)) out$available[i]<-T
+ }
+ if(out$available[i]==T){
+ out$size[i]<-x$size
+ if(out$type[i]=="unk"){
+ # if extension not known, look for envi .hdr file in same directory #
+ if(file.access(paste(file_path_sans_ext(full.names[i]),".hdr",sep=""))==0)
+ out$type[i]<-"envi"
+ }
+ }
+ }
+ return(out)
+}
+
+#make.r.curves.glm <- function(model){
+# tms <- as.matrix(predict(model,type="terms"))
+# mf <- model.frame(model)
+# preds <- list()
+# response <- list()
+# p.names <- colnames(tms)
+# is.fac <- sapply(p.names, function(i) is.factor(mf[, i]))
+# for(i in 1:length(p.names)){
+# if(is.fac[i]){
+# ff <- mf[, p.names[i]]
+# if (!is.null(model$na.action)) ff <- naresid(model$na.action,ff)
+# xx <- as.numeric(ff)
+# ll <- levels(ff)
+# out <- rep(NA,length(ll))
+# for (j in seq_along(ll)) {
+# ww <- which(ff == ll[j])[1]
+# out[j]<-tms[ww,i]
+# #out[j]<-tms[ff==ll[j],i][1]
+# }
+#
+# }
+#
+#
+#
+#data = NULL; envir = environment(formula(model));
+# partial.resid = FALSE; rug = FALSE; terms = NULL; se = FALSE;
+# xlabs = NULL; ylabs = NULL; main = NULL; col.term = 2; lwd.term = 1.5;
+# col.se = "orange"; lty.se = 2; lwd.se = 1; col.res = "gray";
+# cex = 1; pch = par("pch"); col.smth = "darkred"; lty.smth = 2;
+# span.smth = 2/3; ask = dev.interactive() && nb.fig < n.tms;
+# use.factor.levels = TRUE; smooth = NULL; ylim = "common";plot.it=F;
+#terms="yell_250m_evi_16landcovermap_4ag05"
+my.termplot <- function (model, data = NULL, envir = environment(formula(model)),
+ partial.resid = FALSE, rug = FALSE, terms = NULL, se = FALSE,
+ xlabs = NULL, ylabs = NULL, main = NULL, col.term = 2, lwd.term = 1.5,
+ col.se = "orange", lty.se = 2, lwd.se = 1, col.res = "gray",
+ cex = 1, pch = 1, col.smth = "darkred", lty.smth = 2,
+ span.smth = 2/3, ask = dev.interactive() && nb.fig < n.tms,
+ use.factor.levels = TRUE, smooth = NULL, ylim = "common",plot.it=F,
+ ...)
+{ # this function is borrowed from the stats library #
+
+ which.terms <- terms
+ terms <- if (is.null(terms))
+ predict(model, type = "terms", se.fit = se)
+ else predict(model, type = "terms", se.fit = se, terms = terms)
+ n.tms <- ncol(tms <- as.matrix(if (se)
+ terms$fit
+ else terms))
+ mf <- model.frame(model)
+ if (is.null(data))
+ data <- eval(model$call$data, envir)
+ if (is.null(data))
+ data <- mf
+ if (NROW(tms) < NROW(data)) {
+ use.rows <- match(rownames(tms), rownames(data))
+ }
+ else use.rows <- NULL
+ nmt <- colnames(tms)
+ cn <- parse(text = nmt)
+ if (!is.null(smooth))
+ smooth <- match.fun(smooth)
+ if (is.null(ylabs))
+ ylabs <- paste("Partial for", nmt)
+ if (is.null(main))
+ main <- ""
+ else if (is.logical(main))
+ main <- if (main)
+ deparse(model$call, 500)
+ else ""
+ else if (!is.character(main))
+ stop("'main' must be TRUE, FALSE, NULL or character (vector).")
+ main <- rep(main, length.out = n.tms)
+ pf <- envir
+ carrier <- function(term) {
+ if (length(term) > 1)
+ carrier(term[[2]])
+ else eval(term, data, enclos = pf)
+ }
+ carrier.name <- function(term) {
+ if (length(term) > 1)
+ carrier.name(term[[2]])
+ else as.character(term)
+ }
+ if (is.null(xlabs))
+ xlabs <- unlist(lapply(cn, carrier.name))
+ if (partial.resid || !is.null(smooth)) {
+ pres <- residuals(model, "partial")
+ if (!is.null(which.terms))
+ pres <- pres[, which.terms, drop = FALSE]
+ }
+ is.fac <- sapply(nmt, function(i) is.factor(mf[, i]))
+ se.lines <- function(x, iy, i, ff = 2) {
+ tt <- ff * terms$se.fit[iy, i]
+ lines(x, tms[iy, i] + tt, lty = lty.se, lwd = lwd.se,
+ col = col.se)
+ lines(x, tms[iy, i] - tt, lty = lty.se, lwd = lwd.se,
+ col = col.se)
+ }
+ if(plot.it) nb.fig <- prod(par("mfcol"))
+ if (ask & plot.it) {
+ oask <- devAskNewPage(TRUE)
+ on.exit(devAskNewPage(oask))
+ }
+ ylims <- ylim
+ if (identical(ylims, "common")) {
+ ylims <- if (!se)
+ range(tms, na.rm = TRUE)
+ else range(tms + 1.05 * 2 * terms$se.fit, tms - 1.05 *
+ 2 * terms$se.fit, na.rm = TRUE)
+ if (partial.resid)
+ ylims <- range(ylims, pres, na.rm = TRUE)
+ if (rug)
+ ylims[1] <- ylims[1] - 0.07 * diff(ylims)
+ }
+ preds <- list()
+ response <- list()
+ p.names <- xlabs
+ for (i in 1:n.tms) {
+ if (identical(ylim, "free")) {
+ ylims <- range(tms[, i], na.rm = TRUE)
+ if (se)
+ ylims <- range(ylims, tms[, i] + 1.05 * 2 * terms$se.fit[,
+ i], tms[, i] - 1.05 * 2 * terms$se.fit[, i],
+ na.rm = TRUE)
+ if (partial.resid)
+ ylims <- range(ylims, pres[, i], na.rm = TRUE)
+ if (rug)
+ ylims[1] <- ylims[1] - 0.07 * diff(ylims)
+ }
+ if (is.fac[i]) {
+ ff <- mf[, nmt[i]]
+ if (!is.null(model$na.action))
+ ff <- naresid(model$na.action, ff)
+ preds[[i]] <- ll <- levels(ff)
+ xlims <- range(seq_along(ll)) + c(-0.5, 0.5)
+ xx <- as.numeric(ff)
+ response[[i]]<-rep(NA,length(ll))
+ if (rug) {
+ xlims[1] <- xlims[1] - 0.07 * diff(xlims)
+ xlims[2] <- xlims[2] + 0.03 * diff(xlims)
+ }
+
+ if(plot.it){
+ plot(1, 0, type = "n", xlab = xlabs[i], ylab = ylabs[i],
+ xlim = xlims, ylim = ylims, main = main[i], xaxt = "n",
+ ...)
+ if (use.factor.levels)
+ axis(1, at = seq_along(ll), labels = ll, ...)
+ else axis(1)
+ for (j in seq_along(ll)) {
+ ww <- which(ff == ll[j])[c(1, 1)]
+ jf <- j + c(-0.4, 0.4)
+ lines(jf, response[[i]][j]<-tms[ww, i], col = col.term, lwd = lwd.term,...)
+ if (se) se.lines(jf, iy = ww, i = i)
+ }
+ } else {
+ for (j in seq_along(ll)) {
+ ww <- which(ff == ll[j])[c(1, 1)]
+ response[[i]][j]<-tms[ww, i]
+ }
+ }
+ }
+ else {
+ xx <- carrier(cn[[i]])
+ if (!is.null(use.rows))
+ xx <- xx[use.rows]
+ xlims <- range(xx, na.rm = TRUE)
+ if (rug)
+ xlims[1] <- xlims[1] - 0.07 * diff(xlims)
+
+ response[[i]]<- logit(seq(min(tms[,i]),max(tms[,i]),length=100)) #aks
+ preds[[i]]<-seq(min(xx),max(xx),length=100) #aks
+ if(plot.it){
+ oo <- order(xx)
+ plot(xx[oo], logit(tms[oo, i]), type = "l", xlab = xlabs[i],
+ ylab = ylabs[i], xlim = xlims, ylim = logit(ylims),
+ main = main[i], col = col.term, lwd = lwd.term,
+ ...)
+ if (se)
+ se.lines(xx[oo], iy = oo, i = i)
+ }
+ }
+ if(plot.it){
+ if (partial.resid) {
+ if (!is.fac[i] && !is.null(smooth)) {
+ smooth(xx, pres[, i], lty = lty.smth, cex = cex,
+ pch = pch, col = col.res, col.smooth = col.smth,
+ span = span.smth)
+ }
+ else points(xx, pres[, i], cex = cex, pch = pch,
+ col = col.res)
+ }
+ if (rug) {
+ n <- length(xx)
+ lines(rep.int(jitter(xx), rep.int(3, n)), rep.int(ylims[1] +
+ c(0, 0.05, NA) * diff(ylims), n))
+ if (partial.resid)
+ lines(rep.int(xlims[1] + c(0, 0.05, NA) * diff(xlims),
+ n), rep.int(pres[, i], rep.int(3, n)))
+ }
+ }
+ }
+ invisible(list(names=p.names,preds=preds,resp=response))
+}
+
+
+# Interpret command line argurments #
+# Make Function Call #
+ # Interpret command line argurments #
+# Make Function Call #
+make.p.tif=T
+make.binary.tif=T
+simp.method="AIC"
+opt.methods=2
+save.model=FALSE
+MESS=FALSE
+
+Args <- commandArgs(trailingOnly=FALSE)
+
+ for (i in 1:length(Args)){
+ if(Args[i]=="-f") ScriptPath<-Args[i+1]
+ }
+
+ print(Args)
+ for (arg in Args) {
+ argSplit <- strsplit(arg, "=")
+ argSplit[[1]][1]
+ argSplit[[1]][2]
+ if(argSplit[[1]][1]=="c") csv <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="o") output <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mpt") make.p.tif <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mbt") make.binary.tif <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="om") opt.methods <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="savm") save.model <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="sm") simp.method <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mes") MESS <- argSplit[[1]][2]
+ }
+ print(csv)
+ print(output)
+ print(responseCol)
+
+ScriptPath<-dirname(ScriptPath)
+source(paste(ScriptPath,"LoadRequiredCode.r",sep="\\"))
+
+make.p.tif<-as.logical(make.p.tif)
+make.binary.tif<-as.logical(make.binary.tif)
+save.model<-make.p.tif | make.binary.tif
+opt.methods<-as.numeric(opt.methods)
+MESS<-as.logical(MESS)
+
+ fit.glm.fct(ma.name=csv,
+ tif.dir=NULL,output.dir=output,
+ response.col=responseCol,make.p.tif=make.p.tif,make.binary.tif=make.binary.tif,
+ simp.method=simp.method,debug.mode=F,responseCurveForm="pdf",script.name="glm.r",opt.methods=opt.methods,save.model=save.model,MESS=MESS)
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_MARS_pluggable.r b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_MARS_pluggable.r
new file mode 100644
index 0000000..914906f
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_MARS_pluggable.r
@@ -0,0 +1,1697 @@
+# A set of "pluggable" R functions for automated model fitting of glm models to presence/absence data #
+#
+# Modified 12-2-09 to: remove categorical covariates from consideration if they only contain one level
+# ID factor variables based on "categorical" prefix and look for tifs in subdir
+# Give progress reports
+# write large output tif files in blocks to alleviate memory issues
+# various bug fixes
+#
+#
+# Modified 3-4-09 to use a list object for passing of arguements and data
+#
+
+
+# Libraries required to run this program #
+# PresenceAbsence - for ROC plots
+# XML - for XML i/o
+# rgdal - for geotiff i/o
+# sp - used by rdgal library
+# raster for geotiff o
+options(error=NULL)
+
+fit.mars.fct <- function(ma.name,tif.dir=NULL,output.dir=NULL,response.col="^response.binary",make.p.tif=T,make.binary.tif=T,
+ mars.degree=1,mars.penalty=2,responseCurveForm=NULL,debug.mode=T,script.name="mars.r",opt.methods=2,save.model=TRUE,UnitTest=FALSE,MESS=FALSE){
+ # This function fits a stepwise GLM model to presence-absence data.
+ # written by Alan Swanson, 2008-2009
+ # # Maintained and edited by Marian Talbert September 2010-
+ # Arguements.
+ # ma.name: is the name of a .csv file with a model array. full path must be included unless it is in the current
+ # R working directory # THIS FILE CAN NOW INCLUDE AN OPTIONAL COLUMN OF SITE WEIGHTS WHICH MUST BE LABELED "site.weights"
+ # tif.dir: is the directory containing geotiffs for each covariate. only required if geotiffs output of the
+ # response surface is requested # # cov.list.name: is the name of a text file with the names of covariates to be included in models (one per line).
+ # output.dir: is the directory that output files will be stored in. if not given, files will go to the current working directory.
+ # response.col: column number of the model array containing a binary 0/1 response. all other columns will be considered explanatory variables.
+ # make.p.tif: T if a geotiff of the response surface is desired.
+ # make.binary.tif: T if a geotiff of the response surface is desired.
+ # simp.method: model simplification method. valid methods include: "AIC" and "BIC". NOT CURRENTLY FUNCTIONAL
+ # debug.mode: if T, output is directed to the console during the run. also, a pdf is generated which contains response curve plots and perspective plots
+ # showing the effects of interactions deemed important. if F, output is diverted to a text file and the console is kept clear
+ # except for final output of an xml file. in either case, a set of standard output files are created in the output directory.
+ #
+
+ # Value:
+ # returns nothing but generates a number of output files in the directory
+ # "output.dir" named above. These output files consist of:
+ #
+ # glm_output.txt: a text file with fairly detailed results of the final model.
+ # glm_output.xml: an xml-formatted text file with results from the final model.
+ # glm_response_curves.xml: an xml-formatted text file with response curves for
+ # each covariate in the final model.
+ # glm_prob_map.tif: a geotiff of the response surface
+ # glm_bin_map.tif: a geotiff of the binary response surface. threhold is based on the roc curve at the point where sensitivity=specificity.
+ # glm_log.txt: a file containing text output diverted from the console when debug.mode=F
+ # glm_auc_plot.jpg: a jpg file of a ROC plot.
+ # glm_response_curves.pdf: an pdf file with response curves for
+ # each covariate in the final model and perspective plots showing the effect of interactions deemed significant.
+ # only produced when debug.mode=T
+ # # seed=NULL # sets a seed for the algorithm, any inegeger is acceptable
+ # opt.methods=2 # sets the method used for threshold optimization used in the
+ # # the evaluation statistics module
+ # save.model=FALSE # whether the model will be used to later produce tifs
+ # when debug.mode is true, these filenames will include a number in them so that they will not overwrite preexisting files. eg brt_1_output.txt.
+ #
+ times <- as.data.frame(matrix(NA,nrow=7,ncol=1,dimnames=list(c("start","read data","model fit",
+ "model summary","response curves","tif output","done"),c("time"))))
+ times[1,1] <- unclass(Sys.time())
+ t0 <- unclass(Sys.time())
+ #simp.method <- match.arg(simp.method)
+
+ out <- list(
+ input=list(ma.name=ma.name,
+ tif.dir=tif.dir,
+ output.dir=output.dir,
+ response.col=response.col,
+ make.p.tif=make.p.tif,
+ make.binary.tif=make.binary.tif,
+ site.weights=NULL,
+ save.model=save.model,
+ mars.degree=mars.degree,
+ mars.penalty=mars.penalty,
+ model.type="stepwise with pruning",
+ model.source.file=script.name,
+ model.fitting.subset=NULL, # not used.
+ model.family="binomial",
+ run.time=paste(c(format(Sys.time(),"%Y-%m-%d"),format(Sys.time(),"%H:%M:%S")),collapse="T"),
+ sig.test="chi-squared anova p-value",
+ MESS=MESS),
+ dat = list(missing.libs=NULL,
+ output.dir=list(dname=NULL,exist=F,readable=F,writable=F),
+ tif.dir=list(dname=NULL,exist=F,readable=F,writable=F),
+ tif.ind=NULL,
+ tif.names=NULL,
+ bname=NULL,
+ bad.factor.covs=NULL, # factorchange
+ ma=list( status=c(exists=F,readable=F),
+ dims=c(NA,NA),
+ n.pres=c(all=NA,complete=NA,subset=NA),
+ n.abs=c(all=NA,complete=NA,subset=NA),
+ ratio=NA,
+ resp.name=NULL,
+ train.weights=NULL,
+ test.weights=NULL,
+ train.xy=NULL,
+ test.xy=NULL,
+ factor.levels=NA,
+ used.covs=NULL,
+ ma=NULL,
+ ma.subset=NULL,
+ ma.test=NULL)),
+ mods=list(final.mod=NULL,
+ r.curves=NULL,
+ tif.output=list(prob=NULL,bin=NULL),
+ auc.output=NULL,
+ interactions=NULL, # not used #
+ summary=NULL),
+ time=list(strt=unclass(Sys.time()),end=NULL),
+ error.mssg=list(NULL),
+ ec=0 # error count #
+ )
+
+ # load libaries #
+ out <- check.libs(list("PresenceAbsence","rgdal","XML","sp","survival","mda","raster","tcltk2","foreign","ade4"),out)
+
+ # exit program now if there are missing libraries #
+ if(!is.null(out$error.mssg[[1]])){
+ cat(saveXML(mars.to.xml(out),indent=T),'\n')
+ return()
+ }
+
+ # check output dir #
+ out$dat$output.dir <- check.dir(output.dir)
+ if(out$dat$output.dir$writable==F) {out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: output directory",output.dir,"is not writable")
+ out$dat$output.dir$dname <- getwd()
+ }
+
+ # generate a filename for output #
+ if(debug.mode==T){
+ outfile <- paste(bname<-paste(out$dat$output.dir$dname,"/mars_",n<-1,sep=""),"_output.txt",sep="")
+ while(file.access(outfile)==0) outfile<-paste(bname<-paste(out$dat$output.dir$dname,"/mars_",n<-n+1,sep=""),"_output.txt",sep="")
+ capture.output(cat("temp"),file=outfile) # reserve the new basename #
+ } else bname<-paste(out$dat$output.dir$dname,"/mars",sep="")
+ out$dat$bname <- bname
+
+ # sink console output to log file #
+ if(!debug.mode) {sink(logname <- paste(bname,"_log.txt",sep=""));on.exit(sink)} else logname<-NULL
+ options(warn=1)
+
+ # check tif dir #
+ # check tif dir #
+ if(!is.null(tif.dir)){
+ out$dat$tif.dir <- check.dir(tif.dir)
+ if(out$dat$tif.dir$readable==F & (out$input$make.binary.tif | out$input$make.p.tif)) {
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: tif directory",tif.dir,"is not readable")
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ cat(saveXML(brt.to.xml(out),indent=T),'\n')
+ return()
+ }
+ }
+
+
+ # find .tif files in tif dir #
+ if(out$dat$tif.dir$readable) out$dat$tif.names <- list.files(out$dat$tif.dir$dname,pattern=".tif",recursive=T)
+
+ # check for model array #
+ out$input$ma.name <- check.dir(out$input$ma.name)$dname
+
+ if(UnitTest!=FALSE) options(warn=2)
+ out <- read.ma(out)
+ if(UnitTest==1) return(out)
+
+ # exit program now if there are errors in the input data #
+ if(!is.null(out$error.mssg[[1]])){
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ cat(saveXML(mars.to.xml(out),indent=T),'\n')
+ return()
+ }
+
+ cat("\nbegin processing of model array:",out$input$ma.name,"\n")
+ cat("\nfile basename set to:",out$dat$bname,"\n")
+ assign("out",out,envir=.GlobalEnv)
+ if(!debug.mode) {sink();cat("Progress:20%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("20%\n")} ### print time
+ ##############################################################################################################
+ # Begin model fitting #
+ ##############################################################################################################
+
+ # Fit null GLM and run stepwise, then print results #
+ cat("\n","Fitting MARS model","\n")
+ flush.console()
+
+ fit <- mars.glm(data=out$dat$ma$ma, mars.x=c(2:ncol(out$dat$ma$ma)), mars.y=1, mars.degree=out$input$mars.degree, family=out$input$model.family,
+ site.weights=out$dat$ma$train.weights, penalty=out$input$mars.penalty)
+
+ out$mods$final.mod <- fit
+
+ out$mods$final.mod$contributions$var<-names(out$dat$ma$ma)[-1]
+
+ assign("out",out,envir=.GlobalEnv)
+ t3 <- unclass(Sys.time())
+ fit_contribs <- try(mars.contribs(fit))
+ if(class(fit_contribs)=="try-error"){
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]]<- paste("Error summarizing MARS model:",fit_contribs)
+ cat(saveXML(mars.to.xml(out),indent=T),'\n')
+ return()
+ }
+
+ x<-fit_contribs$deviance.table
+ x <- x[x[,2]!=0,]
+ x <- x[order(x[,4]),]
+ row.names(x) <- x[,1]
+ x$df <- -1*x$df
+ x <- x[,-1]
+
+ txt0 <- paste("\nMARS Model Results\n","\n","Data:\n",ma.name,"\n","\n\t n(pres)=",
+ out$dat$ma$n.pres[2],"\n\t n(abs)=",out$dat$ma$n.abs[2],"\n\t n covariates considered=",length(out$dat$ma$used.covs),
+ "\n",
+ "\n total time for model fitting=",round((unclass(Sys.time())-t0)/60,2),"min\n",sep="")
+
+ capture.output(cat(txt0),file=paste(bname,"_output.txt",sep=""))
+
+ cat("\n","Finished with MARS","\n")
+ cat("Summary of Model:","\n")
+ print(out$mods$summary <- x)
+ if(!is.null(out$dat$bad.factor.cols)){
+ cat("\nWarning: the following categorical response variables were removed from consideration\n",
+ "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n\n")
+ }
+ cat("\n","Storing output...","\n","\n")
+ #flush.console()
+ capture.output(cat("\n\nSummary of Model:\n"),file=paste(bname,"_output.txt",sep=""),append=TRUE)
+ capture.output(print(out$mods$summary),file=paste(bname,"_output.txt",sep=""),append=TRUE)
+ if(!is.null(out$dat$bad.factor.cols)){
+ capture.output(cat("\nWarning: the following categorical response variables were removed from consideration\n",
+ "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n"),
+ file=paste(bname,"_output.txt",sep=""),append=T)
+ }
+
+ if(!debug.mode) {sink();cat("Progress:40%\n");flush.console();sink(logname,append=T)} else cat("40%\n")
+
+
+ ##############################################################################################################
+ # Begin model output #
+ ##############################################################################################################
+
+ # Store .jpg ROC plot #
+ auc.output <- make.auc.plot.jpg(out$dat$ma$ma,pred=mars.predict(fit,out$dat$ma$ma)$prediction[,1],
+ plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="MARS",opt.methods=opt.methods,
+ weight=out$dat$ma$train.weights,out=out)
+ out$mods$auc.output<-auc.output
+
+ if(!debug.mode) {sink();cat("Progress:70%\n");flush.console();sink(logname,append=T)} else cat("70%\n")
+
+ # Response curves #
+
+ if(is.null(responseCurveForm)){
+ responseCurveForm<-0}
+
+ if(debug.mode | responseCurveForm=="pdf"){
+ nvar <- nrow(out$mods$summary)
+ pcol <- min(ceiling(sqrt(nvar)),4)
+ prow <- min(ceiling(nvar/pcol),3)
+ r.curves <- try(mars.plot(fit,plot.layout=c(prow,pcol),file.name=paste(bname,"_response_curves.pdf",sep="")))
+
+ } else r.curves<-try(mars.plot(fit,plot.it=F))
+
+ if(class(r.curves)!="try-error") {
+ out$mods$r.curves <- r.curves
+ } else {
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: problem fitting response curves",r.curves)
+ }
+
+ pred.fct<-pred.mars
+
+ assign("out",out,envir=.GlobalEnv)
+
+ save.image(paste(output.dir,"modelWorkspace",sep="\\"))
+ t4 <- unclass(Sys.time())
+ cat("\nfinished with final model summarization, t=",round(t4-t3,2),"sec\n");flush.console()
+ if(!debug.mode) {sink();cat("Progress:80%\n");flush.console();sink(logname,append=T)} else cat("70%\n")
+ # Make .tif of predictions #
+
+ if(out$input$make.p.tif==T | out$input$make.binary.tif==T){
+ if((n.var <- nrow(out$mods$summary))<1){
+ mssg <- "Error producing geotiff output: null model selected by stepwise procedure - pointless to make maps"
+ class(mssg)<-"try-error"
+ } else {
+ cat("\nproducing prediction maps...","\n","\n");flush.console()
+ mssg <- try(proc.tiff(model=out$mods$final.mod,vnames=names(out$dat$ma$ma)[-1],
+ tif.dir=out$dat$tif.dir$dname,filenames=out$dat$tif.ind,pred.fct=pred.mars,factor.levels=out$dat$ma$factor.levels,make.binary.tif=make.binary.tif,
+ thresh=out$mods$auc.output$thresh,make.p.tif=make.p.tif,outfile.p=paste(out$dat$bname,"_prob_map.tif",sep=""),
+ outfile.bin=paste(out$dat$bname,"_bin_map.tif",sep=""),tsize=50.0,NAval=-3000,
+ fnames=out$dat$tif.names,logname=logname,out=out)) #"brt.prob.map.tif"
+ }
+
+ if(class(mssg)=="try-error"){
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("Error producing prediction maps:",mssg)
+ cat(saveXML(mars.to.xml(out),indent=T),'\n')
+ return()
+ } else {
+ if(make.p.tif) out$mods$tif.output$prob <- paste(out$dat$bname,"_prob_map.tif",sep="")
+ if(make.binary.tif) out$mods$tif.output$bin <- paste(out$dat$bname,"_bin_map.tif",sep="")
+ t5 <- unclass(Sys.time())
+ cat("\nfinished with prediction maps, t=",round(t5-t4,2),"sec\n");flush.console()
+ }
+ }
+ if(!debug.mode) {sink();cat("Progress:90%\n");flush.console();sink(logname,append=T)} else cat("90%\n")
+
+ # Evaluation Statistics on Test Data#
+
+ if(!is.null(out$dat$ma$ma.test)) Eval.Stat<-EvaluationStats(out,thresh=auc.output$thresh,train=out$dat$ma$ma,
+ train.pred=mars.predict(fit,out$dat$ma$ma)$prediction[,1],opt.methods)
+
+
+
+ # Write summaries to xml #
+ if(debug.mode) assign("out",out,envir=.GlobalEnv)
+ doc <- mars.to.xml(out)
+
+ cat(paste("\ntotal time=",round((unclass(Sys.time())-t0)/60,2),"min\n\n\n",sep=""))
+ if(!debug.mode) {
+ sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))
+ cat("Progress:100%\n");flush.console()
+ #cat(saveXML(doc,indent=T),'\n')
+ } else #unlink(outfile)
+ capture.output(cat(saveXML(doc,indent=T)),file=paste(out$dat$bname,"_output.xml",sep=""))
+ if(debug.mode) assign("fit",out$mods$final.mod,envir=.GlobalEnv)
+ invisible(out)
+ }
+################################################################################
+########### End fit.mars.fct ####################################
+
+pred.mars <- function(model,x) {
+ # retrieve key items from the global environment #
+ # make predictionss.
+ y <- rep(NA,nrow(x))
+ y[complete.cases(x)] <- as.vector(mars.predict(model,x[complete.cases(x),])$prediction[,1])
+
+#if(sum(is.na(x))/dim(x)[2]!=sum(is.na(y)))
+#h<-is.na(x)
+#h<-apply(h,1,sum)
+#h=h/35
+#f<-is.na(y)
+#which((h-f)!=0,arr.ind=TRUE)
+#b<-cbind(x[which((h-f)!=0,arr.ind=TRUE),],y[which((h-f)!=0,arr.ind=TRUE)])
+
+#which(is.na(y)
+ # encode missing values as -1.
+ y[is.na(y)]<- NaN
+
+ # return predictions.
+ return(y)
+ }
+
+logit <- function(x) 1/(1+exp(-x))
+
+file_path_as_absolute <- function (x){
+ if (!file.exists(epath <- path.expand(x)))
+ stop(gettextf("file '%s' does not exist", x), domain = NA)
+ cwd <- getwd()
+ on.exit(setwd(cwd))
+ if (file_test("-d", epath)) {
+ setwd(epath)
+ getwd()
+ }
+ else {
+ setwd(dirname(epath))
+ file.path(getwd(), basename(epath))
+ }
+}
+#file_path_as_absolute(".")
+
+mars.to.xml <- function(out){
+ require(XML)
+ schema.http="http://www.w3.org/2001/XMLSchema-instance"
+ schema.fname="file:/Users/isfs2/Desktop/Source/2008-04-09/src/gov/nasa/gsfc/quickmap/ModelBuilder/modelRun_output_v2.xsd"
+ xml.out <- newXMLDoc()
+ mr <- newXMLNode("modelRunOutput",doc=xml.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))#,parent=xml.out
+ sm <- newXMLNode("singleModel",parent=mr)
+ bg <- newXMLNode("background",parent=sm)
+ newXMLNode("mdsName",out$input$ma.name,parent=bg)
+ newXMLNode("runDate",out$input$run.time,parent=bg)
+ lc <- newXMLNode("layersConsidered",parent=bg)#, parent = xml.out)
+ kids <- lapply(paste(out$dat$tif.dir$dname,"/",out$dat$tif.names,sep=""),function(x) newXMLNode("layer", x))
+ addChildren(lc, kids)
+ mo <- newXMLNode("modelOutput",parent=sm)
+ newXMLNode("modelType",out$input$model.type,parent=mo)
+ newXMLNode("modelSourceFile",out$input$model.source.file,parent=mo)
+ newXMLNode("devianceExplained",out$mods$auc.output$pct_dev_exp,parent=mo,attrs=list(type="percentage"))
+ newXMLNode("nativeOutput",paste(out$dat$bname,"_output.txt",sep=""),parent=mo)
+ newXMLNode("binaryOutputFile",out$mods$tif.output[[2]],parent=mo)
+ newXMLNode("probOutputFile",out$mods$tif.output[[1]],parent=mo)
+ newXMLNode("auc",out$mods$auc.output$auc,parent=mo)
+ newXMLNode("rocGraphic",out$mods$auc.output$plotname,parent=mo)
+ newXMLNode("rocThresh",out$mods$auc.output$thresh,parent=mo)
+ newXMLNode("modelDeviance",out$mods$auc.output$dev_fit,parent=mo)
+ newXMLNode("nullDeviance",out$mods$auc.output$null_dev,parent=mo)
+ if(is.null(out$mods$r.curves)) rc.name <- NULL else rc.name <- paste(out$dat$bname,"_response_curves.xml",sep="")
+ newXMLNode("responsePlotsFile",rc.name,parent=mo)
+ newXMLNode("significanceDescription",out$input$sig.test,parent=mo)
+ mfp <- newXMLNode("modelFitParmas",parent=mo)
+ newXMLNode("marsDegree",out$input$mars.degree,parent=mfp)
+ newXMLNode("marsPenalty",out$input$mars.penalty,parent=mfp)
+
+ sv <- newXMLNode("significantVariables",parent=mo)
+ if(!is.null(out$mods$summary)) {
+ t.table <- out$mods$summary#$coefficients
+ names(t.table)[3]<-"significanceMeasurement"
+ for(i in 1:nrow(t.table)){
+ x <- newXMLNode("sigVar",parent=sv)
+ newXMLNode(name="name", row.names(t.table)[i],parent=x)
+ kids <- lapply(1:ncol(t.table),function(j) newXMLNode(name=names(t.table)[j], t.table[i,j]))
+ addChildren(x, kids)
+ }
+ }
+
+ if(!is.null(out$mods$r.curves)){
+ r.curves <- out$mods$r.curves
+ factor.levels <- out$dat$ma$factor.levels
+ rc.out <- newXMLDoc()
+ root <- newXMLNode("responseCurves",doc=rc.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))
+ for(i in 1:length(r.curves$names)){
+ if(!is.na(f.index<-match(r.curves$names[i],names(factor.levels)))){
+ vartype <- "factor"} else vartype="continuous"
+ x <- newXMLNode("responseCurve",attrs=list(covariate=r.curves$names[i],type=vartype),parent=root)
+ kids <- lapply(1:length(r.curves$preds[[i]]),function(j){
+ newXMLNode(name="responsePt",parent=x,.children=list(
+ newXMLNode(name="explanatory",as.character(r.curves$preds[[i]])[j]),
+ newXMLNode(name="response",r.curves$resp[[i]][j])))})
+ addChildren(x, kids)
+ }
+ saveXML(rc.out,rc.name,indent=T)
+
+ }
+ if(!is.null(out$error.mssg[[1]])) {
+ kids <- lapply(out$error.mssg,function(j) newXMLNode(name="error",j))
+ addChildren(mo,kids)
+ }
+ return(xml.out)
+ }
+
+
+get.cov.names <- function(model){
+ return(attr(terms(formula(model)),"term.labels"))
+ }
+
+
+check.dir <- function(dname){
+ if(is.null(dname)) dname <- getwd()
+ dname <- gsub("[\\]","/",dname)
+ end.char <- substr(dname,nchar(dname),nchar(dname))
+ if(end.char == "/") dname <- substr(dname,1,nchar(dname)-1)
+ exist <- suppressWarnings(as.numeric(file.access(dname,mode=0))==0) # -1 if bad, 0 if ok #
+ if(exist) dname <- file_path_as_absolute(dname)
+ readable <- suppressWarnings(as.numeric(file.access(dname,mode=4))==0) # -1 if bad, 0 if ok #
+ writable <- suppressWarnings(as.numeric(file.access(dname,mode=2))==0) # -1 if bad, 0 if ok #
+ return(list(dname=dname,exist=exist,readable=readable,writable=writable))
+ }
+
+
+get.image.info <- function(image.names){
+ # this function creates a data.frame with summary image info for a set of images #
+ require(rgdal)
+ n.images <- length(image.names)
+
+ full.names <- image.names
+ out <- data.frame(image=full.names,available=rep(F,n.images),size=rep(NA,n.images),
+ type=factor(rep("unk",n.images),levels=c("asc","envi","tif","unk")))
+ out$type[grep(".tif",image.names)]<-"tif"
+ out$type[grep(".asc",image.names)]<-"asc"
+ for(i in 1:n.images){
+ if(out$type[i]=="tif"){
+ x <-try(GDAL.open(full.names[1],read.only=T))
+ suppressMessages(try(GDAL.close(x)))
+ if(class(x)!="try-error") out$available[i]<-T
+ x<-try(file.info(full.names[i]))
+ } else {
+ x<-try(file.info(full.names[i]))
+ if(!is.na(x$size)) out$available[i]<-T
+ }
+ if(out$available[i]==T){
+ out$size[i]<-x$size
+ if(out$type[i]=="unk"){
+ # if extension not known, look for envi .hdr file in same directory #
+ if(file.access(paste(file_path_sans_ext(full.names[i]),".hdr",sep=""))==0)
+ out$type[i]<-"envi"
+ }
+ }
+ }
+ return(out)
+}
+
+###########################################################################################
+# The following functions are from Elith et al.
+###########################################################################################
+
+"calc.deviance" <-
+function(obs.values, fitted.values, weights = rep(1,length(obs.values)), family=family, calc.mean = TRUE)
+{
+# j. leathwick/j. elith
+#
+# version 2.1 - 5th Sept 2005
+#
+# function to calculate deviance given two vectors of raw and fitted values
+# requires a family argument which is set to binomial by default
+#
+#
+
+if (length(obs.values) != length(fitted.values))
+ stop("observations and predictions must be of equal length")
+
+y_i <- obs.values
+
+u_i <- fitted.values
+
+if (family == "binomial" | family == "bernoulli") {
+
+ deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
+ deviance <- -2 * sum(deviance.contribs * weights)
+
+}
+
+if (family == "poisson" | family == "Poisson") {
+
+ deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
+ deviance <- 2 * sum(deviance.contribs * weights)
+
+}
+
+if (family == "laplace") {
+ deviance <- sum(abs(y_i - u_i))
+ }
+
+if (family == "gaussian") {
+ deviance <- sum((y_i - u_i) * (y_i - u_i))
+ }
+
+
+
+if (calc.mean) deviance <- deviance/length(obs.values)
+
+return(deviance)
+
+}
+
+"calibration" <-
+function(obs, preds, family = family)
+{
+#
+# j elith/j leathwick 17th March 2005
+# calculates calibration statistics for either binomial or count data
+# but the family argument must be specified for the latter
+# a conditional test for the latter will catch most failures to specify
+# the family
+#
+
+if (family == "bernoulli") family <- "binomial"
+pred.range <- max(preds) - min(preds)
+if(pred.range > 1.2 & family == "binomial") {
+print(paste("range of response variable is ", round(pred.range, 2)), sep = "", quote = F)
+print("check family specification", quote = F)
+return()
+}
+if(family == "binomial") {
+pred <- preds + 1e-005
+pred[pred >= 1] <- 0.99999
+mod <- glm(obs ~ log((pred)/(1 - (pred))), family = binomial)
+lp <- log((pred)/(1 - (pred)))
+a0b1 <- glm(obs ~ offset(lp) - 1, family = binomial)
+miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
+ab1 <- glm(obs ~ offset(lp), family = binomial)
+miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
+miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
+}
+if(family == "poisson") {
+mod <- glm(obs ~ log(preds), family = poisson)
+lp <- log(preds)
+a0b1 <- glm(obs ~ offset(lp) - 1, family = poisson)
+miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
+ab1 <- glm(obs ~ offset(lp), family = poisson)
+miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
+miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
+}
+calibration.result <- c(mod$coef, miller1, miller2, miller3)
+names(calibration.result) <- c("intercept", "slope", "testa0b1", "testa0|b1", "testb1|a")
+return(calibration.result)
+}
+
+"mars.contribs" <-
+function (mars.glm.object,sp.no = 1, verbose = TRUE)
+{
+
+# j leathwick/j elith August 2006
+#
+# version 3.1 - developed in R 2.3.1 using mda 0.3-1
+#
+# takes a mars/glm model and uses the updated mars export table
+# stored as the second list item from mars.binomial
+# assessing the contribution of the fitted functions,
+# amalgamating terms for variables as required
+#
+# amended 29/9/04 to pass original mars model details
+# and to return f-statistics
+#
+# amended 7th January to accommodate any glm model family
+#
+# modified 050609 by aks to output a numeric deviance table #
+
+ mars.detail <- mars.glm.object$mars.call
+ pred.names <- mars.detail$predictor.base.names #get the names from the original data
+ n.preds <- length(pred.names)
+
+ spp.names <- mars.detail$y.names
+ family <- mars.detail$family
+
+ m.table <- mars.glm.object$mars.table[-1,]
+ m.table$names1 <- as.character(m.table$names1) #convert from a factor
+
+ x.data <- as.data.frame(eval(mars.glm.object$basis.functions))
+ y.data <- as.data.frame(eval(mars.glm.object$y.values))
+
+ assign("x.data", x.data, pos = 1)
+ assign("y.data", y.data, pos = 1)
+ assign("sp.no", sp.no, pos = 1)
+
+ glm.model <- glm(y.data[,sp.no] ~ .,data = x.data,family = family)
+
+ print(paste("performing backwards drops for mars/glm model for",
+ spp.names[sp.no]),quote=F)
+
+ n.bfs <- length(m.table[,1])
+
+ delta.deviance <- rep(0,n.preds)
+ df <- rep(0,n.preds)
+ signif <- rep(0,n.preds)
+
+ for (i in 1:n.preds) { #start at two because first line is the constant
+
+ # look for variable names in the table matching those in the var list
+
+ var.nos <- grep(as.character(pred.names[i]),m.table$names1)
+
+ #drop.list stores numbers of basis functions to be dropped
+ if (length(var.nos) > 0) {
+ drop.list <- 0 - var.nos
+ x.data.new <- x.data[,drop.list]
+ assign("x.data.new",x.data.new,pos=1)
+
+ if (verbose) {
+ print(paste("Dropping ",pred.names[i],"...",sep=""),
+ quote=FALSE)
+ }
+ x.data.new<-as.data.frame(x.data.new)
+ if(dim(x.data.new)[2]==0){
+ new.model <- glm(y.data[,sp.no] ~ 1, family = family)
+ }else new.model <- glm(y.data[,sp.no] ~ ., data=x.data.new, family = family)
+
+ comparison <- anova(glm.model,new.model,test="Chisq")
+
+ df[i] <- comparison[2,3]
+ delta.deviance[i] <- zapsmall(comparison[2,4],4)
+ signif[i] <- zapsmall(comparison[2,5],6)
+ }
+
+ }
+
+ rm(x.data,y.data,sp.no,pos=1) # tidy up temporary files
+
+ #deviance.table <- as.data.frame(cbind(pred.names,delta.deviance,df,signif))
+ #names(deviance.table) <- c("variable","delta_dev","deg. free.","p-value")
+ deviance.table <- data.frame(variable=pred.names,delta_dev=delta.deviance,df=df,p_value=signif)#aks
+ return(list(mars.call=mars.detail,deviance.table=deviance.table))
+}
+
+"mars.cv" <-
+function (mars.glm.object, nk = 10, sp.no = 1, prev.stratify = F)
+{
+#
+# j. leathwick/j. elith - August 2006
+#
+# version 3.1 - developed in R 2.3.1 using mda 0.3-1
+#
+# function to perform k-fold cross validation
+# with full model perturbation for each subset
+#
+# requires mda library from Cran
+# requires functions mw and calibration
+#
+# takes a mars/glm object produced by mars.glm
+# and first assesses the full model, and then
+# randomly subsets the dataset into nk folds and drops
+# each subset in turn, fitting on remaining data
+# and predicting for withheld data
+#
+# caters for both single species and community models via the argument sp.no
+# for the first, sp.no can be left on its default of 1
+# for community models, sp.no can be varied from 1 to n.spp
+#
+# modified 29/9/04 to
+# 1. return mars analysis details for audit trail
+# 2. calculate roc and calibration on subsets as well as full data
+# returning the mean and se of the ROC scores
+# and the mean calibration statistics
+#
+# modified 8/10/04 to add prevalence stratification
+# modified 7th January to test for binomial family and return if not
+#
+# updated 15th March to cater for both binomial and poisson families
+#
+# updated 16th June 2005 to calculate residual deviance
+#
+
+ data <- mars.glm.object$mars.call$dataframe #get the dataframe name
+ dataframe.name <- deparse(substitute(data))
+
+ data <- as.data.frame(eval(parse(text=data))) #and now the data
+ n.cases <- nrow(data)
+
+ mars.call <- mars.glm.object$mars.call #and the mars call details
+ mars.x <- mars.call$mars.x
+ mars.y <- mars.call$mars.y
+ mars.degree <- mars.call$degree
+ mars.penalty <- mars.call$penalty
+ family <- mars.call$family
+ site.weights <- eval(mars.glm.object$weights$site.weights)
+
+ n.spp <- length(mars.y)
+
+ if (sp.no > n.spp) {
+ print(paste("the value specified for sp.no of",sp.no),quote=F)
+ print(paste("exceeds the total number of species, which is ",n.spp),quote=F)
+ return()
+ }
+
+ xdat <- as.data.frame(data[,mars.x])
+ xdat <- mars.new.dataframe(xdat)[[1]]
+ ydat <- mars.glm.object$y.values[,sp.no]
+ target.sp <- names(data)[mars.y[sp.no]]
+
+ if (prev.stratify) {
+ presence.mask <- ydat == 1
+ absence.mask <- ydat == 0
+ n.pres <- sum(presence.mask)
+ n.abs <- sum(absence.mask)
+ }
+
+ print(paste("Calculating ROC and calibration from full model for",target.sp),quote=F)
+
+ u_i <- mars.glm.object$fitted.values[,sp.no]
+ y_i <- ydat
+
+ if (family == "binomial") {
+ full.resid.deviance <- calc.deviance(y_i,u_i, weights = site.weights, family="binomial")
+ full.test <- roc(y_i, u_i)
+ full.calib <- calibration(y_i, u_i)
+ }
+
+ if (family=="poisson") {
+ full.resid.deviance <- calc.deviance(y_i,u_i, weights = site.weights, family="poisson")
+ full.test <- cor(y_i, u_i)
+ full.calib <- calibration(y_i, u_i, family = "poisson")
+ }
+
+# set up for results storage
+
+ subset.test <- rep(0,nk)
+ subset.calib <- as.data.frame(matrix(0,ncol=5,nrow=nk))
+ names(subset.calib) <- c("intercept","slope","test1","test2","test3")
+ subset.resid.deviance <- rep(0,nk)
+
+# now setup for withholding random subsets
+
+ pred.values <- rep(0, n.cases)
+ fitted.values <- rep(0, n.cases)
+
+ if (prev.stratify) {
+
+ selector <- rep(0,n.cases)
+
+#create a vector of randomised numbers and feed into presences
+
+ temp <- rep(seq(1, nk, by = 1), length = n.pres)
+ temp <- temp[order(runif(n.pres, 1, 100))]
+ selector[presence.mask] <- temp
+
+# and then do the same for absences
+
+ temp <- rep(seq(1, nk, by = 1), length = n.abs)
+ temp <- temp[order(runif(n.abs, 1, 100))]
+ selector[absence.mask] <- temp
+
+ }
+ else { #otherwise make them random with respect to presence/absence
+
+ selector <- rep(seq(1, nk, by = 1), length = n.cases)
+ selector <- selector[order(runif(n.cases, 1, 100))]
+ }
+
+ print("", quote = FALSE)
+ print("Creating predictions for subsets...", quote = F)
+
+ for (i in 1:nk) {
+ cat(i," ")
+ model.mask <- selector != i #used to fit model on majority of data
+ pred.mask <- selector == i #used to identify the with-held subset
+ assign("species.subset", ydat[model.mask], pos = 1)
+ assign("predictor.subset", xdat[model.mask, ], pos = 1)
+
+ # fit new mars model
+
+ mars.object <- mars(y = species.subset, x = predictor.subset,
+ degree = mars.degree, penalty = mars.penalty)
+
+ # and extract basis functions
+
+ n.bfs <- length(mars.object$selected.terms)
+ bf.data <- as.data.frame(mars.object$x)
+ names(bf.data) <- paste("bf",1:n.bfs,sep="")
+ assign("bf.data", bf.data, pos=1)
+
+ # then fit a binomial model to them
+
+ mars.binomial <- glm(species.subset ~ .,data=bf.data[,-1], family= family, maxit = 100)
+
+ pred.basis.functions <- as.data.frame(mda:::model.matrix.mars(mars.object,
+ xdat[pred.mask, ]))
+
+ #now name the bfs to match the approach used in mars.binomial
+
+ names(pred.basis.functions) <- paste("bf",1:n.bfs,sep="")
+
+ # and form predictions for them and evaluate performance
+
+ fitted.values[pred.mask] <- predict(mars.binomial,
+ pred.basis.functions, type = "response")
+
+ y_i <- ydat[pred.mask]
+ u_i <- fitted.values[pred.mask]
+ weights.subset <- site.weights[pred.mask]
+
+ if (family == "binomial") {
+ subset.resid.deviance[i] <- calc.deviance(y_i,u_i,weights = weights.subset, family="binomial")
+ subset.test[i] <- roc(y_i,u_i)
+ subset.calib[i,] <- calibration(y_i, u_i)
+ }
+
+ if (family=="poisson"){
+ subset.resid.deviance[i] <- calc.deviance(y_i,u_i,weights = weights.subset, family="poisson")
+ subset.test[i] <- cor(y_i, u_i)
+ subset.calib[i,] <- calibration(y_i, u_i, family = family)
+ }
+ }
+
+ cat("","\n")
+
+# tidy up temporary files
+
+ rm(species.subset,predictor.subset,bf.data,pos=1)
+
+# and assemble results for return
+
+# mars.detail <- list(dataframe = dataframe.name,
+# x = mars.x, x.names = names(xdat),
+# y = mars.y, y.names = names(data)[mars.y],
+# target.sp = target.sp, degree=mars.degree, penalty = mars.penalty, family = family)
+
+ y_i <- ydat
+ u_i <- fitted.values
+
+ if (family=="binomial") {
+ cv.resid.deviance <- calc.deviance(y_i,u_i,weights = site.weights, family="binomial")
+ cv.test <- roc(y_i, u_i)
+ cv.calib <- calibration(y_i, u_i)
+ }
+
+ if (family=="poisson"){
+ cv.resid.deviance <- calc.deviance(y_i,u_i,weights = site.weights, family="poisson")
+ cv.test <- cor(y_i, u_i)
+ cv.calib <- calibration(y_i, u_i, family = "poisson")
+ }
+
+ subset.test.mean <- mean(subset.test)
+ subset.test.se <- sqrt(var(subset.test))/sqrt(nk)
+
+ subset.test <- list(test.scores = subset.test, subset.test.mean = subset.test.mean,
+ subset.test.se = subset.test.se)
+
+ subset.calib.mean <- apply(subset.calib[,c(1:2)],2,mean)
+ names(subset.calib.mean) <- names(subset.calib)[c(1:2)] #mean only of parameters
+
+ subset.calib <- list(subset.calib = subset.calib,
+ subset.calib.mean = subset.calib.mean)
+
+ subset.deviance.mean <- mean(subset.resid.deviance)
+ subset.deviance.se <- sqrt(var(subset.resid.deviance))/sqrt(nk)
+
+ subset.deviance <- list(subset.deviances = subset.resid.deviance, subset.deviance.mean = subset.deviance.mean,
+ subset.deviance.se = subset.deviance.se)
+
+ return(list(mars.call = mars.call, full.resid.deviance = full.resid.deviance,
+ full.test = full.test, full.calib = full.calib, pooled.deviance = cv.resid.deviance, pooled.test = cv.test,
+ pooled.calib = cv.calib,subset.deviance = subset.deviance, subset.test = subset.test, subset.calib = subset.calib))
+}
+
+"mars.export" <-
+function (object,lineage)
+{
+#
+# j leathwick/j elith August 2006
+#
+# takes a mars model fitted using library mda
+# and extracts the basis functions and their
+# coefficients, returning them as a table
+# caters for models with degree up to 2
+#
+# version 3.1 - developed in R 2.3.1 using mda 0.3-1
+
+ which <- object$selected.terms
+ nterms <- length(which)
+ nspp <- ncol(eval(object$call$y))
+ dir <- object$factor
+ cut <- object$cuts
+ var.names <- dimnames(object$factor)[[2]]
+ p <- length(var.names)
+ coefs <- as.data.frame(object$coefficients)
+ names(coefs) <- names(eval(object$call$y))
+
+# setup storage for results
+
+ names1 <- rep("null", length = nterms)
+ types1 <- rep("null", length = nterms)
+ levels1 <- rep("null", length = nterms)
+ signs1 <- rep(0, length = nterms)
+ cuts1 <- rep(0, length = nterms)
+
+ names2 <- rep("null", length = nterms)
+ types2 <- rep("null", length = nterms)
+ levels2 <- rep("null", length = nterms)
+ signs2 <- rep(0, length = nterms)
+ cuts2 <- rep(0, length = nterms)
+ names1[1] <- "constant"
+ signs1[1] <- 1
+
+# now cycle through the terms
+if(nterms>1){
+ for (i in seq(2, nterms)) {
+ j <- which[i]
+ term.count = 1
+ for (k in 1:p) {
+ if (dir[j, k] != 0) {
+ if (term.count == 1) {
+ n <- match(var.names[k],lineage$full.name)
+ names1[i] <- lineage$base.name[n] #var.names[k]
+ types1[i] <- lineage$type[n]
+ levels1[i] <- lineage$level[n]
+ signs1[i] <- dir[j, k]
+ cuts1[i] <- cut[j, k]
+ term.count <- term.count + 1
+ }
+ else {
+ names2[i] <- var.names[k]
+ n <- match(var.names[k],lineage$full.name)
+ names2[i] <- lineage$base.name[n] #var.names[k]
+ types2[i] <- lineage$type[n]
+ levels2[i] <- lineage$level[n]
+ signs2[i] <- dir[j, k]
+ cuts2[i] <- cut[j, k]
+ }
+ }
+ }
+ }
+ }
+ mars.export.table <- data.frame(names1, types1, levels1, signs1, cuts1,
+ names2, types2, levels2, signs2, cuts2, coefs)
+
+ return(mars.export.table)
+}
+
+"mars.glm" <-
+function (data, # the input data frame
+ mars.x, # column numbers of the predictors
+ mars.y, # column number(s) of the response variable(s)
+ mars.degree = 1, # level of interactions - 1 = zero, 2 = 1st order, etc
+ site.weights = rep(1, nrow(data)), # one weight per site
+ spp.weights = rep(1,length(mars.y)), # one wieght per species
+ penalty = 2, # the default penaly for a mars model
+ family =family) # the family for the glm model
+{
+#
+# j leathwick, j elith - August 2006
+#
+# version 3.1 - developed in R 2.3.1 using mda 0.3-1
+#
+# calculates a mars/glm object in which basis functions are calculated
+# using an initial mars model with single or multiple responses
+# data for individual species are then fitted as glms using the
+# common set of mars basis functions with results returned as a list
+#
+# takes as input a dataset and args selecting x and y variables, and degree of interaction
+# along with site and species weights, the CV penalty, and the glm family argument
+# the latter would normally be one of "binomial" or "poisson" - "gaussian" could be used
+# but in this case the model shouldn't differ from that fitted using mars on its own
+#
+# requires mda and leathwick/elith's mars.export
+#
+# modified 3/11/04 to store information on glm phase convergence
+# and with number of iterations raised to 100 to encourage convergence for low prevalence species
+# modified 4/11/04 to accommodate observation weights in both mars and glm steps
+# modified 12/04 to accommodate non-binomial families
+# modified 11/05 to accommodate factor variables
+# these are done as 0/1 dummy variables in a new dataframe
+# created using mars.new.dataframe
+
+ require(mda)
+
+ n.spp <- length(mars.y)
+
+# setup input data and assign to position one
+
+ dataframe.name <- deparse(substitute(data)) # get the dataframe name
+
+ xdat <- as.data.frame(eval(data[, mars.x])) #form the temporary datasets
+ predictor.base.names <- names(xdat)
+
+# create the new dataframe with dummy vars for factor predictors
+ xdat <- mars.new.dataframe(xdat)
+ lineage <- xdat[[2]] # tracks which variables have had dummy's created
+ xdat <- xdat[[1]]
+ predictor.dummy.names <- names(xdat)
+
+ ydat <- as.data.frame(eval(data[, mars.y]))
+ names(ydat) <- names(data)[mars.y]
+
+ assign("xdat", xdat, pos = 1) #and assign them for later use
+ assign("ydat", ydat, pos = 1)
+
+# create storage space for glm model results
+
+ n.cases <- nrow(xdat)
+
+ fitted.values <- matrix(0,ncol = n.spp, nrow = n.cases)
+ model.residuals <- matrix(0,ncol = n.spp, nrow = n.cases)
+ null.deviances <- rep(0,n.spp)
+ residual.deviances <- rep(0,n.spp)
+ null.dfs <- rep(0,n.spp)
+ residual.dfs <- rep(0,n.spp)
+ converged <- rep(TRUE,n.spp)
+
+# fit the mars model and extract the basis functions
+
+ cat("fitting initial mars model for",n.spp,"responses","\n")
+ cat("followed by a glm model with a family of",family,"\n")
+
+ mars.object <- mars(x = xdat, y = ydat, degree = mars.degree, w = site.weights,
+ wp = spp.weights, penalty = penalty)
+ if(length(mars.object$coefficients)==1) stop("MARS has fit the null model (intercept only) \n new predictors are required")
+ bf.data <- as.data.frame(eval(mars.object$x))
+ n.bfs <- ncol(bf.data)
+ bf.names <- paste("bf", 1:n.bfs, sep = "")
+ names(bf.data) <- bf.names
+ bf.data <- as.data.frame(bf.data[,-1])
+
+ m.table <- as.data.frame(mars.export(mars.object,lineage))
+ names(m.table)[(10 + 1):(10 + n.spp)] <- names(ydat)
+
+ p.values <- matrix(0, ncol = n.spp, nrow = n.bfs)
+ rownames(p.values) <- paste("bf", 1:n.bfs, sep = "")
+ colnames(p.values) <- names(ydat)
+
+# now cycle through the species fitting glm models
+
+ cat("fitting glms for individual responses","\n")
+
+ for (i in 1:n.spp) {
+
+ cat(names(ydat)[i],"\n")
+ model.glm <- glm(ydat[, i] ~ ., data = bf.data, weights = site.weights,
+ family = family, maxit = 100)
+
+# update the coefficients and other results
+
+ # then match names and insert as appropriate
+ m.table[ , i + 10] <- 0 # set all values to zero
+ m.table[ , i + 10] <- model.glm$coefficients # update all the constant
+ sum.table <- summary(model.glm)$coefficients
+ p.values[,i] <- sum.table[,4]
+ fitted.values[,i] <- model.glm$fitted
+ model.residuals[,i] <- resid(model.glm)
+ null.deviances[i] <- model.glm$null.deviance
+ residual.deviances[i] <- model.glm$deviance
+ null.dfs[i] <- model.glm$df.null
+ residual.dfs[i] <- model.glm$df.residual
+ converged[i] <- model.glm$converged
+ }
+
+# now assemble data to be returned
+
+ fitted.values <- as.data.frame(fitted.values)
+ names(fitted.values) <- names(ydat)
+
+ model.residuals <- as.data.frame(model.residuals)
+ names(model.residuals) <- names(ydat)
+
+ deviances <- data.frame(names(ydat),null.deviances,null.dfs,residual.deviances,residual.dfs,converged)
+ names(deviances) <- c("species","null.dev","null.df","resid.dev","resid.df","converged")
+
+ weights = list(site.weights = site.weights, spp.weights = spp.weights)
+
+ mars.detail <- list(dataframe = dataframe.name, mars.x = mars.x,
+ predictor.base.names = predictor.base.names, predictor.dummy.names = predictor.dummy.names,
+ mars.y = mars.y, y.names = names(ydat), degree=mars.degree, penalty = penalty,
+ family = family)
+
+ rm(xdat,ydat,pos=1) #finally, clean up the temporary dataframes
+
+ return(list(mars.table = m.table, basis.functions = bf.data, y.values = ydat,
+ fitted.values = fitted.values, residuals = model.residuals, weights = weights, deviances = deviances,
+ p.values = p.values, mars.call = mars.detail,mars.object=mars.object))
+}
+
+"mars.new.dataframe" <-
+function (input.data)
+{
+#
+# j leathwick, j elith - August 2006
+#
+# version 3.1 - developed in R 2.3.1 using mda 0.3-1
+#
+# takes an input data frame and checks for factor variables
+# converting these to dummy variables, one each for each factor level
+# returning it for use with mars.glm so that factor vars can be included
+# in a mars analysis
+#
+
+ if (!is.data.frame(input.data)) {
+ print("input data must be a dataframe..",quote = FALSE)
+ return()
+ }
+
+ n <- 1
+ for (i in 1:ncol(input.data)) { #first transfer the vector variables
+ if (is.vector(input.data[,i])) {
+ if (n == 1) {
+ output.data <- as.data.frame(input.data[,i])
+ names.list <- names(input.data)[i]
+ var.type <- "vector"
+ factor.level <- "na"
+ }
+ else {
+ output.data[,n] <- input.data[,i]
+ names.list <- c(names.list,names(input.data)[i])
+ var.type <- c(var.type,"vector")
+ factor.level <- c(factor.level,"na")
+ }
+ names(output.data)[n] <- names(input.data)[i]
+ n <- n + 1
+ }
+ }
+
+ for (i in 1:ncol(input.data)) { # and then the factor variables
+ if (is.factor(input.data[,i])) {
+ temp.table <- summary(input.data[,i])
+ for (j in 1:length(temp.table)) {
+ names.list <- c(names.list,names(input.data)[i])
+ var.type <- c(var.type,"factor")
+ factor.level <- c(factor.level,names(temp.table)[j])
+ output.data[,n] <- ifelse(input.data[,i] == names(temp.table)[j],1,0)
+ names(output.data)[n] <- paste(names(input.data)[i],".",names(temp.table)[j],sep="")
+ n <- n + 1
+ }
+ }
+ }
+
+ lineage <- data.frame(names(output.data),names.list,var.type,factor.level)
+ for (i in 1:4) lineage[,i] <- as.character(lineage[,i])
+ names(lineage) <- c("full.name","base.name","type","level")
+
+ return(list(dataframe = output.data, lineage = lineage))
+}
+
+"mars.plot" <-
+function (mars.glm.object, #the input mars object
+ sp.no = 0, # the species number for multi-response models
+ plot.rug=T, # plot a rug of deciles
+ plot.layout = c(3,4), # the plot layout to use
+ file.name = NA, # giving a file name will send results to a pdf
+ plot.it=T) # option for making curves but no plots (aks)
+{
+
+# j leathwick/j elith August 2006
+#
+# version 3.1 - developed in R 2.3.1 using mda 0.3-1
+#
+# requires mars.export of leathwick/elith
+#
+# takes a mars or mars/glm model and either
+# creates a mars export table (vanilla mars object)
+# and works from this or uses the updated mars export table
+# stored as the first list item from mars.binomial
+# plotting out the fitted functions, amalgamating terms
+# for variables and naming the pages as required
+#
+# caters for multispecies mars models by successively plotting
+# all species unless a value other than zero is given for sp.no
+#
+# modified by aks 050609 to only open one plot window and use the record=T option.
+
+ max.plots <- plot.layout[1] * plot.layout[2]
+ if(plot.it){ #aks
+ if (is.na(file.name)) {
+ use.windows = TRUE
+ windows(width = 11, height = 8, record=T) #AKS
+ par(mfrow = plot.layout) #AKS
+ }
+ else {
+ use.windows = FALSE
+ pdf(file=file.name,width = 11, height=8)
+ par(mfrow = plot.layout) #AKS
+ }
+ } else use.windows = FALSE
+
+ if (class(mars.glm.object) == "mars") { #then we have a mars object
+ mars.binomial = FALSE
+ model <- mars.glm.object
+ xdat <- eval(model$call$x)
+ Y <- as.data.frame(eval(model$call$y))
+ n.env <- ncol(xdat)
+ m.table <- mars.export(mars.glm.object)
+ }
+ else {
+ mars.binomial = TRUE
+
+ dat <- mars.glm.object$mars.call$dataframe
+ mars.x <- mars.glm.object$mars.call$mars.x
+ xdat <- as.data.frame(eval(parse(text=dat)))
+ xdat <- xdat[,mars.x]
+
+ m.table <- mars.glm.object[[1]]
+
+ }
+
+ n.bfs <- length(m.table[,1])
+ n.spp <- length(m.table[1,]) - 10
+ r.curves <- list(names=NULL,preds=list(),resp=list()) #aks
+ spp.names <- names(m.table)[(10+1):(10+n.spp)]
+
+ if (sp.no == 0) {
+ wanted.species <- seq(1:n.spp)
+ }
+ else {
+ wanted.species <- sp.no
+ }
+
+ xrange <- matrix(0,nrow = 2,ncol = ncol(xdat))
+ factor.filter <- rep(FALSE,ncol(xdat))
+ for (i in 1:ncol(xdat)) factor.filter[i] <- is.vector(xdat[,i])
+
+ if(sum(factor.filter>1)) {
+ xrange[,factor.filter] <- sapply(xdat[,factor.filter], range)
+ } else xrange[,factor.filter]<-range(xdat[,factor.filter])
+
+ for (i in wanted.species) {
+ n.pages <- 1
+ plotit <- rep(TRUE, n.bfs)
+ print(paste("plotting responses for ",spp.names[i]),quote=F)
+ nplots <- 0
+ cntr <- 1 #aks
+ for (j in 2:n.bfs) {
+ if (m.table$names2[j] == "null") {
+ if (plotit[j]) {
+ varno <- pmatch(as.character(m.table$names1[j]),
+ names(xdat))
+ if (factor.filter[varno]) {
+ Xi <- seq(xrange[1, varno], xrange[2, varno],
+ length = 100)
+ bf <- pmax(0, m.table$signs1[j] * (Xi - m.table$cuts1[j]))
+ bf <- bf * m.table[j, i + 10]
+ bf <- bf - mean(bf)
+ }
+ else {
+ factor.table <- as.data.frame(table(xdat[,varno]))
+ names(factor.table) <- c("levels","coefficients")
+ factor.table$coefficients <- 0
+ level.no <- match(m.table$levels1[j],factor.table$levels)
+ factor.table$coefficients[level.no] <- m.table[j, i + 10]
+ }
+ if (j < n.bfs) {
+ for (k in ((j + 1):n.bfs)) {
+ if (m.table$names1[j] == m.table$names1[k] & m.table$names2[k] == "null") {
+ if (factor.filter[varno]) {
+ bf.add <- pmax(0, m.table$signs1[k] *
+ (Xi - m.table$cuts1[k]))
+ bf.add <- bf.add * m.table[k, i + 10]
+ bf <- bf + bf.add
+ }
+ else {
+ level.no <- match(m.table$levels1[k],factor.table$levels)
+ factor.table$coefficients[level.no] <- m.table[k, i + 10]
+ }
+ plotit[k] <- FALSE
+ }
+ }
+ }
+ #if (nplots == 0) { #AKS
+# if (use.windows) windows(width = 11, height = 8)
+# par(mfrow = plot.layout)
+# }
+ if (factor.filter[varno]) {
+ if(plot.it) plot(Xi, bf, type = "l", xlab = names(xdat)[varno], ylab = "response") #aks
+ if (plot.rug & plot.it) rug(quantile(xdat[,varno], probs = seq(0, 1, 0.1), na.rm = FALSE))
+ r.curves$preds[[cntr]] <- Xi #aks
+ r.curves$resp[[cntr]] <- bf #aks
+ }
+ else {
+ if(plot.it) plot(factor.table$levels, factor.table$coefficients, xlab = names(xdat)[varno]) #aks
+ r.curves$preds[[cntr]] <- factor.table$levels #aks
+ r.curves$resp[[cntr]] <- factor.table$coefficients #aks
+
+ }
+ r.curves$names <- c(r.curves$names,names(xdat)[varno]) #aks
+ cntr <- cntr + 1 #aks
+ nplots = nplots + 1
+ plotit[j] <- FALSE
+ }
+ }
+ else { # case where there is an interaction #
+ if (plotit[j]) {
+ varno1 <- pmatch(as.character(m.table$names1[j]), names(xdat))
+ X1 <- seq(xrange[1, varno1], xrange[2, varno1], length = 20)
+ bf1 <- pmax(0, m.table$signs1[j] * (X1 - m.table$cuts1[j]))
+ varno2 <- pmatch(as.character(m.table$names2[j]), names(xdat))
+ X2 <- seq(xrange[1, varno2], xrange[2, varno2], length = 20)
+ bf2 <- pmax(0, m.table$signs2[j] * (X2 - m.table$cuts2[j]))
+ if(factor.filter[varno1] & factor.filter[varno2]){ #aks
+ zmat <- bf1 %o% bf2
+ zmat <- zmat * m.table[j, i + 10]
+ if (j < n.bfs) {
+ for (k in ((j + 1):n.bfs)) {
+ if (m.table$names1[j] == m.table$names1[k] & m.table$names2[j] == m.table$names2[k]) {
+ bf1 <- pmax(0, m.table$signs1[k] * (X1 - m.table$cuts1[k]))
+ bf2 <- pmax(0, m.table$signs2[j] * (X2 - m.table$cuts2[j]))
+ zmat2 <- bf1 %o% bf2
+ zmat2 <- zmat2 * m.table[j, i + 10]
+ zmat = zmat + zmat2
+ plotit[k] <- FALSE
+ }
+ }
+ }
+ #if (nplots == 0) { #AKS
+ # if (use.windows) windows(width = 11, height = 8)
+ # par(mfrow = plot.layout)
+ # }
+ if(plot.it){
+ persp(x = X1, y = X2, z = zmat, xlab = names(xdat)[varno1],
+ ylab = names(xdat)[varno2], theta = 45, phi = 25) }
+ r.curves$preds[[cntr]] <- X1 #aks
+ r.curves$resp[[cntr]] <- apply(zmat,1,mean,na.rm=T) #aks
+ nplots = nplots + 1
+ } else {
+ r.curves$preds[[cntr]] <- NA #aks
+ r.curves$resp[[cntr]] <- NA #aks
+
+ }
+ r.curves$names <- c(r.curves$names,names(xdat)[varno]) #aks
+ cntr <- cntr + 1 #aks
+ }
+ }
+ if (nplots == 1 & plot.it) {
+ title(paste(spp.names[i], " - page ", n.pages, sep = ""))
+ }
+ if (nplots == max.plots) {
+ nplots = 0
+ n.pages <- n.pages + 1
+ }
+ }
+ }
+ if (!use.windows & plot.it) dev.off()
+ invisible(r.curves) #aks
+}
+
+"mars.plot.fits" <-
+function(mars.glm.object, # the input mars object
+ sp.no = 0, # allows selection of individual spp for multiresponse models
+ mask.presence = FALSE, # plots out just presence records
+ use.factor = FALSE, # draws plots as factors for faster printing
+ plot.layout = c(4,2), # the default plot layout
+ file.name = NA) # allows plotting to a pdf file
+{
+#
+# j leathwick, j elith - August 2006
+#
+# version 3.1 - developed in R 2.3.1 using mda 0.3-1
+#
+# to plot distribution of fitted values in relation to ydat from mars or other p/a models
+# allows masking out of absences to enable focus on sites with high predicted values
+# fitted values = those from model; raw.values = original y values
+# label = text species name; ydat = predictor dataset
+# mask.presence forces function to only plot fitted values for presences
+# use.factor forces to use quicker printing box and whisker plot
+# file.name routes to a pdf file of this name
+#
+
+ max.plots <- plot.layout[1] * plot.layout[2]
+
+ if (is.na(file.name)) { #setup for windows or file output
+ use.windows = TRUE
+ }
+ else {
+ pdf(file.name, width=8, height = 11)
+ par(mfrow = plot.layout)
+ par(cex = 0.5)
+ use.windows = FALSE
+ }
+
+ dat <- mars.glm.object$mars.call$dataframe #get the dataframe name
+ dat <- as.data.frame(eval(parse(text=dat))) #and now the data
+
+ n.cases <- nrow(dat)
+
+ mars.call <- mars.glm.object$mars.call #and the mars call details
+ mars.x <- mars.call$mars.x
+ mars.y <- mars.call$mars.y
+ family <- mars.call$family
+
+ xdat <- as.data.frame(dat[,mars.x])
+ ydat <- as.data.frame(dat[,mars.y])
+
+ n.spp <- ncol(ydat)
+ n.preds <- ncol(xdat)
+
+ fitted.values <- mars.glm.object$fitted.values
+
+ pred.names <- names(dat)[mars.x]
+ spp.names <- names(dat)[mars.y]
+
+ if (sp.no == 0) {
+ wanted.species <- seq(1:n.spp)
+ }
+ else {
+ wanted.species <- sp.no
+ }
+
+ for (i in wanted.species) {
+
+ if (mask.presence) {
+ mask <- ydat[,i] == 1 }
+ else {
+ mask <- rep(TRUE, length = n.cases)
+ }
+
+ robust.max.fit <- approx(ppoints(fitted.values[mask,i]), sort(fitted.values[mask,i]), 0.99) #find 99%ile value
+ nplots <- 0
+
+ for (j in 1:n.preds) {
+ if (use.windows & nplots == 0) {
+ windows(width = 8, height = 11)
+ par(mfrow = plot.layout)
+ par(cex = 0.5)
+ }
+ nplots <- nplots + 1
+ if (is.vector(xdat[,j])) wt.mean <- mean((xdat[mask, j] * fitted.values[mask, i]^5)/mean(fitted.values[mask, i]^5))
+ else wt.mean <- 0
+ if (use.factor) {
+ temp <- factor(cut(xdat[mask, j], breaks = 12))
+ if (family == "binomial") {
+ plot(temp, fitted.values[mask,i], xlab = pred.names[j], ylab = "fitted values", ylim = c(0, 1))
+ }
+ else {
+ plot(temp, fitted.values[mask,i], xlab = pred.names[j], ylab = "fitted values")}
+ }
+ else {
+ if (family == "binomial") {
+ plot(xdat[mask, j], fitted.values[mask,i], xlab = pred.names[j], ylab = "fitted values",
+ ylim = c(0, 1))
+ }
+ else {
+ plot(xdat[mask, j], fitted.values[mask,i], xlab = pred.names[j], ylab = "fitted values")
+ }
+ }
+ abline(h = (0.333 * robust.max.fit$y), lty = 2.)
+ if (nplots == 1) {
+ title(paste(spp.names[i], ", wtm = ", zapsmall(wt.mean, 4.)))}
+ else {
+ title(paste("wtm = ", zapsmall(wt.mean, 4.)))}
+ nplots <- ifelse(nplots == max.plots, 0, nplots)
+ }
+ }
+ if (!use.windows) dev.off()
+}
+
+"mars.predict" <-
+function (mars.glm.object,new.data)
+{
+#
+# j leathwick, j elith - August 2006
+#
+# version 3.1 - developed in R 2.3.1 using mda 0.3-1
+#
+# calculates a mars/glm object in which basis functions are calculated
+# using an initial mars model with single or multiple responses
+# data for individual species are then fitted as glms using the
+# common set of mars basis functions with results returned as a list
+#
+# takes as input a dataset and args selecting x and y variables, and degree of interaction
+# along with site and species weights, the CV penalty, and the glm family argument
+# the latter would normally be one of "binomial" or "poisson" - "gaussian" could be used
+# but in this case the model shouldn't differ from that fitted using mars on its own
+#
+# naming problem for dataframes fixed - je - 15/12/06
+#
+# requires mda and leathwick/elith's mars.export
+#
+ require(mda)
+
+# first recreate both the original mars model and the glm model
+
+# setup input data and create original temporary data
+
+ dataframe.name <- mars.glm.object$mars.call$dataframe # get the dataframe name
+ mars.x <- mars.glm.object$mars.call$mars.x
+ mars.y <- mars.glm.object$mars.call$mars.y
+ n.spp <- length(mars.y)
+ family <- mars.glm.object$mars.call$family
+ mars.degree <- mars.glm.object$mars.call$degree
+ penalty <- mars.glm.object$mars.call$penalty
+ site.weights <- mars.glm.object$weights[[1]]
+ spp.weights <- mars.glm.object$weights[[2]]
+
+ print("creating original data frame...",quote=FALSE)
+
+ base.data <- as.data.frame(eval.parent(parse(text = dataframe.name))) #aks
+
+ x.temp <- eval(base.data[, mars.x]) #form the temporary datasets
+ base.names <- names(x.temp)
+
+ xdat <- mars.new.dataframe(x.temp)[[1]]
+
+ ydat <- as.data.frame(base.data[, mars.y])
+ names(ydat) <- names(base.data)[mars.y]
+
+ assign("xdat", xdat, pos = 1) #and assign them for later use
+ assign("ydat", ydat, pos = 1)
+
+# now create the temporary dataframe for the new data
+
+ print("checking variable matching with new data",quote = FALSE)
+
+ new.names <- names(new.data)
+
+ for (i in 1:length(base.names)) {
+
+ name <- base.names[i]
+
+ if (!(name %in% new.names)) {
+ print(paste("Variable ",name," missing from new data",sep=""),quote = FALSE) #aks
+ return()
+ }
+ }
+
+ print("and creating temporary dataframe for new data...",quote=FALSE)
+
+ selector <- match(names(x.temp),names(new.data))
+
+ pred.dat <- mars.new.dataframe(new.data[,selector])[[1]]
+
+ assign("pred.dat", pred.dat, pos = 1) #and assign them for later use
+
+# fit the mars model and extract the basis functions
+
+ print(paste("re-fitting initial mars model for",n.spp,"responses"),quote = FALSE)
+ print(paste("using glm family of",family),quote = FALSE)
+
+ #mars.fit <- mars(x = xdat, y = ydat, degree = mars.degree, w = site.weights,
+ # wp = spp.weights, penalty = penalty)
+
+ mars.fit <- mars.glm.object$mars.object #AKS
+
+ old.bf.data <- as.data.frame(eval(mars.fit$x))
+ n.bfs <- ncol(old.bf.data)
+ bf.names <- paste("bf", 1:n.bfs, sep = "")
+ old.bf.data <- as.data.frame(old.bf.data[,-1])
+ names(old.bf.data) <- bf.names[-1]
+
+ new.bf.data <- as.data.frame(mda:::model.matrix.mars(mars.fit,pred.dat))
+ new.bf.data <- as.data.frame(new.bf.data[,-1])
+ names(new.bf.data) <- bf.names[-1]
+
+# now cycle through the species fitting glm models
+
+ print("fitting glms for individual responses", quote = F)
+
+ prediction <- as.data.frame(matrix(0, ncol = n.spp, nrow = nrow(pred.dat)))
+ names(prediction) <- names(ydat)
+ standard.errors <- as.data.frame(matrix(0, ncol = n.spp, nrow = nrow(pred.dat)))
+ names(standard.errors) <- names(ydat)
+
+ for (i in 1:n.spp) {
+
+ print(names(ydat)[i], quote = FALSE)
+ model.glm <- glm(ydat[, i] ~ ., data = old.bf.data, weights = site.weights,
+ family = family, maxit = 100)
+ temp <- predict.glm(model.glm,new.bf.data,type="response",se.fit=TRUE)
+ prediction[,i] <- temp[[1]]
+ standard.errors[,i] <- temp[[2]]
+
+ }
+
+ return(list("prediction"=prediction,"ses"=standard.errors))
+}
+
+"roc" <-
+function (obsdat, preddat)
+{
+# code adapted from Ferrier, Pearce and Watson's code, by J.Elith
+#
+# see:
+# Hanley, J.A. & McNeil, B.J. (1982) The meaning and use of the area
+# under a Receiver Operating Characteristic (ROC) curve.
+# Radiology, 143, 29-36
+#
+# Pearce, J. & Ferrier, S. (2000) Evaluating the predictive performance
+# of habitat models developed using logistic regression.
+# Ecological Modelling, 133, 225-245.
+# this is the non-parametric calculation for area under the ROC curve,
+# using the fact that a MannWhitney U statistic is closely related to
+# the area
+#
+ if (length(obsdat) != length(preddat))
+ stop("obs and preds must be equal lengths")
+ n.x <- length(obsdat[obsdat == 0])
+ n.y <- length(obsdat[obsdat == 1])
+ xy <- c(preddat[obsdat == 0], preddat[obsdat == 1])
+ rnk <- rank(xy)
+ wilc <- ((n.x * n.y) + ((n.x * (n.x + 1))/2) - sum(rnk[1:n.x]))/(n.x *
+ n.y)
+ return(round(wilc, 4))
+}
+
+
+
+#set defaults
+make.p.tif=T
+make.binary.tif=T
+mars.degree=1
+mars.penalty=2
+script.name="mars.r"
+opt.methods=2
+save.model=TRUE
+MESS=FALSE
+
+# Interpret command line argurments #
+# Make Function Call #
+Args <- commandArgs(trailingOnly=FALSE)
+
+ for (i in 1:length(Args)){
+ if(Args[i]=="-f") ScriptPath<-Args[i+1]
+ }
+
+ print(Args)
+ for (arg in Args) {
+ argSplit <- strsplit(arg, "=")
+ argSplit[[1]][1]
+ argSplit[[1]][2]
+ if(argSplit[[1]][1]=="c") csv <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="o") output <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mpt") make.p.tif <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mbt") make.binary.tif <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="deg") mars.degree <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="pen") mars.penalty <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="om") opt.methods <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="savm") save.model <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mes") MESS <- argSplit[[1]][2]
+ }
+ print(csv)
+ print(output)
+ print(responseCol)
+
+ScriptPath<-dirname(ScriptPath)
+source(paste(ScriptPath,"LoadRequiredCode.r",sep="\\"))
+print(ScriptPath)
+
+make.p.tif<-as.logical(make.p.tif)
+make.binary.tif<-as.logical(make.binary.tif)
+save.model<-make.p.tif | make.binary.tif
+opt.methods<-as.numeric(opt.methods)
+MESS<-as.logical(MESS)
+
+fit.mars.fct(ma.name=csv,
+ tif.dir=NULL,output.dir=output,
+ response.col=responseCol,make.p.tif=make.p.tif,make.binary.tif=make.binary.tif,
+ mars.degree=mars.degree,mars.penalty=mars.penalty,debug.mode=F,responseCurveForm="pdf",
+ script.name="mars.r",save.model=save.model,opt.methods=as.numeric(opt.methods),MESS=MESS)
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_RF_pluggable.r b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_RF_pluggable.r
new file mode 100644
index 0000000..d6015cc
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_RF_pluggable.r
@@ -0,0 +1,649 @@
+# A set of R functions for automated model fitting of random forest models to presence/absence data #
+#
+# Modified 12-2-09 to: remove categorical covariates from consideration if they only contain one level
+# ID factor variables based on "categorical" prefix and look for tifs in subdir
+# Give progress reports
+# write large output tif files in blocks to alleviate memory issues
+# various bug fixes
+#
+# Adapted from existing pluggable BRT and GLM modules in April 2009 by Alan Swanson
+
+
+# Libraries required to run this program #
+# PresenceAbsence - for ROC plots
+# XML - for XML i/o
+# rgdal - for geotiff i/o
+# RandomForest - duh
+# sp - used by rdgal library
+
+options(error=NULL)
+
+fit.rf.fct <- function(ma.name,tif.dir=NULL,output.dir=NULL,response.col="^response.binary",make.p.tif=T,make.binary.tif=T,
+ debug.mode=F,responseCurveForm="pdf",xtest=NULL,ytest=NULL,n.trees=1000,mtry=NULL, samp.replace=FALSE, sampsize=NULL,nodesize=NULL,maxnodes=NULL,importance=FALSE,
+ localImp=FALSE,nPerm=1,proximity=NULL,oob.prox=proximity,norm.votes=TRUE,do.trace=FALSE,keep.forest=NULL,keep.inbag=FALSE, make.r.curves=T,
+ seed=NULL,script.name="rf.r",opt.methods=2,save.model=TRUE,UnitTest=FALSE,MESS=FALSE){
+ # This function fits a boosted regression tree model to presence-absence data.
+ # written by Alan Swanson, Jan-March 2009
+ # uses code modified from that published in Elith et al 2008
+ # # Maintained and edited by Marian Talbert September 2010-
+ # Arguements.
+ # ma.name: is the name of a .csv file with a model array. full path must be included unless it is in the current
+ # R working directory #
+ # tif.dir: is the directory containing geotiffs for each covariate. only required if geotiffs output of the
+ # response surface is requested # # cov.list.name: is the name of a text file with the names of covariates to be included in models (one per line).
+ # output.dir: is the directory that output files will be stored in. if not given, files will go to the current working directory.
+ # response.col: column number of the model array containing a binary 0/1 response. all other columns will be considered explanatory variables.
+ # make.p.tif: T if a geotiff of the response surface is desired.
+ # make.binary.tif: T if a geotiff of the response surface is desired.
+ # simp.method: model simplification method. valid methods include: "cross-validation", "rel-inf", and "none". "cross-validation" uses the
+ # methods of Elith et al, 2008 for removing covariates that don't contribute to the model. "rel-inf" simply removes covariates that contribute
+ # less than 1%. cross-validation is very slow - it can add up to 10min to a run.
+ # debug.mode: if T, output is directed to the console during the run. also, a pdf is generated which contains response curve plots and perspective plots
+ # showing the effects of interactions deemed important. if F, output is diverted to a text file and the console is kept clear
+ # except for final output of an xml file. in either case, a set of standard output files are created in the output directory.
+ # tc: tree-complexity for brt fits. if specified, this sets the tree-complexity of the final model fit. A lower tree-complexity will be used for
+ # model selection steps. if not set, this will be estimated loosely following the guidelines given by Elith et al, 2008.
+ #
+
+ # Value:
+ # returns nothing but generates a number of output files in the directory
+ # "output.dir" named above. These output files consist of:
+ #
+ # brt_output.txt: a text file with fairly detailed results of the final model.
+ # brt_output.xml: an xml-formatted text file with results from the final model.
+ # brt_response_curves.xml: an xml-formatted text file with response curves for
+ # each covariate in the final model.
+ # brt_prob_map.tif: a geotiff of the response surface
+ # brt_bin_map.tif: a geotiff of the binary response surface. threhold is based on the roc curve at the point where sensitivity=specificity.
+ # brt_log.txt: a file containing text output diverted from the console when debug.mode=F
+ # brt_auc_plot.jpg: a jpg file of a ROC plot.
+ # brt_response_curves.pdf: an pdf file with response curves for
+ # each covariate in the final model and perspective plots showing the effect of interactions deemed significant.
+ # only produced when debug.mode=T
+ # seed=NULL # sets a seed for the algorithm, any inegeger is acceptable
+ # opt.methods=2 # sets the method used for threshold optimization used in the
+ # # the evaluation statistics module
+ # save.model=FALSE # whether the model will be used to later produce tifs
+ #
+ # when debug.mode is true, these filenames will include a number in them so that they will not overwrite preexisting files. eg brt_1_output.txt.
+ #
+ times <- as.data.frame(matrix(NA,nrow=8,ncol=1,dimnames=list(c("start","read data","model tuning","model fit",
+ "model summary","response curves","tif output","done"),c("time"))))
+ times[1,1] <- unclass(Sys.time())
+ t0 <- unclass(Sys.time())
+ #simp.method <- match.arg(simp.method)
+ out <- list(
+ input=list(ma.name=ma.name,
+ tif.dir=tif.dir,
+ output.dir=output.dir,
+ response.col=response.col,
+ save.model=save.model,
+ xtest=xtest,
+ ytest=ytest,
+ n.trees=n.trees,
+ mtry=mtry,
+ samp.replace=samp.replace,
+ sampsize=sampsize,
+ nodesize=nodesize,
+ maxnodes=maxnodes,
+ importance=importance,
+ localImp=localImp,
+ nPerm=nPerm,
+ proximity=proximity,
+ oob.prox=oob.prox,
+ norm.votes=norm.votes,
+ do.trace=do.trace,
+ keep.forest=keep.forest,
+ keep.inbag=keep.inbag,
+ make.p.tif=make.p.tif,
+ make.binary.tif=make.binary.tif,
+ model.type="random forest regression tree",
+ model.source.file=script.name,
+ model.fitting.subset=c(n.pres=50,n.abs=50),#subset used for response curves
+ run.time=paste(c(format(Sys.time(),"%Y-%m-%d"),format(Sys.time(),"%H:%M:%S")),collapse="T"),
+ sig.test="mean decrease in accuracy",
+ MESS=MESS),
+ dat = list(missing.libs=NULL,
+ output.dir=list(dname=NULL,exist=F,readable=F,writable=F),
+ tif.dir=list(dname=NULL,exist=F,readable=F,writable=F),
+ tif.ind=NULL,
+ tif.names=NULL,
+ bname=NULL,
+ bad.factor.covs=NULL, # factorchange
+ ma=list( status=c(exists=F,readable=F),
+ dims=c(NA,NA),
+ n.pres=c(all=NA,complete=NA,subset=NA),
+ n.abs=c(all=NA,complete=NA,subset=NA),
+ ratio=NA,
+ resp.name=NULL,
+ factor.levels=NULL,
+ used.covs=NULL,
+ ma=NULL,
+ ma.subset=NULL,
+ train.xy=NULL,
+ test.xy=NULL,
+ site.weights=NULL),
+ ma.test=NULL),
+ mods=list(parms=list(n.trees=n.trees,mtry=NULL),
+ full.mod=NULL,
+ simp.mod=NULL,
+ final.mod=NULL,
+ r.curves=NULL,
+ tif.output=list(prob=NULL,bin=NULL),
+ auc.output=NULL,
+ interactions=NULL,
+ summary=NULL),
+ time=list(strt=unclass(Sys.time()),end=NULL),
+ error.mssg=list(NULL),
+ ec=0
+ )
+
+ if(!is.null(seed)) set.seed(seed)
+ #if(simplify.brt==T) out$input$simp.method<-"cross-validation" else out$input$simp.method<-">1% rel. influence"
+ # load libaries #
+ out <- check.libs(list("randomForest","PresenceAbsence","rgdal","XML","sp","raster","tcltk2","foreign","ade4"),out)
+
+ # exit program now if there are missing libraries #
+ if(!is.null(out$error.mssg[[1]])){
+ cat(saveXML(rf.to.xml(out),indent=T),'\n')
+ return()
+ }
+
+ # check output dir #
+ out$dat$output.dir <- check.dir(output.dir)
+ if(out$dat$output.dir$writable==F) {out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: output directory",output.dir,"is not writable")
+ out$dat$output.dir$dname <- getwd()
+
+ }
+
+ # generate a filename for output #
+ if(debug.mode==T){
+ outfile <- paste(bname<-paste(out$dat$output.dir$dname,"/rf_",n<-1,sep=""),"_output.txt",sep="")
+ while(file.access(outfile)==0) outfile<-paste(bname<-paste(out$dat$output.dir$dname,"/rf_",n<-n+1,sep=""),"_output.txt",sep="")
+ capture.output(cat("temp"),file=outfile) # reserve the new basename #
+ } else bname <- paste(out$dat$output.dir$dname,"/rf",sep="")
+ out$dat$bname <- bname
+
+ # sink console output to log file #
+ if(!debug.mode) {sink(logname <- paste(bname,"_log.txt",sep=""));on.exit(sink)} else logname<-NULL
+ #options(warn=1)
+
+ # check tif dir #
+ # check tif dir #
+ if(!is.null(tif.dir)){
+ out$dat$tif.dir <- check.dir(tif.dir)
+ if(out$dat$tif.dir$readable==F & (out$input$make.binary.tif | out$input$make.p.tif)) {
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: tif directory",tif.dir,"is not readable")
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ cat(saveXML(brt.to.xml(out),indent=T),'\n')
+ return()
+ }
+ }
+
+
+ # find .tif files in tif dir #
+ if(out$dat$tif.dir$readable) out$dat$tif.names <- list.files(out$dat$tif.dir$dname,pattern=".tif",recursive=T)
+
+ # check for model array #
+ out$input$ma.name <- check.dir(out$input$ma.name)$dname
+ if(UnitTest!=FALSE) options(warn=2)
+ out <- read.ma(out)
+ if(UnitTest==1) return(out)
+ # exit program now if there are errors in the input data #
+ if(!is.null(out$error.mssg[[1]])){
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ cat(saveXML(rf.to.xml(out),indent=T),'\n')
+ return()
+ }
+ t1 <- unclass(Sys.time())
+ cat("\ndone processing data, t=",round(t1-t0,1),"sec\n")
+ cat("\nbegin processing of model array:",out$input$ma.name,"\n")
+ cat("\nfile basename set to:",out$dat$bname,"\n")
+ if(debug.mode) flush.console()
+
+ if(!debug.mode) {sink();cat("Progress:20%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("20%\n")} ### print time
+
+ ##############################################################################################################
+ # Begin model fitting #
+ ##############################################################################################################
+
+
+ # tune the mtry parameter - this controls the number of covariates randomly subset for each split #
+ cat("\ntuning mtry parameter\n")
+
+ x=out$dat$ma$ma[,-1]
+ y=factor(out$dat$ma$ma[,1])
+ if(is.null(mtry)){
+ mtry <- try(tuneRF(x=out$dat$ma$ma[,-1],y=factor(out$dat$ma$ma[,1]),mtryStart=3,importance=TRUE,ntreeTry=100,
+ replace=FALSE, doBest=F, plot=F),silent=T)
+ mtry <- try(mtry[mtry[,2]==min(mtry[,2]),1][1])
+ t2 <- unclass(Sys.time())
+ if(!debug.mode) {sink();cat("Progress:30%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("30%\n")}
+
+ cat("\ndone tuning random forest parameters, t=",round(t2-t1,1),"sec\n")
+ }
+
+ cat("\nnow fitting full random forest model using mtry=",mtry,"\n")
+ if(debug.mode) flush.console()
+
+ rf.full <- randomForest(x=out$dat$ma$ma[,-1],y=factor(out$dat$ma$ma[,1]),xtest=xtest,ytest=ytest,importance=TRUE, ntree=n.trees,
+ mtry=mtry,replace=samp.replace,sampsize=ifelse(is.null(sampsize),(ifelse(samp.replace,nrow(x),ceiling(.632*nrow(x)))),sampsize),
+ nodesize=ifelse(is.null(nodesize),(if (!is.null(y) && !is.factor(y)) 5 else 1),nodesize),maxnodes=maxnodes,
+ localImp=localImp, nPerm=nPerm, keep.forest=ifelse(is.null(keep.forest),!is.null(y) && is.null(xtest),keep.forest),
+ corr.bias=corr.bias, keep.inbag=keep.inbag)
+
+ out$mods$parms$mtry<-mtry
+ out$mods$final.mod <- rf.full
+
+ t3 <- unclass(Sys.time())
+ if(!debug.mode) {sink();cat("Progress:40%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("40%\n")} ### print time
+
+ cat("\nfinished fitting full model, t=",round(t2-t1,1),"sec\nnow computing output stats...\n")
+ if(debug.mode) flush.console()
+
+ ##############################################################################################################
+ # Begin model output #
+ ##############################################################################################################
+
+ # ROC plot #
+
+ model.summary <- try(importance(out$mods$final.mod),silent=T)
+ if(class(model.summary)=="try-error"){
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: can't generate summary of final model:",model.summary)
+ cat(saveXML(rf.to.xml(out),indent=T),'\n')
+ return()
+ } else {
+ model.summary<-model.summary[order(model.summary[,3],decreasing=T),]
+ out$mods$summary <- model.summary
+ }
+
+ txt0 <- paste("Random Forest Modeling Results\n",out$input$run.time,"\n\n",
+ "Data:\n\t",ma.name,
+ "\n\tn(pres)=",out$dat$ma$n.pres[2],
+ "\n\tn(abs)=",out$dat$ma$n.abs[2],
+ "\n\tn covariates considered=",length(out$dat$ma$used.covs),
+ "\n\n","Settings:",
+ "\n\tn covariates considered at each split =",out$mods$parms$mtry,
+ "\n\tn trees=",out$mods$parms$n.tree,
+ "\n\ttotal time for model fitting=",round((unclass(Sys.time())-t0)/60,2),"min\n",sep="")
+ txt1 <- "\nRelative performance of predictors in final model:\n\n"
+ txt2 <- "\nDefault summary of random forest fit:\n"
+ capture.output(cat(txt0),cat(txt1),print(round(model.summary,4)),cat(txt2),print(out$mods$final.mod),file=paste(bname,"_output.txt",sep=""))
+ cat(txt0);cat(txt1);print(round(model.summary,4));cat(txt2);print(out$mods$final.mod);cat("\n\n")
+ if(!is.null(out$dat$bad.factor.cols)){
+ capture.output(cat("\nWarning: the following categorical response variables were removed from consideration\n",
+ "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n"),
+ file=paste(bname,"_output.txt",sep=""),append=T)
+ cat("\nWarning: the following categorical response variables were removed from consideration\n",
+ "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n\n")
+ }
+
+ auc.output <- make.auc.plot.jpg(out$dat$ma$ma,pred=tweak.p(as.vector(predict(out$mods$final.mod,type="prob")[,2])),
+ plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="RF",opt.methods=opt.methods,weight=rep(1,times=dim(out$dat$ma$ma)[1]),out=out)
+
+ if(class(auc.output)=="try-error"){
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("Error making ROC plot:",auc.output)
+ } else { out$mods$auc.output<-auc.output}
+
+
+ #assign("out",out,envir=.GlobalEnv)
+
+ # Text summary #
+
+
+ if(!debug.mode) {sink();cat("Progress:70%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("60%\n")} ### print time
+
+ if(debug.mode) flush.console()
+
+ # Response curves #
+ t4 <- unclass(Sys.time())
+ if(make.r.curves){
+
+ r.curves <- list(names=row.names(out$mods$summary),preds=list(),resp=list())
+ inc <- 10/length(r.curves$names)
+ assign("r.curves",r.curves,envir=.GlobalEnv)
+
+ if(is.null(responseCurveForm)){
+ responseCurveForm<-0}
+
+ if(debug.mode | responseCurveForm=="pdf"){
+ nvar <- nrow(out$mods$summary)
+ pcol <- min(ceiling(sqrt(nvar)),4)
+ prow <- min(ceiling(nvar/pcol),3)
+ pdf(paste(bname,"_response_curves.pdf",sep=""),width=11,height=8.5,onefile=T)
+ par(oma=c(2,2,4,2),mfrow=c(prow,pcol))
+ }
+ for(i in 1:length(r.curves$names)){
+ assign("i",i,envir=.GlobalEnv)
+
+ x<-try(partialPlot(out$mods$final.mod,out$dat$ma$ma.subset,r.curves$names[i],n.pt=50,plot=T,main="",
+ xlab=r.curves$names[i]))
+ if(class(x)=="try-error"){
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))} else graphics.off()
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("ERROR: can't generate response curves:",x)
+ cat(saveXML(rf.to.xml(out),indent=T),'\n')
+ return()
+ } else {
+ r.curves$preds[[i]] <- x$x
+ r.curves$resp[[i]] <- x$y
+ }
+ if(!debug.mode) {sink();cat(paste("Progress:",round(70+i*inc,1),"%\n",sep=""));flush.console();sink(logname,append=T)} else {cat("\n");cat(paste(round(70+i*inc,1),"%\n",sep=""))} ### print time
+ }
+ if(debug.mode) graphics.off()
+ out$mods$r.curves <- r.curves
+ }
+
+ t5 <- unclass(Sys.time())
+ #if(!debug.mode) {sink();cat("80%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("80%\n")} ### print time
+ cat("\nfinished with response curves, t=",round(t5-t4,2),"sec\n")
+ if(debug.mode) flush.console()
+
+ # Make .tif of predictions #
+ out$mods$final.mod$contributions$var<-as.character(row.names(out$mods$summary))
+
+ assign("out",out,envir=.GlobalEnv)
+ save.image(paste(output.dir,"modelWorkspace",sep="\\"))
+ if(out$input$make.p.tif==T | out$input$make.binary.tif==T){
+ cat("\nproducing prediction maps...","\n","\n");flush.console()
+ mssg <- try(proc.tiff(model=out$mods$final.mod,vnames=as.character(row.names(out$mods$summary)),
+ tif.dir=out$dat$tif.dir$dname,filenames=out$dat$tif.ind,pred.fct=rf.predict,factor.levels=out$dat$ma$factor.levels,make.binary.tif=make.binary.tif,
+ thresh=out$mods$auc.output$thresh,make.p.tif=make.p.tif,outfile.p=paste(out$dat$bname,"_prob_map.tif",sep=""),
+ outfile.bin=paste(out$dat$bname,"_bin_map.tif",sep=""),tsize=50.0,NAval=-3000,fnames=out$dat$tif.names,logname=logname,out=out),silent=T) #"brt.prob.map.tif"
+
+ if(class(mssg)=="try-error" | mssg!=0){
+ if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
+ out$ec<-out$ec+1
+ out$error.mssg[[out$ec]] <- paste("Error producing prediction maps:",mssg)
+ cat(saveXML(rf.to.xml(out),indent=T),'\n')
+ return()
+ } else {
+ if(make.p.tif) out$mods$tif.output$prob <- paste(out$dat$bname,"_prob_map.tif",sep="")
+ if(make.binary.tif) out$mods$tif.output$bin <- paste(out$dat$bname,"_bin_map.tif",sep="")
+ t5 <- unclass(Sys.time())
+ cat("\nfinished with prediction maps, t=",round(t5-t4,2),"sec\n");flush.console()
+ }
+ }
+ if(!debug.mode) {sink();cat("Progress:90%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("90%\n")} ### print time
+
+ # Evaluation Statistics on Test Data#
+
+ if(!is.null(out$dat$ma$ma.test)) Eval.Stat<-EvaluationStats(out,thresh=auc.output$thresh,train=out$dat$ma$ma,
+ train.pred=tweak.p(as.vector(predict(out$mods$final.mod,type="prob")[,2])),opt.methods)
+
+
+
+
+ # Write summaries to xml #
+ assign("out",out,envir=.GlobalEnv)
+ doc <- rf.to.xml(out)
+
+ cat(paste("\ntotal time=",round((unclass(Sys.time())-t0)/60,2),"min\n\n\n",sep=""))
+ if(!debug.mode) {
+ sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))
+ cat("Progress:100%\n");flush.console()
+ cat(saveXML(doc,indent=T),'\n')
+ }
+ capture.output(cat(saveXML(doc,indent=T)),file=paste(out$dat$bname,"_output.xml",sep=""))
+ assign("fit",out$mods$final.mod,envir=.GlobalEnv)
+ invisible(out)
+}
+
+rf.predict <- function(model,x) {
+ # retrieve key items from the global environment #
+ # make predictions from complete data only #
+ y <- rep(NA,nrow(x))
+ y[complete.cases(x)] <- as.vector(predict(model,newdata=x[complete.cases(x),],type="prob")[,2])
+
+ # make predictions from full data #
+
+ # encode missing values as -1.
+ y[is.na(y)]<- NaN
+
+ # return predictions.
+ return(y)
+ }
+
+logit <- function(x) 1/(1+exp(-x))
+
+file_path_as_absolute <- function (x){
+ if (!file.exists(epath <- path.expand(x)))
+ stop(gettextf("file '%s' does not exist", x), domain = NA)
+ cwd <- getwd()
+ on.exit(setwd(cwd))
+ if (file_test("-d", epath)) {
+ setwd(epath)
+ getwd()
+ }
+ else {
+ setwd(dirname(epath))
+ file.path(getwd(), basename(epath))
+ }
+}
+#file_path_as_absolute(".")
+
+rf.to.xml <- function(out){
+ require(XML)
+ schema.http="http://www.w3.org/2001/XMLSchema-instance"
+ schema.fname="file:/Users/isfs2/Desktop/Source/2008-04-09/src/gov/nasa/gsfc/quickmap/ModelBuilder/modelRun_output_v2.xsd"
+ xml.out <- newXMLDoc()
+ mr <- newXMLNode("modelRunOutput",doc=xml.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))#,parent=xml.out
+ sm <- newXMLNode("singleModel",parent=mr)
+ bg <- newXMLNode("background",parent=sm)
+ newXMLNode("mdsName",out$input$ma.name,parent=bg)
+ newXMLNode("runDate",out$input$run.time,parent=bg)
+ lc <- newXMLNode("layersConsidered",parent=bg)#, parent = xml.out)
+ kids <- lapply(paste(out$dat$tif.dir$dname,"/",out$dat$tif.names,sep=""),function(x) newXMLNode("layer", x))
+ addChildren(lc, kids)
+ mo <- newXMLNode("modelOutput",parent=sm)
+ newXMLNode("modelType",out$input$model.type,parent=mo)
+ newXMLNode("modelSourceFile",out$input$model.source.file,parent=mo)
+ newXMLNode("devianceExplained",out$mods$auc.output$pct_dev_exp,parent=mo,attrs=list(type="percentage"))
+ newXMLNode("nativeOutput",paste(out$dat$bname,"_output.txt",sep=""),parent=mo)
+ newXMLNode("binaryOutputFile",out$mods$tif.output[[2]],parent=mo)
+ newXMLNode("probOutputFile",out$mods$tif.output[[1]],parent=mo)
+ newXMLNode("auc",out$mods$auc.output$auc,parent=mo)
+ newXMLNode("rocGraphic",out$mods$auc.output$plotname,parent=mo)
+ newXMLNode("rocThresh",out$mods$auc.output$thresh,parent=mo)
+ newXMLNode("modelDeviance",out$mods$auc.output$dev_fit,parent=mo)
+ newXMLNode("nullDeviance",out$mods$auc.output$null_dev,parent=mo)
+ if(is.null(out$mods$r.curves)) rc.name <- NULL else rc.name <- paste(out$dat$bname,"_response_curves.xml",sep="")
+ newXMLNode("responsePlotsFile",rc.name,parent=mo)
+ newXMLNode("significanceDescription",out$input$sig.test,parent=mo)
+ mfp <- newXMLNode("modelFitParmas",parent=mo)
+ newXMLNode("nTrees",out$mods$parms$n.tree,parent=mfp)
+ newXMLNode("mTry",out$mods$parms$mtry,parent=mfp)
+
+ sv <- newXMLNode("significantVariables",parent=mo)
+ if(!is.null(out$mods$summary)) {
+ t.table <- data.frame(significanceMeasurement=out$mods$summary[,3],row.names=row.names(out$mods$summary))
+ for(i in 1:nrow(t.table)){
+ x <- newXMLNode("sigVar",parent=sv)
+ newXMLNode(name="name", row.names(t.table)[i],parent=x)
+ kids <- lapply(1:ncol(t.table),function(j) newXMLNode(name=names(t.table)[j], t.table[i,j]))
+ addChildren(x, kids)
+ }
+ }
+ if(!is.null(out$mods$r.curves)){
+ r.curves <- out$mods$r.curves
+ rc.out <- newXMLDoc()
+ root <- newXMLNode("responseCurves",doc=rc.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))
+ for(i in 1:length(r.curves$names)){
+ vartype <- ifelse(class(r.curves$preds[[i]])=="character","factor","continuous")
+ x <- newXMLNode("responseCurve",attrs=list(covariate=r.curves$names[i],type=vartype),parent=root)
+ kids <- lapply(1:length(r.curves$preds[[i]]),function(j){
+ newXMLNode(name="responsePt",parent=x,.children=list(
+ newXMLNode(name="explanatory",r.curves$preds[[i]][j]),
+ newXMLNode(name="response",r.curves$resp[[i]][j])))})
+ addChildren(x, kids)
+ }
+ saveXML(rc.out,rc.name,indent=T)
+ }
+ if(!is.null(out$error.mssg[[1]])) {
+ kids <- lapply(out$error.mssg,function(j) newXMLNode(name="error",j))
+ addChildren(mo,kids)
+ }
+ return(xml.out)
+ }
+
+
+get.cov.names <- function(model){
+ return(attr(terms(formula(model)),"term.labels"))
+ }
+
+check.dir <- function(dname){
+ if(is.null(dname)) dname <- getwd()
+ dname <- gsub("[\\]","/",dname)
+ end.char <- substr(dname,nchar(dname),nchar(dname))
+ if(end.char == "/") dname <- substr(dname,1,nchar(dname)-1)
+ exist <- suppressWarnings(as.numeric(file.access(dname,mode=0))==0) # -1 if bad, 0 if ok #
+ if(exist) dname <- file_path_as_absolute(dname)
+ readable <- suppressWarnings(as.numeric(file.access(dname,mode=4))==0) # -1 if bad, 0 if ok #
+ writable <- suppressWarnings(as.numeric(file.access(dname,mode=2))==0) # -1 if bad, 0 if ok #
+ return(list(dname=dname,exist=exist,readable=readable,writable=writable))
+ }
+
+
+get.image.info <- function(image.names){
+ # this function creates a data.frame with summary image info for a set of images #
+ require(rgdal)
+ n.images <- length(image.names)
+
+ full.names <- image.names
+ out <- data.frame(image=full.names,available=rep(F,n.images),size=rep(NA,n.images),
+ type=factor(rep("unk",n.images),levels=c("asc","envi","tif","unk")))
+ out$type[grep(".tif",image.names)]<-"tif"
+ out$type[grep(".asc",image.names)]<-"asc"
+ for(i in 1:n.images){
+ if(out$type[i]=="tif"){
+ x <-try(GDAL.open(full.names[1],read.only=T),silent=T)
+ suppressMessages(try(GDAL.close(x),silent=T))
+ if(class(x)!="try-error") out$available[i]<-T
+ x<-try(file.info(full.names[i]))
+ } else {
+ x<-try(file.info(full.names[i]))
+ if(!is.na(x$size)) out$available[i]<-T
+ }
+ if(out$available[i]==T){
+ out$size[i]<-x$size
+ if(out$type[i]=="unk"){
+ # if extension not known, look for envi .hdr file in same directory #
+ if(file.access(paste(file_path_sans_ext(full.names[i]),".hdr",sep=""))==0)
+ out$type[i]<-"envi"
+ }
+ }
+ }
+ return(out)
+}
+
+tweak.p <- function(p){
+ p[p==1]<-max(p[p<1])
+ p[p==0]<-min(p[p>0])
+ return(p)
+ }
+
+
+#
+
+ # Interpret command line argurments #
+# Make Function Call #
+#Set defaults for optional commands
+make.p.tif=T
+make.binary.tif=T
+responseCurveForm="pdf"
+xtest=NULL
+ytest=NULL
+n.trees=1000
+mtry=NULL
+samp.replace=FALSE
+sampsize=NULL
+nodesize=NULL
+maxnodes=NULL
+importance=FALSE
+localImp=FALSE
+nPerm=1
+proximity=NULL
+oob.prox=proximity
+norm.votes=TRUE
+do.trace=FALSE
+keep.forest=NULL
+keep.inbag=FALSE
+make.r.curves=T
+seed=NULL
+opt.methods=2
+save.model=TRUE
+seed=NULL
+MESS=FALSE
+
+Args <- commandArgs(trailingOnly=FALSE)
+
+ for (i in 1:length(Args)){
+ if(Args[i]=="-f") ScriptPath<-Args[i+1]
+ }
+
+ for (arg in Args) {
+ argSplit <- strsplit(arg, "=")
+ argSplit[[1]][1]
+ argSplit[[1]][2]
+ if(argSplit[[1]][1]=="c") csv <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="o") output <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mpt") make.p.tif <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mbt") make.binary.tif <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="xtst") xtest <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="ytst") ytest <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="ntree") n.trees <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mtry") mtry <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="sampR") samp.replace <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="sampS") sampsize <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="nodeS") nodesize <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="maxN") maxnodes <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="impt") importance <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="locImp") localImp <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="nPerm") nPerm <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="prox") proximity <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="oopp") oop.prox <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="NVot") norm.votes <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="Trce") do.trace <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="kf") keep.forest <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="Kbag") keep.inbag <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="curves") make.r.curves <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="om") opt.methods <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="savm") save.model <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="mes") MESS <- argSplit[[1]][2]
+
+ }
+ print(csv)
+ print(output)
+ print(responseCol)
+
+make.p.tif<-as.logical(make.p.tif)
+make.binary.tif<-as.logical(make.binary.tif)
+samp.replace<-as.logical(samp.replace)
+importance<-as.logical(importance)
+localImp<-as.logical(localImp)
+norm.votes<-as.logical(norm.votes)
+do.trace<-as.logical(do.trace)
+keep.inbag<-as.logical(keep.inbag)
+make.r.curves<-as.logical(make.r.curves)
+save.model<-make.p.tif | make.binary.tif
+n.trees<-as.numeric(n.trees)
+opt.methods<-as.numeric(opt.methods)
+ScriptPath<-dirname(ScriptPath)
+MESS<-as.logical(MESS)
+
+source(paste(ScriptPath,"LoadRequiredCode.r",sep="\\"))
+
+fit.rf.fct(ma.name=csv,tif.dir=NULL,output.dir=output,response.col=responseCol,make.p.tif=make.p.tif,make.binary.tif=make.binary.tif,
+ debug.mode=F,responseCurveForm="pdf",xtest=xtest,ytest=ytest,n.trees=n.trees,mtry=mtry,samp.replace=samp.replace, sampsize=sampsize,
+ nodesize=nodesize,maxnodes=maxnodes,importance=importance,
+ localImp=localImp,nPerm=nPerm,proximity=proximity,oob.prox=oob.prox,norm.votes=norm.votes,do.trace=do.trace,keep.forest=keep.forest,
+ keep.inbag=keep.inbag,make.r.curves=make.r.curves,
+ seed=seed,script.name="rf.r",opt.methods=opt.methods,save.model=save.model,MESS=MESS)
+
+
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/FunctionCall.r b/contrib/sahm/pySAHM/Resources/R_Modules/FunctionCall.r
new file mode 100644
index 0000000..4787464
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/FunctionCall.r
@@ -0,0 +1,87 @@
+setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
+source("FIT_BRT_pluggable.r")
+source("FIT_MARS_pluggable.r")
+source("FIT_RF_pluggable.r")
+source("FIT_GLM_pluggable.r")
+
+source("EvaluationStats.r")
+source("TestTrainRocPlot.r")
+source("PredictModel.r")
+source("read.ma.r")
+source("proc.tiff.r")
+
+# Curr
+#trace(proc.tiff,browser)
+#options(error=expression(if(interactive()) recover() else dump.calls()))
+#options(error=NULL)
+
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+ rc="ResponseBinary"
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+ fit.brt.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=F,make.binary.tif=F,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL,opt.methods=1,seed=1,save.model=TRUE)
+
+PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+
+#Now testing to make sure this code works with no test training split
+ma.name<-"H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\ModelOutputCheck\\NewInput.csv"
+ma.name="C:\\VisTrails\\mtalbert_20110406T093111\\sahm4h5b1t.mds"
+
+ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv"
+fit.brt.fct(ma.name=ma.name,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
+
+
+#this is the GLM_pluggable1.r under NewMDSBuilder (Works with new vistrails format)
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110510T100421\\TestTrainingSplit_1.csv"
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+rc="responseCount"
+
+ fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col=rc,make.p.tif=T,make.binary.tif=T,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
+
+
+#Mars check Works with new vistrails format
+ fit.mars.fct(ma.name=ma.name,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
+
+
+fit.rf.fct(ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv",
+ tif.dir=NULL,
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ debug.mode=T,n.trees=1000,ma.test=NULL,make.r.curves=T,script.name="glm.r")
+
+
+
+#this one does not subset paths set up in the old way works with old sahm as well as for
+fit.brt.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,ma.test=NULL,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
+
+
+fit.mars.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+ tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
+
+fit.glm.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+ tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",ma.test=NULL,script.name="glm.r")
+
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/LoadRequiredCode.r b/contrib/sahm/pySAHM/Resources/R_Modules/LoadRequiredCode.r
new file mode 100644
index 0000000..9518b44
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/LoadRequiredCode.r
@@ -0,0 +1,16 @@
+#source(paste(ScriptPath,"EvaluationStats.r",sep="\\"))
+source(paste(ScriptPath,"TestTrainRocPlot.r",sep="\\"))
+source(paste(ScriptPath,"read.ma.r",sep="\\"))
+source(paste(ScriptPath,"proc.tiff.r",sep="\\"))
+source(paste(ScriptPath,"check.libs.r",sep="\\"))
+source(paste(ScriptPath,"modalDialog.r",sep="\\"))
+#replace EvaluationStats with
+source(paste(ScriptPath,"make.auc.r",sep="\\"))
+#source(paste(ScriptPath,"make.poisson.plot.r",sep="\\"))
+#source(paste(ScriptPath,"make.auc.plot.r",sep="\\"))
+source(paste(ScriptPath,"EvalStats.r",sep="\\"))
+source(paste(ScriptPath,"EvalStatsHelperFcts.r",sep="\\"))
+source(paste(ScriptPath,"AppendOut.r",sep="\\"))
+source(paste(ScriptPath,"ResidualImage.r",sep="\\"))
+source(paste(ScriptPath,"Pred.Surface.r",sep="\\"))
+#Fit.Mars
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore.r b/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore.r
new file mode 100644
index 0000000..92b945b
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore.r
@@ -0,0 +1,435 @@
+Pairs.Explore<-function(num.plots=5,min.cor=.7,input.file,output.file,response.col="ResponseBinary",cors.w.highest=FALSE,pres=TRUE,absn=TRUE,bgd=TRUE,Debug=FALSE){
+
+
+ #num.plots=plots per page of display
+ #min.cor=the minimum correlation to be included in determining which set of predictors to display
+ #input.file=a csv assumed to have the new vistrails form with the first several rows specifiying where to find tiffs
+ # and which columns to include in analysis
+ #output.file=...
+ #response.col=name of response column to be removed and used elsewhere
+ #modifications
+ #5/10/2011 altered to handle count data as well presence absence.
+ #any counts higher than or equal to 1 are set to be presence though I might consider
+ #adding the option to have a threshold set instead of using just presence/absence
+
+
+ absn<-as.logical(absn)
+ pres<-as.logical(pres)
+ bgd<-as.logical(bgd)
+ cors.w.highest<-as.logical(cors.w.highest)
+
+ #Read input data and remove any columns to be excluded
+ dat<-read.csv(input.file,skip=3,header=FALSE)
+
+ hl<-readLines(input.file,1)
+ hl=strsplit(hl,',')
+ colnames(dat) = hl[[1]]
+
+ tif.info<-readLines(input.file,3)
+ tif.info<-strsplit(tif.info,',')
+ include<-(as.numeric(tif.info[[2]]))
+
+ #Remove coordinates, response column, site.weights
+ #before exploring predictor relationship
+ rm.cols <- as.vector(na.omit(c(match("x",tolower(names(dat))),match("y",tolower(names(dat))),
+ match("site.weights",tolower(names(dat))),match(tolower(response.col),tolower(names(dat))),match("Split",names(dat)))))
+
+ #remove testing split
+ if(!is.na(match("Split",names(dat)))) dat<-dat[-c(which(dat$Split=="test"),arr.ind=TRUE),]
+
+ include[is.na(include)]<-0
+ rm.cols<-unique(c(rm.cols,which(include==0,arr.ind=TRUE)))
+ response<-dat[,match(tolower(response.col),tolower(names(dat)))]
+
+ dat<-dat[order(response),]
+ response<-response[order(response)]
+
+ #for the purpose of the pairs plot, taking all counts greater than 1 and setting them equal to presence
+ #this is never exported
+ if(response.col=="responseCount") {response[response>=1]<-1
+ }
+
+ #remove any of pres absn or bgd that aren't desired
+ temp<-c(0,1,-9999)
+ temp<-temp[c(absn,pres,bgd)]
+ dat<-dat[response%in%temp,]
+ response<-response[response%in%temp]
+
+
+ if(sum(response==-9999)>1000){
+ s<-sample(which(response==-9999,arr.ind=TRUE),size=(sum(response==-9999)-1000))
+ dat<-dat[-c(s),]
+ response<-response[-c(s)]
+ }
+
+ if (response.col=="responseCount") {
+ TrueResponse<-dat[,match(tolower(response.col),tolower(names(dat)))]
+ } else TrueResponse<-response
+
+ #now remove all columns except predictors
+ dat<-dat[-rm.cols]
+ dat[dat==-9999]<-NA
+ response<-response[complete.cases(dat)]
+ TrueResponse<-TrueResponse[complete.cases(dat)]
+ dat<-dat[complete.cases(dat),]
+
+
+ #dat<-dat[1:2000,]
+ #Remove columns with only one unique value
+ varr <- function(x) var(x,na.rm=TRUE)
+
+ dat<-try(dat[,as.vector(apply(dat,2,varr)==0)!=1],silent=TRUE)
+ if(class(dat)=="try-error") stop("mds file contains nonnumeric columns please remove and continue")
+ #record correlations for later plots
+
+ cmat<-cor(dat,use="pairwise.complete.obs")
+ smat<-cor(dat,method="spearman",use="pairwise.complete.obs")
+ if(dim(dat)[1]<2000){
+ kmat<-cor(dat,method="kendall",use="pairwise.complete.obs")}
+ else {s<-sample(seq(1:dim(dat)[1]),size=2000,replace=FALSE)
+ kmat<-cor(dat[s,],method="kendall",use="pairwise.complete.obs")
+ }
+
+ cmat=pmax(abs(cmat),abs(smat),abs(kmat),na.rm=TRUE)
+
+ High.cor<-sort(apply(abs(cmat)>min.cor,2,sum)-1,decreasing=TRUE)
+
+ #take the top num.plots to put in the pairs plot or if the looking at a single
+ #predictor and other predictors it's correlated with, take the top num.plots-1
+ #of those with which it is correlated
+ {if(cors.w.highest==FALSE){
+ HighToPlot<-dat[,match(names(High.cor),names(dat))[1:min(num.plots,length(High.cor))]]
+ }else{
+ #take the column of the correlation matrix corresponding to the
+ #predictor with the higest number of total correlations record the names
+ #of the predictors that are correlated with this one predictor
+ temp<-cmat[rownames(cmat)==names(High.cor[1]),]
+ CorWHigh<-temp[abs(cmat[,colnames(cmat)==names(High.cor[1])])>min.cor]
+
+ #record counts of total number of correlations with all predictors for those
+ #predictors that are highly correlated with the Highest predictor
+ High.cor<-sort(High.cor[names(CorWHigh)],decreasing=TRUE)
+ HighToPlot<-dat[,match(names(High.cor),names(dat))[1:min(num.plots,length(High.cor))]]
+ }}
+ cor.hightoplot<-abs(cor(HighToPlot,use="pairwise.complete.obs"))
+ diag(cor.hightoplot)<-0
+ cor.range<-c(quantile(as.vector(cor.hightoplot),probs=c(0,.5,.7,.85)),1)
+
+ ## put histograms on the diagonal
+ panel.hist <- function(x, ...)
+ {
+ usr <- par("usr"); on.exit(par(usr))
+ par(usr = c(usr[1:2], 0, 1.5) )
+ h <- hist(x, plot = FALSE)
+ breaks <- h$breaks; nB <- length(breaks)
+ y <- h$counts; y <- y/max(y)
+ rect(breaks[-nB], 0, breaks[-1], y, col="steelblue", ...)
+
+ }
+
+
+ ## put (absolute) correlations on the upper panels,
+ ## with size proportional to the correlations.
+ panel.cor <- function(x, y, digits=2, prefix="", cor.range,cex.cor, ...)
+ {
+ a<-colors()
+ usr <- par("usr"); on.exit(par(usr))
+ par(usr = c(0, 1, 0, 1))
+ r <- abs(cor(x, y,use="pairwise.complete.obs"))
+ spear<-abs(cor(x,y,method="spearman",use="pairwise.complete.obs"))
+ ken<- abs(cor(x,y,method="kendall",use="pairwise.complete.obs"))
+ all.cor<-max(r,spear,ken)
+ #range.seq<-seq(from=cor.range[1],to=cor.range[2],length=20)
+ if(all.cor>=cor.range[4]){
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
+ a[59])} else if(all.cor>=cor.range[3]){
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
+ a[76])} else if(all.cor>=cor.range[2]){
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
+ a[382])}
+ r<-max(all.cor)
+ cex.cor=3
+ txt <- format(c(r, 0.123456789), digits=digits)[1]
+ txt <- paste(prefix, txt, sep="")
+ #if(missing(cex.cor)) cex.cor <- 1.2/strwidth(txt)
+
+ txt2=""
+ if(max(all.cor)>cor.range[2]){
+ if(spear==max(all.cor) && spear!=cor(x,y,use="pairwise.complete.obs")) {txt2 <- " s"
+ } else if(ken==max(all.cor) && ken!=cor(x,y,use="pairwise.complete.obs")){
+ txt2 <-" k"
+ }
+
+ }
+ text(0.5, 0.5, txt, cex = .7+cex.cor * (r-min(cor.range))/(max(cor.range)-min(cor.range)))
+ text(.9,.1,txt2,cex=1.5)
+ }
+
+# #Find a new unique file name (one in the desired directory that hasn't yet been used)
+# outfile <- paste(output.dir,"Predictor_Correlation.pdf",sep="\\")
+# while(file.access(outfile)==0) outfile<-paste(output.dir,"Predictor_Correlation.pdf",sep="\\")
+#
+# options(warn=-1)
+# pdf(outfile,width=11,height=9,onefile=T)
+# MyPairs(HighToPlot,cor.range=cor.range,my.labels=(as.vector(High.cor)[1:num.plots]),
+# lower.panel=panel.smooth,diag.panel=panel.hist, upper.panel=panel.cor,pch=21,bg = c("red","steelblue")[as.factor(response)],col.smooth = "red")
+# graphics.off()
+# options(warn=0)
+#
+# }
+
+
+ #Find a new unique file name (one in the desired directory that hasn't yet been used)
+
+ options(warn=-1)
+ if(Debug==FALSE) jpeg(output.file,width=1000,height=1000,pointsize=13)
+ MyPairs(cbind(TrueResponse,HighToPlot),cor.range=cor.range,my.labels=(as.vector(High.cor)[1:num.plots]),
+ lower.panel=panel.smooth,diag.panel=panel.hist, upper.panel=panel.cor,pch=21,bg = c("green","red","yellow")[factor(response,levels=c(0,1,-9999))],col.smooth = "red")
+
+ if(Debug==FALSE) graphics.off()
+ options(warn=0)
+
+ }
+
+MyPairs<-function (x,my.labels,labels, panel = points, ..., lower.panel = panel,
+ upper.panel = panel, diag.panel = NULL, text.panel = textPanel,
+ label.pos = 0.5 + has.diag/3, cex.labels = NULL, font.labels = 1,
+ row1attop = TRUE, gap = 1,Toplabs=NULL)
+{
+ response<-x[,1]
+ response[response==-9999]<-0
+ x<-x[,2:dim(x)[2]]
+
+ textPanel <- function(x = 0.5, y = 0.5, txt, cex, font) text(x,
+ y, txt, cex = cex, font = font)
+ localAxis <- function(side, x, y, xpd, bg, col = NULL, main,
+ oma, ...) {
+ if (side%%2 == 1)
+ Axis(x, side = side, xpd = NA, ...)
+ else Axis(y, side = side, xpd = NA, ...)
+ }
+ localPlot <- function(..., main, oma, font.main, cex.main) plot(...)
+ localLowerPanel <- function(..., main, oma, font.main, cex.main) lower.panel(...)
+ localUpperPanel <- function(..., main, oma, font.main, cex.main) upper.panel(...)
+ localDiagPanel <- function(..., main, oma, font.main, cex.main) diag.panel(...)
+ dots <- list(...)
+ nmdots <- names(dots)
+ if (!is.matrix(x)) {
+ x <- as.data.frame(x)
+ for (i in seq_along(names(x))) {
+ if (is.factor(x[[i]]) || is.logical(x[[i]]))
+ x[[i]] <- as.numeric(x[[i]])
+ if (!is.numeric(unclass(x[[i]])))
+ stop("non-numeric argument to 'pairs'")
+ }
+ } else if (!is.numeric(x))
+ stop("non-numeric argument to 'pairs'")
+ panel <- match.fun(panel)
+ if ((has.lower <- !is.null(lower.panel)) && !missing(lower.panel))
+ lower.panel <- match.fun(lower.panel)
+ if ((has.upper <- !is.null(upper.panel)) && !missing(upper.panel))
+ upper.panel <- match.fun(upper.panel)
+ if ((has.diag <- !is.null(diag.panel)) && !missing(diag.panel))
+ diag.panel <- match.fun(diag.panel)
+ if (row1attop) {
+ tmp <- lower.panel
+ lower.panel <- upper.panel
+ upper.panel <- tmp
+ tmp <- has.lower
+ has.lower <- has.upper
+ has.upper <- tmp
+ }
+ nc <- ncol(x)
+ if (nc < 2)
+ stop("only one column in the argument to 'pairs'")
+ has.labs <- TRUE
+ if (missing(labels)) {
+ labels <- colnames(x)
+ if (is.null(labels))
+ labels <- paste("var", 1L:nc)
+ }
+ else if (is.null(labels))
+ has.labs <- FALSE
+ oma <- if ("oma" %in% nmdots)
+ dots$oma
+ else NULL
+ main <- if ("main" %in% nmdots)
+ dots$main
+ else NULL
+ if (is.null(oma)) {
+ oma <- c(4, 4, 4, 4)
+ if (!is.null(main))
+ oma[3L] <- 6
+ }
+
+ nCol<-ifelse(length(unique(response))>1,nc+1,nc)
+ j.start<-ifelse(length(unique(response))>1,0,1)
+ opar <- par(mfrow = c(nc, nCol), mar = rep.int(gap/2, 4), oma = oma)
+ on.exit(par(opar))
+ for (i in if (row1attop)
+ 1L:(nc)
+ else nc:1L) for (j in j.start:(nc)) {
+
+
+ if(i==1){ par(mar = c(gap/2,gap/2,gap,gap/2)) #top row add extra room at top
+ if(j==0){
+ par(mar = c(gap/2,gap,gap,gap)) #top left corner room at top and on right
+ localPlot(x[, i],response, xlab = "", ylab = "", axes = FALSE,
+ type="n",...)
+ }else if(j==1) {par(mar = c(gap/2,gap,gap,gap/2)) #extra room on left and topfor second plot top row
+ localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
+ type="n",...)} else {
+ par(mar = c(gap/2,gap/2,gap,gap/2)) #all other top row plots need extra room at top only
+ localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
+ type="n",...)
+ }}else { par(mar = rep.int(gap/2, 4))
+ if(j==0){ par(mar = c(gap/2,gap,gap/2,gap)) #left column needs extra room on right only
+ localPlot(x[, i],response, xlab = "", ylab = "", axes = FALSE,
+ type="n",...)
+ }else if(j==1){ par(mar = c(gap/2,gap,gap/2,gap/2)) #second column needs extra room on left so labels fit
+ localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
+ type="n",...)
+ }else localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
+ type="n",...)}
+ if(j==0) {
+ if(i==1) par(mar=c(gap/2,gap,gap,gap))
+ else par(mar = c(gap/2,gap,gap/2,gap))
+
+ if(i==1) title(main="Response",line=.04,cex.main=1.5)
+
+ box()
+ my.lab<-paste("cor=",round(max(abs(cor(x[,(i)],response,use="pairwise.complete.obs")),abs(cor(x[,(i)],response,method="spearman",use="pairwise.complete.obs")),
+ abs(cor(x[,(i)],response,method="kendall",use="pairwise.complete.obs"))),digits=2),sep="")
+
+ #panel smooth doesn't work for two reasons: one, the response is binary and it requires more than two unique values
+ #second I don't think it can use weights which is necessary with an overwhelming amount of background points so that presnce points
+ #can't be viewed
+ #panel.smooth(as.vector(x[, (i)]), as.vector(jitter(response,factor=.1)),weights=
+ # c(rep(table(response)[2]/table(response)[1],times=table(response)[1]),rep(1,times=table(response)[2])),...)
+
+ if(length(unique(response))>2) panel.smooth(as.vector(x[, (i)]), as.vector(response),...)
+ else my.panel.smooth(as.vector(x[, (i)]), as.vector(response),weights=
+ c(rep(table(response)[2]/table(response)[1],times=table(response)[1]),rep(1,times=table(response)[2])),...)
+
+ title(ylab=paste("cor=",round(max(abs(cor(x[,(i)],response,use="pairwise.complete.obs")),
+ abs(cor(x[,(i)],response,method="spearman",use="pairwise.complete.obs")),abs(cor(x[,(i)],response,method="kendall",use="pairwise.complete.obs"))),digits=2),
+ sep=""),line=.02,cex.lab=1.5)
+ #,y=.85,x=max(x[,(i)])-.2*diff(range(x[,(i)])),cex=1.5)
+
+ } else{
+ if (i == j || (i < j && has.lower) || (i > j && has.upper)) {
+ box()
+ if(i==1) title(main=paste("Total Cor=",my.labels[j],sep=""),line=.04,cex.main=1.5)
+ #if (i == 1 && (!(j%%2) || !has.upper || !has.lower))
+ # localAxis(1 + 2 * row1attop, x[, j], x[, i],
+ # ...)
+ if (i == nc)
+ localAxis(3 - 2 * row1attop, x[, j], x[, i],
+ ...)
+ if (j == 1 && (i!=1 || !has.upper || !has.lower))
+ localAxis(2, x[, j], x[, i], ...)
+ #if (j == nc && (i%%2 || !has.upper || !has.lower))
+ # localAxis(4, x[, j], x[, i], ...)
+ mfg <- par("mfg")
+ if (i == j) {
+ if (has.diag)
+ localDiagPanel(as.vector(x[, i]),...)
+ if (has.labs) {
+ par(usr = c(0, 1, 0, 1))
+ if (is.null(cex.labels)) {
+ l.wid <- strwidth(labels, "user")
+ cex.labels <- max(0.8, min(2, 0.9/max(l.wid)))
+ }
+
+ text.panel(0.5, label.pos, labels[i], cex = cex.labels,
+ font = font.labels)
+ }
+ }
+
+ else if (i < j)
+ if(length(unique(x[,i])>2)){
+ localLowerPanel(as.vector(x[, j]), as.vector(x[,
+ i]), ...) } else {
+ my.panel.smooth(as.vector(x[, j]),as.vector(x[,i]))
+ }
+
+ else localUpperPanel(as.vector(x[, j]), as.vector(x[,
+ i]), ...)
+ if (any(par("mfg") != mfg))
+ stop("the 'panel' function made a new plot")
+ }
+ else par(new = FALSE)
+ }}
+ if (!is.null(main)) {
+ font.main <- if ("font.main" %in% nmdots)
+ dots$font.main
+ else par("font.main")
+ cex.main <- if ("cex.main" %in% nmdots)
+ dots$cex.main
+ else par("cex.main")
+ mtext(main, 3, 3, TRUE, 0.5, cex = cex.main, font = font.main)
+ }
+ invisible(NULL)
+}
+
+
+my.panel.smooth<-function (x, y, col = par("col"), bg = NA, pch = par("pch"),
+ cex = 1, col.smooth = "red", span = 2/3, iter = 3, weights=rep(1,times=length(y)), ...)
+{
+ o<-order(x)
+ points(x, y, pch = pch, col = col, bg = bg, cex = cex)
+ ok <- is.finite(x) & is.finite(y)
+ if (any(ok) && length(unique(x))>3)
+ lines(lowess(x[o],y[o],iter=0),col="red")
+ #lines(smooth.spline(x,w=weights,jitter(y,amount=(max(y)-min(y))/100),nknots=min(length(unique(x)),4)),col="red")
+
+}
+
+
+Args <- commandArgs(T)
+ print(Args)
+ #assign default values
+ num.plots <- 10
+ min.cor <- .7
+ responseCol <- "ResponseBinary"
+ cors.w.highest <- FALSE
+ pres=TRUE
+ absn=TRUE
+ bgd=TRUE
+ #replace the defaults with passed values
+ for (arg in Args) {
+ argSplit <- strsplit(arg, "=")
+ argSplit[[1]][1]
+ argSplit[[1]][2]
+ if(argSplit[[1]][1]=="p") num.plots <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="m") min.cor <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="o") output.file <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="i") infile <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="core") cors.w.highest <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="pres") pres <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="absn") absn <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="bgd") bgd <- argSplit[[1]][2]
+ }
+
+ print(num.plots)
+ print(min.cor)
+ print(output.file)
+ print (infile)
+ print(responseCol)
+ print(cors.w.highest)
+ print(pres)
+ print(absn)
+ print(bgd)
+
+ #Run the Pairs Explore function with these parameters
+ Pairs.Explore(num.plots=num.plots,
+ min.cor=min.cor,
+ input.file=infile,
+ output.file=output.file,
+ response.col=responseCol,
+ cors.w.highest=cors.w.highest,
+ pres,
+ absn,
+ bgd)
+
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore2.r b/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore2.r
new file mode 100644
index 0000000..156e158
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore2.r
@@ -0,0 +1,430 @@
+Pairs.Explore<-function(num.plots=5,min.cor=.7,input.file,output.file,response.col="ResponseBinary",cors.w.highest=FALSE,pres=TRUE,absn=TRUE,bgd=TRUE,Debug=FALSE){
+
+
+ #num.plots=plots per page of display
+ #min.cor=the minimum correlation to be included in determining which set of predictors to display
+ #input.file=a csv assumed to have the new vistrails form with the first several rows specifiying where to find tiffs
+ # and which columns to include in analysis
+ #output.file=...
+ #response.col=name of response column to be removed and used elsewhere
+ #modifications
+ #5/10/2011 altered to handle count data as well presence absence.
+ #any counts higher than or equal to 1 are set to be presence though I might consider
+ #adding the option to have a threshold set instead of using just presence/absence
+
+
+ absn<-as.logical(absn)
+ pres<-as.logical(pres)
+ bgd<-as.logical(bgd)
+ cors.w.highest<-as.logical(cors.w.highest)
+
+ #Read input data and remove any columns to be excluded
+ dat<-read.csv(input.file,skip=3,header=FALSE)
+
+ hl<-readLines(input.file,1)
+ hl=strsplit(hl,',')
+ colnames(dat) = hl[[1]]
+
+ tif.info<-readLines(input.file,3)
+ tif.info<-strsplit(tif.info,',')
+ include<-(as.numeric(tif.info[[2]]))
+
+ #Remove coordinates, response column, site.weights
+ #before exploring predictor relationship
+ rm.cols <- as.vector(na.omit(c(match("x",tolower(names(dat))),match("y",tolower(names(dat))),
+ match("site.weights",tolower(names(dat))),match(tolower(response.col),tolower(names(dat))),match("Split",names(dat)))))
+
+ #remove testing split
+ if(!is.na(match("Split",names(dat)))) dat<-dat[-c(which(dat$Split=="test"),arr.ind=TRUE),]
+
+ include[is.na(include)]<-0
+ rm.cols<-unique(c(rm.cols,which(include==0,arr.ind=TRUE)))
+ response<-dat[,match(tolower(response.col),tolower(names(dat)))]
+
+ dat<-dat[order(response),]
+ response<-response[order(response)]
+
+ #for the purpose of the pairs plot, taking all counts greater than 1 and setting them equal to presence
+ #this is never exported
+ if(response.col=="responseCount") {response[response>=1]<-1
+ }
+
+ #remove any of pres absn or bgd that aren't desired
+ temp<-c(0,1,-9999)
+ temp<-temp[c(absn,pres,bgd)]
+ dat<-dat[response%in%temp,]
+ response<-response[response%in%temp]
+
+
+ if(sum(response==-9999)>1000){
+ s<-sample(which(response==-9999,arr.ind=TRUE),size=(sum(response==-9999)-1000))
+ dat<-dat[-c(s),]
+ response<-response[-c(s)]
+ }
+
+ if (response.col=="responseCount") {
+ TrueResponse<-dat[,match(tolower(response.col),tolower(names(dat)))]
+ } else TrueResponse<-response
+
+ #now remove all columns except predictors
+ dat<-dat[-rm.cols]
+ dat[dat==-9999]<-NA
+ #dat<-dat[1:2000,]
+ #Remove columns with only one unique value
+ varr <- function(x) var(x,na.rm=TRUE)
+
+ dat<-try(dat[,as.vector(apply(dat,2,varr)==0)!=1],silent=TRUE)
+ if(class(dat)=="try-error") stop("mds file contains nonnumeric columns please remove and continue")
+ #record correlations for later plots
+
+ cmat<-cor(dat,use="pairwise.complete.obs")
+ smat<-cor(dat,method="spearman",use="pairwise.complete.obs")
+ if(dim(dat)[1]<2000){
+ kmat<-cor(dat,method="kendall",use="pairwise.complete.obs")}
+ else {s<-sample(seq(1:dim(dat)[1]),size=2000,replace=FALSE)
+ kmat<-cor(dat[s,],method="kendall",use="pairwise.complete.obs")
+ }
+
+ cmat=pmax(abs(cmat),abs(smat),abs(kmat),na.rm=TRUE)
+
+ High.cor<-sort(apply(abs(cmat)>min.cor,2,sum)-1,decreasing=TRUE)
+
+ #take the top num.plots to put in the pairs plot or if the looking at a single
+ #predictor and other predictors it's correlated with, take the top num.plots-1
+ #of those with which it is correlated
+ {if(cors.w.highest==FALSE){
+ HighToPlot<-dat[,match(names(High.cor),names(dat))[1:min(num.plots,length(High.cor))]]
+ }else{
+ #take the column of the correlation matrix corresponding to the
+ #predictor with the higest number of total correlations record the names
+ #of the predictors that are correlated with this one predictor
+ temp<-cmat[rownames(cmat)==names(High.cor[1]),]
+ CorWHigh<-temp[abs(cmat[,colnames(cmat)==names(High.cor[1])])>min.cor]
+
+ #record counts of total number of correlations with all predictors for those
+ #predictors that are highly correlated with the Highest predictor
+ High.cor<-sort(High.cor[names(CorWHigh)],decreasing=TRUE)
+ HighToPlot<-dat[,match(names(High.cor),names(dat))[1:min(num.plots,length(High.cor))]]
+ }}
+ cor.hightoplot<-abs(cor(HighToPlot,use="pairwise.complete.obs"))
+ diag(cor.hightoplot)<-0
+ cor.range<-c(quantile(as.vector(cor.hightoplot),probs=c(0,.5,.7,.85)),1)
+
+ ## put histograms on the diagonal
+ panel.hist <- function(x, ...)
+ {
+ usr <- par("usr"); on.exit(par(usr))
+ par(usr = c(usr[1:2], 0, 1.5) )
+ h <- hist(x, plot = FALSE)
+ breaks <- h$breaks; nB <- length(breaks)
+ y <- h$counts; y <- y/max(y)
+ rect(breaks[-nB], 0, breaks[-1], y, col="steelblue", ...)
+
+ }
+
+
+ ## put (absolute) correlations on the upper panels,
+ ## with size proportional to the correlations.
+ panel.cor <- function(x, y, digits=2, prefix="", cor.range,cex.cor, ...)
+ {
+ a<-colors()
+ usr <- par("usr"); on.exit(par(usr))
+ par(usr = c(0, 1, 0, 1))
+ r <- abs(cor(x, y,use="pairwise.complete.obs"))
+ spear<-abs(cor(x,y,method="spearman",use="pairwise.complete.obs"))
+ ken<- abs(cor(x,y,method="kendall",use="pairwise.complete.obs"))
+ all.cor<-max(r,spear,ken)
+ #range.seq<-seq(from=cor.range[1],to=cor.range[2],length=20)
+ if(all.cor>=cor.range[4]){
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
+ a[59])} else if(all.cor>=cor.range[3]){
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
+ a[76])} else if(all.cor>=cor.range[2]){
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
+ a[382])}
+ r<-max(all.cor)
+ cex.cor=3
+ txt <- format(c(r, 0.123456789), digits=digits)[1]
+ txt <- paste(prefix, txt, sep="")
+ #if(missing(cex.cor)) cex.cor <- 1.2/strwidth(txt)
+
+ txt2=""
+ if(max(all.cor)>cor.range[2]){
+ if(spear==max(all.cor) && spear!=cor(x,y,use="pairwise.complete.obs")) {txt2 <- " s"
+ } else if(ken==max(all.cor) && ken!=cor(x,y,use="pairwise.complete.obs")){
+ txt2 <-" k"
+ }
+
+ }
+ text(0.5, 0.5, txt, cex = .7+cex.cor * (r-min(cor.range))/(max(cor.range)-min(cor.range)))
+ text(.9,.1,txt2,cex=1.5)
+ }
+
+# #Find a new unique file name (one in the desired directory that hasn't yet been used)
+# outfile <- paste(output.dir,"Predictor_Correlation.pdf",sep="\\")
+# while(file.access(outfile)==0) outfile<-paste(output.dir,"Predictor_Correlation.pdf",sep="\\")
+#
+# options(warn=-1)
+# pdf(outfile,width=11,height=9,onefile=T)
+# MyPairs(HighToPlot,cor.range=cor.range,my.labels=(as.vector(High.cor)[1:num.plots]),
+# lower.panel=panel.smooth,diag.panel=panel.hist, upper.panel=panel.cor,pch=21,bg = c("red","steelblue")[as.factor(response)],col.smooth = "red")
+# graphics.off()
+# options(warn=0)
+#
+# }
+
+
+ #Find a new unique file name (one in the desired directory that hasn't yet been used)
+
+ options(warn=-1)
+ if(Debug==FALSE) jpeg(output.file,width=1000,height=1000,pointsize=13)
+ MyPairs(cbind(TrueResponse,HighToPlot),cor.range=cor.range,my.labels=(as.vector(High.cor)[1:num.plots]),
+ lower.panel=panel.smooth,diag.panel=panel.hist, upper.panel=panel.cor,pch=21,bg = c("green","red","yellow")[factor(response,levels=c(0,1,-9999))],col.smooth = "red")
+
+ if(Debug==FALSE) graphics.off()
+ options(warn=0)
+
+ }
+
+MyPairs<-function (x,my.labels,labels, panel = points, ..., lower.panel = panel,
+ upper.panel = panel, diag.panel = NULL, text.panel = textPanel,
+ label.pos = 0.5 + has.diag/3, cex.labels = NULL, font.labels = 1,
+ row1attop = TRUE, gap = 1,Toplabs=NULL)
+{
+ response<-x[,1]
+ response[response==-9999]<-0
+ x<-x[,2:dim(x)[2]]
+
+ textPanel <- function(x = 0.5, y = 0.5, txt, cex, font) text(x,
+ y, txt, cex = cex, font = font)
+ localAxis <- function(side, x, y, xpd, bg, col = NULL, main,
+ oma, ...) {
+ if (side%%2 == 1)
+ Axis(x, side = side, xpd = NA, ...)
+ else Axis(y, side = side, xpd = NA, ...)
+ }
+ localPlot <- function(..., main, oma, font.main, cex.main) plot(...)
+ localLowerPanel <- function(..., main, oma, font.main, cex.main) lower.panel(...)
+ localUpperPanel <- function(..., main, oma, font.main, cex.main) upper.panel(...)
+ localDiagPanel <- function(..., main, oma, font.main, cex.main) diag.panel(...)
+ dots <- list(...)
+ nmdots <- names(dots)
+ if (!is.matrix(x)) {
+ x <- as.data.frame(x)
+ for (i in seq_along(names(x))) {
+ if (is.factor(x[[i]]) || is.logical(x[[i]]))
+ x[[i]] <- as.numeric(x[[i]])
+ if (!is.numeric(unclass(x[[i]])))
+ stop("non-numeric argument to 'pairs'")
+ }
+ } else if (!is.numeric(x))
+ stop("non-numeric argument to 'pairs'")
+ panel <- match.fun(panel)
+ if ((has.lower <- !is.null(lower.panel)) && !missing(lower.panel))
+ lower.panel <- match.fun(lower.panel)
+ if ((has.upper <- !is.null(upper.panel)) && !missing(upper.panel))
+ upper.panel <- match.fun(upper.panel)
+ if ((has.diag <- !is.null(diag.panel)) && !missing(diag.panel))
+ diag.panel <- match.fun(diag.panel)
+ if (row1attop) {
+ tmp <- lower.panel
+ lower.panel <- upper.panel
+ upper.panel <- tmp
+ tmp <- has.lower
+ has.lower <- has.upper
+ has.upper <- tmp
+ }
+ nc <- ncol(x)
+ if (nc < 2)
+ stop("only one column in the argument to 'pairs'")
+ has.labs <- TRUE
+ if (missing(labels)) {
+ labels <- colnames(x)
+ if (is.null(labels))
+ labels <- paste("var", 1L:nc)
+ }
+ else if (is.null(labels))
+ has.labs <- FALSE
+ oma <- if ("oma" %in% nmdots)
+ dots$oma
+ else NULL
+ main <- if ("main" %in% nmdots)
+ dots$main
+ else NULL
+ if (is.null(oma)) {
+ oma <- c(4, 4, 4, 4)
+ if (!is.null(main))
+ oma[3L] <- 6
+ }
+
+ nCol<-ifelse(length(unique(response))>1,nc+1,nc)
+ j.start<-ifelse(length(unique(response))>1,0,1)
+ opar <- par(mfrow = c(nc, nCol), mar = rep.int(gap/2, 4), oma = oma)
+ on.exit(par(opar))
+ for (i in if (row1attop)
+ 1L:(nc)
+ else nc:1L) for (j in j.start:(nc)) {
+
+
+ if(i==1){ par(mar = c(gap/2,gap/2,gap,gap/2)) #top row add extra room at top
+ if(j==0){
+ par(mar = c(gap/2,gap,gap,gap)) #top left corner room at top and on right
+ localPlot(x[, i],response, xlab = "", ylab = "", axes = FALSE,
+ type="n",...)
+ }else if(j==1) {par(mar = c(gap/2,gap,gap,gap/2)) #extra room on left and topfor second plot top row
+ localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
+ type="n",...)} else {
+ par(mar = c(gap/2,gap/2,gap,gap/2)) #all other top row plots need extra room at top only
+ localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
+ type="n",...)
+ }}else { par(mar = rep.int(gap/2, 4))
+ if(j==0){ par(mar = c(gap/2,gap,gap/2,gap)) #left column needs extra room on right only
+ localPlot(x[, i],response, xlab = "", ylab = "", axes = FALSE,
+ type="n",...)
+ }else if(j==1){ par(mar = c(gap/2,gap,gap/2,gap/2)) #second column needs extra room on left so labels fit
+ localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
+ type="n",...)
+ }else localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
+ type="n",...)}
+ if(j==0) {
+ if(i==1) par(mar=c(gap/2,gap,gap,gap))
+ else par(mar = c(gap/2,gap,gap/2,gap))
+
+ if(i==1) title(main="Response",line=.04,cex.main=1.5)
+
+ box()
+ my.lab<-paste("cor=",round(max(abs(cor(x[,(i)],response,use="pairwise.complete.obs")),abs(cor(x[,(i)],response,method="spearman",use="pairwise.complete.obs")),
+ abs(cor(x[,(i)],response,method="kendall",use="pairwise.complete.obs"))),digits=2),sep="")
+
+ #panel smooth doesn't work for two reasons: one, the response is binary and it requires more than two unique values
+ #second I don't think it can use weights which is necessary with an overwhelming amount of background points so that presnce points
+ #can't be viewed
+ #panel.smooth(as.vector(x[, (i)]), as.vector(jitter(response,factor=.1)),weights=
+ # c(rep(table(response)[2]/table(response)[1],times=table(response)[1]),rep(1,times=table(response)[2])),...)
+
+ if(length(unique(response))>2) panel.smooth(as.vector(x[, (i)]), as.vector(response),...)
+ else my.panel.smooth(as.vector(x[, (i)]), as.vector(response),weights=
+ c(rep(table(response)[2]/table(response)[1],times=table(response)[1]),rep(1,times=table(response)[2])),...)
+
+ title(ylab=paste("cor=",round(max(abs(cor(x[,(i)],response,use="pairwise.complete.obs")),
+ abs(cor(x[,(i)],response,method="spearman",use="pairwise.complete.obs")),abs(cor(x[,(i)],response,method="kendall",use="pairwise.complete.obs"))),digits=2),
+ sep=""),line=.02,cex.lab=1.5)
+ #,y=.85,x=max(x[,(i)])-.2*diff(range(x[,(i)])),cex=1.5)
+
+ } else{
+ if (i == j || (i < j && has.lower) || (i > j && has.upper)) {
+ box()
+ if(i==1) title(main=paste("Total Cor=",my.labels[j],sep=""),line=.04,cex.main=1.5)
+ #if (i == 1 && (!(j%%2) || !has.upper || !has.lower))
+ # localAxis(1 + 2 * row1attop, x[, j], x[, i],
+ # ...)
+ if (i == nc)
+ localAxis(3 - 2 * row1attop, x[, j], x[, i],
+ ...)
+ if (j == 1 && (i!=1 || !has.upper || !has.lower))
+ localAxis(2, x[, j], x[, i], ...)
+ #if (j == nc && (i%%2 || !has.upper || !has.lower))
+ # localAxis(4, x[, j], x[, i], ...)
+ mfg <- par("mfg")
+ if (i == j) {
+ if (has.diag)
+ localDiagPanel(as.vector(x[, i]),...)
+ if (has.labs) {
+ par(usr = c(0, 1, 0, 1))
+ if (is.null(cex.labels)) {
+ l.wid <- strwidth(labels, "user")
+ cex.labels <- max(0.8, min(2, 0.9/max(l.wid)))
+ }
+
+ text.panel(0.5, label.pos, labels[i], cex = cex.labels,
+ font = font.labels)
+ }
+ }
+
+ else if (i < j)
+ if(length(unique(x[,i])>2)){
+ localLowerPanel(as.vector(x[, j]), as.vector(x[,
+ i]), ...) } else {
+ my.panel.smooth(as.vector(x[, j]),as.vector(x[,i]))
+ }
+
+ else localUpperPanel(as.vector(x[, j]), as.vector(x[,
+ i]), ...)
+ if (any(par("mfg") != mfg))
+ stop("the 'panel' function made a new plot")
+ }
+ else par(new = FALSE)
+ }}
+ if (!is.null(main)) {
+ font.main <- if ("font.main" %in% nmdots)
+ dots$font.main
+ else par("font.main")
+ cex.main <- if ("cex.main" %in% nmdots)
+ dots$cex.main
+ else par("cex.main")
+ mtext(main, 3, 3, TRUE, 0.5, cex = cex.main, font = font.main)
+ }
+ invisible(NULL)
+}
+
+
+my.panel.smooth<-function (x, y, col = par("col"), bg = NA, pch = par("pch"),
+ cex = 1, col.smooth = "red", span = 2/3, iter = 3, weights=rep(1,times=length(y)), ...)
+{
+ o<-order(x)
+ points(x, y, pch = pch, col = col, bg = bg, cex = cex)
+ ok <- is.finite(x) & is.finite(y)
+ if (any(ok) && length(unique(x))>3)
+ lines(lowess(x[o],y[o],iter=0),col="red")
+ #lines(smooth.spline(x,w=weights,jitter(y,amount=(max(y)-min(y))/100),nknots=min(length(unique(x)),4)),col="red")
+
+}
+
+
+Args <- commandArgs(T)
+ print(Args)
+ #assign default values
+ num.plots <- 10
+ min.cor <- .7
+ responseCol <- "ResponseBinary"
+ cors.w.highest <- FALSE
+ pres=TRUE
+ absn=TRUE
+ bgd=TRUE
+ #replace the defaults with passed values
+ for (arg in Args) {
+ argSplit <- strsplit(arg, "=")
+ argSplit[[1]][1]
+ argSplit[[1]][2]
+ if(argSplit[[1]][1]=="p") num.plots <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="m") min.cor <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="o") output.file <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="i") infile <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="core") cors.w.highest <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="pres") pres <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="absn") absn <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="bgd") bgd <- argSplit[[1]][2]
+ }
+
+ print(num.plots)
+ print(min.cor)
+ print(output.file)
+ print (infile)
+ print(responseCol)
+ print(cors.w.highest)
+ print(pres)
+ print(absn)
+ print(bgd)
+
+ #Run the Pairs Explore function with these parameters
+ Pairs.Explore(num.plots=num.plots,
+ min.cor=min.cor,
+ input.file=infile,
+ output.file=output.file,
+ response.col=responseCol,
+ cors.w.highest=cors.w.highest,
+ pres,
+ absn,
+ bgd)
+
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Pred.Surface.r b/contrib/sahm/pySAHM/Resources/R_Modules/Pred.Surface.r
new file mode 100644
index 0000000..a138e82
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Pred.Surface.r
@@ -0,0 +1,54 @@
+Pred.Surface<-function(object, model, filename="", na.rm=TRUE,NAval) {
+ predrast <- raster(object)
+ filename <- trim(filename)
+ firstrow <- 1
+ firstcol <- 1
+ ncols <- ncol(predrast)
+ lyrnames <- layerNames(object)
+ xylyrnames <- c('x', 'y', lyrnames)
+ v <- matrix(NA, ncol=nrow(predrast), nrow=ncol(predrast))
+ na.rm <- FALSE
+ tr <- blockSize(predrast, n=nlayers(object)+3)
+ ablock <- 1:(ncol(object) * tr$nrows[1])
+ napred <- rep(NA, ncol(predrast)*tr$nrows[1])
+ predrast <- writeStart(predrast, filename=filename,overwrite=TRUE)
+ ############################################################
+ for (i in 1:tr$n) {
+ if (i==tr$n) {
+ ablock <- 1:(ncol(object) * tr$nrows[i])
+ napred <- rep(NA, ncol(predrast) * tr$nrows[i])
+ }
+ rr <- firstrow + tr$row[i] - 1
+ p <- xyFromCell(predrast, ablock + (tr$row[i]-1) * ncol(predrast))
+ p <- na.omit(p)
+ blockvals <- data.frame(x=p[,1], y=p[,2])
+ if (na.rm) {
+ blockvals <- na.omit(blockvals)
+ }
+ if (nrow(blockvals) == 0 ) {
+ predv <- napred
+ } else {
+
+ predv <- predict(model, blockvals)
+ predv[is.na(predv)]<-NAval
+ }
+ if (na.rm) {
+ naind <- as.vector(attr(blockvals, "na.action"))
+ if (!is.null(naind)) {
+ p <- napred
+ p[-naind] <- predv
+ predv <- p
+ rm(p)
+ }
+ }
+
+ # to change factor to numeric; should keep track of this to return a factor type RasterLayer
+ predv = as.numeric(predv)
+ predrast <- writeValues(predrast, predv, tr$row[i])
+ NAvalue(predrast)<-NAval
+ }
+ predrast <- writeStop(predrast)
+ a<-readGDAL(predrast at file@name)
+ writeGDAL(a,predrast at file@name, drivername = "GTiff",setStatistics=TRUE,mvFlag=NAval)
+ return(predrast)
+ }
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/PredictModel.r b/contrib/sahm/pySAHM/Resources/R_Modules/PredictModel.r
new file mode 100644
index 0000000..69383fe
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/PredictModel.r
@@ -0,0 +1,331 @@
+PredictModel<-function(workspace=NULL,new.tifs=NULL,out.dir=NULL,thresh=NULL,make.btif=NULL,make.ptif=NULL){
+
+#This functions separates the step of model fit from producing probability or binary surfaces
+#the default is to read in a workspace and make predictions using the original tiffs supplied
+#but if an mds with new tiff directories are supplied, the function will instead use these
+#options are available for setting the threshold
+#and true and false for whether to make binary or prob.tif
+
+#my stuff to delete
+#workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\")
+#new.tifs<-out$input$ma.name
+#end delete
+
+ load(workspace)
+
+ if(!is.null(new.tifs)){
+
+ ma.name <- new.tifs
+ #get the paths off of the new mds file
+ tif.info<-readLines(ma.name,3)
+ tif.info<-strsplit(tif.info,',')
+ include<-(as.numeric(tif.info[[2]]))
+ paths<-as.character(tif.info[[3]])
+
+ paths<-paths[paths!=""]
+ #this line needs to be changed eventually to deal with locations of model fit covaries from different models
+ if(out$input$model.source.file=="brt.r") {model.covs<-levels(summary(out$mods$final.mod,plotit=FALSE)[,1])
+ pred.fct=brt.predict
+ }
+
+ ma.cols <- match(model.covs,sub(".tif","",basename(paths)))
+ paths<-paths[ma.cols]
+ #checking that all tifs are present
+ if(any(is.na(ma.cols))){
+
+ stop("ERROR: the following geotiff(s) are missing in ",
+ tif.dir,": ",paste(ma.names[-r.col][is.na(ma.cols)],collapse=" ,"),sep="")
+ }
+ #checking that we have read access to all tiffs
+ if(sum(file.access(paths),mode=0)!=0){
+ stop("ERROR: the following geotiff(s) are missing : ",
+ paths[(file.access(paths)!=0),][1],sep="")
+
+ }
+ out$dat$tif.ind<-paths
+ }
+
+ if(out$input$model.source.file=="rf.r") {
+ pred.fct=rf.predict
+ library(randomForest)
+ }
+ if(out$input$model.source.file=="mars.r") {
+ pred.fct=pred.mars
+ library(mda)
+ }
+ if(out$input$model.source.file=="glm.r") pred.fct=glm.predict
+ if(out$input$model.source.file=="brt.r") {
+ pred.fct=brt.predict
+ library(gbm)
+ }
+
+ if(!is.null(thresh))out$mods$auc.output$thresh<-thresh
+ if(!is.null(make.btif)) make.binary.tif<-make.btif
+ if(!is.null(make.ptif)) make.p.tif<-make.ptif
+
+
+ assign("Pred.Surface",Pred.Surface,envir=.GlobalEnv)
+ mssg <- proc.tiff(model=out$mods$final.mod,vnames=as.character(out$mods$final.mod$contributions$var),
+ tif.dir=out$dat$tif.dir$dname,filenames=out$dat$tif.ind,pred.fct=pred.fct,factor.levels=out$dat$ma$factor.levels,make.binary.tif=make.binary.tif,
+ thresh=out$mods$auc.output$thresh,make.p.tif=make.p.tif,outfile.p=paste(out.dir,"prob_map.tif",sep="\\"),
+ outfile.bin=paste(out.dir,"bin_map.tif",sep="\\"),tsize=50.0,NAval=-3000,logname=logname,out=out)
+
+
+}
+
+brt.predict <- function(model,x) {
+ # retrieve key items from the global environment #
+ # make predictions from complete data only #
+ #y <- rep(NA,nrow(x))
+ #y[complete.cases(x)] <- predict.gbm(model, x[complete.cases(x),],model$target.trees,type="response")
+
+ # make predictions from full data #
+ y <- predict.gbm(model,x,model$target.trees,type="response")
+ # encode missing values as -1.
+ a<-complete.cases(x)
+ y[!(a)]<- NaN
+
+ # return predictions.
+ return(y)
+ }
+
+pred.mars <- function(model,x) {
+ # retrieve key items from the global environment #
+ # make predictionss.
+ y <- rep(NA,nrow(x))
+ y[complete.cases(x)] <- as.vector(mars.predict(model,x[complete.cases(x),])$prediction[,1])
+
+#if(sum(is.na(x))/dim(x)[2]!=sum(is.na(y)))
+#h<-is.na(x)
+#h<-apply(h,1,sum)
+#h=h/35
+#f<-is.na(y)
+#which((h-f)!=0,arr.ind=TRUE)
+#b<-cbind(x[which((h-f)!=0,arr.ind=TRUE),],y[which((h-f)!=0,arr.ind=TRUE)])
+
+#which(is.na(y)
+ # encode missing values as -1.
+ y[is.na(y)]<- NaN
+
+ # return predictions.
+ return(y)
+ }
+
+glm.predict <- function(model,x) {
+ # retrieve key items from the global environment #
+ # make predictionss.
+
+ y <- as.vector(predict(model,x,type="response"))
+
+ # encode missing values as -1.
+ y[is.na(y)]<- NaN
+
+ # return predictions.
+ return(y)
+ }
+
+"mars.predict" <-
+function (mars.glm.object,new.data)
+{
+#
+# j leathwick, j elith - August 2006
+#
+# version 3.1 - developed in R 2.3.1 using mda 0.3-1
+#
+# calculates a mars/glm object in which basis functions are calculated
+# using an initial mars model with single or multiple responses
+# data for individual species are then fitted as glms using the
+# common set of mars basis functions with results returned as a list
+#
+# takes as input a dataset and args selecting x and y variables, and degree of interaction
+# along with site and species weights, the CV penalty, and the glm family argument
+# the latter would normally be one of "binomial" or "poisson" - "gaussian" could be used
+# but in this case the model shouldn't differ from that fitted using mars on its own
+#
+# naming problem for dataframes fixed - je - 15/12/06
+#
+# requires mda and leathwick/elith's mars.export
+#
+ require(mda)
+
+# first recreate both the original mars model and the glm model
+
+# setup input data and create original temporary data
+
+ dataframe.name <- mars.glm.object$mars.call$dataframe # get the dataframe name
+ mars.x <- mars.glm.object$mars.call$mars.x
+ mars.y <- mars.glm.object$mars.call$mars.y
+ n.spp <- length(mars.y)
+ family <- mars.glm.object$mars.call$family
+ mars.degree <- mars.glm.object$mars.call$degree
+ penalty <- mars.glm.object$mars.call$penalty
+ site.weights <- mars.glm.object$weights[[1]]
+ spp.weights <- mars.glm.object$weights[[2]]
+
+ print("creating original data frame...",quote=FALSE)
+
+ base.data <- as.data.frame(eval.parent(parse(text = dataframe.name),n=3)) #aks
+
+ x.temp <- eval(base.data[, mars.x]) #form the temporary datasets
+ base.names <- names(x.temp)
+
+ xdat <- mars.new.dataframe(x.temp)[[1]]
+
+ ydat <- as.data.frame(base.data[, mars.y])
+ names(ydat) <- names(base.data)[mars.y]
+
+ assign("xdat", xdat, pos = 1) #and assign them for later use
+ assign("ydat", ydat, pos = 1)
+
+# now create the temporary dataframe for the new data
+
+ print("checking variable matching with new data",quote = FALSE)
+
+ new.names <- names(new.data)
+
+ for (i in 1:length(base.names)) {
+
+ name <- base.names[i]
+
+ if (!(name %in% new.names)) {
+ print(paste("Variable ",name," missing from new data",sep=""),quote = FALSE) #aks
+ return()
+ }
+ }
+
+ print("and creating temporary dataframe for new data...",quote=FALSE)
+
+ selector <- match(names(x.temp),names(new.data))
+
+ pred.dat <- mars.new.dataframe(new.data[,selector])[[1]]
+
+ assign("pred.dat", pred.dat, pos = 1) #and assign them for later use
+
+# fit the mars model and extract the basis functions
+
+ print(paste("re-fitting initial mars model for",n.spp,"responses"),quote = FALSE)
+ print(paste("using glm family of",family),quote = FALSE)
+
+ #mars.fit <- mars(x = xdat, y = ydat, degree = mars.degree, w = site.weights,
+ # wp = spp.weights, penalty = penalty)
+
+ mars.fit <- mars.glm.object$mars.object #AKS
+
+ old.bf.data <- as.data.frame(eval(mars.fit$x))
+ n.bfs <- ncol(old.bf.data)
+ bf.names <- paste("bf", 1:n.bfs, sep = "")
+ old.bf.data <- as.data.frame(old.bf.data[,-1])
+ names(old.bf.data) <- bf.names[-1]
+
+ new.bf.data <- as.data.frame(mda:::model.matrix.mars(mars.fit,pred.dat))
+ new.bf.data <- as.data.frame(new.bf.data[,-1])
+ names(new.bf.data) <- bf.names[-1]
+
+# now cycle through the species fitting glm models
+
+ print("fitting glms for individual responses", quote = F)
+
+ prediction <- as.data.frame(matrix(0, ncol = n.spp, nrow = nrow(pred.dat)))
+ names(prediction) <- names(ydat)
+ standard.errors <- as.data.frame(matrix(0, ncol = n.spp, nrow = nrow(pred.dat)))
+ names(standard.errors) <- names(ydat)
+
+ for (i in 1:n.spp) {
+
+ print(names(ydat)[i], quote = FALSE)
+ model.glm <- glm(ydat[, i] ~ ., data = old.bf.data, weights = site.weights,
+ family = family, maxit = 100)
+ temp <- predict.glm(model.glm,new.bf.data,type="response",se.fit=TRUE)
+ prediction[,i] <- temp[[1]]
+ standard.errors[,i] <- temp[[2]]
+
+ }
+
+ return(list("prediction"=prediction,"ses"=standard.errors))
+}
+
+"mars.new.dataframe" <-
+function (input.data)
+{
+#
+# j leathwick, j elith - August 2006
+#
+# version 3.1 - developed in R 2.3.1 using mda 0.3-1
+#
+# takes an input data frame and checks for factor variables
+# converting these to dummy variables, one each for each factor level
+# returning it for use with mars.glm so that factor vars can be included
+# in a mars analysis
+#
+
+ if (!is.data.frame(input.data)) {
+ print("input data must be a dataframe..",quote = FALSE)
+ return()
+ }
+
+ n <- 1
+ for (i in 1:ncol(input.data)) { #first transfer the vector variables
+ if (is.vector(input.data[,i])) {
+ if (n == 1) {
+ output.data <- as.data.frame(input.data[,i])
+ names.list <- names(input.data)[i]
+ var.type <- "vector"
+ factor.level <- "na"
+ }
+ else {
+ output.data[,n] <- input.data[,i]
+ names.list <- c(names.list,names(input.data)[i])
+ var.type <- c(var.type,"vector")
+ factor.level <- c(factor.level,"na")
+ }
+ names(output.data)[n] <- names(input.data)[i]
+ n <- n + 1
+ }
+ }
+
+ for (i in 1:ncol(input.data)) { # and then the factor variables
+ if (is.factor(input.data[,i])) {
+ temp.table <- summary(input.data[,i])
+ for (j in 1:length(temp.table)) {
+ names.list <- c(names.list,names(input.data)[i])
+ var.type <- c(var.type,"factor")
+ factor.level <- c(factor.level,names(temp.table)[j])
+ output.data[,n] <- ifelse(input.data[,i] == names(temp.table)[j],1,0)
+ names(output.data)[n] <- paste(names(input.data)[i],".",names(temp.table)[j],sep="")
+ n <- n + 1
+ }
+ }
+ }
+
+ lineage <- data.frame(names(output.data),names.list,var.type,factor.level)
+ for (i in 1:4) lineage[,i] <- as.character(lineage[,i])
+ names(lineage) <- c("full.name","base.name","type","level")
+
+ return(list(dataframe = output.data, lineage = lineage))
+}
+
+
+
+
+
+new.tifs=NULL
+# Interpret command line argurments #
+# Make Function Call #
+Args <- commandArgs(trailingOnly=FALSE)
+
+ for (i in 1:length(Args)){
+ if(Args[i]=="-f") ScriptPath<-Args[i+1]
+ }
+
+ for (arg in Args) {
+ argSplit <- strsplit(arg, "=")
+ argSplit[[1]][1]
+ argSplit[[1]][2]
+ if(argSplit[[1]][1]=="ws") ws <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="new.tifs") new.tifs <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="o") out.dir <- argSplit[[1]][2]
+ }
+
+PredictModel(workspace=ws,new.tifs=new.tifs,out.dir=out.dir)
+
+
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/ResidualImage.r b/contrib/sahm/pySAHM/Resources/R_Modules/ResidualImage.r
new file mode 100644
index 0000000..2d0104d
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/ResidualImage.r
@@ -0,0 +1,42 @@
+resid.image<-function(dev.contrib,pred,raw.dat,x,y,model.type,file.name,out){
+ z<-sign(pred-raw.dat)*dev.contrib
+ a<-loess(z~x*y)
+ x.lim<-rep(seq(from=min(out$dat$ma$train.xy[,1]),to=max(out$dat$ma$train.xy[,1]),length=100),each=100)
+ y.lim<-rep(seq(from=min(out$dat$ma$train.xy[,2]),to=max(out$dat$ma$train.xy[,2]),length=100),times=100)
+ z<-predict(a,newdata=cbind("x"=x.lim,"y"=y.lim))
+ x.lim<-seq(from=min(out$dat$ma$train.xy[,1]),to=max(out$dat$ma$train.xy[,1]),length=100)
+ y.lim<-seq(from=min(out$dat$ma$train.xy[,2]),to=max(out$dat$ma$train.xy[,2]),length=100)
+ z<-matrix(data=z,ncol=100,nrow=100,byrow=TRUE)
+ # browser()
+ ########################################### experiment
+ # if(out$input$make.binary.tif==TRUE | out$input$make.p.tif==TRUE){
+ # out$dat$tif.ind[1]
+ # RasterInfo=raster(out$dat$tif.ind[1])
+ # gi <- GDALinfo(out$dat$tif.ind[1])
+ # dims <- as.vector(gi)[1:2]
+ # ps <- as.vector(gi)[6:7]
+ # ll <- as.vector(gi)[4:5]
+ # pref<-attr(gi,"projection")
+
+
+ # }
+
+
+ ##########################################################
+ jpeg(file=paste(file.name,"resid.plot.jpg",sep="/"))
+ par(oma=c(3,3,3,3))
+ layout(matrix(data=c(1,2), nrow=1, ncol=2), widths=c(4,1), heights=c(1,1))
+ image(z,x=x.lim,y=y.lim,col=beachcolours(heightrange=c(min(z),max(z)),sealevel=0,ncolours=length(table(z))),
+ main="Spatial pattern of deviance residuals\n(magnitude and sign)",xlab="X coordinate",ylab="Y coordinate")
+ points(x,y,cex=.5)
+ #image(x=c(1,2),y=sort(unique(z)),z=matrix(data=cbind(rep(sort(unique(z)),times=2)),ncol=2),col=beachcolours(heightrange=c(min(z),max(z)),sealevel=0,ncolours=length(table(z))))
+ par(mar = c(3,2.5,2.5,2))
+ colrange<-seq(from=min(z),to=max(z),length=100)
+ image(1,colrange,
+ matrix(data=colrange, ncol=length(colrange),nrow=1),
+ col=beachcolours(heightrange=c(min(z),max(z)),sealevel=0,ncolours=length(colrange)),
+ xlab="",ylab="",
+ xaxt="n")
+ graphics.off()
+ return(a)
+ }
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/RunMaxEnt.jar b/contrib/sahm/pySAHM/Resources/R_Modules/RunMaxEnt.jar
new file mode 100644
index 0000000..45a9faf
Binary files /dev/null and b/contrib/sahm/pySAHM/Resources/R_Modules/RunMaxEnt.jar differ
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainRocPlot.r b/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainRocPlot.r
new file mode 100644
index 0000000..7e79c14
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainRocPlot.r
@@ -0,0 +1,372 @@
+TestTrainRocPlot<-function (DATA, threshold = 101, find.auc = TRUE, which.model = (1:(ncol(DATA) -
+ 2)), na.rm = FALSE, xlab = "1-Specificity (false positives)",
+ ylab = "Sensitivity (true positives)", main = "ROC Plot",
+ model.names = NULL, color = NULL, line.type = NULL, lwd = 1,
+ mark = 0, mark.numbers = TRUE, mark.color = NULL, opt.thresholds = NULL,
+ opt.methods = NULL, req.sens, req.spec, obs.prev = NULL,
+ smoothing = 1, add.legend = TRUE, legend.text = model.names,
+ legend.cex = 0.8, add.opt.legend = TRUE, opt.legend.text = NULL,
+ opt.legend.cex = 0.7, counter.diagonal = FALSE, pch = NULL,
+ FPC, FNC, cost.line = FALSE,add.roc=FALSE)
+{
+ if (is.data.frame(DATA) == FALSE) {
+ if (is.matrix(DATA) == TRUE) {
+ DATA <- as.data.frame(DATA)
+ }
+ else {
+ stop("'DATA' must be either data frame or matrix")
+ }
+ }
+ OBS <- DATA[, 2]
+ if (length(OBS[OBS == 0]) == 0) {
+ stop("no observed absences in dataset, therefore specificity does not",
+ "exist, and modeling, much less Area Under the Curve, is not very",
+ "meaningful")
+ }
+ if (length(OBS[OBS == 1]) == 0) {
+ stop("no observed presences in dataset, therefore sensitivity does not",
+ "exist, and modeling, much less Area Under the Curve, is not very",
+ "meaningful")
+ }
+ if (is.logical(find.auc) == FALSE) {
+ stop("'find.auc' must be of logical type")
+ }
+ if (is.logical(na.rm) == FALSE) {
+ stop("'na.rm' must be of logical type")
+ }
+ if (is.logical(mark.numbers) == FALSE) {
+ stop("'mark.numbers' must be of logical type!")
+ }
+ if (is.logical(add.legend) == FALSE) {
+ stop("'add.legend' must be of logical type!")
+ }
+ if (is.logical(add.opt.legend) == FALSE) {
+ stop("'add.opt.legend' must be of logical type")
+ }
+ if (is.logical(counter.diagonal) == FALSE) {
+ stop("'counter.diagonal' must be of logical type")
+ }
+ if (length(smoothing) != 1) {
+ stop("'smoothing' must be a single number greater than or equal to 1")
+ }
+ else {
+ if (is.numeric(smoothing) == FALSE) {
+ stop("'smoothing' must be a single number greater than or equal to 1")
+ }
+ else {
+ if (smoothing < 1) {
+ stop("'smoothing' must be a single number greater than or equal to 1")
+ }
+ }
+ }
+ if (sum(is.na(DATA)) > 0) {
+ if (na.rm == TRUE) {
+ NA.rows <- apply(is.na(DATA), 1, sum)
+ warning(length(NA.rows[NA.rows > 0]), " rows ignored due to NA values")
+ DATA <- DATA[NA.rows == 0, ]
+ }
+ else {
+ return(NA)
+ }
+ }
+ DATA[DATA[, 2] > 0, 2] <- 1
+ N.models <- ncol(DATA) - 2
+ if (is.null(obs.prev) == TRUE) {
+ obs.prev <- sum(DATA[, 2])/nrow(DATA)
+ }
+ if (obs.prev < 0 || obs.prev > 1) {
+ stop("'obs.prev' must be a number between zero and one")
+ }
+ if (obs.prev == 0) {
+ warning("because your observed prevalence was zero, results may be strange")
+ }
+ if (obs.prev == 1) {
+ warning("because your observed prevalence was one, results may be strange")
+ }
+ if (min(which.model) < 1 || sum(round(which.model) != which.model) !=
+ 0) {
+ stop("values in 'which.model' must be positive integers")
+ }
+ if (max(which.model) > N.models) {
+ stop("values in 'which.model' must not be greater than number of models in 'DATA'!")
+ }
+ if (is.null(model.names) == TRUE) {
+ model.names <- if (is.null(names(DATA)) == FALSE) {
+ names(DATA)[-c(1, 2)]
+ }
+ else {
+ paste("Model", 1:N.models)
+ }
+ }
+ if (N.models != length(model.names) && (length(which.model) !=
+ 1 || length(model.names) != 1)) {
+ stop("If 'model.names' is specified it must either be a single name, or a vector",
+ "of the same length as the number of model predictions in 'DATA'")
+ }
+ if (is.null(legend.text) == TRUE) {
+ legend.text <- model.names
+ }
+ if (length(legend.text) != N.models) {
+ stop("'opt.legend.text' must be of same length as 'opt.methods'")
+ }
+ DATA <- DATA[, c(1, 2, which.model + 2)]
+ if (length(model.names) != 1) {
+ model.names <- model.names[which.model]
+ }
+ if (length(legend.text) != 1) {
+ legend.text <- legend.text[which.model]
+ }
+ N.dat <- ncol(DATA) - 2
+ if (is.null(obs.prev) == TRUE) {
+ obs.prev <- sum(DATA[, 2])/nrow(DATA)
+ }
+ if (obs.prev < 0 || obs.prev > 1) {
+ stop("'obs.prev' must be a number between zero and one")
+ }
+ mark <- matrix(mark, length(mark), N.dat)
+ if (!is.null(opt.methods) && is.null(opt.thresholds)) {
+ opt.thresholds <- TRUE
+ }
+ if (is.null(opt.methods) && is.null(opt.thresholds)) {
+ opt.thresholds <- FALSE
+ }
+ if (is.null(opt.methods)) {
+ opt.methods <- c(1, 2, 4)
+ }
+ if (is.logical(opt.thresholds) == TRUE) {
+ if (opt.thresholds == TRUE) {
+ POSSIBLE.meth <- c("Default", "Sens=Spec", "MaxSens+Spec",
+ "MaxKappa", "MaxPCC", "PredPrev=Obs", "ObsPrev",
+ "MeanProb", "MinROCdist", "ReqSens", "ReqSpec",
+ "Cost")
+ N.meth <- length(opt.methods)
+ if (is.numeric(opt.methods) == TRUE) {
+ if (sum(opt.methods %in% (1:length(POSSIBLE.meth))) !=
+ N.meth) {
+ stop("invalid optimization method")
+ }
+ else {
+ opt.methods <- POSSIBLE.meth[opt.methods]
+ }
+ }
+ if (sum(opt.methods %in% POSSIBLE.meth) != N.meth) {
+ stop("invalid optimization method")
+ }
+ if (is.null(opt.legend.text) == TRUE) {
+ opt.legend.text <- opt.methods
+ }
+ if (length(opt.legend.text) != N.meth) {
+ stop("'opt.legend.text' must be of same length as 'opt.methods'")
+ }
+ if ("ReqSens" %in% opt.methods) {
+ if (missing(req.sens)) {
+ warning("req.sens defaults to 0.85")
+ req.sens <- 0.85
+ }
+ }
+ if ("ReqSpec" %in% opt.methods) {
+ if (missing(req.spec)) {
+ warning("req.spec defaults to 0.85")
+ req.spec <- 0.85
+ }
+ }
+ if ("Cost" %in% opt.methods) {
+ if (missing(FPC) || missing(FNC)) {
+ warning("costs assumed to be equal")
+ FPC <- 1
+ FNC <- 1
+ }
+ if (FPC <= 0 || FNC <= 0) {
+ stop("costs must be positive")
+ }
+ if (is.logical(cost.line) == FALSE) {
+ stop("'cost.line' must be of logical type")
+ }
+ if (!"Cost" %in% opt.methods) {
+ cost.line <- FALSE
+ }
+ }
+ mark <- optimal.thresholds(DATA = DATA, threshold = threshold,
+ model.names = model.names, na.rm = na.rm, opt.methods = opt.methods,
+ req.sens = req.sens, req.spec = req.spec, obs.prev = obs.prev,
+ smoothing = smoothing, FPC = FPC, FNC = FNC)[,
+ -1, drop = FALSE]
+ if (is.null(pch) == TRUE) {
+ pch <- c(1, 5, 2, 16, 15, 17, 8, 6, 9, 12, 4,
+ 7)[match(opt.methods, POSSIBLE.meth)]
+ }
+ else {
+ pch <- rep(pch, length(opt.methods))[1:length(opt.methods)]
+ }
+ }
+ }
+ if (is.logical(opt.thresholds) == FALSE) {
+ if (!is.numeric(opt.thresholds)) {
+ stop("'opt.thresholds' must be 'TRUE', 'FALSE', or numeric")
+ }
+ if (min(opt.thresholds) < 0) {
+ stop("'opt.thresholds' can not be negative")
+ }
+ if (max(opt.thresholds) > 1) {
+ if (N.thr == 1 && round(opt.thresholds) == opt.thresholds) {
+ opt.thresholds <- seq(length = opt.thresholds,
+ from = 0, to = 1)
+ N.thr <- length(opt.thresholds)
+ }
+ else {
+ stop("non-interger, non-logical 'opt.thresholds' greater than 1")
+ }
+ }
+ N.opt.thresh <- length(opt.thresholds)
+ if (is.null(opt.legend.text)) {
+ opt.legend.text <- rep("threshold", N.opt.thresh)
+ }
+ if (length(opt.legend.text) != N.opt.thresh) {
+ stop("length of 'opt.legend.text' does not match number of specified thresholds")
+ }
+ if (is.null(pch)) {
+ pch <- 1:N.opt.thresh
+ }
+ if (length(pch) != N.opt.thresh) {
+ stop("length of 'pch' does not match number of specified thresholds")
+ }
+ mark <- matrix(opt.thresholds, length(opt.thresholds),
+ N.dat)
+ opt.thresholds = TRUE
+ }
+ if (is.null(pch) == TRUE) {
+ pch <- 16
+ }
+ if (is.null(color) == TRUE) {
+ colors <- rep(1, N.dat)
+ if (is.null(line.type) == TRUE) {
+ line.type <- (1:N.dat) + 1
+ }
+ }
+ else {
+ if (is.logical(color) == TRUE) {
+ if (color == FALSE) {
+ colors <- rep(1, N.dat)
+ if (is.null(line.type) == TRUE) {
+ line.type <- (1:N.dat) + 1
+ }
+ }
+ else {
+ colors <- (1:N.dat) + 1
+ lwd <- 2 * lwd
+ if (is.null(line.type) == TRUE) {
+ line.type <- rep(1, N.dat)
+ }
+ }
+ }
+ else {
+ colors <- rep(color, N.dat)[1:N.dat]
+ lwd <- 2 * lwd
+ if (is.null(line.type) == TRUE) {
+ line.type <- rep(1, N.dat)
+ }
+ }
+ }
+ if (is.null(mark.color) == TRUE) {
+ mark.colors <- colors
+ }
+ else {
+ if (is.logical(mark.color) == TRUE) {
+ if (mark.color == FALSE) {
+ mark.colors <- rep(1, N.dat)
+ }
+ else {
+ mark.colors <- (1:N.dat) + 1
+ }
+ }
+ else {
+ mark.colors <- rep(mark.color, N.dat)[1:N.dat]
+ }
+ }
+ if (is.null(line.type) == FALSE) {
+ if (is.logical(line.type) == TRUE) {
+ if (line.type == FALSE) {
+ line.type <- rep(1, N.dat)
+ }
+ else {
+ line.type <- (1:N.dat) + 1
+ }
+ }
+ else {
+ line.type <- rep(line.type, N.dat)[1:N.dat]
+ }
+ }
+ op <- par(pty = "s")
+ if(add.roc==FALSE){
+ plot(c(0, 1), c(0, 1), type = "n", xlab = xlab, ylab = ylab,
+ main = main)}
+ lines(c(0, 1), c(0, 1), col = "lightgray")
+ if (counter.diagonal == TRUE) {
+ abline(a = 1, b = -1, col = "lightgray")
+ }
+ for (dat in 1:N.dat) {
+ Model.dat <- roc.plot.calculate(DATA = DATA, threshold = threshold,
+ which.model = dat)
+ lines(x = (1 - Model.dat$specificity), y = Model.dat$sensitivity,
+ lty = line.type[dat], lwd = lwd, col = colors[dat])
+ if (max(mark) != 0) {
+ Mark.dat <- roc.plot.calculate(DATA = DATA, threshold = mark[,
+ dat], which.model = dat)
+ Mark.pretty <- round(Mark.dat$threshold, 2)
+ Mark.pretty.char <- as.character(Mark.pretty)
+ Mark.pretty.char[Mark.pretty == 0] <- "0.00"
+ Mark.pretty.char[Mark.pretty == 1] <- "1.00"
+ Mark.pretty.char[nchar(Mark.pretty.char) == 3] <- paste(Mark.pretty.char[nchar(Mark.pretty.char) ==
+ 3], "0", sep = "")
+ if(add.roc==FALSE){
+ points(x = (1 - Mark.dat$specificity), y = Mark.dat$sensitivity,
+ cex = 2, pch = pch, col = mark.colors[dat])
+ if (mark.numbers == TRUE) {
+ text(x = (1 - Mark.dat$specificity), y = Mark.dat$sensitivity -
+ 0.03, labels = Mark.pretty.char, pos = 4, col = mark.colors[dat])
+ }}
+ }
+ if (cost.line == TRUE) {
+ tag <- match("Cost", opt.methods)
+ sl <- (FPC/FNC) * (1 - obs.prev)/obs.prev
+ if (obs.prev == 0) {
+ obs.prev <- 1e-06
+ }
+ abline(a = Mark.dat$sensitivity[tag] - ((1 - Mark.dat$specificity[tag]) *
+ sl), b = sl, col = mark.colors[dat], lty = 3)
+ }
+ }
+ inset <- c(0.02, 0.02)
+ if (opt.thresholds == TRUE && add.opt.legend == TRUE) {
+ if (N.dat == 1) {
+ opt.legend.names <- paste(Mark.pretty.char, opt.legend.text)
+ }
+ else {
+ opt.legend.names <- opt.legend.text
+ }
+ leg.loc <- legend(x = "bottomright", inset = inset, pt.cex = 1,
+ legend = opt.legend.names, pch = pch, bg = "white",
+ cex = opt.legend.cex)
+ inset <- c(0.02, leg.loc$rect$top + 0.05)
+ }
+ if (add.legend == TRUE) {
+ legend.names <- legend.text
+ if (find.auc == TRUE) {
+ AUC <- rep(0, N.dat)
+ for (dat in 1:N.dat) {
+ AUC[dat] <- auc(DATA = DATA, which.model = dat)$AUC
+ }
+ AUC.pretty <- round(AUC, 2)
+ AUC.pretty.char <- as.character(AUC.pretty)
+ AUC.pretty.char[AUC.pretty == 0] <- "0.00"
+ AUC.pretty.char[AUC.pretty == 1] <- "1.00"
+ AUC.pretty.char[nchar(AUC.pretty.char) == 3] <- paste(AUC.pretty.char[nchar(AUC.pretty.char) ==
+ 3], "0", sep = "")
+ legend.names <- paste(AUC.pretty.char, legend.text)
+ }
+ legend(x = "bottomright", inset = inset, legend = legend.names,
+ lty = line.type, col = colors, title = "AUC:", cex = legend.cex,
+ lwd = lwd, bg = "white")
+ }
+ par(op)
+}
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainSplit.r b/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainSplit.r
new file mode 100644
index 0000000..d2564ea
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainSplit.r
@@ -0,0 +1,188 @@
+ TestTrainSplit<-function(input.file,output.file,response.col="ResponseBinary",trainProp=.7,RatioPresAbs=NULL){
+
+#Description:
+#this code takes as input an mds file with the first line being the predictor or
+#response name, the second line an indicator of predictors to include and the
+#third line being paths where tif files can be found. An output file and a
+#response column must also be specified. Given a training proportion, a new
+#column is created indicating whether each observation should be assigned to the
+#test or training split with the correct proportion.
+#trainProp=#obs to be assigned to training split/total sample size
+#his will be balanced with respect to the response in that the training
+#proportion will be matched as close as possible for each level of the response.
+#An optional parameter, RatioPresAbs, can be used to specify if there is a certain
+#ratio of presence to absence points that should be used this ensures the given
+#ratio for all data used in both the test and train split. For categorical data,
+#all responses greater than or equal to 1 will be used to meet this ratio.
+#This option reduces the sample size as some data must be thrown away to meet
+#the constraint of having the desired proportion. Background points are ignored
+#by this module (they are read in, written out, but not assigned to either the
+#test or training split). Output is written to a csv that can be used by the
+#SAHM R modules.
+
+#Written by Marian Talbert 3/23/2011
+#Modified 5/10/2011 to handle count data
+
+
+
+ if(trainProp<=0 | trainProp>1) stop("Train Proportion (trainProp) must be a number between 0 and 1 excluding 0")
+ if(!is.null(RatioPresAbs)) {
+ if(RatioPresAbs<=0) stop("The ratio of presence to absence (RatioPresAbs) must be a \ngreater than 0")}
+
+ #Read input data and remove any columns to be excluded
+ dat.in<-read.csv(input.file,header=FALSE,as.is=TRUE)
+ dat<-as.data.frame(dat.in[4:dim(dat.in)[1],])
+ names(dat)<-dat.in[1,]
+
+ response<-dat[,match(tolower(response.col),tolower(names(dat)))]
+
+ if(sum(as.numeric(response)==0)==0 && !is.null(RatioPresAbs)) stop("The ratio of presence to absence cannot be set with only presence data")
+
+ #Ignoring background data that might be present in the mds
+
+ bg.dat<-dat[response==-9999,]
+
+ if(dim(bg.dat)[1]!=0){
+ dat<-dat[-c(which(response==-9999,arr.ind=TRUE)),]
+ dat.in<-dat.in[-c(which(response==-9999,arr.ind=TRUE)+3),]
+ response<-response[-c(which(response==-9999,arr.ind=TRUE))]
+ bg.dat$TrainSplit=""
+ }
+
+ temp<-if(!is.null(RatioPresAbs))(sum(response>=1)/sum(response==0)==RatioPresAbs)
+ if(is.null(temp)) temp<-FALSE
+ if(is.null(RatioPresAbs)| temp){
+ #Randomly sample presesce absence or counts as close to the size of the training proportion as possible
+
+ #iterate through each unique response and randomly assign the trainProp to be in the training split
+ TrainSplit<-numeric()
+ for(i in sort(as.numeric(unique(response)))){
+ TrainSplit<-c(TrainSplit,sample(which(response==i,arr.ind=TRUE),size=round(sum(response==i)*trainProp)))
+ }
+
+
+ #Take everything not in the training set for the test set
+ TestSplit=which(!(seq(1:length(response)))%in%TrainSplit,arr.ind=TRUE)
+
+ dat$TrainSplit[seq(1:length(response))%in%TrainSplit]<-"train"
+ dat$TrainSplit[seq(1:length(response))%in%TestSplit]<-"test"
+
+ #inserting data must be done in 3 steps because dat.in isn't a proper dataframe in that
+ #not all elements in a column are of the same type
+ dat.in<-dat.in[c(1:3,rownames(dat)),] #removing rows that weren't selected for the test train split
+ dat.in[4:(dim(dat.in)[1]),(dim(dat.in)[2]+1)]<-dat$TrainSplit
+ dat.in[c(1,3),(dim(dat.in)[2])]<-c("Split","")
+ dat.in[2,(dim(dat.in)[2])]<-1
+
+
+ } else { #now considering if there is a desired ratio of presence to absence points
+ if(sum(response>=1)/sum(response==0)>=RatioPresAbs){
+
+ #first determine how many presence points to remove
+ TotToRmv<-(sum(response>=1)-RatioPresAbs*sum(response==0))
+ # if(TotToRmv/sum(response>=1)>.5) {
+ # warning("******************************************\n**** Over 50% of the
+ # presence points were removed to meet the desired ratio of presence to absence \n******************************************")}
+ #determine the number of each count to remove weighted by the reponse and then remove these
+ EachToRmv<-round(TotToRmv*table(response[response!=0])/sum(response!=0))
+ ByCount<-split(cbind(which(response!=0,arr.ind=TRUE)),f=response[response!=0])
+
+ #sampling one from a vector of size 1 actually samples a sequence from 1 to the value in the vector
+ #so correcting this here
+ sam<-function(x,size){if(length(x)==1 & size==1) return(x)
+ else sample(x=x,size=size)}
+
+ RmvIndx<-as.vector(unlist(mapply(sam,x=ByCount,size=EachToRmv)))
+ KeepIndx<-seq(1:length(response))[-c(RmvIndx)]
+ Response<-response[KeepIndx]
+ names(Response)<-KeepIndx
+
+ #now break these into a train an test split while
+ TrainSplit<-numeric()
+
+ for(i in sort(as.numeric(unique(Response)))){
+ TrainSplit<-c(TrainSplit,sample(names(Response[Response==i]),size=round(sum(Response==i)*trainProp)))
+ }
+ TrainSplit<-as.numeric(TrainSplit)
+ #Take everything not in the training set or in the remove list for the test set
+ TestSplit<-seq(from=1,to=length(response))[-c(c(TrainSplit,RmvIndx))]
+
+ dat$TrainSplit[seq(1:length(response))%in%TrainSplit]<-"train"
+ dat$TrainSplit[seq(1:length(response))%in%TestSplit]<-"test"
+
+
+ }
+
+ if(sum(response>=1)/sum(response==0)<RatioPresAbs){
+ browser()
+ #first ballance all responses greater than 1
+ TrainSplit<-numeric()
+ for(i in sort(as.numeric(unique(response[response!=0])))){
+ TrainSplit<-c(TrainSplit,sample(which(response==i,arr.ind=TRUE),size=round(sum(response==i)*trainProp)))
+ }
+ # if((sum(response==0)-sum(response>=1)/RatioPresAbs)/sum(response==0)>.5) {
+ # warning("******************************************\n**** Over 50% of the
+ # absence points were removed to meet the desired ratio of presence to absence \n******************************************")}
+ #now sampling the right number of absence points for the train split
+ TrainSplit<-c(TrainSplit,sample(which(response==0,arr.ind=TRUE),size=round(sum(response>=1)*(1/RatioPresAbs)*trainProp)))
+
+ #Take everything not in the training set for the test set
+ TestSplit=which(!(seq(1:length(response)))%in%TrainSplit,arr.ind=TRUE)
+
+ #now sample some points to remove so we have the correct proportion
+ temp<-sample(which(TestSplit%in%which(response==0,arr.ind=TRUE),arr.ind=TRUE),
+ size=round(sum(TestSplit%in%which(response==0,arr.ind=TRUE))-(1-trainProp)*sum(response>=1)*(1/RatioPresAbs)))
+ TestSplit<-TestSplit[-c(temp)]
+
+ dat$TrainSplit[seq(1:length(response))%in%TrainSplit]<-"train"
+ dat$TrainSplit[seq(1:length(response))%in%TestSplit]<-"test"
+
+ }
+
+ dat<-dat[c(TrainSplit,TestSplit),]
+
+ dat.in<-dat.in[c(1:3,rownames(dat)),] #removing rows that weren't selected for the test train split
+ dat.in[4:(dim(dat.in)[1]),(dim(dat.in)[2]+1)]<-dat$TrainSplit
+ dat.in[c(1,3),(dim(dat.in)[2])]<-c("Split","")
+ dat.in[2,(dim(dat.in)[2])]<-1
+
+
+ }
+
+ if(dim(bg.dat)[1]!=0) {
+ names(bg.dat)<-names(dat.in)
+ dat.in<-rbind(dat.in,bg.dat)}
+
+ #write output files for R modules
+ write.table(dat.in,file=output.file,row.names=FALSE,col.names=FALSE,sep=",",quote=FALSE)
+
+
+ }
+
+
+ #Reading in command line arguments
+ Args <- commandArgs(T)
+ print(Args)
+ #assign default values
+
+ responseCol <- "responseBinary"
+ trainProp=.7
+ RatioPresAbs=NULL
+ #replace the defaults with passed values
+ for (arg in Args) {
+ argSplit <- strsplit(arg, "=")
+ argSplit[[1]][1]
+ argSplit[[1]][2]
+ if(argSplit[[1]][1]=="p") trainProp <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="m") RatioPresAbs <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="o") output.file <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="i") infil <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
+ }
+
+ RatioResAbs<-as.numeric(RatioPresAbs)
+ trainProp<-as.numeric(trainProp)
+
+ #Run the Test training split with these parameters
+ TestTrainSplit(input.file=infil,output.file=output.file,response.col=responseCol,
+ trainProp=trainProp,RatioPresAbs=RatioPresAbs)
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/CallPairsPlot.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/CallPairsPlot.r
new file mode 100644
index 0000000..608b7f3
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/CallPairsPlot.r
@@ -0,0 +1,114 @@
+#Running R from the command line
+#input.file="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv"
+ #output.dir<-"H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck\\"
+ #response.col= "ResponseBinary"
+ #min.cor<-.7
+ #num.plots<-10
+source("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules\\PairsExplore.r")
+
+
+
+num.plots <- 10
+ min.cor <- .7
+ responseCol <- "responseCount"
+ cors.w.highest <- FALSE
+ pres=FALSE
+ absn=TRUE
+ bgd=TRUE
+ #infile="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110510T100421\\TestTrainingSplit_1.csv"
+ infile="I:\\NPS_NPMP_data\\ModelingSession_June\\EAME_MDS.csv"
+ output.file="H:\\Desktop\\SAHM\\Output\\PairsPlot\\pairPres.jpg"
+ Pairs.Explore(num.plots=num.plots,
+ min.cor=min.cor,
+ input.file=infile,
+ output.file=output.file,
+ response.col=responseCol,
+ pres=TRUE,
+ absn=TRUE,
+ bgd=TRUE,
+ Debug=TRUE)
+
+#binary
+input.file="C:\\VisTrails\\EAMEBinTT.csv"
+input.file="C:\\VisTrails\\DICKBinTT.csv"
+input.file="C:\\VisTrails\\HESPBinTT.csv"
+input.file="C:\\VisTrails\\GRSPBinTT.csv"
+responseCol="responseBinary"
+input.file="I:\\SpeciesData\\kudzu\\July2011\\MergedDataset_1.csv"
+#list.files("I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110725T102358")
+Pairs.Explore(num.plots=num.plots,
+ min.cor=min.cor,
+ input.file=input.file,
+ output.file=output.file,
+ response.col=responseCol,
+ pres=TRUE,
+ absn=TRUE,
+ bgd=TRUE,
+ Debug=TRUE)
+
+
+#count
+input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\EAME_MDS.csv"
+input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\DICK_MDS.csv"
+input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\HESP_MDS.csv"
+input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\GRSP_MDS.csv"
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T083827\\MergedDataset_1.csv"
+
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T114212\\MergedDataset_1.csv"
+responseCol="responseBinary"
+Pairs.Explore(num.plots=num.plots,
+ min.cor=min.cor,
+ input.file=input.file,
+ output.file=output.file,
+ response.col=responseCol,
+ pres=TRUE,
+ absn=TRUE,
+ bgd=TRUE,
+ Debug=TRUE)
+
+print(getwd())
+source_pathname = get("PairsExplore",envir = parent.frame())
+source_dirname = dirname(source_pathname )
+setwd(source_dirname)
+print(getwd())
+
+
+frame_files <- lapply(sys.frames(), function(x) x$ofile)
+frame_files <- Filter(Negate(is.null), frame_files)
+PATH <- dirname(frame_files[[length(frame_files)]])
+
+
+as.double.foo <- function(x)
+{
+ str(sys.calls())
+ print(sys.frames())
+ print(sys.parents())
+ print(sys.frame(-1)); print(parent.frame())
+ x
+}
+t2 <- function(x) as.double(x)
+a <- structure(pi, class = "foo")
+t2(a)
+
+library(R.utils)
+print(getAbsolutePath("Pairs.Explore"))
+
+
+Pairs.Explore(num.plots=10,min.cor=.7,input.file="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv",
+output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck\\",
+response.col="ResponseBinary",cors.w.highest=TRUE)
+
+# The BRT Function
+C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\pySAHM\Resources\R_Modules\FIT_BRT_pluggable.r --args c=I:\VisTrails\WorkingFiles\workspace\GYA_demo\test.csv o=C:\temp rc=ResponseBinary
+
+
+C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f H:\Desktop\SAHM\Rcode\PredictorSelection\PairsExplore2.r --args p=10 m=.7 o=H:\Desktop\SAHM\Rcode\ExposingModelParameters\PDFCheck\ i="I:\VisTrails\WorkingFiles\workspace\GYA_demo\test.csv" rc="ResponseBinary" core=TRUE
+
+
+
+if(argSplit[[1]][1]=="p") num.plots <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="m") min.cor <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="o") output.dir <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="i") input.file <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
+ if(argSplit[[1]][1]=="core") cors.w.higest <- argSplit[[1]][2]
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Debugging.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Debugging.r
new file mode 100644
index 0000000..5ae306d
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Debugging.r
@@ -0,0 +1,173 @@
+setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
+source("FIT_BRT_pluggable.r")
+source("FIT_MARS_pluggable.r")
+source("FIT_RF_pluggable.r")
+source("FIT_GLM_pluggable.r")
+
+source("EvaluationStats.r")
+source("TestTrainRocPlot.r")
+source("read.ma.r")
+source("proc.tiff.r")
+source("PredictModel.r")
+
+# Currently testing to see if models work with
+# * new test train split
+# * separation of model fit from prediction
+# * working with count data
+# * producing correct evaluation metrics
+#Future testing will include testing that factor columns are handled correctly
+#trace(proc.tiff,browser)
+#options(error=expression(if(interactive()) recover() else dump.calls()))
+#options(error=NULL)
+#trace(proc.tiff,browser)
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
+output.dir="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\brtoutput_1"
+rc="responseBinary"
+PredictModel(workspace="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T130214\\brtoutput_1\\modelWorkspace",out.dir="C:\\VisTrails")
+PredictModel(workspace="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T130214\\brtoutput_1\\modelWorkspace",out.dir="C:\\VisTrails\\mtalbert_20110505T161105",make.btif=TRUE,make.ptif=TRUE)
+#######################################################
+## BRT TESTING
+
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+ rc="ResponseBinary"
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+
+#this file does have a test training split
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110602T155823\\MergedDataset_1.csv"
+ rc="responseCount"
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T095017\\MergedDataset_2.csv"
+output.dir="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T095017\\brtoutput_1"
+rc="responseBinary"
+
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T134303\\TestTrainingSplit_1.csv"
+output.dir="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T134303\\marsoutput_3"
+rc="responseBinary"
+
+fit.mars.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",model.family="binomial",script.name="mars.r")
+
+fit.brt.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, max.trees = NULL,opt.methods=1,seed=1,save.model=TRUE)
+
+source("FIT_MARS_pluggable.r")
+PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+#########################################################
+## MARS TESTING
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+
+ #this input file does not have a test training split
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+ rc="ResponseBinary"
+
+ #this file does have a test training split
+ input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
+ rc="responseBinary"
+
+fit.mars.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ mars.degree=1,mars.penalty=2,debug.mode=F,responseCurveForm="pdf",model.family="binomial",script.name="mars.r")
+
+PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+#########################################################
+## GLM TESTING
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+ rc="ResponseBinary"
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+
+#this file does have a test training split
+ input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
+ rc="responseBinary"
+
+fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
+
+PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+########################################################
+## RANDOM FOREST TESTING
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+ rc="ResponseBinary"
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+
+#this file does have a test training split
+ input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
+ rc="responseBinary"
+
+fit.rf.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ debug.mode=T,n.trees=1000)
+
+PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+
+#Now testing to make sure this code works with no test training split
+ma.name<-"H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\ModelOutputCheck\\NewInput.csv"
+ma.name="C:\\VisTrails\\mtalbert_20110406T093111\\sahm4h5b1t.mds"
+
+ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv"
+fit.brt.fct(ma.name=ma.name,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
+
+
+#this is the GLM_pluggable1.r under NewMDSBuilder (Works with new vistrails format)
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110510T100421\\TestTrainingSplit_1.csv"
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+rc="responseCount"
+
+ fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col=rc,make.p.tif=T,make.binary.tif=T,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
+
+
+#Mars check Works with new vistrails format
+ fit.mars.fct(ma.name=ma.name,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
+
+
+fit.rf.fct(ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv",
+ tif.dir=NULL,
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ debug.mode=T,n.trees=1000,ma.test=NULL,make.r.curves=T,script.name="glm.r")
+
+
+
+#this one does not subset paths set up in the old way works with old sahm as well as for
+fit.brt.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,ma.test=NULL,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
+
+
+fit.mars.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+ tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
+
+fit.glm.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+ tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",ma.test=NULL,script.name="glm.r")
+
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Dickessel.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Dickessel.r
new file mode 100644
index 0000000..fc80871
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Dickessel.r
@@ -0,0 +1,231 @@
+ setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
+source("FIT_BRT_pluggable.r")
+source("FIT_MARS_pluggable.r")
+source("FIT_RF_pluggable.r")
+source("FIT_GLM_pluggable.r")
+
+source("EvaluationStats.r")
+source("TestTrainRocPlot.r")
+source("read.ma.r")
+source("proc.tiff.r")
+source("PredictModel.r")
+
+# Currently testing to see if models work with
+# * new test train split
+# * separation of model fit from prediction
+# * working with count data
+# * producing correct evaluation metrics
+#Future testing will include testing that factor columns are handled correctly
+#trace(proc.tiff,browser)
+#options(error=expression(if(interactive()) recover() else dump.calls()))
+#options(error=NULL)
+#trace(proc.tiff,browser)
+#################################################################################
+## Testing the code with some dickessel data
+
+ ## EAME
+ input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\EAME_MDS.csv"
+ rc="responseCount"
+ output.dir="C:\\VisTrails\\EAMENoTestTrain"
+
+## DICK
+ input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\DICK_MDS.csv"
+ rc="responseCount"
+ output.dir="C:\\VisTrails\\DICKNoTestTrain"
+
+## HESP
+ input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\HESP_MDS.csv"
+ rc="responseCount"
+ output.dir="C:\\VisTrails\\HESPNoTestTrain"
+
+ ## GRSP
+ input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\GRSP_MDS.csv"
+ rc="responseCount"
+ output.dir="C:\\VisTrails\\GRSPNoTestTrain"
+
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110623T104642\\SelectPredictorsLayers_second_1.csv"
+fit.brt.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "binomial", opt.methods=1,seed=1,save.model=FALSE)
+
+# No Predictions here
+# PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r",model.family="binomial",save.model=FALSE)
+
+ #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+ fit.mars.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",model.family="poisson",script.name="mars.r",save.model=FALSE)
+
+ #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+
+
+#######################################################
+### Now with a test/train split
+#################################################
+## GRSP
+input.file="C:\\VisTrails\\GRSP_TestTrain.csv"
+ rc="responseCount"
+ output.dir="C:\\VisTrails\\GRSPTest"
+
+
+input.file="C:\\VisTrails\\HESP_TestTrain.csv"
+ rc="responseCount"
+ output.dir="C:\\VisTrails\\HESPTest"
+
+input.file="C:\\VisTrails\\EAME_TestTrain.csv"
+ rc="responseCount"
+ output.dir="C:\\VisTrails\\EAMETest"
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T083717\\TestTrainingSplit_1"
+ rc="responseCount"
+ output.dir="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T083717"
+
+############################################################
+### Testing with binary data
+
+ ## EAME
+ input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\EAME_MDS_binary.csv"
+ rc="responseBinary"
+ output.dir="C:\\VisTrails\\EAMEBin"
+
+## DICK
+ input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\DICK_MDS_binary.csv"
+ rc="responseBinary"
+ output.dir="C:\\VisTrails\\DICKBin"
+
+## HESP
+ input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\HESP_MDS_binary.csv"
+ rc="responseBinary"
+ output.dir="C:\\VisTrails\\HESPBin"
+
+ ## GRSP
+ input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\GRSP_MDS_binary.csv"
+ rc="responseBinary"
+ output.dir="C:\\VisTrails\\GRSPBin"
+
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T083717\\TestTrainingSplit_1.csv"
+ rc="responseCount"
+ output.dir="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T083717"
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T113117\\TestTrainingSplit_1.csv"
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T113117\\MergedDataset_2.csv"
+fit.brt.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "binomial", opt.methods=1,seed=1,save.model=FALSE)
+
+# No Predictions here
+# PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r",model.family="binomial",save.model=FALSE)
+
+ #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+ fit.mars.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",model.family="binomial",script.name="mars.r",save.model=FALSE)
+
+ #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+fit.rf.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ debug.mode=T,n.trees=1000,save.model=FALSE)
+
+
+###################################################################################
+## testing with binary with a test train split
+ ## EAME
+ input.file="C:\\VisTrails\\EAMEBinTT.csv"
+ rc="responseBinary"
+ output.dir="C:\\VisTrails\\EAMEBinTT"
+
+## DICK
+ input.file="C:\\VisTrails\\DICKBinTT.csv"
+ rc="responseBinary"
+ output.dir="C:\\VisTrails\\DICKBinTT"
+
+## HESP
+ input.file="C:\\VisTrails\\HESPBinTT.csv"
+ rc="responseBinary"
+ output.dir="C:\\VisTrails\\HESPBinTT"
+
+ ## GRSP
+ input.file="C:\\VisTrails\\GRSPBinTT.csv"
+ rc=r"responseBinary"
+ output.dir="C:\\VisTrails\\GRSPBinTT"
+
+fit.brt.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "binomial", opt.methods=1,seed=1,save.model=FALSE)
+
+# No Predictions here
+# PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r",model.family="binomial",save.model=FALSE)
+
+ #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+ fit.mars.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",model.family="binomial",script.name="mars.r",save.model=FALSE)
+
+ #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+fit.rf.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ debug.mode=T,n.trees=1000,save.model=FALSE)
+
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T083827\\MergedDataset_1.csv"
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T112620\\TestTrainingSplit_1.csv"
+
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T114212\\MergedDataset_1.csv"
+
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T115847\\TestTrainingSplit_2.csv"
+ rc="responseBinary"
+output.dir="C:\\VisTrails"
+
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T134656\\TestTrainingSplit_1.csv"
+rc="responseCount"
+fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=T,make.binary.tif=T,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r",model.family="binomial",save.model=FALSE)
+
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T114212\\MergedDataset_1.csv"
+fit.brt.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "binomial", opt.methods=1,seed=1,save.model=FALSE)
+
+
+C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\pySAHM\Resources\R_Modules\FIT_RF_pluggable.r --args mbt=FALSE mpt=FALSE c=N:\Active\FORT_RAM\VisTrails\workspace\dignizio_20110616T162343\TestTrainingSplit_4.csv o=N:\Active\FORT_RAM\VisTrails\workspace\dignizio_20110616T162343\rfoutput_7 rc=responseBinary
+C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\pySAHM\Resources\R_Modules\PairsExplore.r --args i=N:\Active\FORT_RAM\VisTrails\workspace\talbertc_20110621T083827\MergedDataset_1.csv o=N:\Active\FORT_RAM\VisTrails\workspace\talbertc_20110621T083827\PredictorCorrelation_second_1.jpg m=0.7 rc=responseBinary pres=TRUE absn=TRUE bgd=TRUE
+C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\pySAHM\Resources\R_Modules\FIT_BRT_pluggable.r --args c=N:\Active\FORT_RAM\VisTrails\workspace\talbertc_20110621T105356\TestTrainingSplit_1.csv o=N:\Active\FORT_RAM\VisTrails\workspace\talbertc_20110621T105356\brtoutput_1 rc=responseBinary
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/QuickDebug.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/QuickDebug.r
new file mode 100644
index 0000000..cc1b157
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/QuickDebug.r
@@ -0,0 +1,75 @@
+setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
+setwd("I:\\VisTrails\\Central_VisTrailsInstall\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
+source("FIT_BRT_pluggable.r")
+source("FIT_MARS_pluggable.r")
+source("FIT_RF_pluggable.r")
+source("FIT_GLM_pluggable.r")
+
+source("EvaluationStats.r")
+source("TestTrainRocPlot.r")
+source("read.maNew.r")
+source("proc.tiff.r")
+source("PredictModel.r")
+source("PredictModel.r")
+source("modalDialog.R")
+source("check.libs.r")
+options(error=expression(if(interactive()) recover() else dump.calls()))
+options(error=NULL)
+trace(proc.tiff,browser)
+
+list.files()
+#Testing Compile Output on data with no test train and with a test train
+
+
+input.file="N:/Active/FORT_RAM/VisTrails/workspace/mtalbert_20110817T104421/MergedDataset_1.csv"
+#input.file="N:/Active/FORT_RAM/VisTrails/workspace/mtalbert_20110817T104421/MergedDatasetTestTrain_1.csv"
+
+#No test training split
+
+#this one has a test training split
+
+output.dir="C:\\temp\\SAHMDebugJunk\\BRTOut1"
+rc="responseBinary"
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110824T133049\\CovariateCorrelationOutputMDS_anothertry.csv"
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110825T130119\\CovariateCorrelationOutputMDS_anothertry2.csv"
+#input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110824T133049\\CovariateCorrelationOutputMDS_anothertry2.csv"
+
+##RF
+ fit.rf.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ debug.mode=T,n.trees=1000,opt.methods=5)
+
+ PredictModel(workspace=paste(output.dir,"modelWorkspace",sep="\\"),out.dir=output.dir)
+
+##BRT
+ fit.brt.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, max.trees = NULL,opt.methods=2,seed=1,save.model=TRUE)
+
+ PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+##MARS
+ fit.mars.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ mars.degree=1,mars.penalty=2,debug.mode=F,responseCurveForm="pdf",script.name="mars.r")
+
+ PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+##GLM
+ fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
+
+ PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+
+## Command line
+C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\pySAHM\Resources\R_Modules\FIT_MARS_pluggable.r --args c=I:\VisTrails\WorkingFiles\workspace\talbertc_20110824T133049\CovariateCorrelationOutputMDS_anothertry2.csv o=I:\VisTrails\WorkingFiles\workspace\talbertc_20110824T133049\marsoutput_4 rc=responseBinary
+C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall\vistrails\packages\sahm\pySAHM\Resources\R_Modules\FIT_RF_pluggable.r --args c=I:\VisTrails\WorkingFiles\workspace\talbertc_20110825T130119\CovariateCorrelationOutputMDS_anothertry2.csv o=I:\VisTrails\WorkingFiles\workspace\talbertc_20110825T130119\rfoutput_1 rc=responseBinary
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTestTrainSplit.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTestTrainSplit.r
new file mode 100644
index 0000000..5263aef
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTestTrainSplit.r
@@ -0,0 +1,171 @@
+### This file runs the TestTrainSplit and checks that all ratios end up being what they should if RatioPresAbs is set at an extreme value
+### an excessive number of values are deleted and ratios and be drastically off might want to include future error checking
+setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
+source("TestTrainSplit.r")
+
+input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSetNullModelTest.csv"
+output.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSetNullSplit.csv"
+
+input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSetIncludeTest.csv"
+output.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSetIncludeSplit.csv"
+
+input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+output.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSplitTest.csv"
+
+input.file="N:/Active/FORT_RAM/VisTrails/workspace/mtalbert_20110817T104421/MergedDataset_1.csv"
+input.file="I:/VisTrails/WorkingFiles/workspace/morisettej_20110810T153126/CovariateCorrelationOutputMDS_anothertry.csv"
+output.file="N:/Active/FORT_RAM/VisTrails/workspace/mtalbert_20110817T104421/MergedDatasetTestTrain_1.csv"
+response.col="ResponseBinary"
+
+## Running the code
+TestTrainSplit(input.file,output.file,response.col=response.col,trainProp=.7) #tried also with .8, and no RatioPresAb
+
+## Running some tests on the output
+input.file<-output.file
+dat<-read.csv(input.file,skip=3,header=FALSE)
+
+ hl<-readLines(input.file,1)
+ hl=strsplit(hl,',')
+ colnames(dat) = hl[[1]]
+
+ tif.info<-readLines(input.file,3)
+ tif.info<-strsplit(tif.info,',')
+ include<-(as.numeric(tif.info[[2]]))
+
+# checking that trainProp is correct
+ta<-table(dat$Split,dat$responseBinary)
+ta
+#if there are background points, remove them here
+ta<-ta[-1,]
+ta<-ta[,-1]
+
+#checking that the trainProp was ballanced for each count all of these
+#should be approximately equal to the trainProp this works less well for
+#smaller sample sizes
+ta[2,]/(ta[1,]+ta[2,])
+
+#checks trainProp is correct
+sum(ta[2,])/sum(ta)
+sum(ta[1,])/sum(ta)
+
+#checking ratio of presence to absence should equal RatioPresAbs
+sum(ta[1,2:dim(ta)[2]])/ta[1,1]
+sum(ta[2,2:dim(ta)[2]])/ta[2,1]
+
+#######################################################
+#### testing looking at an mds with counts case 1. appears to be working###########
+input.file<-"H:\\Desktop\\SAHM\\Data\\ChangeFamilyData\\MergedDataSet_1.csv"
+output.file<-"H:\\Desktop\\SAHM\\Output\\TestTrainSplit\\testtrain.mds"
+TestTrainSplit(input.file,output.file,response.col="ResponseCount",trainProp=.7,RatioPresAbs=.9)
+
+input.file<-output.file
+dat<-read.csv(input.file,skip=3,header=FALSE)
+
+ hl<-readLines(input.file,1)
+ hl=strsplit(hl,',')
+ colnames(dat) = hl[[1]]
+
+ tif.info<-readLines(input.file,3)
+ tif.info<-strsplit(tif.info,',')
+ include<-(as.numeric(tif.info[[2]]))
+
+# checking that trainProp is correct
+ta<-table(dat$Split,dat$responseCount)
+ta
+
+#if there are background points, remove them here
+ta<-ta[-1,]
+ta<-ta[,-1]
+
+#checking that the trainProp was ballanced for each count all of these
+#should be approximately equal to the trainProp this works less well for
+#smaller sample sizes
+ta[2,]/(ta[1,]+ta[2,])
+
+#checks trainProp is correct
+sum(ta[2,])/sum(ta)
+sum(ta[1,])/sum(ta)
+
+#checking ratio of presence to absence should equal RatioPresAbs
+sum(ta[1,2:dim(ta)[2]])/ta[1,1]
+sum(ta[2,2:dim(ta)[2]])/ta[2,1]
+
+
+#######################################################
+#### testing looking at an mds with counts case 2. Looks like this is working too###########
+input.file<-"H:\\Desktop\\SAHM\\Data\\ChangeFamilyData\\MergedDataSet_1.csv"
+output.file<-"H:\\Desktop\\SAHM\\Output\\TestTrainSplit\\testtrain.mds"
+TestTrainSplit(input.file,output.file,response.col="ResponseCount",trainProp=.7,RatioPresAbs=.4)
+
+input.file<-output.file
+dat<-read.csv(input.file,skip=3,header=FALSE)
+
+ hl<-readLines(input.file,1)
+ hl=strsplit(hl,',')
+ colnames(dat) = hl[[1]]
+
+ tif.info<-readLines(input.file,3)
+ tif.info<-strsplit(tif.info,',')
+ include<-(as.numeric(tif.info[[2]]))
+
+# checking that trainProp is correct
+ta<-table(dat$Split,dat$responseCount)
+ta
+
+#if there are background points, remove them here
+ta<-ta[-1,]
+ta<-ta[,-1]
+
+#checking that the trainProp was ballanced for each count all of these
+#should be approximately equal to the trainProp this works less well for
+#smaller sample sizes
+ta[2,]/(ta[1,]+ta[2,])
+
+
+#checks trainProp is correct
+sum(ta[2,])/sum(ta)
+sum(ta[1,])/sum(ta)
+
+#checking ratio of presence to absence should equal RatioPresAbs for both the test and train split
+sum(ta[1,2:dim(ta)[2]])/ta[1,1]
+sum(ta[2,2:dim(ta)[2]])/ta[2,1]
+
+
+#######################################################
+#### testing looking at an mds with counts case 3. Without a RatioPresAbs###########
+input.file<-"H:\\Desktop\\SAHM\\Data\\ChangeFamilyData\\MergedDataSet_1.csv"
+output.file<-"H:\\Desktop\\SAHM\\Output\\TestTrainSplit\\testtrain.mds"
+TestTrainSplit(input.file,output.file,response.col="ResponseCount",trainProp=.7)
+
+input.file<-output.file
+dat<-read.csv(input.file,skip=3,header=FALSE)
+
+ hl<-readLines(input.file,1)
+ hl=strsplit(hl,',')
+ colnames(dat) = hl[[1]]
+
+ tif.info<-readLines(input.file,3)
+ tif.info<-strsplit(tif.info,',')
+ include<-(as.numeric(tif.info[[2]]))
+
+# checking that trainProp is correct
+ta<-table(dat$Split,dat$responseCount)
+ta
+
+#if there are background points, remove them here
+ta<-ta[-1,]
+ta<-ta[,-1]
+
+#checking that the trainProp was ballanced for each count all of these
+#should be approximately equal to the trainProp this works less well for
+#smaller sample sizes
+ta[2,]/(ta[1,]+ta[2,])
+
+
+#checks trainProp is correct
+sum(ta[2,])/sum(ta)
+sum(ta[1,])/sum(ta)
+
+#checking ratio of presence to absence should equal RatioPresAbs for both the test and train split
+sum(ta[1,2:dim(ta)[2]])/ta[1,1]
+sum(ta[2,2:dim(ta)[2]])/ta[2,1]
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTests.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTests.r
new file mode 100644
index 0000000..7aba394
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTests.r
@@ -0,0 +1,173 @@
+setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
+source("FIT_BRT_pluggable.r")
+source("FIT_MARS_pluggable.r")
+source("FIT_RF_pluggable.r")
+source("FIT_GLM_pluggable.r")
+source("EvaluationStats.r")
+source("TestTrainRocPlot.r")
+source("read.ma.r")
+source("proc.tiff.r")
+source("PredictModel.r")
+source("PairsExplore.r")
+
+# Currently testing to see if models work with
+# * new test train split
+# * separation of model fit from prediction
+# * working with count data
+# * producing correct evaluation metrics
+#Future testing will include testing that factor columns are handled correctly
+
+
+#################################################################
+## Current test files
+input.file<-vector()
+input.file[1]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullModelTest.csv"
+input.file[2]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullSplit.csv"
+input.file[3]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetIncludeTest.csv"
+input.file[4]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetIncludeSplit.csv"
+input.file[5]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSet_1.csv"
+input.file[6]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSplitTest.csv"
+input.file[7]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullModelTest2.csv"
+output.file<-sub("851/","851/TestOutput/",input.file)
+output.file<-sub(".csv",".jpg",output.file)
+
+#######################################################
+Debug=FALSE
+rc="ResponseBinary"
+output.dir="C:/VisTrails/mtalbert_20110504T132851/TestOutput"
+
+#BRT TEST LIST
+ brt.list<-list()
+ #this is the default scenario
+ brt.list[[1]]<-list(make.p.tif=TRUE,
+ make.binary.tif=TRUE,
+ tc=NULL,
+ n.folds=3,
+ alpha=1,
+ learning.rate=NULL,
+ bag.fraction=.5,
+ model.family="\"bernoulli\"",
+ prev.stratify=TRUE,
+ max.trees=10000,
+ opt.methods=2,
+ seed=NULL,
+ tolerance.method="\"auto\"",
+ tolerance=.001,
+ debug.mode=FALSE)
+ #setting up some alternative scenarios
+ brt.list[[2]]<-brt.list[[1]]
+ brt.list[[2]]$learning.rate=.002
+
+ brt.list[[3]]<-brt.list[[1]]
+ brt.list[[3]]$bag.fraction=1
+ brt.list[[3]]$opt.methods=4
+
+ #which datasets to test with the given set of parameters
+ brt.use.list<-list()
+ brt.use.list[[1]]<-c(3,4,5)
+ brt.use.list[[2]]<-c(5,6,7)
+ brt.use.list[[3]]<-c(3)
+
+#MARS TEST LIST
+ mars.list<-list()
+ #this is the default scenario
+ mars.list[[1]]<-list(make.p.tif=T,
+ make.binary.tif=T,
+ mars.degree=1,
+ mars.penalty=2,
+ model.family="\"binomial\"",
+ script.name="\"mars.r\"",
+ opt.methods=2,
+ save.model=TRUE,
+ debug.mode=FALSE)
+ #setting up some alternative scenarios
+ mars.list[[2]]<-mars.list[[1]]
+ mars.list[[2]]$mars.degree=2
+
+ mars.list[[3]]<-mars.list[[1]]
+ mars.list[[3]]$mars.penalty=3
+ mars.list[[3]]$opt.methods=4
+
+ #which datasets to test with the given set of parameters
+ mars.use.list<-list()
+ mars.use.list[[1]]<-c(3)
+ mars.use.list[[2]]<-c(2,5,6,7)
+ mars.use.list[[3]]<-c(3,4)
+
+#GLM TEST LIST
+ glm.list<-list()
+ #this is the default scenario
+ glm.list[[1]]<-list(make.p.tif=TRUE,
+ make.binary.tif=TRUE,
+ simp.method="\"AIC\"",
+ model.family="\"binomial\"",
+ opt.methods=2,
+ save.model=FALSE,
+ debug.mode=FALSE)
+ #setting up some alternative scenarios
+ glm.list[[2]]<-glm.list[[1]]
+ glm.list[[2]]$simp.method="\"BIC\""
+
+ glm.list[[3]]<-glm.list[[1]]
+ glm.list[[3]]$opt.methods=4
+
+ #which datasets to test with the given set of parameters
+ glm.use.list<-list()
+ glm.use.list[[1]]<-c(1,3)
+ glm.use.list[[2]]<-c(2,5,6,7)
+ glm.use.list[[3]]<-c(1,2,3,4)
+
+#RF TEST LIST
+ rf.list<-list()
+ #this is the default scenario
+ rf.list[[1]]<-list(make.p.tif=T,
+ make.binary.tif=T,
+ responseCurveForm="\"pdf\"",
+ xtest=NULL,
+ ytest=NULL,
+ n.trees=1000,
+ mtry=NULL,
+ samp.replace=FALSE,
+ sampsize=NULL,
+ nodesize=NULL,
+ maxnodes=NULL,
+ importance=FALSE,
+ localImp=FALSE,
+ nPerm=1,
+ proximity=NULL,
+ oob.prox=proximity,
+ norm.votes=TRUE,
+ do.trace=FALSE,
+ keep.forest=NULL,
+ keep.inbag=FALSE,
+ make.r.curves=T,
+ seed=NULL,
+ opt.methods=2,
+ save.model=TRUE,
+ seed=NULL)
+ #setting up some alternative scenarios
+ rf.list[[2]]<-rf.list[[1]]
+ rf.list[[2]]$samp.replace=TRUE
+
+ rf.list[[3]]<-rf.list[[1]]
+ rf.list[[3]]$opt.methods=4
+ rf.list[[3]]$seed=5
+
+ rf.list[[4]]<-rf.list[[1]]
+ rf.list[[4]]$opt.methods=4
+ rf.list[[4]]$seed=5
+
+ #which datasets to test with the given set of parameters
+ rf.use.list<-list()
+ rf.use.list[[1]]<-c(1,3)
+ rf.use.list[[2]]<-c(2,5,6,7)
+ rf.use.list[[3]]<-c(3,4)
+ rf.use.list[[4]]<-c(3,4)
+
+
+parameter.list<-list(brt.list=brt.list,brt.use.list=brt.use.list,mars.list=mars.list,mars.use.list=mars.use.list,
+ glm.list=glm.list,glm.use.list=glm.use.list,rf.list=rf.list,rf.use.list=rf.use.list)
+
+Out<-TestFunction(input.file,parameter.list,Debug,rc,output.dir)
+
+
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/SyntheticData.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/SyntheticData.r
new file mode 100644
index 0000000..48f73f1
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/SyntheticData.r
@@ -0,0 +1,78 @@
+library(raster)
+slopedeg<-raster("C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\slopedeg.tif")
+bio_4<-raster("C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\bio_4_wgs84.tif")
+bio_12<-raster("C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\bio_12_wgs84.tif")
+bio_7<-raster("C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\bio_7_wgs84.tif")
+
+#putting bio_4 on a 0 to 1 range
+temp<-as.matrix(log(bio_4))
+b4<-(log(bio_4)-min(temp))/max(temp-min(temp))
+
+#putting bio_7 on a 0 to 1 range
+temp<-as.matrix(2^bio_7)
+b7<-(2^bio_7-min(temp))/max(temp-min(temp))
+
+#putting slopedeg on a 0 to 1 range
+temp<-as.matrix(slopedeg)
+sld<-(slopedeg-min(temp))/max(temp-min(temp))
+
+#making bio_12 discrete
+temp<-as.matrix(bio_12)
+qan<-quantile(temp,probs=c(.25,.5,.75))
+b12<-.25+.25*(bio_12>=qan[1])+.25*(bio_12>qan[2])+.25*(bio_12>qan[3])
+writeRaster(b12, filename="C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\Cat12_wgs84.tif")
+
+
+#for binomal data
+myFct<-.5*b4*b7+.25*sld+.25*b12+.18
+m<-as.matrix(myFct)
+xcoord<-sample(dim(m)[1],size=200)
+ycoord<-sample(dim(m)[2],size=200)
+cells<-cbind(xcoord,ycoord)
+cellNumbs<-cellFromRowCol(myFct,xcoord,ycoord)
+
+writeRaster(myFct, filename="C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\BinomialSurface.tif")
+
+value<-extract(myFct,cellNumbs)
+responseBinary<-rbinom(length(value),1,value)
+xy = xyFromCell(myFct, cellNumbs)
+
+Binom.out<-as.data.frame(cbind(xy,responseBinary))
+write.table(Binom.out,file="C:\\VisTrails\\mtalbert_20110504T132851\\FieldDatBinom.csv",row.names=FALSE,col.names=TRUE,sep=",",quote=FALSE)
+
+#now for Poisson data generate a lambda surface we want a lot of zeros
+
+PoisFct<-myFct*4
+m<-as.matrix(PoisFct)
+xcoord<-sample(dim(m)[1],size=200)
+ycoord<-sample(dim(m)[2],size=200)
+cells<-cbind(xcoord,ycoord)
+cellNumbs<-cellFromRowCol(PoisFct,xcoord,ycoord)
+
+value<-extract(PoisFct,cellNumbs)
+responseCount<-rpois(length(value),value)
+xy = xyFromCell(myFct, cellNumbs)
+
+par(mfrow=c(2,2))
+plot(as.vector(as.matrix(b4)),as.vector(as.matrix(PoisFct)))
+plot(as.vector(as.matrix(b7)),as.vector(as.matrix(PoisFct)))
+plot(as.vector(as.matrix(sld)),as.vector(as.matrix(PoisFct)))
+plot(as.vector(as.matrix(b12)),as.vector(as.matrix(PoisFct)))
+
+writeRaster(PoisFct, filename="C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\PoissonSurface.tif")
+
+Pois.out<-as.data.frame(cbind(xy,responseCount))
+write.table(Pois.out,file="C:\\VisTrails\\mtalbert_20110504T132851\\FieldDatPois.csv",row.names=FALSE,col.names=TRUE,sep=",",quote=FALSE)
+
+BRT.Out<-raster("C:\\VisTrails\\prob_map.tif")
+BRT.Bin<-raster("C:\\VisTrails\\prob_map.tif")
+resids<-BRT.Out-PoisFct
+
+par(mfrow=c(2,2))
+plot(resids)
+plot(PoisFct)
+plot(BRT.Out)
+
+par(mfrow=c(2,1))
+hist(as.matrix(PoisFct),breaks=40)
+hist(as.matrix(BRT.Out),breaks=40)
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestCountModelRuns.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestCountModelRuns.r
new file mode 100644
index 0000000..cbd6991
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestCountModelRuns.r
@@ -0,0 +1,186 @@
+setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
+source("FIT_BRT_pluggable.r")
+source("FIT_MARS_pluggable.r")
+source("FIT_RF_pluggable.r")
+source("FIT_GLM_pluggable.r")
+
+source("EvaluationStats.r")
+source("TestTrainRocPlot.r")
+source("read.ma.r")
+source("proc.tiff.r")
+source("PredictModel.r")
+
+# Currently testing to see if models work with
+# * new test train split
+# * separation of model fit from prediction
+# * working with count data
+# * producing correct evaluation metrics
+#Future testing will include testing that factor columns are handled correctly
+#trace(proc.tiff,browser)
+#options(error=expression(if(interactive()) recover() else dump.calls()))
+#options(error=NULL)
+#trace(proc.tiff,browser)
+#######################################################
+## Count TESTING
+#this file does not have a test training split but uses Poisson data
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110607T084252\\TestTrainingSplit_2.csv"
+rc="responseCount"
+output.dir="C:\\VisTrails"
+
+fit.brt.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "poisson", opt.methods=1,seed=1,save.model=TRUE)
+
+ PredictModel(workspace=paste("C:\\VisTrails","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+
+fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r",model.family="poisson")
+
+ PredictModel(workspace=paste(output.dir,"modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+fit.mars.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",model.family="poisson",script.name="mars.r")
+
+ PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+############################################################################
+#Making sure some old stuff works here's a presence absence model with no
+rc="ResponseBinary"
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+fit.brt.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", opt.methods=2,seed=1,save.model=TRUE)
+
+PredictModel(workspace=paste("C:\\VisTrails","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+## Now testing GLM model with count data
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110607T084252\\TestTrainingSplit_2.csv"
+ rc="responseCount"
+ output.dir="C:\\VisTrails"
+
+
+
+##this does have a test training split, trying to figure out some good output for evaluation metrics module
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110607T084252\\MergedDataset_2.csv"
+ rc="responseCount"
+
+fit.brt.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "poisson", opt.methods=1,seed=1,save.model=TRUE)
+
+
+#########################################################
+## MARS TESTING
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110607T084252\\MergedDataset_1.csv"
+ rc="responseCount"
+
+
+
+
+#########################################################
+## GLM TESTING
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+ rc="ResponseBinary"
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+
+#this file does have a test training split
+ input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
+ rc="responseBinary"
+
+fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
+
+PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+########################################################
+## RANDOM FOREST TESTING
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+ rc="ResponseBinary"
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+
+#this file does have a test training split
+ input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
+ rc="responseBinary"
+
+fit.rf.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ debug.mode=T,n.trees=1000)
+
+PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+
+#Now testing to make sure this code works with no test training split
+ma.name<-"H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\ModelOutputCheck\\NewInput.csv"
+ma.name="C:\\VisTrails\\mtalbert_20110406T093111\\sahm4h5b1t.mds"
+
+ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv"
+fit.brt.fct(ma.name=ma.name,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
+
+
+#this is the GLM_pluggable1.r under NewMDSBuilder (Works with new vistrails format)
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110510T100421\\TestTrainingSplit_1.csv"
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+rc="responseCount"
+
+ fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col=rc,make.p.tif=T,make.binary.tif=T,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
+
+
+#Mars check Works with new vistrails format
+ fit.mars.fct(ma.name=ma.name,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
+
+
+fit.rf.fct(ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv",
+ tif.dir=NULL,
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ debug.mode=T,n.trees=1000,ma.test=NULL,make.r.curves=T,script.name="glm.r")
+
+
+
+#this one does not subset paths set up in the old way works with old sahm as well as for
+fit.brt.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,ma.test=NULL,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
+
+
+fit.mars.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+ tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
+
+fit.glm.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+ tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",ma.test=NULL,script.name="glm.r")
+
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestFunction2.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestFunction2.r
new file mode 100644
index 0000000..5ad66a1
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestFunction2.r
@@ -0,0 +1,23 @@
+TestFunction<-function(input.file,parameter.list,Debug,rc,output.dir){
+
+ ifelse(Debug,
+ options(error=expression(if(interactive()) recover() else dump.calls())),
+ options(error=NULL))
+ Brt.Out<-list()
+ Mars.Out<-list()
+ Glm.Out<-list()
+ RF.Out<-list()
+ for (i in 1:length(input.file)){
+ Brt.Out[[i]]<-unit.test(i,parameter.list$brt.use.list,parameter.list$brt.list,"brt",outpur.dir,rc)
+ Mars.Out[[i]]<-unit.test(i,parameter.list$mars.use.list,parameter.list$mars.list,"mars",outpur.dir,rc)
+ Glm.Out[[i]]<-unit.test(i,parameter.list$mars.use.list,parameter.list$mars.list,"glm",outpur.dir,rc)
+ RF.Out[[i]]<-unit.test(i,parameter.list$mars.use.list,parameter.list$mars.list,"rf",outpur.dir,rc)
+ } #end file for loop
+
+ options(error=NULL)
+ Out.list=list(Brt.Out=Brt.Out,Mars.Out=Mars.Out,Glm.Out=Glm.Out,RF.Out)
+ return(Out.list)
+}
+
+
+
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns (2).r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns (2).r
new file mode 100644
index 0000000..bc2aef4
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns (2).r
@@ -0,0 +1,148 @@
+setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
+source("FIT_BRT_pluggable.r")
+source("FIT_MARS_pluggable.r")
+source("FIT_RF_pluggable.r")
+source("FIT_GLM_pluggable.r")
+source("EvaluationStats.r")
+source("TestTrainRocPlot.r")
+source("read.ma.r")
+source("proc.tiff.r")
+source("PredictModel.r")
+source("PairsExplore.r")
+
+# Currently testing to see if models work with
+# * new test train split
+# * separation of model fit from prediction
+# * working with count data
+# * producing correct evaluation metrics
+#Future testing will include testing that factor columns are handled correctly
+
+
+#################################################################
+## Current test files
+input.file<-vector()
+input.file[1]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullModelTest.csv"
+input.file[2]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullSplit.csv"
+input.file[3]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetIncludeTest.csv"
+input.file[4]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetIncludeSplit.csv"
+input.file[5]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSet_1.csv"
+input.file[6]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSplitTest.csv"
+input.file[7]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullModelTest2.csv"
+output.file<-sub("851/","851/TestOutput/",input.file)
+output.file<-sub(".csv",".jpg",output.file)
+
+#######################################################
+Debug=FALSE
+rc="ResponseBinary"
+output.dir="C:/VisTrails/mtalbert_20110504T132851/TestOutput"
+
+#BRT TEST LIST
+ brt.list<-list()
+ #this is the default scenario
+ brt.list[[1]]<-list(make.p.tif=TRUE,
+ make.binary.tif=TRUE,
+ tc=NULL,
+ n.folds=3,
+ alpha=1,
+ learning.rate=NULL,
+ bag.fraction=.5,
+ model.family="\"bernoulli\"",
+ prev.stratify=TRUE,
+ max.trees=10000,
+ opt.methods=2,
+ seed=NULL,
+ tolerance.method="\"auto\"",
+ tolerance=.001,
+ debug.mode=FALSE)
+ #setting up some alternative scenarios
+ brt.list[[2]]<-brt.list[[1]]
+ brt.list[[2]]$learning.rate=.002
+
+ brt.list[[3]]<-brt.list[[1]]
+ brt.list[[3]]$bag.fraction=1
+ brt.list[[3]]$opt.methods=4
+
+ #which datasets to test with the given set of parameters
+ brt.use.list<-list()
+ brt.use.list[[1]]<-c(3,4,5)
+ brt.use.list[[2]]<-c(5,6,7)
+ brt.use.list[[3]]<-c(3)
+
+#MARS TEST LIST
+ mars.list<-list()
+ #this is the default scenario
+ mars.list[[1]]<-list(make.p.tif=T,
+ make.binary.tif=T,
+ mars.degree=1,
+ mars.penalty=2,
+ model.family="\"binomial\"",
+ script.name="\"mars.r\"",
+ opt.methods=2,
+ save.model=TRUE,
+ debug.mode=FALSE)
+ #setting up some alternative scenarios
+ mars.list[[2]]<-mars.list[[1]]
+ mars.list[[2]]$mars.degree=2
+
+ mars.list[[3]]<-mars.list[[1]]
+ mars.list[[3]]$mars.penalty=3
+ mars.list[[3]]$opt.methods=4
+
+ #which datasets to test with the given set of parameters
+ mars.use.list<-list()
+ mars.use.list[[1]]<-c(3)
+ mars.use.list[[2]]<-c(2,5,6,7)
+ mars.use.list[[3]]<-c(3,4)
+
+#GLM TEST LIST
+ glm.list<-list()
+ #this is the default scenario
+ glm.list[[1]]<-list(make.p.tif=TRUE,
+ make.binary.tif=TRUE,
+ simp.method="\"AIC\"",
+ model.family="\"binomial\"",
+ opt.methods=2,
+ save.model=FALSE,
+ debug.mode=FALSE)
+ #setting up some alternative scenarios
+ glm.list[[2]]<-glm.list[[1]]
+ glm.list[[2]]$simp.method="\"BIC\""
+
+ glm.list[[3]]<-glm.list[[1]]
+ glm.list[[3]]$opt.methods=4
+
+ #which datasets to test with the given set of parameters
+ glm.use.list<-list()
+ glm.use.list[[1]]<-c(1,3)
+ glm.use.list[[2]]<-c(2,5,6,7)
+ glm.use.list[[3]]<-c(1,2,3,4)
+
+#RF TEST LIST
+ rf.list<-list()
+ #this is the default scenario
+ rf.list[[1]]<-list(make.p.tif=TRUE,
+ make.binary.tif=TRUE,
+ simp.method="\"AIC\"",
+ model.family="\"binomial\"",
+ opt.methods=2,
+ save.model=FALSE,
+ debug.mode=FALSE)
+ #setting up some alternative scenarios
+ rf.list[[2]]<-rf.list[[1]]
+ rf.list[[2]]$simp.method="\"BIC\""
+
+ rf.list[[3]]<-rf.list[[1]]
+ rf.list[[3]]$opt.methods=4
+
+ #which datasets to test with the given set of parameters
+ rf.use.list<-list()
+ rf.use.list[[1]]<-c(1,3)
+ rf.use.list[[2]]<-c(2,5,6,7)
+ rf.use.list[[3]]<-c(1,2,3,4)
+
+parameter.list<-list(brt.list=brt.list,brt.use.list=brt.use.list,mars.list=mars.list,mars.use.list=mars.use.list,
+ glm.list=glm.list,glm.use.list=glm.use.list,rf.list=rf.list,rf.use.list=rf.use.list)
+
+Out<-TestFunction(input.file,parameter.list,Debug,rc,output.dir)
+
+
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns.r
new file mode 100644
index 0000000..3cb9a15
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns.r
@@ -0,0 +1,174 @@
+setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
+source("FIT_BRT_pluggable.r")
+source("FIT_MARS_pluggable.r")
+source("FIT_RF_pluggable.r")
+source("FIT_GLM_pluggable.r")
+
+source("EvaluationStats.r")
+source("TestTrainRocPlot.r")
+source("read.ma.r")
+source("proc.tiff.r")
+source("PredictModel.r")
+
+# Currently testing to see if models work with
+# * new test train split
+# * separation of model fit from prediction
+# * working with count data
+# * producing correct evaluation metrics
+#Future testing will include testing that factor columns are handled correctly
+#trace(proc.tiff,browser)
+#options(error=expression(if(interactive()) recover() else dump.calls()))
+#options(error=NULL)
+#trace(proc.tiff,browser)
+list.files("I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110810T153126")
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110810T153126\\CovariateCorrelationOutputMDS_anothertry.csv"
+output.dir="C:\\temp\\SAHMDebugJunk"
+rc="responseBinary"
+fit.rf.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ debug.mode=T,n.trees=1000)
+
+PredictModel(workspace=paste(output.dir,"modelWorkspace",sep="\\"),out.dir=output.dir)
+
+#######################################################
+## BRT TESTING
+
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+ rc="ResponseBinary"
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+
+#this file does have a test training split
+input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110602T155823\\MergedDataset_1.csv"
+ rc="responseCount"
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T095017\\MergedDataset_2.csv"
+output.dir="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T095017\\brtoutput_1"
+rc="responseBinary"
+
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110804T084435\\CovariateCorrelationOutputMDS_initial.csv"
+output.dir="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110804T084435\\brtoutput_1"
+rc="responseBinary"
+fit.brt.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, max.trees = NULL,opt.methods=1,seed=1,save.model=TRUE)
+
+source("FIT_MARS_pluggable.r")
+PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+#########################################################
+## MARS TESTING
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+
+ #this input file does not have a test training split
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+ rc="ResponseBinary"
+
+ #this file does have a test training split
+ input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
+ rc="responseBinary"
+
+fit.mars.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ mars.degree=1,mars.penalty=2,debug.mode=F,responseCurveForm="pdf",model.family="binomial",script.name="mars.r")
+
+PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+#########################################################
+## GLM TESTING
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+ rc="ResponseBinary"
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+
+#this file does have a test training split
+ input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
+ rc="responseBinary"
+
+fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
+
+PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+########################################################
+## RANDOM FOREST TESTING
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+ rc="ResponseBinary"
+ input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
+
+#this file does have a test training split
+ input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
+ rc="responseBinary"
+
+fit.rf.fct(ma.name=input.file,
+ tif.dir=NULL,
+ output.dir=output.dir,
+ response.col=rc,make.p.tif=F,make.binary.tif=F,
+ debug.mode=T,n.trees=1000)
+
+PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
+
+
+#Now testing to make sure this code works with no test training split
+ma.name<-"H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\ModelOutputCheck\\NewInput.csv"
+ma.name="C:\\VisTrails\\mtalbert_20110406T093111\\sahm4h5b1t.mds"
+
+ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv"
+fit.brt.fct(ma.name=ma.name,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
+
+
+#this is the GLM_pluggable1.r under NewMDSBuilder (Works with new vistrails format)
+input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110510T100421\\TestTrainingSplit_1.csv"
+output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
+rc="responseCount"
+
+ fit.glm.fct(ma.name=input.file,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col=rc,make.p.tif=T,make.binary.tif=T,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
+
+
+#Mars check Works with new vistrails format
+ fit.mars.fct(ma.name=ma.name,
+ tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
+
+
+fit.rf.fct(ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv",
+ tif.dir=NULL,
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ debug.mode=T,n.trees=1000,ma.test=NULL,make.r.curves=T,script.name="glm.r")
+
+
+
+#this one does not subset paths set up in the old way works with old sahm as well as for
+fit.brt.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,ma.test=NULL,alpha=1,script.name="brt.r",
+ learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
+
+
+fit.mars.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+ tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
+
+fit.glm.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
+ tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
+ output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
+ response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
+ simp.method="AIC",debug.mode=T,responseCurveForm="pdf",ma.test=NULL,script.name="glm.r")
+
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestingRandomForest.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestingRandomForest.r
new file mode 100644
index 0000000..b70a563
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestingRandomForest.r
@@ -0,0 +1,17 @@
+dat<-read.csv("C:\\VisTrails\\DICK_MDS_binary.csv")
+
+rf.full <- randomForest(x=dat[,-1],y=factor(dat[,1]),importance=TRUE,
+ ntree=1000, replace=FALSE)
+
+pred<-predict(rf.full, newdata=dat[,-1],type="prob")[,2]
+
+null.dev<-calc.deviance(dat[,1], rep(p.bar,times=length(dat[,1])),family="binomial")*nrow(dat)
+ dev.fit<-calc.deviance(dat[,1], pred, family="binomial")*nrow(dat)
+ dev.exp <- null.dev - dev.fit
+ pct.dev.exp <- dev.exp/null.dev*100
+
+r<-randomForest(x=dat[,-1],y=factor(out$dat$ma$ma[,1]),xtest=xtest,ytest=ytest,importance=TRUE, ntree=n.trees,
+ mtry=mtry,replace=samp.replace,sampsize=ifelse(is.null(sampsize),(ifelse(samp.replace,nrow(x),ceiling(.632*nrow(x)))),sampsize),
+ nodesize=ifelse(is.null(nodesize),(if (!is.null(y) && !is.factor(y)) 5 else 1),nodesize),maxnodes=maxnodes,
+ localImp=localImp, nPerm=nPerm, keep.forest=ifelse(is.null(keep.forest),!is.null(y) && is.null(xtest),keep.forest),
+ corr.bias=corr.bias, keep.inbag=keep.inbag)
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/unit.test.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/unit.test.r
new file mode 100644
index 0000000..83a3985
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/unit.test.r
@@ -0,0 +1,49 @@
+unit.test<-function(i,use.list,model.list,model,outpur.dir,rc){
+ list.fct<-function(x,i) sum(!is.na(match(x=i,table=x)))
+ valid.params<-which(unlist(lapply(use.list,list.fct,i=i))!=0,arr.ind=TRUE)
+ Model.Out<-list()
+ Model.Out[[i]]<-data.frame(list("FctFailed"=rep(FALSE,times=length(valid.params)),
+ "PredictFailed"=rep(FALSE,times=length(valid.params)),
+ "NullDev"=rep(0,times=length(valid.params)),
+ "FitDev"=rep(0,times=length(valid.params)),
+ "Correlation"=rep(0,times=length(valid.params)),
+ "ErrorMessage"=rep("No Error",times=length(valid.params))),row.names=valid.params)
+
+ class(Model.Out[[i]]$ErrorMessage)<-"character"
+ if(length(valid.params)!=0){
+ for(j in 1:length(valid.params)){
+
+ k<-valid.params[j]
+ if(Debug==TRUE) parameter.list$brt.list[[k]]$debug.mode=TRUE
+
+ a<-paste(paste(names(model.list[[k]]),model.list[[k]],sep="="),collapse=",")
+ call.fct<-paste("fit.",model,".fct(ma.name=\"",input.file[i],
+ "\", tif.dir=NULL,output.dir=\"",output.dir,"\", response.col=\"",rc,"\",",a,")",sep="")
+ #Right here I should remove almost everything since all output is written to the global environment
+ call.predict<-"PredictModel(workspace=paste(output.dir,\"modelWorkspace\",sep=\"/\"),out.dir=output.dir)"
+ if(Debug==FALSE) {call.fct<-paste("try(",call.fct,",silent=TRUE)",sep="")
+ call.predict<-paste("try(",call.predict,")",sep="")
+ #so that we don't predict on an old copy in the next loop
+ file.remove(paste(output.dir,"modelWorkspace",sep="/"))
+ }
+
+ fct.output<-eval(parse(text=call.fct))
+ sink()
+ pred.output<-eval(parse(text=call.predict))
+ sink()
+ if(class(fct.output)=="try-error") {
+ Model.Out[[i]][j,1]=TRUE
+ Model.Out[[i]][j,6]=fct.output[1]
+ } else {
+ Model.Out[[i]][j,1]=FALSE
+ Model.Out[[i]][j,3]<-fct.output$mods$auc.output$null.dev
+ Model.Out[[i]][j,4]<-fct.output$mods$auc.output$dev.fit
+ Model.Out[[i]][j,5]<-fct.output$mods$auc.output$correlation
+ }
+ if(class(pred.output)=="try-error") Model.Out[[i]][j,2]=TRUE
+
+ }
+ print(Model.Out)
+ } ## END BRT
+return(Model.Out)
+ }
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/check.libs.r b/contrib/sahm/pySAHM/Resources/R_Modules/check.libs.r
new file mode 100644
index 0000000..49a16bb
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/check.libs.r
@@ -0,0 +1,16 @@
+check.libs <- function(libs,out){
+
+ lib.mssg <- unlist(suppressMessages(suppressWarnings(lapply(libs,require,quietly = T, warn.conflicts=F,character.only=T))))
+ if(any(!lib.mssg)){
+ install.packages(unlist(libs[!lib.mssg]), repos = "http://cran.r-project.org")
+ lib.mssg <- unlist(suppressMessages(suppressWarnings(lapply(unlist(libs[!lib.mssg]),require,quietly = T, warn.conflicts=F,character.only=T))))
+ }
+ if(any(!lib.mssg)) {
+ out$ec <- out$ec+1
+ out$dat$missing.libs <- paste(unlist(libs)[!lib.mssg],collapse="; ")
+ stop("the following package(s) could not be loaded:",out$dat$missing.libs)
+ }
+ return(out)
+ }
+
+
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/make.auc.r b/contrib/sahm/pySAHM/Resources/R_Modules/make.auc.r
new file mode 100644
index 0000000..9e50dfa
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/make.auc.r
@@ -0,0 +1,136 @@
+make.auc.plot.jpg<-function(ma.reduced,pred,plotname,modelname,test.split=FALSE,thresh=NULL,train=NULL,train.pred=NULL,opt.methods=2,weight,out){
+
+ if(is.null(weight)) weight=rep(1,times=dim(ma.reduced)[1])
+ auc.data <- data.frame(ID=1:nrow(ma.reduced),pres.abs=ma.reduced[,1],pred=pred)
+ p.bar <- sum(auc.data$pres.abs * weight) / sum(weight)
+ n.pres <- sum(auc.data$pres.abs>=1)
+ n.abs <- nrow(auc.data)-n.pres
+
+ null.dev<-calc.dev(auc.data$pres.abs, rep(p.bar,times=length(auc.data$pres.abs)), weight, family=out$input$model.family)$deviance*nrow(ma.reduced)
+ dev.fit<-calc.dev(auc.data$pres.abs, pred, weight, family=out$input$model.family)$deviance*nrow(ma.reduced)
+ dev.exp <- null.dev - dev.fit
+ pct.dev.exp <- dev.exp/null.dev*100
+ correlation<-cor(auc.data$pres.abs,pred)
+ residual.smooth.fct<-NULL
+ if(test.split==FALSE) residual.smooth.fct<-resid.image(calc.dev(auc.data$pres.abs, pred, weight, family=out$input$model.family)$dev.cont,pred,
+ auc.data$pres.abs,out$dat$ma$train.xy[,1],out$dat$ma$train.xy[,2],out$input$model.family,out$input$output.dir,out)
+
+ if(is.null(thresh) & out$input$model.family!="poisson"){
+ thresh <- as.numeric(optimal.thresholds(auc.data,opt.methods=opt.methods))[2]
+ }
+
+ if(out$input$model.family%in%c("binomial","bernoulli")){
+ auc.fit <- auc(auc.data,st.dev=T)
+ if(test.split==TRUE){
+ jpeg(file=plotname)
+ d<-data.frame(ID=1:nrow(train),pres.abs=train[,1],pred=train.pred)
+ thresh<- as.numeric(optimal.thresholds(d,opt.methods=opt.methods))[2]
+ TestTrainRocPlot(DATA=d,opt.thresholds=thresh,add.legend=FALSE,lwd=2)
+ TestTrainRocPlot(auc.data,model.names=modelname,opt.thresholds=thresh,add.roc=TRUE,line.type=2,color="red",add.legend=FALSE)
+ legend(x=.66,y=.2,c("Training Split","Testing Split"),lty=2,col=c("black","red"),lwd=2)
+ graphics.off()}
+ else {
+ jpeg(file=plotname)
+ TestTrainRocPlot(auc.data,model.names=modelname,opt.thresholds=thresh)
+ graphics.off()
+ }
+ cmx <- cmx(auc.data,threshold=thresh)
+ PCC <- pcc(cmx,st.dev=F)*100
+ SENS <- sensitivity(cmx,st.dev=F)
+ SPEC <- specificity(cmx,st.dev=F)
+ KAPPA <- Kappa(cmx,st.dev=F)
+ TSS <- SENS+SPEC-1
+ }
+
+ if(out$input$model.family%in%c("poisson")){
+ auc.fit <- auc(auc.data,st.dev=T)
+ if(test.split==FALSE){
+ jpeg(file=plotname)
+ par(mfrow=c(2,2))
+ #plot(out$mods$final.mod)
+ plot(log(pred[pred!=0]),(auc.data$pres.abs[pred!=0]-pred[pred!=0]),xlab="Predicted Values (log scale)",ylab="Residuals",main="Residuals vs Fitted",ylim=c(-3,3))
+ abline(h=0,lty=2)
+ #this is the residual plot from glm but I don't think it will work for anything else
+ qqnorm(residuals(out$mods$final.mod),ylab="Std. deviance residuals")
+ qqline(residuals(out$mods$final.mod))
+ yl <- as.expression(substitute(sqrt(abs(YL)), list(YL = as.name("Std. Deviance Resid"))))
+ plot(log(pred[pred!=0]),sqrt((abs(residuals(out$mods$final.mod,type="deviance")[pred!=0]))),xlab="Predicted Values (log Scale)",ylab=yl)
+ graphics.off()}
+ prediction.error<-sum((auc.data$pres.abs-pred)^2)
+ cmx=PCC=SENS=SPEC=KAPPA=TSS<-NA
+ }
+
+ calibration.stats<-calibration(auc.data$pres.abs, pred, family =out$input$model.family)
+ response<-ma.reduced$response
+
+ capture.output(cat("\n\n============================================================",
+ "\n\nEvaluation Statistics"),file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
+ if(!is.null(out$dat$ma$ma.test))
+ capture.output(cat(" applied to",ifelse(!test.split,"train","test"), "split:\n",sep=" "),
+ file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
+ capture.output(cat( "\n",
+ "\n\t Correlation Coefficient : ",cor.test(pred,response)$estimate,
+ "\n\t NULL Deviance : ",null.dev,
+ "\n\t Fit Deviance : ",dev.fit,
+ "\n\t Explained Deviance : ",dev.exp,
+ "\n\t Percent Deviance Explained : ",pct.dev.exp,
+ file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE))
+
+ if(out$input$model.family%in%c("binomial","bernoulli")){
+ capture.output(cat(
+ "\n\n Threshold Methods based on", switch(opt.methods,
+ "1"=".5 threshold",
+ "2"="Sens=Spec",
+ "3"="maximize (sensitivity+specificity)/2",
+ "4"="maximize Kappa",
+ "5"="maximize percent correctly classified",
+ "6"="predicted prevalence=observed prevalence",
+ "7"="threshold=observed prevalence",
+ "8"="mean predicted probability",
+ "9"="minimize distance between ROC plot and (0,1)",
+ ),
+ "\n\t Threshold : ",
+ thresh,
+ "\n\n\t Confusion Matrix: \n\n"),
+ print.table(cmx),
+ cat("\n\t AUC : ",auc.fit[1,1],
+ "\n\t Percent Correctly Classified : ",PCC,
+ "\n\t Sensitivity : ",SENS,
+ "\n\t Specificity : ",SPEC,
+ "\n\t Kappa : ",KAPPA,
+ "\n\t True Skill Statistic : ",TSS,"\n"),
+ file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
+ }
+
+ capture.output(cat( "\n\n Calibration Statistics",
+ "\n\t Intercept (general calibration) : ",calibration.stats[1],
+ "\n\t Slope (direction and variation in fit) : ",calibration.stats[2],
+ "\n\t Testa0b1 (overall reliability of predictors) : ",calibration.stats[3],
+ "\n\t Testa0|b1(incorrect calibration given correct refinement) : ",calibration.stats[4],
+ "\n\t Testb1|a (refinement given correct calibration) : ",calibration.stats[5],"\n",
+ file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE))
+
+ last.dir<-strsplit(out$input$output.dir,split="\\\\")
+ parent<-sub(paste("\\\\",last.dir[[1]][length(last.dir[[1]])],sep=""),"",out$input$output.dir)
+
+ compile.out<-paste(parent,
+ paste(switch(out$input$model.family,"binomial"="Binary","bernoulli"="Binary","poisson"="Count"),ifelse(!is.null(out$dat$ma$ma.test),"TestTrain",""),
+ "AppendedOutput.csv",sep="."),sep="/")
+
+ if(out$input$model.family%in%c("binomial","bernoulli")){
+ x=data.frame(cbind(c("Correlation Coefficient","Percent Deviance Explained","Percent Correctly Classified","Sensitivity","Specificity"),
+ c(as.vector(cor.test(pred,response)$estimate),pct.dev.exp,PCC,SENS,SPEC)))
+ }else x=data.frame(cbind(c("Correlation Coefficient","Percent Deviance Explained","Prediction Error"),
+ c(as.vector(cor.test(pred,response)$estimate),pct.dev.exp,prediction.error)))
+
+ Header<-cbind(c("","Original Field Data","Field Data Template","PARC Output Folder","PARC Template","Covariate Selection Name",""),
+ c(last.dir[[1]][length(last.dir[[1]])],
+ out$dat$ma$input$OrigFieldData,out$dat$ma$input$FieldDataTemp,out$dat$ma$input$ParcOutputFolder,
+ out$dat$ma$input$ParcTemplate,ifelse(length(out$dat$ma$input$CovSelectName)==0,"NONE",out$dat$ma$input$CovSelectName),""))
+
+AppendOut(compile.out,Header,x,out,test.split,parent=parent)
+
+ return(list(thresh=thresh,cmx=cmx,null.dev=null.dev,dev.fit=dev.fit,dev.exp=dev.exp,pct.dev.exp=pct.dev.exp,auc=auc.fit[1,1],auc.sd=auc.fit[1,2],
+ plotname=plotname,pcc=PCC,sens=SENS,spec=SPEC,kappa=KAPPA,tss=TSS,correlation=correlation,residual.smooth.fct=residual.smooth.fct))
+}
+
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/modalDialog.R b/contrib/sahm/pySAHM/Resources/R_Modules/modalDialog.R
new file mode 100644
index 0000000..0e185ce
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/modalDialog.R
@@ -0,0 +1,46 @@
+#This function was robbed from the dynamicGraphic library
+"modalDialog" <-
+function (title, question, entryInit, top = NULL, entryWidth = 20,
+ returnValOnCancel = "ID_CANCEL", do.grab = FALSE)
+{
+ dlg <- tktoplevel()
+ tkwm.deiconify(dlg)
+ if (do.grab)
+ tkgrab.set(dlg)
+ tkfocus(dlg)
+ tkwm.title(dlg, title)
+ textEntryVarTcl <- tclVar(paste(entryInit))
+ textEntryWidget <- tkentry(dlg, width = paste(entryWidth),
+ textvariable = textEntryVarTcl, background = "white")
+ tkgrid(tklabel(dlg, text = " "))
+ tkgrid(tklabel(dlg, text = question), textEntryWidget)
+ tkgrid(tklabel(dlg, text = " "))
+ ReturnVal <- returnValOnCancel
+ "onOK" <- function() {
+ ReturnVal <<- tclvalue(textEntryVarTcl)
+ tkgrab.release(dlg)
+ tkdestroy(dlg)
+ if (!is.null(top))
+ tkfocus(top)
+ }
+ "onCancel" <- function() {
+ ReturnVal <<- returnValOnCancel
+ tkgrab.release(dlg)
+ tkdestroy(dlg)
+ if (!is.null(top))
+ tkfocus(top)
+ }
+ OK.but <- tkbutton(dlg, text = " OK ", command = onOK)
+ Cancel.but <- tkbutton(dlg, text = " Cancel ", command = onCancel)
+ tkgrid(OK.but, Cancel.but)
+ tkgrid(tklabel(dlg, text = " "))
+ tkfocus(dlg)
+ tkbind(dlg, "<Destroy>", function() {
+ tkgrab.release(dlg)
+ tkfocus(top)
+ })
+ tkbind(textEntryWidget, "<Return>", onOK)
+ tkwait.window(dlg)
+ return(ReturnVal)
+}
+
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/proc.tiff.r b/contrib/sahm/pySAHM/Resources/R_Modules/proc.tiff.r
new file mode 100644
index 0000000..767e335
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/proc.tiff.r
@@ -0,0 +1,212 @@
+proc.tiff<- function(model,vnames,tif.dir=NULL,filenames=NULL,pred.fct,factor.levels=NA,make.binary.tif=F,make.p.tif=T,
+ thresh=0.5,outfile.p="brt.prob.map.tif",outfile.bin="brt.bin.map.tif",tsize=2.0,NAval=-3000,fnames=NULL,logname=NULL,out){
+
+ # vnames,fpath,myfun,make.binary.tif=F,outfile=NA,outfile.bin=NA,output.dir=NA,tsize=10.0,NAval=NA,fnames=NA
+ # Written by Alan Swanson, YERC, 6-11-08
+ # Revised and Edited by Marian Talbert 2010-2011
+ # Description:
+ # This function is used to make predictions using a number of .tiff image inputs
+ # in cases where memory limitations don't allow the full images to be read in.
+ #
+ # Arguments:
+ # vname: names of variables used for prediction. must be same as filenames and variables
+ # in model used for prediction. do not include a .tif extension as this is added in code.
+ # fpath: path to .tif files for predictors. use forward slashes and end with a forward slash ('/').
+ # myfun: prediction function. must generate a vector of predictions using only a
+ # dataframe as input.
+ # outfile: name of output file. placed in same directory as input .tif files. should
+ # have .tif extension in name.
+ # tsize: size of dataframe used for prediction in MB. this controls the size of tiles
+ # extracted from the input files, and the memory usage of this function.
+ # NAval: this is the NAvalue used in the input files.
+ # fnames: if the filenames of input files are different from the variable names used in the
+ # prediction model.
+ #
+ # Modification history:
+ # Fixed problem with NA values causing crash 10/2010
+ # Included code to produce MESS map and Mod map 8/2011
+ # Removed Tiff Directory option as well as some other unused code 10/2011
+ #
+ # Description:
+ # This function reads in a limited number of lines of each image (specified in terms of the
+ # size of the temporary predictor dataframe), applies a user-specified
+ # prediction function, and stores the results as matrix. Alternatively, if an
+ # output file is specified, a file is written directly to that file in .tif format to
+ # the same directory as the input files. Geographic information from the input images
+ # is retained.
+ #
+
+ # Start of function #
+ library(rgdal)
+ library(raster)
+
+ MESS=out$input$MESS
+ if(is.null(thresh)) thresh<-.5
+ nvars<-length(vnames)
+
+# settup up output raster to match input raster
+
+ fullnames <- as.character(filenames[match(vnames,basename(sub(".tif","",filenames)))])
+ goodfiles <- file.access(fullnames)==0
+ if(!all(goodfiles)) stop(paste("ERROR: the following image files are missing:",paste(fullnames[!goodfiles],collapse=", ")))
+
+if(nvars<=1) MESS=FALSE
+ ######################################
+ # get spatial reference info from existing image file
+options(warn=-1)
+ gi <- GDALinfo(fullnames[1])
+options(warn=0)
+ dims <- as.vector(gi)[1:2]
+ ps <- as.vector(gi)[6:7]
+ ll <- as.vector(gi)[4:5]
+ pref<-attr(gi,"projection")
+
+RasterInfo=raster(fullnames[1])
+RasterInfo at file@datanotation<-"FLT4S"
+NAval<- -3.399999999999999961272e+38
+
+#To remove use of the Raster package I need to see if rgdal handles area or point correctly
+if(!is.na(match("AREA_OR_POINT=Point",attr(gi,"mdata")))){
+ xx<-RasterInfo #this shifts by a half pixel
+nrow(xx) <- nrow(xx) - 1
+ncol(xx) <- ncol(xx) - 1
+rs <- res(xx)
+xmin(RasterInfo) <- xmin(RasterInfo) - 0.5 * rs[1]
+xmax(RasterInfo) <- xmax(RasterInfo) - 0.5 * rs[1]
+ymin(RasterInfo) <- ymin(RasterInfo) + 0.5 * rs[2]
+ymax(RasterInfo) <- ymax(RasterInfo) + 0.5 * rs[2]
+ }
+ # calculate position of upper left corner and get geotransform ala http://www.gdal.org/gdal_datamodel.html
+ ul <- c(ll[1],ll[2]+(dims[1])*ps[2])
+ gt<-c(ul[1],ps[1],0,ul[2],0,ps[2])
+
+ # setting tile size
+ MB.per.row<-dims[2]*nvars*32/8/1000/1024
+
+ nrows<-min(round(tsize/MB.per.row),dims[1])
+ bs<-c(nrows,dims[2])
+ nbs <- ceiling(dims[1]/nrows)
+ inc<-round(10/nbs,1)
+
+ chunksize<-bs[1]*bs[2]
+ tr<-blockSize(RasterInfo,chunksize=chunksize)
+
+ continuousRaster<-raster(RasterInfo)
+ continuousRaster <- writeStart(continuousRaster, filename=outfile.p, overwrite=TRUE)
+ if(make.binary.tif) {
+ binaryRaster<-raster(RasterInfo)
+ binaryRaster <- writeStart(binaryRaster, filename=outfile.bin, overwrite=TRUE)}
+ if(MESS) {
+ MessRaster<-raster(RasterInfo)
+ ModRaster<-raster(RasterInfo)
+ MessRaster <- writeStart(MessRaster, filename=sub("bin","mess",outfile.bin), overwrite=TRUE)
+ ModRaster <- writeStart(ModRaster, filename=sub("bin","MoD",outfile.bin), overwrite=TRUE)
+ }
+
+temp <- data.frame(matrix(ncol=nvars,nrow=tr$size*ncol(RasterInfo))) # temp data.frame.
+names(temp) <- vnames
+FactorInd<-which(!is.na(match(names(temp),names(factor.levels))),arr.ind=TRUE)
+ if((nvars-length(FactorInd))==0) MESS<-FALSE #turn this off if only one factor column was selected
+ if(MESS) {
+ pred.rng<-temp
+ CalcMESS<-function(tiff.entry,pred.vect){
+ f<-sum(pred.vect<tiff.entry)/length(pred.vect)*100
+ if(is.na(f)) return(NA)
+ if(f==0) return((tiff.entry-min(pred.vect))/(max(pred.vect)-min(pred.vect))*100)
+ if(0<f & f<=50) return(2*f)
+ if(50<=f & f<100) return(2*(100-f))
+ if(f==100) return((max(pred.vect)-tiff.entry)/(max(pred.vect)-min(pred.vect))*100)
+ else return(NA)
+ }
+ }
+
+ Pred.Surface(object=RasterInfo,model=out$mods$auc.output$residual.smooth.fct,filename=sub("prob_map.tif","resid_map.tif",outfile.p),NAval=NAval)
+
+ min.pred<-1
+ max.pred<-0
+
+ for (i in 1:tr$n) {
+ strt <- c((i-1)*nrows,0)
+ region.dims <- c(min(dims[1]-strt[1],nrows),dims[2])
+ if (i==tr$n) if(is.null(dim(temp))) { temp <- temp[1:(tr$nrows[i]*dims[2])]
+ if(MESS) pred.rng<-pred.rng[1:(tr$nrows[i]*dims[2])]
+ } else {temp <- temp[1:(tr$nrows[i]*dims[2]),]
+ if(MESS) pred.rng<-pred.rng[1:(tr$nrows[i]*dims[2]),]
+ }
+ # for the last tile...
+ for(k in 1:nvars) { # fill temp data frame
+ if(is.null(dim(temp))){
+ temp<- getValuesBlock(raster(fullnames[k]), row=tr$row[i], nrows=tr$size)
+ } else {temp[,k]<- getValuesBlock(raster(fullnames[k]), row=tr$row[i], nrows=tr$size)
+ }
+ if(MESS & !k%in%FactorInd){
+ pred.range<-out$dat$ma$ma[,c(match(sub(".tif","",basename(fullnames[k])),names(out$dat$ma$ma)))]
+ if(nvars>1) pred.rng[,k]<-mapply(CalcMESS,tiff.entry=temp[,k],MoreArgs=list(pred.vect=pred.range))
+ else pred.rng<-mapply(CalcMESS,tiff.entry=temp,MoreArgs=list(pred.vect=pred.range))
+ }
+ }
+ if(MESS & length(FactorInd)>0) pred.rng<-pred.rng[,-c(FactorInd)]
+ temp[temp==NAval] <- NA # replace missing values #
+ temp[is.na(temp)]<-NA #this seemingly worthless line switches NaNs to NA so they aren't predicted
+ if(sum(!is.na(factor.levels))){
+ factor.cols <- match(names(factor.levels),names(temp))
+ if(sum(!is.na(factor.cols))>0){
+ for(j in 1:length(factor.cols)){
+ if(!is.na(factor.cols[j])){
+ temp[,factor.cols[j]] <- factor(temp[,factor.cols[j]],levels=factor.levels[[j]]$number,labels=factor.levels[[j]]$class)
+ }
+ }
+ }}
+ ifelse(sum(!is.na(temp))==0, # does not calculate predictions if all predictors in the region are na
+ preds<-matrix(data=NaN,nrow=region.dims[1],ncol=region.dims[2]),
+ preds <- t(matrix(pred.fct(model,temp),ncol=dims[2],byrow=T)))
+ min.pred<-min(na.omit(preds),min.pred)
+ max.pred<-max(na.omit(preds),max.pred)
+ preds[is.na(preds)]<-NAval
+ ## Writing to the rasters u
+ f<-function(x){
+ if(any(is.na(x))) return(NA)
+ a<-which(x==min(x),arr.ind=TRUE)
+ if(length(a>1)) a<-sample(a,size=1)
+ return(a)
+ }
+ if(MESS) {
+ MessRaster<-writeValues(MessRaster,apply(pred.rng,1,min), tr$row[i])
+ if(!is.null(dim(pred.rng)[2])) a<-apply(as.matrix(pred.rng),1,f)
+ else a<-rep(1,times=length(pred.rng))
+ #if(is.list(a)) a<-unlist(a)
+ ModRaster<-writeValues(ModRaster,a, tr$row[i])
+ }
+ if(make.binary.tif) binaryRaster<-writeValues(binaryRaster,(preds>thresh),tr$row[i])
+ continuousRaster <- writeValues(continuousRaster,preds, tr$row[i])
+ #NAvalue(continuousRaster) <-NAval
+ rm(preds);gc() #why is gc not working on the last call
+}
+
+ continuousRaster <- writeStop(continuousRaster)
+ a<-readGDAL(continuousRaster at file@name)
+ writeGDAL(a,continuousRaster at file@name, drivername = "GTiff",setStatistics=TRUE,mvFlag=NAval)
+
+
+
+ if(make.binary.tif) {
+ writeStop(binaryRaster)
+ a<-readGDAL(binaryRaster at file@name)
+ writeGDAL(a,binaryRaster at file@name, drivername = "GTiff",setStatistics=TRUE,mvFlag=NAval)
+ }
+ if(MESS) {
+ writeStop(MessRaster)
+ a<-readGDAL(MessRaster at file@name)
+ writeGDAL(a,MessRaster at file@name, drivername = "GTiff",setStatistics=TRUE,mvFlag=NAval)
+
+ writeStop(ModRaster)
+ a<-readGDAL(ModRaster at file@name)
+ d<-data.frame(as.integer(seq(1:ncol(pred.rng))),names(pred.rng))
+ names(d)=c("Value","Class")
+ ModRaster at file@datanotation<-"INT1U"
+ write.dbf(d, sub(".tif",".tif.vat.dbf",ModRaster at file@name), factor2char = TRUE, max_nchar = 254)
+ writeGDAL(a,ModRaster at file@name, drivername = "GTiff",setStatistics=TRUE,mvFlag=255,type="UInt16")
+ }
+
+ return(0)
+ }
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/read.ma.r b/contrib/sahm/pySAHM/Resources/R_Modules/read.ma.r
new file mode 100644
index 0000000..f477ebd
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/read.ma.r
@@ -0,0 +1,209 @@
+ read.ma <- function(out){
+
+ ma.name <- out$input$ma.name
+
+ tif.dir <- out$dat$tif.dir$dname
+ out.list <- out$dat$ma
+ out.list$status[1] <- file.access(ma.name,mode=0)==0
+
+ try(ma<-read.csv(ma.name,skip=2))
+ hl<-readLines(ma.name,1)
+ hl=strsplit(hl,',')
+ colnames(ma) = hl[[1]]
+
+ tif.info<-readLines(ma.name,3)
+ tif.info<-strsplit(tif.info,',')
+ temp<-tif.info[[2]]
+ temp[1:3]<-0
+ include<-as.numeric(temp)
+
+ paths<-as.character(tif.info[[3]])
+
+ if(class(ma)=="try-error") stop("Error reading MDS")
+ else out.list$status[2]<-T
+
+ temp<-strsplit(tif.info[[2]][1],split="\\\\")[[1]]
+ out.list$input$FieldDataTemp<-temp[length(temp)]
+
+ temp<-strsplit(tif.info[[2]][2],split="\\\\")[[1]]
+ out.list$input$OrigFieldData<-temp[length(temp)]
+
+ temp<-strsplit(tif.info[[2]][3],split="\\\\")[[1]]
+ out.list$input$CovSelectName<-temp[length(temp)]
+
+ temp<-strsplit(tif.info[[3]][1],split="\\\\")[[1]]
+ out.list$input$ParcTemplate<-temp[length(temp)]
+
+ temp<-strsplit(tif.info[[3]][2],split="\\\\")[[1]]
+ out.list$input$ParcOutputFolder<-temp[length(temp)]
+
+ temp<-strsplit(tif.info[[2]][2],split="\\\\")[[1]]
+ out.list$input$OrigFieldData<-temp[length(temp)]
+
+ r.name <- out$input$response.col
+ if(r.name=="responseCount") out$input$model.family="poisson"
+
+ r.col <- grep(r.name,names(ma))
+ if(length(r.col)==0) stop("Response column was not found")
+ if(length(r.col)>1) stop("Multiple columns matched the response column")
+ rm.list<-r.col
+
+ # remove background points which aren't used here
+ if(length(which(ma[,r.col]==-9999,arr.ind=TRUE))>0) ma<-ma[-c(which(ma[,r.col]==-9999,arr.ind=TRUE)),]
+
+ # remove incomplete cases and warn user if this number is more than 10% of the data
+
+ # find and save xy columns#
+ xy.cols <- na.omit(c(match("x",tolower(names(ma))),match("y",tolower(names(ma)))))
+ if(length(xy.cols)>0) rm.list<-c(rm.list,xy.cols)
+
+ # remove weights column except for Random Forest
+ site.weights<-match("site.weights",tolower(names(ma)))
+ if(!is.na(site.weights)) rm.list<-c(rm.list,site.weights)
+
+ # and index as well
+ split.indx<-match("split",tolower(names(ma)))
+ if(length(na.omit(split.indx))>0) rm.list<-c(rm.list,split.indx)
+
+ #complete the list of columns to include
+ include[is.na(include)]<-0
+ rm.list<-c(rm.list,(which(include!=1,arr.ind=TRUE)))
+ rm.list<-unique(rm.list[!is.na(rm.list)])
+
+ ######################### REMOVING INCOMPLETE CASES ###############
+ #remove incomplete cases but only for include variables
+ all.cases<-nrow(ma)
+ out.list$n.pres[1] <- NA
+ out.list$n.abs[1] <- NA
+ ma<-ma[complete.cases(ma[,-c(rm.list)]),]
+ comp.cases<-nrow(ma)
+ if(comp.cases/all.cases<.9) warning(paste(round((1-comp.cases/all.cases)*100,digits=2),"% of cases were removed because of missing values",sep=""))
+ #########################################################################
+ #split out the weights,response, and xy.columns after removing incomplete cases
+ if(!is.na(site.weights)){
+ out.list$train.weights<-ma[,site.weights]
+ } else out.list$train.weights<-rep(1,times=dim(ma)[1])
+ if(length(xy.cols)>0) out.list$train.xy<-ma[,xy.cols]
+ response<-ma[,r.col]
+
+ ma.names<-names(ma)
+ # tagging factors and looking at their levels
+ factor.cols <- grep("categorical",names(ma))
+ factor.cols <- factor.cols[!is.na(factor.cols)]
+ if(length(factor.cols)==0){
+ out.list$factor.levels <- NA
+ } else {
+ names(ma) <- ma.names <- sub("_categorical","",ma.names)
+ factor.names <- ma.names[factor.cols]
+ factor.levels <- list()
+ for (i in 1:length(factor.cols)){
+ f.col <- factor.cols[i]
+
+ x <- table(ma[,f.col])
+ if(nrow(x)<2){
+ out$dat$bad.factor.cols <- c(out$dat$bad.factor.cols,factor.names[i])
+ }
+ lc.levs <- as.numeric(row.names(x))[x>0] # make sure there is at least one "available" observation at each level
+ lc.levs <- data.frame(number=lc.levs,class=lc.levs)
+ factor.levels[[i]] <- lc.levs
+
+ ma[,f.col] <- factor(ma[,f.col],levels=lc.levs$number,labels=lc.levs$class)
+ }
+
+ names(factor.levels)<-factor.names
+ out.list$factor.levels <- factor.levels
+
+ if(!is.null(out$dat$bad.factor.cols)) rm.list<-c(rm.list,match(out$dat$bad.factor.cols,names(ma)))
+ }
+
+ if(length(which(lapply(apply(ma,2,unique),length)==1,arr.ind=TRUE))>0){
+ rm.list<-c(rm.list,which(lapply(apply(ma,2,unique),length)==1,arr.ind=TRUE))
+ warning(paste("The Following Predictors will be removed because they have only 1 unique value: ",
+ names(which(lapply(apply(ma,2,unique),length)==1,arr.ind=TRUE))))
+ }
+ #remove test training split column if present
+
+ if(length(na.omit(split.indx))>0){
+ split.col<-ma[,split.indx]
+ out.list$ma.test<-ma[split.col=="test",]
+ ma<-ma[split.col=="train",]
+ out.list$test.weights<-out.list$train.weights[split.col=="test"]
+ out.list$train.weights<-out.list$train.weights[split.col=="train"]
+ out.list$test.xy<-out.list$train.xy[split.col=="test",]
+ out.list$train.xy<-out.list$train.xy[split.col=="train",]
+ out.list$n.pres[4] <- sum(out.list$ma.test[,r.col]!=0)
+ out.list$n.abs[4] <- sum(out.list$ma.test[,r.col]==0)
+ }
+
+ # Complete cases n.pres and n.abs must be calculated after splitting data (this is train cases reported)
+ out.list$n.pres[2] <- sum(ma[,r.col]!=0)
+ out.list$n.abs[2] <- sum(ma[,r.col]==0)
+
+ # check that response column contains only 1's and 0's, but not all 1's or all 0's if GLMFamily==binomial
+ if(out$input$model.source.file=="rf.r") out$input$model.family="bernoulli"
+
+ if(tolower(out$input$model.family)=="bernoulli" || tolower(out$input$model.family)=="binomial"){
+ if(any(ma[,r.col]!=1 & ma[,r.col]!=0) | sum(ma[,r.col]==1)==nrow(ma) | sum(ma[,r.col]==0)==nrow(ma))
+ stop("response column (#",r.col,") in ",ma.name," is not binary 0/1",sep="")
+ }
+
+ #check that response column contains at least two unique values for counts
+
+ if(tolower(out$input$model.family)=="poisson"){
+ if(length(table(unique(ma[,r.col])))==1)
+ stop("response column (#",r.col,") in ",ma.name," does not have at least two unique values",sep="")
+ }
+
+ #ma has the first column equal to the response and removes all other remove columns
+ ma <- cbind(ma[,r.col],ma[,-c(rm.list)]) #ma still needs the response column
+ if(length(na.omit(split.indx))>0) out.list$ma.test <- cbind(out.list$ma.test[,r.col],out.list$ma.test[,-c(rm.list)])
+ paths<-paths[-c(rm.list)]
+ include<-include[-c(rm.list)]
+
+ out.list$resp.name <- names(ma)[1]<-"response"
+ if(length(na.omit(split.indx))>0) names(out.list$ma.test)[1]<-"response"
+ ma.names<-names(ma)
+
+ # if producing geotiff output, check to make sure geotiffs are available for each column of the model array #
+ if(out$input$make.binary.tif==T | out$input$make.p.tif==T){
+ #Check that tiffs to be used exist
+ if(sum(file.access(paths),mode=0)!=0){
+ temp<-as.vector(file.access(paths))==-1
+ temp.paths<-paths[temp]
+ stop("the following geotiff(s) are missing:",
+ "\nif these are intentionally left blank, uncheck makeBinMap and makeProbabilityMap options\n",
+ paste(paths[temp],collapse="\n"),sep="")
+ }
+
+ } else out$dat$tif.names <- ma.names[-1]
+
+ out$dat$tif.ind<-paths
+
+ out.list$ma <- ma
+
+ out.list$dims <- dim(out.list$ma)
+ out.list$ratio <- min(sum(out$input$model.fitting.subset)/out.list$dims[1],1)
+ out.list$used.covs <- names(out.list$ma)[-1]
+
+ if(!is.null(out$input$model.fitting.subset)){
+ pres.sample <- sample(c(1:nrow(out.list$ma))[out.list$ma[,1]>=1],min(out.list$n.pres[2],out$input$model.fitting.subset[1]))
+ abs.sample <- sample(c(1:nrow(out.list$ma))[out.list$ma[,1]==0],min(out.list$n.abs[2],out$input$model.fitting.subset[2]))
+ out.list$ma.subset <- out.list$ma[c(pres.sample,abs.sample),]
+ if(out$input$model.source.file!="rf.r") out.list$weight.subset<-out.list$train.weights[c(pres.sample,abs.sample)]
+ out.list$n.pres[3] <- length(pres.sample)
+ out.list$n.abs[3] <- length(abs.sample)
+ } else {
+ out.list$ma.subset <- NULL
+ out.list$weight.subset<-NULL
+ out.list$n.pres[3] <- NA
+ out.list$n.abs[3] <- NA }
+
+if(tolower(out$input$model.family)=="poisson"){
+out.list$ma.subset<-out.list$ma
+out.list$weight.subset<-out.list$train.weights
+}
+
+ out$dat$ma <- out.list
+
+ return(out)
+ }
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/read.maNew.r b/contrib/sahm/pySAHM/Resources/R_Modules/read.maNew.r
new file mode 100644
index 0000000..c2b9004
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/read.maNew.r
@@ -0,0 +1,224 @@
+ read.ma <- function(out){
+
+ ma.name <- out$input$ma.name
+ browser()
+ tif.dir <- out$dat$tif.dir$dname
+ out.list <- out$dat$ma
+ out.list$status[1] <- file.access(ma.name,mode=0)==0
+
+
+ if(is.null(out$input$tif.dir)){
+ try(ma<-read.csv(ma.name,skip=3))
+ hl<-readLines(ma.name,1)
+ hl=strsplit(hl,',')
+ colnames(ma) = hl[[1]]
+
+ tif.info<-readLines(ma.name,3)
+ tif.info<-strsplit(tif.info,',')
+ temp<-tif.info[[2]]
+ temp[1:3]<-0
+ include<-as.numeric(temp)
+
+ paths<-as.character(tif.info[[3]])
+ }
+ if(class(ma)=="try-error") stop("Error reading MDS")
+ else out.list$status[2]<-T
+
+ temp<-strsplit(tif.info[[2]][1],split="\\\\")[[1]]
+ out.list$input$FieldDataTemp<-temp[length(temp)]
+
+ temp<-strsplit(tif.info[[2]][2],split="\\\\")[[1]]
+ out.list$input$OrigFieldData<-temp[length(temp)]
+
+ temp<-strsplit(tif.info[[2]][3],split="\\\\")[[1]]
+ out.list$input$CovSelectName<-temp[length(temp)]
+
+ temp<-strsplit(tif.info[[3]][1],split="\\\\")[[1]]
+ out.list$input$ParcTemplate<-temp[length(temp)]
+
+ temp<-strsplit(tif.info[[3]][2],split="\\\\")[[1]]
+ out.list$input$ParcOutputFolder<-temp[length(temp)]
+
+ temp<-strsplit(tif.info[[2]][2],split="\\\\")[[1]]
+ out.list$input$OrigFieldData<-temp[length(temp)]
+
+ r.name <- out$input$response.col
+ if(r.name=="responseCount") out$input$model.family="poisson"
+
+ r.col <- grep(r.name,names(ma))
+ if(length(r.col)==0) stop("Response column was not found")
+ if(length(r.col)>1) stop("Multiple columns matched the response column")
+ rm.list<-r.col
+
+ # remove background points which aren't used here
+ if(length(which(ma[,r.col]==-9999,arr.ind=TRUE))>0) ma<-ma[-c(which(ma[,r.col]==-9999,arr.ind=TRUE)),]
+ response<-ma[,r.col]
+
+ # find and save xy columns#
+ xy.cols <- na.omit(c(match("x",tolower(names(ma))),match("y",tolower(names(ma)))))
+ if(length(xy.cols)>0) {out.list$train.xy<-ma[,xy.cols]
+ rm.list<-c(rm.list,xy.cols)}
+
+
+ # remove weights column except for Random Forest
+ site.weights<-match("site.weights",tolower(names(ma)))
+ if(!is.na(site.weights)){
+ out.list$train.weights<-ma[,site.weights]
+ rm.list<-c(rm.list,site.weights)
+ } else out.list$train.weights<-rep(1,times=dim(ma)[1]))
+
+
+ ma.names<-names(ma)
+ # tagging factors and looking at their levels
+ factor.cols <- grep("categorical",names(ma))
+ factor.cols <- factor.cols[!is.na(factor.cols)]
+ if(length(factor.cols)==0){
+ out.list$factor.levels <- NA
+ } else {
+ names(ma) <- ma.names <- sub("_categorical","",ma.names)
+ factor.names <- ma.names[factor.cols]
+ factor.levels <- list()
+ for (i in 1:length(factor.cols)){
+ f.col <- factor.cols[i]
+
+ x <- table(ma[,f.col])
+ if(nrow(x)<2){
+ out$dat$bad.factor.cols <- c(out$dat$bad.factor.cols,factor.names[i])
+ }
+ lc.levs <- as.numeric(row.names(x))[x>0] # make sure there is at least one "available" observation at each level
+ lc.levs <- data.frame(number=lc.levs,class=lc.levs)
+ factor.levels[[i]] <- lc.levs
+
+ ma[,f.col] <- factor(ma[,f.col],levels=lc.levs$number,labels=lc.levs$class)
+ }
+
+ names(factor.levels)<-factor.names
+ out.list$factor.levels <- factor.levels
+ }
+
+ #remove test training split column if present
+ split.indx<-match("split",tolower(names(ma)))
+ if(length(na.omit(split.indx))>0){
+ split.col<-ma[,split.indx]
+ out.list$ma.test<-ma[split.col=="test",]
+ ma<-ma[split.col=="train",]
+ out.list$test.weights<-out.list$train.weights[split.col=="test"]
+ out.list$train.weights<-out.list$train.weights[split.col=="train"]
+ out.list$test.xy<-out.list$train.xy[split.col=="test",]
+ out.list$train.xy<-out.list$train.xy[split.col=="train",]
+ rm.list<-c(rm.list,split.indx)
+ }
+
+
+ # check that response column contains only 1's and 0's, but not all 1's or all 0's if GLMFamily==binomial
+ if(out$input$model.source.file=="rf.r") out$input$model.family="bernoulli"
+
+ if(tolower(out$input$model.family)=="bernoulli" || tolower(out$input$model.family)=="binomial"){
+ if(any(ma[,r.col]!=1 & ma[,r.col]!=0) | sum(ma[,r.col]==1)==nrow(ma) | sum(ma[,r.col]==0)==nrow(ma))
+ stop("response column (#",r.col,") in ",ma.name," is not binary 0/1",sep="")
+
+ out.list$n.pres[1] <- sum(ma[,r.col])
+ out.list$n.abs[1] <- nrow(ma)-sum(ma[,r.col])
+ }
+
+
+
+ #check that response column contains at least two unique values for counts
+
+ if(tolower(out$input$model.family)=="poisson"){
+ if(length(table(unique(ma[,r.col])))==1)
+ stop("response column (#",r.col,") in ",ma.name," does not have at least two unique values",sep="")
+
+ out.list$n.pres[1] <- sum(ma[,r.col]!=0)
+ out.list$n.abs[1] <- sum(ma[,r.col]==0)
+ }
+
+ out$dat$ma$resp.name <- names(ma)[r.col]<-"response"
+ out.list$resp.name <- names(ma)[r.col]
+
+ include[is.na(include)]<-0
+ rm.list<-c(rm.list,(which(include!=1,arr.ind=TRUE)))
+ rm.list<-unique(rm.list[!is.na(rm.list)])
+
+ ma <- ma[,-rm.list]
+ if(is.null(out$input$tif.dir)){
+ paths<-paths[-c(rm.list)]
+ include<-include[-c(rm.list)]
+ #ma.names[-c(rm.cols)]
+ }
+
+ ma[ma==-9999]<-NA
+ ma.names<-names(ma)
+ browser()
+ # if producing geotiff output, check to make sure geotiffs are available for each column of the model array #
+ if(out$input$make.binary.tif==T | out$input$make.p.tif==T){
+ #Now check that tiffs to be used exist
+
+ ma.cols <- match(ma.names,sub(".tif","",basename(paths[-r.col])))
+ if(any(is.na(ma.cols))){
+ stop("the following geotiff(s) are missing in ",
+ tif.dir,": ",paste(ma.names[-r.col][is.na(ma.cols)],collapse=" ,"),
+ "\nif these are intentionally left blank, uncheck makeBinMap and makeProbabilityMap options",sep="")
+
+ if(sum(file.access(paths[include==1]),mode=0)!=0)
+ stop("the following geotiff(s) are missing : ",
+ paths[(file.access(paths)!=0),][1],"\nif these are intentionally left blank, uncheck makeBinMap and makeProbabilityMap options", sep="")
+
+ out$dat$tif.ind<-paths
+ }
+
+ if(!is.null(out$input$tif.dir)){
+ tif.names <- out$dat$tif.names
+ ma.cols <- match(ma.names[-r.col],sub(".tif","",basename(tif.names)))
+ if(any(is.na(ma.cols)))stop("the following geotiff(s) are missing in ",
+ tif.dir,": ",paste(ma.names[is.na(ma.cols)],collapse=" ,"),sep="")
+
+ out$dat$tif.names <- tif.names[ma.cols]
+
+ } else out$dat$tif.names <- ma.names
+ #Removing NAs this might be better in a loop
+ out.list$ma <- ma[complete.cases(ma),c(r.col,c(1:ncol(ma))[-r.col])]
+ if(length(na.omit(split.indx))>0) out.list$test.xy<-out.list$test.xy[complete.cases(out.list$ma.test),]
+ out.list$train.xy<-out.list$train.xy[complete.cases(ma),]
+
+ if(!is.null(out.list$ma.test)){
+ if(out$input$model.source.file!="rf.r") out.list$test.weights<- out.list$test.weights[complete.cases(out.list$ma.test)]
+ out.list$ma.test<-out.list$ma.test[complete.cases(out.list$ma.test),c(r.col,c(1:ncol(out.list$ma.test))[-r.col])]
+ if(out$input$model.source.file!="rf.r") out.list$test.weights<- out.list$test.weights[complete.cases(out.list$ma.test)]
+ # out.list$ma.test<-out.list$ma.test[,c(r.col,c(1:ncol(out.list$ma.test))[-r.col])]
+ #if(out$input$model.source.file!="rf.r") out.list$test.weights<- out.list$test.weights
+ out.list$n.pres[4] <- sum(out.list$ma.test[,r.col]!=0)
+ out.list$n.abs[4] <- nrow(out.list$ma.test)-sum(out.list$ma.test[,r.col]!=0)
+ }
+ if(out$input$model.source.file!="rf.r") out.list$train.weights <- out.list$train.weights[complete.cases(ma)]
+ if(!is.null(out$dat$bad.factor.cols)) out.list$ma <- out.list$ma[,-match(out$dat$bad.factor.cols,names(out.list$ma))]
+
+ out.list$dims <- dim(out.list$ma)
+ out.list$ratio <- min(sum(out$input$model.fitting.subset)/out.list$dims[1],1)
+ out.list$n.pres[2] <- sum(out.list$ma[,1]!=0)
+ out.list$n.abs[2] <- nrow(out.list$ma)-sum(out.list$ma[,1]!=0)
+ out.list$used.covs <- names(out.list$ma)[-1]
+
+ if(!is.null(out$input$model.fitting.subset)){
+ pres.sample <- sample(c(1:nrow(out.list$ma))[out.list$ma[,1]>=1],min(out.list$n.pres[2],out$input$model.fitting.subset[1]))
+ abs.sample <- sample(c(1:nrow(out.list$ma))[out.list$ma[,1]==0],min(out.list$n.abs[2],out$input$model.fitting.subset[2]))
+ out.list$ma.subset <- out.list$ma[c(pres.sample,abs.sample),]
+ if(out$input$model.source.file!="rf.r") out.list$weight.subset<-out.list$train.weights[c(pres.sample,abs.sample)]
+ out.list$n.pres[3] <- length(pres.sample)
+ out.list$n.abs[3] <- length(abs.sample)
+ } else {
+ out.list$ma.subset <- NULL
+ out.list$weight.subset<-NULL
+ out.list$n.pres[3] <- NA
+ out.list$n.abs[3] <- NA }
+
+if(tolower(out$input$model.family)=="poisson"){
+out.list$ma.subset<-out.list$ma
+out.list$weight.subset<-out.list$train.weights
+}
+
+
+ out$dat$ma <- out.list
+
+ return(out)
+ }
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/tmp_ThrowsError.r b/contrib/sahm/pySAHM/Resources/R_Modules/tmp_ThrowsError.r
new file mode 100644
index 0000000..a82bea5
--- /dev/null
+++ b/contrib/sahm/pySAHM/Resources/R_Modules/tmp_ThrowsError.r
@@ -0,0 +1 @@
+1 = 2
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/__init__.py b/contrib/sahm/pySAHM/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/contrib/sahm/pySAHM/singlePARC.py b/contrib/sahm/pySAHM/singlePARC.py
new file mode 100644
index 0000000..c1d5dc9
--- /dev/null
+++ b/contrib/sahm/pySAHM/singlePARC.py
@@ -0,0 +1,71 @@
+#!/usr/bin/python
+"""
+This was an experiment to explore breaking the
+individual raster processes into individual
+runs that could be either run on separate
+processes on the same computer with a command line
+popopen perhaps or sent out individually to our
+Condor distributed computing cluster.
+
+"""
+
+
+import glob
+import math
+import os
+import shutil
+import struct
+import sys
+import csv
+
+from optparse import OptionParser
+from multiprocessing import Process, Queue
+
+from osgeo import gdalconst
+from osgeo import gdal
+from osgeo import osr
+
+from numpy import *
+import numpy as np
+
+import utilities
+from PARC import PARC
+
+def main(args_in):
+ """
+ Process commandline Arguments,
+ Create an instance of PARC with the Variables,
+ Kick off the parkFiles function of our PARC instance
+ """
+ # Process command-line args.
+ usageStmt = "usage: %prog [options] <template image> <input dir or list of input files>"
+ desc = "This application projects, aggregates, resamples, and clips imagery."
+
+ parser = OptionParser(usage=usageStmt, description=desc)
+ parser.add_option("-s", dest="source", help="print the names of all known aggregation methods")
+ parser.add_option("-c", dest="categorical")
+ parser.add_option("-d", dest="dest", default="./", help="directory in which to put processed images, defaults to current directory")
+ parser.add_option("-v", dest="verbose", default=False, action="store_true", help="the verbose flag causes diagnostic output to print")
+ parser.add_option("-t", dest="template", help="The template raster used for projection, origin, cell size and extent")
+ parser.add_option("-r", dest="resampling", help="The CSV containing the list of files to process. Format is 'FilePath, Categorical, Resampling, Aggreagtion")
+ parser.add_option("-a", dest="aggregation", default=True, help="'True', 'False' indicating whether to use multiple cores or not")
+ (options, args) = parser.parse_args(args_in)
+
+ ourPARC = PARC()
+ ourPARC.verbose = options.verbose
+ ourPARC.template = options.template
+ outDir = os.path.split(options.dest)[0]
+ ourPARC.outDir = outDir
+ ourPARC.logger = utilities.logger(outDir, ourPARC.verbose)
+ ourPARC.writetolog = ourPARC.logger.writetolog
+ ourPARC.template_params = ourPARC.getRasterParams(options.template)
+ ourPARC.parcFile([options.source, options.categorical, options.resampling, options.aggregation], options.dest)
+
+if __name__ == "__main__":
+ main(sys.argv[1:])
+# try:
+## PARC().testing()
+# sys.exit(PARC().main(sys.argv[1:]))
+# except Exception as e:
+# print e
+# sys.exit(1)
diff --git a/contrib/sahm/pySAHM/singleRasterFormatConverter.py b/contrib/sahm/pySAHM/singleRasterFormatConverter.py
new file mode 100644
index 0000000..99ee88e
--- /dev/null
+++ b/contrib/sahm/pySAHM/singleRasterFormatConverter.py
@@ -0,0 +1,73 @@
+#!/usr/bin/python
+"""
+This script is a wrapper for the
+RasterFormatConverter which allows
+the user to run an individual raster through.
+It is used by RasterFormatConverter itself
+to allow each raster to be spawned off as
+a separate command line to take advantage of
+multiple cores on a machine.
+
+"""
+
+
+import glob
+import math
+import os
+import shutil
+import struct
+import sys
+import csv
+
+from optparse import OptionParser
+from multiprocessing import Process, Queue
+
+from osgeo import gdalconst
+from osgeo import gdal
+from osgeo import osr
+
+from numpy import *
+import numpy as np
+
+import utilities
+from RasterFormatConverter import FormatConverter
+
+def main(argv):
+ usageStmt = "usage: options: -m --MDSFile -o --outputDir -f --format -v --verbose"
+ desc = "Converts all of the tif files specified in an MDS to ASCII format (or optionally other formats)"
+ parser = OptionParser(usage=usageStmt, description=desc)
+
+ parser.add_option("-v",
+ dest="verbose",
+ default=False,
+ action="store_true",
+ help="the verbose flag causes diagnostic output to print.")
+ parser.add_option("-i", "--inputfile",
+ dest="input",
+ help="")
+ parser.add_option("-o", "--outputDir",
+ dest="outputDir",
+ help="Output directory to save files in.")
+ parser.add_option("-f", "--format",
+ dest="format",
+ default='asc',
+ help="The format to convert into. 'bil', 'img', 'tif', 'jpg', 'bmp', 'asc'")
+
+ (options, args) = parser.parse_args(argv)
+
+ ourFC = FormatConverter()
+ ourFC.verbose = options.verbose
+ ourFC.logger = utilities.logger(options.outputDir, ourFC.verbose)
+ ourFC.writetolog = ourFC.logger.writetolog
+ ourFC.outputDir = options.outputDir
+ ourFC.format = options.format
+ ourFC.convertEnvironmentalLayers([options.input, ], options.outputDir, options.format)
+
+if __name__ == "__main__":
+ main(sys.argv[1:])
+# try:
+## PARC().testing()
+# sys.exit(PARC().main(sys.argv[1:]))
+# except Exception as e:
+# print e
+# sys.exit(1)
diff --git a/contrib/sahm/pySAHM/utilities.py b/contrib/sahm/pySAHM/utilities.py
new file mode 100644
index 0000000..53fe97f
--- /dev/null
+++ b/contrib/sahm/pySAHM/utilities.py
@@ -0,0 +1,261 @@
+#!/usr/bin/python
+
+''' These utility functions are shared
+between all of the Python SAHM command line
+modules
+'''
+
+import os, sys
+import time
+import csv
+import string
+
+from osgeo import gdal
+from osgeo import osr
+from osgeo import ogr
+
+_logfile = ''
+_verbose = False
+
+class logger(object):
+ def __init__(self, logfile, verbose):
+ self.logfile = logfile
+ self.verbose = verbose
+
+ #if we mistakenly get a output dir instead of a filename
+ if os.path.isdir(logfile):
+ self.logfile = os.path.join(logfile, 'sessionLog.txt')
+ else:
+ self.logfile = logfile
+
+ if os.path.exists(self.logfile):
+ self.writetolog("\nSession continued\n", True, True)
+ else:
+ logDir = os.path.split(self.logfile)[0]
+ if not os.path.exists(logDir):
+ raise RuntimeError('Directory of specified logfile does not exist.')
+ f = open(self.logfile, "w")
+ del f
+ self.writetolog("\nSession started\n", True, False)
+
+
+ def writetolog(self, msg, addtime=False, printtoscreen=True):
+ '''Opens the log file and writes the passed msg.
+ Optionally adds a time slot to the message and
+ Prints the msg to the screen.
+ If the logfile is not specified tries to use the global variable.
+ '''
+ f = open(self.logfile, "a")
+ if self.verbose and printtoscreen:
+ print msg
+ if addtime:
+ msg = ' at: '.join([msg, time.strftime("%m/%d/%Y %H:%M")])
+ msg = "\n" + msg
+ f.write(msg)
+ del f
+
+class TrappedError(Exception):
+ """Exception class indicating that an anticipated problem
+ was encountered in a specific module
+ """
+ def __init__(self, msg=None):
+ Exception.__init__(self)
+ self.message = msg
+
+
+
+#def createsessionlog(roottempdir, verbose):
+# '''Creates a new log file if one doesn't already exist.
+# If one exists then writes that the session has continued.
+# '''
+# global _logfile, _verbose
+# _verbose = verbose
+#
+# logfile = os.path.join(roottempdir, "sessionLog.txt")
+# _logfile = logfile
+#
+# if os.path.exists(logfile):
+# writetolog("\nSession continued\n", True, True, logfile=logfile)
+# else:
+# f = open(os.path.join(roottempdir, "sessionLog.txt"), "w")
+# del f
+#
+# return logfile
+#
+#def writetolog(msg, addtime=False, printtoscreen=True, logfile=''):
+# '''Opens the log file and writes the passed msg.
+# Optionally adds a time slot to the message and
+# Prints the msg to the screen.
+# If the logfile is not specified tries to use the global variable.
+# '''
+# global _logfile
+# if logfile == '':
+# logfile = _logfile
+#
+# f = open(logfile, "a")
+# if _verbose and printtoscreen:
+# print msg
+# if addtime:
+# msg = ' at: '.join([msg, time.strftime("%m/%d/%Y %H:%M")])
+# msg = "\n" + msg
+# f.write(msg)
+# del f
+
+
+def isMDSFile(MDSFile):
+ '''performs a check to see if a supplied file is in 'MDS' format
+ This means:
+ 1 - The file has three header lines
+ first: x, y, responseBinary or responseCount, a series of covariate names, and an optional Split
+ second: '0', '0', '0', 0 or blanks and 0 or 1 for each covariate indicate use or ignore
+ third: '', '', '', the full path and filename of the tiff covariate layer.
+ 2 - additionally lines contain individual occurance location, response, covariate attributes at that location, and test\train for the Split column
+
+ Values of -9999 in the response column indicate a background point.
+ covariate names ending in '*_categorical' indicate a categorical variable
+
+ The test used in this check are by no means thorough in checking for covariate files
+ existing on the file system, missing values in any columns, appropriate values in
+ the response or Split columns, etc. Instead this function is intended to just give a
+ best guess as to to if this is an MDS.
+ '''
+ MDSreader = csv.reader(open(MDSFile, 'r'))
+ header1 = MDSreader.next()
+ header2 = MDSreader.next()
+ header3 = MDSreader.next()
+
+#These no longer apply with the new agg feature.
+# for i in [0, 1, 2]:
+# if not(header2[0] == '' or header2[0] == '0'):
+# return False
+
+# for item in header2[3:-1]:
+# if not item in ['0', '1']:
+# return False
+
+ return True
+ del MDSreader
+
+def process_waiter(popen, description, que):
+ try:
+ popen.wait()
+ finally:
+ que.put( (description, popen.returncode) )
+
+
+def mds_to_shape(MDSFile, outputfolder):
+
+ #bit of a hack but currently saving the shape file as
+ #three shape files presence, absence, and background
+ #as I'm having trouble getting QGIS to display points
+ #with categorical symbology
+
+ h, t = os.path.split(MDSFile)
+ t_no_ext = os.path.splitext(t)[0]
+ outputfiles = {"pres":os.path.join(outputfolder, t_no_ext + "_pres.shp"),
+ "abs":os.path.join(outputfolder, t_no_ext + "_abs.shp"),
+ "backs":os.path.join(outputfolder, t_no_ext + "_backs.shp")}
+
+ driver = ogr.GetDriverByName('ESRI Shapefile')
+
+ MDSreader = csv.reader(open(MDSFile, 'r'))
+ header1 = MDSreader.next()
+ header2 = MDSreader.next()
+ header3 = MDSreader.next()
+
+ h, t = os.path.split(MDSFile)
+ t_no_ext = os.path.splitext(t)[0]
+#
+
+ for outfile in outputfiles.values():
+ h, t = os.path.split(outfile)
+ if os.path.exists(outfile):
+ os.chdir(h)
+ driver.DeleteDataSource(t)
+
+ ds = driver.CreateDataSource(h)
+
+ preslayer = ds.CreateLayer(t_no_ext + "_pres",
+ geom_type=ogr.wkbPoint)
+ abslayer = ds.CreateLayer(t_no_ext + "_abs",
+ geom_type=ogr.wkbPoint)
+ backslayer = ds.CreateLayer(t_no_ext + "_backs",
+ geom_type=ogr.wkbPoint)
+
+ #cycle through the items in the header and add
+ #these to each output shapefile attribute table
+ fields = {}
+ for field in header1:
+ field_name = Normalized_field_name(field, fields)
+ fields[field_name] = field
+ if field == "Split":
+ #this is the test training split field that we add
+ fieldDefn = ogr.FieldDefn(field_name, ogr.OFTString)
+ else:
+ fieldDefn = ogr.FieldDefn(field_name, ogr.OFTReal)
+
+ preslayer.CreateField(fieldDefn)
+ abslayer.CreateField(fieldDefn)
+ backslayer.CreateField(fieldDefn)
+
+ featureDefn = preslayer.GetLayerDefn()
+
+ #cycle through the rows and add each geometry to the
+ #appropriate shapefile
+ for row in MDSreader:
+ feature = ogr.Feature(featureDefn)
+ point = ogr.Geometry(ogr.wkbPoint)
+
+ point.SetPoint_2D(0, float(row[0]), float(row[1]))
+ feature.SetGeometry(point)
+
+ # for this feature add in each of the attributes from the row
+ header_num = 0
+ for field in header1:
+ short_field = find_key(fields, field)
+ if field == "Split":
+ feature.SetField(short_field, row[header_num])
+ else:
+ feature.SetField(short_field, float(row[header_num]))
+ header_num += 1
+
+ response = float(row[2])
+
+ if abs(response - 0) < 1e-9:
+ abslayer.CreateFeature(feature)
+ elif response > 0:
+ preslayer.CreateFeature(feature)
+ elif abs(response - -9999.0) < 1e-9:
+ backslayer.CreateFeature(feature)
+
+ # close the data sources
+ del MDSreader
+ ds.Destroy()
+
+def Normalized_field_name(field_name, previous_fields):
+ short_name = field_name[:10]
+
+ #remove Non alpha numeric characters
+ short_name = ''.join(ch for ch in short_name if ch in (string.ascii_letters + string.digits + '_'))
+
+ if previous_fields.has_key(short_name):
+ i = 1
+ shorter_name = short_name[:8]
+ short_name = shorter_name + "_" + str(i)
+ while previous_fields.has_key(short_name):
+ i += 1
+ short_name = shorter_name + "_" + str(i)
+ return short_name
+
+def find_key(dic, val):
+ """return the key of dictionary dic given the value
+ from: http://www.daniweb.com/software-development/python/code/217019"""
+ return [k for k, v in dic.iteritems() if v == val][0]
+
+if __name__ == "__main__":
+
+ mds_to_shape(r"I:\VisTrails\WorkingFiles\workspace\talbertc_20110901T175958\CovariateCorrelationOutputMDS_anothertry2.csv", r"I:\VisTrails\WorkingFiles\workspace\talbertc_20110901T175958\CovariateCorrelationOutputMDS_anothertry2.shp")
+ print "done"
+
+
+
diff --git a/contrib/sahm/utils.py b/contrib/sahm/utils.py
new file mode 100644
index 0000000..2933b1d
--- /dev/null
+++ b/contrib/sahm/utils.py
@@ -0,0 +1,481 @@
+'''
+These are utilites used by the VisTrails
+wrappers of the SAHM command line applications
+
+ at author: talbertc
+test
+
+'''
+import os, sys, shutil
+import traceback
+import csv
+import time
+import tempfile
+import subprocess
+
+from PyQt4 import QtCore, QtGui
+
+from core.modules.basic_modules import File, Path, Directory, new_constant, Constant
+from core.modules.vistrails_module import ModuleError
+
+from osgeo import gdalconst
+from osgeo import gdal
+from osgeo import osr
+import numpy
+
+import packages.sahm.pySAHM.utilities as utilities
+import getpass
+
+_roottempdir = ""
+_logger = None
+config = None
+
+def getrasterminmax(filename):
+ dataset = gdal.Open(filename, gdalconst.GA_ReadOnly)
+ band = dataset.GetRasterBand(1)
+
+ min = band.GetMinimum()
+ max = band.GetMaximum()
+
+ try:
+ #our output rasters have approx nodata values
+ #which don't equal the specified nodata.
+ #set the specified to equal what is actually used.
+ if (abs(band.GetNoDataValue() - band.GetMinimum()) < 1e-9 and
+ band.GetNoDataValue() <> band.GetMinimum()):
+ band.SetNoDataValue(band.GetMinimum)
+
+ if min is None or max is None:
+ (min,max) = band.ComputeRasterMinMax(1)
+
+ except:
+ pass
+ return (min, max)
+ dataset = None
+
+def mknextfile(prefix, suffix="", directory=""):
+ global _roottempdir
+ if directory == "":
+ directory = _roottempdir
+ files = os.listdir(directory)
+ seq = 0
+ for f in files:
+ if f.startswith(prefix):
+ old_seq = f.replace(prefix, '')
+ old_seq = old_seq.replace(suffix, '')
+ old_seq = old_seq.replace("_", '')
+ if old_seq.isdigit():
+ if int(old_seq) > seq:
+ seq = int(old_seq)
+ seq += 1
+ filename = prefix + str(seq) + suffix
+ return os.path.join(directory, filename)
+
+def mknextdir(prefix, directory=""):
+ global _roottempdir
+ if directory == "":
+ directory = _roottempdir
+ files = os.listdir(directory)
+ seq = 0
+ for f in files:
+ if (f.startswith(prefix) and
+ not os.path.isfile(f)):
+ f_seq = int(f.replace(prefix, ''))
+ if f_seq > seq:
+ seq = f_seq
+ seq += 1
+ dirname = prefix + str(seq)
+ os.mkdir(os.path.join(directory, dirname))
+ return os.path.join(directory, dirname)
+
+def setrootdir(session_dir):
+ global _roottempdir
+ _roottempdir = session_dir
+
+def createrootdir(rootWorkspace):
+ '''Creates a session Directory which will
+ contain all of the output produced in a single
+ VisTrails/Sahm session.
+ '''
+ global _roottempdir
+ user_nospace = getpass.getuser().split(' ')[0]
+ _roottempdir = os.path.join(rootWorkspace, user_nospace + '_' + time.strftime("%Y%m%dT%H%M%S"))
+ if not os.path.exists(_roottempdir):
+ os.makedirs(_roottempdir)
+
+ return _roottempdir
+
+def map_ports(module, port_map):
+ args = {}
+ for port, (flag, access, required) in port_map.iteritems():
+ if required or module.hasInputFromPort(port):
+ #breakpoint()
+ value = module.forceGetInputListFromPort(port)
+ if len(value) > 1:
+ raise ModuleError(module, 'Multiple items found from Port ' +
+ port + '. Only single entry handled. Please remove extraneous items.')
+ elif len(value) == 0:
+ raise ModuleError(module, 'Multiple items found from Port ' +
+ port + '. Only single entry handled. Please remove extraneous items.')
+ value = module.forceGetInputFromPort(port)
+ if access is not None:
+ value = access(value)
+ if isinstance(value, File) or \
+ isinstance(value, Directory) or \
+ isinstance(value, Path):
+ value = path_port(module, port)
+ args[flag] = value
+ return args
+
+def path_port(module, portName):
+ value = module.forceGetInputListFromPort(portName)
+ if len(value) > 1:
+ raise ModuleError(module, 'Multiple items found from Port ' +
+ portName + '. Only single entry handled. Please remove extraneous items.')
+ value = value[0]
+ path = value.name
+ path.replace("/", os.path.sep)
+ if os.path.exists(path):
+ return path
+ else:
+ raise RuntimeError, 'The indicated file or directory, ' + \
+ path + ', does not exist on the file system. Cannot continue!'
+
+def PySAHM_instance_params(instance, mappedPorts):
+ global _logger
+ instance.__dict__['logger'] = _logger
+ instance.__dict__['verbose'] = _logger.verbose
+ for k, v in mappedPorts.iteritems():
+ instance.__dict__[k] = v
+
+def R_boolean(value):
+ if value:
+ return 'TRUE'
+ else:
+ return 'FALSE'
+
+def dir_path_value(value):
+ val = value.name
+ sep = os.path.sep
+ return val.replace("/", sep)
+
+def create_file_module(fname, f=None):
+ if f is None:
+ f = File()
+ f.name = fname
+ f.upToDate = True
+ return f
+
+def create_dir_module(dname, d=None):
+ if d is None:
+ d = Directory()
+ d.name = dname
+ d.upToDate = True
+ return d
+
+#No longer used
+#def collapse_dictionary(dict):
+# list = []
+# for k,v in dict.items():
+# list.append(k)
+# list.append(v)
+# return list
+
+#def tif_to_color_jpeg(input, output, colorBreaksCSV):
+# writetolog(" running tif_to_color_jpeg()", True, False)
+# writetolog(" input=" + input, False, False)
+# writetolog(" output=" + output, False, False)
+# writetolog(" colorBreaksCSV=" + colorBreaksCSV, False, False)
+# out_bands = 3
+# #output_tmp = mktempfile(prefix='intermediateJpegPic', suffix='.tif')
+# output_tmp = output + ".tmp.tif"
+# # Print some info
+# #print "Creating %s" % (output)
+#
+# #populate the color breaks dictionary
+# # from the colorBreaks CSV
+#
+# csvfile = open(colorBreaksCSV, "r")
+# #dialect = csv.Sniffer().sniff(csvfile.read(1024))
+# reader = csv.reader(csvfile)
+# usedPixels = {}
+# header = reader.next() #skip the header
+#
+# color_dict = {}
+# maxVal = -9999
+# for row in reader:
+# color_dict[float(row[1])] = [row[3], row[4], row[5]]
+# if row[2] > maxVal: maxVal = row[2]
+#
+# #print color_dict
+# # Open source file
+# src_ds = gdal.Open( input )
+# src_band = src_ds.GetRasterBand(1)
+#
+# # create destination file
+# dst_driver = gdal.GetDriverByName('GTiff')
+# dst_ds = dst_driver.Create(output_tmp, src_ds.RasterXSize,
+# src_ds.RasterYSize, out_bands, gdal.GDT_Byte)
+#
+# # create output bands
+# band1 = numpy.zeros([src_ds.RasterYSize, src_ds.RasterXSize])
+# band2 = numpy.zeros([src_ds.RasterYSize, src_ds.RasterXSize])
+# band3 = numpy.zeros([src_ds.RasterYSize, src_ds.RasterXSize])
+#
+# # set the projection and georeferencing info
+# dst_ds.SetProjection( src_ds.GetProjection() )
+# dst_ds.SetGeoTransform( src_ds.GetGeoTransform() )
+#
+# # read the source file
+# #gdal.TermProgress( 0.0 )
+# for iY in range(src_ds.RasterYSize):
+# src_data = src_band.ReadAsArray(0,iY,src_ds.RasterXSize,1)
+# col_values = src_data[0] # array of z_values, one per row in source data
+# for iX in range(src_ds.RasterXSize):
+# z_value = col_values[iX]
+# [R,G,B] = MakeColor(z_value, color_dict, maxVal)
+# band1[iY][iX] = R
+# band2[iY][iX] = G
+# band3[iY][iX] = B
+# #gdal.TermProgress( (iY+1.0) / src_ds.RasterYSize )
+#
+# # write each band out
+# dst_ds.GetRasterBand(1).WriteArray(band1)
+# dst_ds.GetRasterBand(2).WriteArray(band2)
+# dst_ds.GetRasterBand(3).WriteArray(band3)
+#
+# # Create jpeg or rename tmp file
+# jpg_driver = gdal.GetDriverByName("JPEG")
+# jpg_driver.CreateCopy(output, dst_ds, 0 )
+#
+# try:
+# os.remove(output_tmp)
+# except:
+# pass
+#
+# try:
+# GDALClose(output_tmp)
+# except:
+# pass
+#
+# try:
+# os.remove(output_tmp)
+# except:
+# pass
+#
+# dst_ds = None
+# writetolog(" finished running tif_to_color_jpeg()", True, False)
+# return True
+#
+#def MakeColor(z_value, color_dict, maxVal):
+#
+#
+# key_list = color_dict.keys()
+# key_list.sort()
+# while len(key_list) > 0:
+# last_val = key_list[-1]
+# #print "lastVal = ",last_val
+# #print "ZVal = ",z_value
+# if z_value >= last_val and z_value <= maxVal:
+# #"print color for ", z_value, " is ", last_val, " = ", color_dict[last_val]
+# return color_dict[last_val]
+# break
+# else:
+# key_list.remove(last_val)
+#
+# #if we get here something is wrong return black
+# #print "Value not found defaulting to black"
+# return [255, 255, 255]
+
+def MDSresponseCol(MDSFile):
+ csvfile = open(MDSFile, "r")
+ reader = csv.reader(csvfile)
+ header = reader.next() #store the header
+ responseCol = header[2]
+ return responseCol
+
+def print_exc_plus( ):
+ """ Print the usual traceback information, followed by a listing of
+ all the local variables in each frame.
+ lifted from the Python Cookbook
+ """
+ msg = ""
+ tb = sys.exc_info( )[2]
+ while tb.tb_next:
+ tb = tb.tb_next
+ stack = [ ]
+ f = tb.tb_frame
+ while f:
+ if r'\sahm\\' in f.f_code.co_filename:
+ stack.append(f)
+ f = f.f_back
+ stack.reverse( )
+ traceback.print_exc( )
+ msg += "\n" + "Locals by frame, innermost last"
+ for frame in stack:
+ msg += "\n"
+ msg += "\n" + "Frame %s in %s at line %s" % (frame.f_code.co_name,
+ frame.f_code.co_filename,
+ frame.f_lineno)
+ msg += "\n"
+ for key, value in frame.f_locals.items( ):
+ msg += "\t%20s = " % key
+ # we must _absolutely_ avoid propagating exceptions, and str(value)
+ # COULD cause any exception, so we MUST catch any...:
+ try:
+ msg += str(value)
+ except:
+ msg += "<ERROR WHILE PRINTING VALUE>"
+
+ msg += "\n\n" + ' '.join([str(i) for i in sys.exc_info()[:2]])
+
+ return msg
+
+def informative_untrapped_error(instance, name):
+ errorMsg = "An error occurred running " + name + ", error message below: "
+ errorMsg += "\n " + ' '.join([str(i) for i in sys.exc_info()[:2]])
+ try:
+ errorMsg += traceback.format_tb(sys.exc_info()[2], 10)[-2]
+ except IndexError:
+ pass
+ writetolog(print_exc_plus(), False, False)
+ raise ModuleError(instance, errorMsg)
+
+def breakpoint():
+ ''' open up the python debugger here and poke around
+ Very helpful, I should have figured this out ages ago!
+ '''
+ QtCore.pyqtRemoveInputHook()
+ import pdb; pdb.set_trace()
+
+def writetolog(*args, **kwargs):
+ '''Uses the SAHM log file writting function
+ but appends our known logfile to the kwargs.
+ '''
+ global _logger
+ _logger.writetolog(*args, **kwargs)
+
+def createLogger(outputdir, verbose):
+ global _logger
+ _logger = utilities.logger(outputdir, verbose)
+
+def getLogger():
+ global _logger
+ return _logger
+
+def getShortName(fullPathName):
+ if fullPathName.endswith('hdr.adf'):
+ shortname = os.path.split(fullPathName)[0]
+ shortname = os.path.split(shortname)[1]
+ else:
+ shortname = os.path.split(fullPathName)[1]
+ shortname = os.path.splitext(shortname)[0]
+ return shortname
+
+def getRasterName(fullPathName):
+ if fullPathName.endswith('hdr.adf'):
+ rastername = os.path.split(fullPathName)[0]
+ else:
+ rastername = fullPathName
+ return rastername
+
+def getModelsPath():
+ return os.path.join(os.path.dirname(__file__), "pySAHM", "Resources", "R_Modules")
+
+def runRScript(script, args, module=None):
+ global config
+ r_path = config.r_path
+ program = os.path.join(r_path, "i386", "Rterm.exe") #-q prevents program from running
+ scriptFile = os.path.join(getModelsPath(), script)
+
+ command = program + " --vanilla -f " + scriptFile + " --args " + args
+
+ p = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
+ writetolog("\nStarting R Processing of " + script, True)
+ writetolog(" args: " + args, False, False)
+ writetolog(" command: " + command, False, False)
+ ret = p.communicate()
+
+ if 'Error' in ret[1]:
+ msg = "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+ msg +="\n An error was encountered in the R script for this module."
+ msg += "\n The R error message is below: \n"
+ msg += ret[1]
+ writetolog(msg)
+ if module:
+ raise ModuleError(module, msg)
+ else:
+ raise RuntimeError , msg
+
+ if 'Warning' in ret[1]:
+ msg = "The R scipt returned the following warning(s). The R warning message is below - \n"
+ msg += ret[1]
+ writetolog(msg)
+
+ del(ret)
+ writetolog("\nFinished R Processing of " + script, True)
+
+def merge_inputs_csvs(inputCSVs_list, outputFile):
+ oFile = open(outputFile, "wb")
+ outputCSV = csv.writer(oFile)
+ outputCSV.writerow(["PARCOutputFile", "Categorical",
+ "Resampling", "Aggregation", "OriginalFile"])
+ for inputCSV in inputCSVs_list:
+ iFile = open(inputCSV, "rb")
+ inputreader = csv.reader(iFile)
+ inputreader.next()
+ for row in inputreader:
+ outputCSV.writerow(row)
+ iFile.close()
+ oFile.close()
+
+def applyMDS_selection(oldMDS, newMDS):
+ """Takes a selection from a previous MDS and '
+ applies it to a new MDS file.
+ """
+ oldvals = {}
+ if os.path.exists(oldMDS):
+ iFile = open(oldMDS, 'r')
+ previousout = csv.reader(iFile)
+ oldheader1 = previousout.next()
+ oldheader2 = previousout.next()
+ oldvals = dict(zip(oldheader1, oldheader2))
+ iFile.close()
+ del previousout
+
+ tmpnewMDS = newMDS + ".tmp.csv"
+ oFile = open(tmpnewMDS, "wb")
+ tmpOutCSV = csv.writer(oFile)
+ iFile = open(newMDS, "rb")
+ outCSV = csv.reader(iFile)
+
+ oldHeader1 = outCSV.next()
+ oldHeader2 = outCSV.next()
+ oldHeader3 = outCSV.next()
+
+ selectionline = []
+ for i in range(len(oldHeader1)):
+ if oldvals.has_key(oldHeader1[i]) and \
+ oldvals[oldHeader1[i]] == '0':
+ selectionline.append('0')
+ else:
+ selectionline.append('1')
+
+ tmpOutCSV.writerow(oldHeader1)
+ tmpOutCSV.writerow(selectionline)
+ tmpOutCSV.writerow(oldHeader3)
+ for row in outCSV:
+ tmpOutCSV.writerow(row)
+
+ iFile.close()
+ oFile.close()
+ shutil.copyfile(tmpnewMDS, newMDS)
+ os.remove(tmpnewMDS)
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/contrib/sahm/widgets.py b/contrib/sahm/widgets.py
new file mode 100644
index 0000000..4defe99
--- /dev/null
+++ b/contrib/sahm/widgets.py
@@ -0,0 +1,369 @@
+from PyQt4 import QtCore, QtGui
+import os
+
+from core.modules.module_configure import StandardModuleConfigurationWidget
+from core.modules.constant_configuration import ConstantWidgetMixin
+
+class PredictorListWidget(QtGui.QTreeWidget):
+
+ def __init__(self, p_value, available_tree, parent=None):
+
+ self.resamplingMethods = ["nearestneighbor",
+ "bilinear",
+ "cubic",
+ "cubicspline",
+ "lanczos"]
+
+ self.aggregationMethods = ["Min",
+ "Mean",
+ "Max",
+ "Majority",
+ "None"]
+
+ #print "p_value : ", p_value
+ QtGui.QTreeWidget.__init__(self, parent)
+ self.available_tree = available_tree
+ self.setColumnCount(5)
+ self.headerItem().setText(0, "Include")
+ self.setColumnWidth(0,100)
+ self.headerItem().setText(1, "Layer")
+ self.setColumnWidth(1,self.width() - 350)
+ self.headerItem().setText(2, "Categorical")
+ self.setColumnWidth(0,90)
+ self.headerItem().setText(3, "Resampling")
+ self.setColumnWidth(2,125)
+ self.headerItem().setText(4, "Aggregation")
+ self.setColumnWidth(0,125)
+# self.setSelectionBehavior(QtGui.QTreeView.SelectRows)
+
+ self.tree_items = {}
+ for source, file_list in self.available_tree.iteritems():
+ #print source, file_list
+ source_item = QtGui.QTreeWidgetItem([source])
+ self.addTopLevelItem(source_item)
+ for (file, desc, categorical) in file_list:
+ child_item = QtGui.QTreeWidgetItem([file, desc])#, resVal, aggVal])
+ child_item.setFlags(QtCore.Qt.ItemIsUserCheckable |
+ QtCore.Qt.ItemIsEnabled)
+ child_item.setCheckState(0, QtCore.Qt.Unchecked)
+ source_item.addChild(child_item)
+
+ resamplingCB = QtGui.QComboBox(self)
+ resamplingCB.addItems(self.resamplingMethods)
+ aggCB = QtGui.QComboBox(self)
+ aggCB.addItems(self.aggregationMethods)
+ catChk = QtGui.QCheckBox(self)
+# self.connect(aggCB, QtCore.SIGNAL('currentIndexChanged(QString)'), self.testing)
+ if categorical == "N":
+ resamplingCB.setCurrentIndex(1)
+ aggCB.setCurrentIndex(1)
+ curVal = (file, "Bilinear", "Mean")
+ catChk.setCheckState(QtCore.Qt.Unchecked)
+ else:
+ resamplingCB.setCurrentIndex(0)
+ aggCB.setCurrentIndex(3)
+ curVal = (file, "NearestNeighbor", "Majority")
+ catChk.setCheckState(QtCore.Qt.Checked)
+
+ self.setItemWidget(child_item, 2, catChk)
+ self.setItemWidget(child_item, 3, resamplingCB)
+ self.setItemWidget(child_item, 4, aggCB)
+
+# print "The file for dict is ", file
+ self.tree_items[curVal] = child_item
+ self.set_values(p_value)
+
+ def set_values(self, str_value):
+ #print 'set_values:', str_value
+ values = []
+ if str_value:
+ values = eval(str_value)
+ files = {}
+ for k in self.tree_items.iterkeys():
+ files[k[0]] = k[1:]
+ for value in values:
+ if value[0] in files.keys():
+ try:
+ oldValue = (value[0], files[value[0]][0], files[value[0]][1])
+ self.tree_items[oldValue].setCheckState(0, QtCore.Qt.Checked)
+ item = self.itemWidget(self.tree_items[oldValue], 2)
+ if value[1] == '1':
+ item.setCheckState(QtCore.Qt.Checked)
+ else:
+ item.setCheckState(QtCore.Qt.Unchecked)
+ item = self.itemWidget(self.tree_items[oldValue], 3)
+ item.setCurrentIndex(self.resamplingMethods.index(value[2]))
+ item = self.itemWidget(self.tree_items[oldValue], 4)
+ item.setCurrentIndex(self.aggregationMethods.index(value[3]))
+ except ValueError:
+ pass
+
+ def get_values(self):
+ #print 'get_values:'
+ values = []
+ for value, item in self.tree_items.iteritems():
+ #print value, item
+ if item.checkState(0) == QtCore.Qt.Checked:
+ if self.itemWidget(item, 2).checkState() == QtCore.Qt.Checked:
+ categorical = '1'
+ else:
+ categorical = '0'
+ resampleMethod = str(self.itemWidget(item, 3).currentText())
+ aggMethod = str(self.itemWidget(item, 4).currentText())
+
+ values.append((value[0], categorical, resampleMethod, aggMethod))
+# print 'get_vals = ', str(values)
+ return str(values)
+
+ def select_all(self):
+ for value, item in self.tree_items.iteritems():
+ self.tree_items[value].setCheckState(0, QtCore.Qt.Checked)
+
+ def switch_selection(self):
+ for value, item in self.tree_items.iteritems():
+ if item.checkState(0) == QtCore.Qt.Checked:
+ self.tree_items[value].setCheckState(0, QtCore.Qt.Unchecked)
+ else:
+ self.tree_items[value].setCheckState(0, QtCore.Qt.Checked)
+
+ def query_add(self, query_text):
+ for value, item in self.tree_items.iteritems():
+ if str(query_text) in value[0]:
+ self.tree_items[value].setCheckState(0, QtCore.Qt.Checked)
+
+
+
+ def query_remove(self, query_text):
+ for value, item in self.tree_items.iteritems():
+ if str(query_text) in value[0]:
+ self.tree_items[value].setCheckState(0, QtCore.Qt.Unchecked)
+
+class PredictorListConfigurationWidget(PredictorListWidget,
+ ConstantWidgetMixin):
+
+ def __init__(self, param, available_tree, parent=None):
+ """__init__(param: core.vistrail.module_param.ModuleParam,
+ parent: QWidget)
+
+ Initialize the line edit with its contents. Content type is limited
+ to 'int', 'float', and 'string'
+
+ """
+ PredictorListWidget.__init__(self, param.strValue, available_tree,
+ parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ # assert param.namespace == None
+ # assert param.identifier == 'edu.utah.sci.vistrails.basic'
+# self.available_tree = available_tree
+# self.setColumnCount(2)
+# for source, file_list in self.available_tree.iteritems():
+# source_item = QtGui.QTreeWidgetItem([source])
+# self.addTopLevelItem(source_item)
+# for (file, desc) in file_list:
+# child_item = QtGui.QTreeWidgetItem([file, desc])
+# child_item.setFlags(QtCore.Qt.ItemIsUserCheckable |
+# QtCore.Qt.ItemIsEnabled)
+# child_item.setCheckState(0, QtCore.Qt.Unchecked)
+# source_item.addChild(child_item)
+
+ contents = param.strValue
+ contentType = param.type
+
+ # need to deserialize contents and set tree widget accordingly
+ # self.setText(contents)
+ self._contentType = contentType
+# self.connect(self,
+# QtCore.SIGNAL('returnPressed()'),
+# self.update_parent)
+
+ def contents(self):
+ """contents() -> str
+ Re-implement this method to make sure that it will return a string
+ representation of the value that it will be passed to the module
+ As this is a QLineEdit, we just call text()
+
+ """
+ return self.get_values()
+
+ def setContents(self, strValue, silent=True):
+ """setContents(strValue: str) -> None
+ Re-implement this method so the widget can change its value after
+ constructed. If silent is False, it will propagate the event back
+ to the parent.
+ As this is a QLineEdit, we just call setText(strValue)
+ """
+# self.setText(strValue)
+# self.update_text()
+# if not silent:
+# self.update_parent()
+ self.set_values(strValue)
+# self.update_text()
+ if not silent:
+ self.update_parent()
+
+# def update_text(self):
+# """ update_text() -> None
+# Update the text to the result of the evaluation
+
+# """
+# # FIXME: eval should pretty much never be used
+# base = expression.evaluate_expressions(self.text())
+# if self._contentType == 'String':
+# self.setText(base)
+# else:
+# try:
+# self.setText(str(eval(str(base), None, None)))
+# except:
+# self.setText(base)
+
+ def sizeHint(self):
+ return QtCore.QSize(912, 912)
+
+# def sizeHint(self):
+# metrics = QtGui.QFontMetrics(self.font())
+# width = min(metrics.width(self.text())+10,70)
+# return QtCore.QSize(width,
+# metrics.height()+6)
+
+ def minimumSizeHint(self):
+ return self.sizeHint()
+
+ ###########################################################################
+ # event handlers
+
+ def focusInEvent(self, event):
+ """ focusInEvent(event: QEvent) -> None
+ Pass the event to the parent
+
+ """
+ self._contents = self.get_values()
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+ QtGui.QTreeWidget.focusInEvent(self, event)
+
+ def focusOutEvent(self, event):
+ self.update_parent()
+ QtGui.QTreeWidget.focusOutEvent(self, event)
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+
+class PredictorListConfiguration(StandardModuleConfigurationWidget):
+ # FIXME add available_dict as parameter to allow config
+ def __init__(self, module, controller, available_tree, parent=None):
+ StandardModuleConfigurationWidget.__init__(self, module, controller,
+ parent)
+
+ # set title
+ if module.has_annotation_with_key('__desc__'):
+ label = module.get_annotation_by_key('__desc__').value.strip()
+ title = '%s (%s) Module Configuration' % (label, module.name)
+ else:
+ title = '%s Module Configuration' % module.name
+ self.setWindowTitle(title)
+ self.build_gui(available_tree)
+
+ def build_gui(self, available_tree):
+ layout = QtGui.QVBoxLayout()
+ # precompute tree so we only load once
+
+ # factor PredictorListConfigurationWidget so that it can be reused in
+ # both cases
+ self.p_value = ''
+ for function in self.module.functions:
+ if function.name == 'value':
+ self.p_value = function.parameters[0].strValue
+ # should just be able to pass this across to the PredictorList config
+ self.list_config = PredictorListWidget(self.p_value, available_tree)
+ layout.addWidget(self.list_config)
+
+ self.buttonLayout = QtGui.QHBoxLayout()
+ self.buttonLayout.setMargin(5)
+ self.okButton = QtGui.QPushButton('&OK', self)
+ self.okButton.setFixedWidth(110)
+ self.buttonLayout.addWidget(self.okButton)
+ self.cancelButton = QtGui.QPushButton('&Cancel', self)
+ self.cancelButton.setShortcut('Esc')
+ self.cancelButton.setFixedWidth(110)
+ self.buttonLayout.addWidget(self.cancelButton)
+
+ self.selectAllButton = QtGui.QPushButton('&Select All', self)
+ self.selectAllButton.setFixedWidth(110)
+ self.buttonLayout.addWidget(self.selectAllButton)
+
+ self.switchSelectionButton = QtGui.QPushButton('&Switch Selection', self)
+ self.switchSelectionButton.setFixedWidth(110)
+ self.buttonLayout.addWidget(self.switchSelectionButton)
+
+ spacerItem = QtGui.QSpacerItem(10, 0, QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
+ self.buttonLayout.addItem(spacerItem)
+
+ self.queryLabel = QtGui.QLabel("Query")
+ self.buttonLayout.addWidget(self.queryLabel)
+
+ self.queryText = QtGui.QLineEdit(self)
+ self.queryText.setFixedWidth(110)
+ self.buttonLayout.addWidget(self.queryText)
+
+ self.addQuery = QtGui.QPushButton('&Add', self)
+ self.addQuery.setFixedWidth(60)
+ self.buttonLayout.addWidget(self.addQuery)
+
+ self.removeQuery = QtGui.QPushButton('&Remove', self)
+ self.removeQuery.setFixedWidth(60)
+ self.buttonLayout.addWidget(self.removeQuery)
+
+ layout.addLayout(self.buttonLayout)
+ self.connect(self.okButton, QtCore.SIGNAL('clicked(bool)'),
+ self.okTriggered)
+ self.connect(self.cancelButton, QtCore.SIGNAL('clicked(bool)'),
+ self.close)
+ self.connect(self.selectAllButton, QtCore.SIGNAL('clicked(bool)'),
+ self.selectAllTriggered)
+ self.connect(self.switchSelectionButton, QtCore.SIGNAL('clicked(bool)'),
+ self.switchSelectionTriggered)
+ self.connect(self.addQuery, QtCore.SIGNAL('clicked(bool)'),
+ self.queryAdd)
+ self.connect(self.removeQuery, QtCore.SIGNAL('clicked(bool)'),
+ self.queryRemove)
+ self.setLayout(layout)
+
+ def okTriggered(self):
+ str_value = self.list_config.get_values()
+ #print str_value, "=?=", self.p_value
+ if str_value != self.p_value:
+# print 'okTriggered:', str_value
+ functions = [('value', [str_value])]
+ self.controller.update_functions(self.module, functions)
+ self.close()
+
+ def selectAllTriggered(self):
+ self.list_config.select_all()
+
+ def switchSelectionTriggered(self):
+ self.list_config.switch_selection()
+
+ def sizeHint(self):
+ return QtCore.QSize(912, 912)
+
+ def queryAdd(self):
+ self.list_config.query_add(self.queryText.text())
+
+ def queryRemove(self):
+ self.list_config.query_remove(self.queryText.text())
+
+def get_predictor_widget(class_name, tree):
+ def __init__(self, param, parent=None):
+ PredictorListConfigurationWidget.__init__(self, param, tree, parent)
+ class_name += "PredictorListWidget"
+ widget_class = type(class_name, (PredictorListConfigurationWidget,),
+ {'__init__': __init__})
+ return widget_class
+
+def get_predictor_config(class_name, tree):
+ def __init__(self, module, controller, parent=None):
+ PredictorListConfiguration.__init__(self, module, controller, tree,
+ parent)
+ class_name += "PredictorListConfig"
+ widget_class = type(class_name, (PredictorListConfiguration,),
+ {'__init__': __init__})
+ return widget_class
diff --git a/contrib/stem/__init__.py b/contrib/stem/__init__.py
new file mode 100644
index 0000000..b8326dd
--- /dev/null
+++ b/contrib/stem/__init__.py
@@ -0,0 +1,6 @@
+name = 'STEM'
+identifier = 'edu.cornell.birds.stem'
+version = '0.0.2'
+
+def package_dependencies():
+ return ['edu.utah.sci.vistrails.rpy']
diff --git a/contrib/stem/code/STEM_Globals.R b/contrib/stem/code/STEM_Globals.R
new file mode 100644
index 0000000..e0907b9
--- /dev/null
+++ b/contrib/stem/code/STEM_Globals.R
@@ -0,0 +1,236 @@
+
+debugOutput <- FALSE
+# Slash direction for directory creation
+platform = "linux"
+# Possibly Spp names info
+
+# Required Packages
+require(rpart)
+require(mgcv)
+require(gbm)
+require(fields)
+require(splancs)
+require(maps)
+require(maptools)
+
+# Source STEM Libraries
+source(paste(code.directory,"stem.library.A.R",sep=""))
+source(paste(code.directory,"stem.library.B.R",sep=""))
+source(paste(code.directory,"stem.library.ST.R",sep=""))
+
+# Source MORE STEM Functions
+#source(paste(code.directory,"STEM_erd.data.creation.R",sep=""))
+source(paste(code.directory,"STEM_erd.srd.data.subsetting.R",sep=""))
+source(paste(code.directory,"STEM_ModelFitting.R",sep="") )
+source(paste(code.directory,"predict.eBird.ST.matrix.R",sep=""))
+source(paste(code.directory,"STEM_st.matrix.cv.average.R",sep=""))
+
+
+## Name of space time matrix sub-directory
+st.matrix.name <- "stm"
+
+## Name of space time matrix ave map sub-directory
+st.matrix.ave.maps <- "stm.ave.maps"
+
+
+
+# ------------------------
+# Select One Species
+# speciesList - a list of vectors. vector[1] = scientificName & vector[2] = commonName
+# ------------------------
+speciesList <- list(
+c("Hylocichla_mustelina", "Wood_Thrush"))
+#c("Cyanocitta_cristata", "Blue_Jay"))
+#c("Euphagus_carolinus", "Rusty_Blackbird"))
+#c("Turdus_migratorius", "American_Robin"))
+#c("Seiurus_aurocapilla", "Ovenbird"),
+#c("Vireo_olivaceus", "Red-eyed_Vireo"))
+#c("Cardinalis_cardinalis", "Northern_Cardinal"))
+#c("Junco_hyemalis", "Dark-eyed_Junco"),
+#c("Piranga_olivacea", "Scarlet_Tanager"))
+#c("Carduelis_pinus", "Pine_Siskin"))
+#c("Hylocichla_mustelina", "Wood_Thrush"))
+#c("Colinus_virginianus", "Northern_Bobwhite"))
+
+# -----------------------------------------------------
+# SRD maximum sample size - this further restricts SRD
+# in addition to ERD spatial restrictions above)
+# -----------------------------------------------------
+srd.max.sample.size <- 5000
+
+## response.family = "bernoulli" or "gaussian"
+response.family <- "bernoulli"
+
+# ----------------------------------------------------------------------
+# Spatial Extent by Point in Rectangle, Polygon, or ShapeFile
+# ----------------------------------------------------------------------
+#spatial.extent.list <- NULL # Full US
+# -----------
+#spatial.extent.list <- list(type = "rectangle",
+# lat.min = 25.0,
+# lat.max = 50.0,
+# lon.min = -130.0,
+# lon.max = -65.0)
+# -----------
+spatial.extent.list <- list(type = "polygon",
+ # data.frame with named vertices x and y
+ polygon.vertices =
+ data.frame(x = c(-85,-85,-70,-70),
+ y = c(35, 50, 50, 35)) )
+# -----------
+#spatial.extent.list <- list(type="shapefile",
+# shape.dir = data.dir.shapefiles,
+# att.selection.column.name = "BCR",
+# # watch capitalization!
+# shape.filename = "bcr.shp",
+# selected.shape.names = c(13))
+# -----------
+#spatial.extent.list <- list(type="shapefile",
+# shape.dir = data.dir.shapefiles,
+# att.selection.column.name = "STATE_NAME",
+# shape.filename = "STATES.shp",
+# selected.shape.names = c("New York"))
+
+
+# -------------------------------------------------------------------
+# Temporal Extent
+# -------------------------------------------------------------------
+temporal.extent.list <- list(begin.jdate = 1,
+ begin.year = 2006,
+ end.jdate = 366,
+ end.year = 2008)
+iii.year <- 2008
+n.intervals.per.year <-52
+n.intervals <- n.intervals.per.year + 1
+jdate.seq <- seq(from = temporal.extent.list[['begin.jdate']], to = temporal.extent.list[['end.jdate']], length = (n.intervals))
+if (n.intervals > 1) {
+ jdate.seq <- round((jdate.seq[2:n.intervals] + jdate.seq[1:(n.intervals-1)])/2)
+}
+year.seq <- rep(iii.year, length(jdate.seq))
+begin.seq <- 1
+end.seq <- length(jdate.seq)
+
+
+
+# ------------------------
+# Select predictors - must be a subset of what is in erd…..
+# ------------------------
+predictor.names <- c("YEAR", "TIME", "DAY",
+ "EFFORT_HRS", "EFFORT_DISTANCE_KM",
+ "NUMBER_OBSERVERS", "HOUSING_DENSITY",
+ "ELEV_NED",
+ "CAUS_TEMP_AVG",
+ "CAUS_TEMP_MIN", "CAUS_TEMP_MAX",
+ "CAUS_PREC", "CAUS_SNOW",
+ "NLCD2001_FS_C11_750_PLAND", "NLCD2001_FS_C12_750_PLAND",
+ "NLCD2001_FS_C21_750_PLAND", "NLCD2001_FS_C22_750_PLAND",
+ "NLCD2001_FS_C23_750_PLAND", "NLCD2001_FS_C24_750_PLAND",
+ "NLCD2001_FS_C31_750_PLAND", "NLCD2001_FS_C41_750_PLAND",
+ "NLCD2001_FS_C42_750_PLAND", "NLCD2001_FS_C43_750_PLAND",
+ "NLCD2001_FS_C52_750_PLAND", "NLCD2001_FS_C71_750_PLAND",
+ "NLCD2001_FS_C81_750_PLAND", "NLCD2001_FS_C82_750_PLAND",
+ "NLCD2001_FS_C90_750_PLAND", "NLCD2001_FS_C95_750_PLAND")
+
+# -------------------------------------------------------------------
+# Data Splitting Parameters
+# -------------------------------------------------------------------
+split.par.list <- list(grid.cell.min.lat = 0.75,
+ grid.cell.min.lon = 0.75,
+ min.val.cell.locs = 2,
+ fraction.training.data=0.8,
+ mfrac=1.0,
+ plot.it=FALSE)
+
+# -------------------------------------------------------------------
+# CV Fold Splitting Parameters
+# -------------------------------------------------------------------
+cv.folds <- 1
+cv.list <- c(1:cv.folds)
+cv.folds.par.list <- list(grid.cell.min.lat = 0.75,
+ grid.cell.min.lon = 0.75,
+ min.val.cell.locs = 2,
+ fraction.training.data = 0.8,
+ mfrac = 1.0,
+ plot.it = FALSE)
+
+# ---------------------------------------------------------------------
+# STEM Ensemble Design
+# ---------------------------------------------------------------------
+iii.scale <- 2 # largest scale in STEM MS ==> current magic value
+stem.init.par.list <- list(
+ # --------------------------------------------------
+ # Spatial Design
+ # --------------------------------------------------
+ spatial.extent.list = NULL,
+ spatial.region.par.list = list(
+ # Number of MC regionalizations for each time interval
+ n.mc.regions=1,
+ # define minimum area & sample size of rectangles
+ regional.cell.min.lat = 3.00*iii.scale,
+ regional.cell.min.lon = 4.00*iii.scale,
+ # Underlying Coverage Grid
+ # Older declarations
+ # grid.cell.min.lat = 1*(iii.scale^0.5), #5 degrees
+ # grid.cell.min.lon = 1.75*(iii.scale^0.5), # 10 degrees
+ # Simplified
+ grid.cell.min.lat = 3.00*iii.scale/3, #5 degrees
+ grid.cell.min.lon = 4.00*iii.scale/3, # 10 degrees
+ n.centers.per.region = 1, # Density Dependent!!!
+ min.data.size = 10),
+ # --------------------------------------------------
+ # Temporal Design:
+ # Slice year into n.intervals prediction points
+ # --------------------------------------------------
+ n.intervals=60, #add 1! # 81 for migration
+ begin.jdate=1 ,
+ end.jdate = 366,
+ season.window.width=40, #40 # Fitting window
+ prediction.window.width=36, #36
+ # --------------------------------------------------
+ # Sampling
+ # --------------------------------------------------
+ sampling.par.list = list(
+ split.by.location = FALSE,
+ # if TRUE uses locs == ensemble.data.locs
+ ST.basis.rotation = FALSE,
+ # if TRUE assumes {lat,lon} ={$y, $ x}
+ # and julian date == $JDATES
+ p.train=0.75))
+
+base.model.par.list <- rpart.control(cp = 0.01, xval = 0, minbucket = 10)
+
+# ---------------------------------------------------------------------
+# conditioning variables
+# ---------------------------------------------------------------------
+
+conditioning.vars <- list(EFFORT_HRS = 1.0,
+ EFFORT_DISTANCE_KM = 1.0,
+ TIME = 7.0,
+ NUMBER_OBSERVERS = 1.0,
+ I.STATIONARY = 0)
+
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+# ST Matrix Maps
+# (AKA Halloween Maps)
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+
+ns.rows <- 40
+map.plot.pixel.width <- 1000
+z.max <- 0.50
+z.min <- 0.0
+map.filename.tag <- "demo."
+state.map <- TRUE
+state.map.lwd <- 1.0
+county.map <- TRUE
+county.map.lwd <- 0.5
+pred.grid.size <- ns.rows
+## map.plot.width <- map.plot.pixel.width
+map.plot.width <- 1000
+## This is duplicated in stem.init.par.list
+spatial.extent.list <- NULL
+map.tag <- map.filename.tag
+date.bar <- TRUE
+print.date <- TRUE
+## KFW resp.transformation.code <- NULL
diff --git a/contrib/stem/code/STEM_Globals.R.bkup b/contrib/stem/code/STEM_Globals.R.bkup
new file mode 100644
index 0000000..e0907b9
--- /dev/null
+++ b/contrib/stem/code/STEM_Globals.R.bkup
@@ -0,0 +1,236 @@
+
+debugOutput <- FALSE
+# Slash direction for directory creation
+platform = "linux"
+# Possibly Spp names info
+
+# Required Packages
+require(rpart)
+require(mgcv)
+require(gbm)
+require(fields)
+require(splancs)
+require(maps)
+require(maptools)
+
+# Source STEM Libraries
+source(paste(code.directory,"stem.library.A.R",sep=""))
+source(paste(code.directory,"stem.library.B.R",sep=""))
+source(paste(code.directory,"stem.library.ST.R",sep=""))
+
+# Source MORE STEM Functions
+#source(paste(code.directory,"STEM_erd.data.creation.R",sep=""))
+source(paste(code.directory,"STEM_erd.srd.data.subsetting.R",sep=""))
+source(paste(code.directory,"STEM_ModelFitting.R",sep="") )
+source(paste(code.directory,"predict.eBird.ST.matrix.R",sep=""))
+source(paste(code.directory,"STEM_st.matrix.cv.average.R",sep=""))
+
+
+## Name of space time matrix sub-directory
+st.matrix.name <- "stm"
+
+## Name of space time matrix ave map sub-directory
+st.matrix.ave.maps <- "stm.ave.maps"
+
+
+
+# ------------------------
+# Select One Species
+# speciesList - a list of vectors. vector[1] = scientificName & vector[2] = commonName
+# ------------------------
+speciesList <- list(
+c("Hylocichla_mustelina", "Wood_Thrush"))
+#c("Cyanocitta_cristata", "Blue_Jay"))
+#c("Euphagus_carolinus", "Rusty_Blackbird"))
+#c("Turdus_migratorius", "American_Robin"))
+#c("Seiurus_aurocapilla", "Ovenbird"),
+#c("Vireo_olivaceus", "Red-eyed_Vireo"))
+#c("Cardinalis_cardinalis", "Northern_Cardinal"))
+#c("Junco_hyemalis", "Dark-eyed_Junco"),
+#c("Piranga_olivacea", "Scarlet_Tanager"))
+#c("Carduelis_pinus", "Pine_Siskin"))
+#c("Hylocichla_mustelina", "Wood_Thrush"))
+#c("Colinus_virginianus", "Northern_Bobwhite"))
+
+# -----------------------------------------------------
+# SRD maximum sample size - this further restricts SRD
+# in addition to ERD spatial restrictions above)
+# -----------------------------------------------------
+srd.max.sample.size <- 5000
+
+## response.family = "bernoulli" or "gaussian"
+response.family <- "bernoulli"
+
+# ----------------------------------------------------------------------
+# Spatial Extent by Point in Rectangle, Polygon, or ShapeFile
+# ----------------------------------------------------------------------
+#spatial.extent.list <- NULL # Full US
+# -----------
+#spatial.extent.list <- list(type = "rectangle",
+# lat.min = 25.0,
+# lat.max = 50.0,
+# lon.min = -130.0,
+# lon.max = -65.0)
+# -----------
+spatial.extent.list <- list(type = "polygon",
+ # data.frame with named vertices x and y
+ polygon.vertices =
+ data.frame(x = c(-85,-85,-70,-70),
+ y = c(35, 50, 50, 35)) )
+# -----------
+#spatial.extent.list <- list(type="shapefile",
+# shape.dir = data.dir.shapefiles,
+# att.selection.column.name = "BCR",
+# # watch capitalization!
+# shape.filename = "bcr.shp",
+# selected.shape.names = c(13))
+# -----------
+#spatial.extent.list <- list(type="shapefile",
+# shape.dir = data.dir.shapefiles,
+# att.selection.column.name = "STATE_NAME",
+# shape.filename = "STATES.shp",
+# selected.shape.names = c("New York"))
+
+
+# -------------------------------------------------------------------
+# Temporal Extent
+# -------------------------------------------------------------------
+temporal.extent.list <- list(begin.jdate = 1,
+ begin.year = 2006,
+ end.jdate = 366,
+ end.year = 2008)
+iii.year <- 2008
+n.intervals.per.year <-52
+n.intervals <- n.intervals.per.year + 1
+jdate.seq <- seq(from = temporal.extent.list[['begin.jdate']], to = temporal.extent.list[['end.jdate']], length = (n.intervals))
+if (n.intervals > 1) {
+ jdate.seq <- round((jdate.seq[2:n.intervals] + jdate.seq[1:(n.intervals-1)])/2)
+}
+year.seq <- rep(iii.year, length(jdate.seq))
+begin.seq <- 1
+end.seq <- length(jdate.seq)
+
+
+
+# ------------------------
+# Select predictors - must be a subset of what is in erd…..
+# ------------------------
+predictor.names <- c("YEAR", "TIME", "DAY",
+ "EFFORT_HRS", "EFFORT_DISTANCE_KM",
+ "NUMBER_OBSERVERS", "HOUSING_DENSITY",
+ "ELEV_NED",
+ "CAUS_TEMP_AVG",
+ "CAUS_TEMP_MIN", "CAUS_TEMP_MAX",
+ "CAUS_PREC", "CAUS_SNOW",
+ "NLCD2001_FS_C11_750_PLAND", "NLCD2001_FS_C12_750_PLAND",
+ "NLCD2001_FS_C21_750_PLAND", "NLCD2001_FS_C22_750_PLAND",
+ "NLCD2001_FS_C23_750_PLAND", "NLCD2001_FS_C24_750_PLAND",
+ "NLCD2001_FS_C31_750_PLAND", "NLCD2001_FS_C41_750_PLAND",
+ "NLCD2001_FS_C42_750_PLAND", "NLCD2001_FS_C43_750_PLAND",
+ "NLCD2001_FS_C52_750_PLAND", "NLCD2001_FS_C71_750_PLAND",
+ "NLCD2001_FS_C81_750_PLAND", "NLCD2001_FS_C82_750_PLAND",
+ "NLCD2001_FS_C90_750_PLAND", "NLCD2001_FS_C95_750_PLAND")
+
+# -------------------------------------------------------------------
+# Data Splitting Parameters
+# -------------------------------------------------------------------
+split.par.list <- list(grid.cell.min.lat = 0.75,
+ grid.cell.min.lon = 0.75,
+ min.val.cell.locs = 2,
+ fraction.training.data=0.8,
+ mfrac=1.0,
+ plot.it=FALSE)
+
+# -------------------------------------------------------------------
+# CV Fold Splitting Parameters
+# -------------------------------------------------------------------
+cv.folds <- 1
+cv.list <- c(1:cv.folds)
+cv.folds.par.list <- list(grid.cell.min.lat = 0.75,
+ grid.cell.min.lon = 0.75,
+ min.val.cell.locs = 2,
+ fraction.training.data = 0.8,
+ mfrac = 1.0,
+ plot.it = FALSE)
+
+# ---------------------------------------------------------------------
+# STEM Ensemble Design
+# ---------------------------------------------------------------------
+iii.scale <- 2 # largest scale in STEM MS ==> current magic value
+stem.init.par.list <- list(
+ # --------------------------------------------------
+ # Spatial Design
+ # --------------------------------------------------
+ spatial.extent.list = NULL,
+ spatial.region.par.list = list(
+ # Number of MC regionalizations for each time interval
+ n.mc.regions=1,
+ # define minimum area & sample size of rectangles
+ regional.cell.min.lat = 3.00*iii.scale,
+ regional.cell.min.lon = 4.00*iii.scale,
+ # Underlying Coverage Grid
+ # Older declarations
+ # grid.cell.min.lat = 1*(iii.scale^0.5), #5 degrees
+ # grid.cell.min.lon = 1.75*(iii.scale^0.5), # 10 degrees
+ # Simplified
+ grid.cell.min.lat = 3.00*iii.scale/3, #5 degrees
+ grid.cell.min.lon = 4.00*iii.scale/3, # 10 degrees
+ n.centers.per.region = 1, # Density Dependent!!!
+ min.data.size = 10),
+ # --------------------------------------------------
+ # Temporal Design:
+ # Slice year into n.intervals prediction points
+ # --------------------------------------------------
+ n.intervals=60, #add 1! # 81 for migration
+ begin.jdate=1 ,
+ end.jdate = 366,
+ season.window.width=40, #40 # Fitting window
+ prediction.window.width=36, #36
+ # --------------------------------------------------
+ # Sampling
+ # --------------------------------------------------
+ sampling.par.list = list(
+ split.by.location = FALSE,
+ # if TRUE uses locs == ensemble.data.locs
+ ST.basis.rotation = FALSE,
+ # if TRUE assumes {lat,lon} ={$y, $ x}
+ # and julian date == $JDATES
+ p.train=0.75))
+
+base.model.par.list <- rpart.control(cp = 0.01, xval = 0, minbucket = 10)
+
+# ---------------------------------------------------------------------
+# conditioning variables
+# ---------------------------------------------------------------------
+
+conditioning.vars <- list(EFFORT_HRS = 1.0,
+ EFFORT_DISTANCE_KM = 1.0,
+ TIME = 7.0,
+ NUMBER_OBSERVERS = 1.0,
+ I.STATIONARY = 0)
+
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+# ST Matrix Maps
+# (AKA Halloween Maps)
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+
+ns.rows <- 40
+map.plot.pixel.width <- 1000
+z.max <- 0.50
+z.min <- 0.0
+map.filename.tag <- "demo."
+state.map <- TRUE
+state.map.lwd <- 1.0
+county.map <- TRUE
+county.map.lwd <- 0.5
+pred.grid.size <- ns.rows
+## map.plot.width <- map.plot.pixel.width
+map.plot.width <- 1000
+## This is duplicated in stem.init.par.list
+spatial.extent.list <- NULL
+map.tag <- map.filename.tag
+date.bar <- TRUE
+print.date <- TRUE
+## KFW resp.transformation.code <- NULL
diff --git a/contrib/stem/code/STEM_ModelFitting.R b/contrib/stem/code/STEM_ModelFitting.R
new file mode 100644
index 0000000..cde239e
--- /dev/null
+++ b/contrib/stem/code/STEM_ModelFitting.R
@@ -0,0 +1,201 @@
+
+
+# --------------------------------------------------------------------
+# --------------------------------------------------------------------
+#
+# cv.folds = 0 : fit complete training data, no splitting
+# cv.folds >= 1: fit nfold data
+#
+# ---------------------------------------------------------------------
+# Fit & Save The bagged rpart Ensemble
+# ------------------------------------------------
+# Note: Ensemble Model information is autmatically stored
+# with the tag ".ensemble.index.RData" in the model directory.
+# This is essential information along with the
+# ensemble parameter list. So we save that too.
+# ----------------------
+# Brieman rpart parameters
+#control=rpart.control(cp=0,xval=0,minsplit=2))
+# Limit infludence of any one point.
+# And for node-level predictions, it means that a
+# single positive value may have a maximum of
+# 1/minbucket. Which was one
+#parms=list(split="information")) # bernoulli deviance
+# Its huge and all the information is in the index file
+# ---------------------------------------------------------------------
+#
+#
+# TO DO:
+# ** Add functionality for
+# keep.data = TRUE,# verbose = TRUE,
+# and check functionality for RNG.seed in the fit.ensemble()
+# routine.
+# --------------------------------------------------------------------
+# --------------------------------------------------------------------
+# DMF 3.19.10 VT Changes
+# * remove creation of stem.results.directories
+stem <- function(train.data,
+ stem.directory,
+ weights = NULL,
+ offset = NULL,
+ response.family = "bernoulli",
+ cv.folds=0,
+ cv.folds.par.list=NULL,
+ stem.init.par.list,
+ base.model.par.list = NULL,
+ keep.data = TRUE,
+ verbose = TRUE,
+ RNG.seed= 12345,
+ block.save.size=100) # (training sample size x block.save.size )
+{# begin function
+# --------------------------------------------------------------------
+# use constant tag value to simplify inputs
+stem.model.tag <- "stem."
+for (iii.cv in 1:cv.folds){
+ print(paste("iii.cv", iii.cv))
+ # -------------------------------------------------------------
+ # Create Directories
+ # -------------------------------------------------------------
+ if (iii.cv == 1) {
+ system(paste("mkdir ",stem.directory,sep=""), intern=TRUE)
+
+ if( "/" != substring(stem.directory, nchar(stem.directory), nchar(stem.directory))) {
+ stem.model.directory <- paste(stem.directory,"/model/",sep="")
+ }
+ else {
+ stem.model.directory <- paste(stem.directory,"model/",sep="")
+ }
+
+ system(paste("mkdir ",stem.model.directory,sep=""), intern=TRUE)
+ }
+ model.dir <- paste(stem.model.directory,
+ "stem.models.", as.character(iii.cv), "/",sep="")
+ ttt.statement <- paste("mkdir ",model.dir,sep="")
+ #print(ttt.statement)
+ system(ttt.statement, intern=TRUE)
+ #results.dir <- paste(stem.directory,
+ # "stem.results.", as.character(iii.cv), "/",sep="")
+ #ttt.statement <- paste("mkdir ",results.dir,sep="")
+ #print(ttt.statement)
+ #system(ttt.statement, intern=TRUE)
+ # -------------------------------------------------------------
+ # Split-Fold Training Data
+ # -------------------------------------------------------------
+ print(paste("cv.folds", cv.folds))
+ if (cv.folds<=0) {
+ cv.train.data <- list(
+ X = train.data$X,
+ y = train.data$y,
+ locs = train.data$loc,
+ jdates = train.data$jdates)
+ }
+ if (cv.folds>0) {
+ D.split <- maximum.coverage.selection(
+ locs=data.frame(
+ x=train.data$locs$x ,
+ y=train.data$locs$y),
+ jdates=train.data$jdates,
+ grid.cell.min.lat = cv.folds.par.list$grid.cell.min.lat, grid.cell.min.lon = cv.folds.par.list$grid.cell.min.lon, min.val.cell.locs = cv.folds.par.list$min.val.cell.locs, fraction.training.data = cv.folds.par.list$fraction.training.data, mfrac = cv.folds.par.list$mfrac, plot.it=cv.folds.par.list$plot.it)
+ cv.train.data <- list(
+ X = train.data$X[ D.split$train.index, ],
+ y = train.data$y[ D.split$train.index ],
+ locs =
+ list(x=train.data$loc$x[ D.split$train.index ],
+ y=train.data$loc$y[ D.split$train.index ]),
+ jdates = train.data$jdates[ D.split$train.index ])
+
+ }
+ # -------------------------------------------------------------
+ # Create Ensemble based on Training Data
+ # -------------------------------------------------------------
+
+ print("creating ensemble")
+ stem.par.list <- create.simple.STEM.ensemble(
+ ensemble.data.locs = cv.train.data$locs,
+ ensemble.data.jdates = cv.train.data$jdates,
+ #ensemble.model.filename = stem.model.tag,
+ # --------------------------------------------------
+ # Spatial Design
+ # --------------------------------------------------
+ spatial.extent.list = stem.init.par.list$spatial.extent.list , #default to train data convex hull
+ spatial.region.par.list = stem.init.par.list$spatial.region.par.list,
+ #~ # Number of MC regionalizations for each time interval
+ #~ n.mc.regions=1,
+ #~ # Underlying Coverage Grid
+ #~ grid.cell.min.lat = 1.5*(iii.scale^0.5), #5 degrees
+ #~ grid.cell.min.lon = 2*(iii.scale^0.5), # 10 degrees
+ #~ n.centers.per.region = 1, # Density Dependent!!!
+ #~ # Maximum Rectangular Region Growth Factor
+ #~ #max.random.scale.factor = 0.25,
+ #~ # define minimum area & sample size of rectangles
+ #~ regional.cell.min.lat = 3.00*iii.scale,
+ #~ regional.cell.min.lon = 4.00*iii.scale,
+ #~ min.data.size = 25),
+ # --------------------------------------------------
+ # Temporal Design:
+ # Slice year into n.intervals prediction points
+ # --------------------------------------------------
+ n.intervals = stem.init.par.list$n.intervals, #add 1! # 81 for migration
+ begin.jdate= stem.init.par.list$begin.jdate,
+ end.jdate = stem.init.par.list$end.jdate,
+ season.window.width= stem.init.par.list$season.window.width, #40 # Fitting window
+ prediction.window.width=stem.init.par.list$prediction.window.width, #36
+ # --------------------------------------------------
+ # Sampling
+ # --------------------------------------------------
+ sample.ensemble.function = sample.ST.ensemble,
+ sampling.par.list = stem.init.par.list$sampling.par.list,
+ #~ split.by.location = FALSE,
+ #~ # if TRUE uses locs == ensemble.data.locs
+ #~ ST.basis.rotation = FALSE,
+ #~ # if TRUE assumes {lat,lon} ={$y, $ x}
+ #~ # and julian date == $JDATES
+ #~ p.train=0.63),
+ # --------------------------------------------------
+ # Prediction
+ # --------------------------------------------------
+ predict.ensemble.function = predict.ST.ensemble)
+# ---------------------------------------------------------------------
+
+ # -------------------------------------------------------------
+ # STEM Fit
+ # -------------------------------------------------------------
+ print("running fit")
+ D.ttt <- fit.ensemble(
+ train.data = cv.train.data,
+ resp.family= response.family,
+ filename = paste(model.dir,stem.model.tag,sep=""),
+ RNG.seed = RNG.seed,
+ ensemble.par.list = stem.par.list,
+ ensemble.weights = weights,
+ block.save.size=block.save.size,
+ control=base.model.par.list)
+ # ------------------------------------------------------------- # Pack additional info into stem.par.list # -------------------------------------------------------------
+ stem.par.list$cv.fold.train.index <- D.split$train.index
+ stem.par.list$realized.sample.par <- D.ttt$realized.sample.par
+ stem.par.list$RNG.seed <- D.ttt$RNG.seed
+ stem.par.list$function.call <- D.ttt$function.call
+ D.stem <- stem.par.list
+ save(D.stem,
+ file = paste(model.dir, "stem.model.par.list.",
+ iii.cv,".RData" , sep = ""))
+ rm(D.stem, D.split, stem.par.list, D.ttt)
+ ## KFW gc()
+ # ------------------------------------------------------------- # Debug output # -------------------------------------------------------------
+ if (debugOutput == TRUE) {
+ print("----- Memory usage before system() call gc() -----")
+ memoryMsg <- paste("Memory info =", gc(verbose=TRUE), sep=" ")
+ print(memoryMsg)
+ print("----- Memory usage before system() call object.size()-----")
+ mem <- sapply(ls(), function(x) object.size(get(x)))
+ print(mem)
+ print("----- Sum of object.size()-----")
+ print(sum(mem))
+ }
+} ## End for (iii.cv in 1:nnn.cv)
+# -----------------------------------------------------------------------------
+# No Return Value Object
+} # end function
+# --------------------------------------------------------------------
+
+
diff --git a/contrib/stem/code/STEM_erd.srd.data.subsetting.R b/contrib/stem/code/STEM_erd.srd.data.subsetting.R
new file mode 100644
index 0000000..36f6004
--- /dev/null
+++ b/contrib/stem/code/STEM_erd.srd.data.subsetting.R
@@ -0,0 +1,273 @@
+#------------------------------------------------------------------------------
+# I envision ERD data creation this way
+# * STEM_erd.data.creation - processes data from CSV files
+# * STEM_erd.data.subsetting - load and further subset data
+#
+# * Consider SRD & ERD data together as a single functional step
+# because they rely on the same parameters
+# ==> subsetting should also be done together
+#
+# Kevin, we will need to talk about how to incorporate
+# your work on ERD & NDVI data creation.
+# In general we want this to extend to other SRD with
+# temporally varying covariates.
+#
+# Kevin, I dont know where this fits
+#------------------------------------------------------------------------------
+# Load NDVI Data
+#-----------------------------------------------------------------------------
+## KFW
+## vegetationIndexData <- read.csv(file="ebird_reference_data/processed_VI_Data_SRD.csv", na.strings = c("NA", "?"))
+#vegetationIndexData <- matrix(scan("ebird_reference_data/custom_vi.txt"), 18880842, 6, byrow=TRUE)
+#print(class(vegetationIndexData))
+#print(nrow(vegetationIndexData))
+#print(ncol(vegetationIndexData))
+
+testRpyCall <- function(object) {
+ print(class(object))
+ print(object)
+}
+
+
+
+#------------------------------------------------------------------------------
+erd.srd.data.subsetting <- function(
+ erd.data.filename, #erd.data.tag,
+ srd.pred.design.filename,
+ spatial.extent.list,
+ temporal.extent.list,
+ ## KFW speciesList,
+ species.name,
+ predictor.names,
+ response.family,
+ srd.max.sample.size,
+ split.par.list,
+ response.truncation.cutoff=20){
+ #---------------------------------------------------------------------------
+ # Load SRD Data #------------------------------------------------------------------------------------------------------------
+ print(srd.pred.design.filename)
+ load(file=srd.pred.design.filename) # pred.data
+ #dim(pred.data$D.pred)
+ #dim(pred.data$locs)
+ # ----------------------------------------------------------------------
+ # Limit Spatial Extent by Point in Rectangle, Polygon, or ShapeFile
+ # ----------------------------------------------------------------------
+ xxx <- pred.data$locs$x
+ yyy <- pred.data$locs$y
+ region.index <- rep(TRUE, nrow(pred.data$D.pred) )
+ if (!is.null(spatial.extent.list)){
+ ## KFW if (spatial.extent.list$type == "rectangle"){
+ if (spatial.extent.list[['type']] == "rectangle"){
+ ttt.index <- (
+ yyy > spatial.extent.list$lat.min &
+ yyy < spatial.extent.list$lat.max &
+ xxx > spatial.extent.list$lon.min &
+ xxx < spatial.extent.list$lon.max )
+ region.index <- (ttt.index & region.index)
+ }
+ ## KFW if (spatial.extent.list$type == "polygon"){
+ if (spatial.extent.list[['type']] == "polygon"){
+ ttt.index <- point.in.polygon(
+ xxx = xxx,
+ yyy = yyy,
+ polygon.vertices =
+ spatial.extent.list$polygon.vertices)
+ region.index <- (ttt.index & region.index)
+ }
+ ## KFW if (spatial.extent.list$type == "shapefile"){
+ if (spatial.extent.list[['type']] == "shapefile"){
+
+ ttt.index <- point.in.shapefile(
+ sites = data.frame(lon=xxx, lat=yyy),
+ shape.dir=spatial.extent.list$shape.dir,
+ shape.filename=spatial.extent.list$shape.filename,
+ att.selection.column.name=
+ spatial.extent.list$att.selection.column.name,
+ selected.shape.names=
+ spatial.extent.list$selected.shape.names)
+ region.index <- (ttt.index & region.index)
+ }
+ } # if (!is.null(spatial.extent.list)){
+ # ------------------
+ # Subset SRD
+ # ------------------
+ srd.data <-NULL
+ srd.data$D.pred <- pred.data$D.pred[region.index, ]
+ srd.data$locs <- pred.data$locs[region.index, ]
+ #dim(pred.data$D.pred)
+ #dim(pred.data$locs)
+ rm(pred.data)
+ ## KFW gc()
+ # ------------------
+ # Subset SRD
+ # DMF 3.17.10
+ # ------------------
+ if (!is.null(srd.max.sample.size)) {
+ if (nrow(srd.data$D.pred) > srd.max.sample.size){
+ ttt.index <- sample(x=c(1:nrow(srd.data$D.pred)),
+ size=srd.max.sample.size)
+ srd.data$D.pred <- srd.data$D.pred[ttt.index, ]
+ srd.data$locs <- srd.data$locs[ttt.index, ]
+ }
+ }
+ # --------------------------
+
+
+ #-----------------------------------------------------------------------------
+ # Load ERD parameter data & Data
+ #
+ # Wish List for erd.data.creation
+ # ** combine data & parameters into a single list object
+ # ** save only index to identify train & test sets. There is no need to
+ # save entire thing twice.
+ #------------------------------------------------------------------------------
+ #erdParameterListFile <- paste(data.dir, erd.data.tag, "erd.data.par.list.RData", sep="")
+ #load(file=erdParameterListFile) #return.list
+ #D.erd.data.par.list <- return.list
+
+ #erdDataFile <- paste(data.dir, D.erd.data.par.list$erd.data.tag, "erd.data.RData", sep="")
+ load(file=erd.data.filename) # erdDataFile) #D
+ # ----------------------------------------------------------------------
+ # Limit Spatial Extent by Point in Rectangle, Polygon, or ShapeFile
+ # ----------------------------------------------------------------------
+ xxx <- D$LONGITUDE
+ yyy <- D$LATITUDE
+ region.index <- rep(TRUE, nrow(D) )
+ if (!is.null(spatial.extent.list)){
+ ## KFW if (spatial.extent.list$type == "rectangle"){
+ if (spatial.extent.list[['type']] == "rectangle"){
+ ttt.index <- (
+ yyy > spatial.extent.list$lat.min &
+ yyy < spatial.extent.list$lat.max &
+ xxx > spatial.extent.list$lon.min &
+ xxx < spatial.extent.list$lon.max )
+ region.index <- (ttt.index & region.index)
+ }
+ ## KFW if (spatial.extent.list$type == "polygon"){
+ if (spatial.extent.list[['type']] == "polygon"){
+ ttt.index <- point.in.polygon(
+ xxx = xxx,
+ yyy = yyy,
+ polygon.vertices =
+ spatial.extent.list$polygon.vertices)
+ region.index <- (ttt.index & region.index)
+ }
+ ## KFW if (spatial.extent.list$type == "shapefile"){
+ if (spatial.extent.list[['type']] == "shapefile"){
+ ttt.index <- point.in.shapefile(
+ sites = data.frame(lon=xxx, lat=yyy),
+ shape.dir=spatial.extent.list$shape.dir,
+ shape.filename=spatial.extent.list$shape.filename,
+ att.selection.column.name=
+ spatial.extent.list$att.selection.column.name,
+ selected.shape.names=
+ spatial.extent.list$selected.shape.names)
+ region.index <- (ttt.index & region.index)
+ }
+ } # if (!is.null(spatial.extent.list)){
+ # -------------------------------------------------------------------
+ # -------------------------------------------------------------------
+ # Limit Temporal Extent
+ # -------------------------------------------------------------------
+ season.index <- rep(TRUE, nrow(D) )
+ if (!is.null(temporal.extent.list)){
+ # Convert JDATE + YEAR to single temporal index
+ begin.tindex <- temporal.extent.list$begin.year +
+ temporal.extent.list$begin.jdate/366
+ end.tindex <- temporal.extent.list$end.year +
+ temporal.extent.list$end.jdate/366
+ D.tindex <- D$YEAR + D$DAY/366
+ season.index <- D.tindex >= begin.tindex &
+ D.tindex <= end.tindex
+ }
+ # -------------------------------------------------------------------
+ # ST extent
+ # -------------------------------------------------------------------
+ regional.seasonal.index <- region.index & season.index
+ sum(regional.seasonal.index)
+ ebirdReferenceDataFrame <- D[regional.seasonal.index, ]
+ rm(D)
+ ## KFW gc(D)
+ #------------------------------------------------------------------------------------------------------------
+ # Train:Test Set Split : maximum coverage, eq wt train-test split
+ #------------------------------------------------------------------------------------------------------------
+ D.split <- maximum.coverage.selection(locs=data.frame(x=ebirdReferenceDataFrame$LONGITUDE ,
+ y=ebirdReferenceDataFrame$LATITUDE),
+ jdates=ebirdReferenceDataFrame$DAY,
+ # vector length n
+ grid.cell.min.lat = split.par.list$grid.cell.min.lat,
+ grid.cell.min.lon = split.par.list$grid.cell.min.lon,
+ min.val.cell.locs = split.par.list$min.val.cell.locs,
+ fraction.training.data = split.par.list$fraction.training.data,
+ mfrac = split.par.list$mfrac,
+ plot.it=split.par.list$plot.it)
+ # -----------------------------------------------
+ train.index <- D.split$train.index
+ test.index <- D.split$test.index
+ rm(D.split)
+ ## KFW response.index <- names(ebirdReferenceDataFrame) %in% speciesList[[1]][1]
+ response.index <- names(ebirdReferenceDataFrame) %in% species.name
+ predictors.index <- names(ebirdReferenceDataFrame) %in% predictor.names
+ train.data <- NULL
+ test.data <- NULL
+ # ---------------------
+ train.data$X <- ebirdReferenceDataFrame[train.index, predictors.index]
+ ttt.y <- ebirdReferenceDataFrame[, response.index]
+ train.data$y <- ttt.y[train.index]
+ rm(ttt.y)
+ train.data$locs$x <- ebirdReferenceDataFrame$LONGITUDE[train.index]
+ train.data$locs$y <- ebirdReferenceDataFrame$LATITUDE[train.index]
+ train.data$jdates <- ebirdReferenceDataFrame$DAY[train.index]
+ # ------------------------------------
+ test.data$X <- ebirdReferenceDataFrame[test.index,predictors.index]
+ ttt.y <- ebirdReferenceDataFrame[, response.index]
+ test.data$y <- ttt.y[test.index]
+ rm(ttt.y)
+ test.data$locs$x <- ebirdReferenceDataFrame$LONGITUDE[test.index]
+ test.data$locs$y <- ebirdReferenceDataFrame$LATITUDE[test.index]
+ test.data$jdates <- ebirdReferenceDataFrame$DAY[test.index]
+ # --------------------------------------------
+ rm(ebirdReferenceDataFrame)
+ # ----------------------------------------------------------------------
+ # ERD parameters
+ # ----------------------------------------------------------------------
+ #protocol.tag <- D.erd.data.par.list$protocol.tag
+ #c("traveling","stationary") #,"casual.obs")
+ #if (D.erd.data.par.list$response.type == "occurrence") {
+ # resp.family <- "bernoulli" # "gaussian" or "bernoulli"
+ # }
+ #if (D.erd.data.par.list$response.type == "abundance"){
+ # resp.family <- "gaussian" # "gaussian" or "bernoulli"
+ # }
+ # --------------------------------
+ if ( response.family =="bernoulli") {
+ # ------------------------------------
+ # Logical - where the predicted response is the
+ # probability of a positive/True class
+ # -------------------------------------
+ train.data$y <- as.factor( train.data$y > 0) # TRUE if positive
+ test.data$y <- as.factor( test.data$y > 0) # TRUE if positive
+ }
+ # Create Truncated Gaussian Response
+ if ( response.family == "gaussian"){
+ #
+ # truncate responses @ 10
+ #sum(train.data$y > response.truncation.cutoff)
+ train.data$y[train.data$y > response.truncation.cutoff] <- response.truncation.cutoff
+ test.data$y[test.data$y >response.truncation.cutoff] <- response.truncation.cutoff
+ }
+# --------------------------------------------------------------------------
+ return.list <- list(
+ train.index = train.index,
+ test.index = test.index,
+ #protocol.tag=protocol.tag,
+ response.family=response.family,
+ train.data = train.data,
+ test.data = test.data,
+ srd.data = srd.data)
+# --------------------------------------------------------------------------
+ return(return.list)
+ }
+# --------------------------------------------------------------------------
+
+
diff --git a/contrib/stem/code/STEM_st.matrix.cv.average.R b/contrib/stem/code/STEM_st.matrix.cv.average.R
new file mode 100644
index 0000000..7d62b24
--- /dev/null
+++ b/contrib/stem/code/STEM_st.matrix.cv.average.R
@@ -0,0 +1,95 @@
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+# Compute ST Matrix fold-average
+# # DMF 3.19.10
+#
+# The fold-average st.mat predictions produces
+# a single ST matrix object and stores it in the output dir.
+#
+# The idea here is the ST matrix handle is the directory name
+# So, different ST matrices need to live in different directories
+# because each directory will have the same file names.
+#
+# Remember, we are assuming that the loc list is identical for
+# all cv.folds.
+#
+#
+#
+# Inputs
+# stem.dir
+# st.matrix.input.name
+# jdate.seq
+# year.seq
+# Outputs:
+# ST.matrix
+#
+#
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+st.matrix.cv.average <- function(
+ stem.directory, #=stem.directory
+ st.matrix.input.directory, # st.matrix project name #st.matrix.file.tag, # = "demo."
+ cv.list, # = c(1:cv.folds)
+ jdate.seq = jdate.seq,
+ year.seq = year.seq,
+ st.matrix.output.directory){
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+
+ if ("/" == substring(st.matrix.input.directory, nchar(st.matrix.input.directory), nchar(st.matrix.input.directory))) {
+ st.matrix.directory <- st.matrix.input.directory
+ }
+ else {
+ st.matrix.directory <- paste(st.matrix.input.directory, "/", sep="")
+ }
+
+ if ("/" == substring(st.matrix.output.directory, nchar(st.matrix.output.directory), nchar(st.matrix.output.directory))) {
+ st.matrix.output.directory <- st.matrix.output.directory
+ }
+ else {
+ st.matrix.output.directory <- paste(st.matrix.output.directory, "/", sep="")
+ }
+
+ system(paste("mkdir ", st.matrix.output.directory,sep=""), intern=TRUE)
+# -----------------
+for (iii in 1:length(jdate.seq)){
+ cv.pred <- NULL
+ for (iii.cv in cv.list){
+ # --------------------------------------------------------------------
+ # Load data into (location, time) matrix
+ # --------------------------------------------------------------------
+ #results.dir <- paste(stem.directory,"stem.results.",iii.cv, "/",sep="")
+ #stem.ST.matrix.file.tag <-
+ # paste(results.dir,st.matrix.file.tag,"st.matrix.",sep="")
+ results.dir <- paste(st.matrix.directory, "st.matrix.",
+ as.character(iii.cv), "/",sep="")
+ stem.ST.matrix.file.tag <-
+ paste(results.dir,"st.matrix.",sep="")
+ stp.name <- paste(stem.ST.matrix.file.tag,".",iii,".RData",sep="")
+ load(stp.name) # st.pred
+ #names(st.pred) #xxx yyy pred sd
+ if (iii.cv == cv.list[1]) cv.pred <- st.pred$pred
+ if (iii.cv != cv.list[1]) cv.pred <- cv.pred + st.pred$pred
+ } # iii.cv
+ st.pred$pred <- cv.pred/length(cv.list)
+ # -----------------------
+ # Save st.pred
+ # -----------------------
+ # map.dir
+ cv.ave.st.pred.filename <- paste(st.matrix.output.directory,
+ "st.matrix..",iii,".RData",sep="")
+
+ save(st.pred, file = cv.ave.st.pred.filename) # st.pred
+} # end iii - intervals
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+} # end function
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+
+
+
+
+
+
+
diff --git a/contrib/stem/code/predict.eBird.ST.matrix.R b/contrib/stem/code/predict.eBird.ST.matrix.R
new file mode 100644
index 0000000..e46cd31
--- /dev/null
+++ b/contrib/stem/code/predict.eBird.ST.matrix.R
@@ -0,0 +1,200 @@
+
+
+# --------------------------------------------------------------------
#
+# ==> This function is just a CV wrapper to
+# predict.st.matrix.ebird.ref.data!!!
+# ==> Also new is the creation of an "index" file
+# to hold all of the parameters needed to describe
+# the st.matrix (file sequence)
+#
+#
+# The ST Matrix:
+# ------------------
+# Basis for predictive experiments or ST analysis
+# is predictions across a region in space and across.
+# Often we want to know how spatial distrivution changed shrought time.
+#
+# Conceptually the ST Matrix as a data object is a set of
+# prediction across a lattice in space and time.
+# The st.matrix data object is a sequence of files
+# Each one contains the predictions across a set of locations
+# during a single time step.
+# Each file in the sequence contains the predictions across
+# the same set of locations evaluated at each of times
+# in the temporal sequence.
+#
+# One set of ST.matrix files is written for each CV-fold
+# model in cv.list
+#
+# The ST matrix can be thougth of as a source of psuedo-data
+# with 3 added benefits:
+# 1) Cleaned
+# 2) Filled In
+# 3) Uncertainty Estimates
+#
+#
+# File Namining Conventions
+# ---------------------------
+#
+#
+# Naming Standards are being hardcoded for convenience/simplicity
+# For example, one stem analysis per directory means that the
+# STEM objects are uniquely identified by the directory name.
+# So, I fixed the model names by hardcoding
+# stem.model.tag <- "stem."
+#
+# st.matrix Names = paste(results.dir,st.matrix.file.tag,"st.matrix.",
+# [sequence number], ".RData",sep="")
+# These are kept in the CV result directories
+# because they are CV specific.
+#
+# --------------------------------------------------------------------
# --------------------------------------------------------------------
+# DMF 3.19.10 VT modifications
+# * change formal parameter st.matrix.name, # st.matrix project name
+predict.erd.st.matrix <- function(
+ stem.directory, # equivalent to stem.object
+ pred.data, #= srd.data,
+ cv.list, # subset of cv's
+ stem.predictor.names,
+ # --------------
+ st.matrix.name, # st.matrix project name
+ #st.matrix.directory,
+ jdate.seq,
+ year.seq,
+ conditioning.vars){ #= conditioning.vars)
+# --------------------------------------------------------------------
+ stem.model.tag <- "stem." #hardcoded for convenience
+
+ print("**********")
+ print(stem.directory)
+
+
+ if ("/" == substring(stem.directory, nchar(stem.directory), nchar(stem.directory))) {
+ st.matrix.directory <- paste(stem.directory, st.matrix.name, "/", sep="")
+ stem.model.directory <- paste(stem.directory, "model", "/", sep = "")
+ }
+ else {
+ st.matrix.directory <- paste(stem.directory, "/", st.matrix.name, "/", sep="")
+ stem.model.directory <- paste(stem.directory, "/", "model", "/", sep="")
+ }
+
+ system(paste("mkdir ",st.matrix.directory, sep=""), intern=TRUE)
+
+# ---------------------------
+for (iii.cv in cv.list){
+ results.dir <- paste(st.matrix.directory, "st.matrix.",
+ as.character(iii.cv), sep = "")
+ system(paste("mkdir ",results.dir,sep=""), intern=TRUE)
+ # ------
+ model.dir <- paste(stem.model.directory, "stem.models.",
+ as.character(iii.cv), "/", sep="")
+ stem.ST.matrix.file.tag <-
+ paste(results.dir,"/", "st.matrix.",sep="")
+ ## Load nfold specific parameter list
+ load(file = paste(model.dir,
+ "stem.model.par.list.", iii.cv, ".RData" , sep = "")) # D.stem
+ # ----------------------------
+ # Write ST.Matrix object to stem.results directories
+ # ----------------------------
+
+ print(names(pred.data$D.pred))
+ print(nrow(pred.data$D.pred))
+
+
+ predict.st.matrix.ebird.ref.data(
+ prediction.design = pred.data$D.pred,
+ prediction.design.locs = pred.data$locs,
+ # prediction.design.jdates, #not needed here
+ #--------------
+ model.predictor.names = stem.predictor.names,
+ model.filename = #stem.model$ensemble.model.filename,
+ paste(model.dir, stem.model.tag,sep=""),
+ ensemble.par.list = D.stem, #stem.model, #ensemble.par.list,
+ # --------------
+ save.name = stem.ST.matrix.file.tag,
+ # Temporal Sequence
+ jdate.seq =jdate.seq,
+ year.seq =year.seq,
+ # Conditioning Vars - Observation Process Design
+ conditioning.vars = conditioning.vars)
+ # ----------------------
+ # Save Index File
+ # ----------------------
+ st.matrix.list <- list(
+ stem.directory = stem.directory,
+ pred.data.locs = pred.data$locs,
+ cv.number=iii.cv, # subset of cv's
+ stem.predictor.names=stem.predictor.names,
+ # --------------
+ st.matrix.name = st.matrix.name,
+ jdate.seq = jdate.seq,
+ year.seq = year.seq,
+ conditioning.vars=conditioning.vars)
+ filename.tag <-
+ paste(results.dir,"st.matrix.list.",iii.cv,".RData",sep="")
+ save(st.matrix.list, file=filename.tag)
+ # ------------------
+ ## KFW DF
+ ## Local memory recovery block
+ rm(D.stem,st.matrix.list)
+ ## KFW gc()
+} # end iii.cv - data folds
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+## Clear the deck
+rm(list = c("bs.rpart.maps", "conditioning.vars", "create.pd.grid",
+ "create.simple.STEM.ensemble", "D", "data.filename",
+ "D.erd.data.par.list", "D.erd.test.data.par.list",
+ "D.erd.train.data.par.list", "deviance.explained",
+ "ebirdReferenceDataFrame", "ensemble.partial.dependence",
+ "equal.wt.max.coverage.selection", "erdDataFile", "erdParameterListFile",
+ "exp.name", "fit.ensemble", "fit.stem", "halloween.maps", "iii.cv",
+ "iii.year", "initizalize.map.grid", "jdate.seq", "make.erd.data",
+ "make.functional.data.design.matrix", "make.SPAT.COVAR.pred.data",
+ "make.spatial.erd.prediction.design", "map.tag",
+ "maximum.coverage.selection", "model.dir", "monthly.maps", "n.intervals",
+ "n.intervals.per.year", "n.red", "plot.diagnostics",
+ "plot.STEM.temporal.design", "plot.ST.ensemble", "plot.vi.bdt",
+ "point.in.polygon", "point.in.polygon.contours", "point.in.shapefile",
+ "poisson.accuracy", "poisson.deviance", "poisson.pearson", "pop.rpart",
+ "pred.data", "predictive.performance", "predictors.index",
+ "predict.stem.ST.matrix", "predict.ST.ensemble", "predict.st.matrix",
+ "predict.st.matrix.ebird.ref.data", "protocol.tag", "resp.family",
+ "response.index", "response.truncation.cutoff", "results.dir", "return.list",
+ "rotate.ST.basis.pred", "rotate.ST.basis.sample",
+ "rpart.ensemble.diagnostics", "sample.ST.ensemble", "seasonal.window",
+ "smooth.st.predictions", "spatial.density.contours",
+ "spatial.performance.plot", "spp.common.name", "spp.dir", "spp.list",
+ "stateMapEnv", "stem.map.inference.split", "STEM.partial.dependence",
+ "stem.ST.matrix.file.tag", "st.ttt.pred", "summarize.ensemble",
+ "summary.1D.PD.ensemble", "surface.maps", "test.set.prediction.filename",
+ "ttsplit", "ttt.statement", "unique.locs.splitting",
+ "year.seq", "zzz.max"))
+if (debugOutput == TRUE) {
+ rm(list = c("mem", "memoryMsg"))
+}
+## KFW gc()
+# --------------------------------------------------------------------------
+} #end function
+# --------------------------------------------------------------------------
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/contrib/stem/code/stem.library.A.R b/contrib/stem/code/stem.library.A.R
new file mode 100644
index 0000000..60b9074
--- /dev/null
+++ b/contrib/stem/code/stem.library.A.R
@@ -0,0 +1,2088 @@
+
+#--------------------------------------------------------------------------------
+# Predictive.Ensemble.Modeling.Library
+# 1.22.09
+# DMF
+#
+#
+#--------------------------------------------------------------------------------
+#
+# One Stop Shopping for BDT's
+# Bigger vision - this is a flexible bootstrap CV wrapper
+# for predictive modeling.
+#
+#
+# 3.11.09 - Added New STEM Spatial Design
+# Tested standalone
+#
+# Tested with Demo - performed favorably on NE Norcar data
+# compared with BDT!!! Bernoulli -
+# spatial design - no temporal segmentation.
+#
+#New Strategy for saving smaller rpart objects.
+# ----------------------------------------------------
+#Sucess = saving minimal structure for making predicitons
+# & CALCULATING diagnostics (VI's)
+#Test:
+#Pass data frame to predict function.
+#How big are the terms?
+#Can they be left out and still make preds & VI's?
+#--------------------------------------
+# ans <- list(frame = frame, where = where, call = call,
+# terms = Terms, cptable = t(rp$cptable), splits = splits,
+# method = method, parms = init$parms, control = controls,
+# functions = functions)
+# class(ans) <- "rpart"
+#
+#
+# 4/15
+# -------
+# ** sample.ST.ensemble - fixed temporal index problem
+# ** predict.ST.ensemble - fixed temporal index problem
+# ** fixed response factor input
+# ==> This means that the ST ensemble is finally doing
+# what I THOUGHT it was doing all the time.
+# ** reduced memory footprint & speed up run times
+# ==> Run very many more small models - improving
+# ensemble depth.
+#
+# 4.15 TO DO LIST:
+# -------------------------
+# ** Batch processing for Partial Calculations
+# ** I need to figure out some logic to deal with possibilites
+# of region-seasons that do not contain any data, or
+# perhaps do not contain any sampled training data.
+# this will affect sample.ST.ensemble
+# create.ST.ensemble - one option may be to simply exclude them
+# and fit.ST.ensemble & predict.ST.ensemble
+# ** Need to make location information names and parameters
+# consistent across all ST.ensmble functions
+# This means do not assume that train.data$X$x & $X$y are there!!
+# ** sample.ST.ensemble
+# ** missing logic for sampling options
+# ** currently writing $X.loc to the GLOBAL instance
+# of ensemble.par.list. This is BAD - and unnecessary
+# need to clean logic.
+#
+#
+#
+# predict.ST.ensemble - Assumes existance of
+# prediction.design$x, $y, & $JDATE
+#
+#
+#--------------------------------------------------------------------------------
+
+
+
+# ---------------------------------------------------------------------
+# ---------------------------------------------------------------------
+# FUNCTION: Fit and Save BDT Ensemble
+# ---------------------------------------------------------------------
+# ---------------------------------------------------------------------
+# D.Fink
+# Cornell Lab of Ornithology
+# Department of Statistical Science
+# 7.14.08
+#
+# Description
+# -------------
+#
+# Usage:
+# --------
+#
+# Arguments:
+# -----------
+# y response vector
+# X matrix/data.frame of predictors only!!!
+# one predictor per column. Describe how predictors enter model
+# as main effects and interactions of smooth & nonsmooth funcitional
+# forms. Invariant to Monotone transformations.etc.
+# ensemble.weights = from ben's experience rpart likes variances (as
+# opposed to sd or reciprocals of ...)
+# it looks like gam likes st.dev.
+#
+# Value
+# --------
+# ib.sample.index = logical matrix dimension (n x bs.trials)
+# indicates training samples for each ensemble
+#
+# Details
+# --------
+#
+# TO DO List
+# -------------
+#
+# 3.25.09 Added code to pass weights to rpart
+#
+# 4.14.09
+# -------------
+# Modified code to save oob. & ib.sample.index's
+# ** in batches
+# ** to separate file sets
+# This in order to reduce the memory overhead.
+# Both of these matrices were being stored as
+# size = N x (# of ensemble model).
+# Moreover, I almost never use this information for predictions.
+# So, I am going to write it to disk , just in case.
+# Meanwhile - The index file has been modified to hold:
+# # * Number of models in ensemble
+# # * ensemble resp.family
+# # * realized.sample.par
+# and I might add the ensemble.par.list for good measure.
+#
+#
+# **** I NEED LOGIC TO CHECK FOR "NULL" SAMPLES!!!
+#
+#
+# ---------------------------------------------------------------------
+# ---------------------------------------------------------
+# Design Notes:
+#
+# * Individual-Model Paramters will pass through, since cant anticipate
+# how to handle parameters from other models!!!
+# * Ensemble Parameters will be passed with a dedicated list name
+# since this is something that I CAN control
+# ---------------------------------------------------------
+fit.ensemble <- function(
+ train.data,
+ resp.family,
+ RNG.seed = NULL,
+ #sample.ensemble.function,
+ ensemble.par.list=NULL,
+ filename,
+ ensemble.weights=NULL,
+ block.save.size=100, # (training sample size x block.save.size )
+ # Model Parameter Pass Through
+ ...){
+ # ---------------------------------------------------------
+ # Inits
+ # ---------------------------------------------------------
+ function.call <- match.call()
+ ib.sample.index <- NULL
+ oob.sample.index <- NULL
+ realized.sample.par <- NULL
+ n <- length(train.data$y)
+ ensemble.trials <- ensemble.par.list$n.ensemble.models
+ # -----------------------------------------------
+ if (resp.family=="gaussian") bs.method <- "anova"
+ if (resp.family=="bernoulli") bs.method <- "class"
+ if (resp.family=="multiclass") bs.method <- "class"
+ if (resp.family=="poisson") bs.method <- "poisson"
+ # ---------------------------------------------------------
+ # Bootstrap Samples
+ # ---------------------------------------------------------
+ block.number <- 1
+ for (iii in 1:ensemble.trials) {
+ # -------------------------------------
+ # RNG.seed parameter
+ # ------------------------------------------------
+ if (iii==1 & !is.null(RNG.seed)) set.seed(RNG.seed)
+ # --------------------------
+
+ sample.data <- ensemble.par.list$sample.ensemble.function(
+ ensemble.model.number = iii,
+ ensemble.data = train.data,
+ ensemble.par.list = ensemble.par.list,
+ diagnostic.plot = FALSE)
+
+ #cat("fe: iii,",iii, " length(yyy)=", length(sample.data$y),
+ # sum(is.na(sample.data$y)) "\n")
+ #cat("fit.ensemble: iii,",iii, " sum(is.na(yyy))=", sum(is.na(sample.data$y)), "\n")
+ #if (length(sample.data$y) == sum(is.na(sample.data$y)) ){
+ # print(sample.data$y)
+ #}
+ # ---------------------------------------------
+ # Fit Ensemble Member with sampled data
+ # ---------------------------------------
+ # First check for weights
+ if (is.null(ensemble.weights)) {
+ f.rpart <- try(rpart( yyy ~ .,
+ data= data.frame(yyy=sample.data$y,sample.data$X),
+ method=bs.method,
+ ...))
+ # If there is an error, try it again
+ if (class(f.rpart) == "try-error") {
+ cat("fit.ensemble: rpart error \n")
+ f.rpart <- try(rpart( yyy ~ .,
+ data= data.frame(yyy=sample.data$y,sample.data$X),
+ method=bs.method,
+ ...))
+ }
+ }
+ else {
+ f.rpart <- try(rpart( yyy ~ .,
+ data= data.frame(yyy=sample.data$y,sample.data$X),
+ weights= ensemble.weights[sample.data$ib.num.ind],
+ method=bs.method,
+ ...))
+ # If there is an error, try it again
+ if (class(f.rpart) == "try-error") {
+ cat("fit.ensemble: rpart error \n")
+ f.rpart <- try(rpart( yyy ~ .,
+ data= data.frame(yyy=sample.data$y,sample.data$X),
+ weights= ensemble.weights[sample.data$ib.num.ind],
+ method=bs.method,
+ ...))
+ }
+ }
+ # ----------------------
+ # Save Ensemble Model
+ #-----------------------
+ num.txt <- formatC(iii, format="fg", width=6)
+ num.txt <- chartr(" ","0",num.txt)
+ temp.filename <- paste(filename,".",num.txt,".RData",sep="")
+ if (iii == 1) save(f.rpart, file=temp.filename)
+ if (iii > 1) {
+ rpart.parts <-
+ list( frame = f.rpart$frame,
+ where = f.rpart$where, # - vector
+ splits= f.rpart$splits, #- numeric matrix
+ cptable = f.rpart$cptable)
+ if (sum(names(f.rpart) == "csplit") > 0)
+ rpart.parts$csplit <- f.rpart$csplit
+ save(rpart.parts, file=temp.filename)
+ }
+ # --------------------------------
+ # Save sampled data information
+ # --------------------------------
+ ttt.logical <- rep(FALSE, n)
+ ttt.logical[sample.data$oob.num.ind] <- TRUE
+ oob.sample.index <- cbind(oob.sample.index, ttt.logical)
+ ttt.logical <- rep(FALSE, n)
+ ttt.logical[sample.data$ib.num.ind] <- TRUE
+ ib.sample.index <- cbind(ib.sample.index, ttt.logical)
+ # ----------------
+ realized.sample.par <- cbind(realized.sample.par, sample.data$realized.par)
+
+ # ----------------------------------------------------
+ # Block Save of Sampling Index Information
+ # ----------------------------------------------------
+ if ( round(iii/block.save.size) == (iii/block.save.size)) {
+ return.list <- list(oob.sample.index = oob.sample.index,
+ ib.sample.index = ib.sample.index,
+ realized.sample.par = realized.sample.par,
+ function.call = function.call)
+ temp.filename <- paste(filename,".bs.sampling.index.", block.number,".RData",sep="")
+ save(return.list, file=temp.filename)
+ # -------------------------------
+ # Reinitialize Results
+ # -------------------------------
+ ib.sample.index <- NULL
+ oob.sample.index <- NULL
+ # Next block number
+ block.number <- block.number + 1
+ }
+ }# End for(iii) :Bootstrap
+
+ # ---------------------------------------------------------
+ # ----------------------------------------------------
+ # Final Block Save of Sampling Index Information
+ # ----------------------------------------------------
+ if (!is.null(oob.sample.index)){
+ return.list <- list(oob.sample.index = oob.sample.index,
+ ib.sample.index = ib.sample.index,
+ realized.sample.par = realized.sample.par,
+ function.call = function.call)
+ temp.filename <- paste(filename,".bs.sampling.index.",
+ block.number,".RData",sep="")
+ save(return.list, file=temp.filename)
+ rm(ib.sample.index)
+ rm(oob.sample.index)
+ ## KFW gc()
+ }
+ # ---------------------------------------------------------
+ # Return Value
+ # ** I need to return enough information to act as a
+ # handle to the ensemble for prediction, diagnostics, etc.
+ # ** Save all this information as a header/providence
+ # index file with the ensemble itself
+ # ---------------------------------------------------------
+ rm(rpart.parts)
+ rm(num.txt)
+ return.list <- list(realized.sample.par = realized.sample.par,
+ resp.family=resp.family,
+ RNG.seed = RNG.seed,
+ block.save.size=block.save.size,
+ function.call = function.call)
+ temp.filename <- paste(filename,".ensemble.index.RData",sep="")
+ save(return.list, file=temp.filename)
+
+ return(return.list)
+}# End FUNCTION
+# ---------------------------------------------------------
+
+
+
+
+
+# ---------------------------------------------------------------------
+# This is a simple function to compute
+# OOB Predictions,
+# SD,
+# OOB Matrix,
+# * Handle NA's for samples that have not been predited
+# OOB. This is more of a concern when the number of
+# bootstraps is small.
+#
+#
+# OUTPUT:
+# count = (n x 1) vector count of BS reps for each obs
+# mean = (n x 1) vector count of BS reps for each obs
+# sd = OOB.sd,
+# matrix = OOB.pred.index)
+#
+# predict.oob.bdt
+# ---------------------------------------------------------------------
+#predict.oob.bdt <- function(filename, X.train){
+## ---------------------------------------------------------------------
+# # ---------------------------------------------------------
+# # Inits
+# # ---------------------------------------------------------
+# temp.filename <- paste(filename,".ensemble.index.RData",sep="")
+# load(file=temp.filename) #return.list
+# # ---------------------------------------------------------
+# # OOB Predictions - Means & SD's
+# # ---------------------------------------------------------
+# #KISS-Predict entire training set, then extract OOB preds
+# training.pred <- predict.bdt(
+# filename = filename, #model specific stuff stored here
+# prediction.design=X.train)
+# OOB.pred.index <- training.pred$matrix
+# OOB.pred.index[return.list$ib.sample.index==TRUE] <- NA
+# # -------------------
+# OOB.count <- apply(!return.list$ib.sample.index, 1, sum)
+# OOB.pred <- apply(OOB.pred.index, 1, mean, na.rm = TRUE)
+# OOB.sd <- apply(OOB.pred.index, 1, sd, na.rm = TRUE)
+# # ---------------------------------------------------------
+# # Return Value
+# # ---------------------------------------------------------
+# return.list <- list(
+# count = OOB.count,
+# mean = OOB.pred,
+# sd = OOB.sd,
+# matrix = OOB.pred.index)
+# return(return.list)
+## ---------------------------------------------------------
+#}# END OOB FUNCTION
+## ---------------------------------------------------------------------
+## ---------------------------------------------------------------------
+#
+
+# -------------------------------------------------------------------
+# -------------------------------------------------------------------
+# Variable Importances & Summaries
+# DT-rpart Specific Diagnostics
+# -------------------------------------------------------------------
+# -------------------------------------------------------------------
+# var.imp[ ,1]
+# a vector of all the variable importances measured as the empirical
+# improvement in the splitting criterion. Importances are in the
+# same order as the columns in X (design matrix).
+# See above notes for more info.
+# var.imp[ ,2]
+# variable importance weighted by height in tree
+# var.imp[ ,3]
+# variable importance weighted by support - number of data pts affected by
+# split. I need to look at code
+#
+# leaf.count = # of terminal leafs
+# ave.leaf.obs = average number of observations per leaf
+# min.leaf.obs = minimum number of observation in leaf
+# (this value is controled by min.bucket too!)
+#
+# -------------------------------------------------------------------
+rpart.ensemble.diagnostics <- function(
+ filename,
+ ensemble.par.list,
+ X,
+ ensemble.index=NULL){
+# -------------------------------------------------------------------
+
+ # ---------------------------------------------------------
+ # Inits
+ # ---------------------------------------------------------
+
+ bs.trials <- ensemble.par.list$n.ensemble.models
+ # -------------------------------------------------------------------
+ # ** I can pull out the number of predictors
+ # used in the rpart ensemble from the files that
+ # are saved. Then I can remove X.train from the parameter list
+ # -------------------------------------------------------------------
+ # Results
+ # ----------
+ var.imp1 <- matrix(0,NCOL(X), bs.trials)
+ var.imp2 <- matrix(0,NCOL(X), bs.trials)
+ var.imp3 <- matrix(0,NCOL(X), bs.trials)
+ leaf.count <- rep(0,bs.trials)
+ ave.leaf.obs <- rep(0,bs.trials)
+ min.leaf.obs <- rep(0,bs.trials)
+ # ----------------------------------------------------------
+ # Load First Ensemble Model
+ # -----------------------------------------------------------
+ iii <- 1
+ num.txt <- formatC(iii,format="fg", width=6)
+ num.txt <- chartr(" ","0",num.txt)
+ temp.filename <- paste(filename,".",num.txt,".RData",sep="")
+ load( file=temp.filename)
+ # Save ensemble rpart.object stub
+ ttt.rpart <- f.rpart
+ if (is.null(ensemble.index)) ensemble.index <- 1:bs.trials
+ # ----------------------------------------------------------
+ # Loop over Ensemble.Index
+ # KISS - but not the most efficient programming
+ # -----------------------------------------------------------
+ for (iii in 1:length(ensemble.index)){
+ # ----------------------------------------------------------
+ # Load/Construct rpart.object
+ # -----------------------------------------------------------
+ f.rpart <- ttt.rpart
+ if (ensemble.index[iii]!=1){
+ num.txt <- formatC(ensemble.index[iii],format="fg", width=6)
+ num.txt <- chartr(" ","0",num.txt)
+ temp.filename <- paste(filename,".",num.txt,".RData",sep="")
+ load( file=temp.filename) #rpart.parts
+ # Reassemble f.rpart from ttt.rpart stub
+ # ----------------------------
+ f.rpart$frame <- rpart.parts$frame
+ f.rpart$where <- rpart.parts$where
+ f.rpart$splits <- rpart.parts$splits
+ f.rpart$cptable <- rpart.parts$cptable
+ if (sum(names(rpart.parts) == "csplit") > 0)
+ f.rpart$csplit <- rpart.parts$csplit
+ }
+ # -------------------------------------------------------------------
+ # DT-rpart Specific Variable Importance Measures
+ # -------------------------------------------------------------------
+ # Split Variables = row.names(d.rpart$split)
+ # Empirical Improvement = Change in Deviance= d.rpart$split[,3]
+ # var.imp is a vector of all the variable importances in the
+ # same order as the columns in X (design matrix)
+ # -------------------------------------------------------------------
+ # sort out info about leaf nodes (I just want splits!)
+ dnodes <- f.rpart$frame[ f.rpart$frame[ ,1] != "<leaf>", ]
+ ncompete <- dnodes[,7]
+ nsurrogate <- dnodes[,8]
+ nsupport <- dnodes[, 2] # no. of pts affected by split
+ nheight <- as.numeric(row.names(dnodes)) # height in pascal's triange
+ nheight <- floor(log2(nheight)) + 1
+ split.index <- 1 # initialize split index
+ # variable look-up table
+ var.table <- data.frame(pos=seq(1:NCOL(X)), varname=names(X))
+ # add "<leaf>" level to var.table$varname so that var.index works
+ levels(var.table$varname) <- c(levels(var.table$varname),"<leaf>")
+ if (!is.null(f.rpart$split)){
+ # Loop through all splits (rows)
+ for (ii in 1:NROW(dnodes)){
+ # ID split predictor
+ # --------------------------------------------------
+ # Summer & Fall 2007
+ # Generating error number of levels in the factor is different
+ # But I not understand exactly when this error is generated
+ # so I dont know why it occurrs!
+ # ---------------------------------------------------
+
+ var.index <- var.table[as.character(dnodes[ii,1]) == as.character(var.table$varname) , 1]
+ # extract & store improvement in empirical purity from split frame
+ # Use twice emprical improvement to get actual deviance for entropy splitting rule
+ var.imp1[var.index,iii] <- var.imp1[var.index,1] + 2*f.rpart$split[split.index,3]
+ # update current row index in d.rpart$split
+ split.index <- split.index + ncompete[ii] + nsurrogate[ii]+1
+ # variable importance weighted by height in tree
+ var.imp2[var.index,iii] <- var.imp2[var.index,2] + nheight[ii]
+ # variable importance weighted by support
+ var.imp3[var.index,iii] <- var.imp3[var.index,3] + nsupport[ii]
+ } #endfor ii
+ } #end if is.null
+
+
+ # ----------------------------------------------------------
+ # 10.2.07
+ # I need information on ensemble trees to understand laplacian
+ # smoothing.
+ # leaf.count = # of terminal leafs
+ # ave.leaf.obs = average number of observations per leaf
+ # min.leaf.obs = minimum number of observation in leaf
+ # (this value is controled by min.bucket too!)
+ # ----------------------------------------------------------
+ is.leaf.ind <- (f.rpart$frame$var == "<leaf>")
+ leaf.count[iii] <- sum(is.leaf.ind)
+ ave.leaf.obs[iii] <- mean(f.rpart$frame$n[is.leaf.ind])
+ min.leaf.obs[iii] <- min(f.rpart$frame$n[is.leaf.ind])
+ # -------------------------------------------------------------------
+ } #end ensemble.index
+
+ # ----------------------------------------------------------
+ # Return Prediction Matrix
+ # -----------------------------------------------------------
+ return.list <- list(var.imp1 = var.imp1,
+ var.imp2 = var.imp2,
+ var.imp3 = var.imp3,
+ leaf.count = leaf.count,
+ ave.leaf.obs = ave.leaf.obs,
+ min.leaf.obs=min.leaf.obs)
+ return(return.list)
+# ---------------------------------------------------------
+}# End FUNCTION
+# ---------------------------------------------------------
+
+
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+# Variable Importance Barplot
+# -----------------------------------------------------------------------------
+# Daniel Fink
+#
+#
+# Description
+# -----------------
+# This function ....
+# I need to describe what the measure of relative variable importance
+# is and how it is aggregated over the ensemble.
+# * key assumptions
+# * uses, strengths & weaknesses
+#
+#
+# Input
+# ----------
+# vi = (n x 1) numeric vector of VI point estimates
+# where n is the number of Variables
+# barplot
+# vi.mat = ( n x bs.trials) numeric matrix of VI estimates
+# one set of estimates per column.
+# Variabliltiy in estimates plotted with boxplot
+# plot.it=FALSE
+#
+# Output
+# ----------
+# A plot may be produced or the predictive performances for train & test
+# returned.
+#
+# Notes:
+# ---------
+#
+# Further Development:
+# ----------------------------
+# ** common parameter names and calling proceedures for
+# all functions
+# ** return variable importances and names as data.frame
+# -----------------------------------------------------------------------------
+plot.vi.bdt <- function(
+ vi=NULL,
+ vi.mat=NULL,
+ predictor.names,
+ max.vars = 25,
+ file.name = NULL,
+ plot.width = 600,
+ plot.height = 800 ){
+ # --------------------------------------------------------------
+ # VI Point Estimate Plot
+ # --------------------------------------------------------------
+ if (!is.null(vi)) {
+ # --------------------------------------------------------------
+ # Assemble Scaled VI & Names
+ # ---------------------------------------------------------------
+ ttt <- data.frame(Predictor = predictor.names, Deviance = vi/sum(vi)*100)
+ # Re-order ttt in terms of descending Deviance
+ ttt.ind <- order(ttt[,2],decreasing=TRUE)
+ ttt <- ttt[ttt.ind, ]
+ ttt$Predictor <- as.character(ttt$Predictor)
+ # ---------------------------------------------------
+ # Save image to disk
+ # ---------------------------------------------------
+ if (!is.null(file.name)) {
+ png(file=file.name,
+ bg="white",
+ width=plot.width,
+ height=plot.height)
+ }
+
+ # ---------------------------------------------------
+ # Barplot
+ # ---------------------------------------------------
+ xmax <- max(ttt$Deviance) # scale max bar length
+ x.stretch <- 1.4 # scale max bar length
+ nbars <- max.vars # number of bars to plot
+ bar.length <- ttt$Deviance
+ bar.names <- ttt$Predictor
+ tcol <- rainbow(nbars, start = 3/6, end = 4/6)
+ tcol <- tcol[nbars:1] # reorder from dark to light colors
+ barplot(bar.length[1:nbars],
+ horiz=TRUE,
+ xlim=c(0,(xmax*x.stretch)),
+ xlab="Relative Importance",
+ col = tcol,
+ axes=F)
+ axis(1)
+ for (ii in 1:nbars) {
+ text( bar.length[ii] + 1,
+ 1.2*(ii-1) + .75,
+ as.character(bar.names[ii]),
+ cex=0.75,
+ pos=4)
+ }
+ title(main="Ensemble Averages")
+ # ---------------------------------------------------
+ # Save image to disk
+ # ---------------------------------------------------
+ if (!is.null(file.name)) dev.off()
+ }
+
+ # --------------------------------------------------------------
+ # VI Estimates BoxPlot
+ # --------------------------------------------------------------
+ if (!is.null(vi.mat)) {
+ mean.vi <- apply(vi.mat, 1, mean)
+ mean.index <- order(mean.vi, decreasing=TRUE)
+ mean.vi <- mean.vi[mean.index]
+ vi.mat <- vi.mat[mean.index,]/sum(mean.vi)*100
+ mean.vi <- mean.vi/sum(mean.vi)*100
+ predictor.names <- predictor.names[mean.index]
+ # --------------------
+ nbars <- max.vars
+ mean.vi <- mean.vi[c(1:nbars)]
+ predictor.names <- predictor.names[c(1:nbars)]
+ vi.mat <- vi.mat[c(1:nbars), ]
+ ttt.stack <- stack(data.frame(vi.mat))
+ ttt.stack <- data.frame(ttt.stack, var=c(1:nbars))
+ # --------------------
+ xmax <- max(ttt.stack[,1]) # scale max bar length
+ x.stretch <- 1.3 # scale max bar length
+ bar.length <- mean.vi
+ bar.names <- predictor.names
+ tcol <- rainbow(nbars, start = 3/6, end = 4/6)
+ tcol <- tcol[nbars:1] # reorder from dark to light colors
+ # ---------------------------------------------------
+ # Save image to disk
+ # ---------------------------------------------------
+ if (!is.null(file.name)) {
+ png(file=file.name, bg="white",
+ width=plot.width,
+ height=plot.height)
+ }
+
+ # --------------
+
+ boxplot(-values ~ as.factor(var),
+ data = ttt.stack,
+ horizontal=TRUE,
+ outline=FALSE,
+ #xlim=c(0,(nbars)),
+ ylim=c(-(xmax*x.stretch),(.5*xmax)),
+ xlab="Relative Importance",
+ col = tcol,
+ axes=F)
+ axis(1)
+ for (ii in 1:nbars) { #bar.length[ii]
+ #text( ttt.stack$values[ii] + 1, 1.2*(ii-1) + .75,
+ text( 0.5 , 1.*(ii-1) + 1,
+ as.character(bar.names[ii]), cex=1.0, pos=4)
+ }
+ title(main="Ensemble BoxPlot")
+ # ------------
+ # ---------------------------------------------------
+ # Save image to disk
+ # ---------------------------------------------------
+ if (!is.null(file.name)) dev.off()
+ } # end vi.mat
+} # end function
+
+
+# -------------------------------------------------------------------
+# create.pd.grid - Function to Create List of Prediction Grid(s)
+# -------------------------------------------------------------------
+# based on plot.gbm!
+# Input
+# XX - DTM Design matrix
+# arguments that are lists
+# # --------------------------
+# i.var.list = list of i.var vectors
+# for now- these two arguments must be scalars
+# continuous.resolution = list/vector of cont.resolutions
+#
+# Output
+# for each of member of the list, the following objects will be
+# produced:
+# pd.grids
+#
+# Notes:
+# -------
+# There may be times when we actually want to see what the
+# predictions are for NA's - I have left this out, as an extra item.
+# I need to document how I am handling NA's.
+# -------------------------------------------------------------------
+# ---------------------------------------------------------------------
+create.pd.grid <- function(XX,
+ i.var.list,
+ continuous.resolution,
+ na.flag=NULL) {
+ # Cycle through elements of list
+ # --------------------------------
+ pd.grids <- vector(mode="list", length=length(i.var.list))
+ for (iii in 1:length(i.var.list)){
+ i.var <- i.var.list[[iii]]
+
+ # --------------------------------------------
+ # Check User Input
+ # --------------------------------------------
+ if (all(is.character(i.var))) {
+ i <- match(i.var, names(XX))
+ if (any(is.na(i))) {
+ stop("i.var.list contains variables that are not used in model",
+ i.var[is.na(i)])
+ }
+ else {
+ i.var <- i
+ }
+ }
+
+ if ((min(i.var) < 1) || (max(i.var) > length(names(XX)))) {
+ warning("i.var must be between 1 and ", length(names(XX)))
+ }
+
+
+ # --------------------------------------------
+ # Create Prediction Grid
+ # --------------------------------------------
+ # vector produces a vector of the given length and mode.
+ grid.levels <- vector(mode="list", length=length(i.var))
+ for (i in 1:length(i.var)) {
+ X.vars <- XX[ ,i.var[i]]
+ # Check for missing values flag other than "NA"
+ # (for ex. I do not want RF 9e30 flag to affect the
+ # quantile calculations below
+ # ----------------------------------------------
+ if (!is.null(na.flag)){
+ na.ind <- (X.vars == na.flag)
+ # replace with NA's
+ X.vars[na.ind] <- NA
+ }
+
+ # ----------------------
+ # Integer Predictors
+ # ----------------------
+ # continuous resolution - use minimum of either
+ # the range of integers or continuous.resolution
+ if (is.integer(X.vars)) {
+ cont.res <- min((max(X.vars,na.rm=TRUE) - min(X.vars,na.rm=TRUE) + 1), continuous.resolution)
+ grid.levels[[i]] <- seq(min(X.vars,na.rm=TRUE), max(X.vars,na.rm=TRUE), length = cont.res)
+ grid.levels[[i]] <- sort(unique(grid.levels[[i]]))
+ }
+ # ----------------------
+ # Double Predictors
+ # ----------------------
+ if (is.double(X.vars)) {
+ # Sequential Grid
+ # grid.levels[[i]] <- seq(min(XX[ ,i.var[i]],na.rm=TRUE),
+ # max(XX[ ,i.var[i]],na.rm=TRUE),
+ # length = continuous.resolution)
+ # Grid at Equi-spaced Quantiles
+ prob.seq <- seq(from=0, to=1, length= (continuous.resolution+2))
+ # Remove the endpoints of this sequence
+ prob.seq <- prob.seq[2:(continuous.resolution+1)]
+ grid.levels[[i]] <- quantile(X.vars, probs = prob.seq, na.rm = TRUE)
+ grid.levels[[i]] <- sort(unique(grid.levels[[i]]))
+ } #end double
+ # ----------------------
+ # Factors: code levels numerically
+ # ----------------------
+ if (is.factor(X.vars)) {
+ # What happens with missing values here?
+ grid.levels[[i]] <- sort(unique(as.numeric(X.vars) ))
+ } # end factor
+ } #end for i: Making grid.levels
+ # ----------------------
+ pd.grid <- expand.grid(grid.levels)
+ names(pd.grid) <- names(XX)[i.var]
+ # ----------------------------------------
+ pd.grids[[iii]] <- pd.grid
+ } # end for i.var.lists
+
+ return(pd.grids)
+} # end function
+
+
+
+# -------------------------------------------------------------------
+# Predict.pd.grid - Function to make Predictions over PD.grids
+# -------------------------------------------------------------------
+# Input
+# XX = DTM Design matrix
+# pd.quant.grids = create.pd.grid obejct
+# nn.sample = # of randomly selected samples from XX
+# Output
+# list of predictions for each member of the create.pd.grid.object
+#
+#
+#
+# TO DO:
+# --------------------------------
+# 1) Add key parameters to output object!!!
+# partial.dependence.list,
+# continuous.resolution = 15,
+# nn.sample = 500
+#
+# 2) Need to Recode Categorical predictors
+# eg. if BCR was a predictor we would need to recode it
+# to its proper level labels !!!!!
+# Currently, BCR is coded as the number of the LEVEL
+# xxx.grid[,2] <- levels(train.data$X$BCR)[xxx.grid[,2]]
+#
+#
+# HPM Use:
+# HPM will need to store and accululate these predictions or
+# lists of predictions for plotting.
+# ------------------------------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------------------------------
+ensemble.partial.dependence <- function(filename,
+ ensemble.par.list,
+ XX,
+ partial.dependence.list,
+ continuous.resolution = 15,
+ nn.sample = 500) {
+ # ------------------------------------------------------------------------------------------------------
+ # Inits Formal Parameters
+ # ------------------------------------------------------------------------------------------------------
+ # Results
+ pd.means <- vector(mode="list", length=length(partial.dependence.list))
+ pd.matrices <- vector(mode="list", length=length(partial.dependence.list))
+ # ------------------------------------------------------------------------------------------------------
+ # Compute Partial Dependence Quantile Grids
+ # ------------------------------------------------------------------------------------------------------
+ pd.quant.grids <- create.pd.grid(XX=XX,
+ i.var.list=partial.dependence.list,
+ continuous.resolution = continuous.resolution)
+ # ------------------------------------------------------------------------------------------------------
+ # Check Function input
+ # ------------------------------------------------------------------------------------------------------
+ if (nn.sample > NROW(XX)) {
+ nn.sample <- NROW(XX)
+ }
+ # ------------------------------------------------------------------------------------------------------
+ # Random Sample of Data Rows (same sample for all PD elements)
+ # ------------------------------------------------------------------------------------------------------
+ # Sample without replacement from data rows
+ if (nn.sample == NROW(XX)) sample.index <- c(1:NROW(XX))
+ if (nn.sample < NROW(XX)) sample.index <- sample(1:NROW(XX), nn.sample, replace = FALSE)
+
+ # ------------------------------------------------------------------------------------------------------
+ # Find factors in XX
+ # Note : I can not use apply b/c XX is class data.frame
+ # ------------------------------------------------------------------------------------------------------
+ XX.factor.ind <- rep(FALSE, NCOL(XX))
+ ttt <- XX[1,] # it is much faster to search a 1D data.frame!
+ for (ii in 1:NCOL(XX)) XX.factor.ind[ii] <- is.factor(ttt[,ii])
+
+ # Extract an index of column positions for factors (wo zeros!)
+ factor.index <- as.numeric(XX.factor.ind)*seq(1,NCOL(XX))
+ factor.index <- factor.index[factor.index > 0 ]
+ # ------------------------------------------------------------------------------------------------------
+ # Loop Over PD list elements
+ # ------------------------------------------------------------------------------------------------------
+ for (iii in 1:length(pd.quant.grids)){
+ # ------------------------------------
+ # 1. Expand Quantile Grid into PD Prediction Design
+ # 2. BDT Predictions
+ # 3. Assemble Results
+ # ------------------------------------
+ i.var <- match( names(pd.quant.grids[[iii]]), names(XX))
+ XX.sample <- XX[sample.index, setdiff(names(XX), names(XX)[i.var]) ]
+ pd.grid <- pd.quant.grids[[iii]]
+ # ----------------------------
+ # NOTE** The size of the PD design = nn.sample * length(pd.grid)
+ # If this too large, there should be a loop here that can
+ # break this computation into pieces by breaking up
+ # nn.sample
+ # ----------------------------
+ # ------------------------------------------------------------------------------------------------------
+ # Construct Partial Dependence Prediction Data Frame
+ # NOTE: the use of data.matrix converts factors to numerics
+ # ------------------------------------------------------------------------------------------------------
+ # Stack Randomly Sampled Data Rows
+ XX.stack <- kronecker( matrix(1, NROW(pd.grid), 1), data.matrix(XX.sample))
+ XX.stack <- as.data.frame(XX.stack)
+ names(XX.stack) <- names(XX.sample)
+ # Stack Partial Dependence Grids
+ pd.stack <- kronecker( data.matrix(pd.grid), matrix(1, nn.sample, 1))
+ pd.stack <- as.data.frame(pd.stack)
+ names(pd.stack) <- names(pd.grid)
+ PD.prediction.frame <- cbind(pd.stack,XX.stack)
+ # ------------------------------------------------------------------------------------------------------
+ # Reconstruct Factor structure for data.frame
+ # ------------------------------------------------------------------------------------------------------
+ # XX = original data frame that may include factors
+ # PD.prediction.frame = the data.frame currently with numeric
+ # values for all predictors. The prediction data.frame needs
+ # to have the same column/predictor structure as XX
+ # ------------------------------------------------
+ # 1) Reorder PD.prediction.frame to match XX
+ col.order <- match( names(XX), names(PD.prediction.frame))
+ PD.prediction.frame <- PD.prediction.frame[,col.order]
+ # 2) Convert PD.prediction.frame cols to factors
+ for (i in factor.index) {
+ PD.prediction.frame[,i] <- factor(levels(XX[,i])[PD.prediction.frame[,i]], levels=levels(XX[,i]))
+ }
+ # ------------------------------------------------------------------------------------------------------
+ # Ensemble PD Predictions
+ # ------------------------------------------------------------------------------------------------------
+
+ ttt.pred <- ensemble.par.list$predict.ensemble.function(
+ filename = filename,
+ ensemble.par.list = ensemble.par.list,
+ prediction.design= PD.prediction.frame)
+ # BDT ensemble mean predictions
+ pred.X <- ttt.pred$mean
+ pred.X.matrix <- ttt.pred$matrix
+ rm(ttt.pred)
+ # -----------------------------
+ # PD Design Loop would (somewhere?) end here, I think, hmmm
+ # -----------------------------
+ # --------------------------------------------
+ # Ensemble Matrix PD estimates
+ # --------------------------------------------
+ pdf.grid.matrix <- NULL
+ pred.index <- (rep(c(1:NROW(pd.grid)),each=nn.sample))
+ for (jjj in 1:NCOL(pred.X.matrix)){
+ pdf.grid.matrix <- cbind(pdf.grid.matrix, tapply(pred.X.matrix[,jjj], pred.index, mean,na.rm=T))
+ }
+ rm(pred.X.matrix)
+ # --------------------------------------------
+ # Average to get Ensemble average PD estimates
+ # --------------------------------------------
+ pred.index <- (rep(c(1:NROW(pd.grid)), each=nn.sample))
+ ppp <- tapply(pred.X, pred.index, mean,na.rm=T)
+ # recode pd.grid factors
+ f.factor <- rep(FALSE, NCOL(pd.grid))
+ for (i in 1:NCOL(pd.grid)) {
+ col.index <- match( names(pd.grid)[i], names(XX))
+ if (!is.numeric( XX[,col.index] )) {
+ f.factor[i] <- TRUE
+ pd.grid[,i] <- factor(levels(XX[,col.index])[pd.grid[,i]], levels=levels(XX[,col.index]))
+ }
+ } #end for i
+ # Reassociate pd.grid with predictions
+ pdf.grid <- data.frame(pd.grid, pred=ppp)
+
+ # -----------------------------------
+ # Store results in PD.list
+ # -----------------------------------
+ # pd.means = the Partial Dependence Estimate averaged over bags
+ # pd.matrices = the PD estimates, one col per bag/model
+ pd.means[[iii]] <- pdf.grid
+ pd.matrices[[iii]] <- pdf.grid.matrix
+ #names(pdf.grid)
+ #dim(pdf.grid)
+ } # end iii
+
+ return(list(pd.quant.grids=pd.quant.grids, pd.means=pd.means, pd.matrices=pd.matrices))
+} # end function
+
+# ---------------------------------------------------------
+# Summary (TEXT) Function
+# ---------------------------------------------------------
+summarize.ensemble <- function(model.filename,
+ ensemble.par.list,
+ train.data,
+ test.data=NULL,
+ diag.bdt = NULL,
+ oob.pred = NULL,
+ train.pred = NULL,
+ test.pred = NULL){
+ # ---------------------------------------------------------
+ # Inits
+ # ---------------------------------------------------------
+ temp.filename <- paste(model.filename,".ensemble.index.RData",sep="")
+ load(file=temp.filename) #return.list
+ bs.trials <- ensemble.par.list$n.ensemble.models
+ resp.family <- return.list$resp.family
+ # ---------------------------------------------------------
+ cat(" -------------------------------------\n")
+ cat(" Bagged Decision Trees \n")
+ cat(" -------------------------------------\n")
+ cat(" Model Name: ", model.filename , "\n")
+ cat(" Response type = ", resp.family , "\n")
+ cat(" Number of Predictors = ", NCOL(train.data$X) , "\n")
+ cat(" Training sample size = ", NROW(train.data$X) , "\n")
+ cat(" -------------------------------------\n")
+ cat(" Ensemble \n")
+ cat(" -------------------------------------\n")
+ cat(" ensemble size = ", bs.trials,"\n")
+ cat(" Ensemble parameters: \n")
+ for (iii in 2:length(ensemble.par.list)){
+ cat( " ",names(ensemble.par.list)[iii],"\n")
+ }
+ # ----------------------------------------------------
+ # Ensemble size stats
+ # ----------------------------------------------------
+ if (!is.null(diag.bdt)) {
+ cat(" Average # leaves per tree =",
+ mean(diag.bdt$leaf.count) ,"\n")
+ cat(" Average # obs per leaf =",
+ mean(diag.bdt$ave.leaf.obs) ,"\n")
+ cat(" Minimum # obs per leaf =",
+ mean(diag.bdt$min.leaf.obs) ,"\n")
+ }
+ # -----------------------------------------
+ pp <- NULL
+ pp.names <- NULL
+ # -----------------------------------------
+ if (resp.family == "gaussian" | resp.family == "poisson"){
+ if (!is.null(train.pred)) {
+ # -------------------
+ ttt.ind <- (!is.na(train.pred$mean))
+ ttt <- predictive.performance(
+ obs=train.data$y[ttt.ind],
+ ppp=train.pred$mean[ttt.ind],
+ resp.family=resp.family )
+ pp <- cbind(pp, ttt)
+ pp.names <- rbind(pp.names, "Training")
+ }
+ # -----------------
+ if (!is.null(oob.pred)) {
+ ttt.ind <- (oob.pred$count > 0 & !is.na(oob.pred$mean))
+ ttt <- predictive.performance(
+ obs=train.data$y[ttt.ind],
+ ppp=oob.pred$mean[ttt.ind],
+ resp.family=resp.family)
+ pp <- cbind(pp, ttt)
+ pp.names <- rbind(pp.names, "OOB")
+ }
+ # ----------------
+ if (!is.null(test.pred)){
+ ttt.ind <- (!is.na(test.pred$mean))
+ ttt <- predictive.performance(
+ obs=test.data$y[ttt.ind],
+ ppp=test.pred$mean[ttt.ind],
+ resp.family=resp.family)
+ pp <- cbind(pp, ttt)
+ pp.names <- rbind(pp.names, "Test")
+ }
+ if (!is.null(pp)) pp <- data.frame(pp)
+ # -----------------
+ } # end if gaussian or poisson
+ # ----------------------------------------
+ if (resp.family == "bernoulli"){
+ if (!is.null(train.pred)) {
+ # -------------------
+ ttt.ind <- (!is.na(train.pred$mean))
+ ttt <- predictive.performance(
+ obs=train.data$y[ttt.ind],
+ ppp=train.pred$mean[ttt.ind],
+ resp.family=resp.family )
+ pp <- cbind(pp, c(ttt$acc, ttt$rmse, ttt$auc))
+ pp.names <- rbind(pp.names, "Training")
+ }
+ # -----------------
+ if (!is.null(oob.pred)) {
+ ttt.ind <- (oob.pred$count > 0 & !is.na(oob.pred$mean))
+ ttt <- predictive.performance(
+ obs=train.data$y[ttt.ind],
+ ppp=oob.pred$mean[ttt.ind],
+ resp.family=resp.family)
+ pp <- cbind(pp, c(ttt$acc, ttt$rmse, ttt$auc))
+ pp.names <- rbind(pp.names, "OOB")
+ }
+ # ----------------
+ if (!is.null(test.pred)){
+ ttt.ind <- (!is.na(test.pred$mean))
+ ttt <- predictive.performance(
+ obs=test.data$y[ttt.ind],
+ ppp=test.pred$mean[ttt.ind],
+ resp.family=resp.family)
+ pp <- cbind(pp, c(ttt$acc, ttt$rmse, ttt$auc))
+ pp.names <- rbind(pp.names, "Test")
+ }
+ if (!is.null(pp)) pp <- data.frame(pp)
+ # -----------------
+ rownames(pp) <- c("Accuracy", "RMSE", "AUC")
+ } # end if bernoulli
+
+ cat(" -------------------------------------\n")
+ cat(" Predictive Performance \n")
+ cat(" -------------------------------------\n")
+ n.row <- NROW(pp)
+ n.col <- NCOL(pp)
+ for (ii in 1:n.col){
+ cat( " ",pp.names[ii]," ")
+ }
+ cat("\n")
+
+ for (ii in 1:n.row){
+ cat(" ", rownames(pp)[ii], " ")
+ for (jj in 1:n.col) {
+ cat( as.character(format(pp[ii,jj], digits=5))," ")
+ }
+ cat("\n")
+ }
+ # ----------------------------------------------------
+ # Relative Variable Importance -
+ # ----------------------------------------------------
+ if (!is.null(diag.bdt)) {
+ cat(" ---------------------------------------------------------------------\n")
+ cat(" Relative Variable Importance - Top 10 \n")
+ cat(" ---------------------------------------------------------------------\n")
+ # Re-order ttt in terms of descending Deviance
+ ttt <- data.frame(Predictor = c(names(train.data$X)), Deviance = diag.bdt$var.imp1/sum(diag.bdt$var.imp1)*100 )
+ ttt.ind <- order(ttt[,2],decreasing=TRUE)
+ ttt <- ttt[ttt.ind, ]
+ ttt$Predictor <- as.character(ttt$Predictor)
+ for (iii in 1:10) cat(" ", iii, " ",ttt[iii, 2]," ", ttt[iii, 1], "\n")
+ cat(" ---------------------------------------------------------------------\n")
+ cat("\n")
+ cat("\n")
+ }
+}# end summary function
+
+
+# -----------------------------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------------------------
+# Predictive Performance Functions
+# 10.23.08
+#
+# Compute predictive Performance measures. The basic idea is to
+# measure the average distance between observation & prediction.
+# ave (distance(obs - pred))
+# Methods vary according to the family of the response, how the
+# averaging is performed and how distance is measured.
+#
+# ** Assumed that there are no NA's in either obs or predicted.
+#
+# Input:
+# ---------
+# obs = observed response
+# ppp = corresponding predicted response (on response scale!)
+# family = family or name of response type
+#
+# Output:
+# ---------
+# Family = "bernoulli" == binary (numerical? logical?)
+# ------------------------------------------------
+# Family = "gaussian" == numerical
+# ------------------------------------------------
+# Family = "poisson" == counts
+# ------------------------------------------------
+# ** I am no longer computing Pearson's Chi-Squared measure
+# because the predictions in the denominator make is very
+# unstable when there are lots of small predictions.
+# (for the relative abundance analyses)
+# p <- sum( ((yyy - ppp)^2)/(ppp) )
+# ** Deviance Calculations
+#
+# Demo Code:
+# -----------
+# yyy <- p.data$yp
+# ppp <- (d.dtm$pred.Xp)^2 #Untransformed
+# res <- residuals.dtm(obs = yyy,
+# ppp = ppp,
+# family="poisson")
+#
+# Needed:
+# --------------------
+# * More documentation
+# * Example showing ROC curve using pred.obj (ROCR library help(performance))
+# * Add gaussian & binary deviance functions & measures
+# * erorr checking for different types of binary obs & pred
+#
+# -----------------------------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------------------------
+predictive.performance <- function(obs, ppp, resp.family) {
+ if (resp.family=="poisson"){
+ # ----------------------------------
+ MSE <- mean((ppp - obs)^2)
+ R2 <- 1 - mean((ppp - obs)^2)/mean((mean(obs) - obs)^2)
+ MSE.sqrt <- mean((sqrt(ppp) - sqrt(obs))^2)
+ R2.sqrt <- 1 - mean((sqrt(ppp) - sqrt(obs))^2)/
+ mean((mean(sqrt(obs)) - sqrt(obs))^2)
+ MAD <- mean(abs(ppp - obs))
+ rho <- cor(obs,ppp)
+ rho.sqrt <- cor(sqrt(obs),sqrt(ppp))
+ # ----------------------------
+ # Poisson Deviance can not have zero predictions
+ # Substitute predicted zero's with small values
+ # ------------------------------------
+ epsilon <- 1e-8
+ ppp[ppp == 0] <- epsilon
+ # ---------------------------------------------------------
+ null.deviance <- poisson.deviance(
+ yyy=obs,
+ ppp=rep(mean(obs),length(obs) ))
+ obs.deviance <- poisson.deviance(
+ yyy=obs,
+ ppp=ppp)
+ deviance.explained <- (null.deviance - obs.deviance)/null.deviance
+ # ----------------------------------
+ return(list(
+ MSE = MSE,
+ R2=R2,
+ MSE.sqrt = MSE.sqrt,
+ R2.sqrt=R2.sqrt,
+ MAD=MAD,
+ rho=rho,
+ rho.sqrt=rho.sqrt,
+ deviance.explained=deviance.explained,
+ obs.deviance=obs.deviance,
+ null.deviance=null.deviance))
+ }
+
+ if (resp.family=="bernoulli"){
+ acc <- 1 - sum(abs(obs-ppp))/length(ppp)
+ require(ROCR)
+ pred.obj <- prediction(prediction=ppp, labels=as.numeric(obs))
+ perf <- performance(pred.obj, "auc")
+ auc <- perf at y.values[[1]][1]
+ perf <- performance(pred.obj, "rmse")
+ rmse <- perf at y.values[[1]][1]
+ return(list(
+ acc=acc,
+ rmse = rmse,
+ auc = auc,
+ pred.obj = pred.obj))
+ }
+ if (resp.family=="gaussian"){
+ # ----------------------------------
+ MSE <- mean((ppp - obs)^2)
+ R2 <- 1 - mean((ppp - obs)^2)/mean((mean(obs) - obs)^2)
+ MAD <- mean(abs(ppp - obs))
+ rho <- cor(obs,ppp)
+ # ----------------------------
+ return(list(
+ MSE = MSE,
+ R2=R2,
+ MAD=MAD,
+ rho=rho))
+ }
+}
+# -----------------------------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------------------------
+
+
+# -----------------------------------------------------------------------------------------------------------
+# Poisson Predictive Performance Measures
+# -----------------------------------------------------------------------------------------------------------
+# yyy = observations
+# ppp = predicted value - response scale
+#
+# Verified - replicated GAM deviance calcuatlions for poisson
+# -----------------------------------------------------------------------------------------------------------
+poisson.deviance <- function(yyy,ppp){
+ # if predictions (ppp) equal zero we will get underflow
+ # problems from log function.
+ # -------------
+ # break deviance into two pieces - where obs == 0
+ ttt.zero <- (yyy == 0)
+ ttt.pos <- (yyy > 0)
+ dev1 <- sum( (yyy[ttt.zero] - ppp[ttt.zero]) )
+ dev2 <- sum( yyy[ttt.pos]*log(yyy[ttt.pos]/ppp[ttt.pos]) -
+ (yyy[ttt.pos] - ppp[ttt.pos]))
+ dev <- 2*(dev2 - dev1)
+ return(dev)
+}
+# -----------------------------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------------------------
+
+
+# ------------------------------------------------------------------------
+# ------------------------------------------------------------------------
+# Random Train/Test Split
+# ------------------------
+# n = length of index
+# p.train = percentage for training
+#
+# This function simply returns two indices that partition
+# a set of n iterms into two mutually exclusive sets.
+#
+# Demo
+#ttt <- ttsplit(n=100, p.train=0.5)
+#length(ttt$train.index)
+#length(ttt$test.index)
+# ---------------------------------------------------
+ttsplit <- function(n, p.train){
+ train.index <- NULL
+ val.index <- NULL
+ ttt.index <- 1:n
+ nnn.train <- round(n * p.train)
+ nnn.val <- n - nnn.train
+ if (nnn.train <= n)
+ train.index <- sample((1:n), nnn.train)
+ if (nnn.val > 0 ) {
+ full.index <- c(1:n)
+ val.index <- setdiff(full.index, train.index)
+ val.index <- sample( val.index, min(nnn.val, length(val.index)))
+ }
+ return(list(train.index=train.index, test.index=val.index))
+} # end function
+
+# ------------------------------------------------------------------------
+# ------------------------------------------------------------------------
+
+# ------------------------------------------------------------------------
+# ------------------------------------------------------------------------
+# Simple Unique Location Train/Test Splitting
+# 11.3.07
+#
+# Randomly select a unique set of locations for the train and
+# test sets. This function will collect all records for a given
+# location and assign them according to the train/test split.
+# This sampling design does NOT preserve the relative sampling
+# density across locations because there are no repeat locations
+# sampled.
+#
+# Input:
+# ---------
+# locs - location data frame/matrix
+# p.train - proportion of locations for training
+# m.frac - fraction of multiple observations to include for
+# each location
+#
+# Output:
+# ---------
+# unique.index= unique loc index ( I believe that the
+# first instance for each repeated loc is indicated here)
+# train.index.single & test.locs.single
+# index to one observation from a unique set of locations.
+# Train & test sets form a random partition of the locations
+# in the unique.index.
+# train.locs.index & test.locs.index
+# Collect a fraction of available observations at each of
+# the randomly selected training locations. If there are repeat observations at
+# a unique location, then all of these observations will
+# be included in this set. Same for the test set.
+#
+# Demo Code:
+# -----------
+# # Create Data with Repeat Obs at specific locations
+# #nnn <- 10000
+# #locs <- data.frame(x=rnorm(nnn), y=rnorm(nnn))
+# locs <- cc.data$loc
+# ddd <- unique.locs.splitting(locs, p.train=0.75, m.frac=0.5)
+# length(ddd$train.locs.single)
+# length(ddd$train.locs.multiple)
+# length(ddd$test.locs.single)
+# length(ddd$test.locs.multiple)
+# # ----------------------------
+# # Plot Map of Train/Test Sets
+# # ----------------------------
+# plot(locs$x[ddd$train.locs.single],
+# locs$y[ddd$train.locs.single],
+# xlab ="lon", ylab="lon",
+# pch=24,
+# col="red",
+# cex=.5)
+# points(locs$x[ddd$test.locs.single],
+# locs$y[ddd$test.locs.single],
+# col="blue",
+# pch=25,
+# cex=0.5)
+# title(main="eBird Northern Cardinal Summer 2006", font.main = 4 )
+# box(lwd=3.0)
+# require(maps)
+# require(mapdata)
+# map('state',add=TRUE)
+# ------------------------------------------------------------------------
+# ------------------------------------------------------------------------
+unique.locs.splitting <- function(locs, p.train, m.frac=1.0){
+ # Extract unique locs as ttt
+ ttt <- unique(locs)
+ # 1) Randomly select proportion of unique locations
+ split.ind <- ttsplit(n=NROW(ttt), p.train=p.train)
+ train.index <- split.ind$train.index
+ test.index <- split.ind$test.index
+ # ----------------------
+ # 2) Process Test Set
+ test.locs.single <- NULL
+ test.locs.multiple <- NULL
+ for (iii in 1:length(test.index)){
+ temp.ind <- (locs$x == ttt$x[test.index[iii]] &
+ locs$y == ttt$y[test.index[iii]])
+ #Convert to index into locs for matches
+ temp.ind <- as.numeric(temp.ind) * c(1:NROW(locs))
+ temp.ind <- temp.ind[temp.ind > 0]
+ # Random Selection Single
+ temp.ind.single <-temp.ind[
+ sample(1:length(temp.ind), size=1, replace=FALSE) ]
+ test.locs.single<- c(test.locs.single, temp.ind.single)
+ # Random Selection Multiple
+ m.size <- max(1,round(m.frac*length(temp.ind)))
+ temp.ind.multiple <- temp.ind[
+ sample(1:length(temp.ind), size=m.size, replace=FALSE)]
+ test.locs.multiple <- c(test.locs.multiple, temp.ind.multiple)
+ }
+ # -------------------------
+ # 3) Process Train Set
+ train.locs.single <- NULL
+ train.locs.multiple <- NULL
+ for (iii in 1:length(train.index)){
+ temp.ind <- (locs$x == ttt$x[train.index[iii]] &
+ locs$y == ttt$y[train.index[iii]])
+ #Convert to index into locs for matches
+ temp.ind <- as.numeric(temp.ind) * c(1:NROW(locs))
+ temp.ind <- temp.ind[temp.ind > 0]
+ # Random Selection Single
+ temp.ind.single <-temp.ind[
+ sample(1:length(temp.ind), size=1, replace=FALSE) ]
+ train.locs.single<- c(train.locs.single, temp.ind.single)
+ # Random Selection Multiple
+ m.size <- max(1,round(m.frac*length(temp.ind)))
+ temp.ind.multiple <- temp.ind[
+ sample(1:length(temp.ind), size=m.size, replace=FALSE)]
+ train.locs.multiple <- c(train.locs.multiple, temp.ind.multiple)
+ }
+ # -------------------------
+ return(list(train.locs.single = train.locs.single,
+ train.locs.multiple = train.locs.multiple,
+ test.locs.single = test.locs.single,
+ test.locs.multiple = test.locs.multiple,
+ unique.index=as.numeric(rownames(ttt))
+ ))
+} # end function
+# ------------------------------------------------------------------------
+# ------------------------------------------------------------------------
+
+
+
+# ----------------------------------------------------------------------
+# ----------------------------------------------------------------------
+# Loop Over 1 Grid Realization - Compute & Store Distribution
+# ----------------------------------------------------------------------
+# ----------------------------------------------------------------------
+# ----------------------------------------------------------------------
+# Create Train:Test sets with Unique Locations
+# ----------------------------------------------------------------------
+# dsplit <- unique.locs.splitting(locs=cc.data$loc,
+# p.train=fraction.training.data,
+# m.frac=1.0)
+# train.index <- dsplit$train.locs.multiple
+# test.index <- dsplit$test.locs.multiple
+# ---------------------------
+# Maximum Coverage Selection
+# for Train:Test Set
+# ---------------------------
+maximum.coverage.selection <- function(
+ locs, # data.frame(x , y) length n
+ jdates, # vector length n
+ #grid.parameters,
+ grid.cell.min.lat,
+ grid.cell.min.lon,
+ min.val.cell.locs,
+ fraction.training.data,
+ mfrac=1.0,
+ plot.it =FALSE ){
+# ----------------------------------------------------------------
+# RETURN:
+# train.index <-
+# test.index <-
+# -------------------------------------------------------------------
+# Formal test values
+# locs=cc.data$locs data.frame(x , y) length n
+# jdates=cc.data$X$JDATE vector length n
+# grid.parameters,
+# grid.cell.min.lat=1.0
+# grid.cell.min.lon=1.5
+# min.val.cell.locs=5
+# fraction.training.data=0.8
+# mfrac=1.0
+# ----------------------
+ lon.min <- min(locs$x)
+ lon.max <- max(locs$x)
+ lat.min <- min(locs$y)
+ lat.max <- max(locs$y)
+
+ #for (iii.loop in 1:nnn.grids) {
+ iii.loop <- 1
+ # 1) Randomize Coordinate for first grid cell boundary
+ r.lat <- runif(1,min=0, max=grid.cell.min.lat)
+ r.lon <- runif(1,min=0, max=grid.cell.min.lon)
+ # 2) lay down equally spaced grid until x.max reached
+ grid.ttt <- seq(from=(lon.min+r.lon),
+ to=lon.max,
+ by=grid.cell.min.lon)
+ grid.xxx <- c(lon.min, grid.ttt, lon.max)
+ grid.ttt <- seq(from=(lat.min+r.lat),
+ to=lat.max,
+ by=grid.cell.min.lat)
+ grid.yyy <- c(lat.min, grid.ttt, lat.max)
+ # incase of any duplicates!
+ grid.xxx <- sort(unique(grid.xxx))
+ grid.yyy <- sort(unique(grid.yyy))
+ # ---------------------------
+ # Sample Maximal Coverage Validation Data
+ # Then use the rest for Training
+ # ** Take up to the first min.val.cell.locs
+ # ** Then randomly select the rest, by unique loc
+ # ---------------------------
+ kkk <- 0 # counter for grid cell regions
+ nnn.grid.cells <- (length(grid.xxx)-1)*(length(grid.yyy)-1)
+ u.test.locs <- NULL
+ # -----------------------------------------------------------------
+ # Cycle over Columns(xxx_iii) within Given Row (yyy_jjj)
+ # -----------------------------------------------------------------
+ for (jjj in 1:(length(grid.yyy)-1)){
+ for (iii in 1:(length(grid.xxx)-1)){
+ #iii <- 10
+ #jjj <- 20
+
+ kkk <- kkk + 1
+ # --------------------------------
+ xxx <- locs$x
+ yyy <- locs$y
+ cell.index <- xxx >= grid.xxx[iii] & xxx < grid.xxx[iii+1] &
+ yyy >= grid.yyy[jjj] & yyy < grid.yyy[jjj+1]
+ # Check for minimum Prediction Cell Locations
+ # ---------------------------------------------
+ u.locs <- unique(data.frame(x=locs$x[cell.index],
+ y=locs$y[cell.index]))
+ sum(cell.index)
+ dim(u.locs)
+
+ if (NROW(u.locs) <= min.val.cell.locs) {
+ # Randomly Select first min.val.cell.locs
+ u.test.locs <- rbind(u.test.locs,u.locs)
+ }
+ if (NROW(u.locs) > min.val.cell.locs) {
+ # Randomly Select first min.val.cell.locs
+ # Then Randomly split the rest
+ # ---------------------------------
+ ttt.ind <- sample(1:NROW(u.locs), size=min.val.cell.locs)
+ u.test.locs <- rbind(u.test.locs,u.locs[ttt.ind,])
+ u.locs <- u.locs[ (setdiff(1:NROW(u.locs),ttt.ind)) , ]
+ dsplit <- unique.locs.splitting(locs=u.locs,
+ p.train=fraction.training.data,
+ m.frac=1.0)
+ u.test.locs <- rbind(u.test.locs,
+ u.locs[dsplit$test.locs.multiple,])
+ }
+ }}# end grid loop
+ # -----------------------------------------
+ #
+ # -----------------------------------------
+ # Should be locs DF with all unique locs for valiation set
+ # Now, I need to divide data accordingly
+ # ------------------------------
+ test.index <- (locs$x %in% u.test.locs$x) & (locs$y %in% u.test.locs$y)
+ train.index <- !test.index
+ # -------------------------
+ # Test Plot of Grid
+ # -------------------------
+ if ( plot.it == TRUE){
+ plot(1,1,
+ xlim=c(lon.min,lon.max),
+ ylim=c(lat.min, lat.max),
+ type="n",
+ cex=0.25,
+ main =paste("Train=Blue(",sum(train.index),
+ ") Test=Red(",sum(test.index),")"))
+ require(maps)
+ map("state", add=TRUE, col="black", lwd=2)
+ for (jjj in 1:length(grid.yyy)){
+ lines(c(lon.min,lon.max),rep(grid.yyy[jjj],2),col="grey")
+ }
+ for (jjj in 1:length(grid.xxx)){
+ lines(rep(grid.xxx[jjj],2),c(lat.min,lat.max),col="grey")
+ }
+ #dim(u.test.locs)
+ points(locs[train.index,], col="blue", cex=0.5, pch=19)
+ points(u.test.locs, cex=0.5, col=2,pch=19)
+ }
+# ------------------
+return(list( test.index = test.index,
+ train.index = train.index))
+# ---------------------------------------------------------------------------------
+} #end FUNCTION
+# ---------------------------------------------------------------------------------
+
+# ----------------------------------------------------------------------
+# ----------------------------------------------------------------------
+# equal.wt.max.coverage.selection
+# max.uniform.coverage.split
+# DFink
+# 3.22.10
+#
+# This function splits a set of locations into "test" and "training"
+# set with with the goal that the test set meet two objectives:
+# 1) The test set covers the broadest extent possible, and
+# 2) The test set is approximately uniform over the extent.
+#
+# The first goal is met by constructing a randomly located rectangular
+# grid over the extent of the data and then preferentially select
+# test locations that populate as many cells as possible. Within
+# grid cell density is controlled, i.e. made more uniform, by
+# setting the maximum number of unique locations included in cell.
+# Small value of the maximum cell sample size parameter help
+# to produce more uniformly distributed test set samples.
+#
+# Note, if locations are repeated, all the repeats for each location
+# are all assigned to either the test or training sets.
+#
+# Inputs:
+# ---------
+# locs - data frame or list with elements x & y.
+# grid.cell.min.lat - height of grid cells
+# grid.cell.min.lon - width of grid cells
+# max.cell.locs - integer giving maximum number of unique locations
+# per cell
+# plot.it =FALSE - flag for diagnostic plot
+#
+# Outputs:
+# ---------
+# test.index = boolean index of length = nrows(locs)
+# train.index = same.
+#
+# ----------------------------------------------------------------------
+# ----------------------------------------------------------------------
+# Equal Weight with Maximum Coverage Splitting
+# for Train:Test Set
+# ---------------------------
+equal.wt.max.coverage.selection <- function(
+ locs,
+ grid.cell.min.lat,
+ grid.cell.min.lon,
+ max.cell.locs=1,
+ plot.it =FALSE ){
+# ----------------------------------------------------------------
+# Formal test values
+# locs=cc.data$locs data.frame(x , y) length n
+# grid.cell.min.lat=1.0
+# grid.cell.min.lon=1.5
+# max.cell.locs=5
+# ----------------------
+ lon.min <- min(locs$x)
+ lon.max <- max(locs$x)
+ lat.min <- min(locs$y)
+ lat.max <- max(locs$y)
+ iii.loop <- 1
+ # 1) Randomize Coordinate for first grid cell boundary
+ r.lat <- runif(1,min=0, max=grid.cell.min.lat)
+ r.lon <- runif(1,min=0, max=grid.cell.min.lon)
+ # 2) lay down equally spaced grids from min to max
+ grid.ttt <- seq(from=(lon.min+r.lon),
+ to=lon.max,
+ by=grid.cell.min.lon)
+ grid.xxx <- c(lon.min, grid.ttt, lon.max)
+ grid.ttt <- seq(from=(lat.min+r.lat),
+ to=lat.max,
+ by=grid.cell.min.lat)
+ grid.yyy <- c(lat.min, grid.ttt, lat.max)
+ # incase of any duplicates!
+ grid.xxx <- sort(unique(grid.xxx))
+ grid.yyy <- sort(unique(grid.yyy))
+ # ---------------------------------------------------
+ # Sample Maximal Coverage Test Set
+ # Then use the rest for Training
+ # ** Take up to the first max.cell.locs
+ # ** Then randomly select the rest, by unique loc
+ # ---------------------------------------------------
+ kkk <- 0 # counter for grid cell regions
+ nnn.grid.cells <- (length(grid.xxx)-1)*(length(grid.yyy)-1)
+ u.test.locs <- NULL
+ # -----------------------------------------------------------------
+ # Cycle over Columns(xxx_iii) within Given Row (yyy_jjj)
+ # -----------------------------------------------------------------
+ for (jjj in 1:(length(grid.yyy)-1)){
+ for (iii in 1:(length(grid.xxx)-1)){
+ kkk <- kkk + 1
+ xxx <- locs$x
+ yyy <- locs$y
+ cell.index <- xxx >= grid.xxx[iii] & xxx < grid.xxx[iii+1] &
+ yyy >= grid.yyy[jjj] & yyy < grid.yyy[jjj+1]
+ # Check for minimum Prediction Cell Locations
+ # ---------------------------------------------
+ u.locs <- unique(data.frame(x=locs$x[cell.index],
+ y=locs$y[cell.index]))
+ #sum(cell.index)
+ #dim(u.locs)
+ #cat(NROW(u.locs),"\n")
+ #cat( max.cell.locs, "\n")
+ if (NROW(u.locs) <= max.cell.locs) {
+ # Randomly Select first max.cell.locs
+ u.test.locs <- rbind(u.test.locs,u.locs)
+ }
+ if (NROW(u.locs) > max.cell.locs) {
+ # Randomly Select first max.cell.locs
+ # Then Randomly split the rest
+ # ---------------------------------
+ ttt.ind <- sample(1:NROW(u.locs), size=max.cell.locs)
+ u.test.locs <- rbind(u.test.locs,u.locs[ttt.ind,])
+ }
+ }}# end grid loops
+ # -----------------------------------------
+ # Build index into all locations.
+ # ------------------------------
+ test.index <- (locs$x %in% u.test.locs$x) & (locs$y %in% u.test.locs$y)
+ train.index <- !test.index
+ # -------------------------
+ # Test Plot of Grid
+ # -------------------------
+ if ( plot.it == TRUE){
+ plot(1,1,
+ xlim=c(lon.min,lon.max),
+ ylim=c(lat.min, lat.max),
+ type="n",
+ cex=0.25,
+ main =paste("Train=Blue(",sum(train.index),
+ ") Test=Red(",sum(test.index),")"))
+ require(maps)
+ map("state", add=TRUE, col="black", lwd=2)
+ for (jjj in 1:length(grid.yyy)){
+ lines(c(lon.min,lon.max),rep(grid.yyy[jjj],2),col="grey")
+ }
+ for (jjj in 1:length(grid.xxx)){
+ lines(rep(grid.xxx[jjj],2),c(lat.min,lat.max),col="grey")
+ }
+ #dim(u.test.locs)
+ points(locs$x, locs$y, col="blue", cex=0.25, pch=1)
+ points(u.test.locs, cex=0.25, col=2,pch=1)
+ } # plot.it
+# ------------------
+return(list(test.index = test.index,
+ train.index = train.index))
+# ---------------------------------------------------------------------------------
+} #end FUNCTION
+# ---------------------------------------------------------------------------------
+
+
+
+
+
+# ---------------------------------------------------------------------
+# ---------------------------------------------------------------------
+# OOB Diagnositic Plots
+# ---------------------------------------------------------------------
+plot.diagnostics <- function(pred, ensemble.data, resp.family) {
+ # ---------------------------------------------------------------------
+ # ---------------------------------------------------------------------
+ #
+ # pred = test.pred
+ # oob <- FALSE
+ # ensemble.data = test.data
+ # ---------------------------------------------------------------------
+ require(mgcv)
+ par(mfrow=c(3,2))
+ # Plot Residuals
+ # --------------
+ ttt.ind <- !is.na(pred$mean)
+ res <- (ensemble.data$y[ttt.ind] - pred$mean[ttt.ind])
+ hist(res,
+ xlab = "Observation - Prediction",
+ main = "Residuals")
+ lines(c(0,0), c(-9e9,9e9), col="blue")
+ # ------------------------------------
+ # How many models support In-Bag Predicitons
+ # and Out Of Bag/Sample Predictions
+ # --------------------------------------------
+ hist(apply(!is.na(pred$matrix), 1, sum, na.rm=T),
+ main="Ensemble Support",
+ xlab="Number of Models per Prediction")
+ # Note: Zero column is the number of training points
+ # that were never predicted OOB
+ # Plot predictions vs Obs.
+ # ---------------------------
+ ttt.ind <- !is.na(pred$mean)
+ xxx <- pred$mean[ttt.ind]
+ yyy <- ensemble.data$y[ttt.ind]
+ plot(xxx,
+ yyy,
+ xlab="Prediction",
+ ylab="Observation")
+ abline(0,1, col="blue")
+ require(mgcv)
+ d.gam <- gam(yyy ~ s(xxx), data=data.frame(yyy,xxx), gamma=1.2)
+ ttt <- seq(from=min(xxx), to=max(xxx), length=15)
+ p.ttt <- predict(d.gam, newdata=data.frame(xxx=ttt))
+ lines(ttt,p.ttt, col=2)
+ # Mean - Var Scaling
+ # -------------------
+ ttt.ind <- ( !is.na(pred$sd) & !is.na(pred$mean) )
+ xxx <- pred$mean[ttt.ind]
+ yyy <- pred$sd[ttt.ind]
+ plot(xxx,
+ yyy,
+ xlab="Ensemble Pointwise Mean",
+ ylab="Ensemble Pointwise SD")
+ abline(0,1, col="blue")
+ d.gam <- gam(yyy ~ s(xxx), data=data.frame(yyy,xxx), gamma=1.2)
+ ttt <- seq(from=min(xxx), to=max(xxx), length=15)
+ p.ttt <- predict(d.gam, newdata=data.frame(xxx=ttt))
+ lines(ttt,p.ttt, col=2)
+ # ------------------------------
+ # -------------------------------------------------------------
+ # Add Bootstrap Trajectory for MSE(oob.pred, training.obs)
+ # -------------------------------------------------------------
+ if (resp.family=="gaussian" | resp.family=="poisson") {
+ ppp <- pred$matrix # continous.res x btrials
+ j.length <- 25
+ j.ind <- seq(from=1, to=NCOL(ppp), length=j.length)
+ MSE <- rep(0, j.length)
+ for (jjj in 1:j.length){
+ if (jjj == 1) ttt.pred <- ppp[,1]
+ if (jjj > 1) ttt.pred <- apply(ppp[,c(1:j.ind[jjj])],1,
+ mean,
+ na.rm=TRUE)
+ MSE[jjj] <- predictive.performance(obs=ensemble.data$y[!is.na(ttt.pred)],
+ ppp=ttt.pred[!is.na(ttt.pred)],
+ resp.family=resp.family)$MSE
+ }
+ plot(j.ind,
+ MSE,
+ xlab="Ensemble Size",
+ main=" MSE vs Ensemble Size ",
+ type="l", lwd=2)
+ } #
+ # -------------------------------------------------
+ # -------------------------------------------------------------
+ # Add Bootstrap Trajectory for MSE(oob.pred, training.obs)
+ # -------------------------------------------------------------
+ if (resp.family=="bernoulli") {
+ ppp <- pred$matrix # continous.res x btrials
+ j.length <- 25
+ j.ind <- seq(from=1, to=NCOL(ppp), length=j.length)
+ MSE <- rep(0, j.length)
+ for (jjj in 1:j.length){
+ if (jjj == 1) ttt.pred <- ppp[,1]
+ if (jjj > 1) ttt.pred <- apply(ppp[,c(1:j.ind[jjj])],1,
+ mean,
+ na.rm=TRUE)
+ # ---------------------------------------------------------------
+ # This is a hack to accomodate
+ # an error from the ROCR prediction() function
+ # encountered when all the observations are of a
+ # single class!
+ # "Error in prediction(prediction = ppp, labels = as.numeric(obs)) :
+ # "Number of classes is not equal to 2.
+ # ---------------------------------------------------------------
+ if (length((unique(ensemble.data$y[!is.na(ttt.pred)]))) ==2)
+ MSE[jjj] <- predictive.performance(
+ obs=ensemble.data$y[!is.na(ttt.pred)],
+ ppp=ttt.pred[!is.na(ttt.pred)],
+ resp.family=resp.family)$auc
+ }
+ plot(j.ind,
+ MSE,
+ ylim=c(0.5, 1.0),
+ xlab="Ensemble Size",
+ ylab="AUC",
+ main=" AUC vs Ensemble Size ",
+ type="l", lwd=2)
+ } #
+ # -------------------------------------------------
+# -------------------------------------------------------------
+} # end function
+# ---------------------------------------------------------------------
+# ---------------------------------------------------------------------
+
+# ---------------------------------------------------------
+# Simple Plot for 1D PD plots
+#
+# This needs to really be cleaned up
+# ---------------------------------------------------------
+summary.1D.PD.ensemble<- function(filename=NULL,
+ ensemble.par.list,
+ pd.data,
+ pd.bdt.object.name = NULL,
+ continuous.resolution = 15,
+ nn.sample = 100,
+ # ----------------------
+ partial.datafile = NULL,
+ diag.bdt=NULL,
+ n.pd = 4,
+ pd.filename,
+ # ----------------------
+ plot.it = TRUE,
+ plot.range = "common",
+ n.row = 2,
+ n.col =2) {
+ # ---------pd.data------------------------------------------------
+ X.names <- names(pd.data$X)
+ X.factor.ind <- rep(FALSE, NCOL(pd.data$X))
+ ttt <- pd.data$X[1,] # it is much faster to search a 1D data.frame!
+ for (ii in 1:NCOL(pd.data$X))
+ X.factor.ind[ii] <- is.factor(ttt[,ii])
+ # ------------------------------
+ ttt.ind <- order(apply(diag.bdt$var.imp1,1,median), decreasing=TRUE)
+ pd.names <- X.names[ttt.ind]
+ pd.names <- pd.names[1:n.pd]
+ pd.factor.ind <- X.factor.ind[ttt.ind]
+ pd.factor.ind <- pd.factor.ind[1:n.pd]
+ pd.list <- as.list(pd.names)
+
+ if (is.null(pd.bdt.object.name) ){
+ # ------------------------------------------------
+ pd.bdt <- ensemble.partial.dependence(
+ filename = filename,
+ ensemble.par.list = ensemble.par.list,
+ XX = pd.data$X,
+ partial.dependence.list = pd.list,
+ continuous.resolution = continuous.resolution,
+ nn.sample = nn.sample)
+ save(pd.bdt, file=paste(pd.filename,sep=""))
+ }
+
+ if (!is.null(pd.bdt.object.name) ){
+ # ------------------------------------------------
+ load(pd.bdt.object.name) # Assumed name is pd.bdt
+ }
+
+ # ---------------------------
+ if (plot.it == TRUE) {
+ # Calc Centered PD means &
+ # Find y-limits for these plots
+ # --------------------------------
+ y.min <- 0.0
+ y.max <- 0.0
+ for (iii in 1:n.pd) {
+ # Calculate Centered Mean
+ ppp <- pd.bdt$pd.matrices[[iii]]
+ ppp.mean <- apply(ppp, 1, mean, na.rm=T)
+ ppp.mean <- ppp.mean - mean(ppp.mean)
+ y.min <- min(c(y.min,min(ppp.mean)))
+ y.max <- max(c(y.max,max(ppp.mean)))
+ }
+ y.range <- NULL
+ if (plot.range=="common") y.range <- c(y.min, y.max)
+
+ # -------------------------------------------------------------------------------------------------------
+ par(mfrow=c(n.row,n.col), mar=c(2,2,4,2))
+ # mar = c(bottom, left, top, right)
+ for (iii in 1:n.pd) {
+ # --------------------------
+ # Continuous Plot
+ # ----------------------------------
+ if (pd.factor.ind[iii] == FALSE) {
+ xxx <- pd.bdt$pd.quant.grids[[iii]] #
+ ppp <- pd.bdt$pd.matrices[[iii]] # matrix: continous.res x btrials
+ # Change ppp to data.frame
+ ppp <- data.frame(ppp)
+ # Calculate Centered Mean
+ ppp.mean <- apply(ppp, 1, mean, na.rm=T)
+ ppp.center <- mean(ppp.mean)
+ ppp.mean <- ppp.mean - ppp.center
+ #names(ppp) <- as.character(c(1:NCOL(ppp)))
+ #yyy.stacked <- stack(ppp)
+ #yyy.stacked <- as.numeric(yyy.stacked[,1])- ppp.center
+ #xxx.stacked <- rep(as.numeric(xxx[,1]), times=NCOL(ppp))
+ #----
+ plot(xxx[,1],
+ ppp.mean,
+ ylim=y.range ,
+ type = "p",
+ col="black",
+ pch = 19,
+ cex=.75,
+ xlab = " ",
+ main = names(xxx),
+ ylab = " ")
+ abline(0,0)
+
+ # -----------------------------------------------
+ # Plot when there enough unique levels to smooth
+ # ----------------------------------------------
+ if (length(sort(unique(xxx[,1]))) >= 10) {
+ # ----------------------------------------------------
+ yyy.stacked <- ppp.mean
+ xxx.stacked <- xxx[,1]
+ # ---------------
+ require(mgcv)
+ d.gam <- gam( yyy.stacked ~ s(xxx.stacked),
+ gamma=1.2)
+ xxx.pred <- seq(from=min(xxx.stacked),
+ to=max(xxx.stacked),
+ length=25)
+ pred.gam <- predict(d.gam,
+ newdata=data.frame(xxx.stacked=xxx.pred),
+ se.fit=TRUE, type="response")
+ lines(xxx.pred,pred.gam$fit,col="blue", lwd=2.0)
+ }}
+ # ----------------------------------
+ # Factor Plot
+ # ----------------------------------
+ if (pd.factor.ind[iii] == TRUE){
+ xxx <- pd.bdt$pd.quant.grids[[iii]] #
+ ppp <- pd.bdt$pd.matrices[[iii]] # continous.res x btrials
+ # Calculate Centered Mean
+ ppp.mean <- apply(ppp, 1, mean, na.rm=T)
+ ppp.center <- mean(ppp.mean)
+ ppp.mean <- ppp.mean - ppp.center
+ # -----------------------------------------------
+ # Change xxx to class factor for plot
+ # -----------------------------------------------
+ factor.levels <-
+ levels(pd.data$X[, names(pd.data$X) == names(xxx)])
+ xxx.recoded <- factor.levels[ xxx[,1]]
+ plot(as.factor(xxx.recoded),
+ ppp.mean,
+ ylim= y.range,
+ xlab = " ",
+ main = names(xxx),
+ ylab = " ")
+ abline(0,0)
+ }
+ }# end plotting
+ } # end plot.it
+} # end function
+# -------------------------------------------------------------------
+# ---------------------------------------------------------------------
+
+
+
+#------------------------------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------------------------------
+# Extract Seasonal p.data
+# function st.gam relies on this function.
+#
+# 1.13.08
+# Modified to only do a single "training/test" data set
+# and to return only the index (logical index).
+#
+#
+#Demo:
+# -----------
+# ttt.data <- seasonal.window(
+# begin.window=30,
+# end.window=80,
+# p.data=p.data)
+# names(ttt.data$X)
+# dim(ttt.data$X)
+# dim(ttt.data$Xp)
+# sort(unique(ttt.data$X$JDATE))
+#
+#
+# Tree Swallow Notes:
+# ---------------------------------
+ # -----------------------------------------
+ # Define Seasons
+ # -----------------------------------------
+ #ttt<- c( 320, 45, #winter
+ # 45, 110, #spring
+ # 110, 200, #Breeding
+ # 200, 320) # Fall
+ #season.boundaries <- matrix(ttt,4,2, byrow=TRUE)
+#------------------------------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------------------------------
+seasonal.window <- function(
+ begin.window,
+ end.window,
+ p.data){
+ season.boundaries <- matrix(c(begin.window, end.window),
+ 1,2, byrow=TRUE)
+ jjj <- 1
+ winter <- (begin.window > end.window)
+ # -----------------------------------------
+ # Training p.data
+ # -----------------------------------------
+ season.index <- p.data$jdates >= season.boundaries[jjj,1] &
+ p.data$jdates <= season.boundaries[jjj,2]
+ if (winter) { # Winter
+ season.index <- p.data$jdates >= season.boundaries[jjj,1] |
+ p.data$jdates <= season.boundaries[jjj,2]
+ }
+ return(
+ list(
+ #p.data=p.data,
+ season.index = season.index))
+ #season.p.index = season.p.index))
+ } #end function
+# -------------------------------------------------------------------------------------------
+# -------------------------------------------------------------------------------------------
+
+
+## Clear the deck of all local variables
+## rm(list = c("arrival.dates", "begin.date", "bs.rpart.maps", "by.tic", "color.palette", "create.pd.grid", "create.simple.STEM.ensemble", "D.erd.data.par.list", "deviance.explained", "end.date", "ensemble.partial.dependence", "equal.wt.max.coverage.selection", "fit.ensemble", "halloween.colors", "halloween.maps", "iii", "initizalize.map.grid", "jdate.index", "jdate.seq", "jdate.tic.names", "jdate.tics", "j.index", "make.functional.data.design.matrix", "make.SPAT.COVAR.pred.data", "map.i [...]
+## KFW gc()
\ No newline at end of file
diff --git a/contrib/stem/code/stem.library.B.R b/contrib/stem/code/stem.library.B.R
new file mode 100644
index 0000000..3d54a90
--- /dev/null
+++ b/contrib/stem/code/stem.library.B.R
@@ -0,0 +1,2124 @@
+
+# STEM LIBRARY INDEX
+# ---------------------------------------------------------
+# FUNCTION: Create Simple ST Ensemble, 5.1.09
+# * cleaned
+#
+# sample.ST.ensemble <- function( 5.1.09
+# * cleaned, consistent use of locs
+# * STEM ensemble requires ensemble.locs & ensemble.jdates
+# WTIHOUT requiring predictors ($x, $y, & $JDATE)
+# * These predictors are required if basis rotation used!
+#
+# rotate.ST.basis.sample - added ensemble.locs
+# this means that you can split by location within DT
+# without having layt & lon predictors!
+#
+# FUNCTION: Plot STEM Spatial Design
+#
+# FUNCTION: predict.ST.ensemble -
+# explicit locs & jdate incices
+# better handling of null predictions
+# verified
+#
+# FUNCTION: predict.ST.matrix
+# FUNCTION: STEM.partial.dependence
+# ** NOT yet working for lat,lon effects!!!
+#
+#
+# plot ST design Function
+# ---------------------------------------------------------
+# STEM Specific functionality that is Needed:
+# --------------
+# Histogram of ensemble sample sizes
+# Support Map at a point
+# Support Depth Map
+# -------------------------------------------
+
+
+
+
+
+
+
+
+# ---------------------------------------------------------
+# FUNCTION: Create Simple ST Ensemble
+# D Fink
+# 5.1.09
+# ---------------------------------------------------------
+#
+# Becuase the spatial regions are generated randomly, I want
+# to incorporate as much of this variation as possible in
+# the sample. We use a different spatial
+# regionalization for each time interval.
+#
+# Note with spatial design.
+# if locations are only unique locations, then min.data.size
+# if applied to unique locations. Otherwise min.data.size
+# is applied to total number of data pts w/in STEM cell.
+#
+#
+# -----------------------------------------------------------
+# Temporal Design - Seasonal Tiles
+# -----------------------------------------------------------
+# 1) jdate.seq are centers of symmetric temporal window
+# Evenly spaced slices throughout year
+# ** begin.window = vector of jdates for beginning of window
+# centered at jdate.seq
+# ** end.window = same
+# ** begin.pred.window = is the beginning of the prediction
+# window. This controls how the
+# averaging of the ensemble is done.
+# Eg. If prediction.window.width <
+# season.window.width. This can be used to remove bias
+# often encountered when predicting at end of time series.
+# If prediction.window.width > season.window.width
+# then this allows forecasting, predictions beyond the
+# time horizon of the data. This should give a more
+# realistic errors if goal is forecasting.
+# ------------------------------------------------------------
+#
+# INPUT:
+# -----------
+# y = (n x 1) full response vector
+# (Should I remove this or make it optional??)
+# X = (n x p) full design matrix
+#
+# sampling.par.list=NULL
+# split.by.location==TRUE
+# X.loc = data.frame used to split data.
+# note - the NROWS(X.loc) must equal NROWS(X) the
+# training design!!!
+# p.train = proportion data sampled for training
+# # Default ==> Use all available data for
+# # test & training sets by including all replicate locations.
+# m.frac <- 1.0
+# OUTPUT:
+# -------------
+# Regional.polygons = data.frame with components
+# x = vertices of polygons
+# y = vertices of polygons
+# region.code = sequential number code,
+#
+# Cluster.codes = (rows = NROW(ensemble.data$X)
+# cols = n.mc.regions)
+# contains the clusterings for each mc realization
+# regional.polygons = data.frame that defines the regional polygons
+# the partition the global region.
+# Here, regions are defined by clustering algorithm
+# number of polygons = n.region
+# (longitude, latitude, region.number)
+# design.summary <- Center of region mass
+# (good for Knot locations & text titles)
+# ----------------------------------------------------------------------
+# Future Development -
+# ** add logic to cycle through limited
+# number of n.mc.regions for all btrial x n.interval combinations.
+# ------------------------------------------------------------
+create.simple.STEM.ensemble <- function(
+ # Data
+ # ------------------------
+ ensemble.data.locs, # <- data.frame(x=ensemble.data$X$x, y=ensemble.data$X$y)
+ ensemble.data.jdates, # "JDATE" = Julian date from 0 to 365
+ # ------------------------
+ # Spatial Design
+ # ------------------------
+ spatial.region.par.list, # All Random Rectangle Inits
+ # Temporal Design
+ # ------------------------
+ n.intervals, # Slice year into n.intervals prediction points
+ begin.jdate = 0, #
+ end.jdate = 365,
+ season.window.width, # Fitting/Training window width in days
+ prediction.window.width, # Prediction window width in days
+ # Sampling parameters (pass through only)
+ # ------------------------------------
+ sample.ensemble.function,
+ sampling.par.list,
+ predict.ensemble.function,
+ spatial.extent.list=NULL)
+{# ---------------------------------------------------------
+# # ----------------------------------------------------------------------
+# # Formal parameter Test Values
+# # ----------------------------------------------------------------------
+
+# ----------------------------------------------------------------------
+# Temporal Design - Seasonal Tiles
+# ----------------------------------------------------------------------
+ jdate.seq <- seq(from=begin.jdate, to=end.jdate, length=(n.intervals+1))
+ jdate.seq <- round((jdate.seq[2:(n.intervals+1)] + jdate.seq[1:(n.intervals)])/2)
+ begin.window <- jdate.seq - round(season.window.width/2)
+ begin.window[ begin.window < 0 ] <- begin.window[ begin.window < 0 ] + 365
+ end.window <- jdate.seq + round(season.window.width/2)
+ end.window[ end.window > 365 ] <- end.window[ end.window > 365 ] - 365
+ # ----------------------
+ begin.pred.window <- jdate.seq - round(prediction.window.width/2)
+ begin.pred.window[ begin.pred.window < 0 ] <-
+ begin.pred.window[ begin.pred.window < 0 ] +365
+ end.pred.window <- jdate.seq + round(prediction.window.width/2)
+ end.pred.window[ end.pred.window > 365 ] <-
+ end.pred.window[ end.pred.window > 365 ] -365
+
+# ----------------------------------------------------------------------
+# Spatial Design - Random Rectangular Regional Tiles
+# ----------------------------------------------------------------------
+ # --------------------------------------------------------------------------------------------
+ # Inits
+ # --------------------------------------------------------------------------------------------
+ n.mc.regions <- spatial.region.par.list$n.mc.regions
+ # Underlying Coverage Grid
+ grid.cell.min.lat <- spatial.region.par.list$grid.cell.min.lat
+ grid.cell.min.lon <- spatial.region.par.list$grid.cell.min.lon
+ # Randomized Rectangular Regions
+ n.centers.per.region <- spatial.region.par.list$n.centers.per.region
+ regional.cell.min.lat <- spatial.region.par.list$regional.cell.min.lat
+ regional.cell.min.lon <- spatial.region.par.list$regional.cell.min.lon
+ min.data.size <- spatial.region.par.list$min.data.size
+ # Unpack location info
+ # ----------------------
+ xxx <- ensemble.data.locs$x # Longitude
+ yyy <- ensemble.data.locs$y # Longitude
+ lat.min <- min(yyy)
+ lat.max <- max(yyy)
+ lon.min <- min(xxx)
+ lon.max <- max(xxx)
+ iii.count <- 0
+# --------------------------------------------------------------------------------------------
+# Loop MC Regions - one SET of regions for each MC x Time Interval Combination
+# --------------------------------------------------------------------------------------------
+regional.polygons <- NULL
+design.summary <- NULL
+for (iii.interval in 1:n.intervals){
+for (iii.mc.region in 1:(n.mc.regions)){ # 1){ #
+ # ----------------------------------------------------------------------
+ # Define "Coverage" Grid
+ # ----------------------------------------------------------------------
+ # Store grid as x-vector of grid vertices
+ # and y-vector of grid vectices. Both of these are bookended
+ # with their min & max values.
+ # 0) Initialize with x-min,
+ # 1) randomize position of first vertex
+ # 2) lay down equally spaced grid until x.max reached
+ # ** Repeate for y-axis
+ # --------------------------------------------------
+ # --------------------------------------------------
+ # Randomize Coordinate for first grid cell boundary
+ # --------------------------------------------------
+ r.lat <- runif(1,min=0, max=grid.cell.min.lat)
+ r.lon <- runif(1,min=0, max=grid.cell.min.lon)
+ grid.ttt <- seq(from=(lon.min+r.lon),
+ to=lon.max,
+ by=grid.cell.min.lon)
+ grid.xxx <- c(lon.min, grid.ttt, lon.max)
+ grid.ttt <- seq(from=(lat.min+r.lat),
+ to=lat.max,
+ by=grid.cell.min.lat)
+ grid.yyy <- c(lat.min, grid.ttt, lat.max)
+ # incase of any duplicates!
+ grid.xxx <- sort(unique(grid.xxx))
+ grid.yyy <- sort(unique(grid.yyy))
+ # -------------------------
+ # Test Plot of Grid
+ # -------------------------
+ #plot(xxx,yyy, cex=0.25)
+ #require(maps)
+ #map("state", add=TRUE)
+ #for (jjj in 1:length(grid.yyy)){
+ # lines(c(lon.min,lon.max),rep(grid.yyy[jjj],2))
+ # }
+ #for (jjj in 1:length(grid.xxx)){
+ # lines(rep(grid.xxx[jjj],2),c(lat.min,lat.max))
+ # }
+ # --------------------------------------------------------------
+ # -------------------------------------------------------
+ # Cycle over Columns(xxx_iii) within Given Row (yyy_jjj)
+ # Sample Random Centers within Grid Cells
+ # -------------------------------------------------------
+ grid.centers.x <- NULL
+ grid.centers.y <- NULL
+ for (jjj in 1:(length(grid.yyy)-1)){
+ for (iii in 1:(length(grid.xxx)-1)){
+ ttt.index <- xxx >= grid.xxx[iii] & xxx < grid.xxx[iii+1] &
+ yyy >= grid.yyy[jjj] & yyy < grid.yyy[jjj+1]
+ ttt.df <- data.frame(xxx=xxx[ttt.index], yyy=yyy[ttt.index])
+ #ttt.u <- unique(ttt.df)
+ # Check for at least 1 data point in the coverage cell.
+ # If so, then Sample Random Centers
+ # ----------------------------------------
+ if (NROW(ttt.df) > 0 ){
+ n.centers <- n.centers.per.region
+ grid.centers.x <-c(grid.centers.x,
+ runif(n.centers,
+ min=grid.xxx[iii],
+ max=grid.xxx[iii+1]))
+ grid.centers.y <-c(grid.centers.y,
+ runif(n.centers,
+ min=grid.yyy[jjj],
+ max=grid.yyy[jjj+1]))
+ } # endif
+ # ---------------
+ } #iii
+ } #jjj
+ grid.centers <- data.frame(x=grid.centers.x,
+ y=grid.centers.y)
+ rm(grid.centers.x)
+ rm(grid.centers.y)
+ #dim(grid.centers)
+ # plot
+ #points(grid.centers, cex=1.5, pch=19, col=2)
+ # --------------------------------------------------
+ # Filter Grid Centers to lie within Target Boundary
+ # --------------------------------------------------
+ ttt.index <- c(1:NROW(grid.centers))
+ if (!is.null(spatial.extent.list)){
+ if (spatial.extent.list$type == "shapefile"){
+ ttt.index <- point.in.shapefile(
+ sites = data.frame(lon=grid.centers$x,
+ lat=grid.centers$y),
+ shape.dir=spatial.extent.list$shape.dir,
+ shape.filename=spatial.extent.list$shape.filename,
+ att.selection.column.name=
+ spatial.extent.list$att.selection.column.name,
+ selected.shape.names=
+ spatial.extent.list$selected.shape.names)
+ }
+ } # if (!is.null(spatial.extent.list)){
+ # Use Convex Hull around ensemble.data to get approximate boundary
+ # ------------------------------------------------------------
+ if (!is.null(spatial.extent.list)){
+ if (spatial.extent.list$type == "convexhull"){
+ chull.index <- chull(ensemble.data.locs )
+ ttt.index <- point.in.polygon(
+ xxx = grid.centers$x,
+ yyy = grid.centers$y,
+ polygon.vertices = ensemble.data.locs[chull.index,])
+ }}
+ # -----------------------------------------
+ grid.centers <- grid.centers[ttt.index,]
+ # -----------------------------------------
+ # plot check
+ # -----------------------------------------
+ #points(grid.centers, cex=1.0, pch=19, col=3)
+ #cat(dim(grid.centers), "\n")
+ #for (jjj in 1:length(grid.yyy)){
+ # lines(c(lon.min,lon.max),rep(grid.yyy[jjj],2))
+ # }
+ #for (jjj in 1:length(grid.xxx)){
+ # lines(rep(grid.xxx[jjj],2),c(lat.min,lat.max))
+ # }
+ # --------------
+# --------------------------------------------------------------------------------------------
+# Cycle over Regions - Check for minimum data & area requirements
+# Grow Rectanges as necessary
+# --------------------------------------------------------------------------------------------
+ for (iii in 1:NROW(grid.centers)) {
+ # Make Intial Rectangle
+ # ----------------------
+ center.lon <- grid.centers$x[iii]
+ center.lat <- grid.centers$y[iii]
+ r.lat <- regional.cell.min.lat/2
+ r.lon <- regional.cell.min.lon/2
+ regional.rectangle <- data.frame(
+ x= c((center.lon-r.lon), (center.lon-r.lon),
+ (center.lon+r.lon), (center.lon+r.lon), (center.lon- r.lon)),
+ y= c((center.lat-r.lat), (center.lat+r.lat),
+ (center.lat+r.lat), (center.lat-r.lat), (center.lat-r.lat)) )
+ # Clip X & Y coordinates: maximum is
+ # the rectangle bounding the data PLUS
+ # an essential small (epsilon) boundary. This is essential
+ # to include "boundary points" with the point in polygon
+ # routines that I am using. They points that lie
+ # on the lower polygon boundaries.
+ # --------------------------------------------------
+ epsilon <- 1e-10
+ regional.rectangle$x[ regional.rectangle$x > max(xxx)] <- max(xxx)+epsilon
+ regional.rectangle$x[ regional.rectangle$x < min(xxx)] <- min(xxx)-epsilon
+ regional.rectangle$y[ regional.rectangle$y > max(yyy)] <- max(yyy)+epsilon
+ regional.rectangle$y[ regional.rectangle$y < min(yyy)] <- min(yyy)-epsilon
+ # --------------------------
+ # Loop over all ST windows/extents/regions
+ # Record vector of Regional-seasonal sample sizes
+ # Test for minimum sample size requirements
+ # --------------------------
+ # Spatial Region Index
+ rr.index <- point.in.rectangle(
+ xxx = ensemble.data.locs$x,
+ yyy = ensemble.data.locs$y,
+ polygon.vertices = regional.rectangle )
+ # Seasonal Index
+ if ((begin.window[iii.interval] < end.window[iii.interval])) # non-Winter
+ season.index <- ensemble.data.jdates >= begin.window[iii.interval] &
+ ensemble.data.jdates <= end.window[iii.interval]
+ if ((begin.window[iii.interval] > end.window[iii.interval])) # Winter
+ season.index <-ensemble.data.jdates >= begin.window[iii.interval] |
+ ensemble.data.jdates <= end.window[iii.interval]
+ # regional & Seasonal indices
+ ttt.index <- rr.index & season.index
+ # Now see how many unique locations there
+ # are among the selected/identified points
+ # ------------------------------------------
+ u.locs <- unique(data.frame(ensemble.data.locs$x[ttt.index],
+ ensemble.data.locs$y[ttt.index]))
+ # number of unique locs
+ temp.samp.sizes <- NROW(u.locs) #sum(ttt.index)
+ # -------------------------------
+ # If minium data size is met for
+ # ALL Temporal Windows in that region
+ # Then we record its name in the book of
+ # regional names. Otherwise, we ignore that region.
+ # -------------------------------
+ # 4) Summarize Regions
+ # -------------------------------
+ if (temp.samp.sizes > min.data.size) {
+ iii.count <- iii.count + 1
+ regional.polygons <- rbind(regional.polygons,
+ data.frame(
+ regional.rectangle,
+ region.number=rep(iii.count, NROW(regional.rectangle)),
+ region.mc = iii.mc.region,
+ time.intervals=iii.interval))
+ design.summary <- rbind(design.summary,
+ data.frame(
+ x.center=center.lon,
+ y.center=center.lat,
+ region.number=iii.count,
+ region.mc=iii.mc.region,
+ time.intervals=iii.interval,
+ unique.locs = temp.samp.sizes))
+ }
+ # -------------------------------
+ # 5) plot final region
+ # -------------------------------
+ #polygon(regional.rectangle, border=iii+3)
+ #points(center.lon, center.lat, col=iii+3, pch=19)
+ #cat("Region ",iii," :",sum(rr.index),"\n")
+# ------------------------------------------------
+} # end loop over regions iii
+# ------------------------------------------------
+iii.count <- 0
+# ------------------------------------------------
+}} # end loop over MC x Time Interval Combinations
+# --------------------------------------------------------------------------------------------
+ #names(design.summary)
+ #dim(design.summary)
+ #names(regional.polygons)
+ #dim(regional.polygons)
+ # -----------------------------------------------------------------
+ # -------------------------------------------------
+ # Cleanup & Return
+ # -------------------------------------------------
+ return.list <- list(
+ ensemble.data.locs=ensemble.data.locs, # <- data.frame(x=ensemble.data$X$x, y=ensemble.data$X$y)
+ ensemble.data.jdates=ensemble.data.jdates, # "JDATE" = Julian date from 0 to 365
+ # Spatial
+ # --------
+ n.ensemble.models = NROW(design.summary),
+ regional.polygons=regional.polygons,
+ design.summary = design.summary,
+ spatial.region.par.list = spatial.region.par.list,
+ # Temporal
+ # ---------
+ n.intervals=n.intervals, # Slice year into n.intervals prediction points
+ begin.jdate = begin.jdate, #
+ end.jdate = end.jdate,
+ season.window.width=season.window.width, # Fitting/Training window width in days
+ prediction.window.width=prediction.window.width, # Prediction window width in days
+ begin.window=begin.window,
+ end.window=end.window,
+ begin.pred.window=begin.pred.window,
+ end.pred.window=end.pred.window,
+ # Sampling
+ # -----------------------
+ sample.ensemble.function = sample.ensemble.function,
+ sampling.par.list = sampling.par.list,
+ predict.ensemble.function = predict.ensemble.function)
+# ---------------------------------------- -----------------
+ return(return.list)
+# ---------------------------------------- -----------------
+}# end Create STEM ensemble Function
+# ---------------------------------------------------------
+
+
+
+# ---------------------------------------------------------
+# sample.ST.ensemble
+# ---------------------------------------------------------
+# Generate a Sample from a SINGLE ST.ensemble model
+# 4.13.09 - modifications
+# ** if there are no data in stem cell, skip that cell.
+# ---------------------------------------------------------
+sample.ST.ensemble <- function(
+ ensemble.model.number,
+ ensemble.data,
+ ensemble.par.list,
+ diagnostic.plot = FALSE)
+{# -----------------------------------------------------------
+# -----------------------------------------------------------
+# Formal Parameter TEST Values
+# -----------------------------------------------------------
+ #ensemble.model.number <- 100
+ #ensemble.data <- train.data
+# -----------------------------------------------------------
+# Inits
+# -----------------------------------------------------------
+ return.list <- NULL
+ # -----------------
+ n.ensemble.models <- ensemble.par.list$n.ensemble.models
+ # Check ensemble.model.number
+ if (ensemble.model.number > n.ensemble.models)
+ stop(paste("Error: There are only ", n.ensemble.models,
+ " ensemble models. "))
+ # --------
+ ensemble.data.locs <- ensemble.par.list$ensemble.data.locs
+ ensemble.data.jdates <- ensemble.par.list$ensemble.data.jdates
+# -----------------------------------------------------------
+# Select Temporal Window
+# -----------------------------------------------------------
+ iii.interval <-
+ ensemble.par.list$design.summary$time.intervals[ensemble.model.number]
+ sw.obj <- seasonal.window(
+ begin.window = ensemble.par.list$begin.window[iii.interval],
+ end.window = ensemble.par.list$end.window[iii.interval],
+ p.data= ensemble.data)
+
+#cat(" iii.iterval=",iii.interval,
+# ensemble.par.list$begin.window[iii.interval],
+# ensemble.par.list$end.window[iii.interval],"\n")
+#readline()
+#print(
+# cbind(ensemble.par.list$begin.window, ensemble.par.list$end.window) )
+
+
+# -----------------------------------------------------------
+# Check that there are data!!!
+# -----------------------------------------------------------
+ if (sum(sw.obj$season.index) > 0){
+# -----------------------------------------------------------
+# Select Region
+# -----------------------------------------------------------
+ # Index into regional polygons
+ region.number <- ensemble.par.list$design.summary$region.number[ensemble.model.number]
+ region.mc <- ensemble.par.list$design.summary$region.mc[ensemble.model.number]
+ #**** Requires temporal index
+ # *** 4.13 Added temporal interval
+ r.index <- (ensemble.par.list$regional.polygons$region.mc == region.mc &
+ ensemble.par.list$regional.polygons$region.number == region.number &
+ ensemble.par.list$regional.polygons$time.intervals == iii.interval )
+ # Index into p.data Training set
+ region.given.season.index <- point.in.rectangle(
+ # = ttt.data$X$x
+ xxx = ensemble.data.locs$x[sw.obj$season.index],
+ # = ttt.data$X$y
+ yyy = ensemble.data.locs$y[sw.obj$season.index],
+ polygon.vertices = ensemble.par.list$regional.polygons[r.index,1:2])
+# -----------------------------------------------------------
+# Check that there are data!!!
+# -----------------------------------------------------------
+ if (sum(region.given.season.index) > 0){
+ # -----------------------------------------------------------
+ # Indexing Verification
+ # -----------------------------------------------------------
+ # dim(ensemble.data$X) # size training data
+ # # Seasonal index = logical index into training data
+ # length(sw.obj$season.index)
+ # sum( sw.obj$season.index)
+ # # region.given.season.index = logical index into seasonal subset
+ # length(region.given.season.index)
+ # sum(region.given.season.index)
+ # # sample.data$row.index = numeric index into regional-seasonal subset
+ # length(sample.data$row.index)
+ # -------------------------------------
+ # numerical index from training data to
+ # regional-seasonal OOB/IB samples
+ # -------------------------------------
+ seasonal.num.ind <- c(1:length(sw.obj$season.index))[sw.obj$season.index]
+ #length(seasonal.num.ind)
+ reg.sea.num.ind <- seasonal.num.ind[region.given.season.index]
+# -----------------------------------------------------------
+# Sampling and Data Transformations
+# -----------------------------------------------------------
+ # Sample with rotate.ST.basis.sample()
+ sample.data <- rotate.ST.basis.sample(
+ train.data = list(
+ X = ensemble.data$X[reg.sea.num.ind,],
+ y = ensemble.data$y[reg.sea.num.ind]) ,
+ train.locs =ensemble.data.locs[reg.sea.num.ind , ] ,
+ train.jdates = ensemble.data.jdates[reg.sea.num.ind ],
+ sampling.par.list = ensemble.par.list$sampling.par.list)
+
+# -----------------------------------------------------------
+# Check that there are data!!!
+if (length(sample.data$row.index) > 0){
+# ----------------------------------------------
+ # ----------------------------------
+ # Final Indexing Information
+ # ----------------------------------
+ #length(reg.sea.num.ind)
+ ib.reg.sea.num.ind <- reg.sea.num.ind[sample.data$row.index]
+ #length(oob.reg.sea.num.ind)
+ # -----------------------
+ oob.reg.sea.num.ind <- setdiff(reg.sea.num.ind,ib.reg.sea.num.ind)
+ #length(ib.reg.sea.num.ind)
+ #length(oob.reg.sea.num.ind)+ length(ib.reg.sea.num.ind)
+
+# -----------------------------------------
+# Visual Verification Plot
+# Illustrating some fancy sampling!
+# -----------------------------------------
+ if (diagnostic.plot == TRUE) {
+ #windows()
+ # All training points
+ plot( ensemble.data.locs$x, ensemble.data.locs$y, pch=19, cex=0.5)
+ map('state',add=TRUE, lwd=2, col="yellow")
+ map('state',add=TRUE, lwd=1, col="black")
+ # -----------------------------------------------
+ # Seasonal Points
+ points(ensemble.data.locs$x[seasonal.num.ind],
+ ensemble.data.locs$y[seasonal.num.ind],
+ col="red", cex=1.0)
+ # -----------------------------------------------
+ # Regional-Seasonal Points
+ points(ensemble.data.locs$x[reg.sea.num.ind],
+ ensemble.data.locs$y[reg.sea.num.ind],
+ col="blue", cex=1.5)
+ polygon(ensemble.par.list$regional.polygons[r.index,1:2],
+ border="blue")
+ # ----------------------------------------------
+ # IB/OOB points
+ points(ensemble.data.locs$x[oob.reg.sea.num.ind],
+ ensemble.data.locs$y[oob.reg.sea.num.ind],
+ col="green", cex=2.0, lwd=2)
+ points(ensemble.data.locs$x[ib.reg.sea.num.ind],
+ ensemble.data.locs$y[ib.reg.sea.num.ind],
+ col="purple", cex=2.0, lwd=2)
+ }
+ # -------------------------------------------------
+ # Cleanup & Return
+ # -------------------------------------------------
+ return.list <- list(
+ # These are the sampled ("in bag") data
+ X = sample.data$X,
+ y = sample.data$y,
+ # Numerical IB & OOB Indices into formal parameter ensemble.data
+ oob.num.ind = oob.reg.sea.num.ind,
+ ib.num.ind = ib.reg.sea.num.ind,
+ #unique.locs.split = sample.data$dsplit,
+ realized.par = sample.data$realized.par)
+} # seasonal window check end ifs checking for data in stem cell
+} # #sw.obj$season.index
+} # bs - subsampling sampled
+ return(return.list)
+# ---------------------------------------------------------
+}# end Function sample.ST.ensemble
+# ---------------------------------------------------------
+
+
+
+# ---------------------------------------------------------
+# Sample with ST Basis Rotation
+# ---------------------------------------------------------
+# This function is identical to simple.sample,
+# except for the rotation and the sister function
+# rotate.ST.basis.pred()
+# Note: I am going to start with hard coded
+# rotation code.
+#
+#
+# ---------------------------------------------------------
+rotate.ST.basis.sample <- function(
+ train.data,
+ train.locs,
+ train.jdates,
+ sampling.par.list=NULL){
+ # ------------------------------------------------
+ # Inits
+ # ------------------------------------------------
+ n <- NROW(train.data$X)
+ realized.par <- NULL
+ dsplit <- NULL
+ # ------------------------------------------------
+ # Check sampling.par.list for "RND.seed"
+ # ------------------------------------------------
+ if (!is.null(sampling.par.list)) {
+ if (sum(names(sampling.par.list)=="RNG.seed") > 0)
+ set.seed(sampling.par.list$RNG.seed)
+ }
+ # -----------------------------------------------------------
+ # Check for Sampling with ST Basis Rotation
+ # ----------------------------------
+ # requires variables named
+ # "x" - lon coordinate
+ # "y" - lat coordinate
+ # "JDATE" - julian date
+ # --------------
+ # ==> this is a way of introducing Data Transformations
+ # or randomization into the model. perhaps this may be
+ # a nice way of icncorporating latent structure???
+ # -----------------------------------------------------------
+ if (sampling.par.list$ST.basis.rotation == TRUE){
+ # ------------------------------------------------
+ # Random Rotation of "Cartesian" Lat-Lon Plane
+ # and Random cutting of the Julian Date Circle
+ # ------------------------------------------------
+ theta.prime <- runif(1, min=0, max=2*pi)
+ train.data$X$x <- train.data$X$x*cos(theta.prime) - train.data$X$y*sin(theta.prime)
+ train.data$X$y <- train.data$X$x*sin(theta.prime) + train.data$X$y*cos(theta.prime)
+ # ------------------------------------------
+ # Random rotation of Julian Date line
+ theta2.prime <- round(runif(1, min=0, max=365))
+ train.data$X$JDATE <- train.data$X$JDATE + theta2.prime
+ train.data$X$JDATE[train.data$X$JDATE > 365] <- train.data$X$JDATE[train.data$X$JDATE > 365] - 365
+ realized.par <- c(theta.prime, theta2.prime)
+ }
+
+ # -------------------------------------------------
+ # Split Data into Train:Test sets with Unique Locations
+ # -------------------------------------------------
+ if (!is.null(sampling.par.list$split.by.location)){
+ if (sampling.par.list$split.by.location==TRUE){
+ # ------------------------------------
+ # train.locs = data.frame( x, y)
+ # -----
+ # m.frac
+ if (is.null(sampling.par.list$m.frac))
+ # Default ==> Use all available data for
+ # test & training sets by including all replicate locations.
+ m.frac <- 1.0
+ if (!is.null(sampling.par.list$m.frac))
+ m.frac <- sampling.par.list$m.frac
+ # -------
+ # p.train
+ p.train <- NULL
+ if (!is.null(sampling.par.list$p.train))
+ p.train <- sampling.par.list$p.train
+ if (is.null(sampling.par.list$p.train))
+ # Bootstrap proportion as default
+ p.train <- 0.63
+ # --------
+ dsplit <- unique.locs.splitting(
+ locs=train.locs,
+ p.train=p.train,
+ m.frac=m.frac)
+ bindex <- dsplit$train.locs.multiple
+ # default is to pass back train.locs.multiple
+ }}
+
+ # -------------------------------------------------
+ # Split Data Randomly - w/o respect to anything else
+ # -------------------------------------------------
+ if (is.null(sampling.par.list$split.by.location) |
+ (!is.null(sampling.par.list$split.by.location) &
+ sampling.par.list$split.by.location==FALSE)) {
+ # ------------------------------------------------
+ # -------------------------------------------------
+ # Random Sampling
+ # -------------------------------------------------
+ if (!is.null(sampling.par.list$p.train)){
+ bindex <- sample( c(1:n),
+ round(n*sampling.par.list$p.train) ,
+ replace=FALSE)
+ }
+ # Default is to sample with replacement
+ if (is.null(sampling.par.list$p.train))
+ bindex <- round(1 + (n-1)*runif(n))
+ } # end random split
+ # -------------------------------------------------
+
+ # -------------------------------------------------
+ # Cleanup & Return
+ # -------------------------------------------------
+ return.list <- list(
+ X = train.data$X[bindex,],
+ y = train.data$y[bindex],
+ row.index = bindex,
+ unique.locs.split = dsplit,
+ realized.par = realized.par)
+ return(return.list)
+# ---------------------------------------------------------
+}# end Function
+# ---------------------------------------------------------
+
+# ---------------------------------------------------------
+# Predict with ST Basis Rotation
+# ---------------------------------------------------------
+# The prediction-sampling functions need to
+# apply the same design transformations that were
+# used on the training data to subsequent prediction
+# designs. Here the "Cartesian" latxlon and Julian date
+# transformation are performed.
+#
+# INPUT:
+# X = (n x p) full design matrix (unrotated)
+# realized.par = c(theta.prime, theta2.prime)
+# rotation parameters
+#
+# OUTPUT:
+# X = (nnn x ppp) newly rotated prediction matrix
+#
+# NOTE
+# -----------
+# response could be made optional parameter,
+# This might be a nice way to deal with
+# response transformations??? Like
+# box-cox parameterization??
+# ----------------------------------------------
+
+
+# ---------------------------------------------------------
+rotate.ST.basis.pred <- function(X, realized.par){
+ # ----------------------------------------------------------------------
+ # Randomize(Rotate) the predictor.data
+ # 7.17.08
+ # ----------------------------------------------------------------------
+ # Random rotation of "Cartesian" lat-lon plane
+ theta.prime <-realized.par[1]
+ # Random rotation of Julian Date line, Jan 1
+ theta2.prime <- realized.par[2]
+ # ---------------------------------
+ X$x <- X$x*cos(theta.prime) - X$y*sin(theta.prime)
+ X$y <- X$x*sin(theta.prime) + X$y*cos(theta.prime)
+ # ------------------------------------------
+ X$JDATE <- X$JDATE + theta2.prime
+ ttt.ind <- (X$JDATE > 365)
+ X$JDATE[ttt.ind] <- X$JDATE[ttt.ind] - 365
+ # -------------------------------------------------
+ # Cleanup & Return
+ # -------------------------------------------------
+ return(list(X = X))
+# ---------------------------------------------------------
+}# end Function
+# ---------------------------------------------------------
+
+
+
+
+
+# --------------------------------------------------------
+pop.rpart <- function(filename, ensemble.model.number,ttt.rpart){
+ f.rpart <- ttt.rpart
+ num.txt <- formatC(ensemble.model.number,format="fg", width=6)
+ num.txt <- chartr(" ","0",num.txt)
+ temp.filename <- paste(filename,".",num.txt,".RData",sep="")
+ load( file=temp.filename) #rpart.parts
+ # ----------------------------
+ # Reassemble f.rpart from ttt.rpart stub
+ # ----------------------------
+ f.rpart$frame <- rpart.parts$frame
+ f.rpart$where <- rpart.parts$where
+ f.rpart$splits <- rpart.parts$splits
+ f.rpart$cptable <- rpart.parts$cptable
+ if (sum(names(rpart.parts) == "csplit") > 0)
+ f.rpart$csplit <- rpart.parts$csplit
+
+ return(f.rpart)
+}# end function
+
+
+# ---------------------------------------------------------
+# ---------------------------------------------------------
+# Notes: I need to check the resp.family
+# multiclass has not been added - I have not
+# how to handle the MATRIX of class probablities
+#
+# ** ensemble.pred.matrix - could be a VERY large
+# matrix. There are other strategies for dealing with
+# large data sets. This project is geared towards
+# "mid-sized" data sets.
+#
+#
+# # 3.18.09
+# ----------------------------
+# This the first revision to cut down on memory requirements
+# required when (naively) storing ALL ensmble predictions.
+# Here - store only the first two moments - mean & variance's
+# for baggged/ensemble predictions. There is a formal parameter
+# that can be set to store all predictions, if desired
+# matrix.flag = FALSE
+#
+#
+# ensemble.index = (not implemented yet)
+# optional ordered index of ensemble modelsto use for predictions)
+#
+# -----------------------------------------------------------
+# rpart.object$ frame
+# -----------------------------------------------------------
+# frame = data frame with one row for each node in the tree.
+# row.names of frame contain the (unique) node numbers that
+# follow a binary ordering indexed by node depth.
+# Elements of frame include
+# -----------------
+# * var = factor giving the variable used in the split at each node
+# (leaf nodes are denoted by the string <leaf>),
+# * n = size of each node,
+# * wt = sum of case weights for the node,
+# * dev = deviance of each node,
+# * yval = the fitted value of the response at each node, and
+# * splits = two column matrix of left and right split labels for each node.
+#Also included in the frame are
+# * complexity = complexity parameter at which this split will collapse,
+# * ncompete = number of competitor splits retained, and
+# * nsurrogate, the number of surrogate splits retained.
+# * yval2 = contains the number of events at the node (poisson),
+# or a matrix containing the fitted class, the class counts for
+# each node and the class probabilities (classification).
+# -----------------------------------------------------------
+# ---------------------------------------------------------
+# ---------------------------------------------------------
+# ---------------------------------------------------------
+predict.ST.ensemble <- function(
+ filename, # filename of ensemble & index file
+ ensemble.par.list,
+ prediction.design,
+ prediction.design.locs, # required for STEM
+ prediction.design.jdates, # required for STEM
+ matrix.flag = FALSE)
+ #ensemble.index=NULL)
+ #...) # pass through model.specific/predict.rpart parameters
+{
+
+ # ---------------------------------------------------------
+ # Formal Parameter Test Values
+ # ---------------------------------------------------------
+ # filename <- ensemble.model.filename
+ # ensemble.index <- NULL
+ # prediction.design <- train.data$X
+ # matrix.flag <- FALSE
+ # ---------------------------------------------------------
+ # Inits
+ # ---------------------------------------------------------
+ function.call <- match.call()
+ # ---------------------------
+ # Load Ensemble Information
+ # ---------------------------
+ # * Number of models in ensemble
+ # * ensemble resp.family
+ # * realized.sample.par
+ # ----------------------------
+ n.ensemble.models <- ensemble.par.list$n.ensemble.models
+ ensemble.index <- 1:n.ensemble.models
+ ensemble.index <- sort(ensemble.index)
+ # ------------------
+ temp.filename <- paste(filename,".ensemble.index.RData",sep="")
+ load(file=temp.filename) #return.list
+ ens.realized.par <- return.list$realized.sample.par
+ resp.family <- return.list$resp.family
+ rm(return.list)
+ ## KFW gc()
+# -------------------------
+# Extract Time Intervals
+# DMF - 3.17.10
+# added logic
+# -------------------------
+ time.intervals <- sort(unique(ensemble.par.list$design.summary$time.intervals))
+ time.interval.vect <- ensemble.par.list$design.summary$time.intervals
+ # These two parametes define the time intervals
+ # for each unique time interval in the ST ensemble
+ # ==> vector of length(time.intervals)
+ # ---------------------
+ begin.pred.window <- ensemble.par.list$begin.pred.window
+ end.pred.window <- ensemble.par.list$end.pred.window
+ # -----------------------------------------------------------
+ # 3.13.10
+ # Instead of looping over all temporal intervals
+ # I want to identify the subset of temporal intervals
+ # that contain any of the prediction design!!!!
+ #
+ # This should result in speed ups for many predicitons
+ # where the prediction design covers a relatively
+ # small interval of times. Eg. ST matrix and ST PD predictions.
+ # -----------------------------------------------------------
+ ttt.intervals <- rep(FALSE, length(time.intervals))
+ for (iii.time in time.intervals){
+ winter <- begin.pred.window[iii.time] > end.pred.window[iii.time]
+ if (!winter) {
+ pd.season.index <- begin.pred.window[iii.time] <=
+ prediction.design.jdates &
+ prediction.design.jdates <= end.pred.window[iii.time]
+ }
+ else {
+ pd.season.index <- begin.pred.window[iii.time] <=
+ prediction.design.jdates |
+ prediction.design.jdates <= end.pred.window[iii.time]
+ }
+ if (sum(pd.season.index) > 0) ttt.intervals[iii.time] <- TRUE
+ }
+ # Select only the time intervals needed to cover pred.design
+ time.intervals <- time.intervals[ttt.intervals]
+ # ----------------------------------------
+ # Initialize Results/Prediction Vectors
+ # ----------------------------------------
+ ens.count <- rep(0, nrow(prediction.design))
+ ens.moment1<- rep(0, nrow(prediction.design))
+ ens.moment2<- rep(0, nrow(prediction.design))
+ if (matrix.flag==TRUE){
+ ensemble.pred.matrix <- matrix(NA, NROW(prediction.design), NROW(ensemble.par.list$design.summary))
+ }
+
+ # ----------------------------------------------------------
+ # Init: Load First Ensemble Model
+ # -----------------------------------------------------------
+ iii <- 1
+ num.txt <- formatC(iii,format="fg", width=6)
+ num.txt <- chartr(" ","0",num.txt)
+ temp.filename <- paste(filename,".",num.txt,".RData",sep="")
+ load( file=temp.filename)
+
+ # Save ensemble rpart.object stub
+ ## f.rpart is coming from loaded(RData) objects
+ ttt.rpart <- f.rpart
+
+ # ----------------------------------------------------------
+ # A) Loop Over All Seasons & ID Models within Given Season
+ # -----------------------------------------------------------
+ for (iii.time in time.intervals){
+ seasonal.model.index <- c(1:length(time.interval.vect))[time.interval.vect == iii.time]
+ # ----------------------------------------------------------
+ # B) Loop over all MODELS in Specified Season &
+ # Search for Subset of Data within Prediction Season
+ # -----------------------------------------------------------
+ for (ensemble.model.number in seasonal.model.index){
+ winter <- begin.pred.window[iii.time] > end.pred.window[iii.time]
+ if (!winter) {
+ pd.season.index <- begin.pred.window[iii.time] <= prediction.design.jdates &
+ prediction.design.jdates <= end.pred.window[iii.time]
+ }
+ else {
+ pd.season.index <- begin.pred.window[iii.time] <= prediction.design.jdates |
+ prediction.design.jdates <= end.pred.window[iii.time]
+ }
+ # --------------------------------------------------------
+ # 1) Point in Polygon: Are seasonal data in Model Region?
+ # --------------------------------------------------------
+ if (sum(pd.season.index) > 0){
+ # -----------------------------------------------------------
+ # Select Region
+ # -----------------------------------------------------------
+ region.number <- ensemble.par.list$design.summary$region.number[ensemble.model.number]
+ region.mc <- ensemble.par.list$design.summary$region.mc[ensemble.model.number]
+ t.interval <- ensemble.par.list$design.summary$time.intervals[ensemble.model.number]
+ r.index <- (ensemble.par.list$regional.polygons$region.mc == region.mc &
+ ensemble.par.list$regional.polygons$region.number == region.number &
+ ensemble.par.list$regional.polygons$time.intervals == t.interval )
+ # Index into Prediction Design set
+ region.given.season.index <- point.in.rectangle(xxx = prediction.design.locs$x[pd.season.index],
+ yyy = prediction.design.locs$y[pd.season.index],
+ polygon.vertices = ensemble.par.list$regional.polygons[r.index,1:2])
+ # --------------------------------------------------------
+ # 2) Are there data in ensemble.model.number's REGION-SEASON ?
+ # -----------------------------------------------------------
+ if (sum(region.given.season.index) > 0){
+ # -------------------------------------------------
+ # Numeric Indices:
+ # superset/parent: Prediction.design
+ # subset/child : Regional-Seaonal data set
+ # -------------------------------------------------
+ seasonal.num.ind <- c(1:length(pd.season.index))[pd.season.index]
+ reg.sea.num.ind <- seasonal.num.ind[region.given.season.index]
+ # -------------------------------
+ # Regional-seasonal design
+ # ------------------------------
+ X.pred <- prediction.design[ reg.sea.num.ind, ]
+ # -------------------------------------------------
+ # check for Design Transformations, e.g. for basis rotation
+ # -------------------------------------------------
+ if (ensemble.par.list$sampling.par.list$ST.basis.rotation == TRUE){
+ ttt <- rotate.ST.basis.pred(X = X.pred, realized.par=ens.realized.par[,ensemble.model.number])
+ X.pred <- ttt$X
+ rm(ttt)
+ ## KFW gc()
+ }
+ # ----------------------------------------------------------
+ # Load/Construct rpart.object
+ # -----------------------------------------------------------
+
+ if (ensemble.model.number != 1){
+ # ---------------------------------
+ # 5.20.09
+ # Adding Error Trapping code
+ # to deal with the following mysterious message
+ # Error in f.rpart$frame <- rpart.parts$frame :
+ # value of 'SET_ATTRIB' must be a pairlist or NULL, not a 'character'
+ # ---------------------------------
+ f.rpart <- try( pop.rpart(filename, ensemble.model.number, ttt.rpart) )
+ # If there is an error, try it again
+ if (class(f.rpart) == "try-error") {
+ cat("rpart file read error \n")
+ f.rpart <- try( pop.rpart(filename, ensemble.model.number, ttt.rpart) )
+ }
+ } # end ensemble.model.number != 1
+ else {
+ f.rpart <- ttt.rpart
+ }
+
+ # -------------------------------------------------
+ # rpart Predict
+ # ------------------
+ # Note: the predict method for rpart will
+ # not make a prediction on a root node only.
+ # That is, if the rpart model is only a root node
+ # then I need to skip the call to predict - will generate an error
+ # and manually assign all pts the same prediction.
+ # --------------------
+ # 4.9.09
+ # Separate out case when bernoulli because
+ # it requires slightly different call to deal with two classes.
+ # -------------------------------------------------
+ #NROW(f.rpart$frame)
+ if (NROW(f.rpart$frame) == 1) {
+ if (resp.family == "bernoulli"){
+ # yval is the predicted response
+ # In the two class problem, the assumed coding is
+ # a factor with levels "FALSE" and "TRUE".
+ # rpart orders these alphabetically, so
+ # The first class: FALSE
+ # The second class: TRUE
+ # So, if yval are predicted prob for the first class
+ # i.e. FALSE, then I want to use 1-yval as the predicted value
+ # -------------------------------------------------------------
+ ttt.rpart.pred <- rep((1-f.rpart$frame$yval), NROW(X.pred))
+ }
+ if (resp.family =="gaussian"){
+ ttt.rpart.pred <- rep(f.rpart$frame$yval, NROW(X.pred))
+ }# end gaussian
+ } #end stump predictions section
+ # ------------------------------------------
+ # If there is more than just the root node
+ # ------------------------------------------
+ if (NROW(f.rpart$frame) > 1) {
+ if (resp.family=="gaussian"){
+ ttt.rpart.pred <- predict(f.rpart,newdata=X.pred) # ...)
+ }
+ if (resp.family=="bernoulli"){
+ ## ttt.rpart.pred.bern <- predict(f.rpart,newdata=X.pred, type="prob")
+
+ tryCatch ({
+ x.pred.attributes <- attributes(X.pred)
+ f.rpart.attributes <- attributes(f.rpart)
+
+ ## print("start of X.pred attributes")
+ ## print(x.pred.attributes)
+ ## print("end of X.pred attributes")
+
+ if (is.null(x.pred.attributes)) {
+ print("**** NULL X.pred attributes ***")
+ }
+
+ if (is.null(f.rpart.attributes)) {
+ print("**** NULL X.pred attributes ***")
+ }
+
+
+ ## print("start of f.rpart attributes")
+ ## print(f.rpart.attributes)
+ ## print("end of f.rpart attributes")
+ ## print(f.rpart)
+ ## print("======= before predict() ==================================================")
+
+ ttt.rpart.pred.bern <- predict(f.rpart,newdata=X.pred, type="prob");
+
+ ## print("after predict()")
+ },
+ error = function(ex) {
+ print("***** KFW start of catch block")
+
+ x.pred.attributes <- attributes(X.pred)
+ f.rpart.attributes <- attributes(f.rpart)
+
+ print("start of X.pred attributes")
+ print(x.pred.attributes)
+ print("end of X.pred attributes")
+ print("start of f.rpart attributes")
+ print(f.rpart.attributes)
+ print("end of f.rpart attributes")
+ print(f.rpart)
+ print("=========================================================")
+
+ ##
+ ## print("---- prediction.design ---")
+ ##
+ ## print(nrow(prediction.design))
+ ## print(ncol(prediction.design))
+ ##
+ ## for (colIndex in 1:ncol(prediction.design)) {
+ ## message <- paste(colIndex, class(prediction.design[,colIndex]), sep=" ")
+ ## print(message)
+ ## }
+ ##
+ ##
+ stop("ERROR - bailing out!")
+ },
+ finally = {
+ })
+
+ ttt.rpart.pred <- ttt.rpart.pred.bern[,2]
+ }
+ if (resp.family=="poisson") {
+ ttt.rpart.pred <- predict(f.rpart,newdata=X.pred,type="vector") #,...)
+ }
+ }
+
+ #---------------------------------------------------------------
+ # 3. Accumulate Predictions
+ # --------------------------------------------------------------
+ ens.count[reg.sea.num.ind] <- ens.count[reg.sea.num.ind] + 1
+ ens.moment1[reg.sea.num.ind] <- ens.moment1[reg.sea.num.ind] + ttt.rpart.pred
+ ens.moment2[reg.sea.num.ind] <- ens.moment2[reg.sea.num.ind] + ttt.rpart.pred^2
+ # ----------------------------
+ # nrow = NROW(prediction.design)
+ # ncol = number models in ensemble models
+ # ----------------------------
+ if (matrix.flag == TRUE){
+ ensemble.pred.matrix[reg.sea.num.ind,ensemble.model.number] <- ttt.rpart.pred
+ }
+
+ rm(X.pred)
+ } # End REGION-SEASON Prediction
+ } # if data in REGION-SEASON subset
+
+ ## KFW gc()
+ } # end loop over Seasonal ensemble models
+ } # end time interval loop
+
+ # ----------------------------------------------------------
+ # Return Prediction Matrix
+ # -----------------------------------------------------------
+ # 3.18.09 Modifications
+ # -----------------------------------
+ ens.mean <- rep(NA, NROW(prediction.design))
+ ens.var <- rep(NA, NROW(prediction.design))
+ na.ind <- (ens.count > 0)
+ ens.mean[na.ind] <- ens.moment1[na.ind]/ens.count[na.ind]
+ na.ind2 <- (ens.count >= 2)
+ ens.var[na.ind2] <- ens.moment2[na.ind2]/ (ens.count[na.ind2] -1) -
+ (ens.mean[na.ind2]^2)*(ens.count[na.ind2])/(ens.count[na.ind2] -1)
+
+ if (matrix.flag == TRUE) {
+ return.list <- list(
+ mean = ens.mean,
+ sd = sqrt(ens.var),
+ count = ens.count,
+ matrix = ensemble.pred.matrix,
+ function.call = function.call)
+ }
+ else {
+ return.list <- list(
+ mean = ens.mean,
+ sd = sqrt(ens.var),
+ count = ens.count,
+ function.call = function.call)
+ }
+
+ if (matrix.flag==TRUE){
+ rm(ensemble.pred.matrix)
+ }
+
+ ## kfw gc()
+
+ return(return.list)
+}# End FUNCTION
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+
+
+
+
+
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+# BS.RPART Random Space-Time Prediction Function
+# --------------------------------------------------------------------------
+# 1.15.07
+# 7.16.08 - quick & dirty modifications to take into
+# account basis rotations performed in the function
+# ST.BDT.test (located in this file)
+# 1.8.09 - reorganization
+#
+# This function performs two related tasks:
+#
+# 1) Predictor Conditioning
+# 2) Time-Slice Predictions
+#
+# Predictor Conditioning:
+# -----------------------------
+# For many prediction tasks it is necessary to assign constant
+# values to certain predictors. E.g. constructing a prediction
+# design to control for observation effort - by seting effort constant.
+# The conditioning variables and corresponding values are defined
+# in the conditioning.vars list. If the conditioning variable is not
+# present in the predictor.design data frame, it will be added.
+#
+# Time-Slice predictions.
+# ----------------------------
+# We loop though all time slices (defined by julian date AND year)
+# and make the full set of (spatial) predictions. This simple looping
+# proceedure was designed to handle large prediction vectors.
+# For this reason, we decided to cycle throught each ensemble model
+# for EACH time slice. This takes more time to load and reload all
+# of the models, but requires less memory to hold the predictions
+# for ALL time slices simultaneously.
+#
+# The results, i.e. the prediction vectors, are saved into sequentially
+# numbered files, in the same order as the temporal sequence.
+#
+# Like the other functions I am writing, I will begin by keeping
+# this as simple as possible. KISS!!
+#
+# INPUT
+# ------------
+# predictor.design <- data frame of predictors. Including YEAR, JDATE,
+# and the conditioning variables, this should have
+# the same number of predictors are the
+# predictors used in the models.
+# --------------
+# information about the ensemble models
+# ------------------------------------
+# model.predictor.names,
+# bs.rpart.name,
+# bs.rpart.dir,
+# btrials,
+# Save Results to directory and name
+# # --------------
+# save.name,
+# save.dir,
+# Define Temporal Sequence
+# ** jdate.seq and year.seq must be of the same length
+# the code cycles through all pairs of values.
+# jdate.seq,
+# year.seq,
+# Conditioning Variable List - This is how we control for the Observation
+# process.
+# conditioning.vars = NULL
+#
+# OUTPUT
+# ------------
+# call = call,
+# # Saved predictions
+# save.name=save.name,
+# save.dir=save.dir,
+# # Temporal Sequence
+# jdate.seq=jdate.seq,
+# year.seq = year.seq)
+#
+# To do:
+# ---------
+# I need to describe the format of D.pred in detail so that I can
+# generate new sets. Part of this will be to point to/describe the
+# process that Roger and I went through to generate this data.
+#
+# A simple way to do this is to pass the dtm object which
+# should include the names of the predictors!
+# It will also include the bs.trial, and the bs.path and file
+# name information!!!
+#
+# ERROR occurs when there is a predictor.name in "model.predictor.names"
+# but that predictor does not occurr in predictor.design or the
+# conditioning variables. should this happen?
+# If so, I should pass a more intelligible error message to the user.
+#
+# NOTE:
+# When model predicts an NA (e.g. STEM does this when location
+# has no support , i.e. an extrapolation) then this function
+#will just pass NA's through $mean & $sd
+#
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+predict.st.matrix <- function(
+ prediction.design,
+ prediction.design.locs,
+ #prediction.design.jdates = NULL, # required for STEM
+ #--------------
+ model.predictor.names,
+ model.filename,
+ ensemble.par.list,
+ # --------------
+ save.name,
+ # Temporal Sequence
+ jdate.seq,
+ year.seq,
+ # Conditioning Vars - Observation Process Design
+ conditioning.vars = NULL){
+# ---------------------------------------------------
+# prediction.design = pred.data$D.pred
+# prediction.design.locs = pred.data$locs
+# #--------------
+# model.predictor.names = names(train.data$X)
+# model.filename = ensemble.model.filename
+# ensemble.par.list = ensemble.par.list
+# # --------------
+# save.name = st.pred.filename
+# # Temporal Sequence
+# jdate.seq =jdate.seq
+# year.seq =year.seq
+# # Conditioning Vars - Observation Process Design
+# conditioning.vars = conditioning.vars
+# ---------------------------------------------------------
+# Inits
+# ---------------------------------------------------------
+ function.call <- match.call()
+## ------------------------------------------------------------------------
+# Assign and/or Add Conditioning variables as necessary
+# Verified for class numeric
+# Check to make sure that this works with factors -
+# especially if the conditioning value is a level
+# that has NOT been used for training!!!
+# ------------------------------------------------------------------------
+ for (iii in 1:length(conditioning.vars)) {
+ # When conditioning predictor is already in predictor.design
+ if (names(conditioning.vars)[iii] %in% names(prediction.design) ) {
+ pred.index <- names(prediction.design) %in% names(conditioning.vars)[iii]
+ prediction.design[ , pred.index] <- conditioning.vars[[iii]]
+ }
+ # When conditioning predictor is NOT in predictor.design
+ if (!(names(conditioning.vars)[iii] %in% names(prediction.design) )) {
+ ttt.names <- names(prediction.design)
+ ttt <- matrix(conditioning.vars[[iii]], NROW(prediction.design),1)
+ prediction.design <- data.frame(prediction.design, ttt)
+ names(prediction.design) <- c(ttt.names,
+ names(conditioning.vars)[iii])
+ }
+ } # end iii
+
+# ------------------------------------------------------------------------
+# Check to see if any model.predictor.names are missing from predictor.design
+# ------------------------------------------------------------------------
+ # ID predictors in the predictor.design but not in the model.predictors
+ #setdiff(names(prediction.design), model.predictor.names)
+ # These are OK, just extraneous
+ # and the other way around
+ #setdiff(model.predictor.names,names(prediction.design))
+ # year and jdate are OK here, but anything else needs to be flagged
+
+# --------------------------------------------------------------------------
+# Loop over dates in design & make predicitons
+# --------------------------------------------------------------------------
+ for (iii in 1:length(jdate.seq)){
+ # Set prediction design jdate
+ prediction.design.jdates <- rep(jdate.seq[iii],NROW(prediction.design))
+ # Check for predictors called JDATES & YEARS
+ # If so, then impute prediction design values
+ # ----------------------------------------------
+ if ( c("JDATE") %in% model.predictor.names )
+ prediction.design$JDATE <- rep(jdate.seq[iii],NROW(prediction.design))
+ if ( c("YEAR") %in% model.predictor.names )
+ prediction.design$YEAR <- rep(year.seq[iii],NROW(prediction.design))
+ # -----------------------------------------------
+ # Ensemble predictions
+ # -----------------------------------------------
+ #pred.Xp <- ensemble.par.list$predict.ensemble.function(
+ # filename = model.filename,
+ # ensemble.par.list =ensemble.par.list,
+ # prediction.design=predictor.design)
+ # --------------------------------------
+ pred.Xp <- predict.ST.ensemble(
+ filename = model.filename,
+ ensemble.par.list,
+ prediction.design=prediction.design,
+ prediction.design.locs=prediction.design.locs, # required for STEM
+ prediction.design.jdates=prediction.design.jdates, # required for STEM
+ matrix.flag = FALSE)
+ # --------------------------------------------------------------------------
+ # Save predictions to files
+ # --------------------------------------------------------------------------
+ save.filename <- paste(save.name,".",iii,".RData",sep="")
+ st.pred <- data.frame(
+ xxx = prediction.design.locs$x,
+ yyy = prediction.design.locs$y,
+ pred = pred.Xp$mean,
+ sd = pred.Xp$sd)
+ save(st.pred, file=save.filename) # st.pred
+ # Compare to dput or other methods to see if
+ # there is a size advantage
+ # ----------------------------------------------------
+ } # end iii loop
+
+ # ------------------------------------------------------------
+ # Return Values
+ # ------------------------------------------------------------
+ return(function.call)
+} # end function
+# --------------------------------------------------------------------------------------------
+# -------------------------------------------------------------------------------------------
+
+
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+# Modify predict.st.matrix from stem.library.8.18.09.R
+# by
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+predict.st.matrix.ebird.ref.data <- function(
+ prediction.design,
+ prediction.design.locs,
+ #prediction.design.jdates = NULL, # required for STEM
+ #--------------
+ model.predictor.names,
+ model.filename,
+ ensemble.par.list,
+ # --------------
+ save.name,
+ # Temporal Sequence
+ jdate.seq,
+ year.seq,
+ # Conditioning Vars - Observation Process Design
+ conditioning.vars = NULL){
+# ---------------------------------------------------
+# prediction.design = pred.data$D.pred
+# prediction.design.locs = pred.data$locs
+# #--------------
+# model.predictor.names = names(train.data$X)
+# model.filename = ensemble.model.filename
+# ensemble.par.list = ensemble.par.list
+# # --------------
+# save.name = st.pred.filename
+# # Temporal Sequence
+# jdate.seq =jdate.seq
+# year.seq =year.seq
+# # Conditioning Vars - Observation Process Design
+# conditioning.vars = conditioning.vars
+# ---------------------------------------------------------
+# Inits
+# ---------------------------------------------------------
+ function.call <- match.call()
+# ------------------------------------------------------------------------
+# Assign and/or Add Conditioning variables as necessary
+# Verified for class numeric
+# Check to make sure that this works with factors -
+# especially if the conditioning value is a level
+# that has NOT been used for training!!!
+# ------------------------------------------------------------------------
+ for (iii in 1:length(conditioning.vars)) {
+ # When conditioning predictor is already in predictor.design
+ if (names(conditioning.vars)[iii] %in% names(prediction.design) ) {
+ pred.index <- names(prediction.design) %in% names(conditioning.vars)[iii]
+ prediction.design[ , pred.index] <- conditioning.vars[[iii]]
+ }
+ # When conditioning predictor is NOT in predictor.design
+ if (!(names(conditioning.vars)[iii] %in% names(prediction.design) )) {
+ ttt.names <- names(prediction.design)
+ ttt <- matrix(conditioning.vars[[iii]], NROW(prediction.design),1)
+ prediction.design <- data.frame(prediction.design, ttt)
+ names(prediction.design) <- c(ttt.names,
+ names(conditioning.vars)[iii])
+ }
+ } # end iii
+
+# ------------------------------------------------------------------------
+# Check to see if any model.predictor.names are missing from predictor.design
+# ------------------------------------------------------------------------
+ # ID predictors in the predictor.design but not in the model.predictors
+ #setdiff(names(prediction.design), model.predictor.names)
+ # These are OK, just extraneous
+ # and the other way around
+ #setdiff(model.predictor.names,names(prediction.design))
+ # year and jdate are OK here, but anything else needs to be flagged
+
+ ## KFW
+ ## vegetationIndexData <- read.csv(file="ebird_reference_data/processed_VI_Data_SRD.csv", na.strings = c("NA", "?"))
+ ## KFW
+
+# --------------------------------------------------------------------------
+# Loop over dates in design & make predicitons
+# --------------------------------------------------------------------------
+ for (iii in 1:length(jdate.seq)){
+ # Set prediction design jdate
+ prediction.design.jdates <- rep(jdate.seq[iii],NROW(prediction.design))
+ # Check for predictors called JDATES & YEARS
+ # If so, then impute prediction design values
+ # ----------------------------------------------
+ if ( c("DAY") %in% model.predictor.names )
+ prediction.design$DAY <- rep(jdate.seq[iii],NROW(prediction.design))
+ if ( c("YEAR") %in% model.predictor.names )
+ prediction.design$YEAR <- rep(year.seq[iii],NROW(prediction.design))
+
+ # ----------------------------------------------------------------------------------------------------------------------
+ # 8.18.09
+ # -----------------
+ # check for special ebird reference data predictors called
+ # "caus_temp_avg" "caus_temp_min"
+ #[15] "caus_temp_max" "caus_prec"
+ #[17] "caus_snow"
+ #each of these records the climate variable value ( e.g. snow depth )
+ # for month in which observation was made. so, here i
+ # will assume that the requisite us climate are available and then
+ # select the approtiate month for the
+ # corresponding prediction design "observation".
+ # ----------------------------------------------
+ if ( "CAUS_TEMP_AVG" %in% model.predictor.names ) {
+ month.index <- floor(jdate.seq[iii] / (366/12))+1
+ num.txt <- formatC(month.index, format="fg",width=2)
+ num.txt <- chartr(" ","0",num.txt)
+ ttt.pred.name <- paste("CAUS_TEMP_AVG", num.txt,sep="")
+ ## KFW prediction.design$CAUS_TEMP_AVG <-
+ ## KFW prediction.design[ , names(prediction.design) %in% ttt.pred.name]
+
+ prediction.design$CAUS_TEMP_AVG <-
+ as.numeric(prediction.design[ , names(prediction.design) %in% ttt.pred.name])
+ } # end if
+ if ( "CAUS_TEMP_MIN" %in% model.predictor.names ) {
+ month.index <- floor(jdate.seq[iii] / (366/12))+1
+ num.txt <- formatC(month.index, format="fg",width=2)
+ num.txt <- chartr(" ","0",num.txt)
+ ttt.pred.name <- paste("CAUS_TEMP_MIN", num.txt,sep="")
+ ## KFW prediction.design$CAUS_TEMP_MIN <-
+ ## KFW prediction.design[ , names(prediction.design) %in% ttt.pred.name]
+
+ prediction.design$CAUS_TEMP_MIN <-
+ as.numeric(prediction.design[ , names(prediction.design) %in% ttt.pred.name])
+ } # end if
+ if ( "CAUS_TEMP_MAX" %in% model.predictor.names ) {
+ month.index <- floor(jdate.seq[iii] / (366/12))+1
+ num.txt <- formatC(month.index, format="fg",width=2)
+ num.txt <- chartr(" ","0",num.txt)
+ ttt.pred.name <- paste("CAUS_TEMP_MAX", num.txt,sep="")
+ ## KFW prediction.design$CAUS_TEMP_MAX <-
+ ## KFW prediction.design[ , names(prediction.design) %in% ttt.pred.name]
+
+ prediction.design$CAUS_TEMP_MAX <-
+ as.numeric(prediction.design[ , names(prediction.design) %in% ttt.pred.name])
+ } # end if
+ if ( "CAUS_PREC" %in% model.predictor.names ) {
+ month.index <- floor(jdate.seq[iii] / (366/12))+1
+ num.txt <- formatC(month.index, format="fg",width=2)
+ num.txt <- chartr(" ","0",num.txt)
+ ttt.pred.name <- paste("CAUS_PREC", num.txt,sep="")
+ ## KFW prediction.design$CAUS_PREC <-
+ ## KFW prediction.design[ , names(prediction.design) %in% ttt.pred.name]
+
+ prediction.design$CAUS_PREC <-
+ as.numeric(prediction.design[ , names(prediction.design) %in% ttt.pred.name])
+ } # end if
+ if ( "CAUS_SNOW" %in% model.predictor.names ) {
+ month.index <- floor(jdate.seq[iii] / (366/12))+1
+ num.txt <- formatC(month.index, format="fg",width=2)
+ num.txt <- chartr(" ","0",num.txt)
+ ttt.pred.name <- paste("CAUS_SNOW", num.txt,sep="")
+ # Check for Mean snow depth May - Sept
+ snow.check <- month.index >=5 & month.index <=9
+ if (snow.check) ttt.pred <- rep(0,NROW(prediction.design))
+ if (!snow.check) ttt.pred <-
+ prediction.design[ , names(prediction.design) %in% ttt.pred.name]
+ ## KFW prediction.design$CAUS_SNOW <- ttt.pred
+
+ prediction.design$CAUS_SNOW <- as.numeric(ttt.pred)
+ } # end if
+
+
+ ## KFW
+ if ( "NDVI" %in% model.predictor.names ) {
+ ## viDataRecordMask <- vegetationIndexData$YEAR == year.seq[iii] &
+ ## vegetationIndexData$DAY == jdate.seq[iii]
+
+ ## prediction.design$NDVI <- as.numeric(vegetationIndexData$NDVI[viDataRecordMask])
+
+ viDataRecordMask <- vegetationIndexData[,3] == year.seq[iii] &
+ vegetationIndexData[,4] == jdate.seq[iii]
+
+ prediction.design$NDVI <- as.numeric(vegetationIndexData[viDataRecordMask, 5])
+
+
+ ## print(year.seq[iii])
+ ## print(jdate.seq[iii])
+ ## print(prediction.design$NDVI)
+
+ rm(viDataRecordMask)
+ }
+
+ if ( "EVI" %in% model.predictor.names ) {
+ viDataRecordMask <- vegetationIndexData$YEAR == year.seq[iii] &
+ vegetationIndexData$DAY == jdate.seq[iii]
+
+ prediction.design$EVI <- as.numeric(vegetationIndexData$EVI[viDataRecordMask])
+
+ rm(viDataRecordMask)
+ }
+ ## KFW
+
+
+ # -----------------------------------------------
+ # Ensemble predictions
+ # -----------------------------------------------
+ #pred.Xp <- ensemble.par.list$predict.ensemble.function(
+ # filename = model.filename,
+ # ensemble.par.list =ensemble.par.list,
+ # prediction.design=predictor.design)
+ # --------------------------------------
+
+
+ ## print("predict.st.matrix.ebird.ref.data() calling predict.ST.ensemble()")
+
+ pred.Xp <- predict.ST.ensemble(
+ filename = model.filename,
+ ensemble.par.list,
+ prediction.design=prediction.design,
+ prediction.design.locs=prediction.design.locs, # required for STEM
+ prediction.design.jdates=prediction.design.jdates, # required for STEM
+ matrix.flag = FALSE)
+ # --------------------------------------------------------------------------
+ # Save predictions to files
+ # --------------------------------------------------------------------------
+ save.filename <- paste(save.name,".",iii,".RData",sep="")
+ st.pred <- data.frame(
+ xxx = prediction.design.locs$x,
+ yyy = prediction.design.locs$y,
+ pred = pred.Xp$mean,
+ sd = pred.Xp$sd)
+ save(st.pred, file=save.filename) # st.pred
+ # Compare to dput or other methods to see if
+ # there is a size advantage
+ # ----------------------------------------------------
+ } # end iii loop
+
+ # ------------------------------------------------------------
+ # Return Values
+ # ------------------------------------------------------------
+ return(st.pred)
+} # end function
+# --------------------------------------------------------------------------------------------
+# -------------------------------------------------------------------------------------------
+
+
+
+# -------------------------------------------------------------------
+# Predict.pd.grid - Function to make Predictions over PD.grids
+# -------------------------------------------------------------------
+# Input
+# XX = DTM Design matrix
+# pd.quant.grids = create.pd.grid obejct
+# nn.sample = # of randomly selected samples from XX
+# Output
+# list of predictions for each member of the create.pd.grid.object
+#
+# 5.4.09
+# --------------------------------
+# ** Got rid of "matrix" object - only using mean
+# ** STEM additions
+# construct updated prediction.design.locs & prediction.design.jdate
+# ** break appart & sum over nn.sample
+# ** added logic to deal with PD of JDATE and (x,y) locs
+#
+# TO DO:
+# --------------------------------
+# ** collect PD sd estimates!
+# ** Need to Recode Categorical predictors
+# eg. if BCR was a predictor we would need to recode it
+# to its proper level labels !!!!!
+# Currently, BCR is coded as the number of the LEVEL
+# xxx.grid[,2] <- levels(train.data$X$BCR)[xxx.grid[,2]]
+# ** 2.26.10
+# I need to take a single random sample
+# of size nn.sample from an index of length == nrows(prediction.design)
+# then add to it over the batch "samples".
+# This instead of the multiple samples taken one batch at a time.
+# ------------------------------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------------------------------
+STEM.partial.dependence <- function(
+ filename,
+ ensemble.par.list,
+ prediction.design, #XX,
+ prediction.design.locs, # required for STEM
+ prediction.design.jdates, # required for STEM
+ partial.dependence.list,
+ continuous.resolution = 15,
+ nn.sample = 200,
+ batch.size =50 )
+{ # ----------------------------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------------------------------
+# Test Formal Parameters
+# ------------------------------------------------------------------------------------------------------
+# pd.list <- list(
+# "NLCD01_N90A100R5", "JDATE",
+# # 2D Partials
+# c("x", "y"), # lat x lon interaction
+# c("JDATE", "NLCD01_N90A100R5")) # can we pick up change in time of sunrise?
+# filename = ensemble.model.filename
+# ensemble.par.list = ensemble.par.list
+# #XX = train.data$X,
+# prediction.design=train.data$X #XX,
+# prediction.design.locs=ensemble.par.list$ensemble.data.locs # required for STEM
+# prediction.design.jdates=ensemble.par.list$ensemble.data.jdates # required for STEM
+# partial.dependence.list=pd.list
+# continuous.resolution = 30
+# nn.sample = 500
+# batch.size = 50
+# ------------------------------------------------------------------------------------------------------
+# Inits Formal Parameters
+# ------------------------------------------------------------------------------------------------------
+ #temp.filename <- paste(filename,".ensemble.index.RData",sep="")
+ #load(file=temp.filename) #return.list
+ #bs.trials <- NCOL(return.list$ib.sample.index)
+ # Results
+ XX <- prediction.design
+ pd.means <- vector(mode="list", length=length(partial.dependence.list))
+ pd.matrices <- vector(mode="list", length=length(partial.dependence.list))
+# ------------------------------------------------------------------------------------------------------
+# Compute Partial Dependence Quantile Grids
+# ------------------------------------------------------------------------------------------------------
+ pd.quant.grids <- create.pd.grid(
+ XX=XX,
+ i.var.list=partial.dependence.list,
+ continuous.resolution = continuous.resolution)
+# ------------------------------------------------------------------------------------------------------
+# Find factors in XX
+# Note : I can not use apply b/c XX is class data.frame
+# ------------------------------------------------------------------------------------------------------
+ XX.factor.ind <- rep(FALSE, NCOL(XX))
+ ttt <- XX[1,] # it is much faster to search a 1D data.frame!
+ for (ii in 1:NCOL(XX)) XX.factor.ind[ii] <- is.factor(ttt[,ii])
+ # Extract an index of column positions for factors (wo zeros!)
+ factor.index <- as.numeric(XX.factor.ind)*seq(1,NCOL(XX))
+ factor.index <- factor.index[factor.index > 0 ]
+# ------------------------------------------------------------------------------------------------------
+# Loop Over PD list elements
+# ------------------------------------------------------------------------------------------------------
+for (iii in 1:length(pd.quant.grids)){
+ # Initialize Batch Result Vectors
+ ppp.batch <- 0
+ ppp.batch.count <- 0
+ # Calculate # of Batch Loops
+ nnn.batch <- floor(nn.sample/batch.size) +
+ as.numeric(ceiling(nn.sample/batch.size) >
+ floor(nn.sample/batch.size))
+# Begin Batch loop Here
+# -------------------------------
+for ( iii.batch in 1:nnn.batch){
+# -------------------------------
+ batch.sample.size <- min(batch.size, (nn.sample - (iii.batch-1)*batch.size))
+ # ------------------------------------------------------------------------------------------------------
+ # Random Sample of Data Rows (same sample for all PD elements)
+ # ------------------------------------------------------------------------------------------------------
+ # Sample without replacement from data rows
+ if (batch.sample.size >= NROW(XX))
+ sample.index <- sample(1:NROW(XX), batch.sample.size, replace = TRUE)
+ if (batch.sample.size < NROW(XX))
+ sample.index <- sample(1:NROW(XX), batch.sample.size, replace = FALSE)
+ #dim(XX.sample)
+ # ------------------------------------
+ # 1. Expand Quantile Grid into PD Prediction Design
+ # 2. BDT Predictions
+ # 3. Assemble Results
+ # ------------------------------------
+ i.var <- match( names(pd.quant.grids[[iii]]), names(XX))
+ XX.sample <- XX[sample.index, setdiff(names(XX), names(XX)[i.var]) ]
+ pd.grid <- pd.quant.grids[[iii]]
+ # ----------------------------
+ # NOTE** PD design can get big = batch.sample.size * length(pd.grid)
+ # ------------------------------------------------------------------------------------------------------
+ # Construct Partial Dependence Prediction Data Frame
+ # NOTE: the use of data.matrix converts factors to numerics
+ # ------------------------------------------------------------------------------------------------------
+ # Stack Randomly Sampled Data Rows
+ XX.stack <- kronecker( matrix(1, NROW(pd.grid), 1),
+ data.matrix(XX.sample))
+ XX.stack <- as.data.frame(XX.stack)
+ names(XX.stack) <- names(XX.sample)
+ # Stack Partial Dependence Grids
+ pd.stack <- kronecker( data.matrix(pd.grid), matrix(1, batch.sample.size, 1))
+ pd.stack <- as.data.frame(pd.stack)
+ names(pd.stack) <- names(pd.grid)
+ PD.prediction.frame <- cbind(pd.stack,XX.stack)
+ # -------------------------------------------
+ # Stack Location & JDATE indices
+ # Stack Randomly Sampled Data Rows
+ XX.locs.sample <- prediction.design.locs[sample.index,]
+ XX.locs.stack <- kronecker( matrix(1, NROW(pd.grid), 1),
+ data.matrix(XX.locs.sample))
+ XX.locs.stack <- as.data.frame(XX.locs.stack)
+ names(XX.locs.stack) <- names(XX.locs.sample)
+ # -----------
+ XX.jdates.sample <- prediction.design.jdates[sample.index]
+ XX.jdates.stack <- kronecker( matrix(1, NROW(pd.grid), 1),
+ data.matrix(XX.jdates.sample))
+ # -------------------------------------------
+ # **** Check to see if i.var is an index variable.
+ # Currently the ST index variable names are hardcoded to " x, y, or JDATE "
+ #
+ # modified 10.20.09
+ #
+ # If so, then modify parameter indices accordingly
+ # ** Check out the flexible logic - this will work
+ # for any pd.list!
+ # -------------------------------------------
+ # if ("DAY" %in% names(XX)[i.var]) XX.jdates.stack <- pd.stack$DAY
+ # if ("x" %in% names(XX)[i.var]) XX.locs.stack[,1] <- pd.stack$x
+ # if ("y" %in% names(XX)[i.var]) XX.locs.stack[,2] <- pd.stack$y
+ # modified 02.17.10
+ # -------------------
+ # With the separate index variables, there is no need to
+ # treat them specially, whether or not the same index
+ # variables are used as predictors.
+ # Therefore, I removed the lines above.
+
+
+ # ------------------------------------------------------------------------------------------------------
+ # Reconstruct Factor structure for data.frame
+ # ------------------------------------------------------------------------------------------------------
+ # XX = original data frame that may include factors
+ # PD.prediction.frame = the data.frame currently with numeric
+ # values for all predictors. The prediction data.frame needs
+ # to have the same column/predictor structure as XX
+ # ------------------------------------------------
+ # 1) Reorder PD.prediction.frame to match XX
+ col.order <- match( names(XX), names(PD.prediction.frame))
+ PD.prediction.frame <- PD.prediction.frame[,col.order]
+ # 2) Convert PD.prediction.frame cols to factors
+ for (i in factor.index) {
+ PD.prediction.frame[,i] <-
+ factor(levels(XX[,i])[PD.prediction.frame[,i]],
+ levels=levels(XX[,i]))
+ }
+ # ------------------------------------------------------------------------------------------------------
+ # Ensemble PD Predictions
+ # ------------------------------------------------------------------------------------------------------
+ ttt.pred <- predict.ST.ensemble(
+ filename= filename, # filename of ensemble & index file
+ ensemble.par.list = ensemble.par.list,
+ prediction.design= PD.prediction.frame,
+ prediction.design.locs=XX.locs.stack, # required for STEM
+ prediction.design.jdates=XX.jdates.stack, # required for STEM
+ matrix.flag = FALSE)
+ pred.X <- ttt.pred$mean
+ # --------------------------------------------
+ # Average to get Ensemble average PD estimates
+ # --------------------------------------------
+ pred.index <- (rep(c(1:NROW(pd.grid)),each=batch.sample.size))
+ ppp <- tapply(pred.X, pred.index, sum, na.rm=T)
+ ppp.count <- tapply(!is.na(pred.X), pred.index, sum, na.rm=T)
+ # ---------------------------------
+ # Collect the mean (first moment + count)
+ # across batch of partial prediction jobs
+ # ---------------------------------
+ ppp.batch <- ppp.batch + ppp
+ ppp.batch.count <- ppp.batch.count + ppp.count
+ # ---------------------------------
+ # 2.26.10 Cleanup
+ # (incomplete)
+ # ---------------------------------
+ rm(ttt.pred, XX.stack,pd.stack,PD.prediction.frame,
+ XX.locs.stack, XX.jdates.stack)
+ ## KFW gc()
+
+# end Batch loop Here
+# -------------------------
+} # end iii.batch
+# -------------------------
+ if (sum(ppp.batch.count==0) > 0)
+ warning(paste("STEM.partial.dependence: unsupported",
+ "partial predictions, ppp.batch.count==0 "))
+ # Calculate Mean Value and Final Count(support)
+ ppp <- ppp.batch/ppp.batch.count
+ # -------------------------------
+ # recode pd.grid factors
+ f.factor <- rep(FALSE, NCOL(pd.grid))
+ for (i in 1:NCOL(pd.grid)) {
+ col.index <- match( names(pd.grid)[i], names(XX))
+ if (!is.numeric( XX[,col.index] )) {
+ f.factor[i] <- TRUE
+ #if (names(pd.grid[i]) %in% names(XX)[factor.index])
+ pd.grid[,i] <-
+ factor(levels(XX[,col.index])[pd.grid[,i]],
+ levels=levels(XX[,col.index]))}
+ } #end for i - search for factors
+ # Reassociate pd.grid with predictions
+ pdf.grid <- data.frame(pd.grid, pred=ppp)
+ # -----------------------------------
+ # Store results in PD.list
+ # -----------------------------------
+ # pd.means = the Partial Dependence Estimate averaged over bags
+ # pd.matrices = the PD estimates, one col per bag/model
+ pd.means[[iii]] <- pdf.grid
+ #pd.matrices[[iii]] <- pdf.grid.matrix
+ #names(pdf.grid)
+ #dim(pdf.grid)
+} # end iii
+# -----------------
+return(list(
+ pd.quant.grids=pd.quant.grids,
+ pd.means=pd.means))
+ #pd.matrices=pd.matrices))
+} # end function
+# -------------------------------------------------------------------
+# ---------------------------------------------------------------------
+
+
+
+
+# ---------------------------------------------------------------------------------------------------------------------
+# Plot STEM Temporal Design
+# ---------------------------------------------------------------------------------------------------------------------
+plot.STEM.temporal.design<- function(
+ ensemble.par.list)
+ #ensemble.data,
+ #mc.region.x.time.index=1, # value of nnn.spatial.mc)
+ #...) # pass through plotting parameters?
+{# ---------------------------------------------------------
+ #ensemble.par.list
+ p.min <- -1.5
+ p.max <- 1.5
+ # -----------------------------------------------------
+ # Central Julian Calendar Circle
+ # ------------------------------------------------------
+ nnn <- 1000
+ radian.seq <- seq(from=0, to=2*pi, length=nnn)
+ plot( cos(radian.seq),
+ sin(radian.seq),
+ type="l",
+ lwd=3.0,
+ xlab=" ",
+ ylab=" ",
+ xlim = c(p.min,p.max),
+ ylim = c(p.min, p.max),
+ axes = FALSE)
+ # ---------------------------------------------------------
+ # Convert Temporal Sequence times to POSIX
+ # ---------------------------------------------------------
+ #text( -.25, .75,
+ # pos=4, # text is to the left of location
+ # cex = 1.5,
+ # labels=c("Dec/Jan") )
+ # Add notches at 3,6,9, & 12 o'clock
+ n.notches <- 12
+ radian.seq <- seq(from=pi/2, to=5*pi/2, length=(n.notches+1))
+ jdate.ttt <- 365 - radian.seq/2/pi *365 + radian.seq[1]/2/pi *365 + 1
+ jdate.ttt[jdate.ttt > 365] <- jdate.ttt[jdate.ttt > 365] -365
+ jdate.ttt <- jdate.ttt[1:n.notches]
+ p.time <- strptime( x=paste(round(jdate.ttt)), "%j")
+ # Nice function to convert DateTime Classes
+ month.text <- months(p.time, abbreviate = TRUE)
+ date.names <- paste(month.text, " ",p.time$mday,sep="")
+ #p.time
+ #month.text
+ #date.names
+ ttt.min <- 1.0
+ ttt.max <- 1.1
+ inside.scale <- 0.9
+ for (iii in 1:n.notches){
+ lines( c(ttt.min*cos(radian.seq[iii]), ttt.max*cos(radian.seq[iii])),
+ c(ttt.min*sin(radian.seq[iii]), ttt.max*sin(radian.seq[iii])),
+ lwd=2.0)
+ text( inside.scale* cos(radian.seq[iii]) ,
+ inside.scale*sin(radian.seq[iii]),
+ # pos=4, # text is to the left of location
+ # cex = 1.5,
+ labels=c(month.text[iii]) )
+ }
+ # ---------------------------------------------------------
+ # Add Shingles
+ # ---------------------------------------------------------
+ nnn <- length(ensemble.par.list$begin.window)
+ #nnn <- 1
+ inner.radius <- 1.0
+ outer.radius <- 1.5
+ training.window.color <- "blue"
+ inner.pred.radius <- inner.radius + 0.1
+ outer.pred.radius <- outer.radius - 0.1
+ pred.window.color <- "red"
+ # Convert Julian dates into positions on Julian Calendar
+ begin.window.radians <- ensemble.par.list$end.window/365*2*pi + pi/2
+ end.window.radians <- ensemble.par.list$begin.window/365*2*pi + pi/2
+ begin.pred.window.radians <- ensemble.par.list$begin.pred.window/365*2*pi + pi/2
+ end.pred.window.radians <- ensemble.par.list$end.pred.window/365*2*pi + pi/2
+ for (iii in 1:nnn){
+ lines( c( inner.radius*cos(begin.window.radians [iii]),
+ outer.radius*cos(end.window.radians [iii])),
+ c( inner.radius*sin(begin.window.radians [iii]),
+ outer.radius*sin(end.window.radians [iii])),
+ lwd=2.0,
+ col=training.window.color)
+ #lines( c( inner.pred.radius*cos(begin.pred.window.radians [iii]),
+ # outer.pred.radius*cos(end.pred.window.radians [iii])),
+ # c( inner.pred.radius*sin(begin.pred.window.radians [iii]),
+ # outer.pred.radius*sin(end.pred.window.radians [iii])),
+ # lwd=2.0,
+ # col=pred.window.color)
+ }
+ title(main = paste("STEM Temporal Design"),
+ font.main=4, line=2, cex.main=2.0 )
+
+
+ # ---------------------------------------------------------
+ return()
+# ---------------------------------------------------------------------------------------------------------------------
+}# end plot ST ensemble Function
+# ---------------------------------------------------------------------------------------------------------------------
+# ---------------------------------------------------------------------------------------------------------------------
+
+
+
+
+# ---------------------------------------------------------------------------
+# FUNCTION: Plot STEM Spatial Design
+# --------------------------------------
+# Plots a sinlge realization of the STEM Spatial design
+# identified & indexed by its mc.region and time.interval values.
+#
+# # -------------------------------
+# regional.polygons <- rbind(regional.polygons,
+# data.frame(
+# regional.rectangle,
+# region.number=rep(iii, NROW(regional.rectangle)),
+# region.mc = iii.mc.region,
+# time.intervals=iii.interval))
+# ----------------------------------------------------------------------------
+plot.ST.ensemble <- function(
+ ensemble.par.list,
+ # Like JDATE-YEAR.SEQ's These two vectors
+ # define an index PAIR into the ensemble
+ # This means that these have to be the same length!!!!
+ # ----------------------------------------------------
+ mc.regions,
+ time.intervals,
+ ...) # pass through plotting parameters?
+{# ---------------------------------------------------------
+ # mc.regions = c(1)
+ # time.intervals = c(2)
+# -------------------------
+# Inits
+# ------------------------
+ require(maps)
+ regional.polygons <- ensemble.par.list$regional.polygons
+ xxx <- regional.polygons$x
+ yyy <- regional.polygons$y
+ # -------------------------
+ # Plot clusters
+ # ------------------------
+ # Divergent Colors from RColorBrewer
+ col.names <- c( "#E41A1C", "#377EB8", "#4DAF4A",
+ "#984EA3", "#FF7F00", #"#FFFF33", Remove yellow!!
+ "#A65628", "#F781BF", "#999999",
+ "#66C2A5", "#FC8D62", "#8DA0CB",
+ "#E78AC3", "#A6D854", "#FFD92F",
+ "#E5C494", "#B3B3B3")
+ # Repeat colors for large sets of polygons
+ col.names <- rep( col.names, times=1000)
+ # Intialize Plotting Region
+ plot(xxx, yyy, type="n", ...)
+ map('state',add=TRUE, lwd=2, col="yellow")
+ map('state',add=TRUE, lwd=1, col="black")
+ # ------------------------------------------------
+ for (jjj in length(time.intervals)){
+ ttt.index <- regional.polygons$region.mc == mc.regions[jjj] &
+ regional.polygons$time.intervals == time.intervals[jjj]
+ ttt.poly <- regional.polygons[ttt.index,]
+ n.region <- max(ttt.poly$region.number)
+ for (iii in 1:n.region){
+ polygon(ttt.poly[ttt.poly$region.number == iii,],
+ border = col.names[iii],
+ lwd=2.0,
+ density=NULL)
+ #cat("polygon=",iii," Enter to continue","\n") # prompt
+ #ttt.scan <-scan(n=1,what="character")
+ } # end iii
+ } # end jjj
+ # ------------------------------------------------
+ #points(region.centers, col="white", cex=1.5)
+ #points(ensemble.data$X$x,ensemble.data$X$y, col="black", cex=.25)
+ #points(ensemble.data$X$x,ensemble.data$X$y, col="white", cex=.25)
+# ---------------------------------------------------------
+ return()
+# ---------------------------------------------------------
+}# end plot ST ensemble Function
+# ---------------------------------------------------------
+
+
+
diff --git a/contrib/stem/code/stem.library.ST.R b/contrib/stem/code/stem.library.ST.R
new file mode 100644
index 0000000..f795bad
--- /dev/null
+++ b/contrib/stem/code/stem.library.ST.R
@@ -0,0 +1,2430 @@
+
+
+
+# ------------------------------------------------------------------
+# 10.8.08
+# Adding
+# Point in ploygon Function
+# (This is a more basic/generic version of the
+# the point.in.polygon.contours() function in
+# rel.abundance.mapping.functions3.r.
+#
+#
+# 10.6.08
+# Adding Functions:
+# Point in ShapeFile Function
+# NOTE: This function is based on the NCEAS function XXXXXX
+# except that I needed to fix the donut hole problem with
+# the shape files. I need to finish documenting this and
+# send it back to those guys!
+# Initialize Map Gridding
+# Needed ==> a more generic regional.cluster.cloropleth.map()
+#
+# ------------------------------------------------------------------
+
+
+#------------------------------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------------------------------
+# SBT: Better ST Maps
+# -------------------------------------
+# 9.9.08
+#
+# Produce maps and save them to disk.
+# Based on "st.bdt.surface.maps.9.9.R"
+#
+# 10.20.08 Modifications
+# -----------------------------------------
+# 1) Added code include the leading zeros on the map.filename
+# This produces files that will be sequentially ordered in file browsers!
+# Small but important "convenience" modification.
+# 2) Also added call to the function initizalize.map.grid() in
+# st.clustering.functions.2.R format maps automatically
+# 3) Assumed additional parameters
+# begin.seq
+# end.seq
+#
+# 10/24/08
+# -------------------
+# * Added code & switch to deal with sqrt transform
+# # Response Transformation code: resp.transformation.code <- "sqrt"
+# * Excluded the extraneous spatial density contours
+#
+# 11/19/08
+# -------------
+# google earth maps - transparent & no margin plots.
+#
+#
+# REQUIRES
+# ------------------------
+#"eBird taxonomy file.csv",
+#"yelwar.East.travel.spatial.density.contours.RData",se
+ #~ # ------------------------
+ #~ # control.data
+ #~ # ------------------------
+ #~ # (spp.code, spatial.extent, exp.tag, ST.group)
+ #~ # ST groups
+ #~ # A - 156 - 1 per week 2004-06
+ #~ # B - 36 - 1 per month 2004 -2006
+ #~ # C -26 - 1per 2 weeks 2006
+ #~ # ------------------------
+ #~ "amekes", US, stbdt.8.19., B
+ #~ "buffle",US, stbdt.8.19., C
+ #~ "buwwar",East, stbdt.8.19., B
+ #~ "barswa", US, stbdt.9.3.,C
+ #~ "cavswa", SoTX, stbdt.9.3.,C
+ #~ "cliswa", US, stbdt.9.3.,C
+#------------------------------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------------------------------
+
+
+
+## KFW
+require(fields)
+
+
+
+
+
+
+
+# These are legacy code for spatial contours
+# They will need to be intergrated with current functions
+# if this functions stays!
+# -------------------------------------------------------------------
+# Poisson Predictive Performance Measures
+# -------------------------------------------------------------------
+# yyy = observations
+# ppp = predicted value - response scale
+#
+# Verified - replicated GAM deviance calcuatlions for poisson
+poisson.deviance <- function(yyy,ppp){
+ # if predictions (ppp) equal zero we will get underflow
+ # problems from log function.
+ # -------------
+ # break deviance into two pieces - where obs == 0
+ ttt.zero <- (yyy == 0)
+ ttt.pos <- (yyy > 0)
+ dev1 <- sum( (yyy[ttt.zero] - ppp[ttt.zero]) )
+ dev2 <- sum( yyy[ttt.pos]*(log(yyy[ttt.pos])-log(ppp[ttt.pos])) -
+ (yyy[ttt.pos] - ppp[ttt.pos]))
+ dev <- 2*(dev2 - dev1)
+ return(dev)
+ }
+
+deviance.explained <- function(yyy,ppp){
+ null.deviance <- poisson.deviance(yyy, rep(mean(yyy),length(yyy) ))
+ obs.deviance <- poisson.deviance(yyy,ppp)
+ deviance.explained <- (null.deviance - obs.deviance)/null.deviance
+ de <- list(deviance.explained=deviance.explained,
+ obs.deviance=obs.deviance,
+ null.deviance=null.deviance)
+ return(de)
+ }
+
+poisson.pearson <- function(yyy,ppp){
+ p <- sum( ((yyy - ppp)^2)/(ppp) )
+ return(p)
+ }
+
+ # Accuracy of 0-1 Classification for Poisson Regression
+ # ---------------------------------------------------------
+ poisson.accuracy <- function(yyy, ppp, threshold=0.5){
+ y.binary <- as.numeric(yyy > threshold)
+ p.binary <- as.numeric(ppp > threshold)
+ acc <- 1-sum(abs(y.binary - p.binary))/length(y.binary)
+ return(acc)
+ }
+# -------------------------------------------------------------------
+# -------------------------------------------------------------------
+
+
+
+
+
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+# Measure Predictive performance as a function of Spatial Scale
+# -----------------------------------------------------------------------------
+# Daniel Fink
+# 1.9.08
+# 2.7.08 modifications
+#
+# Description
+# -----------------
+# This function Measures the predictive performance as a function of
+# Spatial Scale. It takes the bs.model object from a single test/training
+# split and bins/grids this data across a range of scales. Performance
+# is computed and recorded at each scale and passed back to the user.
+# Predictive performance is computed on the test set.
+# Predictive performance may also be plotted as a function of scale.
+#
+# Currently, the function will take the entire spatial extent analyzed/
+# in the data set, p.data.
+#
+# Input
+# ----------
+# p.data,
+# dtm.obj,
+# grid.size.seq,
+# grid.size.units = "cells",
+# file.name=NULL,
+# plot.it=FALSE,
+# plot.height=600
+# plot.width=800
+#
+# Output
+# ----------
+# pred.performance[iii,1] <- perf.ttt$deviance.explained
+# pred.performance[iii,2] <- perf.ttt$obs.deviance
+# pred.performance[iii,3] <- poisson.pearson(zzz.size[ttt.ind],ppp.size[ttt.ind] )
+# # Total number of grid cells that have test-set observations
+# pred.performance[iii,4] <- NROW(image.pred$ind)
+# # Median # of observations/grid cell, in grid cells with observations
+# pred.performance[iii,5] <- median(image.pred$weights[image.pred$ind])
+# # Grid Size in units of cells
+# pred.performance[iii,6] <- grid.size[iii]
+# # Grid Size in units of (approximate) km^2
+# pred.performance[iii,7] <- grid.size[iii]
+#
+#
+# Notes:
+# ---------
+#
+# Further Development:
+# ----------------------------
+# * include km2 as units
+# Check out the web page at
+# http://www.movable-type.co.uk/scripts/latlong.html
+# for the Haversine formula
+# * inlcude control over spatial.extent
+# -----------------------------------------------------------------------------
+spatial.performance.plot <- function(
+ xxx,
+ yyy,
+ ppp, # predicted
+ zzz, #obs
+ spatial.extent=NULL,
+ #dtm.obj,
+ grid.size.seq,
+ grid.size.ratio = 2,
+ grid.size.units = "cells",
+ # ----------------------------
+ file.name=NULL,
+ plot.it=NULL,
+ span=0.3,
+ plot.height=600,
+ plot.width=800){
+# ------------------------------------------
+# Dummy Values
+# ------------------------------------------
+# xxx = test.data$X$x[subset.index]
+# yyy = test.data$X$y[subset.index]
+# ppp = test.pred$mean[subset.index] predicted
+# zzz = test.data$y[subset.index] observed
+# spatial.extent = spatial.extent
+# grid.size.seq = grid.size.seq
+# grid.size.ratio = 1.0
+# file.name=NULL
+# plot.it=TRUE
+#
+# spatial.extent <- list(
+# # NE Region
+# lat.max = 50.0,
+# lat.min = 25.0,
+# lon.min= -100.0,
+# lon.max = -67.0 )
+# file.name <- FALSE
+# plot.it <- TRUE
+# n.sizes <- 50
+# grid.size.seq <- round(seq(from=5, to=120, length=n.sizes))
+ # -----------------------------------
+ # verification
+ #length(xxx)
+ #length(yyy)
+ #length(ppp)
+ #length(zzz)
+ # image.pred <- as.image(ppp, x= data.frame(xxx,yyy),
+ # nrow=40,
+ # ncol=40, na.rm=TRUE)
+ # image.plot(image.pred)
+ # map('state',add=TRUE, lwd=1, col="grey")
+
+# ------------------------------------------
+# Initial Values
+# ------------------------------------------
+ n.sizes <- length(grid.size.seq)
+ pred.performance <- matrix(0, n.sizes, 20)
+ # Covert grid sizes to both units
+ # -----------------------------------------
+# ------------------------------------------
+# Compute Baseline-Point Performance
+# ------------------------------------------
+ epsilon <- 1e-8
+ #ppp <- ddd$pred.Xp
+ #obs <- p.data$yp
+ obs <- zzz
+ ttt.index <- ppp == 0
+ ppp[ttt.index] <- epsilon
+ ttt.ind <- !is.na(ppp)
+ test.dev <- deviance.explained(obs[ttt.ind],ppp[ttt.ind])$deviance.explained
+ test.pearson <- poisson.pearson(obs[ttt.ind], ppp[ttt.ind])
+
+# ------------------------------------------
+# Compute Performance across scales
+# ------------------------------------------
+ for (iii in 1:n.sizes){
+# -------------------------
+# if (!is.null(spatial.extent)){
+# # Add two points based on spatial extent
+# # Idea is to set spatial extent manually
+# # I should rewrite the binning myself!
+# # small bias caused in perf. metrics
+# ppp.ip <- c(ppp,0,0)
+# zzz.ip <- c(zzz,0,0)
+# xxx.ip <- c(xxx,spatial.extent$lon.min,spatial.extent$lon.max)
+# yyy.ip <- c(yyy,spatial.extent$lat.min,spatial.extent$lat.max)
+# image.pred <- as.image(ppp.ip, x= data.frame(xxx.ip,yyy.ip),
+# nrow=grid.size.seq[iii]*grid.size.ratio,
+# ncol=grid.size.seq[iii] , na.rm=TRUE)
+# image.obs <- as.image(zzz.ip, x= data.frame(xxx.ip,yyy.ip),
+# nrow=grid.size.seq[iii]*grid.size.ratio,
+# ncol=grid.size.seq[iii], na.rm=TRUE)
+# }
+# -----------------------
+ #if (is.null(spatial.extent)){
+ image.pred <- as.image(ppp, x= data.frame(xxx,yyy),
+ nrow=grid.size.seq[iii]*grid.size.ratio,
+ ncol=grid.size.seq[iii] , na.rm=TRUE)
+ image.obs <- as.image(zzz, x= data.frame(xxx,yyy),
+ nrow=grid.size.seq[iii]*grid.size.ratio,
+ ncol=grid.size.seq[iii]) #, na.rm=TRUE)
+ # Form a common na index
+ # ---------------------------
+ ddd.na.ind <- !is.na(image.pred$weights)
+ d2.na.ind <- ddd.na.ind & !is.na(image.obs$weights)
+
+ ppp.size <- image.pred$z[d2.na.ind ]
+ zzz.size <- image.obs$z[d2.na.ind ]
+ length(ppp.size)
+ length(zzz.size)
+
+ # -------------------------------------
+ # Clean Predictions for Dev. Calcs
+ # -------------------------------------
+ # Substitute predicted zero's with small values
+ ttt.index <- ppp.size == 0
+ ppp.size[ttt.index] <- epsilon
+ # Remove any NA's - several occurr with GAM models
+ ttt.ind <- !is.na(ppp.size)
+ # -------------------------------------
+ perf.ttt <- deviance.explained(zzz.size[ttt.ind], ppp.size[ttt.ind])
+ pred.performance[iii,1] <- perf.ttt$deviance.explained
+ pred.performance[iii,2] <- perf.ttt$obs.deviance
+ pred.performance[iii,3] <- poisson.pearson(zzz.size[ttt.ind],ppp.size[ttt.ind] )
+ # Total number of grid cells that have test-set observations
+ # This is the sample size at this scale
+ ip.ind <- !is.na(image.pred$weight)
+ pred.performance[iii,4] <- sum(ip.ind)
+ # Mean Squared error and scaled RMSE
+ pred.performance[iii,5] <- sqrt(
+ mean((zzz.size[ttt.ind]-ppp.size[ttt.ind])^2))
+ pred.performance[iii,6] <- sqrt(
+ mean(((zzz.size[ttt.ind]-ppp.size[ttt.ind])/
+ ppp.size[ttt.ind]) ))
+ # -----------------------------
+ # Add more
+ # -------------------------
+ #MSE
+ pred.performance[iii,11] <- mean((ppp.size - zzz.size)^2)
+
+ #R2
+ pred.performance[iii,12] <- 1 - mean((ppp.size - zzz.size)^2)/
+ mean((mean(zzz.size) - zzz.size)^2)
+ #MSE.sqrt
+ pred.performance[iii,13] <- mean((sqrt(ppp.size) - sqrt(zzz.size))^2)
+ #R2.sqrt
+ pred.performance[iii,14] <- 1 - mean((sqrt(ppp.size) - sqrt(zzz.size))^2)/
+ mean((mean(sqrt(zzz.size)) - sqrt(zzz.size))^2)
+ #MAD
+ pred.performance[iii,15]<- mean(abs(ppp.size - zzz.size))
+ #rho
+ pred.performance[iii,16]<- cor(zzz.size,ppp.size)
+ #rho.sqrt
+ pred.performance[iii,17]<- cor(sqrt(zzz.size),sqrt(ppp.size))
+
+ # --------------------------------
+
+ # Median # of observations/grid cell, in grid cells with observations
+ pred.performance[iii,7] <- median(image.pred$weights[ip.ind])
+ pred.performance[iii,8] <- sd(image.pred$weights[ip.ind])
+ # Grid Size in units of cells
+ pred.performance[iii,9] <- grid.size.seq[iii]
+ # Grid Size in units of (approximate) km^2
+ # --------------------------------------------------
+ # Great Circle Distance Formula using decimal degrees:
+ # Where r is the radius of the earth in whatever units you desire.
+ #r <-3437.74677 (nautical miles)
+ r <- 6378.7 #(kilometers)
+ #r<-3963.0 (statute miles)
+ # Assume we are at centered at 40 Lat and 100 lon
+ lat1 <- 40
+ lon1 <- -100
+ # Step size from image grid
+ lat2 <- lat1 + (image.pred$y[2]- image.pred$y[1])
+ lon2 <- lon1 #+ (image.pred$x[2]- image.pred$x[1])
+ cell.height.km <- r * acos(sin(lat1/57.2958) * sin(lat2/57.2958) +
+ cos(lat1/57.2958) * cos(lat2/57.2958) *
+ cos(lon2/57.2958 -lon1/57.2958))
+ lat2 <- lat1 #+ (image.pred$y[2]- image.pred$y[1])
+ lon2 <- lon1 + (image.pred$x[2]- image.pred$x[1])
+ cell.width.km <- r * acos(sin(lat1/57.2958) * sin(lat2/57.2958) +
+ cos(lat1/57.2958) * cos(lat2/57.2958) *
+ cos(lon2/57.2958 -lon1/57.2958))
+ pred.performance[iii,10] <- cell.width.km*cell.height.km
+ } # end for loop
+ # ----------------------------------------------------------
+# pred.performance
+
+# ------------------------------------------
+# Plot Performance vs Spatial Scale
+# ------------------------------------------
+ if (!is.null(file.name)){
+ png(file=file.name,
+ bg="white",
+ width = plot.width,
+ height = plot.height)
+ }
+ if (!is.null(file.name) | !is.null(plot.it)){
+ # --------------------------------------
+ # ** dual x-labels for # cells and km2 would be cool
+ # ** draw Base-Line at point-level predictive performance
+ # ** adaptively set maximum y-axis value?
+ # ** plot smoothed performance trajectory??
+ # --------------------------------------
+ ymin <- min(c( 0.9*min(pred.performance[,1]), 0.9*test.dev) )
+ ymax <- max( c( 1.1*max(pred.performance[,1]), 1.1*test.dev) )
+ plot(pred.performance[,9],
+ pred.performance[,1],
+ ylim=c(ymin,ymax),
+ type="p",
+ lwd=2.0,
+ col="red",
+ xlab=" # latitude cells ",
+ ylab=" Percent Deviance Explained",
+ main="Performance vs Scale" )
+ # Smoothed Performance
+
+ # Smoothed Performance
+ lines(lowess(pred.performance[,9], pred.performance[,1],
+ f=span),
+ lwd=2.0,
+ col="red")
+ # baseline performance
+ lines(range(pred.performance[,9]),
+ c(test.dev, test.dev),
+ lwd=2.0,
+ col="black")
+
+ }
+ if (!is.null(file.name)) dev.off()
+
+# ------------------------------------------
+# Return Values
+# ------------------------------------------
+return.list <- list(pred.performance=pred.performance,
+ test.dev=test.dev,
+ test.pearson=test.pearson)
+return(return.list)
+# --------------------------------------------------------------------------
+} # end function
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+
+
+
+
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+# Generate Contours for Spatial Density of Given Locations
+# -----------------------------------------------------------------------------
+# Daniel Fink
+# 2.7.08
+#
+# Description
+# -----------------
+# Objectives are to
+# ** estimate 2D KDE over lat & Lon
+# ** second: estimate the SD of prediction error
+# ** exclude/white out lowest level of density surface
+# ** estimate quantiles of density surface estimates
+
+# ----------------------------------------------------------------------
+#
+#
+# Input
+# ----------
+# xxx, yyy - locations
+# contours - vector of numbers
+# density.cutoff
+#
+# Output
+# ----------
+# ** draw contours
+# ** return zzz quantile hieghts that define the contours.
+# This will be a numeric vector with same length as contours
+#
+# Notes:
+# ---------
+#
+# Further Development:
+# ----------------------------
+# ** return density estimate
+# ** pass through to access options on density estimator
+# -----------------------------------------------------------------------------
+spatial.density.contours <- function(
+ xxx, yyy,
+ contours,
+ density.cutoff = 0.1,
+ xgridsize = 40,
+ ygridsize = 40,
+ # ----------------------------
+ file.name =NULL,
+ plot.it =FALSE,
+ plot.height=600,
+ plot.width=800){
+# ------------------------------------------
+# Dummy Values/Calls
+# ------------------------------------------
+
+# ------------------------------------------
+# Inits
+# ------------------------------------------
+ require(GenKern)
+ require(maps)
+ require(fields)
+# -------------------------------------
+# GenKern: Estimate 2D KDE over lat & Lon
+# ----------------------------------
+ # calculate and plot a surface with zero correlation
+ # Notes that KernSur 2D KDE can change dramatically by
+ # changing the bandwidths and correlation.
+ # The selection of grid size determines spatial resoluation
+ # of the contours. Which we want regional.
+ # ------------------------------------------
+ op <- KernSur(xxx,yyy,
+ xgridsize=xgridsize,
+ ygridsize=ygridsize)
+ #correlation=0,
+ #xbandwidth=1,
+ #ybandwidth=1,
+ # Plot level plot of the Density estimate
+ #density.cutoff <- 0.1 # "Zero" Density cutoff
+ # cleans up map and calculations
+ #par(mfrow=c(1,2))
+ image.plot(op$xords, op$yords,
+ log(op$zden+1),
+ zlim = c(density.cutoff, 7),
+ col=terrain.colors(100),
+ #col=heat.colors(100),
+ axes=TRUE,
+ xlab="Longitude",
+ ylab="Latitude",
+ main=" eBird Spatial Log Density " )
+ # Compute quantiles of the Density estimate.
+ # Note however, that this includes all the zeros that are
+ # in the boundary area.
+ # ---------------------------------------------------------
+ # Quantiles for 2004 - 2007 Unique Locations (12008)
+ zzz.quant <- quantile( op$zden[op$zden > density.cutoff],
+ probs = contours) # Defines lower bound for data quality
+ # Quantiles for 2004 - 2007 Unique Locations (12008)
+ #zzz.quant <- quantile( op$zden[op$zden > density.cutoff],
+ # probs =c(0.983, 0.88, 0.65))
+ # Quantiles for 2006 Unique Locations (~6000) #c(0.85, 0.605))
+ # Plot Contours at these levels
+ # ------------------------------
+ #contour(op$xords, op$yords, op$zden, add=TRUE,
+ # levels=zzz.quant,
+ # col=c(1:length(contours))+1,
+ # lwd=2.0)
+ box()
+ # Add political Boundaries
+ map('state',add=TRUE, lwd=2, col="yellow")
+ map('state',add=TRUE, lwd=1, col="black")
+ #points(xxx,yyy, cex=0.25)
+
+ # Calculate All Contour Polygons using contourLines
+ # contour.poly is a list where each element describes
+ # one ploygon. Elements are
+ # $level (this is one of the z.quantiles)
+ # $x
+ # $y (vectors defining boundary of polygon)
+ # -------------------------------------------------
+ contour.polygons <- contourLines(op$xords, op$yords, op$zden,
+ levels=zzz.quant)
+# Return contours as polygons too!!!
+results.list <- list(
+ contours = contours,
+ xxx = xxx,
+ yyy = yyy,
+ log.density.quantiles = zzz.quant,
+ contour.polygons = contour.polygons,
+ density.KernSur.obj = op)
+ return(results.list)
+}#---------------------------------------------------------------------
+#-----------------------------------------------------------------------
+#-----------------------------------------------------------------------
+
+
+
+
+
+
+# --------------------------------------------------------------------------
+# Plot Halloween Maps
+# -----------------------------
+#
+#
+# -------------------------------------
+# There may be a problem with the halloween.maps()
+# code when there are NO missing values and
+# this parameter is used: NA.col="grey20")
+# -------------------------------------
+#
+#
+# jdate.seq
+# year.seq
+# save.name
+# spp.name <- "Yellow Warbler"
+# z.min <-
+# z.max <-
+# If you use the mapping function for a single map, and
+# turn the add=TRUE parameter, then you can add
+# more stuff to the plot. You will need to end it with a call to
+# dev.off()
+#
+# # ----------------------------------------------------------------------
+# # Calculate Indices for Point.in.polygon for Contours
+# # ----------------------------------------------------------------------
+# # Do not filter locations
+# # ------------------------
+# contour.index <- rep(TRUE, length(st.pred$xxx))
+# # Filter locations using archived polygon
+# # --------------------------------
+# sdc.name <- paste(control.dir,
+# "yelwar.East.travel.spatial.density.contours.RData",sep="")
+# load( file=sdc.name) # sd.cont
+# pip.cont <- point.in.polygon.contours( st.pred$xxx, st.pred$yyy,
+# sd.cont$contour.polygons)
+# #contour.index <- pip.cont$contour.index[,1]
+# #
+##
+#
+# #~ # Eg.1. extract individual States
+# #~ #--------------------------------------------------------------
+# #~ sites <- data.frame(lon=st.pred$xxx, lat=st.pred$yyy)
+# #~ shape.dir <-"/mnt/data2/ST.BDT/BDT.shapefiles/"
+# #~ shape.filename <- "STATES.shp"
+# #~ selected.shape.names <- c("New York", "Georgia")
+# #~ att.selection.column.name <- "STATE_NAME"
+# #~ # --------------------------------------------------------------
+# #~ # Eg.2 extract individual BCRs
+# #~ #--------------------------------------------------------------
+# #~ sites <- data.frame(lon=st.pred$xxx, lat=st.pred$yyy)
+# #~ shape.dir <-"/mnt/data2/ST.BDT/BDT.shapefiles/"
+# #~ shape.filename <- "bcr.shp" # watch capitalization!
+# #~ att.selection.column.name <- "BCR"
+## #~ # -------------------------------------------------------------- #~ selected.shape.names <- c(13, 27) # class must match att.selection.column
+##
+#
+# --------------------------------------------------------------------------
+# DMF 3.19.10 modified from halloween.maps in stem.library.ST.R
+# dated 3.16.10
+#
+# I am going to add formal parameters so that
+# we can can specify separate input directories for st.matrix files
+# and separate directories for map sequence outputs
+# --------------------------------------------------------------------------
+st.matrix.maps <- function(
+ st.matrix.directory,
+ map.directory,
+ # --------------
+ #save.dir,
+ #save.name,
+ ## KFW resp.transformation.code = NULL,
+ # ---------------
+ jdate.seq,
+ year.seq,
+ begin.seq,
+ end.seq=length(jdate.seq),
+ # ------------------
+ # output
+ pred.grid.size=NULL,
+ map.plot.width = 1000,
+ spatial.extent.list = NULL,
+ z.max = NULL,
+ z.min = NULL,
+ map.tag = NULL,
+ google.maps=FALSE,
+ add=FALSE,
+ NA.col=NULL,
+ halloween.colors=NULL,
+ title.text = NULL,
+ date.bar = TRUE,
+ # -------------------------------------------
+ # map args
+ # -------------------------------------------
+ county.map = FALSE,
+ state.map=TRUE,
+ world.map=FALSE,
+ state.map.lwd = NULL,
+ state.map.col = NULL,
+ county.map.lwd = NULL,
+ county.map.col = NULL,
+ world.map.lwd = NULL,
+ world.map.col = NULL,
+ # -------------------------
+ print.date=FALSE,
+ # -------------------------
+ ...) {
+# ------------------------------------------------
+
+ if (is.null(state.map.lwd)) state.map.lwd <- 1.5
+ if (is.null(state.map.col)) state.map.col <- "grey"
+ if (is.null(county.map.lwd)) county.map.lwd <- 0.5
+ if (is.null(county.map.col)) county.map.col <- "grey"
+ if (is.null(world.map.lwd)) world.map.lwd <- 2.0
+ if (is.null(world.map.col)) world.map.col <- "white"
+#---------------------------------------------
+
+ if ("/" != substring(map.directory, nchar(map.directory), nchar(map.directory))) {
+ map.directory <- paste(map.directory, "/", sep="")
+ }
+
+ if ("/" != substring(st.matrix.directory, nchar(st.matrix.directory), nchar(st.matrix.directory))) {
+ st.matrix.directory <- paste(st.matrix.directory, "/", sep="")
+ }
+
+ system(paste("mkdir ", map.directory,sep=""), intern=TRUE)
+ # Initialization Info Space-Time Predictions From file
+ # ----------------------------------------------
+ stp.name <- paste(st.matrix.directory,"st.matrix..1.RData",sep="")
+ load(stp.name)
+ # ----------------------------------------------------------------------
+ # Limit Spatial Extent by Point in Polygon or ShapeFile
+ # ----------------------------------------------------------------------
+ contour.index <- rep(TRUE, length(st.pred$xxx))
+ if (!is.null(spatial.extent.list)){
+ if (spatial.extent.list$type == "rectangle"){
+ ttt.index <- ( st.pred$yyy > spatial.extent.list$lat.min &
+ st.pred$yyy < spatial.extent.list$lat.max &
+ st.pred$xxx > spatial.extent.list$lon.min &
+ st.pred$xxx < spatial.extent.list$lon.max )
+ contour.index <- (ttt.index & contour.index)
+ }
+ if (spatial.extent.list$type == "polygon"){
+ ttt.index <- point.in.polygon(
+ xxx = st.pred$xxx,
+ yyy = st.pred$yyy,
+ polygon.vertices =
+ spatial.extent.list$polygon.vertices)
+ contour.index <- (ttt.index & contour.index)
+ }
+ if (spatial.extent.list$type == "shapefile"){
+ ttt.index <- point.in.shapefile(
+ sites = data.frame(lon=st.pred$xxx, lat=st.pred$yyy),
+ shape.dir=spatial.extent.list$shape.dir,
+ shape.filename=spatial.extent.list$shape.filename,
+ att.selection.column.name=
+ spatial.extent.list$att.selection.column.name,
+ selected.shape.names=
+ spatial.extent.list$selected.shape.names)
+ contour.index <- (ttt.index & contour.index)
+ }
+ } # if (!is.null(spatial.extent.list)){
+ # -------------------------------------------------------------------
+ # initizalize.map.grid() formats maps automatically
+ # -------------------------------------------------------------------
+ mapping.spatial.extent <- list(
+ lat.max = max( st.pred$yyy[contour.index]),
+ lat.min = min( st.pred$yyy[contour.index]),
+ lon.min = min( st.pred$xxx[contour.index]),
+ lon.max = max( st.pred$xxx[contour.index]) )
+ map.inits <- initizalize.map.grid(
+ spatial.extent = mapping.spatial.extent,
+ map.plot.width = map.plot.width,
+ pred.grid.size = pred.grid.size)
+ # ----------------------------------------------------------------------
+ # Compute Surface Summaries
+ # ----------------------------------------------------------------------
+ st.summary <- matrix(0,(end.seq-begin.seq+1), 7)
+ for (iii in begin.seq:end.seq){
+ stp.name <- paste(st.matrix.directory,"st.matrix..",iii,".RData",sep="")
+ load(stp.name)
+ # ---------------------------------------------------------------------------
+ # Un-tranform Responses
+ # ---------------------------------------------------------------------------
+ ## KFW if ( resp.transformation.code == "sqrt") {
+ ## KFW st.pred$pred <- (st.pred$pred) ^2
+ ## KFW }
+ # ---------------------------------------------------------------------------
+ st.summary[(iii-begin.seq +1),] <- quantile(st.pred$pred[contour.index],
+ probs=c(0, .1,.25,.5,.75,.9,1),
+ na.rm = TRUE)
+ }
+ # Set minium as min of 10th quantiles
+ if (is.null(z.min)) z.min <- min(st.summary[,2])
+ # Take max as max of 90th quantiles
+ if (is.null(z.max)) z.max <- max(st.summary[,6])
+ # ---------------------------------------------------------
+ # Convert Temporal Sequence times to POSIX
+ # ---------------------------------------------------------
+ p.time <- strptime( x=paste(round(jdate.seq),year.seq), "%j %Y")
+ # Nice function to convert DateTime Classes
+ month.text <- months(p.time, abbreviate = FALSE)
+ date.names <- paste(month.text, " ",p.time$mday,",", year.seq,sep="")
+ # --------------------------------------------------------------
+ # Lookup Common Name in eBird Taxonomy File
+ # --------------------------------------------------------------
+ # datafile <- paste(control.dir,"eBird taxonomy file.csv",sep="")
+ # eBird.taxonomy <- read.csv(file=datafile)
+ # #names(eBird.taxonomy)
+ # spp.name <- eBird.taxonomy$PRIMARY_COM_NAME[
+ # as.character(eBird.taxonomy$SPECIES_CODE) == spp.code ]
+ # --------------------------------------------------------------
+ # Will's Halloween Pallete
+ # --------------------------------------------------------------
+ if (is.null(halloween.colors)){
+ n.red <- 100
+ red.colors <- colorRampPalette(
+ #-----------------------------------------------------------------------------------------
+ # Traditional Halloweeen Map (black under 0.20)
+ # -----------------------------------------------------------------------------------------
+ # c("black","black","#FF7100","white"),
+ # bias=1.9)
+ # -----------------------------------------------------------------------------------------
+ # Low Probability Halloween
+ # -----------------------------------------------------------------------------------------
+ # c("black","grey","#FF7100","yellow","white"),
+ # bias=1.0)
+ # -----------------------------------------------------------------------------------------
+ # Low Probability Halloween 2
+ # -----------------------------------------------------------------------------------------
+ c("black","grey20","#FF7100","white"),
+ bias=2.0)
+ # -----------------------------------------------------------------------------------------
+ # Green Halloween
+ # -----------------------------------------------------------------------------------------
+ #c("black","black","DarkGreen","Green4","Green"),
+ #space = "rgb",
+ }
+ else {
+ n.red <- 100
+ red.colors <- halloween.colors
+ }
+
+ # --------------------------------------------------------------
+ # Loop over Dates
+ # --------------------------------------------------------------
+ for (iii in begin.seq:end.seq){
+ #---------------------------------------------
+ # Load Space-Time Predictions From file
+ # ----------------------------------------------
+ #stp.name <- paste(save.dir,save.name,".",iii,".RData",sep="")
+ stp.name <- paste(st.matrix.directory,"st.matrix..",iii,".RData",sep="")
+ load(stp.name)
+ # ---------------------------------------------------------------------------
+ # Un-tranform Responses
+ # ---------------------------------------------------------------------------
+ ## KFW if ( resp.transformation.code== "sqrt")
+ ## KFW st.pred$pred <- (st.pred$pred) ^2
+ # ---------------------------------------------------------------------------
+ #----------------------------
+ # Surface Height Limits
+ # ----------------------------
+ st.pred$pred[st.pred$pred < z.min] <- z.min
+ st.pred$pred[st.pred$pred > z.max] <- z.max
+ # --------------
+ # --------------
+ num.txt <- formatC(iii,format="fg", width=5)
+ num.txt <- chartr(" ","0",num.txt)
+ map.file.name <- paste(map.directory,map.tag,
+ num.txt,".",jdate.seq[iii],
+ ".",year.seq[iii],".png" ,sep="")
+
+ # --------------------------------------------------------------
+ # "Google".maps == Transparent PNG's
+ # --------------------------------------------------------------
+ # if TRUE then background = Transparent
+ # PNG margins are ajusted.
+ # spatial.extent needs to be communicated to
+ # Google.Earth so that it knows how to overlay image
+ # --------------------------------------------------------------
+ if (!google.maps) {
+ png(file=map.file.name, bg="white",
+ width=map.plot.width,
+ height=map.inits$map.plot.height)
+ par(mar = c(2,4,4,2), bg="black",fg="grey")
+ }
+ if (google.maps) {
+ png(file=map.file.name, bg="transparent",
+ width=map.plot.width,
+ height=map.inits$map.plot.height)
+ par(mar=c(0,0,0,0),bg="black",fg="grey",
+ xpd=TRUE)
+ }
+ # --------------------------------------------------------------
+ # Include Date Bar
+ # --------------------------------------------------------------
+ if (date.bar) {
+ par(plt = c(0.10, 0.883, 0.25, 0.85) )
+ # --------------------------------------------------------
+ # Do not add NA's filled in with given color
+ # --------------------------------------------------------
+ if ( is.null(NA.col) ) {
+ bs.rpart.maps(
+ xxx = st.pred$xxx[contour.index],
+ yyy = st.pred$yyy[contour.index],
+ zzz = st.pred$pred[contour.index],
+ zlim = c(z.min,z.max),
+ pred.grid.size = map.inits$pred.grid.size ,
+ grid.size.ratio = map.inits$grid.size.ratio,
+ axis.args=list(fg="grey", col.axis="grey"),
+ # Less than 1 reduces height,
+ # greater than 1 increase height
+ #for given width
+ col.palette = red.colors(n.red),
+ axes = FALSE,
+ ...)
+ }
+ # --------------------------------------------------------
+ # Add image plot with NA's filled in with given color
+ # --------------------------------------------------------
+ if ( !is.null(NA.col) ) {
+ ttt.st.pred <- rep(NA,length(st.pred$pred))
+ ttt.st.pred[is.na(st.pred$pred)] <- 1
+ ttt.image <- as.image(
+ ttt.st.pred[contour.index],
+ x= data.frame( st.pred$xxx[contour.index],
+ st.pred$yyy[contour.index]),
+ nrow=round(map.inits$pred.grid.size*
+ map.inits$grid.size.ratio), # nrow=X direction
+ ncol=map.inits$pred.grid.size, # ncol=Y direction
+ na.rm=TRUE)
+ image(ttt.image,
+ col=NA.col,
+ # add=TRUE,
+ axes = FALSE,...)
+ if (!is.null(title.text)) {
+ title(main=paste(title.text), col="white",line=0)
+ }
+ bs.rpart.maps(
+ xxx = st.pred$xxx[contour.index],
+ yyy = st.pred$yyy[contour.index],
+ zzz = st.pred$pred[contour.index],
+ zlim = c(z.min,z.max),
+ pred.grid.size = map.inits$pred.grid.size ,
+ grid.size.ratio = map.inits$grid.size.ratio,
+ axis.args=list(fg="grey", col.axis="grey"),
+ # Less than 1 reduces height,
+ # greater than 1 increase height
+ #for given width
+ col.palette = red.colors(n.red),
+ axes = FALSE,
+ add=TRUE,
+ ...)
+ } # !is.null(NA.col)
+ # -------------------------------------------------------------
+ # Add Date Text
+ # -------------------------------------------------------------
+ if (print.date) {
+ #mtext( paste(date.names[iii]), side=3, col="white")
+ text( x= min(st.pred$xxx[contour.index]),
+ y= min(st.pred$yyy[contour.index]),
+ pos=4, #plot to the right
+ labels= date.names[iii])
+ }
+ # -------------------------------------------------------------
+ # Add Political Boundaries
+ # -------------------------------------------------------------
+ if (county.map) map('county',add=TRUE, lwd=county.map.lwd, col=county.map.col)
+ if (state.map) map('state',add=TRUE, lwd=state.map.lwd, col=state.map.col)
+ if (world.map) map('world',add=TRUE, lwd=world.map.lwd, col=world.map.col)
+ # -------------------------------------------------------------
+ # Bottom Date Legend Rectangle
+ # -------------------------------------------------------------
+ # Find the coordinate for the right boundary of
+ # image.plot's "bigplot"
+ right.corner <- image.plot.plt()$bigplot[2]
+ par(plt = c(0.10, right.corner, 0.15, 0.22) )
+ # Set user coordinates for this region
+ par(usr=c(-1,366,0,1))
+ box(lwd=2, col="grey")
+ rect(xleft= (jdate.seq[iii]-2), ybottom=0, xright=(jdate.seq[iii]+2), ytop=2,
+ col=red.colors(n.red)[n.red],
+ border=NA )
+ axis(1, at = c(5, 90, 180, 270, 360),
+ labels = c("Jan", "Apr", "Jun", "Sep", "Dec"),
+ cex=1.5,
+ col="grey",
+ col.axis="grey",
+ font=1)
+ # -------------------------------------------------------------
+ } # end date.bar == TRUE
+ # -------------------------------------------------------------
+
+
+ # --------------------------------------------------------------
+ # Exclude Date Bar
+ # --------------------------------------------------------------
+ if (!date.bar) {
+ # --------------------------------------------------------
+ # Do not add NA's filled in with given color
+ # --------------------------------------------------------
+ if ( is.null(NA.col) ) {
+ bs.rpart.maps(
+ xxx = st.pred$xxx[contour.index],
+ yyy = st.pred$yyy[contour.index],
+ zzz = st.pred$pred[contour.index],
+ zlim = c(z.min,z.max),
+ pred.grid.size = map.inits$pred.grid.size ,
+ grid.size.ratio = map.inits$grid.size.ratio,
+ axis.args=list(fg="grey", col.axis="grey"),
+ # Less than 1 reduces height,
+ # greater than 1 increase height
+ #for given width
+ col.palette = red.colors(n.red),
+ axes = FALSE,
+ ...)
+ }
+ # --------------------------------------------------------
+ # Add image plot with NA's filled in with given color
+ # --------------------------------------------------------
+ if ( !is.null(NA.col) ) {
+ ttt.st.pred <- rep(NA,length(st.pred$pred))
+ ttt.st.pred[is.na(st.pred$pred)] <- 1
+ ttt.image <- as.image(
+ ttt.st.pred[contour.index],
+ x= data.frame( st.pred$xxx[contour.index],
+ st.pred$yyy[contour.index]),
+ nrow=round(map.inits$pred.grid.size*
+ map.inits$grid.size.ratio), # nrow=X direction
+ ncol=map.inits$pred.grid.size, # ncol=Y direction
+ na.rm=TRUE)
+ image(ttt.image,
+ col=NA.col,
+ # add=TRUE,
+ axes = FALSE,...)
+ if (!is.null(title.text)) {
+ title(main=paste(title.text), col="white",line=0)
+ }
+ bs.rpart.maps(
+ xxx = st.pred$xxx[contour.index],
+ yyy = st.pred$yyy[contour.index],
+ zzz = st.pred$pred[contour.index],
+ zlim = c(z.min,z.max),
+ pred.grid.size = map.inits$pred.grid.size ,
+ grid.size.ratio = map.inits$grid.size.ratio,
+ axis.args=list(fg="grey", col.axis="grey"),
+ # Less than 1 reduces height,
+ # greater than 1 increase height
+ #for given width
+ col.palette = red.colors(n.red),
+ axes = FALSE,
+ add=TRUE,
+ ...)
+ } # !is.null(NA.col)
+ # -------------------------------------------------------------
+ # Add Date Text
+ # -------------------------------------------------------------
+ if (print.date) {
+ #mtext( paste(date.names[iii]), side=3, col="white")
+ text( x= min(st.pred$xxx[contour.index]),
+ y= min(st.pred$yyy[contour.index]),
+ pos=4, #plot to the right
+ labels= date.names[iii])
+ }
+ # -------------------------------------------------------------
+ # Add Political Boundaries
+ # -------------------------------------------------------------
+ if (county.map) map('county',add=TRUE, lwd=county.map.lwd, col=county.map.col)
+ if (state.map) map('state',add=TRUE, lwd=state.map.lwd, col=state.map.col)
+ if (world.map) map('world',add=TRUE, lwd=world.map.lwd, col=world.map.col)
+ # -------------------------------------------------------------
+ } # end plotting w/o date bar
+ # -------------------------------------------------------------
+ if (add==FALSE) dev.off()
+ # ---------------------------------------------------------------------------
+ } # iii - loop over dates
+# -----------------------------------------------------------------------------------
+}# end function
+#------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------
+
+
+
+# --------------------------------------------------------------------------
+# Plot Base Surface Maps
+# -----------------------------
+#
+#
+# Results:
+#
+#
+# jdate.seq
+# year.seq
+# save.name
+# spp.name <- "Yellow Warbler"
+# z.min <-
+# z.max <-
+ #----------------------------
+ # google.maps
+ # ---------------------
+ # if TRUE then background = Transparent
+ # PNG margins are ajusted.
+ # spatial.extent needs to be communicated to
+ # Google.Earth so that it knows how to overlay image
+ # ----------------------------
+# --------------------------------------------------------------------------
+surface.maps <- function(
+ save.dir,
+ save.name,
+ jdate.seq,
+ year.seq,
+ begin.seq,
+ end.seq=length(jdate.seq),
+ ## KFW resp.transformation.code = NULL,
+ # output
+ pred.grid.size=NULL,
+ z.max = NULL,
+ z.min = NULL,
+ map.tag,
+ google.maps=FALSE,
+ add=FALSE)
+{
+# ------------------------------------------
+ # call to the function initizalize.map.grid() in
+ # st.clustering.functions.2.R format maps automatically
+ # ---------------------------------------------------------------------------------------------------
+ map.inits <- initizalize.map.grid(spatial.extent=spatial.extent,
+ map.plot.width=map.plot.width,
+ pred.grid.size= pred.grid.size)
+ # Reset this for slightly larger grid cells
+ # Response Transformation code
+ #resp.transformation.code <- "sqrt"
+ # Map surface filename tag
+ #map.tag <- paste(exp.name,"st.map.",sep="")
+ #---------------------------------------------
+ # Initialization Info Space-Time Predictions From file
+ # ----------------------------------------------
+ stp.name <- paste(save.dir,
+ save.name,".",1,".RData",sep="")
+ load(stp.name)
+ # ----------------------------------------------------------------------
+ # Calculate Indices for Point.in.polygon for Contours
+ # ----------------------------------------------------------------------
+ # Do not filter locations
+ # ------------------------
+ contour.index <- rep(TRUE, length(st.pred$xxx))
+ # Filter locations using archived polygon
+ # --------------------------------
+ sdc.name <- paste(control.dir,
+ "yelwar.East.travel.spatial.density.contours.RData",sep="")
+ load( file=sdc.name) # sd.cont
+ pip.cont <- point.in.polygon.contours( st.pred$xxx, st.pred$yyy,
+ sd.cont$contour.polygons)
+ #contour.index <- pip.cont$contour.index[,1]
+ # ----------------------------------------------------------------------
+ # Compute Surface Summaries
+ # ----------------------------------------------------------------------
+ st.summary <- matrix(0,(end.seq-begin.seq+1), 7)
+ for (iii in begin.seq:end.seq){
+ stp.name <- paste(save.dir,
+ save.name,".",iii,".RData",sep="")
+ load(stp.name)
+ # ---------------------------------------------------------------------------
+ # Un-tranform Responses
+ # ---------------------------------------------------------------------------
+ ## KFW if ( resp.transformation.code== "sqrt")
+ ## KFW st.pred$pred <- (st.pred$pred) ^2
+ # ---------------------------------------------------------------------------
+ st.summary[iii,] <- quantile(st.pred$pred[contour.index],
+ probs=c(0, .1,.25,.5,.75,.9,1))
+ }
+ # Set minium as min of 10th quantiles
+ if (is.null(z.min)) z.min <- min(st.summary[,2])
+ # Take max as max of 90th quantiles
+ if (is.null(z.max)) z.max <- max(st.summary[,6])
+
+ # Compute Slice Quantiles
+ #pred.ecdf <- ecdf(st.pred$pred)+
+ #qqq <- pred.ecdf(st.pred$pred)
+ # ---------------------------------------------------------
+ # Convert Temporal Sequence times to POSIX
+ # ---------------------------------------------------------
+ p.time <- strptime( x=paste(round(jdate.seq),year.seq), "%j %Y")
+ # Nice function to convert DateTime Classes
+ month.text <- months(p.time, abbreviate = FALSE)
+ date.names <- paste(month.text, " ",p.time$mday,",", year.seq,sep="")
+ # --------------------------------------------------------------
+ # Lookup Common Name in eBird Taxonomy File
+ # --------------------------------------------------------------
+ datafile <- paste(control.dir,"eBird taxonomy file.csv",sep="")
+ eBird.taxonomy <- read.csv(file=datafile)
+ #names(eBird.taxonomy)
+ spp.name <- eBird.taxonomy$PRIMARY_COM_NAME[
+ as.character(eBird.taxonomy$SPECIES_CODE) == spp.code ]
+ # ------------------------------------
+ # My "Red" Pallete
+ # ------------------------------------
+ n.red <- 100
+ red.colors <- colorRampPalette(
+ c("white","red","#7F0000"),
+ space = "rgb",
+ bias=0.5)
+ # ---------------------------------------
+ for (iii in begin.seq:end.seq){
+ #---------------------------------------------
+ # Load Space-Time Predictions From file
+ # ----------------------------------------------
+ stp.name <- paste(save.dir,
+ save.name,".",iii,".RData",sep="")
+ load(stp.name)
+ # ---------------------------------------------------------------------------
+ # Un-tranform Responses
+ # ---------------------------------------------------------------------------
+ ## KFW if ( resp.transformation.code== "sqrt")
+ ## KFW st.pred$pred <- (st.pred$pred) ^2
+ # ---------------------------------------------------------------------------
+ #----------------------------
+ # Surface Height Limits
+ # ----------------------------
+ st.pred$pred[st.pred$pred < z.min] <- z.min
+ st.pred$pred[st.pred$pred > z.max] <- z.max
+ # --------------
+ # --------------
+ num.txt <- formatC(iii,format="fg", width=5)
+ num.txt <- chartr(" ","0",num.txt)
+ map.file.name <- paste(save.dir,map.tag,
+ num.txt,".",jdate.seq[iii],
+ ".",year.seq[iii],".png" ,sep="")
+
+ #----------------------------
+ # google.maps
+ # ---------------------
+ # if TRUE then background = Transparent
+ # PNG margins are ajusted.
+ # spatial.extent needs to be communicated to
+ # Google.Earth so that it knows how to overlay image
+ # ----------------------------
+ if (!google.maps) {
+ png(file=map.file.name, bg="white",
+ width=map.plot.width,
+ height=map.inits$map.plot.height)
+ par(mfrow=c(1,1), cex=2.0, mar=c(5,4,4,5))
+ }
+ if (google.maps) {
+ png(file=map.file.name, bg="transparent",
+ width=map.plot.width,
+ height=map.inits$map.plot.height)
+ par(mfrow=c(1,1),
+ cex=2.0,
+ mar=c(0,0,0,0),
+ xpd=TRUE)
+ }
+ # ---------------
+ # Plot Surface
+ # ---------------
+ contour.index <- pip.cont$contour.index[,1]
+ bs.rpart.maps(
+ xxx = st.pred$xxx[contour.index],
+ yyy = st.pred$yyy[contour.index],
+ zzz = st.pred$pred[contour.index],
+ zlim = c(z.min,z.max),
+ pred.grid.size = map.inits$pred.grid.size ,
+ grid.size.ratio = map.inits$grid.size.ratio,
+ # Less than 1 reduces height,
+ # greater than 1 increase height
+ #for given width
+ col.palette = red.colors(n.red),
+ #spatial.extent = spatial.extent.map ,
+ xlab= "Longitude",
+ ylab= "Latitude")
+ title(main = paste(spp.name, " ", date.names[iii]) ,
+ font.main=4, line=1, cex.main=3.0 )
+ # -------------------------------------------------------------
+ # Add Polygon Boundaries
+ # -------------------------------------------------------------
+ kk <- 1 # first (lower) quantile
+ hd.index <- pip.cont$contour.level.index ==
+ sd.cont$log.density.quantiles[kk]
+ hd.set <- (1:length(pip.cont$contour.level.index))[hd.index]
+ # There are 9 polygons in this set, but only the first and fourth
+ # are the big important regions
+ for (kkk in c(1,4)){
+ polygon(sd.cont$contour.polygons[[kkk]]) #$x,
+ #sd.cont$contour.polygons[[jjj]]$y,
+ # col= "black", #c.col[kk],
+ #border=TRUE)
+ }
+ # -------------------------------------------------------------
+ # Add Political Boundaries
+ # -------------------------------------------------------------
+ require(maps)
+ map('county',add=TRUE, lwd=2, col="grey")
+ map('state',add=TRUE, lwd=3, col="yellow")
+ map('state',add=TRUE, lwd=2, col="black")
+ # -----------------------------------------------------
+ # -------------------------------------------------------------
+ if (add==FALSE) dev.off()
+ } # iii - st.pred index
+}# end fuction
+#------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------
+
+
+
+# ------------------------------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------------------------------
+# Initialize Map Gridding
+# ------------------------------------------------------------
+# 10.7.08
+#
+# This needs to be cleaned up a bit
+#
+# Input:
+# -------------
+#
+# Output:
+# ----------
+#
+# Examples:
+# ------------------
+# --------------------------------------------------
+ #~ spatial.extent <- list( lat.max = 45.0,
+ #~ lat.min = 39.0,
+ #~ lon.min= -82.5,
+ #~ lon.max = -67.0 )
+ #~ # ----------------------------------------
+ #~ if (spatial.extent.code == "US") {
+ #~ spatial.extent <- spatial.extent.US
+ #~ map.plot.width <- 1800
+ #~ #pred.grid.size <- 100 #height == lat
+ #~ }
+# ------------------------------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------------------------------
+
+
+initizalize.map.grid <- function(
+ spatial.extent=NULL,
+ lat=NULL,
+ lon=NULL,
+ map.plot.width,
+ pred.grid.size=NULL ){
+# Needs either spatial.extent or lat & lon
+# -----------------------------------------------------------------------------
+# ST Surface Plots Inits
+# -----------------------------------------------------------------------------
+#~ Latitude and longitude can be used very simply for plotting
+#~ by setting up a rectangular grid (e.g. like a Simple Cylindrical Projection)
+#~ The question is how to scale the length:width of the rectangles.
+#~ At the equator a degree of latitude is roughly the same length
+#~ in miles as a degree of longitude - ignoring the asphericity of the
+#~ Earth's globe. Thus, at the equator, a square grid would be satisfactory
+#~ for a small map.
+#
+#~ As we move further away from the equator, e.g. where the continental US lies,
+#~ a degree of longitude is shorter in miles, though a degree of latitude
+#~ is much the same. Thus, a square lat-lon grid in the continental US distorts
+# distances, the map being stretched E-W. Using a rectangular lat-lon grid
+# gives a truer picture of everyday miles.
+#
+#~ The ratio of lengths for a degree latitude:longitude approximately corresponds
+#~ to the inverse of the cosine of the latitude. For example, at 40 degrees
+#~ latitude, the ratio of lat:lon is appriximately 1/cos(40 degrees) = 1.31.
+#~ This is the ratio for latitude of Denver,CO Springfield, IL, or Harrisburg, PA.
+#
+#~ This ratio of latitude:longitude is used to determine an appropriate
+#~ ratio of map image size (length & width in pixes) as well to determine
+# grid size ratio so that
+#~ grid cells plotted in the map surface have approximately equal length width & height in miles.
+#~ For simplicity, I use a fixed grid size for mapping. The ratio of
+#~ the length latitude:longitude length of the pixels is adjusted to
+#~ the inverse of the cosine of the latitude from the middle of the spatial
+#~ extent being plotted.
+# -----------------------------------------------------------------------------------------------------
+ # user specified: Width of image (png file) in pixels
+ #map.plot.width <- 1500
+ middle.lat <- mean(spatial.extent$lat.max,spatial.extent$lat.min)
+ pixels.per.degree.lon <- map.plot.width/
+ (spatial.extent$lon.max - spatial.extent$lon.min)
+ length.lat.to.length.lon.ratio <- 1/cos(middle.lat/360*2*pi)
+ pixels.per.degree.lat <- length.lat.to.length.lon.ratio *
+ pixels.per.degree.lon
+ map.plot.height <- round(pixels.per.degree.lat *
+ (spatial.extent$lat.max-spatial.extent$lat.min))
+
+# ------------------------------------------------------------------------
+ # Discretization size
+ # ------------------------------------------------------------------------
+ # Calculate the maximum number of grid cells (minimum grid cell area)
+ # to achieve the 10 random locations per cell from the prediction
+ # grid design.
+ #
+ # NOTE: It appears that with these setting there are FAR more than
+ # 10 random locs per cell!!!!
+ #
+ # The minimum Longitude grid side = . .14436 deg long
+ # At 40 degrees Lat, a change of .14436 lon is 12km in length.
+ # This number comes from the stratified design used to sample the
+ # random locations based on extent and 400 equally spaced lon cells:
+ # .14436 deg long = (-124.72839 - -66.98426)/400
+ #
+ # The minimum Latitude grid side = ..12210 deg lat
+ # At 40 degrees Lat, a change of .12210 lat is 14 km in length.
+ # This number comes from the stratified design used to sample the
+ # random locations based on extent and 200 equally spaced lat cells:
+ # .12210 deg lat= (48.97630 - 24.55572)/200
+ #------------------------------------------------------------------------
+ if (is.null(pred.grid.size)) {
+ # Calculate Maximum pred.grid.size for this region
+ pred.grid.size.max.xxx <-
+ floor( (spatial.extent$lon.max - spatial.extent$lon.min)/.145)
+ pred.grid.size.max.yyy <-
+ floor( (spatial.extent$lat.max - spatial.extent$lat.min)/.123 )
+ if (pred.grid.size.max.xxx < pred.grid.size.max.yyy)
+ pred.grid.size <- floor(pred.grid.size.max.xxx)
+ if (pred.grid.size.max.xxx > pred.grid.size.max.yyy)
+ pred.grid.size <- floor(pred.grid.size.max.yyy)
+ #pred.grid.size
+ }
+ # -------------------------------------------------------------------
+ # User specified: number of latitude cells across spatial.extent
+ #pred.grid.size <- 100
+ # --------------------------------------------------------------------------
+ # longitude cells = pred.grid.size * grid.size.ratio
+ # Note that this ratio really takes into account two
+ # quantities, the ratio of the lat:lon distances on the
+ # surface of the Earth as well as the lat:lon ratio of
+ # the spatial extent.
+ # -------------------------------------------------------------------------
+ cells.per.degree.lat <- pred.grid.size/
+ (spatial.extent$lat.max - spatial.extent$lat.min)
+ cells.per.degree.lon <- cells.per.degree.lat /
+ length.lat.to.length.lon.ratio
+ grid.cell.plot.width <- cells.per.degree.lon *
+ (spatial.extent$lon.max-spatial.extent$lon.min)
+ grid.size.ratio <- grid.cell.plot.width/pred.grid.size
+ #grid.size.ratio
+ #pred.grid.size
+ #grid.cell.plot.width
+
+ # ---------------------------------------------------------------------------------
+ # How long are the sides of a grid cell?
+ # ----------------------------------------------------------------------------------
+ # Assume a grid cell centered at 40 degrees lat
+ # ----------------------------------------------------------------------------------
+ # Formula for distance between two points on a great circle
+ # Each point needs to be expressed in radians
+ # ---------------------------------------------------------------------------------------------
+ lat1<- (40)*pi/180
+ lon1 <- 70*pi/180
+ lat2 <- (40 + 1/cells.per.degree.lat)*pi/180
+ lon2 <- lon1
+ d <- 2*asin(sqrt((sin((lat1-lat2)/2))^2 +
+ cos(lat1)*cos(lat2)*(sin((lon1-lon2)/2))^2))
+ radius.km <- 6371.0
+ lat.distance.km <- radius.km * d
+ # ---------------------------------------------------------------------------------------------
+ lat1<- (40)*pi/180
+ lon1 <- 70*pi/180
+ lon2 <- (70 + 1/cells.per.degree.lon)*pi/180
+ lat2 <- lat1
+ d <- 2*asin(sqrt((sin((lat1-lat2)/2))^2 +
+ cos(lat1)*cos(lat2)*(sin((lon1-lon2)/2))^2))
+ radius.km <- 6371.0
+ lon.distance.km <- radius.km * d
+ # ----------------------------
+
+return(list(
+ pixels.per.degree.lon=pixels.per.degree.lon,
+ pixels.per.degree.lat=pixels.per.degree.lat,
+ map.plot.height=map.plot.height,
+ length.lat.to.length.lon.ratio=length.lat.to.length.lon.ratio,
+ cells.per.degree.lat =cells.per.degree.lat ,
+ cells.per.degree.lon=cells.per.degree.lon,
+ grid.cell.plot.width=grid.cell.plot.width,
+ grid.size.ratio =grid.size.ratio,
+ pred.grid.size=pred.grid.size,
+ lon.distance.km=lon.distance.km,
+ lat.distance.km=lat.distance.km))
+} # end function
+# ------------------------------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------------------------------
+
+# ------------------------------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------------------------------
+# Point in Shapefile Polygon Operation
+# ------------------------------------------------------------
+# 6.3.08
+# 10.6.08
+#
+# This function performs the "Point in shapefile" operation
+# for BCRs and Statenames for a specific set of shapefiles.
+# Because each shape file has its own attr data frame, there are two
+# steps to select shapes:
+# 1) find the att.selection.column of the att.data data.frame
+# 2) search for selected.shape.names in the att.selection.column
+#
+# NOTE: This function is based on the NCEAS function XXXXXX
+# except that I needed to fix the donut hole problem with
+# the shape files. I need to finish documenting this and
+# send it back to those guys!
+#
+# NOTE: 1.9.09
+# ---------------
+# I changed the way that I access attributes -
+# I ran into problems not having S4 objects
+#
+# Input:
+# -------------
+# shape.dir
+# shape.filename
+# sites = data.frame with lat & lon vectors for spatial extent/universe
+# att.selection.column.name = the name of the att.data column
+# selected.shape.names = vector of region/shape names from shape file
+#
+# Output:
+# ----------
+# location.pip - T/F vector the length of the sites
+#
+# Examples:
+# ------------------
+ #~ # --------------------------------------------------------------
+ #~ # Eg.1. extract individual States
+ #~ #--------------------------------------------------------------
+ #~ sites <- data.frame(lon=st.pred$xxx, lat=st.pred$yyy)
+ #~ shape.dir <-"/mnt/data2/ST.BDT/BDT.shapefiles/"
+ #~ shape.filename <- "STATES.shp"
+ #~ selected.shape.names <- c("New York", "Georgia")
+ #~ att.selection.column.name <- "STATE_NAME"
+ #~ # --------------------------------------------------------------
+ #~ # Eg.2 extract individual BCRs
+ #~ #--------------------------------------------------------------
+ #~ sites <- data.frame(lon=st.pred$xxx, lat=st.pred$yyy)
+ #~ shape.dir <-"/mnt/data2/ST.BDT/BDT.shapefiles/"
+ #~ shape.filename <- "bcr.shp" # watch capitalization!
+ #~ att.selection.column.name <- "BCR"
+ #~ selected.shape.names <- c(13, 27) # class must match att.selection.column
+
+ #~ # ------------------------------------------------------------
+ #~ location.pip <- point.in.shapefile(
+ #~ sites,
+ #~ shape.dir,
+ #~ shape.filename,
+ #~ att.selection.column.name,
+ #~ selected.shape.names)
+ #~ plot(sites)
+ #~ points(sites[location.pip,], col="red",cex=0.25)
+# ------------------------------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------------------------------
+point.in.shapefile <- function(
+ sites,
+ shape.dir,
+ shape.filename,
+ att.selection.column.name,
+ selected.shape.names
+ ) {
+# ------------------------------------------------------------------------------------------------------
+ require(maptools)
+ require(splancs)
+ #require(maps)
+ # --------------------------------------------------------------
+ # Read Shape File & Create Map object (using Maptools package)
+ #--------------------------------------------------------------
+ #shape.dir <-"c:\\users\\Research.AKN\\BDT\\Data\\point.in.polygon\\"
+ #shape.dir <- data.dir
+ #shape.filename <- "STATES.shp"
+ #shape.data <- read.shape(paste(shape.dir,shape.filename,sep=""))
+
+ # 2.24.10 Theo Damoulas
+ # The map tools library was "updated"
+ # !!!!!!! function read.shape deprecated use internal ::: to find
+ shape.data <- maptools:::read.shape(paste(shape.dir,shape.filename,sep=""))
+ #maptools:::getinfo.shape(paste(shape.dir,shape.filename,sep=""))
+
+ # --------------------------------------------------------------------------------
+ # Because each shape file has its own attr data frame,
+ # 1) find the att.selection.column.name of the att.data data.frame
+ # 2) search for selected.shape.names in the att.selection.column
+ # --------------------------------------------------------------------------------
+ att.col.index <-( names(shape.data$att.data) %in%
+ att.selection.column.name )
+ #selected.regions <- subset(Map2poly(shape.data),
+ # shape.data$att.data[, att.col.index] %in% selected.shape.names )
+ selected.regions <- subset(maptools:::Map2poly(shape.data),
+ shape.data$att.data[, att.col.index] %in% selected.shape.names )
+
+ # ----------------------------------------------
+ # PIP function
+ # ----------------------------------------------
+ selected.sites <- NULL
+ nnn.regions <- length(selected.regions[])
+ point.in.poly.ind <- NULL
+ for (iii in 1:nnn.regions){
+ # --------------------------------------------------
+ temp.region <- selected.regions[[iii]]
+ # cycle through individual parts within each polygon region
+ # performing the PinP operation one part at a time
+ # instead of one region at a time
+ # ------------------------------------------------
+ attr.temp <- attributes(temp.region)
+ #nParts <- temp.region at nParts
+ nParts <- attr.temp$nParts
+ for (jjj in 1:nParts) {
+ #begin.ttt <- temp.region at pstart$from[jjj]
+ #end.ttt <- temp.region at pstart$to[jjj]
+ begin.ttt <- attr.temp$pstart$from[jjj]
+ end.ttt <- attr.temp$pstart$to[jjj]
+ ttt <- temp.region[begin.ttt:end.ttt,]
+ res <- try(inpip(sites[c("lon","lat")], ttt))
+ # If no errors, collect indices of sites that
+ # are within the set of polygons.
+ if (class(res)=="integer")
+ point.in.poly.ind <- c(point.in.poly.ind,res)
+ } # end for jjj
+ } #end for iii
+ # --------------------------------------------------------
+ # Collect all point in Polygon set
+ # --------------------------------------------------------
+ location.pip <- rep(FALSE, NROW(sites))
+ location.pip[point.in.poly.ind] <- TRUE
+ return(location.pip)
+} # end function
+# ----------------------------------------------------------------------
+# ----------------------------------------------------------------------
+
+
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+# Point-in-Polygon Function
+# -----------------------------------------------------------------------------
+# Daniel Fink
+# 10.08.08
+# 03.17.10
+#
+# Description
+# -----------------
+# For a given set of locations determine if they fall into
+# a sinlge Polygon. Return one index (length of locations).
+#
+# Input
+# ----------
+# xxx, yyy - locations
+# polygon.vertices - data.frame with named vertices x and y
+# corresponding to xxx and yyy coordinates, resp.
+#
+# Output
+# ----------
+# index vector the length of locations
+#
+# Notes:
+# ---------
+#
+# Examples:
+# ----------
+#nnn <- 1000
+#xxx <- rnorm(nnn, mean=0, sd=1)
+#yyy <- rnorm(nnn, mean=0, sd=1)
+#unit.sq.polygon <- data.frame( x=c(0,0,1,1),y=c(0,1,1,0))
+#pip.index <- point.in.polygon(
+# xxx = xxx,
+# yyy = yyy,
+# polygon.vertices = unit.sq.polygon)
+#plot(xxx, yyy, type="n")
+#polygon(unit.sq.polygon, col="blue")
+#points(xxx,yyy)
+#points(xxx[pip.index], yyy[pip.index], pch=19, col="yellow")
+#
+# -----------------------------------------------------------------------------
+point.in.polygon <- function(
+ xxx, yyy,
+ polygon.vertices){
+# ------------------------------------------
+ require(splancs)
+ ttt.index <- inpip(cbind(xxx,yyy),
+ cbind(polygon.vertices$x,
+ polygon.vertices$y))
+ data.index <- rep(FALSE, length(xxx))
+ data.index[ttt.index] <- TRUE
+ return(data.index)
+}#---------------------------------------------------------------------
+#-----------------------------------------------------------------------
+# Drew, Kevin, and the Point in Polygon requires a lot
+# DF: is very general - allows very flexible spatial partions
+# Drew: is computationally intensive
+# Kevin: is easily replaced
+#
+# I have changed the name because point.in.polygon is
+# used LEGITIMATELY used in many other routines.
+# This new function expedites the logic that selects
+# stixels (ST ensemble extents/subsets)
+# predict.ST.ensemble
+# sample.ST.ensemble
+# and create.ST.ensemble
+#
+#
+# ------------------------------------------
+# ------------------------------------------
+## For North America
+##
+## min(x), max(y)
+## -----------------------
+## | |
+## | |
+## | |
+## | |
+## | |
+## | |
+## -----------------------
+## max(x), min(y)
+##
+## This means that even if the base model extents
+## were indeed non-rectangular polgons, then
+## this logic will simply cover each polygon with
+## the smallest covering retangle.
+## This is an interesting idea.
+##
+##
+## Here is another way to do it:
+# The order of the vertices written by create.ST.ensemble is:
+# 1) Lower Left corner
+# 2) Upper Left
+# 3) Upper Right
+# 4) Lower Right
+# ttt.index <- rep(FALSE, length(xxx))
+# ttt.index <- xxx >= polygon.vertices$x[1] &
+# xxx <= polygon.vertices$x[4] &
+# yyy >= polygon.vertices$y[1] &
+# xxx <= polygon.vertices$y[2]
+#
+#-----------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+point.in.rectangle <- function(
+ xxx, yyy,
+ polygon.vertices){
+# ------------------------------------------
+ maxX <- max(polygon.vertices$x)
+ minX <- min(polygon.vertices$x)
+ maxY <- max(polygon.vertices$y)
+ minY <- min(polygon.vertices$y)
+ newDataIndex <- rep(FALSE, length(xxx))
+ locationMask <- xxx <= maxX & xxx >= minX & yyy <= maxY & yyy >= minY
+ newDataIndex[locationMask] <- TRUE
+#### if (isTRUE(all.equal(data.index,newDataIndex)) == FALSE) {
+#### print("~~~~~ point.in.polygon FALSE")
+#### }
+ return(newDataIndex)
+}#---------------------------------------------------------------------
+#-----------------------------------------------------------------------
+#-----------------------------------------------------------------------
+
+
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+# BS.RPART Mapping Plot Function
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+# 1.2.08
+#
+# Description:
+# ----------------
+# This function produces a single map image using fields.
+# No smoothing.
+# Primitive (i.e. rectangular) control of spatial extent
+#
+# INPUT
+# ------------
+# xxx
+# yyy
+# zzz
+#
+# OUTPUT
+# ------------
+#
+# To do:
+# ---------
+#
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+bs.rpart.maps <- function(
+ # Data
+ xxx,
+ yyy,
+ zzz,
+ pred.grid.size = NULL,
+ grid.size.ratio = 2,
+ spatial.extent = NULL,
+ # Save File
+ save.name = NULL,
+ plot.width = 800,
+ plot.height = 600,
+ main.text = NULL,
+ # Pass in other plotting parameters
+ col.palette=NULL,
+ ... )
+{ #begin function
+
+# ------------------------------------------------------
+# Inits
+# ------------------------------------------------------
+ call <- match.call()
+ require(maps)
+ require(fields)
+
+ if (is.null(col.palette)){
+ # Color scheme stolen from sp library
+ col.palette<- c(
+ "#000033FF", "#00003CFF", "#000046FF", "#00004FFF", "#000058FF", "#000061FF",
+ "#00006BFF", "#000074FF", "#00007DFF", "#000086FF", "#000090FF", "#000099FF",
+ "#0000A2FF", "#0000ACFF", "#0000B5FF", "#0000BEFF", "#0000C7FF", "#0000D1FF",
+ "#0000DAFF", "#0000E3FF", "#0000ECFF", "#0000F6FF", "#0000FFFF", "#0700FFFF",
+ "#0E00FFFF", "#1600FFFF", "#1D00FFFF", "#2400FFFF", "#2B00FFFF", "#3300FFFF",
+ "#3A00FFFF", "#4100FFFF", "#4800FFFF", "#5000FFFF", "#5700FFFF", "#5E00FFFF",
+ "#6500FFFF", "#6D00FFFF", "#7400FFFF", "#7B00FFFF", "#8200FFFF", "#8A01FEFF",
+ "#9106F9FF", "#980BF4FF", "#9F0FF0FF", "#A714EBFF", "#AE19E6FF", "#B51DE2FF",
+ "#BC22DDFF", "#C426D9FF", "#CB2BD4FF", "#D230CFFF", "#D934CBFF", "#E139C6FF",
+ "#E83EC1FF", "#EF42BDFF", "#F647B8FF", "#FE4CB3FF", "#FF50AFFF", "#FF55AAFF",
+ "#FF59A6FF", "#FF5EA1FF", "#FF639CFF", "#FF6798FF", "#FF6C93FF", "#FF718EFF",
+ "#FF758AFF", "#FF7A85FF", "#FF7F80FF", "#FF837CFF", "#FF8877FF", "#FF8C73FF",
+ "#FF916EFF", "#FF9669FF", "#FF9A65FF", "#FF9F60FF", "#FFA45BFF", "#FFA857FF",
+ "#FFAD52FF", "#FFB24DFF", "#FFB649FF", "#FFBB44FF", "#FFBF40FF", "#FFC43BFF",
+ "#FFC936FF", "#FFCD32FF", "#FFD22DFF", "#FFD728FF", "#FFDB24FF", "#FFE01FFF",
+ "#FFE51AFF", "#FFE916FF", "#FFEE11FF", "#FFF20DFF", "#FFF708FF", "#FFFC03FF",
+ "#FFFF09FF", "#FFFF26FF", "#FFFF43FF", "#FFFF60FF")}
+
+# ----------------------------------------------
+# Set Spatial Extent
+# ----------------------------------------------
+ if (!is.null(spatial.extent)) {
+ if (is.null(spatial.extent$lat.max)) spatial.extent$lat.max <- max(yyy)
+ if (is.null(spatial.extent$lat.min)) spatial.extent$lat.min <- min(yyy)
+ if (is.null(spatial.extent$lon.min)) spatial.extent$lon.min <- min(xxx)
+ if (is.null(spatial.extent$lon.max)) spatial.extent$lon.max <- max(xxx)
+ x.zoom.ind <- (xxx < spatial.extent$lon.max & xxx > spatial.extent$lon.min)
+ y.zoom.ind <- (yyy < spatial.extent$lat.max & yyy > spatial.extent$lat.min)
+ zoom.ind <- as.logical( x.zoom.ind & y.zoom.ind)
+ #sum(zoom.ind)
+ zzz <- zzz[zoom.ind]
+ xxx <- xxx[zoom.ind]
+ yyy <- yyy[zoom.ind]
+ }
+
+ # ------------------------------------------------------------------------
+ # Discretization size
+ # ------------------------------------------------------------------------
+ # Calculate the maximum number of grid cells(minimum grid cell area)
+ # to achieve the 10 random locations per cell from the prediction
+ # grid design.
+ #
+ # The minimum Longitude grid side = .28872 deg long
+ # This number comes from the stratified design used to sample the
+ # random locations based on extent and 200 equally spaced lon cells:
+ # .28872 deg long = (-124.72839 - -66.98426)/200
+ #
+ # The minimum Latitude grid side = .24421 deg lat
+ # This number comes from the stratified design used to sample the
+ # random locations based on extent and 100 equally spaced lat cells:
+ # .24421 deg lat= (48.97630 - 24.55572)/100
+ #------------------------------------------------------------------------
+ if (is.null(pred.grid.size)) {
+ # Calculate Maximum pred.grid.size for this region
+ pred.grid.size.max.xxx <- floor( (max(xxx) - min(xxx))/.28872 )
+ pred.grid.size.max.yyy <- floor( (max(yyy) - min(yyy))/.24421 )
+ if (pred.grid.size.max.xxx/2 < pred.grid.size.max.yyy)
+ pred.grid.size <- floor(pred.grid.size.max.xxx/2)
+ if (pred.grid.size.max.xxx > pred.grid.size.max.yyy*2)
+ pred.grid.size <- floor(pred.grid.size.max.yyy)
+ #pred.grid.size
+ }
+
+ # ----------------------------------------------
+ # Create Prediction Grid with as.image
+ # ----------------------------------------------
+ ttt.image <- as.image(zzz,
+ x= data.frame(xxx,yyy),
+ nrow=round(pred.grid.size*grid.size.ratio), # nrow=X direction
+ ncol=pred.grid.size, # ncol=Y direction
+ na.rm=TRUE)
+
+ if (!is.null(save.name)){
+ png(file=save.name,
+ bg="white",
+ width = plot.width,
+ height = plot.height)
+ }
+ image.plot(ttt.image,
+ col = col.palette, ...)
+ # zlim=c(0,5))
+ if (!is.null(main.text)){
+ title(main = main.text , font.main=4, line=2)
+ title(main = paste("Spatial Grid:",pred.grid.size,"x",
+ pred.grid.size*2), font.main=4, line=1, cex.main=0.75)}
+
+ # Add political Boundaries
+ # ----------------------------
+ #map('state',add=TRUE, lwd=2, col="yellow")
+ #map('state',add=TRUE, lwd=1.5, col="black")
+
+if (!is.null(save.name)){
+ dev.off()
+ }
+
+# --------------------------------------------------------------------------
+} # end function
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+
+
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+# Point-in-Polygon Contours
+# -----------------------------------------------------------------------------
+# Daniel Fink
+# 2.7.08
+#
+# Description
+# -----------------
+# For a given set of locations determine if they fall into
+# a set of Polygon contours. Return one index (lenght of locations)
+# for each unique level of polygon contours.
+#
+# Also compute quantiles for locations and make a pretty picture.
+#
+# Input
+# ----------
+# xxx, yyy - locations
+# contour.polygons - list of polygon contours from contourLines
+# function
+#
+# Output
+# ----------
+# Return one index (lenght of locations)
+# for each unique level of polygon contours.
+#
+# Notes:
+# ---------
+#
+# Further Development:
+# ----------------------------
+# -----------------------------------------------------------------------------
+point.in.polygon.contours <- function(
+ xxx, yyy,
+ contour.polygons){
+# ------------------------------------------
+# Dummy Values/Calls
+# ------------------------------------------
+ #contour.polygons <- sd.cont$contour.polygons
+# ------------------------------------------
+# Inits
+# ------------------------------------------
+ require(splancs)
+
+# ------------------------------------------
+# Identify unique polygon levels
+# ------------------------------------------
+ level.index <- rep(0,length(contour.polygons))
+ for (iii in 1:length(contour.polygons))
+ level.index[iii] <- contour.polygons[[iii]]$level
+ unique.levels <- sort(unique(level.index))
+ # Matrix of Contour indices
+ contour.index <- matrix(FALSE,length(xxx),length(unique.levels))
+
+ # Cycle through all Polygons in order
+ # ** Do point-in-polygon operations
+ # ** store indices according to polygon level
+ # ----------------------------------------------------------
+ #sum.points <- 0
+ for (jjj in 1:length(contour.polygons)) {
+ ttt.ind <- inpip(cbind(yyy,xxx),
+ cbind(contour.polygons[[jjj]]$y,
+ contour.polygons[[jjj]]$x))
+ # Construct/store contour indices
+ col.index <- (contour.polygons[[jjj]]$level == unique.levels)
+ contour.index[ ttt.ind, col.index] <- TRUE
+ }
+ # -----------------------
+ # Empirical Quantiles
+ empirical.quant <- apply(contour.index, 2, mean)
+
+ # ---------------------------------------------------------
+ # Construct Indices into nonoverlapping contours
+ # ---------------------------------------------------------
+ non.olap.index <- matrix(FALSE, NROW(contour.index),
+ NCOL(contour.index))
+ # Begin with smallest contour
+ non.olap.index[,NCOL(contour.index)] <-
+ contour.index[,NCOL(contour.index)]
+ # Sequentially subtract
+ for (iii in NCOL(contour.index):2){
+ non.olap.index[,(iii-1)] <- (contour.index[,(iii-1)] &
+ !contour.index[,iii])
+ }
+ # % of data in each contour
+ n.contour <- apply(non.olap.index, 2, sum)
+ # ---------------------------------------------------------
+
+# Return contours as polygons too!!!
+results.list <- list(
+ xxx = xxx,
+ yyy = yyy,
+ empirical.quant = empirical.quant,
+ contour.polygons = contour.polygons,
+ contour.index = contour.index,
+ contour.level.index = level.index,
+ non.olap.index = non.olap.index,
+ n.contour = n.contour)
+ return(results.list)
+}#---------------------------------------------------------------------
+#-----------------------------------------------------------------------
+
+
+#-----------------------------------------------------------------------
+# -------------------------------------------------------------------------------
+# Smooth ST Predictions
+#
+# -------------------------------------------------------------------------------
+smooth.st.predictions <- function(
+ kkk, # Single Time slice
+ pred.grid.size, # roughly twice desired plotting resolution
+ gam.smoothing.knots=25,
+ st.rough.dir,
+ st.rough.name ,
+ st.smooth.dir ,
+ st.smooth.name){
+ # ----------------
+ #shape.dir, # <- "C:\\users\\Research.STBDT\\Data\\BDT.shapefiles\\"
+ #shape.filename, # <- "STATES.shp"
+ #selected.state.names = NULL) {
+ # -----------------------------------------------
+ stp.name <- paste(st.rough.dir,st.rough.name,".",kkk,".RData",sep="")
+ load(stp.name) #st.pred
+ require(mgcv)
+ # -----------------------------------------------
+ xxx <- st.pred$xxx
+ yyy <- st.pred$yyy
+ #xxx.name <- "Lon"
+ #yyy.name <- "Lat"
+ zzz <- st.pred$pred
+ # -----------------------------------------------
+ require(mgcv)
+ d.gam <- gam( zzz ~ s(xxx,yyy, k=gam.smoothing.knots))
+ nnn.xxx <- pred.grid.size
+ nnn.yyy <- pred.grid.size
+ xxx.pred <- seq(from=min(xxx),to=max(xxx),length=nnn.xxx)
+ yyy.pred <- seq(from=min(yyy),to=max(yyy),length=nnn.yyy)
+ pred.design <- expand.grid(xxx=xxx.pred, yyy=yyy.pred)
+ # "Fuzz up" Prediction Grid to better fill in image.plot
+ pred.design$xxx <- pred.design$xxx + runif(NROW(pred.design),
+ min = -(abs(xxx.pred[2] - xxx.pred[1]))/2.,
+ max = (abs(xxx.pred[2] - xxx.pred[1]))/2.)
+ pred.design$yyy <- pred.design$yyy + runif(NROW(pred.design),
+ min = -(abs(yyy.pred[2] - yyy.pred[1]))/2.,
+ max = (abs(yyy.pred[2] - yyy.pred[1]))/2.)
+# # -------------------------------------------------------
+# # Cutout US States to reduce prediction time!
+# # --------------------------------------------------------------
+# if (!is.null(selected.state.names)){
+# sites <- data.frame(lon=pred.design$xxx, lat=pred.design$yyy)
+# #shape.dir <- "C:\\users\\Research.STBDT\\Data\\BDT.shapefiles\\"
+# #shape.filename <- "STATES.shp"
+# #selected.shape.names <-
+# # c("New York", "Pennsylvania", "New Jersey",
+# # "Ohio", "West Virginia", "Delaware", "Connecticut",
+# # "Rhode Island", "Massachusetts",
+# # "Vermont", "New Hampshire", "Maine",
+# # "Maryland", "Virginia")
+# att.selection.column.name <- "STATE_NAME"
+# location.pip <- point.in.shapefile(
+# sites,
+# shape.dir,
+# shape.filename,
+# att.selection.column.name,
+# selected.shape.names=selected.state.names)
+# #plot(sites)
+# #points(sites[location.pip,], col="red",cex=0.25)
+# pred.design <- pred.design[ location.pip, ]
+# }
+# # -------------------------------
+ pred.gam <- predict(d.gam,
+ newdata=pred.design,
+ se.fit=FALSE, type="response")
+ st.pred <- data.frame(pred.design, pred=pred.gam)
+ names(st.pred)
+ dim(st.pred)
+ # -----------------------------------------------
+ smooth.filename <- paste(st.smooth.dir,st.smooth.name,".",kkk,".RData",sep="")
+ save(st.pred, file=smooth.filename)
+ # For initialization in Halloween.maps()
+ #smooth.filename <- paste(st.smooth.dir,st.smooth.name,".",1,".RData",sep="")
+ #save(st.pred, file=smooth.filename)
+ # -----------------------------------------------
+ # ------------------------------------------------------------
+ # Return Values
+ # ------------------------------------------------------------
+} # end function
+# --------------------------------------------------------------------------------------------
+# -------------------------------------------------------------------------------------------
+
+
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+# Load & Process SPAT_COVAR Data for Spatial Prediction
+# --------------------------------------------------------------------------
+# This function will load, subsample, and process the Spatial
+# prediction data.
+#
+# Like the other functions I am writing, I will begin by keeping
+# this as simple as possible. KISS!!
+#
+# INPUT
+# ------------
+# INPUT
+# ------------
+# pred.data.file <- character string for file location including directory
+# pred.dir <- "~/norcar.temp/USA Prediction Grid/"
+# pred.data.file <- paste(pred.dir,"Random.locations.NE.10.31.07.csv",sep="")
+#
+#
+# This file is assumed to contain the following fields/information
+#
+# what happens if a field is missing?
+# Should these fields be compared/match to the p.data$X fields used to
+# develop the model?
+#
+#
+# NNN.pred <- (sub)sample size of prediction data file. Defalult = NULL
+# (defaults to whole data set)
+# NNN <- 5000
+# spatial.extent <- list( # NE Region
+# lat.max <- 45.0,
+# lat.min <- 39.0,
+# lon.min <- -82.5,
+# lon.max <- -67.0 )
+#
+# OUTPUT
+# ------------
+# D.pred - prediction data frame
+# locs - locations corresponding to D.pred
+#
+# To do:
+# ---------
+# I need to describe the format of D.pred in detail so that I can
+# generate new sets. Part of this will be to point to/describe the
+# process that Roger and I went through to generate this data.
+#
+# Currently, I have hard coded the list of predictor variables that
+# to be added to D.pred. I would like to add logic to match and
+# keep only those predictors that match a list of predictor names
+# target.var <- names(p.data$X)
+# possibly matching the classes of the variables too. That would
+# be very useful.
+#
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+make.SPAT.COVAR.pred.data <- function(
+ pred.data.file,
+ NNN.pred = NULL,
+ spatial.extent = NULL) {
+# ---------------------------------------------------
+ call <- match.call()
+# ----------------------------------------------
+# Load Data
+# ----------------------------------------------
+ D.pred <- read.csv(file=pred.data.file)
+ #dim(D.pred) #27933 67
+# ----------------------------------------------
+# Set Spatial Extent
+# ----------------------------------------------
+ if (!is.null(spatial.extent)) {
+ xxx <- D.pred$DECIMAL_LONGITUDE
+ yyy <- D.pred$DECIMAL_LATITUDE
+ if (is.null(spatial.extent$lat.max)) spatial.extent$lat.max <- max(yyy)
+ if (is.null(spatial.extent$lat.min)) spatial.extent$lat.min <- min(yyy)
+ if (is.null(spatial.extent$lon.min)) spatial.extent$lon.min <- min(xxx)
+ if (is.null(spatial.extent$lon.max)) spatial.extent$lon.max <- max(xxx)
+ x.zoom.ind <- (xxx < spatial.extent$lon.max & xxx > spatial.extent$lon.min)
+ y.zoom.ind <- (yyy < spatial.extent$lat.max & yyy > spatial.extent$lat.min)
+ zoom.ind <- as.logical( x.zoom.ind & y.zoom.ind)
+ #sum(zoom.ind)
+ D.pred <- D.pred[zoom.ind, ]
+ rm(xxx,yyy)
+ }
+
+# ---------------------------------------------------------------------
+# Convert regional NCLD classes counts to proportions
+# ---------------------------------------------------------------------
+ # Currently, Rogers NLCD neighborhood variables in SPATCOVAR
+ # contain the counts of each landcover class within the given neighborhood.
+ # i.e percentages x 100
+ # # of cells = (a*r)^2
+ #
+ # This was only for earlier version ==>
+ # It should be a non-issue with the "new" version of
+ # "ebird.data.processing.12.03.07.R"
+ # ----------------------------------------------------
+ # NLCD01_CMN" "NLCD01_IMN", are already stored as %'s
+ # However, I am going to include them so that these
+ # predictors are 100% compatible with the ebird predictors.
+ # I need to fix the ebird data!!!
+ # ------------------------------------------------------------
+ nbhd.size <- c("A10R15", "A10R5", "A100R5")
+ nbhd.cell.size <- c(22500,2500,250000)
+ nlcd.vars <- c(
+ "NLCD01_N11", "NLCD01_N12",
+ "NLCD01_N21", "NLCD01_N22",
+ "NLCD01_N23", "NLCD01_N24",
+ "NLCD01_N31", "NLCD01_N41",
+ "NLCD01_N42", "NLCD01_N43",
+ "NLCD01_N52", "NLCD01_N71",
+ "NLCD01_N81", "NLCD01_N82",
+ "NLCD01_N90", "NLCD01_N95")
+ for (iii in 1:3) {
+ regional.nlcd.vars <- paste(nlcd.vars, nbhd.size[iii] ,sep="")
+ D.pred[,names(D.pred) %in% regional.nlcd.vars] <-
+ D.pred[,names(D.pred) %in%
+ regional.nlcd.vars]/nbhd.cell.size[iii]*100
+ }
+# ------------------------------------------------------------
+# Subsampling
+# ------------------------------------------------------------
+ subsample.index <- NULL
+ if (!is.null(NNN.pred)) {
+ if (NNN.pred < NROW(D.pred)){
+ subsample.index <- sample(1:NROW(D.pred), NNN.pred)
+ D.pred <- D.pred[subsample.index, ]
+ }}
+
+# ------------------------------------------------------------
+# Predictor Processing
+# ------------------------------------------------------------
+ y <- D.pred$DECIMAL_LATITUDE
+ x <- D.pred$DECIMAL_LONGITUDE
+ # List of D.NE predictors that need to be removed
+ remove.var <- c( "X", "DECIMAL_LATITUDE_CS", "DECIMAL_LONGITUDE_CS",
+ "NED48_ELEVATION", "BLOCKGROUP_FIPS_ESRI04" ,
+ "DECIMAL_LATITUDE", "DECIMAL_LONGITUDE")
+ # "NLCD01_IMPERV" , "NLCD01_LANDCOVER" )
+ D.pred <- D.pred[ , !(names(D.pred) %in% remove.var) ]
+ # BCR Processing: BCR == 0 occurs at coastline locations
+ # ---------------------------------------------------------------------
+ #points( loc.x[ D.pred$BCR == 0],
+ # loc.y[ D.pred$BCR == 0],
+ # col=4,
+ # cex=3.0,
+ # pch=5)
+ D.pred$BCR[ D.pred$BCR == 0] <- NA
+ D.pred$BCR <- as.factor(D.pred$BCR)
+ D.pred$NLCD01_LANDCOVER <- as.factor(D.pred$NLCD01_LANDCOVER)
+ # Append Lat & lon
+ # ------------------------------------------
+ D.pred <- cbind(D.pred, x, y)
+# ------------------------------------------------------------
+# Return Values
+# ------------------------------------------------------------
+ locs <- data.frame(x = x, y=y)
+ data.list <- list(
+ call = call,
+ locs = locs,
+ D.pred = D.pred,
+ subsample.index=subsample.index)
+ return(data.list)
+} # end function
+
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+
+
+
+
+
+# -----------------------------------------------------------------------------------------------------------
+# Plot Monthly Training Data Map
+# -----------------------------------------------------------------------------------------------------------
+monthly.maps <- function(
+ xxx,
+ yyy,
+ jdates,
+ zzz, # same length as (xxx, yyy, jdates)
+ zzz.index.1, #red obs > pred ===> Predictions too BIG
+ zzz.index.2)
+{# ----------------------------------------
+ mo.txt <- c("Jan","Feb","Mar","Apr","May","Jun",
+ "Jul","Aug","Sep","Oct","Nov","Dec")
+ require(maps)
+ par(mfrow=c(3,4),mar=c(0,0,1,0),cex=1.0)
+ n.period <- 12
+ for (iii in 1:n.period) {
+ #Subseting Criterion
+ # -------------------------------------
+ #ll <- min(jdates)
+ #ul <- max(jdates)
+ #ttt.index <- jdates >= ll & jdates <= ul
+ ll <- (365/n.period)*(iii-1)
+ ul <- (365/n.period)*(iii)
+ ttt.index <- jdates > ll & jdates < ul
+ # --------------------------------------
+ plot( xxx[ttt.index],
+ yyy[ttt.index],
+ #type="n",
+ cex=0.25,
+ pch=19,
+ col="grey",
+ axes = FALSE,
+ main=paste( mo.txt[iii], " ", format(ll, digits=3),":",
+ format(ul, digits=3)," + propor = ",
+ format(sum(zzz[ttt.index] > 0)/ sum(ttt.index),
+ digits=3)))
+ box()
+ # ---------------------------------------
+ # Add negative residuals in blue
+ # RED, neg res ==> ppp> yyy ==> almost all occur when yyy == 0)
+ # ----------------------------------------
+ ttt.index <- jdates > ll & jdates < ul & zzz.index.1
+ points( xxx[ttt.index],
+ yyy[ttt.index],
+ cex=sqrt(abs(zzz[ttt.index])),
+ col="red",
+ #cex=0.25,
+ pch=1)
+ # BLUE ==> ppp < yyy
+ ttt.index <- jdates > ll & jdates < ul & zzz.index.2
+ points( xxx[ttt.index],
+ yyy[ttt.index],
+ cex=sqrt(abs(zzz[ttt.index])),
+ col="blue",
+ #cex=0.25,
+ pch=4)
+ # Add political Boundaries
+ # ----------------------------
+ map('state',add=TRUE, lwd=2, col="yellow")
+ map('state',add=TRUE, lwd=1.5, col="black")
+ } # end iii = months
+
+ # ------------------------------------------------------------
+ # Return Values
+ # ------------------------------------------------------------
+ return()
+} # end function
+# --------------------------------------------------------------------------------------------
+# -------------------------------------------------------------------------------------------
+
+
+# ------------------------------------------------------------------
+# FOR LOOP over time slices (within season)
+# * Load Predicted Surface
+# * Pixelate it
+# * Stack pixelated surface into Clustering design
+# row = pixel/locations, cols= times
+# ==> group trajectories
+# Q: rows come from stack/unstack(ttt.image) ??
+# * END FOR
+#
+# Then cluster the Clustering design
+# Output: each row, i.e. pixel/location will get a cluster
+# label and a silhoullette number
+#
+# Plot these on a map, perhaps one color at a time.
+#
+#
+# Inputs:
+# ---------
+# stp.save.name, #bs.stp.save.name
+# temporal.index,
+# pred.grid.size,
+# grid.size.ratio,
+# spatial.index=NULL This is an index on the prediction vector,
+# usually used to select regions (BCR's or states)
+# Outputs:
+# ---------
+#return.list <- list(call=call,
+# X=X.cluster,
+# X.image = ttt.image)
+# ------------------------------------------------------------------
+make.functional.data.design.matrix <- function(
+ stp.save.dir, #bs.stp.save.dir
+ stp.save.name, #bs.stp.save.name
+ temporal.index,
+ pred.grid.size,
+ grid.size.ratio,
+ spatial.index=NULL){
+ # ----------------------------------
+ call <- match.call()
+ # ------------------------------------------------------------
+ X.cluster <- NULL
+ # ------------------------------------------------
+ for (iii in (temporal.index)){
+ # ----------------------------------------------
+ # Load Space-Time Predictions From file
+ # ----------------------------------------------
+ stp.name <- paste(stp.save.dir,stp.save.name,".",iii,".RData",sep="")
+ load(stp.name) # st.pred
+ # ----------------------------------------------
+ # Spatial Index
+ # ----------------------------------------------
+ if (is.null(spatial.index))
+ spatial.index <- rep(TRUE, length(st.pred$xxx))
+ # ----------------------------------------------
+ # Create Prediction Grid with as.image
+ # ----------------------------------------------
+ xxx <- st.pred$xxx[spatial.index]
+ yyy <- st.pred$yyy[spatial.index]
+ zzz <- st.pred$pred[spatial.index]
+ # ----------------------------------------------
+ # Stack/Unstack using as.image
+ # ----------------------------------------------
+ ttt.image <- as.image(zzz,
+ x= data.frame(xxx,yyy),
+ nrow=round(pred.grid.size*grid.size.ratio), # nrow=X direction
+ ncol=pred.grid.size,
+ na.rm=TRUE) # ncol=Y direction
+ #names(ttt.image)
+ # ---------------------
+ zzz.vector <- rep(0, length( ttt.image$ind[,1] ))
+ for (jjj in 1:length( ttt.image$ind[,1] ))
+ zzz.vector[jjj] <- ttt.image$z[ ttt.image$ind[jjj,1],
+ ttt.image$ind[jjj,2]]
+ #zzz.loc.x <- ttt.image$x[ttt.image$ind[,1]]
+ #zzz.loc.y <- ttt.image$y[ttt.image$ind[,2]]
+ # ---------------------
+ #hist(zzz.vector)
+ #image.plot(ttt.image)
+ #points(ttt.image$x[ttt.image$ind[,1]],
+ # ttt.image$y[ttt.image$ind[,2]],
+ # cex=0.5*zzz.vector ,
+ # col="yellow")
+ # ---------------------
+ # ----------------------------------------------
+ # Add to cluster design
+ # ----------------------------------------------
+ X.cluster <- cbind(X.cluster, zzz.vector)
+ } # end iii
+# ------------------------------------------
+# Return Values
+# ------------------------------------------
+return.list <- list(call=call,
+ X=X.cluster,
+ X.image = ttt.image)
+return(return.list)
+# --------------------------------------------------------------------------
+} # end function
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+# --------------------------------------------------------------------------
+
diff --git a/contrib/stem/current.vt b/contrib/stem/current.vt
new file mode 100644
index 0000000..9a86095
Binary files /dev/null and b/contrib/stem/current.vt differ
diff --git a/contrib/stem/init.py b/contrib/stem/init.py
new file mode 100644
index 0000000..efacabb
--- /dev/null
+++ b/contrib/stem/init.py
@@ -0,0 +1,646 @@
+import os
+
+from core.modules.basic_modules import File, Directory, new_constant
+from core.modules.module_registry import get_module_registry
+from core.modules.vistrails_module import Module, ModuleError, ModuleConnector
+
+reg = get_module_registry()
+RSource = \
+ reg.get_descriptor_by_name('edu.utah.sci.vistrails.rpy', 'RSource').module
+RFigure = reg.get_descriptor_by_name('edu.utah.sci.vistrails.rpy',
+ 'RFigure', 'Figures').module
+
+def create_file_module(fname, f=None):
+ if f is None:
+ f = File()
+ f.name = fname
+ f.upToDate = True
+ return f
+
+def create_dir_module(dname, d=None):
+ if d is None:
+ d = Directory()
+ d.name = dname
+ d.upToDate = True
+ return d
+
+def get_path(fname=''):
+ return os.path.join(os.path.dirname(__file__), fname)
+
+def build_params(input_ports, remap={}):
+ def get_name(port):
+ if port in remap:
+ return remap[port]
+ return port
+ params = ",\n".join(["%s=%s" % (get_name(port[0]), get_name(port[0]))
+ for port in input_ports
+ if port[0] not in remap.keys() or (port[0] in remap.keys() and remap[port[0]] is not None)])
+ return params
+
+
+
+def processActivePortData(inputPorts, object):
+ portData = []
+
+ if object.hasInputFromPort('stem.globals'):
+ stemGlobals = object.getInputFromPort('stem.globals')
+ else :
+ stemGlobals = None
+
+ for port in inputPorts:
+ if port[0] != 'stem.globals' and object.hasInputFromPort(port[0]) and object.getInputFromPort(port[0]) is not None:
+ portData.append((port[0], port[0]))
+ if port[1] == '(edu.utah.sci.vistrails.basic:Directory)' or port[1] == '(edu.utah.sci.vistrails.basic:File)':
+ object.set_variable(port[0], object.getInputFromPort(port[0]).name)
+ else:
+ object.set_variable(port[0], object.getInputFromPort(port[0]))
+ elif stemGlobals:
+ if stemGlobals.global_vars.has_key(port[0]) and stemGlobals.global_vars[port[0]] is not None:
+ portData.append((port[0], port[0]))
+
+ return portData
+
+class STEMConfiguration(RSource):
+ _input_ports = []
+ _output_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)')]
+ def compute(self):
+ self.chdir(get_path())
+ self.run_file(get_path('STEM_Configuration.R'),
+ excluded_outputs=set(['config']))
+ self.setResult('config', self)
+
+class RunModels(RSource):
+ _input_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)'),
+ ('spp.name', '(edu.utah.sci.vistrails.basic:String)'),
+ ('spp.common', '(edu.utah.sci.vistrails.basic:String)')]
+ _output_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)')]
+ def compute(self):
+ self.chdir(get_path())
+ self.set_variable('spp.dir.name', self.getInputFromPort('spp.name'))
+ self.run_file(get_path('STEM_ModelingEngine.R'),
+ excluded_inputs=set(['source', 'config']),
+ excluded_outputs=set(['config']))
+ self.setResult('config', self.getInputFromPort('config'))
+
+class BuildVisualizations(RSource):
+ _input_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)')]
+ _output_ports = [('results.dir',
+ '(edu.utah.sci.vistrails.basic:Directory)')]
+ def compute(self):
+ self.chdir(get_path())
+ self.run_file(get_path('STEM.nfold.pp.comp_2.12.10.R'),
+ excluded_inputs=set(['source', 'config']),
+ excluded_outputs=set(['results.dir']))
+ dname = list(self.get_variable('results.dir'))[0]
+ self.setResult('results.dir', create_dir_module(dname))
+
+class STEMFigure(RFigure):
+ """Write only the R figure code. You do not need the png or pdf
+ graphics setup code or the dev.off calls"""
+ _input_ports = [('results.dir',
+ '(edu.utah.sci.vistrails.basic:Directory)', ),
+ ('pp.metric', '(edu.utah.sci.vistrails.basic:String)')]
+ def compute(self):
+ self.chdir(get_path())
+ self.set_variable('results.dir',
+ self.getInputFromPort('results.dir').name)
+ self.run_figure_file(get_path('STEM_Figure.R'), 'png', 800, 600,
+ excluded_inputs=set(['source',
+ 'results.dir']))
+
+# class STEMCreateData(Module):
+# """Data preparation"""
+# def compute(self):
+# self.run_file(get_path('STEM.erd.data.creation.R'))
+
+class STEMGlobals(RSource):
+ _input_ports = [('debugOutput', '(edu.utah.sci.vistrails.basic:Boolean)'),
+ ('platform', '(edu.utah.sci.vistrails.basic:String)'),
+ ('parent.dir', '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('code.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('species.name', '(edu.utah.sci.vistrails.basic:String)'),
+ ('common.name', '(edu.utah.sci.vistrails.basic:String)'),
+ ('erd.data.file', '(edu.utah.sci.vistrails.basic:File)'),
+ ('srd.pred.design.file', '(edu.utah.sci.vistrails.basic:File)')]
+ _output_ports = [('self', '(edu.cornell.birds.stem:STEMGlobals)')]
+ def compute(self):
+ # run the requires and the loading of STEM libs
+ parent_dir = self.getInputFromPort('parent.dir')
+ self.chdir(self.getInputFromPort('code.directory').name)
+ self.set_variable('parent.dir', parent_dir.name)
+ # FIXME code.directory defaults to parent.dir
+ if not self.hasInputFromPort('code.directory'):
+ self.set_variable('code.directory', parent_dir.name)
+ else:
+ self.set_variable('code.directory',
+ self.getInputFromPort('code.directory').name)
+ self.set_variable('erd.data.filename',
+ ''.join([parent_dir.name, "Data/", self.getInputFromPort('erd.data.file').name]))
+ self.set_variable('srd.pred.design.filename',
+ ''.join([parent_dir.name, "Data/", self.getInputFromPort('srd.pred.design.file').name]))
+ species_name = self.getInputFromPort('species.name')
+ stem_directory = create_dir_module(os.path.join(parent_dir.name, species_name))
+ self.set_variable('stem.directory', stem_directory.name)
+ self.set_variable('species.name', species_name)
+ self.set_variable('common.name', self.getInputFromPort('common.name'))
+
+ # FIXME add erd.data.filename and srd.pred.design.filename
+ # No tags needed, then
+
+ self.run_code(''.join(["source(\"", "STEM_Globals.R", "\")"]),
+ excluded_inputs=set(['source', 'parent.dir',
+ 'code.directory', 'erd.data.file',
+ 'srd.pred.design.file']))
+
+ # FIXME need to actually use and output the globals
+ global_var_list = ['debugOutput',
+ 'platform',
+ 'parent.dir',
+ 'code.directory',
+ 'species.name',
+ 'common.name',
+ 'erd.data.filename',
+ 'srd.pred.design.filename',
+ 'stem.directory',
+ 'spatial.extent.list',
+ 'temporal.extent.list',
+ 'predictor.names',
+ 'response.family',
+ 'cv.folds',
+ 'cv.folds.par.list',
+ 'cv.list',
+ 'stem.init.par.list',
+ 'base.model.par.list',
+ 'srd.max.sample.size',
+ 'split.par.list',
+ 'st.matrix.name',
+ 'jdate.seq',
+ 'year.seq',
+ 'conditioning.vars',
+ 'st.matrix.ave.maps',
+ 'begin.seq',
+ 'end.seq',
+ 'pred.grid.size',
+ 'map.plot.width',
+ 'spatial.extent.list',
+ 'z.max',
+ 'z.min',
+ 'map.tag',
+ 'date.bar',
+ 'print.date',
+ 'county.map',
+ 'county.map.lwd',
+ 'state.map',
+ 'state.map.lwd']
+ self.global_vars = dict((name, self.get_variable(name))
+ for name in global_var_list)
+
+
+class InitERDMapAnalysis(RSource):
+ _input_ports = [('project.directory', '(edu.utah.sci.vistrails.basic:String)'),
+ ('species.directory.nametag', '(edu.utah.sci.vistrails.basic:String)'),
+ ('map.directory.nametag', '(edu.utah.sci.vistrails.basic:String)'),
+ ('map.file.nametag', '(edu.utah.sci.vistrails.basic:String)'),
+ ('map.rows', '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('z.max', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('z.min', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('map.number', '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('lat.max', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('lat.min', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('lon.max', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('lon.min', '(edu.utah.sci.vistrails.basic:Float)')]
+ _output_ports = [('self', '(edu.cornell.birds.stem:InitERDMapAnalysis)')]
+ def compute(self):
+ # run the requires and the loading of STEM libs
+ self.chdir(self.getInputFromPort('project.directory'))
+
+ self.set_variable('project.directory', self.getInputFromPort('project.directory'))
+ self.set_variable('species.directory.nametag', self.getInputFromPort('species.directory.nametag'))
+ self.set_variable('map.directory.nametag', self.getInputFromPort('map.directory.nametag'))
+ self.set_variable('map.file.nametag', self.getInputFromPort('map.file.nametag'))
+ self.set_variable('map.rows', self.getInputFromPort('map.rows'))
+ self.set_variable('z.max', self.getInputFromPort('z.max'))
+ self.set_variable('z.min', self.getInputFromPort('z.min'))
+ self.set_variable('map.number', self.getInputFromPort('map.number'))
+
+ latMax = self.getInputFromPort('lat.max')
+ if latMax:
+ self.set_variable('lat.max', latMax)
+ else:
+ ## self.set_variable('lat.max', "as.null(lat.max)")
+ self.run_code("lat.max <- NULL")
+
+ latMin = self.getInputFromPort('lat.min')
+ if latMin:
+ self.set_variable('lat.min', latMin)
+ else :
+ self.run_code("lat.min <- NULL")
+
+ lonMax = self.getInputFromPort('lon.max')
+ if lonMax:
+ self.set_variable('lon.max', lonMax)
+ else:
+ self.run_code("lon.max <- NULL")
+
+ lonMin = self.getInputFromPort('lon.min')
+ if lonMin:
+ self.set_variable('lon.min', lonMin)
+ else:
+ self.run_code("lon.min <- NULL")
+
+ self.run_code(''.join(["source(\"", self.getInputFromPort('project.directory'), '/code/stem.vt.erd.map.function.R', "\")"]))
+
+ global_var_list = ['project.directory',
+ 'species.directory.nametag',
+ 'map.directory.nametag',
+ 'map.file.nametag',
+ 'map.rows',
+ 'z.max',
+ 'z.min',
+ 'map.number',
+ 'lat.max',
+ 'lat.min',
+ 'lon.max',
+ 'lon.min']
+
+ self.global_vars = dict((name, self.get_variable(name))
+ for name in global_var_list if name is not None)
+
+class PlotERDMaps(RSource):
+ _input_ports = [('stem.globals', '(edu.cornell.birds.stem:InitERDMapAnalysis)'),
+ ('project.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('species.directory.nametag', '(edu.utah.sci.vistrails.basic:String)'),
+ ('map.directory.nametag', '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('map.file.nametag', '(edu.utah.sci.vistrails.basic:File)'),
+ ('map.rows', '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('z.max', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('z.min', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('map.number', '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('lat.max', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('lat.min', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('lon.max', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('lon.min', '(edu.utah.sci.vistrails.basic:Float)')]
+ _output_ports = [('map_file', '(edu.utah.sci.vistrails.basic:File)')]
+
+ def compute(self):
+ ## stem_globals = self.getInputFromPort('stem.globals')
+ ## for k, v in stem_globals.global_vars.iteritems():
+ ## self.set_variable(k,v)
+
+ activePorts = processActivePortData(PlotERDMaps._input_ports, self)
+
+ remap = {'stem.globals': None}
+ params = build_params(activePorts, remap)
+ code_str = "mapFile <-stem.erd.maps(%s)" % params
+
+ self.run_code(code_str)
+
+ self.setResult('map_file', create_file_module(str(list(self.get_variable('mapFile'))[0])))
+
+
+class ERDDataCreation(RSource):
+ _input_ports = [('protocol.tag', '(edu.utah.sci.vistrails.basic:String)'),
+ ('max.effort.hours',
+ '(edu.utah.sci.vistrails.basic:Float)'),
+ ('max.effort.distance.fm',
+ '(edu.utah.sci.vistrails.basic:Float)'),
+ ('min.obs.time', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('max.obs.time', '(edu.utah.sci.vistrails.basic:Float)'),
+ ('response.type', '(edu.utah.sci.vistrails.basic:String)'),
+ ('ebird.data.dir',
+ '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('erd.data.tag', '(edu.utah.sci.vistrails.basic:String)'),
+ ('spatial.erd.tag',
+ '(edu.utah.sci.vistrails.basic:String)'),
+ ('checklist.covariate.names',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('core.covariate.names',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('NLCD.class.neighborhood.size',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('NLCD.names',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('class.level.fragstats',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('landscape.fragstat.tags',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('landscape.neighborhood.size',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)')]
+ _output_ports = [('srd.pred.design.file',
+ '(edu.utah.sci.vistrails.basic:File)'),
+ ('erd.design.file',
+ '(edu.utah.sci.vistrails.basic:File)')]
+ def compute(self):
+ self.chdir(get_path())
+ self.set_variable('ebird.data.dir',
+ self.getInputFromPort('ebird.data.dir').name)
+ self.run_file(get_path('STEM_Globals.R'),
+ excluded_inputs=set(['source', 'ebird.data.dir']))
+ srd_fname = list(self.get_variable('srd.pred.design.filename'))[0]
+ erd_fname = list(self.get_variable('erd.design.filename'))[0]
+ self.setResult('srd.pred.design.file', create_file_module(srd_fname))
+ self.setResult('erd.design.file', create_file_module(erd_fname))
+
+
+class ERDDataSubsetting(RSource):
+ _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
+ ('erd.data.filename', '(edu.utah.sci.vistrails.basic:File)'),
+ ('srd.pred.design.filename', '(edu.utah.sci.vistrails.basic:File)'),
+ ('spatial.extent.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('temporal.extent.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('species.name', '(edu.utah.sci.vistrails.basic:String)'),
+ ('predictor.names', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('response.family', '(edu.utah.sci.vistrails.basic:String)'),
+ ('srd.max.sample.size', '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('split.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)')]
+ _output_ports = [('train.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('test.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('pred.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('stem.predictor.names', '(edu.utah.sci.vistrails.rpy:RVector:Types)')]
+ # Get train.data, test.data, srd.data from eBird.data and expose
+ # these three as the output ports
+ def compute(self):
+ ## stem_globals = self.getInputFromPort('stem.globals')
+ ## for k, v in stem_globals.global_vars.iteritems():
+ ## self.set_variable(k,v)
+
+ activePorts = processActivePortData(ERDDataSubsetting._input_ports, self)
+
+ remap = {'srd.pred.design.file': 'srd.pred.design.filename',
+ 'stem.globals': None}
+ params = build_params(activePorts, remap)
+ code_str = "eBird.data <- erd.srd.data.subsetting(%s)" % params
+
+ self.run_code(code_str,
+ excluded_inputs=set(['source', 'srd.pred.design.file']),
+ excluded_outputs=set(['eBird.data']))
+
+ train = self.get_variable('eBird.data$train.data')
+ test = self.get_variable('eBird.data$test.data')
+ srd = self.get_variable('eBird.data$srd.data')
+
+ self.run_code("stem.predictor.names <- names(eBird.data$train.data$X)")
+ stem_predictor_names = self.get_variable('stem.predictor.names')
+
+ self.setResult('train.data', train)
+ self.setResult('test.data', test)
+ self.setResult('pred.data', srd)
+ self.setResult('stem.predictor.names', stem_predictor_names)
+
+class FitSTEM(RSource):
+ _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
+ ('train.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('stem.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('response.family', '(edu.utah.sci.vistrails.basic:String)'),
+ ('cv.folds', '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('cv.folds.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('stem.init.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('base.model.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)')]
+ _output_ports = [('models.directory', '(edu.utah.sci.vistrails.basic:Directory)')]
+
+ def compute(self):
+ # use a single models dir with a variable number of
+ # subdirectories depending on the cv.folds value
+ # same for results, now -- models/stem.models.[1-10]
+ ## stem_globals = self.getInputFromPort('stem.globals')
+ ## for k, v in stem_globals.global_vars.iteritems():
+ ## self.set_variable(k,v)
+
+ activePorts = processActivePortData(FitSTEM._input_ports, self)
+
+ remap = {'stem.globals': None}
+ params = build_params(activePorts, remap)
+ code_str = "stem(%s)" % params
+
+ self.run_code(code_str)
+
+
+class ERDPredictivePerformance(RSource):
+ _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
+ ('test.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('stem.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('pp.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('cv.list',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('n.mc',
+ '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('grid.cell.min.lat',
+ '(edu.utah.sci.vistrails.basic:Float)'),
+ ('grid.cell.min.lon',
+ '(edu.utah.sci.vistrails.basic:Float)'),
+ ('min.val.cell.locs',
+ '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('threshold',
+ '(edu.utah.sci.vistrails.basic:Float)'),
+ ('min.testset.sample.size',
+ '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('plot.it',
+ '(edu.utah.sci.vistrails.basic:Boolean)')]
+ # pp.directory specifies where, but we can move this, i think
+ _output_ports = [('pp.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)')]
+ def compute(self):
+ self.set_variable('stem.directory',
+ self.getInputFromPort('stem.directory').name)
+ pp_directory = self.getInputFromPort('pp.directory')
+ self.set_variable('pp.directory', pp_directory.name)
+ self.run_file('')
+ self.setResult('pp.directory', pp_directory)
+
+class PredictSTEM(RSource):
+ _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
+ ('stem.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('pred.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('st.pred.tag', '(edu.utah.sci.vistrails.basic:String)'),
+ ('st.prediction.filename',
+ '(edu.utah.sci.vistrails.basic:File)')]
+ _output_ports = [('st.pred', '(edu.utah.sci.vistrails.rpy:RList:Types)')]
+ def compute(self):
+ pas
+
+class ERDPredictSTMatrix(RSource):
+ _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
+ ('stem.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('pred.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('stem.predictor.names',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('st.matrix.name',
+ '(edu.utah.sci.vistrails.basic:String)'),
+ ('jdate.seq',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('year.seq',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('conditioning.vars',
+ '(edu.utah.sci.vistrails.rpy:RList:Types)')]
+ _output_ports = [('st.matrix.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)')]
+ def compute(self):
+ stem_globals = self.getInputFromPort('stem.globals')
+ ## for k, v in stem_globals.global_vars.iteritems():
+ ## self.set_variable(k,v)
+
+ activePorts = processActivePortData(ERDPredictSTMatrix._input_ports, self)
+
+ remap = {'stem.globals': None}
+ params = build_params(activePorts, remap)
+ code_str = "predict.erd.st.matrix(%s)" % params
+
+ self.run_code(code_str)
+
+ if self.hasInputFromPort('stem.directory'):
+ if self.hasInputFromPort('st.matrix.name'):
+ self.setResult('st.matrix.directory', create_dir_module(os.path.join(self.getInputFromPort('stem.directory').name,
+ self.getInputFromPort('st.matrix.name'))))
+ else:
+ self.setResult('st.matrix.directory', create_dir_module(os.path.join(self.getInputFromPort('stem.directory').name,
+ str(list(stem_globals.global_vars['st.matrix.name'])[0]))))
+ else:
+ if self.hasInputFromPort('st.matrix.name'):
+ self.setResult('st.matrix.directory', create_dir_module(os.path.join(str(list(stem_globals.global_vars['stem.directory'])[0]),
+ self.getInputFromPort('st.matrix.name'))))
+ else:
+ self.setResult('st.matrix.directory', create_dir_module(os.path.join(str(list(stem_globals.global_vars['stem.directory'])[0]),
+ str(list(stem_globals.global_vars['st.matrix.name'])[0]))))
+
+
+class STMatrixCVAvg(RSource):
+ _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
+ ('stem.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('st.matrix.input.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('jdate.seq', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('year.seq', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('st.matrix.output.directory', '(edu.utah.sci.vistrails.basic:Directory)')]
+ _output_ports = [('st.matrix.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('map.directory', '(edu.utah.sci.vistrails.basic:Directory)')]
+ def compute(self):
+ self.set_variable('st.matrix.input.directory', self.getInputFromPort('st.matrix.input.directory').name)
+ st_matrix_output_directory = self.getInputFromPort('st.matrix.input.directory')
+ self.set_variable('st.matrix.output.directory', st_matrix_output_directory.name)
+
+ stem_globals = self.getInputFromPort('stem.globals')
+ ## for k, v in stem_globals.global_vars.iteritems():
+ ## self.set_variable(k,v)
+
+ activePorts = processActivePortData(STMatrixCVAvg._input_ports, self)
+
+ remap = {'stem.globals': None}
+ params = build_params(activePorts, remap)
+ code_str = "st.matrix.cv.average(%s)" % params
+
+ self.run_code(code_str)
+
+ self.setResult('st.matrix.directory', st_matrix_output_directory)
+ self.setResult('map.directory', create_dir_module(os.path.join(str(list(stem_globals.global_vars['stem.directory'])[0]),
+ str(list(stem_globals.global_vars['st.matrix.ave.maps'])[0]))))
+
+
+
+class STMatrixMaps(RSource):
+ _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
+ ('st.matrix.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('map.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('jdate.seq',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('year.seq',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('begin.seq',
+ '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('end.seq',
+ '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('pred.grid.size',
+ '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('map.plot.width',
+ '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('spatial.extent.list',
+ '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('z.max',
+ '(edu.utah.sci.vistrails.basic:Float)'),
+ ('z.min',
+ '(edu.utah.sci.vistrails.basic:Float)'),
+ ('map.tag',
+ '(edu.utah.sci.vistrails.basic:String)'),
+ ('date.bar',
+ '(edu.utah.sci.vistrails.basic:Boolean)'),
+ ('print.date',
+ '(edu.utah.sci.vistrails.basic:Boolean)'),
+ ('county.map',
+ '(edu.utah.sci.vistrails.basic:Boolean)'),
+ ('county.map.lwd',
+ '(edu.utah.sci.vistrails.basic:Float)'),
+ ('state.map',
+ '(edu.utah.sci.vistrails.basic:Boolean)'),
+ ('state.map.lwd',
+ '(edu.utah.sci.vistrails.basic:Float)')]
+ _output_ports = [('map.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('map_file_1',
+ '(edu.utah.sci.vistrails.basic:File)')]
+ def compute(self):
+ self.set_variable('st.matrix.directory', ''.join([self.getInputFromPort('st.matrix.directory').name]))
+ map_directory = self.getInputFromPort('map.directory')
+ self.set_variable('map.directory', map_directory.name)
+
+ ## stem_globals = self.getInputFromPort('stem.globals')
+ ## for k, v in stem_globals.global_vars.iteritems():
+ ## self.set_variable(k,v)
+
+ activePorts = processActivePortData(STMatrixMaps._input_ports, self)
+
+ remap = {'stem.globals': None}
+ params = build_params(activePorts, remap)
+ code_str = "st.matrix.maps(%s)" % params
+
+ self.run_code(code_str)
+
+ self.setResult('map.directory', map_directory)
+
+
+
+class ERD_CV_Avg_Maps(RSource):
+ _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
+ ('stem.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('st.matrix.file.tag',
+ '(edu.utah.sci.vistrails.basic:String)'),
+ ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
+ ('maps.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)'),
+ ('map.file.tag', '(edu.utah.sci.vistrails.basic:String)'),
+ ('ns.rows', '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('map.plot.pixel.width',
+ '(edu.utah.sci.vistrails.basic:Integer)'),
+ ('mapping.spatial.extent',
+ '(edu.utah.sci.vistrails.rpy:RList:Types)'),
+ ('z.max', '(edu.utah.sci.vistrails.basic:Float)')]
+ _output_ports = [('erd.cv.avg.maps.directory',
+ '(edu.utah.sci.vistrails.basic:Directory)')]
+ def compute(self):
+ pass
+
+# _modules = [STEMConfiguration,
+# RunModels,
+# BuildVisualizations,
+# STEMFigure]
+
+_modules = [ERDDataCreation,
+ ERDDataSubsetting,
+ FitSTEM,
+ ERDPredictivePerformance,
+ PredictSTEM,
+ ERDPredictSTMatrix,
+ STMatrixCVAvg,
+ STMatrixMaps,
+ # ERD_CV_Avg_Maps,
+ STEMGlobals,
+ InitERDMapAnalysis,
+ PlotERDMaps
+ ]
diff --git a/contrib/stem/mycurrent.vt b/contrib/stem/mycurrent.vt
new file mode 100644
index 0000000..1b3d0d0
Binary files /dev/null and b/contrib/stem/mycurrent.vt differ
diff --git a/contrib/stem/mycurrent2.vt b/contrib/stem/mycurrent2.vt
new file mode 100644
index 0000000..208e254
Binary files /dev/null and b/contrib/stem/mycurrent2.vt differ
diff --git a/contrib/titan/__init__.py b/contrib/titan/__init__.py
new file mode 100644
index 0000000..546fd3f
--- /dev/null
+++ b/contrib/titan/__init__.py
@@ -0,0 +1,59 @@
+###########################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+################################################################################
+# Titan Package for VisTrails (Sandia National Laboratories)
+################################################################################
+
+"""The Titan Informatics Toolkit is a collaborative effort between
+Sandia National Laboratories and Kitware Inc. It represents a
+significant expansion of the Visualization ToolKit (VTK) to support
+the ingestion, processing, and display of informatics data. By
+leveraging the VTK engine, Titan provides a flexible, component
+based, pipeline architecture for the integration and deployment of
+algorithms in the fields of intelligence, semantic graph and
+information analysis.
+
+https://www.kitware.com/InfovisWiki/"""
+
+identifier = 'edu.utah.sci.vistrails.titan'
+name = 'Titan'
+version = '0.1.2'
+
+def package_dependencies():
+ import core.packagemanager
+ manager = core.packagemanager.get_package_manager()
+
+ ret = []
+ #if manager.has_package('edu.utah.sci.vistrails.vtk'):
+ ret.append('edu.utah.sci.vistrails.vtk')
+ #if manager.has_package('edu.utah.sci.vistrails.spreadsheet'):
+ ret.append('edu.utah.sci.vistrails.spreadsheet')
+ return ret
+
+def package_requirements():
+ import core.requirements
+ if not core.requirements.python_module_exists('titan'):
+ raise core.requirements.MissingRequirement('titan')
+ if not core.requirements.python_module_exists('PyQt4'):
+ print 'PyQt4 is not available. There will be no interaction',
+ print 'between Titan and the spreadsheet.'
+ import titan
diff --git a/contrib/titan/base_module.py b/contrib/titan/base_module.py
new file mode 100644
index 0000000..0b74737
--- /dev/null
+++ b/contrib/titan/base_module.py
@@ -0,0 +1,203 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+################################################################################
+# This describes basic modules used by other VTK module
+################################################################################
+import vtk
+from core.modules.module_registry import registry
+from core.modules.vistrails_module import Module, ModuleError
+from itertools import izip
+
+################################################################################
+
+class vtkBaseModule(Module):
+ """
+ vtkBaseModule is the base class for all VTK modules in VisTrails, it acts
+ as a wrapper to direct all input/output ports to appropriate VTK function
+ calls
+
+ """
+
+ def __init__(self):
+ """ vtkBaseModule() -> vtkBaseModule
+ Instantiate an emptt VTK Module with real VTK instance
+
+ """
+ Module.__init__(self)
+ self.vtkInstance = None
+
+ def is_cacheable(self):
+ # VTK objects are by default cacheable only if they're subclasses
+ # of vtkAlgorithm
+ return (issubclass(self.vtkClass, vtk.vtkAlgorithm)
+ and (not issubclass(self.vtkClass, vtk.vtkAbstractMapper)))
+
+ def call_input_function(self, function, params):
+ """self.call_input_function(function, params) -> None
+ Calls the input function on the vtkInstance, or a special
+ input function if one exists in the class."""
+ if hasattr(self, '_special_input_function_' + function):
+ attr = getattr(self, '_special_input_function_' + function)
+ else:
+ try:
+ attr = getattr(self.vtkInstance, function)
+ except AttributeError:
+ # Compensates for overload by exploiting the fact that
+ # no VTK method has underscores.
+ f = function.find('_')
+ if f != -1:
+ function = function[:f]
+ attr = getattr(self.vtkInstance, function)
+ attr(*params)
+ # print "Called ",attr,function,params
+
+ @classmethod
+ def _provide_doc(cls, port_name):
+ f = port_name.find('_')
+ if f != -1:
+ name = port_name[:f]
+ else:
+ name = port_name
+ return getattr(cls.vtkClass, name).__doc__
+
+ @classmethod
+ def provide_input_port_documentation(cls, port_name):
+ return cls._provide_doc(port_name)
+
+ @classmethod
+ def provide_output_port_documentation(cls, port_name):
+ return cls._provide_doc(port_name)
+
+ def compute(self):
+ """ compute() -> None
+ Actually perform real VTK task by directing all input/output ports
+ to VTK function calls
+
+ """
+
+ def call_it(function, p):
+ # Translate between VisTrails objects and VTK objects
+ if p is None:
+ # None indicates a call with no parameters
+ params = []
+ elif type(p) == tuple:
+ # A tuple indicates a call with many parameters
+ params = list(p)
+ else:
+ # Otherwise, it's a single parameter
+ params = [p]
+
+ # Unwraps VTK objects
+ for i in xrange(len(params)):
+ if hasattr(params[i], 'vtkInstance'):
+ params[i] = params[i].vtkInstance
+ try:
+ self.call_input_function(function, params)
+ except Exception, e:
+ msg = 'VTK Exception: '
+ raise ModuleError(self, msg + str(type(e)) + ': ' + str(e))
+
+ # Always re-create vtkInstance module, no caching here
+ if self.vtkInstance:
+ del self.vtkInstance
+ self.vtkInstance = self.vtkClass()
+
+ # We need to call method ports before anything else, and in
+ # the right order.
+
+ # FIXME: This does not belong here, it belongs in the main class
+ # No time for that now
+ methods = self.is_method.values()
+ methods.sort()
+ for value in methods:
+ (_, port) = value
+ conn = self.is_method.inverse[value]
+ p = conn()
+ call_it(port, p)
+
+ # Make sure all input ports are called correctly
+ for (function, connector_list) in self.inputPorts.iteritems():
+ paramList = self.forceGetInputListFromPort(function)
+ if function[:18]=='SetInputConnection':
+ paramList = zip([int(function[18:])]*len(paramList),
+ paramList)
+ function = 'SetInputConnection'
+ if function=='AddInputConnection':
+ desc = registry.get_descriptor_by_name(
+ 'edu.utah.sci.vistrails.vtk',
+ 'vtkAlgorithmOutput')
+ for i in xrange(len(paramList)):
+ if type(paramList[i])==desc.module:
+ paramList[i] = (0, paramList[i])
+ for p,connector in izip(paramList, connector_list):
+ # Don't call method
+ if connector in self.is_method:
+ continue
+ call_it(function, p)
+
+ # Call update if appropriate
+ if hasattr(self.vtkInstance, 'Update'):
+ def ProgressEvent(obj, event):
+ self.logging.update_progress(self, obj.GetProgress())
+ isAlgorithm = issubclass(self.vtkClass, vtk.vtkAlgorithm)
+ if isAlgorithm:
+ cbId = self.vtkInstance.AddObserver('ProgressEvent', ProgressEvent)
+ self.vtkInstance.Update()
+ if isAlgorithm:
+ self.vtkInstance.RemoveObserver(cbId)
+
+ # Then update the output ports also with appropriate function calls
+ for function in self.outputPorts.keys():
+ if function[:13]=='GetOutputPort':
+ i = int(function[13:])
+ vtkOutput = self.vtkInstance.GetOutputPort(i)
+ output = vtkBaseModule.wrapperModule('vtkAlgorithmOutput',
+ vtkOutput)
+ self.setResult(function, output)
+ elif hasattr(self.vtkInstance, function):
+ retValues = getattr(self.vtkInstance, function)()
+ if issubclass(retValues.__class__, vtk.vtkObject):
+ className = retValues.GetClassName()
+ output = vtkBaseModule.wrapperModule(className, retValues)
+ self.setResult(function, output)
+ elif (type(retValues) in [tuple, list]):
+ result = list(retValues)
+ for i in xrange(len(result)):
+ if issubclass(result[i].__class__, vtk.vtkObject):
+ className = result[i].GetClassName()
+ result[i] = vtkBaseModule.wrapperModule(className,
+ result[i])
+ self.setResult(function, type(retValues)(result))
+ else:
+ self.setResult(function, retValues)
+
+ @staticmethod
+ def wrapperModule(classname, instance):
+ """ wrapperModule(classname: str, instance: vtk class) -> Module
+ Create a wrapper module in VisTrails with a vtk instance
+
+ """
+ result = registry.get_descriptor_by_name(
+ 'edu.utah.sci.vistrails.vtk',
+ classname).module()
+ result.vtkInstance = instance
+ return result
diff --git a/contrib/titan/class_tree.py b/contrib/titan/class_tree.py
new file mode 100644
index 0000000..c9f53ff
--- /dev/null
+++ b/contrib/titan/class_tree.py
@@ -0,0 +1,268 @@
+# Author: Prabhu Ramachandran
+# Copyright (c) 2004, Enthought, Inc.
+# License: BSD Style.
+
+"""This module generates the class hierarchy for any given Python
+modules. This can be used (among other things) to generate the
+traitified VTK classes in the correct order.
+
+"""
+
+import __builtin__
+
+
+class TreeNode(object):
+ """Represents a node in the class tree.
+
+ Stores information on the sub and super classes of a particular
+ class. It also stores the inheritance level of the class inside
+ the inheritance tree (essentially how many levels of inheritance
+ are there below this class). This inheritance level is computed
+ when the `get_level` method is called. The `get_level` method
+ works only when the parent information is complete.
+
+ """
+
+ def __init__(self, klass):
+ """Given a class, create a node in the tree.
+
+ Parameters
+ ----------
+ - klass : `class`
+
+ The class which is represented as a node in the tree.
+
+ """
+ self.klass = klass
+ self.name = klass.__name__
+ self.children = []
+ self.parents = []
+ # Uninitialized level is set to None
+ self.level = None
+
+ def add_parent(self, parent):
+ """Add a parent node."""
+ assert isinstance(parent, TreeNode)
+ if parent not in self.parents:
+ self.parents.append(parent)
+
+ def add_child(self, child):
+ """Add a child node. """
+ assert isinstance(child, TreeNode)
+ if child not in self.children:
+ self.children.append(child)
+
+ def get_level(self):
+ """Returns the inheritance level of the node (an int). If the
+ level has not been set, the method computes it. Note however,
+ that this computation will fail if the parent information is
+ incorrect.
+
+ """
+ if not self.level:
+ if self.parents:
+ self.level = max([x.get_level() for x in self.parents]) + 1
+ else:
+ self.level = 0
+ return self.level
+
+ def get_ancestors(self):
+ """Returns a list of ancestor nodes from which this class has
+ descended.
+
+ """
+ def _get_ancestors(node, ancestors):
+ ancestors.extend(node.parents)
+ for p in node.parents:
+ _get_ancestors(p, ancestors)
+ ancestors = []
+ _get_ancestors(self, ancestors)
+ return ancestors
+
+
+class ClassTree(object):
+ """Contains and generates all the class tree information.
+
+ On initialization of the instance, nothing is done. The classes
+ are obtained using the list of modules (or a single module) that
+ is used to initialize the instance. One must then call the
+ `create` method to generate the tree structure. The instance of
+ the class also can be treated as an iterator which iterates over
+ the nodes of the tree.
+
+ There are two ways in which the tree hierarchy is stored. A
+ dictionary mapping class names to the tree node and a tree
+ represented as a list of lists containing the nodes. The tree is
+ organized based on a concept of an inheritance level. A class
+ that has no parent classes (no base classes) is said to be at
+ level zero. If a class inherits successively from 7 classes, it
+ is at level 6. An example of inheritance for a vtkFoo class is
+ given below:
+
+ vtkFoo -> vtkBar -> vtkObject -> vtkObjectBase
+
+ Here, vtkObjectBase has an inheritance level of 0 and vtkFoo a
+ level of 3. One can traverse the tree by using the level as an
+ index and find all the classes at a particular level.
+
+ Here is some example usage of this class::
+
+ >>> import vtk
+ >>> t = ClassTree(vtk)
+ >>> t.create()
+ >>> print t.get_node('vtkObject').name
+ vtkObject
+ >>> print t.get_node('vtkObject').parents[0].name
+ vtkObjectBase
+ >>> print len(t.tree[0])
+ 1
+ >>> t.tree[0][0].name
+ vtkObjectBase
+
+ """
+
+ def __init__(self, modules):
+ """Initialize the instance with the given modules.
+
+ Parameters
+ ----------
+
+ - modules : `sequence` of modules or a module
+
+ This is either a single module or a sequence of modules.
+ The instance uses these list of modules to generate the
+ class tree.
+
+ """
+ self.nodes = {}
+ self.tree = [[]]
+ if not hasattr(modules, '__iter__'):
+ self.modules = [modules]
+ else:
+ self.modules = modules
+
+ def __iter__(self):
+ return iter(self.nodes.values())
+
+ def _generate_hierarchy(self, klass):
+ """Does the hard work of generating the class hierarchy."""
+ node = self.get_node(klass.__name__, create=1)
+ for base in klass.__bases__:
+ base_node = self.get_node_from_class(base, create=1)
+ node.add_parent(base_node)
+ base_node.add_child(node)
+ self._generate_hierarchy(base)
+
+ def get_class(self, name):
+ """Given a class name in the given modules returns the class."""
+ klass = None
+ for m in self.modules:
+ if hasattr(m, name):
+ return getattr(m, name)
+ if hasattr(__builtin__, name):
+ klass = getattr(__builtin__, name)
+ if not klass:
+ try:
+ klass = self.nodes[name].klass
+ except KeyError:
+ raise KeyError, "Cannot find class of name %s"%name
+ return klass
+
+ def add_node(self, klass):
+ """Create a node for the given class."""
+ name = klass.__name__
+ if not self.nodes.has_key(name):
+ node = TreeNode(klass)
+ self.nodes[name] = node
+ return node
+
+ def get_node(self, name, create=0):
+ """Get a node of the given name.
+
+ Parameters
+ ----------
+
+ - name : `str`
+
+ Name of the node to get.
+
+ - create : `boolean`
+
+ If True, a new node will be added if no node of the given
+ name is available. Defaults to False.
+
+ Returns
+ -------
+
+ - `TreeNode`
+
+ """
+ if self.nodes.has_key(name):
+ return self.nodes[name]
+ elif create:
+ return self.add_node(self.get_class(name))
+
+ def get_node_from_class(self, cls, create=0):
+ """Get a node of the given class.
+
+ Parameters
+ ----------
+
+ - cls : `class`
+
+ Class of the node to get.
+
+ - create : `boolean`
+
+ If True, a new node will be added if no node of the given
+ name is available. Defaults to False.
+
+ Returns
+ -------
+
+ - `TreeNode`
+
+ """
+ name = cls.__name__
+ if self.nodes.has_key(name):
+ return self.nodes[name]
+ elif create:
+ return self.add_node(cls)
+
+ def create(self, class_names=None):
+ """This method generates the class tree given an optional list
+ of class names.
+
+ Parameters
+ ----------
+
+ - class_names - `list` of `str`
+
+ An optional list of names of the classes to generate the
+ tree for. Defaults to None where the class list is computed
+ from the modules.
+
+ """
+ if class_names is None:
+ class_names = []
+ for m in self.modules:
+ class_names.extend(dir(m))
+
+ # Generate the nodes.
+ for name in class_names:
+ klass = self.get_class(name)
+ if klass and hasattr(klass, '__bases__'):
+ self._generate_hierarchy(klass)
+
+ # Compute the inheritance level and store the nodes in the tree.
+ for node in self:
+ d = node.get_level()
+ while len(self.tree) <= d:
+ self.tree.append([])
+ self.tree[d].append(node)
+
+ # Sort the nodes alphabetically.
+ def _comp(x, y):
+ return cmp(x.name, y.name)
+ for nodes in self.tree:
+ nodes.sort(_comp)
diff --git a/contrib/titan/fix_classes.py b/contrib/titan/fix_classes.py
new file mode 100644
index 0000000..8181458
--- /dev/null
+++ b/contrib/titan/fix_classes.py
@@ -0,0 +1,51 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+import vtk
+
+################################################################################
+# Some fixed classes that solve a few VTK API issues
+
+# This dictionary stores the patched class to vtk class mapping.
+# This would be naturally better stored as an attribute directly on the
+# patched class. VTK, however, doesn't like class attributes.
+description = {}
+
+# http://www.vtk.org/doc/nightly/html/classvtkImagePlaneWidget.html
+# SetUserControlledLookupTable needs to be set before calling
+# SetLookupTable. VTK should do it automatically, so let's fix it
+
+
+# This fix seems to break on VTK versions larger than 5.0.3. It might also
+# be because of an interaction with python 2.6, but I haven't checked that.
+class vtkImagePlaneWidget_fixed(vtk.vtkImagePlaneWidget):
+ def SetLookupTable(self, lookup_table):
+ self.UserControlledLookupTableOn()
+ vtk.vtkImagePlaneWidget.SetLookupTable(self, lookup_table)
+
+if tuple(vtk.vtkVersion().GetVTKVersion().split('.')) < ('5', '0', '4'):
+ description[vtkImagePlaneWidget_fixed] = vtk.vtkImagePlaneWidget
+else:
+ description[id(vtkImagePlaneWidget_fixed)] = vtk.vtkImagePlaneWidget
+
+# Set docstring to wrap it correctly
+vtkImagePlaneWidget_fixed.SetLookupTable.__doc__ = vtk.vtkImagePlaneWidget.SetLookupTable.__doc__
diff --git a/contrib/titan/hasher.py b/contrib/titan/hasher.py
new file mode 100644
index 0000000..34909ec
--- /dev/null
+++ b/contrib/titan/hasher.py
@@ -0,0 +1,36 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+# This is the user-defined hasher for VTK, that takes into account
+# incoming and outgoing connections
+from core.cache.hasher import Hasher
+
+def vtk_hasher(pipeline, module, chm):
+ outgoing_connections = pipeline.graph.edges_from(module.id)
+ incoming_connections = pipeline.graph.edges_to(module.id)
+ current_hash = Hasher.module_signature(module, chm)
+ chashes = [Hasher.connection_signature(pipeline.connections[c_id])
+ for (_, c_id) in outgoing_connections]
+ chashes += [Hasher.connection_signature(pipeline.connections[c_id])
+ for (_, c_id) in incoming_connections]
+ compound_hash = Hasher.compound_signature(chashes)
+ return Hasher.compound_signature([current_hash, compound_hash])
diff --git a/contrib/titan/init.py b/contrib/titan/init.py
new file mode 100644
index 0000000..070661a
--- /dev/null
+++ b/contrib/titan/init.py
@@ -0,0 +1,1132 @@
+###########################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+################################################################################
+# Titan Package for VisTrails (Sandia National Laboratories)
+################################################################################
+from core.bundles import py_import
+
+pkgs = [ "titan.Antiword",
+#"titan.Clustering",
+"titan.Common",
+"titan.DataAnalysis",
+"titan.GMeans",
+"titan.HDF5",
+#"titan.JSON",
+#"titan.LsaLib",
+"titan.MPIDataAnalysis",
+"titan.MPITextAnalysis",
+"titan.MTGLGraphAnalysis",
+"titan.OWL",
+#"titan.QtGui",
+"titan.StanfordNER",
+"titan.TextAnalysis",
+"titan.Trilinos",
+"titan.Web",
+#"titan.uBLAS",
+"titan.XPDF"]
+
+import sys
+titan2 = []
+for i in pkgs:
+ __import__(i)
+ titan2.append(sys.modules[i])
+
+titan = sys.modules["titan"]
+
+import vtk
+
+in_out_table = {
+
+}
+
+
+from core.utils import all, any, VistrailsInternalError, InstanceObject
+from core.debug import debug
+from core.modules.basic_modules import Integer, Float, String, File, \
+ Variant, Color
+from core.modules.module_registry import get_module_registry
+from core.modules.vistrails_module import new_module, ModuleError
+from base_module import vtkBaseModule
+from class_tree import ClassTree
+from vtk_parser import VTKMethodParser
+import re
+import os.path
+from itertools import izip
+from vtkcell import VTKCell
+import tf_widget
+import offscreen
+import fix_classes
+import inspectors
+from hasher import vtk_hasher
+import sys
+
+################################################################################
+
+# filter some deprecation warnings coming from the fact that vtk calls
+# range() with float parameters
+
+import warnings
+warnings.filterwarnings("ignore",
+ message="integer argument expected, got float")
+
+################################################################################
+
+if tuple(vtk.vtkVersion().GetVTKVersion().split('.')) < ('5', '0', '4'):
+ def get_description_class(klass):
+ """Because sometimes we need to patch VTK classes, the klass that
+ has the methods is different than the klass we want to
+ instantiate. get_description_class makes sure that for patched
+ classes we get the correct one."""
+ try:
+ return fix_classes.description[klass]
+ except KeyError:
+ return klass
+else:
+ # On VTK 5.0.4, we use the id of the class to hash, because it
+ # seems that VTK hasn't implemented hash() correctly for their
+ # classes.
+ def get_description_class(klass):
+ """Because sometimes we need to patch VTK classes, the klass that
+ has the methods is different than the klass we want to
+ instantiate. get_description_class makes sure that for patched
+ classes we get the correct one."""
+ try:
+ return fix_classes.description[id(klass)]
+ except KeyError:
+ return klass
+
+parser = VTKMethodParser()
+
+typeMapDict = {'int': Integer,
+ 'long': Integer,
+ 'float': Float,
+ 'char*': String,
+ 'char *': String,
+ 'string': String,
+ 'char': String,
+ 'const char*': String,
+ 'const char *': String}
+typeMapDictValues = [Integer, Float, String]
+
+file_name_pattern = re.compile('.*FileName$')
+set_file_name_pattern = re.compile('Set.*FileName$')
+
+def resolve_overloaded_name(name, ix, signatures):
+ # VTK supports static overloading, VisTrails does not. The
+ # solution is to check whether the current function has
+ # overloads and change the names appropriately.
+ if len(signatures) == 1:
+ return name
+ else:
+ return name + '_' + str(ix+1)
+
+def typeMap(name, package=None):
+ """ typeMap(name: str) -> Module
+ Convert from C/C++ types into VisTrails Module type
+
+ """
+
+ if package is None:
+ package = identifier
+ if type(name) == tuple:
+ return [typeMap(x, package) for x in name]
+ if name in typeMapDict:
+ return typeMapDict[name]
+ else:
+ registry = get_module_registry()
+
+ if registry.has_descriptor_with_name('edu.utah.sci.vistrails.vtk', name):
+ return registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', name).module
+ elif not registry.has_descriptor_with_name(package, name):
+ return None
+ else:
+ return registry.get_descriptor_by_name(package, name).module
+
+def get_method_signature(method):
+ """ get_method_signature(method: vtkmethod) -> [ret, arg]
+ Re-wrap Prabu's method to increase performance
+
+ """
+ doc = method.__doc__
+ tmptmp = doc.split('\n')
+ tmp = []
+ for l in tmptmp:
+ l = l.strip('\n \t')
+ if l.startswith('V.') or l.startswith('C++:'):
+ tmp.append(l)
+ #else:
+ # tmp[-1] = tmp[-1] + l
+ tmp.append('')
+ sig = []
+ pat = re.compile(r'\b')
+
+ # Remove all the C++ function signatures and V.<method_name> field
+ offset = 2+len(method.__name__)
+ for i in xrange(len(tmp)):
+ s = tmp[i]
+ if s=='': break
+ if i%2==0:
+ x = s.split('->')
+ arg = x[0].strip()[offset:]
+ if len(x) == 1: # No return value
+ ret = None
+ else:
+ ret = x[1].strip()
+
+ # Remove leading and trailing parens for arguments.
+ arg = arg[1:-1]
+ if not arg:
+ arg = None
+ if arg and arg[-1] == ')':
+ arg = arg + ','
+
+ # Now quote the args and eval them. Easy!
+ if ret and ret[:3]!='vtk':
+ try:
+ ret = eval(pat.sub('\"', ret))
+ except:
+ continue
+ if arg:
+ if arg.find('(')!=-1:
+ try:
+ arg = eval(pat.sub('\"', arg))
+ except:
+ continue
+ else:
+ arg = arg.split(', ')
+ if len(arg)>1:
+ arg = tuple(arg)
+ else:
+ arg = arg[0]
+ if type(arg) == str:
+ arg = [arg]
+
+ sig.append(([ret], arg))
+ return sig
+
+def prune_signatures(module, name, signatures, output=False):
+ """prune_signatures tries to remove redundant signatures to reduce
+ overloading. It _mutates_ the given parameter.
+
+ It does this by performing several operations:
+
+ 1) It compares a 'flattened' version of the types
+ against the other 'flattened' signatures. If any of them match, we
+ keep only the 'flatter' ones.
+
+ A 'flattened' signature is one where parameters are not inside a
+ tuple.
+
+ 2) We explicitly forbid a few signatures based on modules and names
+
+ """
+ # yeah, this is Omega(n^2) on the number of overloads. Who cares?
+
+ def flatten(type_):
+ if type_ is None:
+ return []
+ def convert(entry):
+ if type(entry) == tuple:
+ return list(entry)
+ else:
+ assert(type(entry) == str)
+ return [entry]
+ result = []
+ for entry in type_:
+ result.extend(convert(entry))
+ return result
+
+ flattened_entries = [flatten(sig[1]) for
+ sig in signatures]
+ def hit_count(entry):
+ result = 0
+ for entry in flattened_entries:
+ if entry in flattened_entries:
+ result += 1
+ return result
+ hits = [hit_count(entry) for entry in flattened_entries]
+
+ def forbidden(flattened, hit_count, original):
+ if (issubclass(get_description_class(module.vtkClass), vtk.vtk3DWidget) and
+ name == 'PlaceWidget' and
+ flattened == []):
+ return True
+ # We forbid this because addPorts hardcodes this but
+ # SetInputArrayToProcess is an exception for the InfoVis
+ # package
+ if (get_description_class(module.vtkClass) == vtk.vtkAlgorithm and
+ name!='SetInputArrayToProcess'):
+ return True
+ return False
+
+ # This is messy: a signature is only allowed if there's no
+ # explicit disallowing of it. Then, if it's not overloaded,
+ # it is also allowed. If it is overloaded and not the flattened
+ # version, it is pruned. If these are output ports, there can be
+ # no parameters.
+
+ def passes(flattened, hit_count, original):
+ if forbidden(flattened, hit_count, original):
+ return False
+ if hit_count == 1:
+ return True
+ if original[1] is None:
+ return True
+ if output and len(original[1]) > 0:
+ return False
+ if hit_count > 1 and len(original[1]) == len(flattened):
+ return True
+ return False
+
+ signatures[:] = [original for (flattened, hit_count, original)
+ in izip(flattened_entries,
+ hits,
+ signatures)
+ if passes(flattened, hit_count, original)]
+
+ #then we remove the duplicates, if necessary
+ unique_signatures = []
+ [unique_signatures.append(s) for s in signatures if not unique_signatures.count(s)]
+ signatures[:] = unique_signatures
+
+disallowed_classes = set(
+ [
+ 'vtkCriticalSection',
+ 'vtkDataArraySelection',
+ 'vtkDebugLeaks',
+ 'vtkDirectory',
+ 'vtkDynamicLoader',
+ 'vtkFunctionParser',
+ 'vtkGarbageCollector',
+ 'vtkHeap',
+ 'vtkInformationKey',
+ 'vtkInstantiator',
+ 'vtkLogLookupTable', # VTK: use vtkLookupTable.SetScaleToLog10() instead
+ 'vtkMath',
+ 'vtkModelMetadata',
+ 'vtkMultiProcessController',
+ 'vtkMutexLock',
+ 'vtkOutputWindow',
+ 'vtkPriorityQueue',
+ 'vtkReferenceCount',
+ 'vtkRenderWindowCollection',
+ 'vtkRenderWindowInteractor',
+ 'vtkTesting',
+ 'vtkWindow',
+ 'vtkVersion',
+ 'vtkDiffFilter',
+ 'vtkDocumentM3MetaData',
+ 'vtkPPointwiseMutualInformation'
+ #'vtkXMLUtilities',
+ #'vtkXMLShader',
+ #'vtkXMLMaterialReader',
+ #'vtkXMLMaterial',
+ #'vtkXMLDataElement'
+ ])
+
+def is_class_allowed(module):
+ if module is None:
+ return False
+ try:
+ name = module.__name__
+ return not (name in disallowed_classes)
+ except AttributeError:
+ return True
+
+def addAlgorithmPorts(module):
+ """ addAlgorithmPorts(module: Module) -> None
+ If module is a subclass of vtkAlgorithm, this function will add all
+ SetInputConnection([id],[port]) and GetOutputPort([id]) as
+ SetInputConnection{id}([port]) and GetOutputPort{id}.
+
+ """
+ if issubclass(get_description_class(module.vtkClass), vtk.vtkAlgorithm):
+ if get_description_class(module.vtkClass)!=vtk.vtkStructuredPointsGeometryFilter:
+ # We try to instantiate the class here to get the number of
+ # ports and to avoid abstract classes
+ try:
+ instance = module.vtkClass()
+ except TypeError:
+ pass
+ else:
+ registry = get_module_registry()
+ des = registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk',
+ 'vtkAlgorithmOutput')
+ for i in xrange(0,instance.GetNumberOfInputPorts()):
+ registry.add_input_port(module, 'SetInputConnection%d'%i,
+ des.module)
+ for i in xrange(0,instance.GetNumberOfOutputPorts()):
+ registry.add_output_port(module, 'GetOutputPort%d'%i,
+ des.module)
+
+disallowed_set_get_ports = set(['ReferenceCount',
+ 'InputConnection',
+ 'OutputPort',
+ 'Progress',
+ 'ProgressText',
+ 'InputArrayToProcess',
+ ])
+def addSetGetPorts(module, get_set_dict, delayed):
+ """ addSetGetPorts(module: Module, get_set_dict: dict) -> None
+ Convert all Setxxx methods of module into input ports and all Getxxx
+ methods of module into output ports
+
+ Keyword arguments:
+ module --- Module
+ get_set_dict --- the Set/Get method signatures returned by vtk_parser
+
+ """
+
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in get_set_dict.iterkeys():
+ if name in disallowed_set_get_ports: continue
+ getterMethod = getattr(klass, 'Get%s'%name)
+ setterMethod = getattr(klass, 'Set%s'%name)
+ getterSig = get_method_signature(getterMethod)
+ setterSig = get_method_signature(setterMethod)
+
+ if len(getterSig) > 1:
+ prune_signatures(module, 'Get%s'%name, getterSig, output=True)
+ for order, getter in enumerate(getterSig):
+ if getter[1]:
+ debug("Can't handle getter %s (%s) of class %s: Needs input to "
+ "get output" % (order+1, name, klass))
+ continue
+ if len(getter[0]) != 1:
+ debug("Can't handle getter %s (%s) of class %s: More than a "
+ "single output" % (order+1, name, str(klass)))
+ continue
+ class_ = typeMap(getter[0][0])
+ if is_class_allowed(class_):
+ registry.add_output_port(module, 'Get'+name, class_, True)
+ if len(setterSig) > 1:
+ prune_signatures(module, 'Set%s'%name, setterSig)
+ for ix, setter in enumerate(setterSig):
+ if setter[1]==None: continue
+ n = resolve_overloaded_name('Set' + name, ix, setterSig)
+ if len(setter[1]) == 1 and is_class_allowed(typeMap(setter[1][0])):
+ registry.add_input_port(module, n,
+ typeMap(setter[1][0]),
+ setter[1][0] in typeMapDict)
+ else:
+ classes = [typeMap(i) for i in setter[1]]
+ if all(is_class_allowed(x) for x in classes):
+ registry.add_input_port(module, n, classes, True)
+ # Wrap SetFileNames for VisTrails file access
+ if file_name_pattern.match(name):
+ registry.add_input_port(module, 'Set' + name[:-4],
+ (File, 'input file'), False)
+ # Wrap SetRenderWindow for exporters
+ elif name == 'RenderWindow':
+ # cscheid 2008-07-11 This is messy: VTKCell isn't
+ # registered yet, so we can't use it as a port
+ # However, we can't register VTKCell before these either,
+ # because VTKCell requires vtkRenderer. The "right" way would
+ # be to add all modules first, then all ports. However, that would
+ # be too slow.
+ # Workaround: delay the addition of the port by storing
+ # the information in a list
+ if registry.has_module('edu.utah.sci.vistrails.spreadsheet',
+ 'SpreadsheetCell'):
+ delayed.add_input_port.append((module, 'SetVTKCell', VTKCell, False))
+ # Wrap color methods for VisTrails GUI facilities
+ elif name == 'DiffuseColor':
+ registry.add_input_port(module, 'SetDiffuseColorWidget',
+ (Color, 'color'), True)
+ elif name == 'Color':
+ registry.add_input_port(module, 'SetColorWidget',
+ (Color, 'color'), True)
+ elif name == 'AmbientColor':
+ registry.add_input_port(module, 'SetAmbientColorWidget',
+ (Color, 'color'), True)
+ elif name == 'SpecularColor':
+ registry.add_input_port(module, 'SetSpecularColorWidget',
+ (Color, 'color'), True)
+ elif name == 'EdgeColor':
+ registry.add_input_port(module, 'SetEdgeColorWidget',
+ (Color, 'color'), True)
+ elif name == 'Background' :
+ registry.add_input_port(module, 'SetBackgroundWidget',
+ (Color, 'color'), True)
+ elif name == 'Background2' :
+ registry.add_input_port(module, 'SetBackground2Widget',
+ (Color, 'color'), True)
+
+disallowed_toggle_ports = set(['GlobalWarningDisplay',
+ 'Debug',
+ ])
+def addTogglePorts(module, toggle_dict):
+ """ addTogglePorts(module: Module, toggle_dict: dict) -> None
+ Convert all xxxOn/Off methods of module into input ports
+
+ Keyword arguments:
+ module --- Module
+ toggle_dict --- the Toggle method signatures returned by vtk_parser
+
+ """
+ registry = get_module_registry()
+ for name in toggle_dict.iterkeys():
+ if name in disallowed_toggle_ports:
+ continue
+ registry.add_input_port(module, name+'On', [], True)
+ registry.add_input_port(module, name+'Off', [], True)
+
+disallowed_state_ports = set(['SetInputArrayToProcess'])
+def addStatePorts(module, state_dict):
+ """ addStatePorts(module: Module, state_dict: dict) -> None
+ Convert all SetxxxToyyy methods of module into input ports
+
+ Keyword arguments:
+ module --- Module
+ state_dict --- the State method signatures returned by vtk_parser
+
+ """
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in state_dict.iterkeys():
+ for mode in state_dict[name]:
+ # Creates the port Set foo to bar
+ field = 'Set'+name+'To'+mode[0]
+ if field in disallowed_state_ports:
+ continue
+ if not registry.has_input_port(module, field):
+ registry.add_input_port(module, field, [], True)
+
+ # Now create the port Set foo with parameter
+ if hasattr(klass, 'Set%s'%name):
+ setterMethod = getattr(klass, 'Set%s'%name)
+ setterSig = get_method_signature(setterMethod)
+ # if the signature looks like an enum, we'll skip it, it shouldn't
+ # be necessary
+ if len(setterSig) > 1:
+ prune_signatures(module, 'Set%s'%name, setterSig)
+ for ix, setter in enumerate(setterSig):
+ n = resolve_overloaded_name('Set' + name, ix, setterSig)
+ tm = typeMap(setter[1][0])
+ if len(setter[1]) == 1 and is_class_allowed(tm):
+ registry.add_input_port(module, n, tm,
+ setter[1][0] in typeMapDict)
+ else:
+ classes = [typeMap(i) for i in setter[1]]
+ if all(is_class_allowed(x) for x in classes):
+ registry.add_input_port(module, n, classes, True)
+
+disallowed_other_ports = set(
+ [
+ 'BreakOnError',
+ 'DeepCopy',
+ 'FastDelete',
+ 'HasObserver',
+ 'HasExecutive',
+ 'INPUT_ARRAYS_TO_PROCESS',
+ 'INPUT_CONNECTION',
+ 'INPUT_IS_OPTIONAL',
+ 'INPUT_IS_REPEATABLE',
+ 'INPUT_PORT',
+ 'INPUT_REQUIRED_DATA_TYPE',
+ 'INPUT_REQUIRED_FIELDS',
+ 'InvokeEvent',
+ 'IsA',
+ 'Modified',
+ 'NewInstance',
+ 'PrintRevisions',
+ 'RemoveAllInputs',
+ 'RemoveObserver',
+ 'RemoveObservers',
+# 'SafeDownCast',
+# 'SetInputArrayToProcess',
+ 'ShallowCopy',
+ 'Update',
+ 'UpdateInformation',
+ 'UpdateProgress',
+ 'UpdateWholeExtent',
+ ])
+
+force_not_optional_port = set(
+ ['ApplyViewTheme',
+ ])
+
+
+def addOtherPorts(module, other_list):
+ """ addOtherPorts(module: Module, other_list: list) -> None
+ Convert all other ports such as Insert/Add.... into input/output
+
+ Keyword arguments:
+ module --- Module
+ other_dict --- any other method signatures that is not
+ Algorithm/SetGet/Toggle/State type
+
+ """
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in other_list:
+ if name[:3] in ['Add','Set'] or name[:6]=='Insert':
+ if name in disallowed_other_ports:
+ continue
+ method = getattr(klass, name)
+ signatures = ""
+ if not isinstance(method, int):
+ signatures = get_method_signature(method)
+ if len(signatures) > 1:
+ prune_signatures(module, name, signatures)
+ for (ix, sig) in enumerate(signatures):
+ ([result], params) = sig
+ types = []
+ if params:
+ for p in params:
+ t = typeMap(p)
+ if not t:
+ types = None
+ break
+ else: types.append(t)
+ else:
+ types = [[]]
+ if types:
+ if not all(is_class_allowed(x) for x in types):
+ continue
+ n = resolve_overloaded_name(name, ix, signatures)
+ if len(types)<=1:
+ registry.add_input_port(module, n, types[0],
+ types[0] in typeMapDictValues)
+ else:
+ registry.add_input_port(module, n, types, True)
+ else:
+ if name in disallowed_other_ports:
+ continue
+ method = getattr(klass, name)
+ signatures = ""
+ if not isinstance(method, int):
+ signatures = get_method_signature(method)
+ if len(signatures) > 1:
+ prune_signatures(module, name, signatures)
+ for (ix, sig) in enumerate(signatures):
+ ([result], params) = sig
+ types = []
+ if params:
+ types = [typeMap(p) for p in params]
+ else:
+ types = []
+ if not all(is_class_allowed(x) for x in types):
+ continue
+ if types==[] or (result==None):
+ n = resolve_overloaded_name(name, ix, signatures)
+ registry.add_input_port(module, n, types,
+ not (n in force_not_optional_port))
+
+disallowed_get_ports = set([
+ 'GetClassName',
+ 'GetErrorCode',
+ 'GetNumberOfInputPorts',
+ 'GetNumberOfOutputPorts',
+ 'GetOutputPortInformation',
+ 'GetTotalNumberOfInputConnections',
+ ])
+
+def addGetPorts(module, get_list):
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in get_list:
+ if name in disallowed_get_ports:
+ continue
+ method = getattr(klass, name)
+ signatures = get_method_signature(method)
+ if len(signatures) > 1:
+ prune_signatures(module, name, signatures, output=True)
+ for ix, getter in enumerate(signatures):
+ if getter[1] or len(getter[0]) > 1:
+ continue
+ class_ = typeMap(getter[0][0])
+ if is_class_allowed(class_):
+ if len(signatures) > 1:
+ n = name + "_" + str(ix+1)
+ else:
+ n = name
+ registry.add_output_port(module, n, class_, True)
+
+def addPorts(module, delayed):
+ """ addPorts(module: VTK module inherited from Module,
+ delayed: object with add_input_port slot
+ ) -> None
+
+ Search all metamethods of module and add appropriate ports
+
+ ports that cannot be added immediately should be appended to
+ the delayed object that is passed. see the SetRenderWindow cases.
+
+ """
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ registry.add_output_port(module, 'self', module)
+ parser.parse(klass)
+ addAlgorithmPorts(module)
+ addGetPorts(module, parser.get_get_methods())
+ addSetGetPorts(module, parser.get_get_set_methods(), delayed)
+ addTogglePorts(module, parser.get_toggle_methods())
+ addStatePorts(module, parser.get_state_methods())
+ addOtherPorts(module, parser.get_other_methods())
+
+ # CVS version of VTK doesn't support AddInputConnect(vtkAlgorithmOutput)
+ if klass==vtk.vtkAlgorithm:
+ registry.add_input_port(module, 'AddInputConnection',
+ typeMap('vtkAlgorithmOutput'))
+ # vtkWriters have a custom File port
+ elif klass==vtk.vtkWriter:
+ registry.add_output_port(module, 'file',
+ typeMap('File','edu.utah.sci.vistrails.basic'))
+ elif klass==vtk.vtkImageWriter:
+ registry.add_output_port(module, 'file',
+ typeMap('File','edu.utah.sci.vistrails.basic'))
+ elif klass==vtk.vtkVolumeProperty:
+ registry.add_input_port(module, 'SetTransferFunction',
+ typeMap('TransferFunction'))
+ elif klass==vtk.vtkDataSet:
+ registry.add_input_port(module, 'SetPointData', typeMap('vtkPointData'))
+ registry.add_input_port(module, 'SetCallData', typeMap('vtkCellData'))
+ elif klass==vtk.vtkCell:
+ registry.add_input_port(module, 'SetPointIds', typeMap('vtkIdList'))
+
+def setAllPorts(descriptor, delayed):
+ """ setAllPorts(descriptor: ModuleDescriptor) -> None
+ Traverse descriptor and all of its children/grand-children to add all ports
+
+ """
+ addPorts(descriptor.module, delayed)
+ for child in descriptor.children:
+ setAllPorts(child, delayed)
+
+def class_dict(base_module, node):
+ """class_dict(base_module, node) -> dict
+ Returns the class dictionary for the module represented by node and
+ with base class base_module"""
+
+ class_dict_ = {}
+ def update_dict(name, callable_):
+ if class_dict_.has_key(name):
+ class_dict_[name] = callable_(class_dict_[name])
+ elif hasattr(base_module, name):
+ class_dict_[name] = callable_(getattr(base_module, name))
+ else:
+ class_dict_[name] = callable_(None)
+
+ def guarded_SimpleScalarTree_wrap_compute(old_compute):
+ # This builds the scalar tree and makes it cacheable
+
+ def compute(self):
+ self.is_cacheable = lambda *args, **kwargs: True
+ old_compute(self)
+ self.vtkInstance.BuildTree()
+ return compute
+
+ def guarded_SetFileName_wrap_compute(old_compute):
+ # This checks for the presence of file in VTK readers
+ def compute(self):
+
+ # Skips the check if it's a vtkImageReader or vtkPLOT3DReader, because
+ # it has other ways of specifying files, like SetFilePrefix for
+ # multiple files
+ if any(issubclass(self.vtkClass, x)
+ for x in
+ [vtk.vtkBYUReader,
+ vtk.vtkImageReader,
+ vtk.vtkPLOT3DReader,
+ vtk.vtkDICOMImageReader,
+ vtk.vtkTIFFReader]):
+ old_compute(self)
+ return
+ if self.hasInputFromPort('SetFileName'):
+ name = self.getInputFromPort('SetFileName')
+ elif self.hasInputFromPort('SetFile'):
+ name = self.getInputFromPort('SetFile').name
+ else:
+ raise ModuleError(self, 'Missing filename')
+ if not os.path.isfile(name):
+ raise ModuleError(self, 'File does not exist')
+ old_compute(self)
+ return compute
+
+ def compute_SetDiffuseColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetDiffuseColorWidget(self, color):
+ self.vtkInstance.SetDiffuseColor(color.tuple)
+ return call_SetDiffuseColorWidget
+
+ def compute_SetAmbientColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetAmbientColorWidget(self, color):
+ self.vtkInstance.SetAmbientColor(color.tuple)
+ return call_SetAmbientColorWidget
+
+ def compute_SetSpecularColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetSpecularColorWidget(self, color):
+ self.vtkInstance.SetSpecularColor(color.tuple)
+ return call_SetSpecularColorWidget
+
+ def compute_SetColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetColorWidget(self, color):
+ self.vtkInstance.SetColor(color.tuple)
+ return call_SetColorWidget
+
+ def compute_SetEdgeColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetEdgeColorWidget(self, color):
+ self.vtkInstance.SetEdgeColor(color.tuple)
+ return call_SetEdgeColorWidget
+
+ def compute_SetBackgroundWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetBackgroundWidget(self, color):
+ self.vtkInstance.SetBackground(color.tuple)
+ return call_SetBackgroundWidget
+
+ def compute_SetBackground2Widget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetBackground2Widget(self, color):
+ self.vtkInstance.SetBackground2(color.tuple)
+ return call_SetBackground2Widget
+
+ def compute_SetVTKCell(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetRenderWindow(self, cellObj):
+ if cellObj.cellWidget:
+ self.vtkInstance.SetRenderWindow(cellObj.cellWidget.mRenWin)
+ return call_SetRenderWindow
+
+ def compute_SetTransferFunction(old_compute):
+ # This sets the transfer function
+ if old_compute != None:
+ return old_compute
+ def call_SetTransferFunction(self, tf):
+ tf.set_on_vtk_volume_property(self.vtkInstance)
+ return call_SetTransferFunction
+
+ def compute_SetPointData(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetPointData(self, pd):
+ self.vtkInstance.GetPointData().ShallowCopy(pd)
+ return call_SetPointData
+
+ def compute_SetCellData(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetCellData(self, cd):
+ self.vtkInstance.GetCellData().ShallowCopy(cd)
+ return call_SetCellData
+
+ def compute_SetPointIds(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetPointIds(self, point_ids):
+ self.vtkInstance.GetPointIds().SetNumberOfIds(point_ids.GetNumberOfIds())
+ for i in xrange(point_ids.GetNumberOfIds()):
+ self.vtkInstance.GetPointIds().SetId(i, point_ids.GetId(i))
+ return call_SetPointIds
+
+ def guarded_Writer_wrap_compute(old_compute):
+ # The behavior for vtkWriter subclasses is to call Write()
+ # If the user sets a name, we will create a file with that name
+ # If not, we will create a temporary file from the file pool
+ def compute(self):
+ old_compute(self)
+ fn = self.vtkInstance.GetFileName()
+ if not fn:
+ o = self.interpreter.filePool.create_file(suffix='.vtk')
+ self.vtkInstance.SetFileName(o.name)
+ else:
+ o = File()
+ o.name = fn
+ self.vtkInstance.Write()
+ self.setResult('file', o)
+ return compute
+
+ for var in dir(node.klass):
+ # Everyone that has a Set.*FileName should have a Set.*File port too
+ if set_file_name_pattern.match(var):
+ def get_compute_SetFile(method_name):
+ def compute_SetFile(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetFile(self, file_obj):
+ getattr(self.vtkInstance, method_name)(file_obj.name)
+ return call_SetFile
+ return compute_SetFile
+ update_dict('_special_input_function_' + var[:-4],
+ get_compute_SetFile(var))
+
+ if hasattr(node.klass, 'SetFileName'):
+ # ... BUT we only want to check existence of filenames on
+ # readers. VTK is nice enough to be consistent with names, but
+ # this is brittle..
+ if node.klass.__name__.endswith('Reader'):
+ if not node.klass.__name__.endswith('TiffReader'):
+ update_dict('compute', guarded_SetFileName_wrap_compute)
+ if hasattr(node.klass, 'SetRenderWindow'):
+ update_dict('_special_input_function_SetVTKCell',
+ compute_SetVTKCell)
+ #color gui wrapping
+ if hasattr(node.klass, 'SetDiffuseColor'):
+ update_dict('_special_input_function_SetDiffuseColorWidget',
+ compute_SetDiffuseColorWidget)
+ if hasattr(node.klass, 'SetAmbientColor'):
+ update_dict('_special_input_function_SetAmbientColorWidget',
+ compute_SetAmbientColorWidget)
+ if hasattr(node.klass, 'SetSpecularColor'):
+ update_dict('_special_input_function_SetSpecularColorWidget',
+ compute_SetSpecularColorWidget)
+ if hasattr(node.klass, 'SetEdgeColor'):
+ update_dict('_special_input_function_SetEdgeColorWidget',
+ compute_SetEdgeColorWidget)
+ if hasattr(node.klass, 'SetColor'):
+ update_dict('_special_input_function_SetColorWidget',
+ compute_SetColorWidget)
+
+ if (issubclass(node.klass, vtk.vtkRenderer) and
+ hasattr(node.klass, 'SetBackground')):
+ update_dict('_special_input_function_SetBackgroundWidget',
+ compute_SetBackgroundWidget)
+ if (issubclass(node.klass, vtk.vtkRenderer) and
+ hasattr(node.klass, 'SetBackground2')):
+ update_dict('_special_input_function_SetBackground2Widget',
+ compute_SetBackground2Widget)
+ if issubclass(node.klass, vtk.vtkWriter):
+ update_dict('compute', guarded_Writer_wrap_compute)
+
+ if issubclass(node.klass, vtk.vtkScalarTree):
+ update_dict('compute', guarded_SimpleScalarTree_wrap_compute)
+
+ if issubclass(node.klass, vtk.vtkVolumeProperty):
+ update_dict('_special_input_function_SetTransferFunction',
+ compute_SetTransferFunction)
+ if issubclass(node.klass, vtk.vtkDataSet):
+ update_dict('_special_input_function_SetPointData',
+ compute_SetPointData)
+ update_dict('_special_input_function_SetCellData',
+ compute_SetCellData)
+ if issubclass(node.klass, vtk.vtkCell):
+ update_dict('_special_input_function_SetPointIds',
+ compute_SetPointIds)
+ return class_dict_
+
+disallowed_modules = set([
+# 'vtkGeoAlignedImageCache',
+# 'vtkGeoTerrainCache',
+# 'vtkMimeTypeStrategy',
+# 'vtkMPIGroup',
+ 'vtkPlotWriter', # Segfaults when being destroyed (when created without a reference, or when last reference is removed)
+ 'vtkRenderedLandscapeRepresentation' # Segfaults when calling: GetPeakLabelStopWords()
+ ])
+def createModule(baseModule, node):
+ """ createModule(baseModule: a Module subclass, node: TreeNode) -> None
+ Construct a module inherits baseModule with specification from node
+
+ """
+ if node.name in disallowed_modules: return
+ def obsolete_class_list():
+ lst = []
+ items = ['vtkInteractorStyleTrackball',
+ 'vtkStructuredPointsGeometryFilter',
+ 'vtkConstrainedPointHandleRepresentation',
+ 'vtkTypePromotion']
+ def try_to_add_item(item):
+ try:
+ lst.append(getattr(titan, item))
+ except AttributeError:
+ pass
+ for item in items:
+ try_to_add_item(item)
+ return lst
+
+ obsolete_list = obsolete_class_list()
+
+ pack1 = vtk
+ for i in titan2:
+ if getattr(i, node.name, None) != None:
+ pack1 = i
+
+ def is_abstract():
+ """is_abstract tries to instantiate the class. If it's
+ abstract, this will raise."""
+ # Consider obsolete classes abstract
+ if node.klass in obsolete_list:
+ return True
+ try:
+ getattr(pack1, node.name)()
+ except TypeError: # VTK raises type error on abstract classes
+ return True
+ return False
+
+ module = new_module(baseModule, node.name,
+ class_dict(baseModule, node),
+ docstring=getattr(pack1, node.name).__doc__
+ )
+
+ # This is sitting on the class
+ if hasattr(fix_classes, node.klass.__name__ + '_fixed'):
+ module.vtkClass = getattr(fix_classes, node.klass.__name__ + '_fixed')
+ else:
+ module.vtkClass = node.klass
+ registry = get_module_registry()
+ registry.add_module(module, abstract=is_abstract(),
+ signatureCallable=vtk_hasher)
+ for child in node.children:
+ if child.name in disallowed_classes:
+ continue
+ createModule(module, child)
+
+def createAllModules(g):
+ """ createAllModules(g: ClassTree) -> None
+ Traverse the VTK class tree and add all modules into the module registry
+
+ """
+ if tuple(vtk.vtkVersion().GetVTKVersion().split('.')) < ('5', '7', '0'):
+ assert len(g.tree[0]) == 1
+ base = g.tree[0][0]
+ assert base.name == 'vtkObjectBase'
+
+ vtkObjectBase = new_module(vtkBaseModule, 'vtkObjectBase')
+ vtkObjectBase.vtkClass = vtk.vtkObjectBase
+ registry = get_module_registry()
+ registry.add_module(vtkObjectBase)
+ if tuple(vtk.vtkVersion().GetVTKVersion().split('.')) < ('5', '7', '0'):
+ for child in base.children:
+ if child.name in disallowed_classes:
+ continue
+ createModule(vtkObjectBase, child)
+ else:
+ for base in g.tree[0]:
+ for child in base.children:
+ if child.name in disallowed_classes:
+ continue
+ createModule(vtkObjectBase, child)
+
+##############################################################################
+# Convenience methods
+
+def extract_vtk_instance(vistrails_obj):
+ """extract_vtk_instance(vistrails_obj) -> vtk_object
+
+ takes an instance of a VisTrails module that is a subclass
+ of the vtkObjectBase module and returns the corresponding
+ instance."""
+ global identifier
+ vtkObjectBase = registry.get_descriptor_by_name(identifier,
+ 'vtkObjectBase').module
+ assert isinstance(vistrails_obj, vtkObjectBase)
+ return vistrails_obj.vtkInstance
+
+def wrap_vtk_instance(vtk_obj):
+ """wrap_vtk_instance(vtk_object) -> VisTrails module
+
+ takes a vtk instance and returns a corresponding
+ wrapped instance of a VisTrails module"""
+ global identifier
+
+ assert isinstance(vtk_obj, vtk.vtkObjectBase)
+ m = registry.get_descriptor_by_name(identifier,
+ vtk_obj.GetClassName())
+ result = m.module()
+ result.vtkInstance = vtk_obj
+ return result
+
+################################################################################
+
+def initialize():
+ """ initialize() -> None
+ Package-entry to initialize the package
+
+ """
+ # Check VTK version
+ v = vtk.vtkVersion()
+ version = [v.GetVTKMajorVersion(),
+ v.GetVTKMinorVersion(),
+ v.GetVTKBuildVersion()]
+ if version < [5, 0, 0]:
+ raise Exception("You need to upgrade your VTK install to version \
+ > >= 5.0.0")
+ inheritanceGraph = ClassTree(titan2)
+ inheritanceGraph.create()
+
+ # Transfer Function constant
+ tf_widget.initialize()
+
+ delayed = InstanceObject(add_input_port=[])
+ # Add VTK modules
+ registry = get_module_registry()
+ registry.add_module(vtkBaseModule)
+ createAllModules(inheritanceGraph)
+ setAllPorts(registry.get_descriptor_by_name(identifier,
+ 'vtkObjectBase'),
+ delayed)
+
+# # Register the VTKCell and VTKHandler type if the spreadsheet is up
+# if registry.has_module('edu.utah.sci.vistrails.spreadsheet',
+# 'SpreadsheetCell'):
+# import vtkhandler
+# import vtkcell
+# import vtkviewcell
+# vtkhandler.registerSelf()
+# vtkcell.registerSelf()
+# vtkviewcell.registerSelf()
+
+ # register offscreen rendering module
+ offscreen.register_self()
+
+ # Now add all "delayed" ports - see comment on addSetGetPorts
+ for args in delayed.add_input_port:
+
+ registry.add_input_port(*args)
+
+ # register Transfer Function adjustment
+ # This can't be reordered -- TransferFunction needs to go before
+ # vtkVolumeProperty, but vtkScaledTransferFunction needs
+ # to go after vtkAlgorithmOutput
+
+ getter = registry.get_descriptor_by_name
+ registry.add_module(tf_widget.vtkScaledTransferFunction)
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'Input', getter('edu.utah.sci.vistrails.vtk',
+ 'vtkAlgorithmOutput').module)
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'Dataset', getter ('edu.utah.sci.vistrails.vtk',
+ 'vtkDataObject').module)
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'Range', [Float, Float])
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'TransferFunction',
+ tf_widget.TransferFunctionConstant)
+ registry.add_output_port(tf_widget.vtkScaledTransferFunction,
+ 'TransferFunction',
+ tf_widget.TransferFunctionConstant)
+
+
+################################################################################
diff --git a/contrib/titan/inspectors.py b/contrib/titan/inspectors.py
new file mode 100644
index 0000000..f94e2b5
--- /dev/null
+++ b/contrib/titan/inspectors.py
@@ -0,0 +1,232 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+##############################################################################
+# Data inspectors for VTK
+import vtk
+
+from core.modules.vistrails_module import ModuleError
+from core.utils import VistrailsInternalError
+from core.modules.basic_modules import Module, Float, Integer
+from core.modules.module_registry import get_module_registry
+from base_module import vtkBaseModule
+from hasher import vtk_hasher
+
+class vtkBaseInspector(Module):
+
+ @classmethod
+ def register_self(cls, **kwargs):
+ registry = get_module_registry()
+ def resolve_type(t):
+ if type(t) == tuple:
+ return registry.get_descriptor_by_name(*t).module
+ elif type(t) == type:
+ return t
+ else:
+ assert False, ("Unknown type " + str(type(t)))
+
+ registry.add_module(cls, **kwargs)
+ try:
+ ips = cls.input_ports
+ except AttributeError:
+ pass
+ else:
+ for (port_name, types) in ips:
+ registry.add_input_port(cls,
+ port_name,
+ list(resolve_type(t) for t in types))
+
+ try:
+ ops = cls.output_ports
+ except AttributeError:
+ pass
+ else:
+ for (port_name, types) in ops:
+ registry.add_output_port(cls,
+ port_name,
+ list(resolve_type(t) for t in types))
+
+ def auto_set_results(self, vtk_object):
+ for function in self.outputPorts.keys():
+ if hasattr(vtk_object, function):
+ retValues = getattr(vtk_object, function)()
+ if issubclass(retValues.__class__, vtk.vtkObject):
+ className = retValues.GetClassName()
+ output = vtkBaseModule.wrapperModule(className, retValues)
+ self.setResult(function, output)
+ elif type(retValues) in [tuple, list]:
+ result = list(retValues)
+ for i in xrange(len(result)):
+ if issubclass(result[i].__class__, vtk.vtkObject):
+ className = result[i].GetClassName()
+ result[i] = vtkBaseModule.wrapperModule(className,
+ result[i])
+ self.setResult(function, type(retValues)(result))
+ else:
+ self.setResult(function, retValues)
+
+class vtkDataSetInspector(vtkBaseInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInputConnection0"):
+ ic = self.getInputFromPort("SetInputConnection0")
+ port_object = ic.vtkInstance
+ ix = port_object.GetIndex()
+ producer = port_object.GetProducer()
+ try:
+ vtk_object = producer.GetOutput()
+ except AttributeError:
+ raise ModuleError(self,
+ "expected a module that supports GetOutput")
+ elif self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+ input_ports = [('SetInputConnection0',
+ [('edu.utah.sci.vistrails.vtk', 'vtkAlgorithmOutput')]),
+ ('SetInput',
+ [('edu.utah.sci.vistrails.vtk', 'vtkDataSet')]),
+ ]
+ output_ports = [('GetBounds', [Float] * 6),
+ ('GetScalarRange', [Float] * 2),
+ ('GetLength', [Float]),
+ ('GetCenter', [Float] * 3),
+ ('GetNumberOfPoints', [Integer]),
+ ('GetNumberOfCells', [Integer]),
+ ('GetPointData',
+ [('edu.utah.sci.vistrails.vtk', 'vtkPointData')]),
+ ('GetCellData',
+ [('edu.utah.sci.vistrails.vtk', 'vtkCellData')]),
+ ]
+
+class vtkDataSetAttributesInspector(vtkBaseInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+ input_ports = [('SetInput',
+ [('edu.utah.sci.vistrails.vtk', 'vtkDataSetAttributes')]),
+ ]
+ output_ports = [('GetScalars',
+ [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
+ ('GetVectors',
+ [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
+ ('GetNormals',
+ [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
+ ('GetTCoords',
+ [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
+ ('GetTensors',
+ [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
+ ('GetGlobalIds',
+ [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
+ ('GetPedigreeIds',
+ [('edu.utah.sci.vistrails.vtk', 'vtkAbstractArray')]),
+ ]
+
+class vtkDataArrayInspector(vtkBaseInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+ input_ports = [('SetInput',
+ [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')])]
+ output_ports = [('GetMaxNorm', [Float]),
+ ('GetRange', [Float] * 2)]
+
+class vtkPolyDataInspector(vtkDataSetInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInputConnection0"):
+ ic = self.getInputFromPort("SetInputConnection0")
+ port_object = ic.vtkInstance
+ ix = port_object.GetIndex()
+ producer = port_object.GetProducer()
+ try:
+ vtk_object = producer.GetOutput()
+ except AttributeError:
+ raise ModuleError(self,
+ "expected a module that supports GetOutput")
+ elif self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+# Wendel
+ input_ports = [('SetInputConnection0',
+ [('edu.utah.sci.vistrails.vtk', 'vtkAlgorithmOutput')]),
+ ('SetInput',
+ [('edu.utah.sci.vistrails.vtk', 'vtkDataSet')]),
+ ]
+ output_ports = [('GetVerts',
+ [('edu.utah.sci.vistrails.vtk', 'vtkCellArray')]),
+ ('GetLines',
+ [('edu.utah.sci.vistrails.vtk', 'vtkCellArray')]),
+ ('GetPolys',
+ [('edu.utah.sci.vistrails.vtk', 'vtkCellArray')]),
+ ('GetStrips',
+ [('edu.utah.sci.vistrails.vtk', 'vtkCellArray')]),
+ ('GetPoints',
+ [('edu.utah.sci.vistrails.vtk', 'vtkPoints')]),
+ ('GetNumberOfVerts', [Integer]),
+ ('GetNumberOfLines', [Integer]),
+ ('GetNumberOfPolys', [Integer]),
+ ('GetNumberOfStrips', [Integer]),
+ ]
+
+def initialize():
+ vtkBaseInspector.register_self(abstract=True, signatureCallable=vtk_hasher)
+ vtkDataSetInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+ vtkDataSetAttributesInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+ vtkDataArrayInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+ vtkPolyDataInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+
diff --git a/contrib/titan/offscreen.py b/contrib/titan/offscreen.py
new file mode 100644
index 0000000..127ba57
--- /dev/null
+++ b/contrib/titan/offscreen.py
@@ -0,0 +1,62 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+from core.modules.module_registry import get_module_registry
+from core.modules.vistrails_module import Module
+from core.modules.basic_modules import File, Integer
+
+class VTKRenderOffscreen(Module):
+
+ def compute(self):
+ r = self.getInputFromPort("renderer").vtkInstance
+ window = vtk.vtkRenderWindow()
+ w = self.forceGetInputFromPort("width", 512)
+ h = self.forceGetInputFromPort("height", 512)
+ window.OffScreenRenderingOn()
+ window.SetSize(w, h)
+ # r.ResetCamera()
+ window.AddRenderer(r)
+ window.Start()
+ window.Render()
+ win2image = vtk.vtkWindowToImageFilter()
+ win2image.SetInput(window)
+ win2image.Update()
+ writer = vtk.vtkPNGWriter()
+ writer.SetInput(win2image.GetOutput())
+ output = self.interpreter.filePool.create_file(suffix='.png')
+ writer.SetFileName(output.name)
+ writer.Write()
+ window.Finalize()
+ self.setResult("image", output)
+
+def register_self():
+ registry = get_module_registry()
+ r = registry.get_descriptor_by_name(
+ 'edu.utah.sci.vistrails.vtk',
+# Wendel
+ 'vtkRenderer').module
+ registry.add_module(VTKRenderOffscreen)
+ registry.add_input_port(VTKRenderOffscreen, 'renderer', r)
+ registry.add_input_port(VTKRenderOffscreen, 'width', Integer)
+ registry.add_input_port(VTKRenderOffscreen, 'height', Integer)
+ registry.add_output_port(VTKRenderOffscreen, 'image', File)
+
diff --git a/contrib/titan/tf_widget.py b/contrib/titan/tf_widget.py
new file mode 100644
index 0000000..0c52e73
--- /dev/null
+++ b/contrib/titan/tf_widget.py
@@ -0,0 +1,575 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+##############################################################################
+# Transfer Function Widget for VTK
+
+from PyQt4 import QtCore, QtGui
+from core.modules.constant_configuration import ConstantWidgetMixin
+from core.modules.basic_modules import new_constant, init_constant, Module
+from core.utils.color import ColorByName
+import vtk
+import math
+import pickle
+import copy
+
+################################################################################
+# etc
+
+def clamp(v, mn, mx, eps=0.0):
+ mn += eps
+ mx -= eps
+ if v < mn: return mn
+ if v > mx: return mx
+ return v
+
+##############################################################################
+# Transfer Function object
+
+class TransferFunction(object):
+
+ def __init__(self):
+ self._min_range = 0.0
+ self._max_range = 1.0
+ self._pts = []
+
+ def set_range(self, mn, mx):
+ self._min_range = mn
+ self._max_range = mx
+
+ def set_on_vtk_volume_property(self, vtk_volume_property):
+ # Builds the opacity and color functions
+ of = vtk.vtkPiecewiseFunction()
+ cf = vtk.vtkColorTransferFunction()
+ vp = vtk_volume_property
+ for pt in self._pts:
+ (scalar, opacity, color) = pt
+ # Map scalar to tf range
+ s = self._min_range + (self._max_range - self._min_range) * scalar
+ of.AddPoint(s, opacity)
+ cf.AddRGBPoint(s, color[0], color[1], color[2])
+ vp.SetScalarOpacity(of)
+ vp.SetColor(cf)
+
+ def add_point(self, scalar, opacity, color):
+ self._pts.append((scalar, opacity, color))
+ self._pts.sort()
+
+ def get_value(self, scalar):
+ """get_value(scalar): returns the opacity and color
+ linearly interpolated at the value. Useful for
+ adding knots."""
+ ix = 0
+ while ix < len(self._pts) and self._pts[ix][0] > scalar:
+ ix += 1
+ if ix == 0:
+ return (self._pts[0][1], self._pts[0][2])
+ elif ix == len(self._pts):
+ return (self._pts[-1][1], self._pts[-1][2])
+ else:
+ u = ((self._pts[ix][0] - scalar) /
+ (self._pts[ix][0] - self._pts[ix-1][0]))
+ do = self._pts[ix][1] - self._pts[ix-1][1]
+ dr = self._pts[ix][2][0] - self._pts[ix-1][2][0]
+ dg = self._pts[ix][2][1] - self._pts[ix-1][2][1]
+ db = self._pts[ix][2][2] - self._pts[ix-1][2][2]
+ return (self._pts[ix-1][1] + u * do,
+ (self._pts[ix-1][2][0] + u * dr,
+ self._pts[ix-1][2][1] + u * dg,
+ self._pts[ix-1][2][2] + u * db))
+
+ def __copy__(self):
+ result = TransferFunction()
+ result._min_range = self._min_range
+ result._max_range = self._max_range
+ result._pts = copy.copy(self._pts)
+ return result
+
+ def __eq__(self, other):
+ if type(other) != type(self):
+ return False
+ if self._min_range != other._min_range:
+ return False
+ if self._max_range != other._max_range:
+ return False
+ for my_pt, other_pt in zip(self._pts, other._pts):
+ if my_pt != other_pt:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+##############################################################################
+# Graphics Items
+
+class TransferFunctionPoint(QtGui.QGraphicsEllipseItem):
+
+ selection_pens = { True: QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('goldenrod_medium')))),0.012),
+ False: QtGui.QPen() }
+
+ def __init__(self, scalar, opacity, color, parent=None):
+ QtGui.QGraphicsEllipseItem.__init__(self, parent)
+ self._scalar = scalar
+ self._opacity = opacity
+ self._color = QtGui.QColor(color[0]*255,
+ color[1]*255,
+ color[2]*255)
+ self.setPen(QtGui.QPen(QtGui.QColor(0,0,0)))
+ self.setFlag(QtGui.QGraphicsItem.ItemIsMovable)
+ self.setFlag(QtGui.QGraphicsItem.ItemIsSelectable)
+ self.setFlag(QtGui.QGraphicsItem.ItemIsFocusable)
+ self.setZValue(2.0)
+
+ self._sx = 1.0
+ self._sy = 1.0
+ self._left_line = None
+ self._right_line = None
+ self._point = QtCore.QPointF(scalar, opacity)
+ self.refresh()
+
+ self.setToolTip("Double-click to change color\n"
+ "Right-click to remove point\n"
+ "Scalar: %.5f, Opacity: %.5f" % (self._scalar,
+ self._opacity))
+ # This sets up the linked list of Lines
+
+ def keyPressEvent(self, event):
+ if event.key() == QtCore.Qt.Key_Backspace or \
+ event.key() == QtCore.Qt.Key_Delete:
+ self.remove_self()
+
+ def refresh(self):
+ dx = 0.025 / self._sx
+ dy = 0.025 / self._sy
+ # this is the setup
+ self.setBrush(QtGui.QBrush(self._color))
+ self.setRect(-dx,
+ -dy,
+ 2 * dx, 2 * dy)
+ self.setPos(self._scalar,
+ self._opacity)
+
+ def update_scale(self, sx, sy):
+ self._sx = sx
+ self._sy = sy
+ self.refresh()
+
+ def itemChange(self, change, value):
+ if change == QtGui.QGraphicsItem.ItemSelectedChange:
+ self.setPen(self.selection_pens[value.toBool()])
+ if change == QtGui.QGraphicsItem.ItemPositionChange:
+ # moves point
+ pt = value.toPointF()
+ pt.setY(clamp(pt.y(), 0.0, 1.0))
+ self._opacity = pt.y()
+ self._point.setY(pt.y())
+ if not self._left_line:
+ pt.setX(0.0)
+ elif not self._right_line:
+ pt.setX(1.0)
+ else:
+ assert self._left_line._point_right == self
+ assert self._right_line._point_left == self
+ pt.setX(clamp(pt.x(),
+ self._left_line._point_left._point.x(),
+ self._right_line._point_right._point.x(),
+ 1e-6))
+ self._point.setX(pt.x())
+ self._scalar = pt.x()
+ if self._left_line:
+ self._left_line.refresh()
+ if self._right_line:
+ self._right_line.refresh()
+ if self.scene():
+ self.scene()._tf_poly.setup()
+ self.setToolTip("Double-click to change color\n"
+ "Right-click to remove point\n"
+ "Scalar: %.5f, Opacity: %.5f" % (self._scalar,
+ self._opacity))
+ return QtGui.QGraphicsItem.itemChange(self, change,
+ QtCore.QVariant(pt))
+ return QtGui.QGraphicsItem.itemChange(self, change, value)
+
+ def remove_self(self):
+ if not self._left_line or not self._right_line:
+ # Ignore, self is a corner node that can't be removed
+ return
+
+ # Removes the right line and self, re-ties data structure
+ self._left_line._point_right = self._right_line._point_right
+ self._left_line._point_right._left_line = self._left_line
+
+ # be friends with garbage collector
+ self._right_line._point_left = None
+ self._right_line._point_right = None
+ self.scene()._tf_poly.setup()
+ self.scene().removeItem(self._right_line)
+ self.scene().removeItem(self)
+ self._left_line.refresh()
+
+ def mouseDoubleClickEvent(self, event):
+ new_color = QtGui.QColorDialog.getColor(self._color)
+ if not new_color.isValid():
+ return
+ self._color = new_color
+ if self._left_line:
+ self._left_line.refresh()
+ if self._right_line:
+ self._right_line.refresh()
+ self.refresh()
+ self.scene()._tf_poly.setup()
+
+ def mousePressEvent(self, event):
+ if event.button() == QtCore.Qt.RightButton:
+ event.accept()
+ self.remove_self()
+ else:
+ QtGui.QGraphicsEllipseItem.mousePressEvent(self, event)
+
+ def add_self_to_transfer_function(self, tf):
+ tf.add_point(self._scalar,
+ self._opacity,
+ (self._color.redF(),
+ self._color.greenF(),
+ self._color.blueF()))
+
+class TransferFunctionPolygon(QtGui.QGraphicsPolygonItem):
+
+ def __init__(self):
+ QtGui.QGraphicsPolygonItem.__init__(self)
+
+ def setup(self):
+ # This inspects the scene, finds the left-most point, and
+ # then builds the polygon traversing the linked list structure
+ if not self.scene():
+ return
+ pt = self.scene().get_leftmost_point()
+ first_pt = pt
+ self.setZValue(1.25)
+ g = QtGui.QLinearGradient()
+ g.setStart(0.0, 0.5)
+ g.setFinalStop(1.0, 0.5)
+ p = QtGui.QPen()
+ p.setStyle(QtCore.Qt.NoPen)
+ pts = [QtCore.QPointF(pt.x(), 0)]
+ self.setPen(p)
+
+ while 1:
+ c = QtGui.QColor(pt._color)
+ c.setAlphaF(pt._opacity)
+ g.setColorAt(pt._scalar, c)
+ pts.append(pt._point)
+ # move cursor fwd
+ if pt._right_line:
+ pt = pt._right_line._point_right
+ else:
+ break
+ self.setBrush(QtGui.QBrush(g))
+ pts.append(QtCore.QPointF(pt.x(), 0))
+ self.setPolygon(QtGui.QPolygonF(pts))
+
+class TransferFunctionLine(QtGui.QGraphicsPolygonItem):
+
+ def __init__(self, point_left, point_right, parent=None):
+ assert point_right._scalar >= point_left._scalar
+ QtGui.QGraphicsPolygonItem.__init__(self, parent)
+ self._point_left = point_left
+ self._point_right = point_right
+ self._point_left._right_line = self
+ self._point_right._left_line = self
+ self.setup(1.0, 1.0)
+ self._sx = 1.0
+ self._sy = 1.0
+
+ def setup(self, sx, sy):
+ d = self._point_right._point - self._point_left._point
+ d_normal = QtCore.QPointF(d.y(), -d.x())
+ l = math.sqrt(d.x() * d.x() + d.y() * d.y())
+ if l != 0.0:
+ d_normal /= l
+ d_normal *= 0.010
+ d_normal.setX(d_normal.x() / sx)
+ d_normal.setY(d_normal.y() / sy)
+ ps = [self._point_left._point + d_normal,
+ self._point_right._point + d_normal,
+ self._point_right._point - d_normal,
+ self._point_left._point - d_normal]
+ self.setPolygon(QtGui.QPolygonF(ps))
+ self.setZValue(1.5)
+ # Gradient for filling
+ g = QtGui.QLinearGradient()
+ g.setStart(self._point_left._point)
+ g.setFinalStop(self._point_right._point)
+ g.setColorAt(0.0, self._point_left._color)
+ g.setColorAt(1.0, self._point_right._color)
+ self.setBrush(QtGui.QBrush(g))
+ # Gradient for outlining
+ g = QtGui.QLinearGradient()
+ g.setStart(self._point_left._point)
+ g.setFinalStop(self._point_right._point)
+ dark_pl = QtGui.QColor(self._point_left._color.red() * 0.5,
+ self._point_left._color.green() * 0.5,
+ self._point_left._color.blue() * 0.5)
+ dark_pr = QtGui.QColor(self._point_right._color.red() * 0.5,
+ self._point_right._color.green() * 0.5,
+ self._point_right._color.blue() * 0.5)
+ g.setColorAt(0.0, dark_pl)
+ g.setColorAt(1.0, dark_pr)
+ p = QtGui.QPen()
+ p.setBrush(QtGui.QBrush(g))
+ self.setPen(p)
+
+ def update_scale(self, sx, sy):
+ self._sx = sx
+ self._sy = sy
+ self.refresh()
+
+ def refresh(self):
+ self.setup(self._sx, self._sy)
+
+ def mouseDoubleClickEvent(self, event):
+ p = event.scenePos()
+ c_left = self._point_left._color
+ c_right = self._point_right._color
+ u = ((p.x() - self._point_left._point.x()) /
+ (self._point_right._point.x() - self._point_left._point.x()))
+ new_c = (u * c_right.redF() + (1-u) * c_left.redF(),
+ u * c_right.greenF() + (1-u) * c_left.greenF(),
+ u * c_right.blueF() + (1-u) * c_left.blueF())
+ new_point = TransferFunctionPoint(p.x(), p.y(), new_c)
+ new_line = TransferFunctionLine(new_point, self._point_right)
+ new_point._left_line = self
+ self._point_right = new_point
+ self.scene().addItem(new_line)
+ self.scene().addItem(new_point)
+ new_line.update_scale(self._point_left._sx,
+ self._point_left._sy)
+ new_point.update_scale(self._point_left._sx,
+ self._point_left._sy)
+ new_point.refresh()
+ self.refresh()
+
+ def mousePressEvent(self, event):
+ # This needs to be here, otherwise mouseDoubleClickEvent does
+ # not get called.
+ event.accept()
+
+
+##############################################################################
+# Scene, view, widget
+
+class TransferFunctionScene(QtGui.QGraphicsScene):
+
+ def __init__(self, tf, parent=None):
+ QtGui.QGraphicsScene.__init__(self, parent)
+ self._tf_items = []
+ poly = TransferFunctionPolygon()
+ poly.setup()
+ self._tf_poly = poly
+ self.addItem(poly)
+ self.create_tf_items(tf)
+ #current scale
+ self._sx = 1.0
+ self._sy = 1.0
+ # Add outlines
+ line_color = QtGui.QColor(200, 200, 200)
+ pen = QtGui.QPen(line_color)
+ ps = [QtCore.QPointF(0.0, 0.0),
+ QtCore.QPointF(1.0, 0.0),
+ QtCore.QPointF(1.0, 1.0),
+ QtCore.QPointF(0.0, 1.0)]
+ outline = QtGui.QPolygonF(ps)
+ self.addPolygon(outline, pen)
+
+ for i in xrange(51):
+ u = float(i) / 50.0
+ self.addLine(QtCore.QLineF(u, 0.0, u, 1.0), pen)
+ self.addLine(QtCore.QLineF(0.0, u, 1.0, u), pen)
+
+ def reset_transfer_function(self, tf):
+ self.create_tf_items(tf)
+ self.update_scale(self._sx, self._sy)
+ self._tf_poly.setup()
+
+ def removeItem(self, item):
+ if item in self._tf_items:
+ self._tf_items.remove(item)
+ QtGui.QGraphicsScene.removeItem(self, item)
+
+ def addItem(self, item):
+ # Ugly, but hey
+ if isinstance(item, TransferFunctionLine) or \
+ isinstance(item, TransferFunctionPoint):
+ self._tf_items.append(item)
+ QtGui.QGraphicsScene.addItem(self, item)
+
+ def create_tf_items(self, tf):
+ items = copy.copy(self._tf_items)
+ for item in items:
+ self.removeItem(item)
+ self._tf_items = []
+ if len(tf._pts) == 0:
+ pt_left = TransferFunctionPoint(0.0, 0.0, (0.0, 0.0, 0.0))
+ pt_right = TransferFunctionPoint(1.0, 0.0, (0.0, 0.0, 0.0))
+ line = TransferFunctionLine(pt_left, pt_right)
+
+ self.addItem(pt_left)
+ self.addItem(pt_right)
+ self.addItem(line)
+
+ else:
+ pts = [TransferFunctionPoint(*pt)
+ for pt in tf._pts]
+ lines = [TransferFunctionLine(pt_l, pt_r)
+ for (pt_l, pt_r) in zip(pts[:-1], pts[1:])]
+ for pt in pts:
+ self.addItem(pt)
+ for line in lines:
+ self.addItem(line)
+
+ def add_knot(self, scalar, opacity):
+ pass
+
+ def update_scale(self, sx, sy):
+ for item in self._tf_items:
+ item.update_scale(sx, sy)
+ self._sx = sx
+ self._sy = sy
+
+ def get_leftmost_point(self):
+ pt = None
+
+ for item in self._tf_items:
+ if hasattr(item, '_left_line') and not item._left_line:
+ pt = item
+ break
+ assert pt
+ return pt
+
+ def get_transfer_function(self):
+ result = TransferFunction()
+ pt = self.get_leftmost_point()
+ while 1:
+ pt.add_self_to_transfer_function(result)
+ if pt._right_line:
+ pt = pt._right_line._point_right
+ else:
+ break
+ return result
+
+class TransferFunctionView(QtGui.QGraphicsView):
+ def __init__(self, parent=None):
+ QtGui.QGraphicsView.__init__(self, parent)
+ self.setRenderHint(QtGui.QPainter.Antialiasing)
+ self.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ self.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+
+ def resizeEvent(self, event):
+ self.setMatrix(QtGui.QMatrix(event.size().width() / (10.0/9), 0,
+ 0, -event.size().height() / (10.0/9), 0, 0))
+ self.scene().update_scale(event.size().width()/(2000.0/9), event.size().height()/(2000.0/9))
+
+ def focusOutEvent(self, event):
+ self.parent().update_parent()
+ QtGui.QGraphicsView.focusOutEvent(self, event)
+
+default_tf = TransferFunction()
+default_tf.add_point(0.0, 0.0, (0.0, 0.0, 0.0))
+default_tf.add_point(1.0, 0.0, (0.0, 0.0, 0.0))
+
+class TransferFunctionWidget(QtGui.QWidget, ConstantWidgetMixin):
+
+ def __init__(self, param, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ if not param.strValue:
+ self._tf = copy.copy(default_tf)
+ else:
+ self._tf = pickle.loads(param.strValue.decode('hex'))
+ self._scene = TransferFunctionScene(self._tf, self)
+ layout = QtGui.QVBoxLayout()
+ self.setLayout(layout)
+ self._view = TransferFunctionView()
+ self._view.setScene(self._scene)
+ self._view.setMinimumSize(200,200)
+ self._view.show()
+ self._view.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ self._view.setMatrix(QtGui.QMatrix(180, 0, 0, -180, 0, 0))
+ self.setMinimumSize(200,200)
+ caption = QtGui.QLabel("Double-click on the line to add a point")
+ font = QtGui.QFont('Arial', 11)
+ font.setItalic(True)
+ caption.setFont(font)
+ layout.addWidget(self._view)
+ layout.addWidget(caption)
+
+ def contents(self):
+ return pickle.dumps(self._scene.get_transfer_function()).encode('hex')
+
+ def setContents(self, strValue, silent=True):
+ if not strValue:
+ self._tf = copy.copy(default_tf)
+ else:
+ self._tf = pickle.loads(strValue.decode('hex'))
+ self._scene.reset_transfer_function(self._tf)
+ if not silent:
+ self.update_parent()
+
+##############################################################################
+# Helper module to adjust range
+
+class vtkScaledTransferFunction(Module):
+
+ def compute(self):
+ tf = self.getInputFromPort('TransferFunction')
+ new_tf = copy.copy(tf)
+ if self.hasInputFromPort('Input'):
+ port = self.getInputFromPort('Input')
+ algo = port.vtkInstance.GetProducer()
+ output = algo.GetOutput(port.vtkInstance.GetIndex())
+ (new_tf._min_range, new_tf._max_range) = output.GetScalarRange()
+ elif self.hasInputFromPort('Dataset'):
+ algo = self.getInputFromPort('Dataset').vtkInstance
+ output = algo
+ (new_tf._min_range, new_tf._max_range) = output.GetScalarRange()
+ else:
+ (new_tf._min_range, new_tf._max_range) = self.getInputFromPort('Range')
+
+ self.setResult('TransferFunction', new_tf)
+
+string_conversion = staticmethod(lambda x: pickle.dumps(x).encode('hex'))
+conversion = staticmethod(lambda x: pickle.loads(x.decode('hex')))
+validation = staticmethod(lambda x: isinstance(x, TransferFunction))
+TransferFunctionConstant = new_constant('TransferFunction',
+ conversion,
+ default_tf,
+ validation,
+ TransferFunctionWidget)
+TransferFunctionConstant.translate_to_string = string_conversion
+
+##############################################################################
+
+def initialize():
+ init_constant(TransferFunctionConstant)
diff --git a/contrib/titan/vtk_parser.py b/contrib/titan/vtk_parser.py
new file mode 100644
index 0000000..c0479c9
--- /dev/null
+++ b/contrib/titan/vtk_parser.py
@@ -0,0 +1,528 @@
+# Author: Prabhu Ramachandran
+# Copyright (c) 2004, Enthought, Inc.
+# License: BSD Style.
+
+# Modified for VisTrails by the VisTrails team.
+
+"""This module parses the VTK methods, obtains the argument and return
+type information, and organizes them.
+
+"""
+
+pkgs = [ "titan.Antiword", "titan.Common", "titan.DataAnalysis",
+"titan.GMeans", "titan.HDF5", "titan.MPIDataAnalysis", "titan.MPITextAnalysis",
+"titan.MTGLGraphAnalysis", "titan.OWL",
+#"titan.StanfordNER",
+"titan.TextAnalysis", "titan.Trilinos", "titan.Web", "titan.XPDF"]
+titan2 = []
+for i in pkgs:
+ titan2.append(__import__(i))
+
+import vtk
+
+import re
+import class_tree
+import core.debug
+
+log = core.debug.log
+warning = core.debug.warning
+critical = core.debug.critical
+debug = core.debug.debug
+
+class VTKMethodParser(object):
+ """This class provides useful methods for parsing methods of a VTK
+ class or instance.
+
+ The class allows one to categorize the methods of the VTK class
+ and also obtain the method signatures in a form that is easy to
+ use. When the `parse` method is called, it in turn calls the
+ `_organize_methods` method. This method organizes the VTK methods
+ into different instance variables described in the following.
+ `self.toggle_meths` contains a dictionary of all the boolean
+ methods of the form <Value>On/Off. The dictionary keys are
+ strings with the <Value>'s and the value of each item is the
+ default value (0/1) of the item (the example below will clarify
+ this). `self.state_meths` contains a dictionary which collects
+ the Set<Prop>To<Value> type of methods. The key is the <Prop> and
+ the value is a list containing the different string <Value>'s and
+ their corresponding mapped value. The first value in these is the
+ default value of the <Prop>. `self.get_set_meths` will contain a
+ dictionary which collects all the methods of the form
+ Set/Get<Prop> that are not already specified in
+ `self.toggle_meths` or `self.state_meths`. The default value of
+ the Get<Prop> is stored. If the value accepted by the method has
+ a range (via the methods `Get<Prop>MinValue` and
+ `Get<Prop>MaxValue`), then that range is computed and stored.
+ `self.get_meths` stores the methods that are of the form
+ `Get<Prop>`. `self.other_meths` stores the remaining methods.
+ The parsing is quite fast. Parsing every class in the VTK API
+ takes a couple of seconds (on a Pentium III @ 450Mhz).
+
+ Here is an example::
+
+ >>> import vtk
+ >>> p = VTKMethodParser()
+ >>> p.parse(vtk.vtkProperty)
+ >>> print p.get_toggle_methods()
+ {'EdgeVisibility': 0, 'BackfaceCulling': 0, 'FrontfaceCulling': 0}
+ >>> print p.get_state_methods()['Representation']
+ [['Surface', 2], ['Points', 0], ['Surface', 2], ['Wireframe', 1]]
+ >>> print p.get_get_set_methods()['Opacity']
+ (1.0, (0.0, 1.0))
+ >>> print p.get_get_methods()
+ ['GetClassName']
+ >>> print p.get_other_methods()[:3]
+ ['BackfaceRender', 'DeepCopy', 'IsA']
+
+
+ The class also provides a method called `get_method_signature`
+ that obtains the Python method signature given the VTK method
+ object. Here is an example::
+
+ >>> import vtk
+ >>> p = VTKMethodParser()
+ >>> o = vtk.vtkProperty
+ >>> print p.get_method_signature(o.GetClassName)
+ [(['string'], None)]
+ >>> print p.get_method_signature(o.GetColor)[0]
+ ([('float', 'float', 'float')], None)
+ >>> print p.get_method_signature(o.GetColor)[1]
+ ([None], (('float', 'float', 'float'),))
+
+ The `get_method_signature` is fairly efficient and obtaining the
+ signature for every method in every class in the VTK API takes
+ around 6 seconds (on a Pentium III @ 450Mhz).
+
+ """
+
+ def __init__(self, use_tree=True):
+ """Initializes the object.
+
+ Parameters
+ ----------
+
+ - use_tree : `bool`
+
+ If True (default), use a ClassTree instance to obtain a
+ concrete subclass for an abstract base class. This is used
+ only to find the range and default values for some of the
+ methods. If False, no ClassTree instance is created.
+
+ This is optional because, creating a ClassTree is expensive.
+ The parser functionality can be very useful even without the
+ use of a ClassTree. For example, if one wants to save the
+ state of a VTK object one only needs to know the names of
+ the methods and not their default values, ranges etc. In
+ that case using a parser should be cheap.
+
+ """
+ # The ClassTree is needed to find an instantiable child class
+ # for an abstract VTK parent class. This instance is used to
+ # obtain the state values and the ranges of the arguments
+ # accepted by the Get/Set methods that have a
+ # Get<Prop>{MaxValue,MinValue} method.
+ if use_tree:
+ self._tree = class_tree.ClassTree(titan2)
+ self._tree.create()
+ else:
+ self._tree = None
+ self._state_patn = re.compile('To[A-Z0-9]')
+ self._initialize()
+
+ #################################################################
+ # 'VTKMethodParser' interface.
+ #################################################################
+
+ def parse(self, obj, no_warn=True):
+ """Parse the methods for a given VTK object/class.
+
+ Given a VTK class or object, this method parses the methods
+ and orgaizes them into useful categories. The categories and
+ their usage is documented in the documentation for the class.
+
+ Parameters
+ ----------
+
+ - obj : VTK class or instance
+
+ - no_warn : `bool` (default: True)
+
+ If True (default), it suppresses any warnings generated by
+ the VTK object when parsing the methods. This is safe to
+ use.
+
+ """
+ if not hasattr(obj, '__bases__'):
+ klass = obj.__class__
+ else:
+ klass = obj
+
+ methods = self.get_methods(klass)
+
+# Wendel
+ if no_warn:
+ # Save warning setting and shut it off before parsing.
+ warn = vtk.vtkObject.GetGlobalWarningDisplay()
+ if klass.__name__ <> 'vtkObject':
+ vtk.vtkObject.GlobalWarningDisplayOff()
+
+ self._organize_methods(klass, methods)
+
+ if no_warn:
+ # Reset warning status.
+ vtk.vtkObject.SetGlobalWarningDisplay(warn)
+
+ def get_methods(self, klass):
+ """Returns all the relevant methods of the given VTK class."""
+ methods = dir(klass)[:]
+ if hasattr(klass, '__members__'):
+ # Only VTK versions < 4.5 have these.
+ for m in klass.__members__:
+ methods.remove(m)
+
+ return methods
+
+ def get_toggle_methods(self):
+ """Returns a dictionary of the parsed <Value>On/Off methods
+ along with the default value.
+
+ """
+ return self.toggle_meths
+
+ def get_state_methods(self):
+ """Returns a dict of the parsed Set<Prop>To<Value>.
+
+ The keys are the <Prop> string with a list of the different
+ <Value> strings along with their corresponding value (if
+ obtainable). The first value is the default value of the
+ state.
+
+ """
+ return self.state_meths
+
+ def get_get_set_methods(self):
+ """Returns a dict of the parsed Get/Set<Value> methods.
+
+ The keys of the dict are the <Value> strings and contain a
+ two-tuple containing the default value (or None if it is not
+ obtainable for some reason) and a pair of numbers specifying
+ an acceptable range of values (or None if not obtainable).
+
+ """
+ return self.get_set_meths
+
+ def get_get_methods(self):
+ """Return a list of parsed Get<Value> methods.
+
+ All of these methods do NOT have a corresponding Set<Value>.
+
+ """
+ return self.get_meths
+
+ def get_other_methods(self):
+ """Return list of all other methods, that are not
+ categorizable.
+
+ """
+ return self.other_meths
+
+ def get_method_signature(self, method):
+ """Returns information on the Python method signature given
+ the VTK method.
+
+ The doc string of the given method object to get the method
+ signature. The method returns a list of tuples, each of which
+ contains 2 items, the first is a list representing the return
+ value the second represents the arguments to be passed to the
+ function. If the method supports different return values and
+ arguments, this function returns all of their signatures.
+
+ Parameters
+ ----------
+
+ - method : `method`
+
+ A VTK method object.
+
+ """
+ doc = method.__doc__
+ doc = doc[:doc.find('\n\n')]
+ sig = doc.split('\n')
+ sig = [x.strip() for x in sig]
+
+ # Remove all the C++ function signatures.
+ for i in sig[:]:
+ if i[:4] == 'C++:':
+ sig.remove(i)
+
+ # Remove the V.<method_name>
+ sig = [x.replace('V.' + method.__name__, '') for x in sig]
+
+ pat = re.compile(r'\b')
+
+ # Split into [return_value, arguments] after processing them.
+ tmp = list(sig)
+ sig = []
+ for i in tmp:
+ # Split to get return values.
+ x = i.split('->')
+ # Strip each part.
+ x = [y.strip() for y in x]
+
+ if len(x) == 1: # No return value
+ x = [None, x[0]]
+ else:
+ x.reverse()
+
+ ret, arg = x
+
+ # Remove leading and trailing parens for arguments.
+ arg = arg[1:-1]
+ if not arg:
+ arg = None
+ if arg and arg[-1] == ')':
+ arg = arg + ','
+
+ # Now quote the args and eval them. Easy!
+ if ret:
+ ret = eval(pat.sub('\"', ret))
+ if arg:
+ arg = eval(pat.sub('\"', arg))
+ if type(arg) == type('str'):
+ arg = [arg]
+
+ sig.append(([ret], arg))
+
+ return sig
+
+ def get_tree(self):
+ """Return the ClassTree instance used by this class."""
+ return self._tree
+
+ #################################################################
+ # Non-public interface.
+ #################################################################
+
+ def _initialize(self):
+ """Initializes the method categories."""
+ # Collects the <Value>On/Off methods.
+ self.toggle_meths = {}
+ # Collects the Set<Prop>To<Value> methods.
+ self.state_meths = {}
+ # Collects the Set/Get<Value> pairs.
+ self.get_set_meths = {}
+ # Collects the Get<Value> methods.
+ self.get_meths = []
+ # Collects all the remaining methods.
+ self.other_meths = []
+
+ def _organize_methods(self, klass, methods):
+ """Organizes the given methods of a VTK class into different
+ categories.
+
+ Parameters
+ ----------
+
+ - klass : A VTK class
+
+ - methods : `list` of `str`
+
+ A list of the methods to be categorized.
+
+ """
+ self._initialize()
+ meths = methods[:]
+ meths = self._find_toggle_methods(klass, meths)
+ meths = self._find_state_methods(klass, meths)
+ meths = self._find_get_set_methods(klass, meths)
+ meths = self._find_get_methods(klass, meths)
+ self.other_meths = [x for x in meths if '__' not in x]
+
+ def _remove_method(self, meths, method):
+ try:
+ meths.remove(method)
+ except ValueError:
+ pass
+
+ def _find_toggle_methods(self, klass, methods):
+ """Find/store methods of the form <Value>{On,Off} in the given
+ `methods`. Returns the remaining list of methods.
+
+ """
+ meths = methods[:]
+ tm = self.toggle_meths
+ for method in meths[:]:
+ if method[-2:] == 'On':
+ key = method[:-2]
+ if (key + 'Off') in meths and ('Get' + key) in meths:
+ tm[key] = None
+ meths.remove(method)
+ meths.remove(key + 'Off')
+ self._remove_method(meths, 'Set' + key)
+ self._remove_method(meths, 'Get' + key)
+ # get defaults
+ if tm:
+ obj = self._get_instance(klass)
+ if obj:
+ for key in tm:
+ try:
+ tm[key] = getattr(obj, 'Get%s'%key)()
+ except TypeError, e:
+ log("Type error during parsing: class %s will not expose method %s " % (klass.__name__, key))
+ except AttributeError, e:
+ log("Attribute error during parsing: class %s will not expose method %s " % (klass.__name__, key))
+ return meths
+
+ def _find_state_methods(self, klass, methods):
+ """Find/store methods of the form Set<Prop>To<Value> in the
+ given `methods`. Returns the remaining list of methods. The
+ method also computes the mapped value of the different
+ <Values>.
+
+ """
+ # These ignored ones are really not state methods.
+ ignore = ['SetUpdateExtentToWholeExtent']
+ meths = methods[:]
+ sm = self.state_meths
+ for method in meths[:]:
+ if method not in ignore and method[:3] == 'Set':
+ # Methods of form Set<Prop>To<Value>
+ match = self._state_patn.search(method)
+ # Second cond. ensures that this is not an accident.
+ if match and (('Get'+method[3:]) not in meths):
+ key = method[3:match.start()] # The <Prop> part.
+ if (('Get' + key) in methods):
+ val = method[match.start()+2:] # <Value> part.
+ meths.remove(method)
+ if sm.has_key(key):
+ sm[key].append([val, None])
+ else:
+ sm[key] = [[val, None]]
+ meths.remove('Get'+ key)
+ self._remove_method(meths, 'Set'+ key)
+ if ('Get' + key + 'MaxValue') in meths:
+ meths.remove('Get' + key + 'MaxValue')
+ meths.remove('Get' + key + 'MinValue')
+ try:
+ meths.remove('Get' + key + 'AsString')
+ except ValueError:
+ pass
+
+ # Find the values for each of the states, i.e. find that
+ # vtkProperty.SetRepresentationToWireframe() corresponds to
+ # vtkProperty.SetRepresentation(1).
+ if sm:
+ obj = self._get_instance(klass)
+ if obj:
+ for key, values in sm.items():
+ default = getattr(obj, 'Get%s'%key)()
+ for x in values[:]:
+ try:
+ getattr(obj, 'Set%sTo%s'%(key, x[0]))()
+ except:
+ continue
+ val = getattr(obj, 'Get%s'%key)()
+ x[1] = val
+ if val == default:
+ values.insert(0, [x[0], val])
+ return meths
+
+ def _find_get_set_methods(self, klass, methods):
+ """Find/store methods of the form {Get,Set}Prop in the given
+ `methods` and returns the remaining list of methods.
+
+ Note that it makes sense to call this *after*
+ `_find_state_methods` is called in order to avoid incorrect
+ duplication. This method also computes the default value and
+ the ranges of the arguments (when possible) by using the
+ Get<Prop>{MaxValue,MinValue} methods.
+
+ """
+ meths = methods[:]
+ gsm = self.get_set_meths
+
+ for method in meths[:]:
+ # Methods of the Set/Get form.
+ if method in ['Get', 'Set']:
+ # This occurs with the vtkInformation class.
+ continue
+ elif (method[:3] == 'Set') and ('Get' + method[3:]) in methods:
+ key = method[3:]
+ meths.remove('Set' + key)
+ meths.remove('Get' + key)
+ if ('Get' + key + 'MaxValue') in meths:
+ meths.remove('Get' + key + 'MaxValue')
+ meths.remove('Get' + key + 'MinValue')
+ gsm[key] = 1
+ else:
+ gsm[key] = None
+
+ # Find the default and range of the values.
+ if gsm:
+ obj = self._get_instance(klass)
+ if obj:
+ klass_name = klass.__name__
+ for key, value in gsm.items():
+ if klass_name == 'vtkPolyData':
+ # Evil hack, this class segfaults!
+ default = None
+ else:
+ try:
+ default = getattr(obj, 'Get%s'%key)()
+ except TypeError:
+ default = None
+ if value:
+ low = getattr(obj, 'Get%sMinValue'%key)()
+ high = getattr(obj, 'Get%sMaxValue'%key)()
+ gsm[key] = (default, (low, high))
+ else:
+ gsm[key] = (default, None)
+ else:
+ # We still might have methods that have a default range.
+ for key, value in gsm.items():
+ if value == 1:
+ gsm[key] = None
+
+ return meths
+
+ def _find_get_methods(self, klass, methods):
+ """Find/store methods of the form Get<Value> in the given
+ `methods` and returns the remaining list of methods.
+
+ """
+ meths = methods[:]
+ gm = self.get_meths
+ for method in meths[:]:
+ if method == 'Get':
+ # Occurs with vtkInformation
+ continue
+ elif method[:3] == 'Get':
+ gm.append(method)
+ meths.remove(method)
+ return meths
+
+ def _get_instance(self, klass):
+ """Given a VTK class, `klass`, returns an instance of the
+ class.
+
+ If the class is abstract, it uses the class tree to return an
+ instantiable subclass. This is necessary to get the values of
+ the 'state' methods and the ranges for the Get/Set methods.
+
+ """
+ obj = None
+ try:
+ obj = klass()
+ except TypeError:
+ if self._tree:
+ t = self._tree
+ n = t.get_node(klass.__name__)
+# Wendel
+ if n == None:
+ return False
+ for c in n.children:
+ obj = self._get_instance(t.get_class(c.name))
+ if obj:
+ break
+ return obj
+
diff --git a/contrib/titan/vtkcell.py b/contrib/titan/vtkcell.py
new file mode 100644
index 0000000..429c77a
--- /dev/null
+++ b/contrib/titan/vtkcell.py
@@ -0,0 +1,1094 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+################################################################################
+# File QVTKWidget.py
+# File for displaying a vtkRenderWindow in a Qt's QWidget ported from
+# VTK/GUISupport/QVTK. Combine altogether to a single class: QVTKWidget
+################################################################################
+import vtk
+from PyQt4 import QtCore, QtGui
+import sip
+from core import system
+from core.modules.module_registry import get_module_registry
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+import vtkcell_rc
+import gc
+from gui.qt import qt_super
+import core.db.action
+from core.vistrail.action import Action
+from core.vistrail.port import Port
+from core.vistrail import module
+from core.vistrail import connection
+from core.vistrail.module_function import ModuleFunction
+from core.vistrail.module_param import ModuleParam
+from core.vistrail.location import Location
+from core.modules.vistrails_module import ModuleError
+import copy
+
+################################################################################
+
+class VTKCell(SpreadsheetCell):
+ """
+ VTKCell is a VisTrails Module that can display vtkRenderWindow inside a cell
+
+ """
+
+ def __init__(self):
+ SpreadsheetCell.__init__(self)
+ self.cellWidget = None
+
+ def compute(self):
+ """ compute() -> None
+ Dispatch the vtkRenderer to the actual rendering widget
+ """
+ renderers = self.forceGetInputListFromPort('AddRenderer')
+ renderViews = self.forceGetInputListFromPort('SetRenderView')
+ if len(renderViews)>1:
+ raise ModuleError(self, 'There can only be one vtkRenderView '
+ 'per cell')
+ if len(renderViews)==1 and len(renderers)>0:
+ raise ModuleError(self, 'Cannot set both vtkRenderView '
+ 'and vtkRenderer to a cell')
+ renderView = self.forceGetInputFromPort('SetRenderView')
+ iHandlers = self.forceGetInputListFromPort('InteractionHandler')
+ iStyle = self.forceGetInputFromPort('InteractorStyle')
+ picker = self.forceGetInputFromPort('AddPicker')
+ self.cellWidget = self.displayAndWait(QVTKWidget, (renderers, renderView, iHandlers, iStyle, picker))
+
+AsciiToKeySymTable = ( None, None, None, None, None, None, None,
+ None, None,
+ "Tab", None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None,
+ "space", "exclam", "quotedbl", "numbersign",
+ "dollar", "percent", "ampersand", "quoteright",
+ "parenleft", "parenright", "asterisk", "plus",
+ "comma", "minus", "period", "slash",
+ "0", "1", "2", "3", "4", "5", "6", "7",
+ "8", "9", "colon", "semicolon", "less", "equal",
+ "greater", "question",
+ "at", "A", "B", "C", "D", "E", "F", "G",
+ "H", "I", "J", "K", "L", "M", "N", "O",
+ "P", "Q", "R", "S", "T", "U", "V", "W",
+ "X", "Y", "Z", "bracketleft",
+ "backslash", "bracketright", "asciicircum",
+ "underscore",
+ "quoteleft", "a", "b", "c", "d", "e", "f", "g",
+ "h", "i", "j", "k", "l", "m", "n", "o",
+ "p", "q", "r", "s", "t", "u", "v", "w",
+ "x", "y", "z", "braceleft", "bar", "braceright",
+ "asciitilde", "Delete",
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None)
+
+class QVTKWidget(QCellWidget):
+ """
+ QVTKWidget is the actual rendering widget that can display
+ vtkRenderer inside a Qt QWidget
+
+ """
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QVTKWidget(parent: QWidget, f: WindowFlags) -> QVTKWidget
+ Initialize QVTKWidget with a toolbar with its own device
+ context
+
+ """
+ QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
+
+ self.interacting = None
+ self.mRenWin = None
+ self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
+ self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
+ self.setMouseTracking(True)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding))
+ self.toolBarType = QVTKWidgetToolBar
+ self.iHandlers = []
+ self.setAnimationEnabled(True)
+ self.renderer_maps = {}
+
+ def removeObserversFromInteractorStyle(self):
+ """ removeObserversFromInteractorStyle() -> None
+ Remove all python binding from interactor style observers for
+ safely freeing the cell
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.RemoveObservers("InteractionEvent")
+ style.RemoveObservers("EndPickEvent")
+ style.RemoveObservers("CharEvent")
+ style.RemoveObservers("MouseWheelForwardEvent")
+ style.RemoveObservers("MouseWheelBackwardEvent")
+
+ def addObserversToInteractorStyle(self):
+ """ addObserversToInteractorStyle() -> None
+ Assign observer to the current interactor style
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.AddObserver("InteractionEvent", self.interactionEvent)
+ style.AddObserver("EndPickEvent", self.interactionEvent)
+ style.AddObserver("CharEvent", self.charEvent)
+ style.AddObserver("MouseWheelForwardEvent", self.interactionEvent)
+ style.AddObserver("MouseWheelBackwardEvent", self.interactionEvent)
+
+ def deleteLater(self):
+ """ deleteLater() -> None
+ Make sure to free render window resource when
+ deallocating. Overriding PyQt deleteLater to free up
+ resources
+
+ """
+ self.renderer_maps = {}
+ for ren in self.getRendererList():
+ self.mRenWin.RemoveRenderer(ren)
+
+ self.removeObserversFromInteractorStyle()
+
+ self.updateContents(([], None, [], None, None))
+
+ self.SetRenderWindow(None)
+
+ QCellWidget.deleteLater(self)
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple)
+ Updates the cell contents with new vtkRenderer
+
+ """
+ renWin = self.GetRenderWindow()
+ for iHandler in self.iHandlers:
+ if iHandler.observer:
+ iHandler.observer.vtkInstance.SetInteractor(None)
+ iHandler.clear()
+
+ # Remove old renderers first
+ oldRenderers = self.getRendererList()
+ for renderer in oldRenderers:
+ renWin.RemoveRenderer(renderer)
+ renderer.SetRenderWindow(None)
+ del oldRenderers
+
+ (renderers, renderView, self.iHandlers, iStyle, picker) = inputPorts
+ if renderView:
+ renderView.vtkInstance.SetupRenderWindow(renWin)
+ renderers = [renderView.vtkInstance.GetRenderer()]
+ self.renderer_maps = {}
+ for renderer in renderers:
+ if renderView==None:
+ vtkInstance = renderer.vtkInstance
+ renWin.AddRenderer(vtkInstance)
+ self.renderer_maps[vtkInstance] = renderer.moduleInfo['moduleId']
+ else:
+ vtkInstance = renderer
+ if hasattr(vtkInstance, 'IsActiveCameraCreated'):
+ if not vtkInstance.IsActiveCameraCreated():
+ vtkInstance.ResetCamera()
+ else:
+ vtkInstance.ResetCameraClippingRange()
+
+ iren = renWin.GetInteractor()
+ if picker:
+ iren.SetPicker(picker.vtkInstance)
+
+ # Update interactor style
+ self.removeObserversFromInteractorStyle()
+ if renderView==None:
+ if iStyle==None:
+ iStyleInstance = vtk.vtkInteractorStyleTrackballCamera()
+ else:
+ iStyleInstance = iStyle.vtkInstance
+ iren.SetInteractorStyle(iStyleInstance)
+ self.addObserversToInteractorStyle()
+
+ for iHandler in self.iHandlers:
+ if iHandler.observer:
+ iHandler.observer.vtkInstance.SetInteractor(iren)
+ renWin.Render()
+
+ # Capture window into history for playback
+ # Call this at the end to capture the image after rendering
+ QCellWidget.updateContents(self, inputPorts)
+
+ def GetRenderWindow(self):
+ """ GetRenderWindow() -> vtkRenderWindow
+ Return the associated vtkRenderWindow
+
+ """
+ if not self.mRenWin:
+ win = vtk.vtkRenderWindow()
+ win.DoubleBufferOn()
+ self.SetRenderWindow(win)
+ del win
+
+ return self.mRenWin
+
+ def SetRenderWindow(self,w):
+ """ SetRenderWindow(w: vtkRenderWindow)
+ Set a new render window to QVTKWidget and initialize the
+ interactor as well
+
+ """
+ if w == self.mRenWin:
+ return
+
+ if self.mRenWin:
+ if system.systemType!='Linux':
+ self.mRenWin.SetInteractor(None)
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+
+ self.mRenWin = w
+
+ if self.mRenWin:
+ self.mRenWin.Register(None)
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+ if system.systemType=='Linux':
+ try:
+ vp = '_%s_void_p' % (hex(int(QtGui.QX11Info.display()))[2:])
+ except TypeError:
+ #This was change for PyQt4.2
+ if isinstance(QtGui.QX11Info.display(),QtGui.Display):
+ display = sip.unwrapinstance(QtGui.QX11Info.display())
+ vp = '_%s_void_p' % (hex(display)[2:])
+ self.mRenWin.SetDisplayId(vp)
+ self.resizeWindow(1,1)
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ if not self.mRenWin.GetInteractor():
+ iren = vtk.vtkRenderWindowInteractor()
+ if system.systemType=='Darwin':
+ iren.InstallMessageProcOff()
+ iren.SetRenderWindow(self.mRenWin)
+ iren.Initialize()
+ if system.systemType=='Linux':
+ system.XDestroyWindow(self.mRenWin.GetGenericDisplayId(),
+ self.mRenWin.GetGenericWindowId())
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ self.resizeWindow(self.width(), self.height())
+ self.mRenWin.SetPosition(self.x(), self.y())
+
+ def GetInteractor(self):
+ """ GetInteractor() -> vtkInteractor
+ Return the vtkInteractor control this QVTKWidget
+ """
+ return self.GetRenderWindow().GetInteractor()
+
+ def event(self, e):
+ """ event(e: QEvent) -> depends on event type
+ Process window and interaction events
+
+ """
+ if e.type()==QtCore.QEvent.ParentAboutToChange:
+ if self.mRenWin:
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+ else:
+ if e.type()==QtCore.QEvent.ParentChange:
+ if self.mRenWin:
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ if QtCore.QObject.event(self,e):
+ return 1
+
+ if e.type() == QtCore.QEvent.KeyPress:
+ self.keyPressEvent(e)
+ if e.isAccepted():
+ return e.isAccepted()
+
+ return qt_super(QVTKWidget, self).event(e)
+
+ # return QtGui.QWidget.event(self,e)
+ # Was this right? Wasn't this supposed to be QCellWidget.event()?
+
+ def resizeWindow(self, width, height):
+ """ resizeWindow(width: int, height: int) -> None
+ Work around vtk bugs for resizing window
+
+ """
+ ########################################################
+ # VTK - BUGGGGGGGGG - GRRRRRRRRR
+ # This is a 'bug' in vtkWin32OpenGLRenderWindow(.cxx)
+ # If a render window is mapped to screen, the actual
+ # window size is the client area of the window in Win32.
+ # However, this real window size is only updated through
+ # vtkWin32OpenGLRenderWindow::GetSize(). So this has to
+ # be called here to get the cell size correctly. This
+ # invalidates the condition in the next SetSize().
+ # We can use self.mRenWin.SetSize(0,0) here but it will
+ # cause flickering and decrease performance!
+ # SetPosition(curX,curY) also works here but slower.
+ self.mRenWin.GetSize()
+
+ self.mRenWin.SetSize(width, height)
+ if self.mRenWin.GetInteractor():
+ self.mRenWin.GetInteractor().SetSize(width, height)
+
+ def resizeEvent(self, e):
+ """ resizeEvent(e: QEvent) -> None
+ Re-adjust the vtkRenderWindow size then QVTKWidget resized
+
+ """
+ qt_super(QVTKWidget, self).resizeEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.resizeWindow(self.width(), self.height())
+ self.mRenWin.Render()
+
+ def moveEvent(self,e):
+ """ moveEvent(e: QEvent) -> None
+ Echo the move event into vtkRenderWindow
+
+ """
+ qt_super(QVTKWidget, self).moveEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.mRenWin.SetPosition(self.x(),self.y())
+
+ def paintEvent(self, e):
+ """ paintEvent(e: QPaintEvent) -> None
+ Paint the QVTKWidget with vtkRenderWindow
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ if hasattr(self.mRenWin, 'UpdateGLRegion'):
+ self.mRenWin.UpdateGLRegion()
+ self.mRenWin.Render()
+
+ def SelectActiveRenderer(self,iren):
+ """ SelectActiveRenderer(iren: vtkRenderWindowIteractor) -> None
+ Only make the vtkRenderer below the mouse cursor active
+
+ """
+ epos = iren.GetEventPosition()
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ ren.SetInteractive(ren.IsInViewport(epos[0], epos[1]))
+
+ def mousePressEvent(self,e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ isDoubleClick = e.type()==QtCore.QEvent.MouseButtonDblClick
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ ctrl,
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),
+ isDoubleClick,
+ None)
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonPressEvent",
+ QtCore.Qt.MidButton:"MiddleButtonPressEvent",
+ QtCore.Qt.RightButton:"RightButtonPressEvent"}
+
+ self.SelectActiveRenderer(iren)
+
+ if ctrl:
+ e.ignore()
+ return
+
+ self.interacting = self.getActiveRenderer(iren)
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def mouseMoveEvent(self,e):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0), 0, None)
+
+ iren.InvokeEvent("MouseMoveEvent")
+
+ def enterEvent(self,e):
+ """ enterEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("EnterEvent")
+
+ def leaveEvent(self,e):
+ """ leaveEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("LeaveEvent")
+
+ def mouseReleaseEvent(self,e):
+ """ mouseReleaseEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonReleaseEvent",
+ QtCore.Qt.MidButton:"MiddleButtonReleaseEvent",
+ QtCore.Qt.RightButton:"RightButtonReleaseEvent"}
+
+ self.interacting = None
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def keyPressEvent(self,e):
+ """ keyPressEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if e.text().length()>0:
+ ascii_key = e.text().toLatin1()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q', 'e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl,shift,ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyPressEvent")
+
+ if ascii_key:
+ iren.InvokeEvent("CharEvent")
+
+
+ def keyReleaseEvent(self,e):
+ """ keyReleaseEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if e.text().length()>0:
+ ascii_key = e.text().toLatin1()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q','e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl, shift, ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyReleaseEvent")
+
+ def wheelEvent(self,e):
+ """ wheelEvent(e: QWheelEvent) -> None
+ Zoom in/out while scrolling the mouse
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ self.SelectActiveRenderer(iren)
+
+ if e.delta()>0:
+ iren.InvokeEvent("MouseWheelForwardEvent")
+ else:
+ iren.InvokeEvent("MouseWheelBackwardEvent")
+
+ def focusInEvent(self,e):
+ """ focusInEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def focusOutEvent(self,e):
+ """ focusOutEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def contextMenuEvent(self,e):
+ """ contextMenuEvent(e: QContextMenuEvent) -> None
+ Make sure to get the right mouse position for the context menu
+ event, i.e. also the right click
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = int(e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = int(e.modifiers()&QtCore.Qt.ShiftModifier)
+ iren.SetEventInformationFlipY(e.x(),e.y(),ctrl,shift,chr(0),0,None)
+ iren.InvokeEvent("ContextMenuEvent")
+
+ def ascii_to_key_sym(self,i):
+ """ ascii_to_key_sym(i: int) -> str
+ Convert ASCII code into key name
+
+ """
+ global AsciiToKeySymTable
+ return AsciiToKeySymTable[i]
+
+ def qt_key_to_key_sym(self,i):
+ """ qt_key_to_key_sym(i: QtCore.Qt.Keycode) -> str
+ Convert Qt key code into key name
+
+ """
+ handler = {QtCore.Qt.Key_Backspace:"BackSpace",
+ QtCore.Qt.Key_Tab:"Tab",
+ QtCore.Qt.Key_Backtab:"Tab",
+ QtCore.Qt.Key_Return:"Return",
+ QtCore.Qt.Key_Enter:"Return",
+ QtCore.Qt.Key_Shift:"Shift_L",
+ QtCore.Qt.Key_Control:"Control_L",
+ QtCore.Qt.Key_Alt:"Alt_L",
+ QtCore.Qt.Key_Pause:"Pause",
+ QtCore.Qt.Key_CapsLock:"Caps_Lock",
+ QtCore.Qt.Key_Escape:"Escape",
+ QtCore.Qt.Key_Space:"space",
+ QtCore.Qt.Key_End:"End",
+ QtCore.Qt.Key_Home:"Home",
+ QtCore.Qt.Key_Left:"Left",
+ QtCore.Qt.Key_Up:"Up",
+ QtCore.Qt.Key_Right:"Right",
+ QtCore.Qt.Key_Down:"Down",
+ QtCore.Qt.Key_SysReq:"Snapshot",
+ QtCore.Qt.Key_Insert:"Insert",
+ QtCore.Qt.Key_Delete:"Delete",
+ QtCore.Qt.Key_Help:"Help",
+ QtCore.Qt.Key_0:"0",
+ QtCore.Qt.Key_1:"1",
+ QtCore.Qt.Key_2:"2",
+ QtCore.Qt.Key_3:"3",
+ QtCore.Qt.Key_4:"4",
+ QtCore.Qt.Key_5:"5",
+ QtCore.Qt.Key_6:"6",
+ QtCore.Qt.Key_7:"7",
+ QtCore.Qt.Key_8:"8",
+ QtCore.Qt.Key_9:"9",
+ QtCore.Qt.Key_A:"a",
+ QtCore.Qt.Key_B:"b",
+ QtCore.Qt.Key_C:"c",
+ QtCore.Qt.Key_D:"d",
+ QtCore.Qt.Key_E:"e",
+ QtCore.Qt.Key_F:"f",
+ QtCore.Qt.Key_G:"g",
+ QtCore.Qt.Key_H:"h",
+ QtCore.Qt.Key_I:"i",
+ QtCore.Qt.Key_J:"h",
+ QtCore.Qt.Key_K:"k",
+ QtCore.Qt.Key_L:"l",
+ QtCore.Qt.Key_M:"m",
+ QtCore.Qt.Key_N:"n",
+ QtCore.Qt.Key_O:"o",
+ QtCore.Qt.Key_P:"p",
+ QtCore.Qt.Key_Q:"q",
+ QtCore.Qt.Key_R:"r",
+ QtCore.Qt.Key_S:"s",
+ QtCore.Qt.Key_T:"t",
+ QtCore.Qt.Key_U:"u",
+ QtCore.Qt.Key_V:"v",
+ QtCore.Qt.Key_W:"w",
+ QtCore.Qt.Key_X:"x",
+ QtCore.Qt.Key_Y:"y",
+ QtCore.Qt.Key_Z:"z",
+ QtCore.Qt.Key_Asterisk:"asterisk",
+ QtCore.Qt.Key_Plus:"plus",
+ QtCore.Qt.Key_Minus:"minus",
+ QtCore.Qt.Key_Period:"period",
+ QtCore.Qt.Key_Slash:"slash",
+ QtCore.Qt.Key_F1:"F1",
+ QtCore.Qt.Key_F2:"F2",
+ QtCore.Qt.Key_F3:"F3",
+ QtCore.Qt.Key_F4:"F4",
+ QtCore.Qt.Key_F5:"F5",
+ QtCore.Qt.Key_F6:"F6",
+ QtCore.Qt.Key_F7:"F7",
+ QtCore.Qt.Key_F8:"F8",
+ QtCore.Qt.Key_F9:"F9",
+ QtCore.Qt.Key_F10:"F10",
+ QtCore.Qt.Key_F11:"F11",
+ QtCore.Qt.Key_F12:"F12",
+ QtCore.Qt.Key_F13:"F13",
+ QtCore.Qt.Key_F14:"F14",
+ QtCore.Qt.Key_F15:"F15",
+ QtCore.Qt.Key_F16:"F16",
+ QtCore.Qt.Key_F17:"F17",
+ QtCore.Qt.Key_F18:"F18",
+ QtCore.Qt.Key_F19:"F19",
+ QtCore.Qt.Key_F20:"F20",
+ QtCore.Qt.Key_F21:"F21",
+ QtCore.Qt.Key_F22:"F22",
+ QtCore.Qt.Key_F23:"F23",
+ QtCore.Qt.Key_F24:"F24",
+ QtCore.Qt.Key_NumLock:"Num_Lock",
+ QtCore.Qt.Key_ScrollLock:"Scroll_Lock"}
+ if i in handler:
+ return handler[i]
+ else:
+ return "None"
+
+ def getRendererList(self):
+ """ getRendererList() -> list
+ Return a list of vtkRenderer running in this QVTKWidget
+ """
+ result = []
+ renWin = self.GetRenderWindow()
+ renderers = renWin.GetRenderers()
+ renderers.InitTraversal()
+ for i in xrange(renderers.GetNumberOfItems()):
+ result.append(renderers.GetNextItem())
+ return result
+
+ def getActiveRenderer(self, iren):
+ """ getActiveRenderer(iren: vtkRenderWindowwInteractor) -> vtkRenderer
+ Return the active vtkRenderer under mouse
+
+ """
+ epos = list(iren.GetEventPosition())
+ if epos[1]<0:
+ epos[1] = -epos[1]
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ if ren.IsInViewport(epos[0], epos[1]):
+ return ren
+ return None
+
+ def findSheetTabWidget(self):
+ """ findSheetTabWidget() -> QTabWidget
+ Find and return the sheet tab widget
+
+ """
+ p = self.parent()
+ while p:
+ if hasattr(p, 'isSheetTabWidget'):
+ if p.isSheetTabWidget()==True:
+ return p
+ p = p.parent()
+ return None
+
+ def getRenderersInCellList(self, sheet, cells):
+ """ isRendererIn(sheet: spreadsheet.StandardWidgetSheet,
+ cells: [(int,int)]) -> bool
+ Get the list of renderers in side a list of (row, column)
+ cells.
+
+ """
+ rens = []
+ for (row, col) in cells:
+ cell = sheet.getCell(row, col)
+ if hasattr(cell, 'getRendererList'):
+ rens += cell.getRendererList()
+ return rens
+
+ def getSelectedCellWidgets(self):
+ sheet = self.findSheetTabWidget()
+ if sheet:
+ iren = self.mRenWin.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ cells = sheet.getSelectedLocations()
+ if (ren in self.getRenderersInCellList(sheet, cells)):
+ return [sheet.getCell(row, col)
+ for (row, col) in cells
+ if hasattr(sheet.getCell(row, col),
+ 'getRendererList')]
+ return []
+
+ def interactionEvent(self, istyle, name):
+ """ interactionEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure interactions sync across selected renderers
+
+ """
+ if name=='MouseWheelForwardEvent':
+ istyle.OnMouseWheelForward()
+ if name=='MouseWheelBackwardEvent':
+ istyle.OnMouseWheelBackward()
+ ren = self.interacting
+ if not ren:
+ ren = self.getActiveRenderer(istyle.GetInteractor())
+ if ren:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ for cell in self.getSelectedCellWidgets():
+ if cell!=self and hasattr(cell, 'getRendererList'):
+ rens = cell.getRendererList()
+ for r in rens:
+ if r!=ren:
+ dcam = r.GetActiveCamera()
+ dcam.SetPosition(cpos)
+ dcam.SetFocalPoint(cfol)
+ dcam.SetViewUp(cup)
+ r.ResetCameraClippingRange()
+ cell.update()
+
+ def charEvent(self, istyle, name):
+ """ charEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure key presses also sync across selected renderers
+
+ """
+ iren = istyle.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ keyCode = iren.GetKeyCode()
+ if keyCode in ['w','W','s','S','r','R','p','P']:
+ for cell in self.getSelectedCellWidgets():
+ if hasattr(cell, 'GetInteractor'):
+ selectedIren = cell.GetInteractor()
+ selectedIren.SetKeyCode(keyCode)
+ selectedIren.GetInteractorStyle().OnChar()
+ selectedIren.Render()
+ istyle.OnChar()
+
+ def saveToPNG(self, filename):
+ """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
+
+ Save the current widget contents to an image file. If
+ str==None, then it returns the vtkUnsignedCharArray containing
+ the PNG image. Otherwise, the filename is returned.
+
+ """
+ w2i = vtk.vtkWindowToImageFilter()
+ w2i.ReadFrontBufferOff()
+ w2i.SetInput(self.mRenWin)
+ # Render twice to get a clean image on the back buffer
+ self.mRenWin.Render()
+ self.mRenWin.Render()
+ w2i.Update()
+ writer = vtk.vtkPNGWriter()
+ writer.SetInputConnection(w2i.GetOutputPort())
+ if filename!=None:
+ writer.SetFileName(filename)
+ else:
+ writer.WriteToMemoryOn()
+ writer.Write()
+ if filename:
+ return filename
+ else:
+ return writer.GetResult()
+
+ def captureWindow(self):
+ """ captureWindow() -> None
+ Capture the window contents to file
+
+ """
+ fn = QtGui.QFileDialog.getSaveFileName(None,
+ "Save file as...",
+ "screenshot.png",
+ "Images (*.png)")
+ if fn.isNull():
+ return
+ self.saveToPNG(str(fn))
+
+ def grabWindowPixmap(self):
+ """ grabWindowImage() -> QPixmap
+ Widget special grabbing function
+
+ """
+ uchar = self.saveToPNG(None)
+
+ ba = QtCore.QByteArray()
+ buf = QtCore.QBuffer(ba)
+ buf.open(QtCore.QIODevice.WriteOnly)
+ for i in xrange(uchar.GetNumberOfTuples()):
+ c = uchar.GetValue(i)
+ buf.putChar(chr(c))
+ buf.close()
+
+ pixmap = QtGui.QPixmap()
+ pixmap.loadFromData(ba, 'PNG')
+ return pixmap
+
+ def dumpToFile(self, filename):
+ """dumpToFile() -> None
+ Dumps itself as an image to a file, calling saveToPNG
+ """
+ self.saveToPNG(filename)
+
+class QVTKWidgetCapture(QtGui.QAction):
+ """
+ QVTKWidgetCapture is the action to capture the vtk rendering
+ window to an image
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKWidgetCapture(parent: QWidget) -> QVTKWidgetCapture
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/camera.png"),
+ "&Capture image to file",
+ parent)
+ self.setStatusTip("Capture the rendered image to a file")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ cellWidget.captureWindow()
+
+class QVTKWidgetSaveCamera(QtGui.QAction):
+ """
+ QVTKWidgetSaveCamera is the action to capture the current camera
+ of the vtk renderers and save it back to the pipeline
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKWidgetSaveCamera(parent: QWidget) -> QVTKWidgetSaveCamera
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ "Save &Camera",
+ parent)
+ self.setStatusTip("Save current camera views to the pipeline")
+
+ def setCamera(self, controller):
+ ops = []
+ pipeline = controller.current_pipeline
+ cellWidget = self.toolBar.getSnappedWidget()
+ renderers = cellWidget.getRendererList()
+ for ren in renderers:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ rendererId = cellWidget.renderer_maps[ren]
+ # Looking for SetActiveCamera()
+ camera = None
+ renderer = pipeline.modules[rendererId]
+ for c in pipeline.connections.values():
+ if c.destination.moduleId==rendererId:
+ if c.destination.name=='SetActiveCamera':
+ camera = pipeline.modules[c.source.moduleId]
+ break
+
+ if not camera:
+ # Create camera
+ vtk_package = 'edu.utah.sci.vistrails.vtk'
+ camera = controller.create_module(vtk_package, 'vtkCamera', '',
+ 0.0, 0.0)
+ ops.append(('add', camera))
+
+ # Connect camera to renderer
+ camera_conn = controller.create_connection(camera, 'self',
+ renderer,
+ 'SetActiveCamera')
+ ops.append(('add', camera_conn))
+ # update functions
+ def convert_to_str(arglist):
+ new_arglist = []
+ for arg in arglist:
+ new_arglist.append(str(arg))
+ return new_arglist
+ functions = [('SetPosition', convert_to_str(cpos)),
+ ('SetFocalPoint', convert_to_str(cfol)),
+ ('SetViewUp', convert_to_str(cup))]
+ ops.extend(controller.update_functions_ops(camera, functions))
+
+ action = core.db.action.create_action(ops)
+ controller.add_new_action(action)
+ controller.perform_action(action)
+ controller.select_latest_version()
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ visApp = QtCore.QCoreApplication.instance()
+ if hasattr(visApp, 'builderWindow'):
+ builderWindow = visApp.builderWindow
+ if builderWindow:
+ info = self.toolBar.sheet.getCellPipelineInfo(
+ self.toolBar.row, self.toolBar.col)
+ if info:
+ info = info[0]
+ viewManager = builderWindow.viewManager
+ view = viewManager.ensureVistrail(info['locator'])
+ if view:
+ controller = view.controller
+ controller.change_selected_version(info['version'])
+ self.setCamera(controller)
+
+
+class QVTKWidgetToolBar(QCellToolBar):
+ """
+ QVTKWidgetToolBar derives from QCellToolBar to give the VTKCell
+ a customizable toolbar
+
+ """
+ def createToolBar(self):
+ """ createToolBar() -> None
+ This will get call initiallly to add customizable widgets
+
+ """
+ self.appendAction(QVTKWidgetCapture(self))
+ self.addAnimationButtons()
+ self.appendAction(QVTKWidgetSaveCamera(self))
+
+def registerSelf():
+ """ registerSelf() -> None
+ Registry module with the registry
+ """
+ identifier = 'edu.utah.sci.vistrails.vtk'
+ registry = get_module_registry()
+ registry.add_module(VTKCell)
+ registry.add_input_port(VTKCell, "Location", CellLocation)
+ import core.debug
+ for (port,module) in [("AddRenderer",'vtkRenderer'),
+ ("SetRenderView",'vtkRenderView'),
+ ("InteractionHandler",'vtkInteractionHandler'),
+ ("InteractorStyle", 'vtkInteractorStyle'),
+ ("AddPicker",'vtkAbstractPicker')]:
+ try:
+ registry.add_input_port(VTKCell, port,'(%s:%s)'%(identifier,module))
+
+ except Exception, e:
+ core.debug.warning(str(e))
+
+ registry.add_output_port(VTKCell, "self", VTKCell)
diff --git a/contrib/titan/vtkcell_rc.py b/contrib/titan/vtkcell_rc.py
new file mode 100644
index 0000000..8aa8cbf
--- /dev/null
+++ b/contrib/titan/vtkcell_rc.py
@@ -0,0 +1,793 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+# Resource object code
+#
+# Created: Fri Sep 22 09:09:40 2006
+# by: The Resource Compiler for PyQt (Qt v4.1.3)
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore
+
+qt_resource_data = "\
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+"
+
+qt_resource_name = "\
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+\x00\x69\
+\x00\x6d\x00\x61\x00\x67\x00\x65\x00\x73\
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+\x00\x0a\
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+\x00\x10\
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+"
+
+qt_resource_struct = "\
+\x00\x00\x00\x00\x00\x02\x00\x00\x00\x01\x00\x00\x00\x01\
+\x00\x00\x00\x00\x00\x02\x00\x00\x00\x06\x00\x00\x00\x02\
+\x00\x00\x00\x3c\x00\x00\x00\x00\x00\x01\x00\x00\x09\x48\
+\x00\x00\x00\xc8\x00\x00\x00\x00\x00\x01\x00\x00\x25\x33\
+\x00\x00\x00\xa2\x00\x00\x00\x00\x00\x01\x00\x00\x1f\x4a\
+\x00\x00\x00\x12\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\
+\x00\x00\x00\x7c\x00\x00\x00\x00\x00\x01\x00\x00\x15\xb7\
+\x00\x00\x00\x62\x00\x00\x00\x00\x00\x01\x00\x00\x0d\xfd\
+"
+
+def qInitResources():
+ QtCore.qRegisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+def qCleanupResources():
+ QtCore.qUnregisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+qInitResources()
diff --git a/contrib/titan/vtkhandler.py b/contrib/titan/vtkhandler.py
new file mode 100644
index 0000000..b6703a3
--- /dev/null
+++ b/contrib/titan/vtkhandler.py
@@ -0,0 +1,292 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+"""Modules for handling vtkRenderWindowInteractor events"""
+from PyQt4 import QtCore, QtGui
+from core.modules.basic_modules import String
+from core.modules.vistrails_module import Module, NotCacheable
+from core.modules.module_registry import get_module_registry
+from core.modules.module_configure import StandardModuleConfigurationWidget
+from core.modules.python_source_configure import PythonEditor
+from core.vistrail.module_function import ModuleFunction, ModuleParam
+import urllib
+
+################################################################################
+class vtkInteractionHandler(NotCacheable, Module):
+ """
+ vtkInteractionHandler allow users to insert callback code for interacting
+ with the vtkRenderWindowInteractor InteractionEvent
+
+ """
+
+ # Since vtkCommand is not wrapped in Python, we need to hardcoded all events
+ # string from vtkCommand.h
+ vtkEvents = [
+ 'AnyEvent',
+ 'DeleteEvent',
+ 'StartEvent',
+ 'EndEvent',
+ 'RenderEvent',
+ 'ProgressEvent',
+ 'PickEvent',
+ 'StartPickEvent',
+ 'EndPickEvent',
+ 'AbortCheckEvent',
+ 'ExitEvent',
+ 'LeftButtonPressEvent',
+ 'LeftButtonReleaseEvent',
+ 'MiddleButtonPressEvent',
+ 'MiddleButtonReleaseEvent',
+ 'RightButtonPressEvent',
+ 'RightButtonReleaseEvent',
+ 'EnterEvent',
+ 'LeaveEvent',
+ 'KeyPressEvent',
+ 'KeyReleaseEvent',
+ 'CharEvent',
+ 'ExposeEvent',
+ 'ConfigureEvent',
+ 'TimerEvent',
+ 'MouseMoveEvent',
+ 'MouseWheelForwardEvent',
+ 'MouseWheelBackwardEvent',
+ 'ResetCameraEvent',
+ 'ResetCameraClippingRangeEvent',
+ 'ModifiedEvent',
+ 'WindowLevelEvent',
+ 'StartWindowLevelEvent',
+ 'EndWindowLevelEvent',
+ 'ResetWindowLevelEvent',
+ 'SetOutputEvent',
+ 'ErrorEvent',
+ 'WarningEvent',
+ 'StartInteractionEvent',
+ 'InteractionEvent',
+ 'EndInteractionEvent',
+ 'EnableEvent',
+ 'DisableEvent',
+ 'CreateTimerEvent',
+ 'DestroyTimerEvent',
+ 'PlacePointEvent',
+ 'PlaceWidgetEvent',
+ 'CursorChangedEvent',
+ 'ExecuteInformationEvent',
+ 'RenderWindowMessageEvent',
+ 'WrongTagEvent',
+ 'StartAnimationCueEvent',
+ 'AnimationCueTickEvent',
+ 'EndAnimationCueEvent',
+ 'VolumeMapperRenderEndEvent',
+ 'VolumeMapperRenderProgressEvent',
+ 'VolumeMapperRenderStartEvent',
+ 'VolumeMapperComputeGradientsEndEvent',
+ 'VolumeMapperComputeGradientsProgressEvent',
+ 'VolumeMapperComputeGradientsStartEvent',
+ 'WidgetModifiedEvent',
+ 'WidgetValueChangedEvent',
+ 'WidgetActivateEvent',
+ 'ConnectionCreatedEvent',
+ 'ConnectionClosedEvent',
+ 'DomainModifiedEvent',
+ 'PropertyModifiedEvent',
+ 'UpdateEvent',
+ 'RegisterEvent',
+ 'UnRegisterEvent',
+ 'UpdateInformationEvent']
+
+ def __init__(self):
+ Module.__init__(self)
+ self.observer = None
+ self.handler = None
+ self.shareddata = None
+
+ def compute(self):
+ """ compute() -> None
+ Actually compute nothing
+ """
+ self.observer = self.forceGetInputFromPort('Observer')
+ self.handler = self.forceGetInputFromPort('Handler', '')
+ self.shareddata = self.forceGetInputListFromPort('SharedData')
+ if len(self.shareddata)==1:
+ self.shareddata = self.shareddata[0]
+ if self.observer:
+ source = urllib.unquote(self.handler)
+ observer = self.observer.vtkInstance
+ for e in vtkInteractionHandler.vtkEvents:
+ f = e[0].lower() + e[1:]
+ f = f.replace('Event', 'Handler')
+ source += ('\nif locals().has_key("%s"):\n' % f +
+ '\tobserver.AddObserver("%s", ' % e +
+ 'self.eventHandler)\n')
+ exec(source)
+ if hasattr(self.observer.vtkInstance, 'PlaceWidget'):
+ self.observer.vtkInstance.PlaceWidget()
+
+ def eventHandler(self, obj, event):
+ """ eventHandler(obj: vtkObject, event: str) -> None
+ A proxy for all vtk events to direct to the correct calls
+
+ """
+ if self.handler!='':
+ source = urllib.unquote(self.handler)
+ f = event[0].lower() + event[1:]
+ f = f.replace('Event', 'Handler')
+ myGlobals = globals()
+ myGlobals.update({'self':self})
+ exec(source + ('\nif locals().has_key("%s"):\n' % f)+
+ ('\t%s(obj, self.shareddata)' % f)) in myGlobals, locals()
+
+ def clear(self):
+ """ clear() -> None
+ Remove event handler so the object can be freed correctly
+
+ """
+ # Remove all observers
+ if self.observer:
+ for e in vtkInteractionHandler.vtkEvents:
+ self.observer.vtkInstance.RemoveObservers(e)
+ Module.clear(self)
+
+ def repaintCells(self):
+ """ repaintCells() -> None
+ Redraw all cells on the current sheet
+
+ """
+ from packages.spreadsheet.spreadsheet_controller \
+ import spreadsheetController
+ from packages.spreadsheet.spreadsheet_event \
+ import RepaintCurrentSheetEvent
+ spreadsheetController.postEventToSpreadsheet(RepaintCurrentSheetEvent())
+
+class HandlerConfigurationWidget(StandardModuleConfigurationWidget):
+ """
+ HandlerConfigurationWidget is simialr to PythonSource
+ configuration widget except that it doesn't allow add/remove
+ ports. In this configuration widget, the user will enter their
+ python code to handle a specifc event
+
+ """
+ def __init__(self, module, controller, parent=None):
+ """ HandlerConfigurationWidget(module: Module,
+ controller: VistrailController,
+ parent: QWidget)
+ -> HandlerConfigurationWidget
+ Setup the dialog to have a single python source editor and 2
+ buttons
+
+ """
+ StandardModuleConfigurationWidget.__init__(self, module,
+ controller, parent)
+ self.setWindowTitle('Handler Python Script Editor')
+ self.setLayout(QtGui.QVBoxLayout())
+ self.layout().setMargin(0)
+ self.layout().setSpacing(0)
+ self.createEditor()
+ self.createButtonLayout()
+
+ def findHandlerFunction(self):
+ """ findHandlerFunction() -> int
+ Return the function id associated with input port 'source'
+
+ """
+ fid = -1
+ for i in xrange(self.module.getNumFunctions()):
+ if self.module.functions[i].name=='Handler':
+ fid = i
+ break
+ return fid
+
+ def createEditor(self):
+ """ createEditor() -> None
+ Add a python editor into the widget layout
+
+ """
+ self.codeEditor = PythonEditor(self)
+ fid = self.findHandlerFunction()
+ if fid!=-1:
+ f = self.module.functions[fid]
+ self.codeEditor.setPlainText(urllib.unquote(f.params[0].strValue))
+ self.codeEditor.document().setModified(False)
+ self.layout().addWidget(self.codeEditor, 1)
+
+ def createButtonLayout(self):
+ """ createButtonLayout() -> None
+ Construct Ok & Cancel button
+
+ """
+ self.buttonLayout = QtGui.QHBoxLayout()
+ self.buttonLayout.setMargin(5)
+ self.okButton = QtGui.QPushButton('&OK', self)
+ self.okButton.setAutoDefault(False)
+ self.okButton.setFixedWidth(100)
+ self.buttonLayout.addWidget(self.okButton)
+ self.cancelButton = QtGui.QPushButton('&Cancel', self)
+ self.cancelButton.setAutoDefault(False)
+ self.cancelButton.setShortcut('Esc')
+ self.cancelButton.setFixedWidth(100)
+ self.buttonLayout.addWidget(self.cancelButton)
+ self.layout().addLayout(self.buttonLayout)
+ self.connect(self.okButton, QtCore.SIGNAL('clicked(bool)'), self.okTriggered)
+ self.connect(self.cancelButton, QtCore.SIGNAL('clicked(bool)'), self.close)
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+ Return the recommendation size of this widget
+
+ """
+ return QtCore.QSize(512, 512)
+
+ def updateController(self, controller):
+ """ updateController() -> None
+ Based on the input of the python editor, update the vistrail
+ controller appropriately
+
+ """
+ if self.codeEditor.document().isModified():
+ code = urllib.quote(str(self.codeEditor.toPlainText()))
+ functions = [('Handler', [code])]
+ self.controller.update_functions(self.module, functions)
+
+ def okTriggered(self, checked = False):
+ """ okTriggered(checked: bool) -> None
+ Update vistrail controller (if neccesssary) then close the widget
+
+ """
+ self.updateController(self.controller)
+ self.emit(QtCore.SIGNAL('doneConfigure()'))
+ self.close()
+
+
+def registerSelf():
+ """ registerSelf() -> None
+ Registry module with the registry
+ """
+ registry = get_module_registry()
+ vIO = registry.get_descriptor_by_name(
+ 'edu.utah.sci.vistrails.vtk',
+# Wendel
+ 'vtkInteractorObserver').module
+ registry.add_module(vtkInteractionHandler, configureWidgetType=HandlerConfigurationWidget)
+ registry.add_input_port(vtkInteractionHandler, 'Observer', vIO)
+ registry.add_input_port(vtkInteractionHandler, 'Handler', String, True)
+ registry.add_input_port(vtkInteractionHandler, 'SharedData', Module)
+ registry.add_output_port(vtkInteractionHandler, 'self',
+ vtkInteractionHandler)
diff --git a/contrib/titan/vtkviewcell.py b/contrib/titan/vtkviewcell.py
new file mode 100644
index 0000000..a4826d0
--- /dev/null
+++ b/contrib/titan/vtkviewcell.py
@@ -0,0 +1,1032 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+################################################################################
+# File QVTKViewWidget.py
+# File for displaying a vtkRenderWindow in a Qt's QWidget ported from
+# VTK/GUISupport/QVTK. Combine altogether to a single class: QVTKViewWidget
+################################################################################
+import vtk
+from PyQt4 import QtCore, QtGui
+import sip
+from core import system
+from core.modules.module_registry import get_module_registry
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+import vtkcell_rc
+import gc
+from gui.qt import qt_super
+import core.db.action
+from core.vistrail.action import Action
+from core.vistrail.port import Port
+from core.vistrail import module
+from core.vistrail import connection
+from core.vistrail.module_function import ModuleFunction
+from core.vistrail.module_param import ModuleParam
+from core.vistrail.location import Location
+from core.modules.vistrails_module import ModuleError
+import copy
+
+################################################################################
+
+class VTKViewCell(SpreadsheetCell):
+ """
+ VTKViewCell is a VisTrails Module that can display vtkRenderWindow inside a cell
+
+ """
+
+ def __init__(self):
+ SpreadsheetCell.__init__(self)
+ self.cellWidget = None
+
+ def compute(self):
+ """ compute() -> None
+ Dispatch the vtkRenderer to the actual rendering widget
+ """
+ renderView = self.forceGetInputFromPort('SetRenderView')
+ if renderView==None:
+ raise ModuleError(self, 'A vtkRenderView input is required.')
+ self.cellWidget = self.displayAndWait(QVTKViewWidget, (renderView,))
+
+AsciiToKeySymTable = ( None, None, None, None, None, None, None,
+ None, None,
+ "Tab", None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None,
+ "space", "exclam", "quotedbl", "numbersign",
+ "dollar", "percent", "ampersand", "quoteright",
+ "parenleft", "parenright", "asterisk", "plus",
+ "comma", "minus", "period", "slash",
+ "0", "1", "2", "3", "4", "5", "6", "7",
+ "8", "9", "colon", "semicolon", "less", "equal",
+ "greater", "question",
+ "at", "A", "B", "C", "D", "E", "F", "G",
+ "H", "I", "J", "K", "L", "M", "N", "O",
+ "P", "Q", "R", "S", "T", "U", "V", "W",
+ "X", "Y", "Z", "bracketleft",
+ "backslash", "bracketright", "asciicircum",
+ "underscore",
+ "quoteleft", "a", "b", "c", "d", "e", "f", "g",
+ "h", "i", "j", "k", "l", "m", "n", "o",
+ "p", "q", "r", "s", "t", "u", "v", "w",
+ "x", "y", "z", "braceleft", "bar", "braceright",
+ "asciitilde", "Delete",
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None)
+
+class QVTKViewWidget(QCellWidget):
+ """
+ QVTKViewWidget is the actual rendering widget that can display
+ vtkRenderer inside a Qt QWidget
+
+ """
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QVTKViewWidget(parent: QWidget, f: WindowFlags) -> QVTKViewWidget
+ Initialize QVTKViewWidget with a toolbar with its own device
+ context
+
+ """
+ QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
+
+ self.interacting = None
+ self.mRenWin = None
+ self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
+ self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
+ self.setMouseTracking(True)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding))
+ self.toolBarType = QVTKViewWidgetToolBar
+ self.setAnimationEnabled(True)
+
+ def removeObserversFromInteractorStyle(self):
+ """ removeObserversFromInteractorStyle() -> None
+ Remove all python binding from interactor style observers for
+ safely freeing the cell
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.RemoveObservers("InteractionEvent")
+ style.RemoveObservers("EndPickEvent")
+ style.RemoveObservers("CharEvent")
+ style.RemoveObservers("MouseWheelForwardEvent")
+ style.RemoveObservers("MouseWheelBackwardEvent")
+
+ def addObserversToInteractorStyle(self):
+ """ addObserversToInteractorStyle() -> None
+ Assign observer to the current interactor style
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.AddObserver("InteractionEvent", self.interactionEvent)
+ style.AddObserver("EndPickEvent", self.interactionEvent)
+ style.AddObserver("CharEvent", self.charEvent)
+ style.AddObserver("MouseWheelForwardEvent", self.interactionEvent)
+ style.AddObserver("MouseWheelBackwardEvent", self.interactionEvent)
+
+ def deleteLater(self):
+ """ deleteLater() -> None
+ Make sure to free render window resource when
+ deallocating. Overriding PyQt deleteLater to free up
+ resources
+
+ """
+ self.renderer_maps = {}
+ for ren in self.getRendererList():
+ self.mRenWin.RemoveRenderer(ren)
+ self.removeObserversFromInteractorStyle()
+ self.SetRenderWindow(None)
+ QCellWidget.deleteLater(self)
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple)
+ Updates the cell contents with new vtkRenderer
+
+ """
+ (renderView, ) = inputPorts
+ renWin = renderView.vtkInstance.GetRenderWindow()
+ renWin.DoubleBufferOn()
+ self.SetRenderWindow(renWin)
+ renderView.vtkInstance.ResetCamera()
+ self.addObserversToInteractorStyle()
+
+# renWin = self.GetRenderWindow()
+# renderers = [renderView.vtkInstance.GetRenderer()]
+# iren = renWin.GetInteractor()
+ # Update interactor style
+# self.removeObserversFromInteractorStyle()
+# if renderView==None:
+# if iStyle==None:
+# iStyleInstance = vtk.vtkInteractorStyleTrackballCamera()
+# else:
+# iStyleInstance = iStyle.vtkInstance
+# iren.SetInteractorStyle(iStyleInstance)
+# self.addObserversToInteractorStyle()
+ # Capture window into history for playback
+ # Call this at the end to capture the image after rendering
+ QCellWidget.updateContents(self, inputPorts)
+
+ def GetRenderWindow(self):
+ """ GetRenderWindow() -> vtkRenderWindow
+ Return the associated vtkRenderWindow
+
+ """
+ if not self.mRenWin:
+ win = vtk.vtkRenderWindow()
+ win.DoubleBufferOn()
+ self.SetRenderWindow(win)
+ del win
+
+ return self.mRenWin
+
+ def SetRenderWindow(self,w):
+ """ SetRenderWindow(w: vtkRenderWindow)
+ Set a new render window to QVTKViewWidget and initialize the
+ interactor as well
+
+ """
+ if w == self.mRenWin:
+ return
+
+ if self.mRenWin:
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+
+ self.mRenWin = w
+
+ if self.mRenWin:
+ self.mRenWin.Register(None)
+ if system.systemType=='Linux':
+ try:
+ vp = '_%s_void_p' % (hex(int(QtGui.QX11Info.display()))[2:])
+ except TypeError:
+ #This was change for PyQt4.2
+ if isinstance(QtGui.QX11Info.display(),QtGui.Display):
+ display = sip.unwrapinstance(QtGui.QX11Info.display())
+ vp = '_%s_void_p' % (hex(display)[2:])
+ self.mRenWin.SetDisplayId(vp)
+ if not self.mRenWin.GetMapped():
+ self.mRenWin.GetInteractor().Initialize()
+ system.XDestroyWindow(self.mRenWin.GetGenericDisplayId(),
+ self.mRenWin.GetGenericWindowId())
+ self.mRenWin.Finalize()
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ else:
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ def GetInteractor(self):
+ """ GetInteractor() -> vtkInteractor
+ Return the vtkInteractor control this QVTKViewWidget
+ """
+ return self.GetRenderWindow().GetInteractor()
+
+ def event(self, e):
+ """ event(e: QEvent) -> depends on event type
+ Process window and interaction events
+
+ """
+ if e.type()==QtCore.QEvent.ParentAboutToChange:
+ if self.mRenWin:
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+ else:
+ if e.type()==QtCore.QEvent.ParentChange:
+ if self.mRenWin:
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ if QtCore.QObject.event(self,e):
+ return 1
+
+ if e.type() == QtCore.QEvent.KeyPress:
+ self.keyPressEvent(e)
+ if e.isAccepted():
+ return e.isAccepted()
+
+ return qt_super(QVTKViewWidget, self).event(e)
+
+ # return QtGui.QWidget.event(self,e)
+ # Was this right? Wasn't this supposed to be QCellWidget.event()?
+
+ def resizeWindow(self, width, height):
+ """ resizeWindow(width: int, height: int) -> None
+ Work around vtk bugs for resizing window
+
+ """
+ ########################################################
+ # VTK - BUGGGGGGGGG - GRRRRRRRRR
+ # This is a 'bug' in vtkWin32OpenGLRenderWindow(.cxx)
+ # If a render window is mapped to screen, the actual
+ # window size is the client area of the window in Win32.
+ # However, this real window size is only updated through
+ # vtkWin32OpenGLRenderWindow::GetSize(). So this has to
+ # be called here to get the cell size correctly. This
+ # invalidates the condition in the next SetSize().
+ # We can use self.mRenWin.SetSize(0,0) here but it will
+ # cause flickering and decrease performance!
+ # SetPosition(curX,curY) also works here but slower.
+ self.mRenWin.GetSize()
+
+ self.mRenWin.SetSize(width, height)
+ if self.mRenWin.GetInteractor():
+ self.mRenWin.GetInteractor().SetSize(width, height)
+
+ def resizeEvent(self, e):
+ """ resizeEvent(e: QEvent) -> None
+ Re-adjust the vtkRenderWindow size then QVTKViewWidget resized
+
+ """
+ qt_super(QVTKViewWidget, self).resizeEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.resizeWindow(self.width(), self.height())
+ self.mRenWin.Render()
+
+ def moveEvent(self,e):
+ """ moveEvent(e: QEvent) -> None
+ Echo the move event into vtkRenderWindow
+
+ """
+ qt_super(QVTKViewWidget, self).moveEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.mRenWin.SetPosition(self.x(),self.y())
+
+ def paintEvent(self, e):
+ """ paintEvent(e: QPaintEvent) -> None
+ Paint the QVTKViewWidget with vtkRenderWindow
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ if hasattr(self.mRenWin, 'UpdateGLRegion'):
+ self.mRenWin.UpdateGLRegion()
+ self.mRenWin.Render()
+
+ def SelectActiveRenderer(self,iren):
+ """ SelectActiveRenderer(iren: vtkRenderWindowIteractor) -> None
+ Only make the vtkRenderer below the mouse cursor active
+
+ """
+ epos = iren.GetEventPosition()
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ ren.SetInteractive(ren.IsInViewport(epos[0], epos[1]))
+
+ def mousePressEvent(self,e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ isDoubleClick = e.type()==QtCore.QEvent.MouseButtonDblClick
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ ctrl,
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),
+ isDoubleClick,
+ None)
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonPressEvent",
+ QtCore.Qt.MidButton:"MiddleButtonPressEvent",
+ QtCore.Qt.RightButton:"RightButtonPressEvent"}
+
+ self.SelectActiveRenderer(iren)
+
+ if ctrl:
+ e.ignore()
+ return
+
+ self.interacting = self.getActiveRenderer(iren)
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def mouseMoveEvent(self,e):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0), 0, None)
+
+ iren.InvokeEvent("MouseMoveEvent")
+
+ def enterEvent(self,e):
+ """ enterEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("EnterEvent")
+
+ def leaveEvent(self,e):
+ """ leaveEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("LeaveEvent")
+
+ def mouseReleaseEvent(self,e):
+ """ mouseReleaseEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonReleaseEvent",
+ QtCore.Qt.MidButton:"MiddleButtonReleaseEvent",
+ QtCore.Qt.RightButton:"RightButtonReleaseEvent"}
+
+ self.interacting = None
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def keyPressEvent(self,e):
+ """ keyPressEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if e.text().length()>0:
+ ascii_key = e.text().toLatin1()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q', 'e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl,shift,ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyPressEvent")
+
+ if ascii_key:
+ iren.InvokeEvent("CharEvent")
+
+
+ def keyReleaseEvent(self,e):
+ """ keyReleaseEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if e.text().length()>0:
+ ascii_key = e.text().toLatin1()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q','e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl, shift, ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyReleaseEvent")
+
+ def wheelEvent(self,e):
+ """ wheelEvent(e: QWheelEvent) -> None
+ Zoom in/out while scrolling the mouse
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ self.SelectActiveRenderer(iren)
+
+ if e.delta()>0:
+ iren.InvokeEvent("MouseWheelForwardEvent")
+ else:
+ iren.InvokeEvent("MouseWheelBackwardEvent")
+
+ def focusInEvent(self,e):
+ """ focusInEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def focusOutEvent(self,e):
+ """ focusOutEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def contextMenuEvent(self,e):
+ """ contextMenuEvent(e: QContextMenuEvent) -> None
+ Make sure to get the right mouse position for the context menu
+ event, i.e. also the right click
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = int(e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = int(e.modifiers()&QtCore.Qt.ShiftModifier)
+ iren.SetEventInformationFlipY(e.x(),e.y(),ctrl,shift,chr(0),0,None)
+ iren.InvokeEvent("ContextMenuEvent")
+
+ def ascii_to_key_sym(self,i):
+ """ ascii_to_key_sym(i: int) -> str
+ Convert ASCII code into key name
+
+ """
+ global AsciiToKeySymTable
+ return AsciiToKeySymTable[i]
+
+ def qt_key_to_key_sym(self,i):
+ """ qt_key_to_key_sym(i: QtCore.Qt.Keycode) -> str
+ Convert Qt key code into key name
+
+ """
+ handler = {QtCore.Qt.Key_Backspace:"BackSpace",
+ QtCore.Qt.Key_Tab:"Tab",
+ QtCore.Qt.Key_Backtab:"Tab",
+ QtCore.Qt.Key_Return:"Return",
+ QtCore.Qt.Key_Enter:"Return",
+ QtCore.Qt.Key_Shift:"Shift_L",
+ QtCore.Qt.Key_Control:"Control_L",
+ QtCore.Qt.Key_Alt:"Alt_L",
+ QtCore.Qt.Key_Pause:"Pause",
+ QtCore.Qt.Key_CapsLock:"Caps_Lock",
+ QtCore.Qt.Key_Escape:"Escape",
+ QtCore.Qt.Key_Space:"space",
+ QtCore.Qt.Key_End:"End",
+ QtCore.Qt.Key_Home:"Home",
+ QtCore.Qt.Key_Left:"Left",
+ QtCore.Qt.Key_Up:"Up",
+ QtCore.Qt.Key_Right:"Right",
+ QtCore.Qt.Key_Down:"Down",
+ QtCore.Qt.Key_SysReq:"Snapshot",
+ QtCore.Qt.Key_Insert:"Insert",
+ QtCore.Qt.Key_Delete:"Delete",
+ QtCore.Qt.Key_Help:"Help",
+ QtCore.Qt.Key_0:"0",
+ QtCore.Qt.Key_1:"1",
+ QtCore.Qt.Key_2:"2",
+ QtCore.Qt.Key_3:"3",
+ QtCore.Qt.Key_4:"4",
+ QtCore.Qt.Key_5:"5",
+ QtCore.Qt.Key_6:"6",
+ QtCore.Qt.Key_7:"7",
+ QtCore.Qt.Key_8:"8",
+ QtCore.Qt.Key_9:"9",
+ QtCore.Qt.Key_A:"a",
+ QtCore.Qt.Key_B:"b",
+ QtCore.Qt.Key_C:"c",
+ QtCore.Qt.Key_D:"d",
+ QtCore.Qt.Key_E:"e",
+ QtCore.Qt.Key_F:"f",
+ QtCore.Qt.Key_G:"g",
+ QtCore.Qt.Key_H:"h",
+ QtCore.Qt.Key_I:"i",
+ QtCore.Qt.Key_J:"h",
+ QtCore.Qt.Key_K:"k",
+ QtCore.Qt.Key_L:"l",
+ QtCore.Qt.Key_M:"m",
+ QtCore.Qt.Key_N:"n",
+ QtCore.Qt.Key_O:"o",
+ QtCore.Qt.Key_P:"p",
+ QtCore.Qt.Key_Q:"q",
+ QtCore.Qt.Key_R:"r",
+ QtCore.Qt.Key_S:"s",
+ QtCore.Qt.Key_T:"t",
+ QtCore.Qt.Key_U:"u",
+ QtCore.Qt.Key_V:"v",
+ QtCore.Qt.Key_W:"w",
+ QtCore.Qt.Key_X:"x",
+ QtCore.Qt.Key_Y:"y",
+ QtCore.Qt.Key_Z:"z",
+ QtCore.Qt.Key_Asterisk:"asterisk",
+ QtCore.Qt.Key_Plus:"plus",
+ QtCore.Qt.Key_Minus:"minus",
+ QtCore.Qt.Key_Period:"period",
+ QtCore.Qt.Key_Slash:"slash",
+ QtCore.Qt.Key_F1:"F1",
+ QtCore.Qt.Key_F2:"F2",
+ QtCore.Qt.Key_F3:"F3",
+ QtCore.Qt.Key_F4:"F4",
+ QtCore.Qt.Key_F5:"F5",
+ QtCore.Qt.Key_F6:"F6",
+ QtCore.Qt.Key_F7:"F7",
+ QtCore.Qt.Key_F8:"F8",
+ QtCore.Qt.Key_F9:"F9",
+ QtCore.Qt.Key_F10:"F10",
+ QtCore.Qt.Key_F11:"F11",
+ QtCore.Qt.Key_F12:"F12",
+ QtCore.Qt.Key_F13:"F13",
+ QtCore.Qt.Key_F14:"F14",
+ QtCore.Qt.Key_F15:"F15",
+ QtCore.Qt.Key_F16:"F16",
+ QtCore.Qt.Key_F17:"F17",
+ QtCore.Qt.Key_F18:"F18",
+ QtCore.Qt.Key_F19:"F19",
+ QtCore.Qt.Key_F20:"F20",
+ QtCore.Qt.Key_F21:"F21",
+ QtCore.Qt.Key_F22:"F22",
+ QtCore.Qt.Key_F23:"F23",
+ QtCore.Qt.Key_F24:"F24",
+ QtCore.Qt.Key_NumLock:"Num_Lock",
+ QtCore.Qt.Key_ScrollLock:"Scroll_Lock"}
+ if i in handler:
+ return handler[i]
+ else:
+ return "None"
+
+ def getRendererList(self):
+ """ getRendererList() -> list
+ Return a list of vtkRenderer running in this QVTKViewWidget
+ """
+ result = []
+ renWin = self.GetRenderWindow()
+ renderers = renWin.GetRenderers()
+ renderers.InitTraversal()
+ for i in xrange(renderers.GetNumberOfItems()):
+ result.append(renderers.GetNextItem())
+ return result
+
+ def getActiveRenderer(self, iren):
+ """ getActiveRenderer(iren: vtkRenderWindowwInteractor) -> vtkRenderer
+ Return the active vtkRenderer under mouse
+
+ """
+ epos = list(iren.GetEventPosition())
+ if epos[1]<0:
+ epos[1] = -epos[1]
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ if ren.IsInViewport(epos[0], epos[1]):
+ return ren
+ return None
+
+ def findSheetTabWidget(self):
+ """ findSheetTabWidget() -> QTabWidget
+ Find and return the sheet tab widget
+
+ """
+ p = self.parent()
+ while p:
+ if hasattr(p, 'isSheetTabWidget'):
+ if p.isSheetTabWidget()==True:
+ return p
+ p = p.parent()
+ return None
+
+ def getRenderersInCellList(self, sheet, cells):
+ """ isRendererIn(sheet: spreadsheet.StandardWidgetSheet,
+ cells: [(int,int)]) -> bool
+ Get the list of renderers in side a list of (row, column)
+ cells.
+
+ """
+ rens = []
+ for (row, col) in cells:
+ cell = sheet.getCell(row, col)
+ if hasattr(cell, 'getRendererList'):
+ rens += cell.getRendererList()
+ return rens
+
+ def getSelectedCellWidgets(self):
+ sheet = self.findSheetTabWidget()
+ if sheet:
+ iren = self.mRenWin.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ cells = sheet.getSelectedLocations()
+ if (ren in self.getRenderersInCellList(sheet, cells)):
+ return [sheet.getCell(row, col)
+ for (row, col) in cells
+ if hasattr(sheet.getCell(row, col),
+ 'getRendererList')]
+ return []
+
+ def interactionEvent(self, istyle, name):
+ """ interactionEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure interactions sync across selected renderers
+
+ """
+ if name=='MouseWheelForwardEvent':
+ istyle.OnMouseWheelForward()
+ if name=='MouseWheelBackwardEvent':
+ istyle.OnMouseWheelBackward()
+ ren = self.interacting
+ if not ren:
+ ren = self.getActiveRenderer(istyle.GetInteractor())
+ if ren:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ for cell in self.getSelectedCellWidgets():
+ if cell!=self and hasattr(cell, 'getRendererList'):
+ rens = cell.getRendererList()
+ for r in rens:
+ if r!=ren:
+ dcam = r.GetActiveCamera()
+ dcam.SetPosition(cpos)
+ dcam.SetFocalPoint(cfol)
+ dcam.SetViewUp(cup)
+ r.ResetCameraClippingRange()
+ cell.update()
+
+ def charEvent(self, istyle, name):
+ """ charEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure key presses also sync across selected renderers
+
+ """
+ iren = istyle.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ keyCode = iren.GetKeyCode()
+ if keyCode in ['w','W','s','S','r','R','p','P']:
+ for cell in self.getSelectedCellWidgets():
+ if hasattr(cell, 'GetInteractor'):
+ selectedIren = cell.GetInteractor()
+ selectedIren.SetKeyCode(keyCode)
+ selectedIren.GetInteractorStyle().OnChar()
+ selectedIren.Render()
+ istyle.OnChar()
+
+ def saveToPNG(self, filename):
+ """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
+
+ Save the current widget contents to an image file. If
+ str==None, then it returns the vtkUnsignedCharArray containing
+ the PNG image. Otherwise, the filename is returned.
+
+ """
+ w2i = vtk.vtkWindowToImageFilter()
+ w2i.ReadFrontBufferOff()
+ w2i.SetInput(self.mRenWin)
+ # Render twice to get a clean image on the back buffer
+ self.mRenWin.Render()
+ self.mRenWin.Render()
+ w2i.Update()
+ writer = vtk.vtkPNGWriter()
+ writer.SetInputConnection(w2i.GetOutputPort())
+ if filename!=None:
+ writer.SetFileName(filename)
+ else:
+ writer.WriteToMemoryOn()
+ writer.Write()
+ if filename:
+ return filename
+ else:
+ return writer.GetResult()
+
+ def captureWindow(self):
+ """ captureWindow() -> None
+ Capture the window contents to file
+
+ """
+ fn = QtGui.QFileDialog.getSaveFileName(None,
+ "Save file as...",
+ "screenshot.png",
+ "Images (*.png)")
+ if fn.isNull():
+ return
+ self.saveToPNG(str(fn))
+
+ def grabWindowPixmap(self):
+ """ grabWindowImage() -> QPixmap
+ Widget special grabbing function
+
+ """
+ uchar = self.saveToPNG(None)
+
+ ba = QtCore.QByteArray()
+ buf = QtCore.QBuffer(ba)
+ buf.open(QtCore.QIODevice.WriteOnly)
+ for i in xrange(uchar.GetNumberOfTuples()):
+ c = uchar.GetValue(i)
+ buf.putChar(chr(c))
+ buf.close()
+
+ pixmap = QtGui.QPixmap()
+ pixmap.loadFromData(ba, 'PNG')
+ return pixmap
+
+ def dumpToFile(self, filename):
+ """dumpToFile() -> None
+ Dumps itself as an image to a file, calling saveToPNG
+ """
+ self.saveToPNG(filename)
+
+class QVTKViewWidgetCapture(QtGui.QAction):
+ """
+ QVTKViewWidgetCapture is the action to capture the vtk rendering
+ window to an image
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKViewWidgetCapture(parent: QWidget) -> QVTKViewWidgetCapture
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/camera.png"),
+ "&Capture image to file",
+ parent)
+ self.setStatusTip("Capture the rendered image to a file")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ cellWidget.captureWindow()
+
+class QVTKViewWidgetSaveCamera(QtGui.QAction):
+ """
+ QVTKViewWidgetSaveCamera is the action to capture the current camera
+ of the vtk renderers and save it back to the pipeline
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKViewWidgetSaveCamera(parent: QWidget) -> QVTKViewWidgetSaveCamera
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ "Save &Camera",
+ parent)
+ self.setStatusTip("Save current camera views to the pipeline")
+
+ def setCamera(self, controller):
+ ops = []
+ pipeline = controller.current_pipeline
+ cellWidget = self.toolBar.getSnappedWidget()
+ renderers = cellWidget.getRendererList()
+ for ren in renderers:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ rendererId = cellWidget.renderer_maps[ren]
+ # Looking for SetActiveCamera()
+ camera = None
+ renderer = pipeline.modules[rendererId]
+ for c in pipeline.connections.values():
+ if c.destination.moduleId==rendererId:
+ if c.destination.name=='SetActiveCamera':
+ camera = pipeline.modules[c.source.moduleId]
+ break
+
+ if not camera:
+ # Create camera
+ vtk_package = 'edu.utah.sci.vistrails.vtk'
+ camera = controller.create_module(vtk_package, 'vtkCamera', '',
+ 0.0, 0.0)
+ ops.append(('add', camera))
+
+ # Connect camera to renderer
+ camera_conn = controller.create_connection(camera, 'self',
+ renderer,
+ 'SetActiveCamera')
+ ops.append(('add', camera_conn))
+ # update functions
+ def convert_to_str(arglist):
+ new_arglist = []
+ for arg in arglist:
+ new_arglist.append(str(arg))
+ return new_arglist
+ functions = [('SetPosition', convert_to_str(cpos)),
+ ('SetFocalPoint', convert_to_str(cfol)),
+ ('SetViewUp', convert_to_str(cup))]
+ ops.extend(controller.update_functions_ops(camera, functions))
+
+ action = core.db.action.create_action(ops)
+ controller.add_new_action(action)
+ controller.perform_action(action)
+ controller.select_latest_version()
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ visApp = QtCore.QCoreApplication.instance()
+ if hasattr(visApp, 'builderWindow'):
+ builderWindow = visApp.builderWindow
+ if builderWindow:
+ info = self.toolBar.sheet.getCellPipelineInfo(
+ self.toolBar.row, self.toolBar.col)
+ if info:
+ info = info[0]
+ viewManager = builderWindow.viewManager
+ view = viewManager.ensureVistrail(info['locator'])
+ if view:
+ controller = view.controller
+ controller.change_selected_version(info['version'])
+ self.setCamera(controller)
+
+
+class QVTKViewWidgetToolBar(QCellToolBar):
+ """
+ QVTKViewWidgetToolBar derives from QCellToolBar to give the VTKViewCell
+ a customizable toolbar
+
+ """
+ def createToolBar(self):
+ """ createToolBar() -> None
+ This will get call initiallly to add customizable widgets
+
+ """
+ self.appendAction(QVTKViewWidgetCapture(self))
+ self.addAnimationButtons()
+ self.appendAction(QVTKViewWidgetSaveCamera(self))
+
+def registerSelf():
+ """ registerSelf() -> None
+ Registry module with the registry
+ """
+ identifier = 'edu.utah.sci.vistrails.vtk'
+ registry = get_module_registry()
+ registry.add_module(VTKViewCell)
+ registry.add_input_port(VTKViewCell, "Location", CellLocation)
+ import core.debug
+ for (port,module) in [("SetRenderView",'vtkRenderView')]:
+ try:
+ registry.add_input_port(VTKViewCell, port,'(%s:%s)'%(identifier,module))
+
+ except Exception, e:
+ core.debug.warning(str(e))
+
+ registry.add_output_port(VTKViewCell, "self", VTKViewCell)
diff --git a/contrib/trimesh2.py b/contrib/trimesh2.py
new file mode 100644
index 0000000..f00638a
--- /dev/null
+++ b/contrib/trimesh2.py
@@ -0,0 +1,123 @@
+# VisTrails package for trimesh2 support
+# Copyright Carlos Eduardo Scheidegger, 2007
+# Get trimesh2 at www.cs.princeton.edu/gfx/proj/trimesh2/
+# or a patched version with more available file formats
+# at www.sci.utah.edu/~cscheid/software
+
+# License: GPLv2 or later
+
+# ChangeLog:
+
+# 2007-03-13 Carlos Scheidegger <cscheid at juggernaut>
+# * uses core.system.list2cmd to generate command lines.
+# 2007-03-12 Carlos Scheidegger <cscheid at juggernaut>
+# * First release
+##############################################################################
+
+import core.modules
+import core.modules.module_registry
+from core.modules.vistrails_module import Module, ModuleError
+from core.system import list2cmdline
+import os
+
+_mesh_filter_path = None
+
+identifier = 'edu.utah.sci.cscheid.trimesh2'
+version = '0.1'
+name = 'trimesh2'
+
+##############################################################################
+# MeshFilter
+class MeshFilter(Module):
+
+ def guess_input_format(self, input_file_name):
+ i = input_file_name.rfind('.')
+ if i == -1:
+ return None
+ else:
+ return input_file_name[i:]
+
+ def compute(self):
+ self.checkInputPort('input_file')
+ input_file = self.getInputFromPort('input_file')
+ if self.hasInputFromPort('output_format'):
+ output_suffix = self.getInputFromPort('output_format')
+ else:
+ output_suffix = self.guess_input_format(input_file.name)
+ if not output_suffix:
+ output_suffix = '.off'
+ output_file = self.interpreter.filePool.create_file(suffix=output_suffix)
+ values = [_mesh_filter_path,
+ input_file.name,
+ output_file.name]
+ cmdline = list2cmdline(values)
+ print cmdline
+ result = os.system(cmdline)
+ if result != 0:
+ raise ModuleError(self, 'Execution failed')
+ self.setResult('output_file', output_file)
+
+##############################################################################
+# PlanarSubdiv
+class PlanarSubdiv(MeshFilter):
+
+ def compute(self):
+ self.checkInputPort('input_file')
+ self.checkInputPort('iterations')
+ iters = self.getInputFromPort('iterations')
+ if iters < 1:
+ raise ModuleError(self, 'iterations must be >=1')
+ input_file = self.getInputFromPort('input_file')
+ if self.hasInputFromPort('output_format'):
+ output_suffix = self.getInputFromPort('output_format')
+ else:
+ output_suffix = self.guess_input_format(input_file.name)
+ if not output_suffix:
+ output_suffix = '.off'
+ output_file = self.interpreter.filePool.create_file(suffix=output_suffix)
+
+ values = [_mesh_filter_path,
+ input_file.name,
+ '-subdiv',
+ output_file.name]
+ cmdline = list2cmdline(values)
+ print cmdline
+ result = os.system(cmdline)
+ if result != 0:
+ raise ModuleError(self, 'Execution failed')
+
+ for i in xrange(iters-1):
+ cmdline = '%s %s -subdiv %s' % (_mesh_filter_path,
+ output_file.name,
+ output_file.name)
+ print cmdline
+ result = os.system(cmdline)
+ if result != 0:
+ raise ModuleError(self, 'Execution failed')
+
+ self.setResult('output_file', output_file)
+
+
+def initialize(executable_path=None):
+ global _mesh_filter_path
+ if not executable_path:
+ print "Assuming mesh_filter is in path"
+ _mesh_filter_path = 'mesh_filter'
+ else:
+ print "Assuming mesh_filter is in '%s'" % executable_path
+ _mesh_filter_path = executable_path + '/mesh_filter'
+
+ reg = core.modules.module_registry
+
+ reg.add_module(MeshFilter)
+
+ reg.add_input_port(MeshFilter, 'input_file',
+ core.modules.basic_modules.File)
+ reg.add_input_port(MeshFilter, 'output_format',
+ core.modules.basic_modules.String)
+ reg.add_output_port(MeshFilter, 'output_file',
+ core.modules.basic_modules.File)
+
+ reg.add_module(PlanarSubdiv)
+ reg.add_input_port(PlanarSubdiv, 'iterations',
+ core.modules.basic_modules.Integer)
diff --git a/contrib/vtksnl/__init__.py b/contrib/vtksnl/__init__.py
new file mode 100644
index 0000000..03508a3
--- /dev/null
+++ b/contrib/vtksnl/__init__.py
@@ -0,0 +1,53 @@
+###########################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+################################################################################
+# VTK-SNL Package for VisTrails (Sandia National Laboratories)
+################################################################################
+
+"""The Visualization ToolKit (VTK) is an open source, freely available
+software system for 3D computer graphics, image processing, and
+visualization used by thousands of researchers and developers around
+the world. This version of the VTK package requires the Sandia
+National Laboratories version of the VTK libraries.
+
+http://www.vtk.org"""
+
+identifier = 'edu.utah.sci.vistrails.vtksnl'
+name = 'VTKSNL'
+version = '0.9.1'
+
+def package_dependencies():
+ import core.packagemanager
+ manager = core.packagemanager.get_package_manager()
+ if manager.has_package('edu.utah.sci.vistrails.spreadsheet'):
+ return ['edu.utah.sci.vistrails.spreadsheet']
+ else:
+ return []
+
+def package_requirements():
+ import core.requirements
+ if not core.requirements.python_module_exists('vtksnl'):
+ raise core.requirements.MissingRequirement('vtksnl')
+ if not core.requirements.python_module_exists('PyQt4'):
+ print 'PyQt4 is not available. There will be no interaction',
+ print 'between VTK and the spreadsheet.'
+ import vtksnl
diff --git a/contrib/vtksnl/base_module.py b/contrib/vtksnl/base_module.py
new file mode 100644
index 0000000..e9cadac
--- /dev/null
+++ b/contrib/vtksnl/base_module.py
@@ -0,0 +1,203 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+################################################################################
+# This describes basic modules used by other VTK module
+################################################################################
+import vtksnl
+from core.modules.module_registry import registry
+from core.modules.vistrails_module import Module, ModuleError
+from itertools import izip
+
+################################################################################
+
+class vtkBaseModule(Module):
+ """
+ vtkBaseModule is the base class for all VTK modules in VisTrails, it acts
+ as a wrapper to direct all input/output ports to appropriate VTK function
+ calls
+
+ """
+
+ def __init__(self):
+ """ vtkBaseModule() -> vtkBaseModule
+ Instantiate an emptt VTK Module with real VTK instance
+
+ """
+ Module.__init__(self)
+ self.vtkInstance = None
+
+ def is_cacheable(self):
+ # VTK objects are by default cacheable only if they're subclasses
+ # of vtkAlgorithm
+ return (issubclass(self.vtkClass, vtksnl.vtkAlgorithm)
+ and (not issubclass(self.vtkClass, vtksnl.vtkAbstractMapper)))
+
+ def call_input_function(self, function, params):
+ """self.call_input_function(function, params) -> None
+ Calls the input function on the vtkInstance, or a special
+ input function if one exists in the class."""
+ if hasattr(self, '_special_input_function_' + function):
+ attr = getattr(self, '_special_input_function_' + function)
+ else:
+ try:
+ attr = getattr(self.vtkInstance, function)
+ except AttributeError:
+ # Compensates for overload by exploiting the fact that
+ # no VTK method has underscores.
+ f = function.find('_')
+ if f != -1:
+ function = function[:f]
+ attr = getattr(self.vtkInstance, function)
+ attr(*params)
+ # print "Called ",attr,function,params
+
+ @classmethod
+ def _provide_doc(cls, port_name):
+ f = port_name.find('_')
+ if f != -1:
+ name = port_name[:f]
+ else:
+ name = port_name
+ return getattr(cls.vtkClass, name).__doc__
+
+ @classmethod
+ def provide_input_port_documentation(cls, port_name):
+ return cls._provide_doc(port_name)
+
+ @classmethod
+ def provide_output_port_documentation(cls, port_name):
+ return cls._provide_doc(port_name)
+
+ def compute(self):
+ """ compute() -> None
+ Actually perform real VTK task by directing all input/output ports
+ to VTK function calls
+
+ """
+
+ def call_it(function, p):
+ # Translate between VisTrails objects and VTK objects
+ if p is None:
+ # None indicates a call with no parameters
+ params = []
+ elif type(p) == tuple:
+ # A tuple indicates a call with many parameters
+ params = list(p)
+ else:
+ # Otherwise, it's a single parameter
+ params = [p]
+
+ # Unwraps VTK objects
+ for i in xrange(len(params)):
+ if hasattr(params[i], 'vtkInstance'):
+ params[i] = params[i].vtkInstance
+ try:
+ self.call_input_function(function, params)
+ except Exception, e:
+ msg = 'VTK Exception: '
+ raise ModuleError(self, msg + str(type(e)) + ': ' + str(e))
+
+ # Always re-create vtkInstance module, no caching here
+ if self.vtkInstance:
+ del self.vtkInstance
+ self.vtkInstance = self.vtkClass()
+
+ # We need to call method ports before anything else, and in
+ # the right order.
+
+ # FIXME: This does not belong here, it belongs in the main class
+ # No time for that now
+ methods = self.is_method.values()
+ methods.sort()
+ for value in methods:
+ (_, port) = value
+ conn = self.is_method.inverse[value]
+ p = conn()
+ call_it(port, p)
+
+ # Make sure all input ports are called correctly
+ for (function, connector_list) in self.inputPorts.iteritems():
+ paramList = self.forceGetInputListFromPort(function)
+ if function[:18]=='SetInputConnection':
+ paramList = zip([int(function[18:])]*len(paramList),
+ paramList)
+ function = 'SetInputConnection'
+ if function=='AddInputConnection':
+ desc = registry.get_descriptor_by_name(
+ 'edu.utah.sci.vistrails.vtksnl',
+ 'vtkAlgorithmOutput')
+ for i in xrange(len(paramList)):
+ if type(paramList[i])==desc.module:
+ paramList[i] = (0, paramList[i])
+ for p,connector in izip(paramList, connector_list):
+ # Don't call method
+ if connector in self.is_method:
+ continue
+ call_it(function, p)
+
+ # Call update if appropriate
+ if hasattr(self.vtkInstance, 'Update'):
+ def ProgressEvent(obj, event):
+ self.logging.update_progress(self, obj.GetProgress())
+ isAlgorithm = issubclass(self.vtkClass, vtksnl.vtkAlgorithm)
+ if isAlgorithm:
+ cbId = self.vtkInstance.AddObserver('ProgressEvent', ProgressEvent)
+ self.vtkInstance.Update()
+ if isAlgorithm:
+ self.vtkInstance.RemoveObserver(cbId)
+
+ # Then update the output ports also with appropriate function calls
+ for function in self.outputPorts.keys():
+ if function[:13]=='GetOutputPort':
+ i = int(function[13:])
+ vtkOutput = self.vtkInstance.GetOutputPort(i)
+ output = vtkBaseModule.wrapperModule('vtkAlgorithmOutput',
+ vtkOutput)
+ self.setResult(function, output)
+ elif hasattr(self.vtkInstance, function):
+ retValues = getattr(self.vtkInstance, function)()
+ if issubclass(retValues.__class__, vtksnl.vtkObject):
+ className = retValues.GetClassName()
+ output = vtkBaseModule.wrapperModule(className, retValues)
+ self.setResult(function, output)
+ elif (type(retValues) in [tuple, list]):
+ result = list(retValues)
+ for i in xrange(len(result)):
+ if issubclass(result[i].__class__, vtksnl.vtkObject):
+ className = result[i].GetClassName()
+ result[i] = vtkBaseModule.wrapperModule(className,
+ result[i])
+ self.setResult(function, type(retValues)(result))
+ else:
+ self.setResult(function, retValues)
+
+ @staticmethod
+ def wrapperModule(classname, instance):
+ """ wrapperModule(classname: str, instance: vtk class) -> Module
+ Create a wrapper module in VisTrails with a vtk instance
+
+ """
+ result = registry.get_descriptor_by_name(
+ 'edu.utah.sci.vistrails.vtksnl',
+ classname).module()
+ result.vtkInstance = instance
+ return result
diff --git a/contrib/vtksnl/class_tree.py b/contrib/vtksnl/class_tree.py
new file mode 100644
index 0000000..75f8566
--- /dev/null
+++ b/contrib/vtksnl/class_tree.py
@@ -0,0 +1,268 @@
+# Author: Prabhu Ramachandran
+# Copyright (c) 2004, Enthought, Inc.
+# License: BSD Style.
+
+"""This module generates the class hierarchy for any given Python
+modules. This can be used (among other things) to generate the
+traitified VTK classes in the correct order.
+
+"""
+
+import __builtin__
+
+
+class TreeNode(object):
+ """Represents a node in the class tree.
+
+ Stores information on the sub and super classes of a particular
+ class. It also stores the inheritance level of the class inside
+ the inheritance tree (essentially how many levels of inheritance
+ are there below this class). This inheritance level is computed
+ when the `get_level` method is called. The `get_level` method
+ works only when the parent information is complete.
+
+ """
+
+ def __init__(self, klass):
+ """Given a class, create a node in the tree.
+
+ Parameters
+ ----------
+ - klass : `class`
+
+ The class which is represented as a node in the tree.
+
+ """
+ self.klass = klass
+ self.name = klass.__name__
+ self.children = []
+ self.parents = []
+ # Uninitialized level is set to None
+ self.level = None
+
+ def add_parent(self, parent):
+ """Add a parent node."""
+ assert isinstance(parent, TreeNode)
+ if parent not in self.parents:
+ self.parents.append(parent)
+
+ def add_child(self, child):
+ """Add a child node. """
+ assert isinstance(child, TreeNode)
+ if child not in self.children:
+ self.children.append(child)
+
+ def get_level(self):
+ """Returns the inheritance level of the node (an int). If the
+ level has not been set, the method computes it. Note however,
+ that this computation will fail if the parent information is
+ incorrect.
+
+ """
+ if not self.level:
+ if self.parents:
+ self.level = max([x.get_level() for x in self.parents]) + 1
+ else:
+ self.level = 0
+ return self.level
+
+ def get_ancestors(self):
+ """Returns a list of ancestor nodes from which this class has
+ descended.
+
+ """
+ def _get_ancestors(node, ancestors):
+ ancestors.extend(node.parents)
+ for p in node.parents:
+ _get_ancestors(p, ancestors)
+ ancestors = []
+ _get_ancestors(self, ancestors)
+ return ancestors
+
+
+class ClassTree(object):
+ """Contains and generates all the class tree information.
+
+ On initialization of the instance, nothing is done. The classes
+ are obtained using the list of modules (or a single module) that
+ is used to initialize the instance. One must then call the
+ `create` method to generate the tree structure. The instance of
+ the class also can be treated as an iterator which iterates over
+ the nodes of the tree.
+
+ There are two ways in which the tree hierarchy is stored. A
+ dictionary mapping class names to the tree node and a tree
+ represented as a list of lists containing the nodes. The tree is
+ organized based on a concept of an inheritance level. A class
+ that has no parent classes (no base classes) is said to be at
+ level zero. If a class inherits successively from 7 classes, it
+ is at level 6. An example of inheritance for a vtkFoo class is
+ given below:
+
+ vtkFoo -> vtkBar -> vtkObject -> vtkObjectBase
+
+ Here, vtkObjectBase has an inheritance level of 0 and vtkFoo a
+ level of 3. One can traverse the tree by using the level as an
+ index and find all the classes at a particular level.
+
+ Here is some example usage of this class::
+
+ >>> import vtk
+ >>> t = ClassTree(vtk)
+ >>> t.create()
+ >>> print t.get_node('vtkObject').name
+ vtkObject
+ >>> print t.get_node('vtkObject').parents[0].name
+ vtkObjectBase
+ >>> print len(t.tree[0])
+ 1
+ >>> t.tree[0][0].name
+ vtkObjectBase
+
+ """
+
+ def __init__(self, modules):
+ """Initialize the instance with the given modules.
+
+ Parameters
+ ----------
+
+ - modules : `sequence` of modules or a module
+
+ This is either a single module or a sequence of modules.
+ The instance uses these list of modules to generate the
+ class tree.
+
+ """
+ self.nodes = {}
+ self.tree = [[]]
+ if not hasattr(modules, '__iter__'):
+ self.modules = [modules]
+ else:
+ self.modules = modules
+
+ def __iter__(self):
+ return iter(self.nodes.values())
+
+ def _generate_hierarchy(self, klass):
+ """Does the hard work of generating the class hierarchy."""
+ node = self.get_node(klass.__name__, create=1)
+ for base in klass.__bases__:
+ base_node = self.get_node_from_class(base, create=1)
+ node.add_parent(base_node)
+ base_node.add_child(node)
+ self._generate_hierarchy(base)
+
+ def get_class(self, name):
+ """Given a class name in the given modules returns the class."""
+ klass = None
+ for m in self.modules:
+ if hasattr(m, name):
+ return getattr(m, name)
+ if hasattr(__builtin__, name):
+ klass = getattr(__builtin__, name)
+ if not klass:
+ try:
+ klass = self.nodes[name].klass
+ except KeyError:
+ raise KeyError, "Cannot find class of name %s"%name
+ return klass
+
+ def add_node(self, klass):
+ """Create a node for the given class."""
+ name = klass.__name__
+ if not self.nodes.has_key(name):
+ node = TreeNode(klass)
+ self.nodes[name] = node
+ return node
+
+ def get_node(self, name, create=0):
+ """Get a node of the given name.
+
+ Parameters
+ ----------
+
+ - name : `str`
+
+ Name of the node to get.
+
+ - create : `boolean`
+
+ If True, a new node will be added if no node of the given
+ name is available. Defaults to False.
+
+ Returns
+ -------
+
+ - `TreeNode`
+
+ """
+ if self.nodes.has_key(name):
+ return self.nodes[name]
+ elif create:
+ return self.add_node(self.get_class(name))
+
+ def get_node_from_class(self, cls, create=0):
+ """Get a node of the given class.
+
+ Parameters
+ ----------
+
+ - cls : `class`
+
+ Class of the node to get.
+
+ - create : `boolean`
+
+ If True, a new node will be added if no node of the given
+ name is available. Defaults to False.
+
+ Returns
+ -------
+
+ - `TreeNode`
+
+ """
+ name = cls.__name__
+ if self.nodes.has_key(name):
+ return self.nodes[name]
+ elif create:
+ return self.add_node(cls)
+
+ def create(self, class_names=None):
+ """This method generates the class tree given an optional list
+ of class names.
+
+ Parameters
+ ----------
+
+ - class_names - `list` of `str`
+
+ An optional list of names of the classes to generate the
+ tree for. Defaults to None where the class list is computed
+ from the modules.
+
+ """
+ if class_names is None:
+ class_names = []
+ for m in self.modules:
+ class_names.extend(dir(m))
+
+ # Generate the nodes.
+ for name in class_names:
+ klass = self.get_class(name)
+ if klass and hasattr(klass, '__bases__'):
+ self._generate_hierarchy(klass)
+
+ # Compute the inheritance level and store the nodes in the tree.
+ for node in self:
+ d = node.get_level()
+ while len(self.tree) <= d:
+ self.tree.append([])
+ self.tree[d].append(node)
+
+ # Sort the nodes alphabetically.
+ def _comp(x, y):
+ return cmp(x.name, y.name)
+ for nodes in self.tree:
+ nodes.sort(_comp)
diff --git a/contrib/vtksnl/fix_classes.py b/contrib/vtksnl/fix_classes.py
new file mode 100644
index 0000000..90b608d
--- /dev/null
+++ b/contrib/vtksnl/fix_classes.py
@@ -0,0 +1,51 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+import vtksnl
+
+################################################################################
+# Some fixed classes that solve a few VTK API issues
+
+# This dictionary stores the patched class to vtk class mapping.
+# This would be naturally better stored as an attribute directly on the
+# patched class. VTK, however, doesn't like class attributes.
+description = {}
+
+# http://www.vtk.org/doc/nightly/html/classvtkImagePlaneWidget.html
+# SetUserControlledLookupTable needs to be set before calling
+# SetLookupTable. VTK should do it automatically, so let's fix it
+
+
+# This fix seems to break on VTK versions larger than 5.0.3. It might also
+# be because of an interaction with python 2.6, but I haven't checked that.
+class vtkImagePlaneWidget_fixed(vtksnl.vtkImagePlaneWidget):
+ def SetLookupTable(self, lookup_table):
+ self.UserControlledLookupTableOn()
+ vtksnl.vtkImagePlaneWidget.SetLookupTable(self, lookup_table)
+
+if tuple(vtksnl.vtkVersion().GetVTKVersion().split('.')) < ('5', '0', '4'):
+ description[vtkImagePlaneWidget_fixed] = vtksnl.vtkImagePlaneWidget
+else:
+ description[id(vtkImagePlaneWidget_fixed)] = vtksnl.vtkImagePlaneWidget
+
+# Set docstring to wrap it correctly
+vtkImagePlaneWidget_fixed.SetLookupTable.__doc__ = vtksnl.vtkImagePlaneWidget.SetLookupTable.__doc__
diff --git a/contrib/vtksnl/hasher.py b/contrib/vtksnl/hasher.py
new file mode 100644
index 0000000..34909ec
--- /dev/null
+++ b/contrib/vtksnl/hasher.py
@@ -0,0 +1,36 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+# This is the user-defined hasher for VTK, that takes into account
+# incoming and outgoing connections
+from core.cache.hasher import Hasher
+
+def vtk_hasher(pipeline, module, chm):
+ outgoing_connections = pipeline.graph.edges_from(module.id)
+ incoming_connections = pipeline.graph.edges_to(module.id)
+ current_hash = Hasher.module_signature(module, chm)
+ chashes = [Hasher.connection_signature(pipeline.connections[c_id])
+ for (_, c_id) in outgoing_connections]
+ chashes += [Hasher.connection_signature(pipeline.connections[c_id])
+ for (_, c_id) in incoming_connections]
+ compound_hash = Hasher.compound_signature(chashes)
+ return Hasher.compound_signature([current_hash, compound_hash])
diff --git a/contrib/vtksnl/init.py b/contrib/vtksnl/init.py
new file mode 100644
index 0000000..118f102
--- /dev/null
+++ b/contrib/vtksnl/init.py
@@ -0,0 +1,1073 @@
+###########################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+################################################################################
+# VTK-SNL Package for VisTrails (Sandia National Laboratories)
+################################################################################
+
+from core.bundles import py_import
+import vtksnl
+
+from core.utils import all, any, VistrailsInternalError, InstanceObject
+from core.debug import debug
+from core.modules.basic_modules import Integer, Float, String, File, \
+ Variant, Color
+from core.modules.module_registry import get_module_registry
+from core.modules.vistrails_module import new_module, ModuleError
+from base_module import vtkBaseModule
+from class_tree import ClassTree
+from vtk_parser import VTKMethodParser
+import re
+import os.path
+from itertools import izip
+from vtkcell import VTKCell
+import tf_widget
+import offscreen
+import fix_classes
+import inspectors
+from hasher import vtk_hasher
+import sys
+
+################################################################################
+
+# filter some deprecation warnings coming from the fact that vtk calls
+# range() with float parameters
+
+import warnings
+warnings.filterwarnings("ignore",
+ message="integer argument expected, got float")
+
+################################################################################
+
+if tuple(vtksnl.vtkVersion().GetVTKVersion().split('.')) < ('5', '0', '4'):
+ def get_description_class(klass):
+ """Because sometimes we need to patch VTK classes, the klass that
+ has the methods is different than the klass we want to
+ instantiate. get_description_class makes sure that for patched
+ classes we get the correct one."""
+ try:
+ return fix_classes.description[klass]
+ except KeyError:
+ return klass
+else:
+ # On VTK 5.0.4, we use the id of the class to hash, because it
+ # seems that VTK hasn't implemented hash() correctly for their
+ # classes.
+ def get_description_class(klass):
+ """Because sometimes we need to patch VTK classes, the klass that
+ has the methods is different than the klass we want to
+ instantiate. get_description_class makes sure that for patched
+ classes we get the correct one."""
+ try:
+ return fix_classes.description[id(klass)]
+ except KeyError:
+ return klass
+
+parser = VTKMethodParser()
+
+typeMapDict = {'int': Integer,
+ 'long': Integer,
+ 'float': Float,
+ 'char*': String,
+ 'char *': String,
+ 'string': String,
+ 'char': String,
+ 'const char*': String,
+ 'const char *': String}
+typeMapDictValues = [Integer, Float, String]
+
+file_name_pattern = re.compile('.*FileName$')
+set_file_name_pattern = re.compile('Set.*FileName$')
+
+def resolve_overloaded_name(name, ix, signatures):
+ # VTK supports static overloading, VisTrails does not. The
+ # solution is to check whether the current function has
+ # overloads and change the names appropriately.
+ if len(signatures) == 1:
+ return name
+ else:
+ return name + '_' + str(ix+1)
+
+def typeMap(name, package=None):
+ """ typeMap(name: str) -> Module
+ Convert from C/C++ types into VisTrails Module type
+
+ """
+ if package is None:
+ package = identifier
+ if type(name) == tuple:
+ return [typeMap(x, package) for x in name]
+ if name in typeMapDict:
+ return typeMapDict[name]
+ else:
+ registry = get_module_registry()
+ if not registry.has_descriptor_with_name(package, name):
+ return None
+ else:
+ return registry.get_descriptor_by_name(package,
+ name).module
+
+def get_method_signature(method):
+ """ get_method_signature(method: vtkmethod) -> [ret, arg]
+ Re-wrap Prabu's method to increase performance
+
+ """
+ doc = method.__doc__
+ tmptmp = doc.split('\n')
+ tmp = []
+ for l in tmptmp:
+ l = l.strip('\n \t')
+ if l.startswith('V.') or l.startswith('C++:'):
+ tmp.append(l)
+ else:
+ tmp[-1] = tmp[-1] + l
+ tmp.append('')
+ sig = []
+ pat = re.compile(r'\b')
+
+ # Remove all the C++ function signatures and V.<method_name> field
+ offset = 2+len(method.__name__)
+ for i in xrange(len(tmp)):
+ s = tmp[i]
+ if s=='': break
+ if i%2==0:
+ x = s.split('->')
+ arg = x[0].strip()[offset:]
+ if len(x) == 1: # No return value
+ ret = None
+ else:
+ ret = x[1].strip()
+
+ # Remove leading and trailing parens for arguments.
+ arg = arg[1:-1]
+ if not arg:
+ arg = None
+ if arg and arg[-1] == ')':
+ arg = arg + ','
+
+ # Now quote the args and eval them. Easy!
+ if ret and ret[:3]!='vtk':
+ try:
+ ret = eval(pat.sub('\"', ret))
+ except:
+ continue
+ if arg:
+ if arg.find('(')!=-1:
+ try:
+ arg = eval(pat.sub('\"', arg))
+ except:
+ continue
+ else:
+ arg = arg.split(', ')
+ if len(arg)>1:
+ arg = tuple(arg)
+ else:
+ arg = arg[0]
+ if type(arg) == str:
+ arg = [arg]
+
+ sig.append(([ret], arg))
+ return sig
+
+def prune_signatures(module, name, signatures, output=False):
+ """prune_signatures tries to remove redundant signatures to reduce
+ overloading. It _mutates_ the given parameter.
+
+ It does this by performing several operations:
+
+ 1) It compares a 'flattened' version of the types
+ against the other 'flattened' signatures. If any of them match, we
+ keep only the 'flatter' ones.
+
+ A 'flattened' signature is one where parameters are not inside a
+ tuple.
+
+ 2) We explicitly forbid a few signatures based on modules and names
+
+ """
+ # yeah, this is Omega(n^2) on the number of overloads. Who cares?
+
+ def flatten(type_):
+ if type_ is None:
+ return []
+ def convert(entry):
+ if type(entry) == tuple:
+ return list(entry)
+ else:
+ assert(type(entry) == str)
+ return [entry]
+ result = []
+ for entry in type_:
+ result.extend(convert(entry))
+ return result
+
+ flattened_entries = [flatten(sig[1]) for
+ sig in signatures]
+ def hit_count(entry):
+ result = 0
+ for entry in flattened_entries:
+ if entry in flattened_entries:
+ result += 1
+ return result
+ hits = [hit_count(entry) for entry in flattened_entries]
+
+ def forbidden(flattened, hit_count, original):
+ if (issubclass(get_description_class(module.vtkClass), vtksnl.vtk3DWidget) and
+ name == 'PlaceWidget' and
+ flattened == []):
+ return True
+ # We forbid this because addPorts hardcodes this but
+ # SetInputArrayToProcess is an exception for the InfoVis
+ # package
+ if (get_description_class(module.vtkClass) == vtksnl.vtkAlgorithm and
+ name!='SetInputArrayToProcess'):
+ return True
+ return False
+
+ # This is messy: a signature is only allowed if there's no
+ # explicit disallowing of it. Then, if it's not overloaded,
+ # it is also allowed. If it is overloaded and not the flattened
+ # version, it is pruned. If these are output ports, there can be
+ # no parameters.
+
+ def passes(flattened, hit_count, original):
+ if forbidden(flattened, hit_count, original):
+ return False
+ if hit_count == 1:
+ return True
+ if original[1] is None:
+ return True
+ if output and len(original[1]) > 0:
+ return False
+ if hit_count > 1 and len(original[1]) == len(flattened):
+ return True
+ return False
+
+ signatures[:] = [original for (flattened, hit_count, original)
+ in izip(flattened_entries,
+ hits,
+ signatures)
+ if passes(flattened, hit_count, original)]
+
+ #then we remove the duplicates, if necessary
+ unique_signatures = []
+ [unique_signatures.append(s) for s in signatures if not unique_signatures.count(s)]
+ signatures[:] = unique_signatures
+
+disallowed_classes = set(
+ [
+ 'vtkCriticalSection',
+ 'vtkDataArraySelection',
+ 'vtkDebugLeaks',
+ 'vtkDirectory',
+ 'vtkDynamicLoader',
+ 'vtkFunctionParser',
+ 'vtkGarbageCollector',
+ 'vtkHeap',
+ 'vtkInformationKey',
+ 'vtkInstantiator',
+ 'vtkLogLookupTable', # VTK: use vtkLookupTable.SetScaleToLog10() instead
+ 'vtkMath',
+ 'vtkModelMetadata',
+ 'vtkMultiProcessController',
+ 'vtkMutexLock',
+ 'vtkOutputWindow',
+ 'vtkPriorityQueue',
+ 'vtkReferenceCount',
+ 'vtkRenderWindowCollection',
+ 'vtkRenderWindowInteractor',
+ 'vtkTesting',
+ 'vtkWindow',
+ 'vtksnlVersion',
+ 'vtkDiffFilter',
+ 'vtkDocumentM3MetaData'
+ #'vtkXMLUtilities',
+ #'vtkXMLShader',
+ #'vtkXMLMaterialReader',
+ #'vtkXMLMaterial',
+ #'vtkXMLDataElement'
+ ])
+
+def is_class_allowed(module):
+ if module is None:
+ return False
+ try:
+ name = module.__name__
+ return not (name in disallowed_classes)
+ except AttributeError:
+ return True
+
+def addAlgorithmPorts(module):
+ """ addAlgorithmPorts(module: Module) -> None
+ If module is a subclass of vtkAlgorithm, this function will add all
+ SetInputConnection([id],[port]) and GetOutputPort([id]) as
+ SetInputConnection{id}([port]) and GetOutputPort{id}.
+
+ """
+ if issubclass(get_description_class(module.vtkClass), vtksnl.vtkAlgorithm):
+ if get_description_class(module.vtkClass)!=vtksnl.vtkStructuredPointsGeometryFilter:
+ # We try to instantiate the class here to get the number of
+ # ports and to avoid abstract classes
+ try:
+ instance = module.vtkClass()
+ except TypeError:
+ pass
+ else:
+ registry = get_module_registry()
+ des = registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtksnl',
+ 'vtkAlgorithmOutput')
+ for i in xrange(0,instance.GetNumberOfInputPorts()):
+ registry.add_input_port(module, 'SetInputConnection%d'%i,
+ des.module)
+ for i in xrange(0,instance.GetNumberOfOutputPorts()):
+ registry.add_output_port(module, 'GetOutputPort%d'%i,
+ des.module)
+
+disallowed_set_get_ports = set(['ReferenceCount',
+ 'InputConnection',
+ 'OutputPort',
+ 'Progress',
+ 'ProgressText',
+ 'InputArrayToProcess',
+ ])
+def addSetGetPorts(module, get_set_dict, delayed):
+ """ addSetGetPorts(module: Module, get_set_dict: dict) -> None
+ Convert all Setxxx methods of module into input ports and all Getxxx
+ methods of module into output ports
+
+ Keyword arguments:
+ module --- Module
+ get_set_dict --- the Set/Get method signatures returned by vtk_parser
+
+ """
+
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in get_set_dict.iterkeys():
+ if name in disallowed_set_get_ports: continue
+ getterMethod = getattr(klass, 'Get%s'%name)
+ setterMethod = getattr(klass, 'Set%s'%name)
+ getterSig = get_method_signature(getterMethod)
+ setterSig = get_method_signature(setterMethod)
+ if len(getterSig) > 1:
+ prune_signatures(module, 'Get%s'%name, getterSig, output=True)
+ for order, getter in enumerate(getterSig):
+ if getter[1]:
+ debug("Can't handle getter %s (%s) of class %s: Needs input to "
+ "get output" % (order+1, name, klass))
+ continue
+ if len(getter[0]) != 1:
+ debug("Can't handle getter %s (%s) of class %s: More than a "
+ "single output" % (order+1, name, str(klass)))
+ continue
+ class_ = typeMap(getter[0][0])
+ if is_class_allowed(class_):
+ registry.add_output_port(module, 'Get'+name, class_, True)
+ if len(setterSig) > 1:
+ prune_signatures(module, 'Set%s'%name, setterSig)
+ for ix, setter in enumerate(setterSig):
+ if setter[1]==None: continue
+ n = resolve_overloaded_name('Set' + name, ix, setterSig)
+ if len(setter[1]) == 1 and is_class_allowed(typeMap(setter[1][0])):
+ registry.add_input_port(module, n,
+ typeMap(setter[1][0]),
+ setter[1][0] in typeMapDict)
+ else:
+ classes = [typeMap(i) for i in setter[1]]
+ if all(is_class_allowed(x) for x in classes):
+ registry.add_input_port(module, n, classes, True)
+ # Wrap SetFileNames for VisTrails file access
+ if file_name_pattern.match(name):
+ registry.add_input_port(module, 'Set' + name[:-4],
+ (File, 'input file'), False)
+ # Wrap SetRenderWindow for exporters
+ elif name == 'RenderWindow':
+ # cscheid 2008-07-11 This is messy: VTKCell isn't
+ # registered yet, so we can't use it as a port
+ # However, we can't register VTKCell before these either,
+ # because VTKCell requires vtkRenderer. The "right" way would
+ # be to add all modules first, then all ports. However, that would
+ # be too slow.
+ # Workaround: delay the addition of the port by storing
+ # the information in a list
+ if registry.has_module('edu.utah.sci.vistrails.spreadsheet',
+ 'SpreadsheetCell'):
+ delayed.add_input_port.append((module, 'SetVTKCell', VTKCell, False))
+ # Wrap color methods for VisTrails GUI facilities
+ elif name == 'DiffuseColor':
+ registry.add_input_port(module, 'SetDiffuseColorWidget',
+ (Color, 'color'), True)
+ elif name == 'Color':
+ registry.add_input_port(module, 'SetColorWidget',
+ (Color, 'color'), True)
+ elif name == 'AmbientColor':
+ registry.add_input_port(module, 'SetAmbientColorWidget',
+ (Color, 'color'), True)
+ elif name == 'SpecularColor':
+ registry.add_input_port(module, 'SetSpecularColorWidget',
+ (Color, 'color'), True)
+ elif name == 'EdgeColor':
+ registry.add_input_port(module, 'SetEdgeColorWidget',
+ (Color, 'color'), True)
+ elif name == 'Background' :
+ registry.add_input_port(module, 'SetBackgroundWidget',
+ (Color, 'color'), True)
+ elif name == 'Background2' :
+ registry.add_input_port(module, 'SetBackground2Widget',
+ (Color, 'color'), True)
+
+disallowed_toggle_ports = set(['GlobalWarningDisplay',
+ 'Debug',
+ ])
+def addTogglePorts(module, toggle_dict):
+ """ addTogglePorts(module: Module, toggle_dict: dict) -> None
+ Convert all xxxOn/Off methods of module into input ports
+
+ Keyword arguments:
+ module --- Module
+ toggle_dict --- the Toggle method signatures returned by vtk_parser
+
+ """
+ registry = get_module_registry()
+ for name in toggle_dict.iterkeys():
+ if name in disallowed_toggle_ports:
+ continue
+ registry.add_input_port(module, name+'On', [], True)
+ registry.add_input_port(module, name+'Off', [], True)
+
+disallowed_state_ports = set(['SetInputArrayToProcess'])
+def addStatePorts(module, state_dict):
+ """ addStatePorts(module: Module, state_dict: dict) -> None
+ Convert all SetxxxToyyy methods of module into input ports
+
+ Keyword arguments:
+ module --- Module
+ state_dict --- the State method signatures returned by vtk_parser
+
+ """
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in state_dict.iterkeys():
+ for mode in state_dict[name]:
+ # Creates the port Set foo to bar
+ field = 'Set'+name+'To'+mode[0]
+ if field in disallowed_state_ports:
+ continue
+ if not registry.has_input_port(module, field):
+ registry.add_input_port(module, field, [], True)
+
+ # Now create the port Set foo with parameter
+ if hasattr(klass, 'Set%s'%name):
+ setterMethod = getattr(klass, 'Set%s'%name)
+ setterSig = get_method_signature(setterMethod)
+ # if the signature looks like an enum, we'll skip it, it shouldn't
+ # be necessary
+ if len(setterSig) > 1:
+ prune_signatures(module, 'Set%s'%name, setterSig)
+ for ix, setter in enumerate(setterSig):
+ n = resolve_overloaded_name('Set' + name, ix, setterSig)
+ tm = typeMap(setter[1][0])
+ if len(setter[1]) == 1 and is_class_allowed(tm):
+ registry.add_input_port(module, n, tm,
+ setter[1][0] in typeMapDict)
+ else:
+ classes = [typeMap(i) for i in setter[1]]
+ if all(is_class_allowed(x) for x in classes):
+ registry.add_input_port(module, n, classes, True)
+
+disallowed_other_ports = set(
+ [
+ 'BreakOnError',
+ 'DeepCopy',
+ 'FastDelete',
+ 'HasObserver',
+ 'HasExecutive',
+ 'INPUT_ARRAYS_TO_PROCESS',
+ 'INPUT_CONNECTION',
+ 'INPUT_IS_OPTIONAL',
+ 'INPUT_IS_REPEATABLE',
+ 'INPUT_PORT',
+ 'INPUT_REQUIRED_DATA_TYPE',
+ 'INPUT_REQUIRED_FIELDS',
+ 'InvokeEvent',
+ 'IsA',
+ 'Modified',
+ 'NewInstance',
+ 'PrintRevisions',
+ 'RemoveAllInputs',
+ 'RemoveObserver',
+ 'RemoveObservers',
+ 'SafeDownCast',
+# 'SetInputArrayToProcess',
+ 'ShallowCopy',
+ 'Update',
+ 'UpdateInformation',
+ 'UpdateProgress',
+ 'UpdateWholeExtent',
+ ])
+
+force_not_optional_port = set(
+ ['ApplyViewTheme',
+ ])
+
+
+def addOtherPorts(module, other_list):
+ """ addOtherPorts(module: Module, other_list: list) -> None
+ Convert all other ports such as Insert/Add.... into input/output
+
+ Keyword arguments:
+ module --- Module
+ other_dict --- any other method signatures that is not
+ Algorithm/SetGet/Toggle/State type
+
+ """
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in other_list:
+ if name[:3] in ['Add','Set'] or name[:6]=='Insert':
+ if name in disallowed_other_ports:
+ continue
+ method = getattr(klass, name)
+ signatures = get_method_signature(method)
+ if len(signatures) > 1:
+ prune_signatures(module, name, signatures)
+ for (ix, sig) in enumerate(signatures):
+ ([result], params) = sig
+ types = []
+ if params:
+ for p in params:
+ t = typeMap(p)
+ if not t:
+ types = None
+ break
+ else: types.append(t)
+ else:
+ types = [[]]
+ if types:
+ if not all(is_class_allowed(x) for x in types):
+ continue
+ n = resolve_overloaded_name(name, ix, signatures)
+ if len(types)<=1:
+ registry.add_input_port(module, n, types[0],
+ types[0] in typeMapDictValues)
+ else:
+ registry.add_input_port(module, n, types, True)
+ else:
+ if name in disallowed_other_ports:
+ continue
+ method = getattr(klass, name)
+ signatures = get_method_signature(method)
+ if len(signatures) > 1:
+ prune_signatures(module, name, signatures)
+ for (ix, sig) in enumerate(signatures):
+ ([result], params) = sig
+ types = []
+ if params:
+ types = [typeMap(p) for p in params]
+ else:
+ types = []
+ if not all(is_class_allowed(x) for x in types):
+ continue
+ if types==[] or (result==None):
+ n = resolve_overloaded_name(name, ix, signatures)
+ registry.add_input_port(module, n, types,
+ not (n in force_not_optional_port))
+
+disallowed_get_ports = set([
+ 'GetClassName',
+ 'GetErrorCode',
+ 'GetNumberOfInputPorts',
+ 'GetNumberOfOutputPorts',
+ 'GetOutputPortInformation',
+ 'GetTotalNumberOfInputConnections',
+ ])
+
+def addGetPorts(module, get_list):
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in get_list:
+ if name in disallowed_get_ports:
+ continue
+ method = getattr(klass, name)
+ signatures = get_method_signature(method)
+ if len(signatures) > 1:
+ prune_signatures(module, name, signatures, output=True)
+ for ix, getter in enumerate(signatures):
+ if getter[1] or len(getter[0]) > 1:
+ continue
+ class_ = typeMap(getter[0][0])
+ if is_class_allowed(class_):
+ if len(signatures) > 1:
+ n = name + "_" + str(ix+1)
+ else:
+ n = name
+ registry.add_output_port(module, n, class_, True)
+
+def addPorts(module, delayed):
+ """ addPorts(module: VTK module inherited from Module,
+ delayed: object with add_input_port slot
+ ) -> None
+
+ Search all metamethods of module and add appropriate ports
+
+ ports that cannot be added immediately should be appended to
+ the delayed object that is passed. see the SetRenderWindow cases.
+
+ """
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ registry.add_output_port(module, 'self', module)
+ parser.parse(klass)
+ addAlgorithmPorts(module)
+ addGetPorts(module, parser.get_get_methods())
+ addSetGetPorts(module, parser.get_get_set_methods(), delayed)
+ addTogglePorts(module, parser.get_toggle_methods())
+ addStatePorts(module, parser.get_state_methods())
+ addOtherPorts(module, parser.get_other_methods())
+ # CVS version of VTK doesn't support AddInputConnect(vtkAlgorithmOutput)
+ if klass==vtksnl.vtkAlgorithm:
+ registry.add_input_port(module, 'AddInputConnection',
+ typeMap('vtkAlgorithmOutput'))
+ # vtkWriters have a custom File port
+ elif klass==vtksnl.vtkWriter:
+ registry.add_output_port(module, 'file',
+ typeMap('File','edu.utah.sci.vistrails.basic'))
+ elif klass==vtksnl.vtkImageWriter:
+ registry.add_output_port(module, 'file',
+ typeMap('File','edu.utah.sci.vistrails.basic'))
+ elif klass==vtksnl.vtkVolumeProperty:
+ registry.add_input_port(module, 'SetTransferFunction',
+ typeMap('TransferFunction'))
+ elif klass==vtksnl.vtkDataSet:
+ registry.add_input_port(module, 'SetPointData', typeMap('vtkPointData'))
+ registry.add_input_port(module, 'SetCallData', typeMap('vtkCellData'))
+ elif klass==vtksnl.vtkCell:
+ registry.add_input_port(module, 'SetPointIds', typeMap('vtkIdList'))
+
+def setAllPorts(descriptor, delayed):
+ """ setAllPorts(descriptor: ModuleDescriptor) -> None
+ Traverse descriptor and all of its children/grand-children to add all ports
+
+ """
+ addPorts(descriptor.module, delayed)
+ for child in descriptor.children:
+ setAllPorts(child, delayed)
+
+def class_dict(base_module, node):
+ """class_dict(base_module, node) -> dict
+ Returns the class dictionary for the module represented by node and
+ with base class base_module"""
+
+ class_dict_ = {}
+ def update_dict(name, callable_):
+ if class_dict_.has_key(name):
+ class_dict_[name] = callable_(class_dict_[name])
+ elif hasattr(base_module, name):
+ class_dict_[name] = callable_(getattr(base_module, name))
+ else:
+ class_dict_[name] = callable_(None)
+
+ def guarded_SimpleScalarTree_wrap_compute(old_compute):
+ # This builds the scalar tree and makes it cacheable
+
+ def compute(self):
+ self.is_cacheable = lambda *args, **kwargs: True
+ old_compute(self)
+ self.vtkInstance.BuildTree()
+ return compute
+
+ def guarded_SetFileName_wrap_compute(old_compute):
+ # This checks for the presence of file in VTK readers
+ def compute(self):
+
+ # Skips the check if it's a vtkImageReader or vtkPLOT3DReader, because
+ # it has other ways of specifying files, like SetFilePrefix for
+ # multiple files
+ if any(issubclass(self.vtkClass, x)
+ for x in
+ [vtksnl.vtkBYUReader,
+ vtksnl.vtkImageReader,
+ vtksnl.vtkPLOT3DReader,
+ vtksnl.vtkDICOMImageReader,
+ vtksnl.vtkTIFFReader]):
+ old_compute(self)
+ return
+ if self.hasInputFromPort('SetFileName'):
+ name = self.getInputFromPort('SetFileName')
+ elif self.hasInputFromPort('SetFile'):
+ name = self.getInputFromPort('SetFile').name
+ else:
+ raise ModuleError(self, 'Missing filename')
+ if not os.path.isfile(name):
+ raise ModuleError(self, 'File does not exist')
+ old_compute(self)
+ return compute
+
+ def compute_SetDiffuseColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetDiffuseColorWidget(self, color):
+ self.vtkInstance.SetDiffuseColor(color.tuple)
+ return call_SetDiffuseColorWidget
+
+ def compute_SetAmbientColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetAmbientColorWidget(self, color):
+ self.vtkInstance.SetAmbientColor(color.tuple)
+ return call_SetAmbientColorWidget
+
+ def compute_SetSpecularColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetSpecularColorWidget(self, color):
+ self.vtkInstance.SetSpecularColor(color.tuple)
+ return call_SetSpecularColorWidget
+
+ def compute_SetColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetColorWidget(self, color):
+ self.vtkInstance.SetColor(color.tuple)
+ return call_SetColorWidget
+
+ def compute_SetEdgeColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetEdgeColorWidget(self, color):
+ self.vtkInstance.SetEdgeColor(color.tuple)
+ return call_SetEdgeColorWidget
+
+ def compute_SetBackgroundWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetBackgroundWidget(self, color):
+ self.vtkInstance.SetBackground(color.tuple)
+ return call_SetBackgroundWidget
+
+ def compute_SetBackground2Widget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetBackground2Widget(self, color):
+ self.vtkInstance.SetBackground2(color.tuple)
+ return call_SetBackground2Widget
+
+ def compute_SetVTKCell(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetRenderWindow(self, cellObj):
+ if cellObj.cellWidget:
+ self.vtkInstance.SetRenderWindow(cellObj.cellWidget.mRenWin)
+ return call_SetRenderWindow
+
+ def compute_SetTransferFunction(old_compute):
+ # This sets the transfer function
+ if old_compute != None:
+ return old_compute
+ def call_SetTransferFunction(self, tf):
+ tf.set_on_vtk_volume_property(self.vtkInstance)
+ return call_SetTransferFunction
+
+ def compute_SetPointData(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetPointData(self, pd):
+ self.vtkInstance.GetPointData().ShallowCopy(pd)
+ return call_SetPointData
+
+ def compute_SetCellData(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetCellData(self, cd):
+ self.vtkInstance.GetCellData().ShallowCopy(cd)
+ return call_SetCellData
+
+ def compute_SetPointIds(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetPointIds(self, point_ids):
+ self.vtkInstance.GetPointIds().SetNumberOfIds(point_ids.GetNumberOfIds())
+ for i in xrange(point_ids.GetNumberOfIds()):
+ self.vtkInstance.GetPointIds().SetId(i, point_ids.GetId(i))
+ return call_SetPointIds
+
+ def guarded_Writer_wrap_compute(old_compute):
+ # The behavior for vtkWriter subclasses is to call Write()
+ # If the user sets a name, we will create a file with that name
+ # If not, we will create a temporary file from the file pool
+ def compute(self):
+ old_compute(self)
+ fn = self.vtkInstance.GetFileName()
+ if not fn:
+ o = self.interpreter.filePool.create_file(suffix='.vtk')
+ self.vtkInstance.SetFileName(o.name)
+ else:
+ o = File()
+ o.name = fn
+ self.vtkInstance.Write()
+ self.setResult('file', o)
+ return compute
+
+ for var in dir(node.klass):
+ # Everyone that has a Set.*FileName should have a Set.*File port too
+ if set_file_name_pattern.match(var):
+ def get_compute_SetFile(method_name):
+ def compute_SetFile(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetFile(self, file_obj):
+ getattr(self.vtkInstance, method_name)(file_obj.name)
+ return call_SetFile
+ return compute_SetFile
+ update_dict('_special_input_function_' + var[:-4],
+ get_compute_SetFile(var))
+
+ if hasattr(node.klass, 'SetFileName'):
+ # ... BUT we only want to check existence of filenames on
+ # readers. VTK is nice enough to be consistent with names, but
+ # this is brittle..
+ if node.klass.__name__.endswith('Reader'):
+ if not node.klass.__name__.endswith('TiffReader'):
+ update_dict('compute', guarded_SetFileName_wrap_compute)
+ if hasattr(node.klass, 'SetRenderWindow'):
+ update_dict('_special_input_function_SetVTKCell',
+ compute_SetVTKCell)
+ #color gui wrapping
+ if hasattr(node.klass, 'SetDiffuseColor'):
+ update_dict('_special_input_function_SetDiffuseColorWidget',
+ compute_SetDiffuseColorWidget)
+ if hasattr(node.klass, 'SetAmbientColor'):
+ update_dict('_special_input_function_SetAmbientColorWidget',
+ compute_SetAmbientColorWidget)
+ if hasattr(node.klass, 'SetSpecularColor'):
+ update_dict('_special_input_function_SetSpecularColorWidget',
+ compute_SetSpecularColorWidget)
+ if hasattr(node.klass, 'SetEdgeColor'):
+ update_dict('_special_input_function_SetEdgeColorWidget',
+ compute_SetEdgeColorWidget)
+ if hasattr(node.klass, 'SetColor'):
+ update_dict('_special_input_function_SetColorWidget',
+ compute_SetColorWidget)
+ if (issubclass(node.klass, vtksnl.vtkRenderer) and
+ hasattr(node.klass, 'SetBackground')):
+ update_dict('_special_input_function_SetBackgroundWidget',
+ compute_SetBackgroundWidget)
+ if (issubclass(node.klass, vtksnl.vtkRenderer) and
+ hasattr(node.klass, 'SetBackground2')):
+ update_dict('_special_input_function_SetBackground2Widget',
+ compute_SetBackground2Widget)
+ if issubclass(node.klass, vtksnl.vtkWriter):
+ update_dict('compute', guarded_Writer_wrap_compute)
+
+ if issubclass(node.klass, vtksnl.vtkScalarTree):
+ update_dict('compute', guarded_SimpleScalarTree_wrap_compute)
+
+ if issubclass(node.klass, vtksnl.vtkVolumeProperty):
+ update_dict('_special_input_function_SetTransferFunction',
+ compute_SetTransferFunction)
+ if issubclass(node.klass, vtksnl.vtkDataSet):
+ update_dict('_special_input_function_SetPointData',
+ compute_SetPointData)
+ update_dict('_special_input_function_SetCellData',
+ compute_SetCellData)
+ if issubclass(node.klass, vtksnl.vtkCell):
+ update_dict('_special_input_function_SetPointIds',
+ compute_SetPointIds)
+ return class_dict_
+
+disallowed_modules = set([
+# 'vtkGeoAlignedImageCache',
+# 'vtkGeoTerrainCache',
+# 'vtkMimeTypeStrategy',
+# 'vtkMPIGroup',
+ 'vtkPlotWriter', # Segfaults when being destroyed (when created without a reference, or when last reference is removed)
+ 'vtkRenderedLandscapeRepresentation' # Segfaults when calling: GetPeakLabelStopWords()
+ ])
+def createModule(baseModule, node):
+ """ createModule(baseModule: a Module subclass, node: TreeNode) -> None
+ Construct a module inherits baseModule with specification from node
+
+ """
+ if node.name in disallowed_modules: return
+ def obsolete_class_list():
+ lst = []
+ items = ['vtkInteractorStyleTrackball',
+ 'vtkStructuredPointsGeometryFilter',
+ 'vtkConstrainedPointHandleRepresentation',
+ 'vtkTypePromotion']
+ def try_to_add_item(item):
+ try:
+ lst.append(getattr(vtksnl, item))
+ except AttributeError:
+ pass
+ for item in items:
+ try_to_add_item(item)
+ return lst
+
+ obsolete_list = obsolete_class_list()
+
+ def is_abstract():
+ """is_abstract tries to instantiate the class. If it's
+ abstract, this will raise."""
+ # Consider obsolete classes abstract
+ if node.klass in obsolete_list:
+ return True
+ try:
+ getattr(vtksnl, node.name)()
+ except TypeError: # VTK raises type error on abstract classes
+ return True
+ return False
+ module = new_module(baseModule, node.name,
+ class_dict(baseModule, node),
+ docstring=getattr(vtksnl, node.name).__doc__
+ )
+
+ # This is sitting on the class
+ if hasattr(fix_classes, node.klass.__name__ + '_fixed'):
+ module.vtkClass = getattr(fix_classes, node.klass.__name__ + '_fixed')
+ else:
+ module.vtkClass = node.klass
+ registry = get_module_registry()
+ registry.add_module(module, abstract=is_abstract(),
+ signatureCallable=vtk_hasher)
+ for child in node.children:
+ if child.name in disallowed_classes:
+ continue
+ createModule(module, child)
+
+def createAllModules(g):
+ """ createAllModules(g: ClassTree) -> None
+ Traverse the VTK class tree and add all modules into the module registry
+
+ """
+ assert len(g.tree[0]) == 1
+ base = g.tree[0][0]
+ assert base.name == 'vtkObjectBase'
+ vtkObjectBase = new_module(vtkBaseModule, 'vtkObjectBase')
+ vtkObjectBase.vtkClass = vtksnl.vtkObjectBase
+ registry = get_module_registry()
+ registry.add_module(vtkObjectBase)
+ for child in base.children:
+ if child.name in disallowed_classes:
+ continue
+ createModule(vtkObjectBase, child)
+
+##############################################################################
+# Convenience methods
+
+def extract_vtk_instance(vistrails_obj):
+ """extract_vtk_instance(vistrails_obj) -> vtk_object
+
+ takes an instance of a VisTrails module that is a subclass
+ of the vtkObjectBase module and returns the corresponding
+ instance."""
+ global identifier
+ vtkObjectBase = registry.get_descriptor_by_name(identifier,
+ 'vtkObjectBase').module
+ assert isinstance(vistrails_obj, vtkObjectBase)
+ return vistrails_obj.vtkInstance
+
+def wrap_vtk_instance(vtk_obj):
+ """wrap_vtk_instance(vtk_object) -> VisTrails module
+
+ takes a vtk instance and returns a corresponding
+ wrapped instance of a VisTrails module"""
+ global identifier
+
+ assert isinstance(vtk_obj, vtksnl.vtkObjectBase)
+ m = registry.get_descriptor_by_name(identifier,
+ vtk_obj.GetClassName())
+ result = m.module()
+ result.vtkInstance = vtk_obj
+ return result
+
+################################################################################
+
+def initialize():
+ """ initialize() -> None
+ Package-entry to initialize the package
+
+ """
+ # Check VTK version
+ v = vtksnl.vtkVersion()
+ version = [v.GetVTKMajorVersion(),
+ v.GetVTKMinorVersion(),
+ v.GetVTKBuildVersion()]
+ if version < [5, 0, 0]:
+ raise Exception("You need to upgrade your VTK install to version \
+ > >= 5.0.0")
+ inheritanceGraph = ClassTree(vtksnl)
+ inheritanceGraph.create()
+
+ # Transfer Function constant
+ tf_widget.initialize()
+
+ delayed = InstanceObject(add_input_port=[])
+ # Add VTK modules
+ registry = get_module_registry()
+ registry.add_module(vtkBaseModule)
+ createAllModules(inheritanceGraph)
+ setAllPorts(registry.get_descriptor_by_name(identifier,
+ 'vtkObjectBase'),
+ delayed)
+
+ # Register the VTKCell and VTKHandler type if the spreadsheet is up
+ if registry.has_module('edu.utah.sci.vistrails.spreadsheet',
+ 'SpreadsheetCell'):
+ import vtkhandler
+ import vtkcell
+ import vtkviewcell
+ vtkhandler.registerSelf()
+ vtkcell.registerSelf()
+ vtkviewcell.registerSelf()
+
+ # register offscreen rendering module
+ offscreen.register_self()
+
+ # Now add all "delayed" ports - see comment on addSetGetPorts
+ for args in delayed.add_input_port:
+
+ registry.add_input_port(*args)
+
+ # register Transfer Function adjustment
+ # This can't be reordered -- TransferFunction needs to go before
+ # vtkVolumeProperty, but vtkScaledTransferFunction needs
+ # to go after vtkAlgorithmOutput
+
+ getter = registry.get_descriptor_by_name
+ registry.add_module(tf_widget.vtkScaledTransferFunction)
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'Input', getter('edu.utah.sci.vistrails.vtksnl',
+ 'vtkAlgorithmOutput').module)
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'Dataset', getter ('edu.utah.sci.vistrails.vtksnl',
+ 'vtkDataObject').module)
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'Range', [Float, Float])
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'TransferFunction',
+ tf_widget.TransferFunctionConstant)
+ registry.add_output_port(tf_widget.vtkScaledTransferFunction,
+ 'TransferFunction',
+ tf_widget.TransferFunctionConstant)
+ inspectors.initialize()
+
+################################################################################
diff --git a/contrib/vtksnl/inspectors.py b/contrib/vtksnl/inspectors.py
new file mode 100644
index 0000000..9a40acf
--- /dev/null
+++ b/contrib/vtksnl/inspectors.py
@@ -0,0 +1,231 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+##############################################################################
+# Data inspectors for VTK
+
+from core.modules.vistrails_module import ModuleError
+from core.utils import VistrailsInternalError
+from core.modules.basic_modules import Module, Float, Integer
+from core.modules.module_registry import get_module_registry
+import vtksnl
+from base_module import vtkBaseModule
+from hasher import vtk_hasher
+
+class vtkBaseInspector(Module):
+
+ @classmethod
+ def register_self(cls, **kwargs):
+ registry = get_module_registry()
+ def resolve_type(t):
+ if type(t) == tuple:
+ return registry.get_descriptor_by_name(*t).module
+ elif type(t) == type:
+ return t
+ else:
+ assert False, ("Unknown type " + str(type(t)))
+
+ registry.add_module(cls, **kwargs)
+ try:
+ ips = cls.input_ports
+ except AttributeError:
+ pass
+ else:
+ for (port_name, types) in ips:
+ registry.add_input_port(cls,
+ port_name,
+ list(resolve_type(t) for t in types))
+
+ try:
+ ops = cls.output_ports
+ except AttributeError:
+ pass
+ else:
+ for (port_name, types) in ops:
+ registry.add_output_port(cls,
+ port_name,
+ list(resolve_type(t) for t in types))
+
+ def auto_set_results(self, vtk_object):
+ for function in self.outputPorts.keys():
+ if hasattr(vtk_object, function):
+ retValues = getattr(vtk_object, function)()
+ if issubclass(retValues.__class__, vtksnl.vtkObject):
+ className = retValues.GetClassName()
+ output = vtkBaseModule.wrapperModule(className, retValues)
+ self.setResult(function, output)
+ elif type(retValues) in [tuple, list]:
+ result = list(retValues)
+ for i in xrange(len(result)):
+ if issubclass(result[i].__class__, vtksnl.vtkObject):
+ className = result[i].GetClassName()
+ result[i] = vtkBaseModule.wrapperModule(className,
+ result[i])
+ self.setResult(function, type(retValues)(result))
+ else:
+ self.setResult(function, retValues)
+
+class vtkDataSetInspector(vtkBaseInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInputConnection0"):
+ ic = self.getInputFromPort("SetInputConnection0")
+ port_object = ic.vtkInstance
+ ix = port_object.GetIndex()
+ producer = port_object.GetProducer()
+ try:
+ vtk_object = producer.GetOutput()
+ except AttributeError:
+ raise ModuleError(self,
+ "expected a module that supports GetOutput")
+ elif self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+ input_ports = [('SetInputConnection0',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkAlgorithmOutput')]),
+ ('SetInput',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkDataSet')]),
+ ]
+ output_ports = [('GetBounds', [Float] * 6),
+ ('GetScalarRange', [Float] * 2),
+ ('GetLength', [Float]),
+ ('GetCenter', [Float] * 3),
+ ('GetNumberOfPoints', [Integer]),
+ ('GetNumberOfCells', [Integer]),
+ ('GetPointData',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkPointData')]),
+ ('GetCellData',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkCellData')]),
+ ]
+
+class vtkDataSetAttributesInspector(vtkBaseInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+ input_ports = [('SetInput',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkDataSetAttributes')]),
+ ]
+ output_ports = [('GetScalars',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
+ ('GetVectors',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
+ ('GetNormals',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
+ ('GetTCoords',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
+ ('GetTensors',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
+ ('GetGlobalIds',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
+ ('GetPedigreeIds',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkAbstractArray')]),
+ ]
+
+class vtkDataArrayInspector(vtkBaseInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+ input_ports = [('SetInput',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')])]
+ output_ports = [('GetMaxNorm', [Float]),
+ ('GetRange', [Float] * 2)]
+
+class vtkPolyDataInspector(vtkDataSetInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInputConnection0"):
+ ic = self.getInputFromPort("SetInputConnection0")
+ port_object = ic.vtkInstance
+ ix = port_object.GetIndex()
+ producer = port_object.GetProducer()
+ try:
+ vtk_object = producer.GetOutput()
+ except AttributeError:
+ raise ModuleError(self,
+ "expected a module that supports GetOutput")
+ elif self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+ input_ports = [('SetInputConnection0',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkAlgorithmOutput')]),
+ ('SetInput',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkDataSet')]),
+ ]
+ output_ports = [('GetVerts',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkCellArray')]),
+ ('GetLines',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkCellArray')]),
+ ('GetPolys',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkCellArray')]),
+ ('GetStrips',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkCellArray')]),
+ ('GetPoints',
+ [('edu.utah.sci.vistrails.vtksnl', 'vtkPoints')]),
+ ('GetNumberOfVerts', [Integer]),
+ ('GetNumberOfLines', [Integer]),
+ ('GetNumberOfPolys', [Integer]),
+ ('GetNumberOfStrips', [Integer]),
+ ]
+
+def initialize():
+ vtkBaseInspector.register_self(abstract=True, signatureCallable=vtk_hasher)
+ vtkDataSetInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+ vtkDataSetAttributesInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+ vtkDataArrayInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+ vtkPolyDataInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+
diff --git a/contrib/vtksnl/offscreen.py b/contrib/vtksnl/offscreen.py
new file mode 100644
index 0000000..508baa3
--- /dev/null
+++ b/contrib/vtksnl/offscreen.py
@@ -0,0 +1,62 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+import vtksnl
+from core.modules.module_registry import get_module_registry
+from core.modules.vistrails_module import Module
+from core.modules.basic_modules import File, Integer
+
+class VTKRenderOffscreen(Module):
+
+ def compute(self):
+ r = self.getInputFromPort("renderer").vtkInstance
+ window = vtksnl.vtkRenderWindow()
+ w = self.forceGetInputFromPort("width", 512)
+ h = self.forceGetInputFromPort("height", 512)
+ window.OffScreenRenderingOn()
+ window.SetSize(w, h)
+ # r.ResetCamera()
+ window.AddRenderer(r)
+ window.Start()
+ window.Render()
+ win2image = vtksnl.vtkWindowToImageFilter()
+ win2image.SetInput(window)
+ win2image.Update()
+ writer = vtksnl.vtkPNGWriter()
+ writer.SetInput(win2image.GetOutput())
+ output = self.interpreter.filePool.create_file(suffix='.png')
+ writer.SetFileName(output.name)
+ writer.Write()
+ window.Finalize()
+ self.setResult("image", output)
+
+def register_self():
+ registry = get_module_registry()
+ r = registry.get_descriptor_by_name(
+ 'edu.utah.sci.vistrails.vtksnl',
+ 'vtkRenderer').module
+ registry.add_module(VTKRenderOffscreen)
+ registry.add_input_port(VTKRenderOffscreen, 'renderer', r)
+ registry.add_input_port(VTKRenderOffscreen, 'width', Integer)
+ registry.add_input_port(VTKRenderOffscreen, 'height', Integer)
+ registry.add_output_port(VTKRenderOffscreen, 'image', File)
+
diff --git a/contrib/vtksnl/tf_widget.py b/contrib/vtksnl/tf_widget.py
new file mode 100644
index 0000000..7ad6838
--- /dev/null
+++ b/contrib/vtksnl/tf_widget.py
@@ -0,0 +1,575 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+
+##############################################################################
+# Transfer Function Widget for VTK
+
+from PyQt4 import QtCore, QtGui
+from core.modules.constant_configuration import ConstantWidgetMixin
+from core.modules.basic_modules import new_constant, init_constant, Module
+from core.utils.color import ColorByName
+import vtksnl
+import math
+import pickle
+import copy
+
+################################################################################
+# etc
+
+def clamp(v, mn, mx, eps=0.0):
+ mn += eps
+ mx -= eps
+ if v < mn: return mn
+ if v > mx: return mx
+ return v
+
+##############################################################################
+# Transfer Function object
+
+class TransferFunction(object):
+
+ def __init__(self):
+ self._min_range = 0.0
+ self._max_range = 1.0
+ self._pts = []
+
+ def set_range(self, mn, mx):
+ self._min_range = mn
+ self._max_range = mx
+
+ def set_on_vtk_volume_property(self, vtk_volume_property):
+ # Builds the opacity and color functions
+ of = vtksnl.vtkPiecewiseFunction()
+ cf = vtksnl.vtkColorTransferFunction()
+ vp = vtk_volume_property
+ for pt in self._pts:
+ (scalar, opacity, color) = pt
+ # Map scalar to tf range
+ s = self._min_range + (self._max_range - self._min_range) * scalar
+ of.AddPoint(s, opacity)
+ cf.AddRGBPoint(s, color[0], color[1], color[2])
+ vp.SetScalarOpacity(of)
+ vp.SetColor(cf)
+
+ def add_point(self, scalar, opacity, color):
+ self._pts.append((scalar, opacity, color))
+ self._pts.sort()
+
+ def get_value(self, scalar):
+ """get_value(scalar): returns the opacity and color
+ linearly interpolated at the value. Useful for
+ adding knots."""
+ ix = 0
+ while ix < len(self._pts) and self._pts[ix][0] > scalar:
+ ix += 1
+ if ix == 0:
+ return (self._pts[0][1], self._pts[0][2])
+ elif ix == len(self._pts):
+ return (self._pts[-1][1], self._pts[-1][2])
+ else:
+ u = ((self._pts[ix][0] - scalar) /
+ (self._pts[ix][0] - self._pts[ix-1][0]))
+ do = self._pts[ix][1] - self._pts[ix-1][1]
+ dr = self._pts[ix][2][0] - self._pts[ix-1][2][0]
+ dg = self._pts[ix][2][1] - self._pts[ix-1][2][1]
+ db = self._pts[ix][2][2] - self._pts[ix-1][2][2]
+ return (self._pts[ix-1][1] + u * do,
+ (self._pts[ix-1][2][0] + u * dr,
+ self._pts[ix-1][2][1] + u * dg,
+ self._pts[ix-1][2][2] + u * db))
+
+ def __copy__(self):
+ result = TransferFunction()
+ result._min_range = self._min_range
+ result._max_range = self._max_range
+ result._pts = copy.copy(self._pts)
+ return result
+
+ def __eq__(self, other):
+ if type(other) != type(self):
+ return False
+ if self._min_range != other._min_range:
+ return False
+ if self._max_range != other._max_range:
+ return False
+ for my_pt, other_pt in zip(self._pts, other._pts):
+ if my_pt != other_pt:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+##############################################################################
+# Graphics Items
+
+class TransferFunctionPoint(QtGui.QGraphicsEllipseItem):
+
+ selection_pens = { True: QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('goldenrod_medium')))),0.012),
+ False: QtGui.QPen() }
+
+ def __init__(self, scalar, opacity, color, parent=None):
+ QtGui.QGraphicsEllipseItem.__init__(self, parent)
+ self._scalar = scalar
+ self._opacity = opacity
+ self._color = QtGui.QColor(color[0]*255,
+ color[1]*255,
+ color[2]*255)
+ self.setPen(QtGui.QPen(QtGui.QColor(0,0,0)))
+ self.setFlag(QtGui.QGraphicsItem.ItemIsMovable)
+ self.setFlag(QtGui.QGraphicsItem.ItemIsSelectable)
+ self.setFlag(QtGui.QGraphicsItem.ItemIsFocusable)
+ self.setZValue(2.0)
+
+ self._sx = 1.0
+ self._sy = 1.0
+ self._left_line = None
+ self._right_line = None
+ self._point = QtCore.QPointF(scalar, opacity)
+ self.refresh()
+
+ self.setToolTip("Double-click to change color\n"
+ "Right-click to remove point\n"
+ "Scalar: %.5f, Opacity: %.5f" % (self._scalar,
+ self._opacity))
+ # This sets up the linked list of Lines
+
+ def keyPressEvent(self, event):
+ if event.key() == QtCore.Qt.Key_Backspace or \
+ event.key() == QtCore.Qt.Key_Delete:
+ self.remove_self()
+
+ def refresh(self):
+ dx = 0.025 / self._sx
+ dy = 0.025 / self._sy
+ # this is the setup
+ self.setBrush(QtGui.QBrush(self._color))
+ self.setRect(-dx,
+ -dy,
+ 2 * dx, 2 * dy)
+ self.setPos(self._scalar,
+ self._opacity)
+
+ def update_scale(self, sx, sy):
+ self._sx = sx
+ self._sy = sy
+ self.refresh()
+
+ def itemChange(self, change, value):
+ if change == QtGui.QGraphicsItem.ItemSelectedChange:
+ self.setPen(self.selection_pens[value.toBool()])
+ if change == QtGui.QGraphicsItem.ItemPositionChange:
+ # moves point
+ pt = value.toPointF()
+ pt.setY(clamp(pt.y(), 0.0, 1.0))
+ self._opacity = pt.y()
+ self._point.setY(pt.y())
+ if not self._left_line:
+ pt.setX(0.0)
+ elif not self._right_line:
+ pt.setX(1.0)
+ else:
+ assert self._left_line._point_right == self
+ assert self._right_line._point_left == self
+ pt.setX(clamp(pt.x(),
+ self._left_line._point_left._point.x(),
+ self._right_line._point_right._point.x(),
+ 1e-6))
+ self._point.setX(pt.x())
+ self._scalar = pt.x()
+ if self._left_line:
+ self._left_line.refresh()
+ if self._right_line:
+ self._right_line.refresh()
+ if self.scene():
+ self.scene()._tf_poly.setup()
+ self.setToolTip("Double-click to change color\n"
+ "Right-click to remove point\n"
+ "Scalar: %.5f, Opacity: %.5f" % (self._scalar,
+ self._opacity))
+ return QtGui.QGraphicsItem.itemChange(self, change,
+ QtCore.QVariant(pt))
+ return QtGui.QGraphicsItem.itemChange(self, change, value)
+
+ def remove_self(self):
+ if not self._left_line or not self._right_line:
+ # Ignore, self is a corner node that can't be removed
+ return
+
+ # Removes the right line and self, re-ties data structure
+ self._left_line._point_right = self._right_line._point_right
+ self._left_line._point_right._left_line = self._left_line
+
+ # be friends with garbage collector
+ self._right_line._point_left = None
+ self._right_line._point_right = None
+ self.scene()._tf_poly.setup()
+ self.scene().removeItem(self._right_line)
+ self.scene().removeItem(self)
+ self._left_line.refresh()
+
+ def mouseDoubleClickEvent(self, event):
+ new_color = QtGui.QColorDialog.getColor(self._color)
+ if not new_color.isValid():
+ return
+ self._color = new_color
+ if self._left_line:
+ self._left_line.refresh()
+ if self._right_line:
+ self._right_line.refresh()
+ self.refresh()
+ self.scene()._tf_poly.setup()
+
+ def mousePressEvent(self, event):
+ if event.button() == QtCore.Qt.RightButton:
+ event.accept()
+ self.remove_self()
+ else:
+ QtGui.QGraphicsEllipseItem.mousePressEvent(self, event)
+
+ def add_self_to_transfer_function(self, tf):
+ tf.add_point(self._scalar,
+ self._opacity,
+ (self._color.redF(),
+ self._color.greenF(),
+ self._color.blueF()))
+
+class TransferFunctionPolygon(QtGui.QGraphicsPolygonItem):
+
+ def __init__(self):
+ QtGui.QGraphicsPolygonItem.__init__(self)
+
+ def setup(self):
+ # This inspects the scene, finds the left-most point, and
+ # then builds the polygon traversing the linked list structure
+ if not self.scene():
+ return
+ pt = self.scene().get_leftmost_point()
+ first_pt = pt
+ self.setZValue(1.25)
+ g = QtGui.QLinearGradient()
+ g.setStart(0.0, 0.5)
+ g.setFinalStop(1.0, 0.5)
+ p = QtGui.QPen()
+ p.setStyle(QtCore.Qt.NoPen)
+ pts = [QtCore.QPointF(pt.x(), 0)]
+ self.setPen(p)
+
+ while 1:
+ c = QtGui.QColor(pt._color)
+ c.setAlphaF(pt._opacity)
+ g.setColorAt(pt._scalar, c)
+ pts.append(pt._point)
+ # move cursor fwd
+ if pt._right_line:
+ pt = pt._right_line._point_right
+ else:
+ break
+ self.setBrush(QtGui.QBrush(g))
+ pts.append(QtCore.QPointF(pt.x(), 0))
+ self.setPolygon(QtGui.QPolygonF(pts))
+
+class TransferFunctionLine(QtGui.QGraphicsPolygonItem):
+
+ def __init__(self, point_left, point_right, parent=None):
+ assert point_right._scalar >= point_left._scalar
+ QtGui.QGraphicsPolygonItem.__init__(self, parent)
+ self._point_left = point_left
+ self._point_right = point_right
+ self._point_left._right_line = self
+ self._point_right._left_line = self
+ self.setup(1.0, 1.0)
+ self._sx = 1.0
+ self._sy = 1.0
+
+ def setup(self, sx, sy):
+ d = self._point_right._point - self._point_left._point
+ d_normal = QtCore.QPointF(d.y(), -d.x())
+ l = math.sqrt(d.x() * d.x() + d.y() * d.y())
+ if l != 0.0:
+ d_normal /= l
+ d_normal *= 0.010
+ d_normal.setX(d_normal.x() / sx)
+ d_normal.setY(d_normal.y() / sy)
+ ps = [self._point_left._point + d_normal,
+ self._point_right._point + d_normal,
+ self._point_right._point - d_normal,
+ self._point_left._point - d_normal]
+ self.setPolygon(QtGui.QPolygonF(ps))
+ self.setZValue(1.5)
+ # Gradient for filling
+ g = QtGui.QLinearGradient()
+ g.setStart(self._point_left._point)
+ g.setFinalStop(self._point_right._point)
+ g.setColorAt(0.0, self._point_left._color)
+ g.setColorAt(1.0, self._point_right._color)
+ self.setBrush(QtGui.QBrush(g))
+ # Gradient for outlining
+ g = QtGui.QLinearGradient()
+ g.setStart(self._point_left._point)
+ g.setFinalStop(self._point_right._point)
+ dark_pl = QtGui.QColor(self._point_left._color.red() * 0.5,
+ self._point_left._color.green() * 0.5,
+ self._point_left._color.blue() * 0.5)
+ dark_pr = QtGui.QColor(self._point_right._color.red() * 0.5,
+ self._point_right._color.green() * 0.5,
+ self._point_right._color.blue() * 0.5)
+ g.setColorAt(0.0, dark_pl)
+ g.setColorAt(1.0, dark_pr)
+ p = QtGui.QPen()
+ p.setBrush(QtGui.QBrush(g))
+ self.setPen(p)
+
+ def update_scale(self, sx, sy):
+ self._sx = sx
+ self._sy = sy
+ self.refresh()
+
+ def refresh(self):
+ self.setup(self._sx, self._sy)
+
+ def mouseDoubleClickEvent(self, event):
+ p = event.scenePos()
+ c_left = self._point_left._color
+ c_right = self._point_right._color
+ u = ((p.x() - self._point_left._point.x()) /
+ (self._point_right._point.x() - self._point_left._point.x()))
+ new_c = (u * c_right.redF() + (1-u) * c_left.redF(),
+ u * c_right.greenF() + (1-u) * c_left.greenF(),
+ u * c_right.blueF() + (1-u) * c_left.blueF())
+ new_point = TransferFunctionPoint(p.x(), p.y(), new_c)
+ new_line = TransferFunctionLine(new_point, self._point_right)
+ new_point._left_line = self
+ self._point_right = new_point
+ self.scene().addItem(new_line)
+ self.scene().addItem(new_point)
+ new_line.update_scale(self._point_left._sx,
+ self._point_left._sy)
+ new_point.update_scale(self._point_left._sx,
+ self._point_left._sy)
+ new_point.refresh()
+ self.refresh()
+
+ def mousePressEvent(self, event):
+ # This needs to be here, otherwise mouseDoubleClickEvent does
+ # not get called.
+ event.accept()
+
+
+##############################################################################
+# Scene, view, widget
+
+class TransferFunctionScene(QtGui.QGraphicsScene):
+
+ def __init__(self, tf, parent=None):
+ QtGui.QGraphicsScene.__init__(self, parent)
+ self._tf_items = []
+ poly = TransferFunctionPolygon()
+ poly.setup()
+ self._tf_poly = poly
+ self.addItem(poly)
+ self.create_tf_items(tf)
+ #current scale
+ self._sx = 1.0
+ self._sy = 1.0
+ # Add outlines
+ line_color = QtGui.QColor(200, 200, 200)
+ pen = QtGui.QPen(line_color)
+ ps = [QtCore.QPointF(0.0, 0.0),
+ QtCore.QPointF(1.0, 0.0),
+ QtCore.QPointF(1.0, 1.0),
+ QtCore.QPointF(0.0, 1.0)]
+ outline = QtGui.QPolygonF(ps)
+ self.addPolygon(outline, pen)
+
+ for i in xrange(51):
+ u = float(i) / 50.0
+ self.addLine(QtCore.QLineF(u, 0.0, u, 1.0), pen)
+ self.addLine(QtCore.QLineF(0.0, u, 1.0, u), pen)
+
+ def reset_transfer_function(self, tf):
+ self.create_tf_items(tf)
+ self.update_scale(self._sx, self._sy)
+ self._tf_poly.setup()
+
+ def removeItem(self, item):
+ if item in self._tf_items:
+ self._tf_items.remove(item)
+ QtGui.QGraphicsScene.removeItem(self, item)
+
+ def addItem(self, item):
+ # Ugly, but hey
+ if isinstance(item, TransferFunctionLine) or \
+ isinstance(item, TransferFunctionPoint):
+ self._tf_items.append(item)
+ QtGui.QGraphicsScene.addItem(self, item)
+
+ def create_tf_items(self, tf):
+ items = copy.copy(self._tf_items)
+ for item in items:
+ self.removeItem(item)
+ self._tf_items = []
+ if len(tf._pts) == 0:
+ pt_left = TransferFunctionPoint(0.0, 0.0, (0.0, 0.0, 0.0))
+ pt_right = TransferFunctionPoint(1.0, 0.0, (0.0, 0.0, 0.0))
+ line = TransferFunctionLine(pt_left, pt_right)
+
+ self.addItem(pt_left)
+ self.addItem(pt_right)
+ self.addItem(line)
+
+ else:
+ pts = [TransferFunctionPoint(*pt)
+ for pt in tf._pts]
+ lines = [TransferFunctionLine(pt_l, pt_r)
+ for (pt_l, pt_r) in zip(pts[:-1], pts[1:])]
+ for pt in pts:
+ self.addItem(pt)
+ for line in lines:
+ self.addItem(line)
+
+ def add_knot(self, scalar, opacity):
+ pass
+
+ def update_scale(self, sx, sy):
+ for item in self._tf_items:
+ item.update_scale(sx, sy)
+ self._sx = sx
+ self._sy = sy
+
+ def get_leftmost_point(self):
+ pt = None
+
+ for item in self._tf_items:
+ if hasattr(item, '_left_line') and not item._left_line:
+ pt = item
+ break
+ assert pt
+ return pt
+
+ def get_transfer_function(self):
+ result = TransferFunction()
+ pt = self.get_leftmost_point()
+ while 1:
+ pt.add_self_to_transfer_function(result)
+ if pt._right_line:
+ pt = pt._right_line._point_right
+ else:
+ break
+ return result
+
+class TransferFunctionView(QtGui.QGraphicsView):
+ def __init__(self, parent=None):
+ QtGui.QGraphicsView.__init__(self, parent)
+ self.setRenderHint(QtGui.QPainter.Antialiasing)
+ self.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ self.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+
+ def resizeEvent(self, event):
+ self.setMatrix(QtGui.QMatrix(event.size().width() / (10.0/9), 0,
+ 0, -event.size().height() / (10.0/9), 0, 0))
+ self.scene().update_scale(event.size().width()/(2000.0/9), event.size().height()/(2000.0/9))
+
+ def focusOutEvent(self, event):
+ self.parent().update_parent()
+ QtGui.QGraphicsView.focusOutEvent(self, event)
+
+default_tf = TransferFunction()
+default_tf.add_point(0.0, 0.0, (0.0, 0.0, 0.0))
+default_tf.add_point(1.0, 0.0, (0.0, 0.0, 0.0))
+
+class TransferFunctionWidget(QtGui.QWidget, ConstantWidgetMixin):
+
+ def __init__(self, param, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ if not param.strValue:
+ self._tf = copy.copy(default_tf)
+ else:
+ self._tf = pickle.loads(param.strValue.decode('hex'))
+ self._scene = TransferFunctionScene(self._tf, self)
+ layout = QtGui.QVBoxLayout()
+ self.setLayout(layout)
+ self._view = TransferFunctionView()
+ self._view.setScene(self._scene)
+ self._view.setMinimumSize(200,200)
+ self._view.show()
+ self._view.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ self._view.setMatrix(QtGui.QMatrix(180, 0, 0, -180, 0, 0))
+ self.setMinimumSize(200,200)
+ caption = QtGui.QLabel("Double-click on the line to add a point")
+ font = QtGui.QFont('Arial', 11)
+ font.setItalic(True)
+ caption.setFont(font)
+ layout.addWidget(self._view)
+ layout.addWidget(caption)
+
+ def contents(self):
+ return pickle.dumps(self._scene.get_transfer_function()).encode('hex')
+
+ def setContents(self, strValue, silent=True):
+ if not strValue:
+ self._tf = copy.copy(default_tf)
+ else:
+ self._tf = pickle.loads(strValue.decode('hex'))
+ self._scene.reset_transfer_function(self._tf)
+ if not silent:
+ self.update_parent()
+
+##############################################################################
+# Helper module to adjust range
+
+class vtkScaledTransferFunction(Module):
+
+ def compute(self):
+ tf = self.getInputFromPort('TransferFunction')
+ new_tf = copy.copy(tf)
+ if self.hasInputFromPort('Input'):
+ port = self.getInputFromPort('Input')
+ algo = port.vtkInstance.GetProducer()
+ output = algo.GetOutput(port.vtkInstance.GetIndex())
+ (new_tf._min_range, new_tf._max_range) = output.GetScalarRange()
+ elif self.hasInputFromPort('Dataset'):
+ algo = self.getInputFromPort('Dataset').vtkInstance
+ output = algo
+ (new_tf._min_range, new_tf._max_range) = output.GetScalarRange()
+ else:
+ (new_tf._min_range, new_tf._max_range) = self.getInputFromPort('Range')
+
+ self.setResult('TransferFunction', new_tf)
+
+string_conversion = staticmethod(lambda x: pickle.dumps(x).encode('hex'))
+conversion = staticmethod(lambda x: pickle.loads(x.decode('hex')))
+validation = staticmethod(lambda x: isinstance(x, TransferFunction))
+TransferFunctionConstant = new_constant('TransferFunction',
+ conversion,
+ default_tf,
+ validation,
+ TransferFunctionWidget)
+TransferFunctionConstant.translate_to_string = string_conversion
+
+##############################################################################
+
+def initialize():
+ init_constant(TransferFunctionConstant)
diff --git a/contrib/vtksnl/vtk_parser.py b/contrib/vtksnl/vtk_parser.py
new file mode 100644
index 0000000..1624f09
--- /dev/null
+++ b/contrib/vtksnl/vtk_parser.py
@@ -0,0 +1,514 @@
+# Author: Prabhu Ramachandran
+# Copyright (c) 2004, Enthought, Inc.
+# License: BSD Style.
+
+# Modified for VisTrails by the VisTrails team.
+
+"""This module parses the VTK methods, obtains the argument and return
+type information, and organizes them.
+
+"""
+
+import re
+import vtksnl
+import class_tree
+import core.debug
+
+log = core.debug.log
+warning = core.debug.warning
+critical = core.debug.critical
+debug = core.debug.debug
+
+class VTKMethodParser(object):
+ """This class provides useful methods for parsing methods of a VTK
+ class or instance.
+
+ The class allows one to categorize the methods of the VTK class
+ and also obtain the method signatures in a form that is easy to
+ use. When the `parse` method is called, it in turn calls the
+ `_organize_methods` method. This method organizes the VTK methods
+ into different instance variables described in the following.
+ `self.toggle_meths` contains a dictionary of all the boolean
+ methods of the form <Value>On/Off. The dictionary keys are
+ strings with the <Value>'s and the value of each item is the
+ default value (0/1) of the item (the example below will clarify
+ this). `self.state_meths` contains a dictionary which collects
+ the Set<Prop>To<Value> type of methods. The key is the <Prop> and
+ the value is a list containing the different string <Value>'s and
+ their corresponding mapped value. The first value in these is the
+ default value of the <Prop>. `self.get_set_meths` will contain a
+ dictionary which collects all the methods of the form
+ Set/Get<Prop> that are not already specified in
+ `self.toggle_meths` or `self.state_meths`. The default value of
+ the Get<Prop> is stored. If the value accepted by the method has
+ a range (via the methods `Get<Prop>MinValue` and
+ `Get<Prop>MaxValue`), then that range is computed and stored.
+ `self.get_meths` stores the methods that are of the form
+ `Get<Prop>`. `self.other_meths` stores the remaining methods.
+ The parsing is quite fast. Parsing every class in the VTK API
+ takes a couple of seconds (on a Pentium III @ 450Mhz).
+
+ Here is an example::
+
+ >>> import vtk
+ >>> p = VTKMethodParser()
+ >>> p.parse(vtk.vtkProperty)
+ >>> print p.get_toggle_methods()
+ {'EdgeVisibility': 0, 'BackfaceCulling': 0, 'FrontfaceCulling': 0}
+ >>> print p.get_state_methods()['Representation']
+ [['Surface', 2], ['Points', 0], ['Surface', 2], ['Wireframe', 1]]
+ >>> print p.get_get_set_methods()['Opacity']
+ (1.0, (0.0, 1.0))
+ >>> print p.get_get_methods()
+ ['GetClassName']
+ >>> print p.get_other_methods()[:3]
+ ['BackfaceRender', 'DeepCopy', 'IsA']
+
+
+ The class also provides a method called `get_method_signature`
+ that obtains the Python method signature given the VTK method
+ object. Here is an example::
+
+ >>> import vtk
+ >>> p = VTKMethodParser()
+ >>> o = vtk.vtkProperty
+ >>> print p.get_method_signature(o.GetClassName)
+ [(['string'], None)]
+ >>> print p.get_method_signature(o.GetColor)[0]
+ ([('float', 'float', 'float')], None)
+ >>> print p.get_method_signature(o.GetColor)[1]
+ ([None], (('float', 'float', 'float'),))
+
+ The `get_method_signature` is fairly efficient and obtaining the
+ signature for every method in every class in the VTK API takes
+ around 6 seconds (on a Pentium III @ 450Mhz).
+
+ """
+
+ def __init__(self, use_tree=True):
+ """Initializes the object.
+
+ Parameters
+ ----------
+
+ - use_tree : `bool`
+
+ If True (default), use a ClassTree instance to obtain a
+ concrete subclass for an abstract base class. This is used
+ only to find the range and default values for some of the
+ methods. If False, no ClassTree instance is created.
+
+ This is optional because, creating a ClassTree is expensive.
+ The parser functionality can be very useful even without the
+ use of a ClassTree. For example, if one wants to save the
+ state of a VTK object one only needs to know the names of
+ the methods and not their default values, ranges etc. In
+ that case using a parser should be cheap.
+
+ """
+ # The ClassTree is needed to find an instantiable child class
+ # for an abstract VTK parent class. This instance is used to
+ # obtain the state values and the ranges of the arguments
+ # accepted by the Get/Set methods that have a
+ # Get<Prop>{MaxValue,MinValue} method.
+ if use_tree:
+ self._tree = class_tree.ClassTree(vtksnl)
+ self._tree.create()
+ else:
+ self._tree = None
+ self._state_patn = re.compile('To[A-Z0-9]')
+ self._initialize()
+
+ #################################################################
+ # 'VTKMethodParser' interface.
+ #################################################################
+
+ def parse(self, obj, no_warn=True):
+ """Parse the methods for a given VTK object/class.
+
+ Given a VTK class or object, this method parses the methods
+ and orgaizes them into useful categories. The categories and
+ their usage is documented in the documentation for the class.
+
+ Parameters
+ ----------
+
+ - obj : VTK class or instance
+
+ - no_warn : `bool` (default: True)
+
+ If True (default), it suppresses any warnings generated by
+ the VTK object when parsing the methods. This is safe to
+ use.
+
+ """
+ if not hasattr(obj, '__bases__'):
+ klass = obj.__class__
+ else:
+ klass = obj
+
+ methods = self.get_methods(klass)
+
+ if no_warn:
+ # Save warning setting and shut it off before parsing.
+ warn = vtksnl.vtkObject.GetGlobalWarningDisplay()
+ if klass.__name__ <> 'vtkObject':
+ vtksnl.vtkObject.GlobalWarningDisplayOff()
+
+ self._organize_methods(klass, methods)
+
+ if no_warn:
+ # Reset warning status.
+ vtksnl.vtkObject.SetGlobalWarningDisplay(warn)
+
+ def get_methods(self, klass):
+ """Returns all the relevant methods of the given VTK class."""
+ methods = dir(klass)[:]
+ if hasattr(klass, '__members__'):
+ # Only VTK versions < 4.5 have these.
+ for m in klass.__members__:
+ methods.remove(m)
+
+ return methods
+
+ def get_toggle_methods(self):
+ """Returns a dictionary of the parsed <Value>On/Off methods
+ along with the default value.
+
+ """
+ return self.toggle_meths
+
+ def get_state_methods(self):
+ """Returns a dict of the parsed Set<Prop>To<Value>.
+
+ The keys are the <Prop> string with a list of the different
+ <Value> strings along with their corresponding value (if
+ obtainable). The first value is the default value of the
+ state.
+
+ """
+ return self.state_meths
+
+ def get_get_set_methods(self):
+ """Returns a dict of the parsed Get/Set<Value> methods.
+
+ The keys of the dict are the <Value> strings and contain a
+ two-tuple containing the default value (or None if it is not
+ obtainable for some reason) and a pair of numbers specifying
+ an acceptable range of values (or None if not obtainable).
+
+ """
+ return self.get_set_meths
+
+ def get_get_methods(self):
+ """Return a list of parsed Get<Value> methods.
+
+ All of these methods do NOT have a corresponding Set<Value>.
+
+ """
+ return self.get_meths
+
+ def get_other_methods(self):
+ """Return list of all other methods, that are not
+ categorizable.
+
+ """
+ return self.other_meths
+
+ def get_method_signature(self, method):
+ """Returns information on the Python method signature given
+ the VTK method.
+
+ The doc string of the given method object to get the method
+ signature. The method returns a list of tuples, each of which
+ contains 2 items, the first is a list representing the return
+ value the second represents the arguments to be passed to the
+ function. If the method supports different return values and
+ arguments, this function returns all of their signatures.
+
+ Parameters
+ ----------
+
+ - method : `method`
+
+ A VTK method object.
+
+ """
+ doc = method.__doc__
+ doc = doc[:doc.find('\n\n')]
+ sig = doc.split('\n')
+ sig = [x.strip() for x in sig]
+
+ # Remove all the C++ function signatures.
+ for i in sig[:]:
+ if i[:4] == 'C++:':
+ sig.remove(i)
+
+ # Remove the V.<method_name>
+ sig = [x.replace('V.' + method.__name__, '') for x in sig]
+
+ pat = re.compile(r'\b')
+
+ # Split into [return_value, arguments] after processing them.
+ tmp = list(sig)
+ sig = []
+ for i in tmp:
+ # Split to get return values.
+ x = i.split('->')
+ # Strip each part.
+ x = [y.strip() for y in x]
+
+ if len(x) == 1: # No return value
+ x = [None, x[0]]
+ else:
+ x.reverse()
+
+ ret, arg = x
+
+ # Remove leading and trailing parens for arguments.
+ arg = arg[1:-1]
+ if not arg:
+ arg = None
+ if arg and arg[-1] == ')':
+ arg = arg + ','
+
+ # Now quote the args and eval them. Easy!
+ if ret:
+ ret = eval(pat.sub('\"', ret))
+ if arg:
+ arg = eval(pat.sub('\"', arg))
+ if type(arg) == type('str'):
+ arg = [arg]
+
+ sig.append(([ret], arg))
+
+ return sig
+
+ def get_tree(self):
+ """Return the ClassTree instance used by this class."""
+ return self._tree
+
+ #################################################################
+ # Non-public interface.
+ #################################################################
+
+ def _initialize(self):
+ """Initializes the method categories."""
+ # Collects the <Value>On/Off methods.
+ self.toggle_meths = {}
+ # Collects the Set<Prop>To<Value> methods.
+ self.state_meths = {}
+ # Collects the Set/Get<Value> pairs.
+ self.get_set_meths = {}
+ # Collects the Get<Value> methods.
+ self.get_meths = []
+ # Collects all the remaining methods.
+ self.other_meths = []
+
+ def _organize_methods(self, klass, methods):
+ """Organizes the given methods of a VTK class into different
+ categories.
+
+ Parameters
+ ----------
+
+ - klass : A VTK class
+
+ - methods : `list` of `str`
+
+ A list of the methods to be categorized.
+
+ """
+ self._initialize()
+ meths = methods[:]
+ meths = self._find_toggle_methods(klass, meths)
+ meths = self._find_state_methods(klass, meths)
+ meths = self._find_get_set_methods(klass, meths)
+ meths = self._find_get_methods(klass, meths)
+ self.other_meths = [x for x in meths if '__' not in x]
+
+ def _remove_method(self, meths, method):
+ try:
+ meths.remove(method)
+ except ValueError:
+ pass
+
+ def _find_toggle_methods(self, klass, methods):
+ """Find/store methods of the form <Value>{On,Off} in the given
+ `methods`. Returns the remaining list of methods.
+
+ """
+ meths = methods[:]
+ tm = self.toggle_meths
+ for method in meths[:]:
+ if method[-2:] == 'On':
+ key = method[:-2]
+ if (key + 'Off') in meths and ('Get' + key) in meths:
+ tm[key] = None
+ meths.remove(method)
+ meths.remove(key + 'Off')
+ self._remove_method(meths, 'Set' + key)
+ self._remove_method(meths, 'Get' + key)
+ # get defaults
+ if tm:
+ obj = self._get_instance(klass)
+ if obj:
+ for key in tm:
+ try:
+ tm[key] = getattr(obj, 'Get%s'%key)()
+ except TypeError, e:
+ log("Type error during parsing: class %s will not expose method %s " % (klass.__name__, key))
+ except AttributeError, e:
+ log("Attribute error during parsing: class %s will not expose method %s " % (klass.__name__, key))
+ return meths
+
+ def _find_state_methods(self, klass, methods):
+ """Find/store methods of the form Set<Prop>To<Value> in the
+ given `methods`. Returns the remaining list of methods. The
+ method also computes the mapped value of the different
+ <Values>.
+
+ """
+ # These ignored ones are really not state methods.
+ ignore = ['SetUpdateExtentToWholeExtent']
+ meths = methods[:]
+ sm = self.state_meths
+ for method in meths[:]:
+ if method not in ignore and method[:3] == 'Set':
+ # Methods of form Set<Prop>To<Value>
+ match = self._state_patn.search(method)
+ # Second cond. ensures that this is not an accident.
+ if match and (('Get'+method[3:]) not in meths):
+ key = method[3:match.start()] # The <Prop> part.
+ if (('Get' + key) in methods):
+ val = method[match.start()+2:] # <Value> part.
+ meths.remove(method)
+ if sm.has_key(key):
+ sm[key].append([val, None])
+ else:
+ sm[key] = [[val, None]]
+ meths.remove('Get'+ key)
+ self._remove_method(meths, 'Set'+ key)
+ if ('Get' + key + 'MaxValue') in meths:
+ meths.remove('Get' + key + 'MaxValue')
+ meths.remove('Get' + key + 'MinValue')
+ try:
+ meths.remove('Get' + key + 'AsString')
+ except ValueError:
+ pass
+
+ # Find the values for each of the states, i.e. find that
+ # vtkProperty.SetRepresentationToWireframe() corresponds to
+ # vtkProperty.SetRepresentation(1).
+ if sm:
+ obj = self._get_instance(klass)
+ if obj:
+ for key, values in sm.items():
+ default = getattr(obj, 'Get%s'%key)()
+ for x in values[:]:
+ try:
+ getattr(obj, 'Set%sTo%s'%(key, x[0]))()
+ except:
+ continue
+ val = getattr(obj, 'Get%s'%key)()
+ x[1] = val
+ if val == default:
+ values.insert(0, [x[0], val])
+ return meths
+
+ def _find_get_set_methods(self, klass, methods):
+ """Find/store methods of the form {Get,Set}Prop in the given
+ `methods` and returns the remaining list of methods.
+
+ Note that it makes sense to call this *after*
+ `_find_state_methods` is called in order to avoid incorrect
+ duplication. This method also computes the default value and
+ the ranges of the arguments (when possible) by using the
+ Get<Prop>{MaxValue,MinValue} methods.
+
+ """
+ meths = methods[:]
+ gsm = self.get_set_meths
+
+ for method in meths[:]:
+ # Methods of the Set/Get form.
+ if method in ['Get', 'Set']:
+ # This occurs with the vtkInformation class.
+ continue
+ elif (method[:3] == 'Set') and ('Get' + method[3:]) in methods:
+ key = method[3:]
+ meths.remove('Set' + key)
+ meths.remove('Get' + key)
+ if ('Get' + key + 'MaxValue') in meths:
+ meths.remove('Get' + key + 'MaxValue')
+ meths.remove('Get' + key + 'MinValue')
+ gsm[key] = 1
+ else:
+ gsm[key] = None
+
+ # Find the default and range of the values.
+ if gsm:
+ obj = self._get_instance(klass)
+ if obj:
+ klass_name = klass.__name__
+ for key, value in gsm.items():
+ if klass_name == 'vtkPolyData':
+ # Evil hack, this class segfaults!
+ default = None
+ else:
+ try:
+ default = getattr(obj, 'Get%s'%key)()
+ except TypeError:
+ default = None
+ if value:
+ low = getattr(obj, 'Get%sMinValue'%key)()
+ high = getattr(obj, 'Get%sMaxValue'%key)()
+ gsm[key] = (default, (low, high))
+ else:
+ gsm[key] = (default, None)
+ else:
+ # We still might have methods that have a default range.
+ for key, value in gsm.items():
+ if value == 1:
+ gsm[key] = None
+
+ return meths
+
+ def _find_get_methods(self, klass, methods):
+ """Find/store methods of the form Get<Value> in the given
+ `methods` and returns the remaining list of methods.
+
+ """
+ meths = methods[:]
+ gm = self.get_meths
+ for method in meths[:]:
+ if method == 'Get':
+ # Occurs with vtkInformation
+ continue
+ elif method[:3] == 'Get':
+ gm.append(method)
+ meths.remove(method)
+ return meths
+
+ def _get_instance(self, klass):
+ """Given a VTK class, `klass`, returns an instance of the
+ class.
+
+ If the class is abstract, it uses the class tree to return an
+ instantiable subclass. This is necessary to get the values of
+ the 'state' methods and the ranges for the Get/Set methods.
+
+ """
+ obj = None
+ try:
+ obj = klass()
+ except TypeError:
+ if self._tree:
+ t = self._tree
+ n = t.get_node(klass.__name__)
+ for c in n.children:
+ obj = self._get_instance(t.get_class(c.name))
+ if obj:
+ break
+ return obj
+
diff --git a/contrib/vtksnl/vtkcell.py b/contrib/vtksnl/vtkcell.py
new file mode 100644
index 0000000..fa61481
--- /dev/null
+++ b/contrib/vtksnl/vtkcell.py
@@ -0,0 +1,1094 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+################################################################################
+# File QVTKWidget.py
+# File for displaying a vtkRenderWindow in a Qt's QWidget ported from
+# VTK/GUISupport/QVTK. Combine altogether to a single class: QVTKWidget
+################################################################################
+import vtksnl
+from PyQt4 import QtCore, QtGui
+import sip
+from core import system
+from core.modules.module_registry import get_module_registry
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+import vtkcell_rc
+import gc
+from gui.qt import qt_super
+import core.db.action
+from core.vistrail.action import Action
+from core.vistrail.port import Port
+from core.vistrail import module
+from core.vistrail import connection
+from core.vistrail.module_function import ModuleFunction
+from core.vistrail.module_param import ModuleParam
+from core.vistrail.location import Location
+from core.modules.vistrails_module import ModuleError
+import copy
+
+################################################################################
+
+class VTKCell(SpreadsheetCell):
+ """
+ VTKCell is a VisTrails Module that can display vtkRenderWindow inside a cell
+
+ """
+
+ def __init__(self):
+ SpreadsheetCell.__init__(self)
+ self.cellWidget = None
+
+ def compute(self):
+ """ compute() -> None
+ Dispatch the vtkRenderer to the actual rendering widget
+ """
+ renderers = self.forceGetInputListFromPort('AddRenderer')
+ renderViews = self.forceGetInputListFromPort('SetRenderView')
+ if len(renderViews)>1:
+ raise ModuleError(self, 'There can only be one vtkRenderView '
+ 'per cell')
+ if len(renderViews)==1 and len(renderers)>0:
+ raise ModuleError(self, 'Cannot set both vtkRenderView '
+ 'and vtkRenderer to a cell')
+ renderView = self.forceGetInputFromPort('SetRenderView')
+ iHandlers = self.forceGetInputListFromPort('InteractionHandler')
+ iStyle = self.forceGetInputFromPort('InteractorStyle')
+ picker = self.forceGetInputFromPort('AddPicker')
+ self.cellWidget = self.displayAndWait(QVTKWidget, (renderers, renderView, iHandlers, iStyle, picker))
+
+AsciiToKeySymTable = ( None, None, None, None, None, None, None,
+ None, None,
+ "Tab", None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None,
+ "space", "exclam", "quotedbl", "numbersign",
+ "dollar", "percent", "ampersand", "quoteright",
+ "parenleft", "parenright", "asterisk", "plus",
+ "comma", "minus", "period", "slash",
+ "0", "1", "2", "3", "4", "5", "6", "7",
+ "8", "9", "colon", "semicolon", "less", "equal",
+ "greater", "question",
+ "at", "A", "B", "C", "D", "E", "F", "G",
+ "H", "I", "J", "K", "L", "M", "N", "O",
+ "P", "Q", "R", "S", "T", "U", "V", "W",
+ "X", "Y", "Z", "bracketleft",
+ "backslash", "bracketright", "asciicircum",
+ "underscore",
+ "quoteleft", "a", "b", "c", "d", "e", "f", "g",
+ "h", "i", "j", "k", "l", "m", "n", "o",
+ "p", "q", "r", "s", "t", "u", "v", "w",
+ "x", "y", "z", "braceleft", "bar", "braceright",
+ "asciitilde", "Delete",
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None)
+
+class QVTKWidget(QCellWidget):
+ """
+ QVTKWidget is the actual rendering widget that can display
+ vtkRenderer inside a Qt QWidget
+
+ """
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QVTKWidget(parent: QWidget, f: WindowFlags) -> QVTKWidget
+ Initialize QVTKWidget with a toolbar with its own device
+ context
+
+ """
+ QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
+
+ self.interacting = None
+ self.mRenWin = None
+ self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
+ self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
+ self.setMouseTracking(True)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding))
+ self.toolBarType = QVTKWidgetToolBar
+ self.iHandlers = []
+ self.setAnimationEnabled(True)
+ self.renderer_maps = {}
+
+ def removeObserversFromInteractorStyle(self):
+ """ removeObserversFromInteractorStyle() -> None
+ Remove all python binding from interactor style observers for
+ safely freeing the cell
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.RemoveObservers("InteractionEvent")
+ style.RemoveObservers("EndPickEvent")
+ style.RemoveObservers("CharEvent")
+ style.RemoveObservers("MouseWheelForwardEvent")
+ style.RemoveObservers("MouseWheelBackwardEvent")
+
+ def addObserversToInteractorStyle(self):
+ """ addObserversToInteractorStyle() -> None
+ Assign observer to the current interactor style
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.AddObserver("InteractionEvent", self.interactionEvent)
+ style.AddObserver("EndPickEvent", self.interactionEvent)
+ style.AddObserver("CharEvent", self.charEvent)
+ style.AddObserver("MouseWheelForwardEvent", self.interactionEvent)
+ style.AddObserver("MouseWheelBackwardEvent", self.interactionEvent)
+
+ def deleteLater(self):
+ """ deleteLater() -> None
+ Make sure to free render window resource when
+ deallocating. Overriding PyQt deleteLater to free up
+ resources
+
+ """
+ self.renderer_maps = {}
+ for ren in self.getRendererList():
+ self.mRenWin.RemoveRenderer(ren)
+
+ self.removeObserversFromInteractorStyle()
+
+ self.updateContents(([], None, [], None, None))
+
+ self.SetRenderWindow(None)
+
+ QCellWidget.deleteLater(self)
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple)
+ Updates the cell contents with new vtkRenderer
+
+ """
+ renWin = self.GetRenderWindow()
+ for iHandler in self.iHandlers:
+ if iHandler.observer:
+ iHandler.observer.vtkInstance.SetInteractor(None)
+ iHandler.clear()
+
+ # Remove old renderers first
+ oldRenderers = self.getRendererList()
+ for renderer in oldRenderers:
+ renWin.RemoveRenderer(renderer)
+ renderer.SetRenderWindow(None)
+ del oldRenderers
+
+ (renderers, renderView, self.iHandlers, iStyle, picker) = inputPorts
+ if renderView:
+ renderView.vtkInstance.SetupRenderWindow(renWin)
+ renderers = [renderView.vtkInstance.GetRenderer()]
+ self.renderer_maps = {}
+ for renderer in renderers:
+ if renderView==None:
+ vtkInstance = renderer.vtkInstance
+ renWin.AddRenderer(vtkInstance)
+ self.renderer_maps[vtkInstance] = renderer.moduleInfo['moduleId']
+ else:
+ vtkInstance = renderer
+ if hasattr(vtkInstance, 'IsActiveCameraCreated'):
+ if not vtkInstance.IsActiveCameraCreated():
+ vtkInstance.ResetCamera()
+ else:
+ vtkInstance.ResetCameraClippingRange()
+
+ iren = renWin.GetInteractor()
+ if picker:
+ iren.SetPicker(picker.vtkInstance)
+
+ # Update interactor style
+ self.removeObserversFromInteractorStyle()
+ if renderView==None:
+ if iStyle==None:
+ iStyleInstance = vtksnl.vtkInteractorStyleTrackballCamera()
+ else:
+ iStyleInstance = iStyle.vtkInstance
+ iren.SetInteractorStyle(iStyleInstance)
+ self.addObserversToInteractorStyle()
+
+ for iHandler in self.iHandlers:
+ if iHandler.observer:
+ iHandler.observer.vtkInstance.SetInteractor(iren)
+ renWin.Render()
+
+ # Capture window into history for playback
+ # Call this at the end to capture the image after rendering
+ QCellWidget.updateContents(self, inputPorts)
+
+ def GetRenderWindow(self):
+ """ GetRenderWindow() -> vtkRenderWindow
+ Return the associated vtkRenderWindow
+
+ """
+ if not self.mRenWin:
+ win = vtksnl.vtkRenderWindow()
+ win.DoubleBufferOn()
+ self.SetRenderWindow(win)
+ del win
+
+ return self.mRenWin
+
+ def SetRenderWindow(self,w):
+ """ SetRenderWindow(w: vtkRenderWindow)
+ Set a new render window to QVTKWidget and initialize the
+ interactor as well
+
+ """
+ if w == self.mRenWin:
+ return
+
+ if self.mRenWin:
+ if system.systemType!='Linux':
+ self.mRenWin.SetInteractor(None)
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+
+ self.mRenWin = w
+
+ if self.mRenWin:
+ self.mRenWin.Register(None)
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+ if system.systemType=='Linux':
+ try:
+ vp = '_%s_void_p' % (hex(int(QtGui.QX11Info.display()))[2:])
+ except TypeError:
+ #This was change for PyQt4.2
+ if isinstance(QtGui.QX11Info.display(),QtGui.Display):
+ display = sip.unwrapinstance(QtGui.QX11Info.display())
+ vp = '_%s_void_p' % (hex(display)[2:])
+ self.mRenWin.SetDisplayId(vp)
+ self.resizeWindow(1,1)
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ if not self.mRenWin.GetInteractor():
+ iren = vtksnl.vtkRenderWindowInteractor()
+ if system.systemType=='Darwin':
+ iren.InstallMessageProcOff()
+ iren.SetRenderWindow(self.mRenWin)
+ iren.Initialize()
+ if system.systemType=='Linux':
+ system.XDestroyWindow(self.mRenWin.GetGenericDisplayId(),
+ self.mRenWin.GetGenericWindowId())
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ self.resizeWindow(self.width(), self.height())
+ self.mRenWin.SetPosition(self.x(), self.y())
+
+ def GetInteractor(self):
+ """ GetInteractor() -> vtkInteractor
+ Return the vtkInteractor control this QVTKWidget
+ """
+ return self.GetRenderWindow().GetInteractor()
+
+ def event(self, e):
+ """ event(e: QEvent) -> depends on event type
+ Process window and interaction events
+
+ """
+ if e.type()==QtCore.QEvent.ParentAboutToChange:
+ if self.mRenWin:
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+ else:
+ if e.type()==QtCore.QEvent.ParentChange:
+ if self.mRenWin:
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ if QtCore.QObject.event(self,e):
+ return 1
+
+ if e.type() == QtCore.QEvent.KeyPress:
+ self.keyPressEvent(e)
+ if e.isAccepted():
+ return e.isAccepted()
+
+ return qt_super(QVTKWidget, self).event(e)
+
+ # return QtGui.QWidget.event(self,e)
+ # Was this right? Wasn't this supposed to be QCellWidget.event()?
+
+ def resizeWindow(self, width, height):
+ """ resizeWindow(width: int, height: int) -> None
+ Work around vtk bugs for resizing window
+
+ """
+ ########################################################
+ # VTK - BUGGGGGGGGG - GRRRRRRRRR
+ # This is a 'bug' in vtkWin32OpenGLRenderWindow(.cxx)
+ # If a render window is mapped to screen, the actual
+ # window size is the client area of the window in Win32.
+ # However, this real window size is only updated through
+ # vtkWin32OpenGLRenderWindow::GetSize(). So this has to
+ # be called here to get the cell size correctly. This
+ # invalidates the condition in the next SetSize().
+ # We can use self.mRenWin.SetSize(0,0) here but it will
+ # cause flickering and decrease performance!
+ # SetPosition(curX,curY) also works here but slower.
+ self.mRenWin.GetSize()
+
+ self.mRenWin.SetSize(width, height)
+ if self.mRenWin.GetInteractor():
+ self.mRenWin.GetInteractor().SetSize(width, height)
+
+ def resizeEvent(self, e):
+ """ resizeEvent(e: QEvent) -> None
+ Re-adjust the vtkRenderWindow size then QVTKWidget resized
+
+ """
+ qt_super(QVTKWidget, self).resizeEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.resizeWindow(self.width(), self.height())
+ self.mRenWin.Render()
+
+ def moveEvent(self,e):
+ """ moveEvent(e: QEvent) -> None
+ Echo the move event into vtkRenderWindow
+
+ """
+ qt_super(QVTKWidget, self).moveEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.mRenWin.SetPosition(self.x(),self.y())
+
+ def paintEvent(self, e):
+ """ paintEvent(e: QPaintEvent) -> None
+ Paint the QVTKWidget with vtkRenderWindow
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ if hasattr(self.mRenWin, 'UpdateGLRegion'):
+ self.mRenWin.UpdateGLRegion()
+ self.mRenWin.Render()
+
+ def SelectActiveRenderer(self,iren):
+ """ SelectActiveRenderer(iren: vtkRenderWindowIteractor) -> None
+ Only make the vtkRenderer below the mouse cursor active
+
+ """
+ epos = iren.GetEventPosition()
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ ren.SetInteractive(ren.IsInViewport(epos[0], epos[1]))
+
+ def mousePressEvent(self,e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ isDoubleClick = e.type()==QtCore.QEvent.MouseButtonDblClick
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ ctrl,
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),
+ isDoubleClick,
+ None)
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonPressEvent",
+ QtCore.Qt.MidButton:"MiddleButtonPressEvent",
+ QtCore.Qt.RightButton:"RightButtonPressEvent"}
+
+ self.SelectActiveRenderer(iren)
+
+ if ctrl:
+ e.ignore()
+ return
+
+ self.interacting = self.getActiveRenderer(iren)
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def mouseMoveEvent(self,e):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0), 0, None)
+
+ iren.InvokeEvent("MouseMoveEvent")
+
+ def enterEvent(self,e):
+ """ enterEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("EnterEvent")
+
+ def leaveEvent(self,e):
+ """ leaveEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("LeaveEvent")
+
+ def mouseReleaseEvent(self,e):
+ """ mouseReleaseEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonReleaseEvent",
+ QtCore.Qt.MidButton:"MiddleButtonReleaseEvent",
+ QtCore.Qt.RightButton:"RightButtonReleaseEvent"}
+
+ self.interacting = None
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def keyPressEvent(self,e):
+ """ keyPressEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if e.text().length()>0:
+ ascii_key = e.text().toLatin1()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q', 'e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl,shift,ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyPressEvent")
+
+ if ascii_key:
+ iren.InvokeEvent("CharEvent")
+
+
+ def keyReleaseEvent(self,e):
+ """ keyReleaseEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if e.text().length()>0:
+ ascii_key = e.text().toLatin1()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q','e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl, shift, ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyReleaseEvent")
+
+ def wheelEvent(self,e):
+ """ wheelEvent(e: QWheelEvent) -> None
+ Zoom in/out while scrolling the mouse
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ self.SelectActiveRenderer(iren)
+
+ if e.delta()>0:
+ iren.InvokeEvent("MouseWheelForwardEvent")
+ else:
+ iren.InvokeEvent("MouseWheelBackwardEvent")
+
+ def focusInEvent(self,e):
+ """ focusInEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def focusOutEvent(self,e):
+ """ focusOutEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def contextMenuEvent(self,e):
+ """ contextMenuEvent(e: QContextMenuEvent) -> None
+ Make sure to get the right mouse position for the context menu
+ event, i.e. also the right click
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = int(e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = int(e.modifiers()&QtCore.Qt.ShiftModifier)
+ iren.SetEventInformationFlipY(e.x(),e.y(),ctrl,shift,chr(0),0,None)
+ iren.InvokeEvent("ContextMenuEvent")
+
+ def ascii_to_key_sym(self,i):
+ """ ascii_to_key_sym(i: int) -> str
+ Convert ASCII code into key name
+
+ """
+ global AsciiToKeySymTable
+ return AsciiToKeySymTable[i]
+
+ def qt_key_to_key_sym(self,i):
+ """ qt_key_to_key_sym(i: QtCore.Qt.Keycode) -> str
+ Convert Qt key code into key name
+
+ """
+ handler = {QtCore.Qt.Key_Backspace:"BackSpace",
+ QtCore.Qt.Key_Tab:"Tab",
+ QtCore.Qt.Key_Backtab:"Tab",
+ QtCore.Qt.Key_Return:"Return",
+ QtCore.Qt.Key_Enter:"Return",
+ QtCore.Qt.Key_Shift:"Shift_L",
+ QtCore.Qt.Key_Control:"Control_L",
+ QtCore.Qt.Key_Alt:"Alt_L",
+ QtCore.Qt.Key_Pause:"Pause",
+ QtCore.Qt.Key_CapsLock:"Caps_Lock",
+ QtCore.Qt.Key_Escape:"Escape",
+ QtCore.Qt.Key_Space:"space",
+ QtCore.Qt.Key_End:"End",
+ QtCore.Qt.Key_Home:"Home",
+ QtCore.Qt.Key_Left:"Left",
+ QtCore.Qt.Key_Up:"Up",
+ QtCore.Qt.Key_Right:"Right",
+ QtCore.Qt.Key_Down:"Down",
+ QtCore.Qt.Key_SysReq:"Snapshot",
+ QtCore.Qt.Key_Insert:"Insert",
+ QtCore.Qt.Key_Delete:"Delete",
+ QtCore.Qt.Key_Help:"Help",
+ QtCore.Qt.Key_0:"0",
+ QtCore.Qt.Key_1:"1",
+ QtCore.Qt.Key_2:"2",
+ QtCore.Qt.Key_3:"3",
+ QtCore.Qt.Key_4:"4",
+ QtCore.Qt.Key_5:"5",
+ QtCore.Qt.Key_6:"6",
+ QtCore.Qt.Key_7:"7",
+ QtCore.Qt.Key_8:"8",
+ QtCore.Qt.Key_9:"9",
+ QtCore.Qt.Key_A:"a",
+ QtCore.Qt.Key_B:"b",
+ QtCore.Qt.Key_C:"c",
+ QtCore.Qt.Key_D:"d",
+ QtCore.Qt.Key_E:"e",
+ QtCore.Qt.Key_F:"f",
+ QtCore.Qt.Key_G:"g",
+ QtCore.Qt.Key_H:"h",
+ QtCore.Qt.Key_I:"i",
+ QtCore.Qt.Key_J:"h",
+ QtCore.Qt.Key_K:"k",
+ QtCore.Qt.Key_L:"l",
+ QtCore.Qt.Key_M:"m",
+ QtCore.Qt.Key_N:"n",
+ QtCore.Qt.Key_O:"o",
+ QtCore.Qt.Key_P:"p",
+ QtCore.Qt.Key_Q:"q",
+ QtCore.Qt.Key_R:"r",
+ QtCore.Qt.Key_S:"s",
+ QtCore.Qt.Key_T:"t",
+ QtCore.Qt.Key_U:"u",
+ QtCore.Qt.Key_V:"v",
+ QtCore.Qt.Key_W:"w",
+ QtCore.Qt.Key_X:"x",
+ QtCore.Qt.Key_Y:"y",
+ QtCore.Qt.Key_Z:"z",
+ QtCore.Qt.Key_Asterisk:"asterisk",
+ QtCore.Qt.Key_Plus:"plus",
+ QtCore.Qt.Key_Minus:"minus",
+ QtCore.Qt.Key_Period:"period",
+ QtCore.Qt.Key_Slash:"slash",
+ QtCore.Qt.Key_F1:"F1",
+ QtCore.Qt.Key_F2:"F2",
+ QtCore.Qt.Key_F3:"F3",
+ QtCore.Qt.Key_F4:"F4",
+ QtCore.Qt.Key_F5:"F5",
+ QtCore.Qt.Key_F6:"F6",
+ QtCore.Qt.Key_F7:"F7",
+ QtCore.Qt.Key_F8:"F8",
+ QtCore.Qt.Key_F9:"F9",
+ QtCore.Qt.Key_F10:"F10",
+ QtCore.Qt.Key_F11:"F11",
+ QtCore.Qt.Key_F12:"F12",
+ QtCore.Qt.Key_F13:"F13",
+ QtCore.Qt.Key_F14:"F14",
+ QtCore.Qt.Key_F15:"F15",
+ QtCore.Qt.Key_F16:"F16",
+ QtCore.Qt.Key_F17:"F17",
+ QtCore.Qt.Key_F18:"F18",
+ QtCore.Qt.Key_F19:"F19",
+ QtCore.Qt.Key_F20:"F20",
+ QtCore.Qt.Key_F21:"F21",
+ QtCore.Qt.Key_F22:"F22",
+ QtCore.Qt.Key_F23:"F23",
+ QtCore.Qt.Key_F24:"F24",
+ QtCore.Qt.Key_NumLock:"Num_Lock",
+ QtCore.Qt.Key_ScrollLock:"Scroll_Lock"}
+ if i in handler:
+ return handler[i]
+ else:
+ return "None"
+
+ def getRendererList(self):
+ """ getRendererList() -> list
+ Return a list of vtkRenderer running in this QVTKWidget
+ """
+ result = []
+ renWin = self.GetRenderWindow()
+ renderers = renWin.GetRenderers()
+ renderers.InitTraversal()
+ for i in xrange(renderers.GetNumberOfItems()):
+ result.append(renderers.GetNextItem())
+ return result
+
+ def getActiveRenderer(self, iren):
+ """ getActiveRenderer(iren: vtkRenderWindowwInteractor) -> vtkRenderer
+ Return the active vtkRenderer under mouse
+
+ """
+ epos = list(iren.GetEventPosition())
+ if epos[1]<0:
+ epos[1] = -epos[1]
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ if ren.IsInViewport(epos[0], epos[1]):
+ return ren
+ return None
+
+ def findSheetTabWidget(self):
+ """ findSheetTabWidget() -> QTabWidget
+ Find and return the sheet tab widget
+
+ """
+ p = self.parent()
+ while p:
+ if hasattr(p, 'isSheetTabWidget'):
+ if p.isSheetTabWidget()==True:
+ return p
+ p = p.parent()
+ return None
+
+ def getRenderersInCellList(self, sheet, cells):
+ """ isRendererIn(sheet: spreadsheet.StandardWidgetSheet,
+ cells: [(int,int)]) -> bool
+ Get the list of renderers in side a list of (row, column)
+ cells.
+
+ """
+ rens = []
+ for (row, col) in cells:
+ cell = sheet.getCell(row, col)
+ if hasattr(cell, 'getRendererList'):
+ rens += cell.getRendererList()
+ return rens
+
+ def getSelectedCellWidgets(self):
+ sheet = self.findSheetTabWidget()
+ if sheet:
+ iren = self.mRenWin.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ cells = sheet.getSelectedLocations()
+ if (ren in self.getRenderersInCellList(sheet, cells)):
+ return [sheet.getCell(row, col)
+ for (row, col) in cells
+ if hasattr(sheet.getCell(row, col),
+ 'getRendererList')]
+ return []
+
+ def interactionEvent(self, istyle, name):
+ """ interactionEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure interactions sync across selected renderers
+
+ """
+ if name=='MouseWheelForwardEvent':
+ istyle.OnMouseWheelForward()
+ if name=='MouseWheelBackwardEvent':
+ istyle.OnMouseWheelBackward()
+ ren = self.interacting
+ if not ren:
+ ren = self.getActiveRenderer(istyle.GetInteractor())
+ if ren:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ for cell in self.getSelectedCellWidgets():
+ if cell!=self and hasattr(cell, 'getRendererList'):
+ rens = cell.getRendererList()
+ for r in rens:
+ if r!=ren:
+ dcam = r.GetActiveCamera()
+ dcam.SetPosition(cpos)
+ dcam.SetFocalPoint(cfol)
+ dcam.SetViewUp(cup)
+ r.ResetCameraClippingRange()
+ cell.update()
+
+ def charEvent(self, istyle, name):
+ """ charEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure key presses also sync across selected renderers
+
+ """
+ iren = istyle.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ keyCode = iren.GetKeyCode()
+ if keyCode in ['w','W','s','S','r','R','p','P']:
+ for cell in self.getSelectedCellWidgets():
+ if hasattr(cell, 'GetInteractor'):
+ selectedIren = cell.GetInteractor()
+ selectedIren.SetKeyCode(keyCode)
+ selectedIren.GetInteractorStyle().OnChar()
+ selectedIren.Render()
+ istyle.OnChar()
+
+ def saveToPNG(self, filename):
+ """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
+
+ Save the current widget contents to an image file. If
+ str==None, then it returns the vtkUnsignedCharArray containing
+ the PNG image. Otherwise, the filename is returned.
+
+ """
+ w2i = vtksnl.vtkWindowToImageFilter()
+ w2i.ReadFrontBufferOff()
+ w2i.SetInput(self.mRenWin)
+ # Render twice to get a clean image on the back buffer
+ self.mRenWin.Render()
+ self.mRenWin.Render()
+ w2i.Update()
+ writer = vtksnl.vtkPNGWriter()
+ writer.SetInputConnection(w2i.GetOutputPort())
+ if filename!=None:
+ writer.SetFileName(filename)
+ else:
+ writer.WriteToMemoryOn()
+ writer.Write()
+ if filename:
+ return filename
+ else:
+ return writer.GetResult()
+
+ def captureWindow(self):
+ """ captureWindow() -> None
+ Capture the window contents to file
+
+ """
+ fn = QtGui.QFileDialog.getSaveFileName(None,
+ "Save file as...",
+ "screenshot.png",
+ "Images (*.png)")
+ if fn.isNull():
+ return
+ self.saveToPNG(str(fn))
+
+ def grabWindowPixmap(self):
+ """ grabWindowImage() -> QPixmap
+ Widget special grabbing function
+
+ """
+ uchar = self.saveToPNG(None)
+
+ ba = QtCore.QByteArray()
+ buf = QtCore.QBuffer(ba)
+ buf.open(QtCore.QIODevice.WriteOnly)
+ for i in xrange(uchar.GetNumberOfTuples()):
+ c = uchar.GetValue(i)
+ buf.putChar(chr(c))
+ buf.close()
+
+ pixmap = QtGui.QPixmap()
+ pixmap.loadFromData(ba, 'PNG')
+ return pixmap
+
+ def dumpToFile(self, filename):
+ """dumpToFile() -> None
+ Dumps itself as an image to a file, calling saveToPNG
+ """
+ self.saveToPNG(filename)
+
+class QVTKWidgetCapture(QtGui.QAction):
+ """
+ QVTKWidgetCapture is the action to capture the vtk rendering
+ window to an image
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKWidgetCapture(parent: QWidget) -> QVTKWidgetCapture
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/camera.png"),
+ "&Capture image to file",
+ parent)
+ self.setStatusTip("Capture the rendered image to a file")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ cellWidget.captureWindow()
+
+class QVTKWidgetSaveCamera(QtGui.QAction):
+ """
+ QVTKWidgetSaveCamera is the action to capture the current camera
+ of the vtk renderers and save it back to the pipeline
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKWidgetSaveCamera(parent: QWidget) -> QVTKWidgetSaveCamera
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ "Save &Camera",
+ parent)
+ self.setStatusTip("Save current camera views to the pipeline")
+
+ def setCamera(self, controller):
+ ops = []
+ pipeline = controller.current_pipeline
+ cellWidget = self.toolBar.getSnappedWidget()
+ renderers = cellWidget.getRendererList()
+ for ren in renderers:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ rendererId = cellWidget.renderer_maps[ren]
+ # Looking for SetActiveCamera()
+ camera = None
+ renderer = pipeline.modules[rendererId]
+ for c in pipeline.connections.values():
+ if c.destination.moduleId==rendererId:
+ if c.destination.name=='SetActiveCamera':
+ camera = pipeline.modules[c.source.moduleId]
+ break
+
+ if not camera:
+ # Create camera
+ vtk_package = 'edu.utah.sci.vistrails.vtksnl'
+ camera = controller.create_module(vtk_package, 'vtkCamera', '',
+ 0.0, 0.0)
+ ops.append(('add', camera))
+
+ # Connect camera to renderer
+ camera_conn = controller.create_connection(camera, 'self',
+ renderer,
+ 'SetActiveCamera')
+ ops.append(('add', camera_conn))
+ # update functions
+ def convert_to_str(arglist):
+ new_arglist = []
+ for arg in arglist:
+ new_arglist.append(str(arg))
+ return new_arglist
+ functions = [('SetPosition', convert_to_str(cpos)),
+ ('SetFocalPoint', convert_to_str(cfol)),
+ ('SetViewUp', convert_to_str(cup))]
+ ops.extend(controller.update_functions_ops(camera, functions))
+
+ action = core.db.action.create_action(ops)
+ controller.add_new_action(action)
+ controller.perform_action(action)
+ controller.select_latest_version()
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ visApp = QtCore.QCoreApplication.instance()
+ if hasattr(visApp, 'builderWindow'):
+ builderWindow = visApp.builderWindow
+ if builderWindow:
+ info = self.toolBar.sheet.getCellPipelineInfo(
+ self.toolBar.row, self.toolBar.col)
+ if info:
+ info = info[0]
+ viewManager = builderWindow.viewManager
+ view = viewManager.ensureVistrail(info['locator'])
+ if view:
+ controller = view.controller
+ controller.change_selected_version(info['version'])
+ self.setCamera(controller)
+
+
+class QVTKWidgetToolBar(QCellToolBar):
+ """
+ QVTKWidgetToolBar derives from QCellToolBar to give the VTKCell
+ a customizable toolbar
+
+ """
+ def createToolBar(self):
+ """ createToolBar() -> None
+ This will get call initiallly to add customizable widgets
+
+ """
+ self.appendAction(QVTKWidgetCapture(self))
+ self.addAnimationButtons()
+ self.appendAction(QVTKWidgetSaveCamera(self))
+
+def registerSelf():
+ """ registerSelf() -> None
+ Registry module with the registry
+ """
+ identifier = 'edu.utah.sci.vistrails.vtksnl'
+ registry = get_module_registry()
+ registry.add_module(VTKCell)
+ registry.add_input_port(VTKCell, "Location", CellLocation)
+ import core.debug
+ for (port,module) in [("AddRenderer",'vtkRenderer'),
+ ("SetRenderView",'vtkRenderView'),
+ ("InteractionHandler",'vtkInteractionHandler'),
+ ("InteractorStyle", 'vtkInteractorStyle'),
+ ("AddPicker",'vtkAbstractPicker')]:
+ try:
+ registry.add_input_port(VTKCell, port,'(%s:%s)'%(identifier,module))
+
+ except Exception, e:
+ core.debug.warning(str(e))
+
+ registry.add_output_port(VTKCell, "self", VTKCell)
diff --git a/contrib/vtksnl/vtkcell_rc.py b/contrib/vtksnl/vtkcell_rc.py
new file mode 100644
index 0000000..8aa8cbf
--- /dev/null
+++ b/contrib/vtksnl/vtkcell_rc.py
@@ -0,0 +1,793 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+# Resource object code
+#
+# Created: Fri Sep 22 09:09:40 2006
+# by: The Resource Compiler for PyQt (Qt v4.1.3)
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore
+
+qt_resource_data = "\
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+"
+
+qt_resource_name = "\
+\x00\x06\
+\x07\x03\x7d\xc3\
+\x00\x69\
+\x00\x6d\x00\x61\x00\x67\x00\x65\x00\x73\
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+"
+
+qt_resource_struct = "\
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+\x00\x00\x00\x62\x00\x00\x00\x00\x00\x01\x00\x00\x0d\xfd\
+"
+
+def qInitResources():
+ QtCore.qRegisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+def qCleanupResources():
+ QtCore.qUnregisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+qInitResources()
diff --git a/contrib/vtksnl/vtkhandler.py b/contrib/vtksnl/vtkhandler.py
new file mode 100644
index 0000000..36b344c
--- /dev/null
+++ b/contrib/vtksnl/vtkhandler.py
@@ -0,0 +1,291 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+"""Modules for handling vtkRenderWindowInteractor events"""
+from PyQt4 import QtCore, QtGui
+from core.modules.basic_modules import String
+from core.modules.vistrails_module import Module, NotCacheable
+from core.modules.module_registry import get_module_registry
+from core.modules.module_configure import StandardModuleConfigurationWidget
+from core.modules.python_source_configure import PythonEditor
+from core.vistrail.module_function import ModuleFunction, ModuleParam
+import urllib
+
+################################################################################
+class vtkInteractionHandler(NotCacheable, Module):
+ """
+ vtkInteractionHandler allow users to insert callback code for interacting
+ with the vtkRenderWindowInteractor InteractionEvent
+
+ """
+
+ # Since vtkCommand is not wrapped in Python, we need to hardcoded all events
+ # string from vtkCommand.h
+ vtkEvents = [
+ 'AnyEvent',
+ 'DeleteEvent',
+ 'StartEvent',
+ 'EndEvent',
+ 'RenderEvent',
+ 'ProgressEvent',
+ 'PickEvent',
+ 'StartPickEvent',
+ 'EndPickEvent',
+ 'AbortCheckEvent',
+ 'ExitEvent',
+ 'LeftButtonPressEvent',
+ 'LeftButtonReleaseEvent',
+ 'MiddleButtonPressEvent',
+ 'MiddleButtonReleaseEvent',
+ 'RightButtonPressEvent',
+ 'RightButtonReleaseEvent',
+ 'EnterEvent',
+ 'LeaveEvent',
+ 'KeyPressEvent',
+ 'KeyReleaseEvent',
+ 'CharEvent',
+ 'ExposeEvent',
+ 'ConfigureEvent',
+ 'TimerEvent',
+ 'MouseMoveEvent',
+ 'MouseWheelForwardEvent',
+ 'MouseWheelBackwardEvent',
+ 'ResetCameraEvent',
+ 'ResetCameraClippingRangeEvent',
+ 'ModifiedEvent',
+ 'WindowLevelEvent',
+ 'StartWindowLevelEvent',
+ 'EndWindowLevelEvent',
+ 'ResetWindowLevelEvent',
+ 'SetOutputEvent',
+ 'ErrorEvent',
+ 'WarningEvent',
+ 'StartInteractionEvent',
+ 'InteractionEvent',
+ 'EndInteractionEvent',
+ 'EnableEvent',
+ 'DisableEvent',
+ 'CreateTimerEvent',
+ 'DestroyTimerEvent',
+ 'PlacePointEvent',
+ 'PlaceWidgetEvent',
+ 'CursorChangedEvent',
+ 'ExecuteInformationEvent',
+ 'RenderWindowMessageEvent',
+ 'WrongTagEvent',
+ 'StartAnimationCueEvent',
+ 'AnimationCueTickEvent',
+ 'EndAnimationCueEvent',
+ 'VolumeMapperRenderEndEvent',
+ 'VolumeMapperRenderProgressEvent',
+ 'VolumeMapperRenderStartEvent',
+ 'VolumeMapperComputeGradientsEndEvent',
+ 'VolumeMapperComputeGradientsProgressEvent',
+ 'VolumeMapperComputeGradientsStartEvent',
+ 'WidgetModifiedEvent',
+ 'WidgetValueChangedEvent',
+ 'WidgetActivateEvent',
+ 'ConnectionCreatedEvent',
+ 'ConnectionClosedEvent',
+ 'DomainModifiedEvent',
+ 'PropertyModifiedEvent',
+ 'UpdateEvent',
+ 'RegisterEvent',
+ 'UnRegisterEvent',
+ 'UpdateInformationEvent']
+
+ def __init__(self):
+ Module.__init__(self)
+ self.observer = None
+ self.handler = None
+ self.shareddata = None
+
+ def compute(self):
+ """ compute() -> None
+ Actually compute nothing
+ """
+ self.observer = self.forceGetInputFromPort('Observer')
+ self.handler = self.forceGetInputFromPort('Handler', '')
+ self.shareddata = self.forceGetInputListFromPort('SharedData')
+ if len(self.shareddata)==1:
+ self.shareddata = self.shareddata[0]
+ if self.observer:
+ source = urllib.unquote(self.handler)
+ observer = self.observer.vtkInstance
+ for e in vtkInteractionHandler.vtkEvents:
+ f = e[0].lower() + e[1:]
+ f = f.replace('Event', 'Handler')
+ source += ('\nif locals().has_key("%s"):\n' % f +
+ '\tobserver.AddObserver("%s", ' % e +
+ 'self.eventHandler)\n')
+ exec(source)
+ if hasattr(self.observer.vtkInstance, 'PlaceWidget'):
+ self.observer.vtkInstance.PlaceWidget()
+
+ def eventHandler(self, obj, event):
+ """ eventHandler(obj: vtkObject, event: str) -> None
+ A proxy for all vtk events to direct to the correct calls
+
+ """
+ if self.handler!='':
+ source = urllib.unquote(self.handler)
+ f = event[0].lower() + event[1:]
+ f = f.replace('Event', 'Handler')
+ myGlobals = globals()
+ myGlobals.update({'self':self})
+ exec(source + ('\nif locals().has_key("%s"):\n' % f)+
+ ('\t%s(obj, self.shareddata)' % f)) in myGlobals, locals()
+
+ def clear(self):
+ """ clear() -> None
+ Remove event handler so the object can be freed correctly
+
+ """
+ # Remove all observers
+ if self.observer:
+ for e in vtkInteractionHandler.vtkEvents:
+ self.observer.vtkInstance.RemoveObservers(e)
+ Module.clear(self)
+
+ def repaintCells(self):
+ """ repaintCells() -> None
+ Redraw all cells on the current sheet
+
+ """
+ from packages.spreadsheet.spreadsheet_controller \
+ import spreadsheetController
+ from packages.spreadsheet.spreadsheet_event \
+ import RepaintCurrentSheetEvent
+ spreadsheetController.postEventToSpreadsheet(RepaintCurrentSheetEvent())
+
+class HandlerConfigurationWidget(StandardModuleConfigurationWidget):
+ """
+ HandlerConfigurationWidget is simialr to PythonSource
+ configuration widget except that it doesn't allow add/remove
+ ports. In this configuration widget, the user will enter their
+ python code to handle a specifc event
+
+ """
+ def __init__(self, module, controller, parent=None):
+ """ HandlerConfigurationWidget(module: Module,
+ controller: VistrailController,
+ parent: QWidget)
+ -> HandlerConfigurationWidget
+ Setup the dialog to have a single python source editor and 2
+ buttons
+
+ """
+ StandardModuleConfigurationWidget.__init__(self, module,
+ controller, parent)
+ self.setWindowTitle('Handler Python Script Editor')
+ self.setLayout(QtGui.QVBoxLayout())
+ self.layout().setMargin(0)
+ self.layout().setSpacing(0)
+ self.createEditor()
+ self.createButtonLayout()
+
+ def findHandlerFunction(self):
+ """ findHandlerFunction() -> int
+ Return the function id associated with input port 'source'
+
+ """
+ fid = -1
+ for i in xrange(self.module.getNumFunctions()):
+ if self.module.functions[i].name=='Handler':
+ fid = i
+ break
+ return fid
+
+ def createEditor(self):
+ """ createEditor() -> None
+ Add a python editor into the widget layout
+
+ """
+ self.codeEditor = PythonEditor(self)
+ fid = self.findHandlerFunction()
+ if fid!=-1:
+ f = self.module.functions[fid]
+ self.codeEditor.setPlainText(urllib.unquote(f.params[0].strValue))
+ self.codeEditor.document().setModified(False)
+ self.layout().addWidget(self.codeEditor, 1)
+
+ def createButtonLayout(self):
+ """ createButtonLayout() -> None
+ Construct Ok & Cancel button
+
+ """
+ self.buttonLayout = QtGui.QHBoxLayout()
+ self.buttonLayout.setMargin(5)
+ self.okButton = QtGui.QPushButton('&OK', self)
+ self.okButton.setAutoDefault(False)
+ self.okButton.setFixedWidth(100)
+ self.buttonLayout.addWidget(self.okButton)
+ self.cancelButton = QtGui.QPushButton('&Cancel', self)
+ self.cancelButton.setAutoDefault(False)
+ self.cancelButton.setShortcut('Esc')
+ self.cancelButton.setFixedWidth(100)
+ self.buttonLayout.addWidget(self.cancelButton)
+ self.layout().addLayout(self.buttonLayout)
+ self.connect(self.okButton, QtCore.SIGNAL('clicked(bool)'), self.okTriggered)
+ self.connect(self.cancelButton, QtCore.SIGNAL('clicked(bool)'), self.close)
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+ Return the recommendation size of this widget
+
+ """
+ return QtCore.QSize(512, 512)
+
+ def updateController(self, controller):
+ """ updateController() -> None
+ Based on the input of the python editor, update the vistrail
+ controller appropriately
+
+ """
+ if self.codeEditor.document().isModified():
+ code = urllib.quote(str(self.codeEditor.toPlainText()))
+ functions = [('Handler', [code])]
+ self.controller.update_functions(self.module, functions)
+
+ def okTriggered(self, checked = False):
+ """ okTriggered(checked: bool) -> None
+ Update vistrail controller (if neccesssary) then close the widget
+
+ """
+ self.updateController(self.controller)
+ self.emit(QtCore.SIGNAL('doneConfigure()'))
+ self.close()
+
+
+def registerSelf():
+ """ registerSelf() -> None
+ Registry module with the registry
+ """
+ registry = get_module_registry()
+ vIO = registry.get_descriptor_by_name(
+ 'edu.utah.sci.vistrails.vtksnl',
+ 'vtkInteractorObserver').module
+ registry.add_module(vtkInteractionHandler, configureWidgetType=HandlerConfigurationWidget)
+ registry.add_input_port(vtkInteractionHandler, 'Observer', vIO)
+ registry.add_input_port(vtkInteractionHandler, 'Handler', String, True)
+ registry.add_input_port(vtkInteractionHandler, 'SharedData', Module)
+ registry.add_output_port(vtkInteractionHandler, 'self',
+ vtkInteractionHandler)
diff --git a/contrib/vtksnl/vtkviewcell.py b/contrib/vtksnl/vtkviewcell.py
new file mode 100644
index 0000000..1611d95
--- /dev/null
+++ b/contrib/vtksnl/vtkviewcell.py
@@ -0,0 +1,1032 @@
+############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+################################################################################
+# File QVTKViewWidget.py
+# File for displaying a vtkRenderWindow in a Qt's QWidget ported from
+# VTK/GUISupport/QVTK. Combine altogether to a single class: QVTKViewWidget
+################################################################################
+import vtksnl
+from PyQt4 import QtCore, QtGui
+import sip
+from core import system
+from core.modules.module_registry import get_module_registry
+from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+import vtkcell_rc
+import gc
+from gui.qt import qt_super
+import core.db.action
+from core.vistrail.action import Action
+from core.vistrail.port import Port
+from core.vistrail import module
+from core.vistrail import connection
+from core.vistrail.module_function import ModuleFunction
+from core.vistrail.module_param import ModuleParam
+from core.vistrail.location import Location
+from core.modules.vistrails_module import ModuleError
+import copy
+
+################################################################################
+
+class VTKViewCell(SpreadsheetCell):
+ """
+ VTKViewCell is a VisTrails Module that can display vtkRenderWindow inside a cell
+
+ """
+
+ def __init__(self):
+ SpreadsheetCell.__init__(self)
+ self.cellWidget = None
+
+ def compute(self):
+ """ compute() -> None
+ Dispatch the vtkRenderer to the actual rendering widget
+ """
+ renderView = self.forceGetInputFromPort('SetRenderView')
+ if renderView==None:
+ raise ModuleError(self, 'A vtkRenderView input is required.')
+ self.cellWidget = self.displayAndWait(QVTKViewWidget, (renderView,))
+
+AsciiToKeySymTable = ( None, None, None, None, None, None, None,
+ None, None,
+ "Tab", None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None,
+ "space", "exclam", "quotedbl", "numbersign",
+ "dollar", "percent", "ampersand", "quoteright",
+ "parenleft", "parenright", "asterisk", "plus",
+ "comma", "minus", "period", "slash",
+ "0", "1", "2", "3", "4", "5", "6", "7",
+ "8", "9", "colon", "semicolon", "less", "equal",
+ "greater", "question",
+ "at", "A", "B", "C", "D", "E", "F", "G",
+ "H", "I", "J", "K", "L", "M", "N", "O",
+ "P", "Q", "R", "S", "T", "U", "V", "W",
+ "X", "Y", "Z", "bracketleft",
+ "backslash", "bracketright", "asciicircum",
+ "underscore",
+ "quoteleft", "a", "b", "c", "d", "e", "f", "g",
+ "h", "i", "j", "k", "l", "m", "n", "o",
+ "p", "q", "r", "s", "t", "u", "v", "w",
+ "x", "y", "z", "braceleft", "bar", "braceright",
+ "asciitilde", "Delete",
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None)
+
+class QVTKViewWidget(QCellWidget):
+ """
+ QVTKViewWidget is the actual rendering widget that can display
+ vtkRenderer inside a Qt QWidget
+
+ """
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QVTKViewWidget(parent: QWidget, f: WindowFlags) -> QVTKViewWidget
+ Initialize QVTKViewWidget with a toolbar with its own device
+ context
+
+ """
+ QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
+
+ self.interacting = None
+ self.mRenWin = None
+ self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
+ self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
+ self.setMouseTracking(True)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding))
+ self.toolBarType = QVTKViewWidgetToolBar
+ self.setAnimationEnabled(True)
+
+ def removeObserversFromInteractorStyle(self):
+ """ removeObserversFromInteractorStyle() -> None
+ Remove all python binding from interactor style observers for
+ safely freeing the cell
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.RemoveObservers("InteractionEvent")
+ style.RemoveObservers("EndPickEvent")
+ style.RemoveObservers("CharEvent")
+ style.RemoveObservers("MouseWheelForwardEvent")
+ style.RemoveObservers("MouseWheelBackwardEvent")
+
+ def addObserversToInteractorStyle(self):
+ """ addObserversToInteractorStyle() -> None
+ Assign observer to the current interactor style
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.AddObserver("InteractionEvent", self.interactionEvent)
+ style.AddObserver("EndPickEvent", self.interactionEvent)
+ style.AddObserver("CharEvent", self.charEvent)
+ style.AddObserver("MouseWheelForwardEvent", self.interactionEvent)
+ style.AddObserver("MouseWheelBackwardEvent", self.interactionEvent)
+
+ def deleteLater(self):
+ """ deleteLater() -> None
+ Make sure to free render window resource when
+ deallocating. Overriding PyQt deleteLater to free up
+ resources
+
+ """
+ self.renderer_maps = {}
+ for ren in self.getRendererList():
+ self.mRenWin.RemoveRenderer(ren)
+ self.removeObserversFromInteractorStyle()
+ self.SetRenderWindow(None)
+ QCellWidget.deleteLater(self)
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple)
+ Updates the cell contents with new vtkRenderer
+
+ """
+ (renderView, ) = inputPorts
+ renWin = renderView.vtkInstance.GetRenderWindow()
+ renWin.DoubleBufferOn()
+ self.SetRenderWindow(renWin)
+ renderView.vtkInstance.ResetCamera()
+ self.addObserversToInteractorStyle()
+
+# renWin = self.GetRenderWindow()
+# renderers = [renderView.vtkInstance.GetRenderer()]
+# iren = renWin.GetInteractor()
+ # Update interactor style
+# self.removeObserversFromInteractorStyle()
+# if renderView==None:
+# if iStyle==None:
+# iStyleInstance = vtk.vtkInteractorStyleTrackballCamera()
+# else:
+# iStyleInstance = iStyle.vtkInstance
+# iren.SetInteractorStyle(iStyleInstance)
+# self.addObserversToInteractorStyle()
+ # Capture window into history for playback
+ # Call this at the end to capture the image after rendering
+ QCellWidget.updateContents(self, inputPorts)
+
+ def GetRenderWindow(self):
+ """ GetRenderWindow() -> vtkRenderWindow
+ Return the associated vtkRenderWindow
+
+ """
+ if not self.mRenWin:
+ win = vtksnl.vtkRenderWindow()
+ win.DoubleBufferOn()
+ self.SetRenderWindow(win)
+ del win
+
+ return self.mRenWin
+
+ def SetRenderWindow(self,w):
+ """ SetRenderWindow(w: vtkRenderWindow)
+ Set a new render window to QVTKViewWidget and initialize the
+ interactor as well
+
+ """
+ if w == self.mRenWin:
+ return
+
+ if self.mRenWin:
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+
+ self.mRenWin = w
+
+ if self.mRenWin:
+ self.mRenWin.Register(None)
+ if system.systemType=='Linux':
+ try:
+ vp = '_%s_void_p' % (hex(int(QtGui.QX11Info.display()))[2:])
+ except TypeError:
+ #This was change for PyQt4.2
+ if isinstance(QtGui.QX11Info.display(),QtGui.Display):
+ display = sip.unwrapinstance(QtGui.QX11Info.display())
+ vp = '_%s_void_p' % (hex(display)[2:])
+ self.mRenWin.SetDisplayId(vp)
+ if not self.mRenWin.GetMapped():
+ self.mRenWin.GetInteractor().Initialize()
+ system.XDestroyWindow(self.mRenWin.GetGenericDisplayId(),
+ self.mRenWin.GetGenericWindowId())
+ self.mRenWin.Finalize()
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ else:
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ def GetInteractor(self):
+ """ GetInteractor() -> vtkInteractor
+ Return the vtkInteractor control this QVTKViewWidget
+ """
+ return self.GetRenderWindow().GetInteractor()
+
+ def event(self, e):
+ """ event(e: QEvent) -> depends on event type
+ Process window and interaction events
+
+ """
+ if e.type()==QtCore.QEvent.ParentAboutToChange:
+ if self.mRenWin:
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+ else:
+ if e.type()==QtCore.QEvent.ParentChange:
+ if self.mRenWin:
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ if QtCore.QObject.event(self,e):
+ return 1
+
+ if e.type() == QtCore.QEvent.KeyPress:
+ self.keyPressEvent(e)
+ if e.isAccepted():
+ return e.isAccepted()
+
+ return qt_super(QVTKViewWidget, self).event(e)
+
+ # return QtGui.QWidget.event(self,e)
+ # Was this right? Wasn't this supposed to be QCellWidget.event()?
+
+ def resizeWindow(self, width, height):
+ """ resizeWindow(width: int, height: int) -> None
+ Work around vtk bugs for resizing window
+
+ """
+ ########################################################
+ # VTK - BUGGGGGGGGG - GRRRRRRRRR
+ # This is a 'bug' in vtkWin32OpenGLRenderWindow(.cxx)
+ # If a render window is mapped to screen, the actual
+ # window size is the client area of the window in Win32.
+ # However, this real window size is only updated through
+ # vtkWin32OpenGLRenderWindow::GetSize(). So this has to
+ # be called here to get the cell size correctly. This
+ # invalidates the condition in the next SetSize().
+ # We can use self.mRenWin.SetSize(0,0) here but it will
+ # cause flickering and decrease performance!
+ # SetPosition(curX,curY) also works here but slower.
+ self.mRenWin.GetSize()
+
+ self.mRenWin.SetSize(width, height)
+ if self.mRenWin.GetInteractor():
+ self.mRenWin.GetInteractor().SetSize(width, height)
+
+ def resizeEvent(self, e):
+ """ resizeEvent(e: QEvent) -> None
+ Re-adjust the vtkRenderWindow size then QVTKViewWidget resized
+
+ """
+ qt_super(QVTKViewWidget, self).resizeEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.resizeWindow(self.width(), self.height())
+ self.mRenWin.Render()
+
+ def moveEvent(self,e):
+ """ moveEvent(e: QEvent) -> None
+ Echo the move event into vtkRenderWindow
+
+ """
+ qt_super(QVTKViewWidget, self).moveEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.mRenWin.SetPosition(self.x(),self.y())
+
+ def paintEvent(self, e):
+ """ paintEvent(e: QPaintEvent) -> None
+ Paint the QVTKViewWidget with vtkRenderWindow
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ if hasattr(self.mRenWin, 'UpdateGLRegion'):
+ self.mRenWin.UpdateGLRegion()
+ self.mRenWin.Render()
+
+ def SelectActiveRenderer(self,iren):
+ """ SelectActiveRenderer(iren: vtkRenderWindowIteractor) -> None
+ Only make the vtkRenderer below the mouse cursor active
+
+ """
+ epos = iren.GetEventPosition()
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ ren.SetInteractive(ren.IsInViewport(epos[0], epos[1]))
+
+ def mousePressEvent(self,e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ isDoubleClick = e.type()==QtCore.QEvent.MouseButtonDblClick
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ ctrl,
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),
+ isDoubleClick,
+ None)
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonPressEvent",
+ QtCore.Qt.MidButton:"MiddleButtonPressEvent",
+ QtCore.Qt.RightButton:"RightButtonPressEvent"}
+
+ self.SelectActiveRenderer(iren)
+
+ if ctrl:
+ e.ignore()
+ return
+
+ self.interacting = self.getActiveRenderer(iren)
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def mouseMoveEvent(self,e):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0), 0, None)
+
+ iren.InvokeEvent("MouseMoveEvent")
+
+ def enterEvent(self,e):
+ """ enterEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("EnterEvent")
+
+ def leaveEvent(self,e):
+ """ leaveEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("LeaveEvent")
+
+ def mouseReleaseEvent(self,e):
+ """ mouseReleaseEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonReleaseEvent",
+ QtCore.Qt.MidButton:"MiddleButtonReleaseEvent",
+ QtCore.Qt.RightButton:"RightButtonReleaseEvent"}
+
+ self.interacting = None
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def keyPressEvent(self,e):
+ """ keyPressEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if e.text().length()>0:
+ ascii_key = e.text().toLatin1()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q', 'e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl,shift,ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyPressEvent")
+
+ if ascii_key:
+ iren.InvokeEvent("CharEvent")
+
+
+ def keyReleaseEvent(self,e):
+ """ keyReleaseEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if e.text().length()>0:
+ ascii_key = e.text().toLatin1()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q','e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl, shift, ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyReleaseEvent")
+
+ def wheelEvent(self,e):
+ """ wheelEvent(e: QWheelEvent) -> None
+ Zoom in/out while scrolling the mouse
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ self.SelectActiveRenderer(iren)
+
+ if e.delta()>0:
+ iren.InvokeEvent("MouseWheelForwardEvent")
+ else:
+ iren.InvokeEvent("MouseWheelBackwardEvent")
+
+ def focusInEvent(self,e):
+ """ focusInEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def focusOutEvent(self,e):
+ """ focusOutEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def contextMenuEvent(self,e):
+ """ contextMenuEvent(e: QContextMenuEvent) -> None
+ Make sure to get the right mouse position for the context menu
+ event, i.e. also the right click
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = int(e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = int(e.modifiers()&QtCore.Qt.ShiftModifier)
+ iren.SetEventInformationFlipY(e.x(),e.y(),ctrl,shift,chr(0),0,None)
+ iren.InvokeEvent("ContextMenuEvent")
+
+ def ascii_to_key_sym(self,i):
+ """ ascii_to_key_sym(i: int) -> str
+ Convert ASCII code into key name
+
+ """
+ global AsciiToKeySymTable
+ return AsciiToKeySymTable[i]
+
+ def qt_key_to_key_sym(self,i):
+ """ qt_key_to_key_sym(i: QtCore.Qt.Keycode) -> str
+ Convert Qt key code into key name
+
+ """
+ handler = {QtCore.Qt.Key_Backspace:"BackSpace",
+ QtCore.Qt.Key_Tab:"Tab",
+ QtCore.Qt.Key_Backtab:"Tab",
+ QtCore.Qt.Key_Return:"Return",
+ QtCore.Qt.Key_Enter:"Return",
+ QtCore.Qt.Key_Shift:"Shift_L",
+ QtCore.Qt.Key_Control:"Control_L",
+ QtCore.Qt.Key_Alt:"Alt_L",
+ QtCore.Qt.Key_Pause:"Pause",
+ QtCore.Qt.Key_CapsLock:"Caps_Lock",
+ QtCore.Qt.Key_Escape:"Escape",
+ QtCore.Qt.Key_Space:"space",
+ QtCore.Qt.Key_End:"End",
+ QtCore.Qt.Key_Home:"Home",
+ QtCore.Qt.Key_Left:"Left",
+ QtCore.Qt.Key_Up:"Up",
+ QtCore.Qt.Key_Right:"Right",
+ QtCore.Qt.Key_Down:"Down",
+ QtCore.Qt.Key_SysReq:"Snapshot",
+ QtCore.Qt.Key_Insert:"Insert",
+ QtCore.Qt.Key_Delete:"Delete",
+ QtCore.Qt.Key_Help:"Help",
+ QtCore.Qt.Key_0:"0",
+ QtCore.Qt.Key_1:"1",
+ QtCore.Qt.Key_2:"2",
+ QtCore.Qt.Key_3:"3",
+ QtCore.Qt.Key_4:"4",
+ QtCore.Qt.Key_5:"5",
+ QtCore.Qt.Key_6:"6",
+ QtCore.Qt.Key_7:"7",
+ QtCore.Qt.Key_8:"8",
+ QtCore.Qt.Key_9:"9",
+ QtCore.Qt.Key_A:"a",
+ QtCore.Qt.Key_B:"b",
+ QtCore.Qt.Key_C:"c",
+ QtCore.Qt.Key_D:"d",
+ QtCore.Qt.Key_E:"e",
+ QtCore.Qt.Key_F:"f",
+ QtCore.Qt.Key_G:"g",
+ QtCore.Qt.Key_H:"h",
+ QtCore.Qt.Key_I:"i",
+ QtCore.Qt.Key_J:"h",
+ QtCore.Qt.Key_K:"k",
+ QtCore.Qt.Key_L:"l",
+ QtCore.Qt.Key_M:"m",
+ QtCore.Qt.Key_N:"n",
+ QtCore.Qt.Key_O:"o",
+ QtCore.Qt.Key_P:"p",
+ QtCore.Qt.Key_Q:"q",
+ QtCore.Qt.Key_R:"r",
+ QtCore.Qt.Key_S:"s",
+ QtCore.Qt.Key_T:"t",
+ QtCore.Qt.Key_U:"u",
+ QtCore.Qt.Key_V:"v",
+ QtCore.Qt.Key_W:"w",
+ QtCore.Qt.Key_X:"x",
+ QtCore.Qt.Key_Y:"y",
+ QtCore.Qt.Key_Z:"z",
+ QtCore.Qt.Key_Asterisk:"asterisk",
+ QtCore.Qt.Key_Plus:"plus",
+ QtCore.Qt.Key_Minus:"minus",
+ QtCore.Qt.Key_Period:"period",
+ QtCore.Qt.Key_Slash:"slash",
+ QtCore.Qt.Key_F1:"F1",
+ QtCore.Qt.Key_F2:"F2",
+ QtCore.Qt.Key_F3:"F3",
+ QtCore.Qt.Key_F4:"F4",
+ QtCore.Qt.Key_F5:"F5",
+ QtCore.Qt.Key_F6:"F6",
+ QtCore.Qt.Key_F7:"F7",
+ QtCore.Qt.Key_F8:"F8",
+ QtCore.Qt.Key_F9:"F9",
+ QtCore.Qt.Key_F10:"F10",
+ QtCore.Qt.Key_F11:"F11",
+ QtCore.Qt.Key_F12:"F12",
+ QtCore.Qt.Key_F13:"F13",
+ QtCore.Qt.Key_F14:"F14",
+ QtCore.Qt.Key_F15:"F15",
+ QtCore.Qt.Key_F16:"F16",
+ QtCore.Qt.Key_F17:"F17",
+ QtCore.Qt.Key_F18:"F18",
+ QtCore.Qt.Key_F19:"F19",
+ QtCore.Qt.Key_F20:"F20",
+ QtCore.Qt.Key_F21:"F21",
+ QtCore.Qt.Key_F22:"F22",
+ QtCore.Qt.Key_F23:"F23",
+ QtCore.Qt.Key_F24:"F24",
+ QtCore.Qt.Key_NumLock:"Num_Lock",
+ QtCore.Qt.Key_ScrollLock:"Scroll_Lock"}
+ if i in handler:
+ return handler[i]
+ else:
+ return "None"
+
+ def getRendererList(self):
+ """ getRendererList() -> list
+ Return a list of vtkRenderer running in this QVTKViewWidget
+ """
+ result = []
+ renWin = self.GetRenderWindow()
+ renderers = renWin.GetRenderers()
+ renderers.InitTraversal()
+ for i in xrange(renderers.GetNumberOfItems()):
+ result.append(renderers.GetNextItem())
+ return result
+
+ def getActiveRenderer(self, iren):
+ """ getActiveRenderer(iren: vtkRenderWindowwInteractor) -> vtkRenderer
+ Return the active vtkRenderer under mouse
+
+ """
+ epos = list(iren.GetEventPosition())
+ if epos[1]<0:
+ epos[1] = -epos[1]
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ if ren.IsInViewport(epos[0], epos[1]):
+ return ren
+ return None
+
+ def findSheetTabWidget(self):
+ """ findSheetTabWidget() -> QTabWidget
+ Find and return the sheet tab widget
+
+ """
+ p = self.parent()
+ while p:
+ if hasattr(p, 'isSheetTabWidget'):
+ if p.isSheetTabWidget()==True:
+ return p
+ p = p.parent()
+ return None
+
+ def getRenderersInCellList(self, sheet, cells):
+ """ isRendererIn(sheet: spreadsheet.StandardWidgetSheet,
+ cells: [(int,int)]) -> bool
+ Get the list of renderers in side a list of (row, column)
+ cells.
+
+ """
+ rens = []
+ for (row, col) in cells:
+ cell = sheet.getCell(row, col)
+ if hasattr(cell, 'getRendererList'):
+ rens += cell.getRendererList()
+ return rens
+
+ def getSelectedCellWidgets(self):
+ sheet = self.findSheetTabWidget()
+ if sheet:
+ iren = self.mRenWin.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ cells = sheet.getSelectedLocations()
+ if (ren in self.getRenderersInCellList(sheet, cells)):
+ return [sheet.getCell(row, col)
+ for (row, col) in cells
+ if hasattr(sheet.getCell(row, col),
+ 'getRendererList')]
+ return []
+
+ def interactionEvent(self, istyle, name):
+ """ interactionEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure interactions sync across selected renderers
+
+ """
+ if name=='MouseWheelForwardEvent':
+ istyle.OnMouseWheelForward()
+ if name=='MouseWheelBackwardEvent':
+ istyle.OnMouseWheelBackward()
+ ren = self.interacting
+ if not ren:
+ ren = self.getActiveRenderer(istyle.GetInteractor())
+ if ren:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ for cell in self.getSelectedCellWidgets():
+ if cell!=self and hasattr(cell, 'getRendererList'):
+ rens = cell.getRendererList()
+ for r in rens:
+ if r!=ren:
+ dcam = r.GetActiveCamera()
+ dcam.SetPosition(cpos)
+ dcam.SetFocalPoint(cfol)
+ dcam.SetViewUp(cup)
+ r.ResetCameraClippingRange()
+ cell.update()
+
+ def charEvent(self, istyle, name):
+ """ charEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure key presses also sync across selected renderers
+
+ """
+ iren = istyle.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ keyCode = iren.GetKeyCode()
+ if keyCode in ['w','W','s','S','r','R','p','P']:
+ for cell in self.getSelectedCellWidgets():
+ if hasattr(cell, 'GetInteractor'):
+ selectedIren = cell.GetInteractor()
+ selectedIren.SetKeyCode(keyCode)
+ selectedIren.GetInteractorStyle().OnChar()
+ selectedIren.Render()
+ istyle.OnChar()
+
+ def saveToPNG(self, filename):
+ """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
+
+ Save the current widget contents to an image file. If
+ str==None, then it returns the vtkUnsignedCharArray containing
+ the PNG image. Otherwise, the filename is returned.
+
+ """
+ w2i = vtksnl.vtkWindowToImageFilter()
+ w2i.ReadFrontBufferOff()
+ w2i.SetInput(self.mRenWin)
+ # Render twice to get a clean image on the back buffer
+ self.mRenWin.Render()
+ self.mRenWin.Render()
+ w2i.Update()
+ writer = vtksnl.vtkPNGWriter()
+ writer.SetInputConnection(w2i.GetOutputPort())
+ if filename!=None:
+ writer.SetFileName(filename)
+ else:
+ writer.WriteToMemoryOn()
+ writer.Write()
+ if filename:
+ return filename
+ else:
+ return writer.GetResult()
+
+ def captureWindow(self):
+ """ captureWindow() -> None
+ Capture the window contents to file
+
+ """
+ fn = QtGui.QFileDialog.getSaveFileName(None,
+ "Save file as...",
+ "screenshot.png",
+ "Images (*.png)")
+ if fn.isNull():
+ return
+ self.saveToPNG(str(fn))
+
+ def grabWindowPixmap(self):
+ """ grabWindowImage() -> QPixmap
+ Widget special grabbing function
+
+ """
+ uchar = self.saveToPNG(None)
+
+ ba = QtCore.QByteArray()
+ buf = QtCore.QBuffer(ba)
+ buf.open(QtCore.QIODevice.WriteOnly)
+ for i in xrange(uchar.GetNumberOfTuples()):
+ c = uchar.GetValue(i)
+ buf.putChar(chr(c))
+ buf.close()
+
+ pixmap = QtGui.QPixmap()
+ pixmap.loadFromData(ba, 'PNG')
+ return pixmap
+
+ def dumpToFile(self, filename):
+ """dumpToFile() -> None
+ Dumps itself as an image to a file, calling saveToPNG
+ """
+ self.saveToPNG(filename)
+
+class QVTKViewWidgetCapture(QtGui.QAction):
+ """
+ QVTKViewWidgetCapture is the action to capture the vtk rendering
+ window to an image
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKViewWidgetCapture(parent: QWidget) -> QVTKViewWidgetCapture
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/camera.png"),
+ "&Capture image to file",
+ parent)
+ self.setStatusTip("Capture the rendered image to a file")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ cellWidget.captureWindow()
+
+class QVTKViewWidgetSaveCamera(QtGui.QAction):
+ """
+ QVTKViewWidgetSaveCamera is the action to capture the current camera
+ of the vtk renderers and save it back to the pipeline
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKViewWidgetSaveCamera(parent: QWidget) -> QVTKViewWidgetSaveCamera
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ "Save &Camera",
+ parent)
+ self.setStatusTip("Save current camera views to the pipeline")
+
+ def setCamera(self, controller):
+ ops = []
+ pipeline = controller.current_pipeline
+ cellWidget = self.toolBar.getSnappedWidget()
+ renderers = cellWidget.getRendererList()
+ for ren in renderers:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ rendererId = cellWidget.renderer_maps[ren]
+ # Looking for SetActiveCamera()
+ camera = None
+ renderer = pipeline.modules[rendererId]
+ for c in pipeline.connections.values():
+ if c.destination.moduleId==rendererId:
+ if c.destination.name=='SetActiveCamera':
+ camera = pipeline.modules[c.source.moduleId]
+ break
+
+ if not camera:
+ # Create camera
+ vtk_package = 'edu.utah.sci.vistrails.vtksnl'
+ camera = controller.create_module(vtk_package, 'vtkCamera', '',
+ 0.0, 0.0)
+ ops.append(('add', camera))
+
+ # Connect camera to renderer
+ camera_conn = controller.create_connection(camera, 'self',
+ renderer,
+ 'SetActiveCamera')
+ ops.append(('add', camera_conn))
+ # update functions
+ def convert_to_str(arglist):
+ new_arglist = []
+ for arg in arglist:
+ new_arglist.append(str(arg))
+ return new_arglist
+ functions = [('SetPosition', convert_to_str(cpos)),
+ ('SetFocalPoint', convert_to_str(cfol)),
+ ('SetViewUp', convert_to_str(cup))]
+ ops.extend(controller.update_functions_ops(camera, functions))
+
+ action = core.db.action.create_action(ops)
+ controller.add_new_action(action)
+ controller.perform_action(action)
+ controller.select_latest_version()
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ visApp = QtCore.QCoreApplication.instance()
+ if hasattr(visApp, 'builderWindow'):
+ builderWindow = visApp.builderWindow
+ if builderWindow:
+ info = self.toolBar.sheet.getCellPipelineInfo(
+ self.toolBar.row, self.toolBar.col)
+ if info:
+ info = info[0]
+ viewManager = builderWindow.viewManager
+ view = viewManager.ensureVistrail(info['locator'])
+ if view:
+ controller = view.controller
+ controller.change_selected_version(info['version'])
+ self.setCamera(controller)
+
+
+class QVTKViewWidgetToolBar(QCellToolBar):
+ """
+ QVTKViewWidgetToolBar derives from QCellToolBar to give the VTKViewCell
+ a customizable toolbar
+
+ """
+ def createToolBar(self):
+ """ createToolBar() -> None
+ This will get call initiallly to add customizable widgets
+
+ """
+ self.appendAction(QVTKViewWidgetCapture(self))
+ self.addAnimationButtons()
+ self.appendAction(QVTKViewWidgetSaveCamera(self))
+
+def registerSelf():
+ """ registerSelf() -> None
+ Registry module with the registry
+ """
+ identifier = 'edu.utah.sci.vistrails.vtksnl'
+ registry = get_module_registry()
+ registry.add_module(VTKViewCell)
+ registry.add_input_port(VTKViewCell, "Location", CellLocation)
+ import core.debug
+ for (port,module) in [("SetRenderView",'vtkRenderView')]:
+ try:
+ registry.add_input_port(VTKViewCell, port,'(%s:%s)'%(identifier,module))
+
+ except Exception, e:
+ core.debug.warning(str(e))
+
+ registry.add_output_port(VTKViewCell, "self", VTKViewCell)
diff --git a/data/1n25.pdb b/data/1n25.pdb
new file mode 100644
index 0000000..c7b0213
--- /dev/null
+++ b/data/1n25.pdb
@@ -0,0 +1,6334 @@
+HEADER VIRUS/VIRAL PROTEIN 21-OCT-02 1N25
+TITLE CRYSTAL STRUCTURE OF THE SV40 LARGE T ANTIGEN HELICASE
+TITLE 2 DOMAIN
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: LARGE T ANTIGEN;
+COMPND 3 CHAIN: A, B;
+COMPND 4 FRAGMENT: HELICASE DOMAIN;
+COMPND 5 ENGINEERED: YES
+SOURCE MOL_ID: 1;
+SOURCE 2 ORGANISM_SCIENTIFIC: SIMIAN VIRUS 40;
+SOURCE 3 ORGANISM_COMMON: VIRUS;
+SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
+SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA;
+SOURCE 6 EXPRESSION_SYSTEM_STRAIN: XA90;
+SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
+SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-2TK
+KEYWDS HELICASE DOMAIN
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.LI,R.ZHAO,W.LILYESTROM,D.GAI,R.ZHANG,J.A.DECAPRIO,
+AUTHOR 2 E.FANNING,A.JOCHIMIAK,G.SZAKONYI,X.S.CHEN
+REVDAT 1 03-JUN-03 1N25 0
+JRNL AUTH D.LI,R.ZHAO,W.LILYESTROM,D.GAI,R.ZHANG,
+JRNL AUTH 2 J.A.DECAPRIO,E.FANNING,A.JOCHIMIAK,G.SZAKONYI,
+JRNL AUTH 3 X.S.CHEN
+JRNL TITL STRUCTURE OF THE REPLICATIVE HELICASE OF THE
+JRNL TITL 2 ONCOPROTEIN SV40 LARGE TUMOUR ANTIGEN
+JRNL REF NATURE V. 423 512 2003
+JRNL REFN ASTM NATUAS UK ISSN 0028-0836
+REMARK 1
+REMARK 2
+REMARK 2 RESOLUTION. 2.80 ANGSTROMS.
+REMARK 3
+REMARK 3 REFINEMENT.
+REMARK 3 PROGRAM : CNS
+REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
+REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
+REMARK 3 : READ,RICE,SIMONSON,WARREN
+REMARK 3
+REMARK 3 REFINEMENT TARGET : ENGH & HUBER
+REMARK 3
+REMARK 3 DATA USED IN REFINEMENT.
+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80
+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00
+REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
+REMARK 3 OUTLIER CUTOFF HIGH (RMS(ABS(F))) : NULL
+REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.3
+REMARK 3 NUMBER OF REFLECTIONS : 26688
+REMARK 3
+REMARK 3 FIT TO DATA USED IN REFINEMENT.
+REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
+REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
+REMARK 3 R VALUE (WORKING SET) : 0.243
+REMARK 3 FREE R VALUE : 0.276
+REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
+REMARK 3 FREE R VALUE TEST SET COUNT : 1333
+REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
+REMARK 3
+REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
+REMARK 3 TOTAL NUMBER OF BINS USED : 26
+REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80
+REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.84
+REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
+REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 921
+REMARK 3 BIN R VALUE (WORKING SET) : 0.3670
+REMARK 3 BIN FREE R VALUE : 0.3920
+REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00
+REMARK 3 BIN FREE R VALUE TEST SET COUNT : 49
+REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
+REMARK 3
+REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
+REMARK 3 PROTEIN ATOMS : 5806
+REMARK 3 NUCLEIC ACID ATOMS : 0
+REMARK 3 HETEROGEN ATOMS : 0
+REMARK 3 SOLVENT ATOMS : 0
+REMARK 3
+REMARK 3 B VALUES.
+REMARK 3 FROM WILSON PLOT (A**2) : NULL
+REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.79
+REMARK 3 OVERALL ANISOTROPIC B VALUE.
+REMARK 3 B11 (A**2) : 13.86600
+REMARK 3 B22 (A**2) : 13.86600
+REMARK 3 B33 (A**2) : -27.73200
+REMARK 3 B12 (A**2) : 3.91200
+REMARK 3 B13 (A**2) : 0.00000
+REMARK 3 B23 (A**2) : 0.00000
+REMARK 3
+REMARK 3 ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40
+REMARK 3 ESD FROM SIGMAA (A) : 0.57
+REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
+REMARK 3
+REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.47
+REMARK 3 ESD FROM C-V SIGMAA (A) : 0.62
+REMARK 3
+REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
+REMARK 3 BOND LENGTHS (A) : 0.009
+REMARK 3 BOND ANGLES (DEGREES) : 1.37
+REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.54
+REMARK 3 IMPROPER ANGLES (DEGREES) : 0.80
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
+REMARK 3 MAIN-CHAIN BOND (A**2) : 2.953 ; NULL
+REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.570 ; NULL
+REMARK 3 SIDE-CHAIN BOND (A**2) : 4.926 ; NULL
+REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.546 ; NULL
+REMARK 3
+REMARK 3 BULK SOLVENT MODELING.
+REMARK 3 METHOD USED : ANISOTROPIC
+REMARK 3 KSOL : 0.33
+REMARK 3 BSOL : 30.79
+REMARK 3
+REMARK 3 NCS MODEL : NULL
+REMARK 3
+REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
+REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
+REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
+REMARK 3
+REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
+REMARK 3 PARAMETER FILE 2 : ION.PARAM
+REMARK 3 PARAMETER FILE 3 : NULL
+REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
+REMARK 3 TOPOLOGY FILE 2 : ION.TOP
+REMARK 3 TOPOLOGY FILE 3 : NULL
+REMARK 3
+REMARK 3 OTHER REFINEMENT REMARKS: NULL
+REMARK 4
+REMARK 4 1N25 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
+REMARK 100
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-2002.
+REMARK 100 THE RCSB ID CODE IS RCSB017424.
+REMARK 200
+REMARK 200 EXPERIMENTAL DETAILS
+REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
+REMARK 200 DATE OF DATA COLLECTION : 20-JUN-2001
+REMARK 200 TEMPERATURE (KELVIN) : 100.0
+REMARK 200 PH : 7.60
+REMARK 200 NUMBER OF CRYSTALS USED : 1
+REMARK 200
+REMARK 200 SYNCHROTRON (Y/N) : Y
+REMARK 200 RADIATION SOURCE : APS
+REMARK 200 BEAMLINE : 19ID
+REMARK 200 X-RAY GENERATOR MODEL : NULL
+REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
+REMARK 200 WAVELENGTH OR RANGE (A) : 1.074385
+REMARK 200 MONOCHROMATOR : SI 220
+REMARK 200 OPTICS : UNDULATOR A
+REMARK 200
+REMARK 200 DETECTOR TYPE : CCD
+REMARK 200 DETECTOR MANUFACTURER : SBC2 3K X 3K CCD BUILT BY ANL
+REMARK 200 -ECT 210MM X 210MM ACTIVE AREA
+REMARK 200 1.8 SEC READOUT
+REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
+REMARK 200 DATA SCALING SOFTWARE : TRUNCATE
+REMARK 200
+REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27610
+REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800
+REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
+REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
+REMARK 200
+REMARK 200 OVERALL.
+REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4
+REMARK 200 DATA REDUNDANCY : 6.200
+REMARK 200 R MERGE (I) : 0.12500
+REMARK 200 R SYM (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000
+REMARK 200
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90
+REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2
+REMARK 200 DATA REDUNDANCY IN SHELL : 5.40
+REMARK 200 R MERGE FOR SHELL (I) : 0.54400
+REMARK 200 R SYM FOR SHELL (I) : 0.54400
+REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900
+REMARK 200
+REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
+REMARK 200 SOFTWARE USED: SOLVE
+REMARK 200 STARTING MODEL: NULL
+REMARK 200
+REMARK 200 REMARK: NULL
+REMARK 280
+REMARK 280 CRYSTAL
+REMARK 280 SOLVENT CONTENT, VS (%): 64.0
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40
+REMARK 280
+REMARK 280 CRYSTALLIZATION CONDITIONS: GLYCEROL, DTT, HEPES, NACL, ETOH,
+REMARK 280 EDTA, PH 7.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1
+REMARK 290
+REMARK 290 SYMOP SYMMETRY
+REMARK 290 NNNMMM OPERATOR
+REMARK 290 1555 X,Y,Z
+REMARK 290 2555 -Y,X-Y,Z
+REMARK 290 3555 -X+Y,-X,Z
+REMARK 290 4555 Y,X,-Z
+REMARK 290 5555 X-Y,-Y,-Z
+REMARK 290 6555 -X,-X+Y,-Z
+REMARK 290
+REMARK 290 WHERE NNN -> OPERATOR NUMBER
+REMARK 290 MMM -> TRANSLATION VECTOR
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
+REMARK 290 RELATED MOLECULES.
+REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
+REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
+REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
+REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
+REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
+REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
+REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
+REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
+REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
+REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000
+REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
+REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
+REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000
+REMARK 290
+REMARK 290 REMARK: NULL
+REMARK 300
+REMARK 300 BIOMOLECULE: 1
+REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
+REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR
+REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
+REMARK 350
+REMARK 350 GENERATING THE BIOMOLECULE
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
+REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
+REMARK 350
+REMARK 350 BIOMOLECULE: 1
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
+REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 120.32100
+REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000
+REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
+REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 60.16050
+REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 104.20104
+REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
+REMARK 465
+REMARK 465 MISSING RESIDUES
+REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
+REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
+REMARK 465
+REMARK 465 M RES C SSSEQI
+REMARK 465 GLU A 260
+REMARK 465 GLU A 261
+REMARK 465 ALA A 262
+REMARK 465 GLU A 263
+REMARK 465 GLU A 264
+REMARK 465 THR A 265
+REMARK 465 GLU B 260
+REMARK 465 GLU B 261
+REMARK 465 ALA B 262
+REMARK 465 GLU B 263
+REMARK 465 GLU B 264
+REMARK 465 THR B 265
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3)
+REMARK 500
+REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
+REMARK 500 MET A 360 SD MET A 360 CE 0.096
+REMARK 500 MET A 401 SD MET A 401 CE -0.092
+REMARK 500 MET A 528 SD MET A 528 CE -0.069
+REMARK 500 MET A 578 SD MET A 578 CE -0.195
+REMARK 500 MET A 615 CG MET A 615 SD 0.074
+REMARK 500 MET A 615 SD MET A 615 CE -0.109
+REMARK 500 MET B 360 SD MET B 360 CE -0.073
+REMARK 500 MET B 388 SD MET B 388 CE -0.170
+REMARK 500 MET B 412 SD MET B 412 CE -0.057
+REMARK 500 CYS B 443 CB CYS B 443 SG -0.061
+REMARK 500 MET B 528 SD MET B 528 CE -0.095
+REMARK 500 MET B 578 SD MET B 578 CE -0.190
+REMARK 500 MET B 615 SD MET B 615 CE -0.104
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
+REMARK 500
+REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
+REMARK 500 GLY A 480 N - CA - C ANGL. DEV. = 16.4 DEGREES
+REMARK 500 GLY A 503 N - CA - C ANGL. DEV. = 8.3 DEGREES
+REMARK 500 THR A 518 N - CA - C ANGL. DEV. = -8.8 DEGREES
+REMARK 500 ILE A 520 N - CA - C ANGL. DEV. = -8.3 DEGREES
+REMARK 500 MET A 528 CB - CG - SD ANGL. DEV. = -8.6 DEGREES
+REMARK 500 ILE A 623 N - CA - C ANGL. DEV. = 9.4 DEGREES
+REMARK 500 THR B 356 N - CA - C ANGL. DEV. = -9.0 DEGREES
+REMARK 500 ALA B 389 N - CA - C ANGL. DEV. = -9.1 DEGREES
+REMARK 500 GLY B 444 N - CA - C ANGL. DEV. = -9.9 DEGREES
+REMARK 500 ASN B 451 N - CA - C ANGL. DEV. =-10.2 DEGREES
+REMARK 500 ARG B 517 N - CA - C ANGL. DEV. = 9.2 DEGREES
+REMARK 500 THR B 518 N - CA - C ANGL. DEV. =-11.1 DEGREES
+REMARK 500 ILE B 520 N - CA - C ANGL. DEV. = -9.5 DEGREES
+REMARK 500 VAL B 526 N - CA - C ANGL. DEV. = -8.9 DEGREES
+REMARK 500 ASN B 529 N - CA - C ANGL. DEV. = 9.5 DEGREES
+REMARK 500 VAL B 625 N - CA - C ANGL. DEV. = 9.3 DEGREES
+DBREF 1N25 A 260 627 GB 335056 AAB59924 260 627
+DBREF 1N25 B 260 627 GB 335056 AAB59924 260 627
+SEQRES 1 A 368 GLU GLU ALA GLU GLU THR LYS GLN VAL SER TRP LYS LEU
+SEQRES 2 A 368 VAL THR GLU TYR ALA MET GLU THR LYS CYS ASP ASP VAL
+SEQRES 3 A 368 LEU LEU LEU LEU GLY MET TYR LEU GLU PHE GLN TYR SER
+SEQRES 4 A 368 PHE GLU MET CYS LEU LYS CYS ILE LYS LYS GLU GLN PRO
+SEQRES 5 A 368 SER HIS TYR LYS TYR HIS GLU LYS HIS TYR ALA ASN ALA
+SEQRES 6 A 368 ALA ILE PHE ALA ASP SER LYS ASN GLN LYS THR ILE CYS
+SEQRES 7 A 368 GLN GLN ALA VAL ASP THR VAL LEU ALA LYS LYS ARG VAL
+SEQRES 8 A 368 ASP SER LEU GLN LEU THR ARG GLU GLN MET LEU THR ASN
+SEQRES 9 A 368 ARG PHE ASN ASP LEU LEU ASP ARG MET ASP ILE MET PHE
+SEQRES 10 A 368 GLY SER THR GLY SER ALA ASP ILE GLU GLU TRP MET ALA
+SEQRES 11 A 368 GLY VAL ALA TRP LEU HIS CYS LEU LEU PRO LYS MET ASP
+SEQRES 12 A 368 SER VAL VAL TYR ASP PHE LEU LYS CYS MET VAL TYR ASN
+SEQRES 13 A 368 ILE PRO LYS LYS ARG TYR TRP LEU PHE LYS GLY PRO ILE
+SEQRES 14 A 368 ASP SER GLY LYS THR THR LEU ALA ALA ALA LEU LEU GLU
+SEQRES 15 A 368 LEU CYS GLY GLY LYS ALA LEU ASN VAL ASN LEU PRO LEU
+SEQRES 16 A 368 ASP ARG LEU ASN PHE GLU LEU GLY VAL ALA ILE ASP GLN
+SEQRES 17 A 368 PHE LEU VAL VAL PHE GLU ASP VAL LYS GLY THR GLY GLY
+SEQRES 18 A 368 GLU SER ARG ASP LEU PRO SER GLY GLN GLY ILE ASN ASN
+SEQRES 19 A 368 LEU ASP ASN LEU ARG ASP TYR LEU ASP GLY SER VAL LYS
+SEQRES 20 A 368 VAL ASN LEU GLU LYS LYS HIS LEU ASN LYS ARG THR GLN
+SEQRES 21 A 368 ILE PHE PRO PRO GLY ILE VAL THR MET ASN GLU TYR SER
+SEQRES 22 A 368 VAL PRO LYS THR LEU GLN ALA ARG PHE VAL LYS GLN ILE
+SEQRES 23 A 368 ASP PHE ARG PRO LYS ASP TYR LEU LYS HIS CYS LEU GLU
+SEQRES 24 A 368 ARG SER GLU PHE LEU LEU GLU LYS ARG ILE ILE GLN SER
+SEQRES 25 A 368 GLY ILE ALA LEU LEU LEU MET LEU ILE TRP TYR ARG PRO
+SEQRES 26 A 368 VAL ALA GLU PHE ALA GLN SER ILE GLN SER ARG ILE VAL
+SEQRES 27 A 368 GLU TRP LYS GLU ARG LEU ASP LYS GLU PHE SER LEU SER
+SEQRES 28 A 368 VAL TYR GLN LYS MET LYS PHE ASN VAL ALA MET GLY ILE
+SEQRES 29 A 368 GLY VAL LEU ASP
+SEQRES 1 B 368 GLU GLU ALA GLU GLU THR LYS GLN VAL SER TRP LYS LEU
+SEQRES 2 B 368 VAL THR GLU TYR ALA MET GLU THR LYS CYS ASP ASP VAL
+SEQRES 3 B 368 LEU LEU LEU LEU GLY MET TYR LEU GLU PHE GLN TYR SER
+SEQRES 4 B 368 PHE GLU MET CYS LEU LYS CYS ILE LYS LYS GLU GLN PRO
+SEQRES 5 B 368 SER HIS TYR LYS TYR HIS GLU LYS HIS TYR ALA ASN ALA
+SEQRES 6 B 368 ALA ILE PHE ALA ASP SER LYS ASN GLN LYS THR ILE CYS
+SEQRES 7 B 368 GLN GLN ALA VAL ASP THR VAL LEU ALA LYS LYS ARG VAL
+SEQRES 8 B 368 ASP SER LEU GLN LEU THR ARG GLU GLN MET LEU THR ASN
+SEQRES 9 B 368 ARG PHE ASN ASP LEU LEU ASP ARG MET ASP ILE MET PHE
+SEQRES 10 B 368 GLY SER THR GLY SER ALA ASP ILE GLU GLU TRP MET ALA
+SEQRES 11 B 368 GLY VAL ALA TRP LEU HIS CYS LEU LEU PRO LYS MET ASP
+SEQRES 12 B 368 SER VAL VAL TYR ASP PHE LEU LYS CYS MET VAL TYR ASN
+SEQRES 13 B 368 ILE PRO LYS LYS ARG TYR TRP LEU PHE LYS GLY PRO ILE
+SEQRES 14 B 368 ASP SER GLY LYS THR THR LEU ALA ALA ALA LEU LEU GLU
+SEQRES 15 B 368 LEU CYS GLY GLY LYS ALA LEU ASN VAL ASN LEU PRO LEU
+SEQRES 16 B 368 ASP ARG LEU ASN PHE GLU LEU GLY VAL ALA ILE ASP GLN
+SEQRES 17 B 368 PHE LEU VAL VAL PHE GLU ASP VAL LYS GLY THR GLY GLY
+SEQRES 18 B 368 GLU SER ARG ASP LEU PRO SER GLY GLN GLY ILE ASN ASN
+SEQRES 19 B 368 LEU ASP ASN LEU ARG ASP TYR LEU ASP GLY SER VAL LYS
+SEQRES 20 B 368 VAL ASN LEU GLU LYS LYS HIS LEU ASN LYS ARG THR GLN
+SEQRES 21 B 368 ILE PHE PRO PRO GLY ILE VAL THR MET ASN GLU TYR SER
+SEQRES 22 B 368 VAL PRO LYS THR LEU GLN ALA ARG PHE VAL LYS GLN ILE
+SEQRES 23 B 368 ASP PHE ARG PRO LYS ASP TYR LEU LYS HIS CYS LEU GLU
+SEQRES 24 B 368 ARG SER GLU PHE LEU LEU GLU LYS ARG ILE ILE GLN SER
+SEQRES 25 B 368 GLY ILE ALA LEU LEU LEU MET LEU ILE TRP TYR ARG PRO
+SEQRES 26 B 368 VAL ALA GLU PHE ALA GLN SER ILE GLN SER ARG ILE VAL
+SEQRES 27 B 368 GLU TRP LYS GLU ARG LEU ASP LYS GLU PHE SER LEU SER
+SEQRES 28 B 368 VAL TYR GLN LYS MET LYS PHE ASN VAL ALA MET GLY ILE
+SEQRES 29 B 368 GLY VAL LEU ASP
+HET ZN A 700 1
+HET ZN B 700 1
+HETNAM ZN ZINC ION
+FORMUL 3 ZN 2(ZN1 2+)
+HELIX 1 1 SER A 269 LYS A 281 1 13
+HELIX 2 2 ASP A 284 LEU A 293 1 10
+HELIX 3 3 GLU A 294 TYR A 297 5 4
+HELIX 4 4 CYS A 302 LYS A 307 1 6
+HELIX 5 5 GLN A 310 LYS A 315 1 6
+HELIX 6 6 TYR A 316 ALA A 328 1 13
+HELIX 7 7 ASN A 332 LEU A 355 1 24
+HELIX 8 8 THR A 356 PHE A 376 1 21
+HELIX 9 9 ASP A 383 HIS A 395 1 13
+HELIX 10 10 LYS A 400 ASN A 415 1 16
+HELIX 11 11 GLY A 431 GLY A 444 1 14
+HELIX 12 12 ARG A 456 GLY A 462 1 7
+HELIX 13 13 VAL A 463 ILE A 465 5 3
+HELIX 14 14 GLN A 489 ASP A 495 1 7
+HELIX 15 15 LEU A 497 GLY A 503 1 7
+HELIX 16 16 PRO A 534 ALA A 539 1 6
+HELIX 17 17 LYS A 550 ARG A 559 1 10
+HELIX 18 18 GLU A 561 LYS A 566 1 6
+HELIX 19 19 SER A 571 ARG A 583 1 13
+HELIX 20 20 PRO A 584 PHE A 588 5 5
+HELIX 21 21 ALA A 589 LYS A 605 1 17
+HELIX 22 22 SER A 608 MET A 621 1 14
+HELIX 23 23 SER B 269 GLU B 279 1 11
+HELIX 24 24 ASP B 284 LEU B 293 1 10
+HELIX 25 25 GLU B 294 TYR B 297 5 4
+HELIX 26 26 CYS B 302 LYS B 307 1 6
+HELIX 27 27 GLN B 310 LYS B 315 1 6
+HELIX 28 28 TYR B 316 ALA B 328 1 13
+HELIX 29 29 ASN B 332 LEU B 355 1 24
+HELIX 30 30 THR B 356 PHE B 376 1 21
+HELIX 31 31 ASP B 383 LEU B 398 1 16
+HELIX 32 32 LYS B 400 ASN B 415 1 16
+HELIX 33 33 GLY B 431 GLY B 444 1 14
+HELIX 34 34 ARG B 456 GLY B 462 1 7
+HELIX 35 35 VAL B 463 ILE B 465 5 3
+HELIX 36 36 GLN B 489 ASP B 495 1 7
+HELIX 37 37 LEU B 497 ASP B 502 1 6
+HELIX 38 38 PRO B 534 ALA B 539 1 6
+HELIX 39 39 LYS B 550 SER B 560 1 11
+HELIX 40 40 GLU B 561 LYS B 566 1 6
+HELIX 41 41 SER B 571 ARG B 583 1 13
+HELIX 42 42 PRO B 584 PHE B 588 5 5
+HELIX 43 43 ALA B 589 PHE B 607 1 19
+HELIX 44 44 SER B 608 GLY B 622 1 15
+SHEET 1 A 5 GLY A 445 LEU A 448 0
+SHEET 2 A 5 LEU A 469 VAL A 475 1 O VAL A 471 N LEU A 448
+SHEET 3 A 5 GLY A 524 MET A 528 1 O ILE A 525 N PHE A 472
+SHEET 4 A 5 TYR A 421 LYS A 425 1 N PHE A 424 O MET A 528
+SHEET 5 A 5 LYS A 543 ASP A 546 1 O ILE A 545 N LEU A 423
+SHEET 1 B 2 VAL A 507 LYS A 511 0
+SHEET 2 B 2 LEU A 514 GLN A 519 -1 O GLN A 519 N VAL A 507
+SHEET 1 C 5 LYS B 446 LEU B 448 0
+SHEET 2 C 5 VAL B 470 VAL B 475 1 O VAL B 471 N LEU B 448
+SHEET 3 C 5 GLY B 524 MET B 528 1 O THR B 527 N PHE B 472
+SHEET 4 C 5 TYR B 421 LYS B 425 1 N PHE B 424 O VAL B 526
+SHEET 5 C 5 LYS B 543 ASP B 546 1 O ILE B 545 N LEU B 423
+SHEET 1 D 2 VAL B 507 LYS B 511 0
+SHEET 2 D 2 LEU B 514 GLN B 519 -1 O GLN B 519 N VAL B 507
+CRYST1 120.321 120.321 132.202 90.00 90.00 120.00 P 3 2 1 12
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.008311 0.004798 0.000000 0.00000
+SCALE2 0.000000 0.009596 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.007564 0.00000
+ATOM 1 N LYS A 266 44.458 43.722 -0.913 1.00 78.76 N
+ATOM 2 CA LYS A 266 45.695 44.058 -1.666 1.00 79.67 C
+ATOM 3 C LYS A 266 46.880 44.311 -0.754 1.00 83.17 C
+ATOM 4 O LYS A 266 47.722 43.438 -0.543 1.00 81.29 O
+ATOM 5 CB LYS A 266 45.465 45.286 -2.545 1.00 78.46 C
+ATOM 6 CG LYS A 266 45.019 44.931 -3.946 1.00 78.06 C
+ATOM 7 CD LYS A 266 46.037 44.013 -4.599 1.00 76.42 C
+ATOM 8 CE LYS A 266 45.609 43.599 -5.987 1.00 75.78 C
+ATOM 9 NZ LYS A 266 46.626 42.697 -6.594 1.00 77.33 N
+ATOM 10 N GLN A 267 46.954 45.520 -0.220 1.00 83.76 N
+ATOM 11 CA GLN A 267 48.046 45.864 0.670 1.00 82.59 C
+ATOM 12 C GLN A 267 47.527 46.868 1.687 1.00 77.07 C
+ATOM 13 O GLN A 267 47.300 48.035 1.367 1.00 70.67 O
+ATOM 14 CB GLN A 267 49.216 46.436 -0.142 1.00 92.78 C
+ATOM 15 CG GLN A 267 50.558 46.410 0.584 1.00112.09 C
+ATOM 16 CD GLN A 267 50.893 45.038 1.149 1.00120.64 C
+ATOM 17 OE1 GLN A 267 51.357 44.925 2.285 1.00123.65 O
+ATOM 18 NE2 GLN A 267 50.667 43.990 0.355 1.00123.10 N
+ATOM 19 N VAL A 268 47.311 46.392 2.908 1.00 65.08 N
+ATOM 20 CA VAL A 268 46.806 47.239 3.975 1.00 54.25 C
+ATOM 21 C VAL A 268 47.773 48.372 4.244 1.00 49.67 C
+ATOM 22 O VAL A 268 48.984 48.188 4.225 1.00 45.61 O
+ATOM 23 CB VAL A 268 46.609 46.441 5.283 1.00 51.93 C
+ATOM 24 CG1 VAL A 268 45.932 47.311 6.332 1.00 50.50 C
+ATOM 25 CG2 VAL A 268 45.783 45.197 5.007 1.00 53.61 C
+ATOM 26 N SER A 269 47.222 49.550 4.491 1.00 42.47 N
+ATOM 27 CA SER A 269 48.028 50.724 4.785 1.00 38.57 C
+ATOM 28 C SER A 269 48.313 50.842 6.279 1.00 37.02 C
+ATOM 29 O SER A 269 47.508 51.403 7.011 1.00 37.31 O
+ATOM 30 CB SER A 269 47.308 51.988 4.316 1.00 36.94 C
+ATOM 31 OG SER A 269 47.925 53.135 4.865 1.00 35.77 O
+ATOM 32 N TRP A 270 49.453 50.322 6.729 1.00 34.84 N
+ATOM 33 CA TRP A 270 49.826 50.394 8.142 1.00 34.47 C
+ATOM 34 C TRP A 270 49.854 51.843 8.626 1.00 36.89 C
+ATOM 35 O TRP A 270 49.569 52.133 9.787 1.00 35.43 O
+ATOM 36 CB TRP A 270 51.213 49.789 8.364 1.00 30.01 C
+ATOM 37 CG TRP A 270 51.305 48.330 8.150 1.00 25.31 C
+ATOM 38 CD1 TRP A 270 50.766 47.631 7.132 1.00 22.40 C
+ATOM 39 CD2 TRP A 270 52.034 47.385 8.948 1.00 24.93 C
+ATOM 40 NE1 TRP A 270 51.106 46.301 7.231 1.00 23.28 N
+ATOM 41 CE2 TRP A 270 51.884 46.123 8.343 1.00 22.30 C
+ATOM 42 CE3 TRP A 270 52.800 47.485 10.122 1.00 24.62 C
+ATOM 43 CZ2 TRP A 270 52.466 44.966 8.859 1.00 21.50 C
+ATOM 44 CZ3 TRP A 270 53.386 46.324 10.642 1.00 22.83 C
+ATOM 45 CH2 TRP A 270 53.210 45.084 10.008 1.00 21.47 C
+ATOM 46 N LYS A 271 50.199 52.749 7.717 1.00 40.89 N
+ATOM 47 CA LYS A 271 50.301 54.165 8.038 1.00 42.20 C
+ATOM 48 C LYS A 271 48.975 54.744 8.497 1.00 42.18 C
+ATOM 49 O LYS A 271 48.900 55.424 9.517 1.00 39.54 O
+ATOM 50 CB LYS A 271 50.813 54.932 6.821 1.00 45.61 C
+ATOM 51 CG LYS A 271 51.162 56.372 7.116 1.00 52.18 C
+ATOM 52 CD LYS A 271 51.635 57.082 5.873 1.00 55.28 C
+ATOM 53 CE LYS A 271 52.058 58.502 6.200 1.00 56.96 C
+ATOM 54 NZ LYS A 271 52.538 59.205 4.983 1.00 58.32 N
+ATOM 55 N LEU A 272 47.927 54.474 7.734 1.00 41.75 N
+ATOM 56 CA LEU A 272 46.607 54.968 8.079 1.00 41.77 C
+ATOM 57 C LEU A 272 46.188 54.484 9.455 1.00 40.55 C
+ATOM 58 O LEU A 272 45.714 55.266 10.274 1.00 41.22 O
+ATOM 59 CB LEU A 272 45.573 54.511 7.056 1.00 45.58 C
+ATOM 60 CG LEU A 272 45.159 55.560 6.032 1.00 49.61 C
+ATOM 61 CD1 LEU A 272 44.056 54.975 5.176 1.00 53.46 C
+ATOM 62 CD2 LEU A 272 44.671 56.826 6.739 1.00 51.91 C
+ATOM 63 N VAL A 273 46.350 53.191 9.709 1.00 38.10 N
+ATOM 64 CA VAL A 273 45.985 52.642 11.006 1.00 35.48 C
+ATOM 65 C VAL A 273 46.730 53.378 12.126 1.00 35.01 C
+ATOM 66 O VAL A 273 46.175 53.638 13.201 1.00 33.73 O
+ATOM 67 CB VAL A 273 46.292 51.135 11.061 1.00 32.73 C
+ATOM 68 CG1 VAL A 273 46.020 50.599 12.452 1.00 27.49 C
+ATOM 69 CG2 VAL A 273 45.438 50.410 10.025 1.00 30.52 C
+ATOM 70 N THR A 274 47.986 53.726 11.862 1.00 35.07 N
+ATOM 71 CA THR A 274 48.785 54.440 12.840 1.00 37.62 C
+ATOM 72 C THR A 274 48.232 55.844 13.028 1.00 43.27 C
+ATOM 73 O THR A 274 48.231 56.374 14.141 1.00 39.74 O
+ATOM 74 CB THR A 274 50.252 54.544 12.407 1.00 34.96 C
+ATOM 75 OG1 THR A 274 50.851 53.245 12.441 1.00 35.24 O
+ATOM 76 CG2 THR A 274 51.017 55.469 13.339 1.00 33.38 C
+ATOM 77 N GLU A 275 47.766 56.445 11.936 1.00 49.90 N
+ATOM 78 CA GLU A 275 47.214 57.792 11.990 1.00 52.53 C
+ATOM 79 C GLU A 275 45.987 57.804 12.883 1.00 48.41 C
+ATOM 80 O GLU A 275 45.806 58.698 13.707 1.00 43.54 O
+ATOM 81 CB GLU A 275 46.840 58.272 10.591 1.00 65.86 C
+ATOM 82 CG GLU A 275 46.164 59.624 10.593 1.00 93.06 C
+ATOM 83 CD GLU A 275 45.756 60.068 9.215 1.00104.71 C
+ATOM 84 OE1 GLU A 275 45.841 59.243 8.279 1.00108.70 O
+ATOM 85 OE2 GLU A 275 45.343 61.238 9.074 1.00109.07 O
+ATOM 86 N TYR A 276 45.140 56.801 12.715 1.00 40.92 N
+ATOM 87 CA TYR A 276 43.940 56.691 13.525 1.00 33.40 C
+ATOM 88 C TYR A 276 44.363 56.535 14.988 1.00 30.54 C
+ATOM 89 O TYR A 276 43.845 57.220 15.869 1.00 27.65 O
+ATOM 90 CB TYR A 276 43.114 55.490 13.068 1.00 33.41 C
+ATOM 91 CG TYR A 276 41.929 55.197 13.950 1.00 36.52 C
+ATOM 92 CD1 TYR A 276 40.893 56.122 14.096 1.00 37.24 C
+ATOM 93 CD2 TYR A 276 41.856 53.999 14.671 1.00 37.54 C
+ATOM 94 CE1 TYR A 276 39.816 55.863 14.939 1.00 37.19 C
+ATOM 95 CE2 TYR A 276 40.790 53.732 15.512 1.00 37.31 C
+ATOM 96 CZ TYR A 276 39.772 54.665 15.645 1.00 37.89 C
+ATOM 97 OH TYR A 276 38.714 54.392 16.492 1.00 40.18 O
+ATOM 98 N ALA A 277 45.318 55.644 15.240 1.00 28.42 N
+ATOM 99 CA ALA A 277 45.806 55.429 16.597 1.00 27.30 C
+ATOM 100 C ALA A 277 46.291 56.743 17.236 1.00 27.20 C
+ATOM 101 O ALA A 277 45.897 57.082 18.354 1.00 26.98 O
+ATOM 102 CB ALA A 277 46.938 54.382 16.588 1.00 23.86 C
+ATOM 103 N MET A 278 47.149 57.476 16.533 1.00 30.99 N
+ATOM 104 CA MET A 278 47.666 58.740 17.049 1.00 35.54 C
+ATOM 105 C MET A 278 46.589 59.808 17.213 1.00 39.94 C
+ATOM 106 O MET A 278 46.722 60.694 18.057 1.00 39.37 O
+ATOM 107 CB MET A 278 48.772 59.262 16.141 1.00 35.32 C
+ATOM 108 CG MET A 278 50.084 58.515 16.318 1.00 37.07 C
+ATOM 109 SD MET A 278 51.308 59.375 17.330 1.00 36.64 S
+ATOM 110 CE MET A 278 50.257 60.467 18.334 1.00 34.84 C
+ATOM 111 N GLU A 279 45.527 59.718 16.410 1.00 45.14 N
+ATOM 112 CA GLU A 279 44.408 60.666 16.458 1.00 47.29 C
+ATOM 113 C GLU A 279 43.443 60.328 17.617 1.00 48.11 C
+ATOM 114 O GLU A 279 42.838 61.207 18.241 1.00 41.82 O
+ATOM 115 CB GLU A 279 43.661 60.641 15.114 1.00 54.04 C
+ATOM 116 CG GLU A 279 43.583 61.989 14.410 1.00 69.60 C
+ATOM 117 CD GLU A 279 43.865 61.889 12.919 1.00 77.60 C
+ATOM 118 OE1 GLU A 279 43.135 61.158 12.214 1.00 80.48 O
+ATOM 119 OE2 GLU A 279 44.821 62.543 12.446 1.00 80.21 O
+ATOM 120 N THR A 280 43.313 59.037 17.900 1.00 48.69 N
+ATOM 121 CA THR A 280 42.449 58.548 18.963 1.00 44.94 C
+ATOM 122 C THR A 280 43.267 58.525 20.257 1.00 44.45 C
+ATOM 123 O THR A 280 42.723 58.373 21.356 1.00 42.62 O
+ATOM 124 CB THR A 280 41.969 57.116 18.625 1.00 47.20 C
+ATOM 125 OG1 THR A 280 41.123 57.162 17.473 1.00 52.10 O
+ATOM 126 CG2 THR A 280 41.207 56.501 19.782 1.00 54.38 C
+ATOM 127 N LYS A 281 44.581 58.675 20.110 1.00 47.63 N
+ATOM 128 CA LYS A 281 45.490 58.656 21.249 1.00 49.19 C
+ATOM 129 C LYS A 281 45.463 57.267 21.876 1.00 48.67 C
+ATOM 130 O LYS A 281 45.724 57.099 23.068 1.00 54.24 O
+ATOM 131 CB LYS A 281 45.060 59.701 22.279 1.00 49.36 C
+ATOM 132 CG LYS A 281 45.353 61.144 21.890 1.00 47.49 C
+ATOM 133 CD LYS A 281 44.762 62.105 22.922 1.00 46.90 C
+ATOM 134 CE LYS A 281 45.391 63.496 22.846 1.00 46.08 C
+ATOM 135 NZ LYS A 281 46.778 63.540 23.393 1.00 44.64 N
+ATOM 136 N CYS A 282 45.168 56.268 21.055 1.00 48.98 N
+ATOM 137 CA CYS A 282 45.064 54.905 21.533 1.00 49.25 C
+ATOM 138 C CYS A 282 46.374 54.167 21.774 1.00 49.91 C
+ATOM 139 O CYS A 282 47.074 53.804 20.835 1.00 51.42 O
+ATOM 140 CB CYS A 282 44.213 54.101 20.573 1.00 46.97 C
+ATOM 141 SG CYS A 282 43.966 52.455 21.201 1.00 40.88 S
+ATOM 142 N ASP A 283 46.681 53.920 23.043 1.00 47.36 N
+ATOM 143 CA ASP A 283 47.907 53.225 23.421 1.00 44.65 C
+ATOM 144 C ASP A 283 47.664 51.759 23.774 1.00 43.93 C
+ATOM 145 O ASP A 283 48.568 51.074 24.255 1.00 39.51 O
+ATOM 146 CB ASP A 283 48.576 53.937 24.606 1.00 44.58 C
+ATOM 147 CG ASP A 283 47.640 54.114 25.787 1.00 46.75 C
+ATOM 148 OD1 ASP A 283 47.110 53.103 26.297 1.00 48.30 O
+ATOM 149 OD2 ASP A 283 47.430 55.269 26.211 1.00 49.39 O
+ATOM 150 N ASP A 284 46.444 51.281 23.538 1.00 40.95 N
+ATOM 151 CA ASP A 284 46.081 49.888 23.825 1.00 40.00 C
+ATOM 152 C ASP A 284 45.963 49.101 22.515 1.00 38.39 C
+ATOM 153 O ASP A 284 45.175 49.464 21.636 1.00 36.59 O
+ATOM 154 CB ASP A 284 44.746 49.840 24.571 1.00 45.90 C
+ATOM 155 CG ASP A 284 44.389 48.442 25.049 1.00 54.16 C
+ATOM 156 OD1 ASP A 284 44.402 47.491 24.236 1.00 57.69 O
+ATOM 157 OD2 ASP A 284 44.084 48.298 26.248 1.00 58.14 O
+ATOM 158 N VAL A 285 46.726 48.020 22.380 1.00 34.05 N
+ATOM 159 CA VAL A 285 46.675 47.250 21.146 1.00 29.65 C
+ATOM 160 C VAL A 285 45.341 46.555 20.888 1.00 29.63 C
+ATOM 161 O VAL A 285 44.776 46.674 19.802 1.00 29.84 O
+ATOM 162 CB VAL A 285 47.777 46.201 21.084 1.00 27.34 C
+ATOM 163 CG1 VAL A 285 47.800 45.592 19.702 1.00 27.94 C
+ATOM 164 CG2 VAL A 285 49.116 46.834 21.384 1.00 28.25 C
+ATOM 165 N LEU A 286 44.832 45.819 21.869 1.00 30.50 N
+ATOM 166 CA LEU A 286 43.556 45.141 21.678 1.00 31.23 C
+ATOM 167 C LEU A 286 42.409 46.133 21.489 1.00 31.47 C
+ATOM 168 O LEU A 286 41.468 45.877 20.743 1.00 33.17 O
+ATOM 169 CB LEU A 286 43.261 44.206 22.853 1.00 29.32 C
+ATOM 170 CG LEU A 286 43.987 42.858 22.807 1.00 27.27 C
+ATOM 171 CD1 LEU A 286 43.789 42.142 24.118 1.00 27.98 C
+ATOM 172 CD2 LEU A 286 43.466 42.005 21.657 1.00 26.33 C
+ATOM 173 N LEU A 287 42.492 47.277 22.151 1.00 32.01 N
+ATOM 174 CA LEU A 287 41.447 48.279 22.018 1.00 30.98 C
+ATOM 175 C LEU A 287 41.486 48.882 20.623 1.00 29.38 C
+ATOM 176 O LEU A 287 40.457 49.173 20.043 1.00 28.73 O
+ATOM 177 CB LEU A 287 41.618 49.379 23.065 1.00 31.75 C
+ATOM 178 CG LEU A 287 40.501 50.417 23.035 1.00 31.98 C
+ATOM 179 CD1 LEU A 287 39.167 49.733 23.319 1.00 33.54 C
+ATOM 180 CD2 LEU A 287 40.776 51.500 24.054 1.00 32.79 C
+ATOM 181 N LEU A 288 42.681 49.062 20.078 1.00 26.92 N
+ATOM 182 CA LEU A 288 42.805 49.619 18.738 1.00 25.93 C
+ATOM 183 C LEU A 288 42.277 48.635 17.712 1.00 27.61 C
+ATOM 184 O LEU A 288 41.464 48.988 16.856 1.00 27.45 O
+ATOM 185 CB LEU A 288 44.261 49.937 18.411 1.00 23.92 C
+ATOM 186 CG LEU A 288 44.527 50.272 16.936 1.00 21.52 C
+ATOM 187 CD1 LEU A 288 43.758 51.499 16.492 1.00 20.19 C
+ATOM 188 CD2 LEU A 288 46.007 50.510 16.770 1.00 23.14 C
+ATOM 189 N LEU A 289 42.751 47.396 17.804 1.00 29.02 N
+ATOM 190 CA LEU A 289 42.341 46.342 16.886 1.00 29.78 C
+ATOM 191 C LEU A 289 40.827 46.264 16.785 1.00 30.56 C
+ATOM 192 O LEU A 289 40.258 46.381 15.697 1.00 29.97 O
+ATOM 193 CB LEU A 289 42.877 44.995 17.365 1.00 30.20 C
+ATOM 194 CG LEU A 289 42.445 43.786 16.539 1.00 32.47 C
+ATOM 195 CD1 LEU A 289 43.221 43.753 15.238 1.00 33.31 C
+ATOM 196 CD2 LEU A 289 42.692 42.516 17.333 1.00 32.60 C
+ATOM 197 N GLY A 290 40.186 46.061 17.935 1.00 31.54 N
+ATOM 198 CA GLY A 290 38.748 45.949 17.977 1.00 31.64 C
+ATOM 199 C GLY A 290 38.024 47.142 17.390 1.00 33.25 C
+ATOM 200 O GLY A 290 36.953 47.002 16.804 1.00 33.35 O
+ATOM 201 N MET A 291 38.590 48.331 17.534 1.00 33.56 N
+ATOM 202 CA MET A 291 37.919 49.510 17.007 1.00 32.79 C
+ATOM 203 C MET A 291 38.125 49.676 15.515 1.00 32.18 C
+ATOM 204 O MET A 291 37.185 49.993 14.782 1.00 29.93 O
+ATOM 205 CB MET A 291 38.371 50.764 17.755 1.00 34.17 C
+ATOM 206 CG MET A 291 37.883 50.791 19.186 1.00 40.00 C
+ATOM 207 SD MET A 291 38.213 52.345 20.021 1.00 47.45 S
+ATOM 208 CE MET A 291 36.613 53.084 19.764 1.00 46.12 C
+ATOM 209 N TYR A 292 39.339 49.440 15.045 1.00 31.64 N
+ATOM 210 CA TYR A 292 39.569 49.597 13.625 1.00 30.61 C
+ATOM 211 C TYR A 292 38.693 48.640 12.840 1.00 30.33 C
+ATOM 212 O TYR A 292 38.165 49.004 11.791 1.00 32.95 O
+ATOM 213 CB TYR A 292 41.029 49.350 13.271 1.00 30.70 C
+ATOM 214 CG TYR A 292 41.460 50.144 12.075 1.00 31.55 C
+ATOM 215 CD1 TYR A 292 41.531 51.535 12.137 1.00 30.37 C
+ATOM 216 CD2 TYR A 292 41.764 49.512 10.867 1.00 31.91 C
+ATOM 217 CE1 TYR A 292 41.898 52.283 11.017 1.00 31.27 C
+ATOM 218 CE2 TYR A 292 42.128 50.245 9.742 1.00 31.93 C
+ATOM 219 CZ TYR A 292 42.194 51.626 9.825 1.00 31.36 C
+ATOM 220 OH TYR A 292 42.574 52.346 8.725 1.00 31.38 O
+ATOM 221 N LEU A 293 38.533 47.422 13.356 1.00 31.72 N
+ATOM 222 CA LEU A 293 37.725 46.398 12.703 1.00 32.56 C
+ATOM 223 C LEU A 293 36.244 46.754 12.582 1.00 33.99 C
+ATOM 224 O LEU A 293 35.511 46.123 11.816 1.00 34.48 O
+ATOM 225 CB LEU A 293 37.873 45.066 13.437 1.00 30.72 C
+ATOM 226 CG LEU A 293 39.182 44.300 13.219 1.00 28.22 C
+ATOM 227 CD1 LEU A 293 39.293 43.225 14.283 1.00 26.90 C
+ATOM 228 CD2 LEU A 293 39.235 43.705 11.807 1.00 25.91 C
+ATOM 229 N GLU A 294 35.791 47.751 13.331 1.00 36.51 N
+ATOM 230 CA GLU A 294 34.396 48.146 13.226 1.00 37.48 C
+ATOM 231 C GLU A 294 34.181 48.882 11.909 1.00 36.98 C
+ATOM 232 O GLU A 294 33.093 48.838 11.337 1.00 37.79 O
+ATOM 233 CB GLU A 294 33.999 49.053 14.382 1.00 38.80 C
+ATOM 234 CG GLU A 294 34.133 48.398 15.726 1.00 42.71 C
+ATOM 235 CD GLU A 294 33.342 49.111 16.798 1.00 44.92 C
+ATOM 236 OE1 GLU A 294 33.487 50.349 16.935 1.00 46.13 O
+ATOM 237 OE2 GLU A 294 32.575 48.425 17.509 1.00 47.02 O
+ATOM 238 N PHE A 295 35.235 49.547 11.437 1.00 36.80 N
+ATOM 239 CA PHE A 295 35.203 50.308 10.192 1.00 36.65 C
+ATOM 240 C PHE A 295 35.100 49.447 8.920 1.00 38.06 C
+ATOM 241 O PHE A 295 34.784 49.962 7.852 1.00 41.09 O
+ATOM 242 CB PHE A 295 36.458 51.190 10.064 1.00 34.45 C
+ATOM 243 CG PHE A 295 36.716 52.103 11.237 1.00 28.80 C
+ATOM 244 CD1 PHE A 295 35.676 52.604 12.006 1.00 26.98 C
+ATOM 245 CD2 PHE A 295 38.013 52.517 11.527 1.00 27.49 C
+ATOM 246 CE1 PHE A 295 35.934 53.511 13.046 1.00 25.92 C
+ATOM 247 CE2 PHE A 295 38.267 53.424 12.567 1.00 25.37 C
+ATOM 248 CZ PHE A 295 37.233 53.916 13.318 1.00 22.99 C
+ATOM 249 N GLN A 296 35.372 48.151 9.026 1.00 41.46 N
+ATOM 250 CA GLN A 296 35.325 47.246 7.872 1.00 43.34 C
+ATOM 251 C GLN A 296 33.955 47.119 7.193 1.00 45.29 C
+ATOM 252 O GLN A 296 33.822 46.470 6.148 1.00 46.84 O
+ATOM 253 CB GLN A 296 35.752 45.847 8.290 1.00 40.41 C
+ATOM 254 CG GLN A 296 34.576 44.965 8.702 1.00 35.59 C
+ATOM 255 CD GLN A 296 35.033 43.677 9.319 1.00 35.21 C
+ATOM 256 OE1 GLN A 296 35.316 43.621 10.511 1.00 35.54 O
+ATOM 257 NE2 GLN A 296 35.132 42.632 8.508 1.00 36.66 N
+ATOM 258 N TYR A 297 32.931 47.699 7.799 1.00 49.42 N
+ATOM 259 CA TYR A 297 31.597 47.622 7.230 1.00 54.13 C
+ATOM 260 C TYR A 297 31.305 48.903 6.475 1.00 57.45 C
+ATOM 261 O TYR A 297 31.844 49.957 6.808 1.00 57.90 O
+ATOM 262 CB TYR A 297 30.584 47.432 8.342 1.00 55.85 C
+ATOM 263 CG TYR A 297 30.882 46.234 9.196 1.00 56.79 C
+ATOM 264 CD1 TYR A 297 30.788 44.943 8.678 1.00 56.08 C
+ATOM 265 CD2 TYR A 297 31.254 46.387 10.528 1.00 56.58 C
+ATOM 266 CE1 TYR A 297 31.051 43.838 9.474 1.00 55.80 C
+ATOM 267 CE2 TYR A 297 31.521 45.290 11.329 1.00 55.64 C
+ATOM 268 CZ TYR A 297 31.418 44.022 10.802 1.00 55.36 C
+ATOM 269 OH TYR A 297 31.668 42.942 11.614 1.00 56.00 O
+ATOM 270 N SER A 298 30.459 48.819 5.456 1.00 60.51 N
+ATOM 271 CA SER A 298 30.141 50.008 4.684 1.00 60.31 C
+ATOM 272 C SER A 298 29.560 51.029 5.643 1.00 62.98 C
+ATOM 273 O SER A 298 28.634 50.732 6.412 1.00 53.59 O
+ATOM 274 CB SER A 298 29.128 49.707 3.575 1.00 60.41 C
+ATOM 275 OG SER A 298 27.801 49.832 4.051 1.00 68.55 O
+ATOM 276 N PHE A 299 30.135 52.226 5.605 1.00 70.43 N
+ATOM 277 CA PHE A 299 29.692 53.320 6.447 1.00 75.17 C
+ATOM 278 C PHE A 299 28.403 53.835 5.820 1.00 76.91 C
+ATOM 279 O PHE A 299 27.603 54.516 6.464 1.00 78.45 O
+ATOM 280 CB PHE A 299 30.774 54.402 6.479 1.00 80.94 C
+ATOM 281 CG PHE A 299 30.373 55.689 5.831 1.00 93.15 C
+ATOM 282 CD1 PHE A 299 29.946 56.762 6.603 1.00 98.29 C
+ATOM 283 CD2 PHE A 299 30.407 55.827 4.449 1.00 98.25 C
+ATOM 284 CE1 PHE A 299 29.558 57.960 6.007 1.00100.97 C
+ATOM 285 CE2 PHE A 299 30.021 57.020 3.838 1.00100.52 C
+ATOM 286 CZ PHE A 299 29.595 58.090 4.617 1.00101.11 C
+ATOM 287 N GLU A 300 28.209 53.477 4.554 1.00 85.28 N
+ATOM 288 CA GLU A 300 27.027 53.877 3.804 1.00 93.02 C
+ATOM 289 C GLU A 300 25.768 53.306 4.451 1.00 98.29 C
+ATOM 290 O GLU A 300 24.737 53.182 3.796 1.00100.57 O
+ATOM 291 CB GLU A 300 27.095 53.364 2.362 1.00 96.63 C
+ATOM 292 CG GLU A 300 28.484 53.174 1.782 1.00 99.09 C
+ATOM 293 CD GLU A 300 28.436 52.797 0.309 1.00100.18 C
+ATOM 294 OE1 GLU A 300 27.623 51.919 -0.059 1.00100.10 O
+ATOM 295 OE2 GLU A 300 29.213 53.376 -0.481 1.00100.08 O
+ATOM 296 N MET A 301 25.850 52.945 5.726 1.00105.50 N
+ATOM 297 CA MET A 301 24.699 52.380 6.418 1.00104.07 C
+ATOM 298 C MET A 301 24.951 52.309 7.925 1.00 96.31 C
+ATOM 299 O MET A 301 24.012 52.192 8.712 1.00 97.43 O
+ATOM 300 CB MET A 301 24.406 50.977 5.861 1.00109.33 C
+ATOM 301 CG MET A 301 22.926 50.599 5.789 1.00122.12 C
+ATOM 302 SD MET A 301 22.079 51.080 4.247 1.00128.75 S
+ATOM 303 CE MET A 301 21.741 49.459 3.509 1.00130.64 C
+ATOM 304 N CYS A 302 26.224 52.382 8.314 1.00 84.94 N
+ATOM 305 CA CYS A 302 26.635 52.322 9.725 1.00 81.73 C
+ATOM 306 C CYS A 302 25.698 53.097 10.649 1.00 82.88 C
+ATOM 307 O CYS A 302 25.638 54.327 10.591 1.00 85.64 O
+ATOM 308 CB CYS A 302 28.080 52.850 9.881 1.00 75.87 C
+ATOM 309 SG CYS A 302 28.610 53.402 11.543 1.00 58.95 S
+ATOM 310 N LEU A 303 24.964 52.372 11.493 1.00 79.96 N
+ATOM 311 CA LEU A 303 24.052 53.006 12.437 1.00 74.47 C
+ATOM 312 C LEU A 303 24.825 53.665 13.568 1.00 72.34 C
+ATOM 313 O LEU A 303 24.363 54.649 14.147 1.00 61.98 O
+ATOM 314 CB LEU A 303 23.064 51.989 13.020 1.00 76.93 C
+ATOM 315 CG LEU A 303 21.716 51.852 12.303 1.00 83.85 C
+ATOM 316 CD1 LEU A 303 20.805 50.926 13.092 1.00 88.23 C
+ATOM 317 CD2 LEU A 303 21.064 53.227 12.161 1.00 88.93 C
+ATOM 318 N LYS A 304 26.003 53.117 13.873 1.00 65.87 N
+ATOM 319 CA LYS A 304 26.866 53.647 14.927 1.00 62.29 C
+ATOM 320 C LYS A 304 27.254 55.074 14.585 1.00 59.80 C
+ATOM 321 O LYS A 304 27.462 55.909 15.464 1.00 57.26 O
+ATOM 322 CB LYS A 304 28.125 52.788 15.063 1.00 68.05 C
+ATOM 323 CG LYS A 304 27.831 51.352 15.445 1.00 80.77 C
+ATOM 324 CD LYS A 304 29.060 50.586 15.904 1.00 85.84 C
+ATOM 325 CE LYS A 304 28.649 49.195 16.371 1.00 88.26 C
+ATOM 326 NZ LYS A 304 29.799 48.349 16.773 1.00 89.31 N
+ATOM 327 N CYS A 305 27.335 55.334 13.287 1.00 59.51 N
+ATOM 328 CA CYS A 305 27.683 56.640 12.746 1.00 57.56 C
+ATOM 329 C CYS A 305 26.429 57.495 12.663 1.00 56.90 C
+ATOM 330 O CYS A 305 26.410 58.621 13.151 1.00 62.03 O
+ATOM 331 CB CYS A 305 28.263 56.473 11.347 1.00 52.85 C
+ATOM 332 SG CYS A 305 29.564 55.208 11.239 1.00 52.95 S
+ATOM 333 N ILE A 306 25.388 56.951 12.032 1.00 60.49 N
+ATOM 334 CA ILE A 306 24.121 57.664 11.888 1.00 70.12 C
+ATOM 335 C ILE A 306 23.653 58.114 13.265 1.00 73.00 C
+ATOM 336 O ILE A 306 23.259 59.269 13.455 1.00 74.36 O
+ATOM 337 CB ILE A 306 23.011 56.773 11.251 1.00 68.00 C
+ATOM 338 CG1 ILE A 306 23.422 56.330 9.846 1.00 65.88 C
+ATOM 339 CG2 ILE A 306 21.705 57.557 11.166 1.00 67.57 C
+ATOM 340 CD1 ILE A 306 22.407 55.432 9.170 1.00 62.53 C
+ATOM 341 N LYS A 307 23.704 57.199 14.229 1.00 76.09 N
+ATOM 342 CA LYS A 307 23.287 57.526 15.583 1.00 72.32 C
+ATOM 343 C LYS A 307 24.365 58.239 16.403 1.00 67.09 C
+ATOM 344 O LYS A 307 24.117 58.620 17.542 1.00 60.11 O
+ATOM 345 CB LYS A 307 22.801 56.269 16.313 1.00 76.95 C
+ATOM 346 CG LYS A 307 21.450 55.771 15.811 1.00 92.17 C
+ATOM 347 CD LYS A 307 20.821 54.741 16.741 1.00100.72 C
+ATOM 348 CE LYS A 307 19.438 54.327 16.236 1.00104.46 C
+ATOM 349 NZ LYS A 307 18.753 53.346 17.129 1.00105.22 N
+ATOM 350 N LYS A 308 25.550 58.427 15.823 1.00 59.56 N
+ATOM 351 CA LYS A 308 26.651 59.119 16.501 1.00 58.92 C
+ATOM 352 C LYS A 308 26.902 58.586 17.923 1.00 64.36 C
+ATOM 353 O LYS A 308 26.993 59.360 18.881 1.00 61.71 O
+ATOM 354 CB LYS A 308 26.348 60.624 16.561 1.00 55.07 C
+ATOM 355 CG LYS A 308 26.189 61.303 15.201 1.00 52.50 C
+ATOM 356 CD LYS A 308 27.542 61.670 14.586 1.00 51.89 C
+ATOM 357 CE LYS A 308 27.411 62.323 13.198 1.00 50.22 C
+ATOM 358 NZ LYS A 308 28.708 62.882 12.700 1.00 49.81 N
+ATOM 359 N GLU A 309 27.036 57.265 18.039 1.00 71.33 N
+ATOM 360 CA GLU A 309 27.241 56.577 19.316 1.00 72.64 C
+ATOM 361 C GLU A 309 28.564 56.869 20.017 1.00 67.99 C
+ATOM 362 O GLU A 309 28.587 57.165 21.214 1.00 61.21 O
+ATOM 363 CB GLU A 309 27.126 55.066 19.110 1.00 84.01 C
+ATOM 364 CG GLU A 309 25.987 54.641 18.201 1.00109.26 C
+ATOM 365 CD GLU A 309 25.892 53.134 18.065 1.00120.47 C
+ATOM 366 OE1 GLU A 309 26.947 52.495 17.862 1.00124.79 O
+ATOM 367 OE2 GLU A 309 24.768 52.591 18.154 1.00124.00 O
+ATOM 368 N GLN A 310 29.663 56.759 19.272 1.00 60.61 N
+ATOM 369 CA GLN A 310 31.002 56.992 19.813 1.00 53.51 C
+ATOM 370 C GLN A 310 31.822 57.844 18.856 1.00 50.70 C
+ATOM 371 O GLN A 310 32.034 57.471 17.700 1.00 50.89 O
+ATOM 372 CB GLN A 310 31.723 55.663 20.030 1.00 53.87 C
+ATOM 373 CG GLN A 310 31.165 54.801 21.149 1.00 54.31 C
+ATOM 374 CD GLN A 310 31.465 55.355 22.526 1.00 52.49 C
+ATOM 375 OE1 GLN A 310 32.597 55.734 22.820 1.00 52.36 O
+ATOM 376 NE2 GLN A 310 30.453 55.388 23.384 1.00 53.03 N
+ATOM 377 N PRO A 311 32.310 58.997 19.335 1.00 45.68 N
+ATOM 378 CA PRO A 311 33.110 59.911 18.513 1.00 46.38 C
+ATOM 379 C PRO A 311 34.350 59.235 17.944 1.00 47.63 C
+ATOM 380 O PRO A 311 34.780 59.549 16.832 1.00 45.34 O
+ATOM 381 CB PRO A 311 33.450 61.040 19.481 1.00 44.83 C
+ATOM 382 CG PRO A 311 32.301 61.010 20.452 1.00 44.16 C
+ATOM 383 CD PRO A 311 32.122 59.540 20.689 1.00 45.84 C
+ATOM 384 N SER A 312 34.921 58.309 18.713 1.00 48.85 N
+ATOM 385 CA SER A 312 36.114 57.572 18.285 1.00 48.81 C
+ATOM 386 C SER A 312 35.786 56.714 17.057 1.00 47.29 C
+ATOM 387 O SER A 312 36.670 56.198 16.372 1.00 44.34 O
+ATOM 388 CB SER A 312 36.612 56.676 19.422 1.00 51.14 C
+ATOM 389 OG SER A 312 35.594 55.780 19.841 1.00 59.07 O
+ATOM 390 N HIS A 313 34.498 56.580 16.783 1.00 45.05 N
+ATOM 391 CA HIS A 313 34.056 55.793 15.655 1.00 43.34 C
+ATOM 392 C HIS A 313 33.432 56.636 14.544 1.00 43.10 C
+ATOM 393 O HIS A 313 33.909 56.636 13.402 1.00 42.21 O
+ATOM 394 CB HIS A 313 33.041 54.757 16.127 1.00 42.86 C
+ATOM 395 CG HIS A 313 32.443 53.951 15.016 1.00 43.56 C
+ATOM 396 ND1 HIS A 313 33.117 52.920 14.396 1.00 43.88 N
+ATOM 397 CD2 HIS A 313 31.235 54.029 14.406 1.00 43.46 C
+ATOM 398 CE1 HIS A 313 32.349 52.396 13.454 1.00 43.76 C
+ATOM 399 NE2 HIS A 313 31.203 53.055 13.445 1.00 43.67 N
+ATOM 400 N TYR A 314 32.374 57.364 14.881 1.00 43.28 N
+ATOM 401 CA TYR A 314 31.668 58.153 13.884 1.00 44.30 C
+ATOM 402 C TYR A 314 32.403 59.332 13.240 1.00 45.53 C
+ATOM 403 O TYR A 314 31.806 60.065 12.455 1.00 44.80 O
+ATOM 404 CB TYR A 314 30.324 58.614 14.455 1.00 43.58 C
+ATOM 405 CG TYR A 314 30.396 59.740 15.462 1.00 44.86 C
+ATOM 406 CD1 TYR A 314 30.866 61.003 15.096 1.00 44.37 C
+ATOM 407 CD2 TYR A 314 29.939 59.562 16.767 1.00 45.29 C
+ATOM 408 CE1 TYR A 314 30.876 62.056 15.997 1.00 45.24 C
+ATOM 409 CE2 TYR A 314 29.947 60.615 17.682 1.00 45.95 C
+ATOM 410 CZ TYR A 314 30.416 61.857 17.286 1.00 45.59 C
+ATOM 411 OH TYR A 314 30.419 62.905 18.174 1.00 45.85 O
+ATOM 412 N LYS A 315 33.682 59.517 13.566 1.00 46.71 N
+ATOM 413 CA LYS A 315 34.472 60.606 12.989 1.00 47.03 C
+ATOM 414 C LYS A 315 35.580 60.032 12.116 1.00 46.55 C
+ATOM 415 O LYS A 315 36.360 60.777 11.526 1.00 46.18 O
+ATOM 416 CB LYS A 315 35.120 61.464 14.081 1.00 48.16 C
+ATOM 417 CG LYS A 315 34.153 62.153 15.023 1.00 53.01 C
+ATOM 418 CD LYS A 315 34.889 62.929 16.130 1.00 55.42 C
+ATOM 419 CE LYS A 315 35.460 64.261 15.647 1.00 56.95 C
+ATOM 420 NZ LYS A 315 36.411 64.130 14.503 1.00 58.49 N
+ATOM 421 N TYR A 316 35.658 58.708 12.036 1.00 45.41 N
+ATOM 422 CA TYR A 316 36.703 58.088 11.242 1.00 43.87 C
+ATOM 423 C TYR A 316 36.234 56.940 10.369 1.00 43.53 C
+ATOM 424 O TYR A 316 36.970 56.498 9.482 1.00 42.95 O
+ATOM 425 CB TYR A 316 37.830 57.597 12.156 1.00 44.35 C
+ATOM 426 CG TYR A 316 38.382 58.654 13.092 1.00 46.19 C
+ATOM 427 CD1 TYR A 316 37.716 58.989 14.274 1.00 47.17 C
+ATOM 428 CD2 TYR A 316 39.559 59.337 12.784 1.00 46.48 C
+ATOM 429 CE1 TYR A 316 38.215 59.986 15.130 1.00 46.53 C
+ATOM 430 CE2 TYR A 316 40.064 60.330 13.623 1.00 46.53 C
+ATOM 431 CZ TYR A 316 39.389 60.652 14.793 1.00 47.19 C
+ATOM 432 OH TYR A 316 39.876 61.647 15.614 1.00 48.47 O
+ATOM 433 N HIS A 317 35.019 56.451 10.604 1.00 42.74 N
+ATOM 434 CA HIS A 317 34.520 55.329 9.809 1.00 42.88 C
+ATOM 435 C HIS A 317 34.611 55.606 8.312 1.00 48.40 C
+ATOM 436 O HIS A 317 35.125 54.784 7.551 1.00 44.88 O
+ATOM 437 CB HIS A 317 33.074 54.977 10.181 1.00 38.29 C
+ATOM 438 CG HIS A 317 32.600 53.685 9.579 1.00 35.44 C
+ATOM 439 ND1 HIS A 317 31.340 53.174 9.798 1.00 34.68 N
+ATOM 440 CD2 HIS A 317 33.235 52.783 8.794 1.00 34.44 C
+ATOM 441 CE1 HIS A 317 31.219 52.010 9.180 1.00 34.29 C
+ATOM 442 NE2 HIS A 317 32.358 51.752 8.563 1.00 34.04 N
+ATOM 443 N GLU A 318 34.115 56.768 7.903 1.00 57.52 N
+ATOM 444 CA GLU A 318 34.138 57.173 6.503 1.00 64.21 C
+ATOM 445 C GLU A 318 35.550 57.019 5.942 1.00 62.43 C
+ATOM 446 O GLU A 318 35.825 56.147 5.119 1.00 61.63 O
+ATOM 447 CB GLU A 318 33.703 58.636 6.381 1.00 77.63 C
+ATOM 448 CG GLU A 318 32.624 58.916 5.339 1.00100.73 C
+ATOM 449 CD GLU A 318 33.055 58.603 3.918 1.00110.50 C
+ATOM 450 OE1 GLU A 318 32.296 58.938 2.982 1.00113.70 O
+ATOM 451 OE2 GLU A 318 34.146 58.025 3.736 1.00114.14 O
+ATOM 452 N LYS A 319 36.447 57.871 6.417 1.00 58.22 N
+ATOM 453 CA LYS A 319 37.830 57.876 5.973 1.00 52.13 C
+ATOM 454 C LYS A 319 38.534 56.524 5.992 1.00 49.19 C
+ATOM 455 O LYS A 319 39.405 56.259 5.161 1.00 49.24 O
+ATOM 456 CB LYS A 319 38.628 58.869 6.818 1.00 48.75 C
+ATOM 457 CG LYS A 319 40.097 58.916 6.477 1.00 46.93 C
+ATOM 458 CD LYS A 319 40.779 60.000 7.269 1.00 47.21 C
+ATOM 459 CE LYS A 319 42.255 60.120 6.913 1.00 47.29 C
+ATOM 460 NZ LYS A 319 42.854 61.352 7.538 1.00 48.50 N
+ATOM 461 N HIS A 320 38.155 55.660 6.922 1.00 45.92 N
+ATOM 462 CA HIS A 320 38.827 54.376 7.026 1.00 45.26 C
+ATOM 463 C HIS A 320 38.138 53.140 6.465 1.00 46.44 C
+ATOM 464 O HIS A 320 38.730 52.057 6.482 1.00 45.28 O
+ATOM 465 CB HIS A 320 39.231 54.145 8.488 1.00 41.42 C
+ATOM 466 CG HIS A 320 40.308 55.076 8.960 1.00 37.00 C
+ATOM 467 ND1 HIS A 320 41.643 54.876 8.675 1.00 34.20 N
+ATOM 468 CD2 HIS A 320 40.243 56.242 9.645 1.00 35.15 C
+ATOM 469 CE1 HIS A 320 42.352 55.878 9.164 1.00 32.77 C
+ATOM 470 NE2 HIS A 320 41.526 56.722 9.758 1.00 31.78 N
+ATOM 471 N TYR A 321 36.911 53.280 5.966 1.00 47.30 N
+ATOM 472 CA TYR A 321 36.218 52.120 5.411 1.00 48.38 C
+ATOM 473 C TYR A 321 37.184 51.351 4.506 1.00 48.38 C
+ATOM 474 O TYR A 321 37.630 50.254 4.842 1.00 46.70 O
+ATOM 475 CB TYR A 321 34.991 52.537 4.594 1.00 51.57 C
+ATOM 476 CG TYR A 321 34.400 51.387 3.813 1.00 55.99 C
+ATOM 477 CD1 TYR A 321 33.702 50.371 4.460 1.00 59.02 C
+ATOM 478 CD2 TYR A 321 34.613 51.266 2.441 1.00 58.52 C
+ATOM 479 CE1 TYR A 321 33.227 49.252 3.761 1.00 60.96 C
+ATOM 480 CE2 TYR A 321 34.145 50.153 1.728 1.00 61.16 C
+ATOM 481 CZ TYR A 321 33.456 49.145 2.397 1.00 61.32 C
+ATOM 482 OH TYR A 321 33.009 48.029 1.712 1.00 60.75 O
+ATOM 483 N ALA A 322 37.508 51.954 3.366 1.00 47.79 N
+ATOM 484 CA ALA A 322 38.410 51.370 2.380 1.00 46.61 C
+ATOM 485 C ALA A 322 39.545 50.558 2.990 1.00 45.04 C
+ATOM 486 O ALA A 322 39.636 49.346 2.787 1.00 46.87 O
+ATOM 487 CB ALA A 322 38.994 52.474 1.503 1.00 46.20 C
+ATOM 488 N ASN A 323 40.410 51.234 3.738 1.00 42.98 N
+ATOM 489 CA ASN A 323 41.559 50.586 4.353 1.00 41.24 C
+ATOM 490 C ASN A 323 41.213 49.568 5.435 1.00 40.49 C
+ATOM 491 O ASN A 323 41.909 48.564 5.589 1.00 41.21 O
+ATOM 492 CB ASN A 323 42.495 51.633 4.927 1.00 39.68 C
+ATOM 493 CG ASN A 323 43.783 51.039 5.405 1.00 38.56 C
+ATOM 494 OD1 ASN A 323 44.498 50.398 4.636 1.00 38.32 O
+ATOM 495 ND2 ASN A 323 44.097 51.243 6.683 1.00 39.64 N
+ATOM 496 N ALA A 324 40.146 49.826 6.187 1.00 37.41 N
+ATOM 497 CA ALA A 324 39.724 48.907 7.236 1.00 34.71 C
+ATOM 498 C ALA A 324 39.162 47.641 6.596 1.00 33.63 C
+ATOM 499 O ALA A 324 39.267 46.543 7.143 1.00 34.06 O
+ATOM 500 CB ALA A 324 38.673 49.566 8.107 1.00 30.16 C
+ATOM 501 N ALA A 325 38.554 47.809 5.430 1.00 34.53 N
+ATOM 502 CA ALA A 325 37.987 46.692 4.697 1.00 36.08 C
+ATOM 503 C ALA A 325 39.129 45.790 4.241 1.00 38.91 C
+ATOM 504 O ALA A 325 38.994 44.566 4.216 1.00 42.96 O
+ATOM 505 CB ALA A 325 37.207 47.205 3.511 1.00 34.45 C
+ATOM 506 N ILE A 326 40.255 46.399 3.879 1.00 40.72 N
+ATOM 507 CA ILE A 326 41.429 45.644 3.457 1.00 41.75 C
+ATOM 508 C ILE A 326 42.094 45.062 4.713 1.00 41.19 C
+ATOM 509 O ILE A 326 42.686 43.981 4.679 1.00 42.06 O
+ATOM 510 CB ILE A 326 42.454 46.556 2.729 1.00 42.84 C
+ATOM 511 CG1 ILE A 326 41.782 47.277 1.557 1.00 41.51 C
+ATOM 512 CG2 ILE A 326 43.642 45.729 2.246 1.00 41.67 C
+ATOM 513 CD1 ILE A 326 42.688 48.245 0.842 1.00 40.40 C
+ATOM 514 N PHE A 327 41.976 45.795 5.816 1.00 40.10 N
+ATOM 515 CA PHE A 327 42.547 45.399 7.099 1.00 39.71 C
+ATOM 516 C PHE A 327 41.958 44.094 7.586 1.00 40.75 C
+ATOM 517 O PHE A 327 42.683 43.187 7.968 1.00 43.11 O
+ATOM 518 CB PHE A 327 42.272 46.472 8.155 1.00 36.64 C
+ATOM 519 CG PHE A 327 42.877 46.171 9.500 1.00 30.03 C
+ATOM 520 CD1 PHE A 327 44.242 46.336 9.715 1.00 28.79 C
+ATOM 521 CD2 PHE A 327 42.083 45.726 10.552 1.00 27.98 C
+ATOM 522 CE1 PHE A 327 44.805 46.066 10.950 1.00 26.48 C
+ATOM 523 CE2 PHE A 327 42.641 45.451 11.795 1.00 26.00 C
+ATOM 524 CZ PHE A 327 43.999 45.622 11.994 1.00 26.17 C
+ATOM 525 N ALA A 328 40.636 44.006 7.578 1.00 42.18 N
+ATOM 526 CA ALA A 328 39.960 42.811 8.050 1.00 44.94 C
+ATOM 527 C ALA A 328 40.358 41.549 7.282 1.00 48.29 C
+ATOM 528 O ALA A 328 40.020 40.430 7.690 1.00 46.06 O
+ATOM 529 CB ALA A 328 38.456 43.016 7.985 1.00 45.34 C
+ATOM 530 N ASP A 329 41.078 41.721 6.177 1.00 50.33 N
+ATOM 531 CA ASP A 329 41.506 40.578 5.377 1.00 51.25 C
+ATOM 532 C ASP A 329 43.013 40.358 5.433 1.00 49.93 C
+ATOM 533 O ASP A 329 43.569 39.564 4.678 1.00 45.64 O
+ATOM 534 CB ASP A 329 41.045 40.748 3.926 1.00 59.61 C
+ATOM 535 CG ASP A 329 39.785 39.946 3.615 1.00 72.08 C
+ATOM 536 OD1 ASP A 329 39.877 38.697 3.544 1.00 77.68 O
+ATOM 537 OD2 ASP A 329 38.705 40.562 3.450 1.00 77.97 O
+ATOM 538 N SER A 330 43.666 41.064 6.345 1.00 47.77 N
+ATOM 539 CA SER A 330 45.107 40.946 6.528 1.00 44.94 C
+ATOM 540 C SER A 330 45.404 39.716 7.387 1.00 43.21 C
+ATOM 541 O SER A 330 44.584 39.323 8.220 1.00 40.84 O
+ATOM 542 CB SER A 330 45.642 42.211 7.213 1.00 45.37 C
+ATOM 543 OG SER A 330 46.993 42.062 7.615 1.00 50.61 O
+ATOM 544 N LYS A 331 46.568 39.108 7.185 1.00 41.02 N
+ATOM 545 CA LYS A 331 46.937 37.930 7.968 1.00 40.17 C
+ATOM 546 C LYS A 331 47.723 38.244 9.247 1.00 42.07 C
+ATOM 547 O LYS A 331 48.207 37.341 9.921 1.00 38.53 O
+ATOM 548 CB LYS A 331 47.732 36.951 7.109 1.00 40.02 C
+ATOM 549 CG LYS A 331 46.881 36.142 6.168 1.00 43.49 C
+ATOM 550 CD LYS A 331 47.739 35.208 5.343 1.00 45.95 C
+ATOM 551 CE LYS A 331 46.885 34.262 4.506 1.00 46.76 C
+ATOM 552 NZ LYS A 331 47.689 33.086 4.048 1.00 47.56 N
+ATOM 553 N ASN A 332 47.862 39.518 9.583 1.00 43.52 N
+ATOM 554 CA ASN A 332 48.569 39.872 10.805 1.00 43.47 C
+ATOM 555 C ASN A 332 48.178 41.266 11.270 1.00 41.12 C
+ATOM 556 O ASN A 332 48.985 42.202 11.311 1.00 34.12 O
+ATOM 557 CB ASN A 332 50.088 39.741 10.620 1.00 54.19 C
+ATOM 558 CG ASN A 332 50.629 40.618 9.516 1.00 68.01 C
+ATOM 559 OD1 ASN A 332 49.877 41.168 8.713 1.00 76.57 O
+ATOM 560 ND2 ASN A 332 51.949 40.744 9.463 1.00 76.04 N
+ATOM 561 N GLN A 333 46.909 41.378 11.640 1.00 37.13 N
+ATOM 562 CA GLN A 333 46.363 42.631 12.101 1.00 33.91 C
+ATOM 563 C GLN A 333 47.002 43.088 13.410 1.00 33.58 C
+ATOM 564 O GLN A 333 47.311 44.264 13.570 1.00 32.33 O
+ATOM 565 CB GLN A 333 44.846 42.509 12.250 1.00 34.87 C
+ATOM 566 CG GLN A 333 44.284 41.192 11.761 1.00 39.93 C
+ATOM 567 CD GLN A 333 42.791 41.242 11.500 1.00 41.95 C
+ATOM 568 OE1 GLN A 333 42.345 41.857 10.536 1.00 42.03 O
+ATOM 569 NE2 GLN A 333 42.010 40.594 12.362 1.00 43.19 N
+ATOM 570 N LYS A 334 47.228 42.171 14.340 1.00 33.54 N
+ATOM 571 CA LYS A 334 47.828 42.563 15.611 1.00 33.56 C
+ATOM 572 C LYS A 334 49.231 43.169 15.474 1.00 34.00 C
+ATOM 573 O LYS A 334 49.596 44.083 16.217 1.00 29.56 O
+ATOM 574 CB LYS A 334 47.861 41.375 16.577 1.00 37.38 C
+ATOM 575 CG LYS A 334 48.520 41.705 17.901 1.00 46.32 C
+ATOM 576 CD LYS A 334 47.933 40.908 19.047 1.00 50.87 C
+ATOM 577 CE LYS A 334 48.485 41.407 20.375 1.00 53.82 C
+ATOM 578 NZ LYS A 334 47.702 40.919 21.543 1.00 54.15 N
+ATOM 579 N THR A 335 50.016 42.666 14.529 1.00 34.10 N
+ATOM 580 CA THR A 335 51.365 43.180 14.315 1.00 31.59 C
+ATOM 581 C THR A 335 51.245 44.617 13.833 1.00 29.52 C
+ATOM 582 O THR A 335 52.041 45.465 14.191 1.00 28.13 O
+ATOM 583 CB THR A 335 52.118 42.364 13.245 1.00 36.79 C
+ATOM 584 OG1 THR A 335 52.143 40.974 13.610 1.00 45.65 O
+ATOM 585 CG2 THR A 335 53.535 42.866 13.111 1.00 42.57 C
+ATOM 586 N ILE A 336 50.242 44.885 13.009 1.00 27.64 N
+ATOM 587 CA ILE A 336 50.024 46.227 12.494 1.00 26.82 C
+ATOM 588 C ILE A 336 49.666 47.150 13.660 1.00 28.06 C
+ATOM 589 O ILE A 336 50.250 48.220 13.830 1.00 27.95 O
+ATOM 590 CB ILE A 336 48.873 46.238 11.442 1.00 26.63 C
+ATOM 591 CG1 ILE A 336 49.273 45.404 10.214 1.00 24.66 C
+ATOM 592 CG2 ILE A 336 48.531 47.664 11.040 1.00 23.93 C
+ATOM 593 CD1 ILE A 336 48.174 45.293 9.163 1.00 22.99 C
+ATOM 594 N CYS A 337 48.714 46.724 14.478 1.00 30.43 N
+ATOM 595 CA CYS A 337 48.298 47.528 15.619 1.00 32.29 C
+ATOM 596 C CYS A 337 49.440 47.751 16.597 1.00 33.23 C
+ATOM 597 O CYS A 337 49.527 48.795 17.228 1.00 31.18 O
+ATOM 598 CB CYS A 337 47.117 46.863 16.323 1.00 33.35 C
+ATOM 599 SG CYS A 337 45.599 46.894 15.317 1.00 39.71 S
+ATOM 600 N GLN A 338 50.318 46.769 16.722 1.00 35.00 N
+ATOM 601 CA GLN A 338 51.451 46.902 17.619 1.00 36.01 C
+ATOM 602 C GLN A 338 52.274 48.118 17.236 1.00 34.74 C
+ATOM 603 O GLN A 338 52.705 48.881 18.103 1.00 34.53 O
+ATOM 604 CB GLN A 338 52.344 45.664 17.561 1.00 41.23 C
+ATOM 605 CG GLN A 338 52.077 44.651 18.648 1.00 51.41 C
+ATOM 606 CD GLN A 338 52.005 45.291 20.012 1.00 55.66 C
+ATOM 607 OE1 GLN A 338 52.589 46.355 20.245 1.00 56.13 O
+ATOM 608 NE2 GLN A 338 51.295 44.643 20.931 1.00 56.98 N
+ATOM 609 N GLN A 339 52.490 48.300 15.938 1.00 32.27 N
+ATOM 610 CA GLN A 339 53.269 49.426 15.475 1.00 31.10 C
+ATOM 611 C GLN A 339 52.498 50.729 15.636 1.00 30.96 C
+ATOM 612 O GLN A 339 53.090 51.771 15.917 1.00 32.90 O
+ATOM 613 CB GLN A 339 53.674 49.242 14.016 1.00 31.15 C
+ATOM 614 CG GLN A 339 54.781 50.217 13.576 1.00 32.06 C
+ATOM 615 CD GLN A 339 55.455 49.797 12.286 1.00 32.50 C
+ATOM 616 OE1 GLN A 339 55.110 50.280 11.212 1.00 31.82 O
+ATOM 617 NE2 GLN A 339 56.416 48.880 12.389 1.00 31.42 N
+ATOM 618 N ALA A 340 51.182 50.679 15.457 1.00 31.54 N
+ATOM 619 CA ALA A 340 50.365 51.876 15.616 1.00 31.34 C
+ATOM 620 C ALA A 340 50.524 52.369 17.051 1.00 31.80 C
+ATOM 621 O ALA A 340 50.727 53.567 17.304 1.00 33.84 O
+ATOM 622 CB ALA A 340 48.900 51.559 15.337 1.00 32.52 C
+ATOM 623 N VAL A 341 50.445 51.421 17.981 1.00 29.88 N
+ATOM 624 CA VAL A 341 50.555 51.702 19.406 1.00 28.77 C
+ATOM 625 C VAL A 341 51.956 52.149 19.799 1.00 32.27 C
+ATOM 626 O VAL A 341 52.129 53.163 20.476 1.00 28.35 O
+ATOM 627 CB VAL A 341 50.152 50.450 20.213 1.00 25.53 C
+ATOM 628 CG1 VAL A 341 50.529 50.588 21.690 1.00 22.64 C
+ATOM 629 CG2 VAL A 341 48.665 50.242 20.075 1.00 22.06 C
+ATOM 630 N ASP A 342 52.959 51.394 19.370 1.00 36.29 N
+ATOM 631 CA ASP A 342 54.328 51.744 19.694 1.00 39.02 C
+ATOM 632 C ASP A 342 54.586 53.180 19.248 1.00 36.87 C
+ATOM 633 O ASP A 342 55.376 53.901 19.856 1.00 35.16 O
+ATOM 634 CB ASP A 342 55.304 50.792 19.003 1.00 49.20 C
+ATOM 635 CG ASP A 342 55.270 49.396 19.592 1.00 63.23 C
+ATOM 636 OD1 ASP A 342 55.057 49.278 20.818 1.00 70.17 O
+ATOM 637 OD2 ASP A 342 55.471 48.417 18.838 1.00 70.02 O
+ATOM 638 N THR A 343 53.908 53.596 18.186 1.00 32.36 N
+ATOM 639 CA THR A 343 54.071 54.943 17.679 1.00 27.32 C
+ATOM 640 C THR A 343 53.436 55.933 18.641 1.00 27.11 C
+ATOM 641 O THR A 343 53.964 57.024 18.870 1.00 26.54 O
+ATOM 642 CB THR A 343 53.410 55.118 16.309 1.00 23.74 C
+ATOM 643 OG1 THR A 343 54.093 54.316 15.338 1.00 20.28 O
+ATOM 644 CG2 THR A 343 53.480 56.577 15.886 1.00 23.32 C
+ATOM 645 N VAL A 344 52.290 55.560 19.195 1.00 26.83 N
+ATOM 646 CA VAL A 344 51.615 56.439 20.128 1.00 27.04 C
+ATOM 647 C VAL A 344 52.476 56.612 21.374 1.00 26.22 C
+ATOM 648 O VAL A 344 52.557 57.703 21.940 1.00 27.14 O
+ATOM 649 CB VAL A 344 50.229 55.876 20.509 1.00 28.17 C
+ATOM 650 CG1 VAL A 344 49.637 56.666 21.661 1.00 27.35 C
+ATOM 651 CG2 VAL A 344 49.316 55.934 19.309 1.00 28.15 C
+ATOM 652 N LEU A 345 53.125 55.533 21.790 1.00 25.57 N
+ATOM 653 CA LEU A 345 53.983 55.564 22.966 1.00 25.44 C
+ATOM 654 C LEU A 345 55.298 56.280 22.672 1.00 26.26 C
+ATOM 655 O LEU A 345 55.933 56.829 23.576 1.00 26.98 O
+ATOM 656 CB LEU A 345 54.272 54.137 23.432 1.00 23.39 C
+ATOM 657 CG LEU A 345 53.065 53.293 23.829 1.00 20.96 C
+ATOM 658 CD1 LEU A 345 53.516 51.860 23.877 1.00 19.55 C
+ATOM 659 CD2 LEU A 345 52.490 53.731 25.160 1.00 15.63 C
+ATOM 660 N ALA A 346 55.709 56.263 21.408 1.00 27.40 N
+ATOM 661 CA ALA A 346 56.947 56.913 21.004 1.00 28.96 C
+ATOM 662 C ALA A 346 56.774 58.419 21.120 1.00 32.80 C
+ATOM 663 O ALA A 346 57.720 59.141 21.439 1.00 31.41 O
+ATOM 664 CB ALA A 346 57.298 56.532 19.577 1.00 28.77 C
+ATOM 665 N LYS A 347 55.554 58.884 20.862 1.00 35.50 N
+ATOM 666 CA LYS A 347 55.228 60.306 20.940 1.00 36.16 C
+ATOM 667 C LYS A 347 55.104 60.715 22.402 1.00 35.65 C
+ATOM 668 O LYS A 347 55.637 61.745 22.815 1.00 30.50 O
+ATOM 669 CB LYS A 347 53.913 60.583 20.207 1.00 40.88 C
+ATOM 670 CG LYS A 347 53.530 62.050 20.132 1.00 52.30 C
+ATOM 671 CD LYS A 347 54.613 62.851 19.432 1.00 58.83 C
+ATOM 672 CE LYS A 347 54.266 64.333 19.340 1.00 60.27 C
+ATOM 673 NZ LYS A 347 55.388 65.100 18.716 1.00 60.69 N
+ATOM 674 N LYS A 348 54.414 59.889 23.184 1.00 36.12 N
+ATOM 675 CA LYS A 348 54.230 60.173 24.602 1.00 35.77 C
+ATOM 676 C LYS A 348 55.578 60.177 25.283 1.00 37.11 C
+ATOM 677 O LYS A 348 55.728 60.714 26.382 1.00 32.49 O
+ATOM 678 CB LYS A 348 53.291 59.142 25.255 1.00 37.01 C
+ATOM 679 CG LYS A 348 51.838 59.582 25.207 1.00 44.58 C
+ATOM 680 CD LYS A 348 50.819 58.488 25.496 1.00 48.05 C
+ATOM 681 CE LYS A 348 49.404 59.074 25.332 1.00 50.25 C
+ATOM 682 NZ LYS A 348 48.303 58.065 25.335 1.00 50.48 N
+ATOM 683 N ARG A 349 56.564 59.587 24.613 1.00 38.80 N
+ATOM 684 CA ARG A 349 57.914 59.519 25.153 1.00 38.71 C
+ATOM 685 C ARG A 349 58.713 60.760 24.783 1.00 36.32 C
+ATOM 686 O ARG A 349 59.547 61.235 25.553 1.00 32.87 O
+ATOM 687 CB ARG A 349 58.628 58.270 24.632 1.00 45.89 C
+ATOM 688 CG ARG A 349 60.081 58.169 25.048 1.00 59.74 C
+ATOM 689 CD ARG A 349 60.266 58.645 26.473 1.00 67.52 C
+ATOM 690 NE ARG A 349 61.278 57.875 27.179 1.00 71.26 N
+ATOM 691 CZ ARG A 349 61.215 56.557 27.351 1.00 72.35 C
+ATOM 692 NH1 ARG A 349 60.187 55.869 26.860 1.00 71.04 N
+ATOM 693 NH2 ARG A 349 62.171 55.928 28.028 1.00 72.24 N
+ATOM 694 N VAL A 350 58.463 61.275 23.590 1.00 33.56 N
+ATOM 695 CA VAL A 350 59.160 62.451 23.130 1.00 31.43 C
+ATOM 696 C VAL A 350 58.694 63.630 23.944 1.00 33.24 C
+ATOM 697 O VAL A 350 59.504 64.332 24.545 1.00 31.87 O
+ATOM 698 CB VAL A 350 58.883 62.719 21.631 1.00 30.19 C
+ATOM 699 CG1 VAL A 350 59.149 64.194 21.290 1.00 27.51 C
+ATOM 700 CG2 VAL A 350 59.759 61.790 20.774 1.00 28.93 C
+ATOM 701 N ASP A 351 57.385 63.842 23.976 1.00 37.24 N
+ATOM 702 CA ASP A 351 56.833 64.965 24.718 1.00 39.20 C
+ATOM 703 C ASP A 351 57.235 64.902 26.176 1.00 38.93 C
+ATOM 704 O ASP A 351 57.328 65.923 26.859 1.00 34.74 O
+ATOM 705 CB ASP A 351 55.321 64.999 24.559 1.00 46.34 C
+ATOM 706 CG ASP A 351 54.908 65.206 23.119 1.00 57.86 C
+ATOM 707 OD1 ASP A 351 55.516 66.070 22.443 1.00 63.07 O
+ATOM 708 OD2 ASP A 351 53.977 64.511 22.662 1.00 63.84 O
+ATOM 709 N SER A 352 57.510 63.691 26.634 1.00 40.46 N
+ATOM 710 CA SER A 352 57.940 63.463 28.004 1.00 41.25 C
+ATOM 711 C SER A 352 59.253 64.201 28.290 1.00 42.21 C
+ATOM 712 O SER A 352 59.509 64.614 29.419 1.00 40.42 O
+ATOM 713 CB SER A 352 58.123 61.962 28.239 1.00 42.96 C
+ATOM 714 OG SER A 352 58.586 61.686 29.543 1.00 50.07 O
+ATOM 715 N LEU A 353 60.074 64.382 27.261 1.00 43.11 N
+ATOM 716 CA LEU A 353 61.354 65.061 27.425 1.00 42.72 C
+ATOM 717 C LEU A 353 61.441 66.428 26.744 1.00 41.93 C
+ATOM 718 O LEU A 353 62.174 67.306 27.204 1.00 40.44 O
+ATOM 719 CB LEU A 353 62.470 64.168 26.895 1.00 47.94 C
+ATOM 720 CG LEU A 353 62.261 62.688 27.214 1.00 56.76 C
+ATOM 721 CD1 LEU A 353 63.273 61.861 26.454 1.00 60.24 C
+ATOM 722 CD2 LEU A 353 62.371 62.455 28.712 1.00 60.96 C
+ATOM 723 N GLN A 354 60.694 66.613 25.659 1.00 39.45 N
+ATOM 724 CA GLN A 354 60.740 67.867 24.926 1.00 37.20 C
+ATOM 725 C GLN A 354 59.755 68.935 25.356 1.00 37.18 C
+ATOM 726 O GLN A 354 60.040 70.126 25.217 1.00 38.81 O
+ATOM 727 CB GLN A 354 60.563 67.608 23.434 1.00 36.51 C
+ATOM 728 CG GLN A 354 61.468 66.518 22.903 1.00 38.29 C
+ATOM 729 CD GLN A 354 61.682 66.610 21.413 1.00 40.11 C
+ATOM 730 OE1 GLN A 354 60.786 66.996 20.652 1.00 39.79 O
+ATOM 731 NE2 GLN A 354 62.879 66.242 20.980 1.00 41.38 N
+ATOM 732 N LEU A 355 58.601 68.540 25.878 1.00 37.19 N
+ATOM 733 CA LEU A 355 57.614 69.539 26.291 1.00 38.60 C
+ATOM 734 C LEU A 355 57.882 70.190 27.641 1.00 38.12 C
+ATOM 735 O LEU A 355 58.442 69.569 28.540 1.00 37.71 O
+ATOM 736 CB LEU A 355 56.205 68.937 26.292 1.00 39.14 C
+ATOM 737 CG LEU A 355 55.630 68.616 24.910 1.00 40.92 C
+ATOM 738 CD1 LEU A 355 54.140 68.362 25.035 1.00 39.66 C
+ATOM 739 CD2 LEU A 355 55.880 69.781 23.952 1.00 41.33 C
+ATOM 740 N THR A 356 57.491 71.455 27.768 1.00 37.87 N
+ATOM 741 CA THR A 356 57.657 72.188 29.023 1.00 36.78 C
+ATOM 742 C THR A 356 56.460 71.846 29.924 1.00 35.25 C
+ATOM 743 O THR A 356 55.434 71.359 29.450 1.00 34.70 O
+ATOM 744 CB THR A 356 57.696 73.713 28.780 1.00 37.33 C
+ATOM 745 OG1 THR A 356 56.424 74.154 28.280 1.00 37.69 O
+ATOM 746 CG2 THR A 356 58.784 74.058 27.771 1.00 36.36 C
+ATOM 747 N ARG A 357 56.577 72.096 31.217 1.00 32.91 N
+ATOM 748 CA ARG A 357 55.475 71.757 32.096 1.00 33.17 C
+ATOM 749 C ARG A 357 54.184 72.477 31.723 1.00 36.84 C
+ATOM 750 O ARG A 357 53.119 71.856 31.697 1.00 35.12 O
+ATOM 751 CB ARG A 357 55.863 71.998 33.564 1.00 28.89 C
+ATOM 752 CG ARG A 357 56.906 71.001 34.055 1.00 22.61 C
+ATOM 753 CD ARG A 357 57.315 71.218 35.486 1.00 20.66 C
+ATOM 754 NE ARG A 357 56.241 70.843 36.393 1.00 23.55 N
+ATOM 755 CZ ARG A 357 55.851 69.592 36.610 1.00 22.45 C
+ATOM 756 NH1 ARG A 357 56.466 68.599 35.982 1.00 21.93 N
+ATOM 757 NH2 ARG A 357 54.838 69.335 37.436 1.00 20.72 N
+ATOM 758 N GLU A 358 54.263 73.768 31.402 1.00 42.01 N
+ATOM 759 CA GLU A 358 53.048 74.483 31.019 1.00 45.54 C
+ATOM 760 C GLU A 358 52.400 73.833 29.784 1.00 44.88 C
+ATOM 761 O GLU A 358 51.166 73.785 29.675 1.00 40.96 O
+ATOM 762 CB GLU A 358 53.318 75.968 30.750 1.00 52.44 C
+ATOM 763 CG GLU A 358 52.025 76.788 30.787 1.00 67.91 C
+ATOM 764 CD GLU A 358 52.247 78.288 30.713 1.00 74.83 C
+ATOM 765 OE1 GLU A 358 53.139 78.793 31.433 1.00 77.60 O
+ATOM 766 OE2 GLU A 358 51.518 78.965 29.949 1.00 76.31 O
+ATOM 767 N GLN A 359 53.220 73.332 28.860 1.00 43.80 N
+ATOM 768 CA GLN A 359 52.681 72.671 27.678 1.00 40.66 C
+ATOM 769 C GLN A 359 52.059 71.364 28.132 1.00 37.70 C
+ATOM 770 O GLN A 359 50.992 70.987 27.651 1.00 39.76 O
+ATOM 771 CB GLN A 359 53.768 72.381 26.663 1.00 40.42 C
+ATOM 772 CG GLN A 359 54.542 73.593 26.262 1.00 44.30 C
+ATOM 773 CD GLN A 359 55.505 73.303 25.137 1.00 46.12 C
+ATOM 774 OE1 GLN A 359 55.128 73.313 23.962 1.00 46.15 O
+ATOM 775 NE2 GLN A 359 56.758 73.026 25.489 1.00 46.18 N
+ATOM 776 N MET A 360 52.719 70.675 29.061 1.00 32.83 N
+ATOM 777 CA MET A 360 52.168 69.425 29.564 1.00 30.76 C
+ATOM 778 C MET A 360 50.781 69.748 30.092 1.00 32.62 C
+ATOM 779 O MET A 360 49.797 69.063 29.754 1.00 33.06 O
+ATOM 780 CB MET A 360 53.017 68.842 30.699 1.00 28.13 C
+ATOM 781 CG MET A 360 54.296 68.141 30.258 1.00 25.98 C
+ATOM 782 SD MET A 360 55.359 67.650 31.647 1.00 23.38 S
+ATOM 783 CE MET A 360 54.730 65.895 31.940 1.00 19.00 C
+ATOM 784 N LEU A 361 50.696 70.806 30.900 1.00 30.29 N
+ATOM 785 CA LEU A 361 49.412 71.204 31.466 1.00 29.00 C
+ATOM 786 C LEU A 361 48.361 71.562 30.396 1.00 29.14 C
+ATOM 787 O LEU A 361 47.187 71.160 30.489 1.00 23.55 O
+ATOM 788 CB LEU A 361 49.595 72.391 32.424 1.00 31.42 C
+ATOM 789 CG LEU A 361 48.945 72.325 33.821 1.00 32.27 C
+ATOM 790 CD1 LEU A 361 48.349 73.685 34.145 1.00 32.53 C
+ATOM 791 CD2 LEU A 361 47.842 71.260 33.869 1.00 33.31 C
+ATOM 792 N THR A 362 48.776 72.315 29.382 1.00 30.51 N
+ATOM 793 CA THR A 362 47.842 72.708 28.337 1.00 32.94 C
+ATOM 794 C THR A 362 47.289 71.499 27.593 1.00 33.24 C
+ATOM 795 O THR A 362 46.113 71.486 27.213 1.00 34.26 O
+ATOM 796 CB THR A 362 48.489 73.639 27.318 1.00 34.32 C
+ATOM 797 OG1 THR A 362 48.964 74.813 27.983 1.00 38.78 O
+ATOM 798 CG2 THR A 362 47.481 74.031 26.248 1.00 37.61 C
+ATOM 799 N ASN A 363 48.126 70.486 27.374 1.00 33.71 N
+ATOM 800 CA ASN A 363 47.663 69.293 26.667 1.00 33.44 C
+ATOM 801 C ASN A 363 46.593 68.627 27.501 1.00 32.85 C
+ATOM 802 O ASN A 363 45.569 68.183 26.988 1.00 31.77 O
+ATOM 803 CB ASN A 363 48.809 68.320 26.406 1.00 32.84 C
+ATOM 804 CG ASN A 363 49.726 68.795 25.298 1.00 31.77 C
+ATOM 805 OD1 ASN A 363 49.296 69.515 24.399 1.00 31.32 O
+ATOM 806 ND2 ASN A 363 50.990 68.379 25.345 1.00 30.72 N
+ATOM 807 N ARG A 364 46.837 68.576 28.801 1.00 30.84 N
+ATOM 808 CA ARG A 364 45.870 68.004 29.715 1.00 28.85 C
+ATOM 809 C ARG A 364 44.575 68.778 29.527 1.00 28.57 C
+ATOM 810 O ARG A 364 43.503 68.210 29.288 1.00 26.00 O
+ATOM 811 CB ARG A 364 46.356 68.174 31.147 1.00 30.12 C
+ATOM 812 CG ARG A 364 45.358 67.713 32.171 1.00 33.03 C
+ATOM 813 CD ARG A 364 44.991 66.296 31.907 1.00 32.73 C
+ATOM 814 NE ARG A 364 44.083 65.794 32.915 1.00 36.81 N
+ATOM 815 CZ ARG A 364 43.685 64.529 32.974 1.00 38.28 C
+ATOM 816 NH1 ARG A 364 44.126 63.655 32.074 1.00 37.70 N
+ATOM 817 NH2 ARG A 364 42.850 64.133 33.929 1.00 37.61 N
+ATOM 818 N PHE A 365 44.693 70.094 29.628 1.00 28.29 N
+ATOM 819 CA PHE A 365 43.544 70.960 29.473 1.00 28.45 C
+ATOM 820 C PHE A 365 42.799 70.661 28.183 1.00 29.15 C
+ATOM 821 O PHE A 365 41.594 70.400 28.217 1.00 28.82 O
+ATOM 822 CB PHE A 365 43.988 72.430 29.544 1.00 27.14 C
+ATOM 823 CG PHE A 365 44.078 72.960 30.950 1.00 26.64 C
+ATOM 824 CD1 PHE A 365 44.041 72.093 32.042 1.00 28.20 C
+ATOM 825 CD2 PHE A 365 44.161 74.316 31.190 1.00 24.47 C
+ATOM 826 CE1 PHE A 365 44.080 72.583 33.332 1.00 26.00 C
+ATOM 827 CE2 PHE A 365 44.199 74.803 32.476 1.00 24.52 C
+ATOM 828 CZ PHE A 365 44.158 73.941 33.545 1.00 25.17 C
+ATOM 829 N ASN A 366 43.514 70.676 27.059 1.00 32.81 N
+ATOM 830 CA ASN A 366 42.899 70.403 25.764 1.00 35.64 C
+ATOM 831 C ASN A 366 42.162 69.071 25.761 1.00 38.78 C
+ATOM 832 O ASN A 366 41.112 68.931 25.128 1.00 36.88 O
+ATOM 833 CB ASN A 366 43.949 70.418 24.654 1.00 35.50 C
+ATOM 834 CG ASN A 366 44.186 71.807 24.097 1.00 36.88 C
+ATOM 835 OD1 ASN A 366 43.276 72.426 23.546 1.00 39.37 O
+ATOM 836 ND2 ASN A 366 45.409 72.306 24.236 1.00 37.94 N
+ATOM 837 N ASP A 367 42.698 68.091 26.480 1.00 43.70 N
+ATOM 838 CA ASP A 367 42.048 66.785 26.537 1.00 45.66 C
+ATOM 839 C ASP A 367 40.773 66.840 27.364 1.00 43.94 C
+ATOM 840 O ASP A 367 39.787 66.187 27.031 1.00 40.92 O
+ATOM 841 CB ASP A 367 43.008 65.719 27.085 1.00 53.86 C
+ATOM 842 CG ASP A 367 43.937 65.144 26.004 1.00 65.29 C
+ATOM 843 OD1 ASP A 367 43.424 64.577 25.009 1.00 70.52 O
+ATOM 844 OD2 ASP A 367 45.177 65.252 26.153 1.00 69.72 O
+ATOM 845 N LEU A 368 40.779 67.628 28.434 1.00 40.34 N
+ATOM 846 CA LEU A 368 39.576 67.751 29.260 1.00 35.78 C
+ATOM 847 C LEU A 368 38.484 68.524 28.517 1.00 33.38 C
+ATOM 848 O LEU A 368 37.294 68.310 28.741 1.00 29.00 O
+ATOM 849 CB LEU A 368 39.891 68.434 30.597 1.00 37.93 C
+ATOM 850 CG LEU A 368 40.489 67.547 31.700 1.00 40.32 C
+ATOM 851 CD1 LEU A 368 40.691 68.375 32.967 1.00 40.91 C
+ATOM 852 CD2 LEU A 368 39.556 66.368 31.981 1.00 39.89 C
+ATOM 853 N LEU A 369 38.891 69.423 27.634 1.00 31.08 N
+ATOM 854 CA LEU A 369 37.929 70.171 26.857 1.00 30.91 C
+ATOM 855 C LEU A 369 37.300 69.257 25.795 1.00 32.37 C
+ATOM 856 O LEU A 369 36.121 69.389 25.477 1.00 33.46 O
+ATOM 857 CB LEU A 369 38.590 71.384 26.197 1.00 29.40 C
+ATOM 858 CG LEU A 369 38.867 72.563 27.134 1.00 31.37 C
+ATOM 859 CD1 LEU A 369 39.461 73.704 26.326 1.00 31.37 C
+ATOM 860 CD2 LEU A 369 37.571 73.013 27.835 1.00 32.44 C
+ATOM 861 N ASP A 370 38.073 68.334 25.233 1.00 36.20 N
+ATOM 862 CA ASP A 370 37.494 67.433 24.244 1.00 38.67 C
+ATOM 863 C ASP A 370 36.401 66.628 24.952 1.00 39.79 C
+ATOM 864 O ASP A 370 35.316 66.429 24.399 1.00 40.84 O
+ATOM 865 CB ASP A 370 38.565 66.510 23.642 1.00 39.28 C
+ATOM 866 CG ASP A 370 39.552 67.258 22.744 1.00 42.17 C
+ATOM 867 OD1 ASP A 370 39.114 68.092 21.920 1.00 41.41 O
+ATOM 868 OD2 ASP A 370 40.774 67.006 22.849 1.00 45.37 O
+ATOM 869 N ARG A 371 36.689 66.187 26.180 1.00 41.08 N
+ATOM 870 CA ARG A 371 35.729 65.435 27.008 1.00 40.34 C
+ATOM 871 C ARG A 371 34.476 66.267 27.298 1.00 38.57 C
+ATOM 872 O ARG A 371 33.366 65.741 27.367 1.00 37.33 O
+ATOM 873 CB ARG A 371 36.344 65.065 28.361 1.00 41.98 C
+ATOM 874 CG ARG A 371 37.035 63.722 28.447 1.00 44.98 C
+ATOM 875 CD ARG A 371 37.508 63.429 29.884 1.00 46.97 C
+ATOM 876 NE ARG A 371 36.403 63.276 30.840 1.00 48.95 N
+ATOM 877 CZ ARG A 371 36.548 63.150 32.164 1.00 49.50 C
+ATOM 878 NH1 ARG A 371 37.756 63.159 32.719 1.00 47.15 N
+ATOM 879 NH2 ARG A 371 35.476 63.007 32.939 1.00 49.47 N
+ATOM 880 N MET A 372 34.679 67.566 27.511 1.00 36.37 N
+ATOM 881 CA MET A 372 33.594 68.494 27.804 1.00 34.00 C
+ATOM 882 C MET A 372 32.778 68.789 26.554 1.00 34.72 C
+ATOM 883 O MET A 372 31.557 68.929 26.628 1.00 36.19 O
+ATOM 884 CB MET A 372 34.157 69.798 28.386 1.00 29.98 C
+ATOM 885 CG MET A 372 34.636 69.700 29.871 1.00 20.18 C
+ATOM 886 SD MET A 372 35.665 71.068 30.366 1.00 12.54 S
+ATOM 887 CE MET A 372 34.530 72.463 30.198 1.00 15.35 C
+ATOM 888 N ASP A 373 33.449 68.874 25.408 1.00 37.32 N
+ATOM 889 CA ASP A 373 32.762 69.144 24.153 1.00 40.83 C
+ATOM 890 C ASP A 373 31.695 68.083 23.899 1.00 42.07 C
+ATOM 891 O ASP A 373 30.606 68.381 23.419 1.00 45.01 O
+ATOM 892 CB ASP A 373 33.744 69.148 22.978 1.00 42.78 C
+ATOM 893 CG ASP A 373 34.610 70.386 22.941 1.00 45.33 C
+ATOM 894 OD1 ASP A 373 34.069 71.498 23.088 1.00 46.16 O
+ATOM 895 OD2 ASP A 373 35.836 70.249 22.749 1.00 47.15 O
+ATOM 896 N ILE A 374 32.020 66.838 24.218 1.00 41.14 N
+ATOM 897 CA ILE A 374 31.094 65.744 24.019 1.00 39.38 C
+ATOM 898 C ILE A 374 30.059 65.675 25.136 1.00 38.74 C
+ATOM 899 O ILE A 374 28.876 65.538 24.857 1.00 40.82 O
+ATOM 900 CB ILE A 374 31.839 64.405 23.939 1.00 39.05 C
+ATOM 901 CG1 ILE A 374 32.777 64.417 22.739 1.00 37.37 C
+ATOM 902 CG2 ILE A 374 30.846 63.254 23.817 1.00 37.23 C
+ATOM 903 CD1 ILE A 374 33.633 63.180 22.647 1.00 37.48 C
+ATOM 904 N MET A 375 30.493 65.762 26.392 1.00 37.82 N
+ATOM 905 CA MET A 375 29.563 65.713 27.527 1.00 38.23 C
+ATOM 906 C MET A 375 28.381 66.659 27.330 1.00 39.47 C
+ATOM 907 O MET A 375 27.218 66.268 27.469 1.00 41.00 O
+ATOM 908 CB MET A 375 30.248 66.138 28.827 1.00 36.41 C
+ATOM 909 CG MET A 375 31.314 65.215 29.369 1.00 33.48 C
+ATOM 910 SD MET A 375 32.068 66.016 30.795 1.00 27.97 S
+ATOM 911 CE MET A 375 30.738 65.997 31.926 1.00 27.90 C
+ATOM 912 N PHE A 376 28.692 67.912 27.014 1.00 40.75 N
+ATOM 913 CA PHE A 376 27.672 68.936 26.845 1.00 41.94 C
+ATOM 914 C PHE A 376 27.313 69.231 25.392 1.00 43.72 C
+ATOM 915 O PHE A 376 26.780 70.297 25.084 1.00 43.82 O
+ATOM 916 CB PHE A 376 28.141 70.216 27.529 1.00 37.45 C
+ATOM 917 CG PHE A 376 28.648 69.999 28.933 1.00 32.70 C
+ATOM 918 CD1 PHE A 376 27.791 69.560 29.936 1.00 28.61 C
+ATOM 919 CD2 PHE A 376 29.990 70.242 29.251 1.00 32.55 C
+ATOM 920 CE1 PHE A 376 28.257 69.369 31.233 1.00 31.08 C
+ATOM 921 CE2 PHE A 376 30.471 70.053 30.553 1.00 30.28 C
+ATOM 922 CZ PHE A 376 29.605 69.619 31.542 1.00 31.31 C
+ATOM 923 N GLY A 377 27.586 68.280 24.505 1.00 46.34 N
+ATOM 924 CA GLY A 377 27.290 68.484 23.099 1.00 51.35 C
+ATOM 925 C GLY A 377 25.952 67.920 22.664 1.00 54.81 C
+ATOM 926 O GLY A 377 25.177 67.439 23.497 1.00 56.74 O
+ATOM 927 N SER A 378 25.691 67.988 21.356 1.00 56.90 N
+ATOM 928 CA SER A 378 24.454 67.492 20.744 1.00 55.98 C
+ATOM 929 C SER A 378 24.187 66.034 21.093 1.00 59.12 C
+ATOM 930 O SER A 378 23.072 65.669 21.480 1.00 51.38 O
+ATOM 931 CB SER A 378 24.530 67.636 19.224 1.00 54.17 C
+ATOM 932 OG SER A 378 25.638 66.924 18.707 1.00 57.58 O
+ATOM 933 N THR A 379 25.215 65.204 20.932 1.00 63.57 N
+ATOM 934 CA THR A 379 25.115 63.784 21.253 1.00 66.44 C
+ATOM 935 C THR A 379 25.948 63.539 22.509 1.00 63.46 C
+ATOM 936 O THR A 379 27.086 63.073 22.433 1.00 60.51 O
+ATOM 937 CB THR A 379 25.654 62.900 20.106 1.00 78.47 C
+ATOM 938 OG1 THR A 379 27.083 63.003 20.045 1.00 96.49 O
+ATOM 939 CG2 THR A 379 25.064 63.346 18.773 1.00 96.67 C
+ATOM 940 N GLY A 380 25.373 63.885 23.657 1.00 57.83 N
+ATOM 941 CA GLY A 380 26.046 63.720 24.931 1.00 49.07 C
+ATOM 942 C GLY A 380 24.974 63.730 25.995 1.00 47.41 C
+ATOM 943 O GLY A 380 23.859 64.169 25.727 1.00 46.60 O
+ATOM 944 N SER A 381 25.294 63.266 27.199 1.00 45.98 N
+ATOM 945 CA SER A 381 24.311 63.213 28.281 1.00 46.50 C
+ATOM 946 C SER A 381 24.410 64.350 29.291 1.00 46.30 C
+ATOM 947 O SER A 381 23.394 64.852 29.760 1.00 47.53 O
+ATOM 948 CB SER A 381 24.456 61.907 29.036 1.00 48.06 C
+ATOM 949 OG SER A 381 25.741 61.865 29.627 1.00 54.19 O
+ATOM 950 N ALA A 382 25.635 64.744 29.627 1.00 43.09 N
+ATOM 951 CA ALA A 382 25.893 65.800 30.610 1.00 39.82 C
+ATOM 952 C ALA A 382 24.880 66.949 30.687 1.00 37.80 C
+ATOM 953 O ALA A 382 24.413 67.458 29.665 1.00 34.41 O
+ATOM 954 CB ALA A 382 27.301 66.361 30.400 1.00 39.86 C
+ATOM 955 N ASP A 383 24.551 67.339 31.918 1.00 34.30 N
+ATOM 956 CA ASP A 383 23.608 68.434 32.190 1.00 33.80 C
+ATOM 957 C ASP A 383 24.416 69.611 32.745 1.00 34.31 C
+ATOM 958 O ASP A 383 24.625 69.711 33.950 1.00 34.34 O
+ATOM 959 CB ASP A 383 22.583 67.996 33.235 1.00 35.29 C
+ATOM 960 CG ASP A 383 21.481 69.019 33.444 1.00 38.33 C
+ATOM 961 OD1 ASP A 383 21.735 70.227 33.247 1.00 39.88 O
+ATOM 962 OD2 ASP A 383 20.355 68.615 33.822 1.00 40.92 O
+ATOM 963 N ILE A 384 24.852 70.514 31.873 1.00 33.99 N
+ATOM 964 CA ILE A 384 25.687 71.631 32.301 1.00 33.03 C
+ATOM 965 C ILE A 384 25.199 72.436 33.511 1.00 33.49 C
+ATOM 966 O ILE A 384 26.000 72.978 34.273 1.00 31.18 O
+ATOM 967 CB ILE A 384 25.980 72.567 31.107 1.00 33.99 C
+ATOM 968 CG1 ILE A 384 27.301 73.291 31.352 1.00 36.82 C
+ATOM 969 CG2 ILE A 384 24.853 73.549 30.899 1.00 35.47 C
+ATOM 970 CD1 ILE A 384 27.800 74.028 30.136 1.00 39.49 C
+ATOM 971 N GLU A 385 23.892 72.506 33.701 1.00 33.61 N
+ATOM 972 CA GLU A 385 23.347 73.243 34.831 1.00 32.72 C
+ATOM 973 C GLU A 385 23.749 72.556 36.136 1.00 32.78 C
+ATOM 974 O GLU A 385 23.995 73.209 37.148 1.00 31.37 O
+ATOM 975 CB GLU A 385 21.823 73.313 34.706 1.00 34.14 C
+ATOM 976 CG GLU A 385 21.135 74.086 35.810 1.00 38.54 C
+ATOM 977 CD GLU A 385 19.641 73.795 35.893 1.00 40.19 C
+ATOM 978 OE1 GLU A 385 19.259 72.607 36.008 1.00 40.79 O
+ATOM 979 OE2 GLU A 385 18.846 74.755 35.854 1.00 42.23 O
+ATOM 980 N GLU A 386 23.812 71.231 36.107 1.00 33.82 N
+ATOM 981 CA GLU A 386 24.191 70.462 37.287 1.00 36.75 C
+ATOM 982 C GLU A 386 25.692 70.571 37.533 1.00 36.75 C
+ATOM 983 O GLU A 386 26.167 70.412 38.665 1.00 37.20 O
+ATOM 984 CB GLU A 386 23.788 68.995 37.124 1.00 40.88 C
+ATOM 985 CG GLU A 386 22.332 68.714 37.492 1.00 48.69 C
+ATOM 986 CD GLU A 386 21.922 67.277 37.212 1.00 51.43 C
+ATOM 987 OE1 GLU A 386 22.798 66.489 36.795 1.00 52.06 O
+ATOM 988 OE2 GLU A 386 20.729 66.937 37.407 1.00 51.42 O
+ATOM 989 N TRP A 387 26.442 70.856 36.473 1.00 33.05 N
+ATOM 990 CA TRP A 387 27.879 71.019 36.598 1.00 28.82 C
+ATOM 991 C TRP A 387 28.292 72.418 37.080 1.00 25.70 C
+ATOM 992 O TRP A 387 29.373 72.584 37.639 1.00 24.22 O
+ATOM 993 CB TRP A 387 28.556 70.683 35.279 1.00 28.62 C
+ATOM 994 CG TRP A 387 28.604 69.218 35.047 1.00 29.42 C
+ATOM 995 CD1 TRP A 387 27.621 68.436 34.529 1.00 29.34 C
+ATOM 996 CD2 TRP A 387 29.676 68.338 35.396 1.00 30.22 C
+ATOM 997 NE1 TRP A 387 28.010 67.118 34.536 1.00 30.68 N
+ATOM 998 CE2 TRP A 387 29.269 67.030 35.064 1.00 29.27 C
+ATOM 999 CE3 TRP A 387 30.943 68.534 35.967 1.00 30.28 C
+ATOM 1000 CZ2 TRP A 387 30.080 65.916 35.274 1.00 29.25 C
+ATOM 1001 CZ3 TRP A 387 31.757 67.423 36.180 1.00 31.11 C
+ATOM 1002 CH2 TRP A 387 31.318 66.130 35.835 1.00 30.29 C
+ATOM 1003 N MET A 388 27.451 73.427 36.869 1.00 23.71 N
+ATOM 1004 CA MET A 388 27.788 74.761 37.357 1.00 22.54 C
+ATOM 1005 C MET A 388 27.388 74.762 38.822 1.00 21.87 C
+ATOM 1006 O MET A 388 27.943 75.507 39.632 1.00 22.54 O
+ATOM 1007 CB MET A 388 27.043 75.864 36.579 1.00 21.87 C
+ATOM 1008 CG MET A 388 27.724 76.283 35.264 1.00 18.17 C
+ATOM 1009 SD MET A 388 29.400 76.960 35.445 1.00 15.07 S
+ATOM 1010 CE MET A 388 29.023 78.572 36.115 1.00 10.75 C
+ATOM 1011 N ALA A 389 26.428 73.905 39.156 1.00 21.92 N
+ATOM 1012 CA ALA A 389 25.975 73.769 40.535 1.00 24.23 C
+ATOM 1013 C ALA A 389 27.145 73.162 41.291 1.00 25.26 C
+ATOM 1014 O ALA A 389 27.347 73.460 42.474 1.00 24.11 O
+ATOM 1015 CB ALA A 389 24.768 72.845 40.622 1.00 24.33 C
+ATOM 1016 N GLY A 390 27.902 72.306 40.594 1.00 26.35 N
+ATOM 1017 CA GLY A 390 29.071 71.674 41.189 1.00 27.18 C
+ATOM 1018 C GLY A 390 30.133 72.720 41.503 1.00 26.50 C
+ATOM 1019 O GLY A 390 30.788 72.690 42.548 1.00 27.23 O
+ATOM 1020 N VAL A 391 30.300 73.653 40.576 1.00 24.66 N
+ATOM 1021 CA VAL A 391 31.242 74.737 40.750 1.00 23.66 C
+ATOM 1022 C VAL A 391 30.780 75.597 41.932 1.00 22.94 C
+ATOM 1023 O VAL A 391 31.571 75.961 42.811 1.00 23.44 O
+ATOM 1024 CB VAL A 391 31.310 75.591 39.475 1.00 24.96 C
+ATOM 1025 CG1 VAL A 391 32.140 76.859 39.713 1.00 24.27 C
+ATOM 1026 CG2 VAL A 391 31.907 74.747 38.346 1.00 25.40 C
+ATOM 1027 N ALA A 392 29.491 75.904 41.968 1.00 20.41 N
+ATOM 1028 CA ALA A 392 28.974 76.702 43.055 1.00 20.38 C
+ATOM 1029 C ALA A 392 29.279 76.026 44.400 1.00 22.12 C
+ATOM 1030 O ALA A 392 29.744 76.670 45.344 1.00 21.02 O
+ATOM 1031 CB ALA A 392 27.496 76.887 42.885 1.00 19.94 C
+ATOM 1032 N TRP A 393 29.018 74.732 44.502 1.00 23.53 N
+ATOM 1033 CA TRP A 393 29.293 74.026 45.747 1.00 24.55 C
+ATOM 1034 C TRP A 393 30.792 74.042 46.073 1.00 23.78 C
+ATOM 1035 O TRP A 393 31.181 74.210 47.228 1.00 23.31 O
+ATOM 1036 CB TRP A 393 28.813 72.574 45.660 1.00 28.91 C
+ATOM 1037 CG TRP A 393 28.879 71.868 46.976 1.00 33.67 C
+ATOM 1038 CD1 TRP A 393 27.903 71.818 47.940 1.00 34.59 C
+ATOM 1039 CD2 TRP A 393 30.013 71.180 47.521 1.00 35.26 C
+ATOM 1040 NE1 TRP A 393 28.366 71.147 49.045 1.00 35.58 N
+ATOM 1041 CE2 TRP A 393 29.657 70.745 48.815 1.00 35.44 C
+ATOM 1042 CE3 TRP A 393 31.299 70.892 47.036 1.00 35.79 C
+ATOM 1043 CZ2 TRP A 393 30.540 70.035 49.634 1.00 34.69 C
+ATOM 1044 CZ3 TRP A 393 32.172 70.188 47.850 1.00 35.80 C
+ATOM 1045 CH2 TRP A 393 31.788 69.767 49.135 1.00 35.79 C
+ATOM 1046 N LEU A 394 31.627 73.859 45.054 1.00 24.39 N
+ATOM 1047 CA LEU A 394 33.076 73.868 45.239 1.00 24.37 C
+ATOM 1048 C LEU A 394 33.639 75.226 45.636 1.00 25.03 C
+ATOM 1049 O LEU A 394 34.606 75.319 46.402 1.00 28.71 O
+ATOM 1050 CB LEU A 394 33.773 73.415 43.963 1.00 20.59 C
+ATOM 1051 CG LEU A 394 33.890 71.904 43.802 1.00 19.69 C
+ATOM 1052 CD1 LEU A 394 34.407 71.592 42.416 1.00 17.43 C
+ATOM 1053 CD2 LEU A 394 34.812 71.327 44.893 1.00 18.82 C
+ATOM 1054 N HIS A 395 33.036 76.284 45.115 1.00 26.75 N
+ATOM 1055 CA HIS A 395 33.511 77.623 45.407 1.00 29.15 C
+ATOM 1056 C HIS A 395 33.044 78.083 46.785 1.00 30.98 C
+ATOM 1057 O HIS A 395 33.215 79.250 47.151 1.00 32.79 O
+ATOM 1058 CB HIS A 395 33.035 78.575 44.308 1.00 27.42 C
+ATOM 1059 CG HIS A 395 33.895 79.785 44.146 1.00 24.44 C
+ATOM 1060 ND1 HIS A 395 33.844 80.855 45.014 1.00 22.69 N
+ATOM 1061 CD2 HIS A 395 34.842 80.091 43.227 1.00 22.76 C
+ATOM 1062 CE1 HIS A 395 34.724 81.769 44.632 1.00 21.51 C
+ATOM 1063 NE2 HIS A 395 35.339 81.330 43.553 1.00 18.73 N
+ATOM 1064 N CYS A 396 32.461 77.151 47.539 1.00 30.22 N
+ATOM 1065 CA CYS A 396 31.965 77.421 48.885 1.00 29.88 C
+ATOM 1066 C CYS A 396 32.704 76.538 49.873 1.00 28.74 C
+ATOM 1067 O CYS A 396 32.553 76.681 51.092 1.00 26.71 O
+ATOM 1068 CB CYS A 396 30.457 77.130 48.991 1.00 33.03 C
+ATOM 1069 SG CYS A 396 29.304 78.382 48.316 1.00 39.21 S
+ATOM 1070 N LEU A 397 33.492 75.614 49.335 1.00 26.81 N
+ATOM 1071 CA LEU A 397 34.262 74.678 50.147 1.00 25.36 C
+ATOM 1072 C LEU A 397 35.486 75.336 50.759 1.00 25.37 C
+ATOM 1073 O LEU A 397 35.896 75.007 51.874 1.00 25.16 O
+ATOM 1074 CB LEU A 397 34.724 73.508 49.298 1.00 25.97 C
+ATOM 1075 CG LEU A 397 35.596 72.464 49.991 1.00 25.95 C
+ATOM 1076 CD1 LEU A 397 34.789 71.700 51.035 1.00 24.31 C
+ATOM 1077 CD2 LEU A 397 36.136 71.525 48.925 1.00 26.09 C
+ATOM 1078 N LEU A 398 36.070 76.269 50.015 1.00 26.55 N
+ATOM 1079 CA LEU A 398 37.250 76.978 50.466 1.00 25.79 C
+ATOM 1080 C LEU A 398 37.134 78.425 50.031 1.00 24.05 C
+ATOM 1081 O LEU A 398 36.518 78.731 49.010 1.00 28.55 O
+ATOM 1082 CB LEU A 398 38.490 76.336 49.843 1.00 27.44 C
+ATOM 1083 CG LEU A 398 39.627 75.852 50.739 1.00 28.16 C
+ATOM 1084 CD1 LEU A 398 39.109 75.065 51.944 1.00 26.09 C
+ATOM 1085 CD2 LEU A 398 40.537 74.990 49.876 1.00 27.14 C
+ATOM 1086 N PRO A 399 37.722 79.340 50.805 1.00 24.93 N
+ATOM 1087 CA PRO A 399 37.691 80.776 50.503 1.00 25.13 C
+ATOM 1088 C PRO A 399 38.546 81.085 49.281 1.00 26.38 C
+ATOM 1089 O PRO A 399 39.628 80.518 49.122 1.00 29.12 O
+ATOM 1090 CB PRO A 399 38.285 81.410 51.747 1.00 19.95 C
+ATOM 1091 CG PRO A 399 38.081 80.390 52.812 1.00 19.79 C
+ATOM 1092 CD PRO A 399 38.356 79.094 52.106 1.00 22.16 C
+ATOM 1093 N LYS A 400 38.061 81.979 48.423 1.00 29.66 N
+ATOM 1094 CA LYS A 400 38.794 82.364 47.218 1.00 31.32 C
+ATOM 1095 C LYS A 400 39.242 81.103 46.474 1.00 30.51 C
+ATOM 1096 O LYS A 400 40.323 81.063 45.868 1.00 28.23 O
+ATOM 1097 CB LYS A 400 40.003 83.238 47.601 1.00 32.72 C
+ATOM 1098 CG LYS A 400 39.611 84.545 48.278 1.00 33.65 C
+ATOM 1099 CD LYS A 400 40.797 85.335 48.829 1.00 36.43 C
+ATOM 1100 CE LYS A 400 41.431 86.286 47.796 1.00 40.96 C
+ATOM 1101 NZ LYS A 400 42.457 85.684 46.853 1.00 39.75 N
+ATOM 1102 N MET A 401 38.384 80.082 46.528 1.00 26.98 N
+ATOM 1103 CA MET A 401 38.655 78.801 45.897 1.00 23.45 C
+ATOM 1104 C MET A 401 39.235 78.913 44.498 1.00 22.44 C
+ATOM 1105 O MET A 401 40.199 78.219 44.180 1.00 22.39 O
+ATOM 1106 CB MET A 401 37.388 77.936 45.873 1.00 19.42 C
+ATOM 1107 CG MET A 401 37.571 76.528 45.279 1.00 13.83 C
+ATOM 1108 SD MET A 401 39.000 75.607 45.926 1.00 7.98 S
+ATOM 1109 CE MET A 401 38.323 74.598 47.113 1.00 15.86 C
+ATOM 1110 N ASP A 402 38.697 79.802 43.670 1.00 22.47 N
+ATOM 1111 CA ASP A 402 39.211 79.904 42.308 1.00 25.43 C
+ATOM 1112 C ASP A 402 40.633 80.448 42.246 1.00 27.83 C
+ATOM 1113 O ASP A 402 41.372 80.180 41.294 1.00 29.53 O
+ATOM 1114 CB ASP A 402 38.288 80.746 41.434 1.00 25.72 C
+ATOM 1115 CG ASP A 402 38.433 82.201 41.689 1.00 28.47 C
+ATOM 1116 OD1 ASP A 402 39.048 82.899 40.859 1.00 28.54 O
+ATOM 1117 OD2 ASP A 402 37.932 82.649 42.732 1.00 33.58 O
+ATOM 1118 N SER A 403 41.034 81.207 43.256 1.00 28.91 N
+ATOM 1119 CA SER A 403 42.394 81.736 43.275 1.00 27.72 C
+ATOM 1120 C SER A 403 43.320 80.602 43.757 1.00 26.37 C
+ATOM 1121 O SER A 403 44.476 80.479 43.340 1.00 22.80 O
+ATOM 1122 CB SER A 403 42.431 82.944 44.206 1.00 28.27 C
+ATOM 1123 OG SER A 403 41.289 83.764 43.965 1.00 36.54 O
+ATOM 1124 N VAL A 404 42.768 79.755 44.621 1.00 25.55 N
+ATOM 1125 CA VAL A 404 43.477 78.614 45.169 1.00 23.86 C
+ATOM 1126 C VAL A 404 43.878 77.632 44.083 1.00 23.23 C
+ATOM 1127 O VAL A 404 44.984 77.102 44.099 1.00 25.89 O
+ATOM 1128 CB VAL A 404 42.605 77.863 46.171 1.00 21.72 C
+ATOM 1129 CG1 VAL A 404 43.295 76.575 46.595 1.00 22.60 C
+ATOM 1130 CG2 VAL A 404 42.334 78.734 47.367 1.00 21.45 C
+ATOM 1131 N VAL A 405 42.973 77.380 43.144 1.00 22.29 N
+ATOM 1132 CA VAL A 405 43.251 76.441 42.062 1.00 22.38 C
+ATOM 1133 C VAL A 405 44.261 77.034 41.092 1.00 23.76 C
+ATOM 1134 O VAL A 405 45.112 76.332 40.553 1.00 21.51 O
+ATOM 1135 CB VAL A 405 41.946 76.052 41.301 1.00 22.89 C
+ATOM 1136 CG1 VAL A 405 42.263 75.112 40.130 1.00 22.08 C
+ATOM 1137 CG2 VAL A 405 40.981 75.376 42.255 1.00 22.59 C
+ATOM 1138 N TYR A 406 44.163 78.332 40.856 1.00 26.32 N
+ATOM 1139 CA TYR A 406 45.110 78.977 39.960 1.00 27.52 C
+ATOM 1140 C TYR A 406 46.474 78.918 40.645 1.00 27.30 C
+ATOM 1141 O TYR A 406 47.481 78.580 40.030 1.00 24.17 O
+ATOM 1142 CB TYR A 406 44.697 80.434 39.710 1.00 32.08 C
+ATOM 1143 CG TYR A 406 45.749 81.281 39.014 1.00 37.39 C
+ATOM 1144 CD1 TYR A 406 46.126 81.033 37.692 1.00 39.09 C
+ATOM 1145 CD2 TYR A 406 46.354 82.346 39.678 1.00 39.31 C
+ATOM 1146 CE1 TYR A 406 47.080 81.833 37.049 1.00 40.05 C
+ATOM 1147 CE2 TYR A 406 47.303 83.148 39.047 1.00 40.71 C
+ATOM 1148 CZ TYR A 406 47.665 82.891 37.737 1.00 40.85 C
+ATOM 1149 OH TYR A 406 48.608 83.699 37.133 1.00 41.94 O
+ATOM 1150 N ASP A 407 46.494 79.262 41.928 1.00 29.09 N
+ATOM 1151 CA ASP A 407 47.730 79.224 42.683 1.00 30.28 C
+ATOM 1152 C ASP A 407 48.316 77.827 42.593 1.00 29.91 C
+ATOM 1153 O ASP A 407 49.464 77.650 42.203 1.00 33.30 O
+ATOM 1154 CB ASP A 407 47.497 79.555 44.152 1.00 31.80 C
+ATOM 1155 CG ASP A 407 47.280 81.032 44.400 1.00 35.59 C
+ATOM 1156 OD1 ASP A 407 47.949 81.857 43.736 1.00 37.55 O
+ATOM 1157 OD2 ASP A 407 46.449 81.360 45.282 1.00 36.88 O
+ATOM 1158 N PHE A 408 47.521 76.828 42.949 1.00 28.68 N
+ATOM 1159 CA PHE A 408 47.997 75.456 42.910 1.00 26.43 C
+ATOM 1160 C PHE A 408 48.599 75.085 41.560 1.00 24.63 C
+ATOM 1161 O PHE A 408 49.652 74.452 41.499 1.00 24.71 O
+ATOM 1162 CB PHE A 408 46.871 74.485 43.233 1.00 22.03 C
+ATOM 1163 CG PHE A 408 47.290 73.057 43.163 1.00 18.93 C
+ATOM 1164 CD1 PHE A 408 48.128 72.522 44.127 1.00 19.10 C
+ATOM 1165 CD2 PHE A 408 46.883 72.256 42.108 1.00 18.55 C
+ATOM 1166 CE1 PHE A 408 48.561 71.194 44.044 1.00 19.69 C
+ATOM 1167 CE2 PHE A 408 47.304 70.933 42.009 1.00 16.92 C
+ATOM 1168 CZ PHE A 408 48.144 70.399 42.977 1.00 17.84 C
+ATOM 1169 N LEU A 409 47.919 75.463 40.485 1.00 23.47 N
+ATOM 1170 CA LEU A 409 48.387 75.181 39.134 1.00 23.84 C
+ATOM 1171 C LEU A 409 49.743 75.818 38.876 1.00 27.83 C
+ATOM 1172 O LEU A 409 50.609 75.202 38.259 1.00 25.49 O
+ATOM 1173 CB LEU A 409 47.374 75.696 38.105 1.00 22.10 C
+ATOM 1174 CG LEU A 409 46.083 74.884 37.939 1.00 20.48 C
+ATOM 1175 CD1 LEU A 409 45.170 75.536 36.935 1.00 19.00 C
+ATOM 1176 CD2 LEU A 409 46.449 73.476 37.477 1.00 22.01 C
+ATOM 1177 N LYS A 410 49.943 77.044 39.352 1.00 32.67 N
+ATOM 1178 CA LYS A 410 51.225 77.713 39.125 1.00 36.19 C
+ATOM 1179 C LYS A 410 52.325 77.015 39.941 1.00 35.15 C
+ATOM 1180 O LYS A 410 53.461 76.838 39.491 1.00 30.89 O
+ATOM 1181 CB LYS A 410 51.136 79.204 39.492 1.00 45.80 C
+ATOM 1182 CG LYS A 410 51.192 79.491 40.974 1.00 63.96 C
+ATOM 1183 CD LYS A 410 51.124 80.976 41.284 1.00 72.23 C
+ATOM 1184 CE LYS A 410 51.182 81.197 42.795 1.00 74.82 C
+ATOM 1185 NZ LYS A 410 51.046 82.626 43.169 1.00 75.46 N
+ATOM 1186 N CYS A 411 51.965 76.609 41.147 1.00 33.44 N
+ATOM 1187 CA CYS A 411 52.896 75.914 42.000 1.00 30.81 C
+ATOM 1188 C CYS A 411 53.337 74.658 41.239 1.00 28.55 C
+ATOM 1189 O CYS A 411 54.526 74.439 41.044 1.00 31.80 O
+ATOM 1190 CB CYS A 411 52.206 75.535 43.306 1.00 31.63 C
+ATOM 1191 SG CYS A 411 53.297 74.894 44.583 1.00 34.99 S
+ATOM 1192 N MET A 412 52.374 73.858 40.787 1.00 26.53 N
+ATOM 1193 CA MET A 412 52.669 72.630 40.066 1.00 25.54 C
+ATOM 1194 C MET A 412 53.445 72.851 38.777 1.00 28.04 C
+ATOM 1195 O MET A 412 54.302 72.041 38.431 1.00 30.26 O
+ATOM 1196 CB MET A 412 51.378 71.853 39.736 1.00 22.95 C
+ATOM 1197 CG MET A 412 50.562 71.321 40.932 1.00 14.77 C
+ATOM 1198 SD MET A 412 51.499 70.312 42.097 1.00 8.66 S
+ATOM 1199 CE MET A 412 52.088 71.568 43.198 1.00 9.18 C
+ATOM 1200 N VAL A 413 53.155 73.919 38.043 1.00 28.31 N
+ATOM 1201 CA VAL A 413 53.890 74.137 36.798 1.00 28.45 C
+ATOM 1202 C VAL A 413 55.263 74.724 37.051 1.00 30.04 C
+ATOM 1203 O VAL A 413 56.230 74.313 36.440 1.00 29.00 O
+ATOM 1204 CB VAL A 413 53.141 75.065 35.806 1.00 30.11 C
+ATOM 1205 CG1 VAL A 413 54.123 75.645 34.817 1.00 31.81 C
+ATOM 1206 CG2 VAL A 413 52.101 74.283 35.028 1.00 33.51 C
+ATOM 1207 N TYR A 414 55.351 75.695 37.944 1.00 31.77 N
+ATOM 1208 CA TYR A 414 56.633 76.318 38.241 1.00 33.12 C
+ATOM 1209 C TYR A 414 57.593 75.284 38.837 1.00 32.86 C
+ATOM 1210 O TYR A 414 58.811 75.390 38.693 1.00 33.01 O
+ATOM 1211 CB TYR A 414 56.430 77.503 39.198 1.00 36.82 C
+ATOM 1212 CG TYR A 414 55.855 78.743 38.538 1.00 41.97 C
+ATOM 1213 CD1 TYR A 414 54.798 78.653 37.626 1.00 44.77 C
+ATOM 1214 CD2 TYR A 414 56.337 80.014 38.857 1.00 44.97 C
+ATOM 1215 CE1 TYR A 414 54.233 79.799 37.047 1.00 45.26 C
+ATOM 1216 CE2 TYR A 414 55.781 81.170 38.285 1.00 46.06 C
+ATOM 1217 CZ TYR A 414 54.731 81.052 37.385 1.00 45.74 C
+ATOM 1218 OH TYR A 414 54.189 82.179 36.816 1.00 44.79 O
+ATOM 1219 N ASN A 415 57.030 74.279 39.495 1.00 32.00 N
+ATOM 1220 CA ASN A 415 57.809 73.216 40.108 1.00 29.74 C
+ATOM 1221 C ASN A 415 59.142 73.681 40.690 1.00 29.63 C
+ATOM 1222 O ASN A 415 60.213 73.315 40.188 1.00 28.55 O
+ATOM 1223 CB ASN A 415 58.059 72.126 39.078 1.00 28.33 C
+ATOM 1224 CG ASN A 415 58.638 70.890 39.693 1.00 28.81 C
+ATOM 1225 OD1 ASN A 415 59.198 70.056 39.005 1.00 31.76 O
+ATOM 1226 ND2 ASN A 415 58.502 70.759 41.002 1.00 28.27 N
+ATOM 1227 N ILE A 416 59.080 74.467 41.761 1.00 30.66 N
+ATOM 1228 CA ILE A 416 60.289 74.993 42.387 1.00 30.53 C
+ATOM 1229 C ILE A 416 60.752 74.229 43.621 1.00 30.34 C
+ATOM 1230 O ILE A 416 59.983 73.983 44.551 1.00 33.98 O
+ATOM 1231 CB ILE A 416 60.114 76.480 42.748 1.00 31.45 C
+ATOM 1232 CG1 ILE A 416 60.084 77.293 41.453 1.00 30.13 C
+ATOM 1233 CG2 ILE A 416 61.228 76.945 43.691 1.00 31.65 C
+ATOM 1234 CD1 ILE A 416 60.291 78.767 41.646 1.00 33.94 C
+ATOM 1235 N PRO A 417 62.038 73.861 43.658 1.00 35.04 N
+ATOM 1236 CA PRO A 417 62.514 73.119 44.829 1.00 35.17 C
+ATOM 1237 C PRO A 417 62.058 73.703 46.160 1.00 35.90 C
+ATOM 1238 O PRO A 417 62.099 74.913 46.364 1.00 37.52 O
+ATOM 1239 CB PRO A 417 64.040 73.107 44.647 1.00 33.79 C
+ATOM 1240 CG PRO A 417 64.301 74.212 43.633 1.00 31.76 C
+ATOM 1241 CD PRO A 417 63.132 74.155 42.720 1.00 31.43 C
+ATOM 1242 N LYS A 418 61.593 72.819 47.041 1.00 38.21 N
+ATOM 1243 CA LYS A 418 61.108 73.170 48.378 1.00 38.73 C
+ATOM 1244 C LYS A 418 59.857 74.035 48.396 1.00 38.62 C
+ATOM 1245 O LYS A 418 59.533 74.648 49.412 1.00 37.36 O
+ATOM 1246 CB LYS A 418 62.208 73.859 49.187 1.00 41.51 C
+ATOM 1247 CG LYS A 418 63.351 72.954 49.607 1.00 47.93 C
+ATOM 1248 CD LYS A 418 64.339 73.708 50.467 1.00 51.98 C
+ATOM 1249 CE LYS A 418 65.456 72.804 50.964 1.00 54.81 C
+ATOM 1250 NZ LYS A 418 66.452 73.568 51.786 1.00 54.53 N
+ATOM 1251 N LYS A 419 59.148 74.086 47.275 1.00 36.54 N
+ATOM 1252 CA LYS A 419 57.915 74.865 47.186 1.00 33.29 C
+ATOM 1253 C LYS A 419 57.012 74.154 46.189 1.00 31.53 C
+ATOM 1254 O LYS A 419 56.345 74.802 45.378 1.00 32.04 O
+ATOM 1255 CB LYS A 419 58.204 76.266 46.662 1.00 33.55 C
+ATOM 1256 CG LYS A 419 59.081 77.130 47.527 1.00 38.19 C
+ATOM 1257 CD LYS A 419 59.224 78.477 46.836 1.00 40.30 C
+ATOM 1258 CE LYS A 419 59.907 79.527 47.684 1.00 40.35 C
+ATOM 1259 NZ LYS A 419 59.945 80.830 46.960 1.00 39.64 N
+ATOM 1260 N ARG A 420 56.990 72.825 46.252 1.00 28.25 N
+ATOM 1261 CA ARG A 420 56.208 72.019 45.309 1.00 26.37 C
+ATOM 1262 C ARG A 420 55.089 71.189 45.924 1.00 24.71 C
+ATOM 1263 O ARG A 420 54.338 70.537 45.199 1.00 24.40 O
+ATOM 1264 CB ARG A 420 57.152 71.075 44.564 1.00 24.03 C
+ATOM 1265 CG ARG A 420 58.577 71.549 44.598 1.00 23.53 C
+ATOM 1266 CD ARG A 420 59.466 70.696 43.753 1.00 25.58 C
+ATOM 1267 NE ARG A 420 59.706 69.375 44.332 1.00 24.94 N
+ATOM 1268 CZ ARG A 420 59.532 68.236 43.673 1.00 23.58 C
+ATOM 1269 NH1 ARG A 420 59.108 68.248 42.414 1.00 23.34 N
+ATOM 1270 NH2 ARG A 420 59.803 67.087 44.266 1.00 23.07 N
+ATOM 1271 N TYR A 421 54.987 71.206 47.250 1.00 21.14 N
+ATOM 1272 CA TYR A 421 53.982 70.420 47.928 1.00 18.44 C
+ATOM 1273 C TYR A 421 53.014 71.155 48.801 1.00 19.01 C
+ATOM 1274 O TYR A 421 53.368 72.094 49.487 1.00 16.63 O
+ATOM 1275 CB TYR A 421 54.650 69.310 48.737 1.00 16.41 C
+ATOM 1276 CG TYR A 421 54.911 68.102 47.887 1.00 17.95 C
+ATOM 1277 CD1 TYR A 421 55.999 68.067 47.005 1.00 17.12 C
+ATOM 1278 CD2 TYR A 421 54.004 67.028 47.877 1.00 16.87 C
+ATOM 1279 CE1 TYR A 421 56.179 66.995 46.123 1.00 18.25 C
+ATOM 1280 CE2 TYR A 421 54.173 65.957 47.007 1.00 17.30 C
+ATOM 1281 CZ TYR A 421 55.259 65.952 46.129 1.00 18.54 C
+ATOM 1282 OH TYR A 421 55.415 64.929 45.235 1.00 17.50 O
+ATOM 1283 N TRP A 422 51.769 70.708 48.748 1.00 20.35 N
+ATOM 1284 CA TRP A 422 50.696 71.263 49.555 1.00 20.18 C
+ATOM 1285 C TRP A 422 50.239 70.126 50.448 1.00 19.44 C
+ATOM 1286 O TRP A 422 50.263 68.961 50.040 1.00 18.75 O
+ATOM 1287 CB TRP A 422 49.526 71.742 48.682 1.00 21.03 C
+ATOM 1288 CG TRP A 422 49.767 73.063 48.042 1.00 24.75 C
+ATOM 1289 CD1 TRP A 422 50.979 73.606 47.721 1.00 25.95 C
+ATOM 1290 CD2 TRP A 422 48.777 73.972 47.534 1.00 25.60 C
+ATOM 1291 NE1 TRP A 422 50.807 74.791 47.039 1.00 25.74 N
+ATOM 1292 CE2 TRP A 422 49.464 75.040 46.911 1.00 25.72 C
+ATOM 1293 CE3 TRP A 422 47.372 73.985 47.546 1.00 24.93 C
+ATOM 1294 CZ2 TRP A 422 48.798 76.108 46.292 1.00 24.30 C
+ATOM 1295 CZ3 TRP A 422 46.706 75.052 46.930 1.00 25.30 C
+ATOM 1296 CH2 TRP A 422 47.425 76.098 46.314 1.00 25.30 C
+ATOM 1297 N LEU A 423 49.821 70.483 51.657 1.00 20.27 N
+ATOM 1298 CA LEU A 423 49.351 69.527 52.636 1.00 21.39 C
+ATOM 1299 C LEU A 423 47.887 69.777 53.025 1.00 22.94 C
+ATOM 1300 O LEU A 423 47.557 70.818 53.593 1.00 22.15 O
+ATOM 1301 CB LEU A 423 50.234 69.610 53.877 1.00 18.43 C
+ATOM 1302 CG LEU A 423 49.764 68.706 55.016 1.00 17.98 C
+ATOM 1303 CD1 LEU A 423 50.112 67.246 54.667 1.00 14.98 C
+ATOM 1304 CD2 LEU A 423 50.419 69.152 56.334 1.00 15.97 C
+ATOM 1305 N PHE A 424 47.009 68.832 52.706 1.00 23.85 N
+ATOM 1306 CA PHE A 424 45.607 68.983 53.069 1.00 24.69 C
+ATOM 1307 C PHE A 424 45.363 68.188 54.355 1.00 25.99 C
+ATOM 1308 O PHE A 424 45.549 66.963 54.405 1.00 22.30 O
+ATOM 1309 CB PHE A 424 44.685 68.459 51.953 1.00 26.39 C
+ATOM 1310 CG PHE A 424 44.737 69.246 50.664 1.00 26.89 C
+ATOM 1311 CD1 PHE A 424 45.673 70.248 50.464 1.00 27.41 C
+ATOM 1312 CD2 PHE A 424 43.831 68.967 49.640 1.00 27.27 C
+ATOM 1313 CE1 PHE A 424 45.705 70.964 49.270 1.00 27.06 C
+ATOM 1314 CE2 PHE A 424 43.856 69.676 48.441 1.00 26.84 C
+ATOM 1315 CZ PHE A 424 44.794 70.677 48.258 1.00 26.43 C
+ATOM 1316 N LYS A 425 44.961 68.890 55.403 1.00 28.57 N
+ATOM 1317 CA LYS A 425 44.699 68.243 56.677 1.00 30.98 C
+ATOM 1318 C LYS A 425 43.215 68.329 57.005 1.00 30.85 C
+ATOM 1319 O LYS A 425 42.548 69.280 56.593 1.00 30.78 O
+ATOM 1320 CB LYS A 425 45.520 68.906 57.794 1.00 35.03 C
+ATOM 1321 CG LYS A 425 46.554 67.990 58.433 1.00 41.31 C
+ATOM 1322 CD LYS A 425 47.161 68.632 59.674 1.00 45.59 C
+ATOM 1323 CE LYS A 425 48.023 67.647 60.457 1.00 46.44 C
+ATOM 1324 NZ LYS A 425 48.570 68.247 61.707 1.00 46.77 N
+ATOM 1325 N GLY A 426 42.693 67.332 57.724 1.00 31.01 N
+ATOM 1326 CA GLY A 426 41.289 67.361 58.099 1.00 32.00 C
+ATOM 1327 C GLY A 426 40.678 66.015 58.446 1.00 35.55 C
+ATOM 1328 O GLY A 426 41.200 64.970 58.044 1.00 33.53 O
+ATOM 1329 N PRO A 427 39.558 66.007 59.191 1.00 37.74 N
+ATOM 1330 CA PRO A 427 38.878 64.770 59.586 1.00 38.27 C
+ATOM 1331 C PRO A 427 38.339 64.163 58.312 1.00 40.30 C
+ATOM 1332 O PRO A 427 38.594 64.692 57.239 1.00 38.21 O
+ATOM 1333 CB PRO A 427 37.748 65.264 60.483 1.00 38.50 C
+ATOM 1334 CG PRO A 427 38.251 66.583 60.996 1.00 42.02 C
+ATOM 1335 CD PRO A 427 38.875 67.178 59.764 1.00 38.73 C
+ATOM 1336 N ILE A 428 37.587 63.073 58.412 1.00 42.97 N
+ATOM 1337 CA ILE A 428 37.008 62.473 57.214 1.00 45.86 C
+ATOM 1338 C ILE A 428 35.765 63.295 56.881 1.00 47.57 C
+ATOM 1339 O ILE A 428 35.160 63.889 57.770 1.00 45.94 O
+ATOM 1340 CB ILE A 428 36.604 61.007 57.438 1.00 49.52 C
+ATOM 1341 CG1 ILE A 428 36.125 60.395 56.122 1.00 55.62 C
+ATOM 1342 CG2 ILE A 428 35.488 60.923 58.455 1.00 55.35 C
+ATOM 1343 CD1 ILE A 428 35.724 58.951 56.248 1.00 59.07 C
+ATOM 1344 N ASP A 429 35.399 63.341 55.604 1.00 49.26 N
+ATOM 1345 CA ASP A 429 34.240 64.108 55.144 1.00 48.28 C
+ATOM 1346 C ASP A 429 34.363 65.595 55.454 1.00 45.57 C
+ATOM 1347 O ASP A 429 33.440 66.222 55.989 1.00 42.03 O
+ATOM 1348 CB ASP A 429 32.944 63.550 55.739 1.00 56.60 C
+ATOM 1349 CG ASP A 429 32.586 62.189 55.170 1.00 69.73 C
+ATOM 1350 OD1 ASP A 429 32.899 61.948 53.986 1.00 76.05 O
+ATOM 1351 OD2 ASP A 429 31.979 61.367 55.892 1.00 76.93 O
+ATOM 1352 N SER A 430 35.516 66.155 55.109 1.00 41.37 N
+ATOM 1353 CA SER A 430 35.779 67.571 55.323 1.00 37.97 C
+ATOM 1354 C SER A 430 36.009 68.248 53.977 1.00 35.90 C
+ATOM 1355 O SER A 430 35.960 69.472 53.873 1.00 37.01 O
+ATOM 1356 CB SER A 430 37.005 67.749 56.219 1.00 38.99 C
+ATOM 1357 OG SER A 430 38.125 67.087 55.666 1.00 40.94 O
+ATOM 1358 N GLY A 431 36.268 67.441 52.951 1.00 33.34 N
+ATOM 1359 CA GLY A 431 36.483 67.974 51.616 1.00 30.32 C
+ATOM 1360 C GLY A 431 37.860 67.838 50.974 1.00 29.91 C
+ATOM 1361 O GLY A 431 37.956 68.001 49.753 1.00 26.81 O
+ATOM 1362 N LYS A 432 38.910 67.543 51.755 1.00 29.41 N
+ATOM 1363 CA LYS A 432 40.267 67.405 51.198 1.00 29.05 C
+ATOM 1364 C LYS A 432 40.411 66.294 50.165 1.00 28.61 C
+ATOM 1365 O LYS A 432 41.154 66.433 49.181 1.00 24.24 O
+ATOM 1366 CB LYS A 432 41.299 67.192 52.310 1.00 30.36 C
+ATOM 1367 CG LYS A 432 40.790 66.406 53.493 1.00 34.91 C
+ATOM 1368 CD LYS A 432 41.904 66.154 54.495 1.00 35.46 C
+ATOM 1369 CE LYS A 432 42.262 64.691 54.538 1.00 36.42 C
+ATOM 1370 NZ LYS A 432 41.189 63.851 55.148 1.00 35.30 N
+ATOM 1371 N THR A 433 39.699 65.196 50.397 1.00 29.25 N
+ATOM 1372 CA THR A 433 39.733 64.068 49.491 1.00 30.62 C
+ATOM 1373 C THR A 433 39.110 64.476 48.165 1.00 31.14 C
+ATOM 1374 O THR A 433 39.674 64.227 47.102 1.00 30.59 O
+ATOM 1375 CB THR A 433 38.969 62.887 50.076 1.00 33.21 C
+ATOM 1376 OG1 THR A 433 39.575 62.507 51.319 1.00 37.31 O
+ATOM 1377 CG2 THR A 433 38.997 61.709 49.120 1.00 37.45 C
+ATOM 1378 N THR A 434 37.956 65.127 48.227 1.00 30.55 N
+ATOM 1379 CA THR A 434 37.268 65.573 47.012 1.00 28.56 C
+ATOM 1380 C THR A 434 38.112 66.567 46.187 1.00 28.35 C
+ATOM 1381 O THR A 434 38.352 66.353 44.994 1.00 24.93 O
+ATOM 1382 CB THR A 434 35.913 66.235 47.350 1.00 29.51 C
+ATOM 1383 OG1 THR A 434 35.244 65.458 48.344 1.00 34.62 O
+ATOM 1384 CG2 THR A 434 35.029 66.286 46.125 1.00 31.28 C
+ATOM 1385 N LEU A 435 38.572 67.646 46.817 1.00 28.59 N
+ATOM 1386 CA LEU A 435 39.358 68.623 46.081 1.00 28.57 C
+ATOM 1387 C LEU A 435 40.631 67.974 45.542 1.00 29.16 C
+ATOM 1388 O LEU A 435 41.025 68.203 44.397 1.00 29.25 O
+ATOM 1389 CB LEU A 435 39.708 69.835 46.962 1.00 27.52 C
+ATOM 1390 CG LEU A 435 40.379 70.983 46.170 1.00 28.42 C
+ATOM 1391 CD1 LEU A 435 39.458 71.426 45.025 1.00 26.90 C
+ATOM 1392 CD2 LEU A 435 40.688 72.152 47.085 1.00 25.70 C
+ATOM 1393 N ALA A 436 41.264 67.149 46.365 1.00 29.72 N
+ATOM 1394 CA ALA A 436 42.495 66.489 45.955 1.00 30.34 C
+ATOM 1395 C ALA A 436 42.294 65.567 44.752 1.00 28.16 C
+ATOM 1396 O ALA A 436 43.224 65.334 43.965 1.00 26.88 O
+ATOM 1397 CB ALA A 436 43.080 65.719 47.125 1.00 32.21 C
+ATOM 1398 N ALA A 437 41.078 65.049 44.615 1.00 24.35 N
+ATOM 1399 CA ALA A 437 40.734 64.162 43.511 1.00 22.91 C
+ATOM 1400 C ALA A 437 40.536 64.974 42.228 1.00 24.56 C
+ATOM 1401 O ALA A 437 41.082 64.658 41.172 1.00 24.07 O
+ATOM 1402 CB ALA A 437 39.471 63.405 43.853 1.00 21.00 C
+ATOM 1403 N ALA A 438 39.743 66.028 42.325 1.00 24.75 N
+ATOM 1404 CA ALA A 438 39.500 66.888 41.181 1.00 24.65 C
+ATOM 1405 C ALA A 438 40.826 67.490 40.738 1.00 23.95 C
+ATOM 1406 O ALA A 438 41.113 67.570 39.548 1.00 23.71 O
+ATOM 1407 CB ALA A 438 38.523 67.997 41.567 1.00 24.36 C
+ATOM 1408 N LEU A 439 41.631 67.927 41.703 1.00 25.94 N
+ATOM 1409 CA LEU A 439 42.933 68.510 41.390 1.00 26.91 C
+ATOM 1410 C LEU A 439 43.793 67.499 40.616 1.00 28.33 C
+ATOM 1411 O LEU A 439 44.438 67.836 39.621 1.00 28.13 O
+ATOM 1412 CB LEU A 439 43.637 68.951 42.677 1.00 22.58 C
+ATOM 1413 CG LEU A 439 43.188 70.286 43.306 1.00 23.24 C
+ATOM 1414 CD1 LEU A 439 44.031 70.562 44.561 1.00 20.97 C
+ATOM 1415 CD2 LEU A 439 43.342 71.452 42.312 1.00 19.53 C
+ATOM 1416 N LEU A 440 43.766 66.250 41.067 1.00 33.02 N
+ATOM 1417 CA LEU A 440 44.522 65.200 40.407 1.00 35.72 C
+ATOM 1418 C LEU A 440 44.072 65.077 38.957 1.00 36.00 C
+ATOM 1419 O LEU A 440 44.883 65.115 38.041 1.00 34.66 O
+ATOM 1420 CB LEU A 440 44.308 63.865 41.112 1.00 36.87 C
+ATOM 1421 CG LEU A 440 45.604 63.094 41.349 1.00 40.35 C
+ATOM 1422 CD1 LEU A 440 45.275 61.700 41.830 1.00 39.22 C
+ATOM 1423 CD2 LEU A 440 46.432 63.046 40.063 1.00 40.57 C
+ATOM 1424 N GLU A 441 42.767 64.934 38.764 1.00 35.88 N
+ATOM 1425 CA GLU A 441 42.201 64.799 37.431 1.00 34.50 C
+ATOM 1426 C GLU A 441 42.362 66.077 36.608 1.00 33.18 C
+ATOM 1427 O GLU A 441 42.394 66.028 35.375 1.00 31.37 O
+ATOM 1428 CB GLU A 441 40.724 64.422 37.527 1.00 35.60 C
+ATOM 1429 CG GLU A 441 40.008 64.360 36.193 1.00 42.03 C
+ATOM 1430 CD GLU A 441 38.557 63.926 36.333 1.00 45.81 C
+ATOM 1431 OE1 GLU A 441 37.726 64.274 35.458 1.00 47.50 O
+ATOM 1432 OE2 GLU A 441 38.248 63.227 37.319 1.00 47.92 O
+ATOM 1433 N LEU A 442 42.471 67.221 37.278 1.00 31.15 N
+ATOM 1434 CA LEU A 442 42.631 68.473 36.551 1.00 29.12 C
+ATOM 1435 C LEU A 442 44.019 68.518 35.957 1.00 30.61 C
+ATOM 1436 O LEU A 442 44.211 69.034 34.863 1.00 30.16 O
+ATOM 1437 CB LEU A 442 42.444 69.680 37.473 1.00 26.28 C
+ATOM 1438 CG LEU A 442 42.524 71.083 36.841 1.00 24.61 C
+ATOM 1439 CD1 LEU A 442 41.331 71.321 35.914 1.00 21.36 C
+ATOM 1440 CD2 LEU A 442 42.525 72.151 37.942 1.00 23.29 C
+ATOM 1441 N CYS A 443 44.981 67.936 36.667 1.00 35.93 N
+ATOM 1442 CA CYS A 443 46.373 67.954 36.227 1.00 39.99 C
+ATOM 1443 C CYS A 443 46.940 66.675 35.659 1.00 41.61 C
+ATOM 1444 O CYS A 443 47.911 66.717 34.904 1.00 44.32 O
+ATOM 1445 CB CYS A 443 47.271 68.385 37.381 1.00 40.22 C
+ATOM 1446 SG CYS A 443 46.777 69.948 38.115 1.00 43.25 S
+ATOM 1447 N GLY A 444 46.342 65.545 36.011 1.00 43.27 N
+ATOM 1448 CA GLY A 444 46.866 64.277 35.544 1.00 44.42 C
+ATOM 1449 C GLY A 444 47.965 63.884 36.516 1.00 44.11 C
+ATOM 1450 O GLY A 444 48.694 64.735 37.020 1.00 47.39 O
+ATOM 1451 N GLY A 445 48.092 62.599 36.795 1.00 42.70 N
+ATOM 1452 CA GLY A 445 49.107 62.170 37.738 1.00 39.56 C
+ATOM 1453 C GLY A 445 48.577 61.042 38.597 1.00 39.53 C
+ATOM 1454 O GLY A 445 47.368 60.835 38.683 1.00 34.21 O
+ATOM 1455 N LYS A 446 49.467 60.306 39.245 1.00 40.27 N
+ATOM 1456 CA LYS A 446 49.014 59.191 40.058 1.00 39.57 C
+ATOM 1457 C LYS A 446 49.036 59.452 41.564 1.00 37.20 C
+ATOM 1458 O LYS A 446 49.789 60.296 42.070 1.00 32.87 O
+ATOM 1459 CB LYS A 446 49.849 57.946 39.736 1.00 46.40 C
+ATOM 1460 CG LYS A 446 49.968 57.632 38.239 1.00 60.03 C
+ATOM 1461 CD LYS A 446 48.628 57.281 37.597 1.00 66.89 C
+ATOM 1462 CE LYS A 446 48.106 55.925 38.070 1.00 71.12 C
+ATOM 1463 NZ LYS A 446 46.724 55.613 37.556 1.00 71.25 N
+ATOM 1464 N ALA A 447 48.175 58.733 42.272 1.00 35.71 N
+ATOM 1465 CA ALA A 447 48.125 58.832 43.719 1.00 34.62 C
+ATOM 1466 C ALA A 447 49.059 57.726 44.172 1.00 34.60 C
+ATOM 1467 O ALA A 447 49.251 56.744 43.446 1.00 36.80 O
+ATOM 1468 CB ALA A 447 46.724 58.570 44.221 1.00 34.78 C
+ATOM 1469 N LEU A 448 49.650 57.876 45.350 1.00 33.19 N
+ATOM 1470 CA LEU A 448 50.563 56.858 45.840 1.00 32.37 C
+ATOM 1471 C LEU A 448 50.241 56.600 47.308 1.00 33.49 C
+ATOM 1472 O LEU A 448 49.623 57.434 47.971 1.00 29.81 O
+ATOM 1473 CB LEU A 448 52.021 57.327 45.668 1.00 31.16 C
+ATOM 1474 CG LEU A 448 52.411 58.000 44.333 1.00 30.55 C
+ATOM 1475 CD1 LEU A 448 53.903 58.239 44.288 1.00 32.88 C
+ATOM 1476 CD2 LEU A 448 52.025 57.141 43.165 1.00 31.48 C
+ATOM 1477 N ASN A 449 50.642 55.440 47.815 1.00 35.09 N
+ATOM 1478 CA ASN A 449 50.383 55.101 49.207 1.00 35.57 C
+ATOM 1479 C ASN A 449 51.662 54.765 49.946 1.00 36.22 C
+ATOM 1480 O ASN A 449 52.248 53.716 49.734 1.00 35.06 O
+ATOM 1481 CB ASN A 449 49.425 53.928 49.300 1.00 38.86 C
+ATOM 1482 CG ASN A 449 49.323 53.403 50.693 1.00 44.90 C
+ATOM 1483 OD1 ASN A 449 50.193 52.669 51.143 1.00 48.69 O
+ATOM 1484 ND2 ASN A 449 48.276 53.800 51.406 1.00 49.22 N
+ATOM 1485 N VAL A 450 52.081 55.667 50.824 1.00 40.03 N
+ATOM 1486 CA VAL A 450 53.311 55.510 51.590 1.00 41.32 C
+ATOM 1487 C VAL A 450 53.086 54.799 52.924 1.00 43.14 C
+ATOM 1488 O VAL A 450 53.962 54.787 53.780 1.00 46.98 O
+ATOM 1489 CB VAL A 450 53.945 56.894 51.844 1.00 40.29 C
+ATOM 1490 CG1 VAL A 450 55.287 56.758 52.495 1.00 43.35 C
+ATOM 1491 CG2 VAL A 450 54.111 57.616 50.551 1.00 41.70 C
+ATOM 1492 N ASN A 451 51.906 54.212 53.103 1.00 49.01 N
+ATOM 1493 CA ASN A 451 51.595 53.496 54.337 1.00 53.05 C
+ATOM 1494 C ASN A 451 51.985 52.044 54.149 1.00 55.55 C
+ATOM 1495 O ASN A 451 51.192 51.131 54.370 1.00 60.01 O
+ATOM 1496 CB ASN A 451 50.110 53.611 54.647 1.00 51.69 C
+ATOM 1497 CG ASN A 451 49.703 55.025 55.000 1.00 50.87 C
+ATOM 1498 OD1 ASN A 451 50.163 55.580 55.996 1.00 48.70 O
+ATOM 1499 ND2 ASN A 451 48.836 55.619 54.183 1.00 49.34 N
+ATOM 1500 N LEU A 452 53.224 51.847 53.721 1.00 58.16 N
+ATOM 1501 CA LEU A 452 53.748 50.517 53.468 1.00 59.46 C
+ATOM 1502 C LEU A 452 55.043 50.256 54.227 1.00 60.46 C
+ATOM 1503 O LEU A 452 55.661 51.180 54.780 1.00 57.07 O
+ATOM 1504 CB LEU A 452 53.991 50.332 51.969 1.00 60.08 C
+ATOM 1505 CG LEU A 452 52.770 50.476 51.059 1.00 61.67 C
+ATOM 1506 CD1 LEU A 452 53.172 50.190 49.620 1.00 62.13 C
+ATOM 1507 CD2 LEU A 452 51.675 49.518 51.512 1.00 62.46 C
+ATOM 1508 N PRO A 453 55.457 48.979 54.285 1.00 59.30 N
+ATOM 1509 CA PRO A 453 56.693 48.617 54.985 1.00 58.73 C
+ATOM 1510 C PRO A 453 57.861 49.248 54.247 1.00 58.83 C
+ATOM 1511 O PRO A 453 57.962 49.132 53.025 1.00 57.49 O
+ATOM 1512 CB PRO A 453 56.691 47.097 54.909 1.00 58.78 C
+ATOM 1513 CG PRO A 453 55.210 46.783 54.935 1.00 58.69 C
+ATOM 1514 CD PRO A 453 54.686 47.775 53.931 1.00 57.45 C
+ATOM 1515 N LEU A 454 58.727 49.920 54.997 1.00 59.85 N
+ATOM 1516 CA LEU A 454 59.882 50.617 54.440 1.00 62.91 C
+ATOM 1517 C LEU A 454 60.562 49.959 53.232 1.00 68.80 C
+ATOM 1518 O LEU A 454 61.347 50.600 52.541 1.00 65.23 O
+ATOM 1519 CB LEU A 454 60.917 50.854 55.546 1.00 61.42 C
+ATOM 1520 CG LEU A 454 61.971 51.917 55.224 1.00 61.53 C
+ATOM 1521 CD1 LEU A 454 61.399 53.318 55.490 1.00 60.23 C
+ATOM 1522 CD2 LEU A 454 63.211 51.671 56.067 1.00 60.79 C
+ATOM 1523 N ASP A 455 60.259 48.690 52.975 1.00 77.64 N
+ATOM 1524 CA ASP A 455 60.858 47.960 51.857 1.00 81.59 C
+ATOM 1525 C ASP A 455 59.929 47.896 50.650 1.00 80.32 C
+ATOM 1526 O ASP A 455 60.384 47.777 49.512 1.00 72.73 O
+ATOM 1527 CB ASP A 455 61.207 46.539 52.290 1.00 97.12 C
+ATOM 1528 CG ASP A 455 61.694 46.476 53.719 1.00119.52 C
+ATOM 1529 OD1 ASP A 455 62.749 47.078 54.021 1.00131.43 O
+ATOM 1530 OD2 ASP A 455 61.012 45.828 54.543 1.00131.16 O
+ATOM 1531 N ARG A 456 58.625 47.958 50.909 1.00 77.80 N
+ATOM 1532 CA ARG A 456 57.620 47.924 49.851 1.00 73.16 C
+ATOM 1533 C ARG A 456 57.471 49.314 49.217 1.00 67.15 C
+ATOM 1534 O ARG A 456 56.876 49.469 48.151 1.00 67.41 O
+ATOM 1535 CB ARG A 456 56.267 47.465 50.417 1.00 78.55 C
+ATOM 1536 CG ARG A 456 56.309 46.146 51.183 1.00 89.39 C
+ATOM 1537 CD ARG A 456 55.161 45.218 50.769 1.00 94.81 C
+ATOM 1538 NE ARG A 456 55.130 43.977 51.549 1.00 97.11 N
+ATOM 1539 CZ ARG A 456 54.503 43.831 52.716 1.00 96.88 C
+ATOM 1540 NH1 ARG A 456 53.841 44.848 53.250 1.00 96.76 N
+ATOM 1541 NH2 ARG A 456 54.536 42.667 53.350 1.00 96.07 N
+ATOM 1542 N LEU A 457 58.031 50.316 49.886 1.00 60.00 N
+ATOM 1543 CA LEU A 457 57.973 51.705 49.437 1.00 55.70 C
+ATOM 1544 C LEU A 457 58.371 51.911 47.960 1.00 57.21 C
+ATOM 1545 O LEU A 457 57.507 52.104 47.104 1.00 57.05 O
+ATOM 1546 CB LEU A 457 58.856 52.563 50.360 1.00 46.96 C
+ATOM 1547 CG LEU A 457 58.436 53.997 50.720 1.00 38.08 C
+ATOM 1548 CD1 LEU A 457 56.939 54.042 50.994 1.00 33.65 C
+ATOM 1549 CD2 LEU A 457 59.221 54.485 51.939 1.00 31.33 C
+ATOM 1550 N ASN A 458 59.671 51.860 47.674 1.00 57.81 N
+ATOM 1551 CA ASN A 458 60.219 52.049 46.324 1.00 59.86 C
+ATOM 1552 C ASN A 458 59.365 51.619 45.119 1.00 63.06 C
+ATOM 1553 O ASN A 458 59.319 52.330 44.108 1.00 57.73 O
+ATOM 1554 CB ASN A 458 61.587 51.366 46.229 1.00 63.26 C
+ATOM 1555 CG ASN A 458 62.650 52.065 47.060 1.00 68.14 C
+ATOM 1556 OD1 ASN A 458 63.027 53.203 46.774 1.00 70.50 O
+ATOM 1557 ND2 ASN A 458 63.141 51.384 48.096 1.00 70.20 N
+ATOM 1558 N PHE A 459 58.721 50.454 45.207 1.00 66.24 N
+ATOM 1559 CA PHE A 459 57.866 49.950 44.119 1.00 67.09 C
+ATOM 1560 C PHE A 459 56.825 51.037 43.843 1.00 63.56 C
+ATOM 1561 O PHE A 459 56.664 51.503 42.714 1.00 61.87 O
+ATOM 1562 CB PHE A 459 57.173 48.652 44.577 1.00 76.64 C
+ATOM 1563 CG PHE A 459 56.452 47.892 43.482 1.00 90.28 C
+ATOM 1564 CD1 PHE A 459 57.129 47.452 42.344 1.00 95.54 C
+ATOM 1565 CD2 PHE A 459 55.109 47.538 43.637 1.00 95.52 C
+ATOM 1566 CE1 PHE A 459 56.476 46.665 41.380 1.00 97.44 C
+ATOM 1567 CE2 PHE A 459 54.451 46.752 42.681 1.00 97.48 C
+ATOM 1568 CZ PHE A 459 55.137 46.314 41.552 1.00 97.53 C
+ATOM 1569 N GLU A 460 56.142 51.438 44.915 1.00 59.04 N
+ATOM 1570 CA GLU A 460 55.105 52.462 44.881 1.00 55.09 C
+ATOM 1571 C GLU A 460 55.678 53.778 44.357 1.00 51.99 C
+ATOM 1572 O GLU A 460 55.151 54.351 43.406 1.00 52.49 O
+ATOM 1573 CB GLU A 460 54.538 52.659 46.294 1.00 55.44 C
+ATOM 1574 CG GLU A 460 53.302 53.547 46.392 1.00 54.52 C
+ATOM 1575 CD GLU A 460 51.999 52.774 46.265 1.00 54.08 C
+ATOM 1576 OE1 GLU A 460 51.831 51.774 47.001 1.00 54.18 O
+ATOM 1577 OE2 GLU A 460 51.139 53.168 45.443 1.00 52.93 O
+ATOM 1578 N LEU A 461 56.763 54.248 44.969 1.00 44.37 N
+ATOM 1579 CA LEU A 461 57.389 55.500 44.553 1.00 37.91 C
+ATOM 1580 C LEU A 461 57.727 55.536 43.062 1.00 36.85 C
+ATOM 1581 O LEU A 461 57.846 56.614 42.471 1.00 32.48 O
+ATOM 1582 CB LEU A 461 58.664 55.754 45.351 1.00 32.89 C
+ATOM 1583 CG LEU A 461 58.590 55.999 46.859 1.00 28.90 C
+ATOM 1584 CD1 LEU A 461 60.001 56.190 47.395 1.00 27.67 C
+ATOM 1585 CD2 LEU A 461 57.743 57.230 47.173 1.00 26.32 C
+ATOM 1586 N GLY A 462 57.882 54.360 42.456 1.00 35.79 N
+ATOM 1587 CA GLY A 462 58.212 54.287 41.040 1.00 37.35 C
+ATOM 1588 C GLY A 462 57.044 54.651 40.152 1.00 39.12 C
+ATOM 1589 O GLY A 462 57.226 55.044 39.003 1.00 38.84 O
+ATOM 1590 N VAL A 463 55.840 54.509 40.696 1.00 41.77 N
+ATOM 1591 CA VAL A 463 54.609 54.828 39.980 1.00 41.45 C
+ATOM 1592 C VAL A 463 54.616 56.255 39.448 1.00 39.76 C
+ATOM 1593 O VAL A 463 54.061 56.537 38.385 1.00 39.83 O
+ATOM 1594 CB VAL A 463 53.384 54.666 40.910 1.00 43.86 C
+ATOM 1595 CG1 VAL A 463 52.119 55.177 40.221 1.00 46.49 C
+ATOM 1596 CG2 VAL A 463 53.230 53.205 41.299 1.00 47.59 C
+ATOM 1597 N ALA A 464 55.253 57.142 40.204 1.00 36.92 N
+ATOM 1598 CA ALA A 464 55.345 58.557 39.872 1.00 35.38 C
+ATOM 1599 C ALA A 464 56.178 58.867 38.628 1.00 35.94 C
+ATOM 1600 O ALA A 464 56.262 60.018 38.198 1.00 37.48 O
+ATOM 1601 CB ALA A 464 55.897 59.300 41.056 1.00 32.61 C
+ATOM 1602 N ILE A 465 56.793 57.845 38.053 1.00 37.14 N
+ATOM 1603 CA ILE A 465 57.616 58.028 36.872 1.00 38.23 C
+ATOM 1604 C ILE A 465 56.850 58.674 35.730 1.00 41.29 C
+ATOM 1605 O ILE A 465 55.728 58.281 35.438 1.00 41.49 O
+ATOM 1606 CB ILE A 465 58.209 56.671 36.427 1.00 36.25 C
+ATOM 1607 CG1 ILE A 465 59.476 56.395 37.241 1.00 33.89 C
+ATOM 1608 CG2 ILE A 465 58.499 56.659 34.927 1.00 33.71 C
+ATOM 1609 CD1 ILE A 465 60.130 55.073 36.931 1.00 34.55 C
+ATOM 1610 N ASP A 466 57.465 59.671 35.094 1.00 45.08 N
+ATOM 1611 CA ASP A 466 56.865 60.382 33.962 1.00 48.18 C
+ATOM 1612 C ASP A 466 55.600 61.171 34.307 1.00 47.91 C
+ATOM 1613 O ASP A 466 54.991 61.770 33.418 1.00 49.70 O
+ATOM 1614 CB ASP A 466 56.548 59.394 32.829 1.00 54.16 C
+ATOM 1615 CG ASP A 466 57.796 58.922 32.087 1.00 62.44 C
+ATOM 1616 OD1 ASP A 466 58.811 58.634 32.754 1.00 65.42 O
+ATOM 1617 OD2 ASP A 466 57.760 58.827 30.837 1.00 65.51 O
+ATOM 1618 N GLN A 467 55.215 61.185 35.584 1.00 45.79 N
+ATOM 1619 CA GLN A 467 54.006 61.884 36.024 1.00 43.12 C
+ATOM 1620 C GLN A 467 54.139 63.399 36.176 1.00 41.81 C
+ATOM 1621 O GLN A 467 55.230 63.921 36.420 1.00 42.34 O
+ATOM 1622 CB GLN A 467 53.515 61.295 37.348 1.00 42.30 C
+ATOM 1623 CG GLN A 467 53.136 59.844 37.261 1.00 40.84 C
+ATOM 1624 CD GLN A 467 52.066 59.593 36.227 1.00 40.24 C
+ATOM 1625 OE1 GLN A 467 51.844 58.461 35.825 1.00 41.83 O
+ATOM 1626 NE2 GLN A 467 51.391 60.651 35.794 1.00 41.54 N
+ATOM 1627 N PHE A 468 53.011 64.096 36.037 1.00 39.15 N
+ATOM 1628 CA PHE A 468 52.978 65.551 36.163 1.00 36.91 C
+ATOM 1629 C PHE A 468 52.978 65.902 37.634 1.00 36.42 C
+ATOM 1630 O PHE A 468 53.745 66.747 38.090 1.00 38.57 O
+ATOM 1631 CB PHE A 468 51.720 66.127 35.528 1.00 34.90 C
+ATOM 1632 CG PHE A 468 51.656 67.627 35.569 1.00 35.97 C
+ATOM 1633 CD1 PHE A 468 52.425 68.396 34.695 1.00 36.53 C
+ATOM 1634 CD2 PHE A 468 50.825 68.278 36.479 1.00 37.27 C
+ATOM 1635 CE1 PHE A 468 52.365 69.797 34.718 1.00 36.31 C
+ATOM 1636 CE2 PHE A 468 50.756 69.680 36.516 1.00 36.90 C
+ATOM 1637 CZ PHE A 468 51.530 70.444 35.629 1.00 36.82 C
+ATOM 1638 N LEU A 469 52.092 65.262 38.381 1.00 34.84 N
+ATOM 1639 CA LEU A 469 52.029 65.510 39.808 1.00 33.60 C
+ATOM 1640 C LEU A 469 51.598 64.240 40.505 1.00 32.91 C
+ATOM 1641 O LEU A 469 51.053 63.319 39.895 1.00 33.15 O
+ATOM 1642 CB LEU A 469 51.059 66.660 40.140 1.00 31.26 C
+ATOM 1643 CG LEU A 469 49.548 66.444 40.041 1.00 26.83 C
+ATOM 1644 CD1 LEU A 469 49.030 65.673 41.233 1.00 27.39 C
+ATOM 1645 CD2 LEU A 469 48.875 67.787 40.004 1.00 27.02 C
+ATOM 1646 N VAL A 470 51.851 64.205 41.801 1.00 31.41 N
+ATOM 1647 CA VAL A 470 51.516 63.057 42.603 1.00 30.26 C
+ATOM 1648 C VAL A 470 50.679 63.476 43.811 1.00 29.10 C
+ATOM 1649 O VAL A 470 50.793 64.604 44.301 1.00 29.60 O
+ATOM 1650 CB VAL A 470 52.821 62.357 43.044 1.00 26.81 C
+ATOM 1651 CG1 VAL A 470 52.548 61.308 44.092 1.00 24.49 C
+ATOM 1652 CG2 VAL A 470 53.476 61.734 41.824 1.00 23.72 C
+ATOM 1653 N VAL A 471 49.805 62.575 44.254 1.00 26.97 N
+ATOM 1654 CA VAL A 471 48.995 62.834 45.429 1.00 26.13 C
+ATOM 1655 C VAL A 471 49.145 61.702 46.438 1.00 25.75 C
+ATOM 1656 O VAL A 471 48.664 60.592 46.211 1.00 25.66 O
+ATOM 1657 CB VAL A 471 47.520 62.954 45.099 1.00 25.15 C
+ATOM 1658 CG1 VAL A 471 46.728 62.939 46.391 1.00 23.20 C
+ATOM 1659 CG2 VAL A 471 47.250 64.247 44.327 1.00 23.35 C
+ATOM 1660 N PHE A 472 49.826 61.991 47.545 1.00 24.20 N
+ATOM 1661 CA PHE A 472 50.028 61.022 48.619 1.00 24.12 C
+ATOM 1662 C PHE A 472 48.729 60.942 49.426 1.00 26.41 C
+ATOM 1663 O PHE A 472 48.539 61.694 50.378 1.00 24.01 O
+ATOM 1664 CB PHE A 472 51.169 61.477 49.528 1.00 23.65 C
+ATOM 1665 CG PHE A 472 52.544 61.343 48.911 1.00 22.85 C
+ATOM 1666 CD1 PHE A 472 53.155 60.099 48.807 1.00 22.02 C
+ATOM 1667 CD2 PHE A 472 53.241 62.465 48.449 1.00 21.24 C
+ATOM 1668 CE1 PHE A 472 54.444 59.974 48.252 1.00 21.27 C
+ATOM 1669 CE2 PHE A 472 54.532 62.343 47.894 1.00 19.87 C
+ATOM 1670 CZ PHE A 472 55.125 61.106 47.798 1.00 19.62 C
+ATOM 1671 N GLU A 473 47.853 60.018 49.036 1.00 31.45 N
+ATOM 1672 CA GLU A 473 46.556 59.829 49.675 1.00 35.63 C
+ATOM 1673 C GLU A 473 46.561 59.340 51.109 1.00 39.67 C
+ATOM 1674 O GLU A 473 47.068 58.266 51.405 1.00 37.76 O
+ATOM 1675 CB GLU A 473 45.701 58.850 48.887 1.00 37.58 C
+ATOM 1676 CG GLU A 473 45.139 59.355 47.603 1.00 43.95 C
+ATOM 1677 CD GLU A 473 44.237 58.314 46.968 1.00 47.85 C
+ATOM 1678 OE1 GLU A 473 44.166 57.189 47.513 1.00 48.92 O
+ATOM 1679 OE2 GLU A 473 43.607 58.611 45.931 1.00 48.93 O
+ATOM 1680 N ASP A 474 45.944 60.124 51.984 1.00 46.13 N
+ATOM 1681 CA ASP A 474 45.810 59.799 53.398 1.00 49.06 C
+ATOM 1682 C ASP A 474 47.011 59.131 54.043 1.00 46.09 C
+ATOM 1683 O ASP A 474 47.059 57.909 54.203 1.00 44.28 O
+ATOM 1684 CB ASP A 474 44.574 58.928 53.611 1.00 60.47 C
+ATOM 1685 CG ASP A 474 44.394 58.533 55.057 1.00 75.79 C
+ATOM 1686 OD1 ASP A 474 44.505 59.421 55.935 1.00 82.76 O
+ATOM 1687 OD2 ASP A 474 44.140 57.336 55.312 1.00 83.07 O
+ATOM 1688 N VAL A 475 47.980 59.952 54.420 1.00 40.05 N
+ATOM 1689 CA VAL A 475 49.174 59.465 55.064 1.00 33.79 C
+ATOM 1690 C VAL A 475 48.797 59.277 56.514 1.00 34.24 C
+ATOM 1691 O VAL A 475 48.030 60.063 57.062 1.00 31.38 O
+ATOM 1692 CB VAL A 475 50.296 60.498 54.946 1.00 30.34 C
+ATOM 1693 CG1 VAL A 475 51.589 59.950 55.559 1.00 28.93 C
+ATOM 1694 CG2 VAL A 475 50.489 60.858 53.475 1.00 28.17 C
+ATOM 1695 N LYS A 476 49.319 58.235 57.139 1.00 35.78 N
+ATOM 1696 CA LYS A 476 49.007 57.992 58.541 1.00 36.45 C
+ATOM 1697 C LYS A 476 50.241 58.127 59.420 1.00 36.10 C
+ATOM 1698 O LYS A 476 51.339 57.743 59.023 1.00 32.93 O
+ATOM 1699 CB LYS A 476 48.366 56.610 58.702 1.00 41.99 C
+ATOM 1700 CG LYS A 476 46.973 56.519 58.087 1.00 51.65 C
+ATOM 1701 CD LYS A 476 46.336 55.161 58.324 1.00 57.32 C
+ATOM 1702 CE LYS A 476 47.140 54.039 57.666 1.00 60.18 C
+ATOM 1703 NZ LYS A 476 46.566 52.682 57.929 1.00 59.98 N
+ATOM 1704 N GLY A 477 50.047 58.693 60.610 1.00 37.04 N
+ATOM 1705 CA GLY A 477 51.147 58.891 61.540 1.00 39.86 C
+ATOM 1706 C GLY A 477 51.077 58.002 62.767 1.00 42.88 C
+ATOM 1707 O GLY A 477 50.322 57.032 62.797 1.00 41.28 O
+ATOM 1708 N THR A 478 51.862 58.332 63.785 1.00 51.32 N
+ATOM 1709 CA THR A 478 51.868 57.536 64.999 1.00 58.31 C
+ATOM 1710 C THR A 478 51.035 58.159 66.110 1.00 61.69 C
+ATOM 1711 O THR A 478 49.811 57.996 66.144 1.00 67.19 O
+ATOM 1712 CB THR A 478 53.299 57.317 65.505 1.00 59.03 C
+ATOM 1713 OG1 THR A 478 54.046 56.610 64.511 1.00 60.57 O
+ATOM 1714 CG2 THR A 478 53.293 56.489 66.784 1.00 62.62 C
+ATOM 1715 N GLY A 479 51.703 58.867 67.012 1.00 64.56 N
+ATOM 1716 CA GLY A 479 51.026 59.507 68.124 1.00 67.85 C
+ATOM 1717 C GLY A 479 49.540 59.241 68.338 1.00 67.85 C
+ATOM 1718 O GLY A 479 49.129 58.156 68.753 1.00 72.71 O
+ATOM 1719 N GLY A 480 48.742 60.261 68.037 1.00 66.17 N
+ATOM 1720 CA GLY A 480 47.296 60.245 68.208 1.00 58.48 C
+ATOM 1721 C GLY A 480 46.328 59.077 68.065 1.00 56.07 C
+ATOM 1722 O GLY A 480 45.471 59.097 67.187 1.00 49.76 O
+ATOM 1723 N GLU A 481 46.409 58.088 68.944 1.00 54.74 N
+ATOM 1724 CA GLU A 481 45.477 56.963 68.890 1.00 54.80 C
+ATOM 1725 C GLU A 481 44.373 57.227 69.922 1.00 53.97 C
+ATOM 1726 O GLU A 481 43.368 56.506 69.974 1.00 49.04 O
+ATOM 1727 CB GLU A 481 46.182 55.642 69.220 1.00 61.10 C
+ATOM 1728 CG GLU A 481 46.777 55.596 70.624 1.00 76.28 C
+ATOM 1729 CD GLU A 481 47.046 54.186 71.119 1.00 82.33 C
+ATOM 1730 OE1 GLU A 481 47.865 53.478 70.491 1.00 84.24 O
+ATOM 1731 OE2 GLU A 481 46.437 53.790 72.141 1.00 83.95 O
+ATOM 1732 N SER A 482 44.574 58.268 70.738 1.00 51.75 N
+ATOM 1733 CA SER A 482 43.618 58.670 71.779 1.00 48.00 C
+ATOM 1734 C SER A 482 42.416 59.372 71.166 1.00 47.38 C
+ATOM 1735 O SER A 482 41.348 59.458 71.773 1.00 45.39 O
+ATOM 1736 CB SER A 482 44.281 59.620 72.762 1.00 46.01 C
+ATOM 1737 OG SER A 482 45.393 59.005 73.358 1.00 52.47 O
+ATOM 1738 N ARG A 483 42.605 59.881 69.956 1.00 48.45 N
+ATOM 1739 CA ARG A 483 41.547 60.567 69.255 1.00 49.36 C
+ATOM 1740 C ARG A 483 40.994 59.660 68.161 1.00 51.97 C
+ATOM 1741 O ARG A 483 40.381 60.126 67.196 1.00 52.34 O
+ATOM 1742 CB ARG A 483 42.084 61.870 68.671 1.00 47.17 C
+ATOM 1743 CG ARG A 483 42.790 62.747 69.693 1.00 46.02 C
+ATOM 1744 CD ARG A 483 44.093 63.238 69.109 1.00 46.36 C
+ATOM 1745 NE ARG A 483 43.864 63.868 67.813 1.00 46.74 N
+ATOM 1746 CZ ARG A 483 44.810 64.094 66.910 1.00 46.12 C
+ATOM 1747 NH1 ARG A 483 46.060 63.736 67.157 1.00 46.83 N
+ATOM 1748 NH2 ARG A 483 44.507 64.687 65.764 1.00 47.46 N
+ATOM 1749 N ASP A 484 41.223 58.359 68.321 1.00 57.25 N
+ATOM 1750 CA ASP A 484 40.725 57.357 67.385 1.00 61.32 C
+ATOM 1751 C ASP A 484 41.302 57.440 65.982 1.00 59.15 C
+ATOM 1752 O ASP A 484 40.569 57.534 64.996 1.00 60.35 O
+ATOM 1753 CB ASP A 484 39.193 57.422 67.321 1.00 70.82 C
+ATOM 1754 CG ASP A 484 38.544 57.235 68.682 1.00 80.85 C
+ATOM 1755 OD1 ASP A 484 38.734 56.159 69.288 1.00 85.18 O
+ATOM 1756 OD2 ASP A 484 37.841 58.161 69.143 1.00 84.62 O
+ATOM 1757 N LEU A 485 42.624 57.412 65.899 1.00 54.38 N
+ATOM 1758 CA LEU A 485 43.311 57.464 64.614 1.00 47.43 C
+ATOM 1759 C LEU A 485 44.378 56.369 64.565 1.00 44.51 C
+ATOM 1760 O LEU A 485 45.301 56.348 65.381 1.00 46.56 O
+ATOM 1761 CB LEU A 485 43.953 58.839 64.419 1.00 41.09 C
+ATOM 1762 CG LEU A 485 42.978 60.014 64.356 1.00 31.95 C
+ATOM 1763 CD1 LEU A 485 43.749 61.307 64.142 1.00 28.14 C
+ATOM 1764 CD2 LEU A 485 41.993 59.784 63.218 1.00 28.85 C
+ATOM 1765 N PRO A 486 44.253 55.442 63.607 1.00 46.51 N
+ATOM 1766 CA PRO A 486 45.163 54.313 63.397 1.00 46.48 C
+ATOM 1767 C PRO A 486 46.618 54.706 63.183 1.00 46.46 C
+ATOM 1768 O PRO A 486 46.918 55.566 62.356 1.00 49.52 O
+ATOM 1769 CB PRO A 486 44.577 53.633 62.165 1.00 47.65 C
+ATOM 1770 CG PRO A 486 43.125 53.934 62.273 1.00 48.15 C
+ATOM 1771 CD PRO A 486 43.132 55.385 62.656 1.00 47.49 C
+ATOM 1772 N SER A 487 47.518 54.062 63.922 1.00 45.52 N
+ATOM 1773 CA SER A 487 48.952 54.323 63.794 1.00 42.96 C
+ATOM 1774 C SER A 487 49.490 53.704 62.510 1.00 42.14 C
+ATOM 1775 O SER A 487 49.234 52.531 62.224 1.00 39.93 O
+ATOM 1776 CB SER A 487 49.710 53.749 64.996 1.00 40.77 C
+ATOM 1777 OG SER A 487 49.359 54.433 66.189 1.00 42.39 O
+ATOM 1778 N GLY A 488 50.227 54.496 61.735 1.00 40.33 N
+ATOM 1779 CA GLY A 488 50.785 54.007 60.484 1.00 40.29 C
+ATOM 1780 C GLY A 488 52.188 54.530 60.332 1.00 40.43 C
+ATOM 1781 O GLY A 488 52.613 55.354 61.142 1.00 42.17 O
+ATOM 1782 N GLN A 489 52.917 54.073 59.319 1.00 41.28 N
+ATOM 1783 CA GLN A 489 54.293 54.542 59.143 1.00 41.70 C
+ATOM 1784 C GLN A 489 54.471 55.519 57.978 1.00 40.95 C
+ATOM 1785 O GLN A 489 55.585 55.966 57.704 1.00 39.93 O
+ATOM 1786 CB GLN A 489 55.262 53.354 58.977 1.00 43.14 C
+ATOM 1787 CG GLN A 489 55.499 52.490 60.237 1.00 43.91 C
+ATOM 1788 CD GLN A 489 56.128 53.247 61.416 1.00 44.91 C
+ATOM 1789 OE1 GLN A 489 57.201 53.852 61.299 1.00 43.41 O
+ATOM 1790 NE2 GLN A 489 55.453 53.203 62.563 1.00 45.44 N
+ATOM 1791 N GLY A 490 53.371 55.851 57.307 1.00 40.36 N
+ATOM 1792 CA GLY A 490 53.417 56.770 56.181 1.00 38.73 C
+ATOM 1793 C GLY A 490 54.117 58.083 56.480 1.00 37.84 C
+ATOM 1794 O GLY A 490 55.038 58.471 55.763 1.00 37.01 O
+ATOM 1795 N ILE A 491 53.678 58.776 57.528 1.00 37.89 N
+ATOM 1796 CA ILE A 491 54.302 60.044 57.898 1.00 40.48 C
+ATOM 1797 C ILE A 491 55.789 59.821 58.060 1.00 42.37 C
+ATOM 1798 O ILE A 491 56.612 60.572 57.533 1.00 43.73 O
+ATOM 1799 CB ILE A 491 53.798 60.579 59.247 1.00 36.60 C
+ATOM 1800 CG1 ILE A 491 52.342 60.996 59.130 1.00 32.93 C
+ATOM 1801 CG2 ILE A 491 54.645 61.776 59.679 1.00 31.50 C
+ATOM 1802 CD1 ILE A 491 52.143 62.144 58.200 1.00 31.28 C
+ATOM 1803 N ASN A 492 56.113 58.774 58.810 1.00 46.99 N
+ATOM 1804 CA ASN A 492 57.488 58.421 59.087 1.00 49.22 C
+ATOM 1805 C ASN A 492 58.288 58.241 57.820 1.00 48.68 C
+ATOM 1806 O ASN A 492 59.442 58.646 57.756 1.00 49.53 O
+ATOM 1807 CB ASN A 492 57.549 57.147 59.903 1.00 52.76 C
+ATOM 1808 CG ASN A 492 58.620 57.203 60.935 1.00 57.16 C
+ATOM 1809 OD1 ASN A 492 58.485 57.914 61.932 1.00 59.59 O
+ATOM 1810 ND2 ASN A 492 59.716 56.480 60.701 1.00 59.18 N
+ATOM 1811 N ASN A 493 57.676 57.629 56.814 1.00 47.70 N
+ATOM 1812 CA ASN A 493 58.354 57.415 55.539 1.00 46.10 C
+ATOM 1813 C ASN A 493 58.580 58.738 54.818 1.00 45.42 C
+ATOM 1814 O ASN A 493 59.672 58.993 54.330 1.00 44.39 O
+ATOM 1815 CB ASN A 493 57.550 56.469 54.637 1.00 44.35 C
+ATOM 1816 CG ASN A 493 57.441 55.071 55.208 1.00 42.14 C
+ATOM 1817 OD1 ASN A 493 58.304 54.641 55.971 1.00 42.16 O
+ATOM 1818 ND2 ASN A 493 56.392 54.349 54.830 1.00 39.23 N
+ATOM 1819 N LEU A 494 57.549 59.575 54.747 1.00 45.56 N
+ATOM 1820 CA LEU A 494 57.686 60.868 54.087 1.00 45.58 C
+ATOM 1821 C LEU A 494 58.887 61.628 54.637 1.00 46.12 C
+ATOM 1822 O LEU A 494 59.647 62.233 53.874 1.00 45.94 O
+ATOM 1823 CB LEU A 494 56.423 61.719 54.270 1.00 45.72 C
+ATOM 1824 CG LEU A 494 55.250 61.490 53.310 1.00 44.50 C
+ATOM 1825 CD1 LEU A 494 54.083 62.371 53.719 1.00 43.23 C
+ATOM 1826 CD2 LEU A 494 55.681 61.798 51.877 1.00 43.55 C
+ATOM 1827 N ASP A 495 59.063 61.598 55.956 1.00 46.69 N
+ATOM 1828 CA ASP A 495 60.186 62.297 56.564 1.00 48.62 C
+ATOM 1829 C ASP A 495 61.506 61.712 56.061 1.00 51.10 C
+ATOM 1830 O ASP A 495 62.560 62.346 56.166 1.00 48.01 O
+ATOM 1831 CB ASP A 495 60.123 62.205 58.084 1.00 50.47 C
+ATOM 1832 CG ASP A 495 60.492 63.517 58.759 1.00 54.31 C
+ATOM 1833 OD1 ASP A 495 61.458 64.165 58.312 1.00 55.61 O
+ATOM 1834 OD2 ASP A 495 59.821 63.901 59.741 1.00 57.91 O
+ATOM 1835 N ASN A 496 61.445 60.502 55.512 1.00 52.10 N
+ATOM 1836 CA ASN A 496 62.632 59.850 54.973 1.00 50.67 C
+ATOM 1837 C ASN A 496 62.658 60.034 53.465 1.00 46.98 C
+ATOM 1838 O ASN A 496 63.410 59.363 52.773 1.00 45.88 O
+ATOM 1839 CB ASN A 496 62.620 58.355 55.280 1.00 58.59 C
+ATOM 1840 CG ASN A 496 62.272 58.061 56.718 1.00 69.59 C
+ATOM 1841 OD1 ASN A 496 62.747 58.733 57.638 1.00 75.17 O
+ATOM 1842 ND2 ASN A 496 61.443 57.044 56.926 1.00 76.13 N
+ATOM 1843 N LEU A 497 61.817 60.926 52.954 1.00 42.93 N
+ATOM 1844 CA LEU A 497 61.765 61.178 51.520 1.00 42.16 C
+ATOM 1845 C LEU A 497 61.956 62.662 51.196 1.00 48.34 C
+ATOM 1846 O LEU A 497 61.498 63.151 50.158 1.00 44.98 O
+ATOM 1847 CB LEU A 497 60.442 60.678 50.945 1.00 34.22 C
+ATOM 1848 CG LEU A 497 60.168 59.174 51.035 1.00 26.79 C
+ATOM 1849 CD1 LEU A 497 58.732 58.897 50.583 1.00 24.13 C
+ATOM 1850 CD2 LEU A 497 61.172 58.406 50.188 1.00 23.58 C
+ATOM 1851 N ARG A 498 62.647 63.369 52.089 1.00 57.36 N
+ATOM 1852 CA ARG A 498 62.928 64.786 51.898 1.00 62.61 C
+ATOM 1853 C ARG A 498 63.463 65.024 50.490 1.00 62.12 C
+ATOM 1854 O ARG A 498 63.126 66.019 49.865 1.00 54.57 O
+ATOM 1855 CB ARG A 498 63.950 65.269 52.927 1.00 74.56 C
+ATOM 1856 CG ARG A 498 65.308 64.623 52.779 1.00 99.94 C
+ATOM 1857 CD ARG A 498 66.380 65.434 53.479 1.00112.42 C
+ATOM 1858 NE ARG A 498 67.722 64.897 53.248 1.00116.52 N
+ATOM 1859 CZ ARG A 498 68.466 65.154 52.173 1.00117.25 C
+ATOM 1860 NH1 ARG A 498 68.009 65.949 51.213 1.00117.33 N
+ATOM 1861 NH2 ARG A 498 69.672 64.612 52.058 1.00116.82 N
+ATOM 1862 N ASP A 499 64.287 64.098 49.999 1.00 59.10 N
+ATOM 1863 CA ASP A 499 64.870 64.181 48.656 1.00 54.82 C
+ATOM 1864 C ASP A 499 63.790 64.255 47.584 1.00 50.55 C
+ATOM 1865 O ASP A 499 63.803 65.126 46.708 1.00 45.50 O
+ATOM 1866 CB ASP A 499 65.733 62.951 48.382 1.00 65.08 C
+ATOM 1867 CG ASP A 499 67.164 63.141 48.805 1.00 81.10 C
+ATOM 1868 OD1 ASP A 499 67.389 63.808 49.835 1.00 89.63 O
+ATOM 1869 OD2 ASP A 499 68.063 62.614 48.112 1.00 88.92 O
+ATOM 1870 N TYR A 500 62.859 63.317 47.653 1.00 42.63 N
+ATOM 1871 CA TYR A 500 61.787 63.274 46.691 1.00 35.02 C
+ATOM 1872 C TYR A 500 60.927 64.530 46.778 1.00 32.25 C
+ATOM 1873 O TYR A 500 60.728 65.222 45.784 1.00 29.31 O
+ATOM 1874 CB TYR A 500 60.921 62.029 46.923 1.00 35.29 C
+ATOM 1875 CG TYR A 500 61.664 60.720 46.749 1.00 38.26 C
+ATOM 1876 CD1 TYR A 500 62.622 60.305 47.678 1.00 39.95 C
+ATOM 1877 CD2 TYR A 500 61.448 59.920 45.625 1.00 39.68 C
+ATOM 1878 CE1 TYR A 500 63.352 59.127 47.484 1.00 40.39 C
+ATOM 1879 CE2 TYR A 500 62.169 58.745 45.420 1.00 40.34 C
+ATOM 1880 CZ TYR A 500 63.122 58.356 46.349 1.00 40.13 C
+ATOM 1881 OH TYR A 500 63.875 57.227 46.117 1.00 39.16 O
+ATOM 1882 N LEU A 501 60.436 64.836 47.970 1.00 30.01 N
+ATOM 1883 CA LEU A 501 59.558 65.983 48.147 1.00 31.18 C
+ATOM 1884 C LEU A 501 60.010 67.339 47.596 1.00 35.38 C
+ATOM 1885 O LEU A 501 59.345 67.905 46.720 1.00 33.81 O
+ATOM 1886 CB LEU A 501 59.185 66.125 49.626 1.00 28.48 C
+ATOM 1887 CG LEU A 501 58.211 65.083 50.188 1.00 26.35 C
+ATOM 1888 CD1 LEU A 501 58.113 65.252 51.691 1.00 25.75 C
+ATOM 1889 CD2 LEU A 501 56.845 65.231 49.534 1.00 23.28 C
+ATOM 1890 N ASP A 502 61.123 67.875 48.088 1.00 42.45 N
+ATOM 1891 CA ASP A 502 61.547 69.181 47.603 1.00 47.26 C
+ATOM 1892 C ASP A 502 62.357 69.171 46.321 1.00 46.26 C
+ATOM 1893 O ASP A 502 62.699 70.223 45.796 1.00 45.47 O
+ATOM 1894 CB ASP A 502 62.295 69.939 48.693 1.00 57.98 C
+ATOM 1895 CG ASP A 502 63.244 69.067 49.445 1.00 71.37 C
+ATOM 1896 OD1 ASP A 502 63.870 68.203 48.800 1.00 78.52 O
+ATOM 1897 OD2 ASP A 502 63.370 69.251 50.672 1.00 78.06 O
+ATOM 1898 N GLY A 503 62.650 67.979 45.823 1.00 45.47 N
+ATOM 1899 CA GLY A 503 63.392 67.832 44.586 1.00 43.33 C
+ATOM 1900 C GLY A 503 64.374 68.907 44.132 1.00 42.02 C
+ATOM 1901 O GLY A 503 64.105 69.641 43.173 1.00 41.29 O
+ATOM 1902 N SER A 504 65.521 68.993 44.803 1.00 40.38 N
+ATOM 1903 CA SER A 504 66.558 69.953 44.425 1.00 39.58 C
+ATOM 1904 C SER A 504 67.484 69.251 43.428 1.00 40.11 C
+ATOM 1905 O SER A 504 68.134 69.883 42.600 1.00 39.58 O
+ATOM 1906 CB SER A 504 67.348 70.397 45.660 1.00 38.19 C
+ATOM 1907 OG SER A 504 66.546 71.186 46.526 1.00 33.86 O
+ATOM 1908 N VAL A 505 67.516 67.926 43.518 1.00 39.44 N
+ATOM 1909 CA VAL A 505 68.333 67.089 42.645 1.00 38.88 C
+ATOM 1910 C VAL A 505 67.493 65.882 42.196 1.00 40.02 C
+ATOM 1911 O VAL A 505 66.513 65.521 42.852 1.00 37.04 O
+ATOM 1912 CB VAL A 505 69.609 66.583 43.389 1.00 40.41 C
+ATOM 1913 CG1 VAL A 505 70.589 65.948 42.399 1.00 41.74 C
+ATOM 1914 CG2 VAL A 505 70.281 67.740 44.118 1.00 41.22 C
+ATOM 1915 N LYS A 506 67.877 65.270 41.076 1.00 40.38 N
+ATOM 1916 CA LYS A 506 67.165 64.109 40.540 1.00 39.28 C
+ATOM 1917 C LYS A 506 67.172 62.880 41.450 1.00 38.39 C
+ATOM 1918 O LYS A 506 67.885 62.827 42.457 1.00 37.68 O
+ATOM 1919 CB LYS A 506 67.718 63.743 39.157 1.00 40.31 C
+ATOM 1920 CG LYS A 506 67.047 64.513 38.026 1.00 42.43 C
+ATOM 1921 CD LYS A 506 67.786 64.376 36.715 1.00 43.43 C
+ATOM 1922 CE LYS A 506 69.015 65.286 36.677 1.00 46.06 C
+ATOM 1923 NZ LYS A 506 70.051 64.953 37.712 1.00 47.04 N
+ATOM 1924 N VAL A 507 66.370 61.887 41.074 1.00 38.97 N
+ATOM 1925 CA VAL A 507 66.222 60.655 41.849 1.00 40.05 C
+ATOM 1926 C VAL A 507 65.988 59.456 40.920 1.00 42.50 C
+ATOM 1927 O VAL A 507 65.560 59.615 39.773 1.00 41.16 O
+ATOM 1928 CB VAL A 507 65.028 60.809 42.854 1.00 37.56 C
+ATOM 1929 CG1 VAL A 507 64.604 59.465 43.401 1.00 36.32 C
+ATOM 1930 CG2 VAL A 507 65.425 61.733 44.008 1.00 34.76 C
+ATOM 1931 N ASN A 508 66.287 58.258 41.411 1.00 48.25 N
+ATOM 1932 CA ASN A 508 66.096 57.037 40.622 1.00 50.66 C
+ATOM 1933 C ASN A 508 64.786 56.333 41.004 1.00 49.60 C
+ATOM 1934 O ASN A 508 64.545 56.012 42.173 1.00 46.68 O
+ATOM 1935 CB ASN A 508 67.278 56.083 40.829 1.00 58.34 C
+ATOM 1936 CG ASN A 508 68.620 56.724 40.500 1.00 68.38 C
+ATOM 1937 OD1 ASN A 508 69.648 56.048 40.467 1.00 74.62 O
+ATOM 1938 ND2 ASN A 508 68.616 58.030 40.264 1.00 73.70 N
+ATOM 1939 N LEU A 509 63.940 56.099 40.008 1.00 49.76 N
+ATOM 1940 CA LEU A 509 62.648 55.459 40.230 1.00 50.49 C
+ATOM 1941 C LEU A 509 62.626 54.055 39.639 1.00 58.34 C
+ATOM 1942 O LEU A 509 63.294 53.797 38.639 1.00 54.20 O
+ATOM 1943 CB LEU A 509 61.547 56.328 39.616 1.00 44.00 C
+ATOM 1944 CG LEU A 509 60.784 57.250 40.576 1.00 40.53 C
+ATOM 1945 CD1 LEU A 509 61.705 57.803 41.649 1.00 36.48 C
+ATOM 1946 CD2 LEU A 509 60.112 58.362 39.776 1.00 37.88 C
+ATOM 1947 N GLU A 510 61.848 53.156 40.244 1.00 74.63 N
+ATOM 1948 CA GLU A 510 61.798 51.769 39.778 1.00 85.59 C
+ATOM 1949 C GLU A 510 60.443 51.230 39.323 1.00 89.60 C
+ATOM 1950 O GLU A 510 59.388 51.784 39.652 1.00 87.02 O
+ATOM 1951 CB GLU A 510 62.336 50.844 40.868 1.00 95.97 C
+ATOM 1952 CG GLU A 510 63.502 51.418 41.640 1.00120.13 C
+ATOM 1953 CD GLU A 510 64.108 50.419 42.601 1.00130.61 C
+ATOM 1954 OE1 GLU A 510 63.354 49.818 43.393 1.00134.64 O
+ATOM 1955 OE2 GLU A 510 65.343 50.240 42.568 1.00134.85 O
+ATOM 1956 N LYS A 511 60.508 50.125 38.575 1.00100.17 N
+ATOM 1957 CA LYS A 511 59.350 49.410 38.029 1.00106.24 C
+ATOM 1958 C LYS A 511 59.866 48.086 37.454 1.00107.46 C
+ATOM 1959 O LYS A 511 61.075 47.862 37.418 1.00113.88 O
+ATOM 1960 CB LYS A 511 58.677 50.236 36.926 1.00111.48 C
+ATOM 1961 CG LYS A 511 57.475 49.560 36.266 1.00119.83 C
+ATOM 1962 CD LYS A 511 56.830 50.478 35.236 1.00123.38 C
+ATOM 1963 CE LYS A 511 55.726 49.777 34.455 1.00123.83 C
+ATOM 1964 NZ LYS A 511 55.093 50.692 33.458 1.00124.02 N
+ATOM 1965 N LYS A 512 58.960 47.216 37.010 1.00114.93 N
+ATOM 1966 CA LYS A 512 59.337 45.917 36.443 1.00119.36 C
+ATOM 1967 C LYS A 512 60.455 45.210 37.204 1.00124.50 C
+ATOM 1968 O LYS A 512 61.200 44.416 36.625 1.00129.08 O
+ATOM 1969 CB LYS A 512 59.760 46.064 34.978 1.00113.46 C
+ATOM 1970 CG LYS A 512 58.603 46.162 34.008 1.00103.38 C
+ATOM 1971 CD LYS A 512 57.711 44.931 34.088 1.00 98.05 C
+ATOM 1972 CE LYS A 512 56.553 45.025 33.102 1.00 96.64 C
+ATOM 1973 NZ LYS A 512 55.562 43.926 33.276 1.00 96.01 N
+ATOM 1974 N HIS A 513 60.567 45.502 38.496 1.00134.30 N
+ATOM 1975 CA HIS A 513 61.585 44.897 39.351 1.00140.56 C
+ATOM 1976 C HIS A 513 63.012 45.218 38.889 1.00137.57 C
+ATOM 1977 O HIS A 513 63.886 44.351 38.899 1.00143.66 O
+ATOM 1978 CB HIS A 513 61.380 43.375 39.416 1.00146.45 C
+ATOM 1979 CG HIS A 513 61.756 42.766 40.734 1.00151.21 C
+ATOM 1980 ND1 HIS A 513 63.030 42.853 41.258 1.00152.84 N
+ATOM 1981 CD2 HIS A 513 61.025 42.073 41.637 1.00152.67 C
+ATOM 1982 CE1 HIS A 513 63.064 42.238 42.429 1.00153.27 C
+ATOM 1983 NE2 HIS A 513 61.859 41.757 42.681 1.00153.36 N
+ATOM 1984 N LEU A 514 63.232 46.470 38.489 1.00130.89 N
+ATOM 1985 CA LEU A 514 64.537 46.961 38.035 1.00126.77 C
+ATOM 1986 C LEU A 514 64.455 48.481 37.846 1.00126.70 C
+ATOM 1987 O LEU A 514 63.378 49.014 37.581 1.00128.13 O
+ATOM 1988 CB LEU A 514 64.956 46.286 36.718 1.00118.24 C
+ATOM 1989 CG LEU A 514 65.558 44.872 36.762 1.00104.96 C
+ATOM 1990 CD1 LEU A 514 65.826 44.400 35.344 1.00 97.34 C
+ATOM 1991 CD2 LEU A 514 66.854 44.860 37.569 1.00 97.63 C
+ATOM 1992 N ASN A 515 65.585 49.174 37.984 1.00123.51 N
+ATOM 1993 CA ASN A 515 65.626 50.636 37.849 1.00119.16 C
+ATOM 1994 C ASN A 515 65.289 51.190 36.458 1.00114.13 C
+ATOM 1995 O ASN A 515 65.841 50.750 35.446 1.00113.33 O
+ATOM 1996 CB ASN A 515 67.003 51.172 38.278 1.00117.39 C
+ATOM 1997 CG ASN A 515 67.146 51.301 39.792 1.00115.54 C
+ATOM 1998 OD1 ASN A 515 66.924 50.343 40.534 1.00115.73 O
+ATOM 1999 ND2 ASN A 515 67.525 52.491 40.252 1.00115.50 N
+ATOM 2000 N LYS A 516 64.373 52.159 36.425 1.00103.46 N
+ATOM 2001 CA LYS A 516 63.964 52.810 35.180 1.00100.63 C
+ATOM 2002 C LYS A 516 64.426 54.272 35.247 1.00 99.40 C
+ATOM 2003 O LYS A 516 65.570 54.554 35.617 1.00 97.71 O
+ATOM 2004 CB LYS A 516 62.435 52.776 34.997 1.00101.97 C
+ATOM 2005 CG LYS A 516 61.733 51.489 35.408 1.00 97.89 C
+ATOM 2006 CD LYS A 516 62.306 50.244 34.732 1.00 95.97 C
+ATOM 2007 CE LYS A 516 62.030 50.186 33.236 1.00 93.83 C
+ATOM 2008 NZ LYS A 516 62.525 48.891 32.674 1.00 93.26 N
+ATOM 2009 N ARG A 517 63.520 55.194 34.919 1.00 89.03 N
+ATOM 2010 CA ARG A 517 63.809 56.626 34.911 1.00 76.68 C
+ATOM 2011 C ARG A 517 64.425 57.264 36.154 1.00 72.12 C
+ATOM 2012 O ARG A 517 64.208 56.825 37.286 1.00 59.09 O
+ATOM 2013 CB ARG A 517 62.546 57.403 34.548 1.00 74.59 C
+ATOM 2014 CG ARG A 517 62.178 57.324 33.083 1.00 80.58 C
+ATOM 2015 CD ARG A 517 61.724 58.688 32.601 1.00 85.08 C
+ATOM 2016 NE ARG A 517 62.715 59.716 32.912 1.00 86.38 N
+ATOM 2017 CZ ARG A 517 62.517 61.020 32.747 1.00 86.90 C
+ATOM 2018 NH1 ARG A 517 61.360 61.468 32.273 1.00 86.20 N
+ATOM 2019 NH2 ARG A 517 63.479 61.876 33.060 1.00 87.30 N
+ATOM 2020 N THR A 518 65.204 58.315 35.904 1.00 64.50 N
+ATOM 2021 CA THR A 518 65.865 59.105 36.939 1.00 62.32 C
+ATOM 2022 C THR A 518 65.354 60.513 36.653 1.00 60.46 C
+ATOM 2023 O THR A 518 65.369 60.954 35.501 1.00 60.26 O
+ATOM 2024 CB THR A 518 67.404 59.095 36.788 1.00 66.62 C
+ATOM 2025 OG1 THR A 518 67.890 57.748 36.846 1.00 74.37 O
+ATOM 2026 CG2 THR A 518 68.051 59.911 37.902 1.00 73.41 C
+ATOM 2027 N GLN A 519 64.911 61.226 37.683 1.00 56.28 N
+ATOM 2028 CA GLN A 519 64.355 62.557 37.458 1.00 52.54 C
+ATOM 2029 C GLN A 519 64.072 63.284 38.755 1.00 50.17 C
+ATOM 2030 O GLN A 519 64.417 62.813 39.840 1.00 48.30 O
+ATOM 2031 CB GLN A 519 63.030 62.419 36.722 1.00 52.33 C
+ATOM 2032 CG GLN A 519 62.001 61.673 37.574 1.00 51.32 C
+ATOM 2033 CD GLN A 519 60.667 61.487 36.888 1.00 51.87 C
+ATOM 2034 OE1 GLN A 519 60.553 60.728 35.927 1.00 51.92 O
+ATOM 2035 NE2 GLN A 519 59.644 62.184 37.378 1.00 50.98 N
+ATOM 2036 N ILE A 520 63.424 64.438 38.620 1.00 44.28 N
+ATOM 2037 CA ILE A 520 63.024 65.229 39.773 1.00 39.05 C
+ATOM 2038 C ILE A 520 61.704 64.596 40.176 1.00 36.48 C
+ATOM 2039 O ILE A 520 60.799 64.504 39.345 1.00 34.52 O
+ATOM 2040 CB ILE A 520 62.776 66.699 39.382 1.00 38.42 C
+ATOM 2041 CG1 ILE A 520 64.091 67.362 38.973 1.00 37.72 C
+ATOM 2042 CG2 ILE A 520 62.161 67.458 40.547 1.00 37.50 C
+ATOM 2043 CD1 ILE A 520 65.095 67.491 40.100 1.00 37.25 C
+ATOM 2044 N PHE A 521 61.590 64.131 41.419 1.00 31.08 N
+ATOM 2045 CA PHE A 521 60.333 63.514 41.833 1.00 29.96 C
+ATOM 2046 C PHE A 521 59.279 64.566 41.526 1.00 29.94 C
+ATOM 2047 O PHE A 521 59.554 65.762 41.625 1.00 31.08 O
+ATOM 2048 CB PHE A 521 60.329 63.167 43.323 1.00 27.52 C
+ATOM 2049 CG PHE A 521 59.216 62.243 43.717 1.00 25.56 C
+ATOM 2050 CD1 PHE A 521 59.156 60.953 43.210 1.00 25.34 C
+ATOM 2051 CD2 PHE A 521 58.222 62.653 44.600 1.00 25.75 C
+ATOM 2052 CE1 PHE A 521 58.106 60.068 43.584 1.00 25.11 C
+ATOM 2053 CE2 PHE A 521 57.172 61.778 44.977 1.00 24.84 C
+ATOM 2054 CZ PHE A 521 57.119 60.491 44.468 1.00 23.47 C
+ATOM 2055 N PRO A 522 58.064 64.148 41.140 1.00 26.85 N
+ATOM 2056 CA PRO A 522 57.076 65.181 40.836 1.00 26.10 C
+ATOM 2057 C PRO A 522 56.546 65.881 42.066 1.00 24.34 C
+ATOM 2058 O PRO A 522 56.656 65.367 43.181 1.00 24.30 O
+ATOM 2059 CB PRO A 522 55.977 64.418 40.089 1.00 25.17 C
+ATOM 2060 CG PRO A 522 56.653 63.151 39.640 1.00 26.78 C
+ATOM 2061 CD PRO A 522 57.547 62.819 40.794 1.00 25.02 C
+ATOM 2062 N PRO A 523 55.997 67.091 41.872 1.00 21.36 N
+ATOM 2063 CA PRO A 523 55.416 67.916 42.938 1.00 21.51 C
+ATOM 2064 C PRO A 523 54.017 67.354 43.220 1.00 21.96 C
+ATOM 2065 O PRO A 523 53.515 66.524 42.441 1.00 20.82 O
+ATOM 2066 CB PRO A 523 55.358 69.295 42.301 1.00 20.72 C
+ATOM 2067 CG PRO A 523 55.081 68.969 40.837 1.00 18.36 C
+ATOM 2068 CD PRO A 523 56.034 67.824 40.590 1.00 19.50 C
+ATOM 2069 N GLY A 524 53.390 67.780 44.316 1.00 21.33 N
+ATOM 2070 CA GLY A 524 52.066 67.262 44.605 1.00 22.84 C
+ATOM 2071 C GLY A 524 51.373 67.638 45.900 1.00 23.58 C
+ATOM 2072 O GLY A 524 51.606 68.697 46.478 1.00 23.73 O
+ATOM 2073 N ILE A 525 50.502 66.749 46.356 1.00 24.15 N
+ATOM 2074 CA ILE A 525 49.736 66.989 47.569 1.00 26.08 C
+ATOM 2075 C ILE A 525 49.805 65.801 48.524 1.00 24.70 C
+ATOM 2076 O ILE A 525 49.888 64.642 48.109 1.00 27.53 O
+ATOM 2077 CB ILE A 525 48.226 67.196 47.250 1.00 28.51 C
+ATOM 2078 CG1 ILE A 525 48.048 68.207 46.123 1.00 31.26 C
+ATOM 2079 CG2 ILE A 525 47.487 67.663 48.490 1.00 32.03 C
+ATOM 2080 CD1 ILE A 525 46.625 68.310 45.620 1.00 30.68 C
+ATOM 2081 N VAL A 526 49.766 66.099 49.809 1.00 21.78 N
+ATOM 2082 CA VAL A 526 49.735 65.065 50.812 1.00 21.78 C
+ATOM 2083 C VAL A 526 48.401 65.303 51.520 1.00 27.72 C
+ATOM 2084 O VAL A 526 48.135 66.404 52.020 1.00 22.81 O
+ATOM 2085 CB VAL A 526 50.908 65.194 51.819 1.00 19.35 C
+ATOM 2086 CG1 VAL A 526 50.679 64.285 53.015 1.00 15.90 C
+ATOM 2087 CG2 VAL A 526 52.205 64.789 51.158 1.00 14.77 C
+ATOM 2088 N THR A 527 47.545 64.286 51.508 1.00 35.58 N
+ATOM 2089 CA THR A 527 46.246 64.350 52.174 1.00 38.56 C
+ATOM 2090 C THR A 527 46.446 63.643 53.519 1.00 37.40 C
+ATOM 2091 O THR A 527 46.868 62.483 53.571 1.00 36.32 O
+ATOM 2092 CB THR A 527 45.170 63.638 51.351 1.00 47.75 C
+ATOM 2093 OG1 THR A 527 44.166 63.121 52.228 1.00 63.01 O
+ATOM 2094 CG2 THR A 527 45.770 62.515 50.554 1.00 62.65 C
+ATOM 2095 N MET A 528 46.139 64.339 54.608 1.00 37.10 N
+ATOM 2096 CA MET A 528 46.370 63.785 55.937 1.00 36.44 C
+ATOM 2097 C MET A 528 45.167 63.883 56.884 1.00 37.86 C
+ATOM 2098 O MET A 528 44.286 64.727 56.701 1.00 42.10 O
+ATOM 2099 CB MET A 528 47.582 64.511 56.514 1.00 32.35 C
+ATOM 2100 CG MET A 528 48.172 63.935 57.758 1.00 23.82 C
+ATOM 2101 SD MET A 528 49.416 65.106 58.228 1.00 13.96 S
+ATOM 2102 CE MET A 528 50.696 64.566 57.210 1.00 15.97 C
+ATOM 2103 N ASN A 529 45.155 63.049 57.920 1.00 41.20 N
+ATOM 2104 CA ASN A 529 44.031 63.024 58.847 1.00 43.96 C
+ATOM 2105 C ASN A 529 44.166 63.719 60.201 1.00 45.12 C
+ATOM 2106 O ASN A 529 43.329 63.508 61.077 1.00 44.03 O
+ATOM 2107 CB ASN A 529 43.607 61.579 59.097 1.00 46.83 C
+ATOM 2108 CG ASN A 529 42.128 61.449 59.434 1.00 48.41 C
+ATOM 2109 OD1 ASN A 529 41.591 62.174 60.278 1.00 48.15 O
+ATOM 2110 ND2 ASN A 529 41.463 60.512 58.771 1.00 50.44 N
+ATOM 2111 N GLU A 530 45.203 64.523 60.390 1.00 45.45 N
+ATOM 2112 CA GLU A 530 45.388 65.255 61.649 1.00 47.15 C
+ATOM 2113 C GLU A 530 46.342 64.645 62.661 1.00 47.08 C
+ATOM 2114 O GLU A 530 46.170 64.814 63.870 1.00 47.20 O
+ATOM 2115 CB GLU A 530 44.044 65.549 62.349 1.00 47.01 C
+ATOM 2116 CG GLU A 530 43.201 66.604 61.645 1.00 53.61 C
+ATOM 2117 CD GLU A 530 42.154 67.237 62.545 1.00 56.97 C
+ATOM 2118 OE1 GLU A 530 41.139 66.567 62.858 1.00 57.40 O
+ATOM 2119 OE2 GLU A 530 42.353 68.412 62.935 1.00 58.52 O
+ATOM 2120 N TYR A 531 47.350 63.933 62.171 1.00 46.85 N
+ATOM 2121 CA TYR A 531 48.348 63.369 63.059 1.00 45.57 C
+ATOM 2122 C TYR A 531 49.344 64.500 63.247 1.00 44.83 C
+ATOM 2123 O TYR A 531 49.431 65.400 62.408 1.00 44.60 O
+ATOM 2124 CB TYR A 531 49.069 62.195 62.409 1.00 46.77 C
+ATOM 2125 CG TYR A 531 48.178 61.058 62.002 1.00 48.77 C
+ATOM 2126 CD1 TYR A 531 47.438 61.116 60.823 1.00 49.31 C
+ATOM 2127 CD2 TYR A 531 48.062 59.920 62.806 1.00 49.59 C
+ATOM 2128 CE1 TYR A 531 46.596 60.062 60.450 1.00 49.74 C
+ATOM 2129 CE2 TYR A 531 47.224 58.862 62.445 1.00 49.46 C
+ATOM 2130 CZ TYR A 531 46.494 58.942 61.266 1.00 49.67 C
+ATOM 2131 OH TYR A 531 45.658 57.908 60.908 1.00 49.67 O
+ATOM 2132 N SER A 532 50.084 64.465 64.348 1.00 43.29 N
+ATOM 2133 CA SER A 532 51.092 65.485 64.608 1.00 41.35 C
+ATOM 2134 C SER A 532 52.144 65.320 63.523 1.00 40.13 C
+ATOM 2135 O SER A 532 52.379 64.202 63.048 1.00 39.40 O
+ATOM 2136 CB SER A 532 51.722 65.261 65.982 1.00 40.32 C
+ATOM 2137 OG SER A 532 52.071 63.897 66.144 1.00 41.16 O
+ATOM 2138 N VAL A 533 52.770 66.424 63.130 1.00 38.95 N
+ATOM 2139 CA VAL A 533 53.790 66.374 62.089 1.00 39.14 C
+ATOM 2140 C VAL A 533 55.148 66.848 62.581 1.00 39.44 C
+ATOM 2141 O VAL A 533 55.250 67.851 63.289 1.00 41.56 O
+ATOM 2142 CB VAL A 533 53.382 67.232 60.881 1.00 37.85 C
+ATOM 2143 CG1 VAL A 533 54.481 67.213 59.835 1.00 35.93 C
+ATOM 2144 CG2 VAL A 533 52.068 66.710 60.297 1.00 34.58 C
+ATOM 2145 N PRO A 534 56.213 66.116 62.228 1.00 41.51 N
+ATOM 2146 CA PRO A 534 57.568 66.492 62.648 1.00 42.78 C
+ATOM 2147 C PRO A 534 57.961 67.789 61.958 1.00 43.86 C
+ATOM 2148 O PRO A 534 57.706 67.947 60.766 1.00 42.90 O
+ATOM 2149 CB PRO A 534 58.415 65.313 62.173 1.00 43.01 C
+ATOM 2150 CG PRO A 534 57.450 64.157 62.215 1.00 43.46 C
+ATOM 2151 CD PRO A 534 56.204 64.773 61.622 1.00 42.88 C
+ATOM 2152 N LYS A 535 58.577 68.711 62.700 1.00 44.01 N
+ATOM 2153 CA LYS A 535 58.991 70.002 62.141 1.00 42.60 C
+ATOM 2154 C LYS A 535 59.841 69.855 60.868 1.00 41.40 C
+ATOM 2155 O LYS A 535 59.851 70.744 60.011 1.00 35.53 O
+ATOM 2156 CB LYS A 535 59.773 70.819 63.177 1.00 46.80 C
+ATOM 2157 CG LYS A 535 61.278 70.588 63.148 1.00 58.71 C
+ATOM 2158 CD LYS A 535 62.039 71.857 62.759 1.00 64.10 C
+ATOM 2159 CE LYS A 535 63.535 71.576 62.572 1.00 66.00 C
+ATOM 2160 NZ LYS A 535 64.341 72.793 62.237 1.00 66.30 N
+ATOM 2161 N THR A 536 60.562 68.746 60.742 1.00 38.83 N
+ATOM 2162 CA THR A 536 61.377 68.547 59.552 1.00 37.41 C
+ATOM 2163 C THR A 536 60.487 68.245 58.339 1.00 38.15 C
+ATOM 2164 O THR A 536 60.824 68.573 57.197 1.00 37.52 O
+ATOM 2165 CB THR A 536 62.401 67.403 59.768 1.00 39.04 C
+ATOM 2166 OG1 THR A 536 61.718 66.175 60.054 1.00 43.35 O
+ATOM 2167 CG2 THR A 536 63.307 67.740 60.939 1.00 42.50 C
+ATOM 2168 N LEU A 537 59.341 67.622 58.593 1.00 40.53 N
+ATOM 2169 CA LEU A 537 58.409 67.283 57.524 1.00 41.01 C
+ATOM 2170 C LEU A 537 57.581 68.505 57.157 1.00 39.31 C
+ATOM 2171 O LEU A 537 57.428 68.856 55.990 1.00 39.46 O
+ATOM 2172 CB LEU A 537 57.482 66.157 57.978 1.00 44.91 C
+ATOM 2173 CG LEU A 537 56.472 65.695 56.927 1.00 49.35 C
+ATOM 2174 CD1 LEU A 537 57.199 65.183 55.698 1.00 50.49 C
+ATOM 2175 CD2 LEU A 537 55.592 64.611 57.517 1.00 51.83 C
+ATOM 2176 N GLN A 538 57.039 69.141 58.182 1.00 36.88 N
+ATOM 2177 CA GLN A 538 56.222 70.328 58.019 1.00 35.62 C
+ATOM 2178 C GLN A 538 56.879 71.296 57.039 1.00 35.85 C
+ATOM 2179 O GLN A 538 56.214 71.893 56.183 1.00 34.43 O
+ATOM 2180 CB GLN A 538 56.043 70.997 59.385 1.00 34.70 C
+ATOM 2181 CG GLN A 538 54.984 72.075 59.439 1.00 33.65 C
+ATOM 2182 CD GLN A 538 53.622 71.580 58.972 1.00 34.08 C
+ATOM 2183 OE1 GLN A 538 53.117 70.553 59.445 1.00 33.95 O
+ATOM 2184 NE2 GLN A 538 53.017 72.315 58.043 1.00 34.77 N
+ATOM 2185 N ALA A 539 58.197 71.421 57.169 1.00 36.25 N
+ATOM 2186 CA ALA A 539 59.004 72.321 56.350 1.00 36.95 C
+ATOM 2187 C ALA A 539 59.006 72.011 54.865 1.00 38.74 C
+ATOM 2188 O ALA A 539 59.353 72.866 54.051 1.00 39.34 O
+ATOM 2189 CB ALA A 539 60.433 72.329 56.863 1.00 34.84 C
+ATOM 2190 N ARG A 540 58.623 70.796 54.501 1.00 42.74 N
+ATOM 2191 CA ARG A 540 58.620 70.426 53.097 1.00 44.73 C
+ATOM 2192 C ARG A 540 57.359 70.922 52.415 1.00 43.40 C
+ATOM 2193 O ARG A 540 57.282 70.963 51.186 1.00 42.87 O
+ATOM 2194 CB ARG A 540 58.755 68.914 52.962 1.00 50.46 C
+ATOM 2195 CG ARG A 540 59.901 68.354 53.790 1.00 58.88 C
+ATOM 2196 CD ARG A 540 61.226 69.004 53.438 1.00 62.11 C
+ATOM 2197 NE ARG A 540 62.248 68.680 54.425 1.00 63.75 N
+ATOM 2198 CZ ARG A 540 63.553 68.841 54.232 1.00 65.44 C
+ATOM 2199 NH1 ARG A 540 64.005 69.325 53.084 1.00 66.14 N
+ATOM 2200 NH2 ARG A 540 64.411 68.505 55.184 1.00 66.03 N
+ATOM 2201 N PHE A 541 56.375 71.318 53.214 1.00 39.87 N
+ATOM 2202 CA PHE A 541 55.136 71.832 52.651 1.00 36.33 C
+ATOM 2203 C PHE A 541 55.140 73.351 52.616 1.00 34.81 C
+ATOM 2204 O PHE A 541 55.252 74.009 53.648 1.00 35.51 O
+ATOM 2205 CB PHE A 541 53.940 71.326 53.447 1.00 33.49 C
+ATOM 2206 CG PHE A 541 53.853 69.837 53.490 1.00 32.84 C
+ATOM 2207 CD1 PHE A 541 54.276 69.135 54.610 1.00 32.20 C
+ATOM 2208 CD2 PHE A 541 53.401 69.129 52.389 1.00 31.04 C
+ATOM 2209 CE1 PHE A 541 54.254 67.747 54.631 1.00 31.47 C
+ATOM 2210 CE2 PHE A 541 53.377 67.755 52.398 1.00 30.76 C
+ATOM 2211 CZ PHE A 541 53.804 67.056 53.520 1.00 31.43 C
+ATOM 2212 N VAL A 542 55.031 73.903 51.415 1.00 34.35 N
+ATOM 2213 CA VAL A 542 55.026 75.342 51.250 1.00 36.52 C
+ATOM 2214 C VAL A 542 53.661 75.932 51.561 1.00 36.17 C
+ATOM 2215 O VAL A 542 53.522 77.138 51.770 1.00 39.69 O
+ATOM 2216 CB VAL A 542 55.423 75.739 49.814 1.00 36.15 C
+ATOM 2217 CG1 VAL A 542 54.362 75.288 48.821 1.00 32.62 C
+ATOM 2218 CG2 VAL A 542 55.645 77.250 49.749 1.00 34.52 C
+ATOM 2219 N LYS A 543 52.653 75.070 51.598 1.00 35.60 N
+ATOM 2220 CA LYS A 543 51.287 75.501 51.862 1.00 34.36 C
+ATOM 2221 C LYS A 543 50.495 74.419 52.594 1.00 33.74 C
+ATOM 2222 O LYS A 543 50.662 73.238 52.335 1.00 33.88 O
+ATOM 2223 CB LYS A 543 50.589 75.849 50.538 1.00 31.85 C
+ATOM 2224 CG LYS A 543 49.143 76.192 50.720 1.00 31.38 C
+ATOM 2225 CD LYS A 543 48.645 77.191 49.700 1.00 30.19 C
+ATOM 2226 CE LYS A 543 47.261 77.724 50.100 1.00 30.75 C
+ATOM 2227 NZ LYS A 543 46.804 78.891 49.274 1.00 32.15 N
+ATOM 2228 N GLN A 544 49.650 74.820 53.530 1.00 31.21 N
+ATOM 2229 CA GLN A 544 48.819 73.859 54.250 1.00 29.21 C
+ATOM 2230 C GLN A 544 47.384 74.350 54.269 1.00 29.28 C
+ATOM 2231 O GLN A 544 47.122 75.523 54.532 1.00 27.66 O
+ATOM 2232 CB GLN A 544 49.295 73.654 55.686 1.00 27.97 C
+ATOM 2233 CG GLN A 544 48.314 72.844 56.520 1.00 29.44 C
+ATOM 2234 CD GLN A 544 48.879 72.413 57.866 1.00 31.20 C
+ATOM 2235 OE1 GLN A 544 48.159 71.885 58.714 1.00 32.47 O
+ATOM 2236 NE2 GLN A 544 50.170 72.634 58.066 1.00 32.33 N
+ATOM 2237 N ILE A 545 46.457 73.450 53.972 1.00 28.83 N
+ATOM 2238 CA ILE A 545 45.047 73.795 53.957 1.00 29.08 C
+ATOM 2239 C ILE A 545 44.301 72.919 54.947 1.00 29.59 C
+ATOM 2240 O ILE A 545 44.323 71.695 54.838 1.00 30.57 O
+ATOM 2241 CB ILE A 545 44.427 73.591 52.556 1.00 29.20 C
+ATOM 2242 CG1 ILE A 545 45.134 74.479 51.528 1.00 28.79 C
+ATOM 2243 CG2 ILE A 545 42.928 73.900 52.603 1.00 29.95 C
+ATOM 2244 CD1 ILE A 545 44.548 74.369 50.133 1.00 28.13 C
+ATOM 2245 N ASP A 546 43.643 73.549 55.914 1.00 31.76 N
+ATOM 2246 CA ASP A 546 42.887 72.811 56.909 1.00 31.89 C
+ATOM 2247 C ASP A 546 41.421 72.727 56.540 1.00 31.01 C
+ATOM 2248 O ASP A 546 40.743 73.744 56.364 1.00 31.17 O
+ATOM 2249 CB ASP A 546 43.048 73.447 58.288 1.00 34.08 C
+ATOM 2250 CG ASP A 546 44.450 73.301 58.818 1.00 37.82 C
+ATOM 2251 OD1 ASP A 546 44.970 72.171 58.747 1.00 40.48 O
+ATOM 2252 OD2 ASP A 546 45.032 74.297 59.301 1.00 39.17 O
+ATOM 2253 N PHE A 547 40.941 71.497 56.408 1.00 30.35 N
+ATOM 2254 CA PHE A 547 39.553 71.275 56.071 1.00 30.61 C
+ATOM 2255 C PHE A 547 38.798 70.885 57.326 1.00 33.73 C
+ATOM 2256 O PHE A 547 39.272 70.082 58.132 1.00 31.81 O
+ATOM 2257 CB PHE A 547 39.414 70.177 55.004 1.00 27.96 C
+ATOM 2258 CG PHE A 547 40.089 70.510 53.707 1.00 28.24 C
+ATOM 2259 CD1 PHE A 547 41.481 70.391 53.574 1.00 27.61 C
+ATOM 2260 CD2 PHE A 547 39.345 70.984 52.627 1.00 26.45 C
+ATOM 2261 CE1 PHE A 547 42.129 70.745 52.381 1.00 26.76 C
+ATOM 2262 CE2 PHE A 547 39.971 71.345 51.424 1.00 25.92 C
+ATOM 2263 CZ PHE A 547 41.363 71.228 51.296 1.00 27.03 C
+ATOM 2264 N ARG A 548 37.634 71.494 57.500 1.00 39.02 N
+ATOM 2265 CA ARG A 548 36.781 71.203 58.633 1.00 42.85 C
+ATOM 2266 C ARG A 548 35.409 70.955 58.037 1.00 42.12 C
+ATOM 2267 O ARG A 548 34.932 71.724 57.194 1.00 40.04 O
+ATOM 2268 CB ARG A 548 36.766 72.383 59.598 1.00 48.70 C
+ATOM 2269 CG ARG A 548 38.156 72.695 60.088 1.00 62.54 C
+ATOM 2270 CD ARG A 548 38.266 74.050 60.735 1.00 69.07 C
+ATOM 2271 NE ARG A 548 39.663 74.473 60.774 1.00 70.85 N
+ATOM 2272 CZ ARG A 548 40.092 75.589 61.349 1.00 72.04 C
+ATOM 2273 NH1 ARG A 548 39.226 76.403 61.944 1.00 72.77 N
+ATOM 2274 NH2 ARG A 548 41.386 75.892 61.323 1.00 71.92 N
+ATOM 2275 N PRO A 549 34.767 69.851 58.435 1.00 41.98 N
+ATOM 2276 CA PRO A 549 33.446 69.578 57.880 1.00 39.73 C
+ATOM 2277 C PRO A 549 32.502 70.708 58.230 1.00 38.80 C
+ATOM 2278 O PRO A 549 32.520 71.214 59.355 1.00 37.73 O
+ATOM 2279 CB PRO A 549 33.062 68.265 58.544 1.00 39.46 C
+ATOM 2280 CG PRO A 549 34.387 67.609 58.766 1.00 42.04 C
+ATOM 2281 CD PRO A 549 35.207 68.746 59.299 1.00 41.06 C
+ATOM 2282 N LYS A 550 31.706 71.122 57.250 1.00 37.00 N
+ATOM 2283 CA LYS A 550 30.742 72.190 57.451 1.00 37.15 C
+ATOM 2284 C LYS A 550 29.329 71.617 57.283 1.00 40.74 C
+ATOM 2285 O LYS A 550 29.078 70.789 56.408 1.00 35.41 O
+ATOM 2286 CB LYS A 550 30.988 73.335 56.460 1.00 36.51 C
+ATOM 2287 CG LYS A 550 32.344 74.020 56.596 1.00 39.58 C
+ATOM 2288 CD LYS A 550 32.471 75.102 55.538 1.00 43.40 C
+ATOM 2289 CE LYS A 550 33.909 75.557 55.295 1.00 43.64 C
+ATOM 2290 NZ LYS A 550 33.949 76.515 54.131 1.00 42.42 N
+ATOM 2291 N ASP A 551 28.413 72.071 58.133 1.00 45.20 N
+ATOM 2292 CA ASP A 551 27.035 71.601 58.132 1.00 45.25 C
+ATOM 2293 C ASP A 551 26.234 71.996 56.911 1.00 41.40 C
+ATOM 2294 O ASP A 551 25.554 71.154 56.318 1.00 37.47 O
+ATOM 2295 CB ASP A 551 26.331 72.095 59.394 1.00 58.06 C
+ATOM 2296 CG ASP A 551 26.979 71.571 60.652 1.00 74.69 C
+ATOM 2297 OD1 ASP A 551 26.724 70.405 61.004 1.00 82.52 O
+ATOM 2298 OD2 ASP A 551 27.761 72.318 61.278 1.00 84.94 O
+ATOM 2299 N TYR A 552 26.307 73.265 56.524 1.00 37.38 N
+ATOM 2300 CA TYR A 552 25.532 73.690 55.378 1.00 34.50 C
+ATOM 2301 C TYR A 552 25.937 72.967 54.107 1.00 34.55 C
+ATOM 2302 O TYR A 552 25.083 72.636 53.278 1.00 36.77 O
+ATOM 2303 CB TYR A 552 25.586 75.221 55.209 1.00 31.15 C
+ATOM 2304 CG TYR A 552 26.960 75.830 55.060 1.00 30.45 C
+ATOM 2305 CD1 TYR A 552 27.587 75.894 53.812 1.00 30.34 C
+ATOM 2306 CD2 TYR A 552 27.634 76.354 56.159 1.00 28.46 C
+ATOM 2307 CE1 TYR A 552 28.847 76.460 53.664 1.00 27.62 C
+ATOM 2308 CE2 TYR A 552 28.898 76.925 56.018 1.00 27.60 C
+ATOM 2309 CZ TYR A 552 29.496 76.971 54.769 1.00 27.63 C
+ATOM 2310 OH TYR A 552 30.762 77.494 54.624 1.00 27.86 O
+ATOM 2311 N LEU A 553 27.226 72.683 53.958 1.00 35.06 N
+ATOM 2312 CA LEU A 553 27.685 71.991 52.765 1.00 34.33 C
+ATOM 2313 C LEU A 553 27.170 70.571 52.707 1.00 34.59 C
+ATOM 2314 O LEU A 553 26.882 70.046 51.632 1.00 33.13 O
+ATOM 2315 CB LEU A 553 29.203 71.983 52.710 1.00 33.94 C
+ATOM 2316 CG LEU A 553 29.776 73.296 52.177 1.00 36.49 C
+ATOM 2317 CD1 LEU A 553 31.301 73.246 52.238 1.00 37.32 C
+ATOM 2318 CD2 LEU A 553 29.296 73.522 50.746 1.00 35.37 C
+ATOM 2319 N LYS A 554 27.055 69.950 53.872 1.00 35.55 N
+ATOM 2320 CA LYS A 554 26.577 68.585 53.936 1.00 36.32 C
+ATOM 2321 C LYS A 554 25.090 68.585 53.642 1.00 35.94 C
+ATOM 2322 O LYS A 554 24.595 67.720 52.910 1.00 37.28 O
+ATOM 2323 CB LYS A 554 26.830 67.994 55.320 1.00 37.70 C
+ATOM 2324 CG LYS A 554 26.506 66.532 55.404 1.00 38.79 C
+ATOM 2325 CD LYS A 554 26.573 66.051 56.831 1.00 40.86 C
+ATOM 2326 CE LYS A 554 26.189 64.594 56.909 1.00 41.01 C
+ATOM 2327 NZ LYS A 554 26.270 64.104 58.306 1.00 42.37 N
+ATOM 2328 N HIS A 555 24.386 69.565 54.212 1.00 35.62 N
+ATOM 2329 CA HIS A 555 22.948 69.695 54.017 1.00 34.24 C
+ATOM 2330 C HIS A 555 22.655 69.993 52.576 1.00 34.32 C
+ATOM 2331 O HIS A 555 21.641 69.563 52.039 1.00 36.59 O
+ATOM 2332 CB HIS A 555 22.374 70.820 54.862 1.00 32.77 C
+ATOM 2333 CG HIS A 555 22.419 70.552 56.329 1.00 30.74 C
+ATOM 2334 ND1 HIS A 555 22.456 69.274 56.846 1.00 29.93 N
+ATOM 2335 CD2 HIS A 555 22.425 71.390 57.389 1.00 30.93 C
+ATOM 2336 CE1 HIS A 555 22.485 69.340 58.166 1.00 30.18 C
+ATOM 2337 NE2 HIS A 555 22.467 70.611 58.519 1.00 31.41 N
+ATOM 2338 N CYS A 556 23.538 70.754 51.952 1.00 31.90 N
+ATOM 2339 CA CYS A 556 23.358 71.083 50.552 1.00 29.58 C
+ATOM 2340 C CYS A 556 23.342 69.795 49.728 1.00 28.95 C
+ATOM 2341 O CYS A 556 22.460 69.583 48.901 1.00 25.97 O
+ATOM 2342 CB CYS A 556 24.492 71.985 50.078 1.00 29.37 C
+ATOM 2343 SG CYS A 556 24.277 72.506 48.411 1.00 30.69 S
+ATOM 2344 N LEU A 557 24.324 68.935 49.963 1.00 29.67 N
+ATOM 2345 CA LEU A 557 24.411 67.679 49.239 1.00 31.39 C
+ATOM 2346 C LEU A 557 23.208 66.789 49.522 1.00 34.51 C
+ATOM 2347 O LEU A 557 22.699 66.112 48.625 1.00 35.26 O
+ATOM 2348 CB LEU A 557 25.690 66.941 49.616 1.00 30.62 C
+ATOM 2349 CG LEU A 557 26.976 67.618 49.159 1.00 30.57 C
+ATOM 2350 CD1 LEU A 557 28.187 66.791 49.591 1.00 30.21 C
+ATOM 2351 CD2 LEU A 557 26.939 67.771 47.652 1.00 30.61 C
+ATOM 2352 N GLU A 558 22.760 66.779 50.772 1.00 38.85 N
+ATOM 2353 CA GLU A 558 21.611 65.969 51.135 1.00 42.60 C
+ATOM 2354 C GLU A 558 20.424 66.368 50.254 1.00 43.14 C
+ATOM 2355 O GLU A 558 19.583 65.540 49.922 1.00 43.39 O
+ATOM 2356 CB GLU A 558 21.278 66.156 52.625 1.00 47.84 C
+ATOM 2357 CG GLU A 558 22.436 65.763 53.554 1.00 56.71 C
+ATOM 2358 CD GLU A 558 22.133 65.948 55.037 1.00 59.05 C
+ATOM 2359 OE1 GLU A 558 21.654 67.034 55.417 1.00 60.31 O
+ATOM 2360 OE2 GLU A 558 22.393 65.012 55.825 1.00 60.18 O
+ATOM 2361 N ARG A 559 20.365 67.633 49.854 1.00 41.80 N
+ATOM 2362 CA ARG A 559 19.272 68.099 49.013 1.00 38.09 C
+ATOM 2363 C ARG A 559 19.685 68.267 47.560 1.00 35.57 C
+ATOM 2364 O ARG A 559 18.923 68.812 46.758 1.00 34.40 O
+ATOM 2365 CB ARG A 559 18.714 69.427 49.531 1.00 40.61 C
+ATOM 2366 CG ARG A 559 17.888 69.321 50.795 1.00 45.05 C
+ATOM 2367 CD ARG A 559 18.752 69.338 52.024 1.00 48.75 C
+ATOM 2368 NE ARG A 559 17.961 69.263 53.246 1.00 50.23 N
+ATOM 2369 CZ ARG A 559 18.465 69.423 54.466 1.00 50.86 C
+ATOM 2370 NH1 ARG A 559 19.756 69.671 54.619 1.00 51.72 N
+ATOM 2371 NH2 ARG A 559 17.683 69.332 55.534 1.00 50.40 N
+ATOM 2372 N SER A 560 20.881 67.791 47.220 1.00 32.92 N
+ATOM 2373 CA SER A 560 21.390 67.904 45.848 1.00 32.60 C
+ATOM 2374 C SER A 560 22.111 66.615 45.397 1.00 35.73 C
+ATOM 2375 O SER A 560 23.168 66.660 44.774 1.00 31.32 O
+ATOM 2376 CB SER A 560 22.350 69.103 45.760 1.00 28.88 C
+ATOM 2377 OG SER A 560 21.747 70.293 46.254 1.00 25.81 O
+ATOM 2378 N GLU A 561 21.511 65.471 45.693 1.00 39.91 N
+ATOM 2379 CA GLU A 561 22.105 64.178 45.383 1.00 41.05 C
+ATOM 2380 C GLU A 561 22.927 64.098 44.108 1.00 38.26 C
+ATOM 2381 O GLU A 561 23.984 63.454 44.090 1.00 34.27 O
+ATOM 2382 CB GLU A 561 21.032 63.080 45.374 1.00 49.62 C
+ATOM 2383 CG GLU A 561 20.325 62.869 46.709 1.00 65.93 C
+ATOM 2384 CD GLU A 561 18.994 63.606 46.797 1.00 74.51 C
+ATOM 2385 OE1 GLU A 561 18.951 64.836 46.547 1.00 75.86 O
+ATOM 2386 OE2 GLU A 561 17.984 62.943 47.123 1.00 77.77 O
+ATOM 2387 N PHE A 562 22.472 64.749 43.044 1.00 33.66 N
+ATOM 2388 CA PHE A 562 23.211 64.663 41.782 1.00 29.77 C
+ATOM 2389 C PHE A 562 24.693 65.026 41.876 1.00 28.57 C
+ATOM 2390 O PHE A 562 25.503 64.514 41.116 1.00 28.67 O
+ATOM 2391 CB PHE A 562 22.525 65.499 40.688 1.00 28.26 C
+ATOM 2392 CG PHE A 562 22.501 66.973 40.966 1.00 30.44 C
+ATOM 2393 CD1 PHE A 562 23.592 67.778 40.647 1.00 30.82 C
+ATOM 2394 CD2 PHE A 562 21.402 67.553 41.582 1.00 30.45 C
+ATOM 2395 CE1 PHE A 562 23.590 69.131 40.937 1.00 29.40 C
+ATOM 2396 CE2 PHE A 562 21.392 68.907 41.878 1.00 31.34 C
+ATOM 2397 CZ PHE A 562 22.494 69.698 41.553 1.00 31.87 C
+ATOM 2398 N LEU A 563 25.064 65.885 42.817 1.00 27.04 N
+ATOM 2399 CA LEU A 563 26.467 66.261 42.933 1.00 26.12 C
+ATOM 2400 C LEU A 563 27.371 65.086 43.286 1.00 26.19 C
+ATOM 2401 O LEU A 563 28.552 65.083 42.934 1.00 23.62 O
+ATOM 2402 CB LEU A 563 26.649 67.388 43.967 1.00 25.49 C
+ATOM 2403 CG LEU A 563 26.089 68.768 43.592 1.00 23.41 C
+ATOM 2404 CD1 LEU A 563 26.451 69.770 44.671 1.00 21.75 C
+ATOM 2405 CD2 LEU A 563 26.648 69.212 42.250 1.00 22.93 C
+ATOM 2406 N LEU A 564 26.811 64.093 43.974 1.00 29.23 N
+ATOM 2407 CA LEU A 564 27.559 62.900 44.397 1.00 31.91 C
+ATOM 2408 C LEU A 564 27.315 61.714 43.491 1.00 35.23 C
+ATOM 2409 O LEU A 564 28.247 61.058 43.050 1.00 32.79 O
+ATOM 2410 CB LEU A 564 27.168 62.494 45.813 1.00 32.34 C
+ATOM 2411 CG LEU A 564 27.562 63.461 46.928 1.00 34.96 C
+ATOM 2412 CD1 LEU A 564 26.772 63.131 48.192 1.00 36.57 C
+ATOM 2413 CD2 LEU A 564 29.066 63.382 47.175 1.00 33.93 C
+ATOM 2414 N GLU A 565 26.045 61.444 43.226 1.00 41.21 N
+ATOM 2415 CA GLU A 565 25.662 60.331 42.379 1.00 43.98 C
+ATOM 2416 C GLU A 565 26.297 60.450 40.998 1.00 42.31 C
+ATOM 2417 O GLU A 565 26.641 59.446 40.368 1.00 40.14 O
+ATOM 2418 CB GLU A 565 24.141 60.277 42.269 1.00 53.77 C
+ATOM 2419 CG GLU A 565 23.438 60.242 43.615 1.00 71.49 C
+ATOM 2420 CD GLU A 565 21.979 59.843 43.497 1.00 79.84 C
+ATOM 2421 OE1 GLU A 565 21.271 60.421 42.645 1.00 82.86 O
+ATOM 2422 OE2 GLU A 565 21.534 58.954 44.255 1.00 82.42 O
+ATOM 2423 N LYS A 566 26.452 61.673 40.515 1.00 36.96 N
+ATOM 2424 CA LYS A 566 27.060 61.842 39.210 1.00 31.68 C
+ATOM 2425 C LYS A 566 28.524 62.220 39.338 1.00 29.95 C
+ATOM 2426 O LYS A 566 29.136 62.631 38.353 1.00 28.56 O
+ATOM 2427 CB LYS A 566 26.323 62.893 38.392 1.00 31.04 C
+ATOM 2428 CG LYS A 566 24.925 62.485 37.981 1.00 30.61 C
+ATOM 2429 CD LYS A 566 24.327 63.544 37.087 1.00 31.63 C
+ATOM 2430 CE LYS A 566 22.877 63.258 36.792 1.00 33.25 C
+ATOM 2431 NZ LYS A 566 22.292 64.337 35.938 1.00 35.34 N
+ATOM 2432 N ARG A 567 29.075 62.081 40.545 1.00 30.03 N
+ATOM 2433 CA ARG A 567 30.488 62.388 40.815 1.00 30.85 C
+ATOM 2434 C ARG A 567 30.932 63.718 40.212 1.00 31.32 C
+ATOM 2435 O ARG A 567 31.908 63.750 39.449 1.00 32.60 O
+ATOM 2436 CB ARG A 567 31.381 61.302 40.226 1.00 32.09 C
+ATOM 2437 CG ARG A 567 30.977 59.883 40.536 1.00 31.59 C
+ATOM 2438 CD ARG A 567 31.911 58.949 39.808 1.00 32.17 C
+ATOM 2439 NE ARG A 567 31.823 57.572 40.279 1.00 33.38 N
+ATOM 2440 CZ ARG A 567 30.715 56.836 40.235 1.00 33.98 C
+ATOM 2441 NH1 ARG A 567 29.593 57.350 39.742 1.00 33.40 N
+ATOM 2442 NH2 ARG A 567 30.732 55.582 40.675 1.00 33.36 N
+ATOM 2443 N ILE A 568 30.245 64.808 40.550 1.00 30.01 N
+ATOM 2444 CA ILE A 568 30.600 66.095 39.971 1.00 27.25 C
+ATOM 2445 C ILE A 568 31.623 66.883 40.763 1.00 26.36 C
+ATOM 2446 O ILE A 568 32.595 67.372 40.194 1.00 27.51 O
+ATOM 2447 CB ILE A 568 29.344 66.954 39.738 1.00 25.59 C
+ATOM 2448 CG1 ILE A 568 28.507 66.327 38.611 1.00 21.14 C
+ATOM 2449 CG2 ILE A 568 29.738 68.401 39.397 1.00 21.19 C
+ATOM 2450 CD1 ILE A 568 27.170 66.997 38.418 1.00 19.81 C
+ATOM 2451 N ILE A 569 31.439 66.996 42.069 1.00 26.08 N
+ATOM 2452 CA ILE A 569 32.394 67.759 42.849 1.00 29.82 C
+ATOM 2453 C ILE A 569 33.780 67.118 43.037 1.00 32.11 C
+ATOM 2454 O ILE A 569 34.634 67.720 43.677 1.00 35.02 O
+ATOM 2455 CB ILE A 569 31.824 68.116 44.223 1.00 26.08 C
+ATOM 2456 CG1 ILE A 569 31.496 66.852 45.007 1.00 23.22 C
+ATOM 2457 CG2 ILE A 569 30.585 68.956 44.053 1.00 23.63 C
+ATOM 2458 CD1 ILE A 569 30.989 67.129 46.425 1.00 20.64 C
+ATOM 2459 N GLN A 570 34.009 65.916 42.495 1.00 34.80 N
+ATOM 2460 CA GLN A 570 35.312 65.250 42.607 1.00 34.89 C
+ATOM 2461 C GLN A 570 35.952 65.255 41.233 1.00 34.81 C
+ATOM 2462 O GLN A 570 37.078 64.777 41.054 1.00 35.33 O
+ATOM 2463 CB GLN A 570 35.179 63.787 43.030 1.00 36.00 C
+ATOM 2464 CG GLN A 570 34.200 63.498 44.139 1.00 41.20 C
+ATOM 2465 CD GLN A 570 32.929 62.864 43.613 1.00 41.01 C
+ATOM 2466 OE1 GLN A 570 31.943 63.550 43.345 1.00 40.67 O
+ATOM 2467 NE2 GLN A 570 32.955 61.549 43.441 1.00 39.97 N
+ATOM 2468 N SER A 571 35.224 65.782 40.255 1.00 32.92 N
+ATOM 2469 CA SER A 571 35.716 65.830 38.888 1.00 32.56 C
+ATOM 2470 C SER A 571 36.658 67.000 38.583 1.00 32.22 C
+ATOM 2471 O SER A 571 36.415 68.146 38.978 1.00 31.40 O
+ATOM 2472 CB SER A 571 34.537 65.879 37.924 1.00 33.26 C
+ATOM 2473 OG SER A 571 34.991 65.967 36.587 1.00 36.86 O
+ATOM 2474 N GLY A 572 37.738 66.706 37.869 1.00 30.49 N
+ATOM 2475 CA GLY A 572 38.665 67.757 37.495 1.00 28.33 C
+ATOM 2476 C GLY A 572 38.000 68.695 36.502 1.00 28.00 C
+ATOM 2477 O GLY A 572 38.429 69.832 36.307 1.00 25.21 O
+ATOM 2478 N ILE A 573 36.944 68.210 35.859 1.00 28.62 N
+ATOM 2479 CA ILE A 573 36.216 69.022 34.894 1.00 30.13 C
+ATOM 2480 C ILE A 573 35.486 70.155 35.610 1.00 28.00 C
+ATOM 2481 O ILE A 573 35.309 71.237 35.057 1.00 28.80 O
+ATOM 2482 CB ILE A 573 35.211 68.168 34.090 1.00 33.39 C
+ATOM 2483 CG1 ILE A 573 35.979 67.300 33.084 1.00 35.88 C
+ATOM 2484 CG2 ILE A 573 34.195 69.065 33.385 1.00 36.61 C
+ATOM 2485 CD1 ILE A 573 35.102 66.433 32.206 1.00 36.77 C
+ATOM 2486 N ALA A 574 35.067 69.907 36.844 1.00 23.30 N
+ATOM 2487 CA ALA A 574 34.382 70.943 37.598 1.00 19.88 C
+ATOM 2488 C ALA A 574 35.379 72.062 37.897 1.00 18.72 C
+ATOM 2489 O ALA A 574 34.998 73.233 37.973 1.00 16.48 O
+ATOM 2490 CB ALA A 574 33.795 70.363 38.894 1.00 15.66 C
+ATOM 2491 N LEU A 575 36.652 71.700 38.063 1.00 18.22 N
+ATOM 2492 CA LEU A 575 37.687 72.697 38.321 1.00 19.37 C
+ATOM 2493 C LEU A 575 38.075 73.440 37.034 1.00 20.92 C
+ATOM 2494 O LEU A 575 38.330 74.646 37.066 1.00 23.19 O
+ATOM 2495 CB LEU A 575 38.944 72.060 38.949 1.00 18.21 C
+ATOM 2496 CG LEU A 575 38.798 71.577 40.395 1.00 16.66 C
+ATOM 2497 CD1 LEU A 575 40.155 71.205 41.000 1.00 12.34 C
+ATOM 2498 CD2 LEU A 575 38.137 72.700 41.189 1.00 15.57 C
+ATOM 2499 N LEU A 576 38.133 72.740 35.905 1.00 23.59 N
+ATOM 2500 CA LEU A 576 38.478 73.434 34.676 1.00 28.14 C
+ATOM 2501 C LEU A 576 37.336 74.396 34.378 1.00 29.60 C
+ATOM 2502 O LEU A 576 37.551 75.524 33.927 1.00 30.40 O
+ATOM 2503 CB LEU A 576 38.666 72.461 33.507 1.00 30.69 C
+ATOM 2504 CG LEU A 576 39.033 73.131 32.167 1.00 33.82 C
+ATOM 2505 CD1 LEU A 576 40.246 74.034 32.349 1.00 35.33 C
+ATOM 2506 CD2 LEU A 576 39.313 72.073 31.111 1.00 35.40 C
+ATOM 2507 N LEU A 577 36.119 73.936 34.654 1.00 30.84 N
+ATOM 2508 CA LEU A 577 34.909 74.722 34.456 1.00 29.82 C
+ATOM 2509 C LEU A 577 34.907 75.991 35.314 1.00 27.81 C
+ATOM 2510 O LEU A 577 34.486 77.046 34.835 1.00 29.09 O
+ATOM 2511 CB LEU A 577 33.688 73.873 34.792 1.00 31.00 C
+ATOM 2512 CG LEU A 577 32.753 73.586 33.626 1.00 32.52 C
+ATOM 2513 CD1 LEU A 577 31.801 72.471 34.030 1.00 33.21 C
+ATOM 2514 CD2 LEU A 577 32.005 74.862 33.229 1.00 32.18 C
+ATOM 2515 N MET A 578 35.363 75.876 36.569 1.00 26.30 N
+ATOM 2516 CA MET A 578 35.444 77.004 37.506 1.00 26.32 C
+ATOM 2517 C MET A 578 36.415 78.051 36.947 1.00 27.55 C
+ATOM 2518 O MET A 578 36.116 79.262 36.898 1.00 31.15 O
+ATOM 2519 CB MET A 578 35.941 76.509 38.871 1.00 21.73 C
+ATOM 2520 CG MET A 578 36.187 77.590 39.945 1.00 13.18 C
+ATOM 2521 SD MET A 578 36.528 76.887 41.602 1.00 5.56 S
+ATOM 2522 CE MET A 578 38.121 76.967 41.546 1.00 9.41 C
+ATOM 2523 N LEU A 579 37.580 77.571 36.518 1.00 27.27 N
+ATOM 2524 CA LEU A 579 38.601 78.434 35.941 1.00 28.18 C
+ATOM 2525 C LEU A 579 38.023 79.249 34.782 1.00 28.12 C
+ATOM 2526 O LEU A 579 38.117 80.462 34.768 1.00 27.81 O
+ATOM 2527 CB LEU A 579 39.774 77.585 35.445 1.00 25.25 C
+ATOM 2528 CG LEU A 579 40.679 76.989 36.509 1.00 18.84 C
+ATOM 2529 CD1 LEU A 579 41.788 76.205 35.838 1.00 15.97 C
+ATOM 2530 CD2 LEU A 579 41.254 78.106 37.350 1.00 16.17 C
+ATOM 2531 N ILE A 580 37.435 78.550 33.815 1.00 27.08 N
+ATOM 2532 CA ILE A 580 36.815 79.149 32.636 1.00 25.62 C
+ATOM 2533 C ILE A 580 35.802 80.209 33.055 1.00 25.66 C
+ATOM 2534 O ILE A 580 35.665 81.244 32.405 1.00 22.40 O
+ATOM 2535 CB ILE A 580 36.042 78.073 31.800 1.00 27.92 C
+ATOM 2536 CG1 ILE A 580 37.020 77.094 31.152 1.00 28.62 C
+ATOM 2537 CG2 ILE A 580 35.184 78.748 30.726 1.00 28.40 C
+ATOM 2538 CD1 ILE A 580 36.353 76.031 30.329 1.00 27.85 C
+ATOM 2539 N TRP A 581 35.097 79.929 34.146 1.00 24.66 N
+ATOM 2540 CA TRP A 581 34.059 80.808 34.663 1.00 24.36 C
+ATOM 2541 C TRP A 581 34.578 81.996 35.454 1.00 24.88 C
+ATOM 2542 O TRP A 581 33.966 83.052 35.452 1.00 27.10 O
+ATOM 2543 CB TRP A 581 33.106 79.988 35.525 1.00 25.19 C
+ATOM 2544 CG TRP A 581 32.006 80.757 36.163 1.00 26.56 C
+ATOM 2545 CD1 TRP A 581 31.887 81.080 37.487 1.00 27.51 C
+ATOM 2546 CD2 TRP A 581 30.833 81.257 35.521 1.00 26.96 C
+ATOM 2547 NE1 TRP A 581 30.704 81.747 37.711 1.00 27.07 N
+ATOM 2548 CE2 TRP A 581 30.038 81.872 36.522 1.00 27.92 C
+ATOM 2549 CE3 TRP A 581 30.373 81.247 34.199 1.00 27.26 C
+ATOM 2550 CZ2 TRP A 581 28.803 82.468 36.238 1.00 27.55 C
+ATOM 2551 CZ3 TRP A 581 29.146 81.836 33.915 1.00 27.58 C
+ATOM 2552 CH2 TRP A 581 28.373 82.441 34.935 1.00 28.50 C
+ATOM 2553 N TYR A 582 35.706 81.831 36.134 1.00 25.46 N
+ATOM 2554 CA TYR A 582 36.254 82.919 36.925 1.00 24.01 C
+ATOM 2555 C TYR A 582 37.443 83.644 36.314 1.00 24.51 C
+ATOM 2556 O TYR A 582 37.492 84.862 36.273 1.00 25.82 O
+ATOM 2557 CB TYR A 582 36.684 82.395 38.294 1.00 20.52 C
+ATOM 2558 CG TYR A 582 35.587 82.312 39.316 1.00 18.62 C
+ATOM 2559 CD1 TYR A 582 34.873 81.128 39.509 1.00 17.95 C
+ATOM 2560 CD2 TYR A 582 35.251 83.428 40.088 1.00 17.36 C
+ATOM 2561 CE1 TYR A 582 33.839 81.052 40.447 1.00 16.47 C
+ATOM 2562 CE2 TYR A 582 34.224 83.370 41.032 1.00 17.82 C
+ATOM 2563 CZ TYR A 582 33.520 82.174 41.202 1.00 18.33 C
+ATOM 2564 OH TYR A 582 32.503 82.103 42.111 1.00 21.41 O
+ATOM 2565 N ARG A 583 38.417 82.873 35.862 1.00 27.33 N
+ATOM 2566 CA ARG A 583 39.670 83.398 35.331 1.00 27.02 C
+ATOM 2567 C ARG A 583 39.660 84.125 34.002 1.00 26.94 C
+ATOM 2568 O ARG A 583 38.897 83.788 33.085 1.00 27.10 O
+ATOM 2569 CB ARG A 583 40.695 82.261 35.283 1.00 26.13 C
+ATOM 2570 CG ARG A 583 40.994 81.753 36.661 1.00 24.98 C
+ATOM 2571 CD ARG A 583 41.722 82.848 37.368 1.00 26.55 C
+ATOM 2572 NE ARG A 583 41.536 82.857 38.809 1.00 27.71 N
+ATOM 2573 CZ ARG A 583 42.183 83.686 39.620 1.00 26.66 C
+ATOM 2574 NH1 ARG A 583 43.055 84.554 39.114 1.00 24.90 N
+ATOM 2575 NH2 ARG A 583 41.944 83.662 40.925 1.00 26.75 N
+ATOM 2576 N PRO A 584 40.528 85.145 33.887 1.00 28.80 N
+ATOM 2577 CA PRO A 584 40.688 85.975 32.687 1.00 29.47 C
+ATOM 2578 C PRO A 584 41.414 85.191 31.604 1.00 31.56 C
+ATOM 2579 O PRO A 584 42.400 84.512 31.874 1.00 31.06 O
+ATOM 2580 CB PRO A 584 41.487 87.175 33.199 1.00 27.82 C
+ATOM 2581 CG PRO A 584 42.270 86.603 34.347 1.00 25.32 C
+ATOM 2582 CD PRO A 584 41.285 85.702 35.022 1.00 26.93 C
+ATOM 2583 N VAL A 585 40.909 85.283 30.383 1.00 35.75 N
+ATOM 2584 CA VAL A 585 41.472 84.566 29.242 1.00 37.23 C
+ATOM 2585 C VAL A 585 42.999 84.584 29.060 1.00 36.27 C
+ATOM 2586 O VAL A 585 43.583 83.570 28.692 1.00 36.08 O
+ATOM 2587 CB VAL A 585 40.817 85.054 27.935 1.00 40.72 C
+ATOM 2588 CG1 VAL A 585 41.412 84.333 26.748 1.00 46.60 C
+ATOM 2589 CG2 VAL A 585 39.322 84.812 27.995 1.00 46.16 C
+ATOM 2590 N ALA A 586 43.651 85.718 29.305 1.00 34.65 N
+ATOM 2591 CA ALA A 586 45.101 85.796 29.123 1.00 32.54 C
+ATOM 2592 C ALA A 586 45.890 85.047 30.190 1.00 34.09 C
+ATOM 2593 O ALA A 586 47.113 84.964 30.125 1.00 34.63 O
+ATOM 2594 CB ALA A 586 45.538 87.236 29.094 1.00 27.83 C
+ATOM 2595 N GLU A 587 45.191 84.498 31.172 1.00 36.49 N
+ATOM 2596 CA GLU A 587 45.858 83.771 32.237 1.00 37.91 C
+ATOM 2597 C GLU A 587 46.138 82.349 31.751 1.00 38.18 C
+ATOM 2598 O GLU A 587 46.884 81.601 32.395 1.00 37.07 O
+ATOM 2599 CB GLU A 587 44.983 83.777 33.500 1.00 41.13 C
+ATOM 2600 CG GLU A 587 45.765 83.883 34.814 1.00 45.48 C
+ATOM 2601 CD GLU A 587 44.921 84.427 35.968 1.00 48.26 C
+ATOM 2602 OE1 GLU A 587 43.830 83.877 36.217 1.00 48.04 O
+ATOM 2603 OE2 GLU A 587 45.349 85.401 36.630 1.00 49.66 O
+ATOM 2604 N PHE A 588 45.535 81.989 30.611 1.00 37.92 N
+ATOM 2605 CA PHE A 588 45.735 80.676 29.986 1.00 36.59 C
+ATOM 2606 C PHE A 588 46.836 80.829 28.936 1.00 36.70 C
+ATOM 2607 O PHE A 588 47.228 81.949 28.602 1.00 39.31 O
+ATOM 2608 CB PHE A 588 44.463 80.178 29.278 1.00 35.11 C
+ATOM 2609 CG PHE A 588 43.308 79.904 30.197 1.00 33.37 C
+ATOM 2610 CD1 PHE A 588 42.505 80.935 30.647 1.00 33.60 C
+ATOM 2611 CD2 PHE A 588 43.028 78.607 30.614 1.00 35.16 C
+ATOM 2612 CE1 PHE A 588 41.439 80.688 31.497 1.00 33.35 C
+ATOM 2613 CE2 PHE A 588 41.962 78.345 31.469 1.00 34.59 C
+ATOM 2614 CZ PHE A 588 41.167 79.391 31.911 1.00 34.17 C
+ATOM 2615 N ALA A 589 47.332 79.712 28.414 1.00 39.83 N
+ATOM 2616 CA ALA A 589 48.378 79.748 27.390 1.00 43.14 C
+ATOM 2617 C ALA A 589 47.780 80.222 26.064 1.00 47.90 C
+ATOM 2618 O ALA A 589 46.649 79.867 25.729 1.00 47.33 O
+ATOM 2619 CB ALA A 589 49.006 78.355 27.221 1.00 41.05 C
+ATOM 2620 N GLN A 590 48.539 81.020 25.316 1.00 53.41 N
+ATOM 2621 CA GLN A 590 48.071 81.540 24.038 1.00 56.42 C
+ATOM 2622 C GLN A 590 47.367 80.463 23.229 1.00 54.51 C
+ATOM 2623 O GLN A 590 46.179 80.561 22.933 1.00 51.00 O
+ATOM 2624 CB GLN A 590 49.241 82.116 23.241 1.00 66.29 C
+ATOM 2625 CG GLN A 590 48.905 82.420 21.796 1.00 84.97 C
+ATOM 2626 CD GLN A 590 49.975 83.245 21.111 1.00 93.82 C
+ATOM 2627 OE1 GLN A 590 51.172 83.003 21.286 1.00 96.71 O
+ATOM 2628 NE2 GLN A 590 49.550 84.222 20.313 1.00 96.36 N
+ATOM 2629 N SER A 591 48.111 79.429 22.881 1.00 48.00 N
+ATOM 2630 CA SER A 591 47.584 78.313 22.120 1.00 41.22 C
+ATOM 2631 C SER A 591 46.155 77.899 22.462 1.00 38.84 C
+ATOM 2632 O SER A 591 45.393 77.583 21.569 1.00 35.43 O
+ATOM 2633 CB SER A 591 48.506 77.104 22.299 1.00 41.77 C
+ATOM 2634 OG SER A 591 47.896 75.917 21.826 1.00 49.39 O
+ATOM 2635 N ILE A 592 45.784 77.902 23.740 1.00 36.38 N
+ATOM 2636 CA ILE A 592 44.446 77.456 24.143 1.00 34.42 C
+ATOM 2637 C ILE A 592 43.332 78.504 24.318 1.00 34.84 C
+ATOM 2638 O ILE A 592 42.131 78.157 24.349 1.00 34.41 O
+ATOM 2639 CB ILE A 592 44.538 76.592 25.439 1.00 36.98 C
+ATOM 2640 CG1 ILE A 592 44.225 75.137 25.092 1.00 40.69 C
+ATOM 2641 CG2 ILE A 592 43.596 77.099 26.513 1.00 39.89 C
+ATOM 2642 CD1 ILE A 592 44.065 74.234 26.298 1.00 43.91 C
+ATOM 2643 N GLN A 593 43.724 79.773 24.420 1.00 34.78 N
+ATOM 2644 CA GLN A 593 42.779 80.874 24.612 1.00 35.22 C
+ATOM 2645 C GLN A 593 41.567 80.919 23.671 1.00 38.22 C
+ATOM 2646 O GLN A 593 40.448 81.185 24.113 1.00 35.60 O
+ATOM 2647 CB GLN A 593 43.546 82.191 24.571 1.00 31.57 C
+ATOM 2648 CG GLN A 593 44.330 82.411 25.849 1.00 31.00 C
+ATOM 2649 CD GLN A 593 45.340 83.529 25.763 1.00 28.03 C
+ATOM 2650 OE1 GLN A 593 45.091 84.558 25.145 1.00 29.68 O
+ATOM 2651 NE2 GLN A 593 46.483 83.340 26.408 1.00 27.12 N
+ATOM 2652 N SER A 594 41.787 80.648 22.387 1.00 44.66 N
+ATOM 2653 CA SER A 594 40.711 80.647 21.394 1.00 48.05 C
+ATOM 2654 C SER A 594 39.621 79.661 21.806 1.00 46.69 C
+ATOM 2655 O SER A 594 38.425 79.912 21.627 1.00 45.12 O
+ATOM 2656 CB SER A 594 41.251 80.242 20.013 1.00 53.17 C
+ATOM 2657 OG SER A 594 42.339 81.059 19.614 1.00 67.56 O
+ATOM 2658 N ARG A 595 40.043 78.532 22.361 1.00 44.53 N
+ATOM 2659 CA ARG A 595 39.100 77.516 22.782 1.00 41.48 C
+ATOM 2660 C ARG A 595 38.449 77.910 24.108 1.00 38.75 C
+ATOM 2661 O ARG A 595 37.300 77.565 24.379 1.00 40.07 O
+ATOM 2662 CB ARG A 595 39.820 76.177 22.901 1.00 40.52 C
+ATOM 2663 CG ARG A 595 38.916 74.972 22.734 1.00 39.90 C
+ATOM 2664 CD ARG A 595 39.714 73.678 22.555 1.00 39.79 C
+ATOM 2665 NE ARG A 595 38.842 72.512 22.702 1.00 40.19 N
+ATOM 2666 CZ ARG A 595 39.256 71.251 22.661 1.00 39.91 C
+ATOM 2667 NH1 ARG A 595 40.542 70.978 22.474 1.00 39.38 N
+ATOM 2668 NH2 ARG A 595 38.383 70.265 22.821 1.00 39.87 N
+ATOM 2669 N ILE A 596 39.174 78.651 24.932 1.00 36.72 N
+ATOM 2670 CA ILE A 596 38.616 79.070 26.207 1.00 35.68 C
+ATOM 2671 C ILE A 596 37.556 80.162 26.029 1.00 34.31 C
+ATOM 2672 O ILE A 596 36.470 80.067 26.591 1.00 35.99 O
+ATOM 2673 CB ILE A 596 39.728 79.563 27.167 1.00 31.62 C
+ATOM 2674 CG1 ILE A 596 40.638 78.387 27.541 1.00 26.32 C
+ATOM 2675 CG2 ILE A 596 39.113 80.167 28.432 1.00 25.66 C
+ATOM 2676 CD1 ILE A 596 39.931 77.246 28.261 1.00 22.06 C
+ATOM 2677 N VAL A 597 37.871 81.194 25.249 1.00 33.55 N
+ATOM 2678 CA VAL A 597 36.923 82.283 25.010 1.00 36.20 C
+ATOM 2679 C VAL A 597 35.633 81.684 24.490 1.00 40.37 C
+ATOM 2680 O VAL A 597 34.534 82.155 24.794 1.00 39.19 O
+ATOM 2681 CB VAL A 597 37.443 83.290 23.940 1.00 31.54 C
+ATOM 2682 CG1 VAL A 597 36.335 84.274 23.569 1.00 24.61 C
+ATOM 2683 CG2 VAL A 597 38.680 84.035 24.467 1.00 26.58 C
+ATOM 2684 N GLU A 598 35.794 80.631 23.699 1.00 45.55 N
+ATOM 2685 CA GLU A 598 34.682 79.915 23.085 1.00 48.25 C
+ATOM 2686 C GLU A 598 33.768 79.297 24.148 1.00 46.04 C
+ATOM 2687 O GLU A 598 32.546 79.287 23.993 1.00 41.56 O
+ATOM 2688 CB GLU A 598 35.255 78.838 22.168 1.00 57.33 C
+ATOM 2689 CG GLU A 598 34.370 78.382 21.041 1.00 73.73 C
+ATOM 2690 CD GLU A 598 35.137 77.507 20.070 1.00 82.03 C
+ATOM 2691 OE1 GLU A 598 36.109 78.006 19.464 1.00 84.79 O
+ATOM 2692 OE2 GLU A 598 34.782 76.320 19.917 1.00 85.58 O
+ATOM 2693 N TRP A 599 34.362 78.785 25.226 1.00 42.85 N
+ATOM 2694 CA TRP A 599 33.579 78.186 26.308 1.00 38.81 C
+ATOM 2695 C TRP A 599 32.967 79.237 27.223 1.00 37.56 C
+ATOM 2696 O TRP A 599 31.867 79.042 27.738 1.00 39.66 O
+ATOM 2697 CB TRP A 599 34.432 77.233 27.148 1.00 35.24 C
+ATOM 2698 CG TRP A 599 34.335 75.809 26.707 1.00 33.45 C
+ATOM 2699 CD1 TRP A 599 35.197 75.139 25.890 1.00 31.98 C
+ATOM 2700 CD2 TRP A 599 33.269 74.895 27.000 1.00 31.36 C
+ATOM 2701 NE1 TRP A 599 34.733 73.867 25.657 1.00 32.33 N
+ATOM 2702 CE2 TRP A 599 33.552 73.691 26.330 1.00 30.39 C
+ATOM 2703 CE3 TRP A 599 32.106 74.980 27.777 1.00 31.68 C
+ATOM 2704 CZ2 TRP A 599 32.709 72.581 26.390 1.00 29.61 C
+ATOM 2705 CZ3 TRP A 599 31.264 73.867 27.838 1.00 32.24 C
+ATOM 2706 CH2 TRP A 599 31.577 72.685 27.152 1.00 30.62 C
+ATOM 2707 N LYS A 600 33.688 80.338 27.437 1.00 39.23 N
+ATOM 2708 CA LYS A 600 33.203 81.432 28.282 1.00 42.83 C
+ATOM 2709 C LYS A 600 31.910 81.962 27.687 1.00 46.95 C
+ATOM 2710 O LYS A 600 30.915 82.152 28.395 1.00 47.83 O
+ATOM 2711 CB LYS A 600 34.226 82.568 28.347 1.00 41.74 C
+ATOM 2712 CG LYS A 600 35.355 82.326 29.308 1.00 39.47 C
+ATOM 2713 CD LYS A 600 36.473 83.331 29.110 1.00 37.46 C
+ATOM 2714 CE LYS A 600 37.545 83.143 30.172 1.00 38.36 C
+ATOM 2715 NZ LYS A 600 36.987 83.344 31.548 1.00 38.25 N
+ATOM 2716 N GLU A 601 31.939 82.210 26.379 1.00 49.49 N
+ATOM 2717 CA GLU A 601 30.770 82.693 25.675 1.00 48.89 C
+ATOM 2718 C GLU A 601 29.634 81.711 25.921 1.00 46.57 C
+ATOM 2719 O GLU A 601 28.566 82.092 26.398 1.00 43.63 O
+ATOM 2720 CB GLU A 601 31.072 82.805 24.182 1.00 53.59 C
+ATOM 2721 CG GLU A 601 31.778 84.100 23.811 1.00 65.00 C
+ATOM 2722 CD GLU A 601 32.285 84.127 22.375 1.00 70.52 C
+ATOM 2723 OE1 GLU A 601 31.541 83.708 21.453 1.00 72.89 O
+ATOM 2724 OE2 GLU A 601 33.433 84.583 22.173 1.00 72.11 O
+ATOM 2725 N ARG A 602 29.876 80.441 25.610 1.00 43.42 N
+ATOM 2726 CA ARG A 602 28.868 79.406 25.807 1.00 40.54 C
+ATOM 2727 C ARG A 602 28.247 79.632 27.184 1.00 38.64 C
+ATOM 2728 O ARG A 602 27.058 79.918 27.306 1.00 41.31 O
+ATOM 2729 CB ARG A 602 29.526 78.015 25.736 1.00 38.20 C
+ATOM 2730 CG ARG A 602 28.588 76.841 25.406 1.00 33.40 C
+ATOM 2731 CD ARG A 602 27.815 76.343 26.610 1.00 32.51 C
+ATOM 2732 NE ARG A 602 26.890 75.262 26.267 1.00 33.65 N
+ATOM 2733 CZ ARG A 602 27.253 74.090 25.752 1.00 32.11 C
+ATOM 2734 NH1 ARG A 602 28.528 73.825 25.505 1.00 32.37 N
+ATOM 2735 NH2 ARG A 602 26.336 73.171 25.499 1.00 32.57 N
+ATOM 2736 N LEU A 603 29.076 79.526 28.215 1.00 39.29 N
+ATOM 2737 CA LEU A 603 28.631 79.704 29.585 1.00 42.77 C
+ATOM 2738 C LEU A 603 27.896 81.008 29.816 1.00 49.18 C
+ATOM 2739 O LEU A 603 26.808 81.013 30.386 1.00 49.13 O
+ATOM 2740 CB LEU A 603 29.821 79.629 30.532 1.00 37.61 C
+ATOM 2741 CG LEU A 603 30.094 78.300 31.235 1.00 31.25 C
+ATOM 2742 CD1 LEU A 603 29.483 77.143 30.472 1.00 26.77 C
+ATOM 2743 CD2 LEU A 603 31.599 78.130 31.385 1.00 26.71 C
+ATOM 2744 N ASP A 604 28.487 82.114 29.382 1.00 56.19 N
+ATOM 2745 CA ASP A 604 27.860 83.414 29.581 1.00 59.09 C
+ATOM 2746 C ASP A 604 26.483 83.500 28.955 1.00 58.67 C
+ATOM 2747 O ASP A 604 25.570 84.103 29.526 1.00 52.52 O
+ATOM 2748 CB ASP A 604 28.755 84.533 29.051 1.00 69.55 C
+ATOM 2749 CG ASP A 604 29.865 84.903 30.029 1.00 85.72 C
+ATOM 2750 OD1 ASP A 604 29.542 85.264 31.187 1.00 95.13 O
+ATOM 2751 OD2 ASP A 604 31.056 84.835 29.645 1.00 94.11 O
+ATOM 2752 N LYS A 605 26.325 82.866 27.801 1.00 57.42 N
+ATOM 2753 CA LYS A 605 25.056 82.863 27.083 1.00 57.77 C
+ATOM 2754 C LYS A 605 23.979 81.994 27.754 1.00 57.98 C
+ATOM 2755 O LYS A 605 22.831 82.000 27.334 1.00 54.85 O
+ATOM 2756 CB LYS A 605 25.306 82.395 25.638 1.00 65.08 C
+ATOM 2757 CG LYS A 605 24.066 82.186 24.782 1.00 79.80 C
+ATOM 2758 CD LYS A 605 24.438 81.656 23.399 1.00 86.48 C
+ATOM 2759 CE LYS A 605 23.212 81.162 22.622 1.00 88.26 C
+ATOM 2760 NZ LYS A 605 22.581 79.939 23.222 1.00 87.98 N
+ATOM 2761 N GLU A 606 24.338 81.275 28.811 1.00 55.10 N
+ATOM 2762 CA GLU A 606 23.391 80.383 29.490 1.00 48.33 C
+ATOM 2763 C GLU A 606 23.189 80.657 30.965 1.00 42.25 C
+ATOM 2764 O GLU A 606 22.206 80.219 31.561 1.00 33.08 O
+ATOM 2765 CB GLU A 606 23.843 78.929 29.382 1.00 54.95 C
+ATOM 2766 CG GLU A 606 23.339 78.161 28.194 1.00 73.48 C
+ATOM 2767 CD GLU A 606 23.512 76.669 28.400 1.00 82.09 C
+ATOM 2768 OE1 GLU A 606 22.845 76.127 29.310 1.00 84.95 O
+ATOM 2769 OE2 GLU A 606 24.320 76.045 27.670 1.00 85.05 O
+ATOM 2770 N PHE A 607 24.141 81.344 31.571 1.00 35.19 N
+ATOM 2771 CA PHE A 607 24.028 81.625 32.985 1.00 29.64 C
+ATOM 2772 C PHE A 607 24.369 83.063 33.272 1.00 27.29 C
+ATOM 2773 O PHE A 607 25.403 83.577 32.837 1.00 28.17 O
+ATOM 2774 CB PHE A 607 24.970 80.726 33.793 1.00 28.55 C
+ATOM 2775 CG PHE A 607 24.757 79.268 33.571 1.00 24.92 C
+ATOM 2776 CD1 PHE A 607 25.456 78.596 32.579 1.00 24.35 C
+ATOM 2777 CD2 PHE A 607 23.835 78.570 34.337 1.00 23.12 C
+ATOM 2778 CE1 PHE A 607 25.228 77.235 32.358 1.00 25.72 C
+ATOM 2779 CE2 PHE A 607 23.604 77.222 34.124 1.00 23.34 C
+ATOM 2780 CZ PHE A 607 24.293 76.552 33.138 1.00 23.51 C
+ATOM 2781 N SER A 608 23.484 83.716 34.004 1.00 25.52 N
+ATOM 2782 CA SER A 608 23.723 85.097 34.376 1.00 24.81 C
+ATOM 2783 C SER A 608 24.430 85.047 35.720 1.00 26.75 C
+ATOM 2784 O SER A 608 24.391 84.042 36.433 1.00 21.04 O
+ATOM 2785 CB SER A 608 22.408 85.874 34.524 1.00 22.92 C
+ATOM 2786 OG SER A 608 21.711 85.460 35.682 1.00 22.36 O
+ATOM 2787 N LEU A 609 25.094 86.134 36.057 1.00 28.31 N
+ATOM 2788 CA LEU A 609 25.760 86.189 37.326 1.00 28.84 C
+ATOM 2789 C LEU A 609 24.780 85.995 38.461 1.00 26.62 C
+ATOM 2790 O LEU A 609 25.089 85.275 39.400 1.00 26.74 O
+ATOM 2791 CB LEU A 609 26.477 87.520 37.502 1.00 37.70 C
+ATOM 2792 CG LEU A 609 27.982 87.385 37.329 1.00 47.31 C
+ATOM 2793 CD1 LEU A 609 28.643 88.732 37.485 1.00 53.39 C
+ATOM 2794 CD2 LEU A 609 28.503 86.403 38.364 1.00 52.23 C
+ATOM 2795 N SER A 610 23.594 86.597 38.389 1.00 23.81 N
+ATOM 2796 CA SER A 610 22.669 86.441 39.511 1.00 22.92 C
+ATOM 2797 C SER A 610 22.212 84.994 39.704 1.00 21.40 C
+ATOM 2798 O SER A 610 21.977 84.562 40.836 1.00 21.25 O
+ATOM 2799 CB SER A 610 21.466 87.395 39.394 1.00 23.10 C
+ATOM 2800 OG SER A 610 20.607 87.042 38.331 1.00 27.62 O
+ATOM 2801 N VAL A 611 22.112 84.239 38.611 1.00 20.11 N
+ATOM 2802 CA VAL A 611 21.703 82.843 38.692 1.00 19.36 C
+ATOM 2803 C VAL A 611 22.791 82.037 39.413 1.00 19.17 C
+ATOM 2804 O VAL A 611 22.500 81.299 40.366 1.00 21.78 O
+ATOM 2805 CB VAL A 611 21.435 82.266 37.271 1.00 17.03 C
+ATOM 2806 CG1 VAL A 611 21.189 80.762 37.306 1.00 10.43 C
+ATOM 2807 CG2 VAL A 611 20.219 82.949 36.685 1.00 13.05 C
+ATOM 2808 N TYR A 612 24.036 82.178 38.964 1.00 18.86 N
+ATOM 2809 CA TYR A 612 25.146 81.471 39.591 1.00 21.47 C
+ATOM 2810 C TYR A 612 25.282 81.926 41.031 1.00 24.38 C
+ATOM 2811 O TYR A 612 25.589 81.127 41.920 1.00 22.30 O
+ATOM 2812 CB TYR A 612 26.458 81.755 38.865 1.00 20.33 C
+ATOM 2813 CG TYR A 612 27.680 81.268 39.610 1.00 16.74 C
+ATOM 2814 CD1 TYR A 612 28.014 79.919 39.630 1.00 16.03 C
+ATOM 2815 CD2 TYR A 612 28.499 82.155 40.291 1.00 16.43 C
+ATOM 2816 CE1 TYR A 612 29.148 79.447 40.315 1.00 16.15 C
+ATOM 2817 CE2 TYR A 612 29.631 81.709 40.986 1.00 18.51 C
+ATOM 2818 CZ TYR A 612 29.957 80.347 40.991 1.00 18.39 C
+ATOM 2819 OH TYR A 612 31.083 79.904 41.662 1.00 13.95 O
+ATOM 2820 N GLN A 613 25.072 83.220 41.248 1.00 25.82 N
+ATOM 2821 CA GLN A 613 25.149 83.791 42.583 1.00 28.59 C
+ATOM 2822 C GLN A 613 24.105 83.187 43.520 1.00 28.92 C
+ATOM 2823 O GLN A 613 24.356 83.029 44.706 1.00 24.28 O
+ATOM 2824 CB GLN A 613 24.952 85.300 42.533 1.00 35.32 C
+ATOM 2825 CG GLN A 613 26.248 86.055 42.541 1.00 48.52 C
+ATOM 2826 CD GLN A 613 27.222 85.443 43.506 1.00 54.26 C
+ATOM 2827 OE1 GLN A 613 26.846 85.070 44.619 1.00 58.23 O
+ATOM 2828 NE2 GLN A 613 28.480 85.328 43.094 1.00 55.22 N
+ATOM 2829 N LYS A 614 22.932 82.860 42.989 1.00 27.33 N
+ATOM 2830 CA LYS A 614 21.881 82.266 43.795 1.00 23.98 C
+ATOM 2831 C LYS A 614 22.275 80.855 44.197 1.00 20.88 C
+ATOM 2832 O LYS A 614 21.999 80.438 45.316 1.00 18.07 O
+ATOM 2833 CB LYS A 614 20.558 82.247 43.027 1.00 28.47 C
+ATOM 2834 CG LYS A 614 19.354 81.813 43.871 1.00 37.11 C
+ATOM 2835 CD LYS A 614 18.047 82.294 43.231 1.00 42.35 C
+ATOM 2836 CE LYS A 614 16.822 81.630 43.847 1.00 43.48 C
+ATOM 2837 NZ LYS A 614 16.781 80.164 43.532 1.00 44.05 N
+ATOM 2838 N MET A 615 22.914 80.119 43.289 1.00 18.29 N
+ATOM 2839 CA MET A 615 23.349 78.764 43.606 1.00 16.56 C
+ATOM 2840 C MET A 615 24.278 78.795 44.843 1.00 16.45 C
+ATOM 2841 O MET A 615 24.102 78.015 45.797 1.00 15.06 O
+ATOM 2842 CB MET A 615 24.077 78.134 42.406 1.00 14.76 C
+ATOM 2843 CG MET A 615 23.249 78.064 41.100 1.00 13.78 C
+ATOM 2844 SD MET A 615 23.998 77.183 39.622 1.00 9.75 S
+ATOM 2845 CE MET A 615 25.642 77.410 39.893 1.00 10.37 C
+ATOM 2846 N LYS A 616 25.247 79.712 44.838 1.00 19.52 N
+ATOM 2847 CA LYS A 616 26.177 79.837 45.957 1.00 21.30 C
+ATOM 2848 C LYS A 616 25.424 80.166 47.232 1.00 22.53 C
+ATOM 2849 O LYS A 616 25.790 79.709 48.313 1.00 23.38 O
+ATOM 2850 CB LYS A 616 27.217 80.923 45.678 1.00 21.04 C
+ATOM 2851 CG LYS A 616 28.231 80.563 44.577 1.00 20.90 C
+ATOM 2852 CD LYS A 616 29.512 81.404 44.706 1.00 20.31 C
+ATOM 2853 CE LYS A 616 30.320 80.990 45.945 1.00 21.79 C
+ATOM 2854 NZ LYS A 616 31.278 82.030 46.418 1.00 19.43 N
+ATOM 2855 N PHE A 617 24.363 80.957 47.097 1.00 24.76 N
+ATOM 2856 CA PHE A 617 23.537 81.348 48.238 1.00 26.40 C
+ATOM 2857 C PHE A 617 22.796 80.127 48.770 1.00 25.96 C
+ATOM 2858 O PHE A 617 22.663 79.931 49.980 1.00 25.12 O
+ATOM 2859 CB PHE A 617 22.519 82.413 47.823 1.00 29.39 C
+ATOM 2860 CG PHE A 617 21.526 82.758 48.900 1.00 34.26 C
+ATOM 2861 CD1 PHE A 617 21.832 83.705 49.871 1.00 33.58 C
+ATOM 2862 CD2 PHE A 617 20.281 82.121 48.948 1.00 36.63 C
+ATOM 2863 CE1 PHE A 617 20.914 84.019 50.879 1.00 35.37 C
+ATOM 2864 CE2 PHE A 617 19.355 82.424 49.950 1.00 36.25 C
+ATOM 2865 CZ PHE A 617 19.671 83.376 50.919 1.00 36.19 C
+ATOM 2866 N ASN A 618 22.306 79.301 47.853 1.00 27.23 N
+ATOM 2867 CA ASN A 618 21.587 78.097 48.245 1.00 27.67 C
+ATOM 2868 C ASN A 618 22.514 77.156 49.023 1.00 27.35 C
+ATOM 2869 O ASN A 618 22.105 76.587 50.029 1.00 28.30 O
+ATOM 2870 CB ASN A 618 20.964 77.405 47.009 1.00 24.46 C
+ATOM 2871 CG ASN A 618 19.785 78.201 46.419 1.00 21.11 C
+ATOM 2872 OD1 ASN A 618 19.173 79.036 47.100 1.00 19.68 O
+ATOM 2873 ND2 ASN A 618 19.466 77.939 45.157 1.00 19.80 N
+ATOM 2874 N VAL A 619 23.757 77.003 48.567 1.00 28.91 N
+ATOM 2875 CA VAL A 619 24.722 76.154 49.274 1.00 30.25 C
+ATOM 2876 C VAL A 619 24.951 76.706 50.678 1.00 30.14 C
+ATOM 2877 O VAL A 619 24.969 75.963 51.652 1.00 32.11 O
+ATOM 2878 CB VAL A 619 26.090 76.117 48.570 1.00 28.56 C
+ATOM 2879 CG1 VAL A 619 27.103 75.463 49.463 1.00 25.83 C
+ATOM 2880 CG2 VAL A 619 25.990 75.352 47.265 1.00 25.43 C
+ATOM 2881 N ALA A 620 25.135 78.017 50.770 1.00 32.43 N
+ATOM 2882 CA ALA A 620 25.347 78.669 52.057 1.00 34.47 C
+ATOM 2883 C ALA A 620 24.223 78.326 53.039 1.00 34.97 C
+ATOM 2884 O ALA A 620 24.475 78.025 54.209 1.00 39.08 O
+ATOM 2885 CB ALA A 620 25.432 80.177 51.866 1.00 32.79 C
+ATOM 2886 N MET A 621 22.983 78.383 52.559 1.00 34.89 N
+ATOM 2887 CA MET A 621 21.817 78.066 53.381 1.00 34.57 C
+ATOM 2888 C MET A 621 21.591 76.547 53.482 1.00 35.45 C
+ATOM 2889 O MET A 621 20.667 76.098 54.159 1.00 34.35 O
+ATOM 2890 CB MET A 621 20.575 78.715 52.773 1.00 33.54 C
+ATOM 2891 CG MET A 621 20.609 80.226 52.751 1.00 29.11 C
+ATOM 2892 SD MET A 621 20.573 80.916 54.408 1.00 28.26 S
+ATOM 2893 CE MET A 621 22.237 81.591 54.585 1.00 27.21 C
+ATOM 2894 N GLY A 622 22.443 75.777 52.799 1.00 35.73 N
+ATOM 2895 CA GLY A 622 22.332 74.327 52.782 1.00 33.53 C
+ATOM 2896 C GLY A 622 20.992 73.815 52.283 1.00 31.98 C
+ATOM 2897 O GLY A 622 20.355 73.045 52.986 1.00 32.22 O
+ATOM 2898 N ILE A 623 20.566 74.197 51.078 1.00 30.07 N
+ATOM 2899 CA ILE A 623 19.267 73.741 50.591 1.00 32.89 C
+ATOM 2900 C ILE A 623 19.139 73.076 49.217 1.00 33.69 C
+ATOM 2901 O ILE A 623 18.151 72.369 48.954 1.00 36.79 O
+ATOM 2902 CB ILE A 623 18.232 74.874 50.621 1.00 30.24 C
+ATOM 2903 CG1 ILE A 623 18.709 76.044 49.759 1.00 29.79 C
+ATOM 2904 CG2 ILE A 623 17.976 75.291 52.059 1.00 27.93 C
+ATOM 2905 CD1 ILE A 623 17.661 77.097 49.506 1.00 27.29 C
+ATOM 2906 N GLY A 624 20.099 73.272 48.331 1.00 34.27 N
+ATOM 2907 CA GLY A 624 19.954 72.640 47.032 1.00 34.32 C
+ATOM 2908 C GLY A 624 20.329 73.669 46.002 1.00 34.23 C
+ATOM 2909 O GLY A 624 19.533 74.527 45.631 1.00 32.29 O
+ATOM 2910 N VAL A 625 21.570 73.585 45.550 1.00 33.64 N
+ATOM 2911 CA VAL A 625 22.085 74.525 44.586 1.00 33.38 C
+ATOM 2912 C VAL A 625 21.007 74.965 43.604 1.00 33.30 C
+ATOM 2913 O VAL A 625 20.843 76.153 43.347 1.00 35.04 O
+ATOM 2914 CB VAL A 625 23.272 73.912 43.816 1.00 32.55 C
+ATOM 2915 CG1 VAL A 625 24.097 75.018 43.168 1.00 29.70 C
+ATOM 2916 CG2 VAL A 625 24.123 73.095 44.756 1.00 30.89 C
+ATOM 2917 N LEU A 626 20.241 74.010 43.094 1.00 34.40 N
+ATOM 2918 CA LEU A 626 19.212 74.312 42.108 1.00 35.68 C
+ATOM 2919 C LEU A 626 17.853 74.797 42.581 1.00 38.46 C
+ATOM 2920 O LEU A 626 16.930 74.916 41.776 1.00 39.06 O
+ATOM 2921 CB LEU A 626 19.007 73.110 41.198 1.00 31.73 C
+ATOM 2922 CG LEU A 626 20.280 72.622 40.524 1.00 28.36 C
+ATOM 2923 CD1 LEU A 626 19.894 71.560 39.502 1.00 25.73 C
+ATOM 2924 CD2 LEU A 626 21.015 73.799 39.877 1.00 24.32 C
+ATOM 2925 N ASP A 627 17.701 75.077 43.867 1.00 44.95 N
+ATOM 2926 CA ASP A 627 16.412 75.576 44.321 1.00 50.87 C
+ATOM 2927 C ASP A 627 16.258 77.032 43.872 1.00 53.87 C
+ATOM 2928 O ASP A 627 17.278 77.659 43.480 1.00 55.14 O
+ATOM 2929 CB ASP A 627 16.288 75.481 45.846 1.00 53.95 C
+ATOM 2930 CG ASP A 627 16.030 74.064 46.321 1.00 57.53 C
+ATOM 2931 OD1 ASP A 627 15.698 73.194 45.483 1.00 57.84 O
+ATOM 2932 OD2 ASP A 627 16.149 73.819 47.537 1.00 59.41 O
+ATOM 2933 OXT ASP A 627 15.113 77.534 43.922 1.00 56.88 O
+TER 2934 ASP A 627
+ATOM 2935 N LYS B 266 59.471 52.275 -0.025 1.00 86.31 N
+ATOM 2936 CA LYS B 266 60.374 51.550 -0.960 1.00 84.38 C
+ATOM 2937 C LYS B 266 61.457 50.774 -0.231 1.00 86.62 C
+ATOM 2938 O LYS B 266 61.270 49.602 0.109 1.00 85.27 O
+ATOM 2939 CB LYS B 266 61.018 52.529 -1.947 1.00 84.51 C
+ATOM 2940 CG LYS B 266 60.035 53.072 -2.968 1.00 80.32 C
+ATOM 2941 CD LYS B 266 59.411 51.944 -3.789 1.00 77.55 C
+ATOM 2942 CE LYS B 266 58.226 52.441 -4.597 1.00 76.34 C
+ATOM 2943 NZ LYS B 266 57.670 51.378 -5.469 1.00 76.10 N
+ATOM 2944 N GLN B 267 62.588 51.426 0.010 1.00 81.43 N
+ATOM 2945 CA GLN B 267 63.691 50.771 0.694 1.00 75.99 C
+ATOM 2946 C GLN B 267 64.351 51.732 1.678 1.00 72.16 C
+ATOM 2947 O GLN B 267 65.257 52.473 1.311 1.00 64.47 O
+ATOM 2948 CB GLN B 267 64.712 50.276 -0.340 1.00 79.72 C
+ATOM 2949 CG GLN B 267 65.760 49.321 0.206 1.00 90.15 C
+ATOM 2950 CD GLN B 267 65.151 48.081 0.831 1.00 94.61 C
+ATOM 2951 OE1 GLN B 267 64.548 47.249 0.147 1.00 95.63 O
+ATOM 2952 NE2 GLN B 267 65.303 47.954 2.144 1.00 96.24 N
+ATOM 2953 N VAL B 268 63.894 51.726 2.927 1.00 62.73 N
+ATOM 2954 CA VAL B 268 64.466 52.610 3.941 1.00 55.47 C
+ATOM 2955 C VAL B 268 65.918 52.276 4.259 1.00 52.02 C
+ATOM 2956 O VAL B 268 66.355 51.130 4.146 1.00 49.07 O
+ATOM 2957 CB VAL B 268 63.686 52.556 5.270 1.00 56.78 C
+ATOM 2958 CG1 VAL B 268 64.198 53.633 6.216 1.00 60.42 C
+ATOM 2959 CG2 VAL B 268 62.211 52.747 5.014 1.00 62.50 C
+ATOM 2960 N SER B 269 66.659 53.294 4.670 1.00 46.97 N
+ATOM 2961 CA SER B 269 68.059 53.128 5.010 1.00 43.00 C
+ATOM 2962 C SER B 269 68.184 52.901 6.505 1.00 41.62 C
+ATOM 2963 O SER B 269 67.874 53.788 7.302 1.00 44.05 O
+ATOM 2964 CB SER B 269 68.854 54.375 4.617 1.00 40.42 C
+ATOM 2965 OG SER B 269 70.214 54.240 4.990 1.00 36.78 O
+ATOM 2966 N TRP B 270 68.620 51.709 6.888 1.00 39.70 N
+ATOM 2967 CA TRP B 270 68.790 51.405 8.296 1.00 40.19 C
+ATOM 2968 C TRP B 270 70.035 52.136 8.797 1.00 42.41 C
+ATOM 2969 O TRP B 270 70.124 52.488 9.974 1.00 43.04 O
+ATOM 2970 CB TRP B 270 68.957 49.897 8.490 1.00 36.44 C
+ATOM 2971 CG TRP B 270 67.717 49.116 8.179 1.00 32.82 C
+ATOM 2972 CD1 TRP B 270 66.843 49.350 7.162 1.00 28.94 C
+ATOM 2973 CD2 TRP B 270 67.199 47.982 8.902 1.00 30.98 C
+ATOM 2974 NE1 TRP B 270 65.811 48.440 7.205 1.00 28.11 N
+ATOM 2975 CE2 TRP B 270 66.002 47.590 8.261 1.00 27.79 C
+ATOM 2976 CE3 TRP B 270 67.631 47.264 10.032 1.00 30.12 C
+ATOM 2977 CZ2 TRP B 270 65.221 46.513 8.706 1.00 27.65 C
+ATOM 2978 CZ3 TRP B 270 66.847 46.181 10.482 1.00 28.47 C
+ATOM 2979 CH2 TRP B 270 65.655 45.823 9.813 1.00 27.48 C
+ATOM 2980 N LYS B 271 70.982 52.387 7.892 1.00 43.15 N
+ATOM 2981 CA LYS B 271 72.232 53.048 8.259 1.00 42.97 C
+ATOM 2982 C LYS B 271 72.052 54.537 8.464 1.00 42.28 C
+ATOM 2983 O LYS B 271 72.806 55.162 9.196 1.00 38.58 O
+ATOM 2984 CB LYS B 271 73.305 52.797 7.193 1.00 46.26 C
+ATOM 2985 CG LYS B 271 74.736 52.865 7.734 1.00 53.06 C
+ATOM 2986 CD LYS B 271 75.782 52.441 6.700 1.00 56.56 C
+ATOM 2987 CE LYS B 271 76.322 53.620 5.908 1.00 57.17 C
+ATOM 2988 NZ LYS B 271 75.253 54.340 5.169 1.00 58.31 N
+ATOM 2989 N LEU B 272 71.049 55.111 7.817 1.00 40.42 N
+ATOM 2990 CA LEU B 272 70.809 56.535 7.970 1.00 39.09 C
+ATOM 2991 C LEU B 272 70.158 56.800 9.318 1.00 37.51 C
+ATOM 2992 O LEU B 272 70.376 57.851 9.926 1.00 36.91 O
+ATOM 2993 CB LEU B 272 69.922 57.073 6.845 1.00 43.62 C
+ATOM 2994 CG LEU B 272 70.535 58.222 6.032 1.00 47.96 C
+ATOM 2995 CD1 LEU B 272 69.438 58.892 5.232 1.00 50.99 C
+ATOM 2996 CD2 LEU B 272 71.204 59.239 6.951 1.00 50.25 C
+ATOM 2997 N VAL B 273 69.355 55.846 9.782 1.00 34.46 N
+ATOM 2998 CA VAL B 273 68.702 55.964 11.081 1.00 31.40 C
+ATOM 2999 C VAL B 273 69.756 55.736 12.167 1.00 30.01 C
+ATOM 3000 O VAL B 273 69.811 56.475 13.148 1.00 28.25 O
+ATOM 3001 CB VAL B 273 67.552 54.936 11.221 1.00 31.07 C
+ATOM 3002 CG1 VAL B 273 66.858 55.084 12.577 1.00 28.72 C
+ATOM 3003 CG2 VAL B 273 66.550 55.145 10.097 1.00 29.08 C
+ATOM 3004 N THR B 274 70.607 54.729 11.974 1.00 29.08 N
+ATOM 3005 CA THR B 274 71.661 54.442 12.941 1.00 31.40 C
+ATOM 3006 C THR B 274 72.573 55.656 13.089 1.00 36.97 C
+ATOM 3007 O THR B 274 73.070 55.932 14.179 1.00 33.62 O
+ATOM 3008 CB THR B 274 72.511 53.205 12.535 1.00 27.12 C
+ATOM 3009 OG1 THR B 274 71.710 52.027 12.634 1.00 26.37 O
+ATOM 3010 CG2 THR B 274 73.697 53.020 13.472 1.00 24.28 C
+ATOM 3011 N GLU B 275 72.795 56.382 11.997 1.00 44.33 N
+ATOM 3012 CA GLU B 275 73.624 57.576 12.063 1.00 48.98 C
+ATOM 3013 C GLU B 275 72.955 58.529 13.043 1.00 47.13 C
+ATOM 3014 O GLU B 275 73.559 58.979 14.019 1.00 44.34 O
+ATOM 3015 CB GLU B 275 73.706 58.256 10.700 1.00 61.55 C
+ATOM 3016 CG GLU B 275 74.772 57.717 9.786 1.00 85.55 C
+ATOM 3017 CD GLU B 275 74.741 58.391 8.433 1.00 95.88 C
+ATOM 3018 OE1 GLU B 275 74.791 59.640 8.384 1.00 99.15 O
+ATOM 3019 OE2 GLU B 275 74.666 57.669 7.418 1.00 99.19 O
+ATOM 3020 N TYR B 276 71.689 58.828 12.779 1.00 41.64 N
+ATOM 3021 CA TYR B 276 70.938 59.731 13.628 1.00 34.97 C
+ATOM 3022 C TYR B 276 71.055 59.329 15.092 1.00 33.20 C
+ATOM 3023 O TYR B 276 71.281 60.164 15.950 1.00 31.08 O
+ATOM 3024 CB TYR B 276 69.468 59.752 13.210 1.00 31.86 C
+ATOM 3025 CG TYR B 276 68.637 60.668 14.067 1.00 29.83 C
+ATOM 3026 CD1 TYR B 276 68.897 62.037 14.107 1.00 30.09 C
+ATOM 3027 CD2 TYR B 276 67.606 60.167 14.864 1.00 30.82 C
+ATOM 3028 CE1 TYR B 276 68.162 62.882 14.915 1.00 29.94 C
+ATOM 3029 CE2 TYR B 276 66.862 61.005 15.677 1.00 30.77 C
+ATOM 3030 CZ TYR B 276 67.148 62.362 15.693 1.00 30.80 C
+ATOM 3031 OH TYR B 276 66.410 63.201 16.486 1.00 34.43 O
+ATOM 3032 N ALA B 277 70.911 58.047 15.381 1.00 34.29 N
+ATOM 3033 CA ALA B 277 71.003 57.600 16.759 1.00 35.87 C
+ATOM 3034 C ALA B 277 72.387 57.866 17.347 1.00 36.14 C
+ATOM 3035 O ALA B 277 72.499 58.424 18.441 1.00 37.64 O
+ATOM 3036 CB ALA B 277 70.664 56.114 16.852 1.00 36.71 C
+ATOM 3037 N MET B 278 73.433 57.471 16.618 1.00 35.83 N
+ATOM 3038 CA MET B 278 74.817 57.642 17.068 1.00 36.61 C
+ATOM 3039 C MET B 278 75.210 59.080 17.347 1.00 40.00 C
+ATOM 3040 O MET B 278 76.012 59.342 18.232 1.00 37.10 O
+ATOM 3041 CB MET B 278 75.797 57.078 16.041 1.00 35.98 C
+ATOM 3042 CG MET B 278 75.964 55.573 16.058 1.00 38.79 C
+ATOM 3043 SD MET B 278 76.782 54.900 17.532 1.00 41.29 S
+ATOM 3044 CE MET B 278 77.491 56.401 18.327 1.00 38.77 C
+ATOM 3045 N GLU B 279 74.644 60.011 16.589 1.00 42.20 N
+ATOM 3046 CA GLU B 279 74.965 61.423 16.749 1.00 42.49 C
+ATOM 3047 C GLU B 279 74.025 62.122 17.720 1.00 41.80 C
+ATOM 3048 O GLU B 279 74.100 63.332 17.917 1.00 33.64 O
+ATOM 3049 CB GLU B 279 74.939 62.115 15.381 1.00 51.90 C
+ATOM 3050 CG GLU B 279 75.696 61.330 14.314 1.00 73.72 C
+ATOM 3051 CD GLU B 279 75.993 62.135 13.068 1.00 83.44 C
+ATOM 3052 OE1 GLU B 279 75.087 62.858 12.601 1.00 87.47 O
+ATOM 3053 OE2 GLU B 279 77.129 62.034 12.553 1.00 86.16 O
+ATOM 3054 N THR B 280 73.146 61.343 18.334 1.00 40.43 N
+ATOM 3055 CA THR B 280 72.194 61.854 19.304 1.00 37.13 C
+ATOM 3056 C THR B 280 72.490 61.123 20.609 1.00 38.77 C
+ATOM 3057 O THR B 280 71.958 61.456 21.665 1.00 35.72 O
+ATOM 3058 CB THR B 280 70.745 61.578 18.846 1.00 39.27 C
+ATOM 3059 OG1 THR B 280 70.429 62.421 17.730 1.00 47.57 O
+ATOM 3060 CG2 THR B 280 69.769 61.864 19.957 1.00 49.31 C
+ATOM 3061 N LYS B 281 73.376 60.135 20.527 1.00 43.68 N
+ATOM 3062 CA LYS B 281 73.751 59.335 21.685 1.00 45.87 C
+ATOM 3063 C LYS B 281 72.482 58.708 22.261 1.00 45.08 C
+ATOM 3064 O LYS B 281 72.383 58.440 23.457 1.00 45.40 O
+ATOM 3065 CB LYS B 281 74.454 60.220 22.720 1.00 51.30 C
+ATOM 3066 CG LYS B 281 75.735 60.880 22.201 1.00 62.19 C
+ATOM 3067 CD LYS B 281 76.982 60.421 22.977 1.00 67.78 C
+ATOM 3068 CE LYS B 281 78.260 61.108 22.474 1.00 69.13 C
+ATOM 3069 NZ LYS B 281 79.510 60.688 23.190 1.00 68.42 N
+ATOM 3070 N CYS B 282 71.524 58.460 21.372 1.00 44.69 N
+ATOM 3071 CA CYS B 282 70.225 57.895 21.728 1.00 43.41 C
+ATOM 3072 C CYS B 282 70.198 56.383 21.908 1.00 46.14 C
+ATOM 3073 O CYS B 282 70.397 55.630 20.965 1.00 42.02 O
+ATOM 3074 CB CYS B 282 69.192 58.290 20.679 1.00 41.14 C
+ATOM 3075 SG CYS B 282 67.557 57.665 21.058 1.00 43.83 S
+ATOM 3076 N ASP B 283 69.907 55.953 23.130 1.00 49.59 N
+ATOM 3077 CA ASP B 283 69.860 54.531 23.492 1.00 50.83 C
+ATOM 3078 C ASP B 283 68.426 54.072 23.785 1.00 49.49 C
+ATOM 3079 O ASP B 283 68.194 52.926 24.178 1.00 41.18 O
+ATOM 3080 CB ASP B 283 70.735 54.319 24.727 1.00 63.58 C
+ATOM 3081 CG ASP B 283 70.372 55.270 25.853 1.00 82.71 C
+ATOM 3082 OD1 ASP B 283 69.388 54.992 26.570 1.00 92.88 O
+ATOM 3083 OD2 ASP B 283 71.054 56.307 26.009 1.00 92.28 O
+ATOM 3084 N ASP B 284 67.478 54.986 23.587 1.00 45.03 N
+ATOM 3085 CA ASP B 284 66.058 54.732 23.823 1.00 40.02 C
+ATOM 3086 C ASP B 284 65.371 54.385 22.496 1.00 36.23 C
+ATOM 3087 O ASP B 284 65.298 55.222 21.590 1.00 32.64 O
+ATOM 3088 CB ASP B 284 65.411 55.987 24.421 1.00 47.17 C
+ATOM 3089 CG ASP B 284 64.082 55.705 25.109 1.00 57.74 C
+ATOM 3090 OD1 ASP B 284 63.261 54.925 24.577 1.00 62.39 O
+ATOM 3091 OD2 ASP B 284 63.855 56.294 26.187 1.00 63.79 O
+ATOM 3092 N VAL B 285 64.868 53.158 22.384 1.00 32.04 N
+ATOM 3093 CA VAL B 285 64.196 52.718 21.168 1.00 28.26 C
+ATOM 3094 C VAL B 285 62.923 53.504 20.901 1.00 28.27 C
+ATOM 3095 O VAL B 285 62.726 54.038 19.813 1.00 28.51 O
+ATOM 3096 CB VAL B 285 63.831 51.241 21.238 1.00 25.00 C
+ATOM 3097 CG1 VAL B 285 63.281 50.805 19.909 1.00 22.67 C
+ATOM 3098 CG2 VAL B 285 65.057 50.425 21.604 1.00 23.69 C
+ATOM 3099 N LEU B 286 62.039 53.550 21.886 1.00 31.33 N
+ATOM 3100 CA LEU B 286 60.812 54.303 21.726 1.00 33.74 C
+ATOM 3101 C LEU B 286 61.144 55.762 21.406 1.00 33.70 C
+ATOM 3102 O LEU B 286 60.540 56.364 20.521 1.00 35.93 O
+ATOM 3103 CB LEU B 286 59.959 54.224 22.995 1.00 35.23 C
+ATOM 3104 CG LEU B 286 59.062 52.995 23.124 1.00 35.60 C
+ATOM 3105 CD1 LEU B 286 58.140 53.178 24.314 1.00 36.20 C
+ATOM 3106 CD2 LEU B 286 58.249 52.818 21.864 1.00 33.97 C
+ATOM 3107 N LEU B 287 62.103 56.333 22.126 1.00 31.94 N
+ATOM 3108 CA LEU B 287 62.493 57.713 21.875 1.00 30.42 C
+ATOM 3109 C LEU B 287 63.063 57.893 20.454 1.00 30.62 C
+ATOM 3110 O LEU B 287 62.723 58.853 19.762 1.00 30.82 O
+ATOM 3111 CB LEU B 287 63.511 58.171 22.916 1.00 26.17 C
+ATOM 3112 CG LEU B 287 63.963 59.633 22.852 1.00 22.88 C
+ATOM 3113 CD1 LEU B 287 62.757 60.592 22.887 1.00 22.43 C
+ATOM 3114 CD2 LEU B 287 64.890 59.883 24.022 1.00 20.85 C
+ATOM 3115 N LEU B 288 63.916 56.978 20.009 1.00 30.82 N
+ATOM 3116 CA LEU B 288 64.471 57.084 18.665 1.00 31.86 C
+ATOM 3117 C LEU B 288 63.334 57.110 17.653 1.00 32.56 C
+ATOM 3118 O LEU B 288 63.267 57.993 16.793 1.00 32.73 O
+ATOM 3119 CB LEU B 288 65.375 55.897 18.348 1.00 32.38 C
+ATOM 3120 CG LEU B 288 65.996 55.946 16.950 1.00 32.76 C
+ATOM 3121 CD1 LEU B 288 66.849 57.216 16.805 1.00 33.91 C
+ATOM 3122 CD2 LEU B 288 66.839 54.700 16.722 1.00 33.34 C
+ATOM 3123 N LEU B 289 62.456 56.118 17.754 1.00 33.96 N
+ATOM 3124 CA LEU B 289 61.308 56.021 16.872 1.00 35.96 C
+ATOM 3125 C LEU B 289 60.522 57.338 16.879 1.00 36.83 C
+ATOM 3126 O LEU B 289 60.176 57.877 15.827 1.00 37.25 O
+ATOM 3127 CB LEU B 289 60.395 54.890 17.339 1.00 37.04 C
+ATOM 3128 CG LEU B 289 59.044 54.812 16.624 1.00 39.40 C
+ATOM 3129 CD1 LEU B 289 59.255 54.328 15.198 1.00 40.10 C
+ATOM 3130 CD2 LEU B 289 58.109 53.887 17.369 1.00 38.85 C
+ATOM 3131 N GLY B 290 60.237 57.847 18.073 1.00 37.23 N
+ATOM 3132 CA GLY B 290 59.488 59.084 18.193 1.00 36.45 C
+ATOM 3133 C GLY B 290 60.171 60.234 17.488 1.00 36.87 C
+ATOM 3134 O GLY B 290 59.538 60.975 16.733 1.00 35.41 O
+ATOM 3135 N MET B 291 61.465 60.391 17.735 1.00 36.79 N
+ATOM 3136 CA MET B 291 62.217 61.463 17.111 1.00 37.44 C
+ATOM 3137 C MET B 291 62.156 61.357 15.587 1.00 37.26 C
+ATOM 3138 O MET B 291 61.709 62.280 14.892 1.00 37.80 O
+ATOM 3139 CB MET B 291 63.686 61.419 17.540 1.00 40.47 C
+ATOM 3140 CG MET B 291 63.960 61.701 19.001 1.00 46.97 C
+ATOM 3141 SD MET B 291 63.247 63.246 19.528 1.00 50.44 S
+ATOM 3142 CE MET B 291 64.092 64.451 18.429 1.00 51.21 C
+ATOM 3143 N TYR B 292 62.591 60.217 15.067 1.00 34.81 N
+ATOM 3144 CA TYR B 292 62.641 60.028 13.633 1.00 32.12 C
+ATOM 3145 C TYR B 292 61.337 60.248 12.880 1.00 32.36 C
+ATOM 3146 O TYR B 292 61.348 60.789 11.771 1.00 31.76 O
+ATOM 3147 CB TYR B 292 63.207 58.648 13.304 1.00 29.07 C
+ATOM 3148 CG TYR B 292 64.091 58.666 12.078 1.00 27.00 C
+ATOM 3149 CD1 TYR B 292 65.304 59.355 12.079 1.00 25.14 C
+ATOM 3150 CD2 TYR B 292 63.701 58.020 10.905 1.00 26.70 C
+ATOM 3151 CE1 TYR B 292 66.108 59.395 10.946 1.00 25.08 C
+ATOM 3152 CE2 TYR B 292 64.498 58.053 9.762 1.00 26.55 C
+ATOM 3153 CZ TYR B 292 65.697 58.742 9.787 1.00 25.16 C
+ATOM 3154 OH TYR B 292 66.483 58.770 8.655 1.00 24.14 O
+ATOM 3155 N LEU B 293 60.215 59.841 13.463 1.00 32.96 N
+ATOM 3156 CA LEU B 293 58.936 60.009 12.792 1.00 34.10 C
+ATOM 3157 C LEU B 293 58.524 61.466 12.609 1.00 35.67 C
+ATOM 3158 O LEU B 293 57.543 61.757 11.930 1.00 34.88 O
+ATOM 3159 CB LEU B 293 57.855 59.236 13.537 1.00 34.85 C
+ATOM 3160 CG LEU B 293 57.934 57.730 13.271 1.00 38.35 C
+ATOM 3161 CD1 LEU B 293 57.021 56.955 14.206 1.00 38.90 C
+ATOM 3162 CD2 LEU B 293 57.555 57.467 11.814 1.00 39.60 C
+ATOM 3163 N GLU B 294 59.276 62.387 13.193 1.00 37.48 N
+ATOM 3164 CA GLU B 294 58.943 63.798 13.045 1.00 38.99 C
+ATOM 3165 C GLU B 294 59.543 64.360 11.768 1.00 39.03 C
+ATOM 3166 O GLU B 294 59.090 65.379 11.250 1.00 38.64 O
+ATOM 3167 CB GLU B 294 59.476 64.604 14.215 1.00 42.19 C
+ATOM 3168 CG GLU B 294 59.108 64.033 15.541 1.00 50.29 C
+ATOM 3169 CD GLU B 294 59.314 65.017 16.654 1.00 53.28 C
+ATOM 3170 OE1 GLU B 294 60.406 65.619 16.727 1.00 55.56 O
+ATOM 3171 OE2 GLU B 294 58.377 65.185 17.462 1.00 56.22 O
+ATOM 3172 N PHE B 295 60.576 63.701 11.267 1.00 37.85 N
+ATOM 3173 CA PHE B 295 61.225 64.171 10.063 1.00 35.94 C
+ATOM 3174 C PHE B 295 60.489 63.760 8.802 1.00 36.20 C
+ATOM 3175 O PHE B 295 60.932 64.077 7.709 1.00 37.56 O
+ATOM 3176 CB PHE B 295 62.662 63.640 9.971 1.00 36.00 C
+ATOM 3177 CG PHE B 295 63.500 63.895 11.192 1.00 33.88 C
+ATOM 3178 CD1 PHE B 295 63.299 65.027 11.979 1.00 34.40 C
+ATOM 3179 CD2 PHE B 295 64.526 63.016 11.527 1.00 33.37 C
+ATOM 3180 CE1 PHE B 295 64.113 65.279 13.082 1.00 35.16 C
+ATOM 3181 CE2 PHE B 295 65.348 63.254 12.625 1.00 34.75 C
+ATOM 3182 CZ PHE B 295 65.147 64.388 13.408 1.00 34.92 C
+ATOM 3183 N GLN B 296 59.379 63.053 8.936 1.00 39.46 N
+ATOM 3184 CA GLN B 296 58.646 62.614 7.748 1.00 43.33 C
+ATOM 3185 C GLN B 296 57.928 63.754 7.030 1.00 45.50 C
+ATOM 3186 O GLN B 296 57.604 63.647 5.842 1.00 46.04 O
+ATOM 3187 CB GLN B 296 57.622 61.552 8.123 1.00 43.36 C
+ATOM 3188 CG GLN B 296 56.541 62.073 9.028 1.00 43.08 C
+ATOM 3189 CD GLN B 296 55.501 61.033 9.292 1.00 43.93 C
+ATOM 3190 OE1 GLN B 296 55.816 59.937 9.743 1.00 45.16 O
+ATOM 3191 NE2 GLN B 296 54.249 61.359 9.008 1.00 45.76 N
+ATOM 3192 N TYR B 297 57.675 64.832 7.765 1.00 49.91 N
+ATOM 3193 CA TYR B 297 56.995 66.003 7.232 1.00 52.28 C
+ATOM 3194 C TYR B 297 57.998 66.907 6.535 1.00 52.85 C
+ATOM 3195 O TYR B 297 59.174 66.924 6.891 1.00 52.37 O
+ATOM 3196 CB TYR B 297 56.306 66.765 8.366 1.00 55.46 C
+ATOM 3197 CG TYR B 297 55.411 65.893 9.226 1.00 60.11 C
+ATOM 3198 CD1 TYR B 297 54.387 65.131 8.658 1.00 60.32 C
+ATOM 3199 CD2 TYR B 297 55.617 65.793 10.602 1.00 61.87 C
+ATOM 3200 CE1 TYR B 297 53.597 64.287 9.439 1.00 61.37 C
+ATOM 3201 CE2 TYR B 297 54.831 64.950 11.394 1.00 61.93 C
+ATOM 3202 CZ TYR B 297 53.827 64.195 10.807 1.00 61.80 C
+ATOM 3203 OH TYR B 297 53.084 63.318 11.576 1.00 61.03 O
+ATOM 3204 N SER B 298 57.535 67.657 5.536 1.00 54.55 N
+ATOM 3205 CA SER B 298 58.420 68.564 4.807 1.00 54.26 C
+ATOM 3206 C SER B 298 59.022 69.543 5.804 1.00 57.78 C
+ATOM 3207 O SER B 298 58.315 70.094 6.659 1.00 53.69 O
+ATOM 3208 CB SER B 298 57.649 69.328 3.729 1.00 51.76 C
+ATOM 3209 OG SER B 298 56.776 70.280 4.307 1.00 51.11 O
+ATOM 3210 N PHE B 299 60.330 69.744 5.699 1.00 67.50 N
+ATOM 3211 CA PHE B 299 61.035 70.642 6.605 1.00 75.16 C
+ATOM 3212 C PHE B 299 60.907 72.101 6.148 1.00 76.58 C
+ATOM 3213 O PHE B 299 61.306 73.027 6.868 1.00 79.85 O
+ATOM 3214 CB PHE B 299 62.517 70.244 6.689 1.00 81.03 C
+ATOM 3215 CG PHE B 299 63.399 71.022 5.766 1.00 89.07 C
+ATOM 3216 CD1 PHE B 299 64.220 72.031 6.259 1.00 91.52 C
+ATOM 3217 CD2 PHE B 299 63.357 70.793 4.394 1.00 92.58 C
+ATOM 3218 CE1 PHE B 299 64.985 72.804 5.401 1.00 93.46 C
+ATOM 3219 CE2 PHE B 299 64.118 71.563 3.523 1.00 94.19 C
+ATOM 3220 CZ PHE B 299 64.934 72.573 4.028 1.00 94.38 C
+ATOM 3221 N GLU B 300 60.358 72.291 4.950 1.00 82.55 N
+ATOM 3222 CA GLU B 300 60.172 73.624 4.387 1.00 88.29 C
+ATOM 3223 C GLU B 300 59.367 74.511 5.327 1.00 91.18 C
+ATOM 3224 O GLU B 300 59.786 75.618 5.659 1.00 97.37 O
+ATOM 3225 CB GLU B 300 59.472 73.530 3.033 1.00 88.10 C
+ATOM 3226 CG GLU B 300 60.354 72.977 1.928 1.00 83.41 C
+ATOM 3227 CD GLU B 300 59.783 71.726 1.281 1.00 80.11 C
+ATOM 3228 OE1 GLU B 300 58.698 71.808 0.662 1.00 78.42 O
+ATOM 3229 OE2 GLU B 300 60.426 70.660 1.395 1.00 77.59 O
+ATOM 3230 N MET B 301 58.208 74.031 5.754 1.00 92.84 N
+ATOM 3231 CA MET B 301 57.391 74.809 6.671 1.00 92.01 C
+ATOM 3232 C MET B 301 57.487 74.216 8.077 1.00 88.96 C
+ATOM 3233 O MET B 301 56.523 74.278 8.856 1.00 84.33 O
+ATOM 3234 CB MET B 301 55.927 74.834 6.208 1.00 97.69 C
+ATOM 3235 CG MET B 301 55.674 75.604 4.911 1.00105.22 C
+ATOM 3236 SD MET B 301 56.053 74.670 3.406 1.00108.78 S
+ATOM 3237 CE MET B 301 54.460 73.900 3.081 1.00108.86 C
+ATOM 3238 N CYS B 302 58.647 73.639 8.402 1.00 79.72 N
+ATOM 3239 CA CYS B 302 58.841 73.048 9.723 1.00 70.14 C
+ATOM 3240 C CYS B 302 58.966 74.149 10.768 1.00 66.23 C
+ATOM 3241 O CYS B 302 59.919 74.926 10.758 1.00 63.11 O
+ATOM 3242 CB CYS B 302 60.086 72.149 9.752 1.00 65.55 C
+ATOM 3243 SG CYS B 302 60.689 71.769 11.439 1.00 61.97 S
+ATOM 3244 N LEU B 303 57.988 74.208 11.665 1.00 62.86 N
+ATOM 3245 CA LEU B 303 57.983 75.211 12.714 1.00 64.49 C
+ATOM 3246 C LEU B 303 59.033 74.891 13.768 1.00 66.76 C
+ATOM 3247 O LEU B 303 59.713 75.787 14.275 1.00 69.86 O
+ATOM 3248 CB LEU B 303 56.595 75.288 13.350 1.00 61.91 C
+ATOM 3249 CG LEU B 303 55.454 75.620 12.383 1.00 57.69 C
+ATOM 3250 CD1 LEU B 303 54.133 75.686 13.152 1.00 54.85 C
+ATOM 3251 CD2 LEU B 303 55.741 76.952 11.682 1.00 53.50 C
+ATOM 3252 N LYS B 304 59.163 73.609 14.094 1.00 67.18 N
+ATOM 3253 CA LYS B 304 60.136 73.178 15.086 1.00 65.15 C
+ATOM 3254 C LYS B 304 61.512 73.645 14.668 1.00 64.15 C
+ATOM 3255 O LYS B 304 62.286 74.130 15.488 1.00 60.14 O
+ATOM 3256 CB LYS B 304 60.106 71.654 15.240 1.00 66.27 C
+ATOM 3257 CG LYS B 304 58.852 71.176 15.954 1.00 70.91 C
+ATOM 3258 CD LYS B 304 58.809 69.676 16.184 1.00 72.65 C
+ATOM 3259 CE LYS B 304 57.549 69.307 16.957 1.00 73.53 C
+ATOM 3260 NZ LYS B 304 57.318 67.843 16.974 1.00 74.13 N
+ATOM 3261 N CYS B 305 61.804 73.510 13.381 1.00 63.82 N
+ATOM 3262 CA CYS B 305 63.086 73.936 12.838 1.00 64.62 C
+ATOM 3263 C CYS B 305 63.086 75.460 12.767 1.00 65.05 C
+ATOM 3264 O CYS B 305 63.988 76.116 13.280 1.00 68.09 O
+ATOM 3265 CB CYS B 305 63.280 73.363 11.436 1.00 61.96 C
+ATOM 3266 SG CYS B 305 62.726 71.645 11.243 1.00 60.59 S
+ATOM 3267 N ILE B 306 62.064 76.009 12.115 1.00 68.13 N
+ATOM 3268 CA ILE B 306 61.915 77.451 11.969 1.00 75.66 C
+ATOM 3269 C ILE B 306 62.060 78.149 13.319 1.00 75.47 C
+ATOM 3270 O ILE B 306 62.648 79.232 13.404 1.00 75.04 O
+ATOM 3271 CB ILE B 306 60.532 77.816 11.351 1.00 79.19 C
+ATOM 3272 CG1 ILE B 306 60.521 77.459 9.862 1.00 83.79 C
+ATOM 3273 CG2 ILE B 306 60.239 79.298 11.548 1.00 83.04 C
+ATOM 3274 CD1 ILE B 306 59.170 77.620 9.190 1.00 83.47 C
+ATOM 3275 N LYS B 307 61.532 77.531 14.371 1.00 73.50 N
+ATOM 3276 CA LYS B 307 61.623 78.120 15.697 1.00 66.14 C
+ATOM 3277 C LYS B 307 62.810 77.624 16.502 1.00 62.00 C
+ATOM 3278 O LYS B 307 62.996 78.043 17.638 1.00 57.14 O
+ATOM 3279 CB LYS B 307 60.345 77.861 16.484 1.00 64.25 C
+ATOM 3280 CG LYS B 307 59.165 78.677 16.016 1.00 69.33 C
+ATOM 3281 CD LYS B 307 58.076 78.661 17.073 1.00 73.69 C
+ATOM 3282 CE LYS B 307 57.023 79.732 16.813 1.00 76.00 C
+ATOM 3283 NZ LYS B 307 56.037 79.829 17.937 1.00 76.84 N
+ATOM 3284 N LYS B 308 63.603 76.733 15.910 1.00 58.98 N
+ATOM 3285 CA LYS B 308 64.784 76.143 16.551 1.00 61.13 C
+ATOM 3286 C LYS B 308 64.573 75.794 18.026 1.00 64.93 C
+ATOM 3287 O LYS B 308 65.315 76.231 18.907 1.00 67.09 O
+ATOM 3288 CB LYS B 308 65.992 77.065 16.366 1.00 59.90 C
+ATOM 3289 CG LYS B 308 66.350 77.223 14.899 1.00 57.27 C
+ATOM 3290 CD LYS B 308 67.739 77.796 14.673 1.00 55.65 C
+ATOM 3291 CE LYS B 308 68.118 77.714 13.188 1.00 54.38 C
+ATOM 3292 NZ LYS B 308 69.533 78.114 12.928 1.00 54.05 N
+ATOM 3293 N GLU B 309 63.556 74.968 18.259 1.00 69.75 N
+ATOM 3294 CA GLU B 309 63.146 74.522 19.582 1.00 69.05 C
+ATOM 3295 C GLU B 309 63.874 73.272 20.094 1.00 66.42 C
+ATOM 3296 O GLU B 309 63.865 73.004 21.298 1.00 64.00 O
+ATOM 3297 CB GLU B 309 61.633 74.273 19.561 1.00 71.21 C
+ATOM 3298 CG GLU B 309 60.889 75.271 18.673 1.00 81.59 C
+ATOM 3299 CD GLU B 309 59.409 74.953 18.488 1.00 86.43 C
+ATOM 3300 OE1 GLU B 309 59.074 73.797 18.157 1.00 88.15 O
+ATOM 3301 OE2 GLU B 309 58.578 75.872 18.656 1.00 88.22 O
+ATOM 3302 N GLN B 310 64.493 72.500 19.200 1.00 62.07 N
+ATOM 3303 CA GLN B 310 65.213 71.292 19.620 1.00 61.01 C
+ATOM 3304 C GLN B 310 66.362 70.904 18.704 1.00 61.01 C
+ATOM 3305 O GLN B 310 66.152 70.576 17.538 1.00 64.40 O
+ATOM 3306 CB GLN B 310 64.263 70.109 19.721 1.00 61.85 C
+ATOM 3307 CG GLN B 310 63.392 70.115 20.956 1.00 60.20 C
+ATOM 3308 CD GLN B 310 64.181 69.953 22.234 1.00 58.49 C
+ATOM 3309 OE1 GLN B 310 65.065 69.096 22.333 1.00 58.28 O
+ATOM 3310 NE2 GLN B 310 63.854 70.765 23.233 1.00 57.04 N
+ATOM 3311 N PRO B 311 67.596 70.915 19.231 1.00 53.33 N
+ATOM 3312 CA PRO B 311 68.781 70.562 18.443 1.00 54.66 C
+ATOM 3313 C PRO B 311 68.675 69.156 17.859 1.00 54.84 C
+ATOM 3314 O PRO B 311 68.970 68.934 16.682 1.00 49.90 O
+ATOM 3315 CB PRO B 311 69.919 70.680 19.458 1.00 53.22 C
+ATOM 3316 CG PRO B 311 69.403 71.697 20.436 1.00 53.21 C
+ATOM 3317 CD PRO B 311 67.974 71.265 20.612 1.00 55.97 C
+ATOM 3318 N SER B 312 68.245 68.215 18.696 1.00 52.30 N
+ATOM 3319 CA SER B 312 68.092 66.824 18.290 1.00 50.49 C
+ATOM 3320 C SER B 312 67.088 66.712 17.152 1.00 48.57 C
+ATOM 3321 O SER B 312 66.842 65.632 16.623 1.00 46.34 O
+ATOM 3322 CB SER B 312 67.623 65.986 19.477 1.00 52.39 C
+ATOM 3323 OG SER B 312 66.447 66.532 20.041 1.00 60.03 O
+ATOM 3324 N HIS B 313 66.515 67.842 16.771 1.00 47.09 N
+ATOM 3325 CA HIS B 313 65.543 67.843 15.704 1.00 46.06 C
+ATOM 3326 C HIS B 313 65.917 68.737 14.532 1.00 46.44 C
+ATOM 3327 O HIS B 313 66.131 68.247 13.420 1.00 49.98 O
+ATOM 3328 CB HIS B 313 64.190 68.278 16.233 1.00 41.80 C
+ATOM 3329 CG HIS B 313 63.181 68.493 15.154 1.00 37.90 C
+ATOM 3330 ND1 HIS B 313 62.443 67.466 14.610 1.00 37.56 N
+ATOM 3331 CD2 HIS B 313 62.844 69.606 14.463 1.00 37.06 C
+ATOM 3332 CE1 HIS B 313 61.695 67.935 13.628 1.00 35.54 C
+ATOM 3333 NE2 HIS B 313 61.921 69.231 13.518 1.00 35.85 N
+ATOM 3334 N TYR B 314 65.995 70.045 14.782 1.00 48.21 N
+ATOM 3335 CA TYR B 314 66.297 71.003 13.722 1.00 50.55 C
+ATOM 3336 C TYR B 314 67.650 70.840 13.036 1.00 50.42 C
+ATOM 3337 O TYR B 314 67.812 71.242 11.879 1.00 52.24 O
+ATOM 3338 CB TYR B 314 66.110 72.448 14.226 1.00 49.89 C
+ATOM 3339 CG TYR B 314 67.114 72.970 15.244 1.00 47.78 C
+ATOM 3340 CD1 TYR B 314 68.456 73.137 14.912 1.00 46.23 C
+ATOM 3341 CD2 TYR B 314 66.700 73.373 16.520 1.00 46.18 C
+ATOM 3342 CE1 TYR B 314 69.362 73.696 15.818 1.00 45.52 C
+ATOM 3343 CE2 TYR B 314 67.600 73.933 17.437 1.00 44.56 C
+ATOM 3344 CZ TYR B 314 68.931 74.094 17.080 1.00 45.38 C
+ATOM 3345 OH TYR B 314 69.835 74.661 17.964 1.00 43.74 O
+ATOM 3346 N LYS B 315 68.609 70.236 13.734 1.00 47.12 N
+ATOM 3347 CA LYS B 315 69.936 70.016 13.165 1.00 42.83 C
+ATOM 3348 C LYS B 315 69.995 68.802 12.244 1.00 41.78 C
+ATOM 3349 O LYS B 315 71.008 68.572 11.603 1.00 40.97 O
+ATOM 3350 CB LYS B 315 70.976 69.832 14.272 1.00 39.23 C
+ATOM 3351 CG LYS B 315 71.369 71.099 15.012 1.00 35.30 C
+ATOM 3352 CD LYS B 315 72.241 70.770 16.213 1.00 35.35 C
+ATOM 3353 CE LYS B 315 73.383 69.814 15.827 1.00 38.50 C
+ATOM 3354 NZ LYS B 315 74.257 69.364 16.978 1.00 39.22 N
+ATOM 3355 N TYR B 316 68.926 68.017 12.171 1.00 40.36 N
+ATOM 3356 CA TYR B 316 68.955 66.839 11.310 1.00 40.25 C
+ATOM 3357 C TYR B 316 67.728 66.607 10.430 1.00 40.84 C
+ATOM 3358 O TYR B 316 67.746 65.730 9.569 1.00 44.03 O
+ATOM 3359 CB TYR B 316 69.180 65.580 12.148 1.00 39.03 C
+ATOM 3360 CG TYR B 316 70.244 65.701 13.219 1.00 37.49 C
+ATOM 3361 CD1 TYR B 316 69.998 66.416 14.395 1.00 36.49 C
+ATOM 3362 CD2 TYR B 316 71.489 65.088 13.068 1.00 35.85 C
+ATOM 3363 CE1 TYR B 316 70.961 66.512 15.400 1.00 35.10 C
+ATOM 3364 CE2 TYR B 316 72.458 65.178 14.066 1.00 36.39 C
+ATOM 3365 CZ TYR B 316 72.187 65.894 15.228 1.00 35.46 C
+ATOM 3366 OH TYR B 316 73.139 65.990 16.216 1.00 35.68 O
+ATOM 3367 N HIS B 317 66.662 67.376 10.630 1.00 43.49 N
+ATOM 3368 CA HIS B 317 65.446 67.180 9.839 1.00 45.61 C
+ATOM 3369 C HIS B 317 65.678 67.142 8.329 1.00 49.92 C
+ATOM 3370 O HIS B 317 65.214 66.223 7.656 1.00 50.12 O
+ATOM 3371 CB HIS B 317 64.407 68.256 10.185 1.00 42.50 C
+ATOM 3372 CG HIS B 317 63.042 67.994 9.613 1.00 38.56 C
+ATOM 3373 ND1 HIS B 317 61.952 68.788 9.897 1.00 37.03 N
+ATOM 3374 CD2 HIS B 317 62.589 67.024 8.787 1.00 36.40 C
+ATOM 3375 CE1 HIS B 317 60.886 68.318 9.274 1.00 34.43 C
+ATOM 3376 NE2 HIS B 317 61.246 67.247 8.593 1.00 35.39 N
+ATOM 3377 N GLU B 318 66.410 68.115 7.797 1.00 54.61 N
+ATOM 3378 CA GLU B 318 66.633 68.155 6.361 1.00 56.76 C
+ATOM 3379 C GLU B 318 67.372 66.943 5.809 1.00 54.56 C
+ATOM 3380 O GLU B 318 66.913 66.311 4.862 1.00 51.51 O
+ATOM 3381 CB GLU B 318 67.373 69.432 5.966 1.00 65.07 C
+ATOM 3382 CG GLU B 318 66.974 69.938 4.584 1.00 80.29 C
+ATOM 3383 CD GLU B 318 67.888 71.029 4.053 1.00 87.12 C
+ATOM 3384 OE1 GLU B 318 68.064 72.059 4.741 1.00 89.59 O
+ATOM 3385 OE2 GLU B 318 68.426 70.854 2.937 1.00 89.60 O
+ATOM 3386 N LYS B 319 68.513 66.607 6.394 1.00 50.20 N
+ATOM 3387 CA LYS B 319 69.288 65.458 5.917 1.00 45.94 C
+ATOM 3388 C LYS B 319 68.540 64.141 6.047 1.00 43.27 C
+ATOM 3389 O LYS B 319 69.017 63.114 5.584 1.00 42.55 O
+ATOM 3390 CB LYS B 319 70.623 65.346 6.677 1.00 46.28 C
+ATOM 3391 CG LYS B 319 71.459 64.118 6.303 1.00 49.81 C
+ATOM 3392 CD LYS B 319 72.929 64.279 6.697 1.00 52.72 C
+ATOM 3393 CE LYS B 319 73.820 63.252 5.984 1.00 54.35 C
+ATOM 3394 NZ LYS B 319 75.269 63.642 5.961 1.00 52.69 N
+ATOM 3395 N HIS B 320 67.367 64.166 6.665 1.00 39.44 N
+ATOM 3396 CA HIS B 320 66.624 62.933 6.872 1.00 36.27 C
+ATOM 3397 C HIS B 320 65.230 62.896 6.278 1.00 38.06 C
+ATOM 3398 O HIS B 320 64.614 61.831 6.211 1.00 33.79 O
+ATOM 3399 CB HIS B 320 66.559 62.634 8.374 1.00 31.18 C
+ATOM 3400 CG HIS B 320 67.882 62.246 8.964 1.00 26.63 C
+ATOM 3401 ND1 HIS B 320 68.464 61.017 8.745 1.00 25.13 N
+ATOM 3402 CD2 HIS B 320 68.762 62.952 9.709 1.00 25.44 C
+ATOM 3403 CE1 HIS B 320 69.650 60.983 9.325 1.00 24.49 C
+ATOM 3404 NE2 HIS B 320 69.857 62.147 9.917 1.00 25.01 N
+ATOM 3405 N TYR B 321 64.731 64.048 5.843 1.00 41.58 N
+ATOM 3406 CA TYR B 321 63.396 64.099 5.272 1.00 44.15 C
+ATOM 3407 C TYR B 321 63.152 62.855 4.433 1.00 43.01 C
+ATOM 3408 O TYR B 321 62.391 61.969 4.819 1.00 42.61 O
+ATOM 3409 CB TYR B 321 63.217 65.333 4.387 1.00 52.00 C
+ATOM 3410 CG TYR B 321 61.856 65.373 3.732 1.00 62.58 C
+ATOM 3411 CD1 TYR B 321 60.722 65.700 4.466 1.00 67.30 C
+ATOM 3412 CD2 TYR B 321 61.692 65.014 2.394 1.00 67.18 C
+ATOM 3413 CE1 TYR B 321 59.454 65.665 3.889 1.00 69.56 C
+ATOM 3414 CE2 TYR B 321 60.427 64.974 1.807 1.00 69.38 C
+ATOM 3415 CZ TYR B 321 59.311 65.301 2.562 1.00 69.87 C
+ATOM 3416 OH TYR B 321 58.052 65.263 2.000 1.00 70.45 O
+ATOM 3417 N ALA B 322 63.823 62.799 3.291 1.00 41.01 N
+ATOM 3418 CA ALA B 322 63.691 61.691 2.361 1.00 39.13 C
+ATOM 3419 C ALA B 322 63.559 60.345 3.052 1.00 39.76 C
+ATOM 3420 O ALA B 322 62.574 59.636 2.871 1.00 40.55 O
+ATOM 3421 CB ALA B 322 64.883 61.670 1.424 1.00 37.37 C
+ATOM 3422 N ASN B 323 64.559 59.994 3.848 1.00 40.66 N
+ATOM 3423 CA ASN B 323 64.553 58.714 4.534 1.00 40.52 C
+ATOM 3424 C ASN B 323 63.325 58.560 5.437 1.00 38.72 C
+ATOM 3425 O ASN B 323 62.603 57.567 5.351 1.00 38.53 O
+ATOM 3426 CB ASN B 323 65.853 58.562 5.335 1.00 43.51 C
+ATOM 3427 CG ASN B 323 66.192 57.111 5.641 1.00 46.70 C
+ATOM 3428 OD1 ASN B 323 66.229 56.266 4.747 1.00 48.85 O
+ATOM 3429 ND2 ASN B 323 66.452 56.821 6.910 1.00 49.44 N
+ATOM 3430 N ALA B 324 63.078 59.556 6.282 1.00 35.14 N
+ATOM 3431 CA ALA B 324 61.950 59.525 7.207 1.00 33.14 C
+ATOM 3432 C ALA B 324 60.616 59.284 6.506 1.00 33.80 C
+ATOM 3433 O ALA B 324 59.802 58.492 6.967 1.00 33.01 O
+ATOM 3434 CB ALA B 324 61.900 60.833 8.003 1.00 28.88 C
+ATOM 3435 N ALA B 325 60.395 59.977 5.395 1.00 36.17 N
+ATOM 3436 CA ALA B 325 59.156 59.834 4.638 1.00 37.55 C
+ATOM 3437 C ALA B 325 58.941 58.395 4.190 1.00 38.25 C
+ATOM 3438 O ALA B 325 57.800 57.957 4.036 1.00 37.94 O
+ATOM 3439 CB ALA B 325 59.170 60.760 3.426 1.00 38.98 C
+ATOM 3440 N ILE B 326 60.032 57.665 3.965 1.00 38.88 N
+ATOM 3441 CA ILE B 326 59.937 56.262 3.552 1.00 40.33 C
+ATOM 3442 C ILE B 326 59.763 55.389 4.794 1.00 39.45 C
+ATOM 3443 O ILE B 326 59.061 54.373 4.767 1.00 39.20 O
+ATOM 3444 CB ILE B 326 61.209 55.802 2.795 1.00 40.92 C
+ATOM 3445 CG1 ILE B 326 61.465 56.728 1.607 1.00 42.37 C
+ATOM 3446 CG2 ILE B 326 61.043 54.377 2.302 1.00 40.24 C
+ATOM 3447 CD1 ILE B 326 62.680 56.352 0.793 1.00 42.77 C
+ATOM 3448 N PHE B 327 60.417 55.813 5.873 1.00 38.70 N
+ATOM 3449 CA PHE B 327 60.382 55.130 7.157 1.00 36.97 C
+ATOM 3450 C PHE B 327 58.941 55.072 7.634 1.00 35.76 C
+ATOM 3451 O PHE B 327 58.491 54.060 8.172 1.00 36.30 O
+ATOM 3452 CB PHE B 327 61.235 55.909 8.156 1.00 35.76 C
+ATOM 3453 CG PHE B 327 61.344 55.263 9.511 1.00 33.77 C
+ATOM 3454 CD1 PHE B 327 62.111 54.112 9.691 1.00 33.17 C
+ATOM 3455 CD2 PHE B 327 60.714 55.832 10.621 1.00 32.44 C
+ATOM 3456 CE1 PHE B 327 62.251 53.547 10.956 1.00 31.28 C
+ATOM 3457 CE2 PHE B 327 60.852 55.269 11.886 1.00 32.11 C
+ATOM 3458 CZ PHE B 327 61.621 54.129 12.053 1.00 30.41 C
+ATOM 3459 N ALA B 328 58.226 56.168 7.407 1.00 36.03 N
+ATOM 3460 CA ALA B 328 56.829 56.310 7.802 1.00 38.07 C
+ATOM 3461 C ALA B 328 55.878 55.271 7.182 1.00 42.88 C
+ATOM 3462 O ALA B 328 54.810 54.983 7.749 1.00 42.32 O
+ATOM 3463 CB ALA B 328 56.359 57.719 7.464 1.00 34.21 C
+ATOM 3464 N ASP B 329 56.267 54.720 6.028 1.00 48.12 N
+ATOM 3465 CA ASP B 329 55.467 53.715 5.320 1.00 51.93 C
+ATOM 3466 C ASP B 329 56.080 52.315 5.411 1.00 52.24 C
+ATOM 3467 O ASP B 329 55.639 51.391 4.726 1.00 47.12 O
+ATOM 3468 CB ASP B 329 55.320 54.097 3.842 1.00 62.48 C
+ATOM 3469 CG ASP B 329 54.373 55.271 3.623 1.00 77.08 C
+ATOM 3470 OD1 ASP B 329 53.148 55.098 3.813 1.00 84.40 O
+ATOM 3471 OD2 ASP B 329 54.856 56.367 3.258 1.00 83.83 O
+ATOM 3472 N SER B 330 57.103 52.171 6.249 1.00 52.10 N
+ATOM 3473 CA SER B 330 57.787 50.898 6.449 1.00 49.40 C
+ATOM 3474 C SER B 330 57.034 50.044 7.466 1.00 47.75 C
+ATOM 3475 O SER B 330 56.465 50.563 8.429 1.00 46.70 O
+ATOM 3476 CB SER B 330 59.210 51.149 6.940 1.00 50.11 C
+ATOM 3477 OG SER B 330 59.866 49.925 7.214 1.00 59.43 O
+ATOM 3478 N LYS B 331 57.048 48.731 7.265 1.00 47.20 N
+ATOM 3479 CA LYS B 331 56.336 47.817 8.154 1.00 48.09 C
+ATOM 3480 C LYS B 331 57.020 47.406 9.457 1.00 49.60 C
+ATOM 3481 O LYS B 331 56.365 46.897 10.367 1.00 50.18 O
+ATOM 3482 CB LYS B 331 55.929 46.568 7.378 1.00 49.27 C
+ATOM 3483 CG LYS B 331 54.793 46.816 6.419 1.00 52.46 C
+ATOM 3484 CD LYS B 331 54.638 45.666 5.447 1.00 53.69 C
+ATOM 3485 CE LYS B 331 53.451 45.917 4.539 1.00 54.40 C
+ATOM 3486 NZ LYS B 331 53.455 47.327 4.063 1.00 54.52 N
+ATOM 3487 N ASN B 332 58.326 47.613 9.563 1.00 49.40 N
+ATOM 3488 CA ASN B 332 59.018 47.249 10.792 1.00 47.18 C
+ATOM 3489 C ASN B 332 59.894 48.392 11.315 1.00 44.74 C
+ATOM 3490 O ASN B 332 61.114 48.271 11.434 1.00 39.15 O
+ATOM 3491 CB ASN B 332 59.830 45.970 10.570 1.00 53.46 C
+ATOM 3492 CG ASN B 332 60.832 46.099 9.445 1.00 63.24 C
+ATOM 3493 OD1 ASN B 332 60.642 46.878 8.509 1.00 67.50 O
+ATOM 3494 ND2 ASN B 332 61.903 45.318 9.520 1.00 68.90 N
+ATOM 3495 N GLN B 333 59.243 49.510 11.618 1.00 39.07 N
+ATOM 3496 CA GLN B 333 59.911 50.696 12.146 1.00 34.64 C
+ATOM 3497 C GLN B 333 60.655 50.329 13.438 1.00 34.56 C
+ATOM 3498 O GLN B 333 61.814 50.694 13.630 1.00 30.29 O
+ATOM 3499 CB GLN B 333 58.875 51.789 12.430 1.00 35.07 C
+ATOM 3500 CG GLN B 333 58.169 52.351 11.204 1.00 37.13 C
+ATOM 3501 CD GLN B 333 57.029 53.284 11.577 1.00 39.05 C
+ATOM 3502 OE1 GLN B 333 56.555 54.065 10.757 1.00 41.74 O
+ATOM 3503 NE2 GLN B 333 56.574 53.195 12.820 1.00 39.34 N
+ATOM 3504 N LYS B 334 59.972 49.596 14.313 1.00 34.56 N
+ATOM 3505 CA LYS B 334 60.526 49.147 15.590 1.00 33.53 C
+ATOM 3506 C LYS B 334 61.849 48.383 15.399 1.00 32.50 C
+ATOM 3507 O LYS B 334 62.865 48.694 16.025 1.00 29.12 O
+ATOM 3508 CB LYS B 334 59.499 48.251 16.291 1.00 37.90 C
+ATOM 3509 CG LYS B 334 59.924 47.691 17.636 1.00 47.19 C
+ATOM 3510 CD LYS B 334 59.567 48.617 18.792 1.00 52.16 C
+ATOM 3511 CE LYS B 334 59.937 47.975 20.123 1.00 54.06 C
+ATOM 3512 NZ LYS B 334 59.619 48.844 21.287 1.00 55.05 N
+ATOM 3513 N THR B 335 61.837 47.380 14.531 1.00 31.48 N
+ATOM 3514 CA THR B 335 63.034 46.593 14.290 1.00 30.28 C
+ATOM 3515 C THR B 335 64.204 47.459 13.798 1.00 28.26 C
+ATOM 3516 O THR B 335 65.340 47.291 14.249 1.00 29.50 O
+ATOM 3517 CB THR B 335 62.731 45.464 13.291 1.00 32.26 C
+ATOM 3518 OG1 THR B 335 61.695 44.635 13.836 1.00 35.83 O
+ATOM 3519 CG2 THR B 335 63.973 44.608 13.036 1.00 33.46 C
+ATOM 3520 N ILE B 336 63.931 48.381 12.880 1.00 27.09 N
+ATOM 3521 CA ILE B 336 64.969 49.273 12.371 1.00 27.40 C
+ATOM 3522 C ILE B 336 65.602 50.021 13.564 1.00 28.54 C
+ATOM 3523 O ILE B 336 66.824 49.997 13.764 1.00 29.79 O
+ATOM 3524 CB ILE B 336 64.361 50.298 11.363 1.00 22.80 C
+ATOM 3525 CG1 ILE B 336 63.792 49.566 10.154 1.00 18.69 C
+ATOM 3526 CG2 ILE B 336 65.403 51.281 10.891 1.00 17.17 C
+ATOM 3527 CD1 ILE B 336 63.104 50.482 9.171 1.00 15.36 C
+ATOM 3528 N CYS B 337 64.759 50.667 14.367 1.00 31.20 N
+ATOM 3529 CA CYS B 337 65.227 51.411 15.535 1.00 34.00 C
+ATOM 3530 C CYS B 337 66.065 50.564 16.482 1.00 35.43 C
+ATOM 3531 O CYS B 337 66.986 51.068 17.114 1.00 35.01 O
+ATOM 3532 CB CYS B 337 64.045 51.992 16.310 1.00 32.98 C
+ATOM 3533 SG CYS B 337 63.171 53.316 15.443 1.00 37.16 S
+ATOM 3534 N GLN B 338 65.734 49.282 16.591 1.00 38.08 N
+ATOM 3535 CA GLN B 338 66.468 48.381 17.466 1.00 39.30 C
+ATOM 3536 C GLN B 338 67.931 48.354 17.112 1.00 37.85 C
+ATOM 3537 O GLN B 338 68.782 48.654 17.937 1.00 39.68 O
+ATOM 3538 CB GLN B 338 65.919 46.961 17.370 1.00 43.87 C
+ATOM 3539 CG GLN B 338 64.886 46.623 18.423 1.00 51.44 C
+ATOM 3540 CD GLN B 338 65.357 46.954 19.823 1.00 53.05 C
+ATOM 3541 OE1 GLN B 338 66.547 47.184 20.053 1.00 52.69 O
+ATOM 3542 NE2 GLN B 338 64.422 46.972 20.773 1.00 53.74 N
+ATOM 3543 N GLN B 339 68.214 47.988 15.873 1.00 35.50 N
+ATOM 3544 CA GLN B 339 69.583 47.905 15.390 1.00 32.70 C
+ATOM 3545 C GLN B 339 70.329 49.216 15.575 1.00 32.12 C
+ATOM 3546 O GLN B 339 71.527 49.222 15.872 1.00 33.21 O
+ATOM 3547 CB GLN B 339 69.597 47.527 13.910 1.00 31.03 C
+ATOM 3548 CG GLN B 339 70.984 47.315 13.350 1.00 27.08 C
+ATOM 3549 CD GLN B 339 70.953 46.595 12.023 1.00 26.96 C
+ATOM 3550 OE1 GLN B 339 71.117 47.210 10.971 1.00 27.76 O
+ATOM 3551 NE2 GLN B 339 70.729 45.279 12.063 1.00 24.84 N
+ATOM 3552 N ALA B 340 69.625 50.325 15.383 1.00 31.05 N
+ATOM 3553 CA ALA B 340 70.240 51.633 15.531 1.00 30.70 C
+ATOM 3554 C ALA B 340 70.646 51.857 16.981 1.00 31.49 C
+ATOM 3555 O ALA B 340 71.630 52.536 17.267 1.00 33.94 O
+ATOM 3556 CB ALA B 340 69.269 52.704 15.094 1.00 29.70 C
+ATOM 3557 N VAL B 341 69.877 51.277 17.891 1.00 30.39 N
+ATOM 3558 CA VAL B 341 70.130 51.411 19.317 1.00 30.71 C
+ATOM 3559 C VAL B 341 71.216 50.444 19.774 1.00 32.21 C
+ATOM 3560 O VAL B 341 72.079 50.798 20.576 1.00 28.62 O
+ATOM 3561 CB VAL B 341 68.829 51.164 20.127 1.00 31.56 C
+ATOM 3562 CG1 VAL B 341 69.128 51.172 21.635 1.00 31.69 C
+ATOM 3563 CG2 VAL B 341 67.806 52.231 19.779 1.00 30.26 C
+ATOM 3564 N ASP B 342 71.164 49.222 19.267 1.00 32.62 N
+ATOM 3565 CA ASP B 342 72.164 48.233 19.614 1.00 33.29 C
+ATOM 3566 C ASP B 342 73.529 48.766 19.180 1.00 32.48 C
+ATOM 3567 O ASP B 342 74.560 48.431 19.766 1.00 31.50 O
+ATOM 3568 CB ASP B 342 71.852 46.907 18.913 1.00 37.58 C
+ATOM 3569 CG ASP B 342 70.712 46.150 19.579 1.00 45.30 C
+ATOM 3570 OD1 ASP B 342 69.935 46.785 20.325 1.00 48.91 O
+ATOM 3571 OD2 ASP B 342 70.581 44.924 19.356 1.00 49.09 O
+ATOM 3572 N THR B 343 73.518 49.609 18.151 1.00 32.53 N
+ATOM 3573 CA THR B 343 74.738 50.191 17.617 1.00 33.32 C
+ATOM 3574 C THR B 343 75.275 51.195 18.600 1.00 34.53 C
+ATOM 3575 O THR B 343 76.479 51.294 18.795 1.00 35.65 O
+ATOM 3576 CB THR B 343 74.492 50.931 16.288 1.00 33.35 C
+ATOM 3577 OG1 THR B 343 74.164 49.986 15.259 1.00 33.16 O
+ATOM 3578 CG2 THR B 343 75.729 51.727 15.888 1.00 32.79 C
+ATOM 3579 N VAL B 344 74.379 51.957 19.211 1.00 35.21 N
+ATOM 3580 CA VAL B 344 74.803 52.958 20.170 1.00 34.09 C
+ATOM 3581 C VAL B 344 75.256 52.261 21.437 1.00 32.68 C
+ATOM 3582 O VAL B 344 76.235 52.663 22.045 1.00 30.76 O
+ATOM 3583 CB VAL B 344 73.665 53.946 20.481 1.00 37.18 C
+ATOM 3584 CG1 VAL B 344 74.111 54.942 21.522 1.00 39.83 C
+ATOM 3585 CG2 VAL B 344 73.256 54.673 19.206 1.00 39.69 C
+ATOM 3586 N LEU B 345 74.551 51.210 21.833 1.00 31.33 N
+ATOM 3587 CA LEU B 345 74.933 50.466 23.027 1.00 30.01 C
+ATOM 3588 C LEU B 345 76.246 49.749 22.754 1.00 29.83 C
+ATOM 3589 O LEU B 345 77.065 49.567 23.658 1.00 30.36 O
+ATOM 3590 CB LEU B 345 73.863 49.435 23.407 1.00 29.53 C
+ATOM 3591 CG LEU B 345 72.501 49.978 23.857 1.00 30.06 C
+ATOM 3592 CD1 LEU B 345 71.563 48.827 24.094 1.00 29.20 C
+ATOM 3593 CD2 LEU B 345 72.645 50.793 25.138 1.00 30.75 C
+ATOM 3594 N ALA B 346 76.446 49.345 21.501 1.00 29.79 N
+ATOM 3595 CA ALA B 346 77.665 48.643 21.115 1.00 29.54 C
+ATOM 3596 C ALA B 346 78.877 49.572 21.183 1.00 31.30 C
+ATOM 3597 O ALA B 346 79.975 49.159 21.570 1.00 30.44 O
+ATOM 3598 CB ALA B 346 77.518 48.083 19.720 1.00 26.97 C
+ATOM 3599 N LYS B 347 78.675 50.830 20.808 1.00 33.83 N
+ATOM 3600 CA LYS B 347 79.750 51.806 20.834 1.00 35.39 C
+ATOM 3601 C LYS B 347 80.087 52.097 22.295 1.00 36.26 C
+ATOM 3602 O LYS B 347 81.250 52.262 22.655 1.00 33.16 O
+ATOM 3603 CB LYS B 347 79.323 53.085 20.096 1.00 37.67 C
+ATOM 3604 CG LYS B 347 80.354 54.207 20.099 1.00 43.63 C
+ATOM 3605 CD LYS B 347 81.694 53.751 19.545 1.00 47.72 C
+ATOM 3606 CE LYS B 347 82.795 54.786 19.777 1.00 48.27 C
+ATOM 3607 NZ LYS B 347 84.165 54.220 19.504 1.00 48.67 N
+ATOM 3608 N LYS B 348 79.066 52.124 23.142 1.00 38.54 N
+ATOM 3609 CA LYS B 348 79.281 52.391 24.554 1.00 40.37 C
+ATOM 3610 C LYS B 348 79.996 51.242 25.239 1.00 42.08 C
+ATOM 3611 O LYS B 348 80.681 51.436 26.244 1.00 38.28 O
+ATOM 3612 CB LYS B 348 77.950 52.682 25.249 1.00 43.59 C
+ATOM 3613 CG LYS B 348 77.339 53.996 24.807 1.00 53.33 C
+ATOM 3614 CD LYS B 348 76.104 54.352 25.612 1.00 58.30 C
+ATOM 3615 CE LYS B 348 75.608 55.749 25.266 1.00 59.02 C
+ATOM 3616 NZ LYS B 348 74.437 56.117 26.109 1.00 60.12 N
+ATOM 3617 N ARG B 349 79.832 50.042 24.698 1.00 44.90 N
+ATOM 3618 CA ARG B 349 80.487 48.871 25.254 1.00 44.81 C
+ATOM 3619 C ARG B 349 81.959 48.897 24.826 1.00 42.98 C
+ATOM 3620 O ARG B 349 82.850 48.404 25.529 1.00 42.59 O
+ATOM 3621 CB ARG B 349 79.802 47.602 24.744 1.00 47.90 C
+ATOM 3622 CG ARG B 349 80.517 46.326 25.123 1.00 60.28 C
+ATOM 3623 CD ARG B 349 80.859 46.297 26.604 1.00 67.20 C
+ATOM 3624 NE ARG B 349 80.132 45.256 27.327 1.00 70.34 N
+ATOM 3625 CZ ARG B 349 78.808 45.213 27.472 1.00 70.31 C
+ATOM 3626 NH1 ARG B 349 78.038 46.158 26.945 1.00 70.03 N
+ATOM 3627 NH2 ARG B 349 78.249 44.218 28.150 1.00 69.88 N
+ATOM 3628 N VAL B 350 82.215 49.494 23.671 1.00 41.99 N
+ATOM 3629 CA VAL B 350 83.570 49.574 23.162 1.00 42.89 C
+ATOM 3630 C VAL B 350 84.382 50.624 23.908 1.00 42.33 C
+ATOM 3631 O VAL B 350 85.553 50.411 24.200 1.00 45.20 O
+ATOM 3632 CB VAL B 350 83.570 49.897 21.651 1.00 42.12 C
+ATOM 3633 CG1 VAL B 350 84.978 50.240 21.187 1.00 41.20 C
+ATOM 3634 CG2 VAL B 350 83.035 48.703 20.867 1.00 39.28 C
+ATOM 3635 N ASP B 351 83.764 51.756 24.222 1.00 41.66 N
+ATOM 3636 CA ASP B 351 84.471 52.814 24.927 1.00 40.28 C
+ATOM 3637 C ASP B 351 84.756 52.423 26.366 1.00 40.20 C
+ATOM 3638 O ASP B 351 85.732 52.881 26.969 1.00 35.85 O
+ATOM 3639 CB ASP B 351 83.666 54.105 24.886 1.00 40.64 C
+ATOM 3640 CG ASP B 351 83.540 54.652 23.498 1.00 42.17 C
+ATOM 3641 OD1 ASP B 351 84.480 54.434 22.703 1.00 44.45 O
+ATOM 3642 OD2 ASP B 351 82.514 55.308 23.210 1.00 43.39 O
+ATOM 3643 N SER B 352 83.894 51.574 26.909 1.00 39.00 N
+ATOM 3644 CA SER B 352 84.062 51.092 28.269 1.00 39.31 C
+ATOM 3645 C SER B 352 85.386 50.362 28.358 1.00 37.56 C
+ATOM 3646 O SER B 352 86.174 50.578 29.269 1.00 37.89 O
+ATOM 3647 CB SER B 352 82.943 50.114 28.648 1.00 41.62 C
+ATOM 3648 OG SER B 352 81.742 50.788 28.970 1.00 49.00 O
+ATOM 3649 N LEU B 353 85.638 49.506 27.385 1.00 35.98 N
+ATOM 3650 CA LEU B 353 86.855 48.729 27.399 1.00 35.71 C
+ATOM 3651 C LEU B 353 88.065 49.306 26.687 1.00 35.63 C
+ATOM 3652 O LEU B 353 89.122 48.672 26.680 1.00 39.17 O
+ATOM 3653 CB LEU B 353 86.552 47.342 26.845 1.00 34.84 C
+ATOM 3654 CG LEU B 353 85.559 46.567 27.701 1.00 32.99 C
+ATOM 3655 CD1 LEU B 353 85.137 45.313 26.974 1.00 31.38 C
+ATOM 3656 CD2 LEU B 353 86.216 46.235 29.039 1.00 32.04 C
+ATOM 3657 N GLN B 354 87.945 50.496 26.107 1.00 34.01 N
+ATOM 3658 CA GLN B 354 89.077 51.062 25.380 1.00 32.72 C
+ATOM 3659 C GLN B 354 89.514 52.481 25.692 1.00 31.82 C
+ATOM 3660 O GLN B 354 90.638 52.851 25.380 1.00 33.53 O
+ATOM 3661 CB GLN B 354 88.836 50.969 23.875 1.00 30.21 C
+ATOM 3662 CG GLN B 354 88.243 49.657 23.467 1.00 30.42 C
+ATOM 3663 CD GLN B 354 88.562 49.283 22.039 1.00 31.22 C
+ATOM 3664 OE1 GLN B 354 88.504 50.121 21.123 1.00 31.76 O
+ATOM 3665 NE2 GLN B 354 88.891 48.009 21.833 1.00 30.51 N
+ATOM 3666 N LEU B 355 88.658 53.301 26.274 1.00 30.07 N
+ATOM 3667 CA LEU B 355 89.100 54.656 26.543 1.00 30.74 C
+ATOM 3668 C LEU B 355 89.788 54.783 27.893 1.00 31.26 C
+ATOM 3669 O LEU B 355 89.479 54.053 28.843 1.00 31.32 O
+ATOM 3670 CB LEU B 355 87.922 55.619 26.469 1.00 30.80 C
+ATOM 3671 CG LEU B 355 87.202 55.581 25.129 1.00 29.10 C
+ATOM 3672 CD1 LEU B 355 86.028 56.522 25.155 1.00 28.35 C
+ATOM 3673 CD2 LEU B 355 88.174 55.959 24.029 1.00 29.41 C
+ATOM 3674 N THR B 356 90.748 55.698 27.963 1.00 30.32 N
+ATOM 3675 CA THR B 356 91.451 55.956 29.210 1.00 27.99 C
+ATOM 3676 C THR B 356 90.441 56.769 29.983 1.00 27.19 C
+ATOM 3677 O THR B 356 89.513 57.323 29.388 1.00 27.63 O
+ATOM 3678 CB THR B 356 92.685 56.811 28.985 1.00 27.25 C
+ATOM 3679 OG1 THR B 356 92.303 58.065 28.376 1.00 22.76 O
+ATOM 3680 CG2 THR B 356 93.671 56.061 28.103 1.00 24.43 C
+ATOM 3681 N ARG B 357 90.600 56.848 31.293 1.00 27.80 N
+ATOM 3682 CA ARG B 357 89.645 57.605 32.068 1.00 31.82 C
+ATOM 3683 C ARG B 357 89.606 59.082 31.655 1.00 39.66 C
+ATOM 3684 O ARG B 357 88.529 59.702 31.642 1.00 36.19 O
+ATOM 3685 CB ARG B 357 89.938 57.441 33.554 1.00 27.00 C
+ATOM 3686 CG ARG B 357 89.729 56.014 34.042 1.00 22.61 C
+ATOM 3687 CD ARG B 357 90.095 55.866 35.507 1.00 21.02 C
+ATOM 3688 NE ARG B 357 89.191 56.622 36.368 1.00 23.50 N
+ATOM 3689 CZ ARG B 357 87.917 56.304 36.584 1.00 22.05 C
+ATOM 3690 NH1 ARG B 357 87.383 55.237 36.004 1.00 22.06 N
+ATOM 3691 NH2 ARG B 357 87.175 57.057 37.383 1.00 22.73 N
+ATOM 3692 N GLU B 358 90.755 59.646 31.283 1.00 48.78 N
+ATOM 3693 CA GLU B 358 90.751 61.039 30.875 1.00 54.17 C
+ATOM 3694 C GLU B 358 89.879 61.210 29.631 1.00 50.56 C
+ATOM 3695 O GLU B 358 89.065 62.134 29.575 1.00 44.95 O
+ATOM 3696 CB GLU B 358 92.170 61.562 30.615 1.00 70.81 C
+ATOM 3697 CG GLU B 358 92.263 63.089 30.789 1.00102.33 C
+ATOM 3698 CD GLU B 358 93.674 63.645 30.666 1.00115.30 C
+ATOM 3699 OE1 GLU B 358 94.589 63.108 31.329 1.00119.65 O
+ATOM 3700 OE2 GLU B 358 93.862 64.631 29.917 1.00119.28 O
+ATOM 3701 N GLN B 359 90.027 60.325 28.643 1.00 43.72 N
+ATOM 3702 CA GLN B 359 89.208 60.423 27.432 1.00 35.07 C
+ATOM 3703 C GLN B 359 87.743 60.367 27.850 1.00 30.94 C
+ATOM 3704 O GLN B 359 86.893 61.071 27.289 1.00 28.83 O
+ATOM 3705 CB GLN B 359 89.507 59.282 26.469 1.00 32.53 C
+ATOM 3706 CG GLN B 359 90.969 59.120 26.154 1.00 34.68 C
+ATOM 3707 CD GLN B 359 91.224 57.948 25.221 1.00 37.16 C
+ATOM 3708 OE1 GLN B 359 90.667 56.855 25.396 1.00 35.83 O
+ATOM 3709 NE2 GLN B 359 92.075 58.168 24.223 1.00 37.58 N
+ATOM 3710 N MET B 360 87.454 59.527 28.843 1.00 27.62 N
+ATOM 3711 CA MET B 360 86.095 59.408 29.373 1.00 26.56 C
+ATOM 3712 C MET B 360 85.663 60.779 29.912 1.00 27.50 C
+ATOM 3713 O MET B 360 84.619 61.323 29.511 1.00 26.72 O
+ATOM 3714 CB MET B 360 86.036 58.372 30.515 1.00 22.82 C
+ATOM 3715 CG MET B 360 85.872 56.906 30.093 1.00 17.31 C
+ATOM 3716 SD MET B 360 85.841 55.762 31.514 1.00 15.67 S
+ATOM 3717 CE MET B 360 87.195 54.760 31.176 1.00 14.26 C
+ATOM 3718 N LEU B 361 86.481 61.341 30.807 1.00 26.92 N
+ATOM 3719 CA LEU B 361 86.171 62.634 31.401 1.00 26.64 C
+ATOM 3720 C LEU B 361 86.007 63.735 30.363 1.00 26.61 C
+ATOM 3721 O LEU B 361 85.213 64.651 30.562 1.00 25.27 O
+ATOM 3722 CB LEU B 361 87.249 63.058 32.408 1.00 27.64 C
+ATOM 3723 CG LEU B 361 86.838 63.711 33.752 1.00 27.55 C
+ATOM 3724 CD1 LEU B 361 87.946 64.652 34.224 1.00 24.80 C
+ATOM 3725 CD2 LEU B 361 85.513 64.472 33.622 1.00 26.29 C
+ATOM 3726 N THR B 362 86.748 63.665 29.260 1.00 28.11 N
+ATOM 3727 CA THR B 362 86.627 64.704 28.234 1.00 31.93 C
+ATOM 3728 C THR B 362 85.309 64.602 27.455 1.00 33.70 C
+ATOM 3729 O THR B 362 84.704 65.622 27.106 1.00 34.11 O
+ATOM 3730 CB THR B 362 87.781 64.661 27.234 1.00 31.36 C
+ATOM 3731 OG1 THR B 362 89.021 64.783 27.934 1.00 32.92 O
+ATOM 3732 CG2 THR B 362 87.661 65.813 26.255 1.00 32.58 C
+ATOM 3733 N ASN B 363 84.861 63.381 27.173 1.00 34.86 N
+ATOM 3734 CA ASN B 363 83.599 63.223 26.471 1.00 34.56 C
+ATOM 3735 C ASN B 363 82.530 63.846 27.352 1.00 34.02 C
+ATOM 3736 O ASN B 363 81.655 64.557 26.877 1.00 33.97 O
+ATOM 3737 CB ASN B 363 83.278 61.751 26.245 1.00 36.57 C
+ATOM 3738 CG ASN B 363 84.315 61.057 25.394 1.00 38.97 C
+ATOM 3739 OD1 ASN B 363 84.997 61.686 24.588 1.00 39.94 O
+ATOM 3740 ND2 ASN B 363 84.430 59.746 25.561 1.00 40.98 N
+ATOM 3741 N ARG B 364 82.624 63.589 28.650 1.00 33.79 N
+ATOM 3742 CA ARG B 364 81.668 64.138 29.601 1.00 34.11 C
+ATOM 3743 C ARG B 364 81.672 65.657 29.491 1.00 33.81 C
+ATOM 3744 O ARG B 364 80.621 66.286 29.392 1.00 34.79 O
+ATOM 3745 CB ARG B 364 82.039 63.710 31.025 1.00 34.92 C
+ATOM 3746 CG ARG B 364 81.113 64.224 32.100 1.00 35.24 C
+ATOM 3747 CD ARG B 364 79.720 63.681 31.944 1.00 35.27 C
+ATOM 3748 NE ARG B 364 78.778 64.409 32.784 1.00 37.20 N
+ATOM 3749 CZ ARG B 364 77.477 64.144 32.850 1.00 38.31 C
+ATOM 3750 NH1 ARG B 364 76.962 63.160 32.127 1.00 39.70 N
+ATOM 3751 NH2 ARG B 364 76.684 64.871 33.620 1.00 37.31 N
+ATOM 3752 N PHE B 365 82.862 66.244 29.496 1.00 32.52 N
+ATOM 3753 CA PHE B 365 82.991 67.692 29.394 1.00 31.25 C
+ATOM 3754 C PHE B 365 82.386 68.232 28.104 1.00 31.75 C
+ATOM 3755 O PHE B 365 81.663 69.240 28.121 1.00 29.40 O
+ATOM 3756 CB PHE B 365 84.463 68.087 29.517 1.00 30.06 C
+ATOM 3757 CG PHE B 365 84.936 68.179 30.934 1.00 30.36 C
+ATOM 3758 CD1 PHE B 365 84.235 67.545 31.959 1.00 31.72 C
+ATOM 3759 CD2 PHE B 365 86.079 68.900 31.253 1.00 29.41 C
+ATOM 3760 CE1 PHE B 365 84.667 67.630 33.285 1.00 30.86 C
+ATOM 3761 CE2 PHE B 365 86.523 68.993 32.568 1.00 29.08 C
+ATOM 3762 CZ PHE B 365 85.818 68.357 33.588 1.00 30.67 C
+ATOM 3763 N ASN B 366 82.671 67.561 26.989 1.00 30.81 N
+ATOM 3764 CA ASN B 366 82.127 67.987 25.712 1.00 30.95 C
+ATOM 3765 C ASN B 366 80.615 68.018 25.790 1.00 33.38 C
+ATOM 3766 O ASN B 366 79.973 68.962 25.314 1.00 30.44 O
+ATOM 3767 CB ASN B 366 82.573 67.052 24.598 1.00 29.44 C
+ATOM 3768 CG ASN B 366 83.985 67.329 24.156 1.00 29.88 C
+ATOM 3769 OD1 ASN B 366 84.327 68.471 23.875 1.00 30.77 O
+ATOM 3770 ND2 ASN B 366 84.817 66.288 24.090 1.00 31.26 N
+ATOM 3771 N ASP B 367 80.047 66.995 26.415 1.00 37.78 N
+ATOM 3772 CA ASP B 367 78.603 66.926 26.562 1.00 41.01 C
+ATOM 3773 C ASP B 367 78.072 68.084 27.391 1.00 39.56 C
+ATOM 3774 O ASP B 367 77.196 68.822 26.939 1.00 38.85 O
+ATOM 3775 CB ASP B 367 78.198 65.587 27.174 1.00 48.84 C
+ATOM 3776 CG ASP B 367 78.341 64.434 26.187 1.00 60.70 C
+ATOM 3777 OD1 ASP B 367 77.619 64.428 25.166 1.00 66.84 O
+ATOM 3778 OD2 ASP B 367 79.180 63.540 26.420 1.00 67.04 O
+ATOM 3779 N LEU B 368 78.600 68.267 28.594 1.00 35.98 N
+ATOM 3780 CA LEU B 368 78.132 69.375 29.413 1.00 31.25 C
+ATOM 3781 C LEU B 368 78.281 70.658 28.608 1.00 28.73 C
+ATOM 3782 O LEU B 368 77.414 71.526 28.647 1.00 26.95 O
+ATOM 3783 CB LEU B 368 78.928 69.473 30.715 1.00 32.07 C
+ATOM 3784 CG LEU B 368 78.741 68.322 31.712 1.00 33.32 C
+ATOM 3785 CD1 LEU B 368 79.473 68.666 33.002 1.00 32.58 C
+ATOM 3786 CD2 LEU B 368 77.251 68.084 31.981 1.00 32.94 C
+ATOM 3787 N LEU B 369 79.373 70.777 27.862 1.00 28.21 N
+ATOM 3788 CA LEU B 369 79.560 71.969 27.054 1.00 28.53 C
+ATOM 3789 C LEU B 369 78.444 72.025 26.019 1.00 31.16 C
+ATOM 3790 O LEU B 369 77.818 73.077 25.832 1.00 33.08 O
+ATOM 3791 CB LEU B 369 80.928 71.971 26.359 1.00 21.52 C
+ATOM 3792 CG LEU B 369 82.155 72.464 27.146 1.00 16.34 C
+ATOM 3793 CD1 LEU B 369 83.349 72.569 26.186 1.00 12.51 C
+ATOM 3794 CD2 LEU B 369 81.877 73.836 27.781 1.00 13.17 C
+ATOM 3795 N ASP B 370 78.183 70.898 25.358 1.00 36.36 N
+ATOM 3796 CA ASP B 370 77.125 70.853 24.356 1.00 40.75 C
+ATOM 3797 C ASP B 370 75.882 71.552 24.916 1.00 42.57 C
+ATOM 3798 O ASP B 370 75.249 72.355 24.229 1.00 44.78 O
+ATOM 3799 CB ASP B 370 76.795 69.400 23.965 1.00 43.02 C
+ATOM 3800 CG ASP B 370 77.877 68.756 23.073 1.00 48.21 C
+ATOM 3801 OD1 ASP B 370 78.292 69.386 22.068 1.00 50.27 O
+ATOM 3802 OD2 ASP B 370 78.310 67.613 23.366 1.00 50.04 O
+ATOM 3803 N ARG B 371 75.549 71.271 26.174 1.00 43.01 N
+ATOM 3804 CA ARG B 371 74.384 71.888 26.807 1.00 42.46 C
+ATOM 3805 C ARG B 371 74.542 73.386 26.963 1.00 41.54 C
+ATOM 3806 O ARG B 371 73.631 74.160 26.664 1.00 42.36 O
+ATOM 3807 CB ARG B 371 74.160 71.346 28.206 1.00 43.84 C
+ATOM 3808 CG ARG B 371 73.765 69.930 28.310 1.00 45.50 C
+ATOM 3809 CD ARG B 371 73.346 69.746 29.731 1.00 47.79 C
+ATOM 3810 NE ARG B 371 73.457 68.365 30.170 1.00 51.73 N
+ATOM 3811 CZ ARG B 371 73.344 67.990 31.439 1.00 51.00 C
+ATOM 3812 NH1 ARG B 371 73.119 68.909 32.375 1.00 47.19 N
+ATOM 3813 NH2 ARG B 371 73.450 66.704 31.767 1.00 51.17 N
+ATOM 3814 N MET B 372 75.697 73.779 27.486 1.00 39.37 N
+ATOM 3815 CA MET B 372 75.987 75.180 27.715 1.00 37.56 C
+ATOM 3816 C MET B 372 75.759 76.012 26.457 1.00 37.35 C
+ATOM 3817 O MET B 372 75.131 77.072 26.524 1.00 38.99 O
+ATOM 3818 CB MET B 372 77.423 75.337 28.239 1.00 34.77 C
+ATOM 3819 CG MET B 372 77.597 74.865 29.706 1.00 27.50 C
+ATOM 3820 SD MET B 372 79.306 74.596 30.190 1.00 19.75 S
+ATOM 3821 CE MET B 372 79.791 76.258 30.566 1.00 22.14 C
+ATOM 3822 N ASP B 373 76.238 75.538 25.309 1.00 37.88 N
+ATOM 3823 CA ASP B 373 76.029 76.291 24.073 1.00 40.62 C
+ATOM 3824 C ASP B 373 74.527 76.564 23.927 1.00 42.73 C
+ATOM 3825 O ASP B 373 74.115 77.661 23.550 1.00 44.89 O
+ATOM 3826 CB ASP B 373 76.536 75.514 22.852 1.00 37.14 C
+ATOM 3827 CG ASP B 373 78.034 75.274 22.895 1.00 34.93 C
+ATOM 3828 OD1 ASP B 373 78.748 76.081 23.532 1.00 34.98 O
+ATOM 3829 OD2 ASP B 373 78.507 74.286 22.286 1.00 32.01 O
+ATOM 3830 N ILE B 374 73.711 75.568 24.251 1.00 42.40 N
+ATOM 3831 CA ILE B 374 72.273 75.726 24.160 1.00 41.74 C
+ATOM 3832 C ILE B 374 71.657 76.545 25.291 1.00 40.51 C
+ATOM 3833 O ILE B 374 70.911 77.479 25.016 1.00 40.48 O
+ATOM 3834 CB ILE B 374 71.579 74.377 24.111 1.00 43.36 C
+ATOM 3835 CG1 ILE B 374 72.114 73.584 22.927 1.00 45.31 C
+ATOM 3836 CG2 ILE B 374 70.077 74.577 23.998 1.00 43.88 C
+ATOM 3837 CD1 ILE B 374 71.606 72.159 22.878 1.00 48.19 C
+ATOM 3838 N MET B 375 71.939 76.191 26.548 1.00 37.53 N
+ATOM 3839 CA MET B 375 71.389 76.935 27.693 1.00 36.20 C
+ATOM 3840 C MET B 375 71.649 78.425 27.548 1.00 36.07 C
+ATOM 3841 O MET B 375 70.754 79.258 27.747 1.00 36.64 O
+ATOM 3842 CB MET B 375 72.053 76.539 29.010 1.00 33.12 C
+ATOM 3843 CG MET B 375 71.789 75.165 29.530 1.00 32.29 C
+ATOM 3844 SD MET B 375 73.032 74.915 30.784 1.00 27.50 S
+ATOM 3845 CE MET B 375 72.519 76.117 32.007 1.00 27.30 C
+ATOM 3846 N PHE B 376 72.903 78.748 27.240 1.00 37.69 N
+ATOM 3847 CA PHE B 376 73.336 80.130 27.103 1.00 39.07 C
+ATOM 3848 C PHE B 376 73.245 80.650 25.682 1.00 40.59 C
+ATOM 3849 O PHE B 376 73.580 81.800 25.421 1.00 43.00 O
+ATOM 3850 CB PHE B 376 74.766 80.278 27.645 1.00 35.86 C
+ATOM 3851 CG PHE B 376 74.918 79.797 29.068 1.00 30.20 C
+ATOM 3852 CD1 PHE B 376 74.176 80.378 30.094 1.00 26.27 C
+ATOM 3853 CD2 PHE B 376 75.784 78.742 29.377 1.00 29.57 C
+ATOM 3854 CE1 PHE B 376 74.289 79.915 31.409 1.00 27.89 C
+ATOM 3855 CE2 PHE B 376 75.908 78.270 30.690 1.00 26.94 C
+ATOM 3856 CZ PHE B 376 75.158 78.859 31.706 1.00 27.89 C
+ATOM 3857 N GLY B 377 72.795 79.803 24.765 1.00 43.72 N
+ATOM 3858 CA GLY B 377 72.654 80.247 23.392 1.00 46.64 C
+ATOM 3859 C GLY B 377 71.498 81.228 23.283 1.00 47.84 C
+ATOM 3860 O GLY B 377 70.863 81.566 24.300 1.00 47.76 O
+ATOM 3861 N SER B 378 71.214 81.684 22.060 1.00 48.61 N
+ATOM 3862 CA SER B 378 70.118 82.632 21.830 1.00 51.26 C
+ATOM 3863 C SER B 378 68.749 81.961 21.943 1.00 54.56 C
+ATOM 3864 O SER B 378 67.722 82.641 21.957 1.00 51.94 O
+ATOM 3865 CB SER B 378 70.226 83.252 20.447 1.00 49.77 C
+ATOM 3866 OG SER B 378 69.770 82.333 19.476 1.00 49.66 O
+ATOM 3867 N THR B 379 68.747 80.629 22.006 1.00 59.08 N
+ATOM 3868 CA THR B 379 67.517 79.847 22.123 1.00 60.19 C
+ATOM 3869 C THR B 379 67.300 79.401 23.564 1.00 58.26 C
+ATOM 3870 O THR B 379 66.171 79.187 23.991 1.00 54.54 O
+ATOM 3871 CB THR B 379 67.558 78.588 21.228 1.00 68.23 C
+ATOM 3872 OG1 THR B 379 67.627 78.981 19.854 1.00 80.85 O
+ATOM 3873 CG2 THR B 379 66.315 77.740 21.437 1.00 79.96 C
+ATOM 3874 N GLY B 380 68.388 79.257 24.308 1.00 54.69 N
+ATOM 3875 CA GLY B 380 68.275 78.838 25.689 1.00 50.12 C
+ATOM 3876 C GLY B 380 67.628 79.907 26.545 1.00 47.71 C
+ATOM 3877 O GLY B 380 67.400 81.019 26.082 1.00 47.07 O
+ATOM 3878 N SER B 381 67.344 79.568 27.800 1.00 46.66 N
+ATOM 3879 CA SER B 381 66.711 80.488 28.743 1.00 49.51 C
+ATOM 3880 C SER B 381 67.627 80.854 29.915 1.00 50.63 C
+ATOM 3881 O SER B 381 67.268 81.669 30.770 1.00 53.75 O
+ATOM 3882 CB SER B 381 65.434 79.851 29.284 1.00 49.16 C
+ATOM 3883 OG SER B 381 65.707 78.543 29.751 1.00 44.63 O
+ATOM 3884 N ALA B 382 68.814 80.257 29.944 1.00 48.60 N
+ATOM 3885 CA ALA B 382 69.768 80.495 31.019 1.00 46.12 C
+ATOM 3886 C ALA B 382 70.404 81.887 31.044 1.00 45.61 C
+ATOM 3887 O ALA B 382 70.750 82.455 30.002 1.00 40.04 O
+ATOM 3888 CB ALA B 382 70.857 79.430 30.971 1.00 44.23 C
+ATOM 3889 N ASP B 383 70.554 82.416 32.258 1.00 42.31 N
+ATOM 3890 CA ASP B 383 71.162 83.725 32.493 1.00 40.08 C
+ATOM 3891 C ASP B 383 72.584 83.438 32.954 1.00 38.79 C
+ATOM 3892 O ASP B 383 72.813 82.977 34.075 1.00 35.84 O
+ATOM 3893 CB ASP B 383 70.408 84.473 33.596 1.00 45.25 C
+ATOM 3894 CG ASP B 383 70.929 85.884 33.814 1.00 52.61 C
+ATOM 3895 OD1 ASP B 383 72.162 86.090 33.786 1.00 57.72 O
+ATOM 3896 OD2 ASP B 383 70.100 86.791 34.032 1.00 57.22 O
+ATOM 3897 N ILE B 384 73.547 83.710 32.089 1.00 36.75 N
+ATOM 3898 CA ILE B 384 74.928 83.442 32.434 1.00 36.63 C
+ATOM 3899 C ILE B 384 75.405 84.209 33.668 1.00 42.65 C
+ATOM 3900 O ILE B 384 76.306 83.747 34.377 1.00 36.77 O
+ATOM 3901 CB ILE B 384 75.848 83.730 31.249 1.00 33.86 C
+ATOM 3902 CG1 ILE B 384 77.226 83.147 31.536 1.00 34.30 C
+ATOM 3903 CG2 ILE B 384 75.906 85.218 30.986 1.00 33.71 C
+ATOM 3904 CD1 ILE B 384 78.171 83.278 30.382 1.00 37.84 C
+ATOM 3905 N GLU B 385 74.812 85.376 33.925 1.00 50.34 N
+ATOM 3906 CA GLU B 385 75.180 86.160 35.104 1.00 54.17 C
+ATOM 3907 C GLU B 385 74.835 85.359 36.356 1.00 51.51 C
+ATOM 3908 O GLU B 385 75.583 85.356 37.336 1.00 44.78 O
+ATOM 3909 CB GLU B 385 74.411 87.478 35.164 1.00 69.17 C
+ATOM 3910 CG GLU B 385 74.851 88.533 34.185 1.00100.62 C
+ATOM 3911 CD GLU B 385 74.730 89.925 34.780 1.00113.92 C
+ATOM 3912 OE1 GLU B 385 73.719 90.187 35.472 1.00117.90 O
+ATOM 3913 OE2 GLU B 385 75.642 90.754 34.554 1.00118.68 O
+ATOM 3914 N GLU B 386 73.690 84.683 36.311 1.00 45.21 N
+ATOM 3915 CA GLU B 386 73.226 83.893 37.439 1.00 38.46 C
+ATOM 3916 C GLU B 386 74.071 82.651 37.655 1.00 36.10 C
+ATOM 3917 O GLU B 386 74.249 82.195 38.796 1.00 33.10 O
+ATOM 3918 CB GLU B 386 71.753 83.526 37.252 1.00 39.98 C
+ATOM 3919 CG GLU B 386 70.809 84.678 37.565 1.00 47.18 C
+ATOM 3920 CD GLU B 386 69.354 84.315 37.354 1.00 52.36 C
+ATOM 3921 OE1 GLU B 386 68.952 83.218 37.795 1.00 53.77 O
+ATOM 3922 OE2 GLU B 386 68.606 85.127 36.757 1.00 54.49 O
+ATOM 3923 N TRP B 387 74.610 82.111 36.564 1.00 33.02 N
+ATOM 3924 CA TRP B 387 75.458 80.930 36.657 1.00 30.12 C
+ATOM 3925 C TRP B 387 76.887 81.302 37.081 1.00 28.35 C
+ATOM 3926 O TRP B 387 77.689 80.440 37.469 1.00 26.70 O
+ATOM 3927 CB TRP B 387 75.449 80.169 35.327 1.00 31.31 C
+ATOM 3928 CG TRP B 387 74.214 79.364 35.177 1.00 35.49 C
+ATOM 3929 CD1 TRP B 387 72.984 79.808 34.777 1.00 37.06 C
+ATOM 3930 CD2 TRP B 387 74.043 77.992 35.546 1.00 36.75 C
+ATOM 3931 NE1 TRP B 387 72.057 78.796 34.880 1.00 37.94 N
+ATOM 3932 CE2 TRP B 387 72.681 77.671 35.347 1.00 37.24 C
+ATOM 3933 CE3 TRP B 387 74.912 77.001 36.025 1.00 37.30 C
+ATOM 3934 CZ2 TRP B 387 72.165 76.402 35.618 1.00 37.27 C
+ATOM 3935 CZ3 TRP B 387 74.398 75.736 36.294 1.00 37.95 C
+ATOM 3936 CH2 TRP B 387 73.037 75.448 36.088 1.00 37.83 C
+ATOM 3937 N MET B 388 77.203 82.590 37.000 1.00 27.61 N
+ATOM 3938 CA MET B 388 78.513 83.061 37.413 1.00 27.95 C
+ATOM 3939 C MET B 388 78.359 83.515 38.872 1.00 27.72 C
+ATOM 3940 O MET B 388 79.336 83.695 39.603 1.00 29.42 O
+ATOM 3941 CB MET B 388 78.978 84.218 36.513 1.00 26.24 C
+ATOM 3942 CG MET B 388 79.756 83.789 35.246 1.00 22.25 C
+ATOM 3943 SD MET B 388 81.445 83.155 35.517 1.00 14.78 S
+ATOM 3944 CE MET B 388 81.235 81.674 34.892 1.00 18.81 C
+ATOM 3945 N ALA B 389 77.116 83.692 39.295 1.00 28.99 N
+ATOM 3946 CA ALA B 389 76.859 84.082 40.669 1.00 29.51 C
+ATOM 3947 C ALA B 389 77.015 82.770 41.406 1.00 29.60 C
+ATOM 3948 O ALA B 389 77.330 82.733 42.604 1.00 28.45 O
+ATOM 3949 CB ALA B 389 75.429 84.618 40.817 1.00 29.44 C
+ATOM 3950 N GLY B 390 76.792 81.687 40.661 1.00 28.44 N
+ATOM 3951 CA GLY B 390 76.907 80.361 41.234 1.00 27.86 C
+ATOM 3952 C GLY B 390 78.346 79.969 41.506 1.00 26.72 C
+ATOM 3953 O GLY B 390 78.653 79.373 42.549 1.00 26.18 O
+ATOM 3954 N VAL B 391 79.231 80.305 40.565 1.00 25.12 N
+ATOM 3955 CA VAL B 391 80.654 79.999 40.701 1.00 22.35 C
+ATOM 3956 C VAL B 391 81.158 80.742 41.915 1.00 21.36 C
+ATOM 3957 O VAL B 391 81.850 80.186 42.753 1.00 21.06 O
+ATOM 3958 CB VAL B 391 81.454 80.457 39.460 1.00 21.90 C
+ATOM 3959 CG1 VAL B 391 82.905 80.083 39.594 1.00 18.60 C
+ATOM 3960 CG2 VAL B 391 80.879 79.807 38.219 1.00 22.35 C
+ATOM 3961 N ALA B 392 80.776 82.006 42.011 1.00 20.19 N
+ATOM 3962 CA ALA B 392 81.196 82.841 43.119 1.00 20.99 C
+ATOM 3963 C ALA B 392 80.753 82.257 44.463 1.00 21.88 C
+ATOM 3964 O ALA B 392 81.548 82.163 45.412 1.00 22.07 O
+ATOM 3965 CB ALA B 392 80.634 84.256 42.937 1.00 19.27 C
+ATOM 3966 N TRP B 393 79.485 81.874 44.552 1.00 23.98 N
+ATOM 3967 CA TRP B 393 79.004 81.312 45.795 1.00 26.79 C
+ATOM 3968 C TRP B 393 79.793 80.046 46.066 1.00 27.18 C
+ATOM 3969 O TRP B 393 80.424 79.916 47.115 1.00 28.78 O
+ATOM 3970 CB TRP B 393 77.517 80.976 45.721 1.00 28.13 C
+ATOM 3971 CG TRP B 393 76.949 80.598 47.053 1.00 28.90 C
+ATOM 3972 CD1 TRP B 393 76.435 81.441 47.995 1.00 29.54 C
+ATOM 3973 CD2 TRP B 393 76.869 79.282 47.610 1.00 29.83 C
+ATOM 3974 NE1 TRP B 393 76.035 80.733 49.108 1.00 29.88 N
+ATOM 3975 CE2 TRP B 393 76.290 79.404 48.897 1.00 30.35 C
+ATOM 3976 CE3 TRP B 393 77.231 78.011 47.150 1.00 29.12 C
+ATOM 3977 CZ2 TRP B 393 76.064 78.294 49.728 1.00 29.04 C
+ATOM 3978 CZ3 TRP B 393 77.007 76.912 47.978 1.00 28.95 C
+ATOM 3979 CH2 TRP B 393 76.430 77.062 49.250 1.00 27.79 C
+ATOM 3980 N LEU B 394 79.769 79.116 45.116 1.00 26.88 N
+ATOM 3981 CA LEU B 394 80.507 77.868 45.285 1.00 26.43 C
+ATOM 3982 C LEU B 394 81.983 78.112 45.652 1.00 26.41 C
+ATOM 3983 O LEU B 394 82.591 77.326 46.384 1.00 26.77 O
+ATOM 3984 CB LEU B 394 80.411 77.022 44.014 1.00 25.18 C
+ATOM 3985 CG LEU B 394 79.186 76.112 43.910 1.00 27.18 C
+ATOM 3986 CD1 LEU B 394 79.067 75.525 42.509 1.00 27.42 C
+ATOM 3987 CD2 LEU B 394 79.304 74.991 44.952 1.00 30.90 C
+ATOM 3988 N HIS B 395 82.546 79.221 45.184 1.00 26.80 N
+ATOM 3989 CA HIS B 395 83.936 79.517 45.466 1.00 27.58 C
+ATOM 3990 C HIS B 395 84.127 80.050 46.886 1.00 29.81 C
+ATOM 3991 O HIS B 395 85.260 80.315 47.318 1.00 33.66 O
+ATOM 3992 CB HIS B 395 84.469 80.501 44.412 1.00 27.68 C
+ATOM 3993 CG HIS B 395 85.959 80.458 44.231 1.00 26.49 C
+ATOM 3994 ND1 HIS B 395 86.832 81.140 45.052 1.00 24.54 N
+ATOM 3995 CD2 HIS B 395 86.728 79.790 43.338 1.00 25.64 C
+ATOM 3996 CE1 HIS B 395 88.073 80.893 44.675 1.00 25.33 C
+ATOM 3997 NE2 HIS B 395 88.042 80.075 43.636 1.00 23.82 N
+ATOM 3998 N CYS B 396 83.026 80.206 47.618 1.00 32.44 N
+ATOM 3999 CA CYS B 396 83.103 80.687 49.003 1.00 33.22 C
+ATOM 4000 C CYS B 396 82.759 79.559 49.973 1.00 31.28 C
+ATOM 4001 O CYS B 396 82.844 79.721 51.188 1.00 32.73 O
+ATOM 4002 CB CYS B 396 82.165 81.882 49.225 1.00 33.37 C
+ATOM 4003 SG CYS B 396 82.703 83.458 48.456 1.00 32.20 S
+ATOM 4004 N LEU B 397 82.389 78.409 49.414 1.00 30.03 N
+ATOM 4005 CA LEU B 397 82.030 77.234 50.193 1.00 29.91 C
+ATOM 4006 C LEU B 397 83.278 76.533 50.746 1.00 31.11 C
+ATOM 4007 O LEU B 397 83.223 75.915 51.806 1.00 33.59 O
+ATOM 4008 CB LEU B 397 81.221 76.272 49.319 1.00 25.95 C
+ATOM 4009 CG LEU B 397 80.639 74.987 49.941 1.00 23.46 C
+ATOM 4010 CD1 LEU B 397 79.659 75.348 51.058 1.00 18.81 C
+ATOM 4011 CD2 LEU B 397 79.940 74.154 48.860 1.00 17.88 C
+ATOM 4012 N LEU B 398 84.401 76.647 50.036 1.00 30.63 N
+ATOM 4013 CA LEU B 398 85.657 76.031 50.453 1.00 29.96 C
+ATOM 4014 C LEU B 398 86.843 76.866 50.001 1.00 30.06 C
+ATOM 4015 O LEU B 398 86.779 77.587 48.995 1.00 29.42 O
+ATOM 4016 CB LEU B 398 85.812 74.640 49.849 1.00 30.26 C
+ATOM 4017 CG LEU B 398 85.488 73.351 50.596 1.00 28.60 C
+ATOM 4018 CD1 LEU B 398 84.200 73.462 51.357 1.00 29.62 C
+ATOM 4019 CD2 LEU B 398 85.396 72.234 49.571 1.00 29.56 C
+ATOM 4020 N PRO B 399 87.952 76.776 50.744 1.00 36.38 N
+ATOM 4021 CA PRO B 399 89.182 77.511 50.442 1.00 36.28 C
+ATOM 4022 C PRO B 399 89.838 76.882 49.220 1.00 39.84 C
+ATOM 4023 O PRO B 399 89.938 75.656 49.147 1.00 39.96 O
+ATOM 4024 CB PRO B 399 90.021 77.308 51.700 1.00 35.60 C
+ATOM 4025 CG PRO B 399 88.976 77.057 52.778 1.00 36.60 C
+ATOM 4026 CD PRO B 399 88.029 76.146 52.072 1.00 34.07 C
+ATOM 4027 N LYS B 400 90.288 77.714 48.278 1.00 44.16 N
+ATOM 4028 CA LYS B 400 90.932 77.257 47.038 1.00 44.01 C
+ATOM 4029 C LYS B 400 90.087 76.189 46.342 1.00 38.78 C
+ATOM 4030 O LYS B 400 90.597 75.156 45.918 1.00 34.94 O
+ATOM 4031 CB LYS B 400 92.338 76.714 47.327 1.00 53.19 C
+ATOM 4032 CG LYS B 400 93.235 77.700 48.070 1.00 70.95 C
+ATOM 4033 CD LYS B 400 94.708 77.294 48.076 1.00 80.04 C
+ATOM 4034 CE LYS B 400 95.360 77.515 46.710 1.00 83.91 C
+ATOM 4035 NZ LYS B 400 96.831 77.231 46.703 1.00 84.24 N
+ATOM 4036 N MET B 401 88.795 76.475 46.206 1.00 30.38 N
+ATOM 4037 CA MET B 401 87.833 75.556 45.618 1.00 24.59 C
+ATOM 4038 C MET B 401 88.135 75.068 44.204 1.00 23.45 C
+ATOM 4039 O MET B 401 87.888 73.907 43.879 1.00 23.40 O
+ATOM 4040 CB MET B 401 86.422 76.174 45.675 1.00 19.51 C
+ATOM 4041 CG MET B 401 85.328 75.293 45.067 1.00 12.14 C
+ATOM 4042 SD MET B 401 85.121 73.773 45.954 1.00 6.69 S
+ATOM 4043 CE MET B 401 83.678 74.146 46.984 1.00 7.33 C
+ATOM 4044 N ASP B 402 88.654 75.938 43.354 1.00 22.60 N
+ATOM 4045 CA ASP B 402 88.970 75.519 41.996 1.00 23.23 C
+ATOM 4046 C ASP B 402 90.124 74.520 41.978 1.00 22.55 C
+ATOM 4047 O ASP B 402 90.184 73.652 41.108 1.00 22.31 O
+ATOM 4048 CB ASP B 402 89.283 76.737 41.104 1.00 23.95 C
+ATOM 4049 CG ASP B 402 90.457 77.554 41.602 1.00 26.30 C
+ATOM 4050 OD1 ASP B 402 91.611 77.327 41.146 1.00 26.64 O
+ATOM 4051 OD2 ASP B 402 90.208 78.429 42.458 1.00 27.75 O
+ATOM 4052 N SER B 403 91.034 74.646 42.940 1.00 21.07 N
+ATOM 4053 CA SER B 403 92.179 73.754 43.039 1.00 19.49 C
+ATOM 4054 C SER B 403 91.631 72.476 43.656 1.00 19.95 C
+ATOM 4055 O SER B 403 92.106 71.383 43.387 1.00 20.21 O
+ATOM 4056 CB SER B 403 93.259 74.365 43.936 1.00 17.92 C
+ATOM 4057 OG SER B 403 93.552 75.703 43.568 1.00 19.10 O
+ATOM 4058 N VAL B 404 90.606 72.620 44.478 1.00 21.49 N
+ATOM 4059 CA VAL B 404 89.993 71.465 45.087 1.00 23.64 C
+ATOM 4060 C VAL B 404 89.284 70.655 44.007 1.00 22.90 C
+ATOM 4061 O VAL B 404 89.448 69.443 43.933 1.00 25.74 O
+ATOM 4062 CB VAL B 404 88.976 71.872 46.176 1.00 25.78 C
+ATOM 4063 CG1 VAL B 404 88.138 70.663 46.585 1.00 28.47 C
+ATOM 4064 CG2 VAL B 404 89.717 72.423 47.385 1.00 27.06 C
+ATOM 4065 N VAL B 405 88.493 71.322 43.171 1.00 22.93 N
+ATOM 4066 CA VAL B 405 87.784 70.624 42.107 1.00 23.74 C
+ATOM 4067 C VAL B 405 88.766 69.938 41.167 1.00 25.13 C
+ATOM 4068 O VAL B 405 88.593 68.768 40.804 1.00 25.85 O
+ATOM 4069 CB VAL B 405 86.922 71.578 41.272 1.00 20.21 C
+ATOM 4070 CG1 VAL B 405 86.400 70.849 40.031 1.00 17.52 C
+ATOM 4071 CG2 VAL B 405 85.765 72.086 42.102 1.00 15.99 C
+ATOM 4072 N TYR B 406 89.787 70.681 40.762 1.00 27.11 N
+ATOM 4073 CA TYR B 406 90.809 70.164 39.870 1.00 29.13 C
+ATOM 4074 C TYR B 406 91.416 68.876 40.436 1.00 29.32 C
+ATOM 4075 O TYR B 406 91.453 67.842 39.758 1.00 27.58 O
+ATOM 4076 CB TYR B 406 91.888 71.230 39.662 1.00 32.47 C
+ATOM 4077 CG TYR B 406 93.121 70.746 38.933 1.00 38.98 C
+ATOM 4078 CD1 TYR B 406 93.054 70.282 37.612 1.00 40.68 C
+ATOM 4079 CD2 TYR B 406 94.360 70.751 39.563 1.00 39.36 C
+ATOM 4080 CE1 TYR B 406 94.201 69.831 36.945 1.00 41.20 C
+ATOM 4081 CE2 TYR B 406 95.501 70.308 38.912 1.00 40.84 C
+ATOM 4082 CZ TYR B 406 95.423 69.854 37.609 1.00 40.66 C
+ATOM 4083 OH TYR B 406 96.576 69.430 36.994 1.00 40.25 O
+ATOM 4084 N ASP B 407 91.884 68.933 41.679 1.00 27.56 N
+ATOM 4085 CA ASP B 407 92.473 67.761 42.295 1.00 26.28 C
+ATOM 4086 C ASP B 407 91.540 66.553 42.255 1.00 25.90 C
+ATOM 4087 O ASP B 407 91.917 65.475 41.784 1.00 25.12 O
+ATOM 4088 CB ASP B 407 92.865 68.062 43.742 1.00 28.19 C
+ATOM 4089 CG ASP B 407 94.025 69.029 43.841 1.00 31.96 C
+ATOM 4090 OD1 ASP B 407 94.975 68.907 43.044 1.00 35.67 O
+ATOM 4091 OD2 ASP B 407 94.000 69.908 44.724 1.00 32.88 O
+ATOM 4092 N PHE B 408 90.326 66.731 42.759 1.00 23.91 N
+ATOM 4093 CA PHE B 408 89.359 65.652 42.777 1.00 21.79 C
+ATOM 4094 C PHE B 408 89.429 64.957 41.422 1.00 20.53 C
+ATOM 4095 O PHE B 408 89.528 63.741 41.342 1.00 17.94 O
+ATOM 4096 CB PHE B 408 87.951 66.218 43.022 1.00 23.22 C
+ATOM 4097 CG PHE B 408 86.874 65.163 43.157 1.00 24.94 C
+ATOM 4098 CD1 PHE B 408 86.855 64.309 44.247 1.00 23.90 C
+ATOM 4099 CD2 PHE B 408 85.879 65.027 42.176 1.00 25.89 C
+ATOM 4100 CE1 PHE B 408 85.855 63.327 44.361 1.00 27.42 C
+ATOM 4101 CE2 PHE B 408 84.874 64.052 42.279 1.00 25.04 C
+ATOM 4102 CZ PHE B 408 84.862 63.201 43.370 1.00 25.97 C
+ATOM 4103 N LEU B 409 89.387 65.747 40.358 1.00 20.67 N
+ATOM 4104 CA LEU B 409 89.439 65.220 39.000 1.00 21.08 C
+ATOM 4105 C LEU B 409 90.695 64.382 38.777 1.00 23.30 C
+ATOM 4106 O LEU B 409 90.614 63.236 38.336 1.00 20.40 O
+ATOM 4107 CB LEU B 409 89.373 66.374 37.988 1.00 19.20 C
+ATOM 4108 CG LEU B 409 88.064 67.175 38.044 1.00 20.21 C
+ATOM 4109 CD1 LEU B 409 88.050 68.302 37.021 1.00 19.29 C
+ATOM 4110 CD2 LEU B 409 86.906 66.227 37.790 1.00 19.92 C
+ATOM 4111 N LYS B 410 91.859 64.944 39.073 1.00 27.46 N
+ATOM 4112 CA LYS B 410 93.070 64.177 38.884 1.00 30.34 C
+ATOM 4113 C LYS B 410 92.900 62.884 39.663 1.00 29.97 C
+ATOM 4114 O LYS B 410 93.220 61.791 39.177 1.00 28.52 O
+ATOM 4115 CB LYS B 410 94.293 64.943 39.385 1.00 36.27 C
+ATOM 4116 CG LYS B 410 94.772 66.012 38.425 1.00 49.56 C
+ATOM 4117 CD LYS B 410 94.942 65.458 37.013 1.00 55.70 C
+ATOM 4118 CE LYS B 410 95.218 66.568 36.000 1.00 58.66 C
+ATOM 4119 NZ LYS B 410 95.179 66.104 34.582 1.00 58.35 N
+ATOM 4120 N CYS B 411 92.378 63.009 40.874 1.00 29.32 N
+ATOM 4121 CA CYS B 411 92.163 61.844 41.705 1.00 28.44 C
+ATOM 4122 C CYS B 411 91.304 60.816 40.952 1.00 26.76 C
+ATOM 4123 O CYS B 411 91.727 59.688 40.724 1.00 30.38 O
+ATOM 4124 CB CYS B 411 91.479 62.265 43.000 1.00 28.05 C
+ATOM 4125 SG CYS B 411 91.452 61.020 44.289 1.00 31.02 S
+ATOM 4126 N MET B 412 90.112 61.221 40.539 1.00 24.91 N
+ATOM 4127 CA MET B 412 89.201 60.330 39.842 1.00 25.36 C
+ATOM 4128 C MET B 412 89.762 59.737 38.543 1.00 25.86 C
+ATOM 4129 O MET B 412 89.548 58.555 38.237 1.00 27.54 O
+ATOM 4130 CB MET B 412 87.880 61.063 39.554 1.00 22.85 C
+ATOM 4131 CG MET B 412 87.088 61.490 40.794 1.00 16.96 C
+ATOM 4132 SD MET B 412 86.667 60.141 41.922 1.00 10.65 S
+ATOM 4133 CE MET B 412 87.945 60.265 43.088 1.00 10.78 C
+ATOM 4134 N VAL B 413 90.463 60.554 37.769 1.00 23.19 N
+ATOM 4135 CA VAL B 413 91.024 60.080 36.522 1.00 21.94 C
+ATOM 4136 C VAL B 413 92.172 59.115 36.819 1.00 25.81 C
+ATOM 4137 O VAL B 413 92.282 58.062 36.195 1.00 24.95 O
+ATOM 4138 CB VAL B 413 91.542 61.255 35.679 1.00 18.49 C
+ATOM 4139 CG1 VAL B 413 92.507 60.753 34.621 1.00 16.54 C
+ATOM 4140 CG2 VAL B 413 90.388 61.975 35.022 1.00 15.60 C
+ATOM 4141 N TYR B 414 93.014 59.455 37.790 1.00 29.70 N
+ATOM 4142 CA TYR B 414 94.163 58.613 38.125 1.00 32.15 C
+ATOM 4143 C TYR B 414 93.781 57.296 38.754 1.00 32.13 C
+ATOM 4144 O TYR B 414 94.536 56.337 38.668 1.00 31.56 O
+ATOM 4145 CB TYR B 414 95.136 59.361 39.048 1.00 38.69 C
+ATOM 4146 CG TYR B 414 95.925 60.470 38.370 1.00 47.72 C
+ATOM 4147 CD1 TYR B 414 95.579 60.925 37.099 1.00 51.92 C
+ATOM 4148 CD2 TYR B 414 96.991 61.090 39.019 1.00 52.00 C
+ATOM 4149 CE1 TYR B 414 96.267 61.965 36.488 1.00 53.30 C
+ATOM 4150 CE2 TYR B 414 97.691 62.141 38.416 1.00 54.28 C
+ATOM 4151 CZ TYR B 414 97.317 62.573 37.148 1.00 54.23 C
+ATOM 4152 OH TYR B 414 97.979 63.614 36.538 1.00 54.09 O
+ATOM 4153 N ASN B 415 92.608 57.259 39.380 1.00 33.32 N
+ATOM 4154 CA ASN B 415 92.090 56.058 40.041 1.00 33.30 C
+ATOM 4155 C ASN B 415 93.201 55.144 40.569 1.00 32.57 C
+ATOM 4156 O ASN B 415 93.353 54.013 40.120 1.00 33.11 O
+ATOM 4157 CB ASN B 415 91.197 55.280 39.074 1.00 33.28 C
+ATOM 4158 CG ASN B 415 90.386 54.215 39.765 1.00 35.68 C
+ATOM 4159 OD1 ASN B 415 89.926 53.281 39.131 1.00 39.48 O
+ATOM 4160 ND2 ASN B 415 90.198 54.352 41.066 1.00 36.02 N
+ATOM 4161 N ILE B 416 93.961 55.638 41.538 1.00 31.18 N
+ATOM 4162 CA ILE B 416 95.067 54.885 42.103 1.00 29.37 C
+ATOM 4163 C ILE B 416 94.754 54.194 43.438 1.00 28.85 C
+ATOM 4164 O ILE B 416 94.235 54.809 44.362 1.00 29.17 O
+ATOM 4165 CB ILE B 416 96.291 55.831 42.242 1.00 30.86 C
+ATOM 4166 CG1 ILE B 416 96.840 56.133 40.843 1.00 30.56 C
+ATOM 4167 CG2 ILE B 416 97.343 55.236 43.169 1.00 29.05 C
+ATOM 4168 CD1 ILE B 416 97.799 57.284 40.797 1.00 32.19 C
+ATOM 4169 N PRO B 417 95.085 52.900 43.552 1.00 28.06 N
+ATOM 4170 CA PRO B 417 94.852 52.101 44.761 1.00 27.75 C
+ATOM 4171 C PRO B 417 95.007 52.842 46.092 1.00 28.92 C
+ATOM 4172 O PRO B 417 96.052 53.441 46.366 1.00 30.18 O
+ATOM 4173 CB PRO B 417 95.864 50.960 44.616 1.00 25.31 C
+ATOM 4174 CG PRO B 417 95.834 50.712 43.150 1.00 22.69 C
+ATOM 4175 CD PRO B 417 95.865 52.127 42.568 1.00 24.91 C
+ATOM 4176 N LYS B 418 93.953 52.778 46.906 1.00 31.96 N
+ATOM 4177 CA LYS B 418 93.911 53.397 48.230 1.00 35.22 C
+ATOM 4178 C LYS B 418 93.975 54.924 48.248 1.00 36.92 C
+ATOM 4179 O LYS B 418 94.081 55.531 49.319 1.00 36.57 O
+ATOM 4180 CB LYS B 418 95.025 52.816 49.110 1.00 37.80 C
+ATOM 4181 CG LYS B 418 94.870 51.325 49.384 1.00 42.47 C
+ATOM 4182 CD LYS B 418 95.941 50.790 50.316 1.00 43.77 C
+ATOM 4183 CE LYS B 418 95.678 49.324 50.671 1.00 45.28 C
+ATOM 4184 NZ LYS B 418 96.764 48.725 51.511 1.00 45.48 N
+ATOM 4185 N LYS B 419 93.903 55.544 47.071 1.00 34.73 N
+ATOM 4186 CA LYS B 419 93.940 57.000 46.965 1.00 30.63 C
+ATOM 4187 C LYS B 419 92.845 57.468 46.012 1.00 28.61 C
+ATOM 4188 O LYS B 419 93.065 58.335 45.164 1.00 23.59 O
+ATOM 4189 CB LYS B 419 95.302 57.441 46.442 1.00 33.32 C
+ATOM 4190 CG LYS B 419 96.475 56.969 47.285 1.00 40.51 C
+ATOM 4191 CD LYS B 419 97.782 57.349 46.617 1.00 45.23 C
+ATOM 4192 CE LYS B 419 98.985 56.964 47.454 1.00 46.69 C
+ATOM 4193 NZ LYS B 419 100.258 57.360 46.771 1.00 48.03 N
+ATOM 4194 N ARG B 420 91.656 56.893 46.163 1.00 25.51 N
+ATOM 4195 CA ARG B 420 90.539 57.238 45.285 1.00 23.49 C
+ATOM 4196 C ARG B 420 89.234 57.634 45.978 1.00 22.11 C
+ATOM 4197 O ARG B 420 88.225 57.874 45.304 1.00 21.73 O
+ATOM 4198 CB ARG B 420 90.271 56.071 44.325 1.00 22.85 C
+ATOM 4199 CG ARG B 420 90.907 54.778 44.777 1.00 21.96 C
+ATOM 4200 CD ARG B 420 90.600 53.686 43.812 1.00 23.48 C
+ATOM 4201 NE ARG B 420 89.461 52.913 44.281 1.00 23.14 N
+ATOM 4202 CZ ARG B 420 88.648 52.233 43.486 1.00 22.90 C
+ATOM 4203 NH1 ARG B 420 88.844 52.238 42.171 1.00 23.14 N
+ATOM 4204 NH2 ARG B 420 87.652 51.539 44.008 1.00 19.90 N
+ATOM 4205 N TYR B 421 89.254 57.705 47.308 1.00 21.45 N
+ATOM 4206 CA TYR B 421 88.062 58.075 48.045 1.00 21.99 C
+ATOM 4207 C TYR B 421 88.190 59.262 48.961 1.00 23.49 C
+ATOM 4208 O TYR B 421 89.078 59.315 49.808 1.00 25.96 O
+ATOM 4209 CB TYR B 421 87.516 56.894 48.846 1.00 19.53 C
+ATOM 4210 CG TYR B 421 86.541 56.092 48.041 1.00 18.10 C
+ATOM 4211 CD1 TYR B 421 86.984 55.079 47.191 1.00 18.07 C
+ATOM 4212 CD2 TYR B 421 85.184 56.438 48.020 1.00 17.47 C
+ATOM 4213 CE1 TYR B 421 86.106 54.427 46.326 1.00 17.87 C
+ATOM 4214 CE2 TYR B 421 84.290 55.804 47.158 1.00 17.64 C
+ATOM 4215 CZ TYR B 421 84.763 54.801 46.306 1.00 18.55 C
+ATOM 4216 OH TYR B 421 83.920 54.221 45.389 1.00 16.71 O
+ATOM 4217 N TRP B 422 87.280 60.213 48.768 1.00 23.70 N
+ATOM 4218 CA TRP B 422 87.209 61.416 49.573 1.00 22.97 C
+ATOM 4219 C TRP B 422 86.018 61.261 50.499 1.00 24.21 C
+ATOM 4220 O TRP B 422 85.016 60.622 50.162 1.00 21.72 O
+ATOM 4221 CB TRP B 422 87.013 62.635 48.689 1.00 21.55 C
+ATOM 4222 CG TRP B 422 88.213 62.972 47.923 1.00 22.57 C
+ATOM 4223 CD1 TRP B 422 89.218 62.124 47.568 1.00 23.47 C
+ATOM 4224 CD2 TRP B 422 88.571 64.263 47.408 1.00 22.88 C
+ATOM 4225 NE1 TRP B 422 90.188 62.802 46.866 1.00 23.93 N
+ATOM 4226 CE2 TRP B 422 89.817 64.117 46.751 1.00 23.38 C
+ATOM 4227 CE3 TRP B 422 87.958 65.525 47.441 1.00 20.94 C
+ATOM 4228 CZ2 TRP B 422 90.470 65.187 46.127 1.00 22.32 C
+ATOM 4229 CZ3 TRP B 422 88.602 66.588 46.826 1.00 21.75 C
+ATOM 4230 CH2 TRP B 422 89.852 66.412 46.175 1.00 23.52 C
+ATOM 4231 N LEU B 423 86.148 61.862 51.669 1.00 27.32 N
+ATOM 4232 CA LEU B 423 85.124 61.809 52.679 1.00 30.01 C
+ATOM 4233 C LEU B 423 84.595 63.210 52.924 1.00 29.64 C
+ATOM 4234 O LEU B 423 85.335 64.080 53.382 1.00 30.70 O
+ATOM 4235 CB LEU B 423 85.710 61.258 53.984 1.00 31.97 C
+ATOM 4236 CG LEU B 423 84.697 61.192 55.126 1.00 34.79 C
+ATOM 4237 CD1 LEU B 423 83.769 60.025 54.853 1.00 34.51 C
+ATOM 4238 CD2 LEU B 423 85.389 61.035 56.477 1.00 35.42 C
+ATOM 4239 N PHE B 424 83.327 63.436 52.603 1.00 30.55 N
+ATOM 4240 CA PHE B 424 82.716 64.739 52.856 1.00 30.60 C
+ATOM 4241 C PHE B 424 81.980 64.571 54.165 1.00 31.42 C
+ATOM 4242 O PHE B 424 80.929 63.933 54.224 1.00 31.85 O
+ATOM 4243 CB PHE B 424 81.744 65.132 51.744 1.00 28.61 C
+ATOM 4244 CG PHE B 424 82.421 65.606 50.480 1.00 27.26 C
+ATOM 4245 CD1 PHE B 424 83.801 65.479 50.312 1.00 27.28 C
+ATOM 4246 CD2 PHE B 424 81.672 66.183 49.448 1.00 27.55 C
+ATOM 4247 CE1 PHE B 424 84.423 65.922 49.137 1.00 28.10 C
+ATOM 4248 CE2 PHE B 424 82.279 66.627 48.270 1.00 25.97 C
+ATOM 4249 CZ PHE B 424 83.661 66.496 48.115 1.00 26.62 C
+ATOM 4250 N LYS B 425 82.561 65.113 55.225 1.00 33.92 N
+ATOM 4251 CA LYS B 425 81.962 64.992 56.537 1.00 35.95 C
+ATOM 4252 C LYS B 425 81.437 66.348 56.997 1.00 37.29 C
+ATOM 4253 O LYS B 425 82.160 67.347 57.012 1.00 37.80 O
+ATOM 4254 CB LYS B 425 82.992 64.438 57.524 1.00 36.30 C
+ATOM 4255 CG LYS B 425 82.418 63.495 58.565 1.00 37.17 C
+ATOM 4256 CD LYS B 425 83.525 62.989 59.474 1.00 38.59 C
+ATOM 4257 CE LYS B 425 82.970 62.276 60.687 1.00 38.47 C
+ATOM 4258 NZ LYS B 425 83.997 62.255 61.765 1.00 38.51 N
+ATOM 4259 N GLY B 426 80.162 66.392 57.353 1.00 39.53 N
+ATOM 4260 CA GLY B 426 79.609 67.649 57.800 1.00 39.73 C
+ATOM 4261 C GLY B 426 78.213 67.482 58.345 1.00 38.71 C
+ATOM 4262 O GLY B 426 77.588 66.426 58.174 1.00 41.97 O
+ATOM 4263 N PRO B 427 77.708 68.509 59.040 1.00 44.32 N
+ATOM 4264 CA PRO B 427 76.366 68.475 59.613 1.00 43.94 C
+ATOM 4265 C PRO B 427 75.367 68.355 58.486 1.00 45.46 C
+ATOM 4266 O PRO B 427 75.478 67.488 57.624 1.00 49.43 O
+ATOM 4267 CB PRO B 427 76.263 69.819 60.320 1.00 41.75 C
+ATOM 4268 CG PRO B 427 77.660 70.061 60.762 1.00 40.93 C
+ATOM 4269 CD PRO B 427 78.455 69.675 59.536 1.00 42.09 C
+ATOM 4270 N ILE B 428 74.402 69.255 58.493 1.00 50.37 N
+ATOM 4271 CA ILE B 428 73.358 69.275 57.484 1.00 53.16 C
+ATOM 4272 C ILE B 428 73.241 70.731 57.034 1.00 58.56 C
+ATOM 4273 O ILE B 428 73.452 71.653 57.828 1.00 52.38 O
+ATOM 4274 CB ILE B 428 72.036 68.763 58.094 1.00 54.51 C
+ATOM 4275 CG1 ILE B 428 71.083 68.318 56.996 1.00 57.04 C
+ATOM 4276 CG2 ILE B 428 71.405 69.845 58.952 1.00 57.18 C
+ATOM 4277 CD1 ILE B 428 69.930 67.495 57.515 1.00 58.80 C
+ATOM 4278 N ASP B 429 72.926 70.938 55.761 1.00 62.79 N
+ATOM 4279 CA ASP B 429 72.826 72.286 55.217 1.00 63.60 C
+ATOM 4280 C ASP B 429 74.192 72.902 55.403 1.00 58.80 C
+ATOM 4281 O ASP B 429 74.313 74.080 55.699 1.00 54.89 O
+ATOM 4282 CB ASP B 429 71.784 73.111 55.973 1.00 81.05 C
+ATOM 4283 CG ASP B 429 70.428 72.452 55.985 1.00105.52 C
+ATOM 4284 OD1 ASP B 429 70.316 71.344 56.550 1.00118.22 O
+ATOM 4285 OD2 ASP B 429 69.475 73.037 55.429 1.00117.76 O
+ATOM 4286 N SER B 430 75.222 72.081 55.244 1.00 51.30 N
+ATOM 4287 CA SER B 430 76.603 72.530 55.394 1.00 43.99 C
+ATOM 4288 C SER B 430 77.370 72.618 54.071 1.00 40.98 C
+ATOM 4289 O SER B 430 78.511 73.078 54.047 1.00 38.97 O
+ATOM 4290 CB SER B 430 77.344 71.602 56.360 1.00 43.06 C
+ATOM 4291 OG SER B 430 77.010 70.248 56.118 1.00 45.54 O
+ATOM 4292 N GLY B 431 76.743 72.171 52.982 1.00 38.44 N
+ATOM 4293 CA GLY B 431 77.375 72.217 51.674 1.00 35.10 C
+ATOM 4294 C GLY B 431 77.799 70.891 51.050 1.00 34.36 C
+ATOM 4295 O GLY B 431 77.748 70.744 49.818 1.00 33.05 O
+ATOM 4296 N LYS B 432 78.212 69.926 51.878 1.00 32.12 N
+ATOM 4297 CA LYS B 432 78.668 68.634 51.368 1.00 32.02 C
+ATOM 4298 C LYS B 432 77.734 68.008 50.346 1.00 31.35 C
+ATOM 4299 O LYS B 432 78.172 67.533 49.291 1.00 31.31 O
+ATOM 4300 CB LYS B 432 78.902 67.658 52.512 1.00 30.97 C
+ATOM 4301 CG LYS B 432 77.945 67.806 53.651 1.00 33.97 C
+ATOM 4302 CD LYS B 432 78.114 66.665 54.642 1.00 33.09 C
+ATOM 4303 CE LYS B 432 77.045 65.613 54.420 1.00 32.65 C
+ATOM 4304 NZ LYS B 432 75.701 66.159 54.715 1.00 32.69 N
+ATOM 4305 N THR B 433 76.445 67.998 50.655 1.00 28.74 N
+ATOM 4306 CA THR B 433 75.472 67.434 49.737 1.00 26.58 C
+ATOM 4307 C THR B 433 75.498 68.196 48.414 1.00 25.74 C
+ATOM 4308 O THR B 433 75.522 67.600 47.345 1.00 21.86 O
+ATOM 4309 CB THR B 433 74.053 67.456 50.373 1.00 25.90 C
+ATOM 4310 OG1 THR B 433 73.934 66.355 51.290 1.00 26.30 O
+ATOM 4311 CG2 THR B 433 72.974 67.351 49.319 1.00 25.35 C
+ATOM 4312 N THR B 434 75.528 69.518 48.492 1.00 24.32 N
+ATOM 4313 CA THR B 434 75.550 70.343 47.289 1.00 23.06 C
+ATOM 4314 C THR B 434 76.789 70.101 46.420 1.00 24.94 C
+ATOM 4315 O THR B 434 76.662 69.809 45.222 1.00 22.10 O
+ATOM 4316 CB THR B 434 75.451 71.836 47.660 1.00 25.01 C
+ATOM 4317 OG1 THR B 434 74.106 72.116 48.055 1.00 28.10 O
+ATOM 4318 CG2 THR B 434 75.831 72.733 46.486 1.00 26.86 C
+ATOM 4319 N LEU B 435 77.977 70.205 47.023 1.00 27.02 N
+ATOM 4320 CA LEU B 435 79.232 70.003 46.300 1.00 27.60 C
+ATOM 4321 C LEU B 435 79.374 68.595 45.714 1.00 26.87 C
+ATOM 4322 O LEU B 435 79.900 68.425 44.613 1.00 28.49 O
+ATOM 4323 CB LEU B 435 80.425 70.297 47.208 1.00 28.49 C
+ATOM 4324 CG LEU B 435 81.783 70.347 46.489 1.00 28.74 C
+ATOM 4325 CD1 LEU B 435 81.724 71.363 45.356 1.00 30.45 C
+ATOM 4326 CD2 LEU B 435 82.872 70.733 47.479 1.00 29.41 C
+ATOM 4327 N ALA B 436 78.908 67.593 46.454 1.00 26.25 N
+ATOM 4328 CA ALA B 436 78.971 66.210 45.992 1.00 26.41 C
+ATOM 4329 C ALA B 436 78.030 66.035 44.814 1.00 26.58 C
+ATOM 4330 O ALA B 436 78.283 65.228 43.916 1.00 27.34 O
+ATOM 4331 CB ALA B 436 78.575 65.255 47.108 1.00 24.13 C
+ATOM 4332 N ALA B 437 76.938 66.792 44.822 1.00 25.59 N
+ATOM 4333 CA ALA B 437 75.967 66.714 43.741 1.00 26.14 C
+ATOM 4334 C ALA B 437 76.566 67.340 42.484 1.00 27.25 C
+ATOM 4335 O ALA B 437 76.436 66.804 41.380 1.00 27.20 O
+ATOM 4336 CB ALA B 437 74.687 67.442 44.129 1.00 26.75 C
+ATOM 4337 N ALA B 438 77.221 68.479 42.656 1.00 25.80 N
+ATOM 4338 CA ALA B 438 77.835 69.158 41.531 1.00 26.37 C
+ATOM 4339 C ALA B 438 78.969 68.305 40.965 1.00 26.13 C
+ATOM 4340 O ALA B 438 79.121 68.176 39.754 1.00 26.01 O
+ATOM 4341 CB ALA B 438 78.368 70.512 41.974 1.00 26.85 C
+ATOM 4342 N LEU B 439 79.768 67.725 41.852 1.00 26.17 N
+ATOM 4343 CA LEU B 439 80.891 66.898 41.426 1.00 25.76 C
+ATOM 4344 C LEU B 439 80.371 65.665 40.713 1.00 26.00 C
+ATOM 4345 O LEU B 439 80.954 65.219 39.717 1.00 24.83 O
+ATOM 4346 CB LEU B 439 81.746 66.490 42.638 1.00 25.13 C
+ATOM 4347 CG LEU B 439 82.685 67.553 43.231 1.00 24.09 C
+ATOM 4348 CD1 LEU B 439 83.330 67.028 44.498 1.00 22.23 C
+ATOM 4349 CD2 LEU B 439 83.741 67.941 42.208 1.00 23.38 C
+ATOM 4350 N LEU B 440 79.259 65.136 41.230 1.00 27.70 N
+ATOM 4351 CA LEU B 440 78.621 63.954 40.666 1.00 28.33 C
+ATOM 4352 C LEU B 440 78.238 64.223 39.223 1.00 30.13 C
+ATOM 4353 O LEU B 440 78.543 63.421 38.343 1.00 30.22 O
+ATOM 4354 CB LEU B 440 77.376 63.567 41.481 1.00 27.63 C
+ATOM 4355 CG LEU B 440 76.653 62.216 41.255 1.00 26.65 C
+ATOM 4356 CD1 LEU B 440 75.523 62.367 40.254 1.00 25.80 C
+ATOM 4357 CD2 LEU B 440 77.640 61.154 40.801 1.00 26.90 C
+ATOM 4358 N GLU B 441 77.603 65.367 38.974 1.00 31.94 N
+ATOM 4359 CA GLU B 441 77.181 65.716 37.622 1.00 33.09 C
+ATOM 4360 C GLU B 441 78.347 66.116 36.712 1.00 30.87 C
+ATOM 4361 O GLU B 441 78.337 65.851 35.513 1.00 30.94 O
+ATOM 4362 CB GLU B 441 76.145 66.842 37.665 1.00 37.61 C
+ATOM 4363 CG GLU B 441 75.619 67.228 36.288 1.00 46.88 C
+ATOM 4364 CD GLU B 441 74.299 67.969 36.338 1.00 51.32 C
+ATOM 4365 OE1 GLU B 441 74.231 69.035 36.993 1.00 53.39 O
+ATOM 4366 OE2 GLU B 441 73.329 67.481 35.715 1.00 53.42 O
+ATOM 4367 N LEU B 442 79.364 66.739 37.282 1.00 27.62 N
+ATOM 4368 CA LEU B 442 80.515 67.165 36.499 1.00 24.36 C
+ATOM 4369 C LEU B 442 81.257 65.989 35.895 1.00 25.62 C
+ATOM 4370 O LEU B 442 81.726 66.077 34.768 1.00 24.18 O
+ATOM 4371 CB LEU B 442 81.479 67.972 37.370 1.00 20.75 C
+ATOM 4372 CG LEU B 442 82.749 68.466 36.685 1.00 18.25 C
+ATOM 4373 CD1 LEU B 442 82.422 69.620 35.764 1.00 16.40 C
+ATOM 4374 CD2 LEU B 442 83.761 68.893 37.735 1.00 18.89 C
+ATOM 4375 N CYS B 443 81.357 64.888 36.638 1.00 29.46 N
+ATOM 4376 CA CYS B 443 82.073 63.691 36.170 1.00 32.36 C
+ATOM 4377 C CYS B 443 81.265 62.531 35.608 1.00 34.25 C
+ATOM 4378 O CYS B 443 81.818 61.668 34.921 1.00 33.09 O
+ATOM 4379 CB CYS B 443 82.903 63.122 37.302 1.00 31.81 C
+ATOM 4380 SG CYS B 443 84.072 64.275 37.898 1.00 37.05 S
+ATOM 4381 N GLY B 444 79.969 62.511 35.906 1.00 37.65 N
+ATOM 4382 CA GLY B 444 79.121 61.410 35.491 1.00 42.32 C
+ATOM 4383 C GLY B 444 79.126 60.505 36.717 1.00 43.98 C
+ATOM 4384 O GLY B 444 79.887 60.753 37.649 1.00 49.06 O
+ATOM 4385 N GLY B 445 78.294 59.474 36.757 1.00 44.74 N
+ATOM 4386 CA GLY B 445 78.305 58.604 37.923 1.00 42.92 C
+ATOM 4387 C GLY B 445 76.979 58.466 38.649 1.00 42.71 C
+ATOM 4388 O GLY B 445 76.021 59.181 38.359 1.00 41.85 O
+ATOM 4389 N LYS B 446 76.932 57.542 39.607 1.00 42.71 N
+ATOM 4390 CA LYS B 446 75.719 57.285 40.384 1.00 40.08 C
+ATOM 4391 C LYS B 446 75.871 57.449 41.894 1.00 38.23 C
+ATOM 4392 O LYS B 446 76.948 57.237 42.461 1.00 36.96 O
+ATOM 4393 CB LYS B 446 75.218 55.867 40.099 1.00 40.85 C
+ATOM 4394 CG LYS B 446 74.698 55.631 38.689 1.00 43.95 C
+ATOM 4395 CD LYS B 446 73.378 56.343 38.438 1.00 46.70 C
+ATOM 4396 CE LYS B 446 72.712 55.855 37.154 1.00 47.61 C
+ATOM 4397 NZ LYS B 446 71.339 56.435 36.994 1.00 48.16 N
+ATOM 4398 N ALA B 447 74.776 57.832 42.538 1.00 37.92 N
+ATOM 4399 CA ALA B 447 74.757 57.984 43.986 1.00 38.85 C
+ATOM 4400 C ALA B 447 74.339 56.605 44.490 1.00 40.12 C
+ATOM 4401 O ALA B 447 73.619 55.889 43.783 1.00 43.35 O
+ATOM 4402 CB ALA B 447 73.727 59.041 44.399 1.00 39.61 C
+ATOM 4403 N LEU B 448 74.795 56.219 45.683 1.00 38.67 N
+ATOM 4404 CA LEU B 448 74.439 54.911 46.234 1.00 37.24 C
+ATOM 4405 C LEU B 448 74.055 54.971 47.704 1.00 39.96 C
+ATOM 4406 O LEU B 448 74.699 55.666 48.497 1.00 35.95 O
+ATOM 4407 CB LEU B 448 75.597 53.920 46.089 1.00 35.87 C
+ATOM 4408 CG LEU B 448 76.155 53.591 44.709 1.00 34.46 C
+ATOM 4409 CD1 LEU B 448 77.257 52.560 44.848 1.00 35.05 C
+ATOM 4410 CD2 LEU B 448 75.061 53.076 43.830 1.00 34.46 C
+ATOM 4411 N ASN B 449 73.014 54.227 48.066 1.00 41.60 N
+ATOM 4412 CA ASN B 449 72.569 54.173 49.452 1.00 42.60 C
+ATOM 4413 C ASN B 449 72.973 52.831 50.030 1.00 41.43 C
+ATOM 4414 O ASN B 449 72.490 51.791 49.600 1.00 39.25 O
+ATOM 4415 CB ASN B 449 71.057 54.350 49.557 1.00 50.00 C
+ATOM 4416 CG ASN B 449 70.582 54.297 50.986 1.00 60.69 C
+ATOM 4417 OD1 ASN B 449 70.625 53.245 51.619 1.00 68.36 O
+ATOM 4418 ND2 ASN B 449 70.152 55.434 51.516 1.00 65.68 N
+ATOM 4419 N VAL B 450 73.869 52.867 51.008 1.00 42.39 N
+ATOM 4420 CA VAL B 450 74.370 51.657 51.626 1.00 43.90 C
+ATOM 4421 C VAL B 450 73.790 51.452 53.019 1.00 46.33 C
+ATOM 4422 O VAL B 450 74.101 50.469 53.691 1.00 47.15 O
+ATOM 4423 CB VAL B 450 75.911 51.687 51.657 1.00 43.01 C
+ATOM 4424 CG1 VAL B 450 76.458 50.457 52.309 1.00 45.62 C
+ATOM 4425 CG2 VAL B 450 76.435 51.755 50.251 1.00 44.17 C
+ATOM 4426 N ASN B 451 72.953 52.384 53.465 1.00 50.97 N
+ATOM 4427 CA ASN B 451 72.301 52.212 54.753 1.00 52.38 C
+ATOM 4428 C ASN B 451 71.175 51.257 54.384 1.00 52.69 C
+ATOM 4429 O ASN B 451 70.050 51.685 54.139 1.00 50.17 O
+ATOM 4430 CB ASN B 451 71.692 53.515 55.248 1.00 58.27 C
+ATOM 4431 CG ASN B 451 72.593 54.692 55.030 1.00 66.62 C
+ATOM 4432 OD1 ASN B 451 73.686 54.765 55.591 1.00 70.41 O
+ATOM 4433 ND2 ASN B 451 72.142 55.633 54.207 1.00 71.80 N
+ATOM 4434 N LEU B 452 71.482 49.969 54.304 1.00 57.13 N
+ATOM 4435 CA LEU B 452 70.473 48.987 53.930 1.00 60.61 C
+ATOM 4436 C LEU B 452 70.716 47.659 54.647 1.00 63.75 C
+ATOM 4437 O LEU B 452 71.607 47.555 55.497 1.00 69.41 O
+ATOM 4438 CB LEU B 452 70.514 48.758 52.414 1.00 54.90 C
+ATOM 4439 CG LEU B 452 70.287 49.905 51.427 1.00 50.44 C
+ATOM 4440 CD1 LEU B 452 70.412 49.368 50.014 1.00 48.18 C
+ATOM 4441 CD2 LEU B 452 68.918 50.519 51.626 1.00 48.56 C
+ATOM 4442 N PRO B 453 69.898 46.636 54.340 1.00 83.32 N
+ATOM 4443 CA PRO B 453 70.080 45.326 54.977 1.00 84.65 C
+ATOM 4444 C PRO B 453 71.356 44.721 54.394 1.00 83.91 C
+ATOM 4445 O PRO B 453 71.498 44.651 53.173 1.00 88.85 O
+ATOM 4446 CB PRO B 453 68.836 44.557 54.543 1.00 90.04 C
+ATOM 4447 CG PRO B 453 67.809 45.645 54.357 1.00 91.36 C
+ATOM 4448 CD PRO B 453 68.601 46.699 53.642 1.00 84.86 C
+ATOM 4449 N LEU B 454 72.275 44.288 55.254 1.00 83.57 N
+ATOM 4450 CA LEU B 454 73.542 43.727 54.788 1.00 79.96 C
+ATOM 4451 C LEU B 454 73.403 42.727 53.638 1.00 82.24 C
+ATOM 4452 O LEU B 454 74.405 42.295 53.067 1.00 77.88 O
+ATOM 4453 CB LEU B 454 74.303 43.066 55.941 1.00 73.50 C
+ATOM 4454 CG LEU B 454 75.708 42.564 55.575 1.00 68.39 C
+ATOM 4455 CD1 LEU B 454 76.704 43.723 55.579 1.00 65.47 C
+ATOM 4456 CD2 LEU B 454 76.139 41.494 56.560 1.00 67.29 C
+ATOM 4457 N ASP B 455 72.172 42.358 53.294 1.00 87.31 N
+ATOM 4458 CA ASP B 455 71.953 41.418 52.198 1.00 92.70 C
+ATOM 4459 C ASP B 455 71.318 42.099 50.986 1.00 95.57 C
+ATOM 4460 O ASP B 455 71.501 41.666 49.845 1.00 94.38 O
+ATOM 4461 CB ASP B 455 71.097 40.238 52.676 1.00 98.07 C
+ATOM 4462 CG ASP B 455 71.942 39.090 53.243 1.00105.29 C
+ATOM 4463 OD1 ASP B 455 72.820 39.342 54.099 1.00109.17 O
+ATOM 4464 OD2 ASP B 455 71.723 37.929 52.833 1.00109.15 O
+ATOM 4465 N ARG B 456 70.573 43.168 51.237 1.00100.41 N
+ATOM 4466 CA ARG B 456 69.951 43.920 50.158 1.00103.49 C
+ATOM 4467 C ARG B 456 70.958 44.984 49.724 1.00 99.71 C
+ATOM 4468 O ARG B 456 70.591 46.055 49.233 1.00101.80 O
+ATOM 4469 CB ARG B 456 68.651 44.562 50.647 1.00112.19 C
+ATOM 4470 CG ARG B 456 67.580 43.533 50.974 1.00125.10 C
+ATOM 4471 CD ARG B 456 66.300 44.166 51.506 1.00130.45 C
+ATOM 4472 NE ARG B 456 65.248 43.166 51.696 1.00131.93 N
+ATOM 4473 CZ ARG B 456 64.065 43.413 52.254 1.00132.20 C
+ATOM 4474 NH1 ARG B 456 63.776 44.633 52.684 1.00132.19 N
+ATOM 4475 NH2 ARG B 456 63.169 42.442 52.379 1.00131.91 N
+ATOM 4476 N LEU B 457 72.236 44.656 49.910 1.00 90.72 N
+ATOM 4477 CA LEU B 457 73.353 45.535 49.576 1.00 81.96 C
+ATOM 4478 C LEU B 457 73.847 45.320 48.140 1.00 79.50 C
+ATOM 4479 O LEU B 457 73.909 46.270 47.352 1.00 75.68 O
+ATOM 4480 CB LEU B 457 74.494 45.298 50.575 1.00 76.38 C
+ATOM 4481 CG LEU B 457 75.725 46.208 50.574 1.00 70.67 C
+ATOM 4482 CD1 LEU B 457 75.283 47.654 50.694 1.00 69.03 C
+ATOM 4483 CD2 LEU B 457 76.650 45.837 51.731 1.00 67.15 C
+ATOM 4484 N ASN B 458 74.197 44.079 47.802 1.00 73.08 N
+ATOM 4485 CA ASN B 458 74.678 43.755 46.456 1.00 69.84 C
+ATOM 4486 C ASN B 458 73.827 44.447 45.395 1.00 71.95 C
+ATOM 4487 O ASN B 458 74.339 44.882 44.357 1.00 63.80 O
+ATOM 4488 CB ASN B 458 74.643 42.243 46.225 1.00 70.04 C
+ATOM 4489 CG ASN B 458 75.586 41.492 47.144 1.00 73.90 C
+ATOM 4490 OD1 ASN B 458 76.799 41.710 47.124 1.00 76.91 O
+ATOM 4491 ND2 ASN B 458 75.031 40.598 47.955 1.00 76.37 N
+ATOM 4492 N PHE B 459 72.526 44.528 45.676 1.00 72.95 N
+ATOM 4493 CA PHE B 459 71.537 45.172 44.807 1.00 72.96 C
+ATOM 4494 C PHE B 459 72.080 46.535 44.373 1.00 71.07 C
+ATOM 4495 O PHE B 459 72.323 46.776 43.186 1.00 62.90 O
+ATOM 4496 CB PHE B 459 70.227 45.367 45.597 1.00 85.95 C
+ATOM 4497 CG PHE B 459 69.121 46.068 44.832 1.00106.24 C
+ATOM 4498 CD1 PHE B 459 68.191 45.335 44.096 1.00114.37 C
+ATOM 4499 CD2 PHE B 459 68.989 47.457 44.879 1.00114.03 C
+ATOM 4500 CE1 PHE B 459 67.143 45.975 43.421 1.00117.48 C
+ATOM 4501 CE2 PHE B 459 67.948 48.104 44.208 1.00117.01 C
+ATOM 4502 CZ PHE B 459 67.025 47.361 43.479 1.00118.06 C
+ATOM 4503 N GLU B 460 72.281 47.411 45.358 1.00 67.66 N
+ATOM 4504 CA GLU B 460 72.761 48.767 45.124 1.00 62.79 C
+ATOM 4505 C GLU B 460 74.187 48.828 44.578 1.00 56.97 C
+ATOM 4506 O GLU B 460 74.464 49.536 43.609 1.00 54.32 O
+ATOM 4507 CB GLU B 460 72.666 49.580 46.422 1.00 67.31 C
+ATOM 4508 CG GLU B 460 72.275 51.038 46.204 1.00 77.67 C
+ATOM 4509 CD GLU B 460 70.783 51.226 46.004 1.00 82.26 C
+ATOM 4510 OE1 GLU B 460 70.139 50.355 45.383 1.00 83.76 O
+ATOM 4511 OE2 GLU B 460 70.255 52.256 46.464 1.00 84.48 O
+ATOM 4512 N LEU B 461 75.094 48.090 45.201 1.00 49.44 N
+ATOM 4513 CA LEU B 461 76.473 48.093 44.745 1.00 45.10 C
+ATOM 4514 C LEU B 461 76.559 47.792 43.251 1.00 43.19 C
+ATOM 4515 O LEU B 461 77.472 48.253 42.566 1.00 42.65 O
+ATOM 4516 CB LEU B 461 77.294 47.074 45.536 1.00 40.94 C
+ATOM 4517 CG LEU B 461 77.476 47.360 47.032 1.00 37.84 C
+ATOM 4518 CD1 LEU B 461 78.447 46.319 47.604 1.00 33.59 C
+ATOM 4519 CD2 LEU B 461 78.002 48.798 47.265 1.00 34.26 C
+ATOM 4520 N GLY B 462 75.603 47.019 42.750 1.00 41.64 N
+ATOM 4521 CA GLY B 462 75.594 46.679 41.340 1.00 40.36 C
+ATOM 4522 C GLY B 462 75.323 47.877 40.447 1.00 41.30 C
+ATOM 4523 O GLY B 462 75.616 47.837 39.254 1.00 38.56 O
+ATOM 4524 N VAL B 463 74.764 48.943 41.014 1.00 42.70 N
+ATOM 4525 CA VAL B 463 74.469 50.144 40.234 1.00 44.21 C
+ATOM 4526 C VAL B 463 75.757 50.797 39.751 1.00 43.35 C
+ATOM 4527 O VAL B 463 75.762 51.528 38.752 1.00 44.46 O
+ATOM 4528 CB VAL B 463 73.705 51.198 41.067 1.00 48.30 C
+ATOM 4529 CG1 VAL B 463 73.341 52.401 40.188 1.00 51.37 C
+ATOM 4530 CG2 VAL B 463 72.464 50.577 41.679 1.00 52.22 C
+ATOM 4531 N ALA B 464 76.841 50.516 40.473 1.00 41.37 N
+ATOM 4532 CA ALA B 464 78.160 51.073 40.190 1.00 39.33 C
+ATOM 4533 C ALA B 464 78.782 50.578 38.897 1.00 41.81 C
+ATOM 4534 O ALA B 464 79.767 51.145 38.421 1.00 44.34 O
+ATOM 4535 CB ALA B 464 79.087 50.775 41.347 1.00 35.00 C
+ATOM 4536 N ILE B 465 78.200 49.522 38.337 1.00 46.92 N
+ATOM 4537 CA ILE B 465 78.684 48.910 37.107 1.00 51.40 C
+ATOM 4538 C ILE B 465 78.954 49.895 35.985 1.00 55.54 C
+ATOM 4539 O ILE B 465 78.053 50.612 35.559 1.00 55.70 O
+ATOM 4540 CB ILE B 465 77.683 47.857 36.625 1.00 52.72 C
+ATOM 4541 CG1 ILE B 465 77.791 46.628 37.532 1.00 55.93 C
+ATOM 4542 CG2 ILE B 465 77.926 47.524 35.161 1.00 54.61 C
+ATOM 4543 CD1 ILE B 465 76.741 45.567 37.301 1.00 57.56 C
+ATOM 4544 N ASP B 466 80.199 49.918 35.513 1.00 59.32 N
+ATOM 4545 CA ASP B 466 80.621 50.804 34.426 1.00 61.25 C
+ATOM 4546 C ASP B 466 80.513 52.305 34.719 1.00 58.62 C
+ATOM 4547 O ASP B 466 80.692 53.126 33.814 1.00 57.13 O
+ATOM 4548 CB ASP B 466 79.833 50.492 33.146 1.00 70.78 C
+ATOM 4549 CG ASP B 466 80.149 49.123 32.582 1.00 83.85 C
+ATOM 4550 OD1 ASP B 466 81.128 48.506 33.049 1.00 90.84 O
+ATOM 4551 OD2 ASP B 466 79.425 48.670 31.666 1.00 89.90 O
+ATOM 4552 N GLN B 467 80.215 52.669 35.964 1.00 52.29 N
+ATOM 4553 CA GLN B 467 80.107 54.079 36.334 1.00 45.89 C
+ATOM 4554 C GLN B 467 81.499 54.680 36.527 1.00 42.21 C
+ATOM 4555 O GLN B 467 82.383 54.042 37.088 1.00 41.59 O
+ATOM 4556 CB GLN B 467 79.295 54.229 37.624 1.00 45.56 C
+ATOM 4557 CG GLN B 467 77.801 53.982 37.465 1.00 45.85 C
+ATOM 4558 CD GLN B 467 77.185 54.879 36.406 1.00 45.76 C
+ATOM 4559 OE1 GLN B 467 77.309 54.615 35.216 1.00 45.91 O
+ATOM 4560 NE2 GLN B 467 76.537 55.955 36.834 1.00 45.38 N
+ATOM 4561 N PHE B 468 81.690 55.904 36.059 1.00 35.95 N
+ATOM 4562 CA PHE B 468 82.977 56.580 36.190 1.00 31.78 C
+ATOM 4563 C PHE B 468 83.375 56.845 37.648 1.00 30.75 C
+ATOM 4564 O PHE B 468 84.530 56.672 38.017 1.00 31.28 O
+ATOM 4565 CB PHE B 468 82.933 57.889 35.419 1.00 30.08 C
+ATOM 4566 CG PHE B 468 84.199 58.681 35.494 1.00 27.67 C
+ATOM 4567 CD1 PHE B 468 85.318 58.292 34.761 1.00 26.08 C
+ATOM 4568 CD2 PHE B 468 84.266 59.832 36.280 1.00 25.96 C
+ATOM 4569 CE1 PHE B 468 86.488 59.036 34.803 1.00 26.77 C
+ATOM 4570 CE2 PHE B 468 85.424 60.583 36.332 1.00 26.67 C
+ATOM 4571 CZ PHE B 468 86.544 60.188 35.591 1.00 27.18 C
+ATOM 4572 N LEU B 469 82.433 57.297 38.468 1.00 27.72 N
+ATOM 4573 CA LEU B 469 82.717 57.536 39.881 1.00 27.26 C
+ATOM 4574 C LEU B 469 81.433 57.280 40.648 1.00 28.57 C
+ATOM 4575 O LEU B 469 80.335 57.310 40.084 1.00 29.37 O
+ATOM 4576 CB LEU B 469 83.205 58.973 40.148 1.00 25.26 C
+ATOM 4577 CG LEU B 469 82.244 60.152 40.402 1.00 23.80 C
+ATOM 4578 CD1 LEU B 469 81.416 59.922 41.665 1.00 23.69 C
+ATOM 4579 CD2 LEU B 469 83.050 61.442 40.574 1.00 24.39 C
+ATOM 4580 N VAL B 470 81.563 57.048 41.942 1.00 27.95 N
+ATOM 4581 CA VAL B 470 80.403 56.769 42.749 1.00 27.32 C
+ATOM 4582 C VAL B 470 80.290 57.690 43.944 1.00 26.11 C
+ATOM 4583 O VAL B 470 81.289 58.207 44.445 1.00 27.79 O
+ATOM 4584 CB VAL B 470 80.459 55.304 43.229 1.00 27.94 C
+ATOM 4585 CG1 VAL B 470 79.753 55.139 44.567 1.00 27.17 C
+ATOM 4586 CG2 VAL B 470 79.831 54.414 42.181 1.00 27.45 C
+ATOM 4587 N VAL B 471 79.061 57.910 44.391 1.00 24.64 N
+ATOM 4588 CA VAL B 471 78.860 58.719 45.571 1.00 24.06 C
+ATOM 4589 C VAL B 471 77.912 58.015 46.544 1.00 23.72 C
+ATOM 4590 O VAL B 471 76.757 57.742 46.220 1.00 24.86 O
+ATOM 4591 CB VAL B 471 78.308 60.122 45.231 1.00 21.44 C
+ATOM 4592 CG1 VAL B 471 77.979 60.877 46.537 1.00 14.48 C
+ATOM 4593 CG2 VAL B 471 79.334 60.912 44.424 1.00 12.41 C
+ATOM 4594 N PHE B 472 78.442 57.687 47.720 1.00 25.75 N
+ATOM 4595 CA PHE B 472 77.679 57.055 48.795 1.00 29.45 C
+ATOM 4596 C PHE B 472 77.100 58.227 49.584 1.00 35.97 C
+ATOM 4597 O PHE B 472 77.811 58.856 50.377 1.00 31.82 O
+ATOM 4598 CB PHE B 472 78.605 56.253 49.707 1.00 27.11 C
+ATOM 4599 CG PHE B 472 79.238 55.043 49.048 1.00 25.45 C
+ATOM 4600 CD1 PHE B 472 78.652 53.790 49.165 1.00 23.46 C
+ATOM 4601 CD2 PHE B 472 80.440 55.152 48.353 1.00 22.28 C
+ATOM 4602 CE1 PHE B 472 79.250 52.672 48.608 1.00 21.89 C
+ATOM 4603 CE2 PHE B 472 81.041 54.035 47.796 1.00 21.71 C
+ATOM 4604 CZ PHE B 472 80.450 52.800 47.923 1.00 22.09 C
+ATOM 4605 N GLU B 473 75.822 58.521 49.349 1.00 43.95 N
+ATOM 4606 CA GLU B 473 75.158 59.630 50.008 1.00 50.62 C
+ATOM 4607 C GLU B 473 74.627 59.356 51.403 1.00 52.29 C
+ATOM 4608 O GLU B 473 73.969 58.351 51.641 1.00 46.85 O
+ATOM 4609 CB GLU B 473 74.028 60.174 49.134 1.00 62.20 C
+ATOM 4610 CG GLU B 473 74.264 61.590 48.622 1.00 87.71 C
+ATOM 4611 CD GLU B 473 74.395 62.622 49.737 1.00 98.31 C
+ATOM 4612 OE1 GLU B 473 73.475 62.717 50.580 1.00101.96 O
+ATOM 4613 OE2 GLU B 473 75.416 63.344 49.768 1.00101.31 O
+ATOM 4614 N ASP B 474 74.922 60.282 52.313 1.00 53.04 N
+ATOM 4615 CA ASP B 474 74.506 60.225 53.705 1.00 49.97 C
+ATOM 4616 C ASP B 474 74.629 58.864 54.371 1.00 45.96 C
+ATOM 4617 O ASP B 474 73.642 58.284 54.813 1.00 42.30 O
+ATOM 4618 CB ASP B 474 73.075 60.730 53.853 1.00 59.21 C
+ATOM 4619 CG ASP B 474 72.955 61.796 54.909 1.00 74.74 C
+ATOM 4620 OD1 ASP B 474 72.014 61.717 55.723 1.00 83.31 O
+ATOM 4621 OD2 ASP B 474 73.803 62.715 54.919 1.00 82.54 O
+ATOM 4622 N VAL B 475 75.852 58.360 54.440 1.00 42.61 N
+ATOM 4623 CA VAL B 475 76.109 57.091 55.081 1.00 39.96 C
+ATOM 4624 C VAL B 475 75.802 57.316 56.560 1.00 40.87 C
+ATOM 4625 O VAL B 475 76.142 58.363 57.111 1.00 40.16 O
+ATOM 4626 CB VAL B 475 77.580 56.706 54.907 1.00 37.46 C
+ATOM 4627 CG1 VAL B 475 77.783 55.251 55.268 1.00 37.24 C
+ATOM 4628 CG2 VAL B 475 78.009 56.978 53.482 1.00 36.08 C
+ATOM 4629 N LYS B 476 75.144 56.350 57.197 1.00 44.18 N
+ATOM 4630 CA LYS B 476 74.802 56.475 58.614 1.00 45.22 C
+ATOM 4631 C LYS B 476 75.451 55.378 59.439 1.00 45.90 C
+ATOM 4632 O LYS B 476 75.638 54.261 58.954 1.00 43.93 O
+ATOM 4633 CB LYS B 476 73.288 56.420 58.802 1.00 47.29 C
+ATOM 4634 CG LYS B 476 72.550 57.537 58.106 1.00 51.09 C
+ATOM 4635 CD LYS B 476 71.057 57.304 58.117 1.00 53.28 C
+ATOM 4636 CE LYS B 476 70.380 58.208 57.110 1.00 54.71 C
+ATOM 4637 NZ LYS B 476 68.907 58.071 57.150 1.00 55.63 N
+ATOM 4638 N GLY B 477 75.794 55.705 60.682 1.00 49.06 N
+ATOM 4639 CA GLY B 477 76.426 54.733 61.555 1.00 53.66 C
+ATOM 4640 C GLY B 477 75.653 54.486 62.831 1.00 58.13 C
+ATOM 4641 O GLY B 477 74.948 55.368 63.315 1.00 55.95 O
+ATOM 4642 N THR B 478 75.776 53.275 63.366 1.00 67.05 N
+ATOM 4643 CA THR B 478 75.095 52.913 64.602 1.00 73.80 C
+ATOM 4644 C THR B 478 75.719 53.745 65.710 1.00 75.48 C
+ATOM 4645 O THR B 478 75.022 54.451 66.440 1.00 76.87 O
+ATOM 4646 CB THR B 478 75.288 51.426 64.947 1.00 78.75 C
+ATOM 4647 OG1 THR B 478 74.915 50.620 63.824 1.00 85.98 O
+ATOM 4648 CG2 THR B 478 74.422 51.046 66.144 1.00 85.99 C
+ATOM 4649 N GLY B 479 77.039 53.645 65.836 1.00 78.60 N
+ATOM 4650 CA GLY B 479 77.730 54.418 66.846 1.00 80.24 C
+ATOM 4651 C GLY B 479 77.216 55.833 66.693 1.00 81.02 C
+ATOM 4652 O GLY B 479 76.970 56.281 65.572 1.00 82.07 O
+ATOM 4653 N GLY B 480 77.031 56.536 67.802 1.00 81.00 N
+ATOM 4654 CA GLY B 480 76.529 57.893 67.719 1.00 82.35 C
+ATOM 4655 C GLY B 480 75.017 57.884 67.669 1.00 86.16 C
+ATOM 4656 O GLY B 480 74.412 57.153 66.888 1.00 83.18 O
+ATOM 4657 N GLU B 481 74.406 58.724 68.490 1.00 91.11 N
+ATOM 4658 CA GLU B 481 72.957 58.793 68.573 1.00 89.75 C
+ATOM 4659 C GLU B 481 72.574 59.978 69.444 1.00 85.74 C
+ATOM 4660 O GLU B 481 71.595 60.677 69.183 1.00 81.96 O
+ATOM 4661 CB GLU B 481 72.443 57.499 69.197 1.00 95.75 C
+ATOM 4662 CG GLU B 481 73.279 57.063 70.393 1.00112.64 C
+ATOM 4663 CD GLU B 481 72.901 55.694 70.915 1.00120.77 C
+ATOM 4664 OE1 GLU B 481 71.763 55.538 71.407 1.00123.88 O
+ATOM 4665 OE2 GLU B 481 73.743 54.773 70.832 1.00124.11 O
+ATOM 4666 N SER B 482 73.361 60.194 70.490 1.00 82.96 N
+ATOM 4667 CA SER B 482 73.121 61.295 71.403 1.00 83.45 C
+ATOM 4668 C SER B 482 72.944 62.604 70.635 1.00 85.33 C
+ATOM 4669 O SER B 482 71.917 63.264 70.766 1.00 90.55 O
+ATOM 4670 CB SER B 482 74.277 61.407 72.403 1.00 81.55 C
+ATOM 4671 OG SER B 482 75.532 61.215 71.768 1.00 74.27 O
+ATOM 4672 N ARG B 483 73.927 62.963 69.813 1.00 86.74 N
+ATOM 4673 CA ARG B 483 73.865 64.206 69.044 1.00 86.80 C
+ATOM 4674 C ARG B 483 72.710 64.339 68.029 1.00 87.00 C
+ATOM 4675 O ARG B 483 72.752 65.199 67.144 1.00 79.05 O
+ATOM 4676 CB ARG B 483 75.218 64.473 68.358 1.00 90.48 C
+ATOM 4677 CG ARG B 483 75.842 63.281 67.640 1.00 97.49 C
+ATOM 4678 CD ARG B 483 76.573 62.325 68.588 1.00100.20 C
+ATOM 4679 NE ARG B 483 77.886 62.818 69.008 1.00100.82 N
+ATOM 4680 CZ ARG B 483 78.728 62.138 69.787 1.00101.45 C
+ATOM 4681 NH1 ARG B 483 78.400 60.931 70.236 1.00101.17 N
+ATOM 4682 NH2 ARG B 483 79.904 62.664 70.119 1.00101.05 N
+ATOM 4683 N ASP B 484 71.684 63.497 68.174 1.00 82.10 N
+ATOM 4684 CA ASP B 484 70.489 63.530 67.319 1.00 75.79 C
+ATOM 4685 C ASP B 484 70.583 62.845 65.957 1.00 71.38 C
+ATOM 4686 O ASP B 484 69.709 63.016 65.098 1.00 63.51 O
+ATOM 4687 CB ASP B 484 70.033 64.978 67.104 1.00 83.33 C
+ATOM 4688 CG ASP B 484 69.816 65.721 68.404 1.00 96.30 C
+ATOM 4689 OD1 ASP B 484 69.208 65.135 69.323 1.00103.78 O
+ATOM 4690 OD2 ASP B 484 70.242 66.892 68.502 1.00104.24 O
+ATOM 4691 N LEU B 485 71.628 62.057 65.759 1.00 66.69 N
+ATOM 4692 CA LEU B 485 71.809 61.375 64.490 1.00 63.92 C
+ATOM 4693 C LEU B 485 71.226 59.967 64.512 1.00 62.94 C
+ATOM 4694 O LEU B 485 71.479 59.196 65.442 1.00 65.22 O
+ATOM 4695 CB LEU B 485 73.296 61.313 64.156 1.00 64.76 C
+ATOM 4696 CG LEU B 485 74.006 62.665 64.247 1.00 65.73 C
+ATOM 4697 CD1 LEU B 485 75.500 62.499 64.012 1.00 66.40 C
+ATOM 4698 CD2 LEU B 485 73.396 63.612 63.227 1.00 66.43 C
+ATOM 4699 N PRO B 486 70.427 59.618 63.486 1.00 65.55 N
+ATOM 4700 CA PRO B 486 69.776 58.312 63.325 1.00 65.96 C
+ATOM 4701 C PRO B 486 70.731 57.125 63.441 1.00 66.83 C
+ATOM 4702 O PRO B 486 71.912 57.300 63.747 1.00 68.29 O
+ATOM 4703 CB PRO B 486 69.138 58.424 61.944 1.00 65.64 C
+ATOM 4704 CG PRO B 486 68.702 59.851 61.925 1.00 65.07 C
+ATOM 4705 CD PRO B 486 69.925 60.569 62.476 1.00 64.97 C
+ATOM 4706 N SER B 487 70.224 55.924 63.180 1.00 67.36 N
+ATOM 4707 CA SER B 487 71.043 54.721 63.288 1.00 67.47 C
+ATOM 4708 C SER B 487 71.738 54.315 61.983 1.00 65.37 C
+ATOM 4709 O SER B 487 72.943 54.554 61.814 1.00 62.70 O
+ATOM 4710 CB SER B 487 70.189 53.565 63.807 1.00 71.90 C
+ATOM 4711 OG SER B 487 70.984 52.428 64.094 1.00 80.65 O
+ATOM 4712 N GLY B 488 70.992 53.694 61.068 1.00 59.63 N
+ATOM 4713 CA GLY B 488 71.576 53.279 59.798 1.00 53.38 C
+ATOM 4714 C GLY B 488 72.781 52.351 59.909 1.00 51.19 C
+ATOM 4715 O GLY B 488 73.483 52.347 60.920 1.00 46.11 O
+ATOM 4716 N GLN B 489 73.033 51.574 58.860 1.00 51.47 N
+ATOM 4717 CA GLN B 489 74.152 50.635 58.853 1.00 52.08 C
+ATOM 4718 C GLN B 489 75.220 50.920 57.792 1.00 51.27 C
+ATOM 4719 O GLN B 489 76.103 50.095 57.561 1.00 50.23 O
+ATOM 4720 CB GLN B 489 73.625 49.209 58.664 1.00 54.93 C
+ATOM 4721 CG GLN B 489 72.834 48.668 59.842 1.00 61.98 C
+ATOM 4722 CD GLN B 489 73.708 48.338 61.039 1.00 65.32 C
+ATOM 4723 OE1 GLN B 489 74.681 47.586 60.922 1.00 66.90 O
+ATOM 4724 NE2 GLN B 489 73.358 48.886 62.203 1.00 66.19 N
+ATOM 4725 N GLY B 490 75.141 52.079 57.146 1.00 49.30 N
+ATOM 4726 CA GLY B 490 76.116 52.414 56.121 1.00 47.25 C
+ATOM 4727 C GLY B 490 77.573 52.287 56.540 1.00 45.97 C
+ATOM 4728 O GLY B 490 78.335 51.556 55.902 1.00 46.10 O
+ATOM 4729 N ILE B 491 77.962 52.997 57.602 1.00 43.06 N
+ATOM 4730 CA ILE B 491 79.342 52.958 58.094 1.00 38.17 C
+ATOM 4731 C ILE B 491 79.738 51.501 58.314 1.00 40.89 C
+ATOM 4732 O ILE B 491 80.859 51.077 58.006 1.00 35.68 O
+ATOM 4733 CB ILE B 491 79.498 53.700 59.443 1.00 36.14 C
+ATOM 4734 CG1 ILE B 491 78.787 55.051 59.399 1.00 34.17 C
+ATOM 4735 CG2 ILE B 491 80.972 53.915 59.748 1.00 32.76 C
+ATOM 4736 CD1 ILE B 491 79.441 56.072 58.518 1.00 35.07 C
+ATOM 4737 N ASN B 492 78.793 50.739 58.847 1.00 44.31 N
+ATOM 4738 CA ASN B 492 79.012 49.330 59.109 1.00 47.14 C
+ATOM 4739 C ASN B 492 79.320 48.627 57.797 1.00 47.48 C
+ATOM 4740 O ASN B 492 80.295 47.888 57.692 1.00 48.00 O
+ATOM 4741 CB ASN B 492 77.760 48.712 59.717 1.00 54.60 C
+ATOM 4742 CG ASN B 492 78.075 47.734 60.811 1.00 63.99 C
+ATOM 4743 OD1 ASN B 492 78.156 48.108 61.983 1.00 69.01 O
+ATOM 4744 ND2 ASN B 492 78.269 46.470 60.441 1.00 67.45 N
+ATOM 4745 N ASN B 493 78.483 48.871 56.794 1.00 47.26 N
+ATOM 4746 CA ASN B 493 78.651 48.239 55.495 1.00 44.97 C
+ATOM 4747 C ASN B 493 79.909 48.680 54.767 1.00 43.91 C
+ATOM 4748 O ASN B 493 80.635 47.848 54.218 1.00 41.65 O
+ATOM 4749 CB ASN B 493 77.429 48.502 54.613 1.00 45.91 C
+ATOM 4750 CG ASN B 493 76.176 47.838 55.144 1.00 47.47 C
+ATOM 4751 OD1 ASN B 493 76.125 46.624 55.295 1.00 49.98 O
+ATOM 4752 ND2 ASN B 493 75.160 48.634 55.432 1.00 49.48 N
+ATOM 4753 N LEU B 494 80.168 49.984 54.762 1.00 43.52 N
+ATOM 4754 CA LEU B 494 81.348 50.498 54.082 1.00 44.12 C
+ATOM 4755 C LEU B 494 82.577 49.761 54.561 1.00 46.33 C
+ATOM 4756 O LEU B 494 83.437 49.395 53.762 1.00 45.35 O
+ATOM 4757 CB LEU B 494 81.523 52.006 54.323 1.00 42.56 C
+ATOM 4758 CG LEU B 494 80.578 52.959 53.570 1.00 41.07 C
+ATOM 4759 CD1 LEU B 494 80.966 54.377 53.896 1.00 39.22 C
+ATOM 4760 CD2 LEU B 494 80.644 52.724 52.051 1.00 39.99 C
+ATOM 4761 N ASP B 495 82.652 49.522 55.864 1.00 51.79 N
+ATOM 4762 CA ASP B 495 83.805 48.830 56.413 1.00 55.06 C
+ATOM 4763 C ASP B 495 83.959 47.398 55.899 1.00 55.70 C
+ATOM 4764 O ASP B 495 85.048 46.820 55.981 1.00 53.90 O
+ATOM 4765 CB ASP B 495 83.760 48.831 57.934 1.00 60.63 C
+ATOM 4766 CG ASP B 495 85.138 48.986 58.541 1.00 69.57 C
+ATOM 4767 OD1 ASP B 495 86.057 48.243 58.127 1.00 74.01 O
+ATOM 4768 OD2 ASP B 495 85.306 49.853 59.425 1.00 73.94 O
+ATOM 4769 N ASN B 496 82.880 46.832 55.360 1.00 57.46 N
+ATOM 4770 CA ASN B 496 82.918 45.473 54.820 1.00 56.65 C
+ATOM 4771 C ASN B 496 83.121 45.484 53.311 1.00 53.89 C
+ATOM 4772 O ASN B 496 82.941 44.467 52.640 1.00 56.25 O
+ATOM 4773 CB ASN B 496 81.623 44.735 55.131 1.00 58.74 C
+ATOM 4774 CG ASN B 496 81.326 44.697 56.603 1.00 62.52 C
+ATOM 4775 OD1 ASN B 496 82.175 44.324 57.415 1.00 63.47 O
+ATOM 4776 ND2 ASN B 496 80.112 45.083 56.962 1.00 65.34 N
+ATOM 4777 N LEU B 497 83.494 46.643 52.781 1.00 51.11 N
+ATOM 4778 CA LEU B 497 83.710 46.786 51.353 1.00 52.26 C
+ATOM 4779 C LEU B 497 85.083 47.399 51.066 1.00 58.79 C
+ATOM 4780 O LEU B 497 85.283 48.020 50.024 1.00 55.73 O
+ATOM 4781 CB LEU B 497 82.606 47.661 50.758 1.00 45.55 C
+ATOM 4782 CG LEU B 497 81.159 47.225 51.020 1.00 37.73 C
+ATOM 4783 CD1 LEU B 497 80.201 48.377 50.737 1.00 32.55 C
+ATOM 4784 CD2 LEU B 497 80.833 46.023 50.162 1.00 33.77 C
+ATOM 4785 N ARG B 498 86.025 47.219 51.991 1.00 63.77 N
+ATOM 4786 CA ARG B 498 87.377 47.746 51.829 1.00 63.57 C
+ATOM 4787 C ARG B 498 87.965 47.385 50.465 1.00 59.66 C
+ATOM 4788 O ARG B 498 88.796 48.107 49.937 1.00 49.04 O
+ATOM 4789 CB ARG B 498 88.277 47.223 52.948 1.00 74.69 C
+ATOM 4790 CG ARG B 498 88.318 45.721 53.019 1.00101.51 C
+ATOM 4791 CD ARG B 498 89.087 45.230 54.222 1.00115.21 C
+ATOM 4792 NE ARG B 498 89.292 43.784 54.154 1.00120.19 N
+ATOM 4793 CZ ARG B 498 89.944 43.074 55.069 1.00121.23 C
+ATOM 4794 NH1 ARG B 498 90.457 43.678 56.132 1.00121.28 N
+ATOM 4795 NH2 ARG B 498 90.091 41.763 54.916 1.00120.71 N
+ATOM 4796 N ASP B 499 87.515 46.281 49.884 1.00 55.47 N
+ATOM 4797 CA ASP B 499 88.019 45.849 48.584 1.00 52.62 C
+ATOM 4798 C ASP B 499 87.423 46.629 47.424 1.00 51.25 C
+ATOM 4799 O ASP B 499 88.051 46.787 46.369 1.00 53.70 O
+ATOM 4800 CB ASP B 499 87.758 44.358 48.393 1.00 53.32 C
+ATOM 4801 CG ASP B 499 88.850 43.502 48.995 1.00 56.79 C
+ATOM 4802 OD1 ASP B 499 89.484 43.935 49.981 1.00 58.87 O
+ATOM 4803 OD2 ASP B 499 89.072 42.388 48.487 1.00 60.25 O
+ATOM 4804 N TYR B 500 86.203 47.106 47.616 1.00 51.40 N
+ATOM 4805 CA TYR B 500 85.542 47.886 46.588 1.00 51.59 C
+ATOM 4806 C TYR B 500 86.115 49.299 46.635 1.00 49.07 C
+ATOM 4807 O TYR B 500 86.291 49.947 45.611 1.00 52.55 O
+ATOM 4808 CB TYR B 500 84.033 47.963 46.850 1.00 53.59 C
+ATOM 4809 CG TYR B 500 83.310 46.638 46.867 1.00 54.20 C
+ATOM 4810 CD1 TYR B 500 83.570 45.691 47.855 1.00 54.00 C
+ATOM 4811 CD2 TYR B 500 82.354 46.337 45.896 1.00 53.99 C
+ATOM 4812 CE1 TYR B 500 82.896 44.477 47.877 1.00 53.45 C
+ATOM 4813 CE2 TYR B 500 81.674 45.131 45.910 1.00 53.33 C
+ATOM 4814 CZ TYR B 500 81.951 44.204 46.901 1.00 53.46 C
+ATOM 4815 OH TYR B 500 81.288 43.000 46.910 1.00 54.64 O
+ATOM 4816 N LEU B 501 86.418 49.765 47.839 1.00 41.44 N
+ATOM 4817 CA LEU B 501 86.922 51.113 48.024 1.00 36.83 C
+ATOM 4818 C LEU B 501 88.330 51.418 47.545 1.00 40.39 C
+ATOM 4819 O LEU B 501 88.506 52.299 46.710 1.00 33.96 O
+ATOM 4820 CB LEU B 501 86.785 51.522 49.489 1.00 28.32 C
+ATOM 4821 CG LEU B 501 85.355 51.721 49.984 1.00 21.97 C
+ATOM 4822 CD1 LEU B 501 85.384 52.019 51.467 1.00 20.79 C
+ATOM 4823 CD2 LEU B 501 84.686 52.856 49.229 1.00 19.33 C
+ATOM 4824 N ASP B 502 89.334 50.711 48.055 1.00 42.25 N
+ATOM 4825 CA ASP B 502 90.706 51.007 47.634 1.00 43.10 C
+ATOM 4826 C ASP B 502 91.096 50.429 46.289 1.00 39.26 C
+ATOM 4827 O ASP B 502 92.149 50.755 45.738 1.00 32.66 O
+ATOM 4828 CB ASP B 502 91.727 50.612 48.714 1.00 58.00 C
+ATOM 4829 CG ASP B 502 91.299 49.420 49.525 1.00 76.04 C
+ATOM 4830 OD1 ASP B 502 91.052 48.357 48.923 1.00 87.21 O
+ATOM 4831 OD2 ASP B 502 91.219 49.548 50.768 1.00 85.36 O
+ATOM 4832 N GLY B 503 90.220 49.586 45.765 1.00 35.81 N
+ATOM 4833 CA GLY B 503 90.419 48.993 44.459 1.00 32.50 C
+ATOM 4834 C GLY B 503 91.773 48.453 44.060 1.00 31.96 C
+ATOM 4835 O GLY B 503 92.281 48.807 42.993 1.00 29.22 O
+ATOM 4836 N SER B 504 92.352 47.588 44.896 1.00 34.73 N
+ATOM 4837 CA SER B 504 93.643 46.974 44.589 1.00 35.94 C
+ATOM 4838 C SER B 504 93.405 45.872 43.573 1.00 36.94 C
+ATOM 4839 O SER B 504 94.191 45.686 42.650 1.00 38.91 O
+ATOM 4840 CB SER B 504 94.274 46.366 45.839 1.00 36.35 C
+ATOM 4841 OG SER B 504 94.745 47.366 46.723 1.00 37.14 O
+ATOM 4842 N VAL B 505 92.308 45.145 43.751 1.00 38.67 N
+ATOM 4843 CA VAL B 505 91.955 44.057 42.848 1.00 39.92 C
+ATOM 4844 C VAL B 505 90.508 44.225 42.385 1.00 39.99 C
+ATOM 4845 O VAL B 505 89.773 45.047 42.936 1.00 41.32 O
+ATOM 4846 CB VAL B 505 92.125 42.673 43.540 1.00 39.41 C
+ATOM 4847 CG1 VAL B 505 91.978 41.548 42.508 1.00 38.17 C
+ATOM 4848 CG2 VAL B 505 93.494 42.582 44.208 1.00 36.74 C
+ATOM 4849 N LYS B 506 90.107 43.457 41.369 1.00 40.90 N
+ATOM 4850 CA LYS B 506 88.743 43.529 40.838 1.00 41.58 C
+ATOM 4851 C LYS B 506 87.656 43.030 41.799 1.00 41.04 C
+ATOM 4852 O LYS B 506 87.934 42.430 42.838 1.00 43.09 O
+ATOM 4853 CB LYS B 506 88.623 42.742 39.539 1.00 39.44 C
+ATOM 4854 CG LYS B 506 89.467 43.246 38.384 1.00 36.22 C
+ATOM 4855 CD LYS B 506 88.660 43.157 37.084 1.00 34.18 C
+ATOM 4856 CE LYS B 506 89.543 43.113 35.850 1.00 32.63 C
+ATOM 4857 NZ LYS B 506 90.077 41.747 35.649 1.00 35.22 N
+ATOM 4858 N VAL B 507 86.408 43.273 41.418 1.00 41.71 N
+ATOM 4859 CA VAL B 507 85.258 42.893 42.223 1.00 43.67 C
+ATOM 4860 C VAL B 507 84.055 42.491 41.331 1.00 48.45 C
+ATOM 4861 O VAL B 507 83.954 42.896 40.165 1.00 44.17 O
+ATOM 4862 CB VAL B 507 84.916 44.073 43.173 1.00 38.61 C
+ATOM 4863 CG1 VAL B 507 83.492 44.020 43.609 1.00 37.67 C
+ATOM 4864 CG2 VAL B 507 85.805 44.021 44.389 1.00 34.88 C
+ATOM 4865 N ASN B 508 83.155 41.672 41.873 1.00 54.86 N
+ATOM 4866 CA ASN B 508 81.984 41.222 41.114 1.00 57.53 C
+ATOM 4867 C ASN B 508 80.697 41.945 41.524 1.00 56.62 C
+ATOM 4868 O ASN B 508 80.258 41.843 42.666 1.00 47.40 O
+ATOM 4869 CB ASN B 508 81.815 39.707 41.270 1.00 70.65 C
+ATOM 4870 CG ASN B 508 83.047 38.929 40.812 1.00 89.37 C
+ATOM 4871 OD1 ASN B 508 82.995 37.711 40.646 1.00 99.61 O
+ATOM 4872 ND2 ASN B 508 84.158 39.631 40.615 1.00 99.06 N
+ATOM 4873 N LEU B 509 80.100 42.660 40.570 1.00 55.71 N
+ATOM 4874 CA LEU B 509 78.883 43.448 40.792 1.00 54.87 C
+ATOM 4875 C LEU B 509 77.583 42.768 40.331 1.00 59.16 C
+ATOM 4876 O LEU B 509 77.522 42.193 39.247 1.00 52.40 O
+ATOM 4877 CB LEU B 509 79.034 44.809 40.092 1.00 59.48 C
+ATOM 4878 CG LEU B 509 79.910 45.917 40.712 1.00 68.14 C
+ATOM 4879 CD1 LEU B 509 80.983 45.336 41.618 1.00 72.38 C
+ATOM 4880 CD2 LEU B 509 80.534 46.751 39.592 1.00 72.66 C
+ATOM 4881 N GLU B 510 76.540 42.862 41.155 1.00 71.31 N
+ATOM 4882 CA GLU B 510 75.240 42.242 40.858 1.00 75.95 C
+ATOM 4883 C GLU B 510 74.146 43.177 40.339 1.00 75.52 C
+ATOM 4884 O GLU B 510 73.752 44.126 41.014 1.00 77.97 O
+ATOM 4885 CB GLU B 510 74.684 41.540 42.103 1.00 82.26 C
+ATOM 4886 CG GLU B 510 75.286 40.189 42.427 1.00 98.76 C
+ATOM 4887 CD GLU B 510 74.412 39.394 43.390 1.00106.36 C
+ATOM 4888 OE1 GLU B 510 74.139 39.896 44.502 1.00108.51 O
+ATOM 4889 OE2 GLU B 510 73.993 38.270 43.032 1.00109.66 O
+ATOM 4890 N LYS B 511 73.631 42.869 39.153 1.00 82.43 N
+ATOM 4891 CA LYS B 511 72.565 43.652 38.534 1.00 90.15 C
+ATOM 4892 C LYS B 511 71.707 42.671 37.722 1.00 95.24 C
+ATOM 4893 O LYS B 511 72.178 41.586 37.375 1.00104.88 O
+ATOM 4894 CB LYS B 511 73.174 44.723 37.624 1.00 89.47 C
+ATOM 4895 CG LYS B 511 72.188 45.741 37.086 1.00 80.69 C
+ATOM 4896 CD LYS B 511 72.816 46.578 35.974 1.00 74.66 C
+ATOM 4897 CE LYS B 511 71.763 47.407 35.260 1.00 72.51 C
+ATOM 4898 NZ LYS B 511 72.267 47.961 33.980 1.00 71.63 N
+ATOM 4899 N LYS B 512 70.460 43.033 37.419 1.00104.09 N
+ATOM 4900 CA LYS B 512 69.577 42.140 36.662 1.00107.50 C
+ATOM 4901 C LYS B 512 69.266 40.901 37.496 1.00112.77 C
+ATOM 4902 O LYS B 512 68.702 39.925 36.994 1.00109.18 O
+ATOM 4903 CB LYS B 512 70.239 41.705 35.346 1.00102.99 C
+ATOM 4904 CG LYS B 512 69.734 42.424 34.104 1.00 98.78 C
+ATOM 4905 CD LYS B 512 68.296 42.036 33.786 1.00 96.92 C
+ATOM 4906 CE LYS B 512 67.801 42.740 32.531 1.00 96.42 C
+ATOM 4907 NZ LYS B 512 66.380 42.422 32.240 1.00 96.32 N
+ATOM 4908 N HIS B 513 69.651 40.959 38.769 1.00122.75 N
+ATOM 4909 CA HIS B 513 69.449 39.873 39.726 1.00130.20 C
+ATOM 4910 C HIS B 513 70.374 38.690 39.444 1.00127.83 C
+ATOM 4911 O HIS B 513 69.954 37.532 39.502 1.00133.51 O
+ATOM 4912 CB HIS B 513 67.988 39.407 39.714 1.00141.01 C
+ATOM 4913 CG HIS B 513 67.591 38.642 40.940 1.00153.93 C
+ATOM 4914 ND1 HIS B 513 68.193 37.461 41.312 1.00158.69 N
+ATOM 4915 CD2 HIS B 513 66.663 38.907 41.893 1.00158.71 C
+ATOM 4916 CE1 HIS B 513 67.657 37.028 42.439 1.00160.58 C
+ATOM 4917 NE2 HIS B 513 66.726 37.889 42.813 1.00160.70 N
+ATOM 4918 N LEU B 514 71.635 38.994 39.147 1.00125.51 N
+ATOM 4919 CA LEU B 514 72.646 37.978 38.850 1.00123.61 C
+ATOM 4920 C LEU B 514 74.042 38.609 38.935 1.00121.42 C
+ATOM 4921 O LEU B 514 74.190 39.732 39.426 1.00129.84 O
+ATOM 4922 CB LEU B 514 72.421 37.403 37.443 1.00114.80 C
+ATOM 4923 CG LEU B 514 71.203 36.501 37.205 1.00100.99 C
+ATOM 4924 CD1 LEU B 514 70.921 36.382 35.711 1.00 92.56 C
+ATOM 4925 CD2 LEU B 514 71.449 35.132 37.837 1.00 92.50 C
+ATOM 4926 N ASN B 515 75.059 37.889 38.461 1.00114.82 N
+ATOM 4927 CA ASN B 515 76.433 38.401 38.482 1.00110.58 C
+ATOM 4928 C ASN B 515 76.914 38.879 37.112 1.00106.87 C
+ATOM 4929 O ASN B 515 77.419 38.095 36.309 1.00104.06 O
+ATOM 4930 CB ASN B 515 77.406 37.338 39.014 1.00107.23 C
+ATOM 4931 CG ASN B 515 77.504 37.334 40.536 1.00 99.67 C
+ATOM 4932 OD1 ASN B 515 76.576 36.917 41.230 1.00 95.55 O
+ATOM 4933 ND2 ASN B 515 78.633 37.807 41.058 1.00 94.60 N
+ATOM 4934 N LYS B 516 76.748 40.173 36.855 1.00 93.76 N
+ATOM 4935 CA LYS B 516 77.176 40.767 35.595 1.00 83.07 C
+ATOM 4936 C LYS B 516 78.666 41.051 35.727 1.00 80.31 C
+ATOM 4937 O LYS B 516 79.439 40.211 36.193 1.00 70.49 O
+ATOM 4938 CB LYS B 516 76.457 42.097 35.331 1.00 78.96 C
+ATOM 4939 CG LYS B 516 75.028 42.189 35.835 1.00 77.75 C
+ATOM 4940 CD LYS B 516 74.083 41.323 35.028 1.00 78.92 C
+ATOM 4941 CE LYS B 516 74.003 41.774 33.581 1.00 78.76 C
+ATOM 4942 NZ LYS B 516 72.988 40.972 32.845 1.00 79.11 N
+ATOM 4943 N ARG B 517 79.038 42.267 35.346 1.00 73.19 N
+ATOM 4944 CA ARG B 517 80.412 42.741 35.375 1.00 70.93 C
+ATOM 4945 C ARG B 517 81.301 42.469 36.592 1.00 71.67 C
+ATOM 4946 O ARG B 517 80.860 42.494 37.749 1.00 64.37 O
+ATOM 4947 CB ARG B 517 80.439 44.247 35.091 1.00 75.07 C
+ATOM 4948 CG ARG B 517 80.790 44.597 33.659 1.00 85.90 C
+ATOM 4949 CD ARG B 517 81.931 45.604 33.615 1.00 91.17 C
+ATOM 4950 NE ARG B 517 82.559 45.666 32.296 1.00 93.46 N
+ATOM 4951 CZ ARG B 517 83.551 46.490 31.974 1.00 93.61 C
+ATOM 4952 NH1 ARG B 517 84.039 47.334 32.875 1.00 93.21 N
+ATOM 4953 NH2 ARG B 517 84.053 46.471 30.747 1.00 93.07 N
+ATOM 4954 N THR B 518 82.572 42.221 36.274 1.00 71.23 N
+ATOM 4955 CA THR B 518 83.656 41.975 37.222 1.00 67.21 C
+ATOM 4956 C THR B 518 84.582 43.135 36.876 1.00 64.40 C
+ATOM 4957 O THR B 518 85.112 43.184 35.771 1.00 61.53 O
+ATOM 4958 CB THR B 518 84.409 40.672 36.901 1.00 72.54 C
+ATOM 4959 OG1 THR B 518 83.475 39.602 36.714 1.00 82.37 O
+ATOM 4960 CG2 THR B 518 85.374 40.328 38.027 1.00 82.39 C
+ATOM 4961 N GLN B 519 84.778 44.071 37.795 1.00 58.29 N
+ATOM 4962 CA GLN B 519 85.613 45.232 37.489 1.00 54.00 C
+ATOM 4963 C GLN B 519 86.198 45.877 38.730 1.00 50.82 C
+ATOM 4964 O GLN B 519 85.890 45.495 39.856 1.00 51.13 O
+ATOM 4965 CB GLN B 519 84.766 46.296 36.777 1.00 55.88 C
+ATOM 4966 CG GLN B 519 83.695 46.895 37.706 1.00 57.00 C
+ATOM 4967 CD GLN B 519 82.912 48.040 37.089 1.00 57.44 C
+ATOM 4968 OE1 GLN B 519 82.079 47.835 36.206 1.00 56.56 O
+ATOM 4969 NE2 GLN B 519 83.179 49.259 37.558 1.00 56.62 N
+ATOM 4970 N ILE B 520 87.054 46.865 38.513 1.00 42.67 N
+ATOM 4971 CA ILE B 520 87.598 47.599 39.632 1.00 34.90 C
+ATOM 4972 C ILE B 520 86.409 48.478 40.036 1.00 33.07 C
+ATOM 4973 O ILE B 520 85.796 49.124 39.184 1.00 28.62 O
+ATOM 4974 CB ILE B 520 88.758 48.513 39.207 1.00 35.11 C
+ATOM 4975 CG1 ILE B 520 89.901 47.689 38.601 1.00 32.53 C
+ATOM 4976 CG2 ILE B 520 89.244 49.319 40.421 1.00 32.71 C
+ATOM 4977 CD1 ILE B 520 90.838 47.089 39.631 1.00 31.26 C
+ATOM 4978 N PHE B 521 86.052 48.483 41.315 1.00 27.60 N
+ATOM 4979 CA PHE B 521 84.931 49.311 41.754 1.00 26.96 C
+ATOM 4980 C PHE B 521 85.292 50.784 41.518 1.00 29.17 C
+ATOM 4981 O PHE B 521 86.440 51.187 41.698 1.00 26.49 O
+ATOM 4982 CB PHE B 521 84.641 49.077 43.231 1.00 22.67 C
+ATOM 4983 CG PHE B 521 83.277 49.505 43.637 1.00 22.37 C
+ATOM 4984 CD1 PHE B 521 82.161 48.832 43.151 1.00 22.27 C
+ATOM 4985 CD2 PHE B 521 83.096 50.573 44.512 1.00 23.26 C
+ATOM 4986 CE1 PHE B 521 80.879 49.215 43.534 1.00 22.78 C
+ATOM 4987 CE2 PHE B 521 81.811 50.970 44.905 1.00 22.74 C
+ATOM 4988 CZ PHE B 521 80.702 50.288 44.415 1.00 23.77 C
+ATOM 4989 N PRO B 522 84.312 51.608 41.118 1.00 28.76 N
+ATOM 4990 CA PRO B 522 84.634 53.021 40.876 1.00 27.89 C
+ATOM 4991 C PRO B 522 85.091 53.823 42.099 1.00 25.12 C
+ATOM 4992 O PRO B 522 84.781 53.460 43.229 1.00 23.86 O
+ATOM 4993 CB PRO B 522 83.335 53.574 40.269 1.00 31.25 C
+ATOM 4994 CG PRO B 522 82.737 52.373 39.584 1.00 31.91 C
+ATOM 4995 CD PRO B 522 82.957 51.292 40.637 1.00 30.13 C
+ATOM 4996 N PRO B 523 85.854 54.914 41.868 1.00 25.34 N
+ATOM 4997 CA PRO B 523 86.396 55.838 42.867 1.00 22.77 C
+ATOM 4998 C PRO B 523 85.244 56.787 43.190 1.00 21.78 C
+ATOM 4999 O PRO B 523 84.205 56.742 42.531 1.00 27.07 O
+ATOM 5000 CB PRO B 523 87.490 56.585 42.104 1.00 20.38 C
+ATOM 5001 CG PRO B 523 87.648 55.837 40.813 1.00 19.05 C
+ATOM 5002 CD PRO B 523 86.283 55.336 40.530 1.00 20.82 C
+ATOM 5003 N GLY B 524 85.406 57.653 44.178 1.00 21.40 N
+ATOM 5004 CA GLY B 524 84.319 58.563 44.464 1.00 22.26 C
+ATOM 5005 C GLY B 524 84.332 59.282 45.785 1.00 23.31 C
+ATOM 5006 O GLY B 524 85.385 59.516 46.372 1.00 23.22 O
+ATOM 5007 N ILE B 525 83.141 59.635 46.254 1.00 23.81 N
+ATOM 5008 CA ILE B 525 83.006 60.357 47.506 1.00 24.35 C
+ATOM 5009 C ILE B 525 82.097 59.600 48.485 1.00 24.14 C
+ATOM 5010 O ILE B 525 81.291 58.738 48.110 1.00 23.44 O
+ATOM 5011 CB ILE B 525 82.350 61.747 47.276 1.00 24.66 C
+ATOM 5012 CG1 ILE B 525 82.919 62.405 46.025 1.00 24.73 C
+ATOM 5013 CG2 ILE B 525 82.551 62.646 48.499 1.00 23.87 C
+ATOM 5014 CD1 ILE B 525 82.054 63.587 45.515 1.00 23.92 C
+ATOM 5015 N VAL B 526 82.242 59.933 49.754 1.00 24.02 N
+ATOM 5016 CA VAL B 526 81.395 59.369 50.774 1.00 25.08 C
+ATOM 5017 C VAL B 526 80.932 60.598 51.526 1.00 29.69 C
+ATOM 5018 O VAL B 526 81.744 61.326 52.097 1.00 26.11 O
+ATOM 5019 CB VAL B 526 82.156 58.422 51.718 1.00 21.33 C
+ATOM 5020 CG1 VAL B 526 81.392 58.252 53.018 1.00 17.28 C
+ATOM 5021 CG2 VAL B 526 82.305 57.069 51.068 1.00 18.53 C
+ATOM 5022 N THR B 527 79.629 60.858 51.454 1.00 35.18 N
+ATOM 5023 CA THR B 527 79.024 61.992 52.145 1.00 36.85 C
+ATOM 5024 C THR B 527 78.553 61.441 53.496 1.00 34.89 C
+ATOM 5025 O THR B 527 77.903 60.402 53.563 1.00 32.03 O
+ATOM 5026 CB THR B 527 77.854 62.557 51.330 1.00 44.77 C
+ATOM 5027 OG1 THR B 527 77.167 63.551 52.094 1.00 58.56 O
+ATOM 5028 CG2 THR B 527 76.921 61.478 50.967 1.00 57.44 C
+ATOM 5029 N MET B 528 78.886 62.133 54.573 1.00 32.94 N
+ATOM 5030 CA MET B 528 78.547 61.633 55.891 1.00 31.02 C
+ATOM 5031 C MET B 528 78.064 62.736 56.801 1.00 33.51 C
+ATOM 5032 O MET B 528 78.397 63.903 56.595 1.00 34.33 O
+ATOM 5033 CB MET B 528 79.791 60.970 56.465 1.00 27.78 C
+ATOM 5034 CG MET B 528 79.594 60.172 57.717 1.00 24.05 C
+ATOM 5035 SD MET B 528 81.178 59.620 58.243 1.00 15.70 S
+ATOM 5036 CE MET B 528 81.403 58.327 57.168 1.00 19.12 C
+ATOM 5037 N ASN B 529 77.318 62.361 57.837 1.00 40.76 N
+ATOM 5038 CA ASN B 529 76.739 63.342 58.750 1.00 46.59 C
+ATOM 5039 C ASN B 529 77.375 63.607 60.117 1.00 49.12 C
+ATOM 5040 O ASN B 529 76.793 64.331 60.922 1.00 50.16 O
+ATOM 5041 CB ASN B 529 75.260 63.020 58.955 1.00 50.36 C
+ATOM 5042 CG ASN B 529 74.403 64.264 59.027 1.00 54.97 C
+ATOM 5043 OD1 ASN B 529 74.661 65.166 59.831 1.00 56.38 O
+ATOM 5044 ND2 ASN B 529 73.373 64.324 58.182 1.00 56.71 N
+ATOM 5045 N GLU B 530 78.549 63.043 60.379 1.00 55.63 N
+ATOM 5046 CA GLU B 530 79.264 63.246 61.649 1.00 59.39 C
+ATOM 5047 C GLU B 530 79.108 62.165 62.703 1.00 60.38 C
+ATOM 5048 O GLU B 530 78.735 62.443 63.845 1.00 64.07 O
+ATOM 5049 CB GLU B 530 78.915 64.590 62.300 1.00 58.24 C
+ATOM 5050 CG GLU B 530 79.654 65.769 61.724 1.00 58.91 C
+ATOM 5051 CD GLU B 530 79.680 66.941 62.680 1.00 59.79 C
+ATOM 5052 OE1 GLU B 530 78.590 67.454 63.018 1.00 59.81 O
+ATOM 5053 OE2 GLU B 530 80.790 67.345 63.098 1.00 60.50 O
+ATOM 5054 N TYR B 531 79.414 60.933 62.314 1.00 64.49 N
+ATOM 5055 CA TYR B 531 79.349 59.796 63.218 1.00 67.51 C
+ATOM 5056 C TYR B 531 80.783 59.475 63.625 1.00 68.81 C
+ATOM 5057 O TYR B 531 81.684 60.298 63.456 1.00 72.21 O
+ATOM 5058 CB TYR B 531 78.740 58.589 62.505 1.00 67.47 C
+ATOM 5059 CG TYR B 531 77.312 58.783 62.053 1.00 63.74 C
+ATOM 5060 CD1 TYR B 531 76.998 59.676 61.039 1.00 61.45 C
+ATOM 5061 CD2 TYR B 531 76.277 58.056 62.634 1.00 62.54 C
+ATOM 5062 CE1 TYR B 531 75.682 59.839 60.609 1.00 61.78 C
+ATOM 5063 CE2 TYR B 531 74.961 58.212 62.216 1.00 61.73 C
+ATOM 5064 CZ TYR B 531 74.665 59.103 61.202 1.00 61.32 C
+ATOM 5065 OH TYR B 531 73.357 59.248 60.779 1.00 61.16 O
+ATOM 5066 N SER B 532 80.988 58.285 64.176 1.00 68.73 N
+ATOM 5067 CA SER B 532 82.323 57.848 64.562 1.00 65.58 C
+ATOM 5068 C SER B 532 82.750 56.908 63.457 1.00 61.68 C
+ATOM 5069 O SER B 532 82.059 55.929 63.163 1.00 61.98 O
+ATOM 5070 CB SER B 532 82.299 57.100 65.897 1.00 64.61 C
+ATOM 5071 OG SER B 532 82.015 57.983 66.969 1.00 65.04 O
+ATOM 5072 N VAL B 533 83.877 57.210 62.829 1.00 54.21 N
+ATOM 5073 CA VAL B 533 84.351 56.375 61.744 1.00 52.41 C
+ATOM 5074 C VAL B 533 85.524 55.492 62.165 1.00 50.55 C
+ATOM 5075 O VAL B 533 86.591 55.985 62.537 1.00 52.89 O
+ATOM 5076 CB VAL B 533 84.747 57.242 60.525 1.00 50.60 C
+ATOM 5077 CG1 VAL B 533 85.333 56.359 59.421 1.00 45.37 C
+ATOM 5078 CG2 VAL B 533 83.527 57.990 60.009 1.00 44.45 C
+ATOM 5079 N PRO B 534 85.330 54.165 62.119 1.00 41.78 N
+ATOM 5080 CA PRO B 534 86.344 53.172 62.483 1.00 43.63 C
+ATOM 5081 C PRO B 534 87.662 53.473 61.780 1.00 44.32 C
+ATOM 5082 O PRO B 534 87.671 53.833 60.602 1.00 40.60 O
+ATOM 5083 CB PRO B 534 85.728 51.861 62.005 1.00 41.09 C
+ATOM 5084 CG PRO B 534 84.286 52.087 62.193 1.00 40.63 C
+ATOM 5085 CD PRO B 534 84.086 53.505 61.688 1.00 45.14 C
+ATOM 5086 N LYS B 535 88.768 53.326 62.504 1.00 43.32 N
+ATOM 5087 CA LYS B 535 90.084 53.592 61.937 1.00 42.84 C
+ATOM 5088 C LYS B 535 90.273 52.797 60.640 1.00 41.84 C
+ATOM 5089 O LYS B 535 90.882 53.277 59.675 1.00 38.25 O
+ATOM 5090 CB LYS B 535 91.193 53.211 62.921 1.00 46.54 C
+ATOM 5091 CG LYS B 535 92.521 53.824 62.528 1.00 55.47 C
+ATOM 5092 CD LYS B 535 93.714 53.109 63.118 1.00 59.84 C
+ATOM 5093 CE LYS B 535 94.986 53.672 62.494 1.00 61.40 C
+ATOM 5094 NZ LYS B 535 96.181 52.840 62.777 1.00 63.11 N
+ATOM 5095 N THR B 536 89.741 51.582 60.618 1.00 39.34 N
+ATOM 5096 CA THR B 536 89.861 50.753 59.437 1.00 38.15 C
+ATOM 5097 C THR B 536 89.117 51.391 58.255 1.00 37.18 C
+ATOM 5098 O THR B 536 89.494 51.205 57.096 1.00 37.79 O
+ATOM 5099 CB THR B 536 89.324 49.328 59.715 1.00 40.52 C
+ATOM 5100 OG1 THR B 536 88.099 49.409 60.456 1.00 45.16 O
+ATOM 5101 CG2 THR B 536 90.334 48.527 60.515 1.00 42.30 C
+ATOM 5102 N LEU B 537 88.071 52.155 58.546 1.00 35.98 N
+ATOM 5103 CA LEU B 537 87.314 52.810 57.485 1.00 34.50 C
+ATOM 5104 C LEU B 537 87.987 54.128 57.115 1.00 33.99 C
+ATOM 5105 O LEU B 537 88.121 54.472 55.939 1.00 34.34 O
+ATOM 5106 CB LEU B 537 85.881 53.084 57.948 1.00 33.87 C
+ATOM 5107 CG LEU B 537 84.917 53.635 56.898 1.00 32.31 C
+ATOM 5108 CD1 LEU B 537 84.872 52.691 55.695 1.00 31.47 C
+ATOM 5109 CD2 LEU B 537 83.529 53.793 57.511 1.00 31.93 C
+ATOM 5110 N GLN B 538 88.418 54.858 58.136 1.00 32.26 N
+ATOM 5111 CA GLN B 538 89.069 56.144 57.945 1.00 32.32 C
+ATOM 5112 C GLN B 538 90.267 56.028 57.020 1.00 32.28 C
+ATOM 5113 O GLN B 538 90.510 56.903 56.192 1.00 33.63 O
+ATOM 5114 CB GLN B 538 89.530 56.692 59.290 1.00 33.05 C
+ATOM 5115 CG GLN B 538 90.060 58.104 59.233 1.00 30.86 C
+ATOM 5116 CD GLN B 538 88.969 59.117 58.995 1.00 31.61 C
+ATOM 5117 OE1 GLN B 538 87.961 59.127 59.700 1.00 31.47 O
+ATOM 5118 NE2 GLN B 538 89.164 59.986 58.006 1.00 30.90 N
+ATOM 5119 N ALA B 539 91.013 54.937 57.174 1.00 31.18 N
+ATOM 5120 CA ALA B 539 92.210 54.667 56.374 1.00 29.27 C
+ATOM 5121 C ALA B 539 91.867 54.468 54.905 1.00 30.15 C
+ATOM 5122 O ALA B 539 92.739 54.399 54.044 1.00 28.56 O
+ATOM 5123 CB ALA B 539 92.918 53.425 56.918 1.00 25.48 C
+ATOM 5124 N ARG B 540 90.577 54.379 54.632 1.00 33.32 N
+ATOM 5125 CA ARG B 540 90.106 54.179 53.283 1.00 36.18 C
+ATOM 5126 C ARG B 540 90.018 55.472 52.486 1.00 36.77 C
+ATOM 5127 O ARG B 540 89.957 55.435 51.258 1.00 37.56 O
+ATOM 5128 CB ARG B 540 88.749 53.488 53.329 1.00 38.71 C
+ATOM 5129 CG ARG B 540 88.849 52.085 53.885 1.00 44.47 C
+ATOM 5130 CD ARG B 540 89.539 51.167 52.888 1.00 47.50 C
+ATOM 5131 NE ARG B 540 90.207 50.030 53.518 1.00 49.43 N
+ATOM 5132 CZ ARG B 540 91.434 50.062 54.032 1.00 48.57 C
+ATOM 5133 NH1 ARG B 540 92.150 51.177 53.996 1.00 46.65 N
+ATOM 5134 NH2 ARG B 540 91.945 48.970 54.582 1.00 48.87 N
+ATOM 5135 N PHE B 541 90.039 56.613 53.168 1.00 35.50 N
+ATOM 5136 CA PHE B 541 89.924 57.891 52.470 1.00 35.11 C
+ATOM 5137 C PHE B 541 91.221 58.665 52.398 1.00 34.09 C
+ATOM 5138 O PHE B 541 91.826 58.958 53.422 1.00 34.77 O
+ATOM 5139 CB PHE B 541 88.864 58.761 53.140 1.00 35.63 C
+ATOM 5140 CG PHE B 541 87.568 58.040 53.391 1.00 36.31 C
+ATOM 5141 CD1 PHE B 541 87.249 57.588 54.664 1.00 34.86 C
+ATOM 5142 CD2 PHE B 541 86.701 57.761 52.340 1.00 35.27 C
+ATOM 5143 CE1 PHE B 541 86.091 56.868 54.885 1.00 34.78 C
+ATOM 5144 CE2 PHE B 541 85.546 57.043 52.546 1.00 34.36 C
+ATOM 5145 CZ PHE B 541 85.237 56.592 53.822 1.00 36.27 C
+ATOM 5146 N VAL B 542 91.628 59.013 51.181 1.00 30.39 N
+ATOM 5147 CA VAL B 542 92.854 59.754 50.960 1.00 28.60 C
+ATOM 5148 C VAL B 542 92.746 61.241 51.318 1.00 29.50 C
+ATOM 5149 O VAL B 542 93.755 61.923 51.515 1.00 27.64 O
+ATOM 5150 CB VAL B 542 93.281 59.649 49.510 1.00 27.70 C
+ATOM 5151 CG1 VAL B 542 92.278 60.399 48.635 1.00 27.33 C
+ATOM 5152 CG2 VAL B 542 94.708 60.192 49.351 1.00 26.49 C
+ATOM 5153 N LYS B 543 91.521 61.744 51.384 1.00 27.31 N
+ATOM 5154 CA LYS B 543 91.286 63.139 51.730 1.00 25.57 C
+ATOM 5155 C LYS B 543 89.950 63.245 52.464 1.00 25.33 C
+ATOM 5156 O LYS B 543 89.035 62.471 52.200 1.00 22.37 O
+ATOM 5157 CB LYS B 543 91.259 64.002 50.464 1.00 27.69 C
+ATOM 5158 CG LYS B 543 91.029 65.476 50.733 1.00 34.80 C
+ATOM 5159 CD LYS B 543 90.902 66.279 49.441 1.00 38.58 C
+ATOM 5160 CE LYS B 543 90.855 67.790 49.709 1.00 40.40 C
+ATOM 5161 NZ LYS B 543 92.128 68.308 50.301 1.00 41.48 N
+ATOM 5162 N GLN B 544 89.850 64.179 53.403 1.00 25.10 N
+ATOM 5163 CA GLN B 544 88.606 64.380 54.140 1.00 23.94 C
+ATOM 5164 C GLN B 544 88.330 65.867 54.257 1.00 25.40 C
+ATOM 5165 O GLN B 544 89.189 66.631 54.694 1.00 22.78 O
+ATOM 5166 CB GLN B 544 88.673 63.772 55.542 1.00 25.63 C
+ATOM 5167 CG GLN B 544 87.452 64.118 56.391 1.00 29.62 C
+ATOM 5168 CD GLN B 544 87.459 63.466 57.771 1.00 31.02 C
+ATOM 5169 OE1 GLN B 544 86.727 63.893 58.672 1.00 30.20 O
+ATOM 5170 NE2 GLN B 544 88.278 62.426 57.940 1.00 31.34 N
+ATOM 5171 N ILE B 545 87.124 66.270 53.862 1.00 29.80 N
+ATOM 5172 CA ILE B 545 86.715 67.674 53.906 1.00 29.89 C
+ATOM 5173 C ILE B 545 85.609 67.856 54.940 1.00 32.00 C
+ATOM 5174 O ILE B 545 84.626 67.122 54.924 1.00 29.60 O
+ATOM 5175 CB ILE B 545 86.172 68.149 52.528 1.00 31.30 C
+ATOM 5176 CG1 ILE B 545 87.212 67.884 51.438 1.00 32.75 C
+ATOM 5177 CG2 ILE B 545 85.807 69.627 52.590 1.00 32.59 C
+ATOM 5178 CD1 ILE B 545 86.769 68.287 50.056 1.00 34.28 C
+ATOM 5179 N ASP B 546 85.786 68.822 55.840 1.00 39.18 N
+ATOM 5180 CA ASP B 546 84.789 69.108 56.859 1.00 42.46 C
+ATOM 5181 C ASP B 546 84.006 70.321 56.422 1.00 42.27 C
+ATOM 5182 O ASP B 546 84.588 71.366 56.131 1.00 47.75 O
+ATOM 5183 CB ASP B 546 85.435 69.407 58.207 1.00 43.52 C
+ATOM 5184 CG ASP B 546 86.190 68.229 58.758 1.00 46.19 C
+ATOM 5185 OD1 ASP B 546 85.612 67.124 58.839 1.00 44.39 O
+ATOM 5186 OD2 ASP B 546 87.370 68.415 59.117 1.00 49.16 O
+ATOM 5187 N PHE B 547 82.690 70.174 56.348 1.00 43.59 N
+ATOM 5188 CA PHE B 547 81.841 71.290 55.970 1.00 46.11 C
+ATOM 5189 C PHE B 547 81.136 71.751 57.234 1.00 49.70 C
+ATOM 5190 O PHE B 547 80.546 70.935 57.946 1.00 50.27 O
+ATOM 5191 CB PHE B 547 80.793 70.874 54.933 1.00 40.95 C
+ATOM 5192 CG PHE B 547 81.365 70.506 53.597 1.00 33.68 C
+ATOM 5193 CD1 PHE B 547 82.060 69.320 53.432 1.00 30.47 C
+ATOM 5194 CD2 PHE B 547 81.221 71.357 52.506 1.00 30.85 C
+ATOM 5195 CE1 PHE B 547 82.608 68.986 52.196 1.00 30.66 C
+ATOM 5196 CE2 PHE B 547 81.760 71.036 51.274 1.00 29.43 C
+ATOM 5197 CZ PHE B 547 82.457 69.849 51.114 1.00 29.76 C
+ATOM 5198 N ARG B 548 81.226 73.048 57.524 1.00 52.34 N
+ATOM 5199 CA ARG B 548 80.577 73.634 58.696 1.00 52.60 C
+ATOM 5200 C ARG B 548 79.680 74.748 58.177 1.00 51.10 C
+ATOM 5201 O ARG B 548 80.120 75.578 57.387 1.00 47.22 O
+ATOM 5202 CB ARG B 548 81.625 74.173 59.676 1.00 55.79 C
+ATOM 5203 CG ARG B 548 82.181 73.106 60.618 1.00 65.04 C
+ATOM 5204 CD ARG B 548 83.385 73.596 61.394 1.00 70.23 C
+ATOM 5205 NE ARG B 548 84.646 73.309 60.709 1.00 72.67 N
+ATOM 5206 CZ ARG B 548 85.807 73.898 60.997 1.00 73.68 C
+ATOM 5207 NH1 ARG B 548 85.871 74.817 61.957 1.00 74.03 N
+ATOM 5208 NH2 ARG B 548 86.910 73.568 60.335 1.00 73.16 N
+ATOM 5209 N PRO B 549 78.401 74.765 58.596 1.00 50.55 N
+ATOM 5210 CA PRO B 549 77.461 75.795 58.141 1.00 49.15 C
+ATOM 5211 C PRO B 549 78.010 77.201 58.322 1.00 51.07 C
+ATOM 5212 O PRO B 549 78.617 77.523 59.348 1.00 49.36 O
+ATOM 5213 CB PRO B 549 76.222 75.540 59.001 1.00 47.80 C
+ATOM 5214 CG PRO B 549 76.280 74.091 59.280 1.00 47.86 C
+ATOM 5215 CD PRO B 549 77.756 73.895 59.595 1.00 49.19 C
+ATOM 5216 N LYS B 550 77.801 78.038 57.316 1.00 53.39 N
+ATOM 5217 CA LYS B 550 78.277 79.411 57.383 1.00 55.81 C
+ATOM 5218 C LYS B 550 77.091 80.351 57.190 1.00 56.51 C
+ATOM 5219 O LYS B 550 76.328 80.222 56.230 1.00 49.91 O
+ATOM 5220 CB LYS B 550 79.346 79.656 56.311 1.00 62.73 C
+ATOM 5221 CG LYS B 550 80.576 78.748 56.414 1.00 76.31 C
+ATOM 5222 CD LYS B 550 81.472 78.955 55.204 1.00 83.34 C
+ATOM 5223 CE LYS B 550 82.633 77.982 55.150 1.00 84.36 C
+ATOM 5224 NZ LYS B 550 83.429 78.213 53.906 1.00 84.47 N
+ATOM 5225 N ASP B 551 76.946 81.294 58.114 1.00 54.75 N
+ATOM 5226 CA ASP B 551 75.852 82.248 58.086 1.00 51.19 C
+ATOM 5227 C ASP B 551 75.741 83.088 56.819 1.00 47.04 C
+ATOM 5228 O ASP B 551 74.661 83.185 56.224 1.00 40.45 O
+ATOM 5229 CB ASP B 551 75.943 83.151 59.311 1.00 62.13 C
+ATOM 5230 CG ASP B 551 75.846 82.370 60.597 1.00 78.14 C
+ATOM 5231 OD1 ASP B 551 74.795 81.735 60.823 1.00 86.26 O
+ATOM 5232 OD2 ASP B 551 76.825 82.380 61.372 1.00 87.51 O
+ATOM 5233 N TYR B 552 76.842 83.697 56.399 1.00 41.33 N
+ATOM 5234 CA TYR B 552 76.788 84.515 55.200 1.00 35.84 C
+ATOM 5235 C TYR B 552 76.318 83.699 54.005 1.00 32.55 C
+ATOM 5236 O TYR B 552 75.519 84.177 53.207 1.00 33.74 O
+ATOM 5237 CB TYR B 552 78.151 85.177 54.928 1.00 35.09 C
+ATOM 5238 CG TYR B 552 79.346 84.242 54.947 1.00 37.73 C
+ATOM 5239 CD1 TYR B 552 79.933 83.793 53.757 1.00 36.64 C
+ATOM 5240 CD2 TYR B 552 79.924 83.842 56.158 1.00 37.97 C
+ATOM 5241 CE1 TYR B 552 81.066 82.983 53.779 1.00 36.21 C
+ATOM 5242 CE2 TYR B 552 81.058 83.032 56.186 1.00 35.26 C
+ATOM 5243 CZ TYR B 552 81.624 82.612 54.998 1.00 35.39 C
+ATOM 5244 OH TYR B 552 82.768 81.853 55.034 1.00 35.21 O
+ATOM 5245 N LEU B 553 76.787 82.462 53.892 1.00 29.99 N
+ATOM 5246 CA LEU B 553 76.378 81.619 52.777 1.00 30.34 C
+ATOM 5247 C LEU B 553 74.876 81.367 52.821 1.00 32.24 C
+ATOM 5248 O LEU B 553 74.211 81.329 51.787 1.00 32.95 O
+ATOM 5249 CB LEU B 553 77.125 80.283 52.806 1.00 26.05 C
+ATOM 5250 CG LEU B 553 78.627 80.302 52.514 1.00 21.61 C
+ATOM 5251 CD1 LEU B 553 79.167 78.866 52.451 1.00 18.01 C
+ATOM 5252 CD2 LEU B 553 78.872 81.016 51.207 1.00 19.21 C
+ATOM 5253 N LYS B 554 74.350 81.187 54.024 1.00 32.80 N
+ATOM 5254 CA LYS B 554 72.933 80.937 54.202 1.00 34.14 C
+ATOM 5255 C LYS B 554 72.129 82.202 53.865 1.00 35.04 C
+ATOM 5256 O LYS B 554 71.263 82.188 52.971 1.00 30.04 O
+ATOM 5257 CB LYS B 554 72.679 80.521 55.645 1.00 38.40 C
+ATOM 5258 CG LYS B 554 71.237 80.266 55.992 1.00 46.99 C
+ATOM 5259 CD LYS B 554 71.100 80.174 57.493 1.00 51.44 C
+ATOM 5260 CE LYS B 554 69.655 80.017 57.902 1.00 54.33 C
+ATOM 5261 NZ LYS B 554 69.509 80.097 59.384 1.00 55.41 N
+ATOM 5262 N HIS B 555 72.410 83.299 54.565 1.00 35.90 N
+ATOM 5263 CA HIS B 555 71.687 84.542 54.299 1.00 36.37 C
+ATOM 5264 C HIS B 555 71.730 84.828 52.811 1.00 35.55 C
+ATOM 5265 O HIS B 555 70.704 85.085 52.181 1.00 34.65 O
+ATOM 5266 CB HIS B 555 72.317 85.721 55.036 1.00 41.13 C
+ATOM 5267 CG HIS B 555 72.494 85.495 56.505 1.00 48.83 C
+ATOM 5268 ND1 HIS B 555 71.498 84.969 57.301 1.00 50.74 N
+ATOM 5269 CD2 HIS B 555 73.547 85.730 57.321 1.00 51.91 C
+ATOM 5270 CE1 HIS B 555 71.935 84.889 58.545 1.00 53.22 C
+ATOM 5271 NE2 HIS B 555 73.174 85.344 58.586 1.00 52.57 N
+ATOM 5272 N CYS B 556 72.939 84.770 52.264 1.00 35.92 N
+ATOM 5273 CA CYS B 556 73.174 85.012 50.849 1.00 34.28 C
+ATOM 5274 C CYS B 556 72.158 84.310 49.957 1.00 33.23 C
+ATOM 5275 O CYS B 556 71.621 84.909 49.028 1.00 33.41 O
+ATOM 5276 CB CYS B 556 74.580 84.559 50.472 1.00 32.10 C
+ATOM 5277 SG CYS B 556 74.988 85.019 48.804 1.00 33.74 S
+ATOM 5278 N LEU B 557 71.898 83.037 50.235 1.00 34.45 N
+ATOM 5279 CA LEU B 557 70.937 82.287 49.438 1.00 35.25 C
+ATOM 5280 C LEU B 557 69.559 82.894 49.655 1.00 36.39 C
+ATOM 5281 O LEU B 557 68.800 83.091 48.701 1.00 35.72 O
+ATOM 5282 CB LEU B 557 70.925 80.796 49.829 1.00 33.45 C
+ATOM 5283 CG LEU B 557 72.191 79.964 49.599 1.00 30.17 C
+ATOM 5284 CD1 LEU B 557 71.996 78.548 50.100 1.00 27.41 C
+ATOM 5285 CD2 LEU B 557 72.517 79.950 48.118 1.00 28.79 C
+ATOM 5286 N GLU B 558 69.246 83.204 50.913 1.00 38.89 N
+ATOM 5287 CA GLU B 558 67.947 83.795 51.241 1.00 40.45 C
+ATOM 5288 C GLU B 558 67.691 84.977 50.308 1.00 40.75 C
+ATOM 5289 O GLU B 558 66.576 85.173 49.817 1.00 38.31 O
+ATOM 5290 CB GLU B 558 67.919 84.259 52.703 1.00 40.89 C
+ATOM 5291 CG GLU B 558 68.288 83.149 53.691 1.00 45.66 C
+ATOM 5292 CD GLU B 558 68.167 83.552 55.167 1.00 46.54 C
+ATOM 5293 OE1 GLU B 558 68.550 84.695 55.511 1.00 47.65 O
+ATOM 5294 OE2 GLU B 558 67.705 82.712 55.983 1.00 44.57 O
+ATOM 5295 N ARG B 559 68.748 85.740 50.048 1.00 42.94 N
+ATOM 5296 CA ARG B 559 68.665 86.906 49.181 1.00 43.00 C
+ATOM 5297 C ARG B 559 69.026 86.607 47.722 1.00 41.72 C
+ATOM 5298 O ARG B 559 68.899 87.475 46.856 1.00 43.36 O
+ATOM 5299 CB ARG B 559 69.558 88.013 49.741 1.00 43.49 C
+ATOM 5300 CG ARG B 559 69.150 88.474 51.125 1.00 44.54 C
+ATOM 5301 CD ARG B 559 70.102 89.539 51.632 1.00 47.06 C
+ATOM 5302 NE ARG B 559 69.674 90.139 52.896 1.00 48.94 N
+ATOM 5303 CZ ARG B 559 69.542 89.481 54.047 1.00 48.42 C
+ATOM 5304 NH1 ARG B 559 69.806 88.182 54.110 1.00 48.01 N
+ATOM 5305 NH2 ARG B 559 69.141 90.127 55.138 1.00 46.78 N
+ATOM 5306 N SER B 560 69.457 85.376 47.453 1.00 40.36 N
+ATOM 5307 CA SER B 560 69.817 84.971 46.096 1.00 41.52 C
+ATOM 5308 C SER B 560 69.064 83.702 45.691 1.00 46.91 C
+ATOM 5309 O SER B 560 69.626 82.768 45.101 1.00 42.40 O
+ATOM 5310 CB SER B 560 71.324 84.738 45.994 1.00 39.41 C
+ATOM 5311 OG SER B 560 72.033 85.836 46.536 1.00 34.84 O
+ATOM 5312 N GLU B 561 67.780 83.692 46.021 1.00 50.89 N
+ATOM 5313 CA GLU B 561 66.883 82.588 45.718 1.00 50.98 C
+ATOM 5314 C GLU B 561 67.168 81.901 44.384 1.00 46.02 C
+ATOM 5315 O GLU B 561 67.228 80.673 44.317 1.00 40.13 O
+ATOM 5316 CB GLU B 561 65.430 83.082 45.719 1.00 62.52 C
+ATOM 5317 CG GLU B 561 65.242 84.569 46.067 1.00 87.76 C
+ATOM 5318 CD GLU B 561 65.939 85.530 45.094 1.00 98.33 C
+ATOM 5319 OE1 GLU B 561 65.742 85.401 43.866 1.00102.12 O
+ATOM 5320 OE2 GLU B 561 66.678 86.426 45.560 1.00101.30 O
+ATOM 5321 N PHE B 562 67.354 82.686 43.325 1.00 39.42 N
+ATOM 5322 CA PHE B 562 67.586 82.112 41.998 1.00 34.47 C
+ATOM 5323 C PHE B 562 68.663 81.035 41.963 1.00 32.75 C
+ATOM 5324 O PHE B 562 68.687 80.209 41.047 1.00 33.76 O
+ATOM 5325 CB PHE B 562 67.902 83.213 40.967 1.00 32.25 C
+ATOM 5326 CG PHE B 562 69.270 83.835 41.115 1.00 31.72 C
+ATOM 5327 CD1 PHE B 562 70.405 83.199 40.604 1.00 30.49 C
+ATOM 5328 CD2 PHE B 562 69.426 85.062 41.764 1.00 31.44 C
+ATOM 5329 CE1 PHE B 562 71.665 83.770 40.735 1.00 30.13 C
+ATOM 5330 CE2 PHE B 562 70.687 85.638 41.900 1.00 31.42 C
+ATOM 5331 CZ PHE B 562 71.807 84.988 41.382 1.00 30.92 C
+ATOM 5332 N LEU B 563 69.543 81.030 42.959 1.00 31.64 N
+ATOM 5333 CA LEU B 563 70.592 80.037 42.987 1.00 31.20 C
+ATOM 5334 C LEU B 563 70.047 78.649 43.303 1.00 31.79 C
+ATOM 5335 O LEU B 563 70.505 77.648 42.743 1.00 31.86 O
+ATOM 5336 CB LEU B 563 71.652 80.425 44.008 1.00 28.93 C
+ATOM 5337 CG LEU B 563 72.595 81.533 43.568 1.00 26.46 C
+ATOM 5338 CD1 LEU B 563 73.719 81.651 44.603 1.00 22.95 C
+ATOM 5339 CD2 LEU B 563 73.158 81.210 42.177 1.00 24.98 C
+ATOM 5340 N LEU B 564 69.075 78.590 44.209 1.00 33.29 N
+ATOM 5341 CA LEU B 564 68.467 77.320 44.596 1.00 34.99 C
+ATOM 5342 C LEU B 564 67.283 76.989 43.696 1.00 38.54 C
+ATOM 5343 O LEU B 564 67.078 75.835 43.316 1.00 33.31 O
+ATOM 5344 CB LEU B 564 68.013 77.377 46.062 1.00 35.22 C
+ATOM 5345 CG LEU B 564 69.131 77.585 47.092 1.00 37.51 C
+ATOM 5346 CD1 LEU B 564 68.580 77.476 48.491 1.00 37.23 C
+ATOM 5347 CD2 LEU B 564 70.217 76.540 46.882 1.00 38.77 C
+ATOM 5348 N GLU B 565 66.529 78.020 43.335 1.00 41.18 N
+ATOM 5349 CA GLU B 565 65.355 77.858 42.497 1.00 41.24 C
+ATOM 5350 C GLU B 565 65.656 77.362 41.087 1.00 38.17 C
+ATOM 5351 O GLU B 565 64.828 76.702 40.462 1.00 32.32 O
+ATOM 5352 CB GLU B 565 64.564 79.171 42.474 1.00 51.88 C
+ATOM 5353 CG GLU B 565 64.073 79.567 43.869 1.00 74.96 C
+ATOM 5354 CD GLU B 565 63.045 80.687 43.864 1.00 85.67 C
+ATOM 5355 OE1 GLU B 565 63.383 81.811 43.435 1.00 89.25 O
+ATOM 5356 OE2 GLU B 565 61.894 80.443 44.298 1.00 89.23 O
+ATOM 5357 N LYS B 566 66.837 77.659 40.571 1.00 32.85 N
+ATOM 5358 CA LYS B 566 67.155 77.180 39.236 1.00 27.92 C
+ATOM 5359 C LYS B 566 68.180 76.057 39.312 1.00 26.60 C
+ATOM 5360 O LYS B 566 68.826 75.728 38.319 1.00 23.45 O
+ATOM 5361 CB LYS B 566 67.661 78.319 38.354 1.00 29.50 C
+ATOM 5362 CG LYS B 566 66.592 79.341 38.044 1.00 33.82 C
+ATOM 5363 CD LYS B 566 67.145 80.458 37.197 1.00 38.26 C
+ATOM 5364 CE LYS B 566 66.333 81.740 37.386 1.00 40.14 C
+ATOM 5365 NZ LYS B 566 66.894 82.892 36.605 1.00 40.42 N
+ATOM 5366 N ARG B 567 68.317 75.477 40.502 1.00 26.25 N
+ATOM 5367 CA ARG B 567 69.228 74.361 40.720 1.00 26.90 C
+ATOM 5368 C ARG B 567 70.610 74.616 40.132 1.00 27.23 C
+ATOM 5369 O ARG B 567 71.184 73.742 39.477 1.00 27.17 O
+ATOM 5370 CB ARG B 567 68.630 73.092 40.099 1.00 28.45 C
+ATOM 5371 CG ARG B 567 67.252 72.734 40.641 1.00 30.55 C
+ATOM 5372 CD ARG B 567 66.667 71.510 39.957 1.00 32.66 C
+ATOM 5373 NE ARG B 567 65.473 70.977 40.634 1.00 33.99 N
+ATOM 5374 CZ ARG B 567 64.270 71.556 40.639 1.00 33.17 C
+ATOM 5375 NH1 ARG B 567 64.067 72.703 40.005 1.00 32.79 N
+ATOM 5376 NH2 ARG B 567 63.261 70.983 41.278 1.00 33.35 N
+ATOM 5377 N ILE B 568 71.144 75.806 40.391 1.00 28.39 N
+ATOM 5378 CA ILE B 568 72.446 76.213 39.872 1.00 29.40 C
+ATOM 5379 C ILE B 568 73.681 75.784 40.680 1.00 28.96 C
+ATOM 5380 O ILE B 568 74.673 75.327 40.105 1.00 30.88 O
+ATOM 5381 CB ILE B 568 72.502 77.742 39.701 1.00 29.39 C
+ATOM 5382 CG1 ILE B 568 71.299 78.220 38.890 1.00 28.01 C
+ATOM 5383 CG2 ILE B 568 73.797 78.142 38.984 1.00 28.68 C
+ATOM 5384 CD1 ILE B 568 71.215 79.723 38.806 1.00 26.78 C
+ATOM 5385 N ILE B 569 73.634 75.927 41.999 1.00 28.37 N
+ATOM 5386 CA ILE B 569 74.787 75.562 42.799 1.00 28.27 C
+ATOM 5387 C ILE B 569 75.073 74.072 42.876 1.00 29.36 C
+ATOM 5388 O ILE B 569 76.201 73.695 43.214 1.00 29.73 O
+ATOM 5389 CB ILE B 569 74.698 76.122 44.232 1.00 27.13 C
+ATOM 5390 CG1 ILE B 569 73.429 75.648 44.920 1.00 26.59 C
+ATOM 5391 CG2 ILE B 569 74.703 77.633 44.196 1.00 27.10 C
+ATOM 5392 CD1 ILE B 569 73.352 76.081 46.370 1.00 25.04 C
+ATOM 5393 N GLN B 570 74.083 73.221 42.579 1.00 30.71 N
+ATOM 5394 CA GLN B 570 74.312 71.773 42.615 1.00 30.81 C
+ATOM 5395 C GLN B 570 74.601 71.256 41.216 1.00 30.45 C
+ATOM 5396 O GLN B 570 74.623 70.052 40.991 1.00 31.16 O
+ATOM 5397 CB GLN B 570 73.111 70.984 43.140 1.00 32.52 C
+ATOM 5398 CG GLN B 570 72.205 71.682 44.099 1.00 39.62 C
+ATOM 5399 CD GLN B 570 70.986 72.251 43.395 1.00 41.89 C
+ATOM 5400 OE1 GLN B 570 71.080 73.231 42.652 1.00 41.56 O
+ATOM 5401 NE2 GLN B 570 69.836 71.627 43.614 1.00 42.79 N
+ATOM 5402 N SER B 571 74.810 72.154 40.269 1.00 28.18 N
+ATOM 5403 CA SER B 571 75.089 71.723 38.917 1.00 26.50 C
+ATOM 5404 C SER B 571 76.561 71.549 38.627 1.00 26.14 C
+ATOM 5405 O SER B 571 77.394 72.392 38.980 1.00 24.48 O
+ATOM 5406 CB SER B 571 74.519 72.701 37.896 1.00 27.79 C
+ATOM 5407 OG SER B 571 74.958 72.344 36.594 1.00 28.15 O
+ATOM 5408 N GLY B 572 76.871 70.442 37.967 1.00 24.87 N
+ATOM 5409 CA GLY B 572 78.236 70.179 37.584 1.00 23.27 C
+ATOM 5410 C GLY B 572 78.566 71.226 36.542 1.00 23.63 C
+ATOM 5411 O GLY B 572 79.738 71.498 36.284 1.00 24.31 O
+ATOM 5412 N ILE B 573 77.536 71.817 35.935 1.00 23.38 N
+ATOM 5413 CA ILE B 573 77.760 72.851 34.928 1.00 23.54 C
+ATOM 5414 C ILE B 573 78.314 74.088 35.602 1.00 24.08 C
+ATOM 5415 O ILE B 573 79.091 74.843 35.006 1.00 25.62 O
+ATOM 5416 CB ILE B 573 76.470 73.221 34.168 1.00 25.15 C
+ATOM 5417 CG1 ILE B 573 76.270 72.234 33.015 1.00 23.27 C
+ATOM 5418 CG2 ILE B 573 76.539 74.674 33.649 1.00 23.92 C
+ATOM 5419 CD1 ILE B 573 75.128 72.571 32.118 1.00 23.54 C
+ATOM 5420 N ALA B 574 77.917 74.292 36.851 1.00 24.78 N
+ATOM 5421 CA ALA B 574 78.413 75.426 37.599 1.00 24.39 C
+ATOM 5422 C ALA B 574 79.897 75.170 37.817 1.00 24.43 C
+ATOM 5423 O ALA B 574 80.715 76.086 37.741 1.00 26.69 O
+ATOM 5424 CB ALA B 574 77.687 75.534 38.935 1.00 24.17 C
+ATOM 5425 N LEU B 575 80.244 73.912 38.075 1.00 24.36 N
+ATOM 5426 CA LEU B 575 81.635 73.548 38.313 1.00 23.92 C
+ATOM 5427 C LEU B 575 82.493 73.534 37.061 1.00 24.82 C
+ATOM 5428 O LEU B 575 83.705 73.715 37.149 1.00 27.38 O
+ATOM 5429 CB LEU B 575 81.741 72.190 39.014 1.00 20.23 C
+ATOM 5430 CG LEU B 575 81.392 72.206 40.504 1.00 13.79 C
+ATOM 5431 CD1 LEU B 575 81.688 70.840 41.117 1.00 11.67 C
+ATOM 5432 CD2 LEU B 575 82.210 73.274 41.189 1.00 10.18 C
+ATOM 5433 N LEU B 576 81.886 73.319 35.898 1.00 27.18 N
+ATOM 5434 CA LEU B 576 82.668 73.335 34.664 1.00 29.56 C
+ATOM 5435 C LEU B 576 82.973 74.789 34.318 1.00 29.77 C
+ATOM 5436 O LEU B 576 84.008 75.094 33.722 1.00 30.81 O
+ATOM 5437 CB LEU B 576 81.915 72.677 33.500 1.00 30.15 C
+ATOM 5438 CG LEU B 576 82.714 72.613 32.190 1.00 29.10 C
+ATOM 5439 CD1 LEU B 576 84.107 72.032 32.446 1.00 27.96 C
+ATOM 5440 CD2 LEU B 576 81.949 71.784 31.171 1.00 28.76 C
+ATOM 5441 N LEU B 577 82.064 75.682 34.698 1.00 29.22 N
+ATOM 5442 CA LEU B 577 82.256 77.092 34.448 1.00 28.48 C
+ATOM 5443 C LEU B 577 83.354 77.612 35.357 1.00 27.38 C
+ATOM 5444 O LEU B 577 84.090 78.522 34.972 1.00 30.99 O
+ATOM 5445 CB LEU B 577 80.970 77.872 34.713 1.00 26.43 C
+ATOM 5446 CG LEU B 577 80.093 78.201 33.503 1.00 25.60 C
+ATOM 5447 CD1 LEU B 577 78.754 78.735 33.978 1.00 24.76 C
+ATOM 5448 CD2 LEU B 577 80.806 79.225 32.614 1.00 22.63 C
+ATOM 5449 N MET B 578 83.468 77.050 36.561 1.00 25.06 N
+ATOM 5450 CA MET B 578 84.488 77.508 37.497 1.00 25.14 C
+ATOM 5451 C MET B 578 85.902 77.172 37.022 1.00 26.24 C
+ATOM 5452 O MET B 578 86.848 77.937 37.237 1.00 28.66 O
+ATOM 5453 CB MET B 578 84.258 76.892 38.872 1.00 20.36 C
+ATOM 5454 CG MET B 578 85.180 77.463 39.967 1.00 12.03 C
+ATOM 5455 SD MET B 578 85.012 76.614 41.551 1.00 4.67 S
+ATOM 5456 CE MET B 578 86.018 75.416 41.210 1.00 6.52 C
+ATOM 5457 N LEU B 579 86.042 76.020 36.381 1.00 25.53 N
+ATOM 5458 CA LEU B 579 87.334 75.577 35.879 1.00 25.16 C
+ATOM 5459 C LEU B 579 87.745 76.403 34.668 1.00 23.79 C
+ATOM 5460 O LEU B 579 88.891 76.804 34.536 1.00 23.14 O
+ATOM 5461 CB LEU B 579 87.263 74.095 35.493 1.00 27.02 C
+ATOM 5462 CG LEU B 579 86.997 73.035 36.559 1.00 26.12 C
+ATOM 5463 CD1 LEU B 579 86.828 71.682 35.888 1.00 28.03 C
+ATOM 5464 CD2 LEU B 579 88.145 72.993 37.541 1.00 27.24 C
+ATOM 5465 N ILE B 580 86.794 76.644 33.781 1.00 21.37 N
+ATOM 5466 CA ILE B 580 87.049 77.423 32.588 1.00 21.06 C
+ATOM 5467 C ILE B 580 87.415 78.855 32.977 1.00 21.89 C
+ATOM 5468 O ILE B 580 88.192 79.517 32.284 1.00 20.80 O
+ATOM 5469 CB ILE B 580 85.789 77.497 31.683 1.00 22.89 C
+ATOM 5470 CG1 ILE B 580 85.308 76.090 31.317 1.00 24.33 C
+ATOM 5471 CG2 ILE B 580 86.101 78.319 30.428 1.00 21.57 C
+ATOM 5472 CD1 ILE B 580 83.963 76.060 30.571 1.00 22.68 C
+ATOM 5473 N TRP B 581 86.846 79.324 34.085 1.00 22.42 N
+ATOM 5474 CA TRP B 581 87.074 80.684 34.556 1.00 23.19 C
+ATOM 5475 C TRP B 581 88.310 80.905 35.423 1.00 23.60 C
+ATOM 5476 O TRP B 581 88.788 82.033 35.524 1.00 24.88 O
+ATOM 5477 CB TRP B 581 85.819 81.175 35.292 1.00 24.82 C
+ATOM 5478 CG TRP B 581 85.962 82.519 35.975 1.00 29.26 C
+ATOM 5479 CD1 TRP B 581 86.281 82.744 37.292 1.00 30.84 C
+ATOM 5480 CD2 TRP B 581 85.806 83.814 35.377 1.00 29.86 C
+ATOM 5481 NE1 TRP B 581 86.332 84.098 37.546 1.00 31.52 N
+ATOM 5482 CE2 TRP B 581 86.046 84.777 36.390 1.00 31.13 C
+ATOM 5483 CE3 TRP B 581 85.485 84.255 34.089 1.00 29.33 C
+ATOM 5484 CZ2 TRP B 581 85.977 86.157 36.146 1.00 30.40 C
+ATOM 5485 CZ3 TRP B 581 85.417 85.631 33.850 1.00 29.24 C
+ATOM 5486 CH2 TRP B 581 85.661 86.561 34.876 1.00 30.05 C
+ATOM 5487 N TYR B 582 88.834 79.839 36.032 1.00 22.92 N
+ATOM 5488 CA TYR B 582 90.003 79.927 36.917 1.00 20.44 C
+ATOM 5489 C TYR B 582 91.236 79.229 36.401 1.00 21.35 C
+ATOM 5490 O TYR B 582 92.362 79.678 36.601 1.00 19.93 O
+ATOM 5491 CB TYR B 582 89.696 79.287 38.261 1.00 18.43 C
+ATOM 5492 CG TYR B 582 89.131 80.204 39.293 1.00 18.94 C
+ATOM 5493 CD1 TYR B 582 87.758 80.280 39.512 1.00 20.16 C
+ATOM 5494 CD2 TYR B 582 89.970 80.999 40.061 1.00 19.37 C
+ATOM 5495 CE1 TYR B 582 87.224 81.140 40.481 1.00 19.75 C
+ATOM 5496 CE2 TYR B 582 89.459 81.855 41.028 1.00 21.17 C
+ATOM 5497 CZ TYR B 582 88.080 81.921 41.234 1.00 20.39 C
+ATOM 5498 OH TYR B 582 87.577 82.762 42.193 1.00 21.34 O
+ATOM 5499 N ARG B 583 91.009 78.113 35.731 1.00 23.58 N
+ATOM 5500 CA ARG B 583 92.079 77.265 35.251 1.00 23.71 C
+ATOM 5501 C ARG B 583 92.697 77.542 33.883 1.00 23.19 C
+ATOM 5502 O ARG B 583 92.039 78.055 32.985 1.00 24.52 O
+ATOM 5503 CB ARG B 583 91.565 75.827 35.332 1.00 25.54 C
+ATOM 5504 CG ARG B 583 91.256 75.428 36.760 1.00 25.11 C
+ATOM 5505 CD ARG B 583 92.579 75.184 37.434 1.00 28.37 C
+ATOM 5506 NE ARG B 583 92.601 75.424 38.868 1.00 27.98 N
+ATOM 5507 CZ ARG B 583 93.646 75.123 39.634 1.00 25.73 C
+ATOM 5508 NH1 ARG B 583 94.729 74.574 39.094 1.00 21.57 N
+ATOM 5509 NH2 ARG B 583 93.609 75.371 40.935 1.00 27.15 N
+ATOM 5510 N PRO B 584 93.989 77.213 33.722 1.00 28.96 N
+ATOM 5511 CA PRO B 584 94.671 77.432 32.440 1.00 29.39 C
+ATOM 5512 C PRO B 584 94.357 76.329 31.431 1.00 29.56 C
+ATOM 5513 O PRO B 584 94.208 75.163 31.797 1.00 32.28 O
+ATOM 5514 CB PRO B 584 96.154 77.474 32.827 1.00 27.91 C
+ATOM 5515 CG PRO B 584 96.217 76.578 34.036 1.00 25.93 C
+ATOM 5516 CD PRO B 584 94.959 76.940 34.802 1.00 27.78 C
+ATOM 5517 N VAL B 585 94.258 76.716 30.164 1.00 31.08 N
+ATOM 5518 CA VAL B 585 93.967 75.800 29.073 1.00 29.30 C
+ATOM 5519 C VAL B 585 94.782 74.502 29.024 1.00 28.14 C
+ATOM 5520 O VAL B 585 94.218 73.433 28.771 1.00 28.31 O
+ATOM 5521 CB VAL B 585 94.108 76.532 27.730 1.00 28.15 C
+ATOM 5522 CG1 VAL B 585 94.282 75.549 26.601 1.00 29.76 C
+ATOM 5523 CG2 VAL B 585 92.871 77.351 27.489 1.00 29.19 C
+ATOM 5524 N ALA B 586 96.091 74.582 29.262 1.00 26.75 N
+ATOM 5525 CA ALA B 586 96.947 73.390 29.213 1.00 27.32 C
+ATOM 5526 C ALA B 586 96.569 72.335 30.228 1.00 29.91 C
+ATOM 5527 O ALA B 586 97.070 71.214 30.181 1.00 32.05 O
+ATOM 5528 CB ALA B 586 98.398 73.766 29.422 1.00 23.87 C
+ATOM 5529 N GLU B 587 95.699 72.696 31.160 1.00 33.59 N
+ATOM 5530 CA GLU B 587 95.286 71.760 32.176 1.00 35.68 C
+ATOM 5531 C GLU B 587 94.198 70.861 31.640 1.00 36.19 C
+ATOM 5532 O GLU B 587 93.933 69.819 32.218 1.00 38.86 O
+ATOM 5533 CB GLU B 587 94.788 72.511 33.400 1.00 38.20 C
+ATOM 5534 CG GLU B 587 95.550 72.195 34.666 1.00 42.29 C
+ATOM 5535 CD GLU B 587 95.101 73.054 35.820 1.00 45.86 C
+ATOM 5536 OE1 GLU B 587 93.871 73.166 36.011 1.00 46.03 O
+ATOM 5537 OE2 GLU B 587 95.969 73.608 36.534 1.00 45.93 O
+ATOM 5538 N PHE B 588 93.564 71.269 30.541 1.00 35.95 N
+ATOM 5539 CA PHE B 588 92.501 70.476 29.913 1.00 36.51 C
+ATOM 5540 C PHE B 588 93.118 69.511 28.918 1.00 37.14 C
+ATOM 5541 O PHE B 588 94.292 69.633 28.593 1.00 38.75 O
+ATOM 5542 CB PHE B 588 91.518 71.368 29.150 1.00 36.45 C
+ATOM 5543 CG PHE B 588 90.634 72.197 30.026 1.00 36.21 C
+ATOM 5544 CD1 PHE B 588 91.146 73.273 30.737 1.00 36.75 C
+ATOM 5545 CD2 PHE B 588 89.283 71.918 30.118 1.00 36.37 C
+ATOM 5546 CE1 PHE B 588 90.328 74.065 31.522 1.00 36.72 C
+ATOM 5547 CE2 PHE B 588 88.447 72.704 30.905 1.00 38.29 C
+ATOM 5548 CZ PHE B 588 88.970 73.781 31.608 1.00 37.81 C
+ATOM 5549 N ALA B 589 92.328 68.566 28.420 1.00 37.77 N
+ATOM 5550 CA ALA B 589 92.827 67.607 27.435 1.00 38.57 C
+ATOM 5551 C ALA B 589 93.009 68.335 26.105 1.00 41.86 C
+ATOM 5552 O ALA B 589 92.155 69.122 25.704 1.00 37.72 O
+ATOM 5553 CB ALA B 589 91.842 66.461 27.271 1.00 36.76 C
+ATOM 5554 N GLN B 590 94.124 68.070 25.428 1.00 46.88 N
+ATOM 5555 CA GLN B 590 94.427 68.707 24.149 1.00 50.35 C
+ATOM 5556 C GLN B 590 93.180 68.818 23.283 1.00 49.04 C
+ATOM 5557 O GLN B 590 92.843 69.881 22.761 1.00 45.62 O
+ATOM 5558 CB GLN B 590 95.500 67.897 23.409 1.00 61.26 C
+ATOM 5559 CG GLN B 590 95.890 68.423 22.029 1.00 81.11 C
+ATOM 5560 CD GLN B 590 96.529 69.793 22.084 1.00 89.81 C
+ATOM 5561 OE1 GLN B 590 97.215 70.129 23.049 1.00 92.97 O
+ATOM 5562 NE2 GLN B 590 96.322 70.588 21.038 1.00 93.00 N
+ATOM 5563 N SER B 591 92.494 67.695 23.153 1.00 45.69 N
+ATOM 5564 CA SER B 591 91.284 67.594 22.353 1.00 40.32 C
+ATOM 5565 C SER B 591 90.201 68.630 22.602 1.00 37.60 C
+ATOM 5566 O SER B 591 89.499 69.013 21.674 1.00 36.59 O
+ATOM 5567 CB SER B 591 90.668 66.202 22.534 1.00 41.32 C
+ATOM 5568 OG SER B 591 89.274 66.236 22.263 1.00 46.79 O
+ATOM 5569 N ILE B 592 90.055 69.083 23.841 1.00 35.41 N
+ATOM 5570 CA ILE B 592 88.992 70.025 24.163 1.00 33.59 C
+ATOM 5571 C ILE B 592 89.405 71.496 24.291 1.00 34.17 C
+ATOM 5572 O ILE B 592 88.600 72.393 24.058 1.00 33.80 O
+ATOM 5573 CB ILE B 592 88.292 69.577 25.458 1.00 30.85 C
+ATOM 5574 CG1 ILE B 592 86.824 69.941 25.390 1.00 30.49 C
+ATOM 5575 CG2 ILE B 592 88.913 70.248 26.671 1.00 30.28 C
+ATOM 5576 CD1 ILE B 592 86.090 69.588 26.654 1.00 31.95 C
+ATOM 5577 N GLN B 593 90.663 71.729 24.652 1.00 36.82 N
+ATOM 5578 CA GLN B 593 91.206 73.078 24.846 1.00 38.37 C
+ATOM 5579 C GLN B 593 90.673 74.152 23.909 1.00 40.75 C
+ATOM 5580 O GLN B 593 90.234 75.203 24.357 1.00 41.38 O
+ATOM 5581 CB GLN B 593 92.730 73.050 24.738 1.00 34.56 C
+ATOM 5582 CG GLN B 593 93.382 71.997 25.611 1.00 32.36 C
+ATOM 5583 CD GLN B 593 94.881 72.137 25.664 1.00 31.57 C
+ATOM 5584 OE1 GLN B 593 95.469 72.958 24.950 1.00 32.41 O
+ATOM 5585 NE2 GLN B 593 95.518 71.332 26.511 1.00 30.62 N
+ATOM 5586 N SER B 594 90.724 73.899 22.609 1.00 46.33 N
+ATOM 5587 CA SER B 594 90.251 74.884 21.646 1.00 51.04 C
+ATOM 5588 C SER B 594 88.816 75.304 21.928 1.00 50.54 C
+ATOM 5589 O SER B 594 88.433 76.441 21.663 1.00 54.54 O
+ATOM 5590 CB SER B 594 90.364 74.336 20.223 1.00 54.78 C
+ATOM 5591 OG SER B 594 91.715 74.041 19.914 1.00 60.74 O
+ATOM 5592 N ARG B 595 88.029 74.391 22.482 1.00 47.62 N
+ATOM 5593 CA ARG B 595 86.636 74.682 22.784 1.00 44.29 C
+ATOM 5594 C ARG B 595 86.509 75.472 24.090 1.00 41.28 C
+ATOM 5595 O ARG B 595 85.581 76.263 24.262 1.00 43.76 O
+ATOM 5596 CB ARG B 595 85.866 73.371 22.873 1.00 42.18 C
+ATOM 5597 CG ARG B 595 84.379 73.502 22.688 1.00 38.08 C
+ATOM 5598 CD ARG B 595 83.708 72.136 22.690 1.00 36.56 C
+ATOM 5599 NE ARG B 595 82.251 72.250 22.631 1.00 35.93 N
+ATOM 5600 CZ ARG B 595 81.410 71.237 22.817 1.00 34.80 C
+ATOM 5601 NH1 ARG B 595 81.872 70.018 23.081 1.00 36.66 N
+ATOM 5602 NH2 ARG B 595 80.103 71.443 22.737 1.00 35.66 N
+ATOM 5603 N ILE B 596 87.447 75.246 25.005 1.00 36.49 N
+ATOM 5604 CA ILE B 596 87.475 75.937 26.296 1.00 33.41 C
+ATOM 5605 C ILE B 596 87.909 77.396 26.063 1.00 33.42 C
+ATOM 5606 O ILE B 596 87.276 78.335 26.558 1.00 32.93 O
+ATOM 5607 CB ILE B 596 88.490 75.262 27.277 1.00 28.37 C
+ATOM 5608 CG1 ILE B 596 88.040 73.836 27.617 1.00 21.47 C
+ATOM 5609 CG2 ILE B 596 88.658 76.117 28.530 1.00 21.60 C
+ATOM 5610 CD1 ILE B 596 86.697 73.763 28.281 1.00 16.92 C
+ATOM 5611 N VAL B 597 88.994 77.566 25.304 1.00 31.42 N
+ATOM 5612 CA VAL B 597 89.533 78.885 24.980 1.00 33.14 C
+ATOM 5613 C VAL B 597 88.401 79.727 24.419 1.00 36.88 C
+ATOM 5614 O VAL B 597 88.237 80.900 24.753 1.00 35.01 O
+ATOM 5615 CB VAL B 597 90.642 78.799 23.908 1.00 31.52 C
+ATOM 5616 CG1 VAL B 597 90.962 80.204 23.387 1.00 30.13 C
+ATOM 5617 CG2 VAL B 597 91.886 78.148 24.492 1.00 28.29 C
+ATOM 5618 N GLU B 598 87.632 79.089 23.552 1.00 41.56 N
+ATOM 5619 CA GLU B 598 86.475 79.671 22.892 1.00 43.15 C
+ATOM 5620 C GLU B 598 85.555 80.264 23.969 1.00 41.41 C
+ATOM 5621 O GLU B 598 85.078 81.399 23.855 1.00 38.47 O
+ATOM 5622 CB GLU B 598 85.777 78.542 22.134 1.00 49.15 C
+ATOM 5623 CG GLU B 598 84.906 78.923 20.971 1.00 61.07 C
+ATOM 5624 CD GLU B 598 84.336 77.686 20.289 1.00 67.18 C
+ATOM 5625 OE1 GLU B 598 85.117 76.904 19.699 1.00 68.26 O
+ATOM 5626 OE2 GLU B 598 83.106 77.485 20.358 1.00 69.86 O
+ATOM 5627 N TRP B 599 85.329 79.480 25.020 1.00 39.44 N
+ATOM 5628 CA TRP B 599 84.470 79.888 26.127 1.00 37.87 C
+ATOM 5629 C TRP B 599 85.083 80.967 27.033 1.00 36.96 C
+ATOM 5630 O TRP B 599 84.391 81.901 27.462 1.00 35.95 O
+ATOM 5631 CB TRP B 599 84.094 78.661 26.972 1.00 33.82 C
+ATOM 5632 CG TRP B 599 82.751 78.111 26.631 1.00 30.33 C
+ATOM 5633 CD1 TRP B 599 82.477 76.989 25.904 1.00 27.18 C
+ATOM 5634 CD2 TRP B 599 81.486 78.690 26.975 1.00 29.48 C
+ATOM 5635 NE1 TRP B 599 81.122 76.833 25.775 1.00 27.46 N
+ATOM 5636 CE2 TRP B 599 80.485 77.858 26.422 1.00 27.42 C
+ATOM 5637 CE3 TRP B 599 81.102 79.836 27.698 1.00 29.96 C
+ATOM 5638 CZ2 TRP B 599 79.111 78.129 26.564 1.00 28.46 C
+ATOM 5639 CZ3 TRP B 599 79.726 80.116 27.844 1.00 29.63 C
+ATOM 5640 CH2 TRP B 599 78.749 79.257 27.277 1.00 30.20 C
+ATOM 5641 N LYS B 600 86.373 80.817 27.336 1.00 36.77 N
+ATOM 5642 CA LYS B 600 87.087 81.770 28.182 1.00 37.21 C
+ATOM 5643 C LYS B 600 86.883 83.156 27.621 1.00 38.67 C
+ATOM 5644 O LYS B 600 86.468 84.079 28.322 1.00 36.86 O
+ATOM 5645 CB LYS B 600 88.584 81.467 28.196 1.00 36.77 C
+ATOM 5646 CG LYS B 600 88.959 80.195 28.914 1.00 38.05 C
+ATOM 5647 CD LYS B 600 90.457 79.984 28.942 1.00 37.15 C
+ATOM 5648 CE LYS B 600 90.785 78.806 29.841 1.00 37.66 C
+ATOM 5649 NZ LYS B 600 90.263 79.046 31.219 1.00 35.97 N
+ATOM 5650 N GLU B 601 87.181 83.281 26.337 1.00 40.16 N
+ATOM 5651 CA GLU B 601 87.033 84.535 25.634 1.00 40.04 C
+ATOM 5652 C GLU B 601 85.612 85.067 25.775 1.00 39.49 C
+ATOM 5653 O GLU B 601 85.400 86.240 26.086 1.00 39.08 O
+ATOM 5654 CB GLU B 601 87.406 84.325 24.168 1.00 41.16 C
+ATOM 5655 CG GLU B 601 88.907 84.104 23.976 1.00 46.01 C
+ATOM 5656 CD GLU B 601 89.275 83.676 22.571 1.00 49.04 C
+ATOM 5657 OE1 GLU B 601 88.543 84.041 21.624 1.00 50.51 O
+ATOM 5658 OE2 GLU B 601 90.310 82.989 22.417 1.00 50.28 O
+ATOM 5659 N ARG B 602 84.636 84.199 25.568 1.00 40.02 N
+ATOM 5660 CA ARG B 602 83.257 84.618 25.681 1.00 40.79 C
+ATOM 5661 C ARG B 602 83.029 85.140 27.092 1.00 41.63 C
+ATOM 5662 O ARG B 602 82.469 86.220 27.287 1.00 45.68 O
+ATOM 5663 CB ARG B 602 82.340 83.434 25.391 1.00 42.15 C
+ATOM 5664 CG ARG B 602 80.884 83.786 25.200 1.00 41.54 C
+ATOM 5665 CD ARG B 602 80.168 83.834 26.521 1.00 43.37 C
+ATOM 5666 NE ARG B 602 78.726 83.973 26.351 1.00 45.92 N
+ATOM 5667 CZ ARG B 602 77.967 83.121 25.667 1.00 45.85 C
+ATOM 5668 NH1 ARG B 602 78.511 82.056 25.081 1.00 45.69 N
+ATOM 5669 NH2 ARG B 602 76.659 83.332 25.571 1.00 44.44 N
+ATOM 5670 N LEU B 603 83.496 84.380 28.075 1.00 42.62 N
+ATOM 5671 CA LEU B 603 83.323 84.742 29.477 1.00 42.96 C
+ATOM 5672 C LEU B 603 84.104 85.990 29.886 1.00 46.39 C
+ATOM 5673 O LEU B 603 83.606 86.814 30.666 1.00 44.55 O
+ATOM 5674 CB LEU B 603 83.721 83.554 30.350 1.00 38.78 C
+ATOM 5675 CG LEU B 603 82.715 83.088 31.408 1.00 35.66 C
+ATOM 5676 CD1 LEU B 603 81.282 83.232 30.930 1.00 31.14 C
+ATOM 5677 CD2 LEU B 603 83.036 81.631 31.745 1.00 34.19 C
+ATOM 5678 N ASP B 604 85.326 86.117 29.363 1.00 51.12 N
+ATOM 5679 CA ASP B 604 86.195 87.262 29.650 1.00 53.46 C
+ATOM 5680 C ASP B 604 85.687 88.526 28.958 1.00 52.08 C
+ATOM 5681 O ASP B 604 86.035 89.640 29.354 1.00 50.81 O
+ATOM 5682 CB ASP B 604 87.640 86.980 29.207 1.00 60.84 C
+ATOM 5683 CG ASP B 604 88.454 86.252 30.270 1.00 71.18 C
+ATOM 5684 OD1 ASP B 604 88.614 86.801 31.380 1.00 76.81 O
+ATOM 5685 OD2 ASP B 604 88.940 85.133 29.998 1.00 76.01 O
+ATOM 5686 N LYS B 605 84.870 88.348 27.921 1.00 48.81 N
+ATOM 5687 CA LYS B 605 84.289 89.473 27.196 1.00 46.95 C
+ATOM 5688 C LYS B 605 83.033 89.936 27.934 1.00 50.30 C
+ATOM 5689 O LYS B 605 82.627 91.089 27.823 1.00 45.03 O
+ATOM 5690 CB LYS B 605 83.931 89.050 25.769 1.00 45.44 C
+ATOM 5691 CG LYS B 605 83.128 90.076 24.972 1.00 47.62 C
+ATOM 5692 CD LYS B 605 82.743 89.536 23.588 1.00 49.53 C
+ATOM 5693 CE LYS B 605 81.765 90.456 22.843 1.00 48.76 C
+ATOM 5694 NZ LYS B 605 80.397 90.531 23.459 1.00 48.91 N
+ATOM 5695 N GLU B 606 82.448 89.030 28.711 1.00 52.42 N
+ATOM 5696 CA GLU B 606 81.224 89.297 29.468 1.00 50.67 C
+ATOM 5697 C GLU B 606 81.386 89.799 30.902 1.00 44.45 C
+ATOM 5698 O GLU B 606 80.542 90.556 31.392 1.00 35.95 O
+ATOM 5699 CB GLU B 606 80.362 88.036 29.502 1.00 63.61 C
+ATOM 5700 CG GLU B 606 79.649 87.735 28.206 1.00 91.14 C
+ATOM 5701 CD GLU B 606 78.147 87.801 28.367 1.00103.32 C
+ATOM 5702 OE1 GLU B 606 77.661 88.797 28.949 1.00107.69 O
+ATOM 5703 OE2 GLU B 606 77.457 86.865 27.911 1.00107.53 O
+ATOM 5704 N PHE B 607 82.441 89.371 31.589 1.00 35.20 N
+ATOM 5705 CA PHE B 607 82.620 89.788 32.972 1.00 28.14 C
+ATOM 5706 C PHE B 607 84.026 90.236 33.273 1.00 26.21 C
+ATOM 5707 O PHE B 607 84.980 89.634 32.804 1.00 27.06 O
+ATOM 5708 CB PHE B 607 82.265 88.640 33.932 1.00 26.96 C
+ATOM 5709 CG PHE B 607 80.912 88.036 33.684 1.00 25.80 C
+ATOM 5710 CD1 PHE B 607 80.767 86.958 32.819 1.00 24.19 C
+ATOM 5711 CD2 PHE B 607 79.772 88.600 34.256 1.00 26.34 C
+ATOM 5712 CE1 PHE B 607 79.499 86.451 32.516 1.00 24.69 C
+ATOM 5713 CE2 PHE B 607 78.502 88.108 33.966 1.00 24.79 C
+ATOM 5714 CZ PHE B 607 78.363 87.028 33.089 1.00 25.18 C
+ATOM 5715 N SER B 608 84.148 91.287 34.076 1.00 26.77 N
+ATOM 5716 CA SER B 608 85.450 91.798 34.475 1.00 26.54 C
+ATOM 5717 C SER B 608 85.782 91.134 35.803 1.00 28.17 C
+ATOM 5718 O SER B 608 84.891 90.800 36.585 1.00 27.35 O
+ATOM 5719 CB SER B 608 85.406 93.320 34.670 1.00 26.10 C
+ATOM 5720 OG SER B 608 84.706 93.671 35.862 1.00 25.22 O
+ATOM 5721 N LEU B 609 87.067 90.948 36.058 1.00 30.12 N
+ATOM 5722 CA LEU B 609 87.507 90.329 37.290 1.00 31.09 C
+ATOM 5723 C LEU B 609 86.915 91.055 38.491 1.00 31.11 C
+ATOM 5724 O LEU B 609 86.553 90.418 39.482 1.00 32.27 O
+ATOM 5725 CB LEU B 609 89.036 90.353 37.375 1.00 32.84 C
+ATOM 5726 CG LEU B 609 89.648 89.255 38.246 1.00 34.53 C
+ATOM 5727 CD1 LEU B 609 89.329 89.455 39.704 1.00 35.64 C
+ATOM 5728 CD2 LEU B 609 89.085 87.931 37.773 1.00 37.19 C
+ATOM 5729 N SER B 610 86.816 92.382 38.401 1.00 31.01 N
+ATOM 5730 CA SER B 610 86.284 93.200 39.495 1.00 31.60 C
+ATOM 5731 C SER B 610 84.805 92.936 39.761 1.00 31.17 C
+ATOM 5732 O SER B 610 84.356 92.966 40.912 1.00 31.88 O
+ATOM 5733 CB SER B 610 86.505 94.691 39.205 1.00 32.62 C
+ATOM 5734 OG SER B 610 86.038 95.042 37.913 1.00 35.41 O
+ATOM 5735 N VAL B 611 84.053 92.670 38.696 1.00 28.31 N
+ATOM 5736 CA VAL B 611 82.633 92.386 38.820 1.00 24.67 C
+ATOM 5737 C VAL B 611 82.460 91.069 39.554 1.00 25.13 C
+ATOM 5738 O VAL B 611 81.620 90.936 40.450 1.00 24.12 O
+ATOM 5739 CB VAL B 611 81.991 92.287 37.442 1.00 22.21 C
+ATOM 5740 CG1 VAL B 611 80.583 91.738 37.559 1.00 19.87 C
+ATOM 5741 CG2 VAL B 611 81.975 93.666 36.796 1.00 21.68 C
+ATOM 5742 N TYR B 612 83.272 90.096 39.166 1.00 26.41 N
+ATOM 5743 CA TYR B 612 83.235 88.789 39.779 1.00 28.10 C
+ATOM 5744 C TYR B 612 83.660 88.880 41.231 1.00 29.60 C
+ATOM 5745 O TYR B 612 83.066 88.236 42.099 1.00 31.02 O
+ATOM 5746 CB TYR B 612 84.171 87.836 39.045 1.00 29.82 C
+ATOM 5747 CG TYR B 612 84.346 86.526 39.764 1.00 32.12 C
+ATOM 5748 CD1 TYR B 612 83.330 85.578 39.783 1.00 33.78 C
+ATOM 5749 CD2 TYR B 612 85.517 86.243 40.449 1.00 33.26 C
+ATOM 5750 CE1 TYR B 612 83.476 84.366 40.469 1.00 33.67 C
+ATOM 5751 CE2 TYR B 612 85.673 85.039 41.141 1.00 35.34 C
+ATOM 5752 CZ TYR B 612 84.650 84.102 41.147 1.00 34.28 C
+ATOM 5753 OH TYR B 612 84.804 82.911 41.828 1.00 31.38 O
+ATOM 5754 N GLN B 613 84.694 89.670 41.494 1.00 29.32 N
+ATOM 5755 CA GLN B 613 85.189 89.819 42.852 1.00 30.30 C
+ATOM 5756 C GLN B 613 84.146 90.443 43.763 1.00 30.67 C
+ATOM 5757 O GLN B 613 84.081 90.118 44.949 1.00 27.92 O
+ATOM 5758 CB GLN B 613 86.460 90.657 42.869 1.00 32.65 C
+ATOM 5759 CG GLN B 613 87.692 89.903 42.393 1.00 38.10 C
+ATOM 5760 CD GLN B 613 88.025 88.713 43.277 1.00 39.29 C
+ATOM 5761 OE1 GLN B 613 88.140 88.848 44.491 1.00 40.19 O
+ATOM 5762 NE2 GLN B 613 88.184 87.544 42.669 1.00 40.63 N
+ATOM 5763 N LYS B 614 83.320 91.329 43.211 1.00 30.74 N
+ATOM 5764 CA LYS B 614 82.269 91.966 44.003 1.00 29.95 C
+ATOM 5765 C LYS B 614 81.247 90.888 44.387 1.00 27.41 C
+ATOM 5766 O LYS B 614 80.696 90.886 45.495 1.00 26.44 O
+ATOM 5767 CB LYS B 614 81.600 93.085 43.189 1.00 33.43 C
+ATOM 5768 CG LYS B 614 80.596 93.947 43.964 1.00 38.42 C
+ATOM 5769 CD LYS B 614 80.313 95.240 43.194 1.00 43.26 C
+ATOM 5770 CE LYS B 614 79.358 96.179 43.912 1.00 43.23 C
+ATOM 5771 NZ LYS B 614 77.946 95.725 43.782 1.00 43.87 N
+ATOM 5772 N MET B 615 81.016 89.966 43.455 1.00 24.00 N
+ATOM 5773 CA MET B 615 80.089 88.879 43.677 1.00 21.33 C
+ATOM 5774 C MET B 615 80.554 88.079 44.889 1.00 22.27 C
+ATOM 5775 O MET B 615 79.753 87.765 45.761 1.00 23.33 O
+ATOM 5776 CB MET B 615 79.997 87.988 42.429 1.00 17.34 C
+ATOM 5777 CG MET B 615 79.224 88.587 41.252 1.00 8.89 C
+ATOM 5778 SD MET B 615 78.923 87.349 39.957 1.00 6.32 S
+ATOM 5779 CE MET B 615 80.223 87.587 38.908 1.00 11.47 C
+ATOM 5780 N LYS B 616 81.844 87.766 44.969 1.00 24.19 N
+ATOM 5781 CA LYS B 616 82.335 87.006 46.122 1.00 26.58 C
+ATOM 5782 C LYS B 616 82.242 87.863 47.369 1.00 28.53 C
+ATOM 5783 O LYS B 616 81.872 87.381 48.430 1.00 28.60 O
+ATOM 5784 CB LYS B 616 83.796 86.546 45.940 1.00 26.18 C
+ATOM 5785 CG LYS B 616 84.000 85.438 44.912 1.00 26.63 C
+ATOM 5786 CD LYS B 616 85.435 84.879 44.944 1.00 25.69 C
+ATOM 5787 CE LYS B 616 85.681 84.032 46.199 1.00 25.83 C
+ATOM 5788 NZ LYS B 616 87.084 83.551 46.303 1.00 25.31 N
+ATOM 5789 N PHE B 617 82.594 89.140 47.240 1.00 31.53 N
+ATOM 5790 CA PHE B 617 82.543 90.054 48.374 1.00 32.38 C
+ATOM 5791 C PHE B 617 81.129 90.033 48.939 1.00 32.68 C
+ATOM 5792 O PHE B 617 80.929 90.027 50.160 1.00 32.97 O
+ATOM 5793 CB PHE B 617 82.885 91.474 47.941 1.00 33.30 C
+ATOM 5794 CG PHE B 617 82.682 92.487 49.022 1.00 35.32 C
+ATOM 5795 CD1 PHE B 617 83.612 92.627 50.045 1.00 35.64 C
+ATOM 5796 CD2 PHE B 617 81.536 93.275 49.044 1.00 36.93 C
+ATOM 5797 CE1 PHE B 617 83.403 93.534 51.075 1.00 37.00 C
+ATOM 5798 CE2 PHE B 617 81.316 94.187 50.069 1.00 37.37 C
+ATOM 5799 CZ PHE B 617 82.251 94.318 51.087 1.00 37.39 C
+ATOM 5800 N ASN B 618 80.151 90.031 48.035 1.00 34.06 N
+ATOM 5801 CA ASN B 618 78.750 89.993 48.428 1.00 34.93 C
+ATOM 5802 C ASN B 618 78.441 88.721 49.206 1.00 33.90 C
+ATOM 5803 O ASN B 618 77.898 88.779 50.309 1.00 36.07 O
+ATOM 5804 CB ASN B 618 77.841 90.096 47.203 1.00 33.90 C
+ATOM 5805 CG ASN B 618 77.658 91.522 46.749 1.00 33.27 C
+ATOM 5806 OD1 ASN B 618 77.869 92.456 47.532 1.00 34.38 O
+ATOM 5807 ND2 ASN B 618 77.254 91.710 45.489 1.00 32.50 N
+ATOM 5808 N VAL B 619 78.784 87.575 48.632 1.00 31.33 N
+ATOM 5809 CA VAL B 619 78.555 86.302 49.303 1.00 29.38 C
+ATOM 5810 C VAL B 619 79.203 86.385 50.691 1.00 30.70 C
+ATOM 5811 O VAL B 619 78.677 85.870 51.673 1.00 30.97 O
+ATOM 5812 CB VAL B 619 79.183 85.140 48.488 1.00 26.01 C
+ATOM 5813 CG1 VAL B 619 79.149 83.850 49.279 1.00 21.70 C
+ATOM 5814 CG2 VAL B 619 78.438 84.970 47.177 1.00 18.61 C
+ATOM 5815 N ALA B 620 80.337 87.074 50.760 1.00 33.11 N
+ATOM 5816 CA ALA B 620 81.082 87.240 52.005 1.00 35.77 C
+ATOM 5817 C ALA B 620 80.307 88.044 53.047 1.00 36.45 C
+ATOM 5818 O ALA B 620 80.327 87.706 54.231 1.00 38.86 O
+ATOM 5819 CB ALA B 620 82.412 87.911 51.714 1.00 35.97 C
+ATOM 5820 N MET B 621 79.635 89.107 52.601 1.00 38.27 N
+ATOM 5821 CA MET B 621 78.840 89.963 53.484 1.00 39.15 C
+ATOM 5822 C MET B 621 77.419 89.428 53.636 1.00 39.31 C
+ATOM 5823 O MET B 621 76.571 90.085 54.243 1.00 40.32 O
+ATOM 5824 CB MET B 621 78.763 91.386 52.930 1.00 38.75 C
+ATOM 5825 CG MET B 621 80.075 92.175 52.961 1.00 39.00 C
+ATOM 5826 SD MET B 621 80.749 92.490 54.610 1.00 36.57 S
+ATOM 5827 CE MET B 621 82.241 91.479 54.575 1.00 35.60 C
+ATOM 5828 N GLY B 622 77.168 88.245 53.069 1.00 37.36 N
+ATOM 5829 CA GLY B 622 75.855 87.619 53.137 1.00 32.75 C
+ATOM 5830 C GLY B 622 74.714 88.447 52.577 1.00 30.81 C
+ATOM 5831 O GLY B 622 73.750 88.693 53.278 1.00 29.49 O
+ATOM 5832 N ILE B 623 74.793 88.851 51.314 1.00 29.09 N
+ATOM 5833 CA ILE B 623 73.747 89.679 50.733 1.00 29.02 C
+ATOM 5834 C ILE B 623 73.365 89.411 49.288 1.00 30.68 C
+ATOM 5835 O ILE B 623 72.973 90.323 48.579 1.00 32.19 O
+ATOM 5836 CB ILE B 623 74.121 91.173 50.797 1.00 29.79 C
+ATOM 5837 CG1 ILE B 623 75.523 91.368 50.204 1.00 29.85 C
+ATOM 5838 CG2 ILE B 623 74.019 91.688 52.229 1.00 28.46 C
+ATOM 5839 CD1 ILE B 623 75.850 92.788 49.797 1.00 26.72 C
+ATOM 5840 N GLY B 624 73.455 88.189 48.809 1.00 32.90 N
+ATOM 5841 CA GLY B 624 73.054 88.010 47.426 1.00 35.64 C
+ATOM 5842 C GLY B 624 74.039 88.607 46.440 1.00 37.71 C
+ATOM 5843 O GLY B 624 74.286 89.819 46.413 1.00 35.07 O
+ATOM 5844 N VAL B 625 74.592 87.715 45.624 1.00 39.89 N
+ATOM 5845 CA VAL B 625 75.590 88.035 44.618 1.00 40.45 C
+ATOM 5846 C VAL B 625 75.357 89.171 43.635 1.00 40.19 C
+ATOM 5847 O VAL B 625 76.303 89.883 43.300 1.00 40.65 O
+ATOM 5848 CB VAL B 625 75.914 86.797 43.793 1.00 41.40 C
+ATOM 5849 CG1 VAL B 625 77.163 86.157 44.308 1.00 45.21 C
+ATOM 5850 CG2 VAL B 625 74.774 85.821 43.883 1.00 43.70 C
+ATOM 5851 N LEU B 626 74.128 89.358 43.168 1.00 39.16 N
+ATOM 5852 CA LEU B 626 73.886 90.402 42.176 1.00 38.52 C
+ATOM 5853 C LEU B 626 73.542 91.802 42.660 1.00 39.66 C
+ATOM 5854 O LEU B 626 73.046 92.614 41.877 1.00 41.72 O
+ATOM 5855 CB LEU B 626 72.817 89.937 41.188 1.00 35.12 C
+ATOM 5856 CG LEU B 626 73.160 88.620 40.494 1.00 33.02 C
+ATOM 5857 CD1 LEU B 626 72.094 88.294 39.461 1.00 31.33 C
+ATOM 5858 CD2 LEU B 626 74.545 88.729 39.838 1.00 32.12 C
+ATOM 5859 N ASP B 627 73.800 92.100 43.931 1.00 44.14 N
+ATOM 5860 CA ASP B 627 73.501 93.431 44.459 1.00 48.27 C
+ATOM 5861 C ASP B 627 74.465 94.495 43.903 1.00 50.64 C
+ATOM 5862 O ASP B 627 75.657 94.161 43.670 1.00 54.13 O
+ATOM 5863 CB ASP B 627 73.582 93.429 45.994 1.00 49.55 C
+ATOM 5864 CG ASP B 627 72.259 93.058 46.661 1.00 48.92 C
+ATOM 5865 OD1 ASP B 627 71.836 93.789 47.591 1.00 47.20 O
+ATOM 5866 OD2 ASP B 627 71.646 92.040 46.265 1.00 47.20 O
+ATOM 5867 OXT ASP B 627 74.022 95.662 43.729 1.00 54.20 O
+TER 5868 ASP B 627
+HETATM 5869 ZN ZN A 700 30.663 53.669 11.494 1.00 56.10 ZN
+HETATM 5870 ZN ZN B 700 61.548 69.963 11.448 1.00 53.72 ZN
+MASTER 304 0 2 44 14 0 0 6 5868 2 0 58
+END
diff --git a/data/carotid.vtk b/data/carotid.vtk
new file mode 100644
index 0000000..458ebab
--- /dev/null
+++ b/data/carotid.vtk
@@ -0,0 +1,111734 @@
+# vtk DataFile Version 1.0
+Carotid arteries with flow vectors and speed scalars
+ASCII
+DATASET STRUCTURED_POINTS
+DIMENSIONS 76 49 45
+ORIGIN 100.0 80.0 1.0
+ASPECT_RATIO 1.0 1.0 1.0
+
+POINT_DATA 167580
+SCALARS scalars float
+LOOKUP_TABLE default
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diff --git a/data/gktbhL123.vtk b/data/gktbhL123.vtk
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diff --git a/data/head.120.vtk b/data/head.120.vtk
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--- /dev/null
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+
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+
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+
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+
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\ No newline at end of file
diff --git a/data/pdb.pdb b/data/pdb.pdb
new file mode 100644
index 0000000..4cf3e1f
--- /dev/null
+++ b/data/pdb.pdb
@@ -0,0 +1,3025 @@
+HEADER LYASE 23-MAR-06 2DH6
+TITLE CRYSTAL STRUCTURE OF E. COLI APO-TRPB
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: TRYPTOPHAN SYNTHASE BETA SUBUNIT;
+COMPND 3 CHAIN: A;
+COMPND 4 SYNONYM: TRYPTOPHAN SYNTHASE BETA-CHAIN;
+COMPND 5 EC: 4.2.1.20;
+COMPND 6 ENGINEERED: YES
+SOURCE MOL_ID: 1;
+SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
+SOURCE 3 ORGANISM_COMMON: BACTERIA;
+SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
+SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA;
+SOURCE 6 EXPRESSION_SYSTEM_STRAIN: CB149;
+SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
+SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PSTECOTB
+KEYWDS TRYPTOPHAN SYNTHASE, BETA-CHAIN, PLP
+EXPDTA X-RAY DIFFRACTION
+AUTHOR K.NISHIO,Y.MORIMOTO,K.OGASAHARA,N.YASUOKA,K.YUTANI,
+AUTHOR 2 T.TSUKIHARA
+REVDAT 1 24-APR-07 2DH6 0
+JRNL AUTH K.NISHIO,Y.MORIMOTO,K.OGASAHARA,N.YASUOKA,K.YUTANI,
+JRNL AUTH 2 T.TSUKIHARA
+JRNL TITL CRYSTAL STRUCTURE OF TRYPTOPHAN SYNTHASE
+JRNL TITL 2 BETA-SUBUNIT FROM ESCHERICHIA COLI
+JRNL REF TO BE PUBLISHED
+JRNL REFN
+REMARK 1
+REMARK 2
+REMARK 2 RESOLUTION. 3.00 ANGSTROMS.
+REMARK 3
+REMARK 3 REFINEMENT.
+REMARK 3 PROGRAM : CNS 1.1
+REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
+REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
+REMARK 3 : READ,RICE,SIMONSON,WARREN
+REMARK 3
+REMARK 3 REFINEMENT TARGET : NULL
+REMARK 3
+REMARK 3 DATA USED IN REFINEMENT.
+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00
+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.82
+REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
+REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1425358.900
+REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
+REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6
+REMARK 3 NUMBER OF REFLECTIONS : 13244
+REMARK 3
+REMARK 3 FIT TO DATA USED IN REFINEMENT.
+REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
+REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
+REMARK 3 R VALUE (WORKING SET) : 0.206
+REMARK 3 FREE R VALUE : 0.254
+REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
+REMARK 3 FREE R VALUE TEST SET COUNT : 659
+REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010
+REMARK 3
+REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
+REMARK 3 TOTAL NUMBER OF BINS USED : 6
+REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00
+REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19
+REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00
+REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2072
+REMARK 3 BIN R VALUE (WORKING SET) : 0.3140
+REMARK 3 BIN FREE R VALUE : 0.3610
+REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.00
+REMARK 3 BIN FREE R VALUE TEST SET COUNT : 87
+REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.039
+REMARK 3
+REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
+REMARK 3 PROTEIN ATOMS : 2514
+REMARK 3 NUCLEIC ACID ATOMS : 0
+REMARK 3 HETEROGEN ATOMS : 15
+REMARK 3 SOLVENT ATOMS : 23
+REMARK 3
+REMARK 3 B VALUES.
+REMARK 3 FROM WILSON PLOT (A**2) : 85.41
+REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.30
+REMARK 3 OVERALL ANISOTROPIC B VALUE.
+REMARK 3 B11 (A**2) : -0.80000
+REMARK 3 B22 (A**2) : -0.80000
+REMARK 3 B33 (A**2) : 1.61000
+REMARK 3 B12 (A**2) : 0.00000
+REMARK 3 B13 (A**2) : 0.00000
+REMARK 3 B23 (A**2) : 0.00000
+REMARK 3
+REMARK 3 ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32
+REMARK 3 ESD FROM SIGMAA (A) : 0.44
+REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
+REMARK 3
+REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41
+REMARK 3 ESD FROM C-V SIGMAA (A) : 0.55
+REMARK 3
+REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
+REMARK 3 BOND LENGTHS (A) : 0.012
+REMARK 3 BOND ANGLES (DEGREES) : 1.70
+REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80
+REMARK 3 IMPROPER ANGLES (DEGREES) : 0.98
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
+REMARK 3 MAIN-CHAIN BOND (A**2) : 1.800 ; 1.500
+REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.030 ; 2.000
+REMARK 3 SIDE-CHAIN BOND (A**2) : 3.050 ; 2.000
+REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.620 ; 2.500
+REMARK 3
+REMARK 3 BULK SOLVENT MODELING.
+REMARK 3 METHOD USED : FLAT MODEL
+REMARK 3 KSOL : 0.38
+REMARK 3 BSOL : 52.95
+REMARK 3
+REMARK 3 NCS MODEL : NULL
+REMARK 3
+REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
+REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
+REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
+REMARK 3
+REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
+REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM
+REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
+REMARK 3 PARAMETER FILE 4 : ION.PARAM
+REMARK 3 PARAMETER FILE 5 : LIGAND.PARAM
+REMARK 3 PARAMETER FILE 6 : NULL
+REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
+REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP
+REMARK 3 TOPOLOGY FILE 3 : WATER.TOP
+REMARK 3 TOPOLOGY FILE 4 : ION.TOP
+REMARK 3 TOPOLOGY FILE 5 : LIGAND.TOP
+REMARK 3 TOPOLOGY FILE 6 : NULL
+REMARK 3
+REMARK 3 OTHER REFINEMENT REMARKS: NULL
+REMARK 4
+REMARK 4 2DH6 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
+REMARK 100
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-2006.
+REMARK 100 THE RCSB ID CODE IS RCSB025414.
+REMARK 200
+REMARK 200 EXPERIMENTAL DETAILS
+REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
+REMARK 200 DATE OF DATA COLLECTION : 26-OCT-2003
+REMARK 200 TEMPERATURE (KELVIN) : 100.0
+REMARK 200 PH : 6.50
+REMARK 200 NUMBER OF CRYSTALS USED : 2
+REMARK 200
+REMARK 200 SYNCHROTRON (Y/N) : Y
+REMARK 200 RADIATION SOURCE : SPRING-8
+REMARK 200 BEAMLINE : BL44XU
+REMARK 200 X-RAY GENERATOR MODEL : NULL
+REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
+REMARK 200 WAVELENGTH OR RANGE (A) : 0.9
+REMARK 200 MONOCHROMATOR : MIRROR
+REMARK 200 OPTICS : NULL
+REMARK 200
+REMARK 200 DETECTOR TYPE : IMAGE PLATE
+REMARK 200 DETECTOR MANUFACTURER : DIP 6040
+REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
+REMARK 200 DATA SCALING SOFTWARE : SCALA
+REMARK 200
+REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13266
+REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000
+REMARK 200 RESOLUTION RANGE LOW (A) : 46.410
+REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.800
+REMARK 200
+REMARK 200 OVERALL.
+REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
+REMARK 200 DATA REDUNDANCY : 5.200
+REMARK 200 R MERGE (I) : 0.07400
+REMARK 200 R SYM (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
+REMARK 200
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16
+REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
+REMARK 200 DATA REDUNDANCY IN SHELL : 5.30
+REMARK 200 R MERGE FOR SHELL (I) : 0.38900
+REMARK 200 R SYM FOR SHELL (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
+REMARK 200
+REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
+REMARK 200 SOFTWARE USED: CNS
+REMARK 200 STARTING MODEL: CHAIN B OF 1BKS
+REMARK 200
+REMARK 200 REMARK: NULL
+REMARK 280
+REMARK 280 CRYSTAL
+REMARK 280 SOLVENT CONTENT, VS (%): 66.29
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.65
+REMARK 280
+REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE, PH 6.5, VAPOR
+REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 288K
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2
+REMARK 290
+REMARK 290 SYMOP SYMMETRY
+REMARK 290 NNNMMM OPERATOR
+REMARK 290 1555 X,Y,Z
+REMARK 290 2555 -X,-Y,1/2+Z
+REMARK 290 3555 -Y,X,3/4+Z
+REMARK 290 4555 Y,-X,1/4+Z
+REMARK 290 5555 -X,Y,-Z
+REMARK 290 6555 X,-Y,1/2-Z
+REMARK 290 7555 Y,X,1/4-Z
+REMARK 290 8555 -Y,-X,3/4-Z
+REMARK 290
+REMARK 290 WHERE NNN -> OPERATOR NUMBER
+REMARK 290 MMM -> TRANSLATION VECTOR
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
+REMARK 290 RELATED MOLECULES.
+REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.10650
+REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 76.65975
+REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.55325
+REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000
+REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.10650
+REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 25.55325
+REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 76.65975
+REMARK 290
+REMARK 290 REMARK: NULL
+REMARK 300
+REMARK 300 BIOMOLECULE: 1
+REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
+REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR
+REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
+REMARK 350
+REMARK 350 GENERATING THE BIOMOLECULE
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
+REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
+REMARK 350
+REMARK 350 BIOMOLECULE: 1
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
+REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 110.88600
+REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
+REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
+REMARK 465
+REMARK 465 MISSING RESIDUES
+REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
+REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
+REMARK 465
+REMARK 465 M RES C SSSEQI
+REMARK 465 MET A 1
+REMARK 465 THR A 2
+REMARK 465 THR A 3
+REMARK 465 LEU A 4
+REMARK 465 LEU A 5
+REMARK 465 ASN A 6
+REMARK 465 PRO A 7
+REMARK 465 TYR A 8
+REMARK 465 PHE A 9
+REMARK 465 GLY A 10
+REMARK 465 GLU A 11
+REMARK 465 PHE A 12
+REMARK 465 GLY A 13
+REMARK 465 GLY A 14
+REMARK 465 MET A 15
+REMARK 465 TYR A 16
+REMARK 465 GLY A 259
+REMARK 465 HIS A 260
+REMARK 465 GLY A 261
+REMARK 465 ILE A 262
+REMARK 465 GLU A 263
+REMARK 465 THR A 264
+REMARK 465 GLY A 265
+REMARK 465 GLU A 266
+REMARK 465 HIS A 267
+REMARK 465 GLY A 268
+REMARK 465 ALA A 269
+REMARK 465 PRO A 270
+REMARK 465 LEU A 271
+REMARK 465 LYS A 272
+REMARK 465 HIS A 273
+REMARK 465 GLY A 274
+REMARK 465 ARG A 275
+REMARK 465 VAL A 276
+REMARK 465 GLY A 277
+REMARK 465 ILE A 278
+REMARK 465 TYR A 279
+REMARK 465 PHE A 280
+REMARK 465 GLY A 281
+REMARK 465 MET A 282
+REMARK 465 LYS A 283
+REMARK 465 ALA A 284
+REMARK 465 PRO A 285
+REMARK 465 MET A 286
+REMARK 465 MET A 287
+REMARK 465 GLN A 288
+REMARK 465 THR A 289
+REMARK 465 GLU A 290
+REMARK 465 ASP A 291
+REMARK 465 GLY A 292
+REMARK 465 GLN A 293
+REMARK 465 ILE A 294
+REMARK 465 GLU A 295
+REMARK 465 GLU A 296
+REMARK 465 SER A 297
+REMARK 465 TYR A 298
+REMARK 465 SER A 299
+REMARK 465 ILE A 300
+REMARK 465 SER A 301
+REMARK 465 ALA A 302
+REMARK 465 GLY A 303
+REMARK 465 LEU A 304
+REMARK 465 ASP A 305
+REMARK 465 PHE A 306
+REMARK 465 PRO A 307
+REMARK 465 SER A 308
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3)
+REMARK 500
+REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
+REMARK 500 MET A 22 SD MET A 22 CE 0.078
+REMARK 500 MET A 362 SD MET A 362 CE 0.073
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
+REMARK 500
+REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
+REMARK 500 PRO A 56 C - N - CA ANGL. DEV. = 10.2 DEGREES
+REMARK 500 LEU A 59 N - CA - C ANGL. DEV. =-10.1 DEGREES
+REMARK 500 THR A 72 N - CA - C ANGL. DEV. =-10.8 DEGREES
+REMARK 500 GLY A 378 N - CA - C ANGL. DEV. = 16.7 DEGREES
+REMARK 900
+REMARK 900 RELATED ENTRIES
+REMARK 900 RELATED ID: 2DH5 RELATED DB: PDB
+REMARK 900 HOLO-TRPB
+REMARK 999
+REMARK 999 SEQUENCE
+REMARK 999 X (143) OF SEQUENCE DATABASE REFERENCE STANDS
+REMARK 999 FOR ANY RESIDUE, AND THE AUTHOR USED SER.
+DBREF 2DH6 A 1 397 GB 924784 AAA73808 1 397
+SEQADV 2DH6 SER A 143 GB 924784 X 143 SEE REMARK 999
+SEQRES 1 A 397 MET THR THR LEU LEU ASN PRO TYR PHE GLY GLU PHE GLY
+SEQRES 2 A 397 GLY MET TYR VAL PRO GLN ILE LEU MET PRO ALA LEU ARG
+SEQRES 3 A 397 GLN LEU GLU GLU ALA PHE VAL SER ALA GLN LYS ASP PRO
+SEQRES 4 A 397 GLU PHE GLN ALA GLN PHE ASN ASP LEU LEU LYS ASN TYR
+SEQRES 5 A 397 ALA GLY ARG PRO THR ALA LEU THR LYS CYS GLN ASN ILE
+SEQRES 6 A 397 THR ALA GLY THR ASN THR THR LEU TYR LEU LYS ARG GLU
+SEQRES 7 A 397 ASP LEU LEU HIS GLY GLY ALA HIS LYS THR ASN GLN VAL
+SEQRES 8 A 397 LEU GLY GLN ALA LEU LEU ALA LYS ARG MET GLY LYS THR
+SEQRES 9 A 397 GLU ILE ILE ALA GLU THR GLY ALA GLY GLN HIS GLY VAL
+SEQRES 10 A 397 ALA SER ALA LEU ALA SER ALA LEU LEU GLY LEU LYS CYS
+SEQRES 11 A 397 ARG ILE TYR MET GLY ALA LYS ASP VAL GLU ARG GLN SER
+SEQRES 12 A 397 PRO ASN VAL PHE ARG MET ARG LEU MET GLY ALA GLU VAL
+SEQRES 13 A 397 ILE PRO VAL HIS SER GLY SER ALA THR LEU LYS ASP ALA
+SEQRES 14 A 397 CYS ASN GLU ALA LEU ARG ASP TRP SER GLY SER TYR GLU
+SEQRES 15 A 397 THR ALA HIS TYR MET LEU GLY THR ALA ALA GLY PRO HIS
+SEQRES 16 A 397 PRO TYR PRO THR ILE VAL ARG GLU PHE GLN ARG MET ILE
+SEQRES 17 A 397 GLY GLU GLU THR LYS ALA GLN ILE LEU GLU ARG GLU GLY
+SEQRES 18 A 397 ARG LEU PRO ASP ALA VAL ILE ALA CYS VAL GLY GLY GLY
+SEQRES 19 A 397 SER ASN ALA ILE GLY MET PHE ALA ASP PHE ILE ASN GLU
+SEQRES 20 A 397 THR ASN VAL GLY LEU ILE GLY VAL GLU PRO GLY GLY HIS
+SEQRES 21 A 397 GLY ILE GLU THR GLY GLU HIS GLY ALA PRO LEU LYS HIS
+SEQRES 22 A 397 GLY ARG VAL GLY ILE TYR PHE GLY MET LYS ALA PRO MET
+SEQRES 23 A 397 MET GLN THR GLU ASP GLY GLN ILE GLU GLU SER TYR SER
+SEQRES 24 A 397 ILE SER ALA GLY LEU ASP PHE PRO SER VAL GLY PRO GLN
+SEQRES 25 A 397 HIS ALA TYR LEU ASN SER THR GLY ARG ALA ASP TYR VAL
+SEQRES 26 A 397 SER ILE THR ASP ASP GLU ALA LEU GLU ALA PHE LYS THR
+SEQRES 27 A 397 LEU CYS LEU HIS GLU GLY ILE ILE PRO ALA LEU GLU SER
+SEQRES 28 A 397 SER HIS ALA LEU ALA HIS ALA LEU LYS MET MET ARG GLU
+SEQRES 29 A 397 ASN PRO ASP LYS GLU GLN LEU LEU VAL VAL ASN LEU SER
+SEQRES 30 A 397 GLY ARG GLY ASP LYS ASP ILE PHE THR VAL HIS ASP ILE
+SEQRES 31 A 397 LEU LYS ALA ARG GLY GLU ILE
+HET SO4 801 5
+HET SO4 802 5
+HET SO4 803 5
+HETNAM SO4 SULFATE ION
+FORMUL 2 SO4 3(O4 S1 2-)
+FORMUL 5 HOH *23(H2 O1)
+HELIX 1 1 LEU A 21 LYS A 37 1 17
+HELIX 2 2 ASP A 38 GLY A 54 1 17
+HELIX 3 3 GLU A 78 LEU A 81 5 4
+HELIX 4 4 GLY A 84 MET A 101 1 18
+HELIX 5 5 GLY A 113 LEU A 126 1 14
+HELIX 6 6 ALA A 136 ARG A 141 1 6
+HELIX 7 7 GLN A 142 MET A 152 1 11
+HELIX 8 8 THR A 165 SER A 178 1 14
+HELIX 9 9 PRO A 196 PHE A 204 1 9
+HELIX 10 10 ARG A 206 GLY A 221 1 16
+HELIX 11 11 ASN A 236 ALA A 242 1 7
+HELIX 12 12 ASP A 243 ILE A 245 5 3
+HELIX 13 13 GLY A 310 THR A 319 1 10
+HELIX 14 14 THR A 328 GLY A 344 1 17
+HELIX 15 15 ALA A 348 ASN A 365 1 18
+HELIX 16 16 ILE A 384 ARG A 394 1 11
+SHEET 1 A 6 LEU A 59 CYS A 62 0
+SHEET 2 A 6 THR A 72 LYS A 76 -1 O LEU A 73 N CYS A 62
+SHEET 3 A 6 LEU A 371 ASN A 375 1 O VAL A 374 N TYR A 74
+SHEET 4 A 6 ALA A 226 CYS A 230 1 N ILE A 228 O VAL A 373
+SHEET 5 A 6 GLY A 251 PRO A 257 1 O GLY A 251 N VAL A 227
+SHEET 6 A 6 ALA A 322 ILE A 327 1 O VAL A 325 N GLU A 256
+SHEET 1 B 4 GLU A 155 VAL A 159 0
+SHEET 2 B 4 LYS A 129 GLY A 135 1 N ILE A 132 O GLU A 155
+SHEET 3 B 4 GLU A 105 THR A 110 1 N ILE A 106 O LYS A 129
+SHEET 4 B 4 ALA A 184 TYR A 186 1 O HIS A 185 N ILE A 107
+CISPEP 1 ARG A 55 PRO A 56 0 -0.01
+CISPEP 2 HIS A 195 PRO A 196 0 0.29
+CRYST1 110.886 110.886 102.213 90.00 90.00 90.00 P 43 2 2 8
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.009018 0.000000 0.000000 0.00000
+SCALE2 0.000000 0.009018 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.009783 0.00000
+ATOM 1 N VAL A 17 89.425 14.301 -18.452 1.00 86.84 N
+ATOM 2 CA VAL A 17 88.322 14.292 -19.468 1.00 86.19 C
+ATOM 3 C VAL A 17 88.787 13.881 -20.861 1.00 86.01 C
+ATOM 4 O VAL A 17 89.717 14.463 -21.413 1.00 87.98 O
+ATOM 5 CB VAL A 17 87.686 15.677 -19.604 1.00 84.80 C
+ATOM 6 CG1 VAL A 17 86.685 15.677 -20.758 1.00 84.01 C
+ATOM 7 CG2 VAL A 17 87.037 16.068 -18.302 1.00 83.68 C
+ATOM 8 N PRO A 18 88.147 12.872 -21.450 1.00 84.69 N
+ATOM 9 CA PRO A 18 88.576 12.475 -22.792 1.00 85.53 C
+ATOM 10 C PRO A 18 88.482 13.682 -23.731 1.00 86.56 C
+ATOM 11 O PRO A 18 87.465 14.378 -23.761 1.00 86.30 O
+ATOM 12 CB PRO A 18 87.591 11.369 -23.154 1.00 86.13 C
+ATOM 13 CG PRO A 18 86.366 11.713 -22.343 1.00 86.89 C
+ATOM 14 CD PRO A 18 86.951 12.132 -21.023 1.00 84.68 C
+ATOM 15 N GLN A 19 89.550 13.928 -24.486 1.00 87.56 N
+ATOM 16 CA GLN A 19 89.625 15.060 -25.415 1.00 88.01 C
+ATOM 17 C GLN A 19 88.397 15.232 -26.331 1.00 85.50 C
+ATOM 18 O GLN A 19 88.166 16.315 -26.862 1.00 84.73 O
+ATOM 19 CB GLN A 19 90.923 14.966 -26.260 1.00 91.56 C
+ATOM 20 CG GLN A 19 91.018 13.765 -27.258 1.00 97.54 C
+ATOM 21 CD GLN A 19 91.405 12.397 -26.624 1.00100.69 C
+ATOM 22 OE1 GLN A 19 91.289 11.342 -27.271 1.00 98.31 O
+ATOM 23 NE2 GLN A 19 91.876 12.423 -25.371 1.00100.62 N
+ATOM 24 N ILE A 20 87.607 14.175 -26.496 1.00 84.16 N
+ATOM 25 CA ILE A 20 86.420 14.207 -27.357 1.00 82.94 C
+ATOM 26 C ILE A 20 85.223 14.960 -26.756 1.00 83.21 C
+ATOM 27 O ILE A 20 84.353 15.465 -27.484 1.00 82.26 O
+ATOM 28 CB ILE A 20 85.962 12.767 -27.703 1.00 82.26 C
+ATOM 29 CG1 ILE A 20 84.755 12.816 -28.639 1.00 80.80 C
+ATOM 30 CG2 ILE A 20 85.604 12.013 -26.426 1.00 79.92 C
+ATOM 31 CD1 ILE A 20 84.334 11.474 -29.155 1.00 79.46 C
+ATOM 32 N LEU A 21 85.183 15.012 -25.424 1.00 82.95 N
+ATOM 33 CA LEU A 21 84.113 15.691 -24.687 1.00 81.20 C
+ATOM 34 C LEU A 21 84.422 17.159 -24.375 1.00 80.11 C
+ATOM 35 O LEU A 21 83.551 17.872 -23.884 1.00 81.43 O
+ATOM 36 CB LEU A 21 83.827 14.959 -23.366 1.00 79.37 C
+ATOM 37 CG LEU A 21 83.147 13.590 -23.412 1.00 76.91 C
+ATOM 38 CD1 LEU A 21 83.118 13.000 -22.027 1.00 74.74 C
+ATOM 39 CD2 LEU A 21 81.740 13.725 -23.945 1.00 75.83 C
+ATOM 40 N MET A 22 85.653 17.597 -24.645 1.00 77.50 N
+ATOM 41 CA MET A 22 86.065 18.971 -24.392 1.00 73.89 C
+ATOM 42 C MET A 22 85.121 19.998 -24.989 1.00 71.55 C
+ATOM 43 O MET A 22 84.723 20.944 -24.318 1.00 71.82 O
+ATOM 44 CB MET A 22 87.451 19.235 -24.955 1.00 77.66 C
+ATOM 45 CG MET A 22 88.578 18.524 -24.258 1.00 82.67 C
+ATOM 46 SD MET A 22 88.543 18.753 -22.484 1.00 89.63 S
+ATOM 47 CE MET A 22 87.967 20.522 -22.306 1.00 86.21 C
+ATOM 48 N PRO A 23 84.769 19.844 -26.273 1.00 68.13 N
+ATOM 49 CA PRO A 23 83.863 20.783 -26.937 1.00 67.51 C
+ATOM 50 C PRO A 23 82.519 20.916 -26.213 1.00 68.08 C
+ATOM 51 O PRO A 23 82.074 22.030 -25.923 1.00 70.32 O
+ATOM 52 CB PRO A 23 83.706 20.178 -28.324 1.00 65.05 C
+ATOM 53 CG PRO A 23 84.981 19.530 -28.535 1.00 64.84 C
+ATOM 54 CD PRO A 23 85.239 18.838 -27.232 1.00 66.04 C
+ATOM 55 N ALA A 24 81.881 19.774 -25.942 1.00 66.26 N
+ATOM 56 CA ALA A 24 80.593 19.721 -25.249 1.00 61.92 C
+ATOM 57 C ALA A 24 80.640 20.388 -23.872 1.00 59.13 C
+ATOM 58 O ALA A 24 79.761 21.185 -23.526 1.00 57.67 O
+ATOM 59 CB ALA A 24 80.144 18.267 -25.103 1.00 61.30 C
+ATOM 60 N LEU A 25 81.663 20.054 -23.095 1.00 54.63 N
+ATOM 61 CA LEU A 25 81.813 20.617 -21.774 1.00 55.99 C
+ATOM 62 C LEU A 25 82.079 22.120 -21.812 1.00 59.57 C
+ATOM 63 O LEU A 25 81.603 22.846 -20.942 1.00 62.38 O
+ATOM 64 CB LEU A 25 82.930 19.909 -21.025 1.00 51.33 C
+ATOM 65 CG LEU A 25 82.688 18.421 -20.821 1.00 50.95 C
+ATOM 66 CD1 LEU A 25 83.934 17.739 -20.369 1.00 49.96 C
+ATOM 67 CD2 LEU A 25 81.621 18.229 -19.801 1.00 53.70 C
+ATOM 68 N ARG A 26 82.833 22.597 -22.805 1.00 61.72 N
+ATOM 69 CA ARG A 26 83.129 24.030 -22.910 1.00 61.75 C
+ATOM 70 C ARG A 26 81.881 24.834 -23.259 1.00 63.57 C
+ATOM 71 O ARG A 26 81.614 25.872 -22.644 1.00 64.64 O
+ATOM 72 CB ARG A 26 84.214 24.294 -23.951 1.00 60.19 C
+ATOM 73 CG ARG A 26 85.489 24.848 -23.356 1.00 60.94 C
+ATOM 74 CD ARG A 26 86.049 23.883 -22.334 1.00 62.79 C
+ATOM 75 NE ARG A 26 87.373 24.255 -21.816 1.00 67.77 N
+ATOM 76 CZ ARG A 26 87.608 25.147 -20.849 1.00 68.52 C
+ATOM 77 NH1 ARG A 26 86.611 25.800 -20.264 1.00 70.21 N
+ATOM 78 NH2 ARG A 26 88.850 25.368 -20.433 1.00 68.42 N
+ATOM 79 N GLN A 27 81.118 24.364 -24.242 1.00 63.03 N
+ATOM 80 CA GLN A 27 79.897 25.048 -24.628 1.00 64.19 C
+ATOM 81 C GLN A 27 78.885 25.004 -23.484 1.00 65.40 C
+ATOM 82 O GLN A 27 78.002 25.869 -23.376 1.00 63.90 O
+ATOM 83 CB GLN A 27 79.321 24.406 -25.876 1.00 66.09 C
+ATOM 84 CG GLN A 27 79.972 24.926 -27.129 1.00 75.35 C
+ATOM 85 CD GLN A 27 80.182 23.845 -28.173 1.00 81.55 C
+ATOM 86 OE1 GLN A 27 79.214 23.294 -28.722 1.00 86.72 O
+ATOM 87 NE2 GLN A 27 81.453 23.526 -28.453 1.00 81.62 N
+ATOM 88 N LEU A 28 79.017 23.995 -22.623 1.00 64.49 N
+ATOM 89 CA LEU A 28 78.115 23.874 -21.487 1.00 61.54 C
+ATOM 90 C LEU A 28 78.508 24.949 -20.486 1.00 59.62 C
+ATOM 91 O LEU A 28 77.669 25.750 -20.074 1.00 60.71 O
+ATOM 92 CB LEU A 28 78.215 22.490 -20.824 1.00 59.14 C
+ATOM 93 CG LEU A 28 77.211 22.314 -19.677 1.00 56.51 C
+ATOM 94 CD1 LEU A 28 75.811 22.276 -20.251 1.00 53.34 C
+ATOM 95 CD2 LEU A 28 77.505 21.071 -18.890 1.00 54.29 C
+ATOM 96 N GLU A 29 79.783 24.965 -20.105 1.00 56.82 N
+ATOM 97 CA GLU A 29 80.279 25.949 -19.155 1.00 55.54 C
+ATOM 98 C GLU A 29 79.978 27.335 -19.670 1.00 54.80 C
+ATOM 99 O GLU A 29 79.617 28.224 -18.913 1.00 51.20 O
+ATOM 100 CB GLU A 29 81.775 25.792 -18.954 1.00 55.93 C
+ATOM 101 CG GLU A 29 82.431 26.996 -18.329 1.00 59.09 C
+ATOM 102 CD GLU A 29 83.904 26.760 -18.018 1.00 63.86 C
+ATOM 103 OE1 GLU A 29 84.218 26.270 -16.909 1.00 67.14 O
+ATOM 104 OE2 GLU A 29 84.753 27.049 -18.883 1.00 62.41 O
+ATOM 105 N GLU A 30 80.115 27.520 -20.972 1.00 56.15 N
+ATOM 106 CA GLU A 30 79.835 28.825 -21.538 1.00 59.26 C
+ATOM 107 C GLU A 30 78.376 29.162 -21.321 1.00 57.84 C
+ATOM 108 O GLU A 30 78.040 30.263 -20.909 1.00 59.56 O
+ATOM 109 CB GLU A 30 80.140 28.864 -23.036 1.00 62.45 C
+ATOM 110 CG GLU A 30 81.080 30.009 -23.449 1.00 69.44 C
+ATOM 111 CD GLU A 30 80.680 31.398 -22.904 1.00 72.57 C
+ATOM 112 OE1 GLU A 30 79.595 31.928 -23.276 1.00 71.44 O
+ATOM 113 OE2 GLU A 30 81.473 31.955 -22.105 1.00 71.25 O
+ATOM 114 N ALA A 31 77.502 28.215 -21.604 1.00 57.10 N
+ATOM 115 CA ALA A 31 76.088 28.470 -21.425 1.00 58.25 C
+ATOM 116 C ALA A 31 75.707 28.690 -19.951 1.00 58.23 C
+ATOM 117 O ALA A 31 74.886 29.558 -19.650 1.00 57.09 O
+ATOM 118 CB ALA A 31 75.283 27.326 -22.020 1.00 58.31 C
+ATOM 119 N PHE A 32 76.301 27.908 -19.047 1.00 57.46 N
+ATOM 120 CA PHE A 32 76.011 28.013 -17.618 1.00 58.61 C
+ATOM 121 C PHE A 32 76.327 29.397 -17.109 1.00 59.70 C
+ATOM 122 O PHE A 32 75.507 30.053 -16.460 1.00 61.36 O
+ATOM 123 CB PHE A 32 76.838 27.020 -16.809 1.00 58.37 C
+ATOM 124 CG PHE A 32 76.533 27.053 -15.340 1.00 60.38 C
+ATOM 125 CD1 PHE A 32 75.237 26.826 -14.880 1.00 60.40 C
+ATOM 126 CD2 PHE A 32 77.522 27.316 -14.415 1.00 59.98 C
+ATOM 127 CE1 PHE A 32 74.939 26.862 -13.522 1.00 57.57 C
+ATOM 128 CE2 PHE A 32 77.227 27.350 -13.049 1.00 59.81 C
+ATOM 129 CZ PHE A 32 75.932 27.122 -12.610 1.00 58.03 C
+ATOM 130 N VAL A 33 77.550 29.821 -17.392 1.00 59.99 N
+ATOM 131 CA VAL A 33 78.028 31.142 -17.010 1.00 57.76 C
+ATOM 132 C VAL A 33 77.047 32.229 -17.513 1.00 56.04 C
+ATOM 133 O VAL A 33 76.742 33.171 -16.793 1.00 54.86 O
+ATOM 134 CB VAL A 33 79.469 31.351 -17.567 1.00 55.65 C
+ATOM 135 CG1 VAL A 33 79.503 32.497 -18.585 1.00 58.67 C
+ATOM 136 CG2 VAL A 33 80.439 31.575 -16.411 1.00 55.74 C
+ATOM 137 N SER A 34 76.542 32.077 -18.732 1.00 52.93 N
+ATOM 138 CA SER A 34 75.606 33.040 -19.277 1.00 54.56 C
+ATOM 139 C SER A 34 74.281 33.045 -18.560 1.00 58.05 C
+ATOM 140 O SER A 34 73.728 34.100 -18.268 1.00 60.11 O
+ATOM 141 CB SER A 34 75.290 32.747 -20.737 1.00 54.84 C
+ATOM 142 OG SER A 34 74.068 33.383 -21.125 1.00 48.36 O
+ATOM 143 N ALA A 35 73.749 31.850 -18.334 1.00 60.74 N
+ATOM 144 CA ALA A 35 72.455 31.687 -17.699 1.00 59.46 C
+ATOM 145 C ALA A 35 72.512 32.158 -16.276 1.00 60.20 C
+ATOM 146 O ALA A 35 71.507 32.572 -15.713 1.00 60.18 O
+ATOM 147 CB ALA A 35 72.043 30.240 -17.752 1.00 59.87 C
+ATOM 148 N GLN A 36 73.695 32.106 -15.688 1.00 60.79 N
+ATOM 149 CA GLN A 36 73.822 32.537 -14.318 1.00 64.28 C
+ATOM 150 C GLN A 36 73.782 34.082 -14.258 1.00 64.43 C
+ATOM 151 O GLN A 36 73.530 34.688 -13.217 1.00 66.59 O
+ATOM 152 CB GLN A 36 75.118 31.964 -13.731 1.00 65.14 C
+ATOM 153 CG GLN A 36 74.943 31.217 -12.402 1.00 69.04 C
+ATOM 154 CD GLN A 36 76.288 31.003 -11.661 1.00 76.66 C
+ATOM 155 OE1 GLN A 36 77.177 31.886 -11.651 1.00 75.66 O
+ATOM 156 NE2 GLN A 36 76.432 29.836 -11.026 1.00 77.92 N
+ATOM 157 N LYS A 37 74.010 34.720 -15.396 1.00 64.43 N
+ATOM 158 CA LYS A 37 74.015 36.173 -15.463 1.00 61.96 C
+ATOM 159 C LYS A 37 72.684 36.637 -15.985 1.00 64.26 C
+ATOM 160 O LYS A 37 72.492 37.812 -16.236 1.00 67.65 O
+ATOM 161 CB LYS A 37 75.134 36.671 -16.398 1.00 56.55 C
+ATOM 162 CG LYS A 37 76.511 36.704 -15.756 1.00 54.61 C
+ATOM 163 CD LYS A 37 77.602 37.183 -16.701 1.00 54.92 C
+ATOM 164 CE LYS A 37 77.850 36.174 -17.825 1.00 59.16 C
+ATOM 165 NZ LYS A 37 79.027 36.460 -18.715 1.00 57.69 N
+ATOM 166 N ASP A 38 71.747 35.728 -16.169 1.00 65.81 N
+ATOM 167 CA ASP A 38 70.470 36.160 -16.684 1.00 67.40 C
+ATOM 168 C ASP A 38 69.402 36.036 -15.617 1.00 71.32 C
+ATOM 169 O ASP A 38 69.009 34.938 -15.251 1.00 73.15 O
+ATOM 170 CB ASP A 38 70.098 35.348 -17.912 1.00 66.40 C
+ATOM 171 CG ASP A 38 68.862 35.873 -18.583 1.00 68.87 C
+ATOM 172 OD1 ASP A 38 68.526 35.423 -19.705 1.00 70.33 O
+ATOM 173 OD2 ASP A 38 68.218 36.749 -17.973 1.00 69.69 O
+ATOM 174 N PRO A 39 68.914 37.172 -15.091 1.00 74.92 N
+ATOM 175 CA PRO A 39 67.879 37.132 -14.051 1.00 74.49 C
+ATOM 176 C PRO A 39 66.607 36.503 -14.606 1.00 72.70 C
+ATOM 177 O PRO A 39 65.766 36.022 -13.859 1.00 74.82 O
+ATOM 178 CB PRO A 39 67.691 38.602 -13.699 1.00 74.53 C
+ATOM 179 CG PRO A 39 69.012 39.217 -14.063 1.00 74.86 C
+ATOM 180 CD PRO A 39 69.283 38.566 -15.387 1.00 75.12 C
+ATOM 181 N GLU A 40 66.481 36.519 -15.924 1.00 69.35 N
+ATOM 182 CA GLU A 40 65.344 35.931 -16.592 1.00 68.12 C
+ATOM 183 C GLU A 40 65.425 34.406 -16.443 1.00 66.85 C
+ATOM 184 O GLU A 40 64.411 33.719 -16.383 1.00 67.22 O
+ATOM 185 CB GLU A 40 65.385 36.305 -18.061 1.00 71.30 C
+ATOM 186 CG GLU A 40 64.049 36.679 -18.606 1.00 80.03 C
+ATOM 187 CD GLU A 40 63.046 35.563 -18.449 1.00 86.12 C
+ATOM 188 OE1 GLU A 40 63.302 34.457 -18.994 1.00 89.18 O
+ATOM 189 OE2 GLU A 40 62.008 35.793 -17.781 1.00 87.92 O
+ATOM 190 N PHE A 41 66.645 33.881 -16.388 1.00 63.20 N
+ATOM 191 CA PHE A 41 66.862 32.447 -16.240 1.00 58.90 C
+ATOM 192 C PHE A 41 66.509 32.103 -14.822 1.00 58.75 C
+ATOM 193 O PHE A 41 65.574 31.354 -14.556 1.00 58.59 O
+ATOM 194 CB PHE A 41 68.329 32.091 -16.484 1.00 53.71 C
+ATOM 195 CG PHE A 41 68.631 30.631 -16.334 1.00 53.39 C
+ATOM 196 CD1 PHE A 41 68.350 29.733 -17.367 1.00 52.49 C
+ATOM 197 CD2 PHE A 41 69.208 30.139 -15.165 1.00 53.71 C
+ATOM 198 CE1 PHE A 41 68.642 28.371 -17.235 1.00 49.51 C
+ATOM 199 CE2 PHE A 41 69.505 28.772 -15.026 1.00 49.93 C
+ATOM 200 CZ PHE A 41 69.221 27.897 -16.062 1.00 47.79 C
+ATOM 201 N GLN A 42 67.276 32.675 -13.908 1.00 60.78 N
+ATOM 202 CA GLN A 42 67.068 32.449 -12.494 1.00 62.14 C
+ATOM 203 C GLN A 42 65.587 32.618 -12.162 1.00 60.05 C
+ATOM 204 O GLN A 42 65.072 32.012 -11.225 1.00 60.08 O
+ATOM 205 CB GLN A 42 67.920 33.429 -11.688 1.00 64.68 C
+ATOM 206 CG GLN A 42 69.441 33.286 -11.909 1.00 72.60 C
+ATOM 207 CD GLN A 42 70.052 32.070 -11.192 1.00 78.31 C
+ATOM 208 OE1 GLN A 42 69.787 31.833 -9.996 1.00 80.00 O
+ATOM 209 NE2 GLN A 42 70.881 31.302 -11.915 1.00 78.13 N
+ATOM 210 N ALA A 43 64.891 33.419 -12.952 1.00 55.72 N
+ATOM 211 CA ALA A 43 63.486 33.640 -12.692 1.00 55.05 C
+ATOM 212 C ALA A 43 62.680 32.406 -13.030 1.00 56.19 C
+ATOM 213 O ALA A 43 61.842 31.964 -12.252 1.00 55.99 O
+ATOM 214 CB ALA A 43 62.986 34.811 -13.506 1.00 54.28 C
+ATOM 215 N GLN A 44 62.937 31.856 -14.207 1.00 57.28 N
+ATOM 216 CA GLN A 44 62.217 30.694 -14.677 1.00 54.22 C
+ATOM 217 C GLN A 44 62.609 29.500 -13.871 1.00 52.99 C
+ATOM 218 O GLN A 44 61.796 28.607 -13.651 1.00 52.95 O
+ATOM 219 CB GLN A 44 62.540 30.427 -16.136 1.00 56.45 C
+ATOM 220 CG GLN A 44 62.528 31.649 -16.993 1.00 60.47 C
+ATOM 221 CD GLN A 44 62.236 31.318 -18.432 1.00 64.83 C
+ATOM 222 OE1 GLN A 44 62.767 30.342 -18.974 1.00 66.29 O
+ATOM 223 NE2 GLN A 44 61.387 32.133 -19.071 1.00 66.95 N
+ATOM 224 N PHE A 45 63.862 29.470 -13.439 1.00 51.22 N
+ATOM 225 CA PHE A 45 64.325 28.338 -12.656 1.00 52.59 C
+ATOM 226 C PHE A 45 63.571 28.280 -11.336 1.00 52.81 C
+ATOM 227 O PHE A 45 63.297 27.212 -10.792 1.00 53.70 O
+ATOM 228 CB PHE A 45 65.829 28.433 -12.385 1.00 51.64 C
+ATOM 229 CG PHE A 45 66.361 27.284 -11.566 1.00 51.60 C
+ATOM 230 CD1 PHE A 45 67.402 27.471 -10.669 1.00 49.53 C
+ATOM 231 CD2 PHE A 45 65.797 26.013 -11.676 1.00 52.46 C
+ATOM 232 CE1 PHE A 45 67.865 26.422 -9.900 1.00 47.80 C
+ATOM 233 CE2 PHE A 45 66.255 24.964 -10.912 1.00 49.89 C
+ATOM 234 CZ PHE A 45 67.295 25.177 -10.022 1.00 52.00 C
+ATOM 235 N ASN A 46 63.227 29.447 -10.825 1.00 54.86 N
+ATOM 236 CA ASN A 46 62.513 29.532 -9.578 1.00 56.66 C
+ATOM 237 C ASN A 46 61.053 29.178 -9.708 1.00 55.06 C
+ATOM 238 O ASN A 46 60.454 28.623 -8.800 1.00 55.54 O
+ATOM 239 CB ASN A 46 62.663 30.929 -9.006 1.00 62.52 C
+ATOM 240 CG ASN A 46 63.241 30.898 -7.626 1.00 71.44 C
+ATOM 241 OD1 ASN A 46 62.491 30.877 -6.626 1.00 76.86 O
+ATOM 242 ND2 ASN A 46 64.585 30.842 -7.541 1.00 71.19 N
+ATOM 243 N ASP A 47 60.459 29.505 -10.835 1.00 54.83 N
+ATOM 244 CA ASP A 47 59.075 29.170 -10.994 1.00 57.73 C
+ATOM 245 C ASP A 47 58.996 27.644 -11.009 1.00 56.23 C
+ATOM 246 O ASP A 47 58.166 27.056 -10.313 1.00 58.00 O
+ATOM 247 CB ASP A 47 58.526 29.758 -12.291 1.00 65.99 C
+ATOM 248 CG ASP A 47 56.993 29.794 -12.319 1.00 74.84 C
+ATOM 249 OD1 ASP A 47 56.411 29.603 -13.424 1.00 78.60 O
+ATOM 250 OD2 ASP A 47 56.371 30.020 -11.238 1.00 79.34 O
+ATOM 251 N LEU A 48 59.866 26.999 -11.787 1.00 52.41 N
+ATOM 252 CA LEU A 48 59.865 25.542 -11.855 1.00 48.73 C
+ATOM 253 C LEU A 48 60.078 24.965 -10.463 1.00 49.92 C
+ATOM 254 O LEU A 48 59.352 24.049 -10.033 1.00 51.72 O
+ATOM 255 CB LEU A 48 60.956 25.022 -12.793 1.00 42.85 C
+ATOM 256 CG LEU A 48 60.819 25.242 -14.304 1.00 40.60 C
+ATOM 257 CD1 LEU A 48 62.079 24.694 -14.979 1.00 35.46 C
+ATOM 258 CD2 LEU A 48 59.556 24.592 -14.851 1.00 30.14 C
+ATOM 259 N LEU A 49 61.063 25.503 -9.751 1.00 47.17 N
+ATOM 260 CA LEU A 49 61.356 25.034 -8.412 1.00 46.09 C
+ATOM 261 C LEU A 49 60.099 25.058 -7.497 1.00 49.46 C
+ATOM 262 O LEU A 49 59.876 24.145 -6.676 1.00 49.38 O
+ATOM 263 CB LEU A 49 62.488 25.877 -7.852 1.00 41.16 C
+ATOM 264 CG LEU A 49 63.845 25.214 -7.609 1.00 40.32 C
+ATOM 265 CD1 LEU A 49 63.954 23.918 -8.276 1.00 39.81 C
+ATOM 266 CD2 LEU A 49 64.925 26.103 -8.113 1.00 40.63 C
+ATOM 267 N LYS A 50 59.263 26.084 -7.659 1.00 50.12 N
+ATOM 268 CA LYS A 50 58.045 26.217 -6.869 1.00 50.61 C
+ATOM 269 C LYS A 50 57.019 25.227 -7.352 1.00 51.78 C
+ATOM 270 O LYS A 50 56.493 24.398 -6.622 1.00 52.91 O
+ATOM 271 CB LYS A 50 57.429 27.592 -7.044 1.00 51.18 C
+ATOM 272 CG LYS A 50 58.277 28.771 -6.638 1.00 56.28 C
+ATOM 273 CD LYS A 50 57.378 29.837 -6.001 1.00 61.70 C
+ATOM 274 CE LYS A 50 58.136 31.130 -5.721 1.00 66.69 C
+ATOM 275 NZ LYS A 50 57.302 32.109 -4.941 1.00 69.23 N
+ATOM 276 N ASN A 51 56.733 25.320 -8.627 1.00 53.73 N
+ATOM 277 CA ASN A 51 55.731 24.467 -9.192 1.00 55.14 C
+ATOM 278 C ASN A 51 56.030 22.985 -9.257 1.00 56.93 C
+ATOM 279 O ASN A 51 55.110 22.191 -9.122 1.00 59.40 O
+ATOM 280 CB ASN A 51 55.358 25.025 -10.553 1.00 53.30 C
+ATOM 281 CG ASN A 51 54.702 26.389 -10.436 1.00 55.91 C
+ATOM 282 OD1 ASN A 51 53.546 26.482 -10.012 1.00 60.67 O
+ATOM 283 ND2 ASN A 51 55.437 27.455 -10.766 1.00 50.43 N
+ATOM 284 N TYR A 52 57.288 22.578 -9.410 1.00 56.77 N
+ATOM 285 CA TYR A 52 57.537 21.137 -9.527 1.00 57.18 C
+ATOM 286 C TYR A 52 58.369 20.414 -8.491 1.00 58.44 C
+ATOM 287 O TYR A 52 58.371 19.180 -8.470 1.00 57.91 O
+ATOM 288 CB TYR A 52 58.113 20.811 -10.913 1.00 55.86 C
+ATOM 289 CG TYR A 52 57.151 21.129 -12.034 1.00 54.20 C
+ATOM 290 CD1 TYR A 52 57.144 22.387 -12.634 1.00 52.12 C
+ATOM 291 CD2 TYR A 52 56.184 20.213 -12.416 1.00 52.68 C
+ATOM 292 CE1 TYR A 52 56.203 22.726 -13.569 1.00 52.04 C
+ATOM 293 CE2 TYR A 52 55.235 20.541 -13.347 1.00 56.99 C
+ATOM 294 CZ TYR A 52 55.243 21.808 -13.922 1.00 56.74 C
+ATOM 295 OH TYR A 52 54.263 22.153 -14.826 1.00 57.42 O
+ATOM 296 N ALA A 53 59.077 21.166 -7.646 1.00 60.68 N
+ATOM 297 CA ALA A 53 59.941 20.583 -6.611 1.00 58.15 C
+ATOM 298 C ALA A 53 59.484 20.982 -5.222 1.00 57.37 C
+ATOM 299 O ALA A 53 60.234 20.855 -4.248 1.00 57.84 O
+ATOM 300 CB ALA A 53 61.368 21.031 -6.823 1.00 58.20 C
+ATOM 301 N GLY A 54 58.253 21.477 -5.154 1.00 56.65 N
+ATOM 302 CA GLY A 54 57.672 21.901 -3.901 1.00 53.81 C
+ATOM 303 C GLY A 54 58.538 22.826 -3.074 1.00 53.88 C
+ATOM 304 O GLY A 54 58.676 22.591 -1.886 1.00 57.20 O
+ATOM 305 N ARG A 55 59.115 23.874 -3.663 1.00 51.79 N
+ATOM 306 CA ARG A 55 59.950 24.799 -2.887 1.00 48.49 C
+ATOM 307 C ARG A 55 59.273 26.147 -2.628 1.00 45.84 C
+ATOM 308 O ARG A 55 58.423 26.586 -3.397 1.00 47.76 O
+ATOM 309 CB ARG A 55 61.281 25.026 -3.601 1.00 49.81 C
+ATOM 310 CG ARG A 55 62.088 23.746 -3.821 1.00 49.92 C
+ATOM 311 CD ARG A 55 63.555 24.012 -3.590 1.00 51.11 C
+ATOM 312 NE ARG A 55 63.888 24.232 -2.175 1.00 48.43 N
+ATOM 313 CZ ARG A 55 64.047 23.255 -1.287 1.00 49.80 C
+ATOM 314 NH1 ARG A 55 64.347 23.529 -0.027 1.00 46.79 N
+ATOM 315 NH2 ARG A 55 63.907 21.989 -1.667 1.00 53.87 N
+ATOM 316 N PRO A 56 59.626 26.821 -1.530 1.00 41.98 N
+ATOM 317 CA PRO A 56 60.575 26.539 -0.453 1.00 41.58 C
+ATOM 318 C PRO A 56 59.994 25.623 0.587 1.00 41.40 C
+ATOM 319 O PRO A 56 58.804 25.654 0.826 1.00 44.02 O
+ATOM 320 CB PRO A 56 60.799 27.898 0.145 1.00 38.15 C
+ATOM 321 CG PRO A 56 59.456 28.430 0.116 1.00 36.89 C
+ATOM 322 CD PRO A 56 58.977 28.110 -1.277 1.00 38.39 C
+ATOM 323 N THR A 57 60.837 24.827 1.219 1.00 40.86 N
+ATOM 324 CA THR A 57 60.381 23.937 2.260 1.00 41.23 C
+ATOM 325 C THR A 57 60.254 24.823 3.476 1.00 44.58 C
+ATOM 326 O THR A 57 60.818 25.915 3.521 1.00 46.43 O
+ATOM 327 CB THR A 57 61.409 22.885 2.540 1.00 41.75 C
+ATOM 328 OG1 THR A 57 62.662 23.529 2.793 1.00 43.67 O
+ATOM 329 CG2 THR A 57 61.570 21.972 1.344 1.00 40.14 C
+ATOM 330 N ALA A 58 59.522 24.363 4.475 1.00 46.33 N
+ATOM 331 CA ALA A 58 59.340 25.156 5.674 1.00 48.22 C
+ATOM 332 C ALA A 58 60.575 25.108 6.561 1.00 51.26 C
+ATOM 333 O ALA A 58 61.384 24.176 6.463 1.00 53.21 O
+ATOM 334 CB ALA A 58 58.138 24.637 6.446 1.00 46.31 C
+ATOM 335 N LEU A 59 60.734 26.129 7.406 1.00 52.51 N
+ATOM 336 CA LEU A 59 61.831 26.168 8.381 1.00 52.87 C
+ATOM 337 C LEU A 59 61.055 26.237 9.695 1.00 54.29 C
+ATOM 338 O LEU A 59 60.448 27.274 9.990 1.00 58.04 O
+ATOM 339 CB LEU A 59 62.701 27.417 8.234 1.00 48.74 C
+ATOM 340 CG LEU A 59 63.776 27.422 9.332 1.00 52.14 C
+ATOM 341 CD1 LEU A 59 64.878 26.415 9.012 1.00 51.02 C
+ATOM 342 CD2 LEU A 59 64.368 28.801 9.475 1.00 52.81 C
+ATOM 343 N THR A 60 61.041 25.155 10.477 1.00 51.62 N
+ATOM 344 CA THR A 60 60.255 25.196 11.696 1.00 50.31 C
+ATOM 345 C THR A 60 61.000 25.164 13.025 1.00 51.56 C
+ATOM 346 O THR A 60 61.870 24.332 13.281 1.00 50.55 O
+ATOM 347 CB THR A 60 59.108 24.125 11.652 1.00 49.96 C
+ATOM 348 OG1 THR A 60 59.470 22.951 12.367 1.00 48.78 O
+ATOM 349 CG2 THR A 60 58.823 23.730 10.233 1.00 50.81 C
+ATOM 350 N LYS A 61 60.630 26.127 13.862 1.00 52.93 N
+ATOM 351 CA LYS A 61 61.199 26.321 15.177 1.00 53.91 C
+ATOM 352 C LYS A 61 60.681 25.302 16.165 1.00 56.21 C
+ATOM 353 O LYS A 61 59.487 25.156 16.337 1.00 57.80 O
+ATOM 354 CB LYS A 61 60.837 27.713 15.685 1.00 52.42 C
+ATOM 355 CG LYS A 61 61.569 28.080 16.942 1.00 56.56 C
+ATOM 356 CD LYS A 61 60.743 28.907 17.879 1.00 59.72 C
+ATOM 357 CE LYS A 61 60.810 30.387 17.581 1.00 64.87 C
+ATOM 358 NZ LYS A 61 59.925 31.117 18.558 1.00 68.15 N
+ATOM 359 N CYS A 62 61.570 24.595 16.829 1.00 59.80 N
+ATOM 360 CA CYS A 62 61.124 23.631 17.816 1.00 64.38 C
+ATOM 361 C CYS A 62 61.143 24.311 19.175 1.00 66.34 C
+ATOM 362 O CYS A 62 62.181 24.792 19.612 1.00 70.06 O
+ATOM 363 CB CYS A 62 62.050 22.421 17.803 1.00 64.63 C
+ATOM 364 SG CYS A 62 61.980 21.554 16.213 1.00 71.99 S
+ATOM 365 N GLN A 63 60.005 24.395 19.850 1.00 68.99 N
+ATOM 366 CA GLN A 63 60.036 25.045 21.151 1.00 70.54 C
+ATOM 367 C GLN A 63 60.001 24.072 22.310 1.00 70.17 C
+ATOM 368 O GLN A 63 60.646 24.323 23.322 1.00 72.99 O
+ATOM 369 CB GLN A 63 58.919 26.081 21.293 1.00 71.47 C
+ATOM 370 CG GLN A 63 58.947 27.112 20.180 1.00 76.30 C
+ATOM 371 CD GLN A 63 58.289 28.439 20.543 1.00 78.80 C
+ATOM 372 OE1 GLN A 63 58.852 29.243 21.299 1.00 79.77 O
+ATOM 373 NE2 GLN A 63 57.093 28.678 19.999 1.00 78.40 N
+ATOM 374 N ASN A 64 59.283 22.962 22.183 1.00 67.53 N
+ATOM 375 CA ASN A 64 59.253 22.021 23.290 1.00 65.73 C
+ATOM 376 C ASN A 64 60.636 21.509 23.642 1.00 66.22 C
+ATOM 377 O ASN A 64 61.011 21.521 24.807 1.00 67.19 O
+ATOM 378 CB ASN A 64 58.335 20.848 22.991 1.00 63.50 C
+ATOM 379 CG ASN A 64 56.933 21.296 22.677 1.00 66.19 C
+ATOM 380 OD1 ASN A 64 56.438 22.267 23.251 1.00 66.35 O
+ATOM 381 ND2 ASN A 64 56.273 20.592 21.766 1.00 67.25 N
+ATOM 382 N ILE A 65 61.398 21.085 22.637 1.00 66.68 N
+ATOM 383 CA ILE A 65 62.744 20.538 22.840 1.00 64.93 C
+ATOM 384 C ILE A 65 63.768 21.469 23.504 1.00 66.77 C
+ATOM 385 O ILE A 65 64.553 21.037 24.346 1.00 67.65 O
+ATOM 386 CB ILE A 65 63.314 20.020 21.500 1.00 62.12 C
+ATOM 387 CG1 ILE A 65 62.717 18.655 21.204 1.00 63.20 C
+ATOM 388 CG2 ILE A 65 64.812 19.926 21.545 1.00 60.79 C
+ATOM 389 CD1 ILE A 65 63.453 17.895 20.131 1.00 65.90 C
+ATOM 390 N THR A 66 63.764 22.740 23.131 1.00 66.95 N
+ATOM 391 CA THR A 66 64.710 23.680 23.701 1.00 68.25 C
+ATOM 392 C THR A 66 64.223 24.216 25.043 1.00 69.93 C
+ATOM 393 O THR A 66 64.991 24.823 25.788 1.00 70.80 O
+ATOM 394 CB THR A 66 64.931 24.880 22.764 1.00 69.50 C
+ATOM 395 OG1 THR A 66 63.761 25.710 22.760 1.00 71.80 O
+ATOM 396 CG2 THR A 66 65.214 24.407 21.352 1.00 68.48 C
+ATOM 397 N ALA A 67 62.942 24.007 25.338 1.00 71.35 N
+ATOM 398 CA ALA A 67 62.348 24.478 26.589 1.00 70.37 C
+ATOM 399 C ALA A 67 63.320 24.195 27.706 1.00 70.50 C
+ATOM 400 O ALA A 67 63.885 23.105 27.779 1.00 69.55 O
+ATOM 401 CB ALA A 67 61.031 23.772 26.858 1.00 70.86 C
+ATOM 402 N GLY A 68 63.520 25.191 28.561 1.00 70.77 N
+ATOM 403 CA GLY A 68 64.448 25.048 29.662 1.00 69.52 C
+ATOM 404 C GLY A 68 65.878 25.470 29.335 1.00 69.47 C
+ATOM 405 O GLY A 68 66.738 25.391 30.207 1.00 72.58 O
+ATOM 406 N THR A 69 66.163 25.909 28.109 1.00 67.34 N
+ATOM 407 CA THR A 69 67.532 26.305 27.775 1.00 65.93 C
+ATOM 408 C THR A 69 67.545 27.524 26.883 1.00 66.51 C
+ATOM 409 O THR A 69 66.500 27.981 26.430 1.00 65.68 O
+ATOM 410 CB THR A 69 68.286 25.214 27.008 1.00 66.44 C
+ATOM 411 OG1 THR A 69 67.977 25.330 25.614 1.00 66.65 O
+ATOM 412 CG2 THR A 69 67.899 23.824 27.492 1.00 62.61 C
+ATOM 413 N ASN A 70 68.734 28.041 26.605 1.00 67.31 N
+ATOM 414 CA ASN A 70 68.825 29.218 25.755 1.00 70.86 C
+ATOM 415 C ASN A 70 69.053 28.953 24.267 1.00 71.08 C
+ATOM 416 O ASN A 70 69.286 29.894 23.493 1.00 71.62 O
+ATOM 417 CB ASN A 70 69.895 30.163 26.284 1.00 76.50 C
+ATOM 418 CG ASN A 70 69.489 30.810 27.600 1.00 80.96 C
+ATOM 419 OD1 ASN A 70 68.409 31.413 27.704 1.00 82.85 O
+ATOM 420 ND2 ASN A 70 70.347 30.688 28.615 1.00 83.12 N
+ATOM 421 N THR A 71 68.983 27.681 23.866 1.00 68.41 N
+ATOM 422 CA THR A 71 69.133 27.317 22.461 1.00 64.45 C
+ATOM 423 C THR A 71 67.803 27.576 21.752 1.00 62.62 C
+ATOM 424 O THR A 71 66.732 27.395 22.327 1.00 61.84 O
+ATOM 425 CB THR A 71 69.425 25.814 22.273 1.00 65.10 C
+ATOM 426 OG1 THR A 71 70.670 25.473 22.879 1.00 68.32 O
+ATOM 427 CG2 THR A 71 69.491 25.467 20.797 1.00 65.08 C
+ATOM 428 N THR A 72 67.872 28.025 20.508 1.00 60.70 N
+ATOM 429 CA THR A 72 66.677 28.219 19.699 1.00 57.78 C
+ATOM 430 C THR A 72 66.968 27.269 18.550 1.00 58.05 C
+ATOM 431 O THR A 72 67.902 27.506 17.777 1.00 59.97 O
+ATOM 432 CB THR A 72 66.548 29.652 19.170 1.00 54.43 C
+ATOM 433 OG1 THR A 72 66.270 30.525 20.260 1.00 52.12 O
+ATOM 434 CG2 THR A 72 65.411 29.757 18.170 1.00 53.31 C
+ATOM 435 N LEU A 73 66.212 26.177 18.458 1.00 56.11 N
+ATOM 436 CA LEU A 73 66.458 25.209 17.401 1.00 53.97 C
+ATOM 437 C LEU A 73 65.451 25.300 16.271 1.00 56.30 C
+ATOM 438 O LEU A 73 64.244 25.384 16.501 1.00 56.87 O
+ATOM 439 CB LEU A 73 66.459 23.789 17.960 1.00 47.50 C
+ATOM 440 CG LEU A 73 66.673 22.705 16.912 1.00 44.34 C
+ATOM 441 CD1 LEU A 73 68.031 22.856 16.299 1.00 40.13 C
+ATOM 442 CD2 LEU A 73 66.536 21.355 17.536 1.00 39.64 C
+ATOM 443 N TYR A 74 65.973 25.285 15.046 1.00 57.86 N
+ATOM 444 CA TYR A 74 65.175 25.334 13.823 1.00 57.11 C
+ATOM 445 C TYR A 74 65.508 24.152 12.916 1.00 56.77 C
+ATOM 446 O TYR A 74 66.690 23.876 12.658 1.00 58.37 O
+ATOM 447 CB TYR A 74 65.484 26.590 13.018 1.00 57.35 C
+ATOM 448 CG TYR A 74 64.785 27.826 13.458 1.00 57.28 C
+ATOM 449 CD1 TYR A 74 65.443 28.783 14.228 1.00 58.71 C
+ATOM 450 CD2 TYR A 74 63.472 28.065 13.077 1.00 56.00 C
+ATOM 451 CE1 TYR A 74 64.808 29.959 14.606 1.00 60.10 C
+ATOM 452 CE2 TYR A 74 62.825 29.228 13.447 1.00 58.60 C
+ATOM 453 CZ TYR A 74 63.496 30.174 14.211 1.00 60.91 C
+ATOM 454 OH TYR A 74 62.854 31.334 14.568 1.00 65.12 O
+ATOM 455 N LEU A 75 64.481 23.475 12.408 1.00 54.15 N
+ATOM 456 CA LEU A 75 64.703 22.366 11.480 1.00 51.56 C
+ATOM 457 C LEU A 75 64.278 22.840 10.082 1.00 48.56 C
+ATOM 458 O LEU A 75 63.236 23.461 9.918 1.00 47.43 O
+ATOM 459 CB LEU A 75 63.879 21.134 11.901 1.00 53.37 C
+ATOM 460 CG LEU A 75 63.782 20.803 13.410 1.00 54.98 C
+ATOM 461 CD1 LEU A 75 62.801 19.655 13.645 1.00 51.48 C
+ATOM 462 CD2 LEU A 75 65.152 20.468 13.964 1.00 52.73 C
+ATOM 463 N LYS A 76 65.115 22.592 9.086 1.00 47.80 N
+ATOM 464 CA LYS A 76 64.805 22.957 7.705 1.00 46.27 C
+ATOM 465 C LYS A 76 64.072 21.718 7.190 1.00 47.19 C
+ATOM 466 O LYS A 76 64.700 20.691 6.935 1.00 46.71 O
+ATOM 467 CB LYS A 76 66.103 23.180 6.929 1.00 45.37 C
+ATOM 468 CG LYS A 76 65.939 23.486 5.453 1.00 44.90 C
+ATOM 469 CD LYS A 76 65.056 24.692 5.219 1.00 42.70 C
+ATOM 470 CE LYS A 76 64.980 25.007 3.730 1.00 44.26 C
+ATOM 471 NZ LYS A 76 63.971 26.035 3.361 1.00 42.47 N
+ATOM 472 N ARG A 77 62.750 21.818 7.054 1.00 46.06 N
+ATOM 473 CA ARG A 77 61.914 20.700 6.640 1.00 44.01 C
+ATOM 474 C ARG A 77 62.043 20.168 5.203 1.00 46.25 C
+ATOM 475 O ARG A 77 61.120 20.289 4.404 1.00 46.31 O
+ATOM 476 CB ARG A 77 60.441 21.036 6.907 1.00 42.58 C
+ATOM 477 CG ARG A 77 60.124 21.656 8.255 1.00 41.41 C
+ATOM 478 CD ARG A 77 60.423 20.732 9.409 1.00 45.58 C
+ATOM 479 NE ARG A 77 59.854 19.391 9.246 1.00 51.06 N
+ATOM 480 CZ ARG A 77 58.600 19.046 9.538 1.00 52.13 C
+ATOM 481 NH1 ARG A 77 57.761 19.951 10.015 1.00 53.36 N
+ATOM 482 NH2 ARG A 77 58.187 17.789 9.365 1.00 50.72 N
+ATOM 483 N GLU A 78 63.174 19.564 4.863 1.00 48.14 N
+ATOM 484 CA GLU A 78 63.303 18.988 3.530 1.00 49.90 C
+ATOM 485 C GLU A 78 62.579 17.647 3.568 1.00 50.80 C
+ATOM 486 O GLU A 78 62.345 17.033 2.536 1.00 52.19 O
+ATOM 487 CB GLU A 78 64.767 18.752 3.147 1.00 48.61 C
+ATOM 488 CG GLU A 78 65.604 20.009 2.993 1.00 52.93 C
+ATOM 489 CD GLU A 78 65.060 20.985 1.957 1.00 54.42 C
+ATOM 490 OE1 GLU A 78 64.997 20.621 0.764 1.00 55.95 O
+ATOM 491 OE2 GLU A 78 64.701 22.121 2.335 1.00 53.41 O
+ATOM 492 N ASP A 79 62.227 17.212 4.777 1.00 52.10 N
+ATOM 493 CA ASP A 79 61.533 15.943 5.009 1.00 52.35 C
+ATOM 494 C ASP A 79 60.110 15.907 4.480 1.00 52.22 C
+ATOM 495 O ASP A 79 59.545 14.831 4.305 1.00 52.48 O
+ATOM 496 CB ASP A 79 61.509 15.600 6.519 1.00 54.67 C
+ATOM 497 CG ASP A 79 60.637 16.569 7.364 1.00 56.08 C
+ATOM 498 OD1 ASP A 79 60.853 17.799 7.298 1.00 55.96 O
+ATOM 499 OD2 ASP A 79 59.744 16.094 8.114 1.00 55.95 O
+ATOM 500 N LEU A 80 59.526 17.073 4.224 1.00 50.37 N
+ATOM 501 CA LEU A 80 58.162 17.103 3.741 1.00 49.08 C
+ATOM 502 C LEU A 80 58.044 17.057 2.224 1.00 50.61 C
+ATOM 503 O LEU A 80 56.946 16.948 1.690 1.00 54.55 O
+ATOM 504 CB LEU A 80 57.442 18.326 4.293 1.00 47.53 C
+ATOM 505 CG LEU A 80 57.352 18.369 5.823 1.00 48.84 C
+ATOM 506 CD1 LEU A 80 56.356 19.449 6.227 1.00 48.73 C
+ATOM 507 CD2 LEU A 80 56.917 17.020 6.386 1.00 44.55 C
+ATOM 508 N LEU A 81 59.170 17.156 1.528 1.00 50.49 N
+ATOM 509 CA LEU A 81 59.182 17.078 0.072 1.00 49.57 C
+ATOM 510 C LEU A 81 58.851 15.648 -0.293 1.00 51.66 C
+ATOM 511 O LEU A 81 58.834 14.779 0.564 1.00 51.85 O
+ATOM 512 CB LEU A 81 60.570 17.379 -0.455 1.00 45.68 C
+ATOM 513 CG LEU A 81 60.947 18.767 -0.932 1.00 44.38 C
+ATOM 514 CD1 LEU A 81 59.972 19.818 -0.462 1.00 38.08 C
+ATOM 515 CD2 LEU A 81 62.347 19.019 -0.431 1.00 43.11 C
+ATOM 516 N HIS A 82 58.582 15.390 -1.560 1.00 54.70 N
+ATOM 517 CA HIS A 82 58.310 14.028 -1.949 1.00 58.29 C
+ATOM 518 C HIS A 82 59.630 13.478 -2.387 1.00 57.89 C
+ATOM 519 O HIS A 82 60.506 14.239 -2.762 1.00 60.52 O
+ATOM 520 CB HIS A 82 57.294 13.988 -3.066 1.00 67.18 C
+ATOM 521 CG HIS A 82 55.929 13.611 -2.592 1.00 79.31 C
+ATOM 522 ND1 HIS A 82 55.692 12.455 -1.867 1.00 84.56 N
+ATOM 523 CD2 HIS A 82 54.729 14.229 -2.725 1.00 82.57 C
+ATOM 524 CE1 HIS A 82 54.402 12.379 -1.579 1.00 87.32 C
+ATOM 525 NE2 HIS A 82 53.796 13.442 -2.088 1.00 87.44 N
+ATOM 526 N GLY A 83 59.799 12.165 -2.332 1.00 59.92 N
+ATOM 527 CA GLY A 83 61.086 11.573 -2.701 1.00 58.38 C
+ATOM 528 C GLY A 83 61.562 12.042 -4.051 1.00 57.79 C
+ATOM 529 O GLY A 83 60.745 12.367 -4.915 1.00 58.15 O
+ATOM 530 N GLY A 84 62.873 12.101 -4.242 1.00 57.45 N
+ATOM 531 CA GLY A 84 63.397 12.538 -5.533 1.00 55.55 C
+ATOM 532 C GLY A 84 63.351 14.032 -5.822 1.00 53.82 C
+ATOM 533 O GLY A 84 63.904 14.486 -6.831 1.00 51.60 O
+ATOM 534 N ALA A 85 62.679 14.789 -4.954 1.00 52.11 N
+ATOM 535 CA ALA A 85 62.578 16.243 -5.093 1.00 50.22 C
+ATOM 536 C ALA A 85 63.956 16.851 -5.301 1.00 49.66 C
+ATOM 537 O ALA A 85 64.175 17.630 -6.225 1.00 48.85 O
+ATOM 538 CB ALA A 85 61.967 16.839 -3.854 1.00 50.25 C
+ATOM 539 N HIS A 86 64.888 16.490 -4.430 1.00 48.98 N
+ATOM 540 CA HIS A 86 66.224 17.017 -4.544 1.00 51.20 C
+ATOM 541 C HIS A 86 66.904 16.655 -5.867 1.00 53.49 C
+ATOM 542 O HIS A 86 67.837 17.341 -6.284 1.00 57.78 O
+ATOM 543 CB HIS A 86 67.063 16.603 -3.329 1.00 52.13 C
+ATOM 544 CG HIS A 86 66.720 17.359 -2.076 1.00 54.44 C
+ATOM 545 ND1 HIS A 86 67.364 17.150 -0.874 1.00 57.27 N
+ATOM 546 CD2 HIS A 86 65.816 18.344 -1.845 1.00 55.27 C
+ATOM 547 CE1 HIS A 86 66.873 17.972 0.040 1.00 55.44 C
+ATOM 548 NE2 HIS A 86 65.932 18.706 -0.523 1.00 53.99 N
+ATOM 549 N LYS A 87 66.442 15.610 -6.551 1.00 53.66 N
+ATOM 550 CA LYS A 87 67.040 15.262 -7.845 1.00 54.96 C
+ATOM 551 C LYS A 87 66.380 16.143 -8.872 1.00 55.25 C
+ATOM 552 O LYS A 87 67.024 16.629 -9.810 1.00 56.92 O
+ATOM 553 CB LYS A 87 66.799 13.796 -8.206 1.00 55.30 C
+ATOM 554 CG LYS A 87 67.523 12.884 -7.269 1.00 59.08 C
+ATOM 555 CD LYS A 87 67.325 11.415 -7.514 1.00 58.89 C
+ATOM 556 CE LYS A 87 68.175 10.697 -6.482 1.00 58.16 C
+ATOM 557 NZ LYS A 87 68.208 9.247 -6.704 1.00 62.56 N
+ATOM 558 N THR A 88 65.080 16.335 -8.680 1.00 52.74 N
+ATOM 559 CA THR A 88 64.282 17.159 -9.561 1.00 51.57 C
+ATOM 560 C THR A 88 64.900 18.547 -9.578 1.00 51.75 C
+ATOM 561 O THR A 88 64.871 19.245 -10.592 1.00 51.12 O
+ATOM 562 CB THR A 88 62.833 17.195 -9.059 1.00 49.93 C
+ATOM 563 OG1 THR A 88 62.376 15.847 -8.912 1.00 48.08 O
+ATOM 564 CG2 THR A 88 61.930 17.930 -10.038 1.00 46.01 C
+ATOM 565 N ASN A 89 65.474 18.927 -8.442 1.00 52.26 N
+ATOM 566 CA ASN A 89 66.145 20.208 -8.306 1.00 53.91 C
+ATOM 567 C ASN A 89 67.205 20.461 -9.379 1.00 54.46 C
+ATOM 568 O ASN A 89 67.115 21.434 -10.120 1.00 53.15 O
+ATOM 569 CB ASN A 89 66.787 20.301 -6.933 1.00 54.76 C
+ATOM 570 CG ASN A 89 65.822 20.769 -5.892 1.00 56.05 C
+ATOM 571 OD1 ASN A 89 66.088 20.678 -4.700 1.00 56.92 O
+ATOM 572 ND2 ASN A 89 64.686 21.287 -6.335 1.00 55.55 N
+ATOM 573 N GLN A 90 68.215 19.604 -9.484 1.00 55.49 N
+ATOM 574 CA GLN A 90 69.208 19.876 -10.509 1.00 57.17 C
+ATOM 575 C GLN A 90 68.747 19.563 -11.932 1.00 55.04 C
+ATOM 576 O GLN A 90 69.282 20.149 -12.877 1.00 55.43 O
+ATOM 577 CB GLN A 90 70.532 19.174 -10.207 1.00 58.11 C
+ATOM 578 CG GLN A 90 70.601 17.784 -10.676 1.00 67.31 C
+ATOM 579 CD GLN A 90 71.429 16.947 -9.739 1.00 76.61 C
+ATOM 580 OE1 GLN A 90 71.417 15.701 -9.801 1.00 81.27 O
+ATOM 581 NE2 GLN A 90 72.157 17.622 -8.841 1.00 78.98 N
+ATOM 582 N VAL A 91 67.772 18.675 -12.122 1.00 50.98 N
+ATOM 583 CA VAL A 91 67.375 18.441 -13.501 1.00 52.23 C
+ATOM 584 C VAL A 91 66.526 19.597 -14.004 1.00 50.84 C
+ATOM 585 O VAL A 91 66.594 19.952 -15.174 1.00 50.42 O
+ATOM 586 CB VAL A 91 66.607 17.110 -13.740 1.00 52.64 C
+ATOM 587 CG1 VAL A 91 67.478 15.933 -13.410 1.00 50.48 C
+ATOM 588 CG2 VAL A 91 65.335 17.099 -12.956 1.00 58.02 C
+ATOM 589 N LEU A 92 65.715 20.189 -13.138 1.00 50.75 N
+ATOM 590 CA LEU A 92 64.914 21.327 -13.580 1.00 49.99 C
+ATOM 591 C LEU A 92 65.923 22.388 -14.038 1.00 49.31 C
+ATOM 592 O LEU A 92 65.776 22.986 -15.111 1.00 46.55 O
+ATOM 593 CB LEU A 92 64.042 21.845 -12.432 1.00 47.83 C
+ATOM 594 CG LEU A 92 62.869 20.933 -12.069 1.00 47.49 C
+ATOM 595 CD1 LEU A 92 62.118 21.466 -10.855 1.00 46.32 C
+ATOM 596 CD2 LEU A 92 61.935 20.838 -13.264 1.00 45.96 C
+ATOM 597 N GLY A 93 66.958 22.585 -13.222 1.00 48.25 N
+ATOM 598 CA GLY A 93 68.009 23.525 -13.554 1.00 49.35 C
+ATOM 599 C GLY A 93 68.690 23.166 -14.876 1.00 52.32 C
+ATOM 600 O GLY A 93 68.872 24.041 -15.734 1.00 53.92 O
+ATOM 601 N GLN A 94 69.073 21.895 -15.064 1.00 51.49 N
+ATOM 602 CA GLN A 94 69.730 21.485 -16.309 1.00 48.05 C
+ATOM 603 C GLN A 94 68.790 21.400 -17.498 1.00 48.25 C
+ATOM 604 O GLN A 94 69.158 21.778 -18.601 1.00 51.29 O
+ATOM 605 CB GLN A 94 70.430 20.162 -16.131 1.00 44.84 C
+ATOM 606 CG GLN A 94 71.498 20.215 -15.111 1.00 46.83 C
+ATOM 607 CD GLN A 94 72.170 18.876 -14.947 1.00 50.62 C
+ATOM 608 OE1 GLN A 94 72.651 18.297 -15.913 1.00 49.07 O
+ATOM 609 NE2 GLN A 94 72.213 18.375 -13.718 1.00 54.74 N
+ATOM 610 N ALA A 95 67.580 20.901 -17.302 1.00 47.98 N
+ATOM 611 CA ALA A 95 66.641 20.834 -18.416 1.00 46.97 C
+ATOM 612 C ALA A 95 66.522 22.254 -18.947 1.00 46.68 C
+ATOM 613 O ALA A 95 66.614 22.476 -20.147 1.00 45.66 O
+ATOM 614 CB ALA A 95 65.268 20.325 -17.945 1.00 45.72 C
+ATOM 615 N LEU A 96 66.327 23.214 -18.041 1.00 46.93 N
+ATOM 616 CA LEU A 96 66.202 24.613 -18.429 1.00 47.28 C
+ATOM 617 C LEU A 96 67.450 25.082 -19.163 1.00 50.24 C
+ATOM 618 O LEU A 96 67.370 25.763 -20.181 1.00 51.81 O
+ATOM 619 CB LEU A 96 66.013 25.495 -17.213 1.00 46.45 C
+ATOM 620 CG LEU A 96 64.711 26.272 -17.148 1.00 46.53 C
+ATOM 621 CD1 LEU A 96 64.867 27.441 -16.227 1.00 46.61 C
+ATOM 622 CD2 LEU A 96 64.364 26.755 -18.504 1.00 47.60 C
+ATOM 623 N LEU A 97 68.615 24.721 -18.639 1.00 49.95 N
+ATOM 624 CA LEU A 97 69.865 25.111 -19.263 1.00 48.78 C
+ATOM 625 C LEU A 97 69.981 24.555 -20.685 1.00 49.98 C
+ATOM 626 O LEU A 97 70.475 25.232 -21.587 1.00 51.81 O
+ATOM 627 CB LEU A 97 71.026 24.621 -18.412 1.00 46.77 C
+ATOM 628 CG LEU A 97 72.361 25.128 -18.910 1.00 43.76 C
+ATOM 629 CD1 LEU A 97 72.262 26.622 -19.005 1.00 44.44 C
+ATOM 630 CD2 LEU A 97 73.477 24.698 -17.981 1.00 44.70 C
+ATOM 631 N ALA A 98 69.536 23.316 -20.880 1.00 49.14 N
+ATOM 632 CA ALA A 98 69.572 22.685 -22.196 1.00 49.86 C
+ATOM 633 C ALA A 98 68.663 23.438 -23.180 1.00 50.39 C
+ATOM 634 O ALA A 98 69.052 23.725 -24.309 1.00 50.36 O
+ATOM 635 CB ALA A 98 69.136 21.223 -22.090 1.00 49.24 C
+ATOM 636 N LYS A 99 67.448 23.742 -22.745 1.00 49.37 N
+ATOM 637 CA LYS A 99 66.511 24.482 -23.562 1.00 51.40 C
+ATOM 638 C LYS A 99 67.185 25.786 -23.972 1.00 53.98 C
+ATOM 639 O LYS A 99 67.073 26.242 -25.116 1.00 54.67 O
+ATOM 640 CB LYS A 99 65.279 24.797 -22.741 1.00 52.88 C
+ATOM 641 CG LYS A 99 64.020 24.178 -23.264 1.00 57.85 C
+ATOM 642 CD LYS A 99 63.241 25.151 -24.124 1.00 59.52 C
+ATOM 643 CE LYS A 99 61.967 24.489 -24.655 1.00 64.28 C
+ATOM 644 NZ LYS A 99 62.261 23.316 -25.565 1.00 64.54 N
+ATOM 645 N ARG A 100 67.888 26.390 -23.020 1.00 54.14 N
+ATOM 646 CA ARG A 100 68.577 27.633 -23.276 1.00 52.62 C
+ATOM 647 C ARG A 100 69.516 27.370 -24.415 1.00 53.32 C
+ATOM 648 O ARG A 100 69.476 28.085 -25.410 1.00 56.71 O
+ATOM 649 CB ARG A 100 69.387 28.077 -22.057 1.00 55.46 C
+ATOM 650 CG ARG A 100 69.873 29.533 -22.090 1.00 55.34 C
+ATOM 651 CD ARG A 100 69.228 30.310 -20.964 1.00 59.82 C
+ATOM 652 NE ARG A 100 69.686 31.690 -20.834 1.00 63.22 N
+ATOM 653 CZ ARG A 100 70.965 32.053 -20.792 1.00 66.13 C
+ATOM 654 NH1 ARG A 100 71.279 33.340 -20.647 1.00 62.49 N
+ATOM 655 NH2 ARG A 100 71.926 31.128 -20.927 1.00 68.02 N
+ATOM 656 N MET A 101 70.351 26.336 -24.279 1.00 52.04 N
+ATOM 657 CA MET A 101 71.337 25.999 -25.311 1.00 50.74 C
+ATOM 658 C MET A 101 70.705 25.588 -26.617 1.00 49.24 C
+ATOM 659 O MET A 101 71.409 25.262 -27.570 1.00 48.34 O
+ATOM 660 CB MET A 101 72.237 24.867 -24.859 1.00 51.65 C
+ATOM 661 CG MET A 101 73.051 25.178 -23.663 1.00 55.72 C
+ATOM 662 SD MET A 101 74.512 24.158 -23.738 1.00 59.08 S
+ATOM 663 CE MET A 101 73.891 22.676 -22.853 1.00 59.48 C
+ATOM 664 N GLY A 102 69.378 25.585 -26.650 1.00 47.55 N
+ATOM 665 CA GLY A 102 68.676 25.204 -27.853 1.00 47.25 C
+ATOM 666 C GLY A 102 68.713 23.715 -28.140 1.00 48.77 C
+ATOM 667 O GLY A 102 68.469 23.308 -29.287 1.00 48.08 O
+ATOM 668 N LYS A 103 69.022 22.907 -27.116 1.00 48.26 N
+ATOM 669 CA LYS A 103 69.071 21.452 -27.257 1.00 47.03 C
+ATOM 670 C LYS A 103 67.646 20.945 -27.475 1.00 49.28 C
+ATOM 671 O LYS A 103 66.666 21.656 -27.185 1.00 50.12 O
+ATOM 672 CB LYS A 103 69.655 20.793 -26.015 1.00 44.12 C
+ATOM 673 CG LYS A 103 71.045 21.216 -25.671 1.00 42.94 C
+ATOM 674 CD LYS A 103 72.010 20.957 -26.792 1.00 46.12 C
+ATOM 675 CE LYS A 103 73.449 21.346 -26.409 1.00 48.25 C
+ATOM 676 NZ LYS A 103 74.271 21.792 -27.606 1.00 47.96 N
+ATOM 677 N THR A 104 67.531 19.713 -27.970 1.00 49.57 N
+ATOM 678 CA THR A 104 66.224 19.125 -28.270 1.00 49.73 C
+ATOM 679 C THR A 104 66.010 17.758 -27.633 1.00 50.95 C
+ATOM 680 O THR A 104 64.882 17.293 -27.538 1.00 50.91 O
+ATOM 681 CB THR A 104 66.022 19.004 -29.812 1.00 47.33 C
+ATOM 682 OG1 THR A 104 67.251 18.598 -30.435 1.00 48.51 O
+ATOM 683 CG2 THR A 104 65.614 20.320 -30.401 1.00 46.67 C
+ATOM 684 N GLU A 105 67.093 17.105 -27.220 1.00 52.04 N
+ATOM 685 CA GLU A 105 66.979 15.801 -26.590 1.00 52.25 C
+ATOM 686 C GLU A 105 67.843 15.828 -25.348 1.00 52.04 C
+ATOM 687 O GLU A 105 68.750 16.650 -25.225 1.00 48.87 O
+ATOM 688 CB GLU A 105 67.504 14.671 -27.473 1.00 54.07 C
+ATOM 689 CG GLU A 105 67.179 14.713 -28.948 1.00 63.18 C
+ATOM 690 CD GLU A 105 68.443 14.457 -29.771 1.00 69.72 C
+ATOM 691 OE1 GLU A 105 69.295 15.375 -29.758 1.00 75.48 O
+ATOM 692 OE2 GLU A 105 68.614 13.364 -30.399 1.00 69.21 O
+ATOM 693 N ILE A 106 67.567 14.886 -24.451 1.00 52.41 N
+ATOM 694 CA ILE A 106 68.285 14.742 -23.198 1.00 51.35 C
+ATOM 695 C ILE A 106 68.695 13.275 -22.976 1.00 51.31 C
+ATOM 696 O ILE A 106 67.952 12.354 -23.311 1.00 52.69 O
+ATOM 697 CB ILE A 106 67.405 15.278 -22.051 1.00 49.76 C
+ATOM 698 CG1 ILE A 106 67.675 16.762 -21.888 1.00 46.67 C
+ATOM 699 CG2 ILE A 106 67.672 14.539 -20.772 1.00 50.66 C
+ATOM 700 CD1 ILE A 106 66.800 17.384 -20.910 1.00 48.88 C
+ATOM 701 N ILE A 107 69.891 13.083 -22.432 1.00 49.88 N
+ATOM 702 CA ILE A 107 70.446 11.761 -22.171 1.00 50.43 C
+ATOM 703 C ILE A 107 70.733 11.678 -20.675 1.00 51.80 C
+ATOM 704 O ILE A 107 71.373 12.560 -20.118 1.00 50.67 O
+ATOM 705 CB ILE A 107 71.785 11.561 -22.958 1.00 51.48 C
+ATOM 706 CG1 ILE A 107 71.500 11.440 -24.447 1.00 51.52 C
+ATOM 707 CG2 ILE A 107 72.544 10.322 -22.484 1.00 48.76 C
+ATOM 708 CD1 ILE A 107 72.730 11.706 -25.263 1.00 53.31 C
+ATOM 709 N ALA A 108 70.266 10.609 -20.040 1.00 52.48 N
+ATOM 710 CA ALA A 108 70.456 10.401 -18.615 1.00 52.94 C
+ATOM 711 C ALA A 108 70.592 8.913 -18.345 1.00 54.94 C
+ATOM 712 O ALA A 108 70.168 8.098 -19.155 1.00 57.54 O
+ATOM 713 CB ALA A 108 69.252 10.936 -17.855 1.00 49.30 C
+ATOM 714 N GLU A 109 71.200 8.566 -17.217 1.00 55.55 N
+ATOM 715 CA GLU A 109 71.313 7.178 -16.811 1.00 56.32 C
+ATOM 716 C GLU A 109 70.609 7.124 -15.458 1.00 57.80 C
+ATOM 717 O GLU A 109 70.429 8.159 -14.808 1.00 57.39 O
+ATOM 718 CB GLU A 109 72.759 6.748 -16.628 1.00 59.55 C
+ATOM 719 CG GLU A 109 73.398 7.276 -15.373 1.00 66.28 C
+ATOM 720 CD GLU A 109 74.063 8.595 -15.627 1.00 71.94 C
+ATOM 721 OE1 GLU A 109 75.047 8.572 -16.394 1.00 71.28 O
+ATOM 722 OE2 GLU A 109 73.604 9.641 -15.086 1.00 75.92 O
+ATOM 723 N THR A 110 70.225 5.925 -15.018 1.00 58.14 N
+ATOM 724 CA THR A 110 69.530 5.782 -13.740 1.00 55.24 C
+ATOM 725 C THR A 110 69.778 4.413 -13.093 1.00 55.15 C
+ATOM 726 O THR A 110 70.079 3.442 -13.776 1.00 58.80 O
+ATOM 727 CB THR A 110 68.036 6.010 -13.953 1.00 51.82 C
+ATOM 728 OG1 THR A 110 67.361 6.132 -12.696 1.00 48.23 O
+ATOM 729 CG2 THR A 110 67.473 4.873 -14.763 1.00 52.12 C
+ATOM 730 N GLY A 111 69.694 4.355 -11.768 1.00 55.41 N
+ATOM 731 CA GLY A 111 69.892 3.112 -11.042 1.00 54.73 C
+ATOM 732 C GLY A 111 68.552 2.685 -10.469 1.00 55.25 C
+ATOM 733 O GLY A 111 67.887 1.809 -10.999 1.00 56.63 O
+ATOM 734 N ALA A 112 68.145 3.317 -9.381 1.00 56.47 N
+ATOM 735 CA ALA A 112 66.866 3.018 -8.766 1.00 57.06 C
+ATOM 736 C ALA A 112 65.791 3.522 -9.708 1.00 58.71 C
+ATOM 737 O ALA A 112 64.703 2.981 -9.777 1.00 58.44 O
+ATOM 738 CB ALA A 112 66.755 3.743 -7.444 1.00 59.48 C
+ATOM 739 N GLY A 113 66.106 4.579 -10.437 1.00 60.34 N
+ATOM 740 CA GLY A 113 65.134 5.134 -11.344 1.00 60.31 C
+ATOM 741 C GLY A 113 64.682 6.511 -10.904 1.00 62.93 C
+ATOM 742 O GLY A 113 63.969 7.169 -11.656 1.00 64.06 O
+ATOM 743 N GLN A 114 65.064 6.967 -9.707 1.00 63.02 N
+ATOM 744 CA GLN A 114 64.637 8.304 -9.294 1.00 62.88 C
+ATOM 745 C GLN A 114 65.142 9.342 -10.294 1.00 60.76 C
+ATOM 746 O GLN A 114 64.342 10.061 -10.897 1.00 59.55 O
+ATOM 747 CB GLN A 114 65.133 8.659 -7.894 1.00 67.90 C
+ATOM 748 CG GLN A 114 64.336 8.036 -6.749 1.00 74.36 C
+ATOM 749 CD GLN A 114 64.755 8.585 -5.369 1.00 79.89 C
+ATOM 750 OE1 GLN A 114 65.941 8.569 -5.003 1.00 80.85 O
+ATOM 751 NE2 GLN A 114 63.773 9.072 -4.598 1.00 81.89 N
+ATOM 752 N HIS A 115 66.459 9.417 -10.484 1.00 57.94 N
+ATOM 753 CA HIS A 115 67.020 10.377 -11.438 1.00 54.19 C
+ATOM 754 C HIS A 115 66.333 10.259 -12.811 1.00 53.03 C
+ATOM 755 O HIS A 115 65.923 11.272 -13.408 1.00 50.67 O
+ATOM 756 CB HIS A 115 68.518 10.167 -11.596 1.00 51.49 C
+ATOM 757 CG HIS A 115 69.168 11.172 -12.492 1.00 54.08 C
+ATOM 758 ND1 HIS A 115 69.189 12.520 -12.208 1.00 55.53 N
+ATOM 759 CD2 HIS A 115 69.791 11.032 -13.689 1.00 57.28 C
+ATOM 760 CE1 HIS A 115 69.789 13.166 -13.193 1.00 56.75 C
+ATOM 761 NE2 HIS A 115 70.164 12.287 -14.105 1.00 55.82 N
+ATOM 762 N GLY A 116 66.206 9.032 -13.312 1.00 50.22 N
+ATOM 763 CA GLY A 116 65.533 8.849 -14.588 1.00 48.97 C
+ATOM 764 C GLY A 116 64.137 9.476 -14.620 1.00 47.08 C
+ATOM 765 O GLY A 116 63.782 10.187 -15.564 1.00 48.46 O
+ATOM 766 N VAL A 117 63.340 9.213 -13.588 1.00 43.86 N
+ATOM 767 CA VAL A 117 61.997 9.752 -13.512 1.00 41.03 C
+ATOM 768 C VAL A 117 62.061 11.257 -13.440 1.00 43.13 C
+ATOM 769 O VAL A 117 61.152 11.928 -13.898 1.00 43.82 O
+ATOM 770 CB VAL A 117 61.239 9.254 -12.267 1.00 39.62 C
+ATOM 771 CG1 VAL A 117 59.868 9.911 -12.208 1.00 35.53 C
+ATOM 772 CG2 VAL A 117 61.106 7.726 -12.289 1.00 34.51 C
+ATOM 773 N ALA A 118 63.127 11.796 -12.849 1.00 45.06 N
+ATOM 774 CA ALA A 118 63.279 13.256 -12.748 1.00 45.08 C
+ATOM 775 C ALA A 118 63.581 13.849 -14.149 1.00 46.88 C
+ATOM 776 O ALA A 118 62.997 14.873 -14.547 1.00 48.69 O
+ATOM 777 CB ALA A 118 64.387 13.615 -11.742 1.00 34.15 C
+ATOM 778 N SER A 119 64.461 13.191 -14.903 1.00 45.31 N
+ATOM 779 CA SER A 119 64.804 13.655 -16.237 1.00 45.50 C
+ATOM 780 C SER A 119 63.608 13.580 -17.193 1.00 47.92 C
+ATOM 781 O SER A 119 63.393 14.469 -18.025 1.00 47.58 O
+ATOM 782 CB SER A 119 65.935 12.816 -16.757 1.00 43.78 C
+ATOM 783 OG SER A 119 66.829 12.605 -15.697 1.00 46.90 O
+ATOM 784 N ALA A 120 62.829 12.513 -17.082 1.00 48.74 N
+ATOM 785 CA ALA A 120 61.649 12.356 -17.925 1.00 49.95 C
+ATOM 786 C ALA A 120 60.666 13.509 -17.687 1.00 50.28 C
+ATOM 787 O ALA A 120 60.184 14.144 -18.625 1.00 50.67 O
+ATOM 788 CB ALA A 120 60.971 11.028 -17.610 1.00 49.86 C
+ATOM 789 N LEU A 121 60.380 13.752 -16.412 1.00 50.85 N
+ATOM 790 CA LEU A 121 59.469 14.788 -15.966 1.00 49.71 C
+ATOM 791 C LEU A 121 59.929 16.126 -16.497 1.00 49.65 C
+ATOM 792 O LEU A 121 59.201 16.792 -17.243 1.00 49.62 O
+ATOM 793 CB LEU A 121 59.461 14.803 -14.448 1.00 53.68 C
+ATOM 794 CG LEU A 121 58.723 15.866 -13.639 1.00 56.53 C
+ATOM 795 CD1 LEU A 121 58.785 15.460 -12.180 1.00 58.69 C
+ATOM 796 CD2 LEU A 121 59.348 17.231 -13.806 1.00 56.57 C
+ATOM 797 N ALA A 122 61.142 16.523 -16.109 1.00 47.58 N
+ATOM 798 CA ALA A 122 61.696 17.795 -16.556 1.00 43.91 C
+ATOM 799 C ALA A 122 61.599 17.825 -18.063 1.00 44.93 C
+ATOM 800 O ALA A 122 61.213 18.839 -18.646 1.00 45.06 O
+ATOM 801 CB ALA A 122 63.133 17.931 -16.122 1.00 40.34 C
+ATOM 802 N SER A 123 61.922 16.693 -18.691 1.00 46.02 N
+ATOM 803 CA SER A 123 61.874 16.587 -20.147 1.00 46.55 C
+ATOM 804 C SER A 123 60.496 16.778 -20.750 1.00 47.03 C
+ATOM 805 O SER A 123 60.339 17.551 -21.685 1.00 47.72 O
+ATOM 806 CB SER A 123 62.449 15.252 -20.614 1.00 46.69 C
+ATOM 807 OG SER A 123 63.864 15.269 -20.536 1.00 47.64 O
+ATOM 808 N ALA A 124 59.484 16.101 -20.225 1.00 47.27 N
+ATOM 809 CA ALA A 124 58.159 16.258 -20.813 1.00 49.39 C
+ATOM 810 C ALA A 124 57.760 17.715 -20.752 1.00 52.13 C
+ATOM 811 O ALA A 124 57.291 18.298 -21.735 1.00 51.65 O
+ATOM 812 CB ALA A 124 57.160 15.419 -20.078 1.00 48.98 C
+ATOM 813 N LEU A 125 57.963 18.280 -19.567 1.00 54.98 N
+ATOM 814 CA LEU A 125 57.661 19.665 -19.247 1.00 54.95 C
+ATOM 815 C LEU A 125 58.218 20.644 -20.285 1.00 54.72 C
+ATOM 816 O LEU A 125 57.468 21.348 -20.950 1.00 54.08 O
+ATOM 817 CB LEU A 125 58.254 19.958 -17.879 1.00 56.33 C
+ATOM 818 CG LEU A 125 57.616 21.025 -17.026 1.00 56.16 C
+ATOM 819 CD1 LEU A 125 56.115 20.796 -17.018 1.00 58.23 C
+ATOM 820 CD2 LEU A 125 58.204 20.945 -15.620 1.00 55.97 C
+ATOM 821 N LEU A 126 59.534 20.695 -20.424 1.00 53.63 N
+ATOM 822 CA LEU A 126 60.125 21.606 -21.386 1.00 55.31 C
+ATOM 823 C LEU A 126 60.086 21.039 -22.807 1.00 56.74 C
+ATOM 824 O LEU A 126 60.758 21.552 -23.696 1.00 58.28 O
+ATOM 825 CB LEU A 126 61.575 21.895 -21.017 1.00 55.44 C
+ATOM 826 CG LEU A 126 61.822 22.196 -19.554 1.00 54.85 C
+ATOM 827 CD1 LEU A 126 63.282 22.437 -19.335 1.00 59.21 C
+ATOM 828 CD2 LEU A 126 61.056 23.402 -19.166 1.00 55.97 C
+ATOM 829 N GLY A 127 59.329 19.969 -23.017 1.00 54.99 N
+ATOM 830 CA GLY A 127 59.245 19.394 -24.345 1.00 53.74 C
+ATOM 831 C GLY A 127 60.550 18.918 -24.966 1.00 54.55 C
+ATOM 832 O GLY A 127 60.834 19.206 -26.123 1.00 57.21 O
+ATOM 833 N LEU A 128 61.356 18.182 -24.220 1.00 53.71 N
+ATOM 834 CA LEU A 128 62.602 17.666 -24.763 1.00 51.78 C
+ATOM 835 C LEU A 128 62.484 16.146 -24.934 1.00 52.26 C
+ATOM 836 O LEU A 128 61.805 15.479 -24.144 1.00 53.26 O
+ATOM 837 CB LEU A 128 63.749 18.010 -23.821 1.00 49.02 C
+ATOM 838 CG LEU A 128 64.014 19.504 -23.645 1.00 47.07 C
+ATOM 839 CD1 LEU A 128 65.041 19.714 -22.549 1.00 45.27 C
+ATOM 840 CD2 LEU A 128 64.518 20.088 -24.950 1.00 45.15 C
+ATOM 841 N LYS A 129 63.113 15.605 -25.980 1.00 52.27 N
+ATOM 842 CA LYS A 129 63.083 14.164 -26.225 1.00 52.22 C
+ATOM 843 C LYS A 129 64.086 13.556 -25.276 1.00 51.64 C
+ATOM 844 O LYS A 129 65.282 13.863 -25.318 1.00 54.34 O
+ATOM 845 CB LYS A 129 63.452 13.834 -27.666 1.00 53.99 C
+ATOM 846 CG LYS A 129 62.293 14.001 -28.600 1.00 62.36 C
+ATOM 847 CD LYS A 129 62.620 13.502 -30.015 1.00 72.50 C
+ATOM 848 CE LYS A 129 61.403 13.657 -30.987 1.00 76.91 C
+ATOM 849 NZ LYS A 129 60.114 12.997 -30.524 1.00 77.53 N
+ATOM 850 N CYS A 130 63.600 12.664 -24.433 1.00 48.23 N
+ATOM 851 CA CYS A 130 64.436 12.067 -23.413 1.00 46.24 C
+ATOM 852 C CYS A 130 64.762 10.574 -23.566 1.00 45.28 C
+ATOM 853 O CYS A 130 63.884 9.753 -23.813 1.00 45.88 O
+ATOM 854 CB CYS A 130 63.722 12.334 -22.078 1.00 46.83 C
+ATOM 855 SG CYS A 130 64.522 11.816 -20.582 1.00 51.09 S
+ATOM 856 N ARG A 131 66.031 10.215 -23.465 1.00 44.19 N
+ATOM 857 CA ARG A 131 66.364 8.801 -23.488 1.00 44.25 C
+ATOM 858 C ARG A 131 67.241 8.489 -22.268 1.00 46.99 C
+ATOM 859 O ARG A 131 68.248 9.163 -21.997 1.00 45.14 O
+ATOM 860 CB ARG A 131 67.023 8.372 -24.798 1.00 43.41 C
+ATOM 861 CG ARG A 131 68.155 9.177 -25.313 1.00 40.81 C
+ATOM 862 CD ARG A 131 68.643 8.505 -26.570 1.00 41.97 C
+ATOM 863 NE ARG A 131 69.818 9.158 -27.135 1.00 45.75 N
+ATOM 864 CZ ARG A 131 69.782 10.308 -27.788 1.00 44.38 C
+ATOM 865 NH1 ARG A 131 68.630 10.932 -27.956 1.00 45.69 N
+ATOM 866 NH2 ARG A 131 70.891 10.819 -28.281 1.00 46.34 N
+ATOM 867 N ILE A 132 66.826 7.467 -21.524 1.00 47.75 N
+ATOM 868 CA ILE A 132 67.492 7.079 -20.291 1.00 48.43 C
+ATOM 869 C ILE A 132 68.149 5.687 -20.232 1.00 50.06 C
+ATOM 870 O ILE A 132 67.457 4.665 -20.253 1.00 50.48 O
+ATOM 871 CB ILE A 132 66.478 7.181 -19.162 1.00 48.12 C
+ATOM 872 CG1 ILE A 132 65.794 8.552 -19.249 1.00 49.89 C
+ATOM 873 CG2 ILE A 132 67.154 6.914 -17.830 1.00 49.31 C
+ATOM 874 CD1 ILE A 132 64.613 8.756 -18.328 1.00 48.98 C
+ATOM 875 N TYR A 133 69.479 5.643 -20.159 1.00 49.90 N
+ATOM 876 CA TYR A 133 70.168 4.367 -20.049 1.00 49.57 C
+ATOM 877 C TYR A 133 69.979 3.860 -18.640 1.00 49.99 C
+ATOM 878 O TYR A 133 70.015 4.620 -17.686 1.00 49.74 O
+ATOM 879 CB TYR A 133 71.651 4.507 -20.363 1.00 48.70 C
+ATOM 880 CG TYR A 133 71.861 4.793 -21.817 1.00 52.69 C
+ATOM 881 CD1 TYR A 133 71.739 3.785 -22.771 1.00 51.30 C
+ATOM 882 CD2 TYR A 133 72.029 6.099 -22.262 1.00 52.68 C
+ATOM 883 CE1 TYR A 133 71.758 4.080 -24.113 1.00 51.01 C
+ATOM 884 CE2 TYR A 133 72.059 6.398 -23.606 1.00 51.12 C
+ATOM 885 CZ TYR A 133 71.915 5.393 -24.523 1.00 50.42 C
+ATOM 886 OH TYR A 133 71.890 5.724 -25.857 1.00 51.57 O
+ATOM 887 N MET A 134 69.759 2.559 -18.528 1.00 51.96 N
+ATOM 888 CA MET A 134 69.531 1.905 -17.254 1.00 51.46 C
+ATOM 889 C MET A 134 70.027 0.452 -17.345 1.00 53.83 C
+ATOM 890 O MET A 134 69.715 -0.253 -18.307 1.00 54.17 O
+ATOM 891 CB MET A 134 68.031 1.945 -16.934 1.00 46.43 C
+ATOM 892 CG MET A 134 67.686 1.383 -15.597 1.00 45.93 C
+ATOM 893 SD MET A 134 65.963 1.628 -15.158 1.00 52.98 S
+ATOM 894 CE MET A 134 66.058 1.586 -13.363 1.00 43.17 C
+ATOM 895 N GLY A 135 70.827 0.015 -16.370 1.00 55.82 N
+ATOM 896 CA GLY A 135 71.294 -1.366 -16.384 1.00 55.18 C
+ATOM 897 C GLY A 135 70.140 -2.376 -16.403 1.00 56.04 C
+ATOM 898 O GLY A 135 69.116 -2.247 -15.697 1.00 53.35 O
+ATOM 899 N ALA A 136 70.312 -3.404 -17.224 1.00 57.19 N
+ATOM 900 CA ALA A 136 69.309 -4.443 -17.381 1.00 57.18 C
+ATOM 901 C ALA A 136 68.795 -4.980 -16.049 1.00 58.66 C
+ATOM 902 O ALA A 136 67.587 -5.175 -15.879 1.00 55.54 O
+ATOM 903 CB ALA A 136 69.879 -5.549 -18.206 1.00 58.15 C
+ATOM 904 N LYS A 137 69.712 -5.219 -15.111 1.00 61.50 N
+ATOM 905 CA LYS A 137 69.344 -5.719 -13.776 1.00 64.87 C
+ATOM 906 C LYS A 137 68.414 -4.750 -13.052 1.00 65.84 C
+ATOM 907 O LYS A 137 67.438 -5.164 -12.403 1.00 67.63 O
+ATOM 908 CB LYS A 137 70.584 -5.935 -12.904 1.00 64.65 C
+ATOM 909 CG LYS A 137 71.465 -7.074 -13.361 1.00 67.98 C
+ATOM 910 CD LYS A 137 72.721 -7.152 -12.519 1.00 69.14 C
+ATOM 911 CE LYS A 137 73.659 -8.230 -13.028 1.00 69.83 C
+ATOM 912 NZ LYS A 137 74.975 -8.139 -12.340 1.00 72.91 N
+ATOM 913 N ASP A 138 68.723 -3.460 -13.163 1.00 64.83 N
+ATOM 914 CA ASP A 138 67.919 -2.443 -12.523 1.00 61.79 C
+ATOM 915 C ASP A 138 66.580 -2.342 -13.204 1.00 59.39 C
+ATOM 916 O ASP A 138 65.570 -2.158 -12.538 1.00 58.65 O
+ATOM 917 CB ASP A 138 68.631 -1.093 -12.554 1.00 65.28 C
+ATOM 918 CG ASP A 138 69.930 -1.104 -11.765 1.00 68.17 C
+ATOM 919 OD1 ASP A 138 69.911 -1.556 -10.604 1.00 69.43 O
+ATOM 920 OD2 ASP A 138 70.970 -0.656 -12.299 1.00 73.00 O
+ATOM 921 N VAL A 139 66.558 -2.478 -14.526 1.00 55.75 N
+ATOM 922 CA VAL A 139 65.293 -2.391 -15.246 1.00 54.56 C
+ATOM 923 C VAL A 139 64.321 -3.435 -14.730 1.00 56.51 C
+ATOM 924 O VAL A 139 63.112 -3.194 -14.649 1.00 54.19 O
+ATOM 925 CB VAL A 139 65.499 -2.612 -16.733 1.00 52.98 C
+ATOM 926 CG1 VAL A 139 64.206 -2.346 -17.489 1.00 48.93 C
+ATOM 927 CG2 VAL A 139 66.612 -1.711 -17.218 1.00 54.28 C
+ATOM 928 N GLU A 140 64.876 -4.599 -14.383 1.00 61.04 N
+ATOM 929 CA GLU A 140 64.129 -5.744 -13.858 1.00 62.21 C
+ATOM 930 C GLU A 140 63.643 -5.459 -12.467 1.00 62.37 C
+ATOM 931 O GLU A 140 62.448 -5.551 -12.191 1.00 62.67 O
+ATOM 932 CB GLU A 140 65.023 -6.959 -13.787 1.00 67.19 C
+ATOM 933 CG GLU A 140 64.837 -7.956 -14.895 1.00 77.76 C
+ATOM 934 CD GLU A 140 66.072 -8.836 -15.046 1.00 83.93 C
+ATOM 935 OE1 GLU A 140 66.635 -9.258 -13.992 1.00 83.57 O
+ATOM 936 OE2 GLU A 140 66.476 -9.095 -16.215 1.00 87.80 O
+ATOM 937 N ARG A 141 64.577 -5.119 -11.583 1.00 60.69 N
+ATOM 938 CA ARG A 141 64.200 -4.829 -10.219 1.00 61.61 C
+ATOM 939 C ARG A 141 63.626 -3.422 -10.095 1.00 61.77 C
+ATOM 940 O ARG A 141 63.727 -2.827 -9.040 1.00 65.58 O
+ATOM 941 CB ARG A 141 65.403 -5.025 -9.261 1.00 62.05 C
+ATOM 942 CG ARG A 141 66.546 -4.001 -9.347 1.00 71.25 C
+ATOM 943 CD ARG A 141 67.712 -4.228 -8.310 1.00 74.98 C
+ATOM 944 NE ARG A 141 68.930 -4.861 -8.877 1.00 80.88 N
+ATOM 945 CZ ARG A 141 70.143 -4.285 -8.976 1.00 82.05 C
+ATOM 946 NH1 ARG A 141 70.331 -3.043 -8.548 1.00 85.40 N
+ATOM 947 NH2 ARG A 141 71.186 -4.948 -9.492 1.00 77.91 N
+ATOM 948 N GLN A 142 62.987 -2.892 -11.137 1.00 59.77 N
+ATOM 949 CA GLN A 142 62.489 -1.518 -11.052 1.00 58.95 C
+ATOM 950 C GLN A 142 61.318 -1.148 -11.927 1.00 60.25 C
+ATOM 951 O GLN A 142 61.188 -0.005 -12.370 1.00 60.28 O
+ATOM 952 CB GLN A 142 63.617 -0.532 -11.354 1.00 58.24 C
+ATOM 953 CG GLN A 142 64.630 -0.383 -10.248 1.00 55.66 C
+ATOM 954 CD GLN A 142 63.986 0.056 -8.954 1.00 54.55 C
+ATOM 955 OE1 GLN A 142 64.630 0.062 -7.909 1.00 52.04 O
+ATOM 956 NE2 GLN A 142 62.702 0.429 -9.019 1.00 53.06 N
+ATOM 957 N SER A 143 60.452 -2.111 -12.167 1.00 62.06 N
+ATOM 958 CA SER A 143 59.278 -1.890 -12.999 1.00 61.40 C
+ATOM 959 C SER A 143 58.574 -0.550 -12.818 1.00 57.88 C
+ATOM 960 O SER A 143 58.358 0.157 -13.788 1.00 58.02 O
+ATOM 961 CB SER A 143 58.295 -3.025 -12.758 1.00 64.08 C
+ATOM 962 OG SER A 143 58.864 -3.917 -11.799 1.00 71.74 O
+ATOM 963 N PRO A 144 58.212 -0.182 -11.576 1.00 57.13 N
+ATOM 964 CA PRO A 144 57.517 1.076 -11.270 1.00 56.48 C
+ATOM 965 C PRO A 144 58.086 2.336 -11.899 1.00 56.14 C
+ATOM 966 O PRO A 144 57.398 3.009 -12.684 1.00 55.03 O
+ATOM 967 CB PRO A 144 57.557 1.119 -9.755 1.00 56.42 C
+ATOM 968 CG PRO A 144 57.419 -0.298 -9.407 1.00 56.09 C
+ATOM 969 CD PRO A 144 58.423 -0.941 -10.335 1.00 56.94 C
+ATOM 970 N ASN A 145 59.327 2.659 -11.541 1.00 54.85 N
+ATOM 971 CA ASN A 145 59.985 3.831 -12.090 1.00 53.47 C
+ATOM 972 C ASN A 145 60.160 3.709 -13.604 1.00 52.95 C
+ATOM 973 O ASN A 145 60.055 4.701 -14.332 1.00 54.54 O
+ATOM 974 CB ASN A 145 61.331 4.047 -11.410 1.00 55.16 C
+ATOM 975 CG ASN A 145 61.198 4.765 -10.084 1.00 55.97 C
+ATOM 976 OD1 ASN A 145 60.166 5.389 -9.803 1.00 58.87 O
+ATOM 977 ND2 ASN A 145 62.245 4.702 -9.268 1.00 53.66 N
+ATOM 978 N VAL A 146 60.429 2.501 -14.087 1.00 50.20 N
+ATOM 979 CA VAL A 146 60.550 2.310 -15.523 1.00 48.70 C
+ATOM 980 C VAL A 146 59.198 2.613 -16.195 1.00 49.97 C
+ATOM 981 O VAL A 146 59.153 3.250 -17.234 1.00 50.04 O
+ATOM 982 CB VAL A 146 60.996 0.870 -15.858 1.00 46.21 C
+ATOM 983 CG1 VAL A 146 60.894 0.619 -17.373 1.00 40.91 C
+ATOM 984 CG2 VAL A 146 62.437 0.660 -15.370 1.00 44.79 C
+ATOM 985 N PHE A 147 58.101 2.160 -15.585 1.00 52.49 N
+ATOM 986 CA PHE A 147 56.761 2.394 -16.108 1.00 52.40 C
+ATOM 987 C PHE A 147 56.484 3.889 -16.084 1.00 55.14 C
+ATOM 988 O PHE A 147 55.825 4.437 -16.983 1.00 55.78 O
+ATOM 989 CB PHE A 147 55.719 1.659 -15.256 1.00 50.27 C
+ATOM 990 CG PHE A 147 54.278 1.922 -15.678 1.00 50.78 C
+ATOM 991 CD1 PHE A 147 53.906 1.881 -17.014 1.00 47.73 C
+ATOM 992 CD2 PHE A 147 53.295 2.203 -14.727 1.00 48.14 C
+ATOM 993 CE1 PHE A 147 52.600 2.114 -17.389 1.00 47.07 C
+ATOM 994 CE2 PHE A 147 51.984 2.434 -15.101 1.00 45.47 C
+ATOM 995 CZ PHE A 147 51.638 2.391 -16.433 1.00 48.18 C
+ATOM 996 N ARG A 148 56.989 4.549 -15.045 1.00 55.98 N
+ATOM 997 CA ARG A 148 56.806 5.995 -14.901 1.00 56.32 C
+ATOM 998 C ARG A 148 57.543 6.767 -15.993 1.00 52.88 C
+ATOM 999 O ARG A 148 56.976 7.651 -16.640 1.00 51.49 O
+ATOM 1000 CB ARG A 148 57.313 6.477 -13.536 1.00 58.88 C
+ATOM 1001 CG ARG A 148 56.343 6.285 -12.398 1.00 60.17 C
+ATOM 1002 CD ARG A 148 56.851 6.942 -11.111 1.00 62.22 C
+ATOM 1003 NE ARG A 148 56.000 6.555 -9.993 1.00 62.87 N
+ATOM 1004 CZ ARG A 148 56.227 5.504 -9.213 1.00 65.31 C
+ATOM 1005 NH1 ARG A 148 57.303 4.739 -9.414 1.00 62.13 N
+ATOM 1006 NH2 ARG A 148 55.345 5.186 -8.267 1.00 64.75 N
+ATOM 1007 N MET A 149 58.814 6.444 -16.177 1.00 48.46 N
+ATOM 1008 CA MET A 149 59.586 7.134 -17.180 1.00 48.49 C
+ATOM 1009 C MET A 149 58.887 6.989 -18.517 1.00 49.87 C
+ATOM 1010 O MET A 149 58.688 7.970 -19.240 1.00 50.95 O
+ATOM 1011 CB MET A 149 60.999 6.563 -17.250 1.00 45.87 C
+ATOM 1012 CG MET A 149 61.741 6.652 -15.952 1.00 44.71 C
+ATOM 1013 SD MET A 149 63.428 6.145 -16.154 1.00 52.04 S
+ATOM 1014 CE MET A 149 63.490 4.657 -15.155 1.00 48.36 C
+ATOM 1015 N ARG A 150 58.490 5.763 -18.840 1.00 50.93 N
+ATOM 1016 CA ARG A 150 57.822 5.510 -20.102 1.00 49.46 C
+ATOM 1017 C ARG A 150 56.524 6.279 -20.176 1.00 48.16 C
+ATOM 1018 O ARG A 150 56.265 6.951 -21.154 1.00 46.64 O
+ATOM 1019 CB ARG A 150 57.610 4.010 -20.290 1.00 49.35 C
+ATOM 1020 CG ARG A 150 58.892 3.348 -20.759 1.00 53.64 C
+ATOM 1021 CD ARG A 150 58.809 1.840 -20.864 1.00 58.72 C
+ATOM 1022 NE ARG A 150 60.151 1.277 -21.033 1.00 65.73 N
+ATOM 1023 CZ ARG A 150 60.442 -0.017 -20.908 1.00 69.20 C
+ATOM 1024 NH1 ARG A 150 59.465 -0.879 -20.616 1.00 69.44 N
+ATOM 1025 NH2 ARG A 150 61.705 -0.446 -21.048 1.00 65.89 N
+ATOM 1026 N LEU A 151 55.728 6.205 -19.119 1.00 48.10 N
+ATOM 1027 CA LEU A 151 54.457 6.913 -19.055 1.00 48.83 C
+ATOM 1028 C LEU A 151 54.652 8.394 -19.395 1.00 51.31 C
+ATOM 1029 O LEU A 151 53.835 9.030 -20.084 1.00 50.80 O
+ATOM 1030 CB LEU A 151 53.913 6.767 -17.649 1.00 46.72 C
+ATOM 1031 CG LEU A 151 52.485 6.282 -17.457 1.00 49.67 C
+ATOM 1032 CD1 LEU A 151 51.996 5.358 -18.563 1.00 46.19 C
+ATOM 1033 CD2 LEU A 151 52.486 5.574 -16.125 1.00 50.76 C
+ATOM 1034 N MET A 152 55.764 8.926 -18.898 1.00 54.15 N
+ATOM 1035 CA MET A 152 56.145 10.316 -19.086 1.00 54.61 C
+ATOM 1036 C MET A 152 56.643 10.557 -20.511 1.00 54.06 C
+ATOM 1037 O MET A 152 56.962 11.674 -20.904 1.00 56.84 O
+ATOM 1038 CB MET A 152 57.226 10.676 -18.071 1.00 55.93 C
+ATOM 1039 CG MET A 152 56.932 11.928 -17.280 1.00 57.91 C
+ATOM 1040 SD MET A 152 56.792 11.579 -15.529 1.00 59.04 S
+ATOM 1041 CE MET A 152 58.450 11.088 -15.131 1.00 55.03 C
+ATOM 1042 N GLY A 153 56.742 9.500 -21.290 1.00 52.05 N
+ATOM 1043 CA GLY A 153 57.162 9.691 -22.657 1.00 48.08 C
+ATOM 1044 C GLY A 153 58.624 9.509 -22.919 1.00 47.34 C
+ATOM 1045 O GLY A 153 59.048 9.693 -24.042 1.00 47.45 O
+ATOM 1046 N ALA A 154 59.408 9.159 -21.909 1.00 48.51 N
+ATOM 1047 CA ALA A 154 60.835 8.981 -22.139 1.00 47.72 C
+ATOM 1048 C ALA A 154 61.006 7.602 -22.697 1.00 49.69 C
+ATOM 1049 O ALA A 154 60.067 6.813 -22.715 1.00 53.13 O
+ATOM 1050 CB ALA A 154 61.627 9.123 -20.857 1.00 43.66 C
+ATOM 1051 N GLU A 155 62.215 7.326 -23.150 1.00 51.61 N
+ATOM 1052 CA GLU A 155 62.576 6.059 -23.738 1.00 52.95 C
+ATOM 1053 C GLU A 155 63.634 5.435 -22.840 1.00 53.85 C
+ATOM 1054 O GLU A 155 64.684 6.039 -22.619 1.00 56.14 O
+ATOM 1055 CB GLU A 155 63.127 6.324 -25.130 1.00 53.61 C
+ATOM 1056 CG GLU A 155 63.742 5.138 -25.776 1.00 63.31 C
+ATOM 1057 CD GLU A 155 64.307 5.464 -27.137 1.00 68.73 C
+ATOM 1058 OE1 GLU A 155 65.089 6.446 -27.244 1.00 70.54 O
+ATOM 1059 OE2 GLU A 155 63.969 4.734 -28.103 1.00 74.48 O
+ATOM 1060 N VAL A 156 63.367 4.237 -22.322 1.00 53.99 N
+ATOM 1061 CA VAL A 156 64.311 3.563 -21.426 1.00 53.44 C
+ATOM 1062 C VAL A 156 65.137 2.519 -22.153 1.00 53.00 C
+ATOM 1063 O VAL A 156 64.629 1.496 -22.543 1.00 56.37 O
+ATOM 1064 CB VAL A 156 63.598 2.829 -20.254 1.00 53.25 C
+ATOM 1065 CG1 VAL A 156 64.641 2.365 -19.250 1.00 54.90 C
+ATOM 1066 CG2 VAL A 156 62.568 3.728 -19.574 1.00 50.42 C
+ATOM 1067 N ILE A 157 66.424 2.764 -22.300 1.00 52.26 N
+ATOM 1068 CA ILE A 157 67.314 1.837 -22.989 1.00 49.13 C
+ATOM 1069 C ILE A 157 68.007 0.934 -21.971 1.00 49.48 C
+ATOM 1070 O ILE A 157 68.807 1.398 -21.166 1.00 47.65 O
+ATOM 1071 CB ILE A 157 68.379 2.633 -23.766 1.00 47.79 C
+ATOM 1072 CG1 ILE A 157 67.688 3.502 -24.809 1.00 43.99 C
+ATOM 1073 CG2 ILE A 157 69.414 1.718 -24.348 1.00 41.35 C
+ATOM 1074 CD1 ILE A 157 68.607 4.461 -25.427 1.00 46.06 C
+ATOM 1075 N PRO A 158 67.693 -0.371 -21.977 1.00 50.07 N
+ATOM 1076 CA PRO A 158 68.361 -1.239 -21.004 1.00 48.36 C
+ATOM 1077 C PRO A 158 69.780 -1.503 -21.464 1.00 48.52 C
+ATOM 1078 O PRO A 158 70.079 -1.457 -22.653 1.00 51.27 O
+ATOM 1079 CB PRO A 158 67.496 -2.494 -21.005 1.00 46.68 C
+ATOM 1080 CG PRO A 158 67.037 -2.569 -22.418 1.00 48.18 C
+ATOM 1081 CD PRO A 158 66.685 -1.120 -22.748 1.00 49.12 C
+ATOM 1082 N VAL A 159 70.664 -1.766 -20.522 1.00 48.63 N
+ATOM 1083 CA VAL A 159 72.038 -2.031 -20.866 1.00 47.27 C
+ATOM 1084 C VAL A 159 72.456 -3.369 -20.301 1.00 51.16 C
+ATOM 1085 O VAL A 159 72.329 -3.602 -19.107 1.00 51.72 O
+ATOM 1086 CB VAL A 159 72.940 -0.987 -20.289 1.00 44.16 C
+ATOM 1087 CG1 VAL A 159 74.360 -1.264 -20.723 1.00 44.75 C
+ATOM 1088 CG2 VAL A 159 72.472 0.380 -20.694 1.00 39.97 C
+ATOM 1089 N HIS A 160 72.950 -4.254 -21.161 1.00 55.36 N
+ATOM 1090 CA HIS A 160 73.394 -5.566 -20.708 1.00 56.28 C
+ATOM 1091 C HIS A 160 74.901 -5.737 -20.756 1.00 57.26 C
+ATOM 1092 O HIS A 160 75.406 -6.725 -20.241 1.00 59.94 O
+ATOM 1093 CB HIS A 160 72.782 -6.687 -21.539 1.00 53.93 C
+ATOM 1094 CG HIS A 160 71.297 -6.682 -21.557 1.00 54.34 C
+ATOM 1095 ND1 HIS A 160 70.574 -5.782 -22.304 1.00 56.63 N
+ATOM 1096 CD2 HIS A 160 70.391 -7.486 -20.950 1.00 55.41 C
+ATOM 1097 CE1 HIS A 160 69.284 -6.035 -22.163 1.00 57.79 C
+ATOM 1098 NE2 HIS A 160 69.145 -7.063 -21.346 1.00 54.27 N
+ATOM 1099 N SER A 161 75.625 -4.814 -21.378 1.00 57.02 N
+ATOM 1100 CA SER A 161 77.070 -4.972 -21.442 1.00 59.63 C
+ATOM 1101 C SER A 161 77.620 -4.868 -20.031 1.00 61.07 C
+ATOM 1102 O SER A 161 76.895 -4.474 -19.118 1.00 63.84 O
+ATOM 1103 CB SER A 161 77.700 -3.911 -22.356 1.00 62.63 C
+ATOM 1104 OG SER A 161 77.388 -2.584 -21.954 1.00 69.49 O
+ATOM 1105 N GLY A 162 78.885 -5.241 -19.843 1.00 61.74 N
+ATOM 1106 CA GLY A 162 79.489 -5.184 -18.525 1.00 61.11 C
+ATOM 1107 C GLY A 162 78.619 -5.796 -17.434 1.00 62.45 C
+ATOM 1108 O GLY A 162 77.911 -6.777 -17.655 1.00 61.38 O
+ATOM 1109 N SER A 163 78.678 -5.208 -16.246 1.00 63.68 N
+ATOM 1110 CA SER A 163 77.906 -5.676 -15.102 1.00 64.46 C
+ATOM 1111 C SER A 163 76.384 -5.568 -15.262 1.00 63.98 C
+ATOM 1112 O SER A 163 75.629 -6.099 -14.437 1.00 60.36 O
+ATOM 1113 CB SER A 163 78.321 -4.885 -13.865 1.00 66.40 C
+ATOM 1114 OG SER A 163 77.469 -5.199 -12.777 1.00 71.79 O
+ATOM 1115 N ALA A 164 75.943 -4.872 -16.310 1.00 63.90 N
+ATOM 1116 CA ALA A 164 74.521 -4.664 -16.570 1.00 64.03 C
+ATOM 1117 C ALA A 164 73.930 -3.889 -15.419 1.00 65.23 C
+ATOM 1118 O ALA A 164 72.853 -4.221 -14.906 1.00 64.22 O
+ATOM 1119 CB ALA A 164 73.797 -5.972 -16.710 1.00 65.28 C
+ATOM 1120 N THR A 165 74.649 -2.851 -15.017 1.00 65.10 N
+ATOM 1121 CA THR A 165 74.208 -2.009 -13.925 1.00 66.70 C
+ATOM 1122 C THR A 165 74.591 -0.552 -14.149 1.00 65.70 C
+ATOM 1123 O THR A 165 75.086 -0.180 -15.211 1.00 64.21 O
+ATOM 1124 CB THR A 165 74.791 -2.477 -12.579 1.00 67.09 C
+ATOM 1125 OG1 THR A 165 76.224 -2.536 -12.662 1.00 70.16 O
+ATOM 1126 CG2 THR A 165 74.248 -3.832 -12.232 1.00 68.17 C
+ATOM 1127 N LEU A 166 74.371 0.257 -13.120 1.00 64.26 N
+ATOM 1128 CA LEU A 166 74.641 1.669 -13.191 1.00 61.67 C
+ATOM 1129 C LEU A 166 75.930 2.084 -13.892 1.00 62.08 C
+ATOM 1130 O LEU A 166 75.873 2.849 -14.858 1.00 61.93 O
+ATOM 1131 CB LEU A 166 74.589 2.279 -11.796 1.00 57.00 C
+ATOM 1132 CG LEU A 166 74.342 3.777 -11.907 1.00 53.33 C
+ATOM 1133 CD1 LEU A 166 72.989 4.080 -12.525 1.00 50.04 C
+ATOM 1134 CD2 LEU A 166 74.416 4.345 -10.555 1.00 52.62 C
+ATOM 1135 N LYS A 167 77.085 1.606 -13.432 1.00 61.72 N
+ATOM 1136 CA LYS A 167 78.328 2.022 -14.078 1.00 62.35 C
+ATOM 1137 C LYS A 167 78.236 1.743 -15.575 1.00 61.56 C
+ATOM 1138 O LYS A 167 78.745 2.493 -16.397 1.00 61.70 O
+ATOM 1139 CB LYS A 167 79.551 1.338 -13.448 1.00 62.67 C
+ATOM 1140 CG LYS A 167 79.408 -0.159 -13.167 1.00 71.96 C
+ATOM 1141 CD LYS A 167 79.086 -0.499 -11.685 1.00 75.18 C
+ATOM 1142 CE LYS A 167 77.610 -0.260 -11.316 1.00 76.94 C
+ATOM 1143 NZ LYS A 167 77.307 -0.560 -9.876 1.00 76.71 N
+ATOM 1144 N ASP A 168 77.543 0.678 -15.934 1.00 60.58 N
+ATOM 1145 CA ASP A 168 77.378 0.349 -17.336 1.00 60.65 C
+ATOM 1146 C ASP A 168 76.447 1.342 -18.034 1.00 60.19 C
+ATOM 1147 O ASP A 168 76.809 1.934 -19.055 1.00 60.17 O
+ATOM 1148 CB ASP A 168 76.824 -1.065 -17.460 1.00 62.54 C
+ATOM 1149 CG ASP A 168 77.767 -2.092 -16.901 1.00 65.21 C
+ATOM 1150 OD1 ASP A 168 78.821 -2.302 -17.541 1.00 65.37 O
+ATOM 1151 OD2 ASP A 168 77.468 -2.668 -15.826 1.00 64.98 O
+ATOM 1152 N ALA A 169 75.249 1.518 -17.484 1.00 58.37 N
+ATOM 1153 CA ALA A 169 74.277 2.429 -18.058 1.00 57.03 C
+ATOM 1154 C ALA A 169 74.898 3.802 -18.130 1.00 57.54 C
+ATOM 1155 O ALA A 169 74.631 4.572 -19.046 1.00 57.83 O
+ATOM 1156 CB ALA A 169 73.033 2.469 -17.212 1.00 57.84 C
+ATOM 1157 N CYS A 170 75.753 4.099 -17.167 1.00 57.96 N
+ATOM 1158 CA CYS A 170 76.414 5.386 -17.122 1.00 60.24 C
+ATOM 1159 C CYS A 170 77.466 5.534 -18.221 1.00 59.41 C
+ATOM 1160 O CYS A 170 77.523 6.538 -18.925 1.00 58.38 O
+ATOM 1161 CB CYS A 170 77.057 5.566 -15.760 1.00 62.38 C
+ATOM 1162 SG CYS A 170 77.555 7.257 -15.476 1.00 75.35 S
+ATOM 1163 N ASN A 171 78.306 4.521 -18.355 1.00 60.62 N
+ATOM 1164 CA ASN A 171 79.347 4.516 -19.368 1.00 60.69 C
+ATOM 1165 C ASN A 171 78.720 4.602 -20.747 1.00 59.38 C
+ATOM 1166 O ASN A 171 79.270 5.218 -21.656 1.00 56.76 O
+ATOM 1167 CB ASN A 171 80.162 3.229 -19.253 1.00 64.95 C
+ATOM 1168 CG ASN A 171 80.826 2.844 -20.561 1.00 71.53 C
+ATOM 1169 OD1 ASN A 171 81.916 3.327 -20.886 1.00 74.24 O
+ATOM 1170 ND2 ASN A 171 80.159 1.973 -21.336 1.00 75.04 N
+ATOM 1171 N GLU A 172 77.560 3.973 -20.890 1.00 59.52 N
+ATOM 1172 CA GLU A 172 76.843 3.948 -22.150 1.00 61.28 C
+ATOM 1173 C GLU A 172 76.227 5.297 -22.511 1.00 60.89 C
+ATOM 1174 O GLU A 172 76.291 5.719 -23.662 1.00 60.27 O
+ATOM 1175 CB GLU A 172 75.772 2.869 -22.088 1.00 65.87 C
+ATOM 1176 CG GLU A 172 75.667 2.021 -23.352 1.00 74.78 C
+ATOM 1177 CD GLU A 172 77.033 1.608 -23.933 1.00 80.93 C
+ATOM 1178 OE1 GLU A 172 77.863 0.987 -23.204 1.00 80.79 O
+ATOM 1179 OE2 GLU A 172 77.260 1.912 -25.140 1.00 83.75 O
+ATOM 1180 N ALA A 173 75.629 5.974 -21.531 1.00 60.87 N
+ATOM 1181 CA ALA A 173 75.028 7.292 -21.764 1.00 59.87 C
+ATOM 1182 C ALA A 173 76.116 8.240 -22.218 1.00 59.86 C
+ATOM 1183 O ALA A 173 75.956 8.969 -23.193 1.00 59.94 O
+ATOM 1184 CB ALA A 173 74.395 7.828 -20.494 1.00 57.99 C
+ATOM 1185 N LEU A 174 77.224 8.226 -21.489 1.00 60.26 N
+ATOM 1186 CA LEU A 174 78.351 9.072 -21.816 1.00 61.22 C
+ATOM 1187 C LEU A 174 78.804 8.852 -23.265 1.00 61.55 C
+ATOM 1188 O LEU A 174 79.012 9.824 -24.002 1.00 63.41 O
+ATOM 1189 CB LEU A 174 79.502 8.807 -20.843 1.00 62.63 C
+ATOM 1190 CG LEU A 174 80.266 10.064 -20.397 1.00 65.64 C
+ATOM 1191 CD1 LEU A 174 79.268 11.101 -19.826 1.00 64.42 C
+ATOM 1192 CD2 LEU A 174 81.321 9.690 -19.366 1.00 61.54 C
+ATOM 1193 N ARG A 175 78.951 7.595 -23.687 1.00 60.06 N
+ATOM 1194 CA ARG A 175 79.360 7.318 -25.066 1.00 57.52 C
+ATOM 1195 C ARG A 175 78.363 7.927 -26.013 1.00 55.42 C
+ATOM 1196 O ARG A 175 78.739 8.500 -27.021 1.00 53.14 O
+ATOM 1197 CB ARG A 175 79.438 5.825 -25.329 1.00 60.47 C
+ATOM 1198 CG ARG A 175 80.605 5.169 -24.643 1.00 66.12 C
+ATOM 1199 CD ARG A 175 80.510 3.680 -24.763 1.00 70.43 C
+ATOM 1200 NE ARG A 175 80.502 3.269 -26.159 1.00 77.95 N
+ATOM 1201 CZ ARG A 175 80.135 2.056 -26.563 1.00 82.79 C
+ATOM 1202 NH1 ARG A 175 79.745 1.154 -25.664 1.00 83.98 N
+ATOM 1203 NH2 ARG A 175 80.167 1.738 -27.856 1.00 85.11 N
+ATOM 1204 N ASP A 176 77.083 7.794 -25.674 1.00 54.91 N
+ATOM 1205 CA ASP A 176 76.014 8.353 -26.486 1.00 52.10 C
+ATOM 1206 C ASP A 176 76.210 9.863 -26.576 1.00 53.09 C
+ATOM 1207 O ASP A 176 76.283 10.425 -27.666 1.00 54.43 O
+ATOM 1208 CB ASP A 176 74.648 8.055 -25.862 1.00 48.22 C
+ATOM 1209 CG ASP A 176 73.488 8.589 -26.701 1.00 49.58 C
+ATOM 1210 OD1 ASP A 176 73.736 9.339 -27.664 1.00 49.06 O
+ATOM 1211 OD2 ASP A 176 72.319 8.272 -26.405 1.00 46.50 O
+ATOM 1212 N TRP A 177 76.321 10.526 -25.435 1.00 53.49 N
+ATOM 1213 CA TRP A 177 76.466 11.968 -25.463 1.00 54.69 C
+ATOM 1214 C TRP A 177 77.605 12.401 -26.317 1.00 54.72 C
+ATOM 1215 O TRP A 177 77.441 13.262 -27.181 1.00 55.63 O
+ATOM 1216 CB TRP A 177 76.681 12.532 -24.075 1.00 55.47 C
+ATOM 1217 CG TRP A 177 76.718 14.027 -24.028 1.00 55.71 C
+ATOM 1218 CD1 TRP A 177 75.841 14.895 -24.626 1.00 57.49 C
+ATOM 1219 CD2 TRP A 177 77.597 14.830 -23.234 1.00 56.81 C
+ATOM 1220 NE1 TRP A 177 76.116 16.196 -24.239 1.00 58.60 N
+ATOM 1221 CE2 TRP A 177 77.190 16.179 -23.386 1.00 58.32 C
+ATOM 1222 CE3 TRP A 177 78.692 14.541 -22.402 1.00 57.78 C
+ATOM 1223 CZ2 TRP A 177 77.838 17.229 -22.737 1.00 58.42 C
+ATOM 1224 CZ3 TRP A 177 79.336 15.587 -21.757 1.00 56.32 C
+ATOM 1225 CH2 TRP A 177 78.906 16.915 -21.929 1.00 58.90 C
+ATOM 1226 N SER A 178 78.758 11.790 -26.073 1.00 54.71 N
+ATOM 1227 CA SER A 178 79.982 12.135 -26.785 1.00 54.54 C
+ATOM 1228 C SER A 178 79.862 12.011 -28.268 1.00 51.91 C
+ATOM 1229 O SER A 178 80.847 12.081 -28.961 1.00 54.49 O
+ATOM 1230 CB SER A 178 81.140 11.259 -26.333 1.00 56.33 C
+ATOM 1231 OG SER A 178 80.961 9.949 -26.813 1.00 58.84 O
+ATOM 1232 N GLY A 179 78.658 11.804 -28.758 1.00 51.04 N
+ATOM 1233 CA GLY A 179 78.484 11.694 -30.180 1.00 49.81 C
+ATOM 1234 C GLY A 179 77.251 12.470 -30.531 1.00 52.83 C
+ATOM 1235 O GLY A 179 76.872 12.536 -31.694 1.00 54.04 O
+ATOM 1236 N SER A 180 76.608 13.063 -29.528 1.00 55.08 N
+ATOM 1237 CA SER A 180 75.398 13.825 -29.803 1.00 58.05 C
+ATOM 1238 C SER A 180 75.197 15.103 -29.015 1.00 58.95 C
+ATOM 1239 O SER A 180 74.094 15.670 -29.025 1.00 58.59 O
+ATOM 1240 CB SER A 180 74.158 12.929 -29.659 1.00 58.33 C
+ATOM 1241 OG SER A 180 74.237 12.095 -28.521 1.00 56.39 O
+ATOM 1242 N TYR A 181 76.253 15.578 -28.361 1.00 60.70 N
+ATOM 1243 CA TYR A 181 76.151 16.814 -27.581 1.00 63.26 C
+ATOM 1244 C TYR A 181 75.662 18.014 -28.385 1.00 62.26 C
+ATOM 1245 O TYR A 181 75.203 18.993 -27.820 1.00 62.73 O
+ATOM 1246 CB TYR A 181 77.482 17.168 -26.935 1.00 63.33 C
+ATOM 1247 CG TYR A 181 78.638 17.366 -27.895 1.00 67.59 C
+ATOM 1248 CD1 TYR A 181 79.604 16.379 -28.041 1.00 70.23 C
+ATOM 1249 CD2 TYR A 181 78.846 18.589 -28.542 1.00 67.60 C
+ATOM 1250 CE1 TYR A 181 80.756 16.601 -28.783 1.00 72.87 C
+ATOM 1251 CE2 TYR A 181 79.998 18.825 -29.285 1.00 68.93 C
+ATOM 1252 CZ TYR A 181 80.954 17.824 -29.394 1.00 72.14 C
+ATOM 1253 OH TYR A 181 82.142 18.028 -30.060 1.00 73.66 O
+ATOM 1254 N GLU A 182 75.768 17.940 -29.700 1.00 61.76 N
+ATOM 1255 CA GLU A 182 75.311 19.022 -30.544 1.00 62.62 C
+ATOM 1256 C GLU A 182 73.807 19.270 -30.346 1.00 61.35 C
+ATOM 1257 O GLU A 182 73.347 20.398 -30.446 1.00 60.73 O
+ATOM 1258 CB GLU A 182 75.619 18.670 -31.998 1.00 67.94 C
+ATOM 1259 CG GLU A 182 75.461 19.786 -33.029 1.00 75.28 C
+ATOM 1260 CD GLU A 182 76.204 19.466 -34.342 1.00 83.01 C
+ATOM 1261 OE1 GLU A 182 77.469 19.423 -34.334 1.00 83.34 O
+ATOM 1262 OE2 GLU A 182 75.526 19.243 -35.380 1.00 86.01 O
+ATOM 1263 N THR A 183 73.035 18.231 -30.045 1.00 61.08 N
+ATOM 1264 CA THR A 183 71.588 18.412 -29.861 1.00 59.74 C
+ATOM 1265 C THR A 183 71.044 17.850 -28.567 1.00 58.29 C
+ATOM 1266 O THR A 183 69.857 18.018 -28.239 1.00 57.54 O
+ATOM 1267 CB THR A 183 70.774 17.745 -30.976 1.00 59.12 C
+ATOM 1268 OG1 THR A 183 71.554 16.702 -31.581 1.00 54.00 O
+ATOM 1269 CG2 THR A 183 70.312 18.780 -31.983 1.00 58.66 C
+ATOM 1270 N ALA A 184 71.902 17.178 -27.825 1.00 54.30 N
+ATOM 1271 CA ALA A 184 71.424 16.591 -26.608 1.00 52.71 C
+ATOM 1272 C ALA A 184 72.282 16.933 -25.433 1.00 50.97 C
+ATOM 1273 O ALA A 184 73.507 16.898 -25.506 1.00 49.86 O
+ATOM 1274 CB ALA A 184 71.334 15.090 -26.771 1.00 54.07 C
+ATOM 1275 N HIS A 185 71.619 17.291 -24.343 1.00 51.73 N
+ATOM 1276 CA HIS A 185 72.318 17.607 -23.119 1.00 52.01 C
+ATOM 1277 C HIS A 185 72.327 16.331 -22.272 1.00 51.68 C
+ATOM 1278 O HIS A 185 71.369 15.557 -22.231 1.00 50.21 O
+ATOM 1279 CB HIS A 185 71.642 18.766 -22.365 1.00 50.96 C
+ATOM 1280 CG HIS A 185 72.140 18.935 -20.959 1.00 54.00 C
+ATOM 1281 ND1 HIS A 185 73.420 19.357 -20.667 1.00 56.01 N
+ATOM 1282 CD2 HIS A 185 71.558 18.653 -19.767 1.00 54.60 C
+ATOM 1283 CE1 HIS A 185 73.608 19.324 -19.358 1.00 55.09 C
+ATOM 1284 NE2 HIS A 185 72.493 18.900 -18.789 1.00 56.57 N
+ATOM 1285 N TYR A 186 73.453 16.096 -21.633 1.00 52.99 N
+ATOM 1286 CA TYR A 186 73.592 14.948 -20.784 1.00 54.07 C
+ATOM 1287 C TYR A 186 73.207 15.413 -19.364 1.00 55.69 C
+ATOM 1288 O TYR A 186 73.826 16.317 -18.799 1.00 56.48 O
+ATOM 1289 CB TYR A 186 75.036 14.468 -20.862 1.00 52.55 C
+ATOM 1290 CG TYR A 186 75.349 13.368 -19.914 1.00 53.59 C
+ATOM 1291 CD1 TYR A 186 76.524 13.384 -19.191 1.00 58.52 C
+ATOM 1292 CD2 TYR A 186 74.455 12.333 -19.697 1.00 53.70 C
+ATOM 1293 CE1 TYR A 186 76.807 12.405 -18.265 1.00 60.85 C
+ATOM 1294 CE2 TYR A 186 74.729 11.340 -18.767 1.00 57.66 C
+ATOM 1295 CZ TYR A 186 75.911 11.387 -18.052 1.00 59.56 C
+ATOM 1296 OH TYR A 186 76.211 10.436 -17.109 1.00 61.72 O
+ATOM 1297 N MET A 187 72.160 14.808 -18.813 1.00 56.35 N
+ATOM 1298 CA MET A 187 71.662 15.131 -17.484 1.00 57.79 C
+ATOM 1299 C MET A 187 72.436 14.375 -16.423 1.00 60.37 C
+ATOM 1300 O MET A 187 72.267 13.166 -16.264 1.00 62.82 O
+ATOM 1301 CB MET A 187 70.202 14.730 -17.368 1.00 59.25 C
+ATOM 1302 CG MET A 187 69.488 15.329 -16.199 1.00 60.96 C
+ATOM 1303 SD MET A 187 69.010 16.991 -16.640 1.00 67.40 S
+ATOM 1304 CE MET A 187 67.412 16.687 -17.423 1.00 57.53 C
+ATOM 1305 N LEU A 188 73.275 15.078 -15.682 1.00 63.26 N
+ATOM 1306 CA LEU A 188 74.041 14.426 -14.643 1.00 66.37 C
+ATOM 1307 C LEU A 188 73.250 14.308 -13.326 1.00 68.79 C
+ATOM 1308 O LEU A 188 72.594 15.258 -12.887 1.00 66.05 O
+ATOM 1309 CB LEU A 188 75.341 15.180 -14.400 1.00 67.54 C
+ATOM 1310 CG LEU A 188 76.344 14.211 -13.795 1.00 69.13 C
+ATOM 1311 CD1 LEU A 188 76.805 13.271 -14.912 1.00 69.44 C
+ATOM 1312 CD2 LEU A 188 77.499 14.949 -13.162 1.00 69.39 C
+ATOM 1313 N GLY A 189 73.321 13.126 -12.710 1.00 72.63 N
+ATOM 1314 CA GLY A 189 72.622 12.879 -11.461 1.00 78.04 C
+ATOM 1315 C GLY A 189 73.494 13.228 -10.267 1.00 82.37 C
+ATOM 1316 O GLY A 189 73.085 13.958 -9.357 1.00 84.42 O
+ATOM 1317 N THR A 190 74.711 12.703 -10.270 1.00 83.56 N
+ATOM 1318 CA THR A 190 75.648 12.953 -9.191 1.00 84.77 C
+ATOM 1319 C THR A 190 76.227 14.360 -9.377 1.00 87.44 C
+ATOM 1320 O THR A 190 75.978 15.015 -10.407 1.00 87.44 O
+ATOM 1321 CB THR A 190 76.796 11.914 -9.232 1.00 84.30 C
+ATOM 1322 OG1 THR A 190 77.643 12.076 -8.086 1.00 86.30 O
+ATOM 1323 CG2 THR A 190 77.628 12.084 -10.511 1.00 81.25 C
+ATOM 1324 N ALA A 191 76.983 14.818 -8.370 1.00 88.36 N
+ATOM 1325 CA ALA A 191 77.657 16.129 -8.386 1.00 86.76 C
+ATOM 1326 C ALA A 191 79.109 15.869 -8.787 1.00 84.87 C
+ATOM 1327 O ALA A 191 79.906 16.799 -8.945 1.00 85.30 O
+ATOM 1328 CB ALA A 191 77.607 16.784 -6.989 1.00 85.03 C
+ATOM 1329 N ALA A 192 79.420 14.584 -8.959 1.00 82.17 N
+ATOM 1330 CA ALA A 192 80.756 14.122 -9.307 1.00 79.59 C
+ATOM 1331 C ALA A 192 80.923 13.820 -10.789 1.00 78.12 C
+ATOM 1332 O ALA A 192 80.730 12.685 -11.233 1.00 79.23 O
+ATOM 1333 CB ALA A 192 81.090 12.880 -8.485 1.00 78.80 C
+ATOM 1334 N GLY A 193 81.293 14.834 -11.557 1.00 75.20 N
+ATOM 1335 CA GLY A 193 81.482 14.620 -12.976 1.00 73.03 C
+ATOM 1336 C GLY A 193 82.513 15.588 -13.491 1.00 72.34 C
+ATOM 1337 O GLY A 193 83.088 16.334 -12.698 1.00 73.64 O
+ATOM 1338 N PRO A 194 82.770 15.616 -14.806 1.00 70.69 N
+ATOM 1339 CA PRO A 194 83.766 16.549 -15.330 1.00 69.29 C
+ATOM 1340 C PRO A 194 83.246 17.981 -15.193 1.00 68.93 C
+ATOM 1341 O PRO A 194 82.037 18.194 -15.035 1.00 69.27 O
+ATOM 1342 CB PRO A 194 83.868 16.137 -16.786 1.00 69.13 C
+ATOM 1343 CG PRO A 194 82.429 15.842 -17.113 1.00 70.38 C
+ATOM 1344 CD PRO A 194 81.997 15.010 -15.906 1.00 70.70 C
+ATOM 1345 N HIS A 195 84.160 18.950 -15.256 1.00 66.98 N
+ATOM 1346 CA HIS A 195 83.816 20.376 -15.188 1.00 62.37 C
+ATOM 1347 C HIS A 195 83.042 20.661 -16.466 1.00 60.95 C
+ATOM 1348 O HIS A 195 83.359 20.118 -17.519 1.00 62.44 O
+ATOM 1349 CB HIS A 195 85.092 21.217 -15.163 1.00 61.15 C
+ATOM 1350 CG HIS A 195 84.867 22.674 -14.911 1.00 62.14 C
+ATOM 1351 ND1 HIS A 195 84.512 23.170 -13.674 1.00 62.84 N
+ATOM 1352 CD2 HIS A 195 84.943 23.744 -15.739 1.00 59.87 C
+ATOM 1353 CE1 HIS A 195 84.378 24.483 -13.753 1.00 62.54 C
+ATOM 1354 NE2 HIS A 195 84.633 24.856 -14.995 1.00 61.18 N
+ATOM 1355 N PRO A 196 82.049 21.546 -16.409 1.00 59.36 N
+ATOM 1356 CA PRO A 196 81.597 22.304 -15.249 1.00 59.97 C
+ATOM 1357 C PRO A 196 80.479 21.666 -14.420 1.00 62.54 C
+ATOM 1358 O PRO A 196 79.829 22.342 -13.629 1.00 65.01 O
+ATOM 1359 CB PRO A 196 81.159 23.603 -15.888 1.00 57.52 C
+ATOM 1360 CG PRO A 196 80.508 23.120 -17.121 1.00 55.99 C
+ATOM 1361 CD PRO A 196 81.477 22.106 -17.645 1.00 57.13 C
+ATOM 1362 N TYR A 197 80.261 20.367 -14.564 1.00 64.32 N
+ATOM 1363 CA TYR A 197 79.169 19.719 -13.831 1.00 63.59 C
+ATOM 1364 C TYR A 197 79.074 19.954 -12.319 1.00 64.13 C
+ATOM 1365 O TYR A 197 78.076 20.495 -11.832 1.00 65.40 O
+ATOM 1366 CB TYR A 197 79.133 18.215 -14.161 1.00 59.66 C
+ATOM 1367 CG TYR A 197 78.413 17.941 -15.477 1.00 58.40 C
+ATOM 1368 CD1 TYR A 197 77.043 18.142 -15.590 1.00 54.21 C
+ATOM 1369 CD2 TYR A 197 79.107 17.552 -16.619 1.00 58.44 C
+ATOM 1370 CE1 TYR A 197 76.381 17.973 -16.783 1.00 52.90 C
+ATOM 1371 CE2 TYR A 197 78.443 17.380 -17.830 1.00 56.94 C
+ATOM 1372 CZ TYR A 197 77.077 17.595 -17.897 1.00 55.86 C
+ATOM 1373 OH TYR A 197 76.395 17.425 -19.085 1.00 59.61 O
+ATOM 1374 N PRO A 198 80.109 19.588 -11.557 1.00 63.85 N
+ATOM 1375 CA PRO A 198 79.971 19.822 -10.122 1.00 62.00 C
+ATOM 1376 C PRO A 198 79.521 21.234 -9.772 1.00 60.79 C
+ATOM 1377 O PRO A 198 78.863 21.431 -8.760 1.00 63.14 O
+ATOM 1378 CB PRO A 198 81.355 19.480 -9.584 1.00 61.53 C
+ATOM 1379 CG PRO A 198 82.233 19.864 -10.693 1.00 64.29 C
+ATOM 1380 CD PRO A 198 81.509 19.303 -11.898 1.00 64.35 C
+ATOM 1381 N THR A 199 79.857 22.223 -10.590 1.00 58.44 N
+ATOM 1382 CA THR A 199 79.422 23.585 -10.278 1.00 57.34 C
+ATOM 1383 C THR A 199 77.933 23.717 -10.508 1.00 57.53 C
+ATOM 1384 O THR A 199 77.179 24.091 -9.616 1.00 57.81 O
+ATOM 1385 CB THR A 199 80.095 24.618 -11.160 1.00 56.32 C
+ATOM 1386 OG1 THR A 199 81.491 24.628 -10.877 1.00 60.82 O
+ATOM 1387 CG2 THR A 199 79.509 26.003 -10.907 1.00 54.86 C
+ATOM 1388 N ILE A 200 77.528 23.429 -11.735 1.00 56.81 N
+ATOM 1389 CA ILE A 200 76.139 23.496 -12.120 1.00 56.09 C
+ATOM 1390 C ILE A 200 75.294 22.747 -11.096 1.00 55.69 C
+ATOM 1391 O ILE A 200 74.279 23.246 -10.592 1.00 52.74 O
+ATOM 1392 CB ILE A 200 75.970 22.871 -13.488 1.00 57.26 C
+ATOM 1393 CG1 ILE A 200 76.795 23.669 -14.501 1.00 59.23 C
+ATOM 1394 CG2 ILE A 200 74.505 22.831 -13.857 1.00 56.22 C
+ATOM 1395 CD1 ILE A 200 76.855 23.046 -15.878 1.00 61.50 C
+ATOM 1396 N VAL A 201 75.731 21.543 -10.771 1.00 55.13 N
+ATOM 1397 CA VAL A 201 75.001 20.758 -9.807 1.00 56.75 C
+ATOM 1398 C VAL A 201 74.963 21.426 -8.441 1.00 57.25 C
+ATOM 1399 O VAL A 201 73.894 21.569 -7.868 1.00 60.48 O
+ATOM 1400 CB VAL A 201 75.588 19.350 -9.691 1.00 57.85 C
+ATOM 1401 CG1 VAL A 201 75.088 18.677 -8.411 1.00 56.40 C
+ATOM 1402 CG2 VAL A 201 75.183 18.534 -10.935 1.00 58.45 C
+ATOM 1403 N ARG A 202 76.111 21.843 -7.915 1.00 57.23 N
+ATOM 1404 CA ARG A 202 76.124 22.491 -6.611 1.00 55.81 C
+ATOM 1405 C ARG A 202 75.229 23.701 -6.674 1.00 54.52 C
+ATOM 1406 O ARG A 202 74.582 24.056 -5.702 1.00 52.80 O
+ATOM 1407 CB ARG A 202 77.536 22.935 -6.219 1.00 58.67 C
+ATOM 1408 CG ARG A 202 78.498 21.790 -5.847 1.00 66.85 C
+ATOM 1409 CD ARG A 202 79.755 22.308 -5.134 1.00 72.33 C
+ATOM 1410 NE ARG A 202 80.670 23.012 -6.032 1.00 77.77 N
+ATOM 1411 CZ ARG A 202 81.717 22.439 -6.626 1.00 80.96 C
+ATOM 1412 NH1 ARG A 202 81.981 21.147 -6.400 1.00 80.96 N
+ATOM 1413 NH2 ARG A 202 82.483 23.146 -7.465 1.00 80.34 N
+ATOM 1414 N GLU A 203 75.166 24.310 -7.848 1.00 53.93 N
+ATOM 1415 CA GLU A 203 74.387 25.511 -8.017 1.00 53.82 C
+ATOM 1416 C GLU A 203 72.906 25.273 -8.009 1.00 54.22 C
+ATOM 1417 O GLU A 203 72.161 26.061 -7.430 1.00 55.27 O
+ATOM 1418 CB GLU A 203 74.789 26.228 -9.305 1.00 56.38 C
+ATOM 1419 CG GLU A 203 74.353 27.696 -9.367 1.00 60.72 C
+ATOM 1420 CD GLU A 203 75.135 28.629 -8.408 1.00 66.53 C
+ATOM 1421 OE1 GLU A 203 74.785 29.831 -8.387 1.00 67.91 O
+ATOM 1422 OE2 GLU A 203 76.082 28.191 -7.680 1.00 66.18 O
+ATOM 1423 N PHE A 204 72.461 24.201 -8.659 1.00 54.42 N
+ATOM 1424 CA PHE A 204 71.022 23.905 -8.700 1.00 52.76 C
+ATOM 1425 C PHE A 204 70.569 23.134 -7.447 1.00 52.71 C
+ATOM 1426 O PHE A 204 69.543 22.481 -7.443 1.00 53.64 O
+ATOM 1427 CB PHE A 204 70.677 23.134 -9.987 1.00 47.68 C
+ATOM 1428 CG PHE A 204 70.899 23.930 -11.257 1.00 46.50 C
+ATOM 1429 CD1 PHE A 204 71.296 23.302 -12.433 1.00 44.87 C
+ATOM 1430 CD2 PHE A 204 70.720 25.309 -11.282 1.00 44.35 C
+ATOM 1431 CE1 PHE A 204 71.511 24.038 -13.601 1.00 40.99 C
+ATOM 1432 CE2 PHE A 204 70.936 26.036 -12.447 1.00 38.75 C
+ATOM 1433 CZ PHE A 204 71.330 25.395 -13.597 1.00 39.58 C
+ATOM 1434 N GLN A 205 71.341 23.243 -6.375 1.00 53.18 N
+ATOM 1435 CA GLN A 205 71.020 22.584 -5.125 1.00 53.11 C
+ATOM 1436 C GLN A 205 71.171 23.536 -3.954 1.00 51.67 C
+ATOM 1437 O GLN A 205 70.814 23.190 -2.838 1.00 50.53 O
+ATOM 1438 CB GLN A 205 71.971 21.431 -4.879 1.00 58.08 C
+ATOM 1439 CG GLN A 205 71.912 20.339 -5.889 1.00 68.69 C
+ATOM 1440 CD GLN A 205 70.778 19.353 -5.631 1.00 75.76 C
+ATOM 1441 OE1 GLN A 205 70.751 18.268 -6.236 1.00 79.54 O
+ATOM 1442 NE2 GLN A 205 69.833 19.717 -4.736 1.00 75.03 N
+ATOM 1443 N ARG A 206 71.694 24.732 -4.207 1.00 51.73 N
+ATOM 1444 CA ARG A 206 71.974 25.690 -3.137 1.00 51.92 C
+ATOM 1445 C ARG A 206 70.805 26.415 -2.480 1.00 51.59 C
+ATOM 1446 O ARG A 206 71.006 27.094 -1.460 1.00 53.65 O
+ATOM 1447 CB ARG A 206 72.988 26.725 -3.621 1.00 49.16 C
+ATOM 1448 CG ARG A 206 72.377 27.662 -4.594 1.00 52.39 C
+ATOM 1449 CD ARG A 206 73.349 28.647 -5.157 1.00 51.47 C
+ATOM 1450 NE ARG A 206 73.973 29.440 -4.117 1.00 52.89 N
+ATOM 1451 CZ ARG A 206 75.216 29.240 -3.719 1.00 54.65 C
+ATOM 1452 NH1 ARG A 206 75.929 28.275 -4.293 1.00 55.02 N
+ATOM 1453 NH2 ARG A 206 75.743 29.996 -2.765 1.00 51.91 N
+ATOM 1454 N MET A 207 69.600 26.267 -3.036 1.00 50.20 N
+ATOM 1455 CA MET A 207 68.412 26.922 -2.481 1.00 47.63 C
+ATOM 1456 C MET A 207 68.103 26.504 -1.056 1.00 45.77 C
+ATOM 1457 O MET A 207 67.522 27.272 -0.302 1.00 45.64 O
+ATOM 1458 CB MET A 207 67.176 26.687 -3.361 1.00 49.67 C
+ATOM 1459 CG MET A 207 66.803 25.226 -3.613 1.00 55.32 C
+ATOM 1460 SD MET A 207 67.832 24.365 -4.871 1.00 64.94 S
+ATOM 1461 CE MET A 207 67.889 25.548 -6.282 1.00 56.83 C
+ATOM 1462 N ILE A 208 68.489 25.295 -0.671 1.00 45.68 N
+ATOM 1463 CA ILE A 208 68.230 24.851 0.698 1.00 46.01 C
+ATOM 1464 C ILE A 208 68.841 25.858 1.667 1.00 48.01 C
+ATOM 1465 O ILE A 208 68.148 26.383 2.553 1.00 46.46 O
+ATOM 1466 CB ILE A 208 68.833 23.461 0.986 1.00 44.72 C
+ATOM 1467 CG1 ILE A 208 68.230 22.424 0.028 1.00 44.66 C
+ATOM 1468 CG2 ILE A 208 68.578 23.087 2.445 1.00 42.57 C
+ATOM 1469 CD1 ILE A 208 68.847 21.028 0.113 1.00 44.11 C
+ATOM 1470 N GLY A 209 70.138 26.127 1.476 1.00 49.75 N
+ATOM 1471 CA GLY A 209 70.851 27.084 2.305 1.00 48.83 C
+ATOM 1472 C GLY A 209 70.343 28.501 2.074 1.00 48.78 C
+ATOM 1473 O GLY A 209 70.218 29.290 3.016 1.00 49.29 O
+ATOM 1474 N GLU A 210 70.046 28.840 0.823 1.00 47.13 N
+ATOM 1475 CA GLU A 210 69.544 30.170 0.526 1.00 46.64 C
+ATOM 1476 C GLU A 210 68.216 30.419 1.247 1.00 47.30 C
+ATOM 1477 O GLU A 210 68.027 31.470 1.881 1.00 47.46 O
+ATOM 1478 CB GLU A 210 69.385 30.334 -0.970 1.00 45.06 C
+ATOM 1479 CG GLU A 210 70.680 30.179 -1.695 1.00 48.34 C
+ATOM 1480 CD GLU A 210 70.508 30.325 -3.178 1.00 52.70 C
+ATOM 1481 OE1 GLU A 210 69.411 29.975 -3.667 1.00 57.34 O
+ATOM 1482 OE2 GLU A 210 71.459 30.768 -3.865 1.00 55.75 O
+ATOM 1483 N GLU A 211 67.301 29.458 1.172 1.00 45.21 N
+ATOM 1484 CA GLU A 211 66.030 29.614 1.861 1.00 46.10 C
+ATOM 1485 C GLU A 211 66.278 29.717 3.353 1.00 48.21 C
+ATOM 1486 O GLU A 211 65.757 30.612 4.018 1.00 48.09 O
+ATOM 1487 CB GLU A 211 65.126 28.432 1.577 1.00 45.18 C
+ATOM 1488 CG GLU A 211 64.746 28.384 0.146 1.00 45.12 C
+ATOM 1489 CD GLU A 211 64.010 27.144 -0.247 1.00 46.14 C
+ATOM 1490 OE1 GLU A 211 63.824 26.973 -1.483 1.00 47.61 O
+ATOM 1491 OE2 GLU A 211 63.624 26.363 0.658 1.00 44.13 O
+ATOM 1492 N THR A 212 67.085 28.798 3.879 1.00 49.04 N
+ATOM 1493 CA THR A 212 67.396 28.798 5.303 1.00 48.89 C
+ATOM 1494 C THR A 212 67.938 30.140 5.726 1.00 48.62 C
+ATOM 1495 O THR A 212 67.511 30.698 6.749 1.00 49.08 O
+ATOM 1496 CB THR A 212 68.456 27.752 5.666 1.00 49.00 C
+ATOM 1497 OG1 THR A 212 67.960 26.448 5.348 1.00 55.12 O
+ATOM 1498 CG2 THR A 212 68.795 27.816 7.149 1.00 47.11 C
+ATOM 1499 N LYS A 213 68.877 30.664 4.941 1.00 45.22 N
+ATOM 1500 CA LYS A 213 69.483 31.927 5.308 1.00 44.73 C
+ATOM 1501 C LYS A 213 68.457 33.038 5.385 1.00 45.02 C
+ATOM 1502 O LYS A 213 68.357 33.733 6.401 1.00 44.20 O
+ATOM 1503 CB LYS A 213 70.606 32.299 4.341 1.00 42.94 C
+ATOM 1504 CG LYS A 213 71.138 33.700 4.566 1.00 39.01 C
+ATOM 1505 CD LYS A 213 72.633 33.730 4.454 1.00 40.05 C
+ATOM 1506 CE LYS A 213 73.097 33.616 3.034 1.00 41.69 C
+ATOM 1507 NZ LYS A 213 74.601 33.653 2.961 1.00 45.07 N
+ATOM 1508 N ALA A 214 67.678 33.183 4.319 1.00 44.48 N
+ATOM 1509 CA ALA A 214 66.658 34.219 4.263 1.00 43.17 C
+ATOM 1510 C ALA A 214 65.583 34.012 5.335 1.00 43.19 C
+ATOM 1511 O ALA A 214 65.130 34.966 5.982 1.00 41.58 O
+ATOM 1512 CB ALA A 214 66.034 34.235 2.891 1.00 39.27 C
+ATOM 1513 N GLN A 215 65.190 32.757 5.527 1.00 43.72 N
+ATOM 1514 CA GLN A 215 64.167 32.426 6.495 1.00 43.83 C
+ATOM 1515 C GLN A 215 64.615 32.743 7.913 1.00 45.92 C
+ATOM 1516 O GLN A 215 63.864 33.307 8.709 1.00 43.19 O
+ATOM 1517 CB GLN A 215 63.797 30.949 6.362 1.00 41.83 C
+ATOM 1518 CG GLN A 215 63.012 30.662 5.117 1.00 45.70 C
+ATOM 1519 CD GLN A 215 62.559 29.223 5.007 1.00 49.79 C
+ATOM 1520 OE1 GLN A 215 63.371 28.311 4.867 1.00 53.91 O
+ATOM 1521 NE2 GLN A 215 61.256 29.011 5.057 1.00 49.95 N
+ATOM 1522 N ILE A 216 65.857 32.388 8.215 1.00 48.72 N
+ATOM 1523 CA ILE A 216 66.405 32.604 9.538 1.00 51.29 C
+ATOM 1524 C ILE A 216 66.571 34.111 9.836 1.00 54.52 C
+ATOM 1525 O ILE A 216 66.352 34.573 10.969 1.00 52.88 O
+ATOM 1526 CB ILE A 216 67.740 31.799 9.675 1.00 50.03 C
+ATOM 1527 CG1 ILE A 216 67.641 30.837 10.852 1.00 49.54 C
+ATOM 1528 CG2 ILE A 216 68.911 32.714 9.864 1.00 54.62 C
+ATOM 1529 CD1 ILE A 216 67.127 31.493 12.086 1.00 48.15 C
+ATOM 1530 N LEU A 217 66.947 34.882 8.819 1.00 56.02 N
+ATOM 1531 CA LEU A 217 67.099 36.313 9.008 1.00 56.74 C
+ATOM 1532 C LEU A 217 65.733 36.913 9.288 1.00 58.84 C
+ATOM 1533 O LEU A 217 65.578 37.676 10.236 1.00 59.64 O
+ATOM 1534 CB LEU A 217 67.710 36.956 7.771 1.00 55.39 C
+ATOM 1535 CG LEU A 217 69.217 36.726 7.689 1.00 59.03 C
+ATOM 1536 CD1 LEU A 217 69.747 37.438 6.481 1.00 53.66 C
+ATOM 1537 CD2 LEU A 217 69.913 37.220 8.976 1.00 56.80 C
+ATOM 1538 N GLU A 218 64.742 36.559 8.471 1.00 60.04 N
+ATOM 1539 CA GLU A 218 63.384 37.062 8.647 1.00 61.13 C
+ATOM 1540 C GLU A 218 62.789 36.796 10.038 1.00 60.39 C
+ATOM 1541 O GLU A 218 62.107 37.641 10.599 1.00 60.70 O
+ATOM 1542 CB GLU A 218 62.469 36.457 7.587 1.00 65.14 C
+ATOM 1543 CG GLU A 218 60.986 36.779 7.767 1.00 75.18 C
+ATOM 1544 CD GLU A 218 60.672 38.288 7.696 1.00 82.91 C
+ATOM 1545 OE1 GLU A 218 59.484 38.670 7.915 1.00 86.33 O
+ATOM 1546 OE2 GLU A 218 61.607 39.092 7.421 1.00 86.53 O
+ATOM 1547 N ARG A 219 63.054 35.635 10.609 1.00 58.46 N
+ATOM 1548 CA ARG A 219 62.486 35.329 11.903 1.00 59.26 C
+ATOM 1549 C ARG A 219 63.366 35.699 13.082 1.00 61.54 C
+ATOM 1550 O ARG A 219 62.853 36.020 14.138 1.00 62.98 O
+ATOM 1551 CB ARG A 219 62.171 33.837 12.004 1.00 59.81 C
+ATOM 1552 CG ARG A 219 61.302 33.265 10.912 1.00 61.32 C
+ATOM 1553 CD ARG A 219 61.563 31.788 10.883 1.00 68.41 C
+ATOM 1554 NE ARG A 219 60.614 30.970 10.120 1.00 74.39 N
+ATOM 1555 CZ ARG A 219 60.409 31.039 8.804 1.00 76.22 C
+ATOM 1556 NH1 ARG A 219 61.076 31.919 8.056 1.00 77.19 N
+ATOM 1557 NH2 ARG A 219 59.575 30.174 8.224 1.00 76.64 N
+ATOM 1558 N GLU A 220 64.685 35.643 12.917 1.00 63.70 N
+ATOM 1559 CA GLU A 220 65.604 35.932 14.025 1.00 63.85 C
+ATOM 1560 C GLU A 220 66.440 37.186 13.836 1.00 64.09 C
+ATOM 1561 O GLU A 220 67.203 37.568 14.715 1.00 64.40 O
+ATOM 1562 CB GLU A 220 66.541 34.745 14.247 1.00 64.72 C
+ATOM 1563 CG GLU A 220 65.843 33.473 14.683 1.00 66.85 C
+ATOM 1564 CD GLU A 220 65.163 33.624 16.018 1.00 69.01 C
+ATOM 1565 OE1 GLU A 220 65.690 34.380 16.860 1.00 70.94 O
+ATOM 1566 OE2 GLU A 220 64.114 32.979 16.241 1.00 72.12 O
+ATOM 1567 N GLY A 221 66.308 37.815 12.679 1.00 64.32 N
+ATOM 1568 CA GLY A 221 67.045 39.030 12.420 1.00 63.89 C
+ATOM 1569 C GLY A 221 68.551 38.883 12.399 1.00 65.72 C
+ATOM 1570 O GLY A 221 69.259 39.891 12.362 1.00 68.61 O
+ATOM 1571 N ARG A 222 69.052 37.651 12.421 1.00 65.10 N
+ATOM 1572 CA ARG A 222 70.501 37.406 12.386 1.00 63.46 C
+ATOM 1573 C ARG A 222 70.739 36.015 11.831 1.00 62.43 C
+ATOM 1574 O ARG A 222 69.796 35.229 11.745 1.00 66.20 O
+ATOM 1575 CB ARG A 222 71.101 37.503 13.793 1.00 61.35 C
+ATOM 1576 CG ARG A 222 70.247 36.868 14.848 1.00 62.26 C
+ATOM 1577 CD ARG A 222 70.979 36.702 16.143 1.00 62.90 C
+ATOM 1578 NE ARG A 222 72.094 35.766 16.024 1.00 66.20 N
+ATOM 1579 CZ ARG A 222 72.390 34.846 16.943 1.00 68.27 C
+ATOM 1580 NH1 ARG A 222 71.648 34.742 18.040 1.00 70.57 N
+ATOM 1581 NH2 ARG A 222 73.421 34.029 16.774 1.00 67.07 N
+ATOM 1582 N LEU A 223 71.976 35.709 11.448 1.00 57.79 N
+ATOM 1583 CA LEU A 223 72.284 34.385 10.923 1.00 55.77 C
+ATOM 1584 C LEU A 223 72.395 33.409 12.075 1.00 56.33 C
+ATOM 1585 O LEU A 223 72.440 33.814 13.232 1.00 58.91 O
+ATOM 1586 CB LEU A 223 73.594 34.403 10.149 1.00 53.92 C
+ATOM 1587 CG LEU A 223 73.629 35.313 8.928 1.00 53.39 C
+ATOM 1588 CD1 LEU A 223 74.860 34.946 8.133 1.00 50.51 C
+ATOM 1589 CD2 LEU A 223 72.358 35.158 8.077 1.00 50.38 C
+ATOM 1590 N PRO A 224 72.449 32.104 11.783 1.00 56.49 N
+ATOM 1591 CA PRO A 224 72.554 31.129 12.871 1.00 56.34 C
+ATOM 1592 C PRO A 224 73.982 31.041 13.379 1.00 57.98 C
+ATOM 1593 O PRO A 224 74.934 31.355 12.660 1.00 57.15 O
+ATOM 1594 CB PRO A 224 72.147 29.813 12.218 1.00 54.19 C
+ATOM 1595 CG PRO A 224 71.883 30.147 10.761 1.00 54.42 C
+ATOM 1596 CD PRO A 224 72.566 31.435 10.485 1.00 55.46 C
+ATOM 1597 N ASP A 225 74.129 30.594 14.617 1.00 59.46 N
+ATOM 1598 CA ASP A 225 75.442 30.427 15.201 1.00 57.72 C
+ATOM 1599 C ASP A 225 76.080 29.245 14.495 1.00 57.10 C
+ATOM 1600 O ASP A 225 77.217 29.331 14.056 1.00 59.16 O
+ATOM 1601 CB ASP A 225 75.299 30.211 16.698 1.00 59.82 C
+ATOM 1602 CG ASP A 225 74.689 31.428 17.384 1.00 65.15 C
+ATOM 1603 OD1 ASP A 225 75.209 32.538 17.144 1.00 67.26 O
+ATOM 1604 OD2 ASP A 225 73.697 31.298 18.142 1.00 65.60 O
+ATOM 1605 N ALA A 226 75.335 28.156 14.344 1.00 56.87 N
+ATOM 1606 CA ALA A 226 75.846 26.983 13.639 1.00 56.16 C
+ATOM 1607 C ALA A 226 74.742 26.324 12.815 1.00 56.44 C
+ATOM 1608 O ALA A 226 73.556 26.462 13.126 1.00 59.31 O
+ATOM 1609 CB ALA A 226 76.408 25.984 14.625 1.00 55.36 C
+ATOM 1610 N VAL A 227 75.135 25.622 11.757 1.00 54.21 N
+ATOM 1611 CA VAL A 227 74.193 24.902 10.909 1.00 52.64 C
+ATOM 1612 C VAL A 227 74.690 23.461 10.923 1.00 53.84 C
+ATOM 1613 O VAL A 227 75.758 23.183 10.401 1.00 55.40 O
+ATOM 1614 CB VAL A 227 74.212 25.412 9.447 1.00 51.05 C
+ATOM 1615 CG1 VAL A 227 73.483 24.425 8.569 1.00 49.85 C
+ATOM 1616 CG2 VAL A 227 73.565 26.790 9.339 1.00 46.48 C
+ATOM 1617 N ILE A 228 73.931 22.557 11.538 1.00 54.35 N
+ATOM 1618 CA ILE A 228 74.300 21.146 11.630 1.00 53.81 C
+ATOM 1619 C ILE A 228 73.641 20.388 10.485 1.00 56.05 C
+ATOM 1620 O ILE A 228 72.471 20.580 10.184 1.00 57.96 O
+ATOM 1621 CB ILE A 228 73.778 20.501 12.924 1.00 54.98 C
+ATOM 1622 CG1 ILE A 228 73.660 21.539 14.034 1.00 55.29 C
+ATOM 1623 CG2 ILE A 228 74.673 19.364 13.337 1.00 54.21 C
+ATOM 1624 CD1 ILE A 228 74.903 22.270 14.286 1.00 59.53 C
+ATOM 1625 N ALA A 229 74.379 19.505 9.851 1.00 56.54 N
+ATOM 1626 CA ALA A 229 73.817 18.753 8.759 1.00 58.70 C
+ATOM 1627 C ALA A 229 74.625 17.484 8.667 1.00 61.50 C
+ATOM 1628 O ALA A 229 75.849 17.528 8.657 1.00 64.94 O
+ATOM 1629 CB ALA A 229 73.923 19.540 7.477 1.00 55.82 C
+ATOM 1630 N CYS A 230 73.942 16.350 8.627 1.00 62.74 N
+ATOM 1631 CA CYS A 230 74.600 15.067 8.540 1.00 63.30 C
+ATOM 1632 C CYS A 230 75.242 14.913 7.160 1.00 63.88 C
+ATOM 1633 O CYS A 230 74.563 14.904 6.138 1.00 63.09 O
+ATOM 1634 CB CYS A 230 73.567 13.974 8.788 1.00 64.41 C
+ATOM 1635 SG CYS A 230 74.168 12.302 8.544 1.00 73.59 S
+ATOM 1636 N VAL A 231 76.562 14.804 7.125 1.00 66.81 N
+ATOM 1637 CA VAL A 231 77.256 14.652 5.851 1.00 70.40 C
+ATOM 1638 C VAL A 231 77.522 13.183 5.555 1.00 73.58 C
+ATOM 1639 O VAL A 231 77.907 12.421 6.431 1.00 75.22 O
+ATOM 1640 CB VAL A 231 78.599 15.420 5.833 1.00 68.50 C
+ATOM 1641 CG1 VAL A 231 79.437 15.041 7.033 1.00 68.64 C
+ATOM 1642 CG2 VAL A 231 79.350 15.105 4.559 1.00 67.95 C
+ATOM 1643 N GLY A 232 77.306 12.784 4.315 1.00 76.79 N
+ATOM 1644 CA GLY A 232 77.538 11.405 3.964 1.00 80.63 C
+ATOM 1645 C GLY A 232 76.770 11.061 2.711 1.00 85.29 C
+ATOM 1646 O GLY A 232 75.944 10.146 2.734 1.00 89.01 O
+ATOM 1647 N GLY A 233 77.023 11.806 1.630 1.00 86.54 N
+ATOM 1648 CA GLY A 233 76.371 11.560 0.348 1.00 85.99 C
+ATOM 1649 C GLY A 233 74.854 11.471 0.336 1.00 85.84 C
+ATOM 1650 O GLY A 233 74.244 10.841 1.205 1.00 86.32 O
+ATOM 1651 N GLY A 234 74.236 12.091 -0.665 1.00 85.24 N
+ATOM 1652 CA GLY A 234 72.790 12.067 -0.749 1.00 84.91 C
+ATOM 1653 C GLY A 234 72.187 12.719 0.484 1.00 85.88 C
+ATOM 1654 O GLY A 234 70.972 12.682 0.705 1.00 87.81 O
+ATOM 1655 N SER A 235 73.047 13.302 1.312 1.00 84.80 N
+ATOM 1656 CA SER A 235 72.591 13.979 2.517 1.00 82.03 C
+ATOM 1657 C SER A 235 72.255 15.377 2.032 1.00 79.72 C
+ATOM 1658 O SER A 235 71.448 16.085 2.623 1.00 78.76 O
+ATOM 1659 CB SER A 235 73.722 14.060 3.551 1.00 82.56 C
+ATOM 1660 OG SER A 235 74.390 12.818 3.699 1.00 84.00 O
+ATOM 1661 N ASN A 236 72.893 15.749 0.926 1.00 78.02 N
+ATOM 1662 CA ASN A 236 72.728 17.064 0.330 1.00 76.52 C
+ATOM 1663 C ASN A 236 73.112 18.122 1.375 1.00 73.04 C
+ATOM 1664 O ASN A 236 72.394 19.098 1.605 1.00 72.14 O
+ATOM 1665 CB ASN A 236 71.284 17.261 -0.156 1.00 79.65 C
+ATOM 1666 CG ASN A 236 71.194 18.220 -1.349 1.00 83.97 C
+ATOM 1667 OD1 ASN A 236 70.104 18.450 -1.901 1.00 85.62 O
+ATOM 1668 ND2 ASN A 236 72.347 18.781 -1.754 1.00 82.85 N
+ATOM 1669 N ALA A 237 74.255 17.902 2.015 1.00 67.79 N
+ATOM 1670 CA ALA A 237 74.747 18.821 3.014 1.00 62.92 C
+ATOM 1671 C ALA A 237 75.274 20.023 2.258 1.00 62.23 C
+ATOM 1672 O ALA A 237 75.058 21.166 2.651 1.00 62.78 O
+ATOM 1673 CB ALA A 237 75.848 18.171 3.801 1.00 62.25 C
+ATOM 1674 N ILE A 238 75.965 19.761 1.156 1.00 59.96 N
+ATOM 1675 CA ILE A 238 76.507 20.835 0.348 1.00 57.44 C
+ATOM 1676 C ILE A 238 75.411 21.800 -0.018 1.00 58.38 C
+ATOM 1677 O ILE A 238 75.673 22.985 -0.176 1.00 60.11 O
+ATOM 1678 CB ILE A 238 77.097 20.320 -0.952 1.00 56.91 C
+ATOM 1679 CG1 ILE A 238 78.110 19.227 -0.648 1.00 60.48 C
+ATOM 1680 CG2 ILE A 238 77.735 21.455 -1.721 1.00 53.25 C
+ATOM 1681 CD1 ILE A 238 79.088 19.602 0.453 1.00 66.38 C
+ATOM 1682 N GLY A 239 74.188 21.281 -0.168 1.00 58.52 N
+ATOM 1683 CA GLY A 239 73.043 22.109 -0.527 1.00 56.61 C
+ATOM 1684 C GLY A 239 72.702 23.072 0.592 1.00 56.45 C
+ATOM 1685 O GLY A 239 72.367 24.248 0.383 1.00 57.99 O
+ATOM 1686 N MET A 240 72.797 22.571 1.809 1.00 54.40 N
+ATOM 1687 CA MET A 240 72.515 23.402 2.946 1.00 53.93 C
+ATOM 1688 C MET A 240 73.709 24.327 3.261 1.00 54.72 C
+ATOM 1689 O MET A 240 73.499 25.492 3.618 1.00 57.21 O
+ATOM 1690 CB MET A 240 72.156 22.521 4.150 1.00 51.71 C
+ATOM 1691 CG MET A 240 72.041 23.270 5.465 1.00 50.79 C
+ATOM 1692 SD MET A 240 70.878 24.637 5.427 1.00 51.24 S
+ATOM 1693 CE MET A 240 69.504 23.931 6.271 1.00 47.93 C
+ATOM 1694 N PHE A 241 74.945 23.838 3.098 1.00 51.81 N
+ATOM 1695 CA PHE A 241 76.135 24.638 3.422 1.00 50.09 C
+ATOM 1696 C PHE A 241 76.584 25.652 2.392 1.00 51.67 C
+ATOM 1697 O PHE A 241 77.180 26.680 2.735 1.00 49.95 O
+ATOM 1698 CB PHE A 241 77.335 23.744 3.698 1.00 47.45 C
+ATOM 1699 CG PHE A 241 77.205 22.915 4.919 1.00 45.65 C
+ATOM 1700 CD1 PHE A 241 76.610 23.422 6.054 1.00 45.09 C
+ATOM 1701 CD2 PHE A 241 77.692 21.620 4.939 1.00 45.67 C
+ATOM 1702 CE1 PHE A 241 76.496 22.649 7.198 1.00 46.46 C
+ATOM 1703 CE2 PHE A 241 77.586 20.836 6.079 1.00 46.41 C
+ATOM 1704 CZ PHE A 241 76.983 21.354 7.213 1.00 46.84 C
+ATOM 1705 N ALA A 242 76.321 25.352 1.126 1.00 52.31 N
+ATOM 1706 CA ALA A 242 76.739 26.223 0.043 1.00 51.22 C
+ATOM 1707 C ALA A 242 76.645 27.697 0.394 1.00 51.57 C
+ATOM 1708 O ALA A 242 77.663 28.359 0.504 1.00 53.36 O
+ATOM 1709 CB ALA A 242 75.934 25.929 -1.194 1.00 51.93 C
+ATOM 1710 N ASP A 243 75.436 28.204 0.606 1.00 50.25 N
+ATOM 1711 CA ASP A 243 75.263 29.625 0.887 1.00 51.00 C
+ATOM 1712 C ASP A 243 75.842 30.164 2.176 1.00 52.29 C
+ATOM 1713 O ASP A 243 75.704 31.363 2.439 1.00 52.50 O
+ATOM 1714 CB ASP A 243 73.788 30.004 0.835 1.00 53.86 C
+ATOM 1715 CG ASP A 243 73.541 31.323 0.125 1.00 54.52 C
+ATOM 1716 OD1 ASP A 243 74.004 31.458 -1.031 1.00 53.47 O
+ATOM 1717 OD2 ASP A 243 72.865 32.205 0.706 1.00 55.23 O
+ATOM 1718 N PHE A 244 76.475 29.314 2.984 1.00 52.17 N
+ATOM 1719 CA PHE A 244 77.080 29.786 4.242 1.00 53.62 C
+ATOM 1720 C PHE A 244 78.629 29.735 4.211 1.00 55.12 C
+ATOM 1721 O PHE A 244 79.298 30.272 5.101 1.00 55.32 O
+ATOM 1722 CB PHE A 244 76.563 28.958 5.429 1.00 52.17 C
+ATOM 1723 CG PHE A 244 75.107 29.176 5.744 1.00 51.63 C
+ATOM 1724 CD1 PHE A 244 74.689 30.308 6.447 1.00 51.79 C
+ATOM 1725 CD2 PHE A 244 74.150 28.254 5.344 1.00 50.48 C
+ATOM 1726 CE1 PHE A 244 73.331 30.521 6.749 1.00 50.24 C
+ATOM 1727 CE2 PHE A 244 72.797 28.459 5.642 1.00 52.13 C
+ATOM 1728 CZ PHE A 244 72.389 29.601 6.348 1.00 49.57 C
+ATOM 1729 N ILE A 245 79.194 29.090 3.191 1.00 54.65 N
+ATOM 1730 CA ILE A 245 80.643 28.991 3.075 1.00 55.20 C
+ATOM 1731 C ILE A 245 81.295 30.368 3.292 1.00 56.73 C
+ATOM 1732 O ILE A 245 82.350 30.467 3.900 1.00 58.60 O
+ATOM 1733 CB ILE A 245 81.085 28.441 1.671 1.00 56.62 C
+ATOM 1734 CG1 ILE A 245 80.578 27.016 1.439 1.00 56.34 C
+ATOM 1735 CG2 ILE A 245 82.585 28.408 1.588 1.00 56.52 C
+ATOM 1736 CD1 ILE A 245 81.127 26.013 2.429 1.00 56.33 C
+ATOM 1737 N ASN A 246 80.691 31.442 2.794 1.00 57.93 N
+ATOM 1738 CA ASN A 246 81.306 32.748 3.004 1.00 56.18 C
+ATOM 1739 C ASN A 246 80.669 33.595 4.086 1.00 57.30 C
+ATOM 1740 O ASN A 246 80.819 34.812 4.095 1.00 56.67 O
+ATOM 1741 CB ASN A 246 81.378 33.528 1.702 1.00 53.49 C
+ATOM 1742 CG ASN A 246 82.375 32.938 0.752 1.00 53.67 C
+ATOM 1743 OD1 ASN A 246 83.202 32.108 1.147 1.00 52.34 O
+ATOM 1744 ND2 ASN A 246 82.319 33.357 -0.507 1.00 54.78 N
+ATOM 1745 N GLU A 247 79.962 32.935 4.997 1.00 59.13 N
+ATOM 1746 CA GLU A 247 79.313 33.590 6.120 1.00 60.70 C
+ATOM 1747 C GLU A 247 80.158 33.128 7.284 1.00 62.69 C
+ATOM 1748 O GLU A 247 79.656 32.562 8.245 1.00 66.03 O
+ATOM 1749 CB GLU A 247 77.880 33.087 6.259 1.00 58.00 C
+ATOM 1750 CG GLU A 247 76.932 33.671 5.238 1.00 60.69 C
+ATOM 1751 CD GLU A 247 76.755 35.175 5.421 1.00 63.03 C
+ATOM 1752 OE1 GLU A 247 76.014 35.817 4.631 1.00 62.46 O
+ATOM 1753 OE2 GLU A 247 77.363 35.715 6.372 1.00 64.52 O
+ATOM 1754 N THR A 248 81.458 33.370 7.169 1.00 64.29 N
+ATOM 1755 CA THR A 248 82.436 32.934 8.162 1.00 65.20 C
+ATOM 1756 C THR A 248 82.064 32.947 9.627 1.00 63.78 C
+ATOM 1757 O THR A 248 82.544 32.120 10.375 1.00 63.82 O
+ATOM 1758 CB THR A 248 83.775 33.672 7.988 1.00 66.12 C
+ATOM 1759 OG1 THR A 248 83.529 35.042 7.644 1.00 69.60 O
+ATOM 1760 CG2 THR A 248 84.603 33.005 6.889 1.00 65.07 C
+ATOM 1761 N ASN A 249 81.211 33.862 10.051 1.00 65.39 N
+ATOM 1762 CA ASN A 249 80.817 33.901 11.460 1.00 66.91 C
+ATOM 1763 C ASN A 249 79.731 32.845 11.776 1.00 65.17 C
+ATOM 1764 O ASN A 249 79.117 32.855 12.846 1.00 65.49 O
+ATOM 1765 CB ASN A 249 80.316 35.307 11.813 1.00 70.86 C
+ATOM 1766 CG ASN A 249 79.251 35.820 10.823 1.00 78.02 C
+ATOM 1767 OD1 ASN A 249 78.488 36.744 11.144 1.00 80.64 O
+ATOM 1768 ND2 ASN A 249 79.208 35.231 9.608 1.00 77.80 N
+ATOM 1769 N VAL A 250 79.499 31.935 10.837 1.00 63.34 N
+ATOM 1770 CA VAL A 250 78.497 30.889 11.003 1.00 59.46 C
+ATOM 1771 C VAL A 250 79.183 29.551 10.894 1.00 58.33 C
+ATOM 1772 O VAL A 250 79.827 29.252 9.883 1.00 55.90 O
+ATOM 1773 CB VAL A 250 77.411 30.938 9.913 1.00 58.90 C
+ATOM 1774 CG1 VAL A 250 76.458 29.778 10.120 1.00 59.30 C
+ATOM 1775 CG2 VAL A 250 76.659 32.272 9.953 1.00 54.81 C
+ATOM 1776 N GLY A 251 79.017 28.745 11.934 1.00 57.26 N
+ATOM 1777 CA GLY A 251 79.651 27.446 11.988 1.00 56.98 C
+ATOM 1778 C GLY A 251 78.990 26.369 11.177 1.00 59.02 C
+ATOM 1779 O GLY A 251 77.768 26.261 11.154 1.00 60.93 O
+ATOM 1780 N LEU A 252 79.806 25.558 10.517 1.00 59.10 N
+ATOM 1781 CA LEU A 252 79.285 24.476 9.706 1.00 60.66 C
+ATOM 1782 C LEU A 252 79.655 23.113 10.298 1.00 62.82 C
+ATOM 1783 O LEU A 252 80.736 22.599 10.050 1.00 66.07 O
+ATOM 1784 CB LEU A 252 79.820 24.601 8.281 1.00 57.34 C
+ATOM 1785 CG LEU A 252 79.230 25.730 7.441 1.00 55.56 C
+ATOM 1786 CD1 LEU A 252 79.157 27.009 8.196 1.00 55.89 C
+ATOM 1787 CD2 LEU A 252 80.087 25.913 6.248 1.00 57.63 C
+ATOM 1788 N ILE A 253 78.751 22.531 11.082 1.00 63.63 N
+ATOM 1789 CA ILE A 253 78.990 21.230 11.701 1.00 61.40 C
+ATOM 1790 C ILE A 253 78.506 20.143 10.757 1.00 61.85 C
+ATOM 1791 O ILE A 253 77.341 20.120 10.393 1.00 61.56 O
+ATOM 1792 CB ILE A 253 78.197 21.049 13.014 1.00 61.36 C
+ATOM 1793 CG1 ILE A 253 78.301 22.293 13.912 1.00 57.61 C
+ATOM 1794 CG2 ILE A 253 78.689 19.800 13.719 1.00 59.17 C
+ATOM 1795 CD1 ILE A 253 79.614 22.460 14.556 1.00 59.01 C
+ATOM 1796 N GLY A 254 79.406 19.256 10.354 1.00 64.24 N
+ATOM 1797 CA GLY A 254 79.040 18.152 9.484 1.00 64.40 C
+ATOM 1798 C GLY A 254 79.041 16.929 10.382 1.00 66.78 C
+ATOM 1799 O GLY A 254 80.064 16.604 10.996 1.00 65.58 O
+ATOM 1800 N VAL A 255 77.898 16.253 10.480 1.00 68.16 N
+ATOM 1801 CA VAL A 255 77.786 15.086 11.345 1.00 67.54 C
+ATOM 1802 C VAL A 255 77.987 13.759 10.640 1.00 69.53 C
+ATOM 1803 O VAL A 255 77.311 13.443 9.667 1.00 66.20 O
+ATOM 1804 CB VAL A 255 76.440 15.071 12.061 1.00 64.96 C
+ATOM 1805 CG1 VAL A 255 76.386 13.929 13.041 1.00 64.12 C
+ATOM 1806 CG2 VAL A 255 76.246 16.376 12.794 1.00 64.82 C
+ATOM 1807 N GLU A 256 78.943 12.992 11.157 1.00 75.08 N
+ATOM 1808 CA GLU A 256 79.275 11.681 10.623 1.00 80.27 C
+ATOM 1809 C GLU A 256 78.822 10.557 11.538 1.00 83.22 C
+ATOM 1810 O GLU A 256 79.184 10.506 12.723 1.00 82.48 O
+ATOM 1811 CB GLU A 256 80.780 11.566 10.379 1.00 80.85 C
+ATOM 1812 CG GLU A 256 81.229 12.418 9.217 1.00 86.00 C
+ATOM 1813 CD GLU A 256 82.650 12.153 8.794 1.00 86.94 C
+ATOM 1814 OE1 GLU A 256 83.559 12.282 9.647 1.00 88.13 O
+ATOM 1815 OE2 GLU A 256 82.850 11.825 7.601 1.00 87.78 O
+ATOM 1816 N PRO A 257 78.009 9.638 10.992 1.00 86.28 N
+ATOM 1817 CA PRO A 257 77.470 8.478 11.719 1.00 88.00 C
+ATOM 1818 C PRO A 257 78.559 7.569 12.323 1.00 88.10 C
+ATOM 1819 O PRO A 257 79.702 7.571 11.859 1.00 89.54 O
+ATOM 1820 CB PRO A 257 76.634 7.771 10.646 1.00 88.24 C
+ATOM 1821 CG PRO A 257 76.120 8.949 9.806 1.00 87.22 C
+ATOM 1822 CD PRO A 257 77.393 9.762 9.655 1.00 85.91 C
+ATOM 1823 N GLY A 258 78.200 6.803 13.355 1.00 87.45 N
+ATOM 1824 CA GLY A 258 79.153 5.898 13.988 1.00 86.29 C
+ATOM 1825 C GLY A 258 79.618 6.342 15.367 1.00 86.20 C
+ATOM 1826 O GLY A 258 80.677 5.932 15.853 1.00 83.23 O
+ATOM 1827 N VAL A 309 88.042 10.267 -1.156 1.00102.35 N
+ATOM 1828 CA VAL A 309 86.843 9.858 -0.439 1.00102.29 C
+ATOM 1829 C VAL A 309 85.572 10.362 -1.137 1.00102.16 C
+ATOM 1830 O VAL A 309 85.629 10.861 -2.267 1.00100.68 O
+ATOM 1831 CB VAL A 309 86.886 10.364 1.030 1.00101.91 C
+ATOM 1832 CG1 VAL A 309 88.082 9.742 1.756 1.00 99.31 C
+ATOM 1833 CG2 VAL A 309 86.975 11.888 1.060 1.00100.01 C
+ATOM 1834 N GLY A 310 84.430 10.212 -0.466 1.00102.84 N
+ATOM 1835 CA GLY A 310 83.160 10.645 -1.032 1.00104.17 C
+ATOM 1836 C GLY A 310 83.231 12.102 -1.433 1.00105.29 C
+ATOM 1837 O GLY A 310 83.782 12.908 -0.680 1.00106.71 O
+ATOM 1838 N PRO A 311 82.695 12.484 -2.608 1.00105.08 N
+ATOM 1839 CA PRO A 311 82.762 13.896 -3.005 1.00103.98 C
+ATOM 1840 C PRO A 311 82.218 14.851 -1.921 1.00102.37 C
+ATOM 1841 O PRO A 311 82.850 15.864 -1.598 1.00102.68 O
+ATOM 1842 CB PRO A 311 81.953 13.930 -4.315 1.00103.96 C
+ATOM 1843 CG PRO A 311 80.996 12.799 -4.177 1.00103.17 C
+ATOM 1844 CD PRO A 311 81.859 11.716 -3.549 1.00104.90 C
+ATOM 1845 N GLN A 312 81.056 14.513 -1.363 1.00 98.54 N
+ATOM 1846 CA GLN A 312 80.433 15.313 -0.319 1.00 94.24 C
+ATOM 1847 C GLN A 312 81.522 15.886 0.595 1.00 91.39 C
+ATOM 1848 O GLN A 312 81.621 17.095 0.789 1.00 89.63 O
+ATOM 1849 CB GLN A 312 79.485 14.420 0.483 1.00 96.05 C
+ATOM 1850 CG GLN A 312 78.623 15.139 1.505 1.00 98.39 C
+ATOM 1851 CD GLN A 312 77.292 15.605 0.934 1.00101.66 C
+ATOM 1852 OE1 GLN A 312 77.240 16.517 0.103 1.00101.59 O
+ATOM 1853 NE2 GLN A 312 76.205 14.970 1.376 1.00102.01 N
+ATOM 1854 N HIS A 313 82.348 14.997 1.137 1.00 89.36 N
+ATOM 1855 CA HIS A 313 83.436 15.378 2.035 1.00 86.97 C
+ATOM 1856 C HIS A 313 84.503 16.113 1.249 1.00 84.64 C
+ATOM 1857 O HIS A 313 84.996 17.159 1.672 1.00 84.90 O
+ATOM 1858 CB HIS A 313 84.054 14.138 2.691 1.00 88.42 C
+ATOM 1859 CG HIS A 313 83.131 13.424 3.629 1.00 89.39 C
+ATOM 1860 ND1 HIS A 313 82.091 12.630 3.193 1.00 90.86 N
+ATOM 1861 CD2 HIS A 313 83.068 13.416 4.982 1.00 89.78 C
+ATOM 1862 CE1 HIS A 313 81.426 12.166 4.237 1.00 91.92 C
+ATOM 1863 NE2 HIS A 313 81.999 12.628 5.335 1.00 90.79 N
+ATOM 1864 N ALA A 314 84.868 15.536 0.111 1.00 80.49 N
+ATOM 1865 CA ALA A 314 85.848 16.121 -0.774 1.00 74.96 C
+ATOM 1866 C ALA A 314 85.614 17.630 -0.829 1.00 73.97 C
+ATOM 1867 O ALA A 314 86.474 18.417 -0.415 1.00 74.47 O
+ATOM 1868 CB ALA A 314 85.697 15.517 -2.151 1.00 75.67 C
+ATOM 1869 N TYR A 315 84.443 18.034 -1.325 1.00 70.75 N
+ATOM 1870 CA TYR A 315 84.118 19.454 -1.421 1.00 66.85 C
+ATOM 1871 C TYR A 315 84.174 20.140 -0.067 1.00 65.75 C
+ATOM 1872 O TYR A 315 84.858 21.143 0.081 1.00 65.27 O
+ATOM 1873 CB TYR A 315 82.741 19.665 -2.059 1.00 65.07 C
+ATOM 1874 CG TYR A 315 82.258 21.104 -2.012 1.00 63.83 C
+ATOM 1875 CD1 TYR A 315 81.495 21.570 -0.934 1.00 64.20 C
+ATOM 1876 CD2 TYR A 315 82.624 22.016 -3.003 1.00 63.84 C
+ATOM 1877 CE1 TYR A 315 81.113 22.899 -0.832 1.00 62.95 C
+ATOM 1878 CE2 TYR A 315 82.253 23.359 -2.917 1.00 66.05 C
+ATOM 1879 CZ TYR A 315 81.498 23.798 -1.822 1.00 67.87 C
+ATOM 1880 OH TYR A 315 81.167 25.141 -1.694 1.00 70.08 O
+ATOM 1881 N LEU A 316 83.464 19.605 0.919 1.00 64.90 N
+ATOM 1882 CA LEU A 316 83.455 20.192 2.263 1.00 66.59 C
+ATOM 1883 C LEU A 316 84.839 20.388 2.917 1.00 67.33 C
+ATOM 1884 O LEU A 316 85.064 21.331 3.702 1.00 65.92 O
+ATOM 1885 CB LEU A 316 82.588 19.342 3.180 1.00 66.90 C
+ATOM 1886 CG LEU A 316 81.128 19.750 3.266 1.00 66.33 C
+ATOM 1887 CD1 LEU A 316 80.318 18.613 3.849 1.00 67.78 C
+ATOM 1888 CD2 LEU A 316 81.017 20.986 4.122 1.00 65.00 C
+ATOM 1889 N ASN A 317 85.767 19.492 2.613 1.00 67.96 N
+ATOM 1890 CA ASN A 317 87.094 19.611 3.186 1.00 67.83 C
+ATOM 1891 C ASN A 317 87.785 20.804 2.561 1.00 67.76 C
+ATOM 1892 O ASN A 317 88.316 21.651 3.270 1.00 67.53 O
+ATOM 1893 CB ASN A 317 87.893 18.337 2.934 1.00 68.49 C
+ATOM 1894 CG ASN A 317 87.237 17.115 3.543 1.00 68.33 C
+ATOM 1895 OD1 ASN A 317 86.897 17.104 4.726 1.00 67.29 O
+ATOM 1896 ND2 ASN A 317 87.058 16.075 2.736 1.00 70.30 N
+ATOM 1897 N SER A 318 87.745 20.874 1.230 1.00 67.54 N
+ATOM 1898 CA SER A 318 88.369 21.962 0.480 1.00 65.51 C
+ATOM 1899 C SER A 318 87.890 23.354 0.843 1.00 64.51 C
+ATOM 1900 O SER A 318 88.661 24.292 0.774 1.00 66.15 O
+ATOM 1901 CB SER A 318 88.178 21.755 -1.019 1.00 65.02 C
+ATOM 1902 OG SER A 318 86.808 21.769 -1.367 1.00 66.34 O
+ATOM 1903 N THR A 319 86.624 23.506 1.216 1.00 65.61 N
+ATOM 1904 CA THR A 319 86.122 24.833 1.576 1.00 66.58 C
+ATOM 1905 C THR A 319 86.832 25.268 2.841 1.00 67.03 C
+ATOM 1906 O THR A 319 86.882 26.451 3.183 1.00 68.39 O
+ATOM 1907 CB THR A 319 84.616 24.843 1.889 1.00 65.60 C
+ATOM 1908 OG1 THR A 319 84.408 24.389 3.234 1.00 65.17 O
+ATOM 1909 CG2 THR A 319 83.863 23.969 0.910 1.00 63.32 C
+ATOM 1910 N GLY A 320 87.373 24.285 3.540 1.00 66.37 N
+ATOM 1911 CA GLY A 320 88.068 24.573 4.767 1.00 65.95 C
+ATOM 1912 C GLY A 320 87.146 25.041 5.876 1.00 66.38 C
+ATOM 1913 O GLY A 320 87.625 25.531 6.898 1.00 67.55 O
+ATOM 1914 N ARG A 321 85.832 24.917 5.728 1.00 66.26 N
+ATOM 1915 CA ARG A 321 85.034 25.386 6.844 1.00 66.45 C
+ATOM 1916 C ARG A 321 84.006 24.498 7.480 1.00 67.64 C
+ATOM 1917 O ARG A 321 83.073 24.992 8.107 1.00 69.11 O
+ATOM 1918 CB ARG A 321 84.406 26.739 6.552 1.00 62.94 C
+ATOM 1919 CG ARG A 321 84.099 27.047 5.152 1.00 59.72 C
+ATOM 1920 CD ARG A 321 83.812 28.536 5.112 1.00 62.37 C
+ATOM 1921 NE ARG A 321 82.594 28.922 5.846 1.00 61.77 N
+ATOM 1922 CZ ARG A 321 82.539 29.209 7.139 1.00 57.44 C
+ATOM 1923 NH1 ARG A 321 81.390 29.541 7.717 1.00 54.55 N
+ATOM 1924 NH2 ARG A 321 83.641 29.175 7.849 1.00 60.85 N
+ATOM 1925 N ALA A 322 84.188 23.191 7.370 1.00 67.68 N
+ATOM 1926 CA ALA A 322 83.251 22.284 7.999 1.00 68.44 C
+ATOM 1927 C ALA A 322 83.905 21.553 9.175 1.00 69.24 C
+ATOM 1928 O ALA A 322 84.937 20.926 9.010 1.00 70.97 O
+ATOM 1929 CB ALA A 322 82.745 21.292 6.980 1.00 68.84 C
+ATOM 1930 N ASP A 323 83.321 21.652 10.363 1.00 69.76 N
+ATOM 1931 CA ASP A 323 83.841 20.940 11.524 1.00 71.31 C
+ATOM 1932 C ASP A 323 83.145 19.599 11.543 1.00 70.90 C
+ATOM 1933 O ASP A 323 81.931 19.541 11.707 1.00 73.45 O
+ATOM 1934 CB ASP A 323 83.466 21.627 12.833 1.00 74.63 C
+ATOM 1935 CG ASP A 323 83.928 23.041 12.894 1.00 79.67 C
+ATOM 1936 OD1 ASP A 323 85.150 23.246 12.754 1.00 83.28 O
+ATOM 1937 OD2 ASP A 323 83.076 23.945 13.080 1.00 82.80 O
+ATOM 1938 N TYR A 324 83.873 18.510 11.386 1.00 68.81 N
+ATOM 1939 CA TYR A 324 83.189 17.234 11.447 1.00 67.45 C
+ATOM 1940 C TYR A 324 83.063 16.770 12.904 1.00 66.32 C
+ATOM 1941 O TYR A 324 83.869 17.147 13.757 1.00 65.08 O
+ATOM 1942 CB TYR A 324 83.932 16.195 10.614 1.00 64.84 C
+ATOM 1943 CG TYR A 324 83.958 16.514 9.138 1.00 64.57 C
+ATOM 1944 CD1 TYR A 324 83.318 15.687 8.214 1.00 62.69 C
+ATOM 1945 CD2 TYR A 324 84.664 17.620 8.658 1.00 64.26 C
+ATOM 1946 CE1 TYR A 324 83.389 15.948 6.855 1.00 63.87 C
+ATOM 1947 CE2 TYR A 324 84.743 17.892 7.297 1.00 62.99 C
+ATOM 1948 CZ TYR A 324 84.107 17.050 6.405 1.00 66.20 C
+ATOM 1949 OH TYR A 324 84.215 17.290 5.056 1.00 70.01 O
+ATOM 1950 N VAL A 325 82.012 16.002 13.186 1.00 65.12 N
+ATOM 1951 CA VAL A 325 81.781 15.433 14.511 1.00 64.03 C
+ATOM 1952 C VAL A 325 81.091 14.090 14.315 1.00 66.05 C
+ATOM 1953 O VAL A 325 80.478 13.835 13.271 1.00 64.44 O
+ATOM 1954 CB VAL A 325 80.890 16.307 15.402 1.00 62.24 C
+ATOM 1955 CG1 VAL A 325 81.432 17.709 15.444 1.00 60.51 C
+ATOM 1956 CG2 VAL A 325 79.438 16.255 14.919 1.00 63.59 C
+ATOM 1957 N SER A 326 81.199 13.225 15.320 1.00 67.83 N
+ATOM 1958 CA SER A 326 80.600 11.907 15.229 1.00 68.59 C
+ATOM 1959 C SER A 326 79.487 11.717 16.220 1.00 68.05 C
+ATOM 1960 O SER A 326 79.502 12.277 17.320 1.00 68.57 O
+ATOM 1961 CB SER A 326 81.648 10.821 15.454 1.00 70.03 C
+ATOM 1962 OG SER A 326 81.123 9.552 15.106 1.00 73.13 O
+ATOM 1963 N ILE A 327 78.515 10.918 15.812 1.00 67.55 N
+ATOM 1964 CA ILE A 327 77.388 10.624 16.655 1.00 70.03 C
+ATOM 1965 C ILE A 327 77.240 9.114 16.636 1.00 71.95 C
+ATOM 1966 O ILE A 327 77.576 8.459 15.650 1.00 71.54 O
+ATOM 1967 CB ILE A 327 76.115 11.355 16.157 1.00 69.76 C
+ATOM 1968 CG1 ILE A 327 75.705 12.419 17.170 1.00 69.06 C
+ATOM 1969 CG2 ILE A 327 74.967 10.402 16.026 1.00 71.55 C
+ATOM 1970 CD1 ILE A 327 76.737 13.480 17.394 1.00 72.83 C
+ATOM 1971 N THR A 328 76.745 8.580 17.748 1.00 74.81 N
+ATOM 1972 CA THR A 328 76.574 7.145 17.959 1.00 75.31 C
+ATOM 1973 C THR A 328 75.129 6.679 17.932 1.00 77.46 C
+ATOM 1974 O THR A 328 74.246 7.329 18.497 1.00 76.88 O
+ATOM 1975 CB THR A 328 77.092 6.768 19.327 1.00 74.40 C
+ATOM 1976 OG1 THR A 328 76.180 7.266 20.319 1.00 71.83 O
+ATOM 1977 CG2 THR A 328 78.454 7.389 19.559 1.00 73.97 C
+ATOM 1978 N ASP A 329 74.910 5.520 17.324 1.00 78.88 N
+ATOM 1979 CA ASP A 329 73.583 4.933 17.230 1.00 81.11 C
+ATOM 1980 C ASP A 329 72.663 5.189 18.410 1.00 80.55 C
+ATOM 1981 O ASP A 329 71.469 5.409 18.223 1.00 81.67 O
+ATOM 1982 CB ASP A 329 73.699 3.438 17.020 1.00 84.87 C
+ATOM 1983 CG ASP A 329 74.340 3.112 15.718 1.00 90.46 C
+ATOM 1984 OD1 ASP A 329 75.537 3.439 15.563 1.00 96.24 O
+ATOM 1985 OD2 ASP A 329 73.649 2.552 14.838 1.00 95.70 O
+ATOM 1986 N ASP A 330 73.184 5.149 19.627 1.00 78.84 N
+ATOM 1987 CA ASP A 330 72.297 5.404 20.748 1.00 79.51 C
+ATOM 1988 C ASP A 330 71.874 6.857 20.748 1.00 77.35 C
+ATOM 1989 O ASP A 330 70.681 7.157 20.852 1.00 78.88 O
+ATOM 1990 CB ASP A 330 72.951 5.021 22.079 1.00 82.59 C
+ATOM 1991 CG ASP A 330 72.948 3.503 22.315 1.00 84.87 C
+ATOM 1992 OD1 ASP A 330 73.495 3.080 23.356 1.00 85.37 O
+ATOM 1993 OD2 ASP A 330 72.398 2.740 21.469 1.00 84.25 O
+ATOM 1994 N GLU A 331 72.844 7.757 20.597 1.00 74.16 N
+ATOM 1995 CA GLU A 331 72.566 9.197 20.551 1.00 68.48 C
+ATOM 1996 C GLU A 331 71.542 9.487 19.460 1.00 65.22 C
+ATOM 1997 O GLU A 331 70.639 10.292 19.646 1.00 63.64 O
+ATOM 1998 CB GLU A 331 73.852 9.958 20.274 1.00 65.96 C
+ATOM 1999 CG GLU A 331 74.908 9.686 21.298 1.00 61.30 C
+ATOM 2000 CD GLU A 331 76.171 10.448 21.033 1.00 63.55 C
+ATOM 2001 OE1 GLU A 331 76.823 10.176 19.994 1.00 61.44 O
+ATOM 2002 OE2 GLU A 331 76.503 11.325 21.867 1.00 61.05 O
+ATOM 2003 N ALA A 332 71.693 8.816 18.325 1.00 61.50 N
+ATOM 2004 CA ALA A 332 70.766 8.981 17.231 1.00 61.37 C
+ATOM 2005 C ALA A 332 69.371 8.610 17.722 1.00 63.02 C
+ATOM 2006 O ALA A 332 68.459 9.447 17.684 1.00 65.16 O
+ATOM 2007 CB ALA A 332 71.163 8.104 16.068 1.00 56.65 C
+ATOM 2008 N LEU A 333 69.209 7.368 18.193 1.00 63.15 N
+ATOM 2009 CA LEU A 333 67.921 6.876 18.692 1.00 60.56 C
+ATOM 2010 C LEU A 333 67.366 7.747 19.796 1.00 58.60 C
+ATOM 2011 O LEU A 333 66.162 7.934 19.891 1.00 58.41 O
+ATOM 2012 CB LEU A 333 68.056 5.452 19.189 1.00 61.86 C
+ATOM 2013 CG LEU A 333 68.122 4.409 18.074 1.00 67.47 C
+ATOM 2014 CD1 LEU A 333 68.575 3.063 18.637 1.00 70.77 C
+ATOM 2015 CD2 LEU A 333 66.762 4.267 17.432 1.00 69.07 C
+ATOM 2016 N GLU A 334 68.249 8.274 20.630 1.00 56.19 N
+ATOM 2017 CA GLU A 334 67.851 9.163 21.714 1.00 57.83 C
+ATOM 2018 C GLU A 334 67.111 10.314 21.027 1.00 59.67 C
+ATOM 2019 O GLU A 334 65.930 10.580 21.288 1.00 58.28 O
+ATOM 2020 CB GLU A 334 69.112 9.704 22.397 1.00 60.54 C
+ATOM 2021 CG GLU A 334 68.966 10.384 23.761 1.00 61.97 C
+ATOM 2022 CD GLU A 334 68.034 11.572 23.764 1.00 65.49 C
+ATOM 2023 OE1 GLU A 334 66.806 11.356 23.882 1.00 66.73 O
+ATOM 2024 OE2 GLU A 334 68.527 12.718 23.648 1.00 64.64 O
+ATOM 2025 N ALA A 335 67.841 10.988 20.138 1.00 60.09 N
+ATOM 2026 CA ALA A 335 67.333 12.116 19.371 1.00 58.77 C
+ATOM 2027 C ALA A 335 66.056 11.727 18.629 1.00 58.27 C
+ATOM 2028 O ALA A 335 65.014 12.376 18.784 1.00 58.79 O
+ATOM 2029 CB ALA A 335 68.395 12.576 18.379 1.00 57.71 C
+ATOM 2030 N PHE A 336 66.149 10.678 17.816 1.00 54.55 N
+ATOM 2031 CA PHE A 336 65.009 10.210 17.061 1.00 53.53 C
+ATOM 2032 C PHE A 336 63.799 10.160 17.980 1.00 55.62 C
+ATOM 2033 O PHE A 336 62.745 10.723 17.690 1.00 56.95 O
+ATOM 2034 CB PHE A 336 65.283 8.813 16.523 1.00 52.07 C
+ATOM 2035 CG PHE A 336 64.101 8.177 15.852 1.00 50.00 C
+ATOM 2036 CD1 PHE A 336 63.907 8.311 14.480 1.00 49.65 C
+ATOM 2037 CD2 PHE A 336 63.178 7.446 16.594 1.00 48.84 C
+ATOM 2038 CE1 PHE A 336 62.807 7.724 13.849 1.00 50.11 C
+ATOM 2039 CE2 PHE A 336 62.074 6.856 15.978 1.00 50.56 C
+ATOM 2040 CZ PHE A 336 61.888 6.995 14.598 1.00 50.51 C
+ATOM 2041 N LYS A 337 63.951 9.481 19.105 1.00 54.95 N
+ATOM 2042 CA LYS A 337 62.843 9.358 20.018 1.00 55.90 C
+ATOM 2043 C LYS A 337 62.391 10.670 20.603 1.00 56.26 C
+ATOM 2044 O LYS A 337 61.198 10.890 20.784 1.00 58.11 O
+ATOM 2045 CB LYS A 337 63.193 8.391 21.133 1.00 57.71 C
+ATOM 2046 CG LYS A 337 63.098 6.944 20.717 1.00 60.50 C
+ATOM 2047 CD LYS A 337 63.545 6.055 21.852 1.00 65.23 C
+ATOM 2048 CE LYS A 337 63.215 4.598 21.595 1.00 66.53 C
+ATOM 2049 NZ LYS A 337 63.655 3.815 22.787 1.00 71.30 N
+ATOM 2050 N THR A 338 63.342 11.541 20.901 1.00 56.82 N
+ATOM 2051 CA THR A 338 63.041 12.846 21.487 1.00 57.56 C
+ATOM 2052 C THR A 338 62.183 13.741 20.581 1.00 58.58 C
+ATOM 2053 O THR A 338 61.194 14.339 21.034 1.00 58.55 O
+ATOM 2054 CB THR A 338 64.347 13.601 21.801 1.00 58.82 C
+ATOM 2055 OG1 THR A 338 65.227 12.727 22.516 1.00 58.64 O
+ATOM 2056 CG2 THR A 338 64.062 14.880 22.624 1.00 55.48 C
+ATOM 2057 N LEU A 339 62.584 13.839 19.311 1.00 56.40 N
+ATOM 2058 CA LEU A 339 61.887 14.664 18.342 1.00 56.24 C
+ATOM 2059 C LEU A 339 60.453 14.185 18.093 1.00 58.40 C
+ATOM 2060 O LEU A 339 59.542 14.991 17.897 1.00 60.54 O
+ATOM 2061 CB LEU A 339 62.668 14.688 17.035 1.00 54.10 C
+ATOM 2062 CG LEU A 339 62.193 15.645 15.947 1.00 52.36 C
+ATOM 2063 CD1 LEU A 339 62.275 17.071 16.438 1.00 49.87 C
+ATOM 2064 CD2 LEU A 339 63.068 15.461 14.733 1.00 53.51 C
+ATOM 2065 N CYS A 340 60.247 12.874 18.092 1.00 58.03 N
+ATOM 2066 CA CYS A 340 58.913 12.335 17.884 1.00 56.55 C
+ATOM 2067 C CYS A 340 58.022 12.792 19.034 1.00 57.40 C
+ATOM 2068 O CYS A 340 56.932 13.328 18.828 1.00 58.12 O
+ATOM 2069 CB CYS A 340 58.957 10.808 17.881 1.00 54.79 C
+ATOM 2070 SG CYS A 340 59.718 10.048 16.455 1.00 58.57 S
+ATOM 2071 N LEU A 341 58.523 12.575 20.245 1.00 56.75 N
+ATOM 2072 CA LEU A 341 57.827 12.874 21.480 1.00 55.18 C
+ATOM 2073 C LEU A 341 57.527 14.325 21.778 1.00 54.07 C
+ATOM 2074 O LEU A 341 56.453 14.644 22.276 1.00 55.79 O
+ATOM 2075 CB LEU A 341 58.609 12.292 22.658 1.00 56.85 C
+ATOM 2076 CG LEU A 341 57.828 11.476 23.694 1.00 55.95 C
+ATOM 2077 CD1 LEU A 341 58.414 11.745 25.062 1.00 52.74 C
+ATOM 2078 CD2 LEU A 341 56.346 11.860 23.671 1.00 57.85 C
+ATOM 2079 N HIS A 342 58.465 15.206 21.484 1.00 54.14 N
+ATOM 2080 CA HIS A 342 58.269 16.615 21.775 1.00 55.42 C
+ATOM 2081 C HIS A 342 57.851 17.487 20.598 1.00 56.04 C
+ATOM 2082 O HIS A 342 57.103 18.450 20.751 1.00 56.17 O
+ATOM 2083 CB HIS A 342 59.546 17.151 22.396 1.00 58.70 C
+ATOM 2084 CG HIS A 342 59.909 16.451 23.667 1.00 65.72 C
+ATOM 2085 ND1 HIS A 342 59.257 16.692 24.860 1.00 65.85 N
+ATOM 2086 CD2 HIS A 342 60.788 15.450 23.915 1.00 65.35 C
+ATOM 2087 CE1 HIS A 342 59.718 15.868 25.783 1.00 64.28 C
+ATOM 2088 NE2 HIS A 342 60.646 15.104 25.236 1.00 64.25 N
+ATOM 2089 N GLU A 343 58.315 17.147 19.410 1.00 55.59 N
+ATOM 2090 CA GLU A 343 57.982 17.944 18.261 1.00 53.54 C
+ATOM 2091 C GLU A 343 56.944 17.314 17.372 1.00 52.87 C
+ATOM 2092 O GLU A 343 56.377 17.976 16.514 1.00 56.05 O
+ATOM 2093 CB GLU A 343 59.251 18.229 17.483 1.00 54.31 C
+ATOM 2094 CG GLU A 343 60.211 19.077 18.268 1.00 56.22 C
+ATOM 2095 CD GLU A 343 59.510 20.262 18.903 1.00 59.44 C
+ATOM 2096 OE1 GLU A 343 58.447 20.664 18.366 1.00 61.55 O
+ATOM 2097 OE2 GLU A 343 60.022 20.796 19.918 1.00 59.71 O
+ATOM 2098 N GLY A 344 56.680 16.038 17.580 1.00 49.29 N
+ATOM 2099 CA GLY A 344 55.705 15.381 16.749 1.00 47.93 C
+ATOM 2100 C GLY A 344 56.245 15.179 15.355 1.00 46.49 C
+ATOM 2101 O GLY A 344 55.481 15.152 14.393 1.00 48.31 O
+ATOM 2102 N ILE A 345 57.561 15.039 15.242 1.00 45.34 N
+ATOM 2103 CA ILE A 345 58.196 14.818 13.953 1.00 47.30 C
+ATOM 2104 C ILE A 345 59.045 13.549 13.988 1.00 49.50 C
+ATOM 2105 O ILE A 345 59.967 13.443 14.799 1.00 49.40 O
+ATOM 2106 CB ILE A 345 59.128 15.996 13.553 1.00 47.11 C
+ATOM 2107 CG1 ILE A 345 58.376 17.317 13.611 1.00 47.04 C
+ATOM 2108 CG2 ILE A 345 59.636 15.809 12.131 1.00 47.54 C
+ATOM 2109 CD1 ILE A 345 59.181 18.480 13.103 1.00 46.48 C
+ATOM 2110 N ILE A 346 58.736 12.604 13.100 1.00 50.70 N
+ATOM 2111 CA ILE A 346 59.472 11.337 12.985 1.00 53.10 C
+ATOM 2112 C ILE A 346 60.687 11.606 12.083 1.00 53.04 C
+ATOM 2113 O ILE A 346 60.555 11.603 10.858 1.00 56.31 O
+ATOM 2114 CB ILE A 346 58.611 10.223 12.269 1.00 55.67 C
+ATOM 2115 CG1 ILE A 346 57.176 10.200 12.796 1.00 54.89 C
+ATOM 2116 CG2 ILE A 346 59.239 8.861 12.472 1.00 54.11 C
+ATOM 2117 CD1 ILE A 346 57.105 9.968 14.262 1.00 59.04 C
+ATOM 2118 N PRO A 347 61.879 11.830 12.654 1.00 51.38 N
+ATOM 2119 CA PRO A 347 63.019 12.088 11.778 1.00 50.67 C
+ATOM 2120 C PRO A 347 63.558 10.811 11.172 1.00 50.96 C
+ATOM 2121 O PRO A 347 63.259 9.727 11.650 1.00 52.34 O
+ATOM 2122 CB PRO A 347 64.028 12.715 12.723 1.00 49.14 C
+ATOM 2123 CG PRO A 347 63.839 11.910 13.922 1.00 50.83 C
+ATOM 2124 CD PRO A 347 62.312 11.843 14.057 1.00 51.65 C
+ATOM 2125 N ALA A 348 64.337 10.956 10.103 1.00 53.00 N
+ATOM 2126 CA ALA A 348 64.999 9.841 9.430 1.00 53.58 C
+ATOM 2127 C ALA A 348 66.275 9.616 10.260 1.00 58.08 C
+ATOM 2128 O ALA A 348 66.650 10.477 11.068 1.00 58.63 O
+ATOM 2129 CB ALA A 348 65.364 10.226 8.022 1.00 48.87 C
+ATOM 2130 N LEU A 349 66.951 8.484 10.089 1.00 60.50 N
+ATOM 2131 CA LEU A 349 68.142 8.264 10.889 1.00 61.93 C
+ATOM 2132 C LEU A 349 69.230 9.268 10.555 1.00 64.17 C
+ATOM 2133 O LEU A 349 69.924 9.733 11.452 1.00 66.19 O
+ATOM 2134 CB LEU A 349 68.640 6.844 10.712 1.00 64.68 C
+ATOM 2135 CG LEU A 349 67.694 5.804 11.311 1.00 66.45 C
+ATOM 2136 CD1 LEU A 349 68.128 4.439 10.845 1.00 67.37 C
+ATOM 2137 CD2 LEU A 349 67.698 5.885 12.832 1.00 66.12 C
+ATOM 2138 N GLU A 350 69.379 9.620 9.276 1.00 65.05 N
+ATOM 2139 CA GLU A 350 70.374 10.621 8.875 1.00 63.92 C
+ATOM 2140 C GLU A 350 70.117 11.953 9.645 1.00 63.05 C
+ATOM 2141 O GLU A 350 71.035 12.508 10.233 1.00 64.47 O
+ATOM 2142 CB GLU A 350 70.291 10.834 7.369 1.00 66.88 C
+ATOM 2143 CG GLU A 350 71.507 11.464 6.717 1.00 77.19 C
+ATOM 2144 CD GLU A 350 71.312 11.681 5.191 1.00 85.71 C
+ATOM 2145 OE1 GLU A 350 70.588 12.641 4.807 1.00 87.95 O
+ATOM 2146 OE2 GLU A 350 71.873 10.887 4.376 1.00 87.38 O
+ATOM 2147 N SER A 351 68.881 12.458 9.669 1.00 60.73 N
+ATOM 2148 CA SER A 351 68.588 13.697 10.407 1.00 58.59 C
+ATOM 2149 C SER A 351 68.845 13.493 11.888 1.00 57.78 C
+ATOM 2150 O SER A 351 69.325 14.386 12.582 1.00 56.87 O
+ATOM 2151 CB SER A 351 67.107 14.123 10.286 1.00 59.68 C
+ATOM 2152 OG SER A 351 66.656 14.320 8.953 1.00 61.53 O
+ATOM 2153 N SER A 352 68.477 12.315 12.375 1.00 58.27 N
+ATOM 2154 CA SER A 352 68.614 11.990 13.788 1.00 59.86 C
+ATOM 2155 C SER A 352 70.001 12.222 14.350 1.00 59.90 C
+ATOM 2156 O SER A 352 70.142 12.681 15.480 1.00 60.83 O
+ATOM 2157 CB SER A 352 68.180 10.550 14.035 1.00 60.42 C
+ATOM 2158 OG SER A 352 66.819 10.400 13.682 1.00 63.22 O
+ATOM 2159 N HIS A 353 71.027 11.894 13.578 1.00 59.11 N
+ATOM 2160 CA HIS A 353 72.381 12.123 14.037 1.00 60.55 C
+ATOM 2161 C HIS A 353 72.620 13.647 14.099 1.00 61.98 C
+ATOM 2162 O HIS A 353 73.180 14.174 15.063 1.00 61.82 O
+ATOM 2163 CB HIS A 353 73.380 11.475 13.076 1.00 62.23 C
+ATOM 2164 CG HIS A 353 73.320 9.978 13.056 1.00 64.82 C
+ATOM 2165 ND1 HIS A 353 72.299 9.281 12.449 1.00 66.83 N
+ATOM 2166 CD2 HIS A 353 74.159 9.044 13.562 1.00 63.15 C
+ATOM 2167 CE1 HIS A 353 72.513 7.984 12.580 1.00 63.45 C
+ATOM 2168 NE2 HIS A 353 73.636 7.815 13.252 1.00 62.73 N
+ATOM 2169 N ALA A 354 72.194 14.364 13.066 1.00 61.52 N
+ATOM 2170 CA ALA A 354 72.395 15.798 13.067 1.00 60.74 C
+ATOM 2171 C ALA A 354 71.647 16.379 14.245 1.00 60.80 C
+ATOM 2172 O ALA A 354 72.159 17.265 14.926 1.00 63.13 O
+ATOM 2173 CB ALA A 354 71.897 16.412 11.770 1.00 60.93 C
+ATOM 2174 N LEU A 355 70.439 15.877 14.492 1.00 59.22 N
+ATOM 2175 CA LEU A 355 69.645 16.376 15.601 1.00 57.42 C
+ATOM 2176 C LEU A 355 70.281 16.016 16.946 1.00 57.00 C
+ATOM 2177 O LEU A 355 70.153 16.744 17.932 1.00 56.76 O
+ATOM 2178 CB LEU A 355 68.226 15.817 15.542 1.00 55.41 C
+ATOM 2179 CG LEU A 355 67.415 16.306 16.760 1.00 56.24 C
+ATOM 2180 CD1 LEU A 355 67.523 17.840 16.854 1.00 50.61 C
+ATOM 2181 CD2 LEU A 355 65.953 15.839 16.668 1.00 52.65 C
+ATOM 2182 N ALA A 356 70.961 14.879 16.975 1.00 55.24 N
+ATOM 2183 CA ALA A 356 71.614 14.430 18.177 1.00 54.34 C
+ATOM 2184 C ALA A 356 72.708 15.417 18.566 1.00 58.03 C
+ATOM 2185 O ALA A 356 72.851 15.768 19.752 1.00 60.05 O
+ATOM 2186 CB ALA A 356 72.203 13.058 17.956 1.00 51.29 C
+ATOM 2187 N HIS A 357 73.481 15.883 17.582 1.00 58.73 N
+ATOM 2188 CA HIS A 357 74.553 16.806 17.896 1.00 58.00 C
+ATOM 2189 C HIS A 357 74.038 18.141 18.387 1.00 58.37 C
+ATOM 2190 O HIS A 357 74.630 18.750 19.278 1.00 57.48 O
+ATOM 2191 CB HIS A 357 75.450 17.043 16.708 1.00 59.51 C
+ATOM 2192 CG HIS A 357 76.653 17.865 17.048 1.00 64.94 C
+ATOM 2193 ND1 HIS A 357 77.817 17.312 17.538 1.00 64.94 N
+ATOM 2194 CD2 HIS A 357 76.845 19.206 17.045 1.00 65.63 C
+ATOM 2195 CE1 HIS A 357 78.673 18.277 17.819 1.00 65.86 C
+ATOM 2196 NE2 HIS A 357 78.108 19.437 17.531 1.00 65.89 N
+ATOM 2197 N ALA A 358 72.942 18.605 17.798 1.00 59.53 N
+ATOM 2198 CA ALA A 358 72.360 19.882 18.208 1.00 62.15 C
+ATOM 2199 C ALA A 358 71.926 19.704 19.640 1.00 62.35 C
+ATOM 2200 O ALA A 358 72.137 20.574 20.483 1.00 62.57 O
+ATOM 2201 CB ALA A 358 71.154 20.233 17.347 1.00 62.48 C
+ATOM 2202 N LEU A 359 71.320 18.549 19.898 1.00 62.12 N
+ATOM 2203 CA LEU A 359 70.840 18.199 21.225 1.00 61.09 C
+ATOM 2204 C LEU A 359 71.993 18.191 22.219 1.00 59.26 C
+ATOM 2205 O LEU A 359 71.850 18.640 23.351 1.00 57.03 O
+ATOM 2206 CB LEU A 359 70.159 16.834 21.173 1.00 60.49 C
+ATOM 2207 CG LEU A 359 68.642 16.775 21.348 1.00 58.96 C
+ATOM 2208 CD1 LEU A 359 67.969 18.046 20.832 1.00 57.43 C
+ATOM 2209 CD2 LEU A 359 68.144 15.533 20.630 1.00 59.17 C
+ATOM 2210 N LYS A 360 73.142 17.688 21.790 1.00 58.41 N
+ATOM 2211 CA LYS A 360 74.300 17.675 22.667 1.00 58.83 C
+ATOM 2212 C LYS A 360 74.777 19.119 22.917 1.00 60.42 C
+ATOM 2213 O LYS A 360 75.038 19.495 24.054 1.00 60.76 O
+ATOM 2214 CB LYS A 360 75.404 16.845 22.042 1.00 55.74 C
+ATOM 2215 CG LYS A 360 76.553 16.567 22.959 1.00 54.90 C
+ATOM 2216 CD LYS A 360 77.518 15.594 22.289 1.00 56.67 C
+ATOM 2217 CE LYS A 360 76.832 14.258 21.939 1.00 55.66 C
+ATOM 2218 NZ LYS A 360 77.720 13.334 21.176 1.00 54.59 N
+ATOM 2219 N MET A 361 74.866 19.934 21.863 1.00 61.12 N
+ATOM 2220 CA MET A 361 75.297 21.325 22.016 1.00 61.31 C
+ATOM 2221 C MET A 361 74.416 22.069 23.026 1.00 63.50 C
+ATOM 2222 O MET A 361 74.909 22.790 23.892 1.00 64.36 O
+ATOM 2223 CB MET A 361 75.261 22.050 20.666 1.00 59.64 C
+ATOM 2224 CG MET A 361 76.297 21.556 19.672 1.00 57.47 C
+ATOM 2225 SD MET A 361 76.282 22.375 18.061 1.00 57.21 S
+ATOM 2226 CE MET A 361 76.170 24.072 18.480 1.00 51.54 C
+ATOM 2227 N MET A 362 73.106 21.892 22.908 1.00 65.54 N
+ATOM 2228 CA MET A 362 72.159 22.533 23.814 1.00 66.13 C
+ATOM 2229 C MET A 362 72.344 21.991 25.251 1.00 66.31 C
+ATOM 2230 O MET A 362 72.582 22.737 26.200 1.00 64.63 O
+ATOM 2231 CB MET A 362 70.729 22.263 23.327 1.00 64.22 C
+ATOM 2232 CG MET A 362 69.636 22.721 24.283 1.00 63.49 C
+ATOM 2233 SD MET A 362 68.011 22.023 23.900 1.00 64.43 S
+ATOM 2234 CE MET A 362 68.467 20.231 23.663 1.00 57.50 C
+ATOM 2235 N ARG A 363 72.241 20.679 25.392 1.00 66.49 N
+ATOM 2236 CA ARG A 363 72.374 20.044 26.683 1.00 65.59 C
+ATOM 2237 C ARG A 363 73.671 20.364 27.401 1.00 68.49 C
+ATOM 2238 O ARG A 363 73.658 20.580 28.618 1.00 68.99 O
+ATOM 2239 CB ARG A 363 72.199 18.546 26.515 1.00 62.46 C
+ATOM 2240 CG ARG A 363 70.749 18.176 26.247 1.00 60.41 C
+ATOM 2241 CD ARG A 363 70.636 16.781 25.690 1.00 57.80 C
+ATOM 2242 NE ARG A 363 69.252 16.375 25.459 1.00 56.60 N
+ATOM 2243 CZ ARG A 363 68.948 15.243 24.843 1.00 55.83 C
+ATOM 2244 NH1 ARG A 363 69.936 14.467 24.433 1.00 54.57 N
+ATOM 2245 NH2 ARG A 363 67.692 14.886 24.631 1.00 52.88 N
+ATOM 2246 N GLU A 364 74.784 20.409 26.667 1.00 70.94 N
+ATOM 2247 CA GLU A 364 76.077 20.728 27.280 1.00 71.36 C
+ATOM 2248 C GLU A 364 76.010 22.085 27.966 1.00 72.35 C
+ATOM 2249 O GLU A 364 76.173 22.156 29.171 1.00 73.94 O
+ATOM 2250 CB GLU A 364 77.198 20.712 26.253 1.00 71.24 C
+ATOM 2251 CG GLU A 364 78.252 19.688 26.578 1.00 72.38 C
+ATOM 2252 CD GLU A 364 78.708 18.909 25.357 1.00 76.40 C
+ATOM 2253 OE1 GLU A 364 79.166 19.546 24.363 1.00 76.70 O
+ATOM 2254 OE2 GLU A 364 78.604 17.656 25.401 1.00 75.38 O
+ATOM 2255 N ASN A 365 75.782 23.170 27.237 1.00 73.26 N
+ATOM 2256 CA ASN A 365 75.661 24.426 27.952 1.00 75.22 C
+ATOM 2257 C ASN A 365 74.267 25.035 27.822 1.00 75.12 C
+ATOM 2258 O ASN A 365 73.988 25.834 26.917 1.00 75.48 O
+ATOM 2259 CB ASN A 365 76.719 25.437 27.531 1.00 79.46 C
+ATOM 2260 CG ASN A 365 76.994 26.463 28.641 1.00 85.51 C
+ATOM 2261 OD1 ASN A 365 76.135 27.296 28.990 1.00 86.30 O
+ATOM 2262 ND2 ASN A 365 78.188 26.383 29.223 1.00 89.33 N
+ATOM 2263 N PRO A 366 73.367 24.656 28.744 1.00 73.45 N
+ATOM 2264 CA PRO A 366 71.978 25.107 28.816 1.00 72.42 C
+ATOM 2265 C PRO A 366 71.822 26.607 28.772 1.00 72.69 C
+ATOM 2266 O PRO A 366 70.741 27.122 28.455 1.00 74.01 O
+ATOM 2267 CB PRO A 366 71.507 24.527 30.137 1.00 70.87 C
+ATOM 2268 CG PRO A 366 72.235 23.232 30.173 1.00 72.57 C
+ATOM 2269 CD PRO A 366 73.626 23.630 29.767 1.00 71.44 C
+ATOM 2270 N ASP A 367 72.898 27.316 29.076 1.00 71.79 N
+ATOM 2271 CA ASP A 367 72.810 28.752 29.088 1.00 72.55 C
+ATOM 2272 C ASP A 367 73.362 29.472 27.908 1.00 70.93 C
+ATOM 2273 O ASP A 367 72.954 30.592 27.637 1.00 70.35 O
+ATOM 2274 CB ASP A 367 73.452 29.304 30.340 1.00 79.86 C
+ATOM 2275 CG ASP A 367 72.555 29.173 31.536 1.00 86.06 C
+ATOM 2276 OD1 ASP A 367 71.365 29.574 31.420 1.00 88.65 O
+ATOM 2277 OD2 ASP A 367 73.034 28.670 32.584 1.00 91.30 O
+ATOM 2278 N LYS A 368 74.300 28.864 27.206 1.00 69.82 N
+ATOM 2279 CA LYS A 368 74.855 29.545 26.052 1.00 69.49 C
+ATOM 2280 C LYS A 368 73.654 29.881 25.208 1.00 71.05 C
+ATOM 2281 O LYS A 368 72.875 28.995 24.856 1.00 73.73 O
+ATOM 2282 CB LYS A 368 75.795 28.626 25.278 1.00 67.73 C
+ATOM 2283 CG LYS A 368 76.589 29.316 24.199 1.00 64.97 C
+ATOM 2284 CD LYS A 368 77.610 28.353 23.654 1.00 66.28 C
+ATOM 2285 CE LYS A 368 78.627 29.020 22.737 1.00 68.89 C
+ATOM 2286 NZ LYS A 368 79.660 28.021 22.277 1.00 69.89 N
+ATOM 2287 N GLU A 369 73.465 31.159 24.927 1.00 70.20 N
+ATOM 2288 CA GLU A 369 72.346 31.565 24.103 1.00 69.31 C
+ATOM 2289 C GLU A 369 72.795 31.287 22.669 1.00 68.85 C
+ATOM 2290 O GLU A 369 73.532 32.065 22.090 1.00 71.14 O
+ATOM 2291 CB GLU A 369 72.075 33.042 24.332 1.00 71.57 C
+ATOM 2292 CG GLU A 369 71.365 33.739 23.196 1.00 83.60 C
+ATOM 2293 CD GLU A 369 71.005 35.193 23.528 1.00 91.80 C
+ATOM 2294 OE1 GLU A 369 70.518 35.920 22.615 1.00 93.56 O
+ATOM 2295 OE2 GLU A 369 71.208 35.607 24.707 1.00 96.29 O
+ATOM 2296 N GLN A 370 72.371 30.161 22.103 1.00 67.85 N
+ATOM 2297 CA GLN A 370 72.760 29.790 20.743 1.00 64.61 C
+ATOM 2298 C GLN A 370 71.586 29.506 19.794 1.00 64.00 C
+ATOM 2299 O GLN A 370 70.559 28.965 20.202 1.00 64.99 O
+ATOM 2300 CB GLN A 370 73.691 28.583 20.803 1.00 63.27 C
+ATOM 2301 CG GLN A 370 73.135 27.414 21.569 1.00 61.33 C
+ATOM 2302 CD GLN A 370 74.199 26.369 21.862 1.00 64.92 C
+ATOM 2303 OE1 GLN A 370 75.280 26.394 21.266 1.00 62.72 O
+ATOM 2304 NE2 GLN A 370 73.896 25.431 22.774 1.00 65.52 N
+ATOM 2305 N LEU A 371 71.765 29.882 18.527 1.00 61.62 N
+ATOM 2306 CA LEU A 371 70.773 29.722 17.459 1.00 58.03 C
+ATOM 2307 C LEU A 371 71.264 28.670 16.476 1.00 57.54 C
+ATOM 2308 O LEU A 371 72.187 28.907 15.695 1.00 57.20 O
+ATOM 2309 CB LEU A 371 70.608 31.047 16.739 1.00 58.07 C
+ATOM 2310 CG LEU A 371 69.699 31.093 15.528 1.00 57.81 C
+ATOM 2311 CD1 LEU A 371 68.366 30.467 15.895 1.00 56.34 C
+ATOM 2312 CD2 LEU A 371 69.533 32.551 15.075 1.00 56.47 C
+ATOM 2313 N LEU A 372 70.621 27.515 16.489 1.00 55.94 N
+ATOM 2314 CA LEU A 372 71.051 26.409 15.644 1.00 53.83 C
+ATOM 2315 C LEU A 372 70.067 26.025 14.569 1.00 51.61 C
+ATOM 2316 O LEU A 372 68.869 26.171 14.748 1.00 54.88 O
+ATOM 2317 CB LEU A 372 71.282 25.181 16.526 1.00 54.39 C
+ATOM 2318 CG LEU A 372 72.143 25.374 17.776 1.00 53.85 C
+ATOM 2319 CD1 LEU A 372 72.100 24.123 18.626 1.00 54.34 C
+ATOM 2320 CD2 LEU A 372 73.561 25.689 17.364 1.00 54.82 C
+ATOM 2321 N VAL A 373 70.559 25.525 13.449 1.00 47.53 N
+ATOM 2322 CA VAL A 373 69.650 25.059 12.422 1.00 46.19 C
+ATOM 2323 C VAL A 373 70.086 23.641 12.056 1.00 47.63 C
+ATOM 2324 O VAL A 373 71.267 23.382 11.849 1.00 46.82 O
+ATOM 2325 CB VAL A 373 69.671 25.957 11.177 1.00 44.31 C
+ATOM 2326 CG1 VAL A 373 68.939 25.284 10.056 1.00 43.67 C
+ATOM 2327 CG2 VAL A 373 69.006 27.283 11.476 1.00 42.42 C
+ATOM 2328 N VAL A 374 69.138 22.714 12.018 1.00 47.67 N
+ATOM 2329 CA VAL A 374 69.453 21.338 11.662 1.00 48.38 C
+ATOM 2330 C VAL A 374 68.794 21.004 10.343 1.00 47.96 C
+ATOM 2331 O VAL A 374 67.596 21.221 10.169 1.00 48.04 O
+ATOM 2332 CB VAL A 374 68.955 20.324 12.734 1.00 49.64 C
+ATOM 2333 CG1 VAL A 374 69.073 18.861 12.226 1.00 44.97 C
+ATOM 2334 CG2 VAL A 374 69.766 20.497 13.983 1.00 51.45 C
+ATOM 2335 N ASN A 375 69.591 20.481 9.418 1.00 47.01 N
+ATOM 2336 CA ASN A 375 69.084 20.099 8.120 1.00 49.22 C
+ATOM 2337 C ASN A 375 68.393 18.750 8.245 1.00 50.82 C
+ATOM 2338 O ASN A 375 69.018 17.776 8.658 1.00 53.28 O
+ATOM 2339 CB ASN A 375 70.223 19.981 7.117 1.00 47.68 C
+ATOM 2340 CG ASN A 375 69.715 19.938 5.702 1.00 49.33 C
+ATOM 2341 OD1 ASN A 375 69.159 20.907 5.223 1.00 53.40 O
+ATOM 2342 ND2 ASN A 375 69.882 18.814 5.030 1.00 52.31 N
+ATOM 2343 N LEU A 376 67.116 18.670 7.893 1.00 50.82 N
+ATOM 2344 CA LEU A 376 66.415 17.398 7.995 1.00 52.07 C
+ATOM 2345 C LEU A 376 66.511 16.596 6.700 1.00 56.59 C
+ATOM 2346 O LEU A 376 66.035 17.046 5.672 1.00 58.32 O
+ATOM 2347 CB LEU A 376 64.965 17.655 8.355 1.00 48.80 C
+ATOM 2348 CG LEU A 376 64.511 17.106 9.709 1.00 49.39 C
+ATOM 2349 CD1 LEU A 376 65.647 17.042 10.696 1.00 48.10 C
+ATOM 2350 CD2 LEU A 376 63.386 17.976 10.232 1.00 48.51 C
+ATOM 2351 N SER A 377 67.137 15.419 6.753 1.00 62.47 N
+ATOM 2352 CA SER A 377 67.300 14.557 5.576 1.00 69.80 C
+ATOM 2353 C SER A 377 65.955 14.115 4.948 1.00 75.80 C
+ATOM 2354 O SER A 377 65.377 14.882 4.178 1.00 79.43 O
+ATOM 2355 CB SER A 377 68.148 13.325 5.918 1.00 70.12 C
+ATOM 2356 OG SER A 377 67.433 12.383 6.707 1.00 72.27 O
+ATOM 2357 N GLY A 378 65.426 12.920 5.229 1.00 78.55 N
+ATOM 2358 CA GLY A 378 64.170 12.638 4.561 1.00 83.95 C
+ATOM 2359 C GLY A 378 63.246 11.444 4.719 1.00 89.08 C
+ATOM 2360 O GLY A 378 62.082 11.624 5.108 1.00 89.15 O
+ATOM 2361 N ARG A 379 63.712 10.239 4.385 1.00 94.01 N
+ATOM 2362 CA ARG A 379 62.842 9.051 4.473 1.00 97.64 C
+ATOM 2363 C ARG A 379 62.382 8.660 5.893 1.00 98.26 C
+ATOM 2364 O ARG A 379 62.442 7.483 6.281 1.00 97.03 O
+ATOM 2365 CB ARG A 379 63.506 7.859 3.751 1.00 98.03 C
+ATOM 2366 CG ARG A 379 65.005 7.772 3.871 1.00 98.17 C
+ATOM 2367 CD ARG A 379 65.539 6.738 2.892 1.00 99.93 C
+ATOM 2368 NE ARG A 379 66.472 5.797 3.523 1.00103.91 N
+ATOM 2369 CZ ARG A 379 67.703 6.099 3.948 1.00104.42 C
+ATOM 2370 NH1 ARG A 379 68.184 7.332 3.811 1.00102.62 N
+ATOM 2371 NH2 ARG A 379 68.452 5.164 4.527 1.00104.51 N
+ATOM 2372 N GLY A 380 61.889 9.671 6.624 1.00 99.37 N
+ATOM 2373 CA GLY A 380 61.414 9.533 7.998 1.00 99.61 C
+ATOM 2374 C GLY A 380 60.500 8.359 8.272 1.00100.44 C
+ATOM 2375 O GLY A 380 60.649 7.670 9.285 1.00 99.86 O
+ATOM 2376 N ASP A 381 59.549 8.134 7.371 1.00101.00 N
+ATOM 2377 CA ASP A 381 58.622 7.023 7.512 1.00101.37 C
+ATOM 2378 C ASP A 381 58.919 5.890 6.524 1.00 99.89 C
+ATOM 2379 O ASP A 381 58.040 5.102 6.164 1.00 99.39 O
+ATOM 2380 CB ASP A 381 57.178 7.516 7.377 1.00102.85 C
+ATOM 2381 CG ASP A 381 56.738 8.341 8.580 1.00104.87 C
+ATOM 2382 OD1 ASP A 381 57.000 7.901 9.724 1.00105.99 O
+ATOM 2383 OD2 ASP A 381 56.132 9.422 8.391 1.00105.43 O
+ATOM 2384 N LYS A 382 60.176 5.815 6.102 1.00 97.20 N
+ATOM 2385 CA LYS A 382 60.616 4.765 5.199 1.00 95.55 C
+ATOM 2386 C LYS A 382 61.586 3.890 6.014 1.00 95.18 C
+ATOM 2387 O LYS A 382 61.481 2.655 6.031 1.00 94.87 O
+ATOM 2388 CB LYS A 382 61.294 5.390 3.981 1.00 95.57 C
+ATOM 2389 CG LYS A 382 60.491 6.557 3.395 1.00 93.08 C
+ATOM 2390 CD LYS A 382 60.924 6.893 1.975 1.00 91.26 C
+ATOM 2391 CE LYS A 382 60.553 5.776 1.009 1.00 89.86 C
+ATOM 2392 NZ LYS A 382 59.084 5.497 0.995 1.00 87.53 N
+ATOM 2393 N ASP A 383 62.517 4.528 6.717 1.00 93.00 N
+ATOM 2394 CA ASP A 383 63.433 3.769 7.554 1.00 89.31 C
+ATOM 2395 C ASP A 383 62.933 3.836 9.015 1.00 86.97 C
+ATOM 2396 O ASP A 383 63.710 3.880 9.969 1.00 85.65 O
+ATOM 2397 CB ASP A 383 64.878 4.283 7.386 1.00 89.71 C
+ATOM 2398 CG ASP A 383 65.086 5.664 7.946 1.00 88.34 C
+ATOM 2399 OD1 ASP A 383 66.169 6.238 7.703 1.00 86.64 O
+ATOM 2400 OD2 ASP A 383 64.176 6.168 8.635 1.00 90.01 O
+ATOM 2401 N ILE A 384 61.604 3.851 9.145 1.00 84.30 N
+ATOM 2402 CA ILE A 384 60.870 3.852 10.417 1.00 79.77 C
+ATOM 2403 C ILE A 384 60.876 2.383 10.838 1.00 79.99 C
+ATOM 2404 O ILE A 384 60.732 2.042 12.012 1.00 80.46 O
+ATOM 2405 CB ILE A 384 59.389 4.278 10.198 1.00 76.95 C
+ATOM 2406 CG1 ILE A 384 58.596 4.233 11.497 1.00 72.75 C
+ATOM 2407 CG2 ILE A 384 58.716 3.329 9.235 1.00 78.19 C
+ATOM 2408 CD1 ILE A 384 58.627 5.507 12.244 1.00 70.37 C
+ATOM 2409 N PHE A 385 61.041 1.526 9.831 1.00 80.37 N
+ATOM 2410 CA PHE A 385 61.075 0.076 9.982 1.00 78.22 C
+ATOM 2411 C PHE A 385 62.377 -0.424 10.608 1.00 76.05 C
+ATOM 2412 O PHE A 385 62.348 -1.213 11.549 1.00 74.70 O
+ATOM 2413 CB PHE A 385 60.851 -0.574 8.619 1.00 78.57 C
+ATOM 2414 CG PHE A 385 59.485 -0.301 8.032 1.00 82.09 C
+ATOM 2415 CD1 PHE A 385 59.265 -0.403 6.658 1.00 84.79 C
+ATOM 2416 CD2 PHE A 385 58.408 0.015 8.849 1.00 82.35 C
+ATOM 2417 CE1 PHE A 385 57.989 -0.198 6.109 1.00 83.74 C
+ATOM 2418 CE2 PHE A 385 57.129 0.221 8.307 1.00 83.10 C
+ATOM 2419 CZ PHE A 385 56.922 0.113 6.936 1.00 81.89 C
+ATOM 2420 N THR A 386 63.521 0.028 10.109 1.00 74.37 N
+ATOM 2421 CA THR A 386 64.766 -0.427 10.709 1.00 74.19 C
+ATOM 2422 C THR A 386 64.897 0.059 12.149 1.00 74.66 C
+ATOM 2423 O THR A 386 65.682 -0.474 12.925 1.00 75.68 O
+ATOM 2424 CB THR A 386 65.996 -0.001 9.894 1.00 71.90 C
+ATOM 2425 OG1 THR A 386 65.930 1.393 9.604 1.00 66.68 O
+ATOM 2426 CG2 THR A 386 66.056 -0.803 8.600 1.00 73.44 C
+ATOM 2427 N VAL A 387 64.120 1.067 12.510 1.00 75.15 N
+ATOM 2428 CA VAL A 387 64.156 1.561 13.866 1.00 75.26 C
+ATOM 2429 C VAL A 387 63.261 0.647 14.686 1.00 77.29 C
+ATOM 2430 O VAL A 387 63.562 0.325 15.832 1.00 77.22 O
+ATOM 2431 CB VAL A 387 63.662 2.998 13.935 1.00 74.73 C
+ATOM 2432 CG1 VAL A 387 63.530 3.437 15.388 1.00 73.32 C
+ATOM 2433 CG2 VAL A 387 64.644 3.893 13.201 1.00 73.69 C
+ATOM 2434 N HIS A 388 62.154 0.217 14.095 1.00 79.70 N
+ATOM 2435 CA HIS A 388 61.255 -0.693 14.791 1.00 81.27 C
+ATOM 2436 C HIS A 388 62.088 -1.913 15.154 1.00 80.71 C
+ATOM 2437 O HIS A 388 61.964 -2.458 16.246 1.00 80.26 O
+ATOM 2438 CB HIS A 388 60.100 -1.097 13.876 1.00 84.39 C
+ATOM 2439 CG HIS A 388 59.046 -1.916 14.555 1.00 88.33 C
+ATOM 2440 ND1 HIS A 388 57.750 -1.998 14.085 1.00 90.24 N
+ATOM 2441 CD2 HIS A 388 59.092 -2.688 15.667 1.00 89.20 C
+ATOM 2442 CE1 HIS A 388 57.044 -2.782 14.880 1.00 91.29 C
+ATOM 2443 NE2 HIS A 388 57.835 -3.214 15.848 1.00 91.37 N
+ATOM 2444 N ASP A 389 62.948 -2.322 14.221 1.00 80.92 N
+ATOM 2445 CA ASP A 389 63.838 -3.465 14.403 1.00 78.68 C
+ATOM 2446 C ASP A 389 64.872 -3.149 15.469 1.00 78.03 C
+ATOM 2447 O ASP A 389 64.890 -3.785 16.508 1.00 77.40 O
+ATOM 2448 CB ASP A 389 64.518 -3.803 13.087 1.00 77.68 C
+ATOM 2449 CG ASP A 389 63.520 -4.085 11.987 1.00 79.17 C
+ATOM 2450 OD1 ASP A 389 62.403 -4.550 12.310 1.00 79.13 O
+ATOM 2451 OD2 ASP A 389 63.850 -3.857 10.803 1.00 79.79 O
+ATOM 2452 N ILE A 390 65.732 -2.169 15.214 1.00 78.47 N
+ATOM 2453 CA ILE A 390 66.729 -1.760 16.201 1.00 80.70 C
+ATOM 2454 C ILE A 390 66.133 -1.868 17.614 1.00 82.21 C
+ATOM 2455 O ILE A 390 66.775 -2.392 18.522 1.00 84.61 O
+ATOM 2456 CB ILE A 390 67.165 -0.281 15.997 1.00 81.53 C
+ATOM 2457 CG1 ILE A 390 67.818 -0.088 14.628 1.00 80.20 C
+ATOM 2458 CG2 ILE A 390 68.115 0.138 17.112 1.00 81.04 C
+ATOM 2459 CD1 ILE A 390 69.267 -0.497 14.560 1.00 82.28 C
+ATOM 2460 N LEU A 391 64.908 -1.368 17.791 1.00 83.11 N
+ATOM 2461 CA LEU A 391 64.223 -1.404 19.089 1.00 83.92 C
+ATOM 2462 C LEU A 391 63.682 -2.786 19.480 1.00 83.95 C
+ATOM 2463 O LEU A 391 63.881 -3.223 20.606 1.00 82.85 O
+ATOM 2464 CB LEU A 391 63.082 -0.377 19.130 1.00 82.02 C
+ATOM 2465 CG LEU A 391 63.459 1.105 19.108 1.00 79.56 C
+ATOM 2466 CD1 LEU A 391 62.210 1.953 19.019 1.00 78.17 C
+ATOM 2467 CD2 LEU A 391 64.232 1.446 20.352 1.00 80.00 C
+ATOM 2468 N LYS A 392 62.989 -3.475 18.577 1.00 85.78 N
+ATOM 2469 CA LYS A 392 62.494 -4.803 18.928 1.00 89.19 C
+ATOM 2470 C LYS A 392 63.715 -5.672 19.240 1.00 91.13 C
+ATOM 2471 O LYS A 392 63.704 -6.475 20.178 1.00 91.51 O
+ATOM 2472 CB LYS A 392 61.657 -5.411 17.791 1.00 89.47 C
+ATOM 2473 CG LYS A 392 61.143 -6.826 18.089 1.00 89.98 C
+ATOM 2474 CD LYS A 392 59.886 -7.202 17.276 1.00 91.20 C
+ATOM 2475 CE LYS A 392 58.592 -6.640 17.907 1.00 91.19 C
+ATOM 2476 NZ LYS A 392 57.362 -7.096 17.188 1.00 86.27 N
+ATOM 2477 N ALA A 393 64.772 -5.483 18.453 1.00 92.28 N
+ATOM 2478 CA ALA A 393 66.028 -6.192 18.650 1.00 92.10 C
+ATOM 2479 C ALA A 393 66.496 -5.874 20.065 1.00 92.84 C
+ATOM 2480 O ALA A 393 66.285 -6.664 20.979 1.00 93.93 O
+ATOM 2481 CB ALA A 393 67.074 -5.716 17.644 1.00 90.79 C
+ATOM 2482 N ARG A 394 67.113 -4.707 20.236 1.00 92.16 N
+ATOM 2483 CA ARG A 394 67.619 -4.268 21.532 1.00 92.07 C
+ATOM 2484 C ARG A 394 66.660 -4.449 22.713 1.00 92.96 C
+ATOM 2485 O ARG A 394 66.934 -3.971 23.813 1.00 93.36 O
+ATOM 2486 CB ARG A 394 68.060 -2.809 21.430 1.00 91.41 C
+ATOM 2487 CG ARG A 394 69.268 -2.652 20.535 1.00 93.49 C
+ATOM 2488 CD ARG A 394 69.403 -1.270 19.908 1.00 94.71 C
+ATOM 2489 NE ARG A 394 69.924 -0.234 20.801 1.00 95.19 N
+ATOM 2490 CZ ARG A 394 69.214 0.372 21.747 1.00 95.47 C
+ATOM 2491 NH1 ARG A 394 67.941 0.043 21.942 1.00 94.25 N
+ATOM 2492 NH2 ARG A 394 69.771 1.333 22.472 1.00 93.95 N
+ATOM 2493 N GLY A 395 65.537 -5.127 22.480 1.00 93.48 N
+ATOM 2494 CA GLY A 395 64.571 -5.386 23.536 1.00 94.79 C
+ATOM 2495 C GLY A 395 63.766 -4.217 24.082 1.00 96.78 C
+ATOM 2496 O GLY A 395 62.786 -4.441 24.796 1.00 95.92 O
+ATOM 2497 N GLU A 396 64.174 -2.984 23.765 1.00 98.11 N
+ATOM 2498 CA GLU A 396 63.469 -1.786 24.230 1.00 99.11 C
+ATOM 2499 C GLU A 396 62.023 -1.784 23.749 1.00 99.15 C
+ATOM 2500 O GLU A 396 61.187 -1.070 24.301 1.00 98.52 O
+ATOM 2501 CB GLU A 396 64.138 -0.499 23.721 1.00 99.80 C
+ATOM 2502 CG GLU A 396 65.607 -0.317 24.082 1.00102.19 C
+ATOM 2503 CD GLU A 396 66.064 1.142 23.965 1.00103.97 C
+ATOM 2504 OE1 GLU A 396 67.278 1.418 24.106 1.00103.57 O
+ATOM 2505 OE2 GLU A 396 65.204 2.021 23.743 1.00105.40 O
+ATOM 2506 N ILE A 397 61.741 -2.572 22.712 1.00 99.58 N
+ATOM 2507 CA ILE A 397 60.397 -2.650 22.149 1.00100.03 C
+ATOM 2508 C ILE A 397 59.417 -3.050 23.232 1.00101.45 C
+ATOM 2509 O ILE A 397 58.751 -2.140 23.767 1.00103.73 O
+ATOM 2510 CB ILE A 397 60.324 -3.682 20.998 1.00100.17 C
+ATOM 2511 CG1 ILE A 397 58.930 -3.659 20.351 1.00 98.26 C
+ATOM 2512 CG2 ILE A 397 60.701 -5.085 21.520 1.00 98.24 C
+ATOM 2513 CD1 ILE A 397 57.906 -4.572 21.001 1.00 96.68 C
+ATOM 2514 OXT ILE A 397 59.338 -4.255 23.550 1.00101.23 O
+TER 2515 ILE A 397
+HETATM 2516 S SO4 801 69.043 7.012 -9.193 1.00 66.31 S
+HETATM 2517 O1 SO4 801 69.648 5.706 -8.897 1.00 68.30 O
+HETATM 2518 O2 SO4 801 68.821 7.147 -10.634 1.00 69.35 O
+HETATM 2519 O3 SO4 801 67.736 7.108 -8.505 1.00 63.38 O
+HETATM 2520 O4 SO4 801 70.013 8.049 -8.788 1.00 67.40 O
+HETATM 2521 S SO4 802 65.764 12.613 -3.024 1.00122.71 S
+HETATM 2522 O1 SO4 802 64.653 13.293 -2.314 1.00122.21 O
+HETATM 2523 O2 SO4 802 65.491 11.162 -3.117 1.00121.98 O
+HETATM 2524 O3 SO4 802 65.883 13.183 -4.375 1.00122.41 O
+HETATM 2525 O4 SO4 802 67.045 12.824 -2.321 1.00119.97 O
+HETATM 2526 S SO4 803 58.623 31.383 4.559 1.00107.36 S
+HETATM 2527 O1 SO4 803 57.430 32.257 4.562 1.00107.44 O
+HETATM 2528 O2 SO4 803 58.210 30.015 4.932 1.00108.48 O
+HETATM 2529 O3 SO4 803 59.264 31.351 3.223 1.00106.54 O
+HETATM 2530 O4 SO4 803 59.588 31.916 5.543 1.00107.97 O
+HETATM 2531 O HOH 1001 66.831 -5.950 -21.554 1.00 43.58 O
+HETATM 2532 O HOH 1002 65.180 -6.209 -19.516 1.00 41.65 O
+HETATM 2533 O HOH 1003 62.688 29.282 -4.030 1.00 34.17 O
+HETATM 2534 O HOH 1004 67.580 31.198 -8.353 1.00 44.19 O
+HETATM 2535 O HOH 1005 75.239 16.003 -1.158 1.00 39.55 O
+HETATM 2536 O HOH 1006 72.167 30.197 -10.130 1.00 61.12 O
+HETATM 2537 O HOH 1007 56.615 -0.232 -19.458 1.00 45.44 O
+HETATM 2538 O HOH 1008 54.711 11.001 10.088 1.00 50.45 O
+HETATM 2539 O HOH 1009 74.094 25.909 -27.795 1.00 51.85 O
+HETATM 2540 O HOH 1010 57.981 28.061 12.982 1.00 43.12 O
+HETATM 2541 O HOH 1011 56.654 12.901 10.569 1.00 59.80 O
+HETATM 2542 O HOH 1012 56.249 17.358 -10.214 1.00 42.97 O
+HETATM 2543 O HOH 1013 58.199 13.864 8.194 1.00 58.34 O
+HETATM 2544 O HOH 1014 84.797 21.480 -8.429 1.00 47.41 O
+HETATM 2545 O HOH 1015 73.057 8.384 -11.162 1.00 37.43 O
+HETATM 2546 O HOH 1016 61.749 32.271 1.216 1.00 32.23 O
+HETATM 2547 O HOH 1017 56.885 27.950 3.803 1.00 38.41 O
+HETATM 2548 O HOH 1018 57.120 18.339 25.504 1.00 42.95 O
+HETATM 2549 O HOH 1019 73.887 30.162 -24.485 1.00 31.25 O
+HETATM 2550 O HOH 1020 63.805 17.814 26.471 1.00 49.84 O
+HETATM 2551 O HOH 1021 80.312 11.302 0.318 1.00 46.36 O
+HETATM 2552 O HOH 1022 57.406 10.099 -0.875 1.00 58.56 O
+HETATM 2553 O HOH 1023 57.120 -1.779 -16.724 1.00 58.40 O
+CONECT 2516 2517 2518 2519 2520
+CONECT 2517 2516
+CONECT 2518 2516
+CONECT 2519 2516
+CONECT 2520 2516
+CONECT 2521 2522 2523 2524 2525
+CONECT 2522 2521
+CONECT 2523 2521
+CONECT 2524 2521
+CONECT 2525 2521
+CONECT 2526 2527 2528 2529 2530
+CONECT 2527 2526
+CONECT 2528 2526
+CONECT 2529 2526
+CONECT 2530 2526
+MASTER 353 0 3 16 10 0 0 6 2552 1 15 31
+END
diff --git a/data/spx.vtk b/data/spx.vtk
new file mode 100755
index 0000000..7db9582
--- /dev/null
+++ b/data/spx.vtk
@@ -0,0 +1,31678 @@
+# vtk DataFile Version 3.0
+off file: spx.off
+ASCII
+DATASET UNSTRUCTURED_GRID
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diff --git a/data/torus.vtk b/data/torus.vtk
new file mode 100755
index 0000000..20970ca
--- /dev/null
+++ b/data/torus.vtk
@@ -0,0 +1,22046 @@
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diff --git a/data/vslice_circ1.bp b/data/vslice_circ1.bp
new file mode 100644
index 0000000..261fff5
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+97 337408.437500 289107.937500 1.000000
+98 337550.437500 289237.125000 1.000000
+99 337687.375000 289371.687500 1.000000
+100 337819.031250 289511.375000 1.000000
diff --git a/doc/coding_conventions.txt b/doc/coding_conventions.txt
new file mode 100644
index 0000000..5b4f3b6
--- /dev/null
+++ b/doc/coding_conventions.txt
@@ -0,0 +1,149 @@
+Coding Conventions for VisTrails
+--------------------------------------------------------------------------------
+
+Variable naming, spacing
+------------------------
+
+Long version:
+
+ http://www.python.org/dev/peps/pep-0008/
+
+
+Short version:
+
+ Use 4 spaces per indentation level.
+
+ Use spaces, not tabs.
+
+ Hint: if you have a file that uses tabs and you're using emacs:
+
+ M-x mark-whole-buffer
+ M-x untabify
+
+ Limit lines to 79 characters. (Use Python's implied continuation
+ for parentheses, brackets and braces. Or use a backslash):
+
+ if this_is_true and this_other_thing_is_also_true and this_other_thing_makes_this_line_too_long:
+ raise This_is_bad_style
+
+ Fix it like this:
+
+ if (this_is_true and
+ this_other_thing_is_also_true and
+ this_other_thing_makes_this_line_too_long):
+ raise This_is_better_style
+
+ Or like this:
+
+ if this_is_true and \
+ this_other_thing_is_also_true and \
+ this_other_thing_makes_this_line_too_long:
+ raise This_is_not_as_good_but_better_than_long_lines
+
+ Blank lines
+
+ Separate top-level function and class definitions with two
+ blank lines.
+
+ Method definitions inside a class are separated by a single
+ blank line.
+
+ Extra blank lines may be used (sparingly) to separate groups
+ of related functions. Blank lines may be omitted between a
+ bunch of related one-liners (e.g. a set of dummy
+ implementations). Use blank lines in functions, sparingly, to
+ indicate logical sections.
+
+ Whitespace
+
+ Learn by example:
+
+ Yes: spam(ham[1], {eggs: 2})
+ No: spam( ham[ 1 ], { eggs: 2 } )
+
+ Yes: if x == 4: print x, y; x, y = y, x
+ No: if x == 4 : print x , y ; x , y = y , x
+
+ Yes: spam(1)
+ No: spam (1)
+
+ Yes: dict['key'] = list[index]
+ No: dict ['key'] = list [index]
+
+ Yes: def complex(real, imag=0.0): return magic(r=real, i=imag)
+ No: def complex(real, imag = 0.0): return magic(r = real, i = imag)
+
+
+ Comments:
+
+ Read http://www.python.org/dev/peps/pep-0008/
+
+
+ Capitalization:
+
+ class names are CamelCase, while methods and members
+ are_separated_by_underscores. This is not always possible,
+ especially when subclassing from Qt. Everywhere else, this
+ convention should be used. Qt signals are lowerCamelCase, to
+ be consistent with Qt.
+
+ Class members that are Qt objects themselves are probably OK
+ being camelCase, but everything that's possibly public-access
+ (through an API, for example), should be
+ separated_by_underscores.
+
+
+
+Docstrings
+----------
+ We agreed using something a little more compact than the guidelines
+available at:
+ http://www.python.org/dev/peps/pep-0257/
+
+ Examples:
+ If it is an obvious function, we should use something like this:
+ def temporaryDirectory():
+ """ temporaryDirectory() -> str
+ Returns the path to the system's temporary directory """
+ return "/tmp/"
+
+
+ If the function has structured parameters requiring a detailed description,
+ use something like this:
+
+ def complex(real=0.0, imag=0.0):
+ """complex(real=0.0, imag=0.0) -> complex
+ Form a complex number.
+
+ Keyword arguments:
+ real -- the real part
+ imag -- the imaginary part
+
+ """
+ if imag == 0.0 and real == 0.0: return complex_zero
+ ...
+
+
+Importing modules
+-----------------
+
+ Please import the modules using the fully qualified names,
+ even if they are in the right directories. For example, if you
+ have a file inside vistrails/core that imports a module inside
+ vistrails/core/data_structures, do NOT use this
+
+ import data_structures.graph # WRONG, don't do it!
+
+ instead, say
+
+ import core.data_structures.graph # RIGHT
+
+ This allows us to run the modules as standalone classes, which is
+ good for testing purposes.
+
+ Don't use the construct "from foo import *". This also imports the
+ tests from that module. The problem is that the test suite then
+ runs these tests twice. But worse than that is the problem that a
+ module that imports tests from other modules now reports these
+ tests as its own, even though it might have none. This gives us a
+ false sense of test converage which should be avoided.
diff --git a/doc/custom_constants.txt b/doc/custom_constants.txt
new file mode 100644
index 0000000..42365c9
--- /dev/null
+++ b/doc/custom_constants.txt
@@ -0,0 +1,118 @@
+When setting parameters on modules, some value types provide a custom
+widget. For example, VTK allows setting color properties by using
+color chooser widgets. These are defined on a per-constant basis, and
+they are set at module registration time, so you can define your own
+widgets for constants. This file describes how to do just that.
+
+--------------------------------------------------------------------------------
+Creating a new constant
+
+To create a widget for your own module, you first need to make sure
+your module subclasses from Constant, the base class for all constant
+values in VisTrails. If you don't know how to create user-defined
+modules, please check the documentation for that first.
+
+A user-defined constant is a module that should respect a few
+additional requirements. These are documented in the docstring for
+Constant, in core/modules/basic_modules.py, and reproduced here for
+completeness.
+
+ When implementing your own constant, You have to adhere to the
+ following interface:
+
+ Implement the following methods:
+
+ translate_to_python(x): Given a string, translate_to_python
+ must return a python value that will be the value seen by the
+ execution modules.
+
+ For example, translate_to_python called on a float parameter
+ with value '3.15' will return float('3.15').
+
+ translate_to_string(): Return a string representation of the
+ current constant, which will eventually be passed to
+ translate_to_python.
+
+ validate(v): return True if given python value is a plausible
+ value for the constant. It should be implemented such that
+ validate(translate_to_python(x)) == True for all valid x
+
+ A constant must also expose its default value, through the field
+ default_value.
+
+ There are fields you are not allowed to use in your constant classes.
+ These are: 'id', 'interpreter', 'logging' and 'change_parameter'
+
+--------------------------------------------------------------------------------
+GUI widgets
+
+Now that we have a constant class, we need to create a widget that
+allows the custom values to be set.
+
+This can be any PyQt widget, provided that you respect the following
+requirements:
+
+1) Your class should always inherit from
+core.modules.constant_configuration.ConstantMixin, a class mixin that
+provides you with some necessary infrastructure.
+
+2) Your constructor should expect an instance of
+core.vistrail.module_param.ModuleParam and the widget's Qt parent. The
+fields you are probably going to use from ModuleParam are 'type',
+'identifier', 'namespace' and 'strValue'. The first three are used to
+specify the actual type of the class, and 'strValue' is a string
+representation of the value itself, typically obtained by a call to
+translate_to_string() as described above. A typical declaration of the
+constructor then would be
+
+ class MyOwnConstant(SomeQtWidget, ConstantMixin):
+ def __init__(self, param, parent=None):
+ SomeQtWidget.__init__(self, parent)
+ ConstantMixin.__init__(self)
+
+3) You should implement a "contents()" method that returns a string
+representation of the value encoded by the GUI in its current state.
+
+4) Every time a change in the GUI state should be passed to VisTrails,
+you should call update_parent(). Every time this is called a new
+version is created, so make sure you have a reasonable granularity.
+
+--------------------------------------------------------------------------------
+
+Constants during execution
+
+To make writing your own modules more convenient, VisTrails provides a
+certain amount of transparent conversion for some constants. Consider
+this example. A VisTrails pipeline contains a Float module with value
+3.0 connected to port "port1" on a downstream module "Foo" whose
+compute method is as follows:
+
+class Foo(Module):
+ ...
+ def compute(self):
+ ...
+ x = self.getInputFromPort("port1")
+
+In this case, x will be a basic Python value of type 'float', _not_ a
+module of type Float. This automatic conversion happens for only a few
+classes: Boolean, Integer, Null, Float, and String. These get
+translated to the expected python types (Null becomes None).
+
+Note, however, that this translation does _not_ happen for any other
+constant, so if you need programmatic access to a constant in your
+code, you should distinguish between these cases.
+
+--------------------------------------------------------------------------------
+Gotchas, what to watch out for:
+
+If your custom widget is generating errors with tracebacks similar to:
+
+ File "/home/cscheid/vistrails/trunk/vistrails/core/modules/constant_configuration.py", line 43, in update_parent
+
+ if newContents != self._last_contents:
+AttributeError:_last_contents
+
+It probably means you forgot to call the constructor to
+ConstantWidgetMixin.
+
+--------------------------------------------------------------------------------
diff --git a/doc/dist/build_from_source_mac.txt b/doc/dist/build_from_source_mac.txt
new file mode 100644
index 0000000..2d13f84
--- /dev/null
+++ b/doc/dist/build_from_source_mac.txt
@@ -0,0 +1,62 @@
+Building VisTrails from Source
+
+--- Instructions Mac OSX Lion ----
+
+Install the following required software:
+ XCode
+ Command Line Tools (separate download through apple developer web site)
+
+ Python (python.org)
+ make sure to update the PATH to use this python. There's a script that does that in /Applications/Python 2.7/Update Shell Profile.command
+
+ Git
+
+ CMake
+
+ Qt
+
+ Boost (if we want to include text analysis support in VTK (it is currently included in 2.0 but I couldn't get it to work in VTK 5.10 on a Mac)
+
+ VTK
+
+ sip
+
+ PyQt4
+
+ QScintilla and python bindings (read instructions in QScintilla documentation)
+
+ NumPy (Binary installation)
+
+ SciPy (Binary installation)
+
+ Matplotlib (Binary installation)
+
+ suds (patched version)
+
+ MySQLdb (you also need to install MySQL Server so we get the lib and headers)
+
+ libxml2 and libxslt (same versions as in Snow Leopard, instructions here: http://www.vistrails.org/index.php/Mac_Intel_Instructions)
+
+ Numeric 23.8.2 (source files is in ~/src (needed by NumScipy)
+ $ cd ~/src/Numeric-23.8.2
+ $ python setup.py
+
+ fftw3 lib (source files is in ~/src)
+
+ Stockwell (needed by NumSciPy got the files from Erik Anderson the folder is also in ~/src)
+ cd ~/src/stockwell
+ make
+ cp *.so /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/
+ pexpect (easy_install pexpect)
+ psycopg2 (need PostGreSQL)
+ http://www.enterprisedb.com/products-services-training/pgdownload#osx
+ ScientificPython
+ batchq (ALPS) download and install it from https://github.com/troelsfr/BatchQ
+ h5py (ALPS) need to install hdf5 (make sure to --enable-hl)
+
+ download Thuban (http://wald.intevation.org/frs/?group_id=6&release_id=275#thuban-_1.2.2-title-content) and build only libraries/pyshapelib
+for shape files (not sure which package requires this)
+
+ easy_install numexpr
+ easy_install Cython
+ easy_install tables (this didn't work on Lion)
diff --git a/doc/dist/build_from_source_windows.txt b/doc/dist/build_from_source_windows.txt
new file mode 100644
index 0000000..a532653
--- /dev/null
+++ b/doc/dist/build_from_source_windows.txt
@@ -0,0 +1,123 @@
+
+== Windows Build ==
+
+Download and install python from www.python.org. Get both 32-bit and 64-bit versions. Install the 64-bit version in C:\Python27_64 and the 32-bit version in C:\Python27
+
+Download and install msysgit (the windows git user is winbuild and there's no passphrase when generating the ssh keys).
+
+Download and install PyQt4 binary installers (includes sip, Qt and QScintilla)
+
+Download and install active tcl/tk 8.5 both 32-bit and 64-bit versions (make sure to install them in different directories C:\Tcl and C:\Tcl_64
+
+download boost library from www.boost.org and uncompress it to a local folder,
+I had problems building vtk with recent versions of boost, the version I know it works for sure is 1.46.1.
+So extract the zip file to a folder, for example ~/src/boost_1_46_1 vtk will use the same boost for both 32-bit and 64-bit versions
+
+Download and install cmake
+Get vtk source
+uncompress it to (e.g, ~\src\vtk\vtk-5.10.1\
+and rename the VTK folder to src
+create build and build64 folders in ~\src\vtk\vtk-5.10.1
+
+vtk 32-bit:
+ run cmake-gui pointing the src folder to src and build folder to build and press configure
+ select Visual Studio 9 2008
+ mark the following variables:
+ BUILD_SHARED_LIBS
+ VTK_WRAP_PYTHON
+ on the top check Advanced
+ now mark
+ VTK_USE_BOOST
+ VTK_USE_TEXT_ANALYSIS
+ and press configure
+ Set
+ Boost_INCLUDE_DIR to ~/src/boost_1_46_1 (or where you uncompressed boost)
+ make sure it is using the correct versions of tcl and python (they should point to 32-bit installed versions)
+ press configure again and finally press generate
+ now browse to the build directory and open VTK.sln in Visual Studio
+ On the top bar select Release and then build solution (F7)
+If all goes well, you can install vtk python bindings:
+open a command prompt in the build/Wrapping/Python folder and run the following command:
+C:\Python27\python.exe setup.py BUILD_TYPE=Release install
+
+I've created two environment variables called PATH32 and PATH64 configured with
+the environment for each version of VisTrails:
+
+PATH32 = C:\Tcl\bin;C:\Python27\Lib\site-packages\PyQt4;C:\Python27;C:\Python27\Scripts;C:\Users\vistrails\src\vtk\vtk-5.10.1\build\bin\Release;C:\Users\vistrails\code\vistrails\dist\windows\Input
+
+PATH64 = C:\Tcl_64\bin;C:\Python27_64\Lib\site-packages\PyQt4;C:\Python27_64;C:\Python27_64\Scripts;C:\Users\vistrails\src\vtk\vtk-5.10.1\build64\bin\Release;C:\Users\vistrails\code\vistrails\dist\windows\Input
+
+Then, when I need to use the right environment, I just update the PATH
+variable with the right one:
+
+PATH = %PATH64%;%PATH%
+
+vtk 64-bit:
+
+ run cmake-gui again pointing the src folder to src and build folder to build64 and press configure
+ select Visual Studio 9 2008 Win64
+ mark the following variables:
+ BUILD_SHARED_LIBS
+ VTK_WRAP_PYTHON
+on the top check Advanced
+ now mark
+ VTK_USE_BOOST
+ VTK_USE_TEXT_ANALYSIS
+and press configure
+
+ Set
+ Boost_INCLUDE_DIR to ~/src/boost_1_46_1 (or where you uncompressed boost)
+ Boost_LIBRARY_DIRS to ~/src/boost_1_46_1/libs
+
+ make sure it is using the correct versions of tcl and python (they should point to 64-bit installed versions) press configure again and finally press generate now browse to the build64 directory and open VTK.sln in Visual Studio On the top bar select Release and then build solution (F7)
+If all goes well, switch to the 64 bit Path and you can install vtk python bindings:
+open a command prompt in the build64/Wrapping/Python folder and run the following command:
+C:\Python27_64\python.exe setup.py BUILD_TYPE=Release install
+
+Now let's build each configuration at time, starting with the 32-bit version:
+
+== 32-bit version ==
+
+Download and install numpy from numpy.scipy.org (there is a win32 super pack for python 2.7 binary version on source forge)
+
+Download and install scipy from scipy.org (there is a win32 super pack for python 2.7 binary version on source forge)
+
+Download and install matplotlib from matplotlib.org (there is a win32 for python 2.7 version on source forge)
+
+Download and install mysqldb python from source forge, there's a win32 binary installer for python 2.7.
+
+Download and unzip hdf5-1.8.4 from http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.4/bin/windows/hdf5-1.8.4-32bit-VS2008-IVF101.zip
+
+Download fftw (http://www.fftw.org/install/windows.html) from ftp://ftp.fftw.org/pub/fftw/fftw-3.3.3-dll32.zip and extract the zip file to the folder ~/src/fftw-3.3.3-dll32
+
+Download and install setuptools (easy_install)
+
+Download and install the patched version of suds
+
+Copy stockwell files from x86_bin folder to C:\Python27\Lib\site-packages
+st.pyd and sine.pyd
+
+== 64-bit version ==
+
+Go to http://www.lfd.uci.edu/~gohlke/pythonlibs/ and download and
+ install the 64-bit versions of (they are all binaries):
+ numpy (get the MKL version)
+ scipy
+ matplotlib
+ MySQL-python
+ psycopg
+
+Download and unzip hdf5-1.8.4 from http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.4/bin/windows/hdf5-1.8.4-64bit-VS2008-IVF101.zip
+
+Download fftw (http://www.fftw.org/install/windows.html) from
+ftp://ftp.fftw.org/pub/fftw/fftw-3.3.3-dll64.zip and extract the zip
+file to the folder ~/src/fftw-3.3.3-dll64 Follow the instructions on
+the web page to generate the .lib files
+
+Download and install setuptools (easy_install)
+
+Download and install the patched version of suds
+
+Copy stockwell files from x64_bin folder to C:\Python27_64\Lib\site-packages
+st.pyd and sine.pyd
+#Under construction
diff --git a/doc/dist/instructions.txt b/doc/dist/instructions.txt
new file mode 100644
index 0000000..9095b06
--- /dev/null
+++ b/doc/dist/instructions.txt
@@ -0,0 +1,188 @@
+VisTrails Building Binary Releases
+----------------------------------
+
+1. Make sure you can run VisTrails from source on the system you will
+run these instructions. Instructions to build VisTrails from source
+are on build_from_source_mac.txt and build_from_source_windows.txt.
+
+2. Then make sure the system is prepared to package
+VisTrails. Instructions to install the required software are on
+setup_build_system_mac.txt and setup_build_system_windows.txt
+
+3. Now follow the instructions below:
+
+Binary build instructions
+-------------------------
+
+== Preparation ==
+
+These work for making both Mac and Windows releases and need to be
+done only once before generating them. I think it is easier to do on a
+Mac, commit the changes and load them on the Windows machines.
+
+=== Change in Licensing or Update the look and feel in the Mac .dmg
+file ===
+If you ever need to change the VisTrails license or need to change the
+look and feel of the .dmg file we distribute, you can do that by
+opening dist/mac/vistrails.dmgCanvas. In the project settings you can
+update the license text (that one the is displayed when you open
+the .dmg). Else you can control the background image and other
+settings.
+Usually you don't need to touch this file. So go ahead to the next steps.
+
+
+
+Updating version numbers
+
+If there is a version upgrade from 2.0 to 2.1 you need to update the
+ following files (the variable name that needs to be updated are in parentheses:
+ scripts/release_notes.py (release_name)
+ scripts/create_release_wiki_table.py (VT_VERSION)
+ vistrails/core/system/__init__.py (function vistrails_version())
+ dist/mac/setup.py (VERSION)
+ dist/windows/vistrails.iss (AppVerName)
+ dist/windows/vistrailsx64.iss (AppVerName)
+ dist/windows/custom/*.iss (AppVerName)
+ dist/source/make-vistrails-src-release.py (VT_VERSION)
+ doc/usersguide/conf.py
+
+The splash screen also needs to be updated:
+ vistrails/gui/resources/images/vistrails_splash.png
+
+The Adobe Illustrator source file is in the master branch, in
+dist/common/splash folder. You need to install the font file in that
+folder too before opening the .ai file. After the changes, export the
+file to a .png file. Then open it in Photoshop and resize the image to
+546x340 pixels. Then replace the file in
+ vistrails/gui/resources/images/vistrails_splash.png
+
+Commit and push your changes.
+
+Generating the release notes
+
+Make sure scripts/release_notes.py is configured right: look for the variables inside the #### configuration #### section in the file.
+
+In particular, make sure branch has the right branch and commit_start points to the hash tag used on the last release. Also you might need to change release_name as you see fit.
+
+Then run:
+$ cd path/to/scripts
+$ python release_notes.py
+
+This will checkout the branch, process all commits and match them with the trac tickets. It will ask for your login and password on trac to do that. At the end, it will print out a release notes section. Just copy from Release Name.... down to the last item in Bug fixes. All the log messages that were not identified with <bugfix> or <feature> will be print out at the end but they can be ignored. Sometimes just take a look and see if there is something important there that should go as bu [...]
+
+You should paste the text into the dist/mac/Input/README file, just below
+RELEASE NOTES
+-----------------------
+
+Also take a look if there aren't repeated items... They might happen when there are merges across the branches and the commit messages got repeated.
+
+Then do the same into dist/windows/Input/releaseNotes.txt
+
+Then commit and push your changes. Now you are ready to generate the binaries on each platform.
+
+== Mac Binary Instructions ==
+ALPS
+Make sure the latest version of ALPS will be included in the binary.
+Go to http://archive.comp-phys.org/software/vistrails/ and look for the latest version and update dist/mac/make_app (ALPS_VERSION). If there were any changes, commit and push them before following next instructions.
+
+Updating revision numbers
+
+Run git log to know what is the latest hash tag on the release branch and copy the first 12 characters from it. This will be the revision number. There's probably a way to automate this but I didn't have time to look into it.
+
+Update the following files with the "revision number"
+ vistrails/core/system/__init__.py (function vistrails_revision())
+ dist/mac/Input/README (Release Name...)
+ dist/source/make-vistrails-src-release.py (VT_HASH)
+ dist/windows/Input/releaseNotes.txt
+ scripts/create_release_wiki_table.py
+ scripts/release_notes.py
+add and commit the changes. This will be the version released.
+
+Update usersguide paths
+
+Make sure the generated users guide is saved to the correct path by
+editing the following file:
+scripts/build_usersguide.py
+By default it is configured for mac
+
+Now run the following:
+$ cd dist/mac/
+$ ./make_app vistrails-mac-10.6-intel-[VER]-[REV]
+where [VER] should be the vistrails version, and [REV] the revision hash.
+
+at the end you should have a file called vistrails-mac-10.6-intel-[VER]-[REV].dmg that can be tested and uploaded to SourceForge.
+You should have created the folder of the new release on source forge before running the command below
+
+$ scp vistrails-mac-10.6-intel-[VER]-[REV].dmg [SFUSER]@frs.sourceforge.net:/home/frs/project/vistrails/vistrails/v[VER]
+where [SFUSER] is your sourceforge user.
+
+== Windows 32-bit Binary Instructions ==
+Update your local copy so you get the newest changes you pushed from
+the Mac.
+VisTrails needs to be run on Windows before the release so it builds
+all the *.pyc files before hand. This can be done by running:
+$ python -m compileall .
+Also, as we are running both 32-bit and 64-bit versions on the same
+system, make sure the PATH variables are set accordingly to use the
+32-bit version of python, vtk, etc. (if you run vistrails 32-bit) or
+the 64-bit version of python, vtk, etc. (if you run vistrails 64-bit).
+
+ALPS
+Make sure the latest version of ALPS will be included in the binary.
+Go to http://archive.comp-phys.org/software/vistrails/
+Download and uncompress the alps package for windows 32 bit available on http://archive.comp-phys.org/software/vistrails/ into dist/windows/Input/x86/alps_libs folder (it will create a bin and a vistrails folder inside it)
+
+Open dist\windows\vistrails.iss by double-clicking it
+This will launch InnoSetup
+Press the compile script button
+When it finishes a file called dist\windows\Output\vistrails-setup.exe will be created. Rename it according to the release name and create a zip file from it.
+Upload the file to sourceForge (I use WinFTP for this).
+
+Custom 32-bit builds
+For every vistrails-*.iss file in dist/windows/custom folder, run
+InnoSetup. Binaries will be generated in custom/Output folder. Rename it according to the release name and create a zip file from it.
+Upload the file to sourceForge (I use WinFTP for this).
+
+== Windows 64-bit Binary Instructions ==
+
+ALPS
+Make sure the latest version of ALPS will be included in the binary.
+Go to http://archive.comp-phys.org/software/vistrails/
+Download and uncompress the alps package for windows 64 bit available on http://archive.comp-phys.org/software/vistrails/ into dist/windows/Input/x64/alps_libs folder (it will create a bin and a vistrails folder inside it)
+
+Open dist\windows\vistrails_x64.iss by double-clicking it
+This will launch InnoSetup
+Press the compile script button
+When it finishes a file called dist\windows\Output\vistrails-setup.exe will be created. Rename it according to the release name and create a zip file from it.
+Upload the file to sourceForge (I use WinFTP for this).
+
+Custom 64-bit builds
+For every vistrailsx64-*.iss file in dist/windows/custom folder, run
+InnoSetup. Binaries will be generated in custom/Output folder. Rename it according to the release name and create a zip file from it.
+Upload the file to sourceForge (I use WinFTP for this).
+
+
+== Source Distribution Instructions ==
+cd path/to/dist/source
+make sure make-vistrails-src-release.py is updated with the right
+branch VT_BRANCH, VT_VERSION and VT_HASH.
+Also update the SF_USERNAME with the vistrails build username if you
+want to upload directly from the script. I usually don't because I
+don't want to commit the vistrails username to the repository so I
+skip the upload to source forge step and use the scp command line above to
+upload the file using my own user.
+
+All the files you need to upload to source forge using the vistrails
+username are in the vistrails server machine. In the cron directory,
+you can look how it is configured so the nightly builds are uploaded
+every night when there are changes.
+
+to generate the tarball:
+$ python make-vistrails-src-release.py
+It will checkout the hash code defined in the file and rename the
+tarball apropriately.
+
+== Update "Check For Updates" ==
+
+If this is a new stable version, log in to vistrails.org and update the version number in:
+/srv/wiki/vistrails/downloads/dist/release_version.txt
diff --git a/doc/dist/setup_build_system_mac.txt b/doc/dist/setup_build_system_mac.txt
new file mode 100644
index 0000000..b673f12
--- /dev/null
+++ b/doc/dist/setup_build_system_mac.txt
@@ -0,0 +1,55 @@
+# Required software for building binaries
+Install Mercurial http://mercurial.selenic.com/
+
+Checkout and install altgraph
+$ hg clone https://bitbucket.org/ronaldoussoren/altgraph
+$ cd altgraph
+$ python setup.py install
+$ cd ..
+
+Checkout and install macholib
+$ hg clone https://bitbucket.org/ronaldoussoren/macholib
+$ cd macholib
+$ python setup.py install
+$ cd ..
+
+Checkout and install modulegraph
+$ hg clone https://bitbucket.org/ronaldoussoren/modulegraph
+$ cd modulegraph
+$ python setup.py install
+$ cd ..
+
+Checkout and install py2app
+$ hg clone https://bitbucket.org/ronaldoussoren/py2app
+$ cd py2app
+$ python setup.py install
+$ cd ..
+
+Now we need to prepare Qt's plugin libs to be included in the binary because py2app doesn't seem to handle them correctly
+
+Just copy the iconengines and imageformats plugins and run
+vistrails/dist/mac/Input/fix_qtplugin_libs.py on each folder:
+$ cd dist/mac/Input
+$ mkdir plugins
+$ cd plugins
+$ cp -r /Developer/Applications/Qt/plugins/iconengines .
+$ cp -r /Developer/Applications/Qt/plugins/imageformats .
+$ cd ../..
+$ python fix_qtplugin_libs.py Input/plugins/iconengines/
+$ python fix_qtplugin_libs.py Input/plugins/imageformats/
+
+Copy /usr/bin/git to dist/mac/Input
+
+Create a directory alps_libs in Input to store the alps_libs
+
+#GDAL Framework
+Install GDAL Framework Complete 1.8.1 http://www.kyngchaos.com/software/frameworks
+then copy site-packages to python.org directory:
+$ cp -r /Library/Frameworks/GDAL.framework/Versions/1.8/Python/2.7/site-packages/* /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/
+
+#Install DMG Canvas
+Right now the only way is by copying the App from the build
+machine. The developers are now charging for a License when it used to
+be free. DMG Canvas is an application that creates the customized .dmg
+file. It provides a command line tool and we are using it in the main
+make_app script.
diff --git a/doc/dist/setup_build_system_windows.txt b/doc/dist/setup_build_system_windows.txt
new file mode 100644
index 0000000..162dc8d
--- /dev/null
+++ b/doc/dist/setup_build_system_windows.txt
@@ -0,0 +1,61 @@
+
+== Preparing to generate the release ==
+Install InnoDB Setup
+Download and install the QuickStart Pack of Inno Setup from http://www.jrsoftware.org/isdl.php
+
+Checkout VisTrails git repository
+In dist/windows/Input folder create a folder named x86
+Copy python27.dll 32 bit version into the x86 folder
+Inside the x86 folder create a folder called alps_libs
+
+In dist/windows/Input folder create a folder named x64
+Copy python27.dll 64 bit version into the x64 folder
+Inside the x64 folder create a folder called alps_libs
+
+
+== Custom Builds ==
+Inside dist/windows/custom there are scripts for custom builds.
+
+=== GDAL ===
+Download the GDAL files from:
+32-bit:
+http://www.gisinternals.com/sdk/Download.aspx?file=release-1500-gdal-1-9-2-mapserver-6-2-0\gdal-19-1500-core.msi
+http://www.gisinternals.com/sdk/Download.aspx?file=release-1500-gdal-1-9-2-mapserver-6-2-0\GDAL-1.9.2.win32-py2.7.msi
+Install the first file.
+
+Install the second file to a custom Python27
+installation (I believe it can be any folder on your hard drive). I
+copied the installed python files to:
+C:\Users\vistrails\extra_packages\gdal\x86\site-packages
+I then went to the C:\Program Files (x86)\GDAL folder (created by the first
+installer) and copied all the dlls into the osgeo folder inside
+C:\Users\vistrails\extra_packages\gdal\x86\site-packages
+Compiled all .py files with python -m compileall . inside the
+site-packages folder
+
+The script dist/windows/custom/vistrails_gdal.iss will copy the files
+in the binary. Just execute Inno Setup as a normal release. It will
+create a file called vistrails-gdal-setup.exe into
+dist/windows/custom/Output
+
+64-bit:
+http://www.gisinternals.com/sdk/Download.aspx?file=release-1500-x64-gdal-1-9-2-mapserver-6-2-0\gdal-19-1500-x64-core.msi
+http://www.gisinternals.com/sdk/Download.aspx?file=release-1500-x64-gdal-1-9-2-mapserver-6-2-0\GDAL-1.9.2.win-amd64-py2.7.msi
+
+Install the first file.
+
+Install the second file to a custom Python27_64
+installation (I believe it can be any folder on your hard drive). I
+copied the installed python files to:
+C:\Users\vistrails\extra_packages\gdal\x64\site-packages
+I then went to the C:\Program Files\GDAL folder (created by the first
+installer) and copied all the dlls into the osgeo folder inside
+C:\Users\vistrails\extra_packages\gdal\x64\site-packages
+Compiled all .py files with python -m compileall . inside the
+site-packages folder
+
+The script dist/windows/custom/vistrailsx64_gdal.iss will copy the files
+in the binary. Just execute Inno Setup as a normal release. It will
+create a file called vistrails-x64-gdal-setup.exe into
+dist/windows/custom/Output
+
diff --git a/doc/module_registry.txt b/doc/module_registry.txt
new file mode 100644
index 0000000..ef86613
--- /dev/null
+++ b/doc/module_registry.txt
@@ -0,0 +1,14 @@
+--------------------------------------------------------------------------------
+Signatures in calls to add_input_port and add_output_port
+
+A signature given by the user in a call like this
+add_input_port(module, name, signature) should be one of the
+following:
+
+type only: add_input_port(_, _, Float)
+type plus description: add_input_port(_, _, (Float, 'radius'))
+
+multiple parameters, where each parameter can be either of the above:
+add_input_port(_, _, [Float, (Integer, 'count')])
+
+--------------------------------------------------------------------------------
diff --git a/doc/package_system.txt b/doc/package_system.txt
new file mode 100644
index 0000000..e1dcbf6
--- /dev/null
+++ b/doc/package_system.txt
@@ -0,0 +1,99 @@
+FIXME this is old and does not reflect namespaces
+
+on port specs, a name is now of the form
+
+package_identifier:module_name
+
+this means that ":" is no longer allowed on module names.
+
+--------------------------------------------------------------------------------
+
+A package has three "names" associated with it:
+
+- A human-readable name, which is given by the package creator, and is
+ available as the 'name' attribute in the package.
+- A unique identifier, which is given by the package creator, and is
+ available as the 'identifier' attribute in the package
+- A code-path, which is currently given by the package user, and is
+ used by the package manager to get to the package.
+
+These three names are necessary for different reasons. A code-path
+needs to be unique within a VisTrails install so that __import__ is
+well-defined. However, it is not currently under the control of the
+package creator. This is the main identifier for
+core/packagemanager.py, which deals mainly with the executable code
+aspects of VisTrails packages. A human-readable name is necessary for
+the Module Palette in the UI, so that users can quickly see a
+descriptive name for a package. These names might be duplicate across
+a VisTrails install, and they are only cosmetic. A unique identifier
+is necessary for the module registry to distinguish between
+possibly conflicting module names. These are unique across _all_
+VisTrails installs, so users should take extra caution to find unique
+names.
+
+--------------------------------------------------------------------------------
+(The following is not going to be done until 2.0)
+
+So I'm trying to design the packaging system to be reasonably future-proof.
+Here are a few use cases I see:
+
+
+Naming
+
+Use case: You write a package with a module having a certain name. I write a
+package with a module having the same name. VisTrails should handle both of
+them gracefully.
+
+Decision: We will assume a package prefix that is unique among all packages
+("... in the universe"), and educate them to create these correctly. For
+example, packages coming from our group should have an identifier
+"edu.utah.sci.vgc.package_name".
+
+
+Versioning
+
+Use case: I write a package and decide to change its interface. I release a
+new version of the package, which breaks compatibility with the old package.
+VisTrails should realize this and let the user know about obsolete packages,
+vistrail/package mismatches, etc.
+
+Decision: We will allow users to specify the version of a package. Packages
+will have a major.minor.release versioning scheme with specific assumed
+semantics. Major versions will be generally considered to break interfaces.
+Changes in minor versions will have to be fully type-compatible with the
+previous version. For example, version 1.1.0 can only change execution
+behavior, add new ports to modules, or add new modules. Everything else must
+be exactly like 1.0.0. Between 1.1.0 and 1.1.1 there can only be changes in
+execution behavior, documentation, etc: The types must be identical.
+
+Later on (post 1.0), packages can provide meta-information on how to
+automatically upgrade a module from one version to another, in the form of
+rewrite rules.
+
+
+Repositories
+
+When we have the online repository of packages (post 1.0), the repository will
+be able to check for the validity of the typing rules for major and minor
+versions. We should also design the repositories to be distributed. We should
+hold the central one, but we should assume people will eventually want to run
+their own package repositories.
+
+
+Can you guys think of anything?
+Thanks!
+-carlos
+
+--------------------------------------------------------------------------------
+
+Required changes for the new packaging system:
+
+--------------------------------------------------------------------------------
+
+If a package wants to be notified of a missing module, it should
+simply implement a function called "handle_missing_module" that takes
+the name and the namespace of a module that's missing. This function
+should then add the right module (or modules) to the registry. This
+allows configuring some packages (like webservices) to be much less
+annoying.
+
diff --git a/doc/parameter_exploration.txt b/doc/parameter_exploration.txt
new file mode 100644
index 0000000..8ea6504
--- /dev/null
+++ b/doc/parameter_exploration.txt
@@ -0,0 +1,57 @@
+This file describes the API for creating user-defined parameter
+exploration widgets.
+
+--------------------------------------------------------------------------------
+User-defined parameter exploration widgets allow users to define
+methods for performing parameter exploration on user-defined
+constants. If you want to know how to define your own constants,
+please see doc/user_defined_constants.txt.
+
+A user-defined parameter exploration widget is simply a QtGui.QWidget
+subclass that respects a certain small interface. The constant class
+is then made aware of the (possible many) widgets, and VisTrails takes
+care of instantiating them correctly. This is what each of your
+subclasses will have to implement:
+
+- a constructor that takes the parameter exploration information
+
+- a method 'get_values' that will return a list of strings
+ corresponding to the associated values of the exploration
+
+- a field 'exploration_name' that will store the string name to be
+ associated with the particular type of exploration (for example,
+ "HSV Interpolation" or "RGB Interpolation")
+
+- optionally, a method 'size_was_updated', which gets called when the
+ parameter exploration dimension is changed. You can use this to
+ automatically refresh your widget if necessary (the user function
+ editor does this, for example)
+
+--------------------------------------------------------------------------------
+The constructor
+
+The constructor should take two mandatory arguments. The first
+parameter is an instance of ParameterInfo, an object that identifies
+the parameter being changed. The fields you will probably care about
+are 'type', 'identifier', 'namespace' and 'value'. The first three
+will allow you to get to the constant's information in the registry,
+and 'value' is the string representation of the current parameter
+value in the pipeline (typically used as an initialization parameter
+for the widget). The second parameter is an integer corresponding to
+the 'size' of the exploration, the number of steps in that particular
+dimension. The constructor should also accept an optional 'parent'
+parameter, with default value None.
+
+--------------------------------------------------------------------------------
+The get_values method
+
+The 'get_values' method should take a parameter corresponding to the
+size of the exploration, and should return a list of string values
+with length size. These values should correspond to the steps of the
+exploration.
+
+--------------------------------------------------------------------------------
+The size_was_updated method
+
+The 'size_was_updated' method should take a parameter corresponding to
+the new size of the exploration.
diff --git a/doc/pep-0008.txt b/doc/pep-0008.txt
new file mode 100644
index 0000000..3e5ef28
--- /dev/null
+++ b/doc/pep-0008.txt
@@ -0,0 +1,1009 @@
+PEP: 8
+Title: Style Guide for Python Code
+Version: $Revision: cfd6d2cb1ca6 $
+Last-Modified: $Date: 2013/04/19 00:31:05 $
+Author: Guido van Rossum <guido at python.org>,
+ Barry Warsaw <barry at python.org>
+Status: Active
+Type: Process
+Content-Type: text/x-rst
+Created: 05-Jul-2001
+Post-History: 05-Jul-2001
+
+
+Introduction
+============
+
+This document gives coding conventions for the Python code comprising
+the standard library in the main Python distribution. Please see the
+companion informational PEP describing style guidelines for the C code
+in the C implementation of Python [1]_.
+
+This document and PEP 257 (Docstring Conventions) were adapted from
+Guido's original Python Style Guide essay, with some additions from
+Barry's style guide [2]_.
+
+
+A Foolish Consistency is the Hobgoblin of Little Minds
+======================================================
+
+One of Guido's key insights is that code is read much more often than
+it is written. The guidelines provided here are intended to improve
+the readability of code and make it consistent across the wide
+spectrum of Python code. As PEP 20 says, "Readability counts".
+
+A style guide is about consistency. Consistency with this style guide
+is important. Consistency within a project is more important.
+Consistency within one module or function is most important.
+
+But most importantly: know when to be inconsistent -- sometimes the
+style guide just doesn't apply. When in doubt, use your best
+judgment. Look at other examples and decide what looks best. And
+don't hesitate to ask!
+
+Two good reasons to break a particular rule:
+
+1. When applying the rule would make the code less readable, even for
+ someone who is used to reading code that follows the rules.
+
+2. To be consistent with surrounding code that also breaks it (maybe
+ for historic reasons) -- although this is also an opportunity to
+ clean up someone else's mess (in true XP style).
+
+
+Code lay-out
+============
+
+Indentation
+-----------
+
+Use 4 spaces per indentation level.
+
+For really old code that you don't want to mess up, you can continue
+to use 8-space tabs.
+
+Continuation lines should align wrapped elements either vertically
+using Python's implicit line joining inside parentheses, brackets and
+braces, or using a hanging indent. When using a hanging indent the
+following considerations should be applied; there should be no
+arguments on the first line and further indentation should be used to
+clearly distinguish itself as a continuation line.
+
+Yes::
+
+ # Aligned with opening delimiter
+ foo = long_function_name(var_one, var_two,
+ var_three, var_four)
+
+ # More indentation included to distinguish this from the rest.
+ def long_function_name(
+ var_one, var_two, var_three,
+ var_four):
+ print(var_one)
+
+No::
+
+ # Arguments on first line forbidden when not using vertical alignment
+ foo = long_function_name(var_one, var_two,
+ var_three, var_four)
+
+ # Further indentation required as indentation is not distinguishable
+ def long_function_name(
+ var_one, var_two, var_three,
+ var_four):
+ print(var_one)
+
+Optional::
+
+ # Extra indentation is not necessary.
+ foo = long_function_name(
+ var_one, var_two,
+ var_three, var_four)
+
+The closing brace/bracket/parenthesis on multi-line constructs may
+either line up under the last item of the list, as in::
+
+ my_list = [
+ 1, 2, 3,
+ 4, 5, 6,
+ ]
+ result = some_function_that_takes_arguments(
+ 'a', 'b', 'c',
+ 'd', 'e', 'f',
+ )
+
+or it may be lined up under the first character of the line that
+starts the multi-line construct, as in::
+
+ my_list = [
+ 1, 2, 3,
+ 4, 5, 6,
+ ]
+ result = some_function_that_takes_arguments(
+ 'a', 'b', 'c',
+ 'd', 'e', 'f',
+ )
+
+
+Tabs or Spaces?
+---------------
+
+Never mix tabs and spaces.
+
+The most popular way of indenting Python is with spaces only. The
+second-most popular way is with tabs only. Code indented with a
+mixture of tabs and spaces should be converted to using spaces
+exclusively. When invoking the Python command line interpreter with
+the ``-t`` option, it issues warnings about code that illegally mixes
+tabs and spaces. When using ``-tt`` these warnings become errors.
+These options are highly recommended!
+
+For new projects, spaces-only are strongly recommended over tabs.
+Most editors have features that make this easy to do.
+
+Maximum Line Length
+-------------------
+
+Limit all lines to a maximum of 79 characters.
+
+There are still many devices around that are limited to 80 character
+lines; plus, limiting windows to 80 characters makes it possible to
+have several windows side-by-side. The default wrapping on such
+devices disrupts the visual structure of the code, making it more
+difficult to understand. Therefore, please limit all lines to a
+maximum of 79 characters. For flowing long blocks of text (docstrings
+or comments), limiting the length to 72 characters is recommended.
+
+The preferred way of wrapping long lines is by using Python's implied
+line continuation inside parentheses, brackets and braces. Long lines
+can be broken over multiple lines by wrapping expressions in
+parentheses. These should be used in preference to using a backslash
+for line continuation. Make sure to indent the continued line
+appropriately. The preferred place to break around a binary operator
+is *after* the operator, not before it. Some examples::
+
+ class Rectangle(Blob):
+
+ def __init__(self, width, height,
+ color='black', emphasis=None, highlight=0):
+ if (width == 0 and height == 0 and
+ color == 'red' and emphasis == 'strong' or
+ highlight > 100):
+ raise ValueError("sorry, you lose")
+ if width == 0 and height == 0 and (color == 'red' or
+ emphasis is None):
+ raise ValueError("I don't think so -- values are %s, %s" %
+ (width, height))
+ Blob.__init__(self, width, height,
+ color, emphasis, highlight)
+
+Blank Lines
+-----------
+
+Separate top-level function and class definitions with two blank
+lines.
+
+Method definitions inside a class are separated by a single blank
+line.
+
+Extra blank lines may be used (sparingly) to separate groups of
+related functions. Blank lines may be omitted between a bunch of
+related one-liners (e.g. a set of dummy implementations).
+
+Use blank lines in functions, sparingly, to indicate logical sections.
+
+Python accepts the control-L (i.e. ^L) form feed character as
+whitespace; Many tools treat these characters as page separators, so
+you may use them to separate pages of related sections of your file.
+Note, some editors and web-based code viewers may not recognize
+control-L as a form feed and will show another glyph in its place.
+
+Encodings (PEP 263)
+-------------------
+
+Code in the core Python distribution should always use the ASCII or
+Latin-1 encoding (a.k.a. ISO-8859-1). For Python 3.0 and beyond,
+UTF-8 is preferred over Latin-1, see PEP 3120.
+
+Files using ASCII should not have a coding cookie. Latin-1 (or UTF-8)
+should only be used when a comment or docstring needs to mention an
+author name that requires Latin-1; otherwise, using ``\x``, ``\u`` or
+``\U`` escapes is the preferred way to include non-ASCII data in
+string literals.
+
+For Python 3.0 and beyond, the following policy is prescribed for the
+standard library (see PEP 3131): All identifiers in the Python
+standard library MUST use ASCII-only identifiers, and SHOULD use
+English words wherever feasible (in many cases, abbreviations and
+technical terms are used which aren't English). In addition, string
+literals and comments must also be in ASCII. The only exceptions are
+(a) test cases testing the non-ASCII features, and
+(b) names of authors. Authors whose names are not based on the
+latin alphabet MUST provide a latin transliteration of their
+names.
+
+Open source projects with a global audience are encouraged to adopt a
+similar policy.
+
+
+Imports
+-------
+
+- Imports should usually be on separate lines, e.g.::
+
+ Yes: import os
+ import sys
+
+ No: import sys, os
+
+ It's okay to say this though::
+
+ from subprocess import Popen, PIPE
+
+- Imports are always put at the top of the file, just after any module
+ comments and docstrings, and before module globals and constants.
+
+ Imports should be grouped in the following order:
+
+ 1. standard library imports
+ 2. related third party imports
+ 3. local application/library specific imports
+
+ You should put a blank line between each group of imports.
+
+ Put any relevant ``__all__`` specification after the imports.
+
+- Relative imports for intra-package imports are highly discouraged.
+ Always use the absolute package path for all imports. Even now that
+ PEP 328 is fully implemented in Python 2.5, its style of explicit
+ relative imports is actively discouraged; absolute imports are more
+ portable and usually more readable.
+
+- When importing a class from a class-containing module, it's usually
+ okay to spell this::
+
+ from myclass import MyClass
+ from foo.bar.yourclass import YourClass
+
+ If this spelling causes local name clashes, then spell them ::
+
+ import myclass
+ import foo.bar.yourclass
+
+ and use "myclass.MyClass" and "foo.bar.yourclass.YourClass".
+
+
+Whitespace in Expressions and Statements
+========================================
+
+Pet Peeves
+----------
+
+Avoid extraneous whitespace in the following situations:
+
+- Immediately inside parentheses, brackets or braces. ::
+
+ Yes: spam(ham[1], {eggs: 2})
+ No: spam( ham[ 1 ], { eggs: 2 } )
+
+- Immediately before a comma, semicolon, or colon::
+
+ Yes: if x == 4: print x, y; x, y = y, x
+ No: if x == 4 : print x , y ; x , y = y , x
+
+- Immediately before the open parenthesis that starts the argument
+ list of a function call::
+
+ Yes: spam(1)
+ No: spam (1)
+
+- Immediately before the open parenthesis that starts an indexing or
+ slicing::
+
+ Yes: dict['key'] = list[index]
+ No: dict ['key'] = list [index]
+
+- More than one space around an assignment (or other) operator to
+ align it with another.
+
+ Yes::
+
+ x = 1
+ y = 2
+ long_variable = 3
+
+ No::
+
+ x = 1
+ y = 2
+ long_variable = 3
+
+
+Other Recommendations
+---------------------
+
+- Always surround these binary operators with a single space on either
+ side: assignment (``=``), augmented assignment (``+=``, ``-=``
+ etc.), comparisons (``==``, ``<``, ``>``, ``!=``, ``<>``, ``<=``,
+ ``>=``, ``in``, ``not in``, ``is``, ``is not``), Booleans (``and``,
+ ``or``, ``not``).
+
+- If operators with different priorities are used, consider adding
+ whitespace around the operators with the lowest priority(ies). Use
+ your own judgement; however, never use more than one space, and
+ always have the same amount of whitespace on both sides of a binary
+ operator.
+
+ Yes::
+
+ i = i + 1
+ submitted += 1
+ x = x*2 - 1
+ hypot2 = x*x + y*y
+ c = (a+b) * (a-b)
+
+ No::
+
+ i=i+1
+ submitted +=1
+ x = x * 2 - 1
+ hypot2 = x * x + y * y
+ c = (a + b) * (a - b)
+
+- Don't use spaces around the ``=`` sign when used to indicate a
+ keyword argument or a default parameter value.
+
+ Yes::
+
+ def complex(real, imag=0.0):
+ return magic(r=real, i=imag)
+
+ No::
+
+ def complex(real, imag = 0.0):
+ return magic(r = real, i = imag)
+
+- Compound statements (multiple statements on the same line) are
+ generally discouraged.
+
+ Yes::
+
+ if foo == 'blah':
+ do_blah_thing()
+ do_one()
+ do_two()
+ do_three()
+
+ Rather not::
+
+ if foo == 'blah': do_blah_thing()
+ do_one(); do_two(); do_three()
+
+- While sometimes it's okay to put an if/for/while with a small body
+ on the same line, never do this for multi-clause statements. Also
+ avoid folding such long lines!
+
+ Rather not::
+
+ if foo == 'blah': do_blah_thing()
+ for x in lst: total += x
+ while t < 10: t = delay()
+
+ Definitely not::
+
+ if foo == 'blah': do_blah_thing()
+ else: do_non_blah_thing()
+
+ try: something()
+ finally: cleanup()
+
+ do_one(); do_two(); do_three(long, argument,
+ list, like, this)
+
+ if foo == 'blah': one(); two(); three()
+
+Comments
+========
+
+Comments that contradict the code are worse than no comments. Always
+make a priority of keeping the comments up-to-date when the code
+changes!
+
+Comments should be complete sentences. If a comment is a phrase or
+sentence, its first word should be capitalized, unless it is an
+identifier that begins with a lower case letter (never alter the case
+of identifiers!).
+
+If a comment is short, the period at the end can be omitted. Block
+comments generally consist of one or more paragraphs built out of
+complete sentences, and each sentence should end in a period.
+
+You should use two spaces after a sentence-ending period.
+
+When writing English, Strunk and White apply.
+
+Python coders from non-English speaking countries: please write your
+comments in English, unless you are 120% sure that the code will never
+be read by people who don't speak your language.
+
+Block Comments
+--------------
+
+Block comments generally apply to some (or all) code that follows
+them, and are indented to the same level as that code. Each line of a
+block comment starts with a ``#`` and a single space (unless it is
+indented text inside the comment).
+
+Paragraphs inside a block comment are separated by a line containing a
+single ``#``.
+
+Inline Comments
+---------------
+
+Use inline comments sparingly.
+
+An inline comment is a comment on the same line as a statement.
+Inline comments should be separated by at least two spaces from the
+statement. They should start with a # and a single space.
+
+Inline comments are unnecessary and in fact distracting if they state
+the obvious. Don't do this::
+
+ x = x + 1 # Increment x
+
+But sometimes, this is useful::
+
+ x = x + 1 # Compensate for border
+
+Documentation Strings
+---------------------
+
+Conventions for writing good documentation strings
+(a.k.a. "docstrings") are immortalized in PEP 257.
+
+- Write docstrings for all public modules, functions, classes, and
+ methods. Docstrings are not necessary for non-public methods, but
+ you should have a comment that describes what the method does. This
+ comment should appear after the ``def`` line.
+
+- PEP 257 describes good docstring conventions. Note that most
+ importantly, the ``"""`` that ends a multiline docstring should be
+ on a line by itself, and preferably preceded by a blank line, e.g.::
+
+ """Return a foobang
+
+ Optional plotz says to frobnicate the bizbaz first.
+
+ """
+
+- For one liner docstrings, it's okay to keep the closing ``"""`` on
+ the same line.
+
+
+Version Bookkeeping
+===================
+
+If you have to have Subversion, CVS, or RCS crud in your source file,
+do it as follows. ::
+
+ __version__ = "$Revision: cfd6d2cb1ca6 $"
+ # $Source: C:\Users\Remi\Desktop\peps/pep-0008.txt,v $
+
+These lines should be included after the module's docstring, before
+any other code, separated by a blank line above and below.
+
+
+Naming Conventions
+==================
+
+The naming conventions of Python's library are a bit of a mess, so
+we'll never get this completely consistent -- nevertheless, here are
+the currently recommended naming standards. New modules and packages
+(including third party frameworks) should be written to these
+standards, but where an existing library has a different style,
+internal consistency is preferred.
+
+Descriptive: Naming Styles
+--------------------------
+
+There are a lot of different naming styles. It helps to be able to
+recognize what naming style is being used, independently from what
+they are used for.
+
+The following naming styles are commonly distinguished:
+
+- ``b`` (single lowercase letter)
+- ``B`` (single uppercase letter)
+- ``lowercase``
+- ``lower_case_with_underscores``
+- ``UPPERCASE``
+- ``UPPER_CASE_WITH_UNDERSCORES``
+- ``CapitalizedWords`` (or CapWords, or CamelCase -- so named because
+ of the bumpy look of its letters [3]_). This is also sometimes known
+ as StudlyCaps.
+
+ Note: When using abbreviations in CapWords, capitalize all the
+ letters of the abbreviation. Thus HTTPServerError is better than
+ HttpServerError.
+- ``mixedCase`` (differs from CapitalizedWords by initial lowercase
+ character!)
+- ``Capitalized_Words_With_Underscores`` (ugly!)
+
+There's also the style of using a short unique prefix to group related
+names together. This is not used much in Python, but it is mentioned
+for completeness. For example, the ``os.stat()`` function returns a
+tuple whose items traditionally have names like ``st_mode``,
+``st_size``, ``st_mtime`` and so on. (This is done to emphasize the
+correspondence with the fields of the POSIX system call struct, which
+helps programmers familiar with that.)
+
+The X11 library uses a leading X for all its public functions. In
+Python, this style is generally deemed unnecessary because attribute
+and method names are prefixed with an object, and function names are
+prefixed with a module name.
+
+In addition, the following special forms using leading or trailing
+underscores are recognized (these can generally be combined with any
+case convention):
+
+- ``_single_leading_underscore``: weak "internal use" indicator.
+ E.g. ``from M import *`` does not import objects whose name starts
+ with an underscore.
+
+- ``single_trailing_underscore_``: used by convention to avoid
+ conflicts with Python keyword, e.g. ::
+
+ Tkinter.Toplevel(master, class_='ClassName')
+
+- ``__double_leading_underscore``: when naming a class attribute,
+ invokes name mangling (inside class FooBar, ``__boo`` becomes
+ ``_FooBar__boo``; see below).
+
+- ``__double_leading_and_trailing_underscore__``: "magic" objects or
+ attributes that live in user-controlled namespaces.
+ E.g. ``__init__``, ``__import__`` or ``__file__``. Never invent
+ such names; only use them as documented.
+
+Prescriptive: Naming Conventions
+--------------------------------
+
+Names to Avoid
+~~~~~~~~~~~~~~
+
+Never use the characters 'l' (lowercase letter el), 'O' (uppercase
+letter oh), or 'I' (uppercase letter eye) as single character variable
+names.
+
+In some fonts, these characters are indistinguishable from the
+numerals one and zero. When tempted to use 'l', use 'L' instead.
+
+Package and Module Names
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+Modules should have short, all-lowercase names. Underscores can be
+used in the module name if it improves readability. Python packages
+should also have short, all-lowercase names, although the use of
+underscores is discouraged.
+
+Since module names are mapped to file names, and some file systems are
+case insensitive and truncate long names, it is important that module
+names be chosen to be fairly short -- this won't be a problem on Unix,
+but it may be a problem when the code is transported to older Mac or
+Windows versions, or DOS.
+
+When an extension module written in C or C++ has an accompanying
+Python module that provides a higher level (e.g. more object oriented)
+interface, the C/C++ module has a leading underscore
+(e.g. ``_socket``).
+
+Class Names
+~~~~~~~~~~~
+
+Almost without exception, class names use the CapWords convention.
+Classes for internal use have a leading underscore in addition.
+
+Exception Names
+~~~~~~~~~~~~~~~
+
+Because exceptions should be classes, the class naming convention
+applies here. However, you should use the suffix "Error" on your
+exception names (if the exception actually is an error).
+
+Global Variable Names
+~~~~~~~~~~~~~~~~~~~~~
+
+(Let's hope that these variables are meant for use inside one module
+only.) The conventions are about the same as those for functions.
+
+Modules that are designed for use via ``from M import *`` should use
+the ``__all__`` mechanism to prevent exporting globals, or use the
+older convention of prefixing such globals with an underscore (which
+you might want to do to indicate these globals are "module
+non-public").
+
+Function Names
+~~~~~~~~~~~~~~
+
+Function names should be lowercase, with words separated by
+underscores as necessary to improve readability.
+
+mixedCase is allowed only in contexts where that's already the
+prevailing style (e.g. threading.py), to retain backwards
+compatibility.
+
+Function and method arguments
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Always use ``self`` for the first argument to instance methods.
+
+Always use ``cls`` for the first argument to class methods.
+
+If a function argument's name clashes with a reserved keyword, it is
+generally better to append a single trailing underscore rather than
+use an abbreviation or spelling corruption. Thus ``class_`` is better
+than ``clss``. (Perhaps better is to avoid such clashes by using a
+synonym.)
+
+Method Names and Instance Variables
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Use the function naming rules: lowercase with words separated by
+underscores as necessary to improve readability.
+
+Use one leading underscore only for non-public methods and instance
+variables.
+
+To avoid name clashes with subclasses, use two leading underscores to
+invoke Python's name mangling rules.
+
+Python mangles these names with the class name: if class Foo has an
+attribute named ``__a``, it cannot be accessed by ``Foo.__a``. (An
+insistent user could still gain access by calling ``Foo._Foo__a``.)
+Generally, double leading underscores should be used only to avoid
+name conflicts with attributes in classes designed to be subclassed.
+
+Note: there is some controversy about the use of __names (see below).
+
+Constants
+~~~~~~~~~
+
+Constants are usually defined on a module level and written in all
+capital letters with underscores separating words. Examples include
+``MAX_OVERFLOW`` and ``TOTAL``.
+
+Designing for inheritance
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Always decide whether a class's methods and instance variables
+(collectively: "attributes") should be public or non-public. If in
+doubt, choose non-public; it's easier to make it public later than to
+make a public attribute non-public.
+
+Public attributes are those that you expect unrelated clients of your
+class to use, with your commitment to avoid backward incompatible
+changes. Non-public attributes are those that are not intended to be
+used by third parties; you make no guarantees that non-public
+attributes won't change or even be removed.
+
+We don't use the term "private" here, since no attribute is really
+private in Python (without a generally unnecessary amount of work).
+
+Another category of attributes are those that are part of the
+"subclass API" (often called "protected" in other languages). Some
+classes are designed to be inherited from, either to extend or modify
+aspects of the class's behavior. When designing such a class, take
+care to make explicit decisions about which attributes are public,
+which are part of the subclass API, and which are truly only to be
+used by your base class.
+
+With this in mind, here are the Pythonic guidelines:
+
+- Public attributes should have no leading underscores.
+
+- If your public attribute name collides with a reserved keyword,
+ append a single trailing underscore to your attribute name. This is
+ preferable to an abbreviation or corrupted spelling. (However,
+ notwithstanding this rule, 'cls' is the preferred spelling for any
+ variable or argument which is known to be a class, especially the
+ first argument to a class method.)
+
+ Note 1: See the argument name recommendation above for class methods.
+
+- For simple public data attributes, it is best to expose just the
+ attribute name, without complicated accessor/mutator methods. Keep
+ in mind that Python provides an easy path to future enhancement,
+ should you find that a simple data attribute needs to grow
+ functional behavior. In that case, use properties to hide
+ functional implementation behind simple data attribute access
+ syntax.
+
+ Note 1: Properties only work on new-style classes.
+
+ Note 2: Try to keep the functional behavior side-effect free,
+ although side-effects such as caching are generally fine.
+
+ Note 3: Avoid using properties for computationally expensive
+ operations; the attribute notation makes the caller believe that
+ access is (relatively) cheap.
+
+- If your class is intended to be subclassed, and you have attributes
+ that you do not want subclasses to use, consider naming them with
+ double leading underscores and no trailing underscores. This
+ invokes Python's name mangling algorithm, where the name of the
+ class is mangled into the attribute name. This helps avoid
+ attribute name collisions should subclasses inadvertently contain
+ attributes with the same name.
+
+ Note 1: Note that only the simple class name is used in the mangled
+ name, so if a subclass chooses both the same class name and attribute
+ name, you can still get name collisions.
+
+ Note 2: Name mangling can make certain uses, such as debugging and
+ ``__getattr__()``, less convenient. However the name mangling
+ algorithm is well documented and easy to perform manually.
+
+ Note 3: Not everyone likes name mangling. Try to balance the
+ need to avoid accidental name clashes with potential use by
+ advanced callers.
+
+
+Programming Recommendations
+===========================
+
+- Code should be written in a way that does not disadvantage other
+ implementations of Python (PyPy, Jython, IronPython, Cython, Psyco,
+ and such).
+
+ For example, do not rely on CPython's efficient implementation of
+ in-place string concatenation for statements in the form ``a += b``
+ or ``a = a + b``. Those statements run more slowly in Jython. In
+ performance sensitive parts of the library, the ``''.join()`` form
+ should be used instead. This will ensure that concatenation occurs
+ in linear time across various implementations.
+
+- Comparisons to singletons like None should always be done with
+ ``is`` or ``is not``, never the equality operators.
+
+ Also, beware of writing ``if x`` when you really mean ``if x is not
+ None`` -- e.g. when testing whether a variable or argument that
+ defaults to None was set to some other value. The other value might
+ have a type (such as a container) that could be false in a boolean
+ context!
+
+- When implementing ordering operations with rich comparisons, it is
+ best to implement all six operations (``__eq__``, ``__ne__``,
+ ``__lt__``, ``__le__``, ``__gt__``, ``__ge__``) rather than relying
+ on other code to only exercise a particular comparison.
+
+ To minimize the effort involved, the ``functools.total_ordering()``
+ decorator provides a tool to generate missing comparison methods.
+
+ PEP 207 indicates that reflexivity rules *are* assumed by Python.
+ Thus, the interpreter may swap ``y > x`` with ``x < y``, ``y >= x``
+ with ``x <= y``, and may swap the arguments of ``x == y`` and ``x !=
+ y``. The ``sort()`` and ``min()`` operations are guaranteed to use
+ the ``<`` operator and the ``max()`` function uses the ``>``
+ operator. However, it is best to implement all six operations so
+ that confusion doesn't arise in other contexts.
+
+- Use class-based exceptions.
+
+ String exceptions in new code are forbidden, and this language
+ feature has been removed in Python 2.6.
+
+ Modules or packages should define their own domain-specific base
+ exception class, which should be subclassed from the built-in
+ Exception class. Always include a class docstring. E.g.::
+
+ class MessageError(Exception):
+ """Base class for errors in the email package."""
+
+ Class naming conventions apply here, although you should add the
+ suffix "Error" to your exception classes, if the exception is an
+ error. Non-error exceptions need no special suffix.
+
+- When raising an exception, use ``raise ValueError('message')``
+ instead of the older form ``raise ValueError, 'message'``.
+
+ The paren-using form is preferred because when the exception
+ arguments are long or include string formatting, you don't need to
+ use line continuation characters thanks to the containing
+ parentheses. The older form is not legal syntax in Python 3.
+
+- When catching exceptions, mention specific exceptions whenever
+ possible instead of using a bare ``except:`` clause.
+
+ For example, use::
+
+ try:
+ import platform_specific_module
+ except ImportError:
+ platform_specific_module = None
+
+ A bare ``except:`` clause will catch SystemExit and
+ KeyboardInterrupt exceptions, making it harder to interrupt a
+ program with Control-C, and can disguise other problems. If you
+ want to catch all exceptions that signal program errors, use
+ ``except Exception:`` (bare except is equivalent to ``except
+ BaseException:``).
+
+ A good rule of thumb is to limit use of bare 'except' clauses to two
+ cases:
+
+ 1. If the exception handler will be printing out or logging the
+ traceback; at least the user will be aware that an error has
+ occurred.
+
+ 2. If the code needs to do some cleanup work, but then lets the
+ exception propagate upwards with ``raise``. ``try...finally``
+ can be a better way to handle this case.
+
+- Additionally, for all try/except clauses, limit the ``try`` clause
+ to the absolute minimum amount of code necessary. Again, this
+ avoids masking bugs.
+
+ Yes::
+
+ try:
+ value = collection[key]
+ except KeyError:
+ return key_not_found(key)
+ else:
+ return handle_value(value)
+
+ No::
+
+ try:
+ # Too broad!
+ return handle_value(collection[key])
+ except KeyError:
+ # Will also catch KeyError raised by handle_value()
+ return key_not_found(key)
+
+- Context managers should be invoked through separate functions or methods
+ whenever they do something other than acquire and release resources.
+ For example:
+
+ Yes::
+
+ with conn.begin_transaction():
+ do_stuff_in_transaction(conn)
+
+ No::
+
+ with conn:
+ do_stuff_in_transaction(conn)
+
+ The latter example doesn't provide any information to indicate that
+ the __enter__ and __exit__ methods are doing something other than
+ closing the connection after a transaction. Being explicit is
+ important in this case.
+
+- Use string methods instead of the string module.
+
+ String methods are always much faster and share the same API with
+ unicode strings. Override this rule if backward compatibility with
+ Pythons older than 2.0 is required.
+
+- Use ``''.startswith()`` and ``''.endswith()`` instead of string
+ slicing to check for prefixes or suffixes.
+
+ startswith() and endswith() are cleaner and less error prone. For
+ example::
+
+ Yes: if foo.startswith('bar'):
+ No: if foo[:3] == 'bar':
+
+ The exception is if your code must work with Python 1.5.2 (but let's
+ hope not!).
+
+- Object type comparisons should always use isinstance() instead of
+ comparing types directly. ::
+
+ Yes: if isinstance(obj, int):
+
+ No: if type(obj) is type(1):
+
+ When checking if an object is a string, keep in mind that it might
+ be a unicode string too! In Python 2.3, str and unicode have a
+ common base class, basestring, so you can do::
+
+ if isinstance(obj, basestring):
+
+- For sequences, (strings, lists, tuples), use the fact that empty
+ sequences are false. ::
+
+ Yes: if not seq:
+ if seq:
+
+ No: if len(seq)
+ if not len(seq)
+
+- Don't write string literals that rely on significant trailing
+ whitespace. Such trailing whitespace is visually indistinguishable
+ and some editors (or more recently, reindent.py) will trim them.
+
+- Don't compare boolean values to True or False using ``==``. ::
+
+ Yes: if greeting:
+ No: if greeting == True:
+ Worse: if greeting is True:
+
+- The Python standard library will not use function annotations as
+ that would result in a premature commitment to a particular
+ annotation style. Instead, the annotations are left for users to
+ discover and experiment with useful annotation styles.
+
+ Early core developer attempts to use function annotations revealed
+ inconsistent, ad-hoc annotation styles. For example:
+
+ * ``[str]`` was ambiguous as to whether it represented a list of
+ strings or a value that could be either *str* or *None*.
+
+ * The notation ``open(file:(str,bytes))`` was used for a value that
+ could be either *bytes* or *str* rather than a 2-tuple containing
+ a *str* value followed by a *bytes* value.
+
+ * The annotation ``seek(whence:int)`` exhibited a mix of
+ over-specification and under-specification: *int* is too
+ restrictive (anything with ``__index__`` would be allowed) and it
+ is not restrictive enough (only the values 0, 1, and 2 are
+ allowed). Likewise, the annotation ``write(b: bytes)`` was also
+ too restrictive (anything supporting the buffer protocol would be
+ allowed).
+
+ * Annotations such as ``read1(n: int=None)`` were self-contradictory
+ since *None* is not an *int*. Annotations such as
+ ``source_path(self, fullname:str) -> object`` were confusing about
+ what the return type should be.
+
+ * In addition to the above, annotations were inconsistent in the use
+ of concrete types versus abstract types: *int* versus *Integral*
+ and set/frozenset versus MutableSet/Set.
+
+ * Some annotations in the abstract base classes were incorrect
+ specifications. For example, set-to-set operations require
+ *other* to be another instance of *Set* rather than just an
+ *Iterable*.
+
+ * A further issue was that annotations become part of the
+ specification but weren't being tested.
+
+ * In most cases, the docstrings already included the type
+ specifications and did so with greater clarity than the function
+ annotations. In the remaining cases, the docstrings were improved
+ once the annotations were removed.
+
+ * The observed function annotations were too ad-hoc and inconsistent
+ to work with a coherent system of automatic type checking or
+ argument validation. Leaving these annotations in the code would
+ have made it more difficult to make changes later so that
+ automated utilities could be supported.
+
+
+References
+==========
+
+.. [1] PEP 7, Style Guide for C Code, van Rossum
+
+.. [2] Barry's GNU Mailman style guide
+ http://barry.warsaw.us/software/STYLEGUIDE.txt
+
+.. [3] http://www.wikipedia.com/wiki/CamelCase
+
+
+Copyright
+=========
+
+This document has been placed in the public domain.
+
+
+
+..
+ Local Variables:
+ mode: indented-text
+ indent-tabs-mode: nil
+ sentence-end-double-space: t
+ fill-column: 70
+ coding: utf-8
+ End:
diff --git a/doc/pep-0257.txt b/doc/pep-0257.txt
new file mode 100644
index 0000000..58a1ec0
--- /dev/null
+++ b/doc/pep-0257.txt
@@ -0,0 +1,328 @@
+PEP: 257
+Title: Docstring Conventions
+Version: $Revision: e2b5d1a8a663 $
+Last-Modified: $Date: 2009/01/18 09:50:42 $
+Author: David Goodger <goodger at python.org>,
+ Guido van Rossum <guido at python.org>
+Discussions-To: doc-sig at python.org
+Status: Active
+Type: Informational
+Content-Type: text/x-rst
+Created: 29-May-2001
+Post-History: 13-Jun-2001
+
+
+Abstract
+========
+
+This PEP documents the semantics and conventions associated with
+Python docstrings.
+
+
+Rationale
+=========
+
+The aim of this PEP is to standardize the high-level structure of
+docstrings: what they should contain, and how to say it (without
+touching on any markup syntax within docstrings). The PEP contains
+conventions, not laws or syntax.
+
+ "A universal convention supplies all of maintainability, clarity,
+ consistency, and a foundation for good programming habits too.
+ What it doesn't do is insist that you follow it against your will.
+ That's Python!"
+
+ -- Tim Peters on comp.lang.python, 2001-06-16
+
+If you violate these conventions, the worst you'll get is some dirty
+looks. But some software (such as the Docutils_ docstring processing
+system [1]_ [2]_) will be aware of the conventions, so following them
+will get you the best results.
+
+
+Specification
+=============
+
+What is a Docstring?
+--------------------
+
+A docstring is a string literal that occurs as the first statement in
+a module, function, class, or method definition. Such a docstring
+becomes the ``__doc__`` special attribute of that object.
+
+All modules should normally have docstrings, and all functions and
+classes exported by a module should also have docstrings. Public
+methods (including the ``__init__`` constructor) should also have
+docstrings. A package may be documented in the module docstring of
+the ``__init__.py`` file in the package directory.
+
+String literals occurring elsewhere in Python code may also act as
+documentation. They are not recognized by the Python bytecode
+compiler and are not accessible as runtime object attributes (i.e. not
+assigned to ``__doc__``), but two types of extra docstrings may be
+extracted by software tools:
+
+1. String literals occurring immediately after a simple assignment at
+ the top level of a module, class, or ``__init__`` method are called
+ "attribute docstrings".
+
+2. String literals occurring immediately after another docstring are
+ called "additional docstrings".
+
+Please see PEP 258, "Docutils Design Specification" [2]_, for a
+detailed description of attribute and additional docstrings.
+
+XXX Mention docstrings of 2.2 properties.
+
+For consistency, always use ``"""triple double quotes"""`` around
+docstrings. Use ``r"""raw triple double quotes"""`` if you use any
+backslashes in your docstrings. For Unicode docstrings, use
+``u"""Unicode triple-quoted strings"""``.
+
+There are two forms of docstrings: one-liners and multi-line
+docstrings.
+
+
+One-line Docstrings
+--------------------
+
+One-liners are for really obvious cases. They should really fit on
+one line. For example::
+
+ def kos_root():
+ """Return the pathname of the KOS root directory."""
+ global _kos_root
+ if _kos_root: return _kos_root
+ ...
+
+Notes:
+
+- Triple quotes are used even though the string fits on one line.
+ This makes it easy to later expand it.
+
+- The closing quotes are on the same line as the opening quotes. This
+ looks better for one-liners.
+
+- There's no blank line either before or after the docstring.
+
+- The docstring is a phrase ending in a period. It prescribes the
+ function or method's effect as a command ("Do this", "Return that"),
+ not as a description; e.g. don't write "Returns the pathname ...".
+
+- The one-line docstring should NOT be a "signature" reiterating the
+ function/method parameters (which can be obtained by introspection).
+ Don't do::
+
+ def function(a, b):
+ """function(a, b) -> list"""
+
+ This type of docstring is only appropriate for C functions (such as
+ built-ins), where introspection is not possible. However, the
+ nature of the *return value* cannot be determined by introspection,
+ so it should be mentioned. The preferred form for such a docstring
+ would be something like::
+
+ def function(a, b):
+ """Do X and return a list."""
+
+ (Of course "Do X" should be replaced by a useful description!)
+
+
+Multi-line Docstrings
+----------------------
+
+Multi-line docstrings consist of a summary line just like a one-line
+docstring, followed by a blank line, followed by a more elaborate
+description. The summary line may be used by automatic indexing
+tools; it is important that it fits on one line and is separated from
+the rest of the docstring by a blank line. The summary line may be on
+the same line as the opening quotes or on the next line. The entire
+docstring is indented the same as the quotes at its first line (see
+example below).
+
+Insert a blank line before and after all docstrings (one-line or
+multi-line) that document a class -- generally speaking, the class's
+methods are separated from each other by a single blank line, and the
+docstring needs to be offset from the first method by a blank line;
+for symmetry, put a blank line between the class header and the
+docstring. Docstrings documenting functions or methods generally
+don't have this requirement, unless the function or method's body is
+written as a number of blank-line separated sections -- in this case,
+treat the docstring as another section, and precede it with a blank
+line.
+
+The docstring of a script (a stand-alone program) should be usable as
+its "usage" message, printed when the script is invoked with incorrect
+or missing arguments (or perhaps with a "-h" option, for "help").
+Such a docstring should document the script's function and command
+line syntax, environment variables, and files. Usage messages can be
+fairly elaborate (several screens full) and should be sufficient for a
+new user to use the command properly, as well as a complete quick
+reference to all options and arguments for the sophisticated user.
+
+The docstring for a module should generally list the classes,
+exceptions and functions (and any other objects) that are exported by
+the module, with a one-line summary of each. (These summaries
+generally give less detail than the summary line in the object's
+docstring.) The docstring for a package (i.e., the docstring of the
+package's ``__init__.py`` module) should also list the modules and
+subpackages exported by the package.
+
+The docstring for a function or method should summarize its behavior
+and document its arguments, return value(s), side effects, exceptions
+raised, and restrictions on when it can be called (all if applicable).
+Optional arguments should be indicated. It should be documented
+whether keyword arguments are part of the interface.
+
+The docstring for a class should summarize its behavior and list the
+public methods and instance variables. If the class is intended to be
+subclassed, and has an additional interface for subclasses, this
+interface should be listed separately (in the docstring). The class
+constructor should be documented in the docstring for its ``__init__``
+method. Individual methods should be documented by their own
+docstring.
+
+If a class subclasses another class and its behavior is mostly
+inherited from that class, its docstring should mention this and
+summarize the differences. Use the verb "override" to indicate that a
+subclass method replaces a superclass method and does not call the
+superclass method; use the verb "extend" to indicate that a subclass
+method calls the superclass method (in addition to its own behavior).
+
+*Do not* use the Emacs convention of mentioning the arguments of
+functions or methods in upper case in running text. Python is case
+sensitive and the argument names can be used for keyword arguments, so
+the docstring should document the correct argument names. It is best
+to list each argument on a separate line. For example::
+
+ def complex(real=0.0, imag=0.0):
+ """Form a complex number.
+
+ Keyword arguments:
+ real -- the real part (default 0.0)
+ imag -- the imaginary part (default 0.0)
+
+ """
+ if imag == 0.0 and real == 0.0: return complex_zero
+ ...
+
+The BDFL [3]_ recommends inserting a blank line between the last
+paragraph in a multi-line docstring and its closing quotes, placing
+the closing quotes on a line by themselves. This way, Emacs'
+``fill-paragraph`` command can be used on it.
+
+
+Handling Docstring Indentation
+------------------------------
+
+Docstring processing tools will strip a uniform amount of indentation
+from the second and further lines of the docstring, equal to the
+minimum indentation of all non-blank lines after the first line. Any
+indentation in the first line of the docstring (i.e., up to the first
+newline) is insignificant and removed. Relative indentation of later
+lines in the docstring is retained. Blank lines should be removed
+from the beginning and end of the docstring.
+
+Since code is much more precise than words, here is an implementation
+of the algorithm::
+
+ def trim(docstring):
+ if not docstring:
+ return ''
+ # Convert tabs to spaces (following the normal Python rules)
+ # and split into a list of lines:
+ lines = docstring.expandtabs().splitlines()
+ # Determine minimum indentation (first line doesn't count):
+ indent = sys.maxint
+ for line in lines[1:]:
+ stripped = line.lstrip()
+ if stripped:
+ indent = min(indent, len(line) - len(stripped))
+ # Remove indentation (first line is special):
+ trimmed = [lines[0].strip()]
+ if indent < sys.maxint:
+ for line in lines[1:]:
+ trimmed.append(line[indent:].rstrip())
+ # Strip off trailing and leading blank lines:
+ while trimmed and not trimmed[-1]:
+ trimmed.pop()
+ while trimmed and not trimmed[0]:
+ trimmed.pop(0)
+ # Return a single string:
+ return '\n'.join(trimmed)
+
+The docstring in this example contains two newline characters and is
+therefore 3 lines long. The first and last lines are blank::
+
+ def foo():
+ """
+ This is the second line of the docstring.
+ """
+
+To illustrate::
+
+ >>> print repr(foo.__doc__)
+ '\n This is the second line of the docstring.\n '
+ >>> foo.__doc__.splitlines()
+ ['', ' This is the second line of the docstring.', ' ']
+ >>> trim(foo.__doc__)
+ 'This is the second line of the docstring.'
+
+Once trimmed, these docstrings are equivalent::
+
+ def foo():
+ """A multi-line
+ docstring.
+ """
+
+ def bar():
+ """
+ A multi-line
+ docstring.
+ """
+
+
+References and Footnotes
+========================
+
+.. [1] PEP 256, Docstring Processing System Framework, Goodger
+ (http://www.python.org/dev/peps/pep-0256/)
+
+.. [2] PEP 258, Docutils Design Specification, Goodger
+ (http://www.python.org/dev/peps/pep-0258/)
+
+.. [3] Guido van Rossum, Python's creator and Benevolent Dictator For
+ Life.
+
+.. _Docutils: http://docutils.sourceforge.net/
+
+.. _Python Style Guide:
+ http://www.python.org/doc/essays/styleguide.html
+
+.. _Doc-SIG: http://www.python.org/sigs/doc-sig/
+
+
+Copyright
+=========
+
+This document has been placed in the public domain.
+
+
+Acknowledgements
+================
+
+The "Specification" text comes mostly verbatim from the `Python Style
+Guide`_ essay by Guido van Rossum.
+
+This document borrows ideas from the archives of the Python Doc-SIG_.
+Thanks to all members past and present.
+
+
+
+..
+ Local Variables:
+ mode: indented-text
+ indent-tabs-mode: nil
+ fill-column: 70
+ sentence-end-double-space: t
+ End:
diff --git a/doc/signal_mess.txt b/doc/signal_mess.txt
new file mode 100644
index 0000000..543cbca
--- /dev/null
+++ b/doc/signal_mess.txt
@@ -0,0 +1,49 @@
+This is my attempt to tame the current signal mess on VisTrails.
+
+--------------------------------------------------------------------------------
+
+vistrailChanged is emitted by QViewManager.vistrailChanged
+ QViewManager.closeVistrail
+ VistrailController.invalidate_version_tree
+ QVersionTab.vistrailChanged
+
+QVersionTab::vistrailChanged is caught by QViewManager.vistrailChanged
+
+VistrailController::vistrailChanged is caught by QVersionTab.vistrailChanged
+
+VistrailController::vistrailChanged is caught by QQueryTab.vistrailChanged
+
+QViewManager::vistrailChanged is caught by QBuilderWindow.vistrailChanged
+
+invalidate_version_tree
+
+--------------------------------------------------------------------------------
+
+stateChanged is emitted by VistrailController.setChanged
+ VistrailController.setFileName
+
+VistrailController::stateChanged is caught by QVistrailView.stateChanged
+
+--------------------------------------------------------------------------------
+
+versionSelectionChange is emitted by QViewManager.versionSelectionChange
+ QViewManager.redo
+ QViewManager.undo
+ QViewManager.closeVistrail
+ QViewManager.currentChanged
+ QVersionTab.versionSelected
+
+QVersionTab::versionSelectionChange is caught by QVistrailView.versionSelectionChange
+
+QVersionTab::versionSelectionChange is caught by QViewManager.versionSelectionChange
+
+QViewManager::versionSelectionChange is caught by QBuilderWindow.versionSelectionChange
+
+--------------------------------------------------------------------------------
+
+versionWasChanged is emitted by VistrailController.changeSelectedVersion
+ VistrailController.resendVersionWasChanged
+ VistrailController.setVersion
+
+VistrailController::versionWasChanged is caught by QPipelineTab.versionChanged
+
diff --git a/doc/source_tree_overview.tex b/doc/source_tree_overview.tex
new file mode 100644
index 0000000..b41723a
--- /dev/null
+++ b/doc/source_tree_overview.tex
@@ -0,0 +1,102 @@
+% test
+
+\documentclass{article}
+
+\begin{document}
+
+\title{VisTrails Source Tree Overview}
+
+\author{VisTrails development team}
+
+\maketitle
+
+\abstract{This document is intended to provide an overview of the layout of the
+source tree of VisTrails, as presented by a Subversion checkout of
+trunk.}
+
+\section{Basic Directory layout}
+
+\begin{verbatim}
+./
+./dist/
+./examples/
+./examples/data/
+./extensions/
+./packages/
+./scripts/
+./vistrails/
+./vistrails/api/
+./vistrails/core/
+./vistrails/db/
+./vistrails/doc/
+./vistrails/gui/
+./vistrails/packages/
+./vistrails/tests/
+\end{verbatim}
+
+\section{Top-level directories}
+
+The main VisTrails application lives entirely in the vistrails
+subdirectory. All vistrail files with example functionality reside in
+the examples subdirectory, and any necessary data should go in
+examples/data.
+
+The dist subdirectory includes code and documentation necessary to
+create VisTrails stand-alone distributions in several different
+operating systems (Linux, Windows, OS X, etc).
+
+Although originally developed as a stand-alone application, VisTrails
+has now been extended in many ways. These live, unsurprisingly, in the
+extensions directory. Currently, we have mediawiki and latex plugins,
+and a web interface for VisTrails.
+
+Most VisTrails packages should be in the top-level packages
+subdirectory. The reason there exists two packages directories is so
+that we can conveniently select the set of packages that will be
+included in a standard VisTrails distribution. All these default
+packages should be in vistrails/packages. Notice that these packages
+will be included in distributions for different operating systems, so
+try to make sure necessary libraries are available, and that your code
+is portable.
+
+The scripts directory includes various scripts that help the
+administration of VisTrails source code, services and examples.
+
+All documentation for VisTrails developers (including this file)
+reside on doc.
+
+\section{The vistrails directory}
+
+The VisTrails application source tree itself is loosely organized in
+different components that live in different directories. All the basic
+Python classes for modules, connections, workflows, etc live in
+vistrails/core. As a rule of thumb, the classes in the core component
+are agnostic to storage (handled by the db component) and have to user
+interface knowledge (handled by the gui component). This was
+originally intended in part to allow a separation of developers with
+Qt/PyQt4 licenses and developers without Qt/PyQt4 licenses. The db
+component is fairly involved and uses a particular source layout
+intended to simplify the creation of new schemas and versions, as
+described in Section~\ref{sec:db}.
+
+As a general rule, all code that derives from PyQt4 classes should go
+in the vistrails/gui subdirectory. If that is not possible for some
+reason, such code should be clearly marked and documented.
+
+VisTrails can also be used as a library, and the api subdirectory
+includes several helper python functions and classes to access
+VisTrails functionality programmatically. If you intend to write code
+that will script VisTrails executions, or are using the VisTrails
+shell regularly and have a new function that will be handy in that
+scenario, the vistrails/api subdirectory is the correct place to put
+the code.
+
+The testing suite infrastructure lives in vistrails/tests. All the
+necessary files for the test cases, in particular, should be inside
+vistrails/tests/resources.
+
+\subsection{The vistrails/db directory}\label{sec:db}
+
+TBW.
+
+\end{document}
diff --git a/doc/usersguide/Makefile b/doc/usersguide/Makefile
new file mode 100644
index 0000000..5cd524d
--- /dev/null
+++ b/doc/usersguide/Makefile
@@ -0,0 +1,89 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+BUILDDIR = _build
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest
+
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " dirhtml to make HTML files named index.html in directories"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " qthelp to make HTML files and a qthelp project"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+ @echo " changes to make an overview of all changed/added/deprecated items"
+ @echo " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+ -rm -rf $(BUILDDIR)/*
+
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with the" \
+ ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+ @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/VisTrails.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/VisTrails.qhc"
+
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
+ "run these through (pdf)latex."
+
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/doc/usersguide/_static/mystyle.css b/doc/usersguide/_static/mystyle.css
new file mode 100644
index 0000000..0fe6e1a
--- /dev/null
+++ b/doc/usersguide/_static/mystyle.css
@@ -0,0 +1,5 @@
+ at import url("default.css");
+
+.red {
+ color: #ff0000;
+}
\ No newline at end of file
diff --git a/doc/usersguide/analogies.rst b/doc/usersguide/analogies.rst
new file mode 100644
index 0000000..f323e6f
--- /dev/null
+++ b/doc/usersguide/analogies.rst
@@ -0,0 +1,142 @@
+.. _chap-analogies:
+
+***************************************
+Using Analogies to Update Workflows
+***************************************
+
+.. index:: analogy
+
+In Chapter :ref:`chap-version_tree`, we saw how the provenance data maintained by |vistrails| allows you to compare different versions of a workflow. In Chapter :ref:`chap-querying`, you learned how this same provenance information forms the basis of an elegant Query by Example mechanism, letting you find all versions of a workflow that match a given arrangement of modules. In this chapter, we will see yet another benefit of the |vistrails| provenance architecture. Through a process we c [...]
+
+Visualization by Analogy
+========================
+
+The main idea behind visualization by analogy is as follows. Given two versions of a workflow (called the "source" and "target" versions, respectively), |vistrails| can automatically find the differences between them and apply those differences to another (potentially unrelated) workflow. This powerful feature lets you create a new visualization without having to add or remove modules to/from the pipeline. |vistrails| takes care of these details for you behind the scenes.
+
+There are two distinct user interfaces for constructing visualizations by analogy. In the first, you set up the analogy in the ``Visual Diff`` window. In the second, you interact with the Spreadsheet. Both ways are logically equivalent, and which method you use will be largely a matter of personal preference.
+
+Before explaining either approach, however, let's first set up the vistrail that we'll be using as a running example in this chapter.
+
+.. topic:: Try it now!
+
+ Open the :vtl:`vtk\_http.vt` vistrail, located in the examples directory of the |vistrails| distribution. If the ``tetra mesh contour`` version is not selected, go to the ``History`` view and select it. This will be our "source" workflow. Execute this workflow, and take a look at the resultant visualization in the Spreadsheet.
+
+ We will now create our "target" workflow. Switch to the ``Pipeline`` view and add a new module, ``vtkSmoothPolyDataFilter`` between the ``vtkContourFilter`` and ``vtkDataSetMapper`` modules. Your modified pipeline should resemble the one shown in Figure :ref:`Modified pipeline for use in our example <fig-analogy_setupa>`.
+
+ Next, let's adjust some of the parameters for the new module. Select the ``vtkSmoothPolyDataFilter`` module. In the ``Module Information`` panel, select ``SetNumberOfIterations`` and type 20 in the input box. Then, select ``SetRelaxationFactor`` enter 0.5. Now, execute this workflow, and compare the two results in the Spreadsheet.
+
+ Return to the ``History`` view, and give your new version a meaningful tag such as ``smoothed`` (Figure :ref:`Corresponding version tree <fig-analogy_setupb>`). Finally, select the ``Fran Cut`` version and execute it too. Your spreadsheet should now resemble the one shown in Figure :ref:`Analogy example... <fig-analogy_spreadsheet1>`.
+
+.. %\begin{figure}
+.. %\centering
+.. %\includegraphics[width=2in,clip=false]{analogy_setup.png}
+.. %\caption{Modified pipeline for use in our example.}
+.. %\label{fig-analogy_setup}
+.. %\end{figure}
+
+.. fig-analogy_setup
+
+.. _fig-analogy_setupa:
+
+.. figure:: figures/analogies/analogy_setup.png
+ :height: 2in
+ :align: center
+
+ Modified pipeline for use in our example.
+
+.. _fig-analogy_setupb:
+
+.. figure:: figures/analogies/analogy_setup2.png
+ :height: 2in
+ :align: center
+
+ Corresponding version tree.
+
+.. _fig-analogy_spreadsheet1:
+
+.. figure:: figures/analogies/analogy_spreadsheet1.png
+ :width: 5in
+ :align: center
+
+ Analogy example - \(top left\) Original tetrahedral mesh model. \(top right\) Smoothed tetrahedral mesh. \(bottom left\) "Fran Cut" model.
+
+Using the Visual Diff Window
+============================
+
+.. index::
+ pair: analogy; visual diff
+
+By creating an analogy, you're telling |vistrails| to analyze and store the differences between the "source" and "target" versions of a workflow. Then when you apply that analogy to another (perhaps completely different) version of the workflow, |vistrails| attempts to make similar types of changes to this other workflow.
+
+One way to create an analogy is to run a ``Visual Diff`` between the "source" and "target" workflows. Recall from Chapter :ref:`chap-version_tree` that to perform a ``Visual Diff`` between two versions of a workflow, you need to drag the icon for one version atop the icon for the other. However, in the case of analogies, the sequence is important. In order for the analogy to work correctly, the icon for the *source* version of the workflow must be dragged atop the icon for the *target* v [...]
+
+In the toolbar of the ``Diff Properties`` window, there is a button whose tooltip is labeled ``Create Analogy`` (Figure :ref:`Click the Create Analogy button... <fig-analogy_diff>`). Clicking the ``Create Analogy`` will open up a dialog that lets you give this analogy a descriptive name.
+Once the analogy has a name, you can then apply it to any version of the workflow. This is done by returning to the ``History`` view, and selecting then right-clicking the version you want to apply the analogy to. A menu will appear, showing you a list of available analogies. Choose the one you want, and |vistrails| will attempt to apply the selected analogy to this version of the workflow.
+
+.. _fig-analogy_diff:
+
+.. figure:: figures/analogies/analogy_diff.png
+ :width: 4.5in
+ :align: center
+
+ Click the ``Create Analogy`` button in the ``Diff Properties`` window to create a named analogy.
+
+.. topic:: Try it now!
+
+ In the ``History`` view, drag the ``tetra mesh contour`` icon (the "source" version) atop the ``smoothed`` icon (the "target" version). A ``Visual Diff`` window will open. Click the ``Create Analogy`` button in the toolbar and then choose a name for this analogy, for example "SmoothFilter." Close the ``Visual Diff`` window. Select the ``Fran Cut`` icon in the ``History`` view so that it is highlighted, then right-click to access the ``Perform analogy`` menu. Choose the name of the a [...]
+
+.. _fig-analogy_menu:
+
+.. figure:: figures/analogies/analogy_menu.png
+ :width: 3in
+ :align: center
+
+ Access the ``Perform analogy`` menu by right-clicking on a selected icon in the version tree.
+
+.. _fig-analogy_spreadsheet2:
+
+.. figure:: figures/analogies/analogy_spreadsheet2.png
+ :width: 5in
+ :align: center
+
+ Result of applying a smoothing analogy to a different workflow.
+
+Using the Spreadsheet
+=====================
+
+You can also create and apply analogies directly in the Spreadsheet, without the use of the ``Visual Diff`` window. The Spreadsheet uses a simple "drag and drop" interface to manipulate analogies, and many users find it simpler to work with than the method described above. The drawback is that the Spreadsheet does not allow you to name your analogies like the ``Visual Diff`` window does.
+
+The Spreadsheet must be in Editing Mode in order to use analogies. Please refer to Chapter :ref:`chap-spreadsheet` for more information about the Spreadsheet's modes. Identify the two cells representing the "source" and "target" visualizations for which you wish to create an analogy. Drag the ``Create Analogy`` icon *from* the "source" *to* the "target." This creates an analogy that you can use to apply changes to other workflows. To apply an analogy to another version, drag the ``Apply [...]
+
+The following example illustrates how to use analogies within the Spreadsheet. If you completed the previous "Try it now!" exercise, first clear the cell containing the smoothed version of the ``Fran Cut`` model, so that it won't interfere with the present example. The Spreadsheet should again resemble Figure :ref:`Analogy example... <fig-analogy_spreadsheet1>`.
+
+.. topic:: Try it now!
+
+ Switch to the Spreadsheet's Editing Mode by hitting 'Ctrl-Shift-E.' Create the analogy by dragging the ``Create Analogy`` icon from the top-left cell over to the top-right cell (Figure :ref:`Drag the Create Analogy icon from the source cell... <fig-analogies-dnd1>`). Next, apply this analogy to the ``Fran Cut`` model by dragging the ``Apply Analogy`` icon from the bottom-left cell over to the bottom-right cell (Figure :ref:`Drag the Apply Analogy icon from the cell you wish to modify. [...]
+
+.. _fig-analogy_dnd:
+
+.. _fig-analogies-dnd1:
+
+.. figure:: figures/analogies/analogy_dnd1.png
+ :height: 2.5in
+ :align: center
+
+ Drag the ``Create Analogy`` icon *from* the "source" cell *to* the "target" cell to create an analogy.
+
+.. _fig-analogies-dnd2:
+
+.. figure:: figures/analogies/analogy_dnd2.png
+ :height: 2.5in
+ :align: center
+
+ Drag the ``Apply Analogy`` icon *from* the cell you wish to modify *to* an empty cell.
+
+Regardless of whether you use the ``Visual Diff`` interface or the Spreadsheet interface to create your analogy, the end result is the same. To verify this, you can inspect the ``Pipeline`` view for the newly created version of the workflow. All the module(s) necessary to implement the analogy's behavior are automatically inserted by |vistrails| at the correct locations in the pipeline.
+
+Notes
+=====
+
+.. %While it is also possible to create analogies among three or more versions of a workflow, this is an advanced feature and is not covered in this user's guide.
+
+Creating visualizations by analogy is a relatively new feature of |vistrails|, and as such is not yet fully mature. Although it works well for the examples presented herein, our algorithm may fail to create intuitive visualizations on other pipelines. Furthermore, it is not yet possible to save an analogy, nor apply an analogy to a vistrail other than the one in which it was created. Please contact the |vistrails| development team with any bug reports and/or suggestions.
diff --git a/doc/usersguide/batch.rst b/doc/usersguide/batch.rst
new file mode 100644
index 0000000..526a954
--- /dev/null
+++ b/doc/usersguide/batch.rst
@@ -0,0 +1,381 @@
+.. _chap-cli:
+
+**********************
+Command-line Arguments
+**********************
+
+Starting |vistrails| via the Command Line
+=========================================
+
+.. index:: command line arguments
+
+|vistrails| supports a number of command-line arguments that let you modify certain attributes and behaviors of the program. When invoking |vistrails| from the command line, the arguments are placed after the "run.py" filename. For example,
+
+ ``python vistrails/run.py -n``
+
+suppresses the |vistrails| splash screen. Table :ref:`table-batch-cli` contains a complete list of the command line switches supported by \vistrails. Each command line switch has both a short form and a long form. The two forms are logically equivalent, and which one you use is a matter of personal preference. The short form consists of a single minus sign "-" followed by a single letter. The longer form uses two minus signs "--" followed by a descriptive word. For example, the above com [...]
+
+ ``python vistrails/run.py --nosplash``
+
+
+In addition to the explicit switches listed in Table :ref:`table-batch-cli`, the |vistrails| command line also lets you indicate the filename of the vistrail you wish to open. For example, assuming your "examples" directory is one level above your current working directory, this is how you would tell |vistrails| to load the "lung.vt" example at startup:
+
+ ``python vistrails/run.py ../examples/lung.vt``
+
+
+Moreover, if you want |vistrails| to start on a *specific version* of the pipeline within the vistrail, you can indicate that version's tag name on the command line. The filename and version tag should be separated by a colon. For example, to start |vistrails| with the ``colormap`` version of the "lung.vt" vistrail, use:
+
+ ``python vistrails/run.py ../examples/lung.vt:colormap``
+
+
+In the event that the version you want to open contains a space in its tag name, simply surround the entire "filename:tag" pair in double quotes. For example:
+
+ ``python vistrails/run.py "../examples/lung.vt:Axial View"``
+
+
+You can also open up multiple vistrails at once by listing more than one vistrail file on the command line. This causes the vistrails to be opened in separate tabs, just as if you had opened them via the GUI. For example:
+
+ ``python vistrails/run.py ../examples/lung.vt ../examples/head.vt``
+
+
+You can specify version tags in conjunction with multiple filenames. Here is an example of an elaborate command-line invocation that opens two vistrails and sets each one to a specific version:
+
+ ``python vistrails/run.py "../examples/lung.vt:Axial View" ../examples/head.vt:bone``
+
+
+
+.. topic:: Note:
+
+ As of this writing, the |vistrails| development team is refactoring the implementation of many of the command-line switches presented in Table :ref:`table-batch-cli`. As such, depending on your version of |vistrails|, the results you achieve may not match those described. For a list of known issues with the command line switches, please refer to the |vistrails| website.
+
+.. raw::latex
+ \begin{table}
+ \caption{Command line arguments supported by VisTrails.}
+ \label{table:batch:cli}
+ \begin{center}
+ \begin{tabular}{ | l | l | p{3in} | }
+ \hline
+ \textbf{Short form} & \textbf{Long form} & \textbf{Description} \\
+ \hline
+ -h & -$\,$-help & Print a help message and exit. \\
+ \hline
+ -S \emph{/path} & -$\,$-startup=\emph{/path} &
+ Set user configuration directory (default is \texttt{$\sim$/.vistrails})
+ %% (Not fully working. see Ticket 213)
+ \\
+ \hline
+ -? & & Print a help message and exit. \\
+ \hline
+ -v & -$\,$-version & Print version information and exit. \\
+ \hline
+ -V \emph{num} & -$\,$-verbose=\emph{num} &
+ Set verboseness level (0--2, default=0, higher means
+ more verbose). \\
+ \hline
+ -b & -$\,$-noninteractive & Run in non-interactive (batch) mode. \\
+ \hline
+ -n & -$\,$-nosplash & Do not display splash screen on startup. \\
+ \hline
+ -q \emph{file} & -$\,$-quickstart=\emph{file} &
+ Start VisTrails using the specified static registry. \\
+ \hline
+ -c \emph{num} & -$\,$-cache=\emph{num} &
+ Enable/disable caching (0 to disable, nonzero to enable. Default is enabled). \\
+ \hline
+ -m \emph{num} & -$\,$-movies=\emph{num} &
+ Set automatic movie creation on spreadsheet (0 or 1,
+ default=1). Set this to zero to work around VTK bug
+ with offscreen renderer and OpenGL texture3D mappers. \\
+ \hline
+ -s & -$\,$-multiheads & Display the Builder and Spreadsheet on different
+ screens (if available).
+ \\
+ \hline
+ -x & -$\,$-maximized & Maximize Builder and Spreadsheet windows at startup. \\
+ \hline
+ -D & -$\,$-detachHistoryView & Detach the history view from the builder window. \\
+ \hline
+ -l & -$\,$-nologger & Disable logging. \\
+ \hline
+ -d & -$\,$-debugsignals & Debug Qt Signals. \\
+ \hline
+ -a \emph{params} & -$\,$-parameters=\emph{params} &
+ Set workflow parameters (non-interactive mode only). \\
+ \hline
+ -e \emph{dir} & -$\,$-dumpcells=\emph{dir} &
+ Set directory to dump spreadsheet cells before exiting (non-interactive mode only). \\
+ \hline
+ -G & -$\,$-workflowgraph &
+ Save workflow graph in specified directory without running
+ the workflow (non-interactive mode only).
+ \hline
+ -U & -$\,$-evolutiongraph &
+ Save evolution graph in specified directory without running
+ any workflowDump images in pdf format (non-interactive mode only).
+ \hline
+ -p & -$\,$-pdf &
+ Dump images in pdf format (non-interactive mode only).
+ \hline
+ -g & -$\,$-noSingleInstance &
+ Run VisTrails without the single instance restriction. \\
+ \hline
+ -t \emph{host} & -$\,$-host=\emph{host} & Set hostname or IP address of database server. \\
+ \hline
+ -r \emph{port} & -$\,$-port=\emph{port} & Set database port. \\
+ \hline
+ -f \emph{dbName} & -$\,$-db=\emph{dbName} & Set database name. \\
+ \hline
+ -u \emph{userName} & -$\,$-user=\emph{userName} & Set database username. \\
+ \hline
+ \end{tabular}
+ \end{center}
+ \end{table}
+
+.. tabularcolumns:: |l|l|p{7.5cm}|
+
+.. _table-batch-cli:
+
+.. csv-table:: Command line arguments supported by |vistrails|.
+ :header: **Short form**, **Long form**, **Description**
+ :widths: 10, 15, 20
+
+ -h, :math:`--`\ help, Print a help message and exit.
+ -S */path*, -\ -startup=\ */path*, Set user configuration directory (default is :math:`\sim`\ ``/.vistrails``)
+ -?, , Print a help message and exit.
+ -v, --version, Print version information and exit.
+ -V *num*, --verbose=\ *num*, "Set verboseness level (0--2, default=0, higher means more verbose)."
+ -b, --noninteractive, Run in non-interactive (batch) mode.
+ -n, --nosplash, Do not display splash screen on startup.
+ -q *file*, --quickstart=\ *file*, Start VisTrails using the specified static registry.
+ -c *num*, --cache=\ *num*, "Enable/disable caching (0 to disable, nonzero to enable. Default is enabled)."
+ -m *num*, --movies=\ *num*, "Set automatic movie creation on spreadsheet (0 or 1, default=1). Set this to zero to work around VTK bug with offscreen renderer and OpenGL texture3D mappers."
+ -s, --multiheads, Display the Builder and Spreadsheet on different screens (if available).
+ -x, --maximized, Maximize Builder and Spreadsheet windows at startup.
+ -P, --parameterExploration, execute Parameter Exploration.
+ -l, --nologger, Disable logging.
+ -d, --debugsignals, Debug Qt Signals.
+ -a *params*, --parameters=\ *params*, Set workflow parameters (non-interactive mode only).
+ -e *dir*, --dumpcells=\ *dir*, Set directory to dump spreadsheet cells before exiting (non-interactive mode only).
+ -G, --workflowgraph, Save workflow graph in specified directory without running the workflow (non-interactive mode only).
+ -U, --evolutiongraph, Save evolution graph in specified directory without running any workflow (non-interactive mode only).
+ -p, --pdf, Dump images in pdf format (non-interactive mode only).
+ -g, --noSingleInstance, Run VisTrails without the single instance restriction.
+ -t *host*, --host=\ *host*, Set hostname or IP address of database server.
+ -r *port*, --port=\ *port*, Set database port.
+ -f *dbName*, --db=\ *dbName*, Set database name.
+ -u *userName*, --user=\ *userName*, Set database username.
+
+.. index:: configuration directory
+
+Specifying a User Configuration Directory
+=========================================
+
+In addition to the default .vistrails directory, VisTrails allows you to create and use additional configuration directories. First, you will need to create a new directory. This is done by running:
+ ``python vistrails/run.py -S /path_to_new_directory/new_directory_name``.
+
+This will both create a new directory containing default configuration files and directories, and launch VisTrails, which will use the newly created files for configuration. The user is then free to add desired configurations to the new directory. Once a configuration directory exists, subsequent calls using the directory name (``python vistrails/run.py -S /path_to_directory/existing_directory``) will launch VisTrails using the 'existing_directory' for configuration and a new directory [...]
+
+**Note:** If you would like to copy configuration directories, you must change the references in copy_of_directory/startup.xml to point to the new directory instead of the original.
+
+.. _sec-cli-db:
+
+Passing Database Parameters on the Command Line
+===============================================
+
+As discussed in Chapter :ref:`chap-database`, |vistrails| can read and write vistrails stored in a relational database as well as in a filesystem. |vistrails| allows you to specify the name of the database server, the database name, the port number, and the username on the command line. This potentially saves you the trouble of filling out the same information on the database connection dialog. Note that, for security reasons, |vistrails| does not allow you to include a database password [...]
+
+The last four rows of Table :ref:`table-batch-cli` show the command-line switches that pertain to database connectivity. Be advised that these switches were designed primarily for use by VTL files (see Section :ref:`sec-cli-vtl`) and as such, are not necessarily user-friendly. In particular, these switches are ignored unless you also specify the vistrail ID and version name on the command line. For example, to open the ``contour`` version of the the "spx" vistrail (whose ID is 5) from th [...]
+
+ ``python vistrails/run.py -t vistrails.sci.utah.edu -f vistrails -u vistrails 5:contour``
+
+
+Once |vistrails| opens, you will be prompted to enter the password. Upon successful authentication, the vistrail is loaded from the database and opened to the pipeline corresponding to the specified version.
+
+.. _sec-cli-vtl:
+
+Using "Vistrail Link" Files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As discussed in Chapter :ref:`chap-database`, one of the advantages of storing your vistrails on a database is that you can collaborate with others without having to pass around a .vt file or force all users to use a shared filesystem. A disadvantage is that you need to remember the parameters with which to connect to the database. Using a "Vistrail Link" (VTL) file reduces this inconvenience, and also eliminates the need to include the associated command-line switches to connect to the [...]
+
+A VTL is a very small text (XML) file that contains the parameters required to load a vistrail from a database. VTL files are intended for use with a |vistrails|-enabled wiki. You can open a VTL either by saving the file and passing its filename to the command line, or by configuring your web browser to do this for you. Here is the syntax for using a VTL file on the command line:
+
+ ``python vistrails/run.py sample.vtl``
+
+
+Internally, |vistrails| parses the VTL file and loads the vistrail from the database exactly as if you had included its full parameter list on the command line.
+
+.. topic:: Note:
+
+ VTL is a relatively new feature of |vistrails|, and as such is neither fully developed nor completedly documented. Please contact the |vistrails| development team with any bug reports and/or suggestions.
+
+.. _sec-cli-batch:
+
+Running |vistrails| in Batch Mode
+=================================
+
+.. index::
+ single: batch mode
+ single: non-interactive mode
+
+Although |vistrails| is primarily intended to be run as an interactive, graphical client application, it also supports non-interactive use. |vistrails| can thus be invoked programmatically, \eg as part of a shell script. You can tell |vistrails| to start in non-interactive mode by using the "-b" or "--noninteractive" command line switch when launching \vistrails. [#]_
+
+Running |vistrails| in non-interactive mode has little effect, however, without an additional command line argument indicating which vistrail to load. Since we are running |vistrails| as part of a batch process, it only makes sense to execute vistrails whose output is something tangible, such as a file. A vistrail whose only output is an interactive rendering in a ``VTKCell``, for instance, would not be well-suited for running in batch mode.
+
+Consider the following example. The "offscreen.vt" vistrail (included in the "examples" directory) has a variety of output options, depending on which version you select in the ``History`` view (Figure :ref:`The different versions of the offscreen.vt vistrail... <fig-batch-version_tree>`). The version tagged ``only vtk`` displays its output as an interactive VTK rendering. The version tagged ``html`` creates a simple web page in the Spreadsheet. The ``offscreen`` version, however, output [...]
+
+ ``python vistrails/run.py -b ../examples/offscreen.vt:offscreen``
+
+.. _fig-batch-version_tree:
+
+.. figure:: figures/batch/offscreen_version_tree.png
+ :align: center
+ :width: 3in
+
+ The different versions of the "offscreen.vt" vistrail offer various forms of output.
+
+As you would expect, this command runs to completion without opening any windows. Instead, it silently loads the requested pipeline, executes it, and closes.
+Assuming it ran correctly, this pipeline should have created a file named "image.png" in the current directory. When you view this file, it should resemble the picture in Figure :ref:`Running the offscreen version of offscreeen.vt in batch mode... <fig-batch-image_png>`.
+
+.. _fig-batch-image_png:
+
+.. figure:: figures/batch/offscreen_output.png
+ :align: center
+ :width: 2in
+
+ Running the ``offscreen`` version of "offscreen.vt" in batch mode produces an image named "image.png".
+
+Running a Specific Workflow in Batch Mode
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To run a specific workflow in batch mode, call |Vistrails| with the following options:
+
+ ``python vistrails/run.py -b path_to_vistrails_file:pipeline``
+
+where pipeline can be a version **tag name** or version **id**.
+
+.. topic:: Note
+
+ If you downloaded the MacOS X bundle, you can run |vistrails| from the command line via the following commands in the terminal. Change the current directory to wherever VisTrails was installed (often /Applications), and then type: ``Vistrails.app/Contents/MacOS/vistrails [<cmd_line_options>]``
+
+Running a Workflow with Specific Parameters
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+
+An alias is a name assigned to a parameter that allows you to reference that parameter in batch mode. An alias is created by clicking on the type of an existing parameter in VisTrails, then entering a name for it.
+
+.. _fig-batch-create_alias:
+
+.. figure:: figures/batch/create_alias.png
+ :align: center
+ :width: 50%
+
+ Example of creating an alias
+
+Users can change workflow parameters that have an alias through the command line.
+
+For example, offscreen pipeline in offscreen.vt always creates the file called image.png. If you want generate it with a different filename:
+
+``python vistrails/run.py -b ../examples/offscreen.vt:offscreen -a"filename=other.png"``
+
+filename in the example above is the alias name assigned to the parameter in the value method inside the String module. When running a pipeline from the command line, VisTrails will try to start the spreadsheet automatically if the pipeline requires it. For example, this other execution will also start the spreadsheet (attention to how $ characters are escaped when running on bash):
+
+``python vistrails/run.py -b ../examples/head.vt:aliases -a"isovalue=30\$&\$diffuse_color=0.8, 0.4, 0.2"``
+
+You can also execute more than one pipeline on the command line:
+
+``python vistrails/run.py -b ../examples/head.vt:aliases ../examples/spx.vt:spx \ -a"isovalue=30"``
+
+Use the -a parameter only once regardless the number of pipelines.
+
+.. %TODO should we cover aliases here?
+
+Accessing a Database in Batch Mode
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As discussed in Section :ref:`sec-cli-db`, you can specify most of the parameters of your database connection on the command line, but the password must be entered through the GUI. This poses a problem for running |vistrails| in non-interactive mode, since no database connection dialog will be opened. If your batch process needs to access vistrails stored on a database, the current workaround is to create a special account on the database (probably one with read-only access) that does *n [...]
+
+Using |vistrails| as a Server
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. index:: server
+
+Using the VisTrails server mode, it is possible to execute workflows and control VisTrails through another application. For example, the CrowdLabs Web portal (http://www.crowdlabs.org) accesses a VisTrails sever to execute workflows, retrieve and display vistrail trees and workflows.
+
+The way you access the server is by doing XML-RPC calls. In the current VisTrails release, we include a set of PHP scripts that can talk to a VisTrails server instance. They are in "extensions/http" folder. The files are reasonably well documented. Also, it should be not difficult to create python scripts to access the server (just use xmlrpclib module).
+
+Note that the VisTrails server requires the provenance and workflows to be in a database. More detailed instructions on how to setup the server and the database are available in :ref:`chap-vistrails-server` and in :ref:`sec-database-setup`.
+
+If what you want is just to execute a series of workflows in batch mode, a simpler solution would be to use the VisTrails client in batch mode (see Section :ref:`sec-cli-batch`).
+
+Executing Workflows in Parallel
+===============================
+
+The VisTrails server can only execute pipelines in parallel if there's more than one instance of VisTrails running. The command
+
+``self.rpcserver=ThreadedXMLRPCServer((self.temp_xml_rpc_options.server, self.temp_xml_rpc_options.port))``
+
+starts a multithreaded version of the XML-RPC server, so it will create a thread for each request received by the server. The problem is that Qt/PyQT doesn't allow these multiple threads to create GUI objects. Only the main thread can. To overcome this limitation, the multithreaded version can instantiate other single threaded versions of VisTrails and put them in a queue, so workflow executions and other GUI-related requests, such as generating workflow graphs and history trees can be [...]
+
+Note that this infrastructure works on Linux only. To make this work on Windows, you have to create a script similar to start_vistrails_xvfb.sh (located in the scripts folder) where you can send the number of other instances via command-line options to VisTrails. The command line options are:
+
+``python vistrails_server.py -T <ADDRESS> -R <PORT> -O<NUMBER_OF_OTHER_VISTRAILS_INSTANCES> [-M]&``
+
+If you want the main vistrails instance to be multithreaded, use the -M at the end.
+
+After creating this script, update function start_other_instances in vistrails/gui/application_server.py lines 1007-1023 and set the script variable to point to your script. You may also have to change the arguments sent to your script (line 1016: for example, you don't need to set a virtual display). You will need to change the path to the stop_vistrails_server.py script (on line 1026) according to your installation path.
+
+Executing Parameter Explorations from the Command Line
+======================================================
+
+Named parameter explorations can be executed from the command line in different ways using the -P flag. The parameter after the vistrail will then indicate the parameter exploration name in place of the workflow version. To open vistrails and execute a parameter exploration named "final" in terminator.vt run:
+
+``python vistrails/run.py -P terminator.vt:final``
+
+To only show the spreadsheet run:
+
+``python vistrails/run.py -P -i terminator.vt:final``
+
+To execute the spreadsheet in batch mode, and to output the spreadsheet as images to a directory, use the -b flag and specify a directory with the -e flag:
+
+``python vistrails/run.py -P -b -e ./final_images terminator.vt:final``
+
+This will create an image for each cell and also create a composite image for each sheet in the spreadsheet.
+
+
+Finding Methods Via the Command Line
+====================================
+
+We have tried to make some methods more accessible in the console via an api. You can import the api via import api in the console and see the available methods with dir(api). To open a vistrail:
+
+.. code-block:: python
+
+ import api
+ api.open_vistrail_from_file('/Applications/VisTrails/examples/terminator.vt')
+
+To execute a version of a workflow, you currently have to go through the controller:
+
+.. code-block:: python
+
+ api.select_version('Histogram')
+ api.get_current_controller().execute_current_workflow()
+
+Currently, only a subset of VisTrails functionality is directly available from the api. However, since VisTrails is written in python, you can dig down starting with the VistrailsApplication or controller object to expose most of our internal methods. If you have suggestions for calls to be added to the api, please let us know.
+
+One other feature that we're working on, but is still in progress is the ability to construct workflows via the console. For example:
+
+.. code-block:: python
+
+ vtk = load_package('org.vistrails.vistrails.vtk')
+ vtk.vtkDataSetReader() # adds a vtkDataSetReader module to the pipeline
+ # click on the new module
+ a = selected_modules()[0] # get the one currently selected module
+ a.SetFile('/vistrails/examples/data/head120.vtk') # sets the SetFile\
+ parameter for the data set reader
+ b = vtk.vtkContourFilter() # adds a vtkContourFilter module to the\
+ pipeline and saves to var b
+ b.SetInputConnection0(a.GetOutputPort0()) # connects a's GetOutputPort0\
+ port to b's SetInputConnection0
+
+.. rubric:: Footnotes
+.. [#] The parameter "-b" stands for "batch." In this chapter, we use the terms "batch mode" and "non-interactive mode" synonymously.
diff --git a/doc/usersguide/cfassistant.rst b/doc/usersguide/cfassistant.rst
new file mode 100644
index 0000000..0e7e58e
--- /dev/null
+++ b/doc/usersguide/cfassistant.rst
@@ -0,0 +1,145 @@
+.. _chap-controlflow-assistant:
+
+**************************
+The Control Flow Assistant
+**************************
+
+.. index:: control flow assistant
+
+Using the Control Flow Assistant (CFA)
+======================================
+
+In order to simplify the process of creating a control flow loop that uses the Map module, VisTrails has a Control Flow Assistant (CFA).
+To use the CFA, you must:
+
+1) Enable all ports (in the Module Information panel) that you wish to use as inputs or outputs.
+2) Select the modules in the workflow that will form the basis of your mapped input-output loop.
+3) Go to 'Edit->Control Flow Assistant' to launch the CFA using the selected modules.
+4) Select the input ports that you wish to loop over using List modules as input.
+5) Select the output port that you wish to use for the values in the output List.
+6) Click OK, and the CFA will generate the control flow structure as a Group module.
+7) Connect a List input to each of the inputs on the control flow Group.
+8) Connect the Group's output List (output port 'Result') to a suitable module/port, or create a PythonSource module to handle the List output.
+
+Note: All existing connections to input and output ports selected in steps 4 and 5 will be removed.
+
+
+List Input
+^^^^^^^^^^
+
+By default, the List inputs will be used sequentially, one from each List, which requires that all List inputs be the same length. As another option, the Group created by the CFA has a boolean 'UseCartesianProduct' parameter. If this parameter is set to 'true' then the cartesian product of all of the input Lists will be used as the input for the Map. Use caution when using this parameter, as the number of inputs can grow very rapidly with just a few List inputs.
+
+
+List Output
+^^^^^^^^^^^
+
+There are several ways to handle the output List. One option would be to send the output List to a StandardOutput module to display its contents. Another option is to simply ignore the output List, in the case where you just want part of the workflow to execute multiple times using different inputs. For example, if the mapped portion of the workflow contains a VTKCell, and you just want to generate a new VTKCell for each input, you should select the 'self' port of the VTKCell module w [...]
+
+
+Custom List
+^^^^^^^^^^^
+
+For advanced users, the default behavior, or cartesian product behavior may not be sufficient for your needs. If this is the case, the 'UserDefinedInputList' parameter allows you to manually specify the input list. If this parameter is defined, it will override any input lists already defined or connected. The format for this user-provided input list must be a list of lists of tuples. Each inner list represents a single loop execution, and contains tuples (or single values for functi [...]
+
+For example, if the loop has two input functions defined, in order, as SetXY(x, y) and SetZ(z), and we want two executions of the loop, the input list would be:
+[[(x1, y1), z1], [(x2, y2), z2]]
+
+
+Parameter Exploration
+^^^^^^^^^^^^^^^^^^^^^
+
+.. index::
+ pair: parameter exploration; control flow
+ pair: parameters; exploring
+
+One useful purpose for the CFA is to provide a version-based approach to parameter exploration. To create a parameter exploration for a workflow, you could simply select all modules in the workflow, making sure the ports for the desired parameters are enabled, then launch the CFA and select the ports of the parameters you wish to explore. By providing a list for each parameter, you can create a parameter exploration that directly uses the version tree.
+
+.. topic:: Try it Now!
+
+ Processing a List of values with PythonCalc:
+
+ 1) Go to 'Edit->Preferences', select the 'Module Packages' tab, and enable the 'pythonCalc' package if it is not already enabled.
+ 2) Click on File->New to start a new VisTrail.
+ 3) Add the following modules from the module registry to the VisTrail:
+ a) One 'PythonCalc' module from the 'pythonCalc' package
+ b) One 'List' module from the 'Basic Modules' package
+ c) One 'StandardOutput' module from the 'Basic Modules' package
+ 4) Set the List 'value' parameter to: [1.0, 2.0, 3.0, 4.0, 5.0]
+ 5) Set the PythonCalc 'op' parameter to: '*'
+ 6) Set the PythonCalc 'value2' parameter to: 2.0
+ 7) With the PythonCalc module selected, go to 'Edit->Control Flow Assistant' (see Figure :ref:`Example 1.1 <fig-assistant>`):
+
+ a) Click on the input port 'value1' and ensure it is highlighted
+ b) Click on the output port 'value' and ensure it is highlighted
+ c) Click 'OK' to close the window and build the loop structure as a Group module (see Figure :ref:`Example 1.2 <fig-select>`)
+ 8) Connect the 'List' module's output port 'value' to the 'Group' module's input port 'value1'.
+ 9) Connect the 'Group' module's output port 'Result' to the 'StandardOutput' module's input port 'value' (see Figure :ref:`Example 1.3 <fig-pipeline>`)
+ 10) Execute the current workflow.
+ 11) In your Standard Output console, you should see a List containing the computation for each element in the input list: [2.0, 4.0, 6.0, 8.0, 10.0] :vtl:`(Open result) <cfassistant1.vt>`
+
+.. _fig-assistant:
+
+.. figure:: figures/cfassistant/assistant.png
+ :align: center
+ :width: 90%
+
+ Example 1.1 - Running the Control Flow Assistant
+
+.. _fig-select:
+
+.. figure:: figures/cfassistant/port_select.png
+ :align: center
+ :width: 70%
+
+ Example 1.2 - Selecting relevant ports.
+
+.. _fig-pipeline:
+
+.. figure:: figures/cfassistant/pipeline.png
+ :align: center
+ :width: 25%
+
+ Example 1.3 - The connected pipeline.
+
+.. topic:: Try it Now!
+
+ Performing a Parameter Exploration:
+
+ 1) Go to 'File->Open', explore to the VisTrails examples folder, and open :vtl:`spx.vt`.
+ 2) Open the History view and select the version tagged as 'decimate'.
+ 3) Open the Pipeline view.
+ 4) Select the 'vtkContourFilter' module and enable the 'SetValue' input port by clicking to the left of 'SetValue' in the Module Information panel (see Figure :ref:`Example 2.1 <fig-cfassistant-enable-port>`).
+ 5) Click on 'Edit->Select All'.
+ 6) With all modules selected, go to 'Edit->Control Flow Assistant':
+
+ a) Click on the 'vtkContourFilter' module's input port 'SetValue' and ensure it is highlighted
+ b) Click on the 'VTKCell' module's output port 'self' and ensure it is highlighted (see Figure :ref:`Example 2.2 <fig-cfassistant-enable-port>`)
+ c) Click 'OK' to close the window and build the loop structure as a Group module
+ 7) Select the newly created 'Group' module, and set the 'SetValue' parameter to: [(0, 0.5), (0, 0.75), (0, 1.0)]
+ 8) Execute the current workflow.
+ 9) In your VisTrails Spreadsheet, you should see three visualizations, one for each set of input parameters to the 'SetValue' port of 'vtkContourFilter' (see Figure :ref:`Example 2.3 <fig-cfassistant-results>`). :vtl:`(Open result) <cfassistant2.vt>`
+
+.. _fig-cfassistant-enable-port:
+
+.. figure:: figures/cfassistant/enable_port.png
+ :align: center
+ :width: 30%
+
+ Example 2.1 - Enabling a port for use with the control flow assistant.
+
+.. _fig-cfassistant-select:
+
+.. figure:: figures/cfassistant/port_select2.png
+ :align: center
+ :width: 70%
+
+ Example 2.2 - Selecting relevant ports.
+
+.. _fig-cfassistant-results:
+
+.. figure:: figures/cfassistant/results.png
+ :align: center
+ :width: 90%
+
+ Example 2.3 - The spreadsheet results using the list: [(0, 0.5), (0, 0.75), (0, 1.0)] as input to the contour filter via the control flow assistant.
+
diff --git a/doc/usersguide/cltools.rst b/doc/usersguide/cltools.rst
new file mode 100644
index 0000000..9a44c96
--- /dev/null
+++ b/doc/usersguide/cltools.rst
@@ -0,0 +1,264 @@
+.. _chap-cltools:
+
+*************************************************
+Wrapping command line tools using package CLTools
+*************************************************
+
+.. index:: wrapping command line tools using package CLTools
+
+Package CLTools
+===============
+
+The package CLTools provide a way to wrap command line tools so that
+they can be used as modules in VisTrails. It includes a wizard that
+simplifies the creation of wrappers. To use the package, enable
+CLTools in the package configuration window. The package will be empty
+until you add a wrapper for a command line tool. When you have added a
+wrapper you need to reload the wrappers by either pressing the reload
+button in the wizard, reloading the CLTools package, or selecting
+Packages->CLTools->Reload All Scripts on the menu.
+
+Using the CLTools Wizard
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can run the Wizard from within VisTrails. First, make sure the
+CLTools package is enabled. Then, on the menu, select
+Packages->CLTools->Open Wizard.
+
+Or, to launch the wizard from the command line run:
+``python vistrails/package/CLTools/wizard.py``
+
+The wizard allows you to create and edit wrappers for command line
+tools. Input/output ports can be created as arguments to the command
+or using pipes (stdin, stdout, or stderr). :ref:`Figure 1.1
+<fig-cltools-wizard>` shows the main interface. Command line arguments
+can be added, removed and rearranged. Pipes can be added and
+configured. There is a preview line where you can see how your command
+will look when executed. You can also push the preview button to see
+which ports will be available for the vistrails module, as shown in
+the bottom right. This example shows some of the most common ways to
+specify arguments. In order: The standard output is used as a string
+output port, an integer attribute using the **-i** flag, a boolean
+flag **-A** that can be turned on or off, an input file using a
+prefix, an output file using the **-o** flag, and finally a simple
+string input. Note the way arguments correspond to ports in the bottom
+right.
+
+.. _fig-cltools-wizard:
+
+.. figure:: figures/CLTools/wizard.png
+ :align: center
+ :width: 100%
+
+ Figure 1.1 - CLTools Wizard main window
+
+Arguments can represent either input ports, output ports, both, or constant
+strings. Ports can handle different types such as boolean flags,
+strings, integers, floats, or files. Lists of strings and files are also possible. Each
+argument can have a flag before it such as ``-f`` or a prefix such as ``--file=``.
+
+A file ending can be specified for files that are used as outputs using **file suffix**.
+
+You can view and import flags from man and help pages (See :ref:`Figure 1.2
+<fig-cltools-import>`).
+
+.. _fig-cltools-import:
+
+.. figure:: figures/CLTools/import.png
+ :align: center
+ :width: 100%
+
+ Figure 1.2 - Import Arguments Window
+
+Files should be saved as {modulename}.clt in the directory .vistrails/CLTools/
+
+Supported flags::
+
+ -c Import a command with arguments automatically
+ For example, to create a wrapper for ls with two flags -l and -A run:
+ python wizard.py -c ls -l -A
+
+.. topic:: Try it Now!
+
+ Create a wrapper that takes a file as input and generate a file as output using ``-o``. The ports should always be visible. The command looks like::
+
+ filter infile -o outfile
+
+ Your wrapper should look like in figure :ref:`Figure 1.3 <fig-cltools-inputoutput>`. Note that the order of the arguments is always preserved:
+
+.. _fig-cltools-inputoutput:
+
+.. figure:: figures/CLTools/inputoutputfile.png
+ :align: center
+ :width: 100%
+
+ Figure 1.3 - An infile outfile wrapper
+
+Port visibility
+^^^^^^^^^^^^^^^
+
+:ref:`Figure 1.4 <fig-cltools-visibility>` shows how the **visible**
+setting affects ports in VisTrails. Visible ports are meant to be
+connected to other modules, and are shown as square input or output
+ports on the module, while non-visible ports are meant to be optional,
+or added as parameters on the input port list to the right. Non-visible
+ports can be made visible on the module by clicking on the left side
+of the ports pane, so that a eye icon is displayed. The example below has 2 visible input ports and one visible output port. The input list to the right shows available inputs, bot visible and non-visible. The first input in the input list to the right is visible by default,
+which is shown by a greyed-out eye. The second port is non-visible by
+default but has been made visible as shown by the eye icon. The second
+input is non-visible but can be made visible on the module by clicking
+so that the eye icon becomes visible.
+
+.. _fig-cltools-visibility:
+
+.. figure:: figures/CLTools/visibility.png
+ :align: center
+ :width: 70%
+
+ Figure 1.4 - Port visibility in VisTrails
+
+Environment Variables
+^^^^^^^^^^^^^^^^^^^^^
+
+There are three ways to set environment variables in CLTools. If your
+environment variables is platform-dependent, you should set the
+**env** configuration variable for the CLTools package. In VisTrails, go to the
+Preferences->Module Packages dialog, select **CLTools**, make sure it
+is enabled, and select **Configure...**. Set the **env** variable to
+the preferred environment. Separate name and value using **=** and
+variables using **;**, like this::
+
+ PATH=/my/custom/path;DEBUG=;MYVAR=32
+
+If you want to specify the variables in your workflow, you can enable the **env** input port on your module by checking the **env** option in the top toolbar in the CLTools wizard. Then you can specify environment variables either as parameters to your module or by connecting the **env** input port to other modules. Multiple parameters can be specified as a single string or by adding multiple **env** parameters. These variables overrides variables specified using the other two methods.
+
+For modules that always need the same environment variables, they can be added to the module by editing the .clt file directly and adding an **env** entry in the options section as shown below. These variables overrides the ones specified in the CLTools configuration::
+
+ {
+ "command": "ls",
+ "options": {
+ "env": "MYVAR=/my/custom/path;MYVAR2=64"
+ }
+ }
+
+Note that if you replace e.g. the **PATH** variable, you should
+include the existing path, which can be found by running e.g. ``echo
+$PATH`` on the command line.
+
+Setting working directory
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The **Directory** field to the right of the command field can be used
+to specify the working directory where the command will be
+executed. It does **not** specify the directory where the command is
+found. Use the PATH enviroment variable for that.
+
+InputOutput files
+^^^^^^^^^^^^^^^^^
+
+The **InputOutput** port should be used for commands that modifies a
+file in-place, so that it is used both as and input and an output. An
+example of using the InputOutput module is shown in :ref:`Figure 1.5
+<fig-cltools-inputoutputport>`. When executed, the input file will be
+copied to a temporary file before it is passed to the command and used
+as an output. This is because you should not (if you can avoid it)
+modify the inputs to your modules, because they may be used by other
+modules, or re-executed by the same module. It may be useful to set
+the file suffix attribute to make sure the copied file is of the same
+type as the original. There is currently no way of passing the original
+file to the command, since it is discouraged. But if this is
+necessary in a particular case, CLTools can be easily modified to do
+this.
+
+.. _fig-cltools-inputoutputport:
+
+.. figure:: figures/CLTools/inputoutputport.png
+ :align: center
+ :width: 100%
+
+ Figure 1.5 - Example of an InputOutput port
+
+Creating a standalone package
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+When you have a working set of wrappers and want to distribute them,
+you should put them in a separate module package. This allows you to
+name and version your package, and makes sure there are no conflicts
+with modules using the same name as yours. One warning: workflows
+using the old modules will need to be recreated to use the modules in
+this new package instead, so it is better to start building workflows
+after a separate package has been created. Below are the steps to
+follow in order to set up a new package.
+
+1) Create a new directory in ``$HOME/.vistrails/userpackages/``
+2) Copy ``__init__.py`` and ``init.py`` from ``vistrails/packages/CLTools`` to this new directory
+3) Update **name**, **identifier**, and **version** in ``__init__.py`` to the desired values
+4) Move all desired tools (\*.clt files) to this new directory
+5) Enable and test your new package!
+
+File Format
+^^^^^^^^^^^
+
+The wrapper is stored as a `JSON <http://www.json.org/>`_ file and can be edited using a text editor if needed. It uses the following schema:
+
+ROOT is a dict with the following possible keys:
+
+* **command** (required) - value is the command to execute like "cat" or "/home/tommy/cat"
+* **stdin** - handle stdin - value is a 3-list ["port name", CLASS, OPTIONDICT]
+* **stdout** - handle stdout - value is a 3-list ["port name", CLASS, OPTIONDICT]
+* **stderr** - handle stdout - value is a 3-list ["port name", CLASS, OPTIONDICT]
+* **args** - list of ordered arguments that can either be constants, inputs, or outputs. See ARG.
+* **dir** - value is the working directory to execute the command from
+* **options** - a dict of module options - see OPTIONDICT
+
+OPTIONDICT is a dict with module specific options, recognized options are:
+
+* **std_using_files** - connect files to pipes so that they need not be stored in memory. This is useful for large files but may be unsafe since it does not use subprocess.communicate
+* **env** - A list of environment variables to set when executing the command, with entries separated by **;** and key/value pairs separated by **=**. This overrides all other environment variables set, except for the env_port, and should only be used when they are not expected to change. It can only be set by editing the .clt files directly with a text editor.
+* **env_port** - Set to add an input port **env** for specifying the environment variables to use, this overrides all other environment variables set
+
+ARG is a 4-list containing [TYPE, "name", KLASS, ARGOPTIONDICT]
+TYPE is one of:
+
+* **input** - create input port for this arg
+* **output** - create output port for this arg
+* **inputoutput** - create both input and output port for this arg. The type must be **File** and a copy of the original file will be processed and used as output.
+* **constant** - use "port name" directly as a constant string
+
+CLASS indicates the port type and can be one of the following. **String** is used by default.
+
+* **File** - A vistrails **File** type. The filename will be used as the argument
+* **String** - A vistrails **String** type. The string will be used as the argument
+* **Integer** - A vistrails **Integer** type. Its string value will be used as the argument
+* **Float** - A vistrails **Float** type. Its string value will be used as the argument
+* **Flag** - A vistrails **Bool** type. A boolean flag that when set to true will add the value of the argument to the command.
+* **List** - A list of values of the type specified by the **type** option. All values in the list will be added as arguments.
+
+ARGOPTIONDICT is a dict containing argument options. recognized options are:
+
+* **type**: **CLASS** - used by List-types to specify subtype.
+* **flag**: **name** - Append name as a short-style flag before the specified argument. If type is **List** it is appended before each item
+* **prefix**: **name** - Append name as a long-style prefix to the final argument. If it is also a list it is appended to each item.
+* **required**: None - Makes the port always visible in VisTrails.
+* **suffix**: **name** - Specifies the file ending for created files
+
+
+.. topic:: Try it Now!
+
+ Wrap the command "cat" that takes 2 files as input named "first" and "second". Also take a list of files as input named "rest".
+ Catch stdout as file, name it "combined".
+ Catch stderr as string, name it "stderr".
+ Show "first" and "combined" by default.
+
+ Your wrapper should now look like this::
+
+ {"command": "cat",
+ "args": [["input", "first", "File", {"required":""}],
+ ["input", "second", "File", {}],
+ ["input", "rest", "List", {"type":"File"}]],
+ "stdout": ["combined", "File", {"required":""}],
+ "stderr": ["stderr", "String", {}]
+ }
+
+ Save as ``{yourhomedirectory}/.vistrails/CLTools/cat.clt``
+ Reload CLTools package in VisTrails. Test the new module.
diff --git a/doc/usersguide/conf.py b/doc/usersguide/conf.py
new file mode 100644
index 0000000..935f009
--- /dev/null
+++ b/doc/usersguide/conf.py
@@ -0,0 +1,208 @@
+# -*- coding: utf-8 -*-
+#
+# VisTrails documentation build configuration file, created by
+# sphinx-quickstart on Mon Feb 7 21:06:44 2011.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.append(os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.ifconfig', 'sphinx.ext.extlinks']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'VisTrails'
+copyright = u'2013, NYU Poly'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '2.1'
+# The full version, including alpha/beta/rc tags.
+release = '2.1.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+extlinks = {'vtl': ('http://www.vistrails.org/usersguide/v2.1/examples/%sl',
+ '')}
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. Major themes that come with
+# Sphinx are currently 'default' and 'sphinxdoc'.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+html_style = "mystyle.css"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_use_modindex = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'VisTrailsdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+ ('index', 'VisTrails.tex', u'VisTrails Documentation',
+ u'NYU Poly', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+latex_use_parts = True
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'http://docs.python.org/': None}
+
+rst_epilog = """
+.. |vistrails| replace:: VisTrails
+.. |eg| replace:: *e.g.,*\
+.. |etc| replace:: *etc.*\
+"""
diff --git a/doc/usersguide/controlflow.rst b/doc/usersguide/controlflow.rst
new file mode 100644
index 0000000..802e5a0
--- /dev/null
+++ b/doc/usersguide/controlflow.rst
@@ -0,0 +1,593 @@
+.. _chap-controlflow:
+
+*************************
+Control Flow in VisTrails
+*************************
+
+Scientific workflows usually follow a dataflow model, but, in some cases,
+control structures, including loops and conditionals, are necessary to
+accomplish certain tasks. |vistrails| provides the ``Control Flow``
+package to support these and other structures. To create your own ``Control Flow`` modules, please refer to the Developer's Guide (:ref:`chap-controlflowdev`). Or, if you would like to use the Control Flow Assistant, to simplify the process described in this chapter, please refer to :ref:`chap-controlflow-assistant`.
+
+This package also provides some related modules that operate on lists.
+
+The Map operator
+================
+
+In functional programming, ``map`` is a high-order function that applies
+a given function to a list (each element of the list is processed using this
+function) and returns a sequence of results. The ``Map`` module
+provides this functionality for workflows in |vistrails|. Note that this
+module provides simple looping as it can be used to iterate through a list
+of inputs.
+
+The Map module has four input ports:
+
+* "FunctionPort": this port receives the module (via the "self" output port) that represents the function to be applied for each element of the input list; if the function uses more than one module, you must use a ``Group`` (see Chapter :ref:`chap-grouping`) or a ``SubWorkflow`` and connect that composite module to this port;
+* "InputPort": this port receives a list of the names of the input ports that represent the individual arguments of the function;
+* "OutputPort": this port receives the name of the output port that represents the individual result of the function;
+* "InputList": this port receives the input list for the loop; it must be a list of tuples if more than one function input port was chosen.
+
+
+The output port "Result" produces a list of results, one for each element in the input list.
+
+.. topic:: Try it Now!
+
+ To better show how to use the ``Map`` module, let's use a workflow as
+ an example. Inside the "examples" directory of the |vistrails|
+ distribution, open the "triangle_area.vt" vistrail. Now, select the
+ "Surface Area" version. This version basically calculates the area
+ of a given isosurface. We are going to modify this version, in order to
+ calculate the areas of the isosurface given by contour values in a list.
+ Then, we will create a 2D plot to show all the areas.
+
+ Begin by deleting the ``StandardOutput`` modules, and the connection between the ``vtkDataSetReader`` and the ``vtkContourFilter`` modules. Then, drag the following modules to the canvas:
+
+ * ``Map``
+ * ``CartesianProduct``
+ * ``List`` (under "Basic Modules")
+ * ``MplSource`` (under "matplotlib")
+ * ``MplFigure`` (under "matplotlib")
+ * ``MplFigureCell`` (under "matplotlib")
+ * ``InputPort`` (under "Basic Modules") - you will need two of them
+ * ``OutputPort`` (under "Basic Modules")
+ * ``PythonSource`` (under "Basic Modules")
+
+Notice that when you drag ``Map`` to the pipeline canvas it will be drawn in a different shape from the other modules. This is a visual cue to help distinguish control modules from other modules. All control modules have the same shape.
+
+.. topic:: Next Step!
+
+ Select the ``vtkContourFilter`` module and delete its method "SetValue" in the ``Module Information`` tab. Then, make this port visible by clicking on the first column left of its name in the "inputs" tab to toggle the eye icon..
+
+ Connect the modules as shown in Figure :ref:`fig-controlflow-calculate_area`.
+
+.. _fig-controlflow-calculate_area:
+
+.. figure:: figures/controlflow/CalculateArea.png
+ :align: center
+ :width: 1.8in
+
+ Connecting a subset of the modules to be grouped as a ``SubWorkflow``
+
+These modules represent the function we wish to map: each element of the input list will be processed using them. Because we have more than one module, we need to create a ``Group`` or a ``SubWorkflow`` to identify the entire function. The ``InputPort`` and the ``OutputPort`` modules are
+necessary to expose these ports in the ``Group``/``SubWorkflow``
+structure.
+
+.. topic:: Next Step!
+
+ In this example, we will use a ``SubWorkflow`` structure. Select all the modules shown in Figure :ref:`fig-controlflow-calculate_area`, go to the ``Workflow`` menu, and then click on ``Create SubWorkflow``. You can name it ``CalculateArea``. Enable the ``self`` output port in the 'outputs' panel: you will need it to connect to the "Map" module
+
+.. topic:: Note
+
+ When using ``Map``, the module (or subworkflow) used as function port in the map module MUST be a function, i.e., it can only define 1 output port.
+
+.. topic:: Next Step!
+
+ Now, select the ``MplSource`` module and open its configuration dialog. Inside it, add two input ports of type ``List``: "InputList" and "X_Values". Also, copy the code listed below, in order to create the necessary information for the 2D plot, into the source text area and save your changes.
+
+.. code-block:: python
+
+ subplot(212)
+
+ dashes = [1, 3]
+ xaxis = []
+
+ for i in xrange(len(InputList)):
+ xaxis.append(X_Values[i][1])
+
+ l, = plot(xaxis, InputList, marker="o", markerfacecolor="red",
+ markersize=7, label="IsoSurface Areas", linewidth=1.5)
+
+ l.set_dashes(dashes)
+
+.. topic:: Next Step!
+
+ Next, edit the ``PythonSource`` module by adding an output port "result" of type ``List``, copying the following code to the source text area, and saving these changes. The code will create a range of contour values that we will use as our input list.
+
+.. code-block:: python
+
+ result = []
+
+ for i in xrange(4, 256, 4):
+ result.append(i)
+
+.. topic:: Next Step!
+
+ It may be helpful to identify this ``PythonSource`` module by labeling it as ``RangeList``. Connect all the modules as shown in Figure :ref:`fig-controlflow-map_workflow`.
+
+.. _fig-controlflow-map_workflow:
+
+.. figure:: figures/controlflow/Map_Workflow.png
+ :align: center
+ :width: 4in
+
+ All the modules connected in the canvas
+
+.. topic:: Next Step!
+
+ You will set some parameters now:
+
+ * ``HTTPFile``: set the parameter "url" to http://www.sci.utah.edu/~cscheid/stuff/head.120.vtk
+ * ``List``: set the parameter "value" to *[0]*
+ * ``Map``: set the parameter "InputPort" to *["SetValue"]* and the parameter "OutputPort" to *GetSurfaceArea*
+
+
+The workflow is now ready to be executed. When you execute the workflow, you will
+see the SubWorkflow ``CalculateArea`` executing several times (one time
+for each value of the input list). It's important to notice that, although only the
+module connected to ``Map`` (in this example, the SubWorkflow
+``Calculate Area``) will be in the loop, the modules above it will be also
+used in each loop iteration; the difference is that they are going to be executed
+only for the first iteration; in all other iterations, the results will be taken
+from the cache.
+
+When the workflow finishes its execution, the |vistrails| Spreadsheet will contain
+a 2D plot (Figure :ref:`fig-controlflow-map_spreadsheet`).
+
+.. _fig-controlflow-map_spreadsheet:
+
+.. figure:: figures/controlflow/Map_Spreadsheet.png
+ :align: center
+ :width: 100%
+
+ The result in the |vistrails| Spreadsheet
+
+This example can be found in the version "Surface Area with Map", inside
+the :vtl:`triangle_area.vt` vistrail.
+
+
+Filtering results
+=================
+
+When computing large lists of results, it can be useful to selectively reduce the list during execution to avoid unnecessary computation.
+
+The ``Filter`` module was developed to address this issue. It receives an
+input list and, based on a specified boolean condition, returns only elements of
+the list that satisfy the condition. Its ports are the same as those in the
+``Map`` module. The difference between these modules is related to the
+function module: in ``Filter``, the output of that module is not the value to
+keep, but a boolean indicating whether to keep (``True``) or discard
+(``False``) the value from the original list.
+
+.. topic:: Try it Now!
+
+ To better understand how ``Filter`` works, let's modify our earlier example to filter out areas less than 200,000. With the previous vistrail open (you can use the "Surface Area with Map" version), add the following modules to the canvas:
+
+ * ``Filter``
+ * ``PythonSource`` (under "Basic Modules")
+
+ Edit the configuration of ``PythonSource`` by adding an input port of type ``Float`` named "Area", and an output port of type ``Boolean`` named "Condition", and writing the following code inside the source text area:
+
+.. code-block:: python
+
+ if Area > 200000.00:
+ Condition = True
+ else:
+ Condition = False
+
+.. topic:: Next Step!
+
+ Press the ``OK`` button. You can label this ``PythonSource`` as ``FilterCondition``. Now, reorganize the modules in the canvas as shown in Figure :ref:`fig-controlflow-mapandfilter_workflow`.
+
+.. _fig-controlflow-mapandfilter_workflow:
+
+.. figure:: figures/controlflow/MapAndFilter_Workflow.png
+ :align: center
+ :width: 3.8in
+
+ The new organization of the modules in the canvas
+
+.. topic:: Next Step!
+
+ Select the ``Filter`` module and set the values of its parameters to the following:
+
+ * "InputPort": *["Area"]*
+ * "OutputPort": *Condition*
+
+When you execute this workflow, it will generate another plot that is similar to the one from the ``Map`` example, but only areas above 200,000 are considered (Figure :ref:`fig-controlflow-mapandfilter_spreadsheet`).
+
+.. _fig-controlflow-mapandfilter_spreadsheet:
+
+.. figure:: figures/controlflow/MapAndFilter_Spreadsheet.png
+ :align: center
+ :width: 100%
+
+ The result in the |vistrails| spreadsheet
+
+This example is already inside the :vtl:`triangle_area.vt` vistrail, in the
+"Surface Area with Map and Filter" version.
+
+Later in this chapter, you will see how to combine ``Map`` and ``Filter``
+in one single module, by creating your own control structure.
+
+
+Conditional module
+==================
+
+Conditional statements are a very important control flow structure frequently used
+in programming languages, and the ``if`` structure is probably the most
+common of these structures. In scientific workflows, for example, an ``if``
+structure can be used to select the part of the pipeline to be executed based on a
+boolean condition.
+
+For this reason, the ``Control Flow`` package also includes an ``If``
+module. Its input ports are:
+
+* "Condition": this port receives a boolean value that will specify the direction of computation;
+* "TruePort": this port receives the part of the workflow that will be executed if the condition value is ``True``; you don't need to group or make a SubWorkflow in this case: just connect the output port "self" of the last module in this port;
+* "FalsePort": this port receives the part of the workflow that will be executed if the condition value is ``False``; as with the
+* "TruePort" port, you don't need to group or make a SubWorkflow;
+* "TrueOutputPorts": this port receives a list that contains the names of the output ports of the module connected to "TruePort" that you want the result of; this port is optional;
+* "FalseOutputPorts": this port receives a list that contains the names of the output ports of the module connected to "FalsePort" that you want the result of; this port is optional.
+
+
+The ``If`` module has an output port named "Result" that returns a
+list with the results of the specified output ports of "TrueOutputPorts" or
+"FalseOutputPorts", depending on the condition value. If only one output
+port is chosen, the result of this port will not be returned in a list. If
+"TrueOutputPorts" or "FalseOutputPorts" are not enabled,
+"Result" returns ``None``.
+
+Let's do a simple example to show how this module works.
+
+.. topic:: Try it Now!
+
+ Our example will contain 2 different text strings.
+ The string that is used by the workflow will depend on the condition of the ``If`` module.
+ The final text will be rendered in a spreadsheet cell.
+ You can change the final text by changing the condition on the ``If`` module.
+ Create a new workflow and add the following modules:
+
+ * ``Boolean`` (under "Basic Modules")
+ * ``String`` (under "Basic Modules") - you will need two of them
+ * ``If`` (under "Control Flow")
+ * ``WriteFile`` (under "Basic Modules")
+ * ``RichTextCell`` (under "|vistrails| Spreadsheet")
+
+ Name the ``Boolean`` module "Condition", the first ``String`` module
+ "True Branch", and the second ``String`` module "False Branch".
+ Connect the modules as shown in Figure :ref:`fig-controlflow-if_example`.
+ The ``Condition`` should be connected to the "Condition" port on the ``If``
+ module and will determine which of the branches that will be executed.
+ ``True Branch`` should be connected to the "TruePort" on the ``If`` module
+ and will be executed when the ``If`` module evaluates to ``True``.
+ ``False Branch`` should be connected to the "FalsePort" on the ``If``
+ module and will be executed when the ``If`` module evaluates to ``False``.
+ On the ``If`` module, set parameters "TrueOutputPorts" and "FalseOutputPorts"
+ to "['value']". This will tell the ``If`` module to output the "value" port on the
+ ``String`` modules.
+ Finally, set the "value" port on the ``Condition`` module to either ``True`` or
+ ``False``. Execute the workflow and see that the branch specified by the
+ ``If`` condition has been executed.
+
+.. _fig-controlflow-if_example:
+
+.. figure:: figures/controlflow/If_Example.png
+ :align: center
+ :width: 3.0in
+
+ Simple If example
+
+Lets do a more advanced example from the bioinformatics domain. This workflow
+will take a string as the input. If this string is a structure identifier, a
+web service from the European Bioinformatics Institute - EBI (http://www.ebi.ac.uk/)
+is used to put the structure into PDB format (a standard representation for
+macromolecular structure) and the ``VTK`` package is used to show the protein in
+the |vistrails| Spreadsheet. Otherwise, the input is assumed to be invalid and a
+message is generated in the Spreadsheet.
+
+.. topic:: Try it Now!
+
+ First, the EBI's web service must be enabled. For this, you need to add the following url to the ``wsdlList`` configuration:
+
+
+ ``http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl``
+
+
+ Don't forget to ensure that the ``SudsWebServices`` package is enabled in the ``Preferences`` dialog. For more information about web services in |vistrails|, see Chapter :ref:`chap-webservices`.
+
+ Now, you're going to drag the following modules to the canvas:
+
+ * ``If``
+ * ``fetchData`` (under "Methods" for the current web service)
+ * ``WriteFile`` (under "Basic Modules")
+ * ``vtkPDBReader`` (under "VTK")
+ * ``vtkDataSetMapper`` (under "VTK")
+ * ``vtkActor`` (under "VTK")
+ * ``vtkRenderer`` (under "VTK")
+ * ``VTKCell`` (under "VTK")
+ * ``PythonSource`` (under "Basic Modules") - you will need two of them
+ * ``String`` (under "Basic Modules")
+ * ``RichTextCell`` (under "|vistrails| Spreadsheet")
+
+ Set some paremeters of ``fetchData``:
+
+ * "format": *pdb*
+ * "style": *raw*
+
+ Next, connect some modules as shown in Figure :ref:`fig-controlflow-if_group`.
+
+.. _fig-controlflow-if_group:
+
+.. figure:: figures/controlflow/If_Group.png
+ :align: center
+ :width: 1.5in
+
+ Some modules of the workflow connected
+
+The aim of this group of modules is to get the PDB format of the structure ID, through the web service,
+and then make the visualization with the ``VTK`` package. This is the part of the workflow
+that will be executed if the input is a structure identifier.
+
+.. topic:: Next Step!
+
+ Next, select one of the ``PythonSource`` modules and open its configuration dialog. One input port named "Structure", of type ``String``, and one output port named "Is_ID", of type ``Boolean``, must be added, as well as the code below:
+
+.. code-block:: python
+ :linenos:
+
+ if "\n" in Structure:
+ lineLen = Structure.index("\n")
+ else:
+ lineLen = -1
+ if lineLen < 1:
+ lineLen = len(Structure)
+
+ if ":" in Structure:
+ index = Structure.index(":")
+ else:
+ index = -1
+
+ if Structure[0] != "ID " and index > 0 and index < lineLen:
+ Is_ID = True
+ else:
+ Is_ID = False
+
+.. FIXME: there is no way a 1-character string could be equal to "ID "
+
+.. topic:: Next Step!
+
+ Name this module as ``Is_ID``. This module will be the condition for the ``If`` structure.
+
+ Now, select the last ``PythonSource`` module, and, inside its configuration, add one input port of type ``String``, named "Input", and one output port of type ``File``, named "html". Then, copy the code below:
+
+.. code-block:: python
+ :linenos:
+
+ output = self.interpreter.filePool.create_file()
+ f = open(str(output.name), 'w')
+ text = '<HTML><TITLE>Protein Visualization</TITLE><BODY BGCOLOR="#FFFFFF">'
+ f.write(text)
+ text = '<H2>Protein Visualization Workflow</H2>'
+ f.write(text)
+ text = '<H3>The following input is not an ID from a protein:</H3>'
+ text += '<H4>' + Input + '</H4>'
+ text += '<H3>The visualization cannot be done.</H3>'
+ f.write(text)
+
+ text = '</BODY></HTML>'
+ f.write(text)
+
+ self.setResult('html', f)
+
+ f.close()
+
+.. topic:: Next Step!
+
+ Name this ``PythonSource`` as ``Not_ID``. This module will print a message in the |vistrails| Spreadsheet when the input is not a structure identifier.
+
+ Finally, the ``String`` module can be named as ``Workflow_Input``, to make it clear that it takes the input of the workflow. Also, open the configuration dialog of ``RichTextCell`` to enable the output port "self", so it can be connected to the ``If`` module. Then, connect all the modules as shown in Figure :ref:`fig-controlflow-if_workflow`.
+
+.. _fig-controlflow-if_workflow:
+
+.. figure:: figures/controlflow/If_Workflow.png
+ :align: center
+ :width: 3.0in
+
+ All the modules connected
+
+.. topic:: Next Step!
+
+ In order to better organize the disposal of the modules, group all the modules shown in Figure :ref:`fig-controlflow-if_group` by selecting them, going to the ``Edit`` menu and clicking on ``Group``. Name it as ``Generate_Visualization``. Your workflow must correspond to the one shown in Figure :ref:`fig-controlflow-if_workflow_group`.
+
+.. _fig-controlflow-if_workflow_group:
+
+.. figure:: figures/controlflow/If_Workflow_Group.png
+ :align: center
+ :width: 3.8in
+
+ The final workflow, using the ``Group`` structure
+
+Note that this implementation follows exactly the initial specification of the workflow. If the input
+is a structure identifier (``Is_ID`` returns ``True``), ``Generate_Visualization``
+will be executed; otherwise (``Is_ID`` returns ``False``), ``Not_ID``
+and ``RichTextCell`` will create an error message in the |vistrails| Spreadsheet.
+
+.. topic:: Next Step!
+
+ For the workflow execution, set the parameter "value" of the ``Workflow_Input`` module to *PDB:3BG0*. This entry is an ID from a protein; so, the condition will be ``True``, and the ``Generate_Visualization`` group will be executed, generating the visualization shown in Figure :ref:`fig-controlflow-if_spreadsheet_true`.
+
+.. _fig-controlflow-if_spreadsheet_true:
+
+.. figure:: figures/controlflow/If_Spreadsheet_True.png
+ :align: center
+ :width: 100%
+
+ The visualization of the protein in the |vistrails| Spreadsheet
+
+If you change the value from the input port "value" to *protein*, for example, the
+condition will be ``False``, and the message shown in
+Figure :ref:`fig-controlflow-if_spreadsheet_false` will be generated in the Spreadsheet.
+
+.. _fig-controlflow-if_spreadsheet_false:
+
+.. figure:: figures/controlflow/If_Spreadsheet_False.png
+ :align: center
+ :width: 3.8in
+
+ The message in the Spreadsheet, generated when the input is not a structure ID
+
+This example can be found inside the "examples" directory, in the
+:vtl:`protein_visualization.vt` vistrail. It was partially based on the workflow
+"Structure_or_ID", which can be found at http://www.myexperiment.org/workflows/225.
+
+
+While loop
+==========
+
+The while loop is a common construct of programming languages, allowing the
+repetition of an operation until some condition becomes true.
+
+It runs a single module (possibly a Group or Subworkflow) whose ``self`` output
+port is connected to the ``FunctionPort`` input of the ``While`` module (just
+like the ``Map`` module). It gets the value of the ports whose name are set on
+the ConditionPort, OutputPort and StateOutputPorts. As long as the port
+designated by ConditionPort does not return true, the module is run again, with
+on its StateInputPorts the values that were output on the StateOutputPorts in
+the previous run.
+
+.. topic:: Try it Now!
+
+ In this example, we are going to compute the GCD of two integers using
+ Euclid's algorithm. Keep in mind that |vistrails| is meant for data-oriented
+ workflows and that we are twisting it's execution model a little, but this
+ will demonstrate the functionality should you actually need it.
+
+ The modules we are going to need are:
+
+ * ``And``
+ * ``InputPort`` (under "Basic Modules")
+ * ``List`` (under "Basic Modules")
+ * ``PythonSource`` (under "Basic Modules")
+ * 3 ``OutputPort`` (under "Basic Modules")
+ * 2 ``Tuple`` and one ``Untuple`` (under "Basic Modules")
+ * 2 ``PythonCalc`` (under "PythonCalc")
+ * 2 ``If``
+
+ The structure is a little complicated and comports 4 parts (see Figure
+ :ref:`fig-controlflow-gcd`):
+
+ * \(I) compares a and b, and outputs the biggest one as 'result'
+ * \(II) makes the (a, b-a) Tuple (if a < b)
+ * \(III) is like (II) but makes (a-b, b) (if a >= b)
+ * \(IV) sets the 'continue' port, if both a and b are not null.
+
+ The ``Integer`` modules marked 'a' and 'b' are only here to make the workflow
+ clearer, they simply repeat the values from ``Untuple``.
+
+.. _fig-controlflow-gcd:
+
+.. figure:: figures/controlflow/gcd.png
+ :align: center
+ :width: 6in
+
+ The grouped pipeline for Euclid's algorithm
+
+.. topic:: Next Step!
+
+ The ``PythonCalc`` are substractions (operation '-').
+
+ The ``PythonSource`` has two Integer inputs ``a`` and ``b``, and a Boolean ``o``
+ output; the code should be ``o = a < b``
+
+ The ``Tuple`` and ``Untuple`` modules have two ``Integer`` ports each.
+
+ You will need to use the ``List`` module's configuration widget to add one
+ additional port, so you can connect ``a`` and ``b`` to the ``head`` and
+ ``item0`` ports.
+
+ The ``If`` modules each have ``['value']`` for both FalseOutputPorts and
+ TrueOutputPorts.
+
+.. topic:: Next Step!
+
+ Set names on the ``InputPort`` and ``OutputPort`` modules. For example, you
+ can use ``nbs`` for the ``InputPort`` and (from left to right) ``state``,
+ ``result`` and ``continue`` for the ``OutputPort``.
+
+ Once this is done, you can simply select everything and ``Workflow/Group``.
+ Then, add a ``While`` module, fill in the port names, and set the ``nbs``
+ port of the Group to 15 and 6 (or any couple of integers). Also add a
+ ``StandardOutput`` module to display the result.
+
+.. _fig-controlflow-gcd-grouped:
+
+.. figure:: figures/controlflow/gcd-grouped.png
+ :align: center
+ :width: 4.0in
+
+ The final pipeline
+
+
+For loop
+========
+
+The ``For`` module is very similar to ``Map``, except that it uses input values
+from a range. It can be used to make a module or group run several times with
+successive integer input, or just to repeatedly execute a task (optionally
+waiting between each iteration).
+
+
+Boolean operations
+==================
+
+The ``And`` and ``Or`` modules are simple boolean operations. They take a list
+of booleans and output a single boolean. They are useful when building
+workflows with structures that need booleans, such as the ``Filter``, ``While``
+and ``If`` modules.
+
+.. _fig-controlflow-andor:
+
+.. figure:: figures/controlflow/andor.png
+ :align: center
+ :width: 3.2in
+
+ Example usage of And and Or modules; outputs (True, False, True, False)
+
+
+Vector operations
+=================
+
+This packages also provides some general modules for lists, or vectors of
+numbers.
+
+The ``Sum`` module computes the sum of the elements in a list of numbers.
+Example: ``Sum([1, 2, 3]) = 6``
+
+The ``Cross`` module takes two 3-element lists and computes the cross product
+of these vectors. It returns a 3-element list as well.
+Example: ``Cross([1, 2, -1], [0, 2, 5]) = [12, -5, 2]``
+
+The ``Dot`` module performs the dot product of two lists, i.e. returns the sum
+of the pairwise products of the two lists' elements. It is the same thing as
+connecting an ElementwiseProduct to a Sum module.
+Example: ``Dot([2, 0, -1], [4, 2, 3]) = 5``
+
+If ``NumericalProduct`` is true (the default), the ``ElementwiseProduct``
+module outputs a list where each element is the product of the elements of both
+input lists.
+Example: ``ElementwiseProduct([1, 2, 3], [2, 0, -1]) = [2, 0, -3]``
+
+Else, the elements are concatenated instead of multiplied.
+Example: ``ElementwiseProduct([1, 2, 3], [2, 0, -1]) =
+[(1, 2), (2, 0), (3, -1)]``
diff --git a/doc/usersguide/controlflowdev.rst b/doc/usersguide/controlflowdev.rst
new file mode 100644
index 0000000..fdde096
--- /dev/null
+++ b/doc/usersguide/controlflowdev.rst
@@ -0,0 +1,197 @@
+.. _chap-controlflowdev:
+
+***********************************
+Creating a Control Flow Loop Module
+***********************************
+
+This chapter explains how to extend the ``Control Flow`` package by creating additional loop modules. For more information on ``Control Flow`` or the ``Control Flow Assistant``, please refer to :ref:`chap-controlflow` or :ref:`chap-controlflow-assistant` in the User's Guide.
+
+Building your own loop structure
+================================
+
+In functional programming, ``fold`` is a high-order function used to
+encapsulate a pattern of recursion for processing lists. A simple example of a
+``fold`` is summing the elements inside a list. If you ``fold`` the
+list [1, 2, 3, 4] with the sum operator, the result will be (((1+2)+3)+4) = 10. It's
+common to start with an initial value too. In the sum example, the initial value
+would be 0, and the result would be ((((0+1)+2)+3)+4) = 10.
+
+With this function, a programmer can do any type of recursion. In fact, the
+``map`` and ``filter`` functions, shown previously, can be implemented
+with ``fold``. The ``Control Flow`` package provides a ``Fold``
+module to enable this functionality, and the ``Map`` and the ``Filter``
+modules inherit from the ``Fold`` class.
+
+In fact, any control module that has this kind of recursion uses the ``Fold``
+class. To use this functionality for your own control modules, instead of defining
+the ``compute()`` method, you need to define two other methods:
+
+* ``setInitialValue()``: in this method, you will set the initial value of the fold operator through the ``self.initialValue`` attribute;
+* ``operation()``: in this method, you must implement the function to be applied recursively to the elements of the input list (|eg| the sum function). More specifically, you need to define the relationship between the previous iteration's result (``self.partialResult`` attribute) and the current element of the list (``self.element`` attribute); this method must be defined after the ``setInitialValue()`` one.
+
+It's important to notice that all modules inheriting from ``Fold`` will have
+the same ports, as ``Map`` and ``Filter``, but you can add any other
+ports that will be necessary for your control structure. Also, you do not need to use
+the input ports "FunctionPort", "InputPort" and
+"OutputPort". You will only use them when you create an operator like
+``Map`` and ``Filter``, which need a function to be applied for each
+element of the input list.
+
+As an example, we will create a simple ``Sum`` module to better understand the
+idea. Create a new package, and the code inside it would be as follows:
+
+.. role:: red
+
+.. code-block:: python
+ :linenos:
+
+ from controlflow import Fold, registerControl
+
+ version = "0.1"
+ name = "My Control Modules"
+ identifier = "org.vistrails.my_control_modules"
+
+ def package_dependencies():
+ return ["org.vistrails.vistrails.control_flow"]
+
+ class Sum(Fold):
+ def setInitialValue(self):
+ self.initialValue = 0
+
+ def operation(self):
+ self.partialResult += self.element
+
+ def initialize(*args,**keywords):
+ registerControl(Sum)
+
+.. highlight:: python
+ :linenothreshold: 1
+
+.. .. parsed-literal::
+
+ :red:`from controlflow import Fold, registerControl`
+
+ version = "0.1"
+ name = "My Control Modules"
+ identifier = "org.vistrails.my_control_modules"
+
+ :red:`def package_dependencies():`
+ :red:`return ["org.vistrails.vistrails.control_flow"]`
+
+ class Sum(:red:`Fold`):
+ :red:`def setInitialValue(self):`
+ :red:`self.initialValue = 0`
+
+ :red:`def operation(self):`
+ :red:`self.partialResult += self.element`
+
+ def initialize(\*args,**keywords):
+ :red:`registerControl(Sum)`
+
+We begin by importing the ``Fold`` class and the ``registerControl``
+function from the ``Control Flow`` package (Line 1).
+The ``registerControl`` function is used to register the control modules, so
+the shape of them can be set automatically.
+
+Also, define the variables ``version``, ``name`` and
+``identifier``, as it's done for all
+packages. The interpackage dependency (include reference of the package chapter) is
+used too, as ``My Control Modules`` requires a module and a function from
+``Control Flow`` (Lines 7 and 8); in
+this way, |vistrails| can initialize the packages in the correct order. Then, create
+the class ``Sum``, which inherits from ``Fold``. Inside it, set the
+initial value to 0 inside the ``setInitialValue()`` method
+(Lines 11 and 12), and define the sum operator
+inside ``operation()``, as shown clearly by the relation between
+``self.partialResult`` and ``self.element``
+(Lines 14 and 15).
+
+The last thing we must do is define the ``initialize()`` method, so the
+package can be loaded in |vistrails|. However, instead of calling the registry, if you
+do not need any other ports, you just have to call the ``registerControl()``
+function (Line 18).
+
+Save this package and enable it inside |vistrails|. Create a similar workflow as shown
+in Figure :ref:`fig-controlflow-sum_workflow`.
+
+.. _fig-controlflow-sum_workflow:
+
+.. figure:: figures/controlflow/Sum_Workflow.png
+ :align: center
+ :width: 100%
+
+ A workflow using the ``Sum`` module
+
+Upon executing this workflow, the sum ((((0+1)+2)+3)+4), should be printed on your
+terminal as follows:
+
+``10``
+
+Note that the input ports "FunctionPort", "InputPort" and
+"OutputPort" were not necessary for this module. Now, let's see another
+example that does use them. Open the workflow we used to calculate the area of
+isosurfaces (in "triangle_area.vt", "Surface Area with Map
+and Filter" version), and delete the ``Map``, the ``Filter``, and the
+``FilterCondition`` (``PythonSource``) modules.
+
+Now, create a single module that maps the list and filters the results, named as
+``AreaFilter``. Inside your package, add the following class:
+
+.. code-block:: python
+ :linenos:
+
+ class AreaFilter(Fold):
+ def setInitialValue(self):
+ self.initialValue = []
+
+ def operation(self):
+ area = self.elementResult
+
+ if area>200000:
+ self.partialResult.append(area)
+
+.. .. parsed-literal::
+
+ class AreaFilter(:red:`Fold`):
+ :red:`def setInitialValue(self):`
+ .. _ref-areafilter-config1:
+
+ :red:`self.initialValue = []`
+
+ :red:`def operation(self):`
+ :red:`area = self.elementResult`\label{ref:areafilter:config2}
+
+ :red:`if area>200000:`\label{ref:areafilter:config3}
+ :red:`self.partialResult.append(area)`\label{ref:areafilter:config4}
+
+The initial value is an empty list, so the result of each element can be appended to
+it (Line 3). In the ``operation()`` method, the
+``self.elementResult`` attribute is used (Line 6);
+it represents the result of the port chosen in "OutputPort"; so, it means
+that "FunctionPort", "InputPort" and "OutputPort" will have
+connections. In this workflow, ``self.elementResult`` is the area for each
+contour value inside the input list, and, if the area is above 200,000, it will be
+appended to the final result (Lines 8 and 9). We can easily see that this module does exactly
+the same as ``Map`` and ``Filter`` combined.
+
+Don't forget to register this module in the ``initialize()`` function. After
+doing this, save the package and load it again inside |vistrails|. Then, just connect
+``AreaFilter`` as in Figure :ref:`fig-controlflow-areafilter_workflow`.
+
+.. _fig-controlflow-areafilter_workflow:
+
+.. figure:: figures/controlflow/AreaFilter_Workflow.png
+ :align: center
+ :width: 3.8in
+
+ The same workflow, but now with ``AreaFilter``
+
+Now, you must set some values in the following parameters of ``AreaFilter``:
+
+* "InputPort": *["SetValue"]*
+* "OutputPort": *GetSurfaceArea*
+
+When you execute this workflow, the result in the |vistrails| Spreadsheet will be the
+same as shown previously (Figure :ref:`fig-controlflow-mapandfilter_spreadsheet`). It
+shows the flexibility of doing a recursion function by inheriting from
+``Fold``.
diff --git a/doc/usersguide/creating.rst b/doc/usersguide/creating.rst
new file mode 100644
index 0000000..ff9fa1f
--- /dev/null
+++ b/doc/usersguide/creating.rst
@@ -0,0 +1,331 @@
+.. _part2:
+
+.. _chap-creating:
+
+********************************
+Creating and Modifying Workflows
+********************************
+
+.. index:: builder
+
+Working with Modules
+====================
+
+.. index:: modules
+
+In VisTrails, modules are represented by a rectangle in the
+``Pipeline`` view of the Builder. The name of the module is
+shown in bold letters in the middle of the rectangle. The input and
+output ports for the module are denoted by small squares on the top
+and bottom of the module, respectively. Modules are connected
+together to define the dataflow using curved black lines that go from
+output to input ports between modules. Each module may also have
+adjustable parameters that can be viewed when a module is selected.
+Modules can be connected, disconnected, added, and deleted from a
+workflow.
+
+As a running example in this chapter, we will make some changes to the
+"vtk\_book\_3rd\_p189.vt" vistrail, included in the
+"examples" folder of the |vistrails| installation.
+
+.. topic:: Try it now!
+
+ Open the "vtk\_book\_3rd\_p189.vt" vistrail, either by selecting ``File`` :math:`\rightarrow` ``Open`` from the menu, or by clicking the ``Open`` button on the toolbar. After opening this vistrail, select the version labeled ``final``, then click on the ``Pipeline`` toolbar button to enter workflow editing mode.
+
+Adding and Deleting Modules
+===========================
+
+.. index::
+ pair: modules; adding
+
+A list of available modules is displayed
+hierarchically in the ``Modules`` container on the left side
+of the VisTrails Builder (Figure :ref:`The main VisTrails Pipeline... <fig-pipeline_screenshot>`). A core set of basic modules is always
+distributed with the VisTrails system. Other packages, such as VTK,
+are also distributed, but are not necessary for VisTrails and thus can
+be disabled on startup (see Chapter :ref:`chap-packages`). Note, however, that the VTK module *is* required for most of the examples in this book. Depending on
+the number of packages imported on startup, the number of modules to
+select from can be difficult to navigate. Thus, a simple search box
+is provided at the top of the container to narrow the displayed
+results. To add a module to the workflow, simply drag the text from
+the ``Module`` container to the workflow canvas.
+
+.. _fig-pipeline_screenshot:
+
+.. figure:: /figures/creating/pipeline_screenshot_labeled.png
+ :width: 5 in
+ :align: center
+
+ The main |vistrails| Pipeline user interface. The major components are labeled.
+
+.. index::
+ pair: modules; selecting
+ pair: connections; selecting
+
+Modules and
+connections may be selected in multiple ways and are denoted by a
+yellow highlight.
+Besides directly left clicking on the object, a box selection is available by left clicking and dragging over the modules and connections in the canvas. Multiple selection can be performed with the box selection as well as by right clicking on multiple objects with the 'Shift' key pressed.
+
+.. index::
+ pair: modules; deleting
+
+There are several ways to manipulate selected
+modules in the workflow canvas. Moving them is performed by dragging
+a selected module using the left mouse button. Deleting selected
+modules is performed by pressing the 'Delete' key. The modules
+and connections can also be copied and pasted using the
+``Edit`` menu, or with 'Ctrl-C' and 'Ctrl-V', respectively.
+
+.. topic:: Try it now!
+
+ Let's replace the ``vtkQuadric`` module in our example with a ``vtkCylinder`` module instead. To do this, first type "vtkCylinder" into the search box of the ``Module`` container. As the letters are typed, the list filters the available modules to match the query. Select this module and drag the text onto an empty space in the canvas (see Figure :ref:`The vtkCylinder module is added to the canvas <fig-add_and_delete_modulea>`). Then, select the ``vtkQuadric`` module in the canvas a [...]
+
+.. _fig-add_and_delete_modulea:
+
+.. figure:: /figures/creating/add_cylinder.png
+ :height: 1.25in
+ :align: center
+
+ The ``vtkCylinder`` module is added to the canvas.
+
+.. _fig-add_and_delete_moduleb:
+
+.. figure:: /figures/creating/cylinder_not_connected_but_quadric_deleted.png
+ :height: 1.25in
+ :align: center
+
+ The ``vtkQuadric`` module is deleted.
+
+Connecting Modules
+==================
+
+.. index::
+ pair: modules; connecting
+ pair: connections; adding
+ single: ports
+
+Modules are connected in VisTrails through the input and output ports
+at the top and bottom of the module, respectively. By hovering the
+mouse over the box that defines a port, the name and data type are
+shown in a small tooltip. To connect two ports from different
+modules, start by left clicking inside one port, then dragging the
+mouse to the other. The connection line will automatically snap to
+the ports in a module that have a matching datatype. Since multiple
+ports may match, hovering the mouse over the port to confirm the
+desired match may be necessary. Once a suitable match is found,
+releasing the left mouse button will create the connection. Note, a
+connection will only be made if the input and output port's data types
+match. To disconnect a connection between modules, the line between
+the modules can be selected and deleted with the 'Delete' key.
+
+.. topic:: Try it now!
+
+ To connect the ``vtkCylinder`` module to the ``vtkSampleFunction`` module, place the cursor over the only output port on the ``vtkCylinder`` module, located on the bottom right. A tooltip should appear that reads "Output port self (vtkCylinder)." Left click on the port and drag the mouse over the ``vtkSampleFunction`` module. The connection should snap to the fourth input port from the left. Hovering the mouse over this port shows a tooltip that reads "Input port SetImplicitFunctio [...]
+
+.. _fig-add_and_delete_modulec:
+
+.. figure:: /figures/creating/delete_quadric.png
+ :height: 1.25in
+ :align: center
+
+ The connection replaced.
+
+If the ports are not directly compatible, VisTrails may automatically insert a
+conversion module between the two ports. If such a module is about to be used,
+VisTrails will display the connection you are drawing with a dotted line (see
+Figure :ref:`Automatic conversion <fig-automatic_conversion>`).
+
+.. _fig-automatic_conversion:
+
+.. figure:: /figures/creating/automatic_conversion.png
+ :height: 1.25in
+ :align: center
+
+ Insertion of a conversion module
+
+Changing Module Parameters
+==========================
+
+.. index::
+ pair: parameters; changing
+ pair: modules; parameters
+ single: methods
+
+The parameters for a module can be accessed in the
+``Module Information`` tab located on the right side of the
+Builder window. When a module on the canvas is selected, the corresponding
+module information is displayed. The ``Inputs``, ``Outputs``, and ``Annotations`` tabs can be selected to set parameters within the respective categories. To set a parameter, simply click on its name to reveal its input box and enter the desired value. Notice that a ``-`` and ``+`` button appears to the left of the input box. The ``-`` button removes the corresponding input box and the ``+`` button adds one. This allows you to experiment with different values, but only the values in [...]
+
+.. topic:: Try it now!
+
+ To perform a parameter change, select the ``vtkCylinder`` module in the canvas. Select ``SetRadius``, enter 0.25 into the text box and press the 'Enter' key. By executing the workflow, the modified visualization appears in the spreadsheet. Figures :ref:`The module methods... and The results... <fig-parameter_changes>` show the interface and results of the parameter explorations.
+
+.. _fig-parameter_changes:
+
+.. figure:: figures/creating/change_parameter_interface1.png
+ :height: 2.5in
+ :align: center
+
+ The module methods interface is shown with a change of the ``SetRadius`` parameter to 1.0.
+
+.. figure:: figures/creating/cylinder1.png
+ :height: 1.5in
+ :align: center
+
+ The results of the changes are displayed on execution.
+
+.. figure:: figures/creating/change_parameter_interface2.png
+ :height: 2.5in
+ :align: center
+
+ The module methods interface is shown with a change of the ``SetRadius`` parameter to 0.25.
+
+.. figure:: figures/creating/cylinder2.png
+ :height: 1.5in
+ :align: center
+
+ The results of the changes are displayed on execution.
+
+Using Global Variables
+======================
+
+VisTrails supports the use of global variables, which allows the user to create a variable which can be used anywhere within the vistrail. So, if you create a variable of type ``String``, you can assign that variable to any port of type ``String``. This is done by opening the ``Vistrail Variables`` view, creating a variable, and then dragging it to the desired port.
+
+.. topic:: Try it now!
+
+ Open vtk_http.vt and go to the ``Pipeline`` view of the ``Fran Cut Smoothed`` version. Select ``Views`` :math:`\rightarrow` ``Vistrail Variables``. Select the ``String`` module from ``Basic Modules``, drag it over to the ``Vistrail Variables`` tab, and drop it (see Figure :ref:`Create a Variable... <fig-global-create>`). Name it 'Filename1' and assign it the following value: 'http://www.sci.utah.edu/~cscheid/stuff/vtkdata-5.0.2.zip'. Click on ``String``, which is just below ``File [...]
+
+To delete a global variable, simply click on the 'X' button that appears to the right of its name. This will remove the variable, but if any ports are assigned to it, they need to be disconnected. You can do this by right-clicking on the port and selecting ``Disconnect Vistrail Variables`` (see Figure :ref:`Disconnect a Variable... <fig-disconnect>`).
+
+.. _fig-global-create:
+
+.. figure:: /figures/creating/globalcreate.png
+ :width: 2.5in
+
+ Create a Variable - Drag the ``String`` module and drop it in the ``Vistrail Variables`` tab to create a global variable.
+
+.. _fig-global-assign:
+
+.. figure:: /figures/creating/globalassign.png
+ :width: 2.5in
+
+ Assign a Variable - Drag the type from just below the Global Variables name on the ``Vistrail Variables`` tab. Drop it on a port to set the variable.
+
+.. _fig-disconnect:
+
+.. figure:: /figures/creating/disconnect.png
+ :width: 2.5in
+
+ Disconnect a Variable - To disconnect a global variable, right click on the assigned port and select ``Disconnect Vistrail Variables``.
+
+Configuring Module Labels
+=========================
+
+.. index::
+ pair: modules; labels
+
+To give the module a custom name, enter it in the ``Module Information`` tab's ``Name`` box. The modules name will be displayed with the original module name(type) displayed in parenthesis below it.
+
+Configuring Module Ports
+========================
+
+.. index::
+ pair: modules; ports
+ pair: ports; adding
+ pair: ports; deleting
+
+For convenience, all the inputs and outputs of a module are not always
+shown in the canvas as ports. The ports that are shown by default are
+defined with the method signatures of a package. A full list of ports is available in the ``Module Configuraton`` window, which is accessed by clicking on the ``Configure`` button in the module information tab or pressing 'Ctrl-E' when a module is selected. Alternatively, module ports can be enabled/disabled by clicking in the left margin next to the port name in the ``Inputs`` or ``Outputs`` tabs of the ``Module Information`` tab (see Figure :ref:`Enabling the GetRadius port from the [...]
+
+.. %TODO module_configuration.png should be changed to reflect v2.0. Caption: The module configuration window allows the hidden ports to be displayed.
+
+.. topic:: Try it now!
+
+ As an example of configuring a module port, select the ``vtkCylinder`` module in the canvas, select ``Outputs`` from the ``Module Information`` tab, and click in the left margin next to GetRadius (see Figure :ref:`Enabling the GetRadius port from the Module Information tab <fig-enabling_ports>`). A new circle port should appear on the module. Next, add a new ``StandardOutput`` module from the basic modules and connect the output port for ``GetRadius`` to the input port of ``StandardO [...]
+
+.. _fig-enabling_ports:
+
+.. figure:: figures/creating/enabling_ports.png
+ :align: center
+ :width: 4in
+
+ Enabling the GetRadius port from the ``Module Information`` tab.
+
+
+.. _fig-module_configuration:
+
+.. figure:: figures/creating/standard_output_module.png
+ :height: 1.3 in
+ :align: center
+
+ The ``vtkCylinder`` module is configured to show an additional ``GetRadius`` port, which is then connected to a ``StandardOutput`` module.
+
+
+Basic Modules
+=============
+
+.. index::
+ pair: modules; basic
+
+In addition to the modules provided by external
+libraries, VisTrails provides a few basic modules for convenience and
+to facilitate the coupling of multiple packages in one workflow.
+These modules mostly consist of basic data types in Python and some
+manipulators for them. In addition, file manipulation modules are
+provided to read files from disk and write files to disk.
+
+.. _sec-pythonsource:
+
+PythonSource
+^^^^^^^^^^^^
+
+.. index:: PythonSource
+
+Because not every Python operation can be represented as a module, the
+``PythonSource`` module is provided to
+allow you to write Python statements to be executed as part of a
+workflow. By pressing 'Ctrl-E' when a ``PythonSource``
+module is selected in the canvas, a configuration window is opened.
+This window allows you to specify custom input and output ports
+as well as directly enter Python source to be executed in the
+workflow.
+
+.. topic:: Note
+
+ Sometimes is it useful to view the source code that is contained in the ``PythonSource`` module when working with other modules. Since the PythonSource configuration window will disappear when you select a new module, a ``Show read-only window`` button can be used to open a read-only window of the ``PythonSource's`` configuration, which will remain open until it is closed.
+
+.. topic:: Try it now!
+
+ To demonstrate a ``PythonSource`` module, we will output the center of the cylinder using Python instead of the ``StandardOutput`` module. First, add a ``PythonSource`` module to the canvas and remove the ``StandardOutput`` module. Select the ``PythonSource`` module and press 'Ctrl-E' to edit the configuration. In the newly opened configuration window, create a new input port named "radius" of type ``Float``. Next, in the source window enter::
+
+ print radius
+
+ then select ``OK`` to close the window. Finally, connect the ``GetRadius`` output of the ``vtkCylinder`` module to the new input port of ``PythonSource``. Upon execution, the radius of the cylinder is printed to the console as before. Figure :ref:`A PythonSource module can be used to directly insert scripts into the workflow <fig-python_source>` shows the new workflow together with the ``PythonSource`` configuration window.
+
+.. _fig-python_source:
+
+.. figure:: figures/creating/python_source_module.png
+ :height: 1.5in
+ :align: center
+
+ A ``PythonSource`` module can be used to directly insert scripts into the workflow.
+
+.. figure:: figures/creating/python_source_configuration.png
+ :height: 2.5in
+ :align: center
+
+ The configuration window for ``PythonSource`` allows multiple input and output ports to be specified along with the Python code that is to be executed.
+
+**Accessing vtkObjects in PythonSource** When using a ``PythonSource`` module, users will often rely on their knowledge of VTK to interact with VTK modules. It is important to realize that a VTK module is really a wrapping of a vtkObject. The real vtkObject is called vtkInstance, meaning the vtkObject of a module called 'dataset' is called 'dataset.vtkInstance' (see figure :ref:`Accessing vtkObjects... <fig-pythonsource-vtkinstance>`).
+
+.. _fig-pythonsource-vtkinstance:
+
+.. figure:: figures/creating/python_source_instance.png
+ :align: center
+ :width: 4in
+
+ Accessing vtkObjects - The vtkObject of a VTK module, 'dataset', is accessed with 'dataset.vtkInstance'.
+
+.. index:: builder
diff --git a/doc/usersguide/database.rst b/doc/usersguide/database.rst
new file mode 100644
index 0000000..88432ea
--- /dev/null
+++ b/doc/usersguide/database.rst
@@ -0,0 +1,176 @@
+.. _chap-database:
+
+************************
+Connecting to a Database
+************************
+
+.. index:: database
+
+.. \newcommand{\fixme}[1]{***#1}}}
+
+
+As an environment for collaborative scientific exploration, |vistrails|
+supports both stand-alone, file-based storage and relational storage
+of vistrails. With a relational database supporting |vistrails|, multiple users
+can easily collaborate on projects without copying files back and
+forth. At the same time, if you choose to work without being
+connected to a database, you can save your work locally to files.
+Finally, |vistrails| can import and export to both types of storage so
+you can import a vistrail from the database, save it locally as a
+file on your computer, make and save changes, and export those changes
+back to the database. Remember that because the complete workflow
+evolution is always saved, other users will not overwrite your changes, and vice versa. This prevents users from "stepping on each other's feet."
+
+By default, |vistrails| works with local files stored in the
+".vt" format (essentially compressed XML). You can save a vistrail as
+uncompressed XML by saving the file with a ".xml" extension.
+When saving a vistrail, the system displays a standard save dialog.
+These files have a version associated with them so when the schema for
+these files may change, |vistrails| will be able to import older versions.
+The current version of the XML schema can be found in the distribution
+at:
+
+``vistrails/db/versions/v1_0_2/schemas/xml/vistrail.xsd``
+
+where ``v1_0_2`` is the current version.
+
+Setup
+=====
+
+.. index::
+ pair: database; setup
+
+As described earlier, |vistrails| supports relational database storage as well as
+file-based storage. Currently, |vistrails| has been tested with
+MySQL, but in the future, we plan to support most standard relational database systems.
+
+.. _sec-database-setup:
+
+Setting up the database
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Before using |vistrails| with a relational database, you must have a
+database installed and have access to create, access, and
+modify that database. If you are planning to deploy for
+institution-wide access, you should consult your system administrator
+to determine the correct configuration. The database schema for
+|vistrails| can be found in the distribution at:
+
+``vistrails/db/versions/v1_0_2/schemas/sql/vistrails.sql``
+
+where ``v1_0_2`` is the current version. This schema contains a
+sequence of SQL commands that define the tables needed for storing
+vistrails.
+
+After you or someone else has created the database for the vistrails,
+you will need the following information:
+
+#. *hostname*: the name or IP address of the machine that stores the database (``localhost`` if it is your own machine)
+#. *port*: the port number that you connect to the database on
+#. *user*: the username that should be used to access and modify the vistrails database
+#. *password*: the password for the account corresponding to the given user
+#. *database name*: the name of the database where the vistrails are to be stored.
+
+.. _sec-database-config:
+
+Setting up |vistrails|
+^^^^^^^^^^^^^^^^^^^^^^
+
+If you are planning to use the database for most of your work,
+you can configure |vistrails| to open vistrails from the database by
+default. To do so, select the ``Preferences`` option from the ``Edit`` menu. (On Mac OS X, the ``Preferences`` option is found under the ``VisTrails`` menu.) When the ``Preferences`` window opens, select the appropriate option from the "Read/Write to database by default" box in the ``General Configuration`` tab.
+
+.. _sec-database-open:
+
+Opening from a database
+=======================
+
+.. index::
+ pair: database; opening from
+
+To open a vistrail from a relational database, choose the ``Import`` option from the ``File`` menu.
+You should see a dialog like
+the one pictured in Figure :ref:`fig-database-open`.
+(Alternatively, if
+you have set |vistrails| to use a relational database by default
+(see Section :ref:`sec-database-config`), then you should select ``File`` :math:`\rightarrow` ``Open`` from the menu or the ``Open`` button on the toolbar.)
+
+If you have previously connected to databases using |vistrails|, you
+should see a list of these databases in the left column of the dialog. If not,
+you will need to add one. To do so, click the ``+`` icon in the
+lower-left corner. This will bring up a dialog like that shown in
+Figure :ref:`fig-database-create`. To set up a connection, you will
+need the database connection information outlined in
+Section :ref:`sec-database-setup`. After filling in that information,
+you can test the connection by clicking the ``Test`` button.
+If the test succeeds, click the ``Create`` button to add the
+database to the available sources for vistrails.
+
+The database you wish to use should now be listed in the left column.
+Clicking on that row will query the database for a list of vistrails
+available from the database and display them in the right column. To
+open a vistrail, select the desired vistrail and click the
+``Open`` button or simply double-click the vistrail. When
+the vistrail has loaded, you will be able to interact with it in
+exactly the same way as a vistrail loaded from a file.
+
+.. _fig-database-open:
+
+.. figure:: figures/database/open_dialog.png
+ :align: center
+ :width: 3in
+
+ Opening a vistrail from the database
+
+.. _fig-database-create:
+
+.. figure:: figures/database/create_dialog.png
+ :align: center
+ :width: 3in
+
+ Creating a new database connection
+
+Saving to a database
+====================
+
+.. index::
+ pair: database; saving to
+
+If you opened a vistrail from the database, the default save action
+will be to save that vistrail back to the database. There will be no
+dialogs displayed---the database the vistrail was loaded from will be
+automatically updated.
+
+If you opened the vistrail from a file, you will need to select either
+``Save As`` or ``Export`` from the
+``File`` menu, depending on whether |vistrails| uses the
+database by default (see Section :ref:`sec-database-config`). You will
+be shown a dialog similar to the one in
+Figure :ref:`fig-database-save`. As discussed in
+Section :ref:`sec-database-open`, you can create a new connection to the
+database or use an existing one. Note that the name of the vistrail
+must differ from those already stored on the database, and clicking the
+``Save`` button will persist the changes to the database.
+
+.. _fig-database-save:
+
+.. figure:: figures/database/save_dialog.png
+ :align: center
+ :width: 3in
+
+ Saving a vistrail to the database
+
+Known Issues
+============
+
+.. index::
+ pair: database; issues
+
+Currently, saving a vistrail to the database will *overwrite* the
+vistrail currently stored on the database. However, we plan to add
+synchronization soon so that all explorations are captured. Thus, be
+aware that if two users have the same vistrail loaded from the
+database at the same time, and both users save their changes, only the
+second user's changes will be captured.
+
+.. index:: database
diff --git a/doc/usersguide/developer.rst b/doc/usersguide/developer.rst
new file mode 100644
index 0000000..d2cbf9e
--- /dev/null
+++ b/doc/usersguide/developer.rst
@@ -0,0 +1,16 @@
+.. _part3:
+
+#################
+Developer's Guide
+#################
+
+.. toctree::
+ :maxdepth: 2
+
+ packages
+ batch
+ log
+ example_itk
+ controlflowdev
+ parallelization
+ cltools
diff --git a/doc/usersguide/example.rst b/doc/usersguide/example.rst
new file mode 100644
index 0000000..97d66c2
--- /dev/null
+++ b/doc/usersguide/example.rst
@@ -0,0 +1,58 @@
+************
+User's Guide
+************
+
+#################
+Preliminary Pages
+#################
+
+.. toctree::
+ :maxdepth: 1
+
+ preface
+
+############################
+An Introduction to VisTrails
+############################
+
+.. toctree::
+ :maxdepth: 2
+
+ intro2
+ getting_started
+
+#############################
+Learning VisTrails By Example
+#############################
+
+.. toctree::
+ :maxdepth: 2
+
+ creating
+ groups
+ version_tree
+ merging
+ querying
+ spreadsheet
+ tabledata
+ analogies
+ parameter_exploration
+ provenance
+ mashups
+ example_guide
+
+############################################
+Intermediate Concepts and VisTrails Packages
+############################################
+
+.. toctree::
+ :maxdepth: 2
+
+ controlflow
+ cfassistant
+ parallelflow
+ database
+ example_webservices
+ persistence
+ vistrails_server
+ latex
diff --git a/doc/usersguide/example_guide.rst b/doc/usersguide/example_guide.rst
new file mode 100644
index 0000000..1df12af
--- /dev/null
+++ b/doc/usersguide/example_guide.rst
@@ -0,0 +1,229 @@
+.. _chap-example_guide:
+
+********************************
+Module Descriptions and Examples
+********************************
+
+.. index:: VisTrails VTK modules
+
+VisTrails VTK modules
+=====================
+
+Although most VTK modules in VisTrails would be familiar to vtk users, or at least in the vtk documentation, there are a few modules that VisTrails introduces. They are used as follows:
+
+* **PythonSource** - Although a PythonSource is in the Basic Modules list rather than VTK, it is mentioned here for convenience. This module allows you write python statements to be executed as part of the workflow. See Section :ref:`sec-pythonsource` for more information.
+
+* **VTKCell** - VTKCell is a VisTrails module that can display a vtkRenderWindow inside a cell. Simply pass it a vtkRenderer and any additional optional inputs, and it will display the results in the spreadsheet.
+
+* **VTKRenderOffscreen** - Takes the output of a vtkRenderer and produces a PNG image of size width X height. Default values of width and height are 512. The output can then be written to a file using a FileSink.
+
+* **VTKViewCell** - This is similar to the VTKCell except that you pass it a vtkRenderView.
+
+* **vtkInspectors: vtkDataArrayInspector, vtkDataSetAttributesInspector, vtkDataSetInspector, vtkPolyDataInspector** - These inspectors were created to allow easy access to information that is not otherwise exposed by module ports, but would be accessible through vtk objects. This information includes: normals, scalars, tensors, and vectors as well as statistical information such as bounds, center, length, max, min. Looking at the output ports of these inspectors gives an idea of the i [...]
+
+.. index:: vtkInteractionHandler
+
+* **vtkInteractionHandler** - The vtkInteractionHandler is used when a callback function is needed. To setup this handler:
+
+ * Connect the Observer input port to the output port of the object that needs the callback function.
+ * Connect the SharedData input port to the modules that would be passed as parameters to the callback function. Multiple modules can be connected (see terminator.vt - Images Slices SW).
+ * Connect the output port to the VTKCell.
+ * Select configure to write the callback function.
+
+ * Name the function after the event that initiates it, but replace 'Event' with 'Handler'. If the function should be called when a ``StartInteractionEvent`` occurs, the function should be named ``startInteractionHandler``.
+ * The function should take the parameters observer, and shareddata.
+ * Add the contents of the function.
+
+ There are a number of examples that use the vtkInteractionHandler. If there is any confusion, comparing the callback/interaction handler portions of the .py and .vt files in the vtk_examples/GUI directory is helpful.
+
+ **Accessing vtkObjects in vtkInteractionHandler** VtkObjects passed to the vtkInteractionHandler are VisTrails modules. The vtkObject within that module is called a vtkInstance and is accessed by calling myModule.vtkInstance. See Section :ref:`sec-pythonsource` for more information.
+
+* **vtkScaledTransferFunction** - Allows you to add a transfer function through the use of an interactive widget. See head.vt - volume rendering or terminator.vt for example usage.
+
+.. _sec-module-example:
+
+Modules and Corresponding Examples
+==================================
+
+Here we provide a list of the .vt files in the examples directory that use the following modules:
+
+.. index::
+ pair: modules; list of examples
+
+* **AreaFilter**:
+ triangle_area.vt
* **CellLocation**:
+ offscreen.vt, terminator.vt, vtk.vt
* **ConcatenateString**:
+ KEGG_SearchEntities_webservice.vt
* **Cross**:
+ triangle_area.vt
* **fetchData**:
+ structure_or_id_webservice.vt, protein_visualization.vt
* **FileSink**:
+ offscreen.vt - offscreen
* **Filter**:
+ triangle_area.vt
* **If**:
+ structure_or_id_webservice.vt, protein_visualization.vt
* **ImageViewerCell**:
+ r_stats.vt
* **List**:
+ triangle_area.vt
* **Map**:
+ triangle_area.vt
* **MplFigure**:
+ plot.vt, terminator.vt - Histrogram, triangle_area.vt, vtk.vt - Three Cells
* **MplFigureCell**:
+ plot.vt, terminator.vt - Histrogram, triangle_area.vt, vtk.vt - Three Cells
* **MplPlot**:
+ plot.vt, terminator.vt - Histrogram, triangle_area.vt, vtk.vt - Three Cells
* **PythonCalc**:
+ ProbeWithPointWidget.vt, officeTube.vt
* **PythonSource**:
+ infovis.vt, noaa_webservices.vt, offscreen.vt, KEGG_SearchEntities_webservice.vt, chebi_webservice.vt, EMBOSS_webservices.vt, structure_or_id_webservice.vt, vtk_http.vt, protein_visualization.vt, terminator.vt, triangle_area.vt
* **RichTextCell**:
+ noaa_webservices.vt, offscreen.vt, KEGG_SearchEntities_webservice.vt, chebi_webservice.vt, EMBOSS_webservices.vt, protein_visualization.vt
* **RPNGFigure**:
+ r_stats.vt
* **RReadCSV**:
+ r_stats.vt
* **Rsource**:
+ r_stats.vt
* **SheetReference**:
+ offscreen.vt, vtk.vt
* **StandardOutput**:
+ r_stats.vt, triangle_area.vt
* **Tuple**:
+ marching.vt, ProbingWithPlaneWidget.vt, TransformWithBoxWidget.vt, BandContourTerrain.vt, probeComb.vt, ImplicitPlaneWidget.vt, BuildUGrid.vt, ProbeWithPointWidget.vt, VolumeRenderWithBoxWidget.vt, PerlinTerrain.vt
* **Untuple**:
+ probeComb.vt, BandContourTerrain.vt
* **vtk3DSImporter**:
+ flamingo.vt
* **vtkAppendPolyData**:
+ vtk.vt - Implicit Plane Clipper, xyPlot.vt, TransformWithBoxWidget.vt, probeComb.vt, ImplicitPlaneWidget.vt, warpComb.vt
* **vtkAssembly**:
+ assembly.vt
* **vtkAxes**:
+ textOrigin.vt
* **vtkBandedPolyDataContourFilter**:
+ BandContourTerrain.vt
* **vtkBMPReader**:
+ Tplane.vt, imageWarp.vt, GenerateTextureCoords.vt
* **vtkBoxWidget**:
+ TransformWithBoxWidget.vt, VolumeRenderWithBoxWidget.vt, cone.vt - 6
* **vtkBYUReader**:
+ cubeAxes.vt, ClipCow.vt
* **vtkCastToConcrete**:
+ ExtractUGrid.vt
* **vtkCellArray**:
+ constrainedDelaunay.vt, Arrays.vt, CreateStrip.vt
* **vtkClipPolyData**:
+ terminator.vt, vtk.vt - Implicit Plane Clipper, ImplicitPlaneWidget.vt, ClipCow.vt
* **vtkColorTransferFunction**:
+ lung.vt, SimpleRayCast.vt, mummy.xml - volume rendering, SimpleTextureMap2D.vt, VolumeRenderWithBoxWidget.vt
* **vtkCone**:
+ iceCream.vt
* **vtkConeSource**:
+ vtk_book_3rd_p193.vt, vtk.vt - Implicit Plane Clipper, TransformWithBoxWidget.vt, Cone.vt, ImplicitPlaneWidget.vt, ProbeWithPointWidget.vt, assembly.vt
* **vtkConnectivityFilter**:
+ ExtractUGrid.vt, pointToCellData.vt
* **vtkContourFilter**:
+ brain_vistrail.vt, spx.vt, vtk_http.vt, marching.vt, head.vt - alias, mummy.xml - Isosurface, terminator.vt, pointToCellData.vt, triangle_area.vt - CalculateArea, Medical1.vt, hello.vt, VisQuad.vt, probeComb.vt, vtk_book_3rd_p189.vt, Medical2.vt, iceCream.vt, Contours2D.vt, Medical3.vt, PerlinTerrain.vt, ColorIsosurface.vt, PseudoVolumeRendering.vt
* **vtkCubeAxesActor2D**:
+ cubeAxes.vt
* **vtkCubeSource**:
+ assembly.vt, marching.vt
* **vtkCutter**:
+ ClipCow.vt, CutCombustor.vt, PseudoVolumeRendering.vt
* **vtkCylinderSource**:
+ assembly.vt, cylinder.vt
* **vtkDataArrayInspector**:
+ CutCombuster.vt, officeTube.vt
* **vtkDataSetAttributesInspector**:
+ officeTube.vt, CutCombustor.vt
* **vtkDataSetInspector**:
+ ProbingWithPlaneWidget.vt, StreamlinesWithLineWidget.vt, CutCombustor.vt, officeTube.vt, TextureThreshold.vt, BandContourTerrain.vt, probeComb.vt, ProbeWithPointWidget.vt, rainbow.vt, streamSurface.vt, warpComb.vt
* **vtkDataSetMapper**:
+ offscreen.vt, spx.vt, structure_or_id_webservice.vt, vtk_http.vt, SubsampleGrid.vt, TextureThreshold.vt, imageWarp.vt, protein_visualization.vt, head.vt - alias, mummy.xml - Isosurface, terminator.vt - Histogram, pointToCellData.vt, ExtractUGrid.vt, ExtractGeometry.vt, vtk.vt, BuildUGrid.vt, GenerateTextureCoords.vt
* **vtkDataSetReader**:
+ brain_vistrail.vt, vtk_http.vt, triangle_area.vt, ExtractUGrid.vt, vtk.vt
* **vtkDecimatePro**:
+ smoothFran.vt
* **vtkDelaunay2D**:
+ constrainedDelaunay.vt, faultLines.vt
* **vtkDelaunay3D**:
+ GenerateTextureCoords.vt
* **vtkDEMReader**:
+ BandContourTerrain.vt
* **vtkDoubleArray**:
+ Arrays.vt
* **vtkExtractEdges**:
+ constrainedDelaunay.vt, marching.vt
* **vtkExtractGeometry**:
+ ExtractGeometry.vt
* **vtkExtractGrid**:
+ SubsampleGrid.vt, PseudoVolumeRendering.vt - vtkPlane
* **vtkExtractUnstructuredGrid**:
+ ExtractUGrid.vt
* **vtkExtractVOI**:
+ Contours2D.vt
* **vtkFloatArray**:
+ Arrays.vt, BuildUGrid.vt, marching.vt
* **vtkFollower**:
+ textOrigin.vt
* **vtkGeometryFilter**:
+ ExtractUGrid.vt, pointToCellData.vt
* **vtkGlyph3D**:
+ vtk_book_3rd_p193.vt, marching.vt, vtk.vt - Implicit Plane Clipper, TransformWithBoxWidget.vt, ImplicitPlaneWidget.vt, ProbeWithPointWidget.vt, spikeF.vt
* **vtkGraphLayoutView**:
+ infovis.vt
* **vtkHexahedron**:
+ BuildUGrid.vt
* **vtkIcicleView**:
+ infovis.vt
* **vtkIdList**:
+ BuildUGrid.vt, marching.vt
* **vtkImageActor**:
+ Medical3.vt
* **vtkImageDataGeometryFilter**:
+ BandContourTerrain.vt, imageWarp.vt
* **vtkImageLuminance**:
+ imageWarp.vt
* **vtkImageMapToColors**:
+ brain_vistrail.vt, Medical3.vt
* **vtkImageReslice**:
+ terminator.vt
* **vtkImageShiftScale**:
+ lung.vt - raycasted
* **vtkImageShrink3D**:
+ BandContourTerrain.vt
* **vtkImplicitBoolean**:
+ iceCream.vt, ExtractGeometry.vt
* **vtkImplicitModeller**:
+ hello.vt
* **vtkImplicitPlaneWidget**:
+ terminator.vt, vtk.vt, ImplicitPlaneWidget.vt
* **vtkImplicitSum**:
+ PerlinTerrain.vt
* **vtkIntArray**:
+ Arrays.vt
* **vtkInteractionHandler**:
+ ProbingWithPlaneWidget.vt, StreamlinesWithLineWidget.vt, terminator.vt, vtk.vt - Implicit Plane Clipper, TransformWithBoxWidget.vt, Cone.vt - 6 , ImplicitPlaneWidget.vt, ProbeWithPointWidget.vt, VolumeRenderWithBoxWidget.vt
* **vtkInteractorStyleImage**:
+ terminator.vt
* **vtkInteractorStyleTrackballCamera**:
+ Cone.vt - 5
* **vtkLight**:
+ cubeAxes.vt, faultLines.vt
* **vtkLine**:
+ BuildUGrid.vt
* **vtkLineSource**:
+ streamSurface.vt, xyPlot.vt
* **vtkLineWidget**:
+ StreamlinesWithLineWidget.vt
* **vtkLODActor**:
+ TestText.vt, stl.vt, CADPart.vt, vtk.vt - Implicit Plane Clipper, TransformWithBoxWidget.vt, BandContourTerrain.vt, cubeAxes.vt, ImplicitPlaneWidget.vt, FilterCADPart.vt, ColorIsosurface.vt
* **vtkLookupTable**:
+ brain_vistrail.vt, vtk_book_3rd_p193.vt, pointToCellData.vt, BandContourTerrain.vt, ExtractUGrid.vt, Medical3.vt, rainbow.vt, PseudoVolumeRendering.vt
* **vtkMaskPoints**:
+ vtk_book_3rd_p193.vt, spikeF.vt
* **vtkMassProperties**:
+ triangle_area.vt - CalculateArea
* **vtkMergeFilter**:
+ imageWarp.vt
* **vtkOpenGLVolumeTextureMapper3D**:
+ lung.vt - TextureWithShading
* **vtkOutlineFilter**:
+ VisQuad.vt, probeComb.vt, ExtractGeometry.vt, vtk_book_3rd_p189.vt, cubeAxes.vt, VolumeRenderWithBoxWidget.vt, Contours2D.vt, Medical1.vt, Medical2.vt, Medical3.vt
* **vtkPDBReader**:
+ protein_visualization.vt, structure_or_id_webservice.vt
* **vtkPerlinNoise**:
+ PerlinTerrain.vt
* **vtkPiecewiseFunction**:
+ lung.vt, SimpleRayCast.vt, mummy.xml - volume rendering, SimpleTextureMap2D.vt, VolumeRenderWithBoxWidget.vt
* **vtkPixel**:
+ BuildUGrid.vt
* **vtkPlane**:
+ lung.vt - TS and plane, CutCombustor.vt, terminator.vt, vtk.vt - Implicit Plane Clipper, ImplicitPlaneWidget.vt, iceCream.vt, PerlinTerrain.vt, ClipCow.vt
* **vtkPlanes**:
+ VolumeRenderWithBoxWidget.vt
* **vtkPlaneSource**:
+ Tplane.vt, terminator.vt, probeComb.vt
* **vtkPlaneWidget**:
+ ProbingWithPlaneWidget.vt
* **vtkPLOT3DReader**:
+ ProbingWithPlaneWidget.vt, StreamlinesWithLineWidget.vt, CutCombustor.vt, SubsampleGrid.vt, TextureThreshold.vt, xyPlot.vt, probeComb.vt, ProbeWithPointWidget.vt, rainbow.vt, ColorIsosurface.vt, streamSurface.vt, warpComb.vt, PseudoVolumeRendering.vt
* **vtkPointData**:
+ marching.vt, Arrays.vt, BuildUGrid.vt
* **vtkPointDataToCellData**:
+ pointToCellData.vt
* **vtkPoints**:
+ CreateStrip.vt, marching.vt, constrainedDelaunay.vt, Arrays.vt, BuildUGrid.vt
* **vtkPointSource**:
+ GenerateTextureCoords.vt, officeTube.vt
* **vtkPointWidget**:
+ ProbeWithPointWidget.vt
* **vtkPolyData**:
+ CreateStrip.vt, ProbingWithPlaneWidget.vt, constrainedDelaunay.vt, StreamlinesWithLineWidget.vt, Arrays.vt, ProbeWithPointWidget.vt, ClipCow.vt
* **vtkPolyDataInspector**:
+ ClipCow.vt
* **vtkPolyDataNormals**:
+ brain_vistrail.vt, pointToCellData.vt, Medical1.vt , faultLines.vt, ExtractUGrid.vt, smoothFran.vt, cubeAxes.vt, Medical2.vt, Medical3.vt, ClipCow.vt, ColorIsosurface.vt, warpComb.vt, PerlinTerrain.vt, spikeF.vt, PseudoVolumeRendering.vt, BandContourTerrain.vt
* **vtkPolyDataReader**:
+ hello.vt, faultLines.vt, smoothFran.vt, spikeF.vt
* **vtkPolygon**:
+ BuildUGrid.vt
* **vtkPolyLine**:
+ BuildUGrid.vt
* **vtkPolyVertex**:
+ BuildUGrid.vt
* **vtkProbeFilter**:
+ brain_vistrail.vt, ProbingWithPlaneWidget.vt, xyPlot.vt, probeComb.vt, ProbeWithPointWidget.vt
* **vtkProperty2D**:
+ xyPlot.vt
* **vtkPyramid**:
+ BuildUGrid.vt
* **vtkQuad**:
+ BuildUGrid.vt
* **vtkQuadraticDecimation**:
+ spx.vt - Decimate
* **vtkQuadric**:
+ VisQuad.vt, ExtractGeometry.vt, vtk_book_3rd_p189.vt, Contours2D.vt
* **vtkRandomGraphSource**:
+ infovis.vt - hello_world
* **VTKRenderOffscreen**:
+ offscreen.vt
* **vtkRibbonFilter**:
+ StreamlinesWithLineWidget.vt
* **vtkRuledSurfaceFilter**:
+ streamSurface.vt
* **vtkRungeKutta4**:
+ StreamlinesWithLineWidget.vt, officeTube.vt, streamSurface.vt
* **vtkSampleFunction**:
+ VisQuad.vt, ExtractGeometry.vt, vtk_book_3rd_p189.vt, iceCream.vt, Contours2D.vt, PerlinTerrain.vt
* **vtkScaledTransferFunction**:
+ head.vt - volume rendering, terminator.vt
* **vtkShrinkFilter**:
+ ExtractGeometry.vt
* **vtkShrinkPolyData**:
+ marching.vt, filterCADPart.vt
* **vtkSmoothPolyDataFilter**:
+ xyPlot.vt
* **vtkSphere**:
+ iceCream.vt, ExtractGeometry.vt
* **vtkSphereSource**:
+ TestText.vt, marching.vt, assembly.vt, vtk.vt - Implicit Plane Clipper, TransformWithBoxWidget.vt, ImplicitPlaneWidget.vt
* **vtkSTLReader**:
+ stl.vt, CADPart.vt, FilterCADPart.vt
* **vtkStreamLine**:
+ StreamlinesWithLineWidget.vt, officeTube.vt, streamSurface.vt
* **vtkStripper**:
+ brain_vistrail.vt, Medical2.vt, Medical3.vt, ClipCow.vt
* **vtkStructuredGridGeometryFilter**:
+ CutCombuster.vt, officeTube.vt, TextureThreshold.vt, rainbow.vt, warpComb.vt
* **vtkStructuredGridOutlineFilter**:
+ StreamlinesWithLineWidget.vt, officeTube.vt, SubsampleGrid.vt, TextureThreshold.vt, xyPlot.vt, probeComb.vt, ProbeWithPointWidget.vt, rainbow.vt, ColorIsosurface.vt, streamSurface.vt, warpComb.vt, PseudoVolumeRendering.vt, ProbingWithPlaneWidget.vt, CutCombustor.vt
* **vtkStructuredGridReader**:
+ officeTube.vt
* **vtkStructuredPointsReader**:
+ lung.vt, vtk_book_3rd_p193.vt, SimpleRayCast.vt, TextureThreshold.vt, head.vt - volume rendering, mummy.xml - volume rendering, head.vt - alias, mummy.xml - Isosurface, terminator.vt, SimpleTextureMap2D.vt
* **vtkTetra**:
+ BuildUGrid.vt
* **vtkTextActor**:
+ TestText.vt
* **vtkTextProperty**:
+ TestText.vt, xyPlot.vt, cubeAxes.vt
* **vtkTexture**:
+ Tplane.vt, TextureThreshold.vt, terminator.vt, GenerateTextureCoords.vt
* **vtkTextureMapToCylinder**:
+ GenerateTextureCoords.vt
* **vtkThreshold**:
+ pointToCellData.vt
* **vtkThresholdPoints**:
+ vtk_book_3rd_p193.vt, marching.vt
* **vtkThresholdTextureCoords**:
+ TextureThreshold.vt
* **vtkTransform**:
+ marching.vt, terminator.vt, xyPlot.vt, TransformWithBoxWidget.vt, Cone.vt - 6, probeComb.vt, ExtractGeometry.vt, spikeF.vt
* **vtkTransformPolyDataFilter**:
+ marching.vt, xyPlot.vt, probeComb.vt, spikeF.vt
* **vtkTransformTextureCoords**:
+ GenerateTextureCoords.vt
* **vtkTreeMapView**:
+ infovis.vt
* **vtkTreeRingView**:
+ infovis.vt
* **vtkTriangle**:
+ BuildUGrid.vt
* **vtkTriangleFilter**:
+ triangle_area.vt - CalculateArea, ClipCow.vt
* **vtkTriangleStrip**:
+ BuildUGrid.vt
* **vtkTubeFilter**:
+ marching.vt, constrainedDelaunay.vt, officeTube.vt, officeTubes.vt, xyPlot.vt, faultLines.vt, PseudoVolumeRendering.vt
* **vtkUnstructuredGrid**:
+ BuildUGrid.vt, marching.vt
* **vtkUnstructuredGridReader**:
+ offscreen.vt, spx.vt, pointToCellData.vt
* **vtkVectorText**:
+ textOrigin.vt, marching.vt
* **vtkVertex**:
+ BuildUGrid.vt
* **VTKViewCell**:
+ infovis.vt
* **vtkViewTheme**:
+ infovis.vt - cone_layout
* **vtkVolume**:
+ lung.vt, SimpleRayCast.vt, head.vt - volume rendering, mummy.xml - volume rendering, terminator.vt, SimpleTextureMap2D.vt, VolumeRenderWithBoxWidget.vt
* **vtkVolume16Reader**:
+ VolumeRenderWithBoxWidget.vt, Medical1.vt, Medical2.vt, Medical3.vt
* **vtkVolumeProperty**:
+ lung.vt, SimpleRayCast.vt, head.vt - volume rendering, mummy.xml - volume rendering, terminator.vt, SimpleTextureMap2D.vt, VolumeRenderWithBoxWidget.vt
* **vtkVolumeRayCastCompositeFunction**:
+ lung.vt - raycasted, SimpleRayCast.vt, mummy.xml - volume rendering, terminator.vt - SW, VolumeRenderWithBoxWidget.vt
* **vtkVolumeRayCastMapper**:
+ lung.vt - raycasted, SimpleRayCast.vt, mummy.xml - volume rendering, terminator.vt - SW, VolumeRenderWithBoxWidget.vt
* **vtkVolumeTextureMapper2D**:
+ SimpleTextureMap2D.vt
* **vtkVolumeTextureMapper3D**:
+ head.vt - volume rendering, terminator.vt - HW
* **vtkVoxel**:
+ BuildUGrid.vt
* **vtkWarpScalar**:
+ imageWarp.vt, BandContourTerrain.vt, warpComb.vt
* **vtkWarpVector**:
+ pointToCellData.vt, ExtractUGrid.vt
* **vtkWedge**:
+ BuildUGrid.vt
* **vtkWindowLevelLookupTable**:
+ terminator.vt
* **vtkXMLTreeReader**:
+ infovis.vt
* **vtkXYPlotActor**:
+ xyPlot.vt
diff --git a/doc/usersguide/example_itk.rst b/doc/usersguide/example_itk.rst
new file mode 100644
index 0000000..4d727bf
--- /dev/null
+++ b/doc/usersguide/example_itk.rst
@@ -0,0 +1,293 @@
+************
+Example: ITK
+************
+
+Introduction to ITK
+===================
+
+The *Insight Toolkit*, [#]_ or ITK, is an open-source software system initially
+designed to support the Visible Human Project [C1]_.
+ITK is under continual development, being updated to employ
+cutting-edge segmentation and registration algorithms for multiple
+dimensions. For more information about ITK, please refer to [C2]_ and [C3]_.
+
+In order to facilitate the implementation of processing mechanisms
+specific to the medical imaging community, ITK provides a robust set
+of general purpose image processing tools. These image processing
+tools are available to users through the standard ITK Filter interface. Although ITK is implemented in
+C++, through the use of CMake [#]_ and CableSwig [#]_,
+the functionality of ITK is made available to languages such as TCL,
+Java, and Python. In addition, much of the functionality of ITK is also available in a |vistrails| package. The ITK package is not currently included in the binary distribution of |vistrails|, but it may be downloaded separately from the |vistrails| website.
+
+**Note:** The WrapITK library, upon which the |vistrails| ITK package depends, is well-tested on Linux and Mac OS X platforms. It is, however, known to have issues under Windows.
+
+Preparing ITK
+=============
+
+At the time of this writing, the latest stable release of ITK is 3.6.0.
+In order to incorporate the functionality of ITK into the |vistrails|
+system, it first must be built and installed. In the following
+sections, we will describe in detail the process of downloading,
+building, and installing ITK and all the required components needed to
+use it.
+
+Downloading ITK
+^^^^^^^^^^^^^^^
+
+ITK can be downloaded in either source tarballs or via public CVS
+access to the ITK source repository. The following instructions take
+advantage of the CVS source repository; however, source tarballs can
+be downloaded from: http://www.itk.org/
+
+These instructions can be found, in part, at the ITK
+website. To use CVS, you
+must have a CVS client installed on your system. To download the ITK
+library, issue the following commands:
+
+.. parsed-literal::
+
+ cvs -d :pserver:anonymous at www.itk.org:/cvsroot/Insight login
+ *password: insight*
+
+ cvs -d :pserver:anonymous at www.itk.org:/cvsroot/Insight co Insight
+
+Change directory into the newly created ``Insight/Utilities``
+directory and issue the following command:
+
+.. parsed-literal::
+
+ cvs -d :pserver:anonymous at public.kitware.com:/cvsroot/CableSwig co CableSwig
+
+This checkout includes CableSwig in the ITK system,
+allowing it to be built automatically during compilation of ITK
+itself.
+
+Building the ITK Libraries
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+ITK requires CMake to be installed and available on your
+system.
+As of ITK version 3.2.0, CMake version 2.4.6 or greater must be used
+to prevent compilation errors. In order to simplify updating ITK to
+later versions of the software, we perform an out-of-source build. To
+do this, we first create a directory outside the **Insight**
+directory created for us during the CVS checkout process.
+
+.. parsed-literal::
+
+ mkdir itk
+ cd itk
+
+We now run CMake, or the GUI-based version ccmake, in this directory. If you're using Windows, you may wish to run the Windows-specific ``cmake-gui.exe`` instead.
+
+.. parsed-literal::
+
+ ccmake ../Insight
+
+Note: The above command assumes that the **Insight** directory exists
+at the same level as the **itk** directory that we just created.
+
+The following advanced CMake variables must be set to the appropriate values:
+
+.. csv-table::
+ :header: CMake Variable, Value
+
+ BUILD\_SHARED\_LIBS, ON
+ INSTALL\_WRAP\_ITK\_COMPATIBILITY, ON
+ ITK\_CSWIG\_PYTHON, OFF
+ ITK\_USE\_REVIEW, ON
+ USE\_WRAP\_ITK, ON
+ WRAP\_ITK\_PYTHON, ON
+ WRAP\_ITK\_JAVA, OFF
+
+Note: Some CMake variables are only available based on the state of
+others. If a variable is missing from the list, set what is visible
+and re-configure, this will often allow you to see and set additional
+parameters.
+
+After generating the appropriate files and exiting ccmake, the
+standard build process can be completed. To compile (on Linux or Mac OS X), run:
+
+.. parsed-literal::
+
+ make
+ sudo make install
+
+On Windows, the build process is governed by the type of project or Makefile generated by CMake.
+
+.. topic:: Note:
+
+ It is possible to use ITK without installing it. To do this, the environment variables LD\_LIBRARY\_PATH and PYTHONPATH must be set to the appropriate build directories:
+
+ | ``LD_LIBRARY_PATH=/Path_To_itk/bin``
+ | ``PYTHONPATH=/Path_To_itk/Wrapping/WrapITK/Python``
+
+At this point, ITK is build and installed. To validate this, open a
+Python shell and issue the following commands:
+
+.. parsed-literal::
+
+ >>> import itk
+ >>> itk.Image[itk.US,2]
+
+The above commands should both complete without error, and should produce the output:
+
+.. parsed-literal::
+
+ <class 'itkImage.itkImageUS2'>
+
+The WrapITK
+implementation used to wrap ITK for use in Python lazily instantiates
+required classes. This means that even if the import succeeds, the
+instantiation of the above ``itk.Image`` class may fail. This is
+particularly common if the environment variable LD\_LIBRARY\_PATH is incorrectly set.
+
+ITK and |vistrails|
+===================
+
+When built and installed with the appropriate Python bindings
+included, ITK can be used from |vistrails| through the ITK package.
+As mentioned previously, ITK is a third-party package and is not included in the general
+|vistrails| distribution. However, like many third-party packages, it
+is available from the |vistrails| website. [#]_
+
+The |vistrails| ITK package is under continual development with the
+latest versions being announced on the |vistrails| website. After
+downloading the package and extracting it into the ``.vistrails/userpackages`` directory, you can enable it through the ``Module Packages`` tab in the ``Preferences`` dialog. Please refer to Chapter :ref:`chap-packages` for instructions on how to do this.
+
+Upon starting |vistrails|, the ITK package modules will be made
+available to the Builder Window.
+
+ITK Package Organization
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ITK |vistrails| package loosely mimics the ITK functionality
+hierarchy. The package's top level consists of base classes,
+containers, and file readers as shown in Figure :ref:`fig-structure`.
+Also available at the top level is the ``PixelType`` module and the
+specific types used to create and execute ITK-based pipelines.
+
+Currently, the ITK Image Filters are organized into functional groups. The five filter types, as show in Figure :ref:`fig-structurec`, are:
+
+* Feature Extraction Filters
+* Image Intensity Filters
+* Segmentation Filters
+* Image Selection Filters
+* Image Smoothing Filters
+
+All filter types currently have at least one representative ITK filter
+wrapped and usable from within the |vistrails| environment.
+
+.. _fig-structure:
+
+.. figure:: figures/example_itk/package_structure.png
+ :align: center
+ :width: 30%
+
+ \(a\) The |vistrails| ITK Package Structure Overview
+
+.. figure:: figures/example_itk/pixeltypes.png
+ :align: center
+ :width: 30%
+
+ \(b\) The ITK Package Supported PixelTypes
+
+.. _fig-structurec:
+
+.. figure:: figures/example_itk/filtertypes.png
+ :align: center
+ :width: 30%
+
+ \(c\) The ITK Package Filter Structure
+
+Reading DICOM Volumes
+^^^^^^^^^^^^^^^^^^^^^
+
+DICOM is a standard format for exchanging medical images.
+ITK includes DICOM support through the GDCM libraries. [#]_ It is worthwhile to note that at this time these
+libraries are currently not a complete implementation of the DICOM
+standard.
+
+DICOM volumes can be integrated into |vistrails| through the use of
+either the ``GDCMReader`` or ``DICOMReader`` modules in the ITK package.
+For the rest of this example, we will use the ``GDCMReader`` module as
+its performace is slightly higher than the ``DICOMReader``
+implementation.
+
+Figure :ref:`VisTrails workflow utilizing ITK to extract a single slice... <fig-slicer>` shows the use of the ``GDCMReader`` module. In
+order to properly read a DICOM volume, the ``GDCMReader`` must be supplied
+with the dimension of the volume to be read and the directory
+containing the series to read. By default, WrapITK supports
+two- and three-dimensional volumes. In order to include support for
+higher dimensions, the appropriate WrapITK variable must be set within
+CMake, *before* compiling ITK.
+
+Volume Processing With ITK and |vistrails|
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Typically, DICOM volumes are written with no 16-bit unsigned shorts.
+Unfortunately, most systems allow the display of only 8-bit values.
+Because of the higher precision inherent in DICOM data, it is often
+preferable to perform any computation, segmentation, or processing on
+the data prior to rescaling in order to utilize as much information as
+possible.
+
+.. _fig-slicer:
+
+.. figure:: figures/example_itk/itk_slicingpipe.png
+ :align: center
+ :width: 100%
+
+ |vistrails| workflow utilizing ITK to extract a single slice from a DICOM volume. The slice is chosen by first forming a Region to extract. The result is viewed through the use of standard |vistrails| Spreadsheet modules.
+
+Volume Processing With ITK and |vistrails|
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+ITK image filters are
+typically templated based on the dimensionality of the data being
+processed, as well as the data type being processed. In |vistrails|,
+these parameters are handled through the use of ``PixelType`` modules.
+Although any ITK Filter wrapped in \vistrails
+can accept any of these ``PixelType``\ s, the underlying implementation may
+not be compatible with the input ``PixelType``. Using ``PixelType``\ s
+incompatible with the underlying filter implementations is the most
+frequent cause of error when executing otherwise functional pipelines
+in |vistrails|.
+
+.. %%:ref:`fig-pixeltypes`
+
+When processing volumes, it is often necessary to extract a single
+slice from the volume at different stages of the processing pipeline.
+This is possible in |vistrails| through the use of the
+``ExtractImageFilter``. Given a volume, a Region, and Dimensionality
+information, the ``ExtractImageFilter`` can extract a single slice from
+the data volume that can be used in further processing, previewing the
+results, or writing to disk. An example workflow that extracts a slice
+from a DICOM volume can be seen in Figure :ref:`VisTrails workflow utilizing ITK to extract a single slice... <fig-slicer>`.
+
+Visualizing the results
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Although ITK's processing filters and the DICOM standard both support
+16-bit processing and storage, many image viewers are capable of
+displaying in only 8-bit resolution using the unsigned char ``PixelType``.
+Since the output of an ITK processing workflow is an image, it makes
+sense to view it as such. This means that we are required to both
+remap the data values in the image to 8 bits as well as perform a
+casting operation to change the data type from unsigned shorts to
+unsigned chars. These operations are performed through the use of the
+``RescaleIntensityImageFilter`` and the ``CastImageFilter``. Figure :ref:`VisTrails workflow utilizing ITK to extract a single slice... <fig-slicer>` demonstrates the use of the
+``RescaleIntensityImageFilter`` and the ``CastImageFilter`` in conjunction
+with the ``ImageToFile`` and ``ImageViewerCell`` modules to view the resulting slice in the |vistrails| Spreadsheet.
+
+.. rubric:: Footnotes
+.. [#] The Insight Toolkit is sometimes referred to by the longer name *Insight Segmentation and Registration Toolkit*.
+.. [#] CMake cross-platform make system. http://www.cmake.org
+.. [#] CableSwig Interface generator. http://www.itk.org/HTML/CableSwig.html
+.. [#] Please Note: At the time of this writing, the |vistrails| ITK package is not a complete wrapping of all ITK functionality. If you would like to contact the author regarding the wrapped functionality, please do so through the e-mail address on the |vistrails| website.
+.. [#] Grass roots DiCoM Project. http://www.creatis.insa-lyon.fr/Public/Gdcm/
+
+.. rubric:: Citations
+.. [C1] R. A. Banvard, "The visible human project image data set from inception to completion and beyond," Proceedings of CODATA, 2002.
+.. [C2] L. Ibanez, W. Schroeder, L. Ng, and J. Cates, The ITK Software Guide, 2nd ed., Kitware, Inc. ISBN 1-930934-15-7, http://www.itk.org/ItkSoftwareGuide.pdf, 2005.
+.. [C3] T. S. Yoo, M. J. Ackerman, W. E. Lorensen, W. Schroeder, V. Chalana, S. Aylward, D. Metaxes, and R. Whitaker, "Engineering and algorithm design for an image processing API: A technical report on ITK - The Insight Toolkit," Proceedings of Medicine Meets Virtual Reality, pp. 586-592, 2002.
diff --git a/doc/usersguide/example_webservices.rst b/doc/usersguide/example_webservices.rst
new file mode 100644
index 0000000..5ff7a57
--- /dev/null
+++ b/doc/usersguide/example_webservices.rst
@@ -0,0 +1,185 @@
+.. _chap-webservices:
+
+************************
+Example: Web Services
+************************
+
+A *web service* grants you programmatic access to an online data source
+via a straightforward API. In this chapter, you will learn how to invoke web
+services from within |vistrails| workflows. We will build a simple workflow that
+invokes a web service and generates an HTML table with the results. Our current
+example is intentionally simple; for more in-depth examples, please refer to
+the |vistrails| website.
+
+**Where we're going in this chapter:** The European Bioinformatics Institute maintains ChEBI, [#]_ a database of over 15,000 chemical
+compounds. Each entity is referenced by a unique ID number, called
+its *chebiID*. To see an example of the kind of queries we will build in
+this example, go to http://www.ebi.ac.uk/chebi/webServices.do and scroll
+down until you find the web form labeled "getCompleteEntity."
+(Figure :ref:`fig-webservices_webform1`). If you type 15357 into the text
+field, it will return a long string of data in XML format about this
+chemical. We learn, among other things, that this chemical's name
+is *acetylenedicarboxylate(-2)*.
+
+To try another query, scroll down to the area labeled "getOntologyChildren"
+and type 15357 into the text field. This returns an XML representation of this
+chemical's ontology children. In this case, the result is a single
+chemical, *acetylenedicarboxylate(-1)*, whose chebiID is 30782
+(Figure :ref:`fig-webservices_webform2`).
+
+.. _fig-webservices_webform:
+
+.. _fig-webservices_webform1:
+
+.. figure:: figures/example_webservices/webservices_webform.png
+ :width: 3.2in
+ :align: center
+
+ \(a\) Web browser interface for the ChEBI database
+
+.. _fig-webservices_webform2:
+
+.. figure:: figures/example_webservices/webservices_webform_result.png
+ :width: 3.2in
+ :align: center
+
+ \(b\) Results from a "getOntologyChildren" query
+
+In this example, we will build a workflow that accesses a web service to
+perform the second of these two queries. Because we're using a web service, we
+don't need a browser --- we will perform this query programmatically
+within |vistrails|.
+
+Enabling the SUDSWebServices Package
+====================================
+
+In order to use web services in |vistrails|, you need to ensure that the ``SUDSWebServices`` package is enabled in the ``Preferences``
+dialog. (Please refer to Chapter :ref:`chap-packages` for more information on enabling packages.)
+
+Adding Web Service Packages
+===========================
+
+Within the ``Module Packages`` tab of the ``Preferences``
+dialog, click the ``Configure`` button to open the configuration
+dialog for this package(``SUDSWebServices``). Select the ``wsdlList`` and click on the ``Value`` field. This is where you will enter the URL(s) of the web service(s) you wish to access. If there is more than one URL, place a semicolon (;) between each URL, but *not* after the final URL. In other words, the URLs must be semicolon-delimited, but not semicolon-terminated.
+
+For our example, we need the following URL:
+
+``http://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl``
+
+After closing the dialog, you need to reload the ``SUDSWebServices`` package in order to load the changes. Then, close the ``Preferences`` dialog. A new package will be created for each URL provided.
+
+Alternatively, you may add a web service package by clicking the secondary mouse button on the "SUDS Web Services" package in the module palette and entering the corresponding URL. You may remove a web service by clicking the secondary mouse button on the corresponding package in the module palette and selecting ``Remove this Web Service``.
+
+.. %.. figure::
+.. % :align: center
+.. % :height=3in,clip=false]{modules_list.png}
+.. %}
+.. % The available modules in the ``webServices`` module are shown in the ``Modules`` panel.}
+.. %.. _fig-webservices_preferences}
+.. %
+
+Creating a new vistrail
+=======================
+
+After configuring the ``SUDSWebServices`` package properly, there
+will be a ``SUDSWebServices`` entry in your ``Modules``
+panel.
+The ``SUDSWebServices`` package will generate a module for each
+published method in a web service.
+
+.. %Figure TODO.
+
+Start with a new empty workflow in the ``Pipeline`` view, and drag
+the following modules to the canvas.
+
+.. index::
+ pair: modules; adding
+
+* ``String`` (under "Basic Modules")
+* ``getOntologyChildren`` (under "Methods" for the current web service)
+* ``getOntologyChildrenResponse`` (under "Types" for the current web service)
+* ``OntologyDataItemList`` (under "Types" for the current web service)
+* ``PythonSource`` (under "Basic Modules")
+* ``RichTextCell`` (under "Spreadsheet")
+
+As discussed in Chapter :ref:`chap-creating`, ``PythonSource`` has no
+input and output ports by default; we need to create some. Open the
+configuration dialog for ``PythonSource`` by selecting this module in
+the pipeline canvas and typing 'Ctrl-E'. Add a new input port
+named "ontologyDataItemList" of type ``List``, and a new
+output port named "outfile" of type ``File``. (Please refer
+to Chapter :ref:`chap-creating` for more information about configuring and using
+the ``PythonSource`` module.)
+
+We will now add some Python code to this module. This code generates a simple
+HTML table based on the information retrieved from the web service query. Type
+or paste the following source code into the ``PythonSource``
+configuration dialog:
+
+.. code-block:: python
+
+ dataitemlist = self.getInputFromPort("ontologyDataItemList")
+ output1 = self.interpreter.filePool.create_file()
+ f1 = open(str(output1.name), "w")
+ text = "<HTML><TITLE>Chebi WebService</TITLE><BODY BGCOLOR=#FFFFFF>"
+ f1.write(text)
+ text = "<H2>getOntologyChildren Query</H2><BR>"
+ f1.write(text)
+ text = "<CENTER><table border = 1><tr><TH>ChebiId</TH> <TH>ChebiName</TH>"
+ text += "<TH>Comments</TH> <TH>Type</TH> <TH>Status</TH>"
+ text += "<TH>CyclicRelationship</TH></tr>"
+ f1.write(text)
+ for element in dataitemlist:
+ if not hasattr(element,'Comments') or str(element.Comments) == '[]':
+ comment = ""
+ else:
+ comment = str(element.Comments)
+ line = "<tr><td>" + str(element.chebiId) + "</td><td>" + str(element.chebiName)
+ line += "</td><td>" + comment + "</td><td>" + str(element.type) + "</td><td>"
+ line += str(element.status) + "</td><td>" + str(element.cyclicRelationship)
+ line += "</td></tr>"
+ f1.write(line)
+ text = "</table></CENTER></BODY></HTML>"
+ f1.write(text)
+ self.setResult("outfile",output1)
+ f1.close()
+
+Close the dialog. One of the ports we need to use is an optional port. Select the ``OntologyDataItemList`` module and select the ``Outputs`` tab from the ``Module Information`` panel. Click in the left column next to ``ListElement`` so the eye icon appears. Now connect the modules together as shown in Figure :ref:`fig-chebi_pipeline_screenshot`.
+
+.. _fig-chebi_pipeline_screenshot:
+
+.. figure:: figures/example_webservices/only_modules.png
+ :align: center
+ :width: 2.5in
+
+ Our example pipeline
+
+Our workflow is now complete except for one crucial element: the starting point. We need to pass a chebiID string to the workflow in order to look up information about a chemical. We do this by assigning a chebiID string to the ``String`` module at the top of the pipeline. Highlight the ``String`` module in the canvas, then in the ``Module Information`` panel on the right, make sure the ``Inputs`` tab is selected and click on ``value`` and type ``CHEBI:15357`` into the ``String`` inpu [...]
+
+Executing the workflow
+======================
+
+.. index::
+ pair: spreadsheet; RichTextCell
+
+The workflow is now ready to be visualized. Click the ``Execute``
+button to send the current pipeline with the current parameters to
+a ``RichTextCell`` within the |vistrails|
+Spreadsheet. Your result should resemble
+Figure :ref:`fig-webservices_spreadsheet`. As you can see,
+the "ontology children" query returns the same information as before,
+but without the use of a web browser. In addition, we used a small Python
+program (via the ``PythonSource`` module) to transform the raw XML into
+a readable HTML table.
+
+.. _fig-webservices_spreadsheet:
+
+.. figure:: figures/example_webservices/ws_spreadsheet.png
+ :align: center
+ :height: 2.5in
+
+ The HTML table generated by our workflow
+
+.. rubric:: Footnotes
+.. [#] ChEBI is an acronym for Chemical Entities of Biological Interest.
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+***************
+Getting Started
+***************
+
+The |vistrails| system is distributed both as source code and pre-built
+binaries, and instructions for obtaining either can be found at our
+website: http://www.vistrails.org. Because the system is
+written in Python using a Qt interface, it can be run on most
+architectures that support these two components, even if a pre-built
+binary is not available for your system.
+Section :ref:`sec-start-installing` provides instructions to guide you
+through installation procedures, and Section :ref:`sec-start-quick`
+gives a quick orientation and serves as a springboard for
+exploring the different features of |vistrails|.
+
+.. _sec-start-installing:
+
+Installation
+============
+
+There are two types of |vistrails| installations. The first is a
+binary installation that lets you use |vistrails| by running the
+precompiled executable. The second is a full source code installation
+that requires you to install and compile |vistrails| and all of its
+dependencies. Of the two types of installations, the binary version is
+much easier, and we encourage first-time users to use this option
+whenever possible. Precompiled binaries are currently available for
+Microsoft Windows (XP and Vista) and Mac OS X (10.5.x or higher). To
+obtain either a binary or source copy of |vistrails|, please see our
+website: http://www.vistrails.org.
+
+.. _sec-binary_installation_windows:
+
+Installing |vistrails| on Windows XP/Vista
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To install |vistrails| on Windows, download the installation bundle for
+Windows from the |vistrails| website: http://www.vistrails.org.
+Unzip the file using the decompression program of your choice, then
+double-click the executable to begin installation
+(Figure :ref:`Installation wizard for Microsoft Windows XP/Vista<fig-start-windows_installation>`). Follow the prompts in
+the installation wizard to complete the installation process.
+
+.. _fig-start-windows_installation:
+
+.. figure:: /figures/getting_started/windows_installation_wizard.png
+ :width: 4in
+ :align: center
+
+ Installation wizard for Microsoft Windows XP/Vista.
+
+.. _sec-binary_installation_macosx:
+
+Installing |vistrails| on Mac OS X
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To install |vistrails| on Mac OS X, download the installation bundle
+for Mac from the |vistrails| website:
+http://www.vistrails.org. The precompiled binary currently only
+supports Mac OS X 10.5.x or higher. The disk image should be mounted automatically
+(Figure :ref:`Installing VisTrails on Mac OS X <fig-start-mac_installation>`). Once the disk image is mounted, drag the |vistrails| folder to the Applications
+folder to install the software.
+
+.. _fig-start-mac_installation:
+
+.. figure:: /figures/getting_started/mac_post_uncompress_window.png
+ :width: 5in
+ :align: center
+
+ Installing |vistrails| on Mac OS X.
+
+.. _sec-binary_installation_ubuntu:
+
+Installing |vistrails| on Ubuntu Linux
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Although not a binary installation *per se*, installing
+|vistrails| on Ubuntu Linux is nonetheless quite straightforward.
+|vistrails| now interfaces with "apt" directly via a Python API. This
+allows dynamic installation of necessary packages. As a result, you do
+not need to manually install any of the dependent packages. Just
+download the |vistrails| source code and execute it with::
+
+ python vistrails/run.py
+
+and |vistrails| should detect all necessary software and, if necessary,
+ask for your permission to install it.
+
+.. _sec-src_installation:
+
+Installing |vistrails| from source
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Installing |vistrails| from source code is a non-trivial task. Rather
+than listing full compilation instructions in this manual, we instead
+provide a list of software packages upon which |vistrails| is
+dependent, and refer you to the |vistrails| website for additional
+details.
+
+* Python 2.6 or higher
+* Qt 4.4 or higher
+* PyQt4
+* SciPy
+* VTK (needed to run the examples in this book)
+
+There may also be additional dependencies, depending on which optional
+features of |vistrails| you plan to use.
+
+Please refer to http://www.vistrails.org/index.php/Mac_Intel_Instructions for more details.
+
+.. _sec-start-quick:
+
+Quick Start
+===========
+
+On Windows and Mac OS X, you can launch |vistrails| by double-clicking
+on the |vistrails| application icon. In general, however, it is
+possible to start |vistrails| on any system by navigating to the
+directory where the file ``run.py`` is located (usually
+the root directory of your installation) and executing the command::
+
+ python run.py
+
+Depending on a number of factors, it can take a few seconds for the
+system to start up. As |vistrails| loads, you may see some messages
+that detail the packages being loaded and initialized. This is normal
+operation, but if the system fails to load, these messages will
+provide information that may help you understand why.
+
+Installing additional packages
+==============================
+
+|vistrails| releases come with a number of packages already installed. In
+addition to these, you can write your own packages or install packages from
+third-party developers. To do that, just drop the Python module (single file)
+or package (i.e. directory) in ``$HOME/.vistrails/userpackages/`` (|vistrails|
+should automatically create this folder on the first run).
+
+You can then enable and disable standard or user packages from the preferences
+dialog, under the module packages tab.
+
+The Vistrails Builder Window
+============================
+
+After everything has loaded, you will see the |vistrails| Builder window as
+shown in Figure :ref:`fig-start-builder`. If you have enabled the
+|vistrails| Spreadsheet (Packages :math:`\rightarrow` VisTrails Spreadsheet :math:`\rightarrow` Show Spreadsheet), you will also see a second window like that in
+Figure :ref:`fig-start-spreadsheet`. Note that if the spreadsheet window is not visible, it will open upon execution of a workflow that uses it.
+
+.. _fig-start-builder:
+
+.. figure:: /figures/getting_started/builder.png
+ :width: 5in
+
+ |vistrails| Builder Window
+
+.. _fig-start-spreadsheet:
+
+.. figure:: /figures/getting_started/spreadsheet.png
+ :width: 5in
+
+ |vistrails| Spreadsheet Window
+
+The VisTrails Toolbar
+^^^^^^^^^^^^^^^^^^^^^
+
+.. _fig-start-toolbar:
+
+.. figure:: /figures/getting_started/toolbar.png
+ :width: 100%
+
+ |vistrails| Toolbar
+
+.. index:: toolbar
+
+The |vistrails| toolbar both allows you to execute the current workflow or function, and switch between various modes. A brief description of each member of the toolbar follows:
+
+**Pipeline** This view shows the current workflow. See Chapter :ref:`chap-creating` for information about creating a workflow.
+
+**History** This view shows different versions of the workflow(s) as it has progressed over time. See Chapter :ref:`chap-version_tree`.
+
+**Search** Use this mode to search for modules or subpipeline within the current version, the current vistrail, or all vistrails. See Chapter :ref:`chap-querying`.
+
+**Explore** This option allows you to select one or more parameter(s) for which a set of values is created. The workflow is then executed once for each value in the set and displayed in the spreadsheet for comparison purposes. See Chapter :ref:`chap-paramexploration`.
+
+**Provenance** The ``Provenance`` mode shows the user a given vistrail's execution history. When a particular execution is selected, its pipeline view with modules colored according to its associated execution result is shown. See Chapter :ref:`chap-provenance_browser`.
+
+**Mashup** The ``Mashup`` mode allows you to create a small application that allows you to explore different values for a selected set of parameters. See Chapter :ref:`chap-mashups`
+for more information.
+
+**Execute** ``Execute`` will either execute the current pipeline when the ``Pipeline``, ``History``, or ``Provenance`` views are selected, or perform the search or exploration when in ``Search`` or ``Exploration`` mode. This button is disabled for ``Mashup`` mode, or when there is not a current workflow to execute.
+
+The ``New``, ``Open``, and ``Save`` buttons will create, open, and save a vistrail, as expected.
+
+Palettes and Associated Views
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. index::
+ pair: palette; views
+
+**Palettes**
+
+As you can see, the builder window has a center widget with a palette on each side. There are a number of views (listed in the 4th group of the views menu) that when made visible, will be opened in these palettes. In this section, we will discuss how the views are arranged.
+
+Notice that when VisTrails first launches the builder window, both palettes contain two views. The left palette is split so both views are visible, whereas the right palette uses tabs to display one view at a time. By default, additional views will be shown in the right, and lower left panels when they are made visible. To make a view visible, either switch to a mode that requires it, or select it from the views menu. For example, the ``Mashup`` mode will add the ``Mashup Pipel [...]
+
+**Buttons**
+
+Notice that there is a button with a pin icon in the upper right corner of each view (see Figure :ref:`fig-panel-buttons`). If you don't want a view to disappear when you change modes, make sure it is pinned. When the pin points up, it is unpinned and the view is likely to disappear when you change modes.
+
+The other two buttons, the one with the 'X' and the one with the rectangular outlines (see Figure :ref:`fig-panel-buttons`), will either close the view, or undock the view, depending on which one you push. Alternatively, you may undock a view by clicking on the view's title bar and pulling it out of the palette. The view can then either remain in its own window, or can be docked by placing it in either palette.
+
+.. _fig-panel-buttons:
+
+.. figure:: /figures/getting_started/panel_buttons.png
+
+ Buttons - Close, Detach, and Pin
+
+**View Locations**
+
+.. index::
+ pair: view;location
+
+The following table gives the view that is visible in each palette for each of the main views/modes:
+
++-------------++---------------------+--------------------+
+| || Lower Left Palette | Right Palette |
++=============++=====================+====================+
+| Pipeline || Modules | Module Information |
++-------------++---------------------+--------------------+
+| History || Modules | Properties |
++-------------++---------------------+--------------------+
+| Explore || Explore Properties | Set Methods |
++-------------++---------------------+--------------------+
+| Provenance || Modules | Log Details |
++-------------++---------------------+--------------------+
+| Mashup || Mashups Inspector | Mashup Pipeline |
++-------------++---------------------+--------------------+
+
+Notice that the ``Workspace``, ``Diff Properties``, and ``Vistrail Variables`` views are not in the table. That is because, the ``Workspace`` view is always visible, the ``Diff Properties`` view opens in the right palette when a visual diff is performed in the ``History`` view, and the ``Vistrail Variables`` view is opened from the ``Views`` menu. Note: with the ``Vistrail Variables`` view especially, if you don't want it to disappear, you should make sure it is pinned.
+
+The Center Widget
+^^^^^^^^^^^^^^^^^
+
+The center widget is somewhat larger than the side panels as it is intended to be the main workspace. It displays the following views: ``Pipeline``, ``History``, ``Search``- query and results, ``Visual Diff`` results, ``Explore``, ``Provenance``, and ``Mashup``. By default, one view is shown. To open an additional view, type CTRL-t to create a new tab. The new tab starts out in the ``Pipeline`` view, but you are free to change it to any of the other views. Note that the tabs from on [...]
+
+If you would like to see views from more than one vistrail at a time, you may do this by right-clicking on the vistrail (listed in ``Current Vistrails`` of the ``Workspace`` view), and selecting the option to open in a new window. The side palettes will stay with the original window, but can be moved to the current window by selecting ``Dock Palettes`` from the ``Views`` menu.
+
+If you would like to see multiple views from the same vistrail, double-click the title of the view to detach it. It is not possible to reattach the view, so once you are finished with the detached view, you may close it. If you would like the view to be reattached, you should close it and open it again in a new tab.
+
+.. _sec-start-file:
+
+Manipulating |vistrails| Files
+==============================
+
+.. index::
+ pair: open; vistrail
+ pair: open; from a database
+ single: tab
+
+To open a |vistrails| file, or *vistrail*, you can either click the
+``Open`` button in the toolbar or select ``Open`` from the ``File``
+menu. This brings up a standard file dialog where you can select a
+vistrail to open. Vistrails are identified by the ``.vt`` file
+extension. Alternatively, if the vistrail is listed under `My Vistrails` in the ``Workspace Panel``, double clicking its name will open it. When a vistrail is opened, it is listed in the ``Workspace`` (upper left panel) under `Current Vistrails`. Since only one open vistrail is displayed at a time, the ``Workspace`` allows you to select which one to display. Vistrails can also be stored in a database, enabling a central repository for workflows. See Chapter :ref:`chap-database` for mo [...]
+
+.. index::
+ pair: close; vistrail
+ pair: save; vistrail
+
+To close a vistrail, you can either choose the
+``Close`` option from the ``File`` menu or type Ctrl-w. If
+the vistrail has not been saved, you will be asked if you wish to save
+your work. To save a vistrail, there is both a
+button and a menu item in the ``File`` menu. If you would
+like to save the vistrail with a different name or in a different
+location, you can use the ``Save As`` option.
+
+.. _sec-start-basics:
+
+|vistrails| Basics
+==================
+
+.. index::
+ single: workflow
+ pair: modules; definition
+ pair: connections; definition
+
+In general, a *workflow* is a way to structure a complex
+computational process that may involve a variety of different
+resources and services. Instead of trying to keep track of multiple
+programs, scripts, and their dependencies, workflows abstract the
+details of computations and dependencies into a graph consisting of
+computational *modules* and *connections* between these
+modules.
+
+The ``Pipeline`` button on the |vistrails| toolbar accesses VisTrails'
+interface for building workflows. Similar to many existing workflow
+systems, it allows you to interactively create workflows using an
+extensible library of modules and a connection protocol that helps you
+determine how to connect modules. To add a module to a workflow,
+simply drag the module's name from the list of available modules to
+the workflow canvas. Each module has a set of input and output ports,
+and outputs from one module can be connected to inputs of another
+module, provided that the types match. For more information on
+building workflows in |vistrails|, see Chapter :ref:`chap-creating`.
+
+.. index::
+ pair: vistrail; definition
+
+In addition to VisTrail's *Pipeline* interface for manipulating
+individual workflows, the *History* interface (accessed through
+the ``History`` button on the toolbar) contains a number of
+features that function on a collection of workflows.
+A *vistrail* is a collection of
+related workflows. As you explore different computational approaches
+or visualization techniques, a workflow may evolve in a lot of
+directions. |vistrails| captures all of these changes automatically
+and transparently. Thus, you can revisit a previous version of a
+workflow and modify it without worrying about saving intermediate
+versions. This history is displayed by the |vistrails| Version Tree,
+and different ways of interacting with this tree are discussed in
+Chapter :ref:`chap-version_tree`.
+
+With a collection of workflows, one of the necessary tasks is to
+search for specific workflows. VisTrail's search functionality is
+accessed by clicking the ``Query`` button on the toolbar.
+The criteria for these searches may
+vary from finding workflows modified within a specific time frame to
+finding workflows that contain a specific module. Because of the
+version history that |vistrails| captures, these tasks are natural to
+implement and query. |vistrails| has two methods for querying
+workflows, a simple text-based query language and a query-by-example
+canvas that lets you build exactly the workflow structure you
+are looking for. Both of these techniques are described in
+Chapter :ref:`chap-querying`.
+
+The ``Exploration`` button
+allows you to explore workflows by running the same
+workflow with different parameters. Parameter Exploration provides an
+intuitive interface for computing workflows with parameters that vary
+in multiple dimensions. When coupled with the |vistrails| Spreadsheet,
+parameter exploration allows you to quickly compare results and
+discover optimal parameter settings. See
+Chapter :ref:`chap-paramexploration` for specific information on using
+Parameter Exploration.
+
+.. _sec-start-interact:
+
+|vistrails| Interaction
+=======================
+
+Workflow Execution
+^^^^^^^^^^^^^^^^^^
+
+.. index:: execute
+
+The ``Execute`` button on the toolbar serves as the "play" button for
+each of the modes described above. In both the Builder and Version
+Tree modes, it executes the current workflow. In Query mode, it
+executes the query, and in Parameter Exploration mode, it executes the
+workflow for each of the possible parameter settings.
+
+When a workflow is executed, the module color is determined as follows:
+
+ * lilac: module was not executed
+ * yellow: module is currently being executed
+ * green: module was successfully executed
+ * orange: module was cached
+ * red: module execution failed
+
+A popup is shown when executing workflows from the pipeline or history view. The popup shows overall progress, the type of module being executed, and a cancel button. Pressing cancel will show a dialog where you can choose to abort or continue the execution. Note that the cancel button may appear frozen while a module is being executed. This is due to limitations in python.
+
+.. topic:: Note
+
+ VisTrails caches by default, so after a workflow is executed, if none of its parameters change, it won't be executed again.
+
+ If a workflow reads a file using the basic module File, VisTrails does check whether the file was modified since the last run. It does so by keeping a signature that is based on the modification time of the file. And if the file was modified, the File module and all downstream modules (the ones which depend on File) will be executed.
+
+ If you do not want VisTrails to cache executions, you can turn off caching: go to Menu Edit :math:`\rightarrow` Preferences and in the General Configuration tab, change Cache execution results to Never.
+
+ If you would like your input and output data to be versioned, you can use the Persistence package.
+
+Additional Interactions
+^^^^^^^^^^^^^^^^^^^^^^^
+
+.. index:: undo, redo
+
+From the ``Edit`` menu, ``Undo`` and ``Redo`` function in the standard way, but note that these
+actions are implicitly switching between different versions of a
+workflow. Thus, you will notice that as you undo or redo a change to
+a workflow, the selected version in the version tree changes.
+
+.. index:: select, pan, zoom
+
+For all modes except Parameter Exploration, the center pane of
+|vistrails| is a canvas where you can manipulate the current workflow,
+version tree, or query. The buttons on the right side of the toolbar
+allow you to change the default behavior of the primary mouse button
+(the left button for most multiple button mice) within this canvas.
+You can choose the behavior to select items in the scene, pan around
+the scene, or zoom in and out of the scene by selecting the given
+button. In addition, if you are using a 3-button mouse, the right
+button will zoom, and the middle button will pan. To use the zoom
+functionality, click and drag up to zoom out and drag down to zoom in.
+
+.. index:: center
+
+.. topic:: Note
+
+ Pressing Ctrl-R will recenter the window.
+
diff --git a/doc/usersguide/groups.rst b/doc/usersguide/groups.rst
new file mode 100644
index 0000000..f3cae09
--- /dev/null
+++ b/doc/usersguide/groups.rst
@@ -0,0 +1,108 @@
+.. _chap-grouping:
+
+********************************
+Groups and Subworkflows
+********************************
+
+.. _sec-grouping:
+
+Grouping Modules
+================
+
+.. index::
+ pair: modules; grouping
+ pair: modules; ungrouping
+ single: grouping
+
+As the number of modules in a pipeline increases, the pipeline can grow quite large and cumbersome. This also makes the pipeline more difficult to understand and maintain. With any large system, it can be helpful to cluster related pieces together and represent them as a single unit. This idea, called *encapsulation*, is commonly used in computer programming as a way of controlling complexity. |vistrails| likewise supports the grouping of multiple modules together so that they can be tr [...]
+
+Multiple modules are grouped together by first selecting them, and then choosing the ``Group`` option from the ``Edit`` menu. Alternatively, you can use the keyboard shortcut 'Ctrl-G'.
+
+An example may clarify how this works.
+
+.. topic:: Try it now!
+
+ Open :vtl:`vtk_book_3rd_p189.vt`. Select the ``vtkOutlineFilter``, ``vtkPolyDataMapper``, ``vtkProperty``, and ``vtkActor`` modules on the left side of the pipeline, as shown in Figure :ref:`Box selection of four modules <fig-groupinga>`. Type 'Ctrl-G' to group these modules. Notice how the pipeline changes, as shown in Figure :ref:`The modules represented as a single group module <fig-groupingb>`. Since the label "Group" isn't very descriptive, you can change this by selecting the ` [...]
+
+.. _fig-groupinga:
+
+.. figure:: figures/grouping/grouping1.png
+ :height: 2.6in
+ :align: center
+
+ Box selection of four modules.
+
+.. _fig-groupingb:
+
+.. figure:: figures/grouping/grouping2.png
+ :height: 2.6in
+ :align: center
+
+ The modules represented as a single group module.
+
+.. _fig-groupingc:
+
+.. figure:: figures/grouping/grouping4.png
+ :height: 2.6in
+ :align: center
+
+ Renaming the group.
+
+Just as any number of modules may be clustered into a group, any number of groups may be combined with other groups or modules to form still larger groups. This is done in the same way as described above.
+
+Further, the contents of the groups or combinations of groups are revealed through the ``Show Pipeline`` option. First select the ``group`` module in the pipeline and then select ``Show Pipeline`` from the ``Workflow`` menu. The group's contents will be shown in a new tab. If there is a group within a group, selecting the interior ``group`` module and then selecting ``Show Pipeline`` will show the interior group's pipeline in an additional tab.
+
+In addition to viewing the group's contents, any group may be also un-grouped; that is, restored to its individual modules. This is done by selecting the group module in the pipeline, and then choosing the ``Edit`` :math:`\rightarrow` ``Ungroup`` menu option or by pressing 'Ctrl-Shift-G'. A group's pipeline may not be used to ungroup interior groups, however. The tabs opened by the ``Show Pipeline`` command are read only.
+
+.. Groups may only be ungrouped from the pipeline view, and not from the windows that are created when selecting ``Show Pipeline``. Thus, an interior group may only be ungrouped after the group to which is belongs is ungrouped.
+
+.. Combinations of groups may be ungrouped in any order.
+
+.. _sec-grouping-subworkflows:
+
+Subworkflows and Group Modules
+===================================
+
+.. index::
+ pair: modules; subworkflows
+ pair: subworkflows; groups
+ pair: groups; subworkflows
+
+A subworkflow is similar to a group, but has some differences. Here, we will explain the differences to make it easier to understand which one to use when:
+
+ * A subworklow is a VisTrail, and a history of changes to a subworkflow is kept, whereas a group is part of a vistrail. So, if you copy and paste a group, the pasted group won't necessarily be linked to the group's history.
+ * When a subworkflow is created, it is listed in the ``My Subworkflows`` portion of the ``Modules`` panel. It is saved and will be accessible from any vistrail. A group, on the other hand can be named and copied and pasted within a file, or even across files. However, it will not be placed in the modules panel.
+ * Subworkflows can be edited and saved without needing to ungroup and regroup the modules. To edit anything within a group, it first needs to be ungrouped, and then regrouped.
+
+
+Subworkflows
+============
+
+.. index::
+ pair: modules; subworkflows
+ single: subworkflows
+
+To create a subworkflow, select the modules to include and select ``Create Subworkflow`` from the ``Workflow`` menu. See Figure :ref:`Creating a subworkflow <fig-subworkflow>`. You will be prompted to name the subworkflow. The subworkflow will appear in the modules list under ``My Subworkflows.`` Groups can be converted to subworkflows by selecting the ``Convert to Subworkflow`` option.
+
+To edit a subworkflow, select a module of the corresponding subworkflow and select ``Edit Subworkflow`` from the ``Workflow`` menu. This will open the subworkflow's file. If you make changes to the subworkflow and save them, the modules that correspond to the old subworkflow will be marked with a '!', meaning that it is not the latest version. To upgrade to the latest version, either select the triangle in the module's upper right corner and choose ``Upgrade Module``, or delete the ol [...]
+
+.. _fig-subworkflow:
+
+.. figure:: figures/grouping/subworkflow.png
+ :height: 4in
+ :align: center
+
+ Creating a subworkflow.
+
+.. _fig-subworkflow_upgrade:
+
+.. figure:: figures/grouping/subworkflow_upgrade.png
+ :align: center
+ :width: 3in
+
+ Upgrading a subworkflow module that has been edited.
+
+Importing and Exporting Subworkflows
+++++++++++++++++++++++++++++++++++++
+
+Since subworkflows are saved locally, the ``Import Subworkflow`` and ``Export Subworkflow`` options can be used for sharing. For example, to add a subworkflow from an open VisTrail to your local list of ``My Subworkflows`` modules, you would select the subworkflow and select ``Import Subworkflow`` from the ``Workflows`` menu. Alternatively, you can save any number of subworkflows to a package by dragging the subworkflow modules to the canvas, selecting them, selecting ``Export Subworkf [...]
diff --git a/doc/usersguide/index.rst b/doc/usersguide/index.rst
new file mode 100644
index 0000000..7f71717
--- /dev/null
+++ b/doc/usersguide/index.rst
@@ -0,0 +1,20 @@
+.. VisTrails documentation master file, created by
+ sphinx-quickstart on Mon Feb 7 20:45:58 2011.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to VisTrails's documentation!
+=====================================
+
+.. toctree::
+ :maxdepth: 3
+
+ example
+ developer
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`
+
diff --git a/doc/usersguide/intro.rst b/doc/usersguide/intro.rst
new file mode 100644
index 0000000..1076b3c
--- /dev/null
+++ b/doc/usersguide/intro.rst
@@ -0,0 +1,9 @@
+############################
+An Introduction to VisTrails
+############################
+
+.. toctree::
+ :maxdepth: 2
+
+ intro2
+ getting_started
diff --git a/doc/usersguide/intro2.rst b/doc/usersguide/intro2.rst
new file mode 100644
index 0000000..2b46796
--- /dev/null
+++ b/doc/usersguide/intro2.rst
@@ -0,0 +1,85 @@
+******************
+What Is VisTrails?
+******************
+
+VisTrails is a new system that provides data and process management
+support for exploratory computational tasks. It combines features of
+both workflow and visualization systems. Similar to workflow systems, it allows the combination of loosely-coupled resources, specialized
+libraries, and grid and Web services. Similar to some
+visualization systems, it provides a mechanism for parameter
+exploration and comparison of different results. But unlike these other systems,
+VisTrails was designed to manage *exploratory processes* in which
+computational tasks evolve over time as a user iteratively
+formulates and tests hypotheses. A key distinguishing
+feature of VisTrails is its comprehensive provenance infrastructure that
+maintains detailed history information about the steps followed in the
+course of an exploratory task. VisTrails leverages this information to
+provide novel operations and user interfaces that streamline this
+process.
+
+Important Features
+""""""""""""""""""
+One of our main uses for VisTrails has been exploratory visualization,
+but the system is much more general and provides many other features,
+such as:
+
+* *Flexible Provenance Architecture.* VisTrails transparently
+ tracks changes made to workflows, including all the steps followed in the
+ exploration. The system can optionally track run-time information
+ about the execution of workflows (|eg| who executed a module, on
+ which machine, elapsed time |etc|). |vistrails| also provides a
+ flexible annotation framework whereby you can specify
+ application-specific provenance information.
+
+* *Querying and Re-using History.* The provenance
+ information is stored in a structured way. You have a choice of
+ using a relational database (such as MySQL or IBM DB2) or XML files in
+ the file system. The system provides flexible and intuitive query
+ interfaces through which you can explore and reuse provenance
+ information. You can formulate simple keyword-based and selection
+ queries (|eg| find a visualization created by a given user) as well
+ as structured queries (|eg| find visualizations that apply
+ simplification before an isosurface computation for irregular grid
+ data sets).
+
+* *Support for collaborative exploration.* The system can be
+ configured with a database backend that can be used as a shared
+ repository. It also provides a synchronization facility that allows
+ multiple users to collaborate asynchronously and in a disconnected
+ fashion---you can check in and check out changes, akin to a
+ version control system (|eg| SVN: http://subversion.tigris.org).
+
+* *Extensibility.* |vistrails| provides a very simple plugin
+ functionality that can be used to dynamically add packages and
+ libraries. Neither changes to the user interface nor re-compilation
+ of the system are necessary. Because |vistrails| is written in
+ Python, the integration of Python-wrapped libraries is
+ straightforward. For example, a single line in the VisTrails
+ start-up file is needed to import all of VTK's classes.
+* *Scalable Derivation of Data Products and Parameter Exploration.*
+ |vistrails| supports a series of operations
+ for the simultaneous generation of multiple data products, including
+ an interface that allows you to specify sets of values for
+ different parameters in a workflow. The results of a parameter
+ exploration can be displayed side by side in the VisTrails
+ Spreadsheet for easy comparison.
+* *Task Creation by Analogy.* Analogies are supported as
+ first-class operations to guide semi-automated changes to multiple
+ workflows, without requiring you to directly manipulate or edit
+ the workflow specifications.
+
+Obtaining the software
+""""""""""""""""""""""
+
+Visit http://www.vistrails.org to access the VisTrails community
+website. Here you will find information including instructions for
+obtaining the software, online documentation, video tutorials, and
+pointers to papers and presentations.
+
+VisTrails is available as open
+source; it is released under the GPL 2.0 license. The pre-compiled
+versions for Windows and Mac OS X come with an installer and
+include a number of packages, including VTK, matplotlib, and Image
+Magick. Additional packages, including packages written by users, are
+also available (|eg| ITK, Matlab, Metro). Developers can easily add new
+packages using the VisTrails plugin infrastructure.
diff --git a/doc/usersguide/latex.rst b/doc/usersguide/latex.rst
new file mode 100644
index 0000000..5667470
--- /dev/null
+++ b/doc/usersguide/latex.rst
@@ -0,0 +1,260 @@
+***********************************
+Embedding VisTrails Files Via Latex
+***********************************
+
+.. index:
+ pair: embed; latex
+
+The VisTrails Latex extension allows you to embed the result from a VisTrails file into a Latex document. Images to be included in the Latex document will be generated through VisTrails and can be linked to the VisTrails file and version from which it was generated. In other words, Latex calls VisTrails to generate an image for a resulting PDF document. The resulting image can be set up so, when clicked, the generated VisTrails file will be opened in VisTrails.
+
+Latex Setup and Commands
+========================
+
+This section contains instructions for setting up Latex files to use VisTrails. For a complete example of this setup, you may also refer to example.tex in VisTrails' extensions/latex directory.
+
+To use the Latex extension, copy vistrails.sty and includevistrail.py from the extensions/latex directory to the same directory as your .tex files. Then, add the following line to the beginning of the latex file:
+
+``\usepackage{vistrails}``
+
+By default, VisTrails will be executed at www.vistrails.org and the images
+downloaded to your hard drive. This allows any user that downlods your paper to execute the workflows on the server.
+
+Local Setup
+^^^^^^^^^^^
+
+If you want to run a local copy of VisTrails instead, add the following path to your python file or executable:
+
+``\renewcommand{\vistrailspath}{/path/to/vistrails/run.py}``
+
+Depending on how you are running VisTrails and on which OS you are running, the \vistrailspath should be configured appropriately. Please check head.tex in VisTrails' extensions/latex directory for detailed instructions on the configuration for the different platforms.
+
+By default, images are set up to link to their corresponding vistrail. This means that on a local setup, clicking on an image will open the local .vt file or will try to connect to the database if you loaded the vistrail from a database. This may not work when other users click on the images on different machines. However, if you are using your own web server, additional setup is required (see :ref:`sec-latex-setup-using-a-web-server`). Otherwise, to setup the images without links (not [...]
+
+``\renewcommand{\vistrailsdownload}{}``
+
+Finally, if you are running VisTrails from source and don't have
+python on your path, use this to set the python interpreter:
+
+``\renewcommand{\vistrailspythonpath}{/path/to/python/executable}``
+
+**Note:** If you set the \vistrailspythonpath to an invalid path
+VisTrails will use cached files if they exist.
+
+.. _sec-latex-setup-using-a-web-server:
+
+Setup For Use With Files on MediaWiki or a Web Server
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. index:
+ pair: latex embedding; mediawiki
+ pair: latex embedding; web server
+
+Many VisTrails files and/or data are stored in a database that readers
+of a pdf document might not have access to. If the files are also
+accessible through the web, the following instructions explain setup
+that will allow readers to download the VisTrail or workflow through
+MediaWiki or a web server.
+
+**MediaWiki**
+
+To setup your MediaWiki for use with VisTrails:
+
+* In your wiki/extensions folder, create a config.php file based on the config.php.sample file located in VisTrails' extensions/http folder.
+* Copy download.php, functions.php, and vistrailsExtension.php from the extensions/mediawiki folder to your wiki/extentions folder and update these files according to your needs.
+* Configure your .tex files with:
+
+ ``\renewcommand{\vistrailsdownload}{http://yourwebserver.somethingelse/download.php}``
+
+**Web Server**
+
+To configure VisTrails to run on your web server:
+
+* Create a config.php file based on the config.php.sample file located in VisTrails' extensions/http folder.
+* Copy functions.php and downloads.php from the extensions/mediawiki folder and update them according to your needs.
+* Depending on the functionality you want to make available, copy any or all of the following files:
+ - run_vistrails.php - will execute workflows and return images and pdf files
+ - get_db_vistrail_list.php - will return a list of VisTrails available in the database
+ - get_vt_xml.php - will return a VisTrail in xml format
+ - get_wf_pdf.php - will return a workflow graph in pdf format
+ - get_wf_xml.php - will return a workflow in xml format
+* Configure your .tex files with:
+
+ ``\renewcommand{\vistrailspath}{http://yourwebserver.somethingelse/run_vistrails.php}``
+
+ ``\renewcommand{\vistrailsdownload}{http://yourwebserver.somethingelse/download.php}``
+
+Including VisTrails Results in Latex
+====================================
+
+There are two ways of including VisTrails' objects in a Latex file. Usually you start with a workflow in a vistrail (the vistrail can be loaded from a file or from a database):
+
+* In ``History`` view, select the version node representing the workflow.
+* In ``Pipeline`` view, ensure that the workflow is being displayed.
+
+Now you can select ``Publish`` :math:`\rightarrow` ``To Paper...`` to launch a dialog with embedding options (see Figure :ref:`fig-configure-embedding`).
+
+.. _fig-configure-embedding:
+
+.. figure:: figures/latex/embedding.png
+ :align: center
+ :width: 5.5in
+
+ Embedding Options
+
+Then perform the following steps:
+
+* Select the type of object that you would like to display. The choices are: Workflow Results, Workflow Graph, and History Tree Graph.
+* Make sure that ``Latex`` is displayed in the ``In:`` combobox.
+* You should then choose from a number of "Embed" and "Download" options which will be explained in the tables below.
+* Press the "Copy to Clipboard" button
+* Paste clipboard contents into you Latex document
+* Run pdflatex with the -shell-escape option: ``pdflatex -shell-escape example.tex``.
+
+**Note on using local VisTrails files:** Relative or absolute filenames can be used in the .tex file, but absolute filenames are used in the pdf. Thus, if the absolute location of the file has changed, the pdf will need to be regenerated even if the relative location of the file has not changed. Also, the VisTrails ``Embed`` function assumes the .vt file is in the same directory as the .tex file. You will need to change this to an absolute filename if it is not.
+
+.. tabularcolumns:: |p{2.8cm}|p{3.0cm}|p{7.5cm}|
+
+.. _table-options:
+
+.. only:: html
+
+ **Configuration Options**
+
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+ | Option | Latex Flag | Description |
+ +=======================+=======================+==========================================================================+
+ | | Workflow Results | version=<...> | Show the results of the specified version. |
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+ | Workflow Graph | | version=<...> | Show the workflow instead of the results. |
+ | | | showworkflow | |
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+ | | History Tree Graph | showtree | Show the version tree instead of the results. |
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+
+ **Embed Options**
+
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+ | Option | Latex Flag | Description |
+ +=======================+=======================+==========================================================================+
+ | As PDF | | pdf | | Include images as pdf files. If this is not checked, a png image is |
+ | | | used. |
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+ | Smart Tag | tag=<...> | | Allows you to include a version's tag. If a tag is provided, version |
+ | | | can be omitted and buildalways is implicit. |
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+ | Cache Images | | buildalways | | When caching desired, the buildalways flag should not be included. |
+ | | | (do not include | If it is included, VisTrails will be called regardless of whether or |
+ | | for caching) | not it has been called for the same host, db, version, port and vt_id. |
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+ | Include .vtl | | getvtl | | Causes the .vtl file to be downloaded when compiling the pdf file. |
+ | | | This is useful when you want to package the workflows together with |
+ | | | your paper for archiving. |
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+
+ **Download Options**
+
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+ | Option | Latex Flag | Description |
+ +=======================+=======================+==========================================================================+
+ | | Include Workflow | embedworkflow | When clicking on the image in the pdf, download the workflow only. |
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+ | | Execute Workflow | execute | Will cause the workflow to be executed when it is opened. |
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+ | | Include Full Tree | includefulltree | When clicking on the image, download the complete VisTrail. |
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+ | | Show Spreadsheet | showspreadsheetonly | When opening the workflow it will initially only show the spreadsheet. |
+ | Only | execute | The execute option is implicit. |
+ | | | |
+ +-----------------------+-----------------------+--------------------------------------------------------------------------+
+
+.. only:: latex
+
+ .. tabularcolumns:: |p{2.8cm}|p{3.0cm}|p{7.5cm}|
+
+ .. csv-table:: Configuration Options
+ :header: **Option**, **Latex Flag**, **Description**
+
+ Workflow Results, version=<...>, "Show the results of the specified version."
+ , ,
+ Workflow Graph, version=<...>, "Show the workflow instead of the results."
+ ,showworkflow,
+ , ,
+ History Tree Graph, showtree, "Show the version tree instead of the results."
+
+ .. tabularcolumns:: |p{2.8cm}|p{3.0cm}|p{7.5cm}|
+
+ .. csv-table:: Embed Options
+ :header: **Option**, **Latex Flag**, **Description**
+
+ As PDF, pdf, "Download images as pdf files. If this is not checked, a png image is used."
+ , ,
+ Smart Tag, tag=<...>, "Allows you to include a version's tag. If a tag is provided, version can be omitted and buildalways is implicit."
+ , ,
+ Cache Images, buildalways (do not include for caching), "When caching desired, the buildalways flag should not be included. If it is included, VisTrails will be called regardless of whether or not it has been called for the same host, db, version, port and vt_id."
+ , ,
+ Include .vtl, getvtl, "Causes the .vtl file to be downloaded when compiling the pdf file. This is useful when you want to package the workflows together with your paper for archiving."
+
+ .. tabularcolumns:: |p{2.8cm}|p{3.0cm}|p{7.5cm}|
+
+ .. csv-table:: Download Options
+ :header: **Option**, **Latex Flag**, **Description**
+
+ Include Workflow, embedworkflow, "When clicking on the image in the pdf, download the workflow only."
+ , ,
+ Execute Workflow, execute, "Will cause the workflow to be executed when it is opened."
+ , ,
+ Include Full Tree, includefulltree, "When clicking on the image, download the complete VisTrail."
+ , ,
+ Show Spreadsheet Only, showspreadsheetonly, "When opening the workflow it will initially only show the spreadsheet. The execute option is implicit."
+
+Example
+^^^^^^^
+
+The following is an example command for including the execution results the workflow ``aliases`` from examples/head.vt in a pdf and caching the images. When clicking on the images, the user will start |vistrails| showing only the spreadsheet:
+
+| ``\vistrails[filename=head.vt,``
+| ``version=15,``
+| ``pdf,``
+| ``execute,``
+| ``showspreadsheetonly,``
+| ``]{width=0.45\linewidth} %Options you would give to the \includegraphics{} command``.
+
+See head.tex in the extensions/latex directory for a complete example of usage.
+
+Additional Notes
+^^^^^^^^^^^^^^^^
+
+After running at least once, VisTrails will cache the images and latex
+instructions. The latex code will be in the "cached" folder and the images in
+vistrails_images.
+
+Vistrails will create in the current directory a directory called
+vistrails_images/filename_version_options with the png/pdf files generated by the spreadsheet.
+
+Including crowdlabs.org workflow results in Latex
+=================================================
+
+It is also possible to embed results of workflows that are in www.crowdlabs.org.
+
+To use the crowdLabs extension, copy crowdlabs.sty and includecrowdlabs.py from the extensions/latex directory to the same directory as your .tex files. Then, add the following line to the beginning of the latex file:
+
+``\usepackage{crowdlabs}``
+
+
+The vistrail you would like to use must be already in crowdLabs. Visit the page of the workflow, for example, go to:
+
+http://www.crowdlabs.org/vistrails/workflows/details/1046/
+
+And click on the ``Embed this Workflow`` tab located below the image. Copy the snippet in the ``In LaTex`` box:
+
+| ``\vistrail[wfid=1046,``
+| ``buildalways=false]{width=4cm}``
+
+And paste it in the latex file.
+
+Currently crowdLabs supports only embedding workflow results in the png format. Do not use this extension together with the vistrails extension above.
+
+
+
+
+
diff --git a/doc/usersguide/log.rst b/doc/usersguide/log.rst
new file mode 100644
index 0000000..4e20212
--- /dev/null
+++ b/doc/usersguide/log.rst
@@ -0,0 +1,35 @@
+.. _chap-log:
+
+***************************
+Accessing the Execution Log
+***************************
+
+.. index:: log
+
+The code responsible for storing execution information is located in the "core/log" directories, and the code that generates much of that information is in "core/interpreter/cached.py". Modules can add execution-specific annotations to provenance via annotate() calls during execution, but much of the data (like timing and errors) is captured by the LogController and CachedInterpreter (the execution engine) objects. To analyze the log from a vistrail (.vt) file, you might have something l [...]
+
+ import core.log.log
+ import db.services.io
+
+::
+
+ def run(fname):
+ # open the .vt bundle specified by the filename "fname"
+ bundle = db.services.io.open_vistrail_bundle_from_zip_xml(fname)[0]
+ # get the log filename
+ log_fname = bundle.vistrail.db_log_filename
+ if log_fname is not None:
+ # open the log
+ log = db.services.io.open_log_from_xml(log_fname, True)
+ # convert the log from a db object
+ core.log.log.Log.convert(log)
+ for workflow_exec in log.workflow_execs:
+ print 'workflow version:', workflow_exec.parent_version
+ print 'time started:', workflow_exec.ts_start
+ print 'time ended:', workflow_exec.ts_end
+ print 'modules executed:', [i.module_id
+ for i in workflow_exec.item_execs]
+ if __name__ == '__main__':
+ run("some_vistrail.vt")
+
+You should be able to see what information is available by looking at the "core/log" classes.
diff --git a/doc/usersguide/make.bat b/doc/usersguide/make.bat
new file mode 100644
index 0000000..fd22480
--- /dev/null
+++ b/doc/usersguide/make.bat
@@ -0,0 +1,113 @@
+ at ECHO OFF
+
+REM Command file for Sphinx documentation
+
+set SPHINXBUILD=sphinx-build
+set BUILDDIR=_build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+ set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+ :help
+ echo.Please use `make ^<target^>` where ^<target^> is one of
+ echo. html to make standalone HTML files
+ echo. dirhtml to make HTML files named index.html in directories
+ echo. pickle to make pickle files
+ echo. json to make JSON files
+ echo. htmlhelp to make HTML files and a HTML help project
+ echo. qthelp to make HTML files and a qthelp project
+ echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+ echo. changes to make an overview over all changed/added/deprecated items
+ echo. linkcheck to check all external links for integrity
+ echo. doctest to run all doctests embedded in the documentation if enabled
+ goto end
+)
+
+if "%1" == "clean" (
+ for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+ del /q /s %BUILDDIR%\*
+ goto end
+)
+
+if "%1" == "html" (
+ %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+ goto end
+)
+
+if "%1" == "dirhtml" (
+ %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+ goto end
+)
+
+if "%1" == "pickle" (
+ %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+ echo.
+ echo.Build finished; now you can process the pickle files.
+ goto end
+)
+
+if "%1" == "json" (
+ %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+ echo.
+ echo.Build finished; now you can process the JSON files.
+ goto end
+)
+
+if "%1" == "htmlhelp" (
+ %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+ echo.
+ echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+ goto end
+)
+
+if "%1" == "qthelp" (
+ %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+ echo.
+ echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+ echo.^> qcollectiongenerator %BUILDDIR%\qthelp\VisTrails.qhcp
+ echo.To view the help file:
+ echo.^> assistant -collectionFile %BUILDDIR%\qthelp\VisTrails.ghc
+ goto end
+)
+
+if "%1" == "latex" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ echo.
+ echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "changes" (
+ %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+ echo.
+ echo.The overview file is in %BUILDDIR%/changes.
+ goto end
+)
+
+if "%1" == "linkcheck" (
+ %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+ echo.
+ echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+ goto end
+)
+
+if "%1" == "doctest" (
+ %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+ echo.
+ echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+ goto end
+)
+
+:end
diff --git a/doc/usersguide/mashups.rst b/doc/usersguide/mashups.rst
new file mode 100644
index 0000000..dc74619
--- /dev/null
+++ b/doc/usersguide/mashups.rst
@@ -0,0 +1,116 @@
+.. _chap-mashups:
+
+*******
+Mashups
+*******
+
+.. _sec-param-alias:
+
+Creating Parameter Aliases
+==========================
+
+.. index::
+ pair: mashups;aliases
+ pair: mashups;setting parameters
+
+If you would like to be able to explore different values for a specific parameter, you will need to create an alias by double-clicking the parameter in the ``Parameter Aliases`` section. After naming the alias, you can select the alias in the ``Mashup`` tab (center panel), and configure the alias by selecting the ``Display Widget`` type and setting Default values.
+
+Notice that a pipeline can have multiple modules of the same type or name, making it difficult to differentiate between them. These modules are each assigned a number, with the numbers in the ``Annotated Pipeline`` section corresponding to the numbers in the ``Parameter Aliases`` section, making it possible set an alias for the desired module without much confusion. See figure :ref:`Numbered Modules... <fig-righttab>`.
+
+.. _fig-righttab:
+
+.. figure:: figures/mashups/righttab.png
+ :width: 2.5in
+ :align: center
+
+ Numbered Modules - The HTTPFile modules 1 and 2 appear in the annotated pipeline and in the parameter aliases. The annotated pipeline also, numbers the vtkDataSetReader modules (which appear below the respective HTTPFile modules in the pipeline). Their parameters have not been exposed to the mashup, so they do not appear in the Parameter Aliases section.
+
+Finally, not all modules in the ``Annotated Pipeline`` will show up in the ``Parameter Aliases`` section. Only modules whose parameters have been set in the pipeline will appear.
+
+
+Configuring Parameter Aliases
+=============================
+
+.. index::
+ pair: mashups; configuring aliases
+
+As mentioned in section :ref:`sec-param-alias`, aliases are configured in the center panel (the ``Mashup`` tab). This is pretty simple, so here are the steps:
+
+#. Select the alias you wish to configure from the top box in the ``Aliases`` tab. The name and position of the selected alias should be displayed below. Both of these can be changed by editing the ``Name`` and/or ``Order`` values.
+#. Next select the type of widget to display. The choices are combobox, slider, and numeric stepper. The combobox will allow you to enter specific values, whereas the numeric stepper and slider will allow you to scroll through a range of values.
+#. Set the Min Val, Max Val, and Step Size (for slider and numeric stepper only).
+#. Set the Default Value. The default value should already be set based on the value it was given in the pipeline, but you are allowed to change it here if desired.
+#. Enter suggested values. If you have a set of values to suggest to the user through the Mashups interface, you should add them to the values list. You can do this by either clicking the ``...`` button and adding the appropriate values, or by entering the values in the ``Values List`` box in list format.
+#. Finally, you may delete an alias with the ``Delete Alias`` button.
+
+After configuring the necessary aliases, press ``Preview`` to interact with your mashup and to ensure its proper functionality.
+
+Saving a Mashup
+===============
+
+.. index::
+ pair: mashups;saving
+
+Mashups are added the the VisTrail when you press the keep button. However, this changes the VisTrail, but does not save it. To fully save your mashup, you should both press the ``Keep`` button and save the VisTrail.
+
+Managing Multiple Mashups
+=========================
+
+.. index::
+ pair: mashups;naming
+
+The ``Mashups Inspector`` allows you to both rename a mashup, and easily switch between existing mashups.
+
+A Simple Example
+================
+.. topic:: Try it now!
+
+ * Open :vtl:`brain_vistrail.vt`
+ * Choose ``Save As`` and rename the file if you do not want to overwrite the original.
+ * Select the "counter 4" version
+ * Press execute to ensure any necessary upgrades are made
+ * Select ``Mashup`` from the toolbar.
+ * In the Mashup Pipeline tab, look under ``vtkProperty`` :math:`\rightarrow` ``SetOpacity`` and double-click on ``Float``.
+ * Enter "Opacity" in the ``Set Parameter`` box that pops up, then click ``OK``. See figure :ref:`Creating the Opacity Alias <fig-opacityalias>`.
+ * Under ``vtkRenderer`` :math:`\rightarrow` ``SetBackgroundWidget``, double-click on ``Color`` and enter "Background" as the alias. See figure :ref:`Creating the Background Alias <fig-background-create>`.
+ * In the center panel, select the ``Opacity`` alias.
+ * Change the display widget to ``numericstepper``.
+ * Set the ``Min Val``, ``Max Val``, and ``Step Size`` to 0, 1, and 0.1 respectively.
+ * Set the ``Values List`` to [0.3, 0.5]. See figure :ref:`Configuring the Opacity Alias <fig-opacity>`.
+ * Select the ``Background`` alias and make sure the display widget is a ``combobox``.
+ * Select ``Preview``. See figure :ref:`The resulting mashup <fig-mashupcomp>`.
+ * Select ``Tag``, ``No``, and then enter "one" as the new tag name.
+ * Save the file. :vtl:`(Open result) <mashups1.vt>`
+
+.. _fig-opacityalias:
+
+.. figure:: figures/mashups/opacityalias.png
+ :align: center
+ :width: 50%
+
+ Creating the Opacity Alias.
+
+.. _fig-background-create:
+
+.. figure:: figures/mashups/background.png
+ :align: center
+ :width: 35%
+
+ Creating the Background Alias.
+
+.. _fig-opacity:
+
+.. figure:: figures/mashups/aliasconfig.png
+ :align: center
+ :width: 80%
+
+ Configuring the ``Opacity`` alias.
+
+.. _fig-mashupcomp:
+
+.. figure:: figures/mashups/mashupcomp.png
+ :align: center
+ :width: 80%
+
+ The resulting mashup.
+
diff --git a/doc/usersguide/merging.rst b/doc/usersguide/merging.rst
new file mode 100644
index 0000000..ca8211d
--- /dev/null
+++ b/doc/usersguide/merging.rst
@@ -0,0 +1,37 @@
+.. _chap-merging:
+
+*************************
+Merging Two Version Trees
+*************************
+
+.. index:: merging
+
+One of the benefits of having a version tree is that branching allows users to work on multiple workflows within the same file. This is especially useful when workflows are similar or when one workflow provides output for another. However, if a user creates two different workflows in two different files and decides he/she wants them to be part of the same file/history, VisTrails allows file merging.
+
+To merge two files:
+
+ * Open both files
+ * Select one of the files you would like to be merged.
+ * Place you mouse over the ``Merge With`` arrow from the Edit menu. A list of open files should appear.
+ * Select the file that you would like to join with the current (previously selected) file.
+
+The history trees of both files should now be joined and placed in a new file.
+
+Example
+=======
+
+.. _fig-premerge:
+
+.. figure:: figures/merging/premerge.png
+ :align: center
+ :width: 65%
+
+ Merging two vistrails.
+
+.. _fig-postmerge:
+
+.. figure:: figures/merging/postmerge.png
+ :align: center
+ :width: 65%
+
+ The resultant history tree.
diff --git a/doc/usersguide/packages.rst b/doc/usersguide/packages.rst
new file mode 100644
index 0000000..7b61b26
--- /dev/null
+++ b/doc/usersguide/packages.rst
@@ -0,0 +1,1177 @@
+.. _chap-packages:
+
+**************************
+Writing VisTrails Packages
+**************************
+
+Introduction
+============
+
+.. highlight:: python
+ :linenothreshold: 5
+
+.. index::
+ pair: modules; writing new
+ single: packages
+
+.. role:: red
+
+|vistrails| provides a
+plugin infrastructure to integrate user-defined functions and
+libraries. Specifically, users can incorporate their own visualization
+and simulation code into pipelines by defining custom modules (or wrappers). These
+modules are bundled in what we call *packages*. A \vistrails
+package is simply a collection of Python classes stored in one or more
+files, respecting some conventions that will be described shortly.
+Each of these classes will represent a new module. In this chapter, we
+will build progressively more complicated modules.
+Note that even though each section introduces a specific large
+feature of the |vistrails| package mechanism, new small features are
+highlighted and explained as we go along. Because of this, we
+recommend at least skimming through the entire chapter at least once.
+
+Who Should Read This Chapter?
+=============================
+
+This chapter is written for developers who wish to extend |vistrails| with customized modules, tailored for their specific needs. It is assumed that you have experience writing code in the Python programming language. Teaching the syntax of Python is beyond the scope of this manual; for experienced programmers who would like a compact introduction to Python, we recommend the book *Python in a Nutshell* by Alex Martelli (published by O'Reilly).
+
+However, if you do not yet know Python but are familiar with another object-oriented language such as Java or C#, you should be able to get the gist of these examples from looking at the code and by reading our line-by-line commentaries.
+
+.. _sec-packages-simple_example:
+
+A Simple Example
+================
+
+Here is a simplified example of a very simple user-defined module:
+
+.. code-block:: python
+ :linenos:
+
+ class Divide(Module):
+ def compute(self):
+ arg1 = self.getInputFromPort("arg1")
+ arg2 = self.getInputFromPort("arg2")
+ if arg2 == 0.0:
+ raise ModuleError(self, "Division by zero")
+ self.setResult("result", arg1 / arg2)
+
+ _input_ports = [('arg1', '(org.vistrails.vistrails.basic:Float)',\
+ {"labels": str(["dividend"])}),\
+ ('arg2', '(org.vistrails.vistrails.basic:Float)',\
+ {"labels": str(["divisor"])})]
+ _output_ports = [('result', '(org.vistrails.vistrails.basic:Float)',\
+ {"labels": str(["quotient"])})]
+
+ _modules = [Divide]
+ #old syntax
+ #registry.addModule(Divide)
+ #registry.addInputPort(Divide, "arg1", (basic.Float, 'dividend'))
+ #registry.addInputPort(Divide, "arg2", (basic.Float, 'divisor'))
+ #registry.addOutputPort(Divide, "result", (basic.Float, 'quotient'))
+
+New VisTrails modules must subclass from Module, the base class that defines basic functionality. The only required override is the compute() method, which performs the actual module computation. Input and output is specified through ports, which currently have to be explicitly registered with VisTrails. However, this is straightforward, and done through method calls to the module registry. An example of a (slightly) more complicated module follows:
+
+.. include:: pythoncalc.rst
+
+To try this out in VisTrails, save the file above in the ``.vistrails/userpackages`` subdirectory of your home directory, with the filename ``pythoncalc.py``. Then, click on the ``Edit`` menu (or the ``VisTrails`` menu on Mac OS X), select the ``Preferences`` option and select the ``Module Packages`` tab. A dialog similar to what is shown
+in Figure :ref:`All available packages... <fig-packages-enablepackage>` should appear. Select the
+``pythonCalc`` package, then click on
+``Enable``. This should move the package to the
+``Enabled packages`` list. Close the dialog. The package and
+module should now be visible in the VisTrails builder.
+
+.. _fig-packages-enablepackage:
+
+.. figure:: figures/packages/enable_package.png
+ :align: center
+ :width: 100%
+
+ All available packages can be enabled and disabled with the VisTrails preferences dialog.
+
+Now create a workflow similar to what is shown in Figure
+:ref:`A simple workflow that uses PythonCalc... <fig-packages-pythoncalcworkflow>`. When executed, this workflow
+will print the following on your terminal:
+
+``7.0``
+
+.. _fig-packages-pythoncalcworkflow:
+
+.. figure:: figures/packages/pythoncalc_workflow.png
+ :align: center
+ :width: 100%
+
+ A simple workflow that uses ``PythonCalc``, a user-defined module.
+
+
+
+Let's now examine how this works. The first
+two lines simply import required components. The next three lines
+give |vistrails| meta-information about the
+package. ``Version`` is simply information about the package
+version. This might be tied to the underlying library or not. The only
+recommended guideline is that compatibility is not broken across minor
+releases, but this is not enforced in any way. ``Name`` is a
+human-readable name for the package.
+
+.. %\paragraph*{Choosing a good identifier}
+
+The most important piece of metadata,
+however, is the package *identifier*, stored in the variable called
+``identifier``. This is a string that must be globally unique
+across all packages, not only in your system, but in any possible
+system. We recommend using an identifier similar to Java's package
+identifiers. These look essentially like regular DNS names, but the
+word order is reversed. This makes sorting on the strings a lot more
+meaningful. You should generally go for
+``institution.project.packagename`` for a package related to a
+certain project from some institution, and
+``institution.creatorname`` for a personally developed
+package. If you are wrapping third-party functionality, *do not*
+use their institution's DNS, use your own. The rationale for this is
+that the third party itself might decide to create their own |vistrails|
+package, and you do not want to introduce conflicts.
+
+Line 8 is where we actually start defining a new module.
+Every |vistrails| module corresponds
+to a Python class that ultimately derives from the ``Module`` class, which is defined in ``core.modules.vistrails_module``. Each module must implement a ``compute`` method that takes no extra parameters, such as on Line 11. This method
+represents the actual computation that happens in a module.
+This computation typically involves getting the necessary input and
+generating the output. We will now see how that works.
+
+Line 12 shows how to extract input from a
+port. Specifically, we're getting the values passed to input ports
+``value1`` and ``value2``. We then perform some
+operation with these values, and need to report the output on an
+output port, so that it is available for downstream modules. This is
+done on Line 15, where the result is set to port
+``value``.
+
+.. index::
+ pair: modules; ``ModuleError``
+
+Let us now look more carefully at the remainder of the class definition. Notice
+that developers are allowed to define extra helper methods, for example the ``op`` method on Line
+17. These helper methods can naturally use the ports
+API. The other important feature of the ``op`` method is
+*error checking*. ``PythonCalc`` requires a string that
+represents the operation to be performed with the two numbers. If the
+string is invalid, it signals an error by simply raising a Python
+exception, ``ModuleError``, that is provided in
+``core.modules.vistrails_module``. This exception expects two
+parameters: the module that generated the exception (typically
+``self``) and a string describing the error. In the Pipeline view, this error message is displayed in the tooltip that appears when the user "mouses over" the ``PythonCalc`` module icon.
+
+.. index::
+ pair: packages; ``initialize``
+ pair: Module registry; ``add_Module``
+ pair: Module registry; ``add_input_port``
+ pair: Module registry; ``add_output_port``
+
+That is all that it takes in terms of module behavior. The rest of the
+code is meant to interact with |vistrails|, and let the system know
+about the modules and ports being exposed. To do that, you must
+provide a function called ``initialize`` in the main body of the
+package file (the function starting on Line
+27). The first thing is usually to register the
+module itself, such as on Line 33. Then, we need
+to tell |vistrails| about the input and output ports we want to
+expose. Input ports are set with the ``add_input_port`` method
+in the registry, and output ports with ``add_output_port``. These calls take three parameters. The
+first parameter is the module you're adding a new port to. The second
+one is simply the name of the port, and the third one is a description
+of the parameter. In most cases, this is just a pair, where the
+first element is a |vistrails| module representing the module type
+being passed, and the second element is a string describing it.
+Notice that the
+types being used are |vistrails| modules (Line 35),
+and not Python types.
+
+.. %Later, we will see how to pass more complicated data types.
+
+That is it --- you have successfully created a new package and
+module. From now on, we will look at more complicated examples, and
+more advanced features of the package mechanism.
+
+Module documentation
+====================
+
+The docstring you set on your Module subclass will be displayed to the user
+when he clicks on the 'Documentation' button in the 'Module Information' panel.
+Be sure to put a readable description and your usage information there.
+
+If you want to customize that documentation, you can provide a staticmethod or
+classmethod 'get_documentation' on your Module. The string it returns will be
+used as the documentation.
+
+.. code-block:: python
+ :linenos:
+
+ class TestMod(Module):
+ """This very simple module doesn't do anything sensible.
+ """
+
+ @classmethod
+ def get_documentation(cls, docstring, module=None):
+ return docstring.upper()
+
+The function receives two arguments: the string that was about to be used (the
+module's docstring or an empty string), and the module object from the
+pipeline if the documentation was requested for a specific instance of that
+module (else, None is passed).
+
+.. _fig-packages-custom_documentation:
+
+.. figure:: figures/packages/custom_documentation.png
+ :align: center
+
+Creating Reloadable Packages
+============================
+
+When creating or making changes to packages, it is often desirable to reload the package without having to restart |vistrails|. To create a package that is reloadable, users should create a new directory for the package in ``userpackages`` directory. This new directory should have the same name as the package and should contain an ``__init__.py`` file and an ``init.py`` file. The identified, name, version, configuration, and package_dependencies fields/methods should be in ``__init__. [...]
+
+.. code-block:: python
+ :linenos:
+
+ identifier = 'org.vistrails.vistrails.matplotlib'
+ name = 'matplotlib'
+ version = '0.9.0'
+
+ def package_dependencies():
+ import core.packagemanager
+ manager = core.packagemanager.get_package_manager()
+ if manager.has_package('org.vistrails.vistrails.spreadsheet'):
+ return ['org.vistrails.vistrails.spreadsheet']
+ else:
+ return []
+
+ def package_requirements():
+ import core.requirements
+ if not core.requirements.python_module_exists('matplotlib'):
+ raise core.requirements.MissingRequirement('matplotlib')
+ if not core.requirements.python_module_exists('pylab'):
+ raise core.requirements.MissingRequirement('pylab')
+
+Imports (excluding core.configuration), other class definitions, and the initialize method should be in the ``init.py`` file. Finally, to reload a package, select the ``reload`` button from the ``Preferences`` dialog's ``Module Packages`` tab.
+
+.. topic:: Note
+
+ To make the previous example :ref:`sec-packages-simple_example` reloadable, rather than having just one file ``pythoncalc.py``, one would have a ``pythoncalc`` directory with the "version", "name", and "identifier" lines in ``__init__.py`` and all other lines in ``init.py``.
+
+.. _sec-wrapping_cmdline_tools:
+
+Wrapping Command-line tools
+===========================
+
+.. index::
+ pair: packages; wrapping command-line tools
+
+Many existing programs are readily available through a command-line
+interface. Also, many existing workflows are first implemented
+through scripts, which work primarily with command-line
+tools. This section describes how to wrap command-line applications so
+they can be used with VisTrails. We will use as a running example the
+``afront`` package, which wraps ``afront``, a command-line program
+for generating 3D triangle meshes. [#]_ We will wrap the basic
+functionality in three different modules: ``Afront``, ``AfrontIso``, and ``MeshQualityHistogram``.
+
+Each of these modules will be implemented by a Python
+class, and they will all invoke the ``afront`` binary.
+``Afront`` is the base execution module, and
+``AfrontIso`` requires extra parameters on top of the original
+ones. Because of this, we will implement ``AfrontIso`` as a
+subclass of ``Afront``. ``MeshQualityHistogram``,
+however, requires entirely different parameters, and so will not be
+a subclass of ``Afront``. A first attempt at writing this package might look something like this:
+
+.. code-block:: python
+ :linenos:
+
+ from core.modules.vistrails_module import Module
+ ... # other import statements
+
+ name = "Afront"
+ version = "0.1.0"
+ identifier = "edu.utah.vistrails.afront"
+
+ class Afront(Module):
+ def compute(self):
+ ... # invokes afront
+
+ class AfrontIso(Afront):
+ def compute(self):
+ ... # invokes afront with additional parameters
+
+ class MeshQualityHistogram(Module):
+ def compute(self):
+ ... # invokes afront with completely different parameters
+
+ def initialize():
+ ...
+
+Class Mixins
+^^^^^^^^^^^^
+
+While this approach is a good start, it does require significant duplication of effort. Each module must contain code to invoke the ``afront`` binary and pass it some parameters. Since this functionality is required by all three modules, we would like to put this code in a separate class called, say, ``AfrontRun``, and let each of our modules inherit from it. ``AfrontRun`` itself is not a module, and thus does not extend the ``Module`` class. So our three modules will inherit from *both* [...]
+
+.. %It should be clear that all three modules share some functionality (invoking ``afront``), but not all. We would like to avoid duplicate code, but there is not a single class where we can implement the base code. The solution is to create a *mixin class*, where we implement the necessary functionality, and then inherit from both classes. In the following snippets, we will highlight the changes in the code.
+
+.. raw:: latex
+
+ \definecolor{CodeEmph}{rgb}{0.8,0.1,0.1}
+ \newcommand{\important}[1]{\textsl{{\color{CodeEmph}#1}}}
+ \important{hi} hello
+
+.. code-block:: python
+ :linenos:
+
+ from core.modules.vistrails_module import Module, ModuleError
+ from core.system import list2cmdline
+ import os
+
+ class AfrontRun(object):
+ _debug = False
+ def run(self, args):
+ cmd = ['afront', '-nogui'] + args
+ cmdline = list2cmdline(cmd)
+ if self._debug:
+ print cmdline
+ result = os.system(cmdline)
+ if result != 0:
+ raise ModuleError(self, "Execution failed")
+
+ class Afront(Module, AfrontRun):
+ ...
+
+ class MeshQualityHistogram(Module, AfrontRun):
+ ...
+
+.. .. parsed-literal::
+
+ from core.modules.vistrails_module import Module, ModuleError
+ :red:`from core.system import list2cmdline`
+ :red:`import os`
+
+ :red:`class AfrontRun(object):`
+ :red:`_debug = False`
+ :red:`def run(self, args):`
+ :red:`cmd = ['afront', '-nogui'] + args`
+ :red:`cmdline = list2cmdline(cmd)`
+ :red:`if self._debug:`
+ :red:`print cmdline`
+ :red:`result = os.system(cmdline)`
+ :red:`if result != 0:`
+ :red:`raise ModuleError(self, "Execution failed")`
+
+ class Afront(Module, :red:`AfrontRun`):
+ ...
+
+ class MeshQualityHistogram(Module, :red:`AfrontRun`):
+ ...
+
+Now every module in the ``afront`` package has access to
+``run()``. The other new feature in this snippet is
+``list2cmdline``, which turns a list of strings into a command
+line. It does this in a careful way (protecting arguments with spaces,
+for example). Notice that we use a call to a shell
+(``os.system()``) to invoke ``afront``. This is
+frequently the easiest way to get third-party functionality into |vistrails|.
+
+.. _sec-pkg_config:
+
+Package Configuration
+^^^^^^^^^^^^^^^^^^^^^
+
+.. index::
+ pair: packages; configuration
+
+There are two obvious shortcomings in the way ``run()`` is
+implemented. First, the code assumes ``afront`` is available
+in the system path, which might not be true in practice. Second, the
+debugging variable is inaccessible from the GUI, where it could be
+very useful. |vistrails| provides a way to configure a package
+through the |vistrails| ``Preferences`` dialog. It is very simple to provide your own configuration;
+just add a ``configuration`` attribute to your package, as follows:
+
+.. code-block:: python
+ :linenos:
+
+ from core.configuration import ConfigurationObject
+ from core.modules.vistrails_module import Module, ModuleError
+ from core.system import list2cmdline
+ import os
+
+ configuration = ConfigurationObject(path=(None, str),
+ debug=False)
+
+ class AfrontRun(object):
+
+ def run(self, args):
+ if configuration.check('path'): # there's a set directory
+ afront_cmd = configuration.path + '/afront'
+ else: # Assume afront is on path
+ afront_cmd = 'afront'
+ cmd = [afront_cmd, '-nogui'] + args
+ cmdline = list2cmdline(cmd)
+ if configuration.debug:
+ print cmdline
+ ...
+ ...
+
+.. .. parsed-literal::
+
+ :red:`from core.configuration import ConfigurationObject`
+ from core.modules.vistrails_module import Module, ModuleError
+ from core.system import list2cmdline
+ import os
+
+ .. _ref-packages=configconstructor1:
+ :red:`configuration = ConfigurationObject(path=(None, str),`
+ .. _ref-packages-configconstructor2:
+ :red:`debug=False)`
+
+ class AfrontRun(object):
+
+ def run(self, args):
+ .. _ref-packages-configurationcheck:
+ :red:`if configuration.check('path'): # there's a set directory`
+ :red:`afront_cmd = configuration.path + '/afront'`
+ :red:`else: # Assume afront is on path`
+ :red:`afront_cmd = 'afront'`
+ cmd = [:red:`afront_cmd`, '-nogui'] + args
+ cmdline = list2cmdline(cmd)
+ .. _ref-packages-configurationdebug:
+ :red:`if configuration.debug:`
+ print cmdline
+ ...
+ ...
+
+.. index:: ``ConfigurationObject``
+
+Let us first look at how to specify configuration options. Named
+arguments passed to the ``ConfigurationObject`` constructor (Lines 6 and 7) become attributes in the object. If the attribute has a default value, simply pass it to the constructor. If the attribute should be unset by default, pass the constructor a pair whose first element is ``None`` and second element is the *type* of the expected
+parameter. Currently, the valid types are ``bool``,
+``int``, ``float`` and ``str``.
+
+To use the configuration object in your code, you can simply access
+the attributes (as on line 18). This is fine when there is a
+default value set for the attribute. In the case of ``path``,
+however, the absence of a value is encoded by a tuple
+``(None, str)``, so using it directly is inconvenient. That is
+where the ``check()`` method comes in (line 12). It returns ``False``
+if there is no set value, and returns the value otherwise.
+
+Perhaps the biggest advantage of using a configuration object is that the values can
+be changed through a GUI, and they are persistent across VisTrails
+sessions. To configure a package, open the ``Preferences``
+menu (|vistrails|:math:`\rightarrow`
+``Preferences`` on Mac OS X, or ``Edit`` :math:`\rightarrow`
+``Preferences`` on other platforms). Then, select the package you want to
+configure by clicking on it (a package must be enabled to be
+configurable). If the ``Configure`` button is disabled, it
+means the package does not have a configuration object. When you do
+click ``Configure``, a dialog like the one in Figure :ref:`Configuration window for a package... <fig-packages-afrontconfigurationwindow>` will appear.
+
+.. _fig-packages-afrontconfigurationwindow:
+
+.. figure:: figures/packages/afront_configuration_window.png
+ :align: center
+ :width: 40%
+
+ Configuration window for a package that provides a configuration object.
+
+To edit the value for a particular field, double-click on it, and change the
+value. The values set in this dialog are persistent across VisTrails
+sessions, being saved on a per-user basis.
+
+Temporary File Management
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. index::
+ pair: packages; temporary files
+ pair: packages; ``filePool``
+
+Command-line programs typically generate files as outputs. On
+complicated pipelines, many files get created and passed to other
+modules. To facilitate the use of files as communication
+objects, VisTrails provides basic infrastructure for temporary file
+management. This way, package developers do not have to worry about
+file ownership and lifetimes.
+
+To use this infrastructure, it must be possible to tell the program
+being called which filename to use as output. VisTrails can accommodate
+some filename requirements (in particular, specific
+filename extensions might be important in Windows environments, and
+these can be set), but it must be possible to direct the output to a
+certain filename.
+
+We will use ``Afront's compute()`` method to
+illustrate the feature.
+
+.. code-block:: python
+ :linenos:
+
+ ...
+ class Afront(Module, AfrontRun):
+
+ def compute(self):
+ o = self.interpreter.filePool.create_file(suffix='.m')
+ args = []
+ if not self.hasInputFromPort("file"):
+ raise ModuleError(self, "Needs input file")
+ args.append(self.getInputFromPort("file").name)
+ if self.hasInputFromPort("rho"):
+ args.append("-rho")
+ args.append(str(self.getInputFromPort("rho")))
+ if self.hasInputFromPort("eta"):
+ args.append("-reduction")
+ args.append(str(self.getInputFromPort("eta")))
+ args.append("-outname")
+ args.append(o.name)
+ args.append("-tri")
+ self.run(args)
+ self.setResult("output", o)
+ ...
+
+Line 5 shows how to create a temporary file
+during the execution of a pipeline. There are a few new things
+happening, so let us look at them one at a time. Every module holds a
+reference to the current *interpreter*, the object responsible
+for orchestrating the execution of a pipeline. This object has a
+``filePool``, which is what we will use to create a pipeline,
+through the ``create_file`` method. This method takes
+optionally a named parameter ``suffix``, which forces the
+temporary file that will be created to have the right extension.
+
+The file pool returns an instance of ``basic_modules.File``,
+a module that is provided by the basic VisTrails packages. There are
+two important things you should know about ``File``. First, it
+has a ``name`` attribute that stores the name of the file it
+represents. In this case, it is the name of the
+recently-created temporary file. This allows you to safely use this
+file when calling a shell, as seen on Line 17.
+The other important feature is that it can be passed directly to an
+output port, so that this file can be used by subsequent modules. This
+is shown on Line 20.
+
+The above code also introduces the boolean function ``hasInputFromPort`` (see Lines 7, 10, and 13). This is a simple error-checking function that verifies that the port has incoming data before the program attempts to read from it. It is considered good practice to call this function before invoking ``getInputFromPort`` for any input port.
+
+**Accommodating badly-designed programs** Even though it is
+considered bad design for a command-line program not to allow the specification of an output
+filename, there do exist programs that lack this functionality. In this case, a possible
+workaround is to execute the command-line tool, and move the generated
+file to the name given by VisTrails.
+
+Interfacing with the |vistrails| Menu
+=====================================
+
+As we saw in Section :ref:`sec-pkg_config`, using the ``ConfigurationObject`` class is one way to "hook" your custom package into the |vistrails| GUI. However, this is not the only way to integrate your package with the user interface. |vistrails| also supports a mechanism whereby your package can add new options underneath the ``Packages`` menu (Figure :ref:`Packages can integrate their own commands... <fig-packages-package_menu>`).
+
+.. _fig-packages-package_menu:
+
+.. figure:: figures/packages/package_menu.png
+ :align: center
+ :width: 5in
+
+ Packages can integrate their own commands into the main |vistrails| menu.
+
+This is done by adding a function named ``menu_items`` to your main package file. This function takes no parameters, and should return a tuple of pairs for each new menu item to be added. The first element of each pair is the label of the menu item as it should appear in the GUI. The second element of the pair is the name of the callback function to be invoked when the user selects that menu item.
+
+As an example, we include below the implementation of ``menu_items`` from the |vistrails| Spreadsheet package:
+
+.. code-block:: python
+ :linenos:
+
+ def menu_items():
+ """menu_items() -> tuple of (str,function)
+ It returns a list of pairs containing text for the menu and a
+ callback function that will be executed when that menu item is selected.
+ """
+
+ def show_spreadsheet():
+ spreadsheetWindow.show()
+ lst = []
+ lst.append(("Show Spreadsheet", show_spreadsheet))
+ return tuple(lst)
+
+.. .. parsed-literal::
+
+ def menu_items():
+ """menu_items() -> tuple of (str,function)
+ It returns a list of pairs containing text for the menu and a
+ callback function that will be executed when that menu item is selected.
+ """
+
+ def show_spreadsheet():
+ spreadsheetWindow.show()
+ lst = []
+ :red:`lst.append(("Show Spreadsheet", show_spreadsheet))`
+ return tuple(lst)
+
+Writing your own ``menu_items`` function is straightforward; simply use the provided example as a basis, and substitute labels and callback functions as appropriate for your specific module. Although the Spreadsheet package currently only implements one new menu option, you are free to add as many as you see fit; just append additional pairs to the list (see Line 10 of the example code) before the function returns.
+
+The ``Packages`` menu is organized hierarchically, as illustrated in Figure :ref:`Packages can integrate their own commands... <fig-packages-package_menu>`. Each package that contributes a ``menu_items`` function will receive an entry in the ``Packages`` menu. The actual menu items for each package will appear in a submenu.
+
+.. _sec-interpackage_dependencies:
+
+Interpackage Dependencies
+=========================
+
+.. index::
+ pair: packages; dependencies
+
+When creating more sophisticated VisTrails packages, you might want to
+create a new module that requires a module *from another package*. For example, using modules from different packages as
+input ports, or even subclassing modules from other packages, require
+management of interpackage dependencies. VisTrails needs to know about
+these so that packages can be initialized in the correct order. To specify these dependencies, you should add a function named
+``package_dependencies`` to your package. This function should return a list containing the identifier strings of the required packages.
+
+As an example of this function's usage, let's take a look at a (simplified) code segment from the VTK package, which is included in the standard |vistrails| distribution:
+
+.. code-block:: python
+ :linenos:
+
+ def package_dependencies():
+ return ['org.vistrails.vistrails.spreadsheet']
+
+
+As you can see, the ``package_dependencies`` function is quite straightforward; it simply returns a list of the identifiers for the packages required by the VTK package. In this case, the list contains just a single string, as the |vistrails| Spreadsheet is the only package dependency for the VTK package.
+
+The simple approach taken by the above code works well for the majority of cases, but in practice you may want to add some error-checking to your ``package_dependencies`` function. This allows |vistrails| to recover gracefully in the unlikely event that the Spreadsheet package is missing. Below is the complete ``package_dependencies`` function for the VTK package:
+
+.. code-block:: python
+ :linenos:
+
+ def package_dependencies():
+ import core.packagemanager
+ manager = core.packagemanager.get_package_manager()
+ if manager.has_package('org.vistrails.vistrails.spreadsheet'):
+ return ['org.vistrails.vistrails.spreadsheet']
+ else:
+ return []
+
+
+The above code segment also demonstrates the |vistrails| API function ``has_package`` which simply verifies that a given package exists in the system.
+
+Package Requirements
+====================
+
+In Section :ref:`sec-interpackage_dependencies`\ , we saw how packages can depend on other packages. However, some packages may also depend on the presence of external libraries (in the form of Python modules) or executable files in order to run correctly.
+
+Required Python Modules
+^^^^^^^^^^^^^^^^^^^^^^^
+
+To check for the presence of a required Python module, you should add a function named ``package_requirements`` to your package. This function need not return any value; however it may raise exceptions or output error messages as necessary.
+Here is an example of the syntax of the ``package_requirements`` function, taken from the |vistrails| VTK package:
+
+.. code-block:: python
+ :linenos:
+
+ def package_requirements():
+ import core.requirements
+ if not core.requirements.python_module_exists('vtk'):
+ raise core.requirements.MissingRequirement('vtk')
+ if not core.requirements.python_module_exists('PyQt4'):
+ print 'PyQt4 is not available. There will be no interaction',
+ print 'between VTK and the spreadsheet.'
+ import vtk
+
+
+A key element of ``package_requirements`` is the use of the function ``python_module_exists`` (see Lines 3 and 5), which checks whether a given module has been installed in your local Python system.
+
+
+Automatically Installing Python Modules
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A more advanced method is to attempt to install a python module
+automatically using a system package manager. This method currently
+works for apt- and rpm-based systems. By using
+``core.bundles.py_import``, you can attempt to automatically install a
+system dependency, all you need to specify is the python module name
+and the name of the package that contains it. The following example
+can be put in your ``init.py`` file, with the desired module and
+package names changed:
+
+.. code-block:: python
+ :linenos:
+
+ from core.bundles import py_import
+ from core import debug
+ try:
+ pkg_dict = {'linux-ubuntu': 'your-apt-package',
+ 'linux-fedora': 'your-deb-package'}
+ your-py-module = py_import('your-py-module', pkg_dict)
+ except Exception, e:
+ debug.critical("Exception: %s" % e)
+
+Note that, if you use this method, you should not specify it in the
+``package_requirements``, because that would block the install attempt.
+
+Required Executables
+^^^^^^^^^^^^^^^^^^^^
+
+As explained in Section :ref:`sec-wrapping_cmdline_tools`, a common motivation for writing new |vistrails| modules is to wrap existing command-line tools. To this end, the |vistrails| API provides a function called ``executable_file_exists`` which checks for the presence of specific executables on the path.
+
+Here is an example of its usage, taken from the ``initialize`` function of the ``ImageMagick`` package. This package is included in the standard |vistrails| distribution. The following code snippet checks to see if ``convert``, a command-line program associated with the *ImageMagick* suite of graphics utilities, is on the path.
+
+.. code-block:: python
+ :linenos:
+
+ import core.requirements
+
+ ...
+
+ if (not core.requirements.executable_file_exists('convert')):
+ raise core.requirements.MissingRequirement("ImageMagick suite")
+
+Note that this function is not strictly required in order to wrap third party executables into a module. Using a ``Configuration`` object (see Section :ref:`sec-pkg_config`) that lets the user specify the path to an executable may be a cleaner solution.
+
+For additional information or examples of any of the functions described above, please refer to the |vistrails| source code or contact the |vistrails| development team.
+
+Interaction with Caching
+========================
+
+.. index::
+ pair: modules; caching
+
+VisTrails provides a caching mechanism, in which portions of pipelines that are common across different executions are automatically shared. However, some modules should not be shared. Caching control is therefore up to the package developer. By default, caching is enabled. So a developer that doesn't want caching to apply must make small changes to the module. For example, look at the StandardOutput module:
+
+.. code-block:: python
+
+ from core.modules.vistrails_module import Module, newModule, \
+ NotCacheable, ModuleError
+ (...)
+ class StandardOutput(NotCacheable, Module):
+ """StandardOutput is a VisTrails Module that simply prints the
+ value connected on its port to standard output. It is intended
+ mostly as a debugging device."""
+
+ def compute(self):
+ v = self.getInputFromPort("value")
+ print v
+
+By subclassing from ``NotCacheable`` and ``Module`` (or one of its subclasses), we are telling VisTrails not to cache this module, or anything downstream from it.
+
+VisTrails also allows a more sophisticated decision on whether or not to use caching. To do that, a user simply overrides the method ``is_cacheable`` to return the appropriate value (the default implementation returns ``True``). For example, in the `teem <http://teem.sourceforge.net/>` package, there's a module that generates a scalar field with random numbers. This is non-deterministic, so shouldn't be cached. However, this module only generates non-deterministic values in special occa [...]
+
+.. code-block:: python
+
+ class Unu1op(Unu):
+ (...)
+ def is_cacheable(self):
+ return not self.getInputFromPort('op') in ['rand', 'nrand']
+ (...)
+
+Notice that the module explicitly uses inputs to decide whether it should be cached. This allows reasonably fine-grained control over the process.
+
+Customizing Modules and Ports
+=============================
+
+.. index::
+ pair: Module registry; ``-output_ports``
+ pair: Module registry; ``_input_ports``
+ pair: Module registry; ``_modules``
+
+Here we will explore the options for registry initialization of modules and ports which was introduced in Section :ref:`sec-packages-simple_example`. There is a new syntax for specifying modules in packages:
+
+.. code-block:: python
+ :linenos:
+
+ _modules = [MyModule1, (MyModule2, {'option_name' : 'value'})]
+
+Observe that ``_modules`` is assigned a list of modules to be registered, and module options can be provided as keyword arguments by specifying a tuple (class, kwargs). Similarly, ports are defined by providing a list of tuples of the form (portName, portSignature, optional=False, sort_key=-1). For example:
+
+.. code-block:: python
+ :linenos:
+
+ class MyModule(Module):
+ def compute(self):
+ pass
+
+ _input_ports = [('firstInput', String), ('secondInput', Integer, True)]
+ _output_ports = [('firstOutput', String), ('secondOutput', String)]
+
+.. index::
+ pair: port; shortcut
+
+Notice that "String" and "Integer" were used for the portSignature instead of ``org.vistrails.vistrails.basic:String`` and ``org.vistrails.vistrails.basic:Integer``. That is because the current package, ``org.vistrails.vistrails.basic`` is used by default.
+
+.. topic:: Note
+
+ The old syntax (reg.add_module(...), reg.add_input_port(...), and reg.add_output_port(...)) is still supported.
+
+Configuring Modules
+^^^^^^^^^^^^^^^^^^^
+
+.. index::
+ pair: packages; modules
+ pair: modules; visibility
+ pair: modules; namespaces
+
+**Hierarchy and Visibility** There are a few options that assist in the organization and display of modules: ``namespace``, ``abstract``, and ``hide_descriptor``. The ``namespace`` option can be used to define a hierarchy in the module palette, which hierarchies can be nested through the use of the '|' character. For example:
+
+.. code-block:: python
+ :linenos:
+
+ _modules = [MyModule1, (MyModule2, {'namespace': 'MyNamespace'})]
+ or
+ _modules = [MyModule1, (MyModule2, {'namespace': 'ParentNamespace|\
+ ChildNamespace'})]
+
+The other options, ``abstract`` and ``hide_descriptor`` can be used to prevent modules from appearing in the module palette. ``Abstract`` is for use with modules that should never be instantiated in the workflow and will not add the item to the module palette. On the other hand, ``hide-descriptor`` will add the item to the palette, but hides it. This will prevent users from adding the module to a pipeline, but allow code to add it programmatically. To use either of these options, ``a [...]
+
+.. code-block:: python
+ :linenos:
+
+ _modules = [AnotherModule, (InvisibleModule, {'abstract': True})]
+ or
+ _modules = [AnotherModule, (InvisibleModule, {'hide-descriptor': True})]
+
+.. index::
+ pair: modules; shape
+ pair: modules; color
+
+**Defining Module Shapes and Colors** VisTrails allows users to define custom colors and shapes to modules. This must be done at module registration time, by using the ``moduleColor`` and ``moduleFringe`` options. For example:
+
+.. code-block:: python
+
+ _modules = [(Afront, {'moduleColor' : (1.0, 0.0, 0.0),
+ 'moduleFringe' : [(0.0, 0.0),
+ (0.2, 0.0),
+ (0.2, 0.4),
+ (0.0, 0.4),
+ (0.0, 1.0)]})]
+
+.. reg.addModule(Afront,
+ moduleColor=(1.0,0.0,0.0),
+ moduleFringe=[(0.0, 0.0),
+ (0.2, 0.0),
+ (0.2, 0.4),
+ (0.0, 0.4),
+ (0.0, 1.0)])
+
+gives:
+
+.. figure:: figures/packages/CustomColorShape1.png
+ :align: center
+ :width: 2in
+
+and
+
+.. code-block:: python
+
+ _modules = [(Afront, {'moduleColor': (0.4,0.6,0.8),
+ 'moduleFringe' : [(0.0, 0.0),
+ (0.2, 0.0),
+ (0.0, 0.2),
+ (0.2, 0.4),
+ (0.0, 0.6),
+ (0.2, 0.8),
+ (0.0, 1.0)]})]
+
+.. reg = core.modules.module_registry
+.. reg.addModule(Afront,
+ moduleColor=(0.4,0.6,0.8),
+ moduleFringe=[(0.0, 0.0),
+ (0.2, 0.0),
+ (0.0, 0.2),
+ (0.2, 0.4),
+ (0.0, 0.6),
+ (0.2, 0.8),
+ (0.0, 1.0)])
+
+gives:
+
+.. figure:: figures/packages/CustomColorShape2.png
+ :align: center
+ :width: 2in
+
+The moduleColor parameter must be a tuple of three floats between 0 and 1 that specify RGB colors for the module background, while moduleFringe is a list of pairs of floats that specify points as they go around a side of the module (the same one is used to go from the top-right corner to bottom-right corner, and from the bottom-left corner to the top-left one. If this is not enough, let the developers know!)
+
+Alternatively, you can use different fringes for the left and right borders:
+
+.. code-block:: python
+
+ _modules = [(Afront, {'moduleColor': (1.0,0.8,0.6),
+ 'moduleLeftFringe' : [(0.0, 0.0),
+ (-0.2, 0.0),
+ (0.0, 1.0)],
+ 'moduleRightFringe' : [(0.0, 0.0),
+ (0.2, 1.0),
+ (0.0, 1.0)]})]
+
+
+.. reg.addModule(Afront,
+ moduleColor=(1.0,0.8,0.6),
+ moduleLeftFringe=[(0.0, 0.0),
+ (-0.2, 0.0),
+ (0.0, 1.0)],
+ moduleRightFringe=[(0.0, 0.0),
+ (0.2, 1.0),
+ (0.0, 1.0)])
+
+.. figure:: figures/packages/CustomColorShape3.png
+ :align: center
+ :width: 2in
+
+Configuring Ports
+^^^^^^^^^^^^^^^^^
+
+.. index::
+ pair: packages; ports
+ pair: ports; default values
+ pair: ports; labels
+
+**Default Values and Labels** In versions 1.4 and greater, package developers can add labels and default values for parameters. To add this functionality, you need to use the defaults and labels keyword arguments and pass the values as strings. For example,
+
+.. code-block:: python
+ :linenos:
+
+ class TestDefaults(Module):
+ _input_ports = [('f1', '(org.vistrails.vistrails.basic:Float,\
+ org.vistrails.vistrails.basic:String)',
+ {"defaults": str([1.23, "abc"]),
+ "labels": str(["temp", "name"])})]
+ _modules = [TestDefaults]
+
+or in the older syntax,
+
+.. code-block:: python
+ :linenos:
+
+ def initialize():
+ reg = core.modules.module_registry.get_module_registry()
+ reg.add_module(TestDefaults)
+ reg.add_input_port(TestDefaults, "f1", [Float, String],
+ defaults=str([1.23, "abc"]),
+ labels=str(["temp", "name"]))
+
+.. index::
+ pair: ports; optional
+
+**Making a Port Optional** To add a port that is optional, set the optional flag to true:
+
+.. code-block:: python
+ :linenos:
+
+ _input_ports = [('MyPort', '(org.vistrails.vistrails.basic:String)',
+ {"optional": True})]
+
+ reg.add_input_port(MyModule, "MyPort",
+ "(org.vistrails.vistrails.basic:String)",
+ optional=True)
+
+
+.. index::
+ pair: ports; multiple inputs
+
+**Multiple Inputs** For compatibility reasons, we do need to allow multiple connections to an input port. However, most package developers should never have to use this, and so we do our best to hide it. the default behavior for getting inputs from a port, then, is to always return a single input.
+
+If on your module you need multiple inputs connected to a single port, use the 'forceGetInputListFromPort' method. It will return a list of all the data items coming through the port. The spreadsheet package uses this feature, so look there for usage examples (vistrails/packages/spreadsheet/basic_widgets.py)
+
+.. index::
+ pair: ports; port types
+
+**Port Types** To define ports to be of types that are not imported into the package, pass and identifier string as the portSignature:
+
+.. code-block:: python
+ :linenos:
+
+ <module_string> := <package_identifier>:[<namespace>|]<module_name>,
+ <port_signature> := (<module_string>*)
+
+For example,
+
+.. code-block:: python
+
+ registry.add_input_port(MyModule, 'myInputPort', \
+ '(org.vistrails.vistrails.basic:String)')
+
+or
+
+.. code-block:: python
+
+ _input_ports = [('myInputPort', '(org.vistrails.vistrails.basic:String)')]
+
+.. index::
+ pair: ports; input dependency
+
+**Varying Output According to the Input** There are a few ways to tackle this - each has it's own benefits and pitfalls. Firstly, module connections do respect class hierarchies as we're familiar with in object oriented languages. For instance, A module can output a Constant of which String, Float, Integer, etc are specifications. In this way, you can have a subclass of something like MyData be passed out of the module and the connections will be established regardless of the sub-type. T [...]
+
+A second method that is employed in several different packages is the idea of a container class. For instance, the NumSciPy package uses a relatively generic container "Numpy Array" to encapsulate the data. Of course, these encapsulating objects can store dictionaries that other modules can easily access and understand how to operate on. Although this method is slightly more work, the benefits of a stricter typing of ports is beneficial - particularly upon interfacing with other packages [...]
+
+.. index::
+ pair: ports; module connectivity
+
+**Determining Whether or Not a Module is Attached to an Output Port** The outputPorts dictionary of the base Module stores connection information. Thus, you should be able to check
+
+``("myPortName" in self.outputPorts)``
+
+on the parent module to check if there are any downstream connections from the port "myPortName". This might be used, for example, to only set results for output ports that will be used. **Note**, however, that the caching algorithm assumes that all outputs are set so adding a new connection to a previously unconnected output port will not work as desired if that module is cached. For this reason, I would currently recommend making such a module not cacheable. Another possibility is over [...]
+
+.. code-block:: python
+ :linenos:
+
+ class TestModule(Module):
+ _output_ports = [('a1', '(org.vistrails.vistrails.basic:String)'),
+ ('a2', '(org.vistrails.vistrails.basic:String)')]
+ def __init__(self):
+ Module.__init__(self)
+ self._cached_output_ports = set()
+
+ def update(self):
+ if len(set(self.outputPorts) - self._cached_output_ports) > 0:
+ self.upToDate = False
+ Module.update(self)
+
+ def compute(self):
+ if "a1" in self.outputPorts:
+ self.setResult("a1", "test")
+ if "a2" in self.outputPorts:
+ self.setResult("a2", "test2")
+ self._cached_output_ports = set(self.outputPorts)
+
+Generating Modules Dynamically
+==============================
+
+.. index::
+ pair: modules; dynamic
+
+When wrapping existing libraries or trying to generate modules in a more procedural manner, it is useful to dynamically generate modules. In our work, we have created some shortcuts to make this easier. In addition, the list of modules can also be based on the package configuration. Here is some example code:
+
+**__init__.py**
+
+.. code-block:: python
+ :linenos:
+
+ from core.configuration import ConfigurationObject
+
+ identifier = "org.vistrails.dakoop.auto_example"
+ version = "0.0.1"
+ name = "AutoExample"
+
+ configuration = ConfigurationObject(use_b=True)
+
+**init.py**
+
+The expand_ports and build_modules methods are functions to help the construction of the modules easier. The key parts are the new_module call and setting the _modules variable.
+
+.. code-block:: python
+ :linenos:
+
+ from core.modules.vistrails_module import new_module, Module
+
+ identifier = "org.vistrails.dakoop.auto_example"
+
+ def expand_ports(port_list):
+ new_port_list = []
+ for port in port_list:
+ port_spec = port[1]
+ if type(port_spec) == str: # or unicode...
+ if port_spec.startswith('('):
+ port_spec = port_spec[1:]
+ if port_spec.endswith(')'):
+ port_spec = port_spec[:-1]
+ new_spec_list = []
+ for spec in port_spec.split(','):
+ spec = spec.strip()
+ parts = spec.split(':', 1)
+ print 'parts:', parts
+ namespace = None
+ if len(parts) > 1:
+ mod_parts = parts[1].rsplit('|', 1)
+ if len(mod_parts) > 1:
+ namespace, module_name = mod_parts
+ else:
+ module_name = parts[1]
+ if len(parts[0].split('.')) == 1:
+ id_str = 'org.vistrails.vistrails.' + parts[0]
+ else:
+ id_str = parts[0]
+ else:
+ mod_parts = spec.rsplit('|', 1)
+ if len(mod_parts) > 1:
+ namespace, module_name = mod_parts
+ else:
+ module_name = spec
+ id_str = identifier
+ if namespace:
+ new_spec_list.append(id_str + ':' + module_name + \
+ ':' + namespace)
+ else:
+ new_spec_list.append(id_str + ':' + module_name)
+ port_spec = '(' + ','.join(new_spec_list) + ')'
+ new_port_list.append((port[0], port_spec) + port[2:])
+ print new_port_list
+ return new_port_list
+
+ def build_modules(module_descs):
+ new_classes = {}
+ for m_name, m_dict in module_descs:
+ m_doc = m_dict.get("_doc", None)
+ m_inputs = m_dict.get("_inputs", [])
+ m_outputs = m_dict.get("_outputs", [])
+ if "_inputs" in m_dict:
+ del m_dict["_inputs"]
+ if "_outputs" in m_dict:
+ del m_dict["_outputs"]
+ if "_doc" in m_dict:
+ del m_dict["_doc"]
+ klass_dict = {}
+ if "_compute" in m_dict:
+ klass_dict["compute"] = m_dict["_compute"]
+ del m_dict["_compute"]
+ m_class = new_module(Module, m_name, klass_dict, m_doc)
+ m_class._input_ports = expand_ports(m_inputs)
+ m_class._output_ports = expand_ports(m_outputs)
+ new_classes[m_name] = (m_class, m_dict)
+ return new_classes.values()
+
+ def initialize():
+ global _modules
+ def a_compute(self):
+ a = self.getInputFromPort("a")
+ i = 0
+ if self.hasInputFromPort("i"):
+ i = self.getInputFromPort("i")
+ if a == "abc":
+ i += 100
+ self.setResult("b", i)
+
+ module_descs = [("ModuleA", {"_inputs": [("a", "basic:String")],
+ "_outputs": [("b", "basic:Integer")],
+ "_doc": "ModuleA documentation",
+ "_compute": a_compute,
+ "namespace": "Test"}),
+ ("ModuleB", {"_inputs": [("a", "Test|ModuleA")],
+ "_outputs": [("b", "Test|ModuleA")],
+ "_doc": "ModuleB documentation"})
+ ]
+
+ if configuration.use_b:
+ _modules = build_modules(module_descs)
+ else:
+ _modules = build_modules(module_descs[:1])
+
+ _modules = []
+
+For System Administrators
+=========================
+Most users will want to put their custom packages in their
+
+ :math:`\sim`\ ``/.vistrails/userpackages``
+
+directory, as described in Section :ref:`sec-packages-simple_example`. This makes the package available to the current user only. However, if you are a power user or a system administrator, you may wish to make certain packages available to all users of a |vistrails| installation. To do this, copy the appropriate package files and/or directories to the
+
+ ``vistrails/packages``
+
+directory of the |vistrails| distribution.
+The packages will be made visible to users the next time they launch |vistrails|.
+
+.. %Advanced: Wrapping a big API
+.. ============================
+.. %In the future, there will be a walkthrough of the VTK package wrapping mechanism.
+
+.. rubric:: Footnotes
+.. [#] This package is not included in binary distributions of |vistrails|, but is available in the source code distribution. The stand-alone ``Afront`` utility is available at http://afront.sourceforge.net.
+.. [#] Programmers who are more comfortable with single-inheritance languages like Java and C# may be unfamiliar with mixins. A mixin class is similar to an *interface* in Java or C#, except that a mixin provides an implementation as well. Python's support for multiple inheritance allows subclasses to "import" functionality as needed from a mixin class, without artificially cluttering the base class's interface.
diff --git a/doc/usersguide/parallelflow.rst b/doc/usersguide/parallelflow.rst
new file mode 100644
index 0000000..d9d33b0
--- /dev/null
+++ b/doc/usersguide/parallelflow.rst
@@ -0,0 +1,71 @@
+.. _chap-parallelflow:
+
+**************************
+Parallel Flow in VisTrails
+**************************
+
+When dealing with large datasets, the ability to leverage multiple cores or
+machines allows to speed up workflow execution time. VisTrails provides
+support for parallelization of tasks using IPython_.
+
+.. _IPython: http://ipython.org/
+
+Setting up an IPython cluster
+=============================
+
+This package uses the standard IPython.parallel machinery to execute jobs. You
+will need to create and configure the IPython profile that you want |vistrails|
+to use.
+
+|vistrails| is capable of running the ``ipcontroller`` and ``ipengine``
+commands for you to start a controller or a set of engines locally, but for
+more complex setups, you can run ``ipcluster`` yourself from a terminal with
+the necessary options.
+
+Interacting with the cluster
+============================
+
+In the ``Packages/Parallel Flow`` menu, you will find the following options:
+
+Start new engine processes
+ Use ``ipengine`` to start multiple new workers on the machine, using the
+ current IPython profile. These processes will be shutdown on exit, unless
+ detached using Cleanup
+
+Show information on the cluster
+ Indicates whether we are connected to an IPython controller, the number of
+ engines in the cluster, and which processes were started locally. Lists
+ some basic information on each engine.
+
+Change profile
+ Selects a different IPython profile. Performs cleanup first if a cluster
+ was connected.
+
+Cleanup started processes
+ Disconnects from the cluster and "forgets" the processes that were started
+ from |vistrails|. It is either possible to terminate them, or to leave them
+ running in the background (for example, to be reuse by the next |vistrails|
+ session).
+
+Request cluster shutdown
+ Sends the shutdown signal to the controller, regardless of whether it was
+ started locally or not. If accepted, the controller will ask every
+ connected engine to terminate and exit.
+
+Note that when VisTrails is exited, it will shutdown the engines that it
+started. If it started the controller, it will also be shutdown, along with
+every engine that might have connected to it from other machines. To prevent
+that, use the 'cleanup' button and choose not to stop them; they will detach
+from VisTrails and won't be killed automatically. You will still be able to use
+the 'cluster shutdown' button explicitely.
+
+The ``Map`` module
+==================
+
+``Map`` allows you to execute a single module or a ``Group`` in parallel using
+input values taken from a list. It works in exactly the same way as the regular
+``Map`` module from the :ref:`Control Flow <chap-controlflow>` package.
+
+Contrary to the standard ``Map`` module, the elements of the list will be
+submitted to the IPython controller which will execute them in a load-balanced
+manner on the engines currently connected.
diff --git a/doc/usersguide/parallelization.rst b/doc/usersguide/parallelization.rst
new file mode 100644
index 0000000..0bd840c
--- /dev/null
+++ b/doc/usersguide/parallelization.rst
@@ -0,0 +1,56 @@
+.. _chap-parallelization:
+
+******************************************
+Using parallelization in VisTrails modules
+******************************************
+
+This chapters presents different techniques for using parallelization inside
+the code of your |vistrails| modules.
+
+Threading
+=========
+
+|vistrails| is single-threaded: the modules are executed one after the other,
+and while you are free to use threads in your module's ``compute()`` method,
+you should not interact with |vistrails| from other threads.
+
+Note that because of the restrictions of the CPython interpreter, you might not
+improve performance by using this type of parallelization: the interpreter has
+a lock, preventing two threads from executing Python code at the same time. If
+you are not already, consider using packages such as NumPy_ which provides
+efficient numerical functions implemented in C (and parallelizable).
+
+.. _NumPy: http://www.numpy.org/
+
+Multiprocessing
+===============
+
+Use of the ``multiprocessing`` package introduced with Python 2.6 is possible
+in |vistrails|. This is generally the preferred way of performing multiple
+computational tasks in parallel in Python, and will effectively leverage
+multiple cores; please refer to the `official documentation
+<http://docs.python.org/2/library/multiprocessing.html>`_ for more details.
+
+IPython
+=======
+
+You can access IPython clusters through the :ref:`Parallel Flow
+<chap-parallelflow>` package, via the provided API. Simply declare it in your
+package's dependencies, and import ``vistrails.packages.parallelflow.api``.
+This module provides the following:
+
+``get_client(ask=True) -> IPython.parallel.Client or None``
+ Low-level function giving you a Client connected to the cluster, or None.
+ If not connected to a cluster or if no engines are available, the ``ask``
+ parameter controllers whether to offer the user to take automatic action.
+
+``direct_view(ask=True) -> IPython.parallel.DirectView or None``
+ Gives you a view on the engines of the cluster, which you can use to submit
+ tasks. This is currently equivalent to calling ``get_client()[:]``.
+
+ You should probably use ``load_balanced_view()`` instead.
+
+``load_balanced_view(ask=True) -> IPython.parallel.LoadBalancedView or None``
+ Gives you a load-balanced view on the engines of the cluster, which you can *
+ use to submit tasks. It is the preferred way of submitting tasks. This is
+ currently equivalent to calling ``get_client().load_balanced_view()``.
diff --git a/doc/usersguide/parameter_exploration.rst b/doc/usersguide/parameter_exploration.rst
new file mode 100644
index 0000000..82b64f0
--- /dev/null
+++ b/doc/usersguide/parameter_exploration.rst
@@ -0,0 +1,315 @@
+.. _chap-paramexploration:
+
+***********************
+Parameter Exploration
+***********************
+
+.. index::
+ single: parameter exploration
+ pair: parameters; exploring
+
+.. index{parameters!exploring|see{parameter exploration}}
+
+.. %README: This chapter contains a lot of figures. Despite LaTeX's best
+.. %efforts to make the figures and the text "play nice" together, I had
+.. %to insert a few manual pagebreaks to make the layout more smooth.
+.. %Feel free to remove or move them when this chapter gets revised again.
+.. %(draperg 29may2008)
+
+While exploring workflows, one critical task is tweaking parameter
+values to improve simulations or visualizations. |vistrails| contains
+an integrated parameter exploration interface that lets you
+thoroughly explore the parameter space and quickly identify the
+desired settings. By binding parameters to a range of values, you
+can generate a collection of results without having to tediously edit
+the workflow.
+
+.. index::
+ pair: parameter exploration; spreadsheet
+ pair: spreadsheet; parameter exploration
+ single: animation
+
+|vistrails| Parameter Exploration is Spreadsheet-aware, so you can map the
+intermediate results from explorations into cells of the Spreadsheet.
+Because the Spreadsheet provides a multi-view interface that
+makes efficient use of screen space, you can quickly compare the
+results of different parameter settings. The changes in parameters
+can be displayed across rows, columns, and sheets. In addition, parameters can be explored across timesteps, and then displayed in the Spreadsheet as animations. This could be used, for example, to show how pathological tissues and tumors are affected by radiation treatment in a series of scans.
+
+Creating a Parameter Exploration
+================================
+
+To access |vistrails| Parameter Exploration for the currently-active workflow, click
+on the ``Exploration`` button in the |vistrails| toolbar.
+
+The ``Parameter Exploration`` view starts out with a blank central canvas wherein
+exploration parameters can be set up. On the right side of
+the window, there are a variety of panels that control aspects of the
+exploration.
+
+The ``Set Methods`` panel contains the list of parameters that can
+be explored, the ``Annotated Pipeline`` panel displays
+the workflow to be explored and helps resolve ambiguities for parameter
+settings, and the ``Spreadsheet Virtual Cell`` aids users in
+laying out exploration results in the spreadsheet.
+
+.. %(shown in Figure :ref:`fig-fig6_1})
+.. %(See Figure :ref:`fig-paramexp-panels` for a close-up view of each of these panels.)
+.. %.. figure::[h]
+.. % :align: center
+.. % :width=0.7\linewidth,clip=false]{fig6_1.png}}
+.. % Parameter Exploration View}
+.. %.. _fig-fig6_1}
+.. %
+
+.. index::
+ pair: parameter exploration; adding parameters
+
+To add parameters to
+an exploration, simply drag the corresponding method from the
+``Set Methods`` panel to the center canvas. To reduce
+clutter, this panel only shows the methods for which parameters were
+assigned values in the ``Pipeline`` view. See
+Chapter :ref:`chap-creating` for instructions on adding methods and
+parameters to a module.
+
+.. index::
+ pair: parameter exploration; setting values
+
+After dragging a method to the exploration canvas, you can, for each parameter, set the
+collection of values to be explored and the direction in which to
+explore (Figure :ref:`Setting values for parameter exploration <fig-paramexp-adding>`).
+By default, intermediate parameter values are set via linear interpolation. We will discuss other options later.
+
+.. _fig-paramexp-adding:
+
+.. figure:: figures/parameter_exploration/fig6_6.png
+ :align: center
+ :width: 6in
+
+ Setting values for parameter exploration.
+
+.. index::
+ pair: parameter exploration; running
+ pair: parameter exploration; directions
+
+The five column headings in the upper-right corner of the
+main canvas control how the results of the parameter exploration will be displayed in the Spreadsheet. From left to right, the five controls determine:
+
+.. |dirx| image:: figures/parameter_exploration/direction_button_x.png
+ :width: 0.5in
+
+.. |diry| image:: figures/parameter_exploration/direction_button_y.png
+ :width: 0.5in
+
+.. |dirz| image:: figures/parameter_exploration/direction_button_z.png
+ :width: 0.5in
+
+.. |dirtime| image:: figures/parameter_exploration/direction_button_time.png
+ :width: 0.5in
+
+.. |dirno| image:: figures/parameter_exploration/direction_button_no.png
+ :width: 0.5in
+
++-------------+----------------------------------+
+| |dirx| | exploration in the 'x' direction |
++-------------+----------------------------------+
+| |diry| | exploration in the 'y' direction |
++-------------+----------------------------------+
+| |dirz| | exploration in the 'z' direction |
++-------------+----------------------------------+
+| |dirtime| | exploration in time |
++-------------+----------------------------------+
+| |dirno| | none; do not vary this parameter |
++-------------+----------------------------------+
+
+The spinner beneath each
+of these icons lets you control the number of parameter values to be explored in that direction. For each parameter, you must select one of
+the radio buttons corresponding to a direction of exploration ('x', 'y', 'z', time, or none). Note that choosing the final column disables
+exploration for that parameter.
+
+
+To run a parameter exploration,
+click the ``Execute`` button in the |vistrails| toolbar or
+select ``Execute`` from the ``Workflow`` menu.
+
+We now reinforce the above discussion with three examples, motivated by the problem of finding isosurfaces for medical imaging. In the examples that follow, we'll look at determining the interfaces between different types of tissue captured by CT scans.
+
+.. topic:: Try it now!
+
+ To begin, load the :vtl:`terminator.vt` vistrail, select the "Isosurface" node in the version tree, and switch to parameter exploration. From the ``Pipeline Methods`` panel, click and drag the ``SetValue`` method of the ``vtkContourFilter`` module to the center canvas.
+
+ We'd like to compare different values for the isosurfaces so change the start and end values of the "Float" parameter to "30" and "75". Since side-by-side visualization will look better on most monitors, select the radio button below the 'x' dimension control, and increase the value of the control to 2 (see Figure :ref:`Setting values for parameter exploration <fig-paramexp-adding>`). Execute the exploration and switch to the Spreadsheet to view the results. They should match Figure [...]
+
+.. _fig-paramexp-terminator2:
+
+.. figure:: /figures/parameter_exploration/fig6_7.png
+ :align: center
+ :height: 2.2in
+
+ Parameter Exploration of two isovalues as displayed in the Spreadsheet.
+
+.. topic:: Next Step!
+
+ While these two isovalues show interesting features, we may wish to examine other intermediate isosurfaces. To do so, switch back to the main |vistrails| window and increase the number of results to generate in the 'x' direction to four. |vistrails| will calculate the intermediate values via linear interpolation, and your execution of this new exploration should match Figure :ref:`Parameter Exploration of four isovalues... <fig-paramexp-terminator4>`. :vtl:`(Open result) <pe2.vt>`
+
+.. _fig-paramexp-terminator4:
+
+.. figure:: /figures/parameter_exploration/fig6_8.png
+ :align: center
+ :height: 2.2in
+
+ Parameter Exploration of four isovalues as displayed in the Spreadsheet.
+
+In our next example, we demonstrate how multiple parameter values can be explored simultaneously. We will use both ``X`` and ``Y`` exploration directions to change the values of two parameters at the same time in the same spreadsheet.
+
+.. topic:: Try it now!
+
+ In the :vtl:`terminator.vt` example vistrail, make sure you're working with the "Isosurface" version of the workflow, then go to the ``Pipeline`` view. Add the module ``vtkImageResample`` to the pipeline, and insert it between ``vtkStructuredPointsReader`` and ``vtkContourFilter``, connecting the output of the reader to input of the resampler and the output of the resampler to the input of the contour filter as shown in Figure :ref:`Inserting a vtkImageResample module... <fig-paramexp [...]
+ After modifying the workflow, switch back to the ``Exploration`` view. Inside the ``Set Methods`` panel, select the ``SetValue`` method from the ``vtkContourFilter`` module, and drag it to the center canvas. Also select the ``SetAxisMagnificationFactor`` method from the ``vtkImageResample`` module and drag it to the canvas. Set the values as in the previous example, and set the range of the "Float" parameter of "SetAxisMagnificationFactor" to start at 0.2 and end at 1.0. Also, set t [...]
+
+.. _fig-paramexp-vtk_image_resample:
+
+.. figure:: figures/parameter_exploration/vtkImageResample.png
+ :align: center
+ :width: 2in
+
+ Inserting a ``vtkImageResample`` module into the "terminator.vt" example pipeline.
+
+.. _fig-fig6_9:
+
+.. figure:: figures/parameter_exploration/fig6_9.png
+ :align: center
+ :width: 70%
+
+ Setting up parameter exploration.
+
+.. _fig-fig6_10:
+
+.. figure:: figures/parameter_exploration/fig6_10.png
+ :align: center
+ :width: 70%
+
+ Resulting spreadsheet.
+
+ Using parameter exploration with two parameters.
+
+Our third example shows how to create an animation by exploring parameter values in *time*, rather than in 'X' or 'Y'.
+
+.. index:: animation
+
+.. topic:: Try it now!
+
+ To create an animation, we'll use the same :vtl:`terminator <terminator.vt>` example (make sure that you have the "Isosurface" version selected). Follow the same steps as in the first example, but this time, use the range from 30 to 80 and select "time" as the dimension to explore, setting the number of results to generate to 7. See Figure :ref:`Setting up parameter exploration <fig-fig6_11>` to check your settings. After executing, the Spreadsheet will show a *single* cell, but if [...]
+
+.. _fig-fig6_11:
+
+.. figure:: figures/parameter_exploration/fig6_11.png
+ :align: center
+ :width: 5.99in
+
+ Setting up parameter exploration.
+
+.. _fig-fig6_12:
+
+.. figure:: figures/parameter_exploration/fig6_12.png
+ :align: center
+ :width: 50%
+
+ One frame from the resulting animation.
+
+Alternatives to Linear Interpolation
+====================================
+
+In each of the examples above, we used linear interpolation to vary the parameter values in 'X' and 'Y' and time. However, linear interpolation is only one of three methods for exploring a range of parameter values. The other two are to iterate through a simple list of values, or use a user-defined function. You can choose the desired method
+from the drop-down menu on the right side of the parameter input field (Figure :ref:`Choose from linear interpolation, list, or user-defined function <fig-paramexp-popup_menu>`).
+For linear interpolation, the starting and ending values must be
+specified; for a list, the entire comma-separated list must be
+specified, and for a user-defined function, a Python function must be
+specified. For the list and user-defined functions, you can access an
+editor via the '...' button. (See Figure :ref:`Editors for lists of values <fig-paramexp-edit_dialogs>` for examples of the list editor and Python editor widgets.) As an alternative to the list editor,
+you can manually enter a list using Python notation; for example,
+``[30, 36, 45, 75]``. As before, to set the direction in which to explore a
+given parameter, simply select the radio button in the column for the
+specified direction.
+
+.. _fig-paramexp-popup_menu:
+
+.. figure:: figures/parameter_exploration/popup_menu.png
+ :align: center
+ :width: 2in
+
+ Choose from linear interpolation, list, or user-defined function.
+
+.. _fig-paramexp-edit_dialogs:
+
+.. figure:: figures/parameter_exploration/list_edit.png
+ :align: center
+ :height: 2in
+
+ Editors for lists of values.
+
+.. figure:: figures/parameter_exploration/user_func_edit.png
+ :align: center
+ :height: 2in
+
+ Editors for user-defined functions.
+
+In both the ``Set Methods`` and ``Annotated Pipeline`` panels, you may see numbered red circles. See Figure :ref:`The panels of the Parameter Exploration window... <fig-paramexp-virtual_cell>` for an example of what this looks like.
+These circles appear when there is more than one module of a given type in
+a workflow. For each type satisfying this criteria, the instances are
+numbered and displayed so that you can identify which part of the
+pipeline a module in the ``Set Methods`` panel corresponds
+to.
+
+.. _fig-paramexp-panels:
+
+.. figure:: figures/parameter_exploration/set_methods.png
+ :align: center
+ :width: 2.0in
+
+.. figure:: figures/parameter_exploration/annotated_pipeline.png
+ :align: center
+ :width: 2.0in
+
+.. _fig-paramexp-virtual_cell:
+
+.. figure:: figures/parameter_exploration/virtual_cell.png
+ :align: center
+ :width: 2.0in
+
+ The panels of the Parameter Exploration window. ``Set Methods`` (Top) will appear in the right panel and the others will be on the left. The numbered red circles in the ``Annotated Pipeline`` (Middle) distinguish duplicate modules, and the cells in the ``Spreadsheet Virtual Cell`` (Bottom) determine the layout for spreadsheet results.
+
+"Virtual Cell" Layout
+=====================
+
+.. index::
+ pair: spreadsheet; parameter exploration
+ pair: spreadsheet; virtual cell
+
+As stated earlier, the Spreadsheet provides integrated support
+for parameter explorations. Each of the directions of exploration
+corresponds to a visual dimension in the spreadsheet: the 'x'
+direction corresponds to columns; the 'y' direction to rows; the
+'z' direction to sheets; and time to animations. However, when
+a workflow already outputs to more than one cell, you can layout the
+group of cells as it will be replicated during the exploration. For
+example, given a workflow with two output cells and an exploration for
+three parameter values in the 'x' direction, the resulting
+spreadsheet could be :math:`1\times6` or :math:`2\times3`. The
+``Spreadsheet Virtual Cell`` panel controls the layout of
+the pattern. Drag and drop cells to position them. See
+Figures :ref:`The panels of the Parameter Exploration window (Bottom) <fig-paramexp-virtual_cell>` and :ref:`Results of the Virtual Cell arrangement <fig-paramexp-vc_results>`
+for an example.
+
+.. _fig-paramexp-vc_results:
+
+.. figure:: figures/parameter_exploration/fig6_3.png
+ :align: center
+ :width: 70%
+
+ Results of the Virtual Cell arrangement.
+
+.. %TODO insert an example here!
+
+.. index:: parameter exploration
diff --git a/doc/usersguide/persistence.rst b/doc/usersguide/persistence.rst
new file mode 100644
index 0000000..f65570a
--- /dev/null
+++ b/doc/usersguide/persistence.rst
@@ -0,0 +1,165 @@
+.. _chap-persistence:
+
+*************************
+Persistence in VisTrails
+*************************
+
+.. index::persistence
+
+The ``Persistence`` package in Vistrails helps improve reproducibility by associating versions of data files with their provenance, and minimize the need to rerun lengthy executions by keeping intermediate persistent files.
+Although, we will focus primarily on the use of persistent files, persistent directories are used in the same manner. The difference is that a persistent directory deals with multiple files within a directory rather than a single file.
+
+Getting Started With Persistence
+================================
+
+A persistent file is simply a file that is kept in a repository and identified by an id and version string and annotated with a signature and content hash. To begin, notice that there are three persistent file/directory types: input, intermediate, and output. It is helpful to understand the differences among these files as well as their distinguishing characteristics and configuration options.
+
+Input Files
+^^^^^^^^^^^
+
+.. index::
+ pair: persistent files; input
+
+To use a persistent input file, after dragging it onto the canvas, it is necessary to edit the configuration (Ctrl+E). For an input file, one can either create a new reference to an existing local file, or use a file that exists in the database. To create a new reference, select ``Create New Reference`` and either enter the path to the file, or select the folder icon on the right to browse local directories for a file. Then, give the file a name and any appropriate tags to help identi [...]
+
+.. topic:: Note
+
+ A new version of a persistent file is created each time its contents change. A persistent input file will always use the most recent version of a file if it is assigned to the root of the file tree.
+
+The ``PersitentInputFile`` module can also be used to read or write data directly from or to a local file. To use this feature, you will need to set ``localPath`` to point to a local file. This can be done in the Set Methods Panel, the Configuration Dialog, or by connecting a file to the localPath input port. Then, the local file will be read when readLocal is set to true and written when writeLocal is set to true. To do this using the Configuration Dialog, select ``Keep Local Versio [...]
+
+Output Files
+^^^^^^^^^^^^
+
+.. index::
+ pair: persistent files; output
+
+To use a persistent output file, after dragging it onto the canvas, it is necessary to edit the configuration (Ctrl+E). Notice that the Configuration Dialog for the output file is the same as that of the input file except that an option to ``Always Create New Reference`` exists. Selecting this new option will cause a new file to be created and added to the persistent store each time the workflow is executed. The new file does not get a name or tag, so it can be difficult to identify t [...]
+
+If you prefer to have a new version of the file created each time the workflow is changed rather than executed, you should choose either of the other options (``Create New Reference``, or ``Use Existing Reference``). The other two options and the option to read from or write to a local path are used in the same manner as with the input file. However, when the input file is read from a local path, it is not also read from the persistent store. In contrast, when an output file is writte [...]
+
+Intermediate Files
+^^^^^^^^^^^^^^^^^^
+
+.. index::
+ pair: persistent files; intermediate
+
+An intermediate file is the same as the output file except that its contents can be used in further calculations. Thus, lengthy computations upstream of the intermediate file will only be recalculated when the upstream workflow changes, but will not need to be rerun when only the downstream workflow changes. Intermediate files by default are set to always create a new reference. Since these files do not need to be manually annotated or named, configuration is optional, but is the same [...]
+
+Using the Output of One Workflow as Input for Another
+=====================================================
+
+You need to configure the persistence modules using the module's configuration dialog. After adding a PersistentOutputFile to the workflow, click on the triangle in the upper-right corner of the PersistentOutputFile, and select "Edit Configuration" from the menu that appears. In this dialog, select "Create New Reference" and give the reference a name (and any space-delimited tags). Upon running that workflow, the data will be written to the persistent store. In the second workflow where [...]
+
+Managing Files in the Store
+===========================
+
+You may manage the files in the store by selecting ``Packages -> Persistence -> Manage Store``. You are then free to save files from the store to local files, or delete files from the store. However, please be aware that files deleted from the store are not recoverable. Also, for versioned files, a specific version of a file can not be deleted without deleting all versions of that file. To delete all versions of the file, select the root version and press ``Delete``.
+
+Examples
+========
+
+.. topic:: Try it Now!
+
+ **Base Workflow**
+
+ 1) Drag the following modules to the canvas and connect them in the order in which they are named: ``HTTPFile``, ``vtkUnstructuredGridReader``, ``vtkDataSetMapper``, ``vtkActor``, ``vtkRenderer``, ``VTKRenderOffscreen``. Refer to Figure :ref:`Example 1.1 <fig-pers-example-base>` to ensure connections are correct.
+
+ 2) Select the ``HTTPFile`` module and set the url to:
+
+ http://www.vistrails.org/download/download.php?type=DATA&id=spx.vtk
+
+ 3) (Optional) Select the ``vtkRenderer`` module and select ``SetBackgroungWidget`` from the ``Module Information's`` ``Inputs`` tab. Select the background color of your choice.
+
+ **Persistent Output**
+
+ 4) Switch to the ``History`` view and tag the current version as "Base Workflow". Then, switch back to the pipeline view.
+
+ 5) Enable the persistence package.
+
+ 6) Drag the ``PersistentOutputFile`` module to the canvas and connect the output from ``VTKRenderOffscreen`` to its value port. See Figure :ref:`Example 1.2 <fig-pers-example-output>`.
+
+ 7) With the ``PersistentOutputFile`` module selected, press Ctrl-E to edit the module configuration.
+
+ 8) Select ``Create New Reference``, name it "persistence1_1", and give it a "Persistent Output" tag. Select ``Save``.
+
+ 9) Execute the workflow.
+
+ **Persistent Input**
+
+ 10) Switch to the History view again and tag the current version as "Persistent Output". Then, select the root of the version tree and go back to the pipeline view.
+
+ 11) Drag the ``PersistentInputFile`` and ``ImageViewerCell`` modules to the canvas and connect them. See Figure :ref:`Example 1.3 <fig-pers-example-input>`.
+
+ 12) Edit the configuration of the ``PersitentInputFile``. Select "Use Existing Reference" and select the file named "persistence1_1" with the "Persistent Output" tag. Select ``Save``. See Figure :ref:`Example 1.4 <fig-pers-example-conf>`.
+
+ 13) Execute the workflow. An image should be displayed in the VisTrails spreadsheet.
+
+ **Persistent Intermediate**
+
+ 14) Switch to the ``History`` view and tag the version with "Persistent Input", then select the "Base Workflow" version and switch to the pipeline view again.
+
+ 15) Drag the ``PersistentIntermediateFile`` and ``ImageViewerCell`` modules to the canvas and connect them as shown in Figure :ref:`Example 1.5 <fig-pers-example-intermediate>`.
+
+ 16) Execute the workflow.
+
+ 17) In the History view, tag the version with "Persistent Intermediate". See Figure :ref:`Example 1.6 <fig-pers-example-ver>`.
+
+ **Experimentation**
+
+ You can now change the background color in the "Persistent Output" version and execute the pipeline. The changes should show up when you execute the pipeline of the "Persistent Input" version. You can also change the background color in the "Persistent Intermediate" version, but this example merely demonstrates how to use the module. Performance increase will not be seen here due to the lack of lengthy computations.
+
+.. _fig-pers-example-base:
+
+.. |fig1| image:: figures/persistence/base.png
+ :align: top
+
+.. _fig-pers-example-output:
+
+.. |fig2| image:: figures/persistence/output.png
+ :align: top
+
++-----------------------+------------------------------------+
+| |fig1| | |fig2| |
++-----------------------+------------------------------------+
+| Example 1.1 - Base | Example 1.2 - Persistent Output |
+| Workflow - An example | File |
+| pipeline without | |
+| persistence. | |
++-----------------------+------------------------------------+
+
+
+.. _fig-pers-example-input:
+
+.. figure:: figures/persistence/input.png
+ :align: center
+ :width: 30%
+
+ Example 1.3 - Persistent Input File
+
+
+.. _fig-pers-example-conf:
+
+.. figure:: figures/persistence/reference.png
+ :align: center
+ :width: 100%
+
+ Example 1.4 - Selecting an existing reference
+
+
+.. _fig-pers-example-intermediate:
+
+.. figure:: figures/persistence/intermediate.png
+ :align: center
+ :width: 40%
+
+ Example 1.5 - Persistent Intermediate File
+
+
+.. _fig-pers-example-ver:
+
+.. figure:: figures/persistence/versions.png
+ :align: center
+ :width: 70%
+
+ Example 1.6 - The History Tree
diff --git a/doc/usersguide/preface.rst b/doc/usersguide/preface.rst
new file mode 100644
index 0000000..507dca6
--- /dev/null
+++ b/doc/usersguide/preface.rst
@@ -0,0 +1,45 @@
+
+
+*******
+Preface
+*******
+
+Welcome to the *VisTrails User's Guide*. This book has been updated for version 2.1 of the VisTrails software.
+
+VisTrails is a new scientific workflow management system developed at the University of Utah that provides support for data exploration and visualization. For an engineer or scientist, generating and evaluating hypotheses is an interactive process. With each change, a different, albeit related, workflow is created. VisTrails was designed to manage these rapidly-evolving workflows. By automatically managing the data, metadata, and the data exploration process, VisTrails allows you to focu [...]
+
+VisTrails is an open-source software system. You can contribute to
+VisTrails by sharing bug reports, bug fixes, and suggestions with the
+VisTrails community. The easiest way to get started is to sign up for
+the VisTrails Users mailing list. Instructions for doing this can be
+found on the VisTrails web site: www.vistrails.org.
+
+This book is divided into four parts. The first part, :doc:`Introduction
+to VisTrails </intro>`, provides instructions on how to download and install
+the VisTrails software, and introduces you to its user interface. The
+second and longest part, "Learning VisTrails by Example," consists
+of a number of tutorial chapters that guide you, step by step, through
+the features of VisTrails. We encourage you to try out these examples
+for yourself as you read this book. The third part provides information on additional features and packages. The forth and final part is the
+"Developer's Guide" and is intended for programmers who wish to add
+new features, packages, and modules to VisTrails.
+
+We hope that you will find VisTrails to be a useful tool towards
+automating and streamlining your workflows, leading to faster
+discoveries and deeper insight.
+
+For your convenience, the html version of this manual is also available at http://www.vistrails.org/usersguide.
+
+*About the figures:* VisTrails works across multiple platforms, and
+the screenshots shown in this manual reflect this. Hence, some of the
+images in this book may vary slightly from what you see on your
+system, depending on the look and feel of your platform.
+
+Acknowledgements
+================
+VisTrails research and development has
+been funded the Department of Energy SciDAC (VACET and SDM centers),
+the National Science Foundation (grants IIS-0746500, CNS-0751152,
+IIS-0713637, OCE-0424602, IIS-0534628, CNS-0514485, IIS-0513692,
+CNS-0524096, CCF-0401498, OISE-0405402, CCF-0528201, CNS-0551724), and
+IBM Faculty Awards (2005, 2006, 2007, and 2008).
diff --git a/doc/usersguide/preliminary.rst b/doc/usersguide/preliminary.rst
new file mode 100644
index 0000000..5321777
--- /dev/null
+++ b/doc/usersguide/preliminary.rst
@@ -0,0 +1,4 @@
+.. toctree::
+ :maxdepth: 1
+
+ preface
diff --git a/doc/usersguide/provenance.rst b/doc/usersguide/provenance.rst
new file mode 100644
index 0000000..681572d
--- /dev/null
+++ b/doc/usersguide/provenance.rst
@@ -0,0 +1,14 @@
+.. _chap-provenance_browser:
+
+******************
+Provenance Browser
+******************
+
+The ``Provenance Browser`` allows you to browse through all executions performed on a vistrail. When the ``Provenance`` mode is selected, executions are displayed in the ``Log Details`` panel on the right (see figure :ref:`Provenance Browser <fig-browser>`). Selecting an execution from the ``Log Details`` panel will display the pipeline with modules colored according to their execution results. Alternatively, this pipeline is displayed by double-clicking on the execution in the ``Work [...]
+
+.. _fig-browser:
+
+.. figure:: figures/provenance/browser.png
+ :width: 100%
+
+ Provenance Browser - *Left:* The ``Workspace`` has a button to enable/disable executions. When enabled, executions of each tagged version in the vistrail will appear when each respective version is expanded. *Right:* The ``Provenance Browser`` keeps track of all executions whether they belong to tagged versions or not. When selected, the color coded execution pipeline will appear in the center panel.
diff --git a/doc/usersguide/pythoncalc.rst b/doc/usersguide/pythoncalc.rst
new file mode 100644
index 0000000..cbc0758
--- /dev/null
+++ b/doc/usersguide/pythoncalc.rst
@@ -0,0 +1,208 @@
+.. % NB: Please don't break any of the long lines - Verbatim is picky about line breaks
+
+.. index::
+ pair: Module registry; ``addModule``
+ pair: packages; ``initialize``
+ pair: Module registry; ``addInputPort``
+ pair: Module registry; ``addOutputPort``
+ pair: modules; ``ModuleError``
+
+.. role:: red
+
+.. code-block:: python
+ :linenos:
+
+ import core.modules.module_registry
+ from core.modules.vistrails_module import Module, ModuleError
+
+ version = "0.9.0"
+ name = "PythonCalc"
+ identifier = "org.vistrails.vistrails.pythoncalc"
+
+ class PythonCalc(Module):
+ """PythonCalc is a module that performs simple arithmetic operations on its inputs."""
+
+ def compute(self):
+ v1 = self.getInputFromPort("value1")
+ v2 = self.getInputFromPort("value2")
+ result = self.op(v1, v2)
+ self.setResult("value", result)
+
+ def op(self, v1, v2):
+ op = self.getInputFromPort("op")
+ if op == '+': return v1 + v2
+ elif op == '-': return v1 - v2
+ elif op == '*': return v1 * v2
+ elif op == '/': return v1 / v2
+ else: raise ModuleError(self, "unrecognized operation: '%s'" % op)
+
+ ###############################################################################
+
+ def initialize(*args, **keywords):
+
+ # We'll first create a local alias for the module registry so that
+ # we can refer to it in a shorter way.
+ reg = core.modules.module_registry.registry
+
+ # VisTrails cannot currently automatically detect your derived
+ # classes, and the ports that they support as input and
+ # output. Because of this, you as a module developer need to let
+ # VisTrails know that you created a new module. This is done by calling
+ # function addModule:
+ reg.add_module(PythonCalc)
+
+ # In a similar way, you need to report the ports the module wants
+ # to make available. This is done by calling addInputPort and
+ # addOutputPort appropriately. These calls only show how to set up
+ # one-parameter ports. We'll see in later tutorials how to set up
+ # multiple-parameter plots.
+ reg.add_input_port(PythonCalc, "value1",
+ (core.modules.basic_modules.Float, 'the first argument'))
+ reg.add_input_port(PythonCalc, "value2",
+ (core.modules.basic_modules.Float, 'the second argument'))
+ # We declare this port as an enum, so that the user may only select one of
+ # the listed values
+ reg.add_input_port(PythonCalc, "op",
+ (core.modules.basic_modules.String, 'the operation'),
+ entry_types=['enum'], values=["['+', '-', '*', '/']"])
+ reg.add_output_port(PythonCalc, "value",
+ (core.modules.basic_modules.Float, 'the result'))
+
+.. .. code-block:: python
+ :linenos:
+
+ ###############################################################################
+ ##
+ ## Copyright (C) 2011-2014, NYU-Poly.
+ ## Copyright (C) 2006-2011, University of Utah.
+ ## All rights reserved.
+ ## Contact: contact at vistrails.org
+ ##
+ ## This file is part of VisTrails.
+ ##
+ ## "Redistribution and use in source and binary forms, with or without
+ ## modification, are permitted provided that the following conditions are met:
+ ##
+ ## - Redistributions of source code must retain the above copyright notice,
+ ## this list of conditions and the following disclaimer.
+ ## - Redistributions in binary form must reproduce the above copyright
+ ## notice, this list of conditions and the following disclaimer in the
+ ## documentation and/or other materials provided with the distribution.
+ ## - Neither the name of the University of Utah nor the names of its
+ ## contributors may be used to endorse or promote products derived from
+ ## this software without specific prior written permission.
+ ##
+ ## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ ## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+ ## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ ## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+ ## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ ## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ ## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ ## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ ## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+ ## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ ## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+ ##
+ ###############################################################################
+ """This package implements a very simple VisTrails module called
+ PythonCalc. This is intended as a simple example that can be referred
+ to by users to create their own packages and modules later.
+
+ If you're interested in developing new modules for VisTrails, you
+ should also consult the documentation in
+ core/modules/vistrails_module.py.
+ """
+
+ import core.modules
+ import core.modules.module_registry
+ from core.modules.vistrails_module import Module, ModuleError
+
+ ###############################################################################
+ # PythonCalc
+ #
+ # A VisTrails package is simply a Python class that subclasses from
+ # Module. For this class to be executable, it must define a method
+ # compute(self) that will perform the appropriate computations and set
+ # the results.
+ #
+ # Extra helper methods can be defined, as usual. In this case, we're
+ # using a helper method op(self, v1, v2) that performs the right
+ # operations.
+
+ class PythonCalc(Module):
+ """PythonCalc is a module that performs simple arithmetic operations
+ on its inputs."""
+
+ # This constructor is strictly unnecessary. However, some modules
+ # might want to initialize per-object data. When implementing your
+ # own constructor, remember that it must not take any extra
+ # parameters.
+ def __init__(self):
+ Module.__init__(self)
+
+ # This is the method you should implement in every module that
+ # will be executed directly. VisTrails does not use the return
+ # value of this method.
+ def compute(self):
+ # getInputFromPort is a method defined in Module that returns
+ # the value stored at an input port. If there's no value
+ # stored on the port, the method will return None.
+ v1 = self.getInputFromPort("value1")
+ v2 = self.getInputFromPort("value2")
+
+ # You should call setResult to store the appropriate results
+ # on the ports. In this case, we are only storing a
+ # floating-point result, so we can use the number types
+ # directly. For more complicated data, you should
+ # return an instance of a VisTrails Module. This will be made
+ # clear in further examples that use these more complicated data.
+ self.setResult("value", self.op(v1, v2))
+
+ def op(self, v1, v2):
+ op = self.getInputFromPort("op")
+ if op == '+':
+ return v1 + v2
+ elif op == '-':
+ return v1 - v2
+ elif op == '*':
+ return v1 * v2
+ elif op == '/':
+ return v1 / v2
+ # If a module wants to report an error to VisTrails, it should raise
+ # ModuleError with a descriptive error. This allows the interpreter
+ # to capture the error and report it to the caller of the evaluation
+ # function.
+ raise ModuleError(self, "unrecognized operation: '%s'" % op)
+
+ ###############################################################################
+ # the function initialize is called for each package, after all
+ # packages have been loaded. It it used to register the module with
+ # the VisTrails runtime.
+
+ def initialize(*args, **keywords):
+
+ # We'll first create a local alias for the module_registry so that
+ # we can refer to it in a shorter way.
+ reg = core.modules.module_registry
+
+ # VisTrails cannot currently automatically detect your derived
+ # classes, and the ports that they support as input and
+ # output. Because of this, you as a module developer need to let
+ # VisTrails know that you created a new module. This is done by calling
+ # function addModule:
+ reg.addModule(PythonCalc)
+
+ # In a similar way, you need to report the ports the module wants
+ # to make available. This is done by calling addInputPort and
+ # addOutputPort appropriately. These calls only show how to set up
+ # one-parameter ports. We'll see in later tutorials how to set up
+ # multiple-parameter plots.
+ reg.addInputPort(PythonCalc, "value1",
+ (core.modules.basic_modules.Float, 'the first argument'))
+ reg.addInputPort(PythonCalc, "value2",
+ (core.modules.basic_modules.Float, 'the second argument'))
+ reg.addInputPort(PythonCalc, "op",
+ (core.modules.basic_modules.String, 'the operation'))
+ reg.addOutputPort(PythonCalc, "value",
+ (core.modules.basic_modules.Float, 'the result'))
diff --git a/doc/usersguide/querying.rst b/doc/usersguide/querying.rst
new file mode 100644
index 0000000..bfadc67
--- /dev/null
+++ b/doc/usersguide/querying.rst
@@ -0,0 +1,230 @@
+.. _chap-querying:
+
+*************************
+Querying the Version Tree
+*************************
+
+.. role:: red
+
+.. index:: queries
+
+|vistrails| is designed for manipulating collections of workflows, and
+an integral part of this design is the ability to quickly search
+through these collections. |vistrails| provides two methods for
+querying vistrails and workflows. The first is a Query by Example
+interface which allows you to build query workflows and search for
+those with similar structures and parameters. The second is a
+textual interface with a straightforward syntax. For each interface,
+the results are *visual*: each matching version is
+highlighted in the ``History`` view, and if the query
+involves specific workflow characteristics, any matching entities are
+also highlighted in the ``Pipeline`` view for the current
+version.
+
+Query By Example
+================
+
+.. index::
+ pair: queries; by example
+
+One of the problems faced when trying to query a collection of
+workflows is the fact that structure is important. Suppose that you
+want to find only workflows where two modules are used in sequence.
+Instead of trying to translate this into a text-based syntax, it is
+easier to construct this relationship visually. |vistrails| provides such an
+interface which mirrors the ``Pipeline`` view, allowing
+you to construct a (partial) workflow to serve as the search criteria.
+
+To use the Query by Example interface, click on the
+``Search`` button on the toolbar. This view is extremely
+similar to the ``Pipeline`` view and pipelines can be built
+in a similar manner. Just like the ``Pipeline`` view,
+modules are added by dragging them from the list on the left side of
+the window, connections are added by clicking and dragging from a port
+on one module to a corresponding port on another module. Setting module parameters in this view will narrow the search to matching modules whose parameters fall within the specified range of values. Figure :ref:`Example pipeline in Search mode <fig-querying-query>` shows an example pipeline that has been built in the query builder.
+
+.. _fig-querying-query:
+
+.. figure:: figures/querying/query.png
+ :width: 3in
+ :align: center
+
+ Example pipeline in ``Search`` mode.
+
+.. %TODO what are the next few sentences actually trying to say?
+.. %, and parameters can be edited on the right-side of the window. One major difference between the ``Pipeline`` view and the ``Search`` view is that you can use comparison operations in parameter values. For example, instead of searching for a pipeline that contains a Float with a value of ``4.5``, you can search for a pipeline that contains a Float with a value ``'< 4.5'`` or ``'> 4.5'``.
+
+.. index::
+ pair: queries; viewing results
+
+The next step is to decide whether to search the ``Current Vistrail``, ``Current Workflow``, or all ``Open Vistrails``. The results of the first option are displayed on a version tree as well as in the ``Workspace`` panel. Non-matching versions in the version tree will be grayed out while matching versions will be displayed in the tree as normal. In contrast, the ``Workspace`` panel will display matching results and omit versions with no matches. Double-clicking a version from the `` [...]
+
+The remaining two options are ``Current Workflow`` and ``Open Vistrails``. The ``Current Workflow`` option is the simplest and will display the pipeline with matching modules highlighted. The ``Open Vistrails`` option will put all of its results in the ``Workspace`` panel, listing open vistrails with their matching versions. From here, double-clicking on a vistrail will bring up a version tree which emphasizes matching versions, or double-clicking on a version will bring up the assoc [...]
+
+After constructing a pipeline and selecting the appropriate search option, click the ``Execute`` button to begin the query. This button will be available as long as the query window is not empty. However, you may need to press the ``Back to Search`` button to return to the query window to re-execute.
+
+.. topic:: Note
+
+ You may leave the ``Query`` either through use of the toolbar or by pressing the ``Edit`` button. However, the search results will persist until the search is cleared (press ``Clear Search``), returning the workspace to its normal form.
+
+.. topic:: Try it now!
+
+ Let's practice making a simple query. Open the :vtl:`offscreen.vt` example vistrail. Click on the ``Search`` button to enter ``Search`` mode. Create a query like the one shown in Figure :ref:`Example pipeline in Search mode <fig-querying-query>` by dragging the modules ``SheetReference``, ``CellLocation``, and ``RichTextCell`` onto the Search canvas. (These modules can be found under the "|vistrails| Spreadsheet" header in the Modules panel.) Connect the input and output ports of the [...]
+
+
+.. _fig-querying-workspace:
+
+.. figure:: figures/querying/workspace_results.png
+ :align: center
+ :width: 2in
+
+ Workspace - The query results displayed in the workspace.
+
+.. _fig-querying-history:
+
+.. figure:: figures/querying/query2.png
+ :height: 3in
+ :align: center
+
+ History - Search results in the ``History`` view.
+
+.. _fig-querying-pipeline:
+
+.. figure:: figures/querying/query3.png
+ :height: 3in
+ :align: center
+
+ Pipeline - The results in the ``Pipeline`` view.
+
+Note that Query by Example provides the capability to iteratively
+refine searches by adding more criteria. For example, if you were
+interested in workflows that contain a certain module, you may find that
+such a query returns too many results. You could then refine the query
+to find only those workflows where the given module has a parameter
+setting that falls within a given range.
+This is done by specifying parameter values in the ``Methods`` panel on the right side of the window.
+One major difference between the ``Pipeline`` view and the ``Search`` view is that you can use comparison operations, such as '<' and '>', in parameter values. The following example illustrates this.
+
+.. topic:: Try it now!
+
+ Open the :vtl:`terminator.vt` example file, and enter ``Search`` mode. Drag the ``vtkActor`` module from the Modules panel onto the Search canvas. ``Execute`` the query, and see which versions of the workflow contain a ``vtkActor`` module. Select ``Back to Search`` to return to the ``Search`` view, select the ``vtkActor`` module, then select ``RotateZ`` method from the ``Module Information`` tab. In the ``RotateZ`` text field, select ``'>'`` and then enter '90'. When you ``Execute`` t [...]
+
+.. _fig-querying-vtkActor_example:
+
+.. figure:: figures/querying/query_vtkActor.png
+ :width: 3in
+ :align: center
+
+ Query result showing all workflows in the "terminator.vt" example that contain the module ``vtkActor``.
+
+.. figure:: figures/querying/query_vtkActor90.png
+ :width: 3in
+ :align: center
+
+ The same query refined to show only those workflows whose ``RotateZ`` value is greater than 90.
+
+Textual Queries
+===============
+
+.. %Removing this figure as the addition of the next example makes it redundant.
+.. %\begin{figure}
+.. %\centering
+.. %\includegraphics[width=3in]{query4.png}
+.. %\caption{A query made to find any changes made before February 21.}
+.. %\label{fig:querying:date}
+.. %\end{figure}
+
+.. index::
+ pair: queries; textual
+
+There are many ways to search for versions in the version tree using textual queries, but they all rely on a simple
+text box for input. Begin a search by selecting ``Search`` on the toolbar. The search box is at the top of the center panel and has a magnifying glass icon next to it. If you enter query text, |vistrails|
+will attempt to match logical categories, but if your query is more
+specific, |vistrails| has special syntax to markup the query.
+To execute a query, simply press the 'Enter' key after typing your query.
+
+.. raw:: latex
+
+ \linebreak
+
+.. %Figure :ref:`fig-querying-date` shows an example query.
+
+.. _tab-querying-syntax:
+
+.. table:: Syntax for querying specific information using textual queries.
+
+ ============== ================================================================
+ Search Type Syntax
+ ============== ================================================================
+ User name ``user:`` *user name*
+ Annotation ``notes:`` *phrase*
+ Tag ``name:`` *version tag*
+ Date ``before:`` *date* ``|`` *relative time*
+ \ ``after:`` *date* ``|`` *relative time*
+ ============== ================================================================
+
+.. topic:: Note
+
+ Since we allow regular expressions in our search box, question marks are treated as meta-characters. Thus, searching for "?" returns everything and "abc?" will return everything containing "abc". You need to use "\\?" instead to search for "?". So the search for "??" would be "\\?\\?".
+
+Table :ref:`tab-querying-syntax` lists the different ways to markup a
+query. Note that you can search by user name to see which changes a
+particular user has made, and also by date to see which changes were
+made in a specific time frame. When searching by date, you can search
+for all changes before or after a given date or an amount of time
+relative to the present. If searching for changes before or after a
+specific date, the date can be entered in a variety of formats. The
+simplest is '*day* *month* *year*,' but if the
+year is omitted, the current year is used. The month may be specified
+by either its full name or an abbreviation. For example, ``'before: 18 November 2004'`` and ``'after: 20 Dec'`` are both valid queries. If searching by relative time,
+you can prepend the amount of time relative to the present including
+the units to 'ago'. An example of this type of query is
+``'after: 30 minutes ago'``. The available units are seconds,
+minutes, hours, days, months, or years.
+
+You can concatenate simple search statements to create a compound
+query to search across different criteria or for a specific range.
+For example, to search for workflows whose tag includes
+``'brain'`` *and* were created by the user ``'johnsmith'``,
+the query would be ``'name: brain user: johnsmith'``. To search
+for all workflows created between April 1 and June 1, the query would
+be ``'after: April 1 before: June 1'``.
+
+.. topic:: Try it now!
+
+ Open the :vtl:`terminator.vt` example file, and enter ``Search`` mode. Let's look for all workflows that were created after November 24, 2010. In the search box in the ``Search`` panel, type ``'after: 24 nov 2010'`` and press 'Enter'. The expected result is shown in Figure :ref:`Results of a query to find any changes make after November 24, 2010 <fig-querying-july1>`.
+
+.. _fig-querying-july1:
+
+.. figure:: figures/querying/textquery.png
+ :width: 3.5in
+ :align: center
+
+ Results of a query to find any changes made after November 24, 2010.
+
+In addition, |vistrails| keeps track of the most recent textual
+queries, and repeating or clearing these queries can be accomplished by selecting the recent query from the dropdown menu attached to the search box. Finally, the 'X' button next to the search box will reset the query.
+
+.. _sec-querying-results:
+
+Refining the Results
+^^^^^^^^^^^^^^^^^^^^
+
+.. %TODO consider dropping this section, and merging its content into the other sections.
+
+.. index:: search; refine
+
+While in the ``Search`` view, you can select two different
+ways of viewing search results. The magnifying glass icon to the left of the textual search box contains a dropdown menu with two options: "Search" and "Refine" (Figure :ref:`Clicking the button to the left... <fig-querying-search_or_refine>`). The first displays results by simply highlighting the matching nodes while the second condenses the tree to show only the versions that match. For large vistrails, this second method can help you determine relationships between the matching ver [...]
+
+.. %TODO I'm not sure that this button actually works as intended.
+
+.. _fig-querying-search_or_refine:
+
+.. figure:: figures/querying/search_or_refine.png
+ :width: 1.6in
+ :align: center
+
+ Clicking the button to the left of the query text box accesses a dropdown menu.
+
+.. index:: queries
diff --git a/doc/usersguide/spreadsheet.rst b/doc/usersguide/spreadsheet.rst
new file mode 100644
index 0000000..90bbb04
--- /dev/null
+++ b/doc/usersguide/spreadsheet.rst
@@ -0,0 +1,248 @@
+.. _chap-spreadsheet:
+
+***********
+Spreadsheet
+***********
+
+.. index:: spreadsheet
+
+.. _fig-spreadsheet:
+
+.. figure:: figures/spreadsheet/spreadsheet.png
+ :width: 5in
+ :align: center
+
+ The VisTrails Spreadsheet.
+
+As described in Section :ref:`sec-versions-diff`, |vistrails| has a
+powerful built-in mechanism to compare workflows. However, this
+comparison shows changes in the *design* of the workflows, and we
+are often also interested in differences in the *results* of
+workflows. The |vistrails| Spreadsheet provides a simple, flexible,
+and extensible interface to display and compare results from
+workflows. Coupled with the version differences, users can explore
+the evolution of their workflows.
+
+The Spreadsheet package is installed with |vistrails| by default, and
+it can display a variety of data ranging from VTK renderings to
+webpages without additional configuration. To view the spreadsheet if it is hidden, select ``Packages`` :math:`\rightarrow` ``Spreadsheet`` :math:`\rightarrow` ``Show Spreadsheet.``
+
+.. %% TODO add this sentence back in once the Custom Cell chapter is complete!
+.. %In addition to the included types of viewers, users can create and register additional viewers using customized cell widgets (see Chapter :ref:`chap-custom_cells`).
+
+.. _sec-spreadsheet-layout:
+
+The Spreadsheet Layout
+======================
+
+.. index::
+ pair: spreadsheet; layout
+
+As should be expected, the |vistrails| Spreadsheet consists of one or more sheets, each with a customizable number of rows and columns.
+
+.. _sec-spreadsheet-custom:
+
+Custom Layout Options
+^^^^^^^^^^^^^^^^^^^^^
+
+.. index::
+ pair: spreadsheet; rows
+ pair: spreadsheet; columns
+ pair: spreadsheet; cells
+
+To modify the layout for the active sheet, you can change both the number of rows and columns and resize individual cells. The number of rows is controlled by the left spinner in the toolbar and the number of columns by the right spinner. To resize a given row or column, click and drag on one edge of the row or column header. In addition, you can resize an individual cell by moving the mouse to lower-right corner of the cell until the cursor changes and clicking and dragging to the de [...]
+Figure :ref:`Different states of a spreadsheet cell \(d\) <fig-cell_states>`). Note that this will affect the entire
+layout, compressing or expanding rows and columns to generate or fill
+space for the resized cell.
+
+.. index::
+ pair: spreadsheet; default values
+
+To adjust the default number of rows and columns in the spreadsheet: select ``preferences`` from the ``VisTrails`` menu, select ``spreadsheet`` from the ``Enabled Packages`` portion of the ``Module Packages`` tab, press the ``Configure`` button, and adjust the values as for rowCount and colCount as desired.
+
+Multiple Spreadsheets
+^^^^^^^^^^^^^^^^^^^^^
+
+.. index::
+ triple: spreadsheet; sheets; adding
+ triple: spreadsheet; sheets; deleting
+ triple: spreadsheet; sheets; docking
+ triple: spreadsheet; sheets; ordering
+
+|VisTrails| supports the use of multiple spreadsheets which can be added, docked, ordered and deleted. Sheets are added either by clicking the ``New Sheet`` button in the ``Spreadsheet`` toolbar or choosing the menu item with the same name from the ``Main`` menu. Each of these sheets can optionally be displayed as a dock widget separated from the main spreadsheet window by dragging its tab name out of the tab bar at the bottom of the spreadsheet, allowing multiple spreadsheets to be vi [...]
+
+Sending Output to the Spreadsheet
+=================================
+
+.. index::
+ triple: spreadsheet; cells; positioning
+
+Users may send results to the spreadsheet by using a spreadsheet cell. Upon inspecting the VisTrails Spreadsheet package (in the list of packages, to the left of the pipeline builder), one can see there are built-in cells for different kinds of data, e.g., RichTextCell to display HTML and plain text.
+
+By default, an unoccupied cell on the active sheet will be chosen to display the result. However, you can specify in the pipeline exactly where a spreadsheet cell will be placed by using CellLocation and SheetReference. CellLocation specifies the location (row and column) of a cell when connecting to a spreadsheet cell (VTKCell, ImageViewerCell, ...). Similarly, a SheetReference module (when connecting to a CellLocation) will specify which sheet the cell will be put on given its name, mi [...]
+
+Advanced Cell Options
+^^^^^^^^^^^^^^^^^^^^^
+
+.. index::
+ triple: spreadsheet; cells; creating
+
+The user can define new cell types to display application-specific data. For example, we have developed VtkCell, MplFigureCell, and OpenGLCell. It is possible to display pretty much anything on the Spreadsheet!
+
+Examples of writing cell modules can be found in: RichTextCell: packages/spreadsheet/widgets/richtext/richtext.py VTK: packages/vtk/vtkcell.py
+
+Here is the summary of some requirements on a cell widget:
+
+(1) It must be a Qt widget. It should inherit from spreadsheet_cell.QCellWidget in the spreadsheet package. Although any Qt Widget would work, certain features such as animation will not be available (without rewriting it).
+
+(2) It must re-implement the updateContents() function to take a set of inputs (usually coming from input ports of a wrapper Module) and display on the cells. VisTrails uses this function to update/reuse cells on the spreadsheet when new data comes in.
+
+(3) It needs a wrapper VisTrails Module (inherited from basic_widgets.SpreadsheetCell of the spreadsheet package). Inside the compute() method of this module, it may call self.display(CellWidgetType, (inputs)) to trigger the display event on the spreadsheet.
+
+
+Interacting with the Spreadsheet
+================================
+
+.. index::
+ pair: spreadsheet; modes
+
+Currently, there are two operating modes in the Spreadsheet: Interactive Mode and Editing Mode. Interactive Mode allows users to view and interact with the spreadsheet cells, while Editing Mode provides operations for manipulating cells. The modes can be toggled via the ``View`` menu or their corresponding keyboard shortcuts ('Ctrl-Shift-I') and ('Ctrl-Shift-E').
+
+Interactive Mode
+^^^^^^^^^^^^^^^^
+
+.. index::
+ triple: spreadsheet; modes; interactive
+
+In Interactive Mode, users can interact directly with the viewer for an individual cell, interact with multiple cells at once, or change the layout of the sheet. Because cells can differ in their contents, interacting with a cell changes based on the type of data displayed. For example, in a cell displaying VTK data (a ``VTKCell``), a user can rotate, pan, and zoom in or out using the mouse.
+
+.. index::
+ pair: spreadsheet; cells
+
+In a sheet, a cell can be both *active* and *selected*. There can only be one active cell, and that cell is highlighted by a yellow or grey border. Clicking on any cell will make it active. This active cell will respond to keyboard shortcuts as well as mouse input. In constrast to the active cell, one or more cells can be selected, and the active cell need not be selected. To select multiple cells, either click on a row or column heading to toggle selection or 'Ctrl'-click to add or [...]
+
+Depending on the cell type, additional controls may appear in the
+toolbar when a cell is activated. These controls affect only the
+active cell, and change for different cell types. As shown by
+Figure :ref:`Different states of a spreadsheet cell \(d\) <fig-cell_states>`, a cell optimized for rendering 2D images (a ``ImageViewerCell``) adds controls for resizing, flipping, and rotating the image in the active cell.
+
+.. _fig-cell_states:
+
+.. figure:: figures/spreadsheet/cell_states.png
+ :width: 6.5in
+ :align: center
+
+ Different states of a spreadsheet cell. \(a\) inactive and unselected, \(b\) active and unselected, \(c\) active and selected, \(d\) an active cell with its toolbar and resizer.
+
+The Camera
+++++++++++
+Spreadsheet cells that display VTK data typically are associated with a vtkRenderer, which is associated with a vtkCamera. If the camera is not assigned in the workflow, a default one is created. If the rendered geometry is not visible in the window, pressing 'r' will invoke the renderer's ResetCamera() command, which centers the geometry. Also, pressing 'i' will initiate interactions with interactive vtk objects.
+
+Arranging Cells
++++++++++++++++
+
+As described in Section :ref:`sec-spreadsheet-custom`, cells can be
+resized by either resizing rows, columns, or an individual cell. In
+addition to resizing, a row or column can be moved by clicking on its
+header and dragging it along the header bar to the desired position.
+See Section :ref:`sec-spreadsheet-editing` for instructions on moving a
+specific cell to a different location.
+
+Synchronizing Cells
++++++++++++++++++++
+
+Often, when a group of cells all display results from similar workflows, it is useful to interact with all of these cells at the same time. For example, for a group of ``VTKCells``, it is instructive to rotate or zoom in on multiple cells at once and compare the results. For this reason, if a group of cells is selected, mouse and keyboard events for a single cell of the selection are propogated to each of the other selected cells. Currently, this feature only works for ``VTKCells``, b [...]
+
+.. _fig-spreadsheet_sync:
+
+.. figure:: figures/spreadsheet/spreadsheet_sync.png
+ :width: 3in
+ :align: center
+
+ When selecting all cells, interacting with one VTK cell \(A1\) causes the other two VTK cells \(B1 and B2\) to change their camera to the same position.
+
+.. _sec-spreadsheet-editing:
+
+Editing Mode
+^^^^^^^^^^^^
+
+.. index::
+ triple: spreadsheet; modes; editing
+
+Recall that Editing Mode can be entered either by accessing the ``View`` menu or by keying 'Ctrl-Shift-E'. Editing Mode provides more
+operations to layout and organize spreadsheet cells. In this mode,
+the view for each cell is frozen and overlaid with additional
+information and controls (see Figure :ref:`The spreadsheet in editing mode... <fig-editing_mode>`). The top
+of the overlay displays information about which vistrail, version, and
+type of execution were used to generate the cell. The bottom piece of
+the overlay contains a variety of controls to manipulate the cell
+depending on the its state.
+
+Cells can be moved or copied to different locations on the spreadsheet
+by clicking and dragging the appropriate icons (``Move`` or
+``Copy``) for a given cell to its desired location. To move
+a cell to a location on a different sheet, drag the icon over the
+target sheet tab to bring that sheet into focus first and then drop it
+at the desired location. If you move a cell to an already-occupied
+cell, the contents of the two cells will be swapped. See
+Figure :ref:`The spreadsheet in editing mode... <fig-editing_mode>` for an example of swapping two cells.
+
+.. _fig-editing_mode:
+
+.. figure:: figures/spreadsheet/editing_mode.png
+ :width: 6.5in
+ :align: center
+
+ The spreadsheet in Editing Mode. \(a\) All cell widgets are replaced with an information widget \(b\) Two cells are swapped after drag and drop the 'Move' icon from A1 to B1.
+
+Clicking the ``Locate Version`` icon will highlight the node in the version tree (in the ``History`` view) from which the visualization in that cell was generated. The next two icons, ``Create Analogy`` and ``Apply Analogy``, help with creating visualizations by analogy. Please refer to Chapter :ref:`chap-analogies` for information about this feature.
+
+If a cell was generated via parameter exploration (see
+Chapter :ref:`chap-paramexploration`), the ``Create Version``
+button will be available to save the workflow that generated the
+result back to the vistrail. Clicking this button modifies the
+vistrail from which the cell was generated by adding a new version
+with the designated parameter settings. Thus, if you go back to the
+``History`` mode of the |vistrails| Builder for that
+vistrail, you will find that a new version has been added to the
+version tree.
+
+Launching a Web Browser
+=======================
+
+.. index::
+ triple: spreadsheet; cells; web browser
+
+It is sometimes difficult to view web pages within a spreadsheet cell due to limited space. It may therefore be desirable to launch a web browser from within the spreadsheet cell. While this functionality is not provided by |Vistrails|, here are some possible solutions:
+
+(1) You can use parameter exploration to generate multiple sheets so you might have an exploration that opens each page in a new sheet. Use the third column/dimension in the exploration interface to have a parameter span sheets.
+
+(2) The spreadsheet is extensible so you can write a custom spreadsheet cell widget that has a button or label with the desired link (a QLabel with openExternalLinks set to True, for example).
+
+(3) You can tweak the existing RichTextCell by adding the line "self.browser.setOpenExternalLinks(True)" at line 63 of the source file "vistrails/packages/spreadsheet/widgets/richtext/richtext.py". Then, if your workflow creates a file with html markup text like "<a href="http://www.vistrails.org">VisTrails</a>" connected to a RichTextCell, clicking on the rendered link in the cell will open it in a web browser. You need to add the aforementioned line to the source to let Qt know that yo [...]
+
+Saving a Spreadsheet
+====================
+
+.. warning::
+
+ This is currently an experimental feature and as such is not robust. If you rename or move the vistrails used by the saved spreadsheet, the spreadsheet will not load correctly.
+
+.. index::
+ pair: spreadsheet; saving
+
+Because spreadsheets can include several workflow executions or parameter explorations, it is helpful to be
+able to save the layout of the current spreadsheet. To save a
+spreadsheet, simply choose the ``Save`` menu item from the
+``Main`` menu, and complete the dialog. After saving a
+spreadsheet, you can reopen it using the ``Open`` menu item. A whole sheet can also be saved by selecting Export (either from the menu or from the toolbar).
+
+Saving a Spreadsheet Image
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. index::
+ triple: spreadsheet; saving; image
+
+To save an image from the spreadsheet, click on the image's cell to make it active. Then select the camera on the toolbar to take a snapshot. The system will prompt you for the location and file name where it should be saved. The other icons can be used for saving multiple images that can be used for generating an animation on demand.
+
+.. index:: spreadsheet
diff --git a/doc/usersguide/tabledata.rst b/doc/usersguide/tabledata.rst
new file mode 100644
index 0000000..fe1fe7d
--- /dev/null
+++ b/doc/usersguide/tabledata.rst
@@ -0,0 +1,60 @@
+.. _chap-tabledata:
+
+********************
+Tabular data package
+********************
+
+The tabledata package provides facilities to load and manipulate data in table
+formats.
+
+It provides modules to read tables from CSV files and numpy arrays (including
+plain binary files) and extract or convert columns.
+
+.. topic:: Try it Now!
+
+ This example shows how to use tabledata together with matplotlib to
+ visualize trip data from `NYC Citibike's open data
+ <http://www.citibikenyc.com/system-data>`_.
+
+ Note that you can find the completed example here: :vtl:`bikes.vt`.
+
+ Start by dragging the following modules to the canvas:
+
+ * ``HTTPFile`` (from the HTTP package)
+ * ``CSVFile`` (under ``read/csv``)
+ * ``TableCell``
+ * Two ``ExtractColumn`` modules
+ * ``StringToDates`` (under ``convert/dates``)
+ * ``MplLinePlot`` from the matplotlib package
+ * ``MplFigure`` from the matplotlib package
+ * ``MplFigureCell`` from the matplotlib package
+
+ Connect the modules as shown in Figure :ref:`fig-tabledata-pipeline`.
+
+.. _fig-tabledata-pipeline:
+
+.. figure:: figures/tabledata/pipeline.png
+ :align: center
+ :width: 5in
+
+ The pipeline for the Bikes example
+
+.. topic:: Next Step!
+
+ Set the 'url' input of HTTPFile to ``http://www.vistrails.org/download/download.php?type=DATA&id=citibike_from_launch.csv``.
+ Make sure 'header_present' is checked on CSVFile.
+
+ Set the 'column_name' parameters on both ExtractColumn modules to ``Date`` (for the one on the left) and ``Miles traveled today (midnight to 11:59 pm)`` (for the one on the right). Alternatively, you can set column_index to 0 and 3.
+
+
+ The workflow is now ready. On execution, you will see a graphical view of the
+ CSV file as a table, and a line plot showing the variations of the total
+ distance traveled daily.
+
+.. _fig-tabledata-results:
+
+.. figure:: figures/tabledata/results.png
+ :align: center
+ :width: 9in
+
+ The result in the |vistrails| Spreadsheet
diff --git a/doc/usersguide/version_tree.rst b/doc/usersguide/version_tree.rst
new file mode 100644
index 0000000..1afd7ab
--- /dev/null
+++ b/doc/usersguide/version_tree.rst
@@ -0,0 +1,173 @@
+.. _chap-version_tree:
+
+*********************************
+Interacting with the Version Tree
+*********************************
+
+.. index:: versions
+
+Version Tree View
+=================
+
+.. index::
+ pair: versions;viewing
+ single: history
+
+The ``History`` button on the |vistrails| toolbar lets users interact with a workflow history. It consists of a tree view in the center and the ``Properties`` tool container on the right for querying and managing version properties (see Figure :ref:`In History mode, you can examine... <fig-version_tree_screenshot_labeled>`). Versions are displayed as ellipses in the tree view where the root of the tree is displayed at the top of the view. The nodes of the tree correspond to a version of [...]
+
+.. _fig-version_tree_screenshot_labeled:
+
+.. figure:: figures/version_tree/history_view_screenshot_labeled.png
+ :width: 5.5 in
+ :align: center
+
+ In ``History`` mode, you can examine and annotate different versions of a workflow.
+
+.. %TODO hmm... what exactly is the scheme for when version nodes are visible or invisible under the "new regime"?
+
+.. index:: tags
+
+The nodes are displayed as colored ellipses, and are either blue or orange. A blue color denotes that the corresponding version was created by the current user while orange nodes were created by other users. The brightness of each node indicates how recently a version was created; brighter nodes were created more recently than dimmer ones. Each node may also have a *tag* that describes the version, and this tag is displayed as a text label in the center of the ellipse of the correspon [...]
+
+The nodes are connected by a solid line if the child node is a direct descendent of the parent node; that is, if you have made only a single change from the older version to the newer version. By default, only nodes that: are leaves, have more than one child node, are specially tagged (see Section :ref:`sec-adding_deleting_tags`), or are current version will be
+displayed. To save space, other nodes will be "collapsed," or hidden from view. Collapsed nodes are marked by the appearance of a small expansion button along an edge connecting two nodes. Clicking this button expands the
+version tree to reveal the hidden versions (Figure :ref:`To conserve space... <fig-expand_collapse_versions>`). The tree expansion is smoothly
+animated to help you maintain context from one view to the next. Clicking the button a second time collapses the nodes once again. Because most non-trivial changes to a workflow take more than one action, most edges in a the
+version tree will be shown with these expansion buttons.
+
+.. _fig-expand_collapse_versions:
+
+.. figure:: figures/version_tree/collapsed_expanded.png
+ :height: 6in
+ :align: center
+
+ To conserve space, linear sequences of non-tagged nodes may be hidden from view. They can be restored by clicking on the expansion button, which resembles a plus sign (+) inside a small box.
+
+.. %All of the versions are connected to each other by either solid or
+.. %broken lines. A solid line indicates that the child node is a direct
+.. %descendant of the parent node, meaning the user has made only a single
+.. %change from the older version to the newer version. Likewise, a broken
+.. %line indicates that more than one change has been made, but the
+.. %intermediate versions have not been tagged. Because most non-trivial
+.. %changes to a workflow take more than action, most edges in a the
+.. %version tree will be shown as these broken lines.
+
+.. topic:: Try it now!
+
+ To see an example of a version tree, load the example vistrail :vtl:`vtk\_book\_3rd\_p189.vt`. All versions will be shown in orange unless your username happens to be "emanuele." Recall that this tree displays the structure of changes to a workflow, so let's make some changes to see their effect on the version history. In the ``History`` view, select the node tagged ``Almost there``, and then click on the ``Pipeline`` button to switch to a view of the workflow. Select a connection a [...]
+
+.. _fig-creating_versions:
+
+.. _fig-creating_versions_A:
+
+.. figure:: figures/version_tree/creating_versions_A.png
+ :height: 2.8in
+ :align: center
+
+ All versions created by other users are shown in orange.
+
+.. _fig-creating_versions_B:
+
+.. figure:: figures/version_tree/creating_versions_B.png
+ :height: 2.8in
+ :align: center
+
+ Deleting a connection results in a blue version connected by a solid line.
+
+.. _fig-creating_versions_C:
+
+.. figure:: figures/version_tree/creating_versions_C.png
+ :height: 2.8in
+ :align: center
+
+ More interactions on this version cause additional versions to be created. To save space, these intermediate nodes are hidden, and an expansion button appears on the edge between the current node and the last tagged node.
+
+.. _sec-adding_deleting_tags:
+
+Adding and Deleting Tags
+========================
+
+.. index::
+ pair: tags; adding
+ pair: tags; deleting
+
+.. %As noted above, only certain nodes, including specially tagged ones, are shown by default in the version tree. To tag a version, simply add meaningful text to the tag text box in the ``Properties`` container and press 'Enter'. If you would like to change the tag to different text, click in the same text box and modify the string, again hitting 'Enter' when finished. Note that deleting all of the text in the tag field effectively deletes the tag. A second way to delete a tag is to [...]
+
+As noted above, only certain nodes, including specially tagged ones, are shown by default in the version tree. To tag a version, simply
+click inside a selected node and type some meaningful text. The tag is created when you either click outside the node or press 'Enter'. If you would like to change the tag's text, click inside the node again and modify the text as before.
+(Alternately, you can also create and modify tags using the ``Tag`` text field in the ``Properties`` panel.)
+
+Note that deleting all of the text in the tag field effectively deletes the tag. A second way to delete a tag is to click the 'X' button to the right of the text box. Removing a tag from a node may cause it to not be displayed in the default version tree view if it doesn't satisfy any of the other criteria for display.
+
+Upgrading Versions
+==================
+
+.. index::
+ pair: tags; upgrading
+
+As module packages are continuously updated, with new versions being released periodically, VisTrails is set up to automatically incorporate module upgrades into existing workflows before they are executed. In other words, VisTrails upgrades the current vistrail's current version after the execute button is pressed, but prior to execution. When this happens, a new version is created in the version tree and tagged 'Upgrade'. You are then free to rename this version if desired.
+
+After an upgrade, you will not be able to select the original version because the focus is passed to the upgraded version. However, if you right-click on the original version and select 'Display raw pipeline', this version will keep the focus, which allows you to see its pipeline by pressing the ``Pipeline`` button on the toolbar. See figure :ref:`Original Pipeline... <fig-raw-pipeline>`.
+
+.. _fig-raw-pipeline:
+
+.. figure:: figures/version_tree/raw_pipeline.png
+ :align: center
+ :width: 2.5in
+
+ Original Pipeline - This figure shows how to view the original pipeline after an upgrade has occurred.
+
+Finally, although VisTrails tags the new version with 'Upgrade' by default, some users prefer the original version's name to be transferred to the upgraded version. VisTrails will do this if you: select ``Preferences`` from the ``VisTrails`` menu, select the ``Expert Configuration`` tab, and change the ``migrateTags`` value to 'True'.
+
+Adding Version Annotations
+==========================
+
+.. index::
+ pair: versions; annotations
+ single: notes
+
+In addition to the tag field, the ``Properties`` panel displays information about the user who created the selected version
+and when that version was created. Also, the ``Notes`` field which allows users to store notes or annotations related to a version. As with tags, adding notes to a version is as easy as selecting the desired version and modifying the text field. Notes are
+automatically saved when you save the vistrail file. Finally, a thumbnail is displayed in the preview portion of the panel if the version has been successfully executed.
+
+Navigating Versions
+===================
+
+.. index::
+ pair: versions; navigating
+ single: undo
+ single: redo
+
+Clicking on nodes in the version tree is not the only way to navigate different versions of a workflow; you can also use ``Undo`` (Ctrl-z) and ``Redo`` (Ctrl-Shift-z). Because the version tree captures all changes to a workflow, undo and redo not only revert or reinstate changes to a workflow, but also change the currently selected version in the version tree. More precisely, undoing a change in a workflow is exactly the same as selecting the parent of the current node in the version t [...]
+
+.. _sec-versions-diff:
+
+Comparing Versions
+==================
+
+.. index::
+ pair: versions; comparing
+ single: visual diff; see versions, comparing
+ single: diff; see versions, comparing
+
+While selecting versions in the ``History`` view and using the ``Pipeline`` view to examine each version is extremely useful, this approach can be cumbersome when trying to compare two different versions. To help with such a comparison, |vistrails| provides a ``Version Difference`` mechanism for quickly comparing two versions. This is done by dragging one version and dropping it onto another, after which a ``Visual Diff`` tab will open (see Figure :ref:`A Visual Diff showing the differ [...]
+
+.. index::
+ single: legend
+ pair: parameters; differences
+
+In the new tab, the difference is displayed in a manner that is very similar to the pipeline view, but modules and connections are colored based on similarity. Dark gray indicates those modules and connections that are shared between the two versions; orange and blue show modules and connections that exist in one workflow and not the other; and light gray modules are those where parameters between the two versions differ. The Legend, which is displayed in the ``Diff Properties`` panel [...]
+
+.. _fig-visual_diff:
+
+.. figure:: figures/version_tree/visual_diff.png
+ :width: 5in
+ :align: center
+
+ A ``Visual Diff`` showing the difference between version ``z-space`` and version ``textureMapper``.
+
+.. topic:: Try it now!
+
+ To try out this feature, open the :vtl:`lung.vt` example vistrail, and click the ``History`` button. Within the version tree, click and drag the ``z-space`` version to the ``textureMapper`` version. After the diff appears, select ``View`` :math:`\rightarrow` ``Diff Properties`` (if the ``Diff Properties`` panel is not visible), and then click on the ``vtkRenderer`` module to see the parameter differences. We can see that one of the changes from ``z-space`` to ``textureMapper`` was to [...]
+
+.. index:: versions
diff --git a/doc/usersguide/vistrails_server.rst b/doc/usersguide/vistrails_server.rst
new file mode 100644
index 0000000..3610c20
--- /dev/null
+++ b/doc/usersguide/vistrails_server.rst
@@ -0,0 +1,124 @@
+.. _chap-vistrails-server:
+
+***********************
+VisTrails Server Setup
+***********************
+
+.. index:: server
+
+* lets assume that everything is going to be put in the /server dir::
+
+ $ cd /server
+ $ mkdir vistrails
+
+* put VisTrails Source in vistrails/ folder::
+
+ $ cd vistrails
+ $ git clone git://vistrails.org:vistrails.git git # or just download the latest release or nightly build
+
+* make a logs dir for the server::
+
+ $ mkdir logs
+
+* if you are running the server without crowdLabs or as a remote server, you need to create a media directory with the following structure::
+
+ /path/to/media_dir/
+ wf_execution/
+ graphs/
+ workflows/
+ vistrails/
+ medleys/
+ images/
+
+ You can run ``python scripts/create_server_media_dir_structure.py /path/to/media_dir`` to create the directory structure automatically.
+
+* Determine how you will start the vistrails server. You have a choice of using Xvfb or not. If you use it, /server/vistrails/git/scripts/start_vistrails_xvfb.sh is what you will use, otherwise, use start_vistrails.sh
+
+Using Xvfb is slower and not recommended if your workflows will make use of volume rendering or other graphics-card intensive techniques.
+
+.. _sec-server-using-xvfb:
+
+Using Xvfb
+===========
+
+* edit /server/vistrails/git/scripts/start_vistrails_xvfb.sh file and make sure it is consistent with your system setup::
+
+ LOG_DIR=/server/vistrails/logs
+ Xvfb_CMD=/usr/bin/Xvfb
+ VIRTUAL_DISPLAY=":6"
+ VISTRAILS_DIR=/server/vistrails/git/vistrails
+ ADDRESS="<your_server.com>"
+ PORT="8081" #the port where the server will listen for requests
+ CONF_FILE="server.cfg"
+ NUMBER_OF_OTHER_VISTRAILS_INSTANCES="1"
+ MULTI_OPTION="-M" #execute the main instance multithreaded
+
+* The setup above will execute 2 instances of the server. You can add more instances by changing the variable NUMBER_OF_OTHER_VISTRAILS_INSTANCES. When using multiple instances, the ports and virtual displays will be used incrementally, so if the main instance is using port 8081 and virtual display :6, the next instance will use port 8082 and virtual display :7, and so on.
+
+.. _sec-server-using-x-directly:
+
+Connecting to X server directly
+===============================
+
+* If you decide no to use Xvfb, edit /server/vistrails/git/scripts/start_vistrails.sh file and make sure it is consistent with your system setup::
+
+ LOG_DIR=/server/vistrails/logs
+ VISTRAILS_DIR=/server/vistrails/git/vistrails
+ ADDRESS="<your_server.com>"
+ PORT="8081" #the port where the server will listen for requests
+ CONF_FILE="server.cfg"
+ NUMBER_OF_OTHER_VISTRAILS_INSTANCES="2"
+ MULTI_OPTION="-M" #execute the main instance multithreaded
+
+* The setup above will execute 3 instances of the server. You can add or remove more instances by changing the variable NUMBER_OF_OTHER_VISTRAILS_INSTANCES. When using multiple instances, the ports will be used incrementally, so if the main instance is using port 8081, the next instance will use port 8082, and so on.
+
+.. _sec-server-basic-configuration:
+
+Basic Configuration
+===================
+
+* If the vistrails server will receive requests from the outside world and if you are using a firewall, make sure the ports used by the vistrails server are open and accessible.
+
+* create a file called server.cfg in /server/vistrails/git/vistrails/ as follows::
+
+ [access]
+ permitted_addresses = localhost, 127.0.0.1, <crowdlabs-server-address>
+
+ [media]
+ media_dir=/server/crowdlabs/site_media/media
+
+ [database]
+ host = <vistrail database address>
+ read_user = <read user>
+ read_password = <read password>
+ write_user = <write user>
+ write_password = <write user password>
+
+ [script]
+ script_file=/server/vistrails/git/scripts/start_vistrails.sh
+ virtual_display=<virtual display number>
+
+* change permitted_addresses variable in to include the address of the machine running of the crowdLabs server (or other machines you want to be able to connect to the server)::
+
+ [access]
+ permitted_addresses = localhost, 127.0.0.1, <crowdlabs-server-address>
+
+
+* Add the password for the full permission mysql user created in :ref:`VisTrails Database Setup <mysql-full-perm-user>`::
+
+ write_user = <write user>
+ write_password = <write user password>
+
+* Configure the full path to the script file and if you are using Xvfb, also specify the virtual display of the main instance::
+
+ [script]
+ script_file=/server/vistrails/git/scripts/start_vistrails.sh
+ virtual_display=0 #not using any display
+
+* run vistrails in server mode::
+
+ $ cd /server/vistrails/git/scripts
+ # If you are running Xvfb:
+ $ ./start_vistrails_xvfb.sh
+ # Or if you are connecting to X server directly:
+ $ ./start_vistrails.sh
diff --git a/doc/usersguide/vtl/README b/doc/usersguide/vtl/README
new file mode 100644
index 0000000..7bd4c34
--- /dev/null
+++ b/doc/usersguide/vtl/README
@@ -0,0 +1,21 @@
+To link to examples you need to put a vtl file on the server first
+
+To create a link to an example:
+
+1. Create the example in examples/usersguide/, or use an existing example
+
+2. Create a vtl file containing a link to the example like this:
+ <vtlink filename="@examples/usersguide/global_variables.vt" version="60"/>
+ Name it something like global_variables.vtl
+ Place it in the doc/usersguide/vtl directory
+
+3. Create the link in the usersguide like this:
+ Using macro (title will be same as vt filename):
+ :vtl:`terminator.vt`
+ Using macro with custom title:
+ :vtl:`(Open result) <global_variables.vt>`
+ Raw version:
+ `(Open result) <http://www.vistrails.org/usersguide/v2.1/examples/global_variables.vtl>`_
+
+4. Copy the new vtl files to the server:
+ scp doc/usersguide/vtl/* vistrails.org:/srv/wiki/vistrails/usersguide/v2.1/examples/
\ No newline at end of file
diff --git a/doc/usersguide/vtl/bikes.vtl b/doc/usersguide/vtl/bikes.vtl
new file mode 100644
index 0000000..35a3bce
--- /dev/null
+++ b/doc/usersguide/vtl/bikes.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/bikes.vt"/>
diff --git a/doc/usersguide/vtl/brain_vistrail.vtl b/doc/usersguide/vtl/brain_vistrail.vtl
new file mode 100644
index 0000000..847f11d
--- /dev/null
+++ b/doc/usersguide/vtl/brain_vistrail.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/brain_vistrail.vt"/>
diff --git a/doc/usersguide/vtl/cfassistant1.vtl b/doc/usersguide/vtl/cfassistant1.vtl
new file mode 100644
index 0000000..0d85593
--- /dev/null
+++ b/doc/usersguide/vtl/cfassistant1.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/usersguide/cfassistant.vt" version="example1"/>
diff --git a/doc/usersguide/vtl/cfassistant2.vtl b/doc/usersguide/vtl/cfassistant2.vtl
new file mode 100644
index 0000000..154946a
--- /dev/null
+++ b/doc/usersguide/vtl/cfassistant2.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/usersguide/cfassistant.vt" version="example2"/>
diff --git a/doc/usersguide/vtl/global_variables1.vtl b/doc/usersguide/vtl/global_variables1.vtl
new file mode 100644
index 0000000..46cef35
--- /dev/null
+++ b/doc/usersguide/vtl/global_variables1.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/usersguide/global_variables.vt" version="60"/>
diff --git a/doc/usersguide/vtl/lung.vtl b/doc/usersguide/vtl/lung.vtl
new file mode 100644
index 0000000..b199453
--- /dev/null
+++ b/doc/usersguide/vtl/lung.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/lung.vt"/>
diff --git a/doc/usersguide/vtl/mashups1.vtl b/doc/usersguide/vtl/mashups1.vtl
new file mode 100644
index 0000000..6a243f1
--- /dev/null
+++ b/doc/usersguide/vtl/mashups1.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/usersguide/mashups.vt" mashuptrail="9e7148ee-2518-11e3-b863-3c07543dba07" mashupVersion="5"/>
diff --git a/doc/usersguide/vtl/offscreen.vtl b/doc/usersguide/vtl/offscreen.vtl
new file mode 100644
index 0000000..0ce5aed
--- /dev/null
+++ b/doc/usersguide/vtl/offscreen.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/offscreen.vt"/>
diff --git a/doc/usersguide/vtl/pe1.vtl b/doc/usersguide/vtl/pe1.vtl
new file mode 100644
index 0000000..927da63
--- /dev/null
+++ b/doc/usersguide/vtl/pe1.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/usersguide/parameter_exploration.vt" parameterExploration="1"/>
diff --git a/doc/usersguide/vtl/pe2.vtl b/doc/usersguide/vtl/pe2.vtl
new file mode 100644
index 0000000..b9f9abb
--- /dev/null
+++ b/doc/usersguide/vtl/pe2.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/usersguide/parameter_exploration.vt" parameterExploration="2"/>
diff --git a/doc/usersguide/vtl/pe3.vtl b/doc/usersguide/vtl/pe3.vtl
new file mode 100644
index 0000000..f4a4ad2
--- /dev/null
+++ b/doc/usersguide/vtl/pe3.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/usersguide/parameter_exploration.vt" parameterExploration="3"/>
diff --git a/doc/usersguide/vtl/pe4.vtl b/doc/usersguide/vtl/pe4.vtl
new file mode 100644
index 0000000..dda7eb5
--- /dev/null
+++ b/doc/usersguide/vtl/pe4.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/usersguide/parameter_exploration.vt" parameterExploration="4"/>
diff --git a/doc/usersguide/vtl/protein_visualization.vtl b/doc/usersguide/vtl/protein_visualization.vtl
new file mode 100644
index 0000000..1a0887a
--- /dev/null
+++ b/doc/usersguide/vtl/protein_visualization.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/protein_visualization.vt"/>
diff --git a/doc/usersguide/vtl/spx.vtl b/doc/usersguide/vtl/spx.vtl
new file mode 100644
index 0000000..7efe5b8
--- /dev/null
+++ b/doc/usersguide/vtl/spx.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/spx.vt"/>
diff --git a/doc/usersguide/vtl/terminator.vtl b/doc/usersguide/vtl/terminator.vtl
new file mode 100644
index 0000000..5c890af
--- /dev/null
+++ b/doc/usersguide/vtl/terminator.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/terminator.vt"/>
diff --git a/doc/usersguide/vtl/triangle_area.vtl b/doc/usersguide/vtl/triangle_area.vtl
new file mode 100644
index 0000000..565ec42
--- /dev/null
+++ b/doc/usersguide/vtl/triangle_area.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/triangle_area.vt"/>
diff --git a/doc/usersguide/vtl/vtk.vtl b/doc/usersguide/vtl/vtk.vtl
new file mode 100644
index 0000000..2354b88
--- /dev/null
+++ b/doc/usersguide/vtl/vtk.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/vtk.vt"/>
diff --git a/doc/usersguide/vtl/vtk_book_3rd_p189.vtl b/doc/usersguide/vtl/vtk_book_3rd_p189.vtl
new file mode 100644
index 0000000..3fcf15f
--- /dev/null
+++ b/doc/usersguide/vtl/vtk_book_3rd_p189.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/vtk_book_3rd_p189.vt"/>
diff --git a/doc/usersguide/vtl/vtk_http.vtl b/doc/usersguide/vtl/vtk_http.vtl
new file mode 100644
index 0000000..be96537
--- /dev/null
+++ b/doc/usersguide/vtl/vtk_http.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/vtk_http.vt"/>
diff --git a/doc/vistrails.xsd b/doc/vistrails.xsd
new file mode 100644
index 0000000..3d67783
--- /dev/null
+++ b/doc/vistrails.xsd
@@ -0,0 +1,127 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- edited with XMLSpy v2006 sp2 U (http://www.altova.com) by Emanuele Santos (University of UTAH) -->
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="visTrail">
+ <xs:annotation>
+ <xs:documentation>Comment describing your root element</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence maxOccurs="unbounded">
+ <xs:sequence maxOccurs="unbounded">
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="notes" minOccurs="0"/>
+ <xs:choice>
+ <xs:sequence maxOccurs="unbounded">
+ <xs:element name="move">
+ <xs:complexType>
+ <xs:attribute name="dx" type="xs:float"/>
+ <xs:attribute name="dy" type="xs:float"/>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:element name="object">
+ <xs:complexType>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:sequence maxOccurs="unbounded">
+ <xs:element name="set">
+ <xs:complexType>
+ <xs:attribute name="function" type="xs:string"/>
+ <xs:attribute name="functionId" type="xs:int"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="parameter" type="xs:string"/>
+ <xs:attribute name="parameterId" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="value" type="xs:anySimpleType"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:element name="connect">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element name="filterInput">
+ <xs:complexType>
+ <xs:attribute name="destId" type="xs:int"/>
+ <xs:attribute name="destPort" type="xs:int"/>
+ <xs:attribute name="sourceId" type="xs:int"/>
+ <xs:attribute name="sourcePort" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="objectInput">
+ <xs:complexType>
+ <xs:attribute name="destId" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="sourceId" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:sequence maxOccurs="unbounded">
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:attribute name="connectionId" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:sequence maxOccurs="unbounded">
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:attribute name="functionId" type="xs:int"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="parent" type="xs:int"/>
+ <xs:attribute name="time" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="date" type="xs:string" use="optional"/>
+ <xs:attribute name="user" type="xs:string" use="optional"/>
+ <xs:attribute name="notes" type="xs:string" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:sequence minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="time" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:sequence minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="macro">
+ <xs:complexType>
+ <xs:sequence minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:attribute name="time" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="desc" type="xs:string" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/examples/EMBOSS_webservices.vt b/examples/EMBOSS_webservices.vt
new file mode 100644
index 0000000..076a2ce
Binary files /dev/null and b/examples/EMBOSS_webservices.vt differ
diff --git a/examples/KEGGPathway.vt b/examples/KEGGPathway.vt
new file mode 100644
index 0000000..3cb82e8
Binary files /dev/null and b/examples/KEGGPathway.vt differ
diff --git a/examples/KEGG_SearchEntities_webservice.vt b/examples/KEGG_SearchEntities_webservice.vt
new file mode 100644
index 0000000..cf20cbb
Binary files /dev/null and b/examples/KEGG_SearchEntities_webservice.vt differ
diff --git a/examples/KEGG_webservices.vt b/examples/KEGG_webservices.vt
new file mode 100644
index 0000000..4e5ec1f
Binary files /dev/null and b/examples/KEGG_webservices.vt differ
diff --git a/examples/XSLTSample.xsl b/examples/XSLTSample.xsl
new file mode 100644
index 0000000..d291c4a
--- /dev/null
+++ b/examples/XSLTSample.xsl
@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<xsl:stylesheet
+ version="1.0"
+ xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+ <xsl:output method="xml" encoding="UTF-8"/>
+ <xsl:template match="/">
+ <html>
+ <head><title>XSLT Sample</title></head>
+ <body>
+ <h2>The Sequence for the Given Gene is: </h2>
+ <ul>
+ <li>
+ <xsl:value-of select="DDBJXML/SEQUENCE"/>
+ </li>
+ </ul>
+<h3>Please fill in the following inputs and Submit:</h3>
+<xsl:text disable-output-escaping="yes"><![CDATA[
+ <form method="post" action="http://geon01.sdsc.edu:8164/pt2/jsp/ptf.jsp">
+ <b>Program: </b><input name="program" size="20" type="text"><BR>
+ <b>Database: </b><input name="database" size="20" type="text"><BR>
+ <b>Query: </b><input name="query" size="20" type="text"><BR>
+ <INPUT TYPE="submit" VALUE="Make BLAST search using the specified inputs">
+</form>
+]]></xsl:text>
+ </body>
+ </html>
+ </xsl:template>
+</xsl:stylesheet>
diff --git a/examples/afront.xml b/examples/afront.xml
new file mode 100644
index 0000000..ad95b2b
--- /dev/null
+++ b/examples/afront.xml
@@ -0,0 +1,803 @@
+ <visTrail version="0.3.0">
+ <action date="01 Mar 2007 17:56:06" parent="0" time="1" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="0" name="Afront" x="9.0" y="273.0"/>
+ </action>
+ <action date="01 Mar 2007 17:56:12" parent="1" time="2" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="-46.0" dy="-38.0" id="0"/>
+ </action>
+ <action date="01 Mar 2007 17:56:12" parent="2" time="3" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="1" name="File" x="-58.0" y="381.0"/>
+ </action>
+ <action date="01 Mar 2007 17:56:16" parent="3" time="4" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="10.0" dy="-84.0" id="0"/>
+ <move dx="30.0" dy="-45.0" id="1"/>
+ </action>
+ <action date="01 Mar 2007 17:56:16" parent="4" time="5" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="name" functionId="0" moduleId="1" parameter="<no description>" parameterId="0" type="String" value=""/>
+ </action>
+ <action date="01 Mar 2007 17:56:24" parent="5" time="6" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="name" functionId="0" moduleId="1" parameter="<no description>" parameterId="0" type="String" value="/home/cscheid/cscheid_old/meshes/bunny.off"/>
+ </action>
+ <action date="01 Mar 2007 17:56:25" parent="6" time="7" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="name" functionId="0" moduleId="1" parameter="<no description>" parameterId="0" type="String" value="/home/cscheid/cscheid_old/meshes/bunny.off"/>
+ </action>
+ <action date="01 Mar 2007 17:56:29" parent="7" time="8" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="eta" functionId="0" moduleId="0" parameter="eta" parameterId="0" type="Float" value="0.0"/>
+ </action>
+ <action date="01 Mar 2007 17:56:32" parent="8" time="9" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="eta" functionId="0" moduleId="0" parameter="<no description>" parameterId="0" type="Float" value="0.8"/>
+ </action>
+ <action date="01 Mar 2007 17:56:34" parent="9" time="10" user="cscheid" what="deleteFunction">
+ <notes>
+ None
+ </notes>
+ <function functionId="0" moduleId="0"/>
+ </action>
+ <action date="01 Mar 2007 17:56:35" parent="10" time="11" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="rho" functionId="0" moduleId="0" parameter="rho" parameterId="0" type="Float" value="0.0"/>
+ </action>
+ <action date="01 Mar 2007 17:56:37" parent="11" time="12" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="rho" functionId="0" moduleId="0" parameter="<no description>" parameterId="0" type="Float" value="0.8"/>
+ </action>
+ <action date="01 Mar 2007 17:56:38" parent="12" time="13" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="rho" functionId="0" moduleId="0" parameter="<no description>" parameterId="0" type="Float" value="0.8"/>
+ </action>
+ <action date="01 Mar 2007 17:56:41" parent="13" time="14" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="0" destinationModule="Afront" destinationPort="file(File)" id="0" sourceId="1" sourceModule="File" sourcePort="self(File)"/>
+ </action>
+ <action date="01 Mar 2007 17:56:50" parent="14" time="15" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="5.0" dy="26.0" id="0"/>
+ </action>
+ <action date="01 Mar 2007 17:56:50" parent="15" time="16" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="2" name="MeshQualityHistogram" x="35.0" y="46.0"/>
+ </action>
+ <action date="01 Mar 2007 17:56:53" parent="16" time="17" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="-23.0" dy="25.0" id="0"/>
+ </action>
+ <action date="01 Mar 2007 17:56:53" parent="17" time="18" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="2" destinationModule="MeshQualityHistogram" destinationPort="file(File)" id="1" sourceId="0" sourceModule="Afront" sourcePort="output(File)"/>
+ </action>
+ <action date="01 Mar 2007 17:56:57" parent="18" time="19" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="-53.0" dy="26.0" id="2"/>
+ </action>
+ <action date="01 Mar 2007 17:56:57" parent="19" time="20" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="3" name="PythonSource" x="-30.0" y="-86.0"/>
+ </action>
+ <action date="01 Mar 2007 17:58:52" parent="20" time="21" user="cscheid" what="addModulePort">
+ <notes>
+ None
+ </notes>
+ <addPort moduleId="3" portName="input" portSpec="(File)" portType="input"/>
+ </action>
+ <action date="01 Mar 2007 17:58:52" parent="21" time="22" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="String" value="f%20%3D%20self.getInputFromPort%28%27input%27%29%0A%0Av%20%3D%201.0%0Afor%20l%20in%20f.readlines%28%29%3A%0A%20%20%20v%20-%3D%20float%28l%29%20/%20100.0%0A%0Aprint%20%22mesh%20quality%3A%20%22%2C%20v"/>
+ </action>
+ <action date="01 Mar 2007 17:58:54" parent="22" time="23" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="3" destinationModule="PythonSource" destinationPort="input(File)" id="2" sourceId="2" sourceModule="MeshQualityHistogram" sourcePort="output(File)"/>
+ </action>
+ <action date="01 Mar 2007 18:00:32" parent="23" time="24" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="String" value="f%20%3D%20self.getInputFromPort%28%27input%27%29%0A%0Av%20%3D%201.0%0Afor%20l%20in%20file%28f.name%29.readlines%28%29%3A%0A%20%20%20v%20-%3D%20float%28l%29%20/%20100.0%0A%0Aprint%20%22mesh%20quality%3A%20%22%2C%20v"/>
+ </action>
+ <action date="01 Mar 2007 18:00:48" parent="24" time="25" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="String" value="f%20%3D%20self.getInputFromPort%28%27input%27%29%0A%0Av%20%3D%201.0%0Afor%20l%20in%20file%28f.name%29.readlines%28%29%3A%0A%20%20%20print%20l%0A%20%20%20v%20-%3D%20float%28l%29%20/%20100.0%0A%0Aprint%20%22mesh%20quality%3A%20%22%2C%20v"/>
+ </action>
+ <action date="01 Mar 2007 18:09:13" parent="25" time="26" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="String" value="f%20%3D%20self.getInputFromPort%28%27input%27%29%0A%0Av%20%3D%201.0%0Afor%20l%20in%20file%28f.name%29.readlines%28%29%3A%0A%20%20%20v%20-%3D%20float%28l%29%20/%20100.0%0A%0Aprint%20%22mesh%20quality%3A%20%22%2C%20v"/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="0" time="27" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="0" name="vtkDataSetReader" x="50.4689536324" y="-75.039097946"/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="27" time="28" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="1" name="OutputPort" x="66.5683979218" y="-176.342434481"/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="28" time="29" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="2" name="InputPort" x="72.8614246679" y="145.860534924"/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="29" time="30" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="3" name="PythonSource" x="50.127651043" y="23.962638969"/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="30" time="31" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="0" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="31" time="32" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="1" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="32" time="33" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="name" functionId="0" moduleId="2" parameter="<no description>" parameterId="0" type="String" value="input_file"/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="33" time="34" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="2" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="34" time="35" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="String" value="%23%20Extracts%20the%20internal%20file%20name%20so%20VTK%20can%20use%20it%0A%23%20Also%2C%20makes%20local%20copy%20so%20that%20the%20file%20survives%20filepool%0A%23%20cleanup.%0Afrom%20packages.spreadsheet.spreadsheet_controller%20import%20spreadsheetController%0Aself.checkInputPort%28%22file%22%29%0Awindow%20%3D%20spreadsheetController.findSpreadshee [...]
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="35" time="36" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="3" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="36" time="37" user="cscheid" what="addModulePort">
+ <notes>
+ None
+ </notes>
+ <addPort moduleId="3" portName="file" portSpec="(File)" portType="input"/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="37" time="38" user="cscheid" what="addModulePort">
+ <notes>
+ None
+ </notes>
+ <addPort moduleId="3" portName="name" portSpec="(String)" portType="output"/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="38" time="39" user="cscheid" what="addModulePort">
+ <notes>
+ None
+ </notes>
+ <addPort moduleId="3" portName="file" portSpec="(File)" portType="output"/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="39" time="40" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="1" destinationModule="OutputPort" destinationPort="InternalPipe(Module)" id="0" sourceId="0" sourceModule="vtkDataSetReader" sourcePort="GetOutputPort0(vtkAlgorithmOutput)"/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="40" time="41" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="0" destinationModule="vtkDataReader" destinationPort="SetFileName(String)" id="1" sourceId="3" sourceModule="PythonSource" sourcePort="name(String)"/>
+ </action>
+ <action date="01 Mar 2007 18:09:26" parent="41" time="42" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="3" destinationModule="PythonSource" destinationPort="file(File)" id="2" sourceId="2" sourceModule="InputPort" sourcePort="InternalPipe(Variant)"/>
+ </action>
+ <action date="01 Mar 2007 18:10:45" parent="26" time="43" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="4" name="MeshFilter" x="-260.146183261" y="3.39321108601"/>
+ </action>
+ <action date="01 Mar 2007 18:10:48" parent="43" time="44" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="output_format" functionId="0" moduleId="4" parameter="<no description>" parameterId="0" type="String" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:12:31" parent="44" time="45" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="output_format" functionId="0" moduleId="4" parameter="<no description>" parameterId="0" type="String" value=".vtk"/>
+ </action>
+ <action date="01 Mar 2007 18:12:34" parent="45" time="46" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="4" destinationModule="MeshFilter" destinationPort="input_file(File)" id="3" sourceId="0" sourceModule="Afront" sourcePort="output(File)"/>
+ </action>
+ <action date="01 Mar 2007 18:13:38" parent="46" time="47" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="5" name="vtkVistrailsFileReader" x="-272.292020374" y="-128.719864177"/>
+ </action>
+ <action date="01 Mar 2007 18:13:41" parent="47" time="48" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="5" destinationModule="vtkVistrailsFileReader" destinationPort="input_file(File)" id="4" sourceId="4" sourceModule="MeshFilter" sourcePort="output_file(File)"/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="48" time="49" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="6" name="VTKCell" x="-180.664206774" y="-165.520338043"/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="49" time="50" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="7" name="vtkDataSetMapper" x="-237.282186703" y="301.998142802"/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="50" time="51" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="8" name="vtkRenderer" x="-220.460112232" y="-3.1201219181"/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="51" time="52" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="9" name="vtkActor" x="-258.041526728" y="119.069528254"/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="52" time="53" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="6" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="53" time="54" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="ScalarVisibilityOn" functionId="0" moduleId="7" parameter="" parameterId="-1" type="" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="54" time="55" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="7" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="55" time="56" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="8" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="56" time="57" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="9" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="57" time="58" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="6" destinationModule="VTKCell" destinationPort="AddRenderer(vtkRenderer)" id="5" sourceId="8" sourceModule="vtkRenderer" sourcePort="self(vtkRenderer)"/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="58" time="59" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="9" destinationModule="vtkActor" destinationPort="SetMapper(vtkMapper)" id="6" sourceId="7" sourceModule="vtkDataSetMapper" sourcePort="self(vtkDataSetMapper)"/>
+ </action>
+ <action date="01 Mar 2007 18:14:08" parent="59" time="60" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="8" destinationModule="vtkRenderer" destinationPort="AddActor(vtkProp)" id="7" sourceId="9" sourceModule="vtkActor" sourcePort="self(vtkActor)"/>
+ </action>
+ <action date="01 Mar 2007 18:14:14" parent="60" time="61" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="-39.0229417805" dy="-559.894382068" id="6"/>
+ <move dx="-39.0229417805" dy="-559.894382068" id="7"/>
+ <move dx="-39.0229417805" dy="-559.894382068" id="8"/>
+ <move dx="-39.0229417805" dy="-559.894382068" id="9"/>
+ </action>
+ <action date="01 Mar 2007 18:14:14" parent="61" time="62" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="7" destinationModule="vtkAlgorithm" destinationPort="AddInputConnection(vtkAlgorithmOutput)" id="8" sourceId="5" sourceModule="vtkVistrailsFileReader" sourcePort="GetOutputPort0(vtkAlgorithmOutput)"/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="0" time="63" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="0" name="VTKCell" x="-209.687148555" y="-715.414720111"/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="63" time="64" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="1" name="vtkActor" x="-287.064468509" y="-430.824853814"/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="64" time="65" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="2" name="vtkVistrailsFileReader" x="-262.292020374" y="-118.719864177"/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="65" time="66" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="3" name="vtkRenderer" x="-249.483054013" y="-553.014503986"/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="66" time="67" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="4" name="vtkDataSetMapper" x="-266.305128484" y="-247.896239266"/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="67" time="68" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="0" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="68" time="69" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="1" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="69" time="70" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="2" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="70" time="71" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="3" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="71" time="72" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="ScalarVisibilityOn" functionId="0" moduleId="4" parameter="" parameterId="-1" type="" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="72" time="73" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="4" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="73" time="74" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="0" destinationModule="VTKCell" destinationPort="AddRenderer(vtkRenderer)" id="0" sourceId="3" sourceModule="vtkRenderer" sourcePort="self(vtkRenderer)"/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="74" time="75" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="1" destinationModule="vtkActor" destinationPort="SetMapper(vtkMapper)" id="1" sourceId="4" sourceModule="vtkDataSetMapper" sourcePort="self(vtkDataSetMapper)"/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="75" time="76" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="3" destinationModule="vtkRenderer" destinationPort="AddActor(vtkProp)" id="2" sourceId="1" sourceModule="vtkActor" sourcePort="self(vtkActor)"/>
+ </action>
+ <action date="01 Mar 2007 18:14:33" parent="76" time="77" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="4" destinationModule="vtkAlgorithm" destinationPort="AddInputConnection(vtkAlgorithmOutput)" id="3" sourceId="2" sourceModule="vtkVistrailsFileReader" sourcePort="GetOutputPort0(vtkAlgorithmOutput)"/>
+ </action>
+ <action date="01 Mar 2007 18:14:41" parent="77" time="78" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="5" name="InputPort" x="-312.960721232" y="26.921352364"/>
+ </action>
+ <action date="01 Mar 2007 18:14:42" parent="78" time="79" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="2" destinationModule="vtkVistrailsFileReader" destinationPort="input_file(File)" id="4" sourceId="5" sourceModule="InputPort" sourcePort="InternalPipe(Variant)"/>
+ </action>
+ <action date="01 Mar 2007 18:14:56" parent="62" time="80" user="cscheid" what="deleteConnection">
+ <notes>
+ None
+ </notes>
+ <connection connectionId="5"/>
+ <connection connectionId="7"/>
+ <connection connectionId="8"/>
+ <connection connectionId="4"/>
+ <connection connectionId="6"/>
+ </action>
+ <action date="01 Mar 2007 18:14:56" parent="80" time="81" user="cscheid" what="deleteModule">
+ <notes>
+ None
+ </notes>
+ <module moduleId="8"/>
+ <module moduleId="5"/>
+ <module moduleId="7"/>
+ <module moduleId="9"/>
+ <module moduleId="6"/>
+ </action>
+ <action date="01 Mar 2007 18:15:01" parent="81" time="82" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="10" name="MeshCell" x="-269.411673235" y="-189.161387591"/>
+ </action>
+ <action date="01 Mar 2007 18:15:04" parent="82" time="83" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="10" destinationModule="MeshCell" destinationPort="input_file(File)" id="9" sourceId="4" sourceModule="MeshFilter" sourcePort="output_file(File)"/>
+ </action>
+ <action date="01 Mar 2007 18:15:10" parent="83" time="84" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="74.5181223843" dy="-45.8573060826" id="2"/>
+ <move dx="74.5181223843" dy="-45.8573060826" id="3"/>
+ <move dx="11.4643265207" dy="82.1610067314" id="10"/>
+ </action>
+ <action date="01 Mar 2007 18:15:10" parent="84" time="85" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="11" name="MeshFilter" x="-250.146183261" y="13.393211086"/>
+ </action>
+ <action date="01 Mar 2007 18:15:10" parent="85" time="86" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="output_format" functionId="0" moduleId="11" parameter="<no description>" parameterId="0" type="String" value=".vtk"/>
+ </action>
+ <action date="01 Mar 2007 18:15:10" parent="86" time="87" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="11" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:15:13" parent="87" time="88" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="-87.8931699917" dy="179.607782157" id="11"/>
+ </action>
+ <action date="01 Mar 2007 18:15:13" parent="88" time="89" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="11" destinationModule="MeshFilter" destinationPort="input_file(File)" id="10" sourceId="1" sourceModule="File" sourcePort="self(File)"/>
+ </action>
+ <action date="01 Mar 2007 18:15:14" parent="89" time="90" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="12" name="MeshCell" x="-247.947346715" y="-97.000380859"/>
+ </action>
+ <action date="01 Mar 2007 18:15:14" parent="90" time="91" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="12" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:15:17" parent="91" time="92" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="-187.250666504" dy="141.393360421" id="12"/>
+ </action>
+ <action date="01 Mar 2007 18:15:17" parent="92" time="93" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="12" destinationModule="MeshCell" destinationPort="input_file(File)" id="11" sourceId="11" sourceModule="MeshFilter" sourcePort="output_file(File)"/>
+ </action>
+ <action date="01 Mar 2007 18:16:57" parent="93" time="94" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="-265.590231062" dy="-26.7500952149" id="1"/>
+ <move dx="-107.000380859" dy="-204.447156285" id="11"/>
+ <move dx="-11.4643265207" dy="-152.857686942" id="12"/>
+ </action>
+ <action date="01 Mar 2007 18:16:57" parent="94" time="95" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="13" name="MplFigureCell" x="37.0688549561" y="-60.0259508645"/>
+ </action>
+ <action date="01 Mar 2007 18:16:57" parent="95" time="96" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="14" name="MplPlot" x="-104.504769347" y="212.057733157"/>
+ </action>
+ <action date="01 Mar 2007 18:16:57" parent="96" time="97" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="15" name="MplFigure" x="-2.3575207408" y="92.971924974"/>
+ </action>
+ <action date="01 Mar 2007 18:16:57" parent="97" time="98" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="13" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:16:57" parent="98" time="99" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="14" parameter="<no description>" parameterId="0" type="String" value="import%20matplotlib.axes3d%20as%20axes3d%0A%0Afig%20%3D%20gcf%28%29%0A%0Aax3d%20%3D%20axes3d.Axes3D%28fig%29%0Aplt%20%3D%20fig.axes.append%28ax3d%29%0A%0Adelta%20%3D%20pi%20/%20199.0%0Au%20%3D%20arange%280%2C%202%2Api%2B%28delta%2A2%29%2C%20delta%2A2%29%0Av%20%3D%20arange%280%2C%20pi%2Bdelta%2C%20delta%29%0A%0Ax%20%3D%20outer%28cos%28u%29%2Csin%28v%29 [...]
+ </action>
+ <action date="01 Mar 2007 18:16:57" parent="99" time="100" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="14" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:16:57" parent="100" time="101" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="15" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:16:57" parent="101" time="102" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="13" destinationModule="MplFigureCell" destinationPort="FigureManager(MplFigureManager)" id="12" sourceId="15" sourceModule="MplFigure" sourcePort="FigureManager(MplFigureManager)"/>
+ </action>
+ <action date="01 Mar 2007 18:16:58" parent="102" time="103" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="15" destinationModule="MplFigure" destinationPort="Script(String)" id="13" sourceId="14" sourceModule="MplPlot" sourcePort="source(String)"/>
+ </action>
+ <action date="01 Mar 2007 18:19:45" parent="103" time="104" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="-187.250666504" dy="-460.483781913" id="13"/>
+ <move dx="-89.8038910785" dy="-443.287292132" id="14"/>
+ <move dx="-171.96489781" dy="-433.733686698" id="15"/>
+ </action>
+ <action date="01 Mar 2007 18:19:45" parent="104" time="105" user="cscheid" what="addModulePort">
+ <notes>
+ None
+ </notes>
+ <addPort moduleId="14" portName="inputFile" portSpec="(File)" portType="input"/>
+ </action>
+ <action date="01 Mar 2007 18:19:45" parent="105" time="106" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="14" parameter="<no description>" parameterId="0" type="String" value="import%20matplotlib.axes3d%20as%20axes3d%0A%0Afig%20%3D%20gcf%28%29%0A%0Aplot%28array%28%5B0%2C%201%2C%202%2C%203%5D%29%2C%20array%28%5B1%2C%203%2C%201%2C%203%5D%29%29%0A"/>
+ </action>
+ <action date="01 Mar 2007 18:19:52" parent="106" time="107" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="14" destinationModule="MplPlot" destinationPort="inputFile(File)" id="14" sourceId="2" sourceModule="MeshQualityHistogram" sourcePort="output(File)"/>
+ </action>
+ <action date="01 Mar 2007 18:19:53" parent="107" time="108" user="cscheid" what="deleteConnection">
+ <notes>
+ None
+ </notes>
+ <connection connectionId="2"/>
+ </action>
+ <action date="01 Mar 2007 18:19:53" parent="108" time="109" user="cscheid" what="deleteModule">
+ <notes>
+ None
+ </notes>
+ <module moduleId="3"/>
+ </action>
+ <action date="01 Mar 2007 18:21:37" parent="109" time="110" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="14" parameter="<no description>" parameterId="0" type="String" value="import%20matplotlib.axes3d%20as%20axes3d%0A%0Afig%20%3D%20gcf%28%29%0A%0Ax%20%3D%20arange%280.0%2C%201.0%2C%201.0/100.0%29%0Ay%20%3D%20array%28%5Bfloat%28x%29%20for%20x%20in%20file%28inputFile.name%29%5D%29%0A%0Aplot%28x%2C%20y%29%0A"/>
+ </action>
+ <action date="01 Mar 2007 18:23:36" parent="110" time="111" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="14" parameter="<no description>" parameterId="0" type="String" value="import%20matplotlib.axes3d%20as%20axes3d%0A%0AinputFile%20%3D%20self.getInputFromPort%28%27inputFile%27%29%0A%0Afig%20%3D%20gcf%28%29%0A%0Ax%20%3D%20arange%280.0%2C%201.0%2C%201.0/100.0%29%0Ay%20%3D%20array%28%5Bfloat%28x%29%20for%20x%20in%20file%28inputFile.name%29%5D%29%0A%0Aplot%28x%2C%20y%29%0A"/>
+ </action>
+ <action date="01 Mar 2007 18:24:06" parent="111" time="112" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="14" parameter="<no description>" parameterId="0" type="String" value="import%20matplotlib.axes3d%20as%20axes3d%0A%0AinputFile%20%3D%20self.getInputFromPort%28%27inputFile%27%29%0A%0Afig%20%3D%20gcf%28%29%0A%0Ax%20%3D%20arange%280.0%2C%201.0%2C%201.0/100.0%29%0Ay%20%3D%20array%28%5Bfloat%28x%29%20for%20x%20in%20file%28inputFile.name%29%5D%29%0A%0Aprint%20x%0A%0Aprint%20y%0A%0Aplot%28x%2C%20y%29%0A"/>
+ </action>
+ <action date="01 Mar 2007 18:24:38" parent="112" time="113" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="14" parameter="<no description>" parameterId="0" type="String" value="import%20matplotlib.axes3d%20as%20axes3d%0A%0AinputFile%20%3D%20self.getInputFromPort%28%27inputFile%27%29%0A%0Afig%20%3D%20gcf%28%29%0A%0Ax%20%3D%20arange%280.0%2C%201.0%2C%201.0/100.0%29%0Ay%20%3D%20array%28%5Bfloat%28v%29%20for%20v%20in%20file%28inputFile.name%29%5D%29%0A%0Aprint%20x%0A%0Aprint%20y%0A%0Aplot%28x%2C%20y%29%0A"/>
+ </action>
+ <action date="01 Mar 2007 18:25:09" parent="113" time="114" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="244.572299107" dy="150.946965855" id="13"/>
+ <move dx="244.572299107" dy="150.946965855" id="14"/>
+ <move dx="244.572299107" dy="150.946965855" id="15"/>
+ </action>
+ <action date="01 Mar 2007 18:25:09" parent="114" time="115" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="16" name="MplFigure" x="-164.322418551" y="-330.761761724"/>
+ </action>
+ <action date="01 Mar 2007 18:25:09" parent="115" time="116" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="17" name="MplFigureCell" x="-140.181811548" y="-510.509732778"/>
+ </action>
+ <action date="01 Mar 2007 18:25:09" parent="116" time="117" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="18" name="MplPlot" x="-184.308660425" y="-221.229558975"/>
+ </action>
+ <action date="01 Mar 2007 18:25:10" parent="117" time="118" user="cscheid" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="19" name="MeshQualityHistogram" x="66.5181223843" y="36.1426939174"/>
+ </action>
+ <action date="01 Mar 2007 18:25:10" parent="118" time="119" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="16" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:25:10" parent="119" time="120" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="17" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:25:10" parent="120" time="121" user="cscheid" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="18" parameter="<no description>" parameterId="0" type="String" value="import%20matplotlib.axes3d%20as%20axes3d%0A%0AinputFile%20%3D%20self.getInputFromPort%28%27inputFile%27%29%0A%0Afig%20%3D%20gcf%28%29%0A%0Ax%20%3D%20arange%280.0%2C%201.0%2C%201.0/100.0%29%0Ay%20%3D%20array%28%5Bfloat%28v%29%20for%20v%20in%20file%28inputFile.name%29%5D%29%0A%0Aprint%20x%0A%0Aprint%20y%0A%0Aplot%28x%2C%20y%29%0A"/>
+ </action>
+ <action date="01 Mar 2007 18:25:10" parent="121" time="122" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="18" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:25:10" parent="122" time="123" user="cscheid" what="addModulePort">
+ <notes>
+ None
+ </notes>
+ <addPort moduleId="18" portName="inputFile" portSpec="(File)" portType="input"/>
+ </action>
+ <action date="01 Mar 2007 18:25:10" parent="123" time="124" user="cscheid" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="19" value=""/>
+ </action>
+ <action date="01 Mar 2007 18:25:10" parent="124" time="125" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="17" destinationModule="MplFigureCell" destinationPort="FigureManager(MplFigureManager)" id="15" sourceId="16" sourceModule="MplFigure" sourcePort="FigureManager(MplFigureManager)"/>
+ </action>
+ <action date="01 Mar 2007 18:25:10" parent="125" time="126" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="16" destinationModule="MplFigure" destinationPort="Script(String)" id="16" sourceId="18" sourceModule="MplPlot" sourcePort="source(String)"/>
+ </action>
+ <action date="01 Mar 2007 18:25:10" parent="126" time="127" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="18" destinationModule="MplPlot" destinationPort="inputFile(File)" id="17" sourceId="19" sourceModule="MeshQualityHistogram" sourcePort="output(File)"/>
+ </action>
+ <action date="01 Mar 2007 18:25:24" parent="127" time="128" user="cscheid" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="-196.804271938" dy="49.6787482562" id="11"/>
+ <move dx="-196.804271938" dy="49.6787482562" id="12"/>
+ <move dx="-168.143455636" dy="-225.46508824" id="16"/>
+ <move dx="-168.143455636" dy="-225.46508824" id="17"/>
+ <move dx="-168.143455636" dy="-225.46508824" id="18"/>
+ <move dx="-397.429986049" dy="-385.965659529" id="19"/>
+ </action>
+ <action date="01 Mar 2007 18:25:24" parent="128" time="129" user="cscheid" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="19" destinationModule="MeshQualityHistogram" destinationPort="file(File)" id="18" sourceId="1" sourceModule="File" sourcePort="self(File)"/>
+ </action>
+ <tag name="MeshCell" time="79"/>
+ <tag name="vtkVistrailsFileReader" time="42"/>
+ </visTrail>
diff --git a/examples/bikes.vt b/examples/bikes.vt
new file mode 100644
index 0000000..913b8ed
Binary files /dev/null and b/examples/bikes.vt differ
diff --git a/examples/brain_vistrail.vt b/examples/brain_vistrail.vt
new file mode 100644
index 0000000..6eb5f2a
Binary files /dev/null and b/examples/brain_vistrail.vt differ
diff --git a/examples/chebi_webservice.vt b/examples/chebi_webservice.vt
new file mode 100644
index 0000000..88dcaf1
Binary files /dev/null and b/examples/chebi_webservice.vt differ
diff --git a/examples/corie.xml b/examples/corie.xml
new file mode 100644
index 0000000..8640a5c
--- /dev/null
+++ b/examples/corie.xml
@@ -0,0 +1,9009 @@
+ <visTrail version="0.3.1">
+ <action date="20 Feb 2007 22:50:33" parent="0" time="1" user="emanuele" what="addModule">
+ <object cache="1" id="0" name="vtkCornerAnnotation" x="1034.11991838" y="-58.3393925256"/>
+ </action>
+ <action date="20 Feb 2007 22:50:33" parent="1" time="2" user="emanuele" what="addModule">
+ <object cache="1" id="1" name="vtkActor" x="1527.32015179" y="-249.262640518"/>
+ </action>
+ <action date="20 Feb 2007 22:50:33" parent="2" time="3" user="emanuele" what="addModule">
+ <object cache="1" id="2" name="vtkColorTransferFunction" x="688.135907588" y="231.58177416"/>
+ </action>
+ <action date="20 Feb 2007 22:50:33" parent="3" time="4" user="emanuele" what="addModule">
+ <object cache="1" id="3" name="VTKCell" x="1391.97591862" y="-567.894434513"/>
+ </action>
+ <action date="20 Feb 2007 22:50:33" parent="4" time="5" user="emanuele" what="addModule">
+ <object cache="1" id="4" name="vtkConeSource" x="1529.10671562" y="277.773705378"/>
+ </action>
+ <action date="20 Feb 2007 22:50:33" parent="5" time="6" user="emanuele" what="addModule">
+ <object cache="1" id="5" name="vtkRenderer" x="1126.59136348" y="-482.339603991"/>
+ </action>
+ <action date="20 Feb 2007 22:50:33" parent="6" time="7" user="emanuele" what="addModule">
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+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="12.5"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.16"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.73"/>
+ </action>
+ <action date="08 Mar 2007 14:34:37" parent="1268" time="1269" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="12.5"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.164705882353"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.73"/>
+ </action>
+ <action date="08 Mar 2007 14:34:43" parent="1269" time="1270" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="12.5"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.164705882353"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.725490196078"/>
+ </action>
+ <action date="08 Mar 2007 14:34:45" parent="1270" time="1271" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="12.5"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.164705882353"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="7" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.725490196078"/>
+ </action>
+ <action date="08 Mar 2007 14:34:54" parent="1271" time="1272" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="15.0"/>
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.73"/>
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.31"/>
+ </action>
+ <action date="08 Mar 2007 14:35:23" parent="1272" time="1273" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="15.0"/>
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.733333333333"/>
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.31"/>
+ </action>
+ <action date="08 Mar 2007 14:35:27" parent="1273" time="1274" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="15.0"/>
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.733333333333"/>
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="8" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.309803921569"/>
+ </action>
+ <action date="08 Mar 2007 14:35:30" parent="1274" time="1275" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="17.5"/>
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.45"/>
+ </action>
+ <action date="08 Mar 2007 14:35:41" parent="1275" time="1276" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="17.5"/>
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.454901960784"/>
+ </action>
+ <action date="08 Mar 2007 14:35:42" parent="1276" time="1277" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="17.5"/>
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="9" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.454901960784"/>
+ </action>
+ <action date="08 Mar 2007 14:35:53" parent="1277" time="1278" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="20.0"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.93"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:35:54" parent="1278" time="1279" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="20.0"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.93"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:36:07" parent="1279" time="1280" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="20.0"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.933333333333"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:36:10" parent="1280" time="1281" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="20.0"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.933333333333"/>
+ <set alias="" function="AddRGBPoint" functionId="10" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:36:12" parent="1281" time="1282" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="22.5"/>
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.75"/>
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:36:24" parent="1282" time="1283" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="22.5"/>
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.749019607843"/>
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:36:25" parent="1283" time="1284" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="22.5"/>
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.749019607843"/>
+ <set alias="" function="AddRGBPoint" functionId="11" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:36:29" parent="1284" time="1285" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="25.0"/>
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.56"/>
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:36:41" parent="1285" time="1286" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="25.0"/>
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.560784313725"/>
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:36:42" parent="1286" time="1287" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="25.0"/>
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.560784313725"/>
+ <set alias="" function="AddRGBPoint" functionId="12" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:36:57" parent="1287" time="1288" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="13" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="27.5"/>
+ <set alias="" function="AddRGBPoint" functionId="13" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
+ <set alias="" function="AddRGBPoint" functionId="13" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.37"/>
+ <set alias="" function="AddRGBPoint" functionId="13" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:37:04" parent="1288" time="1289" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="13" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="27.5"/>
+ <set alias="" function="AddRGBPoint" functionId="13" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="1.0"/>
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+ </action>
+ <action date="08 Mar 2007 14:37:12" parent="1289" time="1290" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="14" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="30.0"/>
+ <set alias="" function="AddRGBPoint" functionId="14" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.88"/>
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+ </action>
+ <action date="08 Mar 2007 14:37:21" parent="1290" time="1291" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="14" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="30.0"/>
+ <set alias="" function="AddRGBPoint" functionId="14" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.878431372549"/>
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+ </action>
+ <action date="08 Mar 2007 14:37:34" parent="1291" time="1292" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="15" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="32.5"/>
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+ </action>
+ <action date="08 Mar 2007 14:37:37" parent="1292" time="1293" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="15" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="32.5"/>
+ <set alias="" function="AddRGBPoint" functionId="15" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.674509803922"/>
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+ <set alias="" function="AddRGBPoint" functionId="15" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:37:41" parent="1293" time="1294" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="16" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="35.0"/>
+ <set alias="" function="AddRGBPoint" functionId="16" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.49"/>
+ <set alias="" function="AddRGBPoint" functionId="16" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="16" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:37:58" parent="1294" time="1295" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="16" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="35.0"/>
+ <set alias="" function="AddRGBPoint" functionId="16" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.494117647059"/>
+ <set alias="" function="AddRGBPoint" functionId="16" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="16" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:38:04" parent="1295" time="1296" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="35.5"/>
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.49"/>
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:38:08" parent="1296" time="1297" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="35.5"/>
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0"/>
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:38:15" parent="1297" time="1298" user="hvo" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="35.5"/>
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="1" type="Float" value="0.494117647059"/>
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="2" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="17" moduleId="2" parameter="<no description>" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:39:00" parent="1298" time="1299" user="hvo" what="moveModule">
+ <move dx="143.219665953" dy="-132.989689814" id="2"/>
+ </action>
+ <action date="08 Mar 2007 14:39:00" parent="1299" time="1300" user="hvo" what="addConnection">
+ <connect destinationId="73" destinationModule="vtkMapper" destinationPort="SetLookupTable(vtkScalarsToColors)" id="154" sourceId="2" sourceModule="vtkColorTransferFunction" sourcePort="self(vtkColorTransferFunction)"/>
+ </action>
+ <action date="08 Mar 2007 14:39:44" parent="1300" time="1301" user="hvo" what="changeParameter">
+ <set alias="" function="Translate" functionId="0" moduleId="77" parameter="<no description>" parameterId="0" type="Float" value="0"/>
+ <set alias="" function="Translate" functionId="0" moduleId="77" parameter="<no description>" parameterId="1" type="Float" value="0"/>
+ <set alias="" function="Translate" functionId="0" moduleId="77" parameter="<no description>" parameterId="2" type="Float" value="-35"/>
+ </action>
+ <action date="08 Mar 2007 14:39:46" parent="1301" time="1302" user="hvo" what="changeParameter">
+ <set alias="" function="Translate" functionId="0" moduleId="77" parameter="<no description>" parameterId="0" type="Float" value="0"/>
+ <set alias="" function="Translate" functionId="0" moduleId="77" parameter="<no description>" parameterId="1" type="Float" value="0"/>
+ <set alias="" function="Translate" functionId="0" moduleId="77" parameter="<no description>" parameterId="2" type="Float" value="-35"/>
+ </action>
+ <action date="08 Mar 2007 14:40:00" parent="1302" time="1303" user="hvo" what="moveModule">
+ <move dx="64.3027071628" dy="27.767078093" id="71"/>
+ <move dx="0.0" dy="-1.46142516279" id="73"/>
+ </action>
+ <action date="08 Mar 2007 14:40:00" parent="1303" time="1304" user="hvo" what="changeParameter">
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="0" type="Float" value="0.0"/>
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="1" type="Float" value="0.0"/>
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="2" type="Float" value="0.0"/>
+ </action>
+ <action date="08 Mar 2007 14:40:02" parent="1304" time="1305" user="hvo" what="changeParameter">
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="0" type="Float" value="1"/>
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="1" type="Float" value=""/>
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="2" type="Float" value=""/>
+ </action>
+ <action date="08 Mar 2007 14:40:02" parent="1305" time="1306" user="hvo" what="changeParameter">
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="0" type="Float" value="1"/>
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="1" type="Float" value="1"/>
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="2" type="Float" value=""/>
+ </action>
+ <action date="08 Mar 2007 14:40:06" parent="1306" time="1307" user="hvo" what="changeParameter">
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="0" type="Float" value="1"/>
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="1" type="Float" value="1"/>
+ <set alias="" function="SetScale" functionId="0" moduleId="72" parameter="<no description>" parameterId="2" type="Float" value="1000"/>
+ </action>
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+ <tag name="Test2" time="1640"/>
+ <tag name="TimeStep 60" time="161"/>
+ <tag name="webpage 30" time="237"/>
+ <tag name="webpage 60" time="234"/>
+ <tag name="TimeStep 90" time="168"/>
+ <tag name="Test1" time="1546"/>
+ <tag name="Static" time="2439"/>
+ <tag name="TimeStep 30" time="164"/>
+ <tag name="Interactive" time="2524"/>
+ <tag name=" A transect" time="1718"/>
+ <tag name="basic workflow" time="157"/>
+ </visTrail>
diff --git a/examples/gcd.xml b/examples/gcd.xml
new file mode 100644
index 0000000..2734584
--- /dev/null
+++ b/examples/gcd.xml
@@ -0,0 +1,1785 @@
+<vistrail id="" name="" version="1.0.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/vistrail.xsd">
+ <action date="2013-10-14 15:05:53" id="1" prevId="0" session="0" user="Remi">
+ <add id="0" objectId="0" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="0" name="InputPort" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="1" objectId="0" parentObjId="0" parentObjType="module" what="location">
+ <location id="0" x="-127.0" y="52.0" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:05:54" id="2" prevId="1" session="0" user="Remi">
+ <add id="2" objectId="1" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="1" name="InputPort" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="3" objectId="1" parentObjId="1" parentObjType="module" what="location">
+ <location id="1" x="110.0" y="42.0" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:05:56" id="3" prevId="2" session="0" user="Remi">
+ <add id="4" objectId="0" parentObjId="0" parentObjType="module" what="function">
+ <function id="0" name="name" pos="0" />
+ </add>
+ <add id="5" objectId="0" parentObjId="0" parentObjType="function" what="parameter">
+ <parameter alias="" id="0" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:String" val="a" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:05:59" id="4" prevId="3" session="0" user="Remi">
+ <add id="6" objectId="1" parentObjId="1" parentObjType="module" what="function">
+ <function id="1" name="name" pos="0" />
+ </add>
+ <add id="7" objectId="1" parentObjId="1" parentObjType="function" what="parameter">
+ <parameter alias="" id="1" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:String" val="b" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:06:07" id="5" prevId="4" session="0" user="Remi">
+ <change id="8" newObjId="3" oldObjId="0" parentObjId="0" parentObjType="module" what="location">
+ <location id="3" x="-111.0" y="218.0" />
+ </change>
+ <change id="9" newObjId="4" oldObjId="1" parentObjId="1" parentObjType="module" what="location">
+ <location id="4" x="110.0" y="222.0" />
+ </change>
+ </action>
+ <action date="2013-10-14 15:06:07" id="6" prevId="5" session="0" user="Remi">
+ <add id="10" objectId="2" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="2" name="If" namespace="" package="org.vistrails.vistrails.control_flow" version="0.2.3" />
+ </add>
+ <add id="11" objectId="2" parentObjId="2" parentObjType="module" what="location">
+ <location id="2" x="-9.0" y="-2.0" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:06:10" id="7" prevId="6" session="0" user="Remi">
+ <add id="12" objectId="3" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="3" name="OutputPort" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="13" objectId="5" parentObjId="3" parentObjType="module" what="location">
+ <location id="5" x="16.0" y="-102.0" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:06:10" id="8" prevId="7" session="0" user="Remi">
+ <add id="14" objectId="0" parentObjId="" parentObjType="" what="connection">
+ <connection id="0" />
+ </add>
+ <add id="15" objectId="0" parentObjId="0" parentObjType="connection" what="port">
+ <port id="0" moduleId="2" moduleName="If" name="Result" signature="(org.vistrails.vistrails.basic:Variant)" type="source" />
+ </add>
+ <add id="16" objectId="1" parentObjId="0" parentObjType="connection" what="port">
+ <port id="1" moduleId="3" moduleName="OutputPort" name="InternalPipe" signature="(org.vistrails.vistrails.basic:Variant)" type="destination" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:07:17" id="9" prevId="8" session="0" user="Remi">
+ <add id="17" objectId="4" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="4" name="PythonCalc" namespace="" package="org.vistrails.vistrails.pythoncalc" version="0.9.1" />
+ </add>
+ <add id="18" objectId="6" parentObjId="4" parentObjType="module" what="location">
+ <location id="6" x="-217.0" y="86.0" />
+ </add>
+ </action>
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+ <add id="19" objectId="5" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="5" name="PythonSource" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="20" objectId="7" parentObjId="5" parentObjType="module" what="location">
+ <location id="7" x="181.0" y="90.0" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:07:46" id="11" prevId="10" session="0" user="Remi">
+ <add id="21" objectId="0" parentObjId="5" parentObjType="module" what="portSpec">
+ <portSpec id="0" maxConns="-1" minConns="0" name="a" optional="0" sortKey="0" type="input">
+ <portSpecItem default="" entryType="" id="0" label="" module="Integer" namespace="" package="org.vistrails.vistrails.basic" pos="0" values="" />
+ </portSpec>
+ </add>
+ <add id="22" objectId="1" parentObjId="5" parentObjType="module" what="portSpec">
+ <portSpec id="1" maxConns="-1" minConns="0" name="b" optional="0" sortKey="1" type="input">
+ <portSpecItem default="" entryType="" id="1" label="" module="Integer" namespace="" package="org.vistrails.vistrails.basic" pos="0" values="" />
+ </portSpec>
+ </add>
+ <add id="23" objectId="2" parentObjId="5" parentObjType="module" what="portSpec">
+ <portSpec id="2" maxConns="-1" minConns="0" name="o" optional="0" sortKey="0" type="output">
+ <portSpecItem default="" entryType="" id="2" label="" module="Boolean" namespace="" package="org.vistrails.vistrails.basic" pos="0" values="" />
+ </portSpec>
+ </add>
+ <add id="24" objectId="2" parentObjId="5" parentObjType="module" what="function">
+ <function id="2" name="source" pos="0" />
+ </add>
+ <add id="25" objectId="2" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="2" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:String" val="o%20%3D%20a%20%3C%20b" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:07:51" id="12" prevId="11" session="0" user="Remi">
+ <add id="26" objectId="0" parentObjId="5" parentObjType="module" what="annotation">
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+ </add>
+ </action>
+ <action date="2013-10-14 15:07:59" id="13" prevId="12" session="0" user="Remi">
+ <add id="27" objectId="1" parentObjId="" parentObjType="" what="connection">
+ <connection id="1" />
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+ <add id="28" objectId="2" parentObjId="1" parentObjType="connection" what="port">
+ <port id="2" moduleId="0" moduleName="InputPort" name="InternalPipe" signature="(org.vistrails.vistrails.basic:Variant)" type="source" />
+ </add>
+ <add id="29" objectId="3" parentObjId="1" parentObjType="connection" what="port">
+ <port id="3" moduleId="5" moduleName="PythonSource" name="a" signature="(org.vistrails.vistrails.basic:Integer)" type="destination" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:08:00" id="14" prevId="13" session="0" user="Remi">
+ <add id="30" objectId="2" parentObjId="" parentObjType="" what="connection">
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+ <add id="31" objectId="4" parentObjId="2" parentObjType="connection" what="port">
+ <port id="4" moduleId="1" moduleName="InputPort" name="InternalPipe" signature="(org.vistrails.vistrails.basic:Variant)" type="source" />
+ </add>
+ <add id="32" objectId="5" parentObjId="2" parentObjType="connection" what="port">
+ <port id="5" moduleId="5" moduleName="PythonSource" name="b" signature="(org.vistrails.vistrails.basic:Integer)" type="destination" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:08:13" id="15" prevId="14" session="0" user="Remi">
+ <change id="33" newObjId="8" oldObjId="2" parentObjId="2" parentObjType="module" what="location">
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+ </change>
+ </action>
+ <action date="2013-10-14 15:08:13" id="16" prevId="15" session="0" user="Remi">
+ <add id="35" objectId="3" parentObjId="" parentObjType="" what="connection">
+ <connection id="3" />
+ </add>
+ <add id="36" objectId="6" parentObjId="3" parentObjType="connection" what="port">
+ <port id="6" moduleId="5" moduleName="PythonSource" name="o" signature="(org.vistrails.vistrails.basic:Boolean)" type="source" />
+ </add>
+ <add id="37" objectId="7" parentObjId="3" parentObjType="connection" what="port">
+ <port id="7" moduleId="2" moduleName="If" name="Condition" signature="(org.vistrails.vistrails.basic:Boolean)" type="destination" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:08:31" id="17" prevId="16" session="0" user="Remi">
+ <annotation id="1" key="__description__" value="Paste" />
+ <add id="38" objectId="6" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="6" name="PythonCalc" namespace="" package="org.vistrails.vistrails.pythoncalc" version="0.9.1" />
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+ </action>
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+ <delete id="55" objectId="1" parentObjId="" parentObjType="" what="module" />
+ </action>
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+ <location id="87" x="-106.621620243" y="-161.836387869" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:27:40" id="124" prevId="123" session="2" user="Remi">
+ <add id="532" objectId="46" parentObjId="" parentObjType="" what="connection">
+ <connection id="46" />
+ </add>
+ <add id="533" objectId="92" parentObjId="46" parentObjType="connection" what="port">
+ <port id="92" moduleId="24" moduleName="Group" name="self" signature="(org.vistrails.vistrails.basic:Group)" type="source" />
+ </add>
+ <add id="534" objectId="93" parentObjId="46" parentObjType="connection" what="port">
+ <port id="93" moduleId="25" moduleName="While" name="FunctionPort" signature="(org.vistrails.vistrails.basic:Module)" type="destination" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:27:49" id="125" prevId="124" session="2" user="Remi">
+ <add id="535" objectId="13" parentObjId="25" parentObjType="module" what="function">
+ <function id="13" name="StateOutputPorts" pos="0" />
+ </add>
+ <add id="536" objectId="16" parentObjId="13" parentObjType="function" what="parameter">
+ <parameter alias="" id="16" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:List" val="['state']" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:27:56" id="126" prevId="125" session="2" user="Remi">
+ <add id="537" objectId="14" parentObjId="24" parentObjType="group" what="function">
+ <function id="14" name="nbs" pos="0" />
+ </add>
+ <add id="538" objectId="18" parentObjId="14" parentObjType="function" what="parameter">
+ <parameter alias="" id="18" name="<no description>" pos="1" type="org.vistrails.vistrails.basic:Integer" val="" />
+ </add>
+ <add id="539" objectId="17" parentObjId="14" parentObjType="function" what="parameter">
+ <parameter alias="" id="17" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:Integer" val="9" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:27:57" id="127" prevId="126" session="2" user="Remi">
+ <change id="540" newObjId="19" oldObjId="18" parentObjId="14" parentObjType="function" what="parameter">
+ <parameter alias="" id="19" name="<no description>" pos="1" type="org.vistrails.vistrails.basic:Integer" val="12" />
+ </change>
+ </action>
+ <action date="2013-10-14 15:28:02" id="128" prevId="127" session="2" user="Remi">
+ <change id="541" newObjId="20" oldObjId="19" parentObjId="14" parentObjType="function" what="parameter">
+ <parameter alias="" id="20" name="<no description>" pos="1" type="org.vistrails.vistrails.basic:Integer" val="15" />
+ </change>
+ </action>
+ <action date="2013-10-14 15:28:13" id="129" prevId="128" session="2" user="Remi">
+ <add id="542" objectId="15" parentObjId="25" parentObjType="module" what="function">
+ <function id="15" name="StateInputPorts" pos="1" />
+ </add>
+ <add id="543" objectId="21" parentObjId="15" parentObjType="function" what="parameter">
+ <parameter alias="" id="21" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:List" val="['nbs']" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:28:16" id="130" prevId="129" session="2" user="Remi">
+ <add id="544" objectId="16" parentObjId="25" parentObjType="module" what="function">
+ <function id="16" name="OutputPort" pos="2" />
+ </add>
+ <add id="545" objectId="22" parentObjId="16" parentObjType="function" what="parameter">
+ <parameter alias="" id="22" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:String" val="result" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:28:20" id="131" prevId="130" session="2" user="Remi">
+ <add id="546" objectId="26" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="26" name="StandardOutput" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="547" objectId="88" parentObjId="26" parentObjType="module" what="location">
+ <location id="88" x="-16.1836387869" y="-268.458008111" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:28:20" id="132" prevId="131" session="2" user="Remi">
+ <add id="548" objectId="47" parentObjId="" parentObjType="" what="connection">
+ <connection id="47" />
+ </add>
+ <add id="549" objectId="94" parentObjId="47" parentObjType="connection" what="port">
+ <port id="94" moduleId="25" moduleName="While" name="Result" signature="(org.vistrails.vistrails.basic:Variant)" type="source" />
+ </add>
+ <add id="550" objectId="95" parentObjId="47" parentObjType="connection" what="port">
+ <port id="95" moduleId="26" moduleName="StandardOutput" name="value" signature="(org.vistrails.vistrails.basic:Module)" type="destination" />
+ </add>
+ </action>
+ <action date="2013-10-14 15:28:22" id="133" prevId="132" session="2" user="Remi">
+ <change id="551" newObjId="89" oldObjId="88" parentObjId="26" parentObjType="module" what="location">
+ <location id="89" x="-49.5028951127" y="-270.361965616" />
+ </change>
+ </action>
+ <action date="2013-10-14 15:28:57" id="134" prevId="133" session="2" user="Remi">
+ <add id="552" objectId="17" parentObjId="25" parentObjType="module" what="function">
+ <function id="17" name="ConditionPort" pos="3" />
+ </add>
+ <add id="553" objectId="23" parentObjId="17" parentObjType="function" what="parameter">
+ <parameter alias="" id="23" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:String" val="continue" />
+ </add>
+ </action>
+</vistrail>
diff --git a/examples/head.vt b/examples/head.vt
new file mode 100644
index 0000000..0b7c407
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diff --git a/examples/infovis.vt b/examples/infovis.vt
new file mode 100644
index 0000000..799222b
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diff --git a/examples/lung.vt b/examples/lung.vt
new file mode 100644
index 0000000..ce251cd
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diff --git a/examples/matplotlib/Acorr_ex8.vt b/examples/matplotlib/Acorr_ex8.vt
new file mode 100644
index 0000000..f4e9e27
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diff --git a/examples/matplotlib/Arrow_ex9.vt b/examples/matplotlib/Arrow_ex9.vt
new file mode 100644
index 0000000..2643084
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diff --git a/examples/matplotlib/Psd.vt b/examples/matplotlib/Psd.vt
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index 0000000..d671910
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diff --git a/examples/matplotlib/ReadMe.txt b/examples/matplotlib/ReadMe.txt
new file mode 100644
index 0000000..1576b02
--- /dev/null
+++ b/examples/matplotlib/ReadMe.txt
@@ -0,0 +1,23 @@
+(Note: the following *.vt files need to be imported in vistrails and executed)
+The following plots have been plotted with vistrails using matplotlib package.
+
+Arrow_ex9 is an arrow marking downwards. by varying the input coordinates the direction of the arrow can be changed.
+ (x,y,dx,dy) are the required inputs.
+Acorr_ex8 plots an Acorr in matplotlib.
+ (x) is required input.
+Axhspan_ex5 plots the axhspan graph along the x axis.
+ (ymin,ymax) are the required input.
+bar_ex1 represents a mplbar plot.
+ (left,height) are the required parameters.
+hist_ex1 plots a histogram.
+ (x) is the required input.
+line2D_ex4 is a dashed box plot
+ (x) is the required input.
+line2D_ex7 is a dashed line chart with line properties
+ (x,y) are the required input.
+lineplot_ex3 is a simple line chart
+ (x,y) are the reuired input.
+pie_ex1 is a pie chart with shadow
+ (x) is required input which is a list.
+polar_ex10 represents the polar plot with radius and theta as input.
+ (r,theta) are input where theta is 2*pi*r.
\ No newline at end of file
diff --git a/examples/matplotlib/annotate.vt b/examples/matplotlib/annotate.vt
new file mode 100644
index 0000000..e3b9956
Binary files /dev/null and b/examples/matplotlib/annotate.vt differ
diff --git a/examples/matplotlib/axhspan_ex5.vt b/examples/matplotlib/axhspan_ex5.vt
new file mode 100644
index 0000000..12eabe2
Binary files /dev/null and b/examples/matplotlib/axhspan_ex5.vt differ
diff --git a/examples/matplotlib/bar_ex1.vt b/examples/matplotlib/bar_ex1.vt
new file mode 100644
index 0000000..88c4373
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diff --git a/examples/matplotlib/cohere.vt b/examples/matplotlib/cohere.vt
new file mode 100644
index 0000000..c706ee2
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diff --git a/examples/matplotlib/contour.vt b/examples/matplotlib/contour.vt
new file mode 100644
index 0000000..248022a
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diff --git a/examples/matplotlib/contourf.vt b/examples/matplotlib/contourf.vt
new file mode 100644
index 0000000..c54aec7
Binary files /dev/null and b/examples/matplotlib/contourf.vt differ
diff --git a/examples/matplotlib/hist_ex1.vt b/examples/matplotlib/hist_ex1.vt
new file mode 100644
index 0000000..b8533bd
Binary files /dev/null and b/examples/matplotlib/hist_ex1.vt differ
diff --git a/examples/matplotlib/line2d_ex4.vt b/examples/matplotlib/line2d_ex4.vt
new file mode 100644
index 0000000..c0d6443
Binary files /dev/null and b/examples/matplotlib/line2d_ex4.vt differ
diff --git a/examples/matplotlib/line2d_ex7.vt b/examples/matplotlib/line2d_ex7.vt
new file mode 100644
index 0000000..ad5c7e1
Binary files /dev/null and b/examples/matplotlib/line2d_ex7.vt differ
diff --git a/examples/matplotlib/lineplot_ex3.vt b/examples/matplotlib/lineplot_ex3.vt
new file mode 100644
index 0000000..c90a889
Binary files /dev/null and b/examples/matplotlib/lineplot_ex3.vt differ
diff --git a/examples/matplotlib/pcolor.vt b/examples/matplotlib/pcolor.vt
new file mode 100644
index 0000000..0dcd34c
Binary files /dev/null and b/examples/matplotlib/pcolor.vt differ
diff --git a/examples/matplotlib/pie_ex1.vt b/examples/matplotlib/pie_ex1.vt
new file mode 100644
index 0000000..25f3433
Binary files /dev/null and b/examples/matplotlib/pie_ex1.vt differ
diff --git a/examples/matplotlib/polar_ex10.vt b/examples/matplotlib/polar_ex10.vt
new file mode 100644
index 0000000..846b616
Binary files /dev/null and b/examples/matplotlib/polar_ex10.vt differ
diff --git a/examples/matplotlib/scatter.vt b/examples/matplotlib/scatter.vt
new file mode 100644
index 0000000..c002e72
Binary files /dev/null and b/examples/matplotlib/scatter.vt differ
diff --git a/examples/matplotlib/semilog.vt b/examples/matplotlib/semilog.vt
new file mode 100644
index 0000000..94db983
Binary files /dev/null and b/examples/matplotlib/semilog.vt differ
diff --git a/examples/mummy.xml b/examples/mummy.xml
new file mode 100644
index 0000000..95782c8
--- /dev/null
+++ b/examples/mummy.xml
@@ -0,0 +1,552 @@
+ <visTrail version="0.3.0">
+ <action date="05 Jul 2006 11:12:53" parent="0" time="2" user="emanuele" what="addModule">
+ <object cache="1" id="0" name="vtkStructuredPointsReader" x="-0.967032957532" y="1.8021978022"/>
+ </action>
+ <action date="05 Jul 2006 11:13:10" parent="2" time="3" user="emanuele" what="moveModule">
+ <move dx="-2.93040299416" dy="88.6446914673" id="0"/>
+ <move dx="-2.93040299416" dy="88.6446914673" id="0"/>
+ <move dx="-2.93040299416" dy="88.6446914673" id="0"/>
+ <move dx="2.64289617538" dy="149.323638916" id="0"/>
+ </action>
+ <action date="05 Jul 2006 11:14:15" parent="3" time="4" user="emanuele" what="moveModule">
+ <move dx="2.64289617538" dy="149.323638916" id="0"/>
+ <move dx="2.64289617538" dy="149.323638916" id="0"/>
+ <move dx="2.64289617538" dy="149.323638916" id="0"/>
+ <move dx="2.64289617538" dy="149.323638916" id="0"/>
+ <move dx="-4.12526130676" dy="-33.0020904541" id="0"/>
+ <move dx="-4.12526130676" dy="-33.0020904541" id="0"/>
+ </action>
+ <action date="05 Jul 2006 11:14:15" parent="4" time="5" user="emanuele" what="changeParameter">
+ <set alias="" function="SetFileName" functionId="0" moduleId="0" parameter="(unnamed)" parameterId="0" type="String" value=""/>
+ </action>
+ <action date="05 Jul 2006 11:14:41" parent="5" time="6" user="emanuele" what="changeParameter">
+ <set alias="" function="SetFileName" functionId="0" moduleId="0" parameter="(unnamed)" parameterId="0" type="String" value="../examples/data/mummy.128.vtk"/>
+ </action>
+ <action date="05 Jul 2006 11:15:16" parent="6" time="7" user="emanuele" what="addModule">
+ <object cache="0" id="1" name="vtkPiecewiseFunction" x="-32.8559157536" y="204.296605696"/>
+ </action>
+ <action date="05 Jul 2006 11:16:04" parent="7" time="8" user="emanuele" what="moveModule">
+ <move dx="-4.12526130676" dy="-33.0020904541" id="0"/>
+ <move dx="-4.12526130676" dy="-33.0020904541" id="0"/>
+ <move dx="-4.12526130676" dy="-33.0020904541" id="0"/>
+ <move dx="-4.12526130676" dy="-33.0020904541" id="0"/>
+ <move dx="22.0703868866" dy="472.306304932" id="1"/>
+ <move dx="22.0703868866" dy="472.306304932" id="1"/>
+ <move dx="436.661560059" dy="142.583374023" id="1"/>
+ <move dx="-118.076850891" dy="-37.8737068176" id="0"/>
+ <move dx="-2.22786521912" dy="11.1393260956" id="1"/>
+ </action>
+ <action date="05 Jul 2006 11:16:04" parent="8" time="9" user="emanuele" what="changeParameter">
+ <set alias="" function="AddPoint" functionId="0" moduleId="1" parameter="(unnamed)" parameterId="0" type="Float" value="0.0"/>
+ <set alias="" function="AddPoint" functionId="0" moduleId="1" parameter="(unnamed)" parameterId="1" type="Float" value="0.0"/>
+ </action>
+ <action date="05 Jul 2006 11:16:12" parent="9" time="10" user="emanuele" what="changeParameter">
+ <set alias="" function="AddPoint" functionId="0" moduleId="1" parameter="(unnamed)" parameterId="0" type="Float" value="79"/>
+ <set alias="" function="AddPoint" functionId="0" moduleId="1" parameter="(unnamed)" parameterId="1" type="Float" value=""/>
+ </action>
+ <action date="05 Jul 2006 11:16:16" parent="10" time="11" user="emanuele" what="changeParameter">
+ <set alias="" function="AddPoint" functionId="0" moduleId="1" parameter="(unnamed)" parameterId="0" type="Float" value="79"/>
+ <set alias="" function="AddPoint" functionId="0" moduleId="1" parameter="(unnamed)" parameterId="1" type="Float" value="0.0"/>
+ </action>
+ <action date="05 Jul 2006 11:16:21" parent="11" time="12" user="emanuele" what="changeParameter">
+ <set alias="" function="AddPoint" functionId="1" moduleId="1" parameter="(unnamed)" parameterId="0" type="Float" value="0.0"/>
+ <set alias="" function="AddPoint" functionId="1" moduleId="1" parameter="(unnamed)" parameterId="1" type="Float" value="0.0"/>
+ </action>
+ <action date="05 Jul 2006 11:16:27" parent="12" time="13" user="emanuele" what="changeParameter">
+ <set alias="" function="AddPoint" functionId="1" moduleId="1" parameter="(unnamed)" parameterId="0" type="Float" value="80"/>
+ <set alias="" function="AddPoint" functionId="1" moduleId="1" parameter="(unnamed)" parameterId="1" type="Float" value=""/>
+ </action>
+ <action date="05 Jul 2006 11:16:32" parent="13" time="14" user="emanuele" what="changeParameter">
+ <set alias="" function="AddPoint" functionId="1" moduleId="1" parameter="(unnamed)" parameterId="0" type="Float" value="80"/>
+ <set alias="" function="AddPoint" functionId="1" moduleId="1" parameter="(unnamed)" parameterId="1" type="Float" value="0.1"/>
+ </action>
+ <action date="05 Jul 2006 11:16:41" parent="14" time="15" user="emanuele" what="changeParameter">
+ <set alias="" function="AddPoint" functionId="2" moduleId="1" parameter="(unnamed)" parameterId="0" type="Float" value="0.0"/>
+ <set alias="" function="AddPoint" functionId="2" moduleId="1" parameter="(unnamed)" parameterId="1" type="Float" value="0.0"/>
+ </action>
+ <action date="05 Jul 2006 11:16:46" parent="15" time="16" user="emanuele" what="changeParameter">
+ <set alias="" function="AddPoint" functionId="2" moduleId="1" parameter="(unnamed)" parameterId="0" type="Float" value="110"/>
+ <set alias="" function="AddPoint" functionId="2" moduleId="1" parameter="(unnamed)" parameterId="1" type="Float" value=""/>
+ </action>
+ <action date="05 Jul 2006 11:16:52" parent="16" time="17" user="emanuele" what="changeParameter">
+ <set alias="" function="AddPoint" functionId="2" moduleId="1" parameter="(unnamed)" parameterId="0" type="Float" value="110"/>
+ <set alias="" function="AddPoint" functionId="2" moduleId="1" parameter="(unnamed)" parameterId="1" type="Float" value="0.8"/>
+ </action>
+ <action date="05 Jul 2006 11:17:39" parent="17" time="18" user="emanuele" what="moveModule">
+ <move dx="-61.6779518127" dy="-804.616882324" id="1"/>
+ <move dx="-204.864761353" dy="167.841003418" id="1"/>
+ <move dx="17.2777519226" dy="197.460006714" id="0"/>
+ <move dx="197.460021973" dy="88.8570022583" id="1"/>
+ </action>
+ <action date="05 Jul 2006 11:17:39" parent="18" time="19" user="emanuele" what="addModule">
+ <object cache="0" id="2" name="vtkColorTransferFunction" x="332.116694623" y="538.146279974"/>
+ </action>
+ <action date="05 Jul 2006 11:17:55" parent="19" time="20" user="emanuele" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="0" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="1" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="2" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="05 Jul 2006 11:18:03" parent="20" time="21" user="emanuele" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="0" type="Float" value="79.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="1" type="Float" value=""/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="2" type="Float" value=""/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="3" type="Float" value=""/>
+ </action>
+ <action date="05 Jul 2006 11:18:06" parent="21" time="22" user="emanuele" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="0" type="Float" value="79.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="1" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="2" type="Float" value=""/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="3" type="Float" value=""/>
+ </action>
+ <action date="05 Jul 2006 11:18:09" parent="22" time="23" user="emanuele" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="0" type="Float" value="79.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="1" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="2" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="3" type="Float" value=""/>
+ </action>
+ <action date="05 Jul 2006 11:18:13" parent="23" time="24" user="emanuele" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="0" type="Float" value="79.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="1" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="2" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="0" moduleId="2" parameter="(unnamed)" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="05 Jul 2006 11:18:15" parent="24" time="25" user="emanuele" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="0" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="1" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="2" type="Float" value="0.0"/>
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="3" type="Float" value="0.0"/>
+ </action>
+ <action date="05 Jul 2006 11:18:21" parent="25" time="26" user="emanuele" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="0" type="Float" value="80.0"/>
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="1" type="Float" value=""/>
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="2" type="Float" value=""/>
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="3" type="Float" value=""/>
+ </action>
+ <action date="05 Jul 2006 11:18:24" parent="26" time="27" user="emanuele" what="changeParameter">
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="0" type="Float" value="80.0"/>
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="1" type="Float" value="0.8"/>
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="2" type="Float" value=""/>
+ <set alias="" function="AddRGBPoint" functionId="1" moduleId="2" parameter="(unnamed)" parameterId="3" type="Float" value=""/>
+ </action>
+ <action date="05 Jul 2006 11:18:29" parent="27" time="28" user="emanuele" what="changeParameter">
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diff --git a/examples/offscreen.vt b/examples/offscreen.vt
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+ <module cache="1" id="10" name="List" namespace="" package="org.vistrails.vistrails.basic" version="2.1">
+ <location id="10" x="64.5208907006" y="116.834756192" />
+ </module>
+ </workflow>
+ </group>
+ </add>
+ <add id="581" objectId="68" parentObjId="43" parentObjType="group" what="location">
+ <location id="68" x="8.75961968679" y="27.8100671139" />
+ </add>
+ </action>
+ <action date="2013-09-06 11:57:59" id="75" prevId="74" session="3" user="Remi">
+ <annotation id="36" key="__description__" value="Paste" />
+ <add id="582" objectId="44" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="44" name="Integer" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="583" objectId="41" parentObjId="44" parentObjType="module" what="function">
+ <function id="41" name="value" pos="0" />
+ </add>
+ <add id="584" objectId="53" parentObjId="41" parentObjType="function" what="parameter">
+ <parameter alias="" id="53" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:Integer" val="8" />
+ </add>
+ <add id="585" objectId="69" parentObjId="44" parentObjType="module" what="location">
+ <location id="69" x="-119.838926175" y="22.7651006711" />
+ </add>
+ <add id="586" objectId="45" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="45" name="List" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="587" objectId="42" parentObjId="45" parentObjType="module" what="function">
+ <function id="42" name="value" pos="0" />
+ </add>
+ <add id="588" objectId="54" parentObjId="42" parentObjType="function" what="parameter">
+ <parameter alias="" id="54" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:List" val="[2, 3, 5]" />
+ </add>
+ <add id="589" objectId="70" parentObjId="45" parentObjType="module" what="location">
+ <location id="70" x="157.637583893" y="20.1879194631" />
+ </add>
+ </action>
+ <action date="2013-09-06 11:58:08" id="76" prevId="75" session="3" user="Remi">
+ <change id="590" newObjId="71" oldObjId="69" parentObjId="44" parentObjType="module" what="location">
+ <location id="71" x="-87.1946308729" y="149.046979866" />
+ </change>
+ <change id="591" newObjId="72" oldObjId="70" parentObjId="45" parentObjType="module" what="location">
+ <location id="72" x="131.00671141" y="156.77852349" />
+ </change>
+ </action>
+ <action date="2013-09-06 11:58:08" id="77" prevId="76" session="3" user="Remi">
+ <add id="592" objectId="45" parentObjId="" parentObjType="" what="connection">
+ <connection id="45" />
+ </add>
+ <add id="593" objectId="90" parentObjId="45" parentObjType="connection" what="port">
+ <port id="90" moduleId="44" moduleName="Integer" name="value" signature="(org.vistrails.vistrails.basic:Integer)" type="source" />
+ </add>
+ <add id="594" objectId="91" parentObjId="45" parentObjType="connection" what="port">
+ <port id="91" moduleId="43" moduleName="Group" name="genprimes_i" signature="(org.vistrails.vistrails.basic:Integer)" type="destination" />
+ </add>
+ </action>
+ <action date="2013-09-06 11:58:11" id="78" prevId="77" session="3" user="Remi">
+ <add id="595" objectId="46" parentObjId="" parentObjType="" what="connection">
+ <connection id="46" />
+ </add>
+ <add id="596" objectId="92" parentObjId="46" parentObjType="connection" what="port">
+ <port id="92" moduleId="45" moduleName="List" name="value" signature="(org.vistrails.vistrails.basic:List)" type="source" />
+ </add>
+ <add id="597" objectId="93" parentObjId="46" parentObjType="connection" what="port">
+ <port id="93" moduleId="43" moduleName="Group" name="genprimes_previouslist" signature="(org.vistrails.vistrails.basic:List)" type="destination" />
+ </add>
+ </action>
+ <action date="2013-09-06 11:58:20" id="79" prevId="78" session="3" user="Remi">
+ <change id="598" newObjId="55" oldObjId="53" parentObjId="41" parentObjType="function" what="parameter">
+ <parameter alias="" id="55" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:Integer" val="7" />
+ </change>
+ </action>
+ <action date="2013-09-06 11:58:52" id="80" prevId="74" session="3" user="Remi">
+ <add id="599" objectId="46" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="46" name="While" namespace="" package="org.vistrails.vistrails.control_flow" version="0.2.2" />
+ </add>
+ <add id="600" objectId="73" parentObjId="46" parentObjType="module" what="location">
+ <location id="73" x="78.1744966443" y="-132.295302013" />
+ </add>
+ </action>
+ <action date="2013-09-06 11:58:57" id="81" prevId="80" session="3" user="Remi">
+ <change id="601" newObjId="74" oldObjId="73" parentObjId="46" parentObjType="module" what="location">
+ <location id="74" x="88.4832214765" y="-98.7919463087" />
+ </change>
+ </action>
+ <action date="2013-09-06 11:59:02" id="82" prevId="81" session="3" user="Remi">
+ <add id="602" objectId="47" parentObjId="" parentObjType="" what="connection">
+ <connection id="47" />
+ </add>
+ <add id="603" objectId="94" parentObjId="47" parentObjType="connection" what="port">
+ <port id="94" moduleId="43" moduleName="Group" name="self" signature="(org.vistrails.vistrails.basic:Group)" type="source" />
+ </add>
+ <add id="604" objectId="95" parentObjId="47" parentObjType="connection" what="port">
+ <port id="95" moduleId="46" moduleName="While" name="FunctionPort" signature="(org.vistrails.vistrails.basic:Module)" type="destination" />
+ </add>
+ </action>
+ <action date="2013-09-06 11:59:17" id="83" prevId="82" session="3" user="Remi">
+ <add id="605" objectId="43" parentObjId="46" parentObjType="module" what="function">
+ <function id="43" name="MaxIterations" pos="0" />
+ </add>
+ <add id="606" objectId="56" parentObjId="43" parentObjType="function" what="parameter">
+ <parameter alias="" id="56" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:Integer" val="100" />
+ </add>
+ </action>
+ <action date="2013-09-06 11:59:57" id="84" prevId="83" session="3" user="Remi">
+ <add id="607" objectId="44" parentObjId="43" parentObjType="group" what="function">
+ <function id="44" name="genprimes_i" pos="0" />
+ </add>
+ <add id="608" objectId="57" parentObjId="44" parentObjType="function" what="parameter">
+ <parameter alias="" id="57" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:Integer" val="2" />
+ </add>
+ </action>
+ <action date="2013-09-06 12:00:05" id="85" prevId="84" session="3" user="Remi">
+ <add id="609" objectId="45" parentObjId="43" parentObjType="group" what="function">
+ <function id="45" name="genprimes_previouslist" pos="1" />
+ </add>
+ <add id="610" objectId="58" parentObjId="45" parentObjType="function" what="parameter">
+ <parameter alias="" id="58" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:List" val="[]" />
+ </add>
+ </action>
+ <action date="2013-09-06 12:00:18" id="86" prevId="85" session="3" user="Remi">
+ <add id="611" objectId="46" parentObjId="46" parentObjType="module" what="function">
+ <function id="46" name="StateInputPorts" pos="1" />
+ </add>
+ <add id="612" objectId="59" parentObjId="46" parentObjType="function" what="parameter">
+ <parameter alias="" id="59" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:List" val="['genprimes_i', 'genprimes_previouslist']" />
+ </add>
+ </action>
+ <action date="2013-09-06 12:00:37" id="87" prevId="86" session="3" user="Remi">
+ <add id="613" objectId="47" parentObjId="46" parentObjType="module" what="function">
+ <function id="47" name="StateOutputPorts" pos="2" />
+ </add>
+ <add id="614" objectId="60" parentObjId="47" parentObjType="function" what="parameter">
+ <parameter alias="" id="60" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:List" val="['genprimes_next', 'genprimes_newlist']" />
+ </add>
+ </action>
+ <action date="2013-09-06 12:00:49" id="88" prevId="87" session="3" user="Remi">
+ <add id="615" objectId="48" parentObjId="46" parentObjType="module" what="function">
+ <function id="48" name="OutputPort" pos="3" />
+ </add>
+ <add id="616" objectId="61" parentObjId="48" parentObjType="function" what="parameter">
+ <parameter alias="" id="61" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:String" val="genprimes_newlist" />
+ </add>
+ </action>
+ <action date="2013-09-06 12:00:57" id="89" prevId="88" session="3" user="Remi">
+ <add id="617" objectId="47" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="47" name="StandardOutput" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="618" objectId="75" parentObjId="47" parentObjType="module" what="location">
+ <location id="75" x="130.577181208" y="-196.724832215" />
+ </add>
+ </action>
+ <action date="2013-09-06 12:00:57" id="90" prevId="89" session="3" user="Remi">
+ <add id="619" objectId="48" parentObjId="" parentObjType="" what="connection">
+ <connection id="48" />
+ </add>
+ <add id="620" objectId="96" parentObjId="48" parentObjType="connection" what="port">
+ <port id="96" moduleId="46" moduleName="While" name="Result" signature="(org.vistrails.vistrails.basic:Variant)" type="source" />
+ </add>
+ <add id="621" objectId="97" parentObjId="48" parentObjType="connection" what="port">
+ <port id="97" moduleId="47" moduleName="StandardOutput" name="value" signature="(org.vistrails.vistrails.basic:Module)" type="destination" />
+ </add>
+ </action>
+ <action date="2013-09-06 12:06:00" id="91" prevId="90" session="4" user="Remi">
+ <change id="622" newObjId="62" oldObjId="58" parentObjId="45" parentObjType="function" what="parameter">
+ <parameter alias="" id="62" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:List" val="[2]" />
+ </change>
+ </action>
+ <action date="2013-09-06 12:06:04" id="92" prevId="91" session="4" user="Remi">
+ <change id="623" newObjId="63" oldObjId="57" parentObjId="44" parentObjType="function" what="parameter">
+ <parameter alias="" id="63" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:Integer" val="3" />
+ </change>
+ </action>
+ <actionAnnotation actionId="2" date="2013-09-06 11:27:33" id="5" key="__prune__" user="Remi" value="True" />
+ <actionAnnotation actionId="4" date="2013-09-06 11:28:12" id="6" key="__prune__" user="Remi" value="True" />
+ <actionAnnotation actionId="6" date="2013-09-06 11:28:47" id="7" key="__tag__" user="Remi" value="prime_isprime_internal" />
+ <actionAnnotation actionId="27" date="2013-09-06 11:32:46" id="10" key="__tag__" user="Remi" value="test_1_1" />
+ <actionAnnotation actionId="28" date="2013-09-06 11:32:58" id="11" key="__tag__" user="Remi" value="test_1_2" />
+ <actionAnnotation actionId="29" date="2013-09-06 11:33:03" id="13" key="__tag__" user="Remi" value="test_1_3" />
+ <actionAnnotation actionId="30" date="2013-09-06 11:33:35" id="14" key="__tag__" user="Remi" value="prime_isprime_internal grouped" />
+ <actionAnnotation actionId="36" date="2013-09-06 11:34:57" id="16" key="__tag__" user="Remi" value="test_2_1" />
+ <actionAnnotation actionId="33" date="2013-09-06 11:35:02" id="17" key="__prune__" user="Remi" value="True" />
+ <actionAnnotation actionId="37" date="2013-09-06 11:35:24" id="18" key="__tag__" user="Remi" value="test_2_2" />
+ <actionAnnotation actionId="38" date="2013-09-06 11:35:38" id="19" key="__tag__" user="Remi" value="test_2_3" />
+ <actionAnnotation actionId="49" date="2013-09-06 11:38:22" id="23" key="__tag__" user="Remi" value="prime_isprime" />
+ <actionAnnotation actionId="44" date="2013-09-06 11:38:24" id="24" key="__prune__" user="Remi" value="True" />
+ <actionAnnotation actionId="53" date="2013-09-06 11:38:54" id="25" key="__tag__" user="Remi" value="test_3_1" />
+ <actionAnnotation actionId="54" date="2013-09-06 11:38:58" id="26" key="__tag__" user="Remi" value="test_3_2" />
+ <actionAnnotation actionId="55" date="2013-09-06 11:39:37" id="27" key="__tag__" user="Remi" value="prime_isprime grouped" />
+ <actionAnnotation actionId="61" date="2013-09-06 11:40:01" id="28" key="__tag__" user="Remi" value="test_4_1" />
+ <actionAnnotation actionId="62" date="2013-09-06 11:40:16" id="29" key="__tag__" user="Remi" value="test_4_2" />
+ <actionAnnotation actionId="66" date="2013-09-06 11:56:20" id="32" key="__tag__" user="Remi" value="genprimes_internal" />
+ <actionAnnotation actionId="72" date="2013-09-06 11:56:55" id="33" key="__tag__" user="Remi" value="test_5_1" />
+ <actionAnnotation actionId="73" date="2013-09-06 11:57:07" id="34" key="__tag__" user="Remi" value="test_5_2" />
+ <actionAnnotation actionId="74" date="2013-09-06 11:57:46" id="35" key="__tag__" user="Remi" value="genprimes_internal grouped" />
+ <actionAnnotation actionId="78" date="2013-09-06 11:58:28" id="37" key="__tag__" user="Remi" value="test_6_1" />
+ <actionAnnotation actionId="79" date="2013-09-06 11:58:32" id="38" key="__tag__" user="Remi" value="test_6_2" />
+ <actionAnnotation actionId="92" date="2013-09-06 12:06:28" id="40" key="__tag__" user="Remi" value="genprimes" />
+</vistrail>
diff --git a/examples/protein_visualization.vt b/examples/protein_visualization.vt
new file mode 100644
index 0000000..bd59d12
Binary files /dev/null and b/examples/protein_visualization.vt differ
diff --git a/examples/r_stats.vt b/examples/r_stats.vt
new file mode 100644
index 0000000..1d9c5d9
Binary files /dev/null and b/examples/r_stats.vt differ
diff --git a/examples/scripting/README b/examples/scripting/README
new file mode 100644
index 0000000..80dbbb0
--- /dev/null
+++ b/examples/scripting/README
@@ -0,0 +1,11 @@
+This file explains script vtk_book_3rd_p189_script.py. It is a script that generates the same pipeline found in the example vt file with (practically) the same name, and is used to compare the new layout options designed to improve incremental/online layout.
+
+Two options were added to the original layout algorithm:
+
+-preserve_order: this preserves the order in the x-coordinate of existing modules in the pipeline. Modules with no previous x position (new modules) are positioned based on the original layout algorithm which tries to minimize connection crossings.
+
+-no_gaps: this prevents connected modules from being more than one layer (aka row) apart from eachother.
+
+VisTrails files were generated using each of the 4 combinations of the above boolean options. These can be regenerated by changing the parameters in function layoutAndAdd on line 40 of the script, and the output file name at the end of the script. Open these in vistrails and traverse the version tree using undo and redo to see how the pipelines are layed out incrementally.
+
+brain_script.py builds the example pipeline from brain_vistrail.vt, and combined_script.py builds a pipeline of the two combined.
\ No newline at end of file
diff --git a/examples/scripting/brain_from_script.vt b/examples/scripting/brain_from_script.vt
new file mode 100644
index 0000000..d30ae3b
Binary files /dev/null and b/examples/scripting/brain_from_script.vt differ
diff --git a/examples/scripting/brain_script.py b/examples/scripting/brain_script.py
new file mode 100644
index 0000000..292535f
--- /dev/null
+++ b/examples/scripting/brain_script.py
@@ -0,0 +1,110 @@
+import os
+import sys
+
+try:
+ import vistrails
+except:
+ #try to append vistrails source dir relative to examples/scripting
+ this_dir = os.path.split(__file__)[0]
+ sys.path.append(os.path.join(this_dir, '../..'))
+ import vistrails
+
+from vistrails.core.application import init as vt_init
+from vistrails.core.api import Package, get_api
+
+#init vistrails
+vt_app = vt_init()
+vt_app.new_vistrail()
+api = get_api()
+
+httppkg = 'edu.utah.sci.vistrails.http'
+vtkpkg = 'edu.utah.sci.vistrails.vtk'
+
+http = Package(httppkg)
+vtk = Package(vtkpkg)
+
+#start with http file module
+httpFA = http.HTTPFile()
+httpFA.url = \
+ 'http://www.vistrails.org/download/download.php?type=DATA&id=gktbhFA.vtk'
+
+#add and connect vtkDataSetReader
+dataFA = api.add_and_connect_module(vtkpkg, 'vtkDataSetReader', 'SetFile',
+ httpFA, 'file')
+
+#add contour filter
+contour = api.add_and_connect_module(vtkpkg, 'vtkContourFilter',
+ 'SetInputConnection0',
+ dataFA, 'GetOutputPort0')
+contour.SetValue = (0, 0.6)
+
+#add normals, stripper, and probe filter
+normals = api.add_and_connect_module(vtkpkg, 'vtkPolyDataNormals',
+ 'SetInputConnection0',
+ contour, 'GetOutputPort0')
+normals.SetFeatureAngle = 60.0
+
+stripper = api.add_and_connect_module(vtkpkg, 'vtkStripper',
+ 'SetInputConnection0',
+ normals, 'GetOutputPort0')
+
+probe = api.add_and_connect_module(vtkpkg, 'vtkProbeFilter',
+ 'SetInputConnection0',
+ stripper, 'GetOutputPort0')
+
+#build other branch in reverse
+colors = api.add_and_connect_module(vtkpkg, 'vtkImageMapToColors',
+ 'GetOutputPort0',
+ probe, 'SetInputConnection1', True)
+colors.SetOutputFormatToRGBA = True
+
+lookup = api.add_and_connect_module(vtkpkg, 'vtkLookupTable', 'self',
+ colors, 'SetLookupTable', True)
+lookup.SetHueRange = (0.0, 0.8)
+lookup.SetSaturationRange = (0.3, 0.7)
+lookup.SetValueRange = (1.0, 1.0)
+
+dataL123 = api.add_and_connect_module(vtkpkg, 'vtkDataSetReader',
+ 'GetOutputPort0',
+ colors, 'SetInputConnection0', True)
+
+httpL123 = api.add_and_connect_module(httppkg, 'HTTPFile', 'file',
+ dataL123, 'SetFile', True)
+
+httpL123.url = \
+ 'http://www.vistrails.org/download/download.php?type=DATA&id=gktbhL123.vtk'
+
+#finish bottom section
+mapper = api.add_and_connect_module(vtkpkg, 'vtkPolyDataMapper',
+ 'SetInputConnection0',
+ probe, 'GetOutputPort0')
+mapper.ScalarVisibilityOn = True
+
+actor = api.add_and_connect_module(vtkpkg, 'vtkActor', 'SetMapper',
+ mapper, 'self')
+
+prop = api.add_and_connect_module(vtkpkg, 'vtkProperty', 'self',
+ actor, 'SetProperty', True)
+prop.SetDiffuseColor = (1.0, 0.49, 0.25)
+prop.SetOpacity = 0.7
+prop.SetSpecular = 0.3
+prop.SetSpecularPower = 2.0
+
+renderer = api.add_and_connect_module(vtkpkg, 'vtkRenderer', 'AddActor',
+ actor, 'self')
+
+# Thought this used to work. Right now fails to convert to color when executed
+#renderer.SetBackgroundWidget = 'white'
+
+camera = api.add_and_connect_module(vtkpkg, 'vtkCamera', 'self',
+ renderer, 'SetActiveCamera', True)
+camera.SetFocalPoint = (15.666, 40.421, 39.991)
+camera.SetPosition = (207.961, 34.197, 129.680)
+camera.SetViewUp = (0.029, 1.0, 0.008)
+
+
+cell = api.add_and_connect_module(vtkpkg, 'VTKCell', 'AddRenderer',
+ renderer, 'self')
+
+#write to file
+api.save_vistrail('brain_from_script.vt')
diff --git a/examples/scripting/combined_script.py b/examples/scripting/combined_script.py
new file mode 100644
index 0000000..073a596
--- /dev/null
+++ b/examples/scripting/combined_script.py
@@ -0,0 +1,215 @@
+import sys
+sys.path.append('/Users/benbu/src/vistrails/vistrails/')
+
+import vistrails.core.application
+import vistrails.core.db.action
+import vistrails.core.db.locator
+import vistrails.core.modules.module_registry
+
+
+#init vistrails
+vt_app = vistrails.core.application.init()
+controller = vt_app.get_controller()
+registry = vistrails.core.modules.module_registry.get_module_registry()
+
+#========================== convenience methods ================================
+def newModule(package_name, module_name):
+ descriptor = registry.get_descriptor_by_name(package_name, module_name)
+ return controller.create_module_from_descriptor(descriptor)
+
+def newConnection(source, source_port, target, target_port):
+ c = controller.create_connection(source, source_port, target, target_port)
+ return c
+
+def setPortValue(module, port_name, value):
+ function = controller.create_function(module, port_name, [str(value)])
+ module.add_function(function)
+ return
+
+def addToPipeline(items, ops=[]):
+ item_ops = [('add',item) for item in items]
+ action = vistrails.core.db.action.create_action(item_ops + ops)
+ controller.add_new_action(action)
+ version = controller.perform_action(action)
+ controller.change_selected_version(version)
+
+def layoutAndAdd(module, connections):
+ if not isinstance(connections, list):
+ connections = [connections]
+ ops = controller.layout_modules_ops(preserve_order=True,
+ new_modules=[module],
+ new_connections=connections)
+ addToPipeline([module] + connections, ops)
+
+#========================== package prefixes ===================================
+httppkg = 'edu.utah.sci.vistrails.http'
+vtkpkg = 'edu.utah.sci.vistrails.vtk'
+
+#============================ start script =====================================
+
+#start with http file module
+httpFA = newModule(httppkg, 'HTTPFile')
+url = 'http://www.vistrails.org/download/download.php?type=DATA&id=gktbhFA.vtk'
+setPortValue(httpFA, 'url', url)
+
+#add to pipeline
+addToPipeline([httpFA])
+
+#create data set reader module for the gktbhFA.vtk file
+dataFA = newModule(vtkpkg, 'vtkDataSetReader')
+
+#connect modules
+http_dataFA = newConnection(httpFA, 'file', dataFA, 'SetFile')
+
+#layout new modules before adding
+layoutAndAdd(dataFA, http_dataFA)
+
+#add contour filter
+contour = newModule(vtkpkg, 'vtkContourFilter')
+setPortValue(contour, 'SetValue', (0,0.6))
+dataFA_contour = newConnection(dataFA, 'GetOutputPort0',
+ contour, 'SetInputConnection0')
+layoutAndAdd(contour, dataFA_contour)
+
+#add normals, stripper, and probe filter
+normals = newModule(vtkpkg, 'vtkPolyDataNormals') #GetOutputPort0
+setPortValue(normals, 'SetFeatureAngle', 60.0)
+contour_normals = newConnection(contour, 'GetOutputPort0',
+ normals, 'SetInputConnection0')
+layoutAndAdd(normals, contour_normals)
+
+stripper = newModule(vtkpkg, 'vtkStripper') #GetOutputPort0
+normals_stripper = newConnection(normals, 'GetOutputPort0',
+ stripper, 'SetInputConnection0')
+layoutAndAdd(stripper, normals_stripper)
+
+probe = newModule(vtkpkg, 'vtkProbeFilter') #same
+stripper_probe = newConnection(stripper, 'GetOutputPort0',
+ probe, 'SetInputConnection0')
+layoutAndAdd(probe, stripper_probe)
+
+#build other branch in reverse
+colors = newModule(vtkpkg, 'vtkImageMapToColors')
+setPortValue(colors, 'SetOutputFormatToRGBA', True)
+colors_probe = newConnection(colors, 'GetOutputPort0',
+ probe, 'SetInputConnection1')
+layoutAndAdd(colors, colors_probe)
+
+lookup = newModule(vtkpkg, 'vtkLookupTable')
+setPortValue(lookup, 'SetHueRange', (0.0,0.8))
+setPortValue(lookup, 'SetSaturationRange', (0.3,0.7))
+setPortValue(lookup, 'SetValueRange', (1.0,1.0))
+lookup_colors = newConnection(lookup, 'self',
+ colors, 'SetLookupTable')
+layoutAndAdd(lookup, lookup_colors)
+
+dataL123 = newModule(vtkpkg, 'vtkDataSetReader')
+dataL123_colors = newConnection(dataL123, 'GetOutputPort0',
+ colors, 'SetInputConnection0')
+layoutAndAdd(dataL123, dataL123_colors)
+
+httpL123 = newModule(httppkg, 'HTTPFile')
+url = 'http://www.vistrails.org/download/download.php?type=DATA&id=gktbhL123.vtk'
+setPortValue(httpL123, 'url', url)
+httpL123_dataL123 = newConnection(httpL123, 'file',
+ dataL123, 'SetFile')
+layoutAndAdd(httpL123, httpL123_dataL123)
+
+#finish bottom section
+mapper = newModule(vtkpkg, 'vtkPolyDataMapper')
+setPortValue(mapper, 'ScalarVisibilityOn', True)
+probe_mapper = newConnection(probe, 'GetOutputPort0',
+ mapper, 'SetInputConnection0')
+layoutAndAdd(mapper, probe_mapper)
+
+actor = newModule(vtkpkg, 'vtkActor')
+mapper_actor = newConnection(mapper, 'self',
+ actor, 'SetMapper')
+layoutAndAdd(actor, mapper_actor)
+
+prop = newModule(vtkpkg, 'vtkProperty')
+setPortValue(prop, 'SetDiffuseColor', (1.0,0.49,0.25))
+setPortValue(prop, 'SetOpacity', 0.7)
+setPortValue(prop, 'SetSpecular', 0.3)
+setPortValue(prop, 'SetSpecularPower', 2.0)
+prop_actor = newConnection(prop, 'self',
+ actor, 'SetProperty')
+layoutAndAdd(prop, prop_actor)
+
+renderer = newModule(vtkpkg, 'vtkRenderer')
+setPortValue(renderer, 'SetBackgroundWidget', 'white')
+actor_renderer = newConnection(actor, 'self',
+ renderer, 'AddActor')
+layoutAndAdd(renderer, actor_renderer)
+
+camera = newModule(vtkpkg, 'vtkCamera')
+setPortValue(camera, 'SetFocalPoint', (15.666,40.421,39.991))
+setPortValue(camera, 'SetPosition', (207.961,34.197,129.680))
+setPortValue(camera, 'SetViewUp', (0.029, 1.0, 0.008))
+camera_renderer = newConnection(camera, 'self',
+ renderer, 'SetActiveCamera')
+layoutAndAdd(camera, camera_renderer)
+
+#this is missing when running from script??
+# cell = newModule(vtkpkg, 'VTKCell')
+# cell = newModule(vtkpkg, 'vtkCell')
+# renderer_cell = newConnection(renderer, 'self',
+# cell, 'AddRenderer')
+# layoutAndAdd(cell, renderer_cell)
+
+#add book 3rd p189 example
+
+qcActor = newModule(vtkpkg, 'vtkActor')
+qcActor_renderer = newConnection(qcActor, 'self',
+ renderer, 'AddActor')
+layoutAndAdd(qcActor, qcActor_renderer)
+
+qcMapper = newModule(vtkpkg, 'vtkPolyDataMapper')
+qcMapper_actor = newConnection(qcMapper, 'self',
+ qcActor, 'SetMapper')
+layoutAndAdd(qcMapper, qcMapper_actor)
+
+qContour = newModule(vtkpkg, 'vtkContourFilter')
+setPortValue(qContour, 'GenerateValues', (5,0,1.2))
+qContour_mapper = newConnection(qContour, 'GetOutputPort0',
+ qcMapper, 'SetInputConnection0')
+layoutAndAdd(qContour, qContour_mapper)
+
+sample = newModule(vtkpkg, 'vtkSampleFunction')
+setPortValue(sample, 'SetSampleDimensions', (50,50,50))
+sample_qContour = newConnection(sample, 'GetOutputPort0',
+ qContour, 'SetInputConnection0')
+layoutAndAdd(sample, sample_qContour)
+
+quad = newModule(vtkpkg, 'vtkQuadric')
+setPortValue(quad, 'SetCoefficients', (0.5,1,0.2,0,0.1,0,0,0.2,0,0))
+quad_sample = newConnection(quad, 'self',
+ sample, 'SetImplicitFunction')
+layoutAndAdd(quad, quad_sample)
+
+oActor = newModule(vtkpkg, 'vtkActor')
+oActor_renderer = newConnection(oActor, 'self',
+ renderer, 'AddActor')
+layoutAndAdd(oActor, oActor_renderer)
+
+oProp = newModule(vtkpkg, 'vtkProperty')
+setPortValue(oProp, 'SetColor', (0,0,0))
+oProp_actor = newConnection(oProp, 'self',
+ oActor, 'SetProperty')
+layoutAndAdd(oProp, oProp_actor)
+
+oMapper = newModule(vtkpkg, 'vtkPolyDataMapper')
+oMapper_actor = newConnection(oMapper, 'self',
+ oActor, 'SetMapper')
+layoutAndAdd(oMapper, oMapper_actor)
+
+outline = newModule(vtkpkg, 'vtkOutlineFilter')
+outline_mapper = newConnection(outline, 'GetOutputPort0',
+ oMapper, 'SetInputConnection0')
+sample_outline = newConnection(sample, 'GetOutputPort0',
+ outline, 'SetInputConnection0')
+layoutAndAdd(outline, [outline_mapper, sample_outline])
+
+#write to file
+locator = vistrails.core.db.locator.FileLocator('incremental_layout_combined.vt')
+controller.write_vistrail(locator)
diff --git a/examples/scripting/vtk_book_3rd_p189_script.py b/examples/scripting/vtk_book_3rd_p189_script.py
new file mode 100644
index 0000000..b6ca03a
--- /dev/null
+++ b/examples/scripting/vtk_book_3rd_p189_script.py
@@ -0,0 +1,114 @@
+import sys
+sys.path.append('/Users/benbu/src/vistrails/vistrails/')
+
+import vistrails.core.application
+import vistrails.core.db.action
+import vistrails.core.db.locator
+import vistrails.core.modules.module_registry
+
+
+#init vistrails
+vt_app = vistrails.core.application.init()
+controller = vt_app.get_controller()
+registry = vistrails.core.modules.module_registry.get_module_registry()
+
+#========================== convenience methods ================================
+def newModule(package_name, module_name):
+ descriptor = registry.get_descriptor_by_name(package_name, module_name)
+ return controller.create_module_from_descriptor(descriptor)
+
+def newConnection(source, source_port, target, target_port):
+ c = controller.create_connection(source, source_port, target, target_port)
+ return c
+
+def setPortValue(module, port_name, value):
+ function = controller.create_function(module, port_name, [str(value)])
+ module.add_function(function)
+ return
+
+def addToPipeline(items, ops=[]):
+ item_ops = [('add',item) for item in items]
+ action = vistrails.core.db.action.create_action(item_ops + ops)
+ controller.add_new_action(action)
+ version = controller.perform_action(action)
+ controller.change_selected_version(version)
+
+def layoutAndAdd(module, connections):
+ print 'adding %s' % module.name
+ if not isinstance(connections, list):
+ connections = [connections]
+ ops = controller.layout_modules_ops(preserve_order=True, no_gaps=False,
+ new_modules=[module],
+ new_connections=connections)
+ addToPipeline([module] + connections, ops)
+
+#========================== package prefixes ===================================
+httppkg = 'edu.utah.sci.vistrails.http'
+vtkpkg = 'edu.utah.sci.vistrails.vtk'
+
+#============================ start script =====================================
+
+renderer = newModule(vtkpkg, 'vtkRenderer')
+addToPipeline([renderer])
+
+#this is missing when running from script??
+# cell = newModule(vtkpkg, 'VTKCell')
+# cell = newModule(vtkpkg, 'vtkCell')
+# renderer_cell = newConnection(renderer, 'self',
+# cell, 'AddRenderer')
+# layoutAndAdd(cell, renderer_cell)
+
+qcActor = newModule(vtkpkg, 'vtkActor')
+qcActor_renderer = newConnection(qcActor, 'self',
+ renderer, 'AddActor')
+layoutAndAdd(qcActor, qcActor_renderer)
+
+oActor = newModule(vtkpkg, 'vtkActor')
+oActor_renderer = newConnection(oActor, 'self',
+ renderer, 'AddActor')
+layoutAndAdd(oActor, oActor_renderer)
+
+qcMapper = newModule(vtkpkg, 'vtkPolyDataMapper')
+qcMapper_actor = newConnection(qcMapper, 'self',
+ qcActor, 'SetMapper')
+layoutAndAdd(qcMapper, qcMapper_actor)
+
+oProp = newModule(vtkpkg, 'vtkProperty')
+setPortValue(oProp, 'SetColor', (0,0,0))
+oProp_actor = newConnection(oProp, 'self',
+ oActor, 'SetProperty')
+layoutAndAdd(oProp, oProp_actor)
+
+oMapper = newModule(vtkpkg, 'vtkPolyDataMapper')
+oMapper_actor = newConnection(oMapper, 'self',
+ oActor, 'SetMapper')
+layoutAndAdd(oMapper, oMapper_actor)
+
+qContour = newModule(vtkpkg, 'vtkContourFilter')
+setPortValue(qContour, 'GenerateValues', (5,0,1.2))
+qContour_mapper = newConnection(qContour, 'GetOutputPort0',
+ qcMapper, 'SetInputConnection0')
+layoutAndAdd(qContour, qContour_mapper)
+
+sample = newModule(vtkpkg, 'vtkSampleFunction')
+setPortValue(sample, 'SetSampleDimensions', (50,50,50))
+sample_qContour = newConnection(sample, 'GetOutputPort0',
+ qContour, 'SetInputConnection0')
+layoutAndAdd(sample, sample_qContour)
+
+outline = newModule(vtkpkg, 'vtkOutlineFilter')
+outline_mapper = newConnection(outline, 'GetOutputPort0',
+ oMapper, 'SetInputConnection0')
+sample_outline = newConnection(sample, 'GetOutputPort0',
+ outline, 'SetInputConnection0')
+layoutAndAdd(outline, [outline_mapper, sample_outline])
+
+quad = newModule(vtkpkg, 'vtkQuadric')
+setPortValue(quad, 'SetCoefficients', (0.5,1,0.2,0,0.1,0,0,0.2,0,0))
+quad_sample = newConnection(quad, 'self',
+ sample, 'SetImplicitFunction')
+layoutAndAdd(quad, quad_sample)
+
+#write to file
+locator = vistrails.core.db.locator.FileLocator('p189_gaps_preserve_order.vt')
+controller.write_vistrail(locator)
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diff --git a/examples/vtk_book_3rd_p193.vt b/examples/vtk_book_3rd_p193.vt
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diff --git a/examples/vtk_examples/Annotation/TestText.py b/examples/vtk_examples/Annotation/TestText.py
new file mode 100644
index 0000000..289fa76
--- /dev/null
+++ b/examples/vtk_examples/Annotation/TestText.py
@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of 2D text.
+
+import vtk
+
+# Create a sphere source, mapper, and actor
+sphere = vtk.vtkSphereSource()
+
+sphereMapper = vtk.vtkPolyDataMapper()
+sphereMapper.SetInputConnection(sphere.GetOutputPort())
+sphereMapper.GlobalImmediateModeRenderingOn()
+sphereActor = vtk.vtkLODActor()
+sphereActor.SetMapper(sphereMapper)
+
+# Create a scaled text actor.
+# Set the text, font, justification, and properties (bold, italics,
+# etc.).
+textActor = vtk.vtkTextActor()
+textActor.ScaledTextOn()
+textActor.SetDisplayPosition(90, 50)
+textActor.SetInput("This is a sphere")
+
+# Set coordinates to match the old vtkScaledTextActor default value
+textActor.GetPosition2Coordinate().SetCoordinateSystemToNormalizedViewport()
+textActor.GetPosition2Coordinate().SetValue(0.6, 0.1)
+
+tprop = textActor.GetTextProperty()
+tprop.SetFontSize(18)
+tprop.SetFontFamilyToArial()
+tprop.SetJustificationToCentered()
+tprop.BoldOn()
+tprop.ItalicOn()
+tprop.ShadowOn()
+tprop.SetColor(0, 0, 1)
+
+# Create the Renderer, RenderWindow, RenderWindowInteractor
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer; set the background and size; zoom
+# in; and render.
+ren.AddActor2D(textActor)
+ren.AddActor(sphereActor)
+
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(250, 125)
+ren.ResetCamera()
+ren.GetActiveCamera().Zoom(1.5)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Annotation/TestText.vt b/examples/vtk_examples/Annotation/TestText.vt
new file mode 100644
index 0000000..4a53b06
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diff --git a/examples/vtk_examples/Annotation/cubeAxes.py b/examples/vtk_examples/Annotation/cubeAxes.py
new file mode 100644
index 0000000..cffe5ca
--- /dev/null
+++ b/examples/vtk_examples/Annotation/cubeAxes.py
@@ -0,0 +1,118 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of vtkCubeAxesActor2D to indicate
+# the position in space that the camera is currently viewing. The
+# vtkCubeAxesActor2D draws axes on the bounding box of the data set
+# and labels the axes with x-y-z coordinates.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create a vtkBYUReader and read in a data set.
+fohe = vtk.vtkBYUReader()
+fohe.SetGeometryFileName(VTK_DATA_ROOT + "/Data/teapot.g")
+
+# Create a vtkPolyDataNormals filter to calculate the normals of the
+# data set.
+normals = vtk.vtkPolyDataNormals()
+normals.SetInputConnection(fohe.GetOutputPort())
+# Set up the associated mapper and actor.
+foheMapper = vtk.vtkPolyDataMapper()
+foheMapper.SetInputConnection(normals.GetOutputPort())
+foheActor = vtk.vtkLODActor()
+foheActor.SetMapper(foheMapper)
+
+# Create a vtkOutlineFilter to draw the bounding box of the data set.
+# Also create the associated mapper and actor.
+outline = vtk.vtkOutlineFilter()
+outline.SetInputConnection(normals.GetOutputPort())
+mapOutline = vtk.vtkPolyDataMapper()
+mapOutline.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(mapOutline)
+outlineActor.GetProperty().SetColor(0, 0, 0)
+
+# Create a vtkCamera, and set the camera parameters.
+camera = vtk.vtkCamera()
+camera.SetClippingRange(1.60187, 20.0842)
+camera.SetFocalPoint(0.21406, 1.5, 0)
+camera.SetPosition(8.3761, 4.94858, 4.12505)
+camera.SetViewUp(0.180325, 0.549245, -0.815974)
+
+# Create a vtkLight, and set the light parameters.
+light = vtk.vtkLight()
+light.SetFocalPoint(0.21406, 1.5, 0)
+light.SetPosition(8.3761, 4.94858, 4.12505)
+
+# Create the Renderers. Assign them the appropriate viewport
+# coordinates, active camera, and light.
+ren = vtk.vtkRenderer()
+ren.SetViewport(0, 0, 0.5, 1.0)
+ren.SetActiveCamera(camera)
+ren.AddLight(light)
+ren2 = vtk.vtkRenderer()
+ren2.SetViewport(0.5, 0, 1.0, 1.0)
+ren2.SetActiveCamera(camera)
+ren2.AddLight(light)
+
+# Create the RenderWindow and RenderWindowInteractor.
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+renWin.AddRenderer(ren2)
+renWin.SetWindowName("VTK - Cube Axes")
+renWin.SetSize(600, 300)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, and set the background.
+ren.AddViewProp(foheActor)
+ren.AddViewProp(outlineActor)
+ren2.AddViewProp(foheActor)
+ren2.AddViewProp(outlineActor)
+
+ren.SetBackground(0.1, 0.2, 0.4)
+ren2.SetBackground(0.1, 0.2, 0.4)
+
+# Create a text property for both cube axes
+tprop = vtk.vtkTextProperty()
+tprop.SetColor(1, 1, 1)
+tprop.ShadowOn()
+
+# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
+# draw the axes. Add the actor to the renderer.
+axes = vtk.vtkCubeAxesActor2D()
+axes.SetInput(normals.GetOutput())
+axes.SetCamera(ren.GetActiveCamera())
+axes.SetLabelFormat("%6.4g")
+axes.SetFlyModeToOuterEdges()
+axes.SetFontFactor(0.8)
+axes.SetAxisTitleTextProperty(tprop)
+axes.SetAxisLabelTextProperty(tprop)
+ren.AddViewProp(axes)
+
+# Create a vtkCubeAxesActor2D. Use the closest vertex to the camera to
+# determine where to draw the axes. Add the actor to the renderer.
+axes2 = vtk.vtkCubeAxesActor2D()
+axes2.SetViewProp(foheActor)
+axes2.SetCamera(ren2.GetActiveCamera())
+axes2.SetLabelFormat("%6.4g")
+axes2.SetFlyModeToClosestTriad()
+axes2.SetFontFactor(0.8)
+axes2.ScalingOff()
+axes2.SetAxisTitleTextProperty(tprop)
+axes2.SetAxisLabelTextProperty(tprop)
+ren2.AddViewProp(axes2)
+
+# Set up a check for aborting rendering.
+def CheckAbort(obj, event):
+ # obj will be the object generating the event. In this case it
+ # is renWin.
+ if obj.GetEventPending() != 0:
+ obj.SetAbortRender(1)
+
+renWin.AddObserver("AbortCheckEvent", CheckAbort)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Annotation/cubeAxes.vt b/examples/vtk_examples/Annotation/cubeAxes.vt
new file mode 100644
index 0000000..3ceb805
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diff --git a/examples/vtk_examples/Annotation/textOrigin.py b/examples/vtk_examples/Annotation/textOrigin.py
new file mode 100644
index 0000000..54355dd
--- /dev/null
+++ b/examples/vtk_examples/Annotation/textOrigin.py
@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of vtkVectorText and vtkFollower.
+# vtkVectorText is used to create 3D annotation. vtkFollower is used to
+# position the 3D text and to ensure that the text always faces the
+# renderer's active camera (i.e., the text is always readable).
+
+import vtk
+
+# Create the axes and the associated mapper and actor.
+axes = vtk.vtkAxes()
+axes.SetOrigin(0, 0, 0)
+axesMapper = vtk.vtkPolyDataMapper()
+axesMapper.SetInputConnection(axes.GetOutputPort())
+axesActor = vtk.vtkActor()
+axesActor.SetMapper(axesMapper)
+
+# Create the 3D text and the associated mapper and follower (a type of
+# actor). Position the text so it is displayed over the origin of the
+# axes.
+atext = vtk.vtkVectorText()
+atext.SetText("Origin")
+textMapper = vtk.vtkPolyDataMapper()
+textMapper.SetInputConnection(atext.GetOutputPort())
+textActor = vtk.vtkFollower()
+textActor.SetMapper(textMapper)
+textActor.SetScale(0.2, 0.2, 0.2)
+textActor.AddPosition(0, -0.1, 0)
+
+# Create the Renderer, RenderWindow, and RenderWindowInteractor.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer.
+ren.AddActor(axesActor)
+ren.AddActor(textActor)
+
+# Zoom in closer.
+ren.ResetCamera()
+ren.GetActiveCamera().Zoom(1.6)
+
+# Reset the clipping range of the camera; set the camera of the
+# follower; render.
+ren.ResetCameraClippingRange()
+textActor.SetCamera(ren.GetActiveCamera())
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Annotation/textOrigin.vt b/examples/vtk_examples/Annotation/textOrigin.vt
new file mode 100644
index 0000000..03e6e83
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diff --git a/examples/vtk_examples/Annotation/xyPlot.py b/examples/vtk_examples/Annotation/xyPlot.py
new file mode 100644
index 0000000..938dccc
--- /dev/null
+++ b/examples/vtk_examples/Annotation/xyPlot.py
@@ -0,0 +1,195 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of vtkXYPlotActor to display three
+# probe lines using three different techniques. In this example, we
+# are loading data using the vtkPLOT3DReader. We are using the
+# vtkProbeFilter to extract the underlying point data along three
+# probe lines.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create a PLOT3D reader and load the data.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+
+# Create three the line source to use for the probe lines.
+line = vtk.vtkLineSource()
+line.SetResolution(30)
+
+# Move the line into place and create the probe filter. For
+# vtkProbeFilter, the probe line is the input, and the underlying data
+# set is the source.
+transL1 = vtk.vtkTransform()
+transL1.Translate(3.7, 0.0, 28.37)
+transL1.Scale(5, 5, 5)
+transL1.RotateY(90)
+tf = vtk.vtkTransformPolyDataFilter()
+tf.SetInputConnection(line.GetOutputPort())
+tf.SetTransform(transL1)
+probe = vtk.vtkProbeFilter()
+probe.SetInputConnection(tf.GetOutputPort())
+probe.SetSource(pl3d.GetOutput())
+
+# Move the line again and create another probe filter.
+transL2 = vtk.vtkTransform()
+transL2.Translate(9.2, 0.0, 31.20)
+transL2.Scale(5, 5, 5)
+transL2.RotateY(90)
+tf2 = vtk.vtkTransformPolyDataFilter()
+tf2.SetInputConnection(line.GetOutputPort())
+tf2.SetTransform(transL2)
+probe2 = vtk.vtkProbeFilter()
+probe2.SetInputConnection(tf2.GetOutputPort())
+probe2.SetSource(pl3d.GetOutput())
+
+# Move the line again and create a third probe filter.
+transL3 = vtk.vtkTransform()
+transL3.Translate(13.27, 0.0, 33.40)
+transL3.Scale(4.5, 4.5, 4.5)
+transL3.RotateY(90)
+tf3 = vtk.vtkTransformPolyDataFilter()
+tf3.SetInputConnection(line.GetOutputPort())
+tf3.SetTransform(transL3)
+probe3 = vtk.vtkProbeFilter()
+probe3.SetInputConnection(tf3.GetOutputPort())
+probe3.SetSource(pl3d.GetOutput())
+
+# Create a vtkAppendPolyData to merge the output of the three probe
+# filters into one data set.
+appendF = vtk.vtkAppendPolyData()
+appendF.AddInput(probe.GetPolyDataOutput())
+appendF.AddInput(probe2.GetPolyDataOutput())
+appendF.AddInput(probe3.GetPolyDataOutput())
+
+# Create a tube filter to represent the lines as tubes. Set up the
+# associated mapper and actor.
+tuber = vtk.vtkTubeFilter()
+tuber.SetInputConnection(appendF.GetOutputPort())
+tuber.SetRadius(0.1)
+lineMapper = vtk.vtkPolyDataMapper()
+lineMapper.SetInputConnection(tuber.GetOutputPort())
+lineActor = vtk.vtkActor()
+lineActor.SetMapper(lineMapper)
+
+# Create an xy-plot using the output of the 3 probe filters as input.
+# The x-values we are plotting are arc length.
+xyplot = vtk.vtkXYPlotActor()
+xyplot.AddInput(probe.GetOutput())
+xyplot.AddInput(probe2.GetOutput())
+xyplot.AddInput(probe3.GetOutput())
+xyplot.GetPositionCoordinate().SetValue(0.0, 0.67, 0)
+xyplot.GetPosition2Coordinate().SetValue(1.0, 0.33, 0) #relative to Position
+xyplot.SetXValuesToArcLength()
+xyplot.SetNumberOfXLabels(6)
+xyplot.SetTitle("Pressure vs. Arc Length (Zoomed View)")
+xyplot.SetXTitle("")
+xyplot.SetYTitle("P")
+xyplot.SetXRange(.1, .35)
+xyplot.SetYRange(.2, .4)
+xyplot.GetProperty().SetColor(0, 0, 0)
+xyplot.GetProperty().SetLineWidth(2)
+# Set text prop color (same color for backward compat with test)
+# Assign same object to all text props
+tprop = xyplot.GetTitleTextProperty()
+tprop.SetColor(xyplot.GetProperty().GetColor())
+xyplot.SetAxisTitleTextProperty(tprop)
+xyplot.SetAxisLabelTextProperty(tprop)
+
+# Create an xy-plot using the output of the 3 probe filters as input.
+# The x-values we are plotting are normalized arc length.
+xyplot2 = vtk.vtkXYPlotActor()
+xyplot2.AddInput(probe.GetOutput())
+xyplot2.AddInput(probe2.GetOutput())
+xyplot2.AddInput(probe3.GetOutput())
+xyplot2.GetPositionCoordinate().SetValue(0.00, 0.33, 0)
+xyplot2.GetPosition2Coordinate().SetValue(1.0, 0.33, 0) #relative to Position
+xyplot2.SetXValuesToNormalizedArcLength()
+xyplot2.SetNumberOfXLabels(6)
+xyplot2.SetTitle("Pressure vs. Normalized Arc Length")
+xyplot2.SetXTitle("")
+xyplot2.SetYTitle("P")
+xyplot2.PlotPointsOn()
+xyplot2.PlotLinesOff()
+xyplot2.GetProperty().SetColor(1, 0, 0)
+xyplot2.GetProperty().SetPointSize(2)
+# Set text prop color (same color for backward compat with test)
+# Assign same object to all text props
+tprop = xyplot2.GetTitleTextProperty()
+tprop.SetColor(xyplot2.GetProperty().GetColor())
+xyplot2.SetAxisTitleTextProperty(tprop)
+xyplot2.SetAxisLabelTextProperty(tprop)
+
+# Create an xy-plot using the output of the 3 probe filters as input.
+# The x-values we are plotting are the underlying point data values.
+xyplot3 = vtk.vtkXYPlotActor()
+xyplot3.AddInput(probe.GetOutput())
+xyplot3.AddInput(probe2.GetOutput())
+xyplot3.AddInput(probe3.GetOutput())
+xyplot3.GetPositionCoordinate().SetValue(0.0, 0.0, 0)
+xyplot3.GetPosition2Coordinate().SetValue(1.0, 0.33, 0) #relative to Position
+xyplot3.SetXValuesToIndex()
+xyplot3.SetNumberOfXLabels(6)
+xyplot3.SetTitle("Pressure vs. Point Id")
+xyplot3.SetXTitle("Probe Length")
+xyplot3.SetYTitle("P")
+xyplot3.PlotPointsOn()
+xyplot3.GetProperty().SetColor(0, 0, 1)
+xyplot3.GetProperty().SetPointSize(3)
+# Set text prop color (same color for backward compat with test)
+# Assign same object to all text props
+tprop = xyplot3.GetTitleTextProperty()
+tprop.SetColor(xyplot3.GetProperty().GetColor())
+xyplot3.SetAxisTitleTextProperty(tprop)
+xyplot3.SetAxisLabelTextProperty(tprop)
+
+# Draw an outline of the PLOT3D data set.
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+outlineActor.GetProperty().SetColor(0, 0, 0)
+
+# Create the Renderers, RenderWindow, and RenderWindowInteractor.
+ren = vtk.vtkRenderer()
+ren2 = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+renWin.AddRenderer(ren2)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Set the background, viewport (necessary because we want to have the
+# renderers draw to different parts of the render window) of the first
+# renderer. Add the outline and line actors to the renderer.
+ren.SetBackground(0.6784, 0.8471, 0.9020)
+ren.SetViewport(0, 0, .5, 1)
+ren.AddActor(outlineActor)
+ren.AddActor(lineActor)
+
+# Set the background and viewport of the second renderer. Add the
+# xy-plot actors to the renderer. Set the size of the render window.
+ren2.SetBackground(1, 1, 1)
+ren2.SetViewport(0.5, 0.0, 1.0, 1.0)
+ren2.AddActor2D(xyplot)
+ren2.AddActor2D(xyplot2)
+ren2.AddActor2D(xyplot3)
+renWin.SetSize(500, 250)
+
+# Set up the camera parameters.
+cam1 = ren.GetActiveCamera()
+cam1.SetClippingRange(3.95297, 100)
+cam1.SetFocalPoint(8.88908, 0.595038, 29.3342)
+cam1.SetPosition(-12.3332, 31.7479, 41.2387)
+cam1.SetViewUp(0.060772, -0.319905, 0.945498)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Annotation/xyPlot.vt b/examples/vtk_examples/Annotation/xyPlot.vt
new file mode 100644
index 0000000..c638807
Binary files /dev/null and b/examples/vtk_examples/Annotation/xyPlot.vt differ
diff --git a/examples/vtk_examples/DataManipulation/Arrays.py b/examples/vtk_examples/DataManipulation/Arrays.py
new file mode 100644
index 0000000..68cde31
--- /dev/null
+++ b/examples/vtk_examples/DataManipulation/Arrays.py
@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of VTK data arrays as attribute
+# data as well as field data. It creates geometry (vtkPolyData) as
+# well as attribute data explicitly.
+
+import vtk
+
+# Create a float array which represents the points.
+pcoords = vtk.vtkFloatArray()
+# Note that by default, an array has 1 component.
+# We have to change it to 3 for points
+pcoords.SetNumberOfComponents(3)
+# We ask pcoords to allocate room for at least 4 tuples
+# and set the number of tuples to 4.
+pcoords.SetNumberOfTuples(4)
+# Assign each tuple. There are 5 specialized versions of SetTuple:
+# SetTuple1 SetTuple2 SetTuple3 SetTuple4 SetTuple9
+# These take 1, 2, 3, 4 and 9 components respectively.
+pcoords.SetTuple3(0, 0.0, 0.0, 0.0)
+pcoords.SetTuple3(1, 0.0, 1.0, 0.0)
+pcoords.SetTuple3(2, 1.0, 0.0, 0.0)
+pcoords.SetTuple3(3, 1.0, 1.0, 0.0)
+
+# Create vtkPoints and assign pcoords as the internal data array.
+points = vtk.vtkPoints()
+points.SetData(pcoords)
+
+# Create the cells. In this case, a triangle strip with 2 triangles
+# (which can be represented by 4 points)
+strips = vtk.vtkCellArray()
+strips.InsertNextCell(4)
+strips.InsertCellPoint(0)
+strips.InsertCellPoint(1)
+strips.InsertCellPoint(2)
+strips.InsertCellPoint(3)
+
+# Create an integer array with 4 tuples. Note that when using
+# InsertNextValue (or InsertNextTuple1 which is equivalent in
+# this situation), the array will expand automatically
+temperature = vtk.vtkIntArray()
+temperature.SetName("Temperature")
+temperature.InsertNextValue(10)
+temperature.InsertNextValue(20)
+temperature.InsertNextValue(30)
+temperature.InsertNextValue(40)
+
+# Create a double array.
+vorticity = vtk.vtkDoubleArray()
+vorticity.SetName("Vorticity")
+vorticity.InsertNextValue(2.7)
+vorticity.InsertNextValue(4.1)
+vorticity.InsertNextValue(5.3)
+vorticity.InsertNextValue(3.4)
+
+# Create the dataset. In this case, we create a vtkPolyData
+polydata = vtk.vtkPolyData()
+# Assign points and cells
+polydata.SetPoints(points)
+polydata.SetStrips(strips)
+# Assign scalars
+polydata.GetPointData().SetScalars(temperature)
+# Add the vorticity array. In this example, this field
+# is not used.
+polydata.GetPointData().AddArray(vorticity)
+
+# Create the mapper and set the appropriate scalar range
+# (default is (0,1)
+mapper = vtk.vtkPolyDataMapper()
+mapper.SetInput(polydata)
+mapper.SetScalarRange(0, 40)
+
+# Create an actor.
+actor = vtk.vtkActor()
+actor.SetMapper(mapper)
+
+# Create the rendering objects.
+ren = vtk.vtkRenderer()
+ren.AddActor(actor)
+
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/DataManipulation/Arrays.vt b/examples/vtk_examples/DataManipulation/Arrays.vt
new file mode 100644
index 0000000..a759936
Binary files /dev/null and b/examples/vtk_examples/DataManipulation/Arrays.vt differ
diff --git a/examples/vtk_examples/DataManipulation/BuildUGrid.py b/examples/vtk_examples/DataManipulation/BuildUGrid.py
new file mode 100644
index 0000000..f7584e1
--- /dev/null
+++ b/examples/vtk_examples/DataManipulation/BuildUGrid.py
@@ -0,0 +1,386 @@
+#!/usr/bin/env python
+
+# This example shows how to manually construct unstructured grids
+# using Python. Unstructured grids require explicit point and cell
+# representations, so every point and cell must be created, and then
+# added to the vtkUnstructuredGrid instance.
+
+import vtk
+
+# Create several unstructured grids each containing a cell of a
+# different type.
+voxelPoints = vtk.vtkPoints()
+voxelPoints.SetNumberOfPoints(8)
+voxelPoints.InsertPoint(0, 0, 0, 0)
+voxelPoints.InsertPoint(1, 1, 0, 0)
+voxelPoints.InsertPoint(2, 0, 1, 0)
+voxelPoints.InsertPoint(3, 1, 1, 0)
+voxelPoints.InsertPoint(4, 0, 0, 1)
+voxelPoints.InsertPoint(5, 1, 0, 1)
+voxelPoints.InsertPoint(6, 0, 1, 1)
+voxelPoints.InsertPoint(7, 1, 1, 1)
+aVoxel = vtk.vtkVoxel()
+aVoxel.GetPointIds().SetId(0, 0)
+aVoxel.GetPointIds().SetId(1, 1)
+aVoxel.GetPointIds().SetId(2, 2)
+aVoxel.GetPointIds().SetId(3, 3)
+aVoxel.GetPointIds().SetId(4, 4)
+aVoxel.GetPointIds().SetId(5, 5)
+aVoxel.GetPointIds().SetId(6, 6)
+aVoxel.GetPointIds().SetId(7, 7)
+aVoxelGrid = vtk.vtkUnstructuredGrid()
+aVoxelGrid.Allocate(1, 1)
+aVoxelGrid.InsertNextCell(aVoxel.GetCellType(), aVoxel.GetPointIds())
+aVoxelGrid.SetPoints(voxelPoints)
+aVoxelMapper = vtk.vtkDataSetMapper()
+aVoxelMapper.SetInput(aVoxelGrid)
+aVoxelActor = vtk.vtkActor()
+aVoxelActor.SetMapper(aVoxelMapper)
+aVoxelActor.GetProperty().SetDiffuseColor(1, 0, 0)
+
+hexahedronPoints = vtk.vtkPoints()
+hexahedronPoints.SetNumberOfPoints(8)
+hexahedronPoints.InsertPoint(0, 0, 0, 0)
+hexahedronPoints.InsertPoint(1, 1, 0, 0)
+hexahedronPoints.InsertPoint(2, 1, 1, 0)
+hexahedronPoints.InsertPoint(3, 0, 1, 0)
+hexahedronPoints.InsertPoint(4, 0, 0, 1)
+hexahedronPoints.InsertPoint(5, 1, 0, 1)
+hexahedronPoints.InsertPoint(6, 1, 1, 1)
+hexahedronPoints.InsertPoint(7, 0, 1, 1)
+aHexahedron = vtk.vtkHexahedron()
+aHexahedron.GetPointIds().SetId(0, 0)
+aHexahedron.GetPointIds().SetId(1, 1)
+aHexahedron.GetPointIds().SetId(2, 2)
+aHexahedron.GetPointIds().SetId(3, 3)
+aHexahedron.GetPointIds().SetId(4, 4)
+aHexahedron.GetPointIds().SetId(5, 5)
+aHexahedron.GetPointIds().SetId(6, 6)
+aHexahedron.GetPointIds().SetId(7, 7)
+aHexahedronGrid = vtk.vtkUnstructuredGrid()
+aHexahedronGrid.Allocate(1, 1)
+aHexahedronGrid.InsertNextCell(aHexahedron.GetCellType(),
+ aHexahedron.GetPointIds())
+aHexahedronGrid.SetPoints(hexahedronPoints)
+aHexahedronMapper = vtk.vtkDataSetMapper()
+aHexahedronMapper.SetInput(aHexahedronGrid)
+aHexahedronActor = vtk.vtkActor()
+aHexahedronActor.SetMapper(aHexahedronMapper)
+aHexahedronActor.AddPosition(2, 0, 0)
+aHexahedronActor.GetProperty().SetDiffuseColor(1, 1, 0)
+
+tetraPoints = vtk.vtkPoints()
+tetraPoints.SetNumberOfPoints(4)
+tetraPoints.InsertPoint(0, 0, 0, 0)
+tetraPoints.InsertPoint(1, 1, 0, 0)
+tetraPoints.InsertPoint(2, .5, 1, 0)
+tetraPoints.InsertPoint(3, .5, .5, 1)
+aTetra = vtk.vtkTetra()
+aTetra.GetPointIds().SetId(0, 0)
+aTetra.GetPointIds().SetId(1, 1)
+aTetra.GetPointIds().SetId(2, 2)
+aTetra.GetPointIds().SetId(3, 3)
+aTetraGrid = vtk.vtkUnstructuredGrid()
+aTetraGrid.Allocate(1, 1)
+aTetraGrid.InsertNextCell(aTetra.GetCellType(), aTetra.GetPointIds())
+aTetraGrid.SetPoints(tetraPoints)
+aTetraMapper = vtk.vtkDataSetMapper()
+aTetraMapper.SetInput(aTetraGrid)
+aTetraActor = vtk.vtkActor()
+aTetraActor.SetMapper(aTetraMapper)
+aTetraActor.AddPosition(4, 0, 0)
+aTetraActor.GetProperty().SetDiffuseColor(0, 1, 0)
+
+wedgePoints = vtk.vtkPoints()
+wedgePoints.SetNumberOfPoints(6)
+wedgePoints.InsertPoint(0, 0, 1, 0)
+wedgePoints.InsertPoint(1, 0, 0, 0)
+wedgePoints.InsertPoint(2, 0, .5, .5)
+wedgePoints.InsertPoint(3, 1, 1, 0)
+wedgePoints.InsertPoint(4, 1, 0, 0)
+wedgePoints.InsertPoint(5, 1, .5, .5)
+aWedge = vtk.vtkWedge()
+aWedge.GetPointIds().SetId(0, 0)
+aWedge.GetPointIds().SetId(1, 1)
+aWedge.GetPointIds().SetId(2, 2)
+aWedge.GetPointIds().SetId(3, 3)
+aWedge.GetPointIds().SetId(4, 4)
+aWedge.GetPointIds().SetId(5, 5)
+aWedgeGrid = vtk.vtkUnstructuredGrid()
+aWedgeGrid.Allocate(1, 1)
+aWedgeGrid.InsertNextCell(aWedge.GetCellType(), aWedge.GetPointIds())
+aWedgeGrid.SetPoints(wedgePoints)
+aWedgeMapper = vtk.vtkDataSetMapper()
+aWedgeMapper.SetInput(aWedgeGrid)
+aWedgeActor = vtk.vtkActor()
+aWedgeActor.SetMapper(aWedgeMapper)
+aWedgeActor.AddPosition(6, 0, 0)
+aWedgeActor.GetProperty().SetDiffuseColor(0, 1, 1)
+
+pyramidPoints = vtk.vtkPoints()
+pyramidPoints.SetNumberOfPoints(5)
+pyramidPoints.InsertPoint(0, 0, 0, 0)
+pyramidPoints.InsertPoint(1, 1, 0, 0)
+pyramidPoints.InsertPoint(2, 1, 1, 0)
+pyramidPoints.InsertPoint(3, 0, 1, 0)
+pyramidPoints.InsertPoint(4, .5, .5, 1)
+aPyramid = vtk.vtkPyramid()
+aPyramid.GetPointIds().SetId(0, 0)
+aPyramid.GetPointIds().SetId(1, 1)
+aPyramid.GetPointIds().SetId(2, 2)
+aPyramid.GetPointIds().SetId(3, 3)
+aPyramid.GetPointIds().SetId(4, 4)
+aPyramidGrid = vtk.vtkUnstructuredGrid()
+aPyramidGrid.Allocate(1, 1)
+aPyramidGrid.InsertNextCell(aPyramid.GetCellType(), aPyramid.GetPointIds())
+aPyramidGrid.SetPoints(pyramidPoints)
+aPyramidMapper = vtk.vtkDataSetMapper()
+aPyramidMapper.SetInput(aPyramidGrid)
+aPyramidActor = vtk.vtkActor()
+aPyramidActor.SetMapper(aPyramidMapper)
+aPyramidActor.AddPosition(8, 0, 0)
+aPyramidActor.GetProperty().SetDiffuseColor(1, 0, 1)
+
+pixelPoints = vtk.vtkPoints()
+pixelPoints.SetNumberOfPoints(4)
+pixelPoints.InsertPoint(0, 0, 0, 0)
+pixelPoints.InsertPoint(1, 1, 0, 0)
+pixelPoints.InsertPoint(2, 0, 1, 0)
+pixelPoints.InsertPoint(3, 1, 1, 0)
+aPixel = vtk.vtkPixel()
+aPixel.GetPointIds().SetId(0, 0)
+aPixel.GetPointIds().SetId(1, 1)
+aPixel.GetPointIds().SetId(2, 2)
+aPixel.GetPointIds().SetId(3, 3)
+aPixelGrid = vtk.vtkUnstructuredGrid()
+aPixelGrid.Allocate(1, 1)
+aPixelGrid.InsertNextCell(aPixel.GetCellType(), aPixel.GetPointIds())
+aPixelGrid.SetPoints(pixelPoints)
+aPixelMapper = vtk.vtkDataSetMapper()
+aPixelMapper.SetInput(aPixelGrid)
+aPixelActor = vtk.vtkActor()
+aPixelActor.SetMapper(aPixelMapper)
+aPixelActor.AddPosition(0, 0, 2)
+aPixelActor.GetProperty().SetDiffuseColor(0, 1, 1)
+
+quadPoints = vtk.vtkPoints()
+quadPoints.SetNumberOfPoints(4)
+quadPoints.InsertPoint(0, 0, 0, 0)
+quadPoints.InsertPoint(1, 1, 0, 0)
+quadPoints.InsertPoint(2, 1, 1, 0)
+quadPoints.InsertPoint(3, 0, 1, 0)
+aQuad = vtk.vtkQuad()
+aQuad.GetPointIds().SetId(0, 0)
+aQuad.GetPointIds().SetId(1, 1)
+aQuad.GetPointIds().SetId(2, 2)
+aQuad.GetPointIds().SetId(3, 3)
+aQuadGrid = vtk.vtkUnstructuredGrid()
+aQuadGrid.Allocate(1, 1)
+aQuadGrid.InsertNextCell(aQuad.GetCellType(), aQuad.GetPointIds())
+aQuadGrid.SetPoints(quadPoints)
+aQuadMapper = vtk.vtkDataSetMapper()
+aQuadMapper.SetInput(aQuadGrid)
+aQuadActor = vtk.vtkActor()
+aQuadActor.SetMapper(aQuadMapper)
+aQuadActor.AddPosition(2, 0, 2)
+aQuadActor.GetProperty().SetDiffuseColor(1, 0, 1)
+
+trianglePoints = vtk.vtkPoints()
+trianglePoints.SetNumberOfPoints(3)
+trianglePoints.InsertPoint(0, 0, 0, 0)
+trianglePoints.InsertPoint(1, 1, 0, 0)
+trianglePoints.InsertPoint(2, .5, .5, 0)
+triangleTCoords = vtk.vtkFloatArray()
+triangleTCoords.SetNumberOfComponents(3)
+triangleTCoords.SetNumberOfTuples(3)
+triangleTCoords.InsertTuple3(0, 1, 1, 1)
+triangleTCoords.InsertTuple3(1, 2, 2, 2)
+triangleTCoords.InsertTuple3(2, 3, 3, 3)
+aTriangle = vtk.vtkTriangle()
+aTriangle.GetPointIds().SetId(0, 0)
+aTriangle.GetPointIds().SetId(1, 1)
+aTriangle.GetPointIds().SetId(2, 2)
+aTriangleGrid = vtk.vtkUnstructuredGrid()
+aTriangleGrid.Allocate(1, 1)
+aTriangleGrid.InsertNextCell(aTriangle.GetCellType(),
+ aTriangle.GetPointIds())
+aTriangleGrid.SetPoints(trianglePoints)
+aTriangleGrid.GetPointData().SetTCoords(triangleTCoords)
+aTriangleMapper = vtk.vtkDataSetMapper()
+aTriangleMapper.SetInput(aTriangleGrid)
+aTriangleActor = vtk.vtkActor()
+aTriangleActor.SetMapper(aTriangleMapper)
+aTriangleActor.AddPosition(4, 0, 2)
+aTriangleActor.GetProperty().SetDiffuseColor(.3, 1, .5)
+
+polygonPoints = vtk.vtkPoints()
+polygonPoints.SetNumberOfPoints(4)
+polygonPoints.InsertPoint(0, 0, 0, 0)
+polygonPoints.InsertPoint(1, 1, 0, 0)
+polygonPoints.InsertPoint(2, 1, 1, 0)
+polygonPoints.InsertPoint(3, 0, 1, 0)
+aPolygon = vtk.vtkPolygon()
+aPolygon.GetPointIds().SetNumberOfIds(4)
+aPolygon.GetPointIds().SetId(0, 0)
+aPolygon.GetPointIds().SetId(1, 1)
+aPolygon.GetPointIds().SetId(2, 2)
+aPolygon.GetPointIds().SetId(3, 3)
+aPolygonGrid = vtk.vtkUnstructuredGrid()
+aPolygonGrid.Allocate(1, 1)
+aPolygonGrid.InsertNextCell(aPolygon.GetCellType(), aPolygon.GetPointIds())
+aPolygonGrid.SetPoints(polygonPoints)
+aPolygonMapper = vtk.vtkDataSetMapper()
+aPolygonMapper.SetInput(aPolygonGrid)
+aPolygonActor = vtk.vtkActor()
+aPolygonActor.SetMapper(aPolygonMapper)
+aPolygonActor.AddPosition(6, 0, 2)
+aPolygonActor.GetProperty().SetDiffuseColor(1, .4, .5)
+
+triangleStripPoints = vtk.vtkPoints()
+triangleStripPoints.SetNumberOfPoints(5)
+triangleStripPoints.InsertPoint(0, 0, 1, 0)
+triangleStripPoints.InsertPoint(1, 0, 0, 0)
+triangleStripPoints.InsertPoint(2, 1, 1, 0)
+triangleStripPoints.InsertPoint(3, 1, 0, 0)
+triangleStripPoints.InsertPoint(4, 2, 1, 0)
+triangleStripTCoords = vtk.vtkFloatArray()
+triangleStripTCoords.SetNumberOfComponents(3)
+triangleStripTCoords.SetNumberOfTuples(3)
+triangleStripTCoords.InsertTuple3(0, 1, 1, 1)
+triangleStripTCoords.InsertTuple3(1, 2, 2, 2)
+triangleStripTCoords.InsertTuple3(2, 3, 3, 3)
+triangleStripTCoords.InsertTuple3(3, 4, 4, 4)
+triangleStripTCoords.InsertTuple3(4, 5, 5, 5)
+aTriangleStrip = vtk.vtkTriangleStrip()
+aTriangleStrip.GetPointIds().SetNumberOfIds(5)
+aTriangleStrip.GetPointIds().SetId(0, 0)
+aTriangleStrip.GetPointIds().SetId(1, 1)
+aTriangleStrip.GetPointIds().SetId(2, 2)
+aTriangleStrip.GetPointIds().SetId(3, 3)
+aTriangleStrip.GetPointIds().SetId(4, 4)
+aTriangleStripGrid = vtk.vtkUnstructuredGrid()
+aTriangleStripGrid.Allocate(1, 1)
+aTriangleStripGrid.InsertNextCell(aTriangleStrip.GetCellType(),
+ aTriangleStrip.GetPointIds())
+aTriangleStripGrid.SetPoints(triangleStripPoints)
+aTriangleStripGrid.GetPointData().SetTCoords(triangleStripTCoords)
+aTriangleStripMapper = vtk.vtkDataSetMapper()
+aTriangleStripMapper.SetInput(aTriangleStripGrid)
+aTriangleStripActor = vtk.vtkActor()
+aTriangleStripActor.SetMapper(aTriangleStripMapper)
+aTriangleStripActor.AddPosition(8, 0, 2)
+aTriangleStripActor.GetProperty().SetDiffuseColor(.3, .7, 1)
+
+linePoints = vtk.vtkPoints()
+linePoints.SetNumberOfPoints(2)
+linePoints.InsertPoint(0, 0, 0, 0)
+linePoints.InsertPoint(1, 1, 1, 0)
+aLine = vtk.vtkLine()
+aLine.GetPointIds().SetId(0, 0)
+aLine.GetPointIds().SetId(1, 1)
+aLineGrid = vtk.vtkUnstructuredGrid()
+aLineGrid.Allocate(1, 1)
+aLineGrid.InsertNextCell(aLine.GetCellType(), aLine.GetPointIds())
+aLineGrid.SetPoints(linePoints)
+aLineMapper = vtk.vtkDataSetMapper()
+aLineMapper.SetInput(aLineGrid)
+aLineActor = vtk.vtkActor()
+aLineActor.SetMapper(aLineMapper)
+aLineActor.AddPosition(0, 0, 4)
+aLineActor.GetProperty().SetDiffuseColor(.2, 1, 1)
+
+polyLinePoints = vtk.vtkPoints()
+polyLinePoints.SetNumberOfPoints(3)
+polyLinePoints.InsertPoint(0, 0, 0, 0)
+polyLinePoints.InsertPoint(1, 1, 1, 0)
+polyLinePoints.InsertPoint(2, 1, 0, 0)
+aPolyLine = vtk.vtkPolyLine()
+aPolyLine.GetPointIds().SetNumberOfIds(3)
+aPolyLine.GetPointIds().SetId(0, 0)
+aPolyLine.GetPointIds().SetId(1, 1)
+aPolyLine.GetPointIds().SetId(2, 2)
+aPolyLineGrid = vtk.vtkUnstructuredGrid()
+aPolyLineGrid.Allocate(1, 1)
+aPolyLineGrid.InsertNextCell(aPolyLine.GetCellType(),
+ aPolyLine.GetPointIds())
+aPolyLineGrid.SetPoints(polyLinePoints)
+aPolyLineMapper = vtk.vtkDataSetMapper()
+aPolyLineMapper.SetInput(aPolyLineGrid)
+aPolyLineActor = vtk.vtkActor()
+aPolyLineActor.SetMapper(aPolyLineMapper)
+aPolyLineActor.AddPosition(2, 0, 4)
+aPolyLineActor.GetProperty().SetDiffuseColor(1, 1, 1)
+
+vertexPoints = vtk.vtkPoints()
+vertexPoints.SetNumberOfPoints(1)
+vertexPoints.InsertPoint(0, 0, 0, 0)
+aVertex = vtk.vtkVertex()
+aVertex.GetPointIds().SetId(0, 0)
+aVertexGrid = vtk.vtkUnstructuredGrid()
+aVertexGrid.Allocate(1, 1)
+aVertexGrid.InsertNextCell(aVertex.GetCellType(), aVertex.GetPointIds())
+aVertexGrid.SetPoints(vertexPoints)
+aVertexMapper = vtk.vtkDataSetMapper()
+aVertexMapper.SetInput(aVertexGrid)
+aVertexActor = vtk.vtkActor()
+aVertexActor.SetMapper(aVertexMapper)
+aVertexActor.AddPosition(0, 0, 6)
+aVertexActor.GetProperty().SetDiffuseColor(1, 1, 1)
+
+polyVertexPoints = vtk.vtkPoints()
+polyVertexPoints.SetNumberOfPoints(3)
+polyVertexPoints.InsertPoint(0, 0, 0, 0)
+polyVertexPoints.InsertPoint(1, 1, 0, 0)
+polyVertexPoints.InsertPoint(2, 1, 1, 0)
+aPolyVertex = vtk.vtkPolyVertex()
+aPolyVertex.GetPointIds().SetNumberOfIds(3)
+aPolyVertex.GetPointIds().SetId(0, 0)
+aPolyVertex.GetPointIds().SetId(1, 1)
+aPolyVertex.GetPointIds().SetId(2, 2)
+aPolyVertexGrid = vtk.vtkUnstructuredGrid()
+aPolyVertexGrid.Allocate(1, 1)
+aPolyVertexGrid.InsertNextCell(aPolyVertex.GetCellType(),
+ aPolyVertex.GetPointIds())
+aPolyVertexGrid.SetPoints(polyVertexPoints)
+aPolyVertexMapper = vtk.vtkDataSetMapper()
+aPolyVertexMapper.SetInput(aPolyVertexGrid)
+aPolyVertexActor = vtk.vtkActor()
+aPolyVertexActor.SetMapper(aPolyVertexMapper)
+aPolyVertexActor.AddPosition(2, 0, 6)
+aPolyVertexActor.GetProperty().SetDiffuseColor(1, 1, 1)
+
+# Create the usual rendering stuff.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+renWin.SetSize(300, 150)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+ren.SetBackground(.1, .2, .4)
+
+ren.AddActor(aVoxelActor)
+ren.AddActor(aHexahedronActor)
+ren.AddActor(aTetraActor)
+ren.AddActor(aWedgeActor)
+ren.AddActor(aPyramidActor)
+ren.AddActor(aPixelActor)
+ren.AddActor(aQuadActor)
+ren.AddActor(aTriangleActor)
+ren.AddActor(aPolygonActor)
+ren.AddActor(aTriangleStripActor)
+ren.AddActor(aLineActor)
+ren.AddActor(aPolyLineActor)
+ren.AddActor(aVertexActor)
+ren.AddActor(aPolyVertexActor)
+
+ren.ResetCamera()
+ren.GetActiveCamera().Azimuth(30)
+ren.GetActiveCamera().Elevation(20)
+ren.GetActiveCamera().Dolly(2.8)
+ren.ResetCameraClippingRange()
+
+# Render the scene and start interaction.
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/DataManipulation/BuildUGrid.vt b/examples/vtk_examples/DataManipulation/BuildUGrid.vt
new file mode 100644
index 0000000..a082613
Binary files /dev/null and b/examples/vtk_examples/DataManipulation/BuildUGrid.vt differ
diff --git a/examples/vtk_examples/DataManipulation/CreateStrip.py b/examples/vtk_examples/DataManipulation/CreateStrip.py
new file mode 100644
index 0000000..bea887b
--- /dev/null
+++ b/examples/vtk_examples/DataManipulation/CreateStrip.py
@@ -0,0 +1,59 @@
+#!/usr/bin/env python
+
+# This script shows how to manually create a vtkPolyData with a
+# triangle strip.
+
+import vtk
+
+# First we'll create some points.
+points = vtk.vtkPoints()
+points.InsertPoint(0, 0.0, 0.0, 0.0)
+points.InsertPoint(1, 0.0, 1.0, 0.0)
+points.InsertPoint(2, 1.0, 0.0, 0.0)
+points.InsertPoint(3, 1.0, 1.0, 0.0)
+points.InsertPoint(4, 2.0, 0.0, 0.0)
+points.InsertPoint(5, 2.0, 1.0, 0.0)
+points.InsertPoint(6, 3.0, 0.0, 0.0)
+points.InsertPoint(7, 3.0, 1.0, 0.0)
+
+# The cell array can be thought of as a connectivity list. Here we
+# specify the number of points followed by that number of point
+# ids. This can be repeated as many times as there are primitives in
+# the list.
+strips = vtk.vtkCellArray()
+strips.InsertNextCell(8) # number of points
+strips.InsertCellPoint(0)
+strips.InsertCellPoint(1)
+strips.InsertCellPoint(2)
+strips.InsertCellPoint(3)
+strips.InsertCellPoint(4)
+strips.InsertCellPoint(5)
+strips.InsertCellPoint(6)
+strips.InsertCellPoint(7)
+profile = vtk.vtkPolyData()
+profile.SetPoints(points)
+profile.SetStrips(strips)
+
+map = vtk.vtkPolyDataMapper()
+map.SetInput(profile)
+
+strip = vtk.vtkActor()
+strip.SetMapper(map)
+strip.GetProperty().SetColor(0.3800, 0.7000, 0.1600)
+
+# Create the usual rendering stuff.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(strip)
+
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(250, 250)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/DataManipulation/CreateStrip.vt b/examples/vtk_examples/DataManipulation/CreateStrip.vt
new file mode 100644
index 0000000..8cabed3
Binary files /dev/null and b/examples/vtk_examples/DataManipulation/CreateStrip.vt differ
diff --git a/examples/vtk_examples/DataManipulation/marching.py b/examples/vtk_examples/DataManipulation/marching.py
new file mode 100644
index 0000000..e3c2c64
--- /dev/null
+++ b/examples/vtk_examples/DataManipulation/marching.py
@@ -0,0 +1,215 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of the vtkTransformPolyDataFilter
+# to reposition a 3D text string.
+
+import vtk
+from vtk.util.colors import *
+
+# Define a Single Cube
+Scalars = vtk.vtkFloatArray()
+Scalars.InsertNextValue(1.0)
+Scalars.InsertNextValue(0.0)
+Scalars.InsertNextValue(0.0)
+Scalars.InsertNextValue(1.0)
+Scalars.InsertNextValue(0.0)
+Scalars.InsertNextValue(0.0)
+Scalars.InsertNextValue(0.0)
+Scalars.InsertNextValue(0.0)
+
+Points = vtk.vtkPoints()
+Points.InsertNextPoint(0, 0, 0)
+Points.InsertNextPoint(1, 0, 0)
+Points.InsertNextPoint(1, 1, 0)
+Points.InsertNextPoint(0, 1, 0)
+Points.InsertNextPoint(0, 0, 1)
+Points.InsertNextPoint(1, 0, 1)
+Points.InsertNextPoint(1, 1, 1)
+Points.InsertNextPoint(0, 1, 1)
+
+Ids = vtk.vtkIdList()
+Ids.InsertNextId(0)
+Ids.InsertNextId(1)
+Ids.InsertNextId(2)
+Ids.InsertNextId(3)
+Ids.InsertNextId(4)
+Ids.InsertNextId(5)
+Ids.InsertNextId(6)
+Ids.InsertNextId(7)
+
+Grid = vtk.vtkUnstructuredGrid()
+Grid.Allocate(10, 10)
+Grid.InsertNextCell(12, Ids)
+Grid.SetPoints(Points)
+Grid.GetPointData().SetScalars(Scalars)
+
+# Find the triangles that lie along the 0.5 contour in this cube.
+Marching = vtk.vtkContourFilter()
+Marching.SetInput(Grid)
+Marching.SetValue(0, 0.5)
+Marching.Update()
+
+# Extract the edges of the triangles just found.
+triangleEdges = vtk.vtkExtractEdges()
+triangleEdges.SetInputConnection(Marching.GetOutputPort())
+# Draw the edges as tubes instead of lines. Also create the associated
+# mapper and actor to display the tubes.
+triangleEdgeTubes = vtk.vtkTubeFilter()
+triangleEdgeTubes.SetInputConnection(triangleEdges.GetOutputPort())
+triangleEdgeTubes.SetRadius(.005)
+triangleEdgeTubes.SetNumberOfSides(6)
+triangleEdgeTubes.UseDefaultNormalOn()
+triangleEdgeTubes.SetDefaultNormal(.577, .577, .577)
+triangleEdgeMapper = vtk.vtkPolyDataMapper()
+triangleEdgeMapper.SetInputConnection(triangleEdgeTubes.GetOutputPort())
+triangleEdgeMapper.ScalarVisibilityOff()
+triangleEdgeActor = vtk.vtkActor()
+triangleEdgeActor.SetMapper(triangleEdgeMapper)
+triangleEdgeActor.GetProperty().SetDiffuseColor(lamp_black)
+triangleEdgeActor.GetProperty().SetSpecular(.4)
+triangleEdgeActor.GetProperty().SetSpecularPower(10)
+
+# Shrink the triangles we found earlier. Create the associated mapper
+# and actor. Set the opacity of the shrunken triangles.
+aShrinker = vtk.vtkShrinkPolyData()
+aShrinker.SetShrinkFactor(1)
+aShrinker.SetInputConnection(Marching.GetOutputPort())
+aMapper = vtk.vtkPolyDataMapper()
+aMapper.ScalarVisibilityOff()
+aMapper.SetInputConnection(aShrinker.GetOutputPort())
+Triangles = vtk.vtkActor()
+Triangles.SetMapper(aMapper)
+Triangles.GetProperty().SetDiffuseColor(banana)
+Triangles.GetProperty().SetOpacity(.6)
+
+# Draw a cube the same size and at the same position as the one
+# created previously. Extract the edges because we only want to see
+# the outline of the cube. Pass the edges through a vtkTubeFilter so
+# they are displayed as tubes rather than lines.
+CubeModel = vtk.vtkCubeSource()
+CubeModel.SetCenter(.5, .5, .5)
+Edges = vtk.vtkExtractEdges()
+Edges.SetInputConnection(CubeModel.GetOutputPort())
+Tubes = vtk.vtkTubeFilter()
+Tubes.SetInputConnection(Edges.GetOutputPort())
+Tubes.SetRadius(.01)
+Tubes.SetNumberOfSides(6)
+Tubes.UseDefaultNormalOn()
+Tubes.SetDefaultNormal(.577, .577, .577)
+# Create the mapper and actor to display the cube edges.
+TubeMapper = vtk.vtkPolyDataMapper()
+TubeMapper.SetInputConnection(Tubes.GetOutputPort())
+CubeEdges = vtk.vtkActor()
+CubeEdges.SetMapper(TubeMapper)
+CubeEdges.GetProperty().SetDiffuseColor(khaki)
+CubeEdges.GetProperty().SetSpecular(.4)
+CubeEdges.GetProperty().SetSpecularPower(10)
+
+# Create a sphere to use as a glyph source for vtkGlyph3D.
+Sphere = vtk.vtkSphereSource()
+Sphere.SetRadius(0.04)
+Sphere.SetPhiResolution(20)
+Sphere.SetThetaResolution(20)
+# Remove the part of the cube with data values below 0.5.
+ThresholdIn = vtk.vtkThresholdPoints()
+ThresholdIn.SetInput(Grid)
+ThresholdIn.ThresholdByUpper(.5)
+# Display spheres at the vertices remaining in the cube data set after
+# it was passed through vtkThresholdPoints.
+Vertices = vtk.vtkGlyph3D()
+Vertices.SetInputConnection(ThresholdIn.GetOutputPort())
+Vertices.SetSource(Sphere.GetOutput())
+# Create a mapper and actor to display the glyphs.
+SphereMapper = vtk.vtkPolyDataMapper()
+SphereMapper.SetInputConnection(Vertices.GetOutputPort())
+SphereMapper.ScalarVisibilityOff()
+CubeVertices = vtk.vtkActor()
+CubeVertices.SetMapper(SphereMapper)
+CubeVertices.GetProperty().SetDiffuseColor(tomato)
+CubeVertices.GetProperty().SetDiffuseColor(tomato)
+
+# Define the text for the label
+caseLabel = vtk.vtkVectorText()
+caseLabel.SetText("Case 1")
+
+# Set up a transform to move the label to a new position.
+aLabelTransform = vtk.vtkTransform()
+aLabelTransform.Identity()
+aLabelTransform.Translate(-0.2, 0, 1.25)
+aLabelTransform.Scale(.05, .05, .05)
+
+# Move the label to a new position.
+labelTransform = vtk.vtkTransformPolyDataFilter()
+labelTransform.SetTransform(aLabelTransform)
+labelTransform.SetInputConnection(caseLabel.GetOutputPort())
+
+# Create a mapper and actor to display the text.
+labelMapper = vtk.vtkPolyDataMapper()
+labelMapper.SetInputConnection(labelTransform.GetOutputPort())
+
+labelActor = vtk.vtkActor()
+labelActor.SetMapper(labelMapper)
+
+# Define the base that the cube sits on. Create its associated mapper
+# and actor. Set the position of the actor.
+baseModel = vtk.vtkCubeSource()
+baseModel.SetXLength(1.5)
+baseModel.SetYLength(.01)
+baseModel.SetZLength(1.5)
+baseMapper = vtk.vtkPolyDataMapper()
+baseMapper.SetInputConnection(baseModel.GetOutputPort())
+base = vtk.vtkActor()
+base.SetMapper(baseMapper)
+base.SetPosition(.5, -0.09, .5)
+
+# Create the Renderer, RenderWindow, and RenderWindowInteractor
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+renWin.SetSize(640, 480)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer
+ren.AddActor(triangleEdgeActor)
+ren.AddActor(base)
+ren.AddActor(labelActor)
+ren.AddActor(CubeEdges)
+ren.AddActor(CubeVertices)
+ren.AddActor(Triangles)
+
+# Set the background color.
+ren.SetBackground(slate_grey)
+
+# This sets up the right values for case12 of the marching cubes
+# algorithm (routine translated from vtktesting/mccases.tcl).
+def case12(scalars, caselabel, IN, OUT):
+ scalars.InsertValue(0, OUT)
+ scalars.InsertValue(1, IN)
+ scalars.InsertValue(2, OUT)
+ scalars.InsertValue(3, IN)
+ scalars.InsertValue(4, IN)
+ scalars.InsertValue(5, IN)
+ scalars.InsertValue(6, OUT)
+ scalars.InsertValue(7, OUT)
+ if IN == 1:
+ caselabel.SetText("Case 12 - 00111010")
+ else:
+ caselabel.SetText("Case 12 - 11000101")
+
+# Set the scalar values for this case of marching cubes.
+case12(Scalars, caseLabel, 0, 1)
+
+# Force the grid to update.
+Grid.Modified()
+
+# Position the camera.
+ren.ResetCamera()
+ren.GetActiveCamera().Dolly(1.2)
+ren.GetActiveCamera().Azimuth(30)
+ren.GetActiveCamera().Elevation(20)
+ren.ResetCameraClippingRange()
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/DataManipulation/marching.vt b/examples/vtk_examples/DataManipulation/marching.vt
new file mode 100644
index 0000000..a8a6fc9
Binary files /dev/null and b/examples/vtk_examples/DataManipulation/marching.vt differ
diff --git a/examples/vtk_examples/DataManipulation/pointToCellData.py b/examples/vtk_examples/DataManipulation/pointToCellData.py
new file mode 100644
index 0000000..bab4523
--- /dev/null
+++ b/examples/vtk_examples/DataManipulation/pointToCellData.py
@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+
+# This example demonstrates the conversion of point data to cell data.
+# The conversion is necessary because we want to threshold data based
+# on cell scalar values.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Read some data with point data attributes. The data is from a
+# plastic blow molding process (e.g., to make plastic bottles) and
+# consists of two logical components: a mold and a parison. The
+# parison is the hot plastic that is being molded, and the mold is
+# clamped around the parison to form its shape.
+reader = vtk.vtkUnstructuredGridReader()
+reader.SetFileName(VTK_DATA_ROOT + "/Data/blow.vtk")
+reader.SetScalarsName("thickness9")
+reader.SetVectorsName("displacement9")
+
+# Convert the point data to cell data. The point data is passed
+# through the filter so it can be warped. The vtkThresholdFilter then
+# thresholds based on cell scalar values and extracts a portion of the
+# parison whose cell scalar values lie between 0.25 and 0.75.
+p2c = vtk.vtkPointDataToCellData()
+p2c.SetInputConnection(reader.GetOutputPort())
+p2c.PassPointDataOn()
+warp = vtk.vtkWarpVector()
+warp.SetInput(p2c.GetUnstructuredGridOutput())
+thresh = vtk.vtkThreshold()
+thresh.SetInputConnection(warp.GetOutputPort())
+thresh.ThresholdBetween(0.25, 0.75)
+thresh.SetInputArrayToProcess(1, 0, 0, 0, "thickness9")
+#thresh.SetAttributeModeToUseCellData()
+
+# This is used to extract the mold from the parison.
+connect = vtk.vtkConnectivityFilter()
+connect.SetInputConnection(thresh.GetOutputPort())
+connect.SetExtractionModeToSpecifiedRegions()
+connect.AddSpecifiedRegion(0)
+connect.AddSpecifiedRegion(1)
+moldMapper = vtk.vtkDataSetMapper()
+moldMapper.SetInputConnection(reader.GetOutputPort())
+moldMapper.ScalarVisibilityOff()
+moldActor = vtk.vtkActor()
+moldActor.SetMapper(moldMapper)
+moldActor.GetProperty().SetColor(.2, .2, .2)
+moldActor.GetProperty().SetRepresentationToWireframe()
+
+# The threshold filter has been used to extract the parison.
+connect2 = vtk.vtkConnectivityFilter()
+connect2.SetInputConnection(thresh.GetOutputPort())
+parison = vtk.vtkGeometryFilter()
+parison.SetInputConnection(connect2.GetOutputPort())
+normals2 = vtk.vtkPolyDataNormals()
+normals2.SetInputConnection(parison.GetOutputPort())
+normals2.SetFeatureAngle(60)
+lut = vtk.vtkLookupTable()
+lut.SetHueRange(0.0, 0.66667)
+parisonMapper = vtk.vtkPolyDataMapper()
+parisonMapper.SetInputConnection(normals2.GetOutputPort())
+parisonMapper.SetLookupTable(lut)
+parisonMapper.SetScalarRange(0.12, 1.0)
+parisonActor = vtk.vtkActor()
+parisonActor.SetMapper(parisonMapper)
+
+# We generate some contour lines on the parison.
+cf = vtk.vtkContourFilter()
+cf.SetInputConnection(connect2.GetOutputPort())
+cf.SetValue(0, .5)
+contourMapper = vtk.vtkPolyDataMapper()
+contourMapper.SetInputConnection(cf.GetOutputPort())
+contours = vtk.vtkActor()
+contours.SetMapper(contourMapper)
+
+# Create graphics stuff
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(moldActor)
+ren.AddActor(parisonActor)
+ren.AddActor(contours)
+
+ren.ResetCamera()
+ren.GetActiveCamera().Azimuth(60)
+ren.GetActiveCamera().Roll(-90)
+ren.GetActiveCamera().Dolly(2)
+ren.ResetCameraClippingRange()
+
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(750, 400)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/DataManipulation/pointToCellData.vt b/examples/vtk_examples/DataManipulation/pointToCellData.vt
new file mode 100644
index 0000000..99c096a
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diff --git a/examples/vtk_examples/GUI/ImplicitPlaneWidget.py b/examples/vtk_examples/GUI/ImplicitPlaneWidget.py
new file mode 100644
index 0000000..50691db
--- /dev/null
+++ b/examples/vtk_examples/GUI/ImplicitPlaneWidget.py
@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+
+# This example demonstrates how to use the vtkPlaneWidget to probe a
+# dataset and then generate contours on the probed data.
+
+import vtk
+
+# Create a mace out of filters.
+sphere = vtk.vtkSphereSource()
+cone = vtk.vtkConeSource()
+glyph = vtk.vtkGlyph3D()
+glyph.SetInputConnection(sphere.GetOutputPort())
+glyph.SetSource(cone.GetOutput())
+glyph.SetVectorModeToUseNormal()
+glyph.SetScaleModeToScaleByVector()
+glyph.SetScaleFactor(0.25)
+
+# The sphere and spikes are appended into a single polydata.
+# This just makes things simpler to manage.
+apd = vtk.vtkAppendPolyData()
+apd.AddInput(glyph.GetOutput())
+apd.AddInput(sphere.GetOutput())
+
+maceMapper = vtk.vtkPolyDataMapper()
+maceMapper.SetInputConnection(apd.GetOutputPort())
+
+maceActor = vtk.vtkLODActor()
+maceActor.SetMapper(maceMapper)
+maceActor.VisibilityOn()
+
+# This portion of the code clips the mace with the vtkPlanes
+# implicit function. The clipped region is colored green.
+plane = vtk.vtkPlane()
+clipper = vtk.vtkClipPolyData()
+clipper.SetInputConnection(apd.GetOutputPort())
+clipper.SetClipFunction(plane)
+clipper.InsideOutOn()
+
+selectMapper = vtk.vtkPolyDataMapper()
+selectMapper.SetInputConnection(clipper.GetOutputPort())
+
+selectActor = vtk.vtkLODActor()
+selectActor.SetMapper(selectMapper)
+selectActor.GetProperty().SetColor(0, 1, 0)
+selectActor.VisibilityOff()
+selectActor.SetScale(1.01, 1.01, 1.01)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# The callback function
+def myCallback(obj, event):
+ global plane, selectActor
+ obj.GetPlane(plane)
+ selectActor.VisibilityOn()
+
+# Associate the line widget with the interactor
+planeWidget = vtk.vtkImplicitPlaneWidget()
+planeWidget.SetInteractor(iren)
+planeWidget.SetPlaceFactor(1.25)
+planeWidget.SetInput(glyph.GetOutput())
+planeWidget.PlaceWidget()
+planeWidget.AddObserver("InteractionEvent", myCallback)
+
+ren.AddActor(maceActor)
+ren.AddActor(selectActor)
+
+# Add the actors to the renderer, set the background and size
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(300, 300)
+ren.SetBackground(0.1, 0.2, 0.4)
+
+# Start interaction.
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/GUI/ImplicitPlaneWidget.vt b/examples/vtk_examples/GUI/ImplicitPlaneWidget.vt
new file mode 100644
index 0000000..16b6bd9
Binary files /dev/null and b/examples/vtk_examples/GUI/ImplicitPlaneWidget.vt differ
diff --git a/examples/vtk_examples/GUI/ProbeWithPointWidget.py b/examples/vtk_examples/GUI/ProbeWithPointWidget.py
new file mode 100644
index 0000000..5d07070
--- /dev/null
+++ b/examples/vtk_examples/GUI/ProbeWithPointWidget.py
@@ -0,0 +1,102 @@
+#!/usr/bin/env python
+
+# This example demonstrates how to use the vtkPointWidget to probe a
+# dataset and then color the probed point (represented as a cone) as
+# per the probed value and orient it as per the vector.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Start by loading some data.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+
+# The plane widget is used probe the dataset.
+pointWidget = vtk.vtkPointWidget()
+pointWidget.SetInput(pl3d.GetOutput())
+pointWidget.AllOff()
+pointWidget.PlaceWidget()
+point = vtk.vtkPolyData()
+pointWidget.GetPolyData(point)
+
+probe = vtk.vtkProbeFilter()
+probe.SetInput(point)
+probe.SetSource(pl3d.GetOutput())
+
+# create glyph
+cone = vtk.vtkConeSource()
+cone.SetResolution(16)
+
+inspector = vtk.vtkDataSetInspector()
+inspector.SetInputConnection(pl3d.GetOutputPort())
+
+pythoncalc = vtk.PythonCalc()
+pythoncalc.value1(inspector.GetLength())
+pythoncalc.value2(0.1)
+pythoncalc.op('*')
+
+glyph = vtk.vtkGlyph3D()
+glyph.SetInputConnection(probe.GetOutputPort())
+glyph.SetSource(cone.GetOutput())
+glyph.SetVectorModeToUseVector()
+glyph.SetScaleModeToDataScalingOff()
+# glyph.SetScaleFactor(pl3d.GetOutput().GetLength()*0.1)
+glyph.SetScaleFactor(pythoncalc.value())
+glyphMapper = vtk.vtkPolyDataMapper()
+glyphMapper.SetInputConnection(glyph.GetOutputPort())
+glyphActor = vtk.vtkActor()
+glyphActor.SetMapper(glyphMapper)
+glyphActor.VisibilityOff()
+
+# An outline is shown for context.
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Actually set the color and orientation of the probe.
+def BeginInteraction(obj, event):
+ global point, glyphActor
+ obj.GetPolyData(point)
+ glyphActor.VisibilityOn()
+
+def ProbeData(obj, event):
+ obj.GetPolyData(point)
+
+# Associate the line widget with the interactor
+pointWidget.SetInteractor(iren)
+pointWidget.AddObserver("EnableEvent", BeginInteraction)
+pointWidget.AddObserver("StartInteractionEvent", BeginInteraction)
+pointWidget.AddObserver("InteractionEvent", ProbeData)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(outlineActor)
+ren.AddActor(glyphActor)
+
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(300, 300)
+ren.SetBackground(0.1, 0.2, 0.4)
+
+cam1 = ren.GetActiveCamera()
+cam1.SetClippingRange(3.95297, 50)
+cam1.SetFocalPoint(9.71821, 0.458166, 29.3999)
+cam1.SetPosition(2.7439, -37.3196, 38.7167)
+cam1.SetViewUp(-0.16123, 0.264271, 0.950876)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/GUI/ProbeWithPointWidget.vt b/examples/vtk_examples/GUI/ProbeWithPointWidget.vt
new file mode 100644
index 0000000..4fad360
Binary files /dev/null and b/examples/vtk_examples/GUI/ProbeWithPointWidget.vt differ
diff --git a/examples/vtk_examples/GUI/ProbingWithPlaneWidget.py b/examples/vtk_examples/GUI/ProbingWithPlaneWidget.py
new file mode 100644
index 0000000..829fa87
--- /dev/null
+++ b/examples/vtk_examples/GUI/ProbingWithPlaneWidget.py
@@ -0,0 +1,88 @@
+#!/usr/bin/env python
+
+# This example demonstrates how to use the vtkPlaneWidget to probe
+# a dataset and then generate contours on the probed data.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Start by loading some data.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+
+# The plane widget is used probe the dataset.
+planeWidget = vtk.vtkPlaneWidget()
+planeWidget.SetInput(pl3d.GetOutput())
+planeWidget.NormalToXAxisOn()
+planeWidget.SetResolution(20)
+planeWidget.SetRepresentationToOutline()
+planeWidget.PlaceWidget()
+plane = vtk.vtkPolyData()
+planeWidget.GetPolyData(plane)
+
+probe = vtk.vtkProbeFilter()
+probe.SetInput(plane)
+probe.SetSource(pl3d.GetOutput())
+
+contourMapper = vtk.vtkPolyDataMapper()
+contourMapper.SetInputConnection(probe.GetOutputPort())
+contourMapper.SetScalarRange(pl3d.GetOutput().GetScalarRange())
+contourActor = vtk.vtkActor()
+contourActor.SetMapper(contourMapper)
+contourActor.VisibilityOff()
+
+# An outline is shown for context.
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Actually generate contour lines.
+def BeginInteraction(obj, event):
+ global plane, contourActor
+ obj.GetPolyData(plane)
+ contourActor.VisibilityOn()
+
+def ProbeData(obj, event):
+ global plane
+ obj.GetPolyData(plane)
+
+
+# Associate the widget with the interactor
+planeWidget.SetInteractor(iren)
+# Handle the events.
+planeWidget.AddObserver("EnableEvent", BeginInteraction)
+planeWidget.AddObserver("StartInteractionEvent", BeginInteraction)
+planeWidget.AddObserver("InteractionEvent", ProbeData)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(outlineActor)
+ren.AddActor(contourActor)
+
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(300, 300)
+ren.SetBackground(0.1, 0.2, 0.4)
+
+cam1 = ren.GetActiveCamera()
+cam1.SetClippingRange(3.95297, 50)
+cam1.SetFocalPoint(9.71821, 0.458166, 29.3999)
+cam1.SetPosition(2.7439, -37.3196, 38.7167)
+cam1.SetViewUp(-0.16123, 0.264271, 0.950876)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/GUI/ProbingWithPlaneWidget.vt b/examples/vtk_examples/GUI/ProbingWithPlaneWidget.vt
new file mode 100644
index 0000000..fa4a847
Binary files /dev/null and b/examples/vtk_examples/GUI/ProbingWithPlaneWidget.vt differ
diff --git a/examples/vtk_examples/GUI/StreamlinesWithLineWidget.py b/examples/vtk_examples/GUI/StreamlinesWithLineWidget.py
new file mode 100644
index 0000000..f5a522e
--- /dev/null
+++ b/examples/vtk_examples/GUI/StreamlinesWithLineWidget.py
@@ -0,0 +1,139 @@
+#!/usr/bin/env python
+
+# This example demonstrates how to use the vtkLineWidget to seed and
+# manipulate streamlines. Two line widgets are created. One is invoked
+# by pressing 'i', the other by pressing 'L' (capital). Both can exist
+# together.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Start by loading some data.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+
+# The line widget is used seed the streamlines.
+lineWidget = vtk.vtkLineWidget()
+seeds = vtk.vtkPolyData()
+lineWidget.SetInput(pl3d.GetOutput())
+lineWidget.SetAlignToYAxis()
+lineWidget.PlaceWidget()
+lineWidget.GetPolyData(seeds)
+lineWidget.ClampToBoundsOn()
+
+rk4 = vtk.vtkRungeKutta4()
+streamer = vtk.vtkStreamLine()
+streamer.SetInputConnection(pl3d.GetOutputPort())
+streamer.SetSource(seeds)
+streamer.SetMaximumPropagationTime(100)
+streamer.SetIntegrationStepLength(.2)
+streamer.SetStepLength(.001)
+streamer.SetNumberOfThreads(1)
+streamer.SetIntegrationDirectionToForward()
+streamer.VorticityOn()
+streamer.SetIntegrator(rk4)
+rf = vtk.vtkRibbonFilter()
+rf.SetInputConnection(streamer.GetOutputPort())
+rf.SetWidth(0.1)
+rf.SetWidthFactor(5)
+streamMapper = vtk.vtkPolyDataMapper()
+streamMapper.SetInputConnection(rf.GetOutputPort())
+streamMapper.SetScalarRange(pl3d.GetOutput().GetScalarRange())
+streamline = vtk.vtkActor()
+streamline.SetMapper(streamMapper)
+streamline.VisibilityOff()
+
+# The second line widget is used seed more streamlines.
+lineWidget2 = vtk.vtkLineWidget()
+seeds2 = vtk.vtkPolyData()
+lineWidget2.SetInput(pl3d.GetOutput())
+lineWidget2.PlaceWidget()
+lineWidget2.GetPolyData(seeds2)
+lineWidget2.SetKeyPressActivationValue('L')
+
+streamer2 = vtk.vtkStreamLine()
+streamer2.SetInputConnection(pl3d.GetOutputPort())
+streamer2.SetSource(seeds2)
+streamer2.SetMaximumPropagationTime(100)
+streamer2.SetIntegrationStepLength(.2)
+streamer2.SetStepLength(.001)
+streamer2.SetNumberOfThreads(1)
+streamer2.SetIntegrationDirectionToForward()
+streamer2.VorticityOn()
+streamer2.SetIntegrator(rk4)
+rf2 = vtk.vtkRibbonFilter()
+rf2.SetInputConnection(streamer2.GetOutputPort())
+rf2.SetWidth(0.1)
+rf2.SetWidthFactor(5)
+streamMapper2 = vtk.vtkPolyDataMapper()
+streamMapper2.SetInputConnection(rf2.GetOutputPort())
+streamMapper2.SetScalarRange(pl3d.GetOutput().GetScalarRange())
+streamline2 = vtk.vtkActor()
+streamline2.SetMapper(streamMapper2)
+streamline2.VisibilityOff()
+
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Callback functions that actually generate streamlines.
+def BeginInteraction(obj, event):
+ global streamline
+ streamline.VisibilityOn()
+
+def GenerateStreamlines(obj, event):
+ global seeds, renWin
+ obj.GetPolyData(seeds)
+ renWin.Render()
+
+def BeginInteraction2(obj, event):
+ global streamline2
+ streamline2.VisibilityOn()
+
+def GenerateStreamlines2(obj, event):
+ global seeds2, renWin
+ obj.GetPolyData(seeds2)
+ renWin.Render()
+
+# Associate the line widget with the interactor and setup callbacks.
+lineWidget.SetInteractor(iren)
+lineWidget.AddObserver("StartInteractionEvent", BeginInteraction)
+lineWidget.AddObserver("InteractionEvent", GenerateStreamlines)
+
+lineWidget2.SetInteractor(iren)
+lineWidget2.AddObserver("StartInteractionEvent", BeginInteraction2)
+lineWidget2.AddObserver("EndInteractionEvent", GenerateStreamlines2)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(outlineActor)
+ren.AddActor(streamline)
+ren.AddActor(streamline2)
+
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(300, 300)
+ren.SetBackground(0.1, 0.2, 0.4)
+
+cam1 = ren.GetActiveCamera()
+cam1.SetClippingRange(3.95297, 50)
+cam1.SetFocalPoint(9.71821, 0.458166, 29.3999)
+cam1.SetPosition(2.7439, -37.3196, 38.7167)
+cam1.SetViewUp(-0.16123, 0.264271, 0.950876)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/GUI/StreamlinesWithLineWidget.vt b/examples/vtk_examples/GUI/StreamlinesWithLineWidget.vt
new file mode 100644
index 0000000..0e2b157
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diff --git a/examples/vtk_examples/GUI/TransformWithBoxWidget.py b/examples/vtk_examples/GUI/TransformWithBoxWidget.py
new file mode 100644
index 0000000..a04f332
--- /dev/null
+++ b/examples/vtk_examples/GUI/TransformWithBoxWidget.py
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+
+# Demonstrate how to use the vtkBoxWidget to translate, scale, and
+# rotate actors. The basic idea is that the box widget controls an
+# actor's transform. A callback which modifies the transform is
+# invoked as the box widget is manipulated.
+
+import vtk
+
+# Start by creating some simple geometry; in this case a mace.
+sphere = vtk.vtkSphereSource()
+cone = vtk.vtkConeSource()
+glyph = vtk.vtkGlyph3D()
+glyph.SetInputConnection(sphere.GetOutputPort())
+glyph.SetSource(cone.GetOutput())
+glyph.SetVectorModeToUseNormal()
+glyph.SetScaleModeToScaleByVector()
+glyph.SetScaleFactor(0.25)
+appendData = vtk.vtkAppendPolyData()
+appendData.AddInput(glyph.GetOutput())
+appendData.AddInput(sphere.GetOutput())
+maceMapper = vtk.vtkPolyDataMapper()
+maceMapper.SetInputConnection(appendData.GetOutputPort())
+maceActor = vtk.vtkLODActor()
+maceActor.SetMapper(maceMapper)
+maceActor.VisibilityOn()
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# The box widget observes the events invoked by the render window
+# interactor. These events come from user interaction in the render
+# window.
+boxWidget = vtk.vtkBoxWidget()
+boxWidget.SetInteractor(iren)
+boxWidget.SetPlaceFactor(1.25)
+
+# Add the actors to the renderer, set the background and window size.
+ren.AddActor(maceActor)
+ren.SetBackground(0.1, 0.2, 0.4)
+renWin.SetSize(300, 300)
+
+# As the box widget is interacted with, it produces a transformation
+# matrix that is set on the actor.
+t = vtk.vtkTransform()
+def TransformActor(obj, event):
+ global t, maceActor
+ obj.GetTransform(t)
+ maceActor.SetUserTransform(t)
+
+# Place the interactor initially. The actor is used to place and scale
+# the interactor. An observer is added to the box widget to watch for
+# interaction events. This event is captured and used to set the
+# transformation matrix of the actor.
+boxWidget.SetProp3D(maceActor)
+boxWidget.PlaceWidget()
+boxWidget.AddObserver("InteractionEvent", TransformActor)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/GUI/TransformWithBoxWidget.vt b/examples/vtk_examples/GUI/TransformWithBoxWidget.vt
new file mode 100644
index 0000000..40cca2c
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diff --git a/examples/vtk_examples/GUI/VolumeRenderWithBoxWidget.py b/examples/vtk_examples/GUI/VolumeRenderWithBoxWidget.py
new file mode 100644
index 0000000..7b8e549
--- /dev/null
+++ b/examples/vtk_examples/GUI/VolumeRenderWithBoxWidget.py
@@ -0,0 +1,127 @@
+#!/usr/bin/env python
+
+# Demonstrate how to use the vtkBoxWidget to control volume rendering
+# within the interior of the widget.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Load a volume, use the widget to control what's volume
+# rendered. Basically the idea is that the vtkBoxWidget provides a box
+# which clips the volume rendering.
+v16 = vtk.vtkVolume16Reader()
+v16.SetDataDimensions(64, 64)
+v16.GetOutput().SetOrigin(0.0, 0.0, 0.0)
+v16.SetDataByteOrderToLittleEndian()
+v16.SetFilePrefix(VTK_DATA_ROOT+ "/Data/headsq/quarter")
+v16.SetImageRange(1, 93)
+v16.SetDataSpacing(3.2, 3.2, 1.5)
+
+tfun = vtk.vtkPiecewiseFunction()
+tfun.AddPoint(70.0, 0.0)
+tfun.AddPoint(599.0, 0)
+tfun.AddPoint(600.0, 0)
+tfun.AddPoint(1195.0, 0)
+tfun.AddPoint(1200, .2)
+tfun.AddPoint(1300, .3)
+tfun.AddPoint(2000, .3)
+tfun.AddPoint(4095.0, 1.0)
+
+ctfun = vtk.vtkColorTransferFunction()
+ctfun.AddRGBPoint(0.0, 0.5, 0.0, 0.0)
+ctfun.AddRGBPoint(600.0, 1.0, 0.5, 0.5)
+ctfun.AddRGBPoint(1280.0, 0.9, 0.2, 0.3)
+ctfun.AddRGBPoint(1960.0, 0.81, 0.27, 0.1)
+ctfun.AddRGBPoint(4095.0, 0.5, 0.5, 0.5)
+
+compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
+
+volumeMapper = vtk.vtkVolumeRayCastMapper()
+volumeMapper.SetInputConnection(v16.GetOutputPort())
+volumeMapper.SetVolumeRayCastFunction(compositeFunction)
+
+volumeProperty = vtk.vtkVolumeProperty()
+volumeProperty.SetColor(ctfun)
+volumeProperty.SetScalarOpacity(tfun)
+volumeProperty.SetInterpolationTypeToLinear()
+volumeProperty.ShadeOn()
+
+newvol = vtk.vtkVolume()
+newvol.SetMapper(volumeMapper)
+newvol.SetProperty(volumeProperty)
+
+outline = vtk.vtkOutlineFilter()
+outline.SetInputConnection(v16.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# The SetInteractor method is how 3D widgets are associated with the
+# render window interactor. Internally, SetInteractor sets up a bunch
+# of callbacks using the Command/Observer mechanism (AddObserver()).
+boxWidget = vtk.vtkBoxWidget()
+boxWidget.SetInteractor(iren)
+boxWidget.SetPlaceFactor(1.0)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(outlineActor)
+ren.AddVolume(newvol)
+
+ren.SetBackground(0, 0, 0)
+renWin.SetSize(300, 300)
+
+# When interaction starts, the requested frame rate is increased.
+def StartInteraction(obj, event):
+ global renWin
+ renWin.SetDesiredUpdateRate(10)
+
+# When interaction ends, the requested frame rate is decreased to
+# normal levels. This causes a full resolution render to occur.
+def EndInteraction(obj, event):
+ global renWin
+ renWin.SetDesiredUpdateRate(0.001)
+
+# The implicit function vtkPlanes is used in conjunction with the
+# volume ray cast mapper to limit which portion of the volume is
+# volume rendered.
+planes = vtk.vtkPlanes()
+def ClipVolumeRender(obj, event):
+ global planes, volumeMapper
+ obj.GetPlanes(planes)
+ volumeMapper.SetClippingPlanes(planes)
+
+
+# Place the interactor initially. The output of the reader is used to
+# place the box widget.
+boxWidget.SetInput(v16.GetOutput())
+boxWidget.PlaceWidget()
+boxWidget.InsideOutOn()
+boxWidget.AddObserver("StartInteractionEvent", StartInteraction)
+boxWidget.AddObserver("InteractionEvent", ClipVolumeRender)
+boxWidget.AddObserver("EndInteractionEvent", EndInteraction)
+
+outlineProperty = boxWidget.GetOutlineProperty()
+outlineProperty.SetRepresentationToWireframe()
+outlineProperty.SetAmbient(1.0)
+outlineProperty.SetAmbientColor(1, 1, 1)
+outlineProperty.SetLineWidth(3)
+
+selectedOutlineProperty = boxWidget.GetSelectedOutlineProperty()
+selectedOutlineProperty.SetRepresentationToWireframe()
+selectedOutlineProperty.SetAmbient(1.0)
+selectedOutlineProperty.SetAmbientColor(1, 0, 0)
+selectedOutlineProperty.SetLineWidth(3)
+
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/GUI/VolumeRenderWithBoxWidget.vt b/examples/vtk_examples/GUI/VolumeRenderWithBoxWidget.vt
new file mode 100644
index 0000000..0a21a3e
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diff --git a/examples/vtk_examples/IO/flamingo.py b/examples/vtk_examples/IO/flamingo.py
new file mode 100644
index 0000000..14a3f77
--- /dev/null
+++ b/examples/vtk_examples/IO/flamingo.py
@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of vtk3DSImporter.
+# vtk3DSImporter is used to load 3D Studio files. Unlike writers,
+# importers can load scenes (data as well as lights, cameras, actors
+# etc.). Importers will either generate an instance of vtkRenderWindow
+# and/or vtkRenderer or will use the ones you specify.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+
+# Create the importer and read a file
+importer = vtk.vtk3DSImporter()
+importer.ComputeNormalsOn()
+importer.SetFileName(VTK_DATA_ROOT + "/Data/iflamigm.3ds")
+importer.Read()
+
+# Here we let the importer create a renderer and a render window for
+# us. We could have also create and assigned those ourselves like so:
+# renWin = vtk.vtkRenderWindow()
+# importer.SetRenderWindow(renWin)
+
+# Assign an interactor.
+# We have to ask the importer for it's render window.
+# renWin = importer.GetRenderWindow()
+
+ren = importer.GetRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Set the render window's size
+renWin.SetSize(300, 300)
+
+# Set some properties on the renderer.
+# We have to ask the importer for it's renderer.
+# ren = importer.GetRenderer()
+ren.SetBackground(0.1, 0.2, 0.4)
+
+# Position the camera:
+# change view up to +z
+camera = ren.GetActiveCamera()
+camera.SetPosition(0, 1, 0)
+camera.SetFocalPoint(0, 0, 0)
+camera.SetViewUp(0, 0, 1)
+# let the renderer compute good position and focal point
+ren.ResetCamera()
+camera.Dolly(1.4)
+ren.ResetCameraClippingRange()
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/IO/flamingo.vt b/examples/vtk_examples/IO/flamingo.vt
new file mode 100644
index 0000000..9e206eb
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diff --git a/examples/vtk_examples/IO/stl.py b/examples/vtk_examples/IO/stl.py
new file mode 100644
index 0000000..a9cb50d
--- /dev/null
+++ b/examples/vtk_examples/IO/stl.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of vtkSTLReader to load data into
+# VTK from a file. This example also uses vtkLODActor which changes
+# its graphical representation of the data to maintain interactive
+# performance.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create the reader and read a data file. Connect the mapper and
+# actor.
+sr = vtk.vtkSTLReader()
+sr.SetFileName(VTK_DATA_ROOT + "/Data/42400-IDGH.stl")
+
+stlMapper = vtk.vtkPolyDataMapper()
+stlMapper.SetInputConnection(sr.GetOutputPort())
+
+stlActor = vtk.vtkLODActor()
+stlActor.SetMapper(stlMapper)
+
+# Create the Renderer, RenderWindow, and RenderWindowInteractor
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the render; set the background and size
+ren.AddActor(stlActor)
+ren.SetBackground(0.1, 0.2, 0.4)
+renWin.SetSize(500, 500)
+
+# Zoom in closer
+ren.ResetCamera()
+cam1 = ren.GetActiveCamera()
+cam1.Zoom(1.4)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/IO/stl.vt b/examples/vtk_examples/IO/stl.vt
new file mode 100644
index 0000000..5891c13
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diff --git a/examples/vtk_examples/ImageProcessing/Contours2D.py b/examples/vtk_examples/ImageProcessing/Contours2D.py
new file mode 100644
index 0000000..edd434c
--- /dev/null
+++ b/examples/vtk_examples/ImageProcessing/Contours2D.py
@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+
+# This example shows how to sample a mathematical function over a
+# volume. A slice from the volume is then extracted and then contoured
+# to produce 2D contour lines.
+#
+import vtk
+
+# Quadric definition. This is a type of implicit function. Here the
+# coefficients to the equations are set.
+quadric = vtk.vtkQuadric()
+quadric.SetCoefficients(.5, 1, .2, 0, .1, 0, 0, .2, 0, 0)
+
+# The vtkSampleFunction uses the quadric function and evaluates function
+# value over a regular lattice (i.e., a volume).
+sample = vtk.vtkSampleFunction()
+sample.SetSampleDimensions(30, 30, 30)
+sample.SetImplicitFunction(quadric)
+sample.ComputeNormalsOff()
+sample.Update()
+
+# Here a single slice (i.e., image) is extracted from the volume. (Note: in
+# actuality the VOI request causes the sample function to operate on just the
+# slice.)
+extract = vtk.vtkExtractVOI()
+extract.SetInputConnection(sample.GetOutputPort())
+extract.SetVOI(0, 29, 0, 29, 15, 15)
+extract.SetSampleRate(1, 2, 3)
+
+# The image is contoured to produce contour lines. Thirteen contour values
+# ranging from (0,1.2) inclusive are produced.
+contours = vtk.vtkContourFilter()
+contours.SetInputConnection(extract.GetOutputPort())
+contours.GenerateValues(13, 0.0, 1.2)
+
+# The contour lines are mapped to the graphics library.
+contMapper = vtk.vtkPolyDataMapper()
+contMapper.SetInputConnection(contours.GetOutputPort())
+contMapper.SetScalarRange(0.0, 1.2)
+
+contActor = vtk.vtkActor()
+contActor.SetMapper(contMapper)
+
+# Create outline an outline of the sampled data.
+outline = vtk.vtkOutlineFilter()
+outline.SetInputConnection(sample.GetOutputPort())
+
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+outlineActor.GetProperty().SetColor(0, 0, 0)
+
+# Create the renderer, render window, and interactor.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Set the background color to white. Associate the actors with the
+# renderer.
+ren.SetBackground(1, 1, 1)
+ren.AddActor(contActor)
+ren.AddActor(outlineActor)
+
+# Zoom in a little bit.
+ren.ResetCamera()
+ren.GetActiveCamera().Zoom(1.5)
+
+# Initialize and start the event loop.
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/ImageProcessing/Contours2D.vt b/examples/vtk_examples/ImageProcessing/Contours2D.vt
new file mode 100644
index 0000000..93eb1e7
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diff --git a/examples/vtk_examples/Medical/Medical1.py b/examples/vtk_examples/Medical/Medical1.py
new file mode 100644
index 0000000..f3cfa9c
--- /dev/null
+++ b/examples/vtk_examples/Medical/Medical1.py
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+
+# This example reads a volume dataset, extracts an isosurface that
+# represents the skin and displays it.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create the renderer, the render window, and the interactor. The
+# renderer draws into the render window, the interactor enables mouse-
+# and keyboard-based interaction with the scene.
+aRenderer = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(aRenderer)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# The following reader is used to read a series of 2D slices (images)
+# that compose the volume. The slice dimensions are set, and the
+# pixel spacing. The data Endianness must also be specified. The reader
+# usese the FilePrefix in combination with the slice number to construct
+# filenames using the format FilePrefix.%d. (In this case the FilePrefix
+# is the root name of the file: quarter.)
+v16 = vtk.vtkVolume16Reader()
+v16.SetDataDimensions(64, 64)
+v16.SetDataByteOrderToLittleEndian()
+v16.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter")
+v16.SetImageRange(1, 93)
+v16.SetDataSpacing(3.2, 3.2, 1.5)
+
+# An isosurface, or contour value of 500 is known to correspond to the
+# skin of the patient. Once generated, a vtkPolyDataNormals filter is
+# is used to create normals for smooth surface shading during rendering.
+# The triangle stripper is used to create triangle strips from the
+# isosurface these render much faster on may systems.
+skinExtractor = vtk.vtkContourFilter()
+skinExtractor.SetInputConnection(v16.GetOutputPort())
+skinExtractor.SetValue(0, 500)
+skinNormals = vtk.vtkPolyDataNormals()
+skinNormals.SetInputConnection(skinExtractor.GetOutputPort())
+skinNormals.SetFeatureAngle(60.0)
+skinMapper = vtk.vtkPolyDataMapper()
+skinMapper.SetInputConnection(skinNormals.GetOutputPort())
+skinMapper.ScalarVisibilityOff()
+skin = vtk.vtkActor()
+skin.SetMapper(skinMapper)
+
+# An outline provides context around the data.
+outlineData = vtk.vtkOutlineFilter()
+outlineData.SetInputConnection(v16.GetOutputPort())
+mapOutline = vtk.vtkPolyDataMapper()
+mapOutline.SetInputConnection(outlineData.GetOutputPort())
+outline = vtk.vtkActor()
+outline.SetMapper(mapOutline)
+outline.GetProperty().SetColor(0, 0, 0)
+
+# It is convenient to create an initial view of the data. The FocalPoint
+# and Position form a vector direction. Later on (ResetCamera() method)
+# this vector is used to position the camera to look at the data in
+# this direction.
+aCamera = vtk.vtkCamera()
+aCamera.SetViewUp(0, 0, -1)
+aCamera.SetPosition(0, 1, 0)
+aCamera.SetFocalPoint(0, 0, 0)
+aCamera.ComputeViewPlaneNormal()
+
+# Actors are added to the renderer. An initial camera view is created.
+# The Dolly() method moves the camera towards the FocalPoint,
+# thereby enlarging the image.
+aRenderer.AddActor(outline)
+aRenderer.AddActor(skin)
+aRenderer.SetActiveCamera(aCamera)
+aRenderer.ResetCamera()
+aCamera.Dolly(1.5)
+
+# Set a background color for the renderer and set the size of the
+# render window (expressed in pixels).
+aRenderer.SetBackground(1, 1, 1)
+renWin.SetSize(640, 480)
+
+# Note that when camera movement occurs (as it does in the Dolly()
+# method), the clipping planes often need adjusting. Clipping planes
+# consist of two planes: near and far along the view direction. The
+# near plane clips out objects in front of the plane the far plane
+# clips out objects behind the plane. This way only what is drawn
+# between the planes is actually rendered.
+aRenderer.ResetCameraClippingRange()
+
+# Interact with the data.
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Medical/Medical1.vt b/examples/vtk_examples/Medical/Medical1.vt
new file mode 100644
index 0000000..a513f31
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diff --git a/examples/vtk_examples/Medical/Medical2.py b/examples/vtk_examples/Medical/Medical2.py
new file mode 100644
index 0000000..835e9fa
--- /dev/null
+++ b/examples/vtk_examples/Medical/Medical2.py
@@ -0,0 +1,119 @@
+#!/usr/bin/env python
+
+# This example reads a volume dataset, extracts two isosurfaces that
+# represent the skin and bone, and then displays them.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create the renderer, the render window, and the interactor. The
+# renderer draws into the render window, the interactor enables mouse-
+# and keyboard-based interaction with the scene.
+aRenderer = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(aRenderer)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# The following reader is used to read a series of 2D slices (images)
+# that compose the volume. The slice dimensions are set, and the
+# pixel spacing. The data Endianness must also be specified. The reader
+# usese the FilePrefix in combination with the slice number to construct
+# filenames using the format FilePrefix.%d. (In this case the FilePrefix
+# is the root name of the file: quarter.)
+v16 = vtk.vtkVolume16Reader()
+v16.SetDataDimensions(64, 64)
+v16.SetDataByteOrderToLittleEndian()
+v16.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter")
+v16.SetImageRange(1, 93)
+v16.SetDataSpacing(3.2, 3.2, 1.5)
+
+# An isosurface, or contour value of 500 is known to correspond to the
+# skin of the patient. Once generated, a vtkPolyDataNormals filter is
+# is used to create normals for smooth surface shading during rendering.
+# The triangle stripper is used to create triangle strips from the
+# isosurface these render much faster on may systems.
+skinExtractor = vtk.vtkContourFilter()
+skinExtractor.SetInputConnection(v16.GetOutputPort())
+skinExtractor.SetValue(0, 500)
+skinNormals = vtk.vtkPolyDataNormals()
+skinNormals.SetInputConnection(skinExtractor.GetOutputPort())
+skinNormals.SetFeatureAngle(60.0)
+skinStripper = vtk.vtkStripper()
+skinStripper.SetInputConnection(skinNormals.GetOutputPort())
+skinMapper = vtk.vtkPolyDataMapper()
+skinMapper.SetInputConnection(skinStripper.GetOutputPort())
+skinMapper.ScalarVisibilityOff()
+skin = vtk.vtkActor()
+skin.SetMapper(skinMapper)
+skin.GetProperty().SetDiffuseColor(1, .49, .25)
+skin.GetProperty().SetSpecular(.3)
+skin.GetProperty().SetSpecularPower(20)
+
+# An isosurface, or contour value of 1150 is known to correspond to the
+# skin of the patient. Once generated, a vtkPolyDataNormals filter is
+# is used to create normals for smooth surface shading during rendering.
+# The triangle stripper is used to create triangle strips from the
+# isosurface these render much faster on may systems.
+boneExtractor = vtk.vtkContourFilter()
+boneExtractor.SetInputConnection(v16.GetOutputPort())
+boneExtractor.SetValue(0, 1150)
+boneNormals = vtk.vtkPolyDataNormals()
+boneNormals.SetInputConnection(boneExtractor.GetOutputPort())
+boneNormals.SetFeatureAngle(60.0)
+boneStripper = vtk.vtkStripper()
+boneStripper.SetInputConnection(boneNormals.GetOutputPort())
+boneMapper = vtk.vtkPolyDataMapper()
+boneMapper.SetInputConnection(boneStripper.GetOutputPort())
+boneMapper.ScalarVisibilityOff()
+bone = vtk.vtkActor()
+bone.SetMapper(boneMapper)
+bone.GetProperty().SetDiffuseColor(1, 1, .9412)
+
+# An outline provides context around the data.
+outlineData = vtk.vtkOutlineFilter()
+outlineData.SetInputConnection(v16.GetOutputPort())
+mapOutline = vtk.vtkPolyDataMapper()
+mapOutline.SetInputConnection(outlineData.GetOutputPort())
+outline = vtk.vtkActor()
+outline.SetMapper(mapOutline)
+outline.GetProperty().SetColor(0, 0, 0)
+
+# It is convenient to create an initial view of the data. The FocalPoint
+# and Position form a vector direction. Later on (ResetCamera() method)
+# this vector is used to position the camera to look at the data in
+# this direction.
+aCamera = vtk.vtkCamera()
+aCamera.SetViewUp(0, 0, -1)
+aCamera.SetPosition(0, 1, 0)
+aCamera.SetFocalPoint(0, 0, 0)
+aCamera.ComputeViewPlaneNormal()
+
+# Actors are added to the renderer. An initial camera view is created.
+# The Dolly() method moves the camera towards the FocalPoint,
+# thereby enlarging the image.
+aRenderer.AddActor(outline)
+aRenderer.AddActor(skin)
+aRenderer.AddActor(bone)
+aRenderer.SetActiveCamera(aCamera)
+aRenderer.ResetCamera()
+aCamera.Dolly(1.5)
+
+# Set a background color for the renderer and set the size of the
+# render window (expressed in pixels).
+aRenderer.SetBackground(1, 1, 1)
+renWin.SetSize(640, 480)
+
+# Note that when camera movement occurs (as it does in the Dolly()
+# method), the clipping planes often need adjusting. Clipping planes
+# consist of two planes: near and far along the view direction. The
+# near plane clips out objects in front of the plane the far plane
+# clips out objects behind the plane. This way only what is drawn
+# between the planes is actually rendered.
+aRenderer.ResetCameraClippingRange()
+
+# Interact with the data.
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Medical/Medical2.vt b/examples/vtk_examples/Medical/Medical2.vt
new file mode 100644
index 0000000..8af2120
Binary files /dev/null and b/examples/vtk_examples/Medical/Medical2.vt differ
diff --git a/examples/vtk_examples/Medical/Medical3.py b/examples/vtk_examples/Medical/Medical3.py
new file mode 100644
index 0000000..4960597
--- /dev/null
+++ b/examples/vtk_examples/Medical/Medical3.py
@@ -0,0 +1,196 @@
+#!/usr/bin/env python
+
+# This example reads a volume dataset, extracts two isosurfaces that
+# represent the skin and bone, creates three orthogonal planes
+# (saggital, axial, coronal), and displays them.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create the renderer, the render window, and the interactor. The
+# renderer draws into the render window, the interactor enables mouse-
+# and keyboard-based interaction with the scene.
+aRenderer = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(aRenderer)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# The following reader is used to read a series of 2D slices (images)
+# that compose the volume. The slice dimensions are set, and the
+# pixel spacing. The data Endianness must also be specified. The reader
+# usese the FilePrefix in combination with the slice number to construct
+# filenames using the format FilePrefix.%d. (In this case the FilePrefix
+# is the root name of the file: quarter.)
+v16 = vtk.vtkVolume16Reader()
+v16.SetDataDimensions(64, 64)
+v16.SetDataByteOrderToLittleEndian()
+v16.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter")
+v16.SetImageRange(1, 93)
+v16.SetDataSpacing(3.2, 3.2, 1.5)
+
+# An isosurface, or contour value of 500 is known to correspond to the
+# skin of the patient. Once generated, a vtkPolyDataNormals filter is
+# is used to create normals for smooth surface shading during rendering.
+# The triangle stripper is used to create triangle strips from the
+# isosurface these render much faster on may systems.
+skinExtractor = vtk.vtkContourFilter()
+skinExtractor.SetInputConnection(v16.GetOutputPort())
+skinExtractor.SetValue(0, 500)
+skinNormals = vtk.vtkPolyDataNormals()
+skinNormals.SetInputConnection(skinExtractor.GetOutputPort())
+skinNormals.SetFeatureAngle(60.0)
+skinStripper = vtk.vtkStripper()
+skinStripper.SetInputConnection(skinNormals.GetOutputPort())
+skinMapper = vtk.vtkPolyDataMapper()
+skinMapper.SetInputConnection(skinStripper.GetOutputPort())
+skinMapper.ScalarVisibilityOff()
+skin = vtk.vtkActor()
+skin.SetMapper(skinMapper)
+skin.GetProperty().SetDiffuseColor(1, .49, .25)
+skin.GetProperty().SetSpecular(.3)
+skin.GetProperty().SetSpecularPower(20)
+
+# An isosurface, or contour value of 1150 is known to correspond to the
+# skin of the patient. Once generated, a vtkPolyDataNormals filter is
+# is used to create normals for smooth surface shading during rendering.
+# The triangle stripper is used to create triangle strips from the
+# isosurface these render much faster on may systems.
+boneExtractor = vtk.vtkContourFilter()
+boneExtractor.SetInputConnection(v16.GetOutputPort())
+boneExtractor.SetValue(0, 1150)
+boneNormals = vtk.vtkPolyDataNormals()
+boneNormals.SetInputConnection(boneExtractor.GetOutputPort())
+boneNormals.SetFeatureAngle(60.0)
+boneStripper = vtk.vtkStripper()
+boneStripper.SetInputConnection(boneNormals.GetOutputPort())
+boneMapper = vtk.vtkPolyDataMapper()
+boneMapper.SetInputConnection(boneStripper.GetOutputPort())
+boneMapper.ScalarVisibilityOff()
+bone = vtk.vtkActor()
+bone.SetMapper(boneMapper)
+bone.GetProperty().SetDiffuseColor(1, 1, .9412)
+
+# An outline provides context around the data.
+outlineData = vtk.vtkOutlineFilter()
+outlineData.SetInputConnection(v16.GetOutputPort())
+mapOutline = vtk.vtkPolyDataMapper()
+mapOutline.SetInputConnection(outlineData.GetOutputPort())
+outline = vtk.vtkActor()
+outline.SetMapper(mapOutline)
+outline.GetProperty().SetColor(0, 0, 0)
+
+# Now we are creating three orthogonal planes passing through the
+# volume. Each plane uses a different texture map and therefore has
+# diferent coloration.
+
+# Start by creatin a black/white lookup table.
+bwLut = vtk.vtkLookupTable()
+bwLut.SetTableRange(0, 2000)
+bwLut.SetSaturationRange(0, 0)
+bwLut.SetHueRange(0, 0)
+bwLut.SetValueRange(0, 1)
+bwLut.Build()
+
+# Now create a lookup table that consists of the full hue circle (from
+# HSV).
+hueLut = vtk.vtkLookupTable()
+hueLut.SetTableRange(0, 2000)
+hueLut.SetHueRange(0, 1)
+hueLut.SetSaturationRange(1, 1)
+hueLut.SetValueRange(1, 1)
+hueLut.Build()
+
+# Finally, create a lookup table with a single hue but having a range
+# in the saturation of the hue.
+satLut = vtk.vtkLookupTable()
+satLut.SetTableRange(0, 2000)
+satLut.SetHueRange(.6, .6)
+satLut.SetSaturationRange(0, 1)
+satLut.SetValueRange(1, 1)
+satLut.Build()
+
+# Create the first of the three planes. The filter vtkImageMapToColors
+# maps the data through the corresponding lookup table created above.
+# The vtkImageActor is a type of vtkProp and conveniently displays an
+# image on a single quadrilateral plane. It does this using texture
+# mapping and as a result is quite fast. (Note: the input image has to
+# be unsigned char values, which the vtkImageMapToColors produces.)
+# Note also that by specifying the DisplayExtent, the pipeline
+# requests data of this extent and the vtkImageMapToColors only
+# processes a slice of data.
+saggitalColors = vtk.vtkImageMapToColors()
+saggitalColors.SetInputConnection(v16.GetOutputPort())
+saggitalColors.SetLookupTable(bwLut)
+saggital = vtk.vtkImageActor()
+saggital.SetInput(saggitalColors.GetOutput())
+saggital.SetDisplayExtent(32, 32, 0, 63, 0, 92)
+
+# Create the second (axial) plane of the three planes. We use the same
+# approach as before except that the extent differs.
+axialColors = vtk.vtkImageMapToColors()
+axialColors.SetInputConnection(v16.GetOutputPort())
+axialColors.SetLookupTable(hueLut)
+axial = vtk.vtkImageActor()
+axial.SetInput(axialColors.GetOutput())
+axial.SetDisplayExtent(0, 63, 0, 63, 46, 46)
+
+# Create the third (coronal) plane of the three planes. We use the same
+# approach as before except that the extent differs.
+coronalColors = vtk.vtkImageMapToColors()
+coronalColors.SetInputConnection(v16.GetOutputPort())
+coronalColors.SetLookupTable(satLut)
+coronal = vtk.vtkImageActor()
+coronal.SetInput(coronalColors.GetOutput())
+coronal.SetDisplayExtent(0, 63, 32, 32, 0, 92)
+
+# It is convenient to create an initial view of the data. The FocalPoint
+# and Position form a vector direction. Later on (ResetCamera() method)
+# this vector is used to position the camera to look at the data in
+# this direction.
+aCamera = vtk.vtkCamera()
+aCamera.SetViewUp(0, 0, -1)
+aCamera.SetPosition(0, 1, 0)
+aCamera.SetFocalPoint(0, 0, 0)
+aCamera.ComputeViewPlaneNormal()
+
+# Actors are added to the renderer.
+aRenderer.AddActor(outline)
+aRenderer.AddActor(saggital)
+aRenderer.AddActor(axial)
+aRenderer.AddActor(coronal)
+#aRenderer.AddActor(axial)
+#aRenderer.AddActor(coronal)
+aRenderer.AddActor(skin)
+aRenderer.AddActor(bone)
+
+# Turn off bone for this example.
+bone.VisibilityOff()
+
+# Set skin to semi-transparent.
+skin.GetProperty().SetOpacity(0.5)
+
+# An initial camera view is created. The Dolly() method moves
+# the camera towards the FocalPoint, thereby enlarging the image.
+aRenderer.SetActiveCamera(aCamera)
+aRenderer.ResetCamera()
+aCamera.Dolly(1.5)
+
+# Set a background color for the renderer and set the size of the
+# render window (expressed in pixels).
+aRenderer.SetBackground(1, 1, 1)
+renWin.SetSize(640, 480)
+
+# Note that when camera movement occurs (as it does in the Dolly()
+# method), the clipping planes often need adjusting. Clipping planes
+# consist of two planes: near and far along the view direction. The
+# near plane clips out objects in front of the plane the far plane
+# clips out objects behind the plane. This way only what is drawn
+# between the planes is actually rendered.
+aRenderer.ResetCameraClippingRange()
+
+# Interact with the data.
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Medical/Medical3.vt b/examples/vtk_examples/Medical/Medical3.vt
new file mode 100644
index 0000000..8bba608
Binary files /dev/null and b/examples/vtk_examples/Medical/Medical3.vt differ
diff --git a/examples/vtk_examples/Modelling/PerlinTerrain.py b/examples/vtk_examples/Modelling/PerlinTerrain.py
new file mode 100644
index 0000000..ea53af2
--- /dev/null
+++ b/examples/vtk_examples/Modelling/PerlinTerrain.py
@@ -0,0 +1,67 @@
+#!/usr/bin/env python
+
+# This example demonstrates how to combine a "geometric" implicit
+# function with noise at different frequencies to produce the
+# appearance of a landscape.
+
+import vtk
+
+plane = vtk.vtkPlane()
+
+p1 = vtk.vtkPerlinNoise()
+p1.SetFrequency(1, 1, 0)
+
+p2 = vtk.vtkPerlinNoise()
+p2.SetFrequency(3, 5, 0)
+p2.SetPhase(0.5, 0.5, 0)
+
+p3 = vtk.vtkPerlinNoise()
+p3.SetFrequency(16, 16, 0)
+
+sum = vtk.vtkImplicitSum()
+sum.SetNormalizeByWeight(1)
+sum.AddFunction(plane)
+sum.AddFunction(p1, 0.2)
+sum.AddFunction(p2, 0.1)
+sum.AddFunction(p3, 0.02)
+
+sample = vtk.vtkSampleFunction()
+sample.SetImplicitFunction(sum)
+sample.SetSampleDimensions(65, 65, 20)
+sample.SetModelBounds(-1, 1, -1, 1, -0.5, 0.5)
+sample.ComputeNormalsOff()
+surface = vtk.vtkContourFilter()
+surface.SetInputConnection(sample.GetOutputPort())
+surface.SetValue(0, 0.0)
+
+smooth = vtk.vtkPolyDataNormals()
+smooth.SetInputConnection(surface.GetOutputPort())
+smooth.SetFeatureAngle(90)
+
+mapper = vtk.vtkPolyDataMapper()
+mapper.SetInputConnection(smooth.GetOutputPort())
+mapper.ScalarVisibilityOff()
+actor = vtk.vtkActor()
+actor.SetMapper(mapper)
+actor.GetProperty().SetColor(0.4, 0.2, 0.1)
+
+# Create the renderer etc.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(actor)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(500, 500)
+ren.ResetCamera()
+ren.GetActiveCamera().Elevation(-45)
+ren.GetActiveCamera().Azimuth(10)
+ren.GetActiveCamera().Dolly(1.35)
+ren.ResetCameraClippingRange()
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Modelling/PerlinTerrain.vt b/examples/vtk_examples/Modelling/PerlinTerrain.vt
new file mode 100644
index 0000000..60ec1b4
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diff --git a/examples/vtk_examples/Modelling/constrainedDelaunay.py b/examples/vtk_examples/Modelling/constrainedDelaunay.py
new file mode 100644
index 0000000..78bf325
--- /dev/null
+++ b/examples/vtk_examples/Modelling/constrainedDelaunay.py
@@ -0,0 +1,150 @@
+#!/usr/bin/env python
+
+# This example demonstrates how to use a constraint polygon in
+# Delaunay triangulation.
+
+import vtk
+from vtk.util.colors import peacock
+
+# Generate the input points and constrained edges/polygons.
+points = vtk.vtkPoints()
+points.InsertPoint(0, 1, 4, 0)
+points.InsertPoint(1, 3, 4, 0)
+points.InsertPoint(2, 7, 4, 0)
+points.InsertPoint(3, 11, 4, 0)
+points.InsertPoint(4, 13, 4, 0)
+points.InsertPoint(5, 13, 8, 0)
+points.InsertPoint(6, 13, 12, 0)
+points.InsertPoint(7, 10, 12, 0)
+points.InsertPoint(8, 7, 12, 0)
+points.InsertPoint(9, 4, 12, 0)
+points.InsertPoint(10, 1, 12, 0)
+points.InsertPoint(11, 1, 8, 0)
+points.InsertPoint(12, 3.5, 5, 0)
+points.InsertPoint(13, 4.5, 5, 0)
+points.InsertPoint(14, 5.5, 8, 0)
+points.InsertPoint(15, 6.5, 8, 0)
+points.InsertPoint(16, 6.5, 5, 0)
+points.InsertPoint(17, 7.5, 5, 0)
+points.InsertPoint(18, 7.5, 8, 0)
+points.InsertPoint(19, 9, 8, 0)
+points.InsertPoint(20, 9, 5, 0)
+points.InsertPoint(21, 10, 5, 0)
+points.InsertPoint(22, 10, 7, 0)
+points.InsertPoint(23, 11, 5, 0)
+points.InsertPoint(24, 12, 5, 0)
+points.InsertPoint(25, 10.5, 8, 0)
+points.InsertPoint(26, 12, 11, 0)
+points.InsertPoint(27, 11, 11, 0)
+points.InsertPoint(28, 10, 9, 0)
+points.InsertPoint(29, 10, 11, 0)
+points.InsertPoint(30, 9, 11, 0)
+points.InsertPoint(31, 9, 9, 0)
+points.InsertPoint(32, 7.5, 9, 0)
+points.InsertPoint(33, 7.5, 11, 0)
+points.InsertPoint(34, 6.5, 11, 0)
+points.InsertPoint(35, 6.5, 9, 0)
+points.InsertPoint(36, 5, 9, 0)
+points.InsertPoint(37, 4, 6, 0)
+points.InsertPoint(38, 3, 9, 0)
+points.InsertPoint(39, 2, 9, 0)
+polys = vtk.vtkCellArray()
+polys.InsertNextCell(12)
+polys.InsertCellPoint(0)
+polys.InsertCellPoint(1)
+polys.InsertCellPoint(2)
+polys.InsertCellPoint(3)
+polys.InsertCellPoint(4)
+polys.InsertCellPoint(5)
+polys.InsertCellPoint(6)
+polys.InsertCellPoint(7)
+polys.InsertCellPoint(8)
+polys.InsertCellPoint(9)
+polys.InsertCellPoint(10)
+polys.InsertCellPoint(11)
+polys.InsertNextCell(28)
+polys.InsertCellPoint(39)
+polys.InsertCellPoint(38)
+polys.InsertCellPoint(37)
+polys.InsertCellPoint(36)
+polys.InsertCellPoint(35)
+polys.InsertCellPoint(34)
+polys.InsertCellPoint(33)
+polys.InsertCellPoint(32)
+polys.InsertCellPoint(31)
+polys.InsertCellPoint(30)
+polys.InsertCellPoint(29)
+polys.InsertCellPoint(28)
+polys.InsertCellPoint(27)
+polys.InsertCellPoint(26)
+polys.InsertCellPoint(25)
+polys.InsertCellPoint(24)
+polys.InsertCellPoint(23)
+polys.InsertCellPoint(22)
+polys.InsertCellPoint(21)
+polys.InsertCellPoint(20)
+polys.InsertCellPoint(19)
+polys.InsertCellPoint(18)
+polys.InsertCellPoint(17)
+polys.InsertCellPoint(16)
+polys.InsertCellPoint(15)
+polys.InsertCellPoint(14)
+polys.InsertCellPoint(13)
+polys.InsertCellPoint(12)
+
+polyData = vtk.vtkPolyData()
+polyData.SetPoints(points)
+polyData.SetPolys(polys)
+
+# Notice this trick. The SetInput() method accepts a vtkPolyData that
+# is also the input to the Delaunay filter. The points of the
+# vtkPolyData are used to generate the triangulation; the polygons are
+# used to create a constraint region. The polygons are very carefully
+# created and ordered in the right direction to indicate inside and
+# outside of the polygon.
+delny = vtk.vtkDelaunay2D()
+delny.SetInput(polyData)
+delny.SetSource(polyData)
+mapMesh = vtk.vtkPolyDataMapper()
+mapMesh.SetInputConnection(delny.GetOutputPort())
+meshActor = vtk.vtkActor()
+meshActor.SetMapper(mapMesh)
+
+# Now we just pretty the mesh up with tubed edges and balls at the
+# vertices.
+extract = vtk.vtkExtractEdges()
+extract.SetInputConnection(delny.GetOutputPort())
+tubes = vtk.vtkTubeFilter()
+tubes.SetInputConnection(extract.GetOutputPort())
+tubes.SetRadius(0.1)
+tubes.SetNumberOfSides(6)
+mapEdges = vtk.vtkPolyDataMapper()
+mapEdges.SetInputConnection(tubes.GetOutputPort())
+edgeActor = vtk.vtkActor()
+edgeActor.SetMapper(mapEdges)
+edgeActor.GetProperty().SetColor(peacock)
+edgeActor.GetProperty().SetSpecularColor(1, 1, 1)
+edgeActor.GetProperty().SetSpecular(0.3)
+edgeActor.GetProperty().SetSpecularPower(20)
+edgeActor.GetProperty().SetAmbient(0.2)
+edgeActor.GetProperty().SetDiffuse(0.8)
+
+# Create the rendering window, renderer, and interactive renderer
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(meshActor)
+ren.AddActor(edgeActor)
+ren.SetBackground(0, 0, 0)
+renWin.SetSize(450, 300)
+
+ren.ResetCamera()
+ren.GetActiveCamera().Zoom(2)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Modelling/constrainedDelaunay.vt b/examples/vtk_examples/Modelling/constrainedDelaunay.vt
new file mode 100644
index 0000000..9cdfbc8
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diff --git a/examples/vtk_examples/Modelling/faultLines.py b/examples/vtk_examples/Modelling/faultLines.py
new file mode 100644
index 0000000..e3432de
--- /dev/null
+++ b/examples/vtk_examples/Modelling/faultLines.py
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+
+# Create a constrained Delaunay triangulation following fault lines. The
+# fault lines serve as constraint edges in the Delaunay triangulation.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+from vtk.util.colors import *
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Generate some points by reading a VTK data file. The data file also
+# has edges that represent constraint lines. This is originally from a
+# geologic horizon.
+reader = vtk.vtkPolyDataReader()
+reader.SetFileName(VTK_DATA_ROOT + "/Data/faults.vtk")
+
+# Perform a 2D triangulation with constraint edges.
+delny = vtk.vtkDelaunay2D()
+delny.SetInputConnection(reader.GetOutputPort())
+delny.SetSourceConnection(reader.GetOutputPort())
+delny.SetTolerance(0.00001)
+normals = vtk.vtkPolyDataNormals()
+normals.SetInputConnection(delny.GetOutputPort())
+mapMesh = vtk.vtkPolyDataMapper()
+mapMesh.SetInputConnection(normals.GetOutputPort())
+meshActor = vtk.vtkActor()
+meshActor.SetMapper(mapMesh)
+meshActor.GetProperty().SetColor(beige)
+
+# Now pretty up the mesh with tubed edges and balls at the vertices.
+tuber = vtk.vtkTubeFilter()
+tuber.SetInputConnection(reader.GetOutputPort())
+tuber.SetRadius(25)
+mapLines = vtk.vtkPolyDataMapper()
+mapLines.SetInputConnection(tuber.GetOutputPort())
+linesActor = vtk.vtkActor()
+linesActor.SetMapper(mapLines)
+linesActor.GetProperty().SetColor(1, 0, 0)
+linesActor.GetProperty().SetColor(tomato)
+
+# Create graphics objects
+# Create the rendering window, renderer, and interactive renderer
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(linesActor)
+ren.AddActor(meshActor)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(350, 250)
+
+cam1 = vtk.vtkCamera()
+cam1.SetClippingRange(2580, 129041)
+cam1.SetFocalPoint(461550, 6.58e+006, 2132)
+cam1.SetPosition(463960, 6.559e+06, 16982)
+cam1.SetViewUp(-0.321899, 0.522244, 0.78971)
+light = vtk.vtkLight()
+light.SetPosition(0, 0, 1)
+light.SetFocalPoint(0, 0, 0)
+ren.SetActiveCamera(cam1)
+ren.AddLight(light)
+
+ren.GetActiveCamera().Zoom(1.5)
+iren.LightFollowCameraOff()
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Modelling/faultLines.vt b/examples/vtk_examples/Modelling/faultLines.vt
new file mode 100644
index 0000000..0c8ef9b
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diff --git a/examples/vtk_examples/Modelling/hello.py b/examples/vtk_examples/Modelling/hello.py
new file mode 100644
index 0000000..7033dd0
--- /dev/null
+++ b/examples/vtk_examples/Modelling/hello.py
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+
+# This example demonstrates how to use implicit modelling.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+from vtk.util.colors import red, peacock
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create lines which serve as the "seed" geometry. The lines spell the
+# word "hello".
+reader = vtk.vtkPolyDataReader()
+reader.SetFileName(VTK_DATA_ROOT + "/Data/hello.vtk")
+lineMapper = vtk.vtkPolyDataMapper()
+lineMapper.SetInputConnection(reader.GetOutputPort())
+lineActor = vtk.vtkActor()
+lineActor.SetMapper(lineMapper)
+lineActor.GetProperty().SetColor(red)
+
+# Create implicit model with vtkImplicitModeller. This computes a
+# scalar field which is the distance from the generating geometry. The
+# contour filter then extracts the geoemtry at the distance value 0.25
+# from the generating geometry.
+imp = vtk.vtkImplicitModeller()
+imp.SetInputConnection(reader.GetOutputPort())
+imp.SetSampleDimensions(110, 40, 20)
+imp.SetMaximumDistance(0.25)
+imp.SetModelBounds(-1.0, 10.0, -1.0, 3.0, -1.0, 1.0)
+contour = vtk.vtkContourFilter()
+contour.SetInputConnection(imp.GetOutputPort())
+contour.SetValue(0, 0.25)
+impMapper = vtk.vtkPolyDataMapper()
+impMapper.SetInputConnection(contour.GetOutputPort())
+impMapper.ScalarVisibilityOff()
+impActor = vtk.vtkActor()
+impActor.SetMapper(impMapper)
+impActor.GetProperty().SetColor(peacock)
+impActor.GetProperty().SetOpacity(0.5)
+
+# Create the usual graphics stuff.
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(lineActor)
+ren.AddActor(impActor)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(600, 250)
+
+camera = vtk.vtkCamera()
+camera.SetClippingRange(1.81325, 90.6627)
+camera.SetFocalPoint(4.5, 1, 0)
+camera.SetPosition(4.5, 1.0, 6.73257)
+camera.SetViewUp(0, 1, 0)
+camera.Zoom(0.8)
+ren.SetActiveCamera(camera)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Modelling/hello.vt b/examples/vtk_examples/Modelling/hello.vt
new file mode 100644
index 0000000..488f8b4
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diff --git a/examples/vtk_examples/Modelling/iceCream.py b/examples/vtk_examples/Modelling/iceCream.py
new file mode 100644
index 0000000..5cfe59d
--- /dev/null
+++ b/examples/vtk_examples/Modelling/iceCream.py
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+
+# This example demonstrates how to use boolean combinations of implicit
+# functions to create a model of an ice cream cone.
+
+import vtk
+from vtk.util.colors import chocolate, mint
+
+# Create implicit function primitives. These have been carefully
+# placed to give the effect that we want. We are going to use various
+# combinations of these functions to create the shape we want; for
+# example, we use planes intersected with a cone (which is infinite in
+# extent) to get a finite cone.
+cone = vtk.vtkCone()
+cone.SetAngle(20)
+vertPlane = vtk.vtkPlane()
+vertPlane.SetOrigin(.1, 0, 0)
+vertPlane.SetNormal(-1, 0, 0)
+basePlane = vtk.vtkPlane()
+basePlane.SetOrigin(1.2, 0, 0)
+basePlane.SetNormal(1, 0, 0)
+iceCream = vtk.vtkSphere()
+iceCream.SetCenter(1.333, 0, 0)
+iceCream.SetRadius(0.5)
+bite = vtk.vtkSphere()
+bite.SetCenter(1.5, 0, 0.5)
+bite.SetRadius(0.25)
+
+# Combine primitives to build ice-cream cone. Clip the cone with planes.
+theCone = vtk.vtkImplicitBoolean()
+theCone.SetOperationTypeToIntersection()
+theCone.AddFunction(cone)
+theCone.AddFunction(vertPlane)
+theCone.AddFunction(basePlane)
+
+# Take a bite out of the ice cream.
+theCream = vtk.vtkImplicitBoolean()
+theCream.SetOperationTypeToDifference()
+theCream.AddFunction(iceCream)
+theCream.AddFunction(bite)
+
+# The sample function generates a distance function from the implicit
+# function (which in this case is the cone). This is then contoured to
+# get a polygonal surface.
+theConeSample = vtk.vtkSampleFunction()
+theConeSample.SetImplicitFunction(theCone)
+theConeSample.SetModelBounds(-1, 1.5, -1.25, 1.25, -1.25, 1.25)
+theConeSample.SetSampleDimensions(60, 60, 60)
+theConeSample.ComputeNormalsOff()
+theConeSurface = vtk.vtkContourFilter()
+theConeSurface.SetInputConnection(theConeSample.GetOutputPort())
+theConeSurface.SetValue(0, 0.0)
+coneMapper = vtk.vtkPolyDataMapper()
+coneMapper.SetInputConnection(theConeSurface.GetOutputPort())
+coneMapper.ScalarVisibilityOff()
+coneActor = vtk.vtkActor()
+coneActor.SetMapper(coneMapper)
+coneActor.GetProperty().SetColor(chocolate)
+
+# The same here for the ice cream.
+theCreamSample = vtk.vtkSampleFunction()
+theCreamSample.SetImplicitFunction(theCream)
+theCreamSample.SetModelBounds(0, 2.5, -1.25, 1.25, -1.25, 1.25)
+theCreamSample.SetSampleDimensions(60, 60, 60)
+theCreamSample.ComputeNormalsOff()
+theCreamSurface = vtk.vtkContourFilter()
+theCreamSurface.SetInputConnection(theCreamSample.GetOutputPort())
+theCreamSurface.SetValue(0, 0.0)
+creamMapper = vtk.vtkPolyDataMapper()
+creamMapper.SetInputConnection(theCreamSurface.GetOutputPort())
+creamMapper.ScalarVisibilityOff()
+creamActor = vtk.vtkActor()
+creamActor.SetMapper(creamMapper)
+creamActor.GetProperty().SetColor(mint)
+
+# Create the usual rendering stuff
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(coneActor)
+ren.AddActor(creamActor)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(250, 250)
+ren.ResetCamera()
+ren.GetActiveCamera().Roll(90)
+ren.GetActiveCamera().Dolly(1.5)
+ren.ResetCameraClippingRange()
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Modelling/iceCream.vt b/examples/vtk_examples/Modelling/iceCream.vt
new file mode 100644
index 0000000..cccdc33
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diff --git a/examples/vtk_examples/Rendering/CADPart.py b/examples/vtk_examples/Rendering/CADPart.py
new file mode 100644
index 0000000..39182bf
--- /dev/null
+++ b/examples/vtk_examples/Rendering/CADPart.py
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+
+# This simple example shows how to do basic rendering and pipeline
+# creation. It also demonstrates the use of the LODActor.
+
+# Import the VTK-Python module
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+from vtk.util.colors import *
+# Get the location of the data.
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# This creates a polygonal cylinder model with eight circumferential
+# facets.
+part = vtk.vtkSTLReader()
+part.SetFileName(VTK_DATA_ROOT + "/Data/42400-IDGH.stl")
+
+# The mapper is responsible for pushing the geometry into the graphics
+# library. It may also do color mapping, if scalars or other
+# attributes are defined.
+partMapper = vtk.vtkPolyDataMapper()
+partMapper.SetInputConnection(part.GetOutputPort())
+
+# The LOD actor is a special type of actor. It will change appearance
+# in order to render faster. At the highest resolution, it renders
+# ewverything just like an actor. The middle level is a point cloud,
+# and the lowest level is a simple bounding box.
+partActor = vtk.vtkLODActor()
+partActor.SetMapper(partMapper)
+partActor.GetProperty().SetColor(light_grey)
+partActor.RotateX(30.0)
+partActor.RotateY(-45.0)
+
+# Create the graphics structure. The renderer renders into the render
+# window. The render window interactor captures mouse events and will
+# perform appropriate camera or actor manipulation depending on the
+# nature of the events.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(partActor)
+ren.SetBackground(0.1, 0.2, 0.4)
+renWin.SetSize(200, 200)
+
+# We'll zoom in a little by accessing the camera and invoking a "Zoom"
+# method on it.
+ren.ResetCamera()
+ren.GetActiveCamera().Zoom(1.5)
+
+# This starts the event loop.
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Rendering/CADPart.vt b/examples/vtk_examples/Rendering/CADPart.vt
new file mode 100644
index 0000000..688f30c
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diff --git a/examples/vtk_examples/Rendering/Cylinder.py b/examples/vtk_examples/Rendering/Cylinder.py
new file mode 100644
index 0000000..ba4e705
--- /dev/null
+++ b/examples/vtk_examples/Rendering/Cylinder.py
@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+
+# This simple example shows how to do basic rendering and pipeline
+# creation.
+
+import vtk
+# The colors module defines various useful colors.
+from vtk.util.colors import tomato
+
+# This creates a polygonal cylinder model with eight circumferential
+# facets.
+cylinder = vtk.vtkCylinderSource()
+cylinder.SetResolution(8)
+
+# The mapper is responsible for pushing the geometry into the graphics
+# library. It may also do color mapping, if scalars or other
+# attributes are defined.
+cylinderMapper = vtk.vtkPolyDataMapper()
+cylinderMapper.SetInputConnection(cylinder.GetOutputPort())
+
+# The actor is a grouping mechanism: besides the geometry (mapper), it
+# also has a property, transformation matrix, and/or texture map.
+# Here we set its color and rotate it -22.5 degrees.
+cylinderActor = vtk.vtkActor()
+cylinderActor.SetMapper(cylinderMapper)
+cylinderActor.GetProperty().SetColor(tomato)
+cylinderActor.RotateX(30.0)
+cylinderActor.RotateY(-45.0)
+
+# Create the graphics structure. The renderer renders into the render
+# window. The render window interactor captures mouse events and will
+# perform appropriate camera or actor manipulation depending on the
+# nature of the events.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(cylinderActor)
+ren.SetBackground(0.1, 0.2, 0.4)
+renWin.SetSize(200, 200)
+
+# This allows the interactor to initalize itself. It has to be
+# called before an event loop.
+iren.Initialize()
+
+# We'll zoom in a little by accessing the camera and invoking a "Zoom"
+# method on it.
+ren.ResetCamera()
+ren.GetActiveCamera().Zoom(1.5)
+renWin.Render()
+
+# Start the event loop.
+iren.Start()
diff --git a/examples/vtk_examples/Rendering/Cylinder.vt b/examples/vtk_examples/Rendering/Cylinder.vt
new file mode 100644
index 0000000..52efab4
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diff --git a/examples/vtk_examples/Rendering/FilterCADPart.py b/examples/vtk_examples/Rendering/FilterCADPart.py
new file mode 100644
index 0000000..7786e73
--- /dev/null
+++ b/examples/vtk_examples/Rendering/FilterCADPart.py
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+
+# This simple example shows how to do simple filtering in a pipeline.
+# See CADPart.py and Cylinder.py for related information.
+
+import vtk
+from vtk.util.colors import light_grey
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# This creates a polygonal cylinder model with eight circumferential
+# facets.
+part = vtk.vtkSTLReader()
+part.SetFileName(VTK_DATA_ROOT + "/Data/42400-IDGH.stl")
+
+# A filter is a module that takes at least one input and produces at
+# least one output. The SetInput and GetOutput methods are used to do
+# the connection. What is returned by GetOutput is a particulat
+# dataset type. If the type is compatible with the SetInput method,
+# then the filters can be connected together.
+#
+# Here we add a filter that computes surface normals from the geometry.
+shrink = vtk.vtkShrinkPolyData()
+shrink.SetInputConnection(part.GetOutputPort())
+shrink.SetShrinkFactor(0.85)
+
+# The mapper is responsible for pushing the geometry into the graphics
+# library. It may also do color mapping, if scalars or other
+# attributes are defined.
+partMapper = vtk.vtkPolyDataMapper()
+partMapper.SetInputConnection(shrink.GetOutputPort())
+
+# The LOD actor is a special type of actor. It will change appearance
+# in order to render faster. At the highest resolution, it renders
+# ewverything just like an actor. The middle level is a point cloud,
+# and the lowest level is a simple bounding box.
+partActor = vtk.vtkLODActor()
+partActor.SetMapper(partMapper)
+partActor.GetProperty().SetColor(light_grey)
+partActor.RotateX(30.0)
+partActor.RotateY(-45.0)
+
+# Create the graphics structure. The renderer renders into the
+# render window. The render window interactor captures mouse events
+# and will perform appropriate camera or actor manipulation
+# depending on the nature of the events.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(partActor)
+ren.SetBackground(0.1, 0.2, 0.4)
+renWin.SetSize(200, 200)
+
+# We'll zoom in a little by accessing the camera and invoking a "Zoom"
+# method on it.
+ren.ResetCamera()
+ren.GetActiveCamera().Zoom(1.5)
+
+iren.Initialize()
+renWin.Render()
+# Start the event loop.
+iren.Start()
diff --git a/examples/vtk_examples/Rendering/FilterCADPart.vt b/examples/vtk_examples/Rendering/FilterCADPart.vt
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index 0000000..2fbb69e
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diff --git a/examples/vtk_examples/Rendering/TPlane.py b/examples/vtk_examples/Rendering/TPlane.py
new file mode 100644
index 0000000..3b9d402
--- /dev/null
+++ b/examples/vtk_examples/Rendering/TPlane.py
@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+
+# This simple example shows how to do basic texture mapping.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Load in the texture map. A texture is any unsigned char image. If it
+# is not of this type, you will have to map it through a lookup table
+# or by using vtkImageShiftScale.
+bmpReader = vtk.vtkBMPReader()
+bmpReader.SetFileName(VTK_DATA_ROOT + "/Data/masonry.bmp")
+atext = vtk.vtkTexture()
+atext.SetInputConnection(bmpReader.GetOutputPort())
+atext.InterpolateOn()
+
+# Create a plane source and actor. The vtkPlanesSource generates
+# texture coordinates.
+plane = vtk.vtkPlaneSource()
+planeMapper = vtk.vtkPolyDataMapper()
+planeMapper.SetInputConnection(plane.GetOutputPort())
+planeActor = vtk.vtkActor()
+planeActor.SetMapper(planeMapper)
+planeActor.SetTexture(atext)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(planeActor)
+ren.SetBackground(0.1, 0.2, 0.4)
+renWin.SetSize(500, 500)
+
+ren.ResetCamera()
+cam1 = ren.GetActiveCamera()
+cam1.Elevation(-30)
+cam1.Roll(-20)
+ren.ResetCameraClippingRange()
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Rendering/TPlane.vt b/examples/vtk_examples/Rendering/TPlane.vt
new file mode 100644
index 0000000..e896af0
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diff --git a/examples/vtk_examples/Rendering/assembly.py b/examples/vtk_examples/Rendering/assembly.py
new file mode 100644
index 0000000..27d5dcd
--- /dev/null
+++ b/examples/vtk_examples/Rendering/assembly.py
@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of vtkAssembly. In an assembly,
+# the motion of one actor affects the position of other actors.
+
+import vtk
+
+# Create four parts: a top level assembly (in this case, a
+# vtkCylinder) and three primitives (using vtkSphereSource,
+# vtkCubeSource, and vtkConeSource). Set up mappers and actors for
+# each part of the assembly to carry information about material
+# properties and associated geometry.
+sphere = vtk.vtkSphereSource()
+sphereMapper = vtk.vtkPolyDataMapper()
+sphereMapper.SetInputConnection(sphere.GetOutputPort())
+sphereActor = vtk.vtkActor()
+sphereActor.SetMapper(sphereMapper)
+sphereActor.SetOrigin(2, 1, 3)
+sphereActor.RotateY(6)
+sphereActor.SetPosition(2.25, 0, 0)
+sphereActor.GetProperty().SetColor(1, 0, 1)
+
+cube = vtk.vtkCubeSource()
+cubeMapper = vtk.vtkPolyDataMapper()
+cubeMapper.SetInputConnection(cube.GetOutputPort())
+cubeActor = vtk.vtkActor()
+cubeActor.SetMapper(cubeMapper)
+cubeActor.SetPosition(0.0, .25, 0)
+cubeActor.GetProperty().SetColor(0, 0, 1)
+
+cone = vtk.vtkConeSource()
+coneMapper = vtk.vtkPolyDataMapper()
+coneMapper.SetInputConnection(cone.GetOutputPort())
+coneActor = vtk.vtkActor()
+coneActor.SetMapper(coneMapper)
+coneActor.SetPosition(0, 0, .25)
+coneActor.GetProperty().SetColor(0, 1, 0)
+
+# top part of the assembly
+cylinder = vtk.vtkCylinderSource()
+cylinderMapper = vtk.vtkPolyDataMapper()
+cylinderMapper.SetInputConnection(cylinder.GetOutputPort())
+cylinderMapper.SetResolveCoincidentTopologyToPolygonOffset()
+cylinderActor = vtk.vtkActor()
+cylinderActor.SetMapper(cylinderMapper)
+cylinderActor.GetProperty().SetColor(1, 0, 0)
+
+# Create the assembly and add the 4 parts to it. Also set the origin,
+# position and orientation in space.
+assembly = vtk.vtkAssembly()
+assembly.AddPart(cylinderActor)
+assembly.AddPart(sphereActor)
+assembly.AddPart(cubeActor)
+assembly.AddPart(coneActor)
+assembly.SetOrigin(5, 10, 15)
+assembly.AddPosition(5, 0, 0)
+assembly.RotateX(15)
+
+# Create the Renderer, RenderWindow, and RenderWindowInteractor
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(assembly)
+ren.AddActor(coneActor)
+ren.SetBackground(0.1, 0.2, 0.4)
+renWin.SetSize(200, 200)
+
+# Set up the camera to get a particular view of the scene
+camera = vtk.vtkCamera()
+camera.SetClippingRange(21.9464, 30.0179)
+camera.SetFocalPoint(3.49221, 2.28844, -0.970866)
+camera.SetPosition(3.49221, 2.28844, 24.5216)
+camera.SetViewAngle(30)
+camera.SetViewUp(0, 1, 0)
+ren.SetActiveCamera(camera)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Rendering/assembly.vt b/examples/vtk_examples/Rendering/assembly.vt
new file mode 100644
index 0000000..5f767dd
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diff --git a/examples/vtk_examples/Rendering/rainbow.py b/examples/vtk_examples/Rendering/rainbow.py
new file mode 100644
index 0000000..9cbab9d
--- /dev/null
+++ b/examples/vtk_examples/Rendering/rainbow.py
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use and manipulation of lookup tables.
+
+import vtk
+from vtk.util.colors import *
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# First create pipeline a simple pipeline that reads a structure grid
+# and then extracts a plane from the grid. The plane will be colored
+# differently by using different lookup tables.
+#
+# Note: the Update method is manually invoked because it causes the
+# reader to read; later on we use the output of the reader to set
+# a range for the scalar values.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+plane = vtk.vtkStructuredGridGeometryFilter()
+plane.SetInputConnection(pl3d.GetOutputPort())
+plane.SetExtent(1, 100, 1, 100, 7, 7)
+lut = vtk.vtkLookupTable()
+planeMapper = vtk.vtkPolyDataMapper()
+planeMapper.SetLookupTable(lut)
+planeMapper.SetInputConnection(plane.GetOutputPort())
+planeMapper.SetScalarRange(pl3d.GetOutput().GetScalarRange())
+planeActor = vtk.vtkActor()
+planeActor.SetMapper(planeMapper)
+
+# This creates an outline around the data.
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+
+# Much of the following is commented out. To try different lookup tables,
+# uncommented the appropriate portions.
+
+# This creates a black to white lut.
+##lut.SetHueRange(0, 0)
+##lut.SetSaturationRange(0, 0)
+##lut.SetValueRange(0.2, 1.0)
+
+# This creates a red to blue lut.
+##lut.SetHueRange(0.0, 0.667)
+
+# This creates a blue to red lut.
+##lut.SetHueRange(0.667, 0.0)
+
+# This creates a wierd effect. The Build() method causes the lookup
+# table to allocate memory and create a table based on the currect
+# hue, saturation, value, and alpha (transparency) range. Here we then
+# manually overwrite the values generated by the Build() method.
+lut.SetNumberOfColors(256)
+lut.Build()
+for i in range(0, 16):
+ lut.SetTableValue(i*16, red[0], red[1], red[2], 1)
+ lut.SetTableValue(i*16+1, green[0], green[1], green[2], 1)
+ lut.SetTableValue(i*16+2, blue[0], blue[1], blue[2], 1)
+ lut.SetTableValue(i*16+3, black[0], black[1], black[2], 1)
+
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(outlineActor)
+ren.AddActor(planeActor)
+
+ren.SetBackground(0.1, 0.2, 0.4)
+ren.TwoSidedLightingOff()
+
+renWin.SetSize(250, 250)
+
+cam1 = ren.GetActiveCamera()
+cam1.SetClippingRange(3.95297, 50)
+cam1.SetFocalPoint(8.88908, 0.595038, 29.3342)
+cam1.SetPosition(-12.3332, 31.7479, 41.2387)
+cam1.SetViewUp(0.060772, -0.319905, 0.945498)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/Rendering/rainbow.vt b/examples/vtk_examples/Rendering/rainbow.vt
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index 0000000..6ead42d
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diff --git a/examples/vtk_examples/Tutorial/Step1/Cone.py b/examples/vtk_examples/Tutorial/Step1/Cone.py
new file mode 100644
index 0000000..ca13fca
--- /dev/null
+++ b/examples/vtk_examples/Tutorial/Step1/Cone.py
@@ -0,0 +1,72 @@
+#!/usr/bin/env python
+#
+# This example creates a polygonal model of a cone, and then renders it to
+# the screen. It will rotate the cone 360 degrees and then exit. The basic
+# setup of source -> mapper -> actor -> renderer -> renderwindow is
+# typical of most VTK programs.
+#
+
+#
+# First we include the VTK Python packages that will make available
+# all of the VTK commands to Python.
+#
+import vtk
+import time
+
+#
+# Next we create an instance of vtkConeSource and set some of its
+# properties. The instance of vtkConeSource "cone" is part of a visualization
+# pipeline (it is a source process object); it produces data (output type is
+# vtkPolyData) which other filters may process.
+#
+cone = vtk.vtkConeSource()
+cone.SetHeight( 3.0 )
+cone.SetRadius( 1.0 )
+cone.SetResolution( 10 )
+
+#
+# In this example we terminate the pipeline with a mapper process object.
+# (Intermediate filters such as vtkShrinkPolyData could be inserted in
+# between the source and the mapper.) We create an instance of
+# vtkPolyDataMapper to map the polygonal data into graphics primitives. We
+# connect the output of the cone souece to the input of this mapper.
+#
+coneMapper = vtk.vtkPolyDataMapper()
+coneMapper.SetInputConnection( cone.GetOutputPort() )
+
+#
+# Create an actor to represent the cone. The actor orchestrates rendering of
+# the mapper's graphics primitives. An actor also refers to properties via a
+# vtkProperty instance, and includes an internal transformation matrix. We
+# set this actor's mapper to be coneMapper which we created above.
+#
+coneActor = vtk.vtkActor()
+coneActor.SetMapper( coneMapper )
+
+#
+# Create the Renderer and assign actors to it. A renderer is like a
+# viewport. It is part or all of a window on the screen and it is
+# responsible for drawing the actors it has. We also set the background
+# color here
+#
+ren1= vtk.vtkRenderer()
+ren1.AddActor( coneActor )
+ren1.SetBackground( 0.1, 0.2, 0.4 )
+
+#
+# Finally we create the render window which will show up on the screen
+# We put our renderer into the render window using AddRenderer. We also
+# set the size to be 300 pixels by 300
+#
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer( ren1 )
+renWin.SetSize( 300, 300 )
+
+#
+# now we loop over 360 degreeees and render the cone each time
+#
+# for i in range(0,360):
+# time.sleep(0.03)
+
+# renWin.Render()
+# ren1.GetActiveCamera().Azimuth( 1 )
diff --git a/examples/vtk_examples/Tutorial/Step1/Cone.vt b/examples/vtk_examples/Tutorial/Step1/Cone.vt
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diff --git a/examples/vtk_examples/Tutorial/Step2/Cone2.py b/examples/vtk_examples/Tutorial/Step2/Cone2.py
new file mode 100644
index 0000000..d2a7332
--- /dev/null
+++ b/examples/vtk_examples/Tutorial/Step2/Cone2.py
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+#
+#
+# This example shows how to add an observer to a Python program. It extends
+# the Step1/Python/Cone.py Python example (see that example for information on
+# the basic setup).
+#
+# VTK uses a command/observer design pattern. That is, observers watch for
+# particular events that any vtkObject (or subclass) may invoke on
+# itself. For example, the vtkRenderer invokes a "StartEvent" as it begins
+# to render. Here we add an observer that invokes a command when this event
+# is observed.
+#
+
+import vtk
+import time
+
+#
+# define the callback
+#
+def myCallback(obj,string):
+ print "Starting a render"
+
+
+#
+# create the basic pipeline as in Step1
+#
+cone = vtk.vtkConeSource()
+cone.SetHeight( 3.0 )
+cone.SetRadius( 1.0 )
+cone.SetResolution( 10 )
+
+coneMapper = vtk.vtkPolyDataMapper()
+coneMapper.SetInputConnection( cone.GetOutputPort() )
+coneActor = vtk.vtkActor()
+coneActor.SetMapper( coneMapper )
+
+ren1= vtk.vtkRenderer()
+ren1.AddActor( coneActor )
+ren1.SetBackground( 0.1, 0.2, 0.4 )
+
+#
+# Add the observer here
+#
+ren1.AddObserver("StartEvent", myCallback)
+
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer( ren1 )
+renWin.SetSize( 300, 300 )
+
+#
+# now we loop over 360 degreeees and render the cone each time
+#
+# for i in range(0,360):
+# time.sleep(0.03)
+# renWin.Render()
+# ren1.GetActiveCamera().Azimuth( 1 )
+
diff --git a/examples/vtk_examples/Tutorial/Step2/Cone2.vt b/examples/vtk_examples/Tutorial/Step2/Cone2.vt
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diff --git a/examples/vtk_examples/Tutorial/Step3/Cone3.py b/examples/vtk_examples/Tutorial/Step3/Cone3.py
new file mode 100644
index 0000000..0912f50
--- /dev/null
+++ b/examples/vtk_examples/Tutorial/Step3/Cone3.py
@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+#
+# This example demonstrates how to use multiple renderers within a
+# render window. It is a variation of the Cone.py example. Please
+# refer to that example for additional documentation.
+#
+
+import vtk
+import time
+
+#
+# Next we create an instance of vtkConeSource and set some of its
+# properties. The instance of vtkConeSource "cone" is part of a visualization
+# pipeline (it is a source process object); it produces data (output type is
+# vtkPolyData) which other filters may process.
+#
+cone = vtk.vtkConeSource()
+cone.SetHeight( 3.0 )
+cone.SetRadius( 1.0 )
+cone.SetResolution( 10 )
+
+#
+# In this example we terminate the pipeline with a mapper process object.
+# (Intermediate filters such as vtkShrinkPolyData could be inserted in
+# between the source and the mapper.) We create an instance of
+# vtkPolyDataMapper to map the polygonal data into graphics primitives. We
+# connect the output of the cone souece to the input of this mapper.
+#
+coneMapper = vtk.vtkPolyDataMapper()
+coneMapper.SetInputConnection(cone.GetOutputPort())
+
+#
+# Create an actor to represent the cone. The actor orchestrates rendering of
+# the mapper's graphics primitives. An actor also refers to properties via a
+# vtkProperty instance, and includes an internal transformation matrix. We
+# set this actor's mapper to be coneMapper which we created above.
+#
+coneActor = vtk.vtkActor()
+coneActor.SetMapper(coneMapper)
+
+#
+# Create two renderers and assign actors to them. A renderer renders into a
+# viewport within the vtkRenderWindow. It is part or all of a window on the
+# screen and it is responsible for drawing the actors it has. We also set
+# the background color here. In this example we are adding the same actor
+# to two different renderers; it is okay to add different actors to
+# different renderers as well.
+#
+ren1 = vtk.vtkRenderer()
+ren1.AddActor(coneActor)
+ren1.SetBackground(0.1, 0.2, 0.4)
+ren1.SetViewport(0.0, 0.0, 0.5, 1.0)
+
+ren2 = vtk.vtkRenderer()
+ren2.AddActor(coneActor)
+ren2.SetBackground(0.1, 0.2, 0.4)
+ren2.SetViewport(0.5, 0.0, 1.0, 1.0)
+
+#
+# Finally we create the render window which will show up on the screen.
+# We add our two renderers into the render window using AddRenderer. We also
+# set the size to be 600 pixels by 300.
+#
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer( ren1 )
+renWin.AddRenderer( ren2 )
+renWin.SetSize(600, 300)
+
+#
+# Make one camera view 90 degrees from other.
+#
+ren1.ResetCamera()
+ren1.GetActiveCamera().Azimuth(90)
+
+#
+# Now we loop over 360 degreeees and render the cone each time.
+#
+# for i in range(0,360):
+# time.sleep(0.03)
+
+# renWin.Render()
+# ren1.GetActiveCamera().Azimuth( 1 )
+# ren2.GetActiveCamera().Azimuth( 1 )
diff --git a/examples/vtk_examples/Tutorial/Step3/Cone3.vt b/examples/vtk_examples/Tutorial/Step3/Cone3.vt
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index 0000000..6648e35
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diff --git a/examples/vtk_examples/Tutorial/Step4/Cone4.py b/examples/vtk_examples/Tutorial/Step4/Cone4.py
new file mode 100644
index 0000000..05e68e6
--- /dev/null
+++ b/examples/vtk_examples/Tutorial/Step4/Cone4.py
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+#
+# This example demonstrates the creation of multiple actors and the
+# manipulation of their properties and transformations. It is a
+# derivative of Cone.py, see that example for more information.
+#
+
+import vtk
+import time
+
+#
+# Next we create an instance of vtkConeSource and set some of its
+# properties. The instance of vtkConeSource "cone" is part of a visualization
+# pipeline (it is a source process object); it produces data (output type is
+# vtkPolyData) which other filters may process.
+#
+cone = vtk.vtkConeSource ()
+cone.SetHeight( 3.0 )
+cone.SetRadius( 1.0 )
+cone.SetResolution( 10 )
+
+#
+# In this example we terminate the pipeline with a mapper process object.
+# (Intermediate filters such as vtkShrinkPolyData could be inserted in
+# between the source and the mapper.) We create an instance of
+# vtkPolyDataMapper to map the polygonal data into graphics primitives. We
+# connect the output of the cone souece to the input of this mapper.
+#
+coneMapper = vtk.vtkPolyDataMapper()
+coneMapper.SetInputConnection(cone.GetOutputPort())
+
+#
+# Create an actor to represent the first cone. The actor's properties are
+# modified to give it different surface properties. By default, an actor
+# is create with a property so the GetProperty() method can be used.
+#
+coneActor = vtk.vtkActor()
+coneActor.SetMapper(coneMapper)
+coneActor.GetProperty().SetColor(0.2, 0.63, 0.79)
+coneActor.GetProperty().SetDiffuse(0.7)
+coneActor.GetProperty().SetSpecular(0.4)
+coneActor.GetProperty().SetSpecularPower(20)
+
+#
+# Create a property and directly manipulate it. Assign it to the
+# second actor.
+#
+property = vtk.vtkProperty()
+property.SetColor(1.0, 0.3882, 0.2784)
+property.SetDiffuse(0.7)
+property.SetSpecular(0.4)
+property.SetSpecularPower(20)
+
+#
+# Create a second actor and a property. The property is directly
+# manipulated and then assigned to the actor. In this way, a single
+# property can be shared among many actors. Note also that we use the
+# same mapper as the first actor did. This way we avoid duplicating
+# geometry, which may save lots of memory if the geoemtry is large.
+coneActor2 = vtk.vtkActor()
+coneActor2.SetMapper(coneMapper)
+# coneActor2.GetProperty().SetColor(0.2, 0.63, 0.79)
+coneActor2.SetProperty(property)
+coneActor2.SetPosition(0, 2, 0)
+
+#
+# Create the Renderer and assign actors to it. A renderer is like a
+# viewport. It is part or all of a window on the screen and it is responsible
+# for drawing the actors it has. We also set the background color here.
+#
+ren1 = vtk.vtkRenderer()
+ren1.AddActor(coneActor)
+ren1.AddActor(coneActor2)
+ren1.SetBackground(0.1, 0.2, 0.4)
+
+#
+# Finally we create the render window which will show up on the screen
+# We put our renderer into the render window using AddRenderer. We also
+# set the size to be 300 pixels by 300.
+#
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren1)
+renWin.SetSize(300, 300)
+
+#
+# Now we loop over 360 degreeees and render the cone each time.
+#
+# for i in range(0,360):
+# time.sleep(0.03)
+
+# renWin.Render()
+# ren1.GetActiveCamera().Azimuth( 1 )
+
diff --git a/examples/vtk_examples/Tutorial/Step4/Cone4.vt b/examples/vtk_examples/Tutorial/Step4/Cone4.vt
new file mode 100644
index 0000000..300acf9
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diff --git a/examples/vtk_examples/Tutorial/Step5/Cone5.py b/examples/vtk_examples/Tutorial/Step5/Cone5.py
new file mode 100644
index 0000000..1380583
--- /dev/null
+++ b/examples/vtk_examples/Tutorial/Step5/Cone5.py
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+
+#
+# This example introduces the concepts of user interaction with VTK.
+# First, a different interaction style (than the default) is defined.
+# Second, the interaction is started.
+#
+#
+
+import vtk
+
+#
+# Next we create an instance of vtkConeSource and set some of its
+# properties. The instance of vtkConeSource "cone" is part of a visualization
+# pipeline (it is a source process object); it produces data (output type is
+# vtkPolyData) which other filters may process.
+#
+cone = vtk.vtkConeSource()
+cone.SetHeight( 3.0 )
+cone.SetRadius( 1.0 )
+cone.SetResolution( 10 )
+
+#
+# In this example we terminate the pipeline with a mapper process object.
+# (Intermediate filters such as vtkShrinkPolyData could be inserted in
+# between the source and the mapper.) We create an instance of
+# vtkPolyDataMapper to map the polygonal data into graphics primitives. We
+# connect the output of the cone souece to the input of this mapper.
+#
+coneMapper = vtk.vtkPolyDataMapper()
+coneMapper.SetInputConnection(cone.GetOutputPort())
+
+#
+# Create an actor to represent the cone. The actor orchestrates rendering of
+# the mapper's graphics primitives. An actor also refers to properties via a
+# vtkProperty instance, and includes an internal transformation matrix. We
+# set this actor's mapper to be coneMapper which we created above.
+#
+coneActor = vtk.vtkActor()
+coneActor.SetMapper(coneMapper)
+
+#
+# Create the Renderer and assign actors to it. A renderer is like a
+# viewport. It is part or all of a window on the screen and it is responsible
+# for drawing the actors it has. We also set the background color here.
+#
+ren1 = vtk.vtkRenderer()
+ren1.AddActor(coneActor)
+ren1.SetBackground(0.1, 0.2, 0.4)
+
+#
+# Finally we create the render window which will show up on the screen
+# We put our renderer into the render window using AddRenderer. We also
+# set the size to be 300 pixels by 300.
+#
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren1)
+renWin.SetSize(300, 300)
+
+#
+# The vtkRenderWindowInteractor class watches for events (e.g., keypress,
+# mouse) in the vtkRenderWindow. These events are translated into
+# event invocations that VTK understands (see VTK/Common/vtkCommand.h
+# for all events that VTK processes). Then observers of these VTK
+# events can process them as appropriate.
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+#
+# By default the vtkRenderWindowInteractor instantiates an instance
+# of vtkInteractorStyle. vtkInteractorStyle translates a set of events
+# it observes into operations on the camera, actors, and/or properties
+# in the vtkRenderWindow associated with the vtkRenderWinodwInteractor.
+# Here we specify a particular interactor style.
+style = vtk.vtkInteractorStyleTrackballCamera()
+iren.SetInteractorStyle(style)
+
+#
+# Unlike the previous scripts where we performed some operations and then
+# exited, here we leave an event loop running. The user can use the mouse
+# and keyboard to perform the operations on the scene according to the
+# current interaction style.
+#
+
+#
+# Initialize and start the event loop. Once the render window appears, mouse
+# in the window to move the camera. The Start() method executes an event
+# loop which listens to user mouse and keyboard events. Note that keypress-e
+# exits the event loop. (Look in vtkInteractorStyle.h for a summary of events, or
+# the appropriate Doxygen documentation.)
+#
+iren.Initialize()
+iren.Start()
diff --git a/examples/vtk_examples/Tutorial/Step5/Cone5.vt b/examples/vtk_examples/Tutorial/Step5/Cone5.vt
new file mode 100644
index 0000000..029e9a6
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diff --git a/examples/vtk_examples/Tutorial/Step6/Cone6.py b/examples/vtk_examples/Tutorial/Step6/Cone6.py
new file mode 100644
index 0000000..2a47c45
--- /dev/null
+++ b/examples/vtk_examples/Tutorial/Step6/Cone6.py
@@ -0,0 +1,117 @@
+#!/usr/bin/env python
+#
+# This example introduces 3D widgets. 3D widgets take advantage of the
+# event/observer design pattern introduced previously. They typically
+# have a particular representation in the scene which can be interactively
+# selected and manipulated using the mouse and keyboard. As the widgets
+# are manipulated, they in turn invoke events such as StartInteractionEvent,
+# InteractionEvent, and EndInteractionEvent which can be used to manipulate
+# the scene that the widget is embedded in. 3D widgets work in the context
+# of the event loop which was set up in the previous example.
+#
+# Note: there are more 3D widget examples in VTK/Examples/GUI/.
+#
+
+# First we import the VTK Python package that will make available all
+# of the VTK commands to Python.
+import vtk
+
+# Next we create an instance of vtkConeSource and set some of its
+# properties. The instance of vtkConeSource "cone" is part of a
+# visualization pipeline (it is a source process object); it produces
+# data (output type is vtkPolyData) which other filters may process.
+cone = vtk.vtkConeSource()
+cone.SetHeight(3.0)
+cone.SetRadius(1.0)
+cone.SetResolution(10)
+
+# In this example we terminate the pipeline with a mapper process object.
+# (Intermediate filters such as vtkShrinkPolyData could be inserted in
+# between the source and the mapper.) We create an instance of
+# vtkPolyDataMapper to map the polygonal data into graphics primitives. We
+# connect the output of the cone souece to the input of this mapper.
+coneMapper = vtk.vtkPolyDataMapper()
+coneMapper.SetInputConnection(cone.GetOutputPort())
+
+# Create an actor to represent the cone. The actor orchestrates rendering of
+# the mapper's graphics primitives. An actor also refers to properties via a
+# vtkProperty instance, and includes an internal transformation matrix. We
+# set this actor's mapper to be coneMapper which we created above.
+coneActor = vtk.vtkActor()
+coneActor.SetMapper(coneMapper)
+
+# Create the Renderer and assign actors to it. A renderer is like a
+# viewport. It is part or all of a window on the screen and it is
+# responsible for drawing the actors it has. We also set the
+# background color here.
+ren1 = vtk.vtkRenderer()
+ren1.AddActor(coneActor)
+ren1.SetBackground(0.1, 0.2, 0.4)
+
+# Finally we create the render window which will show up on the screen
+# We put our renderer into the render window using AddRenderer. We
+# also set the size to be 300 pixels by 300.
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren1)
+renWin.SetSize(300, 300)
+
+# The vtkRenderWindowInteractor class watches for events (e.g., keypress,
+# mouse) in the vtkRenderWindow. These events are translated into
+# event invocations that VTK understands (see VTK/Common/vtkCommand.h
+# for all events that VTK processes). Then observers of these VTK
+# events can process them as appropriate.
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# By default the vtkRenderWindowInteractor instantiates an instance
+# of vtkInteractorStyle. vtkInteractorStyle translates a set of events
+# it observes into operations on the camera, actors, and/or properties
+# in the vtkRenderWindow associated with the vtkRenderWinodwInteractor.
+# Here we specify a particular interactor style.
+style = vtk.vtkInteractorStyleTrackballCamera()
+iren.SetInteractorStyle(style)
+
+
+# Here we use a vtkBoxWidget to transform the underlying coneActor (by
+# manipulating its transformation matrix). Many other types of widgets
+# are available for use, see the documentation for more details.
+#
+# The SetInteractor method is how 3D widgets are associated with the render
+# window interactor. Internally, SetInteractor sets up a bunch of callbacks
+# using the Command/Observer mechanism (AddObserver()). The place factor
+# controls the initial size of the widget with respect to the bounding box
+# of the input to the widget.
+boxWidget = vtk.vtkBoxWidget()
+boxWidget.SetInteractor(iren)
+boxWidget.SetPlaceFactor(1.25)
+
+# Place the interactor initially. The input to a 3D widget is used to
+# initially position and scale the widget. The EndInteractionEvent is
+# observed which invokes the SelectPolygons callback.
+boxWidget.SetProp3D(coneActor)
+boxWidget.PlaceWidget()
+
+# Similar to Step2/Python/Cone2.py, we define a callback for
+# interaction. As can be seen the callback takes two arguments. The
+# first being the object that generates the event and the second
+# argument the event name (which is a string).
+t = vtk.vtkTransform()
+def myCallback(widget, event_string):
+ boxWidget.GetTransform(t)
+ boxWidget.GetProp3D().SetUserTransform(t)
+
+
+# Now for every interaction event that is generated by the boxWidget,
+# call our callback function.
+boxWidget.AddObserver("InteractionEvent", myCallback)
+
+# Normally the user presses the "i" key to bring a 3D widget to
+# life. Here we will manually enable it so it appears with the cone.
+# boxWidget.On()
+
+# Start the event loop.
+iren.Initialize()
+iren.Start()
+
+# There is no explicit need to free any objects at this point.
+# Once Python exits, memory is automatically freed.
diff --git a/examples/vtk_examples/Tutorial/Step6/Cone6.vt b/examples/vtk_examples/Tutorial/Step6/Cone6.vt
new file mode 100644
index 0000000..ea00e49
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diff --git a/examples/vtk_examples/VisualizationAlgorithms/BandContourTerrain.py b/examples/vtk_examples/VisualizationAlgorithms/BandContourTerrain.py
new file mode 100644
index 0000000..7911b2d
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/BandContourTerrain.py
@@ -0,0 +1,149 @@
+#!/usr/bin/env python
+
+# In this example we show the use of the
+# vtkBandedPolyDataContourFilter. This filter creates separate,
+# constant colored bands for a range of scalar values. Each band is
+# bounded by two scalar values, and the cell data lying within the
+# value has the same cell scalar value.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+
+# The lookup table is similar to that used by maps. Two hues are used:
+# a brown for land, and a blue for water. The value of the hue is
+# changed to give the effect of elevation.
+Scale = 5
+lutWater = vtk.vtkLookupTable()
+lutWater.SetNumberOfColors(10)
+lutWater.SetHueRange(0.58, 0.58)
+lutWater.SetSaturationRange(0.5, 0.1)
+lutWater.SetValueRange(0.5, 1.0)
+lutWater.Build()
+lutLand = vtk.vtkLookupTable()
+lutLand.SetNumberOfColors(10)
+lutLand.SetHueRange(0.1, 0.1)
+lutLand.SetSaturationRange(0.4, 0.1)
+lutLand.SetValueRange(0.55, 0.9)
+lutLand.Build()
+
+
+# The DEM reader reads data and creates an output image.
+demModel = vtk.vtkDEMReader()
+demModel.SetFileName(VTK_DATA_ROOT + "/Data/SainteHelens.dem")
+demModel.Update()
+
+# We shrink the terrain data down a bit to yield better performance for
+# this example.
+shrinkFactor = 4
+shrink = vtk.vtkImageShrink3D()
+shrink.SetShrinkFactors(shrinkFactor, shrinkFactor, 1)
+shrink.SetInputConnection(demModel.GetOutputPort())
+shrink.AveragingOn()
+
+# Convert the image into polygons.
+geom = vtk.vtkImageDataGeometryFilter()
+geom.SetInputConnection(shrink.GetOutputPort())
+
+# Warp the polygons based on elevation.
+warp = vtk.vtkWarpScalar()
+warp.SetInputConnection(geom.GetOutputPort())
+warp.SetNormal(0, 0, 1)
+warp.UseNormalOn()
+warp.SetScaleFactor(Scale)
+
+# Create the contour bands.
+bcf = vtk.vtkBandedPolyDataContourFilter()
+bcf.SetInput(warp.GetPolyDataOutput())
+bcf.GenerateValues(15, demModel.GetOutput().GetScalarRange())
+bcf.SetScalarModeToIndex()
+bcf.GenerateContourEdgesOn()
+
+# Compute normals to give a better look.
+normals = vtk.vtkPolyDataNormals()
+normals.SetInputConnection(bcf.GetOutputPort())
+normals.SetFeatureAngle(60)
+normals.ConsistencyOff()
+normals.SplittingOff()
+
+demMapper = vtk.vtkPolyDataMapper()
+demMapper.SetInputConnection(normals.GetOutputPort())
+demMapper.SetScalarRange(0, 10)
+demMapper.SetLookupTable(lutLand)
+demMapper.SetScalarModeToUseCellData()
+
+demActor = vtk.vtkLODActor()
+demActor.SetMapper(demMapper)
+
+## Create contour edges
+edgeMapper = vtk.vtkPolyDataMapper()
+edgeMapper.SetInput(bcf.GetContourEdgesOutput())
+edgeMapper.SetResolveCoincidentTopologyToPolygonOffset()
+edgeActor = vtk.vtkActor()
+edgeActor.SetMapper(edgeMapper)
+edgeActor.GetProperty().SetColor(0, 0, 0)
+
+## Test clipping
+# Create the contour bands.
+bcf2 = vtk.vtkBandedPolyDataContourFilter()
+bcf2.SetInput(warp.GetPolyDataOutput())
+bcf2.ClippingOn()
+bcf2.GenerateValues(10, 1000, 2000)
+bcf2.SetScalarModeToValue()
+
+# Compute normals to give a better look.
+normals2 = vtk.vtkPolyDataNormals()
+normals2.SetInputConnection(bcf2.GetOutputPort())
+normals2.SetFeatureAngle(60)
+normals2.ConsistencyOff()
+normals2.SplittingOff()
+
+lut = vtk.vtkLookupTable()
+lut.SetNumberOfColors(10)
+demMapper2 = vtk.vtkPolyDataMapper()
+demMapper2.SetInputConnection(normals2.GetOutputPort())
+demMapper2.SetScalarRange(demModel.GetOutput().GetScalarRange())
+demMapper2.SetLookupTable(lut)
+demMapper2.SetScalarModeToUseCellData()
+
+demActor2 = vtk.vtkLODActor()
+demActor2.SetMapper(demMapper2)
+demActor2.AddPosition(0, 15000, 0)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(demActor)
+ren.AddActor(demActor2)
+ren.AddActor(edgeActor)
+
+ren.SetBackground(.4, .4, .4)
+renWin.SetSize(375, 200)
+
+cam = vtk.vtkCamera()
+cam.SetPosition(-17438.8, 2410.62, 25470.8)
+cam.SetFocalPoint(3985.35, 11930.6, 5922.14)
+cam.SetViewUp(0, 0, 1)
+ren.SetActiveCamera(cam)
+ren.ResetCamera()
+cam.Zoom(2)
+
+iren.Initialize()
+iren.SetDesiredUpdateRate(1)
+
+def CheckAbort(obj, event):
+ foo = renWin.GetEventPending()
+ if foo != 0:
+ renWin.SetAbortRender(1)
+
+renWin.AddObserver("AbortCheckEvent", CheckAbort)
+renWin.Render()
+
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/BandContourTerrain.vt b/examples/vtk_examples/VisualizationAlgorithms/BandContourTerrain.vt
new file mode 100644
index 0000000..7cb3857
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diff --git a/examples/vtk_examples/VisualizationAlgorithms/ClipCow.py b/examples/vtk_examples/VisualizationAlgorithms/ClipCow.py
new file mode 100644
index 0000000..78428a4
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/ClipCow.py
@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+
+# In this example vtkClipPolyData is used to cut a polygonal model
+# of a cow in half. In addition, the open clip is closed by triangulating
+# the resulting complex polygons.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+from vtk.util.colors import peacock, tomato
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# First start by reading a cow model. We also generate surface normals for
+# prettier rendering.
+cow = vtk.vtkBYUReader()
+cow.SetGeometryFileName(VTK_DATA_ROOT + "/Data/Viewpoint/cow.g")
+cowNormals = vtk.vtkPolyDataNormals()
+cowNormals.SetInputConnection(cow.GetOutputPort())
+
+# We clip with an implicit function. Here we use a plane positioned near
+# the center of the cow model and oriented at an arbitrary angle.
+plane = vtk.vtkPlane()
+plane.SetOrigin(0.25, 0, 0)
+plane.SetNormal(-1, -1, 0)
+
+# vtkClipPolyData requires an implicit function to define what it is to
+# clip with. Any implicit function, including complex boolean combinations
+# can be used. Notice that we can specify the value of the implicit function
+# with the SetValue method.
+clipper = vtk.vtkClipPolyData()
+clipper.SetInputConnection(cowNormals.GetOutputPort())
+clipper.SetClipFunction(plane)
+clipper.GenerateClipScalarsOn()
+clipper.GenerateClippedOutputOn()
+clipper.SetValue(0.5)
+clipMapper = vtk.vtkPolyDataMapper()
+clipMapper.SetInputConnection(clipper.GetOutputPort())
+clipMapper.ScalarVisibilityOff()
+backProp = vtk.vtkProperty()
+backProp.SetDiffuseColor(tomato)
+clipActor = vtk.vtkActor()
+clipActor.SetMapper(clipMapper)
+clipActor.GetProperty().SetColor(peacock)
+clipActor.SetBackfaceProperty(backProp)
+
+# Here we are cutting the cow. Cutting creates lines where the cut
+# function intersects the model. (Clipping removes a portion of the
+# model but the dimension of the data does not change.)
+#
+# The reason we are cutting is to generate a closed polygon at the
+# boundary of the clipping process. The cutter generates line
+# segments, the stripper then puts them together into polylines. We
+# then pull a trick and define polygons using the closed line
+# segements that the stripper created.
+cutEdges = vtk.vtkCutter()
+cutEdges.SetInputConnection(cowNormals.GetOutputPort())
+cutEdges.SetCutFunction(plane)
+cutEdges.GenerateCutScalarsOn()
+cutEdges.SetValue(0, 0.5)
+cutStrips = vtk.vtkStripper()
+cutStrips.SetInputConnection(cutEdges.GetOutputPort())
+cutStrips.Update()
+cutPoly = vtk.vtkPolyData()
+cutPoly.SetPoints(cutStrips.GetOutput().GetPoints())
+cutPoly.SetPolys(cutStrips.GetOutput().GetLines())
+
+# Triangle filter is robust enough to ignore the duplicate point at
+# the beginning and end of the polygons and triangulate them.
+cutTriangles = vtk.vtkTriangleFilter()
+cutTriangles.SetInput(cutPoly)
+cutMapper = vtk.vtkPolyDataMapper()
+cutMapper.SetInput(cutPoly)
+cutMapper.SetInputConnection(cutTriangles.GetOutputPort())
+cutActor = vtk.vtkActor()
+cutActor.SetMapper(cutMapper)
+cutActor.GetProperty().SetColor(peacock)
+
+# The clipped part of the cow is rendered wireframe.
+restMapper = vtk.vtkPolyDataMapper()
+restMapper.SetInput(clipper.GetClippedOutput())
+restMapper.ScalarVisibilityOff()
+restActor = vtk.vtkActor()
+restActor.SetMapper(restMapper)
+restActor.GetProperty().SetRepresentationToWireframe()
+
+# Create graphics stuff
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(clipActor)
+ren.AddActor(cutActor)
+ren.AddActor(restActor)
+ren.SetBackground(1, 1, 1)
+ren.ResetCamera()
+ren.GetActiveCamera().Azimuth(30)
+ren.GetActiveCamera().Elevation(30)
+ren.GetActiveCamera().Dolly(1.5)
+ren.ResetCameraClippingRange()
+
+renWin.SetSize(300, 300)
+iren.Initialize()
+
+# Lets you move the cut plane back and forth by invoking the function
+# Cut with the appropriate plane value (essentially a distance from
+# the original plane). This is not used in this code but should give
+# you an idea of how to define a function to do this.
+def Cut(v):
+ clipper.SetValue(v)
+ cutEdges.SetValue(0, v)
+ cutStrips.Update()
+ cutPoly.SetPoints(cutStrips.GetOutput().GetPoints())
+ cutPoly.SetPolys(cutStrips.GetOutput().GetLines())
+ cutMapper.Update()
+ renWin.Render()
+
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/ClipCow.vt b/examples/vtk_examples/VisualizationAlgorithms/ClipCow.vt
new file mode 100644
index 0000000..a890d84
Binary files /dev/null and b/examples/vtk_examples/VisualizationAlgorithms/ClipCow.vt differ
diff --git a/examples/vtk_examples/VisualizationAlgorithms/ColorIsosurface.py b/examples/vtk_examples/VisualizationAlgorithms/ColorIsosurface.py
new file mode 100644
index 0000000..9b61c90
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/ColorIsosurface.py
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+
+# This example shows how to color an isosurface with other
+# data. Basically an isosurface is generated, and a data array is
+# selected and used by the mapper to color the surface.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Read some data. The important thing here is to read a function as a
+# data array as well as the scalar and vector. (here function 153 is
+# named "Velocity Magnitude").Later this data array will be used to
+# color the isosurface.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.AddFunction(153)
+pl3d.Update()
+pl3d.DebugOn()
+
+# The contour filter uses the labeled scalar (function number 100
+# above to generate the contour surface; all other data is
+# interpolated during the contouring process.
+iso = vtk.vtkContourFilter()
+iso.SetInputConnection(pl3d.GetOutputPort())
+iso.SetValue(0, .24)
+
+normals = vtk.vtkPolyDataNormals()
+normals.SetInputConnection(iso.GetOutputPort())
+normals.SetFeatureAngle(45)
+
+# We indicate to the mapper to use the velcoity magnitude, which is a
+# vtkDataArray that makes up part of the point attribute data.
+isoMapper = vtk.vtkPolyDataMapper()
+isoMapper.SetInputConnection(normals.GetOutputPort())
+isoMapper.ScalarVisibilityOn()
+isoMapper.SetScalarRange(0, 1500)
+isoMapper.SetScalarModeToUsePointFieldData()
+isoMapper.ColorByArrayComponent("VelocityMagnitude", 0)
+
+isoActor = vtk.vtkLODActor()
+isoActor.SetMapper(isoMapper)
+isoActor.SetNumberOfCloudPoints(1000)
+
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+
+# Create the usual rendering stuff.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(outlineActor)
+ren.AddActor(isoActor)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(500, 500)
+ren.SetBackground(0.1, 0.2, 0.4)
+
+cam1 = ren.GetActiveCamera()
+cam1.SetClippingRange(3.95297, 50)
+cam1.SetFocalPoint(9.71821, 0.458166, 29.3999)
+cam1.SetPosition(2.7439, -37.3196, 38.7167)
+cam1.SetViewUp(-0.16123, 0.264271, 0.950876)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/ColorIsosurface.vt b/examples/vtk_examples/VisualizationAlgorithms/ColorIsosurface.vt
new file mode 100644
index 0000000..e205e01
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diff --git a/examples/vtk_examples/VisualizationAlgorithms/CutCombustor.py b/examples/vtk_examples/VisualizationAlgorithms/CutCombustor.py
new file mode 100644
index 0000000..78a546d
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/CutCombustor.py
@@ -0,0 +1,79 @@
+#!/usr/bin/env python
+
+# This example shows how to use cutting (vtkCutter) and how it
+# compares with extracting a plane from a computational grid.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Read some data.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+
+# The cutter uses an implicit function to perform the cutting.
+# Here we define a plane, specifying its center and normal.
+# Then we assign the plane to the cutter.
+plane = vtk.vtkPlane()
+plane.SetOrigin(pl3d.GetOutput().GetCenter())
+plane.SetNormal(-0.287, 0, 0.9579)
+planeCut = vtk.vtkCutter()
+planeCut.SetInputConnection(pl3d.GetOutputPort())
+planeCut.SetCutFunction(plane)
+cutMapper = vtk.vtkPolyDataMapper()
+cutMapper.SetInputConnection(planeCut.GetOutputPort())
+cutMapper.SetScalarRange(pl3d.GetOutput().GetPointData().GetScalars().GetRange())
+cutActor = vtk.vtkActor()
+cutActor.SetMapper(cutMapper)
+
+# Here we extract a computational plane from the structured grid.
+# We render it as wireframe.
+compPlane = vtk.vtkStructuredGridGeometryFilter()
+compPlane.SetInputConnection(pl3d.GetOutputPort())
+compPlane.SetExtent(0, 100, 0, 100, 9, 9)
+planeMapper = vtk.vtkPolyDataMapper()
+planeMapper.SetInputConnection(compPlane.GetOutputPort())
+planeMapper.ScalarVisibilityOff()
+planeActor = vtk.vtkActor()
+planeActor.SetMapper(planeMapper)
+planeActor.GetProperty().SetRepresentationToWireframe()
+planeActor.GetProperty().SetColor(0, 0, 0)
+
+# The outline of the data puts the data in context.
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+outlineProp = outlineActor.GetProperty()
+outlineProp.SetColor(0, 0, 0)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(outlineActor)
+ren.AddActor(planeActor)
+ren.AddActor(cutActor)
+
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(400, 300)
+
+cam1 = ren.GetActiveCamera()
+cam1.SetClippingRange(11.1034, 59.5328)
+cam1.SetFocalPoint(9.71821, 0.458166, 29.3999)
+cam1.SetPosition(-2.95748, -26.7271, 44.5309)
+cam1.SetViewUp(0.0184785, 0.479657, 0.877262)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/CutCombustor.vt b/examples/vtk_examples/VisualizationAlgorithms/CutCombustor.vt
new file mode 100644
index 0000000..8d8ce2b
Binary files /dev/null and b/examples/vtk_examples/VisualizationAlgorithms/CutCombustor.vt differ
diff --git a/examples/vtk_examples/VisualizationAlgorithms/ExtractGeometry.py b/examples/vtk_examples/VisualizationAlgorithms/ExtractGeometry.py
new file mode 100644
index 0000000..8a6fda3
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/ExtractGeometry.py
@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+
+# This example shows how to extract a piece of a dataset using an
+# implicit function. In this case the implicit function is formed by
+# the boolean combination of two ellipsoids.
+
+import vtk
+
+# Here we create two ellipsoidal implicit functions and boolean them
+# together tto form a "cross" shaped implicit function.
+quadric = vtk.vtkQuadric()
+quadric.SetCoefficients(.5, 1, .2, 0, .1, 0, 0, .2, 0, 0)
+sample = vtk.vtkSampleFunction()
+sample.SetSampleDimensions(50, 50, 50)
+sample.SetImplicitFunction(quadric)
+sample.ComputeNormalsOff()
+trans = vtk.vtkTransform()
+trans.Scale(1, .5, .333)
+sphere = vtk.vtkSphere()
+sphere.SetRadius(0.25)
+sphere.SetTransform(trans)
+trans2 = vtk.vtkTransform()
+trans2.Scale(.25, .5, 1.0)
+sphere2 = vtk.vtkSphere()
+sphere2.SetRadius(0.25)
+sphere2.SetTransform(trans2)
+union = vtk.vtkImplicitBoolean()
+union.AddFunction(sphere)
+union.AddFunction(sphere2)
+union.SetOperationType(0) #union
+
+# Here is where it gets interesting. The implicit function is used to
+# extract those cells completely inside the function. They are then
+# shrunk to help show what was extracted.
+extract = vtk.vtkExtractGeometry()
+extract.SetInputConnection(sample.GetOutputPort())
+extract.SetImplicitFunction(union)
+shrink = vtk.vtkShrinkFilter()
+shrink.SetInputConnection(extract.GetOutputPort())
+shrink.SetShrinkFactor(0.5)
+dataMapper = vtk.vtkDataSetMapper()
+dataMapper.SetInputConnection(shrink.GetOutputPort())
+dataActor = vtk.vtkActor()
+dataActor.SetMapper(dataMapper)
+
+# The outline gives context to the original data.
+outline = vtk.vtkOutlineFilter()
+outline.SetInputConnection(sample.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+outlineProp = outlineActor.GetProperty()
+outlineProp.SetColor(0, 0, 0)
+
+# The usual rendering stuff is created.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(outlineActor)
+ren.AddActor(dataActor)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(500, 500)
+ren.ResetCamera()
+ren.GetActiveCamera().Zoom(1.5)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/ExtractGeometry.vt b/examples/vtk_examples/VisualizationAlgorithms/ExtractGeometry.vt
new file mode 100644
index 0000000..65d11c4
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diff --git a/examples/vtk_examples/VisualizationAlgorithms/ExtractUGrid.py b/examples/vtk_examples/VisualizationAlgorithms/ExtractUGrid.py
new file mode 100644
index 0000000..58ca0f2
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/ExtractUGrid.py
@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+
+# This example shows how to extract portions of an unstructured grid
+# using vtkExtractUnstructuredGrid. vtkConnectivityFilter is also used
+# to extract connected components.
+#
+# The data found here represents a blow molding process. Blow molding
+# requires a mold and parison (hot, viscous plastic) which is shaped
+# by the mold into the final form. The data file contains several steps
+# in time for the analysis.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create a reader to read the unstructured grid data. We use a
+# vtkDataSetReader which means the type of the output is unknown until
+# the data file is read. So we follow the reader with a
+# vtkCastToConcrete and cast the output to vtkUnstructuredGrid.
+reader = vtk.vtkDataSetReader()
+reader.SetFileName(VTK_DATA_ROOT + "/Data/blow.vtk")
+reader.SetScalarsName("thickness9")
+reader.SetVectorsName("displacement9")
+castToUnstructuredGrid = vtk.vtkCastToConcrete()
+castToUnstructuredGrid.SetInputConnection(reader.GetOutputPort())
+warp = vtk.vtkWarpVector()
+warp.SetInput(castToUnstructuredGrid.GetUnstructuredGridOutput())
+
+# The connectivity filter extracts the first two regions. These are
+# know to represent the mold.
+connect = vtk.vtkConnectivityFilter()
+connect.SetInputConnection(warp.GetOutputPort())
+connect.SetExtractionModeToSpecifiedRegions()
+connect.AddSpecifiedRegion(0)
+connect.AddSpecifiedRegion(1)
+moldMapper = vtk.vtkDataSetMapper()
+moldMapper.SetInputConnection(reader.GetOutputPort())
+moldMapper.ScalarVisibilityOff()
+moldActor = vtk.vtkActor()
+moldActor.SetMapper(moldMapper)
+moldActor.GetProperty().SetColor(.2, .2, .2)
+moldActor.GetProperty().SetRepresentationToWireframe()
+
+# Another connectivity filter is used to extract the parison.
+connect2 = vtk.vtkConnectivityFilter()
+connect2.SetInputConnection(warp.GetOutputPort())
+connect2.SetExtractionModeToSpecifiedRegions()
+connect2.AddSpecifiedRegion(2)
+
+# We use vtkExtractUnstructuredGrid because we are interested in
+# looking at just a few cells. We use cell clipping via cell id to
+# extract the portion of the grid we are interested in.
+extractGrid = vtk.vtkExtractUnstructuredGrid()
+extractGrid.SetInputConnection(connect2.GetOutputPort())
+extractGrid.CellClippingOn()
+extractGrid.SetCellMinimum(0)
+extractGrid.SetCellMaximum(23)
+parison = vtk.vtkGeometryFilter()
+parison.SetInputConnection(extractGrid.GetOutputPort())
+normals2 = vtk.vtkPolyDataNormals()
+normals2.SetInputConnection(parison.GetOutputPort())
+normals2.SetFeatureAngle(60)
+lut = vtk.vtkLookupTable()
+lut.SetHueRange(0.0, 0.66667)
+parisonMapper = vtk.vtkPolyDataMapper()
+parisonMapper.SetInputConnection(normals2.GetOutputPort())
+parisonMapper.SetLookupTable(lut)
+parisonMapper.SetScalarRange(0.12, 1.0)
+parisonActor = vtk.vtkActor()
+parisonActor.SetMapper(parisonMapper)
+
+# graphics stuff
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(parisonActor)
+ren.AddActor(moldActor)
+ren.SetBackground(1, 1, 1)
+ren.ResetCamera()
+ren.GetActiveCamera().Azimuth(60)
+ren.GetActiveCamera().Roll(-90)
+ren.GetActiveCamera().Dolly(2)
+ren.ResetCameraClippingRange()
+renWin.SetSize(500, 375)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/ExtractUGrid.vt b/examples/vtk_examples/VisualizationAlgorithms/ExtractUGrid.vt
new file mode 100644
index 0000000..f32b492
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diff --git a/examples/vtk_examples/VisualizationAlgorithms/GenerateTextureCoords.py b/examples/vtk_examples/VisualizationAlgorithms/GenerateTextureCoords.py
new file mode 100644
index 0000000..06b463d
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/GenerateTextureCoords.py
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+
+# This example shows how to generate and manipulate texture coordinates.
+# A random cloud of points is generated and then triangulated with
+# vtkDelaunay3D. Since these points do not have texture coordinates,
+# we generate them with vtkTextureMapToCylinder.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Begin by generating 25 random points in the unit sphere.
+sphere = vtk.vtkPointSource()
+sphere.SetNumberOfPoints(25)
+
+# Triangulate the points with vtkDelaunay3D. This generates a convex hull
+# of tetrahedron.
+delny = vtk.vtkDelaunay3D()
+delny.SetInputConnection(sphere.GetOutputPort())
+delny.SetTolerance(0.01)
+
+# The triangulation has texture coordinates generated so we can map
+# a texture onto it.
+tmapper = vtk.vtkTextureMapToCylinder()
+tmapper.SetInputConnection(delny.GetOutputPort())
+tmapper.PreventSeamOn()
+
+# We scale the texture coordinate to get some repeat patterns.
+xform = vtk.vtkTransformTextureCoords()
+xform.SetInputConnection(tmapper.GetOutputPort())
+xform.SetScale(4, 4, 1)
+
+# vtkDataSetMapper internally uses a vtkGeometryFilter to extract the
+# surface from the triangulation. The output (which is vtkPolyData) is
+# then passed to an internal vtkPolyDataMapper which does the
+# rendering.
+mapper = vtk.vtkDataSetMapper()
+mapper.SetInputConnection(xform.GetOutputPort())
+
+# A texture is loaded using an image reader. Textures are simply images.
+# The texture is eventually associated with an actor.
+bmpReader = vtk.vtkBMPReader()
+bmpReader.SetFileName(VTK_DATA_ROOT + "/Data/masonry.bmp")
+atext = vtk.vtkTexture()
+atext.SetInputConnection(bmpReader.GetOutputPort())
+atext.InterpolateOn()
+triangulation = vtk.vtkActor()
+triangulation.SetMapper(mapper)
+triangulation.SetTexture(atext)
+
+# Create the standard rendering stuff.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(triangulation)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(300, 300)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/GenerateTextureCoords.vt b/examples/vtk_examples/VisualizationAlgorithms/GenerateTextureCoords.vt
new file mode 100644
index 0000000..473a097
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diff --git a/examples/vtk_examples/VisualizationAlgorithms/SubsampleGrid.py b/examples/vtk_examples/VisualizationAlgorithms/SubsampleGrid.py
new file mode 100644
index 0000000..50bec35
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/SubsampleGrid.py
@@ -0,0 +1,67 @@
+#!/usr/bin/env python
+
+# This example demonstrates the subsampling of a structured grid.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Read some structured data.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+
+# Here we subsample the grid. The SetVOI method requires six values
+# specifying (imin,imax, jmin,jmax, kmin,kmax) extents. In this
+# example we extracting a plane. Note that the VOI is clamped to zero
+# (min) and the maximum i-j-k value; that way we can use the
+# -1000,1000 specification and be sure the values are clamped. The
+# SampleRate specifies that we take every point in the i-direction;
+# every other point in the j-direction; and every third point in the
+# k-direction. IncludeBoundaryOn makes sure that we get the boundary
+# points even if the SampleRate does not coincident with the boundary.
+extract = vtk.vtkExtractGrid()
+extract.SetInputConnection(pl3d.GetOutputPort())
+extract.SetVOI(30, 30, -1000, 1000, -1000, 1000)
+extract.SetSampleRate(1, 2, 3)
+extract.IncludeBoundaryOn()
+mapper = vtk.vtkDataSetMapper()
+mapper.SetInputConnection(extract.GetOutputPort())
+mapper.SetScalarRange(.18, .7)
+actor = vtk.vtkActor()
+actor.SetMapper(mapper)
+
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+outlineActor.GetProperty().SetColor(0, 0, 0)
+
+# Add the usual rendering stuff.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(outlineActor)
+ren.AddActor(actor)
+
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(300, 180)
+
+cam1 = ren.GetActiveCamera()
+cam1.SetClippingRange(2.64586, 47.905)
+cam1.SetFocalPoint(8.931, 0.358127, 31.3526)
+cam1.SetPosition(29.7111, -0.688615, 37.1495)
+cam1.SetViewUp(-0.268328, 0.00801595, 0.963294)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/SubsampleGrid.vt b/examples/vtk_examples/VisualizationAlgorithms/SubsampleGrid.vt
new file mode 100644
index 0000000..b1c438d
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diff --git a/examples/vtk_examples/VisualizationAlgorithms/TextureThreshold.py b/examples/vtk_examples/VisualizationAlgorithms/TextureThreshold.py
new file mode 100644
index 0000000..61fb9e8
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/TextureThreshold.py
@@ -0,0 +1,136 @@
+#!/usr/bin/env python
+
+# This example shows how to use a transparent texture map to perform
+# thresholding. The key is the vtkThresholdTextureCoords filter which
+# creates texture coordinates based on a threshold value. These
+# texture coordinates are used in conjuntion with a texture map with
+# varying opacity and intensity to create an inside, transition, and
+# outside region.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Begin by reading some structure grid data.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/bluntfinxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/bluntfinq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+
+# Now extract surfaces from the grid corresponding to boundary
+# geometry. First the wall.
+wall = vtk.vtkStructuredGridGeometryFilter()
+wall.SetInputConnection(pl3d.GetOutputPort())
+wall.SetExtent(0, 100, 0, 0, 0, 100)
+wallMap = vtk.vtkPolyDataMapper()
+wallMap.SetInputConnection(wall.GetOutputPort())
+wallMap.ScalarVisibilityOff()
+wallActor = vtk.vtkActor()
+wallActor.SetMapper(wallMap)
+wallActor.GetProperty().SetColor(0.8, 0.8, 0.8)
+
+# Now the fin.
+fin = vtk.vtkStructuredGridGeometryFilter()
+fin.SetInputConnection(pl3d.GetOutputPort())
+fin.SetExtent(0, 100, 0, 100, 0, 0)
+finMap = vtk.vtkPolyDataMapper()
+finMap.SetInputConnection(fin.GetOutputPort())
+finMap.ScalarVisibilityOff()
+finActor = vtk.vtkActor()
+finActor.SetMapper(finMap)
+finActor.GetProperty().SetColor(0.8, 0.8, 0.8)
+
+# Extract planes to threshold. Start by reading the specially designed
+# texture map that has three regions: an inside, boundary, and outside
+# region. The opacity and intensity of this texture map are varied.
+tmap = vtk.vtkStructuredPointsReader()
+tmap.SetFileName(VTK_DATA_ROOT + "/Data/texThres2.vtk")
+texture = vtk.vtkTexture()
+texture.SetInputConnection(tmap.GetOutputPort())
+texture.InterpolateOff()
+texture.RepeatOff()
+
+# Here are the three planes which will be texture thresholded.
+plane1 = vtk.vtkStructuredGridGeometryFilter()
+plane1.SetInputConnection(pl3d.GetOutputPort())
+plane1.SetExtent(10, 10, 0, 100, 0, 100)
+thresh1 = vtk.vtkThresholdTextureCoords()
+thresh1.SetInputConnection(plane1.GetOutputPort())
+thresh1.ThresholdByUpper(1.5)
+plane1Map = vtk.vtkDataSetMapper()
+plane1Map.SetInputConnection(thresh1.GetOutputPort())
+plane1Map.SetScalarRange(pl3d.GetOutput().GetScalarRange())
+plane1Actor = vtk.vtkActor()
+plane1Actor.SetMapper(plane1Map)
+plane1Actor.SetTexture(texture)
+plane1Actor.GetProperty().SetOpacity(0.999)
+
+plane2 = vtk.vtkStructuredGridGeometryFilter()
+plane2.SetInputConnection(pl3d.GetOutputPort())
+plane2.SetExtent(30, 30, 0, 100, 0, 100)
+thresh2 = vtk.vtkThresholdTextureCoords()
+thresh2.SetInputConnection(plane2.GetOutputPort())
+thresh2.ThresholdByUpper(1.5)
+plane2Map = vtk.vtkDataSetMapper()
+plane2Map.SetInputConnection(thresh2.GetOutputPort())
+plane2Map.SetScalarRange(pl3d.GetOutput().GetScalarRange())
+plane2Actor = vtk.vtkActor()
+plane2Actor.SetMapper(plane2Map)
+plane2Actor.SetTexture(texture)
+plane2Actor.GetProperty().SetOpacity(0.999)
+
+plane3 = vtk.vtkStructuredGridGeometryFilter()
+plane3.SetInputConnection(pl3d.GetOutputPort())
+plane3.SetExtent(35, 35, 0, 100, 0, 100)
+thresh3 = vtk.vtkThresholdTextureCoords()
+thresh3.SetInputConnection(plane3.GetOutputPort())
+thresh3.ThresholdByUpper(1.5)
+plane3Map = vtk.vtkDataSetMapper()
+plane3Map.SetInputConnection(thresh3.GetOutputPort())
+plane3Map.SetScalarRange(pl3d.GetOutput().GetScalarRange())
+plane3Actor = vtk.vtkActor()
+plane3Actor.SetMapper(plane3Map)
+plane3Actor.SetTexture(texture)
+plane3Actor.GetProperty().SetOpacity(0.999)
+
+# For context create an outline around the data.
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+outlineProp = outlineActor.GetProperty()
+outlineProp.SetColor(0, 0, 0)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(outlineActor)
+ren.AddActor(wallActor)
+ren.AddActor(finActor)
+ren.AddActor(plane1Actor)
+ren.AddActor(plane2Actor)
+ren.AddActor(plane3Actor)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(500, 500)
+
+# Set up a nice view.
+cam1 = vtk.vtkCamera()
+cam1.SetClippingRange(1.51176, 75.5879)
+cam1.SetFocalPoint(2.33749, 2.96739, 3.61023)
+cam1.SetPosition(10.8787, 5.27346, 15.8687)
+cam1.SetViewAngle(30)
+cam1.SetViewUp(-0.0610856, 0.987798, -0.143262)
+ren.SetActiveCamera(cam1)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/TextureThreshold.vt b/examples/vtk_examples/VisualizationAlgorithms/TextureThreshold.vt
new file mode 100644
index 0000000..38d24f6
Binary files /dev/null and b/examples/vtk_examples/VisualizationAlgorithms/TextureThreshold.vt differ
diff --git a/examples/vtk_examples/VisualizationAlgorithms/VisQuad.py b/examples/vtk_examples/VisualizationAlgorithms/VisQuad.py
new file mode 100644
index 0000000..bb2b003
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/VisQuad.py
@@ -0,0 +1,59 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of the contour filter, and the use of
+# the vtkSampleFunction to generate a volume of data samples from an
+# implicit function.
+
+import vtk
+
+# VTK supports implicit functions of the form f(x,y,z)=constant. These
+# functions can represent things spheres, cones, etc. Here we use a
+# general form for a quadric to create an elliptical data field.
+quadric = vtk.vtkQuadric()
+quadric.SetCoefficients(.5, 1, .2, 0, .1, 0, 0, .2, 0, 0)
+
+# vtkSampleFunction samples an implicit function over the x-y-z range
+# specified (here it defaults to -1,1 in the x,y,z directions).
+sample = vtk.vtkSampleFunction()
+sample.SetSampleDimensions(30, 30, 30)
+sample.SetImplicitFunction(quadric)
+
+# Create five surfaces F(x,y,z) = constant between range specified. The
+# GenerateValues() method creates n isocontour values between the range
+# specified.
+contours = vtk.vtkContourFilter()
+contours.SetInputConnection(sample.GetOutputPort())
+contours.GenerateValues(5, 0.0, 1.2)
+
+contMapper = vtk.vtkPolyDataMapper()
+contMapper.SetInputConnection(contours.GetOutputPort())
+contMapper.SetScalarRange(0.0, 1.2)
+
+contActor = vtk.vtkActor()
+contActor.SetMapper(contMapper)
+
+# We'll put a simple outline around the data.
+outline = vtk.vtkOutlineFilter()
+outline.SetInputConnection(sample.GetOutputPort())
+
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+outlineActor.GetProperty().SetColor(0,0,0)
+
+# The usual rendering stuff.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+ren.SetBackground(1, 1, 1)
+ren.AddActor(contActor)
+ren.AddActor(outlineActor)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/VisQuad.vt b/examples/vtk_examples/VisualizationAlgorithms/VisQuad.vt
new file mode 100644
index 0000000..297b1a3
Binary files /dev/null and b/examples/vtk_examples/VisualizationAlgorithms/VisQuad.vt differ
diff --git a/examples/vtk_examples/VisualizationAlgorithms/imageWarp.py b/examples/vtk_examples/VisualizationAlgorithms/imageWarp.py
new file mode 100644
index 0000000..4a2c37c
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/imageWarp.py
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+# This example shows how to combine data from both the imaging and
+# graphics pipelines. The vtkMergeFilter is used to merge the data
+# from each together.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Read in an image and compute a luminance value. The image is
+# extracted as a set of polygons (vtkImageDataGeometryFilter). We then
+# will warp the plane using the scalar (luminance) values.
+reader = vtk.vtkBMPReader()
+reader.SetFileName(VTK_DATA_ROOT + "/Data/masonry.bmp")
+luminance = vtk.vtkImageLuminance()
+luminance.SetInputConnection(reader.GetOutputPort())
+geometry = vtk.vtkImageDataGeometryFilter()
+geometry.SetInputConnection(luminance.GetOutputPort())
+warp = vtk.vtkWarpScalar()
+warp.SetInputConnection(geometry.GetOutputPort())
+warp.SetScaleFactor(-0.1)
+
+# Use vtkMergeFilter to combine the original image with the warped
+# geometry.
+merge = vtk.vtkMergeFilter()
+merge.SetGeometry(warp.GetOutput())
+merge.SetScalars(reader.GetOutput())
+mapper = vtk.vtkDataSetMapper()
+mapper.SetInputConnection(merge.GetOutputPort())
+mapper.SetScalarRange(0, 255)
+mapper.ImmediateModeRenderingOff()
+actor = vtk.vtkActor()
+actor.SetMapper(mapper)
+
+# Create renderer stuff
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(actor)
+ren.ResetCamera()
+ren.GetActiveCamera().Azimuth(20)
+ren.GetActiveCamera().Elevation(30)
+ren.SetBackground(0.1, 0.2, 0.4)
+ren.ResetCameraClippingRange()
+
+renWin.SetSize(250, 250)
+
+cam1 = ren.GetActiveCamera()
+cam1.Zoom(1.4)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/imageWarp.vt b/examples/vtk_examples/VisualizationAlgorithms/imageWarp.vt
new file mode 100644
index 0000000..0863754
Binary files /dev/null and b/examples/vtk_examples/VisualizationAlgorithms/imageWarp.vt differ
diff --git a/examples/vtk_examples/VisualizationAlgorithms/officeTube.py b/examples/vtk_examples/VisualizationAlgorithms/officeTube.py
new file mode 100644
index 0000000..ee6556f
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/officeTube.py
@@ -0,0 +1,312 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of a single streamline and the
+# tube filter to create a streamtube.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+from vtk.util.colors import *
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# We read a data file the is a CFD analysis of airflow in an office
+# (with ventilation and a burning cigarette). We force an update so
+# that we can query the output for its length, i.e., the length of the
+# diagonal of the bounding box. This is useful for normalizing the
+# data.
+reader = vtk.vtkStructuredGridReader()
+reader.SetFileName(VTK_DATA_ROOT + "/Data/office.binary.vtk")
+reader.Update()
+
+length = reader.GetOutput().GetLength()
+
+maxVelocity =reader.GetOutput().GetPointData().GetVectors().GetMaxNorm()
+# maxTime = 35.0*length/maxVelocity
+calc1 = vtk.PythonCalc()
+calc1.value1(35.0)
+calc1.value2(length)
+calc1.op('*')
+calc2 = vtk.PythonCalc()
+calc2.value1(calc1.value())
+calc2.value2(maxVelocity)
+calc2.op('/')
+maxTime = calc2.value()
+
+# Now we will generate a single streamline in the data. We select the
+# integration order to use (RungeKutta order 4) and associate it with
+# the streamer. The start position is the position in world space
+# where we want to begin streamline integration; and we integrate in
+# both directions. The step length is the length of the line segments
+# that make up the streamline (i.e., related to display). The
+# IntegrationStepLength specifies the integration step length as a
+# fraction of the cell size that the streamline is in.
+integ = vtk.vtkRungeKutta4()
+streamer = vtk.vtkStreamLine()
+streamer.SetInputConnection(reader.GetOutputPort())
+streamer.SetStartPosition(0.1, 2.1, 0.5)
+streamer.SetMaximumPropagationTime(500)
+streamer.SetStepLength(0.5)
+streamer.SetIntegrationStepLength(0.05)
+streamer.SetIntegrationDirectionToIntegrateBothDirections()
+streamer.SetIntegrator(integ)
+
+# The tube is wrapped around the generated streamline. By varying the
+# radius by the inverse of vector magnitude, we are creating a tube
+# whose radius is proportional to mass flux (in incompressible flow).
+streamTube = vtk.vtkTubeFilter()
+streamTube.SetInputConnection(streamer.GetOutputPort())
+streamTube.SetRadius(0.02)
+streamTube.SetNumberOfSides(12)
+streamTube.SetVaryRadiusToVaryRadiusByVector()
+mapStreamTube = vtk.vtkPolyDataMapper()
+mapStreamTube.SetInputConnection(streamTube.GetOutputPort())
+mapStreamTube.SetScalarRange(reader.GetOutput().GetPointData().GetScalars().GetRange())
+streamTubeActor = vtk.vtkActor()
+streamTubeActor.SetMapper(mapStreamTube)
+streamTubeActor.GetProperty().BackfaceCullingOn()
+
+# From here on we generate a whole bunch of planes which correspond to
+# the geometry in the analysis; tables, bookshelves and so on.
+table1 = vtk.vtkStructuredGridGeometryFilter()
+table1.SetInputConnection(reader.GetOutputPort())
+table1.SetExtent(11, 15, 7, 9, 8, 8)
+mapTable1 = vtk.vtkPolyDataMapper()
+mapTable1.SetInputConnection(table1.GetOutputPort())
+mapTable1.ScalarVisibilityOff()
+table1Actor = vtk.vtkActor()
+table1Actor.SetMapper(mapTable1)
+table1Actor.GetProperty().SetColor(.59, .427, .392)
+
+table2 = vtk.vtkStructuredGridGeometryFilter()
+table2.SetInputConnection(reader.GetOutputPort())
+table2.SetExtent(11, 15, 10, 12, 8, 8)
+mapTable2 = vtk.vtkPolyDataMapper()
+mapTable2.SetInputConnection(table2.GetOutputPort())
+mapTable2.ScalarVisibilityOff()
+table2Actor = vtk.vtkActor()
+table2Actor.SetMapper(mapTable2)
+table2Actor.GetProperty().SetColor(.59, .427, .392)
+
+FilingCabinet1 = vtk.vtkStructuredGridGeometryFilter()
+FilingCabinet1.SetInputConnection(reader.GetOutputPort())
+FilingCabinet1.SetExtent(15, 15, 7, 9, 0, 8)
+mapFilingCabinet1 = vtk.vtkPolyDataMapper()
+mapFilingCabinet1.SetInputConnection(FilingCabinet1.GetOutputPort())
+mapFilingCabinet1.ScalarVisibilityOff()
+FilingCabinet1Actor = vtk.vtkActor()
+FilingCabinet1Actor.SetMapper(mapFilingCabinet1)
+FilingCabinet1Actor.GetProperty().SetColor(.8, .8, .6)
+
+FilingCabinet2 = vtk.vtkStructuredGridGeometryFilter()
+FilingCabinet2.SetInputConnection(reader.GetOutputPort())
+FilingCabinet2.SetExtent(15, 15, 10, 12, 0, 8)
+mapFilingCabinet2 = vtk.vtkPolyDataMapper()
+mapFilingCabinet2.SetInputConnection(FilingCabinet2.GetOutputPort())
+mapFilingCabinet2.ScalarVisibilityOff()
+FilingCabinet2Actor = vtk.vtkActor()
+FilingCabinet2Actor.SetMapper(mapFilingCabinet2)
+FilingCabinet2Actor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1Top = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1Top.SetInputConnection(reader.GetOutputPort())
+bookshelf1Top.SetExtent(13, 13, 0, 4, 0, 11)
+mapBookshelf1Top = vtk.vtkPolyDataMapper()
+mapBookshelf1Top.SetInputConnection(bookshelf1Top.GetOutputPort())
+mapBookshelf1Top.ScalarVisibilityOff()
+bookshelf1TopActor = vtk.vtkActor()
+bookshelf1TopActor.SetMapper(mapBookshelf1Top)
+bookshelf1TopActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1Bottom = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1Bottom.SetInputConnection(reader.GetOutputPort())
+bookshelf1Bottom.SetExtent(20, 20, 0, 4, 0, 11)
+mapBookshelf1Bottom = vtk.vtkPolyDataMapper()
+mapBookshelf1Bottom.SetInputConnection(bookshelf1Bottom.GetOutputPort())
+mapBookshelf1Bottom.ScalarVisibilityOff()
+bookshelf1BottomActor = vtk.vtkActor()
+bookshelf1BottomActor.SetMapper(mapBookshelf1Bottom)
+bookshelf1BottomActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1Front = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1Front.SetInputConnection(reader.GetOutputPort())
+bookshelf1Front.SetExtent(13, 20, 0, 0, 0, 11)
+mapBookshelf1Front = vtk.vtkPolyDataMapper()
+mapBookshelf1Front.SetInputConnection(bookshelf1Front.GetOutputPort())
+mapBookshelf1Front.ScalarVisibilityOff()
+bookshelf1FrontActor = vtk.vtkActor()
+bookshelf1FrontActor.SetMapper(mapBookshelf1Front)
+bookshelf1FrontActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1Back = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1Back.SetInputConnection(reader.GetOutputPort())
+bookshelf1Back.SetExtent(13, 20, 4, 4, 0, 11)
+mapBookshelf1Back = vtk.vtkPolyDataMapper()
+mapBookshelf1Back.SetInputConnection(bookshelf1Back.GetOutputPort())
+mapBookshelf1Back.ScalarVisibilityOff()
+bookshelf1BackActor = vtk.vtkActor()
+bookshelf1BackActor.SetMapper(mapBookshelf1Back)
+bookshelf1BackActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1LHS = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1LHS.SetInputConnection(reader.GetOutputPort())
+bookshelf1LHS.SetExtent(13, 20, 0, 4, 0, 0)
+mapBookshelf1LHS = vtk.vtkPolyDataMapper()
+mapBookshelf1LHS.SetInputConnection(bookshelf1LHS.GetOutputPort())
+mapBookshelf1LHS.ScalarVisibilityOff()
+bookshelf1LHSActor = vtk.vtkActor()
+bookshelf1LHSActor.SetMapper(mapBookshelf1LHS)
+bookshelf1LHSActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1RHS = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1RHS.SetInputConnection(reader.GetOutputPort())
+bookshelf1RHS.SetExtent(13, 20, 0, 4, 11, 11)
+mapBookshelf1RHS = vtk.vtkPolyDataMapper()
+mapBookshelf1RHS.SetInputConnection(bookshelf1RHS.GetOutputPort())
+mapBookshelf1RHS.ScalarVisibilityOff()
+bookshelf1RHSActor = vtk.vtkActor()
+bookshelf1RHSActor.SetMapper(mapBookshelf1RHS)
+bookshelf1RHSActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2Top = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2Top.SetInputConnection(reader.GetOutputPort())
+bookshelf2Top.SetExtent(13, 13, 15, 19, 0, 11)
+mapBookshelf2Top = vtk.vtkPolyDataMapper()
+mapBookshelf2Top.SetInputConnection(bookshelf2Top.GetOutputPort())
+mapBookshelf2Top.ScalarVisibilityOff()
+bookshelf2TopActor = vtk.vtkActor()
+bookshelf2TopActor.SetMapper(mapBookshelf2Top)
+bookshelf2TopActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2Bottom = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2Bottom.SetInputConnection(reader.GetOutputPort())
+bookshelf2Bottom.SetExtent(20, 20, 15, 19, 0, 11)
+mapBookshelf2Bottom = vtk.vtkPolyDataMapper()
+mapBookshelf2Bottom.SetInputConnection(bookshelf2Bottom.GetOutputPort())
+mapBookshelf2Bottom.ScalarVisibilityOff()
+bookshelf2BottomActor = vtk.vtkActor()
+bookshelf2BottomActor.SetMapper(mapBookshelf2Bottom)
+bookshelf2BottomActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2Front = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2Front.SetInputConnection(reader.GetOutputPort())
+bookshelf2Front.SetExtent(13, 20, 15, 15, 0, 11)
+mapBookshelf2Front = vtk.vtkPolyDataMapper()
+mapBookshelf2Front.SetInputConnection(bookshelf2Front.GetOutputPort())
+mapBookshelf2Front.ScalarVisibilityOff()
+bookshelf2FrontActor = vtk.vtkActor()
+bookshelf2FrontActor.SetMapper(mapBookshelf2Front)
+bookshelf2FrontActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2Back = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2Back.SetInputConnection(reader.GetOutputPort())
+bookshelf2Back.SetExtent(13, 20, 19, 19, 0, 11)
+mapBookshelf2Back = vtk.vtkPolyDataMapper()
+mapBookshelf2Back.SetInputConnection(bookshelf2Back.GetOutputPort())
+mapBookshelf2Back.ScalarVisibilityOff()
+bookshelf2BackActor = vtk.vtkActor()
+bookshelf2BackActor.SetMapper(mapBookshelf2Back)
+bookshelf2BackActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2LHS = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2LHS.SetInputConnection(reader.GetOutputPort())
+bookshelf2LHS.SetExtent(13, 20, 15, 19, 0, 0)
+mapBookshelf2LHS = vtk.vtkPolyDataMapper()
+mapBookshelf2LHS.SetInputConnection(bookshelf2LHS.GetOutputPort())
+mapBookshelf2LHS.ScalarVisibilityOff()
+bookshelf2LHSActor = vtk.vtkActor()
+bookshelf2LHSActor.SetMapper(mapBookshelf2LHS)
+bookshelf2LHSActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2RHS = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2RHS.SetInputConnection(reader.GetOutputPort())
+bookshelf2RHS.SetExtent(13, 20, 15, 19, 11, 11)
+mapBookshelf2RHS = vtk.vtkPolyDataMapper()
+mapBookshelf2RHS.SetInputConnection(bookshelf2RHS.GetOutputPort())
+mapBookshelf2RHS.ScalarVisibilityOff()
+bookshelf2RHSActor = vtk.vtkActor()
+bookshelf2RHSActor.SetMapper(mapBookshelf2RHS)
+bookshelf2RHSActor.GetProperty().SetColor(.8, .8, .6)
+
+window = vtk.vtkStructuredGridGeometryFilter()
+window.SetInputConnection(reader.GetOutputPort())
+window.SetExtent(20, 20, 6, 13, 10, 13)
+mapWindow = vtk.vtkPolyDataMapper()
+mapWindow.SetInputConnection(window.GetOutputPort())
+mapWindow.ScalarVisibilityOff()
+windowActor = vtk.vtkActor()
+windowActor.SetMapper(mapWindow)
+windowActor.GetProperty().SetColor(.3, .3, .5)
+
+outlet = vtk.vtkStructuredGridGeometryFilter()
+outlet.SetInputConnection(reader.GetOutputPort())
+outlet.SetExtent(0, 0, 9, 10, 14, 16)
+mapOutlet = vtk.vtkPolyDataMapper()
+mapOutlet.SetInputConnection(outlet.GetOutputPort())
+mapOutlet.ScalarVisibilityOff()
+outletActor = vtk.vtkActor()
+outletActor.SetMapper(mapOutlet)
+outletActor.GetProperty().SetColor(0, 0, 0)
+
+inlet = vtk.vtkStructuredGridGeometryFilter()
+inlet.SetInputConnection(reader.GetOutputPort())
+inlet.SetExtent(0, 0, 9, 10, 0, 6)
+mapInlet = vtk.vtkPolyDataMapper()
+mapInlet.SetInputConnection(inlet.GetOutputPort())
+mapInlet.ScalarVisibilityOff()
+inletActor = vtk.vtkActor()
+inletActor.SetMapper(mapInlet)
+inletActor.GetProperty().SetColor(0, 0, 0)
+
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(reader.GetOutputPort())
+mapOutline = vtk.vtkPolyDataMapper()
+mapOutline.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(mapOutline)
+outlineActor.GetProperty().SetColor(0, 0, 0)
+
+# Now create the usual graphics stuff.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+ren.AddActor(table1Actor)
+ren.AddActor(table2Actor)
+ren.AddActor(FilingCabinet1Actor)
+ren.AddActor(FilingCabinet2Actor)
+ren.AddActor(bookshelf1TopActor)
+ren.AddActor(bookshelf1BottomActor)
+ren.AddActor(bookshelf1FrontActor)
+ren.AddActor(bookshelf1BackActor)
+ren.AddActor(bookshelf1LHSActor)
+ren.AddActor(bookshelf1RHSActor)
+ren.AddActor(bookshelf2TopActor)
+ren.AddActor(bookshelf2BottomActor)
+ren.AddActor(bookshelf2FrontActor)
+ren.AddActor(bookshelf2BackActor)
+ren.AddActor(bookshelf2LHSActor)
+ren.AddActor(bookshelf2RHSActor)
+ren.AddActor(windowActor)
+ren.AddActor(outletActor)
+ren.AddActor(inletActor)
+ren.AddActor(outlineActor)
+ren.AddActor(streamTubeActor)
+
+ren.SetBackground(slate_grey)
+
+# Here we specify a particular view.
+aCamera = vtk.vtkCamera()
+aCamera.SetClippingRange(0.726079, 36.3039)
+aCamera.SetFocalPoint(2.43584, 2.15046, 1.11104)
+aCamera.SetPosition(-4.76183, -10.4426, 3.17203)
+aCamera.SetViewUp(0.0511273, 0.132773, 0.989827)
+aCamera.SetViewAngle(18.604)
+aCamera.Zoom(1.2)
+
+ren.SetActiveCamera(aCamera)
+renWin.SetSize(500, 300)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/officeTube.vt b/examples/vtk_examples/VisualizationAlgorithms/officeTube.vt
new file mode 100644
index 0000000..b537b5c
Binary files /dev/null and b/examples/vtk_examples/VisualizationAlgorithms/officeTube.vt differ
diff --git a/examples/vtk_examples/VisualizationAlgorithms/officeTubes.py b/examples/vtk_examples/VisualizationAlgorithms/officeTubes.py
new file mode 100644
index 0000000..c92f279
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/officeTubes.py
@@ -0,0 +1,320 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of streamlines generated from seeds,
+# combined with a tube filter to create several streamtubes.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+from vtk.util.colors import *
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# We read a data file the is a CFD analysis of airflow in an office
+# (with ventilation and a burning cigarette). We force an update so
+# that we can query the output for its length, i.e., the length of the
+# diagonal of the bounding box. This is useful for normalizing the
+# data.
+reader = vtk.vtkStructuredGridReader()
+reader.SetFileName(VTK_DATA_ROOT + "/Data/office.binary.vtk")
+reader.Update()
+
+length = reader.GetOutput().GetLength()
+
+maxVelocity =reader.GetOutput().GetPointData().GetVectors().GetMaxNorm()
+# maxTime = 35.0*length/maxVelocity
+calc1 = vtk.PythonCalc()
+calc1.value1(35.0)
+calc1.value2(length)
+calc1.op('*')
+calc2 = vtk.PythonCalc()
+calc2.value1(calc1.value())
+calc2.value2(maxVelocity)
+calc2.op('/')
+maxTime = calc2.value()
+
+# Now we will generate multiple streamlines in the data. We create a
+# random cloud of points and then use those as integration seeds. We
+# select the integration order to use (RungeKutta order 4) and
+# associate it with the streamer. The start position is the position
+# in world space where we want to begin streamline integration; and we
+# integrate in both directions. The step length is the length of the
+# line segments that make up the streamline (i.e., related to
+# display). The IntegrationStepLength specifies the integration step
+# length as a fraction of the cell size that the streamline is in.
+
+# Create source for streamtubes
+seeds = vtk.vtkPointSource()
+seeds.SetRadius(0.15)
+seeds.SetCenter(0.1, 2.1, 0.5)
+seeds.SetNumberOfPoints(6)
+
+integ = vtk.vtkRungeKutta4()
+streamer = vtk.vtkStreamLine()
+streamer.SetInputConnection(reader.GetOutputPort())
+streamer.SetSource(seeds.GetOutput())
+streamer.SetMaximumPropagationTime(500)
+streamer.SetStepLength(0.5)
+streamer.SetIntegrationStepLength(0.05)
+streamer.SetIntegrationDirectionToIntegrateBothDirections()
+streamer.SetIntegrator(integ)
+
+# The tube is wrapped around the generated streamline. By varying the
+# radius by the inverse of vector magnitude, we are creating a tube
+# whose radius is proportional to mass flux (in incompressible flow).
+streamTube = vtk.vtkTubeFilter()
+streamTube.SetInputConnection(streamer.GetOutputPort())
+streamTube.SetRadius(0.02)
+streamTube.SetNumberOfSides(12)
+streamTube.SetVaryRadiusToVaryRadiusByVector()
+mapStreamTube = vtk.vtkPolyDataMapper()
+mapStreamTube.SetInputConnection(streamTube.GetOutputPort())
+mapStreamTube.SetScalarRange(reader.GetOutput().GetPointData().GetScalars().GetRange())
+streamTubeActor = vtk.vtkActor()
+streamTubeActor.SetMapper(mapStreamTube)
+streamTubeActor.GetProperty().BackfaceCullingOn()
+
+# From here on we generate a whole bunch of planes which correspond to
+# the geometry in the analysis; tables, bookshelves and so on.
+table1 = vtk.vtkStructuredGridGeometryFilter()
+table1.SetInputConnection(reader.GetOutputPort())
+table1.SetExtent(11, 15, 7, 9, 8, 8)
+mapTable1 = vtk.vtkPolyDataMapper()
+mapTable1.SetInputConnection(table1.GetOutputPort())
+mapTable1.ScalarVisibilityOff()
+table1Actor = vtk.vtkActor()
+table1Actor.SetMapper(mapTable1)
+table1Actor.GetProperty().SetColor(.59, .427, .392)
+
+table2 = vtk.vtkStructuredGridGeometryFilter()
+table2.SetInputConnection(reader.GetOutputPort())
+table2.SetExtent(11, 15, 10, 12, 8, 8)
+mapTable2 = vtk.vtkPolyDataMapper()
+mapTable2.SetInputConnection(table2.GetOutputPort())
+mapTable2.ScalarVisibilityOff()
+table2Actor = vtk.vtkActor()
+table2Actor.SetMapper(mapTable2)
+table2Actor.GetProperty().SetColor(.59, .427, .392)
+
+FilingCabinet1 = vtk.vtkStructuredGridGeometryFilter()
+FilingCabinet1.SetInputConnection(reader.GetOutputPort())
+FilingCabinet1.SetExtent(15, 15, 7, 9, 0, 8)
+mapFilingCabinet1 = vtk.vtkPolyDataMapper()
+mapFilingCabinet1.SetInputConnection(FilingCabinet1.GetOutputPort())
+mapFilingCabinet1.ScalarVisibilityOff()
+FilingCabinet1Actor = vtk.vtkActor()
+FilingCabinet1Actor.SetMapper(mapFilingCabinet1)
+FilingCabinet1Actor.GetProperty().SetColor(.8, .8, .6)
+
+FilingCabinet2 = vtk.vtkStructuredGridGeometryFilter()
+FilingCabinet2.SetInputConnection(reader.GetOutputPort())
+FilingCabinet2.SetExtent(15, 15, 10, 12, 0, 8)
+mapFilingCabinet2 = vtk.vtkPolyDataMapper()
+mapFilingCabinet2.SetInputConnection(FilingCabinet2.GetOutputPort())
+mapFilingCabinet2.ScalarVisibilityOff()
+FilingCabinet2Actor = vtk.vtkActor()
+FilingCabinet2Actor.SetMapper(mapFilingCabinet2)
+FilingCabinet2Actor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1Top = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1Top.SetInputConnection(reader.GetOutputPort())
+bookshelf1Top.SetExtent(13, 13, 0, 4, 0, 11)
+mapBookshelf1Top = vtk.vtkPolyDataMapper()
+mapBookshelf1Top.SetInputConnection(bookshelf1Top.GetOutputPort())
+mapBookshelf1Top.ScalarVisibilityOff()
+bookshelf1TopActor = vtk.vtkActor()
+bookshelf1TopActor.SetMapper(mapBookshelf1Top)
+bookshelf1TopActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1Bottom = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1Bottom.SetInputConnection(reader.GetOutputPort())
+bookshelf1Bottom.SetExtent(20, 20, 0, 4, 0, 11)
+mapBookshelf1Bottom = vtk.vtkPolyDataMapper()
+mapBookshelf1Bottom.SetInputConnection(bookshelf1Bottom.GetOutputPort())
+mapBookshelf1Bottom.ScalarVisibilityOff()
+bookshelf1BottomActor = vtk.vtkActor()
+bookshelf1BottomActor.SetMapper(mapBookshelf1Bottom)
+bookshelf1BottomActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1Front = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1Front.SetInputConnection(reader.GetOutputPort())
+bookshelf1Front.SetExtent(13, 20, 0, 0, 0, 11)
+mapBookshelf1Front = vtk.vtkPolyDataMapper()
+mapBookshelf1Front.SetInputConnection(bookshelf1Front.GetOutputPort())
+mapBookshelf1Front.ScalarVisibilityOff()
+bookshelf1FrontActor = vtk.vtkActor()
+bookshelf1FrontActor.SetMapper(mapBookshelf1Front)
+bookshelf1FrontActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1Back = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1Back.SetInputConnection(reader.GetOutputPort())
+bookshelf1Back.SetExtent(13, 20, 4, 4, 0, 11)
+mapBookshelf1Back = vtk.vtkPolyDataMapper()
+mapBookshelf1Back.SetInputConnection(bookshelf1Back.GetOutputPort())
+mapBookshelf1Back.ScalarVisibilityOff()
+bookshelf1BackActor = vtk.vtkActor()
+bookshelf1BackActor.SetMapper(mapBookshelf1Back)
+bookshelf1BackActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1LHS = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1LHS.SetInputConnection(reader.GetOutputPort())
+bookshelf1LHS.SetExtent(13, 20, 0, 4, 0, 0)
+mapBookshelf1LHS = vtk.vtkPolyDataMapper()
+mapBookshelf1LHS.SetInputConnection(bookshelf1LHS.GetOutputPort())
+mapBookshelf1LHS.ScalarVisibilityOff()
+bookshelf1LHSActor = vtk.vtkActor()
+bookshelf1LHSActor.SetMapper(mapBookshelf1LHS)
+bookshelf1LHSActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf1RHS = vtk.vtkStructuredGridGeometryFilter()
+bookshelf1RHS.SetInputConnection(reader.GetOutputPort())
+bookshelf1RHS.SetExtent(13, 20, 0, 4, 11, 11)
+mapBookshelf1RHS = vtk.vtkPolyDataMapper()
+mapBookshelf1RHS.SetInputConnection(bookshelf1RHS.GetOutputPort())
+mapBookshelf1RHS.ScalarVisibilityOff()
+bookshelf1RHSActor = vtk.vtkActor()
+bookshelf1RHSActor.SetMapper(mapBookshelf1RHS)
+bookshelf1RHSActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2Top = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2Top.SetInputConnection(reader.GetOutputPort())
+bookshelf2Top.SetExtent(13, 13, 15, 19, 0, 11)
+mapBookshelf2Top = vtk.vtkPolyDataMapper()
+mapBookshelf2Top.SetInputConnection(bookshelf2Top.GetOutputPort())
+mapBookshelf2Top.ScalarVisibilityOff()
+bookshelf2TopActor = vtk.vtkActor()
+bookshelf2TopActor.SetMapper(mapBookshelf2Top)
+bookshelf2TopActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2Bottom = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2Bottom.SetInputConnection(reader.GetOutputPort())
+bookshelf2Bottom.SetExtent(20, 20, 15, 19, 0, 11)
+mapBookshelf2Bottom = vtk.vtkPolyDataMapper()
+mapBookshelf2Bottom.SetInputConnection(bookshelf2Bottom.GetOutputPort())
+mapBookshelf2Bottom.ScalarVisibilityOff()
+bookshelf2BottomActor = vtk.vtkActor()
+bookshelf2BottomActor.SetMapper(mapBookshelf2Bottom)
+bookshelf2BottomActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2Front = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2Front.SetInputConnection(reader.GetOutputPort())
+bookshelf2Front.SetExtent(13, 20, 15, 15, 0, 11)
+mapBookshelf2Front = vtk.vtkPolyDataMapper()
+mapBookshelf2Front.SetInputConnection(bookshelf2Front.GetOutputPort())
+mapBookshelf2Front.ScalarVisibilityOff()
+bookshelf2FrontActor = vtk.vtkActor()
+bookshelf2FrontActor.SetMapper(mapBookshelf2Front)
+bookshelf2FrontActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2Back = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2Back.SetInputConnection(reader.GetOutputPort())
+bookshelf2Back.SetExtent(13, 20, 19, 19, 0, 11)
+mapBookshelf2Back = vtk.vtkPolyDataMapper()
+mapBookshelf2Back.SetInputConnection(bookshelf2Back.GetOutputPort())
+mapBookshelf2Back.ScalarVisibilityOff()
+bookshelf2BackActor = vtk.vtkActor()
+bookshelf2BackActor.SetMapper(mapBookshelf2Back)
+bookshelf2BackActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2LHS = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2LHS.SetInputConnection(reader.GetOutputPort())
+bookshelf2LHS.SetExtent(13, 20, 15, 19, 0, 0)
+mapBookshelf2LHS = vtk.vtkPolyDataMapper()
+mapBookshelf2LHS.SetInputConnection(bookshelf2LHS.GetOutputPort())
+mapBookshelf2LHS.ScalarVisibilityOff()
+bookshelf2LHSActor = vtk.vtkActor()
+bookshelf2LHSActor.SetMapper(mapBookshelf2LHS)
+bookshelf2LHSActor.GetProperty().SetColor(.8, .8, .6)
+
+bookshelf2RHS = vtk.vtkStructuredGridGeometryFilter()
+bookshelf2RHS.SetInputConnection(reader.GetOutputPort())
+bookshelf2RHS.SetExtent(13, 20, 15, 19, 11, 11)
+mapBookshelf2RHS = vtk.vtkPolyDataMapper()
+mapBookshelf2RHS.SetInputConnection(bookshelf2RHS.GetOutputPort())
+mapBookshelf2RHS.ScalarVisibilityOff()
+bookshelf2RHSActor = vtk.vtkActor()
+bookshelf2RHSActor.SetMapper(mapBookshelf2RHS)
+bookshelf2RHSActor.GetProperty().SetColor(.8, .8, .6)
+
+window = vtk.vtkStructuredGridGeometryFilter()
+window.SetInputConnection(reader.GetOutputPort())
+window.SetExtent(20, 20, 6, 13, 10, 13)
+mapWindow = vtk.vtkPolyDataMapper()
+mapWindow.SetInputConnection(window.GetOutputPort())
+mapWindow.ScalarVisibilityOff()
+windowActor = vtk.vtkActor()
+windowActor.SetMapper(mapWindow)
+windowActor.GetProperty().SetColor(.3, .3, .5)
+
+outlet = vtk.vtkStructuredGridGeometryFilter()
+outlet.SetInputConnection(reader.GetOutputPort())
+outlet.SetExtent(0, 0, 9, 10, 14, 16)
+mapOutlet = vtk.vtkPolyDataMapper()
+mapOutlet.SetInputConnection(outlet.GetOutputPort())
+mapOutlet.ScalarVisibilityOff()
+outletActor = vtk.vtkActor()
+outletActor.SetMapper(mapOutlet)
+outletActor.GetProperty().SetColor(0, 0, 0)
+
+inlet = vtk.vtkStructuredGridGeometryFilter()
+inlet.SetInputConnection(reader.GetOutputPort())
+inlet.SetExtent(0, 0, 9, 10, 0, 6)
+mapInlet = vtk.vtkPolyDataMapper()
+mapInlet.SetInputConnection(inlet.GetOutputPort())
+mapInlet.ScalarVisibilityOff()
+inletActor = vtk.vtkActor()
+inletActor.SetMapper(mapInlet)
+inletActor.GetProperty().SetColor(0, 0, 0)
+
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(reader.GetOutputPort())
+mapOutline = vtk.vtkPolyDataMapper()
+mapOutline.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(mapOutline)
+outlineActor.GetProperty().SetColor(0, 0, 0)
+
+# Now create the usual graphics stuff.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+ren.AddActor(table1Actor)
+ren.AddActor(table2Actor)
+ren.AddActor(FilingCabinet1Actor)
+ren.AddActor(FilingCabinet2Actor)
+ren.AddActor(bookshelf1TopActor)
+ren.AddActor(bookshelf1BottomActor)
+ren.AddActor(bookshelf1FrontActor)
+ren.AddActor(bookshelf1BackActor)
+ren.AddActor(bookshelf1LHSActor)
+ren.AddActor(bookshelf1RHSActor)
+ren.AddActor(bookshelf2TopActor)
+ren.AddActor(bookshelf2BottomActor)
+ren.AddActor(bookshelf2FrontActor)
+ren.AddActor(bookshelf2BackActor)
+ren.AddActor(bookshelf2LHSActor)
+ren.AddActor(bookshelf2RHSActor)
+ren.AddActor(windowActor)
+ren.AddActor(outletActor)
+ren.AddActor(inletActor)
+ren.AddActor(outlineActor)
+ren.AddActor(streamTubeActor)
+
+ren.SetBackground(slate_grey)
+
+# Here we specify a particular view.
+aCamera = vtk.vtkCamera()
+aCamera.SetClippingRange(0.726079, 36.3039)
+aCamera.SetFocalPoint(2.43584, 2.15046, 1.11104)
+aCamera.SetPosition(-4.76183, -10.4426, 3.17203)
+aCamera.SetViewUp(0.0511273, 0.132773, 0.989827)
+aCamera.SetViewAngle(18.604)
+aCamera.Zoom(1.2)
+
+ren.SetActiveCamera(aCamera)
+renWin.SetSize(500, 300)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/officeTubes.vt b/examples/vtk_examples/VisualizationAlgorithms/officeTubes.vt
new file mode 100644
index 0000000..5f9efa4
Binary files /dev/null and b/examples/vtk_examples/VisualizationAlgorithms/officeTubes.vt differ
diff --git a/examples/vtk_examples/VisualizationAlgorithms/probeComb.py b/examples/vtk_examples/VisualizationAlgorithms/probeComb.py
new file mode 100644
index 0000000..0a323a5
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/probeComb.py
@@ -0,0 +1,123 @@
+#!/usr/bin/env python
+
+# This shows how to probe a dataset with a plane. The probed data is
+# then contoured.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Read data.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+
+# We create three planes and position them in the correct position
+# using transform filters. They are then appended together and used as
+# a probe.
+plane = vtk.vtkPlaneSource()
+plane.SetResolution(50, 50)
+transP1 = vtk.vtkTransform()
+transP1.Translate(3.7, 0.0, 28.37)
+transP1.Scale(5, 5, 5)
+transP1.RotateY(90)
+tpd1 = vtk.vtkTransformPolyDataFilter()
+tpd1.SetInputConnection(plane.GetOutputPort())
+tpd1.SetTransform(transP1)
+outTpd1 = vtk.vtkOutlineFilter()
+outTpd1.SetInputConnection(tpd1.GetOutputPort())
+mapTpd1 = vtk.vtkPolyDataMapper()
+mapTpd1.SetInputConnection(outTpd1.GetOutputPort())
+tpd1Actor = vtk.vtkActor()
+tpd1Actor.SetMapper(mapTpd1)
+tpd1Actor.GetProperty().SetColor(0, 0, 0)
+
+transP2 = vtk.vtkTransform()
+transP2.Translate(9.2, 0.0, 31.20)
+transP2.Scale(5, 5, 5)
+transP2.RotateY(90)
+tpd2 = vtk.vtkTransformPolyDataFilter()
+tpd2.SetInputConnection(plane.GetOutputPort())
+tpd2.SetTransform(transP2)
+outTpd2 = vtk.vtkOutlineFilter()
+outTpd2.SetInputConnection(tpd2.GetOutputPort())
+mapTpd2 = vtk.vtkPolyDataMapper()
+mapTpd2.SetInputConnection(outTpd2.GetOutputPort())
+tpd2Actor = vtk.vtkActor()
+tpd2Actor.SetMapper(mapTpd2)
+tpd2Actor.GetProperty().SetColor(0, 0, 0)
+
+transP3 = vtk.vtkTransform()
+transP3.Translate(13.27, 0.0, 33.30)
+transP3.Scale(5, 5, 5)
+transP3.RotateY(90)
+tpd3 = vtk.vtkTransformPolyDataFilter()
+tpd3.SetInputConnection(plane.GetOutputPort())
+tpd3.SetTransform(transP3)
+outTpd3 = vtk.vtkOutlineFilter()
+outTpd3.SetInputConnection(tpd3.GetOutputPort())
+mapTpd3 = vtk.vtkPolyDataMapper()
+mapTpd3.SetInputConnection(outTpd3.GetOutputPort())
+tpd3Actor = vtk.vtkActor()
+tpd3Actor.SetMapper(mapTpd3)
+tpd3Actor.GetProperty().SetColor(0, 0, 0)
+
+appendF = vtk.vtkAppendPolyData()
+appendF.AddInput(tpd1.GetOutput())
+appendF.AddInput(tpd2.GetOutput())
+appendF.AddInput(tpd3.GetOutput())
+
+# The vtkProbeFilter takes two inputs. One is a dataset to use as the
+# probe geometry (SetInput); the other is the data to probe
+# (SetSource). The output dataset structure (geometry and topology) of
+# the probe is the same as the structure of the input. The probing
+# process generates new data values resampled from the source.
+probe = vtk.vtkProbeFilter()
+probe.SetInputConnection(appendF.GetOutputPort())
+probe.SetSource(pl3d.GetOutput())
+
+contour = vtk.vtkContourFilter()
+contour.SetInputConnection(probe.GetOutputPort())
+contour.GenerateValues(50, pl3d.GetOutput().GetScalarRange())
+contourMapper = vtk.vtkPolyDataMapper()
+contourMapper.SetInputConnection(contour.GetOutputPort())
+contourMapper.SetScalarRange(pl3d.GetOutput().GetScalarRange())
+planeActor = vtk.vtkActor()
+planeActor.SetMapper(contourMapper)
+
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+outlineActor.GetProperty().SetColor(0, 0, 0)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+ren.AddActor(outlineActor)
+ren.AddActor(planeActor)
+ren.AddActor(tpd1Actor)
+ren.AddActor(tpd2Actor)
+ren.AddActor(tpd3Actor)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(400, 400)
+
+ren.ResetCamera()
+cam1 = ren.GetActiveCamera()
+cam1.SetClippingRange(3.95297, 50)
+cam1.SetFocalPoint(8.88908, 0.595038, 29.3342)
+cam1.SetPosition(-12.3332, 31.7479, 41.2387)
+cam1.SetViewUp(0.060772, -0.319905, 0.945498)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/probeComb.vt b/examples/vtk_examples/VisualizationAlgorithms/probeComb.vt
new file mode 100644
index 0000000..6b204a6
Binary files /dev/null and b/examples/vtk_examples/VisualizationAlgorithms/probeComb.vt differ
diff --git a/examples/vtk_examples/VisualizationAlgorithms/smoothFran.py b/examples/vtk_examples/VisualizationAlgorithms/smoothFran.py
new file mode 100644
index 0000000..a640e4d
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/smoothFran.py
@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+
+# This example shows how to use decimation to reduce a polygonal
+# mesh. We also use mesh smoothing and generate surface normals to
+# give a pleasing result.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# We start by reading some data that was originally captured from a
+# Cyberware laser digitizing system.
+fran = vtk.vtkPolyDataReader()
+fran.SetFileName(VTK_DATA_ROOT + "/Data/fran_cut.vtk")
+
+# We want to preserve topology (not let any cracks form). This may
+# limit the total reduction possible, which we have specified at 90%.
+deci = vtk.vtkDecimatePro()
+deci.SetInputConnection(fran.GetOutputPort())
+deci.SetTargetReduction(0.9)
+deci.PreserveTopologyOn()
+smoother = vtk.vtkSmoothPolyDataFilter()
+smoother.SetInputConnection(deci.GetOutputPort())
+smoother.SetNumberOfIterations(50)
+normals = vtk.vtkPolyDataNormals()
+normals.SetInputConnection(smoother.GetOutputPort())
+normals.FlipNormalsOn()
+franMapper = vtk.vtkPolyDataMapper()
+franMapper.SetInputConnection(normals.GetOutputPort())
+franActor = vtk.vtkActor()
+franActor.SetMapper(franMapper)
+franActor.GetProperty().SetColor(1.0, 0.49, 0.25)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(franActor)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(250, 250)
+
+cam1 = vtk.vtkCamera()
+cam1.SetClippingRange(0.0475572, 2.37786)
+cam1.SetFocalPoint(0.052665, -0.129454, -0.0573973)
+cam1.SetPosition(0.327637, -0.116299, -0.256418)
+cam1.SetViewUp(-0.0225386, 0.999137, 0.034901)
+ren.SetActiveCamera(cam1)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/smoothFran.vt b/examples/vtk_examples/VisualizationAlgorithms/smoothFran.vt
new file mode 100644
index 0000000..f937bd3
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diff --git a/examples/vtk_examples/VisualizationAlgorithms/spikeF.py b/examples/vtk_examples/VisualizationAlgorithms/spikeF.py
new file mode 100644
index 0000000..d1e97a2
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/spikeF.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+# This example demonstrates the use of glyphing. We also use a mask filter
+# to select a subset of points to glyph.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Read a data file. This originally was a Cyberware laser digitizer scan
+# of Fran J.'s face. Surface normals are generated based on local geometry
+# (i.e., the polygon normals surrounding eash point are averaged). We flip
+# the normals because we want them to point out from Fran's face.
+fran = vtk.vtkPolyDataReader()
+fran.SetFileName(VTK_DATA_ROOT + "/Data/fran_cut.vtk")
+normals = vtk.vtkPolyDataNormals()
+normals.SetInputConnection(fran.GetOutputPort())
+normals.FlipNormalsOn()
+franMapper = vtk.vtkPolyDataMapper()
+franMapper.SetInputConnection(normals.GetOutputPort())
+franActor = vtk.vtkActor()
+franActor.SetMapper(franMapper)
+franActor.GetProperty().SetColor(1.0, 0.49, 0.25)
+
+# We subsample the dataset because we want to glyph just a subset of
+# the points. Otherwise the display is cluttered and cannot be easily
+# read. The RandonModeOn and SetOnRatio combine to random select one out
+# of every 10 points in the dataset.
+ptMask = vtk.vtkMaskPoints()
+ptMask.SetInputConnection(normals.GetOutputPort())
+ptMask.SetOnRatio(10)
+ptMask.RandomModeOn()
+
+# In this case we are using a cone as a glyph. We transform the cone so
+# its base is at 0,0,0. This is the point where glyph rotation occurs.
+cone = vtk.vtkConeSource()
+cone.SetResolution(6)
+transform = vtk.vtkTransform()
+transform.Translate(0.5, 0.0, 0.0)
+transformF = vtk.vtkTransformPolyDataFilter()
+transformF.SetInputConnection(cone.GetOutputPort())
+transformF.SetTransform(transform)
+
+# vtkGlyph3D takes two inputs: the input point set (SetInput) which can be
+# any vtkDataSet; and the glyph (SetSource) which must be a vtkPolyData.
+# We are interested in orienting the glyphs by the surface normals that
+# we previosuly generated.
+glyph = vtk.vtkGlyph3D()
+glyph.SetInputConnection(ptMask.GetOutputPort())
+glyph.SetSource(transformF.GetOutput())
+glyph.SetVectorModeToUseNormal()
+glyph.SetScaleModeToScaleByVector()
+glyph.SetScaleFactor(0.004)
+spikeMapper = vtk.vtkPolyDataMapper()
+spikeMapper.SetInputConnection(glyph.GetOutputPort())
+spikeActor = vtk.vtkActor()
+spikeActor.SetMapper(spikeMapper)
+spikeActor.GetProperty().SetColor(0.0, 0.79, 0.34)
+
+# Create the RenderWindow, Renderer and both Actors
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(franActor)
+ren.AddActor(spikeActor)
+
+renWin.SetSize(500, 500)
+ren.SetBackground(0.1, 0.2, 0.4)
+
+# Set a nice camera position.
+ren.ResetCamera()
+cam1 = ren.GetActiveCamera()
+cam1.Zoom(1.4)
+cam1.Azimuth(110)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/spikeF.vt b/examples/vtk_examples/VisualizationAlgorithms/spikeF.vt
new file mode 100644
index 0000000..c86a655
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diff --git a/examples/vtk_examples/VisualizationAlgorithms/streamSurface.py b/examples/vtk_examples/VisualizationAlgorithms/streamSurface.py
new file mode 100644
index 0000000..19e62e0
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/streamSurface.py
@@ -0,0 +1,81 @@
+#!/usr/bin/env python
+
+# This example demonstrates the generation of a streamsurface.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Read the data and specify which scalars and vectors to read.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+
+# We use a rake to generate a series of streamline starting points
+# scattered along a line. Each point will generate a streamline. These
+# streamlines are then fed to the vtkRuledSurfaceFilter which stitches
+# the lines together to form a surface.
+rake = vtk.vtkLineSource()
+rake.SetPoint1(15, -5, 32)
+rake.SetPoint2(15, 5, 32)
+rake.SetResolution(21)
+rakeMapper = vtk.vtkPolyDataMapper()
+rakeMapper.SetInputConnection(rake.GetOutputPort())
+rakeActor = vtk.vtkActor()
+rakeActor.SetMapper(rakeMapper)
+
+integ = vtk.vtkRungeKutta4()
+sl = vtk.vtkStreamLine()
+sl.SetInputConnection(pl3d.GetOutputPort())
+sl.SetSource(rake.GetOutput())
+sl.SetIntegrator(integ)
+sl.SetMaximumPropagationTime(0.1)
+sl.SetIntegrationStepLength(0.1)
+sl.SetIntegrationDirectionToBackward()
+sl.SetStepLength(0.001)
+
+# The ruled surface stiches together lines with triangle strips.
+# Note the SetOnRatio method. It turns on every other strip that
+# the filter generates (only when multiple lines are input).
+scalarSurface = vtk.vtkRuledSurfaceFilter()
+scalarSurface.SetInputConnection(sl.GetOutputPort())
+scalarSurface.SetOffset(0)
+scalarSurface.SetOnRatio(2)
+scalarSurface.PassLinesOn()
+scalarSurface.SetRuledModeToPointWalk()
+scalarSurface.SetDistanceFactor(30)
+mapper = vtk.vtkPolyDataMapper()
+mapper.SetInputConnection(scalarSurface.GetOutputPort())
+mapper.SetScalarRange(pl3d.GetOutput().GetScalarRange())
+actor = vtk.vtkActor()
+actor.SetMapper(mapper)
+
+# Put an outline around for context.
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+outlineActor.GetProperty().SetColor(0, 0, 0)
+
+# Now create the usual graphics stuff.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+ren.AddActor(rakeActor)
+ren.AddActor(actor)
+ren.AddActor(outlineActor)
+ren.SetBackground(1, 1, 1)
+
+renWin.SetSize(300, 300)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/streamSurface.vt b/examples/vtk_examples/VisualizationAlgorithms/streamSurface.vt
new file mode 100644
index 0000000..6b99abc
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diff --git a/examples/vtk_examples/VisualizationAlgorithms/warpComb.py b/examples/vtk_examples/VisualizationAlgorithms/warpComb.py
new file mode 100644
index 0000000..de5673d
--- /dev/null
+++ b/examples/vtk_examples/VisualizationAlgorithms/warpComb.py
@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+
+# This example demonstrates how to extract "computational planes" from
+# a structured dataset. Structured data has a natural, logical
+# coordinate system based on i-j-k indices. Specifying imin,imax,
+# jmin,jmax, kmin,kmax pairs can indicate a point, line, plane, or
+# volume of data.
+#
+# In this example, we extract three planes and warp them using scalar
+# values in the direction of the local normal at each point. This
+# gives a sort of "velocity profile" that indicates the nature of the
+# flow.
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Here we read data from a annular combustor. A combustor burns fuel
+# and air in a gas turbine (e.g., a jet engine) and the hot gas
+# eventually makes its way to the turbine section.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+
+# Planes are specified using a imin,imax, jmin,jmax, kmin,kmax
+# coordinate specification. Min and max i,j,k values are clamped to 0
+# and maximum value.
+plane = vtk.vtkStructuredGridGeometryFilter()
+plane.SetInputConnection(pl3d.GetOutputPort())
+plane.SetExtent(10, 10, 1, 100, 1, 100)
+plane2 = vtk.vtkStructuredGridGeometryFilter()
+plane2.SetInputConnection(pl3d.GetOutputPort())
+plane2.SetExtent(30, 30, 1, 100, 1, 100)
+plane3 = vtk.vtkStructuredGridGeometryFilter()
+plane3.SetInputConnection(pl3d.GetOutputPort())
+plane3.SetExtent(45, 45, 1, 100, 1, 100)
+
+# We use an append filter because that way we can do the warping,
+# etc. just using a single pipeline and actor.
+appendF = vtk.vtkAppendPolyData()
+appendF.AddInput(plane.GetOutput())
+appendF.AddInput(plane2.GetOutput())
+appendF.AddInput(plane3.GetOutput())
+warp = vtk.vtkWarpScalar()
+warp.SetInputConnection(appendF.GetOutputPort())
+warp.UseNormalOn()
+warp.SetNormal(1.0, 0.0, 0.0)
+warp.SetScaleFactor(2.5)
+normals = vtk.vtkPolyDataNormals()
+normals.SetInput(warp.GetPolyDataOutput())
+normals.SetFeatureAngle(60)
+planeMapper = vtk.vtkPolyDataMapper()
+planeMapper.SetInputConnection(normals.GetOutputPort())
+planeMapper.SetScalarRange(pl3d.GetOutput().GetScalarRange())
+planeActor = vtk.vtkActor()
+planeActor.SetMapper(planeMapper)
+
+# The outline provides context for the data and the planes.
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outline.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+outlineActor.GetProperty().SetColor(0, 0, 0)
+
+# Create the usual graphics stuff.
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+ren.AddActor(outlineActor)
+ren.AddActor(planeActor)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(500, 500)
+
+# Create an initial view.
+cam1 = ren.GetActiveCamera()
+cam1.SetClippingRange(3.95297, 50)
+cam1.SetFocalPoint(8.88908, 0.595038, 29.3342)
+cam1.SetPosition(-12.3332, 31.7479, 41.2387)
+cam1.SetViewUp(0.060772, -0.319905, 0.945498)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VisualizationAlgorithms/warpComb.vt b/examples/vtk_examples/VisualizationAlgorithms/warpComb.vt
new file mode 100644
index 0000000..624b872
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diff --git a/examples/vtk_examples/VolumeRendering/PseudoVolumeRendering.py b/examples/vtk_examples/VolumeRendering/PseudoVolumeRendering.py
new file mode 100644
index 0000000..7c48e49
--- /dev/null
+++ b/examples/vtk_examples/VolumeRendering/PseudoVolumeRendering.py
@@ -0,0 +1,122 @@
+#!/usr/bin/env python
+
+# Perform psuedo volume rendering in a structured grid by compositing
+# translucent cut planes. This same trick can be used for unstructured
+# grids. Note that for better results, more planes can be created. Also,
+# if your data is vtkImageData, there are much faster methods for volume
+# rendering.
+
+import vtk
+from vtk.util.colors import *
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create pipeline. Read structured grid data.
+pl3d = vtk.vtkPLOT3DReader()
+pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
+pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
+pl3d.SetScalarFunctionNumber(100)
+pl3d.SetVectorFunctionNumber(202)
+pl3d.Update()
+
+# A convenience, use this filter to limit data for experimentation.
+extract = vtk.vtkExtractGrid()
+extract.SetVOI(1, 55, -1000, 1000, -1000, 1000)
+extract.SetInputConnection(pl3d.GetOutputPort())
+
+# The (implicit) plane is used to do the cutting
+plane = vtk.vtkPlane()
+plane.SetOrigin(0, 4, 2)
+plane.SetNormal(0, 1, 0)
+
+# The cutter is set up to process each contour value over all cells
+# (SetSortByToSortByCell). This results in an ordered output of polygons
+# which is key to the compositing.
+cutter = vtk.vtkCutter()
+cutter.SetInputConnection(extract.GetOutputPort())
+cutter.SetCutFunction(plane)
+cutter.GenerateCutScalarsOff()
+cutter.SetSortByToSortByCell()
+
+clut = vtk.vtkLookupTable()
+clut.SetHueRange(0, .67)
+clut.Build()
+
+cutterMapper = vtk.vtkPolyDataMapper()
+cutterMapper.SetInputConnection(cutter.GetOutputPort())
+cutterMapper.SetScalarRange(.18, .7)
+cutterMapper.SetLookupTable(clut)
+
+cut = vtk.vtkActor()
+cut.SetMapper(cutterMapper)
+
+# Add in some surface geometry for interest.
+iso = vtk.vtkContourFilter()
+iso.SetInputConnection(pl3d.GetOutputPort())
+iso.SetValue(0, .22)
+normals = vtk.vtkPolyDataNormals()
+normals.SetInputConnection(iso.GetOutputPort())
+normals.SetFeatureAngle(45)
+isoMapper = vtk.vtkPolyDataMapper()
+isoMapper.SetInputConnection(normals.GetOutputPort())
+isoMapper.ScalarVisibilityOff()
+isoActor = vtk.vtkActor()
+isoActor.SetMapper(isoMapper)
+isoActor.GetProperty().SetDiffuseColor(tomato)
+isoActor.GetProperty().SetSpecularColor(white)
+isoActor.GetProperty().SetDiffuse(.8)
+isoActor.GetProperty().SetSpecular(.5)
+isoActor.GetProperty().SetSpecularPower(30)
+
+outline = vtk.vtkStructuredGridOutlineFilter()
+outline.SetInputConnection(pl3d.GetOutputPort())
+outlineTubes = vtk.vtkTubeFilter()
+outlineTubes.SetInputConnection(outline.GetOutputPort())
+outlineTubes.SetRadius(.1)
+
+outlineMapper = vtk.vtkPolyDataMapper()
+outlineMapper.SetInputConnection(outlineTubes.GetOutputPort())
+outlineActor = vtk.vtkActor()
+outlineActor.SetMapper(outlineMapper)
+
+# Create the RenderWindow, Renderer and Interactor
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Add the actors to the renderer, set the background and size
+ren.AddActor(outlineActor)
+outlineActor.GetProperty().SetColor(banana)
+ren.AddActor(isoActor)
+isoActor.VisibilityOn()
+ren.AddActor(cut)
+opacity = .1
+cut.GetProperty().SetOpacity(1)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(640, 480)
+
+cam1 = ren.GetActiveCamera()
+cam1.SetClippingRange(3.95297, 50)
+cam1.SetFocalPoint(9.71821, 0.458166, 29.3999)
+cam1.SetPosition(2.7439, -37.3196, 38.7167)
+cam1.ComputeViewPlaneNormal()
+cam1.SetViewUp(-0.16123, 0.264271, 0.950876)
+
+# Cut: generates n cut planes normal to camera's view plane
+def Cut(n):
+ global cam1, opacity
+ plane.SetNormal(cam1.GetViewPlaneNormal())
+ plane.SetOrigin(cam1.GetFocalPoint())
+ cutter.GenerateValues(n, -5, 5)
+ clut.SetAlphaRange(opacity, opacity)
+ renWin.Render()
+
+
+# Generate 10 cut planes
+Cut(20)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VolumeRendering/PseudoVolumeRendering.vt b/examples/vtk_examples/VolumeRendering/PseudoVolumeRendering.vt
new file mode 100644
index 0000000..1f61c06
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diff --git a/examples/vtk_examples/VolumeRendering/SimpleRayCast.py b/examples/vtk_examples/VolumeRendering/SimpleRayCast.py
new file mode 100644
index 0000000..6032523
--- /dev/null
+++ b/examples/vtk_examples/VolumeRendering/SimpleRayCast.py
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+
+# This is a simple volume rendering example that uses a
+# vtkVolumeRayCast mapper
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create the standard renderer, render window and interactor
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Create the reader for the data
+reader = vtk.vtkStructuredPointsReader()
+reader.SetFileName(VTK_DATA_ROOT + "/Data/ironProt.vtk")
+
+# Create transfer mapping scalar value to opacity
+opacityTransferFunction = vtk.vtkPiecewiseFunction()
+opacityTransferFunction.AddPoint(20, 0.0)
+opacityTransferFunction.AddPoint(255, 0.2)
+
+# Create transfer mapping scalar value to color
+colorTransferFunction = vtk.vtkColorTransferFunction()
+colorTransferFunction.AddRGBPoint(0.0, 0.0, 0.0, 0.0)
+colorTransferFunction.AddRGBPoint(64.0, 1.0, 0.0, 0.0)
+colorTransferFunction.AddRGBPoint(128.0, 0.0, 0.0, 1.0)
+colorTransferFunction.AddRGBPoint(192.0, 0.0, 1.0, 0.0)
+colorTransferFunction.AddRGBPoint(255.0, 0.0, 0.2, 0.0)
+
+# The property describes how the data will look
+volumeProperty = vtk.vtkVolumeProperty()
+volumeProperty.SetColor(colorTransferFunction)
+volumeProperty.SetScalarOpacity(opacityTransferFunction)
+volumeProperty.ShadeOn()
+volumeProperty.SetInterpolationTypeToLinear()
+
+# The mapper / ray cast function know how to render the data
+compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
+volumeMapper = vtk.vtkVolumeRayCastMapper()
+volumeMapper.SetVolumeRayCastFunction(compositeFunction)
+volumeMapper.SetInputConnection(reader.GetOutputPort())
+
+# The volume holds the mapper and the property and
+# can be used to position/orient the volume
+volume = vtk.vtkVolume()
+volume.SetMapper(volumeMapper)
+volume.SetProperty(volumeProperty)
+
+ren.AddVolume(volume)
+ren.SetBackground(1, 1, 1)
+renWin.SetSize(600, 600)
+renWin.Render()
+
+def CheckAbort(obj, event):
+ if obj.GetEventPending() != 0:
+ obj.SetAbortRender(1)
+
+renWin.AddObserver("AbortCheckEvent", CheckAbort)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VolumeRendering/SimpleRayCast.vt b/examples/vtk_examples/VolumeRendering/SimpleRayCast.vt
new file mode 100644
index 0000000..7cebbd6
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diff --git a/examples/vtk_examples/VolumeRendering/SimpleTextureMap2D.py b/examples/vtk_examples/VolumeRendering/SimpleTextureMap2D.py
new file mode 100644
index 0000000..997f994
--- /dev/null
+++ b/examples/vtk_examples/VolumeRendering/SimpleTextureMap2D.py
@@ -0,0 +1,60 @@
+#!/usr/bin/env python
+
+# This is a simple volume rendering example that uses a
+# vtkVolumeTextureMapper2D mapper
+
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create the standard renderer, render window and interactor
+ren = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Create the reader for the data
+reader = vtk.vtkStructuredPointsReader()
+reader.SetFileName(VTK_DATA_ROOT + "/Data/ironProt.vtk")
+
+# Create transfer mapping scalar value to opacity
+opacityTransferFunction = vtk.vtkPiecewiseFunction()
+opacityTransferFunction.AddPoint(20, 0.0)
+opacityTransferFunction.AddPoint(255, 0.2)
+
+# Create transfer mapping scalar value to color
+colorTransferFunction = vtk.vtkColorTransferFunction()
+colorTransferFunction.AddRGBPoint(0.0, 0.0, 0.0, 0.0)
+colorTransferFunction.AddRGBPoint(64.0, 1.0, 0.0, 0.0)
+colorTransferFunction.AddRGBPoint(128.0, 0.0, 0.0, 1.0)
+colorTransferFunction.AddRGBPoint(192.0, 0.0, 1.0, 0.0)
+colorTransferFunction.AddRGBPoint(255.0, 0.0, 0.2, 0.0)
+
+# The property describes how the data will look
+volumeProperty = vtk.vtkVolumeProperty()
+volumeProperty.SetColor(colorTransferFunction)
+volumeProperty.SetScalarOpacity(opacityTransferFunction)
+
+# The mapper knows how to render the data
+volumeMapper = vtk.vtkVolumeTextureMapper2D()
+volumeMapper.SetInputConnection(reader.GetOutputPort())
+
+# The volume holds the mapper and the property and can be used to
+# position/orient the volume
+volume = vtk.vtkVolume()
+volume.SetMapper(volumeMapper)
+volume.SetProperty(volumeProperty)
+
+ren.AddVolume(volume)
+renWin.Render()
+
+def CheckAbort(obj, event):
+ if obj.GetEventPending() != 0:
+ obj.SetAbortRender(1)
+
+renWin.AddObserver("AbortCheckEvent", CheckAbort)
+
+iren.Initialize()
+renWin.Render()
+iren.Start()
diff --git a/examples/vtk_examples/VolumeRendering/SimpleTextureMap2D.vt b/examples/vtk_examples/VolumeRendering/SimpleTextureMap2D.vt
new file mode 100644
index 0000000..2b8ef23
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diff --git a/examples/vtk_http.vt b/examples/vtk_http.vt
new file mode 100644
index 0000000..e006f58
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diff --git a/extensions/http/README b/extensions/http/README
new file mode 100644
index 0000000..5ef9690
--- /dev/null
+++ b/extensions/http/README
@@ -0,0 +1,11 @@
+This folder contains files for adding vistrails to a regular web server.
+
+Just copy all the files in this directory to the folder where your web server
+files are located.
+Rename config.php.sample to config.php and modify it according to your server
+installation.
+
+More information is documented in the files.
+
+
+
diff --git a/extensions/http/config.php.sample b/extensions/http/config.php.sample
new file mode 100644
index 0000000..ca03a09
--- /dev/null
+++ b/extensions/http/config.php.sample
@@ -0,0 +1,82 @@
+<?php
+////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (C) 2011-2014, NYU-Poly.
+// Copyright (C) 2006-2011, University of Utah.
+// All rights reserved.
+// Contact: contact at vistrails.org
+//
+// This file is part of VisTrails.
+//
+// "Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// - Redistributions of source code must retain the above copyright notice,
+// this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// - Neither the name of the University of Utah nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+// THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+//
+////////////////////////////////////////////////////////////////////////////
+//This file will store the configuration of your server
+// it will be used by all the other php scripts
+// Rename this file to config.php
+
+//This is where the RPC-XML server is running
+$VT_HOST = "localhost";
+$VT_PORT = 8080;
+
+//This controls how VisTrails will be accessed
+//Set it to false if you plan to execute in the command line
+$USE_VISTRAILS_XML_RPC_SERVER = True;
+
+//Set this to False if VisTrails server runs on a different machine
+$USE_LOCAL_VISTRAILS_SERVER = True;
+
+// Change this to point to the folder where run.py is
+// You won't need this if $USE_VISTRAILS_XML_RPC_SERVER is set to True
+// Used in run_vistrails.php
+$PATH_TO_VISTRAILS = '/vistrails/v1.2/vistrails';
+
+// Change this to point to the folder where the images should be generated
+// absoulte path should be used
+$PATH_TO_IMAGES = '/path/to/images/';
+
+// Change this to the web accessible path to the folder where the images were generated
+// Something like http://your.url.com$WEB_PATH_TO_IMAGES
+$WEB_PATH_TO_IMAGES = '/images/';
+
+// Change this to point to the folder where the workflow graphs should be generated
+// absoulte path should be used
+$PATH_TO_GRAPHS = '/path/to/graphs/';
+
+// Change this to the full url pointing to the root where the graphs were generated
+$URL_TO_GRAPHS = "http://your.domain.com/path/to/graphs/";
+
+// Change this to the full url pointing to the download.php script
+$URL_TO_DOWNLOAD = "http://your.domain.com/path/to/download.php";
+
+// Default configuration variables for database
+// They can be changed through the requests in the scripts
+// default database host
+$DB_HOST = 'your.hostname.com';
+// default databse port
+$DB_PORT = '3306';
+// default database name
+$DB_NAME = 'vistrails';
+?>
diff --git a/extensions/http/get_db_vistrail_list.php b/extensions/http/get_db_vistrail_list.php
new file mode 100644
index 0000000..d5830d2
--- /dev/null
+++ b/extensions/http/get_db_vistrail_list.php
@@ -0,0 +1,82 @@
+<?php
+////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (C) 2011-2014, NYU-Poly.
+// Copyright (C) 2006-2011, University of Utah.
+// All rights reserved.
+// Contact: contact at vistrails.org
+//
+// This file is part of VisTrails.
+//
+// "Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// - Redistributions of source code must retain the above copyright notice,
+// this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// - Neither the name of the University of Utah nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+// THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+//
+////////////////////////////////////////////////////////////////////////////
+
+// This file will connect to VisTrails Server and return a page containing the
+// list of vistrails available on the database
+// The url should follow this format:
+// run_vistrails.php?host=vistrails.org&db=vistrails
+// host and db are optional and you can set the default values below
+// if the port is different from the dafault you can also pass the new value on
+// the url
+
+//functions.php is located inside the ./mediawiki folder
+require_once 'functions.php';
+require_once 'config.php';
+
+// set variables with default values
+$host = $DB_HOST;
+$port = $DB_PORT;
+$dbname = $DB_NAME;
+$username = "vtserver";
+
+//Get the variables from the url
+if(array_key_exists('host', $_GET))
+ $host = $_GET['host'];
+if(array_key_exists('db',$_GET))
+ $dbname = $_GET['db'];
+if(array_key_exists('port',$_GET))
+ $port = $_GET['port'];
+
+
+//echo $host . $port . $dbname;
+$request = xmlrpc_encode_request('get_db_vt_list_xml',array($host, $port, $dbname));
+$response = do_call($VT_HOST,$VT_PORT,$request);
+$response = html_entity_decode($response);
+header("Content-Type: text/xml");
+clean_up($response);
+
+
+function clean_up($xmlstring){
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ echo '<?xml version="1.0"?> '."\n";
+ echo $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->string[0]->vistrails[0]->asXML();
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+
+?>
diff --git a/extensions/http/get_vt_xml.php b/extensions/http/get_vt_xml.php
new file mode 100644
index 0000000..e2534b7
--- /dev/null
+++ b/extensions/http/get_vt_xml.php
@@ -0,0 +1,89 @@
+<?php
+////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (C) 2011-2014, NYU-Poly.
+// Copyright (C) 2006-2011, University of Utah.
+// All rights reserved.
+// Contact: contact at vistrails.org
+//
+// This file is part of VisTrails.
+//
+// "Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// - Redistributions of source code must retain the above copyright notice,
+// this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// - Neither the name of the University of Utah nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+// THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+//
+////////////////////////////////////////////////////////////////////////////
+
+// This file will connect to vistrails XML RPC server and return a vistrail in
+// xml format
+// The url should follow this format:
+// get_vt_xml.php?host=vistrails.org&db=vistrails&vt=8
+// host and dbname are optional and you can set the default values below
+// if the port is different from the dafault you can also pass the new value on
+// the url
+//functions.php is located inside the ./mediawiki folder
+require_once 'functions.php';
+require_once 'config.php';
+
+// set variables with default values
+$host = $DB_HOST;
+$port = $DB_PORT;
+$dbname = $DB_NAME;
+$vtid = '';
+$username = "vtserver";
+
+//Get the variables from the url
+if(array_key_exists('host', $_GET))
+ $host = $_GET['host'];
+if(array_key_exists('db',$_GET))
+ $dbname = $_GET['db'];
+if(array_key_exists('port',$_GET))
+ $port = $_GET['port'];
+if(array_key_exists('vt',$_GET))
+ $vtid = $_GET['vt'];
+
+//Check if vtid was provided
+//echo $vtid;
+if($vtid != ''){
+ //echo $host . $port . $dbname . $vtid . $destdit . $version;
+ $request = xmlrpc_encode_request('get_vt_xml',
+ array($host, $port, $dbname, $vtid));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $response = html_entity_decode($response);
+ header("Content-Type: text/xml");
+ clean_up($response);
+}
+else{
+ echo "ERROR: Vistrails id not provided.\n";
+}
+
+function clean_up($xmlstring){
+ try{
+ $node = new SimpleXMLElement($xmlstring);
+ echo '<?xml version="1.0"?> '."\n";
+ echo $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->string[0]->vistrail[0]->asXML();
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+?>
diff --git a/extensions/http/get_wf_pdf.php b/extensions/http/get_wf_pdf.php
new file mode 100644
index 0000000..9937b57
--- /dev/null
+++ b/extensions/http/get_wf_pdf.php
@@ -0,0 +1,137 @@
+<?php
+////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (C) 2011-2014, NYU-Poly.
+// Copyright (C) 2006-2011, University of Utah.
+// All rights reserved.
+// Contact: contact at vistrails.org
+//
+// This file is part of VisTrails.
+//
+// "Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// - Redistributions of source code must retain the above copyright notice,
+// this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// - Neither the name of the University of Utah nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+// THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+//
+////////////////////////////////////////////////////////////////////////////
+
+// This file will connect to VisTrails XML RPC Server and return the url for
+// the pdf file of a workflow.
+// The url should follow this format:
+// get_wf_pdf.php?host=vistrails.org&db=vistrails&vt=8&version=598
+// host and dbname are optional and you can set the default values below
+// if the port is different from the dafault you can also pass the new value on
+// the url
+
+//functions.php is located inside the ./mediawiki folder
+require_once 'functions.php';
+require_once 'config.php';
+
+// set variables with default values
+$host = $DB_HOST;
+$port = $DB_PORT;
+$dbname = $DB_NAME;
+$vtid = '';
+$version = '';
+$username = "vtserver";
+$version_tag = '';
+
+//Get the variables from the url
+if(array_key_exists('host', $_GET))
+ $host = $_GET['host'];
+if(array_key_exists('db',$_GET))
+ $dbname = $_GET['db'];
+if(array_key_exists('port',$_GET))
+ $port = $_GET['port'];
+if(array_key_exists('vt',$_GET))
+ $vtid = $_GET['vt'];
+if(array_key_exists('version',$_GET))
+ $version = $_GET['version'];
+if(array_key_exists('tag',$_GET)){
+ $version_tag = $_GET['tag'];
+ if ($version_tag != ''){
+ $request = xmlrpc_encode_request('get_tag_version',
+ array($host, $port, $dbname, $vtid,
+ $version_tag));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $version = get_version_from_response($response);
+ }
+}
+if(array_key_exists('buildalways',$_GET))
+ $force_build = (bool) $_GET['buildalways'];
+
+//echo $force_build;
+
+//Check if vtid and version were provided
+//echo $vtid . $version;
+if($vtid != '' and $version != ''){
+ //echo $host . $port . $dbname . $vtid . $version;
+ $filename = md5($host . '_'. $dbname .'_' . $port .'_' .$vtid . '_' . $version);
+ $filename = 'workflows/'.$filename . ".pdf";
+ $fullpath = $PATH_TO_GRAPHS. $filename;
+ $cached = file_exists($fullpath);
+ if($USE_LOCAL_VISTRAILS_SERVER or
+ (!$cached or strcasecmp($force_build,'True') == 0)) {
+ $request = xmlrpc_encode_request('get_wf_graph_pdf',
+ array($host, $port, $dbname, $vtid, $version,
+ $USE_LOCAL_VISTRAILS_SERVER));
+ //echo $request;
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $path = clean_up($response, $filename);
+ } else {
+ $path = $filename;
+ }
+ echo "$URL_TO_GRAPHS$path";
+}
+else{
+ echo "ERROR: Vistrails id or version not provided.\n";
+}
+
+function get_version_from_response($xmlstring){
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ return $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->int[0];
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+
+function clean_up($xmlstring, $filename=""){
+ global $PATH_TO_GRAPHS, $USE_LOCAL_VISTRAILS_SERVER;
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ if ($USE_LOCAL_VISTRAILS_SERVER)
+ return $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->string[0];
+ else{
+ $contents = $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->base64[0];
+ $fileHandle = fopen($PATH_TO_GRAPHS. $filename, 'wb') or die("can't open file");
+ fputs($fileHandle, base64_decode($contents));
+ fclose($fileHandle);
+ return $filename;
+ }
+
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+
+?>
diff --git a/extensions/http/get_wf_xml.php b/extensions/http/get_wf_xml.php
new file mode 100644
index 0000000..6e1a59d
--- /dev/null
+++ b/extensions/http/get_wf_xml.php
@@ -0,0 +1,118 @@
+<?php
+////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (C) 2011-2014, NYU-Poly.
+// Copyright (C) 2006-2011, University of Utah.
+// All rights reserved.
+// Contact: contact at vistrails.org
+//
+// This file is part of VisTrails.
+//
+// "Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// - Redistributions of source code must retain the above copyright notice,
+// this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// - Neither the name of the University of Utah nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+// THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+//
+////////////////////////////////////////////////////////////////////////////
+
+// This file will connect to VisTrails XML RPC Server and return a workflow
+// in XML format
+// The url should follow this format:
+// get_wf_xml.php?host=vistrails.org&db=vistrails&vt=8&version=598
+// host and dbname are optional and you can set the default values below
+// if the port is different from the dafault you can also pass the new value on
+// the url
+
+//functions.php is located inside the ./mediawiki folder
+require_once 'functions.php';
+require_once 'config.php';
+
+// set variables with default values
+$host = $DB_HOST;
+$port = $DB_PORT;
+$dbname = $DB_NAME;
+$vtid = '';
+$version = '';
+$username = "vtserver";
+$version_tag = '';
+
+//Get the variables from the url
+if(array_key_exists('host', $_GET))
+ $host = $_GET['host'];
+if(array_key_exists('db',$_GET))
+ $dbname = $_GET['db'];
+if(array_key_exists('port',$_GET))
+ $port = $_GET['port'];
+if(array_key_exists('vt',$_GET))
+ $vtid = $_GET['vt'];
+if(array_key_exists('version',$_GET))
+ $version = $_GET['version'];
+if(array_key_exists('tag',$_GET)){
+ $version_tag = $_GET['tag'];
+ if ($version_tag != ''){
+ $request = xmlrpc_encode_request('get_tag_version',array($host, $port,
+ $dbname, $vtid,
+ $version_tag));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $version = get_version_from_response($response);
+ }
+}
+if(array_key_exists('buildalways',$_GET))
+ $force_build = (bool) $_GET['buildalways'];
+
+//echo $force_build;
+
+//Check if vtid and version were provided
+//echo $vtid . $version;
+if($vtid != '' and $version != ''){
+ //echo $host . $port . $dbname . $vtid . $version;
+ $request = xmlrpc_encode_request('get_wf_xml',
+ array($host, $port, $dbname, $vtid, $version));
+ //echo $request;
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $response = html_entity_decode($response);
+ header("Content-Type: text/xml");
+ clean_up($response);
+}
+else{
+ echo "ERROR: Vistrails id or version not provided.\n";
+}
+
+function get_version_from_response($xmlstring){
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ return $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->int[0];
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+
+function clean_up($xmlstring){
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ echo '<?xml version="1.0"?> '."\n";
+ echo $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->string[0]->workflow[0]->asXML();
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+?>
diff --git a/extensions/http/run_vistrails.php b/extensions/http/run_vistrails.php
new file mode 100644
index 0000000..b6fc09c
--- /dev/null
+++ b/extensions/http/run_vistrails.php
@@ -0,0 +1,270 @@
+<?php
+////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (C) 2011-2014, NYU-Poly.
+// Copyright (C) 2006-2011, University of Utah.
+// All rights reserved.
+// Contact: contact at vistrails.org
+//
+// This file is part of VisTrails.
+//
+// "Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// - Redistributions of source code must retain the above copyright notice,
+// this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// - Neither the name of the University of Utah nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+// THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+//
+////////////////////////////////////////////////////////////////////////////
+
+// This file will execute vistrails and return a page containing the images
+// generated.
+// The url should follow this format:
+// run_vistrails.php?host=vistrails.org&db=vistrails&vt=8&version=598
+// host and dbname are optional and you can set the default values below
+// if the port is different from the dafault you can also pass the new value on
+// the url
+//functions.php is located inside the ./mediawiki folder
+require_once 'functions.php';
+require_once 'config.php';
+
+$SUPPORTED_IMAGE_FILES = array("png", "jpg", "gif");
+
+// set variables with default values
+$host = $DB_HOST;
+$port = $DB_PORT;
+$dbname = $DB_NAME;
+$vtid = '';
+$version = '';
+$username = "vtserver";
+$version_tag = '';
+$force_build = 'False';
+$pdf= 'False';
+$showtree = 'False';
+$showworkflow = 'False';
+
+//Get the variables from the url
+if(array_key_exists('host', $_GET))
+ $host = $_GET['host'];
+if(array_key_exists('db',$_GET))
+ $dbname = $_GET['db'];
+if(array_key_exists('port',$_GET))
+ $port = $_GET['port'];
+if(array_key_exists('vt',$_GET))
+ $vtid = $_GET['vt'];
+if(array_key_exists('version',$_GET))
+ $version = $_GET['version'];
+if(array_key_exists('tag',$_GET)){
+ $version_tag = $_GET['tag'];
+ if ($version_tag != ''){
+ $request = xmlrpc_encode_request('get_tag_version',array($host, $port,
+ $dbname, $vtid,
+ $version_tag));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $version = get_version_from_response($response);
+ }
+}
+if(array_key_exists('buildalways',$_GET))
+ $force_build = $_GET['buildalways'];
+
+if(array_key_exists('pdf',$_GET))
+ $pdf = $_GET['pdf'];
+if(array_key_exists('showworkflow',$_GET))
+ $showworkflow = $_GET['showworkflow'];
+
+if(array_key_exists('showtree',$_GET))
+ $showtree = $_GET['showtree'];
+
+//echo $force_build;
+
+//Check if vtid and version were provided
+if(($vtid != '' and $version != '') or
+ ($vtid != '' and strcasecmp($showtree,'True') == 0)){
+ $pdf_bool = False;
+ $pdf_tag = '';
+ if (strcasecmp($pdf,'True') == 0){
+ $pdf_bool = True;
+ $pdf_tag = '_pdf';
+ }
+ $build_always_bool = False;
+ if (strcasecmp($force_build,'True') == 0)
+ $build_always_bool = True;
+ if (strcasecmp($showtree,'True') == 0){
+ $filename = md5($host . '_'. $dbname .'_' . $port .'_' .$vtid);
+ if ($pdf_bool == True){
+ $func = "get_vt_graph_pdf";
+ $filename = 'vistrails/'.$filename . ".pdf";
+ } else {
+ $func = "get_vt_graph_png";
+ $filename = 'vistrails/'.$filename . ".png";
+ }
+ $request = xmlrpc_encode_request($func, array($host,
+ $port,
+ $dbname,
+ $vtid,
+ $USE_VISTRAILS_XML_RPC_SERVER));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $result = clean_up($response, $filename);
+ if ($pdf_bool == True)
+ $res = '<a href="' . $URL_TO_GRAPHS . $result .
+ '">' . $result . '</a>';
+ else
+ $res = '<img src="'. $URL_TO_GRAPHS . $result.
+ "\" alt=\"vt_id:$vtid\" />";
+ echo $res;
+ }
+ elseif (strcasecmp($showworkflow,'True') == 0){
+ $filename = md5($host . '_'. $dbname .'_' . $port .'_' .$vtid . '_' . $version);
+ if ($pdf_bool == True){
+ $func = "get_wf_graph_pdf";
+ $filename = 'workflows/'.$filename . ".pdf";
+ } else {
+ $func = "get_wf_graph_png";
+ $filename = 'workflows/'.$filename . ".png";
+ }
+ $fullpath = $PATH_TO_GRAPHS. $filename;
+ $cached = file_exists($fullpath);
+ if($USE_LOCAL_VISTRAILS_SERVER or
+ (!$cached or strcasecmp($force_build,'True') == 0)) {
+ $request = xmlrpc_encode_request($func, array($host,
+ $port,
+ $dbname,
+ $vtid,
+ $version));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $result = clean_up($response, $filename);
+ } else {
+ $result = $filename;
+ }
+ if ($pdf_bool == True)
+ $res = '<a href="' . $URL_TO_GRAPHS . $result .
+ '">' . $result . '</a>';
+ else
+ $res = '<img src="'. $URL_TO_GRAPHS . $result.
+ "\" alt=\"vt_id:$vtid version:$version\" />";
+ echo $res;
+ }
+ else{
+ $destdir = $PATH_TO_IMAGES;
+ $destversion = $host . '_'. $dbname .'_' . $port . '_' .$vtid . '_' .
+ $version. $pdf_tag;
+ $destversion = md5($destversion);
+ $destdir = $destdir . $destversion;
+ $result = '';
+ if((!path_exists_and_not_empty($destdir)) or strcasecmp($force_build,'True') == 0) {
+ if (!file_exists($destdir)){
+ mkdir($destdir);//,0770);
+ chmod($destdir,0770);
+ }
+
+ $request = xmlrpc_encode_request('run_from_db',
+ array($host, $port, $dbname, $vtid,
+ $destdir, $version, $pdf_bool,
+ '', $build_always_bool, '',
+ $USE_LOCAL_VISTRAILS_SERVER));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $result = multiple_clean_up($response, $destdir);
+ //echo $result;
+ }
+ $files = scandir($destdir);
+ $n = sizeof($files);
+ if ($n > 2){
+ $res = '';
+ foreach($files as $filename) {
+ if($filename != '.' and $filename != '..'){
+ $info = pathinfo($filename);
+ if ( in_arrayi($info['extension'],$SUPPORTED_IMAGE_FILES)){
+ list($width, $height, $type, $attr) = getimagesize($destdir.'/'.$filename);
+ if ($width > 600)
+ $width = 600;
+ $res = $res . '<img src="'. $WEB_PATH_TO_IMAGES . $destversion.'/'.$filename.
+ "\" alt=\"vt_id:$vtid version:$version\" width=\"$width\"/>";
+ }
+ else{
+ //create an href tag
+ $res = $res . '<a href="' . $WEB_PATH_TO_IMAGES .
+ $destversion.'/'.$filename.'">' . $filename . '</a>';
+ }
+ }
+ }
+ echo $res;
+ }
+ else{
+ echo "ERROR: Vistrails didn't produce any image.\n";
+ echo "This is the output: \n".$result;
+ }
+ }
+}
+else{
+ echo "ERROR: Vistrails id or version not provided.\n";
+}
+
+function get_version_from_response($xmlstring){
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ return $node->params[0]->param[0]->value[0]->int[0];
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+
+function clean_up($xmlstring, $filename=""){
+ global $PATH_TO_GRAPHS, $USE_LOCAL_VISTRAILS_SERVER;
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ if ($USE_LOCAL_VISTRAILS_SERVER)
+ return $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->string[0];
+ else{
+ $contents = $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->base64[0];
+ $fileHandle = fopen($PATH_TO_GRAPHS. $filename, 'wb') or die("can't open file");
+ fputs($fileHandle, base64_decode($contents));
+ fclose($fileHandle);
+ return $filename;
+ }
+
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+
+function multiple_clean_up($xmlstring, $destdir=""){
+ global $USE_LOCAL_VISTRAILS_SERVER;
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ //var_dump($node);
+ if ($USE_LOCAL_VISTRAILS_SERVER)
+ return $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->string[0];
+ else{
+ $contents = $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->struct[0];
+ foreach ($contents as $value){
+ $image_name = (string) $value->name[0];
+ $image_contents = (string) $value->value[0]->base64[0];
+ $fileHandle = fopen($destdir.'/'. $image_name, 'wb') or die("can't open file");
+ fputs($fileHandle, base64_decode($image_contents));
+ fclose($fileHandle);
+ }
+ return $destdir;
+ }
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+
+?>
diff --git a/extensions/latex/Makefile b/extensions/latex/Makefile
new file mode 100644
index 0000000..535fae2
--- /dev/null
+++ b/extensions/latex/Makefile
@@ -0,0 +1,16 @@
+all: example example2 head
+
+example:
+ pdflatex -shell-escape example
+
+example2:
+ pdflatex -shell-escape example2
+ bibtex example2
+ pdflatex -shell-escape example2
+ pdflatex -shell-escape example2
+
+head:
+ pdflatex -shell-escape head
+
+clean:
+ \rm example.pdf example2.pdf head.pdf *.aux *.bbl *.blg *.log *~ *.cmdline *.cmdline.* example.out example2.out head.out
diff --git a/extensions/latex/README b/extensions/latex/README
new file mode 100644
index 0000000..dd30888
--- /dev/null
+++ b/extensions/latex/README
@@ -0,0 +1,91 @@
+This directory contains the vistrails package for latex.
+
+It allows you to include the image generated by vistrails
+by calling vistrails directly.
+
+To use it, copy vistrails.sty and includevistrail.py to the same
+place where your .tex files are.
+
+add the following lines to the beginning of the latex file:
+
+\usepackage{vistrails}
+
+If you want to run a local copy of vistrails (see head.tex file for instructions on the different platforms and versions of latex):
+
+\renewcommand{\vistrailspath}{/path/to/run.py}
+
+If you want to use a media wiki server (see http://www.vistrails.org/usersguide/v2.0/html/latex.html for instructions on how to set up the server), add the following to your tex file:
+
+\renewcommand{\vistrailspath}{http://yourwebserver.somethingelse/run_vistrails.php}
+
+To embed the links in the generated images, use
+\renewcommand{\vistrailsdownload}{http://yourwebserver.somethingelse/download.php}
+or just set to empty to make the images not clickable:
+\renewcommand{\vistrailsdownload}{}
+
+This extension uses python. If you don't have python on your path, use this
+to set the python interpreter:
+
+\renewcommand{\vistrailspythonpath}{python}
+
+
+Then include the following command where you would like to include
+the vistrails images:
+
+\vistrails[host=<your_host>,
+db=vistrails,
+version=<version_number>,
+vtid=<vistrails_id>,
+tag=<tag>
+port=3306,
+buildalways, %will force execution or download
+execute, % vistrails will execute the workflow after the user opens it after clicking on the image
+showspreadsheetonly, % only the spreadsheet will be shown when the user opens the workflow
+pdf, % download images as pdf files
+showworkflow, % show the workflow instead of the results
+showtree, % show version tree instead of the results
+getvtl, % will also download the vistrail/workflow
+]{width=0.45\linewidth}
+
+The tag, port, buildalways, execute, showspreadsheetonly and pdf options are optional.
+The default value for port is 3306.
+If buildalways is provided it will always call
+vistrails, even if it was already called once for the same combination
+of host, db, version, port and vt_id.
+If tag is provided, version can be ommitted and buildalways is implicit.
+execute and showspreasheetonly will affect the link on the generated pdf. If
+execute is provided the workflow will be execute when open, and
+showspreadsheetonly will show initially only the spreadsheet.
+pdf will return the results from the spreadsheet as pdf files
+
+The options inside { } are the options you would give to
+\includegraphics{} command
+
+After running at least once, VisTrails will cache the images and latex
+instructions.
+The latex code will be in the "cached" folder and the images in
+vistrails_images.
+
+If you set the \vistrailspythonpath to a invalid path VisTrails will use
+the cached files.
+
+The option -shell-escape needs to be activated on the latex command line:
+
+pdflatex -shell-escape example.tex
+
+Vistrails will create in the current directory a directory called
+vistrails_images/host_db_vtid_version with the png files generated by
+the spreadsheet.
+
+See head.tex for a complete example of usage.
+
+It is also possible to embed workflow results stored in crowdlabs.org
+
+To use it, copy crowdlabs.sty and includecrowdlabs.py to the same
+place where your .tex files are. Do not use this in conjunction with the vistrails extension.
+
+add the following lines to the beginning of the latex file:
+
+\usepackage{crowdlabs}
+
+Then go to crowdlabs.org and visit the page of the workflow you want to embed and copy the embed to Latex snippet.
diff --git a/extensions/latex/crowdlabs.sty b/extensions/latex/crowdlabs.sty
new file mode 100644
index 0000000..a9ef2f7
--- /dev/null
+++ b/extensions/latex/crowdlabs.sty
@@ -0,0 +1,105 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% Copyright (C) 2011-2014, NYU-Poly.
+%% Copyright (C) 2006-2011, University of Utah.
+%% All rights reserved.
+%% Contact: contact at vistrails.org
+%%
+%% This file is part of VisTrails.
+%%
+%% "Redistribution and use in source and binary forms, with or without
+%% modification, are permitted provided that the following conditions are met:
+%%
+%% - Redistributions of source code must retain the above copyright notice,
+%% this list of conditions and the following disclaimer.
+%% - Redistributions in binary form must reproduce the above copyright
+%% notice, this list of conditions and the following disclaimer in the
+%% documentation and/or other materials provided with the distribution.
+%% - Neither the name of the University of Utah nor the names of its
+%% contributors may be used to endorse or promote products derived from
+%% this software without specific prior written permission.
+%%
+%% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+%% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+%% THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+%% PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+%% CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+%% EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+%% PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+%% OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+%% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+%% OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+%% ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% Note: shell-escape needs to be activated for this to work.
+%% This can either be done by passing -shell-escape as an option to
+%% latex or by adding/changing "shell_escape = t" in your texmf.cnf .
+
+\NeedsTeXFormat{LaTeX2e}[1994/12/01]
+\ProvidesPackage{crowdlabs}[2013/06/07 v0.2 CrowdLabs in LaTeX]
+
+%% keyval package allows us to define arguments in a command as key-value pairs,
+%% which is more convenient
+
+\RequirePackage{graphicx,keyval,ifthen}
+
+%% This is to hide the border of the included image
+\RequirePackage[pdfborder={0 0 0}]{hyperref}
+
+%% we will generate a file for passing to python
+\newwrite\pythonincludein
+
+%% by default we will run vistrails on the web server
+\newcommand{\urlcrowdlabs}{http://www.crowdlabs.org}
+
+%% full path to python or just python if it is on PATH
+\newcommand{\pythonpath}{python}
+
+%% this is for allowing line breaks, empty values in vistrails command's options
+\def\crowdlabs{\kernel at ifnextchar [{\@crowdlabs}{\@crowdlabs[]}}
+
+\def\@crowdlabs[#1]#2{%
+
+%% macros that will be used
+\def\clpdf{false}
+\def\clworkflow{false}
+\def\clvtid{}
+\def\clwfid{}
+\def\clbuildalways{false}
+
+\immediate\openout\pythonincludein=\jobname.crowd.cmdline
+\immediate\write\pythonincludein{url=\urlcrowdlabs}
+\setkeys{cl}{#1}
+
+\ifthenelse{\equal{\clvtid}{}}{% it's a workflow
+ \immediate\write\pythonincludein{wfid=\clwfid}
+ \immediate\write\pythonincludein{workflow=\clworkflow}
+}
+{% else it's a vistrail
+ \immediate\write\pythonincludein{vtid=\clvtid}
+}
+\immediate\write\pythonincludein{buildalways=\clbuildalways}
+\immediate\write\pythonincludein{pdf=\clpdf}
+
+\ifx\@empty#2\@empty
+ \immediate\write\pythonincludein{other=}
+\else
+ \immediate\write\pythonincludein{other=\string#2}
+\fi
+\immediate\closeout\pythonincludein
+\immediate\write18{"\pythonpath" includecrowdlabs.py \jobname.crowd.cmdline > \jobname.crowd.cmdline.tex 2> \jobname.crowd.cmdline.err}
+\immediate\input\jobname.crowd.cmdline.tex
+}
+
+%% key-value pairs for the command's options
+\define at key{cl}{vtid}{\def\clvtid{#1}}
+\define at key{cl}{wfid}{\def\clwfid{#1}}
+\define at key{cl}{showworkflow}[true]{\def\clworkflow{#1}}
+\define at key{cl}{pdf}[true]{\def\clpdf{#1}}
+\define at key{cl}{buildalways}[true]{\def\clbuildalways{#1}}
+
+
+
+
diff --git a/extensions/latex/example.pdf b/extensions/latex/example.pdf
new file mode 100644
index 0000000..83c2057
Binary files /dev/null and b/extensions/latex/example.pdf differ
diff --git a/extensions/latex/example.tex b/extensions/latex/example.tex
new file mode 100644
index 0000000..49fd391
--- /dev/null
+++ b/extensions/latex/example.tex
@@ -0,0 +1,246 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% Copyright (C) 2011-2014, NYU-Poly.
+%% Copyright (C) 2006-2011, University of Utah.
+%% All rights reserved.
+%% Contact: contact at vistrails.org
+%%
+%% This file is part of VisTrails.
+%%
+%% "Redistribution and use in source and binary forms, with or without
+%% modification, are permitted provided that the following conditions are met:
+%%
+%% - Redistributions of source code must retain the above copyright notice,
+%% this list of conditions and the following disclaimer.
+%% - Redistributions in binary form must reproduce the above copyright
+%% notice, this list of conditions and the following disclaimer in the
+%% documentation and/or other materials provided with the distribution.
+%% - Neither the name of the University of Utah nor the names of its
+%% contributors may be used to endorse or promote products derived from
+%% this software without specific prior written permission.
+%%
+%% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+%% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+%% THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+%% PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+%% CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+%% EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+%% PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+%% OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+%% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+%% OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+%% ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\documentclass{article}
+
+%% This file illustrates how to embed images of vistrails published on
+%% crowdLabs. Please refer to
+%% http://www.crowdlabs.org/site_media/static/user_docs/vistrails_usage.html
+%% for instructions on how to publish workflows to crowdLabs and to
+%% http://www.crowdlabs.org/site_media/static/user_docs/embedding.html for
+%% more details about how to use this extension.
+
+%% This is crowdlabs main package
+\usepackage{crowdlabs}
+\usepackage{subfigure}
+
+%% The crowdlabs extension requires python. If your python is not in the path,
+%% uncomment the line below and edit with the path to your python executable
+%\renewcommand{\pythonpath}{C:/Python27/python.exe}
+
+%% You need to enable the crowdlabs package. Make sure crowdlabs.sty is located
+%% in the same directory as the .tex file in which you want to embed the images.
+
+%% If crowdlabs you are using is not on crowdlabs.org,
+%% uncomment the line below and configure it with the current server
+%\renewcommand{\urlcrowdlabs}{http://yourcrowdlabsserver.com}
+
+\title{Embedding workflows in \LaTeX\ using crowdLabs}
+\author{The VisTrails Team}
+\begin{document}
+\maketitle
+\begin{abstract}
+This article shows how to embed images from workflows stored on
+\url{www.crowdlabs.org} in a \LaTeX\ document. The images can be
+workflow results, workflow graphs or VisTrails' history trees.
+\end{abstract}
+
+\begin{figure}[th]
+\begin{center}
+\crowdlabs[wfid=1054,
+buildalways=false]{width=0.50\linewidth}
+\end{center}
+\vspace{-.5cm}
+\caption{Embedding the image generated by the Isosurface workflow. Click on the image to see the details on \url{www.crowdlabs.org}.}
+\label{fig:isosurface}
+\end{figure}
+
+\section{Introduction}
+%% Please refer to \\
+%% http://www.crowdlabs.org/site\_media/static/user\_docs/vistrails\_usage.html
+%% \\
+%% for instructions on how to publish workflows on crowdLabs and to \\
+%% http://www.crowdlabs.org/site\_media/static/user\_docs/embedding.html \\
+%% for more details about how to use this extension.
+
+After uploading your workflows to crowdLabs\footnote{Please visit
+\url{http://www.crowdlabs.org/site_media/static/user_docs/vistrails_usage.html}
+if you need instructions on how to publish workflows to crowdLabs}, you need the following requirements in order to embed the workflows in the \LaTeX\ file:
+\begin{itemize}
+\item Python (\url{www.python.org})
+\item the file \textsf{crowdlabs.sty}
+\item and the file \textsf{includecrowdlabs.py}
+\end{itemize}
+
+Both \textsf{crowdlabs.sty} and \textsf{includecrowdlabs.py} are
+located in the same directory as this document and they should be
+copied to the same folder that your main document is located.
+
+\subsection{Preparing the \LaTeX\ document}
+
+After copying the files, you need to configure your document.In the
+preamble of the \LaTeX\ file add the crowdlabs package:
+\begin{verbatim}
+ \usepackage{crowdlabs}
+\end{verbatim}
+
+As we mentioned before, the crowdLabs package requires Python to
+run. If the python executable is not accessible in the PATH, you will
+need to set the \texttt{\textbackslash pythonpath} command with the correct path for your environment:
+
+\begin{verbatim}
+ \renewcommand{\pythonpath}{C:/Python27/python.exe}
+\end{verbatim}
+
+Also, by default, \url{crowdlabs.org} will be used as the main server, but
+you can use your own crowdLabs server setting the \texttt{\textbackslash urlcrowdlabs} command:
+\begin{verbatim}
+ \renewcommand{\urlcrowdlabs}{http://yourcrowdlabsserver.com}
+\end{verbatim}
+
+\section{Embedding workflows}
+If you go to \url{crowdlabs.org} and visit the details page of the
+workflow you would like to embed, you will see a tab just below the
+resulting image, named \textsf{Embed this Workflow}. Clicking on it,
+will display snippets you can use to embed that particular workflow in
+different types of documents. So copy the text displayed in the
+\textsf{In LaTex} box. For example, we will embed the image produced
+by the workflow
+\textbf{Isosurface}\footnote{\url{http://www.crowdlabs.org/vistrails/workflows/details/1054/}}.
+
+We copied and pasted the following text into this document:
+\begin{verbatim}
+ \crowdlabs[wfid=1054,
+ buildalways=false]{}
+\end{verbatim}
+
+And it generated the image in Figure~\ref{fig:isosurface}. Clicking on the image will take you to that workflow's details page.
+
+\subsection{Controlling the appearance of the image}
+In the \texttt{\textbackslash crowdlabs} command, there are different options to control how the workflow will be embedded. The example above is the simplest way to embed the results of a workflow. To control the size of the image, you write between the curly braces, the options you would normally send to the \texttt{\textbackslash includegraphics} command. For example:
+
+\begin{verbatim}
+ \crowdlabs[wfid=1054,
+ buildalways=false]{width=0.45\linewidth}
+\end{verbatim}
+
+You can also use the \texttt{\textbackslash crowdlabs} command together with the \texttt{\textbackslash subfigure} command:
+\begin{verbatim}
+ \begin{figure}[t]
+ \centering{
+ \subfigure[Isosurface]{\label{fig:isosurface2}
+ \crowdlabs[wfid=1054,
+ buildalways=false]{width=0.35\linewidth}}
+ \subfigure[Volume Rendering]{\label{fig:vr}
+ \crowdlabs[wfid=1046,
+ buildalways=false]{width=0.35\linewidth}} }
+ \end{figure}
+\end{verbatim}
+
+\begin{figure}[t]
+\centering{
+\mbox{\subfigure[Isosurface]
+ {\label{fig:isosurface2}
+ \crowdlabs[wfid=1054,
+ buildalways=false]{width=0.35\linewidth}
+ }
+\subfigure[Volume Rendering]
+ {\label{fig:vr}
+ \crowdlabs[wfid=1046,
+ buildalways=false]{width=0.35\linewidth}
+ }}
+}
+\caption{Using the \texttt{\textbackslash crowdlabs} command with the \texttt{\textbackslash subfigure} command.}
+\label{fig:subfigure}
+\end{figure}
+
+\subsection{Caching images}
+The \textsf{buildalways} option controls whether the images should be cached or not. \textsf{buildalways=false} means that the image will be downloaded only once and every time that you compile your \LaTeX\ document, the image downloaded will be reused. On the other hand, if you set \textsf{buildalways=true}, the image will be downloaded from crowdLabs every time the document is compiled. The images are kept inside the \textsf{crowdlabs\_images} folder.
+
+\subsection{Embedding the workflow graph}
+To embed the workflow graph, just use the \textsf{showworkflow} option inside the \texttt{\textbackslash crowdlabs} command. For example, this is the command to embed the workflow graph that generated Figure~\ref{fig:isosurface}:\\
+
+\begin{verbatim}
+ \crowdlabs[wfid=1054,
+ showworkflow,
+ buildalways=false]{width=0.60\linewidth}
+\end{verbatim}
+
+And it will generate Figure~\ref{fig:workflow}.
+\begin{figure}[th]
+\begin{center}
+\crowdlabs[wfid=1054,
+showworkflow,
+pdf, % use the pdf key to generate in pdf
+buildalways=false]{width=0.60\linewidth}
+\end{center}
+\vspace{-.5cm}
+\caption{Isosurface workflow that generated Figure~\ref{fig:isosurface}}
+\label{fig:workflow}
+\end{figure}
+
+\subsection{Embedding figures in the PDF format}
+If you want to embed the figure in the PDF format, use the \textsf{pdf} option:
+
+\begin{verbatim}
+ \crowdlabs[wfid=1054,
+ showworkflow,
+ pdf,
+ buildalways=false]{width=0.60\linewidth}
+\end{verbatim}
+
+
+\subsection{Embedding VisTrails' history trees}
+
+It is also possible to embed the history tree of a Vistrail. To do that, use the \textsf{vtid=<...>} instead of the \textsf{wfid=<...>} option.
+
+\begin{verbatim}
+ \crowdlabs[vtid=209,
+ buildalways=false]{width=0.90\linewidth}
+\end{verbatim}
+
+To get the \textsf{vtid} of a vistrail, just visit the page of the vistrail in crowdLabs and copy the number that appears in the address bar at the end of the url:
+
+\begin{verbatim}
+ http://www.crowdlabs.org/vistrails/details/209/
+\end{verbatim}
+
+So for the address above, 209 is the \textsf{vtid} of the vistrail \textbf{terminator-latex}.
+
+The command above generates the image in Figure~\ref{fig:tree}.
+\begin{figure}[th]
+\begin{center}
+\crowdlabs[vtid=209,
+% pdf, %uncomment this for using the pdf format
+buildalways=false]{width=0.90\linewidth}
+\end{center}
+\vspace{-.5cm}
+\caption{History tree containing the workflows used in this document}
+\label{fig:tree}
+\end{figure}
+
+The \textsf{pdf} option can also be used if you want to embed the tree in PDF format.
+
+\end{document}
diff --git a/extensions/latex/example2.bib b/extensions/latex/example2.bib
new file mode 100644
index 0000000..ef8a6b4
--- /dev/null
+++ b/extensions/latex/example2.bib
@@ -0,0 +1,3654 @@
+ at Book{Schroeder:2003:VTK,
+ author = {Will Schroeder and Ken Martin and Bill Lorensen},
+ title = {The Visualization Toolkit An Object-Oriented Approach To 3D Graphics},
+ publisher = {Kitware},
+ year = 2003
+}
+
+ at Article{lee at ieee1995,
+ author = {Edward A. Lee and Thomas M. Parks},
+ title = {{Dataflow Process Networks}},
+ journal = {Proceedings of the IEEE},
+ year = {1995},
+ volume = {83},
+ number = {5},
+ pages = {773-801},
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at string{sigmod = "Proc. of ACM SIGMOD"}
+ at string{pods = "Proc. of ACM PODS"}
+ at string{vldb = "Proc. of VLDB"}
+ at string{www = "Proc. of WWW"}
+ at string{sigmod-record = "SIGMOD Record"}
+ at string{aaai = "Proc. of AAAI"}
+ at string{dood = "Proc. of DOOD"}
+ at string{icde = "Proc. of ICDE"}
+% @string{webdb = "Proc. of the Workshop on Web and Databases"}
+ at string{webdb = "Proc. of WebDB"}
+ at string{tods = "ACM TODS"}
+ at string{jiis = "Journal of Intelligent Information Systems"}
+ at string{icdt = "Proc. of ICDT"}
+ at string{dexa = "Proc. of DEXA"}
+ at string{dexaws = "Proc. of DEXA Workshop"}
+ at string{ssdbm = "Proc. of the Conference on Scientific and Statistical Database Management"}
+ at string{jep = "Journal of Electronic Publishing"}
+ at string{vis = "Prof. of IEEE Visualization"}
+ at string{supercomputing = "Prof. of Supercomputing"}
+ at string{spie = "Proc. of SPIE"}
+ at string{siggraph = "Proc. of SIGGRAPH"}
+ at string{lpnmr = "Proc. of the International Conference on
+ Logic Programming and Non-Monotonic Reasoning"}
+ at string{infovis = "Proc. of IEEE Information Visualization Symposium"}
+ at string{volvis = "Proc. IEEE Symposium on Volume
+ Visualization and Graphics"}
+
+ at string{sigmod = "ACM SIGMOD"}
+ at string{pods = " ACM PODS"}
+ at string{vldb = " VLDB"}
+ at string{www = " WWW"}
+ at string{sigmod-record = "SIGMOD Record"}
+ at string{aaai = " AAAI"}
+ at string{dood = " DOOD"}
+ at string{icde = " ICDE"}
+ at string{webdb = "WebDB"}
+ at string{tods = "ACM TODS"}
+ at string{jiis = "Journal of Intelligent Information Systems"}
+ at string{icdt = "ICDT"}
+ at string{dexa = " DEXA"}
+ at string{dexaws = "DEXA Workshop"}
+ at string{ssdbm = "SSDBM"}
+ at string{jep = "Journal of Electronic Publishing"}
+ at string{vis = "IEEE Visualization"}
+ at string{supercomputing = "Supercomputing"}
+ at string{spie = "SPIE"}
+ at string{siggraph = "SIGGRAPH"}
+ at string{lpnmr = "LPNMR"}
+ at string{infovis = "IEEE Information Visualization Symposium"}
+ at string{volvis = "IEEE VolVis"}
+ at string{plilp = "PLILP"}
+ at string{cganda = "IEEE Computer Graphics and Applications"}
+%% {Conference on Innovative Data Systems Research (CIDR)},
+ at string{cidr = "CIDR"}
+ at string{vis = "Proceedings of IEEE Visualization"}
+ at string{infovis = "Proceedings of IEEE Information Visualization Symposium"}
+ at string{volvis = "Proceedings of IEEE VolVis"}
+ at string{spie = "Proceedings of SPIE"}
+ at string{cidr = "Proceedings of CIDR"}
+ at string{eextt = "Proceedings of EEXTT"}
+ at string{cikm = "Proceedings of CIKM"}
+ at string{xsym = "Proceedings of XML Database Symposium (XSym)"}
+ at string{mobilesearch = "Proceedings of the WWW Workshop on Mobile Search"}
+ at string{edbt = "Proceedings of EDBT"}
+ at string{sbbd = "Proceedings of SBBD"}
+ at string{widm = "Proceedings of WIDM"}
+ at string{fsttcs= "Proceedings of FSTTCS"}
+
+ at string{sigmod = "Proceedings of ACM SIGMOD"}
+ at string{pods = "Proceedings of PODS"}
+ at string{vldb = "Proceedings of VLDB"}
+ at string{www = "Proceedings of WWW"}
+ at string{wwwposter = "Poster Proceedings of WWW"}
+ at string{sigmod-record = "SIGMOD Record"}
+ at string{aaai = "Proceedings of AAAI"}
+ at string{dood = "Proceedings of DOOD"}
+ at string{icde = "Proceedings of ICDE"}
+% @string{webdb = "Proceedings of the Workshop on Web and Databases"}
+ at string{webdb = "Proceedings of WebDB"}
+ at string{tods = "ACM TODS"}
+ at string{jiis = "Journal of Intelligent Information Systems"}
+ at string{icdt = "Proceedings of ICDT"}
+ at string{dexa = "Proceedings of DEXA"}
+ at string{scishort = "SCI Institute--Univ. of Utah"}
+
+ at Article{analogy at tvcg2007,
+ author = {C. Scheidegger and H. Vo and D. Koop and J. Freire
+ and C. Silva},
+ title = {Scalable Manipulation Primitives for
+ Visualization Systems},
+ journal = {IEEE Transactions on Visualization and Computer Graphics},
+ year = {2007},
+ OPTvolume = {7},
+ OPTnumber = {3},
+ OPTpages = {275-287},
+ OPTmonth = {July-September},
+ note = {Accepted with minor revisions},
+ OPTannote = {},
+ OPTURL = {http://www.cs.ucdavis.edu/~ma/papers/TVCG2001.pdf}
+}
+
+
+
+ at Book{norman at book1994,
+ author = {Donald A. Norman },
+ title = {Things That Make Us Smart: Defending Human Attributes in the Age of the Machine},
+ publisher = {Addison Wesley},
+ year = {1994},
+}
+
+
+ at Misc{sdm at web,
+ key = {SDM},
+ title = {{Scientific Data Management Center}},
+ note = {\url{http://sdm.lbl.gov/sdmcenter}},
+}
+
+ at Misc{sdm-report-july-sept-2005,
+ key = {SDM},
+ OPTauthor = {},
+ title = {{SDM-Center Quarterly Report}},
+ note = {http://sdmcenter.lbl.gov/quarterly.reports/SDM.quarterly.July-Sept.2005.doc},
+}
+
+
+
+ at inproceedings{brodlie at vis1993,
+ author = {Ken Brodlie and Andrew Poon and Helen Wright and Lesley Brankin and Greg Banecki and Alan Gay},
+ title = {{GRASPARC}: a problem solving environment integrating computation and visualization},
+ booktitle = {IEEE Visualization '93},
+ year = {1993},
+ pages = {102--109},
+ }
+
+ at TechReport{vt-exp,
+ author = {S. Callahan and J. Freire and E. Santos and C. Scheidegger and C. Silva and H. Vo},
+ title = {Using Provenance to Streamline Data Exploration through Visualization},
+ institution = scishort,
+ year = {2006},
+ OPTkey = {},
+ OPTtype = {},
+ number = {UUSCI-2006-016},
+ OPTaddress = {},
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+
+
+ at article{simmhan at sigrec2005,
+ author = {Yogesh L. Simmhan and Beth Plale and Dennis Gannon},
+ title = {A survey of data provenance in e-science},
+ OPTjournal = {SIGMOD Rec.},
+journal = sigmod-record,
+ volume = {34},
+ number = {3},
+ year = {2005},
+ OPTissn = {0163-5808},
+ pages = {31--36},
+ OPTdoi = {http://doi.acm.org/10.1145/1084805.1084812},
+ OPTpublisher = {ACM Press},
+ OPTaddress = {New York, NY, USA},
+ }
+
+
+ at Book{vis-challenges2006,
+ author = {Chris Johnson and Robert Moorhead and Tamara Munzner and Hanspeter Pfister and Penny Rheingans and Terry S. Yoo},
+ ALTeditor = {},
+ title = {NIH/NSF Visualization Research Challenges Report},
+ publisher = {IEEE},
+ year = {2006},
+ OPTkey = {},
+ OPTvolume = {},
+ OPTnumber = {},
+ OPTseries = {},
+ OPTaddress = {},
+ OPTedition = {},
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+
+
+ at Misc{emulab,
+ key = {emulab},
+ OPTauthor = {},
+ title = {{The Emulab Network Emulation Testbed}},
+ OPThowpublished = {},
+ OPTmonth = {},
+ OPTyear = {},
+ note = {\\\url{http://www.emulab.net}},
+ OPTannote = {}
+}
+
+ at InProceedings{eide at usenix2006,
+ author = "Eric Eide and Tim Stack and Leigh Stoller and \freiremarkref{\meabbrev} and Jay Lepreau",
+ title = "Integrated scientific workflow management for the Emulab network testbed",
+ pages = "363--368",
+ year = 2006,
+ booktitle = {Proceedings of USENIX},
+ OPTnote = "To appear"
+}
+
+
+ at InProceedings{Baptista:2003:EOF,
+ author = {A. Baptista and T. Leen and Y. Zhang and A. Chawla
+ and D. Maier and W.-Chi Feng and W.-Chang Feng and
+ J. Walpole and C. Silva and \freiremarkref{\meabbrev}},
+ title = {Environmental Observation and Forecasting Systems:
+ Vision, Challenges and Successes of a Prototype},
+ booktitle = {Conference on Systems Science and Information
+ Technology for Environmental Applications
+ (ISEIS)},
+ year = 2003
+}
+
+ at inproceedings{roberts at vdea2000,
+author = {Jonathan C. Roberts},
+title = {{Multiple-View and Multiform Visualization}},
+OPTmonth = {January},
+year = {2000},
+pages = {176-185},
+keywords = {Visualization, Multiple views, Multiform, Abstraction},
+note = {},
+url = {http://www.cs.ukc.ac.uk/pubs/2000/963},
+OPTbooktitle = {Visual Data Exploration and Analysis VII, Proceedings of SPIE},
+booktitle = spie,
+OPTeditor = {Robert Erbacher and Alex Pang and Craig Wittenbrink and Jonathan Roberts},
+OPTorganization = {IS\&T and SPIE},
+OPTpublication_type = {inproceedings},
+OPTsubmission_id = {26938_949431288},
+OPTvolume = {3960},
+}
+
+ at inproceedings{roberts at iv98,
+author = {Jonathan C. Roberts},
+title = {{On Encouraging Multiple Views for Visualization}},
+month = {July},
+year = {1998},
+pages = {8-14},
+keywords = {visualization, multiple views, multiform, visualization system},
+note = {},
+url = {http://www.cs.ukc.ac.uk/pubs/1998/600},
+ISBN = {0-8186-8509-3},
+ISSN = {1093-9547},
+booktitle = {IV'98 - Proceedings International Conference on Information Visualization },
+editor = {Ebad Banissi and Farzad Khosrowshahi and Muhammad Sarfraz},
+publisher = {IEEE Computer Society},
+}
+
+ at InProceedings{roberts at waltz98,
+ author = {Jonathan C. Roberts},
+ title = {Waltz - Exploratory Visualization Tool For Volume
+ Data, Using Multiform Abstract Displays},
+ OPTbooktitle = {Proceedings of SPIE},
+booktitle = spie,
+ pages = {112-122},
+ year = 1998,
+ volume = 3298
+}
+
+ at InProceedings{pattison-and-phillips,
+ author = {Tim Pattison and Matthew Phillips},
+ title = {View Coordination Architecture for Information
+ Visualization},
+ booktitle = {Proceedings of Australian Symposium on Information
+ Visualization, Sydney, Australia},
+ pages = {165-171},
+ year = 2001
+}
+
+ at inproceedings{ma at vis1999,
+title = {Image Graps- A Novel Interface for Visual Data Exploration},
+booktitle = vis,
+author = {Kwan-Liu Ma },
+year = {1999},
+OPTkeywords = {collaborative visualization, scientific visualization, user interface design, volume rendering.},
+pages = {81-88},
+OPTorganization = {IEEE},
+OPTpublisher = {IEEE},
+OPTeventtime = {October 1999},
+OPTabstract = {For types of data visualization where the cost of producing images is high, and the relationship between the rendering parameters and the image produced is less than clear, a visual representation of the exploration process can make the process more eficient and effective. Image graphs represent not only the results but also the process of data visualization. Each node in an image graph consists of an image and the corresponding visualization parameters used to produce it. [...]
+}
+
+
+
+ at Article{brodlie at cvcgf,
+ author = {K.W. Brodlie and D.A. Duce and J.R. Gallop and J.P.R.B. Walton and J.D. Wood},
+ title = {Distributed and Collaborative Visualization},
+ journal = {Computer Graphics Forum},
+ year = {2004},
+ volume = {23},
+ number = {2},
+ pages = {223-251},
+ OPTannote = {}
+}
+
+ at InProceedings{brodlie at vis2004,
+ author = {Ken Brodlie and David Duce and Julian Gallop and Musbah Sagar and Jeremy Walton and Jason Wood},
+ title = { Visualization in Grid Computing Environments},
+ booktitle = vis,
+ pages = {155-162},
+ year = {2004},
+ OPTnote = {http://www.comp.leeds.ac.uk/vis/gviz/publications/gVizIEEE04.pdf},
+}
+
+
+ at InProceedings{brodlie at vis1997,
+ author = {Jason Wood and Helen Wright and Ken Brodlie},
+ title = {Collaborative Visualization},
+ booktitle = vis,
+ pages = {253-260},
+ year = {1997},
+ OPTnote = {},
+}
+
+
+ at Misc{xquery at w3c,
+ author = {S. Boag and D. Chamberlin and M. Fernandez and D. Florescu and J. Robie and J. Sim\'eon and M. Stefanescu},
+ title = {{XQuery} 1.0: An {XML} Query Language},
+ howpublished = {{W3C} Working Draft},
+ month = jun,
+ year = 2001
+}
+
+ at inproceedings(webvcr at www9,
+author = "V. Anupam and \freiremarkref{\meabbrev} and B. Kumar and D. Lieuwen",
+title = "Automating {Web} Navigation with the {WebVCR}",
+pages = "503-517",
+booktitle = www,
+year={2000},
+optnote={To appear}
+)
+
+
+
+
+ at InProceedings{li at vldb2004,
+ author = {Yunyao Li and Cong Yu and H. V. Jagadish},
+title = {Schema-Free {XQuery}},
+ booktitle = vldb,
+ year = {2004},
+ pages = {72-83},
+}
+
+ at InProceedings{papak at sigmod2005,
+ author = {Yu Xu and Yannis Papakonstantinou},
+title = {Efficient Keyword Search for Smallest {LCAs} in {XML} Databases},
+ booktitle = sigmod,
+ year = {2005},
+ pages = {527-538},
+}
+
+ at InProceedings{freire at sigmod99,
+ author = {H. Davulcu and \freiremarkref{\meabbrev} and M. Kifer and I.V. Ramakrishnan},
+title = {A Layered Architecture for Querying Dynamic Web Content},
+ booktitle = sigmod,
+ year = {1999},
+ pages = {491-502},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+
+ at inproceedings{ives at sigmod99,
+ author = {Zachary G. Ives and
+ Daniela Florescu and
+ Marc Friedman and
+ Alon Y. Levy and
+ Daniel S. Weld},
+ OPTeditor = {Alex Delis and
+ Christos Faloutsos and
+ Shahram Ghandeharizadeh},
+ title = {An Adaptive Query Execution System for Data Integration},
+ OPTbooktitle = {SIGMOD 1999, Proceedings ACM SIGMOD International Conference
+ on Management of Data, June 1-3, 1999, Philadelphia, Pennsylvania,
+ USA},
+ booktitle = sigmod,
+ optpublisher = {ACM Press},
+ year = {1999},
+ isbn = {1-58113-084-8},
+ pages = {299-310},
+}
+
+ at inproceedings{florescu at sigmod99,
+ author = {Daniela Florescu and
+ Alon Y. Levy and
+ Ioana Manolescu and
+ Dan Suciu},
+ OPTeditor = {Alex Delis and
+ Christos Faloutsos and
+ Shahram Ghandeharizadeh},
+ title = {Query Optimization in the Presence of Limited Access Patterns},
+ booktitle = sigmod,
+ OPTbooktitle = {SIGMOD 1999, Proceedings ACM SIGMOD International Conference
+ on Management of Data, June 1-3, 1999, Philadelphia, Pennsylvania,
+ USA},
+ OPTpublisher = {ACM Press},
+ year = {1999},
+ isbn = {1-58113-084-8},
+ pages = {311-322},
+}
+
+ at inproceedings{urhan at sigmod98,
+ author = {Tolga Urhan and
+ Michael J. Franklin and
+ Laurent Amsaleg},
+ OPTeditor = {Laura M. Haas and
+ Ashutosh Tiwary},
+ title = {Cost-Based Query Scrambling for Initial Delays},
+ booktitle = sigmod,
+ OPTbooktitle = {SIGMOD 1998, Proceedings ACM SIGMOD International Conference
+ on Management of Data, June 2-4, 1998, Seattle, Washington, USA},
+ OPTpublisher = {ACM Press},
+ year = {1998},
+ isbn = {0-89791-995-5},
+ pages = {130-141},
+}
+
+
+ at article{ louiqa at vldbj2000,
+ author = "Jean-Robert Gruser and Louiqa Raschid and Vladimir Zadorozhny and Tao Zhan",
+ title = "Learning response time for {WebSources} using query feedback and application in query optimization",
+ journal = "VLDB Journal",
+ volume = "9",
+ number = "1",
+ OPTmonth = "????",
+ pages = "18-37",
+ year = "2000",
+ url = "citeseer.nj.nec.com/gruser99learning.html" }
+
+ at article{ mohan at dataeng95,
+ author = "C. Mohan and Gustavo Alonso and Roger Gunthor and Mohan Kamath",
+ title = "Exotica: A Research Perspective on Workflow Management Systems",
+ journal = "Data Engineering Bulletin",
+ volume = "18",
+ number = "1",
+ pages = "19-26",
+ year = "1995",
+ url = "citeseer.nj.nec.com/mohan95exotica.html" }
+
+
+
+ at InProceedings{foster at ssdbm2002,
+ author = { I. Foster and J. Voeckler and M. Wilde and Y. Zhao},
+ title = {Chimera: A Virtual Data System for Representing, Querying and
+ Automating Data Derivation},
+ booktitle = ssdbm,
+ pages = {37-46},
+ year = {2002},
+}
+
+
+ at inproceedings{levy at vldb96,
+ author = {Alon Y. Levy and
+ Anand Rajaraman and
+ Joann J. Ordille},
+ OPTeditor = {T. M. Vijayaraman and
+ Alejandro P. Buchmann and
+ C. Mohan and
+ Nandlal L. Sarda},
+ title = {Querying Heterogeneous Information Sources Using Source Descriptions},
+ booktitle = vldb,
+ optbooktitle = {VLDB'96, Proceedings of 22th International Conference on Very
+ Large Data Bases, September 3-6, 1996, Mumbai (Bombay), India},
+ publisher = {Morgan Kaufmann},
+ year = {1996},
+ isbn = {1-55860-382-4},
+ pages = {251-262},
+}
+
+
+ at InProceedings{frew at ssdbm2001,
+ author = {James Frew and Rajendra Bose},
+ title = {Earth System Science Workbench: A Data Management Infrastructure for Earth Science Products},
+ booktitle = ssdbm,
+ pages = {180-189},
+ year = {2001},
+}
+
+ at InProceedings{Freire:2000:WSA,
+ author = {Juliana Freire and Bharat Kumar},
+ title = {Web Services and Information Delivery for Diverse
+ Environments},
+ booktitle = {VLDB Workshop on Technologies for E-Services},
+ year = 2000
+}
+
+ at inproceedings{ webviews at www2001,
+ author = "Juliana Freire and Bharat Kumar and Daniel
+ F. Lieuwen",
+ title = "WebViews: accessing personalized web content and
+ services",
+ booktitle = www,
+ pages = "576-586",
+ year = 2001,
+}
+
+
+ at Book{Larson:1996:Syntactica,
+ author = {Richard Larson and David S. Warren and Juliana
+ Freire and Kostis Sagonas},
+ title = {Syntactica},
+ publisher = {MIT Press},
+ year = 1996
+}
+
+ at Book{Larson:1997:Semantica,
+ author = {Richard Larson and David S. Warren and Juliana
+ Freire and Patricia Gomez and Kostis Sagonas},
+ title = {Semantica},
+ publisher = {MIT Press},
+ year = 1997
+}
+
+ at Misc{ogsi,
+ key = {OGSI},
+ OPTauthor = {},
+ title = {OGSI Primer},
+ howpublished = {\url{http://www-unix.globus.org/toolkit}},
+ month = {June},
+ year = {2003},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+
+
+ at Misc{gsfl,
+ key = {GSFL},
+ author = {Sriram Krishnan and Patrick Wagstrom and Gregor von Laszewski},
+ title = {{GSFL}: A Workflow Framework for Grid Services},
+ howpublished = {Argonne National Laboratory, Preprint ANL/MCS-P980-0802},
+}
+
+ at Misc{webservices,
+ key = {Web Services},
+ author = {W3C},
+ title = {Web Services Activity},
+ howpublished = {\url{http://www.w3.org/2002/ws}},
+}
+
+
+ at InProceedings{hull at pods2003,
+ author = {Richard Hull and Michael Benedikt and Vassilis Christophides and Jianwen Su},
+ title = {E-services: a look behind the curtain},
+ OPTcrossref = {},
+ OPTkey = {},
+ booktitle = pods,
+ pages = {2003},
+ year = {1-14},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at Misc{oldxquery at w3c,
+ author = {D. Chamberlin and J. Clark and D. Florescu and J. Robie and J. Sim\'eon and M. Stefanescu},
+ title = {{XQuery} 1.0: An {XML} Query Language},
+ howpublished = {{W3C} Working Draft},
+ month = jun,
+ year = 2001
+}
+
+ at Misc{xerces,
+ key = {Xerces},
+ title = {Xerces Java Parser 1.4.3 },
+ note = {\oneurl{http://xml.apache.org/xerces-j}}
+}
+
+ at Misc{xercesold,
+ key = {Xerces},
+ title = {Xerces {Java} Parser 1.4.3},
+ howpublished = {\url{http://xml.apache.org/xerces-j}},
+ OPTmonth = {},
+ OPTyear = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+
+ at Misc{xpath at w3c,
+ key = {XPath},
+ OPTauthor = {W3C},
+ title = {{XML} Path Language ({XPath}) 2.0},
+ howpublished = {\\\url{http://www.w3.org/TR/xpath20}}
+}
+
+
+
+ at Misc{xslt at w3c,
+ key = {XSLT},
+ OPTauthor = {W3C},
+ title = {{XSL} Transformations ({XSLT})},
+ howpublished = {\url{http://www.w3.org/TR/xslt}}
+}
+
+ at Misc{xhtml at w3c,
+ key = {XHTML},
+ OPTauthor = {W3C},
+ title = {{XHTML}},
+ howpublished = {\url{http://www.w3.org/MarkUp}}
+}
+
+ at Misc{wsdl at w3c,
+ key = {WSDL},
+ OPTauthor = {W3C},
+ title = {Web Service Definition Language (WSDL)},
+ howpublished = {\url{http://www.w3.org/TR/wsdl.html}}
+}
+
+ at Misc{wml,
+ key = {WML},
+ OPTauthor = {W3C},
+ title = {Wireless Markup Language (WML)},
+ howpublished = {\url{http://www1.wapforum.org/tech/terms.asp?doc=WAP-238-WML-20010911-a.pdf}}
+}
+
+
+
+ at Article{xl at deb2001,
+ author = {Daniela Florescu and Donald Kossmann},
+ title = {An {XML} Programming Language for {Web} Service Specification and Composition},
+ journal = {IEEE Data Engineering Bulletin},
+ year = {2001},
+ volume = {24},
+ number = {2},
+ pages = {48-56}
+}
+
+
+ at InProceedings{xl at cidr2003,
+ author = {Daniela Florescu and Andreas Gr�nhagen and Donald Kossmann},
+ title = {{XL}: A Platform for {Web} Services},
+ OPTcrossref = {},
+ OPTkey = {},
+ booktitle = cidr,
+ OPTpages = {},
+ year = {2003},
+ OPTeditor = {},
+ OPTvolume = {},
+ OPTnumber = {},
+ OPTseries = {},
+ OPTaddress = {},
+ OPTmonth = {},
+ OPTorganization = {},
+ OPTpublisher = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at inproceedings{legodb at icde2002,
+ author = {P. Bohannon and \freiremarkref{\meabbrev} and P. Roy and J. Sim\'eon},
+ title = {From {XML} Schema to Relations: A Cost-Based Approach to {XML} Storage},
+ booktitle = icde,
+ OPTpublisher = {IEEE Computer Society},
+ year = {2002},
+ pages = {64-75},
+}
+
+ at Misc{vtk,
+ author = {Kitware},
+ title = {{The Visualization Toolkit}},
+ howpublished = {\url{http://www.vtk.org}}
+}
+
+ at Misc{Darcs,
+ key = {DARCS},
+ author = {David Roundy},
+ title = {Darcs},
+ howpublished = {\url{http://abridgegame.org/darcs}}
+}
+
+ at Misc{kitware,
+ author = {Kitware},
+ title = {{The Visualization Toolkit (VTK) and Paraview}},
+ howpublished = {\url{http://www.kitware.com}}
+}
+
+ at Misc{tcl,
+ author = {John Ousterhout},
+ title = {Tcl/Tk},
+ howpublished = {\url{http://www.tcl.tk}}
+}
+
+ at Misc{python,
+ author = {Guido van Rossum},
+ title = {Python},
+ howpublished = {\url{http://www.python.org}},
+}
+
+ at Misc{dx,
+ author = {IBM},
+ title = {{OpenDX}},
+ howpublished = {\url{http://www.research.ibm.com/dx}},
+}
+
+ at Misc{gtb,
+ author = {Wagner Correa and Louis Bavoil and Shachar Fleishman
+ and Walter Jimenez and James T. Klosowski and
+ Gilberto C. A. G. Martins and Dirce Uesu and Sinesio
+ Pesco and Lourena Rocha and Carlos Eduardo
+ Scheidegger and Claudio T. Silva},
+ title = {Graphics Tool Box (GTB)},
+ howpublished = {\url{http://gtb.sourceforge.net}},
+}
+
+ at Misc{activizcom,
+ author = {Kitware},
+ title = {ActiViz/COM},
+ howpublished = {\url{http://www.kitware.com/products/activiz/activizCOM.html}},
+}
+
+ at Misc{paraview,
+ author = {Kitware},
+ title = {Paraview},
+ howpublished = {\url{http://www.paraview.org}},
+}
+
+ at Article{boukhelifa-and-rodgers,
+ author = {Nadia Boukhelifa and Peter J. Rodgers},
+ title = {A Model and Software System for Coordinated and
+ Multiple Views in Exploratory Visualization},
+ journal = {Information Visualization},
+ year = 2003,
+ volume = 2,
+ number = 4,
+ pages = {258-269}
+}
+
+ at Article{north-and-shneiderman,
+ author = {Chris North and Ben Shneiderman},
+ title = {Snap-Together Visualization: Can Users Construct and
+ Operate Coordinated Visualizations?},
+ journal = {Int. J. Human-Computer Studies},
+ year = 2000,
+ volume = 53,
+ number = {715-739}
+}
+
+ at Article{herman-melancon-marshall,
+ author = {Ivan Herman and Guy Melan�on and M. Scott Marshall},
+ title = {Graph Visualization and Navigation in Information
+ Visualization: A Survey},
+ journal = {IEEE Transactions on Visualization and Computer
+ Graphics},
+ year = 2000,
+ volume = 6,
+ number = 1,
+ pages = {24-43}
+}
+
+ at InProceedings{design-gallery,
+ author = {J. Marks and B. Andalman and P.A. Beardsley and
+ W. Freeman and S. Gibson and J. Hodgins and T. Kang
+ and B. Mirtich and H. Pfister and W. Ruml and
+ K. Ryall and J. Seims and S. Shieber},
+ title = {Design Galleries: A General Approach to Setting
+ Parameters for Computer Graphics and Animation},
+ booktitle = siggraph,
+ pages = {389-400},
+ year = 1997
+}
+
+
+ at InProceedings{roberts,
+ author = {Jonathan C. Roberts},
+ title = {Waltz -- Exploratory Visualization Tool For Volume
+ Data, Using Multiform Abstract Displays},
+ booktitle = spie,
+ pages = {112-122},
+ year = 1998,
+ volume = 3298
+}
+
+ at inproceedings{scirun,
+ author = {Steven G. Parker and Christopher R. Johnson},
+ title = {{SCIRun: a scientific programming environment for
+ computational steering}},
+ booktitle = supercomputing,
+ year = {1995},
+ pages = {52},
+ OPTlocation = {San Diego, California, United States},
+ OPTpublisher = {ACM Press},
+}
+
+
+ at article{avs,
+ OPTauthor = {Craig Upson and Thomas Faulhaber, Jr. and David
+ Kamins and David H. Laidlaw and David Schlegel and
+ Jefrey Vroom and Robert Gurwitz and Andries van Dam},
+ author = {Craig {Upson et al}},
+ title = {The Application Visualization System: A
+ Computational Environment for Scientific
+ Visualization},
+ journal = cganda,
+ volume = 9,
+ number = 4,
+ year = 1989,
+ OPTissn = {0272-1716},
+ pages = {30-42},
+ OPTpublisher = {IEEE Computer Society Press},
+}
+
+ at Unpublished{stc,
+ author = {Antonio Baptista},
+ title = {Science and Technology Center ({STC}) for Coastal
+ Margin Observation and Prediction},
+ note = {Proposal submitted to National Science Foundation}
+}
+
+
+ at Unpublished{corie-itr,
+ author = {Antonio Baptista},
+ title = {ITR/IM+AP: Quality-Scalable Information Flow Systems for Environmental
+Observation and Forecasting},
+ note = {NSF ITR/IM+AP-0121475}
+}
+
+ at Unpublished{uncertainty_vis,
+ author = {Robert B. Gilbert and Fulvio Tonon and \freiremarkref{\meabbrev} and Claudio T. Silva and David R. Maidment},
+ title = {Visualizing Uncertainty with Uncertainty Multiples},
+ note = {To appear in GeoCongress 2006}
+}
+
+ at Misc{GraphViz:2005:GV,
+ author = "David Dobkin and John Ellson and Emden Gansner and Eleftherios Koutsofios
+ Stephen North and Kiem-Phong Vo and Gordon Woodhull",
+ title = "Graphviz 2.2",
+ URL = "http://www.graphviz.org",
+ year = "2005"
+}
+
+
+
+
+ at InProceedings{Ellson:2001:GraphViz,
+ author = {J. Ellson and E. R. Gansner and L. Koutsofios and
+ S.C. North and G. Woodhull},
+ title = {Graphviz - Open Source Graph Drawing Tools},
+ booktitle = {Graph Drawing},
+ year = 2001,
+ pages = {483--485}
+}
+
+ at Article{ludascher at pe2005,
+ author = {B. Lud\"{a}scher and I. Altintas and C. Berkley and D. Higgins and E. Jaeger-Frank and M. Jones and E. Lee and J. Tao and Y. Zhao},
+ title = {{Scientific Workflow Management and the Kepler System}},
+ OPTjournal = {Concurrency and Computation: Practice \& Experience, Special Issue on Scientific Workflows},
+ journal = {Concurrency and Computation: Practice \& Experience},
+ year = {2005},
+ OPTvolume = {},
+ OPTnumber = {},
+ OPTpages = {},
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at inproceedings{stolte at sigmod2003,
+ author = {Etzard Stolte and
+ Christoph von Praun and
+ Gustavo Alonso and
+ Thomas R. Gross},
+ title = {Scientific Data Repositories: Designing for a Moving Target.},
+ booktitle = sigmod,
+ year = {2003},
+ pages = {349-360},
+ ee = {http://www.acm.org/sigmod/sigmod03/eproceedings/papers/r13p03.pdf},
+ OPTcrossref = {DBLP:conf/sigmod/2003},
+ OPTbibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+ at InProceedings{kreuseler at infovis2004,
+ author = {Matthias Kreuseler and Thomas Nocke and Heidrun
+ Schumann},
+ title = {A History Mechanism for Visual Data Mining},
+ booktitle = infovis,
+ pages = {49-56},
+ year = 2004
+}
+
+ at Book{Davis:1994:CCL,
+ author = {Martin D. Davis and Ron Sigal and Elaine Weyuker},
+ title = {Computability, Complexity, and Languages},
+ publisher = {Academic Press},
+ year = 1994
+}
+
+ at Book{Maier:1988:CWL,
+ author = {David Maier and David S. Warren},
+ title = {Computing With Logic: Logic Programming With Prolog},
+ publisher = {Addison-Wesley},
+ year = 1988
+}
+
+ at InProceedings{Rao:1997:XSB,
+ author = {Prasad Rao and Konstantinos Sagonas and Terrance
+ Swift and David Warren and Juliana Freire},
+ title = {{XSB - A System for Efficiently Computing Well
+ Founded Semantics}},
+ booktitle = lpnmr,
+ year = 1997
+}
+
+
+
+ at Article{jankun-kelly at tvcg2001,
+ author = {{T.J.} {Jankun-Kelly} and {Kwan-Liu} Ma},
+ title = {Visualization Exploration and Encapsulation via a Spreadsheet-Like Interface},
+ journal = {IEEE Transactions on Visualization and Computer Graphics},
+ year = {2001},
+ volume = {7},
+ number = {3},
+ pages = {275-287},
+ OPTmonth = {July-September},
+ OPTnote = {},
+ OPTannote = {},
+ OPTURL = {http://www.cs.ucdavis.edu/~ma/papers/TVCG2001.pdf}
+}
+
+
+
+
+ at InProceedings{jankun-kelly at vis2002,
+ author = {{T.J.} {Jankun-Kelly} and {Kwan-Liu} Ma and Michael Gertz},
+ title = {A Model for the Visualization Exploration Process},
+ booktitle = vis,
+ OPTcrossref = {},
+ OPTkey = {},
+ OPTpages = {},
+ year = {2002},
+ OPTeditor = {},
+ OPTvolume = {},
+ OPTnumber = {},
+ OPTseries = {},
+ OPTaddress = {},
+ OPTmonth = {},
+ OPTorganization = {},
+ OPTpublisher = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+
+ at InProceedings{freire at plilp1995,
+ author = {Juliana Freire and Rui Hu and Terrance Swift and David Scott Warren},
+ title = {Exploiting Parallelism in Tabled Evaluations},
+ booktitle = plilp,
+ pages = {115-132},
+ year = {1995},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at Article{buneman at tods2004,
+ author = {Peter Buneman and Sanjeev Khanna and Keishi Tajima and Wang Chiew Tan},
+ title = {Archiving scientific data},
+ journal = {ACM Transactions on Database Systems},
+ year = {2004},
+ OPTkey = {},
+ volume = {29},
+ number = {1},
+ pages = {2-42},
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+
+ at inproceedings{avnur at sigmod2000,
+ author = {Ron Avnur and Joseph M. Hellerstein},
+ title = {Eddies: Continuously Adaptive Query Processing},
+ booktitle = sigmod,
+ year = {2000},
+ pages = {261-272},
+}
+
+
+ at InProceedings{chi at vis1997,
+ author = {Ed {Huai-hsin} Chi and Phillip Barry and John Riedl and Joseph Konstan},
+ title = {A Spreadsheet Approach to Information Visualization},
+ OPTcrossref = {},
+ OPTkey = {},
+ booktitle = infovis,
+ pages = {17-24},
+ year = {1997},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at article{chi at cganda1998,
+ author = {Ed {Huai-hsin} Chi and Phillip Barry and John Riedl and Joseph Konstan},
+ title = {Principles for Information Visualization Spreadsheets},
+ journal = cganda,
+ volume = 18,
+ number = 4,
+ year = 1998,
+ pages = {30-38},
+ OPTpublisher = {IEEE Computer Society Press},
+}
+
+ at InProceedings{levoy at siggraph1994,
+ author = {Mark Levoy},
+ title = {Spreadsheet for Images},
+ booktitle = siggraph,
+ pages = {139-146},
+ year = 1994
+}
+
+ at inproceedings{Chiang:1998:IOI,
+ author = "Yi-Jen Chiang and Cl{\'{a}}udio T. Silva and William
+ J. Schroeder",
+ title = "Interactive Out-Of-Core Isosurface Extraction",
+ year = 1998,
+ booktitle = vis,
+ pages = "167-174",
+}
+
+ at Book{Luebke:2002:LOD,
+ OPTauthor = {David Luebke and Martin Reddy and Jonathan Cohen and
+ Amitabh Varshney and Benjamin Watson and Robert
+ Huebner},
+ author = {David {Luebke et al}},
+ title = {Level of Detail for 3D Graphics},
+ publisher = {Morgan-Kaufmann Publishers},
+ year = 2002
+}
+
+ at inproceedings{Weiler:2000:SLOD,
+ author = {Manfred Weiler and Rudiger Westermann and Chuck
+ Hansen and Kurt Zimmerman and Thomas Ertl},
+ title = {Level-Of-Detail Volume Rendering view 3D Textures},
+ booktitle = {Proceedings of IEEE Volume Visualization 2000},
+ year = {2000}
+}
+
+ at inproceedings{Museth:2004:VIS,
+ author = {Ken Museth and Santiago Lombeyda},
+ title = {TetSplat: Real-time Rendering and Volume Clipping of
+ Large Unstructured Tetrahedral Meshes},
+ booktitle = {Proceedings of IEEE Visualization 2004},
+ year = {2004},
+ pages = {433-440}
+}
+
+ at article{Cignoni:2004:LOD,
+ author = {Paolo Cignoni and Leila De Floriani and Paola
+ Magillo and Enrico Puppo and Roberto Scopigno},
+ title = {Selective Refinement Queries for Volume
+ Visualization of Unstructured Tetrahedral Meshes.},
+ journal = "IEEE Transactions on Visualization and Computer
+ Graphics",
+ volume = 10,
+ number = 1,
+ year = 2004,
+ pages = {29-45},
+}
+
+ at inproceedings{Leven:2002:VV,
+ author = {Joshua Leven and Jason Corso and Jonathan D. Cohen
+ and Subodh Kumar},
+ title = {Interactive Visualization of Unstructured Grids
+ Using Hierarchical 3D Textures},
+ booktitle = volvis,
+ year = {2002},
+ pages = {37-44}
+}
+
+
+ at InProceedings{bright at cidr2005,
+ author = {Laura Bright and David Maier},
+ title = {Deriving and Managing Data Products in an Environmental Observation and Forecasting System},
+ OPTcrossref = {},
+ OPTkey = {},
+ booktitle = cidr,
+ pages = {162-173},
+ year = {2005},
+ OPTeditor = {},
+ OPTvolume = {},
+ OPTnumber = {},
+ OPTseries = {},
+ OPTaddress = {},
+ OPTmonth = {},
+ OPTorganization = {},
+ OPTpublisher = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+
+ at inproceedings{franklin at vldb2004,
+ author = {David T. Liu and Michael J. Franklin},
+ title = {{The Design of GridDB: A Data-Centric Overlay for the Scientific Grid}},
+ booktitle = vldb,
+ year = {2004},
+ pages = {600-611}
+}
+
+ at Misc{thetus,
+ key = {Thetus},
+ title = {Thetus Publisher},
+ URL = {http://www.thetuscorp.com},
+ OPTyear = "2005"
+}
+
+
+ at inproceedings{haas at vldb1999,
+ author = {Mary Tork Roth and Fatma Ozcan and Laura M. Haas},
+ title = {{Cost Models DO Matter: Providing Cost Information for Diverse Data Sources in a Federated System}},
+ booktitle = vldb,
+ year = {1999},
+ pages = {599-610}
+}
+
+ at InProceedings{bavoil at vis2005,
+ author = {L. Bavoil and S. Callahan and P. Crossno and
+ \freiremarkref{\meabbrev} and C. Scheidegger and C. Silva and H. Vo},
+ title = {VisTrails: Enabling Interactive Multiple-View
+ Visualizations},
+ booktitle = vis,
+ pages = {135-142},
+ year = 2005
+}
+
+ at InProceedings{vanwijk at vis2005,
+ author = {Jarke {van Wijk}},
+ title = {The value of visualization},
+ booktitle = vis,
+ OPTpages = {79-86},
+ year = 2005
+}
+
+ at InProceedings{callahan at sciflow2006,
+ author = {S. Callahan and J. Freire and E. Santos and C. Scheidegger and C. Silva and H. Vo},
+ title = { Managing the Evolution of Dataflows with {VisTrails} \emph{(Extended Abstract)}},
+ booktitle = {IEEE Workshop on Workflow and Data Flow for Scientific Applications (SciFlow)},
+ OPTpages = {135--142},
+ year = 2006,
+ OPTnote = {To appear}
+}
+
+ at InProceedings{callahan at sigmod2006,
+ author = {S. Callahan and \freiremarkref{\meabbrev} and E. Santos and C. Scheidegger and C. Silva and H. Vo},
+ title = {{VisTrails: Visualization meets Data Management}},
+ booktitle = sigmod,
+ pages = {745--747},
+ year = 2006,
+ note = {Demo description. }
+}
+
+ at Misc{vistrail at nsf2005,
+ OPTkey = {},
+ author = {\freiremarkref{\meabbrev} and Cl\'audio Silva},
+ title = {Managing Complex Visualizations},
+ OPThowpublished = {},
+ month = jul,
+ year = 2005,
+ OPTnote = {Proposal submitted to the NSF CISE Research Infrastructure
+Program.},
+ note = {NSF CISE-IIS grant \#0513692},
+ OPTannote = {}
+}
+
+ at InProceedings{jimenez at vis2003,
+ author = {W. Herrera-Jimenez and W. Corr\^{e}a and C. Silva
+ and A. Baptista},
+ title = {Visualizing Spatial and Temporal Variability in
+ Coastal Observatories},
+ booktitle = {IEEE Visualization 2003},
+ pages = {269--274},
+ year = 2003
+}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Juliana's %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ at InProceedings{shrex at widm2004,
+ author ={Sihem Amer-Yahia and Fang Du and \freiremarkref{\meabbrev}},
+ title = {{A Comprehensive Solution to the XML-to-Relational
+ Mapping Problem}},
+ pages = {31-38},
+ booktitle = widm,
+ year = 2004,
+}
+
+
+ at InProceedings{barbosa at sbbd2004,
+ OPTauthor = {Luciano Barbosa and Juliana Freire},
+ author = {Luciano Barbosa and \freiremarkref{\meabbrev}},
+ title = {Siphoning Hidden-Web Data through Keyword-Based Interfaces},
+ booktitle = sbbd,
+ pages = {309-321},
+ year = {2004}
+}
+
+ at TechReport{barbosa at techrep2005,
+ OPTauthor = {Luciano Barbosa and Juliana Freire},
+ author = {Luciano Barbosa and \freiremarkref{\meabbrev}},
+ title = {Searching for Hidden-Web Databases},
+ institution = {University of Utah},
+ year = {2005},
+ OPTkey = {},
+ OPTtype = {},
+ OPTnumber = {},
+ OPTaddress = {},
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at TechReport{vistrail at techrep2005,
+ author = {Lois Bavoil and Steven Calahan and Patricia Crossno and \freiremarkref{\meabbrev} and Carlos Scheidegger and Cl\'audio Silva and Huy Vo},
+ title = {VisTrails: Enabling Interactive Multiple-View Visualizations},
+ institution = {University of Utah},
+ year = {2005},
+ OPTkey = {},
+ OPTtype = {},
+ OPTnumber = {},
+ OPTaddress = {},
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+
+
+ at Misc{stc at nsf2004,
+ OPTkey = {},
+ author = {Ant\'onio {Baptista et al}},
+ title = {Science and Tecnology Center (STC) for Coastal
+Margin Observation and Prediction},
+ OPThowpublished = {},
+ OPTmonth = mar,
+ year = 2004,
+ note = {Submitted to NSF. Among the final six proposals recommended for funding
+ by the Blue Ribbon Panel },
+ OPTannote = {}
+}
+
+
+ at Misc{corie at web,
+ key = {CORIE},
+ title = {{CORIE Web site }},
+ note = {\url{http://www.ccalmr.ogi.edu/CORIE}},
+}
+
+
+
+
+ at InProceedings{freire at mobilesearch2002,
+ author = {\freiremarkref{\meabbrev}},
+ title = {Using Wrappers for Device Independent Web Access: Opportunities, Challenges and Limitations (Extended Abstract)},
+ booktitle = mobilesearch,
+ OPTpages = {},
+ year = {2002},
+ note = {Invited paper},
+ OPTannote = {}
+}
+
+
+
+ at inproceedings(webvcr at www9,
+author = "V. Anupam and \freiremarkref{\meabbrev} and B. Kumar and D. Lieuwen",
+title = "Automating {Web} Navigation with the {WebVCR}",
+pages = "503-517",
+booktitle = www,
+year={2000},
+optnote={To appear}
+)
+
+ at misc(xmldm at www2002,
+OPTauthor = "Michael Benedikt and Mary Fernandez and \freiremarkref{Juliana Freire} and Arnaud Sahuguet",
+author = "Michael Benedikt and Mary Fernandez and \freiremarkref{\meabbrev} and Arnaud Sahuguet",
+title = "{XML} and Data Management",
+howpublished = "Full-day tutorial presented at WWW",
+note = "Available at \\ \oneurl{http://www.cse.ogi.edu/$\tilde{\ }$juliana/pub/xml-data-management-slides.pdf}",
+year={2002},
+)
+
+
+ at InProceedings{freire at sigmod99,
+ author = { H. Davulcu and \freiremarkref{\meabbrev} and M. Kifer and I.V. Ramakrishnan},
+title = {A Layered Architecture for Querying Dynamic Web Content},
+ booktitle = sigmod,
+ year = {1999},
+ pages = {491-502},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at InProceedings{Freire:2000:WSA,
+ author = { \freiremarkref{\meabbrev} and Bharat Kumar},
+ title = {Web Services and Information Delivery for Diverse
+ Environments},
+ booktitle = {Proceedings VLDB Workshop on Technologies for E-Services},
+ year = 2000
+}
+
+ at inproceedings{ webviews at www2001,
+ author = " \freiremarkref{\meabbrev} and Bharat Kumar and Daniel
+ F. Lieuwen",
+ title = "WebViews: accessing personalized web content and
+ services",
+ booktitle = www,
+ pages = "576-586",
+ year = 2001,
+}
+
+
+ at Book{Larson:1996:Syntactica,
+ author = { Richard Larson and David S. Warren and \freiremarkref{\meabbrev} and Kostis Sagonas},
+ title = {Syntactica},
+ publisher = {MIT Press},
+ year = 1996
+}
+
+ at Book{Larson:1997:Semantica,
+ author = { Richard Larson and David S. Warren and \freiremarkref{\meabbrev} and Patricia Gomez and Kostis Sagonas},
+ title = {Semantica},
+ publisher = {MIT Press},
+ year = 1997
+}
+
+
+ at inproceedings{statix at sigmod2002,
+ author = { \freiremarkref{\meabbrev} and J. Haritsa and M. Ramanath and P. Roy and J. Sim\'eon},
+ title = {StatiX: Making {XML} Count},
+ booktitle = sigmod,
+ OPTpublisher = {ACM},
+ year = {2002},
+ pages = {181-191},
+}
+
+ at inproceedings{statix at icde2004,
+ author = { \freiremarkref{\meabbrev} and M. Ramanath and L. Zhang},
+ title = {A Flexible Infrastructure for Gathering {XML} Statistics and
+Estimating Query Cardinality},
+ booktitle = icde,
+ OPTpublisher = {ACM},
+ year = {2004},
+ OPTpages = {181-191},
+ note = {To appear}
+}
+
+ at inproceedings{shrex at vldb2004,
+ author = { Fang Du and Sihem Amer-Yahia and \freiremarkref{\meabbrev}},
+ title = { {ShreX}: Managing {XML} Documents in Relational Databases},
+ booktitle = vldb,
+ year = {2004},
+ pages = {1297-1300}
+}
+
+ at inproceedings{imax at icde2005,
+ author = { Maya Ramanath and Lingzhi Zhang and \freiremarkref{\meabbrev} and Jayant Haritsa},
+ title = { {IMAX}: The Big Picture of Dynamic {XML} Statistics},
+ booktitle = icde,
+ year = {2005},
+ pages = {273-284}
+}
+
+ at inproceedings{flexmap at xsym2003,
+ author = {Maya Ramanath and \freiremarkref{\meabbrev} and Jayant Haritsa and Prasan Roy},
+ title = {Searching for Efficient {XML}-to-Relational Mappings},
+ booktitle = xsym,
+ year = {2003},
+ pages = {19-36},
+ OPTnote = {To appear}
+}
+
+ at inproceedings{barbosa at xsym2004,
+ author = {Denilson Barbosa and \freiremarkref{\meabbrev} and Alberto Mendelzon},
+ title = {Information Preservation in {XML}-to-Relational Mappings},
+ booktitle = xsym,
+ year = {2004},
+ pages = {66-81}
+}
+
+
+ at InProceedings{legodb at vldb2002,
+ OPTauthor = {Philip Bohannon and \freiremarkref{\meabbrev} and Jayant Haritsa Maya Ramanath and Prasan Roy J\'er\^ome Sim\'eon},
+ author = { P. Bohannon and \freiremarkref{\meabbrev} and J. Haritsa and M. Ramanath and P. Roy and J. Sim\'eon},
+ title = {LegoDB: Customizing Relational Storage for XML Documents},
+ booktitle = vldb,
+ pages = {1091-1094},
+ year = 2002,
+ OPTaddress = {Honk Kong, China},
+ OPTmonth = aug
+}
+
+ at InProceedings{legodb at icde2003,
+ OPTauthor = {Philip Bohannon and Juliana Freire and Jayant Haritsa Maya Ramanath and Prasan Roy J\'er\^ome Sim\'eon},
+ author = { P. Bohannon and \freiremarkref{\meabbrev} and J. Haritsa and M. Ramanath and P. Roy and J. Sim\'eon},
+ title = {Bridging the {XML}-Relational Divide with {LegoDB}: A Demonstration},
+ booktitle = icde,
+ year = 2003,
+ OPTaddress = {Honk Kong, China},
+ OPTmonth = aug
+}
+
+ at InProceedings{legodb at eextt2002,
+ OPTauthor = {Juliana Freire and J\'er\^ome Sim\'eon},
+ author = {\freiremarkref{\meabbrev} and J. Sim\'eon},
+ title = { Adaptive {XML} Shredding: Architecture, Implementation, and Challenges},
+ booktitle = eextt,
+ pages = {104-116},
+ year = 2002,
+ OPTaddress = {Honk Kong, China},
+ OPTmonth = aug
+}
+
+
+ at inproceedings(veriweb at www2002,
+author = " M. Benedikt and \freiremarkref{\meabbrev} and P. Godefroid",
+title = "VeriWeb: A Platform for Automating Web Site Testing",
+OPTpages = "503-517",
+booktitle = www,
+year={2002},
+)
+
+ at inproceedings(byers at www2001,
+author = " S. Byers and \freiremarkref{\meabbrev} and C.~T.~Silva",
+title = "Efficient Acquisition of Web Data through Restricted Query Interfaces",
+pages = "184-185",
+booktitle = wwwposter,
+year={2001},
+)
+
+ at InProceedings{sihem at icde03,
+ author = {Sihem Amer-Yahia and Yannis Kotidis and Divesh Srivastava},
+ title = {{XML} Publishing: Look at Siblings too!},
+ booktitle = icde,
+ OPTpages = {},
+ year = 2003,
+ note = {Poster paper}
+}
+
+
+
+ at Article{freire at cise2004,
+ author = { \freiremarkref{\meabbrev} and Michael Benedikt},
+ title = {Managing XML Data: An Abridged Overview},
+ journal = {IEEE Computing in Science \& Engineering},
+ year = {2004},
+ OPTkey = {},
+ volume = {6},
+ number = {4},
+ pages = {12-19},
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% XML %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ at InProceedings{sekar at icdt2003,
+ author = {R. Krishnamurthy and V. Chakaravarthy and J. Naughton},
+ title = {On the Difficulty of Finding Optimal Relational Decompositions for {XML} Workloads: a Complexity Theoretic Perspective},
+ booktitle = icdt,
+ pages = {270-284},
+ year = {2003},
+}
+
+ at InProceedings{Shan at vldb99,
+ author = {J. Shanmugasundaram and K. Tufte and G. He and C. Zhang and D. DeWitt and J. Naughton},
+ title = {Relational Databases for Querying {XML} Documents: Limitations and Opportunities},
+ booktitle = vldb,
+ pages = {302-314},
+ year = 1999
+}
+
+ at InProceedings{Deutsch at sigmod99,
+ author = {A. Deutsch and M. Fernandez and D. Suciu},
+ title = {Storing Semi-Structured Data with {STORED}},
+ booktitle = sigmod,
+ pages = {431-442},
+ year = 1999
+}
+
+ at Article{florescu at deb99,
+ author = {D. Florescu and D. Kossman},
+ title = {Storing and Querying XML Data using an RDMBS},
+ journal = {IEEE Data Engineering Bulletin},
+ year = 1999,
+ volume = 22,
+ number = 3,
+ pages = {27-34}
+}
+
+ at InProceedings{schmidt at webdb2000,
+ author = {A. Schmidt and M. Kersten and M. Windhouwer and F. Waas},
+ title = {Efficient Relational Storage and Retrieval of {XML} Documents},
+ booktitle = webdb,
+ pages = {47-52},
+ year = 2000
+}
+
+ at InProceedings{shimura at dexa1999,
+ author = {T. Shimura and M. Yoshikawa and S. Uemura},
+ title = {Storage and Retrieval of {XML} Documents Using Object-Relational Databases},
+ booktitle = dexa,
+ pages = {206-217},
+ year = 1999
+}
+
+ at InProceedings{tatarinov at sigmod2001,
+ author = {Igor Tatarinov and Zachary G. Ives and Alon Y. Halevy and Daniel S. Weld},
+ title = {Updating XML},
+ booktitle = sigmod,
+ OPTpages = {not-available},
+ year = 2001
+}
+
+
+ at MastersThesis{lehti at thesis,
+ author = {Patrick Lehti},
+ title = {Design and Implementation of a Data Manipulation Processor
+for an XML Query Language},
+ school = {Fraunhofer IPSI},
+ year = {2002},
+ OPTkey = {},
+ OPTtype = {},
+ OPTaddress = {},
+ OPTmonth = {},
+ note = {\oneurl{http://www.ipsi.fhg.de/$\tilde{\ }$lehti/diplomarbeit.pdf}},
+ OPTannote = {}
+}
+
+ at InProceedings{Tatarinov at sigmod2002,
+ author = {I. Tatarinov and S. Viglas and K. Beyer and J. Shanmugasundara
+m and E. Shekita and C. Zhang},
+ title = {Storing and Querying Ordered {XML} Using a Relational Database
+ System},
+ booktitle = sigmod,
+ pages = {204-215},
+ year = 2002
+}
+
+ at Misc{excelon,
+ key = {Excelon},
+ title = {Excelon},
+ note = {\oneurl{http://www.exceloncorp.com}}
+}
+
+ at Misc{tamino,
+ key = {Tamino},
+ title = {Tamino},
+ note = {\oneurl{http://www.softwareag.com/tamino}}
+}
+
+ at Misc{xml at oracle,
+ key = {XML SQL},
+ title = {Oracle's {XML} {SQL} Utility},
+ OPThowpublished = {\textsf{\footnotesize http://technet.ora\-cle.com/tech/ xml/oracle\_xsu}},
+ note = {\oneurl{http://technet.ora\-cle.com/tech/xml/oracle\_xsu}},
+ OPTnote = {straightforward mapping from xml into ordbms}
+}
+
+ at Misc{xml at sqlserver,
+ key = {Microsoft Support for XML},
+ title = {Microsoft Support for {XML}},
+ note = {\oneurl{http://msdn.micro\-soft.com/sqlxml}},
+}
+
+ at Misc{xml at db2,
+ key = {IBM DB2 XML Extender},
+ title = {{IBM} {DB2} {XML} {Extender}},
+ note = {\\ \oneurl{http://www4.ibm.com/soft\-ware/ data/db2/extenders/xmlext.html}}
+}
+
+
+ at Misc{oasis,
+ key = {Oasis},
+ title = {The {XML} Cover Pages},
+ note = {\oneurl{http://www.oasis-open.org/cover}}
+}
+
+ at Misc{coverpages,
+ key = {Coverpages},
+ title = {The {XML} Cover Pages},
+ note = {\oneurl{http://xml.coverpages.org}}
+}
+
+
+ at Misc{dtd at w3c,
+ author = {J. Bosac and T. Bray and D. Connolly and E. Maler and G. Nicol and C.~M. Sperberg-McQueen and L. Wood and J. Clark},
+ title = {Guide to the {W3C} {XML} Specification ("{XMLspec}") {DTD}},
+ month = jun,
+ year = 1998
+}
+
+
+ at Misc{xmlspy,
+ key = {Spy},
+ title = {{XML} Spy},
+ note = {\\ \oneurl{http://www.xmlspy.com/}}
+}
+
+ at Misc{infoset at w3c,
+ author = {John Cowan and Richard Tobin},
+ title = {{XML} Information Set},
+ month = oct,
+ year = 2001,
+ note = {{W3C} Recommendation}
+}
+
+ at Misc{xschema at w3c,
+ author = {Henry Thompson and David Beech and Murray Maloney and Noah Mendelsohn},
+ title = {{XML} {Schema} {Part} 1: Structures},
+ howpublished = {{W3C} Working Draft},
+ month = feb,
+ year = 2000
+}
+
+
+ at misc{xml at w3ccomplete,
+ author = {Tim Bray and Jean Paoli and C. M. Sperberg-McQueen},
+ title = {Extensible markup language ({XML}) 1.0},
+ note = {\oneurl{http://www.w3.org/TR/REC-xml}},
+ howpublished = {{W3C} Recommendation},
+ month = feb,
+ year = 1998,
+}
+
+ at Misc{xml at w3c,
+ key = {XML},
+ OPTauthor = {W3C},
+ title = {{Extensible Markup Language (XML)}},
+ howpublished = {\\\url{http://www.w3.org/XML}}
+}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Hidden Web %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ at string{jep = "Journal of Electronic Publishing"}
+
+ at article{ lawrence at science98,
+ author = "Steve Lawrence and C. Lee Giles",
+ title = "Searching the {World Wide Web}",
+ journal = "Science",
+ volume = "280",
+ number = "5360",
+ pages = "98--100",
+ year = "1998",
+ url = "citeseer.nj.nec.com/lawrence98searching.html" }
+
+
+
+ at Book{soumen at mk2002,
+ author = {S. Chakrabarti},
+ title = {Mining the Web: Discovering Knowledge from Hypertext Data},
+ publisher = {Morgan Kaufmann},
+ year = {2002},
+}
+
+ at Misc{mageml,
+ key = {MAGEML},
+ OPTauthor = {},
+ title = {{MAGE-ML}: Microarray Gene Expression Markup Language},
+ OPThowpublished = {\oneurl{http://www.mged.org/Workgroups/MAGE/mage-ml.html}},
+ OPTyear = {},
+ note = {\\ \oneurl{http://www.mged.org/Workgroups/MAGE/mage-ml.html}},
+}
+
+ at Misc{OLDvisitr at nsf2003,
+ OPTkey = {},
+ author = {Cl\'audio Silva and \freiremarkref{\meabbrev} and Ant\'onio Baptista},
+ title = {Middleware Infrastruture for Managing Visualization and Data
+Exploration in Environmental Observation and Forecasting Systems},
+ OPThowpublished = {},
+ month = mar,
+ year = 2003,
+ note = {Medium ITR proposal submitted to the NSF Division of Advanced Computational Infrastructure and Research},
+ OPTannote = {}
+}
+
+ at Misc{dbitr at nsf2003,
+ OPTkey = {},
+ author = {Lois Delcambre and \freiremarkref{\meabbrev} and Paul Gorman
+ and James Larson and David Maier},
+ title = {Taming the Information Jungle - Selecting, Organizing and Analyzing Disparate Information},
+ OPThowpublished = {},
+ month = mar,
+ year = 2003,
+ note = {Medium ITR proposal submitted to the NSF Division of Information
+and Intelligent Systems},
+ OPTannote = {}
+}
+
+ at Misc{cluster at nsf2003,
+ OPTkey = {},
+ author = {\freiremarkref{\meabbrev} and Cl\'audio Silva},
+ title = { A Cluster Infrastructure to Support Retrieval, Management
+and Visualization of Massive Amounts of Data},
+ OPThowpublished = {},
+ month = feb,
+ year = 2003,
+ OPTnote = {Proposal submitted to the NSF CISE Research Infrastructure
+Program.},
+ note = {NSF CISE-RI-MII \emph{0323604}},
+ OPTannote = {}
+}
+
+ at Misc{vistrail at nsf2003,
+ OPTkey = {},
+ author = {Cl\'audio Silva and \freiremarkref{\meabbrev}},
+ title = { VisTrail: A Toolkit for Managing Complex Visualization Processes},
+ OPThowpublished = {},
+ month = jul,
+ year = 2003,
+ note = {Proposal submitted to the NSF Division of Advanced Computational
+Infrastructure \& Research},
+ OPTannote = {}
+}
+
+ at Misc{inria at nsf2003,
+ OPTkey = {},
+ author = {\freiremarkref{\meabbrev} and Michael Benedikt},
+ title = { New Automata and Grammar-based Tools for Web Data
+Processing},
+ OPThowpublished = {},
+ month = may,
+ year = 2003,
+ note = {Proposal submitted to the NSF/INRIA Collaborative Research Program},
+ OPTannote = {}
+}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ at InProceedings{chaudhuri at sigmod98,
+ author = {S. Chaudhuri, V.R. Narasayya},
+ title = {AutoAdmin 'What-if' Index Analysis Utility},
+ booktitle = sigmod,
+ pages = {367-378},
+ year = 1998
+}
+
+ at InProceedings{agrawal at sigmod01,
+ author = {S. Agrawal and S. Chaudhuri and V.R. Narasayya},
+ title = {Materialized View and Index Selection Tool for Microsoft SQL Server 2000},
+ booktitle = sigmod,
+ OPTpages = {},
+ year = {2001},
+ OPTnote = {To appear},
+ OPTannote = {}
+}
+
+ at InProceedings{klettke at webdb2000,
+ author = {M. Klettke and H. Meyer},
+ title = {{XML} and Object-Relational Database Systems - Enhancing Structural Mappings Based on Statistics},
+ booktitle = webdb,
+ pages = {63-68},
+ year = 2000
+}
+
+ at misc(dom at w3c,
+key = "DOM",
+title = "{DOM}",
+note = {\oneurl{http://www.w3.org/DOM}}
+)
+
+ at Article{silkroute at tods2002,
+ author = {Mary F. Fernandez and Yana Kadiyska and Dan Suciu and Atsuyuki Morishima and Wang Chiew Tan},
+ title = {SilkRoute: A framework for publishing relational data in XML},
+ journal = tods,
+ year = {2002},
+ volume = {27},
+ number = {4},
+ pages = {438-493},
+
+}
+
+ at InProceedings{xperanto,
+ author = {M.J. Carey and J. Kiernan and J. Shanmugasundaram and E.J. Shekita and
+ S.N. Subramanian},
+ title = { XPERANTO: Middleware for Publishing
+ Object-Relational Data as XML Documents},
+ booktitle = vldb,
+ pages = {646-648},
+ year = {2000},
+ OPTnote = {Carey at vldb00},
+ OPTannote = {}
+}
+
+ at InProceedings{Agrawal at vldb00,
+ author = {S. Agrawal and S. Chaudhuri and V.R. Narasayya},
+ title = {Automated Selection of Materialized Views and Indexes in {SQL} Databases},
+ booktitle = vldb,
+ pages = {496-505},
+ year = {2000},
+ OPTnote = {To appear},
+ OPTannote = {}
+}
+
+
+ at InProceedings{jirong at dasfaa03,
+ author = {S. Zheng and J-R. Wen and H. Lu},
+ title = {Cost-Driven Storage Schema Selection for {XML}},
+ booktitle = {Proceedings of DASFAA},
+ year = 2003
+}
+
+
+ at InProceedings{sauna at dasfaa2004,
+ author = {Abhijit Kadlag and Amol V. Wanjari and {\freiremarkref{\meabbrev}} and Jayant R. Haritsa},
+ title = {Supporting Exploratory Queries in Databases},
+ booktitle = {Proceedings of DASFAA},
+ pages = {594-605},
+ year = 2004
+}
+
+ at InProceedings{gmap at vldb94,
+ author = {O. Tsatalos and M. Solomon and Y. Ioannidis},
+ title = {The GMAP: A Versatile Tool for Physical Data Independence},
+ booktitle = vldb,
+ pages = {367-378},
+ year = 1994
+}
+
+
+ at InProceedings{rao at sigmod2002,
+ author = {Jun Rao and Chun Zhang and Nimrod Megiddo and Guy M. Lohman},
+ title = {Automating physical database design in a parallel database},
+ booktitle = sigmod,
+ pages = {558-569},
+ year = {2002},
+
+}
+
+ at InProceedings{db2advisor at icde2000,
+ author = {Gary Valentin and Michael Zuliani and Daniel C. Zilio and Guy M. Lohman and Alan Skelley},
+ title = {DB2 Advisor: An Optimizer Smart Enough to Recommend Its Own Indexes},
+ booktitle = icde,
+ OPTpages = {101-110},
+ year = 2000,
+}
+
+ at TechReport{galax at techrep,
+ author = {Byron Choi and Mary Fernandez and Jerome Sim\'eon},
+ title = {The XQuery Formal Semantics: A Foundation for Implementation and Optimization},
+ institution = {AT\&T Research},
+ year = {200},
+ OPTkey = {},
+ OPTtype = {},
+ number = {MS-CIS-02-25},
+ OPTaddress = {},
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at Misc{searchenginewatch,
+ key = {searchenginewatch},
+ OPTauthor = {},
+ title = {Search Engines Size},
+ OPThowpublished = {},
+ month = dec,
+ year = 2001,
+ OPTnote = {\oneurl{http://searchenginewatch.com/reports/article.php/2156481}},
+ OPTannote = {}
+}
+
+
+
+ at Book{googlehacks,
+ OPTauthor = {},
+ editor = {Tara Calishain and Rael Dornfest},
+ title = {Google Hacks: 100 Industrial-Strength Tips \& Tools},
+ publisher = {O'Reilly \& Associates},
+ year = {2003},
+ OPTnote = {},
+}
+
+
+ at Article{soumen at www1999,
+ author = {Soumen Chakrabarti and Martin van den Berg and Byron Dom},
+ title = {Focused Crawling: A New Approach to Topic-Specific Web Resource Discovery},
+ journal = {Computer Networks},
+ volume = {31},
+ number = {11-16},
+ pages = {1623-1640},
+ year = {1999}
+}
+
+ at InProceedings{doan at sigmod01,
+ author = {AnHai Doan and Pedro Domingos and Alon Y. Halevy},
+ title = {Reconciling Schemas of Disparate Data Sources: A Machine-Learning Approach},
+ booktitle = sigmod,
+ OPTpages = {},
+ year = {2001},
+ OPTnote = {To appear},
+ OPTannote = {}
+}
+
+ at Misc{soap at w3c,
+ key = {SOAP},
+ OPTauthor = {},
+ title = {{SOAP} Version 1.2 Part 0: Primer},
+ howpublished = {W3C Recommendation},
+ month = jun,
+ year = {2003},
+ note = {\\ \oneurl{http://www.w3.org/TR/2003/REC-soap12-part0-20030624}},
+ OPTannote = {}
+}
+
+
+
+ at Misc{http at w3c,
+ key = {HTTP},
+ title = {{HTTP} - Hypertext Transfer Protocol},
+ note = {\oneurl{http://www.w3.org/Protocols}},
+}
+
+
+ at Misc{html at w3c,
+ key = {HTML},
+ title = {HyperText Markup Language ({HTML})},
+ note = {\oneurl{http://www.w3.org/MarkUp}}
+}
+
+ at Misc{wsdl at w3c,
+ key = {WSDL},
+ OPTauthor = {W3C},
+ title = {Web Service Definition Language (WSDL)},
+ howpublished = {http://www.w3.org/TR/wsdl.html}
+}
+
+ at InProceedings{webl at www98,
+ author = {T. Kistlera and H. Marais},
+ title = {{WebL}: a programming language for the {Web}},
+ booktitle = www,
+ year = {1998},
+ pages = {283-294},
+ OPTnote = {http://www.research.digital.com/SRC/WebL/index.html},
+ OPTannote = {}
+}
+
+ at Misc{xsym2003,
+ key = {XSym},
+ OPTauthor = {},
+ title = {{XML} {Database} {Symposium} ({XSym2003})},
+ OPThowpublished = {},
+ OPTmonth = {},
+ OPTyear = {},
+ note = {\oneurl{http://www.lirmm.fr/$\tilde{\ }$bella/XSym}},
+ OPTannote = {}
+}
+
+ at Misc{cbr at uw,
+ key = {Columbia},
+ title = {{Columbia Basin Research -- School of Aquatic \& Fishery Sciences}},
+ note = {\oneurl{\\ http://www.cbr.washington.edu}},
+}
+
+ at InProceedings{vianu at icdt2003,
+ author = {Yannis Papakonstantinou and Victor Vianu},
+ title = {Incremental Validation of {XML} Documents},
+ booktitle = icdt,
+ year = 2003,
+ pages = {47-63},
+}
+
+ at InProceedings{braganholo at webdb2003,
+ author = {Vanessa P. Braganholo and Susan B. Davidson and Carlos A. Heuser},
+ title = { On the updatability of {XML} views over relational databases},
+ booktitle = webdb,
+ pages = {31-36},
+ year = 2003
+}
+
+
+ at inproceedings{braganholo at vldb2004,
+ author = {Vanessa P. Braganholo and
+ Susan B. Davidson and
+ Carlos A. Heuser},
+ title = {{From XML View Updates to Relational View Updates: old solutions
+ to a new problem.}},
+ booktitle = {VLDB},
+ year = {2004},
+}
+
+ at Article{nestedrel at acr1986,
+ author = {Stan J. Thomas and Patrick C. Fischer},
+ title = { Nested Relational Structures},
+ journal = {Advances in Computing Research},
+ year = {1986},
+ OPTkey = {},
+ volume = {3},
+ OPTnumber = {},
+ pages = {269-307 },
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at Misc{edr at epa,
+ key = {EPA},
+ title = {Environmental Data Registry -- U.S. Environmental
+Protection Agency},
+ note = {http://www.epa.gov/edr},
+}
+
+ at Misc{cleanair at epa,
+ key = {EPA},
+ title = {Clean Air Markets -- Data and Maps},
+ howpublished = {U.S. Environmental Protection Agency},
+ note = {http://cfpub.epa.gov/gdm},
+}
+ at Misc{inex2005,
+ key = {INEX},
+ OPTauthor = {},
+ title = {{INitiative} for the {Evaluation} of {XML} Retrieval ({INEX})},
+ OPThowpublished = {},
+ OPTmonth = {},
+ OPTyear = {},
+ note = {\\ \url{http://inex.is.informatik.uni-duisburg.de/2005}},
+ OPTannote = {}
+}
+
+ at inproceedings{parsing at cikm2003,
+ author = {Matthias Nicola and Jasmi John},
+ title = {{XML Parsing: a Threat to Database Performance}},
+ booktitle = CIKM,
+ year = {2003},
+ }
+
+ at Misc{dblp,
+ key = {DBLP},
+ OPTauthor = {},
+ title = {{DBLP}},
+ howpublished = {http://dblp.uni-trier.de/xml},
+ OPTmonth = {},
+ OPTyear = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at InProceedings{XSYM03:KKN,
+ author = {Rajasekar Krishnamurthy and Raghav Kaushik and
+ Jeffrey F. Naughton},
+ booktitle = xsym,
+ year = 2003,
+ title = {{XML-SQL Query Translation Literature: the State of
+ the Art and Open Problems}}
+}
+
+ at InProceedings{chaudhuri at icde2004,
+ author = {Surajit Chaudhuri and Zhiyuan Chen,
+ Kyuseok Shim and Yuqing Wu},
+
+ title = {Storing XML (with XSD) in SQL Databases},
+ booktitle = icde,
+ pages = {842},
+ year = 2004,
+}
+
+
+ at InProceedings{toxgene at webdb2002,
+ author = {Denilson Barbosa and Alberto O. Mendelzon and John Keenleyside and Kelly A. Lyons},
+
+ title = {{ToXgene}: An extensible template-based data generator for {XML}},
+ booktitle = webdb,
+ pages = {49-54},
+ year = 2002,
+}
+
+ at InProceedings{xbench at icde2004,
+ author = {{Benjamin Bin} Yao and {M. Tamer} �zsu, Nitin Khandelwal},
+
+ title = {{XBench} Benchmark and Performance Testing of {XML} {DBMSs}},
+ booktitle = icde,
+ pages = {621-633},
+ year = 2004,
+}
+
+ at inproceedings{sihem at edbt2002,
+ author = {Sihem Amer-Yahia and SungRan Cho and Divesh Srivastava},
+ title = {Tree Pattern Relaxation},
+ booktitle = edbt,
+ year = {2002},
+ OPTisbn = {3-540-43324-4},
+ pages = {496-513},
+ OPTpublisher = {Springer-Verlag},
+ OPTaddress = {London, UK},
+ }
+
+
+ at inproceedings{xpathlearner at vldb02,
+ author = {L. Lim and M. Wang and S. Padmanabhan and J. Vitter and R. Parr},
+ title = {{XP}ath{L}earner: An On-Line Self-Tuning Markov Histogream for {XML} Path Selectivity Estimation},
+ booktitle = vldb,
+ pages = {442-453},
+ year = 2002
+}
+
+ at inproceedings{barbosa at icde2004,
+ author = {Denilson Barbosa and Alberto O. Mendelzon and Leonid
+ Libkin and Laurent Mignet and Marcelo Arenas},
+ title = {{Efficient Incremental Validation of XML Documents}},
+ booktitle = icde,
+ year = 2004,
+ OPTpublisher = {IEEE Computer Society},
+}
+
+ at InProceedings{chen at vldb2003,
+ author = {Yi Chen and Susan Davidson and Carmem S. Hara and
+ Yifeng Zheng},
+ title = {{RRXF}: Redundancy reducing {XML} storage in
+ relations},
+ booktitle = vldb,
+ year = 2003,
+}
+
+ at inproceedings{consens at sigmod2005,
+ author = {Mariano Consens and Denilson Barbosa and Adian
+ Teisanu and Laurent Mignet},
+ title = {{Goals and Benchmarks for Autonomic Configuration
+ Recommenders}},
+ booktitle = sigmod,
+ year = 2005,
+ note = {To appear}
+}
+
+ at INPROCEEDINGS{davidson at icde2003,
+ author = {Susan Davidson and Wenfei Fan and Carmem Hara and
+ Jing Qin},
+ booktitle = icde,
+ title = {{Propagating XML Constraints to Relations}},
+ year = 2003
+}
+
+ at InProceedings{kane at cikm2002,
+ author = {Bintou Kane and Hong Su and Elke A. Rundensteiner},
+ title = {{Consistently Updating XML Documents Using
+ Incremental Constraint Check Queries}},
+ booktitle = cikm,
+ year = 2002,
+}
+
+ at InProceedings{donko at icde00,
+ author = {D. Donjerkovic and Y. Ioannidis and R. Ramakrishnan},
+ title = {Dynamic Histograms: Capturing Evolving Data Sets},
+ booktitle = icde,
+ OPTpages = {86},
+ year = 2000
+}
+
+ at inproceedings{multiHistMaint at fsttcs03,
+ author = {S. Muthukrishnan and M. Strauss},
+ title = {Maintenance of Multidimensional Histograms},
+ booktitle = fsttcs,
+ OPTpages = {352-362},
+ year = 2003
+}
+
+ at Misc{repcbr at uw,
+ key = {CBRE},
+ title = {Columbia Basin Research -- University of Washington},
+ note = {\url{http://http://www.cbr.washington.edu}}
+}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+ at inproceedings{papak at icdt2003,
+ author = {Yannis Papakonstantinou and Victor Vianu},
+ title = {Incremental Validation of {XML} Documents},
+ booktitle = {International Conference on Database Theory},
+ pages = {47-63},
+ year = 2003,
+ address = {Siena, Italy},
+ month = {January 8-10}
+}
+
+ at inproceedings{repbarbosa at icde2004,
+ author = {Denilson Barbosa and Alberto O. Mendelzon and Leonid
+ Libkin and Laurent Mignet and Marcelo Arenas},
+ title = {Efficient Incremental Validation of {XML} Documents},
+ booktitle = {International Conference on Data Engineering},
+ year = 2004,
+ note = {To appear}
+}
+
+ at inproceedings{bouchou at dbpl2003,
+ author = {Beatrice Bouchou and Mirian Halfeld-Ferrari-Alvez},
+ title = {{Updates and Incremental Validation of XML
+ Documents}},
+ booktitle = {9th International Conference on Data Base
+ Programming Languages (DBPL)},
+ year = 2003,
+ month = {September 6-8},
+ address = {Potsdam, Germany}
+}
+
+ at InProceedings{OLDtatarinov at sigmod2001,
+ author = {Igor Tatarinov and Zachary G. Ives and Alon Y. Halevy and Daniel S. Weld},
+ title = {Updating XML},
+ booktitle = sigmod,
+ OPTpages = {not-available},
+ year = 2001
+}
+
+ at InProceedings{mchugh at vldb1999,
+ author = {J. McHugh and J. Widom},
+ title = {Query Optimization for {XML}},
+ booktitle = vldb,
+ pages = {315-326},
+ year = {1999},
+}
+
+ at inproceedings{twig at icde2001,
+ author = {Z. Chen and H.V. Jagadish and F. Korn and N. Koudas and S. Muthukrishnan and R.T. Ng and D. Srivastava},
+ title = {Counting Twig Matches in a Tree},
+ booktitle = icde,
+ OPTpublisher = {IEEE Computer Society},
+ year = {2001},
+ pages = {595-604}
+}
+
+ at InProceedings{aboulnaga at vldb2001,
+ author = {A. Aboulnaga and A.R. Alameldeen and J.Naughton},
+ title = {Estimating the Selectivity
+ of {XML} Path Expressions for {Internet} Scale Applications},
+ booktitle = vldb,
+ pages = {591-600},
+ year = 2001
+}
+
+ at InProceedings{jag at edbt2002,
+ author = {Y. Wu and J.~M. Patel and H.~V. Jagadish},
+ title = {Estimating Answer Sizes for XML Queries},
+ booktitle = edbt,
+ year = {2002},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at InProceedings{minos at sigmod2002,
+ author = {N. Polyzotis and M. Garofalakis},
+ title = {Statistical Synopses for Graph Structured {XML} Databases},
+ booktitle = sigmod,
+ year = {2002},
+ pages = {358-369},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at Misc{OLDgalax,
+ key = {Galax},
+ title = {Galax},
+ OPTmonth = oct,
+ OPTyear = 2001,
+ note = {\oneurl{http://db.bell-labs.com/galax}}
+}
+
+
+ at InProceedings{aboulnaga at sigmod1999,
+ author = {A. Aboulnaga and S. Chaudhuri},
+ title = {Self-tuning Histograms: Building Histograms Without Looking at Data},
+ booktitle = sigmod,
+ pages = {181-192},
+ year = {1999}
+}
+
+ at Book{tree-automata,
+ ALTauthor = {},
+ editor = {G. Rozenberg and A. Salomaa},
+ title = {Handbook of formal languages},
+ publisher = {Springer Verlag},
+ year = {1997},
+ volume = {3},
+}
+
+ at Article{ioannidis at tods1993,
+ author = {Y. Ioannidis and S. Christodoulakis},
+ title = {Optimal Histograms for Limiting Worst-Case Error Propagation in the Size of
+ Join Results},
+ journal = tods,
+ year = {1993},
+ OPTkey = {},
+ volume = {18},
+ number = {4},
+ pages = {709-748},
+}
+
+ at InProceedings{kemper at sigmod1990,
+ author = {A. Kemper and G. Moerkotte},
+ title = {Access Support in Object Bases},
+ booktitle = sigmod,
+ pages = {364-374},
+ year = {1990}
+}
+
+ at InProceedings{kemper at vldb1990,
+ author = {A. Kemper and G. Moerkotte},
+ title = {Advanced Query Processing in Object Bases Using Access Support Relations},
+ booktitle = vldb,
+ pages = {290-301},
+ year = {1990}
+}
+
+ at InProceedings{toxin at webdb2001,
+ author = {F. Rizzolo and A. Mendelzon.},
+ title = {Indexing {XML} Data with ToXin},
+ booktitle = {Workshop on the Web and Databases (WebDB},
+ OPTpages = {},
+ year = {2001},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at inproceedings{OLDlegodb at icde2002,
+ author = {P. Bohannon and J. Freire and P. Roy and J. Sim\'eon},
+ title = {From {XML} Schema to Relations: A Cost-Based Approach to {XML} Storage},
+ booktitle = icde,
+ OPTpublisher = {IEEE Computer Society},
+ year = {2002},
+ pages = {64-75},
+ OPTnote = {To appear}
+}
+
+ at Misc{blindlegodb at icde2002,
+ key = {zzz},
+ howpublished = {Reference removed for double-blind review},
+}
+
+ at inproceedings{OLDstatix at sigmod2002,
+ author = { J. Freire and J. Haritsa and M. Ramanath and P. Roy and J. Sim\'eon},
+ title = {StatiX: Making {XML} Count},
+ booktitle = sigmod,
+ OPTpublisher = {ACM},
+ year = {2002},
+ pages = {181-191},
+}
+
+ at inproceedings{DUPstatix at sigmod2002,
+ author = {J. Freire and J. Haritsa and M. Ramanath and P. Roy and J. Sim\'eon},
+ title = {{StatiX}: Making {XML} Count},
+ booktitle = sigmod,
+ OPTpublisher = {ACM},
+ year = {2002},
+ OPTpages = {209-218},
+ note = {To appear}
+}
+
+
+ at TechReport{statix at techrep2002,
+ author = {J. Freire and J. Haritsa and M. Ramanath and P. Roy and J. Sim\'eon},
+ OPTtitle = {{StatiX}: Making {XML} Count},
+ title = {Gathering and Deriving Statistics for {XML} Data},
+ institution = {Bell Labs},
+ year = {2002},
+ OPTkey = {},
+ OPTtype = {},
+ OPTnumber = {},
+ OPTaddress = {},
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+
+ at InProceedings{goldman at vldb97,
+ author = {R. Goldman and J. Widom},
+ title = {DataGuides: Enabling Query Formulation and
+ Optimization in Semistructured Databases},
+ booktitle = vldb,
+ pages = {436-445},
+ year = {1997},
+ OPTnote = {},
+}
+
+ at InProceedings{milo at icdt99,
+ author = {T. Milo and D. Suciu},
+ title = {Index Structures for Path Expressions},
+ booktitle = icdt,
+ pages = {277-295},
+ year = {1999},
+ OPTnote = {},
+}
+
+
+ at InProceedings{DUPaboulnaga at vldb2001,
+ author = {A. Aboulnaga and A.R. Alameldeen and J.Naughton},
+ title = {Estimating the Selectivity
+ of {XML} Path Expressions for {Internet} Scale Applications},
+ booktitle = vldb,
+ pages = {591-600},
+ year = 2001
+}
+
+ at InProceedings{OLDgmap at vldb94,
+ author = {O. Tsatalos and M. Solomon and Y. Ioannidis},
+ title = {The GMAP: A Versatile Tool for Physical Data Independence},
+ booktitle = vldb,
+ pages = {367-378},
+ year = 1994
+}
+
+ at InProceedings{OLDShan at vldb99,
+ author = {J. Shanmugasundaram and K. Tufte and G. He and C. Zhang and D. DeWitt and J. Naughton},
+ title = {Relational Databases for Querying {XML} Documents: Limitations and Opportunities},
+ booktitle = vldb,
+ pages = {302-314},
+ year = 1999
+}
+
+ at InProceedings{Sellis at vldb97,
+ author = {D. Theodoratos and T. K. Sellis},
+ title = {Data Warehouse Configuration},
+ booktitle = vldb,
+ pages = {126-135},
+ year = 1997
+}
+
+ at InProceedings{Carey at vldb99,
+ author = {M. Carey and D. Chamberlin and S. Narayanan and B. Vance and D. Doole and S. Rielau and R. Swagerman and N. Mattos},
+
+ title = {O-O, What Have They Done to DB2},
+ booktitle = vldb,
+ year = 1999
+}
+
+ at InProceedings{OLDDeutsch at sigmod99,
+ author = {A. Deutsch and M. Fernandez and D. Suciu},
+ title = {Storing Semi-Structured Data with {STORED}},
+ booktitle = sigmod,
+ pages = {431-442},
+ year = 1999
+}
+
+ at InProceedings{Deutsch at www99,
+ author = {A. Deutsch and M. Fernandez and D. Florescu and A. Levy and D. Suciu},
+ title = {{XML-QL}: A Query Language for {XML}},
+ booktitle = www,
+ year = 1999
+}
+
+
+ at InProceedings{BROKENFernandez at www9-conf,
+ author = { M.F. Fernandez and W.C. Tan and D. Suciu},
+ title = {SilkRoute: trading between relations and {XML}},
+ booktitle = {WWW9},
+ year = 2000
+}
+
+ at Article{silkroute,
+ author = {M.F. Fernandez and W.C. Tan and D. Suciu},
+ title = {SilkRoute: trading between relations and {XML}},
+ journal = {WWW9/Computer Networks},
+ year = {2000},
+ volume = {33},
+ number = {1-6},
+ pages = {723-745},
+ OPTnote = {},
+ OPTannote = {Fernandez at www00}
+}
+
+
+ at Misc{xql,
+ author = {J. Robie and J. Lapp and D. Schach},
+ title = {{XML} Query Language ({XQL})},
+ howpublished = {http://www.w3.org/TandS/QL/QL98/pp/xql.html},
+ year = 1998
+}
+
+ at Misc{oasis,
+ key = {Oasis},
+ title = {The {XML} Cover Pages},
+ note = {\oneurl{http://www.oasis-open.org/cover}}
+}
+
+
+ at Misc{DUPoasis,
+ OPTauthor = {},
+ key = {Oasis},
+ title = {{XML} Query Language (XQL)},
+ howpublished = {http://www.oasis-open.org},
+ year = 2001
+}
+
+
+ at Misc{tianVarious,
+ author = {F. Tian and D. DeWitt and J. Chen and C. Zhung},
+ title = {The Design and Performance Evaluation of Various {XML} Storage Strategies},
+ howpublished = {http://www.cs.wisc.edu/niagra/Publications.html},
+ year = 2001
+}
+
+ at Book{Raghu at book1997,
+ author = {R. Ramakrishnan},
+ title = {Database Management Systems},
+ publisher = {Morgan Kaufman},
+ year = 1997
+}
+
+ at Misc{html,
+ key = {HTML},
+ title = {www.w3.org/HTML}
+}
+
+ at Misc{OLDxml at w3c,
+ key = {XML},
+ author = {T. Bray and J. Paoli and C. Sperberg-McQueen},
+ title = {Extensible Markup Language ({XML}) 1.0},
+ month = feb,
+ year = 1998,
+ note = {{W3C} recommendation available at http://www.w3.org/TR/1998/REC-xml-19980219}
+}
+
+ at Misc{xquery-requirements at w3org,
+ key = {Requirements},
+ author = {D. Chamberlin and P. Fankhauser and J. Robie},
+ title = {{XML} Query Requirements},
+ month = feb,
+ year = 2001,
+ note = {{W3C} Working Draft available at http://www.w3.org/}
+}
+
+ at Misc{xml-dm at w3org,
+ key = {XDM},
+ author = {M. Fernandez and J. Robie},
+ title = {The {XML} Query Data Model},
+ month = feb,
+ year = 2001,
+ note = {{W3C} Working Draft available at http://www.w3.org/}
+}
+
+ at Misc{xml-algebra at w3org,
+ key = {XAlgebra},
+ author = {P. Fankhauser and M. Fernandez and A. Malhotra and M. Rys and J. Sim\'{e}on and P. Wadler},
+ title = {The {XML} Query Algebra},
+ month = feb,
+ year = 2001,
+ note = {http://www.w3.org/TR/2001/WD-query-algebra-20010215}
+}
+
+ at Misc{xquery at w3crep,
+ author = {S. Boag and D. Chamberlin and M. Fernandez and D. Florescu and J. Robie and J. Sim\'eon and M. Stefanescu},
+ title = {{XQuery} 1.0: An {XML} Query Language},
+ howpublished = {{W3C} Working Draft},
+ month = jun,
+ year = 2001
+}
+
+ at Misc{xquery at w3org,
+ key = {XQuery},
+ author = {D. Chamberlin and D. Florescu and J. Robie and J. Sim\'{e}on and M. Stefanescu},
+ title = {{XQuery}: A Query Language for {XML}},
+ month = feb,
+ year = 2001,
+ note = {{W3C} Working Draft available at http://www.w3.org/}
+}
+
+ at Misc{excelon,
+ key = {EXCELON},
+ title = {Excelon},
+ howpublished = {http://www.odi.com/excelon}
+}
+ at Misc{suciu at ss-tutorial,
+ author = {D. Suciu},
+ title = {From Semi-Structured Data to {XML}},
+ howpublished = {http://www.research.att.com/\verb$~$suciu/slides.ppt},
+ year = 1999,
+ note = {Tutorial presented at VLDB}
+}
+
+ at Book{abiteboul at book1999,
+ author = {S. Abiteboul and P. Buneman and D. Suciu},
+ title = {Data on the {Web}},
+ publisher = {Morgan Kaufmann},
+ year = 1999
+}
+
+ at Article{lore at sigmod-record,
+ author = {J. McHugh and S. Abiteboul and R. Goldman and D. Quass and J. Widom},
+ title = {A Database Management System for Semistructured Data},
+ journal = sigmod-record,
+ year = 1997,
+ volume = 26,
+ number = 3,
+ pages = {54-66},
+ month = sep
+}
+
+ at TechReport{lore at sigrec,
+ author = {J. McHugh and S. Abiteboul and R. Goldman and D. Quass and J. Widom},
+ title = {A Database Management System for Semistructured Data},
+ institution = {Stanford},
+ year = 1997
+}
+
+ at InProceedings{cluet at sigmod98,
+ author = {S. Cluet and C. Delobel and J. Sim\'{e}on and K. Smaga},
+ title = {Your Mediators Need Data Conversion!},
+ booktitle = sigmod,
+ pages = {177-188},
+ year = 1998
+}
+
+ at Misc{widom at xml-note,
+ author = {J. Widom},
+ title = {Data Management for {XML} - Reseach Directions},
+ howpublished = {http://www-db.stanford.edu/\verb$~$widom/xml-whitepaper.html},
+ year = 1999
+}
+
+ at book{ullman at book1,
+AUTHOR = "J. Ullman",
+TITLE = "Principles of Data and Knowledge-base Systems Vol {I}",
+PUBLISHER = "Computer Science Press",
+YEAR = 1989}
+
+ at book{ullman at book2,
+AUTHOR = "J. Ullman",
+TITLE = "Principles of Data and Knowledge-base Systems Vol {II}",
+PUBLISHER = "Computer Science Press",
+YEAR = 1989}
+
+ at Unpublished{dcd,
+ author = {T. Bray and C. Frankston and A. Malhotra},
+ title = {Document Content Description for {XML}},
+ note = {http://www.w3.org/TR/NOTE-dcd},
+ year = 1998
+}
+
+ at Misc{OLDxquery at w3c,
+ author = {D. Chambelin and J. Clark and D. Florescu and Jonathan Robie and J. Sim\'eon and M. Stefanescu},
+ title = {{XQuery} 1.0: An {XML} Query Language},
+ howpublished = {{W3C} Working Draft},
+ month = jun,
+ year = 2001
+}
+
+ at Misc{OLDxschema at w3c,
+ author = {H. Thompson and D. Beech and M. Maloney and N. Mendelsohn},
+ title = {{XML} {Schema} {Part} 1: Structures},
+ howpublished = {{W3C} Working Draft},
+ month = feb,
+ year = 2000
+}
+
+
+ at Misc{OLDdtd at w3c,
+ author = {J. Bosac and T. Bray and D. Connolly and E. Maler and G. Nicol and C.M. Sperberg-McQueen and L. Wood and J. Clark},
+ title = {Guide to the {W3C} {XML} Specification ("{XMLspec}") {DTD}},
+ howpublished = {http://www.w3.org/XML/1998/06/xmlspec-report},
+ month = jun,
+ year = 1998
+}
+
+ at TechReport{florescu at inria99,
+ author = {D. Florescu and D. Kossmann},
+ title = {A Performance Evaluation of Alternative
+Mapping Schemes for Storing {XML} in a Relational Database},
+ institution = {INRIA},
+ year = 1999,
+ number = 3680
+}
+
+ at InProceedings{OLDchaudhuri at sigmod98,
+ author = {S. Chaudhuri, V.R. Narasayya},
+ title = {AutoAdmin 'What-if' Index Analysis Utility},
+ booktitle = sigmod,
+ pages = {367-378},
+ year = 1998
+}
+
+ at InProceedings{selinger at sigmod79,
+ author = {P. Selinger and M. Astrahan and D. Chamberlin and R. Lorie and T. Price},
+ title = {Access Path Selection in a Relational Database Management System},
+ booktitle = sigmod,
+ pages = {23-34},
+ year = 1979
+}
+
+ at inproceedings{Graefe at icde93,
+ author = {G. Graefe and W. McKenna},
+ title = {The Volcano Optimizer Generator: Extensibility and Efficient
+ Search},
+ OPTbooktitle = {Proceedings of the Ninth International Conference on Data Engineering,
+ April 19-23, 1993, Vienna, Austria},
+ booktitle = icde,
+ OPTpublisher = {IEEE Computer Society},
+ year = {1993},
+ OPTisbn = {0-8186-3570-3},
+ pages = {209-218},
+ OPTcrossref = {DBLP:conf/icde/93},
+ bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+ at InProceedings{abiteboul at icdt97,
+ author = {S. Abiteboul},
+ title = {Access Path Selection in a Relational Database Management System},
+ booktitle = icdt,
+ pages = {1-18},
+ year = 1997
+}
+
+ at InProceedings{buneman at pods97,
+ author = {P. Buneman},
+ title = {Semistructured Data},
+ booktitle = pods,
+ pages = {117-121},
+ year = 1997
+}
+
+ at Book{kroenke at book1995,
+ author = {David M. Kroenke},
+ title = {Database Processing: Fundamentals, Design, and Implementation},
+ publisher = {Prentice Hall},
+ year = 1995
+}
+
+ at InProceedings{OLDschmidt at webdb2000,
+ author = {A. Schmidt and M. Kersten and M. Windhouwer and F. Waas},
+ title = {Efficient Relational Storage and Retrieval of {XML} Documents},
+ booktitle = webdb,
+ pages = {47-52},
+ year = 2000
+}
+
+ at InProceedings{kanne at icde2000,
+ author = {C. Kanne and G. Moerkotte},
+ title = {Efficient Storage of {XML} Data},
+ booktitle = icde,
+ pages = 198,
+ year = 2000
+}
+
+ at InProceedings{fiebig at webdb2000,
+ author = {T. Fiebig, G. Moerkotte},
+ title = {Evaluating Queries on Structure with eXtended Access Support Relations},
+ booktitle = webdb,
+ pages = {41-46},
+ year = 2000
+}
+
+ at InProceedings{OLDklettke at webdb2000,
+ author = {M. Klettke and H. Meyer},
+ title = {{XML} and Object-Relational Database Systems - Enhancing Structural Mappings Based on Statistics},
+ booktitle = webdb,
+ pages = {63-68},
+ year = 2000
+}
+
+ at InProceedings{klettke at xml2000,
+ author = {M. Klettke and H. Meyer},
+ title = {Managing {XML} documents in object-relational databases},
+ booktitle = {Proceedings of the {XML} Conference},
+ pages = {63-68},
+ year = 2000
+}
+
+ at InProceedings{kha at icde2001,
+ author = {D. Kha and M. Yoshikawa and S. Uemura},
+ title = {An {XML} Indexing Structure with Relative Region Coordinate},
+ pages = {313-320},
+ booktitle = icde,
+ year = 2001,
+ OPTnote = {To appear}
+}
+
+ at InProceedings{OLDshimura at dexa1999,
+ author = {T. Shimura and M. Yoshikawa and S. Uemura},
+ title = {Storage and Retrieval of {XML} Documents Using Object-Relational Databases},
+ booktitle = dexa,
+ pages = {206-217},
+ year = 1999
+}
+
+ at Book{AbBuSu1999,
+ author = {S. Abiteboul and P. Buneman and D. Suciu},
+ title = {Data on the Web: From Relations to Semistructured Data and {XML}},
+ publisher = {Morgan Kaufmann},
+ year = 1999
+}
+
+
+ at InProceedings{FaKuSi2001,
+ author = {W. Fan and G. Kuper and J. Sim\'eon},
+ title = {A Unified Constraint Model for {XML}},
+ booktitle = WWW,
+ pages = {179-190},
+ year = 2001,
+ address = {Hong Kong, China},
+ month = may,
+ OPTnote = {to appear}
+}
+
+ at InProceedings{PaVi2000,
+ author = {Yannis Papakonstantinou and Victor Vianu},
+ title = {{DTD} Inference for Views of {XML} Data},
+ booktitle = PODS,
+ year = 2000,
+ address = {Dallas, Texas},
+ month = may
+}
+
+ at Book{RoSa1997,
+ editor = {Grzegorz Rozenberg and Arto Salomaa},
+ title = {Handbook of Formal Languages},
+ publisher = {Springer-Verlag},
+ year = 1997
+}
+
+
+ at InProceedings{Agrawal at sigmod01,
+ author = {S. Agrawal and S. Chaudhuri and V.R. Narasayya},
+ title = {Index Tuning Wizard for Microsoft {SQL} Server 2000},
+ booktitle = sigmod,
+ OPTpages = {},
+ year = {2001},
+ note = {To appear},
+ OPTannote = {}
+}
+
+ at InProceedings{DUPmchugh at vldb1999,
+ author = {J. McHugh and J. Widom},
+ title = {Query Optimization for {XML}},
+ booktitle = vldb,
+ pages = {315-326},
+ year = {1999},
+}
+
+ at InProceedings{OLDAgrawal at vldb00,
+ author = {S. Agrawal and S. Chaudhuri and V.R. Narasayya},
+ title = {Automated Selection of Materialized Views and Indexes in {SQL} Databases},
+ booktitle = vldb,
+ pages = {496-505},
+ year = {2000},
+ OPTnote = {To appear},
+ OPTannote = {}
+}
+
+ at Misc{xmlsql at oracle,
+ key = {XML SQL},
+ OPTauthor = {},
+ title = {Oracle's {XML} {SQL} Utility},
+ howpublished = {http://technet.oracle.com/tech/xml/oracle\_xsu},
+ OPTnote = {straightforward mapping from xml into ordbms},
+ OPTannote = {}
+}
+
+ at Article{sqlserverxml at icdebulletin,
+ author = {M. Rhys},
+ title = {State-of-the-art {XML} Support in {RDBMS}: {M}icrosoft {SQL} {S}erver's {XML} Features},
+ journal = {Bulletin of the Technical Committee on Data Engineering} ,
+ year = 2001,
+ volume = 24,
+ number = 2,
+ pages = {3-11},
+ month = jun
+}
+
+
+ at Misc{imdb,
+ key = {IMDB},
+ OPTauthor = {},
+ title = {Internet {Movie} {Database}},
+ howpublished = {\url{http://www.imdb.com}},
+ OPTnote = {Data can be downloaded from {\TTT ftp://ftp.fu-berlin.de/pub/misc/movies/database/tools/}},
+ OPTannote = {}
+}
+
+
+ at InProceedings{OLDxperanto,
+ author = {M.J. Carey and J. Kiernan and J. Shanmugasundaram and E.J. Shekita and
+ S.N. Subramanian},
+ title = { XPERANTO: Middleware for Publishing
+ Object-Relational Data as {XML} Documents},
+ booktitle = vldb,
+ pages = {646-648},
+ year = {2000},
+ OPTnote = {Carey at vldb00},
+ OPTannote = {}
+}
+
+ at InProceedings{HoPi2000,
+ author = {Haruo Hosoya and Benjamin C. Pierce},
+ title = {{XDuce}: an {XML} Processing Language},
+ booktitle = {International Workshop on the Web and Databases (WebDB'2000)},
+ year = 2000,
+ address = {Dallas, Texas},
+ month = may
+}
+
+ at inproceedings{volc:icde93,
+ Author = "Goetz Graefe and William J. McKenna",
+ Title = "The Volcano Optimizer Generator: Extensibility and
+ Efficient Search",
+ Booktitle = icde,
+ Year = 1993}
+
+ at inproceedings{rssb:sigmod00,
+ Author = "P. Roy and S. Seshadri and S. Sudarshan and S.
+Bhobe",
+ Title = "Efficient and Extensible Algorithms for Multi Query
+Optimization",
+pages = "249-260",
+ Booktitle = sigmod,
+ Year = 2000}
+
+ at inproceedings{xtract at sigmod00,
+ Author = "M. Garofalakis and A. Gionis and R. Rastogi and S. Seshadri and K. Shim",
+ Title = "XTRACT: A System for Extracting Document Type
+ Descriptors from {XML} Documents",
+ Booktitle = sigmod,
+ pages = "165-176",
+ Year = 2000}
+
+ at InProceedings{ChAbClSc1994,
+ author = {V. Christophides and S. Abiteboul and S.
+Cluet and M. Scholl},
+ title = {From Structured Documents to Novel Query Facilities},
+ booktitle = SIGMOD,
+ year = 1994,
+ address = {Minneapolis, Minnesota},
+ month = may,
+ pages = {313-324}
+}
+
+
+ at InProceedings{poosala at sigmod1996,
+ author = {V. Poosala and Y. Ioannidis and P. Haas and E. Shekita},
+ title = {Improved Histograms for Selectivity Estimation of Range Predicates},
+ booktitle = sigmod,
+ pages = {294-305},
+ year = {1996},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at InProceedings{poosala at vldb1997,
+ author = {V. Poosala and Y. Ioannidis},
+ title = {Selectivity Estimation Without the Attribute
+ Value Independence Assumption},
+ booktitle = vldb,
+ pages = {486-495},
+ year = {1997},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at InProceedings{yannis at vldb1993,
+ author = {Y. Ioannidis},
+ title = {Universality of Serial Histograms},
+ booktitle = vldb,
+ pages = {256-267},
+ year = {1993},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+
+ at Misc{OLDxerces,
+ key = {Xerces},
+ title = {Xerces Java Parser 1.4.3 },
+ howpublished = {http://xml.apache.org/xerces-j/},
+ OPTmonth = {},
+ OPTyear = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at Misc{xmark,
+ key = {XMark},
+ title = {{XMark}},
+ howpublished = {http://monetdb.cwi.nl/xml},
+}
+
+ at Misc{infoset at w3c,
+ author = {John Cowan and Richard Tobin},
+ title = {{XML} Information Set},
+ month = oct,
+ year = 2001,
+ note = {{W3C} recommendation available at
+ http://www.w3.org/TR/xml-infoset/}
+}
+
+ at Misc{xmlspy,
+ key = {Spy},
+ title = {{XML} Spy},
+ note = {http://www.xmlspy.com/}
+}
+
+ at Misc{schemaformal at w3crepeated,
+ author = {Allen Brown and Matthew Fuchs and Jonathan Robie and
+ Philip Wadler},
+ title = {{XML Schema}: Formal Description},
+ year = 2001,
+ note = {{W3C} Working Draft}
+}
+ at Misc{schemaformal at w3c,
+ author = {Allen Brown and Matthew Fuchs and Jonathan Robie and
+ Philip Wadler},
+ title = {{XML Schema}: Formal Description},
+ year = 2001,
+ note = {{W3C} Working Draft},
+ OPTnote = {{W3C} working draft available at
+ http://www.w3.org/TR/2001/WD-xmlschema-formal-20010320/}
+}
+
+ at InProceedings{xduce,
+ author = {Haruo Hosoya and Jerome Vouillon and Benjamin
+ Pierce},
+ title = {Regular Expression Types for {XML}},
+ booktitle = {Proceedings of the International Conference on
+ Functional Programming (ICFP)},
+ pages = {11-22},
+ year = 2000,
+ month = sep
+}
+
+ at PhdThesis{neumannphd,
+ author = {Andreas Neumann},
+ title = {Parsing and Querying {XML} Documents in {SML}},
+ school = {Universitt Trier},
+ year = 1999,
+ type = {Dissertation},
+ month = dec
+}
+
+ at Misc{DUPgalax,
+ key = {Galax},
+ title = {Galax System},
+ month = oct,
+ year = 2001,
+ note = {http://db.bell-labs.com/galax/}
+}
+
+ at Misc{tata97,
+ author = {H. Comon and M. Dauchet and R. Gilleron and
+ F. Jacquemard and D. Lugiez and S. Tison and M. Tommasi},
+ title = {Tree Automata Techniques and Applications},
+ howpublished = {Available on:
+ http://www.grappa.univ-lille3.fr/tata},
+ year = 1997
+}
+
+ at article{berry86,
+ author = "Gerard Berry and Ravi Sethi",
+ title = "From Regular Expressions to Deterministic Automata",
+ journal = "Theoretical Computer Science",
+ volume = "48",
+ number = "1",
+ pages = "117--126",
+ year = "1986"
+}
+
+
+ at Article{klein1,
+ author = {A. Br\"uggemann-Klein},
+ title = {Regular Expressions into Finite Automata},
+ journal = {TCS},
+ year = 1993,
+ volume = 120,
+ number = 2,
+ pages = {197-213}
+}
+
+ at Article{klein2,
+ author = {A. Br\"uggemann-Klein and D. Wood},
+ title = {One-Unambiguous Regular Languages},
+ journal = {Information and Computation},
+ year = 1998,
+ volume = 140,
+ number = 2,
+ pages = {229-253}
+}
+
+ at InProceedings{DUPminos at sigmod2002,
+ author = {N. Polyzotis and M. Garofalakis},
+ title = {Statistical Synopses for Graph Structured {XML} Databases},
+ booktitle = sigmod,
+ year = {2002},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at InProceedings{minos at vldb2002,
+ author = {N. Polyzotis and M. Garofalakis},
+ title = {Structure and Value Synopses for {XML} Data Graphs},
+ booktitle = vldb,
+ year = {2002},
+ pages = {466-477},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at InProceedings{DUPjag at edbt2002,
+ author = {Y. Wu and J.~M. Patel and H.~V. Jagadish},
+ title = {Estimating Answer Sizes for XML Queries},
+ booktitle = edbt,
+ year = {2002},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at InProceedings{piatetsky-shapiro at sigmod1984,
+ author = {G. Piatetsky-Shapiro and C. Connell},
+ title = {Accurate Estimation of the Number of Tuples Satisfying a Condition},
+ booktitle = sigmod,
+ year = {1984},
+ pages = {256-276},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at InProceedings{xmill at sigmod2000,
+ author = {H. Liefke and D. Suciu},
+ title = {XMill: An Efficient Compressor for XML Data},
+ booktitle = sigmod,
+ pages = {},
+ year = {2000},
+ OPTnote = {},
+}
+
+ at InProceedings{xgrind at icde2002,
+ author = {P. Tolani and J. Haritsa},
+ title = {XGRIND: A Query-friendly XML Compressor},
+ booktitle = icde,
+ pages = {},
+ year = {2002},
+ OPTnote = {},
+}
+
+ at InProceedings{xpress at sigmod2003,
+ author = {J. Min, M. Park and C. Chung},
+ title = {XPRESS: A Queriable Compression for XML data},
+ booktitle = sigmod,
+ pages = {},
+ year = {2003},
+ OPTnote = {},
+}
+
+ at InProceedings{xquec at edbt2004,
+ author = {A. Arion et al},
+ title = {Efficient Query Evaluation over Compressed XML Data},
+ booktitle = edbt,
+ pages = {},
+ year = {2004},
+ OPTnote = {},
+}
+
+ at Article{gmp at tods2002,
+ author = {P. Gibbons, Y. Matias and V. Poosala},
+ title = {Fast Incremental Maintenance of Approximate Histograms},
+ journal = tods,
+ year = {2002},
+ OPTkey = {},
+ volume = {27},
+ number = {3},
+ pages = {261-298},
+}
+
+
+ at PhdThesis{poosala at diss1997,
+ author = {Viswanath Poosala},
+ title = { Histogram-based Estimation Techniques in Databases},
+ school = {University of Wisconsin Madison},
+ year = {1997},
+}
+
+ at MastersThesis{OLDlehti at thesis,
+ author = {Patrick Lehti},
+ title = {Design and Implementation of a Data Manipulation Processor for an XML Query Language},
+ school = {Universit\"{a}t Darmstadt},
+ year = {2001},
+}
+
+Denilson Barbosa, Alberto O. Mendelzon, John Keenleyside, Kelly A. Lyons: .WebDB 2002: 49-54
+
+ at InProceedings{toxgene,
+ author = {Denilson Barbosa and Alberto O. Mendelzon and John Keenleyside and Kelly A. Lyons},
+ title = {{ToXgene}: An extensible template-based data generator for {XML}},
+ booktitle = webdb,
+ pages = {49-54},
+ year = 2002
+}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+ at InProceedings{benedikt at sigmod2003,
+ author = {M. Benedikt and C. Y. Chan and W. Fan and \freiremarkref{\meabbrev} and R. Rastogi},
+title = {Capturing both Types and Constraints in Data Integration},
+ booktitle = sigmod,
+ year = {2003},
+ pages = {277-288},
+ OPTnote = {To appear},
+ OPTannote = {}
+}
+
+ at Misc{Clar1999,
+ author = {James Clark},
+ title = {{XSL} Transformations ({XSLT})},
+ howpublished = {W3C Recommendation},
+ month = nov,
+ year = 1999,
+ note = {\\ \oneurl{http://www.w3.org/TR/xslt}}
+}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ at misc{csilva1,
+ Author = {Bavoil, Louis and Callahan, Steven and Crossno,
+ Patricia and Freire, Juliana and Scheidegger, Carlos
+ and Silva, Claudio T. and Vo, Huy T.},
+ Title = {VisTrails: Enabling Interactive Multiple-View
+ Visualizations},
+ Year = 2005
+}
+
+ at article{csilva2,
+ Author = {Bernardon, Fabio and Pagot, C. and Comba, Joao
+ L. D. and Silva, Claudio T.},
+ Title = {{GPU}-based Tiled Ray Casting using Depth Peeling},
+ Journal = {Journal of Graphics Tools},
+ Year = 2005
+}
+
+ at article{csilva3,
+ Author = {Callahan, Steven and Ikits, Milan and Comba, Joao
+ L. D. and Silva, Claudio T.},
+ Title = {Hardware-Assisted Visibility Sorting for
+ Unstructured Volume Rendering},
+ Journal = {IEEE Transactions on Visualization and Computer
+ Graphics},
+ Year = 2005
+}
+
+ at incollection{csilva4,
+ Author = {Comba, Joao L. D. and Mitchell, Joseph S. B. and
+ Silva, Claudio T.},
+ Title = {On the Convexification of Unstructured Grids From A
+ Scientific Visualization Perspective},
+ BookTitle = {Scientific Visualization: Extracting Information and
+ Knowledge from Scientific Datasets},
+ Editor = {Bonneau, G.-P. and Ertl, T. and Nielson, G. M.},
+ Publisher = {Springer-Verlag},
+ Year = 2005
+}
+
+ at article{csilva5,
+ Author = {Cook, Richard and Max, Nelson and Silva, Claudio
+ T. and Williams, Peter},
+ Title = {Efficient, Exact Visibility Ordering of Unstructured
+ Meshes},
+ Journal = {IEEE Transactions on Visualization and Computer
+ Graphics},
+ Volume = 10,
+ Number = 6,
+ Pages = {695-707},
+ Year = 2004
+}
+
+ at article{csilva6,
+ Author = {Fleishman, Shachar and Cohen-Or, Daniel and Silva,
+ Claudio T.},
+ Title = {Robust Moving-least Squares Fitting With Sharp
+ Features},
+ Journal = {ACM Transactions on Graphics},
+ Year = 2005
+}
+
+ at inproceedings{csilva7,
+ Author = {Pesco, Sinesio and Lindstrom, Peter and Pascucci,
+ Valerio and Silva, Claudio T.},
+ Title = {Implicit Occluders},
+ BookTitle = {IEEE Symposium on Volume Visualization and Graphics
+ 2004},
+ Pages = {47-54},
+ Year = 2004
+}
+
+ at techreport{csilva8,
+ Author = {Scheidegger, Carlos and Fleishman, Shachar and
+ Silva, Claudio T.},
+ Title = {Triangulating Point Set Surfaces with Bounded Error},
+ institution = {University of Utah},
+ Year = 2005
+}
+
+ at techreport{csilva9,
+ Author = {Vo, Huy T. and Callahan, Steven and Lindstrom, Peter
+ and Pascucci, Valerio and Silva, Claudio T.},
+ Title = {Streaming Simplification of Tetrahedral Meshes},
+ institution = {University of Utah},
+ Year = {2005}
+}
+
+ at inproceedings{csilva10,
+ Author = {Uesu, Dirce and Bavoil, Louis and Fleishman, Shachar
+ and Shepherd, Jason F. and Silva, Claudio T.},
+ Title = {Simplification of Unstructured Tetrahedral Meshes by
+ Point Sampling},
+ BookTitle = {Volume Graphics 2005},
+ Year = 2005
+}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ at proceedings{webdb2003,
+ editor = {Vassilis Christophides and
+ \freiremarkref{\meabbrev}},
+ title = {International Workshop on Web and Databases},
+ booktitle = {WebDB},
+ year = {2003},
+ OPTbibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+: , 4th Edition. McGraw-Hill Book Company 2001
+
+ at Book{silber at book,
+ author = {Abraham Silberschatz and Henry F. Korth and S. Sudarshan},
+ title = {Database System Concepts},
+ publisher = {McGraw-Hill},
+ year = {2005},
+}
+
+ at Book{mitchell at book1997,
+ author = {Tom Mitchell},
+ title = {Machine Learning},
+ publisher = {McGraw Hill},
+ year = {1997},
+}
+
+ at Book{baeza at book1999,
+ author = {Ricardo A. Baeza-Yates and Berthier A. Ribeiro-Neto},
+ ALTeditor = {},
+ title = {Modern Information Retrieval},
+ publisher = {ACM Press/Addison-Wesley},
+ year = {1999},
+ OPTnote = {}
+}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ at Article{eureka,
+ author = {John C. Shafer and Rakesh Agrawal},
+ title = {Continuous querying in database-centric Web applications},
+ journal = {Computer Networks},
+ year = {2000},
+ volume = {33},
+ number = {1-6},
+ pages = {519-531},
+}
+
+ at article{mohan at deb1995,
+ author = {C. Mohan and
+ Gustavo Alonso and
+ Roger G{\"u}nth{\"o}r and
+ Mohan Kamath},
+ title = {Exotica: A Research Perspective ob Workflow Management Systems},
+ journal = {IEEE Data Eng. Bull.},
+ volume = {18},
+ number = {1},
+ year = {1995},
+ pages = {19-26},
+ OPTee = {db/journals/debu/MohanAGK95.html},
+ OPTbibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+
+ at TechReport{alonso at ieeeexpert1997,
+ author = {G. Alonso and D. Agrawal and A. {El Abbadi} and C. Mohan},
+ title = {Functionalities and Limitations of Current Workflow Management Systems},
+ institution = {ETH---Zurich},
+ year = {1997},
+ OPTkey = {},
+ OPTtype = {},
+ OPTnumber = {},
+ OPTaddress = {},
+ OPTmonth = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+ at article{lee-dataflow at 2002,
+ author = {Edward A. Lee and Thomas M. Parks},
+ title = {Dataflow process networks},
+ book = {Readings in hardware/software co-design},
+ year = {2002},
+ OPTisbn = {1-55860-702-1},
+ pages = {59-85},
+ OPTpublisher = {Kluwer Academic Publishers},
+ OPTaddress = {Norwell, MA, USA},
+ }
+
+ at InCollection{lee-dataflow at book2002,
+ author = {Edward A. Lee and Thomas M. Parks},
+ title = {Dataflow process networks},
+ editor = {Giovanni {de Micheli} and R. Ernst and Wayne Wolf},
+ booktitle = {Readings in hardware/software co-design},
+ publisher = {Kluwer Academic Publishers},
+ year = {2002},
+ pages = {59-85},
+}
+
+
+ at Book{aalst at book2002,
+ author = {{W. van der} Aalst and {K. van} Hee},
+ title = {Workflow Management: Models, Methods, and
+Systems},
+ publisher = {MIT Press},
+ year = {2002},
+}
+
+ at inproceedings{ailamaki at ssdbm1998,
+ author = {Anastassia Ailamaki and
+ Yannis E. Ioannidis and
+ Miron Livny},
+ OPTeditor = {Maurizio Rafanelli and
+ Matthias Jarke},
+ title = {Scientific Workflow Management by Database Management},
+ OPTbooktitle = {10th International Conference on Scientific and Statistical Database
+ Management, Proceedings, Capri, Italy, July 1-3, 1998},
+ booktitle = {Proceedings of SSDBM},
+ publisher = {IEEE Computer Society},
+ year = {1998},
+ OPTisbn = {0-8186-8575-1},
+ pages = {190-199},
+ OPTee = {db/conf/ssdbm/AilamakiIL98.html},
+ OPTcrossref = {DBLP:conf/ssdbm/98},
+ OPTbibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+ at Misc{taverna,
+ key = {Taverna},
+ title = {{The Taverna Project}},
+ OPTyear = {},
+ note = {\url{http://taverna.sourceforge.net}},
+}
+
+ at Misc{triana,
+ key = {Triana},
+ title = {{The Triana Project}},
+ OPTyear = {},
+ note = {\url{http://www.trianacode.org}},
+}
+
+
+
+ at Misc{euprovenance,
+ key = {Provenance},
+ title = {{The EU Provenance Project}},
+ OPTyear = {},
+ note = {\\\url{http://twiki.gridprovenance.org/bin/view/Provenance}},
+}
+
+
+
+ at InProceedings{gupta at icdt1997,
+ author = {Himanshu Gupta},
+ title = {Selection of Views to Materialize in a Data Warehouse},
+ booktitle = icdt,
+ pages = {98-112},
+ year = 1997
+}
+
+ at InProceedings{gupta at icdt1999,
+ author = {Himanshu Gupta and Inderpal Singh Mumick},
+ title = {Selection of Views to Materialize Under a Maintenance Cost Constraint},
+ booktitle = icdt,
+ pages = {453-470},
+ year = 1999
+}
+
+
+
+ at Misc{sciflow2006,
+ key = {SCIFLOW},
+ title = {{IEEE Workshop on Workflow and Data Flow for Scientific Applications
+(SciFlow 2006)}},
+ note = {\url{http://www.cc.gatech.edu/~cooperb/sciflow06}},
+}
+
+ at Misc{sdm2003,
+ key = {SDM},
+ title = {{Scientific Data Management Framework Workshop}},
+ note = {\\ \url{http://sdm.lbl.gov/$\tilde{ }$arie/sdm/SDM.Framework.wshp.htm}},
+}
+
+
+
+ at Misc{escience2004,
+ key = {escience},
+ title = {{e-Science Grid Environments Workshop}},
+ note = {\url{http://www.nesc.ac.uk/esi}},
+}
+
+
+
+
+ at Article{sigmodrecord at sciflow2005,
+ title = {Special Section on Scientific Workflows },
+ year = {2005},
+ key = {SIGMOD},
+ author = { B. Ludaescher and C.Goble },
+ journal = {ACM SIGMOD Record},
+ volume = {34},
+ number = {3},
+ OPTseries = {},
+ OPTaddress = {},
+ month = sep,
+ OPTorganization = {},
+ OPTpublisher = {},
+ OPTnote = {},
+ OPTannote = {}
+}
+
+Himanshu Gupta, Venky Harinarayan, Anand Rajaraman, Jeffrey D. Ullman: Index Selection for OLAP. ICDE 1997: 208-219
+
+
+ at InProceedings{crossno at vis2004,
+ author = {Patricia Crossno and David H. Rogers and Rebecca M. Brannon and David Coblentz},
+ title = {Visualization of Salt-Induced Stress Perturbations},
+ booktitle = vis,
+ OPTpages = {369-376},
+ year = 2004
+}
+
+ at InProceedings{wilson at vis2005,
+ author = {Andrew Wilson and Rebecca M. Brannon},
+ title = {Exploring 2D Tensor Fields Using Stress Nets},
+ booktitle = vis,
+ OPTpages = {2-9},
+ year = 2005
+}
+
+
+ at InProceedings{levoy at VBC1990,
+ author = {M. Levoy and H. Fuchs and S. Pizer and J. Rosenman and E. L. Chaney and G. W. Sherouse and V. Interrante and J. Kiel},
+ title = {Volume Rendering in Radiation Treatment Planning},
+ booktitle = {Proceedings of the First Conference on Visualization in Biomedical Computing},
+ year = {1990},
+ month = {May},
+}
+
+ at article{pelizzari at CRDI2000,
+ author = {C. A. Pelizzari and G. T. Y. Chen},
+ title = {Volume Visualization in Radiation Treatment Planning},
+ journal = {Critical Reviews in Diagnostic Imaging},
+ volume = {41},
+ number = {6},
+ pages = {379--364},
+ year = {2000}
+}
+
+ at article{jankun-kelly at tvcg2007,
+ author = {T.J. Jankun-Kelly and Kwan-Liu Ma and Michael Gertz},
+ title = {A Model and Framework for Visualization Exploration},
+ year = {2007},
+ journal = {IEEE Transactions on Visualization and Computer Graphics},
+ volume = {13},
+ number = {2},
+ pages = {357--369},
+}
+
+ at article{groth at tvcg2006,
+ author = {Dennis P. Groth and Kristy Streefkerk},
+ title = {Provenance and Annotation for Visual Exploration Systems},
+ journal = {IEEE Transactions on Visualization and Computer Graphics},
+ volume = {12},
+ number = {6},
+ year = {2006},
+ pages = {1500-1510},
+}
+
+ at InProceedings{Freire:2006:IPAW,
+ author = {J. Freire and C. T. Silva and S. P. Callahan and E. Santos and C. E. Scheidegger and H. T. Vo},
+ title = {Managing Rapidly-Evolving Scientific Workflows},
+ booktitle = {International Provenance and Annotation Workshop (IPAW)},
+ year = {2006},
+ pages = {10--18},
+ publisher = {Springer Verlag},
+ series = {LNCS 4145},
+}
+
+ at article{tory05a,
+author = {Melanie Tory and Simeon Potts and Torsten M\"oller},
+title = {A Parallel Coordinates Style Interface for Exploratory Volume Visualization},
+journal = {IEEE Transactions on Visualization and Computer Graphics},
+volume = {11},
+number = {1},
+year = {2005},
+pages = {71--80},
+}
+
+ at article{tory05b,
+author = {Melanie Tory and Torsten M\"oller},
+title = {Evaluating Visualizations: Do Expert Reviews Work?},
+journal = {IEEE Computer Graphics and Applications},
+volume = {25},
+number = {5},
+year = {2005},
+pages = {8--11},
+}
+
+ at article{roth01,
+author = {Mark Derthick and Steven F. Roth},
+title = {Enhancing Data Exploration with a Branching History of User Operations},
+journal = {Knowledge Based Systems},
+volume = {14},
+number = {1--2},
+pages = {65--74},
+year = {2001},
+}
+
+ at book{johnson79,
+author = {Michael R. Garey and David S. Johnson},
+title = {Computers and Intractability: A Guide to the Theory of NP-Completeness},
+publisher = {W. H. Freeman},
+isbn = {0-7167-1045-5},
+pages = {202},
+year = {1979},
+}
+
+ at ARTICLE{myGrid:Challenge06,
+ AUTHOR = {Jun Zhao and Carole Goble and Robert Stevens and Daniele
+ Turi},
+ TITLE = {Mining Taverna's Semantic Web of Provenance},
+ JOURNAL = {Concurrency and Computation: Practice and Experience},
+ YEAR = {2007},
+ OPTKEY = {},
+ OPTVOLUME = {},
+ OPTNUMBER = {},
+ OPTPAGES = {},
+ OPTMONTH = {},
+ OPTNOTE = {},
+ OPTANNOTE = {},
+ ABSTRACT = {Taverna is a workflow workbench and execution environment developed as part of the UK's myGrid project. Taverna's provenance model captures: information about the origin of experimental data results collected during workflow runs; derivation paths that present a datum's lineage; an audit trail of the experiment execution leading to the data; the context of the workflow; and the evidence of the knowledge outcomes as a result of its execution. Flexible and open models are req [...]
+}
diff --git a/extensions/latex/example2.pdf b/extensions/latex/example2.pdf
new file mode 100644
index 0000000..8002563
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diff --git a/extensions/latex/example2.tex b/extensions/latex/example2.tex
new file mode 100644
index 0000000..c0a4027
--- /dev/null
+++ b/extensions/latex/example2.tex
@@ -0,0 +1,218 @@
+\documentclass[11pt,twocolumn]{article}
+
+\usepackage{times}
+\usepackage[letterpaper,hmargin=1in,vmargin=1.25in]{geometry}
+\usepackage{float}
+\usepackage[rflt]{floatflt}
+\usepackage{xspace}
+\usepackage{cite,alltt}
+\usepackage{amsmath,amscd,amssymb}
+\usepackage[pdftex]{graphicx}
+\usepackage{array}
+\usepackage{mathptmx}
+
+\usepackage{crowdlabs}
+\usepackage{subfigure}
+\newcommand{\etc}{\emph{etc.}\xspace}
+\newcommand{\eg}{\emph{e.g.,}\xspace}
+\newcommand{\ie}{\emph{i.e.,}\xspace}
+
+
+\begin{document}
+
+\title{%Provenance for Visualizations: Beyond Reproduciblity\\
+Provenance for Visualizations: Reproducibility and Beyond}
+\author{Cl\'audio T. Silva \and Juliana Freire \and Steven P. Callahan}
+
+\maketitle
+
+\begin{abstract}
+ The demand for the construction of complex visualizations is growing
+ in many disciplines of science, as users are faced with ever
+ increasing volumes of data to analyze. The authors present
+ VisTrails, an open-source provenance management system that provides
+ infrastructure for data exploration and visualization.
+\end{abstract}
+
+\section{Introduction}
+Computing has been an enormous accelerator for science, leading to an
+information explosion in many different fields. Future scientific
+advances depend on our ability to comprehend the vast amounts of
+data currently being produced and acquired.
+%
+To analyze and understand this data, though, we must assemble complex
+computational processes and generate insightful visualizations, which
+often require combining loosely coupled resources, specialized
+libraries, and grid and Web services. Such processes could generate
+yet more data, adding to the information overflow scientists currently
+deal with.
+
+
+Today, the scientific community uses ad hoc approaches to
+data exploration, but such approaches have serious limitations. In
+particular, scientists and engineers must expend substantial effort
+managing data (such as scripts that encode computational tasks, raw
+data, data products, images, and notes) and recording provenance
+information (that is, all the information necessary for reproducing a
+certain piece of data or assertion) so that they can answer basic
+questions: Who created a data product and when? When was it modified,
+and who modified it? What process was used to create the data product?
+Were two data products derived from the same raw data? Not only is
+this process time-consuming, it’s also error-prone.
+
+Without provenance, it’s difficult (and sometimes impossible) to
+reproduce and share results, solve problems collaboratively, validate
+results with different input data, understand the process used to
+solve a particular problem, and reuse the knowledge involved in data
+analysis. In addition, data products’ longevity becomes
+limited—without precise and sufficient information about how the data
+product was generated, its value diminishes significantly.
+
+\begin{figure}[t]
+\centering{
+\includegraphics[width=0.9\linewidth, clip=false]{fig1.png}
+}
+\caption{Dataflow programming for visualization. (a) We commonly use a
+ script to describe a pipeline from existing libraries such as the
+ Visualization Toolkit (VTK). (b) Visual programming interfaces, such
+ as the one VisTrails provides, facilitate the creation and
+ maintenance of these dataflow pipelines. The green rectangles
+ represent modules, and the black lines represent connections.}
+\label{fig:fig1}
+\end{figure}
+
+The lack of adequate provenance support in visualization systems
+motivated us to build VisTrails, an open source provenance-management
+system that provides infrastructure for data exploration and
+visualization through workflows. VisTrails transparently records
+detailed provenance of exploratory computational tasks and leverages
+this information beyond just the ability to reproduce and share
+results. In particular, it uses this information to simplify the
+process of exploring data through visualization.
+
+\section{Visualization Systems}
+
+Visualization systems such as MayaVi
+(\url{http://mayavi.sourceforge.net}) and ParaView
+(\url{www.paraview.org})—which are built on top of Kitware's
+Visualization Toolkit (VTK)~\cite{Schroeder:2003:VTK}~—as well as
+SCIRun (\url{http://software.sci.utah.edu/scirun.html}) enable users
+to interactively create and manipulate complex visualizations. Such
+systems are based on the notion of data flows~\cite{lee at ieee1995}, and
+they provide visual interfaces for producing visualizations by
+assembling pipelines out of modules (or functions) connected in a
+network. SCIRun supports an interface that lets users directly edit
+data flows, giving them complete control. MayaVi and ParaView have a
+different interaction paradigm that implicitly builds data flows as
+the user makes “task-oriented” choices (such as selecting an
+isosurface value).
+
+
+Although these systems let users create complex visualizations, they
+lack the ability to support data exploration at a large scale.
+Notably, they don’t adequately support collaborative creation and
+exploration of multiple visualizations. Because these systems don’t
+distinguish between the definition of a data flow and its instances,
+to execute a given data flow with different parameters (for example,
+different input files), users must manually set these parameters
+through a GUI. Clearly, this process doesn’t scale to more than a few
+visualizations at a time. Additionally, modifications to parameters or
+to a data flow’s definition are destructive—the systems don’t maintain
+any change history. This requires the user to first construct the
+visualization and then remember the input data sets, parameter values,
+and the exact dataflow configuration that led to a particular image.
+
+
+Finally, before constructing a visualization, users must often
+acquire, generate, or transform a given data set—for example, to
+calibrate a simulation, they must obtain data from sensors, generate
+data from a simulation, and finally construct and compare the
+visualization for both data sets. Most visualization systems, however,
+don’t give users adequate support for creating the complex pipelines
+that use multiple libraries and services.
+
+\begin{figure*}[t]
+\centering{
+%\includegraphics[width=0.9\linewidth, clip=false]{fig2.png}
+\crowdlabs[wfid=1046,
+buildalways=false]{width=4cm}
+}
+\caption{The end result of the script or VisTrails pipeline (see
+ Figure~\ref{fig:fig1}) is a set of interactive visualizations.}
+\label{fig:histogram}
+\end{figure*}
+
+\section{VisTrails: Provenance for Visualization}
+VisTrails (\url{www.vistrails.org}) is a new visualization system we
+developed at the University of Utah that provides a comprehensive
+provenance-management infrastructure and can be easily combined with
+existing visualization libraries. Unlike previous systems, VisTrails
+uses an action-based provenance model that uniformly captures changes
+to both parameter values and pipeline definitions by unobtrusively
+tracking all changes that users make to pipelines in an exploration
+task. We refer to this detailed provenance of the pipeline evolution
+as a visualization trail, or vistrail.
+
+The stored provenance ensures that users will be able to
+reproduce the visualizations and lets them easily navigate through the
+space of pipelines created for a given exploration task. The VisTrails
+interface lets users query, interact with, and understand the
+visualization process’s history. In particular, they can return to
+previous versions of a pipeline and change the specification or
+parameters to generate a new visualization without losing previous
+changes.
+
+\begin{figure*}[t]
+\centering{
+%\includegraphics[width=0.9\linewidth, clip=false]{fig2.png}
+\crowdlabs[wfid=1050,
+buildalways=false]{width=4cm}
+}
+\caption{The end result of the script or VisTrails pipeline (see
+ Figure~\ref{fig:fig1}) is a set of interactive visualizations.}
+\label{fig:histogram_pdf}
+\end{figure*}
+
+Another important feature of the action-based provenance model is that
+it enables a series of operations that greatly simplify the
+exploration process and could reduce the time to insight. In
+particular, it allows the flexible reuse of pipelines and provides a
+scalable mechanism for creating and comparing numerous visualizations
+as well as their corresponding pipelines. Although we originally
+built VisTrails to support exploratory visualization tasks, its
+extensible infrastructure lets users integrate a wide range
+of libraries. This makes the system suitable for other exploratory
+tasks, including data mining and integration.
+
+\section{Creating an Interactive Visualization with VisTrails}
+To illustrate the issues involved in creating visualizations and how
+provenance can aid in this process, we present the following scenario,
+common in medical data visualization.
+
+Starting from a volumetric computed tomography (CT) data set, we
+generate different visualizations by exploring the data through volume
+rendering, isosurfacing (extracting a contour), and slicing. Note that
+with proper modifications, this example also works for visualizing
+other types of data (for example, tetrahedral meshes).
+
+\subsection{Dataflow Processing Networks and Visual Programming}
+A useful paradigm for building visualization applications is the
+\emph{dataflow model}. A data flow is a directed graph in which nodes
+represent computations, and edges represent data streams: each node or
+module corresponds to a procedure that’s applied on the input data and
+generates some output data as a result. The data flow in the graph
+determines the order in which a dataflow system executes the
+processing nodes. In visualization, we commonly refer to a dataflow
+network as a visualization pipeline. (For this article, we use the
+terms workflow, data flow, and pipeline interchangeably.)
+Figure~\ref{fig:fig1}b shows an example of the data flow used to
+derive the images shown in Figure~\ref{fig:histogram}. The green
+rectangles represent modules, and the black lines represent
+connections. Most of the modules in Figure~\ref{fig:fig1} are from VTK, and
+labels on each module indicate the corresponding VTK class. In this
+figure, we naturally think of data flowing from top to bottom,
+eventually being rendered and presented for display.
+
+\bibliography{example2}
+\bibliographystyle{abbrv}
+\end{document}
diff --git a/extensions/latex/fig1.png b/extensions/latex/fig1.png
new file mode 100644
index 0000000..82e67a6
Binary files /dev/null and b/extensions/latex/fig1.png differ
diff --git a/extensions/latex/fig2.png b/extensions/latex/fig2.png
new file mode 100644
index 0000000..11ee530
Binary files /dev/null and b/extensions/latex/fig2.png differ
diff --git a/extensions/latex/find.cmd b/extensions/latex/find.cmd
new file mode 100644
index 0000000..2017045
--- /dev/null
+++ b/extensions/latex/find.cmd
@@ -0,0 +1,59 @@
+ at echo off
+setlocal enableextensions enabledelayedexpansion
+
+:: Needs an argument.
+
+if "x%*"=="x" (
+ echo Usage: which ^<progName^>
+ goto :end
+)
+
+:: First check if file exists
+if exist "%*" (
+ echo "%*"
+ goto :end
+)
+
+:: Then try the unadorned filename in PATH.
+
+set fullspec=
+call :find_it %*
+
+:: Then try all adorned filenames in order.
+
+set mypathext=!pathext!
+:loop1
+ :: Stop if found or out of extensions.
+
+ if "x!mypathext!"=="x" goto :loop1end
+
+ :: Get the next extension and try it.
+
+ for /f "delims=;" %%j in ("!mypathext!") do set myext=%%j
+ call :find_it %1!myext!
+
+:: Remove the extension (not overly efficient but it works).
+
+:loop2
+ if not "x!myext!"=="x" (
+ set myext=!myext:~1!
+ set mypathext=!mypathext:~1!
+ goto :loop2
+ )
+ if not "x!mypathext!"=="x" set mypathext=!mypathext:~1!
+
+ goto :loop1
+:loop1end
+
+:end
+endlocal
+goto :eof
+
+:: Function to find and print a file in the path.
+
+:find_it
+ for %%i in (%*) do set fullspec=%%~$PATH:i
+ set z=%fullspec%
+ if not [%fullspec%]==[] set z=%fullspec:\=/%
+ if not "x!z!"=="x" @echo !z!
+ goto :eof
diff --git a/extensions/latex/head.pdf b/extensions/latex/head.pdf
new file mode 100644
index 0000000..fbeb6c1
Binary files /dev/null and b/extensions/latex/head.pdf differ
diff --git a/extensions/latex/head.tex b/extensions/latex/head.tex
new file mode 100644
index 0000000..90e7093
--- /dev/null
+++ b/extensions/latex/head.tex
@@ -0,0 +1,143 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% Copyright (C) 2011-2014, NYU-Poly.
+%% Copyright (C) 2006-2011, University of Utah.
+%% All rights reserved.
+%% Contact: contact at vistrails.org
+%%
+%% This file is part of VisTrails.
+%%
+%% "Redistribution and use in source and binary forms, with or without
+%% modification, are permitted provided that the following conditions are met:
+%%
+%% - Redistributions of source code must retain the above copyright notice,
+%% this list of conditions and the following disclaimer.
+%% - Redistributions in binary form must reproduce the above copyright
+%% notice, this list of conditions and the following disclaimer in the
+%% documentation and/or other materials provided with the distribution.
+%% - Neither the name of the University of Utah nor the names of its
+%% contributors may be used to endorse or promote products derived from
+%% this software without specific prior written permission.
+%%
+%% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+%% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+%% THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+%% PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+%% CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+%% EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+%% PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+%% OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+%% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+%% OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+%% ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\documentclass{article}
+\usepackage{vistrails}
+
+%% uncomment lines below and set to a local path if you want to run vistrails
+%% locally. Otherwise, we will run at www.vistrails.org
+
+%% If you are running on a Mac from a binary distribution uncomment the next 2 lines, modifying them according to your system configuration
+%\renewcommand{\vistrailspath}{/Applications/VisTrails/VisTrails.app/Contents/MacOS/vistrails}
+%\renewcommand{\vistrailsenv}{DYLD_LIBRARY_PATH= }
+
+%% If you are running on Windows from the binary distribution uncommnet the next 3 lines
+%\renewcommand{\vistrailspath}{C:/Program Files (x86)/VisTrails/vistrails/run.py}
+%\renewcommand{\vistrailspythonpath}{C:/Program Files (x86)/VisTrails/Python27/python.exe}
+%\renewcommand{\vistrailsenv}{PATH="C:/Program Files (x86)/VisTrails"}
+
+%% If you are running from source uncomment and modify the lines below
+%% according to your system configuration.
+% \renewcommand{\vistrailspath}{D:/emanuele/vistrails/vistrails/run.py}
+
+%% If using MikTex or cygwin on Windows, you need to set the Path to point to your Qt Libraries
+%\renewcommand{\vistrailsenv}{PATH=D:/Qt/4.6.3/bin}
+
+%% If your python is in the path, you don't need to uncomment the line. Otherwise
+%% add the complete path to your python executable
+%\renewcommand{\vistrailspythonpath}{C:/Python27/python.exe}
+
+\begin{document}
+
+This document shows examples of how to embed a vistrail from a local
+file. The file is head.vt and it is located in the same folder as this
+file.
+
+To build the pdf version of this document, configure this file
+according to your platform and from a terminal window type:
+\begin{verbatim}
+make head
+\end{verbatim}
+
+or
+\begin{verbatim}
+pdflatex -shell-escape head
+\end{verbatim}
+
+Embedding the results of workflow \emph{aliases}:
+\begin{center}
+\vistrail[filename=head.vt,
+version=15]{width=6cm}
+\end{center}
+
+Embedding the workflow \emph{aliases} as a pdf:
+\begin{center}
+\vistrail[filename=head.vt,
+version=15,
+pdf,
+showworkflow]{width=6cm}
+\end{center}
+
+Embedding a workflow as a smart tag (if the tag changes to another
+workflow, the new workflow will be used when the latex file is
+compiled)
+\begin{center}
+\vistrail[filename=head.vt,
+version=42,
+tag={volume rendering},
+buildalways]{width=6cm}
+\end{center}
+
+Embedding the complete tree:
+\begin{center}
+\vistrail[filename=head.vt,
+buildalways,
+showtree]{width=8cm}
+\end{center}
+
+%% Uncomment the following part part for accessing workflows directly
+%% in a database
+
+% Embedding workflow result:
+% \begin{center}
+% \vistrail[host=localhost,
+% db=vistrails,
+% port=3306,
+% vtid=1,
+% version=49]{width=6cm}
+% \end{center}
+
+% Embedding workflow graph as pdf
+% \begin{center}
+% \vistrail[host=localhost,
+% db=vistrails,
+% port=3306,
+% vtid=1,
+% version=49,
+% pdf,
+% showworkflow]{width=6cm}
+% \end{center}
+
+% Embedding the tree
+% \begin{center}
+% \vistrail[host=localhost,
+% db=vistrails,
+% port=3306,
+% vtid=1,
+% buildalways,
+% showtree]{width=8cm}
+% \end{center}
+\end{document}
+
diff --git a/extensions/latex/head.vt b/extensions/latex/head.vt
new file mode 100644
index 0000000..86c6116
Binary files /dev/null and b/extensions/latex/head.vt differ
diff --git a/extensions/latex/includecrowdlabs.py b/extensions/latex/includecrowdlabs.py
new file mode 100755
index 0000000..b83f62b
--- /dev/null
+++ b/extensions/latex/includecrowdlabs.py
@@ -0,0 +1,434 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# This runs on crowdlabs only!!!
+# the input file format should follow this:
+# url=http://www.crowdlabs.org
+# wfid=598
+# vtid=34
+# pdf=true
+# workflow=true
+# buildalways=true
+# other=width=0.45\linewidth
+#
+# buildalways, workflow and pdf are optional
+# at least one of wfid or vtid must be provided
+
+import sys
+import os.path
+import os
+from httplib import HTTP
+from urlparse import urlparse
+import urllib2
+import re
+import logging
+
+debug = True
+logger = None
+
+###############################################################################
+
+def log(msg):
+ global debug, logger
+ if debug:
+ logger.debug(msg)
+
+###############################################################################
+
+def usage():
+ print "Usage: "
+ print " %s path/to/options_file" % sys.argv[0]
+ sys.exit(1)
+
+###############################################################################
+
+def bool_conv(x):
+ """bool_conv(x: str) -> bool
+ Converts a string to boolean.
+
+ """
+ s = str(x).upper()
+ if s == 'TRUE':
+ return True
+ if s == 'FALSE':
+ return False
+
+###############################################################################
+
+def path_exists_and_not_empty(path):
+ """path_exists_and_not_empty(path:str) -> boolean
+ Returns True if given path exists and it's not empty, otherwise returns
+ False.
+
+ """
+ if os.path.exists(path):
+ for root, dirs, file_names in os.walk(path):
+ break
+ if len(file_names) > 0:
+ return True
+ return False
+
+###############################################################################
+
+def build_vistrails_cmd_line(path_to_vistrails, host, db_name, vt_id, version,
+ port, path_to_figures):
+ """ build_vistrails_cmd_line(path_to_vistrails: str, host: str,
+ db_name: str, vt_id: str, version: str,
+ path_to_figures: str) -> str
+ Build the command line to run vistrails with the given parameters.
+ """
+ cmd_line = 'python "%s" -b -e "%s" -t %s -f %s -r %s -u %s "%s:%s" > \
+vistrails.log' % (vt_user,
+ path_to_vistrails,
+ path_to_figures,
+ host,
+ db_name,
+ port,
+ vt_id,
+ version)
+ return cmd_line
+
+###############################################################################
+
+def generate_latex(server_url, wfid, path_to_figures, graphics_options):
+ """generate_latex(wfid: str, execute: bool,
+ showspreadsheetonly: bool, path_to_figures: str,
+ graphics_options: str) -> str
+ This generates a piece of latex code containing the \href command and
+ a \includegraphics command for each image generated.
+ """
+ log("generate_latex")
+ url_params = "details/%s/" % wfid
+ url_params = url_params.replace("%","\%")
+ url = "%s%s"%(server_url,url_params)
+ href = "\href{%s}{" % url
+ for root, dirs, file_names in os.walk(path_to_figures):
+ break
+ n = len(file_names)
+ s = ''
+
+ for f in file_names:
+ filename = os.path.join(path_to_figures,f).replace("%","\%")
+ if graphics_options:
+ s += "\includegraphics[%s]{%s}\n" % (graphics_options, filename)
+ else:
+ s += "\includegraphics{%s}\n" % filename
+ s += "}"
+ return href+s
+
+###############################################################################
+
+def generate_latex_error(error_msg):
+ """ generate_latex_error(error_msg: str) -> str
+ this generates a piece of latex code with an error message.
+ """
+ s = """\\PackageError{vistrails}{ An error occurred when executing vistrails. \\MessageBreak
+%s
+}{vistrails}""" % error_msg
+ return s
+
+###############################################################################
+
+def download(url,filename):
+ try:
+ furl = urllib2.urlopen(url)
+ f = file(filename,'wb')
+ f.write(furl.read())
+ f.close()
+ return True
+ except:
+ return False
+
+###############################################################################
+
+def download_as_text(url):
+ try:
+ furl = urllib2.urlopen(url)
+ s = furl.read()
+ return s
+ except:
+ return None
+
+###############################################################################
+
+def download_workflow(url_crowdlabs, wfid, path_to_figures, wgraph=False,
+ pdf=False, build_always=False):
+ """download_workflow(url_crowdlabs: str, wfid: str, path_to_figures: str,
+ wgraph: bool, pdf: bool, build_always: bool)
+ -> tuple(bool, str)
+ Try to download image from url and returns a tuple containing a boolean
+ saying if it was successful or not and the latex code.
+ """
+ log("download_workflow")
+ if not path_exists_and_not_empty(path_to_figures) or build_always:
+ if not os.path.exists(path_to_figures):
+ os.makedirs(path_to_figures)
+
+ if check_url(url_crowdlabs):
+ website = "://".join(urlparse(url_crowdlabs)[:2])
+ if not wgraph:
+ if not pdf:
+ request = "/vistrails/workflows/generate_visualization_image/%s/"%wfid
+ else:
+ request = "/vistrails/workflows/generate_visualization_pdf/%s/"%wfid
+ else:
+ if not pdf:
+ request = "/vistrails/workflows/generate_pipeline_image/%s/"%wfid
+ else:
+ request = "/vistrails/workflows/generate_pipeline_pdf/%s/"%wfid
+
+ url = url_crowdlabs + request
+ log("from %s"%url)
+ try:
+ page = download_as_text(url)
+ # we will look for a list of comma separated in the html
+ images = page.split(",")
+ if len(images) > 0:
+ failed = False
+ for i in images:
+ msg = ''
+ pngfile = i.strip()
+ if not check_url(pngfile):
+ img = website + pngfile
+ else:
+ img = pngfile
+ if not download(img, os.path.join(path_to_figures,
+ os.path.basename(img))):
+ msg += "Error when download image: %s. <return>" %\
+ img
+ failed = True
+ if not failed:
+ log("success")
+ return (True, generate_latex(url_crowdlabs + "/vistrails/workflows/",
+ wfid,
+ path_to_figures,
+ graphics_options))
+ else:
+ log("failed: %s"%msg)
+ return (False, generate_latex_error(msg))
+ else:
+ msg = "Web server returned: %s" % page
+ log("failed: %s"%msg)
+ return (False, generate_latex_error(msg))
+
+ except Exception, e:
+ log("failed with exception: %s"%str(e))
+ return (False, generate_latex_error(str(e)))
+ else:
+ msg = "Invalid url: %s" % url_crowdlabs
+ return (False, generate_latex_error(msg))
+ else:
+ log("using cached images")
+ return (True, generate_latex(url_crowdlabs + "/vistrails/workflows/",
+ wfid,
+ path_to_figures,
+ graphics_options))
+
+###############################################################################
+
+def download_tree(url_crowdlabs, vtid, path_to_figures, pdf=False,
+ build_always=False):
+ """download_tree(url_crowdlabs: str, vtid: str, path_to_figures: str,
+ pdf: bool, build_always: bool)
+ -> tuple(bool, str)
+ Try to download tree from url and returns a tuple containing a boolean
+ saying if it was successful or not and the latex code.
+ """
+ log("download_tree")
+ if not path_exists_and_not_empty(path_to_figures) or build_always:
+ if not os.path.exists(path_to_figures):
+ os.makedirs(path_to_figures)
+
+ if check_url(url_crowdlabs):
+ website = "://".join(urlparse(url_crowdlabs)[:2])
+ if not pdf:
+ request = "/vistrails/generate_provenance_image/%s/"%vtid
+ else:
+ request = "/vistrails/generate_provenance_pdf/%s/"%vtid
+ url = url_crowdlabs + request
+ log("from %s"%url)
+ try:
+ page = download_as_text(url)
+ # we will look for a list of comma separated in the html
+ images = page.split(",")
+ if len(images) > 0:
+ failed = False
+ for i in images:
+ msg = ''
+ pngfile = i.strip()
+ if not check_url(pngfile):
+ img = website + pngfile
+ else:
+ img = pngfile
+ if not download(img, os.path.join(path_to_figures,
+ os.path.basename(img))):
+ msg += "Error when download image: %s. <return>" %\
+ img
+ failed = True
+ if not failed:
+ log("success")
+ return (True, generate_latex(url_crowdlabs + "/vistrails/", vtid,
+ path_to_figures,
+ graphics_options))
+ else:
+ log("failed: %s"%msg)
+ return (False, generate_latex_error(msg))
+ else:
+ msg = "Web server returned: %s" % page
+ log("failed: %s"%msg)
+ return (False, generate_latex_error(msg))
+
+ except Exception, e:
+ log("failed with exception: %s"%str(e))
+ return (False, generate_latex_error(str(e)))
+ else:
+ msg = "Invalid url: %s" % url_crowdlabs
+ log("failed: %s"%msg)
+ return (False, generate_latex_error(msg))
+ else:
+ log("using cached images")
+ return (True, generate_latex(url_crowdlabs + "/vistrails/", vtid,
+ path_to_figures, graphics_options))
+
+
+###############################################################################
+
+def check_url(url):
+ """check_url(url:str) -> bool
+ Check if a URL exists using the url's header.
+ """
+ try:
+ p = urlparse(url)
+ h = HTTP(p[1])
+ h.putrequest('HEAD', p[2])
+ h.endheaders()
+ if h.getreply()[0] == 200:
+ return True
+ else:
+ return False
+ except:
+ return False
+
+###############################################################################
+
+options_file = None
+try:
+ options_file = open(sys.argv[1])
+except IndexError:
+ usage()
+
+if debug:
+ logger = logging.getLogger("crowdLabsLatex")
+ handler = logging.FileHandler('crowdlabs.log')
+ handler.setFormatter(logging.Formatter('crowdLabsLatex - %(asctime)s %(message)s'))
+ handler.setLevel(logging.DEBUG)
+ logger.setLevel(logging.DEBUG)
+ logger.addHandler(handler)
+ log("***********************************")
+ log("********* SESSION START ***********")
+
+lines = options_file.readlines()
+urlcrowdlabs = None
+wfid = None
+vtid = None
+pdf = False
+wgraph = False
+tree = False
+
+graphics_options = None
+build_always = False
+run_locally = True
+
+for line in lines:
+ args = line.split("=")
+ if len(args) > 2:
+ args[1] = "=".join(args[1:])
+ if args[0] == "url":
+ urlcrowdlabs = args[1].strip(" \n")
+ elif args[0] == "wfid":
+ wfid = args[1].strip(" \n")
+ elif args[0] == "vtid":
+ vtid = args[1].strip(" \n")
+ tree = True
+ elif args[0] == 'pdf':
+ pdf = bool_conv(args[1].strip(" \n"))
+ elif args[0] == 'workflow':
+ wgraph = bool_conv(args[1].strip(" \n"))
+ elif args[0] == "buildalways":
+ build_always = bool_conv(args[1].strip(" \n"))
+ elif args[0] == "other":
+ graphics_options = args[1].strip(" \n")
+
+# then we use the combination wf_wfid or vt_vtid to
+# create a unique folder.
+# TODO: Maybe we should use a hash of this. For now let's keep it
+# legible.
+out_type = "png"
+if pdf:
+ out_type = 'pdf'
+
+if check_url(urlcrowdlabs):
+
+ if wfid is not None:
+ folder_suffix = ""
+ if wgraph:
+ folder_suffix = "_graph"
+ path_to_figures = os.path.join("crowdlabs_images",
+ "wf_%s_%s%s" %(wfid, out_type,folder_suffix))
+ log(path_to_figures)
+ result, latex = download_workflow(urlcrowdlabs, wfid,
+ path_to_figures, wgraph, pdf, build_always)
+
+ elif vtid is not None:
+ path_to_figures = os.path.join("crowdlabs_images",
+ "vt_%s_%s" %(vtid, out_type))
+ log(path_to_figures)
+ result, latex = download_tree(urlcrowdlabs, vtid,
+ path_to_figures, pdf, build_always)
+
+else:
+ result, latex = (False, generate_latex_error("Invalid url %s." % urlcrowdlabs))
+
+# the printed answer will be included inline by the latex compiler.
+print latex
+if result == True:
+ log("********** SESSION END ************")
+ log("***********************************")
+ sys.exit(0)
+else:
+ log("********** SESSION END ************")
+ log("***********************************")
+ sys.exit(1)
diff --git a/extensions/latex/includevistrail.py b/extensions/latex/includevistrail.py
new file mode 100755
index 0000000..ada8adf
--- /dev/null
+++ b/extensions/latex/includevistrail.py
@@ -0,0 +1,1503 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# the input file format should follow this:
+# path=/Users/emanuele/code/vistrails/branches/v1.2/vistrails/run.py
+# python=/path/to/python
+# env=DYLD_LIBRARY_PATH=
+# download=http://url.from.where.download.vt.files
+# host=vistrails.sci.utah.edu
+# user=username
+# db=vistrails
+# filename=path_to_vtfile
+# version=598
+# vtid=8
+# port=3306
+# buildalways=true
+# tag=Some text
+# pdf=false
+# workflow=false
+# tree=false
+# getvtl=false
+# embedworkflow=false
+# includefulltree=false
+# other=width=0.45\linewidth
+#
+# the buildalways and port lines are optional
+# at least a version or a tag must be provided
+# if filename is provided host, db, user and vtid are ignored
+# please notice that the tag has precedence over version. If a tag is passed
+# we will query the database to get the latest version number.
+
+import sys
+import os.path
+import os
+from httplib import HTTP
+from urlparse import urlparse
+import urllib2
+import re
+import logging
+import shlex
+import shutil
+import subprocess
+import platform
+
+systemType = platform.system()
+debug = True
+logger = None
+
+###############################################################################
+
+def log(msg):
+ global debug, logger
+ if debug:
+ logger.debug(msg)
+
+###############################################################################
+
+def usage():
+ print "Usage: "
+ print " %s path/to/options_file" % sys.argv[0]
+ sys.exit(1)
+
+###############################################################################
+
+def bool_conv(x):
+ """bool_conv(x: str) -> bool
+ Converts a string to boolean.
+
+ """
+ s = str(x).upper()
+ if s == 'TRUE':
+ return True
+ if s == 'FALSE':
+ return False
+
+###############################################################################
+
+def path_exists_and_not_empty(path):
+ """path_exists_and_not_empty(path:str) -> boolean
+ Returns True if given path exists and it's not empty, otherwise returns
+ False.
+
+ """
+ if os.path.exists(path):
+ for root, dirs, file_names in os.walk(path):
+ break
+ if len(file_names) > 0:
+ return True
+ return False
+
+###############################################################################
+
+def vtl_exists_in_folder(path):
+ """vtl_exists_in_folder(path:str) -> boolean
+ Returns True if given path contains a *.vtl file, otherwise returns False.
+
+ """
+ for dirpath, dirname,filenames in os.walk(path):
+ for f in filenames:
+ ext = os.path.splitext(f)[1]
+ if ext == ".vtl":
+ return True
+ return False
+
+###############################################################################
+
+def build_vtl_file(download_url, filename, version, tag,
+ execute, showspreadsheetonly, embedWorkflow=False,
+ includeFullTree=False):
+ log("build_vtl_file")
+ try:
+ basename = os.path.splitext(os.path.basename(filename))[0]
+ if version != None:
+ basename += "_%s_%s_%s_%s"%(version,tag,showspreadsheetonly,execute)
+ basename += ".vtl"
+ vtl_filename = os.path.join(download_url, basename)
+ header = '<vtlink filename="%s" version="%s" execute="%s" showSpreadsheetOnly="%s" \
+forceDB="%s" tag="%s"/>'%(filename,#os.path.abspath(filename),
+ str(version),
+ str(execute),
+ str(showspreadsheetonly),
+ str(False),
+ str(tag))
+ except Exception, e:
+ log("Error: %s"%str(e))
+ log("will open %s"%vtl_filename)
+ log("vtlfile contents: %s"%header)
+ f = open(vtl_filename, "w")
+ f.write(header)
+ f.close()
+ return "run:"+ os.path.abspath(vtl_filename).replace("\\","/")
+
+###############################################################################
+
+def build_vtl_db(download_url, host, db_name, vt_id, version, port, tag,
+ execute, showspreadsheetonly, embedWorkflow=False,
+ includeFullTree=False):
+ """build_download_vtl_request(host: str, db_name:str, vt_id: str, version: str,
+ port:str, tag: str, execute: bool,
+ showspreadsheetonly: bool) -> str """
+ log("build_vtl_db")
+ try:
+ basename = "%s_%s_%s_%s_%s_%s_%s_%s_%s.vtl"%(host,
+ db_name,
+ port,
+ vt_id,
+ version,
+ execute,
+ embedWorkflow,
+ includeFullTree,
+ showspreadsheetonly)
+ vtl_filename = os.path.join(download_url, basename)
+ header = '<vtlink host="%s" database="%s" port="%s" vtid="%s" \
+version="%s" execute="%s" showSpreadsheetOnly="%s" forceDB="%s" />'%(
+ host,
+ db_name,
+ str(port),
+ str(vt_id),
+ str(version),
+ str(execute),
+ str(showspreadsheetonly),
+ str(True))
+ except Exception, e:
+ log("Error: %s"%str(e))
+ log("will open %s"%vtl_filename)
+ log("vtlfile contents: %s"%header)
+ f = open(vtl_filename, "w")
+ f.write(header)
+ f.close()
+ return "run:"+ os.path.abspath(vtl_filename)
+
+###############################################################################
+def download(url,filename, folder=None):
+ """download(url:string, filename: string) -> Boolean
+ Downloads a binary file from url to filename and returns True (success)
+ or False (failure)
+
+ """
+ try:
+ furl = urllib2.urlopen(url)
+ if filename is None and folder is not None:
+ info = furl.info()
+ re_filename = re.compile('attachment;filename=(.*vtl)')
+ attach = info.dict['content-disposition']
+ filename = os.path.join(folder,
+ re_filename.match(attach).groups()[0])
+
+ log("downloading file: " + filename)
+ f = file(filename,'wb')
+ f.write(furl.read())
+ f.close()
+ return True
+ except Exception, e:
+ log(str(e))
+ return False
+
+###############################################################################
+
+def download_as_text(url):
+ """download_as_text(url: string) -> string
+ Downloads a url as text. It will return None if it failed.
+
+ """
+ try:
+ furl = urllib2.urlopen(url)
+ s = furl.read()
+ return s
+ except:
+ return None
+
+###############################################################################
+
+def build_download_vtl_request(download_url, host, db_name, vt_id, version, port, tag,
+ execute, showspreadsheetonly, embedWorkflow=False,
+ includeFullTree=False):
+ """build_download_vtl_request(host: str, db_name:str, vt_id: str, version: str,
+ port:str, tag: str, execute: bool,
+ showspreadsheetonly: bool) -> str
+ This generates a piece of latex code containing the \href command and
+ a \includegraphics command for each image generated.
+ """
+
+ url_params = "getvt=%s&db=%s&host=%s&port=%s&tag=%s&\
+execute=%s&showspreadsheetonly=%s&embedWorkflow=%s&includeFullTree=%s" % (vt_id,
+ db_name,
+ host,
+ port,
+ urllib2.quote(tag),
+ execute,
+ showspreadsheetonly,
+ embedWorkflow,
+ includeFullTree)
+ if version is not None:
+ url_params += "&version=%s"%urllib2.quote(version)
+ url_params = url_params.replace("%","\%")
+ url = "%s?%s"%(download_url, url_params)
+
+ return url
+
+###############################################################################
+
+def _download_content(url, request, path_to_figures):
+ """_download_images(url:string, request:string, path_to_figures:string) -> (Boolean,
+ message)
+ Downloads all images and pdf files listed in url and saves them to
+ path_to_figures
+
+ """
+ website = url
+ url = request
+ try:
+ page = download_as_text(url)
+ # we will look for images and other files embedded in the html
+ re_imgs = re.compile('<img[^>]*/>')
+ re_src = re.compile('(.*src=")([^"]*)"')
+ re_a = re.compile('<a[^>]*>[^<]*</a>')
+ re_href = re.compile('(.*href=")([^"]*)"')
+ images = re_imgs.findall(page)
+ files = re_a.findall(page)
+ failed = False
+ msg = ''
+ if len(images) > 0 or len(files) > 0:
+ for i in images:
+ pngfile = re_src.match(i).groups()[1]
+ if not check_url(pngfile):
+ img = website + pngfile
+ else:
+ img = pngfile
+
+ if not download(img, os.path.join(path_to_figures,
+ os.path.basename(img))):
+ msg += "Error when downloading image: %s. <return>" %img
+ failed = True
+
+ for f in files:
+ otherfile = re_href.match(f).groups()[1]
+
+ if not check_url(otherfile):
+ filename = website + otherfile
+ else:
+ filename = otherfile
+
+ if not download(filename, os.path.join(path_to_figures,
+ os.path.basename(filename))):
+ msg += "Error when downloading file: %s. <return>"%filename
+ failed = True
+
+ if not failed :
+ return (True, "")
+ else:
+ return (False, msg)
+ else:
+ msg = "url: '%s' \n returned: %s" % (url,page.strip())
+ return (False, msg)
+
+ except Exception, e:
+ return (False, str(e))
+
+def build_vistrails_cmd_line_db(path_to_vistrails, path_to_python,
+ env_for_vistrails, host,
+ db_name, db_user, vt_id, version, port,
+ path_to_figures, pdf=False, wgraph=False,
+ tree=False):
+ """ build_vistrails_cmd_line_db(path_to_vistrails: str, env_for_vistrails: str,
+ host: str, db_name: str, vt_id: str,
+ version: str, path_to_figures: str,
+ pdf:bool, wgraph:bool, tree: bool) -> list
+ Build the command line to run vistrails with the given parameters.
+ """
+ #dump pdf
+ if pdf:
+ pdfoption = ["-p"]
+ else:
+ pdfoption = []
+ #user
+ if db_user is not None and db_user != "":
+ useroption = ['-u', '%s'%db_user]
+ else:
+ useroption = []
+ #dump tree and workflow graph
+ if wgraph:
+ graphoption = ['-G', '%s'%os.path.abspath(path_to_figures)]
+ elif tree:
+ graphoption = ['-U' ,'%s'%os.path.abspath(path_to_figures)]
+ else:
+ graphoption = ['-e', '%s'%os.path.abspath(path_to_figures)]
+ #don't select a workflow
+ if version is not None:
+ voption = ":%s"%version
+ else:
+ voption = ""
+
+ prefix = ['%s'%path_to_vistrails]
+ if path_to_vistrails.endswith(".py"):
+ prefix = ['%s'%path_to_python,
+ '%s'%path_to_vistrails]
+ cmd_line = prefix + ['-b'] + graphoption + ['-t', host, '-f',db_name] + \
+ useroption + ['-r', port] + pdfoption + [ '%s%s'%(vt_id, voption)]
+ return cmd_line
+
+###############################################################################
+
+def build_vistrails_cmd_line_file(path_to_vistrails, path_to_python,
+ env_for_vistrails, filename,
+ version, path_to_figures, pdf=False,
+ wgraph=False, tree=False):
+ """ build_vistrails_cmd_line_file(path_to_vistrails: str,
+ env_for_vostrails: str, filename: str,
+ version: str, path_to_figures: str,
+ pdf:bool, wgraph:bool, tree: bool) -> str
+ Build the command line to run vistrails with the given parameters.
+ """
+ #dump pdf
+ if pdf:
+ pdfoption = ["-p"]
+ else:
+ pdfoption = []
+ #dump tree and workflow graph
+ if wgraph:
+ graphoption = ['-G','%s'%os.path.abspath(path_to_figures)]
+ elif tree:
+ graphoption = ['-U','%s'%os.path.abspath(path_to_figures)]
+ else:
+ graphoption = ['-e','%s'%os.path.abspath(path_to_figures)]
+ #don't select a workflow
+ if version is not None:
+ voption = ":%s"%version
+ else:
+ voption = ''
+ prefix = ['%s'%path_to_vistrails]
+ if path_to_vistrails.endswith(".py"):
+ prefix = ['%s'%path_to_python,
+ '%s'%path_to_vistrails]
+ cmd_line = prefix + ['-b'] + graphoption + pdfoption + \
+ [ "%s%s"%(os.path.abspath(filename),voption)]
+
+ return cmd_line
+
+###############################################################################
+
+def generate_latex_db(is_local, download_url, host, db_name, vt_id, version, port, tag,
+ execute, showspreadsheetonly, path_to_figures,
+ graphics_options, embedWorkflow=False,
+ includeFullTree=False):
+ """generate_latex(host: str, db_name:str, vt_id: str, version: str,
+ port:str, tag: str, execute: bool,
+ showspreadsheetonly: bool, path_to_figures: str,
+ graphics_options: str, embedWorkflow: bool,
+ includeFullTree:bool) -> str
+ This generates a piece of latex code containing the \href command and
+ a \includegraphics command for each image generated.
+ """
+ if not is_local:
+ if download_url is not None and download_url != "":
+ url = build_download_vtl_request(download_url, host, db_name, vt_id,
+ version, port, tag, execute,
+ showspreadsheetonly,
+ embedWorkflow=embedWorkflow,
+ includeFullTree=includeFullTree)
+ href = "\href{%s}{" % url
+ else:
+ if download_url is not None and download_url != "":
+ url = build_vtl_db(download_url, host, db_name, vt_id,
+ version, port, tag, execute,
+ showspreadsheetonly, embedWorkflow=embedWorkflow,
+ includeFullTree=includeFullTree)
+ href = "\href{%s}{" % url
+ ALLOWED_GRAPHICS = [".png", ".jpg", ".pdf"]
+ images = []
+ for root, dirs, file_names in os.walk(path_to_figures):
+ for f in file_names:
+ ext = os.path.splitext(f)[1]
+ if ext in ALLOWED_GRAPHICS:
+ images.append(f)
+ break
+ n = len(images)
+ s = ''
+
+ for f in images:
+ filename = os.path.join(path_to_figures,f).replace("%","\%")
+ if graphics_options:
+ s += "\includegraphics[%s]{%s}\n" % (graphics_options, filename.replace("\\","/"))
+ else:
+ s += "\includegraphics{%s}\n" % filename.replace("\\","/")
+
+ if download_url is not None and download_url != "":
+ return href + s + "}"
+ else:
+ return s
+
+###############################################################################
+
+def generate_latex_file(download_url, vtfile, version, tag,
+ execute, showspreadsheetonly, path_to_figures,
+ graphics_options,embedWorkflow=False,
+ includeFullTree=False):
+ """generate_latex(host: str, db_name:str, vt_id: str, version: str,
+ port:str, tag: str, execute: bool,
+ showspreadsheetonly: bool, path_to_figures: str,
+ graphics_options: str) -> str
+ This generates a piece of latex code containing the \href command and
+ a \includegraphics command for each image generated.
+ """
+ log("generate_latex_file")
+ if download_url is not None and download_url != "":
+ url = build_vtl_file(download_url, vtfile, version, tag, execute,
+ showspreadsheetonly, embedWorkflow=False)
+ href = "\href{%s}{" % url
+ log(url)
+ ALLOWED_GRAPHICS = [".png", ".jpg", ".pdf"]
+ images = []
+ for root, dirs, file_names in os.walk(path_to_figures):
+ for f in file_names:
+ ext = os.path.splitext(f)[1]
+ if ext in ALLOWED_GRAPHICS:
+ images.append(f)
+ break
+ n = len(images)
+ s = ''
+ for f in images:
+ filename = os.path.join(path_to_figures,f).replace("%","\%")
+ if graphics_options:
+ s += "\includegraphics[%s]{%s}\n" % (graphics_options, filename.replace("\\","/"))
+ else:
+ s += "\includegraphics{%s}\n" % filename.replace("\\","/")
+
+ if download_url is not None and download_url != "":
+ return href + s + "}"
+ else:
+ return s
+
+###############################################################################
+
+def generate_latex_error(error_msg):
+ """ generate_latex_error(error_msg: str) -> str
+ this generates a piece of latex code with an error message.
+ """
+ error_msg = error_msg.replace("\n", "\\MessageBreak ")
+ s = """\\PackageError{vistrails}{ An error occurred when executing vistrails. \\MessageBreak
+%s
+}{}""" % error_msg
+ return s
+
+###############################################################################
+
+def run_vistrails_locally_db(path_to_vistrails, path_to_python,
+ env_for_vistrails, host, db_name,
+ db_user, vt_id,
+ version, port, path_to_figures, build_always=False,
+ tag='', execute=False, showspreadsheetonly=False,
+ pdf=False, embedWorkflow=False,
+ includeFullTree=False):
+ """run_vistrails_locally_db(path_to_vistrails: str, host: str,
+ db_name: str, vt_id: str, version: str, port: str,
+ path_to_figures: str) -> tuple(bool, str)
+ Run vistrails and returns a tuple containing a boolean saying if it was
+ successful or not and the latex code.
+ """
+ v = version
+ if tag != '':
+ v = tag
+ cmd_line = build_vistrails_cmd_line_db(path_to_vistrails, path_to_python,
+ env_for_vistrails,
+ host, db_name, db_user, vt_id,
+ v, port, path_to_figures, pdf)
+ log("run_vistrails_locally_db")
+ log("cmdline: %s"%cmd_line)
+
+ if build_always:
+ #force to remove the folder so we avoid stale results
+ if os.path.exists(path_to_figures):
+ shutil.rmtree(path_to_figures)
+
+ if not os.path.exists(path_to_figures):
+ os.makedirs(path_to_figures)
+
+ if build_always or not path_exists_and_not_empty(path_to_figures):
+ my_env = os.environ
+ sep = ":"
+ if systemType in ["Windows", "Microsoft"]:
+ sep = ";"
+ if env_for_vistrails != '':
+ data = shlex.split(env_for_vistrails)
+ for d in data:
+ (name,val) = d.split("=")
+ pos = val.find("$"+name)
+ if pos != -1:
+ if pos == 0:
+ my_env[name] = my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ if pos + len(name) == len(val) -1:
+ my_env[name] = val[0:pos] + my_env.get(name,'')
+ else:
+ my_env[name] = val[0:pos] + my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ my_env[name] = val
+ log("env: %s"%my_env)
+ if systemType in ['Windows', 'Microsoft']:
+ proc = subprocess.Popen(cmd_line,
+ env=my_env)
+ else:
+ proc = subprocess.Popen(cmd_line, shell=False,
+ env=my_env,
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ close_fds=True)
+ proc.wait()
+ log("result: %s"%proc.returncode)
+ if proc.stdout:
+ lines = proc.stdout.readlines()
+ log("stdout: %s"%lines)
+ if proc.returncode != 0:
+ shutil.rmtree(path_to_figures)
+ msg = "See vistrails.log for more information."
+ return (False, generate_latex_error(msg))
+
+ return (True, generate_latex_db(True,os.getcwd(), host, db_name, vt_id, version, port, tag,
+ execute, showspreadsheetonly,
+ path_to_figures, graphics_options,
+ embedWorkflow, includeFullTree))
+
+###############################################################################
+
+def run_vistrails_locally_file(path_to_vistrails, path_to_python,
+ env_for_vistrails, filename,
+ version, path_to_figures, build_always=False,
+ tag='', execute=False, showspreadsheetonly=False,
+ pdf=False, embedWorkflow=False,
+ includeFullTree=False):
+ """run_vistrails_locally_file(path_to_vistrails: str, filename: str,
+ version: str, path_to_figures: str,
+ build_always:bool, tag:str, execute:bool,
+ showspreadsheetonly:bool, pdf:bool) ->
+ tuple(bool, str)
+ Run vistrails and returns a tuple containing a boolean saying if it was
+ successful or not and the latex code.
+ """
+ v = version
+ if tag != '':
+ v = tag
+ cmd_line = build_vistrails_cmd_line_file(path_to_vistrails, path_to_python,
+ env_for_vistrails,
+ filename, v, path_to_figures,
+ pdf)
+ log("run_vistrails_locally_file")
+ log("cmdline: %s"%cmd_line)
+ if build_always:
+ #force to remove the folder so we avoid stale results
+ if os.path.exists(path_to_figures):
+ shutil.rmtree(path_to_figures)
+
+ if not os.path.exists(path_to_figures):
+ log("creating image path")
+ os.makedirs(path_to_figures)
+
+ if build_always or not path_exists_and_not_empty(path_to_figures):
+ my_env = os.environ
+ sep = ":"
+ if systemType in ["Windows", "Microsoft"]:
+ sep = ";"
+ if env_for_vistrails != '':
+ data = shlex.split(env_for_vistrails)
+ log("env_for_vistrails: %s"%data)
+ for d in data:
+ (name,val) = d.split("=")
+ pos = val.find("$"+name)
+ if pos != -1:
+ if pos == 0:
+ my_env[name] = my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ if pos + len(name) == len(val) -1:
+ my_env[name] = val[0:pos] + my_env.get(name,'')
+ else:
+ my_env[name] = val[0:pos] + my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ my_env[name] = val
+ log("env: %s"%my_env)
+ if systemType in ['Windows', 'Microsoft']:
+ proc = subprocess.Popen(cmd_line,
+ env=my_env,
+ stdout=subprocess.PIPE)
+ else:
+ proc = subprocess.Popen(cmd_line, shell=False,
+ env=my_env,
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ close_fds=True)
+ proc.wait()
+ log("result: %s"%proc.returncode)
+ if proc.stdout:
+ lines = proc.stdout.readlines()
+ log("stdout: %s"%lines)
+ if proc.returncode != 0:
+ shutil.rmtree(path_to_figures)
+ msg = "See vistrails.log for more information."
+ return (False, generate_latex_error(msg))
+ log("will generate latex")
+ try:
+ return (True, generate_latex_file(os.path.dirname(os.path.abspath(filename)),
+ filename, version, tag,
+ execute, showspreadsheetonly,
+ path_to_figures, graphics_options,
+ embedWorkflow, includeFullTree))
+ except Exception, e:
+ log("Error: %s"%str(e))
+###############################################################################
+
+def get_vt_graph_locally_db(path_to_vistrails, path_to_python,
+ env_for_vistrails, host, db_name,
+ db_user, vt_id, port, path_to_figures,
+ build_always=False, pdf=False,
+ embedWorkflow=False, includeFullTree=False):
+ """get_vt_graph_locally_db(path_to_vistrails: str, host: str,
+ db_name: str, vt_id: str, port: str,
+ path_to_figures: str, build_always: bool,
+ pdf:bool) -> tuple(bool, str)
+ Run vistrails for loading a vistrail and dump the tree to a file and
+ returns a tuple containing a boolean saying if it was
+ successful or not and the latex code.
+ """
+ cmd_line = build_vistrails_cmd_line_db(path_to_vistrails, path_to_python,
+ env_for_vistrails,
+ host, db_name, db_user, vt_id,
+ None, port, path_to_figures, pdf, False,
+ True)
+ log("get_vt_graph_locally_db")
+ log("cmdline: %s"%cmd_line)
+ if build_always:
+ #force to remove the folder so we avoid stale results
+ if os.path.exists(path_to_figures):
+ shutil.rmtree(path_to_figures)
+
+ if not os.path.exists(path_to_figures):
+ os.makedirs(path_to_figures)
+
+ if build_always or not path_exists_and_not_empty(path_to_figures):
+ my_env = os.environ
+ sep = ":"
+ if systemType in ["Windows", "Microsoft"]:
+ sep = ";"
+ if env_for_vistrails != '':
+ data = shlex.split(env_for_vistrails)
+ for d in data:
+ (name,val) = d.split("=")
+ pos = val.find("$"+name)
+ if pos != -1:
+ if pos == 0:
+ my_env[name] = my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ if pos + len(name) == len(val) -1:
+ my_env[name] = val[0:pos] + my_env.get(name,'')
+ else:
+ my_env[name] = val[0:pos] + my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ my_env[name] = val
+ log("env: %s"%my_env)
+ if systemType in ['Windows', 'Microsoft']:
+ proc = subprocess.Popen(cmd_line,
+ env=my_env,
+ stdout=subprocess.PIPE)
+ else:
+ proc = subprocess.Popen(cmd_line, shell=False,
+ env=my_env,
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ close_fds=True)
+ proc.wait()
+ log("result: %s"%proc.returncode)
+ if proc.stdout:
+ lines = proc.stdout.readlines()
+ log("stdout: %s"%lines)
+ if proc.returncode != 0:
+ os.rmdir(path_to_figures)
+ msg = "See vistrails.log for more information."
+ return (False, generate_latex_error(msg))
+
+ return (True, generate_latex_db(True, os.getcwd(), host, db_name, vt_id, None, port, '',
+ False, False,
+ path_to_figures, graphics_options,
+ embedWorkflow, includeFullTree))
+
+###############################################################################
+
+def get_vt_graph_locally_file(path_to_vistrails, path_to_python,
+ env_for_vistrails, filename,
+ path_to_figures, build_always=False, pdf=False,
+ embedWorkflow=False, includeFullTree=False):
+ """get_vt_graph_locally_file(path_to_vistrails: str, env_for_vistrails: str,
+ filename: str, version: str,
+ path_to_figures: str,build_always: bool,
+ pdf:bool) -> tuple(bool, str)
+ Run VisTrails to load a workflow and dump the graph to a file and
+ returns a tuple containing a boolean saying whether it was
+ successful and the latex code.
+ """
+ cmd_line = build_vistrails_cmd_line_file(path_to_vistrails,
+ path_to_python,
+ env_for_vistrails,
+ filename, None, path_to_figures,
+ pdf, False, True)
+ log("get_vt_graph_locally_file")
+ log("cmdline: %s"%cmd_line)
+
+ if build_always:
+ #force to remove the folder so we avoid stale results
+ if os.path.exists(path_to_figures):
+ shutil.rmtree(path_to_figures)
+
+ if not os.path.exists(path_to_figures):
+ log(" creating images folder")
+ os.makedirs(path_to_figures)
+
+ if build_always or not path_exists_and_not_empty(path_to_figures):
+ log(" folder was empty or forcing execution")
+ my_env = os.environ
+ sep = ":"
+ if systemType in ["Windows", "Microsoft"]:
+ sep = ";"
+ if env_for_vistrails != '':
+ data = shlex.split(env_for_vistrails)
+ for d in data:
+ (name,val) = d.split("=")
+ pos = val.find("$"+name)
+ if pos != -1:
+ if pos == 0:
+ my_env[name] = my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ if pos + len(name) == len(val) -1:
+ my_env[name] = val[0:pos] + my_env.get(name,'')
+ else:
+ my_env[name] = val[0:pos] + my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ my_env[name] = val
+ log("env: %s"%my_env)
+ if systemType in ['Windows', 'Microsoft']:
+ proc = subprocess.Popen(cmd_line,
+ env=my_env,
+ stdout=subprocess.PIPE)
+ else:
+ proc = subprocess.Popen(cmd_line, shell=False,
+ env=my_env,
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ close_fds=True)
+ proc.wait()
+ log("result: %s"%proc.returncode)
+ if proc.stdout:
+ lines = proc.stdout.readlines()
+ log("stdout: %s"%lines)
+ if proc.returncode != 0:
+ os.rmdir(path_to_figures)
+ msg = "See vistrails.log and vistrails_run.log for more information."
+ return (False, generate_latex_error(msg))
+ else:
+ log(" found cached images")
+
+ return (True, generate_latex_file(os.path.dirname(os.path.abspath(filename)),
+ filename, None, '', False,
+ False, path_to_figures,
+ graphics_options, embedWorkflow,
+ includeFullTree))
+
+###############################################################################
+
+def get_wf_graph_locally_db(path_to_vistrails, path_to_python,
+ env_for_vistrails, host, db_name,
+ db_user, vt_id, version, port, path_to_figures,
+ build_always=False, tag='', pdf=False,
+ embedWorkflow=False, includeFullTree=False):
+ """get_wf_graph_locally_db(path_to_vistrails: str, host: str,
+ db_name: str, vt_id: str, version: str, port: str,
+ path_to_figures: str,build_always: bool,
+ tag: str, pdf:bool) -> tuple(bool, str)
+ Run vistrails for loading a workflow and dump the graph to a file and
+ returns a tuple containing a boolean saying if it was
+ successful or not and the latex code.
+ """
+ v = version
+ if tag != '':
+ v = tag
+ cmd_line = build_vistrails_cmd_line_db(path_to_vistrails,
+ path_to_python, env_for_vistrails,
+ host, db_name, db_user, vt_id,
+ v, port, path_to_figures, pdf,
+ True, False)
+ log("get_wf_graph_locally_db")
+ log("cmdline: %s"%cmd_line)
+ if build_always:
+ #force to remove the folder so we avoid stale results
+ if os.path.exists(path_to_figures):
+ shutil.rmtree(path_to_figures)
+
+ if not os.path.exists(path_to_figures):
+ log(" creating images folder")
+ os.makedirs(path_to_figures)
+
+ if build_always or not path_exists_and_not_empty(path_to_figures):
+ log(" folder was empty or forcing execution")
+ my_env = os.environ
+ sep = ":"
+ if systemType in ["Windows", "Microsoft"]:
+ sep = ";"
+ if env_for_vistrails != '':
+ data = shlex.split(env_for_vistrails)
+ for d in data:
+ (name,val) = d.split("=")
+ pos = val.find("$"+name)
+ if pos != -1:
+ if pos == 0:
+ my_env[name] = my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ if pos + len(name) == len(val) -1:
+ my_env[name] = val[0:pos] + my_env.get(name,'')
+ else:
+ my_env[name] = val[0:pos] + my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ my_env[name] = val
+ log("env: %s"%my_env)
+ if systemType in ['Windows', 'Microsoft']:
+ log("env: %s"%my_env)
+ proc = subprocess.Popen(cmd_line,
+ env=my_env,
+ stdout=subprocess.PIPE)
+ else:
+ proc = subprocess.Popen(cmd_line, shell=False,
+ env=my_env,
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ close_fds=True)
+ proc.wait()
+ log("result: %s"%proc.returncode)
+ if proc.stdout:
+ lines = proc.stdout.readlines()
+ log("stdout: %s"%lines)
+ if proc.returncode != 0:
+ os.rmdir(path_to_figures)
+ msg = "See vistrails.log for more information."
+ return (False, generate_latex_error(msg))
+ else:
+ log(" found cached images")
+
+ return (True, generate_latex_db(True, os.getcwd(), host, db_name, vt_id, version,
+ port, tag, execute, showspreadsheetonly,
+ path_to_figures, graphics_options,
+ embedWorkflow, includeFullTree))
+
+###############################################################################
+
+def get_wf_graph_locally_file(path_to_vistrails, path_to_python,
+ env_for_vistrails, filename,
+ version, path_to_figures, build_always=False,
+ tag='', pdf=False, embedWorkflow=False,
+ includeFullTree=False):
+ """get_wf_graph_locally_file(path_to_vistrails: str, env_for_vistrails: str,
+ filename: str, version: str,
+ path_to_figures: str,build_always: bool,
+ tag: str, pdf:bool) -> tuple(bool, str)
+ Run VisTrails to load a workflow and dump the graph to a file and
+ returns a tuple containing a boolean saying whether it was
+ successful and the latex code.
+ """
+ v = version
+ if tag != '':
+ v = tag
+ cmd_line = build_vistrails_cmd_line_file(path_to_vistrails, path_to_python,
+ env_for_vistrails,
+ filename, v, path_to_figures,
+ pdf, True, False)
+ log("get_wf_graph_locally_file")
+ log("cmdline: %s"%cmd_line)
+ if build_always:
+ #force to remove the folder so we avoid stale results
+ if os.path.exists(path_to_figures):
+ shutil.rmtree(path_to_figures)
+
+ if not os.path.exists(path_to_figures):
+ log(" creating images folder")
+ os.makedirs(path_to_figures)
+
+ if build_always or not path_exists_and_not_empty(path_to_figures):
+ log(" folder was empty or forcing execution")
+ my_env = os.environ
+ sep = ":"
+ if systemType in ["Windows", "Microsoft"]:
+ sep = ";"
+ if env_for_vistrails != '':
+ data = shlex.split(env_for_vistrails)
+ for d in data:
+ (name,val) = d.split("=")
+ pos = val.find("$"+name)
+ if pos != -1:
+ if pos == 0:
+ my_env[name] = my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ if pos + len(name) == len(val) -1:
+ my_env[name] = val[0:pos] + my_env.get(name,'')
+ else:
+ my_env[name] = val[0:pos] + my_env.get(name,'') + \
+ val[pos+len(name)+1:]
+ else:
+ my_env[name] = val
+ log("env: %s"%my_env)
+ if systemType in ['Windows', 'Microsoft']:
+ proc = subprocess.Popen(cmd_line,
+ env=my_env,
+ stdout=subprocess.PIPE)
+ else:
+ proc = subprocess.Popen(cmd_line, shell=False,
+ env=my_env,
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ close_fds=True)
+ proc.wait()
+ log("result: %s"%proc.returncode)
+ if proc.stdout:
+ lines = proc.stdout.readlines()
+ log("stdout: %s"%lines)
+ if proc.returncode != 0:
+ os.rmdir(path_to_figures)
+ msg = "See vistrails.log for more information."
+ return (False, generate_latex_error(msg))
+ else:
+ log(" found cached images")
+ log(" about to return")
+ return (True, generate_latex_file(os.path.dirname(os.path.abspath(filename)),
+ filename, version, tag, execute,
+ showspreadsheetonly, path_to_figures,
+ graphics_options, embedWorkflow,
+ includeFullTree))
+
+###############################################################################
+
+def run_vistrails_remotely(path_to_vistrails, download_url, host, db_name, vt_id,
+ version, port, path_to_figures, build_always=False,
+ tag='', execute=False, showspreadsheetonly=False,
+ pdf=False, embedWorkflow=False,
+ includeFullTree=False):
+ """run_vistrails_remotely(path_to_vistrails: str, download_url: str host: str,
+ db_name: str, vt_id: str, version: str, port: str,
+ path_to_figures: str, build_always: bool,
+ tag:str, execute: bool, showspreadsheetonly: bool,
+ pdf: bool, embedWorkflow:bool,
+ includeFullTree:bool)
+ -> tuple(bool, str)
+ Call vistrails remotely to execute a workflow and returns a tuple
+ containing a boolean saying whether it was successful and the latex
+ code.
+ """
+ log("run_vistrails_remotely")
+ if build_always:
+ #force to remove the folder so we avoid stale results
+ if os.path.exists(path_to_figures):
+ shutil.rmtree(path_to_figures)
+
+ if not path_exists_and_not_empty(path_to_figures) or build_always:
+ if not os.path.exists(path_to_figures):
+ os.makedirs(path_to_figures)
+
+ if check_url(path_to_vistrails):
+ website = "://".join(urlparse(path_to_vistrails)[:2])
+ request = "?host=%s&db=%s&vt=%s&version=%s&port=%s&pdf=%s" % (host,
+ db_name,
+ vt_id,
+ urllib2.quote(version),
+ port,
+ pdf)
+ url = path_to_vistrails + request
+ log("will download from: " + url)
+
+ (result, msg) = _download_content(website, url, path_to_figures)
+ if result == True:
+ log("success")
+ return (result, generate_latex_db(False, download_url, host, db_name, vt_id,
+ version, port, tag, execute,
+ showspreadsheetonly,
+ path_to_figures,
+ graphics_options,
+ embedWorkflow, includeFullTree))
+ else:
+ log("Error: " + msg)
+ return (result, generate_latex_error(msg))
+ else:
+ msg = "Invalid url: %s" % path_to_vistrails
+ log("Error: " + msg)
+ return (False, generate_latex_error(msg))
+ else:
+ log("using cached files")
+ return (True, generate_latex_db(False, download_url, host, db_name, vt_id,
+ version, port, tag, execute,
+ showspreadsheetonly,
+ path_to_figures, graphics_options,
+ embedWorkflow, includeFullTree))
+
+###############################################################################
+
+def get_vt_graph_remotely(path_to_vistrails, download_url, host, db_name, vt_id,
+ port, path_to_figures, build_always=False, pdf=False,
+ embedWorkflow=False, includeFullTree=False):
+ """get_vt_graph_remotely(path_to_vistrails: str, download_url: str, host: str,
+ db_name: str, vt_id: str, port: str,
+ path_to_figures: str, build_always: bool, pdf: bool)
+ -> tuple(bool, str)
+ Get the version tree image of a vistrail and returns a tuple containing
+ a boolean saying whether it was successful and the latex code.
+ """
+ log("get_vt_graph_remotely")
+ if build_always:
+ #force to remove the folder so we avoid stale results
+ if os.path.exists(path_to_figures):
+ shutil.rmtree(path_to_figures)
+
+ if not path_exists_and_not_empty(path_to_figures) or build_always:
+ if not os.path.exists(path_to_figures):
+ os.makedirs(path_to_figures)
+
+ if check_url(path_to_vistrails):
+ website = "://".join(urlparse(path_to_vistrails)[:2])
+ request = "?host=%s&db=%s&vt=%s&port=%s&pdf=%s&showtree=True" % (host,
+ db_name,
+ vt_id,
+ port,
+ pdf)
+ url = path_to_vistrails + request
+ log("will download from: " + url)
+
+ (result, msg) = _download_content(website, url, path_to_figures)
+ if result == True:
+ log("success")
+ return (result, generate_latex_db(False, download_url, host, db_name,
+ vt_id, None,
+ port, '', False,
+ False,
+ path_to_figures,
+ graphics_options,
+ embedWorkflow, includeFullTree))
+ else:
+ log("Error: " + msg)
+ return (result, generate_latex_error(msg))
+ else:
+ msg = "Invalid url: %s" % path_to_vistrails
+ log("Error: " + msg)
+ return (False, generate_latex_error(msg))
+ else:
+ log("using cached files")
+ return (True, generate_latex_db(False, download_url, host, db_name, vt_id,
+ None, port, '',
+ False, False,
+ path_to_figures, graphics_options,
+ embedWorkflow, includeFullTree))
+
+###############################################################################
+
+def get_wf_graph_remotely(path_to_vistrails, download_url, host, db_name, vt_id,
+ version, port, path_to_figures, build_always=False,
+ tag='', pdf=False, embedWorkflow=False,
+ includeFullTree=False):
+ """get_wf_graph_remotely(path_to_vistrails: str, download_url:str, host: str,
+ db_name: str, vt_id: str, version: str, port: str,
+ path_to_figures: str, build_always: bool,
+ tag:str, pdf: bool) -> tuple(bool, str)
+ Get the graph of a workflow and returns a tuple containing a boolean
+ saying whether it was successful and the latex code.
+ """
+ log("get_wf_graph_remotely")
+
+ if build_always:
+ #force to remove the folder so we avoid stale results
+ if os.path.exists(path_to_figures):
+ shutil.rmtree(path_to_figures)
+
+ if not path_exists_and_not_empty(path_to_figures) or build_always:
+ if not os.path.exists(path_to_figures):
+ os.makedirs(path_to_figures)
+
+ if check_url(path_to_vistrails):
+ website = "://".join(urlparse(path_to_vistrails)[:2])
+ request = "?host=%s&db=%s&vt=%s&version=%s&port=%s&pdf=%s&showworkflow=True" % (host,
+ db_name,
+ vt_id,
+ urllib2.quote(version),
+ port,
+ pdf)
+ url = path_to_vistrails + request
+ log("will download from: " + url)
+
+ (result, msg) = _download_content(website, url, path_to_figures)
+ if result == True:
+ log("success")
+ return (result, generate_latex_db(False, download_url, host, db_name,
+ vt_id, version,
+ port, tag, False,
+ False,
+ path_to_figures,
+ graphics_options,
+ embedWorkflow, includeFullTree))
+ else:
+ log("Error: " + msg)
+ return (result, generate_latex_error(msg))
+ else:
+ msg = "Invalid url: %s" % path_to_vistrails
+ log("Error: " + msg)
+ return (False, generate_latex_error(msg))
+ else:
+ log("using cached files")
+ return (True, generate_latex_db(False, download_url, host, db_name, vt_id,
+ version, port, tag,
+ False, False,
+ path_to_figures, graphics_options,
+ embedWorkflow, includeFullTree))
+
+###############################################################################
+
+def check_path(path):
+ """check_path(path:str) -> bool
+ Checks if it's a valid system path.
+ If path is valid, we will update it to be a realpath.
+
+ """
+ result = False
+ new_path = os.path.realpath(path)
+ if os.path.isfile(new_path):
+ path = new_path
+ result = True
+ else:
+ result = False
+ return result
+
+###############################################################################
+
+def check_url(url):
+ try:
+ p = urlparse(url)
+ h = HTTP(p[1])
+ h.putrequest('HEAD', p[2])
+ h.endheaders()
+ if h.getreply()[0] == 200:
+ return True
+ else:
+ return False
+ except Exception, e:
+ log(str(e))
+ return False
+
+###############################################################################
+
+options_file = None
+try:
+ options_file = open(sys.argv[1])
+except IndexError:
+ usage()
+
+if debug:
+ logger = logging.getLogger("VisTrailsLatex")
+ handler = logging.FileHandler('vistrails.log')
+ handler.setFormatter(logging.Formatter('VisTrailsLatex - %(asctime)s %(message)s'))
+ handler.setLevel(logging.DEBUG)
+ logger.setLevel(logging.DEBUG)
+ logger.addHandler(handler)
+ log("***********************************")
+ log("********* SESSION START ***********")
+
+lines = options_file.readlines()
+path_to_vistrails = None
+path_to_python = None
+download_url = None
+env_for_vistrails = None
+host = None
+db_name = None
+db_user = None
+vt_id = None
+filename = None
+version = None
+graphics_options = None
+build_always = False
+port = '3306'
+version_tag = ''
+showspreadsheetonly = False
+execute = False
+pdf = False
+wgraph = False
+tree = False
+getvtl = False
+embedWorkflow=False
+includeFullTree=False
+for line in lines:
+ args = line.split("=")
+ if len(args) > 2:
+ args[1] = "=".join(args[1:])
+ if args[0] == "path":
+ path_to_vistrails = args[1].strip(" \n")
+ elif args[0] == "python":
+ path_to_python = args[1].strip(" \n")
+ elif args[0] == "env":
+ env_for_vistrails = args[1].strip(" \n")
+ elif args[0] == "download":
+ download_url = args[1].strip(" \n")
+ elif args[0] == "host":
+ host = args[1].strip(" \n")
+ elif args[0] == "db":
+ db_name = args[1].strip(" \n")
+ elif args[0] == "user":
+ db_user = args[1].strip(" \n")
+ elif args[0] == "vtid":
+ vt_id = args[1].strip(" \n")
+ elif args[0] == "filename":
+ filename = args[1].strip(" \n")
+ elif args[0] == "version":
+ version = args[1].strip(" \n")
+ elif args[0] == "port":
+ port = args[1].strip(" \n")
+ elif args[0] == "buildalways":
+ build_always = bool_conv(args[1].strip(" \n"))
+ elif args[0] == "tag":
+ version_tag = args[1].strip(" \n")
+ elif args[0] == "execute":
+ execute = bool_conv(args[1].strip(" \n"))
+ elif args[0] == "showspreadsheetonly":
+ showspreadsheetonly = bool_conv(args[1].strip(" \n"))
+ elif args[0] == 'pdf':
+ pdf = bool_conv(args[1].strip(" \n"))
+ elif args[0] == 'workflow':
+ wgraph = bool_conv(args[1].strip(" \n"))
+ elif args[0] == 'tree':
+ tree = bool_conv(args[1].strip(" \n"))
+ elif args[0] == 'getvtl':
+ getvtl = bool_conv(args[1].strip(" \n"))
+ elif args[0] == 'embedworkflow':
+ embedWorkflow = bool_conv(args[1].strip(" \n"))
+ elif args[0] == 'includefulltree':
+ includeFullTree = bool_conv(args[1].strip(" \n"))
+ elif args[0] == "other":
+ graphics_options = args[1].strip(" \n")
+
+if showspreadsheetonly:
+ execute = True
+# then we use the combination host_db_name_port_vt_id_version or
+# filename_version to create a unique folder.
+
+# TODO: Maybe we should use a hash of this. For now let's keep it
+# legible.
+out_type = "png"
+if pdf:
+ out_type = 'pdf'
+if filename is not None:
+ path_to_figures = os.path.join("vistrails_images",
+ "%s_%s_%s" % (filename,
+ version,
+ out_type))
+ if tree:
+ #no need to encode version
+ path_to_figures = os.path.join("vistrails_images",
+ "%s_%s" % (filename, out_type))
+ elif wgraph:
+ path_to_figures = os.path.join("vistrails_images",
+ "%s_%s_%s_graph" % (filename,
+ version,
+ out_type))
+else:
+ path_to_figures = os.path.join("vistrails_images",
+ "%s_%s_%s_%s_%s_%s" % (host, db_name, port,
+ vt_id,
+ version,
+ out_type))
+ if tree:
+ #no need to encode version
+ path_to_figures = os.path.join("vistrails_images",
+ "%s_%s_%s_%s_%s" % (host, db_name, port,
+ vt_id,
+ out_type))
+ elif wgraph:
+ path_to_figures = os.path.join("vistrails_images",
+ "%s_%s_%s_%s_%s_%s_graph" % (host, db_name, port,
+ vt_id,
+ version,
+ out_type))
+# if the path_to_vistrails point to a file that exists on disk, we will use
+# it, else let's assume it's a url (we still check if the url is valid inside
+# the run_vistrails_remotely function)
+log("path_to_figures: %s"%path_to_figures)
+if check_path(path_to_vistrails) and filename is None: #run locally
+ if tree:
+ # we don't need to actually run the workflow, we just get the
+ # tree
+ log("will run get_vt_graph_locally_db")
+ result, latex = get_vt_graph_locally_db(path_to_vistrails,
+ path_to_python,
+ env_for_vistrails, host, db_name,
+ db_user,
+ vt_id, port, path_to_figures,
+ build_always, pdf, embedWorkflow,
+ includeFullTree)
+ elif wgraph:
+ # we don't need to actually run the workflow, we just get the
+ # workflow graph
+ log("will run get_wf_graph_locally_db")
+ result, latex = get_wf_graph_locally_db(path_to_vistrails,
+ path_to_python,
+ env_for_vistrails, host, db_name,
+ db_user,
+ vt_id, version, port, path_to_figures,
+ build_always, version_tag, pdf,
+ embedWorkflow, includeFullTree)
+ else:
+ result, latex = run_vistrails_locally_db(path_to_vistrails,
+ path_to_python,
+ env_for_vistrails, host, db_name,
+ db_user,
+ vt_id, version, port, path_to_figures,
+ build_always, version_tag, execute,
+ showspreadsheetonly, pdf,
+ embedWorkflow, includeFullTree)
+elif check_path(path_to_vistrails) and filename is not None: #run locally
+ if tree:
+ # we don't need to actually run the workflow, we just get the
+ # tree
+ result, latex = get_vt_graph_locally_file(path_to_vistrails,
+ path_to_python,
+ env_for_vistrails, filename,
+ path_to_figures,
+ build_always, pdf,
+ embedWorkflow, includeFullTree)
+ elif wgraph:
+ # we don't need to actually run the workflow, we just get the
+ # workflow graph
+ log("will run get_wf_graph_locally_file")
+ result, latex = get_wf_graph_locally_file(path_to_vistrails,
+ path_to_python,
+ env_for_vistrails, filename,
+ version, path_to_figures,
+ build_always, version_tag, pdf,
+ embedWorkflow, includeFullTree)
+ else:
+ result, latex = run_vistrails_locally_file(path_to_vistrails,
+ path_to_python,
+ env_for_vistrails, filename,
+ version, path_to_figures,
+ build_always, version_tag,
+ execute, showspreadsheetonly,
+ pdf,embedWorkflow,
+ includeFullTree)
+elif (not build_always or
+ (build_always and check_url(path_to_vistrails))): #run from the web
+ if tree:
+ result, latex = get_vt_graph_remotely(path_to_vistrails, download_url,
+ host, db_name,
+ vt_id, port, path_to_figures,
+ build_always, pdf, embedWorkflow,
+ includeFullTree)
+ elif wgraph:
+ result, latex = get_wf_graph_remotely(path_to_vistrails, download_url,
+ host, db_name,
+ vt_id, version, port, path_to_figures,
+ build_always,version_tag, pdf,
+ embedWorkflow, includeFullTree)
+ else:
+ result, latex = run_vistrails_remotely(path_to_vistrails, download_url,
+ host, db_name,
+ vt_id, version, port, path_to_figures,
+ build_always, version_tag, execute,
+ showspreadsheetonly,pdf,
+ embedWorkflow, includeFullTree)
+ #download vtl file
+ if getvtl:
+ if (not build_always and not vtl_exists_in_folder(path_to_figures) or
+ build_always):
+ url = build_download_vtl_request(download_url, host, db_name,
+ vt_id, version, port, version_tag,
+ execute, showspreadsheetonly,
+ embedWorkflow=embedWorkflow,
+ includeFullTree=includeFullTree)
+ log("get_vtl %s"%url)
+ if download(url, filename=None, folder=path_to_figures) == False:
+ log("Error when downloading vtl to %s"%path_to_figures)
+
+
+else:
+ result, latex = (False,
+ generate_latex_error("It is possible that %s is not a valid \
+url nor a valid path to vistrails/run.py or that you don't have an internet connection \
+and some workflows have the buildalways option. If you already have cached files, \
+try removing the buildalways option from vistrails latex command" %\
+ (path_to_vistrails)))
+
+# the printed answer will be included inline by the latex compiler.
+print latex
+if result == True:
+ # we will also create a temporary file that can be used to include the
+ # images directly
+ if not os.path.isdir('cached'):
+ if os.path.exists('cached'):
+ print generate_latex_error("cached exists and it is not a folder")
+ sys.exit(1)
+ else:
+ os.mkdir('cached')
+ if tree:
+ texbasename = "%s_%s_%s_%s_%s.tex" % (host, db_name, port, vt_id,out_type)
+ elif wgraph:
+ texbasename = "%s_%s_%s_%s_%s_%s_graph.tex" % (host, db_name, port, vt_id,
+ version, out_type)
+ else:
+ texbasename = "%s_%s_%s_%s_%s_%s.tex" % (host, db_name, port, vt_id,
+ version, out_type)
+ texfilename = os.path.join('cached', texbasename)
+ texfile = open(texfilename, 'w')
+ texfile.write(latex)
+ texfile.close()
+ log("********** SESSION END ************")
+ log("***********************************")
+ sys.exit(0)
+else:
+ log("********** SESSION END ************")
+ log("***********************************")
+ sys.exit(1)
diff --git a/extensions/latex/vistrails.sty b/extensions/latex/vistrails.sty
new file mode 100644
index 0000000..174fe97
--- /dev/null
+++ b/extensions/latex/vistrails.sty
@@ -0,0 +1,187 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% Copyright (C) 2011-2014, NYU-Poly.
+%% Copyright (C) 2006-2011, University of Utah.
+%% All rights reserved.
+%% Contact: contact at vistrails.org
+%%
+%% This file is part of VisTrails.
+%%
+%% "Redistribution and use in source and binary forms, with or without
+%% modification, are permitted provided that the following conditions are met:
+%%
+%% - Redistributions of source code must retain the above copyright notice,
+%% this list of conditions and the following disclaimer.
+%% - Redistributions in binary form must reproduce the above copyright
+%% notice, this list of conditions and the following disclaimer in the
+%% documentation and/or other materials provided with the distribution.
+%% - Neither the name of the University of Utah nor the names of its
+%% contributors may be used to endorse or promote products derived from
+%% this software without specific prior written permission.
+%%
+%% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+%% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+%% THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+%% PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+%% CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+%% EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+%% PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+%% OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+%% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+%% OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+%% ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% Note: shell-escape needs to be activated for this to work.
+%% This can either be done by passing -shell-escape as an option to
+%% latex or by adding/changing "shell_escape = t" in your texmf.cnf .
+
+\NeedsTeXFormat{LaTeX2e}[1994/12/01]
+\ProvidesPackage{vistrails}[2011/02/10 v0.4 VisTrails in LaTeX]
+
+%% keyval package allows us to define arguments in a command as key-value pairs,
+%% which is more convenient
+%% ifplatform for detecting which version of OS we are running on
+\RequirePackage{graphicx,keyval,ifthen,ifplatform}
+
+%% This is to hide the border of the included image
+\RequirePackage[pdfborder={0 0 0}]{hyperref}
+\hypersetup{extension=notused}
+
+%% we will generate a file for passing to python
+\newwrite\pythonincludein
+
+%% by default we will run vistrails on the web server
+\newcommand{\vistrailspath}{}
+
+%% environment configuration to be set before executing vistrails
+%% for example
+%% \newcommand{\vistrailsenv}{DYLD_LIBRARY_PATH= }
+\newcommand{\vistrailsenv}{}
+
+%% url for downloading the vistrails linked from the images
+%% leave it empty if you don't want to embed a link in the pdf
+\newcommand{\vistrailsdownload}{}
+
+%% full path to python or just python if it is on PATH
+\newcommand{\vistrailspythonpath}{python}
+
+%% this is for allowing line breaks, empty values in vistrails command's options
+\def\vistrail{\kernel at ifnextchar [{\@vistrail}{\@vistrail[]}}
+\def\@vistrail[#1]#2{%
+
+%% macros that will be used
+\def\vthost{vistrails.org}
+\def\vtdb{vistrails}
+\def\vtuser{}
+\def\vtfilename{}
+\def\vtvtid{}
+\def\vtversion{}
+\def\vttag{}
+\def\vtport{3306}
+\def\vtbuildalways{false}
+\def\vtexecute{false}
+\def\vtshowspreadsheetonly{false}
+\def\vtpdf{false}
+\def\vtworkflow{false}
+\def\vttree{false}
+\def\vtgetvtl{false}
+\def\vtembedworkflow{false}
+\def\vtincludefulltree{false}
+\newread\myinput
+%% We use '\jobname.python.temp' to store a unique file saying if python is present
+\ifwindows
+ \immediate\write18{find.cmd \vistrailspythonpath > \jobname.python.temp}
+\else
+ \immediate\write18{type -P "\vistrailspythonpath" > \jobname.python.temp}
+\fi
+\immediate\openin\myinput=\jobname.python.temp
+% The group localizes the change to \endlinechar
+\bgroup
+ \endlinechar=-1
+ \immediate\read\myinput to \localline
+ % Since everything in the group is local, we have to explicitly make the
+ % assignment global
+ \global\let\pythonexists\localline
+\egroup
+\immediate\closein\myinput
+% Clean up after ourselves
+\ifwindows
+ \immediate\write18{del \jobname.python.temp}
+\else
+ \immediate\write18{rm -f -- \jobname.python.temp}
+\fi
+\setkeys{vt}{#1}
+\ifthenelse{\equal{\vtpdf}{true}}{\def\vttype{pdf}}{\def\vttype{png}}
+\ifthenelse{\equal{\pythonexists}{}}{%
+ % python does not exist. Include images directly
+ \ifthenelse{\equal{\vttree}{true}}{%
+ % include version tree image
+ \immediate\input cached/\vthost\string_\vtdb\string_\vtport\string_\vtvtid\string_\vttype.tex
+ }
+ {% else test if don't include the workflow graph
+ \ifthenelse{\equal{\vtworkflow}{false}}{%
+ \immediate\input cached/\vthost\string_\vtdb\string_\vtport\string_\vtvtid\string_\vtversion\string_\vttype.tex
+ }
+ {% else include workflow graph
+ \immediate\input cached/\vthost\string_\vtdb\string_\vtport\string_\vtvtid\string_\vtversion\string_\vttype\string_graph.tex
+ }
+ }
+ }
+ { %else prepare input file for includevistrail.py
+ \immediate\openout\pythonincludein=\jobname.cmdline
+ \immediate\write\pythonincludein{path=\vistrailspath}
+ \immediate\write\pythonincludein{python=\vistrailspythonpath}
+ \immediate\write\pythonincludein{env=\vistrailsenv}
+ \immediate\write\pythonincludein{download=\vistrailsdownload}
+ \ifthenelse{\equal{\vtfilename}{}}{%
+ \immediate\write\pythonincludein{host=\vthost}
+ \immediate\write\pythonincludein{db=\vtdb}
+ \immediate\write\pythonincludein{vtid=\vtvtid}
+ \immediate\write\pythonincludein{user=\vtuser}
+ }
+ {% else it's a filename
+ \immediate\write\pythonincludein{filename=\vtfilename}
+ }
+ \immediate\write\pythonincludein{version=\vtversion}
+ \immediate\write\pythonincludein{tag=\vttag}
+ \immediate\write\pythonincludein{port=\vtport}
+ \immediate\write\pythonincludein{buildalways=\vtbuildalways}
+ \immediate\write\pythonincludein{execute=\vtexecute}
+ \immediate\write\pythonincludein{showspreadsheetonly=\vtshowspreadsheetonly}
+ \immediate\write\pythonincludein{pdf=\vtpdf}
+ \immediate\write\pythonincludein{workflow=\vtworkflow}
+ \immediate\write\pythonincludein{tree=\vttree}
+ \immediate\write\pythonincludein{getvtl=\vtgetvtl}
+ \immediate\write\pythonincludein{embedworkflow=\vtembedworkflow}
+ \immediate\write\pythonincludein{includefulltree=\vtincludefulltree}
+ \ifx\@empty#2\@empty
+ \immediate\write\pythonincludein{other=}
+ \else
+ \immediate\write\pythonincludein{other=\string#2}
+ \fi
+ \immediate\closeout\pythonincludein
+ \immediate\write18{"\vistrailspythonpath" \space includevistrail.py \jobname.cmdline > \jobname.cmdline.tex 2> \jobname.cmdline.err}
+ \immediate\input\jobname.cmdline.tex
+}
+}
+%% key-value pairs for the command's options
+\define at key{vt}{host}[vistrails.org]{\def\vthost{#1}}
+\define at key{vt}{db}[vistrails]{\def\vtdb{#1}}
+\define at key{vt}{user}[vistrails]{\def\vtuser{#1}}
+\define at key{vt}{vtid}{\def\vtvtid{#1}}
+\define at key{vt}{filename}{\def\vtfilename{#1}}
+\define at key{vt}{version}{\def\vtversion{#1}}
+\define at key{vt}{tag}[]{\def\vttag{#1}}
+\define at key{vt}{port}[3306]{\def\vtport{#1}}
+\define at key{vt}{buildalways}[true]{\def\vtbuildalways{#1}}
+\define at key{vt}{execute}[true]{\def\vtexecute{#1}}
+\define at key{vt}{showspreadsheetonly}[true]{\def\vtshowspreadsheetonly{#1}}
+\define at key{vt}{pdf}[true]{\def\vtpdf{#1}}
+\define at key{vt}{showworkflow}[true]{\def\vtworkflow{#1}}
+\define at key{vt}{showtree}[true]{\def\vttree{#1}}
+\define at key{vt}{getvtl}[true]{\def\vtgetvtl{#1}}
+\define at key{vt}{embedworkflow}[true]{\def\vtembedworkflow{#1}}
+\define at key{vt}{includefulltree}[true]{\def\vtincludefulltree{#1}}
+
diff --git a/extensions/mediawiki/README b/extensions/mediawiki/README
new file mode 100644
index 0000000..cb69746
--- /dev/null
+++ b/extensions/mediawiki/README
@@ -0,0 +1,18 @@
+This folder contains files for adding vistrails to mediawiki.
+
+Just copy
+ download.php
+ functions.php
+ vistrailsExtension.php
+ ../http/config.php.sample
+
+to the wiki/extensions/ folder.
+
+Rename config.php.sample to config.php and modify the file according to your needs.
+
+An example of usage is in
+
+http://www.vistrails.org/index.php/Viswiki
+
+
+
diff --git a/extensions/mediawiki/download.php b/extensions/mediawiki/download.php
new file mode 100644
index 0000000..210d339
--- /dev/null
+++ b/extensions/mediawiki/download.php
@@ -0,0 +1,138 @@
+<?php
+////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (C) 2011-2014, NYU-Poly.
+// Copyright (C) 2006-2011, University of Utah.
+// All rights reserved.
+// Contact: contact at vistrails.org
+//
+// This file is part of VisTrails.
+//
+// "Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// - Redistributions of source code must retain the above copyright notice,
+// this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// - Neither the name of the University of Utah nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+// THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+//
+////////////////////////////////////////////////////////////////////////////
+
+require_once 'functions.php';
+require_once 'config.php';
+
+if (array_key_exists('getvt', $_GET)) {
+
+ $host = $DB_HOST;
+ $port = $DB_PORT;
+ $dbname = $_GET["db"];
+ $vtid = $_GET["getvt"];
+ $version = $_GET["version"];
+ $version_tag = '';
+ $execute = 'False';
+ $showspreadsheetonly = 'False';
+ $forceDB = 'False';
+ $includeFullTree = 'False';
+ $embedWorkflow = 'False';
+
+ if(array_key_exists('port', $_GET))
+ $port = $_GET['port'];
+ if(array_key_exists('host', $_GET))
+ $host = $_GET['host'];
+ if(array_key_exists('tag', $_GET))
+ $version_tag = $_GET['tag'];
+ if(array_key_exists('execute', $_GET))
+ $execute = $_GET['execute'];
+ if(array_key_exists('showspreadsheetonly', $_GET))
+ $showspreadsheetonly = $_GET['showspreadsheetonly'];
+ if(array_key_exists('forceDB', $_GET))
+ $forceDB = $_GET['forceDB'];
+ if(array_key_exists('includeFullTree', $_GET))
+ $includeFullTree = $_GET['includeFullTree'];
+ if(array_key_exists('embedWorkflow', $_GET))
+ $embedWorkflow = $_GET['embedWorkflow'];
+
+ $filename = md5($host . '_'. $dbname .'_' . $port .'_' .$vtid . '_' . $version);
+ $filename = $filename . ".vtl";
+
+ //change the address below to appropriate folder
+ //(with read+write access to apache user) if required
+ $fileHandle = fopen($PATH_TO_IMAGES. $filename, 'w') or die("can't open file");
+ $text = '<vtlink database="' . $dbname . '" host="'. $host .
+ '" port="'. $port . '" vtid="' . $vtid . '" execute="'.
+ $execute . '" showSpreadsheetOnly="'. $showspreadsheetonly.
+ '" forceDB="'.$forceDB.'"';
+ if(strcasecmp($embedWorkflow, 'True') == 0){
+ if (strcasecmp($includeFullTree,'True') == 0){
+ $request = xmlrpc_encode_request('get_vt_zip', array($host, $port,
+ $dbname, $vtid));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $vtcontent = get_vt_from_response($response);
+ $text .= ' version="' . $version . '" tag="' . $version_tag .'"';
+ //echo $vtcontent;
+ }
+ else{
+ $request = xmlrpc_encode_request('get_wf_vt_zip', array($host, $port,
+ $dbname, $vtid,
+ $version));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $vtcontent = get_vt_from_response($response);
+ //when a workflow is embedded the version is written only when
+ //forceDB is True. Or else version points to the wrong workflow
+ if (strcasecmp($forceDB, 'True') == 0){
+ $text .= ' version="' . $version . '" tag="' . $version_tag .'"';
+ }
+ }
+ $text .= ' vtcontent="'.$vtcontent .'"';
+ }
+ else{
+ $text .= ' version="' . $version . '" tag="' . $version_tag .'"';
+ }
+ $text .= ' />';
+ fputs($fileHandle, $text);
+ fclose($fileHandle);
+
+ header("Content-Type: text/vistrails");
+ header("Content-Disposition: attachment;filename=" . $filename);
+
+ //the address below should be the same as one above in line 12
+ readfile($PATH_TO_IMAGES.$filename);
+ exit();
+}
+function get_vt_from_response($xmlstring) {
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ return $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->string[0];
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+?>
+
+<html>
+<head>
+<title>Vistrails Download</title>
+<body>
+
+Wrong parameters set!
+
+</body>
+</html>
+<? //Ends ?>
+
diff --git a/extensions/mediawiki/functions.php b/extensions/mediawiki/functions.php
new file mode 100644
index 0000000..1200ff1
--- /dev/null
+++ b/extensions/mediawiki/functions.php
@@ -0,0 +1,81 @@
+<?php
+////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (C) 2011-2014, NYU-Poly.
+// Copyright (C) 2006-2011, University of Utah.
+// All rights reserved.
+// Contact: contact at vistrails.org
+//
+// This file is part of VisTrails.
+//
+// "Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// - Redistributions of source code must retain the above copyright notice,
+// this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// - Neither the name of the University of Utah nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+// THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+//
+////////////////////////////////////////////////////////////////////////////
+
+function do_call($host, $port, $request) {
+
+ $url = "http://$host:$port/";
+ $header[] = "Content-type: text/xml";
+ $header[] = "Content-length: ".strlen($request);
+
+ $ch = curl_init();
+ curl_setopt($ch, CURLOPT_URL, $url);
+ curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
+ curl_setopt($ch, CURLOPT_TIMEOUT, 30);
+ curl_setopt($ch, CURLOPT_HTTPHEADER, $header);
+ curl_setopt($ch, CURLOPT_POSTFIELDS, $request);
+
+ $data = curl_exec($ch);
+ if (curl_errno($ch)) {
+ print curl_error($ch);
+ } else {
+ curl_close($ch);
+ return $data;
+ }
+}
+
+function in_arrayi($needle, $haystack) {
+ return in_array(strtolower($needle), array_map('strtolower', $haystack));
+}
+
+function path_exists_and_not_empty($path){
+ $directory_not_empty = FALSE;
+ if (file_exists($path)){
+ $directory = dir($path);
+
+ while ((FALSE !== ($item = $directory->read())) &&
+ ( ! $directory_not_empty)){
+ // If an item is not "." and "..", then something
+ // exists in the directory and it is not empty
+ if ($item != '.' && $item != '..'){
+ $directory_not_empty = TRUE;
+ }
+ }
+ $directory->close();
+ }
+ return $directory_not_empty;
+}
+
+?>
diff --git a/extensions/mediawiki/vistrailsExtension.php b/extensions/mediawiki/vistrailsExtension.php
new file mode 100644
index 0000000..495e768
--- /dev/null
+++ b/extensions/mediawiki/vistrailsExtension.php
@@ -0,0 +1,271 @@
+<?php
+////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (C) 2011-2014, NYU-Poly.
+// Copyright (C) 2006-2011, University of Utah.
+// All rights reserved.
+// Contact: contact at vistrails.org
+//
+// This file is part of VisTrails.
+//
+// "Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// - Redistributions of source code must retain the above copyright notice,
+// this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// - Neither the name of the University of Utah nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+// THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+//
+////////////////////////////////////////////////////////////////////////////
+require_once 'functions.php';
+require_once 'config.php';
+
+$wgExtensionFunctions[] = 'registerVistrailTag';
+$wgExtensionCredits['parserhook'][] = array(
+ 'name' => 'VistrailTag',
+ 'author' => 'VT',
+ 'url' => 'http://www.vistrails.org/',
+);
+
+$resp_result = '';
+function registerVistrailTag() {
+ global $wgParser;
+ $wgParser->setHook('vistrail', 'printVistrailTag');
+}
+
+function printVistrailTag($input,$params) {
+ global $PATH_TO_IMAGES, $WEB_PATH_TO_IMAGES, $URL_TO_GRAPHS,
+ $PATH_TO_GRAPHS, $VT_HOST, $VT_PORT, $USE_LOCAL_VISTRAILS_SERVER,
+ $USE_VISTRAILS_XML_RPC_SERVER, $PATH_TO_VISTRAILS, $URL_TO_DOWNLOAD,
+ $DB_HOST, $DB_NAME, $DB_PORT;
+ $host = $DB_HOST;
+ $dbname = $DB_NAME;
+ $username = "vtserver";
+ $vtid = "";
+ $version = "";
+ $port = $DB_PORT;
+ $version_tag = "";
+ $execute = "False";
+ $showspreadsheetonly = "False";
+ $force_build = 'False';
+ $embedWorkflow = 'False';
+ $includeFullTree = 'False';
+ $forceDB = 'False';
+ $showTree = 'False';
+ $showWorkflow = 'False';
+ foreach ($params as $key=>$value) {
+ if($key == "vtid")
+ $vtid = $value;
+ if($key == "version")
+ $version = $value;
+ if($key == "host")
+ $host = $value;
+ if($key == "db")
+ $dbname = $value;
+ if($key == "port")
+ $port = $value;
+ if($key == "tag"){
+ $version_tag = $value;
+ if($version_tag != ''){
+ $request = xmlrpc_encode_request('get_tag_version',
+ array($host, $port,
+ $dbname, $vtid,
+ $version_tag));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $version = get_version_from_response($response);
+ //echo $version;
+ }
+ }
+ if ($key == "execute")
+ $execute = $value;
+ if ($key == "showspreadsheetonly")
+ $showspreadsheetonly = $value;
+ if ($key == "buildalways")
+ $force_build = $value;
+ if ($key == 'embedworkflow')
+ $embedWorkflow = $value;
+ if ($key == 'includefulltree')
+ $includeFullTree = $value;
+ if ($key == 'forcedb')
+ $forceDB = $value;
+ if ($key == 'showworkflow')
+ $showWorkflow = $value;
+ if ($key == 'showtree')
+ $showTree = $value;
+ }
+
+ $linkParams = "getvt=" . $vtid . "&version=" . $version . "&db=" .$dbname .
+ "&host=" . $host . "&port=" . $port . "&tag=" .
+ $version_tag . "&execute=" . $execute .
+ "&showspreadsheetonly=" . $showspreadsheetonly .
+ "&embedWorkflow=" . $embedWorkflow . "&includeFullTree=" .
+ $includeFullTree . "&forceDB=" . $forceDB;
+
+ if (strcasecmp($showTree,'True') == 0){
+ $filename = md5($host . '_'. $dbname .'_' . $port .'_' .$vtid);
+ $filename = 'vistrails/'.$filename . ".png";
+ //this request is cached only on the server side
+ $request = xmlrpc_encode_request("get_vt_graph_png", array($host, $port,
+ $dbname, $vtid, $USE_LOCAL_VISTRAILS_SERVER));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $result = clean_up($response, $filename);
+
+ list($width, $height, $type, $attr) = getimagesize($PATH_TO_GRAPHS . $result);
+ if ($width > 400)
+ $width = 400;
+ $res = '<a href="'.$URL_TO_DOWNLOAD.'?' . $linkParams . '">';
+ $res = $res . '<img src="'. $URL_TO_GRAPHS . $result.
+ "\" alt=\"vt_id:$vtid\" width=\"$width\"/>";
+ $res = $res . '</a>';
+ return($res);
+ }
+
+ elseif (strcasecmp($showWorkflow,'True') == 0){
+ $filename = md5($host . '_'. $dbname .'_' . $port .'_' .$vtid . '_' . $version);
+ $filename = 'workflows/'.$filename . ".png";
+ $fullpath = $PATH_TO_GRAPHS. $filename;
+ $cached = file_exists($fullpath);
+ if($USE_LOCAL_VISTRAILS_SERVER or
+ (!$cached or strcasecmp($force_build,'True') == 0)) {
+ $request = xmlrpc_encode_request("get_wf_graph_png", array($host,
+ $port, $dbname, $vtid, $version,
+ $USE_LOCAL_VISTRAILS_SERVER));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $result = clean_up($response, $filename);
+ } else {
+ $result = $filename;
+ }
+ list($width, $height, $type, $attr) = getimagesize($PATH_TO_GRAPHS . $result);
+ if ($width > 400)
+ $width = 400;
+ $res = '<a href="'.$URL_TO_DOWNLOAD.'?' . $linkParams . '">';
+ $res = $res . '<img src="'. $URL_TO_GRAPHS . $result.
+ "\" alt=\"vt_id:$vtid version:$version\" width=\"$width\"/>";
+ $res = $res . '</a>';
+ return($res);
+ }
+
+ else {
+ $result = '';
+ $destdir = $PATH_TO_IMAGES;
+ $destversion = $host . '_'. $dbname .'_' . $port . '_' .$vtid . '_' . $version;
+ $destversion = md5($destversion);
+ $destdir = $destdir . $destversion;
+ $build_always_bool = False;
+ if (strcasecmp($force_build,'True') == 0)
+ $build_always_bool = True;
+ if((!path_exists_and_not_empty($destdir)) or strcasecmp($force_build,'True') == 0) {
+ if(!file_exists($destdir)){
+ mkdir($destdir,0770);
+ chmod($destdir, 0770);
+ }
+ if(!$USE_VISTRAILS_XML_RPC_SERVER){
+ chdir($PATH_TO_VISTRAILS);
+ $setVariables = 'export PATH=$PATH:/usr/bin/X11;export HOME=/var/lib/wwwrun; export TEMP=/tmp; export DISPLAY=localhost:1.0; export LD_LIBRARY_PATH=/usr/local/lib;';
+
+ $mainCommand = 'python vistrails/run.py -b -e '. $destdir.' -t ' .
+ host . ' -r ' . $port . ' -f ' . $dbname . ' -u ' .
+ username . ' "' . $vtid .':' . $version .'"';
+ $result = exec($setVariables.$mainCommand . ' 2>&1', $output, $result);
+ }
+ else {
+ $request = xmlrpc_encode_request('run_from_db',
+ array($host, $port, $dbname, $vtid,
+ $destdir, $version, False, '',
+ $build_always_bool, '',
+ $USE_LOCAL_VISTRAILS_SERVER));
+ $response = do_call($VT_HOST,$VT_PORT,$request);
+ $result = multiple_clean_up($response, $destdir);
+ }
+ }
+ }
+ $files = scandir($destdir);
+ $n = sizeof($files);
+ if($n > 2){
+ $res = '<a href="'.$URL_TO_DOWNLOAD.'?' . $linkParams . '">';
+ foreach($files as $filename) {
+ if($filename != '.' and $filename != '..'){
+ list($width, $height, $type, $attr) = getimagesize($destdir.'/'.$filename);
+ if ($width > 350)
+ $width = 350;
+ $res = $res . '<img src="'.$WEB_PATH_TO_IMAGES . $destversion.'/'.
+ $filename.
+ "\" alt=\"vt_id:$vtid version:$version\" width=\"$width\"/>";
+ }
+ }
+ $res = $res . '</a>';
+ }
+ else{
+ $res = "ERROR: Vistrails didn't produce any image.\n" .
+ "This is the output: \n" . $result;
+ }
+ return($res);
+}
+
+function get_version_from_response($xmlstring){
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ return (string) $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->int[0];
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+
+function clean_up($xmlstring, $filename=""){
+ global $PATH_TO_GRAPHS, $USE_LOCAL_VISTRAILS_SERVER;
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ if ($USE_LOCAL_VISTRAILS_SERVER)
+ return $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->string[0];
+ else{
+ $contents = $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->base64[0];
+ $fileHandle = fopen($PATH_TO_GRAPHS. $filename, 'wb') or die("can't open file");
+ fputs($fileHandle, base64_decode($contents));
+ fclose($fileHandle);
+ return $filename;
+ }
+
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+
+function multiple_clean_up($xmlstring, $destdir=""){
+ global $USE_LOCAL_VISTRAILS_SERVER;
+ try{
+ $node = @new SimpleXMLElement($xmlstring);
+ //var_dump($node);
+ if ($USE_LOCAL_VISTRAILS_SERVER)
+ return $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->string[0];
+ else{
+ $contents = $node->params[0]->param[0]->value[0]->array[0]->data[0]->value[0]->struct[0];
+ foreach ($contents as $value){
+ $image_name = (string) $value->name[0];
+ $image_contents = (string) $value->value[0]->base64[0];
+ $fileHandle = fopen($destdir.'/'. $image_name, 'wb') or die("can't open file");
+ fputs($fileHandle, base64_decode($image_contents));
+ fclose($fileHandle);
+ }
+ return $destdir;
+ }
+ } catch(Exception $e) {
+ echo "bad xml";
+ }
+}
+?>
diff --git a/scripts/build_usersguide.py b/scripts/build_usersguide.py
new file mode 100755
index 0000000..9099572
--- /dev/null
+++ b/scripts/build_usersguide.py
@@ -0,0 +1,169 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This will build the html and the pdf version of the user's guide and put
+them in where defined.
+Please configure the variables below according to your server's setup
+
+"""
+import os
+import os.path
+import re
+import shutil
+import subprocess
+import sys
+import time
+### Begin configuration ###
+# Folder where vistrails is
+PATH_TO_VISTRAILS_GIT = "/Users/emanuele/code/vistrails"
+
+# Folder where the html files will be placed. This script will build
+# the docs in the standard location and move files later
+HTML_FOLDER = None
+
+# Complete file path to where copy final pdf file
+PDF_FILE = "/Users/vistrails/code/vistrails/dist/mac/dist/VisTrails/doc/VisTrails.pdf"
+
+# Should we run a `git pull` before building docs?
+PERFORM_GIT_PULL = True
+
+### End configuration ###
+### The following variables usually don't need to be changed
+USERSGUIDE_SUBPATH = ['doc', 'usersguide']
+GIT_PULL_CMD = ["git", "pull"]
+BUILD_HTML_SUBPATH = ["_build", "html"]
+BUILD_LATEX_SUBPATH = ["_build", "latex"]
+PDF_BUILD_NAME = "VisTrails.pdf"
+if __name__ == '__main__':
+ if (PATH_TO_VISTRAILS_GIT is not None and
+ os.path.exists(PATH_TO_VISTRAILS_GIT)):
+ current_folder = os.getcwd()
+ if PERFORM_GIT_PULL:
+ print "performing git pull in %s..."%PATH_TO_VISTRAILS_GIT
+ os.chdir(PATH_TO_VISTRAILS_GIT)
+ proc = subprocess.Popen(GIT_PULL_CMD,
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT)
+ proc.wait()
+ if proc.returncode != 0:
+ print "ERROR: git pull failed."
+ if proc.stdout:
+ print proc.stdout.readlines()
+
+ os.chdir(os.path.join(PATH_TO_VISTRAILS_GIT,
+ *USERSGUIDE_SUBPATH))
+
+ print "Going into directory %s"%os.getcwd()
+ # now build html documentation
+ print "now building html documentation..."
+ proc = subprocess.Popen(["make", "html"],
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT)
+ proc.wait()
+ if proc.returncode != 0:
+ print "ERROR: make html failed."
+ if proc.stdout:
+ print proc.stdout.readlines()
+ else:
+ # now move files to their final place
+ if HTML_FOLDER is not None:
+ if os.path.exists(HTML_FOLDER):
+ shutil.rmtree(HTML_FOLDER)
+ html_build = os.path.join(os.getcwd(),
+ *BUILD_HTML_SUBPATH)
+
+ shutil.move(html_build, HTML_FOLDER)
+
+ #build latex files
+ print "now preparing latex files..."
+ latex_path = os.path.join(".",
+ *BUILD_LATEX_SUBPATH)
+ if os.path.exists(latex_path):
+ print "removing old %s directory..."%latex_path
+ proc = subprocess.Popen(["rm", "-rf", latex_path],
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT)
+ proc.wait()
+ print "building latex files..."
+ proc = subprocess.Popen(["make", "latex"],
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT)
+ proc.wait()
+ if proc.returncode != 0:
+ print "ERROR: make latex failed."
+ if proc.stdout:
+ print proc.stdout.readlines()
+ else:
+ #now build pdf
+ print "now building pdf file..."
+ os.chdir(os.path.join(os.getcwd(),
+ *BUILD_LATEX_SUBPATH))
+ proc = subprocess.Popen(["make", "all-pdf"],
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT)
+ # when the pdflatex command fails, it waits indefinitely for user
+ #input. We will wait for up to 90 seconds and terminate the process
+ result = None
+ i = 0
+ while (result == None and i < 15):
+ result = proc.poll()
+ time.sleep(20)
+ i += 1
+ print proc.stdout.readlines()
+ sys.stdout.flush()
+ if result == None:
+ proc.terminate()
+ print "ERROR: make all-pdf failed."
+ if proc.stdout:
+ print proc.stdout.readlines()
+ elif proc.returncode != 0:
+ print "ERROR: make all-pdf failed."
+ if proc.stdout:
+ print proc.stdout.readlines()
+ else:
+ #now move file to its final place
+ if PDF_FILE is not None:
+ pdf_build = os.path.join(os.getcwd(),
+ PDF_BUILD_NAME)
+ shutil.move(pdf_build, PDF_FILE)
+ os.chdir(current_folder)
+ print "Done."
+ else:
+ print "PATH_TO_VISTRAILS_GIT was not provided. Exiting."
diff --git a/scripts/convert_files/convert_files.sh b/scripts/convert_files/convert_files.sh
new file mode 100755
index 0000000..410bd5d
--- /dev/null
+++ b/scripts/convert_files/convert_files.sh
@@ -0,0 +1,57 @@
+#!/bin/sh
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+file_list=$1
+shift
+
+for i in `cat $file_list`; do
+ DIR=`dirname $i`
+ VT_FILE=$DIR/`basename $i .vt`_fixed.vt
+ echo $i
+ echo -- UNZIPPING
+ unzip $i
+ echo -- PRETTY PRINTING
+ xmlpp.pl vistrail > vistrail_pp
+ echo -- FIXING
+ ../fix_file.py vistrail_pp $* > vistrail
+ echo -- ZIPPING
+ zip fixed_vistrail.zip vistrail
+ echo -- MOVING
+ mv fixed_vistrail.zip $VT_FILE
+ echo -- CLEANING
+ rm vistrail
+ rm vistrail_pp
+ echo $i
+done
diff --git a/scripts/convert_files/fix_file.py b/scripts/convert_files/fix_file.py
new file mode 100644
index 0000000..25d61c3
--- /dev/null
+++ b/scripts/convert_files/fix_file.py
@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import sys
+import re
+
+re_list = []
+
+if len(sys.argv) < 4:
+ print "Usage:"
+ print "%s file_to_process path_to_data_files data_file_1 data_file_2 ..." % sys.argv[0]
+ sys.exit(1)
+
+for i in xrange(3, len(sys.argv)):
+ re_list.append((sys.argv[i], re.compile(r"val='[^']*" + sys.argv[i] + r"[^']*'")))
+
+f = file(sys.argv[1])
+for l in f:
+ for (s, re_obj) in re_list:
+ l = re_obj.sub("val='" + sys.argv[2] + s + "'", l)
+ print l[:-1]
diff --git a/scripts/create_release_wiki_table.py b/scripts/create_release_wiki_table.py
new file mode 100644
index 0000000..6d83867
--- /dev/null
+++ b/scripts/create_release_wiki_table.py
@@ -0,0 +1,90 @@
+""" This will output text with release information ready to be pasted on the
+wiki page
+
+
+
+"""
+from datetime import date
+#Release version
+VT_VERSION = "2.1.1"
+VT_REVISION = "90975fc00211"
+
+#Sourceforge information
+SF_ROOT_URL = "http://downloads.sourceforge.net/project/vistrails/vistrails/"
+SF_FOLDER_NAME = "v2.1.1"
+SF_DOWNLOAD_URL = "%s%s"%(SF_ROOT_URL,SF_FOLDER_NAME)
+#binaries names
+MAC_64_BIN = "vistrails-mac-10.6-intel-%s-%s.dmg"%(VT_VERSION, VT_REVISION)
+WIN_32_BIN = "vistrails-setup-%s-%s.zip"%(VT_VERSION, VT_REVISION)
+WIN_64_BIN = "vistrails-x64-setup-%s-%s.zip"%(VT_VERSION, VT_REVISION)
+ALL_PLAT_SRC = "vistrails-src-%s-%s.tar.gz"%(VT_VERSION, VT_REVISION)
+#pdf
+USERSGUIDE = "VisTrails.pdf"
+
+#sizes
+MAC_64_SIZE = "182.3 MB"
+WIN_32_SIZE = "125.3 MB"
+WIN_64_SIZE = "150 MB"
+ALL_PLAT_SIZE = "19.2 MB"
+USERSGUIDE_SIZE = "8.7 MB"
+
+def create_text():
+ today = date.today().strftime("%Y-%m-%d")
+
+ text = """|{{Hl4}} colspan="4" |'''%s build %s (%s)''' [[known_issues|Known Issues]] {{SFReleaseNotes\
+ |link=https://sourceforge.net/projects/vistrails/files/vistrails/%s/README/view}}
+|-
+"""%(VT_VERSION, VT_REVISION, today, SF_FOLDER_NAME)
+
+ text += """|
+* {{zip
+ |link=%s/%s
+ |text=%s}}
+|%s
+|i586
+|.zip (32-bit Windows)
+|-
+"""%(SF_DOWNLOAD_URL, WIN_32_BIN, WIN_32_BIN, WIN_32_SIZE)
+
+ text += """|
+* {{zip
+ |link=%s/%s
+ |text=%s}}
+|%s
+|i586
+|.zip (64-bit Windows)
+|-
+"""%(SF_DOWNLOAD_URL, WIN_64_BIN, WIN_64_BIN, WIN_64_SIZE)
+
+ text += """|
+* {{dmg
+ |link=%s/%s
+ |text=%s}}
+|%s
+|Mac OS X 10.6+ x64
+|.dmg (Mac bundle)
+|-
+"""%(SF_DOWNLOAD_URL, MAC_64_BIN, MAC_64_BIN, MAC_64_SIZE)
+
+ text += """|
+* {{targz
+|link=%s/%s
+|text=%s}}
+|%s
+|all
+|Source .tar.gz
+|-
+"""%(SF_DOWNLOAD_URL, ALL_PLAT_SRC, ALL_PLAT_SRC, ALL_PLAT_SIZE)
+ text += """|
+* {{Pdf
+|link=%s/%s
+|text=%s}}
+|%s
+|all
+|.pdf
+|-
+"""%(SF_DOWNLOAD_URL, USERSGUIDE, USERSGUIDE, USERSGUIDE_SIZE)
+ print text
+
+if __name__ == "__main__":
+ create_text()
diff --git a/scripts/create_server_media_dir_structure.py b/scripts/create_server_media_dir_structure.py
new file mode 100644
index 0000000..69d0e6c
--- /dev/null
+++ b/scripts/create_server_media_dir_structure.py
@@ -0,0 +1,99 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This will create the media_dir directory structure required by vistrails
+server when used as a remote server with crowdlabs (www.crowdlabs.org)
+
+usage: python create_server_media_dir_structure.py /path/to/media_dir
+
+If media_dir does not exist, it will be created.
+
+"""
+
+import sys
+import os, os.path
+
+folders = [["wf_execution"],
+ ["graphs", "workflows"],
+ ["graphs", "vistrails"],
+ ["medleys", "images"]]
+def path_exists_and_not_empty(path):
+ """path_exists_and_not_empty(path:str) -> boolean
+ Returns True if given path exists and it's not empty, otherwise returns
+ False.
+
+ """
+ if os.path.exists(path):
+ for root, dirs, file_names in os.walk(path):
+ break
+ if len(file_names) > 0 or len(dirs) > 0:
+ return True
+ return False
+
+if __name__ == "__main__":
+ args = sys.argv
+ error = False
+ if len(args) == 2:
+ media_dir = args[1]
+ else:
+ print "Usage: %s /path/to/media_dir" % args[0]
+ sys.exit(0)
+ if os.path.exists(media_dir):
+ if not os.path.isdir(media_dir):
+ print "Error: %s exists and it is not a directory." %media_dir
+ error = True
+ elif path_exists_and_not_empty(media_dir):
+ print "Error: %s exists and it is not empty. "% media_dir
+ error = True
+ else:
+ print "%s does not exist. Trying to create directory..."%media_dir
+ try:
+ os.mkdir(media_dir)
+ except Exception, e:
+ print "Error creating %s directory: %s" % (media_dir, str(e))
+ error = True
+ if not error:
+ print "Creating inner structure... "
+ for path_list in folders:
+ folder = os.path.join(media_dir, os.path.join(*path_list))
+ print " ", folder
+ try:
+ os.makedirs(folder)
+ except Exception, e:
+ print "Error creating %s directory: %s" % (folder, str(e))
+ print "Done."
+ else:
+ print "There was an error. Please check the messages above. "
+ sys.exit(1)
+
diff --git a/scripts/db_utils.py b/scripts/db_utils.py
new file mode 100644
index 0000000..eaec86e
--- /dev/null
+++ b/scripts/db_utils.py
@@ -0,0 +1,114 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import getopt
+import getpass
+import sys
+
+def usage(usageDict):
+ usageStr = ''
+ unrequired = ''
+ required = ''
+ align_len = 15
+ for (opt, info) in usageDict.iteritems():
+ if info[1]:
+ required += '-%s <%s> ' % (opt[0], info[2])
+ usageStr += ' -%s <%s> %s' % (opt[0], info[2],
+ ' ' * (align_len -
+ len(info[2]) - 3))
+ else:
+ if len(opt) > 1:
+ unrequired += '[-%s <%s>] ' % (opt[0], info[2])
+ usageStr += ' -%s <%s> %s' % (opt[0], info[2],
+ ' ' * (align_len -
+ len(info[2]) - 3))
+ else:
+ unrequired += '[-%s] ' % opt[0]
+ usageStr += ' -%s %s' % (opt[0], ' ' * align_len)
+ usageStr += '%s\n' % info[0]
+ print 'Usage: %s %s %s%s\n%s' % (sys.executable,
+ sys.argv[0],
+ required,
+ unrequired,
+ usageStr)
+
+def parse_db_cmd_line(argv, more_options={}):
+ options = {}
+ optionsUsage = {'t:': ('set database host/port', False, 'host:port'),
+ 'p': ('use password', False),
+ 'u:': ('set database user', False, 'user'),
+ 'D:': ('set database name', False, 'database')
+ }
+ optionsUsage.update(more_options)
+
+ optStr = ''.join(optionsUsage.keys())
+ optKeys = optStr.replace(':','')
+ for idx in xrange(len(optKeys)):
+ options[optKeys[idx]] = False
+
+ try:
+ (optlist, args) = getopt.getopt(argv[1:], optStr)
+ for opt in optlist:
+ if opt[1] is not None and opt[1] != '':
+ options[opt[0][1:]] = opt[1]
+ else:
+ options[opt[0][1:]] = True
+ except getopt.GetoptError:
+ usage(optionsUsage)
+ sys.exit(23)
+
+ for opt, spec in optionsUsage.iteritems():
+ if spec[1] and not options[opt[0]]:
+ usage(optionsUsage)
+ sys.exit(23)
+
+ config = {'host': 'localhost',
+ 'port': 3306,
+ 'user': 'vistrails',
+ 'db': 'vistrails'}
+
+ if options['p']:
+ config['passwd'] = getpass.getpass()
+ if options['t']:
+ host_arr = options['t'].split(':', 1)
+ config['host'] = host_arr[0]
+ if len(host_arr) > 1:
+ config['port'] = int(host_arr[1])
+ if options['u']:
+ config['user'] = options['u']
+ if options['D']:
+ config['db'] = options['D']
+
+ return (config, options)
diff --git a/scripts/delete_from_db.py b/scripts/delete_from_db.py
new file mode 100644
index 0000000..5212fb3
--- /dev/null
+++ b/scripts/delete_from_db.py
@@ -0,0 +1,57 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import os
+import sys
+sys.path.append(os.path.join(os.path.dirname(os.path.dirname(
+ os.path.abspath(__file__))), 'vistrails'))
+from vistrails.db.services import io
+from db_utils import parse_db_cmd_line
+
+def delete_from_db(config, obj_type, obj_id):
+ db_connection = io.open_db_connection(config)
+ io.delete_entity_from_db(db_connection, obj_type, obj_id)
+ io.close_db_connection(db_connection)
+
+if __name__ == '__main__':
+ more_options = {'t:': ('set object type', False, 'obj_type'),
+ 'i:': ('set object id', True, 'obj_id'),
+ }
+ config, options = parse_db_cmd_line(sys.argv, more_options)
+ obj_type = 'vistrail'
+ if options['t']:
+ obj_type = options['t']
+ obj_id = int(options['i'])
+ delete_from_db(config, obj_type, obj_id)
+
diff --git a/scripts/diff_package.py b/scripts/diff_package.py
new file mode 100644
index 0000000..3260e0c
--- /dev/null
+++ b/scripts/diff_package.py
@@ -0,0 +1,101 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""To use this script, run VisTrails with the old version of a package enabled, and choose the Export -> Registry to XML... and save the file. Then, enable the new version of the package and again export the registry to a second XML file. Then, run this script with the package identifier, the old registry's filename, and the new registry's filename as arguments."""
+
+import os
+import sys
+# put the vistrails code on the python path
+sys.path.append(os.path.join(os.path.dirname(os.path.dirname(
+ os.path.abspath(__file__))), "vistrails"))
+
+import vistrails.core.application
+from vistrails.core.modules.module_registry import ModuleRegistry
+from vistrails.db.services.io import open_registry_from_xml
+
+def get_module_name(d):
+ if d.namespace:
+ return "%s|%s" % (d.namespace, d.name)
+ return d.name
+
+def diff_package(pkg_id, reg_fname1, reg_fname2):
+ reg1 = open_registry_from_xml(reg_fname1)
+ ModuleRegistry.convert(reg1)
+ reg2 = open_registry_from_xml(reg_fname2)
+ ModuleRegistry.convert(reg2)
+
+ pkg1 = reg1.get_package_by_name(pkg_id)
+ pkg2 = reg2.get_package_by_name(pkg_id)
+
+ d2_modules_dict = dict(((d2.identifier, d2.name, d2.namespace), d2)
+ for d2 in pkg2.descriptor_list)
+ for d1 in pkg1.descriptor_list:
+ if reg2.has_descriptor_with_name(pkg_id, d1.name, d1.namespace):
+ d2 = reg2.get_descriptor_by_name(pkg_id, d1.name, d1.namespace)
+ d1_port_specs = {}
+ for ps in d1.port_specs_list:
+ d1_port_specs[(ps.name, ps.type)] = ps.sigstring
+ d2_port_specs = {}
+ for ps in d2.port_specs_list:
+ d2_port_specs[(ps.name, ps.type)] = ps.sigstring
+ d2_port_specs_set = set(d2_port_specs.keys())
+ for ps_id, sig1 in d1_port_specs.iteritems():
+ if ps_id not in d2_port_specs:
+ print "added %s port: %s:%s" % \
+ (ps_id[1], get_module_name(d1), ps_id[0])
+ continue
+ d2_port_specs_set.discard(ps_id)
+ if sig1 != d2_port_specs[ps_id]:
+ print "changed %s port: %s:%s" % \
+ (ps_id[1], get_module_name(d1), ps_id[0])
+ print " %s -> %s" % (sig1, d2_port_specs[ps_id])
+ else:
+ # equal
+ pass
+ for ps_id in d2_port_specs_set:
+ print "deleted %s port: %s:%s" % \
+ (ps_id[1], get_module_name(d1), ps_id[0])
+ del d2_modules_dict[(d1.identifier, d1.name, d1.namespace)]
+ else:
+ print "deleted module: %s" % get_module_name(d1)
+ for d2 in d2_modules_dict.itervalues():
+ print "added module: %s" % get_module_name(d2)
+
+if __name__ == '__main__':
+ if len(sys.argv) < 4:
+ print "Usage: %s %s <pkg_identifer> <old_registry> <new_registry>" % \
+ (sys.executable, sys.argv[0])
+ sys.exit(71)
+ vistrails.core.application.init()
+ diff_package(*sys.argv[1:])
diff --git a/scripts/extract.py b/scripts/extract.py
new file mode 100644
index 0000000..5475bfb
--- /dev/null
+++ b/scripts/extract.py
@@ -0,0 +1,58 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore
+import imp
+import sys
+
+def copyDir(src, dst):
+ for info in src.entryInfoList():
+ if info.isDir():
+ dst.mkdir(info.fileName())
+ src.cd(info.fileName())
+ dst.cd(info.fileName())
+ copyDir(src, dst)
+ src.cd('..')
+ dst.cd('..')
+ elif info.isFile():
+ QtCore.QFile.copy(info.filePath(), dst.filePath(info.fileName()))
+
+if __name__=="__main__":
+ if len(sys.argv)!=2:
+ print "Usage: python extract.py resource_rc"
+ sys.exit(0)
+
+ moduleName = sys.argv[1]
+ imp.load_source('resModule', moduleName)
+ copyDir(QtCore.QDir(":"), QtCore.QDir("."))
diff --git a/scripts/force_start_vistrails.py b/scripts/force_start_vistrails.py
new file mode 100755
index 0000000..feb60db
--- /dev/null
+++ b/scripts/force_start_vistrails.py
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This script will read vistrails pids from files, kill them and call
+the script to start vistrails. """
+
+import os.path
+import os
+
+#settings
+LOG_DIR = '/server/vistrails/logs'
+VISTRAILS_SCRIPTS_DIR = '/server/vistrails/trunk/scripts'
+SCRIPT = 'start_vistrails.sh'
+PORTS = ['8081','8082','8083']
+
+
+if __name__ == '__main__':
+ cmds = []
+ for port in PORTS:
+ filename = os.path.join(LOG_DIR,
+ "pid.%s.vistrails"%port)
+ f = open(filename)
+ pid = f.read()
+ f.close()
+ cmd = "kill -9 %s"%pid
+ cmds.append(cmd)
+
+ start_cmd = "nohup " + os.path.join(VISTRAILS_SCRIPTS_DIR,SCRIPT)
+ cmds.append(start_cmd)
+
+ for cmd in cmds:
+ os.system(cmd)
diff --git a/scripts/force_start_vistrails_nonohup.py b/scripts/force_start_vistrails_nonohup.py
new file mode 100755
index 0000000..d5b1a55
--- /dev/null
+++ b/scripts/force_start_vistrails_nonohup.py
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This script will read vistrails pids from files, kill them and call
+the script to start vistrails. """
+
+import os.path
+import os
+
+#settings
+LOG_DIR = '/server/vistrails/logs'
+VISTRAILS_SCRIPTS_DIR = '/server/vistrails/trunk/scripts'
+SCRIPT = 'start_vistrails.sh'
+PORTS = ['8081','8082','8083']
+
+
+if __name__ == '__main__':
+ cmds = []
+ for port in PORTS:
+ filename = os.path.join(LOG_DIR,
+ "pid.%s.vistrails"%port)
+ f = open(filename)
+ pid = f.read()
+ f.close()
+ cmd = "kill -9 %s"%pid
+ cmds.append(cmd)
+
+ start_cmd = os.path.join(VISTRAILS_SCRIPTS_DIR,SCRIPT)
+ cmds.append(start_cmd)
+
+ for cmd in cmds:
+ os.system(cmd)
diff --git a/scripts/gen_vtk_examples/README b/scripts/gen_vtk_examples/README
new file mode 100644
index 0000000..72cea9d
--- /dev/null
+++ b/scripts/gen_vtk_examples/README
@@ -0,0 +1,67 @@
+David Koop
+04/28/2008
+
+These scripts are used to generate VisTrails versions of the vtk
+example python scripts. The general idea is that because most of the
+scripts use qualified vtk calls, we can hijack the "import vtk" call
+and import a vtk class that generates a trace of the pipeline calls.
+From this trace, we can reconstruct a pipeline based on
+function/argument pairs. In addition, we use a set of specialized
+functions to:
+
+ - translate calls to "existing" objects like GetActiveCamera(),
+ GetProperty() to use constructed objects instead
+
+ - translate linked "Get" calls (ie
+ "GetPointData().GetScalars().GetRange()") to use inspectors (part
+ of the VisTrails vtk package).
+
+ - translate other specialized functions calls like observers to work
+ with the VisTrails vtk package
+
+We will use three different directories:
+
+modified_scripts_dir: directory that stores vtk examples with
+ manual modifications to allow better translation.
+intermediate_dir: scratch directory where we attempt to translate all scripts
+out_dir: final directory where initial modified python script and
+ the translated vt file are stored.
+
+To run the entire process:
+
+ python gen_vtk_examples.py <modified_scripts_dir> <intermediate_dir>
+ <out_dir>
+
+Note that the modified_scripts_dir assumes the standard vtk structure
+(ie "DataManipulation/Python/Arrays.py") while the other dirs omit the
+Python subdir (ie "DataManipulation/Arrays.py").
+
+Currently, these scripts work as a 3-step process:
+
+(1) Modify existing vtk python scripts to allow process to work
+correctly (ie use PythonCalc to do arithmetic computations).
+
+(2) Run
+
+ python copy_vtk_examples.py <modified_scripts_dir> <intermediate_dir>
+
+This script will call "convert_to_vt.py" to swap some of the inputs
+and call the translator code at the end of the script and copy this
+file to the output directory. Then, it will run the python script.
+Because we use a class ("vtk_imposter.py") to intercept all vtk calls,
+we end up with a trace of the script. We then invoke "vtk_to_vt.py"
+which translates this class into a pipeline.
+
+(3) Run
+
+ python get_vtk_examples.py examples_list.txt <modified_scripts_dir>
+ <intermediate_dir> <out_dir>
+
+This script copies over the modified python script (not the converted
+script) and the new vistrail to a final output directory. It uses the
+examples_list.txt to determine which scripts it ought to copy ('Y'
+indicates a successsful translation, 'N' indicates an unsuccessful
+translation). This example list is updated **manually**.
+
+Note that "check_diffs.py" can be used to check the differences
+between the original and modified Python scripts.
\ No newline at end of file
diff --git a/scripts/gen_vtk_examples/check_diffs.py b/scripts/gen_vtk_examples/check_diffs.py
new file mode 100644
index 0000000..186c071
--- /dev/null
+++ b/scripts/gen_vtk_examples/check_diffs.py
@@ -0,0 +1,78 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import sys
+import os
+import re
+
+def run(in_dir, out_dir):
+ def collectFilenames(dir):
+ # create the regular expression matcher machines
+ fileNameParser = re.compile('.*\.py')
+
+ result = []
+ for file in os.listdir(dir):
+ # print childDirOrFile
+ childDirOrFile = os.path.join(dir,file)
+ if os.path.isfile(childDirOrFile):
+ # file does match?
+ if fileNameParser.match(childDirOrFile):
+ result.append(childDirOrFile)
+ elif os.path.isdir(childDirOrFile):
+ result += collectFilenames(childDirOrFile)
+ return result
+
+
+ all_files = collectFilenames(in_dir)
+
+ in_base = os.path.basename(in_dir)
+ out_base = os.path.basename(out_dir)
+ for fname in all_files:
+ path_before = os.path.dirname(fname)
+ path_end = os.path.basename(fname)
+ while os.path.basename(path_before) != in_base:
+ path_end = os.path.join(os.path.basename(path_before), path_end)
+ path_before = os.path.dirname(path_before)
+ other_fname = os.path.join(out_dir, path_end)
+
+ cmd_line = "diff %s %s" % (fname, other_fname)
+ print cmd_line
+ os.system(cmd_line)
+
+if __name__ == '__main__':
+ if len(sys.argv) < 3:
+ print 'Usage: python %s <in_directory> <out_directory>' % sys.argv[0]
+ sys.exit(-1)
+ run(*sys.argv[1:])
diff --git a/scripts/gen_vtk_examples/colors.py b/scripts/gen_vtk_examples/colors.py
new file mode 100644
index 0000000..af703d0
--- /dev/null
+++ b/scripts/gen_vtk_examples/colors.py
@@ -0,0 +1,251 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# This module defines many standard colors that should be useful.
+# These colors should be exactly the same as the ones defined in
+# colors.tcl.
+
+# Whites
+antique_white = (0.9804, 0.9216, 0.8431)
+azure = (0.9412, 1.0000, 1.0000)
+bisque = (1.0000, 0.8941, 0.7686)
+blanched_almond = (1.0000, 0.9216, 0.8039)
+cornsilk = (1.0000, 0.9725, 0.8627)
+eggshell = (0.9900, 0.9000, 0.7900)
+floral_white = (1.0000, 0.9804, 0.9412)
+gainsboro = (0.8627, 0.8627, 0.8627)
+ghost_white = (0.9725, 0.9725, 1.0000)
+honeydew = (0.9412, 1.0000, 0.9412)
+ivory = (1.0000, 1.0000, 0.9412)
+lavender = (0.9020, 0.9020, 0.9804)
+lavender_blush = (1.0000, 0.9412, 0.9608)
+lemon_chiffon = (1.0000, 0.9804, 0.8039)
+linen = (0.9804, 0.9412, 0.9020)
+mint_cream = (0.9608, 1.0000, 0.9804)
+misty_rose = (1.0000, 0.8941, 0.8824)
+moccasin = (1.0000, 0.8941, 0.7098)
+navajo_white = (1.0000, 0.8706, 0.6784)
+old_lace = (0.9922, 0.9608, 0.9020)
+papaya_whip = (1.0000, 0.9373, 0.8353)
+peach_puff = (1.0000, 0.8549, 0.7255)
+seashell = (1.0000, 0.9608, 0.9333)
+snow = (1.0000, 0.9804, 0.9804)
+thistle = (0.8471, 0.7490, 0.8471)
+titanium_white = (0.9900, 1.0000, 0.9400)
+wheat = (0.9608, 0.8706, 0.7020)
+white = (1.0000, 1.0000, 1.0000)
+white_smoke = (0.9608, 0.9608, 0.9608)
+zinc_white = (0.9900, 0.9700, 1.0000)
+
+# Greys
+cold_grey = (0.5000, 0.5400, 0.5300)
+dim_grey = (0.4118, 0.4118, 0.4118)
+grey = (0.7529, 0.7529, 0.7529)
+light_grey = (0.8275, 0.8275, 0.8275)
+slate_grey = (0.4392, 0.5020, 0.5647)
+slate_grey_dark = (0.1843, 0.3098, 0.3098)
+slate_grey_light = (0.4667, 0.5333, 0.6000)
+warm_grey = (0.5000, 0.5000, 0.4100)
+
+# Blacks
+black = (0.0000, 0.0000, 0.0000)
+ivory_black = (0.1600, 0.1400, 0.1300)
+lamp_black = (0.1800, 0.2800, 0.2300)
+
+# Reds
+alizarin_crimson = (0.8900, 0.1500, 0.2100)
+brick = (0.6100, 0.4000, 0.1200)
+cadmium_red_deep = (0.8900, 0.0900, 0.0500)
+coral = (1.0000, 0.4980, 0.3137)
+coral_light = (0.9412, 0.5020, 0.5020)
+deep_pink = (1.0000, 0.0784, 0.5765)
+english_red = (0.8300, 0.2400, 0.1000)
+firebrick = (0.6980, 0.1333, 0.1333)
+geranium_lake = (0.8900, 0.0700, 0.1900)
+hot_pink = (1.0000, 0.4118, 0.7059)
+indian_red = (0.6900, 0.0900, 0.1200)
+light_salmon = (1.0000, 0.6275, 0.4784)
+madder_lake_deep = (0.8900, 0.1800, 0.1900)
+maroon = (0.6902, 0.1882, 0.3765)
+pink = (1.0000, 0.7529, 0.7961)
+pink_light = (1.0000, 0.7137, 0.7569)
+raspberry = (0.5300, 0.1500, 0.3400)
+red = (1.0000, 0.0000, 0.0000)
+rose_madder = (0.8900, 0.2100, 0.2200)
+salmon = (0.9804, 0.5020, 0.4471)
+tomato = (1.0000, 0.3882, 0.2784)
+venetian_red = (0.8300, 0.1000, 0.1200)
+
+# Browns
+beige = (0.6400, 0.5800, 0.5000)
+brown = (0.5000, 0.1647, 0.1647)
+brown_madder = (0.8600, 0.1600, 0.1600)
+brown_ochre = (0.5300, 0.2600, 0.1200)
+burlywood = (0.8706, 0.7216, 0.5294)
+burnt_sienna = (0.5400, 0.2100, 0.0600)
+burnt_umber = (0.5400, 0.2000, 0.1400)
+chocolate = (0.8235, 0.4118, 0.1176)
+deep_ochre = (0.4500, 0.2400, 0.1000)
+flesh = (1.0000, 0.4900, 0.2500)
+flesh_ochre = (1.0000, 0.3400, 0.1300)
+gold_ochre = (0.7800, 0.4700, 0.1500)
+greenish_umber = (1.0000, 0.2400, 0.0500)
+khaki = (0.9412, 0.9020, 0.5490)
+khaki_dark = (0.7412, 0.7176, 0.4196)
+light_beige = (0.9608, 0.9608, 0.8627)
+peru = (0.8039, 0.5216, 0.2471)
+rosy_brown = (0.7373, 0.5608, 0.5608)
+raw_sienna = (0.7800, 0.3800, 0.0800)
+raw_umber = (0.4500, 0.2900, 0.0700)
+sepia = (0.3700, 0.1500, 0.0700)
+sienna = (0.6275, 0.3216, 0.1765)
+saddle_brown = (0.5451, 0.2706, 0.0745)
+sandy_brown = (0.9569, 0.6431, 0.3765)
+tan = (0.8235, 0.7059, 0.5490)
+van_dyke_brown = (0.3700, 0.1500, 0.0200)
+
+# Oranges
+cadmium_orange = (1.0000, 0.3800, 0.0100)
+cadmium_red_light = (1.0000, 0.0100, 0.0500)
+carrot = (0.9300, 0.5700, 0.1300)
+dark_orange = (1.0000, 0.5490, 0.0000)
+mars_orange = (0.5900, 0.2700, 0.0800)
+mars_yellow = (0.8900, 0.4400, 0.1000)
+orange = (1.0000, 0.5000, 0.0000)
+orange_red = (1.0000, 0.2706, 0.0000)
+yellow_ochre = (0.8900, 0.5100, 0.0900)
+
+# Yellows
+aureoline_yellow = (1.0000, 0.6600, 0.1400)
+banana = (0.8900, 0.8100, 0.3400)
+cadmium_lemon = (1.0000, 0.8900, 0.0100)
+cadmium_yellow = (1.0000, 0.6000, 0.0700)
+cadmium_yellow_light = (1.0000, 0.6900, 0.0600)
+gold = (1.0000, 0.8431, 0.0000)
+goldenrod = (0.8549, 0.6471, 0.1255)
+goldenrod_dark = (0.7216, 0.5255, 0.0431)
+goldenrod_light = (0.9804, 0.9804, 0.8235)
+goldenrod_pale = (0.9333, 0.9098, 0.6667)
+light_goldenrod = (0.9333, 0.8667, 0.5098)
+melon = (0.8900, 0.6600, 0.4100)
+naples_yellow_deep = (1.0000, 0.6600, 0.0700)
+yellow = (1.0000, 1.0000, 0.0000)
+yellow_light = (1.0000, 1.0000, 0.8784)
+
+# Greens
+chartreuse = (0.4980, 1.0000, 0.0000)
+chrome_oxide_green = (0.4000, 0.5000, 0.0800)
+cinnabar_green = (0.3800, 0.7000, 0.1600)
+cobalt_green = (0.2400, 0.5700, 0.2500)
+emerald_green = (0.0000, 0.7900, 0.3400)
+forest_green = (0.1333, 0.5451, 0.1333)
+green = (0.0000, 1.0000, 0.0000)
+green_dark = (0.0000, 0.3922, 0.0000)
+green_pale = (0.5961, 0.9843, 0.5961)
+green_yellow = (0.6784, 1.0000, 0.1843)
+lawn_green = (0.4863, 0.9882, 0.0000)
+lime_green = (0.1961, 0.8039, 0.1961)
+mint = (0.7400, 0.9900, 0.7900)
+olive = (0.2300, 0.3700, 0.1700)
+olive_drab = (0.4196, 0.5569, 0.1373)
+olive_green_dark = (0.3333, 0.4196, 0.1843)
+permanent_green = (0.0400, 0.7900, 0.1700)
+sap_green = (0.1900, 0.5000, 0.0800)
+sea_green = (0.1804, 0.5451, 0.3412)
+sea_green_dark = (0.5608, 0.7373, 0.5608)
+sea_green_medium = (0.2353, 0.7020, 0.4431)
+sea_green_light = (0.1255, 0.6980, 0.6667)
+spring_green = (0.0000, 1.0000, 0.4980)
+spring_green_medium = (0.0000, 0.9804, 0.6039)
+terre_verte = (0.2200, 0.3700, 0.0600)
+viridian_light = (0.4300, 1.0000, 0.4400)
+yellow_green = (0.6039, 0.8039, 0.1961)
+
+# Cyans
+aquamarine = (0.4980, 1.0000, 0.8314)
+aquamarine_medium = (0.4000, 0.8039, 0.6667)
+cyan = (0.0000, 1.0000, 1.0000)
+cyan_white = (0.8784, 1.0000, 1.0000)
+turquoise = (0.2510, 0.8784, 0.8157)
+turquoise_dark = (0.0000, 0.8078, 0.8196)
+turquoise_medium = (0.2824, 0.8196, 0.8000)
+turquoise_pale = (0.6863, 0.9333, 0.9333)
+
+# Blues
+alice_blue = (0.9412, 0.9725, 1.0000)
+blue = (0.0000, 0.0000, 1.0000)
+blue_light = (0.6784, 0.8471, 0.9020)
+blue_medium = (0.0000, 0.0000, 0.8039)
+cadet = (0.3725, 0.6196, 0.6275)
+cobalt = (0.2400, 0.3500, 0.6700)
+cornflower = (0.3922, 0.5843, 0.9294)
+cerulean = (0.0200, 0.7200, 0.8000)
+dodger_blue = (0.1176, 0.5647, 1.0000)
+indigo = (0.0300, 0.1800, 0.3300)
+manganese_blue = (0.0100, 0.6600, 0.6200)
+midnight_blue = (0.0980, 0.0980, 0.4392)
+navy = (0.0000, 0.0000, 0.5020)
+peacock = (0.2000, 0.6300, 0.7900)
+powder_blue = (0.6902, 0.8784, 0.9020)
+royal_blue = (0.2549, 0.4118, 0.8824)
+slate_blue = (0.4157, 0.3529, 0.8039)
+slate_blue_dark = (0.2824, 0.2392, 0.5451)
+slate_blue_light = (0.5176, 0.4392, 1.0000)
+slate_blue_medium = (0.4824, 0.4078, 0.9333)
+sky_blue = (0.5294, 0.8078, 0.9216)
+sky_blue_deep = (0.0000, 0.7490, 1.0000)
+sky_blue_light = (0.5294, 0.8078, 0.9804)
+steel_blue = (0.2745, 0.5098, 0.7059)
+steel_blue_light = (0.6902, 0.7686, 0.8706)
+turquoise_blue = (0.0000, 0.7800, 0.5500)
+ultramarine = (0.0700, 0.0400, 0.5600)
+
+# Magentas
+blue_violet = (0.5412, 0.1686, 0.8863)
+cobalt_violet_deep = (0.5700, 0.1300, 0.6200)
+magenta = (1.0000, 0.0000, 1.0000)
+orchid = (0.8549, 0.4392, 0.8392)
+orchid_dark = (0.6000, 0.1961, 0.8000)
+orchid_medium = (0.7294, 0.3333, 0.8275)
+permanent_red_violet = (0.8600, 0.1500, 0.2700)
+plum = (0.8667, 0.6275, 0.8667)
+purple = (0.6275, 0.1255, 0.9412)
+purple_medium = (0.5765, 0.4392, 0.8588)
+ultramarine_violet = (0.3600, 0.1400, 0.4300)
+violet = (0.5600, 0.3700, 0.6000)
+violet_dark = (0.5804, 0.0000, 0.8275)
+violet_red = (0.8157, 0.1255, 0.5647)
+violet_red_medium = (0.7804, 0.0824, 0.5216)
+violet_red_pale = (0.8588, 0.4392, 0.5765)
diff --git a/scripts/gen_vtk_examples/convert_to_vt.py b/scripts/gen_vtk_examples/convert_to_vt.py
new file mode 100644
index 0000000..ad600ed
--- /dev/null
+++ b/scripts/gen_vtk_examples/convert_to_vt.py
@@ -0,0 +1,98 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+class ConvertVTKToVT(object):
+ def __init__(self, in_filename, out_py_file):
+ self.in_filename = in_filename
+ self.out_py_file = out_py_file
+
+
+ def run(self):
+ in_file = file(self.in_filename)
+ out_file = file(self.out_py_file, 'w')
+
+ does_continue = False
+ line_count = 0
+ found_starter = False
+ for line in in_file:
+ if line_count == 0:
+ if line.startswith('#!'):
+ found_starter = True
+ else:
+ print >> out_file, \
+ "# This file produced automatically by convert_to_vt.py\n# "
+ elif line_count == 1 and found_starter:
+ print >> out_file, \
+ "# This file produced automatically by convert_to_vt.py\n# "
+ found_starter = False
+
+ if (line.find('import ') != -1 and line.find('vtk') != -1) or \
+ line.find('VTK_DATA_ROOT = ') != -1 or \
+ does_continue:
+ if line.rstrip() == 'import vtk':
+ print >>out_file, 'import sys'
+ print >>out_file, 'sys.path.append' + \
+ '("/vistrails/src/trunk/scripts/gen_vtk_examples")'
+ print >>out_file, 'import vtk_imposter'
+ print >>out_file, 'from colors import *'
+ print >>out_file, 'vtk = vtk_imposter.vtk()'
+ print >>out_file, 'VTK_DATA_ROOT = ""'
+ print >>out_file, ''
+ print >>out_file, '#', line[:-1]
+ else:
+ if line.rstrip()[-1] == '\\':
+ does_continue = True
+ else:
+ does_continue = False
+ print >>out_file, '#', line[:-1]
+ else:
+ out_file.write(line)
+ line_count += 1
+ print >>out_file, '\nif len(sys.argv) > 1:'
+ print >>out_file, ' out_filename = sys.argv[1]'
+ print >>out_file, 'else:'
+ print >>out_file, ' out_filename = None'
+ print >>out_file, 'vtk.to_vt(out_filename)'
+ out_file.close()
+
+
+if __name__ == '__main__':
+ import sys
+ if len(sys.argv) < 3:
+ print 'Usage: %s <in_file> <out_py_file>' % sys.argv[0]
+ sys.exit(0)
+ converter = ConvertVTKToVT(*sys.argv[1:])
+ converter.run()
+
diff --git a/scripts/gen_vtk_examples/copy_vtk_examples.py b/scripts/gen_vtk_examples/copy_vtk_examples.py
new file mode 100644
index 0000000..bc0e20f
--- /dev/null
+++ b/scripts/gen_vtk_examples/copy_vtk_examples.py
@@ -0,0 +1,99 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import sys
+import os
+import re
+from convert_to_vt import ConvertVTKToVT
+
+def run(in_dir, out_dir):
+ def collectFilenames(dir):
+ # create the regular expression matcher machines
+ fileNameParser = re.compile('.*\.py')
+
+ result = []
+ for file in os.listdir(dir):
+ # print childDirOrFile
+ childDirOrFile = os.path.join(dir,file)
+ if os.path.isfile(childDirOrFile):
+ # file does match?
+ if fileNameParser.match(childDirOrFile):
+ result.append(childDirOrFile)
+ elif os.path.isdir(childDirOrFile):
+ result += collectFilenames(childDirOrFile)
+ return result
+
+ all_files = collectFilenames(in_dir)
+ in_base = os.path.basename(in_dir)
+ for fname in all_files:
+ path_before = os.path.dirname(fname)
+ path_end = ''
+ while os.path.basename(path_before) != in_base:
+ if os.path.basename(path_before) != 'Python':
+ if path_end == '':
+ path_end = os.path.basename(path_before)
+ else:
+ path_end = os.path.join(os.path.basename(path_before),
+ path_end)
+ path_before = os.path.dirname(path_before)
+ out_dirname = os.path.join(out_dir, path_end)
+
+ to_make_dirs = []
+ a_dirname = out_dirname
+ while not os.path.exists(a_dirname):
+ to_make_dirs.append(a_dirname)
+ a_dirname = os.path.dirname(a_dirname)
+ # print >>sys.stderr, 'to_make_dirs:', to_make_dirs
+ for a_dirname in reversed(to_make_dirs):
+ # print >>sys.stderr, 'making dir', a_dirname
+ os.mkdir(a_dirname)
+
+ script_name = os.path.basename(fname)
+ vt_name = os.path.splitext(script_name)[0] + '.vt'
+ out_py_name = os.path.join(out_dirname, script_name)
+ out_vt_name = os.path.join(out_dirname, vt_name)
+
+ converter = ConvertVTKToVT(fname, out_py_name)
+ converter.run()
+
+ print >>sys.stderr, "running 'python %s %s'..." % (out_py_name,
+ out_vt_name)
+ os.system('python %s %s' % (out_py_name, out_vt_name))
+
+if __name__ == '__main__':
+ if len(sys.argv) < 3:
+ print 'Usage: %s <in_directory> <out_directory>' % sys.argv[0]
+ sys.exit(-1)
+ run(*sys.argv[1:])
diff --git a/scripts/gen_vtk_examples/examples_list.txt b/scripts/gen_vtk_examples/examples_list.txt
new file mode 100644
index 0000000..f632974
--- /dev/null
+++ b/scripts/gen_vtk_examples/examples_list.txt
@@ -0,0 +1,83 @@
+Annotation/DispAllFonts.py N vtkTkRenderWindowInteractor
+Annotation/TestText.py YC
+Annotation/TestTextOldWay.py N python fails vtkTextMapper error (may work)
+Annotation/annotatePick.py N connections and parameters for Pick
+Annotation/cubeAxes.py Y
+Annotation/labeledMesh.py N cycles (vtkSelectVisiblePoints)
+Annotation/multiLineText.py N ShallowCopy and vtkTextMapper error
+Annotation/textOrigin.py YC
+Annotation/xyPlot.py Y
+DataManipulation/Arrays.py Y
+DataManipulation/BuildUGrid.py YC
+DataManipulation/CreateStrip.py Y
+DataManipulation/FinancialField.py N GetRange()[1] vtkProgrammable*
+DataManipulation/marching.py YC
+DataManipulation/pointToCellData.py YC
+GUI/BoxWidget.py N vtkPlanes -- probably can change to make vtkClipPolyData an input to the vtkInteractionHandler
+GUI/CustomInteraction.py N Observers aren't being added
+GUI/ImagePlaneWidget.py N GetWholeExtent assignment to tuple, others
+GUI/ImageTracerWidget.py N scalar range list index, others
+GUI/ImplicitPlaneWidget.py Y
+GUI/OrthogonalPlanesWithTkPhoto.py N non qualified vtk modules
+GUI/ProbeWithPointWidget.py YM multiplication between function and float
+GUI/ProbingWithPlaneWidget.py Y
+GUI/SphereWidget.py N GetElevationBounds()[0]
+GUI/StreamlinesWithLineWidget.py Y a little buggy on updates
+GUI/TransformWithBoxWidget.py Y
+GUI/VolumeRenderWithBoxWidget.py Y
+IO/flamingo.py YC also background color wrong...
+IO/stl.py YC
+ImageProcessing/Contours2D.py YC
+ImageProcessing/ImageInteractor.py N polyDataMapper error + interactor
+Medical/Medical1.py YC
+Medical/Medical2.py YC
+Medical/Medical3.py YC
+Modelling/DelMesh.py N vtkMath.Random()
+Modelling/Delaunay3D.py N vtkMath.Random()
+Modelling/PerlinTerrain.py YC
+Modelling/SpherePuzzle.py N vtkTkRenderWindowInteractor
+Modelling/constrainedDelaunay.py YC
+Modelling/expCos.py N vtkProgrammableFilter
+Modelling/faultLines.py Y
+Modelling/hello.py YC
+Modelling/iceCream.py YC
+Modelling/procrustesAlignment.py N SetInputConnection(int, object)
+Modelling/reconstructSurface.py N SetExecuteMethod
+ParallelProcessing/MPI/ParallelCone.py N non-qualified vtk modules
+Rendering/CADPart.py YC
+Rendering/CSpline.py N vtkMath.Random()
+Rendering/Cylinder.py YC
+Rendering/FilterCADPart.py YC
+Rendering/RenderLargeImage.py N png image header corrputed
+Rendering/TPlane.py YC
+Rendering/assembly.py Y
+Rendering/rainbow.py Y
+Tutorial/Step1/Cone.py YC
+Tutorial/Step2/Cone2.py YM no observer to do print, removed azimuth loop
+Tutorial/Step3/Cone3.py YMC removed azimuth loop
+Tutorial/Step4/Cone4.py YM removed azimuth loop, extra SetColor
+Tutorial/Step5/Cone5.py Y
+Tutorial/Step6/Cone6.py YM BoxWidget callback and On call
+VisualizationAlgorithms/BandContourTerrain.py Y extra vtkLookupTable
+VisualizationAlgorithms/ClipCow.py YC
+VisualizationAlgorithms/ColorIsosurface.py Y
+VisualizationAlgorithms/CutCombustor.py Y fix SetScalarRange call
+VisualizationAlgorithms/DepthSort.py N Circular vtkActor-vtkDepthSortPolyData
+VisualizationAlgorithms/ExtractGeometry.py Y
+VisualizationAlgorithms/ExtractUGrid.py Y
+VisualizationAlgorithms/GenerateTextureCoords.py Y
+VisualizationAlgorithms/SubsampleGrid.py Y
+VisualizationAlgorithms/TextureThreshold.py Y
+VisualizationAlgorithms/VisQuad.py Y
+VisualizationAlgorithms/deciFran.py P script isn't written correctly!
+VisualizationAlgorithms/imageWarp.py Y
+VisualizationAlgorithms/officeTube.py Y
+VisualizationAlgorithms/officeTubes.py Y
+VisualizationAlgorithms/probeComb.py Y
+VisualizationAlgorithms/smoothFran.py Y
+VisualizationAlgorithms/spikeF.py Y
+VisualizationAlgorithms/streamSurface.py Y
+VisualizationAlgorithms/warpComb.py Y
+VolumeRendering/PseudoVolumeRendering.py Y
+VolumeRendering/SimpleRayCast.py Y
+VolumeRendering/SimpleTextureMap2D.py Y
diff --git a/scripts/gen_vtk_examples/gen_vtk_examples.py b/scripts/gen_vtk_examples/gen_vtk_examples.py
new file mode 100644
index 0000000..ee7ba28
--- /dev/null
+++ b/scripts/gen_vtk_examples/gen_vtk_examples.py
@@ -0,0 +1,50 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import sys
+
+import copy_vtk_examples
+import get_vtk_examples
+
+def run(begin_dir, intermediate_dir, output_dir,
+ examples_list='examples_list.txt'):
+ copy_vtk_examples.run(begin_dir, intermediate_dir)
+ get_vtk_examples.run(begin_dir, intermediate_dir, output_dir, examples_list)
+
+if __name__ == '__main__':
+ if len(sys.argv) < 4:
+ print "Usage: python %s " % sys.argv[0] + \
+ "<begin_dir> <intermediate_dir> <out_dir> [examples_list]"
+ sys.exit(-1)
+ run(*sys.argv[1:])
diff --git a/scripts/gen_vtk_examples/get_vtk_examples.py b/scripts/gen_vtk_examples/get_vtk_examples.py
new file mode 100644
index 0000000..95f254f
--- /dev/null
+++ b/scripts/gen_vtk_examples/get_vtk_examples.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import sys
+import os
+
+def run(py_dirname, in_dirname, out_dirname, filename='examples_list.txt'):
+ f = open(filename)
+ total = 0
+ total_good = 0
+ for line in f:
+ # print line
+ arr = line.rstrip().split(None, 2)
+ total += 1
+ if arr[1][0] == 'Y':
+ total_good += 1
+
+ vt_file = os.path.splitext(arr[0])[0] + '.vt'
+ py_file = arr[0]
+
+ vt_name = os.path.join(in_dirname, vt_file)
+ out_vt_name = os.path.join(out_dirname, vt_file)
+ py_name = os.path.join(py_dirname, py_file)
+
+ py_name = os.path.join(os.path.dirname(py_name),
+ "Python",
+ os.path.basename(py_name))
+ out_py_name = os.path.join(out_dirname, py_file)
+ to_make_dirs = []
+ a_dirname = os.path.dirname(out_vt_name)
+ while not os.path.exists(a_dirname):
+ to_make_dirs.append(a_dirname)
+ a_dirname = os.path.dirname(a_dirname)
+ for a_dirname in reversed(to_make_dirs):
+ # print "os.mkdir('%s')" % a_dirname
+ os.mkdir(a_dirname)
+
+ # print "os.system('cp %s %s')" % (py_name, out_py_name)
+ # print "os.system('cp %s %s')" % (vt_name, out_vt_name)
+ os.system('cp %s %s' % (py_name, out_py_name))
+ os.system('cp %s %s' % (vt_name, out_vt_name))
+ print "%d of %d" % (total_good, total)
+
+if __name__ == '__main__':
+ if len(sys.argv) < 5:
+ print "Usage: python %s " % sys.argv[0] + \
+ "<python_dir> <in_dir> <out_dir> [examples_list]"
+ sys.exit(-1)
+ run(*sys.argv[1:])
diff --git a/scripts/gen_vtk_examples/vtk_imposter.py b/scripts/gen_vtk_examples/vtk_imposter.py
new file mode 100644
index 0000000..5c02174
--- /dev/null
+++ b/scripts/gen_vtk_examples/vtk_imposter.py
@@ -0,0 +1,106 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+class vtk_base(object):
+ def __init__(self, n=None, *args, **kwargs):
+ self._name = n
+ self._args = args
+ self._kwargs = kwargs
+
+ def __call__(self, *args, **kwargs):
+ # print 'calling %s __call__ with' % self.__class__.__name__, \
+ # args, kwargs
+ return self.__class__.__dict__['_call'](self, self.n, *args, **kwargs)
+
+ def __getattr__(self, name):
+ # print 'calling %s __getattr__ with' % self.__class__.__name__, name
+ if name in ('__str__','__repr__'):
+ return lambda: 'instance of %s at %s' % (str(self.__class__),
+ id(self))
+ self.n = name
+ return self
+
+ def _call(self, n, *args, **kwargs):
+ # print 'calling _call with', n, args, kwargs
+ pass
+
+class vtk_function(vtk_base):
+ id_count = 0
+
+ def __init__(self, n=None, parent=None, *args, **kwargs):
+ vtk_base.__init__(self, n, *args, **kwargs)
+ self.parent = parent
+ self.sub_functions = []
+ self.id = vtk_function.id_count
+ vtk_function.id_count += 1
+
+ def _call(self, n, *args, **kwargs):
+ vtk_base._call(self, n, *args, **kwargs)
+ new_sub_function = vtk_function(n, self, *args, **kwargs)
+ self.__dict__['sub_functions'].append(new_sub_function)
+ return new_sub_function
+
+class vtk_module(vtk_base):
+ def __init__(self, n=None, *args, **kwargs):
+ vtk_base.__init__(self, n, *args, **kwargs)
+ self.functions = []
+
+ def _call(self, n, *args, **kwargs):
+ vtk_base._call(self, n, *args, **kwargs)
+ new_function = vtk_function(n, self, *args, **kwargs)
+ self.__dict__['functions'].append(new_function)
+ return new_function
+
+class vtk(vtk_base):
+
+ def __init__(self, n=None, *args, **kwargs):
+ vtk_base.__init__(self, n, *args, **kwargs)
+ self.modules = []
+ # print 'self.__dict__:', self.__dict__
+
+ def _call(self, n, *args, **kwargs):
+ vtk_base._call(self, n, *args, **kwargs)
+ new_module = vtk_module(n, *args, **kwargs)
+ self.__dict__['modules'].append(new_module)
+ return new_module
+
+ def to_vt(self, filename):
+ from vtk_to_vt import VTK2VT
+ my_writer = VTK2VT()
+ for module in self.modules:
+ my_writer.create_module(module)
+ for module in self.modules:
+ my_writer.create_functions(module)
+ my_writer.print_vt(filename)
diff --git a/scripts/gen_vtk_examples/vtk_to_vt.py b/scripts/gen_vtk_examples/vtk_to_vt.py
new file mode 100644
index 0000000..4d2a705
--- /dev/null
+++ b/scripts/gen_vtk_examples/vtk_to_vt.py
@@ -0,0 +1,1117 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import sys
+sys.path.append('/vistrails/src/trunk/vistrails')
+import os
+os.environ['EXECUTABLEPATH'] = ""
+import copy
+import datetime
+import re
+import urllib
+
+from vistrails.db.domain import DBModule, DBConnection, DBPort, DBFunction, \
+ DBParameter, DBLocation, DBPortSpec, DBTag, DBAnnotation, DBVistrail, \
+ DBRegistry
+import vistrails.db.services.io
+from vistrails.db.services.io import SaveBundle
+from vtk_imposter import vtk_module, vtk_function
+
+class VTK2VT(object):
+ vtk_data_url = 'http://www.vtk.org/files/release/5.0/vtkdata-5.0.4.zip'
+ package_name = 'edu.utah.sci.vistrails.vtk'
+ basic_name = 'edu.utah.sci.vistrails.basic'
+ pythoncalc_name = 'edu.utah.sci.vistrails.pythoncalc'
+ http_name = 'edu.utah.sci.vistrails.http'
+ variant_sigstring ='(edu.utah.sci.vistrails.basic:Tuple)'
+ unused_functions = set(['Update',
+ 'Read',
+ 'Write',
+ 'Start',
+ 'Initialize',
+ 'Render',
+ 'PlaceWidget',
+ 'AddObserver',
+ 'SetSize',
+ ])
+ translate_ports = {'SetInputConnection': {None: 'SetInputConnection0'},
+ 'GetOutputPort': {None: 'GetOutputPort0'},
+ 'SetRenderWindow': {None: 'SetVTKCell'},
+ 'SetInteractorStyle': {None: 'InteractorStyle'},
+ 'ResetCamera': {None: 'ResetCamera'},
+ 'AddInput': {None: 'AddInput',
+ 'vtkXYPlotActor': 'AddInput_2'},
+ 'SetInput': {None: 'SetInput',
+ 'vtkPolyDataNormals': 'SetInput_1',
+ 'vtkGlyph3D': 'SetInput_1',
+ 'vtkDelaunay2D': 'SetInput_1',
+ 'vtkDelaunay3D': 'SetInput_1',
+ 'vtkWarpVector': 'SetInput_1',
+ 'vtkContourFilter': 'SetInput_1',
+ 'vtkTubeFilter': 'SetInput_1',
+ 'vtkThresholdPoints': 'SetInput_1',
+ 'vtkProbeFilter': 'SetInput_1',
+ 'vtkTriangleFilter': 'SetInput_1',
+ 'vtkBandedPolyDataContourFilter': \
+ 'SetInput_1',
+ 'vtkWarpScalar': 'SetInput_1'},
+ 'SetSourceConnection': {None: 'SetSourceConnection',
+ 'vtkGlyph3D': \
+ 'SetSourceConnection_2'},
+ 'AddFunction': {None: 'AddFunction',
+ ('vtkImplicitSum', 'vtkPlane'): \
+ 'AddFunction_2',
+ ('vtkImplicitSum', 'Tuple'): \
+ 'AddFunction_1'},
+ 'SetColor': {None: 'SetColor',
+ ('vtkVolumeProperty',
+ 'vtkColorTransferFunction'): \
+ 'SetColor_4',
+ ('vtkVolumeProperty',
+ 'vtkPiecewiseFunction'): \
+ 'SetColor_2'},
+ 'SetScalarOpacity': {None: 'SetScalarOpacity',
+ 'vtkVolumeProperty': \
+ 'SetScalarOpacity_2'},
+ 'SetSource': {None: 'SetSource',
+ 'vtkGlyph3D': 'SetSource_1'},
+ }
+
+ inspector_functions = {'GetScalarRange': 'vtkDataSetInspector',
+ 'GetCenter': 'vtkDataSetInspector',
+ 'GetNumberOfCells': 'vtkDataSetInspector',
+ 'GetNumberOfPoints': 'vtkDataSetInspector',
+ 'GetLength': 'vtkDataSetInspector',
+ 'GetBounds': 'vtkDataSetInspector',
+ 'GetPointData': 'vtkDataSetInspector',
+ 'GetCellData': 'vtkDataSetInspector',
+ 'GetVerts': 'vtkPolyDataInspector',
+ 'GetPoints': 'vtkPolyDataInspector',
+ 'GetLines': 'vtkPolyDataInspector',
+ 'GetStrips': 'vtkPolyDataInspector',
+ 'GetPoints': 'vtkPolyDataInspector',
+ 'GetNumberOfVerts': 'vtkPolyDataInspector',
+ 'GetNumberOfPoints': 'vtkPolyDataInspector',
+ 'GetNumberOfPolys': 'vtkPolyDataInspector',
+ 'GetNumberOfStrips': 'vtkPolyDataInspector',
+ 'GetScalars': 'vtkDataSetAttributesInspector',
+ 'GetVectors': 'vtkDataSetAttributesInspector',
+ 'GetNormals': 'vtkDataSetAttributesInspector',
+ 'GetTCoords': 'vtkDataSetAttributesInspector',
+ 'GetTensors': 'vtkDataSetAttributesInspector',
+ 'GetGlobalIds': 'vtkDataSetAttributesInspector',
+ 'GetPedigreeIds': 'vtkDataSetAttributesInspector',
+ 'GetMaxNorm': 'vtkDataArrayInspector',
+ 'GetRange': 'vtkDataArrayInspector',
+ }
+
+ getters = {'GetProperty': {None: ('SetProperty', 'vtkProperty', None),
+ 'vtkXYPlotActor': ('SetProperty',
+ 'vtkProperty2D', None)},
+ 'GetActiveCamera': {None: ('SetActiveCamera',
+ 'vtkCamera', None)},
+ 'GetTitleTextProperty':{None: ('SetTitleTextProperty',
+ 'vtkTextProperty',
+ [('BoldOn',),
+ ('ItalicOn',),
+ ('ShadowOn',),
+ ('SetFontFamilyToArial',)])},
+ 'GetTextProperty': {None: ('SetTextProperty',
+ 'vtkTextProperty', None)},
+ 'GetPointData': {None: ('SetPointData', 'vtkPointData', None)},
+ 'GetCellData': {None: ('SetCellData', 'vtkCellData', None)},
+ 'GetPointIds': {None: ('SetPointIds', 'vtkIdList', None),
+ 'vtkVoxel': ('SetPointIds', 'vtkIdList',
+ [('SetNumberOfIds', 8)]),
+ 'vtkHexahedron': ('SetPointIds', 'vtkIdList',
+ [('SetNumberOfIds', 8)]),
+ 'vtkTetra': ('SetPointIds', 'vtkIdList',
+ [('SetNumberOfIds', 4)]),
+ 'vtkWedge': ('SetPointIds', 'vtkIdList',
+ [('SetNumberOfIds', 6)]),
+ 'vtkPyramid': ('SetPointIds', 'vtkIdList',
+ [('SetNumberOfIds', 5)]),
+ 'vtkPixel': ('SetPointIds', 'vtkIdList',
+ [('SetNumberOfIds', 4)]),
+ 'vtkQuad': ('SetPointIds', 'vtkIdList',
+ [('SetNumberOfIds', 4)]),
+ 'vtkTriangle': ('SetPointIds', 'vtkIdList',
+ [('SetNumberOfIds', 3)]),
+ 'vtkLine': ('SetPointIds', 'vtkIdList',
+ [('SetNumberOfIds', 2)]),
+ 'vtkVertex': ('SetPointIds', 'vtkIdList',
+ [('SetNumberOfIds', 1)]),
+ },
+ 'GetRenderWindow': {None: ('SetVTKCell', 'VTKCell', None)},
+ }
+
+ set_file_name_pattern = re.compile('Set.*FileName$')
+
+ def __init__(self):
+ self.created_modules = {}
+ self.modules = {}
+ self.vt_modules = {}
+ self.vtk_modules = {}
+ self.connections = {}
+ self.vt_f_connections = {}
+ self.vt_b_connections = {}
+ self.max_module_id = 0
+ self.max_location_id = 0
+ self.max_function_id = 0
+ self.max_parameter_id = 0
+ self.max_connection_id = 0
+ self.max_port_id = 0
+ self.max_port_spec_id = 0
+ self.http_module = None
+
+ r_file = '/vistrails/registry.xml'
+ self.registry = vistrails.db.services.io.open_registry_from_xml(r_file)
+ self.registry_desc_idx = {}
+ for package in self.registry.db_packages:
+ for desc in package.db_module_descriptors:
+ self.registry_desc_idx[desc.db_id] = desc
+
+ def create_module(self, module):
+ # print 'creating module', module._name, id(module)
+ module_name = module._name
+ package_name = self.package_name
+ if module_name == 'vtkRenderWindow':
+ module_name = 'VTKCell'
+ elif module_name == 'vtkRenderWindowInteractor':
+ return
+ elif module_name == 'Tuple' or module_name == 'Unzip':
+ package_name = self.basic_name
+ elif module_name == 'PythonCalc':
+ package_name = self.pythoncalc_name
+ elif module_name == 'HTTPFile':
+ package_name = self.http_name
+ db_module = DBModule(id=self.max_module_id,
+ name=module_name,
+ package=package_name,
+ location=DBLocation(id=self.max_location_id,
+ x=0.0, y=0.0),
+ )
+ self.max_module_id += 1
+ self.max_location_id += 1
+ self.modules[id(module)] = db_module
+ self.vt_modules[db_module.db_id] = db_module
+ self.vtk_modules[id(module)] = module
+ # self.vt_f_connections[db_module.db_id] = []
+ # self.vt_b_connections[db_module.db_id] = []
+
+ def save_modules(self):
+ self.saved_functions = {}
+ for k, module in self.vtk_modules.iteritems():
+ self.saved_functions[k] = module.functions
+ module.functions = []
+
+ def restore_modules(self):
+ for k, module in self.vtk_modules.iteritems():
+ module.functions = self.saved_functions[k]
+
+ def do_layout(self):
+ queue = []
+ # sinks = []
+ vt_b_connections = self.vt_f_connections
+ vt_f_connections = self.vt_b_connections
+ b_connections = copy.deepcopy(vt_b_connections)
+ f_connections = copy.deepcopy(vt_f_connections)
+ for m_id, module in self.vt_modules.iteritems():
+ if m_id not in b_connections:
+ queue.append((module, 0))
+ # if module.db_id not in f_connections:
+ # sinks.append([set([module])])
+
+ # print >>sys.stderr, 'queue:', queue
+ # topological sort
+ t_sort = []
+ for module, level in queue:
+ t_sort.append((module, level))
+ if module.db_id in f_connections:
+ for (next_id, _) in f_connections[module.db_id]:
+ next_module = self.vt_modules[next_id]
+ if next_module.db_id in b_connections:
+ if len(b_connections[next_module.db_id]) == 0:
+ continue
+ remaining_list = b_connections[next_module.db_id][:]
+ for t in remaining_list:
+ if t[0] == module.db_id:
+ b_connections[next_module.db_id].remove(t)
+ if len(b_connections[next_module.db_id]) == 0:
+ queue.append((next_module, level+1))
+
+ # print >>sys.stderr, [(m.db_name, ell) for (m, ell) in t_sort]
+ levels = {}
+ module_levels = {}
+ for (m, ell) in t_sort:
+ if ell not in levels:
+ levels[ell] = []
+ levels[ell].append(m)
+ module_levels[m.db_id] = ell
+
+ for level, m_list in sorted(levels.iteritems()):
+ for i, m in enumerate(m_list):
+ if i >= len(m_list) - 1:
+ continue
+
+ m_next = m_list[i+1]
+ m_idxs = []
+ m_next_idxs = []
+ if m.db_id not in vt_b_connections:
+ continue
+ if m_next.db_id not in vt_b_connections:
+ continue
+ for (n_id, _) in vt_b_connections[m.db_id]:
+ n = self.vt_modules[n_id]
+ n_idx = levels[module_levels[n_id]].index(n)
+ m_idxs.append(n_idx)
+ for (n_id, _) in vt_b_connections[m_next.db_id]:
+ n = self.vt_modules[n_id]
+ n_idx = levels[module_levels[n_id]].index(n)
+ m_next_idxs.append(n_idx)
+ num_overlaps_f = 0
+ num_overlaps_b = 0
+ for m_idx in m_idxs:
+ for m_next_idx in m_next_idxs:
+ if m_idx == m_next_idx:
+ continue
+ elif m_idx < m_next_idx:
+ num_overlaps_b += 1
+ else:
+ num_overlaps_f += 1
+ if num_overlaps_f > num_overlaps_b:
+ # swap
+ swap = m_list[i]
+ m_list[i] = m_list[i+1]
+ m_list[i+1] = swap
+
+ dx = 250.0
+ dy = 100.0
+ current_y = 0.0
+ for level, m_list in levels.iteritems():
+ current_x = - (len(m_list) * dx) / 2.0
+ for m in m_list:
+ m.db_location.db_x = current_x
+ m.db_location.db_y = current_y
+ current_x += dx
+ current_y += dy
+
+ def get_vtk_cell(self, interactor):
+ found_vtk_cell = False
+ if interactor._name == 'vtkRenderWindowInteractor':
+ found_vtk_cell = False
+ for function in interactor.functions:
+ if function._name == 'SetRenderWindow' and \
+ len(function._args) == 1 and \
+ type(function._args[0]) == vtk_module:
+ # use VTKCell to translate calls
+ function_list = interactor.functions
+ module = function._args[0]
+ found_vtk_cell = True
+ break
+ if found_vtk_cell:
+ return (module, function_list)
+ else:
+ print >>sys.stderr, "ERROR: cannot find VTKCell for Interactor"
+ return (None, None)
+
+ def create_functions(self, module, function_list=None, f_pos=0):
+ # print >>sys.stderr, 'creating functions:', module._name
+# import traceback
+# traceback.print_stack(file=sys.stderr)
+ if module._name == 'vtkRenderWindowInteractor':
+ (module, new_function_list) = self.get_vtk_cell(module)
+ if not module:
+ # punt on it in this case
+ return
+ else:
+ function_list = []
+ for function in new_function_list[:]:
+ if type(function.parent) == vtk_module:
+ function.parent = module
+ if function._name != 'SetRenderWindow':
+ function_list.append(function)
+ if function_list is None:
+ function_list = module.functions
+ for function in function_list:
+ # print >>sys.stderr, ' creating:', function._name
+ db_function = self.create_function(function, f_pos)
+ if db_function:
+ self.modules[id(module)].db_add_function(db_function)
+ f_pos += 1
+ return f_pos
+
+ def find_or_create_module(self, function, allow_sub=True):
+# print >>sys.stderr, 'find_or_create:', function._name, \
+# function.parent._name, id(function)
+ parent_name = function.parent._name
+
+# 'GetPositionCoordinate': {None: ('SetPosition',
+# 'vtkCoordinate')},
+# 'GetPosition2Coordinate': {None: ('SetPosition2',
+# 'vtkCoordinate')}
+# }
+
+ # if we have a getter, than check this stuff
+ if function._name.startswith('Get') and len(function._args) == 0 and \
+ len(function.sub_functions) == 1 and \
+ function.sub_functions[0]._name in self.inspector_functions:
+ # print >>sys.stderr, ">> found inspector function"
+ # print >>sys.stderr, " ", function._name, function.parent._name
+ inspector_name = \
+ self.inspector_functions[function.sub_functions[0]._name]
+ key = (id(function.parent), function._name)
+ # print >>sys.stderr, ' ', key
+
+ out_function = function.sub_functions[0]
+ if key in self.created_modules:
+ inspector_module = self.created_modules[key]
+ else:
+ inspector_module = vtk_module(inspector_name)
+ self.create_module(inspector_module)
+ self.created_modules[key] = inspector_module
+
+ # need to attach first piece of call to inspector input
+ in_function = vtk_function('SetInput')
+ in_function.parent = inspector_module
+ function.sub_functions = []
+ in_function._args = [function]
+ inspector_module.functions.append(in_function)
+ self.create_functions(inspector_module, [in_function])
+ # need to attach rest to inspector output
+ found = False
+ out_function.parent = inspector_module
+ for old_function in inspector_module.functions:
+ if old_function._name == out_function._name and \
+ (len(old_function.sub_functions) == 0 or
+ len(out_function.sub_functions) == 0 or
+ old_function.sub_functions[0]._name == \
+ old_function.sub_functions[0]._name):
+ found = True
+ break
+ if not found:
+ inspector_module.functions.append(out_function)
+ self.create_functions(inspector_module, [out_function])
+ return (inspector_module, True)
+ elif function._name in self.getters and \
+ (function._name not in self.inspector_functions or
+ self.inspector_functions[function._name] != \
+ function.parent._name):
+# and len(function.sub_functions) == 1 \
+# and function.sub_functions[0]._name not in \
+# self.inspector_functions:
+ # print >>sys.stderr, '>>', function._name, 'found in getters'
+ if not allow_sub:
+ print >>sys.stderr, "ERROR: sub function has getter"
+ key = (id(function.parent), function._name)
+ if key in self.created_modules:
+ p_module = self.created_modules[key]
+# print >>sys.stderr, "found in created_modules:", \
+# p_module._name
+ return (p_module, False)
+ if parent_name in self.getters[function._name]:
+ (setter, module_name, function_list) = \
+ self.getters[function._name][parent_name]
+ else:
+ (setter, module_name, function_list) = \
+ self.getters[function._name][None]
+# print >>sys.stderr, 'self.getters:', self.getters[function._name]
+ found_setter = False
+ for p_function in function.parent.functions:
+ if p_function._name == setter:
+ found_setter = True
+ for arg in p_function._args:
+ if type(arg) == vtk_module:
+ p_module = arg
+ else:
+ if arg == function:
+ found_setter = False
+ else:
+ p_module = arg.parent
+ if found_setter and type(p_module) != vtk_module:
+ print >>sys.stderr, "ERROR: type of p_module incorrect"
+ found_setter = False
+ if found_setter:
+ # print >>sys.stderr, "found", module_name, p_module._name
+ self.create_functions(p_module, function.sub_functions)
+ return (p_module, False)
+ if not found_setter:
+ # print >>sys.stderr, "doing create for", module_name
+ p_module = \
+ self.create_module_for_get(function, setter, module_name,
+ function_list)
+ # print >>sys.stderr, id(p_module)
+ return (p_module, False)
+ return (None, False)
+
+ def create_module_for_get(self, function, setter, module_name,
+ function_list=None):
+ # create new vtkProperty module
+ # add connection to parent module on SetProperty call
+ # for sub_function in function.sub_functions:
+ # add each sub_function to the vtkProperty module
+ src_module = None
+ # if len(function.sub_functions) > 0:
+
+ db_module = DBModule(id=self.max_module_id,
+ name=module_name,
+ package=self.package_name,
+ location=DBLocation(id=self.max_location_id,
+ x=0.0, y=0.0),
+ )
+ self.max_module_id += 1
+ self.max_location_id += 1
+ src_module = vtk_module(module_name)
+ self.modules[id(src_module)] = db_module
+ self.vt_modules[db_module.db_id] = db_module
+ self.vtk_modules[id(src_module)] = src_module
+ if function_list:
+ src_functions = []
+ for f in function_list:
+ # doesn't work for functions with args yet
+ src_function = vtk_function(f[0])
+ if len(f) > 1:
+ src_function._args = list(f[1:])
+ src_function.parent = src_module
+ src_functions.append(src_function)
+ # print >>sys.stderr, '**', src_function._name
+ # src_module.functions = src_functions
+ self.create_functions(src_module, src_functions)
+ # print >>sys.stderr, "** done with create"
+
+ # self.vt_f_connections[db_module.db_id] = []
+ # self.vt_b_connections[db_module.db_id] = []
+ self.created_modules[(id(function.parent), function._name)] = \
+ src_module
+ dst_function = vtk_function(setter)
+ dst_function.parent = function.parent
+ self.create_connection(src_module, dst_function)
+
+ return src_module
+
+ def create_tuple(self, function):
+ tuple_module = vtk_module('Tuple')
+ tuple_module.blah()
+ self.create_module(tuple_module)
+ db_tuple_module = self.modules[id(tuple_module)]
+ tuple_f_pos = 0
+ final_sigs = []
+ for i, arg in enumerate(function._args):
+ port_spec = DBPortSpec(id=self.max_port_spec_id,
+ name='arg' + str(i),
+ type='input',
+ sigstring=self.variant_sigstring)
+ db_tuple_module.db_add_portSpec(port_spec)
+ self.max_port_spec_id += 1
+ if type(arg) == vtk_module or \
+ type(arg) == vtk_function:
+ # connection
+ tuple_function = vtk_function('arg' + str(i))
+ tuple_function.parent = tuple_module
+ conn = self.create_connection(arg, tuple_function)
+ port_spec.db_sigstring = \
+ conn.db_ports_type_index['source'].db_signature
+ conn.db_ports_type_index['destination'].db_signature = \
+ port_spec.db_sigstring
+ final_sigs.append(port_spec.db_sigstring[1:-1])
+ else:
+ db_parameters = self.get_parameters([arg])
+ db_function = DBFunction(id=self.max_function_id,
+ name='arg' + str(i),
+ pos=tuple_f_pos,
+ parameters=db_parameters,
+ )
+ self.max_function_id += 1
+ tuple_f_pos += 1
+ db_tuple_module.db_add_function(db_function)
+ port_spec.db_sigstring = \
+ "(" + ','.join(p.db_type for p in db_parameters) + ")"
+ final_sigs.extend(p.db_type for p in db_parameters)
+ final_sigstring = "(" + ",".join(final_sigs) + ")"
+ port_spec = DBPortSpec(id=self.max_port_spec_id,
+ name='value',
+ type='output',
+ sigstring=final_sigstring)
+ db_tuple_module.db_add_portSpec(port_spec)
+ self.max_port_spec_id += 1
+ tuple_output = vtk_function('value')
+ tuple_output.parent = tuple_module
+ self.create_connection(tuple_output, function)
+ return tuple_module
+
+ def get_parameters(self, params):
+ def get_type(arg):
+ python_types = {int: 'edu.utah.sci.vistrails.basic:Integer',
+ str: 'edu.utah.sci.vistrails.basic:String',
+ float: 'edu.utah.sci.vistrails.basic:Float',
+ bool: 'edu.utah.sci.vistrails.basic:Boolean'}
+ if type(arg) not in python_types:
+ return None
+ return python_types[type(arg)]
+ # end get_type
+
+ def create_param(arg, position):
+ p_type = get_type(arg)
+ if p_type:
+ p = DBParameter(id=self.max_parameter_id,
+ type=p_type,
+ val=arg,
+ pos=position,
+ )
+ db_parameters.append(p)
+ self.max_parameter_id += 1
+ position += 1
+ return position
+ # end create_param
+
+ db_parameters = []
+ pos = 0
+ for arg in params:
+ if type(arg) == tuple:
+ for tuple_arg in arg:
+ pos = create_param(tuple_arg, pos)
+ else:
+ pos = create_param(arg, pos)
+ return db_parameters
+ # end get_parameters
+
+
+ def create_function(self, function, f_pos, allow_sub=True):
+
+ # print >>sys.stderr, 'type(function.parent):', type(function.parent)
+ db_function = None
+ (p_module, _) = self.find_or_create_module(function, allow_sub)
+ if p_module:
+ # print >>sys.stderr, 'found p_module', p_module._name, 'for', function._name
+ add_functions = []
+ for sub_function in function.sub_functions:
+ if not sub_function._name.startswith('Get'):
+ # print >>sys.stderr, 'adding function:', sub_function._name
+ add_functions.append(sub_function)
+ self.create_functions(p_module, add_functions,
+ len(self.modules[id(p_module)].db_functions))
+# self.create_functions(p_module, function.sub_functions,
+# len(self.modules[id(p_module)].db_functions))
+ db_function = None
+ else:
+ if function._name in self.unused_functions:
+ return None
+ parameters = []
+ connections = []
+ for arg in function._args:
+ if type(arg) == vtk_module or \
+ type(arg) == vtk_function:
+ connections.append(arg)
+ else:
+ parameters.append(arg)
+
+ if len(function._args) == 0 and \
+ len(function.sub_functions) == 0 and \
+ not function._name.startswith('Get'):
+ parameters.append(None)
+ elif function._name.startswith('Get'):
+ parameters = []
+ connections = []
+# if function._name == 'SetScalarRange' and \
+# len(function._args) == 1:
+# # use a vtkDataSetInspector to get scalar range
+# arg = function._args[0]
+# if type(arg) == vtk_function and \
+# type(arg.parent) == vtk_function and \
+# arg._name == 'GetScalarRange' and \
+# arg.parent._name == 'GetOutput':
+# inspector_module = vtk_module('vtkDataSetInspector')
+# inspector_module.SetInputConnection(
+# arg.parent.parent.GetOutputPort())
+# self.create_module(inspector_module)
+# self.create_functions(inspector_module)
+
+# function._args = (inspector_module.GetScalarRange(),)
+# connections = [function._args[0]]
+# elif function._name == 'GenerateValues' and \
+# len(function._args) == 2:
+# # use a vtkDataSetInspector to get scalar range
+# arg = function._args[0]
+# if type(arg) != int:
+# print >>sys.stderr, \
+# "ERROR: GenerateValues first arg type is incorrect"
+# return None
+# arg = function._args[1]
+# if type(arg) == vtk_function and \
+# type(arg.parent) == vtk_function and \
+# arg._name == 'GetScalarRange' and \
+# arg.parent._name == 'GetOutput':
+# inspector_module = vtk_module('vtkDataSetInspector')
+# inspector_module.SetInputConnection(
+# arg.parent.parent.GetOutputPort())
+# self.create_module(inspector_module)
+# self.create_functions(inspector_module)
+
+# function._args = (function._args[0],
+# inspector_module.GetScalarRange())
+# connections = [function._args[1]]
+# parameters = [function._args[0]]
+ if self.set_file_name_pattern.match(function._name) and \
+ type(function.parent) == vtk_module and \
+ len(function._args) == 1 and \
+ type(function._args[0]) == str:
+ # replace SetFileName with a HTTPFile -> Unzip -> SetFile
+ if not self.http_module:
+ self.http_module = vtk_module('HTTPFile')
+ self.http_module.url(self.vtk_data_url)
+ self.create_module(self.http_module)
+ self.create_functions(self.http_module)
+ unzip_module = vtk_module('Unzip')
+ self.create_module(unzip_module)
+ unzip_module.filename_in_archive(function._args[0][1:])
+ unzip_module.archive_file(self.http_module.file())
+ self.create_functions(unzip_module)
+ set_file_function = vtk_function(function._name[:-4])
+ set_file_function.parent = function.parent
+ set_file_function._args = [unzip_module.file()]
+ self.create_functions(function.parent, [set_file_function])
+ return None
+ if function._name == 'SetInteractor' and \
+ len(function._args) == 1 and \
+ type(function._args[0]) == vtk_module and \
+ type(function.parent) == vtk_module:
+ observer_module = function.parent
+ for a_function in observer_module.functions:
+ # right way to do this is to make SharedData a Tuple
+ if a_function._name == 'AddObserver' and \
+ len(a_function._args) == 2:
+ (vtk_cell, _) = self.get_vtk_cell(function._args[0])
+ handler_module = vtk_module('vtkInteractionHandler')
+ handler_module.Observer(function.parent)
+ self.create_module(handler_module)
+ vtk_cell.InteractionHandler(handler_module)
+ for b_index, b_function in \
+ enumerate(vtk_cell.functions):
+ if b_function._name == 'InteractionHandler':
+ break
+ # probably need to make this position right...
+ self.create_functions(vtk_cell, [b_function],
+ len(self.modules[id(vtk_cell)].db_functions))
+ del vtk_cell.functions[b_index]
+
+ # print >>sys.stderr, a_function._args
+ (event_type, python_function) = a_function._args
+ # print >>sys.stderr, 'AddObserver', event_type, \
+ # 'executing'
+ self.save_modules()
+ python_function(observer_module, None)
+ f = event_type[0].lower() + event_type[1:]
+ f = f.replace('Event', 'Handler')
+ handler_code = 'def %s(observer, shareddata):\n' % f
+ # probably need to order the function calls here
+ # ideally, this would be an abstraction of some sort
+ shared_data = set()
+ for s_module in self.vtk_modules.itervalues():
+ if len(s_module.functions) > 0:
+ if not s_module._name == 'vtkRenderWindow':
+ shared_data.add(s_module)
+ # print >>sys.stderr, s_module._name
+ for s_function in s_module.functions:
+ for s_arg in s_function._args:
+ while type(s_arg) == vtk_function:
+ s_arg = s_arg.parent
+ if type(s_arg) == vtk_module:
+ shared_data.add(s_arg)
+ #print >>sys.stderr, s_arg._name
+
+ s_codelines = []
+ s_arg_map = {}
+ s_arg_idx = 1
+
+ if len(shared_data) < 1 or (len(shared_data) == 1 and \
+ observer_module in \
+ shared_data):
+ handler_code += ' pass\n'
+ else:
+ if len(shared_data) > 2:
+ handler_code += ' ('
+ comma = ','
+ else:
+ handler_code += ' '
+ comma = ''
+ for s_module in shared_data:
+ if s_module != observer_module:
+ handler_code += 'arg' + str(s_arg_idx) + \
+ comma
+ s_arg_map[id(s_module)] = s_arg_idx
+ loop_arg_idx = s_arg_idx
+ s_arg_idx += 1
+ else:
+ loop_arg_idx = 0
+ for s_function in s_module.functions:
+ s_line = (s_function.id, loop_arg_idx,
+ s_function)
+ # print >>sys.stderr, "s_line:", s_line
+ s_codelines.append(s_line)
+ if len(shared_data) > 2:
+ handler_code += ') = shareddata\n'
+ else:
+ handler_code += ' = shareddata\n'
+ # need to assign input module names, then write code
+ s_codelines.sort()
+
+ # need to check to see if an arg...
+ for (_, m_idx, s_function) in s_codelines:
+ s_module_name = 'observer' if m_idx == 0 else \
+ 'arg%d.vtkInstance' % m_idx
+ s_function_str = s_function._name
+ while len(s_function.sub_functions) > 0:
+ if len(s_function.sub_functions) > 1:
+ print >> sys.stderr, \
+ "ERROR: too many subfunctions"
+ # FIXME need to do args here, too
+ s_function_str += '().' + \
+ s_function.sub_functions[0]._name
+ s_function = s_function.sub_functions[0]
+ handler_code += ' %s.%s(' % \
+ (s_module_name, s_function_str)
+
+ s_arg_str = ''
+ for arg in s_function._args:
+ if type(arg) == vtk_module:
+ s_module = arg
+ elif type(arg) == vtk_function:
+ s_module = arg.parent
+ else:
+ s_arg_str += arg + ', '
+ continue
+ m_idx = s_arg_map[id(s_module)]
+ s_module_name = 'observer' if m_idx == 0 \
+ else 'arg%d.vtkInstance' % m_idx
+ if type(arg) == vtk_module:
+ s_arg_str += s_module_name
+ else:
+ s_arg_str += s_module_name + \
+ arg._name + '()'
+ handler_code += s_arg_str + ')\n'
+
+
+ self.restore_modules()
+ # print >>sys.stderr, handler_code
+# s_data_function = vtk_function('SharedData')
+# s_data_function.parent = handler_module
+# s_data_function._args = list(shared_data)
+ shared_data.discard(observer_module)
+ shared_data.discard(handler_module)
+ handler_module.SharedData(*shared_data)
+ handler_module.Handler(urllib.quote(handler_code))
+ # print >> sys.stderr, "shared_data", shared_data
+ # functions.append(s_data_function)
+ self.create_functions(handler_module)
+
+ return None
+ elif len(function.sub_functions) == 1:
+ sub_function = function.sub_functions[0]
+ if function._name == 'GetPositionCoordinate' and \
+ sub_function._name == 'SetValue':
+ # print >>sys.stderr, 'sub_function:', sub_function._args[:2]
+ new_function = vtk_function('SetPosition')
+ new_function._args = sub_function._args[:2]
+ new_function._kwargs = sub_function._kwargs
+ new_function.parent = function.parent
+ function = new_function
+ parameters.extend(new_function._args)
+ elif function._name == 'GetPosition2Coordinate' and \
+ sub_function._name == 'SetValue':
+ # print >>sys.stderr, 'sub_function:', sub_function._args[:2]
+ new_function = vtk_function('SetPosition2')
+ new_function._args = sub_function._args[:2]
+ new_function._kwargs = sub_function._kwargs
+ new_function.parent = function.parent
+ function = new_function
+ parameters.extend(new_function._args)
+
+# # we need to use a Tuple module
+# tuple_module = vtk_module('Tuple')
+# self.create_module(tuple_module)
+# new_arg_list = []
+# for arg in function._args:
+# if type(arg) == vtk_module or \
+# type(arg) == vtk_function:
+# self.create_connection(arg, tuple_module)
+# else:
+# new_arg_list.append(arg)
+# tuple_function = vtk_function(
+# function._args =
+
+ if len(connections) > 0:
+ if len(connections) > 1 or len(parameters) > 0:
+ # need tuple
+ tuple_module = self.create_tuple(function)
+ db_function = None
+ else:
+ if allow_sub:
+ for arg in connections:
+ self.create_connection(arg, function)
+ else:
+ print >>sys.stderr, \
+ "ERROR: sub function has connections"
+ elif len(parameters) > 0:
+ db_parameters = self.get_parameters(parameters)
+ db_function = DBFunction(id=self.max_function_id,
+ name=function._name,
+ pos=f_pos,
+ parameters=db_parameters,
+ )
+ self.max_function_id += 1
+ return db_function
+
+ def create_connection(self, src, dst):
+ convert_type_map = {'input': 'destination', 'output': 'source'}
+ def create_port(vtk_module, type, name, other_vtk_module):
+ # print >>sys.stderr, 'creating port:', vtk_module._name, name
+ if id(vtk_module) not in self.modules:
+ print >>sys.stderr, 'ERROR: cannot create port', \
+ vtk_module._name, type, name
+ import traceback
+ traceback.print_stack()
+ return (None, None)
+
+ db_module = self.modules[id(vtk_module)]
+ db_package = \
+ self.registry.db_packages_identifier_index[db_module.db_package]
+ if db_module.db_namespace is None:
+ db_module.db_namespace = ''
+ d_key = (db_module.db_name, db_module.db_namespace)
+ db_module_desc = db_package.db_module_descriptors_name_index[d_key]
+
+ if name in self.translate_ports:
+ if db_module.db_name in self.translate_ports[name]:
+ name = self.translate_ports[name][db_module.db_name]
+ elif (db_module.db_name,
+ other_vtk_module._name) in self.translate_ports[name]:
+ name = self.translate_ports[name][(db_module.db_name,
+ other_vtk_module._name)]
+ else:
+ name = self.translate_ports[name][None]
+
+ ps_key = (name, type)
+ if ps_key in db_module.db_portSpecs_name_index:
+ db_module_desc = db_module
+ while ps_key not in db_module_desc.db_portSpecs_name_index:
+ base_id = db_module_desc.db_base_descriptor_id
+ if base_id < 0:
+ print >>sys.stderr, 'ERROR: cannot create port', \
+ vtk_module._name, type, name
+ import traceback
+ traceback.print_stack()
+ return (None, None)
+ db_module_desc = self.registry_desc_idx[base_id]
+
+ db_port_spec = db_module_desc.db_portSpecs_name_index[ps_key]
+ db_signature = db_port_spec.db_sigstring
+
+ new_port = DBPort(id=self.max_port_id,
+ type=convert_type_map[type],
+ moduleId=db_module.db_id,
+ moduleName=db_module.db_name,
+ name=name,
+ signature=db_signature,
+ )
+ self.max_port_id += 1
+ return (db_module, new_port)
+ # end create_port
+
+ def find_port_info(entity):
+ if type(entity) == vtk_module:
+ if entity._name == 'vtkRenderWindowInteractor':
+ (entity, _) = self.get_vtk_cell(entity)
+ found_module = entity
+ port_name = 'self'
+ elif type(entity) == vtk_function and \
+ type(entity.parent) == vtk_module:
+ (found_module, inspector) = self.find_or_create_module(entity)
+ if found_module:
+ if inspector:
+ port_name = entity._name
+ else:
+ port_name = 'self'
+ else:
+ found_module = entity.parent
+ port_name = entity._name
+ elif type(entity) == vtk_function and \
+ type(entity.parent) == vtk_function:
+ (found_module, _) = self.find_or_create_module(entity.parent)
+ port_name = entity._name
+ if not found_module:
+ print >>sys.stderr, \
+ "ERROR: cannot convert function", entity._name
+
+# elif type(entity) == vtk_function:
+# found_module = self.find_or_create_module(entity)
+# if found_module:
+# port_name = 'self'
+# else:
+# if type(entity.parent) == vtk_function:
+# found_module = self.find_or_create_module(entity.parent)
+# port_name = entity._name
+# if not found_module:
+# print >>sys.stderr, \
+# "ERROR: cannot convert function", entity._name
+# else:
+# found_module = entity.parent
+# port_name = entity._name
+ else:
+ print >>sys.stderr, 'ERROR: cannot deal with type "' + \
+ str(type(entity))
+ found_module = None
+ port_name = None
+ return (found_module, port_name)
+ # end find_port_info
+
+ src_port = None
+ src_module = None
+ dst_port = None
+ dst_module = None
+
+ # print >> sys.stderr, "creating connection:", src._name, dst._name
+
+ (src_vtk_module, src_port_name) = find_port_info(src)
+ (dst_vtk_module, dst_port_name) = find_port_info(dst)
+ if src_vtk_module and dst_vtk_module:
+ (src_module, src_port) = create_port(src_vtk_module, 'output',
+ src_port_name, dst_vtk_module)
+ (dst_module, dst_port) = create_port(dst_vtk_module, 'input',
+ dst_port_name, src_vtk_module)
+
+# if type(src) == vtk_module:
+# src_vtk_module = src
+# (src_module, src_port) = create_port(src, 'source', 'self',
+# dst.parent)
+# elif type(src) == vtk_function:
+# # print >>sys.stderr, 'src:', src._name, src.parent._name
+# src_vtk_module = self.find_or_create_module(src)
+# if src_vtk_module:
+# print >>sys.stderr, '** found early "%s"' % src._name, src_vtk_module._name
+# print >>sys.stderr, 'src_vtk_module:', src_vtk_module._name
+# src_name = 'self'
+# if not src_vtk_module:
+# if type(src.parent) == vtk_function:
+# src_vtk_module = self.find_or_create_module(src.parent)
+# src_name = src._name
+# print >>sys.stderr, 'found src_vtk_module', src_vtk_module._name, 'for', src.parent._name, src_name
+
+# # print >>sys.stderr, "src_vtk_module:", id(src_vtk_module)
+# if not src_vtk_module:
+# print >>sys.stderr, \
+# "ERROR: cannot convert function", src._name
+# else:
+# src_vtk_module = src.parent
+# src_name = src._name
+# if src_vtk_module:
+# (src_module, src_port) = create_port(src_vtk_module, 'source',
+# src_name, dst.parent)
+# else:
+# print >>sys.stderr, 'ERROR: cannot deal with type "' + \
+# str(type(src)) + '"'
+
+# if type(dst) == vtk_function:
+# (dst_module, dst_port) = create_port(dst.parent, 'destination',
+# dst._name, src_vtk_module)
+# else:
+# print >>sys.stderr, 'ERROR: cannot deal with type "' + \
+# str(type(dst)) + '"'
+
+ if not src_module or not dst_module:
+ print >>sys.stderr, 'ERROR: cannot create connection', \
+ src._name, dst._name
+ return None
+# print >>sys.stderr, 'creating connection:', \
+# src_module.db_name, dst_module.db_name
+ connection = DBConnection(id=self.max_connection_id,
+ ports=[src_port, dst_port],
+ )
+ self.max_connection_id += 1
+ key = (id(src_module), id(dst_module))
+ if key not in self.connections:
+ self.connections[key] = []
+ self.connections[key].append(connection)
+ if src_module.db_id not in self.vt_f_connections:
+ self.vt_f_connections[src_module.db_id] = []
+ self.vt_f_connections[src_module.db_id].append((dst_module.db_id,
+ connection))
+ if dst_module.db_id not in self.vt_b_connections:
+ self.vt_b_connections[dst_module.db_id] = []
+ self.vt_b_connections[dst_module.db_id].append((src_module.db_id,
+ connection))
+ return connection
+
+ def print_vt(self, filename=None):
+ import vistrails.db.services.io
+ import vistrails.db.services.action
+
+ action_list = []
+ for module in self.modules.itervalues():
+ # print 'module:', module._name, id(module)
+ action_list.append(('add', module))
+ for connection_list in self.connections.itervalues():
+ for connection in connection_list:
+ # print 'connection:', connection._name, id(connection)
+ action_list.append(('add', connection))
+ self.do_layout()
+ action = vistrails.db.services.action.create_action(action_list)
+ action.db_id = 1
+ action.db_prevId = 0
+ action.db_user = 'dakoop'
+ action.db_date = datetime.datetime.now()
+
+ tag = DBTag(name='Auto-Translated', id=1L)
+
+ op_id = 0
+ for op in action.db_operations:
+ op.db_id = op_id
+ op_id += 1
+ vistrail = DBVistrail(actions=[action], tags=[tag], version='0.9.0')
+ if filename:
+ # f = file(filename, 'w')
+ script_name = os.path.splitext(filename)[0] + '.py'
+
+ # total hack to make this a capital E
+ script_name = 'E' + script_name[3:]
+ annotation = DBAnnotation(id=1,
+ key='notes',
+ value="This workflow was automatically generated from a modified version of the vtk python example script '%s' from the vtk 5.0.4 distribution. In most cases, running this workflow will generate a visualization that is identical to the result from the example script." % script_name)
+ action.db_add_annotation(annotation)
+
+ vistrails.db.services.io.save_bundle_to_zip_xml(SaveBundle(DBVistrail.vtType, vistrail), filename)
+ else:
+ f = None
+ print >>f, vistrails.db.services.io.serialize(vistrail)
+
diff --git a/scripts/mac_update_bin.sh b/scripts/mac_update_bin.sh
new file mode 100755
index 0000000..0c504a0
--- /dev/null
+++ b/scripts/mac_update_bin.sh
@@ -0,0 +1,88 @@
+#!/bin/bash
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+ROOT_DIR_NAME="vistrails"
+EXAMPLES_DIR_NAME="examples"
+BIN_PATH_25="Contents/Resources/lib/python2.5"
+BIN_PATH_26="Contents/Resources/lib/python2.6"
+BIN_PATH_27="Contents/Resources/lib/python2.7"
+OLD_DIRS="api core db gui packages tests"
+
+if [ -z "$1" ] || [ -z "$2" ]
+then
+ echo "usage: $0 <src_dir> <bin_dir>"
+ exit 65
+fi
+
+if [ -e "$2/$BIN_PATH_27" ]
+then
+ BIN_PATH=$BIN_PATH_27
+elif [ -e "$2/$BIN_PATH_26" ]
+then
+ BIN_PATH=$BIN_PATH_26
+elif [ -e "$2/$BIN_PATH_25" ]
+then
+ BIN_PATH=$BIN_PATH_25
+fi
+
+# remove the old lower-level symlinks if they exist
+for dir in $OLD_DIRS
+do
+ if [ -e "$2/$BIN_PATH/$dir" ]
+ then
+ rm -r $2/$BIN_PATH/$dir
+ fi
+done
+
+if [ -e "$2/$BIN_PATH/$ROOT_DIR_NAME" ]
+then
+ rm -r $2/$BIN_PATH/$ROOT_DIR_NAME
+fi
+ln -s -f -F $1/$ROOT_DIR_NAME $2/$BIN_PATH/$ROOT_DIR_NAME
+
+if [ -e "$2/$BIN_PATH/../../run.py" ]
+then
+ rm $2/$BIN_PATH/../../run.py
+fi
+ln -s -f -F $1/$ROOT_DIR_NAME/run.py $2/$BIN_PATH/../../run.py
+
+if [ -e "$2/../$EXAMPLES_DIR_NAME" ]
+then
+ rm -r $2/../$EXAMPLES_DIR_NAME
+fi
+ln -s -f -F $1/$EXAMPLES_DIR_NAME $2/../$EXAMPLES_DIR_NAME
+
+
+exit 0
diff --git a/scripts/merge_vistrails.py b/scripts/merge_vistrails.py
new file mode 100644
index 0000000..79769e7
--- /dev/null
+++ b/scripts/merge_vistrails.py
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+#FIXME !!! DOES NOT MERGE EXECUTION LOGS STORED IN VT FILE !!!
+
+import sys
+if '../vistrails' not in sys.path:
+ sys.path.append('../vistrails')
+
+import vistrails.db.services.vistrail
+from vistrails.db.domain import DBModule, DBConnection, DBPort, DBFunction, \
+ DBParameter, DBLocation, DBPortSpec, DBTag, DBAnnotation, DBVistrail, \
+ DBAction
+from vistrails.db.services import io
+
+def main(out_fname, in_fnames):
+ """main(out_fname: str, in_fnames: list<str>) -> None
+ Combines all vistrails specified in in_fnames into a single vistrail
+ by renumbering their ids
+
+ """
+ # FIXME this breaks when you use abstractions!
+ (save_bundle, vt_save_dir) = io.open_bundle_from_zip_xml(DBVistrail.vtType, in_fnames[0])
+ for in_fname in in_fnames[1:]:
+ (new_save_bundle, new_save_dir) = io.open_bundle_from_zip_xml(DBVistrail.vtType, in_fname)
+ vistrails.db.services.vistrail.merge(save_bundle, new_save_bundle, "", True, vt_save_dir, new_save_dir)
+ io.save_bundle_to_zip_xml(save_bundle, out_fname)
+
+if __name__ == '__main__':
+ if len(sys.argv) < 3:
+ print "Usage: %s [output filename] [list of input vistrails]" % \
+ sys.argv[0]
+ sys.exit(0)
+ main(sys.argv[1], sys.argv[2:])
diff --git a/scripts/module_appearance/main.py b/scripts/module_appearance/main.py
new file mode 100755
index 0000000..714b18a
--- /dev/null
+++ b/scripts/module_appearance/main.py
@@ -0,0 +1,280 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+##############################################################################
+# create_module_appearance.py helps VisTrails package developers customize
+# the appearance of modules in their packages.
+
+from PyQt4 import QtGui, QtCore, Qt
+from module_appearance import Ui_MainWindow
+import sys
+
+default_pen = QtGui.QPen()
+default_pen.setWidth(2)
+default_pen.setColor(QtCore.Qt.black)
+
+selected_pen = QtGui.QPen()
+selected_pen.setWidth(3)
+selected_pen.setColor(QtCore.Qt.yellow)
+
+##############################################################################
+
+class ModuleFringeJoint(QtGui.QGraphicsEllipseItem):
+
+ brush = QtGui.QBrush(QtGui.QColor(192, 192, 192))
+ def __init__(self, leftLine, rightLine):
+ pt = rightLine.line().p1()
+ sz = 5
+ QtGui.QGraphicsEllipseItem.__init__(self, -sz/2, -sz/2, sz, sz)
+ self.setPos(pt)
+ self.leftLine = leftLine
+ self.rightLine = rightLine
+ self.setAcceptHoverEvents(True)
+ self.setPen(default_pen)
+ self.setBrush(self.brush)
+ self.setZValue(1.0)
+ self.setFlag(QtGui.QGraphicsItem.ItemIsMovable, True)
+ self.setFlag(QtGui.QGraphicsItem.ItemIsFocusable, True)
+
+ def removeSelf(self):
+ scene = self.scene()
+ scene.removeItem(self)
+ scene.removeItem(self.rightLine)
+ self.leftLine.rightJoint = self.rightLine.rightJoint
+ self.leftLine.moveRightPoint(self.rightLine.line().p2())
+ if self.rightLine.rightJoint is not None:
+ self.rightLine.rightJoint.leftLine = self.leftLine
+
+ def mouseMoveEvent(self, event):
+ QtGui.QGraphicsItem.mouseMoveEvent(self, event)
+ self.leftLine.moveRightPoint(self.scenePos())
+ self.rightLine.moveLeftPoint(self.scenePos())
+ app.window.update_text_view()
+
+ def keyPressEvent(self, event):
+ if event.matches(QtGui.QKeySequence.Delete):
+ self.removeSelf()
+
+ def hoverEnterEvent(self, event):
+ self.setPen(selected_pen)
+ self.setFocus(QtCore.Qt.OtherFocusReason)
+
+ def hoverLeaveEvent(self, event):
+ self.setPen(default_pen)
+ self.clearFocus()
+
+ @staticmethod
+ def toScene(pt, side):
+ if side == 'left':
+ raise Exception("unimplemented")
+ elif side == 'right':
+ return QtCore.QPointF(pt[0] * 80.0 + 100.0, pt[1] * 80.0 - 40.0)
+ else:
+ raise Exception("side must be either 'right' or 'left'")
+
+ def toVisTrails(self, side):
+ px, py = self.scenePos().x(), self.scenePos().y()
+ if side == 'left':
+ return ((100.0+px)/80.0, (40.0-py)/80.0)
+ elif side == 'right':
+ return ((px-100.0)/80.0, (40.0-py)/80.0)
+ else:
+ raise Exception("side must be either 'right' or 'left'")
+
+class ModuleFringeLine(QtGui.QGraphicsLineItem):
+
+ def __init__(self, leftJoint, rightJoint, *args, **kwargs):
+ QtGui.QGraphicsLineItem.__init__(self, *args, **kwargs)
+ self.setAcceptHoverEvents(True)
+ self.setPen(default_pen)
+ self.setAcceptedMouseButtons(QtCore.Qt.LeftButton)
+ self.leftJoint = leftJoint
+ self.rightJoint = rightJoint
+ self.setZValue(0.0)
+
+ def mouseDoubleClickEvent(self, event):
+ self.createNewLine(event.pos())
+ app.window.update_text_view()
+
+ def hoverEnterEvent(self, event):
+ self.setPen(selected_pen)
+
+ def hoverLeaveEvent(self, event):
+ self.setPen(default_pen)
+
+ def moveLeftPoint(self, pt):
+ self.setLine(QtCore.QLineF(pt, self.line().p2()))
+
+ def moveRightPoint(self, pt):
+ self.setLine(QtCore.QLineF(self.line().p1(), pt))
+
+ def createNewLine(self, pt):
+ old_line = self.line()
+ self.setLine(QtCore.QLineF(old_line.p1(), pt))
+ new_line = QtCore.QLineF(pt, old_line.p2())
+
+ old_joint = self.rightJoint
+
+ new_fringe_line = ModuleFringeLine(None, self.rightJoint, new_line)
+ new_joint = ModuleFringeJoint(self, new_fringe_line)
+
+ self.rightJoint = new_joint
+ new_fringe_line.leftJoint = new_joint
+ if old_joint is not None:
+ old_joint.leftLine = new_fringe_line
+
+ scene = self.scene()
+ scene.addItem(new_fringe_line)
+ scene.addItem(new_joint)
+ return new_fringe_line
+
+##############################################################################
+
+class MainWindow(QtGui.QMainWindow):
+
+ def __init__(self, parent=None):
+ QtGui.QMainWindow.__init__(self)
+ self.ui = Ui_MainWindow()
+ self.ui.setupUi(self)
+ self.gv = self.ui.graphicsView
+ self.setup_graphics_view()
+ self.connect(self.ui.pushButton_Quit,
+ QtCore.SIGNAL("clicked()"),
+ QtGui.qApp.quit)
+ self.connect(self.ui.pushButton_symmetric,
+ QtCore.SIGNAL("clicked()"),
+ self.make_symmetric)
+ self.connect(self.ui.pushButton_mirrored,
+ QtCore.SIGNAL("clicked()"),
+ self.make_mirrored)
+ self.connect(self.ui.pushButton_Clear,
+ QtCore.SIGNAL("clicked()"),
+ self.clear_points)
+
+ def setup_graphics_view(self):
+ self.scene = QtGui.QGraphicsScene()
+ self.gv.setScene(self.scene)
+ self.gv.setBackgroundBrush(QtCore.Qt.gray)
+ pen = QtGui.QPen()
+ pen.setWidth(2)
+ pen.setColor(QtCore.Qt.black)
+
+ self.scene.addLine(-100,-40,100,-40,pen)
+ self.scene.addLine(-100, 40,100, 40,pen)
+
+ # l1 is the left line
+ self.l1 = ModuleFringeLine(None, None, -100, 40, -100, -40)
+
+ # l2 is the right line
+ self.l2 = ModuleFringeLine(None, None, 100, -40, 100, 40)
+
+ self.scene.addItem(self.l1)
+ self.scene.addItem(self.l2)
+
+ self.update_text_view()
+
+ @staticmethod
+ def get_points(line, side):
+ lst = []
+ while not (line.rightJoint is None):
+ lst.append(line.rightJoint.toVisTrails(side))
+ line = line.rightJoint.rightLine
+ return lst
+
+ def update_text_view(self):
+ s = ''
+ left_list = self.get_points(self.l1, 'left')
+ right_list = self.get_points(self.l2, 'right')
+
+ for (preamble, postamble,
+ side, pts) in zip(['reg.add_module(your_class,\n moduleLeftFringe=[(0.0, 0.0), ',
+ ' moduleRightFringe=[(0.0, 0.0), '],
+ ['(0.0, 1.0)],\n', '(0.0, 1.0)])\n'],
+ ['left', 'right'],
+ [left_list, reversed(right_list)]):
+ f = pts
+ s += preamble
+ for p in pts:
+ s += ('(%.4f, %.4f), ' % p)
+ s += postamble
+ self.ui.textEdit.clear()
+ self.ui.textEdit.append(s)
+
+ ##########################################################################
+ # slots
+
+ def make_symmetric(self):
+ while not (self.l2.rightJoint is None):
+ self.l2.rightJoint.removeSelf()
+ l1 = self.l1
+ l2 = self.l2
+ while not (l1.rightJoint is None):
+ t = l1.rightJoint.toVisTrails('left')
+ t = (-t[0], t[1])
+ p = ModuleFringeJoint.toScene(t, 'right')
+ l2 = l2.createNewLine(p)
+ l1 = l1.rightJoint.rightLine
+ self.update_text_view()
+
+ def make_mirrored(self):
+ while not (self.l2.rightJoint is None):
+ self.l2.rightJoint.removeSelf()
+ l1 = self.l1
+ pl = []
+ while not (l1.rightJoint is None):
+ p = l1.rightJoint.scenePos()
+ pl.append(QtCore.QPointF(-p.x(), p.y()))
+ l1 = l1.rightJoint.rightLine
+ l2 = self.l2
+ for p in reversed(pl):
+ l2 = l2.createNewLine(p)
+ self.update_text_view()
+
+ def clear_points(self):
+ while not (self.l2.rightJoint is None):
+ self.l2.rightJoint.removeSelf()
+ while not (self.l1.rightJoint is None):
+ self.l1.rightJoint.removeSelf()
+ self.update_text_view()
+
+##############################################################################
+
+if __name__ == '__main__':
+ app = QtGui.QApplication(sys.argv)
+ app.window = MainWindow()
+ app.window.show()
+ app.exec_()
+
diff --git a/scripts/module_appearance/module_appearance.py b/scripts/module_appearance/module_appearance.py
new file mode 100644
index 0000000..78fd520
--- /dev/null
+++ b/scripts/module_appearance/module_appearance.py
@@ -0,0 +1,109 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# -*- coding: utf-8 -*-
+
+# Form implementation generated from reading ui file 'module_appearance.ui'
+#
+# Created: Mon Oct 11 20:15:11 2010
+# by: PyQt4 UI code generator 4.7.2
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore, QtGui
+
+class Ui_MainWindow(object):
+ def setupUi(self, MainWindow):
+ MainWindow.setObjectName("MainWindow")
+ MainWindow.resize(819, 602)
+ self.centralwidget = QtGui.QWidget(MainWindow)
+ self.centralwidget.setObjectName("centralwidget")
+ self.verticalLayoutWidget = QtGui.QWidget(self.centralwidget)
+ self.verticalLayoutWidget.setGeometry(QtCore.QRect(0, 0, 811, 551))
+ self.verticalLayoutWidget.setObjectName("verticalLayoutWidget")
+ self.verticalLayout = QtGui.QVBoxLayout(self.verticalLayoutWidget)
+ self.verticalLayout.setObjectName("verticalLayout")
+ self.graphicsView = QtGui.QGraphicsView(self.verticalLayoutWidget)
+ self.graphicsView.setObjectName("graphicsView")
+ self.verticalLayout.addWidget(self.graphicsView)
+ self.horizontalLayout_2 = QtGui.QHBoxLayout()
+ self.horizontalLayout_2.setObjectName("horizontalLayout_2")
+ self.textEdit = QtGui.QTextEdit(self.verticalLayoutWidget)
+ self.textEdit.setObjectName("textEdit")
+ self.horizontalLayout_2.addWidget(self.textEdit)
+ self.textEdit_help = QtGui.QTextEdit(self.verticalLayoutWidget)
+ self.textEdit_help.setObjectName("textEdit_help")
+ self.horizontalLayout_2.addWidget(self.textEdit_help)
+ self.verticalLayout.addLayout(self.horizontalLayout_2)
+ self.horizontalLayout = QtGui.QHBoxLayout()
+ self.horizontalLayout.setObjectName("horizontalLayout")
+ self.pushButton_symmetric = QtGui.QPushButton(self.verticalLayoutWidget)
+ self.pushButton_symmetric.setObjectName("pushButton_symmetric")
+ self.horizontalLayout.addWidget(self.pushButton_symmetric)
+ self.pushButton_mirrored = QtGui.QPushButton(self.verticalLayoutWidget)
+ self.pushButton_mirrored.setObjectName("pushButton_mirrored")
+ self.horizontalLayout.addWidget(self.pushButton_mirrored)
+ self.pushButton_Clear = QtGui.QPushButton(self.verticalLayoutWidget)
+ self.pushButton_Clear.setObjectName("pushButton_Clear")
+ self.horizontalLayout.addWidget(self.pushButton_Clear)
+ spacerItem = QtGui.QSpacerItem(40, 20, QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
+ self.horizontalLayout.addItem(spacerItem)
+ self.pushButton_Quit = QtGui.QPushButton(self.verticalLayoutWidget)
+ self.pushButton_Quit.setObjectName("pushButton_Quit")
+ self.horizontalLayout.addWidget(self.pushButton_Quit)
+ self.verticalLayout.addLayout(self.horizontalLayout)
+ MainWindow.setCentralWidget(self.centralwidget)
+ self.statusbar = QtGui.QStatusBar(MainWindow)
+ self.statusbar.setObjectName("statusbar")
+ MainWindow.setStatusBar(self.statusbar)
+
+ self.retranslateUi(MainWindow)
+ QtCore.QMetaObject.connectSlotsByName(MainWindow)
+
+ def retranslateUi(self, MainWindow):
+ MainWindow.setWindowTitle(QtGui.QApplication.translate("MainWindow", "MainWindow", None, QtGui.QApplication.UnicodeUTF8))
+ self.textEdit_help.setHtml(QtGui.QApplication.translate("MainWindow", "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0//EN\" \"http://www.w3.org/TR/REC-html40/strict.dtd\">\n"
+"<html><head><meta name=\"qrichtext\" content=\"1\" /><style type=\"text/css\">\n"
+"p, li { white-space: pre-wrap; }\n"
+"</style></head><body style=\" font-family:\'Sans\'; font-size:10pt; font-weight:400; font-style:normal;\">\n"
+"<p style=\" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\">To edit the shape, double-click the fringe lines and drag the vertices. To delete the vertices, select them and press "Delete" on your keyboard. </p>\n"
+"<p style=\"-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\"></p>\n"
+"<p style=\" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\">The resulting code snippet can be used to generate a module fringe in VisTrails like the one being displayed.</p>\n"
+"<p style=\"-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\"></p>\n"
+"<p style=\" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\">The buttons "Make rotationally symmetric" and "Make mirrored" use the left side of the module to produce the right side. They <span style=\" font-weight:600;\">will erase</span> the decorations on the right side.</p></body></html>", None, QtGui.QApplication.UnicodeUTF8))
+ self.pushButton_symmetric.setText(QtGui.QApplication.translate("MainWindow", "Make rotationally symmetric", None, QtGui.QApplication.UnicodeUTF8))
+ self.pushButton_mirrored.setText(QtGui.QApplication.translate("MainWindow", "Make mirrored", None, QtGui.QApplication.UnicodeUTF8))
+ self.pushButton_Clear.setText(QtGui.QApplication.translate("MainWindow", "Clear", None, QtGui.QApplication.UnicodeUTF8))
+ self.pushButton_Quit.setText(QtGui.QApplication.translate("MainWindow", "Quit", None, QtGui.QApplication.UnicodeUTF8))
+
diff --git a/scripts/module_appearance/module_appearance.ui b/scripts/module_appearance/module_appearance.ui
new file mode 100644
index 0000000..8ac9b8d
--- /dev/null
+++ b/scripts/module_appearance/module_appearance.ui
@@ -0,0 +1,104 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>MainWindow</class>
+ <widget class="QMainWindow" name="MainWindow">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>819</width>
+ <height>602</height>
+ </rect>
+ </property>
+ <property name="windowTitle">
+ <string>MainWindow</string>
+ </property>
+ <widget class="QWidget" name="centralwidget">
+ <widget class="QWidget" name="verticalLayoutWidget">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>811</width>
+ <height>551</height>
+ </rect>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <widget class="QGraphicsView" name="graphicsView"/>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_2">
+ <item>
+ <widget class="QTextEdit" name="textEdit"/>
+ </item>
+ <item>
+ <widget class="QTextEdit" name="textEdit_help">
+ <property name="html">
+ <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Sans'; font-size:10pt; font-weight:400; font-style:normal;">
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">To edit the shape, double-click the fringe lines and drag the vertices. To delete the vertices, select them and press "Delete" on your keyboard. </p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The resulting code snippet can be used to generate a module fringe in VisTrails like the one being displayed.</p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The buttons "Make rotationally symmetric" and "Make mirrored" use the left side of the module to produce the right side. They <span style=" font-weight:600;">will erase</span> the decorations on the right side.</p></body></html></string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout" stretch="0,0,0,0,0">
+ <item>
+ <widget class="QPushButton" name="pushButton_symmetric">
+ <property name="text">
+ <string>Make rotationally symmetric</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_mirrored">
+ <property name="text">
+ <string>Make mirrored</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_Clear">
+ <property name="text">
+ <string>Clear</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_Quit">
+ <property name="text">
+ <string>Quit</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ </widget>
+ <widget class="QStatusBar" name="statusbar"/>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>
diff --git a/scripts/opm/opm2dot.py b/scripts/opm/opm2dot.py
new file mode 100644
index 0000000..a9de8ae
--- /dev/null
+++ b/scripts/opm/opm2dot.py
@@ -0,0 +1,185 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import os
+import sys
+from xml.etree import cElementTree as ElementTree
+
+def run(filename, account=None):
+ root = ElementTree.parse(filename)
+ node_id = 0
+ lookup = {}
+ error_edges = []
+
+ def should_include(obj):
+ if account is None:
+ return True
+ else:
+ for an_account in obj.getiterator('account'):
+ if an_account.get('id') == account:
+ return True
+ return False
+
+ print 'digraph {'
+ print 'edge [dir = "back", style="dashed"];'
+ for process in root.getiterator('processes').next().getiterator('process'):
+ if not should_include(process):
+ continue
+ process_id = process.get('id')
+ error = None
+ for child in process.getiterator('value').next().getchildren():
+ if child.tag == 'moduleExec':
+ process_label = child.get('moduleName')
+ if child.get('completed') == '-1':
+ error = child.get('error')
+ elif child.tag == 'groupExec':
+ process_label = child.get('groupName')
+ if child.get('completed') == '-1':
+ error = child.get('error')
+ if child.tag == 'groupExec':
+ shape = 'hexagon'
+ elif child.tag == 'moduleExec' and child.get('moduleName') == 'Map':
+ shape = 'hexagon'
+ else:
+ shape = 'box'
+ print '%d [label="%s", shape=%s, color=blue];' % \
+ (node_id, process_label, shape)
+ lookup[process_id] = node_id
+ node_id += 1
+ if error is not None:
+ print '%d [label="ERROR: %s", shape=octagon, color=black];' % (node_id,
+ error)
+ error_edges.append((node_id - 1, node_id))
+ node_id += 1
+
+ for artifact in root.getiterator('artifacts').next().getiterator('artifact'):
+ if not should_include(artifact):
+ continue
+ artifact_id = artifact.get('id')
+ for child in artifact.getiterator('value').next().getchildren():
+ if child.tag == 'portSpec':
+ port_name = str(child.get('name'))
+ # artifact_label = '[' + str(child.get('name')) + ']'
+ spec = str(child.get('sigstring'))
+ if spec:
+ artifact_label = port_name + ' = [' + spec[spec.index(':')+1:spec.index(')')] + ']'
+ else:
+ artifact_label = port_name
+ elif child.tag == 'function':
+ artifact_label = str(child.get('name')) + ' = ('
+ comma = ''
+ for param in child.getiterator('parameter'):
+ param_val = param.get('val')
+ if len(param_val) > 32:
+ if param.get('type') == \
+ 'edu.utah.sci.vistrails.basic:File':
+ print >>sys.stderr, "got here"
+ dir_names = []
+ dir_name = param_val
+ while os.path.split(dir_name)[1]:
+ (dir_name, next_name) = os.path.split(dir_name)
+ dir_names.append(next_name)
+ dir_names.append('/')
+ if len(dir_names) <= 1:
+ param_val = param_val
+ dir_names.reverse()
+ if len(dir_names[-1]) > 28:
+ i = 1
+ j = 1
+ arr = dir_names[-1].split('_')
+ while len('_'.join(arr[:i] + ['...'] + arr[-j:])) < 28:
+ if i == j:
+ i += 1
+ else:
+ j += 1
+ dir_names[-1] = '_'.join(arr[:i] + ['...'] + arr[-j:])
+ print >>sys.stderr, dir_names
+ i = 1
+ while (len(os.path.join(dir_names[0], dir_names[1],
+ '...',
+ *dir_names[-i:])) < 32 and
+ i+1 < len(dir_names)):
+ print >>sys.stderr, \
+ len(os.path.join(dir_names[0],
+ dir_names[1],
+ '...',
+ *dir_names[-i:]))
+ i += 1
+ print >>sys.stderr, i
+ param_val = os.path.join(dir_names[0],
+ dir_names[1], '...',
+ *dir_names[-i:])
+ else:
+ param_val = param_val[:24] + '...' + param_val[-8:]
+ artifact_label += comma + param_val
+ comma = ', '
+ artifact_label += ')'
+ else:
+ print >>sys.stderr, "ERROR:", child.tag
+ artifact_label = artifact.get('id')
+ print '%d [label="%s", color=red];' % (node_id, artifact_label)
+ lookup[artifact_id] = node_id
+ node_id += 1
+ for used in root.getiterator('causalDependencies').next().getiterator('used'):
+ if not should_include(used):
+ continue
+
+ print "%d -> %d;" % \
+ (lookup[used.getiterator('cause').next().get('id')],
+ lookup[used.getiterator('effect').next().get('id')])
+ for wgb in root.getiterator('causalDependencies').next().getiterator('wasGeneratedBy'):
+ if not should_include(wgb):
+ continue
+
+ print "%d -> %d;" % \
+ (lookup[wgb.getiterator('cause').next().get('id')],
+ lookup[wgb.getiterator('effect').next().get('id')])
+ for wtb in root.getiterator('causalDependencies').next().getiterator('wasTriggeredBy'):
+ if not should_include(wtb):
+ continue
+ print "%d -> %d;" % \
+ (lookup[wtb.getiterator('cause').next().get('id')],
+ lookup[wtb.getiterator('effect').next().get('id')])
+
+ for error_edge in error_edges:
+ print "%d -> %d;" % error_edge
+ print "}"
+
+
+if __name__ == '__main__':
+ if len(sys.argv) < 2:
+ print "Usage: python %s <opm_file> [account]" % sys.argv[0]
+ sys.exit(42)
+ account = sys.argv[2] if len(sys.argv) > 2 else None
+ run(sys.argv[1], account)
diff --git a/scripts/release_notes.py b/scripts/release_notes.py
new file mode 100755
index 0000000..35ce651
--- /dev/null
+++ b/scripts/release_notes.py
@@ -0,0 +1,326 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""This will write text of a release notes file based on commit messages and trac
+tickets. Use the configuration section below to tune the start and end commits.
+The text will be written to the standard output.
+"""
+
+import xmlrpclib
+import git
+import getpass
+import os
+import sys
+import re
+import tempfile
+import subprocess
+import shutil
+
+#### configuration ####
+commit_start = "90975fc00211" # hash of version used on last release notes
+commit_end = "HEAD" # current hash
+branch = "v2.1" # git branch to be used
+release_name = "2.1.1"
+clonepath = None # set this to the complete path of a vistrails clone to be used
+ # if None, the remote repository will be cloned to a temporary
+ # folder and removed at the end of the script
+#clonepath = '/Users/tommy/git/vistrails'
+cloneremote = 'git://www.vistrails.org/vistrails.git'
+#### end configuration #####
+
+## The script will ask for your Trac user and password
+## so no need to change this now
+username = None
+password = None
+need_cleanup = False
+
+################################################################################
+def userpass(realm, u, may_save):
+ global username
+ global password
+ if not username:
+ print "Username:",
+ sys.stdout.flush()
+ username = raw_input()
+ password = getpass.getpass()
+ return True, username, password, False
+
+################################################################################
+
+def clone_vistrails_git_repository(path_to):
+ global cloneremote
+ cmdlist = ['git', 'clone', cloneremote,
+ path_to]
+ print "Cloning vistrails from:"
+ print " %s to"%cloneremote
+ print " %s"%path_to
+ print "Be patient. This may take a while."
+ process = subprocess.Popen(cmdlist, shell=False,
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ close_fds=True)
+ process.wait()
+ if process.returncode == 0:
+ print "repository is cloned."
+ return process.returncode
+
+################################################################################
+
+def init_repo():
+ global clonepath, need_cleanup, branch
+ ok = False
+ if clonepath is None:
+ clonepath = tempfile.mkdtemp(prefix="vtrel")
+ try:
+ if clone_vistrails_git_repository(clonepath) == 0:
+ ok = True
+ init_branch(clonepath,branch)
+ need_cleanup = True
+ except Exception, e:
+ print "ERROR: Could not clone vistrails repository!"
+ print str(e)
+ shutil.rmtree(clonepath)
+ sys.exit(1)
+ else:
+ init_branch(clonepath,branch)
+ pull_changes(clonepath)
+ ok = True
+ if ok:
+ repo = git.Repo(clonepath)
+ return repo
+ else:
+ print "ERROR: git clone failed."
+ sys.exit(1)
+
+################################################################################
+
+def cleanup_repo():
+ global clonepath, need_cleanup
+ if need_cleanup:
+ shutil.rmtree(clonepath)
+
+################################################################################
+
+def init_branch(path_to, branch):
+ cmdlist = ['git', 'checkout', "%s"%branch]
+ print "Checking out %s branch..."%branch
+ current_dir = os.getcwd()
+ os.chdir(path_to)
+ process = subprocess.Popen(cmdlist, shell=False,
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ close_fds=True)
+ process.wait()
+ lines = process.stdout.readlines()
+ for line in lines:
+ print " ", line
+ if process.returncode == 0:
+ print "Branch %s was checked out."%branch
+ os.chdir(current_dir)
+ return process.returncode
+
+################################################################################
+
+def pull_changes(path_to):
+ cmdlist = ['git', 'pull']
+ print "Pulling changes into the branch..."
+ current_dir = os.getcwd()
+ os.chdir(path_to)
+ process = subprocess.Popen(cmdlist, shell=False,
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ close_fds=True)
+ process.wait()
+ lines = process.stdout.readlines()
+ for line in lines:
+ print " ", line
+ if process.returncode == 0:
+ print "Changes were pulled."
+ os.chdir(current_dir)
+ return process.returncode
+
+################################################################################
+
+def checkout_branch(repo, branch):
+ repobranch = getattr(repo.heads, branch)
+ repobranch.checkout()
+
+##############################################################################
+
+def build_release_notes(repo, branch):
+ global username
+ global password
+ global commit_start, commit_end
+
+ def check_inside_skip(skip_list, message):
+ found = False
+ for s in skip_list:
+ if s.find(message) != -1:
+ found = True
+ break
+ return found
+
+ re_ticket_old = re.compile(r'<ticket>(.*?)</ticket>', re.M | re.S)
+ re_ticket = re.compile(r'^Ticket: (.*?)$', re.M | re.S)
+ re_bugfix_old = re.compile(r'<bugfix>(.*?)</bugfix>', re.M | re.S)
+ re_bugfix = re.compile(r'^Bugfix: (.*?)$', re.M | re.S)
+ re_feature_old = re.compile(r'<feature>(.*?)</feature>', re.M | re.S)
+ re_feature = re.compile(r'^Feature:(.*?)$', re.M | re.S)
+ re_skip = re.compile(r'<skip>(.*?)</skip>', re.M | re.S)
+
+ #build list and dictionary with commits
+ logs = []
+ log_map_time = {}
+ checkout_branch(repo,branch)
+ for c in repo.iter_commits("%s..%s"%(commit_start,commit_end)):
+ logs.append(c)
+ log_map_time[c.hexsha] = c.committed_date
+
+ #populate dictionaries
+ bugfixes = {}
+ tickets = {}
+ features = {}
+ changes = {}
+ ticket_info = {}
+
+ for log in logs:
+ ls = re_skip.findall(log.message)
+ lf = re_feature.findall(log.message)
+ lf.extend(re_feature_old.findall(log.message))
+ lt = re_ticket.findall(log.message)
+ lt.extend(re_ticket_old.findall(log.message))
+ lb = re_bugfix.findall(log.message)
+ lb.extend(re_ticket_old.findall(log.message))
+ for s in ls:
+ changes[s.strip()] = log.hexsha
+ for f in lf:
+ features[f.strip()] = log.hexsha
+ for t in lt:
+ # handle tickets with # (should not be used)
+ t = t.strip()
+ if t.startswith('#'):
+ t = t[1:]
+ try:
+ tickets[int(t)] = log.hexsha
+ except ValueError:
+ pass
+ for b in lb:
+ bugfixes[b.strip()] = log.hexsha
+ if len(ls) == 0 and len(lf) == 0 and len(lt) == 0 and len(lb) == 0:
+ changes[log.message] = log.hexsha
+
+
+ #get ticket summaries from xmlrpc plugin installed on vistrails trac
+ print "Will connect to VisTrails Trac with authentication..."
+ if not username:
+ print "Username:",
+ sys.stdout.flush()
+ username = raw_input()
+ password = getpass.getpass()
+
+ url = "https://%s:%s@www.vistrails.org/login/xmlrpc"%(username,
+ password)
+ server = xmlrpclib.ServerProxy(url)
+ print "downloading tickets.",
+ for (tid,r) in tickets.iteritems():
+ print ".",
+ sys.stdout.flush()
+ try:
+ ticket_info[tid] = server.ticket.get(tid)
+ except Exception, e:
+ tickets.remove(tid)
+ print "commit %s: Could not get info for ticket %s"%(r,tid)
+ print "done."
+
+ #place tickets on bugfixes or enhancements
+ for (tid,r) in tickets.iteritems():
+ txt = "Ticket %s: %s"%(tid,ticket_info[tid][3]['summary'])
+ if ticket_info[tid][3]['type'] == 'enhancement':
+ features[txt] = r
+ elif ticket_info[tid][3]['type'] in ['defect', 'defect+question']:
+ bugfixes[txt] = r
+ else:
+ #put the rest as changes
+ changes[txt] = r
+ if commit_end == "HEAD" and len(logs) > 0:
+ commit_end = logs[0].hexsha
+
+ print
+ print
+ print "Release Name: v%s build %s from %s branch" % (release_name,
+ commit_end[0:12],
+ branch)
+ print
+ print "Enhancements: "
+ times = []
+ for t, r in features.iteritems():
+ times.append((log_map_time[r], t))
+ revisions = sorted(times)
+ revisions.reverse()
+ for (t,text) in revisions:
+ r = features[text]
+ print " - %s (%s)" %(text,r[0:12])
+
+ print
+ print "Bug fixes: "
+ times = []
+ for t, r in bugfixes.iteritems():
+ times.append((log_map_time[r], t))
+ revisions = sorted(times)
+ revisions.reverse()
+ for (t,text) in revisions:
+ r = bugfixes[text]
+ print " - %s (%s)" %(text,r[0:12])
+
+ print
+ print "Other changes: "
+ times = []
+ for t, r in changes.iteritems():
+ times.append((log_map_time[r], t))
+ revisions = sorted(times)
+ revisions.reverse()
+ for (t,text) in revisions:
+ r = changes[text]
+ print " - %s (%s)" %(text.split('\n')[0][0:100],r[0:12])
+
+if __name__ == "__main__":
+ repo = init_repo()
+ build_release_notes(repo, branch)
+ cleanup_repo()
+
+
diff --git a/scripts/restart-vistrails-server.sh b/scripts/restart-vistrails-server.sh
new file mode 100755
index 0000000..a9b1a41
--- /dev/null
+++ b/scripts/restart-vistrails-server.sh
@@ -0,0 +1,40 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+crondir=`pwd`
+export DISPLAY=localhost:1.0
+vistrails_dir="/server/wiki/vistrails/main/vistrails/v1.2/vistrails"
+cd $vistrails_dir
+python stop_vistrails_server.py http://vistrails.sci.utah.edu:8080
+nohup python vistrails_server.py -T vistrails.sci.utah.edu -R 8080&
\ No newline at end of file
diff --git a/scripts/run_vistrails_batch_xvfb.sh b/scripts/run_vistrails_batch_xvfb.sh
new file mode 100755
index 0000000..2c6b79f
--- /dev/null
+++ b/scripts/run_vistrails_batch_xvfb.sh
@@ -0,0 +1,83 @@
+#!/bin/bash
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+#settings
+LOG_DIR=/server/vistrails/logs
+Xvfb_CMD=/usr/bin/Xvfb
+VIRTUAL_DISPLAY=":6"
+VISTRAILS_DIR=/server/vistrails/source
+VT_FILE=""
+WORKFLOW=""
+if (("$#" > "0")); then
+ VIRTUAL_DISPLAY="$1"
+fi
+if (("$#" > "1")); then
+ VT_FILE="$2"
+fi
+if (("$#" > "2")); then
+ WORKFLOW="$3"
+fi
+Xvfb_PARAM="$VIRTUAL_DISPLAY -screen 0 1280x960x24"
+LOG_XVFB="$LOG_DIR/xvfb$VIRTUAL_DISPLAY.log"
+
+#try to find Process ID of running X-Server
+echo "checking if Xvfb is already running..."
+echo "ps -eaf | grep $Xvfb_CMD | grep $VIRTUAL_DISPLAY | awk '{print \$2}'"
+pid=`ps -eaf | grep $Xvfb_CMD | grep $VIRTUAL_DISPLAY | awk '{print \$2}'`
+if [ "$pid" ]; then
+ echo "Xvfb already running [pid=${pid}]"
+else
+ #start a virtual server
+ if [ -x $Xvfb_CMD ]; then
+ $Xvfb_CMD $Xvfb_PARAM>& $LOG_XVFB &
+
+ sleep 5
+
+ #Make sure it started
+ pid=`ps -eaf | grep $Xvfb_CMD | grep $VIRTUAL_DISPLAY | awk '{print $2}'`
+ if [ "$pid" ]; then
+ echo "done."
+ else
+ echo "FAILED."
+ fi
+ else
+ echo "Error: Could not find $Xvfb_CMD. Cannot start Xvfb."
+ fi
+fi
+echo -n "Executing VisTrails on display $VIRTUAL_DISPLAY.0 - "
+cd $VISTRAILS_DIR
+export DISPLAY=$VIRTUAL_DISPLAY
+python vistrails/run.py -b $VT_FILE:$WORKFLOW
+
diff --git a/scripts/sql_delete.py b/scripts/sql_delete.py
new file mode 100644
index 0000000..15090b0
--- /dev/null
+++ b/scripts/sql_delete.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import sys
+if '/vistrails/src/trunk/vistrails' not in sys.path:
+ sys.path.append('/vistrails/src/trunk/vistrails')
+import vistrails.db.services.io
+import urlparse
+import getpass
+
+def run(url, type, id):
+ scheme, rest = url.split('://', 1)
+ url = 'http://' + rest
+ (_, net_loc, db_name, args_str, _) = urlparse.urlsplit(url)
+ db_name = db_name[1:]
+ net_loc_arr = net_loc.split('@',1)
+ if len(net_loc_arr) > 1:
+ user, rest = net_loc_arr
+ else:
+ user = 'root'
+ rest = net_loc_arr[0]
+
+ host_port_arr = rest.split(':', 1)
+ if len(host_port_arr) > 1:
+ host, port = host_port_arr
+ else:
+ host = host_port_arr[0]
+ port = '3306'
+
+ config = {'host': host, 'port': int(port),
+ 'user': user, 'db': db_name}
+ print config
+ try:
+ conn = vistrails.db.services.io.open_db_connection(config)
+ except Exception:
+ passwd = getpass.getpass()
+ config['passwd'] = passwd
+ conn = vistrails.db.services.io.open_db_connection(config)
+
+ vistrails.db.services.io.delete_from_db(conn, type, id)
+
+if __name__ == '__main__':
+ if len(sys.argv) < 4:
+ print "Usage: %s %s <db_connection_str> <type> <id>" % \
+ (sys.executable, sys.argv[0])
+ print " <db_connection_str> := [<user>@]<host>[:<port>]/<db>"
+ print " Password prompt displayed if required"
+ sys.exit(61)
+ run(*sys.argv[1:])
diff --git a/scripts/sql_to_xml.py b/scripts/sql_to_xml.py
new file mode 100644
index 0000000..14ecdf0
--- /dev/null
+++ b/scripts/sql_to_xml.py
@@ -0,0 +1,55 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import sys
+sys.path.append('/vistrails/src/trunk/vistrails')
+from vistrails.db.services import io
+import MySQLdb
+
+def convert_sql_to_xml(filename, id):
+ config = {'host': 'vistrails.sci.utah.edu',
+ 'port': 3306,
+ 'user': 'vistrails',
+ 'passwd': '8edLj4',
+ 'db': 'vistrails'}
+ try:
+ db_connection = io.open_db_connection(config)
+ vistrail = io.open_vistrail_from_db(db_connection, id)
+ io.save_vistrail_to_xml(vistrail, filename)
+ io.close_db_connection(db_connection)
+ except MySQLdb.Error, e:
+ print e
+
+if __name__ == '__main__':
+ convert_sql_to_xml('/tmp/vt_from_db.xml', 4)
diff --git a/scripts/start_vistrails.sh b/scripts/start_vistrails.sh
new file mode 100755
index 0000000..86123f3
--- /dev/null
+++ b/scripts/start_vistrails.sh
@@ -0,0 +1,82 @@
+#!/bin/bash
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+#settings
+LOG_DIR=/server/vistrails/logs
+
+VISTRAILS_DIR=/server/vistrails/trunk/vistrails
+ADDRESS="crowdlabs.sci.utah.edu"
+PORT="8081"
+CONF_FILE="server.cfg"
+NUMBER_OF_OTHER_VISTRAILS_INSTANCES="2"
+MULTI_OPTION="-M"
+if (("$#" > "0")); then
+ VIRTUAL_DISPLAY="$1"
+fi
+if (("$#" > "1")); then
+ ADDRESS="$2"
+fi
+if (("$#" > "2")); then
+ PORT="$3"
+fi
+if (("$#" > "3")); then
+ NUMBER_OF_OTHER_VISTRAILS_INSTANCES="$4"
+fi
+if (("$#" == "5")); then
+ if(("$5" == "0")); then
+ MULTI_OPTION=""
+ else
+ MULTI_OPTION="-M"
+ fi
+fi
+
+PID="$LOG_DIR/pid.$PORT.vistrails"
+
+echo -n "Starting VisTrails in Server Mode on display :0 - "
+cd $VISTRAILS_DIR
+export DISPLAY=:0
+python stop_vistrails_server.py http://$ADDRESS:$PORT
+sleep 5
+#try again because sometimes it doesn't quit
+python stop_vistrails_server.py http://$ADDRESS:$PORT
+
+#finally kill it if it still did not respond because it was hanging
+kill -9 `cat $PID`
+
+export PYTHONPATH=/home/emanuele/src/titan/build/lib:$PYTHONPATH
+export LD_LIBRARY_PATH=/home/emanuele/src/titan/build/lib:$LD_LIBRARY_PATH
+python vistrails_server.py -T $ADDRESS -R $PORT -C $CONF_FILE -O$NUMBER_OF_OTHER_VISTRAILS_INSTANCES $MULTI_OPTION&
+echo $! > $PID
+
diff --git a/scripts/start_vistrails_xvfb.sh b/scripts/start_vistrails_xvfb.sh
new file mode 100755
index 0000000..e57d256
--- /dev/null
+++ b/scripts/start_vistrails_xvfb.sh
@@ -0,0 +1,109 @@
+#!/bin/bash
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+#settings
+LOG_DIR=/server/vistrails/logs
+Xvfb_CMD=/usr/bin/Xvfb
+VIRTUAL_DISPLAY=":6"
+VISTRAILS_DIR=/server/vistrails/git/vistrails
+ADDRESS="vis-7.sci.utah.edu"
+PORT="8081"
+CONF_FILE="server.cfg"
+NUMBER_OF_OTHER_VISTRAILS_INSTANCES="1"
+MULTI_OPTION="-M"
+if (("$#" > "0")); then
+ VIRTUAL_DISPLAY="$1"
+fi
+if (("$#" > "1")); then
+ ADDRESS="$2"
+fi
+if (("$#" > "2")); then
+ PORT="$3"
+fi
+if (("$#" > "3")); then
+ NUMBER_OF_OTHER_VISTRAILS_INSTANCES="$4"
+fi
+if (("$#" == "5")); then
+ if(("$5" == "0")); then
+ MULTI_OPTION=""
+ else
+ MULTI_OPTION="-M"
+ fi
+fi
+
+Xvfb_PARAM="$VIRTUAL_DISPLAY -screen 0 1280x960x24"
+PID="$LOG_DIR/pid.$PORT.vistrails"
+LOG_XVFB="$LOG_DIR/xvfb$VIRTUAL_DISPLAY.log"
+
+#try to find Process ID of running X-Server
+echo "checking if Xvfb is already running..."
+echo "ps -eaf | grep $Xvfb_CMD | grep $VIRTUAL_DISPLAY | awk '{print \$2}'"
+pid=`ps -eaf | grep $Xvfb_CMD | grep $VIRTUAL_DISPLAY | awk '{print \$2}'`
+if [ "$pid" ]; then
+ echo "Xvfb already running [pid=${pid}]"
+else
+ #start a virtual server
+ if [ -x $Xvfb_CMD ]; then
+ $Xvfb_CMD $Xvfb_PARAM>& $LOG_XVFB &
+
+ sleep 5
+
+ #Make sure it started
+ pid=`ps -eaf | grep $Xvfb_CMD | grep $VIRTUAL_DISPLAY | awk '{print $2}'`
+ if [ "$pid" ]; then
+ echo "done."
+ else
+ echo "FAILED."
+ fi
+ else
+ echo "Error: Could not find $Xvfb_CMD. Cannot start Xvfb."
+ fi
+fi
+echo -n "Starting VisTrails in Server Mode on display $VIRTUAL_DISPLAY.0 - "
+cd $VISTRAILS_DIR
+export DISPLAY=$VIRTUAL_DISPLAY
+python stop_vistrails_server.py http://$ADDRESS:$PORT
+#give some time for quitting
+sleep 5
+#try again because sometimes it doesn't quit
+python stop_vistrails_server.py http://$ADDRESS:$PORT
+sleep 5
+
+#finally kill it if it still did not respond because it was hanging
+kill -9 `cat $PID`
+
+python vistrails_server.py -T $ADDRESS -R $PORT -C $CONF_FILE -O$NUMBER_OF_OTHER_VISTRAILS_INSTANCES $MULTI_OPTION&
+echo $! > $PID
+
diff --git a/scripts/system_info.py b/scripts/system_info.py
new file mode 100755
index 0000000..74c554b
--- /dev/null
+++ b/scripts/system_info.py
@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# Basic information
+
+import sys
+import platform
+
+print "Python:"
+print " Basic version: %s.%s.%s" % (sys.version_info[0],
+ sys.version_info[1],
+ sys.version_info[2], )
+print " Full version: " + sys.version.replace('\n', ' ')
+print
+
+def c(s):
+ return s or "<COULD NOT DETERMINE>"
+
+print "System:"
+print " Type: " + c(platform.system())
+print " Architecture: " + c(platform.architecture()[0])
+print " Machine: " + c(platform.machine())
+print " Platform: " + c(platform.platform())
+print " Processor: " + c(platform.processor())
+print
+
+##############################################################################
+
+print "Libraries:"
+
+try:
+ import sip
+ print " sip installed."
+ print " version: " + sip.SIP_VERSION_STR
+except ImportError:
+ print " sip NOT installed."
+print
+
+try:
+ import PyQt4.Qt
+ print " PyQt installed."
+ print " Qt version: " + PyQt4.Qt.QT_VERSION_STR
+ print " PyQt version: " + PyQt4.Qt.PYQT_VERSION_STR
+except ImportError:
+ print " PyQt NOT installed."
+print
+
+try:
+ import vtk
+ print " VTK installed."
+ print " VTK short version: " + vtk.vtkVersion().GetVTKVersion()
+ print " VTK full version: " + vtk.vtkVersion().GetVTKSourceVersion()
+except ImportError:
+ print " VTK NOT installed."
diff --git a/scripts/unzip_vistrail.sh b/scripts/unzip_vistrail.sh
new file mode 100755
index 0000000..8df1878
--- /dev/null
+++ b/scripts/unzip_vistrail.sh
@@ -0,0 +1,42 @@
+#!/bin/bash
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+mkdir $2
+zipfile=`basename $1 .vt`.zip
+cp $1 $2/$zipfile
+pushd $2
+unzip $zipfile
+xmlpp.pl vistrail >vistrail_pp
+popd
diff --git a/scripts/update_copyright_year.py b/scripts/update_copyright_year.py
new file mode 100644
index 0000000..e770b6b
--- /dev/null
+++ b/scripts/update_copyright_year.py
@@ -0,0 +1,73 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# Finds all .py files recursively in current directory (.)
+# and updates 2007 year with 2008 in the file header.
+import re
+import os
+new_copyright = ["## Copyright (C) 2011-2014, NYU-Poly.\n"]
+
+re_copyright = re.compile(r"\s+## Copyright \(C\) 2011-2014, NYU-Poly\.\s+")
+line_copyright = re.compile(r"## Copyright \(C\) 2011-2014, NYU-Poly\.")
+IGNORE_LIST = ["update_copyright_year.py"]
+files = []
+for (path, dnames, fnames) in os.walk('.'):
+ for fn in fnames:
+ if fn not in IGNORE_LIST and fn.endswith(".py"):
+ files.append(os.path.join(path, fn))
+
+print len(files), " files found"
+count = 0
+for fname in files:
+ fin = open(fname)
+ lines = fin.readlines()
+ fin.seek(0)
+ all_lines = fin.read()
+ fin.close()
+ if re_copyright.search(all_lines) > 0:
+ #Search through the first lines because sometimes it's not exactly in the second line:
+ for i in [2,3,4,5]:
+ if line_copyright.search(lines[i]) > 0:
+ print "Updating: %s"%fname
+ newlines = lines[:i]
+ newlines.extend(new_copyright)
+ cropped = lines[i+1:] #Replace by i+1 when it is to update just the year.
+ newlines.extend(cropped)
+ fout = file(fname, 'w')
+ fout.writelines(newlines)
+ fout.close()
+ count += 1
+ break
+
+print count, " files updated"
diff --git a/scripts/update_db.py b/scripts/update_db.py
new file mode 100644
index 0000000..81c7acb
--- /dev/null
+++ b/scripts/update_db.py
@@ -0,0 +1,115 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import os
+import sys
+import tempfile
+sys.path.append(os.path.join(os.path.dirname(os.path.dirname(
+ os.path.abspath(__file__))), 'vistrails'))
+from vistrails.db.services import io
+from vistrails.db.versions import currentVersion
+from db_utils import parse_db_cmd_line
+
+# DO NOT RUN THIS WHILE USERS HAVE ACCESS TO THE DATABASE!
+def update_db(config, new_version=None, tmp_dir=None, restore=False):
+ obj_types = {'vistrail': io.open_bundle_from_db,
+ # 'workflow': io.open_from_db,
+ # 'log': io.open_from_db,
+ # 'registry': io.open_from_db
+ }
+ if new_version is None:
+ new_version = currentVersion
+ if tmp_dir is None:
+ tmp_dir = tempfile.mkdtemp(prefix='vt_db')
+ print 'creating tmpdir:', tmp_dir
+
+ db_connection = io.open_db_connection(config)
+ obj_id_lists = {}
+ filenames = []
+ if restore:
+ for dirpath, dirname, files in os.walk(restore):
+ for fname in files:
+ if fname.endswith('.vt'):
+ filenames.append(os.path.join(restore, fname))
+ else:
+ for obj_type in obj_types:
+ obj_id_lists[obj_type] = io.get_db_object_list(config, obj_type)
+
+ # read data out of database
+ thumbnail_dir = os.path.join(tmp_dir, 'thumbs')
+ os.mkdir(thumbnail_dir)
+ for obj_type, obj_ids in obj_id_lists.iteritems():
+ for (obj_id, _, _) in obj_ids:
+ old_version = io.get_db_object_version(db_connection, obj_id,
+ 'vistrail')
+
+ print 'getting', obj_type, 'id', obj_id
+ local_tmp_dir = os.path.join(tmp_dir, str(obj_id))
+ vt_name = os.path.join(tmp_dir, str(obj_id) + '.vt')
+ filenames.append(vt_name)
+ os.mkdir(local_tmp_dir)
+ res = obj_types[obj_type](obj_type, db_connection, obj_id,
+ thumbnail_dir)
+ io.save_vistrail_bundle_to_zip_xml(res, vt_name, local_tmp_dir)
+
+ # drop the old database
+ # recreate with the new version of the specs
+ io.setup_db_tables(db_connection, None, old_version)
+
+ # add the new data back
+ for filename in filenames:
+ (res, _) = io.open_vistrail_bundle_from_zip_xml(filename)
+ try:
+ io.save_vistrail_bundle_to_db(res, db_connection, 'with_ids')
+ except Exception, e:
+ import traceback
+ print filename, e, traceback.format_exc()
+ io.close_db_connection(db_connection)
+
+if __name__ == '__main__':
+ import vistrails.core.application
+
+ more_options = {'v:': ('set new schema version', False, 'version'),
+ 'd:': ('set temporary directory', False, 'directory'),
+ 'e:': ('restore from directory', False, 'restore')
+ }
+ config, options = parse_db_cmd_line(sys.argv, more_options)
+ new_version = None
+ if options['v']:
+ new_version = options['v']
+
+ vistrails.core.application.init()
+
+ update_db(config, new_version, options['d'], options['e'])
diff --git a/scripts/update_email_contact.py b/scripts/update_email_contact.py
new file mode 100644
index 0000000..d9d8dc1
--- /dev/null
+++ b/scripts/update_email_contact.py
@@ -0,0 +1,37 @@
+# Finds all files matching extensions recursively in current directory (.)
+# and updates tthe contact e-mail address
+
+import re
+import os
+
+OLD_EMAIL = "Copyright (C) 2011-2012, NYU-Poly"
+NEW_EMAIL = "Copyright (C) 2011-2014, NYU-Poly"
+EXTENSIONS = [".py", ".xml", ".xsd", ".php", ".sql", ".sh", ".rst", ".tex",
+ ".txt", "LICENSE", ".iss", ".sty", ".mako"]
+IGNORE_LIST = ["update_email_contact.py"]
+
+files = []
+for (path, dnames, fnames) in os.walk('.'):
+ for fn in fnames:
+ for ext in EXTENSIONS:
+ if fn.endswith(ext) and fn not in IGNORE_LIST:
+ files.append(os.path.join(path, fn))
+ break
+
+print len(files), " files will be processed."
+
+count = 0
+for fname in files:
+ fin = open(fname)
+ all_lines = fin.read()
+ fin.close()
+ pos = all_lines.find(OLD_EMAIL)
+ if pos > -1:
+ print "Updating: %s"%fname
+ newlines = all_lines.replace(OLD_EMAIL, NEW_EMAIL)
+ fout = file(fname, 'w')
+ fout.write(newlines)
+ fout.close()
+ count += 1
+print count, " files updated "
+
\ No newline at end of file
diff --git a/scripts/update_hash.py b/scripts/update_hash.py
new file mode 100755
index 0000000..f3616f3
--- /dev/null
+++ b/scripts/update_hash.py
@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+
+import glob
+import sys
+
+if len(sys.argv)<3:
+ print "Usage: ./update_hash.py old_hash new_hash"
+ sys.exit(-1)
+
+files = ["release_notes.py",
+ "create_release_wiki_table.py",
+ "../vistrails/core/system/__init__.py",
+ "../dist/mac/Input/README",
+ "../dist/windows/Input/releaseNotes.txt",
+ "../dist/source/make-vistrails-src-release.py",
+ "../doc/usersguide/conf.py"]
+
+for path in files:
+ for f in glob.glob(path):
+ print "Updating", f
+
+ file = open(f)
+ text = file.read()
+ file.close()
+
+ text = text.replace(sys.argv[1], sys.argv[2])
+
+ file = open(f, "w")
+ file.write(text)
+ file.close()
diff --git a/scripts/update_to_mod_bsd_license.py b/scripts/update_to_mod_bsd_license.py
new file mode 100644
index 0000000..8c53cd3
--- /dev/null
+++ b/scripts/update_to_mod_bsd_license.py
@@ -0,0 +1,292 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# Finds all .py files recursively in current directory (.)
+# and updates to modified BSD license in the file header.
+import re
+import os
+py_bsd_3_license = """###############################################################################
+##
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""
+xml_bsd_3_license = "<!--"+ py_bsd_3_license + "-->"
+php_bsd_3_license = """////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (C) 2006-2011, University of Utah.
+// All rights reserved.
+// Contact: contact at vistrails.org
+//
+// This file is part of VisTrails.
+//
+// "Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// - Redistributions of source code must retain the above copyright notice,
+// this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// - Neither the name of the University of Utah nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+// THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+//
+////////////////////////////////////////////////////////////////////////////"""
+sql_bsd_3_license = """--#############################################################################
+--
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################"""
+py_old_license = """############################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+############################################################################
+"""
+sql_old_license = """--#########################################################################
+--
+-- Copyright (C) 2006-2010 University of Utah. All rights reserved.
+--
+-- This file is part of VisTrails.
+--
+-- This file may be used under the terms of the GNU General Public
+-- License version 2.0 as published by the Free Software Foundation
+-- and appearing in the file LICENSE.GPL included in the packaging of
+-- this file. Please review the following to ensure GNU General Public
+-- Licensing requirements will be met:
+-- http://www.opensource.org/licenses/gpl-license.php
+--
+-- If you are unsure which license is appropriate for your use (for
+-- instance, you are interested in developing a commercial derivative
+-- of VisTrails), please contact us at contact at vistrails.org.
+--
+-- This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+-- WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+--
+--##########################################################################"""
+xml_old_license = """<!--########################################################################
+##
+## Copyright (C) 2006-2010 University of Utah. All rights reserved.
+##
+## This file is part of VisTrails.
+##
+## This file may be used under the terms of the GNU General Public
+## License version 2.0 as published by the Free Software Foundation
+## and appearing in the file LICENSE.GPL included in the packaging of
+## this file. Please review the following to ensure GNU General Public
+## Licensing requirements will be met:
+## http://www.opensource.org/licenses/gpl-license.php
+##
+## If you are unsure which license is appropriate for your use (for
+## instance, you are interested in developing a commercial derivative
+## of VisTrails), please contact us at contact at vistrails.org.
+##
+## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+##
+#########################################################################-->"""
+
+php_old_license = """////////////////////////////////////////////////////////////////////////////
+//
+// Copyright (C) 2006-2010 University of Utah. All rights reserved.
+//
+// This file is part of VisTrails.
+//
+// This file may be used under the terms of the GNU General Public
+// License version 2.0 as published by the Free Software Foundation
+// and appearing in the file LICENSE.GPL included in the packaging of
+// this file. Please review the following to ensure GNU General Public
+// Licensing requirements will be met:
+// http://www.opensource.org/licenses/gpl-license.php
+//
+// If you are unsure which license is appropriate for your use (for
+// instance, you are interested in developing a commercial derivative
+// of VisTrails), please contact us at contact at vistrails.org.
+//
+// This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+// WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+//
+////////////////////////////////////////////////////////////////////////////"""
+def process_files(files, old_license, new_license, type):
+ count = 0
+ not_found = []
+ gpl_found = []
+ for fname in files:
+ fin = open(fname)
+ all_lines = fin.read()
+ fin.close()
+ pos = all_lines.find(old_license)
+ pos_gen = all_lines.find("GNU General Public")
+ if pos > -1:
+ print "Updating: %s"%fname
+ newlines = all_lines.replace(old_license, new_license)
+ fout = file(fname, 'w')
+ fout.write(newlines)
+ fout.close()
+ count += 1
+ else:
+ if pos_gen > -1:
+ gpl_found.append(fname)
+ else:
+ if all_lines.find(new_license) == -1:
+ print "Appending license to %s"%fname
+ newlines = new_license+"\n"+all_lines
+ fout = file(fname, 'w')
+ fout.write(newlines)
+ fout.close()
+ count +=1
+ print count, " %s files updated"%type
+ print " found reference to gpl in the following files:"
+ for fname in gpl_found:
+ print " ", fname
+
+py_files = []
+xml_files = []
+php_files = []
+sql_files = []
+others = []
+for (path, dnames, fnames) in os.walk('.'):
+ for fn in fnames:
+ if fn.endswith(".py"):
+ py_files.append(os.path.join(path, fn))
+ elif fn.endswith(".xml") or fn.endswith(".xsd"):
+ xml_files.append(os.path.join(path,fn))
+ elif fn.endswith(".php"):
+ php_files.append(os.path.join(path,fn))
+ elif fn.endswith(".sql"):
+ sql_files.append(os.path.join(path,fn))
+ else:
+ others.append(os.path.join(path,fn))
+
+print len(py_files), " python files found"
+process_files(py_files, py_old_license, py_bsd_3_license, 'python')
+
+print len(sql_files), " sql files found"
+process_files(sql_files, sql_old_license, sql_bsd_3_license, 'sql')
+
+print len(xml_files), " xml files found"
+process_files(xml_files, xml_old_license, xml_bsd_3_license, 'xml')
+
+print len(php_files), " php files found"
+process_files(php_files, php_old_license, php_bsd_3_license, 'php')
+
+#print "Ignored files: "
+#for f in others:
+# print f
diff --git a/scripts/update_vistrails_command.py b/scripts/update_vistrails_command.py
new file mode 100755
index 0000000..d59768c
--- /dev/null
+++ b/scripts/update_vistrails_command.py
@@ -0,0 +1,63 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This script assumes that VisTrails.command file is located at ../
+Run this script after you copied the VisTrails folder and run from where it
+is located.
+
+"""
+import os, os.path
+
+if __name__ == "__main__":
+ # get VisTrails folder
+ vt_folder = os.path.abspath(os.path.join(os.path.dirname(__file__),'..'))
+ app_command = os.path.join(vt_folder,'VisTrails.app/Contents/MacOS/vistrails')
+ command_file = os.path.join(vt_folder, 'VisTrails.command')
+
+ file_header = """#This will execute VisTrails in a separate terminal window
+#If you get an error saying:
+#Found another instance of VisTrails running
+#Sending parameters to main instance []
+#Failed: QLocalSocket::connectToServer: Connection refused
+#make sure VisTrails is not already running and simply try to run the script again
+#This might indicate that VisTrails did not quit properly
+
+"""
+ file_contents = "DYLD_LIBRARY_PATH= " + app_command
+ f = open(command_file, 'w')
+ f.write(file_header)
+ f.write(file_contents)
+ f.close()
+
diff --git a/scripts/watch_vistrail_servers.py b/scripts/watch_vistrail_servers.py
new file mode 100644
index 0000000..1396fca
--- /dev/null
+++ b/scripts/watch_vistrail_servers.py
@@ -0,0 +1,167 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import xmlrpclib
+import os
+from subprocess import Popen, PIPE
+from time import sleep
+import smtplib
+from email.mime.text import MIMEText
+import logging
+import logging.handlers
+
+class VistrailWatcher(object):
+ """
+ A class for watching the status of VisTrail Servers running on a machine
+ Servers are pinged and if one down, it is restarted
+ """
+
+ def __init__(self, server, email_addresses, root_virtual_display=None):
+ self.server = server
+ self.root_virtual_display = root_virtual_display
+
+ self.email_addresses = email_addresses
+ self.sender = "vistrails_server_watcher@%s" % server
+
+ self.proxies = {}
+ self.is_down = {}
+
+ self.logger = self.make_logger("vt_watcher.log")
+
+ # find running VisTrails servers
+ proc1 = Popen(["ps", "-eaf"], stdout = PIPE)
+ proc2 = Popen(["grep", "vistrails_server"], stdin=proc1.stdout, stdout=PIPE)
+ proc3 = Popen(["awk", "{print $13}"], stdin=proc2.stdout, stdout=PIPE)
+ out, err = proc3.communicate()
+
+ # get the status servers ports (1 less than normal vt server port)
+ out = out.strip().split('\n')
+ self.ports = [int(x)-1 for x in out[1:]] # exclude multithreaded inst.
+
+ # create proxies
+ for port in self.ports:
+ self.proxies[port] = xmlrpclib.ServerProxy("http://%s:%d" % \
+ (self.server, port))
+ self.is_down[port] = False
+
+ def make_logger(self, filename):
+ """ create logger instance with log file rotation """
+
+ logger = logging.getLogger("VistrailsWatcher")
+ handler = logging.handlers.RotatingFileHandler(filename,
+ maxBytes = 1024*1024,
+ backupCount=5)
+ handler.setFormatter(logging.Formatter('VT Watcher- %(asctime)s '
+ '%(levelname)-8s %(message)s'))
+ handler.setLevel(logging.DEBUG)
+ logger.setLevel(logging.DEBUG)
+ logger.addHandler(handler)
+ return logger
+
+ def send_email(self, msg):
+ """ send email notification that server is down """
+
+ if not self.email_addresses:
+ return
+
+ # Create a text/plain message
+ msg = MIMEText(msg)
+
+ msg['Subject'] = '%s VisTrails Server Down' % self.server
+ msg['From'] = self.sender
+ msg['To'] = ', '.join(self.email_addresses)
+
+ # Send the message via our own SMTP server, but don't include the
+ # envelope header.
+ s = smtplib.SMTP('localhost')
+ s.sendmail(self.sender, self.email_addresses, msg.as_string())
+ s.quit()
+
+ def restart_instance(self, port):
+ """ restart VisTrails Single Tread instance on given port """
+
+ self.logger.info("restarting server on port %s" % port)
+ script = os.path.join("/server/vistrails/git/scripts",
+ "start_vistrails_xvfb.sh")
+
+ instance_virtual_display = self.root_virtual_display + \
+ self.ports.index(port) + 1
+
+ args = [script,":%s" % instance_virtual_display,
+ self.server, str(port+1), '0', '0']
+ try:
+ Popen(args)
+ sleep(20)
+ except Exception, e:
+ self.logger.error("Couldn't start the instance on display:"
+ "%s port: %s") % (instance_virtual_display, port)
+ self.logger.error(str(e))
+
+ def watch(self):
+ """ ping Single Thread VisTrail servers every 5 mins """
+
+ if not self.ports:
+ self.logger.info("no running instances found")
+ print "no running instances found"
+ return
+
+ self.logger.info("watching %s" % str(self.ports))
+ while 1:
+ for port in self.ports:
+ try:
+ if not self.proxies[port].try_ping():
+ if not self.is_down[port]:
+ # first time down, send email
+ self.send_email("%s:%d is down" % (self.server, port))
+ self.logger.info("%s:%d is down" % (self.server, port))
+ self.restart_instance(port)
+ self.is_down[port] = True
+ else:
+ if self.is_down[port]:
+ self.logger.info("%s:%d is back up" % (self.server, port))
+ self.is_down[port] = False
+ except Exception, e:
+ if not self.is_down[port]:
+ # first time down, send email
+ self.send_email("%s:%d is down" % (self.server, port))
+ self.logger.info("%s:%d is down" % (self.server, port))
+ self.restart_instance(port)
+ self.is_down[port] = True
+ sleep(60*5)
+
+
+if __name__ == '__main__':
+ vt_watcher = VistrailWatcher("vis-7.sci.utah.edu", ["phillipmates at gmail.com"], root_virtual_display = 6)
+ vt_watcher.watch()
diff --git a/scripts/win_update_bin.sh b/scripts/win_update_bin.sh
new file mode 100755
index 0000000..8fc9d4e
--- /dev/null
+++ b/scripts/win_update_bin.sh
@@ -0,0 +1,62 @@
+#!/bin/bash
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+SRC_PATH="vistrails"
+BIN_PATH="vistrails"
+
+if [ -z "$1" ] || [ -z "$2" ]
+then
+ echo "usage: $0 <src_dir> <bin_dir>"
+ exit 65
+fi
+curdir=`pwd`
+cd "$1/$SRC_PATH"
+ELEMENTS="*"
+for elem in $ELEMENTS
+do
+ if [ -e "$2/$BIN_PATH/$elem" ]
+ then
+ rm -r "$2/$BIN_PATH/$elem"
+ fi
+ cp -r "$1/$SRC_PATH/$elem" "$2/$BIN_PATH/$elem"
+done
+cd "$curdir"
+
+if [ -e "$2/$BIN_PATH/.svn" ]
+then
+ rm -r "$2/$BIN_PATH/.svn"
+fi
+cp -r "$1/$SRC_PATH/.svn" "$2/$BIN_PATH/.svn"
+exit 0
diff --git a/vistrails/__init__.py b/vistrails/__init__.py
new file mode 100644
index 0000000..68d6941
--- /dev/null
+++ b/vistrails/__init__.py
@@ -0,0 +1,37 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Main file for the VisTrails distribution."""
+
+# FIXME: In the future, bootstrap everything from here.
diff --git a/vistrails/api/__init__.py b/vistrails/api/__init__.py
new file mode 100644
index 0000000..8e873b0
--- /dev/null
+++ b/vistrails/api/__init__.py
@@ -0,0 +1,378 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.gui.application import get_vistrails_application
+
+import unittest
+import copy
+import random
+import vistrails.gui.utils
+
+##############################################################################
+# Exceptions
+
+class NoVistrail(Exception):
+ pass
+
+class NoGUI(Exception):
+ pass
+
+##############################################################################
+
+def switch_to_pipeline_view():
+ """switch_to_pipeline_view():
+
+ Changes current viewing mode to pipeline view in the builder window.
+
+ """
+ get_vistrails_application().builderWindow.qactions['pipeline'].trigger()
+
+def switch_to_history_view():
+ """switch_to_history_view():
+
+ Changes current viewing mode to history view in the builder window.
+
+ """
+ get_vistrails_application().builderWindow.qactions['history'].trigger()
+
+def switch_to_query_view():
+ """switch_to_query_view():
+
+ Changes current viewing mode to query view in the builder window.
+
+ """
+ get_vistrails_application().builderWindow.qactions['search'].trigger()
+
+def switch_to_mashup_view():
+ """switch_to_mashup_view():
+
+ Changes current viewing mode to mashup view in the builder window.
+
+ """
+ get_vistrails_application().builderWindow.qactions['mashup'].trigger()
+
+################################################################################
+# Access to current state
+
+def get_builder_window():
+ """get_builder_window():
+
+ returns the main VisTrails GUI window
+
+ raises NoGUI.
+
+ """
+ try:
+ return get_vistrails_application().builderWindow
+ except AttributeError:
+ raise NoGUI
+
+def get_current_controller():
+ """get_current_controller():
+
+ returns the VistrailController of the currently selected vistrail.
+
+ raises NoVistrail.
+
+ """
+ try:
+ return get_vistrails_application().builderWindow.get_current_controller()
+ except AttributeError:
+ raise NoVistrail
+
+def get_current_vistrail():
+ """get_current_vistrail():
+
+ Returns the currently selected vistrail.
+
+ """
+ return get_current_controller().vistrail
+
+def get_current_vistrail_view():
+ """get_current_vistrail():
+
+ Returns the currently selected vistrail view.
+
+ """
+ view = get_vistrails_application().builderWindow.get_current_view()
+ if view is None:
+ raise NoVistrail
+ return view
+
+def close_current_vistrail(quiet=False):
+ get_vistrails_application().builderWindow.close_vistrail(get_current_vistrail_view())
+
+def get_module_registry():
+ from vistrails.core.modules.module_registry import get_module_registry
+ return get_module_registry()
+
+##############################################################################
+# Do things
+
+def add_module(x, y, identifier, name, namespace, controller=None):
+ if controller is None:
+ controller = get_current_controller()
+ if controller.current_version==-1:
+ controller.change_selected_version(0)
+ result = controller.add_module(x, y, identifier, name, namespace)
+ controller.updatePipelineScene()
+ result = controller.current_pipeline.modules[result.id]
+ return result
+
+def add_module_from_descriptor(descriptor, x=0.0, y=0.0,
+ internal_version=-1, controller=None):
+ if controller is None:
+ controller = get_current_controller()
+ if controller.current_version==-1:
+ controller.change_selected_version(0)
+ result = controller.add_module_from_descriptor(descriptor, x, y,
+ internal_version)
+ controller.updatePipelineScene()
+ result = controller.current_pipeline.modules[result.id]
+ return result
+
+def add_connection(output_id, output_port_spec, input_id, input_port_spec,
+ controller=None):
+ if controller is None:
+ controller = get_current_controller()
+ result = controller.add_connection(output_id, output_port_spec,
+ input_id, input_port_spec)
+ controller.updatePipelineScene()
+ result = controller.current_pipeline.connections[result.id]
+ return result
+
+def create_group(module_ids, connection_ids, controller=None):
+ if controller is None:
+ controller = get_current_controller()
+ controller.create_group(module_ids, connection_ids)
+ controller.updatePipelineScene()
+
+def get_modules_by_name(name, package=None, namespace=None, controller=None):
+ if controller is None:
+ controller = get_current_controller()
+ res = []
+ for module in controller.current_pipeline.modules.itervalues():
+ if (module.name == name and
+ (package is None or module.package == package) and
+ (namespace is None or module.namespace == namespace)):
+ res.append(module)
+ return res
+
+def get_selected_modules(controller=None):
+ if controller is None:
+ controller = get_current_controller()
+ modules = []
+ selected = controller.get_selected_item_ids()
+ if selected is None:
+ return []
+ (sel_module_ids, sel_connection_ids) = selected
+ for m_id in sel_module_ids:
+ modules.append(controller.current_pipeline.modules[m_id])
+ return modules
+
+def change_parameter(module_id, function_name, param_list, function_id=-1L,
+ alias_list=[], controller=None):
+ """change_parameter(module_id: long,
+ function_name: str,
+ param_list: list(str),
+ function_id: long,
+ alias_list: list(str),
+ controller: VistrailController,
+ ) -> None
+ Note: param_list is a list of strings no matter what the parameter type!
+ Note: alias_list will be REMOVED!!
+ """
+ if controller is None:
+ controller = get_current_controller()
+ module = controller.current_pipeline.modules[module_id]
+ controller.update_function(module, function_name, param_list, function_id,
+ alias_list)
+ controller.updatePipelineScene()
+
+def change_parameter_by_id(module_id, function_id, old_param_id, new_value,
+ controller=None):
+ """change_parameter_by_id(module_id: long,
+ function_id: long,
+ old_param_id: long,
+ new_value: str,
+ controller: VistrailController) -> long
+ Returns the id of the new parameter.
+ Note: function_id is the real_id! Use f.real_id to access real_id
+ Note: old_param_id is the real_id! Use p.real_id to access real_id
+ """
+ if controller is None:
+ controller = get_current_controller()
+ module = controller.current_pipeline.modules[module_id]
+ function = module.function_idx[function_id]
+ pos = function.parameter_idx[old_param_id].pos
+ controller.update_parameter(function, old_param_id, new_value)
+ controller.updatePipelineScene()
+ return function.params[pos].real_id
+
+def change_parameter_by_pos(module_id, function_pos, old_param_pos, new_value,
+ controller=None):
+ """change_parameter_by_id(module_id: long,
+ function_pos: int,
+ old_param_pos: int,
+ new_value: str,
+ controller: VistrailController) -> long
+ Returns the id of the new parameter.
+ """
+ if controller is None:
+ controller = get_current_controller()
+ module = controller.current_pipeline.modules[module_id]
+ function = module.functions[function_pos]
+ old_param_id = function.params[old_param_pos].real_id
+ controller.update_parameter(function, old_param_id, new_value)
+ controller.updatePipelineScene()
+ return function.params[old_param_pos].real_id
+
+def add_port_spec(module_id, port_spec, controller=None):
+ if controller is None:
+ controller = get_current_controller()
+ # module = controller.current_pipeline.modules[module_id]
+ controller.add_module_port(module_id, (port_spec.type, port_spec.name,
+ port_spec.sigstring))
+ controller.updatePipelineScene()
+
+##############################################################################
+
+def select_version(version, ctrl=None):
+ """select_version(int or str, ctrl=None):
+
+ Given an integer, selects a version with the given number from the
+ given vistrail (or the current one if no controller is given).
+
+ Given a string, selects a version with that tag.
+
+ """
+ if ctrl is None:
+ ctrl = get_current_controller()
+ vistrail = ctrl.vistrail
+ if isinstance(version, str):
+ version = vistrail.get_tag_str(version).action_id
+ ctrl.change_selected_version(version)
+ ctrl.invalidate_version_tree(False)
+
+def undo():
+ get_current_vistrail_view().undo()
+
+def redo():
+ get_current_vistrail_view().redo()
+
+def get_available_versions():
+ """get_available_version(): ([int], {int: str})
+
+ From the currently selected vistrail, return all available
+ versions and the existing tags.
+
+ """
+ ctrl = get_current_controller()
+ vistrail = ctrl.vistrail
+ return (vistrail.actionMap.keys(), vistrail.get_tagMap())
+
+def open_vistrail_from_file(filename):
+ from vistrails.core.db.locator import FileLocator
+
+ f = FileLocator(filename)
+ view = get_builder_window().open_vistrail(f)
+ return view
+
+def close_vistrail(view, quiet=True):
+ """close_vistrail(view: QVistrailView, quiet:bool)-> None
+ Closes vistrail in view. If quiet is True it will discard changes
+ automatically.
+
+ """
+ get_builder_window().close_vistrail(view, quiet=quiet)
+
+def close_all_vistrails(quiet=True):
+ get_builder_window().close_all_vistrails(quiet)
+
+def new_vistrail():
+ # Returns VistrailView - remember to be consistent about it..
+ get_vistrails_application().builderWindow.new_vistrail(False)
+ result = get_vistrails_application().builderWindow.get_current_view()
+ return result
+
+def get_vistrail_from_file(filename):
+ from vistrails.core.db.locator import FileLocator
+ from vistrails.core.vistrail.vistrail import Vistrail
+ v = FileLocator(filename).load()
+ if not isinstance(v, Vistrail):
+ v = v.vistrail
+ return v
+
+##############################################################################
+# Testing
+
+
+class TestAPI(vistrails.gui.utils.TestVisTrailsGUI):
+
+ def setUp(self):
+ app = vistrails.gui.application.get_vistrails_application()
+ app.builderWindow.auto_view = False
+ app.builderWindow.close_all_vistrails(True)
+
+ def test_close_current_vistrail_no_vistrail(self):
+ self.assertRaises(NoVistrail, lambda: get_current_vistrail_view())
+
+ def test_new_vistrail_no_save(self):
+ v = new_vistrail()
+ import vistrails.gui.vistrail_view
+ assert isinstance(v, vistrails.gui.vistrail_view.QVistrailView)
+ assert not v.controller.changed
+ close_vistrail(v)
+
+ def test_new_vistrail_button_states(self):
+ assert get_vistrails_application().builderWindow.qactions['newVistrail'].isEnabled()
+ assert not get_vistrails_application().builderWindow.qactions['closeVistrail'].isEnabled()
+ assert not get_vistrails_application().builderWindow.qactions['saveFile'].isEnabled()
+ assert not get_vistrails_application().builderWindow.qactions['saveFileAs'].isEnabled()
+ view = new_vistrail()
+ assert get_vistrails_application().builderWindow.qactions['newVistrail'].isEnabled()
+ assert get_vistrails_application().builderWindow.qactions['closeVistrail'].isEnabled()
+ self.assertEqual(get_vistrails_application().builderWindow.qactions['saveFile'].isEnabled(),
+ view.has_changes())
+ assert get_vistrails_application().builderWindow.qactions['saveFileAs'].isEnabled()
+
+ def test_detach_vistrail(self):
+ view = new_vistrail()
+ get_vistrails_application().builderWindow.detach_view(view)
+ get_vistrails_application().builderWindow.attach_view(view)
+ close_vistrail(view)
+
+
+
+
diff --git a/vistrails/core/__init__.py b/vistrails/core/__init__.py
new file mode 100644
index 0000000..cb7e847
--- /dev/null
+++ b/vistrails/core/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+def get_vistrails_application():
+ import vistrails.core.application
+ return vistrails.core.application.get_vistrails_application()
+
+def is_running_gui():
+ return get_vistrails_application() and get_vistrails_application().is_running_gui()
diff --git a/vistrails/core/analogy/__init__.py b/vistrails/core/analogy/__init__.py
new file mode 100644
index 0000000..d1687d7
--- /dev/null
+++ b/vistrails/core/analogy/__init__.py
@@ -0,0 +1,456 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.data_structures.bijectivedict import Bidict
+from itertools import imap, chain
+from vistrails.core.modules.module_registry import get_module_registry, \
+ ModuleRegistryException
+import vistrails.core.db.io
+from vistrails.core.requirements import MissingRequirement
+from vistrails.core.vistrail.module import Module
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.port_spec import PortSpec, PortEndPoint
+import copy
+from vistrails.core.vistrail.pipeline import Pipeline
+
+from eigen import *
+
+##########################################################################
+
+
+_debug = False
+
+def perform_analogy_on_vistrail(vistrail, version_a, version_b, version_c,
+ pipeline_a=None, pipeline_c=None, alpha=0.15):
+ """perform_analogy(vistrail, version_a, version_b, version_c,
+ pipeline_a=None, pipeline_c=None, alpha=0.15): action
+ Creates a new action version_d to the vistrail such that the difference
+ between a and b is the same as between c and d, and returns this
+ action."""
+
+ ############################################################################
+ # STEP 1: find mapping from a to c
+
+ # pipeline_c = Pipeline(vistrail.actionChain(version_c))
+ # pipeline_a = Pipeline(vistrail.actionChain(version_a))
+
+ if _debug:
+ print 'version_a:', version_a
+ print 'version_b:', version_b
+ print 'version_c:', version_c
+
+ if pipeline_a is None:
+ pipeline_a = vistrails.core.db.io.get_workflow(vistrail, version_a)
+ pipeline_a.validate()
+ if pipeline_c is None:
+ pipeline_c = vistrails.core.db.io.get_workflow(vistrail, version_c)
+ pipeline_c.validate()
+
+ e = EigenPipelineSimilarity2(pipeline_a, pipeline_c, alpha=alpha)
+ e._debug = _debug
+
+ (input_module_remap,
+ output_module_remap,
+ combined_module_remap) = e.solve()
+
+ if _debug:
+ print 'Input remap'
+ print input_module_remap
+ print 'Output remap'
+ print output_module_remap
+ print 'Combined remap'
+ print combined_module_remap
+
+ module_remap = combined_module_remap
+ if _debug:
+ print "Computing names..."
+
+ def name_remap(d):
+ return dict([(from_id,
+ pipeline_c.modules[to_id].name)
+ for (from_id, to_id)
+ in d.iteritems()])
+
+ module_name_remap = name_remap(module_remap)
+ input_module_name_remap = name_remap(input_module_remap)
+ output_module_name_remap = name_remap(output_module_remap)
+
+ if _debug:
+ print 'Name remap'
+ print module_name_remap
+
+ # find connection remap
+ connection_remap = {}
+ for a_connect in pipeline_a.connections.itervalues():
+ # FIXME assumes that all connections have both source and dest
+ a_source = a_connect.source.moduleId
+ a_dest = a_connect.destination.moduleId
+ match = None
+ for c_connect in pipeline_c.connections.itervalues():
+ if (output_module_remap[a_source] == c_connect.source.moduleId and
+ input_module_remap[a_dest] == c_connect.destination.moduleId):
+ match = c_connect
+ if (a_connect.source.spec == c_connect.source.spec and
+ a_connect.destination.spec == c_connect.destination.spec):
+ break
+ if match is not None:
+ connection_remap[a_connect.id] = c_connect.id
+ elif _debug:
+ print "failed to find connection match", a_connect.id, a_source, \
+ a_dest
+
+ # find function remap
+
+ # construct total remap
+ id_remap = {}
+ sum_ax = 0.0
+ sum_ay = 0.0
+ sum_cx = 0.0
+ sum_cy = 0.0
+ for (a_id, c_id) in module_remap.iteritems():
+ id_remap[('module', a_id)] = c_id
+ module_a = pipeline_a.modules[a_id]
+ sum_ax += module_a.location.x
+ sum_ay += module_a.location.y
+ module_c = pipeline_c.modules[c_id]
+ sum_cx += module_c.location.x
+ sum_cy += module_c.location.y
+
+ if len(module_remap) != 0:
+ avg_ax = sum_ax / len(module_remap)
+ avg_ay = sum_ay / len(module_remap)
+ avg_cx = sum_cx / len(module_remap)
+ avg_cy = sum_cy / len(module_remap)
+ else:
+ avg_ax = 0.0
+ avg_ay = 0.0
+ avg_cx = 0.0
+ avg_cy = 0.0
+
+# avg_ax = sum_ax / len(module_remap) if len(module_remap) != 0 else 0.0
+# avg_ay = sum_ay / len(module_remap) if len(module_remap) != 0 else 0.0
+# avg_cx = sum_cx / len(module_remap) if len(module_remap) != 0 else 0.0
+# avg_cy = sum_cy / len(module_remap) if len(module_remap) != 0 else 0.0
+
+ for (a_id, c_id) in connection_remap.iteritems():
+ id_remap[('connection', a_id)] = c_id
+ ############################################################################
+ # STEP 2: find actions to be remapped (b-a)
+
+ # this creates a new action with new operations
+ baAction = vistrails.core.db.io.getPathAsAction(vistrail, version_a, version_b, True)
+
+# for operation in baAction.operations:
+# print "ba_op0:", operation.id, operation.vtType, operation.what,
+# print operation.old_obj_id, "to", operation.parentObjType,
+# print operation.parentObjId
+
+ ############################################################################
+ # STEP 3: remap (b-a) using mapping in STEP 1 so it can be applied to c
+
+ # for all module references, update the module ids according to the remap
+ # need to consider modules, parent_obj_ids, ports
+ # if things don't make sense, they're cut out in STEP 4, not here
+
+ reg = get_module_registry()
+ ops = []
+
+ # NOTE !!! delete ops are before any add ops so this is ok !!!
+ # if this changes, this may break
+ c_modules = set(pipeline_c.modules)
+ c_connections = set(pipeline_c.connections)
+ c_locations = dict((m_id, m.location)
+ for (m_id, m) in pipeline_c.modules.iteritems())
+ c_annotations = dict(((m_id, a.key), a) for m_id, m in \
+ pipeline_c.modules.iteritems()
+ for a in m.annotations)
+ c_parameters = dict(((f.real_id, p.pos), p)
+ for m in pipeline_c.modules.itervalues()
+ for f in m.functions
+ for p in f.parameters)
+ conns_to_delete = set()
+
+ for op in baAction.operations:
+ if op.vtType == 'delete':
+ parent_obj_type = op.parentObjType
+ if parent_obj_type == 'abstraction' or parent_obj_type == 'group':
+ parent_obj_type = 'module'
+ if (op.what == 'module' or
+ op.what == 'abstraction' or
+ op.what == 'group'):
+ if module_remap.has_key(op.old_obj_id):
+ remap_id = module_remap[op.old_obj_id]
+ module = pipeline_c.modules[remap_id]
+ graph = pipeline_c.graph
+ for _, c_id in graph.edges_from(remap_id):
+ conn = pipeline_c.connections[c_id]
+ ops.extend(vistrails.core.db.io.create_delete_op_chain(conn))
+ for _, c_id in graph.edges_to(remap_id):
+ conn = pipeline_c.connections[c_id]
+ ops.extend(vistrails.core.db.io.create_delete_op_chain(conn))
+ ops.extend(vistrails.core.db.io.create_delete_op_chain(module))
+ c_modules.discard(remap_id)
+ else:
+ ops.append(op)
+ c_modules.discard(op.old_obj_id)
+ elif op.what == 'connection':
+ if connection_remap.has_key(op.old_obj_id):
+ conn = pipeline_c.connections[connection_remap[ \
+ op.old_obj_id]]
+ ops.extend(vistrails.core.db.io.create_delete_op_chain(conn))
+ c_connections.discard(conn.id)
+ else:
+ ops.append(op)
+ c_connections.discard(op.old_obj_id)
+ elif (parent_obj_type, op.parentObjId) not in id_remap:
+ if op.what == 'location':
+ c_locations.pop(op.parentObjId, None)
+ if op.what == 'annotation':
+ for (m_id, key), a in c_annotations.iteritems():
+ if a.id == op.old_obj_id:
+ c_annotations.pop((m_id, key), None)
+ break
+ if op.what == 'parameter':
+ for (f_id, pos), p in c_parameters.iteritems():
+ if p.real_id == op.old_obj_id:
+ c_parameters.pop((f_id, pos), None)
+ break
+
+ ops.append(op)
+ elif op.vtType == 'add' or op.vtType == 'change':
+ old_id = op.new_obj_id
+ new_id = vistrail.idScope.getNewId(op.what)
+ op.new_obj_id = new_id
+ op.data.db_id = new_id
+ op_what = op.what
+ if op_what == 'abstraction' or op_what == 'group':
+ op_what = 'module'
+ id_remap[(op_what, old_id)] = new_id
+ if (op.what == 'module' or
+ op.what == 'abstraction' or
+ op.what == 'group'):
+ module_name_remap[old_id] = op.data.name
+ c_modules.add(new_id)
+ elif op.what == 'connection':
+ c_connections.add(new_id)
+
+ parent_obj_type = op.parentObjType
+ if parent_obj_type == 'abstraction' or parent_obj_type == 'group':
+ parent_obj_type = 'module'
+ if op.parentObjId is not None and \
+ id_remap.has_key((parent_obj_type, op.parentObjId)):
+ op.parentObjId = id_remap[(parent_obj_type, op.parentObjId)]
+ if op.what == 'location':
+ # need to make this a 'change' if it's an 'add' and
+ # the module already exists
+ if op.vtType == 'add':
+ if op.parentObjId in c_locations:
+ new_op_list = vistrails.core.db.io.create_change_op_chain(
+ c_locations[op.parentObjId], op.data,
+ (op.parentObjType, op.parentObjId))
+ op = new_op_list[0]
+ c_locations[op.parentObjId] = op.data
+ elif op.vtType == 'change':
+ c_locations[op.parentObjId] = op.data
+ elif op.what == 'annotation':
+ if op.vtType == 'add':
+ if (op.parentObjId, op.data.key) in c_annotations:
+ new_op_list = vistrails.core.db.io.create_change_op_chain(
+ c_annotations[(op.parentObjId, op.data.key)],
+ op.data,
+ (Module.vtType, op.parentObjId))
+ op = new_op_list[0]
+ c_annotations[(op.parentObjId, op.data.key)] = op.data
+ elif op.vtType == 'change':
+ c_annotations[(op.parentObjId, op.data.key)] = op.data
+ elif op.what == 'parameter':
+ if op.vtType == 'add':
+ if (op.parentObjId, op.data.pos) in c_parameters:
+ new_op_list = vistrails.core.db.io.create_change_op_chain(
+ c_parameters[(op.parentObjId, op.data.pos)],
+ op.data,
+ (ModuleFunction.vtType, op.parentObjId))
+ op = new_op_list[0]
+ c_parameters[(op.parentObjId, op.data.pos)] = op.data
+ elif op.vtType == 'change':
+ c_parameters[(op.parentObjId, op.data.pos)] = op.data
+ elif op.what == 'port':
+ port = op.data
+ # check the input/output module remaps since that is
+ # what we use to modify the ids
+ if port.type == 'source' and \
+ port.moduleId in output_module_remap:
+ temp_id = output_module_remap[port.moduleId]
+ elif port.type == 'destination' and \
+ port.moduleId in input_module_remap:
+ temp_id = input_module_remap[port.moduleId]
+ else:
+ temp_id = port.moduleId
+ if ('module', temp_id) in id_remap:
+ temp_id = id_remap[('module', temp_id)]
+ if temp_id in c_modules:
+ if port.type == 'source':
+ try:
+ port.moduleName = output_module_name_remap[port.moduleId]
+ port.moduleId = output_module_remap[port.moduleId]
+ m = pipeline_c.modules[port.moduleId]
+ d = m.module_descriptor
+ def remap():
+ port_type = \
+ PortSpec.port_type_map.inverse[port.type]
+ try:
+ pspec = reg.get_port_spec(m.package, m.name,
+ m.namespace,
+ port.name,
+ port_type)
+ except ModuleRegistryException:
+ return False
+ all_ports = reg.all_source_ports(d)
+ # print "pspec", pspec
+ # First try to find a perfect match
+ for (klass_name, ports) in all_ports:
+ for candidate_port in ports:
+ if (candidate_port.type_equals(pspec) and
+ candidate_port.name == port.name):
+ #print "found perfect match"
+ port.spec = candidate_port
+ return True
+ # Now try to find an imperfect one
+ for (klass_name, ports) in all_ports:
+ for candidate_port in ports:
+ print candidate_port
+ if candidate_port.type_equals(pspec):
+ #print "found imperfect match"
+ port.name = candidate_port.name
+ port.spec = candidate_port
+ return True
+ return False
+ if not remap():
+ print "COULD NOT FIND source MATCH!!!"
+ except KeyError:
+ # This happens when the module was added as part of the analogy
+ port.moduleName = module_name_remap[port.moduleId]
+ port.moduleId = id_remap[('module', port.moduleId)]
+ elif port.type == 'destination':
+ try:
+ port.moduleName = input_module_name_remap[port.moduleId]
+ port.moduleId = input_module_remap[port.moduleId]
+ m = pipeline_c.modules[port.moduleId]
+ d = m.module_descriptor
+ def remap():
+ port_type = \
+ PortSpec.port_type_map.inverse[port.type]
+ try:
+ pspec = reg.get_port_spec(m.package, m.name,
+ m.namespace,
+ port.name,
+ port_type)
+ # print "This is the spec", port.spec, \
+ # port.db_spec
+ except ModuleRegistryException:
+ return False
+ all_ports = reg.all_destination_ports(d)
+ # First try to find a perfect match
+ for (klass_name, ports) in all_ports:
+ for candidate_port in ports:
+ if (candidate_port.type_equals(pspec) and
+ candidate_port.name == port.name):
+ # print "found perfect match"
+ port.spec = candidate_port
+ return True
+ # Now try to find an imperfect one
+ for (klass_name, ports) in all_ports:
+ for candidate_port in ports:
+ if candidate_port.type_equals(pspec):
+ # print "found imperfect match"
+ port.name = candidate_port.name
+ port.spec = candidate_port
+ return True
+ return False
+ if not remap():
+ print "COULD NOT FIND destination MATCH!!!"
+ remap()
+ except KeyError:
+ # This happens when the module was added as part of the analogy
+ port.moduleName = module_name_remap[port.moduleId]
+ port.moduleId = id_remap[('module', port.moduleId)]
+ else:
+ # delete the connection since it won't work
+ conns_to_delete.add(op.parentObjId)
+ continue
+ ops.append(op)
+
+ baAction.operations = []
+ for op in ops:
+ if op.what == 'connection' and op.new_obj_id in conns_to_delete:
+ pass
+ elif op.what == 'port' and op.parentObjId in conns_to_delete:
+ pass
+ else:
+ baAction.operations.append(op)
+
+ # baAction.operations = ops
+
+ # baAction should now have remapped everything
+
+ ############################################################################
+ # STEP 4: apply remapped (b-a) to c
+
+ # some actions cannot be applied because they reference stuff that
+ # isn't in c. need to no-op for them
+
+ # want to take the pipeline for c and simply apply (b-a), but return
+ # False for operations that don't make sense.
+
+ # get operationDict for c, do update with baAction but discard ops
+ # that don't make sense
+
+# for operation in baAction.operations:
+# print "ba_op1:", operation.id, operation.vtType, operation.what,
+# print operation.old_obj_id, "to", operation.parentObjType,
+# print operation.parentObjId
+
+ baAction.prevId = version_c
+ vistrails.core.db.io.fixActions(vistrail, version_c, [baAction])
+ for operation in baAction.operations:
+ if operation.what == 'location' and (operation.vtType == 'add' or
+ operation.vtType == 'change'):
+ operation.data.x -= avg_ax - avg_cx
+ operation.data.y -= avg_ay - avg_cy
+# print "ba_op2:", operation.id, operation.vtType, operation.what,
+# print operation.old_obj_id, "to", operation.parentObjType,
+# print operation.parentObjId
+ # this will be taken care by the controller
+ #vistrail.add_action(baAction, version_c)
+ return baAction
diff --git a/vistrails/core/analogy/eigen.py b/vistrails/core/analogy/eigen.py
new file mode 100644
index 0000000..2a81e7e
--- /dev/null
+++ b/vistrails/core/analogy/eigen.py
@@ -0,0 +1,566 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.bundles import py_import
+from vistrails.core.data_structures.bijectivedict import Bidict
+from itertools import imap, chain
+import copy
+
+import math
+import operator
+from pipeline_utils import *
+
+from vistrails.core.utils import append_to_dict_of_lists
+from vistrails.core.system import temporary_directory
+
+import scipy
+
+
+##############################################################################
+# This is the analogy implementation
+
+##############################################################################
+# EigenBase
+
+def mzeros(*args, **kwargs):
+ nkwargs = copy.copy(kwargs)
+ nkwargs['dtype'] = float
+ az = scipy.zeros(*args, **nkwargs)
+ return scipy.matrix(az)
+
+def mones(*args, **kwargs):
+ nkwargs = copy.copy(kwargs)
+ nkwargs['dtype'] = float
+ az = scipy.ones(*args, **nkwargs)
+ return scipy.matrix(az)
+
+#mzeros = lambda *args, **kwargs: scipy.matrix(scipy.zeros(*args, **kwargs))
+# mones = lambda *args, **kwargs: scipy.matrix(scipy.ones(*args, **kwargs))
+
+class EigenBase(object):
+
+ ##########################################################################
+ # Constructor and initialization
+
+ def __init__(self,
+ pipeline1,
+ pipeline2):
+ self._p1 = pipeline1
+ self._p2 = pipeline2
+ self._debug = False
+ self.init_vertex_similarity()
+ self.init_edge_similarity()
+
+ def init_vertex_similarity(self):
+ num_verts_p1 = len(self._p1.graph.vertices)
+ num_verts_p2 = len(self._p2.graph.vertices)
+ m_i = mzeros((num_verts_p1, num_verts_p2))
+ m_o = mzeros((num_verts_p1, num_verts_p2))
+ def get_vertex_map(g):
+ return Bidict([(v, k) for (k, v)
+ in enumerate(g.iter_vertices())])
+ # vertex_maps: vertex_id to matrix index
+ self._g1_vertex_map = get_vertex_map(self._p1.graph)
+ self._g2_vertex_map = get_vertex_map(self._p2.graph)
+ for i in xrange(num_verts_p1):
+ for j in xrange(num_verts_p2):
+ v1_id = self._g1_vertex_map.inverse[i]
+ v2_id = self._g2_vertex_map.inverse[j]
+ (in_s8y, out_s8y) = self.compare_modules(v1_id, v2_id)
+ m_i[i,j] = in_s8y
+ m_o[i,j] = out_s8y
+ # print m_i
+ # print m_o
+ self._input_vertex_s8y = m_i
+ self._output_vertex_s8y = m_o
+ self._vertex_s8y = (m_i + m_o) / 2.0
+
+ def init_edge_similarity(self):
+ def get_edge_map(g):
+ itor = enumerate(imap(lambda x: x[2],
+ g.iter_all_edges()))
+ return Bidict([(v, k) for (k, v)
+ in itor])
+ # edge_maps: edge_id to matrix index
+ self._g1_edge_map = get_edge_map(self._p1.graph)
+ self._g2_edge_map = get_edge_map(self._p2.graph)
+
+ m_e = mzeros((len(self._g1_edge_map),
+ len(self._g2_edge_map)))
+
+ for i in xrange(len(self._g1_edge_map)):
+ for j in xrange(len(self._g2_edge_map)):
+ c1_id = self._g1_edge_map.inverse[i]
+ c2_id = self._g2_edge_map.inverse[j]
+ s8y = self.compare_connections(c1_id, c2_id)
+ m_e[i, j] = s8y
+ self._edge_s8y = m_e
+
+ ##########################################################################
+ # Atomic comparisons for modules and connections
+
+ def create_type_portmap(self, ports):
+ result = {}
+ for port_name, port_descs in ports.iteritems():
+ for port_desc in port_descs:
+ sp = tuple(port_desc)
+ append_to_dict_of_lists(result, sp, port_name)
+ return result
+
+ def compare_modules(self, p1_id, p2_id):
+ """Returns two values \in [0, 1] that is how similar the
+ modules are intrinsically, ie. without looking at
+ neighborhoods. The first value gives similarity wrt input
+ ports, the second to output ports."""
+ (m1_inputs, m1_outputs) = self.get_ports(self._p1.modules[p1_id])
+ (m2_inputs, m2_outputs) = self.get_ports(self._p2.modules[p2_id])
+
+
+ m2_input_hist = self.create_type_portmap(m2_inputs)
+ m2_output_hist = self.create_type_portmap(m2_outputs)
+
+ output_similarity = 0.0
+ total = 0
+ # Outputs can be covariant, inputs can be contravariant
+ # FIXME: subtypes, etc etc
+ for (port_name, port_descs) in m1_outputs.iteritems():
+ # we use max() .. because we want to count
+ # nullary ports as well
+ total_descs = max(len(port_descs), 1)
+ total += total_descs
+ # assert len(port_descs) == 1
+ if (m2_outputs.has_key(port_name) and
+ m2_outputs[port_name] == port_descs):
+ output_similarity += float(total_descs)
+ else:
+ for port_desc in port_descs:
+ port_desc = tuple(port_desc)
+ if m2_output_hist.has_key(port_desc):
+ output_similarity += 1
+ if len(m1_outputs):
+ output_similarity /= total
+ else:
+ output_similarity = 0.2
+
+ if (self._p1.modules[p1_id].name !=
+ self._p2.modules[p2_id].name):
+ output_similarity *= 0.99
+
+ input_similarity = 0.0
+ total = 0
+ # FIXME: consider supertypes, etc etc
+
+ for (port_name, port_descs) in m1_inputs.iteritems():
+ # we use max() .. because we want to count
+ # nullary ports as well
+ total_descs = max(len(port_descs), 1)
+ total += total_descs
+ if (m2_inputs.has_key(port_name) and
+ m2_inputs[port_name] == port_descs):
+ input_similarity += 1.0
+ else:
+ for port_desc in port_descs:
+ port_desc = tuple(port_desc)
+ if m2_input_hist.has_key(port_desc):
+ input_similarity += 1
+
+ if len(m1_inputs):
+ input_similarity /= total
+ else:
+ input_similarity = 0.2
+
+ if (self._p1.modules[p1_id].name !=
+ self._p2.modules[p2_id].name):
+ input_similarity *= 0.99
+
+ return (input_similarity, output_similarity)
+
+ def compare_connections(self, p1_id, p2_id):
+ """Returns a value \in [0, 1] that says how similar
+ the two connections are."""
+ c1 = self._p1.connections[p1_id]
+ c2 = self._p2.connections[p2_id]
+
+ # FIXME: Make this softer in the future
+ if self._debug:
+ print "COMPARING %s:%s -> %s:%s with %s:%s -> %s:%s" % \
+ (self._p1.modules[c1.sourceId].name, c1.source.name,
+ self._p1.modules[c1.destinationId].name, c1.destination.name,
+ self._p2.modules[c2.sourceId].name, c2.source.name,
+ self._p2.modules[c2.destinationId].name, c2.destination.name),
+ if c1.source.name != c2.source.name:
+ if self._debug:
+ print 0.0
+ return 0.0
+ if c1.destination.name != c2.destination.name:
+ if self._debug:
+ print 0.0
+ return 0.0
+
+ m_c1_sid = self._g1_vertex_map[c1.sourceId]
+ m_c1_did = self._g1_vertex_map[c1.destinationId]
+ m_c2_sid = self._g2_vertex_map[c2.sourceId]
+ m_c2_did = self._g2_vertex_map[c2.destinationId]
+
+ if self._debug:
+ print (self._output_vertex_s8y[m_c1_sid, m_c2_sid] +
+ self._input_vertex_s8y[m_c1_did, m_c2_did]) / 2.0
+ return (self._output_vertex_s8y[m_c1_sid, m_c2_sid] +
+ self._input_vertex_s8y[m_c1_did, m_c2_did]) / 2.0
+
+
+ ##########################################################################
+ # Utility
+
+ @staticmethod
+ def pm(m, digits=5):
+ def get_digits(x):
+ if x == 0: return 0
+ return int(math.log(abs(x) * 10.0, 10.0))
+ vd = scipy.vectorize(get_digits)
+ dm = vd(m)
+ widths = dm.max(0)
+ (l, c) = m.shape
+ for i in xrange(l):
+ EigenBase.pv(m[i,:],
+ digits=digits,
+ left_digits=widths)
+
+ @staticmethod
+ def pv(v, digits=5, left_digits=None):
+ # FIXME - some scipy indexing seems to be currently
+ # inconsistent across different deployed versions. Fix this.
+ if isinstance(v, scipy.matrix):
+ v = scipy.array(v)[0]
+ (c,) = v.shape
+ print "[ ",
+ for j in xrange(c):
+ if left_digits != None:
+ d = left_digits[0,j]
+ else:
+ d = 0
+ fmt = ("%" +
+ str(d + digits + 1) +
+ "." + str(digits) + "f ")
+ print (fmt % v[j]),
+ print "]"
+
+ def print_s8ys(self):
+ print "Input s8y"
+ self.pm(self._input_vertex_s8y)
+ print "\nOutput s8y"
+ self.pm(self._output_vertex_s8y)
+ print "\nConnection s8y"
+ self.pm(self._edge_s8y)
+ print "\nCombined s8y"
+ self.pm(self._vertex_s8y)
+
+ # FIXME: move this somewhere decent.
+ def get_ports(self, module, include_optional=False):
+ """get_ports(module) -> (input_ports, output_ports)
+
+ Returns all ports for a given module name, all the way
+ up the class hierarchy."""
+
+ def remove_descriptions(d):
+ def update_elements(spec):
+ return [v.name for v
+ in spec.descriptors()]
+ for k in d.keys():
+ v = update_elements(d[k])
+ if len(v):
+ d[k] = v
+ else:
+ del d[k]
+
+ inputs = dict([(port.name, port) for
+ port in module.destinationPorts()
+ if (not port.optional or include_optional)])
+ outputs = dict([(port.name, port) for
+ port in module.sourcePorts()
+ if (not port.optional or include_optional)])
+
+ remove_descriptions(inputs)
+ remove_descriptions(outputs)
+ return (inputs, outputs)
+
+##############################################################################
+# EigenPipelineSimilarity
+
+class EigenPipelineSimilarity(EigenBase):
+
+ ##########################################################################
+ # Constructor and initialization
+
+ def __init__(self,
+ pipeline1,
+ pipeline2):
+ EigenBase.__init__(self, pipeline1, pipeline2)
+ self.init_operator()
+
+ def init_operator(self):
+ num_verts_p1 = len(self._p1.graph.vertices)
+ num_verts_p2 = len(self._p2.graph.vertices)
+ def ix(a,b): return num_verts_p2 * a + b
+ self._operator = mzeros((num_verts_p1 * num_verts_p2,
+ num_verts_p1 * num_verts_p2))
+
+ u = 0.85
+
+ for i in xrange(num_verts_p1):
+ v1_id = self._g1_vertex_map.inverse[i]
+ for j in xrange(num_verts_p2):
+ ix_ij = ix(i,j)
+ self._operator[ix_ij, ix_ij] = u
+ v2_id = self._g2_vertex_map.inverse[j]
+ def edges(pip, v_id):
+ return chain(imap(lambda (f, t, i): (t, i),
+ self._p1.graph.iter_edges_from(v1_id)),
+ imap(lambda (f, t, i): (f, i),
+ self._p1.graph.iter_edges_to(v1_id)))
+ p1_edges = edges(self._p1, v1_id)
+ p2_edges = edges(self._p2, v2_id)
+ running_sum = 0.0
+ for (_, p1_edge) in p1_edges:
+ for (_, p2_edge) in p2_edges:
+ e1_id = self._g1_edge_map[p1_edge]
+ e2_id = self._g2_edge_map[p2_edge]
+ running_sum += self._edge_s8y[e1_id, e2_id]
+ p1_edges = edges(self._p1, v1_id)
+ p2_edges = edges(self._p2, v2_id)
+ if not running_sum:
+ continue
+ for (p1_v, p1_edge_id) in p1_edges:
+ for (p2_v, p2_edge_id) in p2_edges:
+ e1_id = self._g1_edge_map[p1_edge_id]
+ e2_id = self._g2_edge_map[p2_edge_id]
+ p1_v_id = self._g1_vertex_map[p1_v]
+ p2_v_id = self._g2_vertex_map[p2_v]
+ value = self._edge_s8y[e1_id, e2_id]
+ value *= (1.0 - u) / running_sum
+ self._operator[ix_ij, ix(p1_v_id, p2_v_id)] = value
+
+ ##############################################################################
+ # Solve
+
+ def step(self, m):
+ v = m.reshape(len(self._p1.modules) *
+ len(self._p2.modules))
+ v = scipy.dot(self._operator, v)
+ v = v.reshape(len(self._p1.modules),
+ len(self._p2.modules)).transpose()
+ v = (v / v.sum(0)).transpose()
+ return v
+
+ def solve(self):
+ i = 0
+ while i < 50:
+ i += 1
+ v = self.step(self._vertex_s8y)
+ residue = self._vertex_s8y - v
+ residue *= residue
+ if residue.sum() < 0.0001:
+ break
+ self._vertex_s8y = v
+ mp = [(self._g1_vertex_map.inverse[ix],
+ self._g2_vertex_map.inverse[v])
+ for (ix, v) in
+ enumerate(self._vertex_s8y.argmax(1))]
+ return dict(mp)
+
+##############################################################################
+# EigenPipelineSimilarity2
+
+class EigenPipelineSimilarity2(EigenBase):
+
+ def __init__(self, *args, **kwargs):
+ basekwargs = copy.copy(kwargs)
+ del basekwargs['alpha']
+ EigenBase.__init__(self, *args, **basekwargs)
+ self.init_operator(alpha=kwargs['alpha'])
+
+ def init_operator(self, alpha):
+ def edges(pip, v_id):
+ def from_fn(x): return (x[1], x[2])
+ def to_fn(x): return (x[0], x[2])
+ return chain(imap(from_fn, pip.graph.iter_edges_from(v_id)),
+ imap(to_fn, pip.graph.iter_edges_to(v_id)))
+ num_verts_p1 = len(self._p1.graph.vertices)
+ num_verts_p2 = len(self._p2.graph.vertices)
+ n = num_verts_p1 * num_verts_p2
+ def ix(a,b): return num_verts_p2 * a + b
+ # h is the raw substochastic matrix
+ from scipy import sparse
+ h = sparse.lil_matrix((n, n))
+ # a is the dangling node vector
+ a = mzeros(n)
+ for i in xrange(num_verts_p1):
+ v1_id = self._g1_vertex_map.inverse[i]
+ for j in xrange(num_verts_p2):
+ ix_ij = ix(i,j)
+ v2_id = self._g2_vertex_map.inverse[j]
+ running_sum = 0.0
+ for (_, p1_edge) in edges(self._p1, v1_id):
+ for (_, p2_edge) in edges(self._p2, v2_id):
+ e1_id = self._g1_edge_map[p1_edge]
+ e2_id = self._g2_edge_map[p2_edge]
+ running_sum += self._edge_s8y[e1_id, e2_id]
+ if running_sum == 0.0:
+ a[0, ix_ij] = 1.0
+ continue
+ for (p1_v, p1_edge_id) in edges(self._p1, v1_id):
+ for (p2_v, p2_edge_id) in edges(self._p2, v2_id):
+ e1_id = self._g1_edge_map[p1_edge_id]
+ e2_id = self._g2_edge_map[p2_edge_id]
+ p1_v_id = self._g1_vertex_map[p1_v]
+ p2_v_id = self._g2_vertex_map[p2_v]
+ value = self._edge_s8y[e1_id, e2_id] / running_sum
+ h[ix_ij, ix(p1_v_id, p2_v_id)] = value
+
+ self._alpha = alpha
+ self._n = n
+ self._h = h
+ self._a = a
+ self._e = mones(n) / n
+
+ def step(self, pi_k):
+ r = pi_k * self._h * self._alpha
+ t = pi_k * self._alpha * self._a.transpose()
+ r += self._v * (t[0,0] + 1.0 - self._alpha)
+ return r
+
+ def solve_v(self, s8y):
+ fl = s8y.flatten()
+ self._v = fl / fl.sum()
+ v = copy.copy(self._e)
+ step = 0
+ def write_current_matrix():
+ f = open('%s/%s_%03d.v' % (temporary_directory(),
+ self._debug_matrix_file, step), 'w')
+ x = v.reshape(len(self._p1.modules),
+ len(self._p2.modules))
+ for i in xrange(len(self._p1.modules)):
+ for j in xrange(len(self._p2.modules)):
+ f.write('%f ' % x[i,j])
+ f.write('\n')
+ f.close()
+ while 1:
+ if self._debug:
+ write_current_matrix()
+ new = self.step(v)
+ r = (v-new)
+ r = scipy.multiply(r,r)
+ s = r.sum()
+ if s < 0.0000001 and step >= 10:
+ return v
+ step += 1
+ v = new
+
+ def solve(self):
+ def write_debug_pipeline_positions(pipeline, mmap, f):
+ f.write('%d %d\n' % (len(pipeline.modules),
+ len(pipeline.connections)))
+ for k, v in mmap.iteritems():
+ f.write('%d %d\n' % (k, v))
+ c = pipeline_centroid(pipeline)
+ mn, mx = pipeline_bbox(pipeline)
+ f.write('%f %f %f %f\n' % (mn.x, mn.y, mx.x, mx.y))
+ for i, m in pipeline.modules.iteritems():
+ nc = m.center - c
+ f.write('%d %s %f %f\n' % (i, m.name, nc.x, nc.y))
+ for i, c in pipeline.connections.iteritems():
+ f.write('%d %d %d\n' % (i, c.sourceId, c.destinationId))
+
+ if self._debug:
+ out = open('%s/pipelines.txt' % temporary_directory(), 'w')
+ write_debug_pipeline_positions(self._p1, self._g1_vertex_map, out)
+ write_debug_pipeline_positions(self._p2, self._g2_vertex_map, out)
+ self.print_s8ys()
+
+ self._debug_matrix_file = 'input_matrix'
+ r_in = self.solve_v(self._input_vertex_s8y)
+ self._debug_matrix_file = 'output_matrix'
+ r_out = self.solve_v(self._output_vertex_s8y)
+ r_in = r_in.reshape(len(self._p1.modules),
+ len(self._p2.modules))
+ r_out = r_out.reshape(len(self._p1.modules),
+ len(self._p2.modules))
+
+ s = r_in.sum(1)
+ s[s==0.0] = 1
+ r_in /= s
+
+ s = r_out.sum(1)
+ s[s==0.0] = 1
+ r_out /= s
+
+ r_combined = scipy.multiply(r_in, r_out)
+
+ # Breaks ties on combined similarity
+ r_in = r_in * 0.9 + r_combined * 0.1
+ r_out = r_out * 0.9 + r_combined * 0.1
+
+ if self._debug:
+ print "== G1 =="
+ for (k,v) in sorted(self._g1_vertex_map.iteritems(), key=operator.itemgetter(1)):
+ print v, k, self._p1.modules[k].name
+ print "== G2 =="
+ for (k,v) in sorted(self._g2_vertex_map.iteritems(), key=operator.itemgetter(1)):
+ print v, k, self._p2.modules[k].name
+
+ print "input similarity"
+ self.pm(r_in, digits=3)
+ print "output similarity"
+ self.pm(r_out, digits=3)
+ print "combined similarity"
+ self.pm(r_combined, digits=3)
+
+ inputmap = dict([(self._g1_vertex_map.inverse[ix],
+ self._g2_vertex_map.inverse[v[0,0]])
+ for (ix, v) in
+ enumerate(r_in.argmax(1))])
+ outputmap = dict([(self._g1_vertex_map.inverse[ix],
+ self._g2_vertex_map.inverse[v[0,0]])
+ for (ix, v) in
+ enumerate(r_out.argmax(1))])
+ combinedmap = dict([(self._g1_vertex_map.inverse[ix],
+ self._g2_vertex_map.inverse[v[0,0]])
+ for (ix, v) in
+ enumerate(r_combined.argmax(1))])
+# print inputmap
+# print outputmap
+ return inputmap, outputmap, combinedmap
+
+
+
diff --git a/vistrails/core/analogy/pipeline_utils.py b/vistrails/core/analogy/pipeline_utils.py
new file mode 100644
index 0000000..c9e3f3a
--- /dev/null
+++ b/vistrails/core/analogy/pipeline_utils.py
@@ -0,0 +1,66 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+
+############################################################################
+# Utility functions for debugging on eigen.py
+from vistrails.core.data_structures.point import Point
+
+def smart_sum(v):
+ try:
+ fst = v.next()
+ return sum(v, fst)
+ except:
+ pass
+ fst = v[0]
+ return sum(v[1:], fst)
+
+def pipeline_centroid(pipeline):
+ """Returns the centroid of a given pipeline."""
+ return (smart_sum(x.location for
+ x in pipeline.modules.itervalues()) *
+ (1.0 / len(pipeline.modules)))
+
+def pipeline_bbox(pipeline):
+ mn_x = 1000000000.0
+ mn_y = 1000000000.0
+ mx_x = -1000000000.0
+ mx_y = -1000000000.0
+ for m in pipeline.modules.itervalues():
+ mn_x = min(mn_x, m.location.x)
+ mn_y = min(mn_y, m.location.y)
+ mx_x = max(mx_x, m.location.x)
+ mx_y = max(mx_y, m.location.y)
+ return (Point(mn_x, mn_y), Point(mx_x, mx_y))
diff --git a/vistrails/core/api.py b/vistrails/core/api.py
new file mode 100644
index 0000000..951046c
--- /dev/null
+++ b/vistrails/core/api.py
@@ -0,0 +1,572 @@
+import itertools
+
+import vistrails.core.application
+from vistrails.core.db.locator import FileLocator, untitled_locator
+import vistrails.core.db.io
+from vistrails.core.modules.basic_modules import identifier as basic_pkg
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.modules.utils import create_port_spec_string
+from vistrails.core.packagemanager import get_package_manager
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.vistrail.port_spec import PortSpec
+from vistrails.core.vistrail.vistrail import Vistrail
+
+# from core.modules.package import Package as _Package
+# from core.vistrail.module import Module as _Module
+
+_api = None
+
+def get_api():
+ if _api is None:
+ set_api(VisTrailsAPI())
+ return _api
+
+def set_api(api):
+ global _api
+ _api = api
+
+class Port(object):
+ def __init__(self, module, port_spec):
+ # print 'calling vistrails_port.__init__'
+ self._vistrails_module = module
+ self._port_spec = port_spec
+
+ def __call__(self, *args, **kwargs):
+ if len(args) + len(kwargs) > 0:
+ self._vistrails_module._update_func(self._port_spec,
+ *args, **kwargs)
+ return None
+ return self
+
+class Module(object):
+ def __init__(self, module, *args, **kwargs):
+ self._module = module
+ self._module_desc = self._module.module_descriptor
+ self._package = None # don't think we need this now
+ self.__call__(*args, **kwargs)
+
+ def __call__(self, *args, **kwargs):
+ reg = get_module_registry()
+ if len(args) > 0:
+ constant_desc = reg.get_descriptor_by_name(basic_pkg, "Constant")
+ if reg.is_descriptor_subclass(self._module_desc, constant_desc):
+ kwargs['value'] = args[0]
+
+ for attr_name, value in kwargs.iteritems():
+ self._process_attr_value(attr_name, value)
+ return self
+
+ @staticmethod
+ def create_module(module, *args, **kwargs):
+ m = Module(module)
+ return m
+
+ def _process_attr_value(self, attr_name, value):
+ if self._module.has_port_spec(attr_name, 'input'):
+ port_spec = self._module.get_port_spec(attr_name, 'input')
+
+ args = None
+ # FIXME want this to be any iterable
+ if isinstance(value, tuple):
+ args = value
+ else:
+ args = (value,)
+ self._update_func(port_spec, *args)
+ else:
+ raise AttributeError("type object '%s' has no "
+ "attribute '%s'" % \
+ (self.__class__.__name__,
+ attr_name))
+
+ def __getattr__(self, attr_name):
+ def create_port(port_spec):
+ return Port(self, port_spec)
+
+ if self._module.has_port_spec(attr_name, 'output'):
+ port_spec = \
+ self._module.get_port_spec(attr_name, 'output')
+ return create_port(port_spec)
+ elif self._module.has_port_spec(attr_name, 'input'):
+ port_spec = \
+ self._module.get_port_spec(attr_name, 'input')
+ return create_port(port_spec)
+ else:
+ raise AttributeError("type object '%s' has no "
+ "attribute '%s'" % \
+ (self.__class__.__name__,
+ attr_name))
+
+ def __setattr__(self, attr_name, value):
+ if attr_name.startswith('_'):
+ self.__dict__[attr_name] = value
+ else:
+ self._process_attr_value(attr_name, value)
+
+ def _update_func(self, port_spec, *args, **kwargs):
+ # print 'running _update_func', port_spec.name
+ # print args
+ vt_api = get_api()
+
+ if port_spec.type != 'input':
+ if self._module.has_port_spec(port_spec.name, 'input'):
+ port_spec = \
+ self._module.get_port_spec(port_spec.name, 'input')
+ else:
+ raise TypeError("cannot update an output port spec")
+
+ # FIXME deal with kwargs
+ num_ports = 0
+ num_params = 0
+ for value in args:
+ # print 'processing', type(value), value
+ if isinstance(value, Port):
+ # make connection to specified output port
+ # print 'updating port'
+ num_ports += 1
+ elif isinstance(value, Module):
+ # make connection to 'self' output port of value
+ # print 'updating module'
+ num_ports += 1
+ else:
+ # print 'update literal', type(value), value
+ num_params += 1
+ if num_ports > 1 or (num_ports == 1 and num_params > 0):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ tuple_desc = reg.get_descriptor_by_name(basic_pkg, 'Tuple')
+ tuple_module = vt_api.add_module_from_descriptor(tuple_desc)
+ output_port_spec = PortSpec(id=-1,
+ name='value',
+ type='output',
+ sigstring=port_spec.sigstring)
+ vt_api.add_port_spec(tuple_module, output_port_spec)
+ self._update_func(port_spec, *[tuple_module.value()])
+ assert len(port_spec.descriptors()) == len(args)
+ for i, descriptor in enumerate(port_spec.descriptors()):
+ arg_name = 'arg%d' % i
+ sigstring = create_port_spec_string([descriptor.spec_tuple])
+ tuple_port_spec = PortSpec(id=-1,
+ name=arg_name,
+ type='input',
+ sigstring=sigstring)
+ vt_api.add_port_spec(tuple_module, tuple_port_spec)
+ tuple_module._process_attr_value(arg_name, args[i])
+
+ elif num_ports == 1:
+ other = args[0]
+ if isinstance(other, Port):
+ if other._port_spec.type != 'output':
+ other_module = other._vistrails_module._module
+ if other_module.has_port_spec(port_spec.name,
+ 'output'):
+ other_port_spec = \
+ other_module.get_port_spec(port_spec.name,
+ 'output')
+ else:
+ raise TypeError("cannot update an input "
+ "port spec")
+ else:
+ other_port_spec = other._port_spec
+
+ vt_api.add_connection(other._vistrails_module,
+ other_port_spec,
+ self,
+ port_spec)
+ elif isinstance(other, Module):
+ other_port_spec = \
+ other._module.get_port_spec('self', 'output')
+ vt_api.add_connection(other,
+ other_port_spec,
+ self,
+ port_spec)
+ else:
+ vt_api.change_parameter(self,
+ port_spec.name,
+ [str(x) for x in args])
+
+class Package(object):
+ def __init__(self, identifier, version=''):
+ self._package = None
+ # namespace_dict : {namespace : (namespace_dict, modules)}
+ self._namespaces = ({}, [])
+ reg = get_module_registry()
+ self._package = reg.get_package_by_name(identifier, version)
+ for desc in self._package.descriptor_list:
+ if desc.namespace:
+ namespaces = desc.namespace.split('|')
+ else:
+ namespaces = []
+ cur_namespace = self._namespaces[0]
+ cur_modules = self._namespaces[1]
+ for namespace in namespaces:
+ if namespace not in cur_namespace:
+ cur_namespace[namespace] = ({}, [])
+ cur_modules = cur_namespace[namespace][1]
+ cur_namespace = cur_namespace[namespace][0]
+ cur_modules.append(desc)
+
+ iteritems = [self._namespaces]
+ for (namespaces, modules) in iteritems:
+ modules.sort(key=lambda d: d.name)
+ iteritems = itertools.chain(iteritems, namespaces.itervalues())
+
+ def __getattr__(self, attr_name):
+ reg = get_module_registry()
+ d = reg.get_descriptor_by_name(self._package.identifier,
+ attr_name, '',
+ self._package.version)
+ vt_api = get_api()
+ module = vt_api.add_module_from_descriptor(d)
+ return module
+
+ def get_modules(self, namespace=None):
+ modules = []
+ if namespace == '':
+ modules = [d.name for d in self._namespaces[1]]
+ else:
+ if namespace is None:
+ namespace = ''
+ modules = [d.name for d in self._namespaces[1]]
+ namespaces = sorted(self._namespaces[0].iteritems())
+ else:
+ namespace_dict = self._namespaces[0]
+ descs = self._namespaces[1]
+ for ns in namespace.split('|'):
+ (namespace_dict, descs) = namespace_dict[ns]
+ namespaces = [(namespace, (namespace_dict, descs))]
+
+ for (ns, (child_namespaces, descs)) in namespaces:
+ modules.extend(ns + '|' + d.name for d in descs)
+ namespaces = \
+ itertools.chain([(ns + '|' + c[0], c[1])
+ for c in child_namespaces.iteritems()],
+ namespaces)
+ return modules
+
+ def list_modules(self, namespace=None):
+ for module in self.get_modules(namespace):
+ print module
+
+class VisTrailsAPI(object):
+
+ # !!! Do not pass controller or app unless you know what you are doing !!!
+ def __init__(self, controller=None, app=None):
+ self._controller = controller
+ self._app = app
+ self._packages = None
+ self._old_log = None
+
+ def _get_app(self):
+ if self._app is not None:
+ return self._app
+ return vistrails.core.application.get_vistrails_application()
+ app = property(_get_app)
+
+ # !!! Do not call set_app unless you know what you are doing !!!
+ def set_app(self, app):
+ self._app = app
+
+ def _get_controller(self):
+ if self._controller is not None:
+ return self._controller
+ controller = self.app.get_controller()
+ if controller is None:
+ raise ValueError("You must have a vistrail open before calling "
+ "this API method.")
+ return controller
+ controller = property(_get_controller)
+
+ # !!! Do not call set_controller unless you know what you are doing !!!
+ def set_controller(self, controller=None):
+ self._controller = controller
+
+ def add_module(self, identifier, name, namespace='', internal_version=-1):
+ m = self.controller.add_module(identifier, name, namespace,
+ internal_version=internal_version)
+ # have to go back since there is a copy when the action is performed
+ module = self.controller.current_pipeline.modules[m.id]
+ return Module.create_module(module)
+
+ def add_module_from_descriptor(self, desc):
+ m = self.controller.add_module_from_descriptor(desc)
+ # have to go back since there is a copy when the action is performed
+ module = self.controller.current_pipeline.modules[m.id]
+ return Module.create_module(module)
+
+ def add_connection(self, module_a, port_a, module_b, port_b):
+ conn = self.controller.add_connection(module_a._module.id, port_a,
+ module_b._module.id, port_b)
+
+ def add_port_spec(self, module, port_spec):
+ self.controller.add_module_port(module._module.id,
+ (port_spec.type, port_spec.name,
+ port_spec.sigstring))
+
+ def add_and_connect_module(self,
+ identifier,
+ name,
+ port,
+ module_b,
+ port_b,
+ is_source=False,
+ auto_layout=True,
+ **kwargs):
+ """Adds a module and connects in single action. Returns new module.
+
+ identifier - package identifier for new module
+ name - name of new module
+ module_b - existing module to connect new module to
+ port - port on new module to connect
+ port_b - port on existing module to connect
+ is_source - whether or not new module is source of connection
+ auto_layout - layout pipeline
+ **kwargs - additional arguments to create module
+ """
+
+ module = self.controller.create_module(identifier, name, **kwargs)
+
+ if is_source:
+ source, source_port = module, port
+ target, target_port = module_b._module, port_b
+ else:
+ target, target_port = module, port
+ source, source_port = module_b._module, port_b
+
+ create_conn = self.controller.create_connection
+ conn = create_conn(source, source_port, target, target_port)
+
+ if auto_layout:
+ layout = self.controller.layout_modules_ops
+ layout_ops = layout([], True, [module], [conn], None, True)
+ else:
+ layout_ops = []
+
+ ops = [('add', module), ('add', conn)] + layout_ops
+ action = vistrails.core.db.action.create_action(ops)
+ self.controller.add_new_action(action)
+ version = self.controller.perform_action(action)
+ self.controller.change_selected_version(version)
+
+ # have to go back since there is a copy when the action is performed
+ m = self.controller.current_pipeline.modules[module.id]
+ return Module.create_module(m)
+
+ def change_parameter(self, module, function_name, param_list):
+ self.controller.update_function(module._module, function_name,
+ param_list)
+
+ def execute(self, custom_aliases=None, custom_params=None,
+ extra_info=None, reason='API Pipeline Execution'):
+ return self.controller.execute_current_workflow(custom_aliases, custom_params,
+ extra_info, reason)
+
+ def get_packages(self):
+ if self._packages is None:
+ self._packages = {}
+ self._old_package_ids = {}
+ reg = get_module_registry()
+ for package in reg.package_list:
+ pkg = Package(package.identifier, package.version)
+ self._packages[package.identifier] = pkg
+ for old_name in package.old_identifiers:
+ self._old_package_ids[old_name] = pkg
+ return self._packages
+
+ def list_packages(self):
+ for package in self.get_packages():
+ print package
+
+ def get_package(self, identifier):
+ packages = self.get_packages()
+ if identifier not in packages and identifier in self._old_package_ids:
+ return self._old_package_ids[identifier]
+ else:
+ return packages[identifier]
+
+ def load_package(self, identifier, codepath):
+ packages = self.get_packages()
+ if identifier not in packages:
+ pm = get_package_manager()
+ pm.late_enable_package(codepath)
+ self._packages = None
+ return self.get_package(identifier)
+
+ def list_modules(self):
+ for identifier, package in sorted(self.get_packages().iteritems()):
+ print identifier
+ for module in package.get_modules():
+ print ' --', module
+
+ def _convert_version(self, version):
+ if isinstance(version, basestring):
+ try:
+ version = \
+ self.controller.vistrail.get_version_number(version)
+ except:
+ raise ValueError('Cannot locate version "%s"' % version)
+ return version
+
+ def tag_version(self, tag, version=None):
+ if version is None:
+ version = self.controller.current_version
+ else:
+ version = self._convert_version(version)
+ self.controller.vistrail.set_tag(version, tag)
+
+ def save_vistrail(self, locator_str):
+ return self.app.save_vistrail(locator_str)
+
+ def new_vistrail(self):
+ return bool(self.app.new_vistrail())
+
+ def load_vistrail(self, locator_str):
+ return bool(self.app.open_vistrail(locator_str))
+ open_vistrail = load_vistrail
+
+ def load_workflow(self, locator_str):
+ self.app.open_workflow(locator_str)
+ open_workflow = load_workflow
+
+ def select_version(self, version):
+ self.app.select_version(version)
+
+ def close_vistrail(self):
+ self.app.close_vistrail()
+
+ def get_current_workflow(self):
+ return self.controller.current_pipeline
+
+ def get_all_executions(self):
+ wf_execs = []
+ if (self._old_log is None and
+ hasattr(self.controller.vistrail, 'db_log_filename') and
+ self.controller.vistrail.db_log_filename is not None):
+ self._old_log = \
+ vistrails.core.db.io.open_log(self.controller.vistrail.db_log_filename, True)
+ if self._old_log is not None:
+ wf_execs.extend(self._old_log.workflow_execs)
+ wf_execs.extend(self.controller.log.workflow_execs)
+ return wf_execs
+
+import os
+import unittest
+from vistrails.core.system import temporary_directory
+
+class TestAPI(unittest.TestCase):
+ if not hasattr(unittest.TestCase, 'assertIsInstance'):
+ def assertIsInstance(self, obj, cls, msg=None):
+ assert(isinstance(obj, cls))
+
+ @classmethod
+ def setUpClass(cls):
+ get_api().new_vistrail()
+
+ @classmethod
+ def tearDownClass(cls):
+ get_api().close_vistrail()
+
+ def setUp(self):
+ get_api().controller.change_selected_version(0)
+
+ def get_basic_package(self):
+ basic = get_api().get_package(basic_pkg)
+ self.assertIsInstance(basic, Package)
+ return basic
+
+ def create_modules(self,basic):
+ s1 = basic.String("abc")
+ self.assertIsInstance(s1, Module)
+ s2 = basic.String("def")
+ self.assertIsInstance(s2, Module)
+ return s1, s2
+
+ def test_api(self):
+ self.get_basic_package()
+
+ def test_add_modules(self):
+ basic = self.get_basic_package()
+ s1, s2 = self.create_modules(basic)
+
+ # assert there exist two String modules
+ self.assertEqual(len(get_api().controller.current_pipeline.modules), 2)
+ for m in get_api().controller.current_pipeline.modules.itervalues():
+ self.assertEqual(m.package, basic_pkg)
+ self.assertEqual(m.name, "String")
+
+ def check_connections(self):
+ conns = []
+ modules = get_api().controller.current_pipeline.modules
+ for c in get_api().controller.current_pipeline.connections.itervalues():
+ conns.append((modules[c.sourceId].name, c.source.name,
+ modules[c.destinationId].name, c.destination.name))
+ conns.sort()
+ self.assertEqual(conns,
+ [('String', 'value', 'ConcatenateString', 'str1'),
+ ('String', 'value', 'ConcatenateString', 'str2')])
+
+ def test_add_connections_by_assignment(self):
+ basic = self.get_basic_package()
+ s1, s2 = self.create_modules(basic)
+ c = basic.ConcatenateString()
+ c.str1 = s1.value
+ c.str2 = s2.value
+ self.check_connections()
+
+ def test_add_connections_by_call(self):
+ basic = self.get_basic_package()
+ s1, s2 = self.create_modules(basic)
+ c = basic.ConcatenateString()
+ c.str1(s1.value)
+ c.str2(s2.value)
+ self.check_connections()
+
+ def test_add_connections_by_constructor(self):
+ basic = self.get_basic_package()
+ s1, s2 = self.create_modules(basic)
+ c = basic.ConcatenateString(str1=s1.value, str2=s2.value)
+ self.check_connections()
+
+ def check_parameters(self):
+ params = []
+ for m in get_api().controller.current_pipeline.modules.itervalues():
+ for f in m.functions:
+ params.append((m.name, f.name, f.params[0].strValue))
+ params.sort()
+ self.assertEqual(params,
+ [('String', 'value', 'abc'),
+ ('String', 'value', 'def')])
+
+ def test_add_parameters_by_assignment(self):
+ basic = self.get_basic_package()
+ s1, s2 = self.create_modules(basic)
+ s1.value = "abc"
+ s2.value = "def"
+ self.check_parameters()
+
+ def test_add_parameters_by_call(self):
+ basic = self.get_basic_package()
+ s1, s2 = self.create_modules(basic)
+ s1.value("abc")
+ s2.value("def")
+ self.check_parameters()
+
+ def test_add_parameters_by_constructor(self):
+ basic = self.get_basic_package()
+ s1 = basic.String("abc")
+ s2 = basic.String("def")
+ self.check_parameters()
+
+ def test_write_and_read_vistrail(self):
+ self.assertTrue(get_api().new_vistrail())
+ basic = self.get_basic_package()
+ s1, s2 = self.create_modules(basic)
+ fname = os.path.join(temporary_directory(), "test_write_read.vt")
+ self.assertTrue(get_api().save_vistrail(fname))
+ self.assertTrue(os.path.exists(fname))
+ get_api().close_vistrail()
+ self.assertTrue(get_api().open_vistrail(fname))
+ self.assertEqual(get_api().controller.current_version, 4)
+ get_api().close_vistrail()
+
+if __name__ == '__main__':
+ vistrails.core.application.init()
+ unittest.main()
diff --git a/vistrails/core/application.py b/vistrails/core/application.py
new file mode 100644
index 0000000..9dd3d01
--- /dev/null
+++ b/vistrails/core/application.py
@@ -0,0 +1,833 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import atexit
+import copy
+import os
+import shutil
+import sys
+import tempfile
+import weakref
+import warnings
+
+from vistrails.core import command_line
+from vistrails.core import debug
+from vistrails.core import keychain
+from vistrails.core import system
+from vistrails.core.collection import Collection
+import vistrails.core.configuration
+from vistrails.core.db.locator import BaseLocator, FileLocator, DBLocator, \
+ UntitledLocator
+import vistrails.core.db.io
+import vistrails.core.interpreter.cached
+import vistrails.core.interpreter.default
+import vistrails.core.startup
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.core.utils import InstanceObject, VistrailsWarning
+from vistrails.core.utils.uxml import enter_named_element
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.vistrail.vistrail import Vistrail
+from vistrails.core.vistrail.controller import VistrailController
+from vistrails.db import VistrailsDBException
+
+VistrailsApplication = None
+APP_SUCCESS = 0 # Success exit code
+APP_FAIL = 1 # fialed exit code
+APP_DONE = 2 # Success but shut down prematurely (other instance called)
+
+def finalize_vistrails(app):
+ vistrails.core.interpreter.cached.CachedInterpreter.cleanup()
+
+def get_vistrails_application():
+ global VistrailsApplication
+ if VistrailsApplication is not None:
+ return VistrailsApplication()
+ return None
+
+def set_vistrails_application(app):
+ global VistrailsApplication
+ VistrailsApplication = weakref.ref(app, finalize_vistrails)
+
+def is_running_gui():
+ app = get_vistrails_application()
+ return app.is_running_gui()
+
+def init(options_dict={}, args=None):
+ app = VistrailsCoreApplication()
+ set_vistrails_application(app)
+ app.init(optionsDict=options_dict, args=args)
+ return app
+
+class VistrailsApplicationInterface(object):
+ def __init__(self):
+ self._initialized = False
+ self.notifications = {}
+
+ def setupOptions(self, args=None):
+ """ setupOptions() -> None
+ Check and store all command-line arguments
+
+ """
+ add = command_line.CommandLineParser.add_option
+ add("-S", "--startup", action="store", type="str", default=None,
+ dest="dotVistrails",
+ help="Set startup file (default is ~/.vistrails)")
+ add("-?", action="help",
+ help="show this help message and exit")
+ add("-v", "--version", action="callback",
+ callback=lambda option, opt, value, parser: self.printVersion(),
+ help="print version information and quit")
+ add("-V", "--verbose", action="store", type="int", default=None,
+ dest="verbose", help="set verboseness level (0--2, "
+ "default=0, higher means more verbose)")
+ add("-n", "--nosplash", action="store_false",
+ default = None,
+ help="don't display splash on startup")
+ add("-c", "--cache", action="store", type="int", default=None,
+ dest="cache", help="enable/disable caching")
+ add("-m", "--movies", action="store", type="int", default=None,
+ dest="movies", help="set automatic movie creation on spreadsheet "
+ "(0 or 1, default=1. Set this to zero to work around vtk bug with "
+ "offscreen renderer and opengl texture3d mappers)")
+ add("-s", "--multiheads", action="store_true",
+ default = None,
+ help="display the builder and spreadsheet on different screens "
+ "(if available)")
+ add("-x", "--maximized", action="store_true",
+ default = None,
+ help="Maximize VisTrails windows at startup")
+ add("-b", "--noninteractive", action="store_true",
+ default = None,
+ help="run in non-interactive mode")
+ add("-e", "--dumpcells", action="store", dest="dumpcells",
+ default = None,
+ help="when running in non-interactive mode, directory to dump "
+ "spreadsheet cells before exiting")
+ add("-p", "--pdf", action="store_true",
+ default = None,
+ help="dump files in pdf format (non-interactive mode only)")
+ add("-l", "--nologger", action="store_true",
+ default = None,
+ help="disable the logging")
+ add('--no-logfile', action='store_true',
+ dest='nologfile',
+ default=None,
+ help="Disable the log file (output still happens in terminal)")
+ add("-d", "--debugsignals", action="store_true",
+ default = None,
+ help="debug Qt Signals")
+ add("-a", "--parameters", action="store", dest="parameters",
+ help="workflow parameter settings (non-interactive mode only)")
+ add("-t", "--host", action="store", dest="host",
+ help="hostname or ip address of database server")
+ add("-r", "--port", action="store", type="int", default=3306,
+ dest="port", help="database port")
+ add("-f", "--db", action="store", dest="db",
+ help="database name")
+ add("-u", "--user", action="store", dest="user",
+ help="database username")
+ add("-i", "--showspreadsheetonly", action="store_true",
+ default = None,
+ help="only the spreadsheet will be shown. This implies -w was given.\
+The builder window can be accessed by a spreadsheet menu option.")
+ add("-w", "--executeworkflows", action="store_true",
+ default = None,
+ help="The workflows will be executed")
+ add("-F", "--fixedcells", action="store_true",
+ default = None,
+ help="Use a fixed spreadsheet cell size of 200*180")
+ add("-I", "--workflowinfo", action="store",
+ default = None,
+ help=("Save workflow graph and spec in specified directory "
+ "(only valid in console mode)."))
+ add("-E", "--reviewmode", action="store_true",
+ default = None,
+ help="Show the spreadsheet in the reviewing mode")
+ add("-q", "--quickstart", action="store",
+ help="Start VisTrails using the specified static registry")
+ add("-D", "--detachHistoryView", action="store_true",
+ help="Detach the history view from the builder windows")
+ add("-P", "--parameterExploration", action="store_true",
+ help="Execute Parameter Exploration")
+ add("-G", "--workflowgraph", action="store",
+ default = None,
+ help=("Save workflow graph in specified directory without running "
+ "the workflow (only valid in console mode)."))
+ add("-U", "--evolutiongraph", action="store",
+ default = None,
+ help=("Save evolution graph in specified directory without running "
+ "any workflow (only valid in console mode)."))
+ add("-g", "--noSingleInstance", action="store_true",
+ help=("Run VisTrails without the single instance restriction."))
+ add("--no-bundleinstall", action='store_false',
+ dest='installBundles',
+ help=("Do not try to install missing Python packages "
+ "automatically"))
+ add('--spawned-mode', '--spawned', action='store_true',
+ dest='spawned',
+ help=("Do not use the .vistrails directory, and load packages "
+ "automatically when needed"))
+
+ if args != None:
+ command_line.CommandLineParser.parse_options(args=args)
+ else:
+ command_line.CommandLineParser.parse_options()
+
+ def printVersion(self):
+ """ printVersion() -> None
+ Print version of Vistrail and exit
+
+ """
+ print system.about_string()
+ sys.exit(0)
+
+ def read_dotvistrails_option(self, optionsDict=None):
+ """ read_dotvistrails_option() -> None
+ Check if the user sets a new dotvistrails folder and updates
+ self.temp_configuration with the new value.
+
+ Also handles the 'spawned-mode' option, by using a temporary directory
+ as .vistrails directory, and a specific default configuration.
+ """
+ if optionsDict is None:
+ optionsDict = {}
+ def get(opt):
+ return (optionsDict.get(opt) or
+ command_line.CommandLineParser().get_option(opt))
+
+ if get('spawned'):
+ # Here we are in 'spawned' mode, i.e. we are running
+ # non-interactively as a slave
+ # We are going to create a .vistrails directory as a temporary
+ # directory and copy a specific configuration file
+ # We don't want to load packages that the user might enabled in
+ # this machine's configuration file as it would slow down the
+ # startup time, but we'll load any needed package without
+ # confirmation
+ tmpdir = tempfile.mkdtemp(prefix='vt_spawned_')
+ @atexit.register
+ def clean_dotvistrails():
+ shutil.rmtree(tmpdir, ignore_errors=True)
+ self.temp_configuration.dotVistrails = tmpdir
+ if get('dotVistrails') is not None:
+ debug.warning("--startup option ignored since --spawned-mode "
+ "is used")
+ shutil.copyfile(os.path.join(system.vistrails_root_directory(),
+ 'core', 'resources',
+ 'spawned_startup_xml'),
+ os.path.join(tmpdir, 'startup.xml'))
+ self.temp_configuration.enablePackagesSilently = True
+ self.temp_configuration.nologfile = True
+ self.temp_configuration.singleInstance = False
+ elif get('dotVistrails') is not None:
+ self.temp_configuration.dotVistrails = get('dotVistrails')
+
+ def readOptions(self):
+ """ readOptions() -> None
+ Read arguments from the command line
+
+ """
+ get = command_line.CommandLineParser().get_option
+ if get('nosplash')!=None:
+ self.temp_configuration.showSplash = bool(get('nosplash'))
+ if get('debugsignals')!=None:
+ self.temp_configuration.debugSignals = bool(get('debugsignals'))
+ if get('dotVistrails')!=None:
+ self.temp_configuration.dotVistrails = get('dotVistrails')
+ if get('multiheads')!=None:
+ self.temp_configuration.multiHeads = bool(get('multiheads'))
+ if get('maximized')!=None:
+ self.temp_configuration.maximizeWindows = bool(get('maximized'))
+ if get('movies')!=None:
+ self.temp_configuration.showMovies = bool(get('movies'))
+ if get('cache')!=None:
+ self.temp_configuration.useCache = bool(get('cache'))
+ if get('verbose')!=None:
+ self.temp_configuration.verbosenessLevel = get('verbose')
+ dbg = debug.DebugPrint.getInstance()
+ levels = [dbg.WARNING, dbg.INFO, dbg.DEBUG]
+ dbg.set_message_level(levels[get('verbose')])
+ if get('fixedcells') != None:
+ self.temp_configuration.fixedSpreadsheetCells = str(get('fixedcells'))
+ if get('noninteractive')!=None:
+ self.temp_configuration.interactiveMode = \
+ not bool(get('noninteractive'))
+ if get('workflowinfo') != None:
+ self.temp_configuration.workflowInfo = str(get('workflowinfo'))
+ if get('dumpcells') != None:
+ self.temp_configuration.spreadsheetDumpCells = get('dumpcells')
+ if get('pdf') != None:
+ self.temp_configuration.spreadsheetDumpPDF = get('pdf')
+ if get('workflowgraph') != None:
+ self.temp_configuration.workflowGraph = str(get('workflowgraph'))
+ if get('evolutiongraph') != None:
+ self.temp_configuration.evolutionGraph = str(get('evolutiongraph'))
+ if get('executeworkflows') != None:
+ self.temp_configuration.executeWorkflows = \
+ bool(get('executeworkflows'))
+ if get('showspreadsheetonly') != None:
+ self.temp_configuration.showSpreadsheetOnly = \
+ bool(get('showspreadsheetonly'))
+ # asking to show only the spreadsheet will force the workflows to
+ # be executed
+ if get('reviewmode') != None:
+ self.temp_configuration.reviewMode = bool(get('reviewmode'))
+
+ if self.temp_configuration.showSpreadsheetOnly and not self.temp_configuration.reviewMode:
+ self.temp_configuration.executeWorkflows = True
+
+ self.temp_db_options = InstanceObject(host=get('host'),
+ port=get('port'),
+ db=get('db'),
+ user=get('user'),
+ parameters=get('parameters')
+ )
+ if get('nologger')!=None:
+ self.temp_configuration.nologger = bool(get('nologger'))
+ if get('quickstart') != None:
+ self.temp_configuration.staticRegistry = str(get('quickstart'))
+ if get('parameterExploration')!= None:
+ self.temp_configuration.parameterExploration = \
+ str(get('parameterExploration'))
+ if get('detachHistoryView')!= None:
+ self.temp_configuration.detachHistoryView = bool(get('detachHistoryView'))
+ if get('noSingleInstance')!=None:
+ self.temp_configuration.singleInstance = not bool(get('noSingleInstance'))
+ if get('installBundles')!=None:
+ self.temp_configuration.installBundles = bool(get('installBundles'))
+ self.input = command_line.CommandLineParser().positional_arguments()
+
+ def init(self, optionsDict=None, args=None):
+ """ VistrailsApplicationSingleton(optionDict: dict)
+ -> VistrailsApplicationSingleton
+ Create the application with a dict of settings
+
+ """
+ warnings.simplefilter('once', VistrailsWarning, append=True)
+ # gui.theme.initializeCurrentTheme()
+ # self.connect(self, QtCore.SIGNAL("aboutToQuit()"), self.finishSession)
+
+ # This is the persistent configuration
+ # Setup configuration to default
+ self.configuration = vistrails.core.configuration.default()
+
+ self.keyChain = keychain.KeyChain()
+ self.setupOptions(args)
+
+ # self.temp_configuration is the configuration that will be updated
+ # with the command line and custom options dictionary.
+ # We have to do this because we don't want to make these settings
+ # persistent. This is the actual VisTrails current configuration
+ self.temp_configuration = copy.copy(self.configuration)
+
+ vistrails.core.interpreter.default.connect_to_configuration(self.temp_configuration)
+
+ # now we want to open vistrails and point to a specific version
+ # we will store the version in temp options as it doesn't
+ # need to be persistent. We will do the same to database
+ # information passed in the command line
+ self.temp_db_options = InstanceObject(host=None,
+ port=None,
+ db=None,
+ user=None,
+ vt_id=None,
+ parameters=None
+ )
+
+ # Read only new .vistrails folder option if passed in the command line
+ # or in the optionsDict because this may affect the configuration file
+ # VistrailsStartup will load. This updates self.temp_configuration
+ self.read_dotvistrails_option(optionsDict)
+
+ # the problem here is that if the user pointed to a new .vistrails
+ # folder, the persistent configuration will always point to the
+ # default ~/.vistrails. So we will copy whatever it's on
+ # temp_configuration to the persistent one. In case the configuration
+ # that is on disk is different, it will overwrite this one
+ self.configuration.dotVistrails = self.temp_configuration.dotVistrails
+
+ # During this initialization, VistrailsStartup will load the
+ # configuration from disk and update both configurations
+ self.vistrailsStartup = \
+ vistrails.core.startup.VistrailsStartup(self.configuration,
+ self.temp_configuration)
+
+ # Starting in version 1.2.1 logging is enabled by default.
+ # Users have to explicitly disable it through the command-line
+ self.configuration.nologger = False
+ self.temp_configuration.nologger = False
+
+ if optionsDict:
+ for (k, v) in optionsDict.iteritems():
+ setattr(self.temp_configuration, k, v)
+
+ # Command line options override temp_configuration
+ self.readOptions()
+
+ self.check_all_requirements()
+
+ if self.temp_configuration.check('staticRegistry'):
+ reg = self.temp_configuration.staticRegistry
+ else:
+ reg = None
+ self.vistrailsStartup.set_registry(reg)
+
+ def check_all_requirements(self):
+ # check scipy
+ vistrails.core.requirements.require_python_module('scipy', {
+ 'linux-debian': 'python-scipy',
+ 'linux-ubuntu': 'python-scipy',
+ 'linux-fedora': 'scipy',
+ 'pip': 'scipy'})
+
+ # ZIP manipulations use the command-line executables
+ vistrails.core.requirements.require_executable('zip')
+ vistrails.core.requirements.require_executable('unzip')
+
+ def get_python_environment(self):
+ """get_python_environment(): returns an environment that
+includes local definitions from startup.py. Should only be called
+after self.init()"""
+ return self._python_environment
+
+ def destroy(self):
+ """ destroy() -> None
+ Finalize all packages to, such as, get rid of temp files
+
+ """
+ if hasattr(self, 'vistrailsStartup'):
+ self.vistrailsStartup.destroy()
+ Collection.clearInstance()
+
+ def __del__(self):
+ """ __del__() -> None
+ Make sure to finalize in the destructor
+
+ """
+ self.destroy()
+
+ def _parse_vtinfo(self, info, use_filename=True):
+ name = None
+ version = None
+ if use_filename and os.path.isfile(info):
+ name = info
+ else:
+ data = info.split(":")
+ if len(data) >= 2:
+ if use_filename:
+ if os.path.isfile(str(data[0])):
+ name = str(data[0])
+ else:
+ # maybe we are running on Windows and a full path
+ # was passed as the filename so it has a : separating
+ # the driver letter
+ if system.systemType in ["Windows", "Microsoft"]:
+ if os.path.isfile(":".join(data[:2])):
+ name = ":".join(data[:2])
+ data.pop(0)
+ data[0] = name
+ elif not use_filename:
+ name = str(data[0])
+ # will try to convert version to int
+ # if it fails, it's a tag name
+ try:
+ #maybe a tag name contains ':' in its name
+ #so we need to bring it back together
+ rest = ":".join(data[1:])
+ version = int(rest)
+ except ValueError:
+ version = str(rest)
+ elif len(data) == 1:
+ if use_filename and os.path.isfile(str(data[0])):
+ name = str(data[0])
+ elif not use_filename:
+ name = str(data[0])
+ return (name, version)
+
+ def process_interactive_input(self):
+ pe = None
+ usedb = False
+ if self.temp_db_options.host:
+ usedb = True
+ if self.input:
+ #check if versions are embedded in the filename
+ for filename in self.input:
+ f_name, version = self._parse_vtinfo(filename, not usedb)
+ locator = None
+ if f_name is None:
+ debug.critical("Could not find file %s" % filename)
+ return False
+ elif not usedb:
+ locator = FileLocator(os.path.abspath(f_name))
+ #_vnode and _vtag will be set when a .vtl file is open and
+ # it can be either a FileLocator or a DBLocator
+
+ elif usedb:
+ locator = DBLocator(host=self.temp_db_options.host,
+ port=self.temp_db_options.port,
+ database=self.temp_db_options.db,
+ user='',
+ passwd='',
+ obj_id=f_name,
+ obj_type=None,
+ connection_id=None)
+ if locator:
+ if self.temp_configuration.check('parameterExploration'):
+ pe = version
+ version = None
+ else:
+ if hasattr(locator, '_vnode') and \
+ locator._vnode is not None:
+ version = locator._vnode
+ if hasattr(locator,'_vtag'):
+ # if a tag is set, it should be used instead of the
+ # version number
+ if locator._vtag != '':
+ version = locator._vtag
+ execute = self.temp_configuration.executeWorkflows
+ mashuptrail = None
+ mashupversion = None
+ if hasattr(locator, '_mshptrail'):
+ mashuptrail = locator._mshptrail
+ if hasattr(locator, '_mshpversion'):
+ mashupversion = locator._mshpversion
+ if mashupversion:
+ execute = True
+ if not self.temp_configuration.showSpreadsheetOnly:
+ self.showBuilderWindow()
+ self.builderWindow.open_vistrail_without_prompt(locator,
+ version, execute,
+ mashuptrail=mashuptrail,
+ mashupVersion=mashupversion)
+
+ if self.temp_configuration.check('parameterExploration'):
+ self.builderWindow.executeParameterExploration(pe)
+
+ if self.temp_configuration.reviewMode:
+ self.builderWindow.interactiveExportCurrentPipeline()
+
+ return True
+
+ def finishSession(self):
+ vistrails.core.interpreter.cached.CachedInterpreter.cleanup()
+
+ def save_configuration(self):
+ """ save_configuration() -> None
+ Save the current vistrail configuration to the startup.xml file.
+ This is required to capture changes to the configuration that we
+ make programmatically during the session, ie., browsed directories or
+ window sizes.
+
+ """
+ dom = self.vistrailsStartup.startup_dom()
+ doc = dom.documentElement
+ configuration_element = enter_named_element(doc, 'configuration')
+ doc.removeChild(configuration_element)
+ self.configuration.write_to_dom(dom, doc)
+ self.vistrailsStartup.write_startup_dom(dom)
+ dom.unlink()
+
+ def create_notification(self, notification_id, *args, **kwargs):
+ notifications = self.notifications
+ if notification_id not in notifications:
+ notifications[notification_id] = set()
+ else:
+ print "already added notification", notification_id
+
+ def register_notification(self, notification_id, method, *args, **kwargs):
+ notifications = self.notifications
+ #print '>>> GLOBAL adding notification', notification_id, method
+ #print id(notifications), notifications
+ if notification_id not in notifications:
+ self.create_notification(notification_id)
+ notifications[notification_id].add(method)
+
+ def unregister_notification(self, notification_id, method, *args, **kwargs):
+ notifications = self.notifications
+ #print '>>> GLOBAL remove notification', notification_id, method
+ #print id(notifications), notifications
+ if notification_id in notifications:
+ notifications[notification_id].remove(method)
+
+ def send_notification(self, notification_id, *args):
+ # do global notifications
+ if notification_id in self.notifications:
+ # print 'global notification ', notification_id
+ for m in self.notifications[notification_id]:
+ try:
+ #print " m: ", m
+ m(*args)
+ except Exception, e:
+ import traceback
+ traceback.print_exc()
+
+ def showBuilderWindow(self):
+ pass
+
+ def add_vistrail(self, *objs):
+ """add_vistrail creates and returns a new controller based on the
+ information contained in objs.
+
+ """
+ raise NotImplementedError("Subclass must implement add_vistrail!")
+
+ def ensure_vistrail(self, locator):
+ """ensure_vistrail returns the controller matching the locator if the
+ vistrail is already open, otherwise it returns None.
+
+ """
+ raise NotImplementedError("Subclass must implement ensure_vistrail")
+
+ def select_version(self, version=None):
+ """select_version changes the version of the currently open vistrail
+ to the specified version.
+
+ """
+ raise NotImplementedError("Subclass must implement select_version")
+
+ def get_current_controller(self):
+ """get_current_controller returns the currently active controller, if
+ one exists, otherwise None.
+
+ """
+ raise NotImplementedError("Subclass must implement "
+ "get_current_controller")
+
+ def update_locator(self, old_locator, new_locator):
+ """update_locator updates the application state to ensure that any
+ vistrails referenced by old_locator are now referenced by
+ new_locator.
+
+ """
+ raise NotImplementedError("Subclass must implement update_locator")
+
+ def convert_version(self, version):
+ if isinstance(version, basestring):
+ try:
+ version = \
+ self.get_controller().vistrail.get_version_number(version)
+ except:
+ version = None
+ return version
+
+ def new_vistrail(self):
+ return self.open_vistrail(None)
+
+ def open_vistrail(self, locator=None, version=None, is_abstraction=False):
+ if isinstance(locator, basestring):
+ locator = BaseLocator.from_url(locator)
+ elif locator is None:
+ locator = UntitledLocator()
+
+ controller = self.ensure_vistrail(locator)
+ if controller is None:
+ # vistrail is not already open
+ try:
+ loaded_objs = vistrails.core.db.io.load_vistrail(locator, False)
+ controller = self.add_vistrail(loaded_objs[0], locator,
+ *loaded_objs[1:])
+ if locator.is_untitled():
+ return True
+ controller.is_abstraction = is_abstraction
+ thumb_cache = ThumbnailCache.getInstance()
+ controller.vistrail.thumbnails = controller.find_thumbnails(
+ tags_only=thumb_cache.conf.tagsOnly)
+ controller.vistrail.abstractions = controller.find_abstractions(
+ controller.vistrail, True)
+ controller.vistrail.mashups = controller._mashups
+ collection = Collection.getInstance()
+ url = locator.to_url()
+ entity = collection.updateVistrail(url, controller.vistrail)
+ # add to relevant workspace categories
+ if not controller.is_abstraction:
+ collection.add_to_workspace(entity)
+ collection.commit()
+ except VistrailsDBException, e:
+ import traceback
+ debug.critical(str(e), traceback.format_exc())
+ return None
+ except Exception, e:
+ # debug.critical('An error has occurred', str(e))
+ #print "An error has occurred", str(e)
+ raise
+
+ version = self.convert_version(version)
+ if version is None:
+ controller.select_latest_version()
+ version = controller.current_version
+ self.select_version(version)
+ # flush in case version was upgraded
+ controller.flush_delayed_actions()
+ return True
+
+ def open_workflow(self, locator):
+ if isinstance(locator, basestring):
+ locator = BaseLocator.from_url(locator)
+
+ vistrail = Vistrail()
+ try:
+ if locator is None:
+ return False
+ if locator is not None:
+ workflow = locator.load(Pipeline)
+ action_list = []
+ for module in workflow.module_list:
+ action_list.append(('add', module))
+ for connection in workflow.connection_list:
+ action_list.append(('add', connection))
+ action = vistrails.core.db.action.create_action(action_list)
+ vistrail.add_action(action, 0L)
+ vistrail.update_id_scope()
+ vistrail.addTag("Imported workflow", action.id)
+
+ # FIXME might need different locator?
+ controller = self.add_vistrail(vistrail, locator)
+ except VistrailsDBException, e:
+ import traceback
+ debug.critical(str(e), traceback.format_exc())
+ return None
+ except Exception, e:
+ # debug.critical('An error has occurred', str(e))
+ raise
+
+ controller.select_latest_version()
+ controller.set_changed(True)
+ return True
+
+ def save_vistrail(self, locator=None, controller=None, export=False):
+ if controller is None:
+ controller = self.get_current_controller()
+ if controller is None:
+ return False
+ if locator is None and controller is not None:
+ locator = controller.locator
+ elif isinstance(locator, basestring):
+ locator = BaseLocator.from_url(locator)
+
+ if not locator:
+ return False
+ old_locator = controller.locator
+
+ try:
+ controller.write_vistrail(locator, export=export)
+ except Exception, e:
+ import traceback
+ debug.critical('Failed to save vistrail: %s' % str(e),
+ traceback.format_exc())
+ raise
+ if export:
+ return controller.locator
+
+ self.update_locator(old_locator, controller.locator)
+ # update collection
+ try:
+ thumb_cache = ThumbnailCache.getInstance()
+ controller.vistrail.thumbnails = controller.find_thumbnails(
+ tags_only=thumb_cache.conf.tagsOnly)
+ controller.vistrail.abstractions = controller.find_abstractions(
+ controller.vistrail, True)
+ controller.vistrail.mashups = controller._mashups
+
+ collection = Collection.getInstance()
+ url = locator.to_url()
+ entity = collection.updateVistrail(url, controller.vistrail)
+ # add to relevant workspace categories
+ collection.add_to_workspace(entity)
+ collection.commit()
+ except Exception, e:
+ import traceback
+ debug.critical('Failed to index vistrail', traceback.format_exc())
+ return controller.locator
+
+ def close_vistrail(self, locator=None, controller=None):
+ if controller is None:
+ controller = self.get_current_controller()
+ if controller is None:
+ return False
+ if locator is None and controller is not None:
+ locator = controller.locator
+ elif isinstance(locator, basestring):
+ locator = BaseLocator.from_url(locator)
+
+ controller.close_vistrail(locator)
+ controller.cleanup()
+ self.remove_vistrail(locator)
+
+class VistrailsCoreApplication(VistrailsApplicationInterface):
+ def __init__(self):
+ VistrailsApplicationInterface.__init__(self)
+ self._controllers = {}
+ self._cur_controller = None
+
+ def init(self, optionsDict=None, args=None):
+ VistrailsApplicationInterface.init(self, optionsDict=optionsDict, args=args)
+ self.vistrailsStartup.init()
+
+ def is_running_gui(self):
+ return False
+
+ def get_current_controller(self):
+ return self._cur_controller
+ get_controller = get_current_controller
+
+ def add_vistrail(self, *objs):
+ (vistrail, locator, abstraction_files, thumbnail_files, mashups) = objs
+ controller = VistrailController(*objs)
+ self._controllers[locator] = controller
+ self._cur_controller = controller
+ return self._cur_controller
+
+ def remove_vistrail(self, locator=None):
+ if locator is None and self._cur_controller is not None:
+ locator = self._cur_controller.locator
+ del self._controllers[locator]
+ if len(self._controllers) > 0:
+ self._cur_controller = self._controllers.itervalues().next()
+
+ def ensure_vistrail(self, locator):
+ if locator in self._controllers:
+ self._cur_controller = self._controllers[locator]
+ return self._cur_controller
+ return None
+
+ def update_locator(self, old_locator, new_locator):
+ self._controllers[new_locator] = self._controllers[old_locator]
+ del self._controllers[old_locator]
+
+ def select_version(self, version):
+ if self._cur_controller is not None:
+ self._cur_controller.change_selected_version(version)
+ return True
+ return False
+
diff --git a/vistrails/core/bundles/__init__.py b/vistrails/core/bundles/__init__.py
new file mode 100644
index 0000000..14a819b
--- /dev/null
+++ b/vistrails/core/bundles/__init__.py
@@ -0,0 +1,40 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Package for bundle management. "Bundle" refers to system-level
+packages managed by specialized systems such as RedHat's RPM, Debian
+and Ubuntu's APT, OSX's fink, etc."""
+from vistrails.core.bundles.pyimport import py_import
+from vistrails.core.bundles.installbundle import install
diff --git a/vistrails/core/bundles/installbundle.py b/vistrails/core/bundles/installbundle.py
new file mode 100644
index 0000000..c4f05af
--- /dev/null
+++ b/vistrails/core/bundles/installbundle.py
@@ -0,0 +1,44 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core import is_running_gui
+
+def install(dependency_dictionary):
+ """Tries to install a bundle after a py_import() failed.."""
+
+ if not is_running_gui():
+ return False
+
+ import vistrails.gui.bundles.installbundle
+ return vistrails.gui.bundles.installbundle.install(dependency_dictionary)
diff --git a/vistrails/core/bundles/pyimport.py b/vistrails/core/bundles/pyimport.py
new file mode 100644
index 0000000..f48cb97
--- /dev/null
+++ b/vistrails/core/bundles/pyimport.py
@@ -0,0 +1,92 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""module responsible for smartly importing python modules, checking
+for necessary installs."""
+
+import vistrails.core.bundles.installbundle
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core import debug
+
+##############################################################################
+
+_previously_failed_pkgs = set()
+
+class PyImportException(ImportError):
+ pass
+
+class PyImportBug(PyImportException):
+ pass
+
+def _vanilla_import(module_name):
+ return __import__(module_name, globals(), locals(), [])
+
+def py_import(module_name, dependency_dictionary):
+ """Tries to import a python module, installing if necessary.
+
+ If the import doesn't succeed, we guess which system we are running on and
+ install the corresponding package from the dictionary. We then run the
+ import again.
+ If the installation fails, we won't try to install that same module again
+ for the session.
+ """
+ try:
+ result = _vanilla_import(module_name)
+ return result
+ except ImportError:
+ if not getattr(get_vistrails_configuration(), 'installBundles'):
+ raise
+
+ if module_name in _previously_failed_pkgs:
+ raise PyImportException("Import of Python module '%s' failed again, "
+ "not triggering installation" % module_name)
+ debug.warning("Import of python module '%s' failed. "
+ "Will try to install bundle." % module_name)
+
+ success = vistrails.core.bundles.installbundle.install(dependency_dictionary)
+
+ if not success:
+ _previously_failed_pkgs.add(module_name)
+ raise PyImportException("Installation of Python module '%s' failed." %
+ module_name)
+ try:
+ result = _vanilla_import(module_name)
+ return result
+ except ImportError, e:
+ _previously_failed_pkgs.add(module_name)
+ raise PyImportBug("Installation of package '%s' succeeded, but import "
+ "still fails." % module_name)
+
+##############################################################################
diff --git a/vistrails/core/cache/__init__.py b/vistrails/core/cache/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/core/cache/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/core/cache/hasher.py b/vistrails/core/cache/hasher.py
new file mode 100644
index 0000000..bdbe8b8
--- /dev/null
+++ b/vistrails/core/cache/hasher.py
@@ -0,0 +1,130 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Hasher class for vistrail items."""
+from vistrails.core.cache.utils import hash_list
+
+try:
+ import hashlib
+ sha_hash = hashlib.sha1
+except ImportError:
+ import sha
+ sha_hash = sha.new
+
+##############################################################################
+
+class Hasher(object):
+
+ @staticmethod
+ def parameter_signature(p, constant_hasher_map={}):
+ k = (p.identifier, p.type, p.namespace)
+ custom_hasher = constant_hasher_map.get(k, None)
+ if custom_hasher:
+ return custom_hasher(p)
+ else:
+ hasher = sha_hash()
+ u = hasher.update
+ u(p.type)
+ u(p.identifier)
+ u(p.namespace or "")
+ u(p.strValue)
+ u(p.name)
+ u(p.evaluatedStrValue)
+ return hasher.digest()
+
+ @staticmethod
+ def function_signature(function, constant_hasher_map={}):
+ hasher = sha_hash()
+ u = hasher.update
+ u(function.name)
+ u(function.returnType)
+ u(hash_list(function.params,
+ Hasher.parameter_signature,
+ constant_hasher_map))
+ return hasher.digest()
+
+ @staticmethod
+ def connection_signature(c):
+ hasher = sha_hash()
+ u = hasher.update
+ u(c.source.name)
+ u(c.destination.name)
+ return hasher.digest()
+
+ @staticmethod
+ def connection_subpipeline_signature(c, source_sig, dest_sig):
+ """Returns the signature for the connection, including source
+and dest subpipelines"""
+ hasher = sha_hash()
+ u = hasher.update
+ u(Hasher.connection_signature(c))
+ u(source_sig)
+ u(dest_sig)
+ return hasher.digest()
+
+ @staticmethod
+ def module_signature(obj, constant_hasher_map={}):
+ hasher = sha_hash()
+ u = hasher.update
+ u(obj.module_descriptor.name)
+ u(obj.module_descriptor.package)
+ u(obj.module_descriptor.namespace or '')
+ u(obj.module_descriptor.package_version or '')
+ u(obj.module_descriptor.version or '')
+ u(hash_list(obj.functions, Hasher.function_signature, constant_hasher_map))
+ return hasher.digest()
+
+ @staticmethod
+ def subpipeline_signature(module_sig, upstream_sigs):
+ """Returns the signature for a subpipeline, given the
+signatures for the upstream pipelines and connections.
+
+ WARNING: For efficiency, upstream_sigs is mutated!
+ """
+ hasher = sha_hash()
+ hasher.update(module_sig)
+ upstream_sigs.sort()
+ for pipeline_connection_sig in upstream_sigs:
+ hasher.update(pipeline_connection_sig)
+ return hasher.digest()
+
+ @staticmethod
+ def compound_signature(sig_list):
+ """compound_signature(list of signatures) -> sha digest
+ returns the signature of the compound object formed by the list
+ of signatures, assuming the list order is irrelevant"""
+ hasher = sha_hash()
+ for h in sorted(sig_list):
+ hasher.update(h)
+ return hasher.digest()
diff --git a/vistrails/core/cache/utils.py b/vistrails/core/cache/utils.py
new file mode 100644
index 0000000..137eefd
--- /dev/null
+++ b/vistrails/core/cache/utils.py
@@ -0,0 +1,51 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Helper functions for cache package."""
+
+try:
+ import hashlib
+ sha_hash = hashlib.sha1
+except ImportError:
+ import sha
+ sha_hash = sha.new
+
+##############################################################################
+
+def hash_list(lst, hasher_f, constant_hasher_map={}):
+ hasher = sha_hash()
+ hash_l = [hasher_f(el, constant_hasher_map) for el in lst]
+ hash_l.sort()
+ for hel in hash_l: hasher.update(hel)
+ return hasher.digest()
diff --git a/vistrails/core/collection/__init__.py b/vistrails/core/collection/__init__.py
new file mode 100644
index 0000000..191d745
--- /dev/null
+++ b/vistrails/core/collection/__init__.py
@@ -0,0 +1,391 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import glob
+import os
+import sqlite3
+from itertools import chain
+
+from entity import Entity
+from vistrail import VistrailEntity
+from workflow import WorkflowEntity
+from workflow_exec import WorkflowExecEntity
+from thumbnail import ThumbnailEntity
+from mashup import MashupEntity
+from parameter_exploration import ParameterExplorationEntity
+
+from vistrails.core.db.locator import ZIPFileLocator, DBLocator, FileLocator, BaseLocator
+from vistrails.core.db.io import load_vistrail
+import vistrails.core.system
+import vistrails.db.services.io
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core import debug
+
+schema = ["create table entity(id integer primary key, type integer, "
+ "name text, user integer, mod_time text, create_time text, "
+ "size integer, description text, url text)",
+ "create table entity_children(parent integer, child integer)",
+ "create table entity_workspace(entity integer, workspace text)",
+ "create table workspaces(id text primary key)",
+ "insert into workspaces values ('Default')"]
+
+class Collection(object):
+ entity_types = dict((x.type_id, x)
+ for x in [VistrailEntity, WorkflowEntity,
+ WorkflowExecEntity, ThumbnailEntity,
+ MashupEntity, ParameterExplorationEntity])
+ def __init__(self, database=None):
+ if database is None:
+ self.database = ':memory:'
+ else:
+ self.database = database
+
+ self.entities = {}
+ self.deleted_entities = {}
+ self.temp_entities = {}
+ self.workspaces = {}
+ self.currentWorkspace = 'Default'
+ self.listeners = [] # listens for entity creation removal
+ self.max_id = 0
+
+ if not os.path.exists(self.database):
+ debug.log("'%s' does not exist. Trying to create" % self.database)
+ self.conn = sqlite3.connect(self.database)
+ try:
+ cur = self.conn.cursor()
+ [cur.execute(s) for s in schema]
+ self.conn.commit()
+ except Exception, e:
+ debug.critical("Could not create vistrail index schema",
+ str(e))
+ else:
+ self.conn = sqlite3.connect(self.database)
+ self.load_entities()
+
+ #Singleton technique
+ _instance = None
+
+ @staticmethod
+ def getInstance():
+ if Collection._instance is False:
+ debug.critical("Collection.getInstance() called but the "
+ "Collection has been deleted!")
+ raise RuntimeError("Collection has been deleted!")
+ elif Collection._instance is None:
+ dotVistrails = vistrails.core.system.current_dot_vistrails()
+
+ path = os.path.join(dotVistrails, "index.db")
+ obj = Collection(path)
+ Collection._instance = obj
+ return Collection._instance
+
+ @staticmethod
+ def clearInstance():
+ if Collection._instance:
+ Collection._instance.conn.close()
+ Collection._instance = False
+
+ def add_listener(self, c):
+ """ Add objects that listen to entity creation/removal
+ Object may implement the following method
+ updated(self)
+ """
+ self.listeners.append(c)
+
+ def clear(self):
+ cur = self.conn.cursor()
+ cur.execute('delete from entity;')
+ cur.execute('delete from entity_children;')
+ cur.execute('delete from workspaces;')
+ cur.execute('delete from entity_workspace;')
+
+ def get_current_entities(self):
+ """NOTE: returns an iterator"""
+ return chain(self.entities.itervalues(),
+ self.temp_entities.itervalues())
+
+ def load_entities(self):
+ cur = self.conn.cursor()
+ cur.execute("select max(id) from entity;")
+ for row in cur.fetchall():
+ n = row[0]
+ self.max_id = n if n is not None else 0
+
+ cur.execute("select * from entity;")
+ for row in cur.fetchall():
+ entity = self.load_entity(*row)
+ if entity is not None:
+ self.entities[entity.id] = entity
+
+ # now need to map children to correct places
+ cur.execute("select * from entity_children;")
+ for row in cur.fetchall():
+ if row[0] in self.entities and row[1] in self.entities:
+ self.entities[row[0]].children.append(self.entities[row[1]])
+ self.entities[row[1]].parent = self.entities[row[0]]
+
+ cur.execute("select * from workspaces;")
+ for row in cur.fetchall():
+ self.workspaces[row[0]] = []
+
+ cur.execute("select * from entity_workspace;")
+ for row in cur.fetchall():
+ e_id, workspace = row
+ if e_id in self.entities:
+ if workspace not in self.workspaces:
+ self.workspaces[workspace] = []
+ self.workspaces[workspace].append(self.entities[e_id])
+
+ def save_entities(self):
+ # TODO delete entities with no workspace
+ for entity in self.deleted_entities.itervalues():
+ self.db_delete_entity(entity)
+ self.deleted_entities = {}
+
+ for entity in self.entities.itervalues():
+ if entity.was_updated:
+ self.save_entity(entity)
+
+ cur = self.conn.cursor()
+ cur.execute('delete from workspaces;')
+ cur.executemany("insert into workspaces values (?)",
+ [(i,) for i in self.workspaces])
+
+ cur.execute('delete from entity_workspace;')
+ cur.executemany("insert into entity_workspace values (?, ?)",
+ ((k.id, i) for i,j in self.workspaces.iteritems() for k in j))
+
+ def load_entity(self, *args):
+ if args[1] in Collection.entity_types:
+ entity = Collection.entity_types[args[1]].load(*args)
+ return entity
+ else:
+ debug.critical("Cannot find entity type '%s'" % args[1])
+ return None
+
+ def add_entity(self, entity):
+ """ Adds entities to memory recursively """
+ if entity.id is None:
+ self.max_id += 1
+ entity.id = self.max_id
+ entity.was_updated = True
+ self.entities[entity.id] = entity
+ for child in entity.children:
+ child.parent = entity
+ self.add_entity(child)
+
+ def add_temp_entity(self, entity):
+ """Add an entity to memory only. Used for vistrails that have
+ not been saved."""
+ self.max_id += 1
+ entity.id = self.max_id
+ self.temp_entities[entity.id] = entity
+ for child in entity.children:
+ child.parent = entity
+ self.add_temp_entity(child)
+
+ def is_temp_entity(self, entity):
+ return entity.id in self.temp_entities
+
+ def save_entity(self, entity):
+ """ saves entities to disk """
+ cur = self.conn.cursor()
+ entity_tuple = entity.save()
+ cur.execute("insert or replace into entity values(%s)" % \
+ ','.join(('?',) * len(entity_tuple)), entity_tuple)
+ entity.was_updated = False
+ cur.execute('delete from entity_children where parent=?', (entity.id,))
+ cur.executemany("insert into entity_children values (?, ?)",
+ ((entity.id, child.id) for child in entity.children))
+
+ def commit(self):
+ self.save_entities()
+ self.conn.commit()
+ for o in self.listeners:
+ if hasattr(o, "updated"):
+ o.updated()
+
+ def delete_entity(self, entity):
+ """ Delete entity from memory recursively """
+ if entity.id in self.temp_entities:
+ del self.temp_entities[entity.id]
+ else:
+ self.deleted_entities[entity.id] = entity
+ if entity.id in self.entities:
+ del self.entities[entity.id]
+ for child in entity.children:
+ self.delete_entity(child)
+
+ def add_workspace(self, workspace):
+ if workspace not in self.workspaces:
+ self.workspaces[workspace] = []
+
+ def add_to_workspace(self, entity, workspace=None):
+ if not entity:
+ return
+ if not workspace:
+ workspace = self.currentWorkspace
+ self.add_workspace(workspace)
+ if entity not in self.workspaces[workspace]:
+ self.workspaces[workspace].append(entity)
+
+ def del_from_workspace(self, entity, workspace=None):
+ if not workspace:
+ workspace = self.currentWorkspace
+ if workspace in self.workspaces:
+ if entity in self.workspaces[workspace]:
+ self.workspaces[workspace].remove(entity)
+
+ def delete_workspace(self, workspace):
+ if workspace in self.workspaces:
+ del self.workspaces[workspace]
+
+ def db_delete_entity(self, entity):
+ """ Delete entity from database """
+ cur = self.conn.cursor()
+ if entity.id is not None:
+ cur.execute("delete from entity where id=?", (entity.id,))
+ cur.execute("delete from entity_children where parent=?", (entity.id,))
+ cur.execute("delete from entity_children where child=?", (entity.id,))
+
+ def create_workflow_entity(self, workflow):
+ entity = WorkflowEntity(workflow)
+ self.add_entity(entity)
+ return entity
+
+ def create_vistrail_entity(self, vistrail):
+ entity = VistrailEntity(vistrail)
+ self.add_entity(entity)
+ return entity
+
+ def update_from_database(self, db_locator):
+ # db_conn = db_locator.get_connection()
+ config = (('host', db_locator._host),
+ ('port', int(db_locator._port)),
+ ('db', db_locator._db),
+ ('user', db_locator._user),
+ ('passwd', db_locator._passwd))
+ rows = vistrails.db.services.io.get_db_object_list(dict(config), 'vistrail')
+ for row in rows:
+ if row[0] in [1,]:
+ continue
+ kwargs = {'obj_type': 'vistrail', 'obj_id': row[0]}
+ locator = DBLocator(*[x[1] for x in config], **kwargs)
+ (vistrail, abstractions, thumbnails, mashups) = load_vistrail(locator)
+ vistrail.abstractions = abstractions
+ vistrail.thumbnails = thumbnails
+ vistrail.mashups = mashups
+ self.create_vistrail_entity(vistrail)
+
+ def update_from_directory(self, directory):
+ filenames = glob.glob(os.path.join(directory, '*.vt'))
+ for filename in filenames:
+ locator = FileLocator(filename)
+ url = locator.to_url()
+ self.updateVistrail(url)
+
+ def fromUrl(self, url):
+ """ Check if entity with this url exist in index and return it """
+ for e in self.entities.itervalues():
+ if e.url == url:
+ return e
+ return None
+
+ def urlExists(self, url):
+ """ Check if entity with this url exist """
+ locator = BaseLocator.from_url(url)
+ if locator.is_valid():
+ return True
+ return False
+
+ def updateVistrail(self, url, vistrail=None):
+ """ updateVistrail(self, string:url, Vistrail:vistrail)
+ Update the specified entity url. Delete or reload as necessary.
+ Need to make sure workspaces are updated if the entity is changed.
+ """
+ entities = [e for e in self.entities.itervalues() if e.url == url]
+ entity = entities[0] if len(entities) else None
+ while entity and entity.parent:
+ entity = entity.parent
+ url = entity.url
+ workspaces = [p for p in self.workspaces if entity in self.workspaces[p]]
+ if entity:
+ for p in workspaces:
+ self.del_from_workspace(entity, p)
+ self.delete_entity(entity)
+
+ locator = BaseLocator.from_url(url)
+ if locator.is_valid():
+ if not vistrail:
+ (vistrail, abstractions, thumbnails, mashups) = load_vistrail(locator)
+ vistrail.abstractions = abstractions
+ vistrail.thumbnails = thumbnails
+ vistrail.mashups = mashups
+ entity = self.create_vistrail_entity(vistrail)
+ for p in workspaces:
+ self.add_to_workspace(entity, p)
+ return entity
+ else:
+ # probably an unsaved vistrail
+ pass
+# debug.critical("Locator is not valid!")
+
+def main():
+ import sys
+ sys.path.append('/home/tommy/git/vistrails/vistrails')
+
+ # vistrail = load_vistrail(ZIPFileLocator('/vistrails/examples/spx.vt'))[0]
+# db_locator = DBLocator('vistrails.sci.utah.edu', 3306,
+# 'vistrails', 'vistrails', '8edLj4',
+# obj_id=9, obj_type='vistrail')
+ # vistrail = load_vistrail(db_locator)[0]
+ c = Collection('/home/tommy/git/vistrails/vistrails/core/collection/test.db')
+ c.clear()
+ c.update_from_directory('/home/tommy/git/vistrails/examples')
+# c.update_from_database(db_locator)
+
+ # entity = c.create_vistrail_entity(vistrail)
+ c.entities = {}
+ c.load_entities()
+# print c.entities[2].url
+# locator = BaseLocator.from_url(c.entities[2].url)
+# c.entities[1].description = 'blah blah blah'
+# c.save_entity(c.entities[1])
+# print locator.to_url()
+ # c.load_entities()
+
+# print BaseLocator.from_url('/vistrails/examples/spx.xml').to_url()
+
+if __name__ == '__main__':
+ main()
diff --git a/vistrails/core/collection/entity.py b/vistrails/core/collection/entity.py
new file mode 100644
index 0000000..4daf1e0
--- /dev/null
+++ b/vistrails/core/collection/entity.py
@@ -0,0 +1,119 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.db.locator import BaseLocator
+
+class Entity(object):
+ def __init__(self):
+ self.parent = None
+ self.children = []
+ self.image_fnames = []
+ self.was_updated = False
+ self.is_open = False
+
+ def load(self, *args):
+ (self.id,
+ _,
+ self.name,
+ self.user,
+ self.mod_time,
+ self.create_time,
+ self.size,
+ self.description,
+ self.url) = args
+
+ def save(self):
+ return (self.id,
+ self.type_id,
+ self.name,
+ self.user,
+ self.mod_time,
+ self.create_time,
+ self.size,
+ self.description,
+ self.url)
+
+ def _get_start_date(self):
+ return self.create_time
+ start_date = property(_get_start_date)
+
+ def _get_end_date(self):
+ return self.mod_time
+ end_date = property(_get_end_date)
+
+# # returns string
+# def get_name(self):
+# return self.name
+
+# # returns datetime
+# def get_mod_time(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns datetime
+# def get_create_time(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns string
+# # FIXME: perhaps this should be a User object at some point
+# def get_user(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns tuple (<entity_type>, <entity_id>)
+# def get_id(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns integer
+# def get_size(self):
+# raise RuntimeError("Method is abstract")
+
+# def get_description(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns possibly empty list of Entity objects
+# def get_children(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns list of strings representing paths
+# # FIXME: should this be uris for database access?
+# def get_image_fnames(self):
+# raise RuntimeError("Method is abstract")
+
+ # returns boolean, True if search input is satisfied else False
+ def match(self, search):
+ raise RuntimeError("Method is abstract")
+
+ def locator(self):
+ locator = BaseLocator.from_url(self.url)
+ return locator
+
diff --git a/vistrails/core/collection/mashup.py b/vistrails/core/collection/mashup.py
new file mode 100644
index 0000000..2f88e90
--- /dev/null
+++ b/vistrails/core/collection/mashup.py
@@ -0,0 +1,109 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from entity import Entity
+
+class MashupEntity(Entity):
+ type_id = 5
+
+ def __init__(self, mashup=None):
+ Entity.__init__(self)
+ self.id = None
+ self.update(mashup)
+
+ @staticmethod
+ def load(*args):
+ entity = MashupEntity()
+ Entity.load(entity, *args)
+ return entity
+
+ def update(self, mashup):
+ self.mashup = mashup
+ if self.mashup is not None:
+ self.name = mashup.name \
+ if mashup.name else "Version #" + str(mashup.id)
+ self.user = 'testing'
+ self.mod_time = 'test'
+ self.create_time = 'test'
+ self.size = len(self.mashup.alias_list)
+ self.description = ""
+ self.url = 'test'
+ self.was_updated = True
+
+# self.name = self.workflow.name
+# self.user = self.workflow.user
+# self.mod_time = self.workflow.py_date
+# self.create_time = self.workflow.py_date
+# self.size = len(self.workflow.modules)
+# self.description = self.workflow.notes
+# self.was_updated = True
+
+# # returns string
+# def get_name(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns datetime
+# def get_mod_time(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns datetime
+# def get_create_time(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns string
+# # FIXME: perhaps this should be a User object at some point
+# def get_user(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns tuple (<entity_type>, <entity_id>)
+# def get_id(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns integer
+# def get_size(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns possibly empty list of Entity objects
+# def get_children(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns list of strings representing paths
+# # FIXME: should this be uris for database access?
+# def get_image_fnames(self):
+# raise RuntimeError("Method is abstract")
+
+ # returns boolean, True if search input is satisfied else False
+ def match(self, search):
+ raise RuntimeError("Not implemented")
\ No newline at end of file
diff --git a/vistrails/core/collection/parameter_exploration.py b/vistrails/core/collection/parameter_exploration.py
new file mode 100644
index 0000000..942cf87
--- /dev/null
+++ b/vistrails/core/collection/parameter_exploration.py
@@ -0,0 +1,100 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from entity import Entity
+
+class ParameterExplorationEntity(Entity):
+ type_id = 6
+
+ def __init__(self, pe=None):
+ Entity.__init__(self)
+ self.id = None
+ self.update(pe)
+
+ @staticmethod
+ def load(*args):
+ entity = ParameterExplorationEntity()
+ Entity.load(entity, *args)
+ return entity
+
+ def update(self, pe):
+ self.pe = pe
+ if self.pe is not None:
+ self.name = pe.name
+ self.user = pe.user
+ self.mod_time = pe.date
+ self.create_time = pe.date
+ self.size = len(pe.functions)
+ self.description = ""
+ self.url = 'test'
+ self.was_updated = True
+
+# # returns string
+# def get_name(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns datetime
+# def get_mod_time(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns datetime
+# def get_create_time(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns string
+# # FIXME: perhaps this should be a User object at some point
+# def get_user(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns tuple (<entity_type>, <entity_id>)
+# def get_id(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns integer
+# def get_size(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns possibly empty list of Entity objects
+# def get_children(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns list of strings representing paths
+# # FIXME: should this be uris for database access?
+# def get_image_fnames(self):
+# raise RuntimeError("Method is abstract")
+
+ # returns boolean, True if search input is satisfied else False
+ def match(self, search):
+ raise RuntimeError("Not implemented")
\ No newline at end of file
diff --git a/vistrails/core/collection/schema.sql b/vistrails/core/collection/schema.sql
new file mode 100644
index 0000000..c916c4b
--- /dev/null
+++ b/vistrails/core/collection/schema.sql
@@ -0,0 +1,37 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+create table entity(id integer primary key, type integer, name text, user integer, mod_time text, create_time text, size integer, description text, url text);
+create table entity_children(parent integer, child integer);
+create table type_map(id integer, type string);
\ No newline at end of file
diff --git a/vistrails/core/collection/search.py b/vistrails/core/collection/search.py
new file mode 100644
index 0000000..8628cb2
--- /dev/null
+++ b/vistrails/core/collection/search.py
@@ -0,0 +1,670 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# search functions for entity-type objects
+# notes in plain text, not html, should be fix later
+import re
+import time
+
+from vistrails.core.query import extract_text
+
+import unittest
+import datetime
+import vistrails.core
+
+################################################################################
+
+class SearchParseError(Exception):
+ def __init__(self, *args, **kwargs):
+ Exception.__init__(self, *args, **kwargs)
+
+class SearchStmt(object):
+ def __init__(self, content):
+ self.text = content
+ self.content = re.compile('.*'+content+'.*', re.MULTILINE | re.IGNORECASE)
+
+ def match(self, entity):
+ return True
+
+ def matchModule(self, v, m):
+ return True
+
+ def run(self, v, n):
+ pass
+
+ def __call__(self):
+ """Make SearchStmt behave just like a QueryObject."""
+ return self
+
+class TimeSearchStmt(SearchStmt):
+ oneSecond = 1.0
+ oneMinute = oneSecond * 60.0
+ oneHour = oneMinute * 60.0
+ oneDay = oneHour * 24.0
+ oneWeek = oneDay * 7.0
+ oneMonth = oneDay * 31.0 # wrong, I know
+ oneYear = oneDay * 365.0 # wrong, I know
+ amounts = {'seconds': oneSecond,
+ 'minutes': oneMinute,
+ 'hours': oneHour,
+ 'days': oneDay,
+ 'weeks': oneWeek,
+ 'months': oneMonth,
+ 'years': oneYear}
+ months = {'january': 1,
+ 'february': 2,
+ 'march': 3,
+ 'april': 4,
+ 'may': 5,
+ 'june': 6,
+ 'july': 7,
+ 'august': 8,
+ 'september': 9,
+ 'october': 10,
+ 'november': 11,
+ 'december': 12}
+
+ dateEntry = r'([^\,\/\: ]+)'
+ timeEntry = r'(\d?\d?)'
+ dateSep = r' *[\,\/\- ] *'
+ timeSep = r' *: *'
+ sep = r' *'
+ start = r'^ *'
+ finish = r' *$'
+ twoEntryDate = (dateEntry+
+ dateSep+
+ dateEntry)
+ threeEntryDate = (dateEntry+
+ dateSep+
+ dateEntry+
+ dateSep+
+ dateEntry)
+ twoEntryTime = (timeEntry+
+ timeSep+
+ timeEntry)
+ threeEntryTime = (timeEntry+
+ timeSep+
+ timeEntry+
+ timeSep+
+ timeEntry)
+
+ dateRE = [re.compile((start+
+ twoEntryDate+
+ finish)), # Mar 12 Mar, 12
+ re.compile((start+
+ threeEntryDate+
+ finish)), # Mar, 12, 2006 2006 Mar 12 etc
+ re.compile((start+
+ twoEntryTime+
+ finish)),
+ re.compile((start+
+ threeEntryTime+
+ finish)),
+ re.compile((start+
+ twoEntryDate+
+ sep+
+ twoEntryTime+
+ finish)),
+ re.compile((start+
+ twoEntryDate+
+ sep+
+ threeEntryTime+
+ finish)),
+ re.compile((start+
+ threeEntryDate+
+ sep+
+ twoEntryTime+
+ finish)),
+ re.compile((start+
+ threeEntryDate+
+ sep+
+ threeEntryTime+
+ finish)),
+ re.compile((start+
+ twoEntryTime+
+ sep+
+ twoEntryDate+
+ finish)),
+ re.compile((start+
+ twoEntryTime+
+ sep+
+ threeEntryDate+
+ finish)),
+ re.compile((start+
+ threeEntryTime+
+ sep+
+ twoEntryDate+
+ finish)),
+ re.compile((start+
+ threeEntryTime+
+ sep+
+ threeEntryDate+
+ finish))]
+
+ def __init__(self, date):
+ self.date = self.parseDate(date)
+
+ def parseDate(self, dateStr):
+ def parseAgo(s):
+ [amount, unit] = s.split(' ')
+ try:
+ amount = float(amount)
+ except ValueError:
+ raise SearchParseError("Expected a number, got %s" % amount)
+ if amount <= 0:
+ raise SearchParseError("Expected a positive number, got %s" % amount)
+ unitRe = re.compile('^'+unit)
+ keys = [k
+ for k in TimeSearchStmt.amounts.keys()
+ if unitRe.match(k)]
+ if len(keys) == 0:
+ raise SearchParseError("Time unit unknown: %s" % unit)
+ elif len(keys) > 1:
+ raise SearchParseError("Time unit ambiguous: %s matches %s" % (unit, keys))
+ return round(time.time()) - TimeSearchStmt.amounts[keys[0]] * amount
+
+ def guessDate(unknownEntries, year=None):
+ def guessStrMonth(s):
+ monthRe = re.compile('^'+s)
+ keys = [k
+ for k in TimeSearchStmt.months.keys()
+ if monthRe.match(k)]
+ if len(keys) == 0:
+ raise SearchParseError("Unknown month: %s" % s)
+ elif len(keys) > 1:
+ raise SearchParseError("Ambiguous month: %s matches %s" % (s, keys))
+ return TimeSearchStmt.months[keys[0]]
+ if not year:
+ m = None
+ # First heuristic: if month comes first, then year comes last
+ try:
+ e0 = int(unknownEntries[0])
+ except ValueError:
+ m = guessStrMonth(unknownEntries[0])
+ try:
+ d = int(unknownEntries[1])
+ except ValueError:
+ raise SearchParseError("Expected day, got %s" % unknownEntries[1])
+ try:
+ y = int(unknownEntries[2])
+ except ValueError:
+ raise SearchParseError("Expected year, got %s" % unknownEntries[2])
+ return (y, m, d)
+ # Second heuristic: if month comes last, then year comes first
+ try:
+ e2 = int(unknownEntries[2])
+ except ValueError:
+ m = guessStrMonth(unknownEntries[2])
+ try:
+ d = int(unknownEntries[1])
+ except ValueError:
+ raise SearchParseError("Expected day, got %s" % unknownEntries[1])
+ try:
+ y = int(unknownEntries[0])
+ except ValueError:
+ raise SearchParseError("Expected year, got %s" % unknownEntries[0])
+ return (y, m, d)
+ # If month is the middle one, decide day and year by size
+ # (year is largest, hopefully year was entered using 4 digits)
+ try:
+ e1 = int(unknownEntries[1])
+ except ValueError:
+ m = guessStrMonth(unknownEntries[1])
+ try:
+ d = int(unknownEntries[2])
+ except ValueError:
+ raise SearchParseError("Expected day or year, got %s" % unknownEntries[2])
+ try:
+ y = int(unknownEntries[0])
+ except ValueError:
+ raise SearchParseError("Expected year or year, got %s" % unknownEntries[0])
+ return (max(y,d), m, min(y, d))
+ lst = [(e0,0),(e1,1),(e2,2)]
+ lst.sort()
+ return guessDate([str(lst[0][0]),
+ str(lst[1][0])],
+ year=e2)
+ # We know year, decide month using similar heuristics - try string month first,
+ # then decide which is possible
+ try:
+ e0 = int(unknownEntries[0])
+ except ValueError:
+ m = guessStrMonth(unknownEntries[0])
+ try:
+ d = int(unknownEntries[1])
+ except ValueError:
+ raise SearchParseError("Expected day, got %s" % unknownEntries[1])
+ return (year, m, d)
+ try:
+ e1 = int(unknownEntries[1])
+ except ValueError:
+ m = guessStrMonth(unknownEntries[1])
+ try:
+ d = int(unknownEntries[0])
+ except ValueError:
+ raise SearchParseError("Expected day, got %s" % unknownEntries[0])
+ return (year, m, d)
+ if e0 > 12:
+ return (year, e1, e0)
+ else:
+ return (year, e0, e1)
+
+ dateStr = dateStr.lower().lstrip().rstrip()
+ if dateStr.endswith(" ago"):
+ return parseAgo(dateStr[:-4])
+ if dateStr == "yesterday":
+ lst = list(time.localtime(round(time.time()) - TimeSearchStmt.oneDay))
+ # Reset hour, minute, second
+ lst[3] = 0
+ lst[4] = 0
+ lst[5] = 0
+ return time.mktime(lst)
+ if dateStr == "today":
+ lst = list(time.localtime())
+ # Reset hour, minute, second
+ lst[3] = 0
+ lst[4] = 0
+ lst[5] = 0
+ return time.mktime(lst)
+ if dateStr.startswith("this "):
+ rest = dateStr[5:]
+ lst = list(time.localtime(round(time.time())))
+ if rest == "minute":
+ lst[5] = 0
+ elif rest == "hour":
+ lst[5] = 0
+ lst[4] = 0
+ elif rest == "day":
+ lst[5] = 0
+ lst[4] = 0
+ lst[3] = 0
+ elif rest == "week": # weeks start on monday
+ lst[5] = 0
+ lst[4] = 0
+ lst[3] = 0
+ # This hack saves me the hassle of computing negative days, months, etc
+ lst = list(time.localtime(time.mktime(lst) - TimeSearchStmt.oneDay * lst[6]))
+ elif rest == "month":
+ lst[5] = 0
+ lst[4] = 0
+ lst[3] = 0
+ lst[2] = 1
+ elif rest == "year":
+ lst[5] = 0
+ lst[4] = 0
+ lst[3] = 0
+ lst[2] = 1
+ lst[1] = 1
+ return time.mktime(lst)
+
+ result = [x.match(dateStr) for x in TimeSearchStmt.dateRE]
+ this = list(time.localtime())
+ def setTwoDate(g):
+ d = guessDate(g, year=this[0])
+ this[0] = d[0]
+ this[1] = d[1]
+ this[2] = d[2]
+ def setThreeDate(g):
+ d = guessDate(g)
+ this[0] = d[0]
+ this[1] = d[1]
+ this[2] = d[2]
+ def setTwoTime(g):
+ this[3] = int(g[0])
+ this[4] = int(g[1])
+ this[5] = 0
+ def setThreeTime(g):
+ this[3] = int(g[0])
+ this[4] = int(g[1])
+ this[5] = int(g[2])
+ if result[0]:
+ setTwoDate(result[0].groups())
+ setTwoTime([0,0])
+ elif result[1]:
+ setThreeDate(result[1].groups())
+ setTwoTime([0,0])
+ elif result[2]:
+ setTwoTime(result[2].groups())
+ elif result[3]:
+ setThreeTime(result[3].groups())
+ elif result[4]:
+ g = result[4].groups()
+ setTwoDate([g[0], g[1]])
+ setTwoTime([g[2], g[3]])
+ elif result[5]:
+ g = result[5].groups()
+ setTwoDate([g[0], g[1]])
+ setThreeTime([g[2], g[3], g[4]])
+ elif result[6]:
+ g = result[6].groups()
+ setThreeDate([g[0], g[1], g[2]])
+ setTwoTime([g[3], g[4]])
+ elif result[7]:
+ g = result[7].groups()
+ setThreeDate([g[0], g[1], g[2]])
+ setThreeTime([g[3], g[4], g[5]])
+ elif result[8]:
+ g = result[8].groups()
+ setTwoTime([g[0], g[1]])
+ setTwoDate([g[2], g[3]])
+ elif result[9]:
+ g = result[9].groups()
+ setTwoTime([g[0], g[1]])
+ setThreeDate([g[2], g[3], g[4]])
+ elif result[10]:
+ g = result[10].groups()
+ setThreeTime([g[0], g[1], g[2]])
+ setTwoDate([g[3], g[4]])
+ elif result[11]:
+ g = result[11].groups()
+ setThreeTime([g[0], g[1], g[2]])
+ setThreeDate([g[3], g[4],g[5]])
+ else:
+ raise SearchParseError("Expected a date, got '%s'" % dateStr)
+ return time.mktime(this)
+
+class BeforeSearchStmt(TimeSearchStmt):
+ def match(self, entity):
+ if not entity.mod_time:
+ return False
+ t = time.mktime(time.strptime(entity.mod_time, "%d %b %Y %H:%M:%S"))
+ return t <= self.date
+
+class AfterSearchStmt(TimeSearchStmt):
+ def match(self, entity):
+ if not entity.mod_time:
+ return False
+ t = time.mktime(time.strptime(entity.mod_time, "%d %b %Y %H:%M:%S"))
+ return t >= self.date
+
+class UserSearchStmt(SearchStmt):
+ def match(self, entity):
+ if not entity.user:
+ return False
+ return self.content.match(entity.user)
+
+class NotesSearchStmt(SearchStmt):
+ def match(self, entity):
+ if entity.description:
+ plainNotes = extract_text(entity.description)
+ return self.content.search(plainNotes)
+ return False
+
+class NameSearchStmt(SearchStmt):
+ def match(self, entity):
+ return self.content.match(entity.name)
+
+class AndSearchStmt(SearchStmt):
+ def __init__(self, lst):
+ self.matchList = lst
+ def match(self, entity):
+ for s in self.matchList:
+ if not s.match(entity):
+ return False
+ return True
+
+class OrSearchStmt(SearchStmt):
+ def __init__(self, lst):
+ self.matchList = lst
+ def match(self, entity):
+ for s in self.matchList:
+ if s.match(entity):
+ return True
+ return False
+
+class NotSearchStmt(SearchStmt):
+ def __init__(self, stmt):
+ self.stmt = stmt
+ def match(self, entity):
+ return not self.stmt.match(entity)
+
+class TrueSearch(SearchStmt):
+ def __init__(self):
+ pass
+ def match(self, entity):
+ return True
+
+################################################################################
+
+class SearchCompiler(object):
+ SEPARATOR = -1
+ def __init__(self, searchStr):
+ self.searchStmt = self.compile(searchStr)
+ def compile(self, searchStr):
+ lst = []
+ t1 = searchStr.split(' ')
+ while t1:
+ tok = t1[0]
+ cmd = tok.split(':')
+ if not SearchCompiler.dispatch.has_key(cmd[0]):
+ fun = SearchCompiler.parseAny
+ else:
+ fun = SearchCompiler.dispatch[cmd[0]]
+ if len(cmd) > 1:
+ [search, rest] = fun(self, cmd[1:] + t1[1:])
+ else:
+ [search, rest] = fun(self, t1)
+ lst.append(search)
+ t1 = rest
+ return AndSearchStmt(lst)
+ def parseUser(self, tokStream):
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ return (UserSearchStmt(tokStream[0]), tokStream[1:])
+ def parseAny(self, tokStream):
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ tok = tokStream[0]
+ return (OrSearchStmt([UserSearchStmt(tok),
+ NotesSearchStmt(tok),
+ NameSearchStmt(tok)]), tokStream[1:])
+ def parseNotes(self, tokStream):
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ lst = []
+ while len(tokStream):
+ tok = tokStream[0]
+ if ':' in tok:
+ return (AndSearchStmt(lst), tokStream)
+ lst.append(NotesSearchStmt(tok))
+ tokStream = tokStream[1:]
+ return (AndSearchStmt(lst), [])
+ def parseName(self, tokStream):
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ lst = []
+ while len(tokStream):
+ tok = tokStream[0]
+ if ':' in tok:
+ return (AndSearchStmt(lst), tokStream)
+ lst.append(NameSearchStmt(tok))
+ tokStream = tokStream[1:]
+ return (AndSearchStmt(lst), [])
+ def parseBefore(self, tokStream):
+ old_tokstream = tokStream
+ try:
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ lst = []
+ while len(tokStream):
+ tok = tokStream[0]
+ # ugly, special case times
+ if (':' in tok and
+ not TimeSearchStmt.dateRE[2].match(tok) and
+ not TimeSearchStmt.dateRE[3].match(tok)):
+ return (BeforeSearchStmt(" ".join(lst)), tokStream)
+ lst.append(tok)
+ tokStream = tokStream[1:]
+ return (BeforeSearchStmt(" ".join(lst)), [])
+ except SearchParseError, e:
+ if 'Expected a date' in e.args[0]:
+ try:
+ return self.parseAny(old_tokstream)
+ except SearchParseError, e2:
+ print "Another exception...", e2.args[0]
+ raise e
+ else:
+ raise
+
+ def parseAfter(self, tokStream):
+ try:
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ lst = []
+ while len(tokStream):
+ tok = tokStream[0]
+ # ugly, special case times
+ if (':' in tok and
+ not TimeSearchStmt.dateRE[2].match(tok) and
+ not TimeSearchStmt.dateRE[3].match(tok)):
+ return (AfterSearchStmt(" ".join(lst)), tokStream)
+ lst.append(tok)
+ tokStream = tokStream[1:]
+ return (AfterSearchStmt(" ".join(lst)), [])
+ except SearchParseError, e:
+ if 'Expected a date' in e.args[0]:
+ try:
+ return self.parseAny(['after'] + tokStream)
+ except SearchParseError, e2:
+ print "Another exception...", e2.args[0]
+ raise e
+ else:
+ raise
+
+ dispatch = {'user': parseUser,
+ 'notes': parseNotes,
+ 'before': parseBefore,
+ 'after': parseAfter,
+ 'name': parseName,
+ 'any': parseAny}
+
+
+
+################################################################################
+
+
+class TestSearch(unittest.TestCase):
+ def test1(self):
+ self.assertEquals((TimeSearchStmt('1 day ago').date -
+ TimeSearchStmt('2 days ago').date), TimeSearchStmt.oneDay)
+ def test2(self):
+ self.assertEquals((TimeSearchStmt('12 mar 2006').date -
+ TimeSearchStmt('11 mar 2006').date), TimeSearchStmt.oneDay)
+ def test3(self):
+ # This will fail if year flips during execution. Oh well :)
+ yr = datetime.datetime.today().year
+ self.assertEquals((TimeSearchStmt('12 mar').date -
+ TimeSearchStmt('12 mar %d' % yr).date), 0.0)
+ def test4(self):
+ # This will fail if year flips during execution. Oh well :)
+ yr = datetime.datetime.today().year
+ self.assertEquals((TimeSearchStmt('mar 12').date -
+ TimeSearchStmt('12 mar %d' % yr).date), 0.0)
+ def test5(self):
+ yr = datetime.datetime.today().year
+ self.assertEquals((TimeSearchStmt('03 15').date -
+ TimeSearchStmt('15 mar %d' % yr).date), 0.0)
+ def test6(self):
+ self.assertEquals((TimeSearchStmt('03/15/2006').date -
+ TimeSearchStmt('15 mar 2006').date), 0.0)
+ def test7(self):
+ self.assertEquals((TimeSearchStmt('1 day ago').date -
+ TimeSearchStmt('24 hours ago').date), 0.0)
+ def test8(self):
+ self.assertEquals((TimeSearchStmt('1 hour ago').date -
+ TimeSearchStmt('60 minutes ago').date), 0.0)
+ def test9(self):
+ self.assertEquals((TimeSearchStmt('1 minute ago').date -
+ TimeSearchStmt('60 seconds ago').date), 0.0)
+ def test10(self):
+ self.assertEquals((TimeSearchStmt('1 week ago').date -
+ TimeSearchStmt('7 days ago').date), 0.0)
+ def test11(self):
+ self.assertEquals((TimeSearchStmt('1 month ago').date -
+ TimeSearchStmt('31 days ago').date), 0.0)
+ def test12(self):
+ self.assertEquals(TimeSearchStmt('12 mar 2007 21:00:00').date,
+ TimeSearchStmt('21:00:00 12 mar 2007').date)
+ def test13(self):
+ # This will fail if year flips during execution. Oh well :)
+ yr = datetime.datetime.today().year
+ self.assertEquals(TimeSearchStmt('12 mar %d 21:00' % yr).date,
+ TimeSearchStmt('21:00:00 12 mar').date)
+ def test14(self):
+ self.assertEquals(TimeSearchStmt('13 apr 2006 21:00').date,
+ TimeSearchStmt('04/13/2006 21:00:00').date)
+ def test15(self):
+ import vistrails.core.vistrail
+ from vistrails.core.db.locator import XMLFileLocator
+ import vistrails.core.system
+ v = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/dummy.xml').load()
+ # FIXME: Add notes to this.
+# self.assertTrue(NotesSearchStmt('mapper').match(v.actionMap[36]))
+# self.assertFalse(NotesSearchStmt('-qt-block-indent').match(v.actionMap[36]))
+
+ # test16 and 17 now pass.
+ # def test16(self):
+ # self.assertRaises(SearchParseError, lambda *args: SearchCompiler('before:'))
+ # def test17(self):
+ # self.assertRaises(SearchParseError, lambda *args: SearchCompiler('after:yesterday before:lalala'))
+ def test18(self):
+ self.assertEquals(TimeSearchStmt(' 13 apr 2006 ').date,
+ TimeSearchStmt(' 13 apr 2006 ').date)
+ def test19(self):
+ self.assertEquals(SearchCompiler('before:13 apr 2006 12:34:56').searchStmt.matchList[0].date,
+ BeforeSearchStmt('13 apr 2006 12:34:56').date)
+ def test20(self):
+ self.assertEquals(SearchCompiler('after:yesterday').searchStmt.matchList[0].date,
+ SearchCompiler('before:yesterday').searchStmt.matchList[0].date)
+ def test21(self):
+ self.assertEquals(SearchCompiler('after:today').searchStmt.matchList[0].date,
+ SearchCompiler('before:today').searchStmt.matchList[0].date)
+ def test22(self):
+ self.assertEquals(SearchCompiler('before:today').searchStmt.matchList[0].date,
+ SearchCompiler('before:this day').searchStmt.matchList[0].date)
+ def test23(self):
+ t = time.localtime()
+ import vistrails.core.utils
+ inv = vistrails.core.utils.invert(TimeSearchStmt.months)
+ m = inv[t[1]]
+ self.assertEquals(SearchCompiler('after:%s %s %s' % (t[0], m, t[2])).searchStmt.matchList[0].date,
+ SearchCompiler('after:today').searchStmt.matchList[0].date)
+ def test24(self):
+ # Test compiling these searches
+ SearchCompiler('before')
+ SearchCompiler('after')
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/collection/test.db b/vistrails/core/collection/test.db
new file mode 100644
index 0000000..014d757
Binary files /dev/null and b/vistrails/core/collection/test.db differ
diff --git a/vistrails/core/collection/thumbnail.py b/vistrails/core/collection/thumbnail.py
new file mode 100644
index 0000000..4134dc8
--- /dev/null
+++ b/vistrails/core/collection/thumbnail.py
@@ -0,0 +1,72 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import os
+import stat
+from time import localtime
+from datetime import datetime
+from vistrails.core.thumbnails import ThumbnailCache
+
+from entity import Entity
+
+class ThumbnailEntity(Entity):
+ type_id = 4
+
+ def __init__(self, thumbnail=None):
+ Entity.__init__(self)
+ self.id = None
+ self.update(thumbnail)
+
+ @staticmethod
+ def load(*args):
+ entity = ThumbnailEntity()
+ Entity.load(entity, *args)
+ return entity
+
+ def update(self, thumbnail):
+ self.thumbnail = thumbnail
+ if self.thumbnail is not None:
+ # store in cache if not already there
+ cache = ThumbnailCache.getInstance()
+ cache._copy_thumbnails([thumbnail])
+ self.name = os.path.basename(thumbnail)
+ statinfo = os.stat(self.thumbnail)
+ self.user = statinfo[stat.ST_UID]
+ self.size = statinfo[stat.ST_SIZE]
+ time = datetime(*localtime(statinfo[stat.ST_MTIME])[:6]).strftime('%d %b %Y %H:%M:%S')
+ self.mod_time = ''
+ self.create_time = time
+ self.description = ""
+ self.url = 'test'
+ self.was_updated = True
diff --git a/vistrails/core/collection/vistrail.py b/vistrails/core/collection/vistrail.py
new file mode 100644
index 0000000..38c48a7
--- /dev/null
+++ b/vistrails/core/collection/vistrail.py
@@ -0,0 +1,526 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+import locale
+import sys
+
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.core import debug
+from vistrails.core.query import extract_text
+import vistrails.core.system
+from vistrails.core.db.locator import BaseLocator
+
+from entity import Entity
+from workflow import WorkflowEntity
+from workflow_exec import WorkflowExecEntity
+from thumbnail import ThumbnailEntity
+from mashup import MashupEntity
+from vistrails.core.collection.parameter_exploration import ParameterExplorationEntity
+
+class VistrailEntity(Entity):
+ type_id = 1
+
+ def __init__(self, vistrail=None):
+ Entity.__init__(self)
+ self.id = None
+ self.wf_entity_map = {}
+ self.mshp_entity_map = {}
+ self.pe_entity_map = {}
+ self.wf_exec_entity_map = {}
+ self._vt_tag_map = {}
+ self._mshp_tag_map = {}
+ # self._last_wf_exec_id = None
+ self.reload(vistrail)
+
+ @staticmethod
+ def load(*args):
+ entity = VistrailEntity()
+ Entity.load(entity, *args)
+ return entity
+
+ def create_workflow_entity(self, workflow, action):
+ entity = WorkflowEntity(workflow)
+ self.children.append(entity)
+ entity.parent = self
+ if self.vistrail.has_notes(action.id):
+ plain_notes = extract_text(self.vistrail.get_notes(action.id))
+ entity.description = plain_notes
+ else:
+ entity.description = ''
+ entity.user = action.user
+ entity.mod_time = action.date
+ entity.create_time = action.date
+ locator = BaseLocator.from_url(self.url)
+ locator.kwargs['version_node'] = action.id
+ entity.url = locator.to_url()
+ return entity
+
+ def create_mashup_entity(self, trail_id, mashup, action):
+ entity = MashupEntity(mashup)
+ self.children.append(entity)
+ entity.parent = self
+ vt_version = mashup.version
+ if self.vistrail.has_notes(vt_version):
+ plain_notes = extract_text(self.vistrail.get_notes(vt_version))
+ entity.description = plain_notes
+ else:
+ entity.description = ''
+ entity.user = action.user
+ entity.mod_time = action.date
+ entity.create_time = action.date
+ locator = BaseLocator.from_url(self.url)
+ locator.kwargs['mashuptrail'] = trail_id
+ locator.kwargs['mashup'] = action.id
+ entity.url = locator.to_url()
+ return entity
+
+ def create_parameter_exploration_entity(self, pe):
+ entity = ParameterExplorationEntity(pe)
+ self.children.append(entity)
+ entity.parent = self
+ entity.name = pe.name
+ if pe.name:
+ entity.name = pe.name
+ else:
+ # find logical name using vistrail tag
+ entity.name = "Latest for " + \
+ self.vistrail.get_pipeline_name(pe.action_id)
+ locator = BaseLocator.from_url(self.url)
+ locator.kwargs['parameterExploration'] = pe.id
+ entity.url = locator.to_url()
+ return entity
+
+ def create_wf_exec_entity(self, wf_exec, wf_entity):
+ entity = WorkflowExecEntity(wf_exec)
+ wf_entity.children.append(entity)
+ entity.parent = wf_entity
+ locator = BaseLocator.from_url(self.url)
+ locator.kwargs['workflow_exec'] = entity.name
+ entity.url = locator.to_url()
+ return entity
+
+ def get_vistrail_info(self, vistrail=None):
+ if vistrail is None:
+ vistrail = self.vistrail
+ name = None
+ if vistrail.locator:
+ name = vistrail.locator.short_name
+ if name is None:
+ if vistrail.db_name:
+ name = vistrail.db_name
+ else:
+ name = u"untitled"
+
+ size = vistrail.get_version_count()
+ if size < 1:
+ # empty vistrail
+ user = vistrails.core.system.current_user()
+ mod_time = vistrails.core.system.current_time()
+ create_time = vistrails.core.system.current_time()
+ else:
+ latestVersionId = vistrail.get_latest_version()
+ latestVersion = vistrail.actionMap[latestVersionId]
+ user = latestVersion.user
+ mod_time = latestVersion.date
+ # FIXME: relies on 1 being the first version...
+ firstVersion = vistrail.actionMap[1] \
+ if 1 in vistrail.actionMap else latestVersion
+ create_time = firstVersion.date
+ url = vistrail.locator.to_url() if vistrail.locator else "untitled:"
+ return (name, size, user, mod_time, create_time, url)
+
+ def set_vistrail(self, vistrail):
+ self.vistrail = vistrail
+
+ (self.name, self.size, self.user, self.mod_time, self.create_time, \
+ self.url) = self.get_vistrail_info()
+ self.description = ""
+ self.was_updated = True
+
+ def add_workflow_entity(self, version_id):
+ if version_id not in self.vistrail.actionMap:
+ return
+ action = self.vistrail.actionMap[version_id]
+ tag = None
+ if self.vistrail.has_tag(version_id):
+ tag = self.vistrail.get_tag(version_id)
+ try:
+ workflow = self.vistrail.getPipeline(version_id)
+ except:
+ import traceback
+ debug.critical("Failed to construct pipeline '%s'" %
+ (tag if tag else version_id),
+ traceback.format_exc())
+ workflow = self.vistrail.getPipeline(0)
+ if tag:
+ workflow.name = tag
+ # if workflow already exists, we want to update it...
+ # spin through self.children and look for matching
+ # workflow entity?
+ # self.children.append(WorkflowEntity(workflow))
+ self.wf_entity_map[version_id] = \
+ self.create_workflow_entity(workflow, action)
+
+ # get thumbnail
+ thumbnail = self.vistrail.get_thumbnail(version_id)
+ if thumbnail is not None:
+ cache = ThumbnailCache.getInstance()
+ path = cache.get_abs_name_entry(thumbnail)
+ if path:
+ entity = ThumbnailEntity(path)
+ self.wf_entity_map[action.id].children.append(entity)
+ entity.parent = self.wf_entity_map[action.id]
+ return self.wf_entity_map[version_id]
+
+ def add_mashup_entity(self, mashuptrail, version_id, tag=None):
+ if not hasattr(self.vistrail, 'mashups'):
+ return
+ if mashuptrail not in self.vistrail.mashups:
+ return
+ action = mashuptrail.actionMap[version_id]
+ mashup = mashuptrail.getMashup(version_id)
+ if tag:
+ mashup.name = tag
+ mashup.id = action.id
+ entity_key = (mashuptrail.id,version_id)
+ self.mshp_entity_map[entity_key] = \
+ self.create_mashup_entity(mashuptrail.id, mashup, action)
+ # get thumbnail for the workflow it points
+ thumb_version = mashuptrail.vtVersion
+ thumbnail = self.vistrail.get_thumbnail(thumb_version)
+ if thumbnail is not None:
+ cache = ThumbnailCache.getInstance()
+ path = cache.get_abs_name_entry(thumbnail)
+ if path:
+ entity = ThumbnailEntity(path)
+ mshp_entity = self.mshp_entity_map[entity_key]
+ mshp_entity.children.append(entity)
+ entity.parent = mshp_entity
+ return self.mshp_entity_map[entity_key]
+
+ def add_parameter_exploration_entity(self, pe):
+ if not hasattr(self.vistrail, 'parameter_explorations'):
+ return
+ self.pe_entity_map[pe.name] = \
+ self.create_parameter_exploration_entity(pe)
+ # get thumbnail for the workflow it points
+ thumbnail = self.vistrail.get_thumbnail(pe.action_id)
+ if thumbnail is not None:
+ cache = ThumbnailCache.getInstance()
+ path = cache.get_abs_name_entry(thumbnail)
+ if path:
+ entity = ThumbnailEntity(path)
+ pe_entity = self.pe_entity_map[pe.name]
+ pe_entity.children.append(entity)
+ entity.parent = self
+ return self.pe_entity_map[pe.name]
+
+ def add_wf_exec_entity(self, wf_exec, add_to_map=False):
+ version_id = wf_exec.parent_version
+ is_new = False
+ if version_id not in self.wf_entity_map:
+ is_new = True
+ # FIXME add new workflow entity for this version
+ if version_id not in self.vistrail.actionMap:
+ raise LookupError("Version %d does not occur in vistrail." %
+ version_id)
+ action = self.vistrail.actionMap[version_id]
+ try:
+ workflow = self.vistrail.getPipeline(version_id)
+ except:
+ import traceback
+ if self.vistrail.has_tag(version_id):
+ tag_str = self.vistrail.get_tag(version_id)
+ else:
+ tag_str = str(version_id)
+ debug.critical("Failed to construct pipeline '%s'" % tag_str,
+ traceback.format_exc())
+ workflow = self.vistrail.getPipeline(0)
+ wf_entity = self.create_workflow_entity(workflow, action)
+ self.wf_entity_map[version_id] = wf_entity
+ else:
+ wf_entity = self.wf_entity_map[version_id]
+
+ entity = self.create_wf_exec_entity(wf_exec, wf_entity)
+ if add_to_map:
+ self.wf_exec_entity_map[wf_exec.id] = entity
+ if is_new:
+ return (entity, wf_entity)
+ return (entity, None)
+
+ def add_mashup_entities_from_mashuptrail(self, mashuptrail):
+ added_entry_keys = set()
+ inv_tag_map = {}
+ tagMap = mashuptrail.getTagMap()
+ tags = tagMap.keys()
+ if len(tags) > 0:
+ tags.sort()
+ for tag in tags:
+ version_id = tagMap[tag]
+ inv_tag_map[version_id] = tag
+ action = mashuptrail.actionMap[version_id]
+ mashup = mashuptrail.getMashup(version_id)
+ mashup.name = tag
+ #make sure we identify a mashup by its version
+ mashup.id = action.id
+ entity_key = (mashuptrail.id,version_id)
+ self.mshp_entity_map[entity_key] = \
+ self.create_mashup_entity(mashuptrail.id, mashup, action)
+ added_entry_keys.add(entity_key)
+ # get thumbnail for the workflow it points
+ thumb_version = mashuptrail.vtVersion
+ thumbnail = self.vistrail.get_thumbnail(thumb_version)
+ if thumbnail is not None:
+ cache = ThumbnailCache.getInstance()
+ path = cache.get_abs_name_entry(thumbnail)
+ if path:
+ entity = ThumbnailEntity(path)
+ mshp_entity = self.mshp_entity_map[entity_key]
+ mshp_entity.children.append(entity)
+ entity.parent = mshp_entity
+ return inv_tag_map
+
+ def reload(self, vistrail):
+ if vistrail is not None:
+ self.set_vistrail(vistrail)
+
+ for version_id in self.vistrail.get_tagMap():
+ self.add_workflow_entity(version_id)
+
+ #mashups
+ if hasattr(self.vistrail, 'mashups'):
+ self._mshp_tag_map = {}
+ for mashuptrail in self.vistrail.mashups:
+ self._mshp_tag_map[mashuptrail.id] = \
+ self.add_mashup_entities_from_mashuptrail(mashuptrail)
+
+ #parameter explorations
+ if hasattr(self.vistrail, 'parameter_explorations'):
+ self.pe_entity_map = {}
+ # find named pe's
+ #max_pe = {}
+ for pe in self.vistrail.parameter_explorations:
+ if pe.name:
+ self.pe_entity_map[pe.name] = \
+ self.add_parameter_exploration_entity(pe)
+ # if pe.action_id not in max_pe or max_pe[pe.action_id]<pe.id:
+ # max_pe[pe.action_id] = pe
+
+ #for pe in max_pe.values():
+ # if pe.id not in self.pe_entity_map:
+ # self.pe_entity_map[pe.id] = \
+ # self.add_parameter_exploration_entity(pe)
+
+ # read persisted log entries
+ try:
+ log = vistrail.get_persisted_log()
+ except:
+ import traceback
+ debug.critical("Failed to read log", traceback.format_exc())
+
+ if log is not None:
+ for wf_exec in log.workflow_execs:
+ self.add_wf_exec_entity(wf_exec, False)
+
+ # read unpersisted log entries
+ if vistrail.log is not None:
+ for wf_exec in self.vistrail.log.workflow_execs:
+ self.add_wf_exec_entity(wf_exec, True)
+
+ self._vt_tag_map = copy.copy(self.vistrail.get_tagMap())
+
+ def update_vistrail(self, vistrail):
+ # like set_vistrail but checks everything!
+
+ (name, size, user, mod_time, create_time, url) = \
+ self.get_vistrail_info(vistrail)
+
+ was_updated = False
+ new_entity = False
+ if name != self.name:
+ # self.name = name
+ new_entity = True
+ if size != self.size:
+ self.size = size
+ was_updated = True
+ if user != self.user:
+ self.user = user
+ was_updated = True
+ if mod_time != self.mod_time:
+ self.mod_time = mod_time
+ was_updated = True
+ if create_time != self.create_time:
+ self.create_time = create_time
+ was_updated = True
+ if url != self.url:
+ # self.url = url
+ new_entity = True
+
+ # if we need a new entity, just return, don't update old one
+ if new_entity:
+ return (True, was_updated)
+
+ self.vistrail = vistrail
+ self.vistrail.was_updated = was_updated
+ return (False, was_updated)
+
+ def update_workflows(self):
+ # here we just need to check for changes in tags
+ added_tags = []
+ deleted_tags = []
+ for version_id, tag in self.vistrail.get_tagMap().iteritems():
+ if version_id not in self._vt_tag_map:
+ added_tags.append(self.add_workflow_entity(version_id))
+ elif tag != self._vt_tag_map[version_id]:
+ deleted_tags.append(self.wf_entity_map[version_id])
+ added_tags.append(self.add_workflow_entity(version_id))
+ for version_id, tag in self._vt_tag_map.iteritems():
+ if version_id not in self.vistrail.get_tagMap():
+ deleted_tags.append(self.wf_entity_map[version_id])
+ del self.wf_entity_map[version_id]
+ self._vt_tag_map = copy.copy(self.vistrail.get_tagMap())
+ return (added_tags, deleted_tags)
+
+ def update_log(self):
+ # only need to check non-persisted wf_execs since log is immutable
+ # if vistrail.log.get_last_workflow_exec_id() == self._last_wf_exec_id:
+ # return []
+ added_workflows = []
+ added_wf_execs = []
+ for wf_exec in self.vistrail.log.workflow_execs:
+ if wf_exec.id not in self.wf_exec_entity_map:
+ (exec_entity, wf_entity) = \
+ self.add_wf_exec_entity(wf_exec, True)
+ if wf_entity is not None:
+ added_workflows.append(wf_entity)
+ added_wf_execs.append(exec_entity)
+ return (added_workflows, added_wf_execs)
+
+ def update_mashups(self):
+ added_mashups = []
+ deleted_mashups = []
+ if hasattr(self.vistrail, 'mashups'):
+ for mashuptrail in self.vistrail.mashups:
+ if mashuptrail.id not in self._mshp_tag_map:
+ self._mshp_tag_map[mashuptrail.id] = {}
+ mashup_tag_map = self._mshp_tag_map[mashuptrail.id]
+ tagMap = mashuptrail.getTagMap()
+ #mashups tag map is inverted map[tag] -> version
+ new_mshp_map = {}
+ for tag, version_id in tagMap.iteritems():
+ new_mshp_map[version_id] = tag
+ if version_id not in mashup_tag_map:
+ added_mashups.append(self.add_mashup_entity(mashuptrail, version_id, tag))
+ elif tag != mashup_tag_map[version_id]:
+ deleted_mashups.append(self.mshp_entity_map[(mashuptrail.id,
+ version_id)])
+ added_mashups.append(self.add_mashup_entity(mashuptrail, version_id, tag))
+ for version_id, tag in mashup_tag_map.iteritems():
+ if version_id not in tagMap.values():
+ deleted_mashups.append(self.mshp_entity_map[(mashuptrail.id,
+ version_id)])
+ del self.mshp_entity_map[(mashuptrail.id, version_id)]
+ self._mshp_tag_map[mashuptrail.id] = new_mshp_map
+ return (added_mashups, deleted_mashups)
+
+ def update_parameter_explorations(self):
+ # Check for new or deleted pe:s by id
+ added_pes = []
+ deleted_pes = []
+ if hasattr(self.vistrail, 'parameter_explorations'):
+ for pe in self.vistrail.parameter_explorations:
+ if pe.name and pe.name not in self.pe_entity_map:
+ added_pes.append(self.add_parameter_exploration_entity(pe))
+ for pe_name in self.pe_entity_map.keys():
+ if not self.vistrail.has_named_paramexp(pe_name):
+ deleted_pes.append(self.pe_entity_map[pe_name])
+ del self.pe_entity_map[pe_name]
+ return (added_pes, deleted_pes)
+
+# for key, mashup in self.mshp_entity_map.iteritems():
+# deleted_mashups.append(mashup)
+# self.mshp_entity_map = {}
+#
+# if hasattr(self.vistrail, 'mashups'):
+# for mashuptrail in self.vistrail.mashups:
+# self.mshp_entity_map.update(
+# self.add_mashup_entities_from_mashuptrail(mashuptrail))
+# for key, mashup in self.mshp_entity_map.iteritems():
+# added_mashups.append(mashup)
+# return (added_mashups, deleted_mashups)
+
+# # returns string
+# def get_name(self):
+# return self.vistrail.name
+
+# # returns datetime
+# def get_mod_time(self):
+# return self.vistrail.get_most_recent_action().py_date
+
+# # returns datetime
+# def get_create_time(self):
+# return self.vistrail.get_first_action().py_date
+
+# # returns string
+# # FIXME: perhaps this should be a User object at some point
+# def get_user(self):
+# return self.vistrail.get_most_recent_action().py_date
+
+# # returns tuple (<entity_type>, <entity_id>)
+# def get_id(self):
+# return (self.vistrail.vtType, self.vistrail.id)
+
+# # returns integer
+# def get_size(self):
+# return len(self.vistrail.actionMap)
+
+# # returns possibly empty list of Entity objects
+# def get_children(self):
+# return len(self.vistrail.tagMap)
+
+# # returns list of strings representing paths
+# # FIXME: should this be urls for database access?
+# def get_image_fnames(self):
+# return []
+
+ # returns boolean, True if search input is satisfied else False
+ def match(self, search):
+ # try match on self
+
+
+ # if no match on self, check for a match on all children
+ for child in self.get_children():
+ if child.match(search):
+ return True
diff --git a/vistrails/core/collection/workflow.py b/vistrails/core/collection/workflow.py
new file mode 100644
index 0000000..a5c339f
--- /dev/null
+++ b/vistrails/core/collection/workflow.py
@@ -0,0 +1,109 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from entity import Entity
+
+class WorkflowEntity(Entity):
+ type_id = 2
+
+ def __init__(self, workflow=None):
+ Entity.__init__(self)
+ self.id = None
+ self.update(workflow)
+
+ @staticmethod
+ def load(*args):
+ entity = WorkflowEntity()
+ Entity.load(entity, *args)
+ return entity
+
+ def update(self, workflow):
+ self.workflow = workflow
+ if self.workflow is not None:
+ self.name = workflow.name \
+ if workflow.name else "Version #" + str(workflow.id)
+ self.user = 'testing'
+ self.mod_time = 'test'
+ self.create_time = 'test'
+ self.size = len(self.workflow.modules)
+ self.description = ""
+ self.url = 'test'
+ self.was_updated = True
+
+# self.name = self.workflow.name
+# self.user = self.workflow.user
+# self.mod_time = self.workflow.py_date
+# self.create_time = self.workflow.py_date
+# self.size = len(self.workflow.modules)
+# self.description = self.workflow.notes
+# self.was_updated = True
+
+# # returns string
+# def get_name(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns datetime
+# def get_mod_time(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns datetime
+# def get_create_time(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns string
+# # FIXME: perhaps this should be a User object at some point
+# def get_user(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns tuple (<entity_type>, <entity_id>)
+# def get_id(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns integer
+# def get_size(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns possibly empty list of Entity objects
+# def get_children(self):
+# raise RuntimeError("Method is abstract")
+
+# # returns list of strings representing paths
+# # FIXME: should this be uris for database access?
+# def get_image_fnames(self):
+# raise RuntimeError("Method is abstract")
+
+ # returns boolean, True if search input is satisfied else False
+ def match(self, search):
+ raise RuntimeError("Not implemented")
+
diff --git a/vistrails/core/collection/workflow_exec.py b/vistrails/core/collection/workflow_exec.py
new file mode 100644
index 0000000..f3fef3e
--- /dev/null
+++ b/vistrails/core/collection/workflow_exec.py
@@ -0,0 +1,70 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from entity import Entity
+
+class WorkflowExecEntity(Entity):
+ type_id = 3
+
+ def __init__(self, workflow_exec=None):
+ Entity.__init__(self)
+ self.id = None
+ self.update(workflow_exec)
+
+ @staticmethod
+ def load(*args):
+ entity = WorkflowExecEntity()
+ Entity.load(entity, *args)
+ return entity
+
+ def update(self, workflow_exec):
+ self.workflow_exec = workflow_exec
+ if self.workflow_exec is not None:
+ self.name = "%s" % self.workflow_exec.db_ts_start
+ self.user = self.workflow_exec.user
+ self.mod_time = \
+ self.workflow_exec.ts_end.strftime('%d %b %Y %H:%M:%S') \
+ if self.workflow_exec.ts_end else '1 Jan 0000 00:00:00'
+ self.create_time = \
+ self.workflow_exec.ts_start.strftime('%d %b %Y %H:%M:%S') \
+ if self.workflow_exec.ts_start else '1 Jan 0000 00:00:00'
+ self.size = len(self.workflow_exec.item_execs)
+ self.description = ""
+ self.url = 'test'
+ self.was_updated = True
+
+ # returns boolean, True if search input is satisfied else False
+ def match(self, search):
+ raise NotImplementedError
+
diff --git a/vistrails/core/command_line.py b/vistrails/core/command_line.py
new file mode 100644
index 0000000..386791f
--- /dev/null
+++ b/vistrails/core/command_line.py
@@ -0,0 +1,101 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Very thin convenience wrapper around optparse.OptionParser."""
+
+import optparse
+import sys
+
+class CommandLineParserSingleton(object):
+ """CommandLineParser is a very thin wrapper around
+ optparse.OptionParser to make easier the parsing of command line
+ parameters."""
+ def __call__(self):
+ return self
+
+ def __init__(self):
+ self.parser = optparse.OptionParser()
+ self.options_were_read = False
+ self.args = []
+
+ def init_options(self,args=None):
+ """self.init_options(args: [string]) -> None. Initialize option dictionary,
+ by parsing command line arguments according to the options set
+ by previous add_option calls.
+
+ Few programs should call this. Call self.parse_options() unless
+ you know what you're doing."""
+ if args is None:
+ if hasattr(sys, "argv"):
+ args = sys.argv[1:]
+ else:
+ args = []
+ (self.options, self.args) = self.parser.parse_args(args)
+ self.options_were_read = True
+
+ def add_option(self, *args, **kwargs):
+ """self.add_option(*args, **kwargs) -> None. Adds a new option
+ to the command line parser. Behaves identically to the
+ optparse.OptionParser.add_option."""
+ self.parser.add_option(*args, **kwargs)
+
+ def get_option(self, key):
+ """self.get_option(key) -> value. Returns a value corresponding
+ to the given key that was parsed from the command line. Throws
+ AttributeError if key is not present."""
+ self.parse_options()
+ return getattr(self.options, key)
+
+ def parse_options(self,args=None):
+ """self.parse_options() -> None. Parse command line arguments,
+ according to the options set by previous add_option calls."""
+ if not self.options_were_read:
+ self.init_options(args)
+
+ def get_arg(self,number):
+ """self.get_arg(number) -> value. Returns the value corresponding
+ to the argument at position number from the command line. Returns
+ None if number is greater or equal the number of arguments. """
+ if len(self.args) > number:
+ return self.args[number]
+ else:
+ return None
+
+ def positional_arguments(self):
+ """positional_arguments() -> [string]. Returns a list of strings
+ representing the positional arguments in the command line."""
+ return self.args
+
+# singleton trick
+CommandLineParser = CommandLineParserSingleton()
diff --git a/vistrails/core/common.py b/vistrails/core/common.py
new file mode 100644
index 0000000..8ff715b
--- /dev/null
+++ b/vistrails/core/common.py
@@ -0,0 +1,43 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.utils import \
+ InstanceObject, \
+ lock_method, \
+ enum, \
+ trace_method_args, trace_method_args, bump_trace, report_stack, \
+ memo_method, \
+ all, any, \
+ eprint, \
+ VistrailsInternalError
diff --git a/vistrails/core/configuration.py b/vistrails/core/configuration.py
new file mode 100644
index 0000000..1c928a1
--- /dev/null
+++ b/vistrails/core/configuration.py
@@ -0,0 +1,358 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Configuration variables for controlling specific things in VisTrails."""
+import copy
+import os.path
+import shutil
+import sys
+import tempfile
+import weakref
+
+from vistrails.core import debug
+from vistrails.core import system
+from vistrails.core.utils import (InstanceObject, Ref, append_to_dict_of_lists,
+ VistrailsInternalError)
+from vistrails.core.utils.uxml import (named_elements,
+ elements_filter, eval_xml_value,
+ quote_xml_value)
+
+##############################################################################
+
+class ConfigurationObject(InstanceObject):
+ """A ConfigurationObject is an InstanceObject that respects the
+ following convention: values that are not 'present' in the object
+ should have value (None, type), where type is the type of the
+ expected object.
+
+ ConfigurationObject exists so that the GUI can automatically infer
+ the right types for the widgets.
+
+ """
+
+ def __init__(self, *args, **kwargs):
+ InstanceObject.__init__(self, *args, **kwargs)
+ self.__subscribers__ = {}
+
+ def __setattr__(self, name, value):
+ object.__setattr__(self, name, value)
+ if name == '__subscribers__':
+ return
+ if name in self.__subscribers__:
+ to_remove = []
+ for subscriber in self.__subscribers__[name]:
+ obj = subscriber()
+ if obj:
+ obj(name, value)
+ else:
+ to_remove.append(obj)
+ for ref in to_remove:
+ self.__subscribers__[name].remove(ref)
+
+ def unsubscribe(self, field, callable_):
+ """unsubscribe(field, callable_): remove observer from subject
+ """
+ self.__subscribers__[field].remove(weakref.ref(callable_))
+
+ def subscribe(self, field, callable_):
+ """subscribe(field, callable_): call observer callable_ when
+ self.field is set.
+ """
+ append_to_dict_of_lists(self.__subscribers__, field,
+ Ref(callable_))
+
+ def has(self, key):
+ """has(key) -> bool.
+
+ Returns true if key has valid value in the object.
+ """
+
+ if not hasattr(self, key):
+ return False
+ v = getattr(self, key)
+ if isinstance(v, tuple) and v[0] is None and isinstance(v[1], type):
+ return False
+ return True
+
+ def check(self, key):
+ """check(key) -> obj
+
+ Returns False if key is absent in object, and returns object
+ otherwise.
+ """
+
+ return self.has(key) and getattr(self, key)
+
+ def allkeys(self):
+ """allkeys() -> list of strings
+
+ Returns all options stored in this object.
+ """
+
+ return self.__dict__.keys()
+
+ def keys(self):
+ """keys(self) -> list of strings
+ Returns all public options stored in this object.
+ Public options are keys that do not start with a _
+ """
+ return [k for k in self.__dict__.keys() if not k.startswith('_')]
+
+ def write_to_dom(self, dom, element):
+ conf_element = dom.createElement('configuration')
+ element.appendChild(conf_element)
+ for (key, value) in self.__dict__.iteritems():
+ if key == '__subscribers__':
+ continue
+ key_element = dom.createElement('key')
+ key_element.setAttribute('name', key)
+ if isinstance(value, (int, long, basestring, bool, float)):
+ conf_element.appendChild(key_element)
+ value_element = quote_xml_value(dom, value)
+ key_element.appendChild(value_element)
+ elif isinstance(value, tuple):
+ pass
+ else:
+ assert isinstance(value, ConfigurationObject)
+ conf_element.appendChild(key_element)
+ value.write_to_dom(dom, key_element)
+
+ def set_from_dom_node(self, node):
+ assert str(node.nodeName) == 'configuration'
+ for key in elements_filter(node, lambda node: node.nodeName == 'key'):
+ key_name = str(key.attributes['name'].value)
+ value = [x for x in
+ elements_filter(key, lambda node: node.nodeName in
+ ['unicode', 'bool', 'str', 'int', 'float', 'configuration'])][0]
+ value_type = value.nodeName
+ if value_type == 'configuration':
+ if hasattr(self,key_name):
+ getattr(self, key_name).set_from_dom_node(value)
+ elif value_type in ['bool', 'str', 'int', 'float']:
+ setattr(self, key_name, eval_xml_value(value))
+
+
+ def __copy__(self):
+ result = ConfigurationObject()
+ for (key, value) in self.__dict__.iteritems():
+ setattr(result, key, copy.copy(value))
+ return result
+
+def default():
+ """ default() -> ConfigurationObject
+ Returns the default configuration of VisTrails
+
+ """
+
+ base_dir = {
+ 'abstractionsDirectory': (None, str),
+ 'alwaysShowDebugPopup': False,
+ 'autoConnect': True,
+ 'autosave': True,
+ 'dataDirectory': (None, str),
+ 'dbDefault': False,
+# 'debugSignals': False,
+ 'defaultFileType':system.vistrails_default_file_type(),
+ 'detachHistoryView': False,
+ 'dotVistrails': system.default_dot_vistrails(),
+ 'enablePackagesSilently': False,
+ 'errorOnConnectionTypeerror': False,
+ 'errorOnVariantTypeerror': True,
+ 'executeWorkflows': False,
+ 'fileDirectory': (None, str),
+# 'evolutionGraph': (None, str),
+ 'handlerDontAsk': False,
+ 'installBundles': True,
+ 'installBundlesWithPip': False,
+ 'interactiveMode': True,
+ 'logFile': (None, str),
+ 'logger': default_logger(),
+ 'maxMemory': (None, int),
+ 'maximizeWindows': False,
+ 'maxRecentVistrails': 5,
+ 'migrateTags': False,
+ 'minMemory': (None, int),
+ 'multiHeads': False,
+ 'nologger': True,
+ 'nologfile': False,
+ 'packageDirectory': (None, str),
+ 'pythonPrompt': False,
+ 'recentVistrailList': (None, str),
+ 'repositoryLocalPath': (None, str),
+ 'repositoryHTTPURL': "http://www.vistrails.org/packages",
+ 'reviewMode': False,
+ 'rootDirectory': (None, str),
+ 'runningJobsList': (None, str),
+ 'shell': default_shell(),
+ 'showHistoryViewOnLoad': False,
+ 'showPipelineViewOnLoad': False,
+ 'showScrollbars': True,
+ 'showMovies': True,
+ 'showSplash': True,
+ 'showSpreadsheetOnly': False,
+ 'singleInstance': True,
+ 'spawned': False,
+ 'spreadsheetDumpCells': (None, str),
+ 'spreadsheetDumpPDF': False,
+ 'staticRegistry': (None, str),
+ 'stopOnError': True,
+ 'temporaryDirectory': (None, str),
+ 'thumbs': default_thumbs(),
+ 'upgradeOn': True,
+ 'upgradeDelay': True,
+ 'upgradeModuleFailPrompt': True,
+ 'useCache': True,
+ 'userPackageDirectory': (None, str),
+ 'verbosenessLevel': (None, int),
+# 'workflowGraph': (None, str),
+# 'workflowInfo': (None, str),
+ 'webRepositoryLogin': (None, str),
+ 'webRepositoryURL': "http://www.crowdlabs.org",
+ 'isInServerMode': False,
+ }
+ specific_dir = add_specific_config(base_dir)
+ return ConfigurationObject(**specific_dir)
+
+def default_logger():
+ """default_logger() -> ConfigurationObject
+ Returns the default configuration for the VisTrails logger
+
+ """
+ logger_dir = {
+ 'dbHost': '',
+ 'dbName': '',
+ 'dbPasswd': '',
+ 'dbPort': 0,
+ 'dbUser': '',
+ }
+ return ConfigurationObject(**logger_dir)
+
+def default_shell():
+ """default_shell() -> ConfigurationObject
+ Returns the default configuration for the VisTrails shell
+
+ """
+ if system.systemType == 'Linux':
+ shell_dir = {
+ 'font_face': 'Fixed',
+ 'font_size': 12,
+ }
+ elif system.systemType in ['Windows', 'Microsoft']:
+ shell_dir = {
+ 'font_face': 'Courier New',
+ 'font_size': 8,
+ }
+ elif system.systemType == 'Darwin':
+ shell_dir = {
+ 'font_face': 'Monaco',
+ 'font_size': 12,
+ }
+ else:
+ raise VistrailsInternalError('system type not recognized')
+ return ConfigurationObject(**shell_dir)
+
+def default_thumbs():
+ """default_thumbs() -> ConfigurationObject
+ Returns the default configuration for VisTrails Pipelines Thumbnails
+ """
+ thumbs_dir = {
+ 'autoSave': True,
+ 'cacheDirectory': (None, str),
+ 'cacheSize': 20,
+ 'mouseHover': False,
+ 'tagsOnly': False,
+ }
+ return ConfigurationObject(**thumbs_dir)
+
+def add_specific_config(base_dir):
+ """add_specific_config() -> dict
+ Returns a dict with other specific configuration
+ to the current platform added to base_dir
+
+ """
+ newdir = dict(base_dir)
+ if system.systemType == 'Darwin':
+ newdir['useMacBrushedMetalStyle'] = True
+
+ return newdir
+
+def get_vistrails_persistent_configuration():
+ """get_vistrails_persistent_configuration() -> ConfigurationObject or None
+ Returns the persistent configuration of the application. It returns None if
+ configuration was not found (when running as a bogus application
+ for example.
+ Notice that this function should be use only to write configurations to
+ the user's startup.xml file. Otherwise, use get_vistrails_configuration or
+ get_vistrails_temp_configuration.
+
+ """
+ from vistrails.core.application import get_vistrails_application
+ app = get_vistrails_application()
+ if hasattr(app, 'configuration'):
+ return app.configuration
+ else:
+ return None
+
+def get_vistrails_configuration():
+ """get_vistrails_configuration() -> ConfigurationObject or None
+ Returns the current configuration of the application. It returns None if
+ configuration was not found (when running as a bogus application
+ for example. This configuration is the one that is used just for the
+ current session and is not persistent. To make changes persistent,
+ use get_vistrails_persistent_configuration() instead.
+
+ """
+ from vistrails.core.application import get_vistrails_application
+ app = get_vistrails_application()
+ if hasattr(app, 'temp_configuration'):
+ return app.temp_configuration
+ else:
+ return None
+
+def get_vistrails_temp_configuration():
+ """get_vistrails_temp_configuration() -> ConfigurationObject or None
+ Returns the temp configuration of the application. It returns None if
+ configuration was not found (when running as a bogus application
+ for example. The temp configuration is the one that is used just for the
+ current session and is not persistent. To make changes persistent,
+ use get_vistrails_persistent_configuration() instead.
+
+ """
+ from vistrails.core.application import get_vistrails_application
+ app = get_vistrails_application()
+ if hasattr(app, 'temp_configuration'):
+ return app.temp_configuration
+ else:
+ return None
diff --git a/vistrails/core/console_mode.py b/vistrails/core/console_mode.py
new file mode 100644
index 0000000..196218d
--- /dev/null
+++ b/vistrails/core/console_mode.py
@@ -0,0 +1,395 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" Module used when running vistrails uninteractively """
+from __future__ import absolute_import
+import os.path
+import uuid
+from vistrails.core.application import is_running_gui
+from vistrails.core.configuration import get_vistrails_configuration
+import vistrails.core.interpreter.default
+import vistrails.core.db.io
+from vistrails.core.db.io import load_vistrail
+from vistrails.core.db.locator import XMLFileLocator, ZIPFileLocator
+from vistrails.core import debug
+from vistrails.core.utils import VistrailsInternalError, expression
+from vistrails.core.vistrail.controller import VistrailController
+from vistrails.core.vistrail.vistrail import Vistrail
+
+import vistrails.core.packagemanager
+import vistrails.core.system
+import unittest
+import vistrails.core.vistrail
+import vistrails.db
+
+################################################################################
+
+def run_and_get_results(w_list, parameters='', workflow_info=None,
+ update_vistrail=True, extra_info=None,
+ reason='Console Mode Execution'):
+ """run_and_get_results(w_list: list of (locator, version), parameters: str,
+ workflow_info:str, update_vistrail: boolean,
+ extra_info:dict)
+ Run all workflows in w_list, and returns an interpreter result object.
+ version can be a tag name or a version id.
+
+ """
+ elements = parameters.split("$&$")
+ aliases = {}
+ result = []
+ for locator, workflow in w_list:
+ (v, abstractions , thumbnails, mashups) = load_vistrail(locator)
+ controller = VistrailController(v, locator, abstractions, thumbnails,
+ mashups, auto_save=update_vistrail)
+ if isinstance(workflow, basestring):
+ version = v.get_version_number(workflow)
+ elif isinstance(workflow, (int, long)):
+ version = workflow
+ elif workflow is None:
+ version = controller.get_latest_version_in_graph()
+ else:
+ msg = "Invalid version tag or number: %s" % workflow
+ raise VistrailsInternalError(msg)
+ controller.change_selected_version(version)
+
+ for e in elements:
+ pos = e.find("=")
+ if pos != -1:
+ key = e[:pos].strip()
+ value = e[pos+1:].strip()
+
+ if controller.current_pipeline.has_alias(key):
+ aliases[key] = value
+
+ if workflow_info is not None and controller.current_pipeline is not None:
+ # FIXME DAK: why is this always done?!? there is a flag for it...
+ if is_running_gui():
+ controller.updatePipelineScene()
+ base_fname = "%s_%s_pipeline.pdf" % (locator.short_filename, version)
+ filename = os.path.join(workflow_info, base_fname)
+ controller.current_pipeline_scene.saveToPDF(filename)
+ else:
+ debug.critical("Cannot save pipeline figure when not "
+ "running in gui mode")
+ base_fname = "%s_%s_pipeline.xml" % (locator.short_filename, version)
+ filename = os.path.join(workflow_info, base_fname)
+ vistrails.core.db.io.save_workflow(controller.current_pipeline, filename)
+ if not update_vistrail:
+ conf = get_vistrails_configuration()
+ if conf.has('thumbs'):
+ conf.thumbs.autoSave = False
+
+ (results, _) = \
+ controller.execute_current_workflow(custom_aliases=aliases,
+ extra_info=extra_info,
+ reason=reason)
+ new_version = controller.current_version
+ if new_version != version:
+ debug.warning("Version '%s' (%s) was upgraded. The actual "
+ "version executed was %s" % \
+ (workflow, version, new_version))
+ run = results[0]
+ run.workflow_info = (locator.name, new_version)
+ run.pipeline = controller.current_pipeline
+
+ if update_vistrail:
+ controller.write_vistrail(locator)
+ result.append(run)
+ return result
+
+################################################################################
+
+def get_wf_graph(w_list, workflow_info=None, pdf=False):
+ """run_and_get_results(w_list: list of (locator, version),
+ workflow_info:str, pdf:bool)
+ Load all workflows in wf_list and dump their graph to workflow_info.
+
+ """
+ result = []
+ if is_running_gui():
+ from vistrails.gui.vistrail_controller import VistrailController as \
+ GUIVistrailController
+ for locator, workflow in w_list:
+ try:
+ (v, abstractions , thumbnails, mashups) = load_vistrail(locator)
+ controller = GUIVistrailController(v, locator, abstractions,
+ thumbnails, mashups,
+ auto_save=False)
+ version = None
+ if isinstance(workflow, basestring):
+ version = v.get_version_number(workflow)
+ elif isinstance(workflow, (int, long)):
+ version = workflow
+ elif workflow is None:
+ version = controller.get_latest_version_in_graph()
+ else:
+ msg = "Invalid version tag or number: %s" % workflow
+ raise VistrailsInternalError(msg)
+
+ if (workflow_info is not None and
+ controller.current_pipeline is not None):
+ controller.updatePipelineScene()
+ if pdf:
+ base_fname = "%s_%s_pipeline.pdf" % \
+ (locator.short_filename, version)
+ filename = os.path.join(workflow_info, base_fname)
+ controller.current_pipeline_scene.saveToPDF(filename)
+ else:
+ base_fname = "%s_%s_pipeline.png" % \
+ (locator.short_filename, version)
+ filename = os.path.join(workflow_info, base_fname)
+ controller.current_pipeline_scene.saveToPNG(filename)
+ result.append((True, ""))
+ except Exception, e:
+ result.append((False, str(e)))
+ else:
+ error_str = "Cannot save pipeline figure when not " \
+ "running in gui mode"
+ debug.critical(error_str)
+ result.append((False, error_str))
+ return result
+
+################################################################################
+
+def get_vt_graph(vt_list, tree_info, pdf=False):
+ """get_vt_graph(vt_list: list of locator, tree_info:str)
+ Load all vistrails in vt_list and dump their tree to tree_info.
+
+ """
+ result = []
+ if is_running_gui():
+ from vistrails.gui.vistrail_controller import VistrailController as \
+ GUIVistrailController
+ for locator in vt_list:
+ try:
+ (v, abstractions , thumbnails, mashups) = load_vistrail(locator)
+ controller = GUIVistrailController(v, locator, abstractions,
+ thumbnails, mashups)
+ if tree_info is not None:
+ from vistrails.gui.version_view import QVersionTreeView
+ version_view = QVersionTreeView()
+ version_view.scene().setupScene(controller)
+ if pdf:
+ base_fname = "graph_%s.pdf" % locator.short_filename
+ filename = os.path.join(tree_info, base_fname)
+ version_view.scene().saveToPDF(filename)
+ else:
+ base_fname = "graph_%s.png" % locator.short_filename
+ filename = os.path.join(tree_info, base_fname)
+ version_view.scene().saveToPNG(filename)
+ del version_view
+ result.append((True, ""))
+ except Exception, e:
+ result.append((False, str(e)))
+ else:
+ error_str = "Cannot save version tree figure when not " \
+ "running in gui mode"
+ debug.critical(error_str)
+ result.append((False, error_str))
+ return result
+
+################################################################################
+
+def run(w_list, parameters='', workflow_info=None, update_vistrail=True,
+ extra_info=None, reason="Console Mode Execution"):
+ """run(w_list: list of (locator, version), parameters: str) -> boolean
+ Run all workflows in w_list, version can be a tag name or a version id.
+ Returns list of errors (empty list if there are no errors)
+ """
+ all_errors = []
+ results = run_and_get_results(w_list, parameters, workflow_info,
+ update_vistrail,extra_info, reason)
+ for result in results:
+ (objs, errors, executed) = (result.objects,
+ result.errors, result.executed)
+ for err in sorted(errors.iteritems()):
+ all_errors.append(result.workflow_info + err)
+ return all_errors
+
+def run_parameter_exploration(locator, pe_id, extra_info = {},
+ reason="Console Mode Parameter Exploration Execution"):
+ """run_parameter_exploration(w_list: (locator, version),
+ pe_id: str/int,
+ reason: str) -> (pe_id, [error msg])
+ Run parameter exploration in w, and returns an interpreter result object.
+ version can be a tag name or a version id.
+
+ """
+ if is_running_gui():
+ from vistrails.gui.vistrail_controller import VistrailController as \
+ GUIVistrailController
+ try:
+ (v, abstractions , thumbnails, mashups) = load_vistrail(locator)
+ controller = GUIVistrailController(v, locator, abstractions,
+ thumbnails, mashups)
+ try:
+ pe_id = int(pe_id)
+ pe = controller.vistrail.get_paramexp(pe_id)
+ except ValueError:
+ pe = controller.vistrail.get_named_paramexp(pe_id)
+ controller.change_selected_version(pe.action_id)
+ controller.executeParameterExploration(pe, extra_info=extra_info,
+ showProgress=False)
+ except Exception, e:
+ import traceback
+ return (locator, pe_id, str(e), traceback.format_exc())
+
+def run_parameter_explorations(w_list, extra_info = {},
+ reason="Console Mode Parameter Exploration Execution"):
+ """run(w_list: list of (locator, pe_id), reason: str) -> boolean
+ For each workflow in w_list, run parameter exploration pe_id
+ version can be a tag name or a version id.
+ Returns list of errors (empty list if there are no errors)
+ """
+ all_errors = []
+ for locator, pe_id in w_list:
+ result = run_parameter_exploration(locator, pe_id, reason=reason,
+ extra_info=extra_info)
+ if result:
+ all_errors.append(result)
+ return all_errors
+
+def cleanup():
+ vistrails.core.interpreter.cached.CachedInterpreter.cleanup()
+
+################################################################################
+#Testing
+
+
+class TestConsoleMode(unittest.TestCase):
+
+ @classmethod
+ def setUpClass(cls):
+ manager = vistrails.core.packagemanager.get_package_manager()
+ if manager.has_package('org.vistrails.vistrails.console_mode_test'):
+ return
+
+ d = {'console_mode_test': 'vistrails.tests.resources.'}
+ manager.late_enable_package('console_mode_test',d)
+
+ @classmethod
+ def tearDownClass(cls):
+ manager = vistrails.core.packagemanager.get_package_manager()
+ if manager.has_package('org.vistrails.vistrails.console_mode_test'):
+ manager.late_disable_package('console_mode_test')
+
+ def test1(self):
+ locator = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/dummy.xml')
+ result = run([(locator, "int chain")], update_vistrail=False)
+ self.assertEqual(len(result), 0)
+
+ def test_tuple(self):
+ from vistrails.core.vistrail.module_param import ModuleParam
+ from vistrails.core.vistrail.module_function import ModuleFunction
+ from vistrails.core.utils import DummyView
+ from vistrails.core.vistrail.module import Module
+ import vistrails.db.domain
+
+ id_scope = vistrails.db.domain.IdScope()
+ interpreter = vistrails.core.interpreter.default.get_default_interpreter()
+ v = DummyView()
+ p = vistrails.core.vistrail.pipeline.Pipeline()
+ params = [ModuleParam(id=id_scope.getNewId(ModuleParam.vtType),
+ pos=0,
+ type='Float',
+ val='2.0',
+ ),
+ ModuleParam(id=id_scope.getNewId(ModuleParam.vtType),
+ pos=1,
+ type='Float',
+ val='2.0',
+ )]
+ function = ModuleFunction(id=id_scope.getNewId(ModuleFunction.vtType),
+ name='input')
+ function.add_parameters(params)
+ module = Module(id=id_scope.getNewId(Module.vtType),
+ name='TestTupleExecution',
+ package='org.vistrails.vistrails.console_mode_test',
+ version='0.9.1')
+ module.add_function(function)
+
+ p.add_module(module)
+
+ kwargs = {'locator': XMLFileLocator('foo'),
+ 'current_version': 1L,
+ 'view': v,
+ }
+ interpreter.execute(p, **kwargs)
+
+ def test_python_source(self):
+ locator = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/pythonsource.xml')
+ result = run([(locator,"testPortsAndFail")], update_vistrail=False)
+ self.assertEqual(len(result), 0)
+
+ def test_python_source_2(self):
+ locator = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/pythonsource.xml')
+ result = run_and_get_results([(locator, "test_simple_success")],
+ update_vistrail=False)[0]
+ self.assertEquals(len(result.executed), 1)
+
+ def test_dynamic_module_error(self):
+ locator = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/dynamic_module_error.xml')
+ result = run([(locator, "test")], update_vistrail=False)
+ self.assertNotEqual(len(result), 0)
+
+ def test_change_parameter(self):
+ locator = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/test_change_vistrail.xml')
+ result = run([(locator, "v1")], update_vistrail=False)
+ self.assertEqual(len(result), 0)
+
+ result = run([(locator, "v2")], update_vistrail=False)
+ self.assertEquals(len(result), 0)
+
+ def test_ticket_73(self):
+ # Tests serializing a custom-named module to disk
+ locator = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/test_ticket_73.xml')
+ v = locator.load()
+
+ import tempfile
+ (fd, filename) = tempfile.mkstemp()
+ os.close(fd)
+ locator = XMLFileLocator(filename)
+ try:
+ locator.save(v)
+ finally:
+ os.remove(filename)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/data_structures/__init__.py b/vistrails/core/data_structures/__init__.py
new file mode 100644
index 0000000..210957e
--- /dev/null
+++ b/vistrails/core/data_structures/__init__.py
@@ -0,0 +1,44 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Python package for all data structures that are used throughout
+VisTrails."""
+
+# from core.data_structures.point import Point
+# from core.data_structures.rect import Rect
+# from core.data_structures.graph import Graph
+# from core.data_structures.queue import Queue
+# from core.data_structures.stack import Stack
+# from core.data_structures.bijectivedict import Bidict
+pass
diff --git a/vistrails/core/data_structures/bijectivedict.py b/vistrails/core/data_structures/bijectivedict.py
new file mode 100644
index 0000000..617d8b5
--- /dev/null
+++ b/vistrails/core/data_structures/bijectivedict.py
@@ -0,0 +1,123 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class Bidict(dict):
+ """Subclass of mapping that automatically keeps track of the
+inverse mapping. Note: self.inverse is a simple dict, so it won't keep
+track of deletions directly to self.inverse and things like that. Use
+this for lookups ONLY!. Also, if mapping is not bijective, there's no
+guarantee the inverse mapping will be consistent (particularly in the
+presence of deletions.)"""
+
+ def __init__(self, *args, **kwargs):
+
+ dict.__init__(self, *args, **kwargs)
+ self.inverse = {}
+ for (k, v) in self.iteritems():
+ self.inverse[v] = k
+
+ def __setitem__(self, key, value):
+ dict.__setitem__(self, key, value)
+ self.inverse[value] = key
+
+ def __delitem__(self, key):
+ v = self[key]
+ dict.__delitem__(self, key)
+ # Might not be true if mapping was not bijective
+ if v in self.inverse:
+ del self.inverse[v]
+
+ def __copy__(self):
+ r = Bidict()
+ r.inverse = copy.copy(self.inverse)
+ r.update(self)
+ return r
+
+ def update(self, other):
+ try:
+ for i in other.iterkeys():
+ self[i] = other[i]
+ except:
+ for (k,v) in other:
+ self[k] = v
+
+##############################################################################
+
+import unittest
+
+class TestBidict(unittest.TestCase):
+
+ def test1(self):
+ x = Bidict()
+ for i in xrange(10):
+ x[i] = 9-i
+ for i in xrange(10):
+ self.assertEquals(x[i], 9-i)
+ self.assertEquals(x.inverse[i], 9-i)
+ del x[1]
+ self.assertRaises(KeyError, x.__getitem__, 1)
+ self.assertRaises(KeyError, x.inverse.__getitem__, 8)
+
+ def test_non_bijective(self):
+ """Tests resilience (not correctness!) under non-bijectiveness."""
+ x = Bidict()
+ x[1] = 2
+ x[3] = 2
+ del x[1]
+ del x[3]
+
+ def test_copy(self):
+ """Tests copying a Bidict."""
+ x = Bidict()
+ x[1] = 2
+ x[3] = 4
+ y = copy.copy(x)
+ assert y.inverse[4] == x.inverse[4]
+ assert y.inverse[2] == x.inverse[2]
+
+ def test_update(self):
+ """Tests if updating a bidict with a dict works"""
+ x = {1:2, 3:4}
+ y = Bidict()
+ y.update(x)
+ assert y.inverse[4] == 3
+ assert y.inverse[2] == 1
+
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/data_structures/graph.py b/vistrails/core/data_structures/graph.py
new file mode 100644
index 0000000..68d99c3
--- /dev/null
+++ b/vistrails/core/data_structures/graph.py
@@ -0,0 +1,1135 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import math
+import random
+import copy
+
+from itertools import imap, chain, izip
+
+from vistrails.core.utils import all
+from vistrails.core.data_structures.queue import Queue
+from vistrails.core.data_structures.stack import Stack
+
+import unittest
+import random
+
+################################################################################
+# Graph
+
+class GraphException(Exception):
+ pass
+
+class Graph(object):
+ """Graph holds a graph with possible multiple edges. The
+ datastructures are all dictionary-based, so datatypes more general than ints
+ can be used. For example:
+
+ >>> import graph
+ >>> g = graph.Graph()
+ >>> g.add_vertex('foo')
+ >>> g.add_vertex('bar')
+ >>> g.add_edge('foo', 'bar', 'edge_foo')
+ >>> g.add_edge('foo', 'bar', 'edge_bar')
+ >>> g.add_edge('bar', 'foo', 'edge_back')
+ >>> g.out_degree('foo')
+ 2
+ >>> g.out_degree('bar')
+ 1
+ """
+
+ ##########################################################################
+ # Constructor
+
+ def __init__(self):
+ """ Graph() -> Graph
+ Initialize an empty graph and return nothing
+
+ """
+ self.vertices = {}
+ self.adjacency_list = {}
+ self.inverse_adjacency_list = {}
+
+ @staticmethod
+ def map_vertices(graph, vertex_map=None, edge_map=None):
+ """ map_verices(graph: Graph, vertex_map: dict): Graph
+
+ Creates a new graph that is a mapping of vertex ids through
+ vertex_map.
+
+ """
+ result = Graph()
+ if vertex_map is None:
+ vertex_map = dict((v, v) for v in self.vertices)
+ if edge_map is None:
+ edge_map = {}
+ for vfrom, lto in graph.adjacency_list.iteritems():
+ for (vto, eid) in lto:
+ edge_map[eid] = eid
+ result.vertices = dict((vertex_map[v], True) for v in graph.vertices)
+ for (vto, lto) in graph.adjacency_list.iteritems():
+ result.adjacency_list[vto] = [(vertex_map[to], edge_map[eid]) for (to, eid) in lto]
+ for (vto, lto) in graph.inverse_adjacency_list.iteritems():
+ result.inverse_adjacency_list[vto] = [(vertex_map[to], edge_map[eid]) for (to, eid) in lto]
+ return result
+
+ ##########################################################################
+ # Accessors
+
+ def inverse(self):
+ """inverse() -> Graph
+ Inverse all edge directions on the graph and return a Graph
+
+ """
+ result = copy.copy(self)
+ t = result.adjacency_list
+ result.adjacency_list = result.inverse_adjacency_list
+ result.inverse_adjacency_list = t
+ return result
+
+ def inverse_immutable(self):
+ """inverse_immutable() -> Graph
+
+ Fast version of inverse(), but requires that output not be
+ mutated (it shares with self.)
+ """
+ result = Graph()
+ result.vertices = self.vertices
+ result.adjacency_list = self.inverse_adjacency_list
+ result.inverse_adjacency_list = self.adjacency_list
+ return result
+
+ def undirected_immutable(self):
+ """undirected_immutable() -> Graph
+
+ Creates an undirected version of self. Notice that this
+ version should not be mutated because there is sharing in the
+ adjacency lists and the vertex map.
+
+ Additionally, if self wasn't acyclic, then
+ undirected_immutable() won't be simple.
+ """
+ result = Graph()
+ result.vertices = self.vertices
+ result.adjacency_list = dict((k, (self.adjacency_list[k] +
+ self.inverse_adjacency_list[k]))
+ for k in self.vertices)
+ result.inverse_adjacency_list = result.adjacency_list
+ return result
+
+ def out_degree(self, froom):
+ """ out_degree(froom: id type) -> int
+ Compute the number of edges leaving 'froom' and return an int
+
+ Keyword arguments:
+ froom -- 'immutable' vertex id
+
+ """
+ return len(self.adjacency_list[froom])
+
+ def in_degree(self, to):
+ """ in_degree(to: id type) -> int
+ Compute the number of edges entering 'to' and return an int
+
+ Keyword arguments:
+ to -- 'immutable' vertex id
+
+ """
+ return len(self.inverse_adjacency_list[to])
+
+ def sinks(self):
+ """ sinks() -> list(id type)
+ Find all vertices whose out_degree is zero and return a list of ids
+
+ """
+ return [idx for idx in self.vertices.keys() \
+ if self.out_degree(idx) == 0]
+
+ def sources(self):
+ """ sources() -> list(id type)
+ Find all vertices whose in_degree is zero and return a list of ids
+
+ """
+ return [idx for idx in self.vertices.keys() if self.in_degree(idx) == 0]
+
+ def edges_to(self, id):
+ """ edges_to(id: id type) -> list(list)
+ Find edges entering a vertex id and return a list of tuples (id,id)
+
+ Keyword arguments:
+ id : 'immutable' vertex id
+
+ """
+ return self.inverse_adjacency_list[id]
+
+ def edges_from(self, id):
+ """ edges_from(id: id type) -> list(list)
+ Find edges leaving a vertex id and return a list of tuples (id,id)
+
+ Keyword arguments:
+ id : 'immutable' vertex id
+
+ """
+ return self.adjacency_list[id]
+
+ def get_edge(self, frm, to):
+ """ get_edge(frm, to) -> edge_id
+
+ Returns the id from the edge from->to."""
+ for (t, e_id) in self.edges_from(frm):
+ if t == to:
+ return e_id
+
+ def has_edge(self, frm, to):
+ """ has_edge(frm, to) -> bool
+
+ True if there exists an edge (frm, to)"""
+
+ for (t, _) in self.edges_from(frm):
+ if t == to:
+ return True
+ return False
+
+ ##########################################################################
+ # Mutate graph
+
+ def add_vertex(self, id, data=None):
+ """ add_vertex(id: id type, data) -> None
+ Add a vertex to the graph if it is not already in the graph
+ and return nothing
+
+ Keyword arguments:
+ id -- vertex id
+
+ """
+ if not id in self.vertices:
+ self.vertices[id] = data
+ self.adjacency_list[id] = []
+ self.inverse_adjacency_list[id] = []
+
+ def add_edge(self, froom, to, id=None):
+ """ add_edge(froom: id type, to: id type, id: id type) -> None
+ Add an edge from vertex 'froom' to vertex 'to' and return nothing
+
+ Keyword arguments:
+ froom -- 'immutable' origin vertex id
+ to -- 'immutable' destination vertex id
+ id -- 'immutable' edge id (default None)
+
+ """
+ self.add_vertex(froom)
+ self.add_vertex(to)
+ self.adjacency_list[froom].append((to, id))
+ self.inverse_adjacency_list[to].append((froom, id))
+
+ def delete_vertex(self, id):
+ """ delete_vertex(id: id type) -> None
+ Remove a vertex from graph and return nothing
+
+ Keyword arguments:
+ -- id : 'immutable' vertex id
+
+ """
+
+ for (origin, edge_id) in self.inverse_adjacency_list[id]:
+ t = (id, edge_id)
+ self.adjacency_list[origin].remove(t)
+ for (dest, edge_id) in self.adjacency_list[id]:
+ t = (id, edge_id)
+ self.inverse_adjacency_list[dest].remove(t)
+ del self.adjacency_list[id]
+ del self.inverse_adjacency_list[id]
+ del self.vertices[id]
+
+ class RenameVertexError(GraphException):
+ pass
+
+ def rename_vertex(self, old_vertex, new_vertex):
+ """ rename_vertex(old_vertex, new_vertex) -> None
+
+ renames old_vertex to new_vertex in the graph, updating the edges
+ appropriately. Should not be used to merge vertices, will raise
+ exception if new_vertex exists in graph.
+
+ """
+ if not (old_vertex in self.vertices):
+ raise self.RenameVertexError("vertex '%s' does not exist" % old_vertex)
+ if new_vertex in self.vertices:
+ raise self.RenameVertexError("vertex '%s' already exists" % new_vertex)
+ self.add_vertex(new_vertex)
+
+ # the slice ([:]) is important for copying, since change_edge
+ # mutates the list we'll be traversing
+ for (v_from, e_id) in self.inverse_adjacency_list[old_vertex][:]:
+ self.change_edge(v_from, old_vertex, new_vertex, e_id, e_id)
+
+ self.adjacency_list[new_vertex] = self.adjacency_list[old_vertex]
+ del self.adjacency_list[old_vertex]
+ del self.vertices[old_vertex]
+
+ def change_edge(self, old_froom, old_to, new_to, old_id=None, new_id=None):
+ """ change_edge(old_froom: id, old_to: id, new_to: id,
+ old_id: id, new_id: id) -> None
+ Changes the destination of an edge in a graph **in place**
+
+ Keyword arguments:
+ old_froom -- 'immutable' origin vertex id
+ old_to -- 'immutable' destination vertex id
+ new_to -- 'immutable' destination vertex id
+ old_id -- 'immutable' edge id (default None)
+ new_id -- 'immutable' edge id (default None)
+ """
+
+ if old_id == None:
+ efroom = self.adjacency_list[old_froom]
+ for i, edge in enumerate(efroom):
+ if edge[0] == old_to:
+ old_id = edge[1]
+ forward_idx = i
+ break
+ else:
+ forward_idx = self.adjacency_list[old_froom].index((old_to, old_id))
+
+ self.adjacency_list[old_froom][forward_idx] = ((new_to, new_id))
+ self.inverse_adjacency_list[old_to].remove((old_froom, old_id))
+ self.inverse_adjacency_list[new_to].append((old_froom, new_id))
+
+ def delete_edge(self, froom, to, id=None):
+ """ delete_edge(froom: id type, to: id type, id: id type) -> None
+ Remove an edge from graph and return nothing
+
+ Keyword arguments:
+ froom -- 'immutable' origin vertex id
+ to -- 'immutable' destination vertex id
+ id -- 'immutable' edge id
+
+ """
+ if id is None:
+ efroom = self.adjacency_list[froom]
+ for edge in efroom:
+ if edge[0] == to:
+ id = edge[1]
+ break
+ if id is None:
+ raise GraphException("delete_edge didn't find edge (%s,%s)"%
+ (froom, to))
+ self.adjacency_list[froom].remove((to, id))
+ self.inverse_adjacency_list[to].remove((froom, id))
+
+ ##########################################################################
+ # Graph algorithms
+
+ def closest_vertex(self, frm, target_list):
+ """ closest_vertex(frm, target_list) -> id Uses bfs-like
+ algorithm to find closest vertex to frm in target_list
+
+ """
+ if frm in target_list:
+ return frm
+ target_list = set(target_list)
+ visited = set([frm])
+ parent = {}
+ q = Queue()
+ q.push(frm)
+ while 1:
+ try:
+ current = q.pop()
+ except q.EmptyQueue:
+ raise GraphException("no vertices reachable: %s %s" % (frm, list(target_list)))
+ efrom = self.edges_from(current)
+ for (to, eid) in efrom:
+ if to in target_list:
+ return to
+ if to not in visited:
+ parent[to] = current
+ q.push(to)
+ visited.add(to)
+
+ def bfs(self, frm):
+ """ bfs(frm:id type) -> dict(id type)
+ Perform Breadth-First-Search and return a dict of parent id
+
+ Keyword arguments:
+ frm -- 'immutable' vertex id
+
+ """
+ visited = set([frm])
+ parent = {}
+ q = Queue()
+ q.push(frm)
+ while 1:
+ try:
+ current = q.pop()
+ except q.EmptyQueue:
+ break
+ efrom = self.edges_from(current)
+ for (to, eid) in efrom:
+ if to not in visited:
+ parent[to] = current
+ q.push(to)
+ visited.add(to)
+ return parent
+
+ class GraphContainsCycles(GraphException):
+ def __init__(self, v1, v2):
+ self.back_edge = (v1, v2)
+ def __str__(self):
+ return ("Graph contains cycles: back edge %s encountered" %
+ self.back_edge)
+
+ def dfs(self,
+ vertex_set=None,
+ raise_if_cyclic=False,
+ enter_vertex=None,
+ leave_vertex=None):
+ """ dfs(self,vertex_set=None,raise_if_cyclic=False,enter_vertex=None,
+ leave_vertex=None) -> (discovery, parent, finish)
+ Performs a depth-first search on a graph and returns three dictionaries with
+ relevant information. If vertex_set is not None, then it is used as
+ the list of ids to perform the DFS on.
+
+ See CLRS p. 541.
+
+ enter_vertex, when present, is called just before visiting a vertex
+ for the first time (and only once) with the vertex id as a parameter.
+
+ leave_vertex, when present, is called just after visiting a vertex
+ for the first time (and only once) with the vertex id as a parameter.
+ """
+
+ if not vertex_set:
+ vertex_set = self.vertices
+
+ # Ugly ugly python
+ # http://mail.python.org/pipermail/python-list/2006-April/378964.html
+
+ # We cannot explicitly "del data":
+ # http://www.python.org/dev/peps/pep-0227/
+
+ class Closure(object):
+
+ def clear(self):
+ del self.discovery
+ del self.parent
+ del self.finish
+ del self.t
+
+ # Straight CLRS p.541
+ data = Closure()
+ data.discovery = {} # d in CLRS
+ data.parent = {} # \pi in CLRS
+ data.finish = {} # f in CLRS
+ data.t = 0
+
+ (enter, leave, back, other) = xrange(4)
+
+ # inspired by http://www.ics.uci.edu/~eppstein/PADS/DFS.py
+
+ def handle(v, w, edgetype):
+ data.t += 1
+ if edgetype == enter:
+ data.discovery[v] = data.t
+ if enter_vertex:
+ enter_vertex(w)
+ if v != w:
+ data.parent[w] = v
+ elif edgetype == leave:
+ data.finish[w] = data.t
+ if leave_vertex:
+ leave_vertex(w)
+ elif edgetype == back and raise_if_cyclic:
+ raise self.GraphContainsCycles(v, w)
+
+ visited = set()
+ gray = set()
+ # helper function to build stack structure
+ def st(v): return (v, iter(self.adjacency_list[v]))
+ for vertex in vertex_set:
+ if vertex not in visited:
+ handle(vertex, vertex, enter)
+ visited.add(vertex)
+ stack = Stack()
+ stack.push(st(vertex))
+ gray.add(vertex)
+ while stack.size:
+ parent, children = stack.top()
+ try:
+ child, _ = children.next()
+ if child in visited:
+ handle(parent, child, (child in gray
+ and back
+ or other))
+ else:
+ handle(parent, child, enter)
+ visited.add(child)
+ stack.push(st(child))
+ gray.add(child)
+ except StopIteration:
+ gray.remove(parent)
+ stack.pop()
+ if stack.size:
+ handle(stack.top()[0], parent, leave)
+ handle(vertex, vertex, leave)
+
+ result = (data.discovery, data.parent, data.finish)
+ data.clear()
+ return result
+
+ class VertexHasNoParentError(GraphException):
+ def __init__(self, v):
+ Exception.__init__(self, v)
+ self._v = v
+ def __str__(self):
+ return ("called parent() on vertex '%s', which has no parent nodes"
+ % self._v)
+
+ def parent(self, v):
+ """ parent(v: id type) -> id type
+ Find the parent of vertex v and return an id
+
+ Keyword arguments:
+ v -- 'immutable' vertex id
+
+ raises VertexHasNoParentError is vertex has no parent
+
+ raises KeyError is vertex is not on graph
+
+ """
+ l=self.inverse_adjacency_list[v]
+ if len(l):
+ (froom, a) = l[-1]
+ else:
+ raise self.VertexHasNoParentError(v)
+ return froom
+
+ def vertices_topological_sort(self,vertex_set=None):
+ """ vertices_topological_sort(self,vertex_set=None) ->
+ sequence(vertices) Returns a sequence of all vertices, so that
+ they are in topological sort order (every node traversed is
+ such that their parent nodes have already been
+ traversed). vertex_set is optionally a list of vertices on
+ which to perform the topological sort.
+
+ This is O(n log n) instead of the optimal O(n),
+ """
+ (d, p, f) = self.dfs(vertex_set,raise_if_cyclic=True)
+ # Optimized these three lines into the last one
+ # lst = [(v, k) for (k,v) in f.iteritems()]
+ # lst.sort(reverse=True)
+ # return [v for (k, v) in lst]
+ return [k for (k, _) in sorted(f.iteritems(),
+ key=lambda x: (x[1], x[0]),
+ reverse=True)]
+
+ def topologically_contractible(self, subgraph):
+ """topologically_contractible(subgraph) -> Boolean.
+
+ Returns true if contracting the subgraph to a single vertex
+ doesn't create cycles. This is equivalent to checking whether
+ a pipeline subgraph forms a legal abstraction."""
+ x = copy.copy(self)
+ conns_to_subgraph = self.connections_to_subgraph(subgraph)
+ conns_from_subgraph = self.connections_from_subgraph(subgraph)
+ for v in subgraph.vertices.iterkeys():
+ x.delete_vertex(v)
+ free_vertex = max(subgraph.vertices.iterkeys()) + 1
+ x.add_vertex(free_vertex)
+ for (edge_from, edge_to, edge_id) in conns_to_subgraph:
+ x.add_edge(free_vertex, edge_to)
+ for (edge_from, edge_to, edge_id) in conns_from_subgraph:
+ x.add_edge(edge_from, free_vertex)
+ try:
+ x.vertices_topological_sort()
+ return True
+ except self.GraphContainsCycles:
+ return False
+
+ ##########################################################################
+ # Subgraphs
+
+ def subgraph(self, vertex_set):
+ """ subgraph(vertex_set) -> Graph.
+
+ Returns a subgraph of self containing all vertices and
+ connections between them."""
+ result = Graph()
+ vertex_set = set(vertex_set)
+ # add vertices
+ for vertex in vertex_set:
+ result.add_vertex(vertex)
+ # add edges
+ for vertex_from in vertex_set:
+ for (vertex_to, edge_id) in self.edges_from(vertex_from):
+ if vertex_to in vertex_set:
+ result.add_edge(vertex_from, vertex_to, edge_id)
+ return result
+
+ def connections_to_subgraph(self, subgraph):
+ """connections_to_subgraph(subgraph) -> [(vert_from, vert_to, edge_id)]
+
+ Returns the list of all edges that connect to a vertex \in
+ subgraph. subgraph is assumed to be a subgraph of self"""
+ vertices_to_traverse = set(self.vertices.iterkeys())
+ subgraph_verts = set(subgraph.vertices.iterkeys())
+ vertices_to_traverse -= subgraph_verts
+
+ result = []
+ for v in vertices_to_traverse:
+ for e in self.adjacency_list[v]:
+ (v_to, e_id) = e
+ if v_to in subgraph_verts:
+ result.append((v, v_to, e_id))
+ return result
+
+ def connections_from_subgraph(self, subgraph):
+ """connections_from_subgraph(subgraph) -> [(vert_from, vert_to, edge_id)]
+
+ Returns the list of all edges that connect from a vertex \in
+ subgraph to a vertex \not \in subgraph. subgraph is assumed to
+ be a subgraph of self"""
+ subgraph_verts = set(subgraph.vertices.iterkeys())
+ vertices_to_traverse = subgraph_verts
+
+ result = []
+ for v in vertices_to_traverse:
+ for e in self.adjacency_list[v]:
+ (v_to, e_id) = e
+ if v_to not in subgraph_verts:
+ result.append((v, v_to, e_id))
+ return result
+
+ ##########################################################################
+ # Iterators
+
+
+ def iter_edges_from(self, vertex):
+ """iter_edges_from(self, vertex) -> iterable
+
+ Returns an iterator over all edges in the form
+ (vertex, vert_to, edge_id)."""
+ def fn(edge):
+ (edge_to, edge_id) = edge
+ return (vertex, edge_to, edge_id)
+ return imap(fn, self.adjacency_list[vertex])
+
+ def iter_edges_to(self, vertex):
+ """iter_edges_to(self, vertex) -> iterable
+
+ Returns an iterator over all edges in the form
+ (vertex, vert_to, edge_id)."""
+ def fn(edge):
+ (edge_from, edge_id) = edge
+ return (edge_from, vertex, edge_id)
+ return imap(fn, self.inverse_adjacency_list[vertex])
+
+ def iter_all_edges(self):
+ """iter_all_edges() -> iterable
+
+ Returns an iterator over all edges in the graph in the form
+ (vert_from, vert_to, edge_id)."""
+ verts = self.iter_vertices()
+ edge_itors = imap(self.iter_edges_from, verts)
+ return chain(*[v for v in edge_itors])
+
+ def iter_vertices(self):
+ """iter_vertices() -> iterable
+
+ Returns an iterator over all vertex ids of the graph."""
+ return self.vertices.iterkeys()
+
+ ##########################################################################
+ # Special Python methods
+
+ def __str__(self):
+ """ __str__() -> str
+ Format the graph for serialization and return a string
+
+ """
+ vs = self.vertices.keys()
+ vs.sort()
+ al = []
+ for i in [map(lambda (t, i): (f, t, i), l)
+ for (f, l) in self.adjacency_list.items()]:
+ al.extend(i)
+ al.sort(edge_cmp)
+ return "digraph G { " \
+ + ";".join([str(s) for s in vs]) + ";" \
+ + ";".join(["%s -> %s [label=\"%s\"]" % s for s in al]) + "}"
+
+ def __repr__(self):
+ """ __repr__() -> str
+ Similar to __str__ to re-represent the graph and returns a string
+
+ """
+ return self.__str__()
+
+ def __copy__(self):
+ """ __copy__() -> Graph
+ Make a copy of the graph and return a Graph
+
+ """
+ cp = Graph()
+ cp.vertices = copy.copy(self.vertices)
+ cp.adjacency_list = dict((k, v[:]) for (k,v) in self.adjacency_list.iteritems())
+ cp.inverse_adjacency_list = dict((k, v[:]) for (k,v) in self.inverse_adjacency_list.iteritems())
+ return cp
+
+ def __eq__(self, other):
+ # Does not test isomorphism - vertices must be consistently labeled
+ # might be slow - don't use in tight code
+ if type(self) <> type(other):
+ return False
+ for v in self.vertices:
+ if not v in other.vertices:
+ return False
+ for vfrom, elist in self.adjacency_list.iteritems():
+ for vto, eid in elist:
+ if not other.get_edge(vfrom, vto) == eid:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not (self == other)
+
+ ##########################################################################
+ # Etc
+
+ @staticmethod
+ def from_random(size):
+ """ from_random(size:int) -> Graph
+ Create a DAG with approximately size/e vertices and 3*|vertex| edges
+ and return a Graph
+
+ Keyword arguments:
+ size -- the estimated size of the graph to generate
+
+ """
+ result = Graph()
+ verts = filter(lambda x: x>0, peckcheck.a_list(peckcheck.an_int)(size))
+ for v in verts:
+ result.add_vertex(v)
+ k = size / math.e
+ p = (6*k) / ((k+1)*(k+2))
+ eid = 0
+ for v in verts:
+ for k in verts:
+ if v < k and random.random() > p:
+ result.add_edge(v, k, eid)
+ eid = eid + 1
+ return result
+
+def edge_cmp(v1, v2):
+ """ edge_cmp(v1: id type, v2:id type) -> int
+ Defines how the comparison must be done between edges and return a boolean
+
+ Keyword arguments:
+ v1 -- 'sequence' edge information
+ v2 -- 'sequence' other edge information
+
+ """
+ (from1, to1, id1) = v1
+ (from2, to2, id2) = v2
+ c1 = cmp(from1, from2)
+ if c1:
+ return c1
+ c2 = cmp(to1, to2)
+ if c2:
+ return c2
+ else:
+ return cmp(id1, id2)
+
+################################################################################
+# Unit testing
+
+
+class TestGraph(unittest.TestCase):
+ """ Class to test Graph
+
+ It tests vertex addition, the out_degree of a sink and in_degree of a
+ source consistencies.
+
+ """
+
+ def make_complete(self, v):
+ """returns a complete graph with v verts."""
+ g = Graph()
+ for x in xrange(v):
+ g.add_vertex(x)
+ for f in xrange(v):
+ for t in xrange(f+1, v):
+ g.add_edge(f, t, f * v + t)
+ return g
+
+ def make_linear(self, v, bw=False):
+ """returns a linear graph with v verts. if bw=True, add
+ backward links."""
+ g = Graph()
+ for x in xrange(v):
+ g.add_vertex(x)
+ for x,y in izip(xrange(v-1), xrange(1, v)):
+ g.add_edge(x, y, x)
+ if bw:
+ g.add_edge(y, x, x + v)
+ return g
+
+ def get_default_graph(self):
+ g = Graph()
+ g.add_vertex(0)
+ g.add_vertex(1)
+ g.add_vertex(2)
+ g.add_vertex(3)
+ g.add_vertex(4)
+ g.add_edge(0,1,0)
+ g.add_edge(1,2,1)
+ g.add_edge(0,3,2)
+ g.add_edge(3,2,3)
+ g.add_edge(2,4,4)
+ return g
+
+ def test1(self):
+ """Test adding edges and vertices"""
+ g = Graph()
+ g.add_vertex('0')
+ g.add_vertex('1')
+ g.add_vertex('2')
+ g.add_vertex('3')
+ g.add_edge('0', '1', 0)
+ g.add_edge('1', '2', 1)
+ g.add_edge('2', '3', 2)
+ parent = g.bfs('0')
+ self.assertEquals(parent['3'], '2')
+ self.assertEquals(parent['2'], '1')
+ self.assertEquals(parent['1'], '0')
+
+ def test2(self):
+ """Test bread-first-search"""
+ g = self.get_default_graph()
+ p = g.bfs(0)
+ k = p.keys()
+ k.sort()
+ self.assertEquals(k, [1, 2, 3, 4])
+ inv = g.inverse()
+ p_inv = inv.bfs(4)
+ k2 = p_inv.keys()
+ k2.sort()
+ self.assertEquals(k2, [0, 1, 2, 3])
+
+ def test3(self):
+ """Test sink and source degree consistency"""
+ g = Graph()
+ for i in xrange(100):
+ g.add_vertex(i);
+ for i in xrange(1000):
+ v1 = random.randint(0,99)
+ v2 = random.randint(0,99)
+ g.add_edge(v1, v2, i)
+ sinkResult = [None for i in g.sinks() if g.out_degree(i) == 0]
+ sourceResult = [None for i in g.sources() if g.in_degree(i) == 0]
+ if len(sinkResult) <> len(g.sinks()):
+ assert False
+ if len(sourceResult) <> len(g.sources()):
+ assert False
+
+ def test_remove_vertices(self):
+ g = self.make_linear(5)
+ g.delete_vertex(1)
+ g.delete_vertex(2)
+
+ def test_DFS(self):
+ """Test DFS on graph."""
+ g = self.get_default_graph()
+ g.dfs()
+
+ def test_topological_sort(self):
+ """Test toposort on graph."""
+ g = self.get_default_graph()
+ g.vertices_topological_sort()
+
+ g = self.make_linear(10)
+ r = g.vertices_topological_sort()
+ assert r == [0,1,2,3,4,5,6,7,8,9]
+
+ g = Graph()
+ g.add_vertex('a')
+ g.add_vertex('b')
+ g.add_vertex('c')
+ g.add_edge('a', 'b')
+ g.add_edge('b', 'c')
+ assert g.vertices_topological_sort() == ['a', 'b', 'c']
+
+ def test_limited_DFS(self):
+ """Test DFS on graph using a limited set of starting vertices."""
+ g = self.get_default_graph()
+ g.dfs(vertex_set=[1])
+ g.dfs(vertex_set=[1,3])
+ g.dfs(vertex_set=[1,2])
+
+ def test_limited_topological_sort(self):
+ """Test toposort on graph using a limited set of starting vertices."""
+ g = self.get_default_graph()
+ g.vertices_topological_sort(vertex_set=[1])
+ g.vertices_topological_sort(vertex_set=[1,3])
+ g.vertices_topological_sort(vertex_set=[1,2])
+
+ def test_print_empty_graph(self):
+ """Test print on empty graph"""
+ g = Graph()
+ g.__str__()
+
+ def test_delete(self):
+ """Tests consistency of data structure after deletion."""
+ g = Graph()
+ g.add_vertex(0)
+ g.add_vertex(1)
+ g.add_vertex(2)
+ g.add_edge(0, 1, 0)
+ g.add_edge(1, 2, 1)
+ g.delete_vertex(2)
+ self.assertEquals(g.adjacency_list[1], [])
+
+ def test_raising_DFS(self):
+ """Tests if DFS with cycle-checking will raise exceptions."""
+ g = Graph()
+ g.add_vertex(0)
+ g.add_vertex(1)
+ g.add_vertex(2)
+ g.add_edge(0, 1)
+ g.add_edge(1, 2)
+ g.add_edge(2, 0)
+ with self.assertRaises(Graph.GraphContainsCycles):
+ g.dfs(raise_if_cyclic=True)
+
+ def test_call_inverse(self):
+ """Test if calling inverse methods work."""
+ g = Graph()
+ g.add_vertex(0)
+ g.add_vertex(1)
+ g.add_vertex(2)
+ g.add_edge(0, 1)
+ g.add_edge(1, 2)
+ g.add_edge(2, 0)
+ g2 = g.inverse()
+ g3 = g.inverse_immutable()
+
+ def test_subgraph(self):
+ """Test subgraph routines."""
+ g = self.make_complete(5)
+ sub = g.subgraph([0,1])
+ assert 0 in sub.vertices
+ assert 1 in sub.vertices
+ assert (1,1) in sub.adjacency_list[0]
+ assert (0,1) in sub.inverse_adjacency_list[1]
+
+ g = self.make_linear(3)
+ sub = g.subgraph([0, 2])
+ assert 0 in sub.vertices
+ assert 2 in sub.vertices
+ assert sub.adjacency_list[0] == []
+ assert sub.adjacency_list[2] == []
+
+ def test_connections_to_subgraph(self):
+ """Test connections_to_subgraph."""
+ g = self.make_linear(5)
+ sub = g.subgraph([3])
+ assert len(g.connections_to_subgraph(sub)) == 1
+ g = self.make_linear(5, True)
+ sub = g.subgraph([3])
+ assert len(g.connections_to_subgraph(sub)) == 2
+
+ def test_connections_from_subgraph(self):
+ """Test connections_from_subgraph."""
+ g = self.make_linear(5)
+ sub = g.subgraph([3])
+ assert len(g.connections_from_subgraph(sub)) == 1
+ g = self.make_linear(5, True)
+ sub = g.subgraph([3])
+ assert len(g.connections_from_subgraph(sub)) == 2
+
+ def test_topologically_contractible(self):
+ """Test topologically_contractible."""
+ g = self.make_linear(5)
+ sub = g.subgraph([1, 2])
+ assert g.topologically_contractible(sub)
+ sub = g.subgraph([1, 3])
+ assert not g.topologically_contractible(sub)
+
+ g = Graph()
+ g.add_vertex(0)
+ g.add_vertex(1)
+ g.add_vertex(2)
+ g.add_vertex(3)
+ g.add_edge(0, 1)
+ g.add_edge(2, 3)
+ for i in xrange(1, 16):
+ s = []
+ for j in xrange(4):
+ if i & (1 << j): s.append(j)
+ assert g.topologically_contractible(g.subgraph(s))
+
+ def test_iter_vertices(self):
+ g = self.get_default_graph()
+ l = list(g.iter_vertices())
+ l.sort()
+ assert l == [0,1,2,3,4]
+
+ def test_iter_edges(self):
+ g = self.get_default_graph()
+ l = [v for v in g.iter_all_edges()]
+ l.sort()
+ assert l == [(0,1,0), (0,3,2), (1, 2, 1), (2, 4, 4), (3, 2, 3)]
+
+ def test_iter_edges_empty(self):
+ """Test iterators on empty parts of the graph."""
+ g = Graph()
+ for a in g.iter_vertices():
+ assert False
+ g.add_vertex(0)
+ for a in g.iter_edges_from(0):
+ assert False
+ for a in g.iter_edges_to(0):
+ assert False
+ for a in g.iter_all_edges():
+ assert False
+
+ def test_get_edge_none(self):
+ g = Graph()
+ g.add_vertex(0)
+ g.add_vertex(1)
+ assert g.get_edge(0, 1) == None
+
+ def test_dfs_before(self):
+ g = self.make_linear(10)
+ inc = []
+ dec = []
+ def before(id): inc.append(id)
+ def after(id): dec.append(id)
+ g.dfs(enter_vertex=before,
+ leave_vertex=after)
+ assert inc == [0,1,2,3,4,5,6,7,8,9]
+ assert inc == list(reversed(dec))
+ assert all(a < b for a, b in izip(inc[:-1], inc[1:]))
+ assert all(a > b for a, b in izip(dec[:-1], dec[1:]))
+
+ def test_parent_source(self):
+ g = self.make_linear(10)
+ self.assertRaises(g.VertexHasNoParentError,
+ lambda: g.parent(0))
+ for i in xrange(1, 10):
+ assert g.parent(i) == i-1
+
+ def test_rename_vertex(self):
+ g = self.make_linear(10)
+ self.assertRaises(g.RenameVertexError,
+ lambda: g.rename_vertex(0, 1))
+ assert g.get_edge(0, 1) is not None
+ assert g.get_edge(0, 11) is None
+ g.rename_vertex(1, 11)
+ assert g.get_edge(0, 1) is None
+ assert g.get_edge(0, 11) is not None
+ g.rename_vertex(11, 1)
+ assert g.get_edge(0, 1) is not None
+ assert g.get_edge(0, 11) is None
+
+ def test_delete_get_edge(self):
+ g = self.make_linear(10)
+ self.assertRaises(GraphException, lambda: g.delete_edge(7, 9))
+ assert g.has_edge(7, 8)
+ g.delete_edge(7, 8)
+ assert not g.has_edge(7, 8)
+
+ def test_bfs(self):
+ g = self.make_linear(5)
+ lst = g.bfs(0).items()
+ lst.sort()
+ assert lst == [(1, 0), (2, 1), (3, 2), (4, 3)]
+ lst = g.bfs(2).items()
+ lst.sort()
+ assert lst == [(3, 2), (4, 3)]
+
+ def test_undirected(self):
+ g = self.make_linear(5).undirected_immutable()
+ lst = g.bfs(0).items()
+ lst.sort()
+ assert lst == [(1, 0), (2, 1), (3, 2), (4, 3)]
+ lst = g.bfs(2).items()
+ lst.sort()
+ assert lst == [(0, 1), (1, 2), (3, 2), (4, 3)]
+
+ def test_closest_vertex(self):
+ g = self.make_linear(10)
+ g.delete_edge(7, 8)
+ g = g.undirected_immutable()
+ self.assertRaises(GraphException, lambda: g.closest_vertex(1, [9]))
+ assert g.closest_vertex(3, [2, 6, 7]) == 2
+ assert g.closest_vertex(3, [2, 3, 6, 7]) == 3
+ # Test using dictionary as target_list
+
+ d1 = {2:True, 6:True, 7:False}
+ d2 = {2:True, 6:True, 7:False, 3:False}
+ d3 = {9:True}
+ self.assertRaises(GraphException, lambda: g.closest_vertex(1, d3))
+ assert g.closest_vertex(3, d1) == 2
+ assert g.closest_vertex(3, d2) == 3
+
+ def test_copy_not_share(self):
+ g = self.make_linear(10)
+ g2 = copy.copy(g)
+ for v in g.vertices:
+ assert id(g.adjacency_list[v]) <> id(g2.adjacency_list[v])
+ assert id(g.inverse_adjacency_list[v]) <> id(g2.inverse_adjacency_list[v])
+
+ def test_copy_works(self):
+ g = self.make_linear(10)
+ g2 = copy.copy(g)
+ for v in g.vertices:
+ assert v in g2.vertices
+ assert g2.adjacency_list[v] == g.adjacency_list[v]
+ assert g2.inverse_adjacency_list[v] == g.inverse_adjacency_list[v]
+
+ def test_equals(self):
+ g = self.make_linear(5)
+ assert copy.copy(g) == g
+ g2 = copy.copy(g)
+ g2.add_vertex(10)
+ assert g2 <> g
+
+ def test_map_vertices(self):
+ g = self.make_linear(5)
+ m = {0: 0, 1: 1, 2: 2, 3: 3, 4: 4}
+ assert g == Graph.map_vertices(g, m)
+ m = {0: 5, 1: 6, 2: 7, 3: 8, 4: 9}
+ assert g <> Graph.map_vertices(g, m)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/data_structures/point.py b/vistrails/core/data_structures/point.py
new file mode 100644
index 0000000..9534d2e
--- /dev/null
+++ b/vistrails/core/data_structures/point.py
@@ -0,0 +1,199 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import math
+
+################################################################################
+# Point
+
+class Point(object):
+ """Point is a point in 2D. It behaves as a vector, too, because that's
+ convenient."""
+
+ ##########################################################################
+ # Constructor
+
+ def __init__(self, x=0, y=0):
+ """ Point(x: float, y: float) -> Point
+ Initialize and return a Point
+
+ """
+ self.x = float(x)
+ self.y = float(y)
+
+ # copy is implicit - all fields are immutable
+
+ ##########################################################################
+
+ def reset(self,x,y):
+ """ reset(x: float, y: float) -> None
+ Resets the point to given coordinates and return nothing
+
+ """
+ self.x = float(x)
+ self.y = float(y)
+
+ def is_inside(self, rect):
+ """ is_inside(rect: Rect) -> boolean
+ Check if the point is falling inside rect and return a boolean
+
+ """
+ return (self.x >= rect.lower_left.x and
+ self.x <= rect.upper_right.x and
+ self.y >= rect.lower_left.y and
+ self.y <= rect.upper_right.y)
+
+ def length(self):
+ """ length() -> float
+ Interprets self as a vector to compute the L_2 norm and return a float
+
+ """
+ return math.sqrt(self.x * self.x + self.y * self.y)
+
+ ##########################################################################
+ # Debugging
+
+ def show_comparison(self, other):
+ if type(self) != type(other):
+ print "Type mismatch"
+ return
+ l = (self - other).length()
+ if l >= self.eq_delta:
+ print "Points are too far away:"
+ print self
+ print other
+ else:
+ print "No difference found: delta is %f" % l
+ assert self == other
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ return "(%f, %f)@%X" % (self.x, self.y, id(self))
+
+ def __neg__(self):
+ """ __neg__() -> Point
+ Compute a point p such that: self + p == Point(0,0), and return a Point
+
+ """
+ return Point(-self.x,-self.y)
+
+ def __add__(self, other):
+ """ __add__(other: Point) -> Point
+ Returns a point p such that: self + other == p, and return a Point
+
+ """
+ return Point(self.x + other.x, self.y + other.y)
+
+ def __sub__(self, other):
+ """ __sub__(other: Point) -> Point
+ Returns a point p such that: self - other == p, and return a Point
+
+ """
+ return Point(self.x - other.x, self.y - other.y)
+
+ def __mul__(self, other):
+ """ __mul__(other: float) -> Point
+ Interprets self as a vector to perform a scalar multiplication and
+ return a Point
+
+ """
+ return Point(self.x * other, self.y * other)
+
+ eq_delta = 0.0001
+ def __eq__(self, other):
+ """__eq__(other: Point) -> boolean
+ Two points are equal if they have the same components
+
+ """
+ if type(self) != type(other):
+ return False
+ return (self.x - other.x) ** 2 + (self.y - other.y) ** 2 < 1e-8
+
+ def __ne__(self, other):
+ """__ne__(other: Point) -> boolean
+ Two points are differenr if they don't have the same components
+
+ """
+ return not self.__eq__(other)
+
+ def __rmul__(self, other):
+ """ __rmul__(other: float) -> Point
+ Interprets self as a vector to perform a scalar multiplication and
+ return a Point
+
+ """
+ return Point(self.x * other, self.y * other)
+
+
+################################################################################
+# Unit tests
+
+import unittest
+import random
+
+class TestPoint(unittest.TestCase):
+
+ @staticmethod
+ def assert_double_equals(a, b, eps = 0.00001):
+ assert abs(a-b) < eps
+
+ def test_add_length(self):
+ """Uses triangle inequality to exercise add and length"""
+ for i in xrange(100):
+ x = Point(random.uniform(-1.0, 1.0), random.uniform(-1.0, 1.0))
+ y = Point(random.uniform(-1.0, 1.0), random.uniform(-1.0, 1.0))
+ assert (x+y).length() <= x.length() + y.length()
+
+ def test_mul_length(self):
+ """Uses vector space properties to exercise mul, rmul and length"""
+ for i in xrange(100):
+ x = Point(random.uniform(-1.0, 1.0), random.uniform(-1.0, 1.0))
+ s = random.uniform(0.0, 10.0)
+ self.assert_double_equals(s * x.length(), (s * x).length())
+ self.assert_double_equals(s * x.length(), (x * s).length())
+
+ def test_comparison_operators(self):
+ """ Test comparison operators """
+ a = Point(0, 1)
+ b = Point(0, 1)
+ assert a == b
+ assert a != None
+ b = Point(0, 0.1)
+ assert a != b
+
+if __name__ == '__main__':
+ unittest.main()
+
diff --git a/vistrails/core/data_structures/queue.py b/vistrails/core/data_structures/queue.py
new file mode 100644
index 0000000..634869c
--- /dev/null
+++ b/vistrails/core/data_structures/queue.py
@@ -0,0 +1,232 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+################################################################################
+
+class Queue(object):
+
+ def __init__(self, capacity=8):
+ """ Queue(capacity: int) -> Queue
+ Initialize the queue with a default capacity of zero in size
+
+ """
+ self.__buffer = [None] * capacity
+ self.__capacity = capacity
+ self.__size = 0
+ self.__begin = 0
+ self.__end = 0
+
+ def __len__(self):
+ """ __len__() -> int
+ Compute the number of elements when using the built-in len()
+ and return an int
+
+ """
+ l = self.__end - self.__begin
+ if l < 0:
+ return self.__capacity + l
+ else:
+ return l
+
+ def front(self):
+ """ front() -> element type
+ Get the front of the queue and return an element type
+
+ """
+ return self.__buffer[self.__begin]
+
+ def back(self):
+ """ back() -> element type
+ Get the back (last) element of the queue and return an element type
+
+ """
+ return self.__buffer[(self.__end + self.__capacity - 1) %
+ self.__capacity]
+
+ def push(self, obj):
+ """ push(obj: element type) -> None
+ Push obj onto the back queue and return nothing
+
+ """
+ # olen = len(self)
+ if (self.__end + 1) % self.__capacity == self.__begin:
+ self.__rebuffer(self.__capacity * 2)
+ self.__buffer[self.__end] = obj
+ self.__end += 1
+ if self.__end == self.__capacity:
+ self.__end = 0
+ # nlen = len(self)
+ # assert nlen == olen + 1
+
+ class EmptyQueue(Exception):
+ pass
+
+ def pop(self):
+ """ pop() -> element type
+ Pop the front element of the queue and return an element type
+
+ """
+ # olen = len(self)
+ if len(self) == 0:
+ raise self.EmptyQueue()
+ r = self.__buffer[self.__begin]
+ self.__buffer[self.__begin] = None
+ self.__begin += 1
+ if self.__begin == self.__capacity:
+ self.__begin = 0
+ if self.__capacity > 8 and (self.__capacity / len(self)) >= 4:
+ self.__rebuffer(self.__capacity / 2)
+ # nlen = len(self)
+ # assert olen == nlen + 1
+ return r
+
+ def capacity(self):
+ return self.__capacity
+
+ def __rebuffer(self, newcapacity):
+ """ __rebuffer(newcapacity: int) -> none
+ Reallocate the internal buffer to fit at newcapacity elements and
+ return nothing
+
+ """
+ nb = [None] * newcapacity
+ if self.__begin < self.__end:
+ l = self.__end - self.__begin
+ nb[0:l] = self.__buffer[self.__begin:self.__end]
+ self.__begin = 0
+ self.__end = l
+ else:
+ l1 = self.__capacity - self.__begin
+ l2 = l1 + self.__end
+ nb[0:l1] = self.__buffer[self.__begin:]
+ nb[l1:l2] = self.__buffer[:self.__end]
+ self.__begin = 0
+ self.__end = l2
+ self.__buffer = nb
+ self.__capacity = newcapacity
+
+ def __str__(self):
+ """ __str__() -> str
+ Format the queue for serialization and return a string
+
+ """
+ return str(self.__buffer)
+
+################################################################################
+
+import unittest
+import random
+
+class TestQueue(unittest.TestCase):
+
+ def test_basic(self):
+ """Test push/pop operations"""
+ q = Queue()
+ q.push(1)
+ q.push(2)
+ q.push(3)
+ q.push(4)
+ self.assertEquals(q.pop(), 1)
+ self.assertEquals(q.pop(), 2)
+ self.assertEquals(q.pop(), 3)
+ self.assertEquals(q.pop(), 4)
+
+ def test_expand_basic(self):
+ """Test if the queue is expanding its capacity right with push()"""
+ q = Queue()
+ for i in xrange(512):
+ assert len(q) == i
+ q.push(i)
+ assert len(q) == i+1
+ self.assertEquals(len(q), 512)
+ for i in xrange(512):
+ assert len(q) == 512 - i
+ self.assertEquals(q.pop(), i)
+ assert len(q) == 511 - i
+
+ def test_expand_contract(self):
+ """Test if the queue is expanding and contracting with push()/pop()"""
+ def run_it():
+ pushed = 0
+ popped = 0
+ q = Queue()
+ for t in xrange(100):
+ for i in xrange(100):
+ # Test expand with high probability
+ a = random.choice([0,0,0,0,0,1])
+ if (a == 0) or (len(q) == 0):
+ olen = len(q)
+ q.push(pushed)
+ nlen = len(q)
+ assert nlen == olen+1, "push invariant"
+ pushed += 1
+ else:
+ olen = len(q)
+ v = q.pop()
+ nlen = len(q)
+ assert olen == nlen+1, "pop invariant"
+ self.assertEquals(v, popped)
+ popped += 1
+ for i in xrange(100):
+ # Test contract with high probability
+ a = random.choice([1,1,1,1,1,0])
+ if (a == 0) or (len(q) == 0):
+ olen = len(q)
+ q.push(pushed)
+ nlen = len(q)
+ assert nlen == olen+1, "push invariant"
+ pushed += 1
+ else:
+ olen = len(q)
+ v = q.pop()
+ nlen = len(q)
+ assert olen == nlen+1, "pop invariant"
+ self.assertEquals(v, popped)
+ popped += 1
+ # run test 100 times
+ for i in xrange(1):
+ run_it()
+
+ def test_pop(self):
+ x = Queue()
+ try:
+ x.pop()
+ except x.EmptyQueue:
+ pass
+ else:
+ assert False
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/data_structures/rect.py b/vistrails/core/data_structures/rect.py
new file mode 100644
index 0000000..806042f
--- /dev/null
+++ b/vistrails/core/data_structures/rect.py
@@ -0,0 +1,148 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.core.data_structures.point import Point
+
+import unittest
+import random
+
+################################################################################
+# Rect
+
+class Rect(object):
+ def __init__(self, lower_left=None, upper_right=None):
+ """ Rect(lower_left: Point, upper_right: Point) -> Rect
+ Creates a Rect given the lower_left and the upper_right points. It creates
+ a copy of the given points. Return a Rect
+
+ """
+ if lower_left == None:
+ self.lower_left = Point()
+ else:
+ self.lower_left = copy.copy(lower_left)
+
+ if upper_right == None:
+ self.upper_right = Point()
+ else:
+ self.upper_right = copy.copy(upper_right)
+ self.check_extent()
+
+ @staticmethod
+ def create(left, right, down, up):
+ """ create(left: float, right: float, down: float, up: float) -> Point
+ Creates a Rect from four float extents and return a Rect
+
+ """
+ return Rect(Point(min(left, right),
+ min(up, down)),
+ Point(max(left, right),
+ max(down, up)))
+
+ def set_left(self, x):
+ """ set_left(x: float) -> None
+ Sets the left limit of the Rect and return nothing
+
+ """
+ self.lower_left.x = x
+
+ def set_right(self, x):
+ """ set_right(x: float) -> None
+ Sets the right limit of the Rect and return nothing
+
+ """
+ self.upper_right.x = x
+
+ def set_up(self,y):
+ """ set_up(y: float) -> None
+ Sets the upper limit of the Rect and return nothing
+
+ """
+ self.upper_right.y = y
+
+ def set_down(self, y):
+ """ set_down(y: float) -> None
+ Sets the lower limit of the Rect and return nothing
+
+ """
+ self.lower_left.y = y
+
+ def center(self):
+ """ center() -> Point
+ Compute the center of the Rect and return a Point
+
+ """
+ return (self.upper_right + self.lower_left) * 0.5
+
+ def check_extent(self):
+ """ check_extent() -> None
+ Makes sure left limit is less than right limit, and lower limit is less
+ than upper limit. In other words, ensures that, immediately after the
+ call:
+ self.lower_left.x <= self.upper_right.x and
+ self.lower_left.y <= self.upper_right.y
+
+ """
+ if self.lower_left.x > self.upper_right.x:
+ dlx = self.lower_left.x
+ self.lower_left.x = self.upper_right.x
+ self.upper_right.y = dlx
+
+ if self.lower_left.y > self.upper_right.y:
+ dly = self.lower_left.y
+ self.lower_left.y = self.upper_right.y
+ self.upper_right.y = dly
+
+################################################################################
+# Unit tests
+
+
+class TestRect(unittest.TestCase):
+
+ def test_create(self):
+ """Exercises Rect.create()"""
+ for i in xrange(100):
+ a = random.uniform(-1.0, 1.0)
+ b = random.uniform(-1.0, 1.0)
+ c = random.uniform(-1.0, 1.0)
+ d = random.uniform(-1.0, 1.0)
+
+ r = Rect.create(a, b, c, d)
+ assert r.lower_left.x == min(a, b)
+ assert r.upper_right.x == max(a, b)
+ assert r.lower_left.y == min(c, d)
+ assert r.upper_right.y == max(c, d)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/data_structures/stack.py b/vistrails/core/data_structures/stack.py
new file mode 100644
index 0000000..a4da378
--- /dev/null
+++ b/vistrails/core/data_structures/stack.py
@@ -0,0 +1,103 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Simple stack data structure."""
+
+###############################################################################
+
+class EmptyStack(Exception):
+ pass
+
+
+class Stack(object):
+
+ def __init__(self):
+ object.__init__(self)
+ self.__cell = []
+ self.__size = 0
+
+ def top(self):
+ """Returns the top of the stack."""
+ if not self.__cell:
+ raise EmptyStack()
+ else:
+ return self.__cell[0]
+
+ def push(self, obj):
+ """Pushes an element onto the stack."""
+ self.__cell = [obj, self.__cell]
+ self.__size += 1
+
+ def pop(self):
+ """Pops the top off of the stack."""
+ if not self.__cell:
+ raise EmptyStack()
+ else:
+ self.__cell = self.__cell[1]
+ self.__size -= 1
+
+ def __len__(self):
+ return self.__size
+
+ def __get_size(self):
+ return self.__size
+
+ size = property(__get_size, doc="The size of the stack.")
+
+###############################################################################
+
+import unittest
+
+class TestStack(unittest.TestCase):
+
+ def test_basic(self):
+ s = Stack()
+ self.assertEquals(s.size, 0)
+ s.push(10)
+ self.assertEquals(s.top(), 10)
+ self.assertEquals(len(s), 1)
+ s.pop()
+ self.assertEquals(len(s), 0)
+ self.assertEquals(0, s.size)
+
+ def test_pop_empty_raises(self):
+ s = Stack()
+ self.assertRaises(EmptyStack, s.pop)
+
+ def test_top_empty_raises(self):
+ s = Stack()
+ self.assertRaises(EmptyStack, s.top)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/db/__init__.py b/vistrails/core/db/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/core/db/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/core/db/action.py b/vistrails/core/db/action.py
new file mode 100644
index 0000000..be6c209
--- /dev/null
+++ b/vistrails/core/db/action.py
@@ -0,0 +1,76 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.vistrail.location import Location
+import vistrails.db.services.action
+
+def create_action(op_list):
+ if len(op_list) > 0:
+ from vistrails.core.vistrail.action import Action
+ action = vistrails.db.services.action.create_action(op_list)
+ Action.convert(action)
+ return action
+ return None
+
+def create_action_from_ops(ops, simplify=False):
+ if len(ops) > 0:
+ from vistrails.core.vistrail.action import Action
+ action = vistrails.db.services.action.create_action_from_ops(ops, simplify)
+ Action.convert(action)
+ return action
+ return None
+
+def merge_actions(action_list):
+ ops = []
+ for action in action_list:
+ ops.extend(action.operations)
+ return create_action_from_ops(ops, True)
+
+def create_paste_action(pipeline, id_scope, id_remap=None):
+ action_list = []
+ if id_remap is None:
+ id_remap = {}
+ for module in pipeline.modules.itervalues():
+ module = module.do_copy(True, id_scope, id_remap)
+ action_list.append(('add', module))
+ for connection in pipeline.connections.itervalues():
+ connection = connection.do_copy(True, id_scope, id_remap)
+ action_list.append(('add', connection))
+ action = create_action(action_list)
+
+ # fun stuff to work around bug where pasted entities aren't dirty
+ for (child, _, _) in action.db_children():
+ child.is_dirty = True
+ return action
+
diff --git a/vistrails/core/db/io.py b/vistrails/core/db/io.py
new file mode 100644
index 0000000..589e5c6
--- /dev/null
+++ b/vistrails/core/db/io.py
@@ -0,0 +1,226 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.vistrail.action import Action
+from vistrails.core.log.log import Log
+from vistrails.core.vistrail.operation import AddOp, ChangeOp, DeleteOp
+from vistrails.db.services.io import SaveBundle
+import vistrails.db.services.io
+import vistrails.db.services.vistrail
+import vistrails.db.services.action
+from xml.dom.minidom import parse, getDOMImplementation
+
+def get_db_vistrail_list(config):
+ return vistrails.db.services.io.get_db_object_list(config,'vistrail')
+
+def get_workflow(vt, version):
+ from vistrails.core.vistrail.pipeline import Pipeline
+ workflow = vistrails.db.services.vistrail.materializeWorkflow(vt, version)
+ Pipeline.convert(workflow)
+ return workflow
+
+def open_workflow(filename):
+ from vistrails.core.vistrail.pipeline import Pipeline
+ workflow = vistrails.db.services.io.open_workflow_from_xml(filename)
+ Pipeline.convert(workflow)
+ return workflow
+
+def save_workflow(workflow, filename):
+ vistrails.db.services.io.save_workflow_to_xml(workflow, filename)
+
+def save_vistrail_to_xml(vistrail, filename):
+ vistrails.db.services.io.save_vistrail_to_xml(vistrail, filename)
+
+def load_vistrail(locator, is_abstraction=False):
+ from vistrails.core.vistrail.vistrail import Vistrail
+
+ abstraction_files = []
+ thumbnail_files = []
+ mashups = []
+ vistrail = None
+ if locator is None:
+ vistrail = Vistrail()
+ else:
+ res = locator.load()
+ if type(res) == type(SaveBundle(None)):
+ vistrail = res.vistrail
+ abstraction_files.extend(res.abstractions)
+ thumbnail_files.extend(res.thumbnails)
+ mashups.extend(res.mashups)
+ else:
+ vistrail = res
+ vistrail.is_abstraction = is_abstraction
+ return (vistrail, abstraction_files, thumbnail_files, mashups)
+
+def open_registry(filename):
+ from vistrails.core.modules.module_registry import ModuleRegistry
+ registry = vistrails.db.services.io.open_registry_from_xml(filename)
+ ModuleRegistry.convert(registry)
+ return registry
+
+def unserialize(str, klass):
+ """returns VisTrails entity given an XML serialization
+
+ """
+ obj = vistrails.db.services.io.unserialize(str, klass.vtType)
+ if obj:
+ #maybe we should also put a try except here
+ klass.convert(obj)
+ return obj
+
+def serialize(object):
+ """returns XML serialization for any VisTrails entity
+
+ """
+ return vistrails.db.services.io.serialize(object)
+
+def open_log(fname, was_appended=False):
+ log = vistrails.db.services.io.open_log_from_xml(fname, was_appended)
+ Log.convert(log)
+ return log
+
+
+def merge_logs(new_log, log_fname):
+ log = vistrails.db.services.io.merge_logs(new_log, log_fname)
+ Log.convert(log)
+ return log
+
+def get_workflow_diff(vt_pair_1, vt_pair_2):
+ """get_workflow_diff( tuple(Vistrail, id), tuple(Vistrail, id) ) ->
+ Pipeline, Pipeline, [tuple(id, id)], [tuple(id, id)],
+ [id], [id], [tuple(id, id, list)]
+
+ Return a difference between two workflows referenced as vistrails.
+ """
+
+ from vistrails.core.vistrail.pipeline import Pipeline
+ (v1, v2, pairs, heuristic_pairs, v1_only, v2_only, param_changes, \
+ _, _, _, _) = \
+ vistrails.db.services.vistrail.getWorkflowDiff(vt_pair_1, vt_pair_2, True)
+ Pipeline.convert(v1)
+ Pipeline.convert(v2)
+ return (v1, v2, pairs, heuristic_pairs, v1_only, v2_only, param_changes)
+
+def get_workflow_diff_with_connections(vt_pair_1, vt_pair_2):
+ """get_workflow_diff_with_connections
+
+ Similar to get_workflow_diff but with connection pairings.
+ """
+
+ from vistrails.core.vistrail.pipeline import Pipeline
+ (v1, v2, m_pairs, m_heuristic, v1_only, v2_only, param_changes, \
+ c_pairs, c_heuristic, c1_only, c2_only) = \
+ vistrails.db.services.vistrail.getWorkflowDiff(vt_pair_1, vt_pair_2, False)
+ Pipeline.convert(v1)
+ Pipeline.convert(v2)
+ return (v1, v2, m_pairs, m_heustric, v1_only, v2_only, param_changes,
+ c_pairs, c_heuristic, c1_only, c2_only)
+
+def getPathAsAction(vt, v1, v2, do_copy=False):
+ a = vistrails.db.services.vistrail.getPathAsAction(vt, v1, v2, do_copy)
+ Action.convert(a)
+ return a
+
+def fixActions(vt, v, actions):
+ return vistrails.db.services.vistrail.fixActions(vt, v, actions)
+
+def convert_operation_list(ops):
+ for op in ops:
+ if op.vtType == 'add':
+ AddOp.convert(op)
+ elif op.vtType == 'change':
+ ChangeOp.convert(op)
+ elif op.vtType == 'delete':
+ DeleteOp.convert(op)
+ else:
+ raise TypeError("Unknown operation type '%s'" % op.vtType)
+
+def create_action(action_list):
+ """create_action(action_list: list) -> Action
+ where action_list is a list of tuples
+ (
+ type,
+ object,
+ parent_type=None,
+ parent_id=None,
+ new_obj=None
+ )
+ and the method returns a *single* action that accomplishes all
+ of the operations.
+
+ Examples: create_action([('add', module1), ('delete', connection2)]
+ create_action([('add', param1, 'function', function1),
+ ('change', old_func, new_func, 'module', m1)])
+ Note that create_action([('add', module)]) adds a module and *all* of its
+ children.
+ """
+ action = vistrails.db.services.action.create_action(action_list)
+ Action.convert(action)
+ return action
+
+def create_add_op_chain(object, parent=(None, None)):
+ """create_add_op_chain(object: object,
+ parent=(type : str, id : long)) -> [op]
+ where [op] is a list of operations to add the given object and its
+ children to a workflow.
+ """
+ ops = vistrails.db.services.action.create_add_op_chain(object, parent)
+ convert_operation_list(ops)
+ return ops
+
+def create_change_op_chain(old_obj, new_obj, parent=(None,None)):
+ """create_change_op_chain(old_obj: object, new_obj: object,
+ parent=(type : str, id : long)) -> [op]
+ where [op] is a list of operations to change the given object and its
+ children to the new object in a workflow.
+ """
+ ops = vistrails.db.services.action.create_change_op_chain(old_obj, new_obj, parent)
+ convert_operation_list(ops)
+ return ops
+
+def create_delete_op_chain(object, parent=(None, None)):
+ """create_delete_op_chain(object: object,
+ parent=(type : str, id : long)) -> [op]
+ where [op] is a list of operations to delete the given object and its
+ children from a workflow.
+ """
+ ops = vistrails.db.services.action.create_delete_op_chain(object, parent)
+ convert_operation_list(ops)
+ return ops
+
+def create_temp_folder(prefix='vt_save'):
+ return vistrails.db.services.io.create_temp_folder(prefix=prefix)
+
+def remove_temp_folder(temp_dir):
+ vistrails.db.services.io.remove_temp_folder(temp_dir)
diff --git a/vistrails/core/db/locator.py b/vistrails/core/db/locator.py
new file mode 100644
index 0000000..7a54f0c
--- /dev/null
+++ b/vistrails/core/db/locator.py
@@ -0,0 +1,760 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import base64
+import getpass
+import os.path
+from vistrails.core import get_vistrails_application
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core.system import vistrails_default_file_type, get_elementtree_library, \
+ default_connections_file, vistrails_examples_directory
+from vistrails.core.external_connection import ExtConnectionList, DBConnection
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.core import debug
+from vistrails.db.services.locator import XMLFileLocator as _XMLFileLocator, \
+ DBLocator as _DBLocator, ZIPFileLocator as _ZIPFileLocator, \
+ BaseLocator as _BaseLocator, UntitledLocator as _UntitledLocator
+from vistrails.db.services.io import SaveBundle, test_db_connection
+from vistrails.db import VistrailsDBException
+from vistrails.db.domain import DBWorkflow
+ElementTree = get_elementtree_library()
+
+class BaseLocator(_BaseLocator):
+ @staticmethod
+ def convert_locator(locator):
+ if locator.__class__ == _XMLFileLocator:
+ locator.__class__ = XMLFileLocator
+ elif locator.__class__ == _ZIPFileLocator:
+ locator.__class__ = ZIPFileLocator
+ elif locator.__class__ == _DBLocator:
+ DBLocator.convert(locator)
+ elif locator.__class__ == _UntitledLocator:
+ locator.__class__ = UntitledLocator
+
+ @staticmethod
+ def from_url(url):
+ locator = _BaseLocator.from_url(url)
+ BaseLocator.convert_locator(locator)
+ return locator
+
+class CoreLocator(object):
+ @staticmethod
+ def prompt_autosave(parent_widget):
+ pass # Opens a dialog that prompts the user if they want to
+ # use temporaries
+
+
+ @staticmethod
+ def load_from_gui(parent_widget, obj_type):
+ pass # Opens a dialog that the user will be able to use to
+ # show the right values, and returns a locator suitable
+ # for loading a file
+
+ @staticmethod
+ def save_from_gui(parent_widget, obj_type, locator):
+ pass # Opens a dialog that the user will be able to use to
+ # show the right values, and returns a locator suitable
+ # for saving a file
+
+ def update_from_gui(self, klass=None):
+ pass
+
+ # FIXME Need to do some more intelligent conversions anywhere this
+ # function gets called
+ @staticmethod
+ def get_convert_klass(vt_type):
+ from vistrails.core.vistrail.vistrail import Vistrail
+ from vistrails.core.vistrail.pipeline import Pipeline
+ from vistrails.core.log.log import Log
+ from vistrails.core.modules.module_registry import ModuleRegistry
+ from vistrails.core.log.opm_graph import OpmGraph
+
+ klass_map = {Vistrail.vtType: Vistrail,
+ Pipeline.vtType: Pipeline,
+ Log.vtType: Log,
+ ModuleRegistry.vtType: ModuleRegistry,
+ OpmGraph.vtType: OpmGraph}
+ return klass_map[vt_type]
+
+class UntitledLocator(_UntitledLocator, CoreLocator):
+ def load(self, klass=None):
+ from vistrails.core.vistrail.vistrail import Vistrail
+ if klass is None:
+ klass = Vistrail
+ obj = _UntitledLocator.load(self, klass.vtType)
+ klass.convert(obj)
+ obj.locator = self
+ return obj
+
+class XMLFileLocator(_XMLFileLocator, CoreLocator):
+
+ def __init__(self, filename, **kwargs):
+ _XMLFileLocator.__init__(self, filename, **kwargs)
+
+ def load(self, klass=None):
+ from vistrails.core.vistrail.vistrail import Vistrail
+ if klass is None:
+ klass = Vistrail
+ obj = _XMLFileLocator.load(self, klass.vtType)
+ klass.convert(obj)
+ obj.locator = self
+ return obj
+
+ def save(self, obj):
+ is_bundle = False
+ if type(obj) == type(SaveBundle(None)):
+ is_bundle = True
+ save_bundle = obj
+ obj = save_bundle.get_primary_obj()
+ klass = obj.__class__
+ obj = _XMLFileLocator.save(self, obj, False)
+ klass.convert(obj)
+ obj.locator = self
+ if is_bundle:
+ return SaveBundle(save_bundle.bundle_type, obj)
+ return obj
+
+ def save_as(self, obj, version=None):
+ is_bundle = False
+ if type(obj) == type(SaveBundle(None)):
+ is_bundle = True
+ save_bundle = obj
+ obj = save_bundle.get_primary_obj()
+ klass = obj.__class__
+ obj = _XMLFileLocator.save(self, obj, True, version)
+ klass.convert(obj)
+ obj.locator = self
+ if is_bundle:
+ return SaveBundle(save_bundle.bundle_type, obj)
+ return obj
+
+ ##########################################################################
+
+ def __eq__(self, other):
+ if not isinstance(other, XMLFileLocator):
+ return False
+ return self._name == other._name
+
+ ##########################################################################
+
+ @staticmethod
+ def prompt_autosave(parent_widget):
+ import vistrails.gui.extras.core.db.locator as db_gui
+ return db_gui.get_autosave_prompt(parent_widget)
+
+ @staticmethod
+ def load_from_gui(parent_widget, obj_type):
+ import vistrails.gui.extras.core.db.locator as db_gui
+ return db_gui.get_load_file_locator_from_gui(parent_widget, obj_type)
+
+ @staticmethod
+ def save_from_gui(parent_widget, obj_type, locator=None):
+ import vistrails.gui.extras.core.db.locator as db_gui
+ return db_gui.get_save_file_locator_from_gui(parent_widget, obj_type,
+ locator)
+
+# def update_from_gui(self, parent_widget, klass=None):
+# from core.vistrail.vistrail import Vistrail
+# if klass is None:
+# klass = Vistrail
+# import gui.extras.core.db.locator as db_gui
+# return db_gui.get_load_file_locator_from_gui(parent_widget, klass.vtType)
+
+class DBLocator(_DBLocator, CoreLocator):
+ class getKeyChain(object):
+ def set_key(self, key, passwd):
+ get_vistrails_application().keyChain.set_key(key,passwd)
+
+ def get_key(self, key):
+ return get_vistrails_application().keyChain.get_key(key)
+
+ keyChain = getKeyChain()
+
+ def __init__(self, host, port, database, user, passwd, name=None,
+ **kwargs):
+ _DBLocator.__init__(self, host, port, database, user, passwd, name,
+ **kwargs)
+ self.__list = ExtConnectionList.getInstance(default_connections_file())
+ self.ext_connection_id = -1
+
+ def load(self, klass=None):
+ from vistrails.core.vistrail.vistrail import Vistrail
+ if klass is None:
+ klass = Vistrail
+ save_bundle = _DBLocator.load(self, klass.vtType, ThumbnailCache.getInstance().get_directory())
+ if klass.vtType == DBWorkflow.vtType:
+ wf = save_bundle
+ klass = self.get_convert_klass(wf.vtType)
+ klass.convert(wf)
+ wf.locator = self
+ return wf
+ for obj in save_bundle.get_db_objs():
+ klass = self.get_convert_klass(obj.vtType)
+ klass.convert(obj)
+ obj.locator = self
+ return save_bundle
+
+ def save(self, save_bundle):
+ save_bundle = _DBLocator.save(self, save_bundle, False)
+ for obj in save_bundle.get_db_objs():
+ klass = self.get_convert_klass(obj.vtType)
+ klass.convert(obj)
+ obj.locator = self
+ return save_bundle
+
+ def save_as(self, save_bundle, version=None):
+ save_bundle = _DBLocator.save(self, save_bundle, True, version)
+ for obj in save_bundle.get_db_objs():
+ klass = self.get_convert_klass(obj.vtType)
+ klass.convert(obj)
+ obj.locator = self
+ # Need to copy images into thumbnail cache directory so references
+ # won't become invalid if they are in a temp dir that gets destroyed
+ # when the previous locator is closed
+ import shutil
+ thumb_cache = ThumbnailCache.getInstance()
+ thumb_cache_dir = thumb_cache.get_directory()
+ new_thumbnails = []
+ for thumbnail in save_bundle.thumbnails:
+ if os.path.dirname(thumbnail) == thumb_cache_dir:
+ new_thumbnails.append(thumbnail)
+ else:
+ cachedir_thumbnail = os.path.join(thumb_cache_dir, os.path.basename(thumbnail))
+ try:
+ shutil.copyfile(thumbnail, cachedir_thumbnail)
+ new_thumbnails.append(cachedir_thumbnail)
+ except Exception, e:
+ debug.critical('copying %s -> %s failed: %s' % \
+ (thumbnail, cachedir_thumbnail, str(e)))
+ save_bundle.thumbnails = new_thumbnails
+ # Need to update thumbnail cache in case some references have changed
+ thumb_cache.add_entries_from_files(save_bundle.thumbnails)
+ return save_bundle
+
+ def update_from_gui(self, parent_widget, klass=None):
+ from vistrails.core.vistrail.vistrail import Vistrail
+ import vistrails.gui.extras.core.db.locator as db_gui
+ if klass is None:
+ klass = Vistrail
+ config = self.find_connection_info(self._host, self._port, self._db)
+ if config is None or config['succeeded']==False:
+ config = db_gui.get_db_connection_from_gui(parent_widget,
+ -1,
+ "",
+ self._host,
+ self._port,
+ self._user,
+ self._passwd,
+ self._db)
+
+ if config is not None and config['succeeded'] == True:
+ self._host = config['host']
+ self._port = config['port']
+ self._db = config['db']
+ self._user = config['user']
+ self._passwd = config['passwd']
+ self.ext_connection_id = self.set_connection_info(**config)
+ return True
+
+ return False
+
+ def update_from_console(self):
+ config = self.find_connection_info(self._host, self._port, self._db)
+
+ if config is None:
+ # the problem here is if VisTrails is being run through command
+ # line from LaTex, stdout is being redirected to a log file, so
+ # the user does not see the prompt in raw_input. getpass uses the
+ # controlling terminal so it works fine. Just to make sure he sees
+ # the first message prompt we will the controlling terminal
+ try:
+ f= open('/dev/tty', 'w')
+ f.write("\nConnect to db with username [%s]: "%self._user)
+ f.close()
+ user = raw_input()
+ except:
+ debug.warning("Couldn't write to terminal. Will try stdout")
+ user = raw_input("Connecting to db with username[%s]: "%self._user)
+ try:
+ if user != '':
+ self._user = user
+ passwd = getpass.getpass("password:")
+ self._passwd = passwd
+ config = {'host': self._host,
+ 'port': int(self._port),
+ 'user': self._user,
+ 'passwd': self._passwd,
+ 'db': self._db
+ }
+ test_db_connection(config)
+ config['succeeded'] = True
+ config['name'] = '%s@%s'%(self._user,self._host)
+ config['id'] = -1
+ except VistrailsDBException, e:
+ debug.critical('VisTrails DB Exception', str(e))
+ config['succeeded'] = False
+ except Exception, e2:
+ debug.critical('VisTrails Exception', str(e2))
+ config['succeeded'] = False
+ if config is not None:
+ if config['succeeded'] == False:
+ passwd = getpass.getpass("\nVisTrails DB password for user %s:"%config['user'])
+ self._user = config['user']
+ self._passwd = passwd
+ dbconfig = {'host': self._host,
+ 'port': int(self._port),
+ 'user': self._user,
+ 'passwd': self._passwd,
+ 'db': self._db
+ }
+ try:
+ test_db_connection(dbconfig)
+ config['succeeded'] = True
+ config['passwd'] = self._passwd
+ except VistrailsDBException, e:
+ debug.critical('VisTrails DB Exception', str(e))
+ config['succeeded'] = False
+
+ if config['succeeded'] == True:
+ self._host = config['host']
+ self._port = config['port']
+ self._db = config['db']
+ self._user = config['user']
+ self._passwd = config['passwd']
+ self.ext_connection_id = self.set_connection_info(**config)
+ return True
+ return False
+ return False
+
+ def find_connection_info(self, host, port, db):
+ """find_connection_info(host:str, port: int, db: str) -> dict
+ Returns complete info of a connection with the given parameters
+
+ """
+ id = self.__list.find_db_connection(host,port,db)
+ if id != -1:
+ return self.get_connection_info(id)
+ else:
+ return None
+
+ def get_connection_info(self, id):
+ """get_connection_info(id: int) -> dict
+ Returns info of ExtConnection """
+ conn = self.__list.get_connection(id)
+ if conn != None:
+ succeeded = False
+ key = str(conn.id) + "." + conn.name + "." + conn.host
+ passwd = DBLocator.keyChain.get_key(key)
+ config = {'host': conn.host,
+ 'port': conn.port,
+ 'user': conn.user,
+ 'passwd': passwd}
+ try:
+ test_db_connection(config)
+ succeeded = True
+ except VistrailsDBException:
+ succeeded = False
+
+ config['id'] = conn.id
+ config['name'] = conn.name
+ config['db'] = conn.database
+ config['succeeded'] = succeeded
+ else:
+ config = None
+ return config
+
+ def set_connection_info(self, *args, **kwargs):
+ """set_connection_info(id: int, name: str, host: str, port:int,
+ user:str, passwd:str, db:str) -> None
+ If the connection exists it will update it, else it will add it
+
+ """
+ if kwargs.has_key("id"):
+ id = kwargs["id"]
+ if kwargs.has_key("name"):
+ name = kwargs["name"]
+ if kwargs.has_key("host"):
+ host = kwargs["host"]
+ if kwargs.has_key("port"):
+ port = kwargs["port"]
+ if kwargs.has_key("user"):
+ user = kwargs["user"]
+ if kwargs.has_key("passwd"):
+ passwd = kwargs["passwd"]
+ if kwargs.has_key("db"):
+ db = kwargs["db"]
+
+ conn = DBConnection(id=id,
+ name=name,
+ host=host,
+ port=port,
+ user=user,
+ passwd='',
+ database=db,
+ dbtype='MySQL')
+
+ if self.__list.has_connection(id):
+ self.__list.set_connection(id,conn)
+ else:
+ if conn.id == -1:
+ conn.id = self.__list.get_fresh_id()
+ self.__list.add_connection(conn)
+ key = str(conn.id) + "." + conn.name + "." + conn.host
+ DBLocator.keyChain.set_key(key,passwd)
+ return conn.id
+
+ ##########################################################################
+
+ def __eq__(self, other):
+ if type(other) != type(self):
+ return False
+ return (self._host == other._host and
+ self._port == other._port and
+ self._db == other._db and
+ self._user == other._user and
+ #self._name == other._name and
+ long(self._obj_id) == long(other._obj_id) and
+ self._obj_type == other._obj_type)
+
+ ##########################################################################
+
+ @staticmethod
+ def prompt_autosave(parent_widget):
+ return True
+
+ @staticmethod
+ def load_from_gui(parent_widget, obj_type):
+ import vistrails.gui.extras.core.db.locator as db_gui
+ return db_gui.get_load_db_locator_from_gui(parent_widget, obj_type)
+
+ @staticmethod
+ def save_from_gui(parent_widget, obj_type, locator=None):
+ import vistrails.gui.extras.core.db.locator as db_gui
+ return db_gui.get_save_db_locator_from_gui(parent_widget, obj_type,
+ locator)
+
+ @staticmethod
+ def from_xml(node, include_name=False):
+ locator = _DBLocator.from_xml(node, include_name)
+ locator.__class__ = DBLocator
+ return locator
+
+ @staticmethod
+ def convert(locator):
+ locator.__class__ = DBLocator
+ locator.__list = ExtConnectionList.getInstance(
+ default_connections_file())
+
+class ZIPFileLocator(_ZIPFileLocator, CoreLocator):
+
+ def __init__(self, filename, **kwargs):
+ _ZIPFileLocator.__init__(self, filename, **kwargs)
+
+ def load(self, klass=None):
+ from vistrails.core.vistrail.vistrail import Vistrail
+ if klass is None:
+ klass = Vistrail
+ save_bundle = _ZIPFileLocator.load(self, klass.vtType)
+ for obj in save_bundle.get_db_objs():
+ klass = self.get_convert_klass(obj.vtType)
+ klass.convert(obj)
+ obj.locator = self
+ return save_bundle
+
+ def save(self, save_bundle):
+ save_bundle = _ZIPFileLocator.save(self, save_bundle, False)
+ for obj in save_bundle.get_db_objs():
+ klass = self.get_convert_klass(obj.vtType)
+ klass.convert(obj)
+ obj.locator = self
+ return save_bundle
+
+ def save_as(self, save_bundle, version=None):
+ save_bundle = _ZIPFileLocator.save(self, save_bundle, True, version)
+ for obj in save_bundle.get_db_objs():
+ klass = self.get_convert_klass(obj.vtType)
+ klass.convert(obj)
+ obj.locator = self
+ # Need to update thumbnail cache since files have moved
+ ThumbnailCache.getInstance().add_entries_from_files(save_bundle.thumbnails)
+ return save_bundle
+
+ ##########################################################################
+
+ def __eq__(self, other):
+ if not isinstance(other, ZIPFileLocator):
+ return False
+ return self._name == other._name
+
+ ##########################################################################
+
+ @staticmethod
+ def prompt_autosave(parent_widget):
+ import vistrails.gui.extras.core.db.locator as db_gui
+ return db_gui.get_autosave_prompt(parent_widget)
+
+ @staticmethod
+ def load_from_gui(parent_widget, obj_type):
+ import vistrails.gui.extras.core.db.locator as db_gui
+ return db_gui.get_load_file_locator_from_gui(parent_widget, obj_type)
+
+ @staticmethod
+ def save_from_gui(parent_widget, obj_type, locator=None):
+ import vistrails.gui.extras.core.db.locator as db_gui
+ return db_gui.get_save_file_locator_from_gui(parent_widget, obj_type,
+ locator)
+
+class FileLocator(CoreLocator):
+ def __new__(self, filename=None, **kwargs):
+ if filename:
+ if filename.endswith('.vt'):
+ return ZIPFileLocator(filename, **kwargs)
+ elif filename.endswith('.vtl'):
+ return FileLocator.from_link_file(filename)
+ else:
+ return XMLFileLocator(filename, **kwargs)
+ else:
+ #return class based on default file type
+ if vistrails_default_file_type() == '.vt':
+ return ZIPFileLocator
+ else:
+ return XMLFileLocator
+
+ @staticmethod
+ def prompt_autosave(parent_widget):
+ import vistrails.gui.extras.core.db.locator as db_gui
+ return db_gui.get_autosave_prompt(parent_widget)
+
+ @staticmethod
+ def load_from_gui(parent_widget, obj_type):
+ import vistrails.gui.extras.core.db.locator as db_gui
+ return db_gui.get_load_file_locator_from_gui(parent_widget, obj_type)
+
+ @staticmethod
+ def save_from_gui(parent_widget, obj_type, locator=None):
+ import vistrails.gui.extras.core.db.locator as db_gui
+ return db_gui.get_save_file_locator_from_gui(parent_widget, obj_type,
+ locator)
+
+ @staticmethod
+ def parse(element):
+ """ parse(element) -> XMLFileLocator
+ Parse an XML object representing a locator and returns an
+ XMLFileLocator or a ZIPFileLocator object.
+
+ """
+ if str(element.getAttribute('type')) == 'file':
+ for n in element.childNodes:
+ if n.localName == "name":
+ filename = str(n.firstChild.nodeValue).strip(" \n\t")
+ return FileLocator(filename)
+ return None
+ else:
+ return None
+
+ #ElementTree port
+ @staticmethod
+ def from_xml(node):
+ """from_xml(node:ElementTree.Element) -> XMLFileLocator or None
+ Parse an XML object representing a locator and returns a
+ XMLFileLocator or a ZIPFileLocator object."""
+ if node.tag != 'locator':
+ return None
+ type_ = node.get('type', '')
+ if str(type_) == 'file':
+ for child in node.getchildren():
+ if child.tag == 'name':
+ filename = child.text.encode('latin-1').strip()
+ return FileLocator(filename)
+ return None
+
+ @staticmethod
+ def from_link_file(filename):
+ """from_link_file(filename: str) -> DBLocator
+ This will parse a '.vtl' file and will create a DBLocator. .vtl files
+ are vistrail link files and they are used to point vistrails to open
+ vistrails from the database on the web. """
+ def convert_from_str(value,type):
+ def bool_conv(x):
+ s = str(x).upper()
+ if s == 'TRUE':
+ return True
+ if s == 'FALSE':
+ return False
+
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'bool':
+ return bool_conv(value)
+ elif type == 'base64':
+ return base64.b64decode(value)
+ return None
+
+ def guess_extension_from_contents(contents):
+ if contents.startswith("<vistrail"):
+ return ".xml"
+ else:
+ return ".vt"
+
+ tree = ElementTree.parse(filename)
+ node = tree.getroot()
+ if node.tag != 'vtlink':
+ return None
+ #read attributes
+ data = node.get('host', None)
+ host = convert_from_str(data, 'str')
+ data = node.get('port', None)
+ port = convert_from_str(data,'int')
+ data = node.get('database', None)
+ database = convert_from_str(data,'str')
+ data = node.get('vtid')
+ vt_id = convert_from_str(data, 'int')
+ data = node.get('version')
+ version = convert_from_str(data, 'str')
+ data = node.get('tag')
+ tag = convert_from_str(data, 'str')
+ data = node.get('execute')
+ execute = convert_from_str(data, 'bool')
+ data = node.get('showSpreadsheetOnly')
+ showSpreadsheetOnly = convert_from_str(data, 'bool')
+ data = node.get('url', None)
+ url = convert_from_str(data,'str')
+ data = node.get('vtcontent', None)
+ vtcontent = convert_from_str(data,'base64')
+ data = node.get('filename', None)
+ vtname = convert_from_str(data, 'str')
+ data = node.get('forceDB',None)
+ forceDB = convert_from_str(data,'bool')
+ data = node.get('mashuptrail', None)
+ mashuptrail = convert_from_str(data, 'str')
+ data = node.get('mashupVersion', None)
+ mashupVersion = convert_from_str(data, 'int')
+ data = node.get('parameterExploration', None)
+ parameterExploration = convert_from_str(data, 'int')
+
+ #if execute is False, we will show the builder too
+ if showSpreadsheetOnly and not execute:
+ showSpreadsheetOnly = False
+ try:
+ version = int(version)
+ except:
+ pass
+
+ if tag is None:
+ tag = '';
+
+ ## execute and showSpreadsheetOnly should be written to the current
+ ## configuration
+ config = get_vistrails_configuration()
+ config.executeWorkflows = execute
+ config.showSpreadsheetOnly = showSpreadsheetOnly
+ if not forceDB:
+ if vtcontent is not None:
+ if url is not None:
+ basename = url.split('/')[-1]
+ base,ext = os.path.splitext(basename)
+ dirname = os.path.dirname(filename)
+ fname = os.path.join(dirname,basename)
+ else:
+ basename = os.path.basename(filename)
+ base,ext = os.path.splitext(basename)
+ ext = guess_extension_from_contents(vtcontent)
+ dirname = os.path.dirname(filename)
+ fname = os.path.join(dirname,"%s%s"%(base,ext))
+ create_file = True
+ if os.path.exists(fname): #file was extracted before
+ create_file = False
+ oldf = open(fname)
+ oldcontents = oldf.read()
+ if oldcontents != vtcontent:
+ import vistrails.gui.extras.core.db.locator as db_gui
+ (overwrite, newname) = \
+ db_gui.ask_to_overwrite_file(None, 'vistrail')
+ create_file = True
+ if newname:
+ fname = newname
+ elif overwrite == False:
+ i=1
+ while os.path.exists(fname):
+ newbase = "%s_%s%s" % (base, i, ext)
+ fname = os.path.join(dirname,newbase)
+ i+=1
+
+ if create_file:
+ f = open(fname,'wb')
+ f.write(vtcontent)
+ f.close()
+ return FileLocator(fname, version_node=version, version_tag=tag,
+ mashuptrail=mashuptrail,
+ mashupVersion=mashupVersion,
+ parameterExploration=parameterExploration)
+ if host is not None:
+ user = ""
+ passwd = ""
+
+ return DBLocator(host, port, database,
+ user, passwd, None, obj_id=vt_id,
+ obj_type='vistrail',connection_id=None,
+ version_node=version, version_tag=tag,
+ mashuptrail=mashuptrail,
+ mashupVersion=mashupVersion,
+ parameterExploration=parameterExploration)
+ elif vtname is not None:
+ if os.path.dirname(vtname) == '':
+ #check if file exists in the same directory as the .vtl file
+ dirname = os.path.dirname(filename)
+ newvtname = os.path.join(dirname,vtname)
+ if os.path.exists(newvtname):
+ vtname = newvtname
+ #check for magic strings
+ if "@examples" in vtname:
+ vtname=vtname.replace("@examples", vistrails_examples_directory())
+ return FileLocator(vtname, version_node=version, version_tag=tag,
+ mashuptrail=mashuptrail,
+ mashupVersion=mashupVersion,
+ parameterExploration=parameterExploration)
+
+
+ ##########################################################################
+
+def untitled_locator():
+ return UntitledLocator()
diff --git a/vistrails/core/debug.py b/vistrails/core/debug.py
new file mode 100644
index 0000000..d48826b
--- /dev/null
+++ b/vistrails/core/debug.py
@@ -0,0 +1,314 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import logging
+import logging.handlers
+import inspect
+import os
+import os.path
+import re
+import time
+import vistrails.core
+
+# from core.utils import VersionTooLow
+# from core import system
+
+################################################################################
+
+_warningformat = re.compile(
+ '^(.+):'
+ '([0-9]+): '
+ '([A-Za-z_][A-Za-z0-9_]*): '
+ '((?:.|\n)+)$')
+
+class EmitWarnings(logging.Handler):
+ """A logging Handler that re-logs warning messages in our log format.
+
+ This parses the warnings logged by the standard `warnings` module and
+ writes them to the given logger at level WARNING in the format we use
+ (see DebugPrint#message()).
+ """
+ def __init__(self, logger):
+ logging.Handler.__init__(self)
+ self.logger = logger
+
+ def emit(self, record):
+ # Here we basically do the contrary of warnings:formatwarning()
+ m = _warningformat.match(record.args[0])
+ if m == None:
+ self.logger.warning("(File info not available)\n" +
+ record.args[0])
+ else:
+ filename, lineno, category, message = m.groups()
+ # And here we do self.message()
+ self.logger.warning('%s, line %s\n%s: %s' % (filename, lineno,
+ category, message))
+
+################################################################################
+
+class DebugPrint:
+ """ Class to be used for debugging information.
+
+ Verboseness can be set in the following way:
+ - DebugPrint.CRITICAL
+ Only critical messages will be shown
+ - DebugPrint.WARNING
+ Warnings and critical messages will be shown (default)
+ - DebugPrint.INFO
+ Information, warning and Critical messages will be shown (verbose)
+ - DebugPrint.DEBUG
+ All logging messages will be shown (extra verbose)
+
+ It uses information such as file name and line number only when printing
+ to files and consoles, a stream can be registered to be used in gui.debug.
+ Also, it goes up only one level in the traceback stack,
+ so it will only get information of who called the DebugPrint functions.
+
+ Example of usage:
+ >>> from core import debug
+ >>> debug.DebugPrint.getInstance().set_message_level(
+ debug.DebugPrint.WARNING)
+ # the following messages will be shown
+ >>> debug.critical('This is an error message')
+ >>> debug.warning('This is a warning message')
+ # only warnings and above are shown
+ >>> debug.log('This is a log message and it will not be shown')
+
+ """
+ (CRITICAL, WARNING, INFO, DEBUG) = (logging.CRITICAL,
+ logging.WARNING,
+ logging.INFO,
+ logging.DEBUG) # python logging levels
+ #Singleton technique
+ _instance = None
+ class DebugPrintSingleton():
+ def __call__(self, *args, **kw):
+ if DebugPrint._instance is None:
+ obj = DebugPrint(*args, **kw)
+ DebugPrint._instance = obj
+ return DebugPrint._instance
+
+ getInstance = DebugPrintSingleton()
+
+ def make_logger(self, f=None):
+ self.fhandler = None
+ """self.make_logger_240(file) -> logger. Creates a logging object to
+ be used within the DebugPrint class that sends the debugging
+ output to file.
+ We will configure log so it outputs to both stderr and a file.
+
+ """
+ # Setup root logger
+ self.logger = logging.getLogger('VisLog')
+ self.logger.setLevel(logging.DEBUG)
+ self.format = logging.Formatter("%(asctime)s %(levelname)s:\n%(message)s")
+
+ # Setup warnings logger
+ if hasattr(logging, 'captureWarnings'):
+ wlogger = logging.getLogger('py.warnings')
+ wlogger.propagate = False
+ wlogger.addHandler(EmitWarnings(self.logger))
+ logging.captureWarnings(True)
+
+ # first we define a handler for logging to a file
+ if f:
+ self.set_logfile(f)
+
+ #then we define a handler to log to the console
+ self.console = logging.StreamHandler()
+ self.console.setFormatter(self.format)
+ self.console.setLevel(logging.WARNING)
+ self.logger.addHandler(self.console)
+
+# if system.python_version() <= (2,4,0,'',0):
+# raise VersionTooLow('Python', '2.4.0')
+
+ def __init__(self):
+ self.make_logger()
+ self.app = None
+
+ def set_logfile(self, f):
+ """set_logfile(file) -> None. Redirects debugging
+ output to file."""
+ if f is None:
+ if self.fhandler:
+ self.logger.removeHandler(self.fhandler)
+ self.fhandler = None
+ return
+
+ def rotate_file_if_necessary(filename):
+ statinfo = os.stat(filename)
+ if statinfo.st_size > 1024*1024:
+ #rotate file
+ mincount = 1
+ maxcount = 5
+ count = maxcount
+ newfile = "%s.%s"%(filename, count)
+ while not os.path.exists(newfile) and count >= mincount:
+ count = count - 1
+ newfile = "%s.%s"%(filename, count)
+ if count == 5:
+ os.unlink("%s.%s"%(filename, count))
+ count = 4
+ while count >= mincount:
+ os.rename("%s.%s"%(filename, count), "%s.%s"%(filename, count+1))
+ count = count -1
+ os.rename(filename, "%s.%s"%(filename, mincount))
+
+ try:
+ # there's a problem on Windows with RotatingFileHandler and that
+ # happens when VisTrails starts child processes (it seems related
+ # to the way Windows manages file handlers)
+ # see http://bugs.python.org/issue4749
+ # in this case we will deal with log files differently on Windows:
+ # we will check if we need to rotate the file at the beginning of
+ # the session.
+ import vistrails.core.system
+ if vistrails.core.system.systemType in ["Windows", "Microsoft"]:
+ if not os.path.exists(f):
+ open(f,'w').close()
+ rotate_file_if_necessary(f)
+ handler = logging.FileHandler(f)
+ else:
+ handler = logging.handlers.RotatingFileHandler(f, maxBytes=1024*1024,
+ backupCount=5)
+ handler.setFormatter(self.format)
+ handler.setLevel(logging.DEBUG)
+ if self.fhandler:
+ self.logger.removeHandler(self.fhandler)
+ self.fhandler = handler
+ self.logger.addHandler(handler)
+
+ except Exception, e:
+ self.critical("Could not set log file %s: %s"%(f,str(e)))
+
+ def set_message_level(self,level):
+ """self.set_message_level(level) -> None. Sets the logging
+ verboseness. level must be one of (DebugPrint.CRITICAL,
+ DebugPrint.WARNING, DebugPrint.INFO, DebugPrint.DEBUG)."""
+ self.console.setLevel(level)
+
+ def register_splash(self, app):
+ """ register_splash(self, classname)
+ Registers a method splashMessage(message)
+ """
+ self.app = app
+
+ def splashMessage(self, msg):
+ """ splashMessage(self, string)
+ Writes a splashmessage if app is registered
+ """
+ if self.app:
+ self.app.splashMessage(msg)
+
+ def message(self, caller, msg, details=''):
+ """self.message(caller, str, str) -> str. Returns a string with a
+ formatted message to be send to the debugging output. This
+ should not be called explicitly from userland. Consider using
+ self.log(), self.warning() or self.critical() instead."""
+ msg = (msg + '\n' + details) if details else msg
+ source = inspect.getsourcefile(caller)
+ line = caller.f_lineno
+ if source and line:
+ return source + ", line " + str(line) + "\n" + msg
+ else:
+ return "(File info not available)\n" + msg
+
+ def debug(self, msg, details = ''):
+ """self.log(str, str) -> None. Send information message (low
+ importance) to log with appropriate call site information."""
+ caller = inspect.currentframe().f_back # who called us?
+ self.logger.debug(self.message(caller, msg, details))
+
+ def log(self, msg, details = ''):
+ """self.log(str, str) -> None. Send information message (low
+ importance) to log with appropriate call site information."""
+ caller = inspect.currentframe().f_back # who called us?
+ self.logger.info(self.message(caller, msg, details))
+
+ def warning(self, msg, details = ''):
+ """self.warning(str, str) -> None. Send warning message (medium
+ importance) to log with appropriate call site information."""
+ caller = inspect.currentframe().f_back # who called us?
+ self.logger.warning(self.message(caller, msg, details))
+
+ def critical(self, msg, details = ''):
+ """self.critical(str, str) -> None. Send critical message (high
+ importance) to log with appropriate call site information."""
+ caller = inspect.currentframe().f_back # who called us?
+ self.logger.critical(self.message(caller, msg, details))
+
+splashMessage = DebugPrint.getInstance().splashMessage
+critical = DebugPrint.getInstance().critical
+warning = DebugPrint.getInstance().warning
+log = DebugPrint.getInstance().log
+debug = DebugPrint.getInstance().debug
+
+# critical: terminal, messagebox
+# warning: terminal
+# log : shown if -V 1
+# debug : shown if -V 2
+
+################################################################################
+
+def timecall(method):
+ """timecall is a method decorator that wraps any call in timing calls
+ so we get the total time taken by a function call as a debugging message."""
+ def call(self, *args, **kwargs):
+ caller = inspect.currentframe().f_back
+ start = time.time()
+ method(self, *args, **kwargs)
+ end = time.time()
+ critical("time: %.5s" % (end-start))
+ call.__doc__ = method.__doc__
+ return call
+
+################################################################################
+
+def object_at(desc):
+ """object_at(id) -> object
+
+ id is an int returning from id() or a hex string of id()
+
+ Fetches all live objects, finds the one with given id, and returns
+ it. Warning: THIS IS FOR DEBUGGING ONLY. IT IS SLOW."""
+ if isinstance(desc, int):
+ target_id = desc
+ elif isinstance(desc, basestring):
+ target_id = int(desc, 16) # Reads desc as the hex address
+ import gc
+ for obj in gc.get_objects():
+ if id(obj) == target_id:
+ return obj
+ raise KeyError("Couldn't find object")
diff --git a/vistrails/core/external_connection.py b/vistrails/core/external_connection.py
new file mode 100644
index 0000000..277e18b
--- /dev/null
+++ b/vistrails/core/external_connection.py
@@ -0,0 +1,350 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file contains classes related to loading and saving a set of
+connection objects to an XML file.
+It defines the following
+classes:
+ - ExtConnection
+ - DBConnection
+ - ExtConnectionList
+"""
+import os
+import tempfile
+import unittest
+
+from vistrails.core.utils import VistrailsInternalError, abstract
+from vistrails.core.utils.enum import enum
+from vistrails.core.utils.uxml import named_elements, XMLWrapper
+################################################################################
+
+ConnectionType = enum('ConnectionType',
+ ['DB', 'HTTP', 'Unknown'],
+ "Enumeration of Connection Types")
+
+class ExtConnection(object):
+ """Stores Information for an External Connection"""
+ parseDispatch = {}
+
+ def __init__(self, id=-1, name='', host='', type=ConnectionType.Unknown):
+ """__init__(id: int, name: str, host: str, type: ConnectionType)
+ -> ExtConnection
+ It creates an external connection. Ignoring the connection type, every
+ connection should have at least a name, a hostname and an id """
+ self.id = id
+ self.name = name
+ self.host = host
+ self.type = type
+
+ def serialize(self, dom, element):
+ abstract()
+
+ @staticmethod
+ def parse(element):
+ type = str(element.getAttribute('type'))
+ return ExtConnection.parseDispatch[type](element)
+
+class DBConnection(ExtConnection):
+ """Stores Information for Database Connection """
+ def __init__(self, id=-1, name='', host='', port=0, user='', passwd='',
+ database='', dbtype=''):
+ """__init__(id: int, name: str, host: str, port: int, username: str,
+ passwd: str, database: str, type:ConnectionType)->DBConnection
+ It creates a DBConnection Object
+ """
+ ExtConnection.__init__(self, id, name, host, ConnectionType.DB)
+ self.port = port
+ self.user = user
+ self.passwd = passwd
+ self.database = database
+ self.dbtype = dbtype
+
+ def serialize(self, dom, element):
+ """serialize(dom, element) -> None
+ Convert this object to an XML representation.
+ """
+ conn = dom.createElement('connection')
+ conn.setAttribute('id', str(self.id))
+ conn.setAttribute('name', str(self.name))
+ conn.setAttribute('host', str(self.host))
+ conn.setAttribute('port',str(self.port))
+ conn.setAttribute('user', str(self.user))
+ conn.setAttribute('passwd', str(self.passwd))
+ conn.setAttribute('database', str(self.database))
+ conn.setAttribute('type', str(self.type))
+ conn.setAttribute('dbtype', str(self.dbtype))
+ element.appendChild(conn)
+
+ def __str__(self):
+ """ __str__() -> str - Writes itself as a string """
+ return """<<id= '%s' name='%s' type='%s' host='%s'
+ user='%s' database='%s' dbtype='%s'>>""" % (
+ self.id,
+ self.name,
+ self.type,
+ self.host,
+ self.user,
+ self.database,
+ self.dbtype)
+
+ @staticmethod
+ def parse(element):
+ """ parse(element) -> DBConnection
+ Parse an XML object representing a DBConnection and returns a
+ DBConnection object.
+
+ """
+ conn = DBConnection()
+ conn.type = ConnectionType.DB
+ conn.id = int(element.getAttribute('id'))
+ conn.name = str(element.getAttribute('name'))
+ conn.host = str(element.getAttribute('host'))
+ conn.port = int(element.getAttribute('port'))
+ conn.user = str(element.getAttribute('user'))
+ conn.passwd = str(element.getAttribute('passwd'))
+ conn.database = str(element.getAttribute('database'))
+ conn.dbtype = str(element.getAttribute('dbtype'))
+ return conn
+
+ def __eq__(self, other):
+ """ __eq__(other: DBConnection) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if other == None:
+ return False
+ if self.type != other.type:
+ return False
+ if self.id != other.id:
+ return False
+ if self.name != other.name:
+ return False
+ if self.host != other.host:
+ return False
+ if self.port != other.port:
+ return False
+ if self.user != other.user:
+ return False
+ if self.passwd != other.passwd:
+ return False
+ if self.database != other.database:
+ return False
+ if self.dbtype != other.dbtype:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not (self == other)
+
+ExtConnection.parseDispatch[str(ConnectionType.DB)] = DBConnection.parse
+
+class ExtConnectionList(XMLWrapper):
+ """Class to store and manage a list of connections.
+
+ """
+ _instance = None
+ class ExtConnectionListSingleton(object):
+ def __call__(self, *args, **kw):
+ if ExtConnectionList._instance is None:
+ obj = ExtConnectionList(*args, **kw)
+ ExtConnectionList._instance = obj
+ return ExtConnectionList._instance
+
+ getInstance = ExtConnectionListSingleton()
+
+ def __init__(self, filename=''):
+ """ __init__() -> ExtConnectionList """
+ if not ExtConnectionList._instance:
+ self.__connections = {}
+ self.changed = False
+ self.current_id = 1
+ self.filename = filename
+ self.load_connections()
+ ExtConnectionList._instance = self
+ else:
+ raise RuntimeError, 'Only one instance of ExtConnectionList is \
+allowed!'
+
+ def load_connections(self):
+ """load_connections()-> None
+ Load connections from its internal filename
+
+ """
+ if os.path.exists(self.filename):
+ self.parse(self.filename)
+
+ def add_connection(self, conn):
+ """add_connection(conn: ExtConnection) -> None
+ Adds a connection to the list
+
+ """
+ if self.__connections.has_key(conn.id):
+ msg = "External Connection '%s' with repeated id" % conn.name
+ raise VistrailsInternalError(msg)
+ self.__connections[conn.id] = conn
+ self.current_id = max(self.current_id, conn.id+1)
+ self.serialize()
+
+ def get_connection(self, id):
+ """get_connection(id: int) -> ExtConnection
+ Returns connection object associated with id
+
+ """
+ if self.__connections.has_key(id):
+ return self.__connections[id]
+ else:
+ return None
+
+ def has_connection(self, id):
+ """has_connection(id: int) -> Boolean
+ Returns True if connection with id exists """
+ return self.__connections.has_key(id)
+
+ def find_db_connection(self, host, port, db):
+ """find_db_connection(host: str, port: int, db: str) -> id
+ Returns the id of the first connection that matches the provided
+ parameters. It will return -1 if not found
+
+ """
+ for conn in self.__connections.itervalues():
+ if conn.host == host and conn.port == port and conn.database == db:
+ return conn.id
+ return -1
+
+ def set_connection(self, id, conn):
+ """set_connection(id: int, conn: ExtConnection)- > None
+ Updates the connection with id to be conn
+
+ """
+ if self.__connections.has_key(id):
+ self.__connections[id] = conn
+ self.serialize()
+
+ def remove_connection(self, id):
+ """remove_connection(id: int) -> None
+ Remove connection with id 'id'
+
+ """
+ if self.__connections.has_key(id):
+ del self.__connections[id]
+ self.serialize()
+
+ def clear(self):
+ """ clear() -> None
+ Remove current connections """
+ self.__connections.clear()
+ self.current_id = 1
+
+ def count(self):
+ """count() -> int - Returns the number of connections """
+ return len(self.__connections)
+
+ def items(self):
+ """ items() -> - Returns the connections """
+ return self.__connections.items()
+
+ def parse(self, filename):
+ """parse(filename: str) -> None
+ Loads a list of connections from a XML file, appending it to
+ self.__connections.
+
+ """
+ self.open_file(filename)
+ root = self.dom.documentElement
+ for element in named_elements(root, 'connection'):
+ self.add_connection(ExtConnection.parse(element))
+ self.refresh_current_id()
+
+ def serialize(self):
+ """serialize(filename:str) -> None
+ Writes connection list to given filename.
+
+ """
+ dom = self.create_document('connections')
+ root = dom.documentElement
+
+ for conn in self.__connections.values():
+ conn.serialize(dom, root)
+
+ self.write_document(root, self.filename)
+
+ def refresh_current_id(self):
+ """refresh_current_id() -> None
+ Recomputes the next unused id from scratch
+
+ """
+ self.current_id = max([0] + self.__connections.keys()) + 1
+
+ def get_fresh_id(self):
+ """get_fresh_id() -> int - Returns an unused id. """
+ return self.current_id
+
+
+###############################################################################
+
+class TestConnectionList(unittest.TestCase):
+ def test1(self):
+ """ Exercising writing and reading a file """
+ fd, filename = tempfile.mkstemp(prefix='vt_', suffix='_connections.xml')
+ os.close(fd)
+ try:
+ conns = ExtConnectionList.getInstance()
+ conns.filename = filename
+ conns.clear()
+ conn = DBConnection()
+ conn.id = 1
+ conn.name = 'test'
+ conn.host = 'somehost.com'
+ conn.port = 1234
+ conn.user = 'nobody'
+ conn.passwd = '123'
+ conn.database = 'anydatabase'
+ conn.dbtype = 'MySQL'
+
+ conns.add_connection(conn)
+
+ #reading it again
+ conns.clear()
+ self.assertEquals(conns.count(),0)
+ conns.load_connections()
+ self.assertEquals(conns.count(),1)
+ newconn = conns.get_connection(1)
+ self.assertEqual(conn, newconn)
+ finally:
+ #remove created file
+ os.unlink(filename)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/inspector.py b/vistrails/core/inspector.py
new file mode 100644
index 0000000..6533e04
--- /dev/null
+++ b/vistrails/core/inspector.py
@@ -0,0 +1,247 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Helper classes for inspecting vistrails/pipelines at runtime"""
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.system import get_vistrails_default_pkg_prefix
+################################################################################
+
+class PipelineInspector(object):
+ """
+ PipelineInspector inspects a pipeline to get informations such as
+ the number of spreadsheet cells or compatibility for sub-modules
+
+ """
+ def __init__(self):
+ """ PipelineInspector() -> None
+ Initialize pipeline information
+
+ """
+ # A dict of input port module ids to its name/type
+ self.input_ports = {}
+ self.input_port_by_name = {}
+
+ # A dict of output port module ids to its name/type
+ self.output_ports = {}
+ self.output_port_by_name = {}
+
+ # A list of ids of module of type cell
+ self.spreadsheet_cells = []
+
+ # A dict of ambiguous modules mapped to their annotated id
+ self.annotated_modules = {}
+
+ def inspect(self, pipeline):
+ """ inspect(pipeline: Pipeline) -> None
+ Inspect a pipeline and update information
+
+ """
+ self.inspect_input_output_ports(pipeline)
+ self.inspect_spreadsheet_cells(pipeline)
+ self.inspect_ambiguous_modules(pipeline)
+
+ def has_input_ports(self):
+ """ has_input_ports() -> bool
+ Check if the inspected pipeline has any input ports
+
+ """
+ return len(self.input_ports)>0
+
+ def has_output_ports(self):
+ """ has_output_ports() -> bool
+ Check if the inspected pipeline has any output ports
+
+ """
+ return len(self.output_ports)>0
+
+ def number_of_cells(self):
+ """ number_of_cells() -> int
+ Return the number of cells that will occupied on the spreadsheet
+
+ """
+ return len(self.spreadsheet_cells)
+
+ def is_sub_module(self):
+ """ is_sub_module() -> bool
+ Check whether or not this pipeline is a sub module
+
+ """
+ return self.has_input_ports() or self.has_output_ports()
+
+ def inspect_input_output_ports(self, pipeline):
+ """ inspect_input_output_ports(pipeline: Pipeline) -> None
+ Inspect the pipeline input/output ports, useful for submodule
+
+ """
+ registry = get_module_registry()
+ self.input_ports = {}
+ self.input_port_by_name = {}
+ self.output_ports = {}
+ self.output_port_by_name = {}
+ if not pipeline: return
+ for cId, conn in pipeline.connections.iteritems():
+ src_module = pipeline.modules[conn.source.moduleId]
+ dst_module = pipeline.modules[conn.destination.moduleId]
+ if src_module.name=='InputPort':
+ spec = registry.getInputPortSpec(dst_module,
+ conn.destination.name)
+ name = self.get_port_name(src_module)
+ if name=='':
+ name = conn.destination.name
+ self.input_ports[src_module.id] = (name,
+ spec[0])
+ self.input_port_by_name[name] = src_module.id
+ if dst_module.name=='OutputPort':
+ spec = registry.getOutputPortSpec(src_module,
+ conn.source.name)
+ name = self.get_port_name(dst_module)
+ if name=='':
+ name = conn.source.name
+ self.output_ports[dst_module.id] = (name,
+ spec[0])
+ self.output_port_by_name[name] = dst_module.id
+
+ def get_port_name(self, module):
+ """ get_port_name(module: InputPort/OutputPort) -> str
+ Return the real name of the port module based on 'name' function
+
+ """
+ for f in module.functions:
+ if f.name=='name' and f.params:
+ return f.params[0].strValue
+ return ''
+
+ def inspect_spreadsheet_cells(self, pipeline):
+ """ inspect_spreadsheet_cells(pipeline: Pipeline) -> None
+ Inspect the pipeline to see how many cells is needed
+
+ """
+ registry = get_module_registry()
+ self.spreadsheet_cells = []
+ if not pipeline: return
+
+ def find_spreadsheet_cells(pipeline, root_id=None):
+ if root_id is None:
+ root_id = []
+ # Sometimes we run without the spreadsheet!
+ spreadsheet_pkg = \
+ '%s.spreadsheet' % get_vistrails_default_pkg_prefix()
+ if registry.has_module(spreadsheet_pkg, 'SpreadsheetCell'):
+ # First pass to check cells types
+ cellType = \
+ registry.get_descriptor_by_name(spreadsheet_pkg,
+ 'SpreadsheetCell').module
+ for mId, module in pipeline.modules.iteritems():
+ desc = registry.get_descriptor_by_name(module.package,
+ module.name,
+ module.namespace)
+ if issubclass(desc.module, cellType):
+ self.spreadsheet_cells.append(root_id + [mId])
+
+ for subworkflow_id in self.find_subworkflows(pipeline):
+ subworkflow = pipeline.modules[subworkflow_id]
+ if subworkflow.pipeline is not None:
+ find_spreadsheet_cells(subworkflow.pipeline,
+ root_id + [subworkflow_id])
+
+ find_spreadsheet_cells(pipeline)
+
+ def find_subworkflows(self, pipeline):
+ if not pipeline:
+ return
+ subworkflows = []
+ for m_id, module in pipeline.modules.iteritems():
+ if module.is_abstraction() or module.is_group():
+ subworkflows.append(m_id)
+ return subworkflows
+
+ def inspect_ambiguous_modules(self, pipeline):
+ """ inspect_ambiguous_modules(pipeline: Pipeline) -> None
+ inspect_ambiguous_modules returns a dict of ambiguous modules,
+ i.e. cannot determine the exact module by giving just its
+ name. Then in each group of dupplicate modules, a set of
+ annotated id is generated for them sorted based on their id.
+ The annotated_modules dictionary will map actual module id into
+ their annotated one (if it is ambiguous)
+
+ """
+ self.annotated_modules = {}
+ if not pipeline: return
+
+ orig_pipeline = pipeline
+ count = {}
+ module_name = {}
+ for moduleId in pipeline.modules.iterkeys():
+ module = pipeline.modules[moduleId]
+ if module_name.has_key(module.name): # ambiguous
+ if count[module.name]==1:
+ self.annotated_modules[module_name[module.name]] = 1
+ count[module.name] += 1
+ self.annotated_modules[moduleId] = count[module.name]
+ else:
+ module_name[module.name] = moduleId
+ count[module.name] = 1
+
+ for id_list in self.spreadsheet_cells:
+ pipeline = orig_pipeline
+ # only need to worry about nested cells here
+ if len(id_list) >= 2:
+ id_iter = iter(id_list)
+ m = pipeline.modules[id_iter.next()]
+ for m_id in id_iter:
+ pipeline = m.pipeline
+ m = pipeline.modules[m_id]
+ if m.name in module_name:
+ if count[m.name] == 1:
+ self.annotated_modules[module_name[m.name]] = 1
+ count[m.name] += 1
+ self.annotated_modules[tuple(id_list)] = count[m.name]
+ else:
+ module_name[m.name] = tuple(id_list)
+ count[m.name] = 1
+
+
+# if __name__ == '__main__':
+# from core.startup import VistrailsStartup
+# from core.xml_parser import XMLParser
+# xmlFile = 'C:/cygwin/home/stew/src/vistrails/trunk/examples/vtk.xml'
+# vs = VistrailsStartup()
+# vs.init()
+# parser = XMLParser()
+# parser.openVistrail(xmlFile)
+# vistrail = parser.getVistrail()
+# pipeline = vistrail.getPipeline('Single Renderer')
+# print vistrail.latestTime
diff --git a/vistrails/core/interpreter/__init__.py b/vistrails/core/interpreter/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/core/interpreter/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/core/interpreter/base.py b/vistrails/core/interpreter/base.py
new file mode 100644
index 0000000..d0fc06c
--- /dev/null
+++ b/vistrails/core/interpreter/base.py
@@ -0,0 +1,240 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.data_structures.graph import Graph
+from vistrails.core.utils import expression
+from vistrails.core.utils import trace_method
+from vistrails.core import debug
+import copy
+import parser
+
+##############################################################################
+
+class InternalTuple(object):
+ """Tuple used internally for constant tuples."""
+
+ def _get_length(self, length):
+ return len(self._values)
+ def _set_length(self, length):
+ self._values = [None] * length
+ length = property(_get_length, _set_length)
+
+ def compute(self):
+ return
+
+ def set_input_port(self, index, connector):
+ self._values[index] = connector()
+
+ def get_output(self, port):
+ return tuple(self._values)
+
+ def update(self):
+ pass
+
+##############################################################################
+
+class AbortExecution(Exception):
+ """Internal exception raised to signal the interpreter it should stop.
+ """
+
+##############################################################################
+
+class BaseInterpreter(object):
+
+ def __init__(self):
+ """ BaseInterpreter() -> BaseInterpreter
+ Initialize class members
+
+ """
+ self.done_summon_hook = None
+ self.done_update_hook = None
+
+ def get_name_dependencies(self, astList):
+ """get_name_dependencies(astList) -> list of something
+
+ """
+
+ result = []
+ if astList[0]==1: # NAME token
+ result += [astList[1]]
+ else:
+ for e in astList:
+ if isinstance(e, list):
+ result += self.get_name_dependencies(e)
+ return result
+
+# def build_alias_dictionary(self, pipeline):
+# aliases = {}
+# for mid in pipeline.modules:
+# for f in pipeline.modules[mid].functions:
+# fsig = f.getSignature()
+# for pidx in xrange(len(f.params)):
+# palias = f.params[pidx].alias
+# if palias and palias!='':
+# for f1 in reversed(pipeline.modules[mid].functions):
+# if f1.getSignature()==fsig:
+# p = f1.params[pidx]
+# aliases[palias] = (p.type, expression.parse_expression(str(p.strValue)))
+# break
+# return aliases
+
+ def compute_evaluation_order(self, aliases):
+ # Build the dependencies graph
+ dp = {}
+ for alias,(atype,(base,exp)) in aliases.items():
+ edges = []
+ for e in exp:
+ edges += self.get_name_dependencies()
+ dp[alias] = edges
+
+ # Topological Sort to find the order to compute aliases
+ # Just a slow implementation, O(n^3)...
+ unordered = copy.copy(list(aliases.keys()))
+ ordered = []
+ while unordered:
+ added = []
+ for i in xrange(len(unordered)):
+ ok = True
+ u = unordered[i]
+ for j in xrange(len(unordered)):
+ if i!=j:
+ for v in dp[unordered[j]]:
+ if u==v:
+ ok = False
+ break
+ if not ok: break
+ if ok: added.append(i)
+ if not added:
+ debug.warning('Looping dependencies detected!')
+ break
+ for i in reversed(added):
+ ordered.append(unordered[i])
+ del unordered[i]
+ return ordered
+
+ def evaluate_exp(self, atype, base, exps, aliases):
+ # FIXME: eval should pretty much never be used
+ import datetime
+ for e in exps: base = (base[:e[0]] +
+ str(eval(e[1],
+ {'datetime':locals()['datetime']},
+ aliases)) +
+ base[e[0]:])
+ if not atype in ['string', 'String']:
+ if base=='':
+ base = '0'
+ try:
+ base = eval(base,None,None)
+ except:
+ pass
+ return base
+
+ def resolve_aliases(self, pipeline,
+ customAliases=None):
+ # We don't build the alias dictionary anymore because as we don't
+ # perform expression evaluation anymore, the values won't change.
+ # We only care for custom aliases because they might have a value
+ # different from what it's stored.
+
+ aliases = {}
+ if customAliases:
+ #customAliases can be only a subset of the aliases
+ #so we need to build the Alias Dictionary always
+ for k,v in customAliases.iteritems():
+ aliases[k] = v
+ # no support for expression evaluation. The code that does that is
+ # ugly and dangerous.
+# ordered = self.compute_evaluation_order(aliases)
+# casting = {'int': int, 'float': float, 'double': float, 'string': str,
+# 'Integer': int, 'Float': float, 'String': str}
+# for alias in reversed(ordered):
+# (atype,base) = aliases[alias]
+# #no expression evaluation anymore
+# aliases[alias] = base
+# #value = self.evaluate_exp(atype,base,exps,aliases)
+# #aliases[alias] = value
+ for alias in aliases:
+ try:
+ info = pipeline.aliases[alias]
+ param = pipeline.db_get_object(info[0],info[1])
+ param.strValue = str(aliases[alias])
+ except KeyError:
+ pass
+
+ return aliases
+
+ def update_params(self, pipeline,
+ customParams=None):
+ """update_params(pipeline: Pipeline,
+ customParams=[(vttype, oId, strval)] -> None
+ This will set the new parameter values in the pipeline before
+ execution
+
+ """
+ if customParams:
+ for (vttype, oId, strval) in customParams:
+ try:
+ param = pipeline.db_get_object(vttype,oId)
+ param.strValue = str(strval)
+ except Exception, e:
+ debug.debug("Problem when updating params: %s"%str(e))
+
+ def resolve_variables(self, vistrail_variables, pipeline):
+ for m in pipeline.module_list:
+ if m.is_vistrail_var():
+ vistrail_var = vistrail_variables(m.get_vistrail_var())
+ if vistrail_var is None: # assume set in parameter exploration
+ continue
+ strValue = vistrail_var.value
+ for func in m.functions:
+ if func.name == 'value':
+ func.params[0].strValue = strValue
+
+ def set_done_summon_hook(self, hook):
+ """ set_done_summon_hook(hook: function(pipeline, objects)) -> None
+ Assign a function to call right after every objects has been
+ summoned during execution
+
+ """
+ self.done_summon_hook = hook
+
+ def set_done_update_hook(self, hook):
+ """ set_done_update_hook(hook: function(pipeline, objects)) -> None
+ Assign a function to call right after every objects has been
+ updated
+
+ """
+ self.done_update_hook = hook
+
+##############################################################################
diff --git a/vistrails/core/interpreter/cached.py b/vistrails/core/interpreter/cached.py
new file mode 100644
index 0000000..da79517
--- /dev/null
+++ b/vistrails/core/interpreter/cached.py
@@ -0,0 +1,834 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import base64
+import copy
+import cPickle
+import gc
+
+from vistrails.core.common import InstanceObject, lock_method, \
+ VistrailsInternalError
+from vistrails.core.data_structures.bijectivedict import Bidict
+import vistrails.core.interpreter.base
+from vistrails.core.interpreter.base import AbortExecution
+import vistrails.core.interpreter.utils
+from vistrails.core.log.controller import DummyLogController
+from vistrails.core.modules.basic_modules import identifier as basic_pkg
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.modules.vistrails_module import ModuleConnector, \
+ ModuleHadError, ModuleError, ModuleBreakpoint, ModuleErrors, \
+ ModuleWasSuspended
+from vistrails.core.utils import DummyView
+import vistrails.core.system
+import vistrails.core.vistrail.pipeline
+
+# from core.modules.module_utils import FilePool
+
+##############################################################################
+
+class CachedInterpreter(vistrails.core.interpreter.base.BaseInterpreter):
+
+ def __init__(self):
+ vistrails.core.interpreter.base.BaseInterpreter.__init__(self)
+ self.debugger = None
+ self.create()
+
+ def create(self):
+ # FIXME moved here because otherwise we hit the registry too early
+ from vistrails.core.modules.module_utils import FilePool
+ self._file_pool = FilePool()
+ self._persistent_pipeline = vistrails.core.vistrail.pipeline.Pipeline()
+ self._objects = {}
+ self._executed = {}
+ self.filePool = self._file_pool
+
+ def clear(self):
+ self._file_pool.cleanup()
+ self._persistent_pipeline.clear()
+ for obj in self._objects.itervalues():
+ obj.clear()
+ self._objects = {}
+ self._executed = {}
+
+ def __del__(self):
+ self.clear()
+
+ def clean_modules(self, modules_to_clean):
+ """clean_modules(modules_to_clean: list of persistent module ids)
+
+ Removes modules from the persistent pipeline, and the modules that
+ depend on them."""
+ if not modules_to_clean:
+ return
+ g = self._persistent_pipeline.graph
+ modules_to_clean = (set(modules_to_clean) &
+ set(self._persistent_pipeline.modules.iterkeys()))
+ dependencies = g.vertices_topological_sort(modules_to_clean)
+ for v in dependencies:
+ self._persistent_pipeline.delete_module(v)
+ del self._objects[v]
+
+ def clean_non_cacheable_modules(self):
+ """clean_non_cacheable_modules() -> None
+
+ Removes all modules that are not cacheable from the persistent
+ pipeline, and the modules that depend on them, and
+ previously suspended modules """
+ non_cacheable_modules = [i for
+ (i, mod) in self._objects.iteritems()
+ if not mod.is_cacheable() or \
+ mod.suspended]
+ self.clean_modules(non_cacheable_modules)
+
+ def _clear_package(self, identifier):
+ """clear_package(identifier: str) -> None
+
+ Removes all modules from the given package from the persistent
+ pipeline.
+ """
+ modules = [mod.id
+ for mod in self._persistent_pipeline.module_list
+ if mod.module_descriptor.identifier == identifier]
+ self.clean_modules(modules)
+
+ def setup_pipeline(self, pipeline, **kwargs):
+ """setup_pipeline(controller, pipeline, locator, currentVersion,
+ view, aliases, **kwargs)
+ Matches a pipeline with the persistent pipeline and creates
+ instances of modules that aren't in the cache.
+ """
+ def fetch(name, default):
+ r = kwargs.get(name, default)
+ try:
+ del kwargs[name]
+ except KeyError:
+ pass
+ return r
+ controller = fetch('controller', None)
+ locator = fetch('locator', None)
+ current_version = fetch('current_version', None)
+ view = fetch('view', DummyView())
+ vistrail_variables = fetch('vistrail_variables', None)
+ aliases = fetch('aliases', None)
+ params = fetch('params', None)
+ extra_info = fetch('extra_info', None)
+ logger = fetch('logger', DummyLogController())
+ sinks = fetch('sinks', None)
+ reason = fetch('reason', None)
+ actions = fetch('actions', None)
+ done_summon_hooks = fetch('done_summon_hooks', [])
+ module_executed_hook = fetch('module_executed_hook', [])
+ stop_on_error = fetch('stop_on_error', True)
+
+ reg = get_module_registry()
+
+ if len(kwargs) > 0:
+ raise VistrailsInternalError('Wrong parameters passed '
+ 'to setup_pipeline: %s' % kwargs)
+
+ def create_null():
+ """Creates a Null value"""
+ getter = get_module_registry().get_descriptor_by_name
+ descriptor = getter(basic_pkg, 'Null')
+ return descriptor.module()
+
+ def create_constant(param, module):
+ """Creates a Constant from a parameter spec"""
+ getter = reg.get_descriptor_by_name
+ desc = getter(param.identifier, param.type, param.namespace)
+ constant = desc.module()
+ constant.id = module.id
+# if param.evaluatedStrValue:
+# constant.setValue(param.evaluatedStrValue)
+ if param.strValue != '':
+ constant.setValue(param.strValue)
+ else:
+ constant.setValue( \
+ constant.translate_to_string(constant.default_value))
+ return constant
+
+ ### BEGIN METHOD ###
+
+# if self.debugger:
+# self.debugger.update()
+ to_delete = []
+ errors = {}
+
+ if controller is not None:
+ # Controller is none for sub_modules
+ controller.validate(pipeline)
+ else:
+ pipeline.validate()
+
+ self.resolve_aliases(pipeline, aliases)
+ if vistrail_variables:
+ self.resolve_variables(vistrail_variables, pipeline)
+
+ self.update_params(pipeline, params)
+
+ (tmp_to_persistent_module_map,
+ conn_map,
+ module_added_set,
+ conn_added_set) = self.add_to_persistent_pipeline(pipeline)
+
+ # Create the new objects
+ for i in module_added_set:
+ persistent_id = tmp_to_persistent_module_map[i]
+ module = self._persistent_pipeline.modules[persistent_id]
+ obj = self._objects[persistent_id] = module.summon()
+ obj.interpreter = self
+ obj.id = persistent_id
+ obj.is_breakpoint = module.is_breakpoint
+ obj.signature = module._signature
+
+ # Checking if output should be stored
+ if module.has_annotation_with_key('annotate_output'):
+ annotate_output = module.get_annotation_by_key('annotate_output')
+ #print annotate_output
+ if annotate_output:
+ obj.annotate_output = True
+
+ for f in module.functions:
+ connector = None
+ if len(f.params) == 0:
+ connector = ModuleConnector(create_null(), 'value')
+ elif len(f.params) == 1:
+ p = f.params[0]
+ try:
+ constant = create_constant(p, module)
+ connector = ModuleConnector(constant, 'value')
+ except ValueError, e:
+ err = ModuleError(self, 'Cannot convert parameter '
+ 'value "%s"\n' % p.strValue + str(e))
+ errors[i] = err
+ to_delete.append(obj.id)
+ except Exception, e:
+ err = ModuleError(self, 'Uncaught exception: "%s"' % \
+ p.strValue + str(e))
+ errors[i] = err
+ to_delete.append(obj.id)
+ else:
+ tupleModule = vistrails.core.interpreter.base.InternalTuple()
+ tupleModule.length = len(f.params)
+ for (j,p) in enumerate(f.params):
+ try:
+ constant = create_constant(p, module)
+ constant.update()
+ connector = ModuleConnector(constant, 'value')
+ tupleModule.set_input_port(j, connector)
+ except ValueError, e:
+ err = ModuleError(self, "Cannot convert parameter "
+ "value '%s'\n" % p.strValue + \
+ str(e))
+ errors[i] = err
+ to_delete.append(obj.id)
+ except Exception, e:
+ err = ModuleError(self, 'Uncaught exception: '
+ '"%s"' % p.strValue + str(e))
+ errors[i] = err
+ to_delete.append(obj.id)
+ connector = ModuleConnector(tupleModule, 'value')
+ if connector:
+ obj.set_input_port(f.name, connector, is_method=True)
+
+ # Create the new connections
+ for i in conn_added_set:
+ persistent_id = conn_map[i]
+ conn = self._persistent_pipeline.connections[persistent_id]
+ src = self._objects[conn.sourceId]
+ dst = self._objects[conn.destinationId]
+ conn.makeConnection(src, dst)
+
+ if self.done_summon_hook:
+ self.done_summon_hook(self._persistent_pipeline, self._objects)
+ for callable_ in done_summon_hooks:
+ callable_(self._persistent_pipeline, self._objects)
+
+ tmp_id_to_module_map = {}
+ for i, j in tmp_to_persistent_module_map.iteritems():
+ tmp_id_to_module_map[i] = self._objects[j]
+ return (tmp_id_to_module_map, tmp_to_persistent_module_map.inverse,
+ module_added_set, conn_added_set, to_delete, errors)
+
+ def execute_pipeline(self, pipeline, tmp_id_to_module_map,
+ persistent_to_tmp_id_map, **kwargs):
+ def fetch(name, default):
+ r = kwargs.get(name, default)
+ try:
+ del kwargs[name]
+ except KeyError:
+ pass
+ return r
+ controller = fetch('controller', None)
+ locator = fetch('locator', None)
+ current_version = fetch('current_version', None)
+ view = fetch('view', DummyView())
+ vistrail_variables = fetch('vistrail_variables', None)
+ aliases = fetch('aliases', None)
+ params = fetch('params', None)
+ extra_info = fetch('extra_info', None)
+ logger = fetch('logger', DummyLogController())
+ sinks = fetch('sinks', None)
+ reason = fetch('reason', None)
+ actions = fetch('actions', None)
+ module_executed_hook = fetch('module_executed_hook', [])
+ module_suspended_hook = fetch('module_suspended_hook', [])
+ done_summon_hooks = fetch('done_summon_hooks', [])
+ clean_pipeline = fetch('clean_pipeline', False)
+ stop_on_error = fetch('stop_on_error', True)
+ # parent_exec = fetch('parent_exec', None)
+
+ if len(kwargs) > 0:
+ raise VistrailsInternalError('Wrong parameters passed '
+ 'to execute_pipeline: %s' % kwargs)
+
+ errors = {}
+ executed = {}
+ suspended = {}
+ cached = {}
+
+ # LOGGING SETUP
+ def get_remapped_id(id):
+ return persistent_to_tmp_id_map[id]
+
+ # the executed dict works on persistent ids
+ def add_to_executed(obj):
+ executed[obj.id] = True
+ for callable_ in module_executed_hook:
+ callable_(obj.id)
+
+ # the suspended dict works on persistent ids
+ def add_to_suspended(obj):
+ suspended[obj.id] = obj.suspended
+ for callable_ in module_suspended_hook:
+ callable_(obj.id)
+
+ def set_computing(obj):
+ i = get_remapped_id(obj.id)
+ view.set_module_computing(i)
+
+ # views work on local ids
+ def begin_compute(obj):
+ i = get_remapped_id(obj.id)
+ view.set_module_computing(i)
+
+ reg = get_module_registry()
+ module_name = reg.get_descriptor(obj.__class__).name
+
+ # !!!self.parent_execs is mutated!!!
+ logger.start_execution(obj, i, module_name,
+ parent_execs=self.parent_execs)
+
+ # views and loggers work on local ids
+ def begin_update(obj):
+ i = get_remapped_id(obj.id)
+ view.set_module_active(i)
+
+ def update_cached(obj):
+ cached[obj.id] = True
+ i = get_remapped_id(obj.id)
+
+ reg = get_module_registry()
+ module_name = reg.get_descriptor(obj.__class__).name
+
+ # !!!self.parent_execs is mutated!!!
+ logger.start_execution(obj, i, module_name,
+ parent_execs=self.parent_execs,
+ cached=1)
+ view.set_module_not_executed(i)
+ num_pops = logger.finish_execution(obj,'', self.parent_execs)
+
+ # views and loggers work on local ids
+ def end_update(obj, error='', errorTrace=None, was_suspended = False):
+ i = get_remapped_id(obj.id)
+ if was_suspended:
+ view.set_module_suspended(i, error)
+ error = error.msg
+ elif not error:
+ view.set_module_success(i)
+ else:
+ view.set_module_error(i, error)
+
+ # !!!self.parent_execs is mutated!!!
+ logger.finish_execution(obj, error, self.parent_execs, errorTrace,
+ was_suspended)
+
+ # views and loggers work on local ids
+ def annotate(obj, d):
+ i = get_remapped_id(obj.id)
+ logger.insert_module_annotations(obj, d)
+
+ # views and loggers work on local ids
+ def update_progress(obj, percentage=0.0):
+ i = get_remapped_id(obj.id)
+ view.set_module_progress(i, percentage)
+
+ def add_exec(exec_):
+ logger.add_exec(exec_, self.parent_execs)
+
+ logging_obj = InstanceObject(signalSuccess=add_to_executed,
+ signalSuspended=add_to_suspended,
+ begin_update=begin_update,
+ begin_compute=begin_compute,
+ update_progress=update_progress,
+ end_update=end_update,
+ update_cached=update_cached,
+ set_computing=set_computing,
+ add_exec = add_exec,
+ annotate=annotate,
+ log=logger)
+
+ # PARAMETER CHANGES SETUP
+ parameter_changes = []
+ def change_parameter(obj, name, value):
+ parameter_changes.append((get_remapped_id(obj.id),
+ name, value))
+ def make_change_parameter(obj):
+ return lambda *args: change_parameter(obj, *args)
+
+ # Update **all** modules in the current pipeline
+ for i, obj in tmp_id_to_module_map.iteritems():
+ obj.logging = logging_obj
+ obj.change_parameter = make_change_parameter(obj)
+
+ # Update object pipeline information
+ obj.moduleInfo['locator'] = locator
+ obj.moduleInfo['version'] = current_version
+ obj.moduleInfo['moduleId'] = i
+ obj.moduleInfo['pipeline'] = pipeline
+ obj.moduleInfo['controller'] = controller
+ if extra_info is not None:
+ obj.moduleInfo['extra_info'] = extra_info
+ if reason is not None:
+ obj.moduleInfo['reason'] = reason
+ if actions is not None:
+ obj.moduleInfo['actions'] = actions
+
+ ## Checking 'sinks' from kwargs to resolve only requested sinks
+ # Note that we accept any module in 'sinks', even if it's not actually
+ # a sink in the graph
+ if sinks is not None:
+ persistent_sinks = [tmp_id_to_module_map[sink]
+ for sink in sinks
+ if sink in tmp_id_to_module_map]
+ else:
+ persistent_sinks = [tmp_id_to_module_map[sink]
+ for sink in pipeline.graph.sinks()]
+
+ # Update new sinks
+ for obj in persistent_sinks:
+ abort = False
+ try:
+ obj.update()
+ continue
+ except ModuleWasSuspended:
+ continue
+ except ModuleHadError:
+ pass
+ except AbortExecution:
+ break
+ except ModuleErrors, mes:
+ for me in mes.module_errors:
+ me.module.logging.end_update(me.module, me.msg)
+ errors[me.module.id] = me
+ abort = abort or me.abort
+ except ModuleError, me:
+ me.module.logging.end_update(me.module, me.msg, me.errorTrace)
+ errors[me.module.id] = me
+ abort = me.abort
+ except ModuleBreakpoint, mb:
+ mb.module.logging.end_update(mb.module)
+ errors[mb.module.id] = mb
+ abort = True
+ if stop_on_error or abort:
+ break
+
+ if self.done_update_hook:
+ self.done_update_hook(self._persistent_pipeline, self._objects)
+
+ # objs, errs, and execs are mappings that use the local ids as keys,
+ # as opposed to the persistent ids.
+ # They are thus ideal to external consumption.
+ objs = {}
+ # dict([(i, self._objects[tmp_to_persistent_module_map[i]])
+ # for i in tmp_to_persistent_module_map.keys()])
+ errs = {}
+ execs = {}
+ suspends = {}
+ caches = {}
+
+ to_delete = []
+ for (tmp_id, obj) in tmp_id_to_module_map.iteritems():
+ if clean_pipeline:
+ to_delete.append(obj.id)
+ objs[tmp_id] = obj
+ if obj.id in errors:
+ errs[tmp_id] = errors[obj.id]
+ if not clean_pipeline:
+ to_delete.append(obj.id)
+ if obj.id in executed:
+ execs[tmp_id] = executed[obj.id]
+ elif obj.id in suspended:
+ suspends[tmp_id] = suspended[obj.id]
+ elif obj.id in cached:
+ caches[tmp_id] = cached[obj.id]
+ else:
+ # these modules didn't execute
+ execs[tmp_id] = False
+
+ return (to_delete, objs, errs, execs, suspends, caches, parameter_changes)
+
+ def finalize_pipeline(self, pipeline, to_delete, objs, errs, execs,
+ suspended, cached, **kwargs):
+ def fetch(name, default):
+ r = kwargs.get(name, default)
+ try:
+ del kwargs[name]
+ except KeyError:
+ pass
+ return r
+ view = fetch('view', DummyView())
+ reset_computed = fetch('reset_computed', True)
+
+ self.clean_modules(to_delete)
+
+ for i in objs:
+ if i in errs:
+ view.set_module_error(i, errs[i].msg, errs[i].errorTrace)
+ elif i in suspended and suspended[i]:
+ view.set_module_suspended(i, suspended[i])
+ elif i in execs and execs[i]:
+ view.set_module_success(i)
+ elif i in cached and cached[i]:
+ view.set_module_not_executed(i)
+ else:
+ view.set_module_persistent(i)
+
+ if reset_computed:
+ for module in self._objects.itervalues():
+ module.computed = False
+
+ def unlocked_execute(self, pipeline, **kwargs):
+ """unlocked_execute(pipeline, **kwargs): Executes a pipeline using
+ caching. Caching works by reusing pipelines directly. This
+ means that there exists one global pipeline whose parts get
+ executed over and over again. This allows nested execution."""
+
+ res = self.setup_pipeline(pipeline, **kwargs)
+ modules_added = res[2]
+ conns_added = res[3]
+ to_delete = res[4]
+ errors = res[5]
+ if len(errors) == 0:
+ res = self.execute_pipeline(pipeline, *(res[:2]), **kwargs)
+ else:
+ res = (to_delete, res[0], errors, {}, {}, {}, [])
+ self.finalize_pipeline(pipeline, *(res[:-1]), **kwargs)
+
+ return InstanceObject(objects=res[1],
+ errors=res[2],
+ executed=res[3],
+ suspended=res[4],
+ parameter_changes=res[6],
+ modules_added=modules_added,
+ conns_added=conns_added)
+
+ @lock_method(vistrails.core.interpreter.utils.get_interpreter_lock())
+ def execute(self, pipeline, **kwargs):
+ """execute(pipeline, **kwargs):
+
+ kwargs:
+ controller = fetch('controller', None)
+ locator = fetch('locator', None)
+ current_version = fetch('current_version', None)
+ view = fetch('view', DummyView())
+ aliases = fetch('aliases', None)
+ params = fetch('params', None)
+ extra_info = fetch('extra_info', None)
+ logger = fetch('logger', DummyLogController())
+ reason = fetch('reason', None)
+ actions = fetch('actions', None)
+ done_summon_hooks = fetch('done_summon_hooks', [])
+ module_executed_hook = fetch('module_executed_hook', [])
+
+ Executes a pipeline using caching. Caching works by reusing
+ pipelines directly. This means that there exists one global
+ pipeline whose parts get executed over and over again.
+
+ This function returns a triple of dictionaries (objs, errs, execs).
+
+ objs is a mapping from local ids (the ids in the pipeline) to
+ objects **in the persistent pipeline**. Notice, these are not
+ the objects inside the passed pipeline, but the objects they
+ were mapped to in the persistent pipeline.
+
+ errs is a dictionary from local ids to error messages of modules
+ that might have returns errors.
+
+ execs is a dictionary from local ids to boolean values indicating
+ whether they were executed or not.
+
+ If modules have no error associated with but were not executed, it
+ means they were cached."""
+
+ # Setup named arguments. We don't use named parameters so
+ # that positional parameter calls fail earlier
+ new_kwargs = {}
+ def fetch(name, default):
+ r = kwargs.get(name, default)
+ new_kwargs[name] = r
+ try:
+ del kwargs[name]
+ except KeyError:
+ pass
+ return r
+ controller = fetch('controller', None)
+ locator = fetch('locator', None)
+ current_version = fetch('current_version', None)
+ view = fetch('view', DummyView())
+ vistrail_variables = fetch('vistrail_variables', None)
+ aliases = fetch('aliases', None)
+ params = fetch('params', None)
+ extra_info = fetch('extra_info', None)
+ logger = fetch('logger', DummyLogController())
+ sinks = fetch('sinks', None)
+ reason = fetch('reason', None)
+ actions = fetch('actions', None)
+ done_summon_hooks = fetch('done_summon_hooks', [])
+ module_executed_hook = fetch('module_executed_hook', [])
+ stop_on_error = fetch('stop_on_error', True)
+
+ if len(kwargs) > 0:
+ raise VistrailsInternalError('Wrong parameters passed '
+ 'to execute: %s' % kwargs)
+
+ self.clean_non_cacheable_modules()
+
+# if controller is not None:
+# vistrail = controller.vistrail
+# (pipeline, module_remap) = \
+# core.db.io.expand_workflow(vistrail, pipeline)
+# new_kwargs['module_remap'] = module_remap
+# else:
+# vistrail = None
+
+ if controller is not None:
+ vistrail = controller.vistrail
+ else:
+ vistrail = None
+
+ self.parent_execs = [None]
+ logger.start_workflow_execution(vistrail, pipeline, current_version)
+ self.annotate_workflow_execution(logger, reason, aliases, params)
+ result = self.unlocked_execute(pipeline, **new_kwargs)
+ logger.finish_workflow_execution(result.errors, suspended=result.suspended)
+ self.parent_execs = [None]
+
+ return result
+
+ def annotate_workflow_execution(self, logger, reason, aliases, params):
+ """annotate_workflow_Execution(logger: LogController, reason:str,
+ aliases:dict, params:list)-> None
+ It will annotate the workflow execution in logger with the reason,
+ aliases and params.
+
+ """
+ d = {}
+ d["__reason__"] = reason
+ if aliases is not None and isinstance(aliases, dict):
+ d["__aliases__"] = cPickle.dumps(aliases)
+ if params is not None and isinstance(params, list):
+ d["__params__"] = cPickle.dumps(params)
+ logger.insert_workflow_exec_annotations(d)
+
+ def add_to_persistent_pipeline(self, pipeline):
+ """add_to_persistent_pipeline(pipeline):
+ (module_id_map, connection_id_map, modules_added)
+ Adds a pipeline to the persistent pipeline of the cached interpreter
+ and adds current logging object to each existing module.
+
+ Returns four things: two dictionaries describing the mapping
+ of ids from the passed pipeline to the persistent one (the
+ first one has the module id mapping, the second one has the
+ connection id mapping), a set of all module ids added to the
+ persistent pipeline, and a set of all connection ids added to
+ the persistent pipeline."""
+ module_id_map = Bidict()
+ connection_id_map = Bidict()
+ modules_added = set()
+ connections_added = set()
+ pipeline.refresh_signatures()
+ # we must traverse vertices in topological sort order
+ verts = pipeline.graph.vertices_topological_sort()
+ for new_module_id in verts:
+ new_sig = pipeline.subpipeline_signature(new_module_id)
+ if not self._persistent_pipeline.has_subpipeline_signature(new_sig):
+ # Must add module to persistent pipeline
+ persistent_module = copy.copy(pipeline.modules[new_module_id])
+ persistent_id = self._persistent_pipeline.fresh_module_id()
+ persistent_module.id = persistent_id
+ self._persistent_pipeline.add_module(persistent_module)
+ self._persistent_pipeline.modules[persistent_id]._signature = \
+ base64.b16encode(new_sig).lower()
+ module_id_map[new_module_id] = persistent_id
+ modules_added.add(new_module_id)
+ else:
+ i = self._persistent_pipeline \
+ .subpipeline_id_from_signature(new_sig)
+ module_id_map[new_module_id] = i
+ for connection in pipeline.connections.itervalues():
+ new_sig = pipeline.connection_signature(connection.id)
+ if not self._persistent_pipeline.has_connection_signature(new_sig):
+ # Must add connection to persistent pipeline
+ persistent_connection = copy.copy(connection)
+ persistent_id = self._persistent_pipeline.fresh_connection_id()
+ persistent_connection.id = persistent_id
+ persistent_connection.sourceId = module_id_map[
+ connection.sourceId]
+ persistent_connection.destinationId = module_id_map[
+ connection.destinationId]
+ self._persistent_pipeline.add_connection(persistent_connection)
+ connection_id_map[connection.id] = persistent_id
+ connections_added.add(connection.id)
+ else:
+ i = self._persistent_pipeline \
+ .connection_id_from_signature(new_sig)
+ connection_id_map[connection.id] = i
+ # update persistent signatures
+ self._persistent_pipeline.compute_signatures()
+ return (module_id_map, connection_id_map,
+ modules_added, connections_added)
+
+ def find_persistent_entities(self, pipeline):
+ """returns a map from a pipeline to the persistent pipeline,
+ assuming those pieces exist"""
+ persistent_p = self._persistent_pipeline
+ object_map = {}
+ module_id_map = {}
+ connection_id_map = {}
+ pipeline.refresh_signatures()
+ # we must traverse vertices in topological sort order
+ verts = pipeline.graph.vertices_topological_sort()
+ for module_id in verts:
+ sig = pipeline.subpipeline_signature(module_id)
+ if persistent_p.has_subpipeline_signature(sig):
+ i = persistent_p.subpipeline_id_from_signature(sig)
+ module_id_map[module_id] = i
+ object_map[module_id] = self._objects[i]
+ else:
+ module_id_map[module_id] = None
+ object_map[module_id] = None
+ for connection in pipeline.connections.itervalues():
+ sig = pipeline.connection_signature(connection.id)
+ if persistent_p.has_connection_signature(sig):
+ connection_id_map[connection.id] = \
+ persistent_p.connection_id_from_signature(sig)
+ else:
+ connection_id_map[connection.id] = None
+ return (object_map, module_id_map, connection_id_map)
+
+ __instance = None
+ @staticmethod
+ def get():
+ if not CachedInterpreter.__instance:
+ CachedInterpreter.__instance = CachedInterpreter()
+ return CachedInterpreter.__instance
+
+ @staticmethod
+ def cleanup():
+ if CachedInterpreter.__instance:
+ CachedInterpreter.__instance.clear()
+ objs = gc.collect()
+
+ @staticmethod
+ def flush():
+ if CachedInterpreter.__instance:
+ CachedInterpreter.__instance.clear()
+ CachedInterpreter.__instance.create()
+ objs = gc.collect()
+
+ @staticmethod
+ def clear_package(identifier):
+ if CachedInterpreter.__instance:
+ CachedInterpreter.__instance._clear_package(identifier)
+
+##############################################################################
+# Testing
+
+import unittest
+
+
+class TestCachedInterpreter(unittest.TestCase):
+
+ def test_cache(self):
+ from vistrails.core.db.locator import XMLFileLocator
+ from vistrails.core.vistrail.controller import VistrailController
+ from vistrails.core.db.io import load_vistrail
+
+ """Test if basic caching is working."""
+ locator = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/dummy.xml')
+ (v, abstractions, thumbnails, mashups) = load_vistrail(locator)
+
+ # the controller will take care of upgrades
+ controller = VistrailController(v, locator, abstractions, thumbnails,
+ mashups)
+ p1 = v.getPipeline('int chain')
+ n = v.get_version_number('int chain')
+ controller.change_selected_version(n)
+ controller.flush_delayed_actions()
+ p1 = controller.current_pipeline
+
+ view = DummyView()
+ interpreter = vistrails.core.interpreter.cached.CachedInterpreter.get()
+ result = interpreter.execute(p1,
+ locator=v,
+ current_version=n,
+ view=view,
+ )
+ # to force fresh params
+ p2 = v.getPipeline('int chain')
+ controller.change_selected_version(n)
+ controller.flush_delayed_actions()
+ p2 = controller.current_pipeline
+ result = interpreter.execute(p2,
+ locator=v,
+ current_version=n,
+ view=view,
+ )
+ assert len(result.modules_added) == 1
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/interpreter/default.py b/vistrails/core/interpreter/default.py
new file mode 100644
index 0000000..d169973
--- /dev/null
+++ b/vistrails/core/interpreter/default.py
@@ -0,0 +1,82 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import vistrails.core.interpreter.cached
+import vistrails.core.interpreter.noncached
+
+import unittest
+
+cached_interpreter = vistrails.core.interpreter.cached.CachedInterpreter
+noncached_interpreter = vistrails.core.interpreter.noncached.Interpreter
+__default_interpreter = cached_interpreter
+
+##############################################################################
+
+def set_cache_configuration(field, value):
+ assert field == 'useCache'
+ if value:
+ set_default_interpreter(cached_interpreter)
+ else:
+ set_default_interpreter(noncached_interpreter)
+
+def connect_to_configuration(configuration):
+ configuration.subscribe('useCache', set_cache_configuration)
+
+def get_default_interpreter():
+ """Returns an instance of the default interpreter class."""
+ return __default_interpreter.get()
+
+def set_default_interpreter(interpreter_class):
+ """Sets the default interpreter class."""
+ global __default_interpreter
+ __default_interpreter = interpreter_class
+
+##############################################################################
+
+
+class TestDefaultInterpreter(unittest.TestCase):
+
+ def test_set(self):
+ old_interpreter = type(get_default_interpreter())
+ try:
+ set_default_interpreter(noncached_interpreter)
+ self.assertEquals(type(get_default_interpreter()),
+ noncached_interpreter)
+ set_default_interpreter(cached_interpreter)
+ self.assertEquals(type(get_default_interpreter()),
+ cached_interpreter)
+ finally:
+ set_default_interpreter(old_interpreter)
+ self.assertEquals(type(get_default_interpreter()),
+ old_interpreter)
diff --git a/vistrails/core/interpreter/noncached.py b/vistrails/core/interpreter/noncached.py
new file mode 100644
index 0000000..2666b7d
--- /dev/null
+++ b/vistrails/core/interpreter/noncached.py
@@ -0,0 +1,69 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core import modules
+from vistrails.core.common import *
+from vistrails.core.data_structures.bijectivedict import Bidict
+from vistrails.core.modules.vistrails_module import ModuleConnector, ModuleError
+from vistrails.core.utils import DummyView
+import copy
+import vistrails.core.interpreter.base
+import vistrails.core.interpreter.utils
+import vistrails.core.vistrail.pipeline
+import atexit
+
+# from core.modules.module_utils import FilePool
+
+################################################################################
+
+class Interpreter(vistrails.core.interpreter.cached.CachedInterpreter):
+
+ def clean_non_cacheable_modules(self):
+ non_cacheable_modules = [i for
+ (i, mod) in self._objects.iteritems()]
+ self.clean_modules(non_cacheable_modules)
+
+ __instance = None
+ @staticmethod
+ def get():
+ if not Interpreter.__instance:
+ instance = Interpreter()
+ Interpreter.__instance = instance
+ def cleanup():
+ instance._file_pool.cleanup()
+ atexit.register(cleanup)
+ return Interpreter.__instance
+
+
+################################################################################
diff --git a/vistrails/core/interpreter/utils.py b/vistrails/core/interpreter/utils.py
new file mode 100644
index 0000000..2190f99
--- /dev/null
+++ b/vistrails/core/interpreter/utils.py
@@ -0,0 +1,42 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import threading
+
+##############################################################################
+
+_lock = threading.Lock()
+def get_interpreter_lock():
+ return _lock
diff --git a/vistrails/core/keychain.py b/vistrails/core/keychain.py
new file mode 100644
index 0000000..c0c2ccd
--- /dev/null
+++ b/vistrails/core/keychain.py
@@ -0,0 +1,276 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Keychain keeps a dictionary of key/value pairs.
+It is useful for storing passwords during a vistrails session.
+The values are hashed given the key and the caller object id.
+A value can only be retrieved by the same object that set it.
+Use this at your own risk!
+
+"""
+import inspect
+import os
+import sys
+from vistrails.core import debug
+from vistrails.core.utils import VistrailsInternalError
+from itertools import izip
+
+import struct
+
+import unittest
+try:
+ import hashlib
+ md5_hash = hashlib.md5
+except ImportError:
+ import md5
+ md5_hash = md5.new
+
+##############################################################################
+
+class KeyChain(object):
+ """
+ """
+
+ def __init__(self):
+ """ initializes the internal dictionary"""
+ self.__keys = {}
+
+ def count(self):
+ """count() -> int
+ Returns the number of keys
+
+ """
+ return len(self.__keys.keys())
+
+ def clear(self):
+ """clear() -> None
+ clear the internal dictionary
+ """
+ self.__keys.clear()
+
+ def set_key(self, key, value):
+ """ set_key(key: str, value: str) -> None
+ Sets a key value pair in the internal dictionary
+
+ """
+ #get the arguments of the frame that called us
+ args = inspect.getargvalues(inspect.currentframe().f_back)[3]
+ try:
+ #this will return the instance of the object that called us
+ caller = id(args['self'])
+ newkey = str(caller)+str(key)
+ hashkey = md5_hash(newkey).hexdigest()[:16]
+ cryptvalue = crypt(hashkey,value)
+ self.__keys[hashkey] = cryptvalue
+
+ except KeyError:
+ debug.critical("KeyChain: You need to call this method inside "
+ "another a object's method")
+
+ def get_key(self, key):
+ """ get_key(key:str) -> str
+ Returns the value for the key. Only the object that set the key is
+ able to retrieve its value
+
+ """
+ result = ""
+ #get the arguments of the frame that called us
+ args = inspect.getargvalues(inspect.currentframe().f_back)[3]
+ try:
+ #this will return the instance of the object that called us
+ caller = id(args['self'])
+ newkey = str(caller)+str(key)
+ hashkey = md5_hash(newkey).hexdigest()[:16]
+ if self.__keys.has_key(hashkey):
+ return crypt(hashkey,self.__keys[hashkey])
+ else:
+ debug.debug("KeyChain: the key is not present or only the"
+ " object that set the key can get it")
+ return ""
+ except KeyError:
+ debug.critical("KeyChain: You need to call this method inside "
+ "another object's method")
+
+##############################################################################
+"""
+XTEA Block Encryption Algorithm
+
+Author: Paul Chakravarti (paul_dot_chakravarti_at_mac_dot_com)
+License: Public Domain
+
+This module provides a Python implementation of the XTEA block encryption
+algorithm (http://www.cix.co.uk/~klockstone/xtea.pdf).
+
+The module implements the basic XTEA block encryption algortithm
+(`xtea_encrypt`/`xtea_decrypt`) and also provides a higher level `crypt`
+function which symmetrically encrypts/decrypts a variable length string using
+XTEA in OFB mode as a key generator. The `crypt` function does not use
+`xtea_decrypt` which is provided for completeness only (but can be used
+to support other stream modes - eg CBC/CFB).
+
+This module is intended to provide a simple 'privacy-grade' Python encryption
+algorithm with no external dependencies. The implementation is relatively slow
+and is best suited to small volumes of data. Note that the XTEA algorithm has
+not been subjected to extensive analysis (though is believed to be relatively
+secure - see http://en.wikipedia.org/wiki/XTEA). For applications requiring
+'real' security please use a known and well tested algorithm/implementation.
+
+The security of the algorithm is entirely based on quality (entropy) and
+secrecy of the key. You should generate the key from a known random source and
+exchange using a trusted mechanism. In addition, you should always use a random
+IV to seed the key generator (the IV is not sensitive and does not need to be
+exchanged securely)
+
+ >>> import os
+ >>> iv = 'ABCDEFGH'
+ >>> z = crypt('0123456789012345','Hello There',iv)
+ >>> z.encode('hex')
+ 'fe196d0a40d6c222b9eff3'
+ >>> crypt('0123456789012345',z,iv)
+ 'Hello There'
+
+"""
+
+
+def crypt(key,data,iv='\00\00\00\00\00\00\00\00',n=32):
+ """
+ Encrypt/decrypt variable length string using XTEA cypher as
+ key generator (OFB mode)
+ * key = 128 bit (16 char)
+ * iv = 64 bit (8 char)
+ * data = string (any length)
+
+ >>> import os
+ >>> key = os.urandom(16)
+ >>> iv = os.urandom(8)
+ >>> data = os.urandom(10000)
+ >>> z = crypt(key,data,iv)
+ >>> crypt(key,z,iv) == data
+ True
+
+ """
+ def keygen(key,iv,n):
+ while True:
+ iv = xtea_encrypt(key,iv,n)
+ for k in iv:
+ yield ord(k)
+ xor = [ chr(x^y) for (x,y) in izip(map(ord,data),keygen(key,iv,n))]
+ return "".join(xor)
+
+def xtea_encrypt(key,block,n=32,endian="!"):
+ """
+ Encrypt 64 bit data block using XTEA block cypher
+ * key = 128 bit (16 char)
+ * block = 64 bit (8 char)
+ * n = rounds (default 32)
+ * endian = byte order (see 'struct' doc - default big/network)
+
+ >>> z = xtea_encrypt('0123456789012345','ABCDEFGH')
+ >>> z.encode('hex')
+ 'b67c01662ff6964a'
+
+ Only need to change byte order if sending/receiving from
+ alternative endian implementation
+
+ >>> z = xtea_encrypt('0123456789012345','ABCDEFGH',endian="<")
+ >>> z.encode('hex')
+ 'ea0c3d7c1c22557f'
+
+ """
+ v0,v1 = struct.unpack(endian+"2L",block)
+ k = struct.unpack(endian+"4L",key)
+ sum,delta,mask = 0L,0x9e3779b9L,0xffffffffL
+ for round in xrange(n):
+ v0 = (v0 + (((v1<<4 ^ v1>>5) + v1) ^ (sum + k[sum & 3]))) & mask
+ sum = (sum + delta) & mask
+ v1 = (v1 + (((v0<<4 ^ v0>>5) + v0) ^ (sum + k[sum>>11 & 3]))) & mask
+ return struct.pack(endian+"2L",v0,v1)
+
+def xtea_decrypt(key,block,n=32,endian="!"):
+ """
+ Decrypt 64 bit data block using XTEA block cypher
+ * key = 128 bit (16 char)
+ * block = 64 bit (8 char)
+ * n = rounds (default 32)
+ * endian = byte order (see 'struct' doc - default big/network)
+
+ >>> z = 'b67c01662ff6964a'.decode('hex')
+ >>> xtea_decrypt('0123456789012345',z)
+ 'ABCDEFGH'
+
+ Only need to change byte order if sending/receiving from
+ alternative endian implementation
+
+ >>> z = 'ea0c3d7c1c22557f'.decode('hex')
+ >>> xtea_decrypt('0123456789012345',z,endian="<")
+ 'ABCDEFGH'
+
+ """
+ v0,v1 = struct.unpack(endian+"2L",block)
+ k = struct.unpack(endian+"4L",key)
+ delta,mask = 0x9e3779b9L,0xffffffffL
+ sum = (delta * n) & mask
+ for round in xrange(n):
+ v1 = (v1 - (((v0<<4 ^ v0>>5) + v0) ^ (sum + k[sum>>11 & 3]))) & mask
+ sum = (sum - delta) & mask
+ v0 = (v0 - (((v1<<4 ^ v1>>5) + v1) ^ (sum + k[sum & 3]))) & mask
+ return struct.pack(endian+"2L",v0,v1)
+
+##############################################################################
+
+class A(object):
+ def set_key(self, chain, key, value):
+ chain.set_key(key,value)
+
+ def get_key(self, chain, key):
+ return chain.get_key(key)
+
+class TestKeyChain(unittest.TestCase):
+ def testusage(self):
+ keyChain = KeyChain()
+ this = A()
+ other = A()
+ #test key insertion
+ this.set_key(keyChain, "mykey.name", "value")
+ self.assertEquals(keyChain.count(),1)
+ #test key retrieval
+ value = this.get_key(keyChain, "mykey.name")
+ self.assertEquals(value, "value")
+ #test key protection
+ value = other.get_key(keyChain, "mykey.name")
+ self.assertEquals(value, "")
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/layout/__init__.py b/vistrails/core/layout/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/core/layout/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/core/layout/tree_layout.py b/vistrails/core/layout/tree_layout.py
new file mode 100644
index 0000000..d38c6fd
--- /dev/null
+++ b/vistrails/core/layout/tree_layout.py
@@ -0,0 +1,459 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file has the implementation of an algorithm to layout general
+rooted trees in a nice way. The "lw" in the file name "tree_layout_lw.py"
+stands for (L)inear (W)alker. This code is based on the paper:
+
+ Christoph Buchheim, Michael Junger, and Sebastian Leipert.
+ Improving walker's algorithm to run in linear time.
+ In Stephen G. Kobourov and Michael T. Goodrich, editors, Graph
+ Drawing, volume 2528 of Lecture Notes in Computer Science, pages
+ 344-353. Springer, 2002.
+
+which is a faster (it is linear!) way to compute the tree layout
+proposed by Walker than the algorithm described by him.
+The original paper is:
+
+ John Q. Walker II.
+ A node-positioning algorithm for general trees.
+ Softw., Pract. Exper., 20(7):685-705, 1990.
+
+"""
+
+class TreeLW:
+ """
+ The input to the algorithm must be a tree
+ in this format.
+
+ """
+ def __init__(self):
+ self.nodes = []
+ self.maxLevel = 0
+
+ def root(self):
+ return self.nodes[0]
+
+ def addNode(self, parentNode, width, height, object = None):
+ newNode = NodeLW(width,height,object)
+ self.nodes.append(newNode)
+
+ # add
+ if parentNode != None:
+ parentNode.addChild(newNode)
+
+ # update max level
+ self.maxLevel = max(self.maxLevel,newNode.level)
+ return newNode
+
+ def changeParentOfNodeWithNoParent(self, parentNode, childNode):
+ if childNode.parent != None:
+ raise ValueError("Node already has a parent")
+
+ parentNode.addChild(childNode)
+ maxLevel = self.__dfsUpdateLevel(childNode)
+
+ # update max level
+ self.maxLevel = max(self.maxLevel, maxLevel)
+
+ def __dfsUpdateLevel(self, node):
+ if node.parent == None:
+ node.level = 0
+ else:
+ node.level = node.parent.level + 1
+ maxLevel = node.level
+ for child in node.childs:
+ maxLevel = max(maxLevel, self.__dfsUpdateLevel(child))
+ return maxLevel
+
+ def boundingBox(self):
+ kbb = KeepBoundingBox()
+ for w in self.nodes:
+ kbb.addPoint(w.x-w.width/2.0, w.y-w.height/2.0)
+ kbb.addPoint(w.x+w.width/2.0, w.y+w.height/2.0)
+ return kbb.getBoundingBox()
+
+ def getMaxNodeHeightPerLevel(self):
+ result = [0] * (self.maxLevel+1)
+ for w in self.nodes:
+ level = w.level
+ result[level] = max(result[level],w.height)
+ return result
+
+ @staticmethod
+ def randomTree(n, k=10000000):
+ p = [0] * n
+ import random
+ for i in xrange(1, n):
+ minIndex = max(i-k, 0)
+ index = random.randint(minIndex, i-1) # random number in {0,1,2,...,i-1}
+ p[i] = index
+ t = TreeLW()
+ nodes= []
+ for i in xrange(n):
+ if i==0:
+ parent= None
+ else:
+ parent=nodes[p[i]]
+ width = 5 + 10*random.random()
+ height = 5 + 10*random.random()
+ nodes.append(t.addNode(parent,width,height,i))
+ return t
+
+class KeepBoundingBox:
+ def __init__(self):
+ self.minx = None
+ self.miny = None
+ self.maxx = None
+ self.maxy = None
+ self.size = 0
+
+ def addPoint(self,x,y):
+ if self.minx == None or self.minx > x:
+ self.minx = x
+ if self.miny == None or self.miny > y:
+ self.miny = y
+ if self.maxx == None or self.maxx < x:
+ self.maxx = x
+ if self.maxy == None or self.maxy < y:
+ self.maxy = y
+ self.size = self.size + 1
+
+ def getBoundingBox(self):
+ return [self.minx, self.miny, self.maxx-self.minx, self.maxy - self.miny]
+
+class NodeLW:
+ """
+ Node of the tree with all the auxiliar
+ variables needed to the LW algorithm.
+ The fields width, height and object
+ are given as input. The first two are
+ used to layout while the last one might
+ be used by the user of this class.
+
+ """
+ def __init__(self, width, height, object = None):
+ self.width = width
+ self.height = height
+ self.object = object
+
+ self.childs = []
+
+ self.parent = None
+ self.index = 0
+
+ # level of the node
+ self.level = 0
+
+ # intermediate variables for
+ # layout algorithm
+ self.mod = 0
+ self.prelim = 0
+ self.ancestor = None
+ self.thread = None
+ self.change = 0
+ self.shift = 0
+
+ # final center position
+ self.x = 0
+ self.y = 0
+
+ def getNumChilds(self):
+ return len(self.childs)
+
+ def hasChild(self):
+ return len(self.childs) > 0
+
+ def addChild(self, node):
+ self.childs.append(node)
+ node.index = len(self.childs) - 1
+ node.parent = self
+ node.level = self.level + 1
+
+ def isLeaf(self):
+ return len(self.childs) == 0
+
+ def leftChild(self):
+ return self.childs[0]
+
+ def rightChild(self):
+ return self.childs[len(self.childs)-1]
+
+ def leftSibling(self):
+ if self.index > 0:
+ return self.parent.childs[self.index-1]
+ else:
+ return None
+
+ def leftMostSibling(self):
+ if self.parent != None:
+ return self.parent.childs[0]
+ else:
+ return self
+
+ def isSiblingOf(self, v):
+ return self.parent == v.parent and self.parent != None
+
+class TreeLayoutLW:
+
+ """
+ TreeLayoutLW: the LW stands for Linear Walker.
+
+ This code is based on the paper:
+
+ Christoph Buchheim, Michael Junger, and Sebastian Leipert.
+ Improving walker's algorithm to run in linear time.
+ In Stephen G. Kobourov and Michael T. Goodrich, editors, Graph
+ Drawing, volume 2528 of Lecture Notes in Computer Science, pages
+ 344-353. Springer, 2002.
+
+ which is a faster (linear) way to compute the tree layout
+ proposed by Walker than the algorithm described by him.
+ The original paper is:
+
+ John Q. Walker II.
+ A node-positioning algorithm for general trees.
+ Softw., Pract. Exper., 20(7):685-705, 1990.
+ """
+
+ # vertical alignment of nodes in the
+ # level band: TOP, MIDDLE, BOTTOM
+ TOP = 0
+ MIDDLE = 1
+ BOTTOM = 2
+
+ def __init__(self, tree, vertical_alignment=1, xdistance=10, ydistance=10):
+ self.xdistance = xdistance
+ self.ydistance = ydistance
+ self.tree = tree
+ self.vertical_alignment = vertical_alignment
+ self.treeLayout()
+
+ def treeLayout(self):
+ for v in self.tree.nodes:
+ v.mod = 0
+ v.thread = None
+ v.ancestor = v
+
+ r = self.tree.root()
+ self.firstWalk(r)
+ self.secondWalk(r, -r.prelim)
+ self.setVerticalPositions()
+
+ def setVerticalPositions(self):
+
+ # set y position
+ maxNodeHeightPerLevel = self.tree.getMaxNodeHeightPerLevel()
+ info_level = []
+ position_level = 0
+ for level in xrange(len(maxNodeHeightPerLevel)):
+ height_level = maxNodeHeightPerLevel[level]
+ info_level.append((position_level,height_level))
+ position_level += self.ydistance + height_level
+
+ #
+ for w in self.tree.nodes:
+ level = w.level
+ position_level, height_level = info_level[level]
+ if self.vertical_alignment == TreeLayoutLW.TOP:
+ w.y = position_level + w.height/2.0
+ elif self.vertical_alignment == TreeLayoutLW.MIDDLE:
+ w.y = position_level + height_level/2.0
+ else: # bottom
+ w.y = position_level + height_level - w.height/2.0
+
+
+ def gap(self, v1, v2):
+
+ return self.xdistance + (v1.width + v2.width)/2.0
+
+
+ def firstWalk(self, v):
+
+ if v.isLeaf():
+ v.prelim = 0
+ w = v.leftSibling()
+ if w != None:
+ v.prelim = w.prelim + self.gap(w,v)
+
+ else:
+
+ defaultAncestor = v.leftChild()
+ for w in v.childs:
+ self.firstWalk(w)
+ defaultAncestor = self.apportion(w, defaultAncestor)
+ self.executeShifts(v)
+
+ midpoint = (v.leftChild().prelim + v.rightChild().prelim) / 2.0
+
+ w = v.leftSibling()
+ if w != None:
+ v.prelim = w.prelim + self.gap(w,v)
+ v.mod = v.prelim - midpoint
+ else:
+ v.prelim = midpoint
+
+
+ def apportion(self, v, defaultAncestor):
+
+ """
+ Apportion: to divide and assign proportionally.
+
+ Suppose the the left siblings of "v" are all aligned.
+ Now align the subtree with root "v" (note: the correct
+ alignment of the left siblings of "v" are encoded
+ in the auxiliar variables, the x and y
+ are not correct; only in the end the correct
+ values are assigned to x and y).
+ By property (*) in Section 4 the gratest
+ distinct ancestor of a node "w" in the
+ subtrees at rooted at the left siblings of "v"
+ is w.ancestor if this value is a left sibling
+ of v otherwise it is "defaultAncestor".
+
+ """
+ w = v.leftSibling()
+ if w != None:
+ # p stands for + or plus (right subtree)
+ # m stands for - or minus (left subtree)
+ # i stands for inside
+ # o stands for outside
+ # v stands for vertex
+ # s stands for shift
+ vip = vop = v
+ vim = w
+ vom = vip.leftMostSibling()
+ sip = vip.mod
+ sop = vop.mod
+ sim = vim.mod
+ som = vom.mod
+ while self.nextRight(vim) != None and self.nextLeft(vip) != None:
+
+ vim = self.nextRight(vim)
+ vip = self.nextLeft(vip)
+ vom = self.nextLeft(vom)
+ vop = self.nextRight(vop)
+
+ vop.ancestor = v
+
+ shift = (vim.prelim + sim) - (vip.prelim + sip) + self.gap(vim,vip)
+
+ if shift > 0:
+ self.moveSubtree(self.ancestor(vim,v,defaultAncestor),v,shift)
+ sip += shift
+ sop += shift
+
+ sim += vim.mod
+ sip += vip.mod
+ som += vom.mod
+ sop += vop.mod
+
+ if self.nextRight(vim) != None and self.nextRight(vop) == None:
+ vop.thread = self.nextRight(vim)
+ vop.mod += sim - sop
+
+ if self.nextLeft(vip) != None and self.nextLeft(vom) == None:
+ vom.thread = self.nextLeft(vip)
+ vom.mod += sip - som
+ defaultAncestor = v
+
+ return defaultAncestor
+
+ def nextLeft(self, v):
+ if v.hasChild():
+ return v.leftChild()
+ else:
+ return v.thread
+
+ def nextRight(self, v):
+ if v.hasChild():
+ return v.rightChild()
+ else:
+ return v.thread
+
+ def moveSubtree(self, wm, wp, shift):
+ subtrees = float(wp.index - wm.index)
+ wp.change += -shift/subtrees
+ wp.shift += shift
+ wm.change += shift/subtrees
+ wp.prelim += shift
+ wp.mod += shift
+
+ def executeShifts(self, v):
+ shift = 0
+ change = 0
+ for i in xrange(v.getNumChilds()-1,-1,-1):
+ w = v.childs[i]
+ w.prelim += shift
+ w.mod += shift
+ change += w.change
+ shift += w.shift + change
+
+ def ancestor(self, vim, v, defaultAncestor):
+ if vim.ancestor.isSiblingOf(v):
+ return vim.ancestor
+ else:
+ return defaultAncestor
+
+ def secondWalk(self, v, m):
+ v.x = v.prelim + m
+ for w in v.childs:
+ self.secondWalk(w, m + v.mod)
+
+# graph
+if __name__ == "__main__":
+
+ t = TreeLW()
+
+ a = t.addNode(None,1,1,"a")
+
+ b = t.addNode(a,1,1,"b")
+ c = t.addNode(a,1,1,"c")
+ d = t.addNode(a,1,1,"d")
+
+ e = t.addNode(b,1,1,"e")
+ f = t.addNode(b,1,1,"f")
+ g = t.addNode(d,1,1,"g")
+ h = t.addNode(d,1,1,"h")
+
+ i = t.addNode(f,1,1,"i")
+ j = t.addNode(f,1,1,"j")
+ k = t.addNode(h,1,1,"k")
+ l = t.addNode(h,1,1,"l")
+ m = t.addNode(h,1,1,"m")
+ n = t.addNode(h,1,1,"n")
+ o = t.addNode(h,1,1,"o")
+
+ layout = TreeLayoutLW(t)
+
diff --git a/vistrails/core/layout/version_tree_layout.py b/vistrails/core/layout/version_tree_layout.py
new file mode 100644
index 0000000..4854381
--- /dev/null
+++ b/vistrails/core/layout/version_tree_layout.py
@@ -0,0 +1,203 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""
+Interface Vistrails - TreeLayoutLW to align version trees.
+Originally written by Lauro D. Lins.
+
+"""
+from tree_layout import TreeLW, NodeLW, TreeLayoutLW
+from vistrails.core.data_structures.point import Point
+
+################################################################################
+
+class NodeVistrailsTreeLayoutLW(object):
+ """
+ Preserving the interface that version_view
+ expects with the DotNode.
+
+ """
+ def __init__(self):
+ """ DotNode() -> DotNode
+ Initialize DotNode as a data structure holding geometry info
+
+ """
+ self.p = Point(0,0)
+ self.height = 0.0
+ self.width = 0.0
+ self.id = 0
+
+ def move(self, x, y):
+ """ move(x: float, y: float) -> None
+
+ """
+ self.p.x = self.p.x + x
+ self.p.y = self.p.y + y
+
+class VistrailsTreeLayoutLW(object):
+ """
+ DotLayout is the graph outputed from Dotty which will be used and
+ parsed by version tree view
+
+ """
+ def __init__(self, text_width_f, text_height, text_horizontal_margin,
+ text_vertical_margin):
+ """ DotLayout() -> DotLayout()
+ Initialize DotNode as a data structure holding graph structure
+
+ """
+ self.text_width_f = text_width_f
+ self.text_height = text_height
+ self.text_horizontal_margin = text_horizontal_margin
+ self.text_vertical_margin = text_vertical_margin
+ self.nodes = {}
+ self.height = 0.0
+ self.scale = 0.0
+ self.width = 0.0
+
+ def generateTreeLW(self, vistrail, graph):
+ """ output_vistrail_graph(f: str) -> None
+ Using vistrail and graph to generate layout
+
+ """
+
+ # create list of nodes
+ X = set()
+
+ # include the root manually
+ nodes = [(0,"")]
+ X.add(0)
+
+ # include the tagged nodes
+ for id, tag_name in vistrail.get_tagMap().iteritems():
+ if id in graph.vertices:
+ nodes.append((id, tag_name))
+ X.add(id)
+
+ # mount list of edges (parent, child).
+ # preserving the order given by
+ # "graph.edges_from()".
+ edges = []
+ for id in graph.vertices:
+ froom = graph.edges_from(id)
+ for (first,second) in froom:
+ # print "arc %d -> %d" % (id, first)
+ edges.append((id,first))
+ if id not in X:
+# nodes.append((id," "))
+ nodes.append((id, vistrail.get_description(id)))
+ X.add(id)
+ if first not in X:
+# nodes.append((first," "))
+ nodes.append((first, vistrail.get_description(first)))
+ X.add(first)
+
+ # get widths and heights for the nodes
+ empty_width = self.text_horizontal_margin + self.text_width_f(" " * 5)
+
+ # default height for all nodes
+ height = self.text_height + self.text_vertical_margin
+
+ # create an empty tree
+ tree = TreeLW()
+
+ # create map from id to tree node
+ mapTreeNodes = {}
+
+ # add the remaining nodes
+ for id, tag in nodes:
+ width = self.text_horizontal_margin + self.text_width_f(tag)
+ width = max(width, empty_width)
+ # print "add node to the tree %d %s" % (id, tag)
+ mapTreeNodes[id] = tree.addNode(None,width,height,(id,tag))
+
+ # preserve the order of the edges
+ # to add the childs to their parents
+ for (parentId, childId) in edges:
+ # print "add arc into tree %d -> %d" % (parentId, childId)
+ parent = mapTreeNodes[parentId]
+ child = mapTreeNodes[childId]
+# if child.parent != None:
+# print "child already has a parent!!! %d -> %d" % (parentId, childId)
+# raise ValueError("Node already has a parent")
+ tree.changeParentOfNodeWithNoParent(parent, child)
+
+ # return the tree
+ return tree
+
+ def layout_from(self, vistrail, graph):
+ """ layout_from(vistrail: VisTrail, graph: Graph) -> None
+ Take a graph from VisTrail version and use Dotty to lay it out
+
+ """
+
+ tree = self.generateTreeLW(vistrail, graph)
+
+ min_horizontal_separation = 20
+ min_vertical_separation = 50
+
+ layout = TreeLayoutLW(tree, TreeLayoutLW.TOP,
+ min_horizontal_separation,
+ min_vertical_separation)
+
+ # prepare the result
+ self.nodes = {}
+ for v in tree.nodes:
+ id, tag = v.object
+ newNode = NodeVistrailsTreeLayoutLW()
+ newNode.p = Point(v.x, v.y)
+ newNode.width = v.width
+ newNode.height = v.height
+ newNode.id = id
+ # newNode.label = tag
+ self.nodes[id] = newNode
+
+ # keep track of the bounding box
+ # of the whole tree
+ (minx, miny, width, height) = tree.boundingBox()
+ self.scale = 0.0
+ self.width = width
+ self.height = height
+
+ def move_node(self, id, x, y):
+ """ move_node(id: int, x: float, y: float) -> None
+
+ """
+ self.nodes[id].move(x,y)
+
+ def add_node(self, id, node):
+ """ add_node(id: int, node: NodeVistrailsTreeLayoutLW) -> None
+
+ """
+ self.nodes[id] = node
diff --git a/vistrails/core/layout/workflow_layout.py b/vistrails/core/layout/workflow_layout.py
new file mode 100644
index 0000000..3b4e7e7
--- /dev/null
+++ b/vistrails/core/layout/workflow_layout.py
@@ -0,0 +1,774 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This code creates layouts for workflow digraphs.
+Originally written by Lauro D. Lins.
+
+"""
+
+####################################################
+
+def uniquify(seq, idfun=None):
+ # order preserving
+ if idfun is None:
+ def idfun(x): return x
+ seen = {}
+ result = []
+ for item in seq:
+ marker = idfun(item)
+ # in old Python versions:
+ # if seen.has_key(marker)
+ # but in new ones:
+ if marker in seen: continue
+ seen[marker] = 1
+ result.append(item)
+ return result
+
+
+class Defaults(object):
+ u = 10.0
+ label_margin = 20.0
+
+class Vec2(object):
+ def __init__(self, x, y):
+ self.x = x
+ self.y = y
+ def set(self, x, y):
+ self.x = x
+ self.y = y
+ def __add__(self, other):
+ if isinstance(other, (float, int)):
+ return Vec2(self.x + other, self.y + other)
+ else:
+ return Vec2(self.x + other.x, self.y + other.y)
+ def __radd__(self, other):
+ return self.__add__(other)
+ def __sub__(self, other):
+ if isinstance(other, (float, int)):
+ return Vec2(self.x - other, self.y - other)
+ else:
+ return Vec2(self.x - other.x, self.y - other.y)
+ def __rsub__(self, other):
+ return self.__sub__(other)
+ def __mul__(self, other):
+ if isinstance(other, (float, int)):
+ return Vec2(self.x * other, self.y * other)
+ else:
+ return Vec2(self.x * other.x, self.y * other.y)
+ def __rmul__(self, other):
+ return self.__mul__(other)
+ def dot(self, other):
+ return self.x * other.x + self.y * other.y
+ def __str__(self):
+ return "(%.2f, %.2f)" % (self.x, self.y)
+ def __repr__(self):
+ return "(%.2f, %.2f)" % (self.x, self.y)
+
+####################################################
+
+UNDEFINED_LAYER = None
+INPUT_PORT, OUTPUT_PORT = 1,2
+
+class Pipeline(object):
+
+ def __init__(self):
+ self.modules = []
+ self.connections = []
+
+ def createModule(self, shortname, name, num_input_ports, num_output_ports, prev_x=None):
+ mod = Module(self, len(self.modules), shortname, name, num_input_ports, num_output_ports, prev_x)
+ self.modules.append(mod)
+ return mod
+
+ def createConnection(self, mod_source, port_source_idx, mod_target, port_target_idx):
+ source_port = mod_source.getOutputPort(port_source_idx)
+ target_port = mod_target.getInputPort(port_target_idx)
+
+ conn = Connection(self, source_port, target_port)
+ source_port.addConnection(conn)
+ target_port.addConnection(conn)
+
+ self.connections.append(conn)
+
+ return conn
+
+ # def updateCache(self):
+ # self.cached_num_modules = len(self.modules)
+ # self.cached_num_connections = len(self.connections)
+
+
+
+class Module(object):
+
+ def __init__(self, workflow, key, shortname, name, num_input_ports, num_output_ports, prev_x=None):
+
+ self.workflow = workflow
+ self.key = key
+ self.shortname = shortname
+ self.name = name
+
+ self.input_ports = [ Port(self, INPUT_PORT, i) for i in xrange(num_input_ports ) ]
+ self.output_ports = [ Port(self, OUTPUT_PORT, i) for i in xrange(num_output_ports) ]
+
+ self.layout_layer_number = UNDEFINED_LAYER
+ self.layout_layer_index = 0
+
+ self.cached = False
+ self.cached_in_degree = 0
+ self.cached_out_degree = 0
+
+ self.cached_connections_succ = [] # successor modules
+ self.cached_connections_pred = [] # predecessor modules
+
+ self.cached_succ = [] # successor modules
+ self.cached_pred = [] # predecessor modules
+
+ self.cached_num_succ = 0
+ self.cached_num_pred = 0
+
+ self.flags = 0
+
+ self.layout_pos = Vec2(0,0)
+ self.layout_dim = Vec2(1,1)
+
+ self.prev_x = prev_x
+
+ def clearFlags(self):
+ self.flags = 0
+
+ def updateCache(self):
+ self.cached_in_degree = self.getInDegree()
+ self.cached_out_degree = self.getOutDegree()
+
+ self.cached_connections_succ = [] # successor modules
+ self.cached_connections_pred = [] # predecessor modules
+
+ # cached succ
+ self.cached_succ = []
+ for p in self.output_ports:
+ p.collectOppositeModules(self.cached_succ)
+ self.cached_connections_succ.extend([c for c in p.connections])
+
+ uniquify(self.cached_succ)
+ # print "%s's of cached_succ: " % (self.shortname),
+ # print [m.name for m in self.cached_succ]
+
+
+ # cached pred
+ self.cached_pred = []
+ for p in self.input_ports:
+ p.collectOppositeModules(self.cached_pred)
+ self.cached_connections_pred.extend([c for c in p.connections])
+ uniquify(self.cached_pred)
+
+ self.cached_num_succ = len(self.cached_succ)
+ self.cached_num_pred = len(self.cached_pred)
+
+ self.cached = True
+
+ def getInputPort(self, idx):
+ return self.input_ports[idx]
+
+ def getOutputPort(self, idx):
+ return self.output_ports[idx]
+
+ def getInDegree(self):
+ count = 0
+ for ip in self.input_ports:
+ count += ip.getNumConnections()
+ return count
+
+ def getOutDegree(self):
+ count = 0
+ for ip in self.output_ports:
+ count += ip.getNumConnections()
+ return count
+
+
+
+class Connection(object):
+ def __init__(self, workflow, source_port, target_port):
+ self.workflow = workflow
+ self.source_port = source_port # an output port
+ self.target_port = target_port # an input port
+
+ def getOppositePort(self, port):
+ if self.source_port == port:
+ return self.target_port
+ elif self.target_port == port:
+ return self.source_port
+ else:
+ raise ValueError("oppositePort problem: no opposite port")
+
+
+
+class Port(object):
+
+ def __init__(self, module, kind, index):
+ self.module = module
+ self.kind = kind
+ self.index = index
+ self.connections = []
+
+ self.layout_pos = Vec2(0,0)
+ self.layout_dim = Vec2(1,1)
+
+ def getNumConnections(self):
+ return len(self.connections)
+
+ def addConnection(self, connection):
+ self.connections.append(connection)
+
+ # module is not cached
+ self.module.cached = False
+
+ def collectOppositeModules(self, lst):
+ for c in self.connections:
+ lst.append(c.getOppositePort(self).module)
+
+
+
+class ItemDFS(object):
+ def __init__(self, module, index, max_index):
+ self.module = module
+ self.index = index
+ self.max_index = max_index
+
+ # the creation of ItemDFS implies
+ # that it will be stacked on the DFSIterator
+ # and the module flag goes from 0 to 1
+ self.module.flags = 1
+
+
+
+class DFSIterator(object):
+
+ def __init__(self, workflow, update_module_cache=False):
+ self.stack = []
+
+ # stack source modules
+ for m in workflow.modules:
+
+ m.clearFlags()
+
+ if not m.cached:
+ m.updateCache()
+
+ if m.cached_in_degree == 0: # source modules
+ m.flags = 1
+ self.stack.append(ItemDFS(m,-1,m.cached_num_succ))
+
+
+ def next(self):
+
+ while len(self.stack) > 0:
+
+ top = self.stack[-1]
+ top.index += 1
+ mod = top.module
+
+ #DEBUG
+ #print "pop %s index %d max_index %d" % (mod.shortname, top.index, top.max_index)
+
+ if top.index >= top.max_index:
+ self.stack.pop()
+ return mod
+ else:
+ next_mod = mod.cached_succ[top.index]
+ if next_mod.flags > 0:
+ continue
+ next_mod.flags = 1
+ self.stack.append(ItemDFS(next_mod, -1, next_mod.cached_num_succ))
+
+ return None
+
+class Layer(object):
+
+ def __init__(self, index):
+ self.index = index
+ self.modules = []
+
+ self.y = 0.0
+
+ self.max_module_height = 0.0
+ self.sum_modules_width = 0.0
+
+ def addModule(self, module):
+ self.modules.append(module)
+
+ self.sum_modules_width += module.layout_dim.x
+ self.max_module_height = max(self.max_module_height,module.layout_dim.y)
+
+ # print "addModule(self, module): max_module_height = ", self.max_module_height
+
+
+
+class Layers(object):
+
+ def __init__(self):
+ self.layers = []
+
+ def addModule(self, module, layer_number):
+
+ num_layers = len(self.layers)
+
+ # print "num_layers", num_layers
+ # print "layer_number ", layer_number
+ # print "layers",self.layers
+
+ if layer_number >= num_layers:
+ self.layers.extend([Layer(i) for i in xrange(num_layers,layer_number+1)])
+
+ layer = self.layers[layer_number]
+ layer.addModule(module)
+
+
+class Page(object):
+ def __init__(self, page_x0, page_y0, page_width, page_height):
+ self.x0 = page_x0
+ self.y0 = page_y0
+ self.width = page_width
+ self.height = page_height
+
+ def __str__(self):
+ # print self.x0
+ # print self.y0
+ # print self.width
+ # print self.height
+ return "%.2f %.2f %.2f %.2f" % (self.x0, self.y0, self.width, self.height)
+
+class WorkflowLayout(object):
+ def __init__(self, wf, module_size_f, module_margin, port_size,
+ port_interspace):
+ self.wf = wf
+ self.module_size_f = module_size_f
+ self.module_margin = module_margin
+ self.port_size = port_size
+ self.port_interspace = port_interspace
+
+ #
+ # Compute sizes
+ #
+ def compute_module_sizes(self):
+ wf = self.wf # wf is a workflow
+
+ u = Defaults.u # u is the base unit in points to derive the other sizes
+
+ #
+ # A module visual representation consists of three rows
+ #
+ # first row: input ports
+ # mid row: text label
+ # third row: output ports
+ #
+ row_margin = 0.20 * u
+ row_height = u + 2 * row_margin
+
+ module_height = 3 * row_height # three stripes of
+
+ #DEBUG
+ #print "module_height = ", module_height
+
+ module_text_margin = u
+ module_ports_margin = row_margin
+
+ # port_margin = 0.30 * u
+ # port_interspace = 0.15 * u
+ # port_size = 0.75 * u
+
+ for module in wf.modules:
+ module_width, module_height = self.module_size_f(module)
+
+ # [DK] why do we have to do this here?
+ if not module.cached:
+ module.updateCache()
+
+ max_num_ports = max(len(module.input_ports), len(module.output_ports))
+
+ # ports_width = 2*module_ports_margin + max_num_ports * u + (max_num_ports-1) * module_ports_margin
+ # text_width = 2*module_text_margin + len(module.name) * u * 0.6
+
+ # module_width = max(ports_width, text_width)
+
+ module.layout_pos.set(0,0)
+ module.layout_dim.set(module_width, module_height)
+
+ for port_list, do_reverse, d in [(module.input_ports, False, -1),
+ (module.output_ports, True, 1)]:
+ if do_reverse:
+ port_iter = reversed(port_list)
+ else:
+ port_iter = port_list
+
+ for i, p in enumerate(port_iter):
+ p.layout_pos.set(d * module_width/2.0 -
+ d * self.module_margin[0] -
+ d * (i + 0.5) * self.port_size[0] -
+ d * self.port_interspace * i,
+ d * (module_height/2.0 -
+ self.module_margin[1] -
+ self.port_size[1]))
+ p.layout_dim.set(*self.port_size)
+
+ # for p in module.input_ports:
+ # p.layout_pos.set(-module_width/2.0 + # initial position
+ # port_margin + # ports margin
+ # (p.index + 0.5) * port_size + # widths of previous ports + half port width
+ # port_interspace * p.index, # sum of previous interspace
+ # -module_height / 2.0 + row_height / 2.0 )
+ # p.layout_dim.set(*port_size)
+
+
+ # op = list(module.output_ports)
+ # op.reverse()
+ # for i in xrange(len(op)):
+ # p = op[i]
+ # p.layout_pos.set( module_width/2.0 -
+ # port_margin -
+ # (i + 0.5) * port_size -
+ # port_interspace * i,
+ # +module_height/2.0 - row_height / 2.0 )
+ # p.layout_dim.set(port_size, port_size)
+
+ def assign_modules_to_layers(self):
+ wf = self.wf
+
+ iterator = DFSIterator(wf)
+
+ # topologically sorted permulation of the modules
+ permutation = []
+ while True:
+ mod = iterator.next()
+ if mod == None:
+ break
+ permutation.append(mod)
+ permutation.reverse()
+
+ # define layers
+ i = 0
+ for module in permutation:
+ if module.cached_num_pred == 0:
+ module.layout_layer_number = 0
+ else:
+ module.layout_layer_number = 1 + max([pred.layout_layer_number for pred in module.cached_pred])
+
+ # use permutation index as a the sort key to define
+ # the initial permutation of the modules in each layer
+ module.layout_layer_index = i
+ i += 1
+
+
+ # log
+ # for module in permutation:
+ # print "layer of %s = %d" % (module.shortname, module.layout_layer_number)
+
+ # adjust free modules (a free module in this context is
+ # a module whose minimum successor layer and maximum predecessor layer
+ # have more than one intermediate layer in between
+
+ #
+ # TODO: adjust layer
+ for module in permutation:
+ if module.cached_num_pred == 0 and module.cached_num_succ > 0:
+ module.layout_layer_number = min([succ.layout_layer_number for succ in module.cached_succ]) - 1
+ # else:
+ # a = min([succ.layout_layer_number for succ in module.cached_succ]) - 1
+ # print "layer of %s = %d" % (module.shortname, module.layout_layer_number)
+
+ def assign_module_to_layers_no_gaps(self):
+ if len(self.wf.modules) == 0:
+ return
+
+ visited = set()
+ min_layer = [0]
+ def set_module_layer_number(module, layer_number):
+ module.layout_layer_number = layer_number
+ visited.add(module)
+ min_layer[0] = min(min_layer[0], layer_number)
+ for port in module.input_ports:
+ for conn in port.connections:
+ if conn.source_port.module not in visited:
+ set_module_layer_number(conn.source_port.module, layer_number-1)
+ for port in module.output_ports:
+ for conn in port.connections:
+ if conn.target_port.module not in visited:
+ set_module_layer_number(conn.target_port.module, layer_number+1)
+
+ set_module_layer_number(self.wf.modules[0], 0)
+
+ #adjust all layers numbers so that the min is 0
+ if min_layer[0] < 0:
+ for module in self.wf.modules:
+ module.layout_layer_number -= min_layer[0]
+
+ def assign_module_permutation_to_each_layer(self, preserve_order=False):
+ wf = self.wf
+
+ # create layers
+ layers = Layers()
+ for module in wf.modules:
+ layers.addModule(module, module.layout_layer_number)
+
+ # sort modules by the current value of layout_layer_index
+ for layer in layers.layers:
+ layer.modules.sort(lambda a,b: a.layout_layer_index - b.layout_layer_index)
+ for i in xrange(len(layer.modules)):
+ layer.modules[i].layout_layer_index = i
+
+ #
+ num_layers = len(layers.layers)
+
+ lastModified = [-1 for i in xrange(num_layers)]
+
+ #
+ # sweep down and up reducing the number of crossings
+ # using the barycentric method (heuristic)
+ #
+ iteration = 0
+ updates = len(wf.modules)
+ while updates > 0 and iteration < 100:
+
+ # print "iteration: ", iteration
+
+ updates = 0
+
+ DOWN, UP = 1, -1
+ for direction in [DOWN, UP]:
+
+ # print " direction:", direction
+
+ delta = 1 if direction == DOWN else -1
+
+ i0, i1 = (0,num_layers) if direction == DOWN else (num_layers-1,-1)
+
+ # sweep "direction"
+ for i in xrange(i0+delta,i1,direction):
+ # for i in xrange(2,4):
+
+
+ i_prev = i-delta
+ # print " layer:" , i
+ # print " layer_prev:", i_prev
+
+ layer = layers.layers[i]
+
+ # if one module on layer then continue
+ num_modules = len(layer.modules)
+ if num_modules == 1:
+ continue
+
+ # if nothing chaged on this layer and the "previous" layer (in the sweep direction)
+ # in the last iteration then nothing needs to be done
+ if iteration - lastModified[i_prev] > 1 and \
+ iteration - lastModified[i] > 1:
+ continue
+
+ # apply barycentric permutation to layer "i" using neighbors on layer "i + delta"
+ barycenters = [-1] * num_modules
+ for j in xrange(num_modules):
+
+ module = layer.modules[j]
+ connections = \
+ module.cached_connections_pred \
+ if direction == DOWN else \
+ module.cached_connections_succ
+
+ value = 0.0
+ for c in connections:
+ opposite_port = c.source_port if direction == DOWN else c.target_port
+ value += opposite_port.module.layout_layer_index + opposite_port.index/100.0
+ if len(connections) > 0:
+ value /= 1.0 * len(connections)
+ barycenters[j] = value
+
+ for j in xrange(1,num_modules):
+ if barycenters[j] < 0:
+ barycenters[j] = barycenters[j-1] + 1e-5
+
+ # print " barycenters: ", barycenters
+
+
+ new_order = [(barycenters[j], layer.modules[j]) for j in xrange(num_modules)]
+ new_order.sort()
+
+ # print " indices before: ", [u.layout_layer_index for u in layer.modules]
+ # print " indices after: ", [aux[0] for aux in new_order]
+ # print " names before = ",[mod.name for mod in layer.modules]
+
+ for j in xrange(num_modules):
+ module = new_order[j][1]
+ if module.layout_layer_index != j:
+ # print " module indexed %d goes to index %d" % (module.layout_layer_index,j)
+ lastModified[i] = iteration
+ updates += 1
+
+ if lastModified[i] == iteration:
+ for j in xrange(num_modules):
+ module = new_order[j][1]
+ module.layout_layer_index = j
+
+
+ # sort using the last layout_layer_index
+ layer.modules.sort(lambda a,b: a.layout_layer_index - b.layout_layer_index)
+ # print " names after =",[mod.name for mod in layer.modules]
+
+
+ # print " updates: ", updates
+
+ # iteration
+ iteration += 1
+
+ # break
+ break
+
+ if preserve_order:
+ for layer in layers.layers:
+
+ # sort using the last layout_layer_index
+ layer.modules.sort(key=lambda x: x.layout_layer_index)
+
+ #separate modules that have no previous x value
+ temp = []
+ for i in reversed(range(len(layer.modules))):
+ if layer.modules[i].prev_x is None:
+ temp.append((i,layer.modules.pop(i)))
+
+ #sort on previous x
+ layer.modules.sort(key=lambda x: x.prev_x)
+
+ #put separated modules back in their original slot
+ for item in reversed(temp):
+ layer.modules.insert(item[0],item[1])
+
+ #reassign index
+ for i in range(len(layer.modules)):
+ layer.modules[i].layout_layer_index = i
+
+ #
+ # this method is "friend" of the classes above in the C++ sense:
+ # it can access and modify
+ #
+ def compute_layout(self, layer_x_separation, layer_y_separation):
+ wf = self.wf # wf is a workflow
+
+ # create layers
+ layers = Layers()
+ for module in wf.modules:
+ layers.addModule(module, module.layout_layer_number)
+
+ for layer in layers.layers:# sort using the last layout_layer_index
+ layer.modules.sort(lambda a,b: a.layout_layer_index - b.layout_layer_index)
+
+ # spread layers
+ min_x = max_x = 0.0
+ y = min_y = max_y = 0.0
+
+ top_layer = True
+
+ for layer in layers.layers:
+
+ # print "layer: ", layer.index
+
+ if not top_layer:
+ y += layer_y_separation
+ else:
+ top_layer = False
+
+
+ layer_half_height = layer.max_module_height / 2.0
+
+ # print "layer_half_height", layer_half_height
+
+ y += layer_half_height
+
+
+ # print "layer ", layer.index, " y = ", y
+
+ layer_num_modules = len(layer.modules)
+ layer_width = layer.sum_modules_width + (layer_num_modules-1) * layer_x_separation
+ layer_min_x = -layer_width/2.0
+
+ x = layer_min_x
+
+ # set module positions
+ for i in xrange(layer_num_modules):
+
+ if (i > 0):
+ x += layer_x_separation
+
+ module = layer.modules[i]
+
+ module_half_width = module.layout_dim.x / 2.0
+
+ x += module_half_width
+
+ module.layout_pos.set(x, y)
+
+ x += module_half_width
+
+ layer_max_x = x
+
+ min_x = min(min_x, layer_min_x)
+ max_x = max(max_x, layer_max_x)
+
+ y += layer_half_height
+
+ max_y = y # y only got smaller
+
+
+ #
+ page_x_margin = 3 * Defaults.u
+ page_y_margin = 3 * Defaults.u
+
+ page_util_width = max_x - min_x
+ page_util_height = max_y - min_y
+
+ page_width = page_util_width + page_x_margin * 2
+ page_height = page_util_height + page_y_margin * 2
+
+ page_x0 = -page_width /2.0
+ page_y0 = -page_y_margin
+
+ page = Page(page_x0, page_y0, page_width, page_height)
+
+ return page
+
+ def run_all(self, layer_x_separation=50, layer_y_separation=50, preserve_order=False, no_gaps=False):
+ self.compute_module_sizes()
+ if no_gaps:
+ self.assign_module_to_layers_no_gaps()
+ else:
+ self.assign_modules_to_layers()
+ self.assign_module_permutation_to_each_layer(preserve_order)
+ self.compute_layout(layer_x_separation, layer_y_separation)
\ No newline at end of file
diff --git a/vistrails/core/log/__init__.py b/vistrails/core/log/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/core/log/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/core/log/controller.py b/vistrails/core/log/controller.py
new file mode 100644
index 0000000..bb44e6d
--- /dev/null
+++ b/vistrails/core/log/controller.py
@@ -0,0 +1,362 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.log.workflow_exec import WorkflowExec
+from vistrails.core.log.module_exec import ModuleExec
+from vistrails.core.log.loop_exec import LoopExec
+from vistrails.core.log.group_exec import GroupExec
+from vistrails.core.log.machine import Machine
+from vistrails.core.modules.sub_module import Group, Abstraction
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.vistrail.vistrail import Vistrail
+import vistrails.core.system
+
+class DummyLogController(object):
+ """DummyLogger is a class that has the entire interface for a logger
+ but simply ignores the calls."""
+ def start_workflow_execution(self, *args, **kwargs): pass
+ def finish_workflow_execution(self, *args, **kwargs): pass
+ def create_module_exec(self, *args, **kwargs): pass
+ def create_group_exec(self, *args, **kwargs): pass
+ def create_loop_exec(self, *args, **kwargs): pass
+ def start_execution(self, *args, **kwargs): pass
+ def finish_execution(self, *args, **kwargs): pass
+ def start_module_loop_execution(self, *args, **kwargs): pass
+ def finish_module_loop_execution(self, *args, **kwargs): pass
+ def start_group_loop_execution(self, *args, **kwargs): pass
+ def finish_group_loop_execution(self, *args, **kwargs): pass
+ def start_module_execution(self, *args, **kwargs): pass
+ def finish_module_execution(self, *args, **kwargs): pass
+ def start_group_execution(self, *args, **kwargs): pass
+ def finish_group_execution(self, *args, **kwargs): pass
+ def start_loop_execution(self, *args, **kwargs): pass
+ def finish_loop_execution(self, *args, **kwargs): pass
+ def insert_module_annotations(self, *args, **kwargs): pass
+ def insert_workflow_exec_annotations(self, *args, **kwargs): pass
+ def add_exec(self, *args, **kwargs): pass
+
+class LogControllerFactory(object):
+ _instance = None
+ class LogControllerFactorySingleton(object):
+ def __call__(self, *args, **kw):
+ if LogControllerFactory._instance is None:
+ obj = LogControllerFactory(*args, **kw)
+ LogControllerFactory._instance = obj
+ return LogControllerFactory._instance
+
+ getInstance = LogControllerFactorySingleton()
+
+ def __init__(self):
+ self.machine = Machine(id=-1,
+ name=vistrails.core.system.current_machine(),
+ os=vistrails.core.system.systemType,
+ architecture=vistrails.core.system.current_architecture(),
+ processor=vistrails.core.system.current_processor(),
+ ram=vistrails.core.system.guess_total_memory())
+
+ def create_logger(self, log):
+ return LogController(log, self.machine)
+
+LogControllerFactory.getInstance()
+
+class LogController(object):
+ def __init__(self, log, machine):
+ self.log = log
+ self.workflow_exec = None
+ self.machine = machine
+ to_add = True
+ for machine in self.log.machine_list:
+ if self.machine.equals_no_id(machine):
+ to_add = False
+ self.machine = machine
+ if to_add:
+ self.machine.id = self.log.id_scope.getNewId(Machine.vtType)
+ self.log.add_machine(self.machine)
+
+ def start_workflow_execution(self, vistrail=None, pipeline=None,
+ currentVersion=None):
+ if vistrail is not None:
+ parent_type = Vistrail.vtType
+ parent_id = vistrail.id
+ else:
+ parent_type = Pipeline.vtType
+ parent_id = pipeline.id
+
+ wf_exec_id = self.log.id_scope.getNewId(WorkflowExec.vtType)
+ if vistrail is not None:
+ session = vistrail.current_session
+ else:
+ session = None
+ self.workflow_exec = WorkflowExec(id=wf_exec_id,
+ user=vistrails.core.system.current_user(),
+ ip=vistrails.core.system.current_ip(),
+ vt_version= \
+ vistrails.core.system.vistrails_version(),
+ ts_start=vistrails.core.system.current_time(),
+ parent_type=parent_type,
+ parent_id=parent_id,
+ parent_version=currentVersion,
+ completed=0,
+ session=session)
+ self.log.add_workflow_exec(self.workflow_exec)
+
+ def finish_workflow_execution(self, errors, suspended=False):
+ self.workflow_exec.ts_end = vistrails.core.system.current_time()
+ if suspended:
+ self.workflow_exec.completed = -2
+ elif len(errors) > 0:
+ self.workflow_exec.completed = -1
+ else:
+ self.workflow_exec.completed = 1
+
+ def add_exec(self, exec_, parent_execs):
+ parent_exec = parent_execs[-1]
+ if parent_exec:
+ parent_exec.add_item_exec(exec_)
+ else:
+ self.workflow_exec.add_item_exec(exec_)
+
+ def create_module_exec(self, module, module_id, module_name,
+ cached):
+ m_exec_id = self.log.id_scope.getNewId(ModuleExec.vtType)
+ module_exec = ModuleExec(id=m_exec_id,
+ machine_id=self.machine.id,
+ module_id=module_id,
+ module_name=module_name,
+ cached=cached,
+ ts_start=vistrails.core.system.current_time(),
+ completed=0)
+ return module_exec
+
+ def create_group_exec(self, group, module_id, group_name, cached):
+ g_exec_id = self.log.id_scope.getNewId(GroupExec.vtType)
+ if isinstance(group, Abstraction):
+ group_type = 'SubWorkflow'
+ else:
+ group_type = 'Group'
+ group_exec = GroupExec(id=g_exec_id,
+ machine_id=self.machine.id,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ cached=cached,
+ ts_start=vistrails.core.system.current_time(),
+ completed=0)
+ return group_exec
+
+ def create_loop_exec(self, iteration):
+ l_exec_id = self.log.id_scope.getNewId(LoopExec.vtType)
+ loop_exec = LoopExec(id=l_exec_id,
+ iteration=iteration,
+ ts_start=vistrails.core.system.current_time())
+ return loop_exec
+
+ def start_execution(self, module, module_id, module_name, parent_execs,
+ cached=0):
+ parent_exec = parent_execs[-1]
+ if module.is_looping:
+ parent_exec = self.start_loop_execution(module, module_id,
+ module_name,
+ parent_exec, cached,
+ module.loop_iteration)
+ parent_execs.append(parent_exec)
+
+ if isinstance(module, Group):
+ ret = self.start_group_execution(module, module_id, module_name,
+ parent_exec, cached)
+ if ret is not None:
+ parent_execs.append(ret)
+ else:
+ ret = self.start_module_execution(module, module_id, module_name,
+ parent_exec, cached)
+ if ret is not None:
+ parent_execs.append(ret)
+
+ def finish_execution(self, module, error, parent_execs, errorTrace=None,
+ suspended=False):
+ if isinstance(module, Group):
+ if self.finish_group_execution(module, error, suspended):
+ parent_execs.pop()
+ else:
+ if self.finish_module_execution(module, error, errorTrace, suspended):
+ parent_execs.pop()
+ if module.is_looping:
+ self.finish_loop_execution(module, error, parent_execs.pop(), suspended)
+
+ def start_module_execution(self, module, module_id, module_name,
+ parent_exec, cached):
+ module_exec = self.create_module_exec(module, module_id,
+ module_name,
+ cached)
+ module.module_exec = module_exec
+ if parent_exec:
+ parent_exec.add_item_exec(module_exec)
+ else:
+ self.workflow_exec.add_item_exec(module_exec)
+ if module.is_looping_module:
+ return module_exec
+ return None
+
+ def finish_module_execution(self, module, error, errorTrace=None,
+ suspended=False):
+ if not hasattr(module,'module_exec'):
+ return False
+ module.module_exec.ts_end = vistrails.core.system.current_time()
+ if suspended:
+ module.module_exec.completed = -2
+ module.module_exec.error = error
+ elif not error:
+ module.module_exec.completed = 1
+ else:
+ module.module_exec.completed = -1
+ module.module_exec.error = error
+ if errorTrace:
+ a_id = self.log.id_scope.getNewId(Annotation.vtType)
+ annotation = Annotation(id=a_id,
+ key="errorTrace",
+ value=errorTrace)
+ module.module_exec.add_annotation(annotation)
+ del module.module_exec
+ if module.is_looping_module:
+ return True
+
+ def start_group_execution(self, group, module_id, group_name,
+ parent_exec, cached):
+ group_exec = self.create_group_exec(group, module_id,
+ group_name, cached)
+ group.group_exec = group_exec
+ if parent_exec:
+ parent_exec.add_item_exec(group_exec)
+ else:
+ self.workflow_exec.add_item_exec(group_exec)
+ return group_exec
+
+ def finish_group_execution(self, group, error, suspended=False):
+ if not hasattr(group,'group_exec'):
+ return False
+ group.group_exec.ts_end = vistrails.core.system.current_time()
+ if suspended:
+ group.group_exec.completed = -2
+ group.group_exec.error = error
+ elif not error:
+ group.group_exec.completed = 1
+ else:
+# if group.group_exec.module_execs and group.group_exec.\
+# module_execs[-1].error:
+# error = 'Error in module execution with id %d.'%\
+# group.group_exec.module_execs[-1].id
+# if group.group_exec.group_execs and group.group_exec.\
+# group_execs[-1].error:
+# error = 'Error in group execution with id %d.'%\
+# group.group_exec.group_execs[-1].id
+ group.group_exec.completed = -1
+ group.group_exec.error = error
+ del group.group_exec
+ return True
+
+ def start_loop_execution(self, module, module_id, module_name,
+ parent_exec, cached, iteration):
+ loop_exec = self.create_loop_exec(iteration)
+ if parent_exec:
+ parent_exec.add_loop_exec(loop_exec)
+ else:
+ self.workflow_exec.add_item_exec(loop_exec)
+ return loop_exec
+
+ def finish_loop_execution(self, module, error, loop_exec, suspended=True):
+ if not loop_exec:
+ return False
+ loop_exec.ts_end = vistrails.core.system.current_time()
+ if suspended:
+ loop_exec.completed = -2
+ loop_exec.error = error
+ elif not error:
+ loop_exec.completed = 1
+ else:
+ loop_exec.completed = -1
+ loop_exec.error = error
+ return True
+
+# is_group = isinstance(module, Group)
+# if is_group:
+# module.group_exec.loop_execs[-1].ts_end = core.system.\
+# current_time()
+# if not error:
+# module.group_exec.loop_execs[-1].completed = 1
+# else:
+# if module.group_exec.loop_execs[-1].module_execs and\
+# module.group_exec.loop_execs[-1].module_execs[-1].error:
+# error = 'Error in module execution with id %d.'%\
+# module.group_exec.loop_execs[-1].\
+# module_execs[-1].id
+# if module.group_exec.loop_execs[-1].group_execs and\
+# module.group_exec.loop_execs[-1].group_execs[-1].error:
+# error = 'Error in group execution with id %d.'%\
+# module.group_exec.loop_execs[-1].\
+# group_execs[-1].id
+# module.group_exec.loop_execs[-1].completed = -1
+# module.group_exec.loop_execs[-1].error = error
+# else:
+# module.module_exec.loop_execs[-1].ts_end = core.system.\
+# current_time()
+# if not error:
+# module.module_exec.loop_execs[-1].completed = 1
+# else:
+# module.module_exec.loop_execs[-1].completed = -1
+# module.module_exec.loop_execs[-1].error = error
+# return True
+
+ def insert_module_annotations(self, module, a_dict):
+ for k,v in a_dict.iteritems():
+ a_id = self.log.id_scope.getNewId(Annotation.vtType)
+ annotation = Annotation(id=a_id,
+ key=k,
+ value=v)
+ if hasattr(module, 'is_group'):
+ module.group_exec.add_annotation(annotation)
+ else:
+ module.module_exec.add_annotation(annotation)
+
+ def insert_workflow_exec_annotations(self, a_dict):
+ """insert_workflow_exec_annotations(a_dict)-> None
+ This will create an annotation for each pair in a_dict in
+ self.workflow_exec"""
+ if self.workflow_exec:
+ for k,v in a_dict.iteritems():
+ a_id = self.log.id_scope.getNewId(Annotation.vtType)
+ annotation = Annotation(id=a_id,
+ key=k,
+ value=v)
+ self.workflow_exec.add_annotation(annotation)
diff --git a/vistrails/core/log/group_exec.py b/vistrails/core/log/group_exec.py
new file mode 100644
index 0000000..bd0a75d
--- /dev/null
+++ b/vistrails/core/log/group_exec.py
@@ -0,0 +1,104 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.log.module_exec import ModuleExec
+from vistrails.core.log.loop_exec import LoopExec
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.db.domain import DBGroupExec
+
+class GroupExec(DBGroupExec):
+ """ Class that stores info for logging a group/abstraction execution. """
+
+ def __init__(self, *args, **kwargs):
+ DBGroupExec.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return self.do_copy()
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroupExec.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = GroupExec
+ return cp
+
+ @staticmethod
+ def convert(_group_exec):
+ if _group_exec.__class__ == GroupExec:
+ return
+ _group_exec.__class__ = GroupExec
+ for annotation in _group_exec.annotations:
+ Annotation.convert(annotation)
+ for item_exec in _group_exec.item_execs:
+ if item_exec.vtType == ModuleExec.vtType:
+ ModuleExec.convert(item_exec)
+ elif item_exec.vtType == GroupExec.vtType:
+ GroupExec.convert(item_exec)
+ elif item_exec.vtType == LoopExec.vtType:
+ LoopExec.convert(item_exec)
+
+ ##########################################################################
+ # Properties
+
+ id = DBGroupExec.db_id
+ ts_start = DBGroupExec.db_ts_start
+ ts_end = DBGroupExec.db_ts_end
+ cached = DBGroupExec.db_cached
+ module_id = DBGroupExec.db_module_id
+ group_name = DBGroupExec.db_group_name
+ group_type = DBGroupExec.db_group_type
+ completed = DBGroupExec.db_completed
+ error = DBGroupExec.db_error
+ machine_id = DBGroupExec.db_machine_id
+
+ def _get_duration(self):
+ if self.db_ts_end is not None:
+ return self.db_ts_end - self.db_ts_start
+ return None
+ duration = property(_get_duration)
+
+ def _get_annotations(self):
+ return self.db_annotations
+ def _set_annotations(self, annotations):
+ self.db_annotations = annotations
+ annotations = property(_get_annotations, _set_annotations)
+ def add_annotation(self, annotation):
+ self.db_add_annotation(annotation)
+
+ def _get_item_execs(self):
+ return self.db_item_execs
+ def _set_item_execs(self, item_execs):
+ self.db_item_execs = item_execs
+ item_execs = property(_get_item_execs, _set_item_execs)
+ def add_item_exec(self, item_exec):
+ self.db_add_item_exec(item_exec)
+
diff --git a/vistrails/core/log/log.py b/vistrails/core/log/log.py
new file mode 100644
index 0000000..db05bf2
--- /dev/null
+++ b/vistrails/core/log/log.py
@@ -0,0 +1,103 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+
+from vistrails.core.log.machine import Machine
+from vistrails.core.log.workflow_exec import WorkflowExec
+from vistrails.db.domain import DBLog
+
+class Log(DBLog):
+ """ Class that stores info for logging a workflow execution. """
+
+ def __init__(self, *args, **kwargs):
+ DBLog.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return self.do_copy()
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Log
+ return cp
+
+ @staticmethod
+ def convert(_log):
+ if _log.__class__ == Log:
+ return
+ _log.__class__ = Log
+ for machine in _log.machine_list:
+ Machine.convert(machine)
+ for workflow_exec in _log.workflow_execs:
+ WorkflowExec.convert(workflow_exec)
+
+
+ ##########################################################################
+ # Properties
+
+ def _get_id(self):
+ return self.db_id
+ def _set_id(self, id):
+ self.db_id = id
+ id = property(_get_id, _set_id)
+
+ def _get_machines(self):
+ return self.db_machines_id_index
+ machines = property(_get_machines)
+ def _get_machine_list(self):
+ return self.db_machines
+ machine_list = property(_get_machine_list)
+ def add_machine(self, machine):
+ self.db_add_machine(machine)
+
+ def _get_workflow_execs(self):
+ return self.db_workflow_execs
+ workflow_execs = property(_get_workflow_execs)
+ def add_workflow_exec(self, wf_exec):
+ self.db_add_workflow_exec(wf_exec)
+
+ def delete_all_workflow_execs(self):
+ for wf_exec in copy.copy(self.workflow_execs):
+ self.db_delete_workflow_exec(wf_exec)
+
+ def _get_vistrail_id(self):
+ return self.db_vistrail_id
+ def _set_vistrail_id(self, id):
+ self.db_vistrail_id = id
+ vistrail_id = property(_get_vistrail_id, _set_vistrail_id)
+
+ def get_last_workflow_exec_id(self):
+ if len(self.workflow_execs) < 1:
+ return -1
+ return max(wf_exec.id for wf_exec in self.workflow_execs)
diff --git a/vistrails/core/log/loop_exec.py b/vistrails/core/log/loop_exec.py
new file mode 100644
index 0000000..3b1495b
--- /dev/null
+++ b/vistrails/core/log/loop_exec.py
@@ -0,0 +1,88 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBLoopExec
+
+class LoopExec(DBLoopExec):
+ """ Class that stores info for logging a loop execution. """
+
+ def __init__(self, *args, **kwargs):
+ DBLoopExec.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return self.do_copy()
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLoopExec.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = LoopExec
+ return cp
+
+ @staticmethod
+ def convert(_loop_exec):
+ from vistrails.core.log.module_exec import ModuleExec
+ from vistrails.core.log.group_exec import GroupExec
+
+ if _loop_exec.__class__ == LoopExec:
+ return
+ _loop_exec.__class__ = LoopExec
+ for item_exec in _loop_exec.item_execs:
+ if item_exec.vtType == ModuleExec.vtType:
+ ModuleExec.convert(item_exec)
+ elif item_exec.vtType == GroupExec.vtType:
+ GroupExec.convert(item_exec)
+ elif item_exec.vtType == LoopExec.vtType:
+ LoopExec.convert(item_exec)
+
+ ##########################################################################
+ # Properties
+
+ id = DBLoopExec.db_id
+ ts_start = DBLoopExec.db_ts_start
+ ts_end = DBLoopExec.db_ts_end
+ completed = DBLoopExec.db_completed
+ error = DBLoopExec.db_error
+
+ def _get_duration(self):
+ if self.db_ts_end is not None:
+ return self.db_ts_end - self.db_ts_start
+ return None
+ duration = property(_get_duration)
+
+ def _get_item_execs(self):
+ return self.db_item_execs
+ def _set_item_execs(self, item_execs):
+ self.db_item_execs = item_execs
+ item_execs = property(_get_item_execs, _set_item_execs)
+ def add_item_exec(self, item_exec):
+ self.db_add_item_exec(item_exec)
diff --git a/vistrails/core/log/machine.py b/vistrails/core/log/machine.py
new file mode 100644
index 0000000..14842a1
--- /dev/null
+++ b/vistrails/core/log/machine.py
@@ -0,0 +1,104 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBMachine
+
+class Machine(DBMachine):
+ """ Class that stores info for logging a module execution. """
+
+ def __init__(self, *args, **kwargs):
+ DBMachine.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return self.do_copy()
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Machine
+ return cp
+
+ @staticmethod
+ def convert(_machine):
+ if _machine.__class__ == Machine:
+ return
+ _machine.__class__ = Machine
+
+ ##########################################################################
+ # Properties
+
+ def _get_id(self):
+ return self.db_id
+ def _set_id(self, id):
+ self.db_id = id
+ id = property(_get_id, _set_id)
+
+ def _get_name(self):
+ return self.db_name
+ def _set_name(self, name):
+ self.db_name = name
+ name = property(_get_name, _set_name)
+
+ def _get_os(self):
+ return self.db_os
+ def _set_os(self, os):
+ self.db_os = os
+ os = property(_get_os, _set_os)
+
+ def _get_architecture(self):
+ return self.db_architecture
+ def _set_architecture(self, architecture):
+ self.db_architecture = architecture
+ architecture = property(_get_architecture, _set_architecture)
+
+ def _get_processor(self):
+ return self.db_processor
+ def _set_processor(self, processor):
+ self.db_processor = processor
+ processor = property(_get_processor, _set_processor)
+
+ def _get_ram(self):
+ return self.db_ram
+ def _set_ram(self, ram):
+ self.db_ram = ram
+ ram = property(_get_ram, _set_ram)
+
+ ##########################################################################
+ # Properties
+
+ def equals_no_id(self, other):
+ return (self.name == other.name and
+ self.os == other.os and
+ self.architecture == other.architecture and
+ self.processor == other.processor and
+ self.ram == other.ram)
diff --git a/vistrails/core/log/module_exec.py b/vistrails/core/log/module_exec.py
new file mode 100644
index 0000000..789d044
--- /dev/null
+++ b/vistrails/core/log/module_exec.py
@@ -0,0 +1,97 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.log.loop_exec import LoopExec
+from vistrails.db.domain import DBModuleExec
+
+class ModuleExec(DBModuleExec):
+ """ Class that stores info for logging a module execution. """
+
+ def __init__(self, *args, **kwargs):
+ DBModuleExec.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return self.do_copy()
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = ModuleExec
+ return cp
+
+ @staticmethod
+ def convert(_module_exec):
+ if _module_exec.__class__ == ModuleExec:
+ return
+ _module_exec.__class__ = ModuleExec
+ for annotation in _module_exec.annotations:
+ Annotation.convert(annotation)
+ for loop_exec in _module_exec.loop_execs:
+ LoopExec.convert(loop_exec)
+
+ ##########################################################################
+ # Properties
+
+ id = DBModuleExec.db_id
+ ts_start = DBModuleExec.db_ts_start
+ ts_end = DBModuleExec.db_ts_end
+ cached = DBModuleExec.db_cached
+ completed = DBModuleExec.db_completed
+ module_id = DBModuleExec.db_module_id
+ module_name = DBModuleExec.db_module_name
+ machine_id = DBModuleExec.db_machine_id
+ error = DBModuleExec.db_error
+
+ def _get_duration(self):
+ if self.db_ts_end is not None:
+ return self.db_ts_end - self.db_ts_start
+ return None
+ duration = property(_get_duration)
+
+ def _get_annotations(self):
+ return self.db_annotations
+ def _set_annotations(self, annotations):
+ self.db_annotations = annotations
+ annotations = property(_get_annotations, _set_annotations)
+ def add_annotation(self, annotation):
+ self.db_add_annotation(annotation)
+
+ def _get_loop_execs(self):
+ return self.db_loop_execs
+ def _set_loop_execs(self, loop_execs):
+ self.db_loop_execs = loop_execs
+ loop_execs = property(_get_loop_execs, _set_loop_execs)
+ def add_loop_exec(self, loop_exec):
+ self.db_add_loop_exec(loop_exec)
+
diff --git a/vistrails/core/log/opm_graph.py b/vistrails/core/log/opm_graph.py
new file mode 100644
index 0000000..bd9a2b5
--- /dev/null
+++ b/vistrails/core/log/opm_graph.py
@@ -0,0 +1,88 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBOpmGraph
+
+class OpmGraph(DBOpmGraph):
+ """ Class that stores info for generating OPM Provenance. """
+
+ def __init__(self, *args, **kwargs):
+ if 'log' in kwargs:
+ self.log = kwargs['log']
+ del kwargs['log']
+ else:
+ self.log = None
+ if 'workflow' in kwargs:
+ self.workflow = kwargs['workflow']
+ del kwargs['workflow']
+ elif 'pipeline' in kwargs:
+ self.workflow = kwargs['pipeline']
+ del kwargs['pipeline']
+ else:
+ self.workflow = None
+ if 'registry' in kwargs:
+ self.registry = kwargs['registry']
+ del kwargs['registry']
+ else:
+ self.registry = None
+ if 'version' in kwargs:
+ self.version = kwargs['version']
+ del kwargs['version']
+ else:
+ self.version = None
+ DBOpmGraph.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return self.do_copy()
+
+ def do_copy(self):
+ cp = DBOpmGraph.__copy__(self)
+ cp.__class__ = OpmGraph
+ cp.log = self.log
+ cp.workflow = self.workflow
+ cp.version = self.version
+ cp.registry = self.registry
+ return cp
+
+ @staticmethod
+ def convert(_graph):
+ if _graph.__class__ == OpmGraph:
+ return
+ _graph.__class__ = OpmGraph
+
+ ##########################################################################
+ # Properties
+
+ # No need to do properties right now...
+
diff --git a/vistrails/core/log/prov_document.py b/vistrails/core/log/prov_document.py
new file mode 100644
index 0000000..b9c3117
--- /dev/null
+++ b/vistrails/core/log/prov_document.py
@@ -0,0 +1,85 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBProvDocument
+
+class ProvDocument(DBProvDocument):
+ """ Class that stores info for generating PROV model. """
+
+ def __init__(self, *args, **kwargs):
+ if 'log' in kwargs:
+ self.log = kwargs['log']
+ del kwargs['log']
+ else:
+ self.log = None
+ if 'workflow' in kwargs:
+ self.workflow = kwargs['workflow']
+ del kwargs['workflow']
+ else:
+ self.workflow = None
+ if 'registry' in kwargs:
+ self.registry = kwargs['registry']
+ del kwargs['registry']
+ else:
+ self.registry = None
+ if 'version' in kwargs:
+ self.version = kwargs['version']
+ del kwargs['version']
+ else:
+ self.version = None
+ DBProvDocument.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return self.do_copy()
+
+ def do_copy(self):
+ cp = DBProvDocument.__copy__(self)
+ cp.__class__ = ProvDocument
+ cp.log = self.log
+ cp.workflow = self.workflow
+ cp.version = self.version
+ cp.registry = self.registry
+ return cp
+
+ @staticmethod
+ def convert(_graph):
+ if _graph.__class__ == ProvDocument:
+ return
+ _graph.__class__ = ProvDocument
+
+ ##########################################################################
+ # Properties
+
+ # No need to do properties right now...
+
diff --git a/vistrails/core/log/workflow_exec.py b/vistrails/core/log/workflow_exec.py
new file mode 100644
index 0000000..0ca9dc6
--- /dev/null
+++ b/vistrails/core/log/workflow_exec.py
@@ -0,0 +1,106 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.log.module_exec import ModuleExec
+from vistrails.core.log.group_exec import GroupExec
+from vistrails.core.log.loop_exec import LoopExec
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.db.domain import DBWorkflowExec
+
+class WorkflowExec(DBWorkflowExec):
+ """ Class that stores info for logging a workflow execution. """
+
+ def __init__(self, *args, **kwargs):
+ DBWorkflowExec.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return self.do_copy()
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = WorkflowExec
+ return cp
+
+ @staticmethod
+ def convert(_wf_exec):
+ if _wf_exec.__class__ == WorkflowExec:
+ return
+ _wf_exec.__class__ = WorkflowExec
+ for annotation in _wf_exec.annotations:
+ Annotation.convert(annotation)
+ for item_exec in _wf_exec.item_execs:
+ if item_exec.vtType == ModuleExec.vtType:
+ ModuleExec.convert(item_exec)
+ elif item_exec.vtType == GroupExec.vtType:
+ GroupExec.convert(item_exec)
+ elif item_exec.vtType == LoopExec.vtType:
+ LoopExec.convert(item_exec)
+
+ ##########################################################################
+ # Properties
+
+ id = DBWorkflowExec.db_id
+ user = DBWorkflowExec.db_user
+ ip = DBWorkflowExec.db_ip
+ session = DBWorkflowExec.db_session
+ vt_version = DBWorkflowExec.db_vt_version
+ ts_start = DBWorkflowExec.db_ts_start
+ ts_end = DBWorkflowExec.db_ts_end
+ parent_type = DBWorkflowExec.db_parent_type
+ parent_id = DBWorkflowExec.db_parent_id
+ parent_version = DBWorkflowExec.db_parent_version
+ name = DBWorkflowExec.db_name
+ completed = DBWorkflowExec.db_completed
+
+ def _get_duration(self):
+ if self.db_ts_end is not None:
+ return self.db_ts_end - self.db_ts_start
+ return None
+ duration = property(_get_duration)
+
+ def _get_annotations(self):
+ return self.db_annotations
+ def _set_annotations(self, annotations):
+ self.db_annotations = annotations
+ annotations = property(_get_annotations, _set_annotations)
+ def add_annotation(self, annotation):
+ self.db_add_annotation(annotation)
+
+ def _get_item_execs(self):
+ return self.db_item_execs
+ def _set_item_execs(self, item_execs):
+ self.db_item_execs = item_execs
+ item_execs = property(_get_item_execs, _set_item_execs)
+ def add_item_exec(self, item_exec):
+ self.db_add_item_exec(item_exec)
diff --git a/vistrails/core/mashup/__init__.py b/vistrails/core/mashup/__init__.py
new file mode 100644
index 0000000..3376fe3
--- /dev/null
+++ b/vistrails/core/mashup/__init__.py
@@ -0,0 +1,130 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import uuid
+from datetime import date, datetime
+from time import strptime
+################################################################################
+
+def conv_to_bool(x):
+ if isinstance(x, str):
+ s = str(x).upper()
+ if s == 'TRUE':
+ return True
+ if s == 'FALSE':
+ return False
+ elif isinstance(x, (int, long)):
+ if x == 0:
+ return False
+ else:
+ return True
+ elif isinstance(x, bool):
+ return x
+
+def conv_from_bool(x):
+ if isinstance(x, bool):
+ if x == True:
+ return 1
+ else:
+ return 0
+ elif isinstance(x, (int, long)):
+ return x
+
+def convert_symbols(val):
+ val = val.replace("<", "<")
+ val = val.replace(">", ">")
+ val = val.replace("&","&")
+ return val
+
+
+
+#class XMLObject(object):
+# """Base class for mashup classes"""
+# @staticmethod
+# def convert_from_str(value, type):
+# def bool_conv(x):
+# s = str(x).upper()
+# if s == 'TRUE':
+# return True
+# if s == 'FALSE':
+# return False
+#
+# if value is not None:
+# if type == 'str':
+# return str(value)
+# elif value.strip() != '':
+# if type == 'long':
+# return long(value)
+# elif type == 'float':
+# return float(value)
+# elif type == 'int':
+# return int(value)
+# elif type == 'bool':
+# return bool_conv(value)
+# elif type == 'date':
+# return date(*strptime(value, '%Y-%m-%d')[0:3])
+# elif type == 'datetime':
+# return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+# elif type == 'uuid':
+# return uuid.UUID(value)
+# return None
+#
+# @staticmethod
+# def convert_to_str(value,type):
+# if value is not None:
+# if type == 'date':
+# return value.isoformat()
+# elif type == 'datetime':
+# return value.strftime('%Y-%m-%d %H:%M:%S')
+# else:
+# return str(value)
+# return ''
+#
+# @staticmethod
+# def indent(elem, level=0):
+# i = "\n" + level*" "
+# if len(elem):
+# if not elem.text or not elem.text.strip():
+# elem.text = i + " "
+# if not elem.tail or not elem.tail.strip():
+# elem.tail = i
+# for elem in elem:
+# XMLObject.indent(elem, level+1)
+# if not elem.tail or not elem.tail.strip():
+# elem.tail = i
+# else:
+# if level and (not elem.tail or not elem.tail.strip()):
+# elem.tail = i
+################################################################################
\ No newline at end of file
diff --git a/vistrails/core/mashup/action.py b/vistrails/core/mashup/action.py
new file mode 100644
index 0000000..357aec2
--- /dev/null
+++ b/vistrails/core/mashup/action.py
@@ -0,0 +1,194 @@
+###############################################################################
+##
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+from vistrails.db.domain import DBMashupAction
+from vistrails.core.mashup.mashup import Mashup
+
+class Action(DBMashupAction):
+
+ def __init__(self, id, prevId, user='', mashup=None, date=None):
+ DBMashupAction.__init__(self, id, prevId, date, user, mashup)
+
+ id = DBMashupAction.db_id
+ prevId = DBMashupAction.db_prevId
+ parent_id = DBMashupAction.db_prevId
+ user = DBMashupAction.db_user
+ mashup = DBMashupAction.db_mashup
+
+ def _get_date(self):
+ if self.db_date is not None:
+ return self.db_date.strftime('%d %b %Y %H:%M:%S')
+ return datetime(1900,1,1).strftime('%d %b %Y %H:%M:%S')
+
+ def _set_date(self, date):
+ if isinstance(date, datetime):
+ self.db_date = date
+ elif isinstance(date, basestring) and date.strip() != '':
+ newDate = datetime(*strptime(date, '%d %b %Y %H:%M:%S')[0:6])
+ self.db_date = newDate
+ date = property(_get_date, _set_date)
+
+ @staticmethod
+ def convert(_action):
+ if _action.__class__ == Action:
+ return
+ _action.__class__ = Action
+ Mashup.convert(_action.mashup)
+
+ def __copy__(self):
+ return Action.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMashupAction.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Action
+ Mashup.convert(cp.mashup)
+ return cp
+
+# def toXml(self, node=None):
+# """toXml(node: ElementTree.Element) -> ElementTree.Element
+# writes itself to xml
+# """
+#
+# if node is None:
+# node = ElementTree.Element('action')
+#
+# #set attributes
+# node.set('id', self.convert_to_str(self.id,'long'))
+# node.set('parent_id', self.convert_to_str(self.parent_id,'long'))
+# node.set('user', self.convert_to_str(self.user,'str'))
+# node.set('date', self.convert_to_str(self._date,'datetime'))
+# mnode = ElementTree.SubElement(node, 'mashup')
+# self.mashup.toXml(mnode)
+# return node
+#
+# @staticmethod
+# def fromXml(node):
+# if node.tag != 'action':
+# debug.debug("node.tag != 'action'")
+# return None
+# #read attributes
+# data = node.get('id', None)
+# id = Action.convert_from_str(data, 'long')
+# data = node.get('parent_id', None)
+# parent_id = Action.convert_from_str(data, 'long')
+# data = node.get('user', None)
+# user = Action.convert_from_str(data, 'str')
+# data = node.get('date', None)
+# date = Action.convert_from_str(data, 'datetime')
+# child = node.getchildren()[0]
+# if child.tag == 'mashup':
+# mashup = Mashup.fromXml(child)
+# return Action(id=id, parent_id=parent_id, mashup=mashup, user=user,
+# date=date)
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """ __str__() -> str - Returns a string representation of itself """
+
+ msg = "<<type='%s' id='%s' parent_id='%s' date='%s' user='%s'>>"
+ return msg % (type(self),
+ self.id,
+ self.prevId,
+ self.db_date,
+ self.user)
+
+ def __eq__(self, other):
+ """ __eq__(other: Alias) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.mashup != other.mashup:
+ return False
+ return True
+
+ def __ne__(self, other):
+ """ __ne__(other: Component) -> boolean
+ Returns True if self and other don't have the same attributes.
+ Used by != operator.
+
+ """
+ return not self.__eq__(other)
+################################################################################
+
+import unittest
+from vistrails.db.domain import IdScope
+import copy
+
+class TestAction(unittest.TestCase):
+ def create_action(self, id_scope=IdScope()):
+ from vistrails.core.mashup.component import Component
+ from vistrails.core.mashup.alias import Alias
+ from vistrails.core.mashup.mashup import Mashup
+ c1 = Component(id=id_scope.getNewId('mashup_component'),
+ vttype='parameter', param_id=15L,
+ parent_vttype='function', parent_id=3L, mid=4L,
+ type='String', value='test', p_pos=0, pos=1,
+ strvaluelist='test1,test2', widget="text")
+ a1 = Alias(id=id_scope.getNewId('mashup_alias'), name='alias1', component=c1)
+
+ m = Mashup(id=id_scope.getNewId('mashup'), name='mashup1', vtid='empty.vt',
+ version=15L, alias_list=[a1])
+ action = Action(id=id_scope.getNewId('mashup_action'),
+ prevId=0L,
+ date=datetime(2007,11,18),
+ mashup=m)
+ return action
+
+ def test_copy(self):
+ id_scope = IdScope()
+ a1 = self.create_action(id_scope)
+ a2 = copy.copy(a1)
+ self.assertEquals(a1, a2)
+ self.assertEquals(a1.id, a2.id)
+ a3 = a1.do_copy(True, id_scope, {})
+ self.assertEquals(a1, a3)
+ self.assertNotEquals(a1.id, a3.id)
+
+# def test_serialization(self):
+# a1 = self.create_action()
+# node = a1.toXml()
+# a2 = Action.fromXml(node)
+# self.assertEquals(a1, a2)
+# self.assertEquals(a1.id, a2.id)
+
+ def test_str(self):
+ a1 = self.create_action()
+ str(a1)
diff --git a/vistrails/core/mashup/action_annotation.py b/vistrails/core/mashup/action_annotation.py
new file mode 100644
index 0000000..6cfa589
--- /dev/null
+++ b/vistrails/core/mashup/action_annotation.py
@@ -0,0 +1,176 @@
+###############################################################################
+##
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBMashupActionAnnotation
+from datetime import date, datetime
+from time import strptime
+
+class ActionAnnotation(DBMashupActionAnnotation):
+ def __init__(self, id, action_id, key=None, value=None, user=None, date=None):
+ DBMashupActionAnnotation.__init__(self, id, key, value, action_id, date,
+ user)
+ id = DBMashupActionAnnotation.db_id
+ action_id = DBMashupActionAnnotation.db_action_id
+ key = DBMashupActionAnnotation.db_key
+ value = DBMashupActionAnnotation.db_value
+ user = DBMashupActionAnnotation.db_user
+
+ def _get_date(self):
+ if self.db_date is not None:
+ return self.db_date.strftime('%d %b %Y %H:%M:%S')
+ return datetime(1900,1,1).strftime('%d %b %Y %H:%M:%S')
+
+ def _set_date(self, date):
+ if isinstance(date, datetime):
+ self.db_date = date
+ elif isinstance(date, basestring) and date.strip() != '':
+ newDate = datetime(*strptime(date, '%d %b %Y %H:%M:%S')[0:6])
+ self.db_date = newDate
+ date = property(_get_date, _set_date)
+
+ @staticmethod
+ def convert(_annotation):
+ _annotation.__class__ = ActionAnnotation
+
+ def __copy__(self):
+ return ActionAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMashupActionAnnotation.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = ActionAnnotation
+ return cp
+
+# def toXml(self, node=None):
+# """toXml(node: ElementTree.Element) -> ElementTree.Element
+# writes itself to xml
+# """
+#
+# if node is None:
+# node = ElementTree.Element('actionAnnotation')
+#
+# #set attributes
+# node.set('id', self.convert_to_str(self.id,'long'))
+# node.set('action_id', self.convert_to_str(self.action_id,'long'))
+# node.set('user', self.convert_to_str(self.user,'str'))
+# node.set('key', self.convert_to_str(self.key,'str'))
+# node.set('value', self.convert_to_str(self.value,'str'))
+# node.set('date', self.convert_to_str(self._date,'datetime'))
+# return node
+#
+# @staticmethod
+# def fromXml(node):
+# if node.tag != 'actionAnnotation':
+# debug.debug("node.tag != 'actionAnnotation'")
+# return None
+# #read attributes
+# data = node.get('id', None)
+# id = Action.convert_from_str(data, 'long')
+# data = node.get('action_id', None)
+# action_id = Action.convert_from_str(data, 'long')
+# data = node.get('key', None)
+# key = Action.convert_from_str(data, 'str')
+# data = node.get('value', None)
+# value = Action.convert_from_str(data, 'str')
+# data = node.get('user', None)
+# user = Action.convert_from_str(data, 'str')
+# data = node.get('date', None)
+# date = Action.convert_from_str(data, 'datetime')
+# return ActionAnnotation(id=id, action_id=action_id, key=key, value=value,
+# user=user, date=date)
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of an
+ mashup_actionAnnotation object.
+
+ """
+ rep = ("<mashup_actionAnnotation id=%s action_id=%s key=%s value=%s "
+ "date=%s user=%s</annotation>")
+ return rep % (str(self.id), str(self.action_id), str(self.key),
+ str(self.value), str(self.date), str(self.user))
+
+ def __eq__(self, other):
+ """ __eq__(other: mashup_actionAnnotation) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.key != other.key:
+ return False
+ if self.value != other.value:
+ return False
+ if self.action_id != other.action_id:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+################################################################################
+import unittest
+from vistrails.db.domain import IdScope
+import copy
+
+class TestActionAnnotation(unittest.TestCase):
+ def create_annotation(self, id_scope=IdScope()):
+
+ annotation = \
+ ActionAnnotation(id=id_scope.getNewId('mashup_actionAnnotation'),
+ key='akey', action_id=1L,
+ value='some value', user='test')
+ return annotation
+
+ def test_copy(self):
+ id_scope = IdScope()
+ a1 = self.create_annotation(id_scope)
+ a2 = copy.copy(a1)
+ self.assertEquals(a1, a2)
+ self.assertEquals(a1.id, a2.id)
+ a3 = a1.do_copy(True, id_scope, {})
+ self.assertEquals(a1, a3)
+ self.assertNotEquals(a1.id, a3.id)
+
+# def test_serialization(self):
+# a1 = self.create_annotation()
+# node = a1.toXml()
+# a2 = ActionAnnotation.fromXml(node)
+# self.assertEquals(a1, a2)
+# self.assertEquals(a1.id, a2.id)
+
+ def test_str(self):
+ a1 = self.create_annotation()
+ str(a1)
diff --git a/vistrails/core/mashup/alias.py b/vistrails/core/mashup/alias.py
new file mode 100644
index 0000000..4446cc3
--- /dev/null
+++ b/vistrails/core/mashup/alias.py
@@ -0,0 +1,164 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBMashupAlias
+from vistrails.core.mashup.component import Component
+
+import unittest
+from vistrails.db.domain import IdScope
+import copy
+
+################################################################################
+class Alias(DBMashupAlias):
+ def __init__(self, id, name, component=None):
+ DBMashupAlias.__init__(self, id, name, component)
+
+ id = DBMashupAlias.db_id
+ name = DBMashupAlias.db_name
+ component = DBMashupAlias.db_component
+
+ @staticmethod
+ def convert(_alias):
+ _alias.__class__ = Alias
+ Component.convert(_alias.component)
+
+ def __copy__(self):
+ return Alias.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMashupAlias.do_copy(self, new_ids, id_scope, id_remap)
+ Alias.convert(cp)
+ return cp
+
+ ##########################################################################
+ # Serialization / Unserialization
+
+# def toXml(self, node=None):
+# """toXml(node: ElementTree.Element) -> ElementTree.Element
+# writes itself to xml
+# """
+# if node is None:
+# node = ElementTree.Element('alias')
+#
+# #set attributes
+# node.set('id', self.convert_to_str(self.id,'long'))
+# node.set('name', self.convert_to_str(self.name,'str'))
+# child_ = ElementTree.SubElement(node, 'component')
+# self.component.toXml(child_)
+#
+# return node
+#
+# @staticmethod
+# def fromXml(node):
+# if node.tag != 'alias':
+# return None
+#
+# #read attributes
+# data = node.get('id', None)
+# id = Alias.convert_from_str(data, 'long')
+# data = node.get('name', None)
+# name = Alias.convert_from_str(data, 'str')
+# for child in node.getchildren():
+# if child.tag == "component":
+# component = Component.fromXml(child)
+# alias = Alias(id,name,component)
+# return alias
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """ __str__() -> str - Returns a string representation of itself """
+
+ return ("(Alias id='%s' name='%s' component=%s)@%X" %
+ (self.id,
+ self.name,
+ self.component,
+ id(self)))
+
+ def __eq__(self, other):
+ """ __eq__(other: Alias) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.name != other.name:
+ return False
+ if self.component != other.component:
+ return False
+ return True
+
+ def __ne__(self, other):
+ """ __ne__(other: Component) -> boolean
+ Returns True if self and other don't have the same attributes.
+ Used by != operator.
+
+ """
+ return not self.__eq__(other)
+
+################################################################################
+
+
+class TestAlias(unittest.TestCase):
+ def create_alias(self, id_scope=IdScope()):
+ c1 = Component(id=id_scope.getNewId('mashup_component'),
+ vttype='parameter', param_id=15L,
+ parent_vttype='function', parent_id=3L, mid=4L,
+ type='String', value='test', p_pos=0, pos=1,
+ strvaluelist='test1,test2', widget="text")
+ a1 = Alias(id=id_scope.getNewId('mashup_alias'), name='alias1', component=c1)
+ return a1
+
+ def test_copy(self):
+ id_scope = IdScope()
+ a1 = self.create_alias(id_scope)
+ a2 = copy.copy(a1)
+ self.assertEqual(a1,a2)
+ self.assertEqual(a1.id, a2.id)
+ a3 = a2.do_copy(True, id_scope, {})
+ self.assertEqual(a1,a3)
+ self.assertNotEqual(a1.id, a3.id)
+
+# def test_serialization(self):
+# a1 = self.create_alias()
+# node = a1.toXml()
+# a2 = Alias.fromXml(node)
+# self.assertEqual(a1, a2)
+# self.assertEqual(a1.id, a2.id)
+
+ def test_str(self):
+ a1 = self.create_alias()
+ str(a1)
diff --git a/vistrails/core/mashup/component.py b/vistrails/core/mashup/component.py
new file mode 100644
index 0000000..f29d76a
--- /dev/null
+++ b/vistrails/core/mashup/component.py
@@ -0,0 +1,325 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import urllib
+from vistrails.core.mashup import conv_from_bool, conv_to_bool, convert_symbols
+from vistrails.db.domain import DBMashupComponent
+
+import unittest
+from vistrails.db.domain import IdScope
+import copy
+
+################################################################################
+class Component(DBMashupComponent):
+ def __init__(self, id, vttype, param_id, parent_vttype, parent_id, mid,
+ type, value, p_pos, pos, strvaluelist, minVal="0",
+ maxVal="1", stepSize="1", parent='', seq=0, widget="text"):
+
+ """Component()
+ widget can be: text, slider, combobox, numericstepper, checkbox
+
+ """
+ DBMashupComponent.__init__(self, id, param_id, vttype, parent_vttype,
+ parent_id, p_pos, mid, pos, type, value,
+ minVal, maxVal, stepSize, strvaluelist,
+ widget, seq, parent)
+ if isinstance(seq, bool):
+ self.seq = seq
+
+ id = DBMashupComponent.db_id
+ vttype = DBMashupComponent.db_vttype
+ vtid = DBMashupComponent.db_vtid
+ vtparent_type = DBMashupComponent.db_vtparent_type
+ vtparent_id = DBMashupComponent.db_vtparent_id
+ vtmid = DBMashupComponent.db_vtmid
+ vtpos = DBMashupComponent.db_vtpos
+ pos = DBMashupComponent.db_pos
+ type = DBMashupComponent.db_type
+ minVal = DBMashupComponent.db_minVal
+ maxVal = DBMashupComponent.db_maxVal
+ stepSize = DBMashupComponent.db_stepSize
+ parent = DBMashupComponent.db_parent
+ widget = DBMashupComponent.db_widget
+ strvaluelist = DBMashupComponent.db_strvaluelist
+
+ def _get_seq(self):
+ return conv_to_bool(self.db_seq)
+ def _set_seq(self, s):
+ self.db_seq = conv_from_bool(s)
+ seq = property(_get_seq,_set_seq)
+
+ def _get_val(self):
+ self.db_val = convert_symbols(self.db_val)
+ return self.db_val
+ def _set_val(self, v):
+ self.db_val = v
+ val = property(_get_val,_set_val)
+
+ def _get_valuelist(self):
+ self.strvaluelist = convert_symbols(self.strvaluelist)
+ data = self.strvaluelist.split(',')
+ result = []
+ for d in data:
+ result.append(urllib.unquote_plus(d))
+ return result
+ def _set_valuelist(self, valuelist):
+ q = []
+ for v in valuelist:
+ q.append(urllib.quote_plus(v))
+ self.strvaluelist = ",".join(q)
+ valueList = property(_get_valuelist,_set_valuelist)
+
+ @staticmethod
+ def convert(_component):
+ _component.__class__ = Component
+
+ def __copy__(self):
+ return Component.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ """do_copy() -> Component
+ returns a clone of itself"""
+ cp = DBMashupComponent.do_copy(self, new_ids, id_scope, id_remap)
+ Component.convert(cp)
+ return cp
+
+ ##########################################################################
+ # Serialization / Unserialization
+
+# def toXml(self, node=None):
+# """toXml(node: ElementTree.Element) -> ElementTree.Element
+# writes itself to xml
+# """
+# if node is None:
+# node = ElementTree.Element('component')
+# #set attributes
+# node.set('id', self.convert_to_str(self.id,'long'))
+# node.set('vttype', self.convert_to_str(self.vttype,'str'))
+# node.set('vtid', self.convert_to_str(self.vtid,'long'))
+# node.set('vtparent_type', self.convert_to_str(self.vtparent_type,'str'))
+# node.set('vtparent_id', self.convert_to_str(self.vtparent_id,'long'))
+# node.set('vtmid', self.convert_to_str(self.vtmid,'long'))
+# node.set('vtpos', self.convert_to_str(self.vtpos,'long'))
+#
+# node.set('pos', self.convert_to_str(self.pos,'long'))
+# node.set('type', self.convert_to_str(self.type,'str'))
+#
+# node.set('val', self.convert_to_str(self.val, 'str'))
+# node.set('minVal', self.convert_to_str(self.minVal,'str'))
+# node.set('maxVal', self.convert_to_str(self.maxVal,'str'))
+# node.set('stepSize', self.convert_to_str(self.stepSize,'str'))
+# node.set('valueList',self.convert_to_str(self.strvaluelist,'str'))
+# node.set('parent', self.convert_to_str(self.parent,'str'))
+# node.set('seq', self.convert_to_str(self.seq,'bool'))
+# node.set('widget',self.convert_to_str(self.widget,'str'))
+# return node
+#
+# @staticmethod
+# def fromXml(node):
+# if node.tag != 'component':
+# return None
+#
+# #read attributes
+# data = node.get('id', None)
+# id = Component.convert_from_str(data, 'long')
+# data = node.get('vttype', None)
+# vttype = Component.convert_from_str(data, 'str')
+# data = node.get('vtid', None)
+# vtid = Component.convert_from_str(data, 'long')
+# data = node.get('vtparent_type', None)
+# vtparent_type = Component.convert_from_str(data, 'str')
+# data = node.get('vtparent_id', None)
+# vtparent_id = Component.convert_from_str(data, 'long')
+# data = node.get('vtmid', None)
+# vtmid = Component.convert_from_str(data, 'long')
+# data = node.get('vtpos', None)
+# vtpos = Component.convert_from_str(data, 'long')
+# data = node.get('pos', None)
+# pos = Component.convert_from_str(data, 'long')
+# data = node.get('type', None)
+# type = Component.convert_from_str(data, 'str')
+# data = node.get('val', None)
+# val = Component.convert_from_str(data, 'str')
+# val = val.replace("<", "<")
+# val = val.replace(">", ">")
+# val = val.replace("&","&")
+# data = node.get('minVal', None)
+# minVal = Component.convert_from_str(data, 'str')
+# data = node.get('maxVal', None)
+# maxVal = Component.convert_from_str(data, 'str')
+# data = node.get('stepSize', None)
+# stepSize = Component.convert_from_str(data, 'str')
+# data = node.get('valueList', None)
+# values = Component.convert_from_str(data, 'str')
+# values = values.replace("<", "<")
+# values = values.replace(">", ">")
+# values = values.replace("&","&")
+# data = node.get('parent', None)
+# parent = Component.convert_from_str(data, 'str')
+# data = node.get('seq', None)
+# seq = Component.convert_from_str(data, 'bool')
+# data = node.get('widget', None)
+# widget = Component.convert_from_str(data, 'str')
+#
+# component = Component(id=id, vttype=vttype, param_id=vtid,
+# parent_vttype=vtparent_type,
+# parent_id=vtparent_id, mid=vtmid, type=type,
+# value=val, p_pos=vtpos, pos=pos,
+# minVal=minVal,
+# maxVal=maxVal,
+# stepSize=stepSize,
+# strvaluelist=values,
+# parent=parent,
+# seq=seq,
+# widget=widget)
+# return component
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """ __str__() -> str - Returns a string representation of itself """
+
+ return ("(Component id='%s' vttype='%s' vtid='%s' vtparent_type='%s' \
+vtparent_id='%s' vtmid='%s' vtpos='%s' type='%s' pos='%s' val='%s' minVal='%s' \
+maxVal='%s' stepSize='%s' strvaluelist='%s' parent='%s' seq='%s' widget='%s')@%X" %
+ (self.id,
+ self.vttype,
+ self.vtid,
+ self.vtparent_type,
+ self.vtparent_id,
+ self.vtmid,
+ self.vtpos,
+ self.type,
+ self.pos,
+ self.val,
+ self.minVal,
+ self.maxVal,
+ self.stepSize,
+ self.strvaluelist,
+ self.parent,
+ self.seq,
+ self.widget,
+ id(self)))
+
+ def __eq__(self, other):
+ """ __eq__(other: Component) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.vttype != other.vttype:
+ return False
+ if self.vtid != other.vtid:
+ return False
+ if self.vtparent_type != other.vtparent_type:
+ return False
+ if self.vtparent_id != other.vtparent_id:
+ return False
+ if self.vtmid != other.vtmid:
+ return False
+ if self.vtpos != other.vtpos:
+ return False
+ if self.type != other.type:
+ return False
+ if self.pos != other.pos:
+ return False
+ if self.val != other.val:
+ return False
+ if self.minVal != other.minVal:
+ return False
+ if self.maxVal != other.maxVal:
+ return False
+ if self.stepSize != other.stepSize:
+ return False
+ if self.strvaluelist != other.strvaluelist:
+ return False
+ if self.parent != other.parent:
+ return False
+ if self.seq != other.seq:
+ return False
+ if self.widget != other.widget:
+ return False
+ return True
+
+ def __ne__(self, other):
+ """ __ne__(other: Component) -> boolean
+ Returns True if self and other don't have the same attributes.
+ Used by != operator.
+
+ """
+ return not self.__eq__(other)
+
+################################################################################
+
+
+class TestComponent(unittest.TestCase):
+ def create_component(self, id_scope=IdScope()):
+ c = Component(id=id_scope.getNewId('mashup_component'),
+ vttype='parameter', param_id=15L,
+ parent_vttype='function', parent_id=3L, mid=4L,
+ type='String', value='test', p_pos=0, pos=1,
+ strvaluelist='test1,test2', widget="text")
+ return c
+
+ def test_copy(self):
+ id_scope = IdScope()
+ c1 = self.create_component(id_scope)
+ c2 = copy.copy(c1)
+ self.assertEqual(c1, c2)
+ self.assertEqual(c1.id, c2.id)
+ c3 = c2.do_copy(True, id_scope, {})
+ self.assertEqual(c1,c3)
+ self.assertNotEqual(c1.id, c3.id)
+
+ def test_valuelist(self):
+ c1 = self.create_component()
+ c1.strvaluelist = "1,2,3"
+ self.assertEqual(['1','2','3'], c1.valueList)
+ c1.valueList = ['1','2','3']
+ self.assertEqual(c1.strvaluelist,"1,2,3")
+
+# #testing values with , after serialization
+# c1.valueList = ['a,b,c', '123', ',as']
+# c2 = Component.fromXml(c1.toXml())
+# self.assertEqual(c1.strvaluelist, c2.strvaluelist)
+# self.assertEqual(c1.valueList, c2.valueList)
+# self.assertEqual(c2.valueList, ['a,b,c', '123', ',as'])
+
+ def test_str(self):
+ c1 = self.create_component()
+ str(c1)
+
\ No newline at end of file
diff --git a/vistrails/core/mashup/controller.py b/vistrails/core/mashup/controller.py
new file mode 100644
index 0000000..97b1ab7
--- /dev/null
+++ b/vistrails/core/mashup/controller.py
@@ -0,0 +1,346 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+import os.path
+from vistrails.core.system import current_user, current_time
+from vistrails.core.mashup.alias import Alias
+from vistrails.core.mashup.component import Component
+from vistrails.core.mashup.mashup import Mashup
+
+class MashupController(object):
+ def __init__(self, originalController, vt_controller, vt_version, mshptrail=None):
+ self.vtController = vt_controller
+ self.originalController = originalController
+ self.vtVersion = vt_version
+ self.vtPipeline = self.vtController.vistrail.getPipeline(self.vtVersion)
+ self.vtPipeline.validate()
+ self.mshptrail = mshptrail
+ self.id_scope = mshptrail.id_scope
+ self.currentVersion = -1
+ self.currentMashup = None
+ self._changed = False
+
+ def setChanged(self, on):
+ self._changed = on
+ self.originalController.set_changed(True)
+
+ def setCurrentVersion(self, version):
+ self.currentVersion = version
+ self.vtPipeline = self.vtController.vistrail.getPipeline(self.vtVersion)
+ if version > -1:
+ self.currentMashup = self.mshptrail.getMashup(version)
+ self.updatePipelineAliasesFromCurrentMashup()
+
+ def getVistrailParam(self, alias):
+ if self.vtPipeline:
+ return self.vtPipeline.db_get_object(alias.component.vttype,
+ alias.component.vtid)
+ return None
+
+ def execute(self, params):
+ if self.vtPipeline and self.vtController:
+ mashup_id = self.mshptrail.id
+ mashup_version = self.currentVersion
+ reason = "mashup::%s::%s"%(str(mashup_id), mashup_version)
+ result = self.vtController.execute_current_workflow(custom_params=params,
+ reason=reason)
+ self.originalController.set_changed(True)
+ return result
+ return ([], False)
+
+ def updateCurrentTag(self, name):
+ if self.mshptrail.changeTag(self.currentVersion, name, current_user(),
+ current_time()):
+ self.setChanged(True)
+ return True
+ else:
+ return False
+
+ def moveTag(self, from_version, to_version, name):
+ tag = self.mshptrail.getTagForActionId(from_version)
+ if tag:
+ self.mshptrail.removeTagByActionId(from_version)
+ self.mshptrail.addTag(to_version, tag, user=current_user(),
+ date=current_time())
+
+ def getCurrentTag(self):
+ return self.mshptrail.getTagForActionId(self.currentVersion)
+
+ def versionHasTag(self, version):
+ return self.mshptrail.hasTagForActionId(version)
+
+ def hasTagWithName(self, name):
+ return self.mshptrail.hasTagWithName(name)
+
+ def getVistrailName(self):
+ name = ''
+ locator = self.currentMashup.vtid
+ if locator != None:
+ if locator.name == None:
+ name = ''
+ else:
+ name = os.path.split(locator.name)[1]
+ if name == '':
+ name = self.controller.vtController.name
+ return name
+
+ def resetVistrailPipeline(self):
+ self.vtController.change_selected_version(self.vtVersion)
+
+ def getVistrailWorkflowTag(self):
+ return self.vtController.get_pipeline_name(self.vtVersion)
+
+ def reorderAliases(self, new_order):
+ if self.currentMashup:
+ new_aliases = []
+ pos = 0
+ for old_pos in new_order:
+ alias = copy.copy(self.currentMashup.alias_list[old_pos])
+ alias.component.pos = pos
+ new_aliases.append(alias)
+ pos += 1
+ return self.createMashupVersion(new_aliases, quiet=False)
+
+ def updateAlias(self, alias):
+ """updateAlias(alias)-> long
+ This will create a version with an alias change (can't be a position
+ change). Position changes are taken care in reorderAliases method.
+
+ """
+ #print " controller updateAlias ", alias
+ new_aliases = []
+
+ if self.currentMashup:
+ for a in self.currentMashup.alias_list:
+ if a.id != alias.id:
+ calias = copy.copy(a)
+ else:
+ #print "found alias: ", a
+ calias = copy.copy(alias)
+ new_aliases.append(calias)
+ return self.createMashupVersion(new_aliases, quiet=False)
+
+ def updateAliasFromParam(self, param):
+ add_alias = True
+ new_aliases = []
+ pos = 0
+ for alias in self.currentMashup.alias_list:
+ if alias.component.vtid != param.id:
+ calias = copy.copy(alias)
+ calias.component.pos = pos
+ new_aliases.append(calias)
+ pos += 1
+ else:
+ #print "found alias: ", alias
+ add_alias = False
+ if param.alias != '':
+ new_alias = copy.copy(alias)
+ new_alias.name = param.alias
+ new_aliases.append(new_alias)
+ pos += 1
+ if add_alias:
+ parameter = self.vtPipeline.db_get_object(param.dbtype, param.id)
+ cid = self.id_scope.getNewId('component')
+ aid = self.id_scope.getNewId('alias')
+ component = Component(cid, parameter.vtType,
+ parameter.real_id, param.parent_dbtype,
+ param.parent_id,
+ param.mId, parameter.type,
+ parameter.strValue, parameter.pos,
+ pos, "")
+ alias = Alias(aid, param.alias, component)
+ new_aliases.append(alias)
+ self.vtPipeline.add_alias(param.alias, param.type, param.id,
+ param.parent_dbtype, param.parent_id,
+ param.mId)
+ else:
+ self.vtPipeline.change_alias(param.alias, param.type, param.id,
+ param.parent_dbtype, param.parent_id,
+ param.mId)
+
+ return self.createMashupVersion(new_aliases, quiet=False)
+
+ def updateAliasesFromPipeline(self, pipeline):
+ """updateAliasesFromPipeline(self, pipeline) -> long
+ This will generate a new mashup by updating the aliases of the current
+ mashup according to the aliases in a pipeline. This assumes that the
+ mashup's current aliases are different from pipeline aliases by at most
+ one change (eg., an alias rename, an alias addition, an alias removal)
+
+ """
+ pip_aliases = pipeline.aliases.keys()
+ mashup_aliases = [a.name for a in self.currentMashup.alias_list]
+ new_aliases = []
+ if len(pip_aliases) == len(mashup_aliases):
+ #an alias probably changed its name or its value
+ old_a = None
+ new_a = None
+ for a in self.currentMashup.alias_list:
+ if a.name not in pip_aliases:
+ old_a = copy.copy(a)
+ new_aliases.append(old_a)
+ else:
+ new_aliases.append(a)
+ for a in pip_aliases:
+ if a not in mashup_aliases:
+ new_a = (a, pipeline.aliases[a])
+ if old_a is not None and new_a is not None:
+ (a, info) = new_a
+ parameter = pipeline.db_get_object(info[0],info[1])
+ old_a.name = a
+ old_a.component.vttype = parameter.vtType
+ old_a.component.vtid = parameter.real_id
+ old_a.component.vtparent_type = info[2]
+ old_a.component.vt_parent_id = info[3]
+ old_a.component.mid = info[4]
+ old_a.component.type = parameter.type
+ old_a.component.val = parameter.strValue
+ old_a.component.vtpos = parameter.pos
+
+ elif len(pip_aliases) < len(mashup_aliases):
+ # an alias was removed
+ pos = 0
+ for a in self.currentMashup.alias_list:
+ if a.name in pip_aliases:
+ alias = copy.copy(a)
+ alias.component.pos = pos
+ new_aliases.append(alias)
+ pos += 1
+ else:
+ #an alias was added
+ pos = len(mashup_aliases)
+ new_aliases = [a for a in self.currentMashup.alias_list]
+ for a in pip_aliases:
+ if a not in mashup_aliases:
+ info = pipeline.aliases[a]
+ parameter = pipeline.db_get_object(info[0],info[1])
+ cid = self.id_scope.getNewId('component')
+ aid = self.id_scope.getNewId('alias')
+ component = Component(cid, parameter.vtType,
+ parameter.real_id, info[2], info[3],
+ info[4], parameter.type,
+ parameter.strValue, parameter.pos,
+ pos, "")
+ alias = Alias(aid, a, component)
+ new_aliases.append(alias)
+ pos += 1
+
+ return self.createMashupVersion(new_aliases, quiet=False)
+
+ def updatePipelineAliasesFromCurrentMashup(self):
+ self.resetVistrailPipeline()
+ self.vtPipeline = copy.copy(self.vtController.current_pipeline)
+ #first we clear all aliases in pipeline
+ to_remove = self.vtPipeline.aliases.values()
+ for (type, oId, parentType, parentId, mid) in to_remove:
+ self.vtPipeline.remove_alias(type, oId, parentType, parentId, mid)
+ parameter = self.vtPipeline.db_get_object(type,oId)
+ parameter.alias = ''
+
+ #now we populate the pipeline according to the aliases in the mashup
+ for alias in self.currentMashup.alias_list:
+ self.vtPipeline.add_alias(alias.name, alias.component.vttype,
+ alias.component.vtid,
+ alias.component.vtparent_type,
+ alias.component.vtparent_id,
+ alias.component.vtmid)
+ parameter = self.vtPipeline.db_get_object(alias.component.vttype,
+ alias.component.vtid)
+ parameter.alias = alias.name
+
+ def getMashupName(self, version=-1):
+ action_map = self.mshptrail.actionMap
+ if version == -1:
+ version = self.currentVersion
+ count = 0
+ while True:
+ hasTag = self.mshptrail.hasTagForActionId(version)
+ if hasTag or version <= 1:
+ if hasTag:
+ name = self.mshptrail.getTagForActionId(version)
+ else:
+ name = "ROOT"
+ count_str = ""
+ if count > 0:
+ count_str = " + " + str(count)
+ return name + count_str
+ version = action_map[version].parent_id
+ count += 1
+
+ def findFirstTaggedParent(self, version):
+ action_map = self.mshptrail.actionMap
+ version = action_map[version].parent_id
+ while True:
+ hasTag = self.mshptrail.hasTagForActionId(version)
+ if hasTag or version <= 1:
+ name = ""
+ if hasTag:
+ name = self.mshptrail.getTagForActionId(version)
+ return (version, name)
+ version = action_map[version].parent_id
+
+ def removeAlias(self, name):
+ """removeAlias(name: str) -> long
+ This will create a new version of the mashup without alias name, add it
+ to the trail and set the version as the current version. It will return
+ the version number
+ """
+ new_aliases = []
+ if self.currentMashup:
+ pos = 0
+ for alias in self.currentMashup.alias_list:
+ if alias.name != name:
+ calias = copy.copy(alias)
+ calias.component.pos = pos
+ new_aliases.append(calias)
+ pos += 1
+ return self.createMashupVersion(alias_list=new_aliases, quiet=False)
+
+ def createMashupVersion(self, alias_list, quiet=False):
+ id = self.id_scope.getNewId('mashup')
+ mashup = Mashup(id=id, name="mashup%s"%id,
+ vtid=self.currentMashup.vtid,
+ version=self.currentMashup.version,
+ alias_list=alias_list)
+ currVersion = self.mshptrail.addVersion(parent_id=self.currentVersion,
+ mashup=mashup,
+ user=current_user(),
+ date=current_time())
+ self.mshptrail.currentVersion = currVersion
+ self.currentMashup = mashup
+ #print "created new mashup ", currVersion
+ self.setCurrentVersion(currVersion, quiet)
+ self.setChanged(True)
+ return currVersion
diff --git a/vistrails/core/mashup/mashup.py b/vistrails/core/mashup/mashup.py
new file mode 100644
index 0000000..fd83b10
--- /dev/null
+++ b/vistrails/core/mashup/mashup.py
@@ -0,0 +1,324 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import IdScope
+from vistrails.db.domain import DBMashup
+from vistrails.core.mashup import conv_to_bool, conv_from_bool
+from vistrails.core.mashup.alias import Alias
+from vistrails.core.mashup.component import Component
+from vistrails.core.system import get_elementtree_library
+
+import unittest
+import copy
+
+ElementTree = get_elementtree_library()
+
+class Mashup(DBMashup):
+ def __init__(self, id, name, vtid=None, version=None, alias_list=None,
+ t='vistrail', has_seq=None, layout='', geometry='',
+ id_scope=IdScope()):
+ if has_seq == None:
+ has_seq = 0
+
+ DBMashup.__init__(self, id, name, version, alias_list, t, vtid, layout,
+ geometry, has_seq)
+ self.id_scope = id_scope
+ if has_seq == None:
+ self.has_seq = False
+ if isinstance(self.alias_list, list):
+ for v in self.alias_list:
+ if v.component.seq == True:
+ self.has_seq = True
+ else:
+ self.has_seq = has_seq
+ id = DBMashup.db_id
+ name = DBMashup.db_name
+ version = DBMashup.db_version
+ alias_list = DBMashup.db_aliases
+ aliases = DBMashup.db_aliases
+ vtid = DBMashup.db_vtid
+ type = DBMashup.db_type
+ layout = DBMashup.db_layout
+ geometry = DBMashup.db_geometry
+
+ def _get_has_seq(self):
+ return conv_to_bool(self.db_has_seq)
+ def _set_has_seq(self, s):
+ self.db_has_seq = conv_from_bool(s)
+ has_seq = property(_get_has_seq,_set_has_seq)
+
+ @staticmethod
+ def convert(_mashup):
+ _mashup.__class__ = Mashup
+
+ for alias in _mashup.alias_list:
+ Alias.convert(alias)
+
+ def __copy__(self):
+ return Mashup.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ """do_copy() -> Mashup
+ returns a clone of itself"""
+ cp = DBMashup.do_copy(self, new_ids, id_scope, id_remap)
+ Mashup.convert(cp)
+ return cp
+
+ ##########################################################################
+ # Serialization / Unserialization
+
+# def toXml(self, node=None):
+# """toXml(node: ElementTree.Element) -> ElementTree.Element
+# writes itself to xml
+# """
+#
+# if node is None:
+# node = ElementTree.Element('mashup')
+#
+# #set attributes
+# node.set('id', self.convert_to_str(self.id,'long'))
+# node.set('version', self.convert_to_str(self.version,'long'))
+# node.set('vtid', self.convert_to_str(self.vtid,'str'))
+# node.set('name', self.convert_to_str(self.name,'str'))
+# node.set('type', self.convert_to_str(self.type,'str'))
+# node.set('has_seq', self.convert_to_str(self.has_seq,'bool'))
+# for v in self.alias_list:
+# child_ = ElementTree.SubElement(node, 'alias')
+# v.toXml(child_)
+#
+# layoutnode = ElementTree.SubElement(node,'layout')
+# layoutnode.text = str(self.layout)
+#
+# geomnode = ElementTree.SubElement(node,'geometry')
+# geomnode.text = str(self.geometry)
+#
+# return node
+#
+# @staticmethod
+# def fromXml(node):
+# if node.tag != 'mashup':
+# #print "node.tag != 'mashup'"
+# return None
+# #read attributes
+# data = node.get('id', None)
+# id = Mashup.convert_from_str(data, 'long')
+# data = node.get('name', None)
+# name = Mashup.convert_from_str(data, 'str')
+# data = node.get('version', None)
+# version = Mashup.convert_from_str(data, 'long')
+# data = node.get('vtid', None)
+# vtid = Mashup.convert_from_str(data, 'str')
+# data = node.get('type', None)
+# type = Mashup.convert_from_str(data, 'str')
+# data = node.get('has_seq', None)
+# seq = Component.convert_from_str(data, 'bool')
+# alias_list = []
+# layout = None
+# geometry = None
+# for child in node.getchildren():
+# if child.tag == "alias":
+# alias = Alias.fromXml(child)
+# alias_list.append(alias)
+# if child.tag == "layout":
+# layout = str(child.text).strip(" \n\t")
+# if child.tag == "geometry":
+# geometry = str(child.text).strip(" \n\t")
+# return Mashup(id=id, name=name, vtid=vtid, version=version,
+# alias_list=alias_list, t=type, has_seq=seq,
+# layout=layout, geometry=geometry)
+
+ def loadAliasesFromPipeline(self, pipeline, id_scope):
+ """loadAliasesFromPipelines(pipeline: Pipeline) -> None
+ This will replace current aliases with the ones present in Pipeline
+
+ """
+
+ if pipeline:
+ self.alias_list = []
+ if len(pipeline.aliases) > 0:
+ pos = 0
+ for aname,info in pipeline.aliases.iteritems():
+ parameter = pipeline.db_get_object(info[0],info[1])
+ cid = id_scope.getNewId('component')
+ aid = id_scope.getNewId('alias')
+ component = Component(cid, parameter.vtType,
+ parameter.real_id, info[2], info[3],
+ info[4], parameter.type,
+ parameter.strValue, parameter.pos,
+ pos, "")
+ alias = Alias(aid, aname, component)
+ self.alias_list.append(alias)
+ pos += 1
+
+ def remapPipelineObjects(self, id_remap):
+ for alias in self.alias_list:
+ try:
+ new_pid = id_remap[(alias.component.vtparent_type,
+ alias.component.vtparent_id)]
+ alias.component.vtparent_id = new_pid
+ new_id = id_remap[(alias.component.vttype,alias.component.vtid)]
+ alias.component.vtid = new_id
+ except:
+ pass
+
+ def validateForPipeline(self, pipeline):
+ """validateForPipeline(pipeline) -> None
+ This will make sure that the parameters in the alias list are present
+ in the pipeline. If they were removed, the aliases pointing to it will
+ be removed. This changes the mashup in place """
+ to_remove = []
+ for alias in self.alias_list:
+ try:
+ param = pipeline.db_get_object(alias.component.vttype,
+ alias.component.vtid)
+ except:
+ to_remove.append(alias)
+ for a in to_remove:
+ self.alias_list.remove(a)
+ pos = 0
+ mashup_aliases = []
+ for a in self.alias_list:
+ mashup_aliases.append(a.name)
+ a.component.pos = pos
+ pos+=1
+
+ for a, info in pipeline.aliases.iteritems():
+ if a not in mashup_aliases:
+ parameter = pipeline.db_get_object(info[0],info[1])
+ cid = self.id_scope.getNewId('component')
+ aid = self.id_scope.getNewId('alias')
+ component = Component(cid, parameter.vtType,
+ parameter.real_id, info[2], info[3],
+ info[4], parameter.type,
+ parameter.strValue, parameter.pos,
+ pos, "")
+ newalias = Alias(aid, a, component)
+ self.alias_list.append(newalias)
+ pos +=1
+
+ def getAliasByName(self, name):
+ for alias in self.alias_list:
+ if alias.name == name:
+ return alias
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """ __str__() -> str - Returns a string representation of itself """
+
+ return ("(Mashup id='%s' name='%s' version='%s' vtid='%s' type='%s' \
+layout='%s' geometry='%s' alias_list='%s')@%X" %
+ (self.id,
+ self.name,
+ self.version,
+ self.vtid,
+ self.type,
+ self.layout,
+ self.geometry,
+ self.alias_list,
+ id(self)))
+
+ def __eq__(self, other):
+ """ __eq__(other: Mashup) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.name != other.name:
+ return False
+ if self.vtid != other.vtid:
+ return False
+ if self.version != other.version:
+ return False
+ if self.type != other.type:
+ return False
+ if self.layout != other.layout:
+ return False
+ if self.geometry != other.geometry:
+ return False
+ if len(self.alias_list) != len(other.alias_list):
+ return False
+ for p,q in zip(self.alias_list, other.alias_list):
+ if p != q:
+ return False
+ return True
+
+ def __ne__(self, other):
+ """ __ne__(other: Component) -> boolean
+ Returns True if self and other don't have the same attributes.
+ Used by != operator.
+
+ """
+ return not self.__eq__(other)
+
+################################################################################
+
+
+class TestMashup(unittest.TestCase):
+ def create_mashup(self, id_scope=IdScope()):
+ c1 = Component(id=id_scope.getNewId('component'),
+ vttype='parameter', param_id=15L,
+ parent_vttype='function', parent_id=3L, mid=4L,
+ type='String', value='test', p_pos=0, pos=1,
+ strvaluelist='test1,test2', widget="text")
+ a1 = Alias(id=id_scope.getNewId('alias'), name='alias1', component=c1)
+
+ m = Mashup(id=id_scope.getNewId('mashup'), name='mashup1', vtid='empty.vt',
+ version=15L, alias_list=[a1])
+ return m
+
+ def test_copy(self):
+ id_scope = IdScope()
+ m1 = self.create_mashup(id_scope)
+ m2 = copy.copy(m1)
+ self.assertEqual(m1, m2)
+ self.assertEqual(m1.id, m2.id)
+ m3 = m2.do_copy(True, id_scope, {})
+ self.assertEqual(m1, m3)
+ self.assertNotEqual(m1.id, m3.id)
+
+# def test_serialization(self):
+# m1 = self.create_mashup()
+# node = m1.toXml()
+# m2 = Mashup.fromXml(node)
+# self.assertEqual(m1, m2)
+# self.assertEqual(m1.id, m2.id)
+
+ def test_str(self):
+ m1 = self.create_mashup()
+ str(m1)
+
\ No newline at end of file
diff --git a/vistrails/core/mashup/mashup_trail.py b/vistrails/core/mashup/mashup_trail.py
new file mode 100644
index 0000000..b0e41d6
--- /dev/null
+++ b/vistrails/core/mashup/mashup_trail.py
@@ -0,0 +1,271 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from vistrails.db.domain import IdScope
+from vistrails.db.domain import DBMashuptrail
+from vistrails.core.mashup.action import Action
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.mashup.action_annotation import ActionAnnotation
+
+################################################################################
+
+class Mashuptrail(DBMashuptrail):
+ """ MashupTrail is a class that stores versions of Mashups.
+ For now it keeps a linear history."""
+ def __init__(self, id, vt_version, id_scope=None):
+ DBMashuptrail.__init__(self, None, id, version="", vtVersion=vt_version)
+ self.db_actions = []
+ self.currentVersion = -1
+ self.db_annotations = []
+ self.db_actionAnnotations = []
+ if not id_scope:
+ self.id_scope = IdScope(1L)
+ else:
+ self.id_scope = id_scope
+
+ id = DBMashuptrail.db_name
+ vtVersion = DBMashuptrail.db_vtVersion
+ actions = DBMashuptrail.db_actions
+ annotations = DBMashuptrail.db_annotations
+ actionAnnotations = DBMashuptrail.db_actionAnnotations
+
+ def _get_actionMap(self):
+ return self.db_actions_id_index
+ actionMap = property(_get_actionMap)
+
+ @staticmethod
+ def convert(_mtrail):
+ _mtrail.__class__ = Mashuptrail
+
+ for action in _mtrail.actions:
+ Action.convert(action)
+
+ for annotation in _mtrail.annotations:
+ Annotation.convert(annotation)
+
+ for aannotation in _mtrail.actionAnnotations:
+ ActionAnnotation.convert(aannotation)
+ _mtrail.id_scope = IdScope(1L)
+ _mtrail.updateIdScope()
+
+ def addVersion(self, parent_id, mashup, user, date):
+ id = self.getLatestVersion() + 1
+ mashup.id_scope = self.id_scope
+ mashup.id = id
+ mashup.version = self.vtVersion
+ action = Action(id=id, prevId=parent_id, mashup=mashup,
+ user=user, date=date)
+ self.db_add_action(action)
+
+ return action.id
+
+ def __copy__(self):
+ return Mashuptrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ """do_copy() -> Mashuptrail
+ returns a clone of itself"""
+ cp = DBMashuptrail.do_copy(self, new_ids, id_scope, id_remap)
+ Mashuptrail.convert(cp)
+ cp.currentVersion = self.currentVersion
+ return cp
+
+ def getLatestVersion(self):
+ try:
+ max_ver = max(a.id for a in self.actions)
+ return max_ver
+ except:
+ return 0
+
+ def getMashup(self, version):
+ if version in self.actionMap.keys():
+ return self.actionMap[version].mashup
+ else:
+ return None
+
+ def validateMashupsForPipeline(self, version, pipeline):
+ """validateMashupsForPipeline(version:long, pipeline:Pipeline)->None
+ This will make sure that the aliases present in all mashups are
+ consistent with the current pipeline.
+
+ """
+ for action in self.actions:
+ action.mashup.id_scope = self.id_scope
+ action.mashup.validateForPipeline(pipeline)
+ action.mashup.version = version
+
+ ####################################################################
+ ## Tag manipulation
+ ##
+ def hasTagWithName(self, name):
+ for a in self.actionAnnotations:
+ if a.key == "__tag__":
+ if a.value == name:
+ return True
+ return False
+
+ def hasTagForActionId(self, action_id):
+ for a in self.actionAnnotations:
+ if a.key == "__tag__" and a.action_id == action_id:
+ return True
+ return False
+
+ def getTagForActionId(self, action_id):
+ for a in self.actionAnnotations:
+ if a.key == "__tag__" and a.action_id == action_id:
+ return a.value
+ return ""
+
+ def changeTag(self, action_id, name, user, date):
+ if self.hasTagWithName(name):
+ return False
+ if self.hasTagForActionId(action_id):
+ self.removeTagByActionId(action_id)
+ return self.addTag(action_id, name, user, date)
+
+ def addTag(self, action_id, name, user, date):
+ if not self.hasTagWithName(name):
+ self.addActionAnnotation(action_id=action_id, key="__tag__",
+ value=name, user=user, date=date)
+ return True
+ return False
+
+ def removeTagByActionId(self, action_id):
+ found = None
+ for a in self.actionAnnotations:
+ if a.key == "__tag__" and a.action_id == action_id:
+ found = a
+ break
+ if found:
+ self.actionAnnotations.remove(found)
+
+ def getTagMap(self):
+ """getTagMap() -> dict of tag:action_id"""
+ tagMap = {}
+ for a in self.actionAnnotations:
+ if a.key == "__tag__":
+ tagMap[a.value] = a.action_id
+ return tagMap
+
+ def addActionAnnotation(self, action_id, key, value, user, date):
+ id = self.id_scope.getNewId("mashup_actionAnnotation")
+ annot = ActionAnnotation(id=id, action_id=action_id, key=key,
+ value=value, user=user, date=date)
+ self.actionAnnotations.append(annot)
+
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """ __str__() -> str - Returns a string representation of itself """
+
+ return ("(Mashuptrail id='%s' vtVersion='%s' actions='%s')@%X" %
+ (self.id,
+ self.vtVersion,
+ self.actions,
+ id(self)))
+
+ ######################################################################
+ ## Serialization and Unserialization
+ ##
+# def toXml(self, node=None):
+# """toXml(node: ElementTree.Element) -> ElementTree.Element
+# writes itself to xml
+# """
+#
+# if node is None:
+# node = ElementTree.Element('mashuptrail')
+#
+# #set attributes
+# node.set('id', self.convert_to_str(self.id, 'uuid'))
+# node.set('vtVersion', self.convert_to_str(self.vtVersion,'long'))
+# node.set('version', self.convert_to_str(self.version, 'str'))
+# for action in self.actions:
+# child_ = ElementTree.SubElement(node, 'action')
+# action.toXml(child_)
+# for annot in self.annotations:
+# child_ = ElementTree.SubElement(node, 'actionAnnotation')
+# annot.toXml(child_)
+# return node
+#
+# @staticmethod
+# def fromXml(node):
+# if node.tag != 'mashuptrail':
+# debug.debug("node.tag != 'mashuptrail'")
+# return None
+# #read attributes
+# data = node.get('id', None)
+# id = Mashuptrail.convert_from_str(data, 'uuid')
+# data = node.get('vtVersion', None)
+# vtVersion = Mashuptrail.convert_from_str(data, 'long')
+# data = node.get('version', None)
+# version = Mashuptrail.convert_from_str(data, 'str')
+# actions = []
+# action_map = {}
+# annotations = []
+# for child in node.getchildren():
+# if child.tag == 'action':
+# action = Action.fromXml(child)
+# actions.append(action)
+# action_map[action.id] = action
+# elif child.tag == 'actionAnnotation':
+# annot = ActionAnnotation.fromXml(child)
+# annotations.append(annot)
+#
+# mtrail = Mashuptrail(id,vtVersion)
+# mtrail.version = version
+# mtrail.actions = actions
+# mtrail.actionMap = action_map
+# mtrail.annotations = annotations
+# mtrail.currentVersion = mtrail.getLatestVersion()
+# mtrail.updateIdScope()
+# return mtrail
+
+ ######################################################################
+ ## IdScope
+ ##
+ def updateIdScope(self):
+ for action in self.actions:
+ self.id_scope.updateBeginId('mashup_action', action.id+1)
+ for alias in action.mashup.alias_list:
+ self.id_scope.updateBeginId('mashup_alias', alias.id+1)
+ self.id_scope.updateBeginId('mashup_component', alias.component.id+1)
+ for annotation in self.annotations:
+ self.id_scope.updateBeginId('annotation', annotation.id+1)
+ for aannotation in self.actionAnnotations:
+ self.id_scope.updateBeginId('mashup_actionAnnotation', aannotation.id+1)
+
+
diff --git a/vistrails/core/modules/__init__.py b/vistrails/core/modules/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/core/modules/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/core/modules/abstraction.py b/vistrails/core/modules/abstraction.py
new file mode 100644
index 0000000..aff73cc
--- /dev/null
+++ b/vistrails/core/modules/abstraction.py
@@ -0,0 +1,180 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import os
+import re
+from itertools import chain
+
+from vistrails.core import debug
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core.modules.vistrails_module import Module, ModuleError
+from vistrails.core.modules.sub_module import read_vistrail, new_abstraction, \
+ get_abstraction_dependencies, save_abstraction
+import vistrails.core.modules.module_registry
+from vistrails.core.system import vistrails_version
+from vistrails.core.utils import InvalidPipeline
+
+name = 'My SubWorkflows'
+version = '1.6'
+identifier = 'local.abstractions'
+
+my_vistrails = {}
+
+def initialize(*args, **kwargs):
+ import vistrails.core.packagemanager
+ manager = vistrails.core.packagemanager.get_package_manager()
+
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+# conf = get_vistrails_configuration()
+# if conf.check("userPackageDirectory"):
+# if conf.check('userPackageDirectory'):
+# abstraction_dir = os.path.join(conf.userPackageDirectory,
+# 'abstractions')
+
+# abs_fnames = []
+# p = re.compile(r".*\.vt")
+# for abstraction in os.listdir(abstraction_dir):
+# if p.match(abstraction):
+# abs_fnames.append(os.path.join(abstraction_dir, abstraction))
+ abs_vistrails = my_vistrails
+ last_count = len(my_vistrails) + 1
+
+ missing_depends = {}
+ cannot_load = {}
+ while len(abs_vistrails) > 0 and len(abs_vistrails) < last_count:
+ new_vistrails = {}
+ for (abs_name, abs_info) in abs_vistrails.iteritems():
+ (abs_vistrail, abs_fname, abs_depends) = abs_info
+ packages = get_abstraction_dependencies(abs_vistrail)
+ add_abstraction = True
+ for package, inter_depends in packages.iteritems():
+ if package != identifier:
+ if not manager.has_package(package):
+ add_abstraction = False
+ cannot_load[abs_name] = abs_vistrail
+ break
+ else:
+ for descriptor_info in inter_depends:
+ if not reg.has_descriptor_with_name(*descriptor_info):
+ add_abstraction = False
+ new_vistrails[abs_name] = abs_info
+ missing_depends[abs_name] = "Missing module '%s:%s'"\
+ % (descriptor_info[0],
+ descriptor_info[1])
+ break
+ if add_abstraction:
+ abstraction = None
+ try:
+ abstraction = \
+ new_abstraction(abs_name, abs_vistrail, abs_fname)
+ except InvalidPipeline, e:
+ # handle_invalid_pipeline will raise it's own InvalidPipeline
+ # exception if it fails
+ try:
+ import vistrails.core.vistrail.controller
+ module_version = abs_vistrail.get_latest_version()
+ # Use a "dummy" controller to handle the upgrade
+ controller = vistrails.core.vistrail.controller.VistrailController(abs_vistrail)
+ (new_version, new_pipeline) = \
+ controller.handle_invalid_pipeline(e, long(module_version),
+ abs_vistrail, False, True)
+ del controller
+ save_abstraction(abs_vistrail, abs_fname)
+ abstraction = new_abstraction(abs_name, abs_vistrail, abs_fname,
+ new_version, new_pipeline)
+ except Exception, _e:
+ cannot_load[abs_name] = (abs_vistrail, _e)
+ except Exception, e:
+ cannot_load[abs_name] = (abs_vistrail, e)
+ if abstraction is not None:
+ options = {'namespace': abstraction.uuid,
+ 'hide_namespace': True,
+ 'version': str(abstraction.internal_version)}
+ reg.auto_add_module((abstraction, options))
+ reg.auto_add_ports(abstraction)
+ # print "Added subworkflow", abs_name, abstraction.uuid
+ elif abs_name not in cannot_load:
+ cannot_load[abs_name] = (abs_vistrail, '')
+ last_count = len(abs_vistrails)
+ abs_vistrails = new_vistrails
+
+ for abs_name, (_, e) in cannot_load.iteritems():
+ debug.critical("Cannot load subworkflow '%s'" % abs_name)
+ if e:
+ debug.critical("- %s" % e)
+ for abs_name in abs_vistrails:
+ if abs_name in missing_depends:
+ debug.critical("Cannot load subworkflow '%s'" % abs_name,
+ missing_depends[abs_name])
+ else:
+ debug.critical("Cannot load subworkflow '%s'" % abs_name)
+
+def package_dependencies():
+ import vistrails.core.packagemanager
+ manager = vistrails.core.packagemanager.get_package_manager()
+
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ conf = get_vistrails_configuration()
+ if conf.check("abstractionsDirectory"):
+ abstraction_dir = conf.abstractionsDirectory
+ p = re.compile(r".*\.xml")
+ all_packages = set()
+ for abstraction in os.listdir(abstraction_dir):
+ if p.match(abstraction):
+ abs_fname = os.path.join(abstraction_dir, abstraction)
+ try:
+ vistrail = read_vistrail(abs_fname)
+ dependencies = get_abstraction_dependencies(vistrail)
+ except vistrails.core.modules.module_registry.MissingPackage, e:
+ dependencies = {e._identifier: set()}
+ add_abstraction = True
+ inter_depends = []
+ for package, depends in dependencies.iteritems():
+ if package != identifier:
+ if not manager.has_package(package):
+ add_abstraction = False
+ break
+ else:
+ inter_depends.append(depends)
+ if add_abstraction:
+ # print 'adding', abstraction[:-4]
+ all_packages.update(p for p in dependencies.iterkeys()
+ if p != identifier)
+ my_vistrails[abstraction[:-4]] = \
+ (vistrail, abs_fname, inter_depends)
+ else:
+ debug.critical(("Subworkflow '%s' is missing packages it " +
+ "depends on") % abstraction)
+ # print 'all_packages:', all_packages
+ return list(all_packages)
diff --git a/vistrails/core/modules/basic_modules.py b/vistrails/core/modules/basic_modules.py
new file mode 100644
index 0000000..2a17b6d
--- /dev/null
+++ b/vistrails/core/modules/basic_modules.py
@@ -0,0 +1,1710 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""basic_modules defines basic VisTrails Modules that are used in most
+pipelines."""
+import vistrails.core.cache.hasher
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.modules.vistrails_module import Module, new_module, \
+ Converter, NotCacheable, ModuleError
+import vistrails.core.system
+from vistrails.core.utils import InstanceObject
+from vistrails.core import debug
+
+from abc import ABCMeta
+from itertools import izip
+import os
+import pickle
+import re
+import shutil
+#import zipfile
+import urllib
+
+try:
+ import hashlib
+ sha_hash = hashlib.sha1
+except ImportError:
+ import sha
+ sha_hash = sha.new
+
+###############################################################################
+
+version = '2.1'
+name = 'Basic Modules'
+identifier = 'org.vistrails.vistrails.basic'
+old_identifiers = ['edu.utah.sci.vistrails.basic']
+
+class Constant(Module):
+ """Base class for all Modules that represent a constant value of
+ some type.
+
+ When implementing your own constant, You have to adhere to the
+ following interface:
+
+ Implement the following methods:
+
+ translate_to_python(x): Given a string, translate_to_python
+ must return a python value that will be the value seen by the
+ execution modules.
+
+ For example, translate_to_python called on a float parameter
+ with value '3.15' will return float('3.15').
+
+ translate_to_string(): Return a string representation of the
+ current constant, which will eventually be passed to
+ translate_to_python.
+
+ validate(v): return True if given python value is a plausible
+ value for the constant. It should be implemented such that
+ validate(translate_to_python(x)) == True for all valid x
+
+ A constant must also expose its default value, through the field
+ default_value.
+
+ There are fields you are not allowed to use in your constant classes.
+ These are: 'id', 'interpreter', 'logging' and 'change_parameter'
+
+ You can also define the constant's own GUI widget.
+ See core/modules/constant_configuration.py for details.
+
+ """
+ def compute(self):
+ """Constant.compute() only checks validity (and presence) of
+ input value."""
+ v = self.getInputFromPort("value")
+ b = self.validate(v)
+ if not b:
+ raise ModuleError(self, "Internal Error: Constant failed validation")
+ self.setResult("value", v)
+ self.setResult("value_as_string", self.translate_to_string(v))
+
+ def setValue(self, v):
+ self.setResult("value", self.translate_to_python(v))
+ self.upToDate = True
+
+ def serialize(self):
+ return self.outputPorts['value_as_string']
+
+ def deserialize(self, v):
+ return self.translate_to_python(v)
+
+ @staticmethod
+ def translate_to_string(v):
+ return str(v)
+
+ @staticmethod
+ def get_widget_class():
+ # return StandardConstantWidget
+ return None
+
+ @staticmethod
+ def get_query_widget_class():
+ return None
+
+ @staticmethod
+ def get_param_explore_widget_list():
+ return []
+
+ @staticmethod
+ def query_compute(value_a, value_b, query_method):
+ if query_method == '==' or query_method is None:
+ return (value_a == value_b)
+ elif query_method == '!=':
+ return (value_a != value_b)
+ return False
+
+def new_constant(name, py_conversion=None, default_value=None, validation=None,
+ widget_type=None,
+ str_conversion=None, base_class=Constant,
+ compute=None, query_widget_type=None,
+ query_compute=None,
+ param_explore_widget_list=None):
+ """new_constant(name: str,
+ py_conversion: callable,
+ default_value: python_type,
+ validation: callable,
+ widget_type: (path, name) tuple or QWidget type,
+ str_conversion: callable,
+ base_class: class,
+ compute: callable,
+ query_widget_type: (path, name) tuple or QWidget type,
+ query_compute: static callable,
+ param_explore_widget_list:
+ list((path, name) tuple or QWidget type)) -> Module
+
+ new_constant dynamically creates a new Module derived from
+ Constant with given py_conversion and str_conversion functions, a
+ corresponding python type and a widget type. py_conversion is a
+ python callable that takes a string and returns a python value of
+ the type that the class should hold. str_conversion does the reverse.
+
+ This is the quickest way to create new Constant Modules."""
+
+ d = {}
+
+ if py_conversion is not None:
+ d["translate_to_python"] = py_conversion
+ elif base_class == Constant:
+ raise ValueError("Must specify translate_to_python for constant")
+ else:
+ d["translate_to_python"] = staticmethod(base_class.translate_to_python)
+ if validation is not None:
+ d["validate"] = validation
+ elif base_class == Constant:
+ raise ValueError("Must specify validation for constant")
+ else:
+ d["validate"] = staticmethod(base_class.validate)
+ if default_value is not None:
+ d["default_value"] = default_value
+ elif base_class == Constant:
+ d["default_value"] = None
+ else:
+ d["default_value"] = base_class.default_value
+
+ if str_conversion is not None:
+ d['translate_to_string'] = str_conversion
+ if compute is not None:
+ d['compute'] = compute
+ if query_compute is not None:
+ d['query_compute'] = query_compute
+ if widget_type is not None:
+ @staticmethod
+ def get_widget_class():
+ return widget_type
+ d['get_widget_class'] = get_widget_class
+ if query_widget_type is not None:
+ @staticmethod
+ def get_query_widget_class():
+ return query_widget_type
+ d['get_query_widget_class'] = get_query_widget_class
+ if param_explore_widget_list is not None:
+ @staticmethod
+ def get_param_explore_widget_list():
+ return param_explore_widget_list
+ d['get_param_explore_widget_list'] = get_param_explore_widget_list
+
+ m = new_module(base_class, name, d)
+ m._input_ports = [('value', m)]
+ m._output_ports = [('value', m)]
+ return m
+
+def bool_conv(x):
+ s = str(x).upper()
+ if s == 'TRUE':
+ return True
+ if s == 'FALSE':
+ return False
+ raise ValueError('Boolean from String in VisTrails should be either \
+"true" or "false", got "%s" instead' % x)
+
+def int_conv(x):
+ if x.startswith('0x'):
+ return int(x, 16)
+ else:
+ return int(x)
+
+ at staticmethod
+def numeric_compare(value_a, value_b, query_method):
+ value_a = float(value_a)
+ value_b = float(value_b)
+ if query_method == '==' or query_method is None:
+ return (value_a == value_b)
+ elif query_method == '<':
+ return (value_a < value_b)
+ elif query_method == '>':
+ return (value_a > value_b)
+ elif query_method == '<=':
+ return (value_a <= value_b)
+ elif query_method == '>=':
+ return (value_a >= value_b)
+
+ at staticmethod
+def string_compare(value_a, value_b, query_method):
+ if query_method == '*[]*' or query_method is None:
+ return (value_b in value_a)
+ elif query_method == '==':
+ return (value_a == value_b)
+ elif query_method == '=~':
+ try:
+ m = re.match(value_b, value_a)
+ if m is not None:
+ return (m.end() ==len(value_a))
+ except:
+ pass
+ return False
+
+Boolean = new_constant('Boolean' , staticmethod(bool_conv),
+ False, staticmethod(lambda x: isinstance(x, bool)),
+ widget_type=('vistrails.gui.modules.constant_configuration',
+ 'BooleanWidget'))
+Float = new_constant('Float' , staticmethod(float), 0.0,
+ staticmethod(lambda x: isinstance(x, (int, long, float))),
+ query_widget_type=('vistrails.gui.modules.query_configuration',
+ 'NumericQueryWidget'),
+ query_compute=numeric_compare,
+ param_explore_widget_list=[('vistrails.gui.modules.paramexplore',
+ 'FloatExploreWidget')])
+Integer = new_constant('Integer' , staticmethod(int_conv), 0,
+ staticmethod(lambda x: isinstance(x, (int, long))),
+ base_class=Float,
+ query_widget_type=('vistrails.gui.modules.query_configuration',
+ 'NumericQueryWidget'),
+ query_compute=numeric_compare,
+ param_explore_widget_list=[('vistrails.gui.modules.paramexplore',
+ 'IntegerExploreWidget')])
+String = new_constant('String' , staticmethod(str), "",
+ staticmethod(lambda x: isinstance(x, str)),
+ query_widget_type=('vistrails.gui.modules.query_configuration',
+ 'StringQueryWidget'),
+ query_compute=string_compare,
+ widget_type=('vistrails.gui.modules.constant_configuration',
+ 'StringWidget'))
+
+##############################################################################
+
+class Path(Constant):
+ name = ""
+
+ @staticmethod
+ def translate_to_python(x):
+ result = Path()
+ result.name = x
+ result.setResult("value", result)
+ return result
+
+ @staticmethod
+ def translate_to_string(x):
+ return str(x.name)
+
+ @staticmethod
+ def validate(v):
+ #print 'validating', v
+ #print 'isinstance', isinstance(v, Path)
+ return isinstance(v, Path)
+
+ def get_name(self):
+ n = None
+ if self.hasInputFromPort("value"):
+ n = self.getInputFromPort("value").name
+ if n is None:
+ self.checkInputPort("name")
+ n = self.getInputFromPort("name")
+ return n
+
+ def set_results(self, n):
+ self.name = n
+ self.setResult("value", self)
+ self.setResult("value_as_string", self.translate_to_string(self))
+
+ def compute(self):
+ n = self.get_name()
+ self.set_results(n)
+
+ @staticmethod
+ def get_widget_class():
+ return ("vistrails.gui.modules.constant_configuration",
+ "PathChooserWidget")
+
+Path.default_value = Path()
+
+class File(Path):
+ """File is a VisTrails Module that represents a file stored on a
+ file system local to the machine where VisTrails is running."""
+ @staticmethod
+ def translate_to_python(x):
+ result = File()
+ result.name = x
+ result.setResult("value", result)
+ return result
+
+ def compute(self):
+ n = self.get_name()
+ if (self.hasInputFromPort("create_file") and
+ self.getInputFromPort("create_file")):
+ vistrails.core.system.touch(n)
+ if not os.path.isfile(n):
+ raise ModuleError(self, 'File %r does not exist' % n)
+ self.set_results(n)
+ self.setResult("local_filename", n)
+
+ @staticmethod
+ def get_widget_class():
+ return ("vistrails.gui.modules.constant_configuration",
+ "FileChooserWidget")
+
+File.default_value = File()
+
+class Directory(Path):
+ @staticmethod
+ def translate_to_python(x):
+ result = Directory()
+ result.name = x
+ result.setResult("value", result)
+ return result
+
+ def compute(self):
+ n = self.get_name()
+ if (self.hasInputFromPort("create_directory") and
+ self.getInputFromPort("create_directory")):
+ try:
+ vistrails.core.system.mkdir(n)
+ except Exception, e:
+ raise ModuleError(self, 'mkdir: ' + str(e))
+ if not os.path.isdir(n):
+ raise ModuleError(self, 'Directory "%s" does not exist' % n)
+ self.set_results(n)
+
+ dir_list = os.listdir(n)
+ output_list = []
+ for item in dir_list:
+ full_path = os.path.join(n, item)
+ if os.path.isfile(full_path):
+ file_item = File()
+ file_item.name = full_path
+ file_item.upToDate = True
+ output_list.append(file_item)
+ elif os.path.isdir(full_path):
+ dir_item = Directory()
+ dir_item.name = full_path
+ dir_item.upToDate = True
+ output_list.append(dir_item)
+ self.setResult('itemList', output_list)
+
+ @staticmethod
+ def get_widget_class():
+ return ("vistrails.gui.modules.constant_configuration",
+ "DirectoryChooserWidget")
+
+Directory.default_value = Directory()
+
+def path_parameter_hasher(p):
+ def get_mtime(path):
+ v_list = [int(os.path.getmtime(path))]
+ if os.path.isdir(path):
+ for subpath in os.listdir(path):
+ subpath = os.path.join(path, subpath)
+ if os.path.isdir(subpath):
+ v_list.extend(get_mtime(subpath))
+ return v_list
+
+ h = vistrails.core.cache.hasher.Hasher.parameter_signature(p)
+ try:
+ # FIXME: This will break with aliases - I don't really care that much
+ v_list = get_mtime(p.strValue)
+ except OSError:
+ return h
+ hasher = sha_hash()
+ hasher.update(h)
+ for v in v_list:
+ hasher.update(str(v))
+ return hasher.digest()
+
+##############################################################################
+
+class OutputPath(Path):
+ def get_name(self):
+ n = None
+ if self.hasInputFromPort("value"):
+ n = self.getInputFromPort("value").name
+ if n is None:
+ self.checkInputPort("name")
+ n = self.getInputFromPort("name")
+ return n
+
+ def set_results(self, n):
+ self.name = n
+ self.setResult("value", self)
+ self.setResult("value_as_string", self.translate_to_string(self))
+
+ def compute(self):
+ n = self.get_name()
+ self.set_results(n)
+
+ @staticmethod
+ def get_widget_class():
+ return ("vistrails.gui.modules.constant_configuration",
+ "OutputPathChooserWidget")
+
+OutputPath.default_value = OutputPath()
+
+class FileSink(NotCacheable, Module):
+ """FileSink takes a file and writes it to a user-specified
+ location in the file system. The file is stored at location
+ specified by the outputPath. The overwrite flag allows users to
+ specify whether an existing path should be overwritten."""
+
+ def compute(self):
+ input_file = self.getInputFromPort("file")
+ output_path = self.getInputFromPort("outputPath")
+ full_path = output_path.name
+
+ try:
+ vistrails.core.system.link_or_copy(input_file.name, full_path)
+ except OSError, e:
+ if self.hasInputFromPort("overwrite") and \
+ self.getInputFromPort("overwrite"):
+ try:
+ os.unlink(full_path)
+ vistrails.core.system.link_or_copy(input_file.name, full_path)
+ except OSError:
+ msg = "(override true) Could not create file '%s'" % \
+ full_path
+ raise ModuleError(self, msg)
+ else:
+ msg = "Could not create file '%s': %s" % (full_path, e)
+ raise ModuleError(self, msg)
+
+ if (self.hasInputFromPort("publishFile") and
+ self.getInputFromPort("publishFile") or
+ not self.hasInputFromPort("publishFile")):
+ if self.moduleInfo.has_key('extra_info'):
+ if self.moduleInfo['extra_info'].has_key('pathDumpCells'):
+ folder = self.moduleInfo['extra_info']['pathDumpCells']
+ base_fname = os.path.basename(full_path)
+ (base_fname, file_extension) = os.path.splitext(base_fname)
+ base_fname = os.path.join(folder, base_fname)
+ # make a unique filename
+ filename = base_fname + file_extension
+ counter = 2
+ while os.path.exists(filename):
+ filename = base_fname + "_%d%s" % (counter,
+ file_extension)
+ counter += 1
+ try:
+ vistrails.core.system.link_or_copy(input_file.name, filename)
+ except OSError:
+ msg = "Could not publish file '%s' \n on '%s': %s" % \
+ (full_path, filename, e)
+ # I am not sure whether we should raise an error
+ # I will just print a warning for now (Emanuele)
+ debug.warning("%s" % msg)
+
+class DirectorySink(NotCacheable, Module):
+ """DirectorySink takes a directory and writes it to a
+ user-specified location in the file system. The directory is
+ stored at location specified by the outputPath. The overwrite
+ flag allows users to specify whether an existing path should be
+ overwritten."""
+
+ def compute(self):
+ input_dir = self.getInputFromPort("dir")
+ output_path = self.getInputFromPort("outputPath")
+ full_path = output_path.name
+
+ if os.path.exists(full_path):
+ if (self.hasInputFromPort("overwrite") and
+ self.getInputFromPort("overwrite")):
+ try:
+ if os.path.isfile(full_path):
+ os.remove(full_path)
+ else:
+ shutil.rmtree(full_path)
+ except OSError, e:
+ msg = ('Could not delete existing path "%s" '
+ '(overwrite on)' % full_path)
+ raise ModuleError(self, msg + '\n' + str(e))
+ else:
+ msg = ('Could not write to existing path "%s" '
+ '(overwrite off)' % full_path)
+ raise ModuleError(self, msg)
+
+ try:
+ shutil.copytree(input_dir.name, full_path)
+ except OSError, e:
+ msg = 'Could not copy path from "%s" to "%s"' % \
+ (input_dir.name, full_path)
+ raise ModuleError(self, msg + '\n' + str(e))
+
+##############################################################################
+
+class WriteFile(Converter):
+ """Writes a String to a temporary File.
+ """
+ def compute(self):
+ contents = self.getInputFromPort('in_value')
+ suffix = self.forceGetInputFromPort('suffix', '')
+ result = self.interpreter.filePool.create_file(suffix=suffix)
+ with open(result.name, 'wb') as fp:
+ fp.write(contents)
+ self.setResult('out_value', result)
+
+##############################################################################
+
+class Color(Constant):
+ # We set the value of a color object to be an InstanceObject that
+ # contains a tuple because a tuple would be interpreted as a
+ # type(tuple) which messes with the interpreter
+
+ default_value = InstanceObject(tuple=(1,1,1))
+
+ @staticmethod
+ def translate_to_python(x):
+ return InstanceObject(
+ tuple=tuple([float(a) for a in x.split(',')]))
+
+ @staticmethod
+ def translate_to_string(v):
+ return ','.join('%f' % c for c in v.tuple)
+
+ @staticmethod
+ def validate(x):
+ return isinstance(x, InstanceObject) and hasattr(x, 'tuple')
+
+ @staticmethod
+ def to_string(r, g, b):
+ return "%s,%s,%s" % (r,g,b)
+
+ @staticmethod
+ def get_widget_class():
+ return ("vistrails.gui.modules.constant_configuration", "ColorWidget")
+
+ @staticmethod
+ def get_query_widget_class():
+ return ("vistrails.gui.modules.query_configuration", "ColorQueryWidget")
+
+ @staticmethod
+ def get_param_explore_widget_list():
+ return [('vistrails.gui.modules.paramexplore', 'RGBExploreWidget'),
+ ('vistrails.gui.modules.paramexplore', 'HSVExploreWidget')]
+
+ @staticmethod
+ def query_compute(value_a, value_b, query_method):
+ # SOURCE: http://www.easyrgb.com/index.php?X=MATH
+ def rgb_to_xyz(r, g, b):
+ # r,g,b \in [0,1]
+
+ if r > 0.04045:
+ r = ( ( r + 0.055 ) / 1.055 ) ** 2.4
+ else:
+ r = r / 12.92
+ if g > 0.04045:
+ g = ( ( g + 0.055 ) / 1.055 ) ** 2.4
+ else:
+ g = g / 12.92
+ if b > 0.04045:
+ b = ( ( b + 0.055 ) / 1.055 ) ** 2.4
+ else:
+ b = b / 12.92
+
+ r *= 100
+ g *= 100
+ b *= 100
+
+ # Observer. = 2 deg, Illuminant = D65
+ x = r * 0.4124 + g * 0.3576 + b * 0.1805
+ y = r * 0.2126 + g * 0.7152 + b * 0.0722
+ z = r * 0.0193 + g * 0.1192 + b * 0.9505
+ return (x,y,z)
+
+ def xyz_to_cielab(x,y,z):
+ # Observer= 2 deg, Illuminant= D65
+ ref_x, ref_y, ref_z = (95.047, 100.000, 108.883)
+ x /= ref_x
+ y /= ref_y
+ z /= ref_z
+
+ if x > 0.008856:
+ x = x ** ( 1/3.0 )
+ else:
+ x = ( 7.787 * x ) + ( 16 / 116.0 )
+ if y > 0.008856:
+ y = y ** ( 1/3.0 )
+ else:
+ y = ( 7.787 * y ) + ( 16 / 116.0 )
+ if z > 0.008856:
+ z = z ** ( 1/3.0 )
+ else:
+ z = ( 7.787 * z ) + ( 16 / 116.0 )
+
+ L = ( 116 * y ) - 16
+ a = 500 * ( x - y )
+ b = 200 * ( y - z )
+ return (L, a, b)
+
+ def rgb_to_cielab(r,g,b):
+ return xyz_to_cielab(*rgb_to_xyz(r,g,b))
+
+ value_a_rgb = (float(a) for a in value_a.split(','))
+ value_b_rgb = (float(b) for b in value_b.split(','))
+ value_a_lab = rgb_to_cielab(*value_a_rgb)
+ value_b_lab = rgb_to_cielab(*value_b_rgb)
+
+ # cie76 difference
+ diff = sum((v_1 - v_2) ** 2
+ for v_1, v_2 in izip(value_a_lab, value_b_lab)) ** (0.5)
+
+ # print "CIE 76 DIFFERENCE:", diff
+ if query_method is None:
+ query_method = '2.3'
+ return diff < float(query_method)
+
+##############################################################################
+
+class StandardOutput(NotCacheable, Module):
+ """StandardOutput is a VisTrails Module that simply prints the
+ value connected on its port to standard output. It is intended
+ mostly as a debugging device."""
+
+ def compute(self):
+ v = self.getInputFromPort("value")
+ print v
+
+##############################################################################
+
+# Tuple will be reasonably magic right now. We'll integrate it better
+# with vistrails later.
+# TODO: Check Tuple class, test, integrate.
+class Tuple(Module):
+ """Tuple represents a tuple of values. Tuple might not be well
+ integrated with the rest of VisTrails, so don't use it unless
+ you know what you're doing."""
+
+ def __init__(self):
+ Module.__init__(self)
+ self.input_ports_order = []
+ self.values = tuple()
+
+ def compute(self):
+ values = tuple([self.getInputFromPort(p)
+ for p in self.input_ports_order])
+ self.values = values
+ self.setResult("value", values)
+
+class Untuple(Module):
+ """Untuple takes a tuple and returns the individual values. It
+ reverses the actions of Tuple.
+
+ """
+ def __init__(self):
+ Module.__init__(self)
+ self.output_ports_order = []
+
+ def compute(self):
+ if self.hasInputFromPort("tuple"):
+ tuple = self.getInputFromPort("tuple")
+ values = tuple.values
+ else:
+ values = self.getInputFromPort("value")
+ for p, value in izip(self.output_ports_order, values):
+ self.setResult(p, value)
+
+##############################################################################
+
+# TODO: Create a better Module for ConcatenateString.
+class ConcatenateString(Module):
+ """ConcatenateString takes many strings as input and produces the
+ concatenation as output. Useful for constructing filenames, for
+ example.
+
+ This class will probably be replaced with a better API in the
+ future."""
+
+ fieldCount = 4
+
+ def compute(self):
+ result = ""
+ for i in xrange(self.fieldCount):
+ v = i+1
+ port = "str%s" % v
+ if self.hasInputFromPort(port):
+ inp = self.getInputFromPort(port)
+ result += inp
+ self.setResult("value", result)
+
+##############################################################################
+
+class Not(Module):
+ """Not inverts a Boolean.
+ """
+
+ def compute(self):
+ value = self.getInputFromPort('input')
+ self.setResult('value', not value)
+
+##############################################################################
+# List
+
+# If numpy is available, we consider numpy arrays to be lists as well
+class ListType:
+ __metaclass__ = ABCMeta
+
+ListType.register(list)
+try:
+ import numpy
+except ImportError:
+ numpy = None
+else:
+ ListType.register(numpy.ndarray)
+
+class List(Constant):
+ default_value = []
+
+ def __init__(self):
+ Constant.__init__(self)
+ self.input_ports_order = []
+
+ @staticmethod
+ def validate(x):
+ return isinstance(x, ListType)
+
+ @staticmethod
+ def translate_to_python(v):
+ return eval(v)
+
+ @staticmethod
+ def translate_to_string(v, dims=None):
+ if dims is None:
+ if numpy is not None and isinstance(v, numpy.ndarray):
+ dims = v.ndim
+ else:
+ dims = 1
+ if dims == 1:
+ return '[%s]' % ', '.join(repr(c)
+ for c in v)
+ else:
+ return '[%s]' % ', '.join(List.translate_to_string(c, dims-1)
+ for c in v)
+
+ def compute(self):
+ head, middle, items, tail = [], [], [], []
+ got_value = False
+
+ if self.hasInputFromPort('value'):
+ # run the regular compute here
+ Constant.compute(self)
+ middle = self.outputPorts['value']
+ got_value = True
+ if self.hasInputFromPort('head'):
+ head = self.getInputListFromPort('head')
+ got_value = True
+ if self.input_ports_order:
+ items = [self.getInputFromPort(p)
+ for p in self.input_ports_order]
+ got_value = True
+ if self.hasInputFromPort('tail'):
+ tail = self.getInputFromPort('tail')
+ got_value = True
+
+ if not got_value:
+ self.getInputFromPort('value')
+ self.setResult('value', head + middle + items + tail)
+
+List._input_ports = [('value', List)]
+List._output_ports = [('value', List)]
+
+##############################################################################
+# Dictionary
+
+def dict_conv(v):
+ v_dict = eval(v)
+ return v_dict
+
+def dict_compute(self):
+ d = {}
+ if self.hasInputFromPort('value'):
+ Constant.compute(self)
+ d.update(self.outputPorts['value'])
+ if self.hasInputFromPort('addPair'):
+ pairs_list = self.getInputListFromPort('addPair')
+ d.update(pairs_list)
+ if self.hasInputFromPort('addPairs'):
+ d.update(self.getInputFromPort('addPairs'))
+
+ self.setResult("value", d)
+
+Dictionary = new_constant('Dictionary', staticmethod(dict_conv),
+ {}, staticmethod(lambda x: isinstance(x, dict)),
+ compute=dict_compute)
+
+##############################################################################
+
+# TODO: Null should be a subclass of Constant?
+class Null(Module):
+ """Null is the class of None values."""
+
+ def compute(self):
+ self.setResult("value", None)
+
+##############################################################################
+
+class Unpickle(Module):
+ """Unpickles a string.
+ """
+ def compute(self):
+ value = self.getInputFromPort('input')
+ self.setResult('result', pickle.loads(value))
+
+##############################################################################
+
+class CodeRunnerMixin(object):
+ def __init__(self):
+ self.output_ports_order = []
+ super(CodeRunnerMixin, self).__init__()
+
+ def run_code(self, code_str,
+ use_input=False,
+ use_output=False):
+ """run_code runs a piece of code as a VisTrails module.
+ use_input and use_output control whether to use the inputport
+ and output port dictionary as local variables inside the
+ execution."""
+ import vistrails.core.packagemanager
+ def fail(msg):
+ raise ModuleError(self, msg)
+ def cache_this():
+ self.is_cacheable = lambda *args, **kwargs: True
+ locals_ = locals()
+ if use_input:
+ for k in self.inputPorts:
+ locals_[k] = self.getInputFromPort(k)
+ if use_output:
+ for output_portname in self.output_ports_order:
+ locals_[output_portname] = None
+ _m = vistrails.core.packagemanager.get_package_manager()
+ reg = get_module_registry()
+ locals_.update({'fail': fail,
+ 'package_manager': _m,
+ 'cache_this': cache_this,
+ 'registry': reg,
+ 'self': self})
+ if 'source' in locals_:
+ del locals_['source']
+ exec code_str in locals_, locals_
+ if use_output:
+ for k in self.output_ports_order:
+ if locals_.get(k) != None:
+ self.setResult(k, locals_[k])
+
+##############################################################################
+
+class PythonSource(CodeRunnerMixin, NotCacheable, Module):
+ """PythonSource is a Module that executes an arbitrary piece of
+ Python code.
+
+ It is especially useful for one-off pieces of 'glue' in a
+ pipeline.
+
+ If you want a PythonSource execution to fail, call
+ fail(error_message).
+
+ If you want a PythonSource execution to be cached, call
+ cache_this().
+ """
+
+ def compute(self):
+ s = urllib.unquote(str(self.getInputFromPort('source')))
+ self.run_code(s, use_input=True, use_output=True)
+
+##############################################################################
+
+class SmartSource(NotCacheable, Module):
+
+ def run_code(self, code_str,
+ use_input=False,
+ use_output=False):
+ import vistrails.core.packagemanager
+ def fail(msg):
+ raise ModuleError(self, msg)
+ def cache_this():
+ self.is_cacheable = lambda *args, **kwargs: True
+ locals_ = locals()
+
+ def smart_input_entry(k):
+ v = self.getInputFromPort(k)
+ if isinstance(v, Module) and hasattr(v, 'get_source'):
+ v = v.get_source()
+ return (k, v)
+
+ def get_mro(v):
+ # Tries to get the mro from strange class hierarchies like VTK's
+ try:
+ return v.mro()
+ except AttributeError:
+ def yield_all(v):
+ b = v.__bases__
+ yield v
+ for base in b:
+ g = yield_all(base)
+ while 1: yield g.next()
+ return [x for x in yield_all(v)]
+
+ if use_input:
+ inputDict = dict([smart_input_entry(k)
+ for k in self.inputPorts])
+ locals_.update(inputDict)
+ if use_output:
+ for output_portname in self.output_ports_order:
+ locals_[output_portname] = None
+ _m = vistrails.core.packagemanager.get_package_manager()
+ locals_.update({'fail': fail,
+ 'package_manager': _m,
+ 'cache_this': cache_this,
+ 'self': self})
+ del locals_['source']
+ exec code_str in locals_, locals_
+ if use_output:
+ oports = self.registry.get_descriptor(SmartSource).output_ports
+ for k in self.output_ports_order:
+ if locals_.get(k) != None:
+ v = locals_[k]
+ spec = oports.get(k, None)
+
+ if spec:
+ # See explanation of algo in doc/smart_source_resolution_algo.txt
+ # changed from spec.types()[0]
+ port_vistrail_base_class = spec.descriptors()[0].module
+ mro = get_mro(type(v))
+ source_types = self.registry.python_source_types
+ found = False
+ for python_class in mro:
+ if python_class in source_types:
+ vistrail_classes = [x for x in source_types[python_class]
+ if issubclass(x, port_vistrail_base_class)]
+ if len(vistrail_classes) == 0:
+ # FIXME better error handling
+ raise ModuleError(self, "Module Registry inconsistent")
+ vt_class = vistrail_classes[0]
+ found = True
+ break
+ if found:
+ vt_instance = vt_class()
+ vt_instance.set_source(v)
+ v = vt_instance
+ self.setResult(k, v)
+
+ def compute(self):
+ s = urllib.unquote(str(self.forceGetInputFromPort('source', '')))
+ self.run_code(s, use_input=True, use_output=True)
+
+##############################################################################
+
+def zip_extract_file(archive, filename_in_archive, output_filename):
+ return os.system(
+ "%s > %s" % (
+ vistrails.core.system.list2cmdline([
+ 'unzip',
+ '-p', archive,
+ filename_in_archive]),
+ vistrails.core.system.list2cmdline([output_filename])))
+
+
+def zip_extract_all_files(archive, output_path):
+ return os.system(
+ vistrails.core.system.list2cmdline([
+ 'unzip',
+ archive,
+ '-d', output_path]))
+
+
+class Unzip(Module):
+ """Unzip extracts a file from a ZIP archive."""
+
+ def compute(self):
+ self.checkInputPort("archive_file")
+ self.checkInputPort("filename_in_archive")
+ filename_in_archive = self.getInputFromPort("filename_in_archive")
+ archive_file = self.getInputFromPort("archive_file")
+ if not os.path.isfile(archive_file.name):
+ raise ModuleError(self, "archive file does not exist")
+ suffix = self.interpreter.filePool.guess_suffix(filename_in_archive)
+ output = self.interpreter.filePool.create_file(suffix=suffix)
+ s = zip_extract_file(archive_file.name,
+ filename_in_archive,
+ output.name)
+ if s != 0:
+ raise ModuleError(self, "unzip command failed with status %d" % s)
+ self.setResult("file", output)
+
+
+class UnzipDirectory(Module):
+ """UnzipDirectory extracts every file from a ZIP archive."""
+
+ def compute(self):
+ self.checkInputPort("archive_file")
+ archive_file = self.getInputFromPort("archive_file")
+ if not os.path.isfile(archive_file.name):
+ raise ModuleError(self, "archive file does not exist")
+ output = self.interpreter.filePool.create_directory()
+ s = zip_extract_all_files(archive_file.name,
+ output.name)
+ if s != 0:
+ raise ModuleError(self, "unzip command failed with status %d" % s)
+ self.setResult("directory", output)
+
+##############################################################################
+
+class Round(Converter):
+ """Turns a Float into an Integer.
+ """
+ def compute(self):
+ fl = self.getInputFromPort('in_value')
+ floor = self.getInputFromPort('floor')
+ if floor:
+ integ = int(fl) # just strip the decimals
+ else:
+ integ = int(fl + 0.5) # nearest
+ self.setResult('out_value', integ)
+
+
+class TupleToList(Converter):
+ """Turns a Tuple into a List.
+ """
+ @classmethod
+ def can_convert(cls, sub_descs, super_descs):
+ if len(sub_descs) <= 1:
+ return False
+ reg = get_module_registry()
+ return super_descs == [reg.get_descriptor(List)]
+
+ def compute(self):
+ tu = self.getInputFromPort('in_value')
+ if not isinstance(tu, tuple):
+ raise ModuleError(self, "Input is not a tuple")
+ self.setResult('out_value', list(tu))
+
+##############################################################################
+
+class Variant(Module):
+ """
+ Variant is tracked internally for outputing a variant type on
+ output port. For input port, Module type should be used
+
+ """
+ pass
+
+##############################################################################
+
+class Assert(Module):
+ """
+ Assert is a simple module that conditionally stops the execution.
+ """
+ def compute(self):
+ condition = self.getInputFromPort('condition')
+ if not condition:
+ raise ModuleError(self, "Assert: condition is False",
+ abort=True)
+
+
+class AssertEqual(Module):
+ """
+ AssertEqual works like Assert but compares two values.
+
+ It is provided for convenience.
+ """
+ def compute(self):
+ values = (self.getInputFromPort('value1'),
+ self.getInputFromPort('value2'))
+ if values[0] != values[1]:
+ raise ModuleError(self, "AssertEqual: values are different",
+ abort=True)
+
+##############################################################################
+
+def init_constant(m):
+ reg = get_module_registry()
+
+ reg.add_module(m)
+ reg.add_input_port(m, "value", m)
+ reg.add_output_port(m, "value", m)
+
+def initialize(*args, **kwargs):
+ reg = get_module_registry()
+
+ # !!! is_root should only be set for Module !!!
+ reg.add_module(Module, is_root=True, abstract=True)
+ reg.add_output_port(Module, "self", Module, optional=True)
+
+ reg.add_module(Converter, abstract=True)
+ reg.add_input_port(Converter, 'in_value', Module)
+ reg.add_output_port(Converter, 'out_value', Module)
+
+ reg.add_module(Constant, abstract=True)
+
+ reg.add_module(Boolean)
+ reg.add_module(Float)
+ reg.add_module(Integer)
+ reg.add_module(String,
+ configureWidgetType=("vistrails.gui.modules.string_configure",
+ "TextConfigurationWidget"))
+
+ reg.add_output_port(Constant, "value_as_string", String)
+ reg.add_output_port(String, "value_as_string", String, True)
+
+ reg.add_module(List,
+ configureWidgetType=(
+ "vistrails.gui.modules.list_configuration",
+ "ListConfigurationWidget"))
+ reg.add_input_port(List, "head", Module)
+ reg.add_input_port(List, "tail", List)
+
+ reg.add_module(Path)
+ reg.add_input_port(Path, "value", Path)
+ reg.add_output_port(Path, "value", Path)
+ reg.add_input_port(Path, "name", String, True)
+
+ reg.add_module(File, constantSignatureCallable=path_parameter_hasher)
+ reg.add_input_port(File, "value", File)
+ reg.add_output_port(File, "value", File)
+ reg.add_output_port(File, "self", File, True)
+ reg.add_input_port(File, "create_file", Boolean, True)
+ reg.add_output_port(File, "local_filename", String, True)
+
+ reg.add_module(Directory, constantSignatureCallable=path_parameter_hasher)
+ reg.add_input_port(Directory, "value", Directory)
+ reg.add_output_port(Directory, "value", Directory)
+ reg.add_output_port(Directory, "itemList", List)
+ reg.add_input_port(Directory, "create_directory", Boolean, True)
+
+ reg.add_module(OutputPath)
+ reg.add_output_port(OutputPath, "value", OutputPath)
+
+ reg.add_module(FileSink)
+ reg.add_input_port(FileSink, "file", File)
+ reg.add_input_port(FileSink, "outputPath", OutputPath)
+ reg.add_input_port(FileSink, "overwrite", Boolean, True,
+ defaults="('True',)")
+ reg.add_input_port(FileSink, "publishFile", Boolean, True)
+
+ reg.add_module(DirectorySink)
+ reg.add_input_port(DirectorySink, "dir", Directory)
+ reg.add_input_port(DirectorySink, "outputPath", OutputPath)
+ reg.add_input_port(DirectorySink, "overwrite", Boolean, True,
+ defaults="('True',)")
+
+ reg.add_module(WriteFile)
+ reg.add_input_port(WriteFile, 'in_value', String)
+ reg.add_input_port(WriteFile, 'suffix', String, True, defaults='[""]')
+ reg.add_output_port(WriteFile, 'out_value', File)
+
+ reg.add_module(Color)
+ reg.add_input_port(Color, "value", Color)
+ reg.add_output_port(Color, "value", Color)
+
+ reg.add_module(StandardOutput)
+ reg.add_input_port(StandardOutput, "value", Module)
+
+ reg.add_module(Tuple,
+ configureWidgetType=("vistrails.gui.modules.tuple_configuration",
+ "TupleConfigurationWidget"))
+
+ reg.add_module(Untuple,
+ configureWidgetType=("vistrails.gui.modules.tuple_configuration",
+ "UntupleConfigurationWidget"))
+
+ reg.add_module(ConcatenateString)
+ for i in xrange(ConcatenateString.fieldCount):
+ j = i+1
+ port = "str%s" % j
+ reg.add_input_port(ConcatenateString, port, String)
+ reg.add_output_port(ConcatenateString, "value", String)
+
+ reg.add_module(Not)
+ reg.add_input_port(Not, 'input', Boolean)
+ reg.add_output_port(Not, 'value', Boolean)
+
+ reg.add_module(Dictionary)
+ reg.add_input_port(Dictionary, "addPair", [Module, Module])
+ reg.add_input_port(Dictionary, "addPairs", List)
+
+ reg.add_module(Null, hide_descriptor=True)
+
+ reg.add_module(Variant, abstract=True)
+
+ reg.add_module(Assert)
+ reg.add_input_port(Assert, 'condition', Boolean)
+
+ reg.add_module(AssertEqual)
+ reg.add_input_port(AssertEqual, 'value1', Module)
+ reg.add_input_port(AssertEqual, 'value2', Module)
+
+ reg.add_module(Unpickle, hide_descriptor=True)
+ reg.add_input_port(Unpickle, 'input', String)
+ reg.add_output_port(Unpickle, 'result', Variant)
+
+ reg.add_module(PythonSource,
+ configureWidgetType=("vistrails.gui.modules.python_source_configure",
+ "PythonSourceConfigurationWidget"))
+ reg.add_input_port(PythonSource, 'source', String, True, defaults=str(['']))
+ reg.add_output_port(PythonSource, 'self', Module)
+
+ reg.add_module(SmartSource,
+ configureWidgetType=("vistrails.gui.modules.python_source_configure",
+ "PythonSourceConfigurationWidget"))
+ reg.add_input_port(SmartSource, 'source', String, True, defaults=str(['']))
+
+ reg.add_module(Unzip)
+ reg.add_input_port(Unzip, 'archive_file', File)
+ reg.add_input_port(Unzip, 'filename_in_archive', String)
+ reg.add_output_port(Unzip, 'file', File)
+
+ reg.add_module(UnzipDirectory)
+ reg.add_input_port(UnzipDirectory, 'archive_file', File)
+ reg.add_output_port(UnzipDirectory, 'directory', Directory)
+
+ reg.add_module(Round, hide_descriptor=True)
+ reg.add_input_port(Round, 'in_value', Float)
+ reg.add_output_port(Round, 'out_value', Integer)
+ reg.add_input_port(Round, 'floor', Boolean, optional=True,
+ defaults="('True',)")
+
+ reg.add_module(TupleToList, hide_descriptor=True)
+ reg.add_input_port(TupleToList, 'in_value', Variant)
+ reg.add_output_port(TupleToList, 'out_value', List)
+
+ # initialize the sub_module modules, too
+ import vistrails.core.modules.sub_module
+ vistrails.core.modules.sub_module.initialize(*args, **kwargs)
+
+
+def handle_module_upgrade_request(controller, module_id, pipeline):
+ from vistrails.core.upgradeworkflow import UpgradeWorkflowHandler
+ reg = get_module_registry()
+
+ def outputName_remap(old_conn, new_module):
+ ops = []
+ old_src_module = pipeline.modules[old_conn.source.moduleId]
+ op_desc = reg.get_descriptor(OutputPath)
+ new_x = (old_src_module.location.x + new_module.location.x) / 2.0
+ new_y = (old_src_module.location.y + new_module.location.y) / 2.0
+ op_module = \
+ controller.create_module_from_descriptor(op_desc, new_x, new_y)
+ ops.append(('add', op_module))
+ create_new_connection = UpgradeWorkflowHandler.create_new_connection
+ new_conn_1 = create_new_connection(controller,
+ old_src_module,
+ old_conn.source,
+ op_module,
+ "name")
+ ops.append(('add', new_conn_1))
+ new_conn_2 = create_new_connection(controller,
+ op_module,
+ "value",
+ new_module,
+ "outputPath")
+ ops.append(('add', new_conn_2))
+ return ops
+
+ module_remap = {'FileSink':
+ [(None, '1.6', None,
+ {'dst_port_remap':
+ {'overrideFile': 'overwrite',
+ 'outputName': outputName_remap},
+ 'function_remap':
+ {'overrideFile': 'overwrite',
+ 'outputName': 'outputPath'}})],
+ 'GetItemsFromDirectory':
+ [(None, '1.6', 'Directory',
+ {'dst_port_remap':
+ {'dir': 'value'},
+ 'src_port_remap':
+ {'itemlist': 'itemList'},
+ })],
+ 'InputPort':
+ [(None, '1.6', None,
+ {'dst_port_remap': {'old_name': None}})],
+ 'OutputPort':
+ [(None, '1.6', None,
+ {'dst_port_remap': {'old_name': None}})],
+ 'PythonSource':
+ [(None, '1.6', None, {})],
+ }
+
+ return UpgradeWorkflowHandler.remap_module(controller, module_id, pipeline,
+ module_remap)
+
+
+###############################################################################
+
+import unittest
+
+class TestConcatenateString(unittest.TestCase):
+ @staticmethod
+ def concatenate(**kwargs):
+ from vistrails.tests.utils import execute, intercept_result
+ with intercept_result(ConcatenateString, 'value') as results:
+ errors = execute([
+ ('ConcatenateString', 'org.vistrails.vistrails.basic', [
+ (name, [('String', value)])
+ for name, value in kwargs.iteritems()
+ ]),
+ ])
+ if errors:
+ return None
+ return results
+
+ def test_concatenate(self):
+ """Concatenates strings"""
+ self.assertEqual(self.concatenate(
+ str1="hello ", str2="world"),
+ ["hello world"])
+ self.assertEqual(self.concatenate(
+ str3="hello world"),
+ ["hello world"])
+ self.assertEqual(self.concatenate(
+ str2="hello ", str4="world"),
+ ["hello world"])
+ self.assertEqual(self.concatenate(
+ str1="hello", str3=" ", str4="world"),
+ ["hello world"])
+
+ def test_empty(self):
+ """Runs ConcatenateString with no input"""
+ self.assertEqual(self.concatenate(), [""])
+
+
+class TestNot(unittest.TestCase):
+ def run_pipeline(self, functions):
+ from vistrails.tests.utils import execute, intercept_result
+ with intercept_result(Not, 'value') as results:
+ errors = execute([
+ ('Not', 'org.vistrails.vistrails.basic',
+ functions),
+ ])
+ return errors, results
+
+ def test_true(self):
+ errors, results = self.run_pipeline([
+ ('input', [('Boolean', 'True')])])
+ self.assertFalse(errors)
+ self.assertEqual(len(results), 1)
+ self.assertIs(results[0], False)
+
+ def test_false(self):
+ errors, results = self.run_pipeline([
+ ('input', [('Boolean', 'False')])])
+ self.assertFalse(errors)
+ self.assertEqual(len(results), 1)
+ self.assertIs(results[0], True)
+
+ def test_notset(self):
+ errors, results = self.run_pipeline([])
+ self.assertTrue(errors)
+
+
+class TestList(unittest.TestCase):
+ @staticmethod
+ def build_list(value=None, head=None, tail=None):
+ from vistrails.tests.utils import execute, intercept_result
+ with intercept_result(List, 'value') as results:
+ functions = []
+ def add(n, v, t):
+ if v is not None:
+ for e in v:
+ functions.append(
+ (n, [(t, e)])
+ )
+ add('value', value, 'List')
+ add('head', head, 'String')
+ add('tail', tail, 'List')
+
+ errors = execute([
+ ('List', 'org.vistrails.vistrails.basic', functions),
+ ])
+ if errors:
+ return None
+ # List is a Constant, so the interpreter will set the result 'value'
+ # from the 'value' input port automatically
+ # Ignore these first results
+ return results[-1]
+
+ def test_simple(self):
+ """Tests the default ports of the List module"""
+ self.assertEqual(self.build_list(
+ value=['["a", "b", "c"]']),
+ ["a", "b", "c"])
+ self.assertEqual(self.build_list(
+ head=["d"],
+ value=['["a", "b", "c"]']),
+ ["d", "a", "b", "c"])
+ self.assertEqual(self.build_list(
+ head=["d"],
+ value=['["a", "b", "c"]'],
+ tail=['["e", "f"]']),
+ ["d", "a", "b", "c", "e", "f"])
+ self.assertEqual(self.build_list(
+ value=['[]'],
+ tail=['[]']),
+ [])
+
+ def test_multiple(self):
+ """Tests setting multiple values on a port"""
+ # Multiple values on 'head'
+ self.assertEqual(self.build_list(
+ head=["a", "b"]),
+ ["a", "b"])
+ self.assertEqual(self.build_list(
+ head=["a", "b"],
+ value=['["c", "d"]']),
+ ["a", "b", "c", "d"])
+
+ # Multiple values on 'value'
+ res = self.build_list(value=['["a", "b"]', '["c", "d"]'])
+ self.assertIn(res, [["a", "b"], ["c", "d"]])
+
+ def test_items(self):
+ """Tests the multiple 'itemN' ports"""
+ from vistrails.tests.utils import execute, intercept_result
+ def list_with_items(nb_items, **kwargs):
+ with intercept_result(List, 'value') as results:
+ errors = execute([
+ ('List', 'org.vistrails.vistrails.basic', [
+ (k, [('String', v)])
+ for k, v in kwargs.iteritems()
+ ]),
+ ],
+ add_port_specs=[
+ (0, 'input', 'item%d' % i,
+ '(org.vistrails.vistrails.basic:Module)')
+ for i in xrange(nb_items)
+ ])
+ if errors:
+ return None
+ return results[-1]
+
+ self.assertEqual(
+ list_with_items(2, head="one", item0="two", item1="three"),
+ ["one", "two", "three"])
+
+ # All 'itemN' ports have to be set
+ self.assertIsNone(
+ list_with_items(3, head="one", item0="two", item2="three"))
+
+
+class TestPythonSource(unittest.TestCase):
+ def test_simple(self):
+ """A simple PythonSource returning a string"""
+ import urllib2
+ from vistrails.tests.utils import execute, intercept_result
+ source = 'customout = "nb is %d" % customin'
+ source = urllib2.quote(source)
+ with intercept_result(PythonSource, 'customout') as results:
+ self.assertFalse(execute([
+ ('PythonSource', 'org.vistrails.vistrails.basic', [
+ ('source', [('String', source)]),
+ ('customin', [('Integer', '42')])
+ ]),
+ ('String', 'org.vistrails.vistrails.basic', []),
+ ],
+ [
+ (0, 'customout', 1, 'value'),
+ ],
+ add_port_specs=[
+ (0, 'input', 'customin',
+ 'org.vistrails.vistrails.basic:Integer'),
+ (0, 'output', 'customout',
+ 'org.vistrails.vistrails.basic:String'),
+ ]))
+ self.assertEqual(results[-1], "nb is 42")
+
+
+class TestNumericConversions(unittest.TestCase):
+ def test_full(self):
+ from vistrails.tests.utils import execute, intercept_result
+ with intercept_result(Round, 'out_value') as results:
+ self.assertFalse(execute([
+ ('Integer', 'org.vistrails.vistrails.basic', [
+ ('value', [('Integer', '5')])
+ ]),
+ ('Float', 'org.vistrails.vistrails.basic', []),
+ ('PythonCalc', 'org.vistrails.vistrails.pythoncalc', [
+ ('value2', [('Float', '2.7')]),
+ ('op', [('String', '+')]),
+ ]),
+ ('Round', 'org.vistrails.vistrails.basic', [
+ ('floor', [('Boolean', 'True')]),
+ ]),
+ ],
+ [
+ (0, 'value', 1, 'value'),
+ (1, 'value', 2, 'value1'),
+ (2, 'value', 3, 'in_value'),
+ ]))
+ self.assertEqual(results, [7])
+
+
+class TestUnzip(unittest.TestCase):
+ def test_unzip_file(self):
+ from vistrails.tests.utils import execute, intercept_result
+ from vistrails.core.system import vistrails_root_directory
+ zipfile = os.path.join(vistrails_root_directory(),
+ 'tests', 'resources',
+ 'test_archive.zip')
+ with intercept_result(Unzip, 'file') as outfiles:
+ self.assertFalse(execute([
+ ('Unzip', 'org.vistrails.vistrails.basic', [
+ ('archive_file', [('File', zipfile)]),
+ ('filename_in_archive', [('String', 'file1.txt')]),
+ ]),
+ ]))
+ self.assertEqual(len(outfiles), 1)
+ with open(outfiles[0].name, 'rb') as outfile:
+ self.assertEqual(outfile.read(), "some random\ncontent")
+
+ def test_unzip_all(self):
+ from vistrails.tests.utils import execute, intercept_result
+ from vistrails.core.system import vistrails_root_directory
+ zipfile = os.path.join(vistrails_root_directory(),
+ 'tests', 'resources',
+ 'test_archive.zip')
+ with intercept_result(UnzipDirectory, 'directory') as outdir:
+ self.assertFalse(execute([
+ ('UnzipDirectory', 'org.vistrails.vistrails.basic', [
+ ('archive_file', [('File', zipfile)]),
+ ]),
+ ]))
+ self.assertEqual(len(outdir), 1)
+
+ self.assertEqual(
+ [(d, f) for p, d, f in os.walk(outdir[0].name)],
+ [(['subdir'], ['file1.txt']),
+ ([], ['file2.txt'])])
+
+
+from vistrails.core.configuration import get_vistrails_configuration
+
+class TestTypechecking(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ conf = get_vistrails_configuration()
+ cls.error_all = conf.errorOnConnectionTypeerror
+ cls.error_variant = conf.errorOnVariantTypeerror
+
+ @classmethod
+ def tearDownClass(cls):
+ conf = get_vistrails_configuration()
+ conf.errorOnConnectionTypeerror = cls.error_all
+ conf.errorOnVariantTypeerror = cls.error_variant
+
+ @staticmethod
+ def set_settings(error_all, error_variant):
+ conf = get_vistrails_configuration()
+ conf.errorOnConnectionTypeerror = error_all
+ conf.errorOnVariantTypeerror = error_variant
+
+ def run_test_pipeline(self, result, expected_results, *args, **kwargs):
+ from vistrails.tests.utils import execute, intercept_result
+ for error_all, error_variant, expected in expected_results:
+ self.set_settings(error_all, error_variant)
+ with intercept_result(*result) as results:
+ error = execute(*args, **kwargs)
+ if not expected:
+ self.assertTrue(error)
+ else:
+ self.assertFalse(error)
+ self.assertEqual(results, expected)
+
+ def test_basic(self):
+ import urllib2
+ # Base case: no typing error
+ # This should succeed in every case
+ self.run_test_pipeline(
+ (PythonSource, 'r'),
+ [(False, False, ["test"]),
+ (True, True, ["test"])],
+ [
+ ('PythonSource', 'org.vistrails.vistrails.basic', [
+ ('source', [('String', urllib2.quote('o = "test"'))]),
+ ]),
+ ('PythonSource', 'org.vistrails.vistrails.basic', [
+ ('source', [('String', urllib2.quote('r = i'))])
+ ]),
+ ],
+ [
+ (0, 'o', 1, 'i'),
+ ],
+ add_port_specs=[
+ (0, 'output', 'o',
+ 'org.vistrails.vistrails.basic:String'),
+ (1, 'input', 'i',
+ 'org.vistrails.vistrails.basic:String'),
+ (1, 'output', 'r',
+ 'org.vistrails.vistrails.basic:String')
+ ])
+
+ def test_fake(self):
+ import urllib2
+ # A module is lying, declaring a String but returning an int
+ # This should fail with errorOnConnectionTypeerror=True (not the
+ # default)
+ self.run_test_pipeline(
+ (PythonSource, 'r'),
+ [(False, False, [42]),
+ (False, True, [42]),
+ (True, True, False)],
+ [
+ ('PythonSource', 'org.vistrails.vistrails.basic', [
+ ('source', [('String', urllib2.quote('o = 42'))]),
+ ]),
+ ('PythonSource', 'org.vistrails.vistrails.basic', [
+ ('source', [('String', urllib2.quote('r = i'))])
+ ]),
+ ],
+ [
+ (0, 'o', 1, 'i'),
+ ],
+ add_port_specs=[
+ (0, 'output', 'o',
+ 'org.vistrails.vistrails.basic:String'),
+ (1, 'input', 'i',
+ 'org.vistrails.vistrails.basic:String'),
+ (1, 'output', 'r',
+ 'org.vistrails.vistrails.basic:String')
+ ])
+
+ def test_inputport(self):
+ import urllib2
+ # This test uses an InputPort module, whose output port should not be
+ # considered a Variant port (although it is)
+ self.run_test_pipeline(
+ (PythonSource, 'r'),
+ [(False, False, [42]),
+ (False, True, [42]),
+ (True, True, [42])],
+ [
+ ('InputPort', 'org.vistrails.vistrails.basic', [
+ ('ExternalPipe', [('Integer', '42')]),
+ ]),
+ ('PythonSource', 'org.vistrails.vistrails.basic', [
+ ('source', [('String', urllib2.quote('r = i'))])
+ ]),
+ ],
+ [
+ (0, 'InternalPipe', 1, 'i'),
+ ],
+ add_port_specs=[
+ (1, 'input', 'i',
+ 'org.vistrails.vistrails.basic:String'),
+ (1, 'output', 'r',
+ 'org.vistrails.vistrails.basic:String'),
+ ])
diff --git a/vistrails/core/modules/constant_configuration.py b/vistrails/core/modules/constant_configuration.py
new file mode 100644
index 0000000..ca9064b
--- /dev/null
+++ b/vistrails/core/modules/constant_configuration.py
@@ -0,0 +1,44 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# *** MOVED *** to gui.modules.constant_configuration
+import traceback
+from vistrails.core import debug
+
+from vistrails.gui.modules.constant_configuration import *
+debug.warning("The use of core.modules.constant_configuration is deprecated. "
+ "Please use gui.modules.constant_configuration.",
+ ''.join(traceback.format_stack()))
+
diff --git a/vistrails/core/modules/module_configure.py b/vistrails/core/modules/module_configure.py
new file mode 100644
index 0000000..fa576d4
--- /dev/null
+++ b/vistrails/core/modules/module_configure.py
@@ -0,0 +1,44 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# *** MOVED *** to gui.modules.module_configure
+import traceback
+from vistrails.core import debug
+
+from vistrails.gui.modules.module_configure import *
+debug.warning("The use of core.modules.module_configure is deprecated. "
+ "Please use gui.modules.module_configure.",
+ ''.join(traceback.format_stack()))
+
diff --git a/vistrails/core/modules/module_descriptor.py b/vistrails/core/modules/module_descriptor.py
new file mode 100644
index 0000000..be535ab
--- /dev/null
+++ b/vistrails/core/modules/module_descriptor.py
@@ -0,0 +1,404 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+import pydoc
+
+from vistrails.core import debug
+from vistrails.core.utils import VistrailsInternalError
+from vistrails.core.vistrail.port_spec import PortSpec
+import vistrails.core.modules.module_registry
+from vistrails.core.modules.utils import create_descriptor_string
+from vistrails.db.domain import DBModuleDescriptor
+
+# this is used by add_port to signal a repeated port. Should never
+# happen, but it does. Probably means a bug on the dynamic modules
+# such as MplPlot and Tuple. Of course, that also means that we
+# should be robust in the presence of these errors, since user-defined
+# modules could exhibit this bug
+
+class OverloadedPort(Exception):
+ pass
+
+###############################################################################
+# ModuleDescriptor
+
+class ModuleDescriptor(DBModuleDescriptor):
+ """ModuleDescriptor is a class that holds information about
+ modules in the registry. There exists exactly one ModuleDescriptor
+ for every registered VisTrails module in the system.
+
+ self.module: reference to the python class that defines the module
+ self.name: name of the module
+ self.identifier: identifier of the package that module belongs to
+ self.input_ports: dictionary of names of input ports to the types
+ consumed by the ports
+ self.output_ports: dictionary of names of output ports to the types
+ produces by the ports
+ self.input_ports_optional: dictionary of input port names that records
+ whether ports should show up by default on GUI
+ self.output_ports_optional: dictionary of output port names that records
+ whether ports should show up by default on GUI
+ self.port_order: stores a map from names to numbers to order the ports
+ in the GUI
+
+ self._is_abstract: whether module is abstract
+ self._configuration_widget: reference to the Qt class that provides a
+ custom configuration widget for the class. Note that this can
+ be a tuple (path, name) that will be loaded only when needed via
+ __import__ (! this is preferred !) or as a QWidget (deprecated)
+
+ self._left_fringe and self._right_fringe: lists of 2D points that
+ define a drawing style for modules in the GUI
+ self._module_color: color of the module in the GUI
+
+ self._widget_item: stores a reference to the ModuleTreeWidgetItem so
+ that when ports are added to modules things get correctly updated.
+
+ self._input_port_cache, self._output_port_cache,
+ self._port_caches: Dictionaries for fast port spec lookup,
+ created because port spec lookups are sometimes part of hot code
+ paths and need to go as fast as possible.
+ """
+
+ ##########################################################################
+
+ def __init__(self, *args, **kwargs):
+ self.children = []
+ if 'module' in kwargs:
+ self.module = kwargs['module']
+ if 'name' not in kwargs:
+ kwargs['name'] = self.module.__name__
+ del kwargs['module']
+ else:
+ self.module = None
+ if 'base_descriptor' in kwargs:
+ if kwargs['base_descriptor'] is not None:
+ self._base_descriptor = kwargs['base_descriptor']
+ if 'base_descriptor_id' not in kwargs:
+ kwargs['base_descriptor_id'] = self._base_descriptor.id
+ self._port_count = self._base_descriptor._port_count
+ self._base_descriptor.children.append(self)
+ else:
+ self._base_descriptor = None
+ self._port_count = 0
+ del kwargs['base_descriptor']
+ else:
+ self._base_descriptor = None
+ self._port_count = 0
+ # rename identifier to package for db
+ if 'identifier' in kwargs:
+ if 'package' not in kwargs:
+ kwargs['package'] = kwargs['identifier']
+ del kwargs['identifier']
+ if 'base_descriptor_id' not in kwargs:
+ kwargs['base_descriptor_id'] = -1
+ DBModuleDescriptor.__init__(self, *args, **kwargs)
+ self.set_defaults()
+
+ def set_defaults(self, other=None):
+ if other is None:
+ self._abstraction_refs = 1
+ self._is_abstract = False
+ self._configuration_widget = None
+ self._left_fringe = None
+ self._right_fringe = None
+ self._module_color = None
+ self._hasher_callable = None
+ self._widget_item = None
+ self._is_hidden = False
+ self._namespace_hidden = False
+ self.children = []
+ # The ghost attributes represent the original values
+ # for the descriptor of an upgraded package subworkflow
+ # so it can be displayed with it's original package
+ # rather than 'local.abstractions'
+ self.ghost_identifier = ''
+ self.ghost_package_version = ''
+ self.ghost_namespace = None
+ else:
+ # FIXME this will break things, I think
+ self.children = copy.copy(other.children)
+
+ self._base_descriptor = other._base_descriptor
+ self.module = other.module
+ self._port_count = other._port_count
+ self._abstraction_refs = self._abstraction_refs
+ self._is_abstract = other._is_abstract
+ self._configuration_widget = other._configuration_widget
+ self._left_fringe = other._left_fringe
+ self._right_fringe = other._right_fringe
+ self._module_color = other._module_color
+ self._hasher_callable = other._hasher_callable
+ self._widget_item = other._widget_item
+ self._is_hidden = other._is_hidden
+ self._namespace_hidden = other._namespace_hidden
+ self.ghost_identifier = other.ghost_identifier
+ self.ghost_package_version = other.ghost_package_version
+ self.ghost_namespace = other.ghost_namespace
+ self.port_specs = self.db_portSpecs_name_index
+ if self.version is None:
+ self.version = ''
+ if self.namespace is None:
+ self.namespace = ''
+
+ def __copy__(self):
+ return ModuleDescriptor.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleDescriptor.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = ModuleDescriptor
+ cp.set_defaults(self)
+ return cp
+
+ @staticmethod
+ def convert(_desc):
+ if _desc.__class__ == ModuleDescriptor:
+ return
+ _desc.__class__ = ModuleDescriptor
+
+ for port_spec in _desc.db_portSpecs:
+ PortSpec.convert(port_spec)
+
+ # do more init stuff
+ _desc.children = []
+ _desc.module = None
+ _desc._base_descriptor = None
+ _desc._port_count = 0
+ _desc.set_defaults()
+
+ ##########################################################################
+ # Properties
+
+ id = DBModuleDescriptor.db_id
+ name = DBModuleDescriptor.db_name
+ identifier = DBModuleDescriptor.db_package
+ package = DBModuleDescriptor.db_package
+ namespace = DBModuleDescriptor.db_namespace
+ package_version = DBModuleDescriptor.db_package_version
+ version = DBModuleDescriptor.db_version
+ base_descriptor_id = DBModuleDescriptor.db_base_descriptor_id
+ port_specs_list = DBModuleDescriptor.db_portSpecs
+
+ def _get_base_descriptor(self):
+ if self._base_descriptor is None and self.base_descriptor_id >= 0:
+ from vistrails.core.modules.module_registry import get_module_registry
+ reg = get_module_registry()
+ self._base_descriptor = \
+ reg.descriptors_by_id[self.base_descriptor_id]
+ return self._base_descriptor
+ def _set_base_descriptor(self, base_descriptor):
+ self._base_descriptor = base_descriptor
+ self.base_descriptor_id = base_descriptor.id
+ base_descriptor = property(_get_base_descriptor, _set_base_descriptor)
+
+ def _get_sigstring(self):
+ return create_descriptor_string(self.db_package, self.db_name,
+ self.db_namespace)
+ sigstring = property(_get_sigstring)
+
+ def _get_spec_tuple(self):
+ return (self.package, self.name, self.namespace)
+ spec_tuple = property(_get_spec_tuple)
+
+ def set_module_abstract(self, v):
+ self._is_abstract = v
+
+ def module_abstract(self):
+# if not self.has_ports():
+# return True
+ return self._is_abstract
+
+ def set_configuration_widget(self, configuration_widget_type):
+ """set_configuration_widget(configuration_widget_type:
+ (path, name) tuple or QWidget) -> None
+
+ """
+ self._configuration_widget = configuration_widget_type
+
+ def configuration_widget(self):
+ return self._configuration_widget
+
+ def set_module_color(self, color):
+ if color:
+ assert isinstance(color, tuple)
+ assert len(color) == 3
+ for i in 0,1,2:
+ assert isinstance(color[i], float)
+ self._module_color = color
+
+ def module_color(self):
+ return self._module_color
+
+ def set_module_fringe(self, left_fringe, right_fringe):
+ if left_fringe is None:
+ assert right_fringe is None
+ self._left_fringe = None
+ self._right_fringe = None
+ else:
+ vistrails.core.modules.module_registry._check_fringe(left_fringe)
+ vistrails.core.modules.module_registry._check_fringe(right_fringe)
+ self._left_fringe = left_fringe
+ self._right_fringe = right_fringe
+
+ def module_fringe(self):
+ if self._left_fringe is None and self._right_fringe is None:
+ return None
+ return (self._left_fringe, self._right_fringe)
+
+ def module_documentation(self, module=None):
+ doc = pydoc.getdoc(self.module)
+ if hasattr(self.module, 'get_documentation'):
+ try:
+ doc = self.module.get_documentation(doc, module)
+ except Exception, e:
+ import traceback
+ debug.critical(str(e), traceback.format_exc())
+ doc = doc or "(Error getting documentation)"
+ doc = doc or "(No documentation available)"
+ return doc
+
+ def module_package(self):
+ return self.identifier
+
+ def set_hasher_callable(self, callable_):
+ self._hasher_callable = callable_
+ def hasher_callable(self):
+ return self._hasher_callable
+
+ def _get_is_hidden(self):
+ return self._is_hidden
+ def _set_is_hidden(self, hidden):
+ self._is_hidden = hidden
+ is_hidden = property(_get_is_hidden, _set_is_hidden)
+
+ def _get_namespace_hidden(self):
+ return self._namespace_hidden
+ def _set_namespace_hidden(self, hidden):
+ self._namespace_hidden = hidden
+ namespace_hidden = property(_get_namespace_hidden, _set_namespace_hidden)
+
+ ##########################################################################
+ # Operators
+
+ def __hash__(self):
+ return (type(self), self.package, self.name, self.namespace,
+ self.version).__hash__()
+
+ def __eq__(self, other):
+ return (self.package == other.package and
+ self.name == other.name and
+ self.namespace == other.namespace and
+ self.version == other.version)
+
+ def __str__(self):
+ return ("ModuleDescriptor(id=%s, package=%s, name=%s, namespace=%s, "
+ "version=%s, base_descriptor_id=%s)" % \
+ (self.id, self.package, self.name, self.namespace,
+ self.version, self.base_descriptor_id))
+
+ ##########################################################################
+ # Abstract module detection support
+
+ def set_widget(self, widget_item):
+ self._widget_item = widget_item
+
+ def has_ports(self):
+ """Returns True is module has any ports (this includes
+ superclasses). This method exists to make automatic abstract
+ module detection efficient."""
+ return self._port_count > 0
+
+ def port_count(self):
+ """Return the total number of available for the module."""
+ return self._port_count
+
+ # Signal handling
+ def new_input_port(self):
+ """Updates needed variables when new input port is added
+ to either this module or the superclass."""
+ self._port_count += 1
+ if self._widget_item:
+ self._widget_item.added_input_port()
+ for child in self.children:
+ child.new_input_port()
+
+ def new_output_port(self):
+ """Updates needed variables when new output port is added
+ to either this module or the superclass."""
+ self._port_count += 1
+ if self._widget_item:
+ self._widget_item.added_output_port()
+ for child in self.children:
+ child.new_output_port()
+
+ ##########################################################################
+
+ # port_type is 'input' or 'output'
+ def has_port_spec(self, name, port_type):
+ return self.db_has_portSpec_with_name((name, port_type))
+
+ def get_port_spec(self, name, port_type):
+ if not self.db_has_portSpec_with_name((name, port_type)):
+ raise ValueError("ModuleDescriptor.get_port_spec called when spec "
+ " (%s, %s) doesn't exist" % (name, port_type))
+ return self.db_get_portSpec_by_name((name, port_type))
+
+ def set_port_spec(self, name, port_type, port_spec):
+ self.db_add_portSpec(port_spec)
+
+ def add_port_spec(self, port_spec):
+ self.db_add_portSpec(port_spec)
+
+ def delete_port_spec(self, port_spec):
+ self.db_delete_portSpec(port_spec)
+
+ def delete_input_port(self, name):
+ key = (name, 'input')
+ if key in self.port_specs:
+ self.delete_port_spec(self.port_specs[key])
+ else:
+ raise VistrailsInternalError("delete_input_port called on "
+ "nonexistent port '%s'" % name)
+
+ def delete_output_port(self, name):
+ key = (name, 'output')
+ if key in self.port_specs:
+ self.delete_port_spec(self.port_specs[key])
+ else:
+ raise VistrailsInternalError("delete_output_port called on "
+ "nonexistent port '%s'" % name)
+
+
+
diff --git a/vistrails/core/modules/module_registry.py b/vistrails/core/modules/module_registry.py
new file mode 100644
index 0000000..acdbc02
--- /dev/null
+++ b/vistrails/core/modules/module_registry.py
@@ -0,0 +1,2001 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from itertools import izip, chain
+import copy
+import os
+import tempfile
+import traceback
+import uuid
+
+from vistrails.core import debug, get_vistrails_application
+from vistrails.core.data_structures.graph import Graph
+import vistrails.core.modules
+import vistrails.core.modules.vistrails_module
+from vistrails.core.modules.module_descriptor import ModuleDescriptor
+from vistrails.core.modules.package import Package
+import vistrails.core.modules.utils
+from vistrails.core.utils import VistrailsInternalError, memo_method, \
+ InvalidModuleClass, ModuleAlreadyExists, append_to_dict_of_lists, \
+ all, profile, versions_increasing, InvalidPipeline
+from vistrails.core.system import vistrails_root_directory, vistrails_version, \
+ get_vistrails_basic_pkg_id
+from vistrails.core.vistrail.port import Port, PortEndPoint
+from vistrails.core.vistrail.port_spec import PortSpec
+from vistrails.core.vistrail.port_spec_item import PortSpecItem
+import vistrails.core.cache.hasher
+from vistrails.db.domain import DBRegistry
+
+import unittest
+
+##############################################################################
+
+# This is used by add_module to make sure the fringe specifications
+# make sense
+def _check_fringe(fringe):
+ assert isinstance(fringe, list)
+ assert len(fringe) >= 1
+ for v in fringe:
+ assert isinstance(v, tuple)
+ assert len(v) == 2
+ assert isinstance(v[0], float)
+ assert isinstance(v[1], float)
+
+def _toposort_modules(module_list):
+ """_toposort_modules([class]) -> [class]
+
+ _toposort_modules takes a list of modules and returns them
+ sorted topologically wrt to the subclass relation, such that
+ if a and b are both in the list and issubclass(a,b), then a
+ will appear before b in the resulting order.
+ """
+
+ g = Graph()
+ for m in module_list:
+ if isinstance(m, tuple):
+ g.add_vertex(m[0], m)
+ else:
+ g.add_vertex(m, m)
+ for m in module_list:
+ if isinstance(m, tuple):
+ m = m[0]
+ for subclass in m.mro()[1:]: # skip self
+ if subclass in g.vertices:
+ g.add_edge(subclass, m)
+ return [g.vertices[v] for v in g.vertices_topological_sort()]
+
+def _parse_abstraction_name(filename):
+ # assume only 1 possible prefix or suffix
+ prefixes = ["abstraction_"]
+ suffixes = [".vt", ".xml"]
+ name = os.path.basename(filename)
+ for prefix in prefixes:
+ if name.startswith(prefix):
+ name = name[len(prefix):]
+ break
+ for suffix in suffixes:
+ if name.endswith(suffix):
+ name = name[:-len(suffix)]
+ break
+ return name
+
+def _toposort_abstractions(package, abstraction_list):
+ from vistrails.core.modules.sub_module import find_internal_abstraction_refs
+ g = Graph()
+ for a in abstraction_list:
+ if isinstance(a, tuple):
+ if isinstance(a[1], dict) and 'name' in a[1]:
+ name = (a[1]['name'], a[1].get('namespace', ''))
+ else:
+ name = (_parse_abstraction_name(a[0]), '')
+ g.add_vertex(name, a)
+ else:
+ g.add_vertex((_parse_abstraction_name(a), ''), a)
+ for a in abstraction_list:
+ if isinstance(a, tuple):
+ a = a[0]
+ for ref in find_internal_abstraction_refs(package, a):
+ if ref in g.vertices:
+ g.add_edge(ref, a)
+ return [g.vertices[v] for v in g.vertices_topological_sort()]
+
+###############################################################################
+# ModuleRegistrySignals
+
+class ModuleRegistrySignals(object):
+
+ # # new_module_signal is emitted with descriptor of new module
+ # new_module_signal = QtCore.SIGNAL("new_module")
+ # # new_abstraction_signal is emitted with descriptor of new abstraction
+ # new_abstraction_signal = QtCore.SIGNAL("new_abstraction")
+ # # new_package_signal is emitted with identifier of new package (only for abstractions)
+ # new_package_signal = QtCore.SIGNAL("new_package")
+ # # deleted_module_signal is emitted with descriptor of deleted module
+ # deleted_module_signal = QtCore.SIGNAL("deleted_module")
+ # # deleted_abstraction_signal is emitted with descriptor of deleted abstraction
+ # deleted_abstraction_signal = QtCore.SIGNAL("deleted_abstraction")
+ # # deleted_package_signal is emitted with package identifier
+ # deleted_package_signal = QtCore.SIGNAL("deleted_package")
+ # # new_input_port_signal is emitted with identifier and name of module,
+ # # new port and spec
+ # new_input_port_signal = QtCore.SIGNAL("new_input_port_signal")
+ # # new_output_port_signal is emitted with identifier and name of module,
+ # # new port and spec
+ # new_output_port_signal = QtCore.SIGNAL("new_output_port_signal")
+
+ # show_module_signal = QtCore.SIGNAL("show_module")
+ # hide_module_signal = QtCore.SIGNAL("hide_module")
+ # module_updated_signal = QtCore.SIGNAL("module_updated")
+
+ def __init__(self):
+ app = get_vistrails_application()
+ notifications = ["reg_new_module",
+ "reg_new_abstraction",
+ "reg_new_package",
+ "reg_deleted_module",
+ "reg_deleted_abstraction",
+ "reg_deleted_package",
+ "reg_new_input_port",
+ "reg_new_output_port",
+ "reg_show_module",
+ "reg_hide_module",
+ "reg_module_updated"]
+
+ for notification in notifications:
+ app.create_notification(notification)
+
+ def emit_new_module(self, descriptor):
+ app = get_vistrails_application()
+ app.send_notification("reg_new_module", descriptor)
+ # self.emit(self.new_module_signal, descriptor)
+
+ def emit_new_abstraction(self, descriptor):
+ app = get_vistrails_application()
+ app.send_notification("reg_new_abstraction", descriptor)
+ # self.emit(self.new_abstraction_signal, descriptor)
+
+ def emit_new_package(self, identifier, prepend=False):
+ app = get_vistrails_application()
+ app.send_notification("reg_new_package", identifier, prepend)
+ # self.emit(self.new_package_signal, identifier, prepend)
+
+ def emit_deleted_module(self, descriptor):
+ app = get_vistrails_application()
+ app.send_notification("reg_deleted_module", descriptor)
+ # self.emit(self.deleted_module_signal, descriptor)
+
+ def emit_deleted_abstraction(self, descriptor):
+ app = get_vistrails_application()
+ app.send_notification("reg_deleted_abstraction", descriptor)
+ # self.emit(self.deleted_abstraction_signal, descriptor)
+
+ def emit_deleted_package(self, package):
+ app = get_vistrails_application()
+ app.send_notification("reg_deleted_package", package)
+ # self.emit(self.deleted_package_signal, package)
+
+ def emit_new_input_port(self, identifier, name, port_name, spec):
+ app = get_vistrails_application()
+ app.send_notification("reg_new_input_port", identifier, name,
+ port_name, spec)
+ # self.emit(self.new_input_port_signal, identifier, name, port_name,
+ # spec)
+
+ def emit_new_output_port(self, identifier, name, port_name, spec):
+ app = get_vistrails_application()
+ app.send_notification("reg_new_output_port", identifier, name,
+ port_name, spec)
+ # self.emit(self.new_output_port_signal, identifier, name, port_name,
+ # spec)
+
+ def emit_show_module(self, descriptor):
+ app = get_vistrails_application()
+ app.send_notification("reg_show_module", descriptor)
+ # self.emit(self.show_module_signal, descriptor)
+
+ def emit_hide_module(self, descriptor):
+ app = get_vistrails_application()
+ app.send_notification("reg_hide_module", descriptor)
+ # self.emit(self.hide_module_signal, descriptor)
+
+ def emit_module_updated(self, old_descriptor, new_descriptor):
+ app = get_vistrails_application()
+ app.send_notification("reg_module_updated", old_descriptor,
+ new_descriptor)
+ # self.emit(self.module_updated_signal, old_descriptor, new_descriptor)
+
+###############################################################################
+# ModuleRegistry
+
+# !!!!!! DEPRECATED !!!!!!
+# Use get_module_registry()
+global registry, add_module, add_input_port, has_input_port, add_output_port, \
+ set_current_package, get_descriptor_by_name, get_module_by_name, \
+ get_descriptor
+registry = None
+add_module = None
+add_input_port = None
+has_input_port = None
+add_output_port = None
+set_current_package = None
+get_descriptor_by_name = None
+get_module_by_name = None
+get_descriptor = None
+
+
+class ModuleRegistryException(Exception):
+ def __init__(self, identifier, name=None, namespace=None,
+ package_version=None, module_version=None, module_id=None):
+ Exception.__init__(self)
+ self._identifier = identifier
+ self._name = name
+ self._namespace = namespace
+ self._package_version = package_version
+ self._module_version = module_version
+ self._module_id = module_id
+
+ def __str__(self):
+ p_version_str = ""
+ m_str = ""
+ if self._package_version:
+ p_version_str = " (version '%s')" % self._package_version
+ if self._name:
+ if self._namespace:
+ m_str = " : %s|%s" % (self._namespace, self._name)
+ else:
+ m_str = " : %s" % self._name
+ if self._module_version:
+ m_str += " (version '%s')" % self._module_version
+
+ return "RegistryException: %s%s%s" % (self._identifier,
+ p_version_str, m_str)
+
+ def __eq__(self, other):
+ return type(self) == type(other) and \
+ self._identifier == other._identifier and \
+ self._name == other._name and \
+ self._namespace == other._namespace and \
+ self._package_version == other._package_version and \
+ self._module_version == other._module_version and \
+ self._module_id == other._module_id
+
+ def __hash__(self):
+ return (type(self), self._identifier, self._name, self._namespace,
+ self._package_version, self._module_version,
+ self._module_id).__hash__()
+
+ def _get_module_name(self):
+ if self._namespace:
+ return "%s|%s" % (self._namespace, self._name)
+ return self._name
+ _module_name = property(_get_module_name)
+
+ def _get_package_name(self):
+ if self._package_version:
+ return "%s (version %s)" % (self._identifier,
+ self._package_version)
+ return self._identifier
+ _package_name = property(_get_package_name)
+
+class MissingPackage(ModuleRegistryException):
+ def __init__(self, identifier):
+ ModuleRegistryException.__init__(self, identifier)
+
+ def __str__(self):
+ return "Missing package: %s" % self._identifier
+
+ def _get_module_id(self):
+ return None
+ def _set_module_id(self, m_id):
+ # do not set
+ pass
+ _module_id = property(_get_module_id, _set_module_id)
+
+class MissingModule(ModuleRegistryException):
+ def __init__(self, identifier, name, namespace, package_version=None,
+ module_id=None):
+ ModuleRegistryException.__init__(self, identifier, name, namespace,
+ package_version, None, module_id)
+
+ def __str__(self):
+ return "Missing module %s in package %s" % (self._module_name,
+ self._package_name)
+
+class MissingPackageVersion(ModuleRegistryException):
+ def __init__(self, identifier, version):
+ ModuleRegistryException.__init__(self, identifier, None, None,
+ version)
+
+ def __str__(self):
+ return "Missing version %s of package %s" % \
+ (self._package_version, self._identifier)
+
+class MissingModuleVersion(ModuleRegistryException):
+ def __init__(self, identifier, name, namespace, module_version,
+ package_version=None, module_id=None):
+ ModuleRegistryException.__init__(self, identifier, name, namespace,
+ package_version, module_version, module_id)
+
+ def __str__(self):
+ return "Missing version %s of module %s from package %s" % \
+ (self._module_version, self._module_name, self._package_name)
+
+class AmbiguousResolution(ModuleRegistryException):
+ def __init__(self, name, namespace, matches):
+ ModuleRegistryException.__init__(self, "<unkown package>",
+ name, namespace)
+ self.matches = matches
+
+ def __str__(self):
+ return ("Ambiguous resolution of module %s. Could resolve to:\n%s" % \
+ (self._module_name,
+ ',\n'.join(str(m) for m in self.matches)))
+
+class MissingPort(ModuleRegistryException):
+ def __init__(self, descriptor, port_name, port_type):
+ ModuleRegistryException.__init__(self,
+ descriptor.identifier,
+ descriptor.name,
+ descriptor.namespace)
+ self._port_name = port_name
+ self._port_type = port_type
+
+ def __str__(self):
+ return "Missing %s port %s from module %s in package %s" % \
+ (self._port_type, self._port_name, self._module_name,
+ self._package_name)
+
+class PortMismatch(MissingPort):
+ def __init__(self, identifier, name, namespace, port_name, port_type, port_sigstring):
+ ModuleRegistryException.__init__(self,
+ identifier,
+ name,
+ namespace)
+
+ self._port_name = port_name
+ self._port_type = port_type
+ self._port_sigstring = port_sigstring
+
+ def __str__(self):
+ return ("%s port '%s' of signature '%s' has bad specification"
+ " in module %s of package %s") % \
+ (self._port_type.capitalize(), self._port_name,
+ self._port_sigstring, self._module_name, self._package_name)
+
+class PortsIncompatible(ModuleRegistryException):
+
+ def __init__(self, output_identifier, output_name, output_namespace,
+ output_port, input_identifier, input_name, input_namespace,
+ input_port):
+ ModuleRegistryException.__init__(self, output_identifier, output_name,
+ output_namespace)
+ self._output_port = output_port
+ self._input_identifier = input_identifier
+ self._input_name = input_name
+ self._input_namespace = input_namespace
+ self._input_port = input_port
+
+ def __str__(self):
+ if self._namespace:
+ out_name = "%s:%s|%s" % (self._identifier, self._namespace,
+ self._name)
+ else:
+ out_name = "%s:%s" % (self._identifier, self._name)
+ if self._input_namespace:
+ in_name = "%s:%s|%s" % (self._input_identifier,
+ self._input_namespace,
+ self._input_name)
+ else:
+ in_name = "%s:%s" % (self._input_identifier, self._input_name)
+ return ('Output port "%s" from module "%s" cannot connect to '
+ 'input port "%s" from module "%s".' % (self._output_port,
+ out_name,
+ self._input_port,
+ in_name))
+
+class DuplicateModule(ModuleRegistryException):
+ def __init__(self, old_descriptor, new_identifier, new_name,
+ new_namespace):
+ ModuleRegistryException.__init__(self,
+ new_identifier,
+ new_name,
+ new_namespace)
+ self.old_descriptor = old_descriptor
+
+ def __str__(self):
+ if self.old_descriptor.namespace:
+ old_name = "%s|%s" % (self.old_descriptor.namespace,
+ self.old_descriptor.name)
+ else:
+ old_name = self.old_descriptor.name
+ return ("Module %s in package %s already exists as "
+ "%s in package %s") % \
+ (self._module_name, self._package_name, old_name,
+ self.old_descriptor.identifier)
+
+class DuplicateIdentifier(ModuleRegistryException):
+ def __init__(self, identifier, name, namespace=None,
+ package_version=None, module_version=None):
+ ModuleRegistryException.__init__(self, identifier, name, namespace,
+ package_version, module_version)
+
+ def __str__(self):
+ return "There is already a module %s in package %s" % \
+ (self._module_name, self._package_name)
+
+class InvalidPortSpec(ModuleRegistryException):
+ def __init__(self, descriptor, port_name, port_type, exc):
+ ModuleRegistryException.__init__(self,
+ descriptor.identifier,
+ descriptor.name,
+ descriptor.namespace)
+ self._port_name = port_name
+ self._port_type = port_type[0].capitalize() + port_type[1:]
+ self._exc = exc
+
+ def __str__(self):
+ return ('%s port "%s" from module %s in package %s '
+ 'has bad specification\n %s' % \
+ (self._port_type, self._port_name, self._module_name,
+ self._package_name, str(self._exc)))
+
+class MissingBaseClass(Exception):
+ def __init__(self, base):
+ Exception.__init__(self)
+ self._base = base
+
+ def __str__(self):
+ return "Base class has not been registered : %s" % (self._base.__name__)
+
+class ModuleRegistry(DBRegistry):
+ """ModuleRegistry serves as a registry of VisTrails modules.
+ """
+
+ ##########################################################################
+ # Constructor and copy
+
+ def __init__(self, *args, **kwargs):
+ """ModuleRegistry is the base class for objects that store a hierarchy
+ of registered VisTrails Modules. There is one global registry for the
+ system, and some modules have local registries (in the case of
+ dynamically configurable modules, like PythonSource).
+
+ """
+
+ if 'root_descriptor_id' not in kwargs:
+ kwargs['root_descriptor_id'] = -1
+ DBRegistry.__init__(self, *args, **kwargs)
+
+ self._conversions = dict()
+ self._converters = set()
+
+ self.set_defaults()
+
+ def __copy__(self):
+ ModuleRegistry.do_copy(self)
+
+ def set_defaults(self, other=None):
+ self._root_descriptor = None
+ self.signals = ModuleRegistrySignals()
+ self.setup_indices()
+ if other is None:
+ # _constant_hasher_map stores callables for custom parameter
+ # hashers
+ self._constant_hasher_map = {}
+ basic_pkg = get_vistrails_basic_pkg_id()
+ if basic_pkg in self.packages:
+ self._default_package = self.packages[basic_pkg]
+ self._current_package = self._default_package
+ else:
+ self._default_package = None
+ self._current_package = None
+ else:
+ self._constant_hasher_map = copy.copy(other._constant_hasher_map)
+ self._current_package = \
+ self.packages[other._current_package.identifier]
+ self._default_package = \
+ self.packages[other._default_package.identifier]
+
+ def setup_indices(self):
+ self.descriptors_by_id = {}
+ self.package_versions = self.db_packages_identifier_index
+ self.packages = {}
+ self._module_key_map = {}
+ for pkg in self.package_versions.itervalues():
+ for key in chain(pkg.old_identifiers, [pkg.identifier]):
+ if key in self.packages:
+ old_pkg = self.packages[key]
+ if versions_increasing(old_pkg.version, pkg.version):
+ self.packages[key] = pkg
+ else:
+ self.packages[key] = pkg
+ for descriptor in pkg.descriptor_list:
+ self.descriptors_by_id[descriptor.id] = descriptor
+ k = (descriptor.identifier, descriptor.name,
+ descriptor.namespace, pkg.version, descriptor.version)
+ if descriptor.module is not None:
+ self._module_key_map[descriptor.module] = k
+ for descriptor in self.descriptors_by_id.itervalues():
+ if descriptor.base_descriptor_id in self.descriptors_by_id:
+ base_descriptor = \
+ self.descriptors_by_id[descriptor.base_descriptor_id]
+ if descriptor not in base_descriptor.children:
+ base_descriptor.children.append(descriptor)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBRegistry.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = ModuleRegistry
+ cp.set_defaults(self)
+ return cp
+
+ @staticmethod
+ def convert(_reg):
+ if _reg.__class__ == ModuleRegistry:
+ return
+ _reg.__class__ = ModuleRegistry
+ for package in _reg.package_list:
+ Package.convert(package)
+ _reg.set_defaults()
+
+ def set_global(self):
+ global registry, add_module, add_input_port, has_input_port, \
+ add_output_port, set_current_package, get_descriptor_by_name, \
+ get_module_by_name, get_descriptor
+
+ if registry is not None:
+ raise VistrailsInternalError("Global registry already set.")
+
+ registry = self
+ add_module = self.add_module
+ add_input_port = self.add_input_port
+ has_input_port = self.has_input_port
+ add_output_port = self.add_output_port
+ set_current_package = self.set_current_package
+ get_descriptor_by_name = self.get_descriptor_by_name
+ get_module_by_name = self.get_module_by_name
+ get_descriptor = self.get_descriptor
+
+ ##########################################################################
+ # Properties
+
+ package_list = DBRegistry.db_packages
+ root_descriptor_id = DBRegistry.db_root_descriptor_id
+
+ def _get_root_descriptor(self):
+ if self._root_descriptor is None:
+ if self.root_descriptor_id >= 0:
+ self._root_descriptor = \
+ self.descriptors_by_id[self.root_descriptor_id]
+ return self._root_descriptor
+ def _set_root_descriptor(self, descriptor):
+ self._root_descriptor = descriptor
+ self.root_descriptor_id = descriptor.id
+ root_descriptor = property(_get_root_descriptor, _set_root_descriptor)
+
+ def add_descriptor(self, desc, package=None):
+ if package is None:
+ package = self._default_package
+ # self.descriptors[(desc.package, desc.name, desc.namespace)] = desc
+ self.descriptors_by_id[desc.id] = desc
+ package.add_descriptor(desc)
+ def delete_descriptor(self, desc, package=None):
+ if package is None:
+ try:
+ package = self.packages[desc.identifier]
+ except KeyError:
+ package = self._default_package
+ if desc.base_descriptor_id != -1 and desc.base_descriptor:
+ desc.base_descriptor.children.remove(desc)
+ # del self.descriptors[(desc.package, desc.name, desc.namespace)]
+ del self.descriptors_by_id[desc.id]
+ package.delete_descriptor(desc)
+ def add_package(self, package):
+ DBRegistry.db_add_package(self, package)
+ for key in chain(package.old_identifiers, [package.identifier]):
+ if key in self.packages:
+ old_pkg = self.packages[key]
+ if versions_increasing(old_pkg.version, package.version):
+ self.packages[key] = package
+ else:
+ self.packages[key] = package
+
+ def delete_package(self, package):
+ DBRegistry.db_delete_package(self, package)
+ # FIXME hard to incremental updates here so we'll just recreate
+ # this can be slow
+ self.setup_indices()
+
+ def create_default_package(self):
+ basic_pkg = get_vistrails_basic_pkg_id()
+ default_codepath = os.path.join(vistrails_root_directory(),
+ "core", "modules", "basic_modules.py")
+ self._default_package = \
+ Package(id=self.idScope.getNewId(Package.vtType),
+ codepath=default_codepath,
+ load_configuration=False,
+ identifier=basic_pkg,
+ name='Basic Modules',
+ version=vistrails_version(),
+ description="Basic modules for VisTrails")
+ # FIXME need to serialize old_identifiers!
+ self._default_package.old_identifiers = ['edu.utah.sci.vistrails.basic']
+ self.add_package(self._default_package)
+ return self._default_package
+
+ def has_abs_upgrade(self, identifier, name, namespace='',
+ package_version='', module_version=''):
+
+ # if this fails, we want to raise the exception
+ try:
+ package = self.get_package_by_name(identifier, package_version)
+ except MissingPackageVersion:
+ package = self.get_package_by_name(identifier)
+ return package.has_abs_upgrade(name, namespace, module_version)
+
+ def get_abs_upgrade(self, identifier, name, namespace='',
+ package_version='', module_version=''):
+ try:
+ package = self.get_package_by_name(identifier, package_version)
+ except MissingPackageVersion:
+ package = self.get_package_by_name(identifier)
+ return package.get_abs_upgrade(name, namespace, module_version)
+
+ # def has_abs_upgrade(self, descriptor_info):
+ # return descriptor_info in self._abs_pkg_upgrades
+
+ # def get_abs_upgrade(self, descriptor_info):
+ # if self.has_abs_upgrade(descriptor_info):
+ # return self._abs_pkg_upgrades[descriptor_info]
+ # return None
+
+ ##########################################################################
+ # Per-module registry functions
+
+ def add_hierarchy(self, global_registry, module):
+ # a per-module registry needs to have all the module hierarchy
+ # registered there so that add_module doesn't fail with
+ # missing base class. We do _NOT_ add the ports, so watch out!
+
+ reg = global_registry
+ d = reg.get_descriptor_by_name(module.package, module.name,
+ module.namespace)
+ # we exclude the first module in the hierarchy because it's Module
+ # which we know exists (constructor adds)
+ hierarchy = reg.get_module_hierarchy(d)
+ for desc in reversed(hierarchy[:-1]):
+ old_base = desc.base_descriptor
+ base_descriptor = self.get_descriptor_by_name(old_base.package,
+ old_base.name,
+ old_base.namespace)
+ # FIXME: this package_version should live on descriptor?
+ package = self.get_package_by_name(desc.package)
+ self.update_registry(base_descriptor, desc.module, desc.package,
+ desc.name, desc.namespace, package.version,
+ desc.version)
+
+ def get_package_by_name(self, identifier, package_version=''):
+ package_version = package_version or ''
+ package_version_key = (identifier, package_version)
+# if package_version is not None and package_version.strip() == "":
+# package_version = None
+ try:
+ if not package_version:
+ return self.packages[identifier]
+ else:
+ return self.package_versions[package_version_key]
+ except KeyError:
+ if identifier not in self.packages:
+ raise MissingPackage(identifier)
+ elif package_version and \
+ package_version_key not in self.package_versions:
+ raise MissingPackageVersion(identifier, package_version)
+
+ def get_module_by_name(self, identifier, name, namespace=None):
+ """get_module_by_name(name: string): class
+
+ Returns the VisTrails module (the class) registered under the
+ given name.
+
+ """
+ return self.get_descriptor_by_name(identifier, name, namespace).module
+
+ def has_descriptor_with_name(self, identifier, name, namespace='',
+ package_version='', module_version=''):
+ namespace = namespace or ''
+ package_version = package_version or ''
+ module_version = module_version or ''
+
+ try:
+ if not package_version:
+ package = self.packages[identifier]
+ else:
+ package_version_key = (identifier, package_version)
+ package = self.package_versions[package_version_key]
+ if not module_version:
+ descriptor = package.descriptors[(name, namespace)]
+ else:
+ descriptor_version_key = (name, namespace, module_version)
+ descriptor = \
+ package.descriptor_versions[descriptor_version_key]
+ except KeyError:
+ return False
+ return True
+ has_module = has_descriptor_with_name
+
+ def get_descriptor_by_name(self, identifier, name, namespace='',
+ package_version='', module_version=''):
+ """get_descriptor_by_name(package_identifier : str,
+ module_name : str,
+ namespace : str,
+ package_version : str,
+ module_version : str) -> ModuleDescriptor
+ Gets the specified descriptor from the registry. If you do not
+ specify package_version, you will get the currently loaded version.
+ If you do not specify the module_version, you will get the most recent
+ version. Note that module_version is currently only used for
+ abstractions.
+
+ Raises a ModuleRegistryException if lookup fails.
+ """
+ namespace = namespace or ''
+ package_version = package_version or ''
+ module_version = module_version or ''
+
+ try:
+ package = self.packages[identifier]
+ if package_version:
+ package_version_key = (identifier, package_version)
+ package = self.package_versions[package_version_key]
+ if not module_version:
+ descriptor = package.descriptors[(name, namespace)]
+ else:
+ descriptor_version_key = (name, namespace, module_version)
+ descriptor = \
+ package.descriptor_versions[descriptor_version_key]
+ return descriptor
+ except KeyError:
+ if identifier not in self.packages:
+ raise MissingPackage(identifier)
+ elif (name, namespace) not in package.descriptors:
+ raise MissingModule(identifier, name, namespace,
+ package_version)
+ elif package_version and \
+ package_version_key not in self.package_versions:
+ raise MissingPackageVersion(identifier, package_version)
+ elif module_version and descriptor_version_key not in \
+ package.descriptor_versions:
+ raise MissingModuleVersion(identifier, name, namespace,
+ module_version, package_version)
+ else:
+ raise ModuleRegistryException(identifier, name, namespace,
+ package_version, module_version)
+
+ def get_similar_descriptor(self, identifier, name, namespace=None,
+ package_version=None, module_version=None):
+ try:
+ return self.get_descriptor_by_name(identifier, name, namespace,
+ package_version, module_version)
+ except MissingPackageVersion:
+ return self.get_similar_descriptor(identifier, name, namespace,
+ None, module_version)
+ except MissingModuleVersion:
+ return self.get_similar_descriptor(identifier, name, namespace,
+ package_version, None)
+# except Exception:
+# raise
+
+ return None
+
+ def get_descriptor(self, module):
+ """get_descriptor(module: class) -> ModuleDescriptor
+
+ Returns the ModuleDescriptor of a given vistrails module (a
+ class that subclasses from modules.vistrails_module.Module)
+
+ """
+ # assert isinstance(module, type)
+ # assert issubclass(module, core.modules.vistrails_module.Module)
+ # assert self._module_key_map.has_key(module)
+ k = self._module_key_map[module]
+ return self.get_descriptor_by_name(*k)
+
+ # get_descriptor_from_module is a synonym for get_descriptor
+ get_descriptor_from_module = get_descriptor
+
+ def module_ports(self, p_type, descriptor):
+ return [(p.name, p)
+ for p in descriptor.port_specs_list
+ if p.type == p_type]
+
+ def module_source_ports_from_descriptor(self, do_sort, descriptor):
+ ports = {}
+ for desc in reversed(self.get_module_hierarchy(descriptor)):
+ ports.update(self.module_ports('output', desc))
+ all_ports = ports.values()
+ if do_sort:
+ all_ports.sort(key=lambda x: (x.sort_key, x.id))
+ return all_ports
+
+ def module_source_ports(self, do_sort, identifier, module_name,
+ namespace=None, version=None):
+ descriptor = self.get_descriptor_by_name(identifier, module_name,
+ namespace, version)
+ return self.module_source_ports_from_descriptor(do_sort, descriptor)
+
+ def module_destination_ports_from_descriptor(self, do_sort, descriptor):
+ ports = {}
+ for desc in reversed(self.get_module_hierarchy(descriptor)):
+ ports.update(self.module_ports('input', desc))
+ all_ports = ports.values()
+ if do_sort:
+ all_ports.sort(key=lambda x: (x.sort_key, x.id))
+ return all_ports
+
+ def module_destination_ports(self, do_sort, identifier, module_name,
+ namespace=None, version=None):
+ descriptor = self.get_descriptor_by_name(identifier, module_name,
+ namespace, version)
+ return self.module_destination_ports_from_descriptor(do_sort,
+ descriptor)
+
+ ##########################################################################
+ # Legacy
+
+ def get_descriptor_from_name_only(self, name):
+ """get_descriptor_from_name_only(name) -> descriptor
+
+ This tries to return a descriptor from a name without a
+ package. The call should only be used for converting from
+ legacy vistrails to new ones. For one, it is slow on misses.
+
+ """
+ matches = []
+ for pkg in self.package_list:
+ matches.extend((pkg, key) for key in pkg.descriptors.iterkeys()
+ if key[0] == name)
+# matches = [[(pkg, desc) for desc in pkg.descriptors.iterkeys()
+# if desc[0] == name] for pkg in self.package_list]
+
+# matches = [x for x in
+# self.descriptors.iterkeys()
+# if x[1] == name]
+ if len(matches) == 0:
+ raise MissingModule("<unknown package>", name, None)
+ if len(matches) > 1:
+ matches_str = [(m[0].identifier, m[1][0], m[1][1],
+ m[0].version) for m in matches]
+ raise AmbiguousResolution(name, None, matches_str)
+ (pkg, key) = matches[0]
+ desc = pkg.descriptors[key]
+ result = self.get_descriptor_by_name(pkg.identifier, desc.name,
+ desc.namespace, pkg.version,
+ desc.version)
+ return result
+
+ ##########################################################################
+
+ def module_signature(self, pipeline, module):
+ """Returns signature of a given core.vistrail.Module in the
+ given core.vistrail.Pipeline, possibly using user-defined
+ hasher.
+ """
+ chm = self._constant_hasher_map
+ descriptor = self.get_descriptor_by_name(module.package,
+ module.name,
+ module.namespace)
+ if not descriptor:
+ return vistrails.core.cache.hasher.Hasher.module_signature(module, chm)
+ c = descriptor.hasher_callable()
+ if c:
+ return c(pipeline, module, chm)
+ else:
+ return vistrails.core.cache.hasher.Hasher.module_signature(module, chm)
+
+ def get_module_color(self, identifier, name, namespace=None):
+ return self.get_descriptor_by_name(identifier, name, namespace).module_color()
+
+ def get_module_fringe(self, identifier, name, namespace=None):
+ return self.get_descriptor_by_name(identifier, name, namespace).module_fringe()
+
+ def update_registry(self, base_descriptor, module, identifier, name,
+ namespace, package_version=None, version=None):
+ if namespace is not None and not namespace.strip():
+ namespace = None
+
+ # add to package list, creating new package if necessary
+ if identifier not in self.packages:
+ if self._current_package.identifier == identifier:
+ package = self._current_package
+ else:
+ package_id = self.idScope.getNewId(Package.vtType)
+ package = Package(id=package_id,
+ codepath="",
+ load_configuration=False,
+ name="",
+ identifier=identifier,
+ version=package_version,
+ )
+ self.add_package(package)
+ else:
+ package = self.package_versions[(identifier, package_version)]
+
+ # create descriptor
+ descriptor_id = self.idScope.getNewId(ModuleDescriptor.vtType)
+ descriptor = ModuleDescriptor(id=descriptor_id,
+ module=module,
+ package=identifier,
+ base_descriptor=base_descriptor,
+ name=name,
+ namespace=namespace,
+ package_version=package_version,
+ version=version
+ )
+ self.add_descriptor(descriptor, package)
+
+ # invalidate the map of converters
+ if issubclass(module,
+ vistrails.core.modules.vistrails_module.Converter):
+ self._conversions = dict()
+ self._converters.add(descriptor)
+
+ if module is not None:
+ self._module_key_map[module] = (identifier, name, namespace,
+ package_version, version)
+ return descriptor
+
+ def auto_add_ports(self, module):
+ """auto_add_module(module or (module, kwargs)): add
+ input/output ports to registry. Don't call this directly - it is
+ meant to be used by the packagemanager, when inspecting the package
+ contents."""
+ for (port_key, adder_f) in [('_input_ports', self.add_input_port),
+ ('_output_ports', self.add_output_port)]:
+ if port_key in module.__dict__:
+ for port_info in module.__dict__[port_key]:
+ added = False
+ if isinstance(port_info, PortSpec):
+ # force port type to match list it occurs in
+ # we just need "input" or "output"
+ port_info.type = port_key[1:-6]
+ descriptor = self.get_descriptor(module)
+ self.add_port_spec(descriptor, port_info)
+ added = True
+ elif len(port_info) >= 2:
+ port_name, port_sig = port_info[:2]
+ if len(port_info) > 2 and \
+ isinstance(port_info[2], dict):
+ kwargs = port_info[2]
+ adder_f(module, port_name, port_sig, **kwargs)
+ added = True
+ else:
+ args = port_info[2:]
+ adder_f(module, port_name, port_sig, *args)
+ added = True
+
+ if not added:
+ raise TypeError("Expected (port_name, port_signature, "
+ "kwargs_dict) or (port_name, "
+ "port_signature, *args)")
+
+ def auto_add_module(self, module):
+ """auto_add_module(module or (module, kwargs)): add module
+ to registry. Don't call this directly - it is
+ meant to be used by the packagemanager, when inspecting the package
+ contents."""
+ if isinstance(module, type):
+ return self.add_module(module)
+ elif (isinstance(module, tuple) and
+ len(module) == 2 and
+ isinstance(module[0], type) and
+ isinstance(module[1], dict)):
+ descriptor = self.add_module(module[0], **module[1])
+ return descriptor
+ else:
+ raise TypeError("Expected module or (module, kwargs)")
+
+ def add_module(self, module, **kwargs):
+ """add_module(module: class, **kwargs) -> Tree
+
+ kwargs:
+ name=None,
+ configureWidgetType=None,
+ signatureCallable=None,
+ moduleColor=None,
+ moduleFringe=None,
+ moduleLeftFringe=None,
+ moduleRightFringe=None,
+ abstract=None,
+ package=None,
+ namespace=None,
+ version=None,
+ package_version=None,
+ hide_namespace=False,
+ hide_descriptor=False,
+ is_root=False,
+ ghost_package=None,
+ ghost_package_version=None,
+ ghost_namespace=None,
+
+ Registers a new module with VisTrails. Receives the class
+ itself and an optional name that will be the name of the
+ module (if not given, uses module.__name__). This module will
+ be available for use in pipelines.
+
+ If moduleColor is not None, then registry stores it so that
+ the gui can use it correctly. moduleColor must be a tuple of
+ three floats between 0 and 1.
+
+ if moduleFringe is not None, then registry stores it so that
+ the gui can use it correctly. moduleFringe must be a list of
+ pairs of floating points. The first point must be (0.0, 0.0),
+ and the last must be (0.0, 1.0). This will be used to generate
+ custom lateral fringes for module boxes. It must be the case
+ that all x values must be positive, and all y values must be
+ between 0.0 and 1.0. Alternatively, the user can set
+ moduleLeftFringe and moduleRightFringe to set two different
+ fringes.
+
+ if package is not None, then we override the current package
+ to be the given one. This is only intended to be used with
+ local per-module module registries (in other words: if you
+ don't know what a local per-module registry is, you can ignore
+ this, and never use the 'package' option).
+
+ If namespace is not None, then we associate a namespace with
+ the module. A namespace is essentially appended to the package
+ identifier so that multiple modules inside the same package
+ can share the same name.
+
+ If signatureCallable is not None, then the cache uses this
+ callable as the function to generate the signature for the
+ module in the cache. The function should take three
+ parameters: the pipeline (of type core.vistrail.Pipeline), the
+ module (of type core.vistrail.Module), and a dict that stores
+ parameter hashers. This dict is supposed to be passed to
+ core/cache/hasher.py:Hasher, in case that needs to be called.
+
+ If constantSignatureCallable is not None, then the cache uses
+ this callable as the funciton to generate the signature for
+ the given constant. If this is not None, then the added
+ module must be a subclass of Constant.
+
+ If hide_namespace is True, the ModulePalette will not display
+ the namespace for that module. If hide_descriptor is True,
+ the ModulePalette will not display that module in its list
+ (similar to abstract).
+
+ If is_root is True, the added module will become the root
+ module. Note that this is only possible for the first module
+ added.
+
+ If ghost_package is not None, then the 'ghost_identifier'
+ 'ghost_identifier' is set on the descriptor, which will cause
+ the module to be displayed under that package in the module
+ palette, rather than the package specified by the
+ 'identifier' attribute of the descriptor.
+
+ If ghost_package_version is not None, then the attribute
+ 'ghost_package_version' is set on the descriptor. Currently
+ this value is unused, but eventually if multiple packages
+ with the same identifier but different package versions
+ are loaded simultaneously, this will allow overriding of
+ the package_version to associate with in the module palette.
+
+ If ghost_namespace is not None, the descriptor will be
+ displayed under the specified namespace instead of the
+ 'namespace' attribute of the descriptor.
+
+ Notice: in the future, more named parameters might be added to
+ this method, and the order is not specified. Always call
+ add_module with named parameters.
+
+ """
+ # Setup named arguments. We don't use named parameters so
+ # that positional parameter calls fail earlier
+ def fetch(name, default):
+ r = kwargs.get(name, default)
+ try:
+ del kwargs[name]
+ except KeyError:
+ pass
+ return r
+ name = fetch('name', module.__name__)
+ configureWidgetType = fetch('configureWidgetType', None)
+ signatureCallable = fetch('signatureCallable', None)
+ constantSignatureCallable = fetch('constantSignatureCallable', None)
+ moduleColor = fetch('moduleColor', None)
+ moduleFringe = fetch('moduleFringe', None)
+ moduleLeftFringe = fetch('moduleLeftFringe', None)
+ moduleRightFringe = fetch('moduleRightFringe', None)
+ is_abstract = fetch('abstract', False)
+ identifier = fetch('package', self._current_package.identifier)
+ namespace = fetch('namespace', None)
+ version = fetch('version', None)
+ package_version = fetch('package_version',
+ self._current_package.version)
+ hide_namespace = fetch('hide_namespace', False)
+ hide_descriptor = fetch('hide_descriptor', False)
+ is_root = fetch('is_root', False)
+ ghost_identifier = fetch('ghost_package', None)
+ ghost_package_version = fetch('ghost_package_version', None)
+ ghost_namespace = fetch('ghost_namespace', None)
+
+ if len(kwargs) > 0:
+ raise VistrailsInternalError(
+ 'Wrong parameters passed to addModule: %s' % kwargs)
+
+ package = self.package_versions[(identifier, package_version)]
+ desc_key = (name, namespace, version)
+ if desc_key in package.descriptor_versions:
+ raise ModuleAlreadyExists(identifier, name)
+
+ # We allow multiple inheritance as long as only one of the superclasses
+ # is a subclass of Module.
+ if is_root:
+ base_descriptor = None
+ else:
+ candidates = self.get_subclass_candidates(module)
+ if len(candidates) != 1:
+ raise InvalidModuleClass(module)
+ baseClass = candidates[0]
+ if not self._module_key_map.has_key(baseClass) :
+ raise MissingBaseClass(baseClass)
+ base_descriptor = self.get_descriptor(baseClass)
+
+ if module in self._module_key_map:
+ # This is really obsolete as having two descriptors
+ # pointing to the same module isn't a big deal except to
+ # get_descriptor which shouldn't be used often
+ if identifier != 'local.abstractions':
+ raise DuplicateModule(self.get_descriptor(module), identifier,
+ name, namespace)
+ elif self.has_descriptor_with_name(identifier, name, namespace,
+ package_version, version):
+ raise DuplicateIdentifier(identifier, name, namespace,
+ package_version, version)
+ descriptor = self.update_registry(base_descriptor, module, identifier,
+ name, namespace, package_version,
+ version)
+ if is_root:
+ self.root_descriptor = descriptor
+
+ descriptor.set_module_abstract(is_abstract)
+ descriptor.set_configuration_widget(configureWidgetType)
+ descriptor.is_hidden = hide_descriptor
+ descriptor.namespace_hidden = hide_namespace
+
+ if signatureCallable:
+ descriptor.set_hasher_callable(signatureCallable)
+
+ if constantSignatureCallable:
+ try:
+ basic_pkg = get_vistrails_basic_pkg_id()
+ c = self.get_descriptor_by_name(basic_pkg, 'Constant').module
+ except ModuleRegistryException:
+ msg = "Constant not found - can't set constantSignatureCallable"
+ raise VistrailsInternalError(msg)
+ if not issubclass(module, c):
+ raise TypeError("To set constantSignatureCallable, module " +
+ "must be a subclass of Constant")
+ # FIXME, currently only allow one per hash, no versioning
+ hash_key = (identifier, name, namespace)
+ self._constant_hasher_map[hash_key] = constantSignatureCallable
+ descriptor.set_module_color(moduleColor)
+
+ if moduleFringe:
+ _check_fringe(moduleFringe)
+ leftFringe = list(reversed([(-x, 1.0-y) for (x, y) in moduleFringe]))
+ descriptor.set_module_fringe(leftFringe, moduleFringe)
+ elif moduleLeftFringe and moduleRightFringe:
+ _check_fringe(moduleLeftFringe)
+ _check_fringe(moduleRightFringe)
+ descriptor.set_module_fringe(moduleLeftFringe, moduleRightFringe)
+
+ if ghost_identifier:
+ descriptor.ghost_identifier = ghost_identifier
+ if ghost_package_version:
+ descriptor.ghost_package_version = ghost_package_version
+ if ghost_namespace:
+ descriptor.ghost_namespace = ghost_namespace
+
+ self.signals.emit_new_module(descriptor)
+ if self.is_abstraction(descriptor):
+ self.signals.emit_new_abstraction(descriptor)
+ return descriptor
+
+ def auto_add_subworkflow(self, subworkflow):
+ if isinstance(subworkflow, str):
+ return self.add_subworkflow(subworkflow)
+ elif (isinstance(subworkflow, tuple) and
+ len(subworkflow) == 2 and
+ isinstance(subworkflow[0], str) and
+ isinstance(subworkflow[1], dict)):
+ descriptor = self.add_subworkflow(subworkflow[0], **subworkflow[1])
+ return descriptor
+ else:
+ raise TypeError("Expected filename or (filename, kwargs)")
+
+ def add_subworkflow(self, vt_fname, **kwargs):
+ from vistrails.core.modules.sub_module import new_abstraction, read_vistrail, \
+ get_next_abs_annotation_key
+
+ # vt_fname is relative to the package path
+ if 'package' in kwargs:
+ identifier = kwargs['package']
+ else:
+ identifier = self._current_package.identifier
+ if 'package_version' in kwargs:
+ package_version = kwargs['package_version']
+ else:
+ package_version = self._current_package.version
+ if 'version' in kwargs:
+ version = kwargs['version']
+ else:
+ version = -1L
+ if 'name' in kwargs:
+ name = kwargs['name']
+ else:
+ name = _parse_abstraction_name(vt_fname)
+ kwargs['name'] = name
+
+ package = self.package_versions[(identifier, package_version)]
+ if not os.path.isabs(vt_fname):
+ vt_fname = os.path.join(package.package_dir, vt_fname)
+ else:
+ debug.warning("Using absolute path for subworkflow: '%s'" % \
+ vt_fname)
+
+ vistrail = read_vistrail(vt_fname)
+ namespace = kwargs.get('namespace', '')
+
+ # create module from workflow
+ module = None
+ is_upgraded_abstraction = False
+ try:
+ module = new_abstraction(name, vistrail, vt_fname, version)
+ except InvalidPipeline, e:
+ # This import MUST be delayed until this point or it will fail
+ import vistrails.core.vistrail.controller
+ from vistrails.core.db.io import save_vistrail_to_xml
+ from vistrails.core.modules.abstraction import identifier as \
+ abstraction_pkg, version as abstraction_ver
+ # Use a "dummy" controller to handle the upgrade
+ controller = vistrails.core.vistrail.controller.VistrailController(vistrail)
+ if version == -1L:
+ version = vistrail.get_latest_version()
+ (new_version, new_pipeline) = \
+ controller.handle_invalid_pipeline(e, long(version), vistrail,
+ False, True)
+ del controller
+ vistrail.set_annotation('__abstraction_descriptor_info__',
+ (identifier, name, namespace,
+ package_version, str(version)))
+ vt_save_dir = tempfile.mkdtemp(prefix='vt_upgrade_abs')
+ vt_fname = os.path.join(vt_save_dir, os.path.basename(vt_fname))
+
+
+ # need to create new namespace for upgraded version
+ new_namespace = str(uuid.uuid1())
+ annotation_key = get_next_abs_annotation_key(vistrail)
+ vistrail.set_annotation(annotation_key, new_namespace)
+
+ # FIXME: Should delete this upgrade file when vistrails is exited
+ save_vistrail_to_xml(vistrail, vt_fname)
+ module = new_abstraction(name, vistrail, vt_fname, new_version,
+ new_pipeline)
+ # need to set identifier to local.abstractions and its version
+ kwargs['package'] = abstraction_pkg
+ kwargs['package_version'] = abstraction_ver
+ # only want to change the namespace on the new version
+ # (the one being added to local.abstractions)
+ kwargs['namespace'] = new_namespace
+
+ # Set ghost attributes so module palette shows it in
+ # package instead of 'My Subworkflows'
+ kwargs['ghost_package'] = identifier
+ kwargs['ghost_package_version'] = package_version
+ kwargs['ghost_namespace'] = namespace
+ is_upgraded_abstraction = True
+
+ module.internal_version = str(module.internal_version)
+ kwargs['version'] = module.internal_version
+ descriptor = None
+ if kwargs:
+ descriptor = self.add_module(module, **kwargs)
+ else:
+ descriptor = self.add_module(module)
+ if is_upgraded_abstraction:
+ descriptor_info = (identifier, name, namespace,
+ package_version, str(version))
+ # print 'adding to upgrades:', descriptor_info
+ # print ' ', descriptor.package, descriptor.name, descriptor.namespace, descriptor.version, descriptor.package_version
+ if identifier != abstraction_pkg:
+ info_exc = ModuleRegistryException(*descriptor_info)
+ debug.critical("Module %s in package %s is out-of-date. "
+ "Please check with the package developer for "
+ "a new version." % (info_exc._module_name,
+ info_exc._package_name))
+ package.add_abs_upgrade(descriptor, name, namespace, str(version))
+ self.auto_add_ports(descriptor.module)
+ return descriptor
+
+ def has_input_port(self, module, portName):
+ descriptor = self.get_descriptor(module)
+ # return descriptor.input_ports.has_key(portName)
+ return (portName, 'input') in descriptor.port_specs
+
+ def has_output_port(self, module, portName):
+ descriptor = self.get_descriptor(module)
+ # return descriptor.output_ports.has_key(portName)
+ return (portName, 'output') in descriptor.port_specs
+
+ def create_port_spec(self, name, type, signature=None, sigstring=None,
+ optional=False, sort_key=-1, labels=None,
+ defaults=None, values=None, entry_types=None,
+ docstring=None, shape=None,
+ min_conns=0, max_conns=-1):
+ if signature is None and sigstring is None:
+ raise VistrailsInternalError("create_port_spec: one of signature "
+ "and sigstring must be specified")
+ spec_id = self.idScope.getNewId(PortSpec.vtType)
+ spec = PortSpec(id=spec_id,
+ name=name,
+ type=type,
+ signature=signature,
+ sigstring=sigstring,
+ optional=optional,
+ sort_key=sort_key,
+ labels=labels,
+ defaults=defaults,
+ values=values,
+ entry_types=entry_types,
+ docstring=docstring,
+ shape=shape,
+ min_conns=min_conns,
+ max_conns=max_conns)
+
+ # don't know how many port spec items are created until after...
+ for psi in spec.port_spec_items:
+ psi.id = self.idScope.getNewId(PortSpecItem.vtType)
+ return spec
+
+ def add_port_spec(self, descriptor, spec):
+ # check if the spec is valid
+ try:
+ spec.descriptors()
+ except ModuleRegistryException, e:
+ raise InvalidPortSpec(descriptor, spec.name, spec.type, e)
+
+ descriptor.add_port_spec(spec)
+ if spec.type == 'input':
+ self.signals.emit_new_input_port(descriptor.identifier,
+ descriptor.name, spec.name, spec)
+ elif spec.type == 'output':
+ self.signals.emit_new_output_port(descriptor.identifier,
+ descriptor.name, spec.name, spec)
+
+ def get_port_spec_from_descriptor(self, desc, port_name, port_type):
+ for d in self.get_module_hierarchy(desc):
+ if d.has_port_spec(port_name, port_type):
+ return d.get_port_spec(port_name, port_type)
+
+ # if we don't find it, raise MissingPort exception
+ raise MissingPort(desc, port_name, port_type)
+
+ def get_port_spec(self, package, module_name, namespace,
+ port_name, port_type):
+ desc = self.get_descriptor_by_name(package, module_name, namespace)
+ return self.get_port_spec_from_descriptor(desc, port_name,
+ port_type)
+
+ def has_port_spec_from_descriptor(self, desc, port_name, port_type):
+ for d in self.get_module_hierarchy(desc):
+ if d.has_port_spec(port_name, port_type):
+ return True
+ return False
+
+ def has_port_spec(self, package, module_name, namespace,
+ port_name, port_type):
+ desc = self.get_descriptor_by_name(package, module_name, namespace)
+ return self.has_port_spec_from_descriptor(desc, port_name,
+ port_type)
+
+ def add_port(self, descriptor, port_name, port_type, port_sig=None,
+ port_sigstring=None, optional=False, sort_key=-1,
+ labels=None, defaults=None, values=None, entry_types=None,
+ docstring=None, shape=None, min_conns=0, max_conns=-1):
+ spec = self.create_port_spec(port_name, port_type, port_sig,
+ port_sigstring, optional, sort_key,
+ labels, defaults, values, entry_types,
+ docstring, shape,
+ min_conns, max_conns)
+
+ self.add_port_spec(descriptor, spec)
+
+ def add_input_port(self, module, portName, portSignature, optional=False,
+ sort_key=-1, labels=None, defaults=None, values=None,
+ entry_types=None, docstring=None, shape=None,
+ min_conns=0, max_conns=-1):
+ """add_input_port(module: class,
+ portName: string,
+ portSignature: string,
+ optional: bool,
+ sort_key: int,
+ labels: tuple(string),
+ defaults: tuple(string),
+ values: list(list(string)),
+ entry_types: list(string),
+ docstring: string,
+ shape: tuple,
+ min_conns: int,
+ max_conns: int) -> None
+
+ Registers a new input port with VisTrails. Receives the module
+ that will now have a certain port, a string representing the
+ name, and a signature of the port, described in
+ doc/module_registry.txt. Optionally, it receives whether the
+ input port is optional."""
+ descriptor = self.get_descriptor(module)
+ if isinstance(portSignature, basestring):
+ self.add_port(descriptor, portName, 'input', None, portSignature,
+ optional, sort_key, labels, defaults, values,
+ entry_types, docstring, shape, min_conns, max_conns)
+ else:
+ self.add_port(descriptor, portName, 'input', portSignature, None,
+ optional, sort_key, labels, defaults, values,
+ entry_types, docstring, shape, min_conns, max_conns)
+
+
+ def add_output_port(self, module, portName, portSignature, optional=False,
+ sort_key=-1, docstring=None, shape=None,
+ min_conns=0, max_conns=-1):
+ """add_output_port(module: class,
+ portName: string,
+ portSignature: string,
+ optional: bool,
+ sort_key: int,
+ docstring: string,
+ shape: tuple,
+ min_conns: int,
+ max_conns: int) -> None
+
+ Registers a new output port with VisTrails. Receives the
+ module that will now have a certain port, a string
+ representing the name, and a signature of the port, described
+ in doc/module_registry.txt. Optionally, it receives whether
+ the output port is optional."""
+ descriptor = self.get_descriptor(module)
+ if isinstance(portSignature, basestring):
+ self.add_port(descriptor, portName, 'output', None, portSignature,
+ optional, sort_key, None, None, None, None,
+ docstring, shape, min_conns, max_conns)
+ else:
+ self.add_port(descriptor, portName, 'output', portSignature, None,
+ optional, sort_key, None, None, None, None,
+ docstring, shape, min_conns, max_conns)
+
+ def create_package(self, codepath, load_configuration=True):
+ package_id = self.idScope.getNewId(Package.vtType)
+ package = Package(id=package_id,
+ codepath=codepath,
+ load_configuration=load_configuration)
+ return package
+
+ def initialize_package(self, package):
+ if package.initialized():
+ return
+ debug.splashMessage("Initializing " + package.codepath + "...")
+ debug.log("Initializing " + package.codepath)
+ if (package.identifier, package.version) not in self.package_versions:
+ self.add_package(package)
+ self.set_current_package(package)
+ try:
+ package.initialize()
+ # Perform auto-initialization
+ if hasattr(package.module, '_modules'):
+ modules = package.module._modules
+ if isinstance(modules, dict):
+ module_list = []
+ for namespace, m_list in modules.iteritems():
+ for module in m_list:
+ m_dict = {'namespace': namespace}
+ if isinstance(module, tuple):
+ m_dict.update(module[1])
+ module_list.append((module[0], m_dict))
+ else:
+ module_list.append((module, m_dict))
+ else:
+ module_list = modules
+ modules = _toposort_modules(module_list)
+ # We add all modules before adding ports because
+ # modules inside package might use each other as ports
+ for module in modules:
+ self.auto_add_module(module)
+
+ # allow all modules to auto_add_ports!
+ added_descriptors = set()
+ for descriptor in package.descriptor_list:
+ if hasattr(descriptor, 'module'):
+ self.auto_add_ports(descriptor.module)
+ added_descriptors.add(descriptor)
+ # Perform auto-initialization of abstractions
+ if hasattr(package.module, '_subworkflows'):
+ subworkflows = \
+ _toposort_abstractions(package,
+ package.module._subworkflows)
+ for subworkflow in subworkflows:
+ self.auto_add_subworkflow(subworkflow)
+ for descriptor in package.descriptor_list:
+ if descriptor not in added_descriptors:
+ if hasattr(descriptor, 'module'):
+ self.auto_add_ports(descriptor.module)
+ added_descriptors.add(descriptor)
+ except Exception, e:
+ raise package.InitializationFailed(package,
+ [traceback.format_exc()])
+
+ # The package might have decided to rename itself, let's store that
+ self.set_current_package(None)
+ debug.splashMessage("Initializing " + package.codepath + '... done.')
+ package._initialized = True
+
+ def delete_module(self, identifier, module_name, namespace=None):
+ """deleteModule(module_name): Removes a module from the registry."""
+ descriptor = self.get_descriptor_by_name(identifier, module_name,
+ namespace)
+ assert len(descriptor.children) == 0
+
+ # invalidate the map of converters
+ converter_desc = self.get_descriptor(
+ vistrails.core.modules.vistrails_module.Converter)
+ if self.is_descriptor_subclass(descriptor, converter_desc):
+ self._conversions = dict()
+ self._converters.remove(descriptor)
+
+ self.signals.emit_deleted_module(descriptor)
+ if self.is_abstraction(descriptor):
+ self.signals.emit_deleted_abstraction(descriptor)
+ package = self.packages[descriptor.identifier]
+ self.delete_descriptor(descriptor, package)
+ if descriptor.module is not None:
+ del self._module_key_map[descriptor.module]
+
+ def remove_package(self, package):
+ """remove_package(package) -> None:
+ Removes an entire package from the registry.
+
+ """
+ # graph is the class hierarchy graph for this subset
+ graph = Graph()
+ if package.identifier not in self.packages:
+ raise MissingPackage(package.identifier)
+ package = self.packages[package.identifier]
+ for descriptor in package.descriptor_list:
+ graph.add_vertex(descriptor.sigstring)
+ for descriptor in package.descriptor_list:
+ base_id = descriptor.base_descriptor_id
+ if base_id in package.descriptors_by_id:
+ base_descriptor = \
+ package.descriptors_by_id[descriptor.base_descriptor_id]
+ graph.add_edge(descriptor.sigstring, base_descriptor.sigstring)
+
+ top_sort = graph.vertices_topological_sort()
+ # set up fast removal of model
+ for sigstring in top_sort:
+ self.delete_module(
+ *vistrails.core.modules.utils.parse_descriptor_string(sigstring))
+
+ # Remove upgraded package subworkflows from registry
+ for key, version_dict in package._abs_pkg_upgrades.iteritems():
+ for version, descriptor in version_dict.iteritems():
+ self.delete_module(descriptor.identifier, descriptor.name,
+ descriptor.namespace)
+ package._abs_pkg_upgrades.clear()
+
+ package.unload()
+ self.delete_package(package)
+ self.signals.emit_deleted_package(package)
+
+ def delete_input_port(self, descriptor, port_name):
+ """ Just remove a name input port with all of its specs """
+ descriptor.delete_input_port(port_name)
+
+ def delete_output_port(self, descriptor, port_name):
+ """ Just remove a name output port with all of its specs """
+ descriptor.delete_output_port(port_name)
+
+ def source_ports_from_descriptor(self, descriptor, sorted=True):
+ ports = [p[1] for p in self.module_ports('output', descriptor)]
+ if sorted:
+ ports.sort(key=lambda x: x.name)
+ return ports
+
+ def destination_ports_from_descriptor(self, descriptor, sorted=True):
+ ports = [p[1] for p in self.module_ports('input', descriptor)]
+ if sorted:
+ ports.sort(key=lambda x: x.name)
+ return ports
+
+ def all_source_ports(self, descriptor, sorted=True):
+ """Returns source ports for all hierarchy leading to given module"""
+ getter = self.source_ports_from_descriptor
+ return [(desc.name, getter(desc, sorted))
+ for desc in self.get_module_hierarchy(descriptor)]
+
+ def all_destination_ports(self, descriptor, sorted=True):
+ """Returns destination ports for all hierarchy leading to
+ given module"""
+ getter = self.destination_ports_from_descriptor
+ return [(desc.name, getter(desc, sorted))
+ for desc in self.get_module_hierarchy(descriptor)]
+
+ def get_port_from_all_destinations(self, descriptor, name):
+ """Searches for port identified by name in the destination ports
+ for all hierarchy leading to given module """
+ all_ports = self.all_destination_ports(descriptor)
+ for (klass, port_list) in all_ports:
+ for port in port_list:
+ if port.name == name:
+ return port
+ else:
+ return None
+
+ def is_method(self, port_spec):
+ basic_pkg = get_vistrails_basic_pkg_id()
+ constant_desc = \
+ self.get_descriptor_by_name(basic_pkg, 'Constant')
+ return port_spec.type == 'input' and \
+ all(self.is_descriptor_subclass(d, constant_desc)
+ for d in port_spec.descriptors())
+ is_constant = is_method
+
+ def method_ports(self, module_descriptor):
+ """method_ports(module_descriptor: ModuleDescriptor)
+ -> [PortSpec]}
+
+ Returns a list of port specs that are methods
+ (spec contains only subclasses of Constant).
+
+ """
+ getter = self.module_destination_ports_from_descriptor
+ return [spec for spec in sorted(getter(False, module_descriptor),
+ key=lambda x: x.name)
+ if self.is_method(spec)]
+
+ def port_and_port_spec_match(self, port, port_spec):
+ """port_and_port_spec_match(port: Port | PortSpec,
+ port_spec: PortSpec
+ ) -> bool
+ Checks if port is similar to port_spec or not. These ports must
+ have the same name and type"""
+ if port.type in PortSpec.port_type_map:
+ port_type = port.type
+ elif port.type in PortSpec.port_type_map.inverse:
+ port_type = PortSpec.port_type_map.inverse[port.type]
+ else:
+ raise TypeError('Port type "%s" invalid' % str(port.type))
+ if port_type != port_spec.type:
+ return False
+ if port.name != port_spec.name:
+ return False
+ if port.sigstring == port_spec.sigstring:
+ return True
+ return self.are_specs_matched(port, port_spec)
+
+ def ports_can_connect(self, sourceModulePort, destinationModulePort,
+ allow_conversion=False, out_converters=None):
+ """ports_can_connect(sourceModulePort,destinationModulePort) ->
+ Boolean returns true if there could exist a connection
+ connecting these two ports."""
+ if sourceModulePort.type == destinationModulePort.type:
+ return False
+ return self.are_specs_matched(sourceModulePort, destinationModulePort,
+ allow_conversion=allow_conversion,
+ out_converters=out_converters)
+
+ def is_port_sub_type(self, sub, super):
+ """ is_port_sub_type(sub: Port, super: Port) -> bool
+ Check if port super and sub are similar or not. These ports
+ must have exact name as well as position
+
+ """
+ if sub.type != super.type:
+ return False
+ if sub.name != super.name:
+ return False
+ return self.are_specs_matched(sub, super)
+
+ def get_converters(self, sub_descs, super_descs):
+ key = (tuple(sub_descs), tuple(super_descs))
+
+ # Get the result from the cache
+ try:
+ return self._conversions[key]
+ except KeyError:
+ pass
+
+ converters = []
+
+ # Compute the result
+ for converter in self._converters:
+ if converter.module is (
+ vistrails.core.modules.vistrails_module.Converter):
+ continue
+
+ if converter.module.can_convert(sub_descs, super_descs):
+ converters.append(converter)
+
+ # Store in the cache that there was no result
+ self._conversions[key] = converters
+ return converters
+
+ def are_specs_matched(self, sub, super, allow_conversion=False,
+ out_converters=None):
+ """ are_specs_matched(sub: Port, super: Port) -> bool
+ Check if specs of sub and super port are matched or not
+
+ """
+ basic_pkg = get_vistrails_basic_pkg_id()
+ variant_desc = self.get_descriptor_by_name(basic_pkg, 'Variant')
+ # sometimes sub is coming None
+ # I don't know if this is expected, so I will put a test here
+ sub_descs = []
+ if sub:
+ sub_descs = sub.descriptors()
+ if sub_descs is None:
+ return False
+ elif sub_descs == [variant_desc]:
+ return True
+ super_descs = []
+ if super:
+ super_descs = super.descriptors()
+ if super_descs is None:
+ return False
+ elif super_descs == [variant_desc]:
+ return True
+
+ def check_types(sub_descs, super_descs):
+ for (sub_desc, super_desc) in izip(sub_descs, super_descs):
+ if (sub_desc == variant_desc or super_desc == variant_desc):
+ continue
+ if not self.is_descriptor_subclass(sub_desc, super_desc):
+ return False
+ return True
+
+ if (len(sub_descs) == len(super_descs) and
+ check_types(sub_descs, super_descs)):
+ return True
+
+ if allow_conversion:
+ converters = self.get_converters(sub_descs, super_descs)
+ if converters:
+ if out_converters is not None:
+ out_converters.extend(converters)
+ return True
+
+ return False
+
+ def get_module_hierarchy(self, descriptor):
+ """get_module_hierarchy(descriptor) -> [klass].
+ Returns the module hierarchy all the way to Module, excluding
+ any mixins."""
+ if descriptor.module is None:
+ descriptors = [descriptor]
+ base_id = descriptor.base_descriptor_id
+ while base_id >= 0:
+ descriptor = self.descriptors_by_id[base_id]
+ descriptors.append(descriptor)
+ base_id = descriptor.base_descriptor_id
+ return descriptors
+ return [self.get_descriptor(klass)
+ for klass in descriptor.module.mro()
+ if issubclass(klass, vistrails.core.modules.vistrails_module.Module)]
+
+ def get_input_port_spec(self, module, portName):
+ """ get_input_port_spec(module: Module, portName: str) ->
+ spec-tuple Return the output port of a module given the module
+ and port name.
+
+ FIXME: This should be renamed.
+
+ """
+ descriptor = module.module_descriptor
+ if module.has_port_spec(portName, 'input'):
+ return module.get_port_spec(portName, 'input')
+ return None
+
+ def get_output_port_spec(self, module, portName):
+ """ get_output_port_spec(module: Module, portName: str) -> spec-tuple
+ Return the output port of a module given the module
+ and port name.
+
+ FIXME: This should be renamed.
+
+ """
+ descriptor = module.module_descriptor
+ if module.has_port_spec(portName, 'output'):
+ return module.get_port_spec(portName, 'output')
+ return None
+
+ @staticmethod
+ def get_subclass_candidates(module):
+ """get_subclass_candidates(module) -> [class]
+
+ Tries to eliminate irrelevant mixins for the hierarchy. Returns all
+ base classes that subclass from Module."""
+ return [klass
+ for klass in module.__bases__
+ if issubclass(klass, vistrails.core.modules.vistrails_module.Module)]
+
+ def set_current_package(self, package):
+ """ set_current_package(package: Package) -> None
+ Set the current package for all addModule operations to
+ name. This means that all modules added after this call will
+ be assigned to the specified package. Set package to None to
+ indicate that VisTrails default package should be used instead.
+
+ Do not call this directly. The package manager will call this
+ with the correct value prior to calling 'initialize' on the
+ package.
+
+ """
+ if package is None:
+ package = self._default_package
+ self._current_package = package
+
+ def get_module_package(self, identifier, name, namespace):
+ """ get_module_package(identifier, moduleName: str) -> str
+ Return the name of the package where the module is registered.
+
+ """
+ descriptor = self.get_descriptor_by_name(identifier, name, namespace)
+ return descriptor.module_package()
+
+ def get_configuration_widget(self, identifier, name, namespace):
+ descriptor = self.get_descriptor_by_name(identifier, name, namespace)
+ klass = descriptor.configuration_widget()
+ if isinstance(klass, tuple):
+ (path, klass_name) = klass
+ module = __import__(path, globals(), locals(), [klass_name])
+ klass = getattr(module, klass_name)
+ return klass
+
+ def is_descriptor_subclass(self, sub, super):
+ """is_descriptor_subclass(sub : ModuleDescriptor,
+ super: ModuleDescriptor) -> bool
+
+ """
+ # use issubclass for speed if we've loaded the modules
+ if sub.module is not None and super.module is not None:
+ return issubclass(sub.module, super.module)
+
+ # otherwise, use descriptors themselves
+ if sub == super:
+ return True
+ while sub != self.root_descriptor:
+ sub = sub.base_descriptor
+ if sub == super:
+ return True
+
+ return False
+
+ def find_descriptor_subclass(self, d1, d2):
+ if self.is_descriptor_subclass(d1, d2):
+ return d1
+ elif self.is_descriptor_subclass(d2, d1):
+ return d2
+ return None
+
+ def find_descriptor_superclass(self, d1, d2):
+ """find_descriptor_superclass(d1: ModuleDescriptor,
+ d2: ModuleDescriptor) -> ModuleDescriptor
+ Finds the lowest common superclass descriptor for d1 and d2
+
+ """
+ if self.is_descriptor_subclass(d1, d2):
+ return d2
+ elif self.is_descriptor_subclass(d2, d1):
+ return d1
+
+ d1_list = [d1]
+ while d1 != self.root_descriptor:
+ d1 = d1.base_descriptor
+ d1_list.append(d1)
+ d1_idx = -1
+ while self.is_descriptor_subclass(d2, d1_list[d1_idx]):
+ d1_idx -= 1
+ if d1_idx == -1:
+ return None
+ return d1_list[d1_idx+1]
+
+ def is_abstraction(self, descriptor):
+ basic_pkg = get_vistrails_basic_pkg_id()
+ try:
+ abstraction_desc = self.get_descriptor_by_name(basic_pkg,
+ 'SubWorkflow')
+ except MissingModule:
+ # No abstractions can be loaded before the basic
+ # SubWorkflow descriptor is initialized
+ return False
+ return abstraction_desc != descriptor and \
+ self.is_descriptor_subclass(descriptor, abstraction_desc)
+
+ def show_module(self, descriptor):
+ self.signals.emit_show_module(descriptor)
+ def hide_module(self, descriptor):
+ self.signals.emit_hide_module(descriptor)
+ def update_module(self, old_descriptor, new_descriptor):
+ self.signals.emit_module_updated(old_descriptor, new_descriptor)
+
+ def expand_port_spec_string(self, p_string, cur_package=None,
+ old_style=False):
+ return vistrails.core.modules.utils.expand_port_spec_string(p_string, cur_package,
+ old_style)
+
+###############################################################################
+
+# registry = ModuleRegistry()
+# add_module = registry.add_module
+# add_input_port = registry.add_input_port
+# has_input_port = registry.has_input_port
+# add_output_port = registry.add_output_port
+# set_current_package = registry.set_current_package
+# get_descriptor_by_name = registry.get_descriptor_by_name
+# get_module_by_name = registry.get_module_by_name
+# get_descriptor = registry.get_descriptor
+
+def get_module_registry():
+ global registry
+ if not registry:
+ raise VistrailsInternalError("Registry not constructed yet.")
+ return registry
+
+def module_registry_loaded():
+ global registry
+ return registry is not None
+
+##############################################################################
+
+
+class TestModuleRegistry(unittest.TestCase):
+
+ def test_portspec_construction(self):
+ from vistrails.core.modules.basic_modules import Float, Integer
+ t1 = PortSpec(signature=Float)
+ t2 = PortSpec(signature=[Float])
+ self.assertEquals(t1, t2)
+
+ t1 = PortSpec(signature=[Float, Integer])
+ t2 = PortSpec(signature=[Integer, Float])
+ self.assertNotEquals(t1, t2)
diff --git a/vistrails/core/modules/module_utils.py b/vistrails/core/modules/module_utils.py
new file mode 100644
index 0000000..893a0da
--- /dev/null
+++ b/vistrails/core/modules/module_utils.py
@@ -0,0 +1,167 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# Utilities for user-defined Modules
+import os
+import tempfile
+from vistrails.core.modules import basic_modules
+from vistrails.core.system import link_or_copy
+from vistrails.core.utils import VistrailsInternalError
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core import debug
+
+import unittest
+
+################################################################################
+
+class FilePool(object):
+
+ """FilePool provides a convenient interface for Module developers to
+use temporary files. """
+
+ def __init__(self):
+ d = {'prefix':'vt_tmp'}
+ if get_vistrails_configuration().check('temporaryDirectory'):
+ dir = get_vistrails_configuration().temporaryDirectory
+ if os.path.exists(dir):
+ d['dir'] = dir
+ else:
+ debug.critical("Temporary directory does not exist: %s" % dir)
+
+ self.directory = tempfile.mkdtemp(**d)
+ self.files = {}
+
+ def cleanup(self):
+ """cleanup() -> None
+
+Cleans up the file pool, by removing all temporary files
+and the directory they existed in. Module developers should never
+call this directly."""
+ if not os.path.isdir(self.directory):
+ # cleanup has already happened
+ return
+ try:
+ for root, dirs, files in os.walk(self.directory, topdown=False):
+ for name in files:
+ os.remove(os.path.join(root, name))
+ for name in dirs:
+ os.rmdir(os.path.join(root, name))
+ os.rmdir(self.directory)
+ except OSError, e:
+ raise VistrailsInternalError("Can't remove %s: %s" %
+ (self.directory,
+ str(e)))
+
+ def create_file(self, suffix = '', prefix = 'vt_tmp'):
+ """create_file(suffix='', prefix='vt_tmp') -> File.
+
+Returns a File module representing a writable file for use in modules. To
+avoid race conditions, this file will already exist in the file system."""
+ (fd, name) = tempfile.mkstemp(suffix=suffix,
+ prefix=prefix,
+ dir=self.directory)
+ os.close(fd)
+ result = basic_modules.File()
+ result.name = name
+ result.upToDate = True
+ self.files[name] = result
+ return result
+
+ def create_directory(self, suffix = '', prefix = 'vt_tmp'):
+ """create_directory(suffix='', prefix='vt_tmp') -> Directory.
+
+Returns a Directory module representing a writable directory for use in modules. To
+avoid race conditions, this directory will already exist in the file system."""
+ name = tempfile.mkdtemp(suffix=suffix,
+ prefix=prefix,
+ dir=self.directory)
+ result = basic_modules.Directory()
+ result.name = name
+ result.upToDate = True
+ self.files[name] = result
+ return result
+
+ def guess_suffix(self, file_name):
+ """guess_suffix(file_name) -> String.
+ Tries to guess the suffix of the given filename.
+
+ """
+ return os.path.splitext(file_name)[1]
+
+ def make_local_copy(self, src):
+ """make_local_copy(src) -> File
+
+Returns a file in the filePool that's either a link or a copy of the
+given file path. This ensures the file's longevity when
+necessary. Since it might use a hardlink for speed, modules should
+only use this method if the file is not going to be changed in the
+future."""
+ (fd, name) = tempfile.mkstemp(suffix=self.guess_suffix(src),
+ dir=self.directory)
+ os.close(fd)
+ # FIXME: Watch out for race conditions
+ os.unlink(name)
+ link_or_copy(src, name)
+ result = basic_modules.File()
+ result.name = name
+ result.upToDate = True
+ self.files[name] = result
+ return result
+
+################################################################################
+
+
+class TestFilePool(unittest.TestCase):
+
+ def test_guess_suffix(self):
+ """Tests FilePool.guess_suffix"""
+ x = FilePool()
+ self.assertEquals(x.guess_suffix('asd.foo'), '.foo')
+ self.assertEquals(x.guess_suffix('bar'), '')
+ self.assertEquals(x.guess_suffix('./lalala'), '')
+ self.assertEquals(x.guess_suffix('./lalala.bar'), '.bar')
+ self.assertEquals(x.guess_suffix('user.foo/lalala'), '')
+ x.cleanup()
+ del x
+
+ def test_double_cleanup(self):
+ x = FilePool()
+ x.cleanup()
+ try:
+ x.cleanup()
+ except VistrailsInternalError:
+ self.fail("cleanup failed")
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/modules/package.py b/vistrails/core/modules/package.py
new file mode 100644
index 0000000..0bb64f3
--- /dev/null
+++ b/vistrails/core/modules/package.py
@@ -0,0 +1,765 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+import inspect
+from itertools import chain
+import os
+import re
+import sys
+import traceback
+import xml.dom
+
+from vistrails.core import debug
+from vistrails.core import get_vistrails_application
+from vistrails.core.modules.module_descriptor import ModuleDescriptor
+from vistrails.core.utils import versions_increasing, VistrailsInternalError
+from vistrails.core.utils.uxml import (named_elements, enter_named_element)
+
+from vistrails.db.domain import DBPackage
+
+##############################################################################
+
+class Package(DBPackage):
+ Base, User, Other = 0, 1, 2
+
+ FIX_PACKAGE_NAMES = ["api", "core", "db", "gui", "packages", "tests"]
+
+ class InitializationFailed(Exception):
+ def __init__(self, package, tracebacks):
+ self.package = package
+ self.tracebacks = tracebacks
+ def __str__(self):
+ try:
+ name = self.package.name
+ if name is None:
+ name = 'codepath <%s>' % self.package.codepath
+ except AttributeError:
+ name = 'codepath <%s>' % self.package.codepath
+ return ("Package '%s' failed to initialize because of the "
+ "following exceptions:\n%s" % \
+ (name, "\n".join(self.tracebacks)))
+
+ class LoadFailed(Exception):
+ def __init__(self, package, exception, traceback):
+ self.package = package
+ self.exception = exception
+ self.traceback = traceback
+ def __str__(self):
+ return ("Package '%s' failed to load, raising '%s: %s'. Traceback:\n%s" %
+ (self.package.codepath,
+ self.exception.__class__.__name__,
+ self.exception,
+ self.traceback))
+
+ class MissingDependency(Exception):
+ def __init__(self, package, dependencies):
+ self.package = package
+ self.dependencies = dependencies
+ def __str__(self):
+ def dep_string(dep):
+ retval = dep[0]
+ if dep[1] is not None:
+ retval += ': requires version >= %s' % dep[1]
+ if dep[2] is not None:
+ retval += ' and <= %s' % dep[2]
+ elif dep[2] is not None:
+ retval += ': requires version <= %s' % dep[2]
+ return retval
+
+ return ("Package '%s' has unmet dependencies:\n %s" %
+ (self.package.name,
+ '\n '.join([dep_string(d) for d in self.dependencies])))
+
+ def __init__(self, *args, **kwargs):
+ if 'load_configuration' in kwargs:
+ arg = kwargs['load_configuration']
+ if not isinstance(arg, (int, long)):
+ if isinstance(arg, bool):
+ if arg:
+ kwargs['load_configuration'] = 1
+ else:
+ kwargs['load_configuration'] = 0
+ # kwargs['load_configuration'] = 1 if arg else 0
+ else:
+ raise VistrailsInternalError("Cannot convert "
+ "load_configuration")
+
+ DBPackage.__init__(self, *args, **kwargs)
+ self.set_defaults()
+ self._force_no_unload = None
+ self._force_unload = None
+ self._force_sys_unload = None
+ self._imports_are_good = True
+
+ def __copy__(self):
+ Package.do_copy(self)
+
+ def set_defaults(self, other=None):
+ self.setup_indices()
+ if other is None:
+ self._module = None
+ self._init_module = None
+ self._loaded = False
+ self._initialized = False
+ self._abs_pkg_upgrades = {}
+ self.package_dir = None
+ self.prefix = None
+ self.py_dependencies = set()
+ self.old_identifiers = []
+ else:
+ self._module = other._module
+ self._init_module = other._init_module
+ self._loaded = other._loaded
+ self._initialized = other._initialized
+ self._abs_pkg_upgrades = copy.copy(other._abs_pkg_upgrades)
+ self.package_dir = other.package_dir
+ self.prefix = other.prefix
+ self.py_dependencies = copy.copy(other.py_dependencies)
+ self.old_identifiers = [i for i in self.old_identifiers]
+ # FIXME decide whether we want None or ''
+ if self.version is None:
+ self.version = ''
+
+ def setup_indices(self):
+ self.descriptor_versions = self.db_module_descriptors_name_index
+ self.descriptors_by_id = self.db_module_descriptors_id_index
+ self.descriptors = {}
+ for key, desc in self.descriptor_versions.iteritems():
+ key = key[:2]
+ if key in self.descriptors:
+ old_desc = self.descriptors[key]
+ if versions_increasing(old_desc.version, desc.version):
+ self.descriptors[key] = desc
+ else:
+ self.descriptors[key] = desc
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPackage.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Package
+ cp.set_defaults(self)
+
+ @staticmethod
+ def convert(_package):
+ if _package.__class__ == Package:
+ return
+ _package.__class__ = Package
+
+ for descriptor in _package.db_module_descriptors:
+ ModuleDescriptor.convert(descriptor)
+ _package.set_defaults()
+
+ ##########################################################################
+ # Properties
+
+ id = DBPackage.db_id
+ name = DBPackage.db_name
+ identifier = DBPackage.db_identifier
+ description = DBPackage.db_description
+ version = DBPackage.db_version
+ codepath = DBPackage.db_codepath
+ load_configuration = DBPackage.db_load_configuration
+ descriptor_list = DBPackage.db_module_descriptors
+
+ def add_descriptor(self, desc):
+ self.db_add_module_descriptor(desc)
+ key = (desc.name, desc.namespace)
+ if key in self.descriptors:
+ old_desc = self.descriptors[key]
+ if versions_increasing(old_desc.version, desc.version):
+ self.descriptors[key] = desc
+ else:
+ self.descriptors[key] = desc
+
+ def delete_descriptor(self, desc):
+ self.db_delete_module_descriptor(desc)
+ # FIXME hard to incremental updates here so we'll just recreate
+ # this can be slow
+ self.setup_indices()
+
+ def _get_module(self):
+ return self._module
+ module = property(_get_module)
+
+ def _get_init_module(self):
+ return self._init_module
+ init_module = property(_get_init_module)
+
+ def _get_configuration(self):
+ if hasattr(self._module, 'configuration'):
+ return self._module.configuration
+ else:
+ return None
+ def _set_configuration(self, configuration):
+ if hasattr(self._module, 'configuration'):
+ self._module.configuration = configuration
+ else:
+ raise AttributeError("Can't set configuration on a module "
+ "without one")
+ configuration = property(_get_configuration, _set_configuration)
+
+ ##########################################################################
+ # Operators
+
+ def __hash__(self):
+ if self.identifier and self.version:
+ return (type(self), self.identifier, self.version).__hash__()
+ return (type(self), self.codepath).__hash__()
+
+ def __eq__(self, other):
+ return (type(self) == type(other) and
+ self.identifier == other.identifier and
+ self.version == other.version)
+
+ def __str__(self):
+ return ("Package(id=%s, identifier=%s, version=%s, name=%s, "
+ "codepath=%s") % (self.id, self.identifier,
+ self.version, self.name,
+ self.codepath)
+
+ ##########################################################################
+ # Methods
+
+ _python_lib_regex = re.compile(r'python[0-9.]+[a-z]?/lib/',
+ re.IGNORECASE)
+ _lib_python_regex = re.compile(r'lib/python[0-9.]+[a-z]?/',
+ re.IGNORECASE)
+ def import_override(self, orig_import,
+ name, globals, locals, fromlist, level,
+ package_importing_directly):
+ def in_package_list(pkg_name, pkg_list):
+ if pkg_list is None:
+ return False
+ for pkg in pkg_list:
+ if pkg_name == pkg or pkg_name.startswith(pkg + '.'):
+ return True
+ return False
+
+ def is_sys_pkg(pkg):
+ try:
+ pkg_fname = pkg.__file__
+ except AttributeError:
+ return True
+ if "site-packages" in pkg_fname:
+ return True
+ if os.sep != '/':
+ pkg_fname = pkg_fname.replace(os.sep, '/')
+ return (self._python_lib_regex.search(pkg_fname) or
+ self._lib_python_regex.search(pkg_fname))
+
+ sys_modules = sys.modules.keys()
+
+ def checked_add_package(qual_name, pkg):
+ if qual_name in sys_modules:
+ return
+ if (not in_package_list(qual_name, self._force_no_unload) and
+ (self._force_sys_unload or not is_sys_pkg(pkg)
+ or in_package_list(qual_name, self._force_unload)) and
+ not qual_name.endswith('_rc')):
+ self.py_dependencies.add(qual_name)
+
+ fixed = False
+ try:
+ res = orig_import(name, globals, locals, fromlist, level)
+ except ImportError:
+ if not package_importing_directly:
+ # We only fix stuff imported directly from a package, i.e. we
+ # only tolerate misspellings in the package's code
+ raise
+
+ # backward compatibility for packages that import without
+ # "vistrails." prefix
+ for pkg in Package.FIX_PACKAGE_NAMES:
+ if name == pkg or name.startswith(pkg + '.'):
+ if self._imports_are_good: # only warn first time
+ self._imports_are_good = False
+ debug.warning(
+ "In package '%s', Please use the 'vistrails.' "
+ "prefix when importing vistrails packages." %
+ (self.identifier or self.codepath))
+ fixed = pkg
+ name = "vistrails." + name
+ break
+ if fixed:
+ res = orig_import(name, globals, locals, fromlist, level)
+ else:
+ raise
+ mod = res
+
+ if not fromlist:
+ checked_add_package(mod.__name__, mod)
+ for comp in name.split('.')[1:]:
+ try:
+ mod = getattr(mod, comp)
+ checked_add_package(mod.__name__, mod)
+ except AttributeError:
+ break
+ else:
+ res_name = mod.__name__
+ checked_add_package(mod.__name__, mod)
+ for from_name in fromlist:
+ qual_name = res_name + '.' + from_name
+ checked_add_package(qual_name, mod)
+
+ if fixed and not fromlist:
+ return getattr(res, fixed)
+ else:
+ return res
+
+ def get_py_deps(self):
+ return self.py_dependencies
+
+ def remove_py_deps(self, deps):
+ self.py_dependencies.difference_update(deps)
+
+ def load(self, prefix=None):
+ """load(module=None). Loads package's module.
+
+ If package is already loaded, this is a NOP.
+
+ """
+
+ errors = []
+ if self._loaded:
+ return
+
+ def import_from(p_path):
+ # print 'running import_from'
+ try:
+ # print p_path + self.codepath
+ self.prefix = p_path
+ __import__(p_path + self.codepath,
+ globals(),
+ locals(),
+ [])
+ self._module = module = sys.modules[p_path + self.codepath]
+ self.py_dependencies.add(p_path + self.codepath)
+ self._package_type = self.Base
+
+ if hasattr(module, "_force_no_unload_pkg_list"):
+ self._force_no_unload = module._force_no_unload_pkg_list
+ else:
+ self._force_no_unload = []
+ if hasattr(module, "_force_unload_pkg_list"):
+ self._force_unload = module._force_unload_pkg_list
+ else:
+ self._force_unload = []
+ if hasattr(module, "_force_sys_unload"):
+ self._force_sys_unload = module._force_sys_unload
+ else:
+ self._force_sys_unload = False
+ except ImportError, e:
+ errors.append(traceback.format_exc())
+ self.prefix = None
+ return False
+ return True
+
+ try:
+ if self.prefix is not None:
+ r = not import_from(self.prefix)
+ elif prefix is not None:
+ r = not import_from(prefix)
+ else:
+ r = (not import_from('vistrails.packages.') and
+ not import_from('userpackages.'))
+ except Exception, e:
+ raise self.LoadFailed(self, e, traceback.format_exc())
+
+ if r:
+ raise self.InitializationFailed(self, errors)
+
+ # Sometimes we don't want to change startup.xml, for example
+ # when peeking at a package that's on the available package list
+ # on edit -> preferences. That's what the load_configuration field
+ # is for
+ if self.load_configuration:
+ if hasattr(self._module, 'configuration'):
+ # hold a copy of the initial configuration so it can be reset
+ self._initial_configuration = \
+ copy.copy(self._module.configuration)
+ self.load_persistent_configuration()
+
+ self.set_properties()
+
+ def initialize(self):
+ if not self._loaded:
+ raise VistrailsInternalError("Called initialize() on non-loaded "
+ "Package %s" % self.codepath)
+
+ self.check_requirements()
+
+ try:
+ name = self.prefix + self.codepath + '.init'
+ try:
+ __import__(name, globals(), locals(), [])
+ except ImportError, e:
+ # FIXME !!! Want to differentiate between .init not
+ # existing and an error with an import in the .init
+ # file !!!
+ if str(e) != 'No module named init':
+ raise
+ else:
+ self._init_module = self._module
+ else:
+ self._init_module = sys.modules[name]
+ self.py_dependencies.add(name)
+ # Copy attributes (shallow) from _module into _init_module's namespace and point _module to _init_module
+ module_attributes = ['identifier', 'name', 'version',
+ 'configuration', 'package_dependencies',
+ 'package_requirements',
+ 'can_handle_identifier',
+ 'can_handle_vt_file']
+ for attr in module_attributes:
+ if (hasattr(self._module, attr) and
+ not hasattr(self._init_module, attr)):
+ setattr(self._init_module, attr, getattr(self._module, attr))
+ self._module = self._init_module
+
+ if hasattr(self._init_module, 'initialize'):
+ self._init_module.initialize()
+ except Exception:
+ self.unload()
+ raise
+
+ def unload(self):
+ for path in self.py_dependencies:
+ if path not in sys.modules:
+ # print "skipping %s" % path
+ pass
+ else:
+ # print 'deleting path:', path, path in sys.modules
+ del sys.modules[path]
+ self.py_dependencies.clear()
+ self._loaded = False
+
+ def set_properties(self):
+ # Set properties
+ try:
+ self._loaded = True
+ self.name = self._module.name
+ self.identifier = self._module.identifier
+ self.version = self._module.version
+ if hasattr(self._module, "old_identifiers"):
+ self.old_identifiers = self._module.old_identifiers
+ self.package_dir = os.path.dirname(self._module.__file__)
+ except AttributeError, e:
+ try:
+ v = self._module.__file__
+ except AttributeError:
+ v = self._module
+ raise e
+ descr = inspect.getdoc(self._module)
+ if descr:
+ self.description = re.sub('^ *\n', '', descr.rstrip())
+ else:
+ self.description = "(No description available)"
+
+ def can_handle_all_errors(self):
+ return hasattr(self._init_module, 'handle_all_errors')
+
+ def can_handle_upgrades(self):
+ return hasattr(self._init_module, 'handle_module_upgrade_request')
+
+ def can_handle_identifier(self, identifier):
+ """ Asks package if it can handle this package
+ """
+ try:
+ return (hasattr(self.init_module, 'can_handle_identifier') and
+ self.init_module.can_handle_identifier(identifier))
+ except Exception, e:
+ debug.critical("Got exception calling %s's can_handle_identifier: "
+ "%s: %s" % (self.name,
+ type(e).__name__, ', '.join(e.args)))
+ return False
+
+ def can_handle_vt_file(self, name):
+ """ Asks package if it can handle a file inside a zipped vt file
+ """
+ try:
+ return (hasattr(self.init_module, 'can_handle_vt_file') and
+ self.init_module.can_handle_vt_file(name))
+ except Exception, e:
+ debug.critical("Got exception calling %s's can_handle_vt_file: "
+ "%s: %s" % (self.name,
+ type(e).__name__, ', '.join(e.args)))
+ return False
+
+ def can_handle_missing_modules(self):
+ return hasattr(self._init_module, 'handle_missing_module')
+
+ def handle_all_errors(self, *args, **kwargs):
+ return self._init_module.handle_all_errors(*args, **kwargs)
+
+ def handle_module_upgrade_request(self, *args, **kwargs):
+ return self._init_module.handle_module_upgrade_request(*args, **kwargs)
+
+ def handle_missing_module(self, *args, **kwargs):
+ """report_missing_module(name, namespace):
+
+ Calls the package's module handle_missing_module function, if
+ present, to allow the package to dynamically add a missing
+ module.
+ """
+ return self._init_module.handle_missing_module(*args, **kwargs)
+
+ def add_abs_upgrade(self, new_desc, name, namespace, module_version):
+ key = (name, namespace)
+ if key not in self._abs_pkg_upgrades:
+ self._abs_pkg_upgrades[key] = {}
+ self._abs_pkg_upgrades[key][module_version] = new_desc
+
+ def has_abs_upgrade(self, name, namespace='', module_version=''):
+ key = (name, namespace)
+ if key not in self._abs_pkg_upgrades:
+ return False
+ if module_version and module_version not in self._abs_pkg_upgrades[key]:
+ return False
+ return True
+
+ def get_abs_upgrade(self, name, namespace='', module_version=''):
+ key = (name, namespace)
+ if key in self._abs_pkg_upgrades:
+ if module_version:
+ if module_version in self._abs_pkg_upgrades[key]:
+ return self._abs_pkg_upgrades[key][module_version]
+ else:
+ latest_version = max(self._abs_pkg_upgrades[key].iterkeys())
+ return self._abs_pkg_upgrades[key][latest_version]
+ return None
+
+ def has_contextMenuName(self):
+ return hasattr(self._init_module, 'contextMenuName')
+
+ def contextMenuName(self, signature):
+ return self._init_module.contextMenuName(signature)
+
+ def has_callContextMenu(self):
+ return hasattr(self._init_module, 'callContextMenu')
+
+ def callContextMenu(self, signature):
+ return self._init_module.callContextMenu(signature)
+
+ def loadVistrailFileHook(self, vistrail, tmp_dir):
+ if hasattr(self._init_module, 'loadVistrailFileHook'):
+ try:
+ self._init_module.loadVistrailFileHook(vistrail, tmp_dir)
+ except Exception, e:
+ debug.critical("Got exception in %s's loadVistrailFileHook(): "
+ "%s: %s" % (self.name, type(e).__name__,
+ ', '.join(e.args)))
+
+ def saveVistrailFileHook(self, vistrail, tmp_dir):
+ if hasattr(self._init_module, 'saveVistrailFileHook'):
+ try:
+ self._init_module.saveVistrailFileHook(vistrail, tmp_dir)
+ except Exception, e:
+ debug.critical("Got exception in %s's saveVistrailFileHook(): "
+ "%s: %s" % (self.name, type(e).__name__,
+ ', '.join(e.args)))
+
+ def check_requirements(self):
+ try:
+ callable_ = self._module.package_requirements
+ except AttributeError:
+ return
+ else:
+ callable_()
+
+ def menu_items(self):
+ try:
+ callable_ = self._module.menu_items
+ except AttributeError:
+ return None
+ else:
+ try:
+ return callable_()
+ except Exception, e:
+ debug.critical("Couldn't load menu items for %s: %s: %s" % (
+ self.name, type(e).__name__, ', '.join(e.args)))
+
+ def finalize(self):
+ if not self._initialized:
+ return
+ debug.log("Finalizing %s" % self.name)
+ try:
+ callable_ = self._module.finalize
+ except AttributeError:
+ pass
+ else:
+ try:
+ callable_()
+ except Exception, e:
+ debug.critical("Couldn't finalize %s: %s: %s" % (
+ self.name, type(e).__name__, ', '.join(e.args)))
+ # Save configuration
+ if self.configuration:
+ self.set_persistent_configuration()
+ self.unload()
+ self._module = None
+ self._init_module = None
+ self._initialized = False
+
+ def dependencies(self):
+ try:
+ callable_ = self._module.package_dependencies
+ except AttributeError:
+ deps = []
+ else:
+ try:
+ deps = callable_()
+ except Exception, e:
+ debug.critical("Couldn't get dependencies of %s: %s: %s" % (
+ self.name, type(e).__name__, ', '.join(e.args)))
+
+ if self._module is not None and \
+ hasattr(self._module, '_dependencies'):
+ deps.extend(self._module._dependencies)
+ return deps
+
+ def loaded(self):
+ return self._loaded
+
+ def initialized(self):
+ return self._initialized
+
+ ##########################################################################
+ # Configuration
+
+ def _get_package_node(self, dom, create):
+ doc = dom.documentElement
+ packages = enter_named_element(doc, 'packages')
+ for package_node in named_elements(packages, 'package'):
+ if package_node.attributes['name'].value == self.codepath:
+ return package_node, 'enabled'
+ oldpackages = enter_named_element(doc, 'disabledpackages')
+ for package_node in named_elements(oldpackages, 'package'):
+ if package_node.attributes['name'].value == self.codepath:
+ return package_node, 'disabled'
+
+ if create is None:
+ return None, None
+ else:
+ package_node = dom.createElement('package')
+ package_node.setAttribute('name', self.codepath)
+ if create == 'enabled':
+ packages.appendChild(package_node)
+ elif create == 'disabled':
+ oldpackages.appendChild(package_node)
+ else:
+ raise ValueError
+ get_vistrails_application().vistrailsStartup.write_startup_dom(dom)
+ return package_node, create
+
+ def _move_package_node(self, dom, where, node):
+ doc = dom.documentElement
+ packages = enter_named_element(doc, 'packages')
+ oldpackages = enter_named_element(doc, 'disabledpackages')
+ if where == 'enabled':
+ oldpackages.removeChild(node)
+ packages.appendChild(node)
+ elif where == 'disabled':
+ packages.removeChild(node)
+ oldpackages.appendChild(node)
+ else:
+ raise ValueError
+ get_vistrails_application().vistrailsStartup.write_startup_dom(dom)
+
+ def remove_own_dom_element(self):
+ """Moves the node to the <disabledpackages> section.
+ """
+ dom = get_vistrails_application().vistrailsStartup.startup_dom()
+
+ node, section = self._get_package_node(dom, create='disabled')
+ if section == 'enabled':
+ self._move_package_node(dom, 'disabled', node)
+
+ def reset_configuration(self):
+ """Reset package configuration to original package settings.
+ """
+
+ (dom, element) = self.find_own_dom_element()
+ doc = dom.documentElement
+ configuration = enter_named_element(element, 'configuration')
+ if configuration:
+ element.removeChild(configuration)
+ self.configuration = copy.copy(self._initial_configuration)
+
+ startup = get_vistrails_application().vistrailsStartup
+ startup.write_startup_dom(dom)
+
+ def find_own_dom_element(self):
+ """find_own_dom_element() -> (DOM, Node)
+
+ Opens the startup DOM, looks for the element that belongs to the package,
+ and returns DOM and node. Creates a new one in the <disabledpackages>
+ section if none is found.
+ """
+ dom = get_vistrails_application().vistrailsStartup.startup_dom()
+
+ node, section = self._get_package_node(dom, create='disabled')
+ return (dom, node)
+
+ def load_persistent_configuration(self):
+ (dom, element) = self.find_own_dom_element()
+
+ configuration = enter_named_element(element, 'configuration')
+ if configuration:
+ self.configuration.set_from_dom_node(configuration)
+ dom.unlink()
+
+ def set_persistent_configuration(self):
+ (dom, element) = self.find_own_dom_element()
+ child = enter_named_element(element, 'configuration')
+ if child:
+ element.removeChild(child)
+ self.configuration.write_to_dom(dom, element)
+ get_vistrails_application().vistrailsStartup.write_startup_dom(dom)
+ dom.unlink()
+
+ def create_startup_package_node(self):
+ """Writes the node to the <packages> section.
+
+ If it was in the <disabledpackages> section, move it, else, create it.
+ """
+ dom = get_vistrails_application().vistrailsStartup.startup_dom()
+
+ node, section = self._get_package_node(dom, create='enabled')
+ if section == 'disabled':
+ self._move_package_node(dom, 'enabled', node)
+
+ configuration = enter_named_element(node, 'configuration')
+ if configuration:
+ self.configuration.set_from_dom_node(configuration)
+
+ dom.unlink()
diff --git a/vistrails/core/modules/paramexplore.py b/vistrails/core/modules/paramexplore.py
new file mode 100644
index 0000000..6b8214a
--- /dev/null
+++ b/vistrails/core/modules/paramexplore.py
@@ -0,0 +1,250 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from vistrails.core import debug
+from vistrails.core.modules.basic_modules import Color
+from vistrails.core.utils.color import rgb2hsv, hsv2rgb
+
+
+class BaseLinearInterpolator(object):
+ def __init__(self, ptype, mn, mx, steps):
+ self._ptype = ptype
+ self._mn = mn
+ self._mx = mx
+ self._steps = steps
+
+ def get_values(self):
+ cast = self._ptype
+ begin = self._mn
+ end = self._mx
+ size = self._steps
+ if size <= 1:
+ return [begin]
+ result = [cast(begin + ((end - begin) * i / cast(size - 1)))
+ for i in xrange(size)]
+ return result
+
+
+class IntegerLinearInterpolator(BaseLinearInterpolator):
+ def __init__(self, mn, mx, steps):
+ BaseLinearInterpolator.__init__(self, int, mn, mx, steps)
+
+
+class FloatLinearInterpolator(BaseLinearInterpolator):
+ def __init__(self, mn, mx, steps):
+ BaseLinearInterpolator.__init__(self, float, mn, mx, steps)
+
+
+###############################################################################
+
+class BaseColorInterpolator(object):
+ def __init__(self, ifunc, begin, end, size):
+ self._ifunc = ifunc
+ self.begin = begin
+ self.end = end
+ self.size = size
+
+ def get_values(self):
+ if self.size <= 1:
+ return [self.begin]
+ result = [self._ifunc(self.begin, self.end, self.size, i)
+ for i in xrange(self.size)]
+ return result
+
+
+class RGBColorInterpolator(BaseColorInterpolator):
+ def __init__(self, begin, end, size):
+ def fun(b, e, s, i):
+ b = [float(x) for x in b.split(',')]
+ e = [float(x) for x in e.split(',')]
+ u = float(i) / (float(s) - 1.0)
+ [r,g,b] = [b[i] + u * (e[i] - b[i]) for i in [0,1,2]]
+ return Color.to_string(r, g, b)
+ BaseColorInterpolator.__init__(self, fun, begin, end, size)
+
+
+class HSVColorInterpolator(BaseColorInterpolator):
+ def __init__(self, begin, end, size):
+ BaseColorInterpolator.__init__(self, None, begin, end, size)
+
+ def get_values(self):
+ b = [float(x) for x in self.begin.split(',')]
+ e = [float(x) for x in self.end.split(',')]
+
+ b_hsv = rgb2hsv(b)
+ e_hsv = rgb2hsv(e)
+
+ size_fact = 1.0 / (float(self.size) - 1.0)
+
+ # Ignore the undefined hues
+ if b_hsv[0] is None:
+ b_hsv[0] = e_hsv[0]
+ elif e_hsv[0] is None:
+ e_hsv[0] = b_hsv[0]
+
+ if b_hsv[0] is None:
+ # There is no hue at all!
+ b_hsv[0] = e_hsv[0] = 0.0 # unused value
+ hue_step = 0.0
+ else:
+ # Compute hue
+ # Because the hue is an angle, there is two ways to interpolate it;
+ # choose the shorter path
+ diff1 = e_hsv[0] - b_hsv[0]
+ diff2 = e_hsv[0] - b_hsv[0] + 360.0
+ if diff2 >= 360.0:
+ diff2 -= 360.0
+ assert 0.0 <= diff2 < 360.0
+ if abs(diff1) < abs(diff2):
+ hue_step = diff1
+ else:
+ hue_step = diff2
+
+ colors = []
+ for i in xrange(self.size):
+ u = i * size_fact
+ hue = b_hsv[0] + u * hue_step
+ if hue < 0.0:
+ hue += 360.0
+ elif hue > 360.0:
+ hue -= 360.0
+ colors.append(Color.to_string(*hsv2rgb((
+ hue,
+ b_hsv[1] + u * (e_hsv[1] - b_hsv[1]),
+ b_hsv[2] + u * (e_hsv[2] - b_hsv[2])
+ ))))
+
+ return colors
+
+
+###############################################################################
+
+class UserDefinedFunctionInterpolator(object):
+ def __init__(self, ptype, code, steps):
+ self._ptype = ptype
+ self._code = code
+ self._steps = steps
+ def get_values(self):
+ def get():
+ import code
+ values = []
+ d = {}
+ try:
+ exec(self._code) in {}, d
+ except Exception, e:
+ return [self._ptype.default_value] * self._steps
+ def evaluate(i):
+ try:
+ v = d['value'](i)
+ if v == None:
+ return self._ptype.default_value
+ return v
+ except Exception, e:
+ return str(e)
+ return [evaluate(i) for i in xrange(self._steps)]
+ result = get()
+
+ if not all(self._ptype.validate(x) for x in result):
+ # FIXME: We should throw an error here instead
+ debug.critical(
+ 'Failed Validation',
+ 'One of the <i>%s</i>\'s user defined functions has '
+ 'failed validation, which usually means it generated a '
+ 'value of a type different than that specified by the '
+ 'parameter. Parameter Exploration aborted.' % self._ptype)
+ return None
+ return result
+
+
+################################################################################
+
+import unittest
+
+
+class TestLinearInterpolator(unittest.TestCase):
+ def test_int(self):
+ x = BaseLinearInterpolator(int, 0, 999, 1000)
+ assert x.get_values() == range(1000)
+
+ def test_float(self):
+ # test the property that differences in value must be linearly
+ # proportional to differences in index for a linear interpolation
+ import random
+ s = random.randint(4, 10000)
+ v1 = random.random()
+ v2 = random.random()
+ mn = min(v1, v2)
+ mx = max(v1, v2)
+ x = BaseLinearInterpolator(float, mn, mx, s).get_values()
+ v1 = random.randint(0, s-1)
+ v2 = 0
+ while v2 == v1:
+ v2 = random.randint(0, s-1)
+ v3 = random.randint(0, s-1)
+ v4 = 0
+ while v3 == v4:
+ v4 = random.randint(0, s-1)
+ r1 = (v2 - v1) / (x[v2] - x[v1])
+ r2 = (v4 - v3) / (x[v4] - x[v3])
+ assert abs(r1 - r2) < 1e-6
+
+
+class TestColorInterpolation(unittest.TestCase):
+ def test_rgb_interpolation(self):
+ interp = RGBColorInterpolator('0.5,0.7,0.8', '0.5,0.9,0.3', 6)
+ self.assertEqual(interp.get_values(),
+ ['0.5,0.7,0.8', '0.5,0.74,0.7', '0.5,0.78,0.6',
+ '0.5,0.82,0.5', '0.5,0.86,0.4', '0.5,0.9,0.3'])
+
+ def test_hsv_interpolation(self):
+ tests = [((120.0, 0.8, 0.2), (170.0, 0.5, 0.2),
+ [(120.0, 0.8, 0.2), (130.0, 0.74, 0.2), (140.0, 0.68, 0.2),
+ (150.0, 0.62, 0.2), (160.0, 0.56, 0.2), (170.0, 0.5, 0.2)]),
+ ((260.0, 0.2, 0.7), (40.0, 0.8, 0.1),
+ [(260.0, 0.2, 0.7), (288.0, 0.32, 0.58), (316.0, 0.44, 0.46),
+ (344.0, 0.56, 0.34), (12.0, 0.68, 0.22), (40.0, 0.8, 0.1)])]
+
+ for b, e, expected in tests:
+ b = hsv2rgb(b)
+ e = hsv2rgb(e)
+ interp = HSVColorInterpolator(','.join(str(c) for c in b),
+ ','.join(str(c) for c in e),
+ 6)
+ for i, color in enumerate(interp.get_values()):
+ color = [float(e) for e in color.split(',')]
+ color = rgb2hsv(color)
+ self.assertAlmostEqual(color[0], expected[i][0], delta=0.2)
+ self.assertAlmostEqual(color[1], expected[i][1], delta=0.005)
+ self.assertAlmostEqual(color[2], expected[i][2], delta=0.005)
diff --git a/vistrails/core/modules/python_source_configure.py b/vistrails/core/modules/python_source_configure.py
new file mode 100644
index 0000000..a711b79
--- /dev/null
+++ b/vistrails/core/modules/python_source_configure.py
@@ -0,0 +1,44 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# *** MOVED *** to gui.modules.python_source_configure
+import traceback
+from vistrails.core import debug
+
+from vistrails.gui.modules.python_source_configure import *
+debug.warning("The use of core.modules.python_source_configure is deprecated. "
+ "Please use gui.modules.python_source_configure.",
+ ''.join(traceback.format_stack()))
+
diff --git a/vistrails/core/modules/query_configuration.py b/vistrails/core/modules/query_configuration.py
new file mode 100644
index 0000000..3d1279a
--- /dev/null
+++ b/vistrails/core/modules/query_configuration.py
@@ -0,0 +1,44 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# *** MOVED *** to gui.modules.query_configuration
+import traceback
+from vistrails.core import debug
+
+from vistrails.gui.modules.query_configuration import *
+debug.warning("The use of core.modules.query_configuration is deprecated. "
+ "Please use gui.modules.query_configuration.",
+ ''.join(traceback.format_stack()))
+
diff --git a/vistrails/core/modules/source_configure.py b/vistrails/core/modules/source_configure.py
new file mode 100644
index 0000000..5f804d3
--- /dev/null
+++ b/vistrails/core/modules/source_configure.py
@@ -0,0 +1,44 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# *** MOVED *** to gui.modules.source_configure
+import traceback
+from vistrails.core import debug
+
+from vistrails.gui.modules.source_configure import *
+debug.warning("The use of core.modules.source_configure is deprecated. "
+ "Please use gui.modules.source_configure.",
+ ''.join(traceback.format_stack()))
+
diff --git a/vistrails/core/modules/sub_module.py b/vistrails/core/modules/sub_module.py
new file mode 100644
index 0000000..f6ad512
--- /dev/null
+++ b/vistrails/core/modules/sub_module.py
@@ -0,0 +1,496 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+""" Define facilities for setting up SubModule Module in VisTrails """
+from itertools import izip
+import random
+import uuid
+
+from vistrails.core.cache.hasher import Hasher
+from vistrails.core.cache.utils import hash_list
+from vistrails.core.modules import module_registry
+from vistrails.core.modules.basic_modules import String, Boolean, Variant, \
+ NotCacheable, identifier as basic_pkg
+from vistrails.core.modules.vistrails_module import Module, InvalidOutput, new_module, \
+ ModuleError, ModuleSuspended
+from vistrails.core.utils import ModuleAlreadyExists, DummyView, VistrailsInternalError
+import os.path
+import vistrails.db
+
+try:
+ import hashlib
+ sha_hash = hashlib.sha1
+except ImportError:
+ import sha
+ sha_hash = sha.new
+
+##############################################################################
+
+class InputPort(Module):
+
+ def compute(self):
+ exPipe = self.forceGetInputFromPort('ExternalPipe')
+ if exPipe is not None:
+ self.setResult('InternalPipe', exPipe)
+ else:
+ if self.hasInputFromPort('Default'):
+ self.setResult('InternalPipe',
+ self.getInputFromPort('Default'))
+ else:
+ self.setResult('InternalPipe', InvalidOutput)
+
+###############################################################################
+
+class OutputPort(Module):
+
+ def compute(self):
+ inPipe = self.getInputFromPort('InternalPipe')
+ self.setResult('ExternalPipe', inPipe)
+
+###############################################################################
+
+class Group(Module):
+ def __init__(self):
+ Module.__init__(self)
+ self.is_group = True
+ self.persistent_modules = []
+
+ def compute(self):
+ if not hasattr(self, 'pipeline') or self.pipeline is None:
+ raise VistrailsInternalError("%s cannot execute--" % \
+ self.__class__.__name__ + \
+ "pipeline doesn't exist")
+ elif not hasattr(self, 'input_remap') or self.input_remap is None or \
+ not hasattr(self, 'output_remap') or self.output_remap is None:
+ raise VistrailsInternalError("%s cannot execute--" % \
+ self.__class__.__name__ + \
+ "remap dictionaries don't exist")
+
+ res = self.interpreter.setup_pipeline(self.pipeline)
+ self.persistent_modules = res[0].values()
+ if len(res[5]) > 0:
+ raise ModuleError(self, 'Error(s) inside group:\n' +
+ '\n'.join(me.msg for me in res[5].itervalues()))
+ tmp_id_to_module_map = res[0]
+ for iport_name, conn in self.inputPorts.iteritems():
+ iport_module = self.input_remap[iport_name]
+ iport_obj = tmp_id_to_module_map[iport_module.id]
+ iport_obj.set_input_port('ExternalPipe', conn[0])
+
+ kwargs = {'logger': self.logging.log, 'clean_pipeline': True,
+ 'current_version': self.moduleInfo['version']}
+ module_info_args = set(['locator', 'reason', 'extra_info', 'actions'])
+ for arg in module_info_args:
+ if arg in self.moduleInfo:
+ kwargs[arg] = self.moduleInfo[arg]
+
+# if hasattr(self, 'group_exec'):
+# kwargs['parent_exec'] = self.group_exec
+
+ res = self.interpreter.execute_pipeline(self.pipeline, *(res[:2]),
+ **kwargs)
+ if len(res[2]) > 0:
+ raise ModuleError(self, 'Error(s) inside group:\n' +
+ '\n '.join(me.module.__class__.__name__ + ': ' + \
+ me.msg for me in res[2].itervalues()))
+ if len(res[4]) > 0:
+ # extract messages and previous ModuleSuspended exceptions
+ message = '\n'.join([msg for msg in res[4].itervalues()])
+ children = [tmp_id_to_module_map[module_id]._module_suspended
+ for module_id in res[4]]
+ raise ModuleSuspended(self, message, children=children)
+
+ for oport_name, oport_module in self.output_remap.iteritems():
+ if oport_name is not 'self':
+ # oport_module = self.output_remap[oport_name]
+ oport_obj = tmp_id_to_module_map[oport_module.id]
+ self.setResult(oport_name, oport_obj.get_output('ExternalPipe'))
+ self.interpreter.finalize_pipeline(self.pipeline, *res[:-1],
+ **{'reset_computed': False})
+
+ def is_cacheable(self):
+ return all(m.is_cacheable() for m in self.persistent_modules)
+
+###############################################################################
+
+def coalesce_port_specs(neighbors, type):
+ from vistrails.core.modules.basic_modules import identifier as basic_pkg
+ reg = module_registry.get_module_registry()
+ cur_descs = None
+ if type == 'input':
+ find_common = reg.find_descriptor_subclass
+ common_desc = reg.get_descriptor_by_name(basic_pkg, 'Variant')
+ elif type == 'output':
+ find_common = reg.find_descriptor_superclass
+ common_desc = reg.get_descriptor_by_name(basic_pkg, 'Module')
+ else:
+ raise VistrailsInternalError("Cannot understand type '%s'" % type)
+
+ for (module, port_name) in neighbors:
+ if cur_descs is None:
+ port_spec = module.get_port_spec(port_name, type)
+ cur_descs = port_spec.descriptors()
+ else:
+ next_port_spec = module.get_port_spec(port_name, type)
+ next_descs = next_port_spec.descriptors()
+ if len(cur_descs) != len(next_descs):
+ raise VistrailsInternalError("Cannot have single port "
+ "connect to incompatible "
+ "types")
+ descs = []
+ for cur_desc, next_desc in izip(cur_descs, next_descs):
+ new_desc = find_common(cur_desc, next_desc)
+ if new_desc is None:
+ new_desc = common_desc
+ descs.append(new_desc)
+ cur_descs = descs
+ if cur_descs:
+ sigstring = '(' + ','.join(d.sigstring for d in cur_descs) + ')'
+ else:
+ sigstring = None
+ return sigstring
+
+def get_port_spec_info(pipeline, module):
+ type_map = {'OutputPort': 'output', 'InputPort': 'input'}
+ try:
+ type = type_map[module.name]
+ except KeyError:
+ raise VistrailsInternalError("cannot translate type '%s'" % type)
+ if type == 'input':
+ get_edges = pipeline.graph.edges_from
+ get_port_name = \
+ lambda x: pipeline.connections[x].destination.name
+ elif type == 'output':
+ get_edges = pipeline.graph.edges_to
+ get_port_name = \
+ lambda x: pipeline.connections[x].source.name
+ # conns = get_edges(module.id)
+# for i, m in pipeline.modules.iteritems():
+# print i, m.name
+# for j, c in pipeline.connections.iteritems():
+# print j, c.source.moduleId, c.destination.moduleId
+
+ neighbors = [(pipeline.modules[m_id], get_port_name(c_id))
+ for (m_id, c_id) in get_edges(module.id)]
+ port_name = neighbors[0][1]
+ sigstring = coalesce_port_specs(neighbors, type)
+ old_name = port_name
+ # sigstring = neighbor.get_port_spec(port_name, type).sigstring
+
+ # FIXME check old registry here?
+ port_optional = False
+ for function in module.functions:
+ if function.name == 'name':
+ port_name = function.params[0].strValue
+ if function.name == 'optional':
+ port_optional = function.params[0].strValue == 'True'
+# print 'psi:', port_name, old_name, sigstring
+ return (port_name, sigstring, port_optional, neighbors)
+
+###############################################################################
+
+class Abstraction(Group):
+ def __init__(self):
+ Group.__init__(self)
+
+ # the compute method is inherited from Group!
+
+def read_vistrail(vt_fname):
+ import vistrails.db.services.io
+ from vistrails.core.vistrail.vistrail import Vistrail
+ vistrail = vistrails.db.services.io.open_vistrail_from_xml(vt_fname)
+ Vistrail.convert(vistrail)
+ return vistrail
+
+def read_vistrail_from_db(db_connection, abs_id, version):
+ import vistrails.db.services.io
+ from vistrails.core.vistrail.vistrail import Vistrail
+ vistrail = vistrails.db.services.io.open_vistrail_from_db(db_connection, abs_id, version)
+ Vistrail.convert(vistrail)
+ return vistrail
+
+def get_abs_namespace_info(vistrail):
+ annotation_add = None
+ annotation_key = '__abstraction_uuid__'
+ namespaces = []
+ while vistrail.get_annotation(annotation_key) is not None:
+ namespaces.append(vistrail.get_annotation(annotation_key).value)
+ if annotation_add is None:
+ annotation_add = 2
+ else:
+ annotation_add += 1
+ annotation_key = '__abstraction_uuid_%d__' % annotation_add
+ return namespaces, annotation_add
+
+def get_all_abs_namespaces(vistrail):
+ return get_abs_namespace_info(vistrail)[0]
+
+def get_cur_abs_namespace(vistrail):
+ all_namespaces = get_abs_namespace_info(vistrail)[0]
+ if len(all_namespaces) > 0:
+ return all_namespaces[-1]
+ return None
+
+def get_next_abs_annotation_key(vistrail):
+ annotation_add = get_abs_namespace_info(vistrail)[1]
+ if annotation_add is None:
+ return "__abstraction_uuid__"
+ return "__abstraction_uuid_%d__" % annotation_add
+
+def get_cur_abs_annotation_key(vistrail):
+ annotation_add = get_abs_namespace_info(vistrail)[1]
+ if annotation_add is None:
+ return None
+ elif annotation_add == 2:
+ return '__abstraction_uuid__'
+ return '__abstraction_uuid_%d__' % (annotation_add - 1)
+
+def save_abstraction(vistrail, fname):
+ from vistrails.core.db.io import save_vistrail_to_xml
+
+ # check if vistrail is changed before calling this!
+ new_namespace = str(uuid.uuid1())
+ annotation_key = get_next_abs_annotation_key(vistrail)
+ vistrail.set_annotation(annotation_key, new_namespace)
+ save_vistrail_to_xml(vistrail, fname)
+
+def new_abstraction(name, vistrail, vt_fname=None, internal_version=-1L,
+ pipeline=None):
+ """make_abstraction(name: str,
+ vistrail: (str or Vistrail),
+ registry: ModuleRegistry,
+ vt_fname: str,
+ internal_version: long,
+ pipeline: Pipeline) -> type
+
+ Creates a new VisTrails module that is a subclass of Abstraction
+ according to the vistrail file provided and the version. The version
+ can either be a tag (string) or an id (long)
+ """
+
+ if isinstance(vistrail, basestring):
+ vt_fname = vistrail
+ vistrail = read_vistrail(vistrail)
+ elif vt_fname is None:
+ raise VistrailsInternalError("Abstraction must provide "
+ "vt_fname with vistrail")
+
+ if internal_version == -1L:
+ internal_version = vistrail.get_latest_version()
+ action = vistrail.actionMap[internal_version]
+ if pipeline is None:
+ pipeline = vistrail.getPipeline(internal_version)
+ # try to make the subworkflow work with the package versions we have
+ pipeline.validate()
+ uuid = get_cur_abs_namespace(vistrail)
+
+ if vistrail.has_notes(action.id):
+ docstring = vistrail.get_notes(action.id)
+ else:
+ docstring = None
+
+ d = {}
+ input_modules = []
+ output_modules = []
+ for module in pipeline.module_list:
+ #FIXME make this compare more robust
+ if module.name == 'InputPort' and module.package == basic_pkg:
+ input_modules.append(module)
+ elif module.name == 'OutputPort' and module.package == basic_pkg:
+ output_modules.append(module)
+ input_ports = []
+ output_ports = []
+ input_remap = {}
+ output_remap = {}
+ for module in input_modules:
+ (port_name, sigstring, optional, _) = \
+ get_port_spec_info(pipeline, module)
+ input_ports.append((port_name, sigstring, optional))
+ input_remap[port_name] = module
+ for module in output_modules:
+ (port_name, sigstring, optional, _) = \
+ get_port_spec_info(pipeline, module)
+ output_ports.append((port_name, sigstring, optional))
+ output_remap[port_name] = module
+
+ # necessary for group
+ d['_input_ports'] = input_ports
+ d['_output_ports'] = output_ports
+ d['input_remap'] = input_remap
+ d['output_remap'] = output_remap
+ d['pipeline'] = pipeline
+
+ # abstraction specific
+ d['vt_fname'] = vt_fname
+ d['vistrail'] = vistrail
+ d['internal_version'] = internal_version
+ d['uuid'] = uuid
+
+ # print "input_ports", d['_input_ports']
+ # print "output_ports", d['_output_ports']
+ return new_module(Abstraction, name, d, docstring)
+
+def get_abstraction_dependencies(vistrail, internal_version=-1L):
+ if isinstance(vistrail, basestring):
+ vistrail = read_vistrail(vistrail)
+ if internal_version == -1L:
+ internal_version = vistrail.get_latest_version()
+ # action = vistrail.actionMap[internal_version]
+ pipeline = vistrail.getPipeline(internal_version)
+
+ packages = {}
+ for module in pipeline.module_list:
+ if module.package not in packages:
+ packages[module.package] = set()
+ packages[module.package].add(module.descriptor_info)
+ return packages
+
+def find_internal_abstraction_refs(pkg, vistrail, internal_version=-1L):
+ if isinstance(vistrail, basestring):
+ vistrail = read_vistrail(os.path.join(pkg.package_dir, vistrail))
+ if internal_version == -1L:
+ internal_version = vistrail.get_latest_version()
+ pipeline = vistrail.getPipeline(internal_version)
+ abstractions = []
+ for m in pipeline.module_list:
+ if m.vtType == 'abstraction' and m.package == pkg.identifier:
+ abstractions.append((m.name, m.namespace))
+ return abstractions
+
+def random_signature(pipeline, obj, chm):
+ hasher = sha_hash()
+ hasher.update(str(random.random()))
+ return hasher.digest()
+
+def input_port_signature(pipeline, obj, chm):
+ if hasattr(obj, '_input_port_signature') and \
+ obj._input_port_signature is not None:
+ return obj._input_port_signature
+ return random_signature(pipeline, obj, chm)
+
+def group_signature(pipeline, module, chm):
+ if module._port_specs is None:
+ module.make_port_specs()
+ input_conns = {}
+ input_functions = {}
+ for from_module, c_id in pipeline.graph.edges_to(module.id):
+ conn = pipeline.connections[c_id]
+ if conn.destination.name not in input_conns:
+ input_conns[conn.destination.name] = []
+ input_conns[conn.destination.name].append((from_module, conn))
+ for function in module.functions:
+ if function.name not in input_functions:
+ input_functions[function.name] = []
+ input_functions[function.name].append(function)
+ covered_modules = dict((k, False) for k in module._input_remap)
+ for input_port_name, conn_list in input_conns.iteritems():
+ covered_modules[input_port_name] = True
+ input_module = module._input_remap[input_port_name]
+ upstream_sigs = [(pipeline.subpipeline_signature(m) +
+ Hasher.connection_signature(c))
+ for (m, c) in conn_list]
+ module_sig = Hasher.module_signature(input_module, chm)
+ sig = Hasher.subpipeline_signature(module_sig, upstream_sigs)
+ if input_port_name in input_functions:
+ function_sig = hash_list(input_functions[input_port_name],
+ Hasher.function_signature, chm)
+ sig = Hasher.compound_signature([sig, function_sig])
+ input_module._input_port_signature = sig
+ for input_port_name, done in covered_modules.iteritems():
+ if done:
+ continue
+ covered_modules[input_port_name] = True
+ input_module = module._input_remap[input_port_name]
+ if input_port_name in input_functions:
+ module_sig = Hasher.module_signature(input_module, chm)
+ function_sig = hash_list(input_functions[input_port_name],
+ Hasher.function_signature, chm)
+ sig = Hasher.compound_signature([module_sig, function_sig])
+ else:
+ sig = Hasher.module_signature(input_module, chm)
+ input_module._input_port_signature = sig
+
+ module.pipeline.refresh_signatures()
+
+ sig_list = []
+ sig_list.append(Hasher.module_signature(module, chm))
+ for m_id in module.pipeline.graph.sinks():
+ sig_list.append(module.pipeline.subpipeline_signature(m_id))
+ return Hasher.compound_signature(sig_list)
+
+def parse_abstraction_name(filename, get_all_parts=False):
+ # assume only 1 possible prefix or suffix
+ import re
+ prefixes = ["abstraction_"]
+ suffixes = [".vt", ".xml"]
+ path, fname = os.path.split(filename)
+ hexpat = '[a-fA-F0-9]'
+ uuidpat = hexpat + '{8}-' + hexpat + '{4}-' + hexpat + '{4}-' + hexpat + '{4}-' + hexpat + '{12}'
+ prepat = '|'.join(prefixes).replace('.','\\.')
+ sufpat = '|'.join(suffixes).replace('.','\\.')
+ pattern = re.compile("(" + prepat + ")?(.+?)(\(" + uuidpat + "\))?(" + sufpat + ")", re.DOTALL)
+ matchobj = pattern.match(fname)
+ prefix, absname, uuid, suffix = [matchobj.group(x) or '' for x in xrange(1,5)]
+ if get_all_parts:
+ return (path, prefix, absname, uuid[1:-1], suffix)
+ return absname
+
+
+###############################################################################
+
+def initialize(*args, **kwargs):
+ # These are all from sub_module.py!
+ reg = module_registry.get_module_registry()
+
+ reg.add_module(InputPort, signatureCallable=input_port_signature)
+ reg.add_input_port(InputPort, "name", String, True)
+ reg.add_input_port(InputPort, "optional", Boolean, True)
+ reg.add_input_port(InputPort, "spec", String)
+ reg.add_input_port(InputPort, "ExternalPipe", Variant, True)
+ reg.add_input_port(InputPort, "Default", Variant)
+ reg.add_output_port(InputPort, "InternalPipe", Variant)
+
+ reg.add_module(OutputPort)
+ reg.add_input_port(OutputPort, "name", String, True)
+ reg.add_input_port(OutputPort, "optional", Boolean, True)
+ reg.add_input_port(OutputPort, "spec", String)
+ reg.add_input_port(OutputPort, "InternalPipe", Variant)
+ reg.add_output_port(OutputPort, "ExternalPipe", Variant, True)
+
+ reg.add_module(Group, signatureCallable=group_signature,
+ hide_descriptor=True)
+ reg.add_output_port(Group, "self", Group, True)
+
+ reg.add_module(Abstraction, name="SubWorkflow", hide_descriptor=True)
diff --git a/vistrails/core/modules/tuple_configuration.py b/vistrails/core/modules/tuple_configuration.py
new file mode 100644
index 0000000..d03fb33
--- /dev/null
+++ b/vistrails/core/modules/tuple_configuration.py
@@ -0,0 +1,44 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# *** MOVED *** to gui.modules.tuple_configuration
+import traceback
+from vistrails.core import debug
+
+from vistrails.gui.modules.tuple_configuration import *
+debug.warning("The use of core.modules.tuple_configuration is deprecated. "
+ "Please use gui.modules.tuple_configuration.",
+ ''.join(traceback.format_stack()))
+
diff --git a/vistrails/core/modules/utils.py b/vistrails/core/modules/utils.py
new file mode 100644
index 0000000..9083550
--- /dev/null
+++ b/vistrails/core/modules/utils.py
@@ -0,0 +1,228 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import vistrails.core
+from vistrails.core.system import get_vistrails_default_pkg_prefix
+
+def create_descriptor_string(package, name, namespace=None,
+ use_package=True):
+ package_str = ""
+ namespace_str = ""
+ if use_package:
+ package_str = "%s:" % package
+ if namespace:
+ namespace_str = "%s|" % namespace
+ return "%s%s%s" % (package_str, namespace_str, name)
+
+def parse_descriptor_string(d_string, cur_package=None):
+ """parse_descriptor_string will expand names of modules using
+ information about the current package and allowing shortcuts
+ for any bundled vistrails packages (e.g. "basic" for
+ "org.vistrails.vistrails.basic"). It also allows a nicer
+ format for namespace/module specification (namespace comes
+ fist unlike port specifications where it is after the module
+ name...
+
+ Examples:
+ "persistence:PersistentInputFile", None ->
+ ("org.vistrails.vistrails.persistence", PersistentInputFile", "")
+ "basic:String", None ->
+ ("org.vistrails.vistrails.basic", "String", "")
+ "NamespaceA|NamespaceB|Module", "org.example.my" ->
+ ("org.example.my", "Module", "NamespaceA|NamespaceB")
+ """
+
+ package = ''
+ qual_name = ''
+ name = ''
+ namespace = None
+ parts = d_string.strip().split(':', 1)
+ if len(parts) > 1:
+ qual_name = parts[1]
+ if '.' in parts[0]:
+ package = parts[0]
+ else:
+ package = '%s.%s' % (get_vistrails_default_pkg_prefix(), parts[0])
+ else:
+ qual_name = d_string
+ if cur_package is None:
+ from vistrails.core.modules.module_registry import get_module_registry
+ reg = get_module_registry()
+ if reg._current_package is not None:
+ package = reg._current_package.identifier
+ else:
+ import vistrails.core.modules.basic_modules
+ basic_pkg = vistrails.core.modules.basic_modules.identifier
+ package = basic_pkg
+ else:
+ package = cur_package
+ qual_parts = qual_name.rsplit('|', 1)
+ if len(qual_parts) > 1:
+ namespace, name = qual_parts
+ else:
+ name = qual_name
+ return (package, name, namespace)
+
+def parse_port_spec_item_string(spec, cur_package=None):
+ spec = spec.strip()
+ spec_arr = spec.split(':', 2)
+ if len(spec_arr) > 2:
+ # switch format of spec to more natural
+ # <package>:<namespace>|<name> for descriptor parsing
+ spec = '%s:%s|%s' % (spec_arr[0], spec_arr[2], spec_arr[1])
+ return parse_descriptor_string(spec, cur_package)
+
+def create_port_spec_item_string(package, name, namespace=None,
+ old_style=False):
+ if old_style:
+ if namespace:
+ namespace = ':' + namespace
+ return '%s:%s%s' % (package, name, namespace)
+ else:
+ return create_descriptor_string(package, name, namespace)
+
+def parse_port_spec_string(p_string, cur_package=None):
+ port_spec = p_string.strip()
+ if port_spec.startswith('('):
+ port_spec = port_spec[1:]
+ if port_spec.endswith(')'):
+ port_spec = port_spec[:-1]
+ if port_spec.strip() == '':
+ return []
+
+ specs_list = []
+ for spec in port_spec.split(','):
+ specs_list.append(parse_port_spec_item_string(spec,
+ cur_package))
+ return specs_list
+
+
+def create_port_spec_string(specs_list, old_style=False):
+ return '(' + ','.join(create_port_spec_item_string(
+ *(specs + ((None, old_style) if len(specs) < 3 else (old_style,))))
+ for specs in specs_list) + ')'
+
+def expand_port_spec_string(p_string, cur_package=None,
+ old_style=False):
+ specs_list = parse_port_spec_string(p_string, cur_package)
+ return create_port_spec_string(specs_list, old_style)
+
+
+def make_modules_dict(*dcts, **kwargs):
+ """Makes a dictionary suitable to be exposed as the '_modules' of a package.
+
+ This combines dictionaries hierarchically to make a global dict from other
+ "sub-dicts", allowing to structure a package with subpackages.
+
+ For example, you could have:
+ a/aa.py:
+ _modules = {'aa': [Some, Module]}
+ a/__init__.py:
+ from .aa import _modules as aa_modules
+ from .ab import _modules as bb_modules
+ _modules = make_modules_dict(aa_modules, bb_modules, namespace='a')
+ b.py:
+ _modules = {'b': [Other, Modules]}
+ init.py:
+ from .a import _modules as a_modules
+ from .b import _modules as b_modules
+ _modules = make_modules_dict(a_modules, b_modules)
+
+ The resulting module hierarchy will be:
+ a.aa.Some, a.aa.Module
+ b.Other, b.Modules
+ """
+ namespace = kwargs.pop('namespace', '')
+ if kwargs:
+ raise TypeError("make_modules_dict got unexpected keyword arguments")
+ if namespace:
+ build_namespace = lambda n: '%s|%s' % (namespace, n)
+ else:
+ build_namespace = lambda n: n
+
+ dct = dict()
+ for d in dcts:
+ if not isinstance(d, dict):
+ d = {'': d}
+
+ for subname, sublist in d.iteritems():
+ if subname:
+ name = build_namespace(subname)
+ else:
+ name = namespace
+ dct.setdefault(name, []).extend(sublist)
+
+ return dct
+
+
+###############################################################################
+
+import unittest
+
+
+class UnorderedList(object):
+ def __init__(self, *elems):
+ self._set = set(elems)
+
+ def __eq__(self, other):
+ return set(other) == self._set
+
+ def __str__(self):
+ return 'ul(%s)' % ', '.join(repr(e) for e in self._set)
+
+ def __repr__(self):
+ return str(self)
+
+
+class TestModulesDict(unittest.TestCase):
+ def test_modulesdict(self):
+ ul = UnorderedList
+ pkg_a_aa = {'aa': [1, 2], 'aa|n': [3]}
+ pkg_a_ab = {'ab': [4, 5]}
+ pkg_a = make_modules_dict(pkg_a_aa, pkg_a_ab, [12, 13], namespace='a')
+ self.assertEqual(set(pkg_a.keys()),
+ set(['a', 'a|aa', 'a|aa|n', 'a|ab']))
+ pkg_b = {'b': [6, 7]}
+ glob = [10, 11]
+ more = {'a|aa': [8, 9]}
+ pkg = make_modules_dict(pkg_a, pkg_b, glob, more)
+ self.assertEqual(
+ pkg,
+ {
+ '': ul(10, 11),
+ 'a': ul(12, 13),
+ 'a|aa': ul(1, 2, 8, 9),
+ 'a|aa|n': ul(3),
+ 'a|ab': ul(4, 5),
+ 'b': ul(6, 7)})
diff --git a/vistrails/core/modules/vistrails_module.py b/vistrails/core/modules/vistrails_module.py
new file mode 100644
index 0000000..d2dd47a
--- /dev/null
+++ b/vistrails/core/modules/vistrails_module.py
@@ -0,0 +1,752 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from itertools import izip
+
+from vistrails.core.data_structures.bijectivedict import Bidict
+
+class NeedsInputPort(Exception):
+ def __init__(self, obj, port):
+ self.obj = obj
+ self.port = port
+ def __str__(self):
+ return "Module %s needs port %s" % (self.obj, self.port)
+
+
+class IncompleteImplementation(Exception):
+ def __str__(self):
+ return "Module has incomplete implementation"
+
+
+class MissingModule(Exception):
+ pass
+
+class ModuleBreakpoint(Exception):
+ def __init__(self, module):
+ self.module = module
+ self.msg = "Hit breakpoint"
+ self.errorTrace = ''
+
+ def __str__(self):
+ retstr = "Encoutered breakpoint at Module %s:\n" % (self.module)
+ for k in self.module.__dict__.keys():
+ retstr += "\t%s = %s\n" % (k, self.module.__dict__[k])
+
+ inputs = self.examine_inputs()
+ retstr += "\nModule has inputs:\n"
+
+ for i in inputs.keys():
+ retstr += "\t%s = %s\n" % (i, inputs[i])
+
+ return retstr
+
+ def examine_inputs(self):
+ in_ports = self.module.__dict__["inputPorts"]
+ inputs = {}
+ for p in in_ports:
+ inputs[p] = self.module.getInputListFromPort(p)
+
+ return inputs
+
+class ModuleHadError(Exception):
+ """Exception occurring when a module that failed gets updated again.
+
+ It is caught by the interpreter that doesn't log it.
+ """
+ def __init__(self, module):
+ self.module = module
+
+class ModuleWasSuspended(ModuleHadError):
+ """Exception occurring when a module that was suspended gets updated again.
+ """
+
+class ModuleError(Exception):
+
+ """Exception representing a VisTrails module runtime error. This
+exception is recognized by the interpreter and allows meaningful error
+reporting to the user and to the logging mechanism."""
+
+ def __init__(self, module, errormsg, abort=False):
+ """ModuleError should be passed the module instance that signaled the
+error and the error message as a string."""
+ Exception.__init__(self, errormsg)
+ self.abort = abort # force abort even if stopOnError is False
+ self.module = module
+ self.msg = errormsg
+ import traceback
+ self.errorTrace = traceback.format_exc()
+
+class ModuleSuspended(ModuleError):
+ """Exception representing a VisTrails module being suspended. Raising
+ ModuleSuspended flags that the module is not ready to finish yet and
+ that the workflow should be executed later. A suspended module does
+ not execute the modules downstream but all other branches will be
+ executed. This is useful when executing external jobs where you do not
+ want to block vistrails while waiting for the execution to finish.
+
+ 'queue' is a class instance that should provide a finished() method for
+ checking if the job has finished
+
+ 'children' is a list of ModuleSuspended instances that is used for nested
+ modules
+
+ """
+
+ def __init__(self, module, errormsg, queue=None, children=None):
+ self.queue = queue
+ self.children = children
+ ModuleError.__init__(self, module, errormsg)
+
+class ModuleErrors(Exception):
+ """Exception representing a list of VisTrails module runtime errors.
+ This exception is recognized by the interpreter and allows meaningful
+ error reporting to the user and to the logging mechanism."""
+ def __init__(self, module_errors):
+ """ModuleErrors should be passed a list of ModuleError objects"""
+ Exception.__init__(self, str(tuple(me.msg for me in module_errors)))
+ self.module_errors = module_errors
+
+class _InvalidOutput(object):
+ """ Specify an invalid result
+ """
+ pass
+
+InvalidOutput = _InvalidOutput
+
+################################################################################
+# DummyModuleLogging
+
+class DummyModuleLogging(object):
+ def end_update(self, *args, **kwargs): pass
+ def begin_update(self, *args, **kwargs): pass
+ def begin_compute(self, *args, **kwargs): pass
+ def update_cached(self, *args, **kwargs): pass
+ def signalSuccess(self, *args, **kwargs): pass
+ def annotate(self, *args, **kwargs): pass
+
+_dummy_logging = DummyModuleLogging()
+
+################################################################################
+# Serializable
+
+class Serializable(object):
+ """
+ Serializable is a mixin class used to define methods to serialize and
+ deserialize modules.
+ """
+
+ def serialize(self):
+ """
+ Method used to serialize a module.
+ """
+ raise NotImplementedError('The serialize method is not defined for this module.')
+
+ def deserialize(self):
+ """
+ Method used to deserialize a module.
+ """
+ raise NotImplementedError('The deserialize method is not defined for this module.')
+
+################################################################################
+# Module
+
+class Module(Serializable):
+
+ """Module is the base module from which all module functionality
+is derived from in VisTrails. It defines a set of basic interfaces to
+deal with data input/output (through ports, as will be explained
+later), as well as a basic mechanism for dataflow based updates.
+
+Execution Model
+
+ VisTrails assumes fundamentally that a pipeline is a dataflow. This
+ means that pipeline cycles are disallowed, and that modules are
+ supposed to be free of side-effects. This is obviously not possible
+ in general, particularly for modules whose sole purpose is to
+ interact with operating system resources. In these cases, designing
+ a module is harder -- the side effects should ideally not be exposed
+ to the module interface. VisTrails provides some support for making
+ this easier, as will be discussed later.
+
+ VisTrails caches intermediate results to increase efficiency in
+ exploration. It does so by reusing pieces of pipelines in later
+ executions.
+
+Terminology
+
+ Module Interface: The module interface is the set of input and
+ output ports a module exposes.
+
+Designing New Modules
+
+ Designing new modules is essentially a matter of subclassing this
+ module class and overriding the compute() method. There is a
+ fully-documented example of this on the default package
+ 'pythonCalc', available on the 'packages/pythonCalc' directory.
+
+ Caching
+
+ Caching affects the design of a new module. Most importantly,
+ users have to account for compute() being called more than
+ once. Even though compute() is only called once per individual
+ execution, new connections might mean that previously uncomputed
+ output must be made available.
+
+ Also, operating system side-effects must be carefully accounted
+ for. Some operations are fundamentally side-effectful (creating OS
+ output like uploading a file on the WWW or writing a file to a
+ local hard drive). These modules should probably not be cached at
+ all. VisTrails provides an easy way for modules to report that
+ they should not be cached: simply subclass from the NotCacheable
+ mixin provided in this python module. (NB: In order for the mixin
+ to work appropriately, NotCacheable must appear *BEFORE* any other
+ subclass in the class hierarchy declarations). These modules (and
+ anything that depends on their results) will then never be reused.
+
+
+ Intermediate Files
+
+ Many modules communicate through intermediate files. VisTrails
+ provides automatic filename and handle management to alleviate the
+ burden of determining tricky things (e.g. longevity) of these
+ files. Modules can request temporary file names through the file pool,
+ currently accessible through
+
+ self.interpreter.filePool
+
+ The FilePool class is available in core/modules/module_utils.py -
+ consult its documentation for usage. Notably, using the file pool
+ will make temporary files work correctly with caching, and will
+ make sure the temporaries are correctly removed.
+
+
+
+"""
+
+ def __init__(self):
+ self.inputPorts = {}
+ self.outputPorts = {}
+ self.upToDate = False
+ self.had_error = False
+ self.was_suspended = False
+ self.setResult("self", self) # every object can return itself
+ self.logging = _dummy_logging
+
+ # isMethod stores whether a certain input port is a method.
+ # If so, isMethod maps the port to the order in which it is
+ # stored. This is so that modules that need to know about the
+ # method order can work correctly
+ self.is_method = Bidict()
+ self._latest_method_order = 0
+
+ # Pipeline info that a module should know about This is useful
+ # for a spreadsheet cell to know where it is from. It will be
+ # also used for talking back and forth between the spreadsheet
+ # and the builder besides Parameter Exploration.
+ self.moduleInfo = {
+ 'locator': None,
+ 'controller': None,
+ 'vistrailName': 'Unknown',
+ 'version': -1,
+ 'pipeline': None,
+ 'moduleId': -1,
+ 'reason': 'Pipeline Execution',
+ 'actions': []
+ }
+
+ self.is_breakpoint = False
+
+ # is_looping stores wether the module is a part of a loop
+ self.is_looping = False
+
+ # is_looping_module stores whether the module is a looping module
+ self.is_looping_module = False
+
+ # computed stores wether the module was computed
+ # used for the logging stuff
+ self.computed = False
+
+ self.suspended = False
+
+ self.signature = None
+
+ # stores whether the output of the module should be annotated in the
+ # execution log
+ self.annotate_output = False
+
+ def __copy__(self):
+ """Makes a copy of the input/output ports on shallow copy.
+ """
+ s = super(Module, self)
+ if hasattr(s, '__copy__'):
+ clone = s.__copy__()
+ else:
+ clone = object.__new__(self.__class__)
+ clone.__dict__ = self.__dict__.copy()
+ clone.inputPorts = copy.copy(self.inputPorts)
+ clone.outputPorts = copy.copy(self.outputPorts)
+ clone.outputPorts['self'] = clone
+ return clone
+
+ def clear(self):
+ """clear(self) -> None. Removes all references, prepares for
+deletion."""
+ for connector_list in self.inputPorts.itervalues():
+ for connector in connector_list:
+ connector.clear()
+ self.inputPorts = {}
+ self.outputPorts = {}
+ self.logging = _dummy_logging
+ self.is_method = Bidict()
+ self._latest_method_order = 0
+
+ def is_cacheable(self):
+ """is_cacheable() -> bool. A Module should return whether it
+can be reused across executions. It is safe for a Module to return
+different values in different occasions. In other words, it is
+possible for modules to be cacheable depending on their execution
+context."""
+ return True
+
+ def updateUpstreamPort(self, port):
+ # update single port
+ if port in self.inputPorts:
+ for connector in self.inputPorts[port]:
+ connector.obj.update()
+ if hasattr(connector.obj, 'suspended') and \
+ connector.obj.suspended:
+ self.suspended = connector.obj.suspended
+ for connector in copy.copy(self.inputPorts[port]):
+ if connector.obj.get_output(connector.port) is InvalidOutput:
+ self.removeInputConnector(port, connector)
+
+ def updateUpstream(self):
+ """ updateUpstream() -> None
+ Go upstream from the current module, then update its upstream
+ modules and check input connection based on upstream modules
+ results
+
+ """
+ for connectorList in self.inputPorts.itervalues():
+ for connector in connectorList:
+ connector.obj.update()
+ if hasattr(connector.obj, 'suspended') and \
+ connector.obj.suspended:
+ self.suspended = connector.obj.suspended
+ for iport, connectorList in copy.copy(self.inputPorts.items()):
+ for connector in connectorList:
+ if connector.obj.get_output(connector.port) is InvalidOutput:
+ self.removeInputConnector(iport, connector)
+
+ def update(self):
+ """ update() -> None
+ Check if the module is up-to-date then update the
+ modules. Report to the logger if available
+
+ """
+ if self.had_error:
+ raise ModuleHadError(self)
+ elif self.was_suspended:
+ raise ModuleWasSuspended(self)
+ elif self.computed:
+ return
+ self.logging.begin_update(self)
+ self.updateUpstream()
+ if self.suspended:
+ self.had_error = True
+ return
+ if self.upToDate:
+ if not self.computed:
+ self.logging.update_cached(self)
+ self.computed = True
+ return
+ self.had_error = True # Unset later in this method
+ self.logging.begin_compute(self)
+ try:
+ if self.is_breakpoint:
+ raise ModuleBreakpoint(self)
+ self.compute()
+ self.computed = True
+ except ModuleSuspended, e:
+ self.suspended = e.msg
+ self._module_suspended = e
+ self.had_error, self.was_suspended = False, True
+ self.logging.end_update(self, e, was_suspended=True)
+ self.logging.signalSuspended(self)
+ return
+ except ModuleError, me:
+ if hasattr(me.module, 'interpreter'):
+ raise
+ else:
+ msg = "A dynamic module raised an exception: '%s'"
+ msg %= str(me)
+ raise ModuleError(self, msg)
+ except ModuleErrors:
+ raise
+ except KeyboardInterrupt, e:
+ raise ModuleError(self, 'Interrupted by user')
+ except ModuleBreakpoint:
+ raise
+ except Exception, e:
+ import traceback
+ traceback.print_exc()
+ raise ModuleError(self, 'Uncaught exception: "%s"' % str(e))
+ if self.annotate_output:
+ self.annotate_output_values()
+ self.upToDate = True
+ self.had_error = False
+ self.logging.end_update(self)
+ self.logging.signalSuccess(self)
+
+ def checkInputPort(self, name):
+ """checkInputPort(name) -> None.
+Makes sure input port 'name' is filled."""
+ if not self.hasInputFromPort(name):
+ raise ModuleError(self, "'%s' is a mandatory port" % name)
+
+ def compute(self):
+ pass
+
+ def setResult(self, port, value):
+ self.outputPorts[port] = value
+
+ def annotate_output_values(self):
+ output_values = []
+ for port in self.outputPorts:
+ output_values.append((port, self.outputPorts[port]))
+ self.logging.annotate(self, {'output': output_values})
+
+ def get_output(self, port):
+ # if self.outputPorts.has_key(port) or not self.outputPorts[port]:
+ if port not in self.outputPorts:
+ raise ModuleError(self, "output port '%s' not found" % port)
+ return self.outputPorts[port]
+
+ def getInputConnector(self, inputPort):
+ if not self.inputPorts.has_key(inputPort):
+ raise ModuleError(self, "Missing value from port %s" % inputPort)
+ return self.inputPorts[inputPort][0]
+
+ def getDefaultValue(self, inputPort):
+ reg = self.registry
+
+ d = None
+ try:
+ d = reg.get_descriptor(self.__class__)
+ except:
+ pass
+ if not d:
+ return None
+
+ ps = None
+ try:
+ ps = reg.get_port_spec_from_descriptor(d, inputPort, 'input')
+ except:
+ pass
+ if not ps:
+ return None
+
+ if len(ps.port_spec_items) == 1:
+ psi = ps.port_spec_items[0]
+ if psi.default is not None:
+ m_klass = psi.descriptor.module
+ return m_klass.translate_to_python(psi.default)
+ else:
+ default_val = []
+ default_valid = True
+ for psi in ps.port_spec_items:
+ if psi.default is None:
+ default_valid = False
+ break
+ m_klass = psi.descriptor.module
+ default_val.append(
+ m_klass.translate_to_python(psi.default))
+ if default_valid:
+ return tuple(default_val)
+
+ return None
+
+ def getInputFromPort(self, inputPort, allowDefault=True):
+ if inputPort not in self.inputPorts:
+ if allowDefault and self.registry:
+ defaultValue = self.getDefaultValue(inputPort)
+ if defaultValue is not None:
+ return defaultValue
+ raise ModuleError(self, "Missing value from port %s" % inputPort)
+ # Cannot resolve circular reference here, need to be fixed later
+ from vistrails.core.modules.sub_module import InputPort
+ for conn in self.inputPorts[inputPort]:
+ if isinstance(conn.obj, InputPort):
+ return conn()
+ return self.inputPorts[inputPort][0]()
+
+ def hasInputFromPort(self, inputPort):
+ return self.inputPorts.has_key(inputPort)
+
+ def __str__(self):
+ return "<<%s>>" % str(self.__class__)
+
+ def annotate(self, d):
+ self.logging.annotate(self, d)
+
+ def forceGetInputFromPort(self, inputPort, defaultValue=None):
+ if self.hasInputFromPort(inputPort):
+ return self.getInputFromPort(inputPort)
+ else:
+ return defaultValue
+
+ def set_input_port(self, inputPort, conn, is_method=False):
+ if self.inputPorts.has_key(inputPort):
+ self.inputPorts[inputPort].append(conn)
+ else:
+ self.inputPorts[inputPort] = [conn]
+ if is_method:
+ self.is_method[conn] = (self._latest_method_order, inputPort)
+ self._latest_method_order += 1
+
+ def getInputListFromPort(self, inputPort):
+ if not self.inputPorts.has_key(inputPort):
+ raise ModuleError(self, "Missing value from port %s" % inputPort)
+ # Cannot resolve circular reference here, need to be fixed later
+ from vistrails.core.modules.sub_module import InputPort
+ fromInputPortModule = [connector()
+ for connector in self.inputPorts[inputPort]
+ if isinstance(connector.obj, InputPort)]
+ if len(fromInputPortModule)>0:
+ return fromInputPortModule
+ return [connector() for connector in self.inputPorts[inputPort]]
+
+ def forceGetInputListFromPort(self, inputPort):
+ if not self.inputPorts.has_key(inputPort):
+ return []
+ return self.getInputListFromPort(inputPort)
+
+ def enableOutputPort(self, outputPort):
+ """ enableOutputPort(outputPort: str) -> None
+ Set an output port to be active to store result of computation
+
+ """
+ # Don't reset existing values, it screws up the caching.
+ if not self.outputPorts.has_key(outputPort):
+ self.setResult(outputPort, None)
+
+ def removeInputConnector(self, inputPort, connector):
+ """ removeInputConnector(inputPort: str,
+ connector: ModuleConnector) -> None
+ Remove a connector from the connection list of an input port
+
+ """
+ if self.inputPorts.has_key(inputPort):
+ conList = self.inputPorts[inputPort]
+ if connector in conList:
+ conList.remove(connector)
+ if conList==[]:
+ del self.inputPorts[inputPort]
+
+ def create_instance_of_type(self, ident, name, ns=''):
+ """ Create a vistrails module from the module registry. This creates an instance of the module
+ for use in creating the object output by a Module.
+ """
+ from vistrails.core.modules.module_registry import get_module_registry
+ try:
+ reg = get_module_registry()
+ m = reg.get_module_by_name(ident, name, ns)
+ return m()
+ except:
+ msg = "Cannot get module named " + str(name) + \
+ " with identifier " + str(ident) + " and namespace " + ns
+ raise ModuleError(self, msg)
+
+ @classmethod
+ def provide_input_port_documentation(cls, port_name):
+ return None
+
+ @classmethod
+ def provide_output_port_documentation(cls, port_name):
+ return None
+
+################################################################################
+
+class NotCacheable(object):
+
+ def is_cacheable(self):
+ return False
+
+################################################################################
+
+class Converter(Module):
+ """Base class for automatic conversion modules.
+
+ Modules that subclass Converter will be inserted automatically when
+ connecting incompatible ports, if possible.
+
+ You must override the 'in_value' and 'out_value' ports by providing the
+ types your module actually matches.
+
+ Alternatively, you can override the classmethod can_convert() to provide
+ a custom condition.
+ """
+ @classmethod
+ def can_convert(cls, sub_descs, super_descs):
+ from vistrails.core.modules.module_registry import get_module_registry
+ from vistrails.core.system import get_vistrails_basic_pkg_id
+ reg = get_module_registry()
+ basic_pkg = get_vistrails_basic_pkg_id()
+ variant_desc = reg.get_descriptor_by_name(basic_pkg, 'Variant')
+ desc = reg.get_descriptor(cls)
+
+ def check_types(sub_descs, super_descs):
+ for (sub_desc, super_desc) in izip(sub_descs, super_descs):
+ if (sub_desc == variant_desc or super_desc == variant_desc):
+ continue
+ if not reg.is_descriptor_subclass(sub_desc, super_desc):
+ return False
+ return True
+
+ in_port = reg.get_port_spec_from_descriptor(
+ desc,
+ 'in_value', 'input')
+ if (len(sub_descs) != len(in_port.descriptors()) or
+ not check_types(sub_descs, in_port.descriptors())):
+ return False
+ out_port = reg.get_port_spec_from_descriptor(
+ desc,
+ 'out_value', 'output')
+ if (len(out_port.descriptors()) != len(super_descs)
+ or not check_types(out_port.descriptors(), super_descs)):
+ return False
+
+ return True
+
+ def compute(self):
+ raise NotImplementedError
+
+################################################################################
+
+class ModuleConnector(object):
+ def __init__(self, obj, port, spec=None, typecheck=None):
+ # typecheck is a list of booleans indicating which descriptors to
+ # typecheck
+ self.obj = obj
+ self.port = port
+ self.spec = spec
+ self.typecheck = typecheck
+
+ def clear(self):
+ """clear() -> None. Removes references, prepares for deletion."""
+ self.obj = None
+ self.port = None
+
+ def __call__(self):
+ result = self.obj.get_output(self.port)
+ if self.spec is not None and self.typecheck is not None:
+ descs = self.spec.descriptors()
+ typecheck = self.typecheck
+ if len(descs) == 1:
+ if not typecheck[0]:
+ return result
+ mod = descs[0].module
+ if hasattr(mod, 'validate') and not mod.validate(result):
+ raise ModuleError(self.obj, "Type passed on Variant port "
+ "%s does not match destination type "
+ "%s" % (self.port, descs[0].name))
+ else:
+ if len(typecheck) == 1:
+ if typecheck[0]:
+ typecheck = [True] * len(descs)
+ else:
+ return result
+ if not isinstance(result, tuple):
+ raise ModuleError(self.obj, "Type passed on Variant port "
+ "%s is not a tuple" % self.port)
+ elif len(result) != len(descs):
+ raise ModuleError(self.obj, "Object passed on Variant "
+ "port %s does not have the correct "
+ "length (%d, expected %d)" % (
+ self.port, len(result), len(descs)))
+ for i, desc in enumerate(descs):
+ if not typecheck[i]:
+ continue
+ mod = desc.module
+ if hasattr(mod, 'validate'):
+ if not mod.validate(result[i]):
+ raise ModuleError(
+ self.obj,
+ "Element %d of tuple passed on Variant "
+ "port %s does not match the destination "
+ "type %s" % (i, self.port, desc.name))
+ return result
+
+def new_module(baseModule, name, dict={}, docstring=None):
+ """new_module(baseModule or [baseModule list],
+ name,
+ dict={},
+ docstring=None
+
+ Creates a new VisTrails module dynamically. Exactly one of the
+ elements of the baseModule list (or baseModule itself, in the case
+ it's a single class) should be a subclass of Module.
+ """
+ if isinstance(baseModule, type):
+ assert issubclass(baseModule, Module)
+ superclasses = (baseModule, )
+ elif isinstance(baseModule, list):
+ assert len([x for x in baseModule
+ if issubclass(x, Module)]) == 1
+ superclasses = tuple(baseModule)
+ d = copy.copy(dict)
+ if docstring:
+ d['__doc__'] = docstring
+ return type(name, superclasses, d)
+
+# This is the gist of how type() works. The example is run from a python
+# toplevel
+
+# >>> class X(object):
+# ... def f(self): return 3
+# ...
+# >>> a = X()
+# >>> a.f()
+# 3
+# >>> Y = type('Y', (X, ), {'g': lambda x : 4})
+# >>> b = Y()
+# >>> b.f()
+# 3
+# >>> b.g()
+# 4
+# >>> Z = type('Z', (X, ), {'f': lambda x : 4} )
+# >>> c = Z()
+# >>> c.f()
+# 4
diff --git a/vistrails/core/packagemanager.py b/vistrails/core/packagemanager.py
new file mode 100644
index 0000000..7a5d87b
--- /dev/null
+++ b/vistrails/core/packagemanager.py
@@ -0,0 +1,932 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""The package manager takes care of everything that has got to do
+with handling packages, from setting paths to adding new packages
+to checking dependencies to initializing them."""
+import copy
+import inspect
+import itertools
+import os
+import sys
+import warnings
+
+from vistrails.core import debug, get_vistrails_application
+from vistrails.core.configuration import ConfigurationObject
+import vistrails.core.data_structures.graph
+import vistrails.core.db.io
+from vistrails.core.modules.module_registry import ModuleRegistry, \
+ MissingPackage, MissingPackageVersion
+from vistrails.core.modules.package import Package
+from vistrails.core.utils import VistrailsInternalError, InstanceObject, \
+ versions_increasing, VistrailsDeprecation
+import vistrails.packages
+##############################################################################
+
+
+global _package_manager
+_package_manager = None
+
+class PackageManager(object):
+ # # add_package_menu_signal is emitted with a tuple containing the package
+ # # identifier, package name and the menu item
+ # add_package_menu_signal = QtCore.SIGNAL("add_package_menu")
+ # # remove_package_menu_signal is emitted with the package identifier
+ # remove_package_menu_signal = QtCore.SIGNAL("remove_package_menu")
+ # # package_error_message_signal is emitted with the package identifier,
+ # # package name and the error message
+ # package_error_message_signal = QtCore.SIGNAL("package_error_message_signal")
+ # # reloading_package_signal is emitted when a package reload has disabled
+ # # the packages, but has not yet enabled them
+ # reloading_package_signal = QtCore.SIGNAL("reloading_package_signal")
+
+ class DependencyCycle(Exception):
+ def __init__(self, p1, p2):
+ self._package_1 = p1
+ self._package_2 = p2
+ def __str__(self):
+ return ("Packages '%s' and '%s' have cyclic dependencies" %
+ (self._package_1,
+ self._package_2))
+
+ class PackageInternalError(Exception):
+ def __init__(self, n, d):
+ self._package_name = n
+ self._description = d
+ def __str__(self):
+ return "Package '%s' has a bug: %s" % (self._package_name,
+ self._description)
+
+ def import_packages_module(self):
+ """Imports the packages module using path trickery to find it
+ in the right place.
+
+ """
+ if self._packages is not None:
+ return self._packages
+ # Imports standard packages directory
+ conf = self._configuration
+ old_sys_path = copy.copy(sys.path)
+ if conf.check('packageDirectory'):
+ sys.path.insert(0, conf.packageDirectory)
+ try:
+ import vistrails.packages
+ except ImportError:
+ debug.critical('ImportError: "packages" sys.path: %s' % sys.path)
+ raise
+ finally:
+ sys.path = old_sys_path
+ self._packages = vistrails.packages
+ return vistrails.packages
+
+ def import_user_packages_module(self):
+ """Imports the packages module using path trickery to find it
+ in the right place.
+
+ """
+ if self._userpackages is not None:
+ return self._userpackages
+ # Imports user packages directory
+ conf = self._configuration
+ old_sys_path = copy.copy(sys.path)
+ if conf.check('userPackageDirectory'):
+ sys.path.insert(0, os.path.join(conf.userPackageDirectory,
+ os.path.pardir))
+ try:
+ import userpackages
+ except ImportError:
+ debug.critical('ImportError: "userpackages" sys.path: %s' % sys.path)
+ raise
+ finally:
+ sys.path = old_sys_path
+ os.environ['VISTRAILS_USERPACKAGES_DIR'] = conf.userPackageDirectory
+ self._userpackages = userpackages
+ return userpackages
+
+ def __init__(self, configuration):
+ """__init__(configuration: ConfigurationObject) -> PackageManager
+ configuration is the persistent configuration object of the application.
+
+ """
+ global _package_manager
+ if _package_manager:
+ m = "Package manager can only be constructed once."
+ raise VistrailsInternalError(m)
+ _package_manager = self
+ self._configuration = configuration
+
+ # Contains packages that have not yet been enabled, but exist on the
+ # filesystem
+ self._available_packages = {} # codepath: str -> Package
+ # These other lists contain enabled packages
+ self._package_list = {} # codepath: str -> Package
+ self._package_versions = {} # identifier: str -> version -> Package
+ self._old_identifier_map = {} # old_id: str -> new_id: str
+ self._dependency_graph = vistrails.core.data_structures.graph.Graph()
+
+ self._registry = None
+ self._userpackages = None
+ self._packages = None
+ self._abstraction_pkg = None
+ self._currently_importing_package = None
+
+ def init_registry(self, registry_filename=None):
+ if registry_filename is not None:
+ self._registry = vistrails.core.db.io.open_registry(registry_filename)
+ self._registry.set_global()
+ else:
+ self._registry = ModuleRegistry()
+ self._registry.set_global()
+
+ def setup_basic_package():
+ # setup basic package
+ basic_package = self.add_package('basic_modules')
+ # FIXME need to serialize old_identifiers
+ basic_package.old_identifiers = ['edu.utah.sci.vistrails.basic']
+ self._registry._default_package = basic_package
+ prefix_dictionary = {'basic_modules': 'vistrails.core.modules.'}
+ self.initialize_packages(prefix_dictionary)
+ setup_basic_package()
+
+ self._abstraction_pkg = self.add_package('abstraction', False)
+ # FIXME need to get this info from the package, but cannot
+ # do this since controller isn't imported yet
+ self._abstraction_pkg.identifier = 'local.abstractions'
+ self._abstraction_pkg.name = 'My SubWorkflows'
+ self._abstraction_pkg.version = '1.6'
+ self._registry.add_package(self._abstraction_pkg)
+
+ # Setup a global __import__ hook that calls Package#import_override()
+ # for all imports executed from that package
+ import __builtin__
+ self._orig_import = __builtin__.__import__
+ __builtin__.__import__ = self._import_override
+
+ def _import_override(self,
+ name, globals={}, locals={}, fromlist=[], level=-1):
+ # Get the caller module, using globals (like the original __import
+ # does)
+ try:
+ if globals is None:
+ raise KeyError
+ module = globals['__name__']
+ except KeyError:
+ # Another method of getting the caller module, using the stack
+ caller = inspect.currentframe().f_back
+ module = inspect.getmodule(caller)
+ # Some frames might not be associated to a module, because of the
+ # use of exec for instance; we just skip these until we reach a
+ # valid one
+ while module is None:
+ caller = caller.f_back
+ if caller is None:
+ break
+ module = inspect.getmodule(caller)
+ if module:
+ module = module.__name__
+
+ # Get the Package from the module name
+ if module:
+ importing_pkg = None
+ current = self._currently_importing_package
+ if (current is not None and
+ current.prefix and
+ module.startswith(current.prefix + current.codepath)):
+ importing_pkg = current
+ else:
+ for pkg in itertools.chain(
+ self._package_list.itervalues(),
+ self._available_packages.itervalues()):
+ if (pkg.prefix is not None and
+ module.startswith(pkg.prefix + pkg.codepath)):
+ importing_pkg = pkg
+ break
+
+ # If we are importing directly from a package
+ if importing_pkg is not None:
+ old_current = self._currently_importing_package
+ self._currently_importing_package = importing_pkg
+ result = importing_pkg.import_override(
+ self._orig_import,
+ name, globals, locals, fromlist, level,
+ package_importing_directly=True)
+ self._currently_importing_package = old_current
+ return result
+ # If we are doing it indirectly (from other stuff imported from a
+ # package)
+ elif self._currently_importing_package is not None:
+ return self._currently_importing_package.import_override(
+ self._orig_import,
+ name, globals, locals, fromlist, level,
+ package_importing_directly=False)
+
+ # Else, this is not from a package
+ return self._orig_import(name, globals, locals, fromlist, level)
+
+ def finalize_packages(self):
+ """Finalizes all installed packages. Call this only prior to
+exiting VisTrails."""
+ for package in self._package_list.itervalues():
+ package.finalize()
+ self._package_list = {}
+ self._package_versions = {}
+ self._old_identifier_map = {}
+ global _package_manager
+ _package_manager = None
+
+ def get_available_package(self, codepath):
+ try:
+ pkg = self._available_packages[codepath]
+ except KeyError:
+ pkg = self._registry.create_package(codepath)
+ self._available_packages[codepath] = pkg
+ return pkg
+
+ def add_package(self, codepath, add_to_package_list=True):
+ """Adds a new package to the manager. This does not initialize it.
+To do so, call initialize_packages()"""
+ package = self.get_available_package(codepath)
+ if add_to_package_list:
+ self.add_to_package_list(codepath, package)
+ return package
+
+ def add_to_package_list(self, codepath, package):
+ self._available_packages[codepath] = package
+ self._package_list[codepath] = package
+
+ def initialize_abstraction_pkg(self, prefix_dictionary):
+ if self._abstraction_pkg is None:
+ raise RuntimeError("Subworkflows packages is None")
+ self.add_to_package_list(self._abstraction_pkg.codepath,
+ self._abstraction_pkg)
+ self.late_enable_package(self._abstraction_pkg.codepath,
+ prefix_dictionary, False)
+
+ def remove_old_identifiers(self, identifier):
+ # remove refs in old_identifier_map
+ old_ids = []
+ for old_id, cur_id in self._old_identifier_map.iteritems():
+ if cur_id == identifier:
+ old_ids.append(old_id)
+ for old_id in old_ids:
+ del self._old_identifier_map[old_id]
+
+ def remove_package(self, codepath):
+ """remove_package(name): Removes a package from the system."""
+ pkg = self._package_list[codepath]
+
+ from vistrails.core.interpreter.cached import CachedInterpreter
+ CachedInterpreter.clear_package(pkg.identifier)
+
+ self._dependency_graph.delete_vertex(pkg.identifier)
+ del self._package_versions[pkg.identifier][pkg.version]
+ if len(self._package_versions[pkg.identifier]) == 0:
+ del self._package_versions[pkg.identifier]
+ self.remove_old_identifiers(pkg.identifier)
+ self.remove_menu_items(pkg)
+ pkg.finalize()
+ del self._package_list[codepath]
+ self._registry.remove_package(pkg)
+ app = get_vistrails_application()
+ app.send_notification("package_removed", codepath)
+
+ def has_package(self, identifier, version=None):
+ """has_package(identifer: string) -> Boolean.
+Returns true if given package identifier is present."""
+
+ # check if it's an old identifier
+ identifier = self._old_identifier_map.get(identifier, identifier)
+ if identifier in self._package_versions:
+ return (version is None or
+ version in self._package_versions[identifier])
+ return False
+
+ def look_at_available_package(self, codepath):
+ """look_at_available_package(codepath: string) -> Package
+
+ Returns a Package object for an uninstalled package. This does
+ NOT install a package.
+ """
+ return self.get_available_package(codepath)
+
+ def get_package(self, identifier, version=None):
+ # check if it's an old identifier
+ identifier = self._old_identifier_map.get(identifier, identifier)
+ try:
+ package_versions = self._package_versions[identifier]
+ if version is not None:
+ return package_versions[version]
+ except KeyError:
+ # dynamic packages are only registered in the registry
+ try:
+ return self._registry.get_package_by_name(identifier, version)
+ except MissingPackageVersion:
+ return self._registry.get_package_by_name(identifier)
+
+
+ max_version = '0'
+ max_pkg = None
+ for version, pkg in package_versions.iteritems():
+ if versions_increasing(max_version, version):
+ max_version = version
+ max_pkg = pkg
+ return max_pkg
+
+ def get_package_by_codepath(self, codepath):
+ """get_package_by_codepath(codepath: string) -> Package.
+ Returns a package with given codepath if it is enabled,
+ otherwise throws exception
+ """
+ if codepath not in self._package_list:
+ raise MissingPackage(codepath)
+ else:
+ return self._package_list[codepath]
+
+ def get_package_by_identifier(self, identifier):
+ """get_package_by_identifier(identifier: string) -> Package.
+ Deprecated, use get_package() instead.
+ """
+ warnings.warn(
+ "You should use get_package instead of "
+ "get_package_by_identifier",
+ VistrailsDeprecation,
+ stacklevel=2)
+ return self.get_package(identifier)
+
+ def get_package_configuration(self, codepath):
+ """get_package_configuration(codepath: string) ->
+ ConfigurationObject or None
+
+ Returns the configuration object for the package, if existing,
+ or None. Throws MissingPackage if package doesn't exist.
+ """
+
+ pkg = self.get_package_by_codepath(codepath)
+
+ if not hasattr(pkg.module, 'configuration'):
+ return None
+ else:
+ c = pkg.module.configuration
+ if not isinstance(c, ConfigurationObject):
+ d = "'configuration' attribute should be a ConfigurationObject"
+ raise self.PackageInternalError(codepath, d)
+ return c
+
+ def check_dependencies(self, package, deps):
+ # want to check that necessary version also exists, if specified
+ missing_deps = []
+ for dep in deps:
+ min_version = None
+ max_version = None
+ if isinstance(dep, tuple):
+ identifier = dep[0]
+ if len(dep) > 1:
+ min_version = dep[1]
+ if len(dep) > 2:
+ max_version = dep[2]
+ else:
+ identifier = dep
+
+ # check if it's an old identifier
+ identifier = self._old_identifier_map.get(identifier, identifier)
+ if identifier not in self._package_versions:
+ missing_deps.append((identifier, None, None))
+ else:
+ if min_version is None and max_version is None:
+ continue
+ found_version = False
+ for version, pkg in \
+ self._package_versions[identifier].iteritems():
+ if ((min_version is None or
+ versions_increasing(min_version, version)) and
+ (max_version is None or
+ versions_increasing(version, max_version))):
+ found_version = True
+ if not found_version:
+ missing_deps.append((identifier, min_version, max_version))
+
+ if len(missing_deps) > 0:
+ raise Package.MissingDependency(package, missing_deps)
+ return True
+
+ def add_dependencies(self, package):
+ """add_dependencies(package) -> None. Register all
+ dependencies a package contains by calling the appropriate
+ callback.
+
+ Does not add multiple dependencies - if a dependency is already there,
+ add_dependencies ignores it.
+ """
+ deps = package.dependencies()
+ # FIXME don't hardcode this
+ from vistrails.core.modules.basic_modules import identifier as basic_pkg
+ if package.identifier != basic_pkg:
+ deps.append(basic_pkg)
+
+ self.check_dependencies(package, deps)
+
+ for dep in deps:
+ if isinstance(dep, tuple):
+ dep_name = dep[0]
+ else:
+ dep_name = dep
+ dep_name = self.get_package(dep_name).identifier
+
+ if not self._dependency_graph.has_edge(package.identifier,
+ dep_name):
+ self._dependency_graph.add_edge(package.identifier, dep_name)
+
+ def late_enable_package(self, codepath, prefix_dictionary={},
+ needs_add=True):
+ """late_enable_package enables a package 'late', that is,
+ after VisTrails initialization. All dependencies need to be
+ already enabled.
+ """
+ if needs_add:
+ if codepath in self._package_list:
+ msg = 'duplicate package identifier: %s' % codepath
+ raise VistrailsInternalError(msg)
+ self.add_package(codepath)
+ pkg = self.get_package_by_codepath(codepath)
+ try:
+ pkg.load(prefix_dictionary.get(pkg.codepath, None))
+ pkg.create_startup_package_node()
+ except Exception, e:
+ # invert self.add_package
+ del self._package_list[codepath]
+ raise
+ self._dependency_graph.add_vertex(pkg.identifier)
+ if pkg.identifier not in self._package_versions:
+ self._package_versions[pkg.identifier] = {}
+ self._package_versions[pkg.identifier][pkg.version] = pkg
+ for old_id in pkg.old_identifiers:
+ self._old_identifier_map[old_id] = pkg.identifier
+ try:
+ self.add_dependencies(pkg)
+ #check_requirements is now called in pkg.initialize()
+ #pkg.check_requirements()
+ self._registry.initialize_package(pkg)
+ self._registry.signals.emit_new_package(pkg.identifier, True)
+ app = get_vistrails_application()
+ app.send_notification("package_added", codepath)
+ self.add_menu_items(pkg)
+ except Exception, e:
+ del self._package_versions[pkg.identifier][pkg.version]
+ if len(self._package_versions[pkg.identifier]) == 0:
+ del self._package_versions[pkg.identifier]
+ self.remove_old_identifiers(pkg.identifier)
+ self._dependency_graph.delete_vertex(pkg.identifier)
+ # invert self.add_package
+ del self._package_list[codepath]
+ # if we adding the package to the registry, make sure we
+ # remove it if initialization fails
+ try:
+ self._registry.remove_package(pkg)
+ except MissingPackage:
+ pass
+ raise e
+
+ def late_disable_package(self, codepath):
+ """late_disable_package disables a package 'late', that is,
+ after VisTrails initialization. All reverse dependencies need to be
+ already disabled.
+ """
+ pkg = self.get_package_by_codepath(codepath)
+ self.remove_package(codepath)
+ pkg.remove_own_dom_element()
+
+ def reload_package_disable(self, codepath):
+ # for all reverse dependencies, disable them
+ prefix_dictionary = {}
+ pkg = self.get_package_by_codepath(codepath)
+ reverse_deps = []
+ for dep_id in self.all_reverse_dependencies(pkg.identifier):
+ reverse_deps.append(self.get_package(dep_id))
+
+ for dep_pkg in reverse_deps:
+ prefix_dictionary[dep_pkg.codepath] = dep_pkg.prefix
+ self.late_disable_package(dep_pkg.codepath)
+
+ # Queue the re-enabling of the packages so event loop can free
+ # any QObjects whose deleteLater() method is invoked
+ app = get_vistrails_application()
+ app.send_notification("pm_reloading_package", codepath,
+ reverse_deps, prefix_dictionary)
+ # self.emit(self.reloading_package_signal,
+ # codepath,
+ # reverse_deps,
+ # prefix_dictionary)
+
+ def reload_package_enable(self, reverse_deps, prefix_dictionary):
+ # for all reverse dependencies, enable them
+ for dep_pkg in reversed(reverse_deps):
+ self.late_enable_package(dep_pkg.codepath, prefix_dictionary)
+
+ def initialize_packages(self,prefix_dictionary={}):
+ """initialize_packages(prefix_dictionary={}): None
+
+ Initializes all installed packages. If prefix_dictionary is
+ not {}, then it should be a dictionary from package names to
+ the prefix such that prefix + package_name is a valid python
+ import."""
+
+ packages = self.import_packages_module()
+ userpackages = self.import_user_packages_module()
+
+ failed = []
+ # import the modules
+ for package in self._package_list.itervalues():
+ # print '+ initializing', package.codepath, id(package)
+ if package.initialized():
+ # print '- already initialized'
+ continue
+ try:
+ package.load(prefix_dictionary.get(package.codepath, None))
+ except Package.LoadFailed, e:
+ debug.critical("Package %s failed to load and will be "
+ "disabled" % package.name, str(e))
+ # We disable the package manually to skip over things
+ # we know will not be necessary - the only thing needed is
+ # the reference in the package list
+ package.remove_own_dom_element()
+ failed.append(package)
+ except Package.InitializationFailed, e:
+ debug.critical("Initialization of package <codepath %s> "
+ "failed and will be disabled" % \
+ package.codepath, str(e))
+ # We disable the package manually to skip over things
+ # we know will not be necessary - the only thing needed is
+ # the reference in the package list
+ package.remove_own_dom_element()
+ failed.append(package)
+ else:
+ if package.identifier not in self._package_versions:
+ self._package_versions[package.identifier] = {}
+ self._dependency_graph.add_vertex(package.identifier)
+ elif package.version in \
+ self._package_versions[package.identifier]:
+ raise VistrailsInternalError("Duplicate package version: "
+ "'%s' (version %s) in %s" % \
+ (package.identifier,
+ package.version,
+ package.codepath))
+ else:
+ debug.warning('Duplicate package identifier: %s' % \
+ package.identifier)
+ self._package_versions[package.identifier][package.version] = \
+ package
+ for old_id in package.old_identifiers:
+ self._old_identifier_map[old_id] = package.identifier
+
+ for pkg in failed:
+ del self._package_list[pkg.codepath]
+ failed = []
+
+ # determine dependencies
+ for package in self._package_list.itervalues():
+ try:
+ self.add_dependencies(package)
+ except Package.MissingDependency, e:
+ debug.critical("Dependencies of package %s are missing "
+ "so it will be disabled" % package.name, str(e))
+ except Exception, e:
+ debug.critical("Got an exception while getting dependencies "
+ "of %s so it will be disabled" % package.name,
+ str(e))
+ else:
+ continue
+ package.remove_own_dom_element()
+ self._dependency_graph.delete_vertex(package.identifier)
+ del self._package_versions[package.identifier][package.version]
+ if len(self._package_versions[package.identifier]) == 0:
+ del self._package_versions[package.identifier]
+ self.remove_old_identifiers(package.identifier)
+ failed.append(package)
+
+ for pkg in failed:
+ del self._package_list[pkg.codepath]
+
+ # perform actual initialization
+ try:
+ g = self._dependency_graph.inverse_immutable()
+ sorted_packages = g.vertices_topological_sort()
+ except vistrails.core.data_structures.graph.Graph.GraphContainsCycles, e:
+ raise self.DependencyCycle(e.back_edge[0],
+ e.back_edge[1])
+
+ for name in sorted_packages:
+ pkg = self.get_package(name)
+ if not pkg.initialized():
+ #check_requirements is now called in pkg.initialize()
+ #pkg.check_requirements()
+ try:
+ self._registry.initialize_package(pkg)
+ except Package.InitializationFailed, e:
+ debug.critical("Initialization of package <codepath %s> "
+ "failed and will be disabled" % \
+ pkg.codepath, str(e))
+ # We disable the package manually to skip over things
+ # we know will not be necessary - the only thing needed is
+ # the reference in the package list
+ self.late_disable_package(pkg.codepath)
+# pkg.remove_own_dom_element()
+# failed.append(package)
+ else:
+ self.add_menu_items(pkg)
+ app = get_vistrails_application()
+ app.send_notification("package_added", pkg.codepath)
+
+
+ def add_menu_items(self, pkg):
+ """add_menu_items(pkg: Package) -> None
+ If the package implemented the function menu_items(),
+ the package manager will emit a signal with the menu items to
+ be added to the builder window """
+ items = pkg.menu_items()
+ if items:
+ app = get_vistrails_application()
+ app.send_notification("pm_add_package_menu", pkg.identifier,
+ pkg.name, items)
+ # self.emit(self.add_package_menu_signal,
+ # pkg.identifier,
+ # pkg.name,
+ # items)
+
+ def remove_menu_items(self, pkg):
+ """remove_menu_items(pkg: Package) -> None
+ Send a signal with the pkg identifier. The builder window should
+ catch this signal and remove the package menu items"""
+ if pkg.menu_items():
+ app = get_vistrails_application()
+ app.send_notification("pm_remove_package_menu",
+ pkg.identifier)
+ # self.emit(self.remove_package_menu_signal,
+ # pkg.identifier)
+
+ def show_error_message(self, pkg, msg):
+ """show_error_message(pkg: Package, msg: str) -> None
+ Print a message to standard error output and emit a signal to the
+ builder so if it is possible, a message box is also shown """
+
+ debug.critical("Package %s (%s) says: %s"%(pkg.name,
+ pkg.identifier,
+ msg))
+ app = get_vistrails_application()
+ app.send_notification("pm_package_error_message", pkg.identifier,
+ pkg.name, msg)
+ # self.emit(self.package_error_message_signal,
+ # pkg.identifier,
+ # pkg.name,
+ # msg)
+
+ def enabled_package_list(self):
+ """package_list() -> returns list of all enabled packages."""
+ return self._package_list.values()
+
+ def identifier_is_available(self, identifier):
+ """identifier_is_available(identifier: str) -> Pkg
+
+ returns true if there exists a package with the given
+ identifier in the list of available (ie, disabled) packages.
+
+ If true, returns succesfully loaded, uninitialized package."""
+ for codepath in self.available_package_names_list():
+ pkg = self.get_available_package(codepath)
+ try:
+ pkg.load()
+ if pkg.identifier == identifier:
+ return pkg
+ elif identifier in pkg.old_identifiers:
+ return pkg
+ if (hasattr(pkg._module, "can_handle_identifier") and
+ pkg._module.can_handle_identifier(identifier)):
+ return pkg
+ except pkg.LoadFailed:
+ pass
+ except pkg.InitializationFailed:
+ pass
+ except Exception, e:
+ pass
+ return None
+
+ def available_package_names_list(self):
+ """available_package_names_list() -> returns list with code-paths of all
+ available packages, by looking at the appropriate directories.
+
+ The distinction between package names, identifiers and
+ code-paths is described in doc/package_system.txt
+ """
+
+ pkg_name_set = set()
+
+ def is_vistrails_package(path):
+ return ((path.endswith('.py') and
+ not path.endswith('__init__.py') and
+ os.path.isfile(path)) or
+ os.path.isdir(path) and \
+ os.path.isfile(os.path.join(path, '__init__.py')))
+
+ def search(dirname):
+ for name in os.listdir(dirname):
+ if is_vistrails_package(os.path.join(dirname, name)):
+ if name.endswith('.py'):
+ name = name[:-3]
+ pkg_name_set.add(name)
+
+ # Finds standard packages
+ packages = self.import_packages_module()
+ search(os.path.dirname(packages.__file__))
+ userpackages = self.import_user_packages_module()
+ search(os.path.dirname(userpackages.__file__))
+
+ pkg_name_set.update(self._package_list)
+ return list(pkg_name_set)
+
+ def dependency_graph(self):
+ """dependency_graph() -> Graph. Returns a graph with package
+ dependencies, where u -> v if u depends on v. Vertices are
+ strings representing package names."""
+ return self._dependency_graph
+
+ def can_be_disabled(self, identifier):
+ """Returns whether has no reverse dependencies (other
+ packages that depend on it."""
+ return self._dependency_graph.in_degree(identifier) == 0
+
+ def reverse_dependencies(self, identifier):
+ lst = [x[0] for x in
+ self._dependency_graph.inverse_adjacency_list[identifier]]
+ return lst
+
+ # use this call if we're not necessarily loading
+ def build_dependency_graph(self, pkg_identifiers):
+ dep_graph = vistrails.core.data_structures.graph.Graph()
+
+ def process_dependencies(identifier):
+ dep_graph.add_vertex(identifier)
+ pkg = self.identifier_is_available(identifier)
+ if pkg:
+ deps = pkg.dependencies()
+ for dep in deps:
+ if isinstance(dep, tuple):
+ dep_name = dep[0]
+ else:
+ dep_name = dep
+
+ if dep_name not in self._dependency_graph.vertices and \
+ not dep_graph.has_edge(identifier, dep_name):
+ dep_graph.add_edge(identifier, dep_name)
+ process_dependencies(dep_name)
+
+ for pkg_identifier in pkg_identifiers:
+ process_dependencies(pkg_identifier)
+
+ return dep_graph
+
+ def get_ordered_dependencies(self, dep_graph, identifiers=None):
+ try:
+ sorted_packages = dep_graph.vertices_topological_sort(identifiers)
+ except vistrails.core.data_structures.graph.Graph.GraphContainsCycles, e:
+ raise self.DependencyCycle(e.back_edge[0],
+ e.back_edge[1])
+ return sorted_packages
+
+ def get_all_dependencies(self, identifier, reverse=False, dep_graph=None):
+ if dep_graph is None:
+ dep_graph = self._dependency_graph
+
+ if reverse:
+ adj_list = dep_graph.inverse_adjacency_list
+ else:
+ adj_list = dep_graph.adjacency_list
+
+ all = [identifier]
+ last_adds = [identifier]
+ while len(last_adds) != 0:
+ adds = [x[0] for y in last_adds for x in adj_list[y]]
+ all.extend(adds)
+ last_adds = adds
+
+ seen = set()
+ order = []
+ for pkg in reversed(all):
+ if pkg not in seen:
+ order.append(pkg)
+ seen.add(pkg)
+ return order
+
+ def all_dependencies(self, identifier, dep_graph=None):
+ return self.get_all_dependencies(identifier, False, dep_graph)
+
+ def all_reverse_dependencies(self, identifier, dep_graph=None):
+ return self.get_all_dependencies(identifier, True, dep_graph)
+
+def get_package_manager():
+ global _package_manager
+ if not _package_manager:
+ raise VistrailsInternalError("package manager not constructed yet.")
+ return _package_manager
+
+##############################################################################
+
+import unittest
+
+
+class TestImports(unittest.TestCase):
+ def test_package(self):
+ # Hacks PackageManager so that it temporarily uses our test package
+ # instead of userpackages
+ pm = get_package_manager()
+ from vistrails.tests.resources import import_pkg
+ def fake_userpkg_mod():
+ pm._userpackages = import_pkg
+ return import_pkg
+ old_userpackages = pm._userpackages
+ old_import_userpackages = pm.import_user_packages_module
+ pm._userpackages = import_pkg
+ pm.import_user_packages_module = fake_userpkg_mod
+
+ old_fix_names = list(Package.FIX_PACKAGE_NAMES)
+ Package.FIX_PACKAGE_NAMES.append('tests.resources.import_targets')
+
+ try:
+ # Check the package is in the list
+ available_pkg_names = pm.available_package_names_list()
+ self.assertIn('test_import_pkg', available_pkg_names)
+
+ # Import __init__ and check metadata
+ pkg = pm.look_at_available_package('test_import_pkg')
+ pkg.load('vistrails.tests.resources.import_pkg.')
+ self.assertEqual(pkg.identifier,
+ 'org.vistrails.tests.test_import_pkg')
+ self.assertEqual(pkg.version,
+ '0.42')
+ for n in ['vistrails.tests.resources.import_targets.test1',
+ 'vistrails.tests.resources.import_targets.test2']:
+ self.assertIn(n, sys.modules)
+
+ # Import init.py
+ pm.late_enable_package(
+ 'test_import_pkg',
+ {'test_import_pkg':
+ 'vistrails.tests.resources.import_pkg.'})
+ pkg = pm.get_package_by_codepath('test_import_pkg')
+ for n in ['vistrails.tests.resources.import_targets.test3',
+ 'vistrails.tests.resources.import_targets.test4',
+ 'vistrails.tests.resources.import_targets.test5']:
+ self.assertIn(n, sys.modules)
+
+ # Check dependencies
+ deps = pkg.get_py_deps()
+ for dep in ['vistrails.tests.resources.import_pkg.test_import_pkg',
+ 'vistrails.tests.resources.import_pkg.test_import_pkg.init',
+ 'vistrails.tests.resources.import_pkg.test_import_pkg.module1',
+ 'vistrails.tests.resources.import_pkg.test_import_pkg.module2',
+ 'vistrails.tests.resources.import_targets',
+ 'vistrails.tests.resources.import_targets.test1',
+ 'vistrails.tests.resources.import_targets.test2',
+ 'vistrails.tests.resources.import_targets.test3',
+ 'vistrails.tests.resources.import_targets.test4',
+ 'vistrails.tests.resources.import_targets.test5',
+ 'vistrails.tests.resources.import_targets.test6']:
+ self.assertIn(dep, deps)
+ finally:
+ pm._userpackages = old_userpackages
+ pm.import_user_packages_module = old_import_userpackages
+ Package.FIX_PACKAGE_NAMES = old_fix_names
+ try:
+ pm.late_disable_package('test_import_pkg')
+ except MissingPackage:
+ pass
diff --git a/vistrails/core/packagerepository.py b/vistrails/core/packagerepository.py
new file mode 100644
index 0000000..2a7a9b5
--- /dev/null
+++ b/vistrails/core/packagerepository.py
@@ -0,0 +1,187 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core import debug
+import os
+import vistrails.core.configuration
+import shutil
+import urllib2
+import tempfile
+import os.path
+
+##############################################################################
+# The local codepaths have '.' replaced by '_' because '.' in the names
+# of directories that will be used as python libraries confuses the Python
+# runtime.
+
+##############################################################################
+
+class PackageRepository(object):
+
+ def __init__(self):
+ conf = vistrails.core.configuration.get_vistrails_configuration()
+ if conf.check('userPackageDirectory'):
+ self._upd = conf.userPackageDirectory
+ else:
+ self._upd = conf.get('dotVistrails') + '/.userpackages/'
+
+ def create_main_directory(self, codepath):
+ debug.log("Makedir '%s'" % (os.path.join(self._upd, codepath)))
+ os.mkdir(os.path.join(self._upd, codepath))
+
+ ##########################################################################
+
+ def create_directory(self, codepath, filename):
+ r = os.path.join(self._upd, codepath, filename)
+ debug.log("Makedir '%s'" % r)
+ os.mkdir(r)
+
+ def copy_file(self, codepath, filename, local_name):
+ r = os.path.join(self._upd,
+ codepath, filename)
+ debug.log("Copyfile '%s' to '%s'" % (local_name, r))
+ shutil.copyfile(local_name, r)
+
+ ##########################################################################
+ # implement these
+
+ # def find_package(self, identifier):
+ # pass
+
+ # def install_package(self, identifier):
+ # pass
+
+ ##########################################################################
+
+ class InvalidPackage(Exception):
+ pass
+
+##############################################################################
+
+class LocalPackageRepository(PackageRepository):
+
+ def __init__(self, repository_path):
+ PackageRepository.__init__(self)
+ self._path = repository_path
+
+ def find_package(self, identifier):
+ lst = set(os.listdir(self._path))
+ codepath = identifier.replace('.', '_')
+ if codepath in lst:
+ return codepath
+
+ def install_package(self, codepath):
+ debug.log("package found!")
+ # read manifest
+ try:
+ f = open(os.path.join(self._path, codepath, 'MANIFEST'))
+ except IOError, e:
+ raise InvalidPackage("Package is missing manifest.")
+ # create directory
+ self.create_main_directory(codepath)
+ for l in f:
+ l = l[:-1]
+ if len(l) == 0:
+ continue
+ file_type = l[0]
+ l = l[2:]
+ if file_type == 'D':
+ self.create_directory(codepath, l)
+ elif file_type == 'F':
+ self.copy_file(codepath, l, os.path.join(self._path, codepath, l))
+
+##############################################################################
+
+class HTTPPackageRepository(PackageRepository):
+
+ def __init__(self, repository_url):
+ PackageRepository.__init__(self)
+ self._path = repository_url
+
+ def find_package(self, identifier):
+ identifier = identifier.replace('.', '_')
+ package_url = self._path + '/' + identifier
+ try:
+ f = urllib2.urlopen(package_url)
+ return identifier
+ except urllib2.HTTPError:
+ return None
+
+ def install_package(self, codepath):
+ debug.log("package found!")
+ # read manifest
+ try:
+ f = urllib2.urlopen(self._path + '/' + codepath + '/MANIFEST')
+ except urllib2.HTTPError, e:
+ raise InvalidPackage("Package is missing manifest.")
+ self.create_main_directory(codepath)
+ for l in f:
+ l = l[:-1]
+ if len(l) == 0:
+ continue
+ file_type = l[0]
+ l = l[2:]
+ if file_type == 'D':
+ self.create_directory(codepath, l)
+ elif file_type == 'F':
+ fd, name = tempfile.mkstemp()
+ os.close(fd)
+ try:
+ fout = open(name, 'w')
+ fin = urllib2.urlopen(self._path + '/' + codepath + '/' + l)
+ fout.write(fin.read()) # There should be a better way to do this
+ fin.close()
+ fout.close()
+ self.copy_file(codepath, l, name)
+ finally:
+ os.unlink(name)
+
+##############################################################################
+
+_repository = None
+def get_repository():
+ global _repository
+ if _repository:
+ return _repository
+ import vistrails.core.configuration
+ conf = vistrails.core.configuration.get_vistrails_configuration()
+ if conf.check('repositoryHTTPURL'):
+ _repository = HTTPPackageRepository(conf.repositoryHTTPURL)
+ debug.log("Using HTTP Package Repository @ %s" % conf.repositoryHTTPURL)
+ elif conf.check('repositoryLocalPath'):
+ _repository = LocalPackageRepository(conf.repositoryLocalPath)
+ debug.log("Using Local Repository @ %s" % conf.repositoryLocalPath)
+ else:
+ _repository = None
+ return _repository
diff --git a/vistrails/core/param_explore.py b/vistrails/core/param_explore.py
new file mode 100644
index 0000000..2bbba31
--- /dev/null
+++ b/vistrails/core/param_explore.py
@@ -0,0 +1,263 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""
+This module handles Parameter Exploration in VisTrails
+"""
+from vistrails.core import debug
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+import copy
+
+import unittest
+
+################################################################################
+
+class ParameterExploration(object):
+ """
+ ParameterExploration is a class that will take a pipeline and a
+ set of parameter values and executes all of them
+
+ """
+
+ def __init__(self, specs):
+ """ ParameterExploration(specs: list) -> ParameterExploration
+ Takes a list of interpolator list. The number of items in the
+ list is also the number of dimensions this parameter
+ exploration is going to explore on
+
+ """
+ self.specs = specs
+
+ def explore(self, pipeline):
+ """ explore(pipeline: VisPipeline) -> list[VisPipeline]
+ Apply parameter exploration on multiple dimensions using the
+ values in self.specs
+
+ """
+ pipelineList = [pipeline]
+ for i in xrange(len(self.specs)):
+ pipelineList = self.interpolateList(pipelineList, self.specs[i])
+ return pipelineList
+
+ def interpolateList(self, pipelineList, interpList):
+ """ interpolateList(pipeline: list[VisPipeLine],
+ interpList: InterpolateDiscreteParam)
+ -> list[VisPipeline]
+ Returns a list of interpolated pipelines, by applying the
+ interpolators in a multiplication manner
+
+ """
+ if len(interpList)<1: return pipelineList
+ stepCount = interpList[0].stepCount
+ result = []
+ for step in xrange(stepCount):
+ for pipeline in pipelineList:
+ newp = copy.copy(pipeline)
+ for interp in interpList:
+ interp.perform(newp, step)
+ result.append(newp)
+ return result
+
+class InterpolateDiscreteParam(object):
+ """
+ InterpolateDiscreteParam takes in ranges and a number of
+ steps. Then given a pipeline, it will interpolate and generate a
+ number of steps pipelines with values interpolated between the
+ ranges
+
+ """
+
+ def __init__(self, module, function, ranges, stepCount):
+ """ InterpolateDiscreteParam(module: Module,
+ function: str,
+ ranges: list(tuple),
+ stepCount: int)
+ -> InterpolateDiscreteParam
+
+ Initialize the interpolator with a specific module function
+ given a list of parameter ranges
+
+ Keyword arguments:
+ module --- module id in a pipeline
+ function --- a string express the function name that belongs
+ to module
+
+ ranges --- [tupe(min,max) or tuple(s1,s2..,s{stepCount}],
+ ranges specified for each argument of function
+ where s{i} is of type 'str'
+
+ stepCount --- the number of step for the interpolation
+
+ """
+ self.module = module
+ self.function = function
+ self.stepCount = stepCount
+ self.values = self.interpolate(ranges, stepCount)
+
+ def interpolate(self, ranges, stepCount):
+ """ interpolate(ranges: tuple, stepCount: int) -> list
+
+ This function takes a number of (min,max) or (s1,...sn) to
+ interpolate exact stepCount number of step. The output will be
+ a list of stepCount elements where each of them is (a1,...,an).
+ a{i} is either int or string and n is the number of arguments.
+
+ """
+ params = []
+ for r in ranges:
+ interpolatedValues = []
+ argumentType = type(r[0])
+ if argumentType in [int, float]:
+ for i in xrange(stepCount):
+ if stepCount>1: t = i/float(stepCount-1)
+ else: t = 0
+ interpolatedValues.append(argumentType(r[0]+t*(r[1]-r[0])))
+ elif argumentType==str:
+ interpolatedValues = list(r)
+ else:
+ debug.critical('Cannot interpolate non-cardinal types')
+ assert False
+ params.append(interpolatedValues)
+ return zip(*params)
+
+
+ def perform(self, pipeline, step):
+ """ perform(pipeline: VisPipeline, step: int) -> None
+ This will takes a pipeline and apply the interpolated values
+ at step 'step' to the pipeline. Then return the updated
+ pipeline
+
+ """
+ m = pipeline.modules[self.module.id]
+ f = ModuleFunction()
+ f.name = self.function
+ f.returnType = 'void'
+ value = self.values[step]
+ for v in value:
+ p = ModuleParam()
+ convert = {'int':'Integer', 'str':'String',
+ 'float':'Float', 'double':'Float'}
+ p.type = convert[type(v).__name__]
+ p.strValue = str(v)
+ f.params.append(p)
+ m.functions.append(f)
+
+class ActionBasedParameterExploration(object):
+ """
+ ActionBasedParameterExploration is going to replace
+ ParameterExploration class to perform parameter exploration. It is
+ an action based parameter exploration
+
+ """
+ def explore(self, pipeline, actions, pre_actions=[]):
+ """ explore(pipeline: Pipeline, actions: [action set],
+ pre_actions: [action set]) -> [(pipeline, actions)]
+ Perform the parameter exploration on the pipeline with a set
+ of actions. Each 'action set' represent a tuple of actions that we
+ need to apply on the pipeline at a step in a dimension. For example:
+ actions = [[(action1a, action2a), (action1b, action2b)],
+ [(action3a), (action3b)]]
+
+ which means this is a 2 x 1 parameter exploration resulting of
+ executing 2 pipelines. The first one is
+ pipeline.action1a.action2a.action3a and the second one is
+ pipeline.action1b.action2b.action3b.
+
+ pre_actions are actions that should be applied first to all pipelines
+ and usually contains creation of functions that do not already exist
+
+ The return values are a list of tuples containing interpolated
+ pipeline and a set of actions leading to that interpolated
+ pipeline. This is useful for update the parameter exploration
+ back to the builder.
+
+ """
+ results = []
+ resultActions = []
+
+ def exploreDimension(pipeline, performedActions, dim):
+ """ exploreDimension(pipeline: Pipeline, performedActions: [actions],
+ dim: int) -> None
+ Start applying actions to the pipeline at dimension
+ dim. 'pipeline' will not be modified in the function
+
+ """
+ if dim<0:
+ results.append(pipeline)
+ resultActions.append(performedActions)
+ return
+ currentActions = actions[dim]
+ if len(currentActions)==0:
+ # Ignore empty dimension
+ exploreDimension(pipeline, performedActions, dim-1)
+ return
+ for actionSet in currentActions:
+ currentPipeline = copy.copy(pipeline)
+ currentPeformedActions = copy.copy(performedActions)
+ for action in actionSet:
+ currentPipeline.perform_action(action)
+ currentPeformedActions.append(action)
+ exploreDimension(currentPipeline, currentPeformedActions, dim-1)
+
+ # perform pre_actions
+ currentPipeline = copy.copy(pipeline)
+ for action in pre_actions:
+ currentPipeline.perform_action(action)
+
+ exploreDimension(currentPipeline, pre_actions, len(actions)-1)
+ return (results, resultActions)
+
+################################################################################
+
+
+class TestParameterExploration(unittest.TestCase):
+ """
+ Test if ParameterExploration is executing correctly. For now it is a very
+ simple test to test more of the interpolated values
+
+ """
+ def testInterpolator(self):
+ interpolator = InterpolateDiscreteParam(0, 'testing',
+ [(0,10),
+ (0.0,10.0),
+ ('one', 'two', 'three')],
+ 3)
+ self.assertEqual(interpolator.values,
+ [(0, 0.0, 'one'),
+ (5, 5.0, 'two'),
+ (10, 10.0, 'three')])
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/paramexplore/__init__.py b/vistrails/core/paramexplore/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/core/paramexplore/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/core/paramexplore/function.py b/vistrails/core/paramexplore/function.py
new file mode 100644
index 0000000..e833463
--- /dev/null
+++ b/vistrails/core/paramexplore/function.py
@@ -0,0 +1,201 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This module contains class definitions for:
+
+ * PEFunction
+"""
+from vistrails.db.domain import DBPEFunction, DBPEParameter
+from vistrails.core.paramexplore.param import PEParam
+import copy
+
+import unittest
+from vistrails.db.domain import IdScope
+
+################################################################################
+
+class PEFunction(DBPEFunction):
+ """ Stores a function for a parameter exploration """
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBPEFunction.__init__(self, *args, **kwargs)
+ if self.id is None:
+ self.id = -1
+ if self.module_id is None:
+ self.module_id = -1
+ if self.port_name is None:
+ self.port_name = ""
+ if self.is_alias is None:
+ self.is_alias = 0
+ self.set_defaults()
+
+ def set_defaults(self, other=None):
+ pass
+
+ def __copy__(self):
+ """ __copy__() -> ModuleFunction - Returns a clone of itself """
+ return PEFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPEFunction.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = PEFunction
+ cp.set_defaults(self)
+ return cp
+
+ @staticmethod
+ def convert(_function):
+ if _function.__class__ == PEFunction:
+ return
+ _function.__class__ = PEFunction
+ for _parameter in _function.db_get_parameters():
+ PEParam.convert(_parameter)
+ _function.set_defaults()
+
+ ##########################################################################
+ # Properties
+
+ id = DBPEFunction.db_id
+ module_id = DBPEFunction.db_module_id
+ port_name = DBPEFunction.db_port_name
+ is_alias = DBPEFunction.db_is_alias
+
+ def _get_params(self):
+ self.db_parameters.sort(key=lambda x: x.db_pos)
+ return self.db_parameters
+ def _set_params(self, params):
+ self.db_parameters = params
+
+ parameters = property(_get_params, _set_params)
+ params = property(_get_params, _set_params)
+
+ def add_parameter(self, param):
+ self.db_add_parameter(param)
+ addParameter = add_parameter
+
+ def add_parameters(self, params):
+ for p in params:
+ self.db_add_parameter(p)
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """ __str__() -> str - Returns a string representation of itself """
+ return ("<PEFunction id=%s module_id=%s port_name='%s' is_alias=%s params=%s)@%X" %
+ (self.id,
+ self.module_id,
+ self.port_name,
+ self.is_alias,
+ [str(p) for p in self.params],
+ id(self)))
+
+ def __eq__(self, other):
+ """ __eq__(other: ModuleFunction) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.port_name != other.port_name:
+ return False
+ if self.module_id != other.module_id:
+ return False
+ if self.is_alias != other.is_alias:
+ return False
+ if len(self.params) != len(other.params):
+ return False
+ for p,q in zip(self.params, other.params):
+ if p != q:
+ return False
+ return True
+
+ def __ne__(self, other):
+ """ __ne__(other: ModuleFunction) -> boolean
+ Returns True if self and other don't have the same attributes.
+ Used by != operator.
+
+ """
+ return not self.__eq__(other)
+
+################################################################################
+# Testing
+
+class TestModuleFunction(unittest.TestCase):
+
+ def create_function(self, id_scope=IdScope()):
+ param = PEParam(id=id_scope.getNewId(PEParam.vtType),
+ pos=2,
+ interpolator='Stepper',
+ dimension=4,
+ value='[1, 2]')
+ function = PEFunction(id=id_scope.getNewId(PEFunction.vtType),
+ module_id=7,
+ port_name='value',
+ is_alias=0,
+ parameters=[param])
+ return function
+
+ def test_copy(self):
+ id_scope = IdScope()
+ f1 = self.create_function(id_scope)
+ f2 = copy.copy(f1)
+ self.assertEquals(f1, f2)
+ self.assertEquals(f1.id, f2.id)
+ f3 = f1.do_copy(True, id_scope, {})
+ self.assertEquals(f1, f3)
+ self.assertNotEquals(f1.id, f3.id)
+
+ def testComparisonOperators(self):
+ f = self.create_function()
+ g = self.create_function()
+ self.assertEqual(f, g)
+ g.module_id = 1
+ self.assertNotEqual(f, g)
+ g.module_id = 7
+ g.port_name = "val"
+ self.assertNotEqual(f, g)
+ g.port_name = "value"
+ g.is_alias = 1
+ self.assertNotEqual(f, g)
+
+ def test_str(self):
+ str(self.create_function())
+
+if __name__ == '__main__':
+ unittest.main()
+
diff --git a/vistrails/core/paramexplore/param.py b/vistrails/core/paramexplore/param.py
new file mode 100644
index 0000000..6a79146
--- /dev/null
+++ b/vistrails/core/paramexplore/param.py
@@ -0,0 +1,170 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This module contains class definitions for:
+ * PEParam
+
+ """
+from vistrails.db.domain import DBPEParameter
+
+import unittest
+import copy
+from vistrails.db.domain import IdScope
+
+################################################################################
+
+class PEParam(DBPEParameter):
+ """ Stores a parameter setting for a parameter exploration function """
+
+ ##########################################################################
+ # Constructor
+
+ def __init__(self, *args, **kwargs):
+ DBPEParameter.__init__(self, *args, **kwargs)
+ if self.id is None:
+ self.id = -1
+ if self.pos is None:
+ self.pos = -1
+ if self.interpolator is None:
+ self.interpolator = ""
+ if self.value is None:
+ self.value = ""
+ if self.dimension is None:
+ self.dimension = -1
+
+ def __copy__(self):
+ return PEParam.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPEParameter.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = PEParam
+ return cp
+
+ @staticmethod
+ def convert(_parameter):
+ if _parameter.__class__ == PEParam:
+ return
+ _parameter.__class__ = PEParam
+
+ ##########################################################################
+
+ id = DBPEParameter.db_id
+ pos = DBPEParameter.db_pos
+ interpolator = DBPEParameter.db_interpolator
+ value = DBPEParameter.db_value
+ dimension = DBPEParameter.db_dimension
+
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """ __str__() -> str - Returns a string representation of itself """
+ return ("(PEParam id=%s pos=%s interpolator='%s' value='%s' dimension=%s)@%X" %
+ (self.id,
+ self.pos,
+ self.interpolator,
+ self.value,
+ self.dimension,
+ id(self)))
+
+ def __eq__(self, other):
+ """ __eq__(other: PEParam) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.pos != other.pos:
+ return False
+ if self.interpolator != other.interpolator:
+ return False
+ if self.value != other.value:
+ return False
+ if self.dimension != other.dimension:
+ return False
+ return True
+
+ def __ne__(self, other):
+ """ __ne__(other: ModuleParam) -> boolean
+ Returns True if self and other don't have the same attributes.
+ Used by != operator.
+
+ """
+ return not self.__eq__(other)
+
+###############################################################################
+# Testing
+
+
+class TestModuleParam(unittest.TestCase):
+
+ def create_param(self, id_scope=IdScope()):
+ param = PEParam(id=id_scope.getNewId(PEParam.vtType),
+ pos=1,
+ interpolator='normal-int',
+ value='[1, 2]',
+ dimension=1)
+ return param
+
+ def test_copy(self):
+ id_scope = IdScope()
+ p1 = self.create_param(id_scope)
+ p2 = copy.copy(p1)
+ self.assertEquals(p1, p2)
+ self.assertEquals(p1.id, p2.id)
+ p3 = p1.do_copy(True, id_scope, {})
+ self.assertEquals(p1, p3)
+ self.assertNotEquals(p1.id, p3.id)
+
+ def testComparisonOperators(self):
+ """ Test comparison operators """
+ p = self.create_param()
+ q = self.create_param()
+ self.assertEqual(p, q)
+ q.pos = 2
+ self.assertNotEqual(p, q)
+ q.pos = 1
+ q.interpolator = 'other-int'
+ self.assertNotEqual(p, q)
+ q.interpolator = 'normal-int'
+ q.value = '[1, 3]'
+ self.assertNotEqual(p, q)
+ q.value = '[1, 2]'
+ q.dimension = 2
+ self.assertNotEqual(p, q)
+
+ def test_str(self):
+ str(self.create_param())
diff --git a/vistrails/core/paramexplore/paramexplore.py b/vistrails/core/paramexplore/paramexplore.py
new file mode 100644
index 0000000..df468c9
--- /dev/null
+++ b/vistrails/core/paramexplore/paramexplore.py
@@ -0,0 +1,325 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file contains the definition of the class ParameterExploration """
+
+from xml.sax.saxutils import unescape
+
+import vistrails.core.db.action
+
+from vistrails.db.domain import DBParameterExploration, IdScope
+from vistrails.core.paramexplore.function import PEFunction
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.module import Module
+from vistrails.core.modules.paramexplore import IntegerLinearInterpolator, \
+ FloatLinearInterpolator, RGBColorInterpolator, HSVColorInterpolator,\
+ UserDefinedFunctionInterpolator
+
+
+import unittest
+import copy
+
+###############################################################################
+
+class ParameterExploration(DBParameterExploration):
+ """ParameterExploration
+
+ """
+
+ def __init__(self, *args, **kwargs):
+ DBParameterExploration.__init__(self, *args, **kwargs)
+
+ self.set_defaults()
+
+ def __copy__(self):
+ """ __copy__() -> ParameterExploration - Returns a clone of itself """
+ return ParameterExploration.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameterExploration.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = ParameterExploration
+ cp.set_defaults(self)
+ return cp
+
+ def set_defaults(self, other=None):
+ if other is None:
+ self.changed = False
+ else:
+ self.changed = other.changed
+
+ @staticmethod
+ def convert(_parameter_exploration):
+ _parameter_exploration.__class__ = ParameterExploration
+
+ for function in _parameter_exploration.db_functions:
+ PEFunction.convert(function)
+
+ _parameter_exploration.set_defaults()
+
+ ##########################################################################
+ # Properties
+
+ id = DBParameterExploration.db_id
+ action_id = DBParameterExploration.db_action_id
+ user = DBParameterExploration.db_user
+ date = DBParameterExploration.db_date
+ _dims = DBParameterExploration.db_dims
+ _layout = DBParameterExploration.db_layout
+ name = DBParameterExploration.db_name
+ functions = DBParameterExploration.db_functions
+
+ def get_dims(self):
+ try:
+ return eval(self._dims)
+ except:
+ return []
+ def set_dims(self, d):
+ try:
+ _dims = repr(d)
+ except:
+ _dims = []
+ dims = property(get_dims, set_dims)
+
+ def get_layout(self):
+ try:
+ return eval(self._layout)
+ except:
+ return {}
+ def set_layout(self, l):
+ try:
+ _layout = repr(l)
+ except:
+ _layout = '{}'
+ layout = property(get_layout, set_layout)
+
+ def collectParameterActions(self, pipeline):
+ """ collectParameterActions() -> list
+ Return a list of action lists corresponding to each dimension
+
+ """
+ if not pipeline:
+ return
+ unescape_dict = { "'":"'", '"':'"', '
':'\n' }
+ from vistrails.core.modules.module_registry import get_module_registry
+ reg = get_module_registry()
+ parameterValues = [[], [], [], []]
+ # a list of added functions [(module_id, function_name)] = function
+ added_functions = {}
+ vistrail_vars = []
+ function_actions = []
+ for i in xrange(len(self.functions)):
+ pe_function = self.functions[i]
+ module = pipeline.db_get_object(Module.vtType, pe_function.module_id)
+ # collect overridden vistrail vars
+ if module.is_vistrail_var():
+ vistrail_vars.append(module.get_vistrail_var())
+ port_spec = reg.get_input_port_spec(module, pe_function.port_name)
+ tmp_f_id = -1L
+ tmp_p_id = -1L
+ for param in pe_function.parameters:
+ port_spec_item = port_spec.port_spec_items[param.pos]
+ dim = param.dimension
+ if dim not in [0, 1, 2, 3]:
+ continue
+ count = self.dims[dim]
+ # find interpolator values
+ values = []
+ text = '%s' % unescape(param.value, unescape_dict)
+ if param.interpolator == 'Linear Interpolation':
+ # need to figure out type
+ if port_spec_item.module == "Integer":
+ i_range = eval(text)
+ p_min = int(i_range[0])
+ p_max =int(i_range[1])
+ values = IntegerLinearInterpolator(p_min, p_max,
+ count).get_values()
+ if port_spec_item.module == "Float":
+ i_range = eval(text)
+ p_min = float(i_range[0])
+ p_max =float(i_range[1])
+ values = FloatLinearInterpolator(p_min, p_max,
+ count).get_values()
+ elif param.interpolator == 'RGB Interpolation':
+ i_range = eval(text)
+ p_min = str(i_range[0])
+ p_max =str(i_range[1])
+ values = RGBColorInterpolator(p_min, p_max,
+ count).get_values()
+ elif param.interpolator == 'HSV Interpolation':
+ i_range = eval(text)
+ p_min = str(i_range[0])
+ p_max =str(i_range[1])
+ values = HSVColorInterpolator(p_min, p_max,
+ count).get_values()
+ elif param.interpolator == 'List':
+ p_module = port_spec_item.descriptor.module
+ values = [p_module.translate_to_python(m)
+ for m in eval(text)]
+ elif param.interpolator == 'User-defined Function':
+ p_module = port_spec_item.descriptor.module
+ values = UserDefinedFunctionInterpolator(p_module,
+ text, count).get_values()
+ if not values:
+ return None
+ # find parameter or create one
+ function = [f for f in module.functions
+ if f.name == port_spec.name]
+ if function:
+ function = function[0]
+ else:
+ try:
+ function = added_functions[(module.id,port_spec.name)]
+ except KeyError:
+ # add to function list
+ params = []
+ for psi in port_spec.port_spec_items:
+ parameter = ModuleParam(id=tmp_p_id,
+ pos=psi.pos,
+ name='<no description>',
+ val=psi.default,
+ type=psi.descriptor.sigstring)
+ params.append(parameter)
+ tmp_p_id -= 1
+ function = ModuleFunction(id=tmp_f_id,
+ pos=module.getNumFunctions(),
+ name=port_spec.name,
+ parameters=params)
+ tmp_f_id -= 1
+ added_functions[(module.id, port_spec.name)]=function
+ action = vistrails.core.db.action.create_action([('add',
+ function,
+ module.vtType,
+ module.id)])
+ function_actions.append(action)
+ parameter = function.params[port_spec_item.pos]
+ # find old parameter
+ old_param = parameter
+ actions = []
+ for v in values:
+ desc = port_spec_item.descriptor
+ if not isinstance(v, str):
+ str_value = desc.module.translate_to_string(v)
+ else:
+ str_value = v
+ new_param = ModuleParam(id=tmp_p_id,
+ pos=old_param.pos,
+ name=old_param.name,
+ alias=pe_function.is_alias,
+ val=str_value,
+ type=old_param.type)
+ tmp_p_id -= 1
+ action_spec = ('change', old_param, new_param,
+ function.vtType, function.real_id)
+ action = vistrails.core.db.action.create_action([action_spec])
+ actions.append(action)
+ parameterValues[dim].append(actions)
+ return [zip(*p) for p in parameterValues], function_actions, vistrail_vars
+
+ def __eq__(self, other):
+ """ __eq__(other: ParameterExploration) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.action_id != other.action_id:
+ return False
+ if self._dims != other._dims:
+ return False
+ if self._layout != other._layout:
+ return False
+ if len(self.functions) != len(other.functions):
+ return False
+ for p,q in zip(self.functions, other.functions):
+ if p.real_id != q.real_id or p != q:
+ return False
+ return True
+
+# Testing
+
+
+class TestParameterExploration(unittest.TestCase):
+
+ def create_pe(self, id_scope=IdScope()):
+ pe = ParameterExploration(
+ id=id_scope.getNewId(ParameterExploration.vtType),
+ action_id=6,
+ user='tommy',
+ date='2007-11-23 12:48',
+ dims='[1,2]',
+ layout='{1:"normal"}',
+ name='test-pe',
+ functions=[])
+ return pe
+
+ def test_copy(self):
+ id_scope = IdScope()
+ pe1 = self.create_pe(id_scope)
+ pe2 = copy.copy(pe1)
+ self.assertEquals(pe1, pe2)
+ self.assertEquals(pe1.id, pe2.id)
+ pe3 = pe1.do_copy(True, id_scope, {})
+ self.assertEquals(pe1, pe3)
+ self.assertNotEquals(pe1.id, pe3.id)
+
+ def testComparisonOperators(self):
+ """ Test comparison operators """
+ p = self.create_pe()
+ q = self.create_pe()
+ self.assertEqual(p, q)
+ q.action_id = 8
+ self.assertNotEqual(p, q)
+ q.action_id = 6
+ q.user = 'bobo'
+ self.assertNotEqual(p, q)
+ q.user = 'tommy'
+ q.date = '2008-11-23 12:48'
+ self.assertNotEqual(p, q)
+ q.date = p.date
+ q._dims = '[1,4]'
+ self.assertNotEqual(p, q)
+ q._dims = '[1,2]'
+ q._layout = '{1:"different"}'
+ self.assertNotEqual(p, q)
+ q._layout = p._layout
+ q.name = 'test-pe2'
+ self.assertNotEqual(p, q)
+ q.name = p.name
+ q.functions = [1]
+ self.assertNotEqual(p, q)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/publishing/__init__.py b/vistrails/core/publishing/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/core/publishing/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/core/publishing/parse_latex.py b/vistrails/core/publishing/parse_latex.py
new file mode 100644
index 0000000..ae086f1
--- /dev/null
+++ b/vistrails/core/publishing/parse_latex.py
@@ -0,0 +1,170 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from itertools import izip
+import re
+
+def parse_vt_command(opt_arg, arg):
+ opt_dict = {}
+ for opt_str in opt_arg[1:-1].split(','):
+ opt_str = opt_str.strip()
+ opt_list = opt_str.split('=',1)
+ if len(opt_list) > 1:
+ if opt_list[0].strip():
+ opt_dict[opt_list[0]] = opt_list[1]
+ else:
+ if opt_list[0].strip():
+ opt_dict[opt_list[0]] = None
+ opt_dict['_args'] = arg[1:-1]
+ return opt_dict
+
+def build_vt_command(opt_dict):
+ if '_args' in opt_dict:
+ args = opt_dict['_args']
+ else:
+ args = ''
+ opt_str = ''
+ for k, v in opt_dict.iteritems():
+ if k == '_args':
+ continue
+ if v is None:
+ opt_str += '%s,\n' % k
+ else:
+ opt_str += '%s=%s,\n' % (k,v)
+ if opt_str:
+ full_str = "\\vistrail[%s]{%s}" % (opt_str, args)
+ else:
+ full_str = "\\vistrail{%s}" % args
+ #print '^^ LATEX ^^', opt_dict, full_str
+ return full_str
+
+def parse_latex_file(fname):
+ # vt_begin_re = re.compile(r"% -- VISTRAILS BEGIN --")
+ # vt_end_re = re.compile(r"% -- VISTRAILS END --")
+ vt_begin_re = re.compile(r"^(?:(?:\\%)|[^%])*(\\vistrail[\[\{])")
+
+ # we'll just assume balanced parens here...
+ # vt_end_re = re.compile(r"\}")
+ vt_bracket_re = re.compile(r"[\[\]]")
+ vt_brace_re = re.compile(r"[\{\}]")
+ f = open(fname)
+
+ raw_text = [""]
+ raw_idx = 0
+ vt_text = []
+ for line in f:
+ m = vt_begin_re.search(line)
+ if not m:
+ raw_text[raw_idx] += line
+ else:
+ # print 'found:', m.start(1), m.end(1), line[m.end(1) - 1]
+
+ # first end the current raw_text block
+ raw_text[raw_idx] += line[:m.start(1)]
+ raw_text.append("")
+ raw_idx += 1
+
+ cmd_text = ""
+ # line = line[m.start(1):]
+ line = line[m.end(1)-1:]
+
+ # we'll just assume balanced parens here...
+ if line[0] == '[':
+ brackets_complete = False
+ found_start = False
+ brackets = 0
+ while not brackets_complete:
+ for m in vt_bracket_re.finditer(line):
+ bracket_char = line[m.start()]
+ if bracket_char == '[':
+ brackets += 1
+ found_start = True
+ else:
+ brackets -= 1
+ if found_start and brackets == 0:
+ brackets_complete = True
+ cmd_text += line[:m.end()]
+ line = line[m.end():]
+ break
+ if brackets_complete:
+ break
+ cmd_text += line
+ line = f.next()
+
+ opt_cmd_text = cmd_text
+ cmd_text = ""
+ braces_complete = False
+ found_start = False
+ braces = 0
+ while not braces_complete:
+ for m in vt_brace_re.finditer(line):
+ brace_char = line[m.start()]
+ if brace_char == '{':
+ braces += 1
+ found_start = True
+ else:
+ braces -= 1
+ if found_start and braces == 0:
+ braces_complete = True
+ cmd_text += line[:m.end()]
+ break
+ if braces_complete:
+ break
+ cmd_text += line
+ line = f.next()
+ # print cmd_text
+ vt_text.append((opt_cmd_text,cmd_text))
+ raw_text[raw_idx] += line[m.end():]
+
+ # if vt_begin_re.search(line):
+ # line = f.next()
+ # while not vt_end_re.search(line):
+ # print line.strip()
+ # line = f.next()
+ f.close()
+
+ # vt_text.append(("", ""))
+ #for t, vt in izip(raw_text, vt_text + [("", "")]):
+ #print "RAW:", t
+ #print "VT:", parse_vt_command(*vt)
+ return (raw_text, vt_text)
+
+if __name__ == '__main__':
+ import sys
+ if len(sys.argv) < 2:
+ print "Usage: %s %s <latex-file>" % (sys.executable, sys.argv[0])
+ sys.exit(-1)
+
+ parse_latex_file(sys.argv[1])
diff --git a/vistrails/core/query/__init__.py b/vistrails/core/query/__init__.py
new file mode 100644
index 0000000..1a22cf3
--- /dev/null
+++ b/vistrails/core/query/__init__.py
@@ -0,0 +1,565 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# ################################################################################
+# # QueryWF: Base class for queries over workflows
+
+# class QueryWF(object):
+
+# def __init__(self, transformer, logQueries):
+# self.transformer = transformer
+# self. = logQueries
+
+
+# ################################################################################
+
+# class QueryWFModuleName(QueryWF):
+
+# def __init__(self, name):
+# self.name = name
+
+# def run(self, module):
+# return module.name == self.name
+
+# ################################################################################
+
+# class QueryWFParameter(QueryWF):
+
+# def __init__(self, param, name):
+# self.param = param
+# self.name = name
+
+# def run(self, module):
+# for f in module.functions:
+# if (f.name == name and
+# len(f.params) == 1 and
+# f.params[0].name == self.name:
+# return True
+# return False
+
+# ################################################################################
+
+# class QueryWFAnd(QueryWF):
+
+# def __init__(self, queries):
+# self.queries = queries
+
+# def run(self, module):
+# for query in self.queries:
+# if not query.run(module):
+# return False
+# return True
+
+# ################################################################################
+
+# class QueryWFOr(QueryWF):
+
+# def __init__(self, queries):
+# self.queries = queries
+
+# def run(self, module):
+# for query in self.queries:
+# if query.run(module):
+# return True
+# return False
+
+# ################################################################################
+
+# class QueryWFNot(QueryWF):
+
+# def __init__(self, query):
+# self.query = query
+
+# def run(self, module):
+# return not self.query.run(module)
+
+# ################################################################################
+
+# class QueryWFResultTransformer(object):
+# pass
+
+# ################################################################################
+
+# class QueryWFUpstream(QueryWFResultTransformer):
+
+# def run(self, pipeline, module_ids):
+# result = set()
+# inv_graph = pipeline.graph.inverse()
+# for i in module_ids:
+# result = result.union(set(inv_graph.bfs(i).keys() + [i]))
+# return result
+
+
+# class QueryWFIdentity(QueryWFResultTransformer):
+
+# def run(self, pipeline, module_ids):
+# return module_ids
+
+
+# class QueryWFUnion(QueryWFResultTransformer):
+
+# def __init__(self, queries):
+# self.queries = queries
+
+# def run(self, pipeline, module_ids):
+# result = set()
+# for query in queries:
+# result = result.union(query.run(pipeline, module_ids))
+
+################################################################################
+import xml.sax.saxutils
+
+from vistrails.core.utils import memo_method
+
+# convenience method that does the full html extract if PyQt is loaded
+def extract_text(escaped_html_str):
+ notes = xml.sax.saxutils.unescape(escaped_html_str)
+ try:
+ from PyQt4 import QtGui
+ except ImportError:
+ return str(notes)
+ else:
+ fragment = QtGui.QTextDocumentFragment.fromHtml(notes)
+ return str(fragment.toPlainText())
+
+# The queries are old and are preserved for reference. Some code is
+# quite old (references to vis_application, for example).
+
+class Query(object):
+
+ def upstream(self, graph, id):
+ return graph.bfs(id).keys()
+
+ weekdayMap = {'mo':0, 'tu':1, 'we':2, 'th':3, 'fr':4, 'sa':5, 'su':6}
+
+ def weekday(self, time, weekday):
+ return time.weekday() == self.weekdayMap[weekday.lower()[:2]]
+
+ def computeIndices(self):
+ self.versionDict = {}
+
+ if not len(self.queryResult):
+ return
+ elif len(self.queryResult[0]) == 1:
+ for (v,) in self.queryResult:
+ self.versionDict[v] = {}
+ elif len(self.queryResult[0]) == 2:
+ for (v, m) in self.queryResult:
+ if not self.versionDict.has_key(v):
+ self.versionDict[v] = {m: []}
+ self.versionDict[v][m] = {}
+ else:
+ assert len(self.queryResult[0]) == 3
+ for (v, m, e) in self.queryResult:
+ if not self.versionDict.has_key(v):
+ self.versionDict[v] = {m: [e]}
+ elif not self.versionDict[v].has_key(m):
+ self.versionDict[v][m] = [e]
+ else:
+ self.versionDict[v][m].append(e)
+
+ def match(self, vistrail, action):
+ return action.timestep in self.versionDict
+
+ def matchModule(self, version_id, module):
+ return (self.tupleLength < 2 or
+ (version_id in self.versionDict and
+ module.id in self.versionDict[version_id]))
+
+ def executionInstances(self, version_id, module_id):
+ versionDict = self.versionDict
+ assert self.tupleLength == 3
+ if versionDict[version_id].has_key(module_id):
+ return versionDict[version_id][module_id]
+ else:
+ return None
+
+class Query1a(Query):
+
+ def run(self, vistrail, name):
+ result = []
+ versions = vistrail.get_tagMap().itervalues()
+ for version in versions:
+ p = vistrail.getPipeline(version)
+ for module_id, module in p.modules.iteritems():
+ if module.name == 'FileSink':
+ for f in module.functions:
+ if (f.name == 'outputName' and
+ len(f.params) == 1 and
+ f.params[0].value() == 'atlas-x.gif'):
+ result.append((version, module_id))
+ self.queryResult = result
+ self.tupleLength = 2
+ self.computeIndices()
+ return result
+
+
+class Query1b(Query):
+
+ def run(self, vistrail, name):
+ result = []
+ versions = vistrail.get_tagMap().itervalues()
+ for version in versions:
+ p = vistrail.getPipeline(version)
+ ms = []
+ for module_id, module in p.modules.iteritems():
+ if module.name == 'FileSink':
+ for f in module.functions:
+ if (f.name == 'outputName' and
+ len(f.params) == 1 and
+ f.params[0].value() == 'atlas-x.gif'):
+ ms.append(module_id)
+ s = set()
+ inv_graph = p.graph.inverse()
+ for m in ms:
+ s = s.union(set(inv_graph.bfs(m).keys() + [m]))
+ for m in s:
+ result.append((version, m))
+ self.queryResult = result
+ self.tupleLength = 2
+ self.computeIndices()
+ return result
+
+
+class Query1c(Query):
+
+ def run(self, vistrail, name):
+ import vistrails.gui.vis_application
+ c = vistrails.gui.vis_application.logger.db.cursor()
+ c.execute("""
+ select distinct module_id, wf_version from
+ wf_exec, exec, vistrails
+ where
+ wf_exec.wf_exec_id = exec.wf_exec_id and
+ vistrails.vistrails_name = %s and
+ vistrails.vistrails_id = wf_exec.vistrails_id""", name)
+ lst = list(c.fetchall())
+ versions = set([x[1] for x in lst])
+ executions = set(lst)
+ result = []
+ for version in versions:
+ p = vistrail.getPipeline(int(version))
+ ms = []
+ for module_id, module in p.modules.iteritems():
+ if (module_id, version) not in executions:
+ continue
+ if module.name == 'FileSink':
+ for f in module.functions:
+ if (f.name == 'outputName' and
+ len(f.params) == 1 and
+ f.params[0].value() == 'atlas-x.gif'):
+ ms.append(module_id)
+ s = set()
+ inv_graph = p.graph.inverse()
+ for m in ms:
+ s = s.union(set(inv_graph.bfs(m).keys() + [m]))
+ for m in s:
+ result.append((int(version), m))
+ self.queryResult = result
+ self.tupleLength = 2
+ self.computeIndices()
+ return result
+
+
+class Query2(Query):
+
+ def run(self, vistrail, name):
+ import vistrails.gui.vis_application
+ c = vistrails.gui.vis_application.logger.db.cursor()
+ c.execute("""
+ select distinct module_id, wf_version from
+ wf_exec, exec, vistrails
+ where
+ wf_exec.wf_exec_id = exec.wf_exec_id and
+ vistrails.vistrails_name = %s and
+ vistrails.vistrails_id = wf_exec.vistrails_id""", name)
+ lst = list(c.fetchall())
+ versions = set([x[1] for x in lst])
+ executions = set(lst)
+ result = []
+ for version in versions:
+ p = vistrail.getPipeline(int(version))
+ inv_graph = p.graph.inverse()
+
+ # s = upstream(x) union x where x.name = filesink blablabla
+ s = set()
+ for module_id, module in p.modules.iteritems():
+ if (module_id, version) not in executions:
+ continue
+ if module.name == 'FileSink':
+ for f in module.functions:
+ if (f.name == 'outputName' and
+ len(f.params) == 1 and
+ f.params[0].value() == 'atlas-x.gif'):
+ s = s.union(set(self.upstream(inv_graph, module_id) + [module_id]))
+ break
+
+ # s2 = upstream(y) where y.name = softmean
+ s2 = set()
+ for module_id, module in p.modules.iteritems():
+ if module.name == 'SoftMean':
+ s2 = s2.union(set(self.upstream(inv_graph, module_id) + [module_id]))
+
+ qresult = s - s2
+
+ for m in qresult:
+ result.append((int(version), m))
+ self.queryResult = result
+ self.tupleLength = 2
+ self.computeIndices()
+ return result
+
+
+class Query3(Query):
+
+ def run(self, vistrail, name):
+ import vistrails.gui.vis_application
+ c = vistrails.gui.vis_application.logger.db.cursor()
+ c.execute("""
+ select distinct module_id, wf_version from
+ wf_exec, exec, vistrails
+ where
+ wf_exec.wf_exec_id = exec.wf_exec_id and
+ vistrails.vistrails_name = %s and
+ vistrails.vistrails_id = wf_exec.vistrails_id""", name)
+ lst = list(c.fetchall())
+ versions = set([x[1] for x in lst])
+ executions = set(lst)
+ result = []
+ for version in versions:
+ p = vistrail.getPipeline(int(version))
+ ms = []
+ for module_id, module in p.modules.iteritems():
+ if (module_id, version) not in executions:
+ continue
+ if module.name == 'FileSink':
+ for f in module.functions:
+ if (f.name == 'outputName' and
+ len(f.params) == 1 and
+ f.params[0].value() == 'atlas-x.gif'):
+ ms.append(module_id)
+ s = set()
+ inv_graph = p.graph.inverse()
+ for m in ms:
+ s = s.union(set(inv_graph.bfs(m).keys() + [m]))
+ for m in s:
+ if (p.modules[m].has_annotation_with_key('stage') and
+ p.modules[m].get_annotation_by_key('stage').value in \
+ ['3','4','5']):
+ result.append((int(version), m))
+ self.queryResult = result
+ self.tupleLength = 2
+ self.computeIndices()
+ return result
+
+
+class Query4(Query):
+
+ def run(self, vistrail, name):
+ import vistrails.gui.vis_application
+ c = vistrails.gui.vis_application.logger.db.cursor()
+ c.execute("""
+ select distinct exec.ts_start, exec.ts_end, exec_id, module_id, wf_version from
+ wf_exec, exec, vistrails
+ where
+ exec.module_name = %s and
+ wf_exec.wf_exec_id = exec.wf_exec_id and
+ vistrails.vistrails_name = %s and
+ vistrails.vistrails_id = wf_exec.vistrails_id""", ('AlignWarp', name))
+
+ result = []
+ for ts_start, ts_end, exec_id, module_id, wf_version in c.fetchall():
+ p = vistrail.getPipeline(int(wf_version))
+ m = p.modules[module_id]
+ assert m.name == 'AlignWarp'
+ # We assume here that no module takes longer than a day to execute.
+ wd = 'monday'
+ if self.weekday(ts_start, wd) or self.weekday(ts_end, wd):
+ result.append((wf_version, module_id, exec_id))
+
+ self.queryResult = result
+ self.tupleLength = 3
+ self.computeIndices()
+ return result
+
+class Query5(Query):
+
+ @memo_method
+ def pipeline(self, vistrail, version):
+ return vistrail.getPipeline(version)
+
+ @memo_method
+ def upstream_set(self, graph, m_id):
+ return set(self.upstream(graph, m_id))
+
+ def run(self, vistrail, name):
+ import vistrails.gui.vis_application
+ c = vistrails.gui.vis_application.logger.db.cursor()
+ c.execute("""
+ select distinct
+ wf_exec.wf_version, exec.module_id
+ from
+ wf_exec, exec, annotation, vistrails
+ where
+ wf_exec.wf_exec_id = exec.wf_exec_id and
+ vistrails.vistrails_name = %s and
+ vistrails.vistrails_id = wf_exec.vistrails_id and
+ annotation.exec_id = exec.exec_id and
+ annotation.key = %s and
+ annotation.value = %s""", (name, 'global maximum', '4095'))
+ result = []
+ all = c.fetchall()
+ #print len(all)
+ version_module = {}
+ for wf_version, module_id in all:
+ if not wf_version in version_module:
+ version_module[wf_version] = set([module_id])
+ else:
+ version_module[wf_version].add(module_id)
+ #print vistrail.get_tagMap()
+ for wf_version, module_ids in version_module.iteritems():
+ #print wf_version
+ p = self.pipeline(vistrail, int(wf_version))
+ inv_graph = p.graph.inverse()
+ s = set()
+ for m_id, module in p.modules.iteritems():
+ if module.name == 'FileSink':
+ for f in module.functions:
+ if (f.name == 'outputName' and
+ len(f.params) == 1 and
+ f.params[0].value().find('atlas') != -1):
+ u_id = self.upstream_set(inv_graph, m_id)
+ if module_ids.intersection(u_id):
+ s = s.union(u_id).union(set([m_id]))
+ break
+ for m in s:
+ result.append((int(wf_version), m))
+ self.queryResult = result
+ self.tupleLength = 2
+ self.computeIndices()
+ return result
+
+
+class Query6(Query):
+
+ def run(self, vistrail, name):
+ import vistrails.gui.vis_application
+ c = vistrails.gui.vis_application.logger.db.cursor()
+ c.execute("""
+ select distinct module_id, wf_version from
+ wf_exec, exec, vistrails
+ where
+ exec.module_name = %s and
+ wf_exec.wf_exec_id = exec.wf_exec_id and
+ vistrails.vistrails_name = %s and
+ vistrails.vistrails_id = wf_exec.vistrails_id""", ('SoftMean', name))
+ result = []
+ for (module_id, wf_version) in c.fetchall():
+ p = vistrail.getPipeline(int(wf_version))
+ m = p.modules[module_id]
+ assert m.name == 'SoftMean'
+ inv_graph = p.graph.inverse()
+ up = self.upstream(inv_graph, module_id)
+ up.append(module_id)
+ found = False
+ for up_id in up:
+ up_module = p.modules[up_id]
+ if up_module.name == 'AlignWarp':
+ for f in up_module.functions:
+ if (f.name == 'model' and
+ len(f.params) == 1 and
+ f.params[0].value() == 12):
+ found = True
+ break
+ if found:
+ break
+ if found:
+ for up_id in up:
+ result.append((wf_version, up_id))
+ self.queryResult = result
+ self.tupleLength = 2
+ self.computeIndices()
+ return result
+
+
+class Query8(Query):
+
+ def run(self, vistrail, name):
+ result = []
+ versions = vistrail.get_tagMap().itervalues()
+ for version in versions:
+ s = set()
+ p = vistrail.getPipeline(version)
+ inv_graph = p.graph.inverse()
+ for module_id, module in p.modules.iteritems():
+ if module.name == 'AlignWarp':
+ found = False
+ u_ids = self.upstream(inv_graph, module_id)
+ for i in u_ids:
+ if (p.modules[i].has_annotation_with_key('center')
+ and p.modules[i].get_annotation_by_key('center') \
+ == 'UChicago'):
+ found = True
+ break
+ if found:
+ s = s.union(set(u_ids + [module_id]))
+ for m in s:
+ result.append((version, m))
+ self.queryResult = result
+ self.tupleLength = 2
+ self.computeIndices()
+ return result
+
+
+class Query9(Query):
+
+ def run(self, vistrail, name):
+ result = []
+ versions = vistrail.get_tagMap().itervalues()
+ for version in versions:
+ s = set()
+ p = vistrail.getPipeline(version)
+ inv_graph = p.graph.inverse()
+ for module_id, module in p.modules.iteritems():
+ annot = module.annotations
+ if (module.has_annotation_with_key('studyModality')
+ and module.get_annotation_by_key('studyModality') in \
+ ['visual', 'audio', 'speech']):
+ s = s.union(set(self.upstream(inv_graph, module_id) + [module_id]))
+ for m in s:
+ result.append((version, m))
+ self.queryResult = result
+ self.tupleLength = 2
+ self.computeIndices()
+ return result
diff --git a/vistrails/core/query/combined.py b/vistrails/core/query/combined.py
new file mode 100644
index 0000000..5096d23
--- /dev/null
+++ b/vistrails/core/query/combined.py
@@ -0,0 +1,81 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from version import SearchCompiler
+from visual import VisualQuery
+
+class CombinedSearch(VisualQuery):
+ def __init__(self, search_str=None, pipeline=None, versions_to_check=None):
+ VisualQuery.__init__(self, pipeline, versions_to_check)
+ self.search_str = search_str
+
+ def run(self, vistrail, name):
+ VisualQuery.run(self, vistrail, name)
+ self.search_stmt = SearchCompiler(self.search_str).searchStmt
+
+ def match(self, vistrail, action):
+ if self.queryPipeline is not None and \
+ len(self.queryPipeline.modules) > 0:
+ if action.timestep in self.versionDict:
+ return self.search_stmt.match(vistrail, action)
+ return False
+ else:
+ return self.search_stmt.match(vistrail, action)
+
+ def matchModule(self, version_id, module):
+ if self.queryPipeline is not None and \
+ len(self.queryPipeline.modules) > 0:
+ return VisualQuery.matchModule(self, version_id, module)
+ return True
+
+ def getResultEntity(self, vistrail, versions_to_check):
+ from vistrails.core.collection.vistrail import VistrailEntity
+
+ locators = []
+ vistrail_entity = None
+ for version in versions_to_check:
+ if version in vistrail.actionMap:
+ action = vistrail.actionMap[version]
+ if self.match(vistrail, action):
+ # have a match, get vistrail entity
+ if vistrail_entity is None:
+ vistrail_entity = VistrailEntity()
+ # don't want to add all workflows, executions
+ vistrail_entity.set_vistrail(vistrail)
+ vistrail_entity.add_workflow_entity(version)
+ # FIXME this is not done at the low level but in
+ # Collection class, probably should be reworked
+ vistrail_entity.wf_entity_map[version].parent = \
+ vistrail_entity
+ return vistrail_entity
diff --git a/vistrails/core/query/multiple.py b/vistrails/core/query/multiple.py
new file mode 100644
index 0000000..5a4afb2
--- /dev/null
+++ b/vistrails/core/query/multiple.py
@@ -0,0 +1,78 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.query import Query
+from combined import CombinedSearch
+
+class MultipleSearch(Query):
+ # vistrails_to_check { Vistrail: set(version_ids) }
+ def __init__(self, search_str=None, pipeline=None, entities_to_check={}):
+ self.entities_to_check = entities_to_check
+ self.queryPipeline = pipeline
+ self.search_str = search_str
+ self.queries = {}
+ self.queries_by_vistrail = {}
+ self.cur_vistrail = None
+
+ def setCurrentVistrail(self, vistrail):
+ self.cur_vistrail = vistrail
+
+ def run(self):
+ for entity, versions_to_check in self.entities_to_check.iteritems():
+ query = CombinedSearch(self.search_str, self.queryPipeline,
+ versions_to_check)
+ query.run(entity.vistrail, '')
+ self.queries[entity] = query
+ self.queries_by_vistrail[entity.vistrail] = query
+
+ def match(self, vistrail, action):
+ self.setCurrentVistrail(vistrail)
+ query = self.queries_by_vistrail[vistrail]
+ return query.match(vistrail, action)
+
+ def matchModule(self, version_id, module):
+ query = self.queries_by_vistrail[self.cur_vistrail]
+ return query.matchModule(version_id, module)
+
+ def getResultEntities(self):
+ result_entities = []
+ for entity, query in self.queries.iteritems():
+ versions_to_check = self.entities_to_check[entity]
+ result_entity = query.getResultEntity(entity.vistrail,
+ versions_to_check)
+ if result_entity is not None:
+ # needed for workspace results that are temporary...
+ result_entity._window = entity._window
+ result_entities.append(result_entity)
+ return result_entities
diff --git a/vistrails/core/query/version.py b/vistrails/core/query/version.py
new file mode 100644
index 0000000..4a769e4
--- /dev/null
+++ b/vistrails/core/query/version.py
@@ -0,0 +1,695 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# We need to remove QtGui and QtCore refernce by storing all of our
+# notes in plain text, not html, should be fix later
+from vistrails.core.query import extract_text
+import vistrails.core.utils
+import re
+import time
+
+import unittest
+import datetime
+
+################################################################################
+
+class SearchParseError(Exception):
+ def __init__(self, *args, **kwargs):
+ Exception.__init__(self, *args, **kwargs)
+
+class SearchStmt(object):
+ def __init__(self, content):
+ self.text = content
+ self.content = re.compile('.*'+content+'.*', re.MULTILINE | re.IGNORECASE)
+
+ def match(self, vistrail, action):
+ return True
+
+ def matchModule(self, v, m):
+ return True
+
+ def run(self, v, n):
+ pass
+
+ def __call__(self):
+ """Make SearchStmt behave just like a QueryObject."""
+ return self
+
+class TimeSearchStmt(SearchStmt):
+ oneSecond = 1.0
+ oneMinute = oneSecond * 60.0
+ oneHour = oneMinute * 60.0
+ oneDay = oneHour * 24.0
+ oneWeek = oneDay * 7.0
+ oneMonth = oneDay * 31.0 # wrong, I know
+ oneYear = oneDay * 365.0 # wrong, I know
+ amounts = {'seconds': oneSecond,
+ 'minutes': oneMinute,
+ 'hours': oneHour,
+ 'days': oneDay,
+ 'weeks': oneWeek,
+ 'months': oneMonth,
+ 'years': oneYear}
+ months = {'january': 1,
+ 'february': 2,
+ 'march': 3,
+ 'april': 4,
+ 'may': 5,
+ 'june': 6,
+ 'july': 7,
+ 'august': 8,
+ 'september': 9,
+ 'october': 10,
+ 'november': 11,
+ 'december': 12}
+
+ dateEntry = r'([^\,\/\: ]+)'
+ timeEntry = r'(\d?\d?)'
+ dateSep = r' *[\,\/\- ] *'
+ timeSep = r' *: *'
+ sep = r' *'
+ start = r'^ *'
+ finish = r' *$'
+ twoEntryDate = (dateEntry+
+ dateSep+
+ dateEntry)
+ threeEntryDate = (dateEntry+
+ dateSep+
+ dateEntry+
+ dateSep+
+ dateEntry)
+ twoEntryTime = (timeEntry+
+ timeSep+
+ timeEntry)
+ threeEntryTime = (timeEntry+
+ timeSep+
+ timeEntry+
+ timeSep+
+ timeEntry)
+
+ dateRE = [re.compile((start+
+ twoEntryDate+
+ finish)), # Mar 12 Mar, 12
+ re.compile((start+
+ threeEntryDate+
+ finish)), # Mar, 12, 2006 2006 Mar 12 etc
+ re.compile((start+
+ twoEntryTime+
+ finish)),
+ re.compile((start+
+ threeEntryTime+
+ finish)),
+ re.compile((start+
+ twoEntryDate+
+ sep+
+ twoEntryTime+
+ finish)),
+ re.compile((start+
+ twoEntryDate+
+ sep+
+ threeEntryTime+
+ finish)),
+ re.compile((start+
+ threeEntryDate+
+ sep+
+ twoEntryTime+
+ finish)),
+ re.compile((start+
+ threeEntryDate+
+ sep+
+ threeEntryTime+
+ finish)),
+ re.compile((start+
+ twoEntryTime+
+ sep+
+ twoEntryDate+
+ finish)),
+ re.compile((start+
+ twoEntryTime+
+ sep+
+ threeEntryDate+
+ finish)),
+ re.compile((start+
+ threeEntryTime+
+ sep+
+ twoEntryDate+
+ finish)),
+ re.compile((start+
+ threeEntryTime+
+ sep+
+ threeEntryDate+
+ finish))]
+
+ def __init__(self, date):
+ self.date = self.parseDate(date)
+
+ def parseDate(self, dateStr):
+ def parseAgo(s):
+ [amount, unit] = s.split(' ')
+ try:
+ amount = float(amount)
+ except ValueError:
+ raise SearchParseError("Expected a number, got %s" % amount)
+ if amount <= 0:
+ raise SearchParseError("Expected a positive number, got %s" % amount)
+ unitRe = re.compile('^'+unit)
+ keys = [k
+ for k in TimeSearchStmt.amounts.keys()
+ if unitRe.match(k)]
+ if len(keys) == 0:
+ raise SearchParseError("Time unit unknown: %s" % unit)
+ elif len(keys) > 1:
+ raise SearchParseError("Time unit ambiguous: %s matches %s" % (unit, keys))
+ return round(time.time()) - TimeSearchStmt.amounts[keys[0]] * amount
+
+ def guessDate(unknownEntries, year=None):
+ def guessStrMonth(s):
+ monthRe = re.compile('^'+s)
+ keys = [k
+ for k in TimeSearchStmt.months.keys()
+ if monthRe.match(k)]
+ if len(keys) == 0:
+ raise SearchParseError("Unknown month: %s" % s)
+ elif len(keys) > 1:
+ raise SearchParseError("Ambiguous month: %s matches %s" % (s, keys))
+ return TimeSearchStmt.months[keys[0]]
+ if not year:
+ m = None
+ # First heuristic: if month comes first, then year comes last
+ try:
+ e0 = int(unknownEntries[0])
+ except ValueError:
+ m = guessStrMonth(unknownEntries[0])
+ try:
+ d = int(unknownEntries[1])
+ except ValueError:
+ raise SearchParseError("Expected day, got %s" % unknownEntries[1])
+ try:
+ y = int(unknownEntries[2])
+ except ValueError:
+ raise SearchParseError("Expected year, got %s" % unknownEntries[2])
+ return (y, m, d)
+ # Second heuristic: if month comes last, then year comes first
+ try:
+ e2 = int(unknownEntries[2])
+ except ValueError:
+ m = guessStrMonth(unknownEntries[2])
+ try:
+ d = int(unknownEntries[1])
+ except ValueError:
+ raise SearchParseError("Expected day, got %s" % unknownEntries[1])
+ try:
+ y = int(unknownEntries[0])
+ except ValueError:
+ raise SearchParseError("Expected year, got %s" % unknownEntries[0])
+ return (y, m, d)
+ # If month is the middle one, decide day and year by size
+ # (year is largest, hopefully year was entered using 4 digits)
+ try:
+ e1 = int(unknownEntries[1])
+ except ValueError:
+ m = guessStrMonth(unknownEntries[1])
+ try:
+ d = int(unknownEntries[2])
+ except ValueError:
+ raise SearchParseError("Expected day or year, got %s" % unknownEntries[2])
+ try:
+ y = int(unknownEntries[0])
+ except ValueError:
+ raise SearchParseError("Expected year or year, got %s" % unknownEntries[0])
+ return (max(y,d), m, min(y, d))
+ lst = [(e0,0),(e1,1),(e2,2)]
+ lst.sort()
+ return guessDate([str(lst[0][0]),
+ str(lst[1][0])],
+ year=e2)
+ # We know year, decide month using similar heuristics - try string month first,
+ # then decide which is possible
+ try:
+ e0 = int(unknownEntries[0])
+ except ValueError:
+ m = guessStrMonth(unknownEntries[0])
+ try:
+ d = int(unknownEntries[1])
+ except ValueError:
+ raise SearchParseError("Expected day, got %s" % unknownEntries[1])
+ return (year, m, d)
+ try:
+ e1 = int(unknownEntries[1])
+ except ValueError:
+ m = guessStrMonth(unknownEntries[1])
+ try:
+ d = int(unknownEntries[0])
+ except ValueError:
+ raise SearchParseError("Expected day, got %s" % unknownEntries[0])
+ return (year, m, d)
+ if e0 > 12:
+ return (year, e1, e0)
+ else:
+ return (year, e0, e1)
+
+ dateStr = dateStr.lower().lstrip().rstrip()
+ if dateStr.endswith(" ago"):
+ return parseAgo(dateStr[:-4])
+ if dateStr == "yesterday":
+ lst = list(time.localtime(round(time.time()) - TimeSearchStmt.oneDay))
+ # Reset hour, minute, second
+ lst[3] = 0
+ lst[4] = 0
+ lst[5] = 0
+ return time.mktime(lst)
+ if dateStr == "today":
+ lst = list(time.localtime())
+ # Reset hour, minute, second
+ lst[3] = 0
+ lst[4] = 0
+ lst[5] = 0
+ return time.mktime(lst)
+ if dateStr.startswith("this "):
+ rest = dateStr[5:]
+ lst = list(time.localtime(round(time.time())))
+ if rest == "minute":
+ lst[5] = 0
+ elif rest == "hour":
+ lst[5] = 0
+ lst[4] = 0
+ elif rest == "day":
+ lst[5] = 0
+ lst[4] = 0
+ lst[3] = 0
+ elif rest == "week": # weeks start on monday
+ lst[5] = 0
+ lst[4] = 0
+ lst[3] = 0
+ # This hack saves me the hassle of computing negative days, months, etc
+ lst = list(time.localtime(time.mktime(lst) - TimeSearchStmt.oneDay * lst[6]))
+ elif rest == "month":
+ lst[5] = 0
+ lst[4] = 0
+ lst[3] = 0
+ lst[2] = 1
+ elif rest == "year":
+ lst[5] = 0
+ lst[4] = 0
+ lst[3] = 0
+ lst[2] = 1
+ lst[1] = 1
+ return time.mktime(lst)
+
+ result = [x.match(dateStr) for x in TimeSearchStmt.dateRE]
+ this = list(time.localtime())
+ def setTwoDate(g):
+ d = guessDate(g, year=this[0])
+ this[0] = d[0]
+ this[1] = d[1]
+ this[2] = d[2]
+ def setThreeDate(g):
+ d = guessDate(g)
+ this[0] = d[0]
+ this[1] = d[1]
+ this[2] = d[2]
+ def setTwoTime(g):
+ this[3] = int(g[0])
+ this[4] = int(g[1])
+ this[5] = 0
+ def setThreeTime(g):
+ this[3] = int(g[0])
+ this[4] = int(g[1])
+ this[5] = int(g[2])
+ if result[0]:
+ setTwoDate(result[0].groups())
+ setTwoTime([0,0])
+ elif result[1]:
+ setThreeDate(result[1].groups())
+ setTwoTime([0,0])
+ elif result[2]:
+ setTwoTime(result[2].groups())
+ elif result[3]:
+ setThreeTime(result[3].groups())
+ elif result[4]:
+ g = result[4].groups()
+ setTwoDate([g[0], g[1]])
+ setTwoTime([g[2], g[3]])
+ elif result[5]:
+ g = result[5].groups()
+ setTwoDate([g[0], g[1]])
+ setThreeTime([g[2], g[3], g[4]])
+ elif result[6]:
+ g = result[6].groups()
+ setThreeDate([g[0], g[1], g[2]])
+ setTwoTime([g[3], g[4]])
+ elif result[7]:
+ g = result[7].groups()
+ setThreeDate([g[0], g[1], g[2]])
+ setThreeTime([g[3], g[4], g[5]])
+ elif result[8]:
+ g = result[8].groups()
+ setTwoTime([g[0], g[1]])
+ setTwoDate([g[2], g[3]])
+ elif result[9]:
+ g = result[9].groups()
+ setTwoTime([g[0], g[1]])
+ setThreeDate([g[2], g[3], g[4]])
+ elif result[10]:
+ g = result[10].groups()
+ setThreeTime([g[0], g[1], g[2]])
+ setTwoDate([g[3], g[4]])
+ elif result[11]:
+ g = result[11].groups()
+ setThreeTime([g[0], g[1], g[2]])
+ setThreeDate([g[3], g[4],g[5]])
+ else:
+ raise SearchParseError("Expected a date, got '%s'" % dateStr)
+ return time.mktime(this)
+
+class BeforeSearchStmt(TimeSearchStmt):
+ def match(self, vistrail, action):
+ if not action.date:
+ return False
+ t = time.mktime(time.strptime(action.date, "%d %b %Y %H:%M:%S"))
+ return t <= self.date
+
+class AfterSearchStmt(TimeSearchStmt):
+ def match(self, vistrail, action):
+ if not action.date:
+ return False
+ t = time.mktime(time.strptime(action.date, "%d %b %Y %H:%M:%S"))
+ return t >= self.date
+
+class UserSearchStmt(SearchStmt):
+ def match(self, vistrail, action):
+ if not action.user:
+ return False
+ return self.content.match(action.user)
+
+class NotesSearchStmt(SearchStmt):
+ def match(self, vistrail, action):
+ if vistrail.has_notes(action.id):
+ plainNotes = extract_text(vistrail.get_notes(action.id))
+ return self.content.search(plainNotes)
+ return False
+
+class NameSearchStmt(SearchStmt):
+ def match(self, vistrail, action):
+ m = 0
+ tm = vistrail.get_tagMap()
+ if action.timestep in tm:
+ m = self.content.match(tm[action.timestep])
+ if bool(m) == False:
+ m = self.content.match(vistrail.get_description(action.timestep))
+ return bool(m)
+
+class ModuleSearchStmt(SearchStmt):
+ def match(self, vistrail, action):
+ pipeline = vistrail.getPipeline(action.timestep)
+ for module in pipeline.modules.itervalues():
+ if self.content.match(module.name):
+ return True
+ return False
+
+class AndSearchStmt(SearchStmt):
+ def __init__(self, lst):
+ self.matchList = lst
+ def match(self, vistrail, action):
+ for s in self.matchList:
+ if not s.match(vistrail, action):
+ return False
+ return True
+
+class OrSearchStmt(SearchStmt):
+ def __init__(self, lst):
+ self.matchList = lst
+ def match(self, vistrail, action):
+ for s in self.matchList:
+ if s.match(vistrail, action):
+ return True
+ return False
+
+class NotSearchStmt(SearchStmt):
+ def __init__(self, stmt):
+ self.stmt = stmt
+ def match(self, vistrail, action):
+ return not self.stmt.match(action)
+
+class TrueSearch(SearchStmt):
+ def __init__(self):
+ pass
+ def match(self, vistrail, action):
+ return True
+
+################################################################################
+
+class SearchCompiler(object):
+ SEPARATOR = -1
+ def __init__(self, searchStr):
+ self.searchStmt = self.compile(searchStr)
+ def compile(self, searchStr):
+ lst = []
+ t1 = searchStr.split(' ')
+ while t1:
+ tok = t1[0]
+ cmd = tok.split(':')
+ if not SearchCompiler.dispatch.has_key(cmd[0]):
+ fun = SearchCompiler.parseAny
+ else:
+ fun = SearchCompiler.dispatch[cmd[0]]
+ if len(cmd) > 1:
+ [search, rest] = fun(self, cmd[1:] + t1[1:])
+ else:
+ [search, rest] = fun(self, t1)
+ lst.append(search)
+ t1 = rest
+ return AndSearchStmt(lst)
+ def parseUser(self, tokStream):
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ return (UserSearchStmt(tokStream[0]), tokStream[1:])
+ def parseAny(self, tokStream):
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ tok = tokStream[0]
+ return (OrSearchStmt([UserSearchStmt(tok),
+ NotesSearchStmt(tok),
+ NameSearchStmt(tok)]), tokStream[1:])
+ def parseNotes(self, tokStream):
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ lst = []
+ while len(tokStream):
+ tok = tokStream[0]
+ if ':' in tok:
+ return (AndSearchStmt(lst), tokStream)
+ lst.append(NotesSearchStmt(tok))
+ tokStream = tokStream[1:]
+ return (AndSearchStmt(lst), [])
+ def parseName(self, tokStream):
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ lst = []
+ while len(tokStream):
+ tok = tokStream[0]
+ if ':' in tok:
+ return (AndSearchStmt(lst), tokStream)
+ lst.append(NameSearchStmt(tok))
+ tokStream = tokStream[1:]
+ return (AndSearchStmt(lst), [])
+ def parseModule(self, tokStream):
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ lst = []
+ while len(tokStream):
+ tok = tokStream[0]
+ if ':' in tok:
+ return (AndSearchStmt(lst), tokStream)
+ lst.append(ModuleSearchStmt(tok))
+ tokStream = tokStream[1:]
+ return (AndSearchStmt(lst), [])
+ def parseBefore(self, tokStream):
+ old_tokstream = tokStream
+ try:
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ lst = []
+ while len(tokStream):
+ tok = tokStream[0]
+ # ugly, special case times
+ if (':' in tok and
+ not TimeSearchStmt.dateRE[2].match(tok) and
+ not TimeSearchStmt.dateRE[3].match(tok)):
+ return (BeforeSearchStmt(" ".join(lst)), tokStream)
+ lst.append(tok)
+ tokStream = tokStream[1:]
+ return (BeforeSearchStmt(" ".join(lst)), [])
+ except SearchParseError, e:
+ if 'Expected a date' in e.args[0]:
+ try:
+ return self.parseAny(old_tokstream)
+ except SearchParseError, e2:
+ print "Another exception...", e2.args[0]
+ raise e
+ else:
+ raise
+
+ def parseAfter(self, tokStream):
+ try:
+ if len(tokStream) == 0:
+ raise SearchParseError('Expected token, got end of search')
+ lst = []
+ while len(tokStream):
+ tok = tokStream[0]
+ # ugly, special case times
+ if (':' in tok and
+ not TimeSearchStmt.dateRE[2].match(tok) and
+ not TimeSearchStmt.dateRE[3].match(tok)):
+ return (AfterSearchStmt(" ".join(lst)), tokStream)
+ lst.append(tok)
+ tokStream = tokStream[1:]
+ return (AfterSearchStmt(" ".join(lst)), [])
+ except SearchParseError, e:
+ if 'Expected a date' in e.args[0]:
+ try:
+ return self.parseAny(['after'] + tokStream)
+ except SearchParseError, e2:
+ print "Another exception...", e2.args[0]
+ raise e
+ else:
+ raise
+
+ dispatch = {'user': parseUser,
+ 'notes': parseNotes,
+ 'before': parseBefore,
+ 'after': parseAfter,
+ 'name': parseName,
+ 'module': parseModule,
+ 'any': parseAny}
+
+
+
+################################################################################
+
+
+class TestSearch(unittest.TestCase):
+ def test1(self):
+ self.assertEquals((TimeSearchStmt('1 day ago').date -
+ TimeSearchStmt('2 days ago').date), TimeSearchStmt.oneDay)
+ def test2(self):
+ self.assertEquals((TimeSearchStmt('12 mar 2006').date -
+ TimeSearchStmt('11 mar 2006').date), TimeSearchStmt.oneDay)
+ def test3(self):
+ # This will fail if year flips during execution. Oh well :)
+ yr = datetime.datetime.today().year
+ self.assertEquals((TimeSearchStmt('12 mar').date -
+ TimeSearchStmt('12 mar %d' % yr).date), 0.0)
+ def test4(self):
+ # This will fail if year flips during execution. Oh well :)
+ yr = datetime.datetime.today().year
+ self.assertEquals((TimeSearchStmt('mar 12').date -
+ TimeSearchStmt('12 mar %d' % yr).date), 0.0)
+ def test5(self):
+ yr = datetime.datetime.today().year
+ self.assertEquals((TimeSearchStmt('03 15').date -
+ TimeSearchStmt('15 mar %d' % yr).date), 0.0)
+ def test6(self):
+ self.assertEquals((TimeSearchStmt('03/15/2006').date -
+ TimeSearchStmt('15 mar 2006').date), 0.0)
+ def test7(self):
+ self.assertEquals((TimeSearchStmt('1 day ago').date -
+ TimeSearchStmt('24 hours ago').date), 0.0)
+ def test8(self):
+ self.assertEquals((TimeSearchStmt('1 hour ago').date -
+ TimeSearchStmt('60 minutes ago').date), 0.0)
+ def test9(self):
+ self.assertEquals((TimeSearchStmt('1 minute ago').date -
+ TimeSearchStmt('60 seconds ago').date), 0.0)
+ def test10(self):
+ self.assertEquals((TimeSearchStmt('1 week ago').date -
+ TimeSearchStmt('7 days ago').date), 0.0)
+ def test11(self):
+ self.assertEquals((TimeSearchStmt('1 month ago').date -
+ TimeSearchStmt('31 days ago').date), 0.0)
+ def test12(self):
+ self.assertEquals(TimeSearchStmt('12 mar 2007 21:00:00').date,
+ TimeSearchStmt('21:00:00 12 mar 2007').date)
+ def test13(self):
+ # This will fail if year flips during execution. Oh well :)
+ yr = datetime.datetime.today().year
+ self.assertEquals(TimeSearchStmt('12 mar %d 21:00' % yr).date,
+ TimeSearchStmt('21:00:00 12 mar').date)
+ def test14(self):
+ self.assertEquals(TimeSearchStmt('13 apr 2006 21:00').date,
+ TimeSearchStmt('04/13/2006 21:00:00').date)
+ def test15(self):
+ import vistrails.core.vistrail
+ from vistrails.core.db.locator import XMLFileLocator
+ import vistrails.core.system
+ v = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/dummy.xml').load()
+ # FIXME: Add notes to this.
+# self.assertTrue(NotesSearchStmt('mapper').match(v.actionMap[36]))
+# self.assertFalse(NotesSearchStmt('-qt-block-indent').match(v.actionMap[36]))
+
+ # test16 and 17 now pass.
+ # def test16(self):
+ # self.assertRaises(SearchParseError, lambda *args: SearchCompiler('before:'))
+ # def test17(self):
+ # self.assertRaises(SearchParseError, lambda *args: SearchCompiler('after:yesterday before:lalala'))
+ def test18(self):
+ self.assertEquals(TimeSearchStmt(' 13 apr 2006 ').date,
+ TimeSearchStmt(' 13 apr 2006 ').date)
+ def test19(self):
+ self.assertEquals(SearchCompiler('before:13 apr 2006 12:34:56').searchStmt.matchList[0].date,
+ BeforeSearchStmt('13 apr 2006 12:34:56').date)
+ def test20(self):
+ self.assertEquals(SearchCompiler('after:yesterday').searchStmt.matchList[0].date,
+ SearchCompiler('before:yesterday').searchStmt.matchList[0].date)
+ def test21(self):
+ self.assertEquals(SearchCompiler('after:today').searchStmt.matchList[0].date,
+ SearchCompiler('before:today').searchStmt.matchList[0].date)
+ def test22(self):
+ self.assertEquals(SearchCompiler('before:today').searchStmt.matchList[0].date,
+ SearchCompiler('before:this day').searchStmt.matchList[0].date)
+ def test23(self):
+ t = time.localtime()
+ import vistrails.core.utils
+ inv = vistrails.core.utils.invert(TimeSearchStmt.months)
+ m = inv[t[1]]
+ self.assertEquals(SearchCompiler('after:%s %s %s' % (t[0], m, t[2])).searchStmt.matchList[0].date,
+ SearchCompiler('after:today').searchStmt.matchList[0].date)
+ def test24(self):
+ # Test compiling these searches
+ SearchCompiler('before')
+ SearchCompiler('after')
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/query/visual.py b/vistrails/core/query/visual.py
new file mode 100644
index 0000000..9e87d14
--- /dev/null
+++ b/vistrails/core/query/visual.py
@@ -0,0 +1,239 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core import query
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.utils import append_to_dict_of_lists
+import copy
+import re
+
+################################################################################
+
+class VisualQuery(query.Query):
+
+ def __init__(self, pipeline, versions_to_check):
+ self.queryPipeline = copy.copy(pipeline)
+ self.versions_to_check = versions_to_check
+
+ def heuristicDAGIsomorphism(self,
+ target, template,
+ target_ids, template_ids):
+ resultIds = set()
+ while 1:
+ templateNames = set([(i, template.modules[i].name)
+ for i in template_ids])
+ targetNames = {}
+ for i in target_ids:
+ append_to_dict_of_lists(targetNames, target.modules[i].name, i)
+
+ nextTargetIds = set()
+ nextTemplateIds = set()
+
+ for (i, templateName) in templateNames:
+ if templateName not in targetNames:
+ return (False, resultIds)
+ else:
+ templateModule = template.modules[i]
+ matched = [tId
+ for tId in targetNames[templateName]
+ if self.matchQueryModule(target.modules[tId],
+ templateModule)]
+ resultIds.update(matched)
+ for matchedTargetId in matched:
+ nextTargetIds.update([moduleId for
+ (moduleId, edgeId) in
+ target.graph.edges_from(matchedTargetId)])
+ nextTemplateIds.update([moduleId for
+ (moduleId, edgeId) in
+ template.graph.edges_from(i)])
+
+ if not len(nextTemplateIds):
+ return (True, resultIds)
+
+ target_ids = nextTargetIds
+ template_ids = nextTemplateIds
+
+ def run(self, vistrail, name):
+ result = []
+ self.tupleLength = 2
+ for version in self.versions_to_check:
+ p = vistrail.getPipeline(version)
+ matches = set()
+ queryModuleNameIndex = {}
+ for moduleId, module in p.modules.iteritems():
+ append_to_dict_of_lists(queryModuleNameIndex, module.name, moduleId)
+ for querySourceId in self.queryPipeline.graph.sources():
+ querySourceName = self.queryPipeline.modules[querySourceId].name
+ if not queryModuleNameIndex.has_key(querySourceName):
+ # need to reset matches here!
+ matches = set()
+ continue
+ candidates = queryModuleNameIndex[querySourceName]
+ atLeastOneMatch = False
+ for candidateSourceId in candidates:
+ querySource = self.queryPipeline.modules[querySourceId]
+ candidateSource = p.modules[candidateSourceId]
+ if not self.matchQueryModule(candidateSource,
+ querySource):
+ continue
+ (match, targetIds) = self.heuristicDAGIsomorphism \
+ (template = self.queryPipeline,
+ target = p,
+ template_ids = [querySourceId],
+ target_ids = [candidateSourceId])
+ if match:
+ atLeastOneMatch = True
+ matches.update(targetIds)
+
+ # We always perform AND operation
+ if not atLeastOneMatch:
+ matches = set()
+ break
+
+ for m in matches:
+ result.append((version, m))
+ self.queryResult = result
+ self.computeIndices()
+ return result
+
+ def __call__(self):
+ """Returns a copy of itself. This needs to be implemented so that
+ a visualquery object looks like a class that can be instantiated
+ once per vistrail."""
+ return VisualQuery(self.queryPipeline)
+
+ def matchQueryModule(self, template, target):
+ """ matchQueryModule(template, target: Module) -> bool
+ Return true if the target module can be matched to the
+ template module
+
+ """
+ if target.name != template.name:
+ return False
+ if target.getNumFunctions()>template.getNumFunctions():
+ return False
+ candidateFunctions = {}
+ for fid in xrange(template.getNumFunctions()):
+ f = template.functions[fid]
+ append_to_dict_of_lists(candidateFunctions, f.name, f)
+
+ for f in target.functions:
+ if f.name not in candidateFunctions:
+ return False
+ fNotMatch = True
+ candidates = candidateFunctions[f.name]
+ for cf in candidates:
+ if len(cf.params)!=len(f.params):
+ continue
+ pMatch = True
+ for pid in xrange(len(cf.params)):
+ cp = cf.params[pid]
+ p = f.params[pid]
+ if not self.matchQueryParam(p, cp):
+ pMatch = False
+ break
+ if pMatch:
+ fNotMatch = False
+ break
+ if fNotMatch:
+ return False
+ return True
+
+ def matchQueryParam(self, template, target):
+ """ matchQueryParam(template: Param, target: Param) -> bool
+ Check to see if target can match with a query template
+
+ """
+ if (template.type != target.type or
+ template.identifier != target.identifier or
+ template.namespace != target.namespace):
+ return False
+
+ reg = get_module_registry()
+ desc = reg.get_descriptor_by_name(template.identifier, template.type,
+ template.namespace)
+ return desc.module.query_compute(target.strValue, template.strValue,
+ template.queryMethod)
+
+ # if template.type=='String':
+ # op = template.queryMethod/2
+ # caseInsensitive = template.queryMethod%2==0
+ # templateStr = template.strValue
+ # targetStr = target.strValue
+ # if caseInsensitive:
+ # templateStr = templateStr.lower()
+ # targetStr = targetStr.lower()
+
+ # if op==0:
+ # return templateStr in targetStr
+ # if op==1:
+ # return templateStr==targetStr
+ # if op==2:
+ # try:
+ # mo = re.match(templateStr, targetStr)
+ # if mo!=None:
+ # return mo.end()==len(targetStr)
+ # else:
+ # return False
+ # except:
+ # return False
+ # else:
+ # # FIXME: eval should pretty much never be used
+ # if template.strValue.strip()=='':
+ # return True
+ # realTypeDict = {'Integer': int, 'Float': float}
+ # realType = realTypeDict[template.type]
+ # try:
+ # return realType(template.strValue)==realType(target.strValue)
+ # except: # not a constant
+ # try:
+ # return bool(eval(target.strValue+' '+template.strValue))
+ # except: # not a '<', '>', or '==' expression
+ # try:
+ # s = template.strValue.replace(' ', '')
+ # if s[0]=='(':
+ # mid1 = '<%s)' % target.strValue
+ # if s[0]=='[':
+ # mid1 = '<=%s)' % target.strValue
+ # if s[-1]==')':
+ # mid2 = '(%s<' % target.strValue
+ # if s[-1]==']':
+ # mid2 = '(%s<=' % target.strValue
+
+ # s = s.replace(',', '%s and %s' % (mid1, mid2))
+ # s = '(' + s[1:-1] + ')'
+ # return eval(s)
+ # except:
+ # print 'Invalid query "%s".' % template.strValue
+ # return False
diff --git a/vistrails/core/recent_vistrails.py b/vistrails/core/recent_vistrails.py
new file mode 100644
index 0000000..9f0297c
--- /dev/null
+++ b/vistrails/core/recent_vistrails.py
@@ -0,0 +1,111 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" RecentVistrailList is a Helper class to manage serialization and
+unserialization of a list of locators to XML """
+from vistrails.core.system import get_elementtree_library
+from vistrails.core.db.locator import FileLocator, DBLocator
+
+ElementTree = get_elementtree_library()
+
+class RecentVistrailList(object):
+ def __init__(self):
+ self.maxlocators = 0
+ self.locators = []
+ self.locators_map = {}
+
+ @staticmethod
+ def unserialize(text):
+ """ unserialize(text) -> RecentVistrailList """
+ root = ElementTree.fromstring(text)
+ if root.tag != 'recentVistrails':
+ return None
+ vtlist = RecentVistrailList()
+ for node in root.getchildren():
+ loc = FileLocator.from_xml(node)
+ if loc is None:
+ loc = DBLocator.from_xml(node, include_name=True)
+ if loc is not None:
+ vtlist.locators.append(loc)
+ vtlist.locators_map[loc.name] = loc
+ return vtlist
+
+ def serialize(self, node=None):
+ """serialize(node: ElementTree.Element) -> text
+ Convert this object to an XML representation.
+ """
+ if node is None:
+ node = ElementTree.Element('recentVistrails')
+ for loc in self.locators:
+ childNode = ElementTree.SubElement(node, 'locator')
+ if isinstance(loc, DBLocator):
+ loc.to_xml(childNode, include_name=True)
+ else:
+ loc.to_xml(childNode)
+ return ElementTree.tostring(node)
+
+ def ensure_no_more_than_max(self, max):
+ while len(self.locators) > max:
+ locator = self.locators.pop()
+ del self.locators_map[locator.name]
+
+ self.maxlocators = max
+
+ def add_locator(self, locator):
+ if locator in self.locators:
+ self.locators.remove(locator)
+ self.locators.insert(0, locator)
+ self.locators_map[locator.name] = locator
+
+ self.ensure_no_more_than_max(self.maxlocators)
+
+ def remove_locator(self, locator):
+ if locator in self.locators:
+ self.locators.remove(locator)
+ del self.locators_map[locator.name]
+
+ def length(self):
+ return len(self.locators)
+
+ def get_locator(self, index):
+ try:
+ return self.locators[index]
+ except IndexError:
+ return None
+
+ def get_locator_by_name(self, name):
+ try:
+ return self.locators_map[name]
+ except KeyError:
+ return None
\ No newline at end of file
diff --git a/vistrails/core/repository/__init__.py b/vistrails/core/repository/__init__.py
new file mode 100644
index 0000000..cdc9214
--- /dev/null
+++ b/vistrails/core/repository/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# Nothing here on purpose
+pass
diff --git a/vistrails/core/repository/poster/__init__.py b/vistrails/core/repository/poster/__init__.py
new file mode 100644
index 0000000..bd04291
--- /dev/null
+++ b/vistrails/core/repository/poster/__init__.py
@@ -0,0 +1,67 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# Copyright (c) 2010 Chris AtLee
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+
+"""poster module
+
+Support for streaming HTTP uploads, and multipart/form-data encoding
+
+```poster.version``` is a 3-tuple of integers representing the version number.
+New releases of poster will always have a version number that compares greater
+than an older version of poster.
+New in version 0.6."""
+import vistrails.core.repository.poster.streaminghttp
+import vistrails.core.repository.poster.encode
+
+#version = (0, 7, 0) # Thanks JP!
diff --git a/vistrails/core/repository/poster/encode.py b/vistrails/core/repository/poster/encode.py
new file mode 100644
index 0000000..2905c47
--- /dev/null
+++ b/vistrails/core/repository/poster/encode.py
@@ -0,0 +1,469 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# Copyright (c) 2010 Chris AtLee
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+
+"""multipart/form-data encoding module
+
+This module provides functions that faciliate encoding name/value pairs
+as multipart/form-data suitable for a HTTP POST or PUT request.
+
+multipart/form-data is the standard way to upload files over HTTP"""
+
+__all__ = ['gen_boundary', 'encode_and_quote', 'MultipartParam',
+ 'encode_string', 'encode_file_header', 'get_body_size', 'get_headers',
+ 'multipart_encode']
+
+try:
+ import uuid
+ def gen_boundary():
+ """Returns a random string to use as the boundary for a message"""
+ return uuid.uuid4().hex
+except ImportError:
+ import random, sha
+ def gen_boundary():
+ """Returns a random string to use as the boundary for a message"""
+ bits = random.getrandbits(160)
+ return sha.new(str(bits)).hexdigest()
+
+import urllib, re, os, mimetypes
+
+def encode_and_quote(data):
+ """If ``data`` is unicode, return urllib.quote_plus(data.encode("utf-8"))
+ otherwise return urllib.quote_plus(data)"""
+ if data is None:
+ return None
+
+ if isinstance(data, unicode):
+ data = data.encode("utf-8")
+ return urllib.quote_plus(data)
+
+def _strify(s):
+ """If s is a unicode string, encode it to UTF-8 and return the results,
+ otherwise return str(s), or None if s is None"""
+ if s is None:
+ return None
+ if isinstance(s, unicode):
+ return s.encode("utf-8")
+ return str(s)
+
+class MultipartParam(object):
+ """Represents a single parameter in a multipart/form-data request
+
+ ``name`` is the name of this parameter.
+
+ If ``value`` is set, it must be a string or unicode object to use as the
+ data for this parameter.
+
+ If ``filename`` is set, it is what to say that this parameter's filename
+ is. Note that this does not have to be the actual filename any local file.
+
+ If ``filetype`` is set, it is used as the Content-Type for this parameter.
+ If unset it defaults to "text/plain; charset=utf8"
+
+ If ``filesize`` is set, it specifies the length of the file ``fileobj``
+
+ If ``fileobj`` is set, it must be a file-like object that supports
+ .read().
+
+ Both ``value`` and ``fileobj`` must not be set, doing so will
+ raise a ValueError assertion.
+
+ If ``fileobj`` is set, and ``filesize`` is not specified, then
+ the file's size will be determined first by stat'ing ``fileobj``'s
+ file descriptor, and if that fails, by seeking to the end of the file,
+ recording the current position as the size, and then by seeking back to the
+ beginning of the file.
+
+ ``cb`` is a callable which will be called from iter_encode with (self,
+ current, total), representing the current parameter, current amount
+ transferred, and the total size.
+ """
+ def __init__(self, name, value=None, filename=None, filetype=None,
+ filesize=None, fileobj=None, cb=None):
+ self.name = encode_and_quote(name)
+ self.value = _strify(value)
+ if filename is None:
+ self.filename = None
+ else:
+ if isinstance(filename, unicode):
+ # Encode with XML entities
+ self.filename = filename.encode("ascii", "xmlcharrefreplace")
+ else:
+ self.filename = str(filename)
+ self.filename = self.filename.encode("string_escape").\
+ replace('"', '\\"')
+ self.filetype = _strify(filetype)
+
+ self.filesize = filesize
+ self.fileobj = fileobj
+ self.cb = cb
+
+ if self.value is not None and self.fileobj is not None:
+ raise ValueError("Only one of value or fileobj may be specified")
+
+ if fileobj is not None and filesize is None:
+ # Try and determine the file size
+ try:
+ self.filesize = os.fstat(fileobj.fileno()).st_size
+ except (OSError, AttributeError):
+ try:
+ fileobj.seek(0, 2)
+ self.filesize = fileobj.tell()
+ fileobj.seek(0)
+ except:
+ raise ValueError("Could not determine filesize")
+
+ def __cmp__(self, other):
+ attrs = ['name', 'value', 'filename', 'filetype', 'filesize', 'fileobj']
+ myattrs = [getattr(self, a) for a in attrs]
+ oattrs = [getattr(other, a) for a in attrs]
+ return cmp(myattrs, oattrs)
+
+ def reset(self):
+ if self.fileobj is not None:
+ self.fileobj.seek(0)
+ elif self.value is None:
+ raise ValueError("Don't know how to reset this parameter")
+
+ @classmethod
+ def from_file(cls, paramname, filename):
+ """Returns a new MultipartParam object constructed from the local
+ file at ``filename``.
+
+ ``filesize`` is determined by os.path.getsize(``filename``)
+
+ ``filetype`` is determined by mimetypes.guess_type(``filename``)[0]
+
+ ``filename`` is set to os.path.basename(``filename``)
+ """
+
+ return cls(paramname, filename=os.path.basename(filename),
+ filetype=mimetypes.guess_type(filename)[0],
+ filesize=os.path.getsize(filename),
+ fileobj=open(filename, "rb"))
+
+ @classmethod
+ def from_params(cls, params):
+ """Returns a list of MultipartParam objects from a sequence of
+ name, value pairs, MultipartParam instances,
+ or from a mapping of names to values
+
+ The values may be strings or file objects, or MultipartParam objects.
+ MultipartParam object names must match the given names in the
+ name,value pairs or mapping, if applicable."""
+ if hasattr(params, 'items'):
+ params = params.items()
+
+ retval = []
+ for item in params:
+ if isinstance(item, cls):
+ retval.append(item)
+ continue
+ name, value = item
+ if isinstance(value, cls):
+ assert value.name == name
+ retval.append(value)
+ continue
+ if hasattr(value, 'read'):
+ # Looks like a file object
+ filename = getattr(value, 'name', None)
+ if filename is not None:
+ filetype = mimetypes.guess_type(filename)[0]
+ else:
+ filetype = None
+
+ retval.append(cls(name=name, filename=filename,
+ filetype=filetype, fileobj=value))
+ else:
+ retval.append(cls(name, value))
+ return retval
+
+ def encode_hdr(self, boundary):
+ """Returns the header of the encoding of this parameter"""
+ boundary = encode_and_quote(boundary)
+
+ headers = ["--%s" % boundary]
+
+ if self.filename:
+ disposition = 'form-data; name="%s"; filename="%s"' % (self.name,
+ self.filename)
+ else:
+ disposition = 'form-data; name="%s"' % self.name
+
+ headers.append("Content-Disposition: %s" % disposition)
+
+ if self.filetype:
+ filetype = self.filetype
+ else:
+ filetype = "text/plain; charset=utf-8"
+
+ headers.append("Content-Type: %s" % filetype)
+
+ if self.filesize is not None:
+ headers.append("Content-Length: %i" % self.filesize)
+ else:
+ headers.append("Content-Length: %i" % len(self.value))
+
+ headers.append("")
+ headers.append("")
+
+ return "\r\n".join(headers)
+
+ def encode(self, boundary):
+ """Returns the string encoding of this parameter"""
+ if self.value is None:
+ value = self.fileobj.read()
+ else:
+ value = self.value
+
+ if re.search("^--%s$" % re.escape(boundary), value, re.M):
+ raise ValueError("boundary found in encoded string")
+
+ return "%s%s\r\n" % (self.encode_hdr(boundary), value)
+
+ def iter_encode(self, boundary, blocksize=4096):
+ """Yields the encoding of this parameter
+ If self.fileobj is set, then blocks of ``blocksize`` bytes are read and
+ yielded."""
+ total = self.get_size(boundary)
+ current = 0
+ if self.value is not None:
+ block = self.encode(boundary)
+ current += len(block)
+ yield block
+ if self.cb:
+ self.cb(self, current, total)
+ else:
+ block = self.encode_hdr(boundary)
+ current += len(block)
+ yield block
+ if self.cb:
+ self.cb(self, current, total)
+ last_block = ""
+ encoded_boundary = "--%s" % encode_and_quote(boundary)
+ boundary_exp = re.compile("^%s$" % re.escape(encoded_boundary),
+ re.M)
+ while True:
+ block = self.fileobj.read(blocksize)
+ if not block:
+ current += 2
+ yield "\r\n"
+ if self.cb:
+ self.cb(self, current, total)
+ break
+ last_block += block
+ if boundary_exp.search(last_block):
+ raise ValueError("boundary found in file data")
+ last_block = last_block[-len(encoded_boundary)-2:]
+ current += len(block)
+ yield block
+ if self.cb:
+ self.cb(self, current, total)
+
+ def get_size(self, boundary):
+ """Returns the size in bytes that this param will be when encoded
+ with the given boundary."""
+ if self.filesize is not None:
+ valuesize = self.filesize
+ else:
+ valuesize = len(self.value)
+
+ return len(self.encode_hdr(boundary)) + 2 + valuesize
+
+def encode_string(boundary, name, value):
+ """Returns ``name`` and ``value`` encoded as a multipart/form-data
+ variable. ``boundary`` is the boundary string used throughout
+ a single request to separate variables."""
+
+ return MultipartParam(name, value).encode(boundary)
+
+def encode_file_header(boundary, paramname, filesize, filename=None,
+ filetype=None):
+ """Returns the leading data for a multipart/form-data field that contains
+ file data.
+
+ ``boundary`` is the boundary string used throughout a single request to
+ separate variables.
+
+ ``paramname`` is the name of the variable in this request.
+
+ ``filesize`` is the size of the file data.
+
+ ``filename`` if specified is the filename to give to this field. This
+ field is only useful to the server for determining the original filename.
+
+ ``filetype`` if specified is the MIME type of this file.
+
+ The actual file data should be sent after this header has been sent.
+ """
+
+ return MultipartParam(paramname, filesize=filesize, filename=filename,
+ filetype=filetype).encode_hdr(boundary)
+
+def get_body_size(params, boundary):
+ """Returns the number of bytes that the multipart/form-data encoding
+ of ``params`` will be."""
+ size = sum(p.get_size(boundary) for p in MultipartParam.from_params(params))
+ return size + len(boundary) + 6
+
+def get_headers(params, boundary):
+ """Returns a dictionary with Content-Type and Content-Length headers
+ for the multipart/form-data encoding of ``params``."""
+ headers = {}
+ boundary = urllib.quote_plus(boundary)
+ headers['Content-Type'] = "multipart/form-data; boundary=%s" % boundary
+ headers['Content-Length'] = str(get_body_size(params, boundary))
+ return headers
+
+class multipart_yielder:
+ def __init__(self, params, boundary, cb):
+ self.params = params
+ self.boundary = boundary
+ self.cb = cb
+
+ self.i = 0
+ self.p = None
+ self.param_iter = None
+ self.current = 0
+ self.total = get_body_size(params, boundary)
+
+ def __iter__(self):
+ return self
+
+ def next(self):
+ """generator function to yield multipart/form-data representation
+ of parameters"""
+ if self.param_iter is not None:
+ try:
+ block = self.param_iter.next()
+ self.current += len(block)
+ if self.cb:
+ self.cb(self.p, self.current, self.total)
+ return block
+ except StopIteration:
+ self.p = None
+ self.param_iter = None
+
+ if self.i is None:
+ raise StopIteration
+ elif self.i >= len(self.params):
+ self.param_iter = None
+ self.p = None
+ self.i = None
+ block = "--%s--\r\n" % self.boundary
+ self.current += len(block)
+ if self.cb:
+ self.cb(self.p, self.current, self.total)
+ return block
+
+ self.p = self.params[self.i]
+ self.param_iter = self.p.iter_encode(self.boundary)
+ self.i += 1
+ return self.next()
+
+ def reset(self):
+ self.i = 0
+ self.current = 0
+ for param in self.params:
+ param.reset()
+
+def multipart_encode(params, boundary=None, cb=None):
+ """Encode ``params`` as multipart/form-data.
+
+ ``params`` should be a sequence of (name, value) pairs or MultipartParam
+ objects, or a mapping of names to values.
+ Values are either strings parameter values, or file-like objects to use as
+ the parameter value. The file-like objects must support .read() and either
+ .fileno() or both .seek() and .tell().
+
+ If ``boundary`` is set, then it as used as the MIME boundary. Otherwise
+ a randomly generated boundary will be used. In either case, if the
+ boundary string appears in the parameter values a ValueError will be
+ raised.
+
+ If ``cb`` is set, it should be a callback which will get called as blocks
+ of data are encoded. It will be called with (param, current, total),
+ indicating the current parameter being encoded, the current amount encoded,
+ and the total amount to encode.
+
+ Returns a tuple of `datagen`, `headers`, where `datagen` is a
+ generator that will yield blocks of data that make up the encoded
+ parameters, and `headers` is a dictionary with the assoicated
+ Content-Type and Content-Length headers.
+
+ Examples:
+
+ >>> datagen, headers = multipart_encode( [("key", "value1"), ("key", "value2")] )
+ >>> s = "".join(datagen)
+ >>> assert "value2" in s and "value1" in s
+
+ >>> p = MultipartParam("key", "value2")
+ >>> datagen, headers = multipart_encode( [("key", "value1"), p] )
+ >>> s = "".join(datagen)
+ >>> assert "value2" in s and "value1" in s
+
+ >>> datagen, headers = multipart_encode( {"key": "value1"} )
+ >>> s = "".join(datagen)
+ >>> assert "value2" not in s and "value1" in s
+
+ """
+ if boundary is None:
+ boundary = gen_boundary()
+ else:
+ boundary = urllib.quote_plus(boundary)
+
+ headers = get_headers(params, boundary)
+ params = MultipartParam.from_params(params)
+
+ return multipart_yielder(params, boundary, cb), headers
diff --git a/vistrails/core/repository/poster/streaminghttp.py b/vistrails/core/repository/poster/streaminghttp.py
new file mode 100644
index 0000000..5f1cfd0
--- /dev/null
+++ b/vistrails/core/repository/poster/streaminghttp.py
@@ -0,0 +1,255 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# Copyright (c) 2010 Chris AtLee
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+
+"""Streaming HTTP uploads module.
+
+This module extends the standard httplib and urllib2 objects so that
+iterable objects can be used in the body of HTTP requests.
+
+In most cases all one should have to do is call :func:`register_openers()`
+to register the new streaming http handlers which will take priority over
+the default handlers, and then you can use iterable objects in the body
+of HTTP requests.
+
+**N.B.** You must specify a Content-Length header if using an iterable object
+since there is no way to determine in advance the total size that will be
+yielded, and there is no way to reset an interator.
+
+Example usage:
+
+>>> from StringIO import StringIO
+>>> import urllib2, poster.streaminghttp
+
+>>> opener = poster.streaminghttp.register_openers()
+
+>>> s = "Test file data"
+>>> f = StringIO(s)
+
+>>> req = urllib2.Request("http://localhost:5000", f,
+... {'Content-Length': str(len(s))})
+"""
+
+import httplib, urllib2, socket
+from httplib import NotConnected
+
+__all__ = ['StreamingHTTPConnection', 'StreamingHTTPRedirectHandler',
+ 'StreamingHTTPHandler', 'register_openers']
+
+if hasattr(httplib, 'HTTPS'):
+ __all__.extend(['StreamingHTTPSHandler', 'StreamingHTTPSConnection'])
+
+class _StreamingHTTPMixin:
+ """Mixin class for HTTP and HTTPS connections that implements a streaming
+ send method."""
+ def send(self, value):
+ """Send ``value`` to the server.
+
+ ``value`` can be a string object, a file-like object that supports
+ a .read() method, or an iterable object that supports a .next()
+ method.
+ """
+ # Based on python 2.6's httplib.HTTPConnection.send()
+ if self.sock is None:
+ if self.auto_open:
+ self.connect()
+ else:
+ raise NotConnected()
+
+ # send the data to the server. if we get a broken pipe, then close
+ # the socket. we want to reconnect when somebody tries to send again.
+ #
+ # NOTE: we DO propagate the error, though, because we cannot simply
+ # ignore the error... the caller will know if they can retry.
+ if self.debuglevel > 0:
+ print "send:", repr(value)
+ try:
+ blocksize = 8192
+ if hasattr(value, 'read') :
+ if hasattr(value, 'seek'):
+ value.seek(0)
+ if self.debuglevel > 0:
+ print "sendIng a read()able"
+ data = value.read(blocksize)
+ while data:
+ self.sock.sendall(data)
+ data = value.read(blocksize)
+ elif hasattr(value, 'next'):
+ if hasattr(value, 'reset'):
+ value.reset()
+ if self.debuglevel > 0:
+ print "sendIng an iterable"
+ for data in value:
+ self.sock.sendall(data)
+ else:
+ self.sock.sendall(value)
+ except socket.error, v:
+ if v[0] == 32: # Broken pipe
+ self.close()
+ raise
+
+class StreamingHTTPConnection(_StreamingHTTPMixin, httplib.HTTPConnection):
+ """Subclass of `httplib.HTTPConnection` that overrides the `send()` method
+ to support iterable body objects"""
+
+class StreamingHTTPRedirectHandler(urllib2.HTTPRedirectHandler):
+ """Subclass of `urllib2.HTTPRedirectHandler` that overrides the
+ `redirect_request` method to properly handle redirected POST requests
+
+ This class is required because python 2.5's HTTPRedirectHandler does
+ not remove the Content-Type or Content-Length headers when requesting
+ the new resource, but the body of the original request is not preserved.
+ """
+
+ handler_order = urllib2.HTTPRedirectHandler.handler_order - 1
+
+ # From python2.6 urllib2's HTTPRedirectHandler
+ def redirect_request(self, req, fp, code, msg, headers, newurl):
+ """Return a Request or None in response to a redirect.
+
+ This is called by the http_error_30x methods when a
+ redirection response is received. If a redirection should
+ take place, return a new Request to allow http_error_30x to
+ perform the redirect. Otherwise, raise HTTPError if no-one
+ else should try to handle this url. Return None if you can't
+ but another Handler might.
+ """
+ m = req.get_method()
+ if (code in (301, 302, 303, 307) and m in ("GET", "HEAD")
+ or code in (301, 302, 303) and m == "POST"):
+ # Strictly (according to RFC 2616), 301 or 302 in response
+ # to a POST MUST NOT cause a redirection without confirmation
+ # from the user (of urllib2, in this case). In practice,
+ # essentially all clients do redirect in this case, so we
+ # do the same.
+ # be conciliant with URIs containing a space
+ newurl = newurl.replace(' ', '%20')
+ newheaders = dict((k, v) for k, v in req.headers.items()
+ if k.lower() not in (
+ "content-length", "content-type")
+ )
+ return urllib2.Request(newurl,
+ headers=newheaders,
+ origin_req_host=req.get_origin_req_host(),
+ unverifiable=True)
+ else:
+ raise urllib2.HTTPError(req.get_full_url(), code, msg, headers, fp)
+
+class StreamingHTTPHandler(urllib2.HTTPHandler):
+ """Subclass of `urllib2.HTTPHandler` that uses
+ StreamingHTTPConnection as its http connection class."""
+
+ handler_order = urllib2.HTTPHandler.handler_order - 1
+
+ def http_open(self, req):
+ """Open a StreamingHTTPConnection for the given request"""
+ return self.do_open(StreamingHTTPConnection, req)
+
+ def http_request(self, req):
+ """Handle a HTTP request. Make sure that Content-Length is specified
+ if we're using an interable value"""
+ # Make sure that if we're using an iterable object as the request
+ # body, that we've also specified Content-Length
+ if req.has_data():
+ data = req.get_data()
+ if hasattr(data, 'read') or hasattr(data, 'next'):
+ if not req.has_header('Content-length'):
+ raise ValueError(
+ "No Content-Length specified for iterable body")
+ return urllib2.HTTPHandler.do_request_(self, req)
+
+if hasattr(httplib, 'HTTPS'):
+ class StreamingHTTPSConnection(_StreamingHTTPMixin,
+ httplib.HTTPSConnection):
+ """Subclass of `httplib.HTTSConnection` that overrides the `send()`
+ method to support iterable body objects"""
+
+ class StreamingHTTPSHandler(urllib2.HTTPSHandler):
+ """Subclass of `urllib2.HTTPSHandler` that uses
+ StreamingHTTPSConnection as its http connection class."""
+
+ handler_order = urllib2.HTTPSHandler.handler_order - 1
+
+ def https_open(self, req):
+ return self.do_open(StreamingHTTPSConnection, req)
+
+ def https_request(self, req):
+ # Make sure that if we're using an iterable object as the request
+ # body, that we've also specified Content-Length
+ if req.has_data():
+ data = req.get_data()
+ if hasattr(data, 'read') or hasattr(data, 'next'):
+ if not req.has_header('Content-length'):
+ raise ValueError(
+ "No Content-Length specified for iterable body")
+ return urllib2.HTTPSHandler.do_request_(self, req)
+
+
+def register_openers(cookiejar=None):
+ """Register the streaming http handlers in the global urllib2 default
+ opener object.
+
+ Returns the created OpenerDirector object."""
+ handlers = [StreamingHTTPHandler, StreamingHTTPRedirectHandler]
+ if hasattr(httplib, "HTTPS"):
+ handlers.append(StreamingHTTPSHandler)
+
+ if cookiejar:
+ opener = urllib2.build_opener(urllib2.HTTPCookieProcessor(cookiejar), *handlers)
+ else:
+ opener = urllib2.build_opener(*handlers)
+
+ urllib2.install_opener(opener)
+
+ return opener
diff --git a/vistrails/core/requirements.py b/vistrails/core/requirements.py
new file mode 100644
index 0000000..01b76d5
--- /dev/null
+++ b/vistrails/core/requirements.py
@@ -0,0 +1,94 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""module that allows online inspection of environment to test presence of
+runtime components such as binaries, libraries, other python modules, etc."""
+import sys
+
+import vistrails.core.bundles.installbundle
+from vistrails.core.configuration import get_vistrails_configuration
+import vistrails.core.system
+
+##############################################################################
+
+def python_module_exists(module_name):
+ """python_module_exists(module_name): Boolean.
+Returns if python module of given name can be safely imported."""
+
+ try:
+ sys.modules[module_name]
+ return True
+ except KeyError:
+ pass
+ try:
+ __import__(module_name)
+ return True
+ except ImportError:
+ return False
+
+
+def executable_file_exists(filename):
+ """executable_file_exists(filename): Boolean.
+Returns if certain file is in current path and is executable."""
+ result = vistrails.core.system.executable_is_in_path(filename)
+ if result == "":
+ result = vistrails.core.system.executable_is_in_pythonpath(filename)
+ return result != ""
+
+# FIXME: Add documentation.
+
+def require_python_module(module_name, dep_dict=None):
+ exists = python_module_exists(module_name)
+ if (not exists and
+ dep_dict and
+ getattr(get_vistrails_configuration(), 'installBundles')):
+ vistrails.core.bundles.installbundle.install(dep_dict)
+ exists = python_module_exists(module_name)
+ if not exists:
+ raise MissingRequirement(module_name)
+
+def require_executable(filename):
+ if not executable_file_exists(filename):
+ raise MissingRequirement(filename)
+
+##############################################################################
+
+class MissingRequirement(Exception):
+ """Raise this exception in packages when necessary items are missing."""
+ def __init__(self, req):
+ self.requirement = req
+ def __str__(self):
+ return "Missing Requirement: %s" % self.requirement
+
diff --git a/vistrails/core/resources/default_vistrails_startup b/vistrails/core/resources/default_vistrails_startup
new file mode 100644
index 0000000..0a6c394
--- /dev/null
+++ b/vistrails/core/resources/default_vistrails_startup
@@ -0,0 +1,204 @@
+###############################################################################
+##
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# Vistrails initialization file
+##############################################################################
+
+##############################################################################
+# Basic configuration
+
+# Comment this to use the logging mechanism (which is being
+# overhauled, so right now it's also broken)
+configuration.nologger = True
+
+# Uncomment this to prevent VisTrails's splash screen from appearing
+# configuration.showSplash = False
+
+# Uncomment this to enable VisTrails's python shell by default
+# configuration.pythonPrompt = True
+
+# Uncomment this to switch to the non-caching execution model
+# configuration.useCache = False
+
+# Uncomment this to start VisTrails with maximized windows
+# configuration.maximizeWindows = True
+
+# Uncomment this if you run multiple monitors, to start VisTrails
+# with different windows in different monitors
+# configuration.multiHeads = True
+
+# Set verbosenessLevel to 1 or 2 to enable dumping of non-critical warnings
+# and information messages to stderr.
+# configuration.verbosenessLevel = 1 # 2
+
+##############################################################################
+# VisTrails packages.
+
+# VisTrails packages are collections of modules that provide user-specified
+# functionality to VisTrails. Use addPackage to let VisTrails know which
+# packages you want enabled.
+
+# Interpackage dependencies must currently be handled manually by the user.
+
+# For example, the spreadsheet package depends on VTK for some functionality,
+# so if you want that functionality, you should add the vtk package before
+# the spreadsheet package.
+
+# the vtk package is the main visualization package for VisTrails
+# addPackage('vtk')
+
+# pythonCalc is an example package intended simply to demonstrate how to
+# create new packages
+# addPackage('pythonCalc')
+
+# ImageMagick uses the ImageMagick command-line suite to perform various
+# tasks on images (conversion, filtering, etc).
+#addPackage('ImageMagick')
+
+# The spreadsheet package enables the Visualization Spreadsheet
+# addPackage('spreadsheet')
+
+# The HTTP package provides an easy way to access files from http and use
+# them as regular files in VisTrails pipelines.
+# addPackage('HTTP')
+
+# The pylab (matplotlib) package for plotting and histograms
+# addPackage('pylab')
+
+
+################################################################################
+# Hooks
+
+# Currently, there is only one hook in VisTrails: the startup hook. By adding
+# arbitrary callables to the startup hook, it is possible to run user-defined
+# code after all packages have been initialized, but before VisTrails runs.
+
+# This is intended to show that it is possible to have user-defined code
+# in specific places in VisTrails. If you think you need a hook somewhere that
+# we haven't allowed yet, please let us know, and we'll include it in a future
+# release.
+
+def testHook():
+ """Prints the Module class hierarchy to stdout."""
+ def printTree(n, indent = 0):
+ def iprint(str):
+ print '%s%s' % (" " * indent, str)
+ iprint('Class: %s' % n.descriptor.name)
+ for c in n.children:
+ printTree(c, indent+4)
+
+ import modules
+ import modules.module_registry
+ t = modules.module_registry.registry.classTree
+ printTree(t)
+
+# Uncomment this line to install the startup hook
+# addStartupHook(testHook)
+
+
+##############################################################################
+# If you have an appropriate Qt license, you can install signal inspectors,
+# which might make debugging a whole lot easier. To do that, uncomment the
+# following lines.
+
+
+# import qt
+# connections = {}
+# def connectHandler(*args):
+# """This handler writes all signal connections to /tmp/signalslotnames.txt"""
+# emitter = args[0].__class__.__name__
+# signal = args[1]
+# f = signal.find('(')
+# if f == -1:
+# signal = signal[1:]
+# else:
+# signal = signal[1:f]
+# try:
+# receiver = args[2].im_class.__name__
+# slot = args[2].im_func.__name__
+# except AttributeError:
+# receiver = args[2].__self__.__class__.__name__
+# slot = args[2].__class__.__name__
+# entry = (emitter, signal, receiver, slot)
+# print entry
+# global connections
+# try:
+# connections[emitter].add((signal, receiver, slot))
+# except:
+# connections[emitter] = set(((signal, receiver, slot),))
+# signals = {}
+# slots = {}
+# sig_count = 1
+# slot_count = 1
+# f = open('/tmp/connections.txt', 'w')
+# f.write('digraph {\n')
+# for (k, v) in connections.iteritems():
+# print k, v
+# recs = {}
+# for (sig, rec, sl) in v:
+# if not signals.has_key(sig):
+# signals[sig] = sig_count
+# sig_count += 1
+# if not slots.has_key(sl):
+# slots[sl] = slot_count
+# slot_count += 1
+# try:
+# recs[rec].append( str(signals[sig]) + ':' + str(slots[sl]))
+# except:
+# recs[rec] = [str(signals[sig]) + ':' + str(slots[sl])]
+# for rec, sigslotlist in recs.iteritems():
+# f.write('%s -> %s [label = "%s"];\n' % (k, rec, ";".join(sigslotlist)))
+# # if not entry in connections:
+# # f = open('/tmp/connections.txt', 'a')
+# # f.write("%s %s %s\n" % emi)
+# # f.close()
+# # connections.add(entry)
+# f.write('}\n')
+# f.close()
+# f = open('/tmp/signalslotnames.txt', 'w')
+# sigs = [(v, k) for (k, v) in signals.items()]
+# sigs.sort()
+# sls = [(v, k) for (k, v) in slots.items()]
+# sls.sort()
+# f.write('signals: \n')
+# for (k,v) in sigs:
+# f.write('%s: %s\n' % (k, v))
+# f.write('slots: \n')
+# for (k,v) in sls:
+# f.write('%s: %s\n' % (k, v))
+
+
+# This line hooks connectHandler to Qt's signals. You can use user-defined
+# code here.
+# qt.enableSignalDebugging(connectCall = connectHandler)
diff --git a/vistrails/core/resources/default_vistrails_startup_xml b/vistrails/core/resources/default_vistrails_startup_xml
new file mode 100644
index 0000000..f901b45
--- /dev/null
+++ b/vistrails/core/resources/default_vistrails_startup_xml
@@ -0,0 +1,70 @@
+<startup version="0.1">
+ <configuration>
+ <key name="nologger">
+ <bool value="True"/>
+ </key>
+ </configuration>
+ <packages>
+ <package name="vtk"/>
+ <package name="pythonCalc"/>
+ <package name="spreadsheet"/>
+ <package name="dialogs"/>
+ <package name="HTTP"/>
+ <package name="controlflow"/>
+ <package name="tabledata"/>
+ </packages>
+ <disabledpackages/>
+</startup>
+
+<!--
+ This is what a "regular" startup file looks like.
+
+<startup version="0.1">
+ <configuration>
+ <key name="nologger">
+ <bool value="True"/>
+ </key>
+ <key name="shell">
+ <configuration>
+ <key name="font_face">
+ <str value="Bitstream Vera mono"/>
+ </key>
+ <key name="font_size">
+ <int value="9"/>
+ </key>
+ </configuration>
+ </key>
+ </configuration>
+ <packages>
+ <package name="vtk"/>
+ <package name="spreadsheet"/>
+ <package name="pythonCalc"/>
+ <package name="ImageMagick"/>
+ <package name="HTTP"/>
+ <package name="teem"/>
+ <package name="ectmc"/>
+ <package name="macet"/>
+ <package name="trimesh2"/>
+ <package name="meshutils"/>
+ <package name="afront">
+ <configuration>
+ <key name="debug">
+ <bool value="True"/>
+ </key>
+ </configuration>
+ </package>
+ <package name="metro"/>
+ <package name="console_mode_test"/>
+ <package name="ProteinDataBank"/>
+ <package name="dialogs"/>
+ <package name="SciPy"/>
+ <package name="webServices">
+ <configuration>
+ <key name="wsdlList">
+ <str value=""/>
+ </key>
+ </configuration>
+ </package>
+ </packages>
+</startup>
+-->
diff --git a/vistrails/core/resources/spawned_startup_xml b/vistrails/core/resources/spawned_startup_xml
new file mode 100644
index 0000000..b65ed3a
--- /dev/null
+++ b/vistrails/core/resources/spawned_startup_xml
@@ -0,0 +1,42 @@
+<?xml version="1.0" ?>
+<startup version="0.1">
+ <packages>
+ <package name="spreadsheet">
+ <configuration>
+ <key name="columnCount">
+ <int value="3"/>
+ </key>
+ <key name="rowCount">
+ <int value="2"/>
+ </key>
+ <key name="dumpfileType">
+ <str value="PNG"/>
+ </key>
+ </configuration>
+ </package>
+ <package name="controlflow"/>
+ <package name="abstraction"/>
+ </packages>
+ <disabledpackages/>
+ <configuration>
+ <key name="nologger">
+ <bool value="True"/>
+ </key>
+ <key name="nologfile">
+ <bool value="True"/>
+ </key>
+ <key name="spawned">
+ <bool value="True"/>
+ </key>
+ <key name="shell">
+ <configuration>
+ <key name="font_face">
+ <str value="Bitstream Vera mono"/>
+ </key>
+ <key name="font_size">
+ <int value="9"/>
+ </key>
+ </configuration>
+ </key>
+ </configuration>
+</startup>
diff --git a/vistrails/core/startup.py b/vistrails/core/startup.py
new file mode 100644
index 0000000..3487722
--- /dev/null
+++ b/vistrails/core/startup.py
@@ -0,0 +1,598 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Describes the start-up process of VisTrails"""
+from vistrails.core import debug
+from vistrails.core import system
+from vistrails.core.utils.uxml import named_elements, elements_filter, \
+ eval_xml_value, enter_named_element
+import copy
+import vistrails.core.packagemanager
+import vistrails.core.utils
+import os.path
+import shutil
+import sys
+import tempfile
+import vistrails.core.configuration
+import xml.dom.minidom
+
+################################################################################
+
+class VistrailsStartup(object):
+ """
+ VistrailsStartup is the class that initializes VisTrails based on
+ a configuration. Both application mode (interactive and
+ non-interactive) and import mode of VisTrails use this start up
+ process to install packages and run .vistrails file. The purpose
+ of this class is to separate the initialization process with Qt
+ Application
+
+ """
+
+ def __init__(self, config=None, tempconfig=None):
+ """ VistrailsStartup(config, tempconfig: ConfigurationObject,
+ optionsDict: dict) -> None
+ Setup the configuration. config is the persistent configuration and
+ tempconfig is the current configuration.
+
+ """
+ assert (config is None or
+ isinstance(config, vistrails.core.configuration.ConfigurationObject))
+ assert (tempconfig is None or
+ isinstance(tempconfig, vistrails.core.configuration.ConfigurationObject))
+ if config:
+ self.configuration = config
+ else:
+ self.configuration = vistrails.core.configuration.default()
+ if tempconfig:
+ self.temp_configuration = tempconfig
+ else:
+ self.temp_configuration = copy.copy(self.configuration)
+
+ self.startupHooks = []
+
+ # This needs to be here because we want to log all initialization
+ # steps
+ self.setupLogFile()
+ self._python_environment = self.runDotVistrails()
+ self.load_configuration()
+
+ #the problem is that maybe the logFile now points to a different place
+ self.setupLogFile()
+
+ self.setupDefaultFolders()
+ #package_manager needs the persistent configuration
+ self._package_manager = vistrails.core.packagemanager.PackageManager(
+ self.configuration)
+
+ self._do_load_packages = True
+ self._package_dictionary = {}
+ # stores all packages that must be enabled on startup
+ self._needed_packages = []
+
+ def init(self):
+ """ init() -> None
+ Initialize VisTrails with optionsDict. optionsDict can be
+ another VisTrails Configuration object, e.g. ConfigurationObject
+
+ """
+ if self._do_load_packages:
+ self.load_packages()
+ if self._do_load_packages:
+ # don't call this anymore since we do an add_package for it now
+ # self.setupBaseModules()
+ self.installPackages()
+ self.runStartupHooks()
+
+ def set_needed_packages(self, package_list):
+ self._needed_packages = package_list
+
+ ##########################################################################
+ # startup.xml related
+
+ def startup_dom(self):
+ filename = os.path.join(self.temp_configuration.dotVistrails,'startup.xml')
+ return xml.dom.minidom.parse(filename)
+
+ def write_startup_dom(self, dom):
+ filename = os.path.join(self.temp_configuration.dotVistrails,'startup.xml')
+ f = open(filename, 'w')
+ f.write(dom.toxml())
+
+ def load_configuration(self):
+ """load_configuration() -> None
+ Loads the appropriate configuration from .vistrails/startup.xml.
+ This will overwrite both configuration and temp_configuration
+
+ """
+ dom = self.startup_dom()
+ conf = enter_named_element(dom.documentElement, 'configuration')
+ self.configuration.set_from_dom_node(conf)
+ self.temp_configuration.set_from_dom_node(conf)
+
+ def load_packages(self):
+ """load_packages() -> None
+
+ Loads the appropriate packages from .vistrails/startup.xml.
+ """
+
+ for package_name in self._needed_packages:
+ self._package_manager.add_package(package_name)
+
+ def parse_package(node):
+ is_value = (lambda node: node.nodeName in
+ set(['bool', 'str', 'int', 'float']))
+ package_name = str(node.attributes['name'].value)
+ # FIXME use more robust checks here!
+ if package_name != 'basic_modules' and \
+ package_name != 'abstraction':
+ self._package_manager.add_package(package_name)
+ dom = self.startup_dom()
+ doc = dom.documentElement
+ packages_node = enter_named_element(doc, 'packages')
+ for package_node in named_elements(packages_node, 'package'):
+ parse_package(package_node)
+
+ ##########################################################################
+
+ def get_python_environment(self):
+ """get_python_environment(): returns the python environment generated
+by startup.py. This should only be called after init()."""
+ return self._python_environment
+
+ def create_default_directory(self):
+ if os.path.lexists(self.temp_configuration.dotVistrails):
+ return
+
+ debug.log('Will try to create default directory')
+ try:
+ os.mkdir(self.temp_configuration.dotVistrails)
+ debug.log('Succeeded!')
+ except:
+ debug.critical("""Failed to create initialization directory.
+ This could be an indication of a permissions problem.
+ Make sure parent directory of '%s' is writable."""
+ % self.temp_configuration.dotVistrails)
+ sys.exit(1)
+
+ def runDotVistrails(self):
+ """ runDotVistrails() -> None
+ Setup to run user .vistrails file
+
+ """
+ def addStartupHook(hook):
+ """ addStartupHook(hook: function) -> None
+ Add a hook for start-up after initialization
+
+ """
+ self.startupHooks.append(hook)
+
+ def addPackage(packageName, *args, **keywords):
+ """ addPackage(packageName: str, *args) -> None
+ """
+ self._package_manager.add_package(packageName)
+
+ def create_user_packages_init(userpackagesname):
+ try:
+ name = os.path.join(userpackagesname, '__init__.py')
+ f = open(name, 'w')
+ f.write('pass\n')
+ f.close()
+ except:
+ msg = ("""Failed to create file '%s'. This could indicate a
+ rare combination of a race condition and a permissions problem.
+ Please make sure it is writable.""" % name)
+ debug.critical(msg)
+ sys.exit(1)
+
+ def create_user_packages_dir(userpackagesname=None):
+ debug.warning('Will try to create userpackages directory')
+ if userpackagesname is None:
+ userpackagesname = os.path.join(self.temp_configuration.dotVistrails,
+ 'userpackages')
+ if not os.path.isdir(userpackagesname):
+ try:
+ os.mkdir(userpackagesname)
+ self.configuration.userPackageDirectory = userpackagesname
+ self.temp_configuration.userPackageDirectory = \
+ userpackagesname
+ except:
+ msg = ("""Failed to create userpackages directory: '%s'.
+ This could be an indication of a permissions problem.
+ Make sure directory '%s' in writable.""" %
+ (userpackagesname,
+ self.configuration.dotVistrails))
+ debug.critical(msg)
+ sys.exit(1)
+ create_user_packages_init(userpackagesname)
+
+ def create_thumbnails_dir(thumbnails_dir=None):
+ debug.log('Will try to create thumbnails directory')
+ if thumbnails_dir is None:
+ thumbnails_dir = os.path.join(self.temp_configuration.dotVistrails,
+ 'thumbs')
+
+ if not os.path.isdir(thumbnails_dir):
+ try:
+ os.mkdir(thumbnails_dir)
+ self.configuration.thumbs.cacheDirectory = thumbnails_dir
+ self.temp_configuration.thumbs.cacheDirectory = \
+ thumbnails_dir
+ except:
+ msg = ("Failed to create thumbnails cache directory: '%s'. "
+ "This could be an indication of a permissions "
+ "problem. Make sure directory '%s' is writable." % \
+ (thumbnails_dir,
+ self.configuration.dotVistrails))
+ debug.critical(msg)
+ sys.exit(1)
+
+ def create_abstractions_dir(abstractions_dir=None):
+ debug.log('Will try to create subworkflows directory')
+ abstractions_dir = os.path.join(self.temp_configuration.dotVistrails,
+ 'subworkflows')
+
+ if not os.path.isdir(abstractions_dir):
+ try:
+ os.mkdir(abstractions_dir)
+ self.configuration.abstractionsDirectory = abstractions_dir
+ self.temp_configuration.abstractionsDirectory = \
+ abstractions_dir
+ except:
+ msg = ("Failed to create subworkflows directory: '%s'. "
+ "This could be an indication of a permissions "
+ "problem. Make sure directory '%s' is writable." % \
+ (abstractions_dir,
+ self.configuration.dotVistrails))
+ debug.critical(msg)
+ sys.exit(1)
+# try:
+# root_dir = core.system.vistrails_root_directory()
+# default_file = os.path.join(root_dir,'core','resources',
+# 'abstractions_init')
+# user_file = os.path.join(abstractions_dir, '__init__.py')
+# print 'copying', default_file, '->', abstractions_dir
+# shutil.copyfile(default_file, user_file)
+# debug.log('Succeeded!')
+# except Exception, e:
+# print e
+# debug.critical("Failed to copy default file to abstractions "
+# "package. This could be an indication of a "
+# "permissions problem. Make sure directory "
+# "'%s' is writable" % abstractions_dir)
+# sys.exit(1)
+
+ def install_default_startup():
+ debug.log('Will try to create default startup script')
+ try:
+ root_dir = vistrails.core.system.vistrails_root_directory()
+ default_file = os.path.join(root_dir,'core','resources',
+ 'default_vistrails_startup')
+ user_file = os.path.join(self.temp_configuration.dotVistrails,
+ 'startup.py')
+ shutil.copyfile(default_file,user_file)
+ debug.log('Succeeded!')
+ except:
+ debug.critical("""Failed to copy default file %s.
+ This could be an indication of a permissions problem.
+ Make sure directory '%s' is writable"""
+ % (user_file,self.temp_configuration.dotVistrails))
+ sys.exit(1)
+
+ def install_default_startupxml_if_needed():
+ fname = os.path.join(self.temp_configuration.dotVistrails,
+ 'startup.xml')
+ root_dir = vistrails.core.system.vistrails_root_directory()
+ origin = os.path.join(root_dir, 'core','resources',
+ 'default_vistrails_startup_xml')
+ def skip():
+ if os.path.isfile(fname):
+ try:
+ d = self.startup_dom()
+ v = str(d.getElementsByTagName('startup')[0].attributes['version'].value)
+ r = vistrails.core.utils.version_string_to_list(v)
+ return r >= [0, 1]
+ except:
+ return False
+ else:
+ return False
+ if skip():
+ return
+ try:
+ shutil.copyfile(origin, fname)
+ debug.log('Succeeded!')
+ except:
+ debug.critical("""Failed to copy default configuration
+ file to %s. This could be an indication of a
+ permissions problem. Please make sure '%s' is writable."""
+ % (fname,
+ self.temp_configuration.dotVistrails))
+
+ def execDotVistrails(tried_once=False):
+ """ execDotVistrails() -> None
+ Actually execute the Vistrail initialization
+
+ """
+ # if it is file, then must move old-style .vistrails to
+ # directory.
+ if os.path.isfile(self.temp_configuration.dotVistrails):
+ debug.warning("Old-style initialization hooks. Will try to set things correctly.")
+ (fd, name) = tempfile.mkstemp()
+ os.close(fd)
+ try:
+ shutil.copyfile(self.temp_configuration.dotVistrails, name)
+ try:
+ os.unlink(self.temp_configuration.dotVistrails)
+ except:
+ debug.critical("""Failed to remove old initialization file.
+ This could be an indication of a permissions problem.
+ Make sure file '%s' is writable."""
+ % self.temp_configuration.dotVistrails)
+ sys.exit(1)
+ self.create_default_directory()
+ try:
+ destiny = os.path.join(self.temp_configuration.dotVistrails,
+ 'startup.py')
+ shutil.copyfile(name, destiny)
+ except:
+ debug.critical("""Failed to copy old initialization file to
+ newly-created initialization directory. This must have been
+ a race condition. Please remove '%s' and
+ restart VisTrails."""
+ % self.temp_configuration.dotVistrails)
+ sys.exit(1)
+ debug.critical("Successful move!")
+ finally:
+ try:
+ os.unlink(name)
+ except:
+ debug.warning("Failed to erase temporary file.")
+
+ if os.path.isdir(self.temp_configuration.dotVistrails):
+ if self.temp_configuration.check('userPackageDirectory'):
+ userpackages = self.temp_configuration.userPackageDirectory
+ else:
+ userpackages = os.path.join(self.temp_configuration.dotVistrails,
+ 'userpackages')
+ startup = os.path.join(self.temp_configuration.dotVistrails,
+ 'startup.py')
+ if self.temp_configuration.check('abstractionsDirectory'):
+ abstractions = self.temp_configuration.abstractionsDirectory
+ else:
+ abstractions = os.path.join(self.temp_configuration.dotVistrails,
+ 'subworkflows')
+ if (self.temp_configuration.has('thumbs') and
+ self.temp_configuration.thumbs.check('cacheDirectory')):
+ thumbnails = self.temp_configuration.thumbs.cacheDirectory
+ else:
+ thumbnails = os.path.join(self.temp_configuration.dotVistrails,
+ 'thumbs')
+ if not os.path.isdir(userpackages):
+ create_user_packages_dir(userpackages)
+ if not os.path.isfile(os.path.join(userpackages,
+ '__init__.py')):
+ create_user_packages_init(userpackages)
+ if not os.path.isdir(abstractions):
+ create_abstractions_dir(abstractions)
+ if not os.path.isdir(thumbnails):
+ create_thumbnails_dir(thumbnails)
+ try:
+
+ dotVistrails = open(startup)
+ g = {}
+ localsDir = {'configuration': self.temp_configuration,
+ 'addStartupHook': addStartupHook,
+ 'addPackage': addPackage}
+ old_path = copy.copy(sys.path)
+ sys.path.append(self.temp_configuration.dotVistrails)
+ exec dotVistrails in localsDir
+ sys.path = old_path
+ del localsDir['addPackage']
+ del localsDir['addStartupHook']
+ return localsDir
+ except IOError:
+ if tried_once:
+ debug.critical("""Still cannot find default file.
+ Something has gone wrong. Please make sure ~/.vistrails
+ exists, is writable, and ~/.vistrails/startup.py does
+ not exist.""")
+ sys.exit(1)
+ debug.critical('%s not found' % startup)
+ debug.critical('Will try to install default '
+ 'startup file')
+ install_default_startup()
+ install_default_startupxml_if_needed()
+ return execDotVistrails(True)
+ elif not os.path.lexists(self.temp_configuration.dotVistrails):
+ debug.log('%s not found' % self.temp_configuration.dotVistrails)
+ self.create_default_directory()
+ create_user_packages_dir()
+ create_abstractions_dir()
+ create_thumbnails_dir()
+ install_default_startup()
+ install_default_startupxml_if_needed()
+ return execDotVistrails(True)
+
+ #install_default_startupxml_if_needed()
+ # Now execute the dot vistrails
+ return execDotVistrails()
+
+ def setupDefaultFolders(self):
+ """ setupDefaultFolders() -> None
+ Give default values to folders when there are no values specified
+
+ """
+ if self.temp_configuration.has('rootDirectory'):
+ system.set_vistrails_root_directory(self.temp_configuration.rootDirectory)
+ if self.temp_configuration.has('dataDirectory'):
+ system.set_vistrails_data_directory( \
+ self.temp_configuration.dataDirectory)
+ if self.temp_configuration.has('fileDirectory'):
+ system.set_vistrails_file_directory( \
+ self.temp_configuration.fileDirectory)
+ if (self.temp_configuration.has('verbosenessLevel') and
+ self.temp_configuration.verbosenessLevel != -1):
+ verbose = self.temp_configuration.verbosenessLevel
+ if verbose < 0:
+ msg = ("""Don't know how to set verboseness level to %s - "
+ "setting to the lowest one I know of: 0""" % verbose)
+ debug.critical(msg)
+ verbose = 0
+ if verbose > 2:
+ msg = ("""Don't know how to set verboseness level to %s - "
+ "setting to the highest one I know of: 2""" % verbose)
+ debug.critical(msg)
+ verbose = 2
+ dbg = debug.DebugPrint.getInstance()
+ levels = [dbg.WARNING, dbg.INFO, dbg.DEBUG]
+ dbg.set_message_level(levels[verbose])
+ debug.log("Set verboseness level to %s" % verbose)
+
+ #these checks may need to update the persistent configuration, so
+ # we have to change both objects
+ #userpackages directory
+ if not self.temp_configuration.check('userPackageDirectory'):
+ s = os.path.join(self.temp_configuration.dotVistrails,
+ 'userpackages')
+ self.temp_configuration.userPackageDirectory = s
+ if not self.configuration.check('userPackageDirectory'):
+ s = os.path.join(self.configuration.dotVistrails,
+ 'userpackages')
+ self.configuration.userPackageDirectory = s
+ #abstractions directory
+ if not self.temp_configuration.check('abstractionsDirectory') or \
+ self.temp_configuration.abstractionsDirectory == \
+ os.path.join(self.temp_configuration.userPackageDirectory,
+ 'abstractions'):
+ s = os.path.join(self.temp_configuration.dotVistrails,
+ 'subworkflows')
+ self.temp_configuration.abstractionsDirectory = s
+ if not self.configuration.check('abstractionsDirectory') or \
+ self.configuration.abstractionsDirectory == \
+ os.path.join(self.configuration.userPackageDirectory,
+ 'abstractions'):
+ s = os.path.join(self.configuration.dotVistrails,
+ 'subworkflows')
+ self.configuration.abstractionsDirectory = s
+ #thumbnails directory
+ if self.temp_configuration.has('thumbs'):
+ if not self.temp_configuration.thumbs.check('cacheDirectory'):
+ s = os.path.join(self.temp_configuration.dotVistrails,'thumbs')
+ self.temp_configuration.thumbs.cacheDirectory = s
+ if self.configuration.has('thumbs'):
+ if not self.configuration.thumbs.check('cacheDirectory'):
+ s = os.path.join(self.configuration.dotVistrails, 'thumbs')
+ self.configuration.thumbs.cacheDirectory = s
+
+ def setupLogFile(self):
+ def get_version():
+ import vistrails.core.system
+ version = vistrails.core.system.vistrails_version()
+ return version.replace(".","_")
+ #To make sure we always save a log file name according to the
+ #current version, we will only consider the directory stored in
+ # logFile and append a name with the correct version encoded.
+ if not self.temp_configuration.check('logFile'):
+ s = os.path.join(self.temp_configuration.dotVistrails,
+ 'vistrails_%s.log'%(get_version()))
+ self.temp_configuration.logFile = s
+ else:
+ dirname = os.path.dirname(self.temp_configuration.logFile)
+ self.temp_configuration.logFile = os.path.join(dirname,
+ 'vistrails_%s.log'%(get_version()))
+ if not self.configuration.check('logFile'):
+ # if this was not set before, it should point to the
+ # value in temp_configuration
+ s = os.path.join(self.temp_configuration.dotVistrails,
+ 'vistrails_%s.log'%(get_version()))
+ self.configuration.logFile = s
+ else:
+ dirname = os.path.dirname(self.configuration.logFile)
+ self.configuration.logFile = os.path.join(dirname,
+ 'vistrails_%s.log'%(get_version()))
+ if not os.path.lexists(self.temp_configuration.dotVistrails):
+ self.create_default_directory()
+ if self.configuration.check('nologfile'):
+ debug.DebugPrint.getInstance().set_logfile(None)
+ else:
+ debug.DebugPrint.getInstance().set_logfile(self.temp_configuration.logFile)
+
+ def setupBaseModules(self):
+ """ setupBaseModules() -> None
+ Import basic modules for self-registration. The import here is
+ on purpose, not a typo against the coding rule
+
+ """
+ import vistrails.core.modules.vistrails_module
+ import vistrails.core.modules.basic_modules
+ import vistrails.core.modules.sub_module
+
+ def installPackages(self):
+ """ installPackages() -> None
+ Scheme through packages directory and initialize them all
+ """
+ # Imports standard packages directory
+ self._package_manager.initialize_packages(self._package_dictionary)
+
+ # Enable abstractions
+ import vistrails.core.modules.abstraction
+ abstraction_pkg = "abstraction"
+ abstraction_dict = {abstraction_pkg: 'vistrails.core.modules.'}
+ self._package_manager.initialize_abstraction_pkg(abstraction_dict)
+
+ def runStartupHooks(self):
+ """ runStartupHooks() -> None
+ After initialization, need to run all start up hooks registered
+
+ """
+ for hook in self.startupHooks:
+ try:
+ hook()
+ except Exception, e:
+ debug.critical("Exception raised during hook: %s - %s" %
+ (e.__class__, e))
+
+ def destroy(self):
+ """ destroy() -> None
+ Finalize all packages to, such as, get rid of temp files
+
+ """
+ self._package_manager.finalize_packages()
+
+ def set_registry(self, registry_filename=None):
+ if registry_filename is not None:
+ self._do_load_packages = False
+ self._package_manager.init_registry(registry_filename)
+
diff --git a/vistrails/core/system/__init__.py b/vistrails/core/system/__init__.py
new file mode 100644
index 0000000..6ab99e9
--- /dev/null
+++ b/vistrails/core/system/__init__.py
@@ -0,0 +1,453 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from __future__ import with_statement
+
+import datetime
+import getpass
+import os
+import os.path
+import subprocess
+import sys
+import platform
+import socket
+import urllib2
+from vistrails.core import debug
+from vistrails.core.utils import unimplemented, VistrailsInternalError, Chdir
+
+import unittest
+
+##############################################################################
+
+systemType = platform.system()
+
+if systemType in ['Windows', 'Microsoft']:
+ from vistrails.core.system.windows import guess_total_memory, temporary_directory, \
+ list2cmdline, \
+ home_directory, remote_copy_program, remote_shell_program, \
+ graph_viz_dot_command_line, remove_graph_viz_temporaries, \
+ link_or_copy,executable_is_in_path, executable_is_in_pythonpath, \
+ execute_cmdline, get_executable_path, execute_piped_cmdlines, TestWindows
+
+elif systemType in ['Linux']:
+ from vistrails.core.system.linux import guess_total_memory, temporary_directory, \
+ list2cmdline, \
+ home_directory, remote_copy_program, remote_shell_program, \
+ graph_viz_dot_command_line, remove_graph_viz_temporaries, \
+ link_or_copy, XDestroyWindow, executable_is_in_path, \
+ executable_is_in_pythonpath, execute_cmdline, get_executable_path, \
+ execute_piped_cmdlines, TestLinux
+
+elif systemType in ['Darwin']:
+ from vistrails.core.system.osx import guess_total_memory, temporary_directory, \
+ list2cmdline, \
+ home_directory, remote_copy_program, remote_shell_program, \
+ graph_viz_dot_command_line, remove_graph_viz_temporaries, \
+ link_or_copy, executable_is_in_path, executable_is_in_pythonpath, \
+ execute_cmdline, get_executable_path, execute_piped_cmdlines, TestMacOSX
+else:
+ debug.critical("VisTrails could not detect your operating system.")
+ sys.exit(1)
+
+def touch(file_name):
+ """touch(file_name) -> None Equivalent to 'touch' in a shell. If
+ file exists, updates modified time to current time. If not,
+ creates a new 0-length file.
+
+ """
+ if os.path.isfile(file_name):
+ os.utime(file_name, None)
+ else:
+ open(file_name, 'w')
+
+def mkdir(dir_name):
+ """mkdir(dir_name) -> None Equivalent to 'mkdir' in a shell except
+ that if the directory exists, it will not be overwritten.
+
+ """
+ if not os.path.isdir(dir_name):
+ os.mkdir(dir_name)
+
+##############################################################################
+
+# Makes sure root directory is sensible.
+if __name__ == '__main__':
+ _thisDir = sys.argv[0]
+else:
+ _thisDir = sys.modules[__name__].__file__
+_thisDir = os.path.split(_thisDir)[0]
+__rootDir = os.path.realpath(os.path.join(_thisDir,
+ '..',
+ '..'))
+
+__dataDir = os.path.realpath(os.path.join(__rootDir,
+ 'data'))
+__fileDir = os.path.realpath(os.path.join(__rootDir,
+ '..','examples'))
+
+if systemType in ['Darwin'] and not os.path.exists(__fileDir):
+ # Assume we are running from py2app
+ __fileDir = os.path.realpath(os.path.join(__rootDir,
+ '/'.join(['..']*6),'examples'))
+
+__examplesDir = __fileDir
+
+__defaultFileType = '.vt'
+
+__defaultPkgPrefix = 'org.vistrails.vistrails'
+
+def get_vistrails_default_pkg_prefix():
+ return __defaultPkgPrefix
+
+def get_vistrails_basic_pkg_id():
+ return "%s.basic" % get_vistrails_default_pkg_prefix()
+
+def set_vistrails_data_directory(d):
+ """ set_vistrails_data_directory(d:str) -> None
+ Sets vistrails data directory taking into account environment variables
+
+ """
+ global __dataDir
+ new_d = os.path.expanduser(d)
+ new_d = os.path.expandvars(new_d)
+ while new_d != d:
+ d = new_d
+ new_d = os.path.expandvars(d)
+ __dataDir = os.path.realpath(d)
+
+def set_vistrails_file_directory(d):
+ """ set_vistrails_file_directory(d: str) -> None
+ Sets vistrails file directory taking into accoun environment variables
+
+ """
+ global __fileDir
+ new_d = os.path.expanduser(d)
+ new_d = os.path.expandvars(new_d)
+ while new_d != d:
+ d = new_d
+ new_d = os.path.expandvars(d)
+ __fileDir = os.path.realpath(d)
+
+def set_vistrails_root_directory(d):
+ """ set_vistrails_root_directory(d:str) -> None
+ Sets vistrails root directory taking into account environment variables
+
+ """
+
+ global __rootDir
+ new_d = os.path.expanduser(d)
+ new_d = os.path.expandvars(new_d)
+ while new_d != d:
+ d = new_d
+ new_d = os.path.expandvars(d)
+ __rootDir = os.path.realpath(d)
+
+def set_vistrails_default_file_type(t):
+ """ set_vistrails_default_file_type(t:str) -> None
+ Which file type to use when the user doesn't provide a file extension
+
+ """
+ global __defaultFileType
+ if t in ['.vt', '.xml']:
+ __defaultFileType = t
+ else:
+ __defaultFileType = '.vt'
+
+def vistrails_root_directory():
+ """ vistrails_root_directory() -> str
+ Returns vistrails root directory
+
+ """
+ return __rootDir
+
+def vistrails_file_directory():
+ """ vistrails_file_directory() -> str
+ Returns current vistrails file directory
+
+ """
+ return __fileDir
+
+def vistrails_examples_directory():
+ """ vistrails_file_directory() -> str
+ Returns vistrails examples directory
+
+ """
+ return __examplesDir
+
+def vistrails_data_directory():
+ """ vistrails_data_directory() -> str
+ Returns vistrails data directory
+
+ """
+ return __dataDir
+
+def vistrails_default_file_type():
+ """ vistrails_default_file_type() -> str
+ Returns vistrails file type
+
+ """
+ return __defaultFileType
+
+def packages_directory():
+ """ packages_directory() -> str
+ Returns vistrails packages directory
+
+ """
+ return os.path.join(vistrails_root_directory(),'packages')
+
+def blank_vistrail_file():
+ unimplemented()
+
+def resource_directory():
+ """ resource_directory() -> str
+ Returns vistrails gui resource directory
+
+ """
+ return os.path.join(vistrails_root_directory(),
+ 'gui', 'resources')
+
+def default_options_file():
+ """ default_options_file() -> str
+ Returns vistrails default options file
+
+ """
+ return os.path.join(home_directory(), ".vistrailsrc")
+
+def default_dot_vistrails():
+ """ default_dot_vistrails() -> str
+ Returns the default VisTrails per-user directory.
+
+ """
+ return os.path.join(home_directory(), '.vistrails')
+
+def current_dot_vistrails():
+ """ current_dot_vistrails() -> str
+ Returns the VisTrails per-user directory.
+
+ """
+ from vistrails.core.configuration import get_vistrails_configuration
+ return get_vistrails_configuration().dotVistrails
+
+def default_connections_file():
+ """ default_connections_file() -> str
+ Returns default Vistrails per-user connections file
+
+ """
+ return os.path.join(current_dot_vistrails(), 'connections.xml')
+
+def python_version():
+ """python_version() -> (major, minor, micro, release, serial)
+ Returns python version info."""
+ return sys.version_info
+
+def vistrails_version():
+ """vistrails_version() -> string - Returns the current VisTrails version."""
+ # 0.1 was the Vis2005 version
+ # 0.2 was the SIGMOD demo version
+ # 0.3 was the plugin/vtk version
+ # 0.4 is cleaned up version with new GUI
+ # 1.0 is version with new schema
+ return '2.1.1'
+
+def get_latest_vistrails_version():
+ """get_latest_vistrails_version() -> string - Returns latest vistrails
+ release version as queried from vistrails.org"""
+
+ version = ''
+ version_url = \
+ "http://www.vistrails.org/download/download.php?id=release_version.txt"
+ try:
+ request = urllib2.Request(version_url)
+ get_latest_version = urllib2.urlopen(request)
+ version = get_latest_version.read().strip()
+ except urllib2.HTTPError, err:
+ debug.warning("Unable to check for updates: %s" % str(err))
+ return version
+
+ return version
+
+def new_vistrails_release_exists():
+ """ new_vistrail_release_exists() -> (bool, str)
+ Returns (True, new_version_str) if newer version exists
+
+ """
+
+ local_version = [int(x) for x in vistrails_version().split('.')]
+
+ remote_str = get_latest_vistrails_version()
+ if remote_str:
+ remote_version = [int(x) for x in remote_str.split('.')]
+ else:
+ remote_version = [0]
+
+ if cmp(local_version, remote_version) is -1:
+ return (True, remote_str)
+
+ return (False, None)
+
+def vistrails_revision():
+ """vistrails_revision() -> str
+ When run on a working copy, shows the current svn revision else
+ shows the latest release revision
+
+ """
+ git_dir = os.path.join(vistrails_root_directory(), '..')
+ with Chdir(git_dir):
+ release = "97362185cfd1"
+ import vistrails.core.requirements
+ if vistrails.core.requirements.executable_file_exists('git'):
+ lines = []
+ result = execute_cmdline(['git', 'describe', '--always', '--abbrev=12'],
+ lines)
+ if len(lines) == 1:
+ if result == 0:
+ release = lines[0].strip(" \n")
+ return release
+
+def current_user():
+ return getpass.getuser()
+
+def current_ip():
+ """ current_ip() -> str
+ Gets current IP address trying to avoid the IPv6 interface """
+ try:
+ info = socket.getaddrinfo(socket.gethostname(), None)
+ # Try to find an IPv4
+ for i in info:
+ if i[0] == socket.AF_INET:
+ return i[4][0]
+ # Return any address
+ for i in info:
+ if i[0] in (socket.AF_INET, socket.AF_INET6):
+ return i[4][0]
+ except:
+ return ''
+
+def current_time():
+ """current_time() -> datetime.datetime
+ Returns the current time
+
+ """
+ # FIXME should use DB if available...
+ return datetime.datetime.now()
+
+def current_machine():
+ return socket.getfqdn()
+
+def current_architecture():
+ bit_string = platform.architecture()[0]
+ if bit_string.endswith('bit'):
+ return int(bit_string[:-3])
+ else:
+ return 32 # default value
+
+def current_processor():
+ proc = platform.processor()
+ if not proc:
+ proc = 'n/a'
+ return proc
+
+def short_about_string():
+ return """VisTrails version %s.%s -- contact at vistrails.org""" % \
+ (vistrails_version(), vistrails_revision())
+
+def about_string():
+ """about_string() -> string - Returns the about string for VisTrails."""
+ return """VisTrails version %s.%s -- contact at vistrails.org
+
+Copyright (C) 2011-2014 NYU-Poly. Copyright (C) 2006-2011 University of Utah.
+All rights reserved.
+http://www.vistrails.org
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ * Neither the name of the University of Utah nor the
+ names of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" \
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE \
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE \
+ARE DISCLAIMED. IN NO EVENT SHALL COPYRIGHT HOLDER BE LIABLE FOR ANY DIRECT, \
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, \
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, \
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING \
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, \
+EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.""" % (vistrails_version(),
+ vistrails_revision())
+
+def get_elementtree_library():
+ try:
+ import cElementTree as ElementTree
+ except ImportError:
+ # try python 2.5-style
+ import xml.etree.cElementTree as ElementTree
+ return ElementTree
+
+def execute_cmdline2(cmd_list):
+ return execute_piped_cmdlines([cmd_list])
+
+################################################################################
+
+
+if __name__ == '__main__':
+ unittest.main()
+
+class TestSystem(unittest.TestCase):
+
+ def test_vistrails_revision(self):
+ r = vistrails_root_directory()
+ with Chdir(r):
+ v1 = vistrails_revision()
+ try:
+ with Chdir(os.path.join(r, '..')):
+ self.assertEquals(v1, vistrails_revision())
+ except AssertionError:
+ raise
+ except:
+ pass
+ try:
+ with Chdir(os.path.join(r, '..', '..')):
+ self.assertEquals(v1, vistrails_revision())
+ except AssertionError:
+ raise
+ except:
+ pass
+
+
diff --git a/vistrails/core/system/linux.py b/vistrails/core/system/linux.py
new file mode 100644
index 0000000..cbdf7a5
--- /dev/null
+++ b/vistrails/core/system/linux.py
@@ -0,0 +1,208 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import os
+import re
+import shutil
+from ctypes import CDLL, c_void_p
+from vistrails.core.system.unix import executable_is_in_path,\
+ executable_is_in_pythonpath, list2cmdline, execute_cmdline, \
+ get_executable_path, execute_piped_cmdlines
+
+import unittest
+
+################################################################################
+
+_meminfo_fmt = re.compile(r'([^:]+):\s+([0-9]+)(?: (kB|B))?\n$')
+
+def parse_meminfo():
+ """parse_meminfo() -> dictionary
+ Parses /proc/meminfo and returns appropriate dictionary. Only available on
+ Linux."""
+ info = {}
+ with open('/proc/meminfo') as fp:
+ for line in fp:
+ m = _meminfo_fmt.match(line)
+ if m is None:
+ raise VistrailsInternalError("Invalid format found in "
+ "/proc/meminfo")
+ key, value, unit = m.groups()
+ if unit == 'kB':
+ value = int(value) * 1000
+ else:
+ value = int(value)
+ info[key] = value
+ return info
+
+def guess_total_memory():
+ """ guess_total_memory() -> int
+ Return system memory in bytes.
+
+ """
+ return parse_meminfo()['MemTotal']
+
+def temporary_directory():
+ """ temporary_directory() -> str
+ Returns the path to the system's temporary directory
+
+ """
+ return "/tmp/"
+
+def home_directory():
+ """ home_directory() -> str
+ Returns user's home directory using environment variable $HOME
+
+ """
+ return os.getenv('HOME')
+
+def remote_copy_program():
+ return "scp -p"
+
+def remote_shell_program():
+ return "ssh -p"
+
+def graph_viz_dot_command_line():
+ return 'dot -Tplain -o '
+
+def remove_graph_viz_temporaries():
+ """ remove_graph_viz_temporaries() -> None
+ Removes temporary files generated by dot
+
+ """
+ os.unlink(temporary_directory() + "dot_output_vistrails.txt")
+ os.unlink(temporary_directory() + "dot_tmp_vistrails.txt")
+
+def link_or_copy(src, dst):
+ """link_or_copy(src:str, dst:str) -> None
+ Tries to create a hard link to a file. If it is not possible, it will
+ copy file src to dst
+
+ """
+ # Links if possible, but we're across devices, we need to copy.
+ try:
+ os.link(src, dst)
+ except OSError, e:
+ if e.errno == 18:
+ # Across-device linking is not possible. Let's copy.
+ shutil.copyfile(src, dst)
+ else:
+ raise e
+
+def get_libX11():
+ """ get_libX11() -> CDLL
+ Return the X11 library loaded with ctypes. Only available on
+ Linux. We also need a way to find the correct X11 library name on
+ different machines. Right now, libX11.so.6 is used.
+
+ """
+ from vistrails.core.bundles import py_import
+ ctypes = py_import('ctypes', {
+ 'pip': 'ctypes',
+ 'linux-debian': 'python-ctypes',
+ 'linux-ubuntu': 'python-ctypes',
+ 'linux-fedora': 'python-ctypes'})
+ c_void_p = ctypes.c_void_p
+ CDLL = ctypes.CDLL
+ return CDLL('libX11.so.6')
+
+def XDestroyWindow(displayId, windowId):
+ """ XDestroyWindow(displayId: void_p_str, windowId: void_p_str) -> None
+ Destroy the X window specified by two strings displayId and
+ windowId containing void pointer string of (Display*) and (Window)
+ type.
+ This is specific for VTKCell to remove the top shell window. Since
+ VTK does not expose X11-related functions to Python, we have to
+ use ctypes to hi-jack X11 library and call XDestroyWindow to kill
+ the top-shell widget after reparent the OpenGL canvas to another
+ Qt widget
+
+ """
+ from vistrails.core.bundles import py_import
+ ctypes = py_import('ctypes', {
+ 'pip': 'ctypes',
+ 'linux-debian': 'python-ctypes',
+ 'linux-ubuntu': 'python-ctypes',
+ 'linux-fedora': 'python-ctypes'})
+ c_void_p = ctypes.c_void_p
+ displayPtr = c_void_p(int(displayId[1:displayId.find('_void_p')], 16))
+ windowPtr = c_void_p(int(windowId[1:windowId.find('_void_p')], 16))
+ libx = get_libX11()
+ libx.XDestroyWindow(displayPtr, windowPtr)
+
+################################################################################
+
+
+class TestLinux(unittest.TestCase):
+ """ Class to test Linux specific functions """
+
+ def test1(self):
+ """ Test if guess_total_memory() is returning an int >= 0"""
+ result = guess_total_memory()
+ assert isinstance(result, (int, long))
+ assert result >= 0
+
+ def test2(self):
+ """ Test if home_directory is not empty """
+ result = home_directory()
+ assert result != ""
+
+ def test3(self):
+ """ Test if temporary_directory is not empty """
+ result = temporary_directory()
+ assert result != ""
+
+ def test4(self):
+ """ Test if origin of link_or_copy'ed file is deleteable. """
+ import tempfile
+ import os
+ (fd1, name1) = tempfile.mkstemp()
+ os.close(fd1)
+ (fd2, name2) = tempfile.mkstemp()
+ os.close(fd2)
+ os.unlink(name2)
+ link_or_copy(name1, name2)
+ try:
+ os.unlink(name1)
+ except:
+ self.fail("Should not throw")
+ os.unlink(name2)
+
+ def test_executable_file_in_path(self):
+ # Should exist in any POSIX shell, which is what we have in OSX
+ result = executable_is_in_path('ls')
+ assert os.access(result, os.X_OK)
+
+if __name__ == '__main__':
+ unittest.main()
+
diff --git a/vistrails/core/system/mac_site.py b/vistrails/core/system/mac_site.py
new file mode 100644
index 0000000..3cdac45
--- /dev/null
+++ b/vistrails/core/system/mac_site.py
@@ -0,0 +1,95 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" contains parts from site.py for python2.7 needed when using py2app
+"""
+
+import sys
+
+# for distutils.commands.install
+# These values are initialized by the getuserbase() and getusersitepackages()
+# functions, through the main() function when Python starts.
+USER_SITE = None
+USER_BASE = None
+
+def getuserbase():
+ """Returns the `user base` directory path.
+
+ The `user base` directory can be used to store data. If the global
+ variable ``USER_BASE`` is not initialized yet, this function will also set
+ it.
+ """
+ global USER_BASE
+ if USER_BASE is not None:
+ return USER_BASE
+ from sysconfig import get_config_var
+ USER_BASE = get_config_var('userbase')
+ return USER_BASE
+
+def getusersitepackages():
+ """Returns the user-specific site-packages directory path.
+
+ If the global variable ``USER_SITE`` is not initialized yet, this
+ function will also set it.
+ """
+ global USER_SITE
+ user_base = getuserbase() # this will also set USER_BASE
+
+ if USER_SITE is not None:
+ return USER_SITE
+
+ from sysconfig import get_path
+ import os
+
+ if sys.platform == 'darwin':
+ from sysconfig import get_config_var
+ if get_config_var('PYTHONFRAMEWORK'):
+ USER_SITE = get_path('purelib', 'osx_framework_user')
+ return USER_SITE
+
+ USER_SITE = get_path('purelib', '%s_user' % os.name)
+ return USER_SITE
+
+class _Helper(object):
+ """Define the builtin 'help'.
+ This is a wrapper around pydoc.help (with a twist).
+
+ """
+
+ def __repr__(self):
+ return "Type help() for interactive help, " \
+ "or help(object) for help about object."
+ def __call__(self, *args, **kwds):
+ import pydoc
+ return pydoc.help(*args, **kwds)
\ No newline at end of file
diff --git a/vistrails/core/system/osx.py b/vistrails/core/system/osx.py
new file mode 100644
index 0000000..9547375
--- /dev/null
+++ b/vistrails/core/system/osx.py
@@ -0,0 +1,290 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" Mac OS X specific file """
+
+# from xml import dom
+# from xml.dom.xmlbuilder import DOMInputSource, DOMBuilder
+import xml.etree.cElementTree as ElementTree
+import datetime
+import os
+import shutil
+import subprocess
+import time
+from vistrails.core.system.unix import executable_is_in_path, list2cmdline, \
+ executable_is_in_pythonpath, execute_cmdline, execute_piped_cmdlines
+import vistrails.core.utils
+
+import unittest
+
+###############################################################################
+# Extract system detailed information of a Mac system
+#
+# Based on a Python Cookbook recipe available online :
+# http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/303063
+# and in the Python Coobook, page 418
+# Credit: Brian Quinlan
+#
+# Rewritten to use ElementTree instead of PyXML
+#
+# This recipe uses the system_profiler application to retrieve detailed
+# information about a Mac OS X system. There are two useful ways to use it:
+# the first is to ask for a complete Python datastructure containing
+# information about the system (see OSXSystemProfiler.all()) and the
+# other is two ask for particular keys in the system information database.
+
+def group(lst, n):
+ """group([0,3,4,10,2,3], 2) => [(0,3), (4,10), (2,3)]
+
+ Group a list into consecutive n-tuples. Incomplete tuples are
+ discarded e.g.
+
+ >>> group(range(10), 3)
+ [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
+
+ """
+ return zip(*[lst[i::n] for i in xrange(n)])
+
+class OSXSystemProfiler(object):
+ "Provide information from the Mac OS X System Profiler"
+
+ def __init__(self, category=None, detail=None):
+ """detail can range from -2 to +1, with larger numbers returning more
+ information. Beware of +1, it can take several minutes for
+ system_profiler to generate the data."""
+
+ command = ['system_profiler', '-xml']
+ if category is not None:
+ command.append(str(category))
+ if detail is not None:
+ command.extend(['-detailLevel', '%d' % detail])
+ p = subprocess.Popen(command, stdout=subprocess.PIPE)
+ self.document = ElementTree.parse(p.stdout)
+
+ def _content(self, node):
+ "Get the text node content of an element or an empty string"
+ return (node.text or '')
+
+ def _convert_value_node(self, node):
+ """Convert a 'value' node (i.e. anything but 'key') into a Python data
+ structure"""
+ if node.tag == 'string':
+ return self._content(node)
+ elif node.tag == 'integer':
+ return int(self._content(node))
+ elif node.tag == 'real':
+ return float(self._content(node))
+ elif node.tag == 'date': # <date>2004-07-05T13:29:29Z</date>
+ return datetime.datetime(
+ *time.strptime(self._content(node), '%Y-%m-%dT%H:%M:%SZ')[:5])
+ elif node.tag == 'array':
+ return [self._convert_value_node(n) for n in node.getchildren()]
+ elif node.tag == 'dict':
+ return dict([(self._content(n), self._convert_value_node(m))
+ for n, m in group(node.getchildren(), 2)])
+ else:
+ raise ValueError(node.tag)
+
+ def __getitem__(self, key):
+ nodes = self.document.getiterator('dict')
+ results = []
+ for node in nodes:
+ for child in node:
+ if child.tag == 'key' and child.text == key:
+ v = self._convert_value_node(node)[key]
+ if isinstance(v, dict) and v.has_key('_order'):
+ # this is just information for display
+ pass
+ else:
+ results.append(v)
+ return results
+
+# def all(self):
+# """Return the complete information from the system profiler
+# as a Python data structure"""
+
+# return self._convert_value_node(
+# self.document.documentElement.firstChild)
+
+###############################################################################
+
+def example():
+ from optparse import OptionParser
+ from pprint import pprint
+
+ info = OSXSystemProfiler("SPHardwareDataType")
+ parser = OptionParser()
+ parser.add_option("-f", "--field", action="store", dest="field",
+ help="display the value of the specified field")
+
+ (options, args) = parser.parse_args()
+ if len(args) != 0:
+ parser.error("no arguments are allowed")
+
+ if options.field is not None:
+ pprint(info[options.field])
+ else:
+ # just print some comment keys known to exist in only one important
+ # dictionary
+ for k in ['cpu_type', 'current_processor_speed', 'l2_cache_size',
+ 'physical_memory', 'user_name', 'os_version', 'ip_address']:
+ print '%s: %s' % (k, info[k][0])
+
+###############################################################################
+
+def parse_meminfo():
+ """ parse_meminfo() -> int
+ Uses the system_profiler application to retrieve detailed information
+ about a Mac OS X system. Returns memory size in Megabytes.
+
+ Just use the "SPHardwareDataType" category to limit the amount of
+ information gathered.
+
+ """
+
+ result = -1
+ info = OSXSystemProfiler("SPHardwareDataType")
+ mem = info['physical_memory'][0]
+ # print "*** MEMORY", mem
+ if mem.upper().endswith(' GB'):
+ result = int(float(mem[:-3]) * 1024) * 1L
+ elif mem.upper().endswidth(' MB'):
+ result = int(mem[:-3]) * 1L
+ # print '>>>>', result
+ return result
+
+def guess_total_memory():
+ """ guess_total_memory() -> int
+ Return system memory in bytes. If PyXML is not installed it returns -1
+
+ """
+ return parse_meminfo()
+
+def temporary_directory():
+ """ temporary_directory() -> str
+ Returns the path to the system's temporary directory
+
+ """
+ return "/tmp/"
+
+def home_directory():
+ """ home_directory() -> str
+ Returns user's home directory using environment variable $HOME
+
+ """
+ return os.getenv('HOME')
+
+def remote_copy_program():
+ return "scp -p"
+
+def remote_shell_program():
+ return "ssh -p"
+
+def graph_viz_dot_command_line():
+ """ graph_viz_dot_command_line() -> str
+ Returns dot command line
+
+ """
+ return 'dot -Tplain -o '
+
+def remove_graph_viz_temporaries():
+ """ remove_graph_viz_temporaries() -> None
+ Removes temporary files generated by dot
+
+ """
+ os.unlink(temporary_directory() + "dot_output_vistrails.txt")
+ os.unlink(temporary_directory() + "dot_tmp_vistrails.txt")
+
+def link_or_copy(src, dst):
+ """link_or_copy(src:str, dst:str) -> None
+ Tries to create a hard link to a file. If it is not possible, it will
+ copy file src to dst
+
+ """
+ # Links if possible, but we're across devices, we need to copy.
+ try:
+ os.link(src, dst)
+ except OSError, e:
+ if e.errno == 18:
+ # Across-device linking is not possible. Let's copy.
+ shutil.copyfile(src, dst)
+ else:
+ raise e
+
+def get_executable_path(executable_name):
+ vt_path = os.getenv("EXECUTABLEPATH")
+ if vt_path is not None:
+ vt_path = vt_path.strip()
+ executable_path = \
+ os.path.join(os.path.dirname(vt_path), executable_name)
+ if os.path.exists(executable_path):
+ return executable_path
+ paths = os.environ['PATH']
+ paths = paths.split(os.pathsep)
+ for prefix in paths:
+ path = os.path.join(prefix, executable_name)
+ if os.path.exists(path):
+ return path
+ return None
+
+################################################################################
+
+
+class TestMacOSX(unittest.TestCase):
+ """ Class to test Mac OS X specific functions """
+
+ def test1(self):
+ """ Test if guess_total_memory() is returning an int >= 0"""
+ result = guess_total_memory()
+ assert isinstance(result, (int, long))
+ assert result >= 0
+
+ def test2(self):
+ """ Test if home_directory is not empty """
+ result = home_directory()
+ assert result != ""
+
+ def test3(self):
+ """ Test if temporary_directory is not empty """
+ result = temporary_directory()
+ assert result != ""
+
+ def test_executable_file_in_path(self):
+ # Should exist in any POSIX shell, which is what we have in OSX
+ result = executable_is_in_path('ls')
+ assert result == "/bin/ls" # Any UNIX should respect this.
+
+if __name__ == '__main__':
+ unittest.main()
+
diff --git a/vistrails/core/system/unix.py b/vistrails/core/system/unix.py
new file mode 100644
index 0000000..0cede13
--- /dev/null
+++ b/vistrails/core/system/unix.py
@@ -0,0 +1,125 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Routines common to Linux and OSX."""
+import os
+import os.path
+import stat
+import subprocess
+import sys
+import vistrails.core.utils
+import re
+
+def executable_is_in_path(filename):
+ """executable_is_in_path(filename): string
+ Tests if filename corresponds to an executable file on the path. Returns
+the filename if true, or an empty string if false."""
+ cmdline = ['which','%s' % filename]
+ output = []
+ result = execute_cmdline(cmdline, output)
+ if result == 1:
+ return ""
+ if result != 0:
+ msg = ("'%s' failed. Return code %s. Output: %s" %
+ (cmdline, result, output))
+ raise vistrails.core.utils.VistrailsInternalError(msg)
+ else:
+ output = output[0][:-1]
+ return output
+
+def executable_is_in_pythonpath(filename):
+ """executable_is_in_pythonpath(filename: str)
+ Check if exename can be reached in the PYTHONPATH environment. Return
+ the filename if true, or an empty string if false.
+
+ """
+ pathlist = sys.path
+ for dir in pathlist:
+ fullpath = os.path.join(dir, filename)
+ try:
+ st = os.stat(fullpath)
+ except os.error:
+ continue
+ if stat.S_ISREG(st[stat.ST_MODE]):
+ return filename
+ return ""
+
+def list2cmdline(lst):
+ for el in lst:
+ assert isinstance(el, basestring)
+ return subprocess.list2cmdline(lst)
+
+def execute_cmdline(lst, output):
+ """execute_cmdline(lst: list of str, output)-> int
+ Builds a command line enquoting the arguments properly and executes it
+ using subprocess.Popen. It returns the error code and the output is on 'output'.
+
+ cscheid: why don't we return a tuple of int, lst instead of mutating that list?
+
+ """
+ process = subprocess.Popen(lst, shell=False,
+ stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ close_fds=True)
+ # cscheid: Should this be busy-waiting? What's going on here?
+ result = None
+ while result == None:
+ result = process.poll()
+ output.extend(process.stdout.readlines())
+ return result
+
+def get_executable_path(executable_name):
+ paths = os.environ['PATH']
+ paths = paths.split(os.pathsep)
+ for prefix in paths:
+ path = os.path.join(prefix, executable_name)
+ if os.path.exists(path):
+ return path
+ return None
+
+def execute_piped_cmdlines(cmd_list_list):
+ stdin = subprocess.PIPE
+ for cmd_list in cmd_list_list:
+ cmd_line = list2cmdline(cmd_list)
+ process = subprocess.Popen(cmd_line, shell=True,
+ stdin=stdin,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ close_fds=True)
+ stdin = process.stdout
+ (output, errs) = process.communicate()
+ result = process.returncode
+ return (result, output, errs)
diff --git a/vistrails/core/system/windows.py b/vistrails/core/system/windows.py
new file mode 100644
index 0000000..88e085c
--- /dev/null
+++ b/vistrails/core/system/windows.py
@@ -0,0 +1,250 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import os
+import shutil
+import sys
+import stat
+import subprocess
+import vistrails.core.system
+
+import unittest
+
+try:
+ from ctypes import windll, Structure, c_ulong, c_ulonglong, byref, sizeof
+ importSuccess = True
+
+ class WIN32MEMORYSTATUSEX(Structure):
+ """ Structure that represents memory information returned by
+ Windows API
+
+ """
+ _fields_ = [
+ ('dwLength', c_ulong),
+ ('dwMemoryLoad', c_ulong),
+ ('dwTotalPhys', c_ulonglong),
+ ('dwAvailPhys', c_ulonglong),
+ ('dwTotalPageFile', c_ulonglong),
+ ('dwAvailPageFile', c_ulonglong),
+ ('dwTotalVirtual', c_ulonglong),
+ ('dwAvailVirtual', c_ulonglong),
+ ('dwAvailExtendedVirtual', c_ulonglong),
+ ]
+
+except ImportError:
+ importSuccess = False
+
+##############################################################################
+def parse_meminfo():
+ """
+ parse_meminfo() -> long
+ Calls Windows 32 API GlobalMemoryStatus(Ex) to get memory information
+ It requires ctypes module
+
+ """
+ try:
+ kernel32 = windll.kernel32
+
+ result = WIN32MEMORYSTATUSEX()
+ result.dwLength = sizeof(WIN32MEMORYSTATUSEX)
+ kernel32.GlobalMemoryStatusEx(byref(result))
+ except:
+ return -1
+ return long(result.dwTotalPhys / 1024)
+
+def guess_total_memory():
+ """ guess_total_memory() -> int
+ Return system memory in megabytes. If ctypes is not installed it returns -1
+
+ """
+ if importSuccess:
+ return parse_meminfo()
+ else:
+ return -1
+
+def temporary_directory():
+ """ temporary_directory() -> str
+ Returns the path to the system's temporary directory. Tries to use the $TMP
+ environment variable, if it is present. Else, tries $TEMP, else uses 'c:/'
+
+ """
+ if os.environ.has_key('TMP'):
+ return os.environ['TMP'] + '\\'
+ elif os.environ.has_key('TEMP'):
+ return os.environ['TEMP'] + '\\'
+ else:
+ return 'c:/'
+
+def home_directory():
+ """ home_directory() -> str
+ Returns user's home directory using windows environment variables
+ $HOMEDRIVE and $HOMEPATH
+
+ """
+ if len(os.environ['HOMEPATH']) == 0:
+ return '\\'
+ else:
+ return os.environ['HOMEDRIVE'] + os.environ['HOMEPATH']
+
+def remote_copy_program():
+ return "pscp -P"
+
+def remote_shell_program():
+ return "plink -P"
+
+def graph_viz_dot_command_line():
+ """ graph_viz_dot_command_line() -> str
+ Returns dot command line
+
+ """
+ return 'dot -Tplain -o'
+
+def remove_graph_viz_temporaries():
+ pass
+
+def link_or_copy(src, dst):
+ """link_or_copy(src:str, dst:str) -> None
+ Copies file src to dst
+
+ """
+ shutil.copyfile(src, dst)
+
+def executable_is_in_path(filename):
+ """ executable_is_in_path(filename: str) -> string
+ Check if exename can be reached in the PATH environment. Return
+ the filename if true, or an empty string if false.
+
+ """
+ pathlist = (os.environ['PATH'].split(os.pathsep) +
+ [vistrails.core.system.vistrails_root_directory(),
+ "."])
+ for dir in pathlist:
+ fullpath = os.path.join(dir, filename)
+ try:
+ st = os.stat(fullpath)
+ except os.error:
+ try:
+ st = os.stat(fullpath+'.exe')
+ except:
+ continue
+ if stat.S_ISREG(st[stat.ST_MODE]):
+ return filename
+ return ""
+
+def executable_is_in_pythonpath(filename):
+ """ executable_is_in_pythonpath(filename: str) -> string
+ Check if exename can be reached in the PYTHONPATH environment. Return
+ the filename if true, or an empty string if false.
+
+ """
+ pathlist = sys.path
+ for dir in pathlist:
+ fullpath = os.path.join(dir, filename)
+ try:
+ st = os.stat(fullpath)
+ except os.error:
+ try:
+ st = os.stat(fullpath+'.exe')
+ except:
+ continue
+ if stat.S_ISREG(st[stat.ST_MODE]):
+ return filename
+ return ""
+
+def list2cmdline(lst):
+ for el in lst:
+ assert isinstance(el, basestring)
+ return subprocess.list2cmdline(lst)
+
+def execute_cmdline(lst, output):
+ """execute_cmdline(lst: list of str)-> int Builds a command line
+ enquoting the arguments properly and executes it using popen4. It
+ returns the output on output. popen4 doesn't return a code, so it
+ will always return 0
+
+ """
+ proc = subprocess.Popen(lst, shell=True, stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+ proc.wait()
+ if proc.stdout:
+ output.extend(proc.stdout.readlines())
+ return proc.returncode
+
+def get_executable_path(executable_name):
+ filename = os.path.abspath(os.path.join(os.path.dirname(__file__),'../../../',executable_name))
+ if os.path.exists(filename) or os.path.exists(filename+'.exe'):
+ return filename
+ return None
+
+def execute_piped_cmdlines(cmd_list_list):
+ stdin = subprocess.PIPE
+ for cmd_list in cmd_list_list:
+ cmd_line = list2cmdline(cmd_list)
+ process = subprocess.Popen(cmd_line, shell=True,
+ stdin=stdin,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+ stdin = process.stdout
+ (output, errs) = process.communicate()
+ result = process.returncode
+ return (result, output, errs)
+
+################################################################################
+
+
+class TestWindows(unittest.TestCase):
+ """ Class to test Windows specific functions """
+
+ def test1(self):
+ """ Test if guess_total_memory() is returning an int >= 0"""
+ result = guess_total_memory()
+ assert isinstance(result, (int, long))
+ assert result >= 0
+
+ def test2(self):
+ """ Test if home_directory is not empty """
+ result = home_directory()
+ assert result != ""
+
+ def test3(self):
+ """ Test if temporary_directory is not empty """
+ result = temporary_directory()
+ assert result != ""
+
+ def test_executable_file_in_path(self):
+ result = executable_is_in_path('cmd')
+ assert result != ""
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/theme.py b/vistrails/core/theme.py
new file mode 100644
index 0000000..176aa56
--- /dev/null
+++ b/vistrails/core/theme.py
@@ -0,0 +1,118 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""
+This module describes a core theme structure for VisTrails GUI. It
+specifies measurements
+"""
+
+from vistrails.core.utils.color import ColorByName
+import vistrails.core.system
+################################################################################
+
+class DefaultCoreTheme(object):
+ """
+ This is the default core theme which contains non-qt values,
+ measurements for Vistrail. Other core themes should derive from
+ this class and change appropriate values
+
+ """
+
+ def __init__(self):
+ """ DefaultTheme() -> DefaultTheme
+ This is for initializing all non-Qt values
+
+ """
+ ######################
+ #### MEASUREMENTS ####
+
+ # Padded space of Version shape and its label
+ self.VERSION_LABEL_MARGIN = (60, 35)
+
+ # Padded space of Module shape into its label
+ self.MODULE_LABEL_MARGIN = (20, 20, 20, 15)
+
+ # Margin of Module shape into its ports
+ self.MODULE_PORT_MARGIN = (4, 4, 4, 4)
+
+ # Space between ports inside a module
+ self.MODULE_PORT_SPACE = 4
+
+ # The space added to the end of port shapes before it reaches the
+ # margin of the module
+ self.MODULE_PORT_PADDED_SPACE = 20
+
+ # Width and Height of Port shape
+ self.PORT_WIDTH = 10
+ self.PORT_HEIGHT = 10
+
+ # Width and Height of Configure button shape
+ self.CONFIGURE_WIDTH = 6
+ self.CONFIGURE_HEIGHT = 10
+
+ self.BREAKPOINT_FRINGE = \
+ (((0.0,0.0),(-0.5,0.25),(-0.5,0.75),(0.0,1.0)),
+ ((0.0,0.0),(0.5,0.25),(0.5,0.75),(0.0,1.0)))
+
+
+ # The number of control points when drawing connection curve
+ self.CONNECTION_CONTROL_POINTS = 20
+
+ # Control the size and gap for the 3 little segments when
+ # draw connections between versions
+ self.LINK_SEGMENT_LENGTH = 15
+ self.LINK_SEGMENT_GAP = 5
+ self.LINK_SEGMENT_SQUARE_LENGTH = 12
+
+ # The size of the frame containing the PIP graphics view
+ self.PIP_IN_FRAME_WIDTH = 5
+ self.PIP_OUT_FRAME_WIDTH = 1
+
+ # The size of the frame containing the PIP graphics view
+ self.PIP_DEFAULT_SIZE = (128, 128)
+
+ # The default minimum size of the graphics views
+ self.BOUNDING_RECT_MINIMUM = 512
+
+ # Default Paramter Inspector Window dimension
+ self.VISUAL_DIFF_PARAMETER_WINDOW_SIZE = (348,256)
+
+ # Default legend size (small rectangular shape)
+ self.VISUAL_DIFF_LEGEND_SIZE = (16, 16)
+
+ # Virtual Cell Label default size
+ self.VIRTUAL_CELL_LABEL_SIZE = (40, 40)
+
+ # Query Preview Size
+ self.QUERY_PREVIEW_SIZE = (256, 256)
diff --git a/vistrails/core/thumbnails.py b/vistrails/core/thumbnails.py
new file mode 100644
index 0000000..838905d
--- /dev/null
+++ b/vistrails/core/thumbnails.py
@@ -0,0 +1,291 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+""" Utilities for dealing with the thumbnails """
+import os
+import os.path
+import shutil
+import time
+import uuid
+import mimetypes
+# mimetypes are broken by default on windows so use the builtins
+# Remove line below when it is fixed here: http://bugs.python.org/issue15207
+mimetypes.init(files=[])
+from vistrails.core import debug
+from vistrails.core.configuration import get_vistrails_configuration, \
+ get_vistrails_persistent_configuration
+from vistrails.core.utils import VistrailsInternalError
+
+############################################################################
+class CacheEntry(object):
+ def __init__(self, abs_name, name, time, size):
+ self.abs_name = abs_name
+ self.name = name
+ self.time = time
+ self.size = size
+
+class ThumbnailCache(object):
+ _instance = None
+ IMAGE_MAX_WIDTH = 200
+ SUPPORTED_TYPES = ['image/png','image/jpeg','image/bmp','image/gif']
+ class ThumbnailCacheSingleton(object):
+ def __call__(self, *args, **kw):
+ if ThumbnailCache._instance is None:
+ obj = ThumbnailCache(*args, **kw)
+ ThumbnailCache._instance = obj
+ return ThumbnailCache._instance
+
+ getInstance = ThumbnailCacheSingleton()
+
+ def __init__(self):
+ self.elements = {}
+ self.vtelements = {}
+ self.conf = None
+ conf = get_vistrails_configuration()
+ if conf.has('thumbs'):
+ self.conf = conf.thumbs
+ self.init_cache()
+
+ def get_directory(self):
+ if self.conf.check('cacheDirectory'):
+ thumbnail_dir = self.conf.cacheDirectory
+ if not os.path.exists(thumbnail_dir):
+ raise VistrailsInternalError("Cannot find %s" % thumbnail_dir)
+ return thumbnail_dir
+
+ raise VistrailsInternalError("'thumbs.cacheDirectory' not"
+ " specified in configuration")
+ return None
+
+ def init_cache(self):
+ for root,dirs, files in os.walk(self.get_directory()):
+ for f in files:
+ fname = os.path.join(root,f)
+ statinfo = os.stat(fname)
+ size = int(statinfo[6])
+ time = float(statinfo[8])
+ entry = CacheEntry(fname, f, time, size)
+ self.elements[f] = entry
+
+ def get_abs_name_entry(self,name):
+ """get_abs_name_entry(name) -> str
+ It will look for absolute file path of name in self.elements and
+ self.vtelements. It returns None if item was not found.
+
+ """
+ try:
+ return self.elements[name].abs_name
+ except KeyError, e:
+ try:
+ return self.vtelements[name].abs_name
+ except KeyError, e:
+ return None
+
+ def size(self):
+ size = 0
+ for entry in self.elements.itervalues():
+ size += entry.size
+ return size
+
+ def move_cache_directory(self, sourcedir, destdir):
+ """change_cache_directory(sourcedir: str, dest_dir: str) -> None"
+ Moves files from sourcedir to destdir
+
+ """
+ if os.path.exists(destdir):
+ for entry in self.elements.itervalues():
+ try:
+ srcname = entry.abs_name
+ dstname = os.path.join(destdir,entry.name)
+ shutil.move(srcname,dstname)
+ entry.abs_name = dstname
+
+ except shutil.Error, e:
+ debug.warning("Could not move thumbnail from %s to %s: %s" \
+ % (sourcedir, destdir, str(e)))
+
+ def remove_lru(self,n=1):
+ elements = self.elements.values()
+ elements.sort(key=lambda obj: obj.time)
+ num = min(n,len(elements))
+ debug.debug("Will remove %s elements from cache..."%num)
+ debug.debug("Cache has %s elements and %s bytes"%(len(elements),
+ self.size()))
+ for i in range(num):
+ try:
+ del self.elements[elements[i].name]
+ os.unlink(elements[i].abs_name)
+ except os.error, e:
+ debug.warning("Could not remove file %s: %s" % \
+ (elements[i].abs_name, str(e)))
+ def remove(self,key):
+ if key in self.elements.keys():
+ entry = self.elements[key]
+ del self.elements[key]
+ os.unlink(entry.abs_name)
+ elif key in self.vtelements.keys():
+ entry = self.vtelements[key]
+ del self.vtelements[key]
+ os.unlink(entry.abs_name)
+
+ def clear(self):
+ self.elements = {}
+ self._delete_files(self.get_directory())
+
+ def add_entry_from_cell_dump(self, folder, key=None):
+ """create_entry_from_cell_dump(folder: str) -> str
+ Creates a cache entry from images in folder by merge them in a single
+ image and returns the name of the image in cache.
+ If a valid key is provided, it will use it as the name of the
+ image file.
+
+ """
+
+ image = None
+ thumbnail_fnames = self._get_thumbnail_fnames(folder)
+ if len(thumbnail_fnames) > 0:
+ image = self._merge_thumbnails(thumbnail_fnames)
+ fname = None
+ if image != None and image.width() > 0 and image.height() > 0:
+ fname = "%s.png" % str(uuid.uuid1())
+ abs_fname = self._save_thumbnail(image, fname)
+ statinfo = os.stat(abs_fname)
+ size = int(statinfo[6])
+ time = float(statinfo[8])
+ entry = CacheEntry(abs_fname, fname, time, size)
+ #remove old element
+ if key:
+ self.remove(key)
+ if self.size() + size > self.conf.cacheSize*1024*1024:
+ self.remove_lru(10)
+
+ self.elements[fname] = entry
+ return fname
+
+ def add_entries_from_files(self, absfnames):
+ """add_entries_from_files(absfnames: list of str) -> None
+ In this case the files already exist somewhere on disk.
+ We just keep references to them.
+
+ """
+ for abs_fname in absfnames:
+ fname = os.path.basename(abs_fname)
+ statinfo = os.stat(abs_fname)
+ size = int(statinfo[6])
+ time = float(statinfo[8])
+ entry = CacheEntry(abs_fname, fname, time, size)
+ self.vtelements[fname] = entry
+
+ @staticmethod
+ def _delete_files(dirname):
+ """delete_files(dirname: str) -> None
+ Deletes all files inside dirname
+
+ """
+ try:
+ for root, dirs, files in os.walk(dirname):
+ for fname in files:
+ os.unlink(os.path.join(root,fname))
+
+ except OSError, e:
+ debug.warning("Error when removing thumbnails: %s"%str(e))
+
+ @staticmethod
+ def _get_thumbnail_fnames(folder):
+ """Returns the filenames of the images to be composited in the given
+ folder. (folder: str) -> list(str)
+
+ """
+ fnames = []
+ for root, dirs, files in os.walk(folder):
+ for f in files:
+ ftype = mimetypes.guess_type(f)
+ if ftype[0] in ThumbnailCache.SUPPORTED_TYPES:
+ fnames.append(os.path.join(root,f))
+ return fnames
+
+ @staticmethod
+ def _merge_thumbnails(fnames):
+ """_merge_thumbnails(fnames: list(str)) -> QImage
+ Generates a single image formed by all the images in the fnames list.
+
+ """
+ from PyQt4 import QtCore, QtGui
+ height = 0
+ width = 0
+ pixmaps = []
+ # OS may return wrong order so we need to sort
+ fnames.sort()
+ for fname in fnames:
+ pix = QtGui.QPixmap(fname)
+ if pix.height() > 0 and pix.width() > 0:
+ pixmaps.append(pix)
+ #width += pix.width()
+ #height = max(height, pix.height())
+ height += pix.height()
+ width = max(width,pix.width())
+ if len(pixmaps) > 0 and height > 0 and width > 0:
+ finalImage = QtGui.QImage(width, height, QtGui.QImage.Format_ARGB32)
+ painter = QtGui.QPainter(finalImage)
+ x = 0
+ for pix in pixmaps:
+ painter.drawPixmap(0, x, pix)
+ x += pix.height()
+ painter.end()
+ if width > ThumbnailCache.IMAGE_MAX_WIDTH:
+ finalImage = finalImage.scaledToWidth(ThumbnailCache.IMAGE_MAX_WIDTH,
+ QtCore.Qt.SmoothTransformation)
+ else:
+ finalImage = None
+ return finalImage
+
+ def _save_thumbnail(self, pngimage, fname):
+ """_save_thumbnail(pngimage:QImage, fname: str) -> str
+ Returns the absolute path of the saved image
+
+ """
+ png_fname = os.path.join(self.get_directory(), fname)
+ if os.path.exists(png_fname):
+ os.unlink(png_fname)
+ pngimage.save(png_fname)
+ return png_fname
+
+ def _copy_thumbnails(self, thumbnails):
+ """_copy_thumbnails(thumbnails: list of str) -> None """
+ local_dir = self.get_directory()
+ for thumb in thumbnails:
+ local_thumb = os.path.join(local_dir, os.path.basename(thumb))
+ if os.path.exists(thumb) and not os.path.exists(local_thumb):
+ shutil.copyfile(thumb, local_thumb)
diff --git a/vistrails/core/upgradeworkflow.py b/vistrails/core/upgradeworkflow.py
new file mode 100644
index 0000000..9db165a
--- /dev/null
+++ b/vistrails/core/upgradeworkflow.py
@@ -0,0 +1,578 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""This file contains code to handle InvalidPipeline exceptions that contain
+upgrade requests."""
+from vistrails.core import debug
+import vistrails.core.db.action
+from vistrails.core.modules.module_registry import get_module_registry, \
+ ModuleDescriptor, MissingModule, MissingPort
+from vistrails.core.modules.utils import parse_descriptor_string, \
+ create_descriptor_string, parse_port_spec_string, \
+ create_port_spec_string, expand_port_spec_string
+from vistrails.core.packagemanager import get_package_manager
+from vistrails.core.system import get_vistrails_basic_pkg_id
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.vistrail.connection import Connection
+from vistrails.core.vistrail.port import Port
+from vistrails.core.vistrail.port_spec import PortSpec
+from vistrails.core.utils import versions_increasing
+import copy
+
+##############################################################################
+
+class UpgradeWorkflowError(Exception):
+
+ def __init__(self, msg, module=None, port_name=None, port_type=None):
+ Exception.__init__(self, msg)
+ self._msg = msg
+ self._module = module
+ self._port_name = port_name
+ self._port_type = port_type.lower() if port_type else None
+
+ def __str__(self):
+ return "Upgrading workflow failed.\n" + self._msg
+
+class UpgradeWorkflowHandler(object):
+
+ @staticmethod
+ def dispatch_request(controller, module_id, current_pipeline):
+ reg = get_module_registry()
+ pm = get_package_manager()
+ if module_id not in current_pipeline.modules:
+ # It is possible that some other upgrade request has
+ # already removed the invalid module of this request. In
+ # that case, disregard the request.
+ debug.log("module %s already handled. skipping" % module_id)
+ return []
+ invalid_module = current_pipeline.modules[module_id]
+ pkg = pm.get_package(invalid_module.package)
+ if hasattr(pkg.module, 'handle_module_upgrade_request'):
+ f = pkg.module.handle_module_upgrade_request
+ return f(controller, module_id, current_pipeline)
+ else:
+ debug.log('Package "%s" cannot handle upgrade request. '
+ 'VisTrails will attempt automatic upgrade.' % \
+ pkg.identifier)
+ auto_upgrade = UpgradeWorkflowHandler.attempt_automatic_upgrade
+ return auto_upgrade(controller, current_pipeline, module_id)
+
+ @staticmethod
+ def check_port_spec(module, port_name, port_type, descriptor=None,
+ sigstring=None):
+ from vistrails.core.modules.basic_modules import identifier as basic_pkg
+
+ reg = get_module_registry()
+ found = False
+ try:
+ if descriptor is not None:
+ s = reg.get_port_spec_from_descriptor(descriptor, port_name,
+ port_type)
+ found = True
+
+ spec_tuples = parse_port_spec_string(sigstring, basic_pkg)
+ for i in xrange(len(spec_tuples)):
+ spec_tuple = spec_tuples[i]
+ port_pkg = reg.get_package_by_name(spec_tuple[0])
+ if port_pkg.identifier != spec_tuple[0]:
+ # we have an old identifier
+ spec_tuples[i] = (port_pkg.identifier,) + spec_tuple[1:]
+ sigstring = create_port_spec_string(spec_tuples)
+ # sigstring = expand_port_spec_string(sigstring, basic_pkg)
+ if s.sigstring != sigstring:
+ msg = ('%s port "%s" of module "%s" exists, but '
+ 'signatures differ "%s" != "%s"') % \
+ (port_type.capitalize(), port_name, module.name,
+ s.sigstring, sigstring)
+ raise UpgradeWorkflowError(msg, module, port_name, port_type)
+ except MissingPort:
+ pass
+
+ if not found and \
+ not module.has_portSpec_with_name((port_name, port_type)):
+ msg = '%s port "%s" of module "%s" does not exist.' % \
+ (port_type.capitalize(), port_name, module.name)
+ raise UpgradeWorkflowError(msg, module, port_name, port_type)
+
+ @staticmethod
+ def find_descriptor(controller, pipeline, module_id, desired_version=''):
+ from vistrails.core.modules.abstraction \
+ import identifier as local_abstraction_pkg
+ reg = get_module_registry()
+
+ get_descriptor = reg.get_descriptor_by_name
+ pm = get_package_manager()
+ invalid_module = pipeline.modules[module_id]
+ mpkg, mname, mnamespace, mid = (invalid_module.package,
+ invalid_module.name,
+ invalid_module.namespace,
+ invalid_module.id)
+ pkg = pm.get_package(mpkg)
+ desired_version = ''
+ d = None
+ # don't check for abstraction/subworkflow since the old module
+ # could be a subworkflow
+ if reg.has_abs_upgrade(*invalid_module.descriptor_info):
+ return reg.get_abs_upgrade(*invalid_module.descriptor_info)
+
+ try:
+ try:
+ d = get_descriptor(mpkg, mname, mnamespace, '', desired_version)
+ except MissingModule, e:
+ r = None
+ if pkg.can_handle_missing_modules():
+ r = pkg.handle_missing_module(controller, module_id,
+ pipeline)
+ d = get_descriptor(mpkg, mname, mnamespace, '',
+ desired_version)
+ if not r:
+ raise e
+ except MissingModule, e:
+ return None
+ assert isinstance(d, ModuleDescriptor)
+ return d
+
+ @staticmethod
+ def check_upgrade(pipeline, module_id, d, function_remap={},
+ src_port_remap={}, dst_port_remap={}):
+ invalid_module = pipeline.modules[module_id]
+ def check_connection_port(port):
+ port_type = PortSpec.port_type_map.inverse[port.type]
+ UpgradeWorkflowHandler.check_port_spec(invalid_module,
+ port.name, port_type,
+ d, port.sigstring)
+
+ # check if connections are still valid
+ for _, conn_id in pipeline.graph.edges_from(module_id):
+ port = pipeline.connections[conn_id].source
+ if port.name not in src_port_remap:
+ check_connection_port(port)
+ for _, conn_id in pipeline.graph.edges_to(module_id):
+ port = pipeline.connections[conn_id].destination
+ if port.name not in dst_port_remap:
+ check_connection_port(port)
+
+ # check if function values are still valid
+ for function in invalid_module.functions:
+ # function_spec = function.get_spec('input')
+ if function.name not in function_remap:
+ UpgradeWorkflowHandler.check_port_spec(invalid_module,
+ function.name,
+ 'input', d,
+ function.sigstring)
+
+ @staticmethod
+ def attempt_automatic_upgrade(controller, pipeline, module_id,
+ function_remap={}, src_port_remap={},
+ dst_port_remap={}, annotation_remap={}):
+ """attempt_automatic_upgrade(module_id, pipeline): [Action]
+
+ Attempts to automatically upgrade module by simply adding a
+ new module with the current package version, and recreating
+ all connections and functions. If any of the ports used are
+ not available, raise an exception that will trigger the
+ failure of the entire upgrade.
+
+ attempt_automatic_upgrade returns a list of actions if
+ successful.
+ """
+
+ invalid_module = pipeline.modules[module_id]
+ mpkg, mname, mnamespace, mid = (invalid_module.package,
+ invalid_module.name,
+ invalid_module.namespace,
+ invalid_module.id)
+ d = UpgradeWorkflowHandler.find_descriptor(controller, pipeline,
+ module_id)
+ if not d:
+ if mnamespace:
+ nss = mnamespace + '|' + mname
+ else:
+ nss = mname
+ msg = ("Could not upgrade module %s from package %s.\n" %
+ (mname, mpkg))
+ raise UpgradeWorkflowError(msg)
+
+ UpgradeWorkflowHandler.check_upgrade(pipeline, module_id, d,
+ function_remap,
+ src_port_remap, dst_port_remap)
+
+ # If we passed all of these checks, then we consider module to
+ # be automatically upgradeable. Now create actions that will
+ # delete functions, module, and connections, and add new
+ # module with corresponding functions and connections.
+
+ return UpgradeWorkflowHandler.replace_module(controller, pipeline,
+ module_id, d,
+ function_remap,
+ src_port_remap,
+ dst_port_remap,
+ annotation_remap)
+
+ @staticmethod
+ def create_new_connection(controller, src_module, src_port,
+ dst_module, dst_port):
+ # spec -> name, type, signature
+ output_port_id = controller.id_scope.getNewId(Port.vtType)
+ if isinstance(src_port, basestring):
+ output_port_spec = src_module.get_port_spec(src_port, 'output')
+ output_port = Port(id=output_port_id,
+ spec=output_port_spec,
+ moduleId=src_module.id,
+ moduleName=src_module.name)
+ else:
+ output_port = Port(id=output_port_id,
+ name=src_port.name,
+ type=src_port.type,
+ signature=src_port.signature,
+ moduleId=src_module.id,
+ moduleName=src_module.name)
+
+ input_port_id = controller.id_scope.getNewId(Port.vtType)
+ if isinstance(dst_port, basestring):
+ input_port_spec = dst_module.get_port_spec(dst_port, 'input')
+ input_port = Port(id=input_port_id,
+ spec=input_port_spec,
+ moduleId=dst_module.id,
+ moduleName=dst_module.name)
+ else:
+ input_port = Port(id=input_port_id,
+ name=dst_port.name,
+ type=dst_port.type,
+ signature=dst_port.signature,
+ moduleId=dst_module.id,
+ moduleName=dst_module.name)
+ conn_id = controller.id_scope.getNewId(Connection.vtType)
+ connection = Connection(id=conn_id,
+ ports=[input_port, output_port])
+ return connection
+
+
+
+ @staticmethod
+ def replace_generic(controller, pipeline, old_module, new_module,
+ function_remap={}, src_port_remap={},
+ dst_port_remap={}, annotation_remap={}):
+ ops = []
+ ops.extend(controller.delete_module_list_ops(pipeline, [old_module.id]))
+
+ for annotation in old_module.annotations:
+ if annotation.key not in annotation_remap:
+ annotation_key = annotation.key
+ else:
+ remap = annotation_remap[annotation.key]
+ if remap is None:
+ # don't add the annotation back in
+ continue
+ elif not isinstance(remap, basestring):
+ ops.extend(remap(annotation))
+ continue
+ else:
+ annotation_key = remap
+
+ new_annotation = \
+ Annotation(id=controller.id_scope.getNewId(Annotation.vtType),
+ key=annotation_key,
+ value=annotation.value)
+ new_module.add_annotation(new_annotation)
+
+ if not old_module.is_group() and not old_module.is_abstraction():
+ for port_spec in old_module.port_spec_list:
+ if port_spec.type == 'input':
+ if port_spec.name not in dst_port_remap:
+ spec_name = port_spec.name
+ else:
+ remap = dst_port_remap[port_spec.name]
+ if remap is None:
+ continue
+ elif not isinstance(remap, basestring):
+ ops.extend(remap(port_spec))
+ continue
+ else:
+ spec_name = remap
+ elif port_spec.type == 'output':
+ if port_spec.name not in src_port_remap:
+ spec_name = port_spec.name
+ else:
+ remap = src_port_remap[port_spec.name]
+ if remap is None:
+ continue
+ elif not isinstance(remap, basestring):
+ ops.extend(remap(port_spec))
+ continue
+ else:
+ spec_name = remap
+ new_spec = port_spec.do_copy(True, controller.id_scope, {})
+ new_spec.name = spec_name
+ new_module.add_port_spec(new_spec)
+
+ function_ops = []
+ for function in old_module.functions:
+ if function.name not in function_remap:
+ function_name = function.name
+ else:
+ remap = function_remap[function.name]
+ if remap is None:
+ # don't add the function back in
+ continue
+ elif not isinstance(remap, basestring):
+ function_ops.extend(remap(function, new_module))
+ continue
+ else:
+ function_name = remap
+
+ if len(function.parameters) > 0:
+ new_param_vals, aliases = zip(*[(p.strValue, p.alias)
+ for p in function.parameters])
+ else:
+ new_param_vals = []
+ aliases = []
+ new_function = controller.create_function(new_module,
+ function_name,
+ new_param_vals,
+ aliases)
+ new_module.add_function(new_function)
+
+ # add the new module
+ ops.append(('add', new_module))
+ ops.extend(function_ops)
+
+ create_new_connection = UpgradeWorkflowHandler.create_new_connection
+
+ for _, conn_id in pipeline.graph.edges_from(old_module.id):
+ old_conn = pipeline.connections[conn_id]
+ if old_conn.source.name not in src_port_remap:
+ source_name = old_conn.source.name
+ else:
+ remap = src_port_remap[old_conn.source.name]
+ if remap is None:
+ # don't add this connection back in
+ continue
+ elif not isinstance(remap, basestring):
+ ops.extend(remap(old_conn, new_module))
+ continue
+ else:
+ source_name = remap
+
+ old_dst_module = pipeline.modules[old_conn.destination.moduleId]
+
+ new_conn = create_new_connection(controller,
+ new_module,
+ source_name,
+ old_dst_module,
+ old_conn.destination)
+ ops.append(('add', new_conn))
+
+ for _, conn_id in pipeline.graph.edges_to(old_module.id):
+ old_conn = pipeline.connections[conn_id]
+ if old_conn.destination.name not in dst_port_remap:
+ destination_name = old_conn.destination.name
+ else:
+ remap = dst_port_remap[old_conn.destination.name]
+ if remap is None:
+ # don't add this connection back in
+ continue
+ elif not isinstance(remap, basestring):
+ ops.extend(remap(old_conn, new_module))
+ continue
+ else:
+ destination_name = remap
+
+ old_src_module = pipeline.modules[old_conn.source.moduleId]
+ new_conn = create_new_connection(controller,
+ old_src_module,
+ old_conn.source,
+ new_module,
+ destination_name)
+ ops.append(('add', new_conn))
+
+ return [vistrails.core.db.action.create_action(ops)]
+
+ @staticmethod
+ def replace_group(controller, pipeline, module_id, new_subpipeline):
+ old_group = pipeline.modules[module_id]
+ basic_pkg = get_vistrails_basic_pkg_id()
+ new_group = controller.create_module(basic_pkg, 'Group', '',
+ old_group.location.x,
+ old_group.location.y)
+ new_group.pipeline = new_subpipeline
+ return UpgradeWorkflowHandler.replace_generic(controller, pipeline,
+ old_group, new_group)
+
+ @staticmethod
+ def replace_module(controller, pipeline, module_id, new_descriptor,
+ function_remap={}, src_port_remap={}, dst_port_remap={},
+ annotation_remap={}):
+ old_module = pipeline.modules[module_id]
+ internal_version = -1
+ # try to determine whether new module is an abstraction
+ if (hasattr(new_descriptor, 'module') and
+ hasattr(new_descriptor.module, "vistrail") and
+ hasattr(new_descriptor.module, "internal_version")):
+ internal_version = new_descriptor.version
+ new_module = \
+ controller.create_module_from_descriptor(new_descriptor,
+ old_module.location.x,
+ old_module.location.y,
+ internal_version)
+
+ return UpgradeWorkflowHandler.replace_generic(controller, pipeline,
+ old_module, new_module,
+ function_remap,
+ src_port_remap,
+ dst_port_remap,
+ annotation_remap)
+
+ @staticmethod
+ def remap_module(controller, module_id, pipeline, module_remap):
+
+ """remap_module offers a method to shortcut the
+ specification of upgrades. It is useful when just changing
+ the names of ports or modules, but can also be used to add
+ intermediate modules or change the format of parameters. It
+ is usually called from handle_module_upgrade_request, and the
+ first three arguments are passed from the arguments to that
+ method.
+
+ module_remap specifies all of the changes and is of the format
+ {<old_module_name>: [(<start_version>, <end_version>,
+ <new_module_klass> | <new_module_id> | None,
+ <remap_dictionary>)]}
+ where new_module_klass is the class and new_module_id
+ is a string of the format
+ <package_name>:[<namespace> | ]<module_name>
+ passing None keeps the original name,
+ and remap_dictionary is {<remap_type>:
+ <name_changes>} and <name_changes> is a map from <old_name> to
+ <new_name> or <remap_function>
+ The remap functions are passed the old object and the new
+ module and should return a list of operations with elements of
+ the form ('add', <obj>).
+
+ For example:
+
+ def outputName_remap(old_conn, new_module):
+ ops = []
+ ...
+ return ops
+ module_remap = {'FileSink': [(None, '1.5.1', FileSink,
+ {'dst_port_remap':
+ {'overrideFile': 'overwrite',
+ 'outputName': outputName_remap},
+ 'function_remap':
+ {'overrideFile': 'overwrite',
+ 'outputName': 'outputPath'}}),
+ }
+ """
+
+ reg = get_module_registry()
+
+ old_module = pipeline.modules[module_id]
+ old_desc_str = create_descriptor_string(old_module.package,
+ old_module.name,
+ old_module.namespace,
+ False)
+ # print 'running module_upgrade_request', old_module.name
+ if old_desc_str in module_remap:
+ for upgrade_tuple in module_remap[old_desc_str]:
+ (start_version, end_version, new_module_type, remap) = \
+ upgrade_tuple
+ old_version = old_module.version
+ if ((start_version is None or
+ not versions_increasing(old_version, start_version)) and
+ (end_version is None or
+ versions_increasing(old_version, end_version))):
+ # do upgrade
+
+ if new_module_type is None:
+ try:
+ new_module_desc = \
+ reg.get_descriptor_by_name(old_module.package,
+ old_module.name,
+ old_module.namespace)
+ except MissingModule, e:
+ # if the replacement is an abstraction,
+ # and it has been upgraded, we use that
+ if reg.has_abs_upgrade(old_module.package,
+ old_module.name,
+ old_module.namespace):
+ new_module_desc = \
+ reg.get_abs_upgrade(old_module.package,
+ old_module.name,
+ old_module.namespace)
+ else:
+ raise e
+ elif isinstance(new_module_type, basestring):
+ d_tuple = parse_descriptor_string(new_module_type,
+ old_module.package)
+ try:
+ new_module_desc = \
+ reg.get_descriptor_by_name(*d_tuple)
+ except MissingModule, e:
+ # if the replacement is an abstraction,
+ # and it has been upgraded, we use that
+ if reg.has_abs_upgrade(*d_tuple):
+ new_module_desc = reg.get_abs_upgrade(*d_tuple)
+ else:
+ raise e
+ else: # we have a klass for get_descriptor
+ new_module_desc = reg.get_descriptor(new_module_type)
+
+ src_port_remap = remap.get('src_port_remap', {})
+ dst_port_remap = remap.get('dst_port_remap', {})
+ # !!! we're going to let dst_port_remap serve as a
+ # base for function_remap but the developer is
+ # responsible for knowing that anything beyond name
+ # remaps requires different functions
+ function_remap = copy.copy(dst_port_remap)
+ function_remap.update(remap.get('function_remap', {}))
+ annotation_remap = remap.get('annotation_remap', {})
+ action_list = \
+ UpgradeWorkflowHandler.replace_module(controller,
+ pipeline,
+ module_id,
+ new_module_desc,
+ function_remap,
+ src_port_remap,
+ dst_port_remap,
+ annotation_remap)
+ return action_list
+
+ # otherwise, just try to automatic upgrade
+ # attempt_automatic_upgrade
+ return UpgradeWorkflowHandler.attempt_automatic_upgrade(controller,
+ pipeline,
+ module_id)
+
diff --git a/vistrails/core/utils/__init__.py b/vistrails/core/utils/__init__.py
new file mode 100644
index 0000000..1b09d76
--- /dev/null
+++ b/vistrails/core/utils/__init__.py
@@ -0,0 +1,644 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""
+This module defines common functions and exception class definitions
+used all over VisTrails.
+"""
+from __future__ import with_statement
+
+import vistrails.core.debug
+from vistrails.core.utils.enum import enum
+from vistrails.core.utils.timemethod import time_method, time_call
+from vistrails.core.utils.tracemethod import trace_method, bump_trace, report_stack, \
+ trace_method_options, trace_method_args
+from vistrails.core.utils.color import ColorByName
+from vistrails.core.utils.lockmethod import lock_method
+import copy
+import errno
+import itertools
+import os
+import sys
+import weakref
+
+
+import unittest
+import tempfile
+
+################################################################################
+
+def invert(d):
+ """invert(dict) -> dict. Returns an inverted dictionary by
+ switching key-value pairs. If you use this repeatedly,
+ consider switching the underlying data structure to a
+ core.data_structures.bijectivedict.Bidict instead."""
+ return dict([[v,k] for k,v in d.items()])
+
+################################################################################
+
+def unimplemented():
+ """Raises UnimplementedException."""
+ raise UnimplementedException()
+
+def abstract():
+ """Raises AbstractException."""
+ raise AbstractException()
+
+class VistrailsWarning(Warning):
+ pass
+
+class VistrailsDeprecation(VistrailsWarning):
+ pass
+
+################################################################################
+
+class NoMakeConnection(Exception):
+ """NoMakeConnection is raised when a VisConnection doesn't know
+ how to create a live version of itself. This is an internal error
+ that should never be seen by a user. Please report a bug if you
+ see this."""
+ def __init__(self, conn):
+ self.conn = conn
+ def __str__(self):
+ return "Connection %s has no makeConnection method" % self.conn
+
+class NoSummon(Exception):
+ """NoSummon is raised when a VisObject doesn't know how to create
+ a live version of itself. This is an internal error that should
+ never be seen by a user. Please report a bug if you see this."""
+ def __init__(self, obj):
+ self.obj = obj
+ def __str__(self):
+ return "Module %s has no summon method" % self.obj
+
+class UnimplementedException(Exception):
+ """UnimplementedException is raised when some interface hasn't
+ been implemented yet. This is an internal error that should never
+ be seen by a user. Please report a bug if you see this."""
+ def __str__(self):
+ return "Object is Unimplemented"
+
+class AbstractException(Exception):
+ """AbstractException is raised when an abstract method is called.
+ This is an internal error that should never be seen by a
+ user. Please report a bug if you see this."""
+ def __str__(self):
+ return "Abstract Method was called"
+
+class VistrailsInternalError(Exception):
+ """VistrailsInternalError is raised when an unexpected internal
+ inconsistency happens. This is (clearly) an internal error that
+ should never be seen by a user. Please report a bug if you see
+ this."""
+ def __init__(self, msg):
+ self.emsg = msg
+ def __str__(self):
+ return "Vistrails Internal Error: " + str(self.emsg)
+
+class VersionTooLow(Exception):
+ """VersionTooLow is raised when you're running an outdated version
+ of some necessary software or package."""
+ def __init__(self, sw, required_version):
+ self.sw = sw
+ self.required_version = required_version
+ def __str__(self):
+ return ("Your version of '" +
+ self.sw +
+ "' is too low. Please upgrade to " +
+ self.required_version +
+ " or later")
+
+class InvalidModuleClass(Exception):
+ """InvalidModuleClass is raised when there's something wrong with
+a class that's being registered as a module within VisTrails."""
+
+ def __init__(self, klass):
+ self.klass = klass
+
+ def __str__(self):
+ return ("class '%s' cannot be registered in VisTrails. Please" +
+ " consult the documentation.") % self.klass.__name__
+
+class ModuleAlreadyExists(Exception):
+ """ModuleAlreadyExists is raised when trying to add a class that
+ is already in the module registry."""
+
+ def __init__(self, identifier, moduleName):
+ self._identifier = identifier
+ self._name = moduleName
+
+ def __str__(self):
+ return ("'%s, %s' cannot be registered in VisTrails because of another "
+ "module with the same identifier and name already exists." %
+ (self._identifier,
+ self._name))
+
+class PortAlreadyExists(Exception):
+ """PortAlreadyExists is raised when trying to add a PortSpec that
+ has the same name and type as an existing PortSpec."""
+
+ def __init__(self, identifier, module_name, port_type, port_name):
+ self._identifier = identifier
+ self._module_name = module_name
+ self._port_type = port_type
+ self._port_name = port_name
+
+ def __str__(self):
+ return "Module '%s:%s' already contains an %s port named '%s'" % \
+ (self._identifier, self._module_name, self._port_type,
+ self._port_name)
+
+class InvalidPipeline(Exception):
+ """InvalidPipeline is raised when a pipeline cannot be instantiated due
+ to missing information in the registry, like unloaded packages or missing
+ modules.
+
+ parameters:
+
+ exception_set: list of all exceptions related to why this is an
+ invalid pipeline
+
+ pipeline: pipeline that is invalid (potentially incomplete, in the
+ case where modules could not be found, etc). This is stored here
+ so that pipeline upgrades can be performed appropriately. Since
+ Controller.do_version_switch (sensibly) bails before setting the
+ invalid pipeline to current_pipeline and the new value to
+ current_version, these need to percolate through the exceptions so
+ the values can be fixed.
+
+ version: version id of the pipeline in the vistrail
+ """
+ def __init__(self, exception_set, pipeline=None, version=None):
+ self._exception_set = exception_set
+ #the problem here is that sometimes the pipeline can't be copied when
+ # it is invalid. So if it throws an Exception, we will just ignore
+ try:
+ self._pipeline = copy.copy(pipeline)
+ except:
+ self._pipeline = None
+ self._version = version
+
+ def __str__(self):
+ return "Pipeline has errors. Please see the detailed message for more information.\n " + \
+ '\n '.join(line for e in self._exception_set
+ for line in str(e).splitlines())
+
+ def get_exception_set(self):
+ return self._exception_set
+
+################################################################################
+
+# Only works for functions with NO kwargs!
+def memo_method(method):
+ """memo_method is a method decorator that memoizes results of the
+ decorated method, trading off memory for time by caching previous
+ results of the calls."""
+ attrname = "_%s_memo_result" % id(method)
+ memo = {}
+ def decorated(self, *args):
+ try:
+ return memo[args]
+ except KeyError:
+ result = method(self, *args)
+ memo[args] = result
+ return result
+ warn = "(This is a memoized method: Don't mutate the return value you're given.)"
+ if method.__doc__:
+ decorated.__doc__ = method.__doc__ + "\n\n" + warn
+ else:
+ decorated.__doc__ = warn
+ return decorated
+
+##############################################################################
+# Profiling, utilities
+
+_profiled_list = []
+def profile(func):
+ """profile is a method decorator that profiles the calls of a
+ given method using cProfile. You need to get the decorated method
+ programmatically later to get to the profiler stats. It will be
+ available as the attribute 'profiler_object' on the decorated
+ result.
+
+ From there, you can simply call save_all_profiles(), and that will
+ take the list of all profiled methods and save them to different
+ files.
+
+ If you like manual labor, you probably want to do something like this:
+
+ >>> po = ...... .profiler_object
+ >>> po.dump_stats('/tmp/some_temporary_file')
+ >>> import pstats
+ >>> ps = pstats.Stats('/tmp/some_temporary_file')
+ >>> ps.sort_stats('time') # or cumtime, or calls, or others - see doc
+ >>> ps.print_stats()
+
+ """
+
+ # Notice that on ubuntu you will need
+ # sudo apt-get install python-profiler
+
+ try:
+ import cProfile as prof
+ except ImportError:
+ import profile as prof
+
+ pobject = prof.Profile()
+ def method(*args, **kwargs):
+ return pobject.runcall(func, *args, **kwargs)
+
+ method.profiler_object = pobject
+ _profiled_list.append((func.__name__, method))
+ return method
+
+def get_profiled_methods():
+ return _profiled_list
+
+def save_profile_to_disk(callable_, filename):
+ callable_.profiler_object.dump_stats(filename)
+
+def save_all_profiles():
+ # This is internal because core.system imports core.utils... :/
+ import vistrails.core.system
+ td = vistrails.core.system.temporary_directory()
+ for (name, method) in get_profiled_methods():
+ fout = td + name + '.pyp'
+ #print fout
+ method.profiler_object.dump_stats(fout)
+
+##############################################################################
+
+def debug(func):
+ """debug is a method decorator that invokes the python integrated
+ debugger in a given method. Use it to step through tricky
+ code. Note that pdb is not integrated with emacs or anything like
+ that, so you'll need a shell to see what's going on.
+
+ """
+ import pdb
+
+ def method(*args, **kwargs):
+ return pdb.runcall(func, *args, **kwargs)
+ return method
+
+################################################################################
+
+# Write our own all() and any() if python version < 2.5
+if sys.version_info < (2, 5):
+ def any(iterable):
+ """any(iterable) -> Boolean - Returns true if any element
+ is true. This is meant to be the equivalent of python 2.5's any
+ when running on python < 2.5"""
+ for b in iterable:
+ if b:
+ return True
+ return False
+
+ def all(iterable):
+ """all(iterable) -> Boolean - Returns true if no elements are
+ False. This is meant to be the equivalent of python 2.5's
+ all() when running on python < 2.5"""
+ for b in iterable:
+ if not b:
+ return False
+ return True
+else:
+ import __builtin__
+ any = __builtin__.any
+ all = __builtin__.all
+
+def iter_index(iterable, item):
+ """iter_index(iterable, item) -> int - Iterates through iterator
+ until item is found, and returns the index inside the iterator.
+
+ iter_index is analogous to list.index for iterators."""
+ try:
+ itor = itertools.izip(iterable, itertools.count(0))
+ return itertools.dropwhile(lambda (v,c): v != item, itor).next()[1]
+ except StopIteration:
+ return -1
+
+
+def eprint(*args):
+ """eprint(*args) -> False - Prints the arguments, then returns
+ false. Useful inside a lambda expression, for example."""
+ for v in args:
+ print v,
+ print
+
+def uniq(l):
+ """uniq(l) -> List. Returns a new list consisting of elements that
+ test pairwise different for equality. Requires all elements to be
+ sortable, and runs in O(n log n) time."""
+ if len(l) == 0:
+ return []
+ a = copy.copy(l)
+ a.sort()
+ l1 = a[:-1]
+ l2 = a[1:]
+ return [a[0]] + [next for (i, next) in itertools.izip(l1, l2) if i != next]
+
+class InstanceObject(object):
+ """InstanceObject is a convenience class created to facilitate
+ creating of one-off objects with many fields. It simply translates
+ the passed kwargs on the constructor to a set of fields with
+ the right values."""
+ def __init__(self, **kw):
+ self.__dict__.update(kw)
+
+ def __str__(self):
+ pre = "(%s " % self.__class__.__name__
+ items = [('%s: %s' % (k, str(v)))
+ for (k, v)
+ in sorted(self.__dict__.items())]
+ items_str = ('\n' + (' ' * len(pre))).join(items)
+ post = ')@%X' % id(self)
+ return pre + items_str + post
+
+ def write_source(self, prefix=""):
+ result = ""
+ for (k, v) in sorted(self.__dict__.items()):
+ if isinstance(v, InstanceObject):
+ newprefix = prefix + "." + k
+ result += v.write_source(newprefix)
+ else:
+ result += prefix
+ result += "." + str(k) + " = "
+ if isinstance(v, basestring):
+ result += "'" + str(v) + "'\n"
+ else:
+ result += str(v) + "\n"
+ return result
+
+def append_to_dict_of_lists(dict, key, value):
+ """Appends /value/ to /dict/[/key/], or creates entry such that
+ /dict/[/key/] == [/value/]."""
+ try:
+ dict[key].append(value)
+ except KeyError:
+ dict[key] = [value]
+
+def version_string_to_list(version):
+ """version_string_to_list converts a version string to a list of
+ numbers and strings:
+
+ version_string('0.1') -> [0, 1]
+ version_string('0.9.9alpha') -> [0, 9, '9alpha']
+
+ """
+ def convert(value):
+ try:
+ return int(value)
+ except ValueError:
+ return value
+ return [convert(value) for value in version.split('.')]
+
+def versions_increasing(v1, v2):
+ v1_list = v1.split('.')
+ v1_list.reverse()
+ v2_list = v2.split('.')
+ v2_list.reverse()
+ try:
+ while len(v1_list) > 0 and len(v2_list) > 0:
+ v1_num = int(v1_list.pop())
+ v2_num = int(v2_list.pop())
+ if v1_num < v2_num:
+ return True
+ elif v1_num > v2_num:
+ return False
+ if len(v1_list) < len(v2_list):
+ return True
+ elif len(v1_list) > len(v2_list):
+ return False
+ except ValueError:
+ vistrails.core.debug.critical("Cannot compare versions whose components " +
+ "are not integers")
+ return False
+
+
+##############################################################################
+# DummyView & DummyScene
+
+class DummyScene(object):
+ def __init(self):
+ self.current_version = -1
+ self.current_pipeline = None
+ def get_selected_module_ids(self):
+ return []
+ def flushMoveActions(self, *args, **kwargs): pass
+
+class DummyView(object):
+ def __init__(self):
+ self._scene = DummyScene()
+ def set_module_active(self, *args, **kwargs): pass
+ def set_module_computing(self, *args, **kwargs): pass
+ def set_module_success(self, *args, **kwargs): pass
+ def set_module_suspended(self, *args, **kwargs): pass
+ def set_module_error(self, *args, **kwargs): pass
+ def set_module_not_executed(self, *args, **kwargs): pass
+ def set_module_progress(self, *args, **kwargs): pass
+ def set_module_persistent(self, *args, **kwargs): pass
+ def flushMoveActions(self, *args, **kwargs): pass
+ def scene(self):
+ return self._scene
+##############################################################################
+# FIXME: Add tests
+def no_interrupt(callable_, *args, **kwargs):
+ """no_interrupt(callable_, *args, **kwargs) -> return arguments
+ from callable.
+
+ Calls callable_ with *args and **kwargs and keeps retrying as long as call
+is interrupted by the OS. This makes calling read more convenient when
+using output from the subprocess module."""
+ while True:
+ try:
+ return callable_(*args, **kwargs)
+ except IOError, e:
+ if e.errno == errno.EINTR:
+ continue
+ else:
+ raise
+
+################################################################################
+# class for creating weak references to bound methods
+# based on recipe http://code.activestate.com/recipes/81253/
+# converted to work also in python 2.6.x without using deprecated methods
+# not tested in python 2.5.x but it should work
+class Ref(object):
+ """ Wraps any callable, most importantly a bound method, in a way that
+ allows a bound method's object to be GC'ed, while providing the same
+ interface as a normal weak reference. """
+ def __init__(self, fn):
+ try:
+ #try getting object, function, and class
+ o, f, c = fn.im_self, fn.im_func, fn.im_class
+ except AttributeError: #it's not a bound method
+ self._obj = None
+ self._func = fn
+ self._clas = None
+ else: #it's a bound method
+ if o is None: self._obj = None #... actually UN-bound
+ else: self._obj = weakref.ref(o)
+ self._func = f
+ self._clas = None
+
+ def __call__(self):
+ if self._obj is None: return self._func
+ elif self._obj() is None: return None
+ try:
+ import types
+ instance_method = types.MethodType
+ except ImportError:
+ #new is deprecated in python 2.6
+ import new
+ instance_method = new.instancemethod
+ return instance_method(self._func, self._obj(), self._clas)
+
+################################################################################
+
+class Chdir(object):
+ def __init__(self, dirname):
+ self._old_dir = os.getcwd()
+ self._new_dir = dirname
+
+ def __enter__(self):
+ os.chdir(self._new_dir)
+
+ def __exit__(self, *args):
+ os.chdir(self._old_dir)
+################################################################################
+
+
+
+class _TestRegularFibo(object):
+ def __init__(self):
+ self.calls = 0
+
+ def f(self, x):
+ self.calls += 1
+ if x == 0: return 0
+ if x == 1: return 1
+ return self.f(x-1) + self.f(x-2)
+
+class _TestMemoFibo(_TestRegularFibo):
+ f = memo_method(_TestRegularFibo.f)
+
+class TestCommon(unittest.TestCase):
+ def test_append_to_dict_of_lists(self):
+ f = {}
+ self.assertEquals(f.has_key(1), False)
+ append_to_dict_of_lists(f, 1, 1)
+ self.assertEquals(f.has_key(1), True)
+ self.assertEquals(f[1], [1])
+ append_to_dict_of_lists(f, 1, 1)
+ self.assertEquals(f.has_key(1), True)
+ self.assertEquals(f[1], [1, 1])
+ append_to_dict_of_lists(f, 1, 2)
+ self.assertEquals(f.has_key(1), True)
+ self.assertEquals(f[1], [1, 1, 2])
+ append_to_dict_of_lists(f, 2, "Foo")
+ self.assertEquals(f.has_key(2), True)
+ self.assertEquals(f[2], ["Foo"])
+
+ def test_memo(self):
+ regular = _TestRegularFibo()
+ r1 = regular.f(20)
+ memoized = _TestMemoFibo()
+ r2 = memoized.f(20)
+ self.assertEqual(r1, 6765)
+ self.assertEqual(r2, 6765)
+ self.assertLess(memoized.calls, regular.calls)
+ self.assertEqual(regular.calls, 21891)
+ self.assertEqual(memoized.calls, 21)
+
+ def test_memo_2(self):
+ count = [0]
+ class C1(object):
+ pass
+ class C2(object):
+ pass
+ class TestClassMemo(object):
+ def __init__(self, cell):
+ self.cell = cell
+ @memo_method
+ def f(self, cl, x):
+ self.cell[0] += 1
+ return x
+ t = TestClassMemo(count)
+ self.assertEquals(count[0], 0)
+ t.f(C1, 0)
+ self.assertEquals(count[0], 1)
+ t.f(C1, 0)
+ self.assertEquals(count[0], 1)
+ t.f(C1, 1)
+ self.assertEquals(count[0], 2)
+ t.f(C2, 0)
+ self.assertEquals(count[0], 3)
+
+ def test_version_string_to_list(self):
+ self.assertEquals(version_string_to_list("0.1"), [0, 1])
+ self.assertEquals(version_string_to_list("1.0.2"), [1, 0, 2])
+ self.assertEquals(version_string_to_list("1.0.2beta"), [1, 0, '2beta'])
+
+ def test_ref(self):
+ class C(object):
+ def f(self):
+ return 'hello'
+ c = C()
+ cf = weakref.ref(c.f)
+ #bound methods behave not as expected. You want cf() not to be None
+ self.assertEquals(cf(), None)
+ #so we use the new class
+ cf = Ref(c.f)
+ #it behaves as expected
+ self.assertEquals(cf()(),'hello')
+ del c
+ #and after deletion the reference is dead
+ self.assertEquals(cf(), None)
+
+ def test_chdir(self):
+ def raise_exception():
+ with Chdir(tempfile.gettempdir()):
+ raise Exception
+
+ currentpath = os.getcwd()
+ with Chdir(tempfile.gettempdir()):
+ pass
+ self.assertEquals(os.getcwd(), currentpath)
+
+ self.assertRaises(Exception, raise_exception)
+ self.assertEquals(os.getcwd(), currentpath)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/utils/color.py b/vistrails/core/utils/color.py
new file mode 100644
index 0000000..0b20b30
--- /dev/null
+++ b/vistrails/core/utils/color.py
@@ -0,0 +1,452 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""
+Contain color related utilities such as color look up by name or
+color defines
+"""
+
+################################################################################
+
+class ColorByName(object):
+ """
+ Provides a list of colors that can be queried by name
+
+ """
+ colors = { 'antique_white' : [ 0.9804, 0.9216, 0.8431 ],
+ 'azure' : [ 0.9412, 1.0000, 1.0000 ],
+ 'bisque' : [ 1.0000, 0.8941, 0.7686 ],
+ 'blanched_almond' : [ 1.0000, 0.9216, 0.8039 ],
+ 'cornsilk' : [ 1.0000, 0.9725, 0.8627 ],
+ 'eggshell' : [ 0.9900, 0.9000, 0.7900 ],
+ 'floral_white' : [ 1.0000, 0.9804, 0.9412 ],
+ 'gainsboro' : [ 0.8627, 0.8627, 0.8627],
+ 'ghost_white' : [ 0.9725, 0.9725, 1.0000],
+ 'honeydew' : [ 0.9412, 1.0000, 0.9412 ],
+ 'ivory' : [ 1.0000, 1.0000, 0.9412 ],
+ 'lavender' : [ 0.9020, 0.9020, 0.9804],
+ 'lavender_blush' : [1.0000, 0.9412, 0.9608 ],
+ 'lemon_chiffon' : [1.0000, 0.9804, 0.8039 ],
+ 'linen' : [ 0.9804, 0.9412, 0.9020 ],
+ 'mint_cream' : [ 0.9608, 1.0000, 0.9804 ],
+ 'misty_rose' : [ 1.0000, 0.8941, 0.8824 ],
+ 'moccasin' : [ 1.0000, 0.8941, 0.7098 ],
+ 'navajo_white' : [ 1.0000, 0.8706, 0.6784 ],
+ 'old_lace' : [ 0.9922, 0.9608, 0.9020 ],
+ 'papaya_whip' : [ 1.0000, 0.9373, 0.8353 ],
+ 'peach_puff' : [ 1.0000, 0.8549, 0.7255 ],
+ 'seashell' : [ 1.0000, 0.9608, 0.9333 ],
+ 'snow' : [ 1.0000, 0.9804, 0.9804 ],
+ 'thistle' : [ 0.8471, 0.7490, 0.8471 ],
+ 'titanium_white' : [ 0.9900, 1.0000, 0.9400 ],
+ 'wheat' : [ 0.9608, 0.8706, 0.7020 ],
+ 'white' : [ 1.0000, 1.0000, 1.0000 ],
+ 'white_smoke' : [ 0.9608, 0.9608, 0.9608 ],
+ 'zinc_white' : [ 0.9900, 0.9700, 1.0000 ],
+
+ #Greys
+ 'cold_grey' : [ 0.5000, 0.5400, 0.5300 ],
+ 'light_dim_grey' : [ 0.45, 0.45, 0.45 ],
+ 'dim_grey' : [ 0.4118, 0.4118, 0.4118 ],
+ 'dark_dim_grey' : [ 0.35, 0.35, 0.35 ],
+ 'grey' : [ 0.7529, 0.7529, 0.7529 ],
+ 'very_light_grey' : [ 0.95, 0.95, 0.95 ],
+ 'light_grey' : [ 0.8275, 0.8275, 0.8275 ],
+ 'slate_grey' : [ 0.4392, 0.5020, 0.5647 ],
+ 'slate_grey_dark' : [ 0.1843, 0.3098, 0.3098 ],
+ 'slate_grey_light' : [ 0.4667, 0.5333, 0.6000 ],
+ 'warm_grey' : [ 0.5000, 0.5000, 0.4100 ],
+
+ #Blacks
+ 'black' : [ 0.0000, 0.0000, 0.0000],
+ 'ivory_black' : [ 0.1600, 0.1400, 0.1300 ],
+ 'lamp_black' : [ 0.1800, 0.2800, 0.2300 ],
+
+ #Reds
+ 'alizarin_crimson' : [ 0.8900, 0.1500, 0.2100 ],
+ 'brick' : [ 0.6100, 0.4000, 0.1200 ],
+ 'cadmium_red_deep' : [ 0.8900, 0.0900, 0.0500 ],
+ 'coral' : [ 1.0000, 0.4980, 0.3137 ],
+ 'coral_light' : [ 0.9412, 0.5020, 0.5020 ],
+ 'deep_pink' : [ 1.0000, 0.0784, 0.5765],
+ 'english_red' : [ 0.8300, 0.2400, 0.1000 ],
+ 'firebrick' : [ 0.6980, 0.1333, 0.1333 ],
+ 'geranium_lake' : [ 0.8900, 0.0700, 0.1900 ],
+ 'hot_pink' : [ 1.0000, 0.4118, 0.7059 ],
+ 'indian_red' : [ 0.6900, 0.0900, 0.1200 ],
+ 'light_salmon' : [ 1.0000, 0.6275, 0.4784 ],
+ 'madder_lake_deep' :[ 0.8900, 0.1800, 0.1900 ],
+ 'maroon' : [0.6902, 0.1882, 0.3765 ],
+ 'pink' : [ 1.0000, 0.7529, 0.7961 ],
+ 'pink_light' : [ 1.0000, 0.7137, 0.7569 ],
+ 'raspberry' : [ 0.5300, 0.1500, 0.3400 ],
+ 'red': [ 1.0000, 0.0000, 0.0000 ],
+ 'rose_madder' : [ 0.8900, 0.2100, 0.2200 ],
+ 'salmon' : [ 0.9804, 0.5020, 0.4471 ],
+ 'tomato': [ 1.0000, 0.3882, 0.2784 ],
+ 'venetian_red' : [ 0.8300, 0.1000, 0.1200 ],
+
+ #Browns
+ 'beige' : [ 0.6400, 0.5800, 0.5000 ],
+ 'brown' : [ 0.5000, 0.1647, 0.1647 ],
+ 'brown_madder' : [ 0.8600, 0.1600, 0.1600 ],
+ 'brown_ochre': [ 0.5300, 0.2600, 0.1200 ],
+ 'burlywood' : [ 0.8706, 0.7216, 0.5294 ],
+ 'burnt_sienna' : [ 0.5400, 0.2100, 0.0600 ],
+ 'burnt_umber' : [ 0.5400, 0.2000, 0.1400 ],
+ 'chocolate' : [ 0.8235, 0.4118, 0.1176 ],
+ 'deep_ochre' : [ 0.4500, 0.2400, 0.1000 ],
+ 'flesh': [ 1.0000, 0.4900, 0.2500 ],
+ 'flesh_ochre': [ 1.0000, 0.3400, 0.1300 ],
+ 'gold_ochre': [ 0.7800, 0.4700, 0.1500 ],
+ 'greenish_umber': [ 1.0000, 0.2400, 0.0500 ],
+ 'khaki': [ 0.9412, 0.9020, 0.5490 ],
+ 'khaki_dark': [ 0.7412, 0.7176, 0.4196 ],
+ 'light_beige': [ 0.9608, 0.9608, 0.8627 ],
+ 'peru': [ 0.8039, 0.5216, 0.2471 ],
+ 'rosy_brown': [ 0.7373, 0.5608, 0.5608 ],
+ 'raw_sienna': [ 0.7800, 0.3800, 0.0800 ],
+ 'raw_umber': [ 0.4500, 0.2900, 0.0700 ],
+ 'sepia': [ 0.3700, 0.1500, 0.0700 ],
+ 'sienna': [ 0.6275, 0.3216, 0.1765 ],
+ 'saddle_brown': [ 0.5451, 0.2706, 0.0745 ],
+ 'sandy_brown': [ 0.9569, 0.6431, 0.3765 ],
+ 'tan': [ 0.8235, 0.7059, 0.5490 ],
+ 'van_dyke_brown': [ 0.3700, 0.1500, 0.0200 ],
+
+ #Oranges
+ 'cadmium_orange': [ 1.0000, 0.3800, 0.0100 ],
+ 'cadmium_red_light': [ 1.0000, 0.0100, 0.0500 ],
+ 'carrot': [ 0.9300, 0.5700, 0.1300 ],
+ 'dark_orange': [ 1.0000, 0.5490, 0.0000 ],
+ 'mars_orange': [ 0.5900, 0.2700, 0.0800 ],
+ 'mars_yellow': [ 0.8900, 0.4400, 0.1000 ],
+ 'orange': [ 1.0000, 0.5000, 0.0000 ],
+ 'orange_red': [ 1.0000, 0.2706, 0.0000 ],
+ 'yellow_ochre': [ 0.8900, 0.5100, 0.0900 ],
+
+ #Yellows
+ 'aureoline_yellow': [ 1.0000, 0.6600, 0.1400 ],
+ 'banana': [ 0.8900, 0.8100, 0.3400 ],
+ 'cadmium_lemon': [ 1.0000, 0.8900, 0.0100 ],
+ 'cadmium_yellow': [ 1.0000, 0.6000, 0.0700 ],
+ 'cadmium_yellow_light': [ 1.0000, 0.6900, 0.0600 ],
+ 'gold': [ 1.0000, 0.8431, 0.0000 ],
+ 'goldenrod': [ 0.8549, 0.6471, 0.1255 ],
+ 'goldenrod_medium': [0.8549, 0.6971, 0.2255],
+ 'goldenrod_dark': [ 0.7216, 0.5255, 0.0431 ],
+ 'goldenrod_light': [ 0.9804, 0.9804, 0.8235 ],
+ 'goldenrod_pale': [ 0.9333, 0.9098, 0.6667 ],
+ 'light_goldenrod': [ 0.9333, 0.8667, 0.5098 ],
+ 'melon': [ 0.8900, 0.6600, 0.4100 ],
+ 'naples_yellow_deep': [ 1.0000, 0.6600, 0.0700 ],
+ 'yellow': [ 1.0000, 1.0000, 0.0000 ],
+ 'yellow_light': [ 1.0000, 1.0000, 0.8784 ],
+
+ #Greens
+ 'chartreuse': [ 0.4980, 1.0000, 0.0000 ],
+ 'chrome_oxide_green': [ 0.4000, 0.5000, 0.0800 ],
+ 'cinnabar_green': [ 0.3800, 0.7000, 0.1600 ],
+ 'cobalt_green': [ 0.2400, 0.5700, 0.2500 ],
+ 'emerald_green': [ 0.0000, 0.7900, 0.3400 ],
+ 'forest_green': [ 0.1333, 0.5451, 0.1333 ],
+ 'green': [ 0.0000, 1.0000, 0.0000 ],
+ 'green_dark': [ 0.0000, 0.3922, 0.0000 ],
+ 'green_pale': [ 0.5961, 0.9843, 0.5961 ],
+ 'green_yellow': [ 0.6784, 1.0000, 0.1843 ],
+ 'lawn_green': [ 0.4863, 0.9882, 0.0000 ],
+ 'lime_green': [ 0.1961, 0.8039, 0.1961 ],
+ 'mint': [ 0.7400, 0.9900, 0.7900 ],
+ 'olive': [ 0.2300, 0.3700, 0.1700 ],
+ 'olive_drab': [ 0.4196, 0.5569, 0.1373 ],
+ 'olive_green_dark': [ 0.3333, 0.4196, 0.1843 ],
+ 'permanent_green': [ 0.0400, 0.7900, 0.1700 ],
+ 'sap_green': [ 0.1900, 0.5000, 0.0800 ],
+ 'sea_green': [ 0.1804, 0.5451, 0.3412 ],
+ 'sea_green_dark': [ 0.5608, 0.7373, 0.5608 ],
+ 'sea_green_medium': [ 0.2353, 0.7020, 0.4431 ],
+ 'sea_green_light': [ 0.1255, 0.6980, 0.6667 ],
+ 'spring_green': [ 0.0000, 1.0000, 0.4980 ],
+ 'spring_green_medium': [ 0.0000, 0.9804, 0.6039 ],
+ 'terre_verte': [ 0.2200, 0.3700, 0.0600 ],
+ 'viridian_light': [ 0.4300, 1.0000, 0.4400 ],
+ 'yellow_green': [ 0.6039, 0.8039, 0.1961 ],
+
+ #Cyans
+ 'aquamarine': [ 0.4980, 1.0000, 0.8314 ],
+ 'aquamarine_medium': [ 0.4000, 0.8039, 0.6667 ],
+ 'cyan': [ 0.0000, 1.0000, 1.0000 ],
+ 'cyan_white': [ 0.8784, 1.0000, 1.0000 ],
+ 'turquoise': [ 0.2510, 0.8784, 0.8157 ],
+ 'turquoise_dark': [ 0.0000, 0.8078, 0.8196 ],
+ 'turquoise_medium': [ 0.2824, 0.8196, 0.8000 ],
+ 'turquoise_pale': [ 0.6863, 0.9333, 0.9333 ],
+
+ #Blues
+ 'alice_blue': [ 0.9412, 0.9725, 1.0000 ],
+ 'blue': [ 0.0000, 0.0000, 1.0000 ],
+ 'blue_light': [ 0.6784, 0.8471, 0.9020 ],
+ 'blue_medium': [ 0.0000, 0.0000, 0.8039 ],
+ 'cadet': [ 0.3725, 0.6196, 0.6275 ],
+ 'cobalt': [ 0.2400, 0.3500, 0.6700 ],
+ 'cornflower': [ 0.3922, 0.5843, 0.9294 ],
+ 'desatcornflower': [ 0.5138, 0.6098, 0.7835 ],
+ 'cerulean': [ 0.0200, 0.7200, 0.8000 ],
+ 'dodger_blue': [ 0.1176, 0.5647, 1.0000 ],
+ 'indigo': [ 0.0300, 0.1800, 0.3300 ],
+ 'manganese_blue': [ 0.0100, 0.6600, 0.6200 ],
+ 'midnight_blue': [ 0.0980, 0.0980, 0.4392 ],
+ 'navy': [ 0.0000, 0.0000, 0.5020 ],
+ 'peacock': [ 0.2000, 0.6300, 0.7900 ],
+ 'powder_blue': [ 0.6902, 0.8784, 0.9020 ],
+ 'royal_blue': [ 0.2549, 0.4118, 0.8824 ],
+ 'slate_blue': [ 0.4157, 0.3529, 0.8039 ],
+ 'slate_blue_dark': [ 0.2824, 0.2392, 0.5451 ],
+ 'slate_blue_light': [ 0.5176, 0.4392, 1.0000 ],
+ 'slate_blue_medium': [ 0.4824, 0.4078, 0.9333 ],
+ 'sky_blue': [ 0.5294, 0.8078, 0.9216 ],
+ 'sky_blue_deep': [ 0.0000, 0.7490, 1.0000 ],
+ 'sky_blue_light': [ 0.5294, 0.8078, 0.9804 ],
+ 'steel_blue': [ 0.2745, 0.5098, 0.7059 ],
+ 'steel_blue_light': [ 0.6902, 0.7686, 0.8706 ],
+ 'turquoise_blue': [ 0.0000, 0.7800, 0.5500 ],
+ 'ultramarine': [ 0.0700, 0.0400, 0.5600 ],
+
+ #Magentas
+ 'blue_violet': [ 0.5412, 0.1686, 0.8863 ],
+ 'cobalt_violet_deep': [ 0.5700, 0.1300, 0.6200 ],
+ 'magenta': [ 1.0000, 0.0000, 1.0000 ],
+ 'orchid': [ 0.8549, 0.4392, 0.8392 ],
+ 'orchid_dark': [ 0.6000, 0.1961, 0.8000 ],
+ 'orchid_medium': [ 0.7294, 0.3333, 0.8275 ],
+ 'permanent_red_violet': [ 0.8600, 0.1500, 0.2700 ],
+ 'plum': [ 0.8667, 0.6275, 0.8667 ],
+ 'purple': [ 0.6275, 0.1255, 0.9412 ],
+ 'purple_medium': [ 0.5765, 0.4392, 0.8588 ],
+ 'ultramarine_violet': [ 0.3600, 0.1400, 0.4300 ],
+ 'violet': [ 0.5600, 0.3700, 0.6000 ],
+ 'violet_dark': [ 0.5804, 0.0000, 0.8275 ],
+ 'violet_red': [ 0.8157, 0.1255, 0.5647 ],
+ 'violet_red_medium': [ 0.7804, 0.0824, 0.5216 ],
+ 'violet_red_pale': [ 0.8588, 0.4392, 0.5765 ] }
+ @staticmethod
+ def get(name):
+ """ get(str) -> Color
+ This is a static method returning a color with the
+ given name or black if name not found. Alpha channel is also
+ included
+
+ """
+ if name in ColorByName.colors:
+ return ColorByName.colors[name] + [1.0]
+ else:
+ return [0.0, 0.0, 0.0, 1.0]
+
+ @staticmethod
+ def get_int(name):
+ """ get_int(str) -> Color in int range
+ Similar to get() but color ranges are from 0 to 255
+
+ """
+ if name in ColorByName.colors:
+ return [int(ColorByName.colors[name][0]*255),
+ int(ColorByName.colors[name][1]*255),
+ int(ColorByName.colors[name][2]*255),
+ 255]
+ else:
+ return [0, 0, 0, 255]
+
+ @staticmethod
+ def get_no_alpha(name):
+ """ get_no_alpha(str) -> Color
+ This is a static method returning a color with the given name
+ or black if name not found. Alpha channel is not included
+
+ """
+ if name in ColorByName.colors:
+ return ColorByName.colors[name]+[] # to make copy
+ else:
+ return [0.0, 0.0, 0.0]
+
+ @staticmethod
+ def get_no_alpha_int(name):
+ """ get_no_alpha_int(str) -> Color in int range
+ Similar to get_no_alpha() but color ranges are from 0 to 255
+
+ """
+ if name in ColorByName.colors:
+ return [int(ColorByName.colors[name][0]*255),
+ int(ColorByName.colors[name][1]*255),
+ int(ColorByName.colors[name][2]*255)]
+ else:
+ return [0, 0, 0]
+
+class ColorManipulator(object):
+ """
+ ColorManipulator is a class containing color-manipulation routines
+
+ """
+ @staticmethod
+ def multiply(color, ratio):
+ """ multiply(color: list, ratio: float) -> Color
+ This is a static method returning a color that has its RGB to
+ be only a ratio of color
+
+ """
+ result = []
+ for i in xrange(len(color)):
+ if i<3:
+ result.append(color[i]*ratio)
+ else:
+ return result + color[3:]
+ return color
+
+################################################################################
+
+def rgb2hsv(rgb):
+ """Converts RGB to HSV.
+
+ Note that H may be None when S is 0 (for grey colors).
+ """
+ r, g, b = rgb
+ minimum = min(r, g, b)
+ maximum = max(r, g, b)
+
+ v = maximum
+
+ delta = maximum - minimum
+
+ if delta != 0:
+ s = delta / maximum
+ else:
+ # h is undefined
+ s = 0
+ h = None
+ return (h, s, v)
+
+ if r == maximum:
+ h = (g - b) / delta # between yellow & magenta
+ elif g == maximum:
+ h = 2 + (b - r) / delta # between cyan & yellow
+ else:
+ h = 4 + (r - g) / delta # between magenta & cyan
+
+ h *= 60 # degrees
+
+ if h < 0:
+ h += 360
+
+ return (h, s, v)
+
+
+def hsv2rgb(hsv):
+ """Converts HSV to RGB.
+
+ Accepts H=None when S=0.
+ """
+ h, s, v = hsv
+
+ if s == 0:
+ return (v, v, v)
+
+ h /= 60
+ i = int(h)
+ f = h - i # factorial part
+ p = v * (1 - s)
+ q = v * (1 - s * f)
+ t = v * (1 - s * (1 - f))
+
+ if i == 0:
+ return (v, t, p)
+ elif i == 1:
+ return (q, v, p)
+ elif i == 2:
+ return (p, v, t)
+ elif i == 3:
+ return (p, q, v)
+ elif i == 4:
+ return (t, p, v)
+ else: # i == 5
+ return (v, p, q)
+
+################################################################################
+
+import unittest
+
+class TestColorByName(unittest.TestCase):
+ """
+ A few simple tests to make sure ColorByName is working as expected
+
+ """
+ def test_alpha_channel(self):
+ self.assertEquals(ColorByName.get('blue'),
+ [0.0, 0.0, 1.0 , 1.0])
+ self.assertEquals(ColorByName.get_no_alpha('red'),
+ [1.0, 0.0, 0.0])
+ self.assertEquals(ColorByName.get('not exist'),
+ [0.0, 0.0, 0.0, 1.0]),
+ self.assertEquals(ColorByName.get_no_alpha('another not exist'),
+ [0.0, 0.0, 0.0]),
+
+
+class TestColorConversion(unittest.TestCase):
+ colors = [(0.0, 0.0, 0.0), (1.0, 0.0, 0.0), (1.0, 0.8, 0.3),
+ (0.9, 0.0, 0.6), (0.4, 0.4, 0.4), (1.0, 1.0, 1.0)]
+
+ def test_hsv_conversions(self):
+ for color in self.colors:
+ res = hsv2rgb(rgb2hsv(color))
+ for i in xrange(3):
+ self.assertAlmostEqual(color[i], res[i])
+
+ def test_hsv_with_qt(self):
+ try:
+ from PyQt4 import QtGui
+ except ImportError:
+ self.skipTest("QtGui not available")
+ for color in self.colors:
+ our_hsv = rgb2hsv(color)
+ qcolor = QtGui.QColor(*[int(color[i]*255) for i in xrange(3)])
+ qt_hsv = [qcolor.hueF(), qcolor.saturationF(), qcolor.valueF()]
+ if qt_hsv[0] == -1.0:
+ qt_hsv[0] = None
+ else:
+ self.assertAlmostEqual(our_hsv[0], qt_hsv[0] * 360.0,
+ delta=0.2)
+ self.assertAlmostEqual(our_hsv[1], qt_hsv[1], delta=0.005)
+ self.assertAlmostEqual(our_hsv[2], qt_hsv[2], delta=0.005)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/utils/enum.py b/vistrails/core/utils/enum.py
new file mode 100644
index 0000000..3ab79b0
--- /dev/null
+++ b/vistrails/core/utils/enum.py
@@ -0,0 +1,142 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""enum helps create enumeration classes.
+
+"""
+from itertools import izip
+
+def enum(className, enumValues, doc = None):
+ """enum(className: str, enumValues: [str], doc = None) -> class.
+ Creates a new enumeration class. For example:
+
+ >>> import enum
+ >>> Colors = enum.enum('Colors',
+ ['Red', 'Green', 'Blue'],
+ "Enumeration of primary colors")
+
+ will create a class that can be used as follows:
+
+ >>> x = Colors.Red
+ >>> y = Colors.Blue
+ >>> x == y
+ False
+ >>> z = Colors.REd
+ Traceback (most recent call last):
+ File "<stdin>", line 1, in ?
+ AttributeError: type object 'Colors' has no attribute 'REd'
+ >>> z = Colors.Red
+ >>> z == x
+ True
+ >>> x.__doc__
+ 'Enumeration of primary colors'
+
+ """
+ def __init__(self, v):
+ self.__v = v
+
+ def str(v):
+ return the_enum.st[v]
+
+ def __str__(self):
+ return the_enum.str(self.__v)
+
+ def __repr__(self):
+ return className + "." + the_enum.str(self.__v)
+
+ def __eq__(self, other):
+ try:
+ return (self.__v == other.__v and
+ self.__className == other.__className)
+ except AttributeError:
+ return False
+
+ def __ne__(self, other):
+ return not (self == other)
+
+ def from_str(v):
+ return the_enum(the_enum.st.index(v))
+
+ the_enum = type(className, (object, ),
+ {'__init__': __init__,
+ 'str': staticmethod(str),
+ 'from_str': staticmethod(from_str),
+ '__str__': __str__,
+ '__repr__': __repr__,
+ 'st': enumValues,
+ '__className': className,
+ '__eq__': __eq__,
+ '__ne__': __ne__,
+ '__doc__': doc,
+ '__hash__': lambda self: self.__v})
+ for (v, x) in izip(enumValues, xrange(len(enumValues))):
+ setattr(the_enum, v, the_enum(x))
+ return the_enum
+
+################################################################################
+
+import unittest
+
+class TestEnum(unittest.TestCase):
+
+ def test1(self):
+ e1 = enum('e1', ['v1', 'v2', 'v3'])
+ self.assertEquals(e1.v1, e1.v1)
+ self.assertEquals(e1.v2, e1.v2)
+ self.assertEquals(e1.v3, e1.v3)
+ self.assertNotEquals(e1.v1, e1.v2)
+ self.assertNotEquals(e1.v1, e1.v3)
+ self.assertNotEquals(e1.v2, e1.v3)
+ self.assertNotEquals(e1.v2, e1.v1)
+ self.assertNotEquals(e1.v3, e1.v1)
+ self.assertNotEquals(e1.v3, e1.v2)
+
+ def test2(self):
+ e1 = enum('e1', ['v1', 'v2', 'v3'])
+ e2 = enum('e1', ['v1', 'v2', 'v3'])
+ self.assertEquals(e1.v1, e2.v1)
+
+ def test3(self):
+ e1 = enum('e1', ['v1', 'v2', 'v3'])
+ self.assertNotEquals(e1.v1, 5)
+
+ def test4(self):
+ e2 = enum('e1', ['v1', 'v2', 'v3'])
+ x = e2.v2
+ import copy
+ y = copy.copy(x)
+ self.assertEquals(x, y)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/utils/expression.py b/vistrails/core/utils/expression.py
new file mode 100644
index 0000000..98b9bb4
--- /dev/null
+++ b/vistrails/core/utils/expression.py
@@ -0,0 +1,82 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" Helper functions for parsing and evaluating expressions """
+
+################################################################################
+
+def evaluate_expressions(expressions):
+ """ evaluate_expressions(expressions: str) -> int/float/string
+ Evaluate the contents of the line edit inside each '$' pair
+
+ """
+
+ # FIXME: eval should pretty much never be used
+ (base, exps) = parse_expression(str(expressions))
+ for e in exps:
+ try:
+ base = base[:e[0]] + unicode(eval(e[1],None,None)) + base[e[0]:]
+ except:
+ base = base[:e[0]] + '$' + e[1] + '$' + base[e[0]:]
+ return base
+
+def parse_expression(expression):
+ """ parse_expression(expression: str) -> output (see below)
+ Parse the mixed expression string into expressions and string
+ constants
+
+ Keyword arguments:
+ output - (simplified string, [(pos:exp),(pos:exp),...]
+ simplified string: the string without any '$exp$'. All
+ $$ will be replace by a single $.
+ (pos:exp) - the expression to be computed and where it should be
+ inserted back to the simplified string, starting from
+ the end of the string.
+
+ """
+ import re
+ output = expression
+ result = []
+ p = re.compile(r'\$[^$]+\$')
+ e = p.finditer(output)
+ if e:
+ offset = 0
+ for s in e:
+ exp = s.group()
+ result.append((s.span()[0]-offset, exp[1:len(exp)-1]))
+ offset += s.span()[1]-s.span()[0]
+ result.reverse()
+ output = p.sub('', output)
+ output.replace('$$','$')
+ return (output, result)
diff --git a/vistrails/core/utils/gcutils.py b/vistrails/core/utils/gcutils.py
new file mode 100644
index 0000000..172130c
--- /dev/null
+++ b/vistrails/core/utils/gcutils.py
@@ -0,0 +1,73 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Utilities for debugging garbage collection, leaked memory, etc."""
+
+import gc
+
+def get_objects_by_typename():
+ gc.collect()
+ x = {}
+ for obj in gc.get_objects():
+ t = type(obj).__name__
+ if t in x:
+ x[t].append(obj)
+ else:
+ x[t] = [obj]
+ return x
+
+def get_objects_by_livecount(obj_dict=None):
+ if not obj_dict:
+ obj_dict = get_objects_by_typename()
+ else:
+ gc.collect()
+ lst = [(len(val), k) for (k, val) in obj_dict.iteritems()]
+ lst.sort()
+ return lst
+
+def get_referrers(obj, path=None):
+ if not path:
+ path = []
+ referrers = gc.get_referrers(obj)
+ for edge in path:
+ referrers = gc.get_referrers(referrers[edge])
+ return referrers
+
+def count_object_by_name(name):
+ objects = get_objects_by_livecount()
+ for (count, oName) in objects:
+ if oName==name:
+ return count
+ return 0
diff --git a/vistrails/core/utils/lockmethod.py b/vistrails/core/utils/lockmethod.py
new file mode 100644
index 0000000..9006415
--- /dev/null
+++ b/vistrails/core/utils/lockmethod.py
@@ -0,0 +1,99 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+def lock_method(lock):
+
+ def decorator(method):
+ def decorated(self, *args, **kwargs):
+ try:
+ lock.acquire()
+ result = method(self, *args, **kwargs)
+ finally:
+ lock.release()
+ return result
+ decorated.func_doc = method.__doc__
+ return decorated
+
+ return decorator
+
+##############################################################################
+
+import unittest
+import threading
+
+class TestLockMethod(unittest.TestCase):
+
+ lock = threading.Lock()
+ @lock_method(lock)
+ def foo(self):
+ self.assertEquals(self.lock.locked(), True)
+
+ @lock_method(lock)
+ def foo_throws(self):
+ raise Exception()
+
+ @lock_method(lock)
+ def foo_finally(self):
+ try:
+ raise Exception
+ return False
+ finally:
+ return True
+
+ @lock_method(lock)
+ def foo_docstring(self):
+ """FOO"""
+ pass
+
+ def test_common(self):
+ self.assertEquals(self.lock.locked(), False)
+ self.foo()
+ self.assertEquals(self.lock.locked(), False)
+
+ def test_throws(self):
+ self.assertEquals(self.lock.locked(), False)
+ self.assertRaises(Exception, self.foo_throws)
+ self.assertEquals(self.lock.locked(), False)
+
+ def test_finally(self):
+ self.assertEquals(self.lock.locked(), False)
+ self.assertEquals(self.foo_finally(), True)
+ self.assertEquals(self.lock.locked(), False)
+
+ def test_docstring(self):
+ self.assertEquals(self.foo_docstring.__doc__, "FOO")
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/utils/timemethod.py b/vistrails/core/utils/timemethod.py
new file mode 100644
index 0000000..f43b8d4
--- /dev/null
+++ b/vistrails/core/utils/timemethod.py
@@ -0,0 +1,57 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Defines a time decorator that times function calls."""
+
+import time
+
+def time_method(method):
+ def decorated(self, *args, **kwargs):
+ t = time.time()
+ try:
+ return method(self, *args, **kwargs)
+ finally:
+ print time.time() - t
+ return decorated
+
+def time_call(callable_):
+ def decorated(*args, **kwargs):
+ t = time.time()
+ try:
+ return callable_(*args, **kwargs)
+ finally:
+ print time.time() - t
+ return decorated
+
+##############################################################################
diff --git a/vistrails/core/utils/tracemethod.py b/vistrails/core/utils/tracemethod.py
new file mode 100644
index 0000000..6054dbd
--- /dev/null
+++ b/vistrails/core/utils/tracemethod.py
@@ -0,0 +1,176 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Defines a trace decorator that traces function calls. This is not currently
+thread-safe. It won't crash, but the bump() printouts might not be correct.
+
+Also defines report_stack, a decorator that dumps the traceback whenever
+a method gets called."""
+import sys
+import traceback
+from vistrails.core.data_structures.stack import Stack
+
+import unittest
+import tempfile
+import os
+
+_output_file = sys.stderr
+
+__current_method_name = Stack()
+
+def _indent():
+ _output_file.write(' ' * (len(__current_method_name)-1))
+
+def trace_method_options(method,
+ with_args=False,
+ with_kwargs=False,
+ with_return=False):
+ """trace_method_options is a method decorator that traces
+ entry-exit of functions. It also prints args, kwargs and return
+ values if optional parameters with_args, with_kwargs and
+ with_return are set to True."""
+ def decorated(self, *args, **kwargs):
+ __current_method_name.push([method.__name__, 0])
+ try:
+ _indent()
+ _output_file.write(method.__name__ + ".enter")
+ if with_args:
+ _output_file.write(" (args: ")
+ _output_file.write(str([str(arg) for arg in args]))
+ _output_file.write(")")
+ if with_kwargs:
+ _output_file.write(" (kwargs: ")
+ kwarglist = [(k, str(v)) for (k,v) in kwargs.iteritems()]
+ kwarglist.sort()
+ _output_file.write(str(kwarglist))
+ _output_file.write(")")
+ _output_file.write('\n')
+ result = method(self, *args, **kwargs)
+ _indent()
+ _output_file.write(method.__name__ + ".exit")
+ if with_return:
+ _output_file.write(" (return: %s)" % str(result))
+ _output_file.write('\n')
+ finally:
+ __current_method_name.pop()
+ return result
+ return decorated
+
+def trace_method(method):
+ return trace_method_options(method)
+
+def trace_method_args(method):
+ return trace_method_options(method, with_args=True)
+
+def bump_trace():
+ __current_method_name.top()[1] += 1
+ _indent()
+ _output_file.write('%s.%s\n' % tuple(__current_method_name.top()))
+
+def report_stack(method):
+ def decorated(self, *args, **kwargs):
+ print "-" * 78
+ try:
+ print "Method: " + method.im_class.__name__ + '.' + method.__name__
+ except:
+ pass
+ try:
+ print "Function: " + method.func_name
+ except:
+ pass
+ traceback.print_stack()
+ print "-" * 78
+ return method(self, *args, **kwargs)
+ return decorated
+
+###############################################################################
+
+
+ at trace_method
+def test_fun(p1):
+ return p1 + 5
+
+ at trace_method
+def test_fun_2(p1):
+ bump_trace()
+ result = test_fun(p1) + 3
+ bump_trace()
+ return result
+
+class TestTraceMethod(unittest.TestCase):
+
+ def test_trace_1(self):
+ global _output_file
+ (fd, name) = tempfile.mkstemp()
+ os.close(fd)
+ try:
+ _output_file = open(name, 'w')
+
+ x = test_fun(10)
+ self.assertEquals(x, 15)
+
+ _output_file.close()
+ _output_file = sys.stderr
+
+ output = "".join(open(name, 'r').readlines())
+ self.assertEquals(output,
+ 'test_fun.enter\n' +
+ 'test_fun.exit\n')
+ finally:
+ os.unlink(name)
+
+ def test_trace_2(self):
+ global _output_file
+ (fd, name) = tempfile.mkstemp()
+ os.close(fd)
+ _output_file = open(name, 'w')
+
+ x = test_fun_2(10)
+ self.assertEquals(x, 18)
+
+ _output_file.close()
+ _output_file = sys.stderr
+
+ output = "".join(open(name, 'r').readlines())
+ self.assertEquals(output,
+ 'test_fun_2.enter\n' +
+ 'test_fun_2.1\n' +
+ ' test_fun.enter\n' +
+ ' test_fun.exit\n' +
+ 'test_fun_2.2\n' +
+ 'test_fun_2.exit\n')
+ os.unlink(name)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/utils/uxml.py b/vistrails/core/utils/uxml.py
new file mode 100644
index 0000000..3d93a38
--- /dev/null
+++ b/vistrails/core/utils/uxml.py
@@ -0,0 +1,246 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.dom import minidom
+import xml.parsers.expat
+import __builtin__
+
+def eval_xml_value(node):
+ """eval_xml_value(node) -> value
+
+ evaluates an xml node as the following examples:
+
+ <str value='foo'/> -> 'foo'
+ <int value='3'/> -> 3
+ <float value='3.141592'> -> 3.141592
+ <bool value='False'> -> False
+ """
+
+ key_name = node.nodeName
+ type_ = getattr(__builtin__, key_name)
+ str_value = str(node.attributes['value'].value)
+
+ # Tricky case bool('False') == True
+ if type_ == bool:
+ if str_value == 'True':
+ return True
+ elif str_value == 'False':
+ return False
+ else:
+ raise ValueError("eval_xml_value: Bogus bool value '%s'" % str_value)
+ return type_(str_value)
+
+def quote_xml_value(dom, value):
+ """quote_xml_value(dom, value) -> value
+
+ quotes a value as an xml node so that
+ eval_xml_value(quote_xml_value(dom, value)) == value
+
+ <str value='foo'/> <- 'foo'
+ <int value='3'/> <- 3
+ <float value='3.141592'> <- 3.141592
+ <bool value='False'> <- False
+ """
+
+ el = dom.createElement(type(value).__name__)
+ el.setAttribute('value', str(value))
+ return el
+
+def named_elements(element, elname):
+ """named_elements(element, elname) -> Node
+ Helper function that iterates over the element child Nodes searching
+ for node with name elname.
+
+ """
+ for node in element.childNodes:
+ if node.nodeName == elname:
+ yield node
+
+def enter_named_element(element, elname):
+ """enter_named_element(element, elname) -> Node
+ Returns first child of element with name elname
+
+ """
+ for node in named_elements(element, elname):
+ return node
+ return None
+
+def elements_filter(element, element_predicate):
+ """elements_filter(element, element_predicate) -> Node iterator
+ Helper function that iterates over the element child Nodes searching
+ for nodes that pass element_predicate, that is, node for which
+
+ element_predicate(node) == True
+
+ """
+ for node in element.childNodes:
+ if element_predicate(node):
+ yield node
+
+class XMLWrapper(object):
+ """Helper to parse a general XML file. It provides functions to open and
+ close files.
+ It must be subclassed to parse specifi files. """
+
+ class XMLParseError(Exception):
+
+
+ def __init__(self, line, char, code):
+ self._line = line
+ self._char = char
+ self._code = code
+
+ def __str__(self):
+ return ("XML Parse error at line %s, col %s: %s" %
+ (self._line,
+ self._char,
+ xml.parsers.expat.ErrorString(self._code)))
+
+ def open_file(self, filename):
+ """open_file(filename: str) -> None
+ Parses an XML file.
+
+ """
+ self.filename = filename
+ try:
+ self.dom = minidom.parse(filename)
+ except xml.parsers.expat.ExpatError, e:
+ raise self.XMLParseError(e.lineno, e.offset, e.code)
+
+ def create_document_from_string(self, text):
+ """parse_string(text:str) -> dom
+ Parses an xml string and returns the DOM object
+
+ """
+ try:
+ dom = minidom.parseString(text)
+ except xml.parsers.expat.ExpatError, e:
+ raise self.XMLParseError(e.lineno, e.offset, e.code)
+ return dom
+
+ def close_file(self):
+ """close_file() -> None
+ Removes the association with the XML file loaded by open_file
+ method.
+
+ """
+ if self.dom:
+ self.dom.unlink()
+ self.filename = None
+ self.dom = None
+
+ def create_document(self, nodename):
+ """create_document(nodename: str) -> xml element
+ Creates a documentElement
+
+ """
+ impl = minidom.getDOMImplementation()
+ dom = impl.createDocument(None, nodename, None)
+ return dom
+
+ def write_document(self, root, filename):
+ """write_document(root:xml element, filename: str) -> None
+ Save as an XML file
+
+ """
+ output_file = open(filename,'w')
+ root.writexml(output_file, " ", " ", '\n')
+ output_file.close()
+
+ def __str__(self):
+ """ __str__() -> str
+ Returns the XML that self.dom represents as a string
+
+ """
+ return self.dom.toprettyxml()
+
+################################################################################
+# Testing
+
+import unittest
+
+class TestXmlUtils(unittest.TestCase):
+ def test_named_elements(self):
+ """ Exercises searching for elements """
+ xmlStr = """<root>
+ <child>
+ <grandchild></grandchild>
+ <grandchild></grandchild>
+ </child>
+ <child></child>
+ </root>"""
+ dom = minidom.parseString(xmlStr)
+ root = dom.documentElement
+ childcount = 0
+ for node in named_elements(root,'child'):
+ childcount += 1
+ self.assertEquals(childcount,2)
+
+ grandchildcount = 0
+ for node in named_elements(root,'grandchild'):
+ grandchildcount += 1
+ self.assertEquals(grandchildcount,0)
+
+ def test_eval_quote(self):
+ xmlStr = """<root>
+ <child>
+ <grandchild></grandchild>
+ <grandchild></grandchild>
+ </child>
+ <child></child>
+ </root>"""
+ dom = minidom.parseString(xmlStr)
+ def do_it_1(v):
+ q = quote_xml_value(dom, v)
+ v2 = eval_xml_value(q)
+ self.assertEquals(v, v2)
+ def do_it_2(q):
+ q = minidom.parseString(q).documentElement
+ v = eval_xml_value(q)
+ self.assertEquals(q.toxml(), quote_xml_value(dom, v).toxml())
+ do_it_1(2)
+ do_it_1(3.0)
+ do_it_1(False)
+ do_it_1(True)
+ do_it_1('Foobar')
+ do_it_1('with<brackets>')
+
+ do_it_2('<str value="Foo"/>')
+ do_it_2('<bool value="False"/>')
+ do_it_2('<bool value="True"/>')
+ do_it_2('<int value="3"/>')
+ do_it_2('<float value="4.0"/>')
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/vistrails/core/vistrail/__init__.py b/vistrails/core/vistrail/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/core/vistrail/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/core/vistrail/abstraction.py b/vistrails/core/vistrail/abstraction.py
new file mode 100644
index 0000000..d0faf55
--- /dev/null
+++ b/vistrails/core/vistrail/abstraction.py
@@ -0,0 +1,198 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+
+from vistrails.core.modules.module_registry import get_module_registry
+import vistrails.core.modules.sub_module
+from vistrails.core.utils import VistrailsInternalError
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.vistrail.location import Location
+from vistrails.core.vistrail.module import Module
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.db.domain import DBAbstraction
+
+import unittest
+
+class Abstraction(DBAbstraction, Module):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBAbstraction.__init__(self, *args, **kwargs)
+ if self.cache is None:
+ self.cache = 1
+ if self.id is None:
+ self.id = -1
+ if self.location is None:
+ self.location = Location(x=-1.0, y=-1.0)
+ if self.name is None:
+ self.name = ''
+ if self.package is None:
+ self.package = ''
+ if self.version is None:
+ self.version = ''
+ self.set_defaults()
+
+ def set_defaults(self, other=None):
+ Module.set_defaults(self, other)
+ self._is_latest_version = True
+ self.check_latest_version()
+ # if other is None:
+ # self._is_latest_version = True
+ # else:
+ # self._is_latest_version = other._is_latest_version
+
+ def setup_indices(self):
+ pass
+
+ def __copy__(self):
+ return Abstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Abstraction
+ cp.set_defaults(self)
+ return cp
+
+ @staticmethod
+ def convert(_abstraction):
+ if _abstraction.__class__ == Abstraction:
+ return
+ _abstraction.__class__ = Abstraction
+ if _abstraction.db_location:
+ Location.convert(_abstraction.db_location)
+ for _function in _abstraction.db_functions:
+ ModuleFunction.convert(_function)
+ for _annotation in _abstraction.db_get_annotations():
+ Annotation.convert(_annotation)
+ _abstraction.set_defaults()
+
+ ##########################################################################
+ # Properties
+
+ # We need to repeat these here because Module uses DBModule. ...
+ id = DBAbstraction.db_id
+ cache = DBAbstraction.db_cache
+ annotations = DBAbstraction.db_annotations
+ location = DBAbstraction.db_location
+ center = DBAbstraction.db_location
+ name = DBAbstraction.db_name
+ label = DBAbstraction.db_name
+ namespace = DBAbstraction.db_namespace
+ package = DBAbstraction.db_package
+ version = DBAbstraction.db_version
+ internal_version = DBAbstraction.db_internal_version
+
+ def is_abstraction(self):
+ return True
+
+ def check_latest_version(self):
+ reg = get_module_registry()
+ try:
+ desc = reg.get_descriptor_by_name(self.package, self.name,
+ self.namespace)
+ except:
+ # Should only get here if the abstraction's descriptor was
+ # removed from the registry which only happens when the
+ # abstraction should be destroyed.
+ self._is_latest_version = False
+ return
+ latest_version = desc.module.vistrail.get_latest_version()
+ self._is_latest_version = \
+ (long(latest_version) == long(self.internal_version))
+
+ def is_latest_version(self):
+ return self._is_latest_version
+
+ def _get_pipeline(self):
+ return self.module_descriptor.module.pipeline
+ pipeline = property(_get_pipeline)
+
+ def _get_vistrail(self):
+ return self.module_descriptor.module.vistrail
+ vistrail = property(_get_vistrail)
+
+ # override db-mirrored accesses in Module
+ port_specs = {}
+ port_spec_list = []
+ _input_port_specs = []
+ _output_port_specs = []
+
+ def has_portSpec_with_name(self, name):
+ return False
+ def get_portSpec_by_name(self, name):
+ return None
+ def add_port_spec(self, port_spec):
+ raise VistrailsInternalError("Cannot add port spec to abstraction")
+ def delete_port_spec(self, port_spec):
+ raise VistrailsInternalError("Cannot delete port spec from abstraction")
+
+ ##########################################################################
+
+ def get_port_spec_info(self, module):
+ return vistrails.core.modules.sub_module.get_port_spec_info(self.pipeline,
+ module)
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of an Abstraction
+ object.
+
+ """
+# rep = '<abstraction id="%s" name="%s">' + \
+# '<actions>%s</actions>' + \
+# '<tags>%s</tags>' + \
+# '</abstraction>'
+# return rep % (str(self.id), str(self.name),
+# [str(a) for a in self.action_list],
+# [str(t) for t in self.tag_list])
+ rep = '<abstraction id="%s" name="%s"/>'
+ return rep % (str(self.id), str(self.name))
+
+ def __eq__(self, other):
+ """ __eq__(other: Abstraction) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
diff --git a/vistrails/core/vistrail/action.py b/vistrails/core/vistrail/action.py
new file mode 100644
index 0000000..565e2bb
--- /dev/null
+++ b/vistrails/core/vistrail/action.py
@@ -0,0 +1,280 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from datetime import date, datetime
+from time import strptime
+
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.vistrail.operation import AddOp, ChangeOp, DeleteOp
+from vistrails.db.domain import DBAction
+from itertools import izip
+
+import unittest
+import vistrails.core
+
+class Action(DBAction):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBAction.__init__(self, *args, **kwargs)
+ if self.timestep is None:
+ self.timestep = -1
+ if self.parent is None:
+ self.parent = -1
+ if self.user is None:
+ self.user = ''
+ if self.expand is None:
+ self.expand = 0
+
+ def __copy__(self):
+ return Action.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Action
+ return cp
+
+ ##########################################################################
+ # Constants
+
+ ANNOTATION_DESCRIPTION = '__description__'
+ ANNOTATION_ANALOGY_INFO = '__analogy_info__'
+
+ ##########################################################################
+ # Properties
+
+ id = DBAction.db_id
+ timestep = DBAction.db_id
+ parent = DBAction.db_prevId
+ prevId = DBAction.db_prevId
+ session = DBAction.db_session
+ user = DBAction.db_user
+ expand = 0
+ annotations = DBAction.db_annotations
+ operations = DBAction.db_operations
+
+ def _get_date(self):
+ if self.db_date is not None:
+ return self.db_date.strftime('%d %b %Y %H:%M:%S')
+ return datetime(1900,1,1).strftime('%d %b %Y %H:%M:%S')
+
+ def _set_date(self, date):
+ if isinstance(date, datetime):
+ self.db_date = date
+ elif isinstance(date, basestring) and date.strip() != '':
+ newDate = datetime(*strptime(date, '%d %b %Y %H:%M:%S')[0:6])
+ self.db_date = newDate
+ date = property(_get_date, _set_date)
+
+ def has_annotation_with_key(self, key):
+ return self.db_has_annotation_with_key(key)
+ def get_annotation_by_key(self, key):
+ return self.db_get_annotation_by_key(key)
+ def add_annotation(self, annotation):
+ self.db_add_annotation(annotation)
+ def delete_annotation(self, annotation):
+ self.db_delete_annotation(annotation)
+
+ def _get_description(self):
+ if self.db_has_annotation_with_key(self.ANNOTATION_DESCRIPTION):
+ return \
+ self.db_get_annotation_by_key(self.ANNOTATION_DESCRIPTION).value
+ return None
+ description = property(_get_description)
+
+ def _get_analogy_info(self):
+ if self.db_has_annotation_with_key(self.ANNOTATION_ANALOGY_INFO):
+ ann = self.db_get_annotation_by_key(self.ANNOTATION_ANALOGY_INFO)
+ return ann.value
+ return None
+ analogy_info = property(_get_analogy_info)
+
+ def add_operation(self, operation):
+ self.db_operations.db_add_operation(operation)
+
+ ##########################################################################
+ # DB Conversion
+
+ @staticmethod
+ def convert(_action):
+ if _action.__class__ == Action:
+ return
+ _action.__class__ = Action
+ for _annotation in _action.annotations:
+ Annotation.convert(_annotation)
+ for _operation in _action.operations:
+ if _operation.vtType == 'add':
+ AddOp.convert(_operation)
+ elif _operation.vtType == 'change':
+ ChangeOp.convert(_operation)
+ elif _operation.vtType == 'delete':
+ DeleteOp.convert(_operation)
+ else:
+ raise TypeError("Unknown operation type '%s'" %
+ _operation.vtType)
+
+ ##########################################################################
+ # Operators
+
+ def __eq__(self, other):
+ """ __eq__(other: Module) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if len(self.annotations) != len(other.annotations):
+ return False
+ if len(self.operations) != len(other.operations):
+ return False
+ for f,g in zip(self.annotations, other.annotations):
+ if f != g:
+ return False
+ for f,g in zip(self.operations, other.operations):
+ if f != g:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+
+ def __str__(self):
+ """__str__() -> str
+ Returns a string representation of an action object.
+
+ """
+ msg = "<<type='%s' timestep='%s' parent='%s' date='%s'" + \
+ "user='%s'>>"
+ return msg % (type(self),
+ self.timestep,
+ self.parent,
+ self.date,
+ self.user)
+
+################################################################################
+# Unit tests
+
+class TestAction(unittest.TestCase):
+
+ def create_action(self, id_scope=None):
+ from vistrails.core.modules.basic_modules import identifier as basic_pkg
+ from vistrails.core.vistrail.action import Action
+ from vistrails.core.vistrail.module import Module
+ from vistrails.core.vistrail.module_function import ModuleFunction
+ from vistrails.core.vistrail.module_param import ModuleParam
+ from vistrails.core.vistrail.operation import AddOp
+ from vistrails.db.domain import IdScope
+ from datetime import datetime
+
+ if id_scope is None:
+ id_scope = IdScope()
+ param = ModuleParam(id=id_scope.getNewId(ModuleParam.vtType),
+ type='Integer',
+ val='1')
+ function = ModuleFunction(id=id_scope.getNewId(ModuleFunction.vtType),
+ name='value',
+ parameters=[param])
+ m = Module(id=id_scope.getNewId(Module.vtType),
+ name='Float',
+ package=basic_pkg,
+ functions=[function])
+
+ add_op = AddOp(id=id_scope.getNewId('operation'),
+ what='module',
+ objectId=m.id,
+ data=m)
+ action = Action(id=id_scope.getNewId(Action.vtType),
+ prevId=0,
+ date=datetime(2007,11,18),
+ operations=[add_op])
+ return action
+
+ def test_copy(self):
+ import copy
+ from vistrails.db.domain import IdScope
+
+ id_scope = IdScope()
+ a1 = self.create_action(id_scope)
+ a2 = copy.copy(a1)
+ self.assertEquals(a1, a2)
+ self.assertEquals(a1.id, a2.id)
+ a3 = a1.do_copy(True, id_scope, {})
+ self.assertEquals(a1, a3)
+ self.assertNotEquals(a1.id, a3.id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ a1 = self.create_action()
+ xml_str = vistrails.core.db.io.serialize(a1)
+ a2 = vistrails.core.db.io.unserialize(xml_str, Action)
+ self.assertEquals(a1, a2)
+ self.assertEquals(a1.id, a2.id)
+
+ def test1(self):
+ """Exercises aliasing on modules"""
+ import vistrails.core.vistrail
+ from vistrails.core.db.locator import XMLFileLocator
+ v = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/dummy.xml').load()
+ p1 = v.getPipeline('final')
+ p2 = v.getPipeline('final')
+ self.assertEquals(len(p1.modules), len(p2.modules))
+ for k in p1.modules.keys():
+ if p1.modules[k] is p2.modules[k]:
+ self.fail("didn't expect aliases in two different pipelines")
+
+ def test2(self):
+ """Exercises aliasing on points"""
+ import vistrails.core.vistrail
+ from vistrails.core.db.locator import XMLFileLocator
+ import vistrails.core.system
+ v = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/dummy.xml').load()
+ p1 = v.getPipeline('final')
+ v.getPipeline('final')
+ p2 = v.getPipeline('final')
+ m1s = p1.modules.items()
+ m2s = p2.modules.items()
+ m1s.sort()
+ m2s.sort()
+ for ((i1,m1),(i2,m2)) in izip(m1s, m2s):
+ self.assertEquals(m1.center.x, m2.center.x)
+ self.assertEquals(m1.center.y, m2.center.y)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/vistrail/action_annotation.py b/vistrails/core/vistrail/action_annotation.py
new file mode 100644
index 0000000..782c51e
--- /dev/null
+++ b/vistrails/core/vistrail/action_annotation.py
@@ -0,0 +1,144 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBActionAnnotation
+
+import unittest
+import copy
+import vistrails.core
+
+class ActionAnnotation(DBActionAnnotation):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBActionAnnotation.__init__(self, *args, **kwargs)
+ if self.id is None:
+ self.id = -1
+
+ def __copy__(self):
+ return ActionAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBActionAnnotation.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = ActionAnnotation
+ return cp
+
+ @staticmethod
+ def convert(_annotation):
+ _annotation.__class__ = ActionAnnotation
+
+ ##########################################################################
+ # Properties
+
+ id = DBActionAnnotation.db_id
+ key = DBActionAnnotation.db_key
+ value = DBActionAnnotation.db_value
+ action_id = DBActionAnnotation.db_action_id
+ date = DBActionAnnotation.db_date
+ user = DBActionAnnotation.db_user
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of an
+ ActionAnnotation object.
+
+ """
+ rep = ("<actionAnnotation id=%s action_id=%s key=%s value=%s "
+ "date=%s user=%s</annotation>")
+ return rep % (str(self.id), str(self.action_id), str(self.key),
+ str(self.value), str(self.date), str(self.user))
+
+ def __eq__(self, other):
+ """ __eq__(other: ActionAnnotation) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.key != other.key:
+ return False
+ if self.value != other.value:
+ return False
+ if self.action_id != other.action_id:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+################################################################################
+# Unit tests
+
+
+class TestActionAnnotation(unittest.TestCase):
+
+ def create_annotation(self, id_scope=None):
+ from vistrails.db.domain import IdScope
+
+ if id_scope is None:
+ id_scope = IdScope()
+ annotation = \
+ ActionAnnotation(id=id_scope.getNewId(ActionAnnotation.vtType),
+ key='akey', action_id=1L,
+ value='some value', user='test')
+ return annotation
+
+ def test_copy(self):
+ from vistrails.db.domain import IdScope
+ id_scope = IdScope()
+
+ a1 = self.create_annotation(id_scope)
+ a2 = copy.copy(a1)
+ self.assertEquals(a1, a2)
+ self.assertEquals(a1.id, a2.id)
+ a3 = a1.do_copy(True, id_scope, {})
+ self.assertEquals(a1, a3)
+ self.assertNotEquals(a1.id, a3.id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ a1 = self.create_annotation()
+ xml_str = vistrails.core.db.io.serialize(a1)
+ a2 = vistrails.core.db.io.unserialize(xml_str, ActionAnnotation)
+ self.assertEquals(a1, a2)
+ self.assertEquals(a1.id, a2.id)
+
+ def test_str(self):
+ a1 = self.create_annotation()
+ str(a1)
diff --git a/vistrails/core/vistrail/annotation.py b/vistrails/core/vistrail/annotation.py
new file mode 100644
index 0000000..6b38855
--- /dev/null
+++ b/vistrails/core/vistrail/annotation.py
@@ -0,0 +1,136 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBAnnotation
+
+import unittest
+import copy
+import vistrails.core
+
+class Annotation(DBAnnotation):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBAnnotation.__init__(self, *args, **kwargs)
+ if self.id is None:
+ self.id = -1
+
+ def __copy__(self):
+ return Annotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Annotation
+ return cp
+
+ @staticmethod
+ def convert(_annotation):
+ _annotation.__class__ = Annotation
+
+ ##########################################################################
+ # Properties
+
+ id = DBAnnotation.db_id
+ key = DBAnnotation.db_key
+ value = DBAnnotation.db_value
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of an Annotation
+ object.
+
+ """
+ rep = "<annotation id=%s key=%s value=%s</annotation>"
+ return rep % (str(self.id), str(self.key), str(self.value))
+
+ def __eq__(self, other):
+ """ __eq__(other: Annotation) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.key != other.key:
+ return False
+ if self.value != other.value:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+################################################################################
+# Unit tests
+
+
+class TestAnnotation(unittest.TestCase):
+
+ def create_annotation(self, id_scope=None):
+ from vistrails.db.domain import IdScope
+
+ if id_scope is None:
+ id_scope = IdScope()
+ annotation = Annotation(id=id_scope.getNewId(Annotation.vtType),
+ key='akey %s',
+ value='some value %s')
+ return annotation
+
+ def test_copy(self):
+ from vistrails.db.domain import IdScope
+ id_scope = IdScope()
+
+ a1 = self.create_annotation(id_scope)
+ a2 = copy.copy(a1)
+ self.assertEquals(a1, a2)
+ self.assertEquals(a1.id, a2.id)
+ a3 = a1.do_copy(True, id_scope, {})
+ self.assertEquals(a1, a3)
+ self.assertNotEquals(a1.id, a3.id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ a1 = self.create_annotation()
+ xml_str = vistrails.core.db.io.serialize(a1)
+ a2 = vistrails.core.db.io.unserialize(xml_str, Annotation)
+ self.assertEquals(a1, a2)
+ self.assertEquals(a1.id, a2.id)
+
+ def test_str(self):
+ a1 = self.create_annotation()
+ str(a1)
diff --git a/vistrails/core/vistrail/connection.py b/vistrails/core/vistrail/connection.py
new file mode 100644
index 0000000..8d93bf2
--- /dev/null
+++ b/vistrails/core/vistrail/connection.py
@@ -0,0 +1,408 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.configuration import get_vistrails_configuration
+""" This python module defines Connection class.
+"""
+import copy
+from vistrails.db.domain import DBConnection
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.modules.vistrails_module import ModuleConnector
+from vistrails.core.vistrail.port import PortEndPoint, Port
+
+import unittest
+from vistrails.db.domain import IdScope
+
+################################################################################
+
+Variant_desc = None
+InputPort_desc = None
+
+def moduleConnection(conn):
+ """moduleConnection(conn)-> function
+ Returns a function to build a module connection
+
+ """
+ def theFunction(src, dst):
+ global Variant_desc, InputPort_desc
+ if Variant_desc is None:
+ reg = get_module_registry()
+ Variant_desc = reg.get_descriptor_by_name(
+ 'org.vistrails.vistrails.basic', 'Variant')
+ InputPort_desc = reg.get_descriptor_by_name(
+ 'org.vistrails.vistrails.basic', 'InputPort')
+
+ iport = conn.destination.name
+ oport = conn.source.name
+ src.enableOutputPort(oport)
+ conf = get_vistrails_configuration()
+ error_on_others = getattr(conf, 'errorOnConnectionTypeerror')
+ error_on_variant = (error_on_others or
+ getattr(conf, 'errorOnVariantTypeerror'))
+ errors = [error_on_others, error_on_variant]
+ if isinstance(src, InputPort_desc.module):
+ typecheck = [False]
+ else:
+ typecheck = [errors[desc is Variant_desc]
+ for desc in conn.source.spec.descriptors()]
+ dst.set_input_port(
+ iport,
+ ModuleConnector(src, oport, conn.destination.spec, typecheck))
+ return theFunction
+
+################################################################################
+
+class Connection(DBConnection):
+ """ A Connection is a connection between two modules.
+ Right now there's only Module connections.
+
+ """
+
+ ##########################################################################
+ # Constructors and copy
+
+ @staticmethod
+ def from_port_specs(source, dest):
+ """from_port_specs(source: PortSpec, dest: PortSpec) -> Connection
+ Static method that creates a Connection given source and
+ destination ports.
+
+ """
+ conn = Connection()
+ conn.source = copy.copy(source)
+ conn.destination = copy.copy(dest)
+ return conn
+
+ @staticmethod
+ def fromID(id):
+ """fromTypeID(id: int) -> Connection
+ Static method that creates a Connection given an id.
+
+ """
+ conn = Connection()
+ conn.id = id
+ conn.source.endPoint = PortEndPoint.Source
+ conn.destination.endPoint = PortEndPoint.Destination
+ return conn
+
+ def __init__(self, *args, **kwargs):
+ """__init__() -> Connection
+ Initializes source and destination ports.
+
+ """
+ DBConnection.__init__(self, *args, **kwargs)
+ if self.id is None:
+ self.db_id = -1
+ if not len(self.ports) > 0:
+ self.source = Port(type='source')
+ self.destination = Port(type='destination')
+# self.source.endPoint = PortEndPoint.Source
+# self.destination.endPoint = PortEndPoint.Destination
+ self.makeConnection = moduleConnection(self)
+
+ def __copy__(self):
+ """__copy__() -> Connection - Returns a clone of self.
+
+ """
+ return Connection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Connection
+ cp.makeConnection = moduleConnection(cp)
+ for port in cp.ports:
+ Port.convert(port)
+ return cp
+
+ ##########################################################################
+
+ @staticmethod
+ def convert(_connection):
+# print "ports: %s" % _Connection._get_ports(_connection)
+ if _connection.__class__ == Connection:
+ return
+ _connection.__class__ = Connection
+
+ for port in _connection.ports:
+ Port.convert(port)
+
+# _connection.sourceInfo = \
+# (_connection.source.moduleName, _connection.source.sig)
+# _connection.destinationInfo = \
+# (_connection.destination.moduleName, _connection.destination.sig)
+# # print _connection.sourceInfo
+# # print _connection.destinationInfo
+# portFromRepresentation = registry.portFromRepresentation
+# newSource = \
+# portFromRepresentation(_connection.source.moduleName,
+# _connection.source.sig,
+# PortEndPoint.Source, None, True)
+# newDestination = \
+# portFromRepresentation(_connection.destination.moduleName,
+# _connection.destination.sig,
+# PortEndPoint.Destination, None, True)
+# newSource.moduleId = _connection.source.moduleId
+# newDestination.moduleId = _connection.destination.moduleId
+# _connection.source = newSource
+# _connection.destination = newDestination
+ _connection.makeConnection = moduleConnection(_connection)
+
+
+ ##########################################################################
+ # Debugging
+
+ def show_comparison(self, other):
+ if type(other) != type(self):
+ print "Type mismatch"
+ return
+ if self.__source != other.__source:
+ print "Source mismatch"
+ self.__source.show_comparison(other.__source)
+ return
+ if self.__dest != other.__dest:
+ print "Dest mismatch"
+ self.__dest.show_comparison(other.__dest)
+ return
+ print "no difference found"
+ assert self == other
+
+ ##########################################################################
+ # Properties
+
+ id = DBConnection.db_id
+ ports = DBConnection.db_ports
+
+ def add_port(self, port):
+ self.db_add_port(port)
+
+ def _get_sourceId(self):
+ """ _get_sourceId() -> int
+ Returns the module id of source port. Do not use this function,
+ use sourceId property: c.sourceId
+
+ """
+ return self.source.moduleId
+
+ def _set_sourceId(self, id):
+ """ _set_sourceId(id : int) -> None
+ Sets this connection source id. It updates both self.__source.moduleId
+ and self.__source.id. Do not use this function, use sourceId
+ property: c.sourceId = id
+
+ """
+ self.source.moduleId = id
+ self.source.id = id
+ sourceId = property(_get_sourceId, _set_sourceId)
+
+ def _get_destinationId(self):
+ """ _get_destinationId() -> int
+ Returns the module id of dest port. Do not use this function,
+ use sourceId property: c.destinationId
+
+ """
+ return self.destination.moduleId
+
+ def _set_destinationId(self, id):
+ """ _set_destinationId(id : int) -> None
+ Sets this connection destination id. It updates self.__dest.moduleId.
+ Do not use this function, use destinationId property:
+ c.destinationId = id
+
+ """
+ self.destination.moduleId = id
+ destinationId = property(_get_destinationId, _set_destinationId)
+
+ def _get_type(self):
+ """_get_type() -> VistrailModuleType - Returns this connection type.
+ Do not use this function, use type property: c.type = t
+
+ """
+ return self.source.type
+
+ def _set_type(self, t):
+ """ _set_type(t: VistrailModuleType) -> None
+ Sets this connection type and updates self.__source.type and
+ self.__dest.type. It also updates the correct makeConnection function.
+ Do not use this function, use type property: c.type = t
+
+ """
+ self.source.type = t
+ self.destination.type = t
+ self.updateMakeConnection()
+ type = property(_get_type, _set_type)
+
+ def _get_source(self):
+ """_get_source() -> Port
+ Returns source port. Do not use this function, use source property:
+ c.source
+
+ """
+ try:
+ return self.db_get_port_by_type('source')
+ except KeyError:
+ pass
+ return None
+
+ def _set_source(self, source):
+ """_set_source(source: Port) -> None
+ Sets this connection source port. It also updates this connection
+ makeConnection function. Do not use this function, use source
+ property instead: c.source = source
+
+ """
+ try:
+ port = self.db_get_port_by_type('source')
+ self.db_delete_port(port)
+ except KeyError:
+ pass
+ if source is not None:
+ self.db_add_port(source)
+ source = property(_get_source, _set_source)
+
+ def _get_destination(self):
+ """_get_destination() -> Port
+ Returns destination port. Do not use this function, use destination
+ property: c.destination
+
+ """
+# return self.db_ports['destination']
+ try:
+ return self.db_get_port_by_type('destination')
+ except KeyError:
+ pass
+ return None
+
+ def _set_destination(self, dest):
+ """_set_destination(dest: Port) -> None
+ Sets this connection destination port. It also updates this connection
+ makeConnection function. Do not use this function, use destination
+ property instead: c.destination = dest
+
+ """
+ try:
+ port = self.db_get_port_by_type('destination')
+ self.db_delete_port(port)
+ except KeyError:
+ pass
+ if dest is not None:
+ self.db_add_port(dest)
+ destination = property(_get_destination, _set_destination)
+ dest = property(_get_destination, _set_destination)
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of a Connection
+ object.
+
+ """
+ rep = "<connection id='%s'>%s%s</connection>"
+ return rep % (str(self.id), str(self.source), str(self.destination))
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+ def __eq__(self, other):
+ if type(other) != type(self):
+ return False
+ return (self.source == other.source and
+ self.dest == other.dest)
+
+ def equals_no_id(self, other):
+ """Checks equality up to ids (connection and ports)."""
+ if type(self) != type(other):
+ return False
+ return (self.source.equals_no_id(other.source) and
+ self.dest.equals_no_id(other.dest))
+
+################################################################################
+# Testing
+
+
+class TestConnection(unittest.TestCase):
+
+ def create_connection(self, id_scope=IdScope()):
+ from vistrails.core.vistrail.port import Port
+ from vistrails.core.modules.basic_modules import identifier as basic_pkg
+ source = Port(id=id_scope.getNewId(Port.vtType),
+ type='source',
+ moduleId=21L,
+ moduleName='String',
+ name='value',
+ signature='(%s:String)' % basic_pkg)
+ destination = Port(id=id_scope.getNewId(Port.vtType),
+ type='destination',
+ moduleId=20L,
+ moduleName='Float',
+ name='value',
+ signature='(%s:Float)' % basic_pkg)
+ connection = Connection(id=id_scope.getNewId(Connection.vtType),
+ ports=[source, destination])
+ return connection
+
+ def test_copy(self):
+ id_scope = IdScope()
+
+ c1 = self.create_connection(id_scope)
+ c2 = copy.copy(c1)
+ self.assertEquals(c1, c2)
+ self.assertEquals(c1.id, c2.id)
+ c3 = c1.do_copy(True, id_scope, {})
+ self.assertEquals(c1, c3)
+ self.assertNotEquals(c1.id, c3.id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ c1 = self.create_connection()
+ xml_str = vistrails.core.db.io.serialize(c1)
+ c2 = vistrails.core.db.io.unserialize(xml_str, Connection)
+ self.assertEquals(c1, c2)
+ self.assertEquals(c1.id, c2.id)
+
+ def testModuleConnection(self):
+ a = Connection.fromID(0)
+ c = moduleConnection(a)
+ def bogus(asd):
+ return 3
+ assert type(c) == type(bogus)
+
+ def testEmptyConnection(self):
+ """Tests sane initialization of empty connection"""
+ c = Connection()
+ self.assertEquals(c.source.endPoint, PortEndPoint.Source)
+ self.assertEquals(c.destination.endPoint, PortEndPoint.Destination)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/vistrail/controller.py b/vistrails/core/vistrail/controller.py
new file mode 100644
index 0000000..03a4bd4
--- /dev/null
+++ b/vistrails/core/vistrail/controller.py
@@ -0,0 +1,3891 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from itertools import izip
+import os
+import uuid
+import shutil
+import tempfile
+
+from vistrails.core.configuration import get_vistrails_configuration, \
+ get_vistrails_persistent_configuration
+import vistrails.core.db.action
+import vistrails.core.db.io
+import vistrails.core.db.locator
+from vistrails.core import debug
+from vistrails.core.data_structures.graph import Graph
+from vistrails.core.interpreter.default import get_default_interpreter
+from vistrails.core.layout.workflow_layout import WorkflowLayout, \
+ Pipeline as LayoutPipeline, Defaults as LayoutDefaults
+from vistrails.core.log.controller import LogControllerFactory, DummyLogController
+from vistrails.core.log.log import Log
+from vistrails.core.modules.abstraction import identifier as abstraction_pkg, \
+ version as abstraction_ver
+from vistrails.core.modules.basic_modules import identifier as basic_pkg
+import vistrails.core.modules.module_registry
+from vistrails.core.modules.module_registry import ModuleRegistryException, \
+ MissingModuleVersion, MissingModule, MissingPackageVersion, MissingPort, \
+ MissingPackage, PortsIncompatible
+from vistrails.core.modules.package import Package
+from vistrails.core.modules.sub_module import new_abstraction, read_vistrail, \
+ get_all_abs_namespaces, get_cur_abs_namespace, get_cur_abs_annotation_key, \
+ get_next_abs_annotation_key, save_abstraction, parse_abstraction_name
+from vistrails.core.packagemanager import PackageManager, get_package_manager
+import vistrails.core.packagerepository
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.core.upgradeworkflow import UpgradeWorkflowHandler, UpgradeWorkflowError
+from vistrails.core.utils import VistrailsInternalError, PortAlreadyExists, DummyView, \
+ InvalidPipeline
+from vistrails.core.system import vistrails_default_file_type
+from vistrails.core.vistrail.abstraction import Abstraction
+from vistrails.core.vistrail.action import Action
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.vistrail.connection import Connection
+from vistrails.core.vistrail.group import Group
+from vistrails.core.vistrail.location import Location
+from vistrails.core.vistrail.module import Module, ModuleFunction, ModuleParam
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.vistrail.port import Port
+from vistrails.core.vistrail.port_spec import PortSpec
+from vistrails.core.vistrail.port_spec_item import PortSpecItem
+from vistrails.core.vistrail.vistrail import Vistrail
+from vistrails.core.theme import DefaultCoreTheme
+from vistrails.db import VistrailsDBException
+from vistrails.db.domain import IdScope, DBWorkflowExec
+from vistrails.db.services.io import create_temp_folder, remove_temp_folder
+from vistrails.db.services.io import SaveBundle, open_vt_log_from_db
+from vistrails.db.services.vistrail import getSharedRoot
+from vistrails.core.utils import any
+
+def vt_action(description_or_f=None):
+ def get_f(f, description=None):
+ def new_f(self, *args, **kwargs):
+ self.flush_delayed_actions()
+ action = f(self, *args, **kwargs)
+ if action is not None:
+ self.add_new_action(action, description)
+ self.perform_action(action)
+ return action
+ return new_f
+
+ if isinstance(description_or_f, basestring):
+ d = description_or_f
+ def wrap(f):
+ return get_f(f, d)
+ return wrap
+ else:
+ return get_f(description_or_f)
+
+class CompareThumbnailsError(Exception):
+
+ def __init__(self, msg, first=None, second=None):
+ Exception.__init__(self, msg)
+ self._msg = msg
+ self._first = first
+ self._second = second
+
+ def __str__(self):
+ return "Comparing thumbnails failed.\n%s\n%s\n%s" % \
+ (self._msg, self._first, self._second)
+
+class VistrailController(object):
+ def __init__(self, vistrail=None, locator=None, abstractions=None,
+ thumbnails=None, mashups=None, id_scope=None,
+ set_log_on_vt=True, auto_save=True):
+ self.vistrail = None
+ self.locator = None
+ self._auto_save = auto_save
+ self.name = ''
+ self.file_name = ''
+ self.is_abstraction = False
+ self.changed = False
+
+ # if _cache_pipelines is True, cache pipelines to speed up
+ # version switching
+ self._cache_pipelines = True
+ self.flush_pipeline_cache()
+ self._current_full_graph = None
+ self._current_terse_graph = None
+ self.num_versions_always_shown = 1
+
+ # if self.search is True, vistrail is currently being searched
+ self.search = None
+ self.search_str = None
+ # If self.refine is True, search mismatches are hidden instead
+ # of ghosted
+ self.refine = False
+ self.full_tree = False
+
+ self._asked_packages = set()
+ self._delayed_actions = []
+ self._delayed_paramexps = []
+ self._delayed_mashups = []
+ self._loaded_abstractions = {}
+
+ # This will just store the mashups in memory and send them to SaveBundle
+ # when writing the vistrail
+ self._mashups = []
+
+ # the redo stack stores the undone action ids
+ # (undo is automatic with us, through the version tree)
+ self.redo_stack = []
+
+ # this is a reference to the current parameter exploration
+ self.current_parameter_exploration = None
+
+ # theme used to estimate module size for layout
+ self.layoutTheme = DefaultCoreTheme()
+
+ self.set_vistrail(vistrail, locator,
+ abstractions=abstractions,
+ thumbnails=thumbnails,
+ mashups=mashups,
+ id_scope=id_scope,
+ set_log_on_vt=set_log_on_vt)
+
+ # allow gui.vistrail_controller to reference individual views
+ def _get_current_version(self):
+ return self._current_version
+ def _set_current_version(self, version):
+ self._current_version = version
+ current_version = property(_get_current_version, _set_current_version)
+
+ def _get_current_pipeline(self):
+ return self._current_pipeline
+ def _set_current_pipeline(self, pipeline):
+ self._current_pipeline = pipeline
+ current_pipeline = property(_get_current_pipeline, _set_current_pipeline)
+
+ def flush_pipeline_cache(self):
+ self._pipelines = {0: Pipeline()}
+
+ def logging_on(self):
+ return not get_vistrails_configuration().check('nologger')
+
+ def get_logger(self):
+ if self.logging_on():
+ return LogControllerFactory.getInstance().create_logger(self.log)
+ else:
+ return DummyLogController()
+
+ def get_locator(self):
+ return self.locator
+
+ def set_vistrail(self, vistrail, locator, abstractions=None,
+ thumbnails=None, mashups=None, id_scope=None,
+ set_log_on_vt=True):
+ self.vistrail = vistrail
+ self.id_scope = id_scope
+ self.current_session = -1
+ self.log = Log()
+ if self.vistrail is not None:
+ self.id_scope = self.vistrail.idScope
+ self.current_session = self.vistrail.idScope.getNewId("session")
+ self.vistrail.current_session = self.current_session
+ if set_log_on_vt:
+ self.vistrail.log = self.log
+ if abstractions is not None:
+ self.ensure_abstractions_loaded(self.vistrail, abstractions)
+ if thumbnails is not None:
+ ThumbnailCache.getInstance().add_entries_from_files(thumbnails)
+ if mashups is not None:
+ self._mashups = mashups
+ self.current_version = -1
+ self.current_pipeline = Pipeline()
+ if self.locator != locator and self.locator is not None:
+ self.locator.clean_temporaries()
+ self.locator = locator
+ if self.locator is not None:
+ self.set_file_name(locator.name)
+ else:
+ self.set_file_name('')
+ if self.locator and self.locator.has_temporaries():
+ self.set_changed(True)
+ if self.vistrail is not None:
+ self.recompute_terse_graph()
+
+ def close_vistrail(self, locator):
+ if not self.vistrail.is_abstraction:
+ self.unload_abstractions()
+ if locator is not None:
+ locator.clean_temporaries()
+ locator.close()
+
+ def cleanup(self):
+ pass
+
+ def set_id_scope(self, id_scope):
+ self.id_scope = id_scope
+
+ def set_changed(self, changed):
+ """ set_changed(changed: bool) -> None
+ Set the current state of changed and emit signal accordingly
+
+ """
+ if changed!=self.changed:
+ self.changed = changed
+
+ def set_file_name(self, file_name):
+ """ set_file_name(file_name: str) -> None
+ Change the controller file name
+
+ """
+ if file_name == None:
+ file_name = ''
+ if self.file_name!=file_name:
+ self.file_name = file_name
+ self.name = os.path.split(file_name)[1]
+ if self.name=='':
+ self.name = 'untitled%s'%vistrails_default_file_type()
+
+ def check_alias(self, name):
+ """check_alias(alias) -> Boolean
+ Returns True if current pipeline has an alias named name """
+ # FIXME Why isn't this call on the pipeline?
+ return self.current_pipeline.has_alias(name)
+
+ def check_vistrail_variable(self, name):
+ """check_vistrail_variable(var) -> Boolean
+ Returns True if vistrail has a variable named name """
+ if self.vistrail:
+ return self.vistrail.has_vistrail_var(name)
+ return False
+
+ def set_vistrail_variable(self, name, value=None, set_changed=True):
+ """set_vistrail_variable(var) -> Boolean
+ Returns True if vistrail variable was changed """
+ if self.vistrail:
+ changed = self.vistrail.set_vistrail_var(name, value)
+ if changed and set_changed:
+ self.set_changed(changed)
+ return changed
+ return False
+
+ def get_vistrail_variable(self, name):
+ if self.vistrail:
+ return self.vistrail.get_vistrail_var(name)
+ return None
+
+ def get_vistrail_variable_by_uuid(self, uuid):
+ if self.vistrail:
+ return self.vistrail.db_get_vistrailVariable_by_uuid(uuid)
+ return None
+
+ def get_vistrail_variables(self):
+ """get_vistrail_variables() -> list
+ Returns the list of vistrail variables """
+ if self.vistrail:
+ return self.vistrail.vistrail_vars
+ return []
+
+ def get_vistrail_variable_name_by_uuid(self, uuid):
+ """def get_vistrail_variable_name_by_uuid(uuid: str) -> dict
+ Returns the var name for vistrail variable with uuid """
+ if self.vistrail and self.vistrail.db_has_vistrailVariable_with_uuid(uuid):
+ return self.vistrail.db_get_vistrailVariable_by_uuid(uuid).name
+
+ def find_vistrail_var_module(self, var_uuid):
+ for m in self.current_pipeline.modules.itervalues():
+ if m.is_vistrail_var() and m.get_vistrail_var() == var_uuid:
+ return m
+ return None
+
+ def get_vistrail_var_pairs(self, to_module, port_name, var_uuid=None):
+ connections = self.get_connections_to(self.current_pipeline,
+ [to_module.id], port_name)
+ pipeline = self.current_pipeline
+ v_pairs = {}
+ for connection in connections:
+ m = pipeline.modules[connection.source.moduleId]
+ if m.is_vistrail_var():
+ if var_uuid is None or m.get_vistrail_var() == var_uuid:
+ if m.id not in v_pairs:
+ v_pairs[m.id] = []
+ v_pairs[m.id].append(connection)
+ return v_pairs
+
+ def create_vistrail_var_module(self, descriptor, x, y, var_uuid):
+ m = self.create_module_from_descriptor(descriptor, x, y)
+ a = Annotation(id=self.id_scope.getNewId(Annotation.vtType),
+ key=Module.VISTRAIL_VAR_ANNOTATION,
+ value=var_uuid)
+ m.add_annotation(a)
+ f = self.create_function(m, "value")
+ m.add_function(f)
+ return m
+
+ def check_vistrail_var_connected(self, v_module, to_module, to_port):
+ connections = self.get_connections_to(self.current_pipeline,
+ [to_module.id], to_port)
+ for connection in connections:
+ if connection.source.moduleId == v_module.id:
+ return True
+ return False
+
+ def check_has_vistrail_var_connected(self, to_module, port_name):
+ connections = self.get_connections_to(self.current_pipeline,
+ [to_module.id], port_name)
+ pipeline = self.current_pipeline
+ for connection in connections:
+ if pipeline.modules[connection.source.moduleId].is_vistrail_var():
+ return True
+ return False
+
+ @vt_action("Connected vistrail variable")
+ def connect_vistrail_var_action(self, connection, module=None):
+ ops = []
+ if module is not None:
+ ops.append(('add', module))
+ ops.append(('add', connection))
+ action = vistrails.core.db.action.create_action(ops)
+ return action
+
+ def connect_vistrail_var(self, descriptor, var_uuid,
+ to_module, to_port, x, y):
+ ops = []
+ new_module = None
+ v_module = self.find_vistrail_var_module(var_uuid)
+ if v_module is None:
+ v_module = self.create_vistrail_var_module(descriptor, x, y,
+ var_uuid)
+ new_module = v_module
+ elif self.check_vistrail_var_connected(v_module, to_module, to_port):
+ return (None, None)
+
+ c = self.create_connection(v_module, "value", to_module, to_port)
+ action = self.connect_vistrail_var_action(c, new_module)
+ return (c, new_module)
+
+ def delete_modules_and_connections(self, modules, connections):
+ ops = []
+ ops.extend([('delete', c) for c in connections])
+ ops.extend([('delete', m) for m in modules])
+ if len(ops) > 0:
+ action = vistrails.core.db.action.create_action(ops)
+ return action
+ return None
+
+ @vt_action("Disconnected vistrail variable")
+ def disconnect_vistrail_vars(self, modules, connections):
+ return self.delete_modules_and_connections(modules, connections)
+
+ def get_disconnect_vistrail_vars(self, to_module, to_port,
+ to_var_uuid=None):
+ to_delete_modules = []
+ to_delete_conns = []
+ v_pairs = self.get_vistrail_var_pairs(to_module, to_port, to_var_uuid)
+ for (v_module_id, v_conns) in v_pairs.iteritems():
+ to_delete_conns.extend(v_conns)
+ total_conns = self.get_connections_from(self.current_pipeline,
+ [v_module_id])
+ # remove v_module if it isn't connected to others
+ if (len(total_conns) - len(v_conns)) < 1:
+ to_delete_modules.append(
+ self.current_pipeline.modules[v_module_id])
+
+ # action = self.delete_modules_and_connections(to_delete_modules,
+ # to_delete_conns)
+ # if action:
+ # self.vistrail.change_description("Disconnected Vistrail Variables",
+ # action.id)
+ return (to_delete_modules, to_delete_conns)
+
+ def getParameterExplorationById(self, id):
+ """ getParameterExplorationById(self, id) -> ParameterExploration
+ Returns a ParameterExploration given its id
+ """
+ if self.vistrail and \
+ self.vistrail.db_has_parameter_exploration_with_id(id):
+ return self.vistrail.db_get_parameter_exploration_by_id(id)
+ return None
+
+ def getLatestParameterExplorationByVersion(self, id):
+ """ getLatestParameterExplorationByVersion(self, version) ->
+ ParameterExploration
+ Returns a parameter exploration given its action_id and
+ that it has not been named
+ """
+ for i in xrange(len(self.vistrail.db_parameter_explorations)):
+ pe = self.vistrail.db_parameter_explorations[i]
+ if pe.action_id == id and not pe.name:
+ return pe
+ return None
+
+ def invalidate_version_tree(self, *args, **kwargs):
+ """ invalidate_version_tree(self, *args, **kwargs) -> None
+ Does nothing, gui/vistrail_controller.py does, though
+ """
+ pass
+
+ ##########################################################################
+ # Actions, etc
+
+ def has_move_actions(self):
+ return False
+
+ def flush_move_actions(self):
+ return False
+
+ def migrate_tags(self, from_version, to_version, vistrail=None):
+ if vistrail is None:
+ vistrail = self.vistrail
+ tag = vistrail.get_tag(from_version)
+ if tag:
+ vistrail.set_tag(from_version, "")
+ vistrail.set_tag(to_version, tag)
+ notes = vistrail.get_notes(from_version)
+ if notes:
+ vistrail.set_notes(from_version, "")
+ vistrail.set_notes(to_version, notes)
+
+ def flush_delayed_actions(self):
+ start_version = self.current_version
+ desc_key = Action.ANNOTATION_DESCRIPTION
+ added_upgrade = False
+ should_migrate_tags = get_vistrails_configuration().check("migrateTags")
+ for action in self._delayed_actions:
+ self.vistrail.add_action(action, start_version,
+ self.current_session)
+ # HACK to populate upgrade information
+ if (action.has_annotation_with_key(desc_key) and
+ action.get_annotation_by_key(desc_key).value == 'Upgrade'):
+ self.vistrail.set_upgrade(start_version, str(action.id))
+ if should_migrate_tags:
+ self.migrate_tags(start_version, action.id)
+ self.current_version = action.id
+ start_version = action.id
+ added_upgrade = True
+ for pe in self._delayed_paramexps:
+ pe.action_id = self.current_version
+ self.vistrail.db_add_parameter_exploration(pe)
+ for mashup in self._delayed_mashups:
+ # mashup is a mashuptrail.
+ # We need to update all action id references.
+ mashup.vtVersion = self.current_version
+ for action in mashup.actions:
+ action.mashup.version = self.current_version
+ self._mashups.append(mashup)
+
+ #self.vistrail.db_add_parameter_exploration(pe)
+ # We have to do moves after the delayed actions because the pipeline
+ # may have been updated
+ added_moves = self.flush_move_actions()
+ self._delayed_actions = []
+ self._delayed_paramexps = []
+ self._delayed_mashups = []
+ if added_upgrade or added_moves:
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(False)
+
+ def perform_action(self, action):
+ """ performAction(action: Action) -> timestep
+
+ Performs given action on current pipeline.
+
+ """
+ if action is not None:
+ self.current_pipeline.perform_action(action)
+ self.current_version = action.db_id
+ return action.db_id
+ return None
+
+ def add_new_action(self, action, description=None):
+ """add_new_action(action) -> None
+
+ Call this function to add a new action to the vistrail being
+ controlled by the vistrailcontroller.
+
+ FIXME: In the future, this function should watch the vistrail
+ and get notified of the change.
+
+ """
+ if action is not None:
+ if self.current_version == -1:
+ self.change_selected_version(0)
+ self.vistrail.add_action(action, self.current_version,
+ self.current_session)
+ if description is not None:
+ self.vistrail.change_description(description, action.id)
+ self.set_changed(True)
+ self.current_version = action.db_id
+ self.recompute_terse_graph()
+
+ def create_module_from_descriptor(self, *args, **kwargs):
+ return self.create_module_from_descriptor_static(self.id_scope,
+ *args, **kwargs)
+
+ @staticmethod
+ def create_module_from_descriptor_static(id_scope, descriptor,
+ x=0.0, y=0.0,
+ internal_version=-1):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ package = reg.get_package_by_name(descriptor.identifier)
+ loc_id = id_scope.getNewId(Location.vtType)
+ location = Location(id=loc_id,
+ x=x,
+ y=y,
+ )
+ if internal_version > -1:
+ # only get the current namespace if this is a local subworkflow
+ if package == abstraction_pkg:
+ namespace = get_cur_abs_namespace(descriptor.module.vistrail)
+ else:
+ namespace = descriptor.namespace
+ abstraction_id = id_scope.getNewId(Abstraction.vtType)
+ module = Abstraction(id=abstraction_id,
+ name=descriptor.name,
+ package=descriptor.identifier,
+ namespace=namespace,
+ version=package.version,
+ location=location,
+ internal_version=internal_version,
+ )
+ elif descriptor.identifier == basic_pkg and \
+ descriptor.name == 'Group':
+ group_id = id_scope.getNewId(Group.vtType)
+ module = Group(id=group_id,
+ name=descriptor.name,
+ package=descriptor.identifier,
+ namespace=descriptor.namespace,
+ version=package.version,
+ location=location,
+ )
+ else:
+ module_id = id_scope.getNewId(Module.vtType)
+ module = Module(id=module_id,
+ name=descriptor.name,
+ package=descriptor.identifier,
+ namespace=descriptor.namespace,
+ version=package.version,
+ location=location,
+ )
+ module.is_valid = True
+ return module
+
+ def create_module(self, *args, **kwargs):
+ return self.create_module_static(self.id_scope, *args, **kwargs)
+
+ @staticmethod
+ def create_module_static(id_scope, identifier, name, namespace='',
+ x=0.0, y=0.0, internal_version=-1):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ d = reg.get_descriptor_by_name(identifier, name, namespace)
+ static_call = VistrailController.create_module_from_descriptor_static
+ return static_call(id_scope, d, x, y, internal_version)
+
+ def create_connection_from_ids(self, output_id, output_port_spec,
+ input_id, input_port_spec):
+ output_module = self.current_pipeline.modules[output_id]
+ input_module = self.current_pipeline.modules[input_id]
+ return self.create_connection(output_module, output_port_spec,
+ input_module, input_port_spec)
+
+ def create_connection(self, *args, **kwargs):
+ return self.create_connection_static(self.id_scope, *args, **kwargs)
+
+ @staticmethod
+ def create_connection_static(id_scope, output_module, output_port_spec,
+ input_module, input_port_spec):
+ if isinstance(output_port_spec, basestring):
+ output_port_spec = \
+ output_module.get_port_spec(output_port_spec, 'output')
+ if isinstance(input_port_spec, basestring):
+ input_port_spec = \
+ input_module.get_port_spec(input_port_spec, 'input')
+ if output_port_spec is None:
+ raise VistrailsInternalError("output port spec is None")
+ if input_port_spec is None:
+ raise VistrailsInternalError("input port spec is None")
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ if not reg.ports_can_connect(output_port_spec, input_port_spec):
+ raise PortsIncompatible(output_module.package,
+ output_module.name,
+ output_module.namespace,
+ output_port_spec.name,
+ input_module.package,
+ input_module.name,
+ input_module.namespace,
+ input_port_spec.name)
+ output_port_id = id_scope.getNewId(Port.vtType)
+ output_port = Port(id=output_port_id,
+ spec=output_port_spec,
+ moduleId=output_module.id,
+ moduleName=output_module.name)
+ input_port_id = id_scope.getNewId(Port.vtType)
+ input_port = Port(id=input_port_id,
+ spec=input_port_spec,
+ moduleId=input_module.id,
+ moduleName=input_module.name)
+ conn_id = id_scope.getNewId(Connection.vtType)
+ connection = Connection(id=conn_id,
+ ports=[input_port, output_port])
+ return connection
+
+ def create_param(self, *args, **kwargs):
+ return self.create_param_static(self.id_scope, *args, **kwargs)
+
+ @staticmethod
+ def create_param_static(id_scope, port_spec, pos, value, alias='',
+ query_method=None):
+ param_id = id_scope.getNewId(ModuleParam.vtType)
+ descriptor = port_spec.descriptors()[pos]
+ param_type = descriptor.sigstring
+ # FIXME add/remove description
+ # FIXME make ModuleParam constructor accept port_spec
+ new_param = ModuleParam(id=param_id,
+ pos=pos,
+ name='<no description>',
+ alias=alias,
+ val=value,
+ type=param_type,
+ )
+
+ # FIXME probably should put this in the ModuleParam constructor
+ new_param.queryMethod = query_method
+ return new_param
+
+ def create_params(self, *args, **kwargs):
+ return self.create_params_static(self.id_scope, *args, **kwargs)
+
+ @staticmethod
+ def create_params_static(id_scope, port_spec, values, aliases=[],
+ query_methods=[]):
+ params = []
+ for i in xrange(len(port_spec.descriptors())):
+ if i < len(values):
+ value = str(values[i])
+ else:
+ value = None
+ if i < len(aliases):
+ alias = str(aliases[i])
+ else:
+ alias = ''
+ if i < len(query_methods):
+ query_method = query_methods[i]
+ else:
+ query_method = None
+ param = VistrailController.create_param_static(id_scope, port_spec,
+ i, value, alias,
+ query_method)
+ params.append(param)
+ return params
+
+ def create_function(self, *args, **kwargs):
+ return self.create_function_static(self.id_scope, *args, **kwargs)
+
+ @staticmethod
+ def create_function_static(id_scope, module, function_name,
+ param_values=[], aliases=[], query_methods=[]):
+ port_spec = module.get_port_spec(function_name, 'input')
+ if len(param_values) <= 0 and port_spec.defaults is not None:
+ param_values = port_spec.defaults
+
+ f_id = id_scope.getNewId(ModuleFunction.vtType)
+ new_function = ModuleFunction(id=f_id,
+ pos=module.getNumFunctions(),
+ name=function_name,
+ )
+ new_function.is_valid = True
+ new_params = \
+ VistrailController.create_params_static(id_scope, port_spec,
+ param_values, aliases,
+ query_methods)
+ new_function.add_parameters(new_params)
+ return new_function
+
+ def create_functions(self, *args, **kwargs):
+ return self.create_functions_static(self.id_scope, *args, **kwargs)
+
+ @staticmethod
+ def create_functions_static(id_scope, module, functions):
+ """create_functions(module: Module,
+ functions: [function_name: str,
+ param_values: [str]])
+ -> [ModuleFunction]
+
+ """
+ new_functions = []
+ static_call = VistrailController.create_function_static
+ for f in functions:
+ new_functions.append(static_call(id_scope, module, *f))
+ return new_functions
+
+ def create_port_spec(self, *args, **kwargs):
+ return self.create_port_spec_static(self.id_scope, *args, **kwargs)
+
+ @staticmethod
+ def create_port_spec_static(id_scope, module, port_type, port_name,
+ port_sigstring, port_sort_key=-1):
+ p_id = id_scope.getNewId(PortSpec.vtType)
+ port_spec = PortSpec(id=p_id,
+ type=port_type,
+ name=port_name,
+ sigstring=port_sigstring,
+ sort_key=port_sort_key,
+ )
+ # don't know how many port spec items are created until after...
+ for psi in port_spec.port_spec_items:
+ psi.id = id_scope.getNewId(PortSpecItem.vtType)
+ return port_spec
+
+ def get_module_connection_ids(self, module_ids, graph):
+ connection_ids = set()
+ for module_id in module_ids:
+ for v, id in graph.edges_from(module_id):
+ connection_ids.add(id)
+ for v, id in graph.edges_to(module_id):
+ connection_ids.add(id)
+ return connection_ids
+
+ def delete_module_list_ops(self, pipeline, module_ids):
+ graph = pipeline.graph
+ connect_ids = self.get_module_connection_ids(module_ids, graph)
+ ops = []
+ for c_id in connect_ids:
+ ops.append(('delete', pipeline.connections[c_id]))
+ for m_id in module_ids:
+ ops.append(('delete', pipeline.modules[m_id]))
+ return ops
+
+ def update_port_spec_ops(self, module, deleted_ports, added_ports):
+ op_list = []
+ deleted_port_info = set()
+ changed_port_info = set()
+ for p in deleted_ports:
+ port_info = (p[1], p[0])
+ if module.has_portSpec_with_name(port_info):
+ port = module.get_portSpec_by_name(port_info)
+ deleted_port_info.add(port_info + (port.sigstring,))
+ for p in added_ports:
+ port_info = (p[1], p[0], p[2])
+ if port_info in deleted_port_info:
+ changed_port_info.add(port_info[:2])
+
+ # Remove any connections related to deleted ports
+ for c in self.current_pipeline.connections.itervalues():
+ if ((c.sourceId == module.id and
+ any(c.source.name == p[1] for p in deleted_ports
+ if (p[1], p[0]) not in changed_port_info)) or
+ (c.destinationId == module.id and
+ any(c.destination.name == p[1] for p in deleted_ports
+ if (p[1], p[0]) not in changed_port_info))):
+ op_list.append(('delete', c))
+
+ # Remove any functions related to deleted ports
+ for p in deleted_ports:
+ if (p[1], p[0]) not in changed_port_info:
+ for function in module.functions:
+ if function.name == p[1]:
+ op_list.append(('delete', function,
+ Module.vtType, module.id))
+
+ # Remove all deleted ports
+ # !! Reset delted_port_info to not store sigstring
+ deleted_port_info = set()
+ for p in deleted_ports:
+ port_info = (p[1], p[0])
+ if module.has_portSpec_with_name(port_info):
+ port_spec = module.get_portSpec_by_name(port_info)
+ op_list.append(('delete', port_spec, Module.vtType, module.id))
+ deleted_port_info.add(port_info)
+
+ # Add all added ports
+ for p in added_ports:
+ if (p[1], p[0]) not in deleted_port_info and \
+ module.has_port_spec(p[1], p[0]):
+ raise PortAlreadyExists(module.package, module.name, p[0], p[1])
+ port_spec = self.create_port_spec(module, *p)
+ op_list.append(('add', port_spec, Module.vtType, module.id))
+ return op_list
+
+ def update_function_ops(self, module, function_name, param_values=[],
+ old_id=-1L, should_replace=True, aliases=[],
+ query_methods=[]):
+ """NOTE: aliases will be removed in the future!"""
+ op_list = []
+ port_spec = module.get_port_spec(function_name, 'input')
+
+ if should_replace and old_id < 0:
+ for old_function in module.functions:
+ if old_function.name == function_name:
+ old_id = old_function.real_id
+
+ # ensure that replacements don't happen for functions that
+ # shouldn't be replaced
+ if should_replace and old_id >= 0:
+ function = module.function_idx[old_id]
+ if param_values is None:
+ op_list.append(('delete', function, module.vtType, module.id))
+ else:
+ for i, new_param_value in enumerate(param_values):
+ old_param = function.params[i]
+ if ((len(aliases) > i and old_param.alias != aliases[i]) or
+ (len(query_methods) > i and
+ old_param.queryMethod != query_methods[i]) or
+ (old_param.strValue != new_param_value)):
+ if len(aliases) > i:
+ alias = aliases[i]
+ else:
+ alias = ''
+ if len(query_methods) > i:
+ query_method = query_methods[i]
+ else:
+ query_method = None
+ new_param = self.create_param(port_spec, i,
+ new_param_value, alias,
+ query_method)
+ op_list.append(('change', old_param, new_param,
+ function.vtType, function.real_id))
+ elif param_values is not None:
+ if len(param_values) < 1:
+ new_function = self.create_function(module, function_name,
+ param_values, aliases,
+ query_methods)
+ op_list.append(('add', new_function,
+ module.vtType, module.id))
+ else:
+ psis = port_spec.port_spec_items
+ found = False
+ for param_value, psi in izip(param_values, psis):
+ if param_value != psi.default:
+ found = True
+ break
+ if found:
+ new_function = self.create_function(module, function_name,
+ param_values, aliases,
+ query_methods)
+ op_list.append(('add', new_function,
+ module.vtType, module.id))
+ return op_list
+
+ def update_functions_ops(self, module, functions):
+ """update_functions_ops(module: Module,
+ functions: [function_name: str,
+ param_values: [str],
+ old_id: long (-1)
+ should_replace: bool (True)])
+ -> [Op]
+ Returns a list of operations that will create and update the
+ functions of the specified module with new values.
+
+ """
+ op_list = []
+ for f in functions:
+ op_list.extend(self.update_function_ops(module, *f))
+ return op_list
+
+ def create_updated_parameter(self, old_param, new_value):
+ """update_parameter(old_param: ModuleParam, new_value: str)
+ -> ModuleParam
+ Generates a change parameter action if the value is different
+
+ """
+ if old_param.strValue == new_value:
+ return None
+
+ param_id = self.id_scope.getNewId(ModuleParam.vtType)
+ new_param = ModuleParam(id=param_id,
+ pos=old_param.pos,
+ name=old_param.name,
+ alias=old_param.alias,
+ val=new_value,
+ type=old_param.typeStr,
+ )
+ return new_param
+
+ def update_annotation_ops(self, module, annotations):
+ """update_annotation_ops(module: Module, annotations: [(str, str)])
+ -> [operation_list]
+
+ """
+ op_list = []
+ for (key, value) in annotations:
+ a_id = self.id_scope.getNewId(Annotation.vtType)
+ annotation = Annotation(id=a_id,
+ key=key,
+ value=value,
+ )
+ if module.has_annotation_with_key(key):
+ old_annotation = module.get_annotation_by_key(key)
+ op_list.append(('change', old_annotation, annotation,
+ module.vtType, module.id))
+ else:
+ op_list.append(('add', annotation, module.vtType, module.id))
+ return op_list
+
+ def check_subworkflow_versions(self, changed_subworkflow_desc):
+ if self.current_pipeline is not None:
+ self.current_pipeline.check_subworkflow_versions()
+
+ @vt_action
+ def add_module_action(self, module):
+ action = vistrails.core.db.action.create_action([('add', module)])
+ return action
+
+ def add_module_from_descriptor(self, descriptor, x=0.0, y=0.0,
+ internal_version=-1):
+ module = self.create_module_from_descriptor(descriptor, x, y,
+ internal_version)
+ action = self.add_module_action(module)
+ return module
+
+
+ def add_module(self, identifier, name, namespace='', x=0.0, y=0.0,
+ internal_version=-1):
+ """ addModule(x: int, y: int, identifier, name: str, namespace='')
+ -> Module
+ Add a new module into the current pipeline
+
+ """
+ module = self.create_module(identifier, name, namespace, x, y,
+ internal_version)
+ action = self.add_module_action(module)
+ return module
+
+ def delete_module(self, module_id):
+ """ delete_module(module_id: int) -> version id
+ Delete a module from the current pipeline
+
+ """
+ return self.delete_module_list([module_id])
+
+ def create_module_list_deletion_action(self, pipeline, module_ids):
+ """ create_module_list_deletion_action(
+ pipeline: Pipeline,
+ module_ids: [int]) -> Action
+ Create action that will delete multiple modules from the given pipeline.
+
+ """
+ ops = self.delete_module_list_ops(pipeline, module_ids)
+ return vistrails.core.db.action.create_action(ops)
+
+ @vt_action
+ def delete_module_list(self, module_ids):
+ """ delete_module_list(module_ids: [int]) -> [version id]
+ Delete multiple modules from the current pipeline
+
+ """
+ action = self.create_module_list_deletion_action(self.current_pipeline,
+ module_ids)
+ return action
+
+ def move_modules_ops(self, move_list):
+ """ move_module_list(move_list: [(id,x,y)]) -> [operations]
+ Returns the operations that will move each module to its
+ specified location
+
+ """
+ operations = []
+ for (id, x, y) in move_list:
+ module = self.current_pipeline.get_module_by_id(id)
+ if module.location:
+ if module.location.x == x and module.location.y == y:
+ continue
+ loc_id = self.vistrail.idScope.getNewId(Location.vtType)
+ location = Location(id=loc_id, x=x, y=y)
+ if module.location and module.location.id != -1:
+ old_location = module.location
+ operations.append(('change', old_location, location,
+ module.vtType, module.id))
+ else:
+ #should probably be an error
+ operations.append(('add', location, module.vtType, module.id))
+ return operations
+
+ def move_module_list(self, move_list):
+ """ move_module_list(move_list: [(id,x,y)]) -> [version id]
+ Move all modules to a new location. No flushMoveActions is
+ allowed to to emit to avoid recursive actions
+
+ """
+ action_list = self.move_modules_ops(move_list)
+ action = vistrails.core.db.action.create_action(action_list)
+ self.add_new_action(action)
+ return self.perform_action(action)
+
+ @vt_action
+ def add_connection_action(self, connection):
+ action = vistrails.core.db.action.create_action([('add', connection)])
+ return action
+
+ def add_connection(self, output_id, output_port_spec,
+ input_id, input_port_spec):
+ """ add_connection(output_id: long,
+ output_port_spec: PortSpec | str,
+ input_id: long,
+ input_port_spec: PortSpec | str) -> Connection
+ Add a new connection into Vistrail
+
+ """
+ connection = \
+ self.create_connection_from_ids(output_id, output_port_spec,
+ input_id, input_port_spec)
+ action = self.add_connection_action(connection)
+ return connection
+
+ def delete_connection(self, id):
+ """ delete_connection(id: int) -> version id
+ Delete a connection with id 'id'
+
+ """
+ return self.delete_connection_list([id])
+
+ @vt_action
+ def delete_connection_list(self, connect_ids):
+ """ delete_connection_list(connect_ids: list) -> version id
+ Delete a list of connections
+
+ """
+ action_list = []
+ for c_id in connect_ids:
+ action_list.append(('delete',
+ self.current_pipeline.connections[c_id]))
+ action = vistrails.core.db.action.create_action(action_list)
+ return action
+
+ @vt_action
+ def add_function_action(self, module, function):
+ action = vistrails.core.db.action.create_action([('add', function,
+ module.vtType, module.id)])
+ return action
+
+ def add_function(self, module, function_name):
+ function = self.create_function(module, function_name)
+ action = self.add_function_action(module, function)
+ return function
+
+ @vt_action
+ def update_function(self, module, function_name, param_values, old_id=-1L,
+ aliases=[], query_methods=[], should_replace=True):
+ op_list = self.update_function_ops(module, function_name, param_values,
+ old_id, aliases=aliases,
+ query_methods=query_methods,
+ should_replace=should_replace)
+ if len(op_list) > 0:
+ action = vistrails.core.db.action.create_action(op_list)
+ return action
+ return None
+
+ @vt_action
+ def update_parameter(self, function, old_param_id, new_value):
+ old_param = function.parameter_idx[old_param_id]
+ new_param = self.create_updated_parameter(old_param, new_value)
+ if new_param is None:
+ return None
+ op = ('change', old_param, new_param,
+ function.vtType, function.real_id)
+ action = vistrails.core.db.action.create_action([op])
+ return action
+
+ @vt_action
+ def delete_method(self, function_pos, module_id):
+ """ delete_method(function_pos: int, module_id: int) -> version id
+ Delete a method with function_pos from module module_id
+
+ """
+
+ module = self.current_pipeline.get_module_by_id(module_id)
+ function = module.functions[function_pos]
+ action = vistrails.core.db.action.create_action([('delete', function,
+ module.vtType, module.id)])
+ return action
+
+ @vt_action
+ def delete_function(self, real_id, module_id):
+ module = self.current_pipeline.get_module_by_id(module_id)
+ function = module.get_function_by_real_id(real_id)
+ action = vistrails.core.db.action.create_action([('delete', function,
+ module.vtType, module.id)])
+ return action
+
+ @vt_action
+ def delete_annotation(self, key, module_id):
+ """ delete_annotation(key: str, module_id: long) -> version_id
+ Deletes an annotation from a module
+
+ """
+ module = self.current_pipeline.get_module_by_id(module_id)
+ annotation = module.get_annotation_by_key(key)
+ action = vistrails.core.db.action.create_action([('delete', annotation,
+ module.vtType, module.id)])
+ return action
+
+ @vt_action
+ def add_annotation(self, pair, module_id):
+ """ add_annotation(pair: (str, str), moduleId: int)
+ Add/Update a key/value pair annotation into the module of
+ moduleId
+
+ """
+ assert isinstance(pair[0], basestring)
+ assert isinstance(pair[1], basestring)
+ if pair[0].strip()=='':
+ return
+
+ module = self.current_pipeline.get_module_by_id(module_id)
+ a_id = self.vistrail.idScope.getNewId(Annotation.vtType)
+ annotation = Annotation(id=a_id,
+ key=pair[0],
+ value=pair[1],
+ )
+ if module.has_annotation_with_key(pair[0]):
+ old_annotation = module.get_annotation_by_key(pair[0])
+ action = \
+ vistrails.core.db.action.create_action([('change', old_annotation,
+ annotation,
+ module.vtType, module.id)])
+ else:
+ action = vistrails.core.db.action.create_action([('add', annotation,
+ module.vtType,
+ module.id)])
+ return action
+
+ def update_functions_ops_from_ids(self, module_id, functions):
+ module = self.current_pipeline.modules[module_id]
+ return self.update_functions_ops(module, functions)
+
+ def update_port_spec_ops_from_ids(self, module_id, deleted_ports,
+ added_ports):
+ module = self.current_pipeline.modules[module_id]
+ return self.update_port_spec_ops(module, deleted_ports, added_ports)
+
+ @vt_action
+ def update_functions(self, module, functions):
+ op_list = self.update_functions_ops(module, functions)
+ if len(op_list) > 0:
+ action = vistrails.core.db.action.create_action(op_list)
+ else:
+ action = None
+ return action
+
+ @vt_action
+ def update_ports_and_functions(self, module_id, deleted_ports, added_ports,
+ functions):
+ op_list = self.update_port_spec_ops_from_ids(module_id, deleted_ports,
+ added_ports)
+ op_list.extend(self.update_functions_ops_from_ids(module_id, functions))
+ action = vistrails.core.db.action.create_action(op_list)
+ return action
+
+ @vt_action
+ def update_ports(self, module_id, deleted_ports, added_ports):
+ op_list = self.update_port_spec_ops_from_ids(module_id, deleted_ports,
+ added_ports)
+ action = vistrails.core.db.action.create_action(op_list)
+ return action
+
+ def has_module_port(self, module_id, port_tuple):
+ """ has_module_port(module_id: int, port_tuple: (str, str)): bool
+ Parameters
+ ----------
+
+ - module_id : 'int'
+ - port_tuple : (portType, portName)
+
+ Returns true if there exists a module port in this module with given params
+
+ """
+ (type, name) = port_tuple
+ module = self.current_pipeline.get_module_by_id(module_id)
+ return len([x for x in module.db_portSpecs
+ if x.name == name and x.type == type]) > 0
+
+ @vt_action
+ def add_module_port(self, module_id, port_tuple):
+ """ add_module_port(module_id: int, port_tuple: (str, str, list)
+ Parameters
+ ----------
+
+ - module_id : 'int'
+ - port_tuple : (portType, portName, portSpec)
+
+ """
+ module = self.current_pipeline.get_module_by_id(module_id)
+ p_id = self.vistrail.idScope.getNewId(PortSpec.vtType)
+ port_spec = PortSpec(id=p_id,
+ type=port_tuple[0],
+ name=port_tuple[1],
+ sigstring=port_tuple[2],
+ )
+ # don't know how many port spec items are created until after...
+ for psi in port_spec.port_spec_items:
+ psi.id = self.vistrail.idScope.getNewId(PortSpecItem.vtType)
+ action = vistrails.core.db.action.create_action([('add', port_spec,
+ module.vtType, module.id)])
+ return action
+
+ @vt_action
+ def delete_module_port(self, module_id, port_tuple):
+ """
+ Parameters
+ ----------
+
+ - module_id : 'int'
+ - port_tuple : (portType, portName, portSpec)
+
+ """
+ spec_id = -1
+ module = self.current_pipeline.get_module_by_id(module_id)
+ port_spec = module.get_portSpec_by_name((port_tuple[1], port_tuple[0]))
+ action_list = [('delete', port_spec, module.vtType, module.id)]
+ for function in module.functions:
+ if function.name == port_spec.name:
+ action_list.append(('delete', function,
+ module.vtType, module.id))
+ action = vistrails.core.db.action.create_action(action_list)
+ return action
+
+ def create_group(self, module_ids, connection_ids):
+ self.flush_delayed_actions()
+ (group, connections) = \
+ self.build_group(self.current_pipeline,
+ module_ids, connection_ids)
+ op_list = []
+ op_list.extend(('delete', self.current_pipeline.connections[c_id])
+ for c_id in connection_ids)
+ op_list.extend(('delete', self.current_pipeline.modules[m_id])
+ for m_id in module_ids)
+ op_list.append(('add', group))
+ op_list.extend(('add', c) for c in connections)
+ action = vistrails.core.db.action.create_action(op_list)
+ self.add_new_action(action)
+# for op in action.operations:
+# print op.vtType, op.what, op.old_obj_id, op.new_obj_id
+ result = self.perform_action(action)
+ return group
+
+ def create_abstraction(self, module_ids, connection_ids, name):
+ self.flush_delayed_actions()
+ (abstraction, connections) = \
+ self.build_abstraction(self.current_pipeline,
+ module_ids, connection_ids, name)
+ op_list = []
+ op_list.extend(('delete', self.current_pipeline.connections[c_id])
+ for c_id in connection_ids)
+ op_list.extend(('delete', self.current_pipeline.modules[m_id])
+ for m_id in module_ids)
+ op_list.append(('add', abstraction))
+ op_list.extend(('add', c) for c in connections)
+ action = vistrails.core.db.action.create_action(op_list)
+ self.add_new_action(action)
+ result = self.perform_action(action)
+ return abstraction
+
+ def create_abstractions_from_groups(self, group_ids):
+ for group_id in group_ids:
+ self.create_abstraction_from_group(group_id)
+
+ def create_abstraction_from_group(self, group_id, name=""):
+ self.flush_delayed_actions()
+ name = self.get_abstraction_name(name)
+
+ (abstraction, connections) = \
+ self.build_abstraction_from_group(self.current_pipeline,
+ group_id, name)
+
+ op_list = []
+ getter = self.get_connections_to_and_from
+ op_list.extend(('delete', c)
+ for c in getter(self.current_pipeline, [group_id]))
+ op_list.append(('delete', self.current_pipeline.modules[group_id]))
+ op_list.append(('add', abstraction))
+ op_list.extend(('add', c) for c in connections)
+ action = vistrails.core.db.action.create_action(op_list)
+ self.add_new_action(action)
+ result = self.perform_action(action)
+ return abstraction
+
+
+ def ungroup_set(self, module_ids):
+ self.flush_delayed_actions()
+ for m_id in module_ids:
+ self.create_ungroup(m_id)
+
+ def create_ungroup(self, module_id):
+ (modules, connections) = \
+ self.build_ungroup(self.current_pipeline, module_id)
+ pipeline = self.current_pipeline
+ old_conn_ids = self.get_module_connection_ids([module_id],
+ pipeline.graph)
+ op_list = []
+ op_list.extend(('delete', pipeline.connections[c_id])
+ for c_id in old_conn_ids)
+ op_list.append(('delete', pipeline.modules[module_id]))
+ op_list.extend(('add', m) for m in modules)
+ op_list.extend(('add', c) for c in connections)
+ action = vistrails.core.db.action.create_action(op_list)
+ self.add_new_action(action)
+ res = self.perform_action(action)
+ self.validate(self.current_pipeline, False)
+ return res
+
+
+
+ ##########################################################################
+ # Methods to access/find pipeline information
+
+ def get_connections_to(self, pipeline, module_ids, port_name=None):
+ connection_ids = set()
+ graph = pipeline.graph
+ for m_id in module_ids:
+ for _, id in graph.edges_to(m_id):
+ connection_ids.add(id)
+ return [pipeline.connections[c_id] for c_id in connection_ids
+ if port_name is None or \
+ pipeline.connections[c_id].destination.name == port_name]
+
+ def get_connections_from(self, pipeline, module_ids, port_name=None):
+ connection_ids = set()
+ graph = pipeline.graph
+ for m_id in module_ids:
+ for _, id in graph.edges_from(m_id):
+ connection_ids.add(id)
+ return [pipeline.connections[c_id] for c_id in connection_ids
+ if port_name is None or \
+ pipeline.connections[c_id].source.name == port_name]
+
+ def get_connections_to_and_from(self, pipeline, module_ids):
+ connection_ids = set()
+ graph = pipeline.graph
+ for m_id in module_ids:
+ for _, id in graph.edges_from(m_id):
+ connection_ids.add(id)
+ for _, id in graph.edges_to(m_id):
+ connection_ids.add(id)
+ return [pipeline.connections[c_id] for c_id in connection_ids]
+
+ ##########################################################################
+ # Grouping/abstraction
+
+ def get_avg_location(self, modules):
+ if len(modules) < 1:
+ return (0.0, 0.0)
+
+ sum_x = 0.0
+ sum_y = 0.0
+ for module in modules:
+ sum_x += module.location.x
+ sum_y += module.location.y
+ return (sum_x / len(modules), sum_y / len(modules))
+
+ def translate_modules(self, modules, x, y):
+ for module in modules:
+ module.location.x -= x
+ module.location.y -= y
+
+ def center_modules(self, modules):
+ (avg_x, avg_y) = self.get_avg_location(modules)
+ self.translate_modules(modules, avg_x, avg_y)
+
+ @staticmethod
+ def get_neighbors(pipeline, module, upstream=True):
+# for i, m in pipeline.modules.iteritems():
+# print i, m.name
+# for j, c in pipeline.connections.iteritems():
+# print j, c.source.moduleId, c.destination.moduleId
+
+ neighbors = []
+ if upstream:
+ get_edges = pipeline.graph.edges_to
+ get_port_name = \
+ lambda x: pipeline.connections[x].source.name
+ else:
+ get_edges = pipeline.graph.edges_from
+ get_port_name = \
+ lambda x: pipeline.connections[x].destination.name
+ for (m_id, conn_id) in get_edges(module.id):
+ neighbors.append((pipeline.modules[m_id], get_port_name(conn_id)))
+ return neighbors
+
+ @staticmethod
+ def get_upstream_neighbors(pipeline, module):
+ return VistrailController.get_neighbors(pipeline, module, True)
+ @staticmethod
+ def get_downstream_neighbors(pipeline, module):
+ return VistrailController.get_neighbors(pipeline, module, False)
+
+ def check_subpipeline_port_names(self):
+ def create_name(base_name, names):
+ if base_name in names:
+ port_name = base_name + '_' + str(names[base_name])
+ names[base_name] += 1
+ else:
+ port_name = base_name
+ names[base_name] = 2
+ return port_name
+
+ in_names = {}
+ out_names = {}
+ in_cur_names = []
+ out_cur_names = []
+ in_process_list = []
+ out_process_list = []
+ pipeline = self.current_pipeline
+ for m in pipeline.module_list:
+ if m.package == basic_pkg and (m.name == 'InputPort' or
+ m.name == 'OutputPort'):
+ if m.name == 'InputPort':
+ neighbors = self.get_downstream_neighbors(pipeline, m)
+ names = in_names
+ cur_names = in_cur_names
+ process_list = in_process_list
+ elif m.name == 'OutputPort':
+ neighbors = self.get_upstream_neighbors(pipeline, m)
+ names = out_names
+ cur_names = out_cur_names
+
+ if len(neighbors) < 1:
+ # print "not adding, no neighbors"
+ # don't add it!
+ continue
+
+ name_function = None
+ base_name = None
+ for function in m.functions:
+ if function.name == 'name':
+ name_function = function
+ if len(function.params) > 0:
+ base_name = function.params[0].strValue
+ if base_name is not None:
+ cur_names.append(base_name)
+ else:
+ base_name = neighbors[0][1]
+ if base_name == 'self':
+ base_name = neighbors[0][0].name
+ process_list.append((m, base_name))
+
+ op_list = []
+ for (port_type, names, cur_names, process_list) in \
+ [("input", in_names, in_cur_names, in_process_list), \
+ ("output", out_names, out_cur_names, out_process_list)]:
+ cur_names.sort()
+ last_name = None
+ for name in cur_names:
+ if name == last_name:
+ msg = 'Cannot assign the name "%s" to more ' \
+ 'than one %s port' % (name, port_type)
+ raise RuntimeError(msg)
+ last_name = name
+ idx = name.rfind("_")
+ if idx < 0:
+ names[name] = 2
+ else:
+ base_name = None
+ try:
+ val = int(name[idx+1:])
+ base_name = name[:idx]
+ except ValueError:
+ pass
+ if base_name is not None and base_name in names:
+ cur_val = names[base_name]
+ if val >= cur_val:
+ names[base_name] = val + 1
+ else:
+ names[name] = 2
+
+ for (m, base_name) in process_list:
+ port_name = create_name(base_name, names)
+ # FIXME use update_function when it is moved to
+ # core (see core_no_gui branch)
+ ops = self.update_function_ops(m, 'name',
+ [port_name])
+ op_list.extend(ops)
+ self.flush_delayed_actions()
+ action = vistrails.core.db.action.create_action(op_list)
+ if action is not None:
+ self.add_new_action(action)
+ self.perform_action(action)
+ return action
+
+ def create_subpipeline(self, full_pipeline, module_ids, connection_ids,
+ id_remap, id_scope=None):
+ if not id_scope:
+ id_scope = IdScope(1, {Group.vtType: Module.vtType,
+ Abstraction.vtType: Module.vtType})
+ old_id_scope = self.id_scope
+ self.set_id_scope(id_scope)
+
+ connections = [full_pipeline.connections[c_id]
+ for c_id in connection_ids]
+
+ pipeline = Pipeline()
+ pipeline.id = None # get rid of id so that sql saves correctly
+
+ in_names = {}
+ out_names = {}
+ def create_name(base_name, names):
+ if base_name in names:
+ port_name = base_name + '_' + str(names[base_name])
+ names[base_name] += 1
+ else:
+ port_name = base_name
+ names[base_name] = 2
+ return port_name
+
+ for m in full_pipeline.module_list:
+ if m.id not in module_ids:
+ continue
+ if m.package == basic_pkg and (m.name == 'InputPort' or
+ m.name == 'OutputPort'):
+ if m.name == 'InputPort':
+ neighbors = self.get_downstream_neighbors(full_pipeline, m)
+ names = in_names
+ elif m.name == 'OutputPort':
+ neighbors = self.get_upstream_neighbors(full_pipeline, m)
+ names = out_names
+ if len(neighbors) < 1:
+ # print "not adding, no neighbors"
+ # don't add it!
+ continue
+
+ m = m.do_copy(True, id_scope, id_remap)
+ name_function = None
+ for function in m.functions:
+ if function.name == 'name':
+ name_function = function
+ base_name = function.params[0].strValue
+ if name_function is None:
+ base_name = neighbors[0][1]
+ if base_name == 'self':
+ base_name = neighbors[0][0].name
+ port_name = create_name(base_name, names)
+ if name_function is not None:
+ name_function.params[0].strValue = port_name
+ else:
+ functions = [('name', [port_name])]
+ for f in self.create_functions(m, functions):
+ m.add_function(f)
+ pipeline.add_module(m)
+ else:
+ pipeline.add_module(m.do_copy(True, id_scope, id_remap))
+
+ # translate group to center
+ (avg_x, avg_y) = self.get_avg_location(pipeline.module_list)
+ self.translate_modules(pipeline.module_list, avg_x, avg_y)
+ module_index = dict([(m.id, m) for m in pipeline.module_list])
+
+ def create_port(port_type, other_port, other_module, old_module, names):
+ x = old_module.location.x
+ y = old_module.location.y
+ module_name = port_type.capitalize() + 'Port'
+ base_name = other_port.name
+ if base_name == 'self':
+ base_name = other_module.name
+ port_name = create_name(base_name, names)
+ module = self.create_module(basic_pkg, module_name, '',
+ x - avg_x, y - avg_y)
+ functions = [('name', [port_name])]
+ for f in self.create_functions(module, functions):
+ module.add_function(f)
+
+ return (module, 'InternalPipe', port_name)
+
+ def add_to_pipeline(port_type, port, other_port, names):
+ old_module = full_pipeline.modules[port.moduleId]
+ old_port_name = port.name
+ port_name = other_port.name
+ module_id = id_remap[(Module.vtType, other_port.moduleId)]
+ module = module_index[module_id]
+ key = (module_id, port_name, port_type)
+ if key in existing_ports:
+ (new_module, new_port, new_name) = existing_ports[key]
+ else:
+ (new_module, new_port, new_name) = \
+ create_port(port_type, other_port, module,
+ old_module, names)
+ existing_ports[key] = (new_module, new_port, new_name)
+ pipeline.add_module(new_module)
+ if port_type == 'input':
+ # print "output:", new_module.name, new_module.id, new_name
+ # print "input:", module.name, module.id, port_name
+ new_conn = self.create_connection(new_module, new_port,
+ module, port_name)
+ elif port_type == 'output':
+ # print "output:", module.name, module.id, port_name
+ # print "input:", new_module.name, new_module.id, new_name
+ new_conn = self.create_connection(module, port_name,
+ new_module, new_port)
+ else:
+ raise VistrailsInternalError("port_type incorrect")
+ pipeline.add_connection(new_conn)
+ return (old_module, old_port_name, new_name)
+
+
+ outside_connections = []
+ existing_ports = {}
+ for connection in connections:
+ all_inside = True
+ all_outside = True
+ for port in connection.ports:
+ if not (Module.vtType, port.moduleId) in id_remap:
+ all_inside = False
+ else:
+ all_outside = False
+
+ # if a connection has an "external" connection, we need to
+ # create an input port or output port module
+ if all_inside:
+ pipeline.add_connection(connection.do_copy(True, id_scope,
+ id_remap))
+ else:
+ old_in_module = None
+ old_out_module = None
+ if (Module.vtType, connection.source.moduleId) not in id_remap:
+ (old_out_module, old_out_port, old_in_port) = \
+ add_to_pipeline('input', connection.source,
+ connection.destination, in_names)
+ elif (Module.vtType, connection.destination.moduleId) \
+ not in id_remap:
+ (old_in_module, old_in_port, old_out_port) = \
+ add_to_pipeline('output', connection.destination,
+ connection.source, out_names)
+ outside_connections.append((old_out_module, old_out_port,
+ old_in_module, old_in_port))
+
+ self.set_id_scope(old_id_scope)
+ return (pipeline, outside_connections)
+
+ def get_connections_to_subpipeline(self, module, partial_connections):
+ connections = []
+ for (out_module, out_port, in_module, in_port) in partial_connections:
+ if out_module is None:
+ out_module = module
+ if in_module is None:
+ in_module = module
+ connections.append(self.create_connection(out_module, out_port,
+ in_module, in_port))
+ return connections
+
+ def build_group(self, full_pipeline, module_ids, connection_ids):
+ id_remap = {}
+ (pipeline, outside_connections) = \
+ self.create_subpipeline(full_pipeline, module_ids, connection_ids,
+ id_remap)
+
+ # now group to vistrail
+ (avg_x, avg_y) = self.get_avg_location([full_pipeline.modules[m_id]
+ for m_id in module_ids])
+ group = self.create_module(basic_pkg, 'Group', '', avg_x, avg_y)
+ group.pipeline = pipeline
+
+ connections = \
+ self.get_connections_to_subpipeline(group, outside_connections)
+
+ return (group, connections)
+
+ def build_abstraction(self, full_pipeline, module_ids,
+ connection_ids, name):
+ id_remap = {}
+ (pipeline, outside_connections) = \
+ self.create_subpipeline(full_pipeline, module_ids, connection_ids,
+ id_remap)
+
+ # save vistrail
+ abs_vistrail = self.create_vistrail_from_pipeline(pipeline)
+ abs_vistrail.name = name
+ abs_vistrail.change_description("Copied from pipeline", 1L)
+ abs_fname = self.save_abstraction(abs_vistrail)
+
+ # need to late enable stuff on the abstraction_pkg package
+ self.add_abstraction_to_registry(abs_vistrail, abs_fname, name,
+ None, "1")
+ namespace = get_cur_abs_namespace(abs_vistrail)
+ (avg_x, avg_y) = self.get_avg_location([full_pipeline.modules[m_id]
+ for m_id in module_ids])
+ abstraction = self.create_module(abstraction_pkg, name, namespace,
+ avg_x, avg_y, 1L)
+ connections = self.get_connections_to_subpipeline(abstraction,
+ outside_connections)
+ return (abstraction, connections)
+
+ def build_abstraction_from_group(self, full_pipeline, group_id, name):
+ if name is None:
+ return
+ group = self.current_pipeline.modules[group_id]
+ abs_vistrail = self.create_vistrail_from_pipeline(group.pipeline)
+ abs_vistrail.name = name
+ abs_vistrail.change_description("Created from group", 1L)
+ abs_fname = self.save_abstraction(abs_vistrail)
+
+ group_connections = self.get_connections_to_and_from(full_pipeline,
+ [group_id])
+ outside_connections = []
+ for c in group_connections:
+ out_module = full_pipeline.modules[c.source.moduleId]
+ out_port = c.source.name
+ in_module = full_pipeline.modules[c.destination.moduleId]
+ in_port = c.destination.name
+ if c.source.moduleId == group_id:
+ out_module = None
+ if c.destination.moduleId == group.id:
+ in_module = None
+ outside_connections.append((out_module, out_port,
+ in_module, in_port))
+
+ # need to late enable stuff on the 'local.abstractions' package
+ self.add_abstraction_to_registry(abs_vistrail, abs_fname, name,
+ None, "1")
+ namespace = get_cur_abs_namespace(abs_vistrail)
+ abstraction = self.create_module(abstraction_pkg, name, namespace,
+ group.location.x, group.location.y,
+ 1L)
+ connections = self.get_connections_to_subpipeline(abstraction,
+ outside_connections)
+ return (abstraction, connections)
+
+ def create_vistrail_from_pipeline(self, pipeline):
+ abs_vistrail = Vistrail()
+
+ id_remap = {}
+ action = vistrails.core.db.action.create_paste_action(pipeline,
+ abs_vistrail.idScope,
+ id_remap)
+ abs_vistrail.add_action(action, 0L, 0)
+ return abs_vistrail
+
+ def get_abstraction_dir(self):
+ conf = get_vistrails_configuration()
+ if conf.check('abstractionsDirectory'):
+ abstraction_dir = conf.abstractionsDirectory
+ if not os.path.exists(abstraction_dir):
+ raise VistrailsInternalError("Cannot find %s" % \
+ abstraction_dir)
+ return abstraction_dir
+ else:
+ raise VistrailsInternalError("'abstractionsDirectory' not"
+ " specified in configuration")
+ return None
+
+ def get_abstraction_desc(self, package, name, namespace, module_version=None):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ if reg.has_descriptor_with_name(package, name, namespace,
+ None, module_version):
+ return reg.get_descriptor_by_name(package, name,
+ namespace, None, module_version)
+ return None
+
+ def add_abstraction_to_registry(self, abs_vistrail, abs_fname, name,
+ namespace=None, module_version=None,
+ is_global=True, avail_fnames=[]):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ cur_namespace = get_cur_abs_namespace(abs_vistrail)
+ if namespace is None:
+ namespace = cur_namespace
+ if module_version is None:
+ module_version = -1L
+
+ self.ensure_abstractions_loaded(abs_vistrail, avail_fnames)
+ try:
+ abstraction = new_abstraction(name, abs_vistrail, abs_fname,
+ long(module_version))
+ except InvalidPipeline, e:
+ # handle_invalid_pipeline will raise it's own InvalidPipeline
+ # exception if it fails
+
+ # use a new controller that is tied to the abstraction
+ # vistrail to process exceptions, also force upgrades to
+ # be immediately incorporated, use self.__class_ to create
+ # controller so user is prompted if in GUI mode
+ abs_controller = self.__class__(abs_vistrail, auto_save=False)
+ (new_version, new_pipeline) = \
+ abs_controller.handle_invalid_pipeline(e, long(module_version),
+ force_no_delay=True)
+ try:
+ abstraction = new_abstraction(name, abs_vistrail, abs_fname,
+ new_version)
+ except InvalidPipeline, e:
+ # we need to process a second InvalidPipeline exception
+ # because the first may be simply for a missing package,
+ # then we hit upgrades with the second one
+
+ (new_version, new_pipeline) = \
+ abs_controller.handle_invalid_pipeline(e, new_version,
+ force_no_delay=True)
+ del abs_controller
+
+ save_abstraction(abs_vistrail, abs_fname)
+ self.set_changed(True)
+ abstraction = new_abstraction(name, abs_vistrail, abs_fname,
+ new_version, new_pipeline)
+ module_version = str(new_version)
+
+ all_namespaces = get_all_abs_namespaces(abs_vistrail)
+
+ old_desc = None
+ for ns in all_namespaces:
+ try:
+ desc = reg.get_similar_descriptor(abstraction_pkg,
+ name,
+ ns)
+ if not desc.is_hidden:
+ old_desc = desc
+ # print "found old_desc", old_desc.name, old_desc.version
+ break
+ except ModuleRegistryException, e:
+ pass
+
+ global_hide = not is_global or old_desc is not None
+ newest_desc = None
+ requested_desc = None
+ for ns in all_namespaces:
+ hide_descriptor = (ns != cur_namespace) or global_hide
+ # print '()()() adding abstraction', namespace
+ if reg.has_descriptor_with_name(abstraction_pkg,
+ name,
+ ns,
+ abstraction_ver,
+ str(module_version)):
+ # don't add something twice
+ continue
+ new_desc = reg.auto_add_module((abstraction,
+ {'package': abstraction_pkg,
+ 'package_version': abstraction_ver,
+ 'namespace': ns,
+ 'version': str(module_version),
+ 'hide_namespace': True,
+ 'hide_descriptor': hide_descriptor,
+ }))
+ if ns == cur_namespace:
+ newest_desc = new_desc
+ if ns == namespace:
+ requested_desc = new_desc
+ reg.auto_add_ports(abstraction)
+ if old_desc is not None:
+ # print '$$$ calling update_module'
+ reg.update_module(old_desc, newest_desc)
+ return requested_desc
+
+# package = reg.get_package_by_name(abstraction_pkg)
+# for desc in package.descriptor_versions.itervalues():
+# print desc.package, desc.name, desc.namespace, desc.version
+
+ def abstraction_exists(self, name):
+ # FIXME need to check directory in case abstraction was not
+ # loaded due to dependencies.
+ # FIXME, also need to check this for groups, probably
+ abstraction_dir = self.get_abstraction_dir()
+ vt_fname = os.path.join(abstraction_dir, name + '.xml')
+ return os.path.exists(vt_fname)
+
+ def load_abstraction(self, abs_fname, is_global=True, abs_name=None,
+ module_version=None, avail_fnames=[]):
+ if abs_name is None:
+ abs_name = parse_abstraction_name(abs_fname)
+ if abs_fname in self._loaded_abstractions:
+ abs_vistrail = self._loaded_abstractions[abs_fname]
+ else:
+ abs_vistrail = read_vistrail(abs_fname)
+ self._loaded_abstractions[abs_fname] = abs_vistrail
+
+ # print "LOAD_VT NAMESPACES:", get_all_abs_namespaces(abs_vistrail)
+
+ abstraction_uuid = get_cur_abs_namespace(abs_vistrail)
+ if abstraction_uuid is None:
+ # No current uuid exists - generate one
+ abstraction_uuid = str(uuid.uuid1())
+ abs_vistrail.set_annotation('__abstraction_uuid__', abstraction_uuid)
+ origin_uuid = abs_vistrail.get_annotation('__abstraction_origin_uuid__')
+ if origin_uuid is None:
+ # No origin uuid exists - set to current uuid (for backwards compatibility)
+ origin_uuid = abstraction_uuid
+ abs_vistrail.set_annotation('__abstraction_origin_uuid__', origin_uuid)
+ else:
+ origin_uuid = origin_uuid.value
+
+ if module_version is None:
+ module_version = str(abs_vistrail.get_latest_version())
+ elif isinstance(module_version, (int, long)):
+ module_version = str(module_version)
+ # If an upgraded version has already been created, we want to use that rather than loading the old version.
+ # This step also avoid duplication of abstraction upgrades. Otherwise, when we try to add the old version
+ # to the registry, it raises an InvalidPipeline exception and automatically tries to handle it by creating
+ # another upgrade for the old version.
+ upgrade_version = abs_vistrail.get_upgrade(long(module_version))
+ if upgrade_version is not None:
+ old_version = module_version
+ module_version = str(upgrade_version)
+
+ desc = self.get_abstraction_desc(abstraction_pkg, abs_name,
+ abstraction_uuid, module_version)
+ if desc is None:
+ #print "adding version", module_version, "of", abs_name, "(namespace: %s)"%abstraction_uuid, "to registry"
+ desc = self.add_abstraction_to_registry(abs_vistrail, abs_fname,
+ abs_name, None,
+ module_version,
+ is_global, avail_fnames)
+ #if desc.version != module_version:
+ #print "upgraded version", module_version, "of", abs_name, "(namespace: %s)"%abstraction_uuid, "to version", desc.version, "and namespace", desc.namespace
+# else:
+# if upgrade_version is not None:
+# print "version", old_version, "of", abs_name, "(namespace: %s)"%abstraction_uuid, "already in registry as upgraded version", module_version
+# else:
+# print "version", module_version, "of", abs_name, "(namespace: %s)"%abstraction_uuid, "already in registry"
+ return desc
+
+ def unload_abstractions(self):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ for abs_fname, abs_vistrail in self._loaded_abstractions.iteritems():
+ abs_name = parse_abstraction_name(abs_fname)
+ # FIXME? do we need to remove all versions (call
+ # delete_module over and over?)
+ for namespace in get_all_abs_namespaces(abs_vistrail):
+ try:
+ reg.delete_module(abstraction_pkg, abs_name, namespace)
+ except:
+ pass
+ self._loaded_abstractions.clear()
+
+ # for abs_fname, abs_vistrail in self._loaded_abstractions.iteritems():
+ # abs_desc_info = abs_vistrail.get_annotation('__abstraction_descriptor_info__')
+ # if abs_desc_info is not None:
+ # abs_desc_info = eval(abs_desc_info.value)
+ # # Don't unload package abstractions that have been
+ # # upgraded by this controller (during a manual version
+ # # upgrade) because that would also unload the version
+ # # in the module palette
+ # if abs_desc_info[2] == abs_vistrail.get_annotation('__abstraction_uuid__').value:
+ # continue
+ # abs_name = parse_abstraction_name(abs_fname)
+ # abs_namespace = abs_vistrail.get_annotation('__abstraction_uuid__').value
+ # try:
+ # descriptor = self.get_abstraction_descriptor(abs_name, abs_namespace)
+ # print "removing all versions of", abs_name, "from registry (namespace: %s)"%abs_namespace
+ # while descriptor is not None:
+ # reg = core.modules.module_registry.get_module_registry()
+ # reg.delete_module(abstraction_pkg, abs_name, abs_namespace)
+ # descriptor = self.get_abstraction_descriptor(abs_name, abs_namespace)
+ # except:
+ # # No versions of the abstraction exist in the registry now
+ # pass
+ # self._loaded_abstractions.clear()
+
+# def update_abstraction(self, abstraction, new_actions):
+# module_version = abstraction.internal_version
+# if isinstance(module_version, basestring):
+# module_version = int(module_version)
+# abstraction_uuid = \
+# abstraction.vistrail.get_annotation('__abstraction_uuid__').value
+# upgrade_action = self.create_upgrade_action(new_actions)
+#
+# a = (abstraction.vistrail,
+# module_version)
+#
+# desc = self.get_abstraction_desc(abstraction.name, abstraction_uuid,
+# new_version)
+# if desc is None:
+# # desc = self.add_abstraction_to_registry(abstraction.vistrail,
+# # abstraction.
+# pass
+# # FIXME finish this!
+
+
+
+
+ def manage_package_names(self, vistrail, package):
+ vistrail = copy.copy(vistrail)
+ dependencies = []
+ for action in vistrail.actions:
+ for operation in action.operations:
+ if (operation.vtType == 'add' or
+ operation.vtType == 'change'):
+ if (operation.what == 'abstraction' and
+ operation.data.package == abstraction_pkg):
+ operation.data.package = package
+ elif (operation.what == 'abstraction' or
+ operation.what == 'module' or
+ operation.what == 'group'):
+ dependencies.append(operation.data.package)
+
+ return (vistrail, dependencies)
+
+ def save_abstraction(self, vistrail, name=None, package=None,
+ save_dir=None, overwrite=False):
+ if (package is None) != (save_dir is None):
+ raise VistrailsInternalError("Must set both package and "
+ "save_dir or neither")
+ if name is None:
+ name = vistrail.name
+
+ if package is None and self.abstraction_exists(name):
+ raise VistrailsInternalError("Abstraction with name '%s' already "
+ "exists" % name)
+
+ # Set uuid's (this is somewhat tricky because of backwards
+ # compatibility - there was originally only
+ # '__abstraction_uuid__' and no origin, so we have to handle
+ # cases where a uuid is set, but hasn't been set as the origin
+ # yet).
+ new_uuid = str(uuid.uuid1())
+ if vistrail.get_annotation('__abstraction_origin_uuid__') is None:
+ # No origin uuid exists
+ current_uuid = vistrail.get_annotation('__abstraction_uuid__')
+ if current_uuid is None:
+ # No current uuid exists - generate one and use it as
+ # origin and current uuid
+ vistrail.set_annotation('__abstraction_origin_uuid__', new_uuid)
+ # vistrail.set_annotation('__abstraction_uuid__', new_uuid)
+ else:
+ # A current uuid exists - set it as origin and
+ # generate a new current uuid
+ vistrail.set_annotation('__abstraction_origin_uuid__',
+ current_uuid.value)
+ # vistrail.set_annotation('__abstraction_uuid__', str(uuid.uuid1()))
+ # else:
+ # # Origin uuid exists - just generate a new current uuid
+ # vistrail.set_annotation('__abstraction_uuid__', str(uuid.uuid1()))
+ annotation_key = get_next_abs_annotation_key(vistrail)
+ vistrail.set_annotation(annotation_key, new_uuid)
+
+ if save_dir is None:
+ save_dir = self.get_abstraction_dir()
+ vt_fname = os.path.join(save_dir, name + '.xml')
+ if not overwrite and os.path.exists(vt_fname):
+ raise VistrailsInternalError("'%s' already exists" % \
+ vt_fname)
+ vistrails.core.db.io.save_vistrail_to_xml(vistrail, vt_fname)
+ return vt_fname
+
+ def upgrade_abstraction_module(self, module_id, test_only=False):
+ """upgrade_abstraction_module(module_id, test_only) -> None or
+ (preserved: bool, missing_ports: list)
+
+ If test_only is False, attempts to automatically upgrade an
+ abstraction by adding a new abstraction with the current package
+ version, and recreates all connections and functions. If any
+ of the ports/functions used are not available, they are not
+ reconnected/readded to the new abstraction.
+
+ If test_only is True, (preserved: bool, missing_ports: list)
+ is returned, where 'preserved' is a boolean that is True
+ if the abstraction can be replaced with all functions and
+ connections preserved. If 'preserved' is True, then
+ 'missing_ports' is an empty list, otherwise it contains a
+ list of tuples (port_type: str, port_name: str) of all
+ ports that have been removed.
+
+ """
+ # get the new descriptor first
+ invalid_module = self.current_pipeline.modules[module_id]
+ # make sure that we don't get an obselete descriptor
+ invalid_module._module_descriptor = None
+ abs_fname = invalid_module.module_descriptor.module.vt_fname
+ #print "&&& abs_fname", abs_fname
+ (path, prefix, abs_name, abs_namespace, suffix) = \
+ parse_abstraction_name(abs_fname, True)
+ # abs_vistrail = invalid_module.vistrail
+ abs_vistrail = read_vistrail(abs_fname)
+ abs_namespace = get_cur_abs_namespace(abs_vistrail)
+ lookup = {(abs_name, abs_namespace): abs_fname}
+ descriptor_info = invalid_module.descriptor_info
+ newest_version = str(abs_vistrail.get_latest_version())
+ #print '&&& check_abstraction', abs_namespace, newest_version
+ d = self.check_abstraction((descriptor_info[0],
+ descriptor_info[1],
+ abs_namespace,
+ descriptor_info[3],
+ newest_version),
+ lookup)
+
+ failed = True
+ src_ports_gone = {}
+ dst_ports_gone = {}
+ fns_gone = {}
+ missing_ports = []
+ check_upgrade = UpgradeWorkflowHandler.check_upgrade
+ while failed:
+ try:
+ check_upgrade(self.current_pipeline, module_id, d,
+ function_remap=fns_gone,
+ src_port_remap=src_ports_gone,
+ dst_port_remap=dst_ports_gone)
+ if test_only:
+ return (len(missing_ports) == 0, missing_ports)
+ failed = False
+ except UpgradeWorkflowError, e:
+ if test_only:
+ missing_ports.append((e._port_type, e._port_name))
+ if e._module is None or e._port_type is None or \
+ e._port_name is None:
+ raise e
+ # Remove the offending connection/function by remapping to None
+ if e._port_type == 'output':
+ src_ports_gone[e._port_name] = None
+ elif e._port_type == 'input':
+ dst_ports_gone[e._port_name] = None
+ fns_gone[e._port_name] = None
+ else:
+ raise e
+ upgrade_action = \
+ UpgradeWorkflowHandler.replace_module(self, self.current_pipeline,
+ module_id, d,
+ fns_gone,
+ src_ports_gone,
+ dst_ports_gone)[0]
+ self.flush_delayed_actions()
+ self.add_new_action(upgrade_action)
+ self.perform_action(upgrade_action)
+ self.vistrail.change_description("Upgrade Subworkflow",
+ self.current_version)
+
+ def get_abstraction_descriptor(self, name, namespace=None):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ return reg.get_descriptor_by_name(abstraction_pkg, name, namespace)
+
+# def load_abstraction(self, abs_fname, abs_name=None):
+# if abs_name is None:
+# abs_name = os.path.basename(abs_fname)[12:-4]
+# abs_vistrail = read_vistrail(abs_fname)
+# abstraction_uuid = \
+# abs_vistrail.get_annotation('__abstraction_uuid__').value
+# if self.abstraction_exists(abs_name):
+# descriptor = self.get_abstraction_descriptor(abs_name)
+# if descriptor.module.uuid == abstraction_uuid:
+# return
+# if self.abstraction_exists(abs_name, abstraction_uuid):
+# descriptor = \
+# self.get_abstraction_descriptor(abs_name, abstraction_uuid)
+# descriptor._abstraction_refs += 1
+# # print 'load ref_count:', descriptor.abstraction_refs
+# return
+
+# self.add_abstraction(abs_vistrail, abs_fname, abs_name,
+# abstraction_uuid)
+
+# def unload_abstraction(self, name, namespace):
+# if self.abstraction_exists(name):
+# descriptor = self.get_abstraction_descriptor(name, namespace)
+# descriptor._abstraction_refs -= 1
+# # print 'unload ref_count:', descriptor.abstraction_refs
+# if descriptor._abstraction_refs < 1:
+# # unload abstraction
+# print "deleting module:", name, namespace
+# reg = core.modules.module_registry.get_module_registry()
+# reg.delete_module(abstraction_pkg, name, namespace)
+
+ def import_abstraction(self, new_name, package, name, namespace,
+ module_version=None):
+ # copy from a local namespace to local.abstractions
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ descriptor = self.get_abstraction_desc(package, name, namespace, str(module_version))
+ if descriptor is None:
+ # if not self.abstraction_exists(name):
+ raise VistrailsInternalError("Abstraction %s|%s (package: %s) not on registry" %\
+ (name, namespace, package))
+ # FIXME have save_abstraction take abs_fname as argument and do
+ # shutil copy
+ # abs_fname = descriptor.module.vt_fname
+ abs_vistrail = descriptor.module.vistrail
+ # Strip the descriptor info annotation before saving so the imported version will be editable
+ abs_desc_info = abs_vistrail.get_annotation('__abstraction_descriptor_info__')
+ if abs_desc_info is not None:
+ abs_vistrail.set_annotation('__abstraction_descriptor_info__', None)
+ abs_fname = self.save_abstraction(abs_vistrail, new_name)
+ # Duplicate the vistrail and set the uuid and descriptor annotation back on the original vistrail
+ imported_vistrail = read_vistrail(abs_fname)
+ annotation_key = get_next_abs_annotation_key(abs_vistrail)
+ abs_vistrail.set_annotation(annotation_key, namespace)
+ if abs_desc_info is not None:
+ abs_vistrail.set_annotation('__abstraction_descriptor_info__', abs_desc_info.value)
+ #if new_name == name and package == abstraction_pkg:
+ # reg.show_module(descriptor)
+ # descriptor.module.vt_fname = abs_fname
+ #else:
+ new_desc = self.add_abstraction_to_registry(imported_vistrail, abs_fname, new_name,
+ None, str(module_version))
+ reg.show_module(new_desc)
+
+ def export_abstraction(self, new_name, pkg_name, dir, package, name, namespace,
+ module_version):
+ descriptor = self.get_abstraction_desc(package, name, namespace, module_version)
+ if descriptor is None:
+ raise VistrailsInternalError("Abstraction %s|%s (package: %s) not on registry" %\
+ (name, namespace, package))
+
+ abs_vistrail = descriptor.module.vistrail
+ (abs_vistrail, dependencies) = self.manage_package_names(abs_vistrail,
+ pkg_name)
+ abs_fname = self.save_abstraction(abs_vistrail, new_name, pkg_name,
+ dir)
+ return (os.path.basename(abs_fname), dependencies)
+
+ def find_abstractions(self, vistrail, recurse=False):
+ abstractions = {}
+ for action in vistrail.actions:
+ for operation in action.operations:
+ if operation.vtType == 'add' or \
+ operation.vtType == 'change':
+ if operation.data is not None and operation.data.vtType == Abstraction.vtType:
+ abstraction = operation.data
+ if abstraction.package == abstraction_pkg:
+ key = abstraction.descriptor_info
+ if key not in abstractions:
+ abstractions[key] = []
+ abstractions[key].append(abstraction)
+ if recurse:
+ for abstraction_list in abstractions.values():
+ for abstraction in abstraction_list[:]:
+ try:
+ vistrail = abstraction.vistrail
+ except MissingPackageVersion, e:
+ try:
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ abstraction._module_descriptor = \
+ reg.get_similar_descriptor(
+ *abstraction.descriptor_info)
+ vistrail = abstraction.vistrail
+ except Exception, e:
+ # ignore because there will be a load attempt later
+ continue
+ except Exception, e:
+ # ignore because there will be a load attempt later
+ continue
+ r_abstractions = self.find_abstractions(vistrail, recurse)
+ for k,v in r_abstractions.iteritems():
+ if k not in abstractions:
+ abstractions[k] = []
+ abstractions[k].extend(v)
+ return abstractions
+
+ def check_abstraction(self, descriptor_tuple, lookup):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ try:
+ descriptor = reg.get_descriptor_by_name(*descriptor_tuple)
+ if not os.path.exists(descriptor.module.vt_fname):
+ # print "abstraction path doesn't exist"
+ reg.delete_descriptor(descriptor)
+ raise MissingModule(descriptor_tuple[0],
+ descriptor_tuple[1],
+ descriptor_tuple[2],
+ descriptor_tuple[4])
+ return descriptor
+ except MissingPackageVersion, e:
+ if descriptor_tuple[3] != '':
+ new_desc = (descriptor_tuple[0],
+ descriptor_tuple[1],
+ descriptor_tuple[2],
+ '',
+ descriptor_tuple[4])
+ return self.check_abstraction(new_desc, lookup)
+ else:
+ raise
+ except MissingModuleVersion, e:
+ if descriptor_tuple[4] != '':
+ other_desc = reg.get_descriptor_by_name(descriptor_tuple[0],
+ descriptor_tuple[1],
+ descriptor_tuple[2],
+ descriptor_tuple[3],
+ '')
+ new_desc = \
+ self.load_abstraction(other_desc.module.vt_fname,
+ False, descriptor_tuple[1],
+ descriptor_tuple[4])
+ descriptor_tuple = (new_desc.package, new_desc.name,
+ new_desc.namespace, new_desc.package_version,
+ str(new_desc.version))
+ return self.check_abstraction(descriptor_tuple, lookup)
+ else:
+ raise
+ except MissingModule, e:
+ if (descriptor_tuple[1], descriptor_tuple[2]) not in lookup:
+ if (descriptor_tuple[1], None) not in lookup:
+ raise
+ abs_fnames = lookup[(descriptor_tuple[1], None)]
+ else:
+ abs_fnames = [lookup[(descriptor_tuple[1], descriptor_tuple[2])]]
+ for abs_fname in abs_fnames:
+ new_desc = \
+ self.load_abstraction(abs_fname, False,
+ descriptor_tuple[1],
+ descriptor_tuple[4],
+ [v for k, v in lookup.iteritems()
+ if k[1] != None])
+ descriptor_tuple = (new_desc.package, new_desc.name,
+ new_desc.namespace, new_desc.package_version,
+ str(new_desc.version))
+ return self.check_abstraction(descriptor_tuple, lookup)
+ return None
+
+ def ensure_abstractions_loaded(self, vistrail, abs_fnames):
+ lookup = {}
+ for abs_fname in abs_fnames:
+ path, prefix, abs_name, abs_namespace, suffix = parse_abstraction_name(abs_fname, True)
+ # abs_name = os.path.basename(abs_fname)[12:-4]
+ lookup[(abs_name, abs_namespace)] = abs_fname
+ if (abs_name, None) not in lookup:
+ lookup[(abs_name, None)] = []
+ lookup[(abs_name, None)].append(abs_fname)
+
+ # we're going to recurse manually (see
+ # add_abstraction_to_regsitry) because we can't call
+ # abstraction.vistrail until the module is loaded.
+ abstractions = self.find_abstractions(vistrail)
+ for descriptor_info, abstraction_list in abstractions.iteritems():
+ # print 'checking for abstraction "' + str(abstraction.name) + '"'
+ try:
+ descriptor = self.check_abstraction(descriptor_info,
+ lookup)
+ for abstraction in abstraction_list:
+ abstraction.module_descriptor = descriptor
+ except InvalidPipeline, e:
+ debug.critical("Error loading abstraction '%s'" % \
+ descriptor_info[1], str(e))
+
+ def build_ungroup(self, full_pipeline, module_id):
+
+ group = full_pipeline.modules[module_id]
+ if group.vtType == Group.vtType:
+ pipeline = group.pipeline
+ elif group.vtType == Abstraction.vtType:
+ pipeline = group.summon().pipeline
+ else:
+ print 'not a group or abstraction?'
+ return
+
+ pipeline.ensure_connection_specs()
+
+ modules = []
+ connections = []
+ id_remap = {}
+ for module in pipeline.module_list:
+ # FIXME have better checks for this
+ if module.package != basic_pkg or (module.name != 'InputPort' and
+ module.name != 'OutputPort'):
+ modules.append(module.do_copy(True, self.id_scope, id_remap))
+ self.translate_modules(modules, -group.location.x, -group.location.y)
+ module_index = dict([(m.id, m) for m in modules])
+
+ open_ports = {}
+ for connection in pipeline.connection_list:
+ all_inside = True
+ all_outside = True
+ for port in connection.ports:
+ if (Module.vtType, port.moduleId) not in id_remap:
+ all_inside = False
+ else:
+ all_outside = False
+
+ if all_inside:
+ connections.append(connection.do_copy(True, self.id_scope,
+ id_remap))
+ else:
+ if (Module.vtType, connection.source.moduleId) not in id_remap:
+ port_module = \
+ pipeline.modules[connection.source.moduleId]
+ port_type = 'input'
+ elif (Module.vtType, connection.destination.moduleId) \
+ not in id_remap:
+ port_module = \
+ pipeline.modules[connection.destination.moduleId]
+ port_type = 'output'
+ else:
+ continue
+
+ (port_name, _, _, neighbors) = \
+ group.get_port_spec_info(port_module)
+ new_neighbors = \
+ [(module_index[id_remap[(Module.vtType, m.id)]], n)
+ for (m, n) in neighbors
+ if (Module.vtType, m.id) in id_remap]
+ open_ports[(port_name, port_type)] = new_neighbors
+
+ for connection in full_pipeline.connection_list:
+ if connection.source.moduleId == group.id:
+ key = (connection.source.name, 'output')
+ if key not in open_ports:
+ continue
+ neighbors = open_ports[key]
+ input_module = \
+ full_pipeline.modules[connection.destination.moduleId]
+ input_port = connection.destination.name
+ for (output_module, output_port) in neighbors:
+ connections.append(self.create_connection(output_module,
+ output_port,
+ input_module,
+ input_port))
+ elif connection.destination.moduleId == group.id:
+ key = (connection.destination.name, 'input')
+ if key not in open_ports:
+ continue
+ neighbors = open_ports[key]
+ output_module = \
+ full_pipeline.modules[connection.source.moduleId]
+ output_port = connection.source.name
+ for (input_module, input_port) in neighbors:
+ connections.append(self.create_connection(output_module,
+ output_port,
+ input_module,
+ input_port))
+ # end for
+
+ return (modules, connections)
+
+ def find_thumbnails(self, tags_only=True):
+ thumbnails = []
+ thumb_cache = ThumbnailCache.getInstance()
+ for action in self.vistrail.actions:
+ if self.vistrail.has_thumbnail(action.id):
+ thumbnail = self.vistrail.get_thumbnail(action.id)
+ if tags_only and not self.vistrail.has_tag(action.timestep):
+ thumb_cache.remove(thumbnail)
+ self.vistrail.set_thumbnail(action.timestep, "")
+ else:
+ abs_fname = thumb_cache.get_abs_name_entry(thumbnail)
+ if abs_fname is not None:
+ thumbnails.append(abs_fname)
+ else:
+ self.vistrail.set_thumbnail(action.timestep, "")
+ return thumbnails
+
+ def add_parameter_changes_from_execution(self, pipeline, version,
+ parameter_changes):
+ """add_parameter_changes_from_execution(pipeline, version,
+ parameter_changes) -> int.
+
+ Adds new versions to the current vistrail as a result of an
+ execution. Returns the version number of the new version."""
+
+ current_pipeline = self.current_pipeline
+ current_version = self.current_version
+
+ self.current_pipeline = pipeline
+ self.current_version = version
+
+ op_list = []
+ for (m_id, function_name, param_values) in parameter_changes:
+ try:
+ param_values_len = len(param_values)
+ except TypeError:
+ param_values = [param_values]
+ # FIXME should use registry to determine parameter types
+ # and then call the translate_to_string method on each
+ # parameter
+ param_values = [str(x) for x in param_values]
+ module = self.current_pipeline.modules[m_id]
+ # FIXME remove this code when aliases move
+ old_id = -1
+ for old_function in module.functions:
+ if old_function.name == function_name:
+ old_id = old_function.real_id
+
+ # ensure that replacements don't happen for functions that
+ # shouldn't be replaced
+ aliases = []
+ if old_id >= 0:
+ function = module.function_idx[old_id]
+ for i in xrange(len(param_values)):
+ aliases.append(function.params[i].alias)
+
+ op_list.extend(self.update_function_ops(module, function_name,
+ param_values,
+ should_replace=True,
+ aliases=aliases))
+
+ action = vistrails.core.db.action.create_action(op_list)
+ self.add_new_action(action)
+
+ self.current_pipeline = current_pipeline
+ self.current_version = current_version
+
+ return action.id
+
+ ##########################################################################
+ # Workflow Execution
+
+ def execute_workflow_list(self, vistrails):
+ """execute_workflow_list(vistrails: list) -> (results, bool)"""
+
+ stop_on_error = getattr(get_vistrails_configuration(),
+ 'stopOnError')
+ interpreter = get_default_interpreter()
+ changed = False
+ results = []
+ for vis in vistrails:
+ error = None
+ (locator, version, pipeline, view, aliases, params, reason, sinks, extra_info) = vis
+ temp_folder_used = False
+ if (not extra_info or not extra_info.has_key('pathDumpCells') or
+ not extra_info['pathDumpCells']):
+ if extra_info is None:
+ extra_info = {}
+ extra_info['pathDumpCells'] = create_temp_folder(prefix='vt_thumb')
+ temp_folder_used = True
+#
+ kwargs = {'locator': locator,
+ 'current_version': version,
+ 'view': view,
+ 'logger': self.get_logger(),
+ 'controller': self,
+ 'aliases': aliases,
+ 'params': params,
+ 'reason': reason,
+ 'sinks': sinks,
+ 'extra_info': extra_info,
+ 'stop_on_error': stop_on_error,
+ }
+ if self.get_vistrail_variables():
+ kwargs['vistrail_variables'] = \
+ self.get_vistrail_variable_by_uuid
+ result = interpreter.execute(pipeline, **kwargs)
+
+ thumb_cache = ThumbnailCache.getInstance()
+
+ if len(result.errors) == 0 and \
+ (thumb_cache.conf.autoSave or 'compare_thumbnails' in extra_info):
+ old_thumb_name = self.vistrail.get_thumbnail(version)
+ if 'compare_thumbnails' in extra_info:
+ old_thumb_name = None
+ fname = thumb_cache.add_entry_from_cell_dump(
+ extra_info['pathDumpCells'],
+ old_thumb_name)
+ if 'compare_thumbnails' in extra_info:
+ # check thumbnail difference
+ prev = None
+ if self.vistrail.has_thumbnail(version):
+ prev = thumb_cache.get_abs_name_entry(self.vistrail.get_thumbnail(version))
+ elif version in self.vistrail.actionMap and \
+ int(self.vistrail.get_upgrade(self.vistrail.actionMap[version].parent)) == version and \
+ self.vistrail.has_thumbnail(self.vistrail.actionMap[version].parent):
+ prev = thumb_cache.get_abs_name_entry(self.vistrail.get_thumbnail(self.vistrail.actionMap[version].parent))
+ else:
+ error = CompareThumbnailsError("No thumbnail exist for version %s" % version)
+ if prev:
+ if not prev:
+ error = CompareThumbnailsError("No thumbnail file exist for version %s" % version)
+ elif not fname:
+ raise CompareThumbnailsError("No thumbnail generated")
+ else:
+ next = thumb_cache.get_abs_name_entry(fname)
+ if not next:
+ raise CompareThumbnailsError("No thumbnail file generated for version %s" % version)
+ else:
+ min_err = extra_info['compare_thumbnails'](prev, next)
+ treshold = 0.1
+ if min_err > treshold:
+ raise CompareThumbnailsError("Thumbnails are different with value %s" % min_err, prev, next)
+
+ if fname is not None:
+ self.vistrail.set_thumbnail(version, fname)
+ changed = True
+
+ if temp_folder_used:
+ remove_temp_folder(extra_info['pathDumpCells'])
+
+ if result.parameter_changes:
+ l = result.parameter_changes
+ self.add_parameter_changes_from_execution(pipeline, version, l)
+ changed = True
+
+ results.append(result)
+ if error:
+ result.errors[version] = error
+ return ([result], False)
+ if self.logging_on():
+ self.set_changed(True)
+
+ if interpreter.debugger:
+ interpreter.debugger.update_values()
+ return (results,changed)
+
+ def execute_current_workflow(self, custom_aliases=None, custom_params=None,
+ extra_info=None, reason='Pipeline Execution',
+ sinks=None):
+ """ execute_current_workflow(custom_aliases: dict,
+ custom_params: list,
+ extra_info: dict) -> (list, bool)
+ Execute the current workflow (if exists)
+ custom_params is a list of tuples (vttype, oId, newval) with new values
+ for parameters
+ extra_info is a dictionary containing extra information for execution.
+ As we want to make the executions thread safe, we will pass information
+ specific to each pipeline through extra_info
+ As, an example, this will be useful for telling the spreadsheet where
+ to dump the images.
+ """
+ self.flush_delayed_actions()
+ if self.current_pipeline:
+ locator = self.get_locator()
+ if locator:
+ locator.clean_temporaries()
+ if self._auto_save:
+ locator.save_temporary(self.vistrail)
+ view = DummyView()
+ return self.execute_workflow_list([(self.locator,
+ self.current_version,
+ self.current_pipeline,
+ view,
+ custom_aliases,
+ custom_params,
+ reason,
+ sinks,
+ extra_info)])
+
+ def recompute_terse_graph(self):
+ # get full version tree (including pruned nodes) this tree is
+ # kept updated all the time. This data is read only and should
+ # not be updated!
+ fullVersionTree = self.vistrail.tree.getVersionTree()
+
+ # create tersed tree
+ x = [(0,None)]
+ tersedVersionTree = Graph()
+
+ # cache actionMap and tagMap because they're properties, sort
+ # of slow
+ am = self.vistrail.actionMap
+ tm = self.vistrail.get_tagMap()
+ last_n = self.vistrail.getLastActions(self.num_versions_always_shown)
+
+ while 1:
+ try:
+ (current,parent)=x.pop()
+ except IndexError:
+ break
+
+ # mount childs list
+ if current in am and self.vistrail.is_pruned(current):
+ children = []
+ else:
+ children = \
+ [to for (to, _) in fullVersionTree.adjacency_list[current]
+ if (to in am) and (not self.vistrail.is_pruned(to) or \
+ to == self.current_version)]
+
+ if (self.full_tree or
+ (current == 0) or # is root
+ (current in tm) or # hasTag:
+ (len(children) <> 1) or # not oneChild:
+ (current == self.current_version) or # isCurrentVersion
+ (am[current].expand) or # forced expansion
+ (current in last_n)): # show latest
+
+ # yes it will! this needs to be here because if we
+ # are refining version view receives the graph without
+ # the non matching elements
+ if( (not self.refine) or
+ (self.refine and not self.search) or
+ (current == 0) or
+ (self.refine and self.search and
+ self.search.match(self.vistrail,am[current]) or
+ current == self.current_version)):
+ # add vertex...
+ tersedVersionTree.add_vertex(current)
+
+ # ...and the parent
+ if parent is not None:
+ tersedVersionTree.add_edge(parent,current,0)
+
+ # update the parent info that will be used by the
+ # childs of this node
+ parentToChildren = current
+ else:
+ parentToChildren = parent
+ else:
+ parentToChildren = parent
+
+ for child in reversed(children):
+ x.append((child, parentToChildren))
+
+ self._current_terse_graph = tersedVersionTree
+ self._current_full_graph = self.vistrail.tree.getVersionTree()
+
+ # def refine_graph(self, step=1.0):
+ # """ refine_graph(step: float in [0,1]) -> (Graph, Graph)
+ # Refine the graph of the current vistrail based the search
+ # status of the controller. It also return the full graph as a
+ # reference
+
+ # """
+
+ # if self._current_full_graph is None:
+ # self.recompute_terse_graph()
+ # return (self._current_terse_graph, self._current_full_graph,
+ # self._current_graph_layout)
+
+ def get_latest_version_in_graph(self):
+ if not self._current_terse_graph:
+ # DAK do we want refine_graph here?
+ # (current, full, layout) = self.refine_graph()
+ self.recompute_terse_graph()
+ if self._current_terse_graph:
+ return max(self._current_terse_graph.iter_vertices())
+ return max(self.actions)
+
+ def select_latest_version(self):
+ """ select_latest_version() -> None
+ Try to select the latest visible version on the tree
+
+ """
+ self.change_selected_version(self.get_latest_version_in_graph())
+
+ def enable_missing_package(self, identifier, deps):
+ """callback for try_to_enable_package"""
+ return True
+
+ def install_missing_package(self, identifier):
+ """callback for try_to_enable_package"""
+ return True
+
+ def try_to_enable_package(self, identifier, dep_graph, confirmed=False):
+ """try_to_enable_package(identifier: str,
+ dep_graph: Graph,
+ confirmed: boolean)
+ Returns True if changes have been made to the registry, which
+ means reloading a pipeline that previously failed with missing
+ packages might work now. dep_graph will enable any
+ dependencies. Setting confirmed to True will bypass prompts
+ for later enables.
+ """
+
+ pm = get_package_manager()
+ pkg = pm.identifier_is_available(identifier)
+ if pkg and not pm.has_package(pkg.identifier):
+ deps = pm.all_dependencies(identifier, dep_graph)[:-1]
+ if pkg.identifier in self._asked_packages:
+ return False
+ if not confirmed and \
+ not self.enable_missing_package(pkg.identifier, deps):
+ self._asked_packages.add(pkg.identifier)
+ return False
+ # Ok, user wants to late-enable it. Let's give it a shot
+ try:
+ pm.late_enable_package(pkg.codepath)
+ pkg = pm.get_package_by_codepath(pkg.codepath)
+ if pkg.identifier != identifier:
+ # pkg is probably a parent of the "identifier" package
+ # try to load it
+ if hasattr(pkg.module, "can_handle_identifier") and \
+ pkg.module.can_handle_identifier(identifier):
+ pkg.init_module.load_from_identifier(identifier)
+ except pkg.MissingDependency, e:
+ for dependency in e.dependencies:
+ print 'MISSING DEPENDENCY:', dependency
+ if not self.try_to_enable_package(dependency[0], dep_graph,
+ True):
+ return False
+ return self.try_to_enable_package(pkg.identifier, dep_graph, True)
+ except pkg.InitializationFailed:
+ self._asked_packages.add(pkg.identifier)
+ raise
+ # there's a new package in the system, so we retry
+ # changing the version by recursing, since other
+ # packages/modules might still be needed.
+ self._asked_packages.add(pkg.identifier)
+ return True
+ # identifier may refer to a subpackage
+ if pkg and pkg.identifier != identifier and \
+ hasattr(pkg.module, "can_handle_identifier") and \
+ pkg.module.can_handle_identifier(identifier) and \
+ hasattr(pkg.init_module, "load_from_identifier"):
+ pkg.init_module.load_from_identifier(identifier)
+ return True
+ # Package is not available, let's try to fetch it
+ rep = vistrails.core.packagerepository.get_repository()
+ if rep:
+ codepath = rep.find_package(identifier)
+ if codepath and self.install_missing_package(identifier):
+ rep.install_package(codepath)
+ return self.try_to_enable_package(identifier, dep_graph, True)
+ self._asked_packages.add(identifier)
+ return False
+
+ def set_action_annotation(self, action, key, value, id_scope=None):
+ if id_scope is None:
+ id_scope = self.id_scope
+ if action.has_annotation_with_key(key):
+ old_annotation = action.get_annotation_by_key(key)
+ if old_annotation.value == value:
+ return False
+ action.delete_annotation(old_annotation)
+ if value.strip() != '':
+ annotation = \
+ Annotation(id=id_scope.getNewId(Annotation.vtType),
+ key=key,
+ value=value,
+ )
+ action.add_annotation(annotation)
+
+ def get_upgrade_module_remap(self, actions):
+ """Try to get a module remap when possible. This uses the fact that
+ most generic actions will have a single delete module action
+ and a single add module action.
+
+ """
+ is_full_remap = True
+ remap = {}
+ for action in actions:
+ d_module_ids = []
+ a_module_ids = []
+ for op in action.operations:
+ if op.vtType == 'delete' and op.what == 'module':
+ d_module_ids.append(op.db_objectId)
+ if op.vtType == 'add' and op.what == 'module':
+ a_module_ids.append(op.db_objectId)
+ if len(d_module_ids) == 1 and len(a_module_ids) == 1:
+ remap[(Module.vtType, d_module_ids[0])] = a_module_ids[0]
+ elif len(d_module_ids) + len(a_module_ids) > 0:
+ is_full_remap = False
+ return (remap, is_full_remap)
+
+ def get_simple_upgrade_remap(self, actions):
+ """Try to get module/function/parameter remaps when possible. This
+ uses the fact that most remaps only changes names and number of
+ deletes/adds are the same and adds are done in the reverse order of
+ deletes.
+ """
+ is_full_remap = True
+ remap = {}
+ for action in actions:
+ delete_ops = []
+ add_ops = []
+ for op in action.operations:
+ if op.vtType == 'delete':
+ delete_ops.append(op)
+ if op.vtType == 'add':
+ add_ops.append(op)
+ if len(delete_ops) != len(add_ops):
+ return (remap, False)
+ add_ops.reverse()
+ for deleted, added in zip(delete_ops, add_ops):
+ if deleted.what != added.what:
+ return (remap, False)
+ if added.what == 'module':
+ remap[(Module.vtType, deleted.db_objectId)] = added.db_objectId
+ if added.what == 'function':
+ if len(delete_ops) != len(add_ops):
+ return (remap, False)
+ remap[(ModuleFunction.vtType, deleted.db_objectId)] = added.db_objectId
+ if added.what == 'parameter':
+ if len(delete_ops) != len(add_ops):
+ return (remap, False)
+ remap[(ModuleParam.vtType, deleted.db_objectId)] = added.db_objectId
+ return (remap, is_full_remap)
+
+ def create_upgrade_action(self, actions):
+ new_action = vistrails.core.db.action.merge_actions(actions)
+ self.set_action_annotation(new_action, Action.ANNOTATION_DESCRIPTION,
+ "Upgrade")
+ return new_action
+
+ def handle_invalid_pipeline(self, e, new_version, vistrail=None,
+ report_all_errors=False, force_no_delay=False):
+ load_other_versions = False
+ # print 'running handle_invalid_pipeline'
+ if vistrail is None:
+ vistrail = self.vistrail
+ pm = get_package_manager()
+ root_exceptions = e.get_exception_set()
+ missing_packages = {}
+ def process_missing_packages(exception_set):
+ for err in exception_set:
+ err._was_handled = False
+ # print '--- trying to fix', str(err)
+ # FIXME need to get module_id from these exceptions
+ # when possible! need to integrate
+ # report_missing_module and handle_module_upgrade
+ if isinstance(err, InvalidPipeline):
+ process_missing_packages(err.get_exception_set())
+ elif isinstance(err, MissingPackage):
+ #check if the package was already installed before (because
+ #it was in the dependency list of a previous package
+ if err._identifier not in missing_packages:
+ missing_packages[err._identifier] = []
+ missing_packages[err._identifier].append(err)
+
+ process_missing_packages(root_exceptions)
+ new_exceptions = []
+
+ dep_graph = pm.build_dependency_graph(missing_packages.keys())
+ # for identifier, err_list in missing_packages.iteritems():
+ for identifier in pm.get_ordered_dependencies(dep_graph):
+ # print 'testing identifier', identifier
+ if not pm.has_package(identifier):
+ try:
+ # print 'trying to enable package'
+ if not self.try_to_enable_package(identifier, dep_graph):
+ pass
+ # print 'failed to enable package'
+ # if not report_all_errors:
+ # raise err
+ else:
+ for err in missing_packages[identifier]:
+ err._was_handled = True
+ except Exception, new_e:
+ print '&&& hit other exception'
+ new_exceptions.append(new_e)
+ if not report_all_errors:
+ raise new_e
+ else:
+ if identifier in missing_packages.iterkeys():
+ for err in missing_packages[identifier]:
+ err._was_handled = True
+ # else assume the package was already enabled
+
+ if len(new_exceptions) > 0:
+ # got new exceptions
+ pass
+
+ def process_package_versions(exception_set):
+ for err in exception_set:
+ if err._was_handled:
+ continue
+ if isinstance(err, InvalidPipeline):
+ process_package_versions(err.get_exception_set())
+ if isinstance(err, MissingPackageVersion):
+ # try and load other version of package?
+ err._was_handled = True
+ pass
+
+ # instead of upgrading, may wish to load the old version of
+ # the package if possible
+ if load_other_versions:
+ process_package_versions(root_exceptions)
+
+ def process_package_exceptions(exception_set, pipeline):
+ new_actions = []
+ package_errs = {}
+ for err in exception_set:
+ if err._was_handled:
+ continue
+ # print '+++ trying to fix', str(err)
+ if isinstance(err, InvalidPipeline):
+ id_scope = IdScope(1, {Group.vtType: Module.vtType,
+ Abstraction.vtType: Module.vtType})
+ id_remap = {}
+ new_pipeline = err._pipeline.do_copy(True, id_scope,
+ id_remap)
+ new_exception_set = []
+ for sub_err in err.get_exception_set():
+ key = (Module.vtType, sub_err._module_id)
+ if key in id_remap:
+ sub_err._module_id = id_remap[key]
+ new_exception_set.append(sub_err)
+ else:
+ new_exception_set.append(sub_err)
+
+ # set id to None so db saves correctly
+ new_pipeline.id = None
+ old_id_scope = self.id_scope
+ self.id_scope = id_scope
+ inner_actions = \
+ process_package_exceptions(new_exception_set,
+ new_pipeline)
+ self.id_scope = old_id_scope
+ if len(inner_actions) > 0:
+ # create action that recreates group/subworkflow
+ old_module = pipeline.modules[err._module_id]
+ if old_module.is_group():
+ my_actions = \
+ UpgradeWorkflowHandler.replace_group(
+ self, pipeline, old_module.id, new_pipeline)
+ for action in my_actions:
+ pipeline.perform_action(action)
+ new_actions.extend(my_actions)
+# This code shouldn't ever be reachable because invalid abstraction pipelines are handled when they're initially loaded.
+# elif old_module.is_abstraction():
+# # add new version to the abstraction
+# # then update the current pipeline by replacing
+# # abstraction module
+#
+# # FIXME finish this code
+# my_actions = \
+# UpgradeWorkflowHandler.replace_abstraction(
+# self, pipeline, old_module.id, inner_actions)
+# for action in my_actions:
+# pipeline.perform_action(action)
+# new_actions.extend(my_actions)
+
+ elif (isinstance(err, MissingModule) or
+ isinstance(err, MissingPackageVersion) or
+ isinstance(err, MissingModuleVersion)):
+ if err._identifier not in package_errs:
+ package_errs[err._identifier] = []
+ package_errs[err._identifier].append(err)
+
+ for identifier, err_list in package_errs.iteritems():
+ try:
+ pkg = pm.get_package(identifier)
+ except MissingPackage:
+ # cannot get the package we need
+ continue
+ details = '\n'.join(str(e) for e in err_list)
+ debug.log('Processing upgrades in package "%s"' %
+ identifier, details)
+ if pkg.can_handle_all_errors():
+ try:
+ actions = pkg.handle_all_errors(self, err_list,
+ pipeline)
+ if actions is not None:
+ for action in actions:
+ pipeline.perform_action(action)
+ new_actions.extend(actions)
+ for err in err_list:
+ err._was_handled = True
+ except Exception, new_e:
+ new_exceptions.append(new_e)
+ if not report_all_errors:
+ return new_actions
+# elif pkg.can_handle_upgrades():
+# print ' handle upgrades'
+# for err in err_list:
+# try:
+# actions = pkg.handle_module_upgrade_request(
+# self, err._module_id, pipeline)
+# if actions is not None:
+# print 'handled', pipeline.modules[err._module_id].name
+# for action in actions:
+# pipeline.perform_action(action)
+# new_actions.extend(actions)
+# print 'OK'
+# err._was_handled = True
+# except Exception, new_e:
+# new_exceptions.append(new_e)
+# if not report_all_errors:
+# return
+ else:
+ # print ' default upgrades'
+ # process default upgrades
+ # handler = UpgradeWorkflowHandler(self, pipeline)
+ for err in err_list:
+ try:
+ actions = UpgradeWorkflowHandler.dispatch_request(
+ self, err._module_id, pipeline)
+ if actions is not None:
+ for action in actions:
+ pipeline.perform_action(action)
+ new_actions.extend(actions)
+ err._was_handled = True
+ except Exception, new_e:
+ import traceback
+ traceback.print_exc()
+ new_exceptions.append(new_e)
+
+ if pkg.can_handle_missing_modules():
+ for err in err_list + new_exceptions:
+ if hasattr(err, '_was_handled') and err._was_handled:
+ continue
+ if isinstance(err, MissingModule):
+ try:
+ res = pkg.handle_missing_module(self,
+ err._module_id,
+ pipeline)
+ # need backward compatibility
+ if res is True:
+ err._was_handled = True
+ elif res is False:
+ pass
+ else:
+ actions = res
+ if actions is not None:
+ for action in actions:
+ pipeline.perform_action(action)
+ new_actions.extend(actions)
+ err._was_handled = True
+ except Exception, new_e:
+ new_exceptions.append(new_e)
+ if not report_all_errors:
+ return new_actions
+ return new_actions
+
+ if get_vistrails_configuration().check('upgradeOn'):
+ cur_pipeline = copy.copy(e._pipeline)
+ # note that cur_pipeline is modified to be the result of
+ # applying the actions in new_actions
+ new_actions = process_package_exceptions(root_exceptions,
+ cur_pipeline)
+ else:
+ new_actions = []
+ cur_pipeline = e._pipeline
+
+ if len(new_actions) > 0:
+ upgrade_action = self.create_upgrade_action(new_actions)
+ param_exps = self.vistrail.get_paramexps(new_version)
+ new_param_exps = []
+ if len(param_exps) > 0:
+ (module_remap, is_complete) = \
+ self.get_upgrade_module_remap(new_actions)
+ if is_complete:
+ for pe in param_exps:
+ new_pe = pe.do_copy(True, self.id_scope, module_remap)
+ new_param_exps.append(new_pe)
+ else:
+ debug.warning("Cannot translate old parameter "
+ "explorations through upgrade.")
+ mashup = None
+ if hasattr(self, "_mashups"):
+ for mashuptrail in self._mashups:
+ if mashuptrail.vtVersion == new_version:
+ mashup = mashuptrail
+ new_mashups = []
+ if mashup:
+ (mfp_remap, is_complete) = \
+ self.get_simple_upgrade_remap(new_actions)
+ if is_complete:
+ # FIXME: we should move the remapping to the db layer
+ # But we need to fix the schema by making functions/params
+ # foreign keys
+
+ #mashup = mashup.do_copy(True, self.id_scope, mfp_remap)
+ #mashup.id = uuid.uuid1()
+ # we move it to the new version so that references still work
+ self._mashups.remove(mashup)
+
+ for action in mashup.actions:
+ for alias in action.mashup.aliases:
+ c = alias.component
+ if (Module.vtType, c.vtmid) in mfp_remap:
+ c.vtmid = mfp_remap[(Module.vtType, c.vtmid)]
+ if (ModuleFunction.vtType,
+ c.vtparent_id) in mfp_remap:
+ c.vtparent_id=mfp_remap[(ModuleFunction.vtType,
+ c.vtparent_id)]
+ if (ModuleParam.vtType, c.vtid) in mfp_remap:
+ c.vtid = mfp_remap[(ModuleParam.vtType,
+ c.vtid)]
+ mashup.currentVersion = mashup.getLatestVersion()
+
+ new_mashups.append(mashup)
+ else:
+ debug.warning("Cannot translate old mashup "
+ "through upgrade.")
+
+ if get_vistrails_configuration().check('upgradeDelay') and not force_no_delay:
+ self._delayed_actions.append(upgrade_action)
+ self._delayed_paramexps.extend(new_param_exps)
+ self._delayed_mashups.extend(new_mashups)
+ else:
+ vistrail.add_action(upgrade_action, new_version,
+ self.current_session)
+ vistrail.set_upgrade(new_version, str(upgrade_action.id))
+ if get_vistrails_configuration().check("migrateTags"):
+ self.migrate_tags(new_version, upgrade_action.id, vistrail)
+ new_version = upgrade_action.id
+ for pe in new_param_exps:
+ pe.action_id = new_version
+ self.vistrail.db_add_parameter_exploration(pe)
+ for mashup in new_mashups:
+ mashup.vtVersion = self.current_version
+ for action in mashup.actions:
+ action.mashup.version = self.current_version
+ self._mashups.append(mashup)
+
+ self.set_changed(True)
+ self.recompute_terse_graph()
+
+ def check_exceptions(exception_set):
+ unhandled_exceptions = []
+ for err in exception_set:
+ if isinstance(err, InvalidPipeline):
+ sub_exceptions = check_exceptions(err.get_exception_set())
+ if len(sub_exceptions) > 0:
+ new_err = InvalidPipeline(sub_exceptions,
+ err._pipeline,
+ err._version)
+ unhandled_exceptions.append(new_err)
+ else:
+ if not err._was_handled:
+ unhandled_exceptions.append(err)
+ return unhandled_exceptions
+
+ left_exceptions = check_exceptions(root_exceptions)
+ if len(left_exceptions) > 0 or len(new_exceptions) > 0:
+ details = '\n'.join(set(str(e) for e in left_exceptions + \
+ new_exceptions))
+ # debug.critical("Some exceptions could not be handled", details)
+ raise InvalidPipeline(left_exceptions + new_exceptions,
+ cur_pipeline, new_version)
+ return (new_version, cur_pipeline)
+
+ def validate(self, pipeline, raise_exception=True):
+ vistrail_vars = self.get_vistrail_variables()
+ pipeline.validate(raise_exception, vistrail_vars)
+
+ def do_version_switch(self, new_version, report_all_errors=False,
+ do_validate=True, from_root=False):
+ """ do_version_switch(new_version: int,
+ resolve_all_errors: boolean) -> None
+ Change the current vistrail version into new_version, reporting
+ either the first error or all errors.
+
+ """
+
+ # This is tricky code, so watch carefully before you change
+ # it. The biggest problem is that we want to perform state
+ # changes only after all exceptions have been handled, but
+ # creating a pipeline every time is too slow. The solution
+ # then is to mutate currentPipeline, and in case exceptions
+ # are thrown, we roll back by rebuilding the pipeline from
+ # scratch as the first thing on the exception handler, so to
+ # the rest of the exception handling code, things look
+ # stateless.
+
+ def get_cost(descendant, ancestor):
+ cost = 0
+ am = self.vistrail.actionMap
+ if descendant == -1:
+ descendant = 0
+ while descendant != ancestor:
+ descendant = am[descendant].parent
+ cost += 1
+ return cost
+
+ def switch_version(version, allow_fail=False):
+ if self.current_version != -1 and not self.current_pipeline:
+ debug.warning("current_version is not -1 and "
+ "current_pipeline is None")
+ if version != self.current_version:
+ # clear delayed actions
+ # FIXME: invert the delayed actions and integrate them into
+ # the general_action_chain?
+ if len(self._delayed_actions) > 0:
+ self._delayed_actions = []
+ self.current_pipeline = Pipeline()
+ self.current_version = 0
+ if version == -1:
+ return None
+
+ # now we reuse some existing pipeline, even if it's the
+ # empty one for version zero
+ #
+ # The available pipelines are in self._pipelines, plus
+ # the current pipeline.
+ # Fast check: do we have to change anything?
+ if from_root:
+ result = self.vistrail.getPipeline(version)
+ elif version == self.current_version:
+ # we don't even need to check connection specs or
+ # registry
+ return self.current_pipeline
+ # Fast check: if target is cached, copy it and we're done.
+ elif version in self._pipelines:
+ result = copy.copy(self._pipelines[version])
+ else:
+ # Find the closest upstream pipeline to the current one
+ cv = self._current_full_graph.inverse_immutable().closest_vertex
+ closest = cv(version, self._pipelines)
+ cost_to_closest_version = get_cost(version, closest)
+ # Now we have to decide between the closest pipeline
+ # to version and the current pipeline
+ shared_parent = getSharedRoot(self.vistrail,
+ [self.current_version,
+ version])
+ cost_common_to_old = get_cost(self.current_version,
+ shared_parent)
+ cost_common_to_new = get_cost(version, shared_parent)
+ cost_to_current_version = cost_common_to_old + \
+ cost_common_to_new
+ # FIXME I'm assuming copying the pipeline has zero cost.
+ # Formulate a better cost model
+ if cost_to_closest_version < cost_to_current_version:
+ if closest == 0:
+ result = self.vistrail.getPipeline(version)
+ else:
+ result = copy.copy(self._pipelines[closest])
+ action = self.vistrail.general_action_chain(closest,
+ version)
+ result.perform_action(action)
+ else:
+ action = \
+ self.vistrail.general_action_chain(self.current_version,
+ version)
+ if self.current_version == -1 or self.current_version == 0:
+ result = Pipeline()
+ else:
+ result = copy.copy(self.current_pipeline)
+ result.perform_action(action)
+ if self._cache_pipelines and \
+ self.vistrail.has_tag(long(version)):
+ # stash a copy for future use
+ if do_validate:
+ try:
+ self.validate(result)
+ except InvalidPipeline:
+ if not allow_fail:
+ raise
+ else:
+ self._pipelines[version] = copy.copy(result)
+ else:
+ self._pipelines[version] = copy.copy(result)
+ if do_validate:
+ try:
+ self.validate(result)
+ except InvalidPipeline:
+ if not allow_fail:
+ raise
+ return result
+ # end switch_version
+
+ try:
+ self.current_pipeline = switch_version(new_version)
+ self.current_version = new_version
+ except InvalidPipeline, e:
+ # print 'EXCEPTION'
+ # print e
+ new_error = None
+
+ # DAK !!! don't need to rollback anymore!!!!
+ # we don't update self.current_pipeline until we actually
+ # get the result back
+
+ start_version = new_version
+ upgrade_version = self.vistrail.get_upgrade(new_version)
+ was_upgraded = False
+ if upgrade_version is not None:
+ try:
+ upgrade_version = int(upgrade_version)
+ if (upgrade_version in self.vistrail.actionMap and \
+ not self.vistrail.is_pruned(upgrade_version)):
+ self.current_pipeline = switch_version(upgrade_version)
+ new_version = upgrade_version
+ self.current_version = new_version
+ # print 'self.current_version:', self.current_version
+ was_upgraded = True
+ except InvalidPipeline:
+ # try to handle using the handler and create
+ # new upgrade
+ pass
+ if not was_upgraded:
+ try:
+ try:
+ (new_version, pipeline) = \
+ self.handle_invalid_pipeline(e, new_version,
+ self.vistrail,
+ report_all_errors)
+ except InvalidPipeline, e:
+ pipeline = e._pipeline
+ # check that we handled the invalid pipeline
+ # correctly
+ try:
+ self.validate(pipeline)
+ # this means that there was a new exception after handling
+ # the invalid pipeline and we should handle it again.
+ except InvalidPipeline, e:
+ (new_version, pipeline) = \
+ self.handle_invalid_pipeline(e, new_version,
+ self.vistrail,
+ report_all_errors)
+ # check that we handled the invalid pipeline
+ # correctly
+ self.validate(pipeline)
+ self.current_pipeline = pipeline
+ self.current_version = new_version
+ except InvalidPipeline, e:
+ # display invalid pipeline?
+ # import traceback
+ # traceback.print_exc()
+ new_error = e
+
+ # just do the version switch, anyway, but alert the
+ # user to the remaining issues
+ self.current_pipeline = e._pipeline
+ new_version = e._version
+ self.current_version = new_version
+
+ if new_version != start_version:
+ self.invalidate_version_tree(False)
+ if new_error is not None:
+ raise new_error
+
+ def change_selected_version(self, new_version, report_all_errors=True,
+ do_validate=True, from_root=False):
+ try:
+ self.do_version_switch(new_version, report_all_errors,
+ do_validate, from_root)
+ except InvalidPipeline, e:
+ # FIXME: do error handling through central switch that produces gui
+ # or core.debug messages as specified
+ def process_err(err):
+ if isinstance(err, Package.InitializationFailed):
+ msg = ('Package "%s" failed during initialization. '
+ 'Please contact the developer of that package '
+ 'and report a bug.' % err.package.name)
+ debug.critical(msg)
+ elif isinstance(err, MissingPackage):
+ msg = ('Cannot find package "%s" in '
+ 'list of available packages. '
+ 'Please install it first.' % err._identifier)
+ debug.critical(msg)
+ elif issubclass(err.__class__, MissingPort):
+ msg = ('Cannot find %s port "%s" for module "%s" '
+ 'in loaded package "%s". A different package '
+ 'version might be necessary.') % \
+ (err._port_type, err._port_name,
+ err._module_name, err._package_name)
+ debug.critical(msg)
+ else:
+ debug.critical(str(err))
+
+ if report_all_errors:
+ for err in e._exception_set:
+ process_err(err)
+ elif len(e._exception_set) > 0:
+ process_err(e._exception_set.__iter__().next())
+ except Exception, e:
+ import traceback
+ debug.critical(str(e), traceback.format_exc())
+
+ def write_temporary(self):
+ if self.vistrail and self.changed:
+ locator = self.get_locator()
+ if locator:
+ locator.save_temporary(self.vistrail)
+
+ def write_abstractions(self, locator, save_bundle, abstractions,
+ abs_save_dir):
+ def make_abstraction_path_unique(abs_fname, namespace):
+ # Constructs the abstraction name using the namespace to
+ # prevent conflicts and copies the abstraction to the new
+ # path so save_bundle has a valid file
+ path, prefix, absname, old_ns, suffix = \
+ parse_abstraction_name(abs_fname, True)
+ new_abs_fname = os.path.join(abs_save_dir,
+ '%s%s(%s)%s' % (prefix, absname,
+ namespace, suffix))
+ # print " $@$@$ new_abs_fname:", new_abs_fname
+ shutil.copy(abs_fname, new_abs_fname)
+ return new_abs_fname
+
+ included_abstractions = {}
+ for abstraction_list in abstractions.itervalues():
+ for abstraction in abstraction_list:
+ abs_module = abstraction.module_descriptor.module
+ namespaces = set(get_all_abs_namespaces(abstraction.vistrail))
+ if abs_module is not None:
+ abs_fname = abs_module.vt_fname
+ path, prefix, abs_name, old_ns, suffix = \
+ parse_abstraction_name(abs_fname, True)
+ # do our indexing by abstraction name
+ # we know that abstractions with different names
+ # cannot overlap, but those that have the same
+ # name may or may not
+ if abs_name not in included_abstractions:
+ included_abstractions[abs_name] = [(abstraction,
+ namespaces)]
+ else:
+ # only keep abstractions that don't repeat what
+ # others already cover
+ new_list = []
+ found = False
+ for (i_abs, i_namespaces) in \
+ included_abstractions[abs_name]:
+ if not (i_namespaces < namespaces):
+ new_list.append((i_abs, i_namespaces))
+ if i_namespaces >= namespaces:
+ found = True
+ # only add new one once
+ if not found:
+ new_list.append((abstraction, namespaces))
+ included_abstractions[abs_name] = new_list
+
+ for abs_name, abstraction_list in included_abstractions.iteritems():
+ for (abstraction, _) in abstraction_list:
+ abs_module = abstraction.module_descriptor.module
+ if abs_module is None:
+ continue
+ abs_fname = abs_module.vt_fname
+ if not os.path.exists(abs_fname):
+ # Write vistrail to disk if the file no longer
+ # exists (if temp file was deleted)
+ abs_fname = os.path.join(abs_save_dir,
+ abstraction.name + '.xml')
+ save_abstraction(abstraction.vistrail, abs_fname)
+ namespace = get_cur_abs_namespace(abstraction.vistrail)
+ abs_unique_name = make_abstraction_path_unique(abs_fname,
+ namespace)
+ save_bundle.abstractions.append(abs_unique_name)
+
+ def write_vistrail(self, locator, version=None, export=False):
+ """write_vistrail(locator,version) -> Boolean
+ It will return a boolean that tells if the tree needs to be
+ invalidated
+ export=True means you should not update the current controller"""
+ result = False
+ if self.vistrail and (self.changed or self.locator != locator):
+ # FIXME create this on-demand?
+ abs_save_dir = tempfile.mkdtemp(prefix='vt_abs')
+ is_abstraction = self.vistrail.is_abstraction
+ if is_abstraction and self.changed:
+ # first update any names if necessary
+ self.check_subpipeline_port_names()
+ new_namespace = str(uuid.uuid1())
+ annotation_key = get_next_abs_annotation_key(self.vistrail)
+ self.vistrail.set_annotation(annotation_key, new_namespace)
+ save_bundle = SaveBundle(self.vistrail.vtType)
+ if export:
+ save_bundle.vistrail = self.vistrail.do_copy()
+ if isinstance(locator, vistrails.core.db.locator.DBLocator):
+ save_bundle.vistrail.db_log_filename = None
+ else:
+ save_bundle.vistrail = self.vistrail
+ if self.log and len(self.log.workflow_execs) > 0:
+ save_bundle.log = self.log
+ abstractions = self.find_abstractions(self.vistrail, True)
+ self.write_abstractions(locator, save_bundle, abstractions,
+ abs_save_dir)
+ thumb_cache = ThumbnailCache.getInstance()
+ if thumb_cache.conf.autoSave:
+ save_bundle.thumbnails = self.find_thumbnails(
+ tags_only=thumb_cache.conf.tagsOnly)
+
+ #mashups
+ save_bundle.mashups = self._mashups
+ # FIXME hack to use db_currentVersion for convenience
+ # it's not an actual field
+ self.vistrail.db_currentVersion = self.current_version
+ if self.locator != locator:
+ # check for db log
+ log = Log()
+ if isinstance(self.locator, vistrails.core.db.locator.DBLocator):
+ connection = self.locator.get_connection()
+ db_log = open_vt_log_from_db(connection,
+ self.vistrail.db_id)
+ Log.convert(db_log)
+ for workflow_exec in db_log.workflow_execs:
+ workflow_exec.db_id = \
+ log.id_scope.getNewId(DBWorkflowExec.vtType)
+ log.db_add_workflow_exec(workflow_exec)
+ # add recent log entries
+ if self.log and len(self.log.workflow_execs) > 0:
+ for workflow_exec in self.log.db_workflow_execs:
+ workflow_exec = copy.copy(workflow_exec)
+ workflow_exec.db_id = \
+ log.id_scope.getNewId(DBWorkflowExec.vtType)
+ log.db_add_workflow_exec(workflow_exec)
+ if len(log.workflow_execs) > 0:
+ save_bundle.log = log
+ old_locator = self.get_locator()
+ if not export:
+ self.locator = locator
+ save_bundle = locator.save_as(save_bundle, version)
+ new_vistrail = save_bundle.vistrail
+ if isinstance(locator, vistrails.core.db.locator.DBLocator):
+ new_vistrail.db_log_filename = None
+ locator.kwargs['obj_id'] = new_vistrail.db_id
+ if not export:
+ # DAK don't think is necessary since we have a new
+ # namespace for an abstraction on each save
+ # Unload abstractions from old namespace
+ # self.unload_abstractions()
+ # Load all abstractions from new namespaces
+ self.ensure_abstractions_loaded(new_vistrail,
+ save_bundle.abstractions)
+ conf = get_vistrails_configuration()
+ if conf.has('runningJobsList') and conf.runningJobsList:
+ conf_jobs = conf.runningJobsList.split(';')
+ conf_jobs = [job.replace(old_locator.to_url(),
+ locator.to_url()) for job in conf_jobs]
+ conf.runningJobsList = ';'.join(conf_jobs)
+ get_vistrails_persistent_configuration(
+ ).runningJobsList = conf.runningJobsList
+ self.set_file_name(locator.name)
+ if old_locator and not export:
+ old_locator.clean_temporaries()
+ old_locator.close()
+ self.flush_pipeline_cache()
+ self.change_selected_version(new_vistrail.db_currentVersion,
+ from_root=True)
+ else:
+ save_bundle = self.locator.save(save_bundle)
+ new_vistrail = save_bundle.vistrail
+ # Load any abstractions that were given new namespaces
+ self.ensure_abstractions_loaded(new_vistrail,
+ save_bundle.abstractions)
+ # FIXME abstractions only work with FileLocators right now
+ if is_abstraction:
+ new_vistrail.is_abstraction = True
+ if isinstance(self.locator, (
+ vistrails.core.db.locator.XMLFileLocator,
+ vistrails.core.db.locator.ZIPFileLocator)):
+ filename = self.locator.name
+ if filename in self._loaded_abstractions:
+ del self._loaded_abstractions[filename]
+ # we don't know if the subworkflow should be shown
+ # if it doesn't currently exist, we don't want to add it
+ # if it does, we will replace it via upgrade module
+ # so it is not global
+ self.load_abstraction(filename, False)
+
+ # reg = core.modules.module_registry.get_module_registry()
+ # for desc in reg.get_package_by_name('local.abstractions').descriptor_list:
+ # print desc.name, desc.namespace, desc.version
+ if not export:
+ if id(self.vistrail) != id(new_vistrail):
+ new_version = new_vistrail.db_currentVersion
+ # FIXME have to figure out what to do here !!!
+ self.set_vistrail(new_vistrail, locator)
+ self.change_selected_version(new_version)
+ result = True
+ if self.log:
+ self.log.delete_all_workflow_execs()
+ self.set_changed(False)
+ locator.clean_temporaries()
+
+ # delete any temporary subworkflows
+ try:
+ for root, _, files in os.walk(abs_save_dir, topdown=False):
+ for name in files:
+ os.remove(os.path.join(root, name))
+ os.rmdir(abs_save_dir)
+ except OSError, e:
+ raise VistrailsDBException("Can't remove %s: %s" % \
+ (abs_save_dir, str(e)))
+ return result
+
+
+ def write_workflow(self, locator):
+ if self.current_pipeline:
+ pipeline = Pipeline()
+ # pipeline.set_abstraction_map(self.vistrail.abstractionMap)
+ for module in self.current_pipeline.modules.itervalues():
+ # if module.vtType == AbstractionModule.vtType:
+ # abstraction = \
+ # pipeline.abstraction_map[module.abstraction_id]
+ # pipeline.add_abstraction(abstraction)
+ pipeline.add_module(module)
+ for connection in self.current_pipeline.connections.itervalues():
+ pipeline.add_connection(connection)
+ save_bundle = SaveBundle(pipeline.vtType,workflow=pipeline)
+ locator.save_as(save_bundle)
+
+ def write_log(self, locator):
+ if self.log:
+ if self.vistrail.db_log_filename is not None:
+ log = vistrails.core.db.io.merge_logs(self.log,
+ self.vistrail.db_log_filename)
+ else:
+ log = self.log
+ #print log
+ save_bundle = SaveBundle(log.vtType,log=log)
+ locator.save_as(save_bundle)
+
+ def read_log(self):
+ """ Returns the saved log from zip or DB
+
+ """
+ return self.vistrail.get_persisted_log()
+
+ def write_registry(self, locator):
+ registry = vistrails.core.modules.module_registry.get_module_registry()
+ save_bundle = SaveBundle(registry.vtType, registry=registry)
+ locator.save_as(save_bundle)
+
+ def update_checkout_version(self, app=''):
+ self.vistrail.update_checkout_version(app)
+
+ def reset_redo_stack(self):
+ self.redo_stack = []
+
+ def undo(self):
+ """Performs one undo step, moving up the version tree."""
+ action_map = self.vistrail.actionMap
+ old_action = action_map.get(self.current_version, None)
+ self.redo_stack.append(self.current_version)
+ self.show_parent_version()
+ new_action = action_map.get(self.current_version, None)
+ return (old_action, new_action)
+ # self.set_pipeline_selection(old_action, new_action, 'undo')
+ # return self.current_version
+
+ def redo(self):
+ """Performs one redo step if possible, moving down the version tree."""
+ action_map = self.vistrail.actionMap
+ old_action = action_map.get(self.current_version, None)
+ if len(self.redo_stack) < 1:
+ debug.critical("Redo on an empty redo stack. Ignoring.")
+ return
+ next_version = self.redo_stack[-1]
+ self.redo_stack = self.redo_stack[:-1]
+ self.show_child_version(next_version)
+ new_action = action_map[self.current_version]
+ return (old_action, new_action)
+ # self.set_pipeline_selection(old_action, new_action, 'redo')
+ # return next_version
+
+ def can_redo(self):
+ return (len(self.redo_stack) > 0)
+
+ def can_undo(self):
+ return self.current_version > 0
+
+ def layout_modules(self, old_modules=[], preserve_order=False,
+ new_modules=[], new_connections=[], module_size_func=None, no_gaps=False):
+ """Lays out modules and returns the new version.
+
+ If old_modules are not specified, all modules in current pipeline are used.
+ If preserve_order is True, modules in each row will be ordered based on
+ their current x value
+ new_modules ignore preserve_order, and don't need exist yet in the pipeline
+ new_connections associated with new_modules
+ module_size_func is used to determine size of a module. It takes a
+ vistrails.core.layout.workflow_layout.Module object and returns a (width, height)
+ tuple.
+ If no_gaps is True, all connected modules will be at most 1 layer above or
+ below their child or parent respectively
+ """
+
+ #fixes issue when opening old vistrails that needs upgrade
+ self.flush_delayed_actions()
+
+ action_list = self.layout_modules_ops(old_modules, preserve_order,
+ new_modules, new_connections, module_size_func, no_gaps)
+ if(len(action_list) > 0):
+ action = vistrails.core.db.action.create_action(action_list)
+ self.add_new_action(action)
+ version = self.perform_action(action)
+ self.change_selected_version(version)
+ return version
+ return self.current_version
+
+ def layout_modules_ops(self, old_modules=[], preserve_order=False,
+ new_modules=[], new_connections=[], module_size_func=None, no_gaps=False):
+ """Returns operations needed to layout the modules.
+
+ If old_modules are not specified, all modules in current pipeline are used.
+ If preserve_order is True, modules in each row will be ordered based on
+ their current x value
+ new_modules ignore preserve_order, and don't need exist yet in the pipeline
+ new_connections associated with new_modules
+ module_size_func is used to determine size of a module. It takes a
+ vistrails.core.layout.workflow_layout.Module object and returns a (width, height)
+ tuple.
+ If no_gaps is True, all connected modules will be at most 1 layer above or
+ below their child or parent respectively
+ """
+
+ connected_input_ports = set(
+ c.destination.spec for c in self.current_pipeline.connection_list)
+ connected_input_ports.update(
+ c.destination.spec for c in new_connections)
+ connected_output_ports = set(
+ c.source.spec for c in self.current_pipeline.connection_list)
+ connected_output_ports.update(
+ c.source.spec for c in new_connections)
+ connected_ports = connected_input_ports | connected_output_ports
+
+ def get_visible_port_names(port_list, visible_ports):
+ output_list = []
+ visible_list = []
+ for i, p in enumerate(port_list):
+ if not p.optional:
+ output_list.append(p.name)
+ elif p.name in visible_ports or p in connected_ports:
+ visible_list.append(p.name)
+ output_list.extend(visible_list)
+ return output_list
+
+ if not old_modules or len(old_modules) == 0:
+ old_modules = self.current_pipeline.modules.values()
+
+ #create layout objects
+ layoutPipeline = LayoutPipeline()
+
+ module_info = {} # {id: (module, layoutModule, in_port_names=[], out_port_names=[])}
+
+ #add modules to layout, and find their visible ports
+ def _add_layout_module(module, prev_x):
+ in_ports = get_visible_port_names(module.destinationPorts(),
+ module.visible_input_ports)
+ out_ports = get_visible_port_names(module.sourcePorts(),
+ module.visible_output_ports)
+
+ layoutModule = layoutPipeline.createModule(module.id,
+ module.name,
+ len(in_ports),
+ len(out_ports),
+ prev_x)
+
+ module_info[module.id] = (module, layoutModule, in_ports, out_ports)
+
+ for module in old_modules:
+ _add_layout_module(module, module.location.x)
+
+ for module in new_modules:
+ _add_layout_module(module, None)
+
+ #add connections to layout
+ old_ids = [module.id for module in old_modules]
+ old_conns = self.get_connections_to(self.current_pipeline, old_ids)
+ for conn in old_conns + new_connections:
+ if conn.source.moduleId in module_info:
+ layoutPipeline.createConnection(
+ module_info[conn.source.moduleId][1],
+ module_info[conn.source.moduleId][3].index(conn.source.name),
+ module_info[conn.destination.moduleId][1],
+ module_info[conn.destination.moduleId][2].index(conn.destination.name))
+
+ #set default module size function if needed
+ paddedPortWidth = self.layoutTheme.PORT_WIDTH + self.layoutTheme.MODULE_PORT_SPACE
+ def estimate_module_size(module):
+ width = max(len(module.name)*6 + self.layoutTheme.MODULE_LABEL_MARGIN[0] + self.layoutTheme.MODULE_LABEL_MARGIN[1],
+ len(module_info[module.shortname][2]) * paddedPortWidth + self.layoutTheme.MODULE_PORT_PADDED_SPACE,
+ len(module_info[module.shortname][3]) * paddedPortWidth + self.layoutTheme.MODULE_PORT_PADDED_SPACE)
+ height = LayoutDefaults.u * 5 #todo, fix these sizes
+ return (width, height)
+ if module_size_func is None:
+ module_size_func = estimate_module_size
+
+ workflowLayout = WorkflowLayout(layoutPipeline,
+ module_size_func,
+ self.layoutTheme.MODULE_PORT_MARGIN,
+ (self.layoutTheme.PORT_WIDTH, self.layoutTheme.PORT_HEIGHT),
+ self.layoutTheme.MODULE_PORT_SPACE)
+
+ #do layout with layer x and y separation of 50
+ workflowLayout.run_all(50,50,preserve_order,no_gaps)
+
+ #maintain center
+ center_x, center_y = self.get_avg_location([item[0] for item in module_info.values()])
+ new_center_x = sum([m.layout_pos.x for m in layoutPipeline.modules]) / len(layoutPipeline.modules)
+ new_center_y = -sum([m.layout_pos.y for m in layoutPipeline.modules]) / len(layoutPipeline.modules)
+ offset_x = center_x - new_center_x
+ offset_y = center_y - new_center_y
+
+ #generate module move list
+ moves = []
+ for (module, layoutModule, _, _) in module_info.values():
+ new_x = layoutModule.layout_pos.x+offset_x
+ new_y = -layoutModule.layout_pos.y+offset_y
+ if module.id in self.current_pipeline.modules:
+ moves.append((module.id, new_x, new_y))
+ else:
+ #module doesn't exist in pipeline yet, just change x,y
+ module.location.x = new_x
+ module.location.y = new_y
+
+ #return module move operations
+ return self.move_modules_ops(moves)
+
+
diff --git a/vistrails/core/vistrail/group.py b/vistrails/core/vistrail/group.py
new file mode 100644
index 0000000..7a74879
--- /dev/null
+++ b/vistrails/core/vistrail/group.py
@@ -0,0 +1,344 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from itertools import izip
+
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.vistrail.location import Location
+from vistrails.core.vistrail.module import Module
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.port_spec import PortSpec, PortEndPoint
+from vistrails.db.domain import DBGroup
+
+from vistrails.core.utils import NoSummon, VistrailsInternalError, report_stack
+from vistrails.core.modules.basic_modules import identifier as basic_pkg, \
+ version as basic_pkg_version
+import vistrails.core.modules.sub_module
+import vistrails.core.modules.module_registry
+from vistrails.core.modules.module_registry import get_module_registry, ModuleRegistry
+
+import unittest
+from vistrails.db.domain import IdScope
+
+class Group(DBGroup, Module):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ if 'pipeline' in kwargs:
+ kwargs['workflow'] = kwargs['pipeline']
+ del kwargs['pipeline']
+ DBGroup.__init__(self, *args, **kwargs)
+ if self.cache is None:
+ self.cache = 1
+ if self.id is None:
+ self.id = -1
+ if self.location is None:
+ self.location = Location(x=-1.0, y=-1.0)
+ if self.name is None:
+ self.name = ''
+ if self.package is None:
+ self.package = ''
+ if self.version is None:
+ self.version = ''
+ self.set_defaults()
+
+ def set_defaults(self, other=None):
+ Module.set_defaults(self, other)
+
+ def setup_indices(self):
+ # delay this until needed (on materialize)
+ self._port_specs = None
+ self._port_specs_id_index = None
+ # self.make_port_specs()
+
+ def __copy__(self):
+ return Group.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroup.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Group
+ cp.set_defaults(self)
+ return cp
+
+ @staticmethod
+ def convert(_group):
+ if _group.__class__ == Group:
+ return
+ _group.__class__ = Group
+ if _group.db_location:
+ Location.convert(_group.db_location)
+ if _group.db_workflow:
+ from vistrails.core.vistrail.pipeline import Pipeline
+ Pipeline.convert(_group.db_workflow)
+ for _function in _group.db_functions:
+ ModuleFunction.convert(_function)
+ for _annotation in _group.db_get_annotations():
+ Annotation.convert(_annotation)
+ _group.set_defaults()
+
+ ##########################################################################
+ # Properties
+
+ # We need to repeat these here because Module uses DBModule. ...
+ id = DBGroup.db_id
+ cache = DBGroup.db_cache
+ annotations = DBGroup.db_annotations
+ location = DBGroup.db_location
+ center = DBGroup.db_location
+ # version = DBGroup.db_version
+ # name = DBGroup.db_name
+ # label = DBGroup.db_name
+ # namespace = DBGroup.db_namespace
+ # package = DBGroup.db_package
+
+ name = 'Group'
+ label = 'Group'
+ package = basic_pkg
+ namespace = None
+ version = basic_pkg_version
+ internal_version = ''
+
+ def summon(self):
+ result = self.module_descriptor.module()
+ result.pipeline = self.pipeline
+ if self._port_specs is None:
+ self.make_port_specs()
+ result.input_remap = self._input_remap
+ result.output_remap = self._output_remap
+ if self.cache != 1:
+ result.is_cacheable = lambda *args: False
+ if hasattr(result, 'input_ports_order'):
+ result.input_ports_order = [p.name for p in self.destinationPorts()]
+ if hasattr(result, 'output_ports_order'):
+ result.output_ports_order = [p.name for p in self.sourcePorts()]
+ result.registry = get_module_registry()
+ return result
+
+ def is_group(self):
+ return True
+
+ def _get_pipeline(self):
+ return self.db_workflow
+ def _set_pipeline(self, pipeline):
+ self.db_workflow = pipeline
+ self.setup_indices()
+ pipeline = property(_get_pipeline, _set_pipeline)
+ workflow = pipeline
+
+ # override these from the Module class with defaults
+ # these are "local" port_specs, but Group's are "registry"
+ def _get_port_specs(self):
+ if self._port_specs_id_index is None:
+ if self._port_specs is None:
+ self.make_port_specs()
+ self._port_specs_id_index = {}
+ self._port_specs_id_index = \
+ dict([(p.id, p) for p in self._port_specs.itervalues()])
+ return self._port_specs_id_index
+ port_specs = property(_get_port_specs)
+
+ def _get_port_spec_list(self):
+ if self._port_specs is None:
+ self.make_port_specs()
+ return self._port_specs.values()
+ port_spec_list = property(_get_port_spec_list)
+
+ def has_portSpec_with_name(self, name):
+ if self._port_specs is None:
+ self.make_port_specs()
+ return name in self._port_specs
+
+ def get_portSpec_by_name(self, name):
+ if self._port_specs is None:
+ self.make_port_specs()
+ if name in self._port_specs:
+ return self._port_specs[name]
+ return None
+
+ def add_port_spec(self, spec):
+ # operate on self._port_specs instead of db level
+ if self._port_specs is None:
+ self.make_port_specs()
+ self._port_specs[(spec.name, spec.type)] = spec
+ self.port_specs[spec.id] = spec
+ if spec.type == 'input':
+ self._input_port_specs.append(spec)
+ elif spec.type == 'output':
+ self._output_port_specs.append(spec)
+ def delete_port_spec(self, spec):
+ if spec.type == 'input':
+ self._input_port_specs.remove(spec)
+ elif spec.type == 'output':
+ self._output_port_specs.remove(spec)
+ # operate on self._port_specs instead of db level
+ del self._port_specs[(spec.name, spec.type)]
+ del self.port_specs[spec.id]
+
+ def _get_input_port_specs(self):
+ if self._port_specs is None:
+ self.make_port_specs()
+ return Module._get_input_port_specs(self)
+ input_port_specs = property(_get_input_port_specs)
+ def _get_output_port_specs(self):
+ if self._port_specs is None:
+ self.make_port_specs()
+ return Module._get_output_port_specs(self)
+ output_port_specs = property(_get_output_port_specs)
+
+ def get_port_spec_info(self, module):
+ return vistrails.core.modules.sub_module.get_port_spec_info(self.pipeline,
+ module)
+
+ def make_port_specs(self):
+ self._port_specs = {}
+ self._input_port_specs = []
+ self._output_port_specs = []
+ self._input_remap = {}
+ self._output_remap = {}
+ if self.pipeline is None:
+ return
+
+ registry = get_module_registry()
+ for module in self.pipeline.module_list:
+ if module.name == 'OutputPort' and module.package == basic_pkg:
+ (port_name, sigstring, optional, _) = \
+ self.get_port_spec_info(module)
+ port_spec = registry.create_port_spec(port_name, 'output',
+ None, sigstring,
+ optional)
+ self._port_specs[(port_name, 'output')] = port_spec
+ self._output_port_specs.append(port_spec)
+ self._output_remap[port_name] = module
+ elif module.name == 'InputPort' and module.package == basic_pkg:
+ (port_name, sigstring, optional, _) = \
+ self.get_port_spec_info(module)
+ port_spec = registry.create_port_spec(port_name, 'input',
+ None, sigstring,
+ optional)
+ self._port_specs[(port_name, 'input')] = port_spec
+ self._input_port_specs.append(port_spec)
+ self._input_remap[port_name] = module
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of an
+ GroupModule object.
+
+ """
+ rep = '<group id="%s">'
+ rep += str(self.location)
+ rep += str(self.functions)
+ rep += str(self.annotations)
+ rep += '</group>'
+ return rep % str(self.id)
+
+ def __eq__(self, other):
+ """ __eq__(other: GroupModule) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(other) != type(self):
+ return False
+ if self.location != other.location:
+ return False
+ if len(self.functions) != len(other.functions):
+ return False
+ if len(self.annotations) != len(other.annotations):
+ return False
+ for f,g in izip(self.functions, other.functions):
+ if f != g:
+ return False
+ for f,g in izip(self.annotations, other.annotations):
+ if f != g:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+
+################################################################################
+# Testing
+
+
+class TestGroup(unittest.TestCase):
+
+ def create_group(self, id_scope=IdScope()):
+ from vistrails.core.vistrail.location import Location
+ from vistrails.core.vistrail.module_function import ModuleFunction
+ from vistrails.core.vistrail.module_param import ModuleParam
+
+ params = [ModuleParam(id=id_scope.getNewId(ModuleParam.vtType),
+ type='Int',
+ val='1')]
+ functions = [ModuleFunction(id=id_scope.getNewId(ModuleFunction.vtType),
+ name='value',
+ parameters=params)]
+ location = Location(id=id_scope.getNewId(Location.vtType),
+ x=12.342,
+ y=-19.432)
+ module = \
+ Group(id=id_scope.getNewId(Group.vtType),
+ location=location,
+ functions=functions,
+ )
+ return module
+
+ def test_copy(self):
+ """Check that copy works correctly"""
+
+ id_scope = IdScope()
+ m1 = self.create_group(id_scope)
+ m2 = copy.copy(m1)
+ self.assertEquals(m1, m2)
+ self.assertEquals(m1.id, m2.id)
+ m3 = m1.do_copy(True, id_scope, {})
+ self.assertEquals(m1, m3)
+ self.assertNotEquals(m1.id, m3.id)
+
+ def test_serialization(self):
+ """ Check that serialize and unserialize are working properly """
+ import vistrails.core.db.io
+
+ m1 = self.create_group()
+ xml_str = vistrails.core.db.io.serialize(m1)
+ m2 = vistrails.core.db.io.unserialize(xml_str, Group)
+ self.assertEquals(m1, m2)
+ self.assertEquals(m1.id, m2.id)
diff --git a/vistrails/core/vistrail/location.py b/vistrails/core/vistrail/location.py
new file mode 100644
index 0000000..de71bd1
--- /dev/null
+++ b/vistrails/core/vistrail/location.py
@@ -0,0 +1,199 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.data_structures.point import Point
+from vistrails.db.domain import DBLocation
+
+import unittest
+import copy
+import random
+from vistrails.db.domain import IdScope
+import vistrails.core
+
+class Location(DBLocation, Point):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBLocation.__init__(self, *args, **kwargs)
+ if self.id is None:
+ self.id = -1
+
+ def __copy__(self):
+ return Location.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Location
+ return cp
+
+ ##########################################################################
+ # DB Conversion
+
+ @staticmethod
+ def convert(_location):
+ _location.__class__ = Location
+
+ ##########################################################################
+ # Properties
+
+ id = DBLocation.db_id
+ x = DBLocation.db_x
+ y = DBLocation.db_y
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of an Annotation
+ object.
+
+ """
+ rep = "<location id=%s x=%s y=%s/>"
+ return rep % (str(self.id), str(self.x), str(self.y))
+
+
+ eq_delta = 0.0001
+ def __eq__(self, other):
+ """ __eq__(other: Location) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(other) != type(self):
+ return False
+ # Skip property lookup for performance
+ return ((self._db_x - other._db_x) ** 2 +
+ (self._db_y - other._db_y)) ** 2 < 1e-8
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+ def __neg__(self):
+ """ __neg__() -> Location
+ Compute a point p such that: self + p == Location(0,0),
+ and return a Location
+
+ """
+ return Location(x=-self.db_x,y=-self.db_y)
+
+ def __add__(self, other):
+ """ __add__(other: Location) -> Location
+ Returns a point p such that: self + other == p, and return a Location
+
+ """
+ return Location(x=(self.db_x + other.db_x), y=(self.db_y + other.db_y))
+
+ def __sub__(self, other):
+ """ __sub__(other: Location) -> Location
+ Returns a point p such that: self - other == p, and return a Location
+
+ """
+ return Location(x=(self.db_x - other.db_x), y=(self.db_y - other.db_y))
+
+ def __mul__(self, other):
+ """ __mul__(other: float) -> Location
+ Interprets self as a vector to perform a scalar multiplication and
+ return a Location
+
+ """
+ return Location(x=(self.db_x * other), y=(self.db_y * other))
+
+ def __rmul__(self, other):
+ """ __rmul__(other: float) -> Location
+ Interprets self as a vector to perform a scalar multiplication and
+ return a Location
+
+ """
+ return Location(x=(self.db_x * other), y=(self.db_y * other))
+
+################################################################################
+# Testing
+
+
+class TestLocation(unittest.TestCase):
+
+ @staticmethod
+ def assert_double_equals(a, b, eps = 0.00001):
+ assert abs(a-b) < eps
+
+ def create_location(self, id_scope=IdScope()):
+ location = Location(id=id_scope.getNewId(Location.vtType),
+ x=12.34567,
+ y=14.65431)
+ return location
+
+ def test_copy(self):
+ id_scope = IdScope()
+
+ loc1 = self.create_location(id_scope)
+ loc2 = copy.copy(loc1)
+ self.assertEquals(loc1, loc2)
+ self.assertEquals(loc1.id, loc2.id)
+ loc3 = loc1.do_copy(True, id_scope, {})
+ self.assertEquals(loc1, loc3)
+ self.assertNotEquals(loc1.id, loc3.id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ loc1 = self.create_location()
+ xml_str = vistrails.core.db.io.serialize(loc1)
+ loc2 = vistrails.core.db.io.unserialize(xml_str, Location)
+ self.assertEquals(loc1, loc2)
+ self.assertEquals(loc1.id, loc2.id)
+
+ def test_add_length(self):
+ """Uses triangle inequality to exercise add and length"""
+ for i in xrange(100):
+ x = Location(x=random.uniform(-1.0, 1.0), y=random.uniform(-1.0, 1.0))
+ y = Location(x=random.uniform(-1.0, 1.0), y=random.uniform(-1.0, 1.0))
+ assert (x+y).length() <= x.length() + y.length()
+
+ def test_mul_length(self):
+ """Uses vector space properties to exercise mul, rmul and length"""
+ for i in xrange(100):
+ x = Location(x=random.uniform(-1.0, 1.0), y=random.uniform(-1.0, 1.0))
+ s = random.uniform(0.0, 10.0)
+ self.assert_double_equals(s * x.length(), (s * x).length())
+ self.assert_double_equals(s * x.length(), (x * s).length())
+
+ def test_comparison_operators(self):
+ """ Test comparison operators """
+ a = Location(x=0, y=1)
+ b = Location(x=0, y=1)
+ assert a == b
+ assert a != None
+ b = Location(x=0, y=0.1)
+ assert a != b
diff --git a/vistrails/core/vistrail/module.py b/vistrails/core/vistrail/module.py
new file mode 100644
index 0000000..3360e14
--- /dev/null
+++ b/vistrails/core/vistrail/module.py
@@ -0,0 +1,526 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# Check for testing
+""" This module defines the class Module
+"""
+import copy
+from itertools import izip
+import weakref
+
+from vistrails.db.domain import DBModule
+from vistrails.core.data_structures.point import Point
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.vistrail.location import Location
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.port import Port, PortEndPoint
+from vistrails.core.vistrail.port_spec import PortSpec
+from vistrails.core.utils import NoSummon, VistrailsInternalError, report_stack
+from vistrails.core.modules.module_descriptor import OverloadedPort
+from vistrails.core.modules.module_registry import get_module_registry, ModuleRegistry
+
+import unittest
+import vistrails.core
+
+################################################################################
+
+# A Module stores not only the information, but a method (summon) that
+# creates a 'live' object, subclass of core/modules/vistrail_module/Module
+
+class Module(DBModule):
+ """ Represents a module from a Pipeline """
+
+ ##########################################################################
+ # Constructor and copy
+
+ def __init__(self, *args, **kwargs):
+ DBModule.__init__(self, *args, **kwargs)
+ if self.cache is None:
+ self.cache = 1
+ if self.id is None:
+ self.id = -1
+ if self.location is None:
+ self.location = Location(x=-1.0, y=-1.0)
+ if self.name is None:
+ self.name = ''
+ if self.package is None:
+ self.package = ''
+ if self.version is None:
+ self.version = ''
+ self.set_defaults()
+
+ def set_defaults(self, other=None):
+ if other is None:
+ self.portVisible = set()
+ self.visible_input_ports = set()
+ self.visible_output_ports = set()
+ self.connected_input_ports = {}
+ self.connected_output_ports = {}
+ self.is_valid = False
+ self.is_breakpoint = False
+ self.is_watched = False
+ self._descriptor_info = None
+ self._module_descriptor = None
+ else:
+ self.portVisible = copy.copy(other.portVisible)
+ self.visible_input_ports = copy.copy(other.visible_input_ports)
+ self.visible_output_ports = copy.copy(other.visible_output_ports)
+ self.connected_input_ports = copy.copy(other.connected_input_ports)
+ self.connected_output_ports = \
+ copy.copy(other.connected_output_ports)
+ self.is_valid = other.is_valid
+ self.is_breakpoint = other.is_breakpoint
+ self.is_watched = other.is_watched
+ self._descriptor_info = None
+ self._module_descriptor = other._module_descriptor
+ if not self.namespace:
+ self.namespace = None
+ self.function_idx = self.db_functions_id_index
+ self.setup_indices()
+
+ def setup_indices(self):
+ self._input_port_specs = []
+ self._output_port_specs = []
+ for port_spec in self.port_spec_list:
+ if port_spec.type == 'input':
+ self._input_port_specs.append(port_spec)
+ elif port_spec.type == 'output':
+ self._output_port_specs.append(port_spec)
+
+ def __copy__(self):
+ """__copy__() -> Module - Returns a clone of itself"""
+ return Module.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Module
+ cp.set_defaults(self)
+ return cp
+
+ @staticmethod
+ def convert(_module):
+ if _module.__class__ == Module:
+ return
+ _module.__class__ = Module
+ for _port_spec in _module.db_portSpecs:
+ PortSpec.convert(_port_spec)
+ if _module.db_location:
+ Location.convert(_module.db_location)
+ for _function in _module.db_functions:
+ ModuleFunction.convert(_function)
+ for _annotation in _module.db_get_annotations():
+ Annotation.convert(_annotation)
+ _module.set_defaults()
+
+ ##########################################################################
+ # CONSTANTS
+
+ VISTRAIL_VAR_ANNOTATION = '__vistrail_var__'
+
+ ##########################################################################
+
+ id = DBModule.db_id
+ cache = DBModule.db_cache
+ annotations = DBModule.db_annotations
+ location = DBModule.db_location
+ center = DBModule.db_location
+ name = DBModule.db_name
+ label = DBModule.db_name
+ namespace = DBModule.db_namespace
+ package = DBModule.db_package
+ version = DBModule.db_version
+ port_spec_list = DBModule.db_portSpecs
+ internal_version = ''
+
+ # type check this (list, hash)
+ def _get_functions(self):
+ self.db_functions.sort(key=lambda x: x.db_pos)
+ return self.db_functions
+ def _set_functions(self, functions):
+ # want to convert functions to hash...?
+ self.db_functions = functions
+ functions = property(_get_functions, _set_functions)
+ def add_function(self, function):
+ self.db_add_function(function)
+ def has_function_with_real_id(self, f_id):
+ return self.db_has_function_with_id(f_id)
+ def get_function_by_real_id(self, f_id):
+ return self.db_get_function_by_id(f_id)
+
+ def add_annotation(self, annotation):
+ self.db_add_annotation(annotation)
+ def delete_annotation(self, annotation):
+ self.db_delete_annotation(annotation)
+ def has_annotation_with_key(self, key):
+ return self.db_has_annotation_with_key(key)
+ def get_annotation_by_key(self, key):
+ return self.db_get_annotation_by_key(key)
+ def toggle_breakpoint(self):
+ self.is_breakpoint = not self.is_breakpoint
+ def toggle_watched(self):
+ self.is_watched = not self.is_watched
+
+ def is_vistrail_var(self):
+ return self.has_annotation_with_key(Module.VISTRAIL_VAR_ANNOTATION)
+ def get_vistrail_var(self):
+ return self.get_annotation_by_key(Module.VISTRAIL_VAR_ANNOTATION).value
+
+ def _get_port_specs(self):
+ return self.db_portSpecs_id_index
+ port_specs = property(_get_port_specs)
+ def has_portSpec_with_name(self, name):
+ return self.db_has_portSpec_with_name(name)
+ def get_portSpec_by_name(self, name):
+ return self.db_get_portSpec_by_name(name)
+ def add_port_spec(self, spec):
+ DBModule.db_add_portSpec(self, spec)
+ if spec.type == 'input':
+ self._input_port_specs.append(spec)
+ elif spec.type == 'output':
+ self._output_port_specs.append(spec)
+ # override DBModule.db_add_portSpec so that _*_port_specs are updated
+ db_add_portSpec = add_port_spec
+ def delete_port_spec(self, spec):
+ if spec.type == 'input':
+ self._input_port_specs.remove(spec)
+ elif spec.type == 'output':
+ self._output_port_specs.remove(spec)
+ DBModule.db_delete_portSpec(self, spec)
+ # override DBModule.db_delete_portSpec so that _*_port_specs are updated
+ db_delete_portSpec = delete_port_spec
+
+ def _get_input_port_specs(self):
+ return sorted(self._input_port_specs,
+ key=lambda x: (x.sort_key, x.id))
+ input_port_specs = property(_get_input_port_specs)
+ def _get_output_port_specs(self):
+ return sorted(self._output_port_specs,
+ key=lambda x: (x.sort_key, x.id), reverse=True)
+ output_port_specs = property(_get_output_port_specs)
+
+ def _get_descriptor_info(self):
+ if self._descriptor_info is None:
+ self._descriptor_info = (self.package, self.name,
+ self.namespace, self.version,
+ str(self.internal_version))
+ return self._descriptor_info
+ descriptor_info = property(_get_descriptor_info)
+
+ def _get_module_descriptor(self):
+ if self._module_descriptor is None or \
+ self._module_descriptor() is None:
+ reg = get_module_registry()
+ self._module_descriptor = \
+ weakref.ref(reg.get_descriptor_by_name(*self.descriptor_info))
+ return self._module_descriptor()
+ def _set_module_descriptor(self, descriptor):
+ self._module_descriptor = weakref.ref(descriptor)
+ module_descriptor = property(_get_module_descriptor,
+ _set_module_descriptor)
+
+ def get_port_spec(self, port_name, port_type):
+ """get_port_spec(port_name: str, port_type: str: ['input' | 'output'])
+ -> PortSpec
+
+ """
+ if self.has_portSpec_with_name((port_name, port_type)):
+ return self.get_portSpec_by_name((port_name, port_type))
+ desc = self.module_descriptor
+ reg = get_module_registry()
+ return reg.get_port_spec_from_descriptor(desc, port_name, port_type)
+
+ def has_port_spec(self, port_name, port_type):
+ if self.has_portSpec_with_name((port_name, port_type)):
+ return True
+ reg = get_module_registry()
+ desc = self.module_descriptor
+ return reg.has_port_spec_from_descriptor(desc, port_name, port_type)
+
+ def summon(self):
+ result = self.module_descriptor.module()
+ if self.cache != 1:
+ result.is_cacheable = lambda *args: False
+ if hasattr(result, 'input_ports_order'):
+ result.input_ports_order = [p.name for p in self.input_port_specs]
+ if hasattr(result, 'output_ports_order'):
+ result.output_ports_order = [p.name for p in self.output_port_specs]
+ # output_ports are reversed for display purposes...
+ result.output_ports_order.reverse()
+ # FIXME this may not be quite right because we don't have self.registry
+ # anymore. That said, I'm not sure how self.registry would have
+ # worked for hybrids...
+ result.registry = get_module_registry()
+ return result
+
+ def is_group(self):
+ return False
+ def is_abstraction(self):
+ return False
+
+ def getNumFunctions(self):
+ """getNumFunctions() -> int - Returns the number of functions """
+ return len(self.functions)
+
+ def sourcePorts(self):
+ """sourcePorts() -> list of Port
+ Returns list of source (output) ports module supports.
+
+ """
+ registry = get_module_registry()
+ desc = self.module_descriptor
+ ports = registry.module_source_ports_from_descriptor(True, desc)
+ ports.extend(self.output_port_specs)
+ return ports
+
+ def destinationPorts(self):
+ """destinationPorts() -> list of Port
+ Returns list of destination (input) ports module supports
+
+ """
+ registry = get_module_registry()
+ desc = self.module_descriptor
+ ports = registry.module_destination_ports_from_descriptor(True, desc)
+ ports.extend(self.input_port_specs)
+ return ports
+
+ ##########################################################################
+ # Debugging
+
+ def show_comparison(self, other):
+ if type(other) != type(self):
+ print "Type mismatch"
+ print type(self), type(other)
+ elif self.id != other.id:
+ print "id mismatch"
+ print self.id, other.id
+ elif self.name != other.name:
+ print "name mismatch"
+ print self.name, other.name
+ elif self.cache != other.cache:
+ print "cache mismatch"
+ print self.cache, other.cache
+ elif self.location != other.location:
+ print "location mismatch"
+ # FIXME Location has no show_comparison
+ # self.location.show_comparison(other.location)
+ elif len(self.functions) != len(other.functions):
+ print "function length mismatch"
+ print len(self.functions), len(other.functions)
+ else:
+ for f, g in izip(self.functions, other.functions):
+ if f != g:
+ print "function mismatch"
+ f.show_comparison(g)
+ return
+ print "No difference found"
+ assert self == other
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str Returns a string representation of itself. """
+ def get_name():
+ if self.namespace:
+ return self.namespace + '|' + self.name
+ return self.name
+ return ("(Module '%s:%s' id=%s functions:%s port_specs:%s annotations:%s)@%X" %
+ (self.package,
+ get_name(),
+ self.id,
+ [str(f) for f in self.functions],
+ [str(port_spec) for port_spec in self.db_portSpecs],
+ [str(a) for a in self.annotations],
+ id(self)))
+
+ def __eq__(self, other):
+ """ __eq__(other: Module) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(other) != type(self):
+ return False
+ if self.name != other.name:
+ return False
+ if self.namespace != other.namespace:
+ return False
+ if self.package != other.package:
+ return False
+ if self.cache != other.cache:
+ return False
+ if self.location != other.location:
+ return False
+ if len(self.functions) != len(other.functions):
+ return False
+ if len(self.annotations) != len(other.annotations):
+ return False
+ for f, g in izip(self.functions, other.functions):
+ if f != g:
+ return False
+ for f, g in izip(self.annotations, other.annotations):
+ if f != g:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+ ##########################################################################
+ # Properties
+
+
+################################################################################
+# Testing
+
+
+class TestModule(unittest.TestCase):
+
+ def create_module(self, id_scope=None):
+ from vistrails.core.modules.basic_modules import identifier as basic_pkg
+ from vistrails.db.domain import IdScope
+ if id_scope is None:
+ id_scope = IdScope()
+
+ params = [ModuleParam(id=id_scope.getNewId(ModuleParam.vtType),
+ type='Int',
+ val='1')]
+ functions = [ModuleFunction(id=id_scope.getNewId(ModuleFunction.vtType),
+ name='value',
+ parameters=params)]
+ module = Module(id=id_scope.getNewId(Module.vtType),
+ name='Float',
+ package=basic_pkg,
+ functions=functions)
+ return module
+
+ def test_copy(self):
+ """Check that copy works correctly"""
+ from vistrails.db.domain import IdScope
+
+ id_scope = IdScope()
+ m1 = self.create_module(id_scope)
+ m2 = copy.copy(m1)
+ self.assertEquals(m1, m2)
+ self.assertEquals(m1.id, m2.id)
+ m3 = m1.do_copy(True, id_scope, {})
+ self.assertEquals(m1, m3)
+ self.assertNotEquals(m1.id, m3.id)
+
+ def test_serialization(self):
+ """ Check that serialize and unserialize are working properly """
+ import vistrails.core.db.io
+
+ m1 = self.create_module()
+ xml_str = vistrails.core.db.io.serialize(m1)
+ m2 = vistrails.core.db.io.unserialize(xml_str, Module)
+ self.assertEquals(m1, m2)
+ self.assertEquals(m1.id, m2.id)
+
+ def testEq(self):
+ """Check correctness of equality operator."""
+ x = Module()
+ self.assertNotEquals(x, None)
+
+ def testAccessors(self):
+ """Check that accessors are working."""
+ x = Module()
+ self.assertEquals(x.id, -1)
+ x.id = 10
+ self.assertEquals(x.id, 10)
+ self.assertEquals(x.cache, 1)
+ x.cache = 1
+ self.assertEquals(x.cache, 1)
+ self.assertEquals(x.location.x, -1.0)
+ x.location = Location(x=1, y=x.location.y)
+ self.assertEquals(x.location.x, 1)
+ self.assertEquals(x.name, "")
+
+ def testSummonModule(self):
+ """Check that summon creates a correct module"""
+ from vistrails.core.modules.basic_modules import identifier as basic_pkg
+
+ x = Module()
+ x.name = "String"
+ x.package = basic_pkg
+ try:
+ registry = get_module_registry()
+ c = x.summon()
+ m = registry.get_descriptor_by_name(basic_pkg, 'String').module
+ assert isinstance(c, m)
+ except NoSummon:
+ msg = "Expected to get a String object, got a NoSummon exception"
+ self.fail(msg)
+
+ def test_constructor(self):
+ m1_param = ModuleParam(val="1.2",
+ type="Float",
+ alias="",
+ )
+ m1_function = ModuleFunction(name="value",
+ parameters=[m1_param],
+ )
+ m1 = Module(id=0,
+ name='Float',
+ functions=[m1_function],
+ )
+
+ m2 = Module()
+ m2.name = "Float"
+ m2.id = 0
+ f = ModuleFunction()
+ f.name = "value"
+ m2.functions.append(f)
+ param = ModuleParam()
+ param.strValue = "1.2"
+ param.type = "Float"
+ param.alias = ""
+ f.params.append(param)
+ assert m1 == m2
+
+ def test_str(self):
+ m = Module(id=0,
+ name='Float',
+ functions=[ModuleFunction(name='value',
+ parameters=[ModuleParam(type='Int',
+ val='1',
+ )],
+ )],
+ )
+ str(m)
+
+if __name__ == '__main__':
+ unittest.main()
+
diff --git a/vistrails/core/vistrail/module_function.py b/vistrails/core/vistrail/module_function.py
new file mode 100644
index 0000000..b3f819a
--- /dev/null
+++ b/vistrails/core/vistrail/module_function.py
@@ -0,0 +1,300 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This module contains class definitions for:
+
+ * ModuleFunction
+"""
+from vistrails.db.domain import DBFunction
+from vistrails.core.modules.utils import create_port_spec_string
+from vistrails.core.utils import enum, VistrailsInternalError, all, eprint
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.port_spec import PortSpec
+from itertools import izip
+import copy
+
+import unittest
+import copy
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.db.domain import IdScope
+import vistrails.core
+
+################################################################################
+
+PipelineElementType = enum('PipelineElementType',
+ ['Module', 'Connection', 'Function', 'Parameter'])
+
+################################################################################
+
+class ModuleFunction(DBFunction):
+ __fields__ = ['name', 'returnType', 'params']
+ """ Stores a function from a vistrail module """
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBFunction.__init__(self, *args, **kwargs)
+ if self.name is None:
+ self.name = ""
+ if self.real_id is None:
+ self.real_id = -1
+ if self.pos is None:
+ self.pos = -1
+ self.set_defaults()
+
+ def set_defaults(self, other=None):
+ if other is None:
+ self.returnType = "void"
+ self.is_valid = False
+ else:
+ self.returnType = other.returnType
+ self.is_valid = other.is_valid
+ self.parameter_idx = self.db_parameters_id_index
+
+ def __copy__(self):
+ """ __copy__() -> ModuleFunction - Returns a clone of itself """
+ return ModuleFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = ModuleFunction
+ cp.set_defaults(self)
+ return cp
+
+ @staticmethod
+ def convert(_function):
+ if _function.__class__ == ModuleFunction:
+ return
+ _function.__class__ = ModuleFunction
+ for _parameter in _function.db_get_parameters():
+ ModuleParam.convert(_parameter)
+ _function.set_defaults()
+
+ ##########################################################################
+ # Properties
+
+ id = DBFunction.db_pos
+ pos = DBFunction.db_pos
+ real_id = DBFunction.db_id
+ name = DBFunction.db_name
+
+ def _get_sigstring(self):
+ return create_port_spec_string([p.spec_tuple for p in self.params])
+ sigstring = property(_get_sigstring)
+
+ def _get_params(self):
+ self.db_parameters.sort(key=lambda x: x.db_pos)
+ return self.db_parameters
+ def _set_params(self, params):
+ self.db_parameters = params
+ # If you're mutating the params property, watch out for the sort
+ # gotcha: every time you use the params on reading position,
+ # they get resorted
+ params = property(_get_params, _set_params)
+ parameters = property(_get_params, _set_params)
+
+ def add_parameter(self, param):
+ self.db_add_parameter(param)
+ addParameter = add_parameter
+
+ def add_parameters(self, params):
+ for p in params:
+ self.db_add_parameter(p)
+
+ ##########################################################################
+
+ def getNumParams(self):
+ """ getNumParams() -> int Returns the number of params. """
+ return len(self.params)
+
+ def serialize(self, doc, element):
+ """serialize(doc, element) -> None - Writes itself in XML """
+ child = doc.createElement('function')
+ child.setAttribute('name',self.name)
+ child.setAttribute('returnType',self.type)
+ for p in self.params:
+ p.serialize(doc,child)
+ element.appendChild(child)
+
+ def get_spec(self, port_type):
+ """ get_spec(port_type) -> PortSpec
+
+ Returns a PortSpec corresponding to the function parameter
+ types set. This is useful to make module functions look more
+ like they are 'regular' modules and connections (which is what
+ they get compiled down to in execution).
+
+ port_type is either 'input' or 'output', as strings, which
+ simply gets set on the spec being returned.
+ """
+ assert port_type == 'input' or port_type == 'output'
+ result = PortSpec(sigstring=self.sigstring)
+ result.type = port_type
+ return result
+
+ ##########################################################################
+ # Debugging
+
+ def show_comparison(self, other):
+ if type(self) != type(other):
+ print "type mismatch"
+ return
+ if self.name != other.name:
+ print "name mismatch"
+ return
+ if self.returnType != other.returnType:
+ print "return type mismatch"
+ return
+ if len(self.params) != len(other.params):
+ print "params length mismatch"
+ return
+ for p,q in izip(self.params, other.params):
+ if p != q:
+ print "params mismatch"
+ p.show_comparison(q)
+ return
+ print "no difference found"
+ assert self == other
+ return
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """ __str__() -> str - Returns a string representation of itself """
+ return ("<function id='%s' pos='%s' name='%s' params=%s)@%X" %
+ (self.real_id,
+ self.pos,
+ self.name,
+ [str(p) for p in self.params],
+ id(self)))
+
+ def __eq__(self, other):
+ """ __eq__(other: ModuleFunction) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.name != other.name:
+ return False
+ if self.returnType != other.returnType:
+ return False
+ if len(self.params) != len(other.params):
+ return False
+ for p,q in zip(self.params, other.params):
+ if p != q:
+ return False
+ return True
+
+ def __ne__(self, other):
+ """ __ne__(other: ModuleFunction) -> boolean
+ Returns True if self and other don't have the same attributes.
+ Used by != operator.
+
+ """
+ return not self.__eq__(other)
+
+################################################################################
+# Testing
+
+
+#TODO add more meaningful tests
+
+class TestModuleFunction(unittest.TestCase):
+
+ def create_function(self, id_scope=IdScope()):
+ param = ModuleParam(id=id_scope.getNewId(ModuleParam.vtType),
+ pos=2,
+ type='Int',
+ val='1')
+ function = ModuleFunction(id=id_scope.getNewId(ModuleFunction.vtType),
+ pos=0,
+ name='value',
+ parameters=[param])
+ return function
+
+ def test_copy(self):
+ id_scope = IdScope()
+ f1 = self.create_function(id_scope)
+ f2 = copy.copy(f1)
+ self.assertEquals(f1, f2)
+ self.assertEquals(f1.id, f2.id)
+ f3 = f1.do_copy(True, id_scope, {})
+ self.assertEquals(f1, f3)
+ self.assertNotEquals(f1.real_id, f3.real_id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ f1 = self.create_function()
+ xml_str = vistrails.core.db.io.serialize(f1)
+ f2 = vistrails.core.db.io.unserialize(xml_str, ModuleFunction)
+ self.assertEquals(f1, f2)
+ self.assertEquals(f1.real_id, f2.real_id)
+
+ def testComparisonOperators(self):
+ f = ModuleFunction()
+ f.name = "value"
+ param = ModuleParam()
+ param.strValue = "1.2"
+ param.type = "Float"
+ param.alias = ""
+ f.addParameter(param)
+ g = ModuleFunction()
+ g.name = "value"
+ param = ModuleParam()
+ param.strValue = "1.2"
+ param.type = "Float"
+ param.alias = ""
+ g.addParameter(param)
+ assert f == g
+ param = ModuleParam()
+ param.strValue = "1.2"
+ param.type = "Float"
+ param.alias = ""
+ g.addParameter(param)
+ assert f != g
+
+ def test_str(self):
+ f = ModuleFunction(name='value',
+ parameters=[ModuleParam(type='Float',
+ val='1.2')],
+ )
+ str(f)
+
+if __name__ == '__main__':
+ unittest.main()
+
diff --git a/vistrails/core/vistrail/module_param.py b/vistrails/core/vistrail/module_param.py
new file mode 100644
index 0000000..0c8bc90
--- /dev/null
+++ b/vistrails/core/vistrail/module_param.py
@@ -0,0 +1,403 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This module contains class definitions for:
+ * ModuleParam
+
+ """
+from vistrails.db.domain import DBParameter
+from vistrails.core.modules.utils import parse_port_spec_item_string, \
+ create_port_spec_item_string
+from vistrails.core.utils import enum
+
+import unittest
+import copy
+from vistrails.db.domain import IdScope
+import vistrails.core
+from vistrails.core.system import get_vistrails_basic_pkg_id
+
+################################################################################
+
+class ModuleParam(DBParameter):
+ """ Stores a parameter setting for a vistrail function """
+
+ ##########################################################################
+ # Constructor
+
+ def __init__(self, *args, **kwargs):
+ if 'identifier' in kwargs:
+ identifier = kwargs['identifier']
+ del kwargs['identifier']
+ else:
+ identifier = None
+ if 'namespace' in kwargs:
+ namespace = kwargs['namespace']
+ del kwargs['namespace']
+ else:
+ namespace = None
+ DBParameter.__init__(self, *args, **kwargs)
+ if self.real_id is None:
+ self.real_id = -1
+ if self.strValue is None:
+ self.strValue = ""
+ if self.alias is None:
+ self.alias = ""
+ if self.pos is None:
+ self.pos = -1
+ if self.name is None:
+ self.name = ""
+
+ self.minValue = ""
+ self.maxValue = ""
+ self.evaluatedStrValue = ""
+
+ self.parse_db_type()
+ if identifier:
+ self.identifier = identifier
+ if namespace:
+ self.namespace = namespace
+
+ # This is used for visual query and will not get serialized
+ self.queryMethod = None
+
+ # this is used for parameter settings
+ self._port_spec_item = None
+
+ # Used by constant widgets to determine how default is displayed
+ self.param_exists = True
+
+ def __copy__(self):
+ return ModuleParam.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = ModuleParam
+ cp.minValue = self.minValue
+ cp.maxValue = self.maxValue
+ cp.evaluatedStrValue = self.evaluatedStrValue
+ cp.queryMethod = self.queryMethod
+ cp._port_spec_item = self._port_spec_item
+
+ # cp.identifier = self.identifier
+ # cp.namespace = self.namespace
+ # cp._type = self._type
+ cp.parse_db_type()
+
+ return cp
+
+ @staticmethod
+ def convert(_parameter):
+ if _parameter.__class__ == ModuleParam:
+ return
+ _parameter.__class__ = ModuleParam
+ _parameter.queryMethod = None
+ _parameter.minValue = ""
+ _parameter.maxValue = ""
+ _parameter.evaluatedStrValue = ""
+ _parameter._port_spec_item = None
+
+ # _parameter.identifier = ""
+ # _parameter.namespace = ""
+ # _parameter._type = ""
+ # _parameter.parse_type_str(_parameter.db_type)
+ _parameter.parse_db_type()
+
+ ##########################################################################
+
+ id = DBParameter.db_pos
+ pos = DBParameter.db_pos
+ real_id = DBParameter.db_id
+ name = DBParameter.db_name
+ typeStr = DBParameter.db_type
+ strValue = DBParameter.db_val
+ alias = DBParameter.db_alias
+
+ def parse_db_type(self):
+ if self.db_type:
+ (self._identifier, self._type, self._namespace) = \
+ parse_port_spec_item_string(self.db_type,
+ get_vistrails_basic_pkg_id())
+ else:
+ self._identifier = None
+ self._type = None
+ self._namespace = None
+
+ def update_db_type(self):
+ if not self._type:
+ self.db_type = None
+ else:
+ self.db_type = create_port_spec_item_string(self._identifier,
+ self._type,
+ self._namespace)
+
+ def _get_type(self):
+ if not hasattr(self, '_type'):
+ self.parse_db_type()
+ return self._type
+ def _set_type(self, type):
+ self._type = type
+ self.update_db_type()
+ type = property(_get_type, _set_type)
+
+ def _get_namespace(self):
+ if not hasattr(self, '_namespace'):
+ self.parse_db_type()
+ return self._namespace
+ def _set_namespace(self, namespace):
+ self._namespace = namespace
+ self.update_db_type()
+ namespace = property(_get_namespace, _set_namespace)
+
+ def _get_identifier(self):
+ if not hasattr(self, '_identifier'):
+ self.parse_db_type()
+ return self._identifier
+ def _set_identifier(self, identifier):
+ self._identifier = identifier
+ self.update_db_type()
+ identifier = property(_get_identifier, _set_identifier)
+
+ def _get_port_spec_item(self):
+ return self._port_spec_item
+ def _set_port_spec_item(self, psi):
+ self._port_spec_item = psi
+ port_spec_item = property(_get_port_spec_item, _set_port_spec_item)
+
+ def _get_spec_tuple(self):
+ return (self._identifier, self._type, self._namespace)
+ spec_tuple = property(_get_spec_tuple)
+
+ def serialize(self, dom, element):
+ """ serialize(dom, element) -> None
+ Writes itself in XML
+
+ """
+ child = dom.createElement('param')
+ child.setAttribute('name',self.name)
+ ctype = dom.createElement('type')
+ cval = dom.createElement('val')
+ calias = dom.createElement('alias')
+ ttype = dom.createTextNode(self.typeStr)
+ tval = dom.createTextNode(self.strValue)
+ talias = dom.createTextNode(self.alias)
+ child.appendchild(ctype)
+ child.appendChild(cval)
+ ctype.appendChild(ttype)
+ cval.appendChild(tval)
+ calias.appendChild(talias)
+ element.appendChild(child)
+
+ def value(self):
+ """ value() -> any type
+ Returns its strValue as a python type.
+
+ """
+ from vistrails.core.modules.module_registry import get_module_registry
+ module = get_module_registry().get_module_by_name(self.identifier,
+ self.type,
+ self.namespace)
+ if self.strValue == "":
+ self.strValue = module.default_value
+ return module.default_value
+ return module.translate_to_python(self.strValue)
+
+ ##########################################################################
+ # Debugging
+
+ def show_comparison(self, other):
+ if type(self) != type(other):
+ print "type mismatch"
+ return
+ if self.typeStr != other.typeStr:
+ print "paramtype mismatch"
+ return
+ if self.strValue != other.strValue:
+ print "strvalue mismatch"
+ return
+ if self.name != other.name:
+ print "name mismatch"
+ return
+ if self.alias != other.alias:
+ print "alias mismatch"
+ return
+ if self.minValue != other.minValue:
+ print "minvalue mismatch"
+ return
+ if self.maxValue != other.maxValue:
+ print "maxvalue mismatch"
+ return
+ if self.evaluatedStrValue != other.evaluatedStrValue:
+ print "evaluatedStrValue mismatch"
+ return
+ print "no difference found"
+ assert self == other
+ return
+
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """ __str__() -> str - Returns a string representation of itself """
+ if self.minValue != "":
+ assert False
+ else:
+ return ("(Param '%s' db_type='%s' strValue='%s' real_id='%s' pos='%s' identifier='%s' alias='%s' namespace='%s')@%X" %
+ (self.name,
+ self.db_type,
+ self.strValue,
+ self.real_id,
+ self.pos,
+ self.identifier,
+ self.alias,
+ self.namespace,
+ id(self)))
+
+ def __eq__(self, other):
+ """ __eq__(other: ModuleParam) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.type != other.type:
+ return False
+ if self.strValue != other.strValue:
+ return False
+ if self.name != other.name:
+ return False
+ if self.alias != other.alias:
+ return False
+ if self.minValue != other.minValue:
+ return False
+ if self.maxValue != other.maxValue:
+ return False
+ if self.evaluatedStrValue != other.evaluatedStrValue:
+ return False
+ return True
+
+ def __ne__(self, other):
+ """ __ne__(other: ModuleParam) -> boolean
+ Returns True if self and other don't have the same attributes.
+ Used by != operator.
+
+ """
+ return not self.__eq__(other)
+
+###############################################################################
+# Testing
+
+
+class TestModuleParam(unittest.TestCase):
+
+ def create_param(self, id_scope=IdScope()):
+ param = ModuleParam(id=id_scope.getNewId(ModuleParam.vtType),
+ pos=2,
+ type='Int',
+ val='1')
+ return param
+
+ def test_copy(self):
+ id_scope = IdScope()
+ p1 = self.create_param(id_scope)
+ p2 = copy.copy(p1)
+ self.assertEquals(p1, p2)
+ self.assertEquals(p1.id, p2.id)
+ p3 = p1.do_copy(True, id_scope, {})
+ self.assertEquals(p1, p3)
+ self.assertNotEquals(p1.real_id, p3.real_id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ p1 = self.create_param()
+ xml_str = vistrails.core.db.io.serialize(p1)
+ p2 = vistrails.core.db.io.unserialize(xml_str, ModuleParam)
+ self.assertEquals(p1, p2)
+ self.assertEquals(p1.real_id, p2.real_id)
+
+ def testValue(self):
+ """ Test values returned by value() function """
+ basic_pkg = get_vistrails_basic_pkg_id()
+
+ p = ModuleParam()
+ p.type = "Float"
+ p.identifier = basic_pkg
+ assert p.value() == 0.0
+ p.strValue = "1.5"
+ assert p.value() == 1.5
+
+ p.type = "Integer"
+ p.identifier = basic_pkg
+ p.strValue = ""
+ assert p.value() == 0
+ p.strValue = "2"
+ assert p.value() == 2
+
+ p.type = "String"
+ p.identifier = basic_pkg
+ p.strValue = ""
+ assert p.value() == ""
+ p.strValue = "test"
+ assert p.value() == "test"
+
+ p.type = "Boolean"
+ p.identifier = basic_pkg
+ p.strValue = ""
+ assert p.value() == False
+ p.strValue = "False"
+ assert p.value() == False
+ p.strValue = "True"
+ assert p.value() == True
+
+ def testComparisonOperators(self):
+ """ Test comparison operators """
+ p = ModuleParam()
+ q = ModuleParam()
+ assert p == q
+ q.type = "Float"
+ assert p != q
+
+ def test_str(self):
+ p = ModuleParam(type='Float', val='1.5')
+ str(p)
+
+
+ def test_parse(self):
+ basic_pkg = get_vistrails_basic_pkg_id()
+
+ p = ModuleParam(type='Integer', val='1.5')
+ self.assertEqual(p.identifier, basic_pkg)
+ self.assertEqual(p.type, 'Integer')
+ self.assertFalse(p.namespace)
diff --git a/vistrails/core/vistrail/operation.py b/vistrails/core/vistrail/operation.py
new file mode 100644
index 0000000..bcb4f78
--- /dev/null
+++ b/vistrails/core/vistrail/operation.py
@@ -0,0 +1,413 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBAdd, DBChange, DBDelete
+from vistrails.db.domain import DBAnnotation, DBAbstraction, DBConnection, DBGroup, \
+ DBLocation, DBModule, DBFunction, DBPluginData, DBParameter, DBPort, \
+ DBPortSpec
+
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.vistrail.abstraction import Abstraction
+from vistrails.core.vistrail.connection import Connection
+from vistrails.core.vistrail.group import Group
+from vistrails.core.vistrail.location import Location
+from vistrails.core.vistrail.module import Module
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.plugin_data import PluginData
+from vistrails.core.vistrail.port import Port
+from vistrails.core.vistrail.port_spec import PortSpec
+
+import unittest
+import copy
+from vistrails.db.domain import IdScope
+import vistrails.core
+
+def convert_data(_data):
+ map = {
+ DBAnnotation.vtType: Annotation,
+ DBAbstraction.vtType: Abstraction,
+ DBConnection.vtType: Connection,
+ DBLocation.vtType: Location,
+ DBModule.vtType: Module,
+ DBFunction.vtType: ModuleFunction,
+ DBGroup.vtType: Group,
+ DBParameter.vtType: ModuleParam,
+ DBPluginData.vtType: PluginData,
+ DBPort.vtType: Port,
+ DBPortSpec.vtType: PortSpec,
+ }
+ try:
+ map[_data.vtType].convert(_data)
+ except KeyError:
+ raise TypeError('cannot convert data of type %s' % _data.vtType)
+
+class AddOp(DBAdd):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBAdd.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return AddOp.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = AddOp
+ return cp
+
+ @staticmethod
+ def convert(_add_op):
+ if _add_op.__class__ == AddOp:
+ return
+ _add_op.__class__ = AddOp
+ if _add_op.data is not None:
+ convert_data(_add_op.data)
+ ##########################################################################
+ # Properties
+
+ id = DBAdd.db_id
+ what = DBAdd.db_what
+ objectId = DBAdd.db_objectId
+ old_obj_id = DBAdd.db_objectId
+ new_obj_id = DBAdd.db_objectId
+ parentObjId = DBAdd.db_parentObjId
+ parentObjType = DBAdd.db_parentObjType
+ data = DBAdd.db_data
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of an Annotation
+ object.
+
+ """
+
+ rep = ("<add id=%s what=%s objectId=%s parentObjId=%s" + \
+ " parentObjType=%s>") % (str(self.id), str(self.what), str(self.objectId),
+ str(self.parentObjId), str(self.parentObjType))
+ rep += str(self.data) + "</add>"
+ return rep
+
+ # FIXME expand this
+ def __eq__(self, other):
+ """ __eq__(other: AddOp) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(other) != type(self):
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+class ChangeOp(DBChange):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBChange.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return ChangeOp.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = ChangeOp
+ return cp
+
+ @staticmethod
+ def convert(_change_op):
+ if _change_op.__class__ == ChangeOp:
+ return
+ _change_op.__class__ = ChangeOp
+ if _change_op.data is not None:
+ convert_data(_change_op.data)
+
+ ##########################################################################
+ # Properties
+
+ id = DBChange.db_id
+ what = DBChange.db_what
+ oldObjId = DBChange.db_oldObjId
+ old_obj_id = DBChange.db_oldObjId
+ newObjId = DBChange.db_newObjId
+ new_obj_id = DBChange.db_newObjId
+ parentObjId = DBChange.db_parentObjId
+ parentObjType = DBChange.db_parentObjType
+ data = DBChange.db_data
+
+ # def _get_id(self):
+ # return self.db_id
+ # def _set_id(self, id):
+ # self.db_id = id
+ # id = property(_get_id, _set_id)
+
+ # def _get_what(self):
+ # return self.db_what
+ # def _set_what(self, what):
+ # self.db_what = what
+ # what = property(_get_what, _set_what)
+
+ # def _get_oldObjId(self):
+ # return self.db_oldObjId
+ # def _set_oldObjId(self, oldObjId):
+ # self.db_oldObjId = oldObjId
+ # oldObjId = property(_get_oldObjId, _set_oldObjId)
+ # old_obj_id = property(_get_oldObjId, _set_oldObjId)
+
+ # def _get_newObjId(self):
+ # return self.db_newObjId
+ # def _set_newObjId(self, newObjId):
+ # self.db_newObjId = newObjId
+ # newObjId = property(_get_newObjId, _set_newObjId)
+ # new_obj_id = property(_get_newObjId, _set_newObjId)
+
+ # def _get_parentObjId(self):
+ # return self.db_parentObjId
+ # def _set_parentObjId(self, parentObjId):
+ # self.db_parentObjId = parentObjId
+ # parentObjId = property(_get_parentObjId, _set_parentObjId)
+
+ # def _get_parentObjType(self):
+ # return self.db_parentObjType
+ # def _set_parentObjType(self, parentObjType):
+ # self.db_parentObjType = parentObjType
+ # parentObjType = property(_get_parentObjType, _set_parentObjType)
+
+ # def _get_data(self):
+ # return self.db_data
+ # def _set_data(self, data):
+ # self.db_data = data
+ # data = property(_get_data, _set_data)
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of an Annotation
+ object.
+
+ """
+ rep = "<change id=%s what=%s oldId=%s newId=%s parentObjId=%s" + \
+ " parentObjType=%s>" + str(self.data) + "</change>"
+ return rep % (str(self.id), str(self.what), str(self.oldObjId),
+ str(self.newObjId), str(self.parentObjId),
+ str(self.parentObjType))
+
+ # FIXME expand this
+ def __eq__(self, other):
+ """ __eq__(other: ChangeOp) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(other) != type(self):
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+class DeleteOp(DBDelete):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBDelete.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return DeleteOp.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DeleteOp
+ return cp
+
+ @staticmethod
+ def convert(_delete_op):
+ _delete_op.__class__ = DeleteOp
+
+ ##########################################################################
+ # Properties
+
+ id = DBDelete.db_id
+ what = DBDelete.db_what
+ objectId = DBDelete.db_objectId
+ old_obj_id = DBDelete.db_objectId
+ new_obj_id = DBDelete.db_objectId
+ parentObjId = DBDelete.db_parentObjId
+ parentObjType = DBDelete.db_parentObjType
+
+ # def _get_id(self):
+ # return self.db_id
+ # def _set_id(self, id):
+ # self.db_id = id
+ # id = property(_get_id, _set_id)
+
+ # def _get_what(self):
+ # return self.db_what
+ # def _set_what(self, what):
+ # self.db_what = what
+ # what = property(_get_what, _set_what)
+
+ # def _get_objectId(self):
+ # return self.db_objectId
+ # def _set_objectId(self, objectId):
+ # self.db_objectId = objectId
+ # objectId = property(_get_objectId, _set_objectId)
+ # old_obj_id = property(_get_objectId, _set_objectId)
+ # new_obj_id = property(_get_objectId, _set_objectId)
+
+ # def _get_parentObjId(self):
+ # return self.db_parentObjId
+ # def _set_parentObjId(self, parentObjId):
+ # self.db_parentObjId = parentObjId
+ # parentObjId = property(_get_parentObjId, _set_parentObjId)
+
+ # def _get_parentObjType(self):
+ # return self.db_parentObjType
+ # def _set_parentObjType(self, parentObjType):
+ # self.db_parentObjType = parentObjType
+ # parentObjType = property(_get_parentObjType, _set_parentObjType)
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of an Annotation
+ object.
+
+ """
+ rep = "<delete id=%s what=%s objectId=%s parentObjId=%s" + \
+ " parentObjType=%s/>"
+ return rep % (str(self.id), str(self.what), str(self.objectId),
+ str(self.parentObjId), str(self.parentObjType))
+
+ # FIXME expand this
+ def __eq__(self, other):
+ """ __eq__(other: DeleteOp) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(other) != type(self):
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+################################################################################
+# Unit tests
+
+
+class TestOperation(unittest.TestCase):
+
+ def create_ops(self, id_scope=IdScope()):
+ from vistrails.core.modules.basic_modules import identifier as basic_pkg
+ from vistrails.core.vistrail.module import Module
+ from vistrails.core.vistrail.module_function import ModuleFunction
+ from vistrails.core.vistrail.module_param import ModuleParam
+ from vistrails.core.vistrail.annotation import Annotation
+
+ if id_scope is None:
+ id_scope = IdScope(remap={AddOp.vtType: 'operation',
+ ChangeOp.vtType: 'operation',
+ DeleteOp.vtType: 'operation'})
+
+ m = Module(id=id_scope.getNewId(Module.vtType),
+ name='Float',
+ package=basic_pkg)
+ add_op = AddOp(id=id_scope.getNewId(AddOp.vtType),
+ what=Module.vtType,
+ objectId=m.id,
+ data=m)
+ function = ModuleFunction(id=id_scope.getNewId(ModuleFunction.vtType),
+ name='value')
+ change_op = ChangeOp(id=id_scope.getNewId(ChangeOp.vtType),
+ what=ModuleFunction.vtType,
+ oldObjId=2,
+ newObjId=function.real_id,
+ parentObjId=m.id,
+ parentObjType=Module.vtType,
+ data=function)
+ param = ModuleParam(id=id_scope.getNewId(ModuleParam.vtType),
+ type='Float',
+ val='1.0')
+
+ delete_op = DeleteOp(id=id_scope.getNewId(DeleteOp.vtType),
+ what=ModuleParam.vtType,
+ objectId=param.real_id,
+ parentObjId=function.real_id,
+ parentObjType=ModuleFunction.vtType)
+
+ annotation = Annotation(id=id_scope.getNewId(Annotation.vtType),
+ key='foo',
+ value='bar')
+ add_annotation = AddOp(id=id_scope.getNewId(AddOp.vtType),
+ what=Annotation.vtType,
+ objectId=m.id,
+ data=annotation)
+
+ return [add_op, change_op, delete_op, add_annotation]
+
+ def test_copy(self):
+ id_scope = IdScope(remap={AddOp.vtType: 'operation',
+ ChangeOp.vtType: 'operation',
+ DeleteOp.vtType: 'operation'})
+ for op1 in self.create_ops(id_scope):
+ op2 = copy.copy(op1)
+ self.assertEquals(op1, op2)
+ self.assertEquals(op1.id, op2.id)
+ op3 = op1.do_copy(True, id_scope, {})
+ self.assertEquals(op1, op3)
+ self.assertNotEquals(op1.id, op3.id)
+ if hasattr(op1, 'data'):
+ self.assertNotEquals(op1.data.db_id, op3.data.db_id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ for op1 in self.create_ops():
+ xml_str = vistrails.core.db.io.serialize(op1)
+ op2 = vistrails.core.db.io.unserialize(xml_str, op1.__class__)
+ self.assertEquals(op1, op2)
+ self.assertEquals(op1.id, op2.id)
diff --git a/vistrails/core/vistrail/pipeline.py b/vistrails/core/vistrail/pipeline.py
new file mode 100644
index 0000000..fba8463
--- /dev/null
+++ b/vistrails/core/vistrail/pipeline.py
@@ -0,0 +1,1698 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+##TODO Tests
+""" This module defines the class Pipeline """
+from vistrails.core.cache.hasher import Hasher
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core.data_structures.bijectivedict import Bidict
+from vistrails.core.data_structures.graph import Graph
+from vistrails.core import debug
+from vistrails.core.modules.module_descriptor import ModuleDescriptor
+from vistrails.core.modules.module_registry import get_module_registry, \
+ ModuleRegistryException, MissingModuleVersion, MissingPackage, PortMismatch
+from vistrails.core.system import get_vistrails_default_pkg_prefix, \
+ get_vistrails_basic_pkg_id
+from vistrails.core.utils import VistrailsInternalError
+from vistrails.core.utils import expression, append_to_dict_of_lists
+from vistrails.core.utils.uxml import named_elements
+from vistrails.core.vistrail.abstraction import Abstraction
+from vistrails.core.vistrail.connection import Connection
+from vistrails.core.vistrail.group import Group
+from vistrails.core.vistrail.module import Module
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.plugin_data import PluginData
+from vistrails.core.vistrail.port import Port, PortEndPoint
+from vistrails.core.vistrail.port_spec import PortSpec
+from vistrails.db.domain import DBWorkflow
+import vistrails.core.vistrail.action
+from vistrails.core.utils import profile, InvalidPipeline, versions_increasing
+
+from xml.dom.minidom import getDOMImplementation, parseString
+import copy
+
+import unittest
+from vistrails.core.vistrail.abstraction import Abstraction
+from vistrails.core.vistrail.connection import Connection
+from vistrails.core.vistrail.location import Location
+from vistrails.core.vistrail.module import Module
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.port import Port
+from vistrails.db.domain import IdScope
+
+##############################################################################
+
+class MissingVistrailVariable(Exception):
+ def __init__(self, var_uuid, identifier, name, namespace):
+ self._var_uuid = var_uuid
+ self._identifier = identifier
+ self._name = name
+ self._namespace = namespace
+
+ def __str__(self):
+ return "Missing Vistrail Variable '%s' of type %s from package %s" % (self._var_uuid,
+ self._module_name, self._identifier)
+
+ def __eq__(self, other):
+ return type(self) == type(other) and \
+ self._var_uuid == other._var_uuid and \
+ self._identifier == other._identifier and \
+ self._name == other._name and \
+ self._namespace == other._namespace
+
+ def __hash__(self):
+ return (type(self), self._var_uuid, self._identifier,
+ self._name, self._namespace).__hash__()
+
+ def _get_module_name(self):
+ if self._namespace:
+ return "%s|%s" % (self._namespace, self._name)
+ return self._name
+ _module_name = property(_get_module_name)
+
+class MissingFunction(Exception):
+ def __init__(self, name, module_name, module_id=None):
+ self.name = name
+ self.module_name = module_name
+ self.module_id = module_id
+
+ def __str__(self):
+ return ("Missing Function '%s' on module '%s'%s" %
+ (self.name, self.module_name, " (id %d)" % self.module_id if
+ self.module_id is not None else ""))
+
+class CycleInPipeline(Exception):
+ def __str__(self):
+ return "Pipeline contains a cycle"
+
+class Pipeline(DBWorkflow):
+ """ A Pipeline is a set of modules and connections between them. """
+
+ def __init__(self, *args, **kwargs):
+ """ __init__() -> Pipelines
+ Initializes modules, connections and graph.
+
+ """
+ self.clear()
+
+ DBWorkflow.__init__(self, *args, **kwargs)
+ if self.id is None:
+ self.id = 0
+ if self.name is None:
+ self.name = 'untitled'
+ self.set_defaults()
+
+ def set_defaults(self, other=None):
+ if other is None:
+ self.is_valid = False
+ self.aliases = Bidict()
+ self._subpipeline_signatures = Bidict()
+ self._module_signatures = Bidict()
+ self._connection_signatures = Bidict()
+ else:
+ self.is_valid = other.is_valid
+ self.aliases = Bidict([(k,copy.copy(v))
+ for (k,v) in other.aliases.iteritems()])
+ self._connection_signatures = \
+ Bidict([(k,copy.copy(v))
+ for (k,v) in other._connection_signatures.iteritems()])
+ self._subpipeline_signatures = \
+ Bidict([(k,copy.copy(v))
+ for (k,v) in other._subpipeline_signatures.iteritems()])
+ self._module_signatures = \
+ Bidict([(k,copy.copy(v))
+ for (k,v) in other._module_signatures.iteritems()])
+
+ self.graph = Graph()
+ for module in self.module_list:
+ self.graph.add_vertex(module.id)
+ # there should be another way to do this
+ m_id = module.id
+ for fun in module.functions:
+ for par in fun.parameters:
+ self.change_alias(par.alias,
+ par.vtType,
+ par.real_id,
+ fun.vtType,
+ fun.real_id,
+ m_id)
+ module.connected_input_ports = {}
+ module.connected_output_ports = {}
+
+ for connection in self.connection_list:
+ self.graph.add_edge(connection.source.moduleId,
+ connection.destination.moduleId,
+ connection.id)
+ c = connection
+ source_name = c.source.name
+ output_ports = self.modules[c.sourceId].connected_output_ports
+ if source_name not in output_ports:
+ output_ports[source_name] = 0
+ output_ports[source_name] += 1
+
+ dest_name = c.destination.name
+ input_ports = self.modules[c.destinationId].connected_input_ports
+ if dest_name not in input_ports:
+ input_ports[dest_name] = 0
+ input_ports[dest_name] += 1
+
+ def __copy__(self):
+ """ __copy__() -> Pipeline - Returns a clone of itself """
+ return Pipeline.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Pipeline
+ cp.set_defaults(self)
+ return cp
+
+ @staticmethod
+ def convert(_workflow):
+ if _workflow.__class__ == Pipeline:
+ return
+ # do clear plus get the modules and connections
+ _workflow.__class__ = Pipeline
+ for _module in _workflow.db_modules:
+ if _module.vtType == Module.vtType:
+ Module.convert(_module)
+ elif _module.vtType == Abstraction.vtType:
+ Abstraction.convert(_module)
+ elif _module.vtType == Group.vtType:
+ Group.convert(_module)
+ for _connection in _workflow.db_connections:
+ Connection.convert(_connection)
+ for _plugin_data in _workflow.db_plugin_datas:
+ PluginData.convert(_plugin_data)
+ _workflow.set_defaults()
+
+ ##########################################################################
+
+ def find_method(self, module_id, parameter_name):
+ """find_method(module_id, parameter_name) -> int.
+
+ Finds the function_id for a given method name.
+ Returns -1 if method name is not there.
+
+ WARNING: Might not work for overloaded methods (where types
+ also matter)
+ """
+ try:
+ return [f.name
+ for f
+ in self.get_module_by_id(module_id).functions].index(parameter_name)
+ except ValueError:
+ return -1
+
+ ##########################################################################
+ # Properties
+
+ id = DBWorkflow.db_id
+ name = DBWorkflow.db_name
+ plugin_datas = DBWorkflow.db_plugin_datas
+
+ def _get_modules(self):
+ return self.db_modules_id_index
+ modules = property(_get_modules)
+ def _get_module_list(self):
+ return self.db_modules
+ module_list = property(_get_module_list)
+
+ def _get_connections(self):
+ return self.db_connections_id_index
+ connections = property(_get_connections)
+ def _get_connection_list(self):
+ return self.db_connections
+ connection_list = property(_get_connection_list)
+
+ def clear(self):
+ """clear() -> None. Erases pipeline contents."""
+ if hasattr(self, 'db_modules'):
+ for module in self.db_modules:
+ self.db_delete_module(module)
+ if hasattr(self, 'db_connections'):
+ for connection in self.db_connections:
+ self.db_delete_connection(connection)
+ self.graph = Graph()
+ self.aliases = Bidict()
+ self._subpipeline_signatures = Bidict()
+ self._module_signatures = Bidict()
+ self._connection_signatures = Bidict()
+
+ def get_tmp_id(self, type):
+ """get_tmp_id(type: str) -> long
+ returns a temporary id for a workflow item. Use the idScope on the
+ vistrail for permanent ids.
+ """
+
+ return -self.tmp_id.getNewId(type)
+
+ def fresh_module_id(self):
+ return self.get_tmp_id(Module.vtType)
+ def fresh_connection_id(self):
+ return self.get_tmp_id(Connection.vtType)
+
+ def check_connection(self, c):
+ """check_connection(c: Connection) -> boolean
+ Checks semantics of connection
+
+ """
+ if c.source.endPoint != Port.SourceEndPoint:
+ return False
+ if c.destination.endPoint != Port.DestinationEndPoint:
+ return False
+ if not self.has_module_with_id(c.sourceId):
+ return False
+ if not self.has_module_with_id(c.destinationId):
+ return False
+ if c.source.type != c.destination.type:
+ return False
+ return True
+
+ def connects_at_port(self, p):
+ """ connects_at_port(p: Port) -> list of Connection
+ Returns a list of Connections that connect at port p
+
+ """
+ result = []
+ if p.endPoint == Port.DestinationEndPoint:
+ el = self.graph.edges_to(p.moduleId)
+ for (edgeto, edgeid) in el:
+ dest = self.connection[edgeid].destination
+ if VTKRTTI().intrinsicPortEqual(dest, p):
+ result.append(self.connection[edgeid])
+ elif p.endPoint == Port.SourceEndPoint:
+ el = self.graph.edges_from(p.moduleId)
+ for (edgeto, edgeid) in el:
+ source = self.connection[edgeid].source
+ if VTKRTTI().intrinsicPortEqual(source, p):
+ result.append(self.connection[edgeid])
+ else:
+ raise VistrailsInternalError("port with bogus information")
+ return result
+
+ def connections_to_module(self, moduleId):
+ """ connections_to_module(int moduleId) -> list of module ids
+ returns a list of module ids that are inputs to the given moduleId
+
+ """
+
+ modules = []
+ for edge in self.graph.edges_to(moduleId):
+ modules.append(self.modules[edge[0]].id)
+ return modules
+
+ def get_inputPort_modules(self, moduleId, portName):
+ """ get_inputPort_modules(int moduleId, string portName)-> list of module ids
+ returns a list of module ids that are the input to a given port
+ on a given module
+
+ """
+ modules = []
+ for edge in self.graph.edges_to(moduleId):
+ if self.connections[edge[1]].destination.name == portName:
+ modules.append(self.modules[edge[0]].id)
+ return modules
+
+ def get_outputPort_modules(self, moduleId, portName):
+ """ get_outputPort_modules(int moduleId, string portName)-> list of module ids
+ returns a list of module ids that are the output to a given port
+ on a given module
+ """
+ modules = []
+ for edge in self.graph.edges_from(moduleId):
+ if self.connections[edge[1]].source.name == portName:
+ modules.append(self.modules[edge[0]].id)
+ return modules
+
+ def perform_action_chain(self, actionChain):
+ # BEWARE: if actionChain is long, you're probably better off
+ # going through general_action_chain, because it optimizes
+ # away unnecessary operations.
+ for action in actionChain:
+ self.perform_action(action)
+
+ def perform_action(self, action):
+# print "+++"
+# for operation in action.operations:
+# print operation.vtType, operation.what, operation.old_obj_id, \
+# operation.new_obj_id, operation.parentObjType, operation.parentObjId
+# print "---"
+ for operation in action.operations:
+ self.perform_operation(operation)
+
+ def perform_operation_chain(self, opChain):
+ for op in opChain:
+ self.perform_operation(op)
+
+ def perform_operation(self, op):
+ # print "doing %s %s %s" % (op.id, op.vtType, op.what)
+ if op.db_what == 'abstraction' or op.db_what == 'group':
+ what = 'module'
+ else:
+ what = op.db_what
+ funname = '%s_%s' % (op.vtType, what)
+ try:
+ f = getattr(self, funname)
+ except AttributeError:
+ db_funname = 'db_%s_object' % op.vtType
+ try:
+ f = getattr(self, db_funname)
+ except AttributeError:
+ msg = "Pipeline cannot execute '%s %s' operation" % \
+ (op.vtType, op.what)
+ raise VistrailsInternalError(msg)
+
+ if op.vtType == 'add':
+ f(op.data, op.parentObjType, op.parentObjId)
+ elif op.vtType == 'delete':
+ f(op.objectId, op.what, op.parentObjType, op.parentObjId)
+ elif op.vtType == 'change':
+ f(op.oldObjId, op.data, op.parentObjType, op.parentObjId)
+
+ def add_module(self, m, *args):
+ """add_module(m: Module) -> None
+ Add new module to pipeline
+
+ """
+ if self.has_module_with_id(m.id):
+ raise VistrailsInternalError("duplicate module id: %d" % m.id )
+# self.modules[m.id] = copy.copy(m)
+# if m.vtType == Abstraction.vtType:
+# m.abstraction = self.abstraction_map[m.abstraction_id]
+ self.db_add_object(m)
+ self.graph.add_vertex(m.id)
+
+ def change_module(self, old_id, m, *args):
+ if not self.has_module_with_id(old_id):
+ raise VistrailsInternalError("module %s doesn't exist" % old_id)
+ self.db_change_object(old_id, m)
+ self.graph.delete_vertex(old_id)
+ self.graph.add_vertex(m.id)
+
+ def delete_module(self, id, *args):
+ """delete_module(id:int) -> None
+ Delete a module from pipeline given an id.
+
+ """
+ if not self.has_module_with_id(id):
+ raise VistrailsInternalError("id missing in modules")
+
+ # we're hiding the necessary operations by doing this!
+ for (_, conn_id) in self.graph.adjacency_list[id][:]:
+ self.delete_connection(conn_id)
+ for (_, conn_id) in self.graph.inverse_adjacency_list[id][:]:
+ self.delete_connection(conn_id)
+
+ # self.modules.pop(id)
+ self.db_delete_object(id, Module.vtType)
+ self.graph.delete_vertex(id)
+ if id in self._module_signatures:
+ del self._module_signatures[id]
+ if id in self._subpipeline_signatures:
+ del self._subpipeline_signatures[id]
+
+ def add_connection(self, c, *args):
+ """add_connection(c: Connection) -> None
+ Add new connection to pipeline.
+
+ """
+ if self.has_connection_with_id(c.id):
+ raise VistrailsInternalError("duplicate connection id " + str(c.id))
+# self.connections[c.id] = copy.copy(c)
+ self.db_add_object(c)
+ if c.source is not None and c.destination is not None:
+ assert(c.sourceId != c.destinationId)
+ self.graph.add_edge(c.sourceId, c.destinationId, c.id)
+ self.ensure_connection_specs([c.id])
+
+ source_name = c.source.name
+ output_ports = self.modules[c.sourceId].connected_output_ports
+ if source_name not in output_ports:
+ output_ports[source_name] = 0
+ output_ports[source_name] += 1
+
+ dest_name = c.destination.name
+ input_ports = self.modules[c.destinationId].connected_input_ports
+ if dest_name not in input_ports:
+ input_ports[dest_name] = 0
+ input_ports[dest_name] += 1
+
+ def change_connection(self, old_id, c, *args):
+ """change_connection(old_id: long, c: Connection) -> None
+ Deletes connection identified by old_id and adds connection c
+
+ """
+ if not self.has_connection_with_id(old_id):
+ raise VistrailsInternalError("connection %s doesn't exist" % old_id)
+
+ old_conn = self.connections[old_id]
+ if old_conn.source is not None and old_conn.destination is not None:
+ self.graph.delete_edge(old_conn.sourceId, old_conn.destinationId,
+ old_conn.id)
+ if self.graph.out_degree(old_conn.sourceId) < 1:
+ self.modules[old_conn.sourceId].connected_output_ports.discard(
+ conn.source.name)
+ if self.graph.in_degree(old_conn.destinationId) < 1:
+ connected_input_ports = \
+ self.modules[old_conn.destinationId].connected_input_ports
+ connected_input_ports.discard(conn.destination.name)
+
+ if old_id in self._connection_signatures:
+ del self._connection_signatures[old_id]
+ self.db_change_object(old_id, c)
+ if c.source is not None and c.destination is not None:
+ assert(c.sourceId != c.destinationId)
+ self.graph.add_edge(c.sourceId, c.destinationId, c.id)
+ self.ensure_connection_specs([c.id])
+ self.modules[c.sourceId].connected_output_ports.add(c.source.name)
+ self.modules[c.destinationId].connected_input_ports.add(
+ c.destination.name)
+
+ def delete_connection(self, id, *args):
+ """ delete_connection(id:int) -> None
+ Delete connection identified by id from pipeline.
+
+ """
+
+ if not self.has_connection_with_id(id):
+ raise VistrailsInternalError("id %s missing in connections" % id)
+ conn = self.connections[id]
+ # self.connections.pop(id)
+ self.db_delete_object(id, 'connection')
+ if conn.source is not None and conn.destination is not None and \
+ (conn.destinationId, conn.id) in \
+ self.graph.edges_from(conn.sourceId):
+ self.graph.delete_edge(conn.sourceId, conn.destinationId, conn.id)
+
+ c = conn
+ source_name = c.source.name
+ output_ports = self.modules[c.sourceId].connected_output_ports
+ output_ports[source_name] -= 1
+
+ dest_name = c.destination.name
+ input_ports = self.modules[c.destinationId].connected_input_ports
+ input_ports[dest_name] -= 1
+
+ if id in self._connection_signatures:
+ del self._connection_signatures[id]
+
+ def add_parameter(self, param, parent_type, parent_id):
+ self.db_add_object(param, parent_type, parent_id)
+ if not self.has_alias(param.alias):
+ self.change_alias(param.alias,
+ param.vtType,
+ param.real_id,
+ parent_type,
+ parent_id,
+ None)
+
+ def delete_parameter(self, param_id, param_type, parent_type, parent_id):
+ self.db_delete_object(param_id, ModuleParam.vtType,
+ parent_type, parent_id)
+ self.remove_alias(ModuleParam.vtType, param_id, parent_type,
+ parent_id, None)
+
+ def change_parameter(self, old_param_id, param, parent_type, parent_id):
+ self.remove_alias(ModuleParam.vtType, old_param_id,
+ parent_type, parent_id, None)
+ self.db_change_object(old_param_id, param,
+ parent_type, parent_id)
+ if not self.has_alias(param.alias):
+ self.change_alias(param.alias,
+ param.vtType,
+ param.real_id,
+ parent_type,
+ parent_id,
+ None)
+
+ def add_port(self, port, parent_type, parent_id):
+ self.db_add_object(port, parent_type, parent_id)
+ connection = self.connections[parent_id]
+ if connection.source is not None and \
+ connection.destination is not None:
+ self.graph.add_edge(connection.sourceId,
+ connection.destinationId,
+ connection.id)
+ c = connection
+ source_name = c.source.name
+ output_ports = self.modules[c.sourceId].connected_output_ports
+ if source_name not in output_ports:
+ output_ports[source_name] = 0
+ output_ports[source_name] += 1
+
+ dest_name = c.destination.name
+ input_ports = self.modules[c.destinationId].connected_input_ports
+ if dest_name not in input_ports:
+ input_ports[dest_name] = 0
+ input_ports[dest_name] += 1
+
+ def delete_port(self, port_id, port_type, parent_type, parent_id):
+ conn = self.connections[parent_id]
+ if len(conn.ports) >= 2:
+ self.graph.delete_edge(conn.sourceId,
+ conn.destinationId,
+ conn.id)
+ c = conn
+ source_name = c.source.name
+ output_ports = self.modules[c.sourceId].connected_output_ports
+ output_ports[source_name] -= 1
+
+ dest_name = c.destination.name
+ input_ports = self.modules[c.destinationId].connected_input_ports
+ input_ports[dest_name] -= 1
+
+ self.db_delete_object(port_id, Port.vtType, parent_type, parent_id)
+
+ def change_port(self, old_port_id, port, parent_type, parent_id):
+ connection = self.connections[parent_id]
+ if len(connection.ports) >= 2:
+ source_list = self.graph.adjacency_list[connection.sourceId]
+ source_list.remove((connection.destinationId, connection.id))
+ dest_list = \
+ self.graph.inverse_adjacency_list[connection.destinationId]
+ dest_list.remove((connection.sourceId, connection.id))
+ self.db_change_object(old_port_id, port, parent_type, parent_id)
+ if len(connection.ports) >= 2:
+ source_list = self.graph.adjacency_list[connection.sourceId]
+ source_list.append((connection.destinationId, connection.id))
+ dest_list = \
+ self.graph.inverse_adjacency_list[connection.destinationId]
+ dest_list.append((connection.sourceId, connection.id))
+
+ def add_port_to_registry(self, portSpec, moduleId):
+ m = self.get_module_by_id(moduleId)
+ m.add_port_spec(portSpec)
+
+ def add_portSpec(self, port_spec, parent_type, parent_id):
+ # self.db_add_object(port_spec, parent_type, parent_id)
+ self.add_port_to_registry(port_spec, parent_id)
+
+ def delete_port_from_registry(self, id, moduleId):
+ m = self.get_module_by_id(moduleId)
+ portSpec = m.port_specs[id]
+ m.delete_port_spec(portSpec)
+
+ def delete_portSpec(self, spec_id, portSpec_type, parent_type, parent_id):
+ self.delete_port_from_registry(spec_id, parent_id)
+ # self.db_delete_object(spec_id, PortSpec.vtType, parent_type, parent_id)
+
+ def change_portSpec(self, old_spec_id, port_spec, parent_type, parent_id):
+ self.delete_port_from_registry(old_spec_id, parent_id)
+ # self.db_change_object(old_spec_id, port_spec, parent_type, parent_id)
+ self.add_port_to_registry(port_spec, parent_id)
+
+ def add_alias(self, name, type, oId, parentType, parentId, mId):
+ """add_alias(name: str, oId: int, parentType:str, parentId: int,
+ mId: int) -> None
+ Add alias to pipeline
+
+ """
+ if self.has_alias(name):
+ raise VistrailsInternalError("duplicate alias")
+ if mId is not None:
+ self.aliases[name] = (type, oId, parentType, parentId, mId)
+ else:
+ mid = None
+ for _mod in self.modules.itervalues():
+ for _fun in _mod.functions:
+ for _par in _fun.parameters:
+ if (_par.vtType == type and _par.real_id == oId and
+ _fun.vtType == parentType and
+ _fun.real_id == parentId):
+ mid = _mod.id
+ break
+ if mid is not None:
+ self.aliases[name] = (type, oId, parentType, parentId, mid)
+
+ def remove_alias_by_name(self, name):
+ """remove_alias_by_name(name: str) -> None
+ Remove alias with given name """
+ if self.has_alias(name):
+ del self.aliases[name]
+
+ def remove_alias(self, type, oId, parentType, parentId, mId):
+ """remove_alias(name: str, type:str, oId: int, parentType: str,
+ parentId: int, mId: int)-> None
+ Remove alias identified by oId """
+ if mId is not None:
+ try:
+ oldname = self.aliases.inverse[(type,oId, parentType, parentId, mId)]
+ del self.aliases[oldname]
+ except KeyError:
+ pass
+ else:
+ oldname = None
+ for aname,(t,o,pt,pid,mid) in self.aliases.iteritems():
+ if (t == type and o == oId and pt == parentType and
+ pid == parentId):
+ oldname = aname
+ break
+ if oldname:
+ del self.aliases[oldname]
+
+ def change_alias(self, name, type, oId, parentType, parentId, mId):
+ """change_alias(name: str, type:str oId:int, parentType:str,
+ parentId:int, mId: int)-> None
+ Change alias if name is non empty. Else remove alias
+
+ """
+ if name == "":
+ self.remove_alias(type, oId, parentType, parentId, mId)
+ else:
+ if not self.has_alias(name):
+ self.remove_alias(type, oId, parentType, parentId, mId)
+ self.add_alias(name, type, oId, parentType, parentId, mId)
+
+ def get_alias_str_value(self, name):
+ """ get_alias_str_value(name: str) -> str
+ returns the strValue of the parameter with alias name
+
+ """
+ try:
+ what, oId, parentType, parentId, mId = self.aliases[name]
+ except KeyError:
+ return ''
+ else:
+ if what == 'parameter':
+ parameter = self.db_get_object(what, oId)
+ return parameter.strValue
+ else:
+ raise VistrailsInternalError("only parameters are supported")
+
+ def set_alias_str_value(self, name, value):
+ """ set_alias_str_value(name: str, value: str) -> None
+ sets the strValue of the parameter with alias name
+
+ """
+ try:
+ what, oId, parentType, parentId, mId = self.aliases[name]
+ except KeyError:
+ pass
+ else:
+ if what == 'parameter':
+ #FIXME: check if a change parameter action needs to be generated
+ parameter = self.db_get_object(what, oId)
+ parameter.strValue = str(value)
+ else:
+ raise VistrailsInternalError("only parameters are supported")
+
+ def get_module_by_id(self, id):
+ """get_module_by_id(id: int) -> Module
+ Accessor. id is the Module id.
+
+ """
+ result = self.modules[id]
+ if result.vtType != Abstraction.vtType and \
+ result.vtType != Group.vtType and result.package is None:
+ registry = get_module_registry()
+ debug.critical('module %d is missing package' % id)
+ descriptor = registry.get_descriptor_from_name_only(result.name)
+ result.package = descriptor.identifier
+ return result
+
+ def get_connection_by_id(self, id):
+ """get_connection_by_id(id: int) -> Connection
+ Accessor. id is the Connection id.
+
+ """
+ self.ensure_connection_specs([id])
+ return self.connections[id]
+
+ def module_count(self):
+ """ module_count() -> int
+ Returns the number of modules in the pipeline.
+
+ """
+ return len(self.modules)
+
+ def connection_count(self):
+ """connection_count() -> int
+ Returns the number of connections in the pipeline.
+
+ """
+ return len(self.connections)
+
+ def has_module_with_id(self, id):
+ """has_module_with_id(id: int) -> boolean
+ Checks whether given module exists.
+
+ """
+ return id in self.modules
+
+ def has_connection_with_id(self, id):
+ """has_connection_with_id(id: int) -> boolean
+ Checks whether given connection exists.
+
+ """
+ return id in self.connections
+
+ def has_alias(self, name):
+ """has_alias(name: str) -> boolean
+ Checks whether given alias exists.
+
+ """
+ return name in self.aliases
+
+ def out_degree(self, id):
+ """out_degree(id: int) -> int - Returns the out-degree of a module. """
+ return self.graph.out_degree(id)
+
+ ##########################################################################
+ # Caching-related
+
+ # Modules
+
+ def module_signature(self, module_id):
+ """module_signature(module_id): string
+ Returns the signature for the module with given module_id."""
+ try:
+ return self._module_signatures[module_id]
+ except KeyError:
+ registry = get_module_registry()
+ m = self.modules[module_id]
+ sig = registry.module_signature(self, m)
+ self._module_signatures[module_id] = sig
+ return sig
+
+ def module_id_from_signature(self, signature):
+ """module_id_from_signature(sig): int
+ Returns the module_id that corresponds to the given signature.
+ This must have been previously computed."""
+ return self._module_signatures.inverse[signature]
+
+ def has_module_signature(self, signature):
+ return signature in self._module_signatures.inverse
+
+ # Subpipelines
+
+ def subpipeline_signature(self, module_id, visited_ids=None):
+ """subpipeline_signature(module_id): string
+ Returns the signature for the subpipeline whose sink id is module_id."""
+ if visited_ids is None:
+ visited_ids = set([module_id])
+ elif module_id in visited_ids:
+ raise CycleInPipeline()
+ try:
+ return self._subpipeline_signatures[module_id]
+ except KeyError:
+ upstream_sigs = [(self.subpipeline_signature(
+ m,
+ visited_ids | set([module_id])) +
+ Hasher.connection_signature(
+ self.connections[edge_id]))
+ for (m, edge_id) in
+ self.graph.edges_to(module_id)]
+ module_sig = self.module_signature(module_id)
+ sig = Hasher.subpipeline_signature(module_sig,
+ upstream_sigs)
+ self._subpipeline_signatures[module_id] = sig
+ return sig
+
+ def subpipeline_id_from_signature(self, signature):
+ """subpipeline_id_from_signature(sig): int
+ Returns the module_id that corresponds to the given signature.
+ This must have been previously computed."""
+ return self._subpipeline_signatures.inverse[signature]
+
+ def has_subpipeline_signature(self, signature):
+ return signature in self._subpipeline_signatures.inverse
+
+ # Connections
+
+ def connection_signature(self, connection_id):
+ """connection_signature(id): string
+ Returns the signature for the connection with given id."""
+ try:
+ return self._connection_signatures[connection_id]
+ except KeyError:
+ c = self.connections[connection_id]
+ source_sig = self.subpipeline_signature(c.sourceId)
+ dest_sig = self.subpipeline_signature(c.destinationId)
+ sig = Hasher.connection_subpipeline_signature(c, source_sig,
+ dest_sig)
+ self._connection_signatures[connection_id] = sig
+ return sig
+
+ def connection_id_from_signature(self, signature):
+ return self._connection_signatures.inverse[signature]
+
+ def has_connection_signature(self, signature):
+ return signature in self._connection_signatures.inverse
+
+ def refresh_signatures(self):
+ self._connection_signatures = {}
+ self._subpipeline_signatures = {}
+ self._module_signatures = {}
+ self.compute_signatures()
+
+ def compute_signatures(self):
+ """compute_signatures(): compute all module and subpipeline signatures
+ for this pipeline."""
+ for i in self.modules.iterkeys():
+ self.subpipeline_signature(i)
+ for c in self.connections.iterkeys():
+ self.connection_signature(c)
+
+ def get_subpipeline(self, module_set):
+ """get_subpipeline([module_id] or subgraph) -> Pipeline
+
+ Returns a subset of the current pipeline with the modules passed
+ in as module_ids and the internal connections between them."""
+ if isinstance(module_set, list):
+ subgraph = self.graph.subgraph(module_set)
+ elif isinstance(module_set, Graph):
+ subgraph = module_set
+ else:
+ raise TypeError("Expected list of ints or graph")
+ result = Pipeline()
+ for module_id in subgraph.iter_vertices():
+ result.add_module(copy.copy(self.modules[module_id]))
+ for (conn_from, conn_to, conn_id) in subgraph.iter_all_edges():
+ result.add_connection(copy.copy(self.connections[conn_id]))
+ # TODO : I haven't finished this yet. -cscheid
+ raise NotImplementedError
+ return result
+
+ ##########################################################################
+ # Registry-related
+
+ def validate(self, raise_exception=True, vistrail_vars={}):
+ # want to check entire pipeline and reconcile it with the
+ # registry - if anything fails, generate invalid pipeline with
+ # the errors
+ exceptions = set()
+ try:
+ self.ensure_modules_are_on_registry()
+ except InvalidPipeline, e:
+ exceptions.update(e.get_exception_set())
+
+ # do this before we check connection specs because it is
+ # possible that a subpipeline invalidates the module, meaning
+ # we shouldn't check the connection specs
+ for module in self.modules.itervalues():
+ if module.is_valid and (module.is_group() or
+ module.is_abstraction()):
+ try:
+ subpipeline = module.pipeline
+ if subpipeline is not None:
+ subpipeline.validate()
+ except InvalidPipeline, e:
+ module.is_valid = False
+ e._module_id = module.id
+ exceptions.add(e)
+ if module.is_abstraction():
+ try:
+ desc = module.module_descriptor
+ if long(module.internal_version) != long(desc.version):
+ exceptions.add(MissingModuleVersion(desc.package, desc.name, desc.namespace, desc.version, desc.package_version, module.id))
+ except:
+ pass
+ try:
+ self.ensure_port_specs()
+ except InvalidPipeline, e:
+ exceptions.update(e.get_exception_set())
+ try:
+ self.ensure_connection_specs()
+ except InvalidPipeline, e:
+ exceptions.update(e.get_exception_set())
+ try:
+ self.ensure_functions()
+ except InvalidPipeline, e:
+ exceptions.update(e.get_exception_set())
+ try:
+ self.ensure_vistrail_variables(vistrail_vars)
+ except InvalidPipeline, e:
+ exceptions.update(e.get_exception_set())
+
+ self.check_subworkflow_versions()
+
+ if len(exceptions) > 0:
+ if raise_exception:
+ raise InvalidPipeline(exceptions, self)
+ else:
+ self.is_valid = False
+ return False
+
+ self.is_valid = True
+ return True
+
+ def ensure_old_modules_have_package_names(self):
+ """ensure_old_modules_have_package_names()
+
+ Makes sure each module has a package associated with it.
+
+ """
+ for i in self.modules.iterkeys():
+ self.get_module_by_id(i)
+
+ def ensure_connection_specs(self, connection_ids=None):
+ """ensure_connection_specs(connection_ids=None) -> None.
+
+ Computes the specs for the connections in connection_ids. If
+ connection_ids is None, computes it for every connection in the pipeline.
+ """
+ exceptions = set()
+
+ # print 'ensure_connection_specs:', sorted(self.modules.keys())
+
+ def find_spec(port):
+ port.is_valid = False
+ module = self.get_module_by_id(port.moduleId)
+ port_type_map = PortSpec.port_type_map
+ try:
+ # print 'running get_port_spec', port.name
+ port.spec = module.get_port_spec(port.name,
+ port_type_map.inverse[port.type])
+ # print 'got spec', spec, spec.sigstring
+ except ModuleRegistryException, e:
+ # debug.critical('CONNECTION EXCEPTION: %s' % e)
+ exceptions.add(e)
+ else:
+ if port.spec.is_valid:
+ port.is_valid = True
+
+ if connection_ids is None:
+ connection_ids = self.connections.iterkeys()
+ for conn_id in connection_ids:
+ conn = self.connections[conn_id]
+ # print 'checking connection', conn_id, conn.source.moduleId, conn.source.moduleName, conn.source.name, conn.destination.moduleId, conn.destination.moduleName, conn.destination.name
+ src_module = self.modules[conn.source.moduleId]
+ if src_module.is_valid:
+ # print 'src_module:', src_module.name, src_module.id
+ find_spec(conn.source)
+
+ dst_module = self.modules[conn.destination.moduleId]
+ if dst_module.is_valid:
+ # print 'dst_module:', dst_module.name, dst_module.id
+ find_spec(conn.destination)
+
+ # if not conn.source.spec:
+ # conn.source.spec = find_spec(conn.source)
+ # if not conn.destination.spec:
+ # conn.destination.spec = find_spec(conn.destination)
+ # print 'source spec:', conn.source.spec.sigstring
+ # print 'dest spec:', conn.destination.spec.sigstring
+
+ if len(exceptions) > 0:
+ raise InvalidPipeline(exceptions, self)
+
+ def ensure_modules_are_on_registry(self, module_ids=None):
+ """ensure_modules_are_on_registry(module_ids: optional list of module ids) -> None
+
+ Queries the module registry for the module information in the
+ given modules. The only goal of this function is to trigger
+ exceptions in the registry that will be treated somewhere else
+ in the calling stack.
+
+ If modules are not on registry, the registry will raise
+ ModuleRegistryException exceptions that should be caught and handled.
+
+ if no module_ids list is given, we assume every module in the pipeline.
+ """
+ def find_descriptors(pipeline, module_ids=None):
+ registry = get_module_registry()
+ conf = get_vistrails_configuration()
+ if module_ids == None:
+ module_ids = pipeline.modules.iterkeys()
+ exceptions = set()
+ for mid in module_ids:
+ module = pipeline.modules[mid]
+ module.is_valid = False
+ if not module.version:
+ module.version = '0'
+ try:
+ # FIXME check for upgrades, otherwise use similar
+ # descriptor, the old behavior
+ descriptor = module.module_descriptor
+ except ModuleRegistryException, e:
+ e._module_id = mid
+ exceptions.add(e)
+ else:
+ module.is_valid = True
+ return exceptions
+ # end find_descriptors
+
+ exceptions = find_descriptors(self, module_ids)
+ if len(exceptions) > 0:
+ raise InvalidPipeline(exceptions, self)
+
+ def ensure_functions(self):
+ exceptions = set()
+ reg = get_module_registry()
+ for module in self.modules.itervalues():
+ for function in module.functions:
+ is_valid = True
+ if module.is_valid and not module.has_port_spec(function.name,
+ 'input'):
+ is_valid = False
+ e = MissingFunction(function.name, module.name, module.id)
+ e._module_id = module.id
+ exceptions.add(e)
+ pos_map = {}
+ for p in function.parameters:
+ if p.identifier == '':
+ idn = get_vistrails_basic_pkg_id()
+ else:
+ idn = p.identifier
+
+ try:
+ desc = reg.get_module_by_name(idn,
+ p.type,
+ p.namespace)
+ except ModuleRegistryException, e:
+ is_valid = False
+ e._module_id = module.id
+ exceptions.add(e)
+
+ if p.pos in pos_map:
+ is_valid = False
+ e = VistrailsInternalError("Module %d has multiple "
+ "values for parameter %d "
+ "of function %s (%d)" % \
+ (module.id,
+ p.pos,
+ function.name,
+ function.real_id))
+ exceptions.add(e)
+ pos_map[p.pos] = p
+ function.is_valid = is_valid
+ if len(exceptions) > 0:
+ raise InvalidPipeline(exceptions, self)
+
+ def ensure_vistrail_variables(self, vistrail_vars):
+ var_uuids = [var.uuid for var in vistrail_vars]
+ exceptions = set()
+ for module in self.modules.itervalues():
+ if module.is_vistrail_var():
+ # first check if value is already set
+ # (used by parameter explorations)
+ value_set = False
+ for func in module.functions:
+ if func.name == 'value':
+ if func.params[0].strValue:
+ value_set = True
+ continue
+ if value_set:
+ continue
+ var_uuid = module.get_vistrail_var()
+ if var_uuid not in var_uuids:
+ e = MissingVistrailVariable(var_uuid, module.package,
+ module.name, module.namespace)
+ exceptions.add(e)
+ if len(exceptions) > 0:
+ raise InvalidPipeline(exceptions, self)
+
+ def ensure_port_specs(self):
+ exceptions = set()
+ for module in self.modules.itervalues():
+ # if module.is_valid:
+ try:
+ for port_spec in module.port_specs.itervalues():
+ try:
+ port_spec.descriptors()
+ except MissingPackage, e:
+ port_spec.is_valid = False
+ e._module_id = module.id
+ exceptions.add(e)
+ except ModuleRegistryException, e:
+ e = PortMismatch(module.package, module.name,
+ module.namespace, port_spec.name,
+ port_spec.type, port_spec.sigstring)
+ port_spec.is_valid = False
+ e._module_id = module.id
+ exceptions.add(e)
+ except ModuleRegistryException, e:
+ if module.is_valid:
+ module.is_valid = False
+
+ if len(exceptions) > 0:
+ raise InvalidPipeline(exceptions, self)
+
+ def check_subworkflow_versions(self):
+ reg = get_module_registry()
+ for module in self.modules.itervalues():
+ if module.is_valid and module.is_abstraction():
+ module.check_latest_version()
+
+ ##########################################################################
+ # Debugging
+
+ def show_comparison(self, other):
+ if type(other) != type(self):
+ print "type mismatch"
+ return
+ if len(self.module_list) != len(other.module_list):
+ print "module lists of different sizes"
+ return
+ if len(self.connection_list) != len(other.connection_list):
+ print "Connection lists of different sizes"
+ return
+ for m_id, m in self.modules.iteritems():
+ if not m_id in other.modules:
+ print "module %d in self but not in other" % m_id
+ return
+ if m <> other.modules[m_id]:
+ print "module %s in self doesn't match module %s in other" % (m, other.modules[m_id])
+ return
+ for m_id, m in other.modules.iteritems():
+ if not m_id in self.modules:
+ print "module %d in other but not in self" % m_id
+ return
+ # no need to check equality since this was already done before
+ for c_id, c in self.connections.iteritems():
+ if not c_id in other.connections:
+ print "connection %d in self but not in other" % c_id
+ return
+ if c <> other.connections[c_id]:
+ print "connection %s in self doesn't match connection %s in other" % (c, other.connections[c_id])
+ return
+ for c_id, c, in other.connections.iteritems():
+ if not c_id in self.connections:
+ print "connection %d in other but not in self" % c_id
+ return
+ # no need to check equality since this was already done before
+ assert self == other
+
+ ##########################################################################
+ # Operators
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+# There's a bug in this code that's not easily worked around: if
+# modules are in different order in the list, there's no easy way to
+# check for equality. The solution is to move to a check that
+# takes module and connection ids into account.
+# def __eq__(self, other):
+# if type(other) != type(self):
+# return False
+# if len(self.module_list) != len(other.module_list):
+# return False
+# if len(self.connection_list) != len(other.connection_list):
+# return False
+# for f, g in zip(self.module_list, other.module_list):
+# if f != g:
+# return False
+# for f, g in zip(self.connection_list, other.connection_list):
+# if f != g:
+# return False
+# return True
+
+ def __eq__(self, other):
+ if type(other) != type(self):
+ return False
+ if len(self.module_list) != len(other.module_list):
+ return False
+ if len(self.connection_list) != len(other.connection_list):
+ return False
+ for m_id, m in self.modules.iteritems():
+ if not m_id in other.modules:
+ return False
+ if m <> other.modules[m_id]:
+ return False
+ for m_id, m in other.modules.iteritems():
+ if not m_id in self.modules:
+ return False
+ # no need to check equality since this was already done before
+ for c_id, c in self.connections.iteritems():
+ if not c_id in other.connections:
+ return False
+ if c <> other.connections[c_id]:
+ return False
+ for c_id, c, in other.connections.iteritems():
+ if not c_id in self.connections:
+ return False
+ # no need to check equality since this was already done before
+ return True
+
+ def __str__(self):
+ return ("(Pipeline Modules: %s Graph:%s)@%X" %
+ ([(m, str(v)) for (m,v) in sorted(self.modules.items())],
+ str(self.graph),
+ id(self)))
+
+
+################################################################################
+
+
+class TestPipeline(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ # make sure pythonCalc is loaded
+ from vistrails.core.packagemanager import get_package_manager
+ pm = get_package_manager()
+ if 'pythonCalc' not in pm._package_list: # pragma: no cover # pragma: no partial
+ pm.late_enable_package('pythonCalc')
+
+ def create_default_pipeline(self, id_scope=None):
+ if id_scope is None:
+ id_scope = IdScope()
+
+ p = Pipeline()
+ p.id = id_scope.getNewId(Pipeline.vtType)
+
+ def module1(p):
+ def f1():
+ f = ModuleFunction()
+ f.real_id = id_scope.getNewId(ModuleFunction.vtType)
+ f.name = 'op'
+ f.returnType = 'void'
+ param = ModuleParam()
+ param.type = 'String'
+ param.strValue = '+'
+ f.params.append(param)
+ return f
+ def f2():
+ f = ModuleFunction()
+ f.real_id = id_scope.getNewId(ModuleFunction.vtType)
+ f.name = 'value1'
+ f.returnType = 'void'
+ param = ModuleParam()
+ param.type = 'Float'
+ param.strValue = '2.0'
+ f.params.append(param)
+ return f
+ def f3():
+ f = ModuleFunction()
+ f.real_id = id_scope.getNewId(ModuleFunction.vtType)
+ f.name = 'value2'
+ f.returnType = 'void'
+ param = ModuleParam()
+ param.type = 'Float'
+ param.strValue = '4.0'
+ f.params.append(param)
+ return f
+ m = Module()
+ m.id = id_scope.getNewId(Module.vtType)
+ m.name = 'PythonCalc'
+ m.package = '%s.pythoncalc' % get_vistrails_default_pkg_prefix()
+ m.functions.append(f1())
+ return m
+
+ def module2(p):
+ def f1():
+ f = ModuleFunction()
+ f.real_id = id_scope.getNewId(ModuleFunction.vtType)
+ f.name = 'op'
+ f.returnType = 'void'
+ param = ModuleParam()
+ param.type = 'String'
+ param.strValue = '+'
+ f.params.append(param)
+ return f
+ m = Module()
+ m.id = id_scope.getNewId(Module.vtType)
+ m.name = 'PythonCalc'
+ m.package = '%s.pythoncalc' % get_vistrails_default_pkg_prefix()
+ m.functions.append(f1())
+ return m
+ m1 = module1(p)
+ p.add_module(m1)
+ m2 = module1(p)
+ p.add_module(m2)
+ m3 = module2(p)
+ p.add_module(m3)
+
+ c1 = Connection()
+ c1.sourceId = m1.id
+ c1.destinationId = m3.id
+ c1.source.id = id_scope.getNewId(Port.vtType)
+ c1.destination.id = id_scope.getNewId(Port.vtType)
+ c1.source.name = 'value'
+ c1.source.moduleName = 'PythonCalc'
+ c1.destination.name = 'value1'
+ c1.destination.moduleName = 'PythonCalc'
+ c1.id = id_scope.getNewId(Connection.vtType)
+ p.add_connection(c1)
+
+ c2 = Connection()
+ c2.sourceId = m2.id
+ c2.destinationId = m3.id
+ c2.source.id = id_scope.getNewId(Port.vtType)
+ c2.destination.id = id_scope.getNewId(Port.vtType)
+ c2.source.name = 'value'
+ c2.source.moduleName = 'PythonCalc'
+ c2.destination.name = 'value2'
+ c2.destination.moduleName = 'PythonCalc'
+ c2.id = id_scope.getNewId(Connection.vtType)
+
+ p.add_connection(c2)
+ p.compute_signatures()
+ return p
+
+ def create_pipeline2(self, id_scope=None):
+ basic_pkg = get_vistrails_basic_pkg_id()
+ if id_scope is None:
+ id_scope = IdScope(remap={Abstraction.vtType: Module.vtType})
+
+ param1 = ModuleParam(id=id_scope.getNewId(ModuleParam.vtType),
+ type='Int',
+ val='1')
+ param2 = ModuleParam(id=id_scope.getNewId(ModuleParam.vtType),
+ type='Float',
+ val='1.3456')
+ func1 = ModuleFunction(id=id_scope.getNewId(ModuleFunction.vtType),
+ name='value',
+ parameters=[param1])
+ func2 = ModuleFunction(id=id_scope.getNewId(ModuleFunction.vtType),
+ name='floatVal',
+ parameters=[param2])
+ loc1 = Location(id=id_scope.getNewId(Location.vtType),
+ x=12.342,
+ y=-19.432)
+ loc2 = Location(id=id_scope.getNewId(Location.vtType),
+ x=21.34,
+ y=456.234)
+ m1 = Module(id=id_scope.getNewId(Module.vtType),
+ package=basic_pkg,
+ name='String',
+ location=loc1,
+ functions=[func1])
+ m2 = Abstraction(id=id_scope.getNewId(Abstraction.vtType),
+ internal_version=13,
+ location=loc2,
+ functions=[func2])
+ source = Port(id=id_scope.getNewId(Port.vtType),
+ type='source',
+ moduleId=m1.id,
+ moduleName='String',
+ name='value',
+ signature='(%s:String)' % basic_pkg)
+ destination = Port(id=id_scope.getNewId(Port.vtType),
+ type='destination',
+ moduleId=m2.id,
+ moduleName='Abstraction',
+ name='self',
+ signature='()')
+ c1 = Connection(id=id_scope.getNewId(Connection.vtType),
+ ports=[source, destination])
+ pipeline = Pipeline(id=id_scope.getNewId(Pipeline.vtType),
+ modules=[m1, m2],
+ connections=[c1])
+ return pipeline
+
+ def setUp(self):
+ self.pipeline = self.create_default_pipeline()
+ self.sink_id = 2
+
+ def test_create_pipeline_signature(self):
+ self.pipeline.subpipeline_signature(self.sink_id)
+
+ def test_delete_signatures(self):
+ """Makes sure signatures are deleted when other things are."""
+ p = self.create_default_pipeline()
+ m_sig_size_before = len(p._module_signatures)
+ c_sig_size_before = len(p._connection_signatures)
+ p_sig_size_before = len(p._subpipeline_signatures)
+ p.delete_connection(0)
+ p.delete_module(0)
+ m_sig_size_after = len(p._module_signatures)
+ c_sig_size_after = len(p._connection_signatures)
+ p_sig_size_after = len(p._subpipeline_signatures)
+ self.assertNotEquals(m_sig_size_before, m_sig_size_after)
+ self.assertNotEquals(c_sig_size_before, c_sig_size_after)
+ self.assertNotEquals(p_sig_size_before, p_sig_size_after)
+
+ def test_delete_connections(self):
+ p = self.create_default_pipeline()
+ p.delete_connection(0)
+ p.delete_connection(1)
+ p.delete_module(2)
+ self.assertEquals(len(p.connections), 0)
+
+ def test_basic(self):
+ """Makes sure pipeline can be created, modules and connections
+ can be added and deleted."""
+ p = self.create_default_pipeline()
+
+ def test_copy(self):
+ id_scope = IdScope()
+
+ p1 = self.create_default_pipeline(id_scope)
+ p2 = copy.copy(p1)
+ self.assertEquals(p1, p2)
+ self.assertEquals(p1.id, p2.id)
+ p3 = p1.do_copy(True, id_scope, {})
+ self.assertNotEquals(p1, p3)
+ self.assertNotEquals(p1.id, p3.id)
+
+ def test_copy2(self):
+ import vistrails.core.db.io
+
+ # nedd to id modules and abstraction_modules with same counter
+ id_scope = IdScope(remap={Abstraction.vtType: Module.vtType})
+
+ p1 = self.create_pipeline2(id_scope)
+ p2 = copy.copy(p1)
+ self.assertEquals(p1, p2)
+ self.assertEquals(p1.id, p2.id)
+ p3 = p1.do_copy(True, id_scope, {})
+ self.assertNotEquals(p1, p3)
+ self.assertNotEquals(p1.id, p3.id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ p1 = self.create_default_pipeline()
+ xml_str = vistrails.core.db.io.serialize(p1)
+ p2 = vistrails.core.db.io.unserialize(xml_str, Pipeline)
+ self.assertEquals(p1, p2)
+ self.assertEquals(p1.id, p2.id)
+
+ def test_serialization2(self):
+ import vistrails.core.db.io
+ p1 = self.create_pipeline2()
+ xml_str = vistrails.core.db.io.serialize(p1)
+ p2 = vistrails.core.db.io.unserialize(xml_str, Pipeline)
+ self.assertEquals(p1, p2)
+ self.assertEquals(p1.id, p2.id)
+
+ def test_aliases(self):
+ """ Exercises aliases manipulation """
+ import vistrails.core.db.action
+ from vistrails.core.db.locator import XMLFileLocator
+ import vistrails.core.system
+ v = XMLFileLocator( \
+ vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/test_alias.xml').load()
+
+ p1 = v.getPipeline('alias')
+ p2 = v.getPipeline('alias')
+
+ # testing removing an alias
+ old_param = p1.modules[0].functions[0].params[0]
+ func = p1.modules[0].functions[0]
+ #old_id = p1.modules[0].functions[0].params[0].db_id
+ #old_f_id = p1.modules[0].functions[0].db_id
+ new_param = ModuleParam(id=-1,
+ pos=old_param.pos,
+ name=old_param.name,
+ alias="",
+ val=str(1.0),
+ type=old_param.type)
+ action_spec = ('change', old_param, new_param,
+ func.vtType, func.real_id)
+ action = vistrails.core.db.action.create_action([action_spec])
+ p1.perform_action(action)
+ self.assertEquals(p1.has_alias('v1'),False)
+ v1 = p2.aliases['v1']
+ old_param2 = p2.modules[0].functions[0].params[0]
+ new_param2 = ModuleParam(id=old_param.real_id,
+ pos=old_param.pos,
+ name=old_param.name,
+ alias="v1",
+ val=str(v),
+ type=old_param.type)
+ func2 = p2.modules[0].functions[0]
+ action2 = vistrails.core.db.action.create_action([('change',
+ old_param2,
+ new_param2,
+ func2.vtType,
+ func2.real_id)
+ ])
+ p2.perform_action(action2)
+ self.assertEquals(v1, p2.aliases['v1'])
+
+ def test_module_signature(self):
+ """Tests signatures for modules with similar (but not equal)
+ parameter specs."""
+ pycalc_pkg = '%s.pythoncalc' % get_vistrails_default_pkg_prefix()
+ p1 = Pipeline()
+ p1_functions = [ModuleFunction(name='value1',
+ parameters=[ModuleParam(type='Float',
+ val='1.0',
+ )],
+ ),
+ ModuleFunction(name='value2',
+ parameters=[ModuleParam(type='Float',
+ val='2.0',
+ )],
+ )]
+ p1.add_module(Module(name='PythonCalc',
+ package=pycalc_pkg,
+ id=3,
+ functions=p1_functions))
+
+ p2 = Pipeline()
+ p2_functions = [ModuleFunction(name='value1',
+ parameters=[ModuleParam(type='Float',
+ val='2.0',
+ )],
+ ),
+ ModuleFunction(name='value2',
+ parameters=[ModuleParam(type='Float',
+ val='1.0',
+ )],
+ )]
+ p2.add_module(Module(name='PythonCalc',
+ package=pycalc_pkg,
+ id=3,
+ functions=p2_functions))
+
+ self.assertNotEquals(p1.module_signature(3),
+ p2.module_signature(3))
+
+ def test_find_method(self):
+ p1 = Pipeline()
+ p1_functions = [ModuleFunction(name='i1',
+ parameters=[ModuleParam(type='Float',
+ val='1.0',
+ )],
+ ),
+ ModuleFunction(name='i2',
+ parameters=[ModuleParam(type='Float',
+ val='2.0',
+ )],
+ )]
+ p1.add_module(Module(name='CacheBug',
+ package='%s.console_mode_test' % \
+ get_vistrails_default_pkg_prefix(),
+ id=3,
+ functions=p1_functions))
+
+ self.assertEquals(p1.find_method(3, 'i1'), 0)
+ self.assertEquals(p1.find_method(3, 'i2'), 1)
+ self.assertEquals(p1.find_method(3, 'i3'), -1)
+ self.assertRaises(KeyError, p1.find_method, 4, 'i1')
+
+ def test_str(self):
+ p1 = Pipeline()
+ p1_functions = [ModuleFunction(name='i1',
+ parameters=[ModuleParam(type='Float',
+ val='1.0',
+ )],
+ ),
+ ModuleFunction(name='i2',
+ parameters=[ModuleParam(type='Float',
+ val='2.0',
+ )],
+ )]
+ p1.add_module(Module(name='CacheBug',
+ package='%s.console_mode_test' % \
+ get_vistrails_default_pkg_prefix(),
+ id=3,
+ functions=p1_functions))
+ str(p1)
+
+ def test_pipeline_equality_module_list_out_of_order(self):
+ p1 = Pipeline()
+ p1.add_module(Module(name='Foo',
+ package='bar',
+ id=0,
+ functions=[]))
+ p1.add_module(Module(name='Foo2',
+ package='bar',
+ id=1,
+ functions=[]))
+ p2 = Pipeline()
+ p2.add_module(Module(name='Foo2',
+ package='bar',
+ id=1,
+ functions=[]))
+ p2.add_module(Module(name='Foo',
+ package='bar',
+ id=0,
+ functions=[]))
+ assert p1 == p2
+
+# def test_subpipeline(self):
+# p = self.create_default_pipeline()
+# p2 = p.get_subpipeline([0, 1])
+# for m in p2.modules:
+# print m
+# for c in p2.connections:
+# print c
+
+ def test_incorrect_port_spec(self):
+ import vistrails.core.modules.basic_modules
+ p = Pipeline()
+ basic_version = vistrails.core.modules.basic_modules.version
+ basic_pkg = vistrails.core.modules.basic_modules.identifier
+ m1 = Module(name="String",
+ package=basic_pkg,
+ version=basic_version,
+ id=1L)
+ m2 = Module(name="String",
+ package=basic_pkg,
+ version=basic_version,
+ id=2L)
+ source = Port(id=1L,
+ type='source',
+ moduleId=m1.id,
+ moduleName='String',
+ name='value',
+ signature='(%s:StringBean)' % basic_pkg)
+ destination = Port(id=2L,
+ type='destination',
+ moduleId=m2.id,
+ moduleName='String',
+ name='value',
+ signature='(%s:NString)' % basic_pkg)
+ c1 = Connection(id=1L,
+ ports=[source, destination])
+ p.add_module(m1)
+ p.add_module(m2)
+ p.add_connection(c1)
+ p.ensure_modules_are_on_registry()
+ p.ensure_connection_specs()
+ p_source = p.connections[c1.id].source
+ p_destination = p.connections[c1.id].destination
+ self.assertEqual(p_source.signature, '(%s:String)' % basic_pkg)
+ self.assertEqual(len(p_source.descriptors()), 1)
+ self.assertEqual(p_destination.signature, '(%s:String)' % basic_pkg)
+ self.assertEqual(len(p_destination.descriptors()), 1)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/vistrail/plugin_data.py b/vistrails/core/vistrail/plugin_data.py
new file mode 100644
index 0000000..c36b901
--- /dev/null
+++ b/vistrails/core/vistrail/plugin_data.py
@@ -0,0 +1,101 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBPluginData
+
+import unittest
+import copy
+import random
+from vistrails.db.domain import IdScope
+import vistrails.core
+
+class PluginData(DBPluginData):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBPluginData.__init__(self, *args, **kwargs)
+ if self.id is None:
+ self.id = -1
+
+ def __copy__(self):
+ return PluginData.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPluginData.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = PluginData
+ return cp
+
+ ##########################################################################
+ # DB Conversion
+
+ @staticmethod
+ def convert(_plugin_data):
+ _plugin_data.__class__ = PluginData
+
+ ##########################################################################
+ # Properties
+
+ id = DBPluginData.db_id
+ data = DBPluginData.db_data
+
+ ##########################################################################
+ # Operators
+
+ def __eq__(self, other):
+ if type(other) != type(self):
+ return False
+ return self.data == other.data
+
+################################################################################
+# Testing
+
+
+class TestPluginData(unittest.TestCase):
+
+ def create_data(self, id=1, data=""):
+ return PluginData(id=id, data=data)
+
+ def test_create(self):
+ self.create_data(2, "testing the data field")
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ p_data1 = self.create_data()
+ xml_str = vistrails.core.db.io.serialize(p_data1)
+ p_data2 = vistrails.core.db.io.unserialize(xml_str, PluginData)
+ self.assertEquals(p_data1, p_data2)
+ self.assertEquals(p_data1.id, p_data2.id)
+
diff --git a/vistrails/core/vistrail/port.py b/vistrails/core/vistrail/port.py
new file mode 100644
index 0000000..3f17a62
--- /dev/null
+++ b/vistrails/core/vistrail/port.py
@@ -0,0 +1,303 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This module contains class definitions for:
+ * Port
+
+ """
+from vistrails.db.domain import DBPort
+from vistrails.core.utils import VistrailsInternalError, all
+from vistrails.core.vistrail.port_spec import PortSpec, PortEndPoint
+import vistrails.core.modules.vistrails_module
+import copy
+
+import unittest
+from vistrails.db.domain import IdScope
+
+################################################################################
+
+class Port(DBPort):
+ """ A port denotes one endpoint of a Connection.
+
+ self.spec: list of list of (module, str)
+
+ """
+
+ ##########################################################################
+ # Constructor and copy
+
+ def __init__(self, *args, **kwargs):
+ """The preferred way to create a port is to pass a PortSpec with
+ new information. The construcotr pulls name, type, and signature
+ info from the PortSpec.
+
+ Example: Port(id=<id>, spec=<port_spec>, moduleId=<id>,
+ moduleName=<name>)
+
+ You can also pass the name, type, and signature, separately.
+
+ Example: Port(id=<id>, name=<name>, type=[source|destination],
+ signature=<sig>, moduleId=<id>, moduleName=<name>)
+
+ """
+
+ self._spec = None
+ self._descriptors = None
+ if 'spec' in kwargs:
+ self._spec = kwargs['spec']
+ del kwargs['spec']
+ if 'name' not in kwargs:
+ kwargs['name'] = self._spec.name
+ if 'type' not in kwargs:
+ if self._spec.type in PortSpec.port_type_map:
+ kwargs['type'] = PortSpec.port_type_map[self._spec.type]
+ if 'signature' not in kwargs:
+ kwargs['signature'] = self._spec.sigstring
+# else:
+# self.spec = None
+ if 'id' not in kwargs:
+ kwargs['id'] = -1
+ if 'moduleId' not in kwargs:
+ kwargs['moduleId'] = 0
+ if 'moduleName' not in kwargs:
+ kwargs['moduleName'] = ""
+ if 'name' not in kwargs:
+ kwargs['name'] = ""
+ if 'signature' not in kwargs:
+ kwargs['signature'] = ""
+
+ DBPort.__init__(self, *args, **kwargs)
+
+ self.set_defaults()
+
+# # if there is no spec, create it
+# spec_type = PortSpec.port_type_map.inverse[self.type]
+# self._spec = PortSpec(name=self.name,
+# type=spec_type,
+# sigstring=self.signature)
+
+ def set_defaults(self, other=None):
+ if other is None:
+ self.is_valid = False
+ else:
+ self.is_valid = other.is_valid
+ self._spec = copy.copy(other._spec)
+ self._descriptors = copy.copy(other._descriptors)
+
+ def __copy__(self):
+ return Port.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Port
+ cp.set_defaults(self)
+ return cp
+
+ @staticmethod
+ def convert(_port):
+ if _port.__class__ == Port:
+ return
+ _port.__class__ = Port
+ _port._spec = None
+ _port._descriptors = None
+ _port.set_defaults()
+
+ ##########################################################################
+ # Properties
+
+ id = DBPort.db_id
+ moduleId = DBPort.db_moduleId
+ moduleName = DBPort.db_moduleName
+ name = DBPort.db_name
+ type = DBPort.db_type
+
+ def _get_endPoint(self):
+ if self.db_type in PortSpec.end_point_map:
+ return PortSpec.end_point_map[self.db_type]
+ return PortEndPoint.Invalid
+ def _set_endPoint(self, endPoint):
+ if endPoint in PortSpec.end_point_map.inverse:
+ self.db_type = PortSpec.end_point_map.inverse[endPoint]
+ else:
+ self.db_type = 'invalid'
+ endPoint = property(_get_endPoint, _set_endPoint)
+
+ def _get_signature(self):
+ if not self.db_signature and self.spec is not None:
+ self.db_signature = self.spec.sigstring
+ return self.db_signature
+ def _set_signature(self, signature):
+ self.db_signature = signature
+ signature = property(_get_signature, _set_signature)
+ sigstring = signature
+
+ def _get_spec(self):
+ return self._spec
+ def _set_spec(self, spec):
+ self._spec = spec
+ if self._spec is not None:
+ self.name = self._spec.name
+ self.type = PortSpec.port_type_map[self._spec.type]
+ self.signature = self._spec.sigstring
+ # self.find_port_types()
+ else:
+ self.signature = ""
+ spec = property(_get_spec, _set_spec)
+
+ # FIXME get rid of this one?
+ def _get_sig(self):
+ return self.name + self.signature
+ sig = property(_get_sig)
+
+ def descriptors(self):
+ if self._spec is not None:
+ return self._spec.descriptors()
+ return None
+
+ # return self._descriptors
+
+ ##########################################################################
+ # Debugging
+
+ def show_comparison(self, other):
+ if type(self) != type(other):
+ print "Type mismatch"
+ elif self.endPoint != other.endPoint:
+ print "endpoint mismatch"
+ elif self.moduleName != other.moduleName:
+ print "moduleName mismatch"
+ elif self.name != other.name:
+ print "name mismatch"
+ elif self.spec != other.spec:
+ print "spec mismatch"
+ else:
+ print "no difference found"
+ assert self == other
+
+ ##########################################################################
+ # Operators
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+ def __eq__(self, other):
+ if type(self) != type(other):
+ return False
+ return (self.endPoint == other.endPoint and
+# FIXME module id can change...
+# self.moduleId == other.moduleId and
+ self.moduleName == other.moduleName and
+ self.name == other.name and
+ self.signature == other.signature)
+
+ def __str__(self):
+ """ __str__() -> str
+ Returns a string representation of a Port object. """
+ return '<Port endPoint="%s" moduleId=%s name=%s ' \
+ 'type=Module %s/>' % (self.endPoint,
+ self.moduleId,
+ self.name,
+ self.spec)
+
+ def equals_no_id(self, other):
+ if type(self) != type(other):
+ return False
+ return (self.endPoint == other.endPoint and
+ self.moduleName == other.moduleName and
+ self.name == other.name and
+ self.signature == other.signature)
+
+###############################################################################
+
+
+if __name__ == '__main__':
+ import vistrails.core.modules.basic_modules
+ import vistrails.core.modules.module_registry
+
+from vistrails.core.system import get_vistrails_basic_pkg_id
+
+class TestPort(unittest.TestCase):
+ def setUp(self):
+ self.registry = vistrails.core.modules.module_registry.get_module_registry()
+
+ def create_port(self, id_scope=IdScope()):
+ port = Port(id=id_scope.getNewId(Port.vtType),
+ type='source',
+ moduleId=12L,
+ moduleName='String',
+ name='value',
+ signature='(%s:String)' % get_vistrails_basic_pkg_id())
+ return port
+
+ def test_copy(self):
+ id_scope = IdScope()
+
+ p1 = self.create_port(id_scope)
+ p2 = copy.copy(p1)
+ self.assertEquals(p1, p2)
+ self.assertEquals(p1.id, p2.id)
+ p3 = p1.do_copy(True, id_scope, {})
+ self.assertEquals(p1, p3)
+ self.assertNotEquals(p1.id, p3.id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ p1 = self.create_port()
+ xml_str = vistrails.core.db.io.serialize(p1)
+ p2 = vistrails.core.db.io.unserialize(xml_str, Port)
+ self.assertEquals(p1, p2)
+ self.assertEquals(p1.id, p2.id)
+
+ def testPort(self):
+ x = Port()
+ a = str(x)
+
+ def test_registry_port_subtype(self):
+ """Test registry isPortSubType"""
+ descriptor = self.registry.get_descriptor_by_name( \
+ get_vistrails_basic_pkg_id(), 'String')
+ ports = self.registry.source_ports_from_descriptor(descriptor)
+ assert self.registry.is_port_sub_type(ports[0], ports[0])
+
+ def test_registry_ports_can_connect(self):
+ """Test registry isPortSubType"""
+ descriptor = self.registry.get_descriptor_by_name( \
+ get_vistrails_basic_pkg_id(), 'String')
+ oport = self.registry.source_ports_from_descriptor(descriptor)[0]
+ iport = self.registry.destination_ports_from_descriptor(descriptor)[0]
+ assert self.registry.ports_can_connect(oport, iport)
+
+if __name__ == '__main__':
+ unittest.main()
+
diff --git a/vistrails/core/vistrail/port_spec.py b/vistrails/core/vistrail/port_spec.py
new file mode 100644
index 0000000..948c6c0
--- /dev/null
+++ b/vistrails/core/vistrail/port_spec.py
@@ -0,0 +1,522 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from itertools import izip
+import operator
+
+from vistrails.core.data_structures.bijectivedict import Bidict
+from vistrails.core.modules.utils import create_port_spec_string, parse_port_spec_string
+from vistrails.core.system import get_vistrails_basic_pkg_id
+from vistrails.core.utils import enum, VistrailsInternalError
+from vistrails.core.vistrail.port_spec_item import PortSpecItem
+from vistrails.db.domain import DBPortSpec
+
+import unittest
+import copy
+from vistrails.db.domain import IdScope
+import vistrails.core
+
+################################################################################
+
+PortEndPoint = enum('PortEndPoint',
+ ['Invalid', 'Source', 'Destination'])
+
+################################################################################
+
+class PortSpec(DBPortSpec):
+
+ port_type_map = Bidict([('input', 'destination'),
+ ('output', 'source'),
+ ('invalid', 'invalid')])
+ end_point_map = Bidict([('source', PortEndPoint.Source),
+ ('destination', PortEndPoint.Destination),
+ ('invalid', PortEndPoint.Invalid)])
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ signature = None
+ if 'signature' in kwargs:
+ signature = kwargs['signature']
+ del kwargs['signature']
+ sigstring = None
+ if 'sigstring' in kwargs:
+ sigstring = kwargs['sigstring']
+ del kwargs['sigstring']
+ defaults = None
+ if 'defaults' in kwargs:
+ defaults = kwargs['defaults']
+ del kwargs['defaults']
+ labels = None
+ if 'labels' in kwargs:
+ labels = kwargs['labels']
+ del kwargs['labels']
+ values = None
+ if 'values' in kwargs:
+ values = kwargs['values']
+ del kwargs['values']
+ entry_types = None
+ if 'entry_types' in kwargs:
+ entry_types = kwargs['entry_types']
+ del kwargs['entry_types']
+
+ if 'items' in kwargs and 'portSpecItems' not in kwargs:
+ kwargs['portSpecItems'] = kwargs['items']
+ del kwargs['items']
+
+ if 'optional' not in kwargs:
+ kwargs['optional'] = 0 # False
+ elif not isinstance(kwargs['optional'], (int, long)):
+ if isinstance(kwargs['optional'], bool):
+ if kwargs['optional']:
+ kwargs['optional'] = 1
+ else:
+ kwargs['optional'] = 0
+ else:
+ raise VistrailsInternalError("Cannot parse 'optional' kw "
+ "-- must be an int or bool")
+ if 'min_conns' not in kwargs:
+ kwargs['min_conns'] = 0
+ elif kwargs['optional'] == 1 and kwargs['min_conns'] > 0:
+ raise VistrailsInternalError("A mandatory port cannot be set "
+ "to optional")
+ if 'max_conns' not in kwargs:
+ kwargs['max_conns'] = -1
+ if kwargs['min_conns'] >= 0 and kwargs['max_conns'] >= 0 and \
+ kwargs['min_conns'] > kwargs['max_conns']:
+ raise VistrailsInternalError("Minimum number of connections "
+ "cannot be greater than maximum "
+ "number of connections")
+
+ if 'sort_key' not in kwargs:
+ kwargs['sort_key'] = -1
+ if 'id' not in kwargs:
+ kwargs['id'] = -1
+ if 'tooltip' in kwargs:
+ self._tooltip = kwargs['tooltip']
+ del kwargs['tooltip']
+ else:
+ self._tooltip = None
+
+ if 'docstring' in kwargs:
+ self._docstring = kwargs['docstring']
+ del kwargs['docstring']
+ else:
+ self._docstring = None
+ if 'shape' in kwargs:
+ self._shape = kwargs['shape']
+ del kwargs['shape']
+ else:
+ self._shape = None
+
+ DBPortSpec.__init__(self, *args, **kwargs)
+
+ if sum(1 for container in (self.port_spec_items, signature, sigstring)
+ if container) > 1:
+ raise ValueError("Please specify only one of portSpecItems,"
+ " signature, or sigstring kwargs.")
+ self.create_spec_items(self.port_spec_items, signature, sigstring,
+ defaults, labels, values, entry_types)
+
+ self._short_sigstring = None
+ # if signature is not None:
+ # self.create_entries(signature)
+ # if not self.sigstring and self._entries is not None:
+ # # create sigstring from entries
+ # self.create_sigstring_and_descriptors()
+# DAKOOP: removed this---we will check in module_registry and pipeline
+# validation, this way, we can let errors go all the way up
+# elif self._entries is None and self.sigstring:
+# # create entries from sigstring
+# self.create_entries_and_descriptors()
+# else:
+# raise VistrailsInternalError("Need to specify signature or "
+# "sigstring to create PortSpec")
+ # if self._entries is not None and self._tooltip is None:
+ # self.create_tooltip()
+ self.is_valid = True
+
+ def __copy__(self):
+ return PortSpec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec.do_copy(self, new_ids, id_scope, id_remap)
+ cp._short_sigstring = self._short_sigstring
+ cp._tooltip = self._tooltip
+ cp._shape = self._shape
+ cp._docstring = self._docstring
+ cp.is_valid = self.is_valid
+ cp.__class__ = PortSpec
+ # if cp._entries is not None:
+ # cp.create_tooltip()
+ return cp
+
+ @staticmethod
+ def convert(_port_spec):
+ from vistrails.core.modules.module_registry import module_registry_loaded, \
+ ModuleRegistryException
+ if _port_spec.__class__ == PortSpec:
+ return
+ _port_spec.__class__ = PortSpec
+ for _port_spec_item in _port_spec.db_portSpecItems:
+ PortSpecItem.convert(_port_spec_item)
+ _port_spec._short_sigstring = None
+ _port_spec._tooltip = None
+ _port_spec._shape = None
+ _port_spec._docstring = None
+ _port_spec.is_valid = True
+
+ _port_spec.port_spec_items.sort(key=operator.attrgetter('db_pos'))
+
+ @staticmethod
+ def from_sigstring(sigstring):
+ """from_sig(sigstring: string) -> PortSpec
+
+ Returns a portspec from the given sigstring.
+
+ """
+ return PortSpec(sigstring=sigstring)
+
+ ##########################################################################
+ # Properties
+
+ id = DBPortSpec.db_id
+ name = DBPortSpec.db_name
+ type = DBPortSpec.db_type
+ optional = DBPortSpec.db_optional
+ sort_key = DBPortSpec.db_sort_key
+ min_conns = DBPortSpec.db_min_conns
+ max_conns = DBPortSpec.db_max_conns
+ port_spec_items = DBPortSpec.db_portSpecItems
+ items = DBPortSpec.db_portSpecItems
+
+ def _get_sigstring(self):
+ return create_port_spec_string([i.spec_tuple
+ for i in self.port_spec_items])
+ sigstring = property(_get_sigstring)
+
+ def is_mandatory(self):
+ return (self.min_conns > 0)
+
+ def _get_labels(self):
+ return [i.label for i in self.port_spec_items]
+ labels = property(_get_labels)
+
+ def _get_defaults(self):
+ return [i.default for i in self.port_spec_items]
+ defaults = property(_get_defaults)
+
+ def _get_short_sigstring(self):
+ if self._short_sigstring is None:
+ self.create_tooltip()
+ return self._short_sigstring
+ short_sigstring = property(_get_short_sigstring)
+
+ def _get_signature(self):
+ signature = []
+ for i in self.port_spec_items:
+ signature.append((i.descriptor.module, i.label))
+ return signature
+ signature = property(_get_signature)
+
+ def toolTip(self):
+ if self._tooltip is None:
+ self.create_tooltip()
+ return self._tooltip
+
+ def shape(self):
+ return self._shape
+
+ def docstring(self):
+ return self._docstring
+
+ def descriptors(self):
+ return [i.descriptor for i in self.port_spec_items]
+
+ ##########################################################################
+ # Methods
+
+ def _resize_attrs(self, target, *lists):
+ for rlist in lists:
+ if len(target) > len(rlist):
+ rlist.extend(None for i in xrange(len(target)-len(rlist)))
+
+ def _set_attrs(self, item, *attrs):
+ attr_order = ['default', 'label', 'values', 'entry_type']
+ if item is None:
+ kwargs = dict(izip(attr_order, attrs))
+ return kwargs
+ else:
+ for (attr_key, attr) in izip(attr_order, attrs):
+ if attr is not None:
+ setattr(item, attr_key, attr)
+
+
+ def create_spec_items(self, items=None, signature=None, sigstring=None,
+ defaults=None, labels=None, values=None,
+ entry_types=None):
+ if defaults is None:
+ defaults = []
+ elif isinstance(defaults, basestring):
+ defaults = eval(defaults)
+ if labels is None:
+ labels = []
+ elif isinstance(labels, basestring):
+ labels = eval(labels)
+ if values is None:
+ values = []
+ elif isinstance(values, basestring):
+ values = eval(values)
+ if entry_types is None:
+ entry_types = []
+ elif isinstance(entry_types, basestring):
+ entry_types = eval(entry_types)
+ attrs = [defaults, labels, values, entry_types]
+ if items:
+ self.set_items(items, *attrs)
+ elif signature is not None:
+ items = self.get_items_from_entries(signature, *attrs)
+ elif sigstring is not None:
+ items = self.get_items_from_sigstring(sigstring, *attrs)
+ self.port_spec_items = items
+
+ def set_items(self, items, *attrs):
+ self._resize_attrs(items, *attrs)
+ for i, item_tuple in enumerate(izip(items, *attrs)):
+ item_tuple[0].pos = i
+ self._set_attrs(*item_tuple)
+
+ def get_items_from_entries(self, signature, *attrs):
+ # This is reasonably messy code. The intent is that a
+ # signature given by the user in a call like this
+ # add_input_port(module, name, signature) should be one of the
+ # following:
+
+ # type only: add_input_port(_, _, Float)
+ # type plus description: add_input_port(_, _, (Float, 'radius'))
+
+ # multiple parameters, where each parameter can be either of the above:
+ # add_input_port(_, _, [Float, (Integer, 'count')])
+
+ from vistrails.core.modules.module_registry import get_module_registry
+ registry = get_module_registry()
+ entries = []
+ def canonicalize(sig_item):
+ if isinstance(sig_item, tuple):
+ # assert len(sig_item) == 2
+ # assert isinstance(sig_item[0], type)
+ # assert isinstance(sig_item[1], str)
+ descriptor = registry.get_descriptor(sig_item[0])
+ label = sig_item[1]
+ return (descriptor, label)
+ elif isinstance(sig_item, list):
+ descriptor = registry.get_descriptor_by_name(
+ get_vistrails_basic_pkg_id(), 'List')
+ return (descriptor, None)
+ else:
+ # isinstance(sig_item, type):
+ return (registry.get_descriptor(sig_item), None)
+
+ # def _add_entry(sig_item):
+ ps_items = []
+ if not isinstance(signature, list):
+ signature = [signature]
+ self._resize_attrs(signature, *attrs)
+ for i, item_tuple in enumerate(izip(signature, *attrs)):
+ descriptor, item_label = canonicalize(item_tuple[0])
+ kwargs = self._set_attrs(None, *item_tuple[1:])
+ if not kwargs['label']:
+ if item_label != "<no description>":
+ kwargs['label'] = item_label
+ ps_item = PortSpecItem(pos=i,
+ package=descriptor.identifier,
+ module=descriptor.name,
+ namespace=descriptor.namespace,
+ **kwargs)
+ ps_items.append(ps_item)
+ return ps_items
+
+ def get_items_from_sigstring(self, sigstring, *attrs):
+ ps_items = []
+ specs_list = parse_port_spec_string(sigstring)
+ if len(specs_list) == 0:
+ return ps_items
+
+ self._resize_attrs(specs_list, *attrs)
+ for i, item_tuple in enumerate(izip(specs_list, *attrs)):
+ kwargs = self._set_attrs(None, *item_tuple[1:])
+ ps_item = PortSpecItem(pos=i,
+ package=item_tuple[0][0],
+ module=item_tuple[0][1],
+ namespace=item_tuple[0][2],
+ **kwargs)
+ ps_items.append(ps_item)
+ return ps_items
+
+ def create_tooltip(self):
+ """Creates a short_sigstring that does not include package names for
+ use with the tooltip. Note, however, that such sigstrings
+ can't be used to reconstruct a spec. They should only be used
+ for human-readable purposes.
+ """
+
+ self._short_sigstring = \
+ "(" + ",".join(d.name for d in self.descriptors()) + ")"
+ if self.type in ['input', 'output']:
+ port_string = self.type.capitalize()
+ else:
+ port_string = 'Invalid'
+ self._tooltip = "%s port %s\n%s" % (port_string,
+ self.name,
+ self._short_sigstring)
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of an PortSpec
+ object.
+
+ """
+ rep = "<portSpec id=%s name=%s type=%s signature=%s />"
+ return rep % (str(self.id), str(self.name),
+ str(self.type), str(self.sigstring))
+
+ def __eq__(self, other):
+ """ __eq__(other: PortSpec) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if self is None and other is None:
+ return True
+ if type(self) != type(other) or \
+ self.name != other.name or \
+ self.type != other.type:
+ return False
+ if len(self.descriptors()) != len(other.descriptors()):
+ return False
+ for (mine, their) in izip(self.descriptors(), other.descriptors()):
+ if mine != their:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+ def type_equals(self, other):
+ """type_equals(other: PortSpec) -> Bool
+
+ Checks equality ignoring description strings. Only cares about types.
+ Does not do subtyping or supertyping: match must be perfect.
+
+ """
+ if self is None and other is None:
+ return True
+ if len(self.descriptors()) != len(other.descriptors()):
+ return False
+ for (mine, their) in izip(self.descriptors(), other.descriptors()):
+ if mine != their:
+ return False
+ return True
+
+ def key_no_id(self):
+ """key_no_id(): tuple. returns a tuple that identifies
+ the port without caring about ids. Used for sorting
+ port lists."""
+ return (self.type,
+ self.name,
+ self.signature)
+
+################################################################################
+# Testing
+
+
+class TestPortSpec(unittest.TestCase):
+
+ def create_port_spec(self, id_scope=IdScope()):
+ # FIXME add a valid port spec
+ port_spec = PortSpec(id=id_scope.getNewId(PortSpec.vtType),
+ name='SetValue',
+ type='input',
+ sigstring='(%s:String)' % \
+ get_vistrails_basic_pkg_id(),
+ )
+ return port_spec
+
+ def test_copy(self):
+ id_scope = IdScope()
+
+ s1 = self.create_port_spec(id_scope)
+ s2 = copy.copy(s1)
+ self.assertEquals(s1, s2)
+ self.assertEquals(s1.id, s2.id)
+ s3 = s1.do_copy(True, id_scope, {})
+ self.assertEquals(s1, s3)
+ self.assertNotEquals(s1.id, s3.id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ s1 = self.create_port_spec()
+ xml_str = vistrails.core.db.io.serialize(s1)
+ s2 = vistrails.core.db.io.unserialize(xml_str, PortSpec)
+ self.assertEquals(s1, s2)
+ self.assertEquals(s1.id, s2.id)
+
+ def test_create_from_signature(self):
+ from vistrails.core.modules.basic_modules import Float
+ port_spec = PortSpec(id=-1,
+ name="SetXYZ",
+ type='input',
+ signature=[(Float, "x"), (Float, "y"),
+ (Float, "z")])
+
+ def test_create_from_items(self):
+ basic_pkg = get_vistrails_basic_pkg_id()
+ item_a = PortSpecItem(pos=0,
+ package=basic_pkg,
+ module="Integer",
+ label="a",
+ default="123")
+ item_b = PortSpecItem(pos=1,
+ package=basic_pkg,
+ module="String",
+ label="b",
+ default="abc")
+ port_spec = PortSpec(id=-1,
+ name="SetValue",
+ type='input',
+ portSpecItems=[item_a, item_b])
+
diff --git a/vistrails/core/vistrail/port_spec_item.py b/vistrails/core/vistrail/port_spec_item.py
new file mode 100644
index 0000000..8d53e6b
--- /dev/null
+++ b/vistrails/core/vistrail/port_spec_item.py
@@ -0,0 +1,219 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.core.modules.utils import parse_port_spec_item_string, \
+ create_port_spec_item_string
+from vistrails.db.domain import DBPortSpecItem
+
+import unittest
+from vistrails.db.domain import IdScope
+
+class PortSpecItem(DBPortSpecItem):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ if "sigstring" in kwargs:
+ sigstring = kwargs["sigstring"]
+ del kwargs["sigstring"]
+
+ (package, module, namespace) = \
+ parse_port_spec_item_string(sigstring)
+ if "package" not in kwargs:
+ kwargs["package"] = package
+ if "module" not in kwargs:
+ kwargs["module"] = module
+ if "namespace" not in kwargs:
+ kwargs["namespace"] = namespace
+ if "values" in kwargs:
+ if (kwargs["values"] is not None and
+ not isinstance(kwargs["values"], basestring)):
+ kwargs["values"] = str(kwargs["values"])
+ if 'id' not in kwargs:
+ kwargs['id'] = -1
+
+ def update_identifier(identifier):
+ """check for changed identifiers (e.g. edu.utah.sci.vistrails ->
+ org.vistrails.vistrails) and use the current one.
+
+ """
+ from vistrails.core.modules.module_registry import \
+ get_module_registry, MissingPackage
+ reg = get_module_registry()
+ try:
+ identifier = reg.get_package_by_name(identifier).identifier
+ except MissingPackage:
+ # catch this later, just trying to ensure that old
+ # identifiers are updated
+ pass
+ return identifier
+
+ # args[3] is the package argument
+ # FIXME this is schema-dependent...
+ if len(args) > 3:
+ args[3] = update_identifier(args[3])
+ if "package" in kwargs:
+ kwargs["package"] = update_identifier(kwargs["package"])
+ DBPortSpecItem.__init__(self, *args, **kwargs)
+ self.set_defaults()
+
+ def set_defaults(self, other=None):
+ if other is None:
+ self._values = None
+ self._sigstring = None
+ self._descriptor = None
+ else:
+ self._values = copy.copy(other._values)
+ self._sigstring = other._sigstring
+ self._descriptor = other._descriptor
+
+ def __copy__(self):
+ """__copy__() -> PortSpecItem - Returns a clone of itself"""
+ return self.do_copy()
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpecItem.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = PortSpecItem
+ cp.set_defaults(self)
+ return cp
+
+ @staticmethod
+ def convert(_portSpecItem):
+ if _portSpecItem.__class__ == PortSpecItem:
+ return
+ _portSpecItem.__class__ = PortSpecItem
+ _portSpecItem.set_defaults()
+
+ id = DBPortSpecItem.db_id
+ pos = DBPortSpecItem.db_pos
+ label = DBPortSpecItem.db_label
+ default = DBPortSpecItem.db_default
+ entry_type = DBPortSpecItem.db_entry_type
+
+ def _get_module(self):
+ return self.db_module
+ def _set_module(self, module):
+ if self.db_module != module:
+ self._sigstring = None
+ self._descriptor = None
+ self.db_module = module
+ module = property(_get_module, _set_module)
+
+ def _get_package(self):
+ return self.db_package
+ def _set_package(self, package):
+ if self.db_package != package:
+ self._sigstring = None
+ self._descriptor = None
+ self.db_package = package
+ package = property(_get_package, _set_package)
+
+ def _get_namespace(self):
+ return self.db_namespace
+ def _set_namespace(self, ns):
+ if self.db_namespace != ns:
+ self._sigstring = None
+ self._descriptor = None
+ self.db_namespace = ns
+ namespace = property(_get_namespace, _set_namespace)
+
+ def _get_sigstring(self):
+ if self._sigstring is None:
+ self._sigstring = create_port_spec_item_string(self.package,
+ self.module,
+ self.namespace)
+ return self._sigstring
+ sigstring = property(_get_sigstring)
+
+ def _get_descriptor(self):
+ if self._descriptor is None:
+ from vistrails.core.modules.module_registry import get_module_registry
+ reg = get_module_registry()
+ if self.package is None:
+ self._descriptor = \
+ reg.get_descriptor_from_name_only(self.module)
+ self.db_package = self._descriptor.identifier
+ self.db_namespace = self._descriptor.namespace
+ else:
+ self._descriptor = reg.get_descriptor_by_name(self.package,
+ self.module,
+ self.namespace)
+ return self._descriptor
+ descriptor = property(_get_descriptor)
+
+ def _get_values(self):
+ if self._values is None:
+ # don't use eval here...
+ self._values = eval(self.db_values)
+ return self._values
+ def _set_values(self, values):
+ if not isinstance(values, basestring):
+ self._values = values
+ self.db_values = str(values)
+ else:
+ self.db_values = values
+ # don't use eval here...
+ self._values = eval(values)
+ values = property(_get_values, _set_values)
+
+ def _get_spec_tuple(self):
+ return (self.package, self.module, self.namespace)
+ spec_tuple = property(_get_spec_tuple)
+
+################################################################################
+# Testing
+
+from vistrails.core.system import get_vistrails_basic_pkg_id
+
+class TestPortSpecItem(unittest.TestCase):
+ def create_port_spec_item(self):
+ return PortSpecItem(id=0, pos=0,
+ module="String",
+ package=get_vistrails_basic_pkg_id(),
+ label="testLabel",
+ default="abc",
+ values=["abc", "def", "ghi"],
+ entry_type="enum")
+
+ def test_change_descriptor(self):
+ psi = self.create_port_spec_item()
+ d1 = psi.descriptor
+ s1 = psi.sigstring
+ psi.module = "Integer"
+ d2 = psi.descriptor
+ s2 = psi.sigstring
+ assert(d1 != d2)
+ assert(s1 != s2)
diff --git a/vistrails/core/vistrail/tag.py b/vistrails/core/vistrail/tag.py
new file mode 100644
index 0000000..fdfbfa3
--- /dev/null
+++ b/vistrails/core/vistrail/tag.py
@@ -0,0 +1,121 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBTag
+
+import unittest
+import copy
+from vistrails.db.domain import IdScope
+import vistrails.core
+
+class Tag(DBTag):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBTag.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return Tag.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Tag
+ return cp
+
+ @staticmethod
+ def convert(_tag):
+ _tag.__class__ = Tag
+
+ ##########################################################################
+ # Properties
+
+ id = DBTag.db_id
+ time = DBTag.db_id
+ name = DBTag.db_name
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of a Tag
+ object.
+
+ """
+ rep = "<tag name=%s time=%s />"
+ return rep % (str(self.name), str(self.time))
+
+ def __eq__(self, other):
+ """ __eq__(other: Annotation) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(other) != type(self):
+ return False
+ return self.name == other.name
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+################################################################################
+# Testing
+
+
+class TestTag(unittest.TestCase):
+
+ def create_tag(self, id_scope=IdScope()):
+ tag = Tag(id=id_scope.getNewId(Tag.vtType),
+ name='blah')
+ return tag
+
+ def test_copy(self):
+ id_scope = IdScope()
+
+ t1 = self.create_tag(id_scope)
+ t2 = copy.copy(t1)
+ self.assertEquals(t1, t2)
+ self.assertEquals(t1.id, t2.id)
+ t3 = t1.do_copy(True, id_scope, {})
+ self.assertEquals(t1, t3)
+ self.assertNotEquals(t1.id, t3.id)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ t1 = self.create_tag()
+ xml_str = vistrails.core.db.io.serialize(t1)
+ t2 = vistrails.core.db.io.unserialize(xml_str, Tag)
+ self.assertEquals(t1, t2)
+ self.assertEquals(t1.id, t2.id)
diff --git a/vistrails/core/vistrail/vistrail.py b/vistrails/core/vistrail/vistrail.py
new file mode 100644
index 0000000..07ef0ea
--- /dev/null
+++ b/vistrails/core/vistrail/vistrail.py
@@ -0,0 +1,1382 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.paramexplore.paramexplore import ParameterExploration
+
+import copy
+import datetime
+import getpass
+
+from vistrails.db.domain import DBVistrail
+from vistrails.db.services.io import open_vt_log_from_db, open_log_from_xml
+from vistrails.core.db.locator import DBLocator
+from vistrails.core.log.log import Log
+from vistrails.core.data_structures.graph import Graph
+from vistrails.core.data_structures.bijectivedict import Bidict
+from vistrails.core import debug
+import vistrails.core.db.io
+from vistrails.core.utils import VistrailsInternalError, \
+ InvalidPipeline
+from vistrails.core.vistrail.action import Action
+from vistrails.core.vistrail.action_annotation import ActionAnnotation
+from vistrails.core.vistrail.vistrailvariable import VistrailVariable
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.vistrail.module import Module
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.operation import AddOp, ChangeOp, DeleteOp
+from vistrails.core.vistrail.plugin_data import PluginData
+
+import unittest
+import copy
+import random
+
+""" This file contains the definition of the class Vistrail """
+
+
+################################################################################
+
+class Vistrail(DBVistrail):
+ """Vistrail is the base class for storing versioned pipelines.
+
+ Because of the automatic loading from the db layer, the fields in
+ the class will seem mysterious.
+
+ self.currentVersion: version of the schema being used for this vistrail
+ (Do not confuse with the currently selected version on the controller)
+
+ self.actions: list of core/vistrail/action/Action objects
+
+ self.actionMap: dictionary from version number to action object.
+
+ Simple use cases:
+
+ To get a version number given a tag name, use
+ get_tag_str(tag_name).action_id
+
+ """
+
+ def __init__(self, locator=None):
+ DBVistrail.__init__(self)
+
+ self.locator = locator
+ self.set_defaults()
+
+ def __copy__(self):
+ """ __copy__() -> Vistrail - Returns a clone of itself """
+ return Vistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = Vistrail
+ cp.locator = copy.copy(self.locator)
+ cp.set_defaults(self)
+ return cp
+
+ def set_defaults(self, other=None):
+ if other is None:
+ self.changed = False
+ self.currentVersion = -1
+ self.savedQueries = []
+ self.is_abstraction = False
+ else:
+ self.changed = other.changed
+ self.currentVersion = other.currentVersion
+ self.savedQueries = copy.copy(other.savedQueries)
+ self.is_abstraction = other.is_abstraction
+
+ # object to keep explicit expanded
+ # version tree always updated
+ self.tree = ExplicitExpandedVersionTree(self)
+ # add all versions to the trees
+ for action in sorted(self.actions, key=lambda a: a.id):
+ self.tree.addVersion(action.id, action.prevId)
+
+ @staticmethod
+ def convert(_vistrail):
+ _vistrail.__class__ = Vistrail
+
+ for action in _vistrail.actions:
+ Action.convert(action)
+# for tag in _vistrail.tags:
+# Tag.convert(tag)
+ for annotation in _vistrail.annotations:
+ Annotation.convert(annotation)
+ for annotation in _vistrail.action_annotations:
+ ActionAnnotation.convert(annotation)
+
+ for variable in _vistrail.vistrail_variables:
+ VistrailVariable.convert(variable)
+
+ for pe in _vistrail.parameter_explorations:
+ ParameterExploration.convert(pe)
+
+ _vistrail.set_defaults()
+
+ ##########################################################################
+ # Constants
+
+ TAG_ANNOTATION = '__tag__'
+ NOTES_ANNOTATION = '__notes__'
+ PARAMEXP_ANNOTATION = '__paramexp__'
+ THUMBNAIL_ANNOTATION = '__thumb__'
+ PRUNE_ANNOTATION = '__prune__'
+ UPGRADE_ANNOTATION = '__upgrade__'
+# VARIABLES_ANNOTATION = '__vistrail_vars__'
+
+ ##########################################################################
+ # Properties
+
+ id = DBVistrail.db_id
+ actions = DBVistrail.db_actions # This is now read-write
+ tags = DBVistrail.db_tags # This is now read-write
+ annotations = DBVistrail.db_annotations
+ action_annotations = DBVistrail.db_actionAnnotations
+ vistrail_variables = DBVistrail.db_vistrailVariables
+ parameter_explorations = DBVistrail.db_parameter_explorations
+
+ def _get_actionMap(self):
+ return self.db_actions_id_index
+ actionMap = property(_get_actionMap)
+
+ def get_annotation(self, key):
+ if self.db_has_annotation_with_key(key):
+ return self.db_get_annotation_by_key(key)
+ return None
+
+ def set_annotation(self, key, value):
+ if self.db_has_annotation_with_key(key):
+ old_annotation = self.db_get_annotation_by_key(key)
+ if old_annotation.value == value:
+ return False
+ self.db_delete_annotation(old_annotation)
+ if not (value is None or (isinstance(value, str) and value.strip() == '')):
+ annotation = Annotation(id=self.idScope.getNewId(Annotation.vtType),
+ key=key,
+ value=value,
+ )
+ self.db_add_annotation(annotation)
+ return True
+
+ def _get_plugin_info(self):
+ annotation = self.get_annotation("__plugin_info__")
+ if annotation is not None:
+ return annotation.value
+ else:
+ return ""
+# return annotation.value if annotation is not None else ""
+ def _set_plugin_info(self, value):
+ return self.set_annotation("__plugin_info__", value)
+ plugin_info = property(_get_plugin_info, _set_plugin_info)
+
+ def _get_database_info(self):
+ annotation = self.get_annotation("__database_info__")
+ if annotation is not None:
+ return annotation.value
+ else:
+ return ""
+# return annotation.value if annotation is not None else ""
+ def _set_database_info(self, value):
+ return self.set_annotation("__database_info__", value)
+ database_info = property(_get_database_info, _set_database_info)
+
+ def _get_vistrail_vars(self):
+ return self.vistrail_variables
+
+ def _set_vistrail_vars(self, vars):
+ self.vistrail_variables = vars
+ vistrail_vars = property(_get_vistrail_vars, _set_vistrail_vars)
+
+ def has_vistrail_var(self, name):
+ return self.db_has_vistrailVariable_with_name(name)
+
+ def get_vistrail_var(self, name):
+ if self.has_vistrail_var(name):
+ return self.db_get_vistrailVariable_by_name(name)
+ return None
+
+ def set_vistrail_var(self, name, var):
+ if self.db_has_vistrailVariable_with_name(name):
+ old_var = self.db_get_vistrailVariable_by_name(name)
+ if var and old_var == var:
+ return False
+ self.db_delete_vistrailVariable(old_var)
+ if var:
+ self.db_add_vistrailVariable(var)
+ return True
+
+ def getVersionName(self, version):
+ """ getVersionName(version) -> str
+ Returns the name of a version, if it exists. Returns an empty string
+ if it doesn't.
+
+ """
+ if self.has_tag(version):
+ return self.get_tag(version)
+ return ""
+
+ def get_pipeline_name(self, version):
+ tag_map = self.get_tagMap()
+ action_map = self.actionMap
+ count = 0
+ while True:
+ if version in tag_map or version <= 0:
+ if version in tag_map:
+ name = tag_map[version]
+ else:
+ name = "ROOT"
+ count_str = ""
+ if count > 0:
+ count_str = " + " + str(count)
+ return name + count_str
+ version = action_map[version].parent
+ count += 1
+
+ def get_version_count(self):
+ """get_version_count() -> Integer
+ Returns the total number of versions in this vistrail.
+
+ """
+ return len(self.actionMap)
+
+ def get_version_number(self, version):
+ """get_version_number(version) -> Integer
+ Returns the version number given a tag.
+
+ """
+ return self.get_tag_str(version).action_id
+
+ def get_latest_version(self):
+ """get_latest_version() -> Integer
+ Returns the latest version id for the vistrail.
+
+ FIXME: Running time O(|versions|)
+
+ FIXME: Check if pruning is handled correctly here.
+
+ """
+ try:
+ desc_key = Action.ANNOTATION_DESCRIPTION
+ # Get the max id of all actions (excluding upgrade actions)
+ max_ver = max(v.id for v in self.actions if not self.is_pruned(v.id) and not (v.has_annotation_with_key(desc_key) and v.get_annotation_by_key(desc_key).value == 'Upgrade'))
+ # If that action has an upgrade, use it
+ if self.has_upgrade(max_ver):
+ max_ver = long(self.get_upgrade(max_ver))
+ return max_ver
+ except:
+ return 0
+
+ def getPipeline(self, version):
+ """getPipeline(number or tagname) -> Pipeline
+ Return a pipeline object given a version number or a version name.
+
+ """
+ try:
+ return Vistrail.getPipelineDispatcher[type(version)](self, version)
+ except Exception, e:
+ raise InvalidPipeline([e])
+
+ def getPipelineVersionName(self, version):
+ """getPipelineVersionName(version:str) -> Pipeline
+ Returns a pipeline given a version name. If version name doesn't exist
+ it will return None.
+
+ """
+ if self.has_tag_str(version):
+ number = self.get_tag_str(version).action_id
+ return self.getPipelineVersionNumber(number)
+ else:
+ return None
+
+ def getPipelineVersionNumber(self, version):
+ """getPipelineVersionNumber(version:int) -> Pipeline
+ Returns a pipeline given a version number.
+
+ """
+ workflow = vistrails.core.db.io.get_workflow(self, version)
+ return workflow
+
+ def make_actions_from_diff(self, diff):
+ """ make_actions_from_diff(diff) -> [action]
+ Returns a sequence of actions that performs the diff.
+
+ (The point is that this might be smaller than the
+ algebra-based one).
+ """
+ (p1,
+ p2,
+ m_shared,
+ m_to_be_deleted,
+ m_to_be_added,
+ parameter_changes,
+ c_shared,
+ c_to_be_deleted,
+ c_to_be_added) = (diff.p1,
+ diff.p2,
+ diff.v1andv2,
+ diff.v1only,
+ diff.v2only,
+ diff.paramchanged,
+ diff.c1andc2,
+ diff.c1only,
+ diff.c2only)
+
+ p1_c = copy.copy(p1)
+ result = []
+
+ module_id_remap = Bidict()
+ module_id_remap.update(m_shared)
+
+ connection_id_remap = Bidict()
+ connection_id_remap.update(c_shared)
+
+ for ((m_id_from, m_id_to), _) in parameter_changes:
+ module_id_remap[m_id_from] = m_id_to
+
+ # First all the modules to get the remap
+ for p2_m_id in m_to_be_added:
+ add_module = AddModuleAction()
+ add_module.module = copy.copy(p2.modules[p2_m_id])
+ add_module.module.id = p1_c.fresh_module_id()
+ module_id_remap[add_module.module.id] = p2_m_id
+ result.append(add_module)
+ add_module.perform(p1_c)
+
+
+ # Then all the connections using the remap
+ for p2_c_id in c_to_be_added:
+ c2 = p2.connections[p2_c_id]
+ add_connection = AddConnectionAction()
+ new_c = copy.copy(c2)
+ add_connection.connection = new_c
+ new_c.id = p1_c.fresh_connection_id()
+ new_c.sourceId = module_id_remap.inverse[c2.sourceId]
+ new_c.destinationId = module_id_remap.inverse[c2.destinationId]
+ connection_id_remap[c2.id] = new_c.id
+ result.append(add_connection)
+ add_connection.perform(p1_c)
+
+
+ # Now delete all connections:
+ delete_conns = DeleteConnectionAction()
+ delete_conns.ids = copy.copy(c_to_be_deleted)
+ if len(delete_conns.ids) > 0:
+ delete_conns.perform(p1_c)
+ result.append(delete_conns)
+
+ # And then all the modules
+ delete_modules = DeleteModuleAction()
+ delete_modules.ids = copy.copy(m_to_be_deleted)
+ if len(delete_modules.ids) > 0:
+ delete_modules.perform(p1_c)
+ result.append(delete_modules)
+
+ # From now on, module_id_remap is not necessary, we can act
+ # on p1 ids without worry. (they still exist)
+
+ # Now move everyone
+ move_action = MoveModuleAction()
+ for (p1_m_id, p2_m_id) in m_shared.iteritems():
+ delta = p2.modules[p2_m_id].location - p1.modules[p1_m_id].location
+ move_action.addMove(p1_m_id, delta.x, delta.y)
+ move_action.perform(p1_c)
+ result.append(move_action)
+
+ # Now change parameters
+ def make_param_change(fto_name, fto_params,
+ m_id, f_id, m):
+ action = ChangeParameterAction()
+ for (p_id, param) in enumerate(fto_params):
+ p_name = m.functions[f_id].params[p_id].name
+ p_alias = m.functions[f_id].params[p_id].alias
+ (p_type, p_value) = param
+ action.addParameter(m_id, f_id, p_id, fto_name,
+ p_name, p_value, p_type, p_alias)
+ return action
+
+ if len(parameter_changes):
+ # print parameter_changes
+ for ((m_from_id, m_to_id), plist) in parameter_changes:
+ m_from = p1.modules[m_to_id]
+ for ((ffrom_name, ffrom_params),
+ (fto_name, fto_params)) in plist:
+ for (f_id, f) in enumerate(m_from.functions):
+ if f.name != fto_name: continue
+ new_action = make_param_change(fto_name,
+ fto_params,
+ m_from_id,
+ f_id,
+ m_from)
+ new_action.perform(p1_c)
+ result.append(new_action)
+
+ return (result,
+ module_id_remap,
+ connection_id_remap)
+
+ def get_pipeline_diff_with_connections(self, v1, v2):
+ """like get_pipeline_diff but returns connection info
+ Keyword arguments:
+ v1 --- the first version number
+ v2 --- the second version number
+ return --- (p1, p2: VistrailPipeline,
+ [shared modules (id in v1, id in v2) ...],
+ [shared modules [heuristic match] (id in v1, id in v2)],
+ [v1 not v2 modules],
+ [v2 not v1 modules],
+ [parameter-changed modules (see-below)],
+ [shared connections (id in v1, id in v2) ...],
+ [shared connections [heuristic] (id in v1, id in v2)],
+ [c1 not in v2 connections],
+ [c2 not in v1 connections])
+
+ parameter-changed modules = [((module id in v1, module id in v2),
+ [(function in v1, function in v2)...]),
+ ...]
+
+ """
+ return vistrails.core.db.io.get_workflow_diff_with_connections((self, v1),
+ (self, v2))
+
+ def get_pipeline_diff(self, v1, v2):
+ """ get_pipeline_diff(v1: int, v2: int) -> tuple
+ Perform a diff between 2 versions, this will obtain the shared
+ modules by getting shared nodes on the version tree. After,
+ that, it will perform a heuristic algorithm to match
+ signatures of modules to get more shared/diff modules. The
+ heuristic is O(N^2), where N = the number of modules
+
+ Keyword arguments:
+ v1 --- the first version number
+ v2 --- the second version number
+ return --- (p1, p2: VistrailPipeline,
+ [shared modules (id in v1, id in v2) ...],
+ [shared modules [heuristic match] (id in v1, id in v2)],
+ [v1 not v2 modules],
+ [v2 not v1 modules],
+ [parameter-changed modules (see-below)])
+
+ parameter-changed modules = [((module id in v1, module id in v2),
+ [(function in v1, function in v2)...]),
+ ...]
+
+ """
+ return vistrails.core.db.io.get_workflow_diff((self, v1), (self, v2))
+
+ def getFirstCommonVersion(self, v1, v2):
+ """ Returns the first version that it is common to both v1 and v2
+ Parameters
+ ----------
+ - v1 : 'int'
+ version number 1
+
+ - v2 : 'int'
+ version number 2
+
+ """
+ if (v1<=0 or v2<=0):
+ return 0
+
+ t1 = set()
+ t1.add(v1)
+ t = self.actionMap[v1].parent
+ while t != 0:
+ t1.add(t)
+ t = self.actionMap[t].parent
+
+ t = v2
+ while t != 0:
+ if t in t1:
+ return t
+ t = self.actionMap[t].parent
+ return 0
+
+ def getLastCommonVersion(self, v):
+ """getLastCommonVersion(v: Vistrail) -> int
+ Returns the last version that is common to this vistrail and v
+
+ """
+ # TODO: There HAS to be a better way to do this...
+ common = []
+ for action in self.actionMap:
+ if(v.hasVersion(action.timestep)):
+ common.append(action.timestep)
+
+ timestep = 0
+ for time in common:
+ if time > timestep:
+ timestep = time
+
+ return timestep
+
+ def general_action_chain(self, v1, v2):
+ """general_action_chain(v1, v2): Returns an action that turns
+ pipeline v1 into v2."""
+
+ return vistrails.core.db.io.getPathAsAction(self, v1, v2)
+
+ def actionChain(self, t, start=0):
+ """ actionChain(t:int, start=0) -> [Action]
+ Returns the action chain (list of Action) necessary to recreate a
+ pipeline from a certain time
+
+ """
+ assert t >= start
+ if t == start:
+ return []
+ result = []
+ action = self.actionMap[t]
+
+ while 1:
+ result.append(action)
+ if action.timestep == start:
+ break
+ if action.parent == start:
+ if start != 0:
+ action = self.actionMap[action.parent]
+ break
+ action = self.actionMap[action.parent]
+ result.reverse()
+ return result
+
+ def update_object(self, obj, **kwargs):
+ self.db_update_object(obj, **kwargs)
+
+ def add_action(self, action, parent, session=None):
+ # FIXME: this should go to core.db.io
+ Action.convert(action)
+ if action.id < 0:
+ action.id = self.idScope.getNewId(action.vtType)
+ action.prevId = parent
+ action.date = self.getDate()
+ action.user = self.getUser()
+ if session is not None:
+ action.session = session
+ for op in action.operations:
+ if op.id < 0:
+ op.id = self.idScope.getNewId('operation')
+ if op.vtType == 'add' or op.vtType == 'change':
+ self.db_add_object(op.db_data)
+ self.addVersion(action)
+
+# def add_abstraction(self, abstraction):
+# Abstraction.convert(abstraction)
+# if abstraction.id < 0:
+# abstraction.id = self.idScope.getNewId(abstraction.vtType)
+# action_remap = {}
+# for action in abstraction.actions.itervalues():
+# if action.id < 0:
+# new_id = abstraction.idScope.getNewId(action.vtType)
+# action_remap[action.id] = new_id
+# action.id = new_id
+# action.date = self.getDate()
+# action.user = self.getUser()
+# for op in action.operations:
+# if op.id < 0:
+# op.id = self.idScope.getNewId('operation')
+# for action in abstraction.actions.itervalues():
+# if action.prevId < 0:
+# action.prevId = action_remap[action.prevId]
+
+# self.db_add_abstraction(abstraction)
+
+ def getLastActions(self, n):
+ """ getLastActions(n: int) -> list of ids
+ Returns the last n actions performed
+ """
+ last_n = []
+ num_actions = len(self.actionMap)
+ if num_actions < n:
+ n = num_actions
+ if n > 0:
+ sorted_keys = sorted(self.actionMap.keys())
+ last_n = sorted_keys[num_actions-n:num_actions-1]
+ return last_n
+
+ def hasVersion(self, version):
+ """hasVersion(version:int) -> boolean
+ Returns True if version with given timestamp exists
+
+ """
+ return version in self.actionMap
+
+ def addVersion(self, action):
+ """ addVersion(action: Action) -> None
+ Adds new version to vistrail
+
+ """
+ if action.timestep in self.actionMap:
+ raise VistrailsInternalError("existing timestep: %d" %
+ action.timestep)
+ self.db_add_action(action)
+ self.changed = True
+
+ # signal to update explicit tree
+ self.tree.addVersion(action.id, action.prevId)
+
+ def hasTag(self, tag):
+ """ hasTag(tag) -> boolean
+ Returns True if a tag with given name or number exists
+
+ """
+ if isinstance(tag, (int, long)):
+ return self.has_tag(tag)
+ elif isinstance(tag, basestring):
+ return self.has_tag_str(tag)
+
+ def addTag(self, version_name, version_number):
+ """addTag(version_name, version_number) -> None
+ Adds new tag to vistrail
+
+ """
+ if version_name == '':
+ return None
+ if self.has_tag(version_number):
+ debug.log("Version is already tagged")
+ raise VersionAlreadyTagged()
+ if self.has_tag_str(version_name):
+ debug.log("Tag already exists")
+ raise TagExists()
+ self.set_tag(version_number, version_name)
+
+ def changeTag(self, version_name, version_number):
+ """changeTag(version_name, version_number) -> None
+ Changes the old tag of version_number to version_name in the
+ vistrail. If version_name is empty, this version will be
+ untagged.
+
+ """
+ if not self.has_tag(version_number):
+ debug.log("Version is not tagged")
+ raise VersionNotTagged()
+ if self.get_tag(version_number) == version_name:
+ return None
+ if self.has_tag_str(version_name):
+ debug.log("Tag already exists")
+ raise TagExists()
+ self.set_tag(version_number, version_name)
+
+ def has_action_annotation(self, action_id, key):
+ return self.db_has_actionAnnotation_with_action_id((action_id, key))
+
+ def get_action_annotation(self, action_id, key):
+ if self.has_action_annotation(action_id, key):
+ return self.db_get_actionAnnotation_by_action_id((action_id, key))
+ return None
+
+ def delete_action_annotation(self, action_id, key):
+ annotation = self.get_action_annotation(action_id, key)
+ self.db_delete_actionAnnotation(annotation)
+
+ def set_action_annotation(self, action_id, key, value):
+ changed = False
+ if self.has_action_annotation(action_id, key):
+ annotation = self.get_action_annotation(action_id, key)
+ if annotation.value == value:
+ return False
+ self.db_delete_actionAnnotation(annotation)
+ changed = True
+ if value is not None and value.strip() != '':
+ new_id = self.idScope.getNewId(ActionAnnotation.vtType)
+ annotation = ActionAnnotation(id=new_id,
+ action_id=action_id,
+ key=key,
+ value=value,
+ date=self.getDate(),
+ user=self.getUser())
+ #print 'doing addAnnotation', action_id, key, value
+ self.db_add_actionAnnotation(annotation)
+ changed = True
+ if changed:
+ self.changed = True
+ return True
+ return False
+
+ def get_tagMap(self):
+ tagMap = {}
+ for annotation in self.action_annotations:
+ if annotation.db_key == Vistrail.TAG_ANNOTATION:
+ tagMap[annotation.db_action_id] = annotation.db_value
+ return tagMap
+ def has_tag_str(self, value):
+ return self.db_has_actionAnnotation_with_key((Vistrail.TAG_ANNOTATION,
+ value))
+ def get_tag_str(self, value):
+ return self.db_get_actionAnnotation_by_key((Vistrail.TAG_ANNOTATION,
+ value))
+ def has_tag(self, action_id):
+ return self.has_action_annotation(action_id, Vistrail.TAG_ANNOTATION)
+ def get_tag(self, action_id):
+ a = self.get_action_annotation(action_id, Vistrail.TAG_ANNOTATION)
+ if a is not None:
+ return a.value
+ return None
+ def set_tag(self, action_id, value):
+ return self.set_action_annotation(action_id, Vistrail.TAG_ANNOTATION,
+ value)
+
+ def has_notes(self, action_id):
+ return self.has_action_annotation(action_id, Vistrail.NOTES_ANNOTATION)
+ def get_notes(self, action_id):
+ a = self.get_action_annotation(action_id, Vistrail.NOTES_ANNOTATION)
+ if a is not None:
+ return a.value
+ return None
+ def set_notes(self, action_id, value):
+ return self.set_action_annotation(action_id, Vistrail.NOTES_ANNOTATION,
+ value)
+
+ def has_paramexp(self, action_id):
+ """ Check if vistrail has a latest paramexp for action action_id
+ """
+ return len(self.get_paramexps(action_id))>0
+ def get_paramexp(self, action_id):
+ """ Check if vistrail has a default paramexp for action action_id
+ and returns it (using latest id)
+ """
+ pes = self.get_paramexps(action_id)
+ if not len(pes):
+ return None
+ pes.sort(key=lambda x: x.id)
+ return pes[-1]
+ def get_paramexps(self, action_id):
+ """ return all pe:s for this action
+ """
+ return [pe for pe in self.parameter_explorations if pe.action_id == action_id]
+ def has_named_paramexp(self, name):
+ """ Check if vistrail has a paramexp named "name"
+ """
+ if not name:
+ return False
+ for pe in self.parameter_explorations:
+ if pe.name == name:
+ return True
+ return False
+ def get_named_paramexp(self, name):
+ """ Returns the paramexp named "name" or None
+ """
+ for pe in self.parameter_explorations:
+ if pe.name == name:
+ return pe
+ return None
+ def delete_paramexp(self, param_exp):
+ self.db_delete_parameter_exploration(param_exp)
+ def add_paramexp(self, param_exp):
+ param_exp.id = self.idScope.getNewId(param_exp.vtType)
+ self.db_add_parameter_exploration(param_exp)
+
+ def has_thumbnail(self, action_id):
+ return self.has_action_annotation(action_id,
+ Vistrail.THUMBNAIL_ANNOTATION)
+ def get_thumbnail(self, action_id):
+ a = self.get_action_annotation(action_id,
+ Vistrail.THUMBNAIL_ANNOTATION)
+ if a is not None:
+ return a.value
+ return None
+ def set_thumbnail(self, action_id, value):
+ return self.set_action_annotation(action_id,
+ Vistrail.THUMBNAIL_ANNOTATION,
+ value)
+
+ def has_prune(self, action_id):
+ return self.has_action_annotation(action_id, Vistrail.PRUNE_ANNOTATION)
+ def get_prune(self, action_id):
+ a = self.get_action_annotation(action_id, Vistrail.PRUNE_ANNOTATION)
+ if a is not None:
+ return a.value
+ return None
+ def set_prune(self, action_id, value):
+ if isinstance(value, bool):
+ value = str(value)
+ return self.set_action_annotation(action_id, Vistrail.PRUNE_ANNOTATION,
+ value)
+ def is_pruned(self, action_id):
+ return self.get_prune(action_id) == str(True)
+
+ def has_upgrade(self, action_id):
+ return self.has_action_annotation(action_id,
+ Vistrail.UPGRADE_ANNOTATION)
+ def get_upgrade(self, action_id, root_level=True):
+ a = self.get_action_annotation(action_id, Vistrail.UPGRADE_ANNOTATION)
+ if a is not None:
+ # Recurse to get the newest upgrade in case there are
+ # multiple chained upgrades
+ return self.get_upgrade(long(a.value), False)
+ if root_level:
+ return None
+ return action_id
+ def set_upgrade(self, action_id, value):
+ return self.set_action_annotation(action_id,
+ Vistrail.UPGRADE_ANNOTATION,
+ value)
+
+ def change_annotation(self, key, value, version_number):
+ """ change_annotation(key:str, value:str, version_number:long) -> None
+ Changes the annotation of (key, value) for version version_number
+
+ """
+
+ if version_number in self.actionMap:
+ action = self.actionMap[version_number]
+ if action.has_annotation_with_key(key):
+ old_annotation = action.get_annotation_by_key(key)
+ if old_annotation.value == value:
+ return False
+ action.delete_annotation(old_annotation)
+ if value.strip() != '':
+ annotation = \
+ Annotation(id=self.idScope.getNewId(Annotation.vtType),
+ key=key,
+ value=value,
+ )
+ action.add_annotation(annotation)
+ self.changed = True
+ return True
+ return False
+
+ def change_description(self, description, version_number):
+ """ change_description(description:str, version_number:int) -> None
+ Changes the description of a version
+
+ """
+
+ return self.change_annotation(Action.ANNOTATION_DESCRIPTION,
+ description, version_number)
+
+ def change_analogy_info(self, analogy_info, version_number):
+ """ change_analogy_info(analogy_info:str, version_number:int) -> None
+ Changes the analogy information of a version
+
+ """
+
+ return self.change_annotation(Action.ANNOTATION_ANALOGY_INFO,
+ analogy_info, version_number)
+
+ def get_description(self, version_number):
+ """ get_description(version_number: int) -> str
+ Compute the description of a version
+
+ """
+ description = "Other action"
+ if not version_number:
+ description = "" # Root node
+ elif version_number in self.actionMap:
+ action = self.actionMap[version_number]
+ # if a description has been manually set, return that value
+ if action.description is not None:
+ return action.description
+ ops = action.operations
+ added_modules = 0
+ added_functions = 0
+ added_parameters = 0
+ added_connections = 0
+ added_annotations = 0
+ added_ports = 0
+ moved_modules = 0
+ changed_parameters = 0
+ changed_annotations = 0
+ deleted_modules = 0
+ deleted_connections = 0
+ deleted_parameters = 0
+ deleted_functions = 0
+ deleted_annotations = 0
+ deleted_ports = 0
+ for op in ops:
+ if op.vtType == 'add':
+ if op.what == 'module':
+ added_modules+=1
+ elif op.what == 'connection':
+ added_connections+=1
+ elif op.what == 'function':
+ added_functions+=1
+ elif op.what == 'parameter':
+ added_parameters+=1
+ elif op.what == 'annotation':
+ added_annotations+=1
+ elif op.what == 'portSpec':
+ added_ports += 1
+ elif op.vtType == 'change':
+ if op.what == 'parameter':
+ changed_parameters+=1
+ elif op.what == 'location':
+ moved_modules+=1
+ elif op.what == 'annotation':
+ changed_annotations+=1
+ elif op.vtType == 'delete':
+ if op.what == 'module':
+ deleted_modules+=1
+ elif op.what == 'connection':
+ deleted_connections+=1
+ elif op.what == 'function':
+ deleted_functions+=1
+ elif op.what == 'parameter':
+ deleted_parameters+=1
+ elif op.what == 'annotation':
+ deleted_annotations+=1
+ elif op.what == 'portSpec':
+ deleted_ports += 1
+ else:
+ raise TypeError("Unknown operation type '%s'" % op.vtType)
+
+ if added_modules:
+ description = "Added module"
+ if added_modules > 1:
+ description += "s"
+ elif added_connections:
+ description = "Added connection"
+ if added_connections > 1:
+ description += "s"
+ elif added_functions or added_parameters:
+ description = "Added parameter"
+ if added_functions > 1 or added_parameters > 1:
+ description += "s"
+ elif added_annotations:
+ description = "Added annotation"
+ if added_annotations > 1:
+ description += "s"
+ elif added_ports:
+ description = "Added port"
+ if added_ports > 1:
+ description += "s"
+ elif changed_parameters:
+ description = "Changed parameter"
+ if changed_parameters > 1:
+ description += "s"
+ elif moved_modules:
+ description = "Moved module"
+ if moved_modules > 1:
+ description += "s"
+ elif changed_annotations:
+ description = "Changed annotation"
+ if changed_annotations > 1:
+ description += "s"
+ elif deleted_modules:
+ description = "Deleted module"
+ if deleted_modules > 1:
+ description += "s"
+ elif deleted_connections:
+ description = "Deleted connection"
+ if deleted_connections > 1:
+ description += "s"
+ elif deleted_parameters or deleted_functions:
+ description = "Deleted parameter"
+ if deleted_parameters > 1 or deleted_functions > 1:
+ description += "s"
+ elif deleted_annotations:
+ description = "Deleted annotation"
+ if deleted_annotations > 1:
+ description += "s"
+ elif deleted_ports:
+ description = "Deleted port"
+ if deleted_ports > 1:
+ description += "s"
+ return description
+
+ # FIXME: remove this function (left here only for transition)
+ def getVersionGraph(self):
+ """getVersionGraph() -> Graph
+ Returns the version graph
+
+ """
+ result = Graph()
+ result.add_vertex(0)
+
+ # the sorting is for the display using graphviz
+ # we want to always add nodes from left to right
+ for action in sorted(self.actionMap.itervalues(),
+ key=lambda x: x.timestep):
+ # We need to check the presence of the parent's timestep
+ # on the graph because it might have been previously
+ # pruned. Remember that pruning is only marked for the
+ # topmost invisible action.
+ if (action.parent in result.vertices and
+ not self.is_pruned(action.id)):
+ result.add_edge(action.parent,
+ action.timestep,
+ 0)
+ return result
+
+ def getDate(self):
+ """ getDate() -> str - Returns the current date and time. """
+ # return time.strftime("%d %b %Y %H:%M:%S", time.localtime())
+ return datetime.datetime.now()
+
+ def getUser(self):
+ """ getUser() -> str - Returns the username. """
+ return getpass.getuser()
+
+ def serialize(self, filename):
+ pass
+
+ def pruneVersion(self, version):
+ """ pruneVersion(version: int) -> None
+ Add a version into the prunedVersion set
+
+ """
+ tagMap = self.get_tagMap()
+ if version!=0: # not root
+ def delete_tag(version):
+ if version in tagMap:
+ # delete tag
+ self.set_tag(version, '')
+ current_graph = self.getVersionGraph()
+ current_graph.dfs(vertex_set=[version], enter_vertex=delete_tag)
+ self.set_prune(version, str(True))
+
+ # self.prunedVersions.add(version)
+
+ def hideVersion(self, version):
+ """ hideVersion(version: int) -> None
+ Set the prune flag for the version
+
+ """
+ if version != 0:
+ self.set_prune(version, str(True))
+
+ def showVersion(self, version):
+ """ showVersion(version: int) -> None
+ Set the prune flag for the version
+
+ """
+ if version != 0:
+ self.set_prune(version, str(False))
+
+ def expandVersion(self, version):
+ """ expandVersion(version: int) -> None
+ Set the expand flag for the version
+
+ """
+ if version!=0: # not root
+ self.actionMap[version].expand = 1
+
+ def collapseVersion(self, version):
+ """ collapseVersion(version: int) -> None
+ Reset the expand flag for the version
+
+ """
+ if version!=0:
+ self.actionMap[version].expand = 0
+
+ def setSavedQueries(self, savedQueries):
+ """ setSavedQueries(savedQueries: list of (str, str, str)) -> None
+ Set the saved queries of this vistrail
+
+ """
+ self.savedQueries = savedQueries
+
+ # Dispatch in runtime according to type
+ getPipelineDispatcher = {}
+ getPipelineDispatcher[type(0)] = getPipelineVersionNumber
+ getPipelineDispatcher[type(0L)] = getPipelineVersionNumber
+ getPipelineDispatcher[type('0')] = getPipelineVersionName
+
+ class InvalidAbstraction(Exception):
+ pass
+
+ def get_persisted_log(self):
+ """
+ Returns the log object for this vistrail if available
+ """
+ log = Log()
+ if isinstance(self.locator, vistrails.core.db.locator.ZIPFileLocator):
+ if self.db_log_filename is not None:
+ log = open_log_from_xml(self.db_log_filename, True)
+ if isinstance(self.locator, vistrails.core.db.locator.DBLocator):
+ connection = self.locator.get_connection()
+ log = open_vt_log_from_db(connection, self.db_id)
+ Log.convert(log)
+ return log
+
+ def get_used_packages(self):
+ package_list = {}
+ for action in self.actions:
+ for op in action.operations:
+ try:
+ if isinstance(op, AddOp) and op.what == 'module':
+ package_list[op.data.package] = op.data.package
+ except:
+ pass
+ return package_list
+
+
+##############################################################################
+
+class ExplicitExpandedVersionTree(object):
+ """
+ Keep explicit expanded and tersed version
+ trees.
+ """
+ def __init__(self, vistrail):
+ self.vistrail = vistrail
+ self.expandedVersionTree = Graph()
+ self.expandedVersionTree.add_vertex(0)
+ self.tersedVersionTree = Graph()
+
+ def addVersion(self, id, prevId):
+ # print "add version %d child of %d" % (id, prevId)
+ self.expandedVersionTree.add_vertex(id)
+ self.expandedVersionTree.add_edge(prevId,id,0)
+
+ def getVersionTree(self):
+ return self.expandedVersionTree
+
+##############################################################################
+
+class VersionAlreadyTagged(Exception):
+ def __str__(self):
+ return "Version is already tagged"
+ pass
+
+class TagExists(Exception):
+ def __str__(self):
+ return "Tag already exists"
+ pass
+
+class VersionNotTagged(Exception):
+ def __str__(self):
+ return "Version is not tagged"
+ pass
+
+##############################################################################
+# Testing
+
+from vistrails.core.system import get_vistrails_basic_pkg_id
+
+class TestVistrail(unittest.TestCase):
+
+ def create_vistrail(self):
+ vistrail = Vistrail()
+
+ m = Module(id=vistrail.idScope.getNewId(Module.vtType),
+ name='Float',
+ package=get_vistrails_basic_pkg_id())
+ add_op = AddOp(id=vistrail.idScope.getNewId(AddOp.vtType),
+ what=Module.vtType,
+ objectId=m.id,
+ data=m)
+ function_id = vistrail.idScope.getNewId(ModuleFunction.vtType)
+ function = ModuleFunction(id=function_id,
+ name='value')
+ change_op = ChangeOp(id=vistrail.idScope.getNewId(ChangeOp.vtType),
+ what=ModuleFunction.vtType,
+ oldObjId=2,
+ newObjId=function.real_id,
+ parentObjId=m.id,
+ parentObjType=Module.vtType,
+ data=function)
+ param = ModuleParam(id=vistrail.idScope.getNewId(ModuleParam.vtType),
+ type='Integer',
+ val='1')
+ delete_op = DeleteOp(id=vistrail.idScope.getNewId(DeleteOp.vtType),
+ what=ModuleParam.vtType,
+ objectId=param.real_id,
+ parentObjId=function.real_id,
+ parentObjType=ModuleFunction.vtType)
+
+ action1 = Action(id=vistrail.idScope.getNewId(Action.vtType),
+ operations=[add_op])
+ action2 = Action(id=vistrail.idScope.getNewId(Action.vtType),
+ operations=[change_op, delete_op])
+
+ vistrail.add_action(action1, 0)
+ vistrail.add_action(action2, action1.id)
+ vistrail.addTag('first action', action1.id)
+ vistrail.addTag('second action', action2.id)
+ return vistrail
+
+ def test_get_tag_str(self):
+ v = self.create_vistrail()
+ self.failUnlessRaises(KeyError, lambda: v.get_tag_str('not here'))
+ v.get_tag_str('first action')
+ v.get_tag_str('second action')
+
+ def test_copy(self):
+ v1 = self.create_vistrail()
+ v2 = copy.copy(v1)
+ v3 = v1.do_copy(True, v1.idScope, {})
+ # FIXME add checks for equality
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ v1 = self.create_vistrail()
+ xml_str = vistrails.core.db.io.serialize(v1)
+ v2 = vistrails.core.db.io.unserialize(xml_str, Vistrail)
+ # FIXME add checks for equality
+
+ def test1(self):
+ import vistrails.core.vistrail
+ from vistrails.core.db.locator import XMLFileLocator
+ import vistrails.core.system
+ v = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/dummy.xml').load()
+ #testing nodes in different branches
+ v1 = 36
+ v2 = 41
+ p1 = v.getFirstCommonVersion(v1,v2)
+ p2 = v.getFirstCommonVersion(v2,v1)
+ self.assertEquals(p1,p2)
+
+ #testing nodes in the same branch
+ v1 = 15
+ v2 = 36
+ p1 = v.getFirstCommonVersion(v1,v2)
+ p2 = v.getFirstCommonVersion(v2,v1)
+ self.assertEquals(p1,p2)
+
+ if p1 == 0 or p2 == 0:
+ self.fail("vistrails tree is not single rooted.")
+
+ def test2(self):
+ import vistrails.core.vistrail
+ from vistrails.core.db.locator import XMLFileLocator
+ import vistrails.core.system
+ v = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/dummy.xml').load()
+ #testing diff
+ v1 = 17
+ v2 = 27
+ v3 = 22
+ v.get_pipeline_diff(v1,v2)
+ v.get_pipeline_diff(v1,v3)
+
+ def test_empty_action_chain(self):
+ """Tests calling action chain on empty version."""
+ v = Vistrail()
+ p = v.getPipeline(0)
+
+ def test_empty_action_chain_2(self):
+ from vistrails.core.db.locator import XMLFileLocator
+ import vistrails.core.system
+ v = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/dummy.xml').load()
+ assert v.actionChain(17, 17) == []
+
+ def test_get_version_negative_one(self):
+ """Tests getting the 'no version' vistrail. This should raise
+ VistrailsDBException.
+
+ """
+ v = Vistrail()
+ self.assertRaises(InvalidPipeline, lambda: v.getPipeline(-1))
+
+ def test_version_graph(self):
+ from vistrails.core.db.locator import XMLFileLocator
+ import vistrails.core.system
+ v = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/dummy.xml').load()
+ v.getVersionGraph()
+
+ def test_plugin_info(self):
+ import vistrails.core.db.io
+ plugin_info_str = "this is a test of plugin_info"
+ v1 = self.create_vistrail()
+ v1.plugin_info = plugin_info_str
+ xml_str = vistrails.core.db.io.serialize(v1)
+ v2 = vistrails.core.db.io.unserialize(xml_str, Vistrail)
+ assert plugin_info_str == v2.plugin_info
+
+ def test_database_info(self):
+ import vistrails.core.db.io
+ database_info_str = "db.hostname.edu:3306:TABLE_NAME"
+ v1 = self.create_vistrail()
+ v1.database_info = database_info_str
+ xml_str = vistrails.core.db.io.serialize(v1)
+ v2 = vistrails.core.db.io.unserialize(xml_str, Vistrail)
+ assert database_info_str == v2.database_info
+
+ def test_plugin_data(self):
+ import vistrails.core.db.io
+ v1 = self.create_vistrail()
+ plugin_data_str = "testing plugin_data"
+ p = PluginData(id=v1.idScope.getNewId(PluginData.vtType),
+ data=plugin_data_str)
+ add_op = AddOp(id=v1.idScope.getNewId(AddOp.vtType),
+ what=PluginData.vtType,
+ objectId=p.id,
+ data=p)
+ action = Action(id=v1.idScope.getNewId(Action.vtType),
+ operations=[add_op])
+ v1.add_action(action, 0)
+ workflow = v1.getPipeline(action.id)
+ p2 = workflow.plugin_datas[0]
+ assert plugin_data_str == p2.data
+
+ def test_inverse(self):
+ """Test if inverses and general_action_chain are working by
+ doing a lot of action-based transformations on a pipeline and
+ checking against another way of getting the same one."""
+ def check_pipelines(p, p2):
+ if p != p2:
+ p.show_comparison(p2)
+ return False
+ return True
+ from vistrails.core.db.locator import XMLFileLocator
+ from vistrails.core.db.locator import FileLocator
+ import vistrails.core.system
+ import sys
+
+ def do_test(filename, locator_class, old_v=None, new_v=None):
+ v = locator_class(vistrails.core.system.vistrails_root_directory() +
+ filename).load()
+ if not isinstance(v, Vistrail):
+ v = v.vistrail
+ version_ids = v.actionMap.keys()
+ if old_v is None:
+ old_v = random.choice(version_ids)
+ p = v.getPipeline(old_v)
+
+ def do_single_test(start_v, end_v):
+ p2 = v.getPipeline(end_v)
+ a = v.general_action_chain(start_v, end_v)
+ p.perform_action(a)
+ #if not check_pipelines(p, p2):
+ # print start_v, end_v
+
+ assert p == p2
+
+ if new_v is not None:
+ do_single_test(old_v, new_v)
+ else:
+ for i in xrange(10):
+ new_v = random.choice(version_ids)
+ do_single_test(old_v, new_v)
+ old_v = new_v
+
+
+ do_test('/tests/resources/dummy.xml', XMLFileLocator)
+ do_test('/tests/resources/terminator.vt', FileLocator)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/core/vistrail/vistrailvariable.py b/vistrails/core/vistrail/vistrailvariable.py
new file mode 100644
index 0000000..19a9eeb
--- /dev/null
+++ b/vistrails/core/vistrail/vistrailvariable.py
@@ -0,0 +1,135 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBVistrailVariable
+
+import unittest
+import copy
+import vistrails.core
+
+class VistrailVariable(DBVistrailVariable):
+
+ ##########################################################################
+ # Constructors and copy
+
+ def __init__(self, *args, **kwargs):
+ DBVistrailVariable.__init__(self, *args, **kwargs)
+
+ def __copy__(self):
+ return VistrailVariable.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrailVariable.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = VistrailVariable
+ return cp
+
+ @staticmethod
+ def convert(_vistrailvariable):
+ _vistrailvariable.__class__ = VistrailVariable
+
+ ##########################################################################
+ # Properties
+
+ name = DBVistrailVariable.db_name
+ uuid = DBVistrailVariable.db_uuid
+ package = DBVistrailVariable.db_package
+ module = DBVistrailVariable.db_module
+ namespace = DBVistrailVariable.db_namespace
+ value = DBVistrailVariable.db_value
+
+ ##########################################################################
+ # Operators
+
+ def __str__(self):
+ """__str__() -> str - Returns a string representation of a
+ VistrailVariable object.
+
+ """
+ rep = "<vistrailvariable name=%s uuid=%s package=%s module=%s \
+namespace=%s value=%s</vistrailvariable>"
+ return rep % (str(self.name), str(self.uuid), str(self.package),
+ str(self.module), str(self.namespace), str(self.value))
+
+ def __eq__(self, other):
+ """ __eq__(other: VistrailVariable) -> boolean
+ Returns True if self and other have the same attributes. Used by ==
+ operator.
+
+ """
+ if type(self) != type(other):
+ return False
+ if self.name != other.name:
+ return False
+ if self.uuid != other.uuid:
+ return False
+ if self.package != other.package:
+ return False
+ if self.module != other.module:
+ return False
+ if self.namespace != other.namespace:
+ return False
+ if self.value != other.value:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+################################################################################
+# Unit tests
+
+
+class TestVistrailVariable(unittest.TestCase):
+
+ def create_vv(self):
+ var = VistrailVariable('a','false uuid','pack','module',"ns","3.14")
+ return var
+
+ def test_copy(self):
+ a1 = self.create_vv()
+ a2 = copy.copy(a1)
+ self.assertEquals(a1, a2)
+ a3 = a1.do_copy()
+ self.assertEquals(a1, a3)
+
+ def test_serialization(self):
+ import vistrails.core.db.io
+ a1 = self.create_vv()
+ xml_str = vistrails.core.db.io.serialize(a1)
+ a2 = vistrails.core.db.io.unserialize(xml_str, VistrailVariable)
+ self.assertEquals(a1, a2)
+
+ def test_str(self):
+ a1 = self.create_vv()
+ str(a1)
diff --git a/vistrails/db/__init__.py b/vistrails/db/__init__.py
new file mode 100644
index 0000000..fc3514e
--- /dev/null
+++ b/vistrails/db/__init__.py
@@ -0,0 +1,45 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+class VistrailsDBException(Exception):
+ """VistrailsDBException is raised when there is any exception in the
+ db code for VisTrails
+
+ """
+ def __init__(self, msg):
+ self.msg = msg
+ def __str__(self):
+ return "VistrailsDBException: " + str(self.msg)
+
diff --git a/vistrails/db/bin/README b/vistrails/db/bin/README
new file mode 100644
index 0000000..184396f
--- /dev/null
+++ b/vistrails/db/bin/README
@@ -0,0 +1,27 @@
+To generate code for the vistrails database interaction automatically,
+you will need to run generate.py with a directory of specs files.
+
+Usage: python generate.py -v <version> [-a] [-m] [-n] [-p] [-s] [-d <dir>] [-x] [-b <dir>]
+ -a generate all database information (-p -s -x)
+ -m make all directories
+ -n do not change current version
+ -p generate python domain classes
+ -s generate sql schema and persistence classes
+ -d <dir> versions directory
+ -x generate xml schema and persistence classes
+ -v <version> vistrail version tag
+ -b <dir> base directory
+
+If you have not created any directory structure for the version,
+common usage would be something like
+
+python generate.py -v 0.6.0 -m -a -n
+
+with -n depending on whether you wish to change the current version or not.
+
+In the specs file, you can create indexes using the index attribute
+for a property. You can specify multiple indexes by delimiting them
+with spaces. You can specify a composite index by separating the
+fields by a colon. Finally, you can specify that an index is not 1-1
+with '!' as the starting character; this allows us to ignore KeyErrors
+on the deletes from that dictionary.
\ No newline at end of file
diff --git a/vistrails/db/bin/__init__.py b/vistrails/db/bin/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/bin/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/bin/auto_gen_objects.py b/vistrails/db/bin/auto_gen_objects.py
new file mode 100644
index 0000000..e994737
--- /dev/null
+++ b/vistrails/db/bin/auto_gen_objects.py
@@ -0,0 +1,417 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+def capitalizeOne(str):
+ result = ''
+ strs = str.split('_')
+ for a_str in strs:
+ result += a_str[0].upper() + a_str[1:]
+ return result
+
+class Field:
+ def __init__(self, params):
+ self.params = params
+
+ def getName(self):
+ try:
+ return self.params['name']
+ except KeyError:
+ try:
+ return self.params['object']
+ except KeyError:
+ pass
+ return None
+
+ def getPluralName(self):
+ try:
+ return self.params['pluralName']
+ except KeyError:
+ pass
+ return "%ss" % Field.getName(self)
+
+ def getIterator(self):
+ if Field.getType(self) == 'hash':
+ return Field.getFieldName(self) + '.itervalues()'
+ return Field.getFieldName(self)
+
+ def getPrivateIterator(self):
+ if Field.getType(self) == 'hash':
+ return Field.getPrivateName(self) + '.itervalues()'
+ return Field.getPrivateName(self)
+
+ def getRegularIterator(self):
+ if Field.getType(self) == 'hash':
+ return Field.getRegularName(self) + '.itervalues()'
+ return Field.getRegularName(self)
+
+ def getSingleName(self):
+ return Field.getName(self)
+
+ def getRegularName(self):
+ if Field.isPlural(self):
+ return Field.getPluralName(self)
+ return Field.getName(self)
+
+ def getPythonName(self):
+ return 'db_' + Field.getName(self)
+
+ def getFieldName(self):
+ return 'db_' + Field.getRegularName(self)
+
+ def getDefineAccessor(self):
+ return '__get_%s' % Field.getFieldName(self)
+
+ def getDefineMutator(self):
+ return '__set_%s' % Field.getFieldName(self)
+
+ def getAccessor(self):
+ return 'db_get_%s' % Field.getRegularName(self)
+
+ def getMutator(self):
+ return 'db_set_%s' % Field.getRegularName(self)
+
+ def getAppender(self):
+ return 'db_add_%s' % Field.getSingleName(self)
+
+ def getLookup(self):
+ return 'db_get_%s' % Field.getSingleName(self)
+
+ def getModifier(self):
+ return 'db_change_%s' % Field.getSingleName(self)
+
+ def getRemover(self):
+ return 'db_delete_%s' % Field.getSingleName(self)
+
+ def getList(self):
+ return 'db_get_%s' % Field.getRegularName(self)
+
+ def getListValues(self):
+ if Field.getType(self) == 'hash':
+ return Field.getPrivateName(self) + '.values()'
+ return Field.getPrivateName(self)
+
+ def getPrivateName(self):
+ return '_%s' % Field.getFieldName(self)
+
+ def getMapping(self):
+ try:
+ return self.params['mapping']
+ except KeyError:
+ pass
+ return 'one-to-one'
+
+ def getType(self):
+ try:
+ return self.params['type']
+ except KeyError:
+ pass
+ return 'str'
+
+ def getPythonType(self):
+ return Field.getType(self)
+
+ def getIndices(self):
+ try:
+ str = self.params['index']
+ indices = str.split()
+ for i, index in enumerate(indices):
+ compound_idx = index.split(':')
+ if len(compound_idx) > 1:
+ indices[i] = compound_idx
+ return indices
+ except KeyError:
+ pass
+ return []
+
+ def getAllIndices(self):
+ indices = []
+ if self.isReference():
+ if self.isPlural():
+ ref_obj = self.getReferencedObject()
+ key = ref_obj.getKey()
+ if key is not None:
+ indices.append(key.getRegularName())
+ for index in self.getIndices():
+ if isinstance(index, list):
+ index_field = []
+ for piece in index:
+ ignore_del_err = False
+ if piece[0] == '!':
+ piece = piece[1:]
+ ignore_del_err = True
+ ref_field = ref_obj.getField(piece)
+ if ref_field is not None:
+ if ignore_del_err:
+ index_field.append('!' + ref_field.getRegularName())
+ else:
+ index_field.append(ref_field.getRegularName())
+ if len(index_field) > 1:
+ indices.append(index_field)
+ elif len(index_field) > 0:
+ indices.append(index_field[0])
+ else:
+ ignore_del_err = False
+ if index[0] == '!':
+ index = index[1:]
+ ignore_del_err = True
+ index_field = ref_obj.getField(index)
+ if index_field is not None:
+ if ignore_del_err:
+ indices.append('!' + index_field.getRegularName())
+ else:
+ indices.append(index_field.getRegularName())
+ return indices
+
+ def isInverse(self):
+ try:
+ return self.params['inverse'] == 'true'
+ except KeyError:
+ pass
+ return False
+
+ def isPlural(self):
+ return self.getMapping() == 'one-to-many' or \
+ self.getMapping() == 'many-to-many'
+
+ def shouldExpand(self):
+ return self.params.get('expand','true') == 'true'
+
+ def shouldExpandAction(self):
+ return self.params.get('expandAction', 'true') == 'true'
+
+ def hasDiscriminator(self):
+ return self.params.has_key('discriminator')
+
+ def getDiscriminator(self):
+ try:
+ return self.params['discriminator']
+ except KeyError:
+ pass
+ return None
+
+class Choice(Field):
+ def __init__(self, params, properties):
+ Field.__init__(self, params)
+ self.properties = properties
+
+ def __str__(self):
+ return 'choice: %s\nparams:\n\t%s\nprops:\n\t%s' % \
+ (self.getName(), self.params, self.properties)
+
+ def isReference(self):
+ if len(self.properties) > 0:
+ return self.properties[0].isReference()
+ return False
+
+ def getReference(self):
+ if len(self.properties) > 0:
+ return self.properties[0].getReference()
+ return None
+
+ def getReferencedObject(self):
+ if len(self.properties) > 0:
+ return self.properties[0].getReferencedObject()
+
+ def isChoice(self):
+ return True
+
+class Property(Field):
+ def __init__(self, params, specs):
+ Field.__init__(self, params)
+ self.specs = specs
+ self.referencedObject = None
+
+ def __str__(self):
+ return 'property: %s\nparams:\n\t%s\nspecs:\n\t%s' % \
+ (self.getName(), self.params, self.specs)
+
+ def getReference(self):
+ try:
+ return self.params['object']
+ except KeyError:
+ pass
+ return ''
+
+ def getReferencedObject(self):
+ return self.referencedObject
+
+ def setReferencedObject(self, obj):
+ self.referencedObject = obj
+
+ def isReference(self):
+ try:
+ return self.params['ref'] == 'true'
+ except KeyError:
+ pass
+ return False
+
+ def isPrimaryKey(self):
+ try:
+ return self.params['primaryKey'] == 'true'
+ except KeyError:
+ pass
+ return False
+
+ def isForeignKey(self):
+ try:
+ return self.params['foreignKey'] == 'true'
+ except KeyError:
+ pass
+ return False
+
+ def isChoice(self):
+ return False
+
+class Object:
+ def __init__(self, params, properties, layouts, choices):
+ self.params = params
+ self.properties = properties
+ self.layouts = layouts
+ self.choices = choices
+
+ def __str__(self):
+ propStr = ''
+ for property in self.properties:
+ propStr += '\t%s\n' % property
+ choiceStr = ''
+ for choice in self.choices:
+ choiceStr += '\t%s\n' % choice
+ return 'params:\n\t%s\nlayouts\n\t%s\n' % \
+ (self.params, self.layouts) + \
+ 'properites:\n%s\nchoices:\n%s\n' % \
+ (propStr, choiceStr)
+
+ def getName(self):
+ try:
+ return self.params['name']
+ except KeyError:
+ pass
+ return None
+
+ def getField(self, field_name):
+ for property in self.properties:
+ if Property.getName(property) == field_name:
+ return property
+ for choice in self.choices:
+ if Choice.getName(choice) == field_name:
+ return choice
+ return None
+
+ def getRegularName(self):
+ return Object.getName(self)
+
+ def getPythonName(self):
+ return 'db_' + Object.getName(self)
+
+ def getClassName(self):
+ try:
+ return self.params['className']
+ except KeyError:
+ pass
+ return 'DB%s' % capitalizeOne(Object.getName(self))
+
+ def getChildren(self):
+ return 'db_children'
+
+ def getKey(self):
+ for property in self.properties:
+ if property.isPrimaryKey():
+ return property
+ return None
+
+ def getSingleProperties(self):
+ return [p for p in self.properties if not p.isPlural()]
+
+ def getPluralProperties(self):
+ return [p for p in self.properties if p.isPlural and not p.isInverse()]
+
+ def getForeignKeys(self):
+ return [p for p in self.properties if p.isForeignKey()]
+
+ def getReferences(self):
+ return self.getReferenceProperties() + self.getReferenceChoices()
+
+ def getNonInverseReferences(self):
+ return [ref for ref in self.getReferences() if not ref.isInverse()]
+
+ def getReferenceProperties(self):
+ return [p for p in self.properties if p.isReference()]
+
+ def getReferenceChoices(self):
+ return [c for c in self.choices if c.isReference()]
+
+ def getNonReferenceProperties(self):
+ return [p for p in self.properties if not p.isReference()]
+
+ def getInverseProperties(self):
+ return [p for p in self.properties if p.isInverse()]
+
+ def getNonInverseProperties(self):
+ return [p for p in self.properties if not p.isInverse()]
+
+ def getPythonVarNames(self):
+ return [field.getRegularName() for field in self.getPythonFields()]
+
+ def getPythonFields(self):
+ return [c for c in self.choices if not c.isInverse()] + \
+ [p for p in self.properties if not p.isInverse()]
+
+ def getPythonPluralFields(self):
+ return [f for f in self.getPythonFields() if f.isPlural()]
+
+ def getPythonLists(self):
+ return [f for f in self.getPythonPluralFields()
+ if f.getPythonType() != 'hash']
+
+ def getPythonHashes(self):
+ return [f for f in self.getPythonPluralFields()
+ if f.getPythonType() == 'hash']
+
+ def getDiscriminatorProperty(self, dName):
+ try:
+ for property in self.properties:
+ if property.getName() == dName:
+ return property
+ except KeyError:
+ pass
+ return None
+
+ def getConstructorNames(self):
+ return [f.getRegularName() for f in self.getPythonFields()]
+
+ def getCopyNames(self):
+ return [(f.getRegularName(), f.getPrivateName())
+ for f in self.getPythonFields()
+ if not f.isPlural() and not f.isReference()]
diff --git a/vistrails/db/bin/generate.py b/vistrails/db/bin/generate.py
new file mode 100644
index 0000000..c3d624a
--- /dev/null
+++ b/vistrails/db/bin/generate.py
@@ -0,0 +1,382 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""auto-generates code given specs"""
+
+# requires mako python package (easy_install Mako) and
+# uses emacs via subprocess call for python indentation
+# the emacs call is slow because it checks all of the indentation
+
+from mako.template import Template
+
+import os
+import re
+import shutil
+import subprocess
+import sys
+import tempfile
+import getopt
+from parser import AutoGenParser
+import xml_gen_objects
+import sql_gen_objects
+
+BASE_DIR = os.path.dirname(os.getcwd())
+
+DOMAIN_INIT = """from auto_gen import *"""
+PERSISTENCE_INIT = \
+"""from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+"""
+COPYRIGHT_NOTICE = \
+"""###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""
+
+def preprocess_template(in_fname, out_fname=None):
+ in_file = open(in_fname)
+ if out_fname is not None:
+ out_file = open(out_fname, 'w')
+ else:
+ out_file = sys.stdout
+
+ single_slash = re.compile(r'\s*\\$')
+ double_slash = re.compile(r'\s*\\\\$')
+ triple_slash = re.compile(r'\s*\\\\\\$')
+ slash_bang = re.compile(r'\s*\\!$')
+ python_block = re.compile(r'^\s+<%')
+ strip_whitespace = False
+ for line in in_file:
+ if strip_whitespace:
+ line = line.lstrip()
+ if python_block.search(line):
+ line = python_block.sub(r'<%', line)
+ if triple_slash.search(line):
+ line = triple_slash.sub(r' ${"\\\\"}', line)
+ strip_whitespace = False
+ elif double_slash.search(line):
+ line = double_slash.sub(r'\\', line)
+ strip_whitespace = False
+ elif slash_bang.search(line):
+ line = line[:-3].rstrip()
+ strip_whitespace = True
+ elif single_slash.search(line):
+ line = line[:-2].rstrip() + ' '
+ strip_whitespace = True
+ else:
+ strip_whitespace = False
+ out_file.write(line)
+
+ if out_fname is not None:
+ out_file.close()
+ in_file.close()
+
+def indent_python(fname):
+ subprocess.Popen(["emacs", "-batch", fname, "-f", "mark-whole-buffer",
+ "-f", "indent-region", "-f", "save-buffer", "-kill"],
+ stdout=subprocess.PIPE).communicate()
+
+def run_template(template_fname, objects, version, version_string, output_file,
+ indent=False):
+ [prefix, suffix] = os.path.basename(template_fname).split('.', 1)
+ (fd, p_fname) = tempfile.mkstemp(prefix=prefix, suffix=suffix)
+ os.close(fd)
+ try:
+ preprocess_template(template_fname, p_fname)
+ template = Template(filename=p_fname, module_directory='/tmp/mako')
+
+ f = open(output_file, 'w')
+ f.write(template.render(objs=objects,
+ version=version,
+ version_string=version_string))
+ f.close()
+ if indent:
+ indent_python(output_file)
+ finally:
+ os.remove(p_fname)
+
+def usage(usageDict):
+ usageStr = ''
+ unrequired = ''
+ required = ''
+ for (opt, info) in usageDict.iteritems():
+ if info[1]:
+ required += '-%s <%s> ' % (opt[0], info[2])
+ usageStr += ' -%s <%s> ' % (opt[0], info[2])
+ else:
+ if len(opt) > 1:
+ unrequired += '[-%s <%s>] ' % (opt[0], info[2])
+ usageStr += ' -%s <%s> ' % (opt[0], info[2])
+ else:
+ unrequired += '[-%s] ' % opt[0]
+ usageStr += ' -%s ' % opt[0]
+ usageStr += '%s\n' % info[0]
+ print 'Usage: python generate.py %s%s\n%s' % (required,
+ unrequired,
+ usageStr)
+
+def dirStructure(baseDir):
+ dirs = {}
+ dirs['base'] = baseDir
+ dirs['specs'] = os.path.join(dirs['base'], 'specs')
+ dirs['persistence'] = os.path.join(dirs['base'], 'persistence')
+ dirs['domain'] = os.path.join(dirs['base'], 'domain')
+ dirs['schemas'] = os.path.join(dirs['base'], 'schemas')
+ dirs['xmlPersistence'] = os.path.join(dirs['persistence'], 'xml')
+ dirs['sqlPersistence'] = os.path.join(dirs['persistence'], 'sql')
+ dirs['xmlSchema'] = os.path.join(dirs['schemas'], 'xml')
+ dirs['sqlSchema'] = os.path.join(dirs['schemas'], 'sql')
+ return dirs
+
+def makeAllDirs(dirs):
+ for (name, dir) in dirs.iteritems():
+ if not os.path.exists(dir):
+ print "creating directory '%s'" % dir
+ os.makedirs(dir)
+ if name not in set(['specs', 'schemas', 'xmlSchema', 'sqlSchema']):
+ init_file = os.path.join(dir, '__init__.py')
+ if not os.path.exists(init_file):
+ print "creating file '%s'" % init_file
+ f = open(init_file, 'w')
+ f.write(COPYRIGHT_NOTICE)
+ if name == 'domain':
+ f.write(DOMAIN_INIT)
+ elif name == 'persistence':
+ f.write(PERSISTENCE_INIT)
+ else:
+ f.write('pass')
+ f.close()
+
+def main(argv=None):
+ options = {}
+ objects = None
+
+ optionsUsage = {'a': ('generate all database information (-p -s -x)',
+ False),
+ 'b:': ('base directory', False, 'dir'),
+ 'd:': ('versions directory', False, 'dir'),
+ 'p': ('generate python domain classes', False),
+ 's': ('generate sql schema and persistence classes', False),
+ 'x': ('generate xml schema and persistence classes', False),
+ 'v:': ('vistrail version tag', True, 'version'),
+ 'm': ('make all directories', False),
+ 'n': ('do not change current version', False)}
+
+ optStr = ''.join(optionsUsage.keys())
+ optKeys = optStr.replace(':','')
+ for idx in xrange(len(optKeys)):
+ options[optKeys[idx]] = False
+
+ try:
+ (optlist, args) = getopt.getopt(sys.argv[1:], optStr)
+ for opt in optlist:
+ if opt[1] is not None and opt[1] != '':
+ options[opt[0][1:]] = opt[1]
+ else:
+ options[opt[0][1:]] = True
+ except getopt.GetoptError:
+ usage(optionsUsage)
+ return
+
+ if options['b']:
+ baseDir = options['b']
+ else:
+ baseDir = BASE_DIR
+ baseDirs = dirStructure(baseDir)
+
+ if not options['v']:
+ usage(optionsUsage)
+ return
+
+ version = options['v']
+ # make sure version use dot-style
+ assert(len(version.split('.'))==3)
+ versionName = 'v' + version.replace('.', '_')
+ if options['d']:
+ versionsDir = options['d']
+ else:
+ versionsDir = os.path.join(baseDir, 'versions')
+ versionDir = os.path.join(versionsDir, versionName)
+ versionDirs = dirStructure(versionDir)
+
+ print baseDirs
+ print versionDirs
+
+ if options['m']:
+ makeAllDirs(baseDirs)
+ makeAllDirs(versionDirs)
+
+ # check whether we should use existing specs for version
+ use_base_specs = True
+ if options['n'] and os.path.exists(versionDirs['specs']):
+ for file in os.listdir(versionDirs['specs']):
+ if file.endswith('.xml'):
+ # assume we've already copied the specs
+ use_base_specs = False
+
+ if use_base_specs:
+ # copy specs to version
+ print "copying base specs to version directory..."
+ for file in os.listdir(baseDirs['specs']):
+ if file.endswith('.xml'):
+ print 'copying %s' % file
+ filename = os.path.join(baseDirs['specs'], file)
+ toFile = os.path.join(versionDirs['specs'], file)
+ shutil.copyfile(filename, toFile)
+ else:
+ print "using existing specs from version directory..."
+
+ if options['p'] or options['a']:
+ # generate python domain objects
+ print "generating python domain objects..."
+ if objects is None:
+ parser = AutoGenParser()
+ objects = parser.parse(versionDirs['specs'])
+ run_template('templates/domain.py.mako', objects, version, versionName,
+ os.path.join(versionDirs['domain'], 'auto_gen.py'),
+ True)
+
+ if not options['n']:
+ domainFile = os.path.join(baseDirs['domain'], '__init__.py')
+ f = open(domainFile, 'w')
+ f.write(COPYRIGHT_NOTICE)
+ f.write('from vistrails.db.versions.%s.domain import *\n' % \
+ versionName)
+ f.close()
+
+ if options['x'] or options['a']:
+ # generate xml schema and dao objects
+ print "generating xml schema and dao objects..."
+ if objects is None:
+ parser = AutoGenParser()
+ objects = parser.parse(versionDirs['specs'])
+ xml_objects = xml_gen_objects.convert(objects)
+
+ run_template('templates/xml_schema.xsd.mako',
+ xml_gen_objects.convert_schema_order(xml_objects,
+ 'vistrail'),
+ version, versionName,
+ os.path.join(versionDirs['xmlSchema'], 'vistrail.xsd'),
+ False)
+
+ run_template('templates/xml_schema.xsd.mako',
+ xml_gen_objects.convert_schema_order(xml_objects,
+ 'workflow'),
+ version, versionName,
+ os.path.join(versionDirs['xmlSchema'], 'workflow.xsd'),
+ False)
+
+ run_template('templates/xml_schema.xsd.mako',
+ xml_gen_objects.convert_schema_order(xml_objects,
+ 'log'),
+ version, versionName,
+ os.path.join(versionDirs['xmlSchema'], 'log.xsd'),
+ False)
+
+ run_template('templates/xml.py.mako', xml_objects, version, versionName,
+ os.path.join(versionDirs['xmlPersistence'], 'auto_gen.py'),
+ True)
+
+ if options['s'] or options['a']:
+ # generate sql schema and dao objects
+ print "generating sql schema and dao objects..."
+ if objects is None:
+ parser = AutoGenParser()
+ objects = parser.parse(versionDirs['specs'])
+ sql_objects = sql_gen_objects.convert(objects)
+
+ run_template('templates/sql_schema.sql.mako', sql_objects,
+ version, versionName,
+ os.path.join(versionDirs['sqlSchema'], 'vistrails.sql'),
+ False)
+
+ run_template('templates/sql_delete.sql.mako', sql_objects,
+ version, versionName,
+ os.path.join(versionDirs['sqlSchema'],
+ 'vistrails_drop.sql'),
+ False)
+
+ run_template('templates/sql.py.mako', sql_objects,
+ version, versionName,
+ os.path.join(versionDirs['sqlPersistence'], 'auto_gen.py'),
+ True)
+
+ if not options['n']:
+ domainFile = os.path.join(baseDirs['persistence'], '__init__.py')
+ f = open(domainFile, 'w')
+ f.write(COPYRIGHT_NOTICE)
+ f.write('from vistrails.db.versions.%s.persistence import *\n' % \
+ versionName)
+ f.close()
+
+if __name__ == '__main__':
+ main()
diff --git a/vistrails/db/bin/parser.py b/vistrails/db/bin/parser.py
new file mode 100644
index 0000000..68dfbf1
--- /dev/null
+++ b/vistrails/db/bin/parser.py
@@ -0,0 +1,130 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import os
+from xml.dom import minidom, Node
+from auto_gen_objects import Object, Property, Choice
+
+class AutoGenParser:
+ def __init__(self):
+ pass
+
+ def parse(self, dir):
+ objects = {}
+ for file in os.listdir(dir):
+ if file.endswith('.xml'):
+ filename = os.path.join(dir, file)
+ # print filename
+ dom = minidom.parse(filename)
+ domObjects = dom.getElementsByTagName('object')
+ for node in domObjects:
+ curObject = self.parseObject(node)
+ objects[curObject.getName()] = curObject
+
+ # set the referenced objects here
+ for obj in objects.itervalues():
+ for prop in obj.properties:
+ if prop.getReference():
+ try:
+ prop.setReferencedObject(objects[prop.getReference()])
+ except KeyError:
+ print 'error:', prop.getReference()
+ for choice in obj.choices:
+ for prop in choice.properties:
+ if prop.getReference():
+ try:
+ prop.setReferencedObject(
+ objects[prop.getReference()])
+ except KeyError:
+ print 'error:', prop.getReference()
+
+ return objects.values()
+
+ def parseObject(self, node):
+ params = {}
+ properties = []
+ choices = []
+ layouts = None
+ for attr in node.attributes.keys():
+ params[attr] = node.attributes.get(attr).value
+ for child in node.childNodes:
+ if child.nodeType == Node.ELEMENT_NODE:
+ if child.nodeName == 'layout':
+ layouts = self.parseLayouts(child)
+ elif child.nodeName == 'property':
+ property = self.parseProperty(child)
+ properties.append(property)
+ elif child.nodeName == 'choice':
+ choice = self.parseChoice(child)
+ choices.append(choice)
+ return Object(params, properties, layouts, choices)
+
+ def parseLayouts(self, node):
+ layouts = {}
+ for child in node.childNodes:
+ if child.nodeType == Node.ELEMENT_NODE:
+ layouts[child.nodeName] = self.parseDataToDict(child)
+ return layouts
+
+ def parseProperty(self, node):
+ params = {}
+ specs = {}
+ for attr in node.attributes.keys():
+ params[attr] = node.attributes.get(attr).value
+ for child in node.childNodes:
+ if child.nodeType == Node.ELEMENT_NODE:
+ specs[child.nodeName] = self.parseDataToDict(child)
+ return Property(params, specs)
+
+ def parseChoice(self, node):
+ params = {}
+ properties = []
+ for attr in node.attributes.keys():
+ params[attr] = node.attributes.get(attr).value
+ for child in node.childNodes:
+ if child.nodeType == Node.ELEMENT_NODE and \
+ child.nodeName == 'property':
+ properties.append(self.parseProperty(child))
+ return Choice(params, properties)
+
+ def parseDataToDict(self, node):
+ dict = {}
+ if node.nodeType == Node.ELEMENT_NODE:
+ for attr in node.attributes.keys():
+ dict[attr] = node.attributes.get(attr).value
+ for child in node.childNodes:
+ if child.nodeType == Node.ELEMENT_NODE:
+ dict[child.nodeName] = child.childNodes[0].data
+ return dict
diff --git a/vistrails/db/bin/sql_gen_objects.py b/vistrails/db/bin/sql_gen_objects.py
new file mode 100644
index 0000000..cf72c4b
--- /dev/null
+++ b/vistrails/db/bin/sql_gen_objects.py
@@ -0,0 +1,242 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen_objects import Object, Property, Choice
+
+SQL_TYPE = 'sql'
+
+class SQLObject(Object):
+ @staticmethod
+ def convert(obj):
+ if SQL_TYPE in obj.layouts:
+ obj.__class__ = SQLObject
+ for prop in obj.properties:
+ prop.__class__ = SQLProperty
+ for choice in obj.choices:
+ choice.__class__ = SQLChoice
+ for prop in choice.properties:
+ prop.__class__ = SQLProperty
+
+ def getName(self):
+ try:
+ return self.layouts[SQL_TYPE]['table']
+ except KeyError:
+ pass
+ return Object.getName(self)
+
+ def getSQLFields(self):
+ return self.getSQLProperties() + self.getSQLChoices()
+
+ def getSQLProperties(self):
+ return [p for p in self.properties if p.hasSpec()]
+
+ def getSQLChoices(self):
+ return [c for c in self.choices if c.hasSpec()]
+
+ def getSQLInverses(self):
+ return [f for f in self.getSQLFields() if f.isInverse()]
+
+ def getSQLInverseRefs(self):
+ return [f for f in self.getSQLFields()
+ if f.isInverse() and f.isReference()]
+
+ def getSQLColumns(self):
+ return [f.getColumn() for f in self.getSQLFields()]
+
+ def getSQLReferences(self):
+ return ([p for p in self.properties
+ if p.isReference() and not p.isInverse()] +
+ [c for c in self.choices
+ if c.isReference() and not c.isInverse()])
+
+ def getNormalSQLColumns(self):
+ return [p for p in self.properties if not p.isInverse() and \
+ not p.isPrimaryKey() and not p.isReference() and \
+ p.hasSpec()]
+
+ def getNormalSQLColumnsAndKey(self):
+ return self.getNormalSQLColumns() + [self.getKey()]
+
+ def getSQLConstructorPairs(self):
+ return [(f.getRegularName(), f.getRegularName())
+ for f in self.getNormalSQLColumnsAndKey()]
+
+ def getSQLColumnsAndKey(self):
+ return [p.getColumnn() for p in self.getNormalSQLColumnsAndKey()]
+
+ def getSQLReferenceProperties(self):
+ return [p for p in self.properties
+ if not p.isInverse() and p.isReference()]
+
+ def getSQLForeignKeys(self):
+ return [p for p in self.properties
+ if p.isInverse() and p.isForeignKey()]
+
+ def getSQLReferencedField(self, refObj):
+ if refObj is not None:
+ # find inverse
+ for refProp in refObj.properties:
+ if refProp.isReference() and \
+ refProp.isInverse() and \
+ refProp.getReference() == self.getRegularName():
+ return (refProp, False)
+ for choice in refObj.choices:
+ for refProp in self.getSQLPropertiesForChoice(choice):
+ if refProp.isReference() and \
+ refProp.getReference() == self.getRegularName():
+ return (choice, True)
+ return (None, False)
+
+ def get_sql_referenced(self, ref_obj, inverse=False):
+ if ref_obj is not None:
+ for ref_prop in ref_obj.properties:
+ if not (inverse ^ ref_prop.isInverse()) and \
+ ref_prop.isReference() and \
+ ref_prop.getReference() == self.getRegularName():
+ return (ref_prop, False)
+ for choice in ref_obj.choices:
+ if inverse ^ choice.isInverse():
+ continue
+ for ref_prop in choice.properties:
+ if ref_prop.isReference() and \
+ ref_prop.getReference() == self.getRegularName():
+ return (choice, True)
+ raise RuntimeError("didn't work", ref_obj.getRegularName(),
+ self.getRegularName())
+
+class SQLProperty (Property):
+ def hasSpec(self):
+ try:
+ sqlSpec = self.specs[SQL_TYPE]
+ return True
+ except KeyError:
+ pass
+ return False
+
+ def getName(self):
+ try:
+ return self.specs[SQL_TYPE]['name']
+ except KeyError:
+ pass
+ return Property.getName(self)
+
+ def getColumn(self):
+ try:
+ return self.specs[SQL_TYPE]['column']
+ except KeyError:
+ pass
+ return self.getName()
+
+ def getType(self):
+ try:
+ return self.specs[SQL_TYPE]['type']
+ except KeyError:
+ pass
+ return 'int'
+
+ def getGlobalName(self):
+ try:
+ return self.specs[SQL_TYPE]['globalName']
+ except KeyError:
+ pass
+ return ''
+
+ def isText(self):
+ if string.find(self.getType().upper(), 'CHAR') != -1 or \
+ string.find(self.getType().upper(), 'DATE') != -1:
+ return True
+ return False
+
+ def isAutoInc(self):
+ try:
+ # FIXME include "and isPrimaryKey()" ?
+ return self.specs[SQL_TYPE]['autoInc'] == 'true' and \
+ self.isPrimaryKey()
+ except KeyError:
+ pass
+ return False
+
+ def isGlobal(self):
+ try:
+ return self.specs[SQL_TYPE]['global'] == 'true'
+ except KeyError:
+ pass
+ return False
+
+class SQLChoice(Choice):
+ def hasSpec(self):
+ if self.properties[0].hasSpec():
+ return True
+ return False
+
+ def getSpec(self):
+ if self.hasSpec():
+ return self.properties[0]
+ return None
+
+ def getColumn(self):
+ for property in self.properties:
+ if property.hasSpec():
+ break
+ try:
+ return property.specs[SQL_TYPE]['column']
+ except KeyError:
+ pass
+ return self.getName()
+
+ def isGlobal(self):
+ try:
+ return self.properties[0].specs[SQL_TYPE]['global'] == 'true'
+ except KeyError:
+ pass
+ return False
+
+ def getGlobalName(self):
+ try:
+ return self.properties[0].specs[SQL_TYPE]['globalName']
+ except KeyError:
+ pass
+ return ''
+
+ def getSQLProperties(self):
+ return [p for p in self.properties if p.hasSpec()]
+
+def convert(objects):
+ sql_objects = []
+ for obj in objects:
+ if SQL_TYPE in obj.layouts:
+ SQLObject.convert(obj)
+ sql_objects.append(obj)
+ return sql_objects
diff --git a/vistrails/db/bin/templates/domain.py.mako b/vistrails/db/bin/templates/domain.py.mako
new file mode 100644
index 0000000..5e2b456
--- /dev/null
+++ b/vistrails/db/bin/templates/domain.py.mako
@@ -0,0 +1,504 @@
+<%
+def getIndexName(index):
+ if type(index) == type([]):
+ # return '_'.join(index)
+ if index[0][0] == '!':
+ return index[0][1:]
+ return index[0]
+ else:
+ if index[0] == '!':
+ return index[1:]
+ return index
+
+def getIndexKey(field_str, index):
+ if type(index) == type([]):
+ if index[0][0] == '!':
+ index = [index[0][1:]] + index[1:]
+ return '(' + field_str + '.db_' + \
+ (',' + field_str + '.db_').join(index) + ')'
+ else:
+ if index[0] == '!':
+ index = index[1:]
+ return field_str + '.db_' + index
+
+def shouldIgnoreIndexDelete(index):
+ if type(index) == type([]):
+ return index[0][0] == '!'
+ return index[0] == '!'
+%> \\
+<%text>###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+</%text>
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+% for obj in objs:
+class ${obj.getClassName()}(object):
+
+ vtType = '${obj.getRegularName()}'
+
+ def __init__(self, ${', '.join(['%s=None' % n \
+ for n in obj.getConstructorNames()])}):
+ % for field in obj.getPythonFields():
+ % if field.isReference() and not field.isInverse():
+ self.db_deleted_${field.getRegularName()} = []
+ % endif
+ % if field.isPlural():
+ % for index in field.getAllIndices():
+ self.db_${field.getRegularName()}_${getIndexName(index)}_index = {}
+ % endfor
+ if ${field.getRegularName()} is None:
+ % if field.getPythonType() == 'hash':
+ self.${field.getPrivateName()} = {}
+ % else:
+ self.${field.getPrivateName()} = []
+ % endif
+ else:
+ self.${field.getPrivateName()} = ${field.getRegularName()}
+ % if len(field.getAllIndices()) > 0:
+ % if field.getPythonType() == 'hash':
+ for v in self.${field.getPrivateName()}.itervalues():
+ % else:
+ for v in self.${field.getPrivateName()}:
+ % endif
+ % for index in field.getAllIndices():
+ self.db_${field.getRegularName()}_${getIndexName(index)}_ \!
+ index[${getIndexKey('v', index)}] = v
+ % endfor
+ % endif
+ % else:
+ self.${field.getPrivateName()} = ${field.getRegularName()}
+ % endif
+ % endfor
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return ${obj.getClassName()}.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = ${obj.getClassName()}( \!
+ ${',\n'.join(['%s=self.%s' % f for f in obj.getCopyNames()])})
+ % for field in obj.getPythonFields():
+ % if field.isPlural():
+ if self.${field.getPrivateName()} is None:
+ % if field.getPythonType() == 'hash':
+ cp.${field.getPrivateName()} = {}
+ % else:
+ cp.${field.getPrivateName()} = []
+ % endif
+ else:
+ % if field.getPythonType() == 'hash':
+ % if field.shouldExpand():
+ cp.${field.getPrivateName()} = \
+ dict([(k, v.do_copy(new_ids, id_scope, id_remap)) \
+ for (k,v) in self.${field.getPrivateName()}.iteritems()])
+ % else:
+ cp.${field.getPrivateName()} = \
+ dict([(k, v.do_copy()) \
+ for (k,v) in self.${field.getPrivateName()}.iteritems()])
+ % endif
+ % else:
+ % if field.shouldExpand():
+ cp.${field.getPrivateName()} = \
+ [v.do_copy(new_ids, id_scope, id_remap) \
+ for v in self.${field.getPrivateName()}]
+ % else:
+ cp.${field.getPrivateName()} = \
+ [v.do_copy() for v in self.${field.getPrivateName()}]
+ % endif
+ % endif
+ % else:
+ % if field.isReference():
+ if self.${field.getPrivateName()} is not None:
+ % if field.shouldExpand():
+ cp.${field.getPrivateName()} = \
+ self.${field.getPrivateName()}.do_copy(new_ids, id_scope, \
+ id_remap)
+ % else:
+ cp.${field.getPrivateName()} = \
+ self.${field.getPrivateName()}.do_copy()
+ % endif
+ % endif
+ % endif
+ % endfor
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ % if len(obj.getForeignKeys()) > 0:
+ % for field in obj.getForeignKeys():
+ <%
+ if field.hasDiscriminator():
+ disc_prop = obj.getDiscriminatorProperty( \
+ field.getDiscriminator())
+ lookup_str = "self.%s" % disc_prop.getPrivateName()
+ else:
+ ref_obj = field.getReferencedObject()
+ lookup_str = "'%s'" % ref_obj.getRegularName()
+ %> \\
+ if hasattr(self, '${field.getFieldName()}') and \
+ (${lookup_str}, self.${field.getPrivateName()}) in id_remap:
+ cp.${field.getPrivateName()} = \
+ id_remap[(${lookup_str}, \
+ self.${field.getPrivateName()})]
+ % endfor
+ % endif
+
+ # recreate indices and set flags
+ % for field in obj.getPythonFields():
+ % if len(field.getAllIndices()) > 0:
+ % for index in field.getAllIndices():
+ cp.db_${field.getRegularName()}_${getIndexName(index)}_index = \
+ dict((${getIndexKey('v', index)}, v) \
+ for v in cp.${field.getPrivateIterator()})
+ % endfor
+ % endif
+ % endfor
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ ## create static update_version
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = ${obj.getClassName()}()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ % for field in obj.getPythonFields():
+ if '${field.getRegularName()}' in class_dict:
+ res = class_dict['${field.getRegularName()}'](old_obj, trans_dict)
+ % if field.isPlural():
+ for obj in res:
+ new_obj.${field.getAppender()}(obj)
+ % else:
+ new_obj.${field.getFieldName()} = res
+ % endif
+ elif hasattr(old_obj, '${field.getFieldName()}') and \
+ old_obj.${field.getFieldName()} is not None:
+ % if field.isReference():
+ ## refObj = field.getReferencedObject()
+ % if field.isPlural():
+ for obj in old_obj.${field.getIterator()}:
+ % if field.isChoice():
+ <% cond = 'if' %> \\
+ % for prop in field.properties:
+ ## if prop.isReference():
+ ## propRefObj = prop.getReferencedObject()
+ ${cond} obj.vtType == \
+ '${prop.getReferencedObject().getRegularName()}':
+ new_obj.${field.getAppender()}( \!
+ ${prop.getReferencedObject().getClassName()}. \!
+ update_version(obj, trans_dict))
+ <% cond = 'elif' %> \\
+ % endfor
+ % else:
+ new_obj.${field.getAppender()}( \!
+ ${field.getReferencedObject().getClassName()}. \!
+ update_version(obj, trans_dict))
+ % endif
+ % else:
+ obj = old_obj.${field.getFieldName()}
+ % if field.isChoice():
+ <% cond = 'if' %> \\
+ % for prop in field.properties:
+ ## if prop.isReference():
+ ## propRefObj = prop.getReferencedObject()
+ ${cond} obj.vtType == \
+ '${prop.getReferencedObject().getRegularName()}':
+ new_obj.${field.getAppender()}( \!
+ ${prop.getReferencedObject().getClassName()}. \!
+ update_version(obj, trans_dict))
+ <% cond = 'elif' %> \\
+ % endfor
+ % else:
+ new_obj.${field.getAppender()}( \!
+ ${field.getReferencedObject().getClassName()}. \!
+ update_version(obj, trans_dict))
+ % endif
+ % endif
+ % if not field.isInverse():
+ if hasattr(old_obj, 'db_deleted_${field.getRegularName()}') \
+ and hasattr(new_obj, 'db_deleted_${field.getRegularName()}'):
+ ## refObj = field.getReferencedObject()
+ for obj in old_obj.db_deleted_${field.getRegularName()}:
+ % if field.isChoice():
+ <% cond = 'if' %> \\
+ % for prop in field.properties:
+ ## if prop.isReference():
+ ## propRefObj = prop.getReferencedObject()
+ ${cond} obj.vtType == \
+ '${prop.getReferencedObject().getRegularName()}':
+ n_obj = ${prop.getReferencedObject().getClassName()}. \!
+ update_version(obj, trans_dict)
+ new_obj.db_deleted_${field.getRegularName()}.append(n_obj)
+ <% cond = 'elif' %> \\
+ % endfor
+ % else:
+ n_obj = ${field.getReferencedObject().getClassName()}. \!
+ update_version(obj, trans_dict)
+ new_obj.db_deleted_${field.getRegularName()}.append(n_obj)
+ % endif
+ % endif
+ % else:
+ new_obj.${field.getFieldName()} = old_obj.${field.getFieldName()}
+ % endif
+ % endfor
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ ## create child methods
+ def ${obj.getChildren()}(self, parent=(None,None), orphan=False, for_action=False):
+ % if not any([not ref.isInverse() and ref.shouldExpand() \
+ for ref in obj.getReferences()]):
+ return [(self, parent[0], parent[1])]
+ % else:
+ children = []
+ % for ref in obj.getReferences():
+ % if not ref.isInverse() and ref.shouldExpand():
+ ## refObj = ref.getReferencedObject()
+ % if not ref.shouldExpandAction():
+ if not for_action:
+ % if not ref.isPlural():
+ if self.${ref.getPrivateName()} is not None:
+ children.extend(self.${ref.getPrivateName()}. \!
+ ${ref.getReferencedObject().getChildren()}( \!
+ (self.vtType, self.db_id), orphan, for_action))
+ % else:
+ for child in self.${ref.getIterator()}:
+ children.extend(child.${ref.getReferencedObject().getChildren()}( \!
+ (self.vtType, self.db_id), orphan, for_action))
+ % endif
+ % else:
+ % if not ref.isPlural():
+ if self.${ref.getPrivateName()} is not None:
+ children.extend(self.${ref.getPrivateName()}. \!
+ ${ref.getReferencedObject().getChildren()}( \!
+ (self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self.${ref.getPrivateName()} = None
+ % else:
+ to_del = []
+ for child in self.${ref.getIterator()}:
+ children.extend(child.${ref.getReferencedObject().getChildren()}( \!
+ (self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.${ref.getRemover()}(child)
+ % endif
+ % endif
+ % endif
+ % endfor
+ children.append((self, parent[0], parent[1]))
+ return children
+ % endif
+ ## get deleted method
+ def db_deleted_children(self, remove=False):
+ children = []
+ % if len(obj.getNonInverseReferences()) > 0:
+ % for ref in obj.getNonInverseReferences():
+ children.extend(self.db_deleted_${ref.getRegularName()})
+ % endfor
+ if remove:
+ % for ref in obj.getNonInverseReferences():
+ self.db_deleted_${ref.getRegularName()} = []
+ % endfor
+ % endif
+ return children
+ ## dirty method
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ % for ref in obj.getNonInverseReferences():
+ % if not ref.isPlural():
+ if self.${ref.getPrivateName()} is not None and \
+ self.${ref.getPrivateName()}.has_changes():
+ return True
+ % else:
+ for child in self.${ref.getPrivateIterator()}:
+ if child.has_changes():
+ return True
+ % endif
+ % endfor
+ return False
+ ## create methods
+ % for field in obj.getPythonFields():
+ def ${field.getDefineAccessor()}(self):
+ return self.${field.getPrivateName()}
+ def ${field.getDefineMutator()}(self, ${field.getRegularName()}):
+ self.${field.getPrivateName()} = ${field.getRegularName()}
+ self.is_dirty = True
+ ${field.getFieldName()} = property(${field.getDefineAccessor()}, \
+ ${field.getDefineMutator()})
+ % if not field.isPlural():
+ def ${field.getAppender()}(self, ${field.getName()}):
+ self.${field.getPrivateName()} = ${field.getName()}
+ def ${field.getModifier()}(self, ${field.getName()}):
+ self.${field.getPrivateName()} = ${field.getName()}
+ def ${field.getRemover()}(self, ${field.getName()}):
+ % if field.isReference() and not field.isInverse():
+ if not self.is_new:
+ self.db_deleted_${field.getRegularName()}.append( \!
+ self.${field.getPrivateName()})
+ % endif
+ self.${field.getPrivateName()} = None
+ % else:
+ def ${field.getList()}(self):
+ return self.${field.getListValues()}
+ def ${field.getAppender()}(self, ${field.getName()}):
+ self.is_dirty = True
+ % if field.getPythonType() == 'hash':
+ self.${field.getPrivateName()}[${field.getName()}. \!
+ ${field.getReferencedObject().getKey().getPythonName()}] = \
+ ${field.getName()}
+ % else:
+ self.${field.getPrivateName()}.append(${field.getName()})
+ % endif
+ % for index in field.getAllIndices():
+ self.db_${field.getRegularName()}_${getIndexName(index)}_index[ \!
+ ${getIndexKey(field.getName(), index)}] = ${field.getName()}
+ % endfor
+ def ${field.getModifier()}(self, ${field.getName()}):
+ self.is_dirty = True
+ % if field.getPythonType() == 'hash':
+ ## childObj = field.getReferencedObject()
+ self.${field.getPrivateName()}[${field.getName()}. \!
+ ${field.getReferencedObject().getKey().getPythonName()}] = \
+ ${field.getName()}
+ % else:
+ ## childObj = field.getReferencedObject()
+ % if field.getReferencedObject().getKey() is not None:
+ found = False
+ for i in xrange(len(self.${field.getPrivateName()})):
+ if self.${field.getPrivateName()}[i]. \!
+ ${field.getReferencedObject().getKey().getPythonName()} == \
+ ${field.getName()}. \!
+ ${field.getReferencedObject().getKey().getPythonName()}:
+ self.${field.getPrivateName()}[i] = ${field.getName()}
+ found = True
+ break
+ if not found:
+ self.${field.getPrivateName()}.append(${field.getName()})
+ % else:
+ self.${field.getPrivateName()}.append(${field.getName()})
+ % endif
+ % endif
+ % for index in field.getAllIndices():
+ self.db_${field.getRegularName()}_${getIndexName(index)}_index[ \!
+ ${getIndexKey(field.getName(), index)}] = ${field.getName()}
+ % endfor
+ def ${field.getRemover()}(self, ${field.getName()}):
+ self.is_dirty = True
+ % if field.getPythonType() == 'hash':
+ ## childObj = field.getReferencedObject()
+ if not self.${field.getPrivateName()}[${field.getName()}. \!
+ ${field.getReferencedObject().getKey().getPythonName()}].is_new:
+ self.db_deleted_${field.getRegularName()}.append( \!
+ self.${field.getPrivateName()}[${field.getName()}. \!
+ ${field.getReferencedObject().getKey().getPythonName()}])
+ del self.${field.getPrivateName()}[${field.getName()}. \!
+ ${field.getReferencedObject().getKey().getPythonName()}]
+ % else:
+ % if field.getReferencedObject().getKey() is None:
+ raise Exception('Cannot delete a non-keyed object')
+ % else:
+ for i in xrange(len(self.${field.getPrivateName()})):
+ if self.${field.getPrivateName()}[i]. \!
+ ${field.getReferencedObject().getKey().getPythonName()} == \
+ ${field.getName()}. \!
+ ${field.getReferencedObject().getKey().getPythonName()}:
+ if not self.${field.getPrivateName()}[i].is_new:
+ self.db_deleted_${field.getRegularName()}.append( \!
+ self.${field.getPrivateName()}[i])
+ del self.${field.getPrivateName()}[i]
+ break
+ % endif
+ % endif
+ % for index in field.getAllIndices():
+ % if shouldIgnoreIndexDelete(index):
+ try:
+ del self.db_${field.getRegularName()}_${getIndexName(index)}_ \!
+ index[${getIndexKey(field.getName(), index)}]
+ except KeyError:
+ pass
+ % else:
+ del self.db_${field.getRegularName()}_${getIndexName(index)}_ \!
+ index[${getIndexKey(field.getName(), index)}]
+ % endif
+ % endfor
+ def ${field.getLookup()}(self, key):
+ % if field.getPythonType() == 'hash':
+ if key in self.${field.getPrivateName()}:
+ return self.${field.getPrivateName()}[key]
+ return None
+ % else:
+ % if field.getReferencedObject().getKey() is not None:
+ for i in xrange(len(self.${field.getPrivateName()})):
+ if self.${field.getPrivateName()}[i]. \!
+ ${field.getReferencedObject().getKey().getPythonName()} == key:
+ return self.${field.getPrivateName()}[i]
+ % endif
+ return None
+ % endif
+ % endif
+ % for index in field.getAllIndices():
+ def db_get_${field.getSingleName()}_by_${getIndexName(index)}(self, key):
+ return self.db_${field.getRegularName()}_ \!
+ ${getIndexName(index)}_index[key]
+ def db_has_${field.getSingleName()}_with_${getIndexName(index)}(self, key):
+ return key in self.db_${field.getRegularName()}_ \!
+ ${getIndexName(index)}_index
+ % endfor
+
+ % endfor
+ % if obj.getKey() is not None:
+ def getPrimaryKey(self):
+ return self.${obj.getKey().getPrivateName()}
+ % else:
+
+ % endif
+
+% endfor
diff --git a/vistrails/db/bin/templates/sql.py.mako b/vistrails/db/bin/templates/sql.py.mako
new file mode 100644
index 0000000..f74ad9f
--- /dev/null
+++ b/vistrails/db/bin/templates/sql.py.mako
@@ -0,0 +1,306 @@
+<%text>###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+</%text>
+"""generated automatically by auto_dao.py"""
+
+from sql_dao import SQLDAO
+from vistrails.db.versions.${version_string}.domain import *
+
+% for obj in objs:
+class ${obj.getClassName()}SQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = '${obj.getName()}'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ ## get_sql_columns
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['${"', '".join(obj.getSQLColumns())}']
+ table = '${obj.getName()}'
+ whereMap = global_props
+ orderBy = '${obj.getKey().getName()}'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, \
+ lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ % for count, field in enumerate(obj.getSQLFields()):
+ ${field.getRegularName()} = \
+ self.convertFromDB(row[${count}], '${field.getPythonType()}', \
+ '${field.getType()}')
+ % if field.isGlobal():
+ global_props['${field.getGlobalName()}'] = \
+ self.convertToDB(${field.getRegularName()}, \
+ '${field.getPythonType()}', \
+ '${field.getType()}')
+ % endif
+ % endfor
+
+ ${obj.getRegularName()} = ${obj.getClassName()} \!
+ (${',\n'.join('%s=%s' % p
+ for p in obj.getSQLConstructorPairs())})
+ % for field in obj.getSQLInverses():
+ ${obj.getRegularName()}.${field.getFieldName()} = \
+ ${field.getRegularName()}
+ % endfor
+ ${obj.getRegularName()}.is_dirty = False
+ res[('${obj.getRegularName()}', \
+ ${obj.getKey().getRegularName()})] = ${obj.getRegularName()}
+ return res
+
+ ## get_sql_select
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['${"', '".join(obj.getSQLColumns())}']
+ table = '${obj.getName()}'
+ whereMap = global_props
+ orderBy = '${obj.getKey().getName()}'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, \
+ lock)
+
+ ## process_sql_columns
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ % for count, field in enumerate(obj.getSQLFields()):
+ ${field.getRegularName()} = \
+ self.convertFromDB(row[${count}], '${field.getPythonType()}', \
+ '${field.getType()}')
+ % if field.isGlobal():
+ global_props['${field.getGlobalName()}'] = \
+ self.convertToDB(${field.getRegularName()}, \
+ '${field.getPythonType()}', \
+ '${field.getType()}')
+ % endif
+ % endfor
+
+ ${obj.getRegularName()} = ${obj.getClassName()} \!
+ (${',\n'.join('%s=%s' % p
+ for p in obj.getSQLConstructorPairs())})
+ % for field in obj.getSQLInverses():
+ ${obj.getRegularName()}.${field.getFieldName()} = \
+ ${field.getRegularName()}
+ % endfor
+ ${obj.getRegularName()}.is_dirty = False
+ res[('${obj.getRegularName()}', \
+ ${obj.getKey().getRegularName()})] = ${obj.getRegularName()}
+ return res
+
+ ## from_sql_fast
+ def from_sql_fast(self, obj, all_objects):
+ % if len(obj.getSQLInverseRefs()) < 1:
+ pass
+ % endif
+ % for backRef in obj.getSQLInverseRefs():
+ <% cond = "if" %> \\
+ % if backRef.isChoice():
+ % for prop in backRef.properties:
+ ${cond} obj.${obj.getDiscriminatorProperty( \!
+ backRef.getDiscriminator()).getFieldName()} == \
+ '${prop.getReferencedObject().getRegularName()}':
+ p = all_objects[('${prop.getReferencedObject().getRegularName()}', \
+ obj.${backRef.getFieldName()})]
+ p.${obj.get_sql_referenced(prop.getReferencedObject())[0] \!
+ .getAppender()}(obj)
+ <% cond = "elif" %> \\
+ % endfor
+ % else:
+ if ('${backRef.getReferencedObject().getRegularName()}', \
+ obj.${backRef.getFieldName()}) in all_objects:
+ p = all_objects[( \!
+ '${backRef.getReferencedObject().getRegularName()}', \
+ obj.${backRef.getFieldName()})]
+ p.${obj.get_sql_referenced(backRef.getReferencedObject())[0]. \!
+ getAppender()}(obj)
+ % endif
+ % endfor
+
+ ## set_sql_columns
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['${"', '".join(obj.getSQLColumns())}']
+ table = '${obj.getName()}'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.${obj.getKey().getFieldName()} is not None:
+ keyStr = self.convertToDB(obj.${obj.getKey().getFieldName()}, \
+ '${obj.getKey().getPythonType()}', \
+ '${obj.getKey().getType()}')
+ whereMap['${obj.getKey().getColumn()}'] = keyStr
+ columnMap = {}
+ % for field in obj.getSQLFields():
+ if hasattr(obj, '${field.getPythonName()}') and \
+ obj.${field.getPythonName()} is not None:
+ columnMap['${field.getColumn()}'] = \\\
+ self.convertToDB(obj.${field.getFieldName()}, \
+ '${field.getPythonType()}', \
+ '${field.getType()}')
+ % endfor
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ % if obj.getKey().isAutoInc():
+ if obj.${obj.getKey().getPythonName()} is None:
+ obj.${obj.getKey().getPythonName()} = lastId
+ keyStr = self.convertToDB(obj.${obj.getKey().getPythonName()}, \
+ '${obj.getKey().getPythonType()}', \
+ '${obj.getKey().getType()}')
+ % endif
+ % for prop in obj.getNormalSQLColumnsAndKey():
+ % if prop.isGlobal():
+ if hasattr(obj, '${prop.getPythonName()}') and \
+ obj.${prop.getPythonName()} is not None:
+ global_props['${prop.getGlobalName()}'] = \
+ self.convertToDB(obj.${prop.getPythonName()}, \
+ '${prop.getPythonType()}', \
+ '${prop.getType()}')
+ % endif
+ % endfor
+
+ ## set_sql_command
+ ## returns the sql command for saving this object or none if already up to date
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['${"', '".join(obj.getSQLColumns())}']
+ table = '${obj.getName()}'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.${obj.getKey().getFieldName()} is not None:
+ keyStr = self.convertToDB(obj.${obj.getKey().getFieldName()}, \
+ '${obj.getKey().getPythonType()}', \
+ '${obj.getKey().getType()}')
+ whereMap['${obj.getKey().getColumn()}'] = keyStr
+ columnMap = {}
+ % for field in obj.getSQLFields():
+ if hasattr(obj, '${field.getPythonName()}') and \
+ obj.${field.getPythonName()} is not None:
+ columnMap['${field.getColumn()}'] = \\\
+ self.convertToDB(obj.${field.getFieldName()}, \
+ '${field.getPythonType()}', \
+ '${field.getType()}')
+ % endfor
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ ## set_sql_process
+ ## takes the generated id and updates the object
+ def set_sql_process(self, obj, global_props, lastId):
+ % if obj.getKey().isAutoInc():
+ if obj.${obj.getKey().getPythonName()} is None:
+ obj.${obj.getKey().getPythonName()} = lastId
+ keyStr = self.convertToDB(obj.${obj.getKey().getPythonName()}, \
+ '${obj.getKey().getPythonType()}', \
+ '${obj.getKey().getType()}')
+ % endif
+ % for prop in obj.getNormalSQLColumnsAndKey():
+ % if prop.isGlobal():
+ if hasattr(obj, '${prop.getPythonName()}') and \
+ obj.${prop.getPythonName()} is not None:
+ global_props['${prop.getGlobalName()}'] = \
+ self.convertToDB(obj.${prop.getPythonName()}, \
+ '${prop.getPythonType()}', \
+ '${prop.getType()}')
+ % endif
+ % endfor
+ pass
+
+ ## to_sql_fast
+ def to_sql_fast(self, obj, do_copy=True):
+ % if len(obj.getSQLReferences()) < 1:
+ pass
+ % endif
+ % for ref in obj.getSQLReferences():
+ % if ref.isPlural():
+ for child in obj.${ref.getIterator()}:
+ % else:
+ if obj.${ref.getFieldName()} is not None:
+ child = obj.${ref.getFieldName()}
+ % endif
+ % if obj.get_sql_referenced(ref.getReferencedObject(), True)[1]:
+ child.${ref.getReferencedObject().getDiscriminatorProperty( \!
+ obj.get_sql_referenced(ref.getReferencedObject(), \
+ True)[0].getDiscriminator()). \!
+ getFieldName()} = obj.vtType
+ child.${obj.get_sql_referenced(ref.getReferencedObject(), \
+ True)[0].getFieldName()} = \
+ obj.db_id
+ % else:
+ child.${obj.get_sql_referenced(ref.getReferencedObject(), \
+ True)[0].getFieldName()} = \
+ obj.db_id
+ % endif
+ % endfor
+
+ ## delete_sql_column
+ def delete_sql_column(self, db, obj, global_props):
+ table = '${obj.getName()}'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.${obj.getKey().getFieldName()} is not None:
+ keyStr = self.convertToDB(obj.${obj.getKey().getFieldName()}, \
+ '${obj.getKey().getPythonType()}', \
+ '${obj.getKey().getType()}')
+ whereMap['${obj.getKey().getColumn()}'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+% endfor
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ % for obj in objs:
+ if '${obj.getRegularName()}' not in self:
+ self['${obj.getRegularName()}'] = \
+ ${obj.getClassName()}SQLDAOBase(self)
+ % endfor
diff --git a/vistrails/db/bin/templates/sql_delete.sql.mako b/vistrails/db/bin/templates/sql_delete.sql.mako
new file mode 100644
index 0000000..fcd9736
--- /dev/null
+++ b/vistrails/db/bin/templates/sql_delete.sql.mako
@@ -0,0 +1,42 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+DROP TABLE IF EXISTS `vistrails_version`;
+
+DROP TABLE IF EXISTS thumbnail;
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS ${', '.join(['%s' % obj.getName() for obj in objs])};
diff --git a/vistrails/db/bin/templates/sql_schema.sql.mako b/vistrails/db/bin/templates/sql_schema.sql.mako
new file mode 100644
index 0000000..0410f55
--- /dev/null
+++ b/vistrails/db/bin/templates/sql_schema.sql.mako
@@ -0,0 +1,77 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+CREATE TABLE `vistrails_version`(`version` char(16)) engine=InnoDB;
+INSERT INTO `vistrails_version`(`version`) VALUES ('${version}');
+
+CREATE TABLE thumbnail(
+ id int not null auto_increment primary key,
+ file_name varchar(255),
+ image_bytes mediumblob,
+ last_modified datetime
+) engine=InnoDB;
+
+-- generated automatically by auto_dao.py
+
+% for obj in objs:
+CREATE TABLE ${obj.getName()}(
+% for i, prop in enumerate(obj.getSQLProperties() + obj.getSQLChoices()):
+ % if prop.isChoice():
+ % if prop.isInverse():
+ % if i != len(obj.getSQLProperties() + obj.getSQLChoices()) - 1:
+ ${prop.getSpec().getColumn()} ${prop.getSpec().getType()},
+ % else:
+ ${prop.getSpec().getColumn()} ${prop.getSpec().getType()}
+ % endif
+ % endif
+ % else:
+ % if i != len(obj.getSQLProperties() + obj.getSQLChoices()) - 1:
+ % if prop.isAutoInc():
+ ${prop.getColumn()} ${prop.getType()} not null auto_increment primary key,
+ % else:
+ ${prop.getColumn()} ${prop.getType()},
+ % endif
+ % else:
+ % if prop.isAutoInc():
+ ${prop.getColumn()} ${prop.getType()} not null auto_increment primary key
+ % else:
+ ${prop.getColumn()} ${prop.getType()}
+ % endif
+ % endif
+ % endif
+% endfor
+) engine=InnoDB;
+
+% endfor
\ No newline at end of file
diff --git a/vistrails/db/bin/templates/xml.py.mako b/vistrails/db/bin/templates/xml.py.mako
new file mode 100644
index 0000000..93a0e91
--- /dev/null
+++ b/vistrails/db/bin/templates/xml.py.mako
@@ -0,0 +1,228 @@
+<%text>###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+</%text>
+"""generated automatically by auto_dao.py"""
+
+from vistrails.core.system import get_elementtree_library
+ElementTree = get_elementtree_library()
+
+from xml_dao import XMLDAO
+from vistrails.db.versions.${version_string}.domain import *
+
+% for obj in objs:
+class ${obj.getClassName()}XMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ ## define fromXML function
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != '${obj.getName()}':
+ return None
+ % if len(obj.getXMLAttributes()) > 0:
+
+ # read attributes
+ % for prop in obj.getXMLAttributes():
+ data = node.get('${prop.getName()}', None)
+ ${prop.getRegularName()} = \
+ self.convertFromStr(data, '${prop.getPythonType()}')
+ % endfor
+ % endif
+ % if len(obj.getXMLElements()) + len(obj.getXMLChoices()) > 0:
+
+ % for field in obj.getXMLElements() + obj.getXMLChoices():
+ % if not field.isPlural():
+ ${field.getRegularName()} = None
+ % else:
+ % if field.getPythonType() == 'hash':
+ ${field.getRegularName()} = {}
+ % else:
+ ${field.getRegularName()} = []
+ % endif
+ % endif
+ % endfor
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ <% cond = 'if' %> \\
+ % for field in obj.getXMLElements() + obj.getXMLChoices():
+ % if field.isChoice():
+ % for prop in field.getXMLProperties():
+ ${cond} child_tag == '${prop.getXMLPropertyName()}':
+ % if prop.isReference():
+ _data = self.getDao('${prop.getReference()}').fromXML(child)
+ % else:
+ _data = self.convertFromStr(child.text, \!
+ '${prop.getPythonType()}')
+ % endif
+ % if field.isPlural():
+ % if field.getPythonType() == 'hash':
+ % if not field.isReference():
+ raise Exception("Cannot generate hash for non-referenced field")
+ % endif
+ ${field.getRegularName()}[_data. \!
+ ${field.getReferencedObject().getKey().getFieldName()}] = \
+ _data
+ % else:
+ ${field.getRegularName()}.append(_data)
+ % endif
+ % else:
+ ${field.getRegularName()} = _data
+ % endif
+ <% cond = 'elif' %> \\
+ % endfor
+ % else:
+ ${cond} child_tag == '${field.getXMLPropertyName()}':
+ % if field.isReference():
+ _data = self.getDao('${field.getReference()}').fromXML(child)
+ % else:
+ _data = self.convertFromStr(child.text, \!
+ '${field.getPythonType()}')
+ % endif
+ % if field.isPlural():
+ % if field.getPythonType() == 'hash':
+ % if not field.isReference():
+ raise Exception("Cannot generate hash for non-referenced field")
+ % endif
+ ${field.getRegularName()}[_data. \!
+ ${field.getReferencedObject().getKey().getFieldName()}] = \
+ _data
+ % else:
+ ${field.getRegularName()}.append(_data)
+ % endif
+ % else:
+ ${field.getRegularName()} = _data
+ % endif
+ <% cond = 'elif' %> \\
+ % endif
+ % endfor
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+ % endif
+
+ obj = ${obj.getClassName()}( \!
+ ${',\n'.join(['%s=%s' % f for f in obj.getConstructorPairs()])})
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, ${obj.getRegularName()}, node=None):
+ ## if not ${obj.getRegularName()}.has_changes():
+ ## return
+ if node is None:
+ node = ElementTree.Element('${obj.getName()}')
+ % if len(obj.getXMLAttributes()) > 0:
+
+ # set attributes
+ % for prop in obj.getXMLAttributes():
+ node.set('${prop.getName()}', \!
+ self.convertToStr(${obj.getRegularName()}. \!
+ ${prop.getFieldName()}, \
+ '${prop.getPythonType()}'))
+ % endfor
+ % endif
+
+ % if len(obj.getXMLElements()) + len(obj.getXMLChoices()) > 0:
+ # set elements
+ % for field in obj.getXMLElements() + obj.getXMLChoices():
+ ${field.getRegularName()} = \
+ ${obj.getRegularName()}.${field.getFieldName()}
+ % if field.isReference():
+ % if field.isPlural():
+ for ${field.getSingleName()} in ${field.getRegularIterator()}:
+ % else:
+ if ${field.getSingleName()} is not None:
+ % endif
+ % if field.isChoice():
+ <% cond = 'if' %> \\
+ % for prop in field.getXMLProperties():
+ ${cond} ${field.getSingleName()}.vtType == '${prop.getReference()}':
+ % if prop.isReference():
+ childNode = ElementTree.SubElement(node, \
+ '${prop.getReferencedObject().getName()}')
+ self.getDao('${prop.getReference()}').toXML( \!
+ ${field.getSingleName()}, childNode)
+ % else:
+ childNode = ElementTree.SubElement(node, \
+ '${prop.getXMLPropertyName()}')
+ childNode.text = self.convertToStr(${prop.getSingleName()}, \
+ '${prop.getPythonType()}')
+ % endif
+ <% cond = 'elif' %> \\
+ % endfor
+ % else:
+ if (${field.getRegularName()} is not None) and (${field.getRegularName()} != ""):
+ childNode = ElementTree.SubElement(node, \
+ '${field.getReferencedObject().getName()}')
+ self.getDao('${field.getReference()}').toXML( \!
+ ${field.getSingleName()}, childNode)
+ % endif
+ % else:
+ if (${field.getRegularName()} is not None) and (${field.getRegularName()} != ""):
+ childNode = ElementTree.SubElement(node, '${field.getXMLPropertyName()}')
+ childNode.text = self.convertToStr(${field.getSingleName()}, \
+ '${field.getPythonType()}')
+ % endif
+ % endfor
+
+ % endif
+ return node
+
+% endfor
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ % for obj in objs:
+ if '${obj.getRegularName()}' not in self:
+ self['${obj.getRegularName()}'] = \
+ ${obj.getClassName()}XMLDAOBase(self)
+ % endfor
diff --git a/vistrails/db/bin/templates/xml_schema.xsd.mako b/vistrails/db/bin/templates/xml_schema.xsd.mako
new file mode 100644
index 0000000..c722630
--- /dev/null
+++ b/vistrails/db/bin/templates/xml_schema.xsd.mako
@@ -0,0 +1,103 @@
+<%
+def writeElement(prop):
+ if prop.isReference():
+ if prop.getName() == prop.getReferencedObject().getName():
+ return '<xs:element ref="%s" minOccurs="%s" maxOccurs="%s"/>' % \
+ (prop.getName(), prop.getMinOccurs(), prop.getMaxOccurs())
+ else:
+ return ('<xs:element name="%s" ref="%s" minOccurs="%s" ' + \
+ 'maxOccurs="%s"/>') % \
+ (prop.getName(), prop.getReferencedObject().getName(),
+ prop.getMinOccurs(), prop.getMaxOccurs())
+
+ return '<xs:element name="%s" minOccurs="%s" maxOccurs="%s"/>' % \
+ (prop.getName(), prop.getMinOccurs(), prop.getMaxOccurs())
+%> \\
+<%text><!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+</%text>
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ % for obj in objs:
+ <${obj.getNodeType()} name="${obj.getName()}">
+ % if len(obj.getXMLElements()) + len(obj.getXMLAttributes()) + \
+ len(obj.getXMLChoices()) > 0:
+ <xs:complexType>
+ % if len(obj.getXMLElements()) > 0:
+ <xs:sequence>
+ % for prop in obj.getXMLElements():
+ ${writeElement(prop)}
+ % endfor
+ % for choice in obj.getXMLChoices():
+ <xs:choice>
+ % for prop in choice.getXMLProperties():
+ % if prop.hasSpec() and not prop.isInferred():
+ % if prop.getNodeType() == 'xs:attribute':
+ <xs:attribute name="${prop.getName()}" \
+ type="${prop.getAttributeType()}"${prop.getAttributeUseText()}/>
+ % elif prop.getNodeType() == 'xs:element':
+ ${writeElement(prop)}
+ % endif
+ % endif
+ % endfor
+ </xs:choice>
+ % endfor
+ </xs:sequence>
+ % else:
+ % for choice in obj.getXMLChoices():
+ <xs:choice>
+ % for prop in choice.getXMLProperties():
+ % if prop.hasSpec() and not prop.isInferred():
+ % if prop.getNodeType() == 'xs:attribute':
+ <xs:attribute name="${prop.getName()}" \
+ type="${prop.getAttributeType()}"${prop.getAttributeUseText()}/>
+ % elif prop.getNodeType() == 'xs:element':
+ ${writeElement(prop)}
+ % endif
+ % endif
+ % endfor
+ </xs:choice>
+ % endfor
+ % endif
+ % for prop in obj.getXMLAttributes():
+ <xs:attribute name="${prop.getName()}" \
+ type="${prop.getAttributeType()}"${prop.getAttributeUseText()}/>
+ % endfor
+ </xs:complexType>
+ % endif
+ </${obj.getNodeType()}>
+ % endfor
+</xs:schema>
diff --git a/vistrails/db/bin/xml_gen_objects.py b/vistrails/db/bin/xml_gen_objects.py
new file mode 100644
index 0000000..d89aec0
--- /dev/null
+++ b/vistrails/db/bin/xml_gen_objects.py
@@ -0,0 +1,208 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen_objects import Object, Property, Choice
+
+XML_TYPE = 'xml'
+
+class XMLObject(Object):
+ @staticmethod
+ def convert(obj):
+ if XML_TYPE in obj.layouts:
+ obj.__class__ = XMLObject
+ for prop in obj.properties:
+ prop.__class__ = XMLProperty
+ for choice in obj.choices:
+ choice.__class__ = XMLChoice
+ for prop in choice.properties:
+ prop.__class__ = XMLProperty
+
+ def getName(self):
+ try:
+ return self.layouts[XML_TYPE]['name']
+ except KeyError:
+ pass
+ return Object.getName(self)
+
+ def getNodeType(self):
+ try:
+ return self.layouts[XML_TYPE]['nodeType']
+ except KeyError:
+ pass
+ return 'xs:element'
+
+ def getXMLAttributes(self):
+ return [p for p in self.properties if p.hasSpec() and \
+ not p.isInferred() and p.getNodeType() == 'xs:attribute']
+
+ def getXMLElements(self):
+ return [p for p in self.properties if p.hasSpec() and \
+ not p.isInferred() and p.getNodeType() == 'xs:element']
+
+ def getXMLChoices(self):
+ return [c for c in self.choices if not c.isInverse() and \
+ any([p.hasSpec() for p in c.properties])]
+
+ def isXMLChoice(self):
+ return False
+
+ def getXMLInferredProperties(self):
+ return [p for p in self.properties if p.isInferred()]
+
+ def getConstructorPairs(self):
+ return [(f.getRegularName(), f.getRegularName())
+ for f in self.getPythonFields() if f.hasSpec()]
+
+class XMLProperty(Property):
+ def hasSpec(self):
+ return self.specs.has_key(XML_TYPE)
+
+ def getName(self):
+ try:
+ return self.specs[XML_TYPE]['name']
+ except KeyError:
+ pass
+ return Property.getName(self)
+
+ def getNodeType(self):
+ try:
+ return self.specs[XML_TYPE]['nodeType']
+ except KeyError:
+ pass
+ return 'xs:attribute'
+
+ def getAttributeType(self):
+ try:
+ return self.specs[XML_TYPE]['type']
+ except KeyError:
+ pass
+ return 'xs:string'
+
+ def getAttributeUse(self):
+ try:
+ return self.specs[XML_TYPE]['use']
+ except KeyError:
+ pass
+ return None
+
+ def getAttributeUseText(self):
+ if self.getAttributeUse() is not None:
+ return ' use=%s' & self.getAttributeUse()
+ return ''
+
+ def getChoice(self):
+ try:
+ return self.specs[XML_TYPE]['choice']
+ except KeyError:
+ pass
+ return None
+
+ def isInferred(self):
+ try:
+ return self.specs[XML_TYPE]['inferred'] == 'true'
+ except KeyError:
+ pass
+ return False
+
+ def getXMLPropertyName(self):
+ if self.isReference():
+ refObj = self.getReferencedObject()
+ return refObj.getName()
+ return self.getName()
+
+ def getMinOccurs(self):
+ return '0'
+
+ def getMaxOccurs(self):
+ if self.isReference() and self.getMapping() != 'one-to-many':
+ return '1'
+ return 'unbounded'
+
+class XMLChoice(Choice):
+ def hasSpec(self):
+ return self.properties[0].hasSpec()
+
+ def getXMLProperties(self):
+ return [p for p in self.properties if p.hasSpec()]
+
+ def getXMLAttributes(self):
+ return [p for p in self.properties if p.hasSpec() and \
+ not p.isInferred() and p.getNodeType() == 'xs:attribute']
+
+ def getXMLElements(self):
+ return [p for p in self.properties if p.hasSpec() and \
+ not p.isInferred() and p.getNodeType() == 'xs:element']
+
+ def getXMLInferredProperties(self):
+ return [p for p in self.properties if p.isInferred()]
+
+ def isXMLChoice(self):
+ return True
+
+def convert(objects):
+ xml_objects = []
+ for obj in objects:
+ if XML_TYPE in obj.layouts:
+ XMLObject.convert(obj)
+ xml_objects.append(obj)
+ return xml_objects
+
+def convert_schema_order(objects, root_type):
+ ref_objects = []
+ cur_objects = []
+ for obj in objects:
+ if obj.getName() == root_type:
+ ref_objects = [obj]
+ cur_objects = [obj]
+ break
+ if len(ref_objects) < 1:
+ raise ValueError("Cannot find root %s" % root_type)
+ while len(cur_objects) > 0:
+ next_objects = []
+ for obj in cur_objects:
+ for prop in obj.getXMLElements():
+ if prop.isReference() and \
+ prop.getReferencedObject() not in ref_objects and \
+ prop.getReferencedObject() not in next_objects:
+ next_objects.append(prop.getReferencedObject())
+ for choice in obj.getXMLChoices():
+ for prop in choice.getXMLElements():
+ if prop.isReference() and \
+ prop.getReferencedObject() not in ref_objects and \
+ prop.getReferencedObject() not in next_objects:
+ next_objects.append(prop.getReferencedObject())
+ ref_objects.extend(next_objects)
+ cur_objects = next_objects
+ return ref_objects
diff --git a/vistrails/db/domain/__init__.py b/vistrails/db/domain/__init__.py
new file mode 100644
index 0000000..947b0dc
--- /dev/null
+++ b/vistrails/db/domain/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.versions.v1_0_3.domain import *
diff --git a/vistrails/db/persistence/__init__.py b/vistrails/db/persistence/__init__.py
new file mode 100644
index 0000000..06d6c7d
--- /dev/null
+++ b/vistrails/db/persistence/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.versions.v1_0_3.persistence import *
diff --git a/vistrails/db/services/__init__.py b/vistrails/db/services/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/services/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/services/abstraction.py b/vistrails/db/services/abstraction.py
new file mode 100644
index 0000000..43a7b51
--- /dev/null
+++ b/vistrails/db/services/abstraction.py
@@ -0,0 +1,57 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBWorkflow
+from vistrails.db.services.action_chain import getActionChain, getCurrentOperationDict, \
+ getCurrentOperations
+
+def getNewObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_newObjId
+ return operation.db_objectId
+
+def update_id_scope(vistrail):
+ for action in vistrail.db_actions:
+ vistrail.idScope.updateBeginId('action', action.db_id+1)
+ for operation in action.db_operations:
+ vistrail.idScope.updateBeginId('operation', operation.db_id+1)
+ if operation.vtType == 'add' or operation.vtType == 'change':
+ # update ids of data
+ vistrail.idScope.updateBeginId(operation.db_what,
+ getNewObjId(operation)+1)
+ if operation.db_data is None:
+ if operation.vtType == 'change':
+ operation.db_objectId = operation.db_oldObjId
+ for annotation in action.db_annotations:
+ vistrail.idScope.updateBeginId('annotation', annotation.db_id+1)
diff --git a/vistrails/db/services/action.py b/vistrails/db/services/action.py
new file mode 100644
index 0000000..f2acbf5
--- /dev/null
+++ b/vistrails/db/services/action.py
@@ -0,0 +1,174 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.services.action_chain import simplify_ops
+from vistrails.db.domain import DBAction, DBAdd, DBDelete, DBChange
+import copy
+
+def create_delete_op_chain(object, parent=(None, None)):
+ opChain = []
+ for (obj, parentType, parentId) in object.db_children(parent,
+ for_action=True):
+ op = DBDelete(id=-1,
+ what=obj.vtType,
+ objectId=obj.db_id,
+ parentObjType=parentType,
+ parentObjId=parentId,
+ )
+ opChain.append(op)
+ return opChain
+
+def create_add_op_chain(object, parent=(None, None)):
+ opChain = []
+ object = copy.copy(object)
+ adds = object.db_children(parent, True, for_action=True)
+ adds.reverse()
+ for (obj, parentType, parentId) in adds:
+ op = DBAdd(id=-1,
+ what=obj.vtType,
+ objectId=obj.db_id,
+ parentObjType=parentType,
+ parentObjId=parentId,
+ data=obj,
+ )
+ opChain.append(op)
+ return opChain
+
+def create_change_op_chain(old_obj, new_obj, parent=(None,None)):
+ opChain = []
+ new_obj = copy.copy(new_obj)
+ deletes = old_obj.db_children(parent, for_action=True)
+ deletes.pop()
+ for (obj, parentType, parentId) in deletes:
+ op = DBDelete(id=-1,
+ what=obj.vtType,
+ objectId=obj.db_id,
+ parentObjType=parentType,
+ parentObjId=parentId,
+ )
+ opChain.append(op)
+
+ adds = new_obj.db_children(parent, True, for_action=True)
+ (obj, parentType, parentId) = adds.pop()
+ op = DBChange(id=-1,
+ what=obj.vtType,
+ oldObjId=old_obj.db_id,
+ newObjId=obj.db_id,
+ parentObjType=parentType,
+ parentObjId=parentId,
+ data=new_obj,
+ )
+ opChain.append(op)
+
+ adds.reverse()
+ for (obj, parentType, parentId) in adds:
+ op = DBAdd(id=-1,
+ what=obj.vtType,
+ objectId=obj.db_id,
+ parentObjType=parentType,
+ parentObjId=parentId,
+ data=obj,
+ )
+ return opChain
+
+def create_copy_op_chain(object, parent=(None,None), id_scope=None):
+ opChain = []
+ id_remap = {}
+ object = copy.copy(object)
+
+ adds = object.db_children(parent, True, for_action=True)
+ adds.reverse()
+ for (obj, parentType, parentId) in adds:
+ if parentId is not None:
+ parentId = id_remap[(parentType, parentId)]
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ op = DBAdd(id=-1,
+ what=obj.vtType,
+ objectId=obj.db_id,
+ parentObjType=parentType,
+ parentObjId=parentId,
+ data=obj,
+ )
+ opChain.append(op)
+ return opChain
+
+
+def create_action(action_list):
+ """create_action(action_list: list) -> DBAction
+ where action_list is a list of tuples
+ (
+ type,
+ object,
+ new_obj=None,
+ parent_type=None,
+ parent_id=None,
+ )
+ Example: create_action([('add', module1), ('delete', connection2)]
+
+ """
+ ops = []
+ for tuple in action_list:
+ if tuple[0] == 'add' and len(tuple) >= 2:
+ if len(tuple) >= 4:
+ ops.extend(create_add_op_chain(tuple[1], (tuple[2], tuple[3])))
+ else:
+ ops.extend(create_add_op_chain(tuple[1]))
+ elif tuple[0] == 'delete' and len(tuple) >= 2:
+ if len(tuple) >= 4:
+ ops.extend(create_delete_op_chain(tuple[1],
+ (tuple[2], tuple[3])))
+ else:
+ ops.extend(create_delete_op_chain(tuple[1]))
+ elif tuple[0] == 'change' and len(tuple) >= 3:
+ if len(tuple) >= 5:
+ ops.extend(create_change_op_chain(tuple[1], tuple[2],
+ (tuple[3], tuple[4])))
+ else:
+ ops.extend(create_change_op_chain(tuple[1], tuple[2]))
+ else:
+ msg = "unable to interpret action tuple " + tuple.__str__()
+ raise ValueError(msg)
+ action = DBAction(id=-1,
+ operations=ops)
+ return action
+
+def create_action_from_ops(ops, simplify=False):
+ if simplify:
+ ops = simplify_ops(ops)
+
+ action = DBAction(id=-1,
+ operations=ops)
+ return action
diff --git a/vistrails/db/services/action_chain.py b/vistrails/db/services/action_chain.py
new file mode 100644
index 0000000..b5a23c1
--- /dev/null
+++ b/vistrails/db/services/action_chain.py
@@ -0,0 +1,128 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+def getActionChain(obj, version, start=0):
+ result = []
+ currentId = version
+ while currentId > start: #and currentId > 0:
+ action = obj.db_get_action_by_id(currentId)
+ result.append(action)
+ currentId = action.db_prevId
+ result.reverse()
+ return result
+
+def simplify_ops(ops):
+ addDict = {}
+ deleteDict = {}
+ for op_count, op in enumerate(ops):
+ op.db_id = -op_count - 1
+ if op.vtType == 'add':
+ addDict[(op.db_what, op.db_objectId)] = op
+ elif op.vtType == 'delete':
+ try:
+ del addDict[(op.db_what, op.db_objectId)]
+ except KeyError:
+ deleteDict[(op.db_what, op.db_objectId)] = op
+ elif op.vtType == 'change':
+ try:
+ k = addDict[(op.db_what, op.db_oldObjId)]
+ except KeyError:
+ addDict[(op.db_what, op.db_newObjId)] = op
+ else:
+ old_old_id = getOldObjId(k)
+ del addDict[(op.db_what, op.db_oldObjId)]
+ addDict[(op.db_what, op.db_newObjId)] = \
+ DBChange(id=opCount,
+ what=op.db_what,
+ oldObjId=old_old_id,
+ newObjId=op.db_newObjId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=op.db_data,
+ )
+
+ deletes = deleteDict.values()
+ deletes.sort(key=lambda x: -x.db_id) # faster than sort(lambda x, y: -cmp(x.db_id, y.db_id))
+ adds = addDict.values()
+ adds.sort(key=lambda x: -x.db_id) # faster than sort(lambda x, y: -cmp(x.db_id, y.db_id))
+ return deletes + adds
+
+def getCurrentOperationDict(actions, currentOperations=None):
+ if currentOperations is None:
+ currentOperations = {}
+
+ # note that this operation assumes unique ids for each operation's data
+ # any add adds to the dict, delete removes from the dict, and
+ # change replaces the current value in the dict
+ for action in actions:
+ for operation in action.db_operations:
+ operationvtType = operation.vtType
+ d = operation.__dict__
+ if operationvtType == 'add':
+ currentOperations[(d['_db_what'],
+ d['_db_objectId'])] = \
+ operation
+ elif operationvtType == 'delete':
+ what = d['_db_what']
+ objectId = d['_db_objectId']
+ t = (what, objectId)
+ try:
+ del currentOperations[t]
+ except KeyError:
+ msg = "Illegal delete operation: %d" % d['_db_id']
+ raise RuntimeError(msg)
+ elif operationvtType == 'change':
+ what = d['_db_what']
+ objectId = d['_db_oldObjId']
+ t = (what, objectId)
+ try:
+ del currentOperations[t]
+ except KeyError:
+ msg = "Illegal change operation: %d" % d['_db_id']
+ raise RuntimeError(msg)
+ currentOperations[(what,
+ d['_db_newObjId'])] = operation
+ else:
+ msg = "Unrecognized operation '%s'" % operation.vtType
+ raise TypeError(msg)
+
+ return currentOperations
+
+def getCurrentOperations(actions):
+ # sort the values left in the hash and return the list
+ sortedOperations = getCurrentOperationDict(actions).values()
+ sortedOperations.sort(key=lambda x: x.db_id)
+ return sortedOperations
+
diff --git a/vistrails/db/services/io.py b/vistrails/db/services/io.py
new file mode 100644
index 0000000..d155cec
--- /dev/null
+++ b/vistrails/db/services/io.py
@@ -0,0 +1,1905 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from __future__ import with_statement
+
+from datetime import datetime
+from vistrails.core import debug
+from vistrails.core.bundles import py_import
+from vistrails.core.system import get_elementtree_library, temporary_directory,\
+ execute_cmdline, systemType, get_executable_path
+from vistrails.core.utils import Chdir
+from vistrails.core.log.log import Log
+from vistrails.core.mashup.mashup_trail import Mashuptrail
+from vistrails.core.modules.sub_module import get_cur_abs_namespace,\
+ parse_abstraction_name, read_vistrail_from_db
+
+import vistrails.core.requirements
+
+import sys
+import os
+import os.path
+import shutil
+import tempfile
+import copy
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.domain import DBVistrail, DBWorkflow, DBLog, DBAbstraction, DBGroup, \
+ DBRegistry, DBWorkflowExec, DBOpmGraph, DBProvDocument, DBAnnotation, \
+ DBMashuptrail
+import vistrails.db.services.abstraction
+import vistrails.db.services.log
+import vistrails.db.services.opm
+import vistrails.db.services.prov
+import vistrails.db.services.registry
+import vistrails.db.services.workflow
+import vistrails.db.services.vistrail
+from vistrails.db.versions import getVersionDAO, currentVersion, getVersionSchemaDir, \
+ translate_vistrail, translate_workflow, translate_log, translate_registry
+
+import unittest
+import vistrails.core.system
+
+ElementTree = get_elementtree_library()
+
+CONNECT_TIMEOUT = 15
+
+_db_lib = None
+def get_db_lib():
+ global _db_lib
+ if _db_lib is None:
+ MySQLdb = py_import('MySQLdb', {
+ 'pip': 'mysql-python',
+ 'linux-debian': 'python-mysqldb',
+ 'linux-ubuntu': 'python-mysqldb',
+ 'linux-fedora': 'MySQL-python'})
+ # import sqlite3
+ _db_lib = MySQLdb
+ return _db_lib
+def set_db_lib(lib):
+ global _db_lib
+ _db_lib = lib
+
+
+class SaveBundle(object):
+ """Transient bundle of objects to be saved or loaded.
+ The bundle type MUST be specified in the constructor; it should be
+ the the vtType of the primary object in the bundle. This parameter
+ identifies which object is the primary object when mutiple objects
+ are stored in the bundle.
+
+ Args is the (unordered) list of objects to be included in the bundle
+ (vistrail, workflow, log, registry, opm_graph). Any args without a
+ 'vtType' attribute are explicitly ignored (including any args=None).
+
+ As kwargs, you can specify 'abstractions=[]' or 'thumbnails=[]',
+ both of which should be a list of filenames as strings. You can also
+ specify the other bundle objects as kwargs, but abstractions and
+ thumbnails cannot be args, since they are both lists, and there is no
+ vtType to differentiate between them.
+
+ As a final option, you can directly set the objects in the bundle,
+ self.vistrail = vistrail_object, self.thumbnails = thumbs_list, etc.,
+ before passing the SaveBundle to a locator. Both abstractions and
+ thumbnails are intialized for convenience so that you can directly
+ append to them when using this step-by-step bundle creation method.
+
+ """
+
+ def __init__(self, bundle_type, *args, **kwargs):
+ self.bundle_type = bundle_type
+ self.vistrail = None
+ self.workflow = None
+ self.log = None
+ self.registry = None
+ self.opm_graph = None
+ self.abstractions = []
+ self.thumbnails = []
+ self.mashups = []
+ # Make all args into attrs using vtType as attr name
+ # This requires that attr names in this class match the vtTypes
+ # i.e. if arg's vtType is 'vistrail', self.vistrail = arg, etc...
+ for arg in args:
+ if hasattr(arg, 'vtType'):
+ setattr(self, arg.vtType, arg)
+ # Make all keyword args directly into attrs
+ for (k,v) in kwargs.iteritems():
+ setattr(self, k, v)
+
+ def get_db_objs(self):
+ """Gets a list containing only the DB* objects in the bundle"""
+ return [obj for obj in self.__dict__.itervalues() if obj is not None and not isinstance(obj, (list, basestring))]
+
+ def get_primary_obj(self):
+ """get_primary_obj() -> DB*
+ Gets the bundle's primary DB* object based on the bundle type.
+ """
+ return getattr(self, self.bundle_type)
+
+ def __copy__(self):
+ return SaveBundle.do_copy(self)
+
+ def do_copy(self):
+ cp = SaveBundle(self.bundle_type)
+ cp.vistrail = copy.copy(self.vistrail)
+ cp.workflow = copy.copy(self.workflow)
+ cp.log = copy.copy(self.log)
+ cp.registry = copy.copy(self.registry)
+ cp.opm_graph = copy.copy(self.opm_graph)
+ for a in self.abstractions:
+ cp.abstractions.append(a)
+
+ for t in self.thumbnails:
+ cp.thumbnails.append(t)
+
+ return cp
+
+def format_prepared_statement(statement):
+ """format_prepared_statement(statement: str) -> str
+ Formats a prepared statement for compatibility with the currently
+ loaded database library's paramstyle.
+
+ Currently only supports 'qmark' and 'format' paramstyles.
+ May be expanded later to allow for more compatibility options
+ on input and output. See PEP 249 for more info.
+
+ """
+ style = get_db_lib().paramstyle
+ if style == 'format':
+ return statement.replace("?", "%s")
+ elif style == 'qmark':
+ return statement.replace("%s", "?")
+ return statement
+
+def open_db_connection(config):
+
+ if config is None:
+ msg = "You need to provide valid config dictionary"
+ raise VistrailsDBException(msg)
+ if 'connect_timeout' not in config:
+ config['connect_timeout'] = CONNECT_TIMEOUT
+ try:
+ # FIXME allow config to be kwargs and args?
+ db_connection = get_db_lib().connect(**config)
+ #db_connection = get_db_lib().connect(config)
+ return db_connection
+ except get_db_lib().Error, e:
+ # should have a DB exception type
+ msg = "cannot open connection (%d: %s)" % (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+
+def close_db_connection(db_connection):
+ if db_connection is not None:
+ db_connection.close()
+
+def test_db_connection(config):
+ """testDBConnection(config: dict) -> None
+ Tests a connection raising an exception in case of error.
+
+ """
+ #print "Testing config", config
+ if 'connect_timeout' not in config:
+ config['connect_timeout'] = CONNECT_TIMEOUT
+ try:
+ db_connection = get_db_lib().connect(**config)
+ close_db_connection(db_connection)
+ except get_db_lib().Error, e:
+ msg = "connection test failed (%d: %s)" % (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+ except TypeError, e:
+ msg = "connection test failed (%s)" %str(e)
+ raise VistrailsDBException(msg)
+
+def ping_db_connection(db_connection):
+ """ping_db_connection(db_connection) -> boolean
+ It will ping the database to check if the connection is alive.
+ It returns True if it is, False otherwise.
+ This can be used for preventing the "MySQL Server has gone away" error.
+ """
+ try:
+ db_connection.ping()
+ except get_db_lib().OperationalError:
+ return False
+ return True
+
+def translate_to_tbl_name(obj_type):
+ map = {DBVistrail.vtType: 'vistrail',
+ DBWorkflow.vtType: 'workflow',
+ DBLog.vtType: 'log_tbl',
+ DBRegistry.vtType: 'registry',
+ DBAbstraction.vtType: 'abstraction',
+ DBMashuptrail.vtType: 'mashuptrail',
+ DBAnnotation.vtType: 'annotation',
+ }
+ return map[obj_type]
+
+def date_to_str(date):
+ return date.strftime('%Y-%m-%d %H:%M:%S')
+
+def get_db_object_list(config, obj_type):
+
+ result = []
+ db = open_db_connection(config)
+
+ #FIXME Create a DBGetVistrailListSQLDAOBase for this
+ # and maybe there's another way to build this query
+ command = """SELECT o.id, o.name, o.last_modified
+ FROM %s o ORDER BY o.name"""
+
+ # if it is a vistrail we need to remove abstractions
+ if obj_type == DBVistrail.vtType:
+ id_key = '__abstraction_uuid__'
+ command = """SELECT o.id, o.name, o.last_modified
+ FROM %s o"""
+ command += """ WHERE o.id not in ( SELECT o.id
+ FROM %s o, %s a
+ WHERE o.id = a.parent_id AND '%s' = a.parent_type AND a.akey = '%s')
+ ORDER BY o.name""" % (translate_to_tbl_name(obj_type),
+ translate_to_tbl_name(DBAnnotation.vtType),
+ translate_to_tbl_name(obj_type),
+ id_key)
+# command = """SELECT o.id, v.name, a.date, a.user
+# FROM %s o, action a,
+# (SELECT a.entity_id, MAX(a.date) as recent, a.user
+# FROM action a
+# GROUP BY entity_id) latest
+# WHERE o.id = latest.entity_id
+# AND a.entity_id = o.id
+# AND a.date = latest.recent
+# """ % obj_type
+
+ try:
+ c = db.cursor()
+ c.execute(command % translate_to_tbl_name(obj_type))
+ rows = c.fetchall()
+ result = rows
+ c.close()
+ close_db_connection(db)
+
+ except get_db_lib().Error, e:
+ msg = "Couldn't get list of vistrails objects from db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+ return result
+
+def get_db_object_modification_time(db_connection, obj_id, obj_type):
+ command = """
+ SELECT o.last_modified
+ FROM %s o
+ WHERE o.id = %s
+ """
+
+ try:
+ db_connection.begin()
+ c = db_connection.cursor()
+ c.execute(command % (translate_to_tbl_name(obj_type), obj_id))
+ db_connection.commit()
+ time = c.fetchall()[0][0]
+ c.close()
+ except get_db_lib().Error, e:
+ msg = "Couldn't get object modification time from db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+ return time
+
+def get_db_object_version(db_connection, obj_id, obj_type):
+ command = """
+ SELECT o.version
+ FROM %s o
+ WHERE o.id = %s
+ """
+
+ try:
+ c = db_connection.cursor()
+ #print command % (translate_to_tbl_name(obj_type), obj_id)
+ c.execute(command % (translate_to_tbl_name(obj_type), obj_id))
+ version = c.fetchall()[0][0]
+ c.close()
+ except get_db_lib().Error, e:
+ msg = "Couldn't get object version from db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+ return version
+
+def get_db_version(db_connection):
+ command = """
+ SELECT `version`
+ FROM `vistrails_version`
+ """
+
+ try:
+ c = db_connection.cursor()
+ c.execute(command)
+ version = c.fetchall()[0][0]
+ c.close()
+ except get_db_lib().Error, e:
+ # just return None if we hit an error
+ return None
+ return version
+
+def get_db_id_from_name(db_connection, obj_type, name):
+ command = """
+ SELECT o.id
+ FROM %s o
+ WHERE o.name = '%s'
+ """
+
+ try:
+ c = db_connection.cursor()
+ c.execute(command % (translate_to_tbl_name(obj_type), name))
+ rows = c.fetchall()
+ if len(rows) != 1:
+ if len(rows) == 0:
+ c.close()
+ msg = "Cannot find object of type '%s' named '%s'" % \
+ (obj_type, name)
+ raise VistrailsDBException(msg)
+ elif len(rows) > 1:
+ c.close()
+ msg = "Found more than one object of type '%s' named '%s'" % \
+ (obj_type, name)
+ raise VistrailsDBException(msg)
+ else:
+ c.close()
+ return int(rows[0][0])
+ except get_db_lib().Error, e:
+ c.close()
+ msg = "Connection error when trying to get db id from name"
+ raise VistrailsDBException(msg)
+
+def get_db_abstraction_modification_time(db_connection, abstraction):
+ id_key = '__abstraction_vistrail_id__'
+ command = """
+ SELECT o.last_modified
+ FROM %s o, %s a
+ WHERE o.id = %s AND
+ o.id = a.parent_id AND
+ '%s' = a.parent_type AND
+ a.akey = '""" + id_key + """' AND
+ a.value = '%s'
+ """
+
+ if abstraction.db_has_annotation_with_key(id_key):
+ id_value = abstraction.db_get_annotation_by_key(id_key).db_value
+ else:
+ return None
+
+ try:
+ c = db_connection.cursor()
+ c.execute(command % (translate_to_tbl_name(DBVistrail.vtType),
+ translate_to_tbl_name(DBAnnotation.vtType),
+ abstraction.db_id,
+ translate_to_tbl_name(DBVistrail.vtType),
+ id_value))
+ modtime = c.fetchall()[0][0]
+ c.close()
+ except get_db_lib().Error, e:
+ msg = "Couldn't get modification time from db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+ return modtime
+
+def get_db_abstraction_ids_from_vistrail(db_connection, vt_id):
+ """ get_db_abstractions_from_vistrail(db_connection: DBConnection,
+ vt_id: int): List
+ Returns abstractions associated with a vistrail
+ """
+
+ id_key = '__abstraction_vistrail_id__'
+ return get_db_ids_from_vistrail(db_connection, vt_id, id_key)
+
+def get_db_mashuptrail_ids_from_vistrail(db_connection, vt_id):
+ """ get_db_mashuptrail_ids_from_vistrail(db_connection: DBConnection,
+ vt_id: int): List
+ Returns mashuptrails associated with a vistrail
+ """
+ id_key = '__mashuptrail_vistrail_id__'
+ return get_db_ids_from_vistrail(db_connection, vt_id, id_key)
+
+def get_db_ids_from_vistrail(db_connection, vt_id, id_key):
+ """ get_db_ids_from_vistrail(db_connection: DBConnection,
+ vt_id: int, id_key: str): List
+ Returns object ids associated with a vistrail by an annotation
+ """
+ command = """
+ SELECT a.parent_id FROM %s a
+ WHERE a.akey = '%s' AND a.value = '%s'"""
+
+ try:
+ c = db_connection.cursor()
+ c.execute(command%(translate_to_tbl_name(DBAnnotation.vtType), id_key, vt_id))
+ abs_ids = c.fetchall()
+ c.close()
+ except get_db_lib().Error, e:
+ msg = "Couldn't get object ids from db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+ return [i[0] for i in abs_ids]
+
+def get_matching_abstraction_id(db_connection, abstraction):
+ last_action_id = -1
+ last_action = None
+ for action in abstraction.db_actions:
+ if action.db_id > last_action_id:
+ last_action_id = action.db_id
+ last_action = action
+
+ command = """
+ SELECT g.id
+ FROM abstraction g, action a
+ WHERE g.name = '%s'
+ AND a.entity_type = 'abstraction'
+ AND a.entity_id = g.id
+ AND a.user = '%s'
+ AND a.date = '%s'
+ AND a.id = %s
+ """
+
+ id = None
+ try:
+ c = db_connection.cursor()
+ c.execute(command % (abstraction.db_name,
+ last_action.db_user,
+ date_to_str(last_action.db_date),
+ last_action.db_id))
+ result = c.fetchall()
+ c.close()
+ if len(result) > 0:
+ #print 'got result:', result
+ id = result[0][0]
+ except get_db_lib().Error, e:
+ msg = "Couldn't get object modification time from db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+ return id
+
+def setup_db_tables(db_connection, version=None, old_version=None):
+ if version is None:
+ version = currentVersion
+ if old_version is None:
+ old_version = version
+ try:
+ def execute_file(c, f):
+ cmd = ""
+# auto_inc_str = 'auto_increment'
+# not_null_str = 'not null'
+# engine_str = 'engine=InnoDB;'
+ for line in f:
+# if line.find(auto_inc_str) > 0:
+# num = line.find(auto_inc_str)
+# line = line[:num] + line[num+len(auto_inc_str):]
+# if line.find(not_null_str) > 0:
+# num = line.find(not_null_str)
+# line = line[:num] + line[num+len(not_null_str):]
+ line = line.strip()
+ if cmd or not line.startswith('--'):
+ cmd += line
+ ending = line
+ else:
+ ending = None
+ if ending and ending[-1] == ';':
+ # FIXME engine stuff switch for MySQLdb, sqlite3
+ cmd = cmd.rstrip()
+# if cmd.endswith(engine_str):
+# cmd = cmd[:-len(engine_str)] + ';'
+ #print cmd
+ c.execute(cmd)
+ cmd = ""
+
+ # delete tables
+ c = db_connection.cursor()
+ schemaDir = getVersionSchemaDir(old_version)
+ f = open(os.path.join(schemaDir, 'vistrails_drop.sql'))
+ execute_file(c, f)
+# db_script = f.read()
+# c.execute(db_script)
+ c.close()
+ f.close()
+
+ # create tables
+ c = db_connection.cursor()
+ schemaDir = getVersionSchemaDir(version)
+ f = open(os.path.join(schemaDir, 'vistrails.sql'))
+ execute_file(c, f)
+# db_script = f.read()
+# c.execute(db_script)
+ f.close()
+ c.close()
+ except get_db_lib().Error, e:
+ raise VistrailsDBException("unable to create tables: " + str(e))
+
+##############################################################################
+# General I/O
+
+def open_from_xml(filename, type):
+ if type == DBVistrail.vtType:
+ return open_vistrail_from_xml(filename)
+ elif type == DBWorkflow.vtType:
+ return open_workflow_from_xml(filename)
+ elif type == DBLog.vtType:
+ return open_log_from_xml(filename)
+ elif type == DBRegistry.vtType:
+ return open_registry_from_xml(filename)
+ else:
+ raise VistrailsDBException("cannot open object of type "
+ "'%s' from xml" % type)
+
+def save_to_xml(obj, filename, version=None):
+ if obj.vtType == DBVistrail.vtType:
+ return save_vistrail_to_xml(obj, filename, version)
+ elif obj.vtType == DBWorkflow.vtType:
+ return save_workflow_to_xml(obj, filename, version)
+ elif obj.vtType == DBLog.vtType:
+ return save_log_to_xml(obj, filename, version)
+ elif obj.vtType == DBRegistry.vtType:
+ return save_registry_to_xml(obj, filename, version)
+ elif obj.vtType == DBOpmGraph.vtType:
+ return save_opm_to_xml(obj, filename, version)
+ elif obj.vtType == DBProvDocument.vtType:
+ return save_prov_to_xml(obj, filename, version)
+ else:
+ raise VistrailsDBException("cannot save object of type "
+ "'%s' to xml" % type)
+
+def open_bundle_from_zip_xml(bundle_type, filename):
+ if bundle_type == DBVistrail.vtType:
+ return open_vistrail_bundle_from_zip_xml(filename)
+ else:
+ raise VistrailsDBException("cannot open bundle of type '%s' from zip" %\
+ bundle_type)
+
+def save_bundle_to_zip_xml(save_bundle, filename, tmp_dir=None, version=None):
+ bundle_type = save_bundle.bundle_type
+ if bundle_type == DBVistrail.vtType:
+ return save_vistrail_bundle_to_zip_xml(save_bundle, filename, tmp_dir, version)
+ elif bundle_type == DBLog.vtType:
+ return save_log_bundle_to_xml(save_bundle, filename, version)
+ elif bundle_type == DBWorkflow.vtType:
+ return save_workflow_bundle_to_xml(save_bundle, filename, version)
+ elif bundle_type == DBRegistry.vtType:
+ return save_registry_bundle_to_xml(save_bundle, filename, version)
+ else:
+ raise VistrailsDBException("cannot save bundle of type '%s' to zip" % \
+ bundle_type)
+
+def open_bundle_from_db(bundle_type, connection, primary_obj_id, tmp_dir=None):
+ if bundle_type == DBVistrail.vtType:
+ return open_vistrail_bundle_from_db(connection, primary_obj_id, tmp_dir)
+ else:
+ raise VistrailsDBException("cannot open bundle of type '%s' from db" %\
+ bundle_type)
+
+def save_bundle_to_db(save_bundle, connection, do_copy=False, version=None):
+ bundle_type = save_bundle.bundle_type
+ if bundle_type == DBVistrail.vtType:
+ return save_vistrail_bundle_to_db(save_bundle, connection, do_copy, version)
+ elif bundle_type == DBLog.vtType:
+ return save_log_bundle_to_db(save_bundle, connection, do_copy, version)
+ elif bundle_type == DBWorkflow.vtType:
+ return save_workflow_bundle_to_db(save_bundle, connection, do_copy, version)
+ elif bundle_type == DBRegistry.vtType:
+ return save_registry_bundle_to_db(save_bundle, connection, do_copy, version)
+ else:
+ raise VistrailsDBException("cannot save bundle of type '%s' to db" % \
+ bundle_type)
+
+def open_from_db(db_connection, type, obj_id):
+ if type == DBVistrail.vtType:
+ return open_vistrail_from_db(db_connection, obj_id)
+ elif type == DBWorkflow.vtType:
+ return open_workflow_from_db(db_connection, obj_id)
+ elif type == DBLog.vtType:
+ return open_log_from_db(db_connection, obj_id)
+ elif type == DBRegistry.vtType:
+ return open_registry_from_db(db_connection, obj_id)
+ else:
+ raise VistrailsDBException("cannot open object of type '%s' from db" % \
+ type)
+
+def save_to_db(obj, db_connection, do_copy=False):
+ if obj.vtType == DBVistrail.vtType:
+ return save_vistrail_to_db(obj, db_connection, do_copy)
+ elif obj.vtType == DBWorkflow.vtType:
+ return save_workflow_to_db(obj, db_connection, do_copy)
+ elif obj.vtType == DBLog.vtType:
+ return save_log_to_db(obj, db_connection, do_copy)
+ elif obj.vtType == DBRegistry.vtType:
+ return save_registry_to_db(obj, db_connection, do_copy)
+ else:
+ raise VistrailsDBException("cannot save object of type '%s' to db" % \
+ type)
+
+def delete_from_db(db_connection, type, obj_id):
+ if type in [DBVistrail.vtType, DBWorkflow.vtType, DBLog.vtType,
+ DBRegistry.vtType]:
+ return delete_entity_from_db(db_connection, type, obj_id)
+
+def close_zip_xml(temp_dir):
+ """close_zip_xml(temp_dir: string) -> None
+ Removes any temporary files for a vistrails file
+
+ temp_dir: directory storing any persistent files
+ """
+ if temp_dir is None:
+ return
+ if not os.path.isdir(temp_dir):
+ if os.path.isfile(temp_dir):
+ os.remove(temp_dir)
+
+ # cleanup has already happened
+ return
+ try:
+ for root, dirs, files in os.walk(temp_dir, topdown=False):
+ for name in files:
+ os.remove(os.path.join(root, name))
+ for name in dirs:
+ os.rmdir(os.path.join(root, name))
+ os.rmdir(temp_dir)
+ except OSError, e:
+ raise VistrailsDBException("Can't remove %s: %s" % (temp_dir, str(e)))
+
+def serialize(object):
+ daoList = getVersionDAO(currentVersion)
+ return daoList.serialize(object)
+
+def unserialize(str, obj_type):
+ daoList = getVersionDAO(currentVersion)
+ return daoList.unserialize(str, obj_type)
+
+##############################################################################
+# Vistrail I/O
+
+def open_vistrail_from_xml(filename):
+ """open_vistrail_from_xml(filename) -> Vistrail"""
+ tree = ElementTree.parse(filename)
+ version = get_version_for_xml(tree.getroot())
+ try:
+ daoList = getVersionDAO(version)
+ vistrail = daoList.open_from_xml(filename, DBVistrail.vtType, tree)
+ vistrail = translate_vistrail(vistrail, version)
+ vistrails.db.services.vistrail.update_id_scope(vistrail)
+ except VistrailsDBException, e:
+ if str(e).startswith('VistrailsDBException: Cannot find DAO for'):
+ msg = "This vistrail was created by a newer version of VisTrails "
+ msg += "and cannot be opened."
+ raise VistrailsDBException(msg)
+ raise e
+
+ return vistrail
+
+def open_vistrail_bundle_from_zip_xml(filename):
+ """open_vistrail_bundle_from_zip_xml(filename) -> SaveBundle
+ Open a vistrail from a zip compressed format.
+ It expects that the vistrail file inside archive has name 'vistrail',
+ the log inside archive has name 'log',
+ abstractions inside archive have prefix 'abstraction_',
+ and thumbnails inside archive are '.png' files in 'thumbs' dir
+
+ """
+
+ vistrails.core.requirements.require_executable('unzip')
+
+ vt_save_dir = tempfile.mkdtemp(prefix='vt_save')
+ output = []
+ cmdline = ['unzip', '-q','-o','-d', vt_save_dir, filename]
+ result = execute_cmdline(cmdline, output)
+
+ if result != 0 and len(output) != 0:
+ raise VistrailsDBException("Unzip of '%s' failed" % filename)
+
+ vistrail = None
+ log = None
+ log_fname = None
+ abstraction_files = []
+ unknown_files = []
+ thumbnail_files = []
+ mashups = []
+ try:
+ for root, dirs, files in os.walk(vt_save_dir):
+ for fname in files:
+ if fname == 'vistrail' and root == vt_save_dir:
+ vistrail = open_vistrail_from_xml(os.path.join(root, fname))
+ elif fname == 'log' and root == vt_save_dir:
+ # FIXME read log to get execution info
+ # right now, just ignore the file
+ log = None
+ log_fname = os.path.join(root, fname)
+ # log = open_log_from_xml(os.path.join(root, fname))
+ # objs.append(DBLog.vtType, log)
+ elif fname.startswith('abstraction_'):
+ abstraction_file = os.path.join(root, fname)
+ abstraction_files.append(abstraction_file)
+ elif (fname.endswith('.png') and
+ root == os.path.join(vt_save_dir,'thumbs')):
+ thumbnail_file = os.path.join(root, fname)
+ thumbnail_files.append(thumbnail_file)
+ elif root == os.path.join(vt_save_dir,'mashups'):
+ mashup_file = os.path.join(root, fname)
+ mashup = open_mashuptrail_from_xml(mashup_file)
+ mashups.append(mashup)
+ else:
+ handled = False
+ from vistrails.core.packagemanager import get_package_manager
+ pm = get_package_manager()
+ for package in pm.enabled_package_list():
+ if package.can_handle_vt_file(fname):
+ handled = True
+ continue
+ if not handled:
+ unknown_files.append(os.path.join(root, fname))
+ except OSError, e:
+ raise VistrailsDBException("Error when reading vt file")
+ if len(unknown_files) > 0:
+ raise VistrailsDBException("Unknown files in vt file: %s" % \
+ unknown_files)
+ if vistrail is None:
+ raise VistrailsDBException("vt file does not contain vistrail")
+ vistrail.db_log_filename = log_fname
+
+ # call package hooks
+ from vistrails.core.packagemanager import get_package_manager
+ pm = get_package_manager()
+ for package in pm.enabled_package_list():
+ package.loadVistrailFileHook(vistrail, vt_save_dir)
+
+ save_bundle = SaveBundle(DBVistrail.vtType, vistrail, log,
+ abstractions=abstraction_files,
+ thumbnails=thumbnail_files, mashups=mashups)
+ return (save_bundle, vt_save_dir)
+
+def open_vistrail_bundle_from_db(db_connection, vistrail_id, tmp_dir=None):
+ """open_vistrail_bundle_from_db(db_connection, id: long, tmp_dir: str) -> SaveBundle
+ Open a vistrail bundle from the database.
+
+ """
+ vt_abs_dir = tempfile.mkdtemp(prefix='vt_abs')
+ vistrail = open_vistrail_from_db(db_connection, vistrail_id)
+ # FIXME open log from db
+ log = None
+ # open abstractions from db
+ abstractions = []
+ try:
+ for abs_id in get_db_abstraction_ids_from_vistrail(db_connection, vistrail.db_id):
+ abs = read_vistrail_from_db(db_connection, abs_id, vistrail.db_version)
+ abs_fname = '%s%s(%s)%s' % ('abstraction_', abs.db_name,
+ get_cur_abs_namespace(abs), '.xml')
+ fname = os.path.join(vt_abs_dir, abs_fname)
+ save_vistrail_to_xml(abs, fname)
+ abstractions.append(fname)
+ except Exception, e:
+ import traceback
+ debug.critical('Could not load abstraction from database: %s' % str(e),
+ traceback.format_exc())
+ # open mashuptrails from db
+ mashuptrails = []
+ try:
+ for mashup_id in get_db_mashuptrail_ids_from_vistrail(db_connection, vistrail.db_id):
+ mashup = open_mashuptrail_from_db(db_connection, mashup_id)
+ mashuptrails.append(mashup)
+ except Exception, e:
+ import traceback
+ debug.critical('Could not load mashuptrail from database: %s' % str(e),
+ traceback.format_exc())
+ thumbnails = open_thumbnails_from_db(db_connection, DBVistrail.vtType,
+ vistrail_id, tmp_dir)
+ return SaveBundle(DBVistrail.vtType, vistrail, log,
+ abstractions=abstractions, thumbnails=thumbnails,
+ mashups=mashuptrails)
+
+def open_vistrail_from_db(db_connection, id, lock=False, version=None):
+ """open_vistrail_from_db(db_connection, id : long, lock: bool,
+ version: str)
+ -> DBVistrail
+
+ """
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ if version is None:
+ version = get_db_object_version(db_connection, id, DBVistrail.vtType)
+ dao_list = getVersionDAO(version)
+ vistrail = \
+ dao_list.open_from_db(db_connection, DBVistrail.vtType, id, lock)
+ vistrail = translate_vistrail(vistrail, version)
+ for db_action in vistrail.db_get_actions():
+ db_action.db_operations.sort(key=lambda x: x.db_id)
+ vistrails.db.services.vistrail.update_id_scope(vistrail)
+ return vistrail
+
+def save_vistrail_to_xml(vistrail, filename, version=None):
+ tags = {'xmlns:xsi': 'http://www.w3.org/2001/XMLSchema-instance',
+ 'xsi:schemaLocation': 'http://www.vistrails.org/vistrail.xsd'
+ }
+ if version is None:
+ version = currentVersion
+ if not vistrail.db_version:
+ vistrail.db_version = currentVersion
+
+ # current_action holds the current action id
+ # (used by the controller--write_vistrail)
+ current_action = 0L
+ if hasattr(vistrail, 'db_currentVersion'):
+ current_action = vistrail.db_currentVersion
+
+ vistrail = translate_vistrail(vistrail, vistrail.db_version, version)
+
+ daoList = getVersionDAO(version)
+ daoList.save_to_xml(vistrail, filename, tags, version)
+ vistrail = translate_vistrail(vistrail, version)
+ vistrail.db_currentVersion = current_action
+ return vistrail
+
+def save_vistrail_bundle_to_zip_xml(save_bundle, filename, vt_save_dir=None, version=None):
+ """save_vistrail_bundle_to_zip_xml(save_bundle: SaveBundle, filename: str,
+ vt_save_dir: str, version: str)
+ -> (save_bundle: SaveBundle, vt_save_dir: str)
+
+ save_bundle: a SaveBundle object containing vistrail data to save
+ filename: filename to save to
+ vt_save_dir: directory storing any previous files
+
+ Generates a zip compressed version of vistrail.
+ It raises an Exception if there was an error.
+
+ """
+
+ vistrails.core.requirements.require_executable('zip')
+
+ if save_bundle.vistrail is None:
+ raise VistrailsDBException('save_vistrail_bundle_to_zip_xml failed, '
+ 'bundle does not contain a vistrail')
+ if not vt_save_dir:
+ vt_save_dir = tempfile.mkdtemp(prefix='vt_save')
+ # abstractions are saved in the root of the zip file
+ # abstraction_dir = os.path.join(vt_save_dir, 'abstractions')
+ #thumbnails and mashups have their own folder
+ thumbnail_dir = os.path.join(vt_save_dir, 'thumbs')
+ mashup_dir = os.path.join(vt_save_dir, 'mashups')
+
+ # Save Vistrail
+ xml_fname = os.path.join(vt_save_dir, 'vistrail')
+ save_vistrail_to_xml(save_bundle.vistrail, xml_fname, version)
+
+ # Save Log
+ if save_bundle.vistrail.db_log_filename is not None:
+ xml_fname = os.path.join(vt_save_dir, 'log')
+ if save_bundle.vistrail.db_log_filename != xml_fname:
+ shutil.copyfile(save_bundle.vistrail.db_log_filename, xml_fname)
+ save_bundle.vistrail.db_log_filename = xml_fname
+
+ if save_bundle.log is not None:
+ xml_fname = os.path.join(vt_save_dir, 'log')
+ save_log_to_xml(save_bundle.log, xml_fname, version, True)
+ save_bundle.vistrail.db_log_filename = xml_fname
+
+ # Save Abstractions
+ saved_abstractions = []
+ for obj in save_bundle.abstractions:
+ if isinstance(obj, basestring):
+ # FIXME we should have an abstraction directory here instead
+ # of the abstraction_ prefix...
+ if not os.path.basename(obj).startswith('abstraction_'):
+ obj_fname = 'abstraction_' + os.path.basename(obj)
+ else:
+ obj_fname = os.path.basename(obj)
+ # xml_fname = os.path.join(abstraction_dir, obj_fname)
+ xml_fname = os.path.join(vt_save_dir, obj_fname)
+ saved_abstractions.append(xml_fname)
+ # if not os.path.exists(abstraction_dir):
+ # os.mkdir(abstraction_dir)
+ # print "obj:", obj
+ # print "xml_fname:", xml_fname
+ if obj != xml_fname:
+ # print 'copying %s -> %s' % (obj, xml_fname)
+ try:
+ shutil.copyfile(obj, xml_fname)
+ except Exception, e:
+ saved_abstractions.pop()
+ debug.critical('copying %s -> %s failed: %s' % \
+ (obj, xml_fname, str(e)))
+ else:
+ raise VistrailsDBException('save_vistrail_bundle_to_zip_xml failed, '
+ 'abstraction list entry must be a filename')
+ # Save Thumbnails
+ saved_thumbnails = []
+ for obj in save_bundle.thumbnails:
+ if isinstance(obj, basestring):
+ obj_fname = os.path.basename(obj)
+ png_fname = os.path.join(thumbnail_dir, obj_fname)
+ saved_thumbnails.append(png_fname)
+ if not os.path.exists(thumbnail_dir):
+ os.mkdir(thumbnail_dir)
+
+ try:
+ shutil.copyfile(obj, png_fname)
+ except shutil.Error, e:
+ #files are the same no need to show warning
+ saved_thumbnails.pop()
+ except IOError, e2:
+ saved_thumbnails.pop()
+ debug.warning('copying thumbnail %s -> %s failed: %s' % \
+ (obj, png_fname, str(e2)))
+ else:
+ raise VistrailsDBException('save_vistrail_bundle_to_zip_xml failed, '
+ 'thumbnail list entry must be a filename')
+ # Save Mashups
+ #print " mashups:"
+ if len(save_bundle.mashups) > 0 and not os.path.exists(mashup_dir):
+ os.mkdir(mashup_dir)
+ for obj in save_bundle.mashups:
+ #print " ", obj
+ try:
+ xml_fname = os.path.join(mashup_dir, str(obj.id))
+ save_mashuptrail_to_xml(obj, xml_fname)
+ except Exception, e:
+ raise VistrailsDBException('save_vistrail_bundle_to_zip_xml failed, '
+ 'when saving mashup: %s'%str(e))
+
+ # call package hooks
+ # it will fail if package manager has not been constructed yet
+ try:
+ from vistrails.core.packagemanager import get_package_manager
+ pm = get_package_manager()
+ for package in pm.enabled_package_list():
+ package.saveVistrailFileHook(save_bundle.vistrail, vt_save_dir)
+ except Exception, e:
+ debug.warning("Could not call package hooks", str(e))
+ tmp_zip_dir = tempfile.mkdtemp(prefix='vt_zip')
+ tmp_zip_file = os.path.join(tmp_zip_dir, "vt.zip")
+ output = []
+ rel_vt_save_dir = os.path.split(vt_save_dir)[1]
+
+ # on windows, we assume zip.exe is in the current directory when
+ # running from the binary install
+ zipcmd = 'zip'
+ if systemType in ['Windows', 'Microsoft']:
+ zipcmd = get_executable_path('zip.exe')
+ if not zipcmd or not os.path.exists(zipcmd):
+ zipcmd = 'zip.exe' #assume zip is in path
+ cmdline = [zipcmd, '-r', '-q', tmp_zip_file, '.']
+ try:
+ #if we want that directories are also stored in the zip file
+ # we need to run from the vt directory
+ with Chdir(vt_save_dir):
+ result = execute_cmdline(cmdline,output)
+ #print result, output
+ if result != 0 or len(output) != 0:
+ for line in output:
+ if line.find('deflated') == -1:
+ raise VistrailsDBException(" ".join(output))
+ shutil.copyfile(tmp_zip_file, filename)
+ finally:
+ os.unlink(tmp_zip_file)
+ os.rmdir(tmp_zip_dir)
+ save_bundle = SaveBundle(save_bundle.bundle_type, save_bundle.vistrail, save_bundle.log, thumbnails=saved_thumbnails, abstractions=saved_abstractions)
+ return (save_bundle, vt_save_dir)
+
+def save_vistrail_bundle_to_db(save_bundle, db_connection, do_copy=False, version=None):
+ if save_bundle.vistrail is None:
+ raise VistrailsDBException('save_vistrail_bundle_to_db failed, '
+ 'bundle does not contain a vistrail')
+ vistrail = save_vistrail_to_db(save_bundle.vistrail, db_connection, do_copy, version)
+ log = None
+ if save_bundle.vistrail.db_log_filename is not None:
+ if save_bundle.log is not None:
+ log = merge_logs(save_bundle.log,
+ save_bundle.vistrail.db_log_filename)
+ else:
+ log = open_log_from_xml(save_bundle.vistrail.db_log_filename, True)
+ elif save_bundle.log is not None:
+ log = save_bundle.log
+ if log is not None:
+ # Set foreign key 'vistrail_id' for the log to point at its vistrail
+ log.db_vistrail_id = vistrail.db_id
+ log = save_log_to_db(log, db_connection, do_copy, version)
+ save_abstractions_to_db(save_bundle.abstractions, vistrail.db_id, db_connection, do_copy)
+ save_mashuptrails_to_db(save_bundle.mashups, vistrail.db_id, db_connection, do_copy)
+ save_thumbnails_to_db(save_bundle.thumbnails, db_connection)
+ return SaveBundle(DBVistrail.vtType, vistrail, log, abstractions=list(save_bundle.abstractions), thumbnails=list(save_bundle.thumbnails))
+
+def save_vistrail_to_db(vistrail, db_connection, do_copy=False, version=None):
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ if version is None:
+ version = get_db_version(db_connection)
+ if version is None:
+ version = currentVersion
+ if not vistrail.db_version:
+ vistrail.db_version = currentVersion
+
+ dao_list = getVersionDAO(version)
+
+ # db_connection.begin()
+
+ # current_action holds the current action id
+ # (used by the controller--write_vistrail)
+ current_action = 0L
+ if hasattr(vistrail, 'db_currentVersion'):
+ current_action = vistrail.db_currentVersion
+
+ if not do_copy and vistrail.db_last_modified is not None:
+ new_time = get_db_object_modification_time(db_connection,
+ vistrail.db_id,
+ DBVistrail.vtType)
+ if new_time > vistrail.db_last_modified:
+ # need synchronization
+ old_vistrail = open_vistrail_from_db(db_connection,
+ vistrail.db_id,
+ True, version)
+ old_vistrail = translate_vistrail(old_vistrail, version)
+ # the "old" one is modified and changes integrated
+ current_action = \
+ vistrails.db.services.vistrail.synchronize(old_vistrail, vistrail,
+ current_action)
+ vistrail = old_vistrail
+ vistrail.db_last_modified = get_current_time(db_connection)
+
+ vistrail = translate_vistrail(vistrail, vistrail.db_version, version)
+ # get saved workflows from db
+ workflowIds = get_saved_workflows(vistrail, db_connection)
+ #print "Workflows already saved:", workflowIds
+ dao_list.save_to_db(db_connection, vistrail, do_copy)
+ vistrail = translate_vistrail(vistrail, version)
+ vistrail.db_currentVersion = current_action
+
+ # update all missing tagged workflows
+ tagMap = {}
+ for annotation in vistrail.db_actionAnnotations:
+ if annotation.db_key == '__tag__':
+ tagMap[annotation.db_action_id] = annotation.db_value
+ wfToSave = []
+ for id, name in tagMap.iteritems():
+ if id not in workflowIds:
+ #print "creating workflow", vistrail.db_id, id, name,
+ workflow = vistrails.db.services.vistrail.materializeWorkflow(vistrail, id)
+ workflow.db_id = None
+ workflow.db_vistrail_id = vistrail.db_id
+ workflow.db_parent_id = id
+ workflow.db_group = id
+ workflow.db_last_modified=vistrail.db_get_action_by_id(id).db_date
+ workflow.db_name = name
+ workflow = translate_workflow(workflow, currentVersion, version)
+ wfToSave.append(workflow)
+ #print "done"
+ if wfToSave:
+ dao_list.save_many_to_db(db_connection, wfToSave, True)
+ db_connection.commit()
+ return vistrail
+
+##############################################################################
+# Workflow I/O
+
+def open_workflow_from_xml(filename):
+ """open_workflow_from_xml(filename) -> DBWorkflow"""
+ tree = ElementTree.parse(filename)
+ version = get_version_for_xml(tree.getroot())
+ daoList = getVersionDAO(version)
+ workflow = daoList.open_from_xml(filename, DBWorkflow.vtType, tree)
+ workflow = translate_workflow(workflow, version)
+ vistrails.db.services.workflow.update_id_scope(workflow)
+ return workflow
+
+def open_workflow_from_db(db_connection, id, lock=False, version=None):
+ """open_workflow_from_db(db_connection, id : long: lock: bool,
+ version: str)
+ -> DBWorkflow
+
+ """
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ if version is None:
+ version = get_db_object_version(db_connection, id, DBWorkflow.vtType)
+ dao_list = getVersionDAO(version)
+ workflow = \
+ dao_list.open_from_db(db_connection, DBWorkflow.vtType, id, lock)
+ workflow = translate_workflow(workflow, version)
+ return workflow
+
+def save_workflow_to_xml(workflow, filename, version=None):
+ tags = {'xmlns:xsi': 'http://www.w3.org/2001/XMLSchema-instance',
+ 'xsi:schemaLocation': 'http://www.vistrails.org/workflow.xsd'
+ }
+ if version is None:
+ version = currentVersion
+ if not workflow.db_version:
+ workflow.db_version = currentVersion
+ workflow = translate_workflow(workflow, workflow.db_version, version)
+
+ daoList = getVersionDAO(version)
+ daoList.save_to_xml(workflow, filename, tags, version)
+ workflow = translate_workflow(workflow, version)
+ return workflow
+
+def save_workflow_bundle_to_xml(save_bundle, filename, version=None):
+ if save_bundle.workflow is None:
+ raise VistrailsDBException('save_workflow_bundle_to_xml failed, '
+ 'bundle does not contain a workflow')
+ workflow = save_workflow_to_xml(save_bundle.workflow, filename, version)
+ return SaveBundle(DBWorkflow.vtType, workflow=workflow)
+
+def save_workflow_to_db(workflow, db_connection, do_copy=False, version=None):
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ if version is None:
+ version = get_db_version(db_connection)
+ if version is None:
+ version = currentVersion
+ if not workflow.db_version:
+ workflow.db_version = currentVersion
+ workflow = translate_workflow(workflow, workflow.db_version, version)
+ dao_list = getVersionDAO(version)
+
+ db_connection.begin()
+ workflow.db_last_modified = get_current_time(db_connection)
+ dao_list.save_to_db(db_connection, workflow, do_copy)
+ db_connection.commit()
+ workflow = translate_workflow(workflow, version)
+ return workflow
+
+def save_workflow_bundle_to_db(save_bundle, db_connection, do_copy=False,
+ version=None):
+ if save_bundle.workflow is None:
+ raise VistrailsDBException('save_workflow_bundle_to_db failed, '
+ 'bundle does not contain a workflow')
+ workflow = save_workflow_to_db(save_bundle.workflow, db_connection, do_copy,
+ version)
+ return SaveBundle(DBWorkflow.vtType, workflow=workflow)
+
+def get_saved_workflows(vistrail, db_connection):
+ """ Returns list of action id:s representing populated workflows """
+ if not vistrail.db_id:
+ return []
+ c = db_connection.cursor()
+ c.execute("SELECT parent_id FROM workflow WHERE vistrail_id=%s;", (vistrail.db_id,))
+ ids = [i[0] for i in c.fetchall()]
+ c.close()
+ return ids
+
+##############################################################################
+# Logging I/O
+
+def open_log_from_xml(filename, was_appended=False):
+ """open_log_from_xml(filename) -> DBLog"""
+ if was_appended:
+ parser = ElementTree.XMLTreeBuilder()
+ parser.feed("<log>\n")
+ f = open(filename, "rb")
+ parser.feed(f.read())
+ parser.feed("</log>\n")
+ root = parser.close()
+ workflow_execs = []
+ for node in root:
+ version = get_version_for_xml(node)
+ daoList = getVersionDAO(version)
+ workflow_exec = \
+ daoList.read_xml_object(DBWorkflowExec.vtType, node)
+ if version != currentVersion:
+ # if version is wrong, dump this into a dummy log object,
+ # then translate, then get workflow_exec back
+ log = DBLog()
+ translate_log(log, currentVersion, version)
+ log.db_add_workflow_exec(workflow_exec)
+ log = translate_log(log, version)
+ workflow_exec = log.db_workflow_execs[0]
+ workflow_execs.append(workflow_exec)
+ log = DBLog(workflow_execs=workflow_execs)
+ vistrails.db.services.log.update_ids(log)
+ else:
+ tree = ElementTree.parse(filename)
+ version = get_version_for_xml(tree.getroot())
+ daoList = getVersionDAO(version)
+ log = daoList.open_from_xml(filename, DBLog.vtType, tree)
+ log = translate_log(log, version)
+ vistrails.db.services.log.update_id_scope(log)
+ return log
+
+def open_log_from_db(db_connection, id, lock=False, version=None):
+ """open_log_from_db(db_connection, id : long: lock: bool, version: str)
+ -> DBLog
+
+ """
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ if version is None:
+ version = get_db_object_version(db_connection, id, DBLog.vtType)
+ dao_list = getVersionDAO(version)
+ log = dao_list.open_from_db(db_connection, DBLog.vtType, id, lock)
+ log = translate_log(log, version)
+ return log
+
+def open_vt_log_from_db(db_connection, vt_id, version=None):
+ """ return the logs for the specified vistrail """
+ if version is None:
+ version = get_db_object_version(db_connection, vt_id, DBVistrail.vtType)
+ dao_list = getVersionDAO(version)
+ ids = []
+ if db_connection is not None:
+ try:
+ c = db_connection.cursor()
+ # FIXME MySQL versus sqlite3
+ res = c.execute("SELECT id FROM log_tbl WHERE vistrail_id=%s;", (vt_id,))
+ ids = [i[0] for i in c.fetchall()]
+ c.close()
+ except get_db_lib().Error, e:
+ debug.critical("Error getting log id:s %d: %s" % (e.args[0], e.args[1]))
+ log = DBLog()
+ if hasattr(dao_list, 'open_many_from_db'): # does not exist pre 1.0.2
+ logs = dao_list.open_many_from_db(db_connection, DBLog.vtType, ids)
+ else:
+ logs = [dao_list.open_from_db(db_connection, DBLog.vtType, id) \
+ for id in ids]
+ for new_log in logs:
+ for workflow_exec in new_log.db_workflow_execs:
+ workflow_exec.db_id = log.id_scope.getNewId(DBWorkflowExec.vtType)
+ log.db_add_workflow_exec(workflow_exec)
+ log = translate_log(log, version)
+ return log
+
+def save_log_to_xml(log, filename, version=None, do_append=False):
+ if version is None:
+ version = currentVersion
+ if not log.db_version:
+ log.db_version = currentVersion
+ log = translate_log(log, log.db_version, version)
+
+ daoList = getVersionDAO(version)
+ if do_append:
+ log_file = open(filename, 'ab')
+ for workflow_exec in log.db_workflow_execs:
+ # cannot do correct numbering here...
+ # but need to save so that we can use it for deletes
+ wf_exec_id = workflow_exec.db_id
+ workflow_exec.db_id = -1L
+ daoList.save_to_xml(workflow_exec, log_file, {}, version)
+ workflow_exec.db_id = wf_exec_id
+ log_file.close()
+ else:
+ tags = {'xmlns:xsi': 'http://www.w3.org/2001/XMLSchema-instance',
+ 'xsi:schemaLocation': 'http://www.vistrails.org/log.xsd'
+ }
+ daoList.save_to_xml(log, filename, tags, version)
+ log = translate_log(log, version)
+ return log
+
+def save_log_bundle_to_xml(save_bundle, filename, version=None):
+ if save_bundle.log is None:
+ raise VistrailsDBException('save_log_bundle_to_xml failed, '
+ 'bundle does not contain a log')
+
+ log = save_log_to_xml(save_bundle.log, filename, version)
+ return SaveBundle(DBLog.vtType, log=log)
+
+def save_log_to_db(log, db_connection, do_copy=False, version=None):
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ if version is None:
+ version = get_db_version(db_connection)
+ if version is None:
+ version = currentVersion
+ if not log.db_version:
+ log.db_version = currentVersion
+ log = translate_log(log, log.db_version, version)
+ dao_list = getVersionDAO(version)
+
+ db_connection.begin()
+ log.db_last_modified = get_current_time(db_connection)
+ dao_list.save_to_db(db_connection, log, do_copy)
+ db_connection.commit()
+ log = translate_log(log, version)
+ return log
+
+def save_log_bundle_to_db(save_bundle, db_connection, do_copy=False,
+ version=None):
+ if save_bundle.log is None:
+ raise VistrailsDBException('save_log_bundle_to_db failed, '
+ 'bundle does not contain a log')
+
+ log = save_log_to_db(save_bundle.log, db_connection, do_copy, version)
+ return SaveBundle(DBLog.vtType, log=log)
+
+def merge_logs(new_log, vt_log_fname):
+ log = open_log_from_xml(vt_log_fname, True)
+ for workflow_exec in new_log.db_workflow_execs:
+ workflow_exec.db_id = log.id_scope.getNewId(DBWorkflowExec.vtType)
+ log.db_add_workflow_exec(workflow_exec)
+ return log
+
+##############################################################################
+# OPM I/O
+
+def save_opm_to_xml(opm_graph, filename, version=None):
+ # FIXME, we're using workflow, version, and log here...
+ # which aren't in DBOpmGraph...
+ if version is None:
+ version = currentVersion
+ daoList = getVersionDAO(version)
+ tags = {'xmlns': 'http://openprovenance.org/model/v1.01.a',
+ }
+ opm_graph = vistrails.db.services.opm.create_opm(opm_graph.workflow,
+ opm_graph.version,
+ opm_graph.log,
+ opm_graph.registry)
+ daoList.save_to_xml(opm_graph, filename, tags, version)
+ return opm_graph
+
+##############################################################################
+# PROV I/O
+
+def save_prov_to_xml(prov_document, filename, version=None):
+ # FIXME, we're using workflow, version, and log here...
+ # which aren't in DBProvDocument...
+ if version is None:
+ version = currentVersion
+ daoList = getVersionDAO(version)
+ tags = {'xmlns:prov': 'http://www.w3.org/ns/prov#',
+ 'xmlns:dcterms': 'http://purl.org/dc/terms/',
+ 'xmlns:vt': 'http://www.vistrails.org/registry.xsd',
+ }
+ prov_document = vistrails.db.services.prov.create_prov(prov_document.workflow,
+ prov_document.version,
+ prov_document.log)
+ daoList.save_to_xml(prov_document, filename, tags, version)
+ return prov_document
+
+##############################################################################
+# Registry I/O
+
+def open_registry_from_xml(filename):
+ tree = ElementTree.parse(filename)
+ version = get_version_for_xml(tree.getroot())
+ daoList = getVersionDAO(version)
+ registry = daoList.open_from_xml(filename, DBRegistry.vtType, tree)
+ registry = translate_registry(registry, version)
+ vistrails.db.services.registry.update_id_scope(registry)
+ return registry
+
+def open_registry_from_db(db_connection, id, lock=False, version=None):
+ """open_registry_from_db(db_connection, id : long: lock: bool,
+ version: str) -> DBRegistry
+
+ """
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ if version is None:
+ version = get_db_object_version(db_connection, id, DBRegistry.vtType)
+ dao_list = getVersionDAO(version)
+ registry = dao_list.open_from_db(db_connection, DBRegistry.vtType, id, lock)
+ registry = translate_registry(registry, version)
+ return registry
+
+def save_registry_to_xml(registry, filename, version=None):
+ tags = {'xmlns:xsi': 'http://www.w3.org/2001/XMLSchema-instance',
+ 'xsi:schemaLocation': 'http://www.vistrails.org/registry.xsd'
+ }
+ if version is None:
+ version = currentVersion
+ if not registry.db_version:
+ registry.db_version = currentVersion
+ registry = translate_registry(registry, registry.db_version, version)
+
+ daoList = getVersionDAO(version)
+ daoList.save_to_xml(registry, filename, tags, version)
+ registry = translate_registry(registry, version)
+ return registry
+
+def save_registry_bundle_to_xml(save_bundle, filename, version=None):
+ if save_bundle.registry is None:
+ raise VistrailsDBException('save_registry_bundle_to_xml failed, '
+ 'bundle does not contain a registry')
+
+ registry = save_registry_to_xml(save_bundle.registry, filename, version)
+ return SaveBundle(DBRegistry.vtType, registry=registry)
+
+def save_registry_to_db(registry, db_connection, do_copy=False, version=None):
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ if version is None:
+ version = get_db_version(db_connection)
+ if version is None:
+ version = currentVersion
+ if not registry.db_version:
+ registry.db_version = currentVersion
+ registry = translate_registry(registry, registry.db_version, version)
+ dao_list = getVersionDAO(version)
+
+ db_connection.begin()
+ registry.db_last_modified = get_current_time(db_connection)
+ dao_list.save_to_db(db_connection, registry, do_copy)
+ db_connection.commit()
+ registry = translate_registry(registry, version)
+ return registry
+
+def save_registry_bundle_to_db(save_bundle, db_connection, do_copy=False,
+ version=None):
+ if save_bundle.registry is None:
+ raise VistrailsDBException('save_registry_bundle_to_db failed, '
+ 'bundle does not contain a registry')
+
+ registry = save_registry_to_db(save_bundle.registry, db_connection, do_copy,
+ version)
+ return SaveBundle(DBRegistry.vtType, registry=registry)
+
+##############################################################################
+# Abstraction I/O
+
+def open_abstraction_from_db(db_connection, id, lock=False):
+ """open_abstraction_from_db(db_connection, id : long: lock: bool)
+ -> DBAbstraction
+ DEPRECATED
+ """
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ abstraction = read_sql_objects(db_connection, DBAbstraction.vtType,
+ id, lock)[0]
+
+ # not sure where this really should be done...
+ # problem is that db reads the add ops, then change ops, then delete ops
+ # need them ordered by their id
+ for db_action in abstraction.db_get_actions():
+ db_action.db_operations.sort(key=lambda x: x.db_id)
+ vistrails.db.services.abstraction.update_id_scope(abstraction)
+ return abstraction
+
+def save_abstraction_to_db(abstraction, db_connection, do_copy=False):
+ """ DEPRECATED """
+ db_connection.begin()
+ if abstraction.db_last_modified is None:
+ do_copy = True
+ if not do_copy:
+ match_id = get_matching_abstraction_id(db_connection, abstraction)
+ # FIXME remove print
+ #print 'match_id:', match_id
+ if match_id is not None:
+ abstraction.db_id = match_id
+ abstraction.is_new = False
+ else:
+ do_copy = True
+ new_time = get_db_object_modification_time(db_connection,
+ abstraction.db_id,
+ DBAbstraction.vtType)
+ if new_time > abstraction.db_last_modified:
+ # need synchronization
+ # FIXME remove print
+ #print '*** doing synchronization ***'
+ old_abstraction = open_abstraction_from_db(db_connection,
+ abstraction.db_id,
+ True)
+ # the "old" one is modified and changes integrated
+ vistrails.db.services.vistrail.synchronize(old_abstraction, abstraction,
+ 0L)
+ abstraction = old_abstraction
+ if do_copy:
+ abstraction.db_id = None
+ abstraction.db_last_modified = get_current_time(db_connection)
+ write_sql_objects(db_connection, [abstraction], do_copy)
+ db_connection.commit()
+ return abstraction
+
+def save_abstractions_to_db(abstractions, vt_id, db_connection, do_copy=False):
+ """save_abstraction_to_db(abs: DBVistrail, db_connection) -> None
+ Saves an abstraction to db, and updating existing abstractions
+
+ """
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+
+ for abs_name in abstractions:
+ try:
+ abs = open_vistrail_from_xml(abs_name)
+ abs.db_name = parse_abstraction_name(abs_name)
+ id_key = '__abstraction_vistrail_id__'
+ id_value = str(vt_id)
+ if abs.db_has_annotation_with_key(id_key):
+ annotation = abs.db_get_annotation_by_key(id_key)
+ annotation.db_value = id_value
+ else:
+ annotation=DBAnnotation(abs.idScope.getNewId(DBAnnotation.vtType),
+ id_key, id_value)
+ abs.db_add_annotation(annotation)
+ db_mod_time = None if not abs.db_id else \
+ get_db_abstraction_modification_time(db_connection, abs)
+
+ if db_mod_time:
+ delete_entity_from_db(db_connection, abs.vtType, abs.db_id)
+
+ abs.db_id = None
+ abs.db_last_modified = get_current_time(db_connection)
+ version = get_db_version(db_connection)
+ version = version if version else currentVersion
+ if not abs.db_version:
+ abs.db_version = currentVersion
+ abs = translate_vistrail(abs, abs.db_version, version)
+ # Always copy for now
+ getVersionDAO(version).save_to_db(db_connection, abs, True)
+ db_connection.commit()
+
+ except Exception, e:
+ debug.critical('Could not save abstraction to db: %s' % str(e))
+
+##############################################################################
+# Thumbnail I/O
+
+def open_thumbnails_from_db(db_connection, obj_type, obj_id, tmp_dir=None):
+ """open_thumbnails_from_db(db_connection, obj_type: DB*,
+ obj_id: long, tmp_dir: str) -> [str]
+
+ Gets a list of all thumbnails associated with this object from the
+ annotations table in the db (by comparing obj_type with the column
+ 'entity_type' and obj_id with the column 'entity_id') and for any
+ thumbnails not found in tmp_dir, they are retreived from the db and
+ saved into tmp_dir.
+ Returns a list of absolute file paths for all thumbnails associated
+ with this object that exist in tmp_dir after the function has run.
+
+ """
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ if tmp_dir is None:
+ return []
+
+ # First get associated file names from annotation table
+ prepared_statement = format_prepared_statement(
+ """
+ SELECT a.value
+ FROM annotation a
+ WHERE a.akey = '__thumb__' AND a.entity_id = ? AND a.entity_type = ?
+ """)
+ try:
+ c = db_connection.cursor()
+ c.execute(prepared_statement, (obj_id, obj_type))
+ file_names = [file_name for (file_name,) in c.fetchall()]
+ c.close()
+ except get_db_lib().Error, e:
+ msg = "Couldn't get thumbnails list from db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+
+ # Next get all thumbnails from the db that aren't already in tmp_dir
+ get_db_file_names = [fname for fname in file_names if fname not in os.listdir(tmp_dir)]
+ for file_name in get_db_file_names:
+ prepared_statement = format_prepared_statement(
+ """
+ SELECT t.image_bytes
+ FROM thumbnail t
+ WHERE t.file_name = ?
+ """)
+ try:
+ c = db_connection.cursor()
+ c.execute(prepared_statement, (file_name,))
+ row = c.fetchone()
+ c.close()
+ except get_db_lib().Error, e:
+ msg = "Couldn't get thumbnail from db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+ if row is not None:
+ image_bytes = row[0]
+ try:
+ absfname = os.path.join(tmp_dir, file_name)
+ image_file = open(absfname, 'wb')
+ image_file.write(image_bytes)
+ image_file.close()
+ except IOError, e:
+ msg = "Couldn't write thumbnail file to disk: %s" % absfname
+ raise VistrailsDBException(msg)
+ else:
+ debug.warning("db: Referenced thumbnail not found locally or in the database: '%s'" % file_name)
+ # Return only thumbnails that now exist locally
+ return [os.path.join(tmp_dir, file_name) for file_name in file_names if file_name in os.listdir(tmp_dir)]
+
+def save_thumbnails_to_db(absfnames, db_connection):
+ """save_thumbnails_to_db(absfnames: list, db_connection) -> None
+ Saves all thumbnails from a list of local absolute file paths into the db,
+ except those already present on the db.
+
+ """
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ if absfnames is None or len(absfnames) == 0:
+ return None
+
+ # Determine which thumbnails already exist in db
+ statement = """
+ SELECT t.file_name
+ FROM thumbnail t
+ WHERE t.file_name IN %s
+ """
+ check_file_names = [os.path.basename(absfname).replace("'", "''").replace("\\", "\\\\") for absfname in absfnames]
+ # SQL syntax needs SOMETHING if list is empty - use filename that's illegal on all platforms
+ check_file_names.append(':/')
+ sql_in_token = str(tuple(check_file_names))
+ try:
+ c = db_connection.cursor()
+ c.execute(statement % sql_in_token)
+ db_file_names = [file_name for (file_name,) in c.fetchall()]
+ c.close()
+ except get_db_lib().Error, e:
+ msg = "Couldn't check which thumbnails already exist in db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+ insert_absfnames = [absfname for absfname in absfnames if os.path.basename(absfname) not in db_file_names]
+
+ # Save any thumbnails that don't already exist in db
+ prepared_statement = format_prepared_statement(
+ """
+ INSERT INTO thumbnail(file_name, image_bytes, last_modified)
+ VALUES (?, ?, ?)
+ """)
+ try:
+ c = db_connection.cursor()
+ for absfname in insert_absfnames:
+ image_file = open(absfname, 'rb')
+ image_bytes = image_file.read()
+ image_file.close()
+ c.execute(prepared_statement, (os.path.basename(absfname), image_bytes, get_current_time(db_connection).strftime('%Y-%m-%d %H:%M:%S')))
+ db_connection.commit()
+ c.close()
+ except IOError, e:
+ msg = "Couldn't read thumbnail file for writing to db: %s" % absfname
+ raise VistrailsDBException(msg)
+ except get_db_lib().Error, e:
+ msg = "Couldn't insert thumbnail into db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+ return None
+##############################################################################
+# Mashup I/O
+def open_mashuptrail_from_xml(filename):
+ """open_mashuptrail_from_xml(filename) -> Mashuptrail"""
+ tree = ElementTree.parse(filename)
+ version = get_version_for_xml(tree.getroot())
+ # this is here because initially the version in the mashuptrail file was
+ # independent of VisTrails schema version. So if the version was "0.1.0" we
+ # can safely upgrade it directly to 1.0.3 as it was the first version when
+ # the mashuptrail started to use the same vistrails schema version
+ old_version = version
+ if version == "0.1.0":
+ version = "1.0.3"
+ try:
+ daoList = getVersionDAO(version)
+ mashuptrail = daoList.open_from_xml(filename, DBMashuptrail.vtType, tree)
+ if old_version == "0.1.0":
+ mashuptrail.db_version = version
+ Mashuptrail.convert(mashuptrail)
+ mashuptrail.currentVersion = mashuptrail.getLatestVersion()
+ mashuptrail.updateIdScope()
+ except VistrailsDBException, e:
+ msg = "There was a problem when reading mashups from the xml file: "
+ msg += str(e)
+ raise VistrailsDBException(msg)
+ return mashuptrail
+
+def save_mashuptrail_to_xml(mashuptrail, filename, version=None):
+ tags = {'xmlns:xsi': 'http://www.w3.org/2001/XMLSchema-instance',
+ 'xsi:schemaLocation': 'http://www.vistrails.org/mashup.xsd'
+ }
+ if version is None:
+ version = currentVersion
+
+ if not mashuptrail.db_version:
+ mashuptrail.db_version = version
+
+ #FIXME: This must be enabled at some point
+ #mashuptrail = translate_mashuptrail(mashuptrail, mashuptrail.db_version, version)
+ daoList = getVersionDAO(version)
+ daoList.save_to_xml(mashuptrail, filename, tags, version)
+ return mashuptrail
+
+def open_mashuptrail_from_db(db_connection, mashup_id, lock=False):
+ """open_mashuptrail_from_db(filename) -> Mashuptrail"""
+
+ version = get_db_object_version(db_connection, mashup_id, DBMashuptrail.vtType)
+ try:
+ daoList = getVersionDAO(version)
+ mashuptrail = daoList.open_from_db(db_connection, DBMashuptrail.vtType, mashup_id, lock)
+ Mashuptrail.convert(mashuptrail)
+ mashuptrail.currentVersion = mashuptrail.getLatestVersion()
+ mashuptrail.updateIdScope()
+ except VistrailsDBException, e:
+ msg = "There was a problem when reading mashups from the db file: "
+ msg += str(e)
+ raise VistrailsDBException(msg)
+ return mashuptrail
+
+def save_mashuptrails_to_db(mashuptrails, vt_id, db_connection, do_copy=False):
+ """save_mashuptrails_to_db(mashuptrails: DBMashuptrail, vt_id: int,
+ db_connection, do_copy: bool) -> None
+ Saves a list of mashuptrails to the db, and replacing existing mashuptrails
+
+ """
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+
+ old_ids = get_db_mashuptrail_ids_from_vistrail(db_connection, vt_id)
+ for mashuptrail in mashuptrails:
+ try:
+ id_key = '__mashuptrail_vistrail_id__'
+ id_value = str(vt_id)
+ if mashuptrail.db_has_annotation_with_key(id_key):
+ annotation = mashuptrail.db_get_annotation_by_key(id_key)
+ annotation.db_value = id_value
+ else:
+ annotation=DBAnnotation(mashuptrail.id_scope.getNewId(DBAnnotation.vtType),
+ id_key, id_value)
+ mashuptrail.db_add_annotation(annotation)
+
+ if mashuptrail.db_id in old_ids:
+ delete_entity_from_db(db_connection, mashuptrail.vtType, mashuptrail.db_id)
+
+ # add vt_id to mashups
+ for action in mashuptrail.db_actions:
+ action.db_mashup.db_vtid = vt_id
+ mashuptrail.db_last_modified = get_current_time(db_connection)
+ mashuptrail.db_id = None
+ version = get_db_version(db_connection)
+ version = version if version else currentVersion
+ if not mashuptrail.db_version:
+ mashuptrail.db_version = currentVersion
+ #FIXME: This must be enabled at some point
+ #mashuptrail = translate_vistrail(mashuptrail, mashuptrail.db_version, version)
+ # Always copy for now
+ getVersionDAO(version).save_to_db(db_connection, mashuptrail, True)
+ db_connection.commit()
+
+ except Exception, e:
+ debug.critical('Could not save mashuptrail to db: %s' % str(e))
+
+##############################################################################
+# I/O Utilities
+
+def delete_entity_from_db(db_connection, type, obj_id):
+ if db_connection is None:
+ msg = "Need to call open_db_connection() before reading"
+ raise VistrailsDBException(msg)
+ version = get_db_version(db_connection)
+ if version is None:
+ version = currentVersion
+ dao_list = getVersionDAO(version)
+ dao_list.delete_from_db(db_connection, type, obj_id)
+ db_connection.commit()
+
+def get_version_for_xml(root):
+ version = root.get('version', None)
+ if version is not None:
+ return version
+ msg = "Cannot find version information"
+ raise VistrailsDBException(msg)
+
+def get_type_for_xml(root):
+ return root.tag
+
+def get_current_time(db_connection=None):
+ timestamp = datetime.now()
+ if db_connection is not None:
+ try:
+ c = db_connection.cursor()
+ # FIXME MySQL versus sqlite3
+ c.execute("SELECT NOW();")
+ # c.execute("SELECT DATETIME('NOW');")
+ row = c.fetchone()
+ if row:
+ # FIXME MySQL versus sqlite3
+ timestamp = row[0]
+ # timestamp = datetime.strptime(row[0], '%Y-%m-%d %H:%M:%S')
+ c.close()
+ except get_db_lib().Error, e:
+ debug.critical("Logger Error %d: %s" % (e.args[0], e.args[1]))
+
+ return timestamp
+
+def create_temp_folder(prefix='vt_save'):
+ return tempfile.mkdtemp(prefix=prefix)
+
+def remove_temp_folder(temp_dir):
+ if temp_dir is None:
+ return
+ if not os.path.isdir(temp_dir):
+ if os.path.isfile(temp_dir):
+ os.remove(temp_dir)
+
+ # cleanup has already happened
+ return
+ try:
+ for root, dirs, files in os.walk(temp_dir, topdown=False):
+ for name in files:
+ os.remove(os.path.join(root, name))
+ for name in dirs:
+ os.rmdir(os.path.join(root, name))
+ os.rmdir(temp_dir)
+ except OSError, e:
+ raise VistrailsDBException("Can't remove %s: %s" % (temp_dir, str(e)))
+
+##############################################################################
+# Testing
+
+
+class TestDBIO(unittest.TestCase):
+ def test1(self):
+ """test importing an xml file"""
+
+ vistrail = open_vistrail_from_xml( \
+ os.path.join(vistrails.core.system.vistrails_root_directory(),
+ 'tests/resources/dummy.xml'))
+ assert vistrail is not None
+
+ def test2(self):
+ """test importing an xml file"""
+
+ vistrail = open_vistrail_from_xml( \
+ os.path.join(vistrails.core.system.vistrails_root_directory(),
+ 'tests/resources/dummy_new.xml'))
+ assert vistrail is not None
+
+ def test3(self):
+ """test importing a vt file"""
+
+ # FIXME include abstractions
+ (save_bundle, vt_save_dir) = open_bundle_from_zip_xml( \
+ DBVistrail.vtType,
+ os.path.join(vistrails.core.system.vistrails_root_directory(),
+ 'tests/resources/dummy_new.vt'))
+ assert save_bundle.vistrail is not None
+
+ def test4(self):
+ """ test saving a vt file """
+
+ # FIXME include abstractions
+ testdir = tempfile.mkdtemp(prefix='vt_')
+ filename = os.path.join(testdir, 'dummy_new.vt')
+
+ try:
+ (save_bundle, vt_save_dir) = open_bundle_from_zip_xml(
+ DBVistrail.vtType,
+ os.path.join(vistrails.core.system.vistrails_root_directory(),
+ 'tests/resources/dummy_new.vt'))
+ try:
+ save_bundle_to_zip_xml(save_bundle, filename, vt_save_dir)
+ if os.path.isfile(filename):
+ os.unlink(filename)
+ except Exception, e:
+ self.fail(str(e))
+ finally:
+ os.rmdir(testdir)
diff --git a/vistrails/db/services/locator.py b/vistrails/db/services/locator.py
new file mode 100644
index 0000000..ab9ac51
--- /dev/null
+++ b/vistrails/db/services/locator.py
@@ -0,0 +1,1235 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import cgi
+from datetime import datetime, date
+import hashlib
+import locale
+import os.path
+import re
+import sys
+from time import strptime
+import urllib
+import urlparse
+import uuid
+
+import vistrails.core.system
+from vistrails.db.services import io
+from vistrails.db.services.io import SaveBundle
+from vistrails.db.domain import DBVistrail, DBWorkflow
+from vistrails.db import VistrailsDBException
+from vistrails.core import debug
+from vistrails.core.system import get_elementtree_library, systemType
+
+ElementTree = get_elementtree_library()
+
+
+_drive_regex = re.compile(r"/*([a-zA-Z]:/.+)$")
+def pathname2url(path):
+ """ Takes an absolute filename and turns it into a file:// URL.
+
+ While urllib.pathname2url seems like a good idea, it doesn't appear
+ to do anything sensible in practice on Windows.
+ """
+ if path.startswith('file://'):
+ path = urllib.unquote(path[7:])
+ if systemType in ('Windows', 'Microsoft'):
+ path = path.replace('\\', '/')
+ match = _drive_regex.match(path)
+ if match is not None:
+ path = '/%s' % match.group(1)
+ path = urllib.quote(path, safe='/:')
+ return path
+
+
+def url2pathname(urlpath):
+ """ Takes a file:// URL and turns it into a filename.
+ """
+ path = urllib.url2pathname(urlpath)
+ if systemType in ('Windows', 'Microsoft'):
+ path = path.replace('/', '\\')
+ path = path.lstrip('\\')
+ return path
+
+
+class BaseLocator(object):
+
+ def load(self):
+ raise NotImplementedError("load is not implemented")
+
+ def save(self, obj, do_copy=True, version=None):
+ """Saves an object in the given place.
+
+ """
+ raise NotImplementedError("save is not implemented")
+
+ def save_as(self, obj, version=None):
+ return self.save(obj, True, version) # calls save by default
+
+ def close(self):
+ """Closes locator.
+
+ """
+ pass
+
+ def is_valid(self):
+ """Returns true if locator refers to a valid object.
+
+ """
+ raise NotImplementedError("is_valid is not implemented")
+
+ def get_temporary(self):
+ return None
+
+ def has_temporaries(self):
+ return self.get_temporary() is not None
+
+ def clean_temporaries(self):
+ pass
+
+ def save_temporary(self, obj):
+ pass
+
+ def serialize(self, dom, element):
+ """Serializes this locator to XML.
+
+ """
+ raise NotImplementedError("serialize is not implemented")
+
+ def to_xml(self, node=None):
+ """ElementTree port of serialize.
+
+ """
+ raise NotImplementedError("to_xml is not implemented")
+
+ @staticmethod
+ def parse(element):
+ """Parse an XML object representing a locator and returns a Locator.
+
+ """
+ raise NotImplementedError("parse is not implemented")
+
+ @staticmethod
+ def convert_filename_to_url(filename):
+ """ Converts a local filename to a file:// URL.
+
+ All file:// URLs are absolute, so abspath() will be used on the
+ argument.
+ """
+ exts = ["vt", "xml"]
+ q_mark = False
+ query_str_idx = None
+ for match in re.finditer("\.(%s)(\??)" % "|".join(exts), filename):
+ if match.group(2):
+ if q_mark:
+ raise VistrailsDBException('Ambiguous URI with '
+ 'multiple question '
+ 'marks: "%s"' % filename)
+ else:
+ q_mark = True
+ query_str_idx = match.end()
+ if q_mark:
+ args_str = filename[query_str_idx-1:]
+ filename = filename[:query_str_idx-1]
+ else:
+ args_str = ""
+
+ return 'file://%s%s' % (pathname2url(os.path.abspath(filename)),
+ urllib.quote(args_str, safe='/?=&'))
+
+ @staticmethod
+ def from_url(url):
+ """Assumes a valid URL if the scheme is specified. For example,
+ 'file:///C:/My%20Documents/test.vt'. If only a filename is
+ specified, it converts the filename to a URL.
+
+ """
+ if '://' in url:
+ scheme = url.split('://', 1)[0]
+ elif url.startswith('untitled:'):
+ scheme = 'untitled'
+ else:
+ scheme = 'file'
+ url = BaseLocator.convert_filename_to_url(url)
+ if scheme == 'untitled':
+ return UntitledLocator.from_url(url)
+ elif scheme == 'db':
+ return DBLocator.from_url(url)
+ elif scheme == 'file':
+ old_uses_query = urlparse.uses_query
+ urlparse.uses_query = urlparse.uses_query + ['file']
+ scheme, host, path, query, fragment = urlparse.urlsplit(str(url))
+ urlparse.uses_query = old_uses_query
+ path = url2pathname(path)
+ if path.endswith(".vt"):
+ return ZIPFileLocator.from_url(url)
+ elif path.endswith(".xml"):
+ return XMLFileLocator.from_url(url)
+ return None
+
+ @staticmethod
+ def parse_args(arg_str):
+ args = {}
+ parsed_dict = cgi.parse_qs(arg_str)
+ if 'type' in parsed_dict:
+ args['obj_type'] = parsed_dict['type'][0]
+ if 'id' in parsed_dict:
+ args['obj_id'] = parsed_dict['id'][0]
+ args['version_node'] = None
+ args['version_tag'] = None
+ if 'workflow' in parsed_dict:
+ workflow_arg = parsed_dict['workflow'][0]
+ try:
+ args['version_node'] = int(workflow_arg)
+ except ValueError:
+ args['version_tag'] = workflow_arg
+ if 'workflow_exec' in parsed_dict:
+ args['workflow_exec'] = parsed_dict['workflow_exec'][0]
+ if 'parameterExploration' in parsed_dict:
+ args['parameterExploration'] = \
+ parsed_dict['parameterExploration'][0]
+ if 'mashuptrail' in parsed_dict:
+ args['mashuptrail'] = parsed_dict['mashuptrail'][0]
+ # should use mashupVersion, but also allow (and preserve) mashup
+ if 'mashupVersion' in parsed_dict:
+ args['mashupVersion'] = parsed_dict['mashupVersion'][0]
+ elif 'mashup' in parsed_dict:
+ args['mashup'] = parsed_dict['mashup'][0]
+ if 'workflow_exec' in parsed_dict:
+ args['workflow_exec'] = parsed_dict['workflow_exec'][0]
+ return args
+
+ @staticmethod
+ def generate_args(args):
+ generate_dict = {}
+ if 'obj_type' in args and args['obj_type']:
+ generate_dict['type'] = args['obj_type']
+ if 'obj_id' in args and args['obj_id']:
+ generate_dict['id'] = args['obj_id']
+ if 'version_node' in args and args['version_node']:
+ generate_dict['workflow'] = args['version_node']
+ elif 'version_tag' in args and args['version_tag']:
+ generate_dict['workflow'] = args['version_tag']
+ if 'parameterExploration' in args and args['parameterExploration']:
+ generate_dict['parameterExploration'] = args['parameterExploration']
+ if 'mashuptrail' in args and args['mashuptrail']:
+ generate_dict['mashuptrail'] = args['mashuptrail']
+ if 'mashupVersion' in args and args['mashupVersion']:
+ generate_dict['mashupVersion'] = args['mashupVersion']
+ elif 'mashup' in args and args['mashup']:
+ generate_dict['mashup'] = args['mashup']
+ if 'workflow_exec' in args and args['workflow_exec']:
+ generate_dict['workflow_exec'] = args['workflow_exec']
+ return urllib.urlencode(generate_dict)
+
+
+ def _get_name(self):
+ return None # Returns a name that will be displayed for the object
+ name = property(_get_name)
+
+ def _get_short_filename(self):
+ """ Returns a short name that can be used to derive other filenames
+ """
+ return None
+ short_filename = property(_get_short_filename)
+
+ def _get_short_name(self):
+ """ Returns a short name that can be used for display
+ """
+ return None
+ short_name = property(_get_short_name)
+
+ ###########################################################################
+ # Operators
+
+ def __eq__(self, other):
+ pass # Implement equality
+
+ def __ne__(self, other):
+ pass # Implement nonequality
+
+ def __hash__(self):
+ return hash(self.name)
+
+ def is_untitled(self):
+ return False
+
+class SaveTemporariesMixin(object):
+ """A mixin class that saves temporary copies of a file. It requires
+ self.name to exist for proper functioning.
+
+ """
+
+ @staticmethod
+ def get_autosave_dir():
+ dot_vistrails = vistrails.core.system.current_dot_vistrails()
+ auto_save_dir = os.path.join(dot_vistrails, "autosave")
+ if not os.path.exists(auto_save_dir):
+ # !!! we assume dot_vistrails exists !!!
+ os.mkdir(auto_save_dir)
+ if not os.path.isdir(auto_save_dir):
+ raise VistrailsDBException('Auto-save path "%s" is not a '
+ 'directory' % auto_save_dir)
+ return auto_save_dir
+
+ def get_temp_basename(self):
+ return self.name
+
+ def save_temporary(self, obj):
+ fname = self._find_latest_temporary()
+ new_temp_fname = self._next_temporary(fname)
+ io.save_to_xml(obj, new_temp_fname)
+
+ def clean_temporaries(self):
+ """_remove_temporaries() -> None
+
+ Erases all temporary files.
+
+ """
+ def remove_it(fname):
+ os.unlink(fname)
+ self._iter_temporaries(remove_it)
+
+ def encode_name(self, filename):
+ """encode_name(filename) -> str
+ Encodes a file path using urllib.quoteplus
+
+ """
+ name = urllib.quote_plus(filename) + '_tmp_'
+ return os.path.join(self.get_autosave_dir(), name)
+
+ def _iter_temporaries(self, f):
+ """_iter_temporaries(f): calls f with each temporary file name, in
+ sequence.
+
+ """
+ latest = None
+ current = 0
+ while True:
+ fname = self.encode_name(self.get_temp_basename()) + str(current)
+ if os.path.isfile(fname):
+ f(fname)
+ current += 1
+ else:
+ break
+
+ def _find_latest_temporary(self):
+ """_find_latest_temporary(): String or None.
+
+ Returns the latest temporary file saved, if it exists. Returns
+ None otherwise.
+
+ """
+ latest = [None]
+ def set_it(fname):
+ latest[0] = fname
+ self._iter_temporaries(set_it)
+ return latest[0]
+
+ def _next_temporary(self, temporary):
+ """_find_latest_temporary(string or None): String
+
+ Returns the next suitable temporary file given the current
+ latest one.
+
+ """
+ if temporary == None:
+ return self.encode_name(self.get_temp_basename()) + '0'
+ else:
+ split = temporary.rfind('_')+1
+ base = temporary[:split]
+ number = int(temporary[split:])
+ return base + str(number+1)
+
+class UntitledLocator(SaveTemporariesMixin, BaseLocator):
+ UNTITLED_NAME = "Untitled"
+ UNTITLED_PREFIX = UNTITLED_NAME + "_"
+
+ def __init__(self, my_uuid=None, **kwargs):
+ if my_uuid is not None:
+ self._uuid = my_uuid
+ else:
+ self._uuid = uuid.uuid4()
+ self._vnode = kwargs.get('version_node', None)
+ self._vtag = kwargs.get('version_tag', '')
+ self._mshptrail = kwargs.get('mashuptrail', None)
+ if 'mashupVersion' in kwargs:
+ self._mshpversion = kwargs.get('mashupVersion', None)
+ else:
+ self._mshpversion = kwargs.get('mashup', None)
+ self._parameterexploration = kwargs.get('parameterExploration', None)
+ self.kwargs = kwargs
+
+ def load(self, type):
+ fname = self.get_temporary()
+ if fname:
+ obj = io.open_from_xml(fname, type)
+ else:
+ obj = DBVistrail()
+ obj.locator = self
+ return obj
+
+ def is_valid(self):
+ return False
+
+ def get_temp_basename(self):
+ return UntitledLocator.UNTITLED_PREFIX + self._uuid.hex
+
+ def get_temporary(self):
+ return self._find_latest_temporary()
+
+ def _get_name(self):
+ return UntitledLocator.UNTITLED_NAME
+ name = property(_get_name)
+
+ def _get_short_filename(self):
+ return self._get_name()
+ short_filename = property(_get_short_filename)
+
+ def _get_short_name(self):
+ return self._get_name().decode('ascii')
+ short_name = property(_get_short_name)
+
+ @staticmethod
+ def from_url(url):
+ if not url.startswith('untitled:'):
+ raise VistrailsDBException("URL does not start with untitled:")
+
+ rest = url[9:]
+ my_uuid = None
+ if len(rest) >= 32:
+ try:
+ my_uuid = uuid.UUID(rest[:32])
+ rest = rest[32:]
+ except ValueError:
+ pass
+ if not rest:
+ kwargs = dict()
+ elif rest[0] == '?':
+ kwargs = BaseLocator.parse_args(rest[1:])
+ else:
+ raise ValueError
+ return UntitledLocator(my_uuid, **kwargs)
+
+ def to_url(self):
+ args_str = BaseLocator.generate_args(self.kwargs)
+ url_tuple = ('untitled', '', self._uuid.hex, args_str, '')
+ return urlparse.urlunsplit(url_tuple)
+
+ def __hash__(self):
+ return self._uuid.int
+
+ def __eq__(self, other):
+ if type(other) != type(self):
+ return False
+ return (self._uuid == other._uuid)
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+ def is_untitled(self):
+ return True
+
+ @classmethod
+ def all_untitled_temporaries(cls):
+ autosave_dir = SaveTemporariesMixin.get_autosave_dir()
+ fnames = []
+ for fname in os.listdir(autosave_dir):
+ if fname.startswith(cls.UNTITLED_PREFIX) and \
+ os.path.isfile(os.path.join(autosave_dir, fname)):
+ fnames.append(fname)
+ locators = {}
+ for fname in fnames:
+ uuid_start = len(cls.UNTITLED_PREFIX)
+ my_uuid = uuid.UUID(fname[uuid_start:uuid_start+32])
+ if my_uuid not in locators:
+ locators[my_uuid] = cls(my_uuid)
+ return locators.values()
+
+class XMLFileLocator(BaseLocator, SaveTemporariesMixin):
+ def __init__(self, filename, **kwargs):
+ self._name = filename
+ self._vnode = kwargs.get('version_node', None)
+ self._vtag = kwargs.get('version_tag', '')
+ self._mshptrail = kwargs.get('mashuptrail', None)
+ if 'mashupVersion' in kwargs:
+ self._mshpversion = kwargs.get('mashupVersion', None)
+ else:
+ self._mshpversion = kwargs.get('mashup', None)
+ self._parameterexploration = kwargs.get('parameterExploration', None)
+ self.kwargs = kwargs
+
+ def load(self, type):
+ fname = self.get_temporary()
+ if fname:
+ obj = io.open_from_xml(fname, type)
+ else:
+ obj = io.open_from_xml(self._name, type)
+ obj.locator = self
+ return obj
+
+ def save(self, obj, do_copy=True, version=None):
+ is_bundle = False
+ if type(obj) == type(SaveBundle(None)):
+ is_bundle = True
+ save_bundle = obj
+ obj = save_bundle.get_primary_obj()
+ obj = io.save_to_xml(obj, self._name, version)
+ obj.locator = self
+ # Only remove the temporaries if save succeeded!
+ self.clean_temporaries()
+ if is_bundle:
+ return SaveBundle(save_bundle.bundle_type, obj)
+ return obj
+
+ def is_valid(self):
+ return os.path.isfile(self._name)
+
+ def get_temporary(self):
+ return self._find_latest_temporary()
+
+ def _get_name(self):
+ return str(self._name)
+ name = property(_get_name)
+
+ def _get_short_filename(self):
+ return os.path.splitext(os.path.basename(self._name))[0]
+ short_filename = property(_get_short_filename)
+
+ def _get_short_name(self):
+ name = self._get_short_filename()
+ enc = sys.getfilesystemencoding() or locale.getpreferredencoding()
+ return name.decode(enc)
+ short_name = property(_get_short_name)
+
+ @classmethod
+ def from_url(cls, url):
+ if '://' in url:
+ scheme, path = url.split('://', 1)
+ if scheme != 'file':
+ raise ValueError
+ else:
+ url = BaseLocator.convert_filename_to_url(url)
+
+ old_uses_query = urlparse.uses_query
+ urlparse.uses_query = urlparse.uses_query + ['file']
+ scheme, host, path, args_str, fragment = urlparse.urlsplit(url)
+ urlparse.uses_query = old_uses_query
+ # De-urlencode pathname
+ path = url2pathname(str(path))
+ kwargs = BaseLocator.parse_args(args_str)
+
+ return cls(os.path.abspath(path), **kwargs)
+
+ def to_url(self):
+ args_str = BaseLocator.generate_args(self.kwargs)
+ url_tuple = ('file', '',
+ pathname2url(os.path.abspath(self._name)),
+ args_str, '')
+ return urlparse.urlunsplit(url_tuple)
+
+ def serialize(self, dom, element):
+ """serialize(dom, element) -> None
+ Convert this object to an XML representation.
+
+ """
+ locator = dom.createElement('locator')
+ locator.setAttribute('type', 'file')
+ node = dom.createElement('name')
+ filename = dom.createTextNode(str(self._name))
+ node.appendChild(filename)
+ locator.appendChild(node)
+ element.appendChild(locator)
+
+ @staticmethod
+ def parse(element):
+ """ parse(element) -> XMLFileLocator or None
+ Parse an XML object representing a locator and returns a
+ XMLFileLocator object.
+
+ """
+ if str(element.getAttribute('type')) == 'file':
+ for n in element.childNodes:
+ if n.localName == "name":
+ filename = str(n.firstChild.nodeValue).strip(" \n\t")
+ return XMLFileLocator(filename)
+ return None
+ else:
+ return None
+
+ #ElementTree port
+ def to_xml(self, node=None):
+ """to_xml(node: ElementTree.Element) -> ElementTree.Element
+ Convert this object to an XML representation.
+ """
+ if node is None:
+ node = ElementTree.Element('locator')
+
+ node.set('type', 'file')
+ childnode = ElementTree.SubElement(node,'name')
+ childnode.text = self._name.decode('latin-1')
+ return node
+
+ @staticmethod
+ def from_xml(node):
+ """from_xml(node:ElementTree.Element) -> XMLFileLocator or None
+ Parse an XML object representing a locator and returns a
+ XMLFileLocator object."""
+ if node.tag != 'locator':
+ return None
+
+ #read attributes
+ data = node.get('type', '')
+ type = str(data)
+ if type == 'file':
+ for child in node.getchildren():
+ if child.tag == 'name':
+ filename = child.text.encode('latin-1').strip()
+ return XMLFileLocator(filename)
+ return None
+
+ def __str__(self):
+ return '<%s vistrail_name="%s" />' % (self.__class__.__name__, self._name)
+
+ ###########################################################################
+ # Operators
+
+ def __eq__(self, other):
+ if not isinstance(other, XMLFileLocator):
+ return False
+ return self._name == other._name
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+class ZIPFileLocator(XMLFileLocator):
+ """Files are compressed in zip format. The temporaries are
+ still in xml"""
+ def __init__(self, filename, **kwargs):
+ XMLFileLocator.__init__(self, filename, **kwargs)
+ self.tmp_dir = None
+
+ def load(self, type):
+ fname = self.get_temporary()
+ if fname:
+ from vistrails.db.domain import DBVistrail
+ obj = io.open_from_xml(fname, type)
+ return SaveBundle(DBVistrail.vtType, obj)
+ else:
+ (save_bundle, tmp_dir) = io.open_bundle_from_zip_xml(type, self._name)
+ self.tmp_dir = tmp_dir
+ for obj in save_bundle.get_db_objs():
+ obj.locator = self
+ return save_bundle
+
+ def save(self, save_bundle, do_copy=True, version=None):
+ if do_copy:
+ # make sure we create a fresh temporary directory if we're
+ # duplicating the vistrail
+ tmp_dir = None
+ else:
+ # otherwise, use the existing temp directory if one is set
+ tmp_dir = self.tmp_dir
+ (save_bundle, tmp_dir) = io.save_bundle_to_zip_xml(save_bundle, self._name, tmp_dir, version)
+ self.tmp_dir = tmp_dir
+ for obj in save_bundle.get_db_objs():
+ obj.locator = self
+ # Only remove the temporaries if save succeeded!
+ self.clean_temporaries()
+ return save_bundle
+
+ def close(self):
+ if self.tmp_dir is not None:
+ io.close_zip_xml(self.tmp_dir)
+ self.tmp_dir = None
+
+ ###########################################################################
+ # Operators
+
+ def __eq__(self, other):
+ if not isinstance(other, ZIPFileLocator):
+ return False
+ return self._name == other._name
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+ @staticmethod
+ def parse(element):
+ """ parse(element) -> ZIPFileLocator or None
+ Parse an XML object representing a locator and returns a
+ ZIPFileLocator object.
+
+ """
+ if str(element.getAttribute('type')) == 'file':
+ for n in element.childNodes:
+ if n.localName == "name":
+ filename = str(n.firstChild.nodeValue).strip(" \n\t")
+ return ZIPFileLocator(filename)
+ return None
+ else:
+ return None
+
+ #ElementTree port
+ @staticmethod
+ def from_xml(node):
+ """from_xml(node:ElementTree.Element) -> ZIPFileLocator or None
+ Parse an XML object representing a locator and returns a
+ ZIPFileLocator object."""
+ if node.tag != 'locator':
+ return None
+
+ #read attributes
+ data = node.get('type', '')
+ type = str(data)
+ if type == 'file':
+ for child in node.getchildren():
+ if child.tag == 'name':
+ filename = child.text.encode('latin-1').strip()
+ return ZIPFileLocator(filename)
+ return None
+ return None
+
+# class URLLocator(ZIPFileLocator):
+# def load(self, type):
+
+class DBLocator(BaseLocator):
+ cache = {}
+ cache_timestamps = {}
+ connections = {}
+ cache_connections = {}
+
+ def __init__(self, host, port, database, user, passwd, name=None,
+ **kwargs):
+ self._host = host
+ self._port = int(port)
+ self._db = database
+ self._user = user
+ self._passwd = passwd
+ self._name = name
+ self._hash = ''
+ self.kwargs = kwargs
+ self._obj_id = self.kwargs.get('obj_id', None)
+ self._obj_type = self.kwargs.get('obj_type', None)
+ self._conn_id = self.kwargs.get('connection_id', None)
+ self._vnode = self.kwargs.get('version_node', None)
+ self._vtag = self.kwargs.get('version_tag', None)
+ self._mshptrail = self.kwargs.get('mashuptrail', None)
+ if 'mashupVersion' in self.kwargs:
+ self._mshpversion = self.kwargs.get('mashupVersion', None)
+ else:
+ self._mshpversion = self.kwargs.get('mashup', None)
+ self._parameterexploration = self.kwargs.get('parameterExploration', None)
+
+ def _get_host(self):
+ return self._host
+ host = property(_get_host)
+
+ def _get_port(self):
+ return self._port
+ port = property(_get_port)
+
+ def _get_db(self):
+ return self._db
+ db = property(_get_db)
+
+ def _get_obj_id(self):
+ return self._obj_id
+ obj_id = property(_get_obj_id)
+
+ def _get_obj_type(self):
+ return self._obj_type
+ obj_type = property(_get_obj_type)
+
+ def _get_connection_id(self):
+ return self._conn_id
+ connection_id = property(_get_connection_id)
+
+ def _get_name(self):
+ return self._host + ':' + str(self._port) + ':' + self._db + ':' + \
+ str(self._name)
+ name = property(_get_name)
+
+ def _get_short_filename(self):
+ return str(self._name)
+ short_filename = property(_get_short_filename)
+
+ def _get_short_name(self):
+ name = self._name
+ if not isinstance(name, unicode):
+ name = name.decode('ascii')
+ return name
+ short_name = property(_get_short_name)
+
+ def hash(self):
+ node = self.to_xml()
+ xml_string = ElementTree.tostring(node)
+ #print "hash", xml_string
+ return hashlib.sha224(xml_string).hexdigest()
+
+ def is_valid(self):
+ if self._conn_id is not None \
+ and self._conn_id in DBLocator.connections:
+ return True
+ try:
+ self.get_connection()
+ except:
+ return False
+ return True
+
+ def get_connection(self):
+ if self._conn_id is not None \
+ and DBLocator.connections.has_key(self._conn_id):
+ connection = DBLocator.connections[self._conn_id]
+ if io.ping_db_connection(connection):
+ return connection
+ else:
+ if self._conn_id is None:
+ if DBLocator.cache_connections.has_key(self._hash):
+ connection = DBLocator.cache_connections[self._hash]
+ if io.ping_db_connection(connection):
+ debug.log("Reusing cached connection")
+ return connection
+
+ if len(DBLocator.connections.keys()) == 0:
+ self._conn_id = 1
+ else:
+ self._conn_id = max(DBLocator.connections.keys()) + 1
+ config = {'host': self._host,
+ 'port': self._port,
+ 'db': self._db,
+ 'user': self._user,
+ 'passwd': self._passwd}
+ #print "config:", config
+ connection = io.open_db_connection(config)
+
+ DBLocator.connections[self._conn_id] = connection
+ DBLocator.cache_connections[self._hash] = connection
+ return connection
+
+ def load(self, type, tmp_dir=None):
+ self._hash = self.hash()
+ #print "LLoad Big|type", type
+ if DBLocator.cache.has_key(self._hash):
+ save_bundle = DBLocator.cache[self._hash]
+ obj = save_bundle.get_primary_obj()
+
+ ts = self.get_db_modification_time(obj.vtType)
+ #debug.log("cached time: %s, db time: %s"%(DBLocator.cache_timestamps[self._hash],ts))
+ if DBLocator.cache_timestamps[self._hash] == ts:
+ #debug.log("using cached vistrail")
+ self._name = obj.db_name
+ # If thumbnail cache was cleared, get thumbs from db
+ if tmp_dir is not None:
+ for absfname in save_bundle.thumbnails:
+ if not os.path.isfile(absfname):
+ save_bundle.thumbnails = io.open_thumbnails_from_db(self.get_connection(), type, self.obj_id, tmp_dir)
+ break
+ return save_bundle
+ #debug.log("loading vistrail from db")
+ connection = self.get_connection()
+ if type == DBWorkflow.vtType:
+ return io.open_from_db(connection, type, self.obj_id)
+ save_bundle = io.open_bundle_from_db(type, connection, self.obj_id, tmp_dir)
+ primary_obj = save_bundle.get_primary_obj()
+ self._name = primary_obj.db_name
+ #print "locator db name:", self._name
+ for obj in save_bundle.get_db_objs():
+ obj.locator = self
+
+ _hash = self.hash()
+ DBLocator.cache[self._hash] = save_bundle.do_copy()
+ DBLocator.cache_timestamps[self._hash] = primary_obj.db_last_modified
+ return save_bundle
+
+ def save(self, save_bundle, do_copy=False, version=None):
+ connection = self.get_connection()
+ for obj in save_bundle.get_db_objs():
+ obj.db_name = self._name
+ save_bundle = io.save_bundle_to_db(save_bundle, connection, do_copy, version)
+ primary_obj = save_bundle.get_primary_obj()
+ self._obj_id = primary_obj.db_id
+ self._obj_type = primary_obj.vtType
+ for obj in save_bundle.get_db_objs():
+ obj.locator = self
+ #update the cache with a copy of the new bundle
+ self._hash = self.hash()
+ DBLocator.cache[self._hash] = save_bundle.do_copy()
+ DBLocator.cache_timestamps[self._hash] = primary_obj.db_last_modified
+ return save_bundle
+
+ def get_db_modification_time(self, obj_type=None):
+ if obj_type is None:
+ if self.obj_type is None:
+ obj_type = DBVistrail.vtType
+ else:
+ obj_type = self.obj_type
+
+ ts = io.get_db_object_modification_time(self.get_connection(),
+ self.obj_id,
+ obj_type)
+ ts = datetime(*strptime(str(ts).strip(), '%Y-%m-%d %H:%M:%S')[0:6])
+ return ts
+
+ def serialize(self, dom, element):
+ """serialize(dom, element) -> None
+ Convert this object to an XML representation.
+
+ """
+ locator = dom.createElement('locator')
+ locator.setAttribute('type', 'db')
+ locator.setAttribute('host', str(self._host))
+ locator.setAttribute('port', str(self._port))
+ locator.setAttribute('db', str(self._db))
+ locator.setAttribute('vt_id', str(self._obj_id))
+ node = dom.createElement('name')
+ filename = dom.createTextNode(str(self._name))
+ node.appendChild(filename)
+ locator.appendChild(node)
+ element.appendChild(locator)
+
+ @staticmethod
+ def parse(element):
+ """ parse(element) -> DBFileLocator or None
+ Parse an XML object representing a locator and returns a
+ DBFileLocator object.
+
+ """
+ if str(element.getAttribute('type')) == 'db':
+ host = str(element.getAttribute('host'))
+ port = int(element.getAttribute('port'))
+ database = str(element.getAttribute('db'))
+ vt_id = str(element.getAttribute('vt_id'))
+ user = ""
+ passwd = ""
+ for n in element.childNodes:
+ if n.localName == "name":
+ name = str(n.firstChild.nodeValue).strip(" \n\t")
+ #print host, port, database, name, vt_id
+ return DBLocator(host, port, database,
+ user, passwd, name, vt_id, None)
+ return None
+ else:
+ return None
+
+ @staticmethod
+ def from_url(url):
+ format = re.compile(
+ r"^"
+ "([a-zA-Z0-9_-]+)://" # scheme
+ "(?:"
+ "([^:@]+)" # user name
+ "(?:([^:@]+))?" # password
+ "@)?"
+ "([^/]+)" # net location
+ "/([^?]+)" # database name
+ "(?:\?(.+))?" # query arguments
+ "$")
+ match = format.match(url)
+ if match is None:
+ return ValueError
+ else:
+ scheme, user, passwd, net_loc, db_name, args_str = match.groups('')
+ if ':' in net_loc:
+ host, port = net_loc.rsplit(':', 1)
+ else:
+ host, port = net_loc, None
+ db_name = urllib.unquote(str(db_name))
+ kwargs = BaseLocator.parse_args(args_str)
+ return DBLocator(host, port, db_name, user, passwd, **kwargs)
+
+ def to_url(self):
+ # FIXME may also want to allow database type to be encoded in
+ # scheme (ie mysql://host/db, sqlite3://path/to)
+ net_loc = '%s:%s' % (self._host, self._port)
+ args_str = BaseLocator.generate_args(self.kwargs)
+ # query_str = '%s=%s' % (self._obj_type, self._obj_id)
+ url_tuple = ('db', net_loc, urllib.quote(self._db, ''), args_str, '')
+ return urlparse.urlunsplit(url_tuple)
+
+ #ElementTree port
+ def to_xml(self, node=None, include_name = False):
+ """to_xml(node: ElementTree.Element) -> ElementTree.Element
+ Convert this object to an XML representation.
+ """
+ if node is None:
+ node = ElementTree.Element('locator')
+
+ node.set('type', 'db')
+ node.set('host', str(self._host))
+ node.set('port', str(self._port))
+ node.set('db', str(self._db))
+ node.set('vt_id', str(self._obj_id))
+ node.set('user', str(self._user))
+ if include_name:
+ childnode = ElementTree.SubElement(node,'name')
+ childnode.text = str(self._name)
+ return node
+
+ @staticmethod
+ def from_xml(node, include_name=False):
+ """from_xml(node:ElementTree.Element) -> DBLocator or None
+ Parse an XML object representing a locator and returns a
+ DBLocator object."""
+
+ def convert_from_str(value,type):
+ def bool_conv(x):
+ s = str(x).upper()
+ if s == 'TRUE':
+ return True
+ if s == 'FALSE':
+ return False
+
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'bool':
+ return bool_conv(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ if node.tag != 'locator':
+ return None
+
+ #read attributes
+ data = node.get('type', '')
+ type = convert_from_str(data, 'str')
+
+ if type == 'db':
+ data = node.get('host', None)
+ host = convert_from_str(data, 'str')
+ data = node.get('port', None)
+ port = convert_from_str(data,'int')
+ data = node.get('db', None)
+ database = convert_from_str(data,'str')
+ data = node.get('vt_id')
+ vt_id = convert_from_str(data, 'str')
+ data = node.get('user')
+ user = convert_from_str(data, 'str')
+ passwd = ""
+ name = None
+ if include_name:
+ for child in node.getchildren():
+ if child.tag == 'name':
+ name = str(child.text).strip(" \n\t")
+ return DBLocator(host, port, database,
+ user, passwd, name, obj_id=vt_id, obj_type='vistrail')
+ else:
+ return None
+
+ def __str__(self):
+ return '<DBLocator host="%s" port="%s" database="%s" vistrail_id="%s" \
+vistrail_name="%s"/>' % ( self._host, self._port, self._db,
+ self._obj_id, self._name)
+
+ ###########################################################################
+ # Operators
+
+ def __eq__(self, other):
+ if type(other) != type(self):
+ return False
+ return (self._host == other._host and
+ self._port == other._port and
+ self._db == other._db and
+ self._user == other._user and
+ #self._name == other._name and
+ long(self._obj_id) == long(other._obj_id) and
+ self._obj_type == other._obj_type)
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+
+import unittest
+
+class TestLocators(unittest.TestCase):
+ if not hasattr(unittest.TestCase, 'assertIsInstance'):
+ def assertIsInstance(self, obj, cls, msg=None):
+ assert(isinstance(obj, cls))
+ def assertIsNone(self, obj):
+ self.assertEqual(obj, None)
+
+ @staticmethod
+ def path2url(fname):
+ path = os.path.abspath(fname)
+ path = path.replace(os.sep, '/')
+ if path.startswith('/'):
+ path = path[1:]
+ return "file:///%s" % urllib.quote(path, '/:')
+
+ def test_convert_filename(self):
+ # Test both systemTypes
+ global systemType
+ old_systemType = systemType
+ # Don't use abspath, it would cause Linux tests to fail on Windows
+ # we are using abspaths anyway
+ old_abspath = os.path.abspath
+ os.path.abspath = lambda x: x
+ try:
+ systemType = 'Linux'
+ self.assertEqual(
+ BaseLocator.convert_filename_to_url(
+ '/a dir/test.vt?v=a\xE9&b'),
+ 'file:///a%20dir/test.vt?v=a%E9&b')
+ systemType = 'Windows'
+ self.assertEqual(
+ BaseLocator.convert_filename_to_url(
+ 'C:\\a dir\\test.vt?v=a\xE9&b'),
+ 'file:///C:/a%20dir/test.vt?v=a%E9&b')
+ finally:
+ systemType = old_systemType
+ os.path.abspath = old_abspath
+
+ def test_parse_untitled(self):
+ loc_str = "untitled:e78394a73b87429e952b71b858e03242?workflow=42"
+ loc = BaseLocator.from_url(loc_str)
+ self.assertIsInstance(loc, UntitledLocator)
+ self.assertEqual(loc.kwargs['version_node'], 42)
+ self.assertEqual(loc._uuid,
+ uuid.UUID('e78394a73b87429e952b71b858e03242'))
+ self.assertEqual(loc.to_url(), loc_str)
+
+ def test_untitled_no_uuid(self):
+ loc_str = "untitled:"
+ loc = BaseLocator.from_url(loc_str)
+ self.assertIsInstance(loc, UntitledLocator)
+ # make sure it adds a uuid
+ self.assertEqual(len(loc.to_url()), 41)
+
+ def test_parse_zip_file(self):
+ loc_str = self.path2url(
+ "/vistrails/tmp/test_parse_zip_file \xE9 \xEA.vt")
+ loc_str += "?workflow=abc"
+ loc = BaseLocator.from_url(loc_str)
+ self.assertIsInstance(loc, ZIPFileLocator)
+ self.assertEqual(loc.kwargs['version_tag'], "abc")
+ self.assertEqual(loc.short_filename, "test_parse_zip_file \xE9 \xEA")
+ self.assertEqual(loc.to_url(), loc_str)
+
+ def test_parse_zip_file_no_scheme(self):
+ loc_str = os.path.abspath(
+ "../tmp/test_parse_zip_file_no_scheme \xE9 \xEA.vt")
+ loc_str += "?workflow=abc"
+ loc = BaseLocator.from_url(loc_str)
+ self.assertIsInstance(loc, ZIPFileLocator)
+ self.assertEqual(loc.kwargs['version_tag'], "abc")
+ self.assertEqual(loc.short_filename,
+ "test_parse_zip_file_no_scheme \xE9 \xEA")
+ loc_str = loc_str.replace(os.sep, '/')
+ if loc_str[0] == '/':
+ loc_str = loc_str[1:]
+ loc_str = "file:///%s" % urllib.quote(loc_str, '/:?=')
+ self.assertEqual(loc.to_url(), loc_str)
+
+ def test_parse_xml_file(self):
+ loc_str = self.path2url(
+ "/vistrails/tmp/test_parse_xml_file \xE9 \xEA.xml")
+ loc = BaseLocator.from_url(loc_str)
+ self.assertIsInstance(loc, XMLFileLocator)
+ self.assertEqual(loc.short_filename, "test_parse_xml_file \xE9 \xEA")
+ self.assertEqual(loc.to_url(), loc_str)
+
+ def test_short_names(self):
+ enc = sys.getfilesystemencoding() or locale.getpreferredencoding()
+ if (enc.lower() not in ('mbcs', 'utf-8', 'utf8',
+ 'latin-1', 'iso-8859-1', 'iso-8859-15')):
+ self.skipTest("unusual encoding on this system: %r" % enc)
+ if enc.lower() in ('mbcs', 'latin-1', 'iso-8859-1', 'iso-8859-15'):
+ fname = "test_short_names \xE9 \xEA"
+ elif enc.lower() in ('utf8', 'utf-8'):
+ fname = "test_short_names \xC3\xA9 \xC3\xAA"
+ else:
+ self.skipTest("unusual encoding on this system: %r" % enc)
+ loc = BaseLocator.from_url("../%s.xml" % fname)
+ self.assertEqual(loc.short_filename, fname)
+ self.assertEqual(loc.short_name, u"test_short_names \xE9 \xEA")
+
+ def test_win_xml_file(self):
+ try:
+ import ntpath
+ import nturl2path
+ except ImportError:
+ return self.skipTest("Do not have ntpath or nturl2path installed.")
+
+ global systemType
+ old_sys_type = systemType
+ old_path = os.path
+ old_pathname2url = urllib.pathname2url
+ old_url2pathname = urllib.url2pathname
+ systemType = 'Windows'
+ os.path = ntpath
+ urllib.pathname2url = nturl2path.pathname2url
+ urllib.url2pathname = nturl2path.url2pathname
+ try:
+ loc_str = "C:\\vt?dir\\tmp\\test_win_xml_file.xml?workflow=3"
+ loc = BaseLocator.from_url(loc_str)
+ self.assertIsInstance(loc, XMLFileLocator)
+ self.assertEqual(loc.short_filename, "test_win_xml_file")
+ self.assertEqual(loc.kwargs['version_node'], 3)
+ self.assertEqual(
+ loc.to_url(),
+ "file:///C:/vt%3Fdir/tmp/test_win_xml_file.xml?workflow=3")
+ finally:
+ systemType = old_sys_type
+ os.path = old_path
+ urllib.pathname2url = old_pathname2url
+ urllib.url2pathname = old_url2pathname
+
+ def test_parse_db(self):
+ loc_str = "db://localhost:3306/vistrails?workflow=42"
+ loc = BaseLocator.from_url(loc_str)
+ self.assertIsInstance(loc, DBLocator)
+ self.assertEqual(loc.kwargs['version_node'], 42)
+ self.assertEqual(loc._host, "localhost")
+ self.assertEqual(loc._port, 3306)
+ self.assertEqual(loc._db, "vistrails")
+ self.assertEqual(loc.to_url(), loc_str)
+
+ def test_parse_bad_url(self):
+ loc_str = "http://blah.com/"
+ loc = BaseLocator.from_url(loc_str)
+ self.assertIsNone(loc)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/db/services/log.py b/vistrails/db/services/log.py
new file mode 100644
index 0000000..d5df8e6
--- /dev/null
+++ b/vistrails/db/services/log.py
@@ -0,0 +1,45 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBWorkflowExec
+
+def update_id_scope(log):
+ if hasattr(log, 'update_id_scope'):
+ log.update_id_scope()
+ else:
+ pass
+
+def update_ids(log):
+ for workflow_exec in log.db_workflow_execs:
+ workflow_exec.db_id = log.id_scope.getNewId(DBWorkflowExec.vtType)
diff --git a/vistrails/db/services/opm.py b/vistrails/db/services/opm.py
new file mode 100644
index 0000000..d5d00a9
--- /dev/null
+++ b/vistrails/db/services/opm.py
@@ -0,0 +1,780 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+import sys
+from vistrails.core.system import get_vistrails_default_pkg_prefix, \
+ get_vistrails_basic_pkg_id
+import vistrails.db.services.io
+from vistrails.db.domain import DBOpmProcess, DBOpmArtifact, DBOpmUsed, \
+ DBOpmWasGeneratedBy, DBOpmProcessIdCause, DBOpmProcessIdEffect, \
+ DBOpmArtifactIdCause, DBOpmArtifactIdEffect, DBOpmRole, DBOpmAccountId, \
+ DBOpmAccount, DBOpmAccounts, DBOpmGraph, DBOpmArtifacts, \
+ DBOpmDependencies, DBOpmProcesses, DBOpmProcessValue, DBOpmArtifactValue, \
+ IdScope, DBGroupExec, DBLoopExec, DBModuleExec, DBOpmOverlaps, DBPort, \
+ DBConnection, DBGroup, DBPortSpec, DBOpmWasTriggeredBy, DBFunction, \
+ DBParameter
+from vistrails.db.services.vistrail import materializeWorkflow
+
+sys.path.append('/vistrails/src/trunk/vistrails')
+
+def create_process(item_exec, account, id_scope):
+ return DBOpmProcess(id='p' + str(id_scope.getNewId(DBOpmProcess.vtType)),
+ value=DBOpmProcessValue(item_exec),
+ accounts=[DBOpmAccountId(id=account.db_id)])
+
+def create_process_manual(p_str, account, id_scope):
+ item_exec = DBModuleExec(id=-1,
+ module_name=p_str,
+ module_id=-1,
+ completed=1,
+ )
+ return DBOpmProcess(id='p' + str(id_scope.getNewId(DBOpmProcess.vtType)),
+ value=DBOpmProcessValue(item_exec),
+ accounts=[DBOpmAccountId(id=account.db_id)])
+
+def create_artifact_from_filename(filename, account, id_scope):
+ parameter = DBParameter(id=-1,
+ pos=0,
+ type='%s:File' % get_vistrails_basic_pkg_id(),
+ val=filename)
+ function = DBFunction(id=-1,
+ name="file",
+ pos=0,
+ parameters=[parameter])
+ return DBOpmArtifact(id='a' + str(id_scope.getNewId(DBOpmArtifact.vtType)),
+ value=DBOpmArtifactValue(function),
+ accounts=[DBOpmAccountId(id=account.db_id)])
+
+def create_artifact_from_db_tuple(db_tuple, account, id_scope):
+ parameters = []
+ for db_str in db_tuple:
+ parameter = DBParameter(id=-1,
+ pos=0,
+ type='%s:String' % get_vistrails_basic_pkg_id(),
+ val=db_str)
+ parameters.append(parameter)
+ function = DBFunction(id=-1,
+ name="dbEntry",
+ pos=0,
+ parameters=parameters)
+ return DBOpmArtifact(id='a' + str(id_scope.getNewId(DBOpmArtifact.vtType)),
+ value=DBOpmArtifactValue(function),
+ accounts=[DBOpmAccountId(id=account.db_id)])
+
+def create_artifact_from_function(function, account, id_scope):
+ return DBOpmArtifact(id='a' + str(id_scope.getNewId(DBOpmArtifact.vtType)),
+ value=DBOpmArtifactValue(function),
+ accounts=[DBOpmAccountId(id=account.db_id)])
+
+def create_artifact_from_port_spec(port_spec, account, id_scope):
+ return DBOpmArtifact(id='a' + str(id_scope.getNewId(DBOpmArtifact.vtType)),
+ value=DBOpmArtifactValue(port_spec),
+ accounts=[DBOpmAccountId(id=account.db_id)])
+
+def create_used(process, artifact, account, id_scope):
+ return DBOpmUsed(effect=DBOpmProcessIdEffect(id=process.db_id),
+ role=DBOpmRole(value="in"),
+ cause=DBOpmArtifactIdCause(id=artifact.db_id),
+ accounts=[DBOpmAccountId(id=account.db_id)])
+
+def create_was_generated_by(artifact, process, account, id_scope):
+ return DBOpmWasGeneratedBy(effect=DBOpmArtifactIdEffect(id=artifact.db_id),
+ role=DBOpmRole(value="out"),
+ cause=DBOpmProcessIdCause(id=process.db_id),
+ accounts=[DBOpmAccountId(id=account.db_id)])
+
+def create_was_triggered_by(process1, process2, account, id_scope):
+ return DBOpmWasTriggeredBy(effect=DBOpmProcessIdEffect(id=process1.db_id),
+ role=DBOpmRole(value="control"),
+ cause=DBOpmProcessIdCause(id=process2.db_id),
+ accounts=[DBOpmAccountId(id=account.db_id)])
+
+def create_account(depth, id_scope):
+ account_id = id_scope.getNewId(DBOpmAccount.vtType)
+ account = DBOpmAccount(id='acct' + str(account_id),
+ value=str(depth))
+ return account
+
+def create_opm(workflow, version, log, reg):
+ id_scope = IdScope()
+ processes = []
+ # conn_artifacts = {}
+ artifacts = []
+ dependencies = []
+ accounts = []
+ depth_accounts = {}
+ file_artifacts = {}
+ db_artifacts = {}
+
+ def do_create_process(workflow, item_exec, account, module_processes):
+ process = create_process(item_exec, account, id_scope)
+ print 'adding process', process.db_id,
+ if hasattr(item_exec, 'db_module_name'):
+ print item_exec.db_module_name
+ elif hasattr(item_exec, 'db_group_nane'):
+ print item_exec.db_module_name
+ processes.append(process)
+ module = workflow.db_modules_id_index[item_exec.db_module_id]
+ module_processes[module.db_id] = (module, process)
+
+ def get_package(reg, pkg_identifier, pkg_version=''):
+ if not pkg_version:
+ # spin and get current package
+ for pkg in reg.db_packages:
+ if pkg.db_identifier == pkg_identifier:
+ break
+ pkg = None
+ else:
+ pkg = reg.db_packages_identifier_index[(pkg_identifier,
+ pkg_version)]
+ return pkg
+
+ def process_exec(item_exec, workflow, account, upstream_lookup,
+ downstream_lookup, depth, conn_artifacts=None,
+ function_artifacts=None, module_processes=None,
+ in_upstream_artifacts={}, in_downstream_artifacts={},
+ add_extras=False):
+
+ print 'in_upstream:', [(n, x.db_id)
+ for n, x_list in in_upstream_artifacts.iteritems() for x in x_list]
+ print 'in_downstream:', [(n, x.db_id)
+ for n, x_list in in_downstream_artifacts.iteritems() for x in x_list]
+ # FIXME merge conn_artifacts and function_artifacts
+ # problem is that a conn_artifact is OUTPUT while function_artifact
+ # is INPUT
+ if conn_artifacts is None:
+ conn_artifacts = {}
+ if function_artifacts is None:
+ function_artifacts = {}
+ if module_processes is None:
+ module_processes = {}
+# while item_exec.vtType == DBLoopExec.vtType:
+# item_exec = item_exec.db_item_execs[0]
+ (module, process) = module_processes[item_exec.db_module_id]
+
+ def process_connection(conn):
+ source = conn.db_ports_type_index['source']
+ source_t = (source.db_moduleId, source.db_name)
+ in_cache = False
+ print '!!! processing', source_t
+ if source_t in conn_artifacts:
+ artifact = conn_artifacts[source_t]
+ in_cache = True
+ else:
+ # key off source module and port name
+ # get descriptor from registry and then port_spec
+ # store port_spec as artifact
+
+ if source.db_moduleId < 0:
+ dest = conn.db_ports_type_index['destination']
+ module = source.db_module
+ else:
+ module = workflow.db_modules_id_index[source.db_moduleId]
+ print module.db_name, module.db_id
+
+ pkg = get_package(reg, module.db_package, module.db_version)
+
+ if not module.db_namespace:
+ module_namespace = ''
+ else:
+ module_namespace = module.db_namespace
+ module_desc = \
+ pkg.db_module_descriptors_name_index[(module.db_name,
+ module_namespace,
+ '')]
+ # FIXME make work for module port_specs, too
+ # for example, a PythonSource with a given port in
+ # module.db_portSpecs
+ port_spec = None
+ spec_t = (source.db_name, 'output')
+ if spec_t in module.db_portSpecs_name_index:
+ port_spec = module.db_portSpecs_name_index[spec_t]
+ while port_spec is None and \
+ module_desc.db_id != reg.db_root_descriptor_id:
+ if spec_t in module_desc.db_portSpecs_name_index:
+ port_spec = module_desc.db_portSpecs_name_index[spec_t]
+ base_id = module_desc.db_base_descriptor_id
+
+ # inefficient spin through db_packages but we do
+ # not have the descriptors_by_id index that exists
+ # on core.module_registry.ModuleRegistry here
+ module_desc = None
+ for pkg in reg.db_packages:
+ if base_id in pkg.db_module_descriptors_id_index:
+ module_desc = \
+ pkg.db_module_descriptors_id_index[base_id]
+ break
+ if module_desc is None:
+ raise KeyError("Cannot find base descriptor id %d" %
+ base_id)
+ # pkg = get_package(reg, module_desc.db_package,
+ # module_desc.db_package_version)
+ # module_desc = pkg.db_module_descriptors_id_index[base_id]
+ if port_spec is None:
+ port_spec = module_desc.db_portSpecs_name_index[spec_t]
+ print module_desc.db_name
+
+ artifact = \
+ create_artifact_from_port_spec(port_spec, account, id_scope)
+ artifacts.append(artifact)
+ print 'adding conn_artifact', artifact.db_id, source_t, \
+ source.db_moduleName
+ conn_artifacts[source_t] = artifact
+ return (artifact, in_cache)
+
+ def process_map(module, found_input_ports, found_output_ports):
+ print "*** Processing Map"
+ if depth+1 in depth_accounts:
+ account = depth_accounts[depth+1]
+ else:
+ account = create_account(depth+1, id_scope)
+ accounts.append(account)
+ depth_accounts[depth+1] = account
+
+ # need to have process that extracts artifacts for each iteration
+ input_list_artifact = found_input_ports['InputList']
+ result_artifact = found_output_ports.get('Result', None)
+ input_port_list = \
+ eval(found_input_ports['InputPort'].db_parameters[0].db_val)
+ output_port = \
+ found_input_ports['OutputPort'].db_parameters[0].db_val
+
+ s_process = create_process_manual('Split', account, id_scope)
+ processes.append(s_process)
+ dependencies.append(create_used(s_process,
+ input_list_artifact,
+ account,
+ id_scope))
+ # need to have process that condenses artifacts from each iteration
+ if result_artifact is not None:
+ j_process = create_process_manual('Join', account, id_scope)
+ processes.append(j_process)
+ for loop_exec in item_exec.db_loop_execs:
+ loop_up_artifacts = {}
+ loop_down_artifacts = {}
+ for input_name in input_port_list:
+ port_spec = DBPortSpec(id=-1,
+ name=input_name,
+ type='output')
+ s_artifact = \
+ create_artifact_from_port_spec(port_spec, account,
+ id_scope)
+ artifacts.append(s_artifact)
+ dependencies.append(create_was_generated_by(s_artifact,
+ s_process,
+ account,
+ id_scope))
+ if input_name not in loop_up_artifacts:
+ loop_up_artifacts[input_name] = []
+ loop_up_artifacts[input_name].append(s_artifact)
+
+ # process output_port
+ if loop_exec.db_completed == 1:
+ port_spec = DBPortSpec(id=-1,
+ name=output_port,
+ type='output')
+ o_artifact = \
+ create_artifact_from_port_spec(port_spec, account,
+ id_scope)
+ artifacts.append(o_artifact)
+ if output_port not in loop_down_artifacts:
+ loop_down_artifacts[output_port] = []
+ loop_down_artifacts[output_port].append(o_artifact)
+
+ if result_artifact is not None:
+ dependencies.append(create_used(j_process, o_artifact,
+ account, id_scope))
+
+ # now process a loop_exec
+ for child_exec in loop_exec.db_item_execs:
+ do_create_process(workflow, child_exec, account,
+ module_processes)
+ for child_exec in loop_exec.db_item_execs:
+ process_exec(child_exec, workflow, account, upstream_lookup,
+ downstream_lookup, depth+1, conn_artifacts,
+ function_artifacts, module_processes,
+ loop_up_artifacts, loop_down_artifacts, True)
+
+ # need to set Return artifact and connect j_process to it
+ if result_artifact is not None:
+ dependencies.append(create_was_generated_by(result_artifact,
+ j_process,
+ account,
+ id_scope))
+
+ def process_group(module, found_input_ports, found_output_ports):
+ # identify depth and create new account if necessary
+ # recurse with new account
+ # need to link to upstream and downstream correctly
+ workflow = module.db_workflow
+ # run the whole upstream construction, etc, using this exec
+ # and the group's workflow
+ if depth+1 in depth_accounts:
+ account = depth_accounts[depth+1]
+ else:
+ account = create_account(depth+1, id_scope)
+ accounts.append(account)
+ depth_accounts[depth+1] = account
+ process_workflow(workflow, item_exec, account,
+ out_upstream_artifacts,
+ out_downstream_artifacts, depth+1)
+
+ def process_port_module(module, found_input_ports, found_output_ports):
+ port_name = found_input_ports['name'].db_parameters[0].db_val
+ if module.db_name == 'InputPort':
+ if port_name in in_upstream_artifacts:
+ for artifact in in_upstream_artifacts[port_name]:
+ dependencies.append(create_used(process, artifact,
+ account, id_scope))
+ elif module.db_name == 'OutputPort':
+ if port_name in in_downstream_artifacts:
+ for artifact in in_downstream_artifacts[port_name]:
+ dependencies.append(create_was_generated_by(artifact,
+ process,
+ account,
+ id_scope))
+
+ def process_if_module(module, found_input_ports, found_output_ports):
+ print 'processing IFFFF'
+ # need to decide which path was taken?
+ # check which module was executed, then know which branch was
+ # taken?
+ true_conn = found_input_ports['TruePort']
+ false_conn = found_input_ports['FalsePort']
+ true_id = true_conn.db_ports_type_index['source'].db_moduleId
+ false_id = false_conn.db_ports_type_index['source'].db_moduleId
+ print '$$ TRUE ID:', true_id
+ print '$$ FALSE ID:', false_id
+ for x,y in module_processes.iteritems():
+ print x, ':', y
+ if true_id in module_processes:
+ cond_process = module_processes[true_id][1]
+ elif false_id in module_processes:
+ cond_process = module_processes[false_id][1]
+ else:
+ raise RuntimeError("cannot process if")
+ # FIXME: assume true for now
+ # eventually need to check which module_id was execed for this
+ # current item exec
+ dependencies.append(create_was_triggered_by(cond_process,
+ process,
+ account,
+ id_scope))
+
+ if add_extras:
+ print '***adding extras'
+ out_upstream_artifacts = copy.copy(in_upstream_artifacts)
+ out_downstream_artifacts = copy.copy(in_downstream_artifacts)
+ for port_name, artifact_list in in_upstream_artifacts.iteritems():
+ for artifact in artifact_list:
+ dependencies.append(create_used(process, artifact,
+ account, id_scope))
+ for port_name, artifact_list in in_downstream_artifacts.iteritems():
+ for artifact in artifact_list:
+ # conn_artifacts[(port_name, 'output')] = artifact
+ dependencies.append(create_was_generated_by(artifact,
+ process,
+ account,
+ id_scope))
+ else:
+ out_upstream_artifacts = {}
+ out_downstream_artifacts = {}
+
+
+ ctrl_flow_pkg = '%s.control_flow' % get_vistrails_default_pkg_prefix()
+ basic_pkg = get_vistrails_basic_pkg_id()
+ all_special_ports = {'%s:Map' % ctrl_flow_pkg:
+ [{'InputPort': False,
+ 'OutputPort': False,
+ 'InputList': True,
+ 'FunctionPort': False},
+ {'Result': True},
+ process_map],
+ '%s:Group' % basic_pkg:
+ [{},
+ {},
+ process_group],
+ '%s:InputPort' % basic_pkg:
+ [{'name': False,
+ 'spec': False,
+ 'old_name': False},
+ {},
+ process_port_module],
+ '%s:OutputPort' % basic_pkg:
+ [{'name': False,
+ 'spec': False,
+ 'old_name': False},
+ {},
+ process_port_module],
+ '%s:If' % ctrl_flow_pkg:
+ [{'TruePort': False,
+ 'FalsePort': False},
+ {},
+ process_if_module],
+ }
+
+ module_desc_str = module.db_package + ':' + module.db_name
+ special_ports = all_special_ports.get(module_desc_str, [{}, {}, None])
+ found_input_ports = {}
+ found_output_ports = {}
+
+ # process used_files annotations
+ # process generated_tables annotations:
+ for annotation in item_exec.db_annotations:
+ def process_db_tuple(db_tuple):
+ db_tuple = (str(db_tuple[0]),) + db_tuple[1:]
+ if db_tuple not in db_artifacts:
+ artifact = create_artifact_from_db_tuple(db_tuple,
+ account,
+ id_scope)
+ artifacts.append(artifact)
+ db_artifacts[db_tuple] = artifact
+ else:
+ artifact = db_artifacts[db_tuple]
+ if int(artifact.db_accounts[0].db_id[4:]) > \
+ int(account.db_id[4:]):
+ artifact.db_accounts[0] = account
+ return artifact
+
+ if annotation.db_key == 'used_files':
+ used_files = eval(annotation.db_value)
+ for fname in used_files:
+ if fname not in file_artifacts:
+ artifact = create_artifact_from_filename(fname,
+ account,
+ id_scope)
+ artifacts.append(artifact)
+ file_artifacts[fname] = artifact
+ else:
+ artifact = file_artifacts[fname]
+ if int(artifact.db_accounts[0].db_id[4:]) > \
+ int(account.db_id[4:]):
+ artifact.db_accounts[0] = account
+ dependencies.append(create_used(process, artifact,
+ account, id_scope))
+ elif annotation.db_key == 'generated_tables':
+ generated_tables = eval(annotation.db_value)
+ for db_tuple in generated_tables:
+ artifact = process_db_tuple(db_tuple)
+ dependencies.append(create_was_generated_by(artifact,
+ process,
+ account,
+ id_scope))
+ elif annotation.db_key == 'used_tables':
+ used_tables = eval(annotation.db_value)
+ for db_tuple in used_tables:
+ artifact = process_db_tuple(db_tuple)
+ dependencies.append(create_used(process, artifact,
+ account, id_scope))
+
+ # process functions
+ for function in module.db_functions:
+ # FIXME let found_input_ports, found_output_ports store lists?
+ if function.db_name in special_ports[0]:
+ if not special_ports[0][function.db_name]:
+ found_input_ports[function.db_name] = function
+ continue
+ function_t = (module.db_id, function.db_name)
+ if function_t in function_artifacts:
+ artifact = function_artifacts[function_t]
+ if int(artifact.db_accounts[0].db_id[4:]) > \
+ int(account.db_id[4:]):
+ artifact.db_accounts[0] = account
+ else:
+ artifact = create_artifact_from_function(function,
+ account,
+ id_scope)
+ print 'adding artifact', artifact.db_id
+ artifacts.append(artifact)
+ function_artifacts[function_t] = artifact
+ if function.db_name in special_ports[0]:
+ found_input_ports[function.db_name] = artifact
+ if function.db_name not in out_upstream_artifacts:
+ out_upstream_artifacts[function.db_name] = []
+ out_upstream_artifacts[function.db_name].append(artifact)
+ dependencies.append(create_used(process, artifact, account,
+ id_scope))
+
+ # process connections
+ if module.db_id in upstream_lookup:
+ for conns in upstream_lookup[module.db_id].itervalues():
+ for conn in conns:
+ dest = conn.db_ports_type_index['destination']
+ if dest.db_name in special_ports[0]:
+ if not special_ports[0][dest.db_name]:
+ found_input_ports[dest.db_name] = conn
+ continue
+ (artifact, in_cache) = process_connection(conn)
+ if dest.db_name in special_ports[0]:
+ found_input_ports[dest.db_name] = artifact
+ if dest.db_name not in out_upstream_artifacts:
+ out_upstream_artifacts[dest.db_name] = []
+ out_upstream_artifacts[dest.db_name].append(artifact)
+ print 'adding dependency (pa)', process.db_id, \
+ artifact.db_id
+ dependencies.append(create_used(process, artifact,
+ account, id_scope))
+
+ if item_exec.db_completed == 1:
+ if module.db_id in downstream_lookup:
+ # check if everything completed successfully for this?
+ for conns in downstream_lookup[module.db_id].itervalues():
+ for conn in conns:
+ source = conn.db_ports_type_index['source']
+ if source.db_name in special_ports[1]:
+ if not special_ports[1][source.db_name]:
+ found_output_ports[source.db_name] = conn
+ continue
+ dest = conn.db_ports_type_index['destination']
+ dest_module = \
+ workflow.db_modules_id_index[dest.db_moduleId]
+ dest_desc_str = dest_module.db_package + ':' + \
+ dest_module.db_name
+ dest_special_ports = all_special_ports.get(dest_desc_str,
+ [{}, {}, None])
+ if dest.db_name in dest_special_ports[0] and \
+ not dest_special_ports[0][dest.db_name]:
+ print 'skipping', dest.db_name
+ continue
+ (artifact, in_cache) = process_connection(conn)
+ if not in_cache:
+ if source.db_name in special_ports[1]:
+ found_output_ports[source.db_name] = artifact
+ if source.db_name not in out_downstream_artifacts:
+ out_downstream_artifacts[source.db_name] = []
+ out_downstream_artifacts[source.db_name].append(artifact)
+ print 'adding dependency (ap)', artifact.db_id, \
+ process.db_id
+ dependencies.append(create_was_generated_by(artifact,
+ process,
+ account,
+ id_scope))
+
+ if special_ports[2] is not None:
+ special_ports[2](module, found_input_ports, found_output_ports)
+
+ def process_workflow(workflow, parent_exec, account, upstream_artifacts={},
+ downstream_artifacts={}, depth=0, top_version=False):
+ # create process for each module_exec
+ # for each module, find parameters and upstream connections
+ # tie them in
+ # each connection's source port is
+ # associated with a transient data item
+ # use wasDerivedBy and used relationships to tie things together
+ # check run-time annotations?
+ print 'processing workflow', parent_exec
+
+ upstream_lookup = {}
+ downstream_lookup = {}
+ for connection in workflow.db_connections:
+ source = connection.db_ports_type_index['source']
+ if source.db_moduleId not in downstream_lookup:
+ downstream_lookup[source.db_moduleId] = {}
+ if source.db_name not in downstream_lookup[source.db_moduleId]:
+ downstream_lookup[source.db_moduleId][source.db_name] = []
+ downstream_lookup[source.db_moduleId][source.db_name].append(connection)
+
+ dest = connection.db_ports_type_index['destination']
+ if dest.db_moduleId not in upstream_lookup:
+ upstream_lookup[dest.db_moduleId] = {}
+ if dest.db_name not in upstream_lookup[dest.db_moduleId]:
+ upstream_lookup[dest.db_moduleId][dest.db_name] = []
+ upstream_lookup[dest.db_moduleId][dest.db_name].append(connection)
+
+ conn_artifacts = {}
+ function_artifacts = {}
+ module_processes = {}
+ print ' upstream_lookup:'
+ lookup = upstream_lookup
+ for id, name_list in lookup.iteritems():
+ print ' ', id, ':', name_list.keys()
+
+ print ' downstream_lookup:'
+ lookup = downstream_lookup
+ for id, name_list in lookup.iteritems():
+ print ' ', id, ':', name_list.keys()
+
+ # print ' upstream_lookup:', upstream_lookup
+ # print ' downstream_lookup:', downstream_lookup
+ if top_version:
+ for workflow_exec in parent_exec.db_workflow_execs:
+ if workflow_exec.db_parent_version != version:
+ continue
+ conn_artifacts = {}
+ function_artifacts = {}
+ module_processes = {}
+ upstream_artifacts = {}
+ downstream_artifacts = {}
+ for item_exec in workflow_exec.db_item_execs:
+ do_create_process(workflow, item_exec, account,
+ module_processes)
+ for item_exec in workflow_exec.db_item_execs:
+ process_exec(item_exec, workflow, account,
+ upstream_lookup, downstream_lookup,
+ depth, conn_artifacts, function_artifacts,
+ module_processes,
+ upstream_artifacts, downstream_artifacts)
+ else:
+ for item_exec in parent_exec.db_item_execs:
+ do_create_process(workflow, item_exec, account,
+ module_processes)
+ for item_exec in parent_exec.db_item_execs:
+ process_exec(item_exec, workflow, account, upstream_lookup,
+ downstream_lookup, depth, conn_artifacts,
+ function_artifacts, module_processes,
+ upstream_artifacts, downstream_artifacts)
+
+ account_id = id_scope.getNewId(DBOpmAccount.vtType)
+ account = DBOpmAccount(id='acct' + str(account_id),
+ value=str(0))
+ accounts.append(account)
+ depth_accounts[0] = account
+ process_workflow(workflow, log, account, {}, {}, 0, True)
+
+ #print processes
+ #print dependencies
+ max_depth = max(depth_accounts)
+ def add_finer_depths(objs, exclude_groups=False, exclude_deps=False,
+ p_ids=set()):
+ new_p_ids = []
+ for obj in objs:
+ can_update=True
+ if exclude_groups:
+ if obj.db_value.db_value.vtType == DBGroupExec.vtType:
+ new_p_ids.append(obj.db_id)
+ can_update = False
+ elif obj.db_value.db_value.vtType == DBModuleExec.vtType and \
+ len(obj.db_value.db_value.db_loop_execs) > 0:
+ new_p_ids.append(obj.db_id)
+ can_update = False
+
+ if exclude_deps:
+ if ((obj.vtType == DBOpmWasGeneratedBy.vtType and
+ obj.db_cause.db_id in p_ids) or
+ (obj.vtType == DBOpmUsed.vtType and
+ obj.db_effect.db_id in p_ids)):
+ can_update = False
+ if can_update:
+ min_depth = int(obj.db_accounts[0].db_id[4:])
+ for i in xrange(min_depth+1, max_depth+1):
+ obj.db_add_account(DBOpmAccountId(id='acct' + str(i)))
+ return new_p_ids
+
+ # FIXME: also exclude group dependencies (used, wasGeneratedBy)...
+ p_ids = add_finer_depths(processes, True)
+ print p_ids
+ add_finer_depths(artifacts)
+ add_finer_depths(dependencies, False, True, set(p_ids))
+
+ overlaps = []
+ for i in xrange(max_depth+1):
+ for j in xrange(i+1, max_depth+1):
+ ids = [DBOpmAccountId(id='acct' + str(i)),
+ DBOpmAccountId(id='acct' + str(j))]
+ overlaps.append(DBOpmOverlaps(opm_account_ids=ids))
+
+ opm_graph = DBOpmGraph(accounts=DBOpmAccounts(accounts=accounts,
+ opm_overlapss=overlaps),
+ processes=DBOpmProcesses(processs=processes),
+ artifacts=\
+ DBOpmArtifacts(artifacts=artifacts),
+ dependencies=\
+ DBOpmDependencies(dependencys=dependencies),
+ )
+ return opm_graph
+
+def add_module_descriptor_index(registry):
+ registry.db_module_descriptors_id_index = {}
+ for package in registry.db_packages:
+ for module_descriptor in package.db_module_descriptors:
+ registry.db_module_descriptors_id_index[module_descriptor.db_id] =\
+ module_descriptor
+
+def add_group_portSpecs_index(workflow):
+ basic_pkg = get_vistrails_basic_pkg_id()
+ def process_group(group):
+ def get_port_name(module):
+ port_name = None
+ for function in module.db_functions:
+ if function.db_name == 'name':
+ port_name = function.db_parameters[0].db_val
+ return port_name
+ g_workflow = group.db_workflow
+ group.db_portSpecs_name_index = {}
+ for module in g_workflow.db_modules:
+ if module.db_name == 'InputPort' and module.db_package == basic_pkg:
+ port_name = get_port_name(module)
+ # FIXME add sigstring to DBPortSpec
+ group.db_portSpecs_name_index[(port_name, 'input')] = \
+ DBPortSpec(id=-1,
+ name=port_name,
+ type='input')
+ elif module.db_name == 'OutputPort' and \
+ module.db_package == basic_package:
+ port_name = get_port_name(module)
+ # FIXME add sigstring to DBPortSpec
+ group.db_portSpecs_name_index[(port_name, 'output')] = \
+ DBPortSpec(id=-1,
+ name=port_name,
+ type='output')
+ elif module.db_name == 'Group' and module.db_package == basic_pkg:
+ process_group(module)
+
+ for module in workflow.db_modules:
+ if module.vtType == DBGroup.vtType:
+ process_group(module)
+
+def create_opm_from_vistrail(vistrail, version, log, registry):
+ workflow = materializeWorkflow(vistrail, version)
+ add_group_portSpecs_index(workflow)
+ add_module_descriptor_index(registry)
+ return create_opm(workflow, version, log, registry)
+
+def run(vistrail_xml, version, log_xml, registry_xml, output_fname):
+ from vistrails.db.persistence import DAOList
+
+ vistrail = vistrails.db.services.io.open_vistrail_from_xml(vistrail_xml)
+ log = vistrails.db.services.io.open_log_from_xml(log_xml)
+ registry = vistrails.db.services.io.open_registry_from_xml(registry_xml)
+ opm_graph = create_opm_from_vistrail(vistrail, int(version), log, registry)
+ dao_list = DAOList()
+ dao_list.save_to_xml(opm_graph, output_fname, {})
+
+if __name__ == '__main__':
+ if len(sys.argv) < 5:
+ print "Usage: python %s <vt_xml> <version> <log_xml> <registry_xml> <out_xml>" % sys.argv[0]
+ sys.exit(1)
+ run(*sys.argv[1:])
+
diff --git a/vistrails/db/services/prov.py b/vistrails/db/services/prov.py
new file mode 100644
index 0000000..61999da
--- /dev/null
+++ b/vistrails/db/services/prov.py
@@ -0,0 +1,585 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+import sys
+import os
+#sys.path.append(os.getenv('VISTRAILS', ''))
+import vistrails.db.services.io
+from vistrails.db.domain import DBProvDocument, DBProvEntity, DBProvActivity, \
+ DBProvAgent, DBProvGeneration, DBProvUsage, DBProvAssociation, \
+ DBVtConnection, DBRefProvEntity, DBRefProvPlan, DBRefProvActivity, \
+ DBRefProvAgent, DBIsPartOf, IdScope, DBGroupExec, DBLoopExec, DBModuleExec, \
+ DBWorkflowExec, DBFunction, DBParameter, DBGroup, DBAbstraction
+from vistrails.db.services.vistrail import materializeWorkflow
+
+def create_prov_document(entities, activities, agents, connections, usages,
+ generations, associations):
+ return DBProvDocument(prov_entitys=entities,
+ prov_activitys=activities,
+ prov_agents=agents,
+ vt_connections=connections,
+ prov_usages=usages,
+ prov_generations=generations,
+ prov_associations=associations)
+
+def create_prov_entity_from_workflow(id_scope, workflow):
+ return DBProvEntity(id='e' + str(id_scope.getNewId(DBProvEntity.vtType)),
+ vt_id=workflow.db_id,
+ prov_type='prov:Plan',
+ prov_label=workflow._db_name,
+ prov_value=None,
+ vt_type='vt:workflow',
+ vt_desc=None,
+ vt_package=None,
+ vt_version=workflow._db_version,
+ vt_cache=None,
+ vt_location_x=None,
+ vt_location_y=None,
+ is_part_of=None)
+
+def create_prov_entity_from_module(id_scope, module, is_part_of):
+
+ # getting module label defined by the user
+ desc = None
+ for db_annotation in module.db_annotations:
+ if db_annotation._db_key == '__desc__':
+ desc = db_annotation._db_value
+ break
+
+ return DBProvEntity(id='e' + str(id_scope.getNewId(DBProvEntity.vtType)),
+ vt_id=module._db_id,
+ prov_type='prov:Plan',
+ prov_label=module.db_name,
+ prov_value=None,
+ vt_type='vt:module',
+ vt_desc=desc,
+ vt_package=module.db_package,
+ vt_version=module.db_version,
+ vt_cache=module.db_cache,
+ vt_location_x=module.db_location._db_x,
+ vt_location_y=module.db_location._db_y,
+ is_part_of=is_part_of)
+
+def create_is_part_of(prov_object):
+ return DBIsPartOf(prov_ref=prov_object._db_id)
+
+def create_prov_entity_from_group(id_scope, group, is_part_of):
+
+ # getting group label defined by the user
+ desc = None
+ for db_annotation in group.db_annotations:
+ if db_annotation._db_key == '__desc__':
+ desc = db_annotation._db_value
+ break
+
+ return DBProvEntity(id='e' + str(id_scope.getNewId(DBProvEntity.vtType)),
+ vt_id=group.db_id,
+ prov_type='prov:Plan',
+ prov_label=group.db_name,
+ prov_value=None,
+ vt_type='vt:group',
+ vt_desc=desc,
+ vt_package=None,
+ vt_version=None,
+ vt_cache=group.db_cache,
+ vt_location_x=group.db_location._db_x,
+ vt_location_y=group.db_location._db_y,
+ is_part_of=is_part_of)
+
+def create_prov_entity_from_abstraction(id_scope, abstraction, is_part_of):
+
+ # getting abstraction label defined by the user
+ desc = None
+ for db_annotation in abstraction.db_annotations:
+ if db_annotation._db_key == '__desc__':
+ desc = db_annotation._db_value
+ break
+
+ return DBProvEntity(id='e' + str(id_scope.getNewId(DBProvEntity.vtType)),
+ vt_id=abstraction.db_id,
+ prov_type='prov:Plan',
+ prov_label=abstraction.db_name,
+ prov_value=None,
+ vt_type='vt:subworkflow',
+ vt_desc=desc,
+ vt_package=None,
+ vt_version=None,
+ vt_cache=abstraction.db_cache,
+ vt_location_x=abstraction.db_location._db_x,
+ vt_location_y=abstraction.db_location._db_y,
+ is_part_of=is_part_of)
+
+def create_prov_entity_from_function(id_scope, function):
+ values = []
+ types = []
+ aliases = []
+ for parameter in function._db_parameters:
+ values.append(str(parameter._db_val))
+ types.append(str(parameter._db_type))
+ if parameter._db_alias:
+ aliases.append(parameter._db_alias)
+ else:
+ aliases.append('None')
+
+ value = ''
+ type = ''
+ alias = None
+ if len(values) == 1:
+ value = values[0]
+ type = types[0]
+ alias = aliases[0]
+ elif len(values) > 1:
+ value = '(' + ','.join(values) + ')'
+ type = '(' + ','.join(types) + ')'
+ alias = '(' + ','.join(aliases) + ')'
+
+ return DBProvEntity(id='e' + str(id_scope.getNewId(DBProvEntity.vtType)),
+ vt_id=function.db_id,
+ prov_type='vt:data',
+ prov_label=function.db_name,
+ prov_value=value,
+ vt_type=type,
+ vt_desc=alias,
+ vt_package=None,
+ vt_version=None,
+ vt_cache=None,
+ vt_location_x=None,
+ vt_location_y=None,
+ is_part_of=None)
+
+def create_prov_entity_for_data(id_scope, conn):
+ return DBProvEntity(id='e' + str(id_scope.getNewId(DBProvEntity.vtType)),
+ vt_id=conn.db_id,
+ prov_type='vt:data',
+ prov_label=None,
+ prov_value=None,
+ vt_type=None,
+ vt_desc=None,
+ vt_package=None,
+ vt_version=None,
+ vt_cache=None,
+ vt_location_x=None,
+ vt_location_y=None,
+ is_part_of=None)
+
+def create_vt_connection(id_scope, source, dest, mapping):
+ return DBVtConnection(id='c' + str(id_scope.getNewId(DBVtConnection.vtType)),
+ vt_source=mapping[source._db_moduleId]._db_id,
+ vt_dest=mapping[dest._db_moduleId]._db_id,
+ vt_source_port=source.db_name,
+ vt_dest_port=dest.db_name,
+ vt_source_signature=source._db_signature,
+ vt_dest_signature=dest._db_signature)
+
+def create_prov_agent_from_user(id_scope, user):
+ return DBProvAgent(id='ag' + str(id_scope.getNewId(DBProvAgent.vtType)),
+ vt_id=None,
+ prov_type='prov:Person',
+ prov_label=user,
+ vt_machine_os=None,
+ vt_machine_architecture=None,
+ vt_machine_processor=None,
+ vt_machine_ram=None)
+
+def create_prov_agent_from_machine(id_scope, machine):
+ return DBProvAgent(id='ag' + str(id_scope.getNewId(DBProvAgent.vtType)),
+ vt_id=machine.db_id,
+ prov_type='vt:machine',
+ prov_label=machine.db_name,
+ vt_machine_os=machine._db_os,
+ vt_machine_architecture=machine._db_architecture,
+ vt_machine_processor=machine._db_processor,
+ vt_machine_ram=machine._db_ram)
+
+def create_prov_association(prov_activity, prov_agent, prov_entity):
+ ref_prov_activity = DBRefProvActivity(prov_ref=prov_activity._db_id)
+ ref_prov_agent = DBRefProvAgent(prov_ref=prov_agent._db_id)
+ ref_prov_entity = DBRefProvPlan(prov_ref=prov_entity._db_id)
+
+ return DBProvAssociation(prov_activity=ref_prov_activity,
+ prov_agent=ref_prov_agent,
+ prov_plan=ref_prov_entity,
+ prov_role=None)
+
+def create_prov_activity_from_wf_exec(id_scope, wf_exec):
+ return DBProvActivity(id='a' + str(id_scope.getNewId(DBProvActivity.vtType)),
+ vt_id=wf_exec._db_id,
+ startTime=wf_exec._db_ts_start,
+ endTime=wf_exec._db_ts_end,
+ vt_type='vt:wf_exec',
+ vt_cached=None,
+ vt_completed=wf_exec._db_completed,
+ vt_machine_id=None,
+ vt_error=None,
+ is_part_of=None)
+
+def create_prov_activity_from_exec(id_scope, module_exec, machine_id, is_part_of):
+ type = ''
+ if module_exec.vtType == DBModuleExec.vtType:
+ type = 'vt:module_exec'
+ elif module_exec.vtType == DBGroupExec.vtType:
+ type = 'vt:group_exec'
+ else:
+ # something is wrong...
+ pass
+ return DBProvActivity(id='a' + str(id_scope.getNewId(DBProvActivity.vtType)),
+ vt_id=module_exec._db_id,
+ startTime=module_exec._db_ts_start,
+ endTime=module_exec._db_ts_end,
+ vt_type=type,
+ vt_cached=module_exec._db_cached,
+ vt_completed=module_exec._db_completed,
+ vt_machine_id=machine_id,
+ vt_error=module_exec._db_error,
+ is_part_of=is_part_of)
+
+def create_prov_usage(prov_activity, prov_entity):
+ ref_prov_activity = DBRefProvActivity(prov_ref=prov_activity._db_id)
+ ref_prov_entity = DBRefProvEntity(prov_ref=prov_entity._db_id)
+
+ return DBProvUsage(prov_activity=ref_prov_activity,
+ prov_entity=ref_prov_entity,
+ prov_role=None)
+
+def create_prov_generation(prov_entity, prov_activity):
+ ref_prov_entity = DBRefProvEntity(prov_ref=prov_entity._db_id)
+ ref_prov_activity = DBRefProvActivity(prov_ref=prov_activity._db_id)
+
+ return DBProvGeneration(prov_entity=ref_prov_entity,
+ prov_activity=ref_prov_activity,
+ prov_role=None)
+
+def create_prov(workflow, version, log):
+ id_scope = IdScope()
+ entities = []
+ activities = []
+ agents = []
+ connections = []
+ usages = []
+ generations = []
+ associations = []
+
+ # mapping between VT ids and PROV objects
+ entities_map = {}
+ agents_map = {}
+
+ # mapping between module ids and their functions
+ module_functions = {}
+
+ # mapping between module ids and module objects
+ module_list = {}
+
+ # mapping between module ids and source connections
+ source_conn = {}
+
+ # mapping between module ids and destination connections
+ dest_conn = {}
+
+ # mapping between connection ids and PROV entities for data
+ prov_data_conn = {}
+
+ # mapping between function ids and their PROV entities
+ prov_functions = {}
+
+ # mapping of machine ids to corresponding PROV agents
+ machines = {}
+
+ ############################################################################
+ def get_modules_and_conn(prov_workflow, workflow):
+
+ # modules
+ for module in workflow._db_modules:
+# print "Entity name:", module.name
+# print module.id
+
+ module_list[module._db_id] = module
+
+ # group
+ if module.vtType == DBGroup.vtType:
+ vt_part = create_is_part_of(prov_workflow)
+ prov_group = create_prov_entity_from_group(id_scope=id_scope,
+ group=module,
+ is_part_of=vt_part)
+ entities_map[module._db_id] = prov_group
+ entities.append(prov_group)
+ get_modules_and_conn(prov_group, module.db_workflow)
+
+ # abstraction (subworkflow)
+ elif module.vtType == DBAbstraction.vtType:
+ vt_part = create_is_part_of(prov_workflow)
+ prov_abstraction = create_prov_entity_from_abstraction(id_scope=id_scope,
+ abstraction=module,
+ is_part_of=vt_part)
+ entities_map[module._db_id] = prov_abstraction
+ entities.append(prov_abstraction)
+ #get_modules_and_conn(prov_abstraction, module.db_workflow)
+
+ # module
+ else:
+ vt_part = create_is_part_of(prov_workflow)
+ prov_module = create_prov_entity_from_module(id_scope=id_scope,
+ module=module,
+ is_part_of=vt_part)
+ entities_map[module._db_id] = prov_module
+ entities.append(prov_module)
+
+ module_functions[module._db_id] = module._db_functions
+ for function in module._db_functions:
+ prov_data = create_prov_entity_from_function(id_scope, function)
+ prov_functions[function.db_id] = prov_data
+
+ # connections
+ for conn in workflow._db_connections:
+ # storing information about connections
+ # used to create entities for input and output data
+ source = conn.db_ports_type_index['source']
+ dest = conn.db_ports_type_index['destination']
+ if not source_conn.has_key(source._db_moduleId):
+ source_conn[source._db_moduleId] = []
+ if not dest_conn.has_key(dest._db_moduleId):
+ dest_conn[dest._db_moduleId] = []
+ source_conn[source._db_moduleId].append(conn)
+ dest_conn[dest._db_moduleId].append(conn)
+
+ prov_data = create_prov_entity_for_data(id_scope, conn)
+ prov_data_conn[conn.db_id] = [prov_data, False]
+
+ vt_connection = create_vt_connection(id_scope, source, dest, entities_map)
+ connections.append(vt_connection)
+
+ return True
+ ############################################################################
+
+ def get_execs(exec_, parent_exec, prov_agent):
+
+ # module or group execution
+ if exec_.vtType != DBLoopExec.vtType:
+
+# print "Exec name:", exec_.module_name
+# print exec_.module_id
+
+ # machine (PROV agent)
+ machine_id = None
+# prov_machine = machines[exec_.machine_id][0]
+# machine_id = prov_machine._db_id
+# if not machines[exec_.machine_id][1]:
+# agents.append(prov_machine)
+# machines[exec_.machine_id][1] = True
+
+ # PROV activity
+ vt_part = create_is_part_of(parent_exec)
+ prov_activity = create_prov_activity_from_exec(id_scope,
+ exec_,
+ machine_id,
+ vt_part)
+
+ try:
+ functions = module_functions[exec_._db_module_id]
+ except:
+ activities.append(prov_activity)
+ return True
+
+ for function in functions:
+ prov_data = prov_functions[function.db_id]
+
+ prov_usage = create_prov_usage(prov_activity, prov_data)
+ usages.append(prov_usage)
+
+ if dest_conn.has_key(exec_._db_module_id):
+ connections = dest_conn[exec_._db_module_id]
+ for connection in connections:
+ prov_input_data, inserted = prov_data_conn[connection.db_id]
+ if not inserted:
+ entities.append(prov_input_data)
+ prov_data_conn[connection.db_id][1] = True
+
+ prov_usage = create_prov_usage(prov_activity, prov_input_data)
+ usages.append(prov_usage)
+
+ if (prov_activity._db_vt_error == None) or (prov_activity._db_vt_error == ''):
+ if source_conn.has_key(exec_._db_module_id):
+ connections = source_conn[exec_._db_module_id]
+ for connection in connections:
+ prov_output_data, inserted = prov_data_conn[connection.db_id]
+ if not inserted:
+ entities.append(prov_output_data)
+ prov_data_conn[connection.db_id][1] = True
+
+ prov_generation = create_prov_generation(prov_output_data, prov_activity)
+ generations.append(prov_generation)
+
+ activities.append(prov_activity)
+
+ # PROV entity associated
+ prov_module_entity = entities_map[exec_._db_module_id]
+ prov_association = create_prov_association(prov_activity, prov_agent, prov_module_entity)
+ associations.append(prov_association)
+
+ if exec_.vtType == DBModuleExec.vtType:
+ for loop_exec in exec_._db_loop_execs:
+ get_execs(loop_exec, prov_activity, prov_agent)
+ elif exec_.vtType == DBGroupExec.vtType:
+ for item in exec_._db_item_execs:
+ get_execs(item, prov_activity, prov_agent)
+ else:
+ # something is wrong...
+ pass
+
+ # loop execution
+ elif exec_.vtType == DBLoopExec.vtType:
+ # here, the parent execution is related to the ControlFlow:Map module
+ # TODO: should get the input values from Map, and create Function +
+ # Parameter?
+
+ # there must be only one item exec per loop exec - otherwise, something
+ # is wrong
+ item_exec = exec_.item_execs[0]
+ get_execs(item_exec, parent_exec, prov_agent)
+
+ else:
+ # something is wrong...
+ pass
+
+ return True
+ ############################################################################
+
+ # workflow
+ prov_workflow = create_prov_entity_from_workflow(id_scope, workflow)
+ entities_map[workflow.db_id] = prov_workflow
+ entities.append(prov_workflow)
+
+ # getting modules and connections
+ get_modules_and_conn(prov_workflow, workflow)
+
+ # storing input data
+ for id in prov_functions:
+ entities.append(prov_functions[id])
+
+ # machines
+ for machine in log._db_machines:
+ machines[machine.db_id] = (create_prov_agent_from_machine(id_scope, machine), False)
+
+ # executions
+ for exec_ in log._db_workflow_execs:
+ if exec_._db_parent_version != version:
+ continue
+ prov_agent = None
+ if exec_._db_user not in agents_map:
+ prov_agent = create_prov_agent_from_user(id_scope, exec_._db_user)
+ agents_map[exec_._db_user] = prov_agent
+ agents.append(prov_agent)
+ else:
+ prov_agent = agents_map[exec_._db_user]
+
+ # creating PROV activity
+ prov_activity = create_prov_activity_from_wf_exec(id_scope, exec_)
+ activities.append(prov_activity)
+
+ # creating association with PROV entity
+ prov_association = create_prov_association(prov_activity, prov_agent, prov_workflow)
+
+ for item in exec_._db_item_execs:
+ get_execs(item, prov_activity, prov_agent)
+
+ # PROV Document
+ return create_prov_document(entities=entities,
+ activities=activities,
+ agents=agents,
+ connections=connections,
+ usages=usages,
+ generations=generations,
+ associations=associations)
+
+def add_group_portSpecs_index(workflow):
+ basic_pkg = get_vistrails_basic_pkg_id()
+ def process_group(group):
+ def get_port_name(module):
+ port_name = None
+ for function in module._db_functions:
+ if function.db_name == 'name':
+ port_name = function.db_parameters[0].db_val
+ return port_name
+ g_workflow = group.db_workflow
+ group.db_portSpecs_name_index = {}
+ for module in g_workflow.db_modules:
+ if module.db_name == 'InputPort' and module.db_package == basic_pkg:
+ port_name = get_port_name(module)
+ # FIXME add sigstring to DBPortSpec
+ group.db_portSpecs_name_index[(port_name, 'input')] = \
+ DBPortSpec(id=-1,
+ name=port_name,
+ type='input')
+ elif module.db_name == 'OutputPort' and \
+ module.db_package == basic_pkg:
+ port_name = get_port_name(module)
+ # FIXME add sigstring to DBPortSpec
+ group.db_portSpecs_name_index[(port_name, 'output')] = \
+ DBPortSpec(id=-1,
+ name=port_name,
+ type='output')
+ elif module.db_name == 'Group' and module.db_package == basic_pkg:
+ process_group(module)
+
+ for module in workflow.db_modules:
+ if module.vtType == DBGroup.vtType:
+ process_group(module)
+
+def create_prov_from_vistrail(vistrail, version, log):
+ workflow = materializeWorkflow(vistrail, version)
+ add_group_portSpecs_index(workflow)
+ return create_prov(workflow, version, log)
+
+def run(vistrail_xml, version, log_xml, output_fname):
+ from vistrails.db.persistence import DAOList
+ from vistrails.core.vistrail.vistrail import Vistrail
+ import vistrails.db.services.io
+
+ vistrail = vistrails.db.services.io.open_vistrail_from_xml(vistrail_xml)
+ log = vistrails.db.services.io.open_log_from_xml(log_xml, was_appended=True)
+ version_id = vistrail.db_get_actionAnnotation_by_key((Vistrail.TAG_ANNOTATION, version)).db_action_id
+ prov_document = create_prov_from_vistrail(vistrail, int(version_id), log)
+ dao_list = DAOList()
+ tags = {'xmlns:prov': 'http://www.w3.org/ns/prov#',
+ 'xmlns:dcterms': 'http://purl.org/dc/terms/',
+ 'xmlns:vt': 'http://www.vistrails.org/registry.xsd',
+ }
+ dao_list.save_to_xml(prov_document, output_fname, tags)
+
+if __name__ == '__main__':
+ if len(sys.argv) < 4:
+ print "Usage: python %s <vt_xml> <version> <log_xml> <out_xml>" % sys.argv[0]
+ sys.exit(1)
+ run(*sys.argv[1:])
+
diff --git a/vistrails/db/services/query.py b/vistrails/db/services/query.py
new file mode 100644
index 0000000..9861e94
--- /dev/null
+++ b/vistrails/db/services/query.py
@@ -0,0 +1,262 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db import VistrailsDBException
+from vistrails.db.services.io import open_db_connection, close_db_connection, get_db_lib
+
+def runWorkflowQuery(config, vistrail=None, version=None, fromTime=None,
+ toTime=None, user=None, offset=0, limit=100, modules=[], thumbs=None):
+ # returns list of workflows:
+ # (vistrail name, vistrail id, id, name, date, user, thumb)
+ result = []
+ db = open_db_connection(config)
+ select_part = \
+ """SELECT DISTINCT v.name, v.id, w.parent_id, a1.value,
+ action.date, action.user"""
+ from_part = \
+ """FROM workflow w"""
+ # "tag name" exist in workflow table but may have been changed
+ # so we use value from the vistrail __tag__ annotation
+ where_part = \
+ """WHERE w.entity_type='workflow'"""
+ limit_part = 'LIMIT %s, %s' % (int(offset), int(limit))
+
+ if vistrail:
+ try:
+ where_part += " AND v.id=%s" % int(vistrail)
+ except ValueError:
+ where_part += " AND v.name=%s" % \
+ db.escape(vistrail, get_db_lib().converters.conversions)
+ if version:
+ try:
+ where_part += " AND w.parent_id=%s" % int(version)
+ except ValueError:
+ where_part += " AND a1.value=%s" % \
+ db.escape(version, get_db_lib().converters.conversions)
+ if fromTime:
+ where_part += " AND w.last_modified>%s" % \
+ db.escape(fromTime, get_db_lib().converters.conversions)
+ if toTime:
+ where_part += " AND w.last_modified<%s" % \
+ db.escape(toTime, get_db_lib().converters.conversions)
+ if user:
+ where_part += " AND action.user=%s" % \
+ db.escape(user, get_db_lib().converters.conversions)
+ next_port = 1
+ old_alias = None
+ for i, module, connected in zip(range(1,len(modules)+1), *zip(*modules)):
+ module = module.lower()
+ alias = "m%s"%i
+ from_part += \
+ """ JOIN module {0} ON
+ ({0}.parent_id=w.id AND {0}.entity_type=w.entity_type AND
+ {0}.name={1})
+ """.format(alias,
+ db.escape(module, get_db_lib().converters.conversions))
+ if connected:
+ p1_alias, p2_alias=("port%s"%next_port), ("port%s"%(next_port+1))
+ next_port += 2
+ from_part += \
+ """ JOIN port {0} ON
+ ({0}.entity_id=w.id AND {0}.entity_type=w.entity_type AND
+ {0}.moduleId={1}.id AND {0}.type='source')""".format(
+ p1_alias, old_alias)
+ from_part += \
+ """ JOIN port {0} ON
+ ({0}.entity_id=w.id AND {0}.entity_type=w.entity_type AND
+ {0}.moduleId={1}.id AND {0}.type='destination' AND
+ {0}.parent_id = {2}.parent_id)""".format(
+ p2_alias, alias, p1_alias)
+ old_alias = alias
+ from_part += \
+ """ JOIN vistrail v ON w.vistrail_id = v.id JOIN
+ action ON action.entity_id=w.vistrail_id AND
+ action.id=w.parent_id LEFT JOIN
+ action_annotation a1 ON
+ a1.entity_id=w.vistrail_id AND
+ a1.action_id=w.parent_id AND
+ (a1.akey='__tag__' OR a1.akey IS NULL)"""
+ if thumbs:
+ select_part += ', t.image_bytes'
+ from_part += """ LEFT JOIN action_annotation a2 ON
+ (a2.entity_id=w.vistrail_id AND
+ a2.action_id=w.parent_id AND
+ (a2.akey='__thumb__' OR
+ a2.akey IS NULL)) LEFT JOIN
+ thumbnail t ON a2.value=t.file_name"""
+ else:
+ select_part += ', NULL'
+
+ command = ' '.join([select_part, from_part, where_part, limit_part]) + ';'
+ #print command
+ try:
+ c = db.cursor()
+ c.execute(command)
+ rows = c.fetchall()
+ result = rows
+ c.close()
+ except get_db_lib().Error, e:
+ msg = "Couldn't perform query on db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+
+ # count all rows when offset = 0
+ if 0 == offset:
+ select_part = 'SELECT count(0)'
+ command = ' '.join([select_part,from_part,where_part]) +';'
+ #print command
+ try:
+ c = db.cursor()
+ c.execute(command)
+ res = c.fetchall()
+ result= (result, res[0][0])
+ c.close()
+ except get_db_lib().Error, e:
+ msg = "Couldn't perform query on db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+
+ close_db_connection(db)
+ return result
+
+def runLogQuery(config, vistrail=None, version=None, fromTime=None, toTime=None,
+ user=None, completed=None, offset=0, limit=100, modules=[],
+ thumbs=None):
+ # returns list of workflow executions:
+ # (vistrail name, vistrail id, log id, workflow id, workflow name,
+ # execution id, start time, end time, user, completed, thumb)
+ result = []
+ db = open_db_connection(config)
+ select_part = \
+ """SELECT DISTINCT v.name, v.id, w.entity_id,
+ w.parent_version, a1.value, w.id,
+ w.ts_start, w.ts_end, w.user, w.completed"""
+ from_part = \
+ """FROM workflow_exec w JOIN
+ log_tbl l ON (l.id = w.entity_id) JOIN
+ vistrail v ON (l.vistrail_id = v.id) LEFT JOIN
+ action_annotation a1 ON (a1.entity_id=v.id AND
+ a1.action_id=w.parent_version)"""
+ where_part = \
+ """WHERE w.parent_type='vistrail' AND
+ w.entity_type='log' AND
+ (a1.akey='__tag__' OR a1.akey IS NULL)"""
+ limit_part = 'LIMIT %s, %s' % (int(offset), int(limit))
+
+ if vistrail:
+ try:
+ where_part += " AND v.id=%s" % int(vistrail)
+ except ValueError:
+ where_part += " AND v.name=%s" % \
+ db.escape(vistrail, get_db_lib().converters.conversions)
+ if version:
+ try:
+ where_part += " AND w.parent_version=%s" % int(version)
+ except ValueError:
+ where_part += " AND a1.value=%s" % \
+ db.escape(version, get_db_lib().converters.conversions)
+ if fromTime:
+ where_part += " AND w.ts_end>%s" % \
+ db.escape(fromTime, get_db_lib().converters.conversions)
+ if toTime:
+ where_part += " AND w.ts_start<%s" % \
+ db.escape(toTime, get_db_lib().converters.conversions)
+ if user:
+ where_part += " AND w.user=%s" % \
+ db.escape(user, get_db_lib().converters.conversions)
+ completed_dict = {'no':0, 'yes':1, 'ok':1}
+ if completed is not None:
+ try:
+ int(completed)
+ except ValueError:
+ completed = completed_dict.get(str(completed).lower(), -1)
+ where_part += " AND w.completed=%s" % completed
+ if thumbs:
+ select_part += ', t.image_bytes'
+ from_part += """ LEFT JOIN action_annotation a2 ON
+ (a2.entity_id=v.id AND
+ a2.action_id=w.parent_version) LEFT JOIN
+ thumbnail t ON a2.value=t.file_name"""
+ where_part += " AND (a2.akey='__thumb__' OR a2.akey IS NULL)"
+ else:
+ select_part += ', NULL'
+
+ # TODO nested module executions are not detected
+ for i, module, mCompleted in zip(range(1,len(modules)+1), *zip(*modules)):
+ alias = "m%s"%i
+ from_part += \
+ """ JOIN module_exec %s ON
+ (%s.parent_id=w.id AND
+ %s.entity_id=w.entity_id AND
+ %s.entity_type=w.entity_type)
+ """.replace('%s', alias)
+ where_part += \
+ """ AND %s.parent_type='workflow_exec'
+ AND %s.module_name=%s """ % (alias, alias,
+ db.escape(module.lower(), get_db_lib().converters.conversions) )
+ if mCompleted is not None:
+ mCompleted = completed_dict.get(str(mCompleted).lower(), -1)
+ where_part += """ AND %s.completed=%s""" % (alias, mCompleted)
+
+ command = ' '.join([select_part, from_part, where_part, limit_part]) + ';'
+ #print command
+ try:
+ c = db.cursor()
+ c.execute(command)
+ rows = c.fetchall()
+ result = rows
+ c.close()
+ except get_db_lib().Error, e:
+ msg = "Couldn't perform query on db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+
+ # count all rows when offset = 0
+ if 0 == offset:
+ select_part = 'SELECT count(0)'
+ command = ' '.join([select_part,from_part,where_part]) +';'
+ #print command
+ try:
+ c = db.cursor()
+ c.execute(command)
+ res = c.fetchall()
+ result= (result, res[0][0])
+ c.close()
+ except get_db_lib().Error, e:
+ msg = "Couldn't perform query on db (%d : %s)" % \
+ (e.args[0], e.args[1])
+ raise VistrailsDBException(msg)
+
+ close_db_connection(db)
+ return result
diff --git a/vistrails/db/services/registry.py b/vistrails/db/services/registry.py
new file mode 100644
index 0000000..062e6ce
--- /dev/null
+++ b/vistrails/db/services/registry.py
@@ -0,0 +1,48 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBPackage, DBModuleDescriptor, DBPortSpec
+
+def update_id_scope(registry):
+ if hasattr(registry, 'update_id_scope'):
+ registry.update_id_scope()
+ else:
+ for package in registry.db_packages:
+ registry.idScope.updateBeginId(DBPackage.vtType, package.db_id+1)
+ for descriptor in package.db_module_descriptors:
+ registry.idScope.updateBeginId(DBModuleDescriptor.vtType,
+ descriptor.db_id+1)
+ for port_spec in descriptor.db_portSpecs:
+ registry.idScope.updateBeginId(DBPortSpec.vtType,
+ port_spec.db_id+1)
diff --git a/vistrails/db/services/vistrail.py b/vistrails/db/services/vistrail.py
new file mode 100644
index 0000000..d3caef8
--- /dev/null
+++ b/vistrails/db/services/vistrail.py
@@ -0,0 +1,1354 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.domain import DBWorkflow, DBAdd, DBDelete, DBAction, DBAbstraction, \
+ DBModule, DBConnection, DBPort, DBFunction, DBParameter, DBGroup
+from vistrails.db.services.action_chain import getActionChain, getCurrentOperationDict, \
+ getCurrentOperations, simplify_ops
+from vistrails.db import VistrailsDBException
+
+import copy
+import datetime
+import getpass
+
+import unittest
+import vistrails.core.system
+
+def update_id_scope(vistrail):
+ if hasattr(vistrail, 'update_id_scope'):
+ vistrail.update_id_scope()
+ else:
+ for action in vistrail.db_actions:
+ vistrail.idScope.updateBeginId('action', action.db_id+1)
+ if action.db_session is not None:
+ vistrail.idScope.updateBeginId('session', action.db_session + 1)
+ for operation in action.db_operations:
+ vistrail.idScope.updateBeginId('operation', operation.db_id+1)
+ if operation.vtType == 'add' or operation.vtType == 'change':
+ # update ids of data
+ vistrail.idScope.updateBeginId(operation.db_what,
+ getNewObjId(operation)+1)
+ if operation.db_data is None:
+ if operation.vtType == 'change':
+ operation.db_objectId = operation.db_oldObjId
+ vistrail.db_add_object(operation.db_data)
+ for annotation in action.db_annotations:
+ vistrail.idScope.updateBeginId('annotation', annotation.db_id+1)
+
+def materializeWorkflow(vistrail, version):
+ # construct path up through tree and perform each action
+ if vistrail.db_has_action_with_id(version):
+ workflow = DBWorkflow()
+ #for action in getActionChain(vistrail, version):
+ # oldPerformAction(action, workflow)
+ performActions(getActionChain(vistrail, version),
+ workflow)
+ workflow.db_id = version
+ workflow.db_vistrailId = vistrail.db_id
+ return workflow
+ elif version == 0:
+ return DBWorkflow()
+ else:
+ raise VistrailsDBException("invalid workflow version %s" % version)
+
+def performAction(action, workflow):
+ if action.actionType == 'add':
+ for operation in action.db_operations:
+ workflow.db_add_object(operation.db_data,
+ operation.db_parentObjType,
+ operation.db_parentObjId)
+ elif action.actionType == 'change':
+ for operation in action.db_operations:
+ workflow.db_change_object(operation.db_data,
+ operation.db_parentObjType,
+ operation.db_parentObjId)
+ elif action.actionType == 'delete':
+ for operation in action.operations:
+ workflow.db_delete_object(operation.db_objectId,
+ operation.db_what,
+ operation.db_parentObjType,
+ operation.db_parentObjId)
+ else:
+ msg = "Unrecognized action type '%s'" % action.db_actionType
+ raise TypeError(msg)
+
+def performDeletes(deleteOps, workflow):
+ for operation in deleteOps:
+ workflow.db_delete_object(getOldObjId(operation), operation.db_what,
+ operation.db_parentObjType,
+ operation.db_parentObjId)
+
+def performAdds(addOps, workflow):
+ for operation in addOps:
+# print "operation %d: %s %s" % (operation.db_id, operation.vtType,
+# operation.db_what)
+# print " to: %s %s" % (operation.db_parentObjType,
+# operation.db_parentObjId)
+ workflow.db_add_object(operation.db_data,
+ operation.db_parentObjType,
+ operation.db_parentObjId)
+
+def performActions(actions, workflow):
+ # get the current actions and run addObject on the workflow
+ # note that delete actions have been removed and
+ # a change after an add is effectively an add if the add is discarded
+ performAdds(getCurrentOperations(actions), workflow)
+
+def synchronize(old_vistrail, new_vistrail, current_action_id):
+ id_remap = {}
+ for action in new_vistrail.db_actions:
+ if action.is_new:
+ new_action = action.do_copy(True, old_vistrail.idScope, id_remap)
+ old_vistrail.db_add_action(new_action)
+ else:
+ # it must exist in the old vistrail, too
+ old_action = old_vistrail.db_actions_id_index[action.db_id]
+ # use knowledge that we replace old notes...
+ for annotation in action.db_deleted_annotations:
+ if old_action.db_has_annotation_with_id(annotation.db_id):
+ old_action.db_delete_annotation(annotation)
+ else:
+ # FIXME conflict!
+ # we know that the annotation that was there isn't anymore
+ #print 'possible notes conflict'
+ if old_action.db_has_annotation_with_key('notes'):
+ old_annotation = \
+ old_action.db_get_annotation_by_key('notes')
+ old_action.db_delete_annotation(old_annotation)
+ else:
+ # we don't have to do anything
+ pass
+ for annotation in action.db_annotations:
+ if annotation.is_new:
+ new_annotation = annotation.do_copy(True,
+ old_vistrail.idScope,
+ id_remap)
+ old_action.db_add_annotation(new_annotation)
+
+ for tag in new_vistrail.db_deleted_tags:
+ if old_vistrail.db_has_tag_with_id(tag.db_id):
+ old_vistrail.db_delete_tag(tag)
+ else:
+ # FIXME conflict!
+ # we know the tag that was there isn't anymore
+ #print 'possible tag conflict'
+ # we don't have to do anything here, though
+ pass
+
+ for tag in new_vistrail.db_tags:
+ if tag.is_new:
+ new_tag = tag.do_copy(False)
+ # remap id
+ try:
+ new_tag.db_id = id_remap[(DBAction.vtType, new_tag.db_id)]
+ except KeyError:
+ pass
+ try:
+ old_tag = old_vistrail.db_tags_name_index[new_tag.db_name]
+ except KeyError:
+ # FIXME conflict!
+ #print "tag conflict--name already used"
+ old_vistrail.db_delete_tag(old_tag)
+ try:
+ old_tag = old_vistrail.db_tags_id_index[new_tag.db_id]
+ except KeyError:
+ #print 'possible tag conflict -- WILL NOT GET HERE!'
+ old_vistrail.db_delete_tag(old_tag)
+ old_vistrail.db_add_tag(new_tag)
+
+ new_action_id = \
+ id_remap.get((DBAction.vtType, current_action_id), current_action_id)
+ old_vistrail.db_currentVersion = new_action_id
+ return new_action_id
+
+def merge(sb, next_sb, app='', interactive = False, tmp_dir = '', next_tmp_dir = ''):
+ """ def merge(sb: SaveBundle, next_sb: SaveBundle, app: str,
+ interactive: bool, tmp_dir: str, next_tmp_dir: str) -> None
+ Merges two save bundles that has been annotated with checkout
+ information from a database.
+ All changes from next_sb are appended onto sb. The changes in sb can
+ then be uploaded to the database and use as the new working copy.
+ first sb is the old one from db, last vt is the new one.
+ if interactive is gui.merge_gui.MergeGui then the tmp_dir's must be set.
+ """
+ vt = sb.vistrail
+ next_vt = next_sb.vistrail
+ merge_gui = interactive
+ MergeGUI = merge_gui.MergeGUI if merge_gui else False
+ skip = 0
+
+ id_remap = {}
+
+ checkout_key = "__checkout_version_"
+ action_key = checkout_key + app
+ annotation_key = action_key + '_annotationhash'
+ action_annotation_key = action_key + '_actionannotationhash'
+
+ # find the highest common checkin id
+ checkinId = 0
+ if len(app) and next_vt.db_has_annotation_with_key(action_key):
+ co = next_vt.db_get_annotation_by_key(action_key)
+ #print "found checkin id annotation"
+ checkinId = int(co._db_value)
+ else:
+ #print "calculating checkin id"
+ # create unique identifiers for all actions
+ actions = []
+ actionDict = {}
+ for action in vt.db_actions:
+ unique = action._db_user + str(action._db_date)
+ copy_no = 0
+ while (unique + str(copy_no)) in actionDict:
+ copy_no += 1
+ unique = unique + str(copy_no)
+ actions.append(unique)
+ actionDict[unique] = action
+ actionNexts = []
+ actionDictNext = {}
+ for action in next_vt.db_actions:
+ unique = action._db_user + str(action._db_date)
+ copy_no = 0
+ while (unique + str(copy_no)) in actionDictNext:
+ copy_no += 1
+ unique = unique + str(copy_no)
+ actionNexts.append(unique)
+ actionDictNext[unique] = action
+
+ # find last checkin action (only works for centralized syncs)
+ while checkinId < len(actions) and checkinId < len(actionNexts) and \
+ actions[checkinId] == actionNexts[checkinId]:
+ checkinId += 1
+ if checkinId > 0:
+ checkinId = actionDict[actions[checkinId-1]].db_id
+ #print "checkinId:", checkinId
+
+ # delete previous checkout annotations in vt
+ deletekeys = [action_key,annotation_key,action_annotation_key]
+ for key in deletekeys:
+ while vt.db_has_annotation_with_key(key):
+ a = vt.db_get_annotation_by_key(key)
+ vt.db_delete_annotation(a)
+
+ # check if someone else have changed the annotations
+ mergeAnnotations = True
+ if len(app) and next_vt.db_has_annotation_with_key(annotation_key):
+ #print "found annotationhash"
+ co = next_vt.db_get_annotation_by_key(annotation_key)
+ old_hash = co._db_value
+ mergeAnnotations = (old_hash != vt.hashAnnotations())
+ #print "merge annotations:", mergeAnnotations
+
+ # check if someone else have changed the action annotations
+ mergeActionAnnotations = True
+ if len(app) and next_vt.db_has_annotation_with_key(action_annotation_key):
+ #print "found actionannotationhash"
+ co = next_vt.db_get_annotation_by_key(action_annotation_key)
+ old_hash = co._db_value
+ mergeActionAnnotations = (old_hash != vt.hashActionAnnotations())
+ #print "merge actionannotations:", mergeActionAnnotations
+
+ ################## merge actions ######################
+ for action in next_vt.db_actions:
+ # check for identical actions
+ if action._db_id > checkinId:
+ new_action = action.do_copy(True, vt.idScope, id_remap)
+ vt.db_add_action(new_action)
+
+ ################## merge annotations ##################
+ if not mergeAnnotations:
+ # delete removed annotations
+ for annotation in [a for a in vt.db_annotations]:
+ if not next_vt.db_has_annotation_with_id(annotation.db_id):
+ # delete it
+ vt.db_delete_annotation(annotation)
+ # add new and update changed annotations
+ for annotation in next_vt.db_annotations:
+ if not vt.db_has_annotation_with_id(annotation.db_id):
+ # new annotation
+ new_annotation = annotation.do_copy(True, vt.idScope, id_remap)
+ vt.db_add_annotation(new_annotation)
+ else:
+ old_annotation = vt.db_get_annotation_by_id(annotation.db_id)
+ if old_annotation.db_key != annotation.db_key:
+ # key changed
+ old_annotation.db_key = annotation.db_key
+ if old_annotation.db_value != annotation.db_value:
+ # value changed
+ old_annotation.db_value = annotation.db_value
+ else:
+ annotations = {}
+ # create dict with keys and values
+ for annotation in vt.db_annotations:
+ if annotation.db_key not in annotations:
+ annotations[annotation.db_key] = []
+ if annotation.db_value not in annotations[annotation.db_key]:
+ annotations[annotation.db_key].append(annotation.db_value)
+ # add nonexisting key-value pairs
+ for annotation in next_vt.db_annotations:
+ if annotation.db_key not in annotations or \
+ annotation.db_value not in annotations[annotation.db_key]:
+ new_annotation = annotation.do_copy(True, vt.idScope, id_remap)
+ vt.db_add_annotation(new_annotation)
+
+ ################# merge action annotations ############
+ if not mergeActionAnnotations:
+ # delete removed action annotations
+ for annotation in [a for a in vt.db_actionAnnotations]:
+ if not next_vt.db_has_actionAnnotation_with_id(annotation.db_id):
+ # delete it
+ vt.db_delete_actionAnnotation(annotation)
+ if annotation.db_key == '__thumb__' and len(sb.thumbnails) > 0:
+ # remove thumb
+ thumb = '/'.join(sb.thumbnails[0].split(
+ '/')[:-1]) + '/' + annotation.db_value
+ if thumb in sb.thumbnails:
+ sb.thumbnails.remove(thumb)
+
+ # add new and update changed annotations
+ for annotation in next_vt.db_actionAnnotations:
+ if not vt.db_has_actionAnnotation_with_id(annotation.db_id):
+ # new actionAnnotation
+ annotation = annotation.do_copy(True, vt.idScope, id_remap)
+ vt.db_add_actionAnnotation(annotation)
+ if annotation.db_key == '__thumb__' and \
+ len(next_sb.thumbnails) > 0:
+ # add thumb
+ thumb = '/'.join(next_sb.thumbnails[0].split(
+ '/')[:-1])+'/'+ annotation.db_value
+ if thumb not in sb.thumbnails:
+ sb.thumbnails.append(thumb)
+ else:
+ old_annotation = \
+ vt.db_get_actionAnnotation_by_id(annotation.db_id)
+ if old_annotation.db_value != annotation.db_value:
+ # value changed
+ if annotation.db_key == '__thumb__' and \
+ len(sb.thumbnails) > 0:
+ # remove thumb
+ thumb = '/'.join(sb.thumbnails[0].split(
+ '/')[:-1]) + '/' + old_annotation.db_value
+ if thumb in sb.thumbnails:
+ sb.thumbnails.remove(thumb)
+ if annotation.db_key == '__thumb__' and \
+ len(next_sb.thumbnails) > 0:
+ # add thumb
+ thumb = '/'.join(next_sb.thumbnails[0].split(
+ '/')[:-1])+'/'+ annotation.db_value
+ if thumb not in sb.thumbnails:
+ sb.thumbnails.append(thumb)
+ old_annotation.db_value = annotation.db_value
+ old_annotation.db_date = annotation.db_date
+ old_annotation.db_user = annotation.db_user
+ else:
+ # construct old action index (oas)
+ oas = {}
+ for a in vt.db_actionAnnotations:
+ if not a.db_action_id in oas:
+ oas[a.db_action_id] = {}
+ if not a.db_key in oas[a.db_action_id]:
+ oas[a.db_action_id][a.db_key] = []
+ oas[a.db_action_id][a.db_key].append(a)
+ # merge per action
+ for new_annotation in next_vt.db_actionAnnotations:
+ # keep both upgrades but update action id in new
+ if new_annotation.db_key == '__upgrade__':
+ value = int(new_annotation.db_value)
+ if ('action', value) in id_remap:
+ new_annotation.db_value = str(id_remap[('action', value)])
+ annotation = new_annotation.do_copy(True, vt.idScope, id_remap)
+ vt.db_add_actionAnnotation(annotation)
+ elif new_annotation.db_action_id <= checkinId and \
+ new_annotation.db_key in oas[new_annotation.db_action_id]:
+ old_action = oas[new_annotation.db_action_id]
+ # we have a conflict
+ # tags should be merged (the user need to resolve)
+ if new_annotation.db_key == '__tag__':
+ # there is only one
+ old_annotation = old_action[new_annotation.db_key][0]
+ if old_annotation.db_value != new_annotation.db_value:
+ value = old_annotation.db_value + " or " + \
+ new_annotation.db_value
+ if interactive:
+ if skip == 1:
+ pass
+ elif skip == 2:
+ old_annotation.db_value=new_annotation.db_value
+ old_annotation.db_date = new_annotation.db_date
+ old_annotation.db_user = new_annotation.db_user
+ else:
+ v, value = MergeGUI.resolveTags(
+ old_annotation, new_annotation, value)
+ if v == merge_gui.CHOICE_OTHER_ALL:
+ skip = 1
+ elif v == merge_gui.CHOICE_OTHER:
+ pass
+ elif v == merge_gui.CHOICE_RESOLVED:
+ #print "Tag resolved:", value
+ old_annotation.db_value = value
+ old_annotation.db_date = \
+ new_annotation.db_date
+ old_annotation.db_user = \
+ new_annotation.db_user
+ pass
+ elif v == merge_gui.CHOICE_OWN:
+ old_annotation.db_value = \
+ new_annotation.db_value
+ old_annotation.db_date = \
+ new_annotation.db_date
+ old_annotation.db_user = \
+ new_annotation.db_user
+ elif v == merge_gui.CHOICE_OWN_ALL:
+ old_annotation.db_value = \
+ new_annotation.db_value
+ old_annotation.db_date = \
+ new_annotation.db_date
+ old_annotation.db_user = \
+ new_annotation.db_user
+ skip = 2
+ else:
+ old_annotation.db_value = value
+ old_annotation.db_date = new_annotation.db_date
+ old_annotation.db_user = new_annotation.db_user
+ # notes should be merged (the user need to resolve)
+ elif new_annotation.db_key == '__notes__':
+ # there is only one
+ old_annotation = old_action[new_annotation.db_key][0]
+ if new_annotation.db_value != old_annotation.db_value:
+ value = ("#### conflicting versions! ####<br/>" +
+ "## Other version at %s by %s:%s<br/>" +
+ "## Your version at %s by %s:%s") % \
+ (str(old_annotation.db_date), old_annotation.db_user,
+ old_annotation.db_value, str(new_annotation.db_date),
+ new_annotation.db_user, new_annotation.db_value)
+ if interactive:
+ if skip == 1:
+ pass
+ elif skip == 2:
+ old_annotation.db_value=new_annotation.db_value
+ old_annotation.db_date = new_annotation.db_date
+ old_annotation.db_user = new_annotation.db_user
+ else:
+ v, value = MergeGUI.resolveNotes(
+ old_annotation, new_annotation, value)
+ if v == merge_gui.CHOICE_OTHER_ALL:
+ skip = 1
+ elif v == merge_gui.CHOICE_OTHER:
+ pass
+ elif v == merge_gui.CHOICE_RESOLVED:
+ #print "Note resolved:", value
+ old_annotation.db_value = value
+ old_annotation.db_date = \
+ new_annotation.db_date
+ old_annotation.db_user = \
+ new_annotation.db_user
+ pass
+ elif v == merge_gui.CHOICE_OWN:
+ old_annotation.db_value = \
+ new_annotation.db_value
+ old_annotation.db_date = \
+ new_annotation.db_date
+ old_annotation.db_user = \
+ new_annotation.db_user
+ elif v == merge_gui.CHOICE_OWN_ALL:
+ old_annotation.db_value = \
+ new_annotation.db_value
+ old_annotation.db_date = \
+ new_annotation.db_date
+ old_annotation.db_user = \
+ new_annotation.db_user
+ skip = 2
+ else:
+ old_annotation.db_value = value
+ old_annotation.db_date = new_annotation.db_date
+ old_annotation.db_user = new_annotation.db_user
+
+ # thumbs should be updated (we loose the other update)
+ elif new_annotation.db_key == '__thumb__':
+ # there is only one
+ old_annotation = old_action[new_annotation.db_key][0]
+ if new_annotation.db_value != old_annotation.db_value:
+ if interactive:
+ if skip == 1:
+ pass
+ elif skip == 2:
+ thumb = '/'.join(sb.thumbnails[0].split(
+ '/')[:-1])+'/'+ old_annotation.db_value
+ if thumb in sb.thumbnails:
+ sb.thumbnails.remove(thumb)
+ old_annotation.db_value=new_annotation.db_value
+ old_annotation.db_date = new_annotation.db_date
+ old_annotation.db_user = new_annotation.db_user
+ thumb = '/'.join(next_sb.thumbnails[0].split(
+ '/')[:-1])+'/'+ new_annotation.db_value
+ if thumb not in sb.thumbnails:
+ sb.thumbnails.append(thumb)
+ else:
+ v = MergeGUI.resolveThumbs(old_annotation,
+ new_annotation, tmp_dir, next_tmp_dir)
+ if v == merge_gui.CHOICE_OTHER_ALL:
+ skip = 1
+ elif v == merge_gui.CHOICE_OTHER:
+ pass
+ elif v in (merge_gui.CHOICE_OWN,
+ merge_gui.CHOICE_OWN_ALL):
+ thumb = '/'.join(sb.thumbnails[0].split(
+ '/')[:-1])+'/'+ old_annotation.db_value
+ if thumb in sb.thumbnails:
+ sb.thumbnails.remove(thumb)
+ old_annotation.db_value = \
+ new_annotation.db_value
+ old_annotation.db_date = \
+ new_annotation.db_date
+ old_annotation.db_user = \
+ new_annotation.db_user
+ thumb='/'.join(next_sb.thumbnails[0].split(
+ '/')[:-1])+'/'+ new_annotation.db_value
+ if thumb not in sb.thumbnails:
+ sb.thumbnails.append(thumb)
+ if v == merge_gui.CHOICE_OWN_ALL:
+ skip = 2
+ else:
+ thumb = '/'.join(sb.thumbnails[0].split(
+ '/')[:-1])+'/'+ old_annotation.db_value
+ if thumb in sb.thumbnails:
+ sb.thumbnails.remove(thumb)
+ old_annotation.db_value = new_annotation.db_value
+ old_annotation.db_date = new_annotation.db_date
+ old_annotation.db_user = new_annotation.db_user
+ thumb = '/'.join(next_sb.thumbnails[0].split(
+ '/')[:-1])+'/'+ new_annotation.db_value
+ if thumb not in sb.thumbnails:
+ sb.thumbnails.append(thumb)
+ elif new_annotation.db_key == '__prune__': # keep old
+ pass
+ # others should be appended if not already there
+ else:
+ values = []
+ for old_annotation in old_action[new_annotation.db_key]:
+ values.append(old_annotation.db_value)
+ if new_annotation.db_value not in values:
+ annotation = new_annotation.do_copy(True, vt.idScope, \
+ id_remap)
+ vt.db_add_actionAnnotation(annotation)
+ else:
+ annotation = new_annotation.do_copy(True, vt.idScope, id_remap)
+ vt.db_add_actionAnnotation(annotation)
+ if annotation.db_key == '__thumb__':
+ thumb = '/'.join(next_sb.thumbnails[0].split('/')[:-1]) + \
+ '/' + annotation.db_value
+ if thumb not in sb.thumbnails:
+ sb.thumbnails.append(thumb)
+ # make this a valid checked out version
+ if len(app):
+ vt.update_checkout_version(app)
+
+################################################################################
+# Analogy methods
+
+def find_data(what, id, op_dict):
+ try:
+ return op_dict[(what, id)].db_data
+ except KeyError:
+ msg = 'cannot find data (%s, %s)' % (what, id)
+ raise KeyError(msg)
+
+def invertOperations(op_dict, adds, deletes, do_copy=False):
+ inverse_ops = []
+ deletes.reverse()
+ for op in deletes:
+ data = find_data(op.db_what, getOldObjId(op), op_dict)
+ if do_copy:
+ data = copy.copy(data)
+ inv_op = DBAdd(id=-1,
+ what=op.db_what,
+ objectId=getOldObjId(op),
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data
+ )
+ inverse_ops.append(inv_op)
+ adds.reverse()
+ for op in adds:
+ inv_op = DBDelete(id=-1,
+ what=op.db_what,
+ objectId=getNewObjId(op),
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ )
+ inverse_ops.append(inv_op)
+ return inverse_ops
+
+def normalOperations(adds, deletes, do_copy=False):
+ new_ops = []
+ for op in deletes:
+ new_op = DBDelete(id=-1,
+ what=op.db_what,
+ objectId=getOldObjId(op),
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ )
+ new_ops.append(new_op)
+ for op in adds:
+ data = op.db_data
+ if do_copy:
+ data = copy.copy(op.db_data)
+ new_op = DBAdd(id=-1,
+ what=op.db_what,
+ objectId=getNewObjId(op),
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data)
+ new_ops.append(new_op)
+ return new_ops
+
+def getPathAsAction(vistrail, v1, v2, do_copy=False):
+ sharedRoot = getSharedRoot(vistrail, [v1, v2])
+ sharedActionChain = getActionChain(vistrail, sharedRoot)
+ sharedOperationDict = getCurrentOperationDict(sharedActionChain)
+ v1Actions = getActionChain(vistrail, v1, sharedRoot)
+ v2Actions = getActionChain(vistrail, v2, sharedRoot)
+ (v1AddDict, v1DeleteDict) = getOperationDiff(v1Actions,
+ sharedOperationDict)
+ (v2AddDict, v2DeleteDict) = getOperationDiff(v2Actions,
+ sharedOperationDict)
+
+ # need to invert one of them (v1)
+ v1Adds = v1AddDict.values()
+ v1Adds.sort(key=lambda x: x.db_id) # faster than sort(lambda x, y: cmp(x.db_id, y.db_id))
+ v1Deletes = v1DeleteDict.values()
+ v1Deletes.sort(key=lambda x: x.db_id) # faster than sort(lambda x, y: cmp(x.db_id, y.db_id))
+ v1InverseOps = \
+ invertOperations(sharedOperationDict, v1Adds, v1Deletes, do_copy)
+
+ # need to normalize ops of the other (v2)
+ v2Adds = v2AddDict.values()
+ v2Adds.sort(key=lambda x: x.db_id) # faster than sort(lambda x, y: cmp(x.db_id, y.db_id))
+ v2Deletes = v2DeleteDict.values()
+ v2Deletes.sort(key=lambda x: x.db_id) # faster than sort(lambda x, y: cmp(x.db_id, y.db_id))
+ v2Ops = normalOperations(v2Adds, v2Deletes, do_copy)
+
+ allOps = v1InverseOps + v2Ops
+ simplifiedOps = simplify_ops(allOps)
+ return DBAction(id=-1,
+ operations=simplifiedOps,
+ )
+
+def addAndFixActions(startDict, actions):
+ curDict = copy.copy(startDict)
+ # print curDict
+ for action in actions:
+# print "fixing action:", action.db_id
+ new_ops = []
+ for op in action.db_operations:
+# print "op:", op.vtType, op.db_what, getOldObjId(op)
+# print " ", op.db_parentObjType, op.db_parentObjId
+ if op.vtType == 'add':
+ if op.db_parentObjId is None or \
+ curDict.has_key((op.db_parentObjType,
+ op.db_parentObjId)):
+ curDict[(op.db_what, op.db_objectId)] = op
+ new_ops.append(op)
+ elif op.vtType == 'change':
+ if curDict.has_key((op.db_what, op.db_oldObjId)) and \
+ (op.db_parentObjId is None or \
+ curDict.has_key((op.db_parentObjType,
+ op.db_parentObjId))):
+ del curDict[(op.db_what, op.db_oldObjId)]
+ curDict[(op.db_what, op.db_newObjId)] = op
+ new_ops.append(op)
+ elif op.vtType == 'delete':
+ if (op.db_parentObjId is None or
+ curDict.has_key((op.db_parentObjType,
+ op.db_parentObjId))) and \
+ curDict.has_key((op.db_what, op.db_objectId)):
+ del curDict[(op.db_what, op.db_objectId)]
+ new_ops.append(op)
+ action.db_operations = new_ops
+ return curDict
+
+def fixActions(vistrail, v, actions):
+ startingChain = getActionChain(vistrail, v)
+ startingDict = getCurrentOperationDict(startingChain)
+ addAndFixActions(startingDict, actions)
+
+################################################################################
+# Diff methods
+
+def getSharedRoot(vistrail, versions):
+ # base case is 0
+ current = copy.copy(versions)
+ while 0 not in current:
+ maxId = max(current)
+ if current.count(maxId) == len(current):
+ return maxId
+ else:
+ newId = vistrail.db_get_action_by_id(maxId).db_prevId
+ for i, v in enumerate(current):
+ if v == maxId:
+ current[i] = newId
+ return 0
+
+def getOperationDiff(actions, operationDict):
+ addDict = {}
+ deleteDict = {}
+ for action in actions:
+# print 'action: %d' % action.db_id
+ for operation in action.db_operations:
+ if operation.vtType == 'add':
+# print "add: %s %s" % (operation.db_what,
+# operation.db_objectId)
+ addDict[(operation.db_what,
+ operation.db_objectId)] = operation
+ elif operation.vtType == 'delete':
+# print "del: %s %s" % (operation.db_what,
+# operation.db_objectId)
+ if operationDict.has_key((operation.db_what,
+ operation.db_objectId)):
+ deleteDict[(operation.db_what,
+ operation.db_objectId)] = operation
+# del operationDict[(operation.db_what,
+# operation.db_objectId)]
+ elif addDict.has_key((operation.db_what,
+ operation.db_objectId)):
+ del addDict[(operation.db_what,
+ operation.db_objectId)]
+ else:
+ pass
+ elif operation.vtType == 'change':
+# print "chg: %s %s %s" % (operation.db_what,
+# operation.db_oldObjId,
+# operation.db_newObjId)
+ if operationDict.has_key((operation.db_what,
+ operation.db_oldObjId)):
+ deleteDict[(operation.db_what,
+ operation.db_oldObjId)] = operation
+# del operationDict[(operation.db_what,
+# operation.db_oldObjId)]
+ elif addDict.has_key((operation.db_what,
+ operation.db_oldObjId)):
+ del addDict[(operation.db_what, operation.db_oldObjId)]
+
+ addDict[(operation.db_what,
+ operation.db_newObjId)] = operation
+ else:
+ msg = "Unrecognized operation '%s'" % operation.vtType
+ raise TypeError(msg)
+
+ return (addDict, deleteDict)
+
+def updateOperationDict(operationDict, deleteOps, addOps):
+ for operation in deleteOps:
+ if operationDict.has_key((operation.db_what, getOldObjId(operation))):
+ del operationDict[(operation.db_what, getOldObjId(operation))]
+ else:
+ msg = "Illegal operation: " + operation
+ for operation in addOps:
+ operationDict[(operation.db_what, getNewObjId(operation))] = operation
+ return operationDict
+
+def getObjects(actions):
+ objects = {}
+ for action in actions:
+ for operation in action.db_operations:
+ if not objects.has_key(operation.db_what):
+ objects[operation.db_what] = []
+ object = copy.copy(operation.db_data)
+ objects[operation.db_what].append(object)
+ return objects
+
+def getVersionDifferences(vistrail, versions):
+ sharedRoot = getSharedRoot(vistrail, versions)
+ sharedActionChain = getActionChain(vistrail, sharedRoot)
+ sharedOperationDict = getCurrentOperationDict(sharedActionChain)
+
+ vOnlySorted = []
+ for v in versions:
+ vActions = getActionChain(vistrail, v, sharedRoot)
+ (vAddDict, vDeleteDict) = getOperationDiff(vActions,
+ sharedOperationDict)
+ vOnlyAdds = vAddDict.values()
+ vOnlyAdds.sort(key=lambda x: x.db_id)
+ vOnlyDeletes = vDeleteDict.values()
+ vOnlyDeletes.sort(key=lambda x: x.db_id)
+ vOpDict = copy.copy(sharedOperationDict)
+ updateOperationDict(vOpDict, vOnlyDeletes, vOnlyAdds)
+ vOps = vOpDict.values()
+ vOps.sort(key=lambda x: x.db_id)
+ vOnlySorted.append((vOnlyAdds, vOnlyDeletes, vOps))
+
+ sharedOps = sharedOperationDict.values()
+ sharedOps.sort(key=lambda x: x.db_id)
+
+ return (sharedOps, vOnlySorted)
+
+def heuristicModuleMatch(m1, m2):
+ """takes two modules and returns 1 if exact match,
+ 0 if module names match, -1 if no match
+
+ """
+ if m1.db_name == m2.db_name and m1.db_namespace == m2.db_namespace and \
+ m1.db_package == m2.db_package:
+ if m1.vtType == 'group':
+ # check if we have __desc__ annotation
+ m1_desc = None
+ m2_desc = None
+ if '__desc__' in m1.db_annotations_key_index:
+ m1_desc = m1.db_annotations_key_index['__desc__']
+ if '__desc__' in m2.db_annotations_key_index:
+ m2_desc = m2.db_annotations_key_index['__desc__']
+ if not (m1_desc and m2_desc and m1_desc == m2_desc):
+ # if desc's don't exactly match, return 0
+ # else continue and check functions
+ # FIXME: maybe we should check functions here
+ return 0
+
+ m1_functions = copy.copy(m1.db_get_functions())
+ m2_functions = copy.copy(m2.db_get_functions())
+ if len(m1_functions) != len(m2_functions):
+ return 0
+ for f1 in m1_functions[:]:
+ match = None
+ for f2 in m2_functions:
+ isMatch = heuristicFunctionMatch(f1, f2)
+ if isMatch == 1:
+ match = f2
+ break
+ if match is not None:
+ m1_functions.remove(f1)
+ m2_functions.remove(f2)
+ else:
+ return 0
+ if len(m1_functions) == len(m2_functions) == 0:
+ return 1
+ else:
+ return 0
+ return -1
+
+def heuristicFunctionMatch(f1, f2):
+ """takes two functions and returns 1 if exact match,
+ 0 if function names match, -1 if no match
+
+ """
+ if f1.db_name == f2.db_name:
+ f1_parameters = copy.copy(f1.db_get_parameters())
+ f2_parameters = copy.copy(f2.db_get_parameters())
+ if len(f1_parameters) != len(f2_parameters):
+ return 0
+ for p1 in f1_parameters[:]:
+ match = None
+ for p2 in f2_parameters:
+ isMatch = heuristicParameterMatch(p1, p2)
+ if isMatch == 1:
+ match = p2
+ break
+ if match is not None:
+ f1_parameters.remove(p1)
+ f2_parameters.remove(match)
+ else:
+ return 0
+ if len(f1_parameters) == len(f2_parameters) == 0:
+ return 1
+ else:
+ return 0
+ return -1
+
+def heuristicParameterMatch(p1, p2):
+ """takes two parameters and returns 1 if exact match,
+ 0 if partial match (types match), -1 if no match
+
+ """
+ if p1.db_type == p2.db_type and p1.db_pos == p2.db_pos:
+ if p1.db_val == p2.db_val:
+ return 1
+ else:
+ return 0
+ return -1
+
+def heuristicConnectionMatch(c1, c2):
+ """takes two connections and returns 1 if exact match,
+ 0 if partial match (currently undefined), -1 if no match
+
+ """
+ c1_ports = copy.copy(c1.db_get_ports())
+ c2_ports = copy.copy(c2.db_get_ports())
+ for p1 in c1_ports[:]:
+ match = None
+ for p2 in c2_ports:
+ isMatch = heuristicPortMatch(p1, p2)
+ if isMatch == 1:
+ match = p2
+ break
+ elif isMatch == 0:
+ match = p2
+ if match is not None:
+ c1_ports.remove(p1)
+ c2_ports.remove(match)
+ else:
+ return -1
+ if len(c1_ports) == len(c2_ports) == 0:
+ return 1
+ return -1
+
+def heuristicPortMatch(p1, p2):
+ """takes two ports and returns 1 if exact match,
+ 0 if partial match, -1 if no match
+
+ """
+ if p1.db_moduleId == p2.db_moduleId:
+ return 1
+ elif p1.db_type == p2.db_type and \
+ p1.db_moduleName == p2.db_moduleName and \
+ p1.sig == p2.sig:
+ return 0
+ return -1
+
+def function_sig(function):
+ return (function.db_name,
+ [(param.db_type, param.db_val)
+ for param in function.db_get_parameters()])
+
+def getParamChanges(m1, m2, same_vt=True, heuristic_match=True):
+ paramChanges = []
+ # need to check to see if any children of m1 and m2 are affected
+ m1_functions = m1.db_get_functions()
+ m2_functions = m2.db_get_functions()
+ m1_unmatched = []
+ m2_unmatched = []
+ if same_vt:
+ for f1 in m1_functions:
+ # see if m2 has f1, too
+ f2 = m2.db_get_function(f1.db_id)
+ if f2 is None:
+ m1_unmatched.append(f1)
+ else:
+ # function is same, check if parameters have changed
+ if heuristic_match:
+ matchValue = heuristicFunctionMatch(f1, f2)
+ if matchValue != 1:
+ paramChanges.append((function_sig(f1),
+ function_sig(f2)))
+ else:
+ paramChanges.append((function_sig(f1), function_sig(f2)))
+ for f2 in m2_functions:
+ # see if m1 has f2, too
+ if m1.db_get_function(f2.db_id) is None:
+ m2_unmatched.append(f2)
+ else:
+ m1_unmatched.extend(m1_functions)
+ m2_unmatched.extend(m2_functions)
+
+# functionMatch = True
+# f1_params = f1.db_get_parameters()
+# f2_params = f2.db_get_parameters()
+# for p1 in f1_params:
+# if f2.db_get_parameter(p1.db_id) is None:
+# functionMatch = False
+# m1_unmatched.append(f1)
+# break
+# for p2 in f2_params:
+# if f1.db_get_parameter(p2.db_id) is None:
+# functionMatch = False
+# m2_unmatched.append(f2)
+# break
+# if functionMatch:
+
+ if len(m1_unmatched) + len(m2_unmatched) > 0:
+ if heuristic_match and len(m1_unmatched) > 0 and len(m2_unmatched) > 0:
+ # do heuristic matches
+ for f1 in m1_unmatched[:]:
+ matched = False
+ matchValue = 0
+ for f2 in m2_unmatched:
+ matchValue = heuristicFunctionMatch(f1, f2)
+ if matchValue == 1:
+ # best match so quit
+ matched = f1
+ break
+ elif matchValue == 0:
+ # match, but not exact so continue to look
+ matched = f1
+ if matched:
+ if matchValue != 1:
+ paramChanges.append((function_sig(f1),
+ function_sig(f2)))
+ m1_unmatched.remove(f1)
+ m2_unmatched.remove(f2)
+
+ for f in m1_unmatched:
+ paramChanges.append((function_sig(f), (None, None)))
+ for f in m2_unmatched:
+ paramChanges.append(((None, None), function_sig(f)))
+
+ return paramChanges
+
+def getOldObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_oldObjId
+ return operation.db_objectId
+
+def getNewObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_newObjId
+ return operation.db_objectId
+
+def setOldObjId(operation, id):
+ if operation.vtType == 'change':
+ operation.db_oldObjId = id
+ else:
+ operation.db_objectId = id
+
+def setNewObjId(operation, id):
+ if operation.vtType == 'change':
+ operation.db_newObjId = id
+ else:
+ operation.db_objectId = id
+
+def getWorkflowDiffCommon(vistrail, v1, v2, heuristic_match=True):
+ (sharedOps, vOnlyOps) = \
+ getVersionDifferences(vistrail, [v1, v2])
+
+ sharedWorkflow = DBWorkflow()
+ performAdds(sharedOps, sharedWorkflow)
+
+ # FIXME better to do additional ops (and do deletes) or do this?
+ v1Workflow = DBWorkflow()
+ v1Ops = vOnlyOps[0][2]
+ performAdds(v1Ops, v1Workflow)
+
+ v2Workflow = DBWorkflow()
+ v2Ops = vOnlyOps[1][2]
+ performAdds(v2Ops, v2Workflow)
+
+ # FIXME connections do not check their ports
+ sharedModuleIds = []
+ sharedConnectionIds = []
+ sharedFunctionIds = {}
+ for op in sharedOps:
+ if op.what == 'module' or op.what == 'abstraction' or \
+ op.what == 'group':
+ sharedModuleIds.append(getNewObjId(op))
+ elif op.what == 'connection':
+ sharedConnectionIds.append(getNewObjId(op))
+ elif op.what == 'function':
+ sharedFunctionIds[getNewObjId(op)] = op.db_parentObjId
+
+ vOnlyModules = []
+ vOnlyConnections = []
+ paramChgModules = {}
+ for (vAdds, vDeletes, _) in vOnlyOps:
+ moduleDeleteIds = []
+ connectionDeleteIds = []
+ for op in vDeletes:
+ if op.what == 'module' or op.what == 'abstraction' or \
+ op.what == 'group':
+ moduleDeleteIds.append(getOldObjId(op))
+ if getOldObjId(op) in sharedModuleIds:
+ sharedModuleIds.remove(getOldObjId(op))
+ if paramChgModules.has_key(getOldObjId(op)):
+ del paramChgModules[getOldObjId(op)]
+ elif op.what == 'function' and \
+ (op.db_parentObjType == 'module' or
+ op.db_parentObjType == 'abstraction' or
+ op.db_parentObjType == 'group') and \
+ op.db_parentObjId in sharedModuleIds:
+ # have a function change
+ paramChgModules[op.db_parentObjId] = None
+ sharedModuleIds.remove(op.db_parentObjId)
+ elif op.what == 'parameter' and op.db_parentObjType == 'function' \
+ and sharedFunctionIds.has_key(op.db_parentObjId):
+ # have a parameter change
+ moduleId = sharedFunctionIds[op.db_parentObjId]
+ if moduleId in sharedModuleIds:
+ paramChgModules[moduleId] = None
+ sharedModuleIds.remove(moduleId)
+ elif op.what == 'connection':
+ connectionDeleteIds.append(getOldObjId(op))
+ if getOldObjId(op) in sharedConnectionIds:
+ sharedConnectionIds.remove(getOldObjId(op))
+
+ moduleAddIds = []
+ connectionAddIds = []
+ for op in vAdds:
+ if op.what == 'module' or op.what == 'abstraction' or \
+ op.what == 'group':
+ moduleAddIds.append(getNewObjId(op))
+ elif (op.what == 'function' and
+ (op.db_parentObjType == 'module' or
+ op.db_parentObjType == 'abstraction' or
+ op.db_parentObjType == 'group') and
+ op.db_parentObjId in sharedModuleIds):
+ # have a function change
+ paramChgModules[op.db_parentObjId] = None
+ sharedModuleIds.remove(op.db_parentObjId)
+ elif op.what == 'parameter' and op.db_parentObjType == 'function' \
+ and sharedFunctionIds.has_key(op.db_parentObjId):
+ # have a parameter change
+ moduleId = sharedFunctionIds[op.db_parentObjId]
+ if moduleId in sharedModuleIds:
+ paramChgModules[moduleId] = None
+ sharedModuleIds.remove(moduleId)
+ elif op.what == 'connection':
+ connectionAddIds.append(getOldObjId(op))
+
+ vOnlyModules.append((moduleAddIds, moduleDeleteIds))
+ vOnlyConnections.append((connectionAddIds, connectionDeleteIds))
+
+ sharedModulePairs = [(id, id) for id in sharedModuleIds]
+ v1Only = vOnlyModules[0][0]
+ v2Only = vOnlyModules[1][0]
+ for id in vOnlyModules[1][1]:
+ if id not in vOnlyModules[0][1]:
+ v1Only.append(id)
+ for id in vOnlyModules[0][1]:
+ if id not in vOnlyModules[1][1]:
+ v2Only.append(id)
+
+ sharedConnectionPairs = [(id, id) for id in sharedConnectionIds]
+ c1Only = vOnlyConnections[0][0]
+ c2Only = vOnlyConnections[1][0]
+ for id in vOnlyConnections[1][1]:
+ if id not in vOnlyConnections[0][1]:
+ c1Only.append(id)
+ for id in vOnlyConnections[0][1]:
+ if id not in vOnlyConnections[1][1]:
+ c2Only.append(id)
+
+ paramChgModulePairs = [(id, id) for id in paramChgModules.keys()]
+
+ # print "^^^^ SHARED MODULE PAIRS:", sharedModulePairs
+ if heuristic_match:
+ (heuristicModulePairs, heuristicConnectionPairs, v1Only, v2Only, \
+ c1Only, c2Only) = do_heuristic_diff(v1Workflow, v2Workflow, \
+ v1Only, v2Only, \
+ c1Only, c2Only)
+ paramChgModulePairs.extend(heuristicModulePairs)
+
+ (heuristicModulePairs, paramChanges) = \
+ check_params_diff(v1Workflow, v2Workflow, paramChgModulePairs,
+ True, heuristic_match)
+
+ return (v1Workflow, v2Workflow,
+ sharedModulePairs, heuristicModulePairs, v1Only, v2Only,
+ paramChanges, sharedConnectionPairs, heuristicConnectionPairs,
+ c1Only, c2Only)
+
+def do_heuristic_diff(v1Workflow, v2Workflow, v1_modules, v2_modules,
+ v1_connections, v2_connections):
+ # add heuristic matches
+ heuristicModulePairs = []
+ heuristicConnectionPairs = []
+ paramChgModulePairs = []
+
+ v1Only = copy.copy(v1_modules)
+ v2Only = copy.copy(v2_modules)
+ c1Only = copy.copy(v1_connections)
+ c2Only = copy.copy(v2_connections)
+
+ # we now check all heuristic pairs for parameter changes
+ # match modules
+ # for (m1_id, m2_id) in paramChgModulePairs[:]:
+ # m1 = v1Workflow.db_get_module(m1_id)
+ # m2 = v2Workflow.db_get_module(m2_id)
+ # if heuristicModuleMatch(m1, m2) == 1:
+ # # paramChgModulePairs.remove((m1_id, m2_id))
+ # # heuristicModulePairs.append((m1_id, m2_id))
+ # pass
+
+ for m1_id in v1Only[:]:
+ m1 = v1Workflow.db_get_module(m1_id)
+ match = None
+ for m2_id in v2Only:
+ m2 = v2Workflow.db_get_module(m2_id)
+ isMatch = heuristicModuleMatch(m1, m2)
+ if isMatch == 1:
+ match = (m1_id, m2_id)
+ break
+ elif isMatch == 0:
+ match = (m1_id, m2_id)
+ if match is not None:
+ v1Only.remove(match[0])
+ v2Only.remove(match[1])
+ # we now check all heuristic pairs for parameter changes
+ heuristicModulePairs.append(match)
+ # paramChgModulePairs.append(match)
+
+ # match connections
+ for c1_id in c1Only[:]:
+ c1 = v1Workflow.db_get_connection(c1_id)
+ match = None
+ for c2_id in c2Only:
+ c2 = v2Workflow.db_get_connection(c2_id)
+ isMatch = heuristicConnectionMatch(c1, c2)
+ if isMatch == 1:
+ match = (c1_id, c2_id)
+ break
+ elif isMatch == 0:
+ match = (c1_id, c2_id)
+ if match is not None:
+ # don't have port changes yet
+ c1Only.remove(match[0])
+ c2Only.remove(match[1])
+ heuristicConnectionPairs.append(match)
+
+ return (heuristicModulePairs, heuristicConnectionPairs, v1Only, v2Only,
+ c1Only, c2Only)
+
+def check_params_diff(v1Workflow, v2Workflow, paramChgModulePairs,
+ same_vt=True, heuristic_match=True):
+ matched = []
+ paramChanges = []
+ # print "^^^^ PARAM CHG PAIRS:", paramChgModulePairs
+ for (m1_id, m2_id) in paramChgModulePairs:
+ m1 = v1Workflow.db_get_module(m1_id)
+ m2 = v2Workflow.db_get_module(m2_id)
+ moduleParamChanges = getParamChanges(m1, m2, same_vt, heuristic_match)
+ if len(moduleParamChanges) > 0:
+ paramChanges.append(((m1_id, m2_id), moduleParamChanges))
+ else:
+ # heuristicModulePairs.append((m1_id, m2_id))
+ matched.append((m1_id, m2_id))
+
+ return (matched, paramChanges)
+
+def getWorkflowDiff(vt_pair_1, vt_pair_2, heuristic_match=True):
+ (vistrail_1, v_1) = vt_pair_1
+ (vistrail_2, v_2) = vt_pair_2
+
+ if vistrail_1 == vistrail_2:
+ return getWorkflowDiffCommon(vistrail_1, v_1, v_2, heuristic_match)
+
+ workflow_1 = materializeWorkflow(vistrail_1, v_1)
+ workflow_2 = materializeWorkflow(vistrail_2, v_2)
+ modules_1 = workflow_1.db_modules_id_index.keys()
+ modules_2 = workflow_2.db_modules_id_index.keys()
+ conns_1 = workflow_1.db_connections_id_index.keys()
+ conns_2 = workflow_2.db_connections_id_index.keys()
+
+ if heuristic_match:
+ (m_matches, c_matches, modules_1, modules_2, conns_1, conns_2) = \
+ do_heuristic_diff(workflow_1, workflow_2, modules_1, modules_2, \
+ conns_1, conns_2)
+ (m_matches, param_changes) = check_params_diff(workflow_1, workflow_2,
+ m_matches, False,
+ heuristic_match)
+ return (workflow_1, workflow_2, [], m_matches, modules_1, modules_2,
+ param_changes, [], c_matches, conns_1, conns_2)
+
+ return (workflow_1, workflow_2, [], [], modules_1, modules_2, [], [], [],
+ conns_1, conns_2)
+
+################################################################################
+
+
+class TestDBVistrailService(unittest.TestCase):
+ def test_parameter_heuristic(self):
+ from vistrails.core.vistrail.module_param import ModuleParam
+
+ param1 = ModuleParam(id=0, pos=0, type='String', val='abc')
+ param2 = ModuleParam(id=1, pos=0, type='String', val='abc')
+ param3 = ModuleParam(id=2, pos=1, type='Float', val='1.0')
+ param4 = ModuleParam(id=3, pos=0, type='String', val='def')
+ param5 = ModuleParam(id=4, pos=1, type='String', val='abc')
+
+ # test basic equality
+ assert heuristicParameterMatch(param1, param2) == 1
+ # test basic inequality
+ assert heuristicParameterMatch(param1, param3) == -1
+ # test partial match
+ assert heuristicParameterMatch(param1, param4) == 0
+ # test position inequality
+ assert heuristicParameterMatch(param1, param5) == -1
+
+ def test_function_heuristic(self):
+ from vistrails.core.vistrail.module_param import ModuleParam
+ from vistrails.core.vistrail.module_function import ModuleFunction
+
+ param1 = ModuleParam(id=0, pos=0, type='String', val='abc')
+ param2 = ModuleParam(id=1, pos=1, type='Float', val='1.0')
+ param3 = ModuleParam(id=2, pos=0, type='String', val='abc')
+ param4 = ModuleParam(id=3, pos=1, type='Float', val='1.0')
+ param5 = ModuleParam(id=4, pos=0, type='String', val='abc')
+ param6 = ModuleParam(id=5, pos=1, type='Float', val='2.0')
+
+ function1 = ModuleFunction(name='f1', parameters=[param1, param2])
+ function2 = ModuleFunction(name='f1', parameters=[param3, param4])
+ function3 = ModuleFunction(name='f1', parameters=[param5, param6])
+ function4 = ModuleFunction(name='f2', parameters=[param1, param2])
+ function5 = ModuleFunction(name='f1', parameters=[param1])
+
+ # test basic equality
+ assert heuristicFunctionMatch(function1, function2) == 1
+ # test partial match
+ assert heuristicFunctionMatch(function1, function3) == 0
+ # test basic inequality
+ assert heuristicFunctionMatch(function1, function4) == -1
+ # test length inequality
+ assert heuristicFunctionMatch(function1, function5) == 0
+
+ def test_module_heuristic(self):
+ from vistrails.core.vistrail.module_param import ModuleParam
+ from vistrails.core.vistrail.module_function import ModuleFunction
+ from vistrails.core.vistrail.module import Module
+
+ param1 = ModuleParam(id=0, pos=0, type='String', val='abc')
+ param2 = ModuleParam(id=1, pos=1, type='Float', val='1.0')
+ param3 = ModuleParam(id=2, pos=0, type='String', val='abc')
+ param4 = ModuleParam(id=3, pos=1, type='Float', val='1.0')
+ param5 = ModuleParam(id=4, pos=0, type='Integer', val='2')
+ param6 = ModuleParam(id=5, pos=0, type='Integer', val='2')
+
+ function1 = ModuleFunction(name='f1', parameters=[param1, param2])
+ function2 = ModuleFunction(name='f1', parameters=[param3, param4])
+ function3 = ModuleFunction(name='f2', parameters=[param5])
+ function4 = ModuleFunction(name='f2', parameters=[param6])
+ function5 = ModuleFunction(name='f1', parameters=[param2, param4])
+ function6 = ModuleFunction(name='f2', parameters=[param5])
+
+ module1 = Module(name='m1', functions=[function1, function3])
+ module2 = Module(name='m1', functions=[function2, function4])
+ module3 = Module(name='m2', functions=[function1, function2])
+ module4 = Module(name='m1', functions=[function5])
+ module5 = Module(name='m1', functions=[function5, function6])
+
+ # test basic equality
+ assert heuristicModuleMatch(module1, module2) == 1
+ # test basic inequality
+ assert heuristicModuleMatch(module1, module3) == -1
+ # test length inequality
+ assert heuristicModuleMatch(module1, module4) == 0
+ # test parameter change inequality
+ assert heuristicModuleMatch(module1, module5) == 0
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/db/services/workflow.py b/vistrails/db/services/workflow.py
new file mode 100644
index 0000000..cbbb77c
--- /dev/null
+++ b/vistrails/db/services/workflow.py
@@ -0,0 +1,42 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+def update_id_scope(workflow):
+ if hasattr(workflow, 'update_id_scope'):
+ workflow.update_id_scope()
+ else:
+ pass
+
+
diff --git a/vistrails/db/specs/all.xml b/vistrails/db/specs/all.xml
new file mode 100644
index 0000000..ab07b76
--- /dev/null
+++ b/vistrails/db/specs/all.xml
@@ -0,0 +1,3823 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<objects>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ABSTRACTION +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="internal_version" type="str">
+ <xml name="internalVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ACTION ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long" foreignKey="true" object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="vistrail" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ADD +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ACTION_ANNOTATION +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="actionAnnotation">
+ <layout>
+ <xml nodeType="xs:element"/>
+ <sql table="action_annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="action_id" type="long" foreignKey="true" object="action">
+ <xml name="actionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ANNOTATION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="workflow_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="mashuptrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VISTRAIL_VARIABLE +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vistrailVariable">
+ <layout>
+ <xml nodeType="xs:element"/>
+ <sql table="vistrail_variable"/>
+ </layout>
+
+ <property name="name" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="name" type="varchar(255)"/>
+ </property>
+
+ <property name="uuid" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="uuid" type="char(36)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="package" type="varchar(255)"/>
+ </property>
+
+ <property name="module" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="module" type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="namespace" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="value" type="varchar(8191)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CHANGE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CONNECTION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- DELETE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- FUNCTION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group" parentClass="module">
+ <layout>
+ <xml name="group" nodeType="xs:element"/>
+ <sql table="group_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow" type="object" mapping="one-to-one"
+ expand="false">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOCATION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MACHINE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:long"/>
+ <sql type="bigint"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOOP_EXEC +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="loop_exec">
+ <layout>
+ <xml name="loopExec" nodeType="xs:element"/>
+ <sql table="loop_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <!--<property name="input" type="str">
+ <xml name="input" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>-->
+
+ <property name="iteration" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP_EXEC ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group_exec">
+ <layout>
+ <xml name="groupExec" nodeType="xs:element"/>
+ <sql table="group_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="group_name" type="str">
+ <xml name="groupName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="group_type" type="str">
+ <xml name="groupType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <!--<property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>-->
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_EXEC +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OTHER +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PARAMETER +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PLUGIN DATA +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="plugin_data">
+ <layout>
+ <xml name="plugin_data" nodeType="xs:element"/>
+ <sql table="plugin_data"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="data" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORT ++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="signature" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORTSPEC ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="optional" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="sort_key" type="int">
+ <xml name="sortKey" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="portSpecItem" type="list"
+ mapping="one-to-many" expandAction="false">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="min_conns" type="int">
+ <xml name="minConns" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="max_conns" type="int">
+ <xml name="maxConns" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="module_descriptor">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORTSPECITEM ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="portSpecItem">
+ <layout>
+ <xml name="portSpecItem" nodeType="xs:element"/>
+ <sql table="port_spec_item"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="label" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="default" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="_default" type="varchar(4095)"/>
+ </property>
+
+ <property name="values" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="_values" type="mediumtext"/>
+ </property>
+
+ <property name="entry_type" type="str">
+ <xml name="entryType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="portSpec" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_DESCRIPTOR +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_descriptor">
+ <layout>
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ <sql table="module_descriptor"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package_version" type="str">
+ <xml name="packageVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="base_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="baseDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="package" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ <!--
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="registry">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="package">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+ -->
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PACKAGE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="package">
+ <layout>
+ <xml name="package" nodeType="xs:element"/>
+ <sql table="package"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="identifier" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="codepath" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="load_configuration" type="int">
+ <xml name="loadConfiguration" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="description" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property ref="true" object="module_descriptor" type="list"
+ mapping="one-to-many" index="name:namespace:version">
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="registry" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REGISTRY ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="registry">
+ <layout>
+ <xml name="registry" nodeType="xs:element"/>
+ <sql table="registry"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="root_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="rootDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <!-- <xml nodeType="xs:attribute" type="xs:string"/> -->
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="package" type="list"
+ mapping="one-to-many" index="identifier:version">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- TAG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VISTRAIL ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="vistrailVariable" type="list" mapping="one-to-many"
+ index="uuid">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="parameter_exploration" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="actionAnnotation" type="list"
+ mapping="one-to-many" index="action_id:key !key:value">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstraction" ref="true" object="abstraction">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group" ref="true" object="group">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="plugin_data" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="group" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW_EXEC +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PE_PARAMETER ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="pe_parameter" className="DBPEParameter">
+ <layout>
+ <xml name="peParameter" nodeType="xs:element"/>
+ <sql table="pe_parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="interpolator" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="dimension" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <property ref="true" type="long" object="pe_function" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PE_FUNCTION +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="pe_function" className="DBPEFunction">
+ <layout>
+ <xml name="peFunction" nodeType="xs:element"/>
+ <sql table="pe_function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="port_name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="is_alias" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" name="parameter" object="pe_parameter" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <property ref="true" type="long" object="parameter_exploration"
+ inverse="true" mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PARAMETER_EXPLORATION +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="parameter_exploration">
+ <layout>
+ <xml name="parameterExploration" nodeType="xs:element"/>
+ <sql table="parameter_exploration"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="action_id" type="long" foreignKey="true" object="action">
+ <xml name="actionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="dims" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="layout" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" name="function" object="pe_function" type="list"
+ mapping="one-to-many" index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MASHUP_ACTION +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="mashup_action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="mashup_action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long" foreignKey="true" object="mashup_action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="mashup" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="mashuptrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--+++++++++++++++++++++++++++++-->
+ <!-- MASHUP_ACTION_ANNOTATION +++-->
+ <!--+++++++++++++++++++++++++++++-->
+
+ <object name="mashup_actionAnnotation">
+ <layout>
+ <xml name="actionAnnotation" nodeType="xs:element"/>
+ <sql table="mashup_action_annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="action_id" type="long" foreignKey="true" object="mashup_action">
+ <xml name="action_id" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="mashuptrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MASHUPTRAIL +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="mashuptrail">
+ <layout>
+ <xml name="mashuptrail" nodeType="xs:element"/>
+ <sql table="mashuptrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml name="id" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(36)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="vtVersion" type="long">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql column="vt_version" type="int"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property name="action" ref="true" object="mashup_action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="actionAnnotation" ref="true" object="mashup_actionAnnotation" type="list"
+ mapping="one-to-many" index="action_id:key !key:value">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--+++++++++++++++++++++++++++++-->
+ <!-- MASHUP_ALIAS +++++++++++++++-->
+ <!--+++++++++++++++++++++++++++++-->
+
+ <object name="mashup_alias">
+ <layout>
+ <xml name="alias" nodeType="xs:element"/>
+ <sql table="mashup_alias"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="component" ref="true" object="mashup_component" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parent" ref="true" object="mashup" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MASHUP_COMPONENT ++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="mashup_component">
+ <layout>
+ <xml name="component" nodeType="xs:element"/>
+ <sql table="mashup_component"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vtid" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vttype" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="vtparent_type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(32)"/>
+ </property>
+
+ <property name="vtparent_id" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vtpos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vtmid" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="minVal" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="maxVal" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="stepSize" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="strvaluelist" type="str">
+ <xml name="valueList" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="widget" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="seq" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="mashup_alias" type="long" mapping="one-to-one"
+ inverse="true">
+ <sql column="alias_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MASHUP ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="mashup">
+ <layout>
+ <xml name="mashup" nodeType="xs:element"/>
+ <sql table="mashup"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="alias" pluralName="aliases" type= "list" ref="true"
+ object="mashup_alias" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="vtid" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="layout" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="geometry" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="has_seq" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent" ref="true" object="mashup_action" type="long"
+ mapping="one-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_GRAPH +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_graph">
+ <layout>
+ <xml name="opmGraph" nodeType="xs:element"/>
+ <!-- <sql table="opm_graph"/> -->
+ </layout>
+
+ <property name="accounts" ref="true" object="opm_accounts"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="processes" ref="true" object="opm_processes"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="artifacts" ref="true" object="opm_artifacts"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="agents" ref="true" object="opm_agents"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="dependencies" ref="true" object="opm_dependencies"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNTS ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_accounts">
+ <layout>
+ <xml name="accounts" nodeType="xs:element"/>
+ <!-- <sql table="accounts"/> -->
+ </layout>
+
+ <property name="account" ref="true" object="opm_account" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="opm_overlaps" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNT +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_account">
+ <layout>
+ <xml name="account" nodeType="xs:element"/>
+ <!-- <sql table="account"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_OVERLAPS ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_overlaps">
+ <layout>
+ <xml name="overlaps" nodeType="xs:element"/>
+ <!-- <sql table="overlaps"/> -->
+ </layout>
+
+ <property ref="true" object="opm_account_id" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACTS +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifacts">
+ <layout>
+ <xml name="artifacts" nodeType="xs:element"/>
+ <!-- <sql table="artifacts"/> -->
+ </layout>
+
+ <property name="artifact" ref="true" object="opm_artifact" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_VALUE ++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_value">
+ <layout>
+ <xml name="value" nodeType="xs:element"/>
+ <!-- <sql table="artifact_value"/> -->
+ </layout>
+
+ <choice name="value" type="object" mapping="one-to-one">
+ <property ref="true" object="portSpec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact">
+ <layout>
+ <xml name="artifact" nodeType="xs:element"/>
+ <!-- <sql table="artifact"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" ref="true" object="opm_artifact_value" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESSES +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_processes">
+ <layout>
+ <xml name="processes" nodeType="xs:element"/>
+ <!-- <sql table="processes"/> -->
+ </layout>
+
+ <property name="process" ref="true" object="opm_process" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_VALUE +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_value">
+ <layout>
+ <xml name="value" nodeType="xs:element"/>
+ <!-- <sql table="process_value"/> -->
+ </layout>
+
+ <choice name="value" type="object" mapping="one-to-one">
+ <property ref="true" object="module_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process">
+ <layout>
+ <xml name="process" nodeType="xs:element"/>
+ <!-- <sql table="process"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" ref="true" object="opm_process_value" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENTS ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agents">
+ <layout>
+ <xml name="agents" nodeType="xs:element"/>
+ <!-- <sql table="agents"/> -->
+ </layout>
+
+ <property name="agent" ref="true" object="opm_agent" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENT +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agent">
+ <layout>
+ <xml name="agent" nodeType="xs:element"/>
+ <!-- <sql table="agent"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type=""/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_DEPENDENCIES ++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_dependencies">
+ <layout>
+ <xml name="causalDependencies" nodeType="xs:element"/>
+ <!-- <sql table="causal_dependencies"/> -->
+ </layout>
+
+ <choice name="dependency" type="list" mapping="one-to-many">
+ <property name="used" ref="true" object="opm_used">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_generated_by" ref="true"
+ object="opm_was_generated_by">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_triggered_by" ref="true"
+ object="opm_was_triggered_by">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_derived_from" ref="true"
+ object="opm_was_derived_from">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_controlled_by" ref="true"
+ object="opm_was_controlled_by">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_TIME ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_time">
+ <layout>
+ <xml name="time" nodeType="xs:element"/>
+ <!-- <sql table="time"/> -->
+ </layout>
+
+ <property name="no_later_than" type="datetime">
+ <xml name="noLaterThan" nodeType="xs:attribute" type="xs:dateTime"/>
+ <!-- <sql type="datetime"/> -->
+ </property>
+
+ <property name="no_earlier_than" type="datetime">
+ <xml name="noEarlierThan" nodeType="xs:attribute" type="xs:dateTime"/>
+ <!-- <sql type="datetime"/> -->
+ </property>
+
+ <property name="clock_id" type="str">
+ <xml name="clockId" nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNT_ID ++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_account_id">
+ <layout>
+ <xml name="account" nodeType="xs:element"/>
+ <!-- <sql table="account_id"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_account">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_ID_CAUSE ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_id_cause">
+ <layout>
+ <xml name="cause" nodeType="xs:element"/>
+ <!-- <sql table="process_id_cause"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_process">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_ID_EFFECT +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_id_effect">
+ <layout>
+ <xml name="effect" nodeType="xs:element"/>
+ <!-- <sql table="process_id_effect"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_process">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_ID_CAUSE +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_id_cause">
+ <layout>
+ <xml name="cause" nodeType="xs:element"/>
+ <!-- <sql table="artifact_id_cause"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_artifact">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_ID_EFFECT ++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_id_effect">
+ <layout>
+ <xml name="effect" nodeType="xs:element"/>
+ <!-- <sql table="artifact_id_effect"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_artifact">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENT_ID ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agent_id">
+ <layout>
+ <xml name="agent" nodeType="xs:element"/>
+ <!-- <sql table="agent_id"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_agent">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ROLE ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_role">
+ <layout>
+ <xml name="role" nodeType="xs:element"/>
+ <!-- <sql table="role"/> -->
+ </layout>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(4095)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_USED ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_used">
+ <layout>
+ <xml name="used" nodeType="xs:element"/>
+ <!-- <sql table="used"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_artifact_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_GENERATED_BY ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_generated_by">
+ <layout>
+ <xml name="wasGeneratedBy" nodeType="xs:element"/>
+ <!-- <sql table="was_generated_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_artifact_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_process_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_CONTROLLED_BY +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_controlled_by">
+ <layout>
+ <xml name="wasControlledBy" nodeType="xs:element"/>
+ <!-- <sql table="was_controlled_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_agent_id"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="start" ref="true" object="opm_time" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="end" ref="true" object="opm_time" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_DERIVED_FROM ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_derived_from">
+ <layout>
+ <xml name="wasDerivedFrom" nodeType="xs:element"/>
+ <!-- <sql table="was_derived_from"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_artifact_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_artifact_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_TRIGGERED_BY ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_triggered_by">
+ <layout>
+ <xml name="wasTriggeredBy" nodeType="xs:element"/>
+ <!-- <sql table="was_triggered_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_process_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_DOCUMENT +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_document">
+ <layout>
+ <xml name="prov:document" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_entity" ref="true" object="prov_entity" type="list"
+ mapping="one-to-many">
+ <xml name="prov:entity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_activity" ref="true" object="prov_activity" type="list"
+ mapping="one-to-many">
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_agent" ref="true" object="prov_agent" type="list"
+ mapping="one-to-many">
+ <xml name="prov:agent" nodeType="xs:element"/>
+ </property>
+
+ <property name="vt_connection" ref="true" object="vt_connection" type="list"
+ mapping="one-to-many">
+ <xml name="vt:connection" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_usage" ref="true" object="prov_usage" type="list"
+ mapping="one-to-many">
+ <xml name="prov:used" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_generation" ref="true" object="prov_generation" type="list"
+ mapping="one-to-many">
+ <xml name="prov:wasGeneratedBy" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_association" ref="true" object="prov_association" type="list"
+ mapping="one-to-many">
+ <xml name="prov:wasAssociatedWith" nodeType="xs:element"/>
+ </property>
+
+ <!--<property name="vt_part" ref="true" object="vt_part" type="list"
+ mapping="one-to-many">
+ <xml name="vt:isPartOf" nodeType="xs:element"/>
+ </property>-->
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_ENTITY +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_entity">
+ <layout>
+ <xml name="prov:entity" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml name="prov:id" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="prov_type" type="str">
+ <xml name="prov:type" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="prov_label" type="str">
+ <xml name="prov:label" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="prov_value" type="str">
+ <xml name="prov:value" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_id" type="str">
+ <xml name="vt:id" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_type" type="str">
+ <xml name="vt:type" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_desc" type="str">
+ <xml name="vt:desc" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_package" type="str">
+ <xml name="vt:package" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vt:version" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_cache" type="str">
+ <xml name="vt:cache" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_location_x" type="str">
+ <xml name="vt:location_x" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_location_y" type="str">
+ <xml name="vt:location_y" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="is_part_of" ref="true" object="is_part_of" type="str">
+ <xml name="dcterms:isPartOf" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REF_PROV_ENTITY +++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="ref_prov_entity">
+ <layout>
+ <xml name="prov:entity" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_ref" type="str" foreignKey="true" object="prov_entity">
+ <xml name="prov:ref" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REF_PROV_PLAN +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="ref_prov_plan">
+ <layout>
+ <xml name="prov:plan" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_ref" type="str" foreignKey="true" object="prov_entity">
+ <xml name="prov:ref" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_ACTIVITY +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_activity">
+ <layout>
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml name="prov:id" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="startTime" type="str">
+ <xml name="prov:startTime" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="endTime" type="str">
+ <xml name="prov:endTime" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_id" type="str" primaryKey="true">
+ <xml name="vt:id" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_type" type="str">
+ <xml name="vt:type" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_cached" type="str">
+ <xml name="vt:cached" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_completed" type="str">
+ <xml name="vt:completed" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_machine_id" type="str">
+ <xml name="vt:machine_id" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_error" type="str">
+ <xml name="vt:error" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="is_part_of" ref="true" object="is_part_of" type="str">
+ <xml name="dcterms:isPartOf" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REF_PROV_ACTIVITY +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="ref_prov_activity">
+ <layout>
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_ref" type="str" foreignKey="true" object="prov_activity">
+ <xml name="prov:ref" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_AGENT ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_agent">
+ <layout>
+ <xml name="prov:agent" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml name="prov:id" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="vt_id" type="str">
+ <xml name="vt:id" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="prov_type" type="str">
+ <xml name="prov:type" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="prov_label" type="str">
+ <xml name="prov:label" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_machine_os" type="str">
+ <xml name="vt:machine_os" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_machine_architecture" type="str">
+ <xml name="vt:machine_architecture" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_machine_processor" type="str">
+ <xml name="vt:machine_processor" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_machine_ram" type="str">
+ <xml name="vt:machine_ram" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REF_PROV_AGENT ++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="ref_prov_agent">
+ <layout>
+ <xml name="prov:agent" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_ref" type="str" foreignKey="true" object="prov_agent">
+ <xml name="prov:ref" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VT_CONNECTION +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vt_connection">
+ <layout>
+ <xml name="vt:connection" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml name="id" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="vt_source" type="str">
+ <xml name="vt:source" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_dest" type="str">
+ <xml name="vt:dest" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_source_port" type="str">
+ <xml name="vt:source_port" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_dest_port" type="str">
+ <xml name="vt:dest_port" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_source_signature" type="str">
+ <xml name="vt:source_signature" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_dest_signature" type="str">
+ <xml name="vt:dest_signature" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_USAGE ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_usage">
+ <layout>
+ <xml name="prov:used" nodeType="xs:element"/>
+ </layout>
+
+ <!--<property name="id" type="str" primaryKey="true">
+ <xml name="id" nodeType="xs:attribute" type="xs:string"/>
+ </property>-->
+
+ <property name="prov_activity" ref="true" object="ref_prov_activity" type="str">
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_entity" ref="true" object="ref_prov_entity" type="str">
+ <xml name="prov:entity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_role" type="str">
+ <xml name="prov:role" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_GENERATION +++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_generation">
+ <layout>
+ <xml name="prov:wasGeneratedBy" nodeType="xs:element"/>
+ </layout>
+
+ <!--<property name="id" type="str" primaryKey="true">
+ <xml name="id" nodeType="xs:attribute" type="xs:string"/>
+ </property>-->
+
+ <property name="prov_entity" ref="true" object="ref_prov_entity" type="str">
+ <xml name="prov:entity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_activity" ref="true" object="ref_prov_activity" type="str">
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_role" type="str">
+ <xml name="prov:role" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_ASSOCIATION ++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_association">
+ <layout>
+ <xml name="prov:wasAssociatedWith" nodeType="xs:element"/>
+ </layout>
+
+ <!--<property name="id" type="str" primaryKey="true">
+ <xml name="id" nodeType="xs:attribute" type="xs:string"/>
+ </property>-->
+
+ <property name="prov_activity" ref="true" object="ref_prov_activity" type="str">
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_agent" ref="true" object="ref_prov_agent" type="str">
+ <xml name="prov:agent" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_plan" ref="true" object="ref_prov_plan" type="str">
+ <xml name="prov:plan" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_role" type="str">
+ <xml name="prov:role" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- IS_PART_OF ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="is_part_of">
+ <layout>
+ <xml name="dcterms:isPartOf" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_ref" type="str">
+ <xml name="prov:ref" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+ </object>
+
+</objects>
diff --git a/vistrails/db/tests/__init__.py b/vistrails/db/tests/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/db/tests/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/db/tests/setup_db_tables.py b/vistrails/db/tests/setup_db_tables.py
new file mode 100644
index 0000000..00f9fde
--- /dev/null
+++ b/vistrails/db/tests/setup_db_tables.py
@@ -0,0 +1,65 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# MACOSX binary install stuff
+import os
+import sys
+from vistrails.db.services import io
+
+sys.path.append("../..")
+
+def setup_tables(host, port, user, passwd, db):
+ config = {'host': host,
+ 'port': port,
+ 'user': user,
+ 'passwd': passwd,
+ 'db': db}
+
+ try:
+ db_connection = io.open_db_connection(config)
+ io.setup_db_tables(db_connection)
+ except Exception, e:
+ print e
+
+if __name__ == '__main__':
+ args = sys.argv
+ if len(args) > 4:
+ host = str(args[1])
+ port = 3306
+ user = str(args[2])
+ passwd = str(args[3])
+ db = str(args[4])
+ setup_tables(host, port, user, passwd, db)
+ else:
+ print "Usage: %s host user passwd db" % args[0]
diff --git a/vistrails/db/tests/sql_to_xml.py b/vistrails/db/tests/sql_to_xml.py
new file mode 100644
index 0000000..e9ff98c
--- /dev/null
+++ b/vistrails/db/tests/sql_to_xml.py
@@ -0,0 +1,69 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# MACOSX binary install stuff
+import os
+
+import MySQLdb
+
+from vistrails.db.services import io
+import vistrails.tests
+
+if __name__ != '__main__':
+ import vistrails.tests
+ raise vistrails.tests.NotModule('This should not be imported as a module')
+
+os.environ['EXECUTABLEPATH'] = '/vistrails/VisTrails.app/Contents/MacOS'
+
+
+
+def convert_sql_to_xml(filename, id):
+ config = {'host': 'localhost',
+ 'port': 3306,
+ 'user': 'vistrails',
+ 'passwd': 'vistrailspwd',
+ 'db': 'vistrails'}
+ try:
+ dbConnection = io.open_db_connection(config)
+ vistrail = io.open_vistrail_from_db(dbConnection, id)
+ io.setDBParameters(vistrail, config)
+ io.save_vistrail_to_xml(vistrail, filename)
+ io.close_db_connection(dbConnection)
+ except MySQLdb.Error, e:
+ print e
+
+if __name__ == '__main__':
+ convert_sql_to_xml('/vistrails/vtk_http_from_db.xml', 1)
+ # convert_sql_to_xml('/vistrails/head_from_db.xml', 1)
+ # convert_sql_to_xml('/vistrails/lung_from_db.xml', 2)
diff --git a/vistrails/db/tests/xml_to_sql.py b/vistrails/db/tests/xml_to_sql.py
new file mode 100644
index 0000000..d599836
--- /dev/null
+++ b/vistrails/db/tests/xml_to_sql.py
@@ -0,0 +1,69 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# MACOSX binary install stuff
+import os
+
+from vistrails.db.services import io
+
+os.environ['EXECUTABLEPATH'] = '/vistrails/VisTrails.app/Contents/MacOS'
+
+
+def convert_xml_to_sql(filename):
+ config = {'host': 'localhost',
+ 'port': 3306,
+ 'user': 'vistrails',
+ 'passwd': 'vistrailspwd',
+ 'db': 'vistrails'}
+
+ try:
+ vistrail = io.open_vistrail_from_xml(filename)
+ dbConnection = io.open_db_connection(config)
+
+ print dbConnection.get_server_info()
+ print dbConnection.get_host_info()
+ print dbConnection.stat()
+ print str(dbConnection)
+
+ io.save_vistrail_to_db(vistrail, dbConnection)
+ io.close_db_connection(dbConnection)
+ print 'db_id: ', vistrail.db_id
+
+ except Exception, e:
+ print e
+
+if __name__ == '__main__':
+ # convert_xml_to_sql('/vistrails/vtk_http_new.xml')
+ convert_xml_to_sql('/vistrails/examples/head.xml')
+ # convert_xml_to_sql('/vistrails/examples/lung.xml')
diff --git a/vistrails/db/versions/__init__.py b/vistrails/db/versions/__init__.py
new file mode 100644
index 0000000..ad96364
--- /dev/null
+++ b/vistrails/db/versions/__init__.py
@@ -0,0 +1,165 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from itertools import izip
+import os
+
+from vistrails.core.system import vistrails_root_directory
+from vistrails.db import VistrailsDBException
+
+currentVersion = '1.0.3'
+
+def getVersionDAO(version=None):
+ if version is None:
+ version = currentVersion
+ persistence_dir = 'vistrails.db.versions.' + get_version_name(version) + \
+ '.persistence'
+ try:
+ persistence = __import__(persistence_dir, {}, {}, [''])
+ except ImportError as e:
+ if str(e).startswith('No module named v'):
+ # assume version is not available
+ msg = "Cannot find DAO for version '%s'" % version
+ raise VistrailsDBException(msg)
+ # assume other error
+ import traceback
+ raise VistrailsDBException(traceback.format_exc())
+ return persistence.DAOList()
+
+def translate_object(obj, method_name, version=None, target_version=None):
+ if version is None:
+ version = obj.version
+ if target_version is None:
+ target_version = currentVersion
+
+ version_map = {
+ '0.3.0': '0.3.1',
+ '0.3.1': '0.6.0',
+ '0.5.0': '0.6.0',
+ '0.6.0': '0.7.0',
+ '0.7.0': '0.8.0',
+ '0.8.0': '0.8.1',
+ '0.8.1': '0.9.0',
+ '0.9.0': '0.9.1',
+ '0.9.1': '0.9.3',
+ '0.9.2': '0.9.3',
+ '0.9.3': '0.9.4',
+ '0.9.4': '0.9.5',
+ '0.9.5': '1.0.0',
+ '1.0.0': '1.0.1',
+ '1.0.1': '1.0.2',
+ '1.0.2': '1.0.3',
+ }
+
+ rev_version_map = {
+ '1.0.3': '1.0.2',
+ '1.0.2': '1.0.1',
+ '1.0.1': '1.0.0',
+ '1.0.0': '0.9.5',
+ '0.9.5': '0.9.4',
+ '0.9.4': '0.9.3',
+ }
+
+ def get_translate_module(map, start_version, end_version):
+ translate_dir = 'vistrails.db.versions.' + \
+ get_version_name(end_version) + '.translate.' + \
+ get_version_name(start_version)
+ return __import__(translate_dir, {}, {}, [''])
+
+ path = []
+ old_tuple = version.split('.')
+ new_tuple = target_version.split('.')
+ map = version_map
+ for i, j in izip(old_tuple, new_tuple):
+ if i < j:
+ # forward
+ break
+ elif i > j:
+ # reverse
+ map = rev_version_map
+ break
+
+ # don't get stuck in an infinite loop
+ count = 0
+ while version != target_version:
+ if count > len(map):
+ break
+ next_version = map[version]
+ try:
+ translate_module = get_translate_module(map, version, next_version)
+ except Exception, e:
+ import traceback
+ raise VistrailsDBException("Cannot translate version: "
+ "error loading translation version %s method '%s': %s" % \
+ (version, method_name, traceback.format_exc()))
+ if not hasattr(translate_module, method_name):
+ raise VistrailsDBException("Cannot translate version: "
+ "version %s missing method '%s'" % \
+ (version, method_name))
+ obj = getattr(translate_module, method_name)(obj)
+ version = next_version
+ count += 1
+
+ if version != target_version:
+ msg = "An error occurred when translating,"
+ msg += "only able to translate to version '%s'" % version
+ raise VistrailsDBException(msg)
+
+ return obj
+
+def translate_vistrail(vistrail, version=None, target_version=None):
+ return translate_object(vistrail, 'translateVistrail', version,
+ target_version)
+
+def translate_workflow(workflow, version=None, target_version=None):
+ return translate_object(workflow, 'translateWorkflow', version,
+ target_version)
+
+def translate_log(log, version=None, target_version=None):
+ return translate_object(log, 'translateLog', version, target_version)
+
+def translate_registry(registry, version=None, target_version=None):
+ return translate_object(registry, 'translateRegistry', version,
+ target_version)
+
+def get_version_name(version_no):
+ return 'v' + version_no.replace('.', '_')
+
+def getVersionSchemaDir(version=None):
+ if version is None:
+ version = currentVersion
+ versionName = get_version_name(version)
+ schemaDir = os.path.join(vistrails_root_directory(), 'db', 'versions',
+ versionName, 'schemas', 'sql')
+ return schemaDir
diff --git a/vistrails/db/versions/v0_3_0/__init__.py b/vistrails/db/versions/v0_3_0/__init__.py
new file mode 100644
index 0000000..a6ad05c
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.3.0'
diff --git a/vistrails/db/versions/v0_3_0/domain/__init__.py b/vistrails/db/versions/v0_3_0/domain/__init__.py
new file mode 100644
index 0000000..1870fdf
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/domain/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
diff --git a/vistrails/db/versions/v0_3_0/domain/auto_gen.py b/vistrails/db/versions/v0_3_0/domain/auto_gen.py
new file mode 100644
index 0000000..9a5f3e6
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/domain/auto_gen.py
@@ -0,0 +1,876 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+class DBChangeParameter(object):
+
+ vtType = 'changeParameter'
+
+ def __init__(self, moduleId=None, alias=None, functionId=None, function=None, parameterId=None, parameter=None, type=None, value=None):
+ self.__db_moduleId = moduleId
+ self.__db_alias = alias
+ self.__db_functionId = functionId
+ self.__db_function = function
+ self.__db_parameterId = parameterId
+ self.__db_parameter = parameter
+ self.__db_type = type
+ self.__db_value = value
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_alias(self):
+ return self.__db_alias
+ def __set_db_alias(self, alias):
+ self.__db_alias = alias
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self.__db_alias = alias
+ def db_change_alias(self, alias):
+ self.__db_alias = alias
+ def db_delete_alias(self, alias):
+ self.__db_alias = None
+
+ def __get_db_functionId(self):
+ return self.__db_functionId
+ def __set_db_functionId(self, functionId):
+ self.__db_functionId = functionId
+ db_functionId = property(__get_db_functionId, __set_db_functionId)
+ def db_add_functionId(self, functionId):
+ self.__db_functionId = functionId
+ def db_change_functionId(self, functionId):
+ self.__db_functionId = functionId
+ def db_delete_functionId(self, functionId):
+ self.__db_functionId = None
+
+ def __get_db_function(self):
+ return self.__db_function
+ def __set_db_function(self, function):
+ self.__db_function = function
+ db_function = property(__get_db_function, __set_db_function)
+ def db_add_function(self, function):
+ self.__db_function = function
+ def db_change_function(self, function):
+ self.__db_function = function
+ def db_delete_function(self, function):
+ self.__db_function = None
+
+ def __get_db_parameterId(self):
+ return self.__db_parameterId
+ def __set_db_parameterId(self, parameterId):
+ self.__db_parameterId = parameterId
+ db_parameterId = property(__get_db_parameterId, __set_db_parameterId)
+ def db_add_parameterId(self, parameterId):
+ self.__db_parameterId = parameterId
+ def db_change_parameterId(self, parameterId):
+ self.__db_parameterId = parameterId
+ def db_delete_parameterId(self, parameterId):
+ self.__db_parameterId = None
+
+ def __get_db_parameter(self):
+ return self.__db_parameter
+ def __set_db_parameter(self, parameter):
+ self.__db_parameter = parameter
+ db_parameter = property(__get_db_parameter, __set_db_parameter)
+ def db_add_parameter(self, parameter):
+ self.__db_parameter = parameter
+ def db_change_parameter(self, parameter):
+ self.__db_parameter = parameter
+ def db_delete_parameter(self, parameter):
+ self.__db_parameter = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_moduleId
+
+"""generated automatically by auto_dao.py"""
+
+class DBDeleteFunction(object):
+
+ vtType = 'deleteFunction'
+
+ def __init__(self, moduleId=None, functionId=None):
+ self.__db_moduleId = moduleId
+ self.__db_functionId = functionId
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_functionId(self):
+ return self.__db_functionId
+ def __set_db_functionId(self, functionId):
+ self.__db_functionId = functionId
+ db_functionId = property(__get_db_functionId, __set_db_functionId)
+ def db_add_functionId(self, functionId):
+ self.__db_functionId = functionId
+ def db_change_functionId(self, functionId):
+ self.__db_functionId = functionId
+ def db_delete_functionId(self, functionId):
+ self.__db_functionId = None
+
+ def getPrimaryKey(self):
+ return self.__db_moduleId
+
+"""generated automatically by auto_dao.py"""
+
+class DBDeleteConnection(object):
+
+ vtType = 'deleteConnection'
+
+ def __init__(self, connectionId=None):
+ self.__db_connectionId = connectionId
+ def __get_db_connectionId(self):
+ return self.__db_connectionId
+ def __set_db_connectionId(self, connectionId):
+ self.__db_connectionId = connectionId
+ db_connectionId = property(__get_db_connectionId, __set_db_connectionId)
+ def db_add_connectionId(self, connectionId):
+ self.__db_connectionId = connectionId
+ def db_change_connectionId(self, connectionId):
+ self.__db_connectionId = connectionId
+ def db_delete_connectionId(self, connectionId):
+ self.__db_connectionId = None
+
+ def getPrimaryKey(self):
+ return self.__db_connectionId
+
+"""generated automatically by auto_dao.py"""
+
+class DBAddModule(object):
+
+ vtType = 'addModule'
+
+ def __init__(self, id=None, cache=None, name=None, x=None, y=None):
+ self.__db_id = id
+ self.__db_cache = cache
+ self.__db_name = name
+ self.__db_x = x
+ self.__db_y = y
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_cache(self):
+ return self.__db_cache
+ def __set_db_cache(self, cache):
+ self.__db_cache = cache
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self.__db_cache = cache
+ def db_change_cache(self, cache):
+ self.__db_cache = cache
+ def db_delete_cache(self, cache):
+ self.__db_cache = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_x(self):
+ return self.__db_x
+ def __set_db_x(self, x):
+ self.__db_x = x
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self.__db_x = x
+ def db_change_x(self, x):
+ self.__db_x = x
+ def db_delete_x(self, x):
+ self.__db_x = None
+
+ def __get_db_y(self):
+ return self.__db_y
+ def __set_db_y(self, y):
+ self.__db_y = y
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self.__db_y = y
+ def db_change_y(self, y):
+ self.__db_y = y
+ def db_delete_y(self, y):
+ self.__db_y = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+"""generated automatically by auto_dao.py"""
+
+class DBDeleteAnnotation(object):
+
+ vtType = 'deleteAnnotation'
+
+ def __init__(self, moduleId=None, key=None):
+ self.__db_moduleId = moduleId
+ self.__db_key = key
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def getPrimaryKey(self):
+ return self.__db_moduleId
+
+"""generated automatically by auto_dao.py"""
+
+class DBDeleteModulePort(object):
+
+ vtType = 'deleteModulePort'
+
+ def __init__(self, moduleId=None, portType=None, portName=None):
+ self.__db_moduleId = moduleId
+ self.__db_portType = portType
+ self.__db_portName = portName
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_portType(self):
+ return self.__db_portType
+ def __set_db_portType(self, portType):
+ self.__db_portType = portType
+ db_portType = property(__get_db_portType, __set_db_portType)
+ def db_add_portType(self, portType):
+ self.__db_portType = portType
+ def db_change_portType(self, portType):
+ self.__db_portType = portType
+ def db_delete_portType(self, portType):
+ self.__db_portType = None
+
+ def __get_db_portName(self):
+ return self.__db_portName
+ def __set_db_portName(self, portName):
+ self.__db_portName = portName
+ db_portName = property(__get_db_portName, __set_db_portName)
+ def db_add_portName(self, portName):
+ self.__db_portName = portName
+ def db_change_portName(self, portName):
+ self.__db_portName = portName
+ def db_delete_portName(self, portName):
+ self.__db_portName = None
+
+ def getPrimaryKey(self):
+ return self.__db_moduleId
+
+"""generated automatically by auto_dao.py"""
+
+class DBDeleteModule(object):
+
+ vtType = 'deleteModule'
+
+ def __init__(self, moduleId=None):
+ self.__db_moduleId = moduleId
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def getPrimaryKey(self):
+ return self.__db_moduleId
+
+"""generated automatically by auto_dao.py"""
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, time=None, name=None):
+ self.__db_time = time
+ self.__db_name = name
+ def __get_db_time(self):
+ return self.__db_time
+ def __set_db_time(self, time):
+ self.__db_time = time
+ db_time = property(__get_db_time, __set_db_time)
+ def db_add_time(self, time):
+ self.__db_time = time
+ def db_change_time(self, time):
+ self.__db_time = time
+ def db_delete_time(self, time):
+ self.__db_time = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def getPrimaryKey(self):
+ return self.__db_time
+
+"""generated automatically by auto_dao.py"""
+
+class DBAddModulePort(object):
+
+ vtType = 'addModulePort'
+
+ def __init__(self, moduleId=None, portType=None, portName=None, portSpec=None):
+ self.__db_moduleId = moduleId
+ self.__db_portType = portType
+ self.__db_portName = portName
+ self.__db_portSpec = portSpec
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_portType(self):
+ return self.__db_portType
+ def __set_db_portType(self, portType):
+ self.__db_portType = portType
+ db_portType = property(__get_db_portType, __set_db_portType)
+ def db_add_portType(self, portType):
+ self.__db_portType = portType
+ def db_change_portType(self, portType):
+ self.__db_portType = portType
+ def db_delete_portType(self, portType):
+ self.__db_portType = None
+
+ def __get_db_portName(self):
+ return self.__db_portName
+ def __set_db_portName(self, portName):
+ self.__db_portName = portName
+ db_portName = property(__get_db_portName, __set_db_portName)
+ def db_add_portName(self, portName):
+ self.__db_portName = portName
+ def db_change_portName(self, portName):
+ self.__db_portName = portName
+ def db_delete_portName(self, portName):
+ self.__db_portName = None
+
+ def __get_db_portSpec(self):
+ return self.__db_portSpec
+ def __set_db_portSpec(self, portSpec):
+ self.__db_portSpec = portSpec
+ db_portSpec = property(__get_db_portSpec, __set_db_portSpec)
+ def db_add_portSpec(self, portSpec):
+ self.__db_portSpec = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.__db_portSpec = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.__db_portSpec = None
+
+ def getPrimaryKey(self):
+ return self.__db_moduleId
+
+"""generated automatically by auto_dao.py"""
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, time=None, parent=None, user=None, what=None, date=None, notes=None, datas=None):
+ self.__db_time = time
+ self.__db_parent = parent
+ self.__db_user = user
+ self.__db_what = what
+ self.__db_date = date
+ self.__db_notes = notes
+ if datas is None:
+ self.__db_datas = []
+ else:
+ self.__db_datas = datas
+ def __get_db_time(self):
+ return self.__db_time
+ def __set_db_time(self, time):
+ self.__db_time = time
+ db_time = property(__get_db_time, __set_db_time)
+ def db_add_time(self, time):
+ self.__db_time = time
+ def db_change_time(self, time):
+ self.__db_time = time
+ def db_delete_time(self, time):
+ self.__db_time = None
+
+ def __get_db_parent(self):
+ return self.__db_parent
+ def __set_db_parent(self, parent):
+ self.__db_parent = parent
+ db_parent = property(__get_db_parent, __set_db_parent)
+ def db_add_parent(self, parent):
+ self.__db_parent = parent
+ def db_change_parent(self, parent):
+ self.__db_parent = parent
+ def db_delete_parent(self, parent):
+ self.__db_parent = None
+
+ def __get_db_user(self):
+ return self.__db_user
+ def __set_db_user(self, user):
+ self.__db_user = user
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self.__db_user = user
+ def db_change_user(self, user):
+ self.__db_user = user
+ def db_delete_user(self, user):
+ self.__db_user = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_date(self):
+ return self.__db_date
+ def __set_db_date(self, date):
+ self.__db_date = date
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self.__db_date = date
+ def db_change_date(self, date):
+ self.__db_date = date
+ def db_delete_date(self, date):
+ self.__db_date = None
+
+ def __get_db_notes(self):
+ return self.__db_notes
+ def __set_db_notes(self, notes):
+ self.__db_notes = notes
+ db_notes = property(__get_db_notes, __set_db_notes)
+ def db_add_notes(self, notes):
+ self.__db_notes = notes
+ def db_change_notes(self, notes):
+ self.__db_notes = notes
+ def db_delete_notes(self, notes):
+ self.__db_notes = None
+
+ def __get_db_datas(self):
+ return self.__db_datas
+ def __set_db_datas(self, datas):
+ self.__db_datas = datas
+ db_datas = property(__get_db_datas, __set_db_datas)
+ def db_get_datas(self):
+ return self.__db_datas
+ def db_add_data(self, data):
+ self.__db_datas.append(data)
+ def db_change_data(self, data):
+ found = False
+ for i in xrange(len(self.__db_datas)):
+ if self.__db_datas[i].db_id == data.db_id:
+ self.__db_datas[i] = data
+ found = True
+ break
+ if not found:
+ self.__db_datas.append(data)
+ def db_delete_data(self, data):
+ for i in xrange(len(self.__db_datas)):
+ if self.__db_datas[i].db_id == data.db_id:
+ del self.__db_datas[i]
+ break
+ def db_get_data(self, key):
+ for i in xrange(len(self.__db_datas)):
+ if self.__db_datas[i].db_id == data.db_id:
+ return self.__db_datas[i]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_time
+
+"""generated automatically by auto_dao.py"""
+
+class DBAddConnection(object):
+
+ vtType = 'addConnection'
+
+ def __init__(self, id=None, destinationId=None, destinationModule=None, destinationPort=None, sourceId=None, sourceModule=None, sourcePort=None):
+ self.__db_id = id
+ self.__db_destinationId = destinationId
+ self.__db_destinationModule = destinationModule
+ self.__db_destinationPort = destinationPort
+ self.__db_sourceId = sourceId
+ self.__db_sourceModule = sourceModule
+ self.__db_sourcePort = sourcePort
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_destinationId(self):
+ return self.__db_destinationId
+ def __set_db_destinationId(self, destinationId):
+ self.__db_destinationId = destinationId
+ db_destinationId = property(__get_db_destinationId, __set_db_destinationId)
+ def db_add_destinationId(self, destinationId):
+ self.__db_destinationId = destinationId
+ def db_change_destinationId(self, destinationId):
+ self.__db_destinationId = destinationId
+ def db_delete_destinationId(self, destinationId):
+ self.__db_destinationId = None
+
+ def __get_db_destinationModule(self):
+ return self.__db_destinationModule
+ def __set_db_destinationModule(self, destinationModule):
+ self.__db_destinationModule = destinationModule
+ db_destinationModule = property(__get_db_destinationModule, __set_db_destinationModule)
+ def db_add_destinationModule(self, destinationModule):
+ self.__db_destinationModule = destinationModule
+ def db_change_destinationModule(self, destinationModule):
+ self.__db_destinationModule = destinationModule
+ def db_delete_destinationModule(self, destinationModule):
+ self.__db_destinationModule = None
+
+ def __get_db_destinationPort(self):
+ return self.__db_destinationPort
+ def __set_db_destinationPort(self, destinationPort):
+ self.__db_destinationPort = destinationPort
+ db_destinationPort = property(__get_db_destinationPort, __set_db_destinationPort)
+ def db_add_destinationPort(self, destinationPort):
+ self.__db_destinationPort = destinationPort
+ def db_change_destinationPort(self, destinationPort):
+ self.__db_destinationPort = destinationPort
+ def db_delete_destinationPort(self, destinationPort):
+ self.__db_destinationPort = None
+
+ def __get_db_sourceId(self):
+ return self.__db_sourceId
+ def __set_db_sourceId(self, sourceId):
+ self.__db_sourceId = sourceId
+ db_sourceId = property(__get_db_sourceId, __set_db_sourceId)
+ def db_add_sourceId(self, sourceId):
+ self.__db_sourceId = sourceId
+ def db_change_sourceId(self, sourceId):
+ self.__db_sourceId = sourceId
+ def db_delete_sourceId(self, sourceId):
+ self.__db_sourceId = None
+
+ def __get_db_sourceModule(self):
+ return self.__db_sourceModule
+ def __set_db_sourceModule(self, sourceModule):
+ self.__db_sourceModule = sourceModule
+ db_sourceModule = property(__get_db_sourceModule, __set_db_sourceModule)
+ def db_add_sourceModule(self, sourceModule):
+ self.__db_sourceModule = sourceModule
+ def db_change_sourceModule(self, sourceModule):
+ self.__db_sourceModule = sourceModule
+ def db_delete_sourceModule(self, sourceModule):
+ self.__db_sourceModule = None
+
+ def __get_db_sourcePort(self):
+ return self.__db_sourcePort
+ def __set_db_sourcePort(self, sourcePort):
+ self.__db_sourcePort = sourcePort
+ db_sourcePort = property(__get_db_sourcePort, __set_db_sourcePort)
+ def db_add_sourcePort(self, sourcePort):
+ self.__db_sourcePort = sourcePort
+ def db_change_sourcePort(self, sourcePort):
+ self.__db_sourcePort = sourcePort
+ def db_delete_sourcePort(self, sourcePort):
+ self.__db_sourcePort = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+"""generated automatically by auto_dao.py"""
+
+class DBMoveModule(object):
+
+ vtType = 'moveModule'
+
+ def __init__(self, id=None, dx=None, dy=None):
+ self.__db_id = id
+ self.__db_dx = dx
+ self.__db_dy = dy
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_dx(self):
+ return self.__db_dx
+ def __set_db_dx(self, dx):
+ self.__db_dx = dx
+ db_dx = property(__get_db_dx, __set_db_dx)
+ def db_add_dx(self, dx):
+ self.__db_dx = dx
+ def db_change_dx(self, dx):
+ self.__db_dx = dx
+ def db_delete_dx(self, dx):
+ self.__db_dx = None
+
+ def __get_db_dy(self):
+ return self.__db_dy
+ def __set_db_dy(self, dy):
+ self.__db_dy = dy
+ db_dy = property(__get_db_dy, __set_db_dy)
+ def db_add_dy(self, dy):
+ self.__db_dy = dy
+ def db_change_dy(self, dy):
+ self.__db_dy = dy
+ def db_delete_dy(self, dy):
+ self.__db_dy = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+"""generated automatically by auto_dao.py"""
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, version=None, actions=None, tags=None):
+ self.__db_version = version
+ if actions is None:
+ self.__db_actions = {}
+ else:
+ self.__db_actions = actions
+ if tags is None:
+ self.__db_tags = {}
+ else:
+ self.__db_tags = tags
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_actions(self):
+ return self.__db_actions
+ def __set_db_actions(self, actions):
+ self.__db_actions = actions
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self.__db_actions.values()
+ def db_add_action(self, action):
+ self.__db_actions[action.db_time] = action
+ def db_change_action(self, action):
+ self.__db_actions[action.db_time] = action
+ def db_delete_action(self, action):
+ del self.__db_actions[action.db_time]
+ def db_get_action(self, key):
+ if self.__db_actions.has_key(key):
+ return self.__db_actions[key]
+ return None
+
+ def __get_db_tags(self):
+ return self.__db_tags
+ def __set_db_tags(self, tags):
+ self.__db_tags = tags
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self.__db_tags.values()
+ def db_add_tag(self, tag):
+ self.__db_tags[tag.db_time] = tag
+ def db_change_tag(self, tag):
+ self.__db_tags[tag.db_time] = tag
+ def db_delete_tag(self, tag):
+ del self.__db_tags[tag.db_time]
+ def db_get_tag(self, key):
+ if self.__db_tags.has_key(key):
+ return self.__db_tags[key]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_version
+
+"""generated automatically by auto_dao.py"""
+
+class DBChangeAnnotation(object):
+
+ vtType = 'changeAnnotation'
+
+ def __init__(self, moduleId=None, key=None, value=None):
+ self.__db_moduleId = moduleId
+ self.__db_key = key
+ self.__db_value = value
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_moduleId
+
diff --git a/vistrails/db/versions/v0_3_0/persistence/__init__.py b/vistrails/db/versions/v0_3_0/persistence/__init__.py
new file mode 100644
index 0000000..fca428d
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/persistence/__init__.py
@@ -0,0 +1,53 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from xml.auto_gen import XMLDAOListBase
+import xml.io
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ return xml.io.open_from_xml(filename, vtType, self['xml'])
+
+ def save_to_xml(self, obj, filename):
+ xml.io.save_to_xml(obj, filename, self['xml'])
+
+ def serialize(self, obj):
+ return xml.io.serialize(obj, self['xml'])
+
+ def unserialize(self, str, type):
+ return xml.io.unserialize(str, type, self['xml'])
diff --git a/vistrails/db/versions/v0_3_0/persistence/xml/__init__.py b/vistrails/db/versions/v0_3_0/persistence/xml/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_3_0/persistence/xml/auto_gen.py b/vistrails/db/versions/v0_3_0/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..7371db2
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/persistence/xml/auto_gen.py
@@ -0,0 +1,638 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from vistrails.db.versions.v0_3_0.persistence.xml.xml_dao import XMLDAO
+from vistrails.db.versions.v0_3_0.domain.auto_gen import *
+
+class DBChangeParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'set':
+ return None
+
+ # read attributes
+ moduleId = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ alias = self.convertFromStr(self.getAttribute(node, 'alias'), 'str')
+ functionId = self.convertFromStr(self.getAttribute(node, 'functionId'), 'long')
+ function = self.convertFromStr(self.getAttribute(node, 'function'), 'str')
+ parameterId = self.convertFromStr(self.getAttribute(node, 'parameterId'), 'long')
+ parameter = self.convertFromStr(self.getAttribute(node, 'parameter'), 'str')
+ type = self.convertFromStr(self.getAttribute(node, 'type'), 'str')
+ value = self.convertFromStr(self.getAttribute(node, 'value'), 'str')
+
+ return DBChangeParameter(moduleId=moduleId,
+ alias=alias,
+ functionId=functionId,
+ function=function,
+ parameterId=parameterId,
+ parameter=parameter,
+ type=type,
+ value=value)
+
+ def toXML(self, changeParameter, doc):
+ node = doc.createElement('set')
+
+ # set attributes
+ node.setAttribute('moduleId',self.convertToStr(changeParameter.db_moduleId, 'long'))
+ node.setAttribute('alias',self.convertToStr(changeParameter.db_alias, 'str'))
+ node.setAttribute('functionId',self.convertToStr(changeParameter.db_functionId, 'long'))
+ node.setAttribute('function',self.convertToStr(changeParameter.db_function, 'str'))
+ node.setAttribute('parameterId',self.convertToStr(changeParameter.db_parameterId, 'long'))
+ node.setAttribute('parameter',self.convertToStr(changeParameter.db_parameter, 'str'))
+ node.setAttribute('type',self.convertToStr(changeParameter.db_type, 'str'))
+ node.setAttribute('value',self.convertToStr(changeParameter.db_value, 'str'))
+
+ return node
+
+class DBDeleteFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'function':
+ return None
+
+ # read attributes
+ moduleId = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ functionId = self.convertFromStr(self.getAttribute(node, 'functionId'), 'long')
+
+ return DBDeleteFunction(moduleId=moduleId,
+ functionId=functionId)
+
+ def toXML(self, deleteFunction, doc):
+ node = doc.createElement('function')
+
+ # set attributes
+ node.setAttribute('moduleId',self.convertToStr(deleteFunction.db_moduleId, 'long'))
+ node.setAttribute('functionId',self.convertToStr(deleteFunction.db_functionId, 'long'))
+
+ return node
+
+class DBDeleteConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'connection':
+ return None
+
+ # read attributes
+ connectionId = self.convertFromStr(self.getAttribute(node, 'connectionId'), 'long')
+
+ return DBDeleteConnection(connectionId=connectionId)
+
+ def toXML(self, deleteConnection, doc):
+ node = doc.createElement('connection')
+
+ # set attributes
+ node.setAttribute('connectionId',self.convertToStr(deleteConnection.db_connectionId, 'long'))
+
+ return node
+
+class DBAddModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'object':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ cache = self.convertFromStr(self.getAttribute(node, 'cache'), 'int')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ x = self.convertFromStr(self.getAttribute(node, 'x'), 'float')
+ y = self.convertFromStr(self.getAttribute(node, 'y'), 'float')
+
+ return DBAddModule(id=id,
+ cache=cache,
+ name=name,
+ x=x,
+ y=y)
+
+ def toXML(self, addModule, doc):
+ node = doc.createElement('object')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(addModule.db_id, 'long'))
+ node.setAttribute('cache',self.convertToStr(addModule.db_cache, 'int'))
+ node.setAttribute('name',self.convertToStr(addModule.db_name, 'str'))
+ node.setAttribute('x',self.convertToStr(addModule.db_x, 'float'))
+ node.setAttribute('y',self.convertToStr(addModule.db_y, 'float'))
+
+ return node
+
+class DBDeleteAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'annotation':
+ return None
+
+ # read attributes
+ moduleId = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ key = self.convertFromStr(self.getAttribute(node, 'key'), 'str')
+
+ return DBDeleteAnnotation(moduleId=moduleId,
+ key=key)
+
+ def toXML(self, deleteAnnotation, doc):
+ node = doc.createElement('annotation')
+
+ # set attributes
+ node.setAttribute('moduleId',self.convertToStr(deleteAnnotation.db_moduleId, 'long'))
+ node.setAttribute('key',self.convertToStr(deleteAnnotation.db_key, 'str'))
+
+ return node
+
+class DBDeleteModulePortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'deletePort':
+ return None
+
+ # read attributes
+ moduleId = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ portType = self.convertFromStr(self.getAttribute(node, 'portType'), 'str')
+ portName = self.convertFromStr(self.getAttribute(node, 'portName'), 'str')
+
+ return DBDeleteModulePort(moduleId=moduleId,
+ portType=portType,
+ portName=portName)
+
+ def toXML(self, deleteModulePort, doc):
+ node = doc.createElement('deletePort')
+
+ # set attributes
+ node.setAttribute('moduleId',self.convertToStr(deleteModulePort.db_moduleId, 'long'))
+ node.setAttribute('portType',self.convertToStr(deleteModulePort.db_portType, 'str'))
+ node.setAttribute('portName',self.convertToStr(deleteModulePort.db_portName, 'str'))
+
+ return node
+
+class DBDeleteModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'module':
+ return None
+
+ # read attributes
+ moduleId = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+
+ return DBDeleteModule(moduleId=moduleId)
+
+ def toXML(self, deleteModule, doc):
+ node = doc.createElement('module')
+
+ # set attributes
+ node.setAttribute('moduleId',self.convertToStr(deleteModule.db_moduleId, 'long'))
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'tag':
+ return None
+
+ # read attributes
+ time = self.convertFromStr(self.getAttribute(node, 'time'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+ return DBTag(time=time,
+ name=name)
+
+ def toXML(self, tag, doc):
+ node = doc.createElement('tag')
+
+ # set attributes
+ node.setAttribute('time',self.convertToStr(tag.db_time, 'long'))
+ node.setAttribute('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBAddModulePortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'addPort':
+ return None
+
+ # read attributes
+ moduleId = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ portType = self.convertFromStr(self.getAttribute(node, 'portType'), 'str')
+ portName = self.convertFromStr(self.getAttribute(node, 'portName'), 'str')
+ portSpec = self.convertFromStr(self.getAttribute(node, 'portSpec'), 'str')
+
+ return DBAddModulePort(moduleId=moduleId,
+ portType=portType,
+ portName=portName,
+ portSpec=portSpec)
+
+ def toXML(self, addModulePort, doc):
+ node = doc.createElement('addPort')
+
+ # set attributes
+ node.setAttribute('moduleId',self.convertToStr(addModulePort.db_moduleId, 'long'))
+ node.setAttribute('portType',self.convertToStr(addModulePort.db_portType, 'str'))
+ node.setAttribute('portName',self.convertToStr(addModulePort.db_portName, 'str'))
+ node.setAttribute('portSpec',self.convertToStr(addModulePort.db_portSpec, 'str'))
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'action':
+ return None
+
+ datas = []
+
+ # read attributes
+ time = self.convertFromStr(self.getAttribute(node, 'time'), 'long')
+ parent = self.convertFromStr(self.getAttribute(node, 'parent'), 'long')
+ user = self.convertFromStr(self.getAttribute(node, 'user'), 'str')
+ what = self.convertFromStr(self.getAttribute(node, 'what'), 'str')
+ date = self.convertFromStr(self.getAttribute(node, 'date'), 'str')
+
+ notes = None
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'notes':
+ notes = self.convertFromStr(child.firstChild.nodeValue,'str')
+ elif what == 'addModule' and child.nodeName == 'object':
+ data = self.getDao('addModule').fromXML(child)
+ datas.append(data)
+ what = 'addModule'
+ elif what == 'addConnection' and child.nodeName == 'connect':
+ data = self.getDao('addConnection').fromXML(child)
+ datas.append(data)
+ what = 'addConnection'
+ elif what == 'changeParameter' and child.nodeName == 'set':
+ data = self.getDao('changeParameter').fromXML(child)
+ datas.append(data)
+ what = 'changeParameter'
+ elif what == 'changeAnnotation' and child.nodeName == 'set':
+ data = self.getDao('changeAnnotation').fromXML(child)
+ datas.append(data)
+ what = 'changeAnnotation'
+ elif what == 'addModulePort' and child.nodeName == 'addPort':
+ data = self.getDao('addModulePort').fromXML(child)
+ datas.append(data)
+ what = 'addModulePort'
+ elif what == 'moveModule' and child.nodeName == 'move':
+ data = self.getDao('moveModule').fromXML(child)
+ datas.append(data)
+ what = 'moveModule'
+ elif what == 'deleteModule' and child.nodeName == 'module':
+ data = self.getDao('deleteModule').fromXML(child)
+ datas.append(data)
+ what = 'deleteModule'
+ elif what == 'deleteConnection' and child.nodeName == 'connection':
+ data = self.getDao('deleteConnection').fromXML(child)
+ datas.append(data)
+ what = 'deleteConnection'
+ elif what == 'deleteFunction' and child.nodeName == 'function':
+ data = self.getDao('deleteFunction').fromXML(child)
+ datas.append(data)
+ what = 'deleteFunction'
+ elif what == 'deleteAnnotation' and child.nodeName == 'annotation':
+ data = self.getDao('deleteAnnotation').fromXML(child)
+ datas.append(data)
+ what = 'deleteAnnotation'
+ elif what == 'deleteModulePort' and child.nodeName == 'deletePort':
+ data = self.getDao('deleteModulePort').fromXML(child)
+ datas.append(data)
+ what = 'deleteModulePort'
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ return DBAction(time=time,
+ parent=parent,
+ user=user,
+ what=what,
+ date=date,
+ notes=notes,
+ datas=datas)
+
+ def toXML(self, action, doc):
+ node = doc.createElement('action')
+
+ # set attributes
+ node.setAttribute('time',self.convertToStr(action.db_time, 'long'))
+ node.setAttribute('parent',self.convertToStr(action.db_parent, 'long'))
+ node.setAttribute('user',self.convertToStr(action.db_user, 'str'))
+ node.setAttribute('what',self.convertToStr(action.db_what, 'str'))
+ node.setAttribute('date',self.convertToStr(action.db_date, 'str'))
+
+ # set elements
+ if action.db_notes is not None:
+ child = action.db_notes
+ notesNode = doc.createElement('notes')
+ notesText = doc.createTextNode(self.convertToStr(child, 'str'))
+ notesNode.appendChild(notesText)
+ node.appendChild(notesNode)
+ datas = action.db_datas
+ for data in datas:
+ if action.db_what == 'addModule':
+ node.appendChild(self.getDao('addModule').toXML(data, doc))
+ elif action.db_what == 'addConnection':
+ node.appendChild(self.getDao('addConnection').toXML(data, doc))
+ elif action.db_what == 'changeParameter':
+ node.appendChild(self.getDao('changeParameter').toXML(data, doc))
+ elif action.db_what == 'changeAnnotation':
+ node.appendChild(self.getDao('changeAnnotation').toXML(data, doc))
+ elif action.db_what == 'addModulePort':
+ node.appendChild(self.getDao('addModulePort').toXML(data, doc))
+ elif action.db_what == 'moveModule':
+ node.appendChild(self.getDao('moveModule').toXML(data, doc))
+ elif action.db_what == 'deleteModule':
+ node.appendChild(self.getDao('deleteModule').toXML(data, doc))
+ elif action.db_what == 'deleteConnection':
+ node.appendChild(self.getDao('deleteConnection').toXML(data, doc))
+ elif action.db_what == 'deleteFunction':
+ node.appendChild(self.getDao('deleteFunction').toXML(data, doc))
+ elif action.db_what == 'deleteAnnotation':
+ node.appendChild(self.getDao('deleteAnnotation').toXML(data, doc))
+ elif action.db_what == 'deleteModulePort':
+ node.appendChild(self.getDao('deleteModulePort').toXML(data, doc))
+
+ return node
+
+class DBAddConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'connect':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ destinationId = self.convertFromStr(self.getAttribute(node, 'destinationId'), 'long')
+ destinationModule = self.convertFromStr(self.getAttribute(node, 'destinationModule'), 'str')
+ destinationPort = self.convertFromStr(self.getAttribute(node, 'destinationPort'), 'str')
+ sourceId = self.convertFromStr(self.getAttribute(node, 'sourceId'), 'long')
+ sourceModule = self.convertFromStr(self.getAttribute(node, 'sourceModule'), 'str')
+ sourcePort = self.convertFromStr(self.getAttribute(node, 'sourcePort'), 'str')
+
+ return DBAddConnection(id=id,
+ destinationId=destinationId,
+ destinationModule=destinationModule,
+ destinationPort=destinationPort,
+ sourceId=sourceId,
+ sourceModule=sourceModule,
+ sourcePort=sourcePort)
+
+ def toXML(self, addConnection, doc):
+ node = doc.createElement('connect')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(addConnection.db_id, 'long'))
+ node.setAttribute('destinationId',self.convertToStr(addConnection.db_destinationId, 'long'))
+ node.setAttribute('destinationModule',self.convertToStr(addConnection.db_destinationModule, 'str'))
+ node.setAttribute('destinationPort',self.convertToStr(addConnection.db_destinationPort, 'str'))
+ node.setAttribute('sourceId',self.convertToStr(addConnection.db_sourceId, 'long'))
+ node.setAttribute('sourceModule',self.convertToStr(addConnection.db_sourceModule, 'str'))
+ node.setAttribute('sourcePort',self.convertToStr(addConnection.db_sourcePort, 'str'))
+
+ return node
+
+class DBMoveModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'move':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ dx = self.convertFromStr(self.getAttribute(node, 'dx'), 'float')
+ dy = self.convertFromStr(self.getAttribute(node, 'dy'), 'float')
+
+ return DBMoveModule(id=id,
+ dx=dx,
+ dy=dy)
+
+ def toXML(self, moveModule, doc):
+ node = doc.createElement('move')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(moveModule.db_id, 'long'))
+ node.setAttribute('dx',self.convertToStr(moveModule.db_dx, 'float'))
+ node.setAttribute('dy',self.convertToStr(moveModule.db_dy, 'float'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'visTrail':
+ return None
+
+ actions = {}
+ tags = {}
+
+ # read attributes
+ version = self.convertFromStr(self.getAttribute(node, 'version'), 'str')
+
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'action':
+ action = self.getDao('action').fromXML(child)
+ actions[action.db_time] = action
+ elif child.nodeName == 'tag':
+ tag = self.getDao('tag').fromXML(child)
+ tags[tag.db_time] = tag
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ return DBVistrail(version=version,
+ actions=actions,
+ tags=tags)
+
+ def toXML(self, vistrail, doc):
+ node = doc.createElement('visTrail')
+
+ # set attributes
+ node.setAttribute('version',self.convertToStr(vistrail.db_version, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions.itervalues():
+ node.appendChild(self.getDao('action').toXML(action, doc))
+ tags = vistrail.db_tags
+ for tag in tags.itervalues():
+ node.appendChild(self.getDao('tag').toXML(tag, doc))
+
+ return node
+
+class DBChangeAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'set':
+ return None
+
+ # read attributes
+ moduleId = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ key = self.convertFromStr(self.getAttribute(node, 'key'), 'str')
+ value = self.convertFromStr(self.getAttribute(node, 'value'), 'str')
+
+ return DBChangeAnnotation(moduleId=moduleId,
+ key=key,
+ value=value)
+
+ def toXML(self, changeAnnotation, doc):
+ node = doc.createElement('set')
+
+ # set attributes
+ node.setAttribute('moduleId',self.convertToStr(changeAnnotation.db_moduleId, 'long'))
+ node.setAttribute('key',self.convertToStr(changeAnnotation.db_key, 'str'))
+ node.setAttribute('value',self.convertToStr(changeAnnotation.db_value, 'str'))
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'changeParameter' not in self:
+ self['changeParameter'] = DBChangeParameterXMLDAOBase(self)
+ if 'deleteFunction' not in self:
+ self['deleteFunction'] = DBDeleteFunctionXMLDAOBase(self)
+ if 'deleteConnection' not in self:
+ self['deleteConnection'] = DBDeleteConnectionXMLDAOBase(self)
+ if 'addModule' not in self:
+ self['addModule'] = DBAddModuleXMLDAOBase(self)
+ if 'deleteAnnotation' not in self:
+ self['deleteAnnotation'] = DBDeleteAnnotationXMLDAOBase(self)
+ if 'deleteModulePort' not in self:
+ self['deleteModulePort'] = DBDeleteModulePortXMLDAOBase(self)
+ if 'deleteModule' not in self:
+ self['deleteModule'] = DBDeleteModuleXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'addModulePort' not in self:
+ self['addModulePort'] = DBAddModulePortXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'addConnection' not in self:
+ self['addConnection'] = DBAddConnectionXMLDAOBase(self)
+ if 'moveModule' not in self:
+ self['moveModule'] = DBMoveModuleXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'changeAnnotation' not in self:
+ self['changeAnnotation'] = DBChangeAnnotationXMLDAOBase(self)
diff --git a/vistrails/db/versions/v0_3_0/persistence/xml/io.py b/vistrails/db/versions/v0_3_0/persistence/xml/io.py
new file mode 100644
index 0000000..0b01c45
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/persistence/xml/io.py
@@ -0,0 +1,95 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.parsers.expat import ExpatError
+import xml.dom.minidom
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_3_0 import version as my_version
+
+def parse_xml_file(filename):
+ try:
+ return xml.dom.minidom.parse(filename)
+ except xml.parsers.expat.ExpatError, e:
+ msg = 'XML parse error at line %s, col %s: %s' % \
+ (e.lineno, e.offset, e.code)
+ raise VistrailsDBException(msg)
+
+def write_xml_file(filename, dom, prettyprint=True):
+ output = open(filename, 'w')
+ if prettyprint:
+ dom.writexml(output, '',' ','\n')
+ else:
+ dom.writexml(output)
+ output.close()
+
+def read_xml_object(vtType, node, dao_list):
+ return dao_list[vtType].fromXML(node)
+
+def write_xml_object(obj, dom, dao_list, node=None):
+ res_node = dao_list[obj.vtType].toXML(obj, dom, node)
+ return res_node
+
+def open_from_xml(filename, vtType, dao_list):
+ """open_from_xml(filename) -> DBVistrail"""
+ dom = parse_xml_file(filename)
+ vistrail = read_xml_object(vtType, dom.documentElement, dao_list)
+ dom.unlink()
+ return vistrail
+
+def save_to_xml(obj, filename, dao_list):
+ dom = xml.dom.minidom.getDOMImplementation().createDocument(None, None,
+ None)
+ root = write_xml_object(obj, dom, dao_list)
+ dom.appendChild(root)
+ if obj.vtType == 'vistrail':
+ root.setAttribute('version', my_version)
+ root.setAttribute('xmlns:xsi',
+ 'http://www.w3.org/2001/XMLSchema-instance')
+ root.setAttribute('xsi:schemaLocation',
+ 'http://www.vistrails.org/vistrail.xsd')
+ write_xml_file(filename, dom)
+ dom.unlink()
+
+def serialize(object, dao_list):
+ dom = xml.dom.minidom.getDOMImplementation().createDocument(None, None,
+ None)
+ root = write_xml_object(object, dom, dao_list)
+ dom.appendChild(root)
+ return dom.toxml()
+
+def unserialize(str, obj_type):
+ dom = xml.dom.minidom.parseString(str)
+ return read_xml_object(obj_type, dom.documentElement, dao_list)
+
diff --git a/vistrails/db/versions/v0_3_0/persistence/xml/xml_dao.py b/vistrails/db/versions/v0_3_0/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..de42aa2
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/persistence/xml/xml_dao.py
@@ -0,0 +1,77 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v0_3_0/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_3_0/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..b0a275e
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/schemas/xml/vistrail.xsd
@@ -0,0 +1,161 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="visTrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="notes" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element name="addModule" ref="object" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="addConnection" ref="connect" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="changeParameter" ref="set" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="changeAnnotation" ref="set" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="addModulePort" ref="addPort" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="moveModule" ref="move" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="deleteModule" ref="module" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="deleteConnection" ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="deleteFunction" ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="deleteAnnotation" ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="deleteModulePort" ref="deletePort" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="time" type="xs:int"/>
+ <xs:attribute name="parent" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="date" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="time" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="object">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connect">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="destinationId" type="xs:int"/>
+ <xs:attribute name="destinationModule" type="xs:string"/>
+ <xs:attribute name="destinationPort" type="xs:string"/>
+ <xs:attribute name="sourceId" type="xs:int"/>
+ <xs:attribute name="sourceModule" type="xs:string"/>
+ <xs:attribute name="sourcePort" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="set">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ <xs:attribute name="functionId" type="xs:int"/>
+ <xs:attribute name="function" type="xs:string"/>
+ <xs:attribute name="parameterId" type="xs:int"/>
+ <xs:attribute name="parameter" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="set">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="addPort">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="portType" type="xs:string"/>
+ <xs:attribute name="portName" type="xs:string"/>
+ <xs:attribute name="portSpec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="move">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="dx" type="xs:float"/>
+ <xs:attribute name="dy" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:attribute name="connectionId" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="functionId" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="deletePort">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="portType" type="xs:string"/>
+ <xs:attribute name="portName" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_3_0/specs/action.xml b/vistrails/db/versions/v0_3_0/specs/action.xml
new file mode 100644
index 0000000..104c998
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/action.xml
@@ -0,0 +1,101 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ </layout>
+
+ <property name="time" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="parent" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="date" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="notes" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what" mapping="one-to-many">
+ <property ref="true" object="addModule" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="addConnection" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="changeParameter" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="changeAnnotation" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="addModulePort" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="moveModule" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="deleteModule" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="deleteConnection" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="deleteFunction" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="deleteAnnotation" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="deleteModulePort" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/addConnection.xml b/vistrails/db/versions/v0_3_0/specs/addConnection.xml
new file mode 100644
index 0000000..99599cf
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/addConnection.xml
@@ -0,0 +1,68 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="addConnection">
+ <layout>
+ <xml name="connect" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="destinationId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="destinationModule" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="destinationPort" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="sourceId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="sourceModule" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="sourcePort" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/addModule.xml b/vistrails/db/versions/v0_3_0/specs/addModule.xml
new file mode 100644
index 0000000..d3584c1
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/addModule.xml
@@ -0,0 +1,60 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="addModule">
+ <layout>
+ <xml name="object" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/addModulePort.xml b/vistrails/db/versions/v0_3_0/specs/addModulePort.xml
new file mode 100644
index 0000000..5f83e50
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/addModulePort.xml
@@ -0,0 +1,56 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="addModulePort">
+ <layout>
+ <xml name="addPort" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="portType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="portName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="portSpec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/changeAnnotation.xml b/vistrails/db/versions/v0_3_0/specs/changeAnnotation.xml
new file mode 100644
index 0000000..3915523
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/changeAnnotation.xml
@@ -0,0 +1,52 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="changeAnnotation">
+ <layout>
+ <xml name="set" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/changeParameter.xml b/vistrails/db/versions/v0_3_0/specs/changeParameter.xml
new file mode 100644
index 0000000..8a8de86
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/changeParameter.xml
@@ -0,0 +1,72 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="changeParameter">
+ <layout>
+ <xml name="set" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="functionId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="function" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="parameterId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="parameter" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/deleteAnnotation.xml b/vistrails/db/versions/v0_3_0/specs/deleteAnnotation.xml
new file mode 100644
index 0000000..e20c4ae
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/deleteAnnotation.xml
@@ -0,0 +1,48 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="deleteAnnotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/deleteConnection.xml b/vistrails/db/versions/v0_3_0/specs/deleteConnection.xml
new file mode 100644
index 0000000..8ff250a
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/deleteConnection.xml
@@ -0,0 +1,44 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="deleteConnection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ </layout>
+
+ <property name="connectionId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/deleteFunction.xml b/vistrails/db/versions/v0_3_0/specs/deleteFunction.xml
new file mode 100644
index 0000000..d647c15
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/deleteFunction.xml
@@ -0,0 +1,48 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="deleteFunction">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="functionId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/deleteModule.xml b/vistrails/db/versions/v0_3_0/specs/deleteModule.xml
new file mode 100644
index 0000000..a07f569
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/deleteModule.xml
@@ -0,0 +1,44 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="deleteModule">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/deleteModulePort.xml b/vistrails/db/versions/v0_3_0/specs/deleteModulePort.xml
new file mode 100644
index 0000000..e6e6a7c
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/deleteModulePort.xml
@@ -0,0 +1,52 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="deleteModulePort">
+ <layout>
+ <xml name="deletePort" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="portType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="portName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/moveModule.xml b/vistrails/db/versions/v0_3_0/specs/moveModule.xml
new file mode 100644
index 0000000..3712805
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/moveModule.xml
@@ -0,0 +1,52 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="moveModule">
+ <layout>
+ <xml name="move" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="dx" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ </property>
+
+ <property name="dy" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/tag.xml b/vistrails/db/versions/v0_3_0/specs/tag.xml
new file mode 100644
index 0000000..6022ef3
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/tag.xml
@@ -0,0 +1,48 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ </layout>
+
+ <property name="time" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_0/specs/vistrail.xml b/vistrails/db/versions/v0_3_0/specs/vistrail.xml
new file mode 100644
index 0000000..aa68d46
--- /dev/null
+++ b/vistrails/db/versions/v0_3_0/specs/vistrail.xml
@@ -0,0 +1,52 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="vistrail">
+ <layout>
+ <xml name="visTrail" nodeType="xs:element"/>
+ </layout>
+
+ <property name="version" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property ref="true" object="action" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/__init__.py b/vistrails/db/versions/v0_3_1/__init__.py
new file mode 100644
index 0000000..1ba86e3
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.3.1'
diff --git a/vistrails/db/versions/v0_3_1/domain/__init__.py b/vistrails/db/versions/v0_3_1/domain/__init__.py
new file mode 100644
index 0000000..fb50f24
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/domain/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.versions.v0_3_0.domain import *
diff --git a/vistrails/db/versions/v0_3_1/persistence/__init__.py b/vistrails/db/versions/v0_3_1/persistence/__init__.py
new file mode 100644
index 0000000..47924e5
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/persistence/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.versions.v0_3_0.persistence import DAOList
diff --git a/vistrails/db/versions/v0_3_1/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_3_1/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..b0a275e
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/schemas/xml/vistrail.xsd
@@ -0,0 +1,161 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="visTrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="notes" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element name="addModule" ref="object" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="addConnection" ref="connect" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="changeParameter" ref="set" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="changeAnnotation" ref="set" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="addModulePort" ref="addPort" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="moveModule" ref="move" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="deleteModule" ref="module" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="deleteConnection" ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="deleteFunction" ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="deleteAnnotation" ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="deleteModulePort" ref="deletePort" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="time" type="xs:int"/>
+ <xs:attribute name="parent" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="date" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="time" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="object">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connect">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="destinationId" type="xs:int"/>
+ <xs:attribute name="destinationModule" type="xs:string"/>
+ <xs:attribute name="destinationPort" type="xs:string"/>
+ <xs:attribute name="sourceId" type="xs:int"/>
+ <xs:attribute name="sourceModule" type="xs:string"/>
+ <xs:attribute name="sourcePort" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="set">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ <xs:attribute name="functionId" type="xs:int"/>
+ <xs:attribute name="function" type="xs:string"/>
+ <xs:attribute name="parameterId" type="xs:int"/>
+ <xs:attribute name="parameter" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="set">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="addPort">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="portType" type="xs:string"/>
+ <xs:attribute name="portName" type="xs:string"/>
+ <xs:attribute name="portSpec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="move">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="dx" type="xs:float"/>
+ <xs:attribute name="dy" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:attribute name="connectionId" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="functionId" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="deletePort">
+ <xs:complexType>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="portType" type="xs:string"/>
+ <xs:attribute name="portName" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_3_1/specs/action.xml b/vistrails/db/versions/v0_3_1/specs/action.xml
new file mode 100644
index 0000000..104c998
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/action.xml
@@ -0,0 +1,101 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ </layout>
+
+ <property name="time" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="parent" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="date" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="notes" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what" mapping="one-to-many">
+ <property ref="true" object="addModule" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="addConnection" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="changeParameter" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="changeAnnotation" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="addModulePort" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="moveModule" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="deleteModule" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="deleteConnection" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="deleteFunction" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="deleteAnnotation" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="deleteModulePort" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/addConnection.xml b/vistrails/db/versions/v0_3_1/specs/addConnection.xml
new file mode 100644
index 0000000..99599cf
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/addConnection.xml
@@ -0,0 +1,68 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="addConnection">
+ <layout>
+ <xml name="connect" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="destinationId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="destinationModule" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="destinationPort" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="sourceId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="sourceModule" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="sourcePort" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/addModule.xml b/vistrails/db/versions/v0_3_1/specs/addModule.xml
new file mode 100644
index 0000000..d3584c1
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/addModule.xml
@@ -0,0 +1,60 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="addModule">
+ <layout>
+ <xml name="object" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/addModulePort.xml b/vistrails/db/versions/v0_3_1/specs/addModulePort.xml
new file mode 100644
index 0000000..5f83e50
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/addModulePort.xml
@@ -0,0 +1,56 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="addModulePort">
+ <layout>
+ <xml name="addPort" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="portType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="portName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="portSpec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/changeAnnotation.xml b/vistrails/db/versions/v0_3_1/specs/changeAnnotation.xml
new file mode 100644
index 0000000..3915523
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/changeAnnotation.xml
@@ -0,0 +1,52 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="changeAnnotation">
+ <layout>
+ <xml name="set" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/changeParameter.xml b/vistrails/db/versions/v0_3_1/specs/changeParameter.xml
new file mode 100644
index 0000000..8a8de86
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/changeParameter.xml
@@ -0,0 +1,72 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="changeParameter">
+ <layout>
+ <xml name="set" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="functionId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="function" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="parameterId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="parameter" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/deleteAnnotation.xml b/vistrails/db/versions/v0_3_1/specs/deleteAnnotation.xml
new file mode 100644
index 0000000..e20c4ae
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/deleteAnnotation.xml
@@ -0,0 +1,48 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="deleteAnnotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/deleteConnection.xml b/vistrails/db/versions/v0_3_1/specs/deleteConnection.xml
new file mode 100644
index 0000000..8ff250a
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/deleteConnection.xml
@@ -0,0 +1,44 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="deleteConnection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ </layout>
+
+ <property name="connectionId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/deleteFunction.xml b/vistrails/db/versions/v0_3_1/specs/deleteFunction.xml
new file mode 100644
index 0000000..d647c15
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/deleteFunction.xml
@@ -0,0 +1,48 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="deleteFunction">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="functionId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/deleteModule.xml b/vistrails/db/versions/v0_3_1/specs/deleteModule.xml
new file mode 100644
index 0000000..a07f569
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/deleteModule.xml
@@ -0,0 +1,44 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="deleteModule">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/deleteModulePort.xml b/vistrails/db/versions/v0_3_1/specs/deleteModulePort.xml
new file mode 100644
index 0000000..e6e6a7c
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/deleteModulePort.xml
@@ -0,0 +1,52 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="deleteModulePort">
+ <layout>
+ <xml name="deletePort" nodeType="xs:element"/>
+ </layout>
+
+ <property name="moduleId" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="portType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="portName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/moveModule.xml b/vistrails/db/versions/v0_3_1/specs/moveModule.xml
new file mode 100644
index 0000000..3712805
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/moveModule.xml
@@ -0,0 +1,52 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="moveModule">
+ <layout>
+ <xml name="move" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="dx" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ </property>
+
+ <property name="dy" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/tag.xml b/vistrails/db/versions/v0_3_1/specs/tag.xml
new file mode 100644
index 0000000..6022ef3
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/tag.xml
@@ -0,0 +1,48 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ </layout>
+
+ <property name="time" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/specs/vistrail.xml b/vistrails/db/versions/v0_3_1/specs/vistrail.xml
new file mode 100644
index 0000000..aa68d46
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/specs/vistrail.xml
@@ -0,0 +1,52 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="vistrail">
+ <layout>
+ <xml name="visTrail" nodeType="xs:element"/>
+ </layout>
+
+ <property name="version" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property ref="true" object="action" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_3_1/translate/__init__.py b/vistrails/db/versions/v0_3_1/translate/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_3_1/translate/v0_3_0.py b/vistrails/db/versions/v0_3_1/translate/v0_3_0.py
new file mode 100644
index 0000000..13ecea7
--- /dev/null
+++ b/vistrails/db/versions/v0_3_1/translate/v0_3_0.py
@@ -0,0 +1,47 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+def translateVistrail(_vistrail):
+ # FIXME should this be a deepcopy?
+ vistrail = copy.deepcopy(_vistrail)
+ for action in vistrail.db_get_actions():
+# print 'translating action %s' % action.db_time
+ if action.db_what == 'addModule':
+ if action.db_datas[0].db_cache == 0:
+ action.db_datas[0].db_cache = 1
+ vistrail.db_version = '0.3.1'
+ return vistrail
diff --git a/vistrails/db/versions/v0_5_0/__init__.py b/vistrails/db/versions/v0_5_0/__init__.py
new file mode 100644
index 0000000..81e9321
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.5.0'
diff --git a/vistrails/db/versions/v0_5_0/domain/__init__.py b/vistrails/db/versions/v0_5_0/domain/__init__.py
new file mode 100644
index 0000000..f9f4892
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/domain/__init__.py
@@ -0,0 +1,38 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from workflow import DBWorkflow
+from vistrail import DBVistrail
diff --git a/vistrails/db/versions/v0_5_0/domain/auto_gen.py b/vistrails/db/versions/v0_5_0/domain/auto_gen.py
new file mode 100644
index 0000000..ef7ae65
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/domain/auto_gen.py
@@ -0,0 +1,2696 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, spec=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_type = type
+ self.__db_spec = spec
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBPortSpec()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_name = self.db_name
+ cp.is_dirty = self.is_dirty
+ cp.db_type = self.db_type
+ cp.is_dirty = self.is_dirty
+ cp.db_spec = self.db_spec
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_spec(self):
+ return self.__db_spec
+ def __set_db_spec(self, spec):
+ self.__db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self.__db_spec = spec
+ def db_change_spec(self, spec):
+ self.__db_spec = spec
+ def db_delete_spec(self, spec):
+ self.__db_spec = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self.__db_id = id
+ self.__db_cache = cache
+ self.__db_name = name
+ self.__db_location = location
+ if functions is None:
+ self.__db_functions = []
+ else:
+ self.__db_functions = functions
+ if annotations is None:
+ self.__db_annotations = {}
+ else:
+ self.__db_annotations = annotations
+ if portSpecs is None:
+ self.__db_portSpecs = []
+ else:
+ self.__db_portSpecs = portSpecs
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBModule()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_cache = self.db_cache
+ cp.is_dirty = self.is_dirty
+ cp.db_name = self.db_name
+ cp.is_dirty = self.is_dirty
+ cp.db_location = self.db_location
+ cp.is_dirty = self.is_dirty
+ if self.db_functions is None:
+ cp.db_functions = None
+ else:
+ cp.db_functions = [copy.copy(v) for v in self.db_functions]
+ cp.is_dirty = self.is_dirty
+ if self.db_annotations is None:
+ cp.db_annotations = None
+ else:
+ cp.db_annotations = dict([(k,copy.copy(v)) for (k,v) in self.db_annotations.iteritems()])
+ cp.is_dirty = self.is_dirty
+ if self.db_portSpecs is None:
+ cp.db_portSpecs = None
+ else:
+ cp.db_portSpecs = [copy.copy(v) for v in self.db_portSpecs]
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.extend(self.db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_location = None
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_functions = []
+ for child in self.db_annotations.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_annotations = {}
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_portSpecs = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_cache(self):
+ return self.__db_cache
+ def __set_db_cache(self, cache):
+ self.__db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self.__db_cache = cache
+ def db_change_cache(self, cache):
+ self.__db_cache = cache
+ def db_delete_cache(self, cache):
+ self.__db_cache = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_location(self):
+ return self.__db_location
+ def __set_db_location(self, location):
+ self.__db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self.__db_location = location
+ def db_change_location(self, location):
+ self.__db_location = location
+ def db_delete_location(self, location):
+ self.__db_location = None
+
+ def __get_db_functions(self):
+ return self.__db_functions
+ def __set_db_functions(self, functions):
+ self.__db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self.__db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self.__db_functions.append(function)
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ self.__db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self.__db_functions.append(function)
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ del self.__db_functions[i]
+ break
+ def db_get_function(self, key):
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == key:
+ return self.__db_functions[i]
+ return None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations.values()
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ del self.__db_annotations[annotation.db_id]
+ def db_get_annotation(self, key):
+ if self.__db_annotations.has_key(key):
+ return self.__db_annotations[key]
+ return None
+
+ def __get_db_portSpecs(self):
+ return self.__db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self.__db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self.__db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self.__db_portSpecs.append(portSpec)
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == portSpec.db_id:
+ self.__db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self.__db_portSpecs.append(portSpec)
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == portSpec.db_id:
+ del self.__db_portSpecs[i]
+ break
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == key:
+ return self.__db_portSpecs[i]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBSession(object):
+
+ vtType = 'session'
+
+ def __init__(self, id=None, user=None, ip=None, visVersion=None, tsStart=None, tsEnd=None, machineId=None, wfExecs=None):
+ self.__db_id = id
+ self.__db_user = user
+ self.__db_ip = ip
+ self.__db_visVersion = visVersion
+ self.__db_tsStart = tsStart
+ self.__db_tsEnd = tsEnd
+ self.__db_machineId = machineId
+ if wfExecs is None:
+ self.__db_wfExecs = {}
+ else:
+ self.__db_wfExecs = wfExecs
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBSession()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_user = self.db_user
+ cp.is_dirty = self.is_dirty
+ cp.db_ip = self.db_ip
+ cp.is_dirty = self.is_dirty
+ cp.db_visVersion = self.db_visVersion
+ cp.is_dirty = self.is_dirty
+ cp.db_tsStart = self.db_tsStart
+ cp.is_dirty = self.is_dirty
+ cp.db_tsEnd = self.db_tsEnd
+ cp.is_dirty = self.is_dirty
+ cp.db_machineId = self.db_machineId
+ cp.is_dirty = self.is_dirty
+ if self.db_wfExecs is None:
+ cp.db_wfExecs = None
+ else:
+ cp.db_wfExecs = dict([(k,copy.copy(v)) for (k,v) in self.db_wfExecs.iteritems()])
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ for child in self.db_wfExecs.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_wfExecs = {}
+ children.extend(self.db_log.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_log = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_user(self):
+ return self.__db_user
+ def __set_db_user(self, user):
+ self.__db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self.__db_user = user
+ def db_change_user(self, user):
+ self.__db_user = user
+ def db_delete_user(self, user):
+ self.__db_user = None
+
+ def __get_db_ip(self):
+ return self.__db_ip
+ def __set_db_ip(self, ip):
+ self.__db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self.__db_ip = ip
+ def db_change_ip(self, ip):
+ self.__db_ip = ip
+ def db_delete_ip(self, ip):
+ self.__db_ip = None
+
+ def __get_db_visVersion(self):
+ return self.__db_visVersion
+ def __set_db_visVersion(self, visVersion):
+ self.__db_visVersion = visVersion
+ self.is_dirty = True
+ db_visVersion = property(__get_db_visVersion, __set_db_visVersion)
+ def db_add_visVersion(self, visVersion):
+ self.__db_visVersion = visVersion
+ def db_change_visVersion(self, visVersion):
+ self.__db_visVersion = visVersion
+ def db_delete_visVersion(self, visVersion):
+ self.__db_visVersion = None
+
+ def __get_db_tsStart(self):
+ return self.__db_tsStart
+ def __set_db_tsStart(self, tsStart):
+ self.__db_tsStart = tsStart
+ self.is_dirty = True
+ db_tsStart = property(__get_db_tsStart, __set_db_tsStart)
+ def db_add_tsStart(self, tsStart):
+ self.__db_tsStart = tsStart
+ def db_change_tsStart(self, tsStart):
+ self.__db_tsStart = tsStart
+ def db_delete_tsStart(self, tsStart):
+ self.__db_tsStart = None
+
+ def __get_db_tsEnd(self):
+ return self.__db_tsEnd
+ def __set_db_tsEnd(self, tsEnd):
+ self.__db_tsEnd = tsEnd
+ self.is_dirty = True
+ db_tsEnd = property(__get_db_tsEnd, __set_db_tsEnd)
+ def db_add_tsEnd(self, tsEnd):
+ self.__db_tsEnd = tsEnd
+ def db_change_tsEnd(self, tsEnd):
+ self.__db_tsEnd = tsEnd
+ def db_delete_tsEnd(self, tsEnd):
+ self.__db_tsEnd = None
+
+ def __get_db_machineId(self):
+ return self.__db_machineId
+ def __set_db_machineId(self, machineId):
+ self.__db_machineId = machineId
+ self.is_dirty = True
+ db_machineId = property(__get_db_machineId, __set_db_machineId)
+ def db_add_machineId(self, machineId):
+ self.__db_machineId = machineId
+ def db_change_machineId(self, machineId):
+ self.__db_machineId = machineId
+ def db_delete_machineId(self, machineId):
+ self.__db_machineId = None
+
+ def __get_db_wfExecs(self):
+ return self.__db_wfExecs
+ def __set_db_wfExecs(self, wfExecs):
+ self.__db_wfExecs = wfExecs
+ self.is_dirty = True
+ db_wfExecs = property(__get_db_wfExecs, __set_db_wfExecs)
+ def db_get_wfExecs(self):
+ return self.__db_wfExecs.values()
+ def db_add_wfExec(self, wfExec):
+ self.is_dirty = True
+ self.__db_wfExecs[wfExec.db_id] = wfExec
+ def db_change_wfExec(self, wfExec):
+ self.is_dirty = True
+ self.__db_wfExecs[wfExec.db_id] = wfExec
+ def db_delete_wfExec(self, wfExec):
+ self.is_dirty = True
+ del self.__db_wfExecs[wfExec.db_id]
+ def db_get_wfExec(self, key):
+ if self.__db_wfExecs.has_key(key):
+ return self.__db_wfExecs[key]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, sig=None):
+ self.__db_id = id
+ self.__db_type = type
+ self.__db_moduleId = moduleId
+ self.__db_moduleName = moduleName
+ self.__db_sig = sig
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBPort()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_type = self.db_type
+ cp.is_dirty = self.is_dirty
+ cp.db_moduleId = self.db_moduleId
+ cp.is_dirty = self.is_dirty
+ cp.db_moduleName = self.db_moduleName
+ cp.is_dirty = self.is_dirty
+ cp.db_sig = self.db_sig
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self.__db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self.__db_moduleName = None
+
+ def __get_db_sig(self):
+ return self.__db_sig
+ def __set_db_sig(self, sig):
+ self.__db_sig = sig
+ self.is_dirty = True
+ db_sig = property(__get_db_sig, __set_db_sig)
+ def db_add_sig(self, sig):
+ self.__db_sig = sig
+ def db_change_sig(self, sig):
+ self.__db_sig = sig
+ def db_delete_sig(self, sig):
+ self.__db_sig = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, sessions=None, machines=None):
+ self.__db_id = id
+ if sessions is None:
+ self.__db_sessions = {}
+ else:
+ self.__db_sessions = sessions
+ if machines is None:
+ self.__db_machines = {}
+ else:
+ self.__db_machines = machines
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBLog()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ if self.db_sessions is None:
+ cp.db_sessions = None
+ else:
+ cp.db_sessions = dict([(k,copy.copy(v)) for (k,v) in self.db_sessions.iteritems()])
+ cp.is_dirty = self.is_dirty
+ if self.db_machines is None:
+ cp.db_machines = None
+ else:
+ cp.db_machines = dict([(k,copy.copy(v)) for (k,v) in self.db_machines.iteritems()])
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ for child in self.db_sessions.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_sessions = {}
+ for child in self.db_machines.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_machines = {}
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_sessions(self):
+ return self.__db_sessions
+ def __set_db_sessions(self, sessions):
+ self.__db_sessions = sessions
+ self.is_dirty = True
+ db_sessions = property(__get_db_sessions, __set_db_sessions)
+ def db_get_sessions(self):
+ return self.__db_sessions.values()
+ def db_add_session(self, session):
+ self.is_dirty = True
+ self.__db_sessions[session.db_id] = session
+ def db_change_session(self, session):
+ self.is_dirty = True
+ self.__db_sessions[session.db_id] = session
+ def db_delete_session(self, session):
+ self.is_dirty = True
+ del self.__db_sessions[session.db_id]
+ def db_get_session(self, key):
+ if self.__db_sessions.has_key(key):
+ return self.__db_sessions[key]
+ return None
+
+ def __get_db_machines(self):
+ return self.__db_machines
+ def __set_db_machines(self, machines):
+ self.__db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self.__db_machines.values()
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self.__db_machines[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ self.__db_machines[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ del self.__db_machines[machine.db_id]
+ def db_get_machine(self, key):
+ if self.__db_machines.has_key(key):
+ return self.__db_machines[key]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_os = os
+ self.__db_architecture = architecture
+ self.__db_processor = processor
+ self.__db_ram = ram
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBMachine()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_name = self.db_name
+ cp.is_dirty = self.is_dirty
+ cp.db_os = self.db_os
+ cp.is_dirty = self.is_dirty
+ cp.db_architecture = self.db_architecture
+ cp.is_dirty = self.is_dirty
+ cp.db_processor = self.db_processor
+ cp.is_dirty = self.is_dirty
+ cp.db_ram = self.db_ram
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.extend(self.db_log.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_log = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_os(self):
+ return self.__db_os
+ def __set_db_os(self, os):
+ self.__db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self.__db_os = os
+ def db_change_os(self, os):
+ self.__db_os = os
+ def db_delete_os(self, os):
+ self.__db_os = None
+
+ def __get_db_architecture(self):
+ return self.__db_architecture
+ def __set_db_architecture(self, architecture):
+ self.__db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self.__db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self.__db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self.__db_architecture = None
+
+ def __get_db_processor(self):
+ return self.__db_processor
+ def __set_db_processor(self, processor):
+ self.__db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self.__db_processor = processor
+ def db_change_processor(self, processor):
+ self.__db_processor = processor
+ def db_delete_processor(self, processor):
+ self.__db_processor = None
+
+ def __get_db_ram(self):
+ return self.__db_ram
+ def __set_db_ram(self, ram):
+ self.__db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self.__db_ram = ram
+ def db_change_ram(self, ram):
+ self.__db_ram = ram
+ def db_delete_ram(self, ram):
+ self.__db_ram = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None, data=None):
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_objectId = objectId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.__db_data = data
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBAdd()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_what = self.db_what
+ cp.is_dirty = self.is_dirty
+ cp.db_objectId = self.db_objectId
+ cp.is_dirty = self.is_dirty
+ cp.db_parentObjId = self.db_parentObjId
+ cp.is_dirty = self.is_dirty
+ cp.db_parentObjType = self.db_parentObjType
+ cp.is_dirty = self.is_dirty
+ cp.db_data = self.db_data
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.extend(self.db_action.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_action = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_objectId(self):
+ return self.__db_objectId
+ def __set_db_objectId(self, objectId):
+ self.__db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self.__db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def __get_db_data(self):
+ return self.__db_data
+ def __set_db_data(self, data):
+ self.__db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self.__db_data = data
+ def db_change_data(self, data):
+ self.__db_data = data
+ def db_delete_data(self, data):
+ self.__db_data = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self.__db_id = id
+ self.__db_key = key
+ self.__db_value = value
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBOther()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_key = self.db_key
+ cp.is_dirty = self.is_dirty
+ cp.db_value = self.db_value
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self.__db_id = id
+ self.__db_x = x
+ self.__db_y = y
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBLocation()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_x = self.db_x
+ cp.is_dirty = self.is_dirty
+ cp.db_y = self.db_y
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_x(self):
+ return self.__db_x
+ def __set_db_x(self, x):
+ self.__db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self.__db_x = x
+ def db_change_x(self, x):
+ self.__db_x = x
+ def db_delete_x(self, x):
+ self.__db_x = None
+
+ def __get_db_y(self):
+ return self.__db_y
+ def __set_db_y(self, y):
+ self.__db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self.__db_y = y
+ def db_change_y(self, y):
+ self.__db_y = y
+ def db_delete_y(self, y):
+ self.__db_y = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBWfExec(object):
+
+ vtType = 'wfExec'
+
+ def __init__(self, id=None, tsStart=None, tsEnd=None, wfVersion=None, vistrailId=None, vistrailName=None, execRecs=None):
+ self.__db_id = id
+ self.__db_tsStart = tsStart
+ self.__db_tsEnd = tsEnd
+ self.__db_wfVersion = wfVersion
+ self.__db_vistrailId = vistrailId
+ self.__db_vistrailName = vistrailName
+ if execRecs is None:
+ self.__db_execRecs = {}
+ else:
+ self.__db_execRecs = execRecs
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBWfExec()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_tsStart = self.db_tsStart
+ cp.is_dirty = self.is_dirty
+ cp.db_tsEnd = self.db_tsEnd
+ cp.is_dirty = self.is_dirty
+ cp.db_wfVersion = self.db_wfVersion
+ cp.is_dirty = self.is_dirty
+ cp.db_vistrailId = self.db_vistrailId
+ cp.is_dirty = self.is_dirty
+ cp.db_vistrailName = self.db_vistrailName
+ cp.is_dirty = self.is_dirty
+ if self.db_execRecs is None:
+ cp.db_execRecs = None
+ else:
+ cp.db_execRecs = dict([(k,copy.copy(v)) for (k,v) in self.db_execRecs.iteritems()])
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.extend(self.db_session.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_session = None
+ for child in self.db_execRecs.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_execRecs = {}
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_tsStart(self):
+ return self.__db_tsStart
+ def __set_db_tsStart(self, tsStart):
+ self.__db_tsStart = tsStart
+ self.is_dirty = True
+ db_tsStart = property(__get_db_tsStart, __set_db_tsStart)
+ def db_add_tsStart(self, tsStart):
+ self.__db_tsStart = tsStart
+ def db_change_tsStart(self, tsStart):
+ self.__db_tsStart = tsStart
+ def db_delete_tsStart(self, tsStart):
+ self.__db_tsStart = None
+
+ def __get_db_tsEnd(self):
+ return self.__db_tsEnd
+ def __set_db_tsEnd(self, tsEnd):
+ self.__db_tsEnd = tsEnd
+ self.is_dirty = True
+ db_tsEnd = property(__get_db_tsEnd, __set_db_tsEnd)
+ def db_add_tsEnd(self, tsEnd):
+ self.__db_tsEnd = tsEnd
+ def db_change_tsEnd(self, tsEnd):
+ self.__db_tsEnd = tsEnd
+ def db_delete_tsEnd(self, tsEnd):
+ self.__db_tsEnd = None
+
+ def __get_db_wfVersion(self):
+ return self.__db_wfVersion
+ def __set_db_wfVersion(self, wfVersion):
+ self.__db_wfVersion = wfVersion
+ self.is_dirty = True
+ db_wfVersion = property(__get_db_wfVersion, __set_db_wfVersion)
+ def db_add_wfVersion(self, wfVersion):
+ self.__db_wfVersion = wfVersion
+ def db_change_wfVersion(self, wfVersion):
+ self.__db_wfVersion = wfVersion
+ def db_delete_wfVersion(self, wfVersion):
+ self.__db_wfVersion = None
+
+ def __get_db_vistrailId(self):
+ return self.__db_vistrailId
+ def __set_db_vistrailId(self, vistrailId):
+ self.__db_vistrailId = vistrailId
+ self.is_dirty = True
+ db_vistrailId = property(__get_db_vistrailId, __set_db_vistrailId)
+ def db_add_vistrailId(self, vistrailId):
+ self.__db_vistrailId = vistrailId
+ def db_change_vistrailId(self, vistrailId):
+ self.__db_vistrailId = vistrailId
+ def db_delete_vistrailId(self, vistrailId):
+ self.__db_vistrailId = None
+
+ def __get_db_vistrailName(self):
+ return self.__db_vistrailName
+ def __set_db_vistrailName(self, vistrailName):
+ self.__db_vistrailName = vistrailName
+ self.is_dirty = True
+ db_vistrailName = property(__get_db_vistrailName, __set_db_vistrailName)
+ def db_add_vistrailName(self, vistrailName):
+ self.__db_vistrailName = vistrailName
+ def db_change_vistrailName(self, vistrailName):
+ self.__db_vistrailName = vistrailName
+ def db_delete_vistrailName(self, vistrailName):
+ self.__db_vistrailName = None
+
+ def __get_db_execRecs(self):
+ return self.__db_execRecs
+ def __set_db_execRecs(self, execRecs):
+ self.__db_execRecs = execRecs
+ self.is_dirty = True
+ db_execRecs = property(__get_db_execRecs, __set_db_execRecs)
+ def db_get_execRecs(self):
+ return self.__db_execRecs.values()
+ def db_add_execRec(self, execRec):
+ self.is_dirty = True
+ self.__db_execRecs[execRec.db_id] = execRec
+ def db_change_execRec(self, execRec):
+ self.is_dirty = True
+ self.__db_execRecs[execRec.db_id] = execRec
+ def db_delete_execRec(self, execRec):
+ self.is_dirty = True
+ del self.__db_execRecs[execRec.db_id]
+ def db_get_execRec(self, key):
+ if self.__db_execRecs.has_key(key):
+ return self.__db_execRecs[key]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self.__db_id = id
+ self.__db_pos = pos
+ self.__db_name = name
+ self.__db_type = type
+ self.__db_val = val
+ self.__db_alias = alias
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBParameter()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_pos = self.db_pos
+ cp.is_dirty = self.is_dirty
+ cp.db_name = self.db_name
+ cp.is_dirty = self.is_dirty
+ cp.db_type = self.db_type
+ cp.is_dirty = self.is_dirty
+ cp.db_val = self.db_val
+ cp.is_dirty = self.is_dirty
+ cp.db_alias = self.db_alias
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_pos(self):
+ return self.__db_pos
+ def __set_db_pos(self, pos):
+ self.__db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self.__db_pos = pos
+ def db_change_pos(self, pos):
+ self.__db_pos = pos
+ def db_delete_pos(self, pos):
+ self.__db_pos = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_val(self):
+ return self.__db_val
+ def __set_db_val(self, val):
+ self.__db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self.__db_val = val
+ def db_change_val(self, val):
+ self.__db_val = val
+ def db_delete_val(self, val):
+ self.__db_val = None
+
+ def __get_db_alias(self):
+ return self.__db_alias
+ def __set_db_alias(self, alias):
+ self.__db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self.__db_alias = alias
+ def db_change_alias(self, alias):
+ self.__db_alias = alias
+ def db_delete_alias(self, alias):
+ self.__db_alias = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self.__db_id = id
+ self.__db_pos = pos
+ self.__db_name = name
+ if parameters is None:
+ self.__db_parameters = []
+ else:
+ self.__db_parameters = parameters
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBFunction()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_pos = self.db_pos
+ cp.is_dirty = self.is_dirty
+ cp.db_name = self.db_name
+ cp.is_dirty = self.is_dirty
+ if self.db_parameters is None:
+ cp.db_parameters = None
+ else:
+ cp.db_parameters = [copy.copy(v) for v in self.db_parameters]
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_parameters = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_pos(self):
+ return self.__db_pos
+ def __set_db_pos(self, pos):
+ self.__db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self.__db_pos = pos
+ def db_change_pos(self, pos):
+ self.__db_pos = pos
+ def db_delete_pos(self, pos):
+ self.__db_pos = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_parameters(self):
+ return self.__db_parameters
+ def __set_db_parameters(self, parameters):
+ self.__db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self.__db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self.__db_parameters.append(parameter)
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == parameter.db_id:
+ self.__db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self.__db_parameters.append(parameter)
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == parameter.db_id:
+ del self.__db_parameters[i]
+ break
+ def db_get_parameter(self, key):
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == key:
+ return self.__db_parameters[i]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, id=None, name=None, modules=None, connections=None, annotations=None, others=None):
+ self.__db_id = id
+ self.__db_name = name
+ if modules is None:
+ self.__db_modules = {}
+ else:
+ self.__db_modules = modules
+ if connections is None:
+ self.__db_connections = {}
+ else:
+ self.__db_connections = connections
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ if others is None:
+ self.__db_others = []
+ else:
+ self.__db_others = others
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBWorkflow()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_name = self.db_name
+ cp.is_dirty = self.is_dirty
+ if self.db_modules is None:
+ cp.db_modules = None
+ else:
+ cp.db_modules = dict([(k,copy.copy(v)) for (k,v) in self.db_modules.iteritems()])
+ cp.is_dirty = self.is_dirty
+ if self.db_connections is None:
+ cp.db_connections = None
+ else:
+ cp.db_connections = dict([(k,copy.copy(v)) for (k,v) in self.db_connections.iteritems()])
+ cp.is_dirty = self.is_dirty
+ if self.db_annotations is None:
+ cp.db_annotations = None
+ else:
+ cp.db_annotations = [copy.copy(v) for v in self.db_annotations]
+ cp.is_dirty = self.is_dirty
+ if self.db_others is None:
+ cp.db_others = None
+ else:
+ cp.db_others = [copy.copy(v) for v in self.db_others]
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ for child in self.db_modules.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_modules = {}
+ for child in self.db_connections.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_connections = {}
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_annotations = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_others = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_modules(self):
+ return self.__db_modules
+ def __set_db_modules(self, modules):
+ self.__db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self.__db_modules.values()
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self.__db_modules[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ self.__db_modules[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ del self.__db_modules[module.db_id]
+ def db_get_module(self, key):
+ if self.__db_modules.has_key(key):
+ return self.__db_modules[key]
+ return None
+
+ def __get_db_connections(self):
+ return self.__db_connections
+ def __set_db_connections(self, connections):
+ self.__db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self.__db_connections.values()
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self.__db_connections[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ self.__db_connections[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ del self.__db_connections[connection.db_id]
+ def db_get_connection(self, key):
+ if self.__db_connections.has_key(key):
+ return self.__db_connections[key]
+ return None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ del self.__db_annotations[i]
+ break
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+
+ def __get_db_others(self):
+ return self.__db_others
+ def __set_db_others(self, others):
+ self.__db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self.__db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self.__db_others.append(other)
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == other.db_id:
+ self.__db_others[i] = other
+ found = True
+ break
+ if not found:
+ self.__db_others.append(other)
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == other.db_id:
+ del self.__db_others[i]
+ break
+ def db_get_other(self, key):
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == key:
+ return self.__db_others[i]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, id=None, prevId=None, date=None, user=None, operations=None):
+ self.__db_id = id
+ self.__db_prevId = prevId
+ self.__db_date = date
+ self.__db_user = user
+ if operations is None:
+ self.__db_operations = []
+ else:
+ self.__db_operations = operations
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBAction()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_prevId = self.db_prevId
+ cp.is_dirty = self.is_dirty
+ cp.db_date = self.db_date
+ cp.is_dirty = self.is_dirty
+ cp.db_user = self.db_user
+ cp.is_dirty = self.is_dirty
+ if self.db_operations is None:
+ cp.db_operations = None
+ else:
+ cp.db_operations = [copy.copy(v) for v in self.db_operations]
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_prevId(self):
+ return self.__db_prevId
+ def __set_db_prevId(self, prevId):
+ self.__db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self.__db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self.__db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self.__db_prevId = None
+
+ def __get_db_date(self):
+ return self.__db_date
+ def __set_db_date(self, date):
+ self.__db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self.__db_date = date
+ def db_change_date(self, date):
+ self.__db_date = date
+ def db_delete_date(self, date):
+ self.__db_date = None
+
+ def __get_db_user(self):
+ return self.__db_user
+ def __set_db_user(self, user):
+ self.__db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self.__db_user = user
+ def db_change_user(self, user):
+ self.__db_user = user
+ def db_delete_user(self, user):
+ self.__db_user = None
+
+ def __get_db_operations(self):
+ return self.__db_operations
+ def __set_db_operations(self, operations):
+ self.__db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self.__db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self.__db_operations.append(operation)
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == operation.db_id:
+ self.__db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self.__db_operations.append(operation)
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == operation.db_id:
+ del self.__db_operations[i]
+ break
+ def db_get_operation(self, key):
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == key:
+ return self.__db_operations[i]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self.__db_id = id
+ self.__db_key = key
+ self.__db_value = value
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBAnnotation()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_key = self.db_key
+ cp.is_dirty = self.is_dirty
+ cp.db_value = self.db_value
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None, data=None):
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_oldObjId = oldObjId
+ self.__db_newObjId = newObjId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.__db_data = data
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBChange()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_what = self.db_what
+ cp.is_dirty = self.is_dirty
+ cp.db_oldObjId = self.db_oldObjId
+ cp.is_dirty = self.is_dirty
+ cp.db_newObjId = self.db_newObjId
+ cp.is_dirty = self.is_dirty
+ cp.db_parentObjId = self.db_parentObjId
+ cp.is_dirty = self.is_dirty
+ cp.db_parentObjType = self.db_parentObjType
+ cp.is_dirty = self.is_dirty
+ cp.db_data = self.db_data
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.extend(self.db_action.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_action = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_oldObjId(self):
+ return self.__db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self.__db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self.__db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self.__db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def __get_db_data(self):
+ return self.__db_data
+ def __set_db_data(self, data):
+ self.__db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self.__db_data = data
+ def db_change_data(self, data):
+ self.__db_data = data
+ def db_delete_data(self, data):
+ self.__db_data = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBMacro(object):
+
+ vtType = 'macro'
+
+ def __init__(self, id=None, name=None, descrptn=None, actions=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_descrptn = descrptn
+ if actions is None:
+ self.__db_actions = {}
+ else:
+ self.__db_actions = actions
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBMacro()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_name = self.db_name
+ cp.is_dirty = self.is_dirty
+ cp.db_descrptn = self.db_descrptn
+ cp.is_dirty = self.is_dirty
+ if self.db_actions is None:
+ cp.db_actions = None
+ else:
+ cp.db_actions = dict([(k,copy.copy(v)) for (k,v) in self.db_actions.iteritems()])
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ for child in self.db_actions.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_actions = {}
+ children.extend(self.db_vistrail.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_vistrail = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_descrptn(self):
+ return self.__db_descrptn
+ def __set_db_descrptn(self, descrptn):
+ self.__db_descrptn = descrptn
+ self.is_dirty = True
+ db_descrptn = property(__get_db_descrptn, __set_db_descrptn)
+ def db_add_descrptn(self, descrptn):
+ self.__db_descrptn = descrptn
+ def db_change_descrptn(self, descrptn):
+ self.__db_descrptn = descrptn
+ def db_delete_descrptn(self, descrptn):
+ self.__db_descrptn = None
+
+ def __get_db_actions(self):
+ return self.__db_actions
+ def __set_db_actions(self, actions):
+ self.__db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self.__db_actions.values()
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self.__db_actions[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ self.__db_actions[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ del self.__db_actions[action.db_id]
+ def db_get_action(self, key):
+ if self.__db_actions.has_key(key):
+ return self.__db_actions[key]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self.__db_id = id
+ self.db_type_index = {}
+ if ports is None:
+ self.__db_ports = []
+ else:
+ self.__db_ports = ports
+ for v in self.__db_ports:
+ self.db_type_index[v.db_type] = v
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBConnection()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ if self.db_ports is None:
+ cp.db_ports = None
+ else:
+ cp.db_ports = [copy.copy(v) for v in self.db_ports]
+ for v in cp.__db_ports:
+ cp.db_type_index[v.db_type] = v
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_ports = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_ports(self):
+ return self.__db_ports
+ def __set_db_ports(self, ports):
+ self.__db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self.__db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self.__db_ports.append(port)
+ self.db_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == port.db_id:
+ self.__db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self.__db_ports.append(port)
+ self.db_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == port.db_id:
+ del self.__db_ports[i]
+ break
+ del self.db_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == key:
+ return self.__db_ports[i]
+ return None
+ def db_get_port_by_type(self, key):
+ return self.db_type_index[key]
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, name=None, time=None):
+ self.__db_name = name
+ self.__db_time = time
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBTag()
+ cp.db_name = self.db_name
+ cp.is_dirty = self.is_dirty
+ cp.db_time = self.db_time
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.extend(self.db_vistrail.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_vistrail = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_time(self):
+ return self.__db_time
+ def __set_db_time(self, time):
+ self.__db_time = time
+ self.is_dirty = True
+ db_time = property(__get_db_time, __set_db_time)
+ def db_add_time(self, time):
+ self.__db_time = time
+ def db_change_time(self, time):
+ self.__db_time = time
+ def db_delete_time(self, time):
+ self.__db_time = None
+
+ def getPrimaryKey(self):
+ return self.__db_name
+
+class DBExecRec(object):
+
+ vtType = 'execRec'
+
+ def __init__(self, id=None, tsStart=None, tsEnd=None, moduleId=None, moduleName=None, annotations=None):
+ self.__db_id = id
+ self.__db_tsStart = tsStart
+ self.__db_tsEnd = tsEnd
+ self.__db_moduleId = moduleId
+ self.__db_moduleName = moduleName
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBExecRec()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_tsStart = self.db_tsStart
+ cp.is_dirty = self.is_dirty
+ cp.db_tsEnd = self.db_tsEnd
+ cp.is_dirty = self.is_dirty
+ cp.db_moduleId = self.db_moduleId
+ cp.is_dirty = self.is_dirty
+ cp.db_moduleName = self.db_moduleName
+ cp.is_dirty = self.is_dirty
+ if self.db_annotations is None:
+ cp.db_annotations = None
+ else:
+ cp.db_annotations = [copy.copy(v) for v in self.db_annotations]
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_annotations = []
+ children.extend(self.db_wfExec.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_wfExec = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_tsStart(self):
+ return self.__db_tsStart
+ def __set_db_tsStart(self, tsStart):
+ self.__db_tsStart = tsStart
+ self.is_dirty = True
+ db_tsStart = property(__get_db_tsStart, __set_db_tsStart)
+ def db_add_tsStart(self, tsStart):
+ self.__db_tsStart = tsStart
+ def db_change_tsStart(self, tsStart):
+ self.__db_tsStart = tsStart
+ def db_delete_tsStart(self, tsStart):
+ self.__db_tsStart = None
+
+ def __get_db_tsEnd(self):
+ return self.__db_tsEnd
+ def __set_db_tsEnd(self, tsEnd):
+ self.__db_tsEnd = tsEnd
+ self.is_dirty = True
+ db_tsEnd = property(__get_db_tsEnd, __set_db_tsEnd)
+ def db_add_tsEnd(self, tsEnd):
+ self.__db_tsEnd = tsEnd
+ def db_change_tsEnd(self, tsEnd):
+ self.__db_tsEnd = tsEnd
+ def db_delete_tsEnd(self, tsEnd):
+ self.__db_tsEnd = None
+
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self.__db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self.__db_moduleName = None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ del self.__db_annotations[i]
+ break
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, version=None, name=None, dbHost=None, dbPort=None, dbName=None, actions=None, tags=None, macros=None):
+ self.__db_id = id
+ self.__db_version = version
+ self.__db_name = name
+ self.__db_dbHost = dbHost
+ self.__db_dbPort = dbPort
+ self.__db_dbName = dbName
+ if actions is None:
+ self.__db_actions = {}
+ else:
+ self.__db_actions = actions
+ if tags is None:
+ self.__db_tags = {}
+ else:
+ self.__db_tags = tags
+ if macros is None:
+ self.__db_macros = {}
+ else:
+ self.__db_macros = macros
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBVistrail()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_version = self.db_version
+ cp.is_dirty = self.is_dirty
+ cp.db_name = self.db_name
+ cp.is_dirty = self.is_dirty
+ cp.db_dbHost = self.db_dbHost
+ cp.is_dirty = self.is_dirty
+ cp.db_dbPort = self.db_dbPort
+ cp.is_dirty = self.is_dirty
+ cp.db_dbName = self.db_dbName
+ cp.is_dirty = self.is_dirty
+ if self.db_actions is None:
+ cp.db_actions = None
+ else:
+ cp.db_actions = dict([(k,copy.copy(v)) for (k,v) in self.db_actions.iteritems()])
+ cp.is_dirty = self.is_dirty
+ if self.db_tags is None:
+ cp.db_tags = None
+ else:
+ cp.db_tags = dict([(k,copy.copy(v)) for (k,v) in self.db_tags.iteritems()])
+ cp.is_dirty = self.is_dirty
+ if self.db_macros is None:
+ cp.db_macros = None
+ else:
+ cp.db_macros = dict([(k,copy.copy(v)) for (k,v) in self.db_macros.iteritems()])
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ for child in self.db_actions.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_actions = {}
+ for child in self.db_tags.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_tags = {}
+ for child in self.db_macros.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_macros = {}
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_dbHost(self):
+ return self.__db_dbHost
+ def __set_db_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ self.is_dirty = True
+ db_dbHost = property(__get_db_dbHost, __set_db_dbHost)
+ def db_add_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ def db_change_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ def db_delete_dbHost(self, dbHost):
+ self.__db_dbHost = None
+
+ def __get_db_dbPort(self):
+ return self.__db_dbPort
+ def __set_db_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ self.is_dirty = True
+ db_dbPort = property(__get_db_dbPort, __set_db_dbPort)
+ def db_add_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ def db_change_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ def db_delete_dbPort(self, dbPort):
+ self.__db_dbPort = None
+
+ def __get_db_dbName(self):
+ return self.__db_dbName
+ def __set_db_dbName(self, dbName):
+ self.__db_dbName = dbName
+ self.is_dirty = True
+ db_dbName = property(__get_db_dbName, __set_db_dbName)
+ def db_add_dbName(self, dbName):
+ self.__db_dbName = dbName
+ def db_change_dbName(self, dbName):
+ self.__db_dbName = dbName
+ def db_delete_dbName(self, dbName):
+ self.__db_dbName = None
+
+ def __get_db_actions(self):
+ return self.__db_actions
+ def __set_db_actions(self, actions):
+ self.__db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self.__db_actions.values()
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self.__db_actions[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ self.__db_actions[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ del self.__db_actions[action.db_id]
+ def db_get_action(self, key):
+ if self.__db_actions.has_key(key):
+ return self.__db_actions[key]
+ return None
+
+ def __get_db_tags(self):
+ return self.__db_tags
+ def __set_db_tags(self, tags):
+ self.__db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self.__db_tags.values()
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ del self.__db_tags[tag.db_name]
+ def db_get_tag(self, key):
+ if self.__db_tags.has_key(key):
+ return self.__db_tags[key]
+ return None
+
+ def __get_db_macros(self):
+ return self.__db_macros
+ def __set_db_macros(self, macros):
+ self.__db_macros = macros
+ self.is_dirty = True
+ db_macros = property(__get_db_macros, __set_db_macros)
+ def db_get_macros(self):
+ return self.__db_macros.values()
+ def db_add_macro(self, macro):
+ self.is_dirty = True
+ self.__db_macros[macro.db_id] = macro
+ def db_change_macro(self, macro):
+ self.is_dirty = True
+ self.__db_macros[macro.db_id] = macro
+ def db_delete_macro(self, macro):
+ self.is_dirty = True
+ del self.__db_macros[macro.db_id]
+ def db_get_macro(self, key):
+ if self.__db_macros.has_key(key):
+ return self.__db_macros[key]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_objectId = objectId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+
+ def __copy__(self):
+ cp = DBDelete()
+ cp.db_id = self.db_id
+ cp.is_dirty = self.is_dirty
+ cp.db_what = self.db_what
+ cp.is_dirty = self.is_dirty
+ cp.db_objectId = self.db_objectId
+ cp.is_dirty = self.is_dirty
+ cp.db_parentObjId = self.db_parentObjId
+ cp.is_dirty = self.is_dirty
+ cp.db_parentObjType = self.db_parentObjType
+ cp.is_dirty = self.is_dirty
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.extend(self.db_action.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_action = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_objectId(self):
+ return self.__db_objectId
+ def __set_db_objectId(self, objectId):
+ self.__db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self.__db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
diff --git a/vistrails/db/versions/v0_5_0/domain/id_scope.py b/vistrails/db/versions/v0_5_0/domain/id_scope.py
new file mode 100644
index 0000000..3f151ff
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/domain/id_scope.py
@@ -0,0 +1,65 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L):
+ self.ids = {}
+ self.beginId = beginId
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ if self.ids.has_key(objType):
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ else:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ if not self.ids.has_key(objType) or self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v0_5_0/domain/vistrail.py b/vistrails/db/versions/v0_5_0/domain/vistrail.py
new file mode 100644
index 0000000..4ca792e
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/domain/vistrail.py
@@ -0,0 +1,43 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBVistrail as _DBVistrail
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope()
+ self.idScope.setBeginId('action', 1)
diff --git a/vistrails/db/versions/v0_5_0/domain/workflow.py b/vistrails/db/versions/v0_5_0/domain/workflow.py
new file mode 100644
index 0000000..97cb040
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/domain/workflow.py
@@ -0,0 +1,116 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1)
+
+ def __copy__(self):
+ cp = _DBWorkflow.__copy__(self)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.objects = {}
+ for (child, _, _) in cp.db_children():
+ cp.addToIndex(child)
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ def addToIndex(self, object):
+ self.objects[(object.vtType, object.getPrimaryKey())] = object
+
+ def deleteFromIndex(self, object):
+ del self.objects[(object.vtType, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_add_object(self, object, parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_add_%s' % object.vtType
+ objCopy = copy.copy(object)
+ getattr(parentObj, funname)(objCopy)
+ self.addToIndex(objCopy)
+
+ def db_change_object(self, object, parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_change_%s' % object.vtType
+ objCopy = copy.copy(object)
+ getattr(parentObj, funname)(objCopy)
+ self.addToIndex(objCopy)
+
+ def db_delete_object(self, objId, objType,
+ parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_get_%s' % objType
+ try:
+ object = getattr(parentObj, funname)(objId)
+ except AttributeError:
+ attr_name = 'db_%s' % objType
+ object = getattr(parentObj, attr_name)
+ funname = 'db_delete_%s' % objType
+ getattr(parentObj, funname)(object)
+ self.deleteFromIndex(object)
diff --git a/vistrails/db/versions/v0_5_0/persistence/__init__.py b/vistrails/db/versions/v0_5_0/persistence/__init__.py
new file mode 100644
index 0000000..0a10c9d
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/persistence/__init__.py
@@ -0,0 +1,55 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+import xml.io
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ return xml.io.open_from_xml(filename, vtType, self['xml'])
+
+ def save_to_xml(self, obj, filename):
+ xml.io.save_to_xml(obj, filename, self['xml'])
+
+ def serialize(self, obj):
+ return xml.io.serialize(obj, self['xml'])
+
+ def unserialize(self, str, type):
+ return xml.io.unserialize(str, type, self['xml'])
diff --git a/vistrails/db/versions/v0_5_0/persistence/sql/__init__.py b/vistrails/db/versions/v0_5_0/persistence/sql/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_5_0/persistence/sql/auto_gen.py b/vistrails/db/versions/v0_5_0/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..a8da624
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/persistence/sql/auto_gen.py
@@ -0,0 +1,2228 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v0_5_0.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'type', 'spec', 'id']
+ table = 'port_spec'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(22)')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[3], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ portSpec = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ spec=spec)
+ portSpec.is_dirty = False
+ list.append(portSpec)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'port_spec'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(22)')
+ if obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['cache', 'name', 'id']
+ table = 'module'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ cache = self.convertFromDB(row[0], 'int', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('location').fromSQL(db, None, foreignKey, globalProps)
+ if len(res) > 0:
+ location = res[0]
+ else:
+ location = None
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('function').fromSQL(db, None, foreignKey, globalProps)
+ functions = res
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ annotations = {}
+ for obj in res:
+ annotations[obj.db_id] = obj
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('portSpec').fromSQL(db, None, foreignKey, globalProps)
+ portSpecs = res
+
+ module = DBModule(id=id,
+ cache=cache,
+ name=name,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ module.is_dirty = False
+ list.append(module)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'module'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ child = obj.db_location
+ if child is not None:
+ self.getDao('location').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_functions:
+ self.getDao('function').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_annotations.itervalues():
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_portSpecs:
+ self.getDao('portSpec').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBSessionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['user', 'ip', 'vis_ver', 'ts_start', 'tsEnd', 'machine_id', 'id']
+ table = 'session'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ user = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ visVersion = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ tsStart = self.convertFromDB(row[3], 'datetime', 'datetime')
+ tsEnd = self.convertFromDB(row[4], 'datetime', 'datetime')
+ machineId = self.convertFromDB(row[5], 'long', 'int')
+ id = self.convertFromDB(row[6], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ foreignKey = {'session_id': keyStr}
+ res = self.getDao('wfExec').fromSQL(db, None, foreignKey, globalProps)
+ wfExecs = {}
+ for obj in res:
+ wfExecs[obj.db_id] = obj
+
+ session = DBSession(id=id,
+ user=user,
+ ip=ip,
+ visVersion=visVersion,
+ tsStart=tsStart,
+ tsEnd=tsEnd,
+ machineId=machineId,
+ wfExecs=wfExecs)
+ session.is_dirty = False
+ list.append(session)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'session'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if obj.db_visVersion is not None:
+ columnMap['vis_ver'] = \
+ self.convertToDB(obj.db_visVersion, 'str', 'varchar(255)')
+ if obj.db_tsStart is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_tsStart, 'datetime', 'datetime')
+ if obj.db_tsEnd is not None:
+ columnMap['tsEnd'] = \
+ self.convertToDB(obj.db_tsEnd, 'datetime', 'datetime')
+ if obj.db_machineId is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machineId, 'long', 'int')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ foreignKey = {'session_id': keyStr}
+ for child in obj.db_wfExecs.itervalues():
+ self.getDao('wfExec').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['type', 'moduleId', 'moduleName', 'sig', 'id']
+ table = 'port'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ type = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[1], 'long', 'int')
+ moduleName = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ sig = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ port = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ sig=sig)
+ port.is_dirty = False
+ list.append(port)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'port'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if obj.db_sig is not None:
+ columnMap['sig'] = \
+ self.convertToDB(obj.db_sig, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['id']
+ table = 'log_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ foreignKey = {'log_id': keyStr}
+ res = self.getDao('session').fromSQL(db, None, foreignKey, globalProps)
+ sessions = {}
+ for obj in res:
+ sessions[obj.db_id] = obj
+
+ foreignKey = {'log_id': keyStr}
+ res = self.getDao('machine').fromSQL(db, None, foreignKey, globalProps)
+ machines = {}
+ for obj in res:
+ machines[obj.db_id] = obj
+
+ log = DBLog(id=id,
+ sessions=sessions,
+ machines=machines)
+ log.is_dirty = False
+ list.append(log)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'log_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ foreignKey = {'log_id': keyStr}
+ for child in obj.db_sessions.itervalues():
+ self.getDao('session').toSQL(db, child, foreignKey, globalProps)
+
+ foreignKey = {'log_id': keyStr}
+ for child in obj.db_machines.itervalues():
+ self.getDao('machine').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'os', 'architecture', 'processor', 'ram', 'id']
+ table = 'machine'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[4], 'int', 'int')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ machine = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ machine.is_dirty = False
+ list.append(machine)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'machine'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['what', 'object_id', 'par_obj_id', 'par_obj_type', 'id']
+ table = 'add_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ what = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[1], 'long', 'int')
+ parentObjId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjType = self.convertFromDB(row[3], 'str', 'char(16)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ data = None
+ if what == 'module':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('module').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'location':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('location').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'annotation':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'function':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('function').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'connection':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('connection').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'port':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('port').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'parameter':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('parameter').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'portSpec':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('portSpec').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'other':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('other').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+
+ add = DBAdd(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ add.is_dirty = False
+ list.append(add)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'add_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ child = obj.db_data
+ if child.vtType == 'module':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('module').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'location':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('location').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'annotation':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'function':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('function').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'connection':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('connection').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'port':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('port').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'parameter':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('parameter').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'portSpec':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('portSpec').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'other':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('other').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['okey', 'value', 'id']
+ table = 'other'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ key = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ other = DBOther(id=id,
+ key=key,
+ value=value)
+ other.is_dirty = False
+ list.append(other)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'other'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['x', 'y', 'id']
+ table = 'location'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ x = self.convertFromDB(row[0], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ location = DBLocation(id=id,
+ x=x,
+ y=y)
+ location.is_dirty = False
+ list.append(location)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'location'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBWfExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['ts_start', 'ts_end', 'wfVersion', 'vistrail_id', 'vistrail_name', 'id']
+ table = 'wf_exec'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ tsStart = self.convertFromDB(row[0], 'datetime', 'datetime')
+ tsEnd = self.convertFromDB(row[1], 'datetime', 'datetime')
+ wfVersion = self.convertFromDB(row[2], 'int', 'int')
+ vistrailId = self.convertFromDB(row[3], 'long', 'int')
+ vistrailName = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ foreignKey = {'wf_exec_id': keyStr}
+ res = self.getDao('execRec').fromSQL(db, None, foreignKey, globalProps)
+ execRecs = {}
+ for obj in res:
+ execRecs[obj.db_id] = obj
+
+ wfExec = DBWfExec(id=id,
+ tsStart=tsStart,
+ tsEnd=tsEnd,
+ wfVersion=wfVersion,
+ vistrailId=vistrailId,
+ vistrailName=vistrailName,
+ execRecs=execRecs)
+ wfExec.is_dirty = False
+ list.append(wfExec)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'wf_exec'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_tsStart is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_tsStart, 'datetime', 'datetime')
+ if obj.db_tsEnd is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_tsEnd, 'datetime', 'datetime')
+ if obj.db_wfVersion is not None:
+ columnMap['wfVersion'] = \
+ self.convertToDB(obj.db_wfVersion, 'int', 'int')
+ if obj.db_vistrailId is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if obj.db_vistrailName is not None:
+ columnMap['vistrail_name'] = \
+ self.convertToDB(obj.db_vistrailName, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ foreignKey = {'wf_exec_id': keyStr}
+ for child in obj.db_execRecs.itervalues():
+ self.getDao('execRec').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['pos', 'name', 'type', 'val', 'alias', 'id']
+ table = 'parameter'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ pos = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[3], 'str', 'varchar(8192)')
+ alias = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ parameter = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ parameter.is_dirty = False
+ list.append(parameter)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'parameter'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8192)')
+ if obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['pos', 'name', 'id']
+ table = 'function'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ pos = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('function','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('parameter').fromSQL(db, None, foreignKey, globalProps)
+ parameters = res
+
+ function = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ function.is_dirty = False
+ list.append(function)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'function'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('function','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_parameters:
+ self.getDao('parameter').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'id']
+ table = 'workflow'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[1], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('module').fromSQL(db, None, foreignKey, globalProps)
+ modules = {}
+ for obj in res:
+ modules[obj.db_id] = obj
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('connection').fromSQL(db, None, foreignKey, globalProps)
+ connections = {}
+ for obj in res:
+ connections[obj.db_id] = obj
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ annotations = res
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('other').fromSQL(db, None, foreignKey, globalProps)
+ others = res
+
+ workflow = DBWorkflow(id=id,
+ name=name,
+ modules=modules,
+ connections=connections,
+ annotations=annotations,
+ others=others)
+ workflow.is_dirty = False
+ list.append(workflow)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'workflow'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_modules.itervalues():
+ self.getDao('module').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_connections.itervalues():
+ self.getDao('connection').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_annotations:
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_others:
+ self.getDao('other').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['prev_id', 'date', 'user', 'id']
+ table = 'action'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ prevId = self.convertFromDB(row[0], 'long', 'int')
+ date = self.convertFromDB(row[1], 'datetime', 'datetime')
+ user = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[3], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ operations = []
+
+ foreignKey = {'action_id': keyStr}
+ res = self.getDao('add').fromSQL(db, None, foreignKey, globalProps)
+ operations.extend(res)
+
+ foreignKey = {'action_id': keyStr}
+ res = self.getDao('delete').fromSQL(db, None, foreignKey, globalProps)
+ operations.extend(res)
+
+ foreignKey = {'action_id': keyStr}
+ res = self.getDao('change').fromSQL(db, None, foreignKey, globalProps)
+ operations.extend(res)
+
+ action = DBAction(id=id,
+ prevId=prevId,
+ date=date,
+ user=user,
+ operations=operations)
+ action.is_dirty = False
+ list.append(action)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'action'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ for child in obj.db_operations:
+ if child.vtType == 'add':
+ foreignKey = {'action_id' : keyStr}
+ self.getDao('add').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'delete':
+ foreignKey = {'action_id' : keyStr}
+ self.getDao('delete').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'change':
+ foreignKey = {'action_id' : keyStr}
+ self.getDao('change').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['akey', 'value', 'id']
+ table = 'annotation'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ key = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ annotation = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ annotation.is_dirty = False
+ list.append(annotation)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'annotation'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'id']
+ table = 'change_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ what = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[1], 'long', 'int')
+ newObjId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ data = None
+ if what == 'module':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('module').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'location':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('location').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'annotation':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'function':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('function').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'connection':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('connection').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'port':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('port').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'parameter':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('parameter').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'portSpec':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('portSpec').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'other':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('other').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+
+ change = DBChange(id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ change.is_dirty = False
+ list.append(change)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'change_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ child = obj.db_data
+ if child.vtType == 'module':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('module').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'location':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('location').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'annotation':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'function':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('function').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'connection':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('connection').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'port':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('port').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'parameter':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('parameter').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'portSpec':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('portSpec').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'other':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('other').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBMacroSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'descrptn', 'id']
+ table = 'macro'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ descrptn = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('macro','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('action').fromSQL(db, None, foreignKey, globalProps)
+ actions = {}
+ for obj in res:
+ actions[obj.db_id] = obj
+
+ macro = DBMacro(id=id,
+ name=name,
+ descrptn=descrptn,
+ actions=actions)
+ macro.is_dirty = False
+ list.append(macro)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'macro'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if obj.db_descrptn is not None:
+ columnMap['descrptn'] = \
+ self.convertToDB(obj.db_descrptn, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('macro','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_actions.itervalues():
+ self.getDao('action').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['id']
+ table = 'connection_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('connection','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('port').fromSQL(db, None, foreignKey, globalProps)
+ ports = res
+
+ connection = DBConnection(id=id,
+ ports=ports)
+ connection.is_dirty = False
+ list.append(connection)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'connection_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('connection','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_ports:
+ self.getDao('port').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['time', 'name']
+ table = 'tag'
+ whereMap = {}
+ orderBy = 'name'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'str', 'varchar(255)')
+ whereMap['name'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ time = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ keyStr = self.convertToDB(name,'str','varchar(255)')
+
+ tag = DBTag(name=name,
+ time=time)
+ tag.is_dirty = False
+ list.append(tag)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if obj.is_dirty:
+ columns = ['name']
+ table = 'tag'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['name'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_time is not None:
+ columnMap['time'] = \
+ self.convertToDB(obj.db_time, 'long', 'int')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['name'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBExecRecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['ts_start', 'ts_end', 'module_id', 'module_name', 'id']
+ table = 'exec'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ tsStart = self.convertFromDB(row[0], 'datetime', 'datetime')
+ tsEnd = self.convertFromDB(row[1], 'datetime', 'datetime')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('execRec','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ annotations = res
+
+ execRec = DBExecRec(id=id,
+ tsStart=tsStart,
+ tsEnd=tsEnd,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ annotations=annotations)
+ execRec.is_dirty = False
+ list.append(execRec)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'exec'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_tsStart is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_tsStart, 'datetime', 'datetime')
+ if obj.db_tsEnd is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_tsEnd, 'datetime', 'datetime')
+ if obj.db_moduleId is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if obj.db_moduleName is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('execRec','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_annotations:
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['version', 'name', 'id']
+ table = 'vistrail'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ version = self.convertFromDB(row[0], 'str', 'char(16)')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ if globalProps is None:
+ globalProps = {}
+ globalProps['vt_id'] = self.convertToDB(id, 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('vistrail','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('action').fromSQL(db, None, foreignKey, globalProps)
+ actions = {}
+ for obj in res:
+ actions[obj.db_id] = obj
+
+ foreignKey = None
+ res = self.getDao('tag').fromSQL(db, None, foreignKey, globalProps)
+ tags = {}
+ for obj in res:
+ tags[obj.db_name] = obj
+
+ foreignKey = None
+ res = self.getDao('macro').fromSQL(db, None, foreignKey, globalProps)
+ macros = {}
+ for obj in res:
+ macros[obj.db_id] = obj
+
+ vistrail = DBVistrail(id=id,
+ version=version,
+ name=name,
+ actions=actions,
+ tags=tags,
+ macros=macros)
+ vistrail.is_dirty = False
+ list.append(vistrail)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'vistrail'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ if obj.db_id is not None:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if globalProps is None:
+ globalProps = {}
+ globalProps['vt_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+
+ discStr = self.convertToDB('vistrail','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_actions.itervalues():
+ self.getDao('action').toSQL(db, child, foreignKey, globalProps)
+
+ foreignKey = None
+ for child in obj.db_tags.itervalues():
+ self.getDao('tag').toSQL(db, child, foreignKey, globalProps)
+
+ foreignKey = None
+ for child in obj.db_macros.itervalues():
+ self.getDao('macro').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['what', 'object_id', 'par_obj_id', 'par_obj_type', 'id']
+ table = 'delete_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ what = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[1], 'long', 'int')
+ parentObjId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjType = self.convertFromDB(row[3], 'str', 'char(16)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ delete = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ delete.is_dirty = False
+ list.append(delete)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'delete_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'session' not in self:
+ self['session'] = DBSessionSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'wfExec' not in self:
+ self['wfExec'] = DBWfExecSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'macro' not in self:
+ self['macro'] = DBMacroSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'execRec' not in self:
+ self['execRec'] = DBExecRecSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
diff --git a/vistrails/db/versions/v0_5_0/persistence/sql/sql_dao.py b/vistrails/db/versions/v0_5_0/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..f632eb8
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/persistence/sql/sql_dao.py
@@ -0,0 +1,141 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return "'" + str(value) + "'"
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ return str(value)
+ elif type == 'int':
+ return str(value)
+ elif type == 'date':
+ return "'" + value.isoformat() + "'"
+ elif type == 'datetime':
+ return "'" + value.strftime('%Y-%m-%d %H:%M:%S') + "'"
+ else:
+ return str(value)
+
+ return "''"
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ return dbCommand
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ valueStr = ', '.join(values)
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s)""" % \
+ (table, columnStr, valueStr)
+ return dbCommand
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ setStr += '%s %s = %s' % (comma, column, value)
+ comma = ','
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """UPDATE %s SET %s WHERE %s""" % \
+ (table, setStr, whereStr)
+ return dbCommand
+
+ def executeSQL(self, db, dbCommand, isFetch):
+ # print 'dbCommand: %s' % dbCommand
+ data = None
+ cursor = db.cursor()
+ cursor.execute(dbCommand)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ cursor.close()
+ return data
diff --git a/vistrails/db/versions/v0_5_0/persistence/xml/__init__.py b/vistrails/db/versions/v0_5_0/persistence/xml/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_5_0/persistence/xml/auto_gen.py b/vistrails/db/versions/v0_5_0/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..ed948a6
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/persistence/xml/auto_gen.py
@@ -0,0 +1,1266 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from xml_dao import XMLDAO
+from vistrails.db.versions.v0_5_0.domain import *
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'portSpec':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ type = self.convertFromStr(self.getAttribute(node, 'type'), 'str')
+ spec = self.convertFromStr(self.getAttribute(node, 'spec'), 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, doc):
+ node = doc.createElement('portSpec')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.setAttribute('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.setAttribute('spec',self.convertToStr(portSpec.db_spec, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'module':
+ return None
+
+ functions = []
+ portSpecs = []
+
+ annotations = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ cache = self.convertFromStr(self.getAttribute(node, 'cache'), 'int')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+ location = None
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'location':
+ location = self.getDao('location').fromXML(child)
+ elif child.nodeName == 'function':
+ function = self.getDao('function').fromXML(child)
+ functions.append(function)
+ elif child.nodeName == 'annotation':
+ annotation = self.getDao('annotation').fromXML(child)
+ annotations[annotation.db_id] = annotation
+ elif child.nodeName == 'portSpec':
+ portSpec = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(portSpec)
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, doc):
+ node = doc.createElement('module')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(module.db_id, 'long'))
+ node.setAttribute('cache',self.convertToStr(module.db_cache, 'int'))
+ node.setAttribute('name',self.convertToStr(module.db_name, 'str'))
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ node.appendChild(self.getDao('location').toXML(location, doc))
+ functions = module.db_functions
+ for function in functions:
+ node.appendChild(self.getDao('function').toXML(function, doc))
+ annotations = module.db_annotations
+ for annotation in annotations.itervalues():
+ node.appendChild(self.getDao('annotation').toXML(annotation, doc))
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ node.appendChild(self.getDao('portSpec').toXML(portSpec, doc))
+
+ return node
+
+class DBSessionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'session':
+ return None
+
+ wfExecs = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ user = self.convertFromStr(self.getAttribute(node, 'user'), 'str')
+ ip = self.convertFromStr(self.getAttribute(node, 'ip'), 'str')
+ visVersion = self.convertFromStr(self.getAttribute(node, 'visVersion'), 'str')
+ tsStart = self.convertFromStr(self.getAttribute(node, 'tsStart'), 'datetime')
+ tsEnd = self.convertFromStr(self.getAttribute(node, 'tsEnd'), 'datetime')
+ machineId = self.convertFromStr(self.getAttribute(node, 'machineId'), 'long')
+
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'wfExec':
+ wfExec = self.getDao('wfExec').fromXML(child)
+ wfExecs[wfExec.db_id] = wfExec
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBSession(id=id,
+ user=user,
+ ip=ip,
+ visVersion=visVersion,
+ tsStart=tsStart,
+ tsEnd=tsEnd,
+ machineId=machineId,
+ wfExecs=wfExecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, session, doc):
+ node = doc.createElement('session')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(session.db_id, 'long'))
+ node.setAttribute('user',self.convertToStr(session.db_user, 'str'))
+ node.setAttribute('ip',self.convertToStr(session.db_ip, 'str'))
+ node.setAttribute('visVersion',self.convertToStr(session.db_visVersion, 'str'))
+ node.setAttribute('tsStart',self.convertToStr(session.db_tsStart, 'datetime'))
+ node.setAttribute('tsEnd',self.convertToStr(session.db_tsEnd, 'datetime'))
+ node.setAttribute('machineId',self.convertToStr(session.db_machineId, 'long'))
+
+ # set elements
+ wfExecs = session.db_wfExecs
+ for wfExec in wfExecs.itervalues():
+ node.appendChild(self.getDao('wfExec').toXML(wfExec, doc))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'port':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ type = self.convertFromStr(self.getAttribute(node, 'type'), 'str')
+ moduleId = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ moduleName = self.convertFromStr(self.getAttribute(node, 'moduleName'), 'str')
+ sig = self.convertFromStr(self.getAttribute(node, 'sig'), 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ sig=sig)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, doc):
+ node = doc.createElement('port')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(port.db_id, 'long'))
+ node.setAttribute('type',self.convertToStr(port.db_type, 'str'))
+ node.setAttribute('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.setAttribute('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.setAttribute('sig',self.convertToStr(port.db_sig, 'str'))
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'log':
+ return None
+
+ sessions = {}
+ machines = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'session':
+ session = self.getDao('session').fromXML(child)
+ sessions[session.db_id] = session
+ elif child.nodeName == 'machine':
+ machine = self.getDao('machine').fromXML(child)
+ machines[machine.db_id] = machine
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBLog(id=id,
+ sessions=sessions,
+ machines=machines)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, doc):
+ node = doc.createElement('log')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(log.db_id, 'long'))
+
+ # set elements
+ sessions = log.db_sessions
+ for session in sessions.itervalues():
+ node.appendChild(self.getDao('session').toXML(session, doc))
+ machines = log.db_machines
+ for machine in machines.itervalues():
+ node.appendChild(self.getDao('machine').toXML(machine, doc))
+
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'machine':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ os = self.convertFromStr(self.getAttribute(node, 'os'), 'str')
+ architecture = self.convertFromStr(self.getAttribute(node, 'architecture'), 'str')
+ processor = self.convertFromStr(self.getAttribute(node, 'processor'), 'str')
+ ram = self.convertFromStr(self.getAttribute(node, 'ram'), 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, doc):
+ node = doc.createElement('machine')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(machine.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(machine.db_name, 'str'))
+ node.setAttribute('os',self.convertToStr(machine.db_os, 'str'))
+ node.setAttribute('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.setAttribute('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.setAttribute('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'add':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ what = self.convertFromStr(self.getAttribute(node, 'what'), 'str')
+ objectId = self.convertFromStr(self.getAttribute(node, 'objectId'), 'long')
+ parentObjId = self.convertFromStr(self.getAttribute(node, 'parentObjId'), 'long')
+ parentObjType = self.convertFromStr(self.getAttribute(node, 'parentObjType'), 'str')
+
+ data = None
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'module':
+ data = self.getDao('module').fromXML(child)
+ elif child.nodeName == 'location':
+ data = self.getDao('location').fromXML(child)
+ elif child.nodeName == 'annotation':
+ data = self.getDao('annotation').fromXML(child)
+ elif child.nodeName == 'function':
+ data = self.getDao('function').fromXML(child)
+ elif child.nodeName == 'connection':
+ data = self.getDao('connection').fromXML(child)
+ elif child.nodeName == 'port':
+ data = self.getDao('port').fromXML(child)
+ elif child.nodeName == 'parameter':
+ data = self.getDao('parameter').fromXML(child)
+ elif child.nodeName == 'portSpec':
+ data = self.getDao('portSpec').fromXML(child)
+ elif child.nodeName == 'other':
+ data = self.getDao('other').fromXML(child)
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBAdd(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, doc):
+ node = doc.createElement('add')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(add.db_id, 'long'))
+ node.setAttribute('what',self.convertToStr(add.db_what, 'str'))
+ node.setAttribute('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.setAttribute('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.setAttribute('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # set elements
+ data = add.db_data
+ if data.vtType == 'module':
+ node.appendChild(self.getDao('module').toXML(data, doc))
+ elif data.vtType == 'location':
+ node.appendChild(self.getDao('location').toXML(data, doc))
+ elif data.vtType == 'annotation':
+ node.appendChild(self.getDao('annotation').toXML(data, doc))
+ elif data.vtType == 'function':
+ node.appendChild(self.getDao('function').toXML(data, doc))
+ elif data.vtType == 'connection':
+ node.appendChild(self.getDao('connection').toXML(data, doc))
+ elif data.vtType == 'port':
+ node.appendChild(self.getDao('port').toXML(data, doc))
+ elif data.vtType == 'parameter':
+ node.appendChild(self.getDao('parameter').toXML(data, doc))
+ elif data.vtType == 'portSpec':
+ node.appendChild(self.getDao('portSpec').toXML(data, doc))
+ elif data.vtType == 'other':
+ node.appendChild(self.getDao('other').toXML(data, doc))
+
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'other':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ key = self.convertFromStr(self.getAttribute(node, 'key'), 'str')
+
+ value = None
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'value':
+ value = self.convertFromStr(child.firstChild.nodeValue,'str')
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, doc):
+ node = doc.createElement('other')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(other.db_id, 'long'))
+ node.setAttribute('key',self.convertToStr(other.db_key, 'str'))
+
+ # set elements
+ if other.db_value is not None:
+ child = other.db_value
+ valueNode = doc.createElement('value')
+ valueText = doc.createTextNode(self.convertToStr(child, 'str'))
+ valueNode.appendChild(valueText)
+ node.appendChild(valueNode)
+
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'location':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ x = self.convertFromStr(self.getAttribute(node, 'x'), 'float')
+ y = self.convertFromStr(self.getAttribute(node, 'y'), 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, doc):
+ node = doc.createElement('location')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(location.db_id, 'long'))
+ node.setAttribute('x',self.convertToStr(location.db_x, 'float'))
+ node.setAttribute('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBWfExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'wfExec':
+ return None
+
+ execRecs = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ tsStart = self.convertFromStr(self.getAttribute(node, 'tsStart'), 'datetime')
+ tsEnd = self.convertFromStr(self.getAttribute(node, 'tsEnd'), 'datetime')
+ wfVersion = self.convertFromStr(self.getAttribute(node, 'wfVersion'), 'int')
+ vistrailId = self.convertFromStr(self.getAttribute(node, 'vistrailId'), 'long')
+ vistrailName = self.convertFromStr(self.getAttribute(node, 'vistrailName'), 'str')
+
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'execRec':
+ execRec = self.getDao('execRec').fromXML(child)
+ execRecs[execRec.db_id] = execRec
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBWfExec(id=id,
+ tsStart=tsStart,
+ tsEnd=tsEnd,
+ wfVersion=wfVersion,
+ vistrailId=vistrailId,
+ vistrailName=vistrailName,
+ execRecs=execRecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, wfExec, doc):
+ node = doc.createElement('wfExec')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(wfExec.db_id, 'long'))
+ node.setAttribute('tsStart',self.convertToStr(wfExec.db_tsStart, 'datetime'))
+ node.setAttribute('tsEnd',self.convertToStr(wfExec.db_tsEnd, 'datetime'))
+ node.setAttribute('wfVersion',self.convertToStr(wfExec.db_wfVersion, 'int'))
+ node.setAttribute('vistrailId',self.convertToStr(wfExec.db_vistrailId, 'long'))
+ node.setAttribute('vistrailName',self.convertToStr(wfExec.db_vistrailName, 'str'))
+
+ # set elements
+ execRecs = wfExec.db_execRecs
+ for execRec in execRecs.itervalues():
+ node.appendChild(self.getDao('execRec').toXML(execRec, doc))
+
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'parameter':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ pos = self.convertFromStr(self.getAttribute(node, 'pos'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ type = self.convertFromStr(self.getAttribute(node, 'type'), 'str')
+ val = self.convertFromStr(self.getAttribute(node, 'val'), 'str')
+ alias = self.convertFromStr(self.getAttribute(node, 'alias'), 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, doc):
+ node = doc.createElement('parameter')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(parameter.db_id, 'long'))
+ node.setAttribute('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.setAttribute('name',self.convertToStr(parameter.db_name, 'str'))
+ node.setAttribute('type',self.convertToStr(parameter.db_type, 'str'))
+ node.setAttribute('val',self.convertToStr(parameter.db_val, 'str'))
+ node.setAttribute('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'function':
+ return None
+
+ parameters = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ pos = self.convertFromStr(self.getAttribute(node, 'pos'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'parameter':
+ parameter = self.getDao('parameter').fromXML(child)
+ parameters.append(parameter)
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, doc):
+ node = doc.createElement('function')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(function.db_id, 'long'))
+ node.setAttribute('pos',self.convertToStr(function.db_pos, 'long'))
+ node.setAttribute('name',self.convertToStr(function.db_name, 'str'))
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ node.appendChild(self.getDao('parameter').toXML(parameter, doc))
+
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'workflow':
+ return None
+
+ annotations = []
+ others = []
+
+ modules = {}
+ connections = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'module':
+ module = self.getDao('module').fromXML(child)
+ modules[module.db_id] = module
+ elif child.nodeName == 'connection':
+ connection = self.getDao('connection').fromXML(child)
+ connections[connection.db_id] = connection
+ elif child.nodeName == 'annotation':
+ annotation = self.getDao('annotation').fromXML(child)
+ annotations.append(annotation)
+ elif child.nodeName == 'other':
+ other = self.getDao('other').fromXML(child)
+ others.append(other)
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBWorkflow(id=id,
+ name=name,
+ modules=modules,
+ connections=connections,
+ annotations=annotations,
+ others=others)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, doc):
+ node = doc.createElement('workflow')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(workflow.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(workflow.db_name, 'str'))
+
+ # set elements
+ modules = workflow.db_modules
+ for module in modules.itervalues():
+ node.appendChild(self.getDao('module').toXML(module, doc))
+ connections = workflow.db_connections
+ for connection in connections.itervalues():
+ node.appendChild(self.getDao('connection').toXML(connection, doc))
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ node.appendChild(self.getDao('annotation').toXML(annotation, doc))
+ others = workflow.db_others
+ for other in others:
+ node.appendChild(self.getDao('other').toXML(other, doc))
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'action':
+ return None
+
+ operations = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ prevId = self.convertFromStr(self.getAttribute(node, 'prevId'), 'long')
+ date = self.convertFromStr(self.getAttribute(node, 'date'), 'datetime')
+ user = self.convertFromStr(self.getAttribute(node, 'user'), 'str')
+
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'add':
+ operation = self.getDao('add').fromXML(child)
+ operations.append(operation)
+ elif child.nodeName == 'delete':
+ operation = self.getDao('delete').fromXML(child)
+ operations.append(operation)
+ elif child.nodeName == 'change':
+ operation = self.getDao('change').fromXML(child)
+ operations.append(operation)
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBAction(id=id,
+ prevId=prevId,
+ date=date,
+ user=user,
+ operations=operations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, doc):
+ node = doc.createElement('action')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(action.db_id, 'long'))
+ node.setAttribute('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.setAttribute('date',self.convertToStr(action.db_date, 'datetime'))
+ node.setAttribute('user',self.convertToStr(action.db_user, 'str'))
+
+ # set elements
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ node.appendChild(self.getDao('add').toXML(operation, doc))
+ elif operation.vtType == 'delete':
+ node.appendChild(self.getDao('delete').toXML(operation, doc))
+ elif operation.vtType == 'change':
+ node.appendChild(self.getDao('change').toXML(operation, doc))
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'annotation':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ key = self.convertFromStr(self.getAttribute(node, 'key'), 'str')
+ value = self.convertFromStr(self.getAttribute(node, 'value'), 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, doc):
+ node = doc.createElement('annotation')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(annotation.db_id, 'long'))
+ node.setAttribute('key',self.convertToStr(annotation.db_key, 'str'))
+ node.setAttribute('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'change':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ what = self.convertFromStr(self.getAttribute(node, 'what'), 'str')
+ oldObjId = self.convertFromStr(self.getAttribute(node, 'oldObjId'), 'long')
+ newObjId = self.convertFromStr(self.getAttribute(node, 'newObjId'), 'long')
+ parentObjId = self.convertFromStr(self.getAttribute(node, 'parentObjId'), 'long')
+ parentObjType = self.convertFromStr(self.getAttribute(node, 'parentObjType'), 'str')
+
+ data = None
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'module':
+ data = self.getDao('module').fromXML(child)
+ elif child.nodeName == 'location':
+ data = self.getDao('location').fromXML(child)
+ elif child.nodeName == 'annotation':
+ data = self.getDao('annotation').fromXML(child)
+ elif child.nodeName == 'function':
+ data = self.getDao('function').fromXML(child)
+ elif child.nodeName == 'connection':
+ data = self.getDao('connection').fromXML(child)
+ elif child.nodeName == 'port':
+ data = self.getDao('port').fromXML(child)
+ elif child.nodeName == 'parameter':
+ data = self.getDao('parameter').fromXML(child)
+ elif child.nodeName == 'portSpec':
+ data = self.getDao('portSpec').fromXML(child)
+ elif child.nodeName == 'other':
+ data = self.getDao('other').fromXML(child)
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBChange(id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, doc):
+ node = doc.createElement('change')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(change.db_id, 'long'))
+ node.setAttribute('what',self.convertToStr(change.db_what, 'str'))
+ node.setAttribute('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.setAttribute('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.setAttribute('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.setAttribute('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # set elements
+ data = change.db_data
+ if data.vtType == 'module':
+ node.appendChild(self.getDao('module').toXML(data, doc))
+ elif data.vtType == 'location':
+ node.appendChild(self.getDao('location').toXML(data, doc))
+ elif data.vtType == 'annotation':
+ node.appendChild(self.getDao('annotation').toXML(data, doc))
+ elif data.vtType == 'function':
+ node.appendChild(self.getDao('function').toXML(data, doc))
+ elif data.vtType == 'connection':
+ node.appendChild(self.getDao('connection').toXML(data, doc))
+ elif data.vtType == 'port':
+ node.appendChild(self.getDao('port').toXML(data, doc))
+ elif data.vtType == 'parameter':
+ node.appendChild(self.getDao('parameter').toXML(data, doc))
+ elif data.vtType == 'portSpec':
+ node.appendChild(self.getDao('portSpec').toXML(data, doc))
+ elif data.vtType == 'other':
+ node.appendChild(self.getDao('other').toXML(data, doc))
+
+ return node
+
+class DBMacroXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'macro':
+ return None
+
+ actions = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ descrptn = self.convertFromStr(self.getAttribute(node, 'descrptn'), 'str')
+
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'action':
+ action = self.getDao('action').fromXML(child)
+ actions[action.db_id] = action
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBMacro(id=id,
+ name=name,
+ descrptn=descrptn,
+ actions=actions)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, macro, doc):
+ node = doc.createElement('macro')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(macro.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(macro.db_name, 'str'))
+ node.setAttribute('descrptn',self.convertToStr(macro.db_descrptn, 'str'))
+
+ # set elements
+ actions = macro.db_actions
+ for action in actions.itervalues():
+ node.appendChild(self.getDao('action').toXML(action, doc))
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'connection':
+ return None
+
+ ports = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'port':
+ port = self.getDao('port').fromXML(child)
+ ports.append(port)
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, doc):
+ node = doc.createElement('connection')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(connection.db_id, 'long'))
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ node.appendChild(self.getDao('port').toXML(port, doc))
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'tag':
+ return None
+
+ # read attributes
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ time = self.convertFromStr(self.getAttribute(node, 'time'), 'long')
+
+ obj = DBTag(name=name,
+ time=time)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, doc):
+ node = doc.createElement('tag')
+
+ # set attributes
+ node.setAttribute('name',self.convertToStr(tag.db_name, 'str'))
+ node.setAttribute('time',self.convertToStr(tag.db_time, 'long'))
+
+ return node
+
+class DBExecRecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'exec':
+ return None
+
+ annotations = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ tsStart = self.convertFromStr(self.getAttribute(node, 'tsStart'), 'datetime')
+ tsEnd = self.convertFromStr(self.getAttribute(node, 'tsEnd'), 'datetime')
+ moduleId = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ moduleName = self.convertFromStr(self.getAttribute(node, 'moduleName'), 'str')
+
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'annotation':
+ annotation = self.getDao('annotation').fromXML(child)
+ annotations.append(annotation)
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBExecRec(id=id,
+ tsStart=tsStart,
+ tsEnd=tsEnd,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, execRec, doc):
+ node = doc.createElement('exec')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(execRec.db_id, 'long'))
+ node.setAttribute('tsStart',self.convertToStr(execRec.db_tsStart, 'datetime'))
+ node.setAttribute('tsEnd',self.convertToStr(execRec.db_tsEnd, 'datetime'))
+ node.setAttribute('moduleId',self.convertToStr(execRec.db_moduleId, 'long'))
+ node.setAttribute('moduleName',self.convertToStr(execRec.db_moduleName, 'str'))
+
+ # set elements
+ annotations = execRec.db_annotations
+ for annotation in annotations:
+ node.appendChild(self.getDao('annotation').toXML(annotation, doc))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'vistrail':
+ return None
+
+ actions = {}
+ tags = {}
+ macros = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ version = self.convertFromStr(self.getAttribute(node, 'version'), 'str')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ dbHost = self.convertFromStr(self.getAttribute(node, 'dbHost'), 'str')
+ dbPort = self.convertFromStr(self.getAttribute(node, 'dbPort'), 'int')
+ dbName = self.convertFromStr(self.getAttribute(node, 'dbName'), 'str')
+
+
+ # read children
+ for child in node.childNodes:
+ if child.nodeName == 'action':
+ action = self.getDao('action').fromXML(child)
+ actions[action.db_id] = action
+ elif child.nodeName == 'tag':
+ tag = self.getDao('tag').fromXML(child)
+ tags[tag.db_name] = tag
+ elif child.nodeName == 'macro':
+ macro = self.getDao('macro').fromXML(child)
+ macros[macro.db_id] = macro
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ dbHost=dbHost,
+ dbPort=dbPort,
+ dbName=dbName,
+ actions=actions,
+ tags=tags,
+ macros=macros)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, doc):
+ node = doc.createElement('vistrail')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.setAttribute('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.setAttribute('name',self.convertToStr(vistrail.db_name, 'str'))
+ node.setAttribute('dbHost',self.convertToStr(vistrail.db_dbHost, 'str'))
+ node.setAttribute('dbPort',self.convertToStr(vistrail.db_dbPort, 'int'))
+ node.setAttribute('dbName',self.convertToStr(vistrail.db_dbName, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions.itervalues():
+ node.appendChild(self.getDao('action').toXML(action, doc))
+ tags = vistrail.db_tags
+ for tag in tags.itervalues():
+ node.appendChild(self.getDao('tag').toXML(tag, doc))
+ macros = vistrail.db_macros
+ for macro in macros.itervalues():
+ node.appendChild(self.getDao('macro').toXML(macro, doc))
+
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'delete':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ what = self.convertFromStr(self.getAttribute(node, 'what'), 'str')
+ objectId = self.convertFromStr(self.getAttribute(node, 'objectId'), 'long')
+ parentObjId = self.convertFromStr(self.getAttribute(node, 'parentObjId'), 'long')
+ parentObjType = self.convertFromStr(self.getAttribute(node, 'parentObjType'), 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, doc):
+ node = doc.createElement('delete')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(delete.db_id, 'long'))
+ node.setAttribute('what',self.convertToStr(delete.db_what, 'str'))
+ node.setAttribute('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.setAttribute('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.setAttribute('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'session' not in self:
+ self['session'] = DBSessionXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'wfExec' not in self:
+ self['wfExec'] = DBWfExecXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'macro' not in self:
+ self['macro'] = DBMacroXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'execRec' not in self:
+ self['execRec'] = DBExecRecXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
diff --git a/vistrails/db/versions/v0_5_0/persistence/xml/io.py b/vistrails/db/versions/v0_5_0/persistence/xml/io.py
new file mode 100644
index 0000000..661d937
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/persistence/xml/io.py
@@ -0,0 +1,95 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.parsers.expat import ExpatError
+import xml.dom.minidom
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_5_0 import version as my_version
+
+def parse_xml_file(filename):
+ try:
+ return xml.dom.minidom.parse(filename)
+ except xml.parsers.expat.ExpatError, e:
+ msg = 'XML parse error at line %s, col %s: %s' % \
+ (e.lineno, e.offset, e.code)
+ raise VistrailsDBException(msg)
+
+def write_xml_file(filename, dom, prettyprint=True):
+ output = open(filename, 'w')
+ if prettyprint:
+ dom.writexml(output, '',' ','\n')
+ else:
+ dom.writexml(output)
+ output.close()
+
+def read_xml_object(vtType, node, dao_list):
+ return dao_list[vtType].fromXML(node)
+
+def write_xml_object(obj, dom, dao_list, node=None):
+ res_node = dao_list[obj.vtType].toXML(obj, dom, node)
+ return res_node
+
+def open_from_xml(filename, vtType, dao_list):
+ """open_from_xml(filename) -> DBVistrail"""
+ dom = parse_xml_file(filename)
+ vistrail = read_xml_object(vtType, dom.documentElement, dao_list)
+ dom.unlink()
+ return vistrail
+
+def save_to_xml(obj, filename, dao_list):
+ dom = xml.dom.minidom.getDOMImplementation().createDocument(None, None,
+ None)
+ root = write_xml_object(obj, dom, dao_list)
+ dom.appendChild(root)
+ if obj.vtType == 'vistrail':
+ root.setAttribute('version', my_version)
+ root.setAttribute('xmlns:xsi',
+ 'http://www.w3.org/2001/XMLSchema-instance')
+ root.setAttribute('xsi:schemaLocation',
+ 'http://www.vistrails.org/vistrail.xsd')
+ write_xml_file(filename, dom)
+ dom.unlink()
+
+def serialize(object, dao_list):
+ dom = xml.dom.minidom.getDOMImplementation().createDocument(None, None,
+ None)
+ root = write_xml_object(object, dom, dao_list)
+ dom.appendChild(root)
+ return dom.toxml()
+
+def unserialize(str, obj_type):
+ dom = xml.dom.minidom.parseString(str)
+ return read_xml_object(obj_type, dom.documentElement, dao_list)
+
diff --git a/vistrails/db/versions/v0_5_0/persistence/xml/xml_dao.py b/vistrails/db/versions/v0_5_0/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..de42aa2
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/persistence/xml/xml_dao.py
@@ -0,0 +1,77 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v0_5_0/schemas/sql/vistrails.sql b/vistrails/db/versions/v0_5_0/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..8d403eb
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/schemas/sql/vistrails.sql
@@ -0,0 +1,236 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(22),
+ type varchar(255),
+ spec varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE session(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ vis_ver varchar(255),
+ ts_start datetime,
+ tsEnd datetime,
+ machine_id int,
+ log_id int,
+ vt_id int
+);
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ sig varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE log_tbl(
+ id int,
+ vt_id int
+);
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ log_id int,
+ vt_id int
+);
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+);
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE wf_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ wfVersion int,
+ vistrail_id int,
+ vistrail_name varchar(255),
+ session_id int,
+ vt_id int
+);
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8192),
+ alias varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE workflow(
+ id int,
+ name varchar(255),
+ vt_id int
+);
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ user varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+);
+
+CREATE TABLE macro(
+ id int,
+ name varchar(255),
+ descrptn varchar(255),
+ vt_id int
+);
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE tag(
+ name varchar(255),
+ time int,
+ vt_id int
+);
+
+CREATE TABLE exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ module_id int,
+ module_name varchar(255),
+ wf_exec_id int,
+ vt_id int
+);
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ version char(16),
+ name varchar(255)
+);
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+);
+
diff --git a/vistrails/db/versions/v0_5_0/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v0_5_0/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..fcb4304
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,38 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, session, port, log_tbl, machine, add_tbl, other, location, wf_exec, parameter, function, workflow, action, annotation, change_tbl, macro, connection_tbl, tag, exec, vistrail, delete_tbl
diff --git a/vistrails/db/versions/v0_5_0/schemas/xml/log.xsd b/vistrails/db/versions/v0_5_0/schemas/xml/log.xsd
new file mode 100644
index 0000000..1871490
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/schemas/xml/log.xsd
@@ -0,0 +1,102 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="log">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="session" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="machine" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="session">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="wfExec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="ip" type="xs:string"/>
+ <xs:attribute name="visVersion" type="xs:string"/>
+ <xs:attribute name="tsStart" type="xs:dateTime"/>
+ <xs:attribute name="tsEnd" type="xs:dateTime"/>
+ <xs:attribute name="machineId" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="machine">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="os" type="xs:string"/>
+ <xs:attribute name="architecture" type="xs:string"/>
+ <xs:attribute name="processor" type="xs:string"/>
+ <xs:attribute name="ram" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="wfExec">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="execRec" ref="exec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="tsStart" type="xs:dateTime"/>
+ <xs:attribute name="tsEnd" type="xs:dateTime"/>
+ <xs:attribute name="wfVersion" type="xs:int"/>
+ <xs:attribute name="vistrailId" type="xs:int"/>
+ <xs:attribute name="vistrailName" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="exec">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="tsStart" type="xs:dateTime"/>
+ <xs:attribute name="tsEnd" type="xs:dateTime"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_5_0/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_5_0/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..23bdc68
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/schemas/xml/vistrail.xsd
@@ -0,0 +1,213 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="macro" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="dbHost" type="xs:string"/>
+ <xs:attribute name="dbPort" type="xs:int"/>
+ <xs:attribute name="dbName" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="user" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="time" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="macro">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="descrptn" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="sig" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_5_0/schemas/xml/workflow.xsd b/vistrails/db/versions/v0_5_0/schemas/xml/workflow.xsd
new file mode 100644
index 0000000..d24c9f8
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/schemas/xml/workflow.xsd
@@ -0,0 +1,131 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="workflow">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="module" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ <xs:attribute name="relative" type="xs:boolean"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="sig" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_5_0/specs/action.xml b/vistrails/db/versions/v0_5_0/specs/action.xml
new file mode 100644
index 0000000..2847761
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/action.xml
@@ -0,0 +1,104 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+<!--
+ <property name="actionType" type="str">
+ <xml inferred="true" choice="operation"/>
+ <sql column="action_type" type="char(16)"/>
+ </property>
+
+discriminator="actionType"
+-->
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="macro">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/add.xml b/vistrails/db/versions/v0_5_0/specs/add.xml
new file mode 100644
index 0000000..0973246
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/add.xml
@@ -0,0 +1,107 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/annotation.xml b/vistrails/db/versions/v0_5_0/specs/annotation.xml
new file mode 100644
index 0000000..58d4dd6
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/annotation.xml
@@ -0,0 +1,89 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml name="id" nodeType="xs:attribute" type="xs:int"/>
+ <sql column="id" type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml name="key" nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="execRec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/change.xml b/vistrails/db/versions/v0_5_0/specs/change.xml
new file mode 100644
index 0000000..178a19b
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/change.xml
@@ -0,0 +1,112 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/connection.xml b/vistrails/db/versions/v0_5_0/specs/connection.xml
new file mode 100644
index 0000000..781b127
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/connection.xml
@@ -0,0 +1,86 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+<!--
+ <property name="source" ref="true" object="port" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="destination" ref="true" object="port" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+-->
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/delete.xml b/vistrails/db/versions/v0_5_0/specs/delete.xml
new file mode 100644
index 0000000..9df9273
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/delete.xml
@@ -0,0 +1,77 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/execRec.xml b/vistrails/db/versions/v0_5_0/specs/execRec.xml
new file mode 100644
index 0000000..29f48ee
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/execRec.xml
@@ -0,0 +1,81 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="execRec">
+ <layout>
+ <xml name="exec" nodeType="xs:element"/>
+ <sql table="exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="tsStart" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql column="ts_start" type="datetime"/>
+ </property>
+
+ <property name="tsEnd" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql column="ts_end" type="datetime"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="module_id" type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="module_name" type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="wfExec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/function.xml b/vistrails/db/versions/v0_5_0/specs/function.xml
new file mode 100644
index 0000000..8254645
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/function.xml
@@ -0,0 +1,83 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/location.xml b/vistrails/db/versions/v0_5_0/specs/location.xml
new file mode 100644
index 0000000..6e56055
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/location.xml
@@ -0,0 +1,80 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_5_0/specs/log.xml b/vistrails/db/versions/v0_5_0/specs/log.xml
new file mode 100644
index 0000000..53d3d43
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/log.xml
@@ -0,0 +1,60 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="session" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/machine.xml b/vistrails/db/versions/v0_5_0/specs/machine.xml
new file mode 100644
index 0000000..bae6103
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/machine.xml
@@ -0,0 +1,82 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/macro.xml b/vistrails/db/versions/v0_5_0/specs/macro.xml
new file mode 100644
index 0000000..6c5fb37
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/macro.xml
@@ -0,0 +1,72 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="macro">
+ <layout>
+ <xml name="macro" nodeType="xs:element"/>
+ <sql table="macro"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="descrptn" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="action" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="vistrail" type="long" mapping="many-to-one"
+ inverse="true">
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
+
+
diff --git a/vistrails/db/versions/v0_5_0/specs/module.xml b/vistrails/db/versions/v0_5_0/specs/module.xml
new file mode 100644
index 0000000..922ac2b
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/module.xml
@@ -0,0 +1,95 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/other.xml b/vistrails/db/versions/v0_5_0/specs/other.xml
new file mode 100644
index 0000000..40e1388
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/other.xml
@@ -0,0 +1,79 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/parameter.xml b/vistrails/db/versions/v0_5_0/specs/parameter.xml
new file mode 100644
index 0000000..23236b5
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/parameter.xml
@@ -0,0 +1,94 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8192)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/port.xml b/vistrails/db/versions/v0_5_0/specs/port.xml
new file mode 100644
index 0000000..2a369ff
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/port.xml
@@ -0,0 +1,90 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="sig" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/portSpec.xml b/vistrails/db/versions/v0_5_0/specs/portSpec.xml
new file mode 100644
index 0000000..e42a5f0
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/portSpec.xml
@@ -0,0 +1,84 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(22)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/session.xml b/vistrails/db/versions/v0_5_0/specs/session.xml
new file mode 100644
index 0000000..0b1a03d
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/session.xml
@@ -0,0 +1,91 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="session">
+ <layout>
+ <xml name="session" type="xs:element"/>
+ <sql table="session"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="visVersion" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="vis_ver" type="varchar(255)"/>
+ </property>
+
+ <property name="tsStart" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql column="ts_start" type="datetime"/>
+ </property>
+
+ <property name="tsEnd" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql coumn="ts_end" type="datetime"/>
+ </property>
+
+ <property name="machineId" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="machine_id" type="int"/>
+ </property>
+
+ <property ref="true" object="wfExec" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/tag.xml b/vistrails/db/versions/v0_5_0/specs/tag.xml
new file mode 100644
index 0000000..22af100
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/tag.xml
@@ -0,0 +1,61 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="name" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="time" type="long" foreignKey="true" object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="vistrail" type="long" mapping="many-to-one"
+ inverse="true">
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/vistrail.xml b/vistrails/db/versions/v0_5_0/specs/vistrail.xml
new file mode 100644
index 0000000..9ffbb79
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/vistrail.xml
@@ -0,0 +1,80 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="vt_id"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="dbHost" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="dbPort" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="dbName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property ref="true" object="action" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="macro" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/wfExec.xml b/vistrails/db/versions/v0_5_0/specs/wfExec.xml
new file mode 100644
index 0000000..aa56ca6
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/wfExec.xml
@@ -0,0 +1,86 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="wfExec">
+ <layout>
+ <xml name="wfExec" nodeType="xs:element"/>
+ <sql table="wf_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="tsStart" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql column="ts_start" type="datetime"/>
+ </property>
+
+ <property name="tsEnd" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql column="ts_end" type="datetime"/>
+ </property>
+
+ <property name="wfVersion" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql colunn="wf_version" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="vistrail_id" type="int"/>
+ </property>
+
+ <property name="vistrailName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="vistrail_name" type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="session" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="session_id" type="int"/>
+ </property>
+
+ <property ref="true" object="execRec" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_5_0/specs/workflow.xml b/vistrails/db/versions/v0_5_0/specs/workflow.xml
new file mode 100644
index 0000000..4f3a576
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/specs/workflow.xml
@@ -0,0 +1,74 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="module" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="connection" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_5_0/translate/__init__.py b/vistrails/db/versions/v0_5_0/translate/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_5_0/translate/v0_3_1.py b/vistrails/db/versions/v0_5_0/translate/v0_3_1.py
new file mode 100644
index 0000000..eff91ce
--- /dev/null
+++ b/vistrails/db/versions/v0_5_0/translate/v0_3_1.py
@@ -0,0 +1,754 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import sys
+import copy
+from datetime import datetime
+from time import strptime
+
+from vistrails.core.data_structures.graph import Graph
+from vistrails.db.versions.v0_5_0.domain import DBVistrail, DBAction, DBTag, DBModule, \
+ DBConnection, DBPortSpec, DBFunction, DBParameter, DBLocation, DBAdd, \
+ DBChange, DBDelete, DBAnnotation, DBPort
+
+def convertDate(date):
+ if date is not None and date != '':
+ return datetime(*strptime(date, '%d %b %Y %H:%M:%S')[0:6])
+ return datetime(1900, 1, 1)
+
+def translateVistrail(_vistrail):
+ vistrail = DBVistrail()
+ for _action in _vistrail.db_get_actions():
+# print 'translating action %s' % _action.db_time
+ functionName = 'translate%s%sAction' % \
+ (_action.db_what[0].upper(), _action.db_what[1:])
+ thisModule = sys.modules[__name__]
+ action = getattr(thisModule, functionName)(_action)
+ vistrail.db_add_action(action)
+ for _tag in _vistrail.db_get_tags():
+ tag = DBTag(time=_tag.db_time,
+ name=_tag.db_name)
+ vistrail.db_add_tag(tag)
+
+ convertIds(vistrail)
+# for action in vistrail.getActions():
+# print '%s %s' % (action.id, action.operations)
+ vistrail.db_version = '0.5.0'
+ return vistrail
+
+def translateAddModuleAction(_action):
+ operations = []
+ for _module in _action.db_datas:
+ module = DBModule(id=_module.db_id,
+ name=_module.db_name,
+ cache=1,
+ location=DBLocation(id=_module.db_id,
+ x=_module.db_x,
+ y=_module.db_y))
+ module.db_location.relative = False
+ operation = DBAdd(id=_action.db_time,
+ what='module',
+ objectId=_module.db_id,
+ data=module)
+ operations.append(operation)
+
+ action = DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations)
+ return action
+
+def translateAddConnectionAction(_action):
+ operations = []
+ for _connection in _action.db_datas:
+ source = DBPort(id=_connection.db_id,
+ type='source',
+ moduleId=_connection.db_sourceId,
+ moduleName=_connection.db_sourceModule,
+ sig=_connection.db_sourcePort)
+ destination = DBPort(id=_connection.db_id,
+ type='destination',
+ moduleId=_connection.db_destinationId,
+ moduleName=_connection.db_destinationModule,
+ sig=_connection.db_destinationPort)
+ connection = DBConnection(id=_connection.db_id,
+ ports=[source, destination])
+ operation = DBAdd(id=_action.db_time,
+ what='connection',
+ objectId=_connection.db_id,
+ data=connection)
+ operations.append(operation)
+
+ action = DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations)
+ return action
+
+def translateChangeParameterAction(_action):
+ operations = []
+ for _set in _action.db_datas:
+ parameter = DBParameter(id=_set.db_parameterId,
+ pos=_set.db_parameterId,
+ name=_set.db_parameter,
+ alias=_set.db_alias,
+ val=_set.db_value,
+ type=_set.db_type)
+ function = DBFunction(id=_set.db_functionId,
+ pos=_set.db_functionId,
+ name=_set.db_function,
+ parameters=[parameter])
+ operation = DBChange(id=_action.db_time,
+ what='function',
+ oldObjId=_set.db_functionId,
+ parentObjId=_set.db_moduleId,
+ parentObjType='module',
+ data=function)
+ operations.append(operation)
+
+ action = DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations)
+ return action
+
+def translateAddModulePortAction(_action):
+ operations = []
+ for _portSpec in _action.db_datas:
+ # ids need to be checked
+ portSpec = DBPortSpec(id=_portSpec.db_moduleId,
+ name=_portSpec.db_portName,
+ type=_portSpec.db_portType,
+ spec=_portSpec.db_portSpec)
+ operation = DBAdd(id=_action.db_time,
+ what='portSpec',
+ objectId=(_portSpec.db_portName,
+ _portSpec.db_portType),
+ parentObjId=_portSpec.db_moduleId,
+ parentObjType='module',
+ data=portSpec)
+ operations.append(operation)
+
+ action = DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations)
+ return action
+
+def translateChangeAnnotationAction(_action):
+ operations = []
+ for _annotation in _action.db_datas:
+ if _annotation.db_key.strip() != '' or \
+ _annotation.db_value.strip() != '':
+ annotation = DBAnnotation(id=-1,
+ key=_annotation.db_key,
+ value=_annotation.db_value)
+ operation = DBChange(id=_action.db_time,
+ what='annotation',
+ oldObjId=_annotation.db_key,
+ parentObjId=_annotation.db_moduleId,
+ parentObjType='module',
+ data=annotation)
+ operations.append(operation)
+
+ action = DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations)
+ return action
+
+def translateDeleteModuleAction(_action):
+ operations = []
+ for _module in _action.db_datas:
+ operation = DBDelete(id=_action.db_time,
+ what='module',
+ objectId=_module.db_moduleId)
+ operations.append(operation)
+
+ action = DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations)
+ return action
+
+def translateDeleteConnectionAction(_action):
+ operations = []
+ for _connection in _action.db_datas:
+ operation = DBDelete(id=_action.db_time,
+ what='connection',
+ objectId=_connection.db_connectionId)
+ operations.append(operation)
+
+ action = DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations)
+ return action
+
+def translateDeleteFunctionAction(_action):
+ operations = []
+ for _function in _action.db_datas:
+ operation = DBDelete(id=_action.db_time,
+ what='function',
+ objectId=_function.db_functionId,
+ parentObjId=_function.db_moduleId,
+ parentObjType='module')
+ operations.append(operation)
+
+ action = DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations)
+ return action
+
+def translateDeleteAnnotationAction(_action):
+ operations = []
+ for _annotation in _action.db_datas:
+ operation = DBDelete(id=_action.db_time,
+ what='annotation',
+ objectId=_annotation.db_key)
+ operations.append(operation)
+
+ action = DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations)
+ return action
+
+def translateDeleteModulePortAction(_action):
+ operations = []
+ for _portSpec in _action.db_datas:
+ operation = DBDelete(id=_action.db_time,
+ what='portSpec',
+ objectId=(_portSpec.db_portName,
+ _portSpec.db_portType),
+ parentObjId=_portSpec.db_moduleId,
+ parentObjType='module')
+ operations.append(operation)
+
+ action = DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations)
+ return action
+
+def translateMoveModuleAction(_action):
+ operations = []
+ for _location in _action.db_datas:
+ location = DBLocation(id=_location.db_id,
+ x=_location.db_dx,
+ y=_location.db_dy)
+ location.relative = True
+
+ operation = DBChange(id=_action.db_time,
+ what='location',
+ oldObjId=_location.db_id,
+ parentObjId=_location.db_id,
+ parentObjType='module',
+ data=location)
+ operations.append(operation)
+
+ action = DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations)
+ return action
+
+
+### UPDATE IDS ###
+
+def convertIds(vistrail):
+ actions = vistrail.db_get_actions()
+ actions.sort(key=lambda x: x.db_id)
+ objectDict = {}
+# refDict = {'objectDict': objectDict}
+
+ graph = Graph()
+ for action in actions:
+ graph.add_vertex(action.db_id)
+ graph.add_edge(action.db_prevId, action.db_id)
+
+ def convertAction(actionId):
+ if actionId == 0:
+ return
+
+ allOps = []
+ action = vistrail.db_get_action(actionId)
+# objectDict = refDict['objectDict']
+# if action.actionType == 'delete' or action.actionType == 'change':
+# action.objectDict = copy.deepcopy(objectDict)
+# else:
+# action.objectDict = objectDict
+ for operation in action.db_get_operations():
+ allOps.extend(convertOperation(vistrail,
+ objectDict,
+ operation.vtType,
+ operation))
+ action.db_operations = allOps
+
+ def removeObjects(actionId):
+ if actionId == 0:
+ return
+# print "removeObjects(%s)" % actionId
+ action = vistrail.db_get_action(actionId)
+
+ # need to reverse ops here
+ reverseOps = action.db_get_operations()
+ reverseOps.reverse()
+ for operation in reverseOps:
+ parentList = getTypeIdList(operation)
+ removeObject(operation.db_what,
+ operation.db_oldId,
+ objectDict,
+ parentList[:-1])
+ reverseOps.reverse()
+
+
+ graph.dfs(enter_vertex=convertAction,
+ leave_vertex=removeObjects)
+
+def getTypeIdList(operation):
+ if operation.db_what in ('module', 'connection'):
+ return [(operation.db_what, operation.db_oldId)]
+ elif operation.db_what in \
+ ('function', 'portSpec', 'location', 'annotation'):
+ return [('module', operation.db_oldParentId),
+ (operation.db_what, operation.db_oldId)]
+ elif operation.db_what in ('port'):
+ return [('connection', operation.db_oldParentId),
+ (operation.db_what, operation.db_oldId)]
+ elif operation.db_what in ('parameter'):
+ return [('module', operation.db_moduleId),
+ ('function', operation.db_oldParentId),
+ ('parameter', operation.db_oldId)]
+ else:
+ print "unknown type: '%s'" % operation.db_what
+ return [(operation.db_what, operation.db_oldId)]
+
+def getOldId(object):
+ if object.vtType == 'annotation':
+ return object.db_key
+ elif object.vtType == 'port':
+ return object.db_type
+ elif object.vtType == 'portSpec':
+ return (object.db_name, object.db_type)
+ else:
+ return object.getPrimaryKey()
+
+def getChildren(object):
+ childList = []
+ if object.vtType == 'module':
+ childList = object.db_get_functions() + \
+ object.db_get_portSpecs() + \
+ object.db_get_annotations()
+ childList.append(object.db_location)
+ object.db_functions = []
+ object.db_portSpecs = []
+ object.db_annotations = {}
+ object.db_location = None
+ elif object.vtType == 'connection':
+ childList = object.db_get_ports()
+ object.db_ports = []
+ elif object.vtType == 'function':
+ childList = object.db_get_parameters()
+ object.db_parameters = []
+ return childList
+
+def captureObject(object, objectDict, newId, parentList):
+
+# print "capturing %s" % object
+ currentDict = objectDict
+ for key in parentList:
+ (objType, objId) = key
+# (currentId, newDict, _) = currentDict[(objType, objId)]
+# currentDict = newDict
+ (objList, curIdx) = currentDict[(objType, objId)]
+ currentDict = objList[curIdx][1]
+ oldId = getOldId(object)
+# print "capture: %s %s" % (object.vtType, oldId)
+# currentDict[(object.vtType, oldId)] = (newId, {}, object)
+ if not currentDict.has_key((object.vtType, oldId)):
+ currentDict[(object.vtType, oldId)] = ([], -1)
+ (curList, curIdx) = currentDict[(object.vtType, oldId)]
+ curList.append((newId, {}, object, curIdx))
+ currentDict[(object.vtType, oldId)] = (curList, len(curList) - 1)
+
+def captureDelete(objType, objId, objectDict, parentList):
+ currentDict = objectDict
+ for (aType, aId) in parentList:
+# (currentId, newDict, _) = currentDict[(objType, objId)]
+# currentDict = newDict
+ (objList, curIdx) = currentDict[(aType, aId)]
+ currentDict = objList[curIdx][1]
+
+# print "captureDelete: %s %s" % (objType, objId)
+ if not currentDict.has_key((objType, objId)):
+ raise Exception("invalid delete")
+ (curList, curIdx) = currentDict[(objType, objId)]
+ curList.append((-1, {}, None, curIdx))
+ currentDict[(objType, objId)] = (curList, len(curList) - 1)
+
+def removeObject(oldObjType, oldId, objectDict, parentList):
+# print '%s %s' % (oldObjType, oldId)
+# print objectDict
+# print parentList
+
+ try:
+ currentDict = objectDict
+ for key in parentList:
+ (objType, objId) = key
+# (currentId, newDict, _) = currentDict[(objType, objId)]
+# currentDict = newDict
+ (objList, objIdx) = currentDict[(objType, objId)]
+ currentDict = objList[objIdx][1]
+# print "remove: %s %s" % (oldObjType, oldId)
+ (curList, curIdx) = currentDict[(oldObjType, oldId)]
+# print "ok"
+ newIdx = curList[curIdx][3]
+# del curList[curIdx]
+ currentDict[(oldObjType, oldId)] = (curList, newIdx)
+ except KeyError:
+ print "cannot remove (%s, %s)" % (oldObjType, oldId)
+ print parentList
+ print objList
+ print "index: %s" % objIdx
+
+def findNewId(typeIdList, objectDict):
+ try:
+ currentDict = objectDict
+ for key in typeIdList:
+# (currentId, currentDict, currentObj) = currentDict[key]
+ (objList, curIdx) = currentDict[key]
+ if curIdx == -1:
+ return (None, None)
+ (currentId, currentDict, currentObj, _) = objList[curIdx]
+ if currentId == -1:
+ return (None, None)
+ return (currentId, currentObj)
+ except KeyError:
+ pass
+ return (None, None)
+
+def getChildList(typeIdList, objectDict):
+ try:
+ currentDict = objectDict
+ for (objType, objOldId) in typeIdList:
+# (currentId, currentDict, _) = currentDict[(objType, objOldId)]
+ (objList, curIdx) = currentDict[(objType, objOldId)]
+ if curIdx == -1:
+ return {}
+ currentDict = objList[curIdx][1]
+ return currentDict
+ except KeyError:
+ pass
+ return {}
+
+def createOperation(actionType, objId, objType, parentId, parentType,
+ object=None):
+ if actionType == 'add':
+ operation = DBAdd(what=objType,
+ objectId=objId,
+ parentObjId=parentId,
+ parentObjType=parentType,
+ data=object)
+
+ elif actionType == 'change':
+ operation = DBChange(what=objType,
+ oldObjId=objId,
+ parentObjId=parentId,
+ parentObjType=parentType,
+ data=object)
+ elif actionType == 'delete':
+ operation = DBDelete(what=objType,
+ objectId=objId,
+ parentObjId=parentId,
+ parentObjType=parentType)
+ else:
+ msg = "Cannot find actionType='%s'" % actionType
+ raise Exception(msg)
+
+ return operation
+
+def convertChangeToAdd(operation):
+ return DBAdd(what=operation.db_what,
+ objectId=operation.db_newObjId,
+ parentObjId=operation.db_parentObjId,
+ parentObjType=operation.db_parentObjType,
+ data=operation.db_data)
+
+def convertOperation(vistrail, objectDict, actionType, operation):
+ newOps = []
+ if actionType == 'add':
+ object = operation.db_data
+ if object.vtType == 'parameter' and object.db_pos == -1:
+ return newOps
+ operation.db_oldId = operation.db_objectId
+ if operation.db_what == 'annotation':
+ operation.db_oldId = object.db_key
+ elif operation.db_what == 'port':
+ operation.db_oldId = object.db_type
+ operation.db_oldParentId = operation.db_parentObjId
+ parentList = getTypeIdList(operation)
+
+
+ newId = vistrail.idScope.getNewId(object.vtType)
+ captureObject(object, objectDict, newId, parentList[:-1])
+ operation.db_objectId = newId
+ oldId = object.getPrimaryKey()
+ if object.vtType == 'annotation':
+ oldId = object.db_key
+ elif object.vtType == 'port':
+ oldId = object.db_type
+ if hasattr(object, 'db_id'):
+ object.db_id = newId
+
+ # set parent ids correctly...
+ operation.db_id = vistrail.idScope.getNewId('operation')
+ if operation.db_parentObjId is not None:
+ oldParentObjId = operation.db_parentObjId
+ operation.db_parentObjId = findNewId(parentList[:-1], objectDict)[0]
+ if object.vtType == 'port':
+ object.db_moduleId = \
+ findNewId([('module', object.db_moduleId)], objectDict)[0]
+# if object.vtType == 'connection':
+# for port in object.db_ports.itervalues():
+# port.db_moduleId = \
+# findNewId([('module', port.db_moduleId)], objectDict)[0]
+
+ newOps.append(operation)
+
+ # set child operations
+ children = getChildren(object)
+ for child in children:
+ # hack to get around fact that location ids are wrong
+ if child.vtType == 'location':
+ child.db_id = oldId
+ newOp = createOperation('add',
+ child.getPrimaryKey(),
+ child.vtType,
+ oldId,
+ object.vtType,
+ child)
+
+ # hack to get moduleId at parameter level
+ if child.vtType == 'parameter':
+ newOp.db_moduleId = oldParentObjId
+ newOps.extend(convertOperation(vistrail,
+ objectDict,
+ 'add',
+ newOp))
+ newOp.db_parentObjId = newId
+ elif actionType == 'change':
+ object = operation.db_data
+ if object.vtType == 'parameter' and object.db_pos == -1:
+ return newOps
+ operation.db_oldId = operation.db_oldObjId
+ if operation.db_what == 'annotation':
+ operation.db_oldId = object.db_key
+ elif operation.db_what == 'port':
+ operation.db_oldId = object.db_type
+ operation.db_oldParentId = operation.db_parentObjId
+ parentList = getTypeIdList(operation)
+
+ # need to get changed id as new id if have one
+ (foundId, foundObj) = findNewId(parentList, objectDict)
+ if foundId is not None:
+ if foundObj.vtType == 'function' and \
+ foundObj.db_pos == object.db_pos and \
+ foundObj.db_name == object.db_name:
+ # don't create new function, convert parameter
+ for parameter in object.db_parameters:
+ newOp = createOperation('change',
+ parameter.getPrimaryKey(),
+ parameter.vtType,
+ object.getPrimaryKey(),
+ object.vtType,
+ parameter)
+ newOp.db_moduleId = operation.db_parentObjId
+ newOps.extend(convertOperation(vistrail,
+ objectDict,
+ 'change',
+ newOp))
+ newOp.db_parentObjId = foundId
+ return newOps
+ else:
+ if foundObj.vtType == 'location' and object.relative == True:
+ object.db_x += foundObj.db_x
+ object.db_y += foundObj.db_y
+ object.relative = False
+ # get new id for new object
+ newId = vistrail.idScope.getNewId(object.vtType)
+ operation.db_oldObjId = foundId
+ operation.db_newObjId = newId
+ else:
+ # get new id for new object
+ newId = vistrail.idScope.getNewId(object.vtType)
+ operation.db_oldObjId = -1
+ operation.db_newObjId = newId
+ anOldId = operation.db_oldId
+ anOldParentId = operation.db_parentObjId
+ if hasattr(operation,'db_moduleId'):
+ aModuleId = operation.db_moduleId
+ else:
+ aModuleId = None
+ operation = convertChangeToAdd(operation)
+ operation.db_oldId = anOldId
+ operation.db_oldParentId = operation.db_parentObjId
+ operation.db_moduleId = aModuleId
+
+ # need to do child deletes first
+ childDict = getChildList(parentList, objectDict)
+ for k,v in childDict.items():
+ (objType, objId) = k
+# (newId, newDict) = v
+# print 'creating delete for %s' % objType
+ newOp = createOperation('delete',
+ objId,
+ objType,
+ object.getPrimaryKey(),
+ object.vtType)
+ # hack to get moduleId at parameter level
+ if objType == 'parameter':
+ newOp.db_moduleId = operation.db_parentObjId
+ newOps.extend(convertOperation(vistrail,
+ objectDict,
+ 'delete',
+ newOp))
+ newOp.db_parentObjId = newId
+ # don't reverse -- ordering is correct
+ # newOps.reverse()
+
+ # set new object id
+ captureObject(object, objectDict, newId, parentList[:-1])
+# operation.db_objectId = newId
+ oldId = object.getPrimaryKey()
+ if object.vtType == 'annotation':
+ oldId = object.db_key
+ elif object.vtType == 'port':
+ oldId = object.db_type
+ if hasattr(object, 'db_id'):
+ object.db_id = newId
+
+ # set parent ids correctly...
+ operation.db_id = vistrail.idScope.getNewId('operation')
+ if operation.db_parentObjId is not None:
+ oldParentObjId = operation.db_parentObjId
+ operation.db_parentObjId = findNewId(parentList[:-1], objectDict)[0]
+ if object.vtType == 'port':
+ object.db_moduleId = \
+ findNewId([('module', object.db_moduleId)], objectDict)[0]
+# if object.vtType == 'connection':
+# for port in object.db_ports.itervalues():
+# port.db_moduleId = \
+# findNewId([('module', port.db_moduleId)], objectDict)[0]
+ newOps.append(operation)
+
+ # set child operations
+ children = getChildren(operation.db_data)
+ for child in children:
+# print 'creating add for %s' % child.vtType
+ newOp = createOperation('add',
+ child.getPrimaryKey(),
+ child.vtType,
+ oldId,
+ object.vtType,
+ child)
+ # hack to get moduleId at parameter level
+ if child.vtType == 'parameter':
+ newOp.db_moduleId = oldParentObjId
+ newOps.extend(convertOperation(vistrail,
+ objectDict,
+ 'add',
+ newOp))
+ newOp.db_parentObjId = newId
+ elif actionType == 'delete':
+ operation.db_oldId = operation.db_objectId
+# if operation.db_what == 'annotation':
+# operation.db_oldId = object.db_key
+# elif operation.db_what == 'port':
+# operation.db_oldId = object.db_type
+ operation.db_oldParentId = operation.db_parentObjId
+ parentList = getTypeIdList(operation)
+
+ # get new id for delete operation
+ (newId, _) = findNewId(parentList, objectDict)
+# print 'found new id: %s' % newId
+ if newId is None:
+ msg = "Cannot find id: %s" % parentList
+ print msg
+# raise Exception(msg)
+ return []
+
+ # need to do child deletes first
+ childDict = getChildList(parentList, objectDict)
+ for k,v in childDict.items():
+ (objType, objId) = k
+# (newId, newDict) = v
+ newOp = createOperation('delete',
+ objId,
+ objType,
+ operation.db_objectId,
+ operation.db_what)
+ # hack to get moduleId at parameter level
+ if objType == 'parameter':
+ newOp.db_moduleId = operation.db_parentObjId
+ newOps.extend(convertOperation(vistrail,
+ objectDict,
+ 'delete',
+ newOp))
+ newOp.db_parentObjId = newId
+# newOps.reverse()
+
+ captureDelete(operation.db_what, operation.db_objectId, objectDict,
+ parentList[:-1])
+ operation.db_objectId = newId
+
+ # set parent ids correctly
+ operation.db_id = vistrail.idScope.getNewId('operation')
+ if operation.db_parentObjId is not None:
+ operation.db_parentObjId = findNewId(parentList[:-1], objectDict)[0]
+ newOps.append(operation)
+
+ return newOps
diff --git a/vistrails/db/versions/v0_6_0/__init__.py b/vistrails/db/versions/v0_6_0/__init__.py
new file mode 100644
index 0000000..c015978
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.6.0'
diff --git a/vistrails/db/versions/v0_6_0/domain/__init__.py b/vistrails/db/versions/v0_6_0/domain/__init__.py
new file mode 100644
index 0000000..f9f4892
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/domain/__init__.py
@@ -0,0 +1,38 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from workflow import DBWorkflow
+from vistrail import DBVistrail
diff --git a/vistrails/db/versions/v0_6_0/domain/auto_gen.py b/vistrails/db/versions/v0_6_0/domain/auto_gen.py
new file mode 100644
index 0000000..a95442a
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/domain/auto_gen.py
@@ -0,0 +1,3284 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, spec=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_type = type
+ self.__db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBPortSpec()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_type = self.db_type
+ cp.db_spec = self.db_spec
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_spec(self):
+ return self.__db_spec
+ def __set_db_spec(self, spec):
+ self.__db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self.__db_spec = spec
+ def db_change_spec(self, spec):
+ self.__db_spec = spec
+ def db_delete_spec(self, spec):
+ self.__db_spec = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, package=None, version=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self.__db_id = id
+ self.__db_cache = cache
+ self.__db_name = name
+ self.__db_package = package
+ self.__db_version = version
+ self.__db_location = location
+ if functions is None:
+ self.__db_functions = []
+ else:
+ self.__db_functions = functions
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self.__db_annotations = {}
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations.itervalues():
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self.__db_portSpecs = {}
+ else:
+ self.__db_portSpecs = portSpecs
+ for v in self.__db_portSpecs.itervalues():
+ self.db_portSpecs_name_index[v.db_name] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBModule()
+ cp.db_id = self.db_id
+ cp.db_cache = self.db_cache
+ cp.db_name = self.db_name
+ cp.db_package = self.db_package
+ cp.db_version = self.db_version
+ cp.db_location = self.db_location
+ if self.db_functions is None:
+ cp.db_functions = None
+ else:
+ cp.db_functions = [copy.copy(v) for v in self.db_functions]
+ if self.db_annotations is None:
+ cp.db_annotations = None
+ else:
+ cp.db_annotations = dict([(k,copy.copy(v)) for (k,v) in self.db_annotations.iteritems()])
+ for v in cp.__db_annotations.itervalues():
+ cp.db_annotations_key_index[v.db_key] = v
+ if self.db_portSpecs is None:
+ cp.db_portSpecs = None
+ else:
+ cp.db_portSpecs = dict([(k,copy.copy(v)) for (k,v) in self.db_portSpecs.iteritems()])
+ for v in cp.__db_portSpecs.itervalues():
+ cp.db_portSpecs_name_index[v.db_name] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_location is not None:
+ children.extend(self.db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_portSpecs.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_location is not None and self.db_location.has_changes():
+ return True
+ for child in self.db_functions:
+ if child.has_changes():
+ return True
+ for child in self.db_annotations.itervalues():
+ if child.has_changes():
+ return True
+ for child in self.db_portSpecs.itervalues():
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_cache(self):
+ return self.__db_cache
+ def __set_db_cache(self, cache):
+ self.__db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self.__db_cache = cache
+ def db_change_cache(self, cache):
+ self.__db_cache = cache
+ def db_delete_cache(self, cache):
+ self.__db_cache = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_package(self):
+ return self.__db_package
+ def __set_db_package(self, package):
+ self.__db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self.__db_package = package
+ def db_change_package(self, package):
+ self.__db_package = package
+ def db_delete_package(self, package):
+ self.__db_package = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_location(self):
+ return self.__db_location
+ def __set_db_location(self, location):
+ self.__db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self.__db_location = location
+ def db_change_location(self, location):
+ self.__db_location = location
+ def db_delete_location(self, location):
+ self.__db_location = None
+
+ def __get_db_functions(self):
+ return self.__db_functions
+ def __set_db_functions(self, functions):
+ self.__db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self.__db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self.__db_functions.append(function)
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ self.__db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self.__db_functions.append(function)
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ del self.__db_functions[i]
+ break
+ def db_get_function(self, key):
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == key:
+ return self.__db_functions[i]
+ return None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations.values()
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ del self.__db_annotations[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ if self.__db_annotations.has_key(key):
+ return self.__db_annotations[key]
+ return None
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return self.db_annotations_key_index.has_key(key)
+
+ def __get_db_portSpecs(self):
+ return self.__db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self.__db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self.__db_portSpecs.values()
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self.__db_portSpecs[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[portSpec.db_name] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ self.__db_portSpecs[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[portSpec.db_name] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ del self.__db_portSpecs[portSpec.db_id]
+ del self.db_portSpecs_name_index[portSpec.db_name]
+ def db_get_portSpec(self, key):
+ if self.__db_portSpecs.has_key(key):
+ return self.__db_portSpecs[key]
+ return None
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return self.db_portSpecs_name_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBTag()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('action', obj.db_id)):
+ obj.db_id = id_remap[('action', obj.db_id)]
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, sig=None):
+ self.__db_id = id
+ self.__db_type = type
+ self.__db_moduleId = moduleId
+ self.__db_moduleName = moduleName
+ self.__db_sig = sig
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBPort()
+ cp.db_id = self.db_id
+ cp.db_type = self.db_type
+ cp.db_moduleId = self.db_moduleId
+ cp.db_moduleName = self.db_moduleName
+ cp.db_sig = self.db_sig
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('module', obj.db_moduleId)):
+ obj.db_moduleId = id_remap[('module', obj.db_moduleId)]
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self.__db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self.__db_moduleName = None
+
+ def __get_db_sig(self):
+ return self.__db_sig
+ def __set_db_sig(self, sig):
+ self.__db_sig = sig
+ self.is_dirty = True
+ db_sig = property(__get_db_sig, __set_db_sig)
+ def db_add_sig(self, sig):
+ self.__db_sig = sig
+ def db_change_sig(self, sig):
+ self.__db_sig = sig
+ def db_delete_sig(self, sig):
+ self.__db_sig = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, workflow_execs=None, machines=None):
+ self.__db_id = id
+ if workflow_execs is None:
+ self.__db_workflow_execs = {}
+ else:
+ self.__db_workflow_execs = workflow_execs
+ if machines is None:
+ self.__db_machines = {}
+ else:
+ self.__db_machines = machines
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBLog()
+ cp.db_id = self.db_id
+ if self.db_workflow_execs is None:
+ cp.db_workflow_execs = None
+ else:
+ cp.db_workflow_execs = dict([(k,copy.copy(v)) for (k,v) in self.db_workflow_execs.iteritems()])
+ if self.db_machines is None:
+ cp.db_machines = None
+ else:
+ cp.db_machines = dict([(k,copy.copy(v)) for (k,v) in self.db_machines.iteritems()])
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_workflow_execs.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self.db_machines.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_workflow_execs.itervalues():
+ if child.has_changes():
+ return True
+ for child in self.db_machines.itervalues():
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_workflow_execs(self):
+ return self.__db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self.__db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self.__db_workflow_execs.values()
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self.__db_workflow_execs[workflow_exec.db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self.__db_workflow_execs[workflow_exec.db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ del self.__db_workflow_execs[workflow_exec.db_id]
+ def db_get_workflow_exec(self, key):
+ if self.__db_workflow_execs.has_key(key):
+ return self.__db_workflow_execs[key]
+ return None
+
+ def __get_db_machines(self):
+ return self.__db_machines
+ def __set_db_machines(self, machines):
+ self.__db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self.__db_machines.values()
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self.__db_machines[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ self.__db_machines[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ del self.__db_machines[machine.db_id]
+ def db_get_machine(self, key):
+ if self.__db_machines.has_key(key):
+ return self.__db_machines[key]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None, module_execs=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_os = os
+ self.__db_architecture = architecture
+ self.__db_processor = processor
+ self.__db_ram = ram
+ if module_execs is None:
+ self.__db_module_execs = []
+ else:
+ self.__db_module_execs = module_execs
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBMachine()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_os = self.db_os
+ cp.db_architecture = self.db_architecture
+ cp.db_processor = self.db_processor
+ cp.db_ram = self.db_ram
+ if self.db_module_execs is None:
+ cp.db_module_execs = None
+ else:
+ cp.db_module_execs = [copy.copy(v) for v in self.db_module_execs]
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_module_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_os(self):
+ return self.__db_os
+ def __set_db_os(self, os):
+ self.__db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self.__db_os = os
+ def db_change_os(self, os):
+ self.__db_os = os
+ def db_delete_os(self, os):
+ self.__db_os = None
+
+ def __get_db_architecture(self):
+ return self.__db_architecture
+ def __set_db_architecture(self, architecture):
+ self.__db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self.__db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self.__db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self.__db_architecture = None
+
+ def __get_db_processor(self):
+ return self.__db_processor
+ def __set_db_processor(self, processor):
+ self.__db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self.__db_processor = processor
+ def db_change_processor(self, processor):
+ self.__db_processor = processor
+ def db_delete_processor(self, processor):
+ self.__db_processor = None
+
+ def __get_db_ram(self):
+ return self.__db_ram
+ def __set_db_ram(self, ram):
+ self.__db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self.__db_ram = ram
+ def db_change_ram(self, ram):
+ self.__db_ram = ram
+ def db_delete_ram(self, ram):
+ self.__db_ram = None
+
+ def __get_db_module_execs(self):
+ return self.__db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self.__db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self.__db_module_execs
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self.__db_module_execs.append(module_exec)
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ self.__db_module_execs[i] = module_exec
+ found = True
+ break
+ if not found:
+ self.__db_module_execs.append(module_exec)
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ del self.__db_module_execs[i]
+ break
+ def db_get_module_exec(self, key):
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == key:
+ return self.__db_module_execs[i]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None, data=None):
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_objectId = objectId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.__db_data = data
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBAdd()
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_objectId = self.db_objectId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+ cp.db_data = self.db_data
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_data is not None:
+ children.extend(self.db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_data is not None and self.db_data.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_objectId(self):
+ return self.__db_objectId
+ def __set_db_objectId(self, objectId):
+ self.__db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self.__db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def __get_db_data(self):
+ return self.__db_data
+ def __set_db_data(self, data):
+ self.__db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self.__db_data = data
+ def db_change_data(self, data):
+ self.__db_data = data
+ def db_delete_data(self, data):
+ self.__db_data = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self.__db_id = id
+ self.__db_key = key
+ self.__db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBOther()
+ cp.db_id = self.db_id
+ cp.db_key = self.db_key
+ cp.db_value = self.db_value
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self.__db_id = id
+ self.__db_x = x
+ self.__db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBLocation()
+ cp.db_id = self.db_id
+ cp.db_x = self.db_x
+ cp.db_y = self.db_y
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_x(self):
+ return self.__db_x
+ def __set_db_x(self, x):
+ self.__db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self.__db_x = x
+ def db_change_x(self, x):
+ self.__db_x = x
+ def db_delete_x(self, x):
+ self.__db_x = None
+
+ def __get_db_y(self):
+ return self.__db_y
+ def __set_db_y(self, y):
+ self.__db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self.__db_y = y
+ def db_change_y(self, y):
+ self.__db_y = y
+ def db_delete_y(self, y):
+ self.__db_y = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, id=None, user=None, ip=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, name=None, module_execs=None):
+ self.__db_id = id
+ self.__db_user = user
+ self.__db_ip = ip
+ self.__db_vt_version = vt_version
+ self.__db_ts_start = ts_start
+ self.__db_ts_end = ts_end
+ self.__db_parent_id = parent_id
+ self.__db_parent_type = parent_type
+ self.__db_parent_version = parent_version
+ self.__db_name = name
+ if module_execs is None:
+ self.__db_module_execs = {}
+ else:
+ self.__db_module_execs = module_execs
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBWorkflowExec()
+ cp.db_id = self.db_id
+ cp.db_user = self.db_user
+ cp.db_ip = self.db_ip
+ cp.db_vt_version = self.db_vt_version
+ cp.db_ts_start = self.db_ts_start
+ cp.db_ts_end = self.db_ts_end
+ cp.db_parent_id = self.db_parent_id
+ cp.db_parent_type = self.db_parent_type
+ cp.db_parent_version = self.db_parent_version
+ cp.db_name = self.db_name
+ if self.db_module_execs is None:
+ cp.db_module_execs = None
+ else:
+ cp.db_module_execs = dict([(k,copy.copy(v)) for (k,v) in self.db_module_execs.iteritems()])
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_execs.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_module_execs.itervalues():
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_user(self):
+ return self.__db_user
+ def __set_db_user(self, user):
+ self.__db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self.__db_user = user
+ def db_change_user(self, user):
+ self.__db_user = user
+ def db_delete_user(self, user):
+ self.__db_user = None
+
+ def __get_db_ip(self):
+ return self.__db_ip
+ def __set_db_ip(self, ip):
+ self.__db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self.__db_ip = ip
+ def db_change_ip(self, ip):
+ self.__db_ip = ip
+ def db_delete_ip(self, ip):
+ self.__db_ip = None
+
+ def __get_db_vt_version(self):
+ return self.__db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self.__db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self.__db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self.__db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self.__db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self.__db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self.__db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self.__db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self.__db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self.__db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self.__db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self.__db_parent_version = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_module_execs(self):
+ return self.__db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self.__db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self.__db_module_execs.values()
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self.__db_module_execs[module_exec.db_id] = module_exec
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ self.__db_module_execs[module_exec.db_id] = module_exec
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ del self.__db_module_execs[module_exec.db_id]
+ def db_get_module_exec(self, key):
+ if self.__db_module_execs.has_key(key):
+ return self.__db_module_execs[key]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self.__db_id = id
+ self.__db_pos = pos
+ self.__db_name = name
+ if parameters is None:
+ self.__db_parameters = []
+ else:
+ self.__db_parameters = parameters
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBFunction()
+ cp.db_id = self.db_id
+ cp.db_pos = self.db_pos
+ cp.db_name = self.db_name
+ if self.db_parameters is None:
+ cp.db_parameters = None
+ else:
+ cp.db_parameters = [copy.copy(v) for v in self.db_parameters]
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_pos(self):
+ return self.__db_pos
+ def __set_db_pos(self, pos):
+ self.__db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self.__db_pos = pos
+ def db_change_pos(self, pos):
+ self.__db_pos = pos
+ def db_delete_pos(self, pos):
+ self.__db_pos = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_parameters(self):
+ return self.__db_parameters
+ def __set_db_parameters(self, parameters):
+ self.__db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self.__db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self.__db_parameters.append(parameter)
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == parameter.db_id:
+ self.__db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self.__db_parameters.append(parameter)
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == parameter.db_id:
+ del self.__db_parameters[i]
+ break
+ def db_get_parameter(self, key):
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == key:
+ return self.__db_parameters[i]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, name=None, actions=None, tags=None):
+ self.__db_id = id
+ self.__db_name = name
+ if actions is None:
+ self.__db_actions = {}
+ else:
+ self.__db_actions = actions
+ self.db_tags_name_index = {}
+ if tags is None:
+ self.__db_tags = {}
+ else:
+ self.__db_tags = tags
+ for v in self.__db_tags.itervalues():
+ self.db_tags_name_index[v.db_name] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBAbstraction()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ if self.db_actions is None:
+ cp.db_actions = None
+ else:
+ cp.db_actions = dict([(k,copy.copy(v)) for (k,v) in self.db_actions.iteritems()])
+ if self.db_tags is None:
+ cp.db_tags = None
+ else:
+ cp.db_tags = dict([(k,copy.copy(v)) for (k,v) in self.db_tags.iteritems()])
+ for v in cp.__db_tags.itervalues():
+ cp.db_tags_name_index[v.db_name] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_actions.itervalues():
+ if child.has_changes():
+ return True
+ for child in self.db_tags.itervalues():
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_actions(self):
+ return self.__db_actions
+ def __set_db_actions(self, actions):
+ self.__db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self.__db_actions.values()
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self.__db_actions[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ self.__db_actions[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ del self.__db_actions[action.db_id]
+ def db_get_action(self, key):
+ if self.__db_actions.has_key(key):
+ return self.__db_actions[key]
+ return None
+
+ def __get_db_tags(self):
+ return self.__db_tags
+ def __set_db_tags(self, tags):
+ self.__db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self.__db_tags.values()
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ del self.__db_tags[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ if self.__db_tags.has_key(key):
+ return self.__db_tags[key]
+ return None
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return self.db_tags_name_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, id=None, name=None, modules=None, connections=None, annotations=None, others=None, abstractionRefs=None):
+ self.__db_id = id
+ self.__db_name = name
+ if modules is None:
+ self.__db_modules = {}
+ else:
+ self.__db_modules = modules
+ if connections is None:
+ self.__db_connections = {}
+ else:
+ self.__db_connections = connections
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ if others is None:
+ self.__db_others = []
+ else:
+ self.__db_others = others
+ if abstractionRefs is None:
+ self.__db_abstractionRefs = {}
+ else:
+ self.__db_abstractionRefs = abstractionRefs
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBWorkflow()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ if self.db_modules is None:
+ cp.db_modules = None
+ else:
+ cp.db_modules = dict([(k,copy.copy(v)) for (k,v) in self.db_modules.iteritems()])
+ if self.db_connections is None:
+ cp.db_connections = None
+ else:
+ cp.db_connections = dict([(k,copy.copy(v)) for (k,v) in self.db_connections.iteritems()])
+ if self.db_annotations is None:
+ cp.db_annotations = None
+ else:
+ cp.db_annotations = [copy.copy(v) for v in self.db_annotations]
+ if self.db_others is None:
+ cp.db_others = None
+ else:
+ cp.db_others = [copy.copy(v) for v in self.db_others]
+ if self.db_abstractionRefs is None:
+ cp.db_abstractionRefs = None
+ else:
+ cp.db_abstractionRefs = dict([(k,copy.copy(v)) for (k,v) in self.db_abstractionRefs.iteritems()])
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_modules.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module(child)
+ to_del = []
+ for child in self.db_connections.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_connection(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_other(child)
+ to_del = []
+ for child in self.db_abstractionRefs.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_abstractionRef(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_modules.itervalues():
+ if child.has_changes():
+ return True
+ for child in self.db_connections.itervalues():
+ if child.has_changes():
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ for child in self.db_others:
+ if child.has_changes():
+ return True
+ for child in self.db_abstractionRefs.itervalues():
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_modules(self):
+ return self.__db_modules
+ def __set_db_modules(self, modules):
+ self.__db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self.__db_modules.values()
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self.__db_modules[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ self.__db_modules[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ del self.__db_modules[module.db_id]
+ def db_get_module(self, key):
+ if self.__db_modules.has_key(key):
+ return self.__db_modules[key]
+ return None
+
+ def __get_db_connections(self):
+ return self.__db_connections
+ def __set_db_connections(self, connections):
+ self.__db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self.__db_connections.values()
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self.__db_connections[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ self.__db_connections[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ del self.__db_connections[connection.db_id]
+ def db_get_connection(self, key):
+ if self.__db_connections.has_key(key):
+ return self.__db_connections[key]
+ return None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ del self.__db_annotations[i]
+ break
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+
+ def __get_db_others(self):
+ return self.__db_others
+ def __set_db_others(self, others):
+ self.__db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self.__db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self.__db_others.append(other)
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == other.db_id:
+ self.__db_others[i] = other
+ found = True
+ break
+ if not found:
+ self.__db_others.append(other)
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == other.db_id:
+ del self.__db_others[i]
+ break
+ def db_get_other(self, key):
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == key:
+ return self.__db_others[i]
+ return None
+
+ def __get_db_abstractionRefs(self):
+ return self.__db_abstractionRefs
+ def __set_db_abstractionRefs(self, abstractionRefs):
+ self.__db_abstractionRefs = abstractionRefs
+ self.is_dirty = True
+ db_abstractionRefs = property(__get_db_abstractionRefs, __set_db_abstractionRefs)
+ def db_get_abstractionRefs(self):
+ return self.__db_abstractionRefs.values()
+ def db_add_abstractionRef(self, abstractionRef):
+ self.is_dirty = True
+ self.__db_abstractionRefs[abstractionRef.db_id] = abstractionRef
+ def db_change_abstractionRef(self, abstractionRef):
+ self.is_dirty = True
+ self.__db_abstractionRefs[abstractionRef.db_id] = abstractionRef
+ def db_delete_abstractionRef(self, abstractionRef):
+ self.is_dirty = True
+ del self.__db_abstractionRefs[abstractionRef.db_id]
+ def db_get_abstractionRef(self, key):
+ if self.__db_abstractionRefs.has_key(key):
+ return self.__db_abstractionRefs[key]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAbstractionRef(object):
+
+ vtType = 'abstractionRef'
+
+ def __init__(self, id=None, abstraction_id=None, version=None):
+ self.__db_id = id
+ self.__db_abstraction_id = abstraction_id
+ self.__db_version = version
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBAbstractionRef()
+ cp.db_id = self.db_id
+ cp.db_abstraction_id = self.db_abstraction_id
+ cp.db_version = self.db_version
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_abstraction_id(self):
+ return self.__db_abstraction_id
+ def __set_db_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ self.is_dirty = True
+ db_abstraction_id = property(__get_db_abstraction_id, __set_db_abstraction_id)
+ def db_add_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ def db_change_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ def db_delete_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self.__db_id = id
+ self.__db_key = key
+ self.__db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBAnnotation()
+ cp.db_id = self.db_id
+ cp.db_key = self.db_key
+ cp.db_value = self.db_value
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None, data=None):
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_oldObjId = oldObjId
+ self.__db_newObjId = newObjId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.__db_data = data
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBChange()
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_oldObjId = self.db_oldObjId
+ cp.db_newObjId = self.db_newObjId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+ cp.db_data = self.db_data
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_data is not None:
+ children.extend(self.db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_data is not None and self.db_data.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_oldObjId(self):
+ return self.__db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self.__db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self.__db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self.__db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def __get_db_data(self):
+ return self.__db_data
+ def __set_db_data(self, data):
+ self.__db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self.__db_data = data
+ def db_change_data(self, data):
+ self.__db_data = data
+ def db_delete_data(self, data):
+ self.__db_data = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self.__db_id = id
+ self.__db_pos = pos
+ self.__db_name = name
+ self.__db_type = type
+ self.__db_val = val
+ self.__db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBParameter()
+ cp.db_id = self.db_id
+ cp.db_pos = self.db_pos
+ cp.db_name = self.db_name
+ cp.db_type = self.db_type
+ cp.db_val = self.db_val
+ cp.db_alias = self.db_alias
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_pos(self):
+ return self.__db_pos
+ def __set_db_pos(self, pos):
+ self.__db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self.__db_pos = pos
+ def db_change_pos(self, pos):
+ self.__db_pos = pos
+ def db_delete_pos(self, pos):
+ self.__db_pos = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_val(self):
+ return self.__db_val
+ def __set_db_val(self, val):
+ self.__db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self.__db_val = val
+ def db_change_val(self, val):
+ self.__db_val = val
+ def db_delete_val(self, val):
+ self.__db_val = None
+
+ def __get_db_alias(self):
+ return self.__db_alias
+ def __set_db_alias(self, alias):
+ self.__db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self.__db_alias = alias
+ def db_change_alias(self, alias):
+ self.__db_alias = alias
+ def db_delete_alias(self, alias):
+ self.__db_alias = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self.__db_id = id
+ self.db_ports_type_index = {}
+ if ports is None:
+ self.__db_ports = []
+ else:
+ self.__db_ports = ports
+ for v in self.__db_ports:
+ self.db_ports_type_index[v.db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBConnection()
+ cp.db_id = self.db_id
+ if self.db_ports is None:
+ cp.db_ports = None
+ else:
+ cp.db_ports = [copy.copy(v) for v in self.db_ports]
+ for v in cp.__db_ports:
+ cp.db_ports_type_index[v.db_type] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_ports(self):
+ return self.__db_ports
+ def __set_db_ports(self, ports):
+ self.__db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self.__db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self.__db_ports.append(port)
+ self.db_ports_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == port.db_id:
+ self.__db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self.__db_ports.append(port)
+ self.db_ports_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == port.db_id:
+ del self.__db_ports[i]
+ break
+ del self.db_ports_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == key:
+ return self.__db_ports[i]
+ return None
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return self.db_ports_type_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, id=None, prevId=None, date=None, user=None, annotations=None, operations=None):
+ self.__db_id = id
+ self.__db_prevId = prevId
+ self.__db_date = date
+ self.__db_user = user
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self.__db_annotations = {}
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations.itervalues():
+ self.db_annotations_key_index[v.db_key] = v
+ if operations is None:
+ self.__db_operations = []
+ else:
+ self.__db_operations = operations
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBAction()
+ cp.db_id = self.db_id
+ cp.db_prevId = self.db_prevId
+ cp.db_date = self.db_date
+ cp.db_user = self.db_user
+ if self.db_annotations is None:
+ cp.db_annotations = None
+ else:
+ cp.db_annotations = dict([(k,copy.copy(v)) for (k,v) in self.db_annotations.iteritems()])
+ for v in cp.__db_annotations.itervalues():
+ cp.db_annotations_key_index[v.db_key] = v
+ if self.db_operations is None:
+ cp.db_operations = None
+ else:
+ cp.db_operations = [copy.copy(v) for v in self.db_operations]
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_operations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_annotations.itervalues():
+ if child.has_changes():
+ return True
+ for child in self.db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_prevId(self):
+ return self.__db_prevId
+ def __set_db_prevId(self, prevId):
+ self.__db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self.__db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self.__db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self.__db_prevId = None
+
+ def __get_db_date(self):
+ return self.__db_date
+ def __set_db_date(self, date):
+ self.__db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self.__db_date = date
+ def db_change_date(self, date):
+ self.__db_date = date
+ def db_delete_date(self, date):
+ self.__db_date = None
+
+ def __get_db_user(self):
+ return self.__db_user
+ def __set_db_user(self, user):
+ self.__db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self.__db_user = user
+ def db_change_user(self, user):
+ self.__db_user = user
+ def db_delete_user(self, user):
+ self.__db_user = None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations.values()
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ del self.__db_annotations[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ if self.__db_annotations.has_key(key):
+ return self.__db_annotations[key]
+ return None
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return self.db_annotations_key_index.has_key(key)
+
+ def __get_db_operations(self):
+ return self.__db_operations
+ def __set_db_operations(self, operations):
+ self.__db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self.__db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self.__db_operations.append(operation)
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == operation.db_id:
+ self.__db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self.__db_operations.append(operation)
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == operation.db_id:
+ del self.__db_operations[i]
+ break
+ def db_get_operation(self, key):
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == key:
+ return self.__db_operations[i]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_objectId = objectId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBDelete()
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_objectId = self.db_objectId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_objectId(self):
+ return self.__db_objectId
+ def __set_db_objectId(self, objectId):
+ self.__db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self.__db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, version=None, name=None, dbHost=None, dbPort=None, dbName=None, actions=None, tags=None, abstractions=None):
+ self.__db_id = id
+ self.__db_version = version
+ self.__db_name = name
+ self.__db_dbHost = dbHost
+ self.__db_dbPort = dbPort
+ self.__db_dbName = dbName
+ if actions is None:
+ self.__db_actions = {}
+ else:
+ self.__db_actions = actions
+ self.db_tags_name_index = {}
+ if tags is None:
+ self.__db_tags = {}
+ else:
+ self.__db_tags = tags
+ for v in self.__db_tags.itervalues():
+ self.db_tags_name_index[v.db_name] = v
+ if abstractions is None:
+ self.__db_abstractions = {}
+ else:
+ self.__db_abstractions = abstractions
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBVistrail()
+ cp.db_id = self.db_id
+ cp.db_version = self.db_version
+ cp.db_name = self.db_name
+ cp.db_dbHost = self.db_dbHost
+ cp.db_dbPort = self.db_dbPort
+ cp.db_dbName = self.db_dbName
+ if self.db_actions is None:
+ cp.db_actions = None
+ else:
+ cp.db_actions = dict([(k,copy.copy(v)) for (k,v) in self.db_actions.iteritems()])
+ if self.db_tags is None:
+ cp.db_tags = None
+ else:
+ cp.db_tags = dict([(k,copy.copy(v)) for (k,v) in self.db_tags.iteritems()])
+ for v in cp.__db_tags.itervalues():
+ cp.db_tags_name_index[v.db_name] = v
+ if self.db_abstractions is None:
+ cp.db_abstractions = None
+ else:
+ cp.db_abstractions = dict([(k,copy.copy(v)) for (k,v) in self.db_abstractions.iteritems()])
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self.db_abstractions.itervalues():
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_abstraction(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_actions.itervalues():
+ if child.has_changes():
+ return True
+ for child in self.db_tags.itervalues():
+ if child.has_changes():
+ return True
+ for child in self.db_abstractions.itervalues():
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_dbHost(self):
+ return self.__db_dbHost
+ def __set_db_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ self.is_dirty = True
+ db_dbHost = property(__get_db_dbHost, __set_db_dbHost)
+ def db_add_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ def db_change_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ def db_delete_dbHost(self, dbHost):
+ self.__db_dbHost = None
+
+ def __get_db_dbPort(self):
+ return self.__db_dbPort
+ def __set_db_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ self.is_dirty = True
+ db_dbPort = property(__get_db_dbPort, __set_db_dbPort)
+ def db_add_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ def db_change_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ def db_delete_dbPort(self, dbPort):
+ self.__db_dbPort = None
+
+ def __get_db_dbName(self):
+ return self.__db_dbName
+ def __set_db_dbName(self, dbName):
+ self.__db_dbName = dbName
+ self.is_dirty = True
+ db_dbName = property(__get_db_dbName, __set_db_dbName)
+ def db_add_dbName(self, dbName):
+ self.__db_dbName = dbName
+ def db_change_dbName(self, dbName):
+ self.__db_dbName = dbName
+ def db_delete_dbName(self, dbName):
+ self.__db_dbName = None
+
+ def __get_db_actions(self):
+ return self.__db_actions
+ def __set_db_actions(self, actions):
+ self.__db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self.__db_actions.values()
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self.__db_actions[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ self.__db_actions[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ del self.__db_actions[action.db_id]
+ def db_get_action(self, key):
+ if self.__db_actions.has_key(key):
+ return self.__db_actions[key]
+ return None
+
+ def __get_db_tags(self):
+ return self.__db_tags
+ def __set_db_tags(self, tags):
+ self.__db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self.__db_tags.values()
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ del self.__db_tags[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ if self.__db_tags.has_key(key):
+ return self.__db_tags[key]
+ return None
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return self.db_tags_name_index.has_key(key)
+
+ def __get_db_abstractions(self):
+ return self.__db_abstractions
+ def __set_db_abstractions(self, abstractions):
+ self.__db_abstractions = abstractions
+ self.is_dirty = True
+ db_abstractions = property(__get_db_abstractions, __set_db_abstractions)
+ def db_get_abstractions(self):
+ return self.__db_abstractions.values()
+ def db_add_abstraction(self, abstraction):
+ self.is_dirty = True
+ self.__db_abstractions[abstraction.db_id] = abstraction
+ def db_change_abstraction(self, abstraction):
+ self.is_dirty = True
+ self.__db_abstractions[abstraction.db_id] = abstraction
+ def db_delete_abstraction(self, abstraction):
+ self.is_dirty = True
+ del self.__db_abstractions[abstraction.db_id]
+ def db_get_abstraction(self, key):
+ if self.__db_abstractions.has_key(key):
+ return self.__db_abstractions[key]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, module_id=None, module_name=None, annotations=None):
+ self.__db_id = id
+ self.__db_ts_start = ts_start
+ self.__db_ts_end = ts_end
+ self.__db_module_id = module_id
+ self.__db_module_name = module_name
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBModuleExec()
+ cp.db_id = self.db_id
+ cp.db_ts_start = self.db_ts_start
+ cp.db_ts_end = self.db_ts_end
+ cp.db_module_id = self.db_module_id
+ cp.db_module_name = self.db_module_name
+ if self.db_annotations is None:
+ cp.db_annotations = None
+ else:
+ cp.db_annotations = [copy.copy(v) for v in self.db_annotations]
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def copy_with_new_ids(self, parent, id_scope, id_remap):
+ cp = copy.copy(self)
+ children = cp.db_children(parent, False)
+ for (obj, _, _) in children:
+ new_id = id_scope.getNewId(obj.vtType)
+ id_remap[(obj.vtType, obj.db_id)] = new_id
+ obj.db_id = new_id
+ for (obj, _, _) in children:
+ if id_remap.has_key(('module', obj.db_module_id)):
+ obj.db_module_id = id_remap[('module', obj.db_module_id)]
+ if id_remap.has_key(('vistrail', obj.db_vistrailId)):
+ obj.db_vistrailId = id_remap[('vistrail', obj.db_vistrailId)]
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_ts_start(self):
+ return self.__db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self.__db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self.__db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self.__db_ts_end = None
+
+ def __get_db_module_id(self):
+ return self.__db_module_id
+ def __set_db_module_id(self, module_id):
+ self.__db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self.__db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self.__db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self.__db_module_id = None
+
+ def __get_db_module_name(self):
+ return self.__db_module_name
+ def __set_db_module_name(self, module_name):
+ self.__db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self.__db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self.__db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self.__db_module_name = None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ del self.__db_annotations[i]
+ break
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
diff --git a/vistrails/db/versions/v0_6_0/domain/id_scope.py b/vistrails/db/versions/v0_6_0/domain/id_scope.py
new file mode 100644
index 0000000..3f151ff
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/domain/id_scope.py
@@ -0,0 +1,65 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L):
+ self.ids = {}
+ self.beginId = beginId
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ if self.ids.has_key(objType):
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ else:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ if not self.ids.has_key(objType) or self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v0_6_0/domain/vistrail.py b/vistrails/db/versions/v0_6_0/domain/vistrail.py
new file mode 100644
index 0000000..4ca792e
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/domain/vistrail.py
@@ -0,0 +1,43 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBVistrail as _DBVistrail
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope()
+ self.idScope.setBeginId('action', 1)
diff --git a/vistrails/db/versions/v0_6_0/domain/workflow.py b/vistrails/db/versions/v0_6_0/domain/workflow.py
new file mode 100644
index 0000000..97cb040
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/domain/workflow.py
@@ -0,0 +1,116 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1)
+
+ def __copy__(self):
+ cp = _DBWorkflow.__copy__(self)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.objects = {}
+ for (child, _, _) in cp.db_children():
+ cp.addToIndex(child)
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ def addToIndex(self, object):
+ self.objects[(object.vtType, object.getPrimaryKey())] = object
+
+ def deleteFromIndex(self, object):
+ del self.objects[(object.vtType, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_add_object(self, object, parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_add_%s' % object.vtType
+ objCopy = copy.copy(object)
+ getattr(parentObj, funname)(objCopy)
+ self.addToIndex(objCopy)
+
+ def db_change_object(self, object, parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_change_%s' % object.vtType
+ objCopy = copy.copy(object)
+ getattr(parentObj, funname)(objCopy)
+ self.addToIndex(objCopy)
+
+ def db_delete_object(self, objId, objType,
+ parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_get_%s' % objType
+ try:
+ object = getattr(parentObj, funname)(objId)
+ except AttributeError:
+ attr_name = 'db_%s' % objType
+ object = getattr(parentObj, attr_name)
+ funname = 'db_delete_%s' % objType
+ getattr(parentObj, funname)(object)
+ self.deleteFromIndex(object)
diff --git a/vistrails/db/versions/v0_6_0/persistence/__init__.py b/vistrails/db/versions/v0_6_0/persistence/__init__.py
new file mode 100644
index 0000000..0a10c9d
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/persistence/__init__.py
@@ -0,0 +1,55 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+import xml.io
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ return xml.io.open_from_xml(filename, vtType, self['xml'])
+
+ def save_to_xml(self, obj, filename):
+ xml.io.save_to_xml(obj, filename, self['xml'])
+
+ def serialize(self, obj):
+ return xml.io.serialize(obj, self['xml'])
+
+ def unserialize(self, str, type):
+ return xml.io.unserialize(str, type, self['xml'])
diff --git a/vistrails/db/versions/v0_6_0/persistence/sql/__init__.py b/vistrails/db/versions/v0_6_0/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_6_0/persistence/sql/auto_gen.py b/vistrails/db/versions/v0_6_0/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..dffd921
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/persistence/sql/auto_gen.py
@@ -0,0 +1,4069 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v0_6_0.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(22)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[4], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[5], 'long', 'int')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ spec=spec,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_vistrailId = vistrailId
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(22)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'type', 'spec', 'id']
+ table = 'port_spec'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(22)')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[3], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ portSpec = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ spec=spec)
+ portSpec.is_dirty = False
+ list.append(portSpec)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'port_spec'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(22)')
+ if obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'cache', 'name', 'package', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[3], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[5], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ parent = self.convertFromDB(row[7], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ package=package,
+ version=version,
+ id=id)
+ module.db_parentType = parentType
+ module.db_vistrailId = vistrailId
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'package', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations.itervalues():
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs.itervalues():
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['cache', 'name', 'package', 'version', 'id']
+ table = 'module'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ cache = self.convertFromDB(row[0], 'int', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[2], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('location').fromSQL(db, None, foreignKey, globalProps)
+ if len(res) > 0:
+ location = res[0]
+ else:
+ location = None
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('function').fromSQL(db, None, foreignKey, globalProps)
+ functions = res
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ annotations = {}
+ for obj in res:
+ annotations[obj.db_id] = obj
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('portSpec').fromSQL(db, None, foreignKey, globalProps)
+ portSpecs = {}
+ for obj in res:
+ portSpecs[obj.db_id] = obj
+
+ module = DBModule(id=id,
+ cache=cache,
+ name=name,
+ package=package,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ module.is_dirty = False
+ list.append(module)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'module'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ child = obj.db_location
+ if child is not None:
+ self.getDao('location').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_functions:
+ self.getDao('function').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_annotations.itervalues():
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_portSpecs.itervalues():
+ self.getDao('portSpec').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[3], 'long', 'int')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_parentType = parentType
+ tag.db_vistrailId = vistrailId
+ tag.db_parent = parent
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_tag(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'tag'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'id']
+ table = 'tag'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[1], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ tag = DBTag(id=id,
+ name=name)
+ tag.is_dirty = False
+ list.append(tag)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'tag'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'sig', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ sig = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[5], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ parent = self.convertFromDB(row[7], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ sig=sig,
+ id=id)
+ port.db_parentType = parentType
+ port.db_vistrailId = vistrailId
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'sig', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_sig') and obj.db_sig is not None:
+ columnMap['sig'] = \
+ self.convertToDB(obj.db_sig, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['type', 'moduleId', 'moduleName', 'sig', 'id']
+ table = 'port'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ type = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[1], 'long', 'int')
+ moduleName = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ sig = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ port = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ sig=sig)
+ port.is_dirty = False
+ list.append(port)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'port'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if obj.db_sig is not None:
+ columnMap['sig'] = \
+ self.convertToDB(obj.db_sig, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'vt_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ vistrailId = self.convertFromDB(row[1], 'long', 'int')
+
+ log = DBLog(id=id)
+ log.db_vistrailId = vistrailId
+ log.is_dirty = False
+ res[('log', id)] = log
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'vt_id']
+ table = 'log_tbl'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_workflow_execs.itervalues():
+ child.db_log = obj.db_id
+ for child in obj.db_machines.itervalues():
+ child.db_log = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['id']
+ table = 'log_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ foreignKey = {'log_id': keyStr}
+ res = self.getDao('workflow_exec').fromSQL(db, None, foreignKey, globalProps)
+ workflow_execs = {}
+ for obj in res:
+ workflow_execs[obj.db_id] = obj
+
+ foreignKey = {'log_id': keyStr}
+ res = self.getDao('machine').fromSQL(db, None, foreignKey, globalProps)
+ machines = {}
+ for obj in res:
+ machines[obj.db_id] = obj
+
+ log = DBLog(id=id,
+ workflow_execs=workflow_execs,
+ machines=machines)
+ log.is_dirty = False
+ list.append(log)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'log_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ foreignKey = {'log_id': keyStr}
+ for child in obj.db_workflow_execs.itervalues():
+ self.getDao('workflow_exec').toSQL(db, child, foreignKey, globalProps)
+
+ foreignKey = {'log_id': keyStr}
+ for child in obj.db_machines.itervalues():
+ self.getDao('machine').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'module_exec_id']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ module_execs = self.convertFromDB(row[8], 'long', 'int')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'module_exec_id']
+ table = 'machine'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_module_exec') and obj.db_module_exec is not None:
+ columnMap['module_exec_id'] = \
+ self.convertToDB(obj.db_module_execs, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_module_execs:
+ child.db_machine_id = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'os', 'architecture', 'processor', 'ram', 'id']
+ table = 'machine'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[4], 'int', 'int')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ foreignKey = {'machine_id': keyStr}
+ res = self.getDao('module_exec').fromSQL(db, None, foreignKey, globalProps)
+ module_execs = res
+
+ machine = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ module_execs=module_execs)
+ machine.is_dirty = False
+ list.append(machine)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'machine'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ foreignKey = {'machine_id': keyStr}
+ for child in obj.db_module_execs:
+ self.getDao('module_exec').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_vistrailId = vistrailId
+ add.is_dirty = False
+ res[('add', id)] = add
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'add_tbl'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['what', 'object_id', 'par_obj_id', 'par_obj_type', 'id']
+ table = 'add_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ what = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[1], 'long', 'int')
+ parentObjId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjType = self.convertFromDB(row[3], 'str', 'char(16)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ data = None
+ if what == 'module':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('module').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'location':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('location').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'annotation':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'function':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('function').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'connection':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('connection').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'port':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('port').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'parameter':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('parameter').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'portSpec':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('portSpec').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'abstractionRef':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('abstractionRef').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'other':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('other').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+
+ add = DBAdd(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ add.is_dirty = False
+ list.append(add)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'add_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ child = obj.db_data
+ if child.vtType == 'module':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('module').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'location':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('location').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'annotation':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'function':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('function').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'connection':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('connection').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'port':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('port').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'parameter':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('parameter').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'portSpec':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('portSpec').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'abstractionRef':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('abstractionRef').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'other':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('other').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'okey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_vistrailId = vistrailId
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['okey', 'value', 'id']
+ table = 'other'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ key = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ other = DBOther(id=id,
+ key=key,
+ value=value)
+ other.is_dirty = False
+ list.append(other)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'other'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'x', 'y', 'parent_type', 'vt_id', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_vistrailId = vistrailId
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'vt_id', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['x', 'y', 'id']
+ table = 'location'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ x = self.convertFromDB(row[0], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ location = DBLocation(id=id,
+ x=x,
+ y=y)
+ location.is_dirty = False
+ list.append(location)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'location'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'log_id', 'vt_id']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ vt_version = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[4], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[5], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[6], 'long', 'int')
+ parent_type = self.convertFromDB(row[7], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[8], 'long', 'int')
+ name = self.convertFromDB(row[9], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[10], 'long', 'int')
+ vistrailId = self.convertFromDB(row[11], 'long', 'int')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_vistrailId = vistrailId
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'log_id', 'vt_id']
+ table = 'workflow_exec'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_module_execs.itervalues():
+ child.db_workflow_exec = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'id']
+ table = 'workflow_exec'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ user = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vt_version = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[3], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[4], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[5], 'long', 'int')
+ parent_type = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[7], 'long', 'int')
+ name = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[9], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ foreignKey = {'wf_exec_id': keyStr}
+ res = self.getDao('module_exec').fromSQL(db, None, foreignKey, globalProps)
+ module_execs = {}
+ for obj in res:
+ module_execs[obj.db_id] = obj
+
+ workflow_exec = DBWorkflowExec(id=id,
+ user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ module_execs=module_execs)
+ workflow_exec.is_dirty = False
+ list.append(workflow_exec)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'workflow_exec'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ foreignKey = {'wf_exec_id': keyStr}
+ for child in obj.db_module_execs.itervalues():
+ self.getDao('module_exec').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'pos', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_vistrailId = vistrailId
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['pos', 'name', 'id']
+ table = 'function'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ pos = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('function','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('parameter').fromSQL(db, None, foreignKey, globalProps)
+ parameters = res
+
+ function = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ function.is_dirty = False
+ list.append(function)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'function'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('function','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_parameters:
+ self.getDao('parameter').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'name', 'vt_id']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[2], 'long', 'int')
+
+ abstraction = DBAbstraction(name=name,
+ id=id)
+ abstraction.db_vistrail = vistrail
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_abstraction(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'vt_id']
+ table = 'abstraction'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_actions.itervalues():
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags.itervalues():
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'id']
+ table = 'abstraction'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[1], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('abstraction','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('action').fromSQL(db, None, foreignKey, globalProps)
+ actions = {}
+ for obj in res:
+ actions[obj.db_id] = obj
+
+ discStr = self.convertToDB('abstraction','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('tag').fromSQL(db, None, foreignKey, globalProps)
+ tags = {}
+ for obj in res:
+ tags[obj.db_id] = obj
+
+ abstraction = DBAbstraction(id=id,
+ name=name,
+ actions=actions,
+ tags=tags)
+ abstraction.is_dirty = False
+ list.append(abstraction)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'abstraction'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('abstraction','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_actions.itervalues():
+ self.getDao('action').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('abstraction','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_tags.itervalues():
+ self.getDao('tag').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'name', 'vt_id']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrailId = self.convertFromDB(row[2], 'long', 'int')
+
+ workflow = DBWorkflow(name=name,
+ id=id)
+ workflow.db_vistrailId = vistrailId
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'vt_id']
+ table = 'workflow'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_modules.itervalues():
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_connections.itervalues():
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_abstractionRefs.itervalues():
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'id']
+ table = 'workflow'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[1], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('module').fromSQL(db, None, foreignKey, globalProps)
+ modules = {}
+ for obj in res:
+ modules[obj.db_id] = obj
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('connection').fromSQL(db, None, foreignKey, globalProps)
+ connections = {}
+ for obj in res:
+ connections[obj.db_id] = obj
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ annotations = res
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('other').fromSQL(db, None, foreignKey, globalProps)
+ others = res
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('abstractionRef').fromSQL(db, None, foreignKey, globalProps)
+ abstractionRefs = {}
+ for obj in res:
+ abstractionRefs[obj.db_id] = obj
+
+ workflow = DBWorkflow(id=id,
+ name=name,
+ modules=modules,
+ connections=connections,
+ annotations=annotations,
+ others=others,
+ abstractionRefs=abstractionRefs)
+ workflow.is_dirty = False
+ list.append(workflow)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'workflow'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_modules.itervalues():
+ self.getDao('module').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_connections.itervalues():
+ self.getDao('connection').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_annotations:
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_others:
+ self.getDao('other').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_abstractionRefs.itervalues():
+ self.getDao('abstractionRef').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBAbstractionRefSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'abstraction_id', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ abstraction_id = self.convertFromDB(row[1], 'long', 'int')
+ version = self.convertFromDB(row[2], 'long', 'int')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ abstractionRef = DBAbstractionRef(abstraction_id=abstraction_id,
+ version=version,
+ id=id)
+ abstractionRef.db_parentType = parentType
+ abstractionRef.db_vistrailId = vistrailId
+ abstractionRef.db_parent = parent
+ abstractionRef.is_dirty = False
+ res[('abstractionRef', id)] = abstractionRef
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_abstractionRef(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'abstraction_id', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_abstraction_id') and obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['abstraction_id', 'version', 'id']
+ table = 'abstraction_ref'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ abstraction_id = self.convertFromDB(row[0], 'long', 'int')
+ version = self.convertFromDB(row[1], 'long', 'int')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ abstractionRef = DBAbstractionRef(id=id,
+ abstraction_id=abstraction_id,
+ version=version)
+ abstractionRef.is_dirty = False
+ list.append(abstractionRef)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'abstraction_ref'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'long', 'int')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'akey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_vistrailId = vistrailId
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['akey', 'value', 'id']
+ table = 'annotation'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ key = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[1], 'str', 'varchar(8191)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ annotation = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ annotation.is_dirty = False
+ list.append(annotation)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'annotation'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_vistrailId = vistrailId
+ change.is_dirty = False
+ res[('change', id)] = change
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'change_tbl'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'id']
+ table = 'change_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ what = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[1], 'long', 'int')
+ newObjId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ data = None
+ if what == 'module':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('module').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'location':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('location').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'annotation':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'function':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('function').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'connection':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('connection').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'port':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('port').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'parameter':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('parameter').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'portSpec':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('portSpec').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'abstractionRef':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('abstractionRef').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'other':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('other').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+
+ change = DBChange(id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ change.is_dirty = False
+ list.append(change)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'change_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ child = obj.db_data
+ if child.vtType == 'module':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('module').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'location':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('location').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'annotation':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'function':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('function').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'connection':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('connection').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'port':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('port').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'parameter':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('parameter').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'portSpec':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('portSpec').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'abstractionRef':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('abstractionRef').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'other':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('other').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'vt_id', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_vistrailId = vistrailId
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'vt_id', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['pos', 'name', 'type', 'val', 'alias', 'id']
+ table = 'parameter'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ pos = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[3], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ parameter = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ parameter.is_dirty = False
+ list.append(parameter)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'parameter'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'parent_type', 'vt_id', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[2], 'long', 'int')
+ parent = self.convertFromDB(row[3], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_vistrailId = vistrailId
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'vt_id', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['id']
+ table = 'connection_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('connection','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('port').fromSQL(db, None, foreignKey, globalProps)
+ ports = res
+
+ connection = DBConnection(id=id,
+ ports=ports)
+ connection.is_dirty = False
+ list.append(connection)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'connection_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('connection','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_ports:
+ self.getDao('port').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'prev_id', 'date', 'user', 'parent_type', 'vt_id', 'parent_id']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ user = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[4], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[5], 'long', 'int')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ user=user,
+ id=id)
+ action.db_parentType = parentType
+ action.db_vistrailId = vistrailId
+ action.db_parent = parent
+ action.is_dirty = False
+ res[('action', id)] = action
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_action(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'user', 'parent_type', 'vt_id', 'parent_id']
+ table = 'action'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_annotations.itervalues():
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['prev_id', 'date', 'user', 'id']
+ table = 'action'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ prevId = self.convertFromDB(row[0], 'long', 'int')
+ date = self.convertFromDB(row[1], 'datetime', 'datetime')
+ user = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[3], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('action','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ annotations = {}
+ for obj in res:
+ annotations[obj.db_id] = obj
+
+ operations = []
+
+ foreignKey = {'action_id': keyStr}
+ res = self.getDao('add').fromSQL(db, None, foreignKey, globalProps)
+ operations.extend(res)
+
+ foreignKey = {'action_id': keyStr}
+ res = self.getDao('delete').fromSQL(db, None, foreignKey, globalProps)
+ operations.extend(res)
+
+ foreignKey = {'action_id': keyStr}
+ res = self.getDao('change').fromSQL(db, None, foreignKey, globalProps)
+ operations.extend(res)
+
+ action = DBAction(id=id,
+ prevId=prevId,
+ date=date,
+ user=user,
+ annotations=annotations,
+ operations=operations)
+ action.is_dirty = False
+ list.append(action)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'action'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('action','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_annotations.itervalues():
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+
+ for child in obj.db_operations:
+ if child.vtType == 'add':
+ foreignKey = {'action_id' : keyStr}
+ self.getDao('add').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'delete':
+ foreignKey = {'action_id' : keyStr}
+ self.getDao('delete').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'change':
+ foreignKey = {'action_id' : keyStr}
+ self.getDao('change').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_vistrailId = vistrailId
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'delete_tbl'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['what', 'object_id', 'par_obj_id', 'par_obj_type', 'id']
+ table = 'delete_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ what = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[1], 'long', 'int')
+ parentObjId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjType = self.convertFromDB(row[3], 'str', 'char(16)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ delete = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ delete.is_dirty = False
+ list.append(delete)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'delete_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'version', 'name']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['vt_id'] = self.convertToDB(id, 'long', 'int')
+ version = self.convertFromDB(row[1], 'str', 'char(16)')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+
+ vistrail = DBVistrail(version=version,
+ name=name,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'version', 'name']
+ table = 'vistrail'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ global_props['vt_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_actions.itervalues():
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags.itervalues():
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_abstractions.itervalues():
+ child.db_vistrail = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['version', 'name', 'id']
+ table = 'vistrail'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ version = self.convertFromDB(row[0], 'str', 'char(16)')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ if globalProps is None:
+ globalProps = {}
+ globalProps['vt_id'] = self.convertToDB(id, 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('vistrail','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('action').fromSQL(db, None, foreignKey, globalProps)
+ actions = {}
+ for obj in res:
+ actions[obj.db_id] = obj
+
+ discStr = self.convertToDB('vistrail','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('tag').fromSQL(db, None, foreignKey, globalProps)
+ tags = {}
+ for obj in res:
+ tags[obj.db_id] = obj
+
+ foreignKey = {'vt_id': keyStr}
+ res = self.getDao('abstraction').fromSQL(db, None, foreignKey, globalProps)
+ abstractions = {}
+ for obj in res:
+ abstractions[obj.db_id] = obj
+
+ vistrail = DBVistrail(id=id,
+ version=version,
+ name=name,
+ actions=actions,
+ tags=tags,
+ abstractions=abstractions)
+ vistrail.is_dirty = False
+ list.append(vistrail)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'vistrail'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ if obj.db_id is not None:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if globalProps is None:
+ globalProps = {}
+ globalProps['vt_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+
+ discStr = self.convertToDB('vistrail','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_actions.itervalues():
+ self.getDao('action').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('vistrail','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_tags.itervalues():
+ self.getDao('tag').toSQL(db, child, foreignKey, globalProps)
+
+ foreignKey = {'vt_id': keyStr}
+ for child in obj.db_abstractions.itervalues():
+ self.getDao('abstraction').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'ts_start', 'ts_end', 'module_id', 'module_name', 'machine_id', 'wf_exec_id', 'vt_id']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ module_id = self.convertFromDB(row[3], 'long', 'int')
+ module_name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ machine_id = self.convertFromDB(row[5], 'long', 'int')
+ workflow_exec = self.convertFromDB(row[6], 'long', 'int')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ module_id=module_id,
+ module_name=module_name,
+ id=id)
+ module_exec.db_machine_id = machine_id
+ module_exec.db_workflow_exec = workflow_exec
+ module_exec.db_vistrailId = vistrailId
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('machine', obj.db_machine_id)]
+ p.db_add_module_exec(obj)
+ p = all_objects[('workflow_exec', obj.db_workflow_exec)]
+ p.db_add_module_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'module_id', 'module_name', 'machine_id', 'wf_exec_id', 'vt_id']
+ table = 'module_exec'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_workflow_exec') and obj.db_workflow_exec is not None:
+ columnMap['wf_exec_id'] = \
+ self.convertToDB(obj.db_workflow_exec, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['ts_start', 'ts_end', 'module_id', 'module_name', 'id']
+ table = 'module_exec'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ ts_start = self.convertFromDB(row[0], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[1], 'datetime', 'datetime')
+ module_id = self.convertFromDB(row[2], 'long', 'int')
+ module_name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('module_exec','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ annotations = res
+
+ module_exec = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ module_id=module_id,
+ module_name=module_name,
+ annotations=annotations)
+ module_exec.is_dirty = False
+ list.append(module_exec)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'module_exec'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('module_exec','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_annotations:
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefSQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v0_6_0/persistence/sql/sql_dao.py b/vistrails/db/versions/v0_6_0/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..7f92a24
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/persistence/sql/sql_dao.py
@@ -0,0 +1,141 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return "'" + str(value).replace("'", "''") + "'"
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ return str(value)
+ elif type == 'int':
+ return str(value)
+ elif type == 'date':
+ return "'" + value.isoformat() + "'"
+ elif type == 'datetime':
+ return "'" + value.strftime('%Y-%m-%d %H:%M:%S') + "'"
+ else:
+ return str(value)
+
+ return "''"
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ return dbCommand
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ valueStr = ', '.join(values)
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s)""" % \
+ (table, columnStr, valueStr)
+ return dbCommand
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ setStr += '%s %s = %s' % (comma, column, value)
+ comma = ','
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """UPDATE %s SET %s WHERE %s""" % \
+ (table, setStr, whereStr)
+ return dbCommand
+
+ def executeSQL(self, db, dbCommand, isFetch):
+ print 'db: %s' % dbCommand
+ data = None
+ cursor = db.cursor()
+ cursor.execute(dbCommand)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ cursor.close()
+ return data
diff --git a/vistrails/db/versions/v0_6_0/persistence/xml/__init__.py b/vistrails/db/versions/v0_6_0/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_6_0/persistence/xml/auto_gen.py b/vistrails/db/versions/v0_6_0/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..78e1469
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/persistence/xml/auto_gen.py
@@ -0,0 +1,1749 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from xml_dao import XMLDAO
+from vistrails.db.versions.v0_6_0.domain import *
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'portSpec':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ type = self.convertFromStr(self.getAttribute(node, 'type'), 'str')
+ spec = self.convertFromStr(self.getAttribute(node, 'spec'), 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, doc, node):
+ if node is None:
+ node = doc.createElement('portSpec')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.setAttribute('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.setAttribute('spec',self.convertToStr(portSpec.db_spec, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'module':
+ return None
+
+ functions = []
+
+ annotations = {}
+ portSpecs = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ cache = self.convertFromStr(self.getAttribute(node, 'cache'), 'int')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ package = self.convertFromStr(self.getAttribute(node, 'package'), 'str')
+ version = self.convertFromStr(self.getAttribute(node, 'version'), 'str')
+
+ location = None
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'location':
+ location = self.getDao('location').fromXML(child)
+ elif child.nodeName == 'function':
+ function = self.getDao('function').fromXML(child)
+ functions.append(function)
+ elif child.nodeName == 'annotation':
+ annotation = self.getDao('annotation').fromXML(child)
+ annotations[annotation.db_id] = annotation
+ elif child.nodeName == 'portSpec':
+ portSpec = self.getDao('portSpec').fromXML(child)
+ portSpecs[portSpec.db_id] = portSpec
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ package=package,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, doc, node):
+ if node is None:
+ node = doc.createElement('module')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(module.db_id, 'long'))
+ node.setAttribute('cache',self.convertToStr(module.db_cache, 'int'))
+ node.setAttribute('name',self.convertToStr(module.db_name, 'str'))
+ node.setAttribute('package',self.convertToStr(module.db_package, 'str'))
+ node.setAttribute('version',self.convertToStr(module.db_version, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ if nodeMap.has_key(('location', location.db_id)):
+ childNode = nodeMap[('location', location.db_id)]
+ del nodeMap[('location', location.db_id)]
+ else:
+ childNode = doc.createElement('location')
+ node.appendChild(childNode)
+ self.getDao('location').toXML(location, doc, childNode)
+ functions = module.db_functions
+ for function in functions:
+ if nodeMap.has_key(('function', function.db_id)):
+ childNode = nodeMap[('function', function.db_id)]
+ del nodeMap[('function', function.db_id)]
+ else:
+ childNode = doc.createElement('function')
+ node.appendChild(childNode)
+ self.getDao('function').toXML(function, doc, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations.itervalues():
+ if nodeMap.has_key(('annotation', annotation.db_id)):
+ childNode = nodeMap[('annotation', annotation.db_id)]
+ del nodeMap[('annotation', annotation.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(annotation, doc, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs.itervalues():
+ if nodeMap.has_key(('portSpec', portSpec.db_id)):
+ childNode = nodeMap[('portSpec', portSpec.db_id)]
+ del nodeMap[('portSpec', portSpec.db_id)]
+ else:
+ childNode = doc.createElement('portSpec')
+ node.appendChild(childNode)
+ self.getDao('portSpec').toXML(portSpec, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'tag':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, doc, node):
+ if node is None:
+ node = doc.createElement('tag')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(tag.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'port':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ type = self.convertFromStr(self.getAttribute(node, 'type'), 'str')
+ moduleId = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ moduleName = self.convertFromStr(self.getAttribute(node, 'moduleName'), 'str')
+ sig = self.convertFromStr(self.getAttribute(node, 'sig'), 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ sig=sig)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, doc, node):
+ if node is None:
+ node = doc.createElement('port')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(port.db_id, 'long'))
+ node.setAttribute('type',self.convertToStr(port.db_type, 'str'))
+ node.setAttribute('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.setAttribute('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.setAttribute('sig',self.convertToStr(port.db_sig, 'str'))
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'log':
+ return None
+
+ workflow_execs = {}
+ machines = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'workflowExec':
+ workflow_exec = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs[workflow_exec.db_id] = workflow_exec
+ elif child.nodeName == 'machine':
+ machine = self.getDao('machine').fromXML(child)
+ machines[machine.db_id] = machine
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBLog(id=id,
+ workflow_execs=workflow_execs,
+ machines=machines)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, doc, node):
+ if node is None:
+ node = doc.createElement('log')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(log.db_id, 'long'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs.itervalues():
+ if nodeMap.has_key(('workflow_exec', workflow_exec.db_id)):
+ childNode = nodeMap[('workflow_exec', workflow_exec.db_id)]
+ del nodeMap[('workflow_exec', workflow_exec.db_id)]
+ else:
+ childNode = doc.createElement('workflow_exec')
+ node.appendChild(childNode)
+ self.getDao('workflow_exec').toXML(workflow_exec, doc, childNode)
+ machines = log.db_machines
+ for machine in machines.itervalues():
+ if nodeMap.has_key(('machine', machine.db_id)):
+ childNode = nodeMap[('machine', machine.db_id)]
+ del nodeMap[('machine', machine.db_id)]
+ else:
+ childNode = doc.createElement('machine')
+ node.appendChild(childNode)
+ self.getDao('machine').toXML(machine, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'machine':
+ return None
+
+ module_execs = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ os = self.convertFromStr(self.getAttribute(node, 'os'), 'str')
+ architecture = self.convertFromStr(self.getAttribute(node, 'architecture'), 'str')
+ processor = self.convertFromStr(self.getAttribute(node, 'processor'), 'str')
+ ram = self.convertFromStr(self.getAttribute(node, 'ram'), 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ module_execs=module_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, doc, node):
+ if node is None:
+ node = doc.createElement('machine')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(machine.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(machine.db_name, 'str'))
+ node.setAttribute('os',self.convertToStr(machine.db_os, 'str'))
+ node.setAttribute('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.setAttribute('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.setAttribute('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'add':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ what = self.convertFromStr(self.getAttribute(node, 'what'), 'str')
+ objectId = self.convertFromStr(self.getAttribute(node, 'objectId'), 'long')
+ parentObjId = self.convertFromStr(self.getAttribute(node, 'parentObjId'), 'long')
+ parentObjType = self.convertFromStr(self.getAttribute(node, 'parentObjType'), 'str')
+
+ data = None
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'module':
+ data = self.getDao('module').fromXML(child)
+ elif child.nodeName == 'location':
+ data = self.getDao('location').fromXML(child)
+ elif child.nodeName == 'annotation':
+ data = self.getDao('annotation').fromXML(child)
+ elif child.nodeName == 'function':
+ data = self.getDao('function').fromXML(child)
+ elif child.nodeName == 'connection':
+ data = self.getDao('connection').fromXML(child)
+ elif child.nodeName == 'port':
+ data = self.getDao('port').fromXML(child)
+ elif child.nodeName == 'parameter':
+ data = self.getDao('parameter').fromXML(child)
+ elif child.nodeName == 'portSpec':
+ data = self.getDao('portSpec').fromXML(child)
+ elif child.nodeName == 'abstractionRef':
+ data = self.getDao('abstractionRef').fromXML(child)
+ elif child.nodeName == 'other':
+ data = self.getDao('other').fromXML(child)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBAdd(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, doc, node):
+ if node is None:
+ node = doc.createElement('add')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(add.db_id, 'long'))
+ node.setAttribute('what',self.convertToStr(add.db_what, 'str'))
+ node.setAttribute('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.setAttribute('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.setAttribute('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ data = add.db_data
+ if data.vtType == 'module':
+ if nodeMap.has_key(('module', data.db_id)):
+ childNode = nodeMap[('module', data.db_id)]
+ del nodeMap[('module', data.db_id)]
+ else:
+ childNode = doc.createElement('module')
+ node.appendChild(childNode)
+ self.getDao('module').toXML(data, doc, childNode)
+ elif data.vtType == 'location':
+ if nodeMap.has_key(('location', data.db_id)):
+ childNode = nodeMap[('location', data.db_id)]
+ del nodeMap[('location', data.db_id)]
+ else:
+ childNode = doc.createElement('location')
+ node.appendChild(childNode)
+ self.getDao('location').toXML(data, doc, childNode)
+ elif data.vtType == 'annotation':
+ if nodeMap.has_key(('annotation', data.db_id)):
+ childNode = nodeMap[('annotation', data.db_id)]
+ del nodeMap[('annotation', data.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(data, doc, childNode)
+ elif data.vtType == 'function':
+ if nodeMap.has_key(('function', data.db_id)):
+ childNode = nodeMap[('function', data.db_id)]
+ del nodeMap[('function', data.db_id)]
+ else:
+ childNode = doc.createElement('function')
+ node.appendChild(childNode)
+ self.getDao('function').toXML(data, doc, childNode)
+ elif data.vtType == 'connection':
+ if nodeMap.has_key(('connection', data.db_id)):
+ childNode = nodeMap[('connection', data.db_id)]
+ del nodeMap[('connection', data.db_id)]
+ else:
+ childNode = doc.createElement('connection')
+ node.appendChild(childNode)
+ self.getDao('connection').toXML(data, doc, childNode)
+ elif data.vtType == 'port':
+ if nodeMap.has_key(('port', data.db_id)):
+ childNode = nodeMap[('port', data.db_id)]
+ del nodeMap[('port', data.db_id)]
+ else:
+ childNode = doc.createElement('port')
+ node.appendChild(childNode)
+ self.getDao('port').toXML(data, doc, childNode)
+ elif data.vtType == 'parameter':
+ if nodeMap.has_key(('parameter', data.db_id)):
+ childNode = nodeMap[('parameter', data.db_id)]
+ del nodeMap[('parameter', data.db_id)]
+ else:
+ childNode = doc.createElement('parameter')
+ node.appendChild(childNode)
+ self.getDao('parameter').toXML(data, doc, childNode)
+ elif data.vtType == 'portSpec':
+ if nodeMap.has_key(('portSpec', data.db_id)):
+ childNode = nodeMap[('portSpec', data.db_id)]
+ del nodeMap[('portSpec', data.db_id)]
+ else:
+ childNode = doc.createElement('portSpec')
+ node.appendChild(childNode)
+ self.getDao('portSpec').toXML(data, doc, childNode)
+ elif data.vtType == 'abstractionRef':
+ if nodeMap.has_key(('abstractionRef', data.db_id)):
+ childNode = nodeMap[('abstractionRef', data.db_id)]
+ del nodeMap[('abstractionRef', data.db_id)]
+ else:
+ childNode = doc.createElement('abstractionRef')
+ node.appendChild(childNode)
+ self.getDao('abstractionRef').toXML(data, doc, childNode)
+ elif data.vtType == 'other':
+ if nodeMap.has_key(('other', data.db_id)):
+ childNode = nodeMap[('other', data.db_id)]
+ del nodeMap[('other', data.db_id)]
+ else:
+ childNode = doc.createElement('other')
+ node.appendChild(childNode)
+ self.getDao('other').toXML(data, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'other':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ key = self.convertFromStr(self.getAttribute(node, 'key'), 'str')
+
+ value = None
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'value':
+ value = self.convertFromStr(child.firstChild.nodeValue,'str')
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, doc, node):
+ if node is None:
+ node = doc.createElement('other')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(other.db_id, 'long'))
+ node.setAttribute('key',self.convertToStr(other.db_key, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ if other.db_value is not None:
+ child = other.db_value
+ if nodeMap.has_key(('value',child.db_id)):
+ childNode = nodeMap[('value',child.db_id)]
+ del nodeMap[('value', child.db_id)]
+ textNode = childNode.firstChild
+ textNode.replaceWholeText(self.convertToStr(child, 'str'))
+ else:
+ childNode = doc.createElement('value')
+ node.appendChild(childNode)
+ textNode = doc.createTextNode(self.convertToStr(child, 'str'))
+ childNode.appendChild(textNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'location':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ x = self.convertFromStr(self.getAttribute(node, 'x'), 'float')
+ y = self.convertFromStr(self.getAttribute(node, 'y'), 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, doc, node):
+ if node is None:
+ node = doc.createElement('location')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(location.db_id, 'long'))
+ node.setAttribute('x',self.convertToStr(location.db_x, 'float'))
+ node.setAttribute('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'workflowExec':
+ return None
+
+ module_execs = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ user = self.convertFromStr(self.getAttribute(node, 'user'), 'str')
+ ip = self.convertFromStr(self.getAttribute(node, 'ip'), 'str')
+ vt_version = self.convertFromStr(self.getAttribute(node, 'vtVersion'), 'str')
+ ts_start = self.convertFromStr(self.getAttribute(node, 'tsStart'), 'datetime')
+ ts_end = self.convertFromStr(self.getAttribute(node, 'tsEnd'), 'datetime')
+ parent_id = self.convertFromStr(self.getAttribute(node, 'parentId'), 'long')
+ parent_type = self.convertFromStr(self.getAttribute(node, 'parentType'), 'str')
+ parent_version = self.convertFromStr(self.getAttribute(node, 'parentVersion'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'moduleExec':
+ module_exec = self.getDao('module_exec').fromXML(child)
+ module_execs[module_exec.db_id] = module_exec
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBWorkflowExec(id=id,
+ user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ module_execs=module_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, doc, node):
+ if node is None:
+ node = doc.createElement('workflowExec')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.setAttribute('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.setAttribute('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.setAttribute('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.setAttribute('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.setAttribute('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.setAttribute('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.setAttribute('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.setAttribute('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.setAttribute('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ module_execs = workflow_exec.db_module_execs
+ for module_exec in module_execs.itervalues():
+ if nodeMap.has_key(('module_exec', module_exec.db_id)):
+ childNode = nodeMap[('module_exec', module_exec.db_id)]
+ del nodeMap[('module_exec', module_exec.db_id)]
+ else:
+ childNode = doc.createElement('module_exec')
+ node.appendChild(childNode)
+ self.getDao('module_exec').toXML(module_exec, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'function':
+ return None
+
+ parameters = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ pos = self.convertFromStr(self.getAttribute(node, 'pos'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'parameter':
+ parameter = self.getDao('parameter').fromXML(child)
+ parameters.append(parameter)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, doc, node):
+ if node is None:
+ node = doc.createElement('function')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(function.db_id, 'long'))
+ node.setAttribute('pos',self.convertToStr(function.db_pos, 'long'))
+ node.setAttribute('name',self.convertToStr(function.db_name, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ if nodeMap.has_key(('parameter', parameter.db_id)):
+ childNode = nodeMap[('parameter', parameter.db_id)]
+ del nodeMap[('parameter', parameter.db_id)]
+ else:
+ childNode = doc.createElement('parameter')
+ node.appendChild(childNode)
+ self.getDao('parameter').toXML(parameter, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'abstraction':
+ return None
+
+ actions = {}
+ tags = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'action':
+ action = self.getDao('action').fromXML(child)
+ actions[action.db_id] = action
+ elif child.nodeName == 'tag':
+ tag = self.getDao('tag').fromXML(child)
+ tags[tag.db_id] = tag
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBAbstraction(id=id,
+ name=name,
+ actions=actions,
+ tags=tags)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, doc, node):
+ if node is None:
+ node = doc.createElement('abstraction')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(abstraction.db_name, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ actions = abstraction.db_actions
+ for action in actions.itervalues():
+ if nodeMap.has_key(('action', action.db_id)):
+ childNode = nodeMap[('action', action.db_id)]
+ del nodeMap[('action', action.db_id)]
+ else:
+ childNode = doc.createElement('action')
+ node.appendChild(childNode)
+ self.getDao('action').toXML(action, doc, childNode)
+ tags = abstraction.db_tags
+ for tag in tags.itervalues():
+ if nodeMap.has_key(('tag', tag.db_id)):
+ childNode = nodeMap[('tag', tag.db_id)]
+ del nodeMap[('tag', tag.db_id)]
+ else:
+ childNode = doc.createElement('tag')
+ node.appendChild(childNode)
+ self.getDao('tag').toXML(tag, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'workflow':
+ return None
+
+ annotations = []
+ others = []
+
+ modules = {}
+ connections = {}
+ abstractionRefs = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'module':
+ module = self.getDao('module').fromXML(child)
+ modules[module.db_id] = module
+ elif child.nodeName == 'connection':
+ connection = self.getDao('connection').fromXML(child)
+ connections[connection.db_id] = connection
+ elif child.nodeName == 'annotation':
+ annotation = self.getDao('annotation').fromXML(child)
+ annotations.append(annotation)
+ elif child.nodeName == 'other':
+ other = self.getDao('other').fromXML(child)
+ others.append(other)
+ elif child.nodeName == 'abstractionRef':
+ abstractionRef = self.getDao('abstractionRef').fromXML(child)
+ abstractionRefs[abstractionRef.db_id] = abstractionRef
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBWorkflow(id=id,
+ name=name,
+ modules=modules,
+ connections=connections,
+ annotations=annotations,
+ others=others,
+ abstractionRefs=abstractionRefs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, doc, node):
+ if node is None:
+ node = doc.createElement('workflow')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(workflow.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(workflow.db_name, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ modules = workflow.db_modules
+ for module in modules.itervalues():
+ if nodeMap.has_key(('module', module.db_id)):
+ childNode = nodeMap[('module', module.db_id)]
+ del nodeMap[('module', module.db_id)]
+ else:
+ childNode = doc.createElement('module')
+ node.appendChild(childNode)
+ self.getDao('module').toXML(module, doc, childNode)
+ connections = workflow.db_connections
+ for connection in connections.itervalues():
+ if nodeMap.has_key(('connection', connection.db_id)):
+ childNode = nodeMap[('connection', connection.db_id)]
+ del nodeMap[('connection', connection.db_id)]
+ else:
+ childNode = doc.createElement('connection')
+ node.appendChild(childNode)
+ self.getDao('connection').toXML(connection, doc, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ if nodeMap.has_key(('annotation', annotation.db_id)):
+ childNode = nodeMap[('annotation', annotation.db_id)]
+ del nodeMap[('annotation', annotation.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(annotation, doc, childNode)
+ others = workflow.db_others
+ for other in others:
+ if nodeMap.has_key(('other', other.db_id)):
+ childNode = nodeMap[('other', other.db_id)]
+ del nodeMap[('other', other.db_id)]
+ else:
+ childNode = doc.createElement('other')
+ node.appendChild(childNode)
+ self.getDao('other').toXML(other, doc, childNode)
+ abstractionRefs = workflow.db_abstractionRefs
+ for abstractionRef in abstractionRefs.itervalues():
+ if nodeMap.has_key(('abstractionRef', abstractionRef.db_id)):
+ childNode = nodeMap[('abstractionRef', abstractionRef.db_id)]
+ del nodeMap[('abstractionRef', abstractionRef.db_id)]
+ else:
+ childNode = doc.createElement('abstractionRef')
+ node.appendChild(childNode)
+ self.getDao('abstractionRef').toXML(abstractionRef, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBAbstractionRefXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'abstractionRef':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ abstraction_id = self.convertFromStr(self.getAttribute(node, 'abstractionId'), 'long')
+ version = self.convertFromStr(self.getAttribute(node, 'version'), 'long')
+
+ obj = DBAbstractionRef(id=id,
+ abstraction_id=abstraction_id,
+ version=version)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstractionRef, doc, node):
+ if node is None:
+ node = doc.createElement('abstractionRef')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(abstractionRef.db_id, 'long'))
+ node.setAttribute('abstractionId',self.convertToStr(abstractionRef.db_abstraction_id, 'long'))
+ node.setAttribute('version',self.convertToStr(abstractionRef.db_version, 'long'))
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'annotation':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ key = self.convertFromStr(self.getAttribute(node, 'key'), 'str')
+ value = self.convertFromStr(self.getAttribute(node, 'value'), 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, doc, node):
+ if node is None:
+ node = doc.createElement('annotation')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(annotation.db_id, 'long'))
+ node.setAttribute('key',self.convertToStr(annotation.db_key, 'str'))
+ node.setAttribute('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'change':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ what = self.convertFromStr(self.getAttribute(node, 'what'), 'str')
+ oldObjId = self.convertFromStr(self.getAttribute(node, 'oldObjId'), 'long')
+ newObjId = self.convertFromStr(self.getAttribute(node, 'newObjId'), 'long')
+ parentObjId = self.convertFromStr(self.getAttribute(node, 'parentObjId'), 'long')
+ parentObjType = self.convertFromStr(self.getAttribute(node, 'parentObjType'), 'str')
+
+ data = None
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'module':
+ data = self.getDao('module').fromXML(child)
+ elif child.nodeName == 'location':
+ data = self.getDao('location').fromXML(child)
+ elif child.nodeName == 'annotation':
+ data = self.getDao('annotation').fromXML(child)
+ elif child.nodeName == 'function':
+ data = self.getDao('function').fromXML(child)
+ elif child.nodeName == 'connection':
+ data = self.getDao('connection').fromXML(child)
+ elif child.nodeName == 'port':
+ data = self.getDao('port').fromXML(child)
+ elif child.nodeName == 'parameter':
+ data = self.getDao('parameter').fromXML(child)
+ elif child.nodeName == 'portSpec':
+ data = self.getDao('portSpec').fromXML(child)
+ elif child.nodeName == 'abstractionRef':
+ data = self.getDao('abstractionRef').fromXML(child)
+ elif child.nodeName == 'other':
+ data = self.getDao('other').fromXML(child)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBChange(id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, doc, node):
+ if node is None:
+ node = doc.createElement('change')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(change.db_id, 'long'))
+ node.setAttribute('what',self.convertToStr(change.db_what, 'str'))
+ node.setAttribute('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.setAttribute('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.setAttribute('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.setAttribute('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ data = change.db_data
+ if data.vtType == 'module':
+ if nodeMap.has_key(('module', data.db_id)):
+ childNode = nodeMap[('module', data.db_id)]
+ del nodeMap[('module', data.db_id)]
+ else:
+ childNode = doc.createElement('module')
+ node.appendChild(childNode)
+ self.getDao('module').toXML(data, doc, childNode)
+ elif data.vtType == 'location':
+ if nodeMap.has_key(('location', data.db_id)):
+ childNode = nodeMap[('location', data.db_id)]
+ del nodeMap[('location', data.db_id)]
+ else:
+ childNode = doc.createElement('location')
+ node.appendChild(childNode)
+ self.getDao('location').toXML(data, doc, childNode)
+ elif data.vtType == 'annotation':
+ if nodeMap.has_key(('annotation', data.db_id)):
+ childNode = nodeMap[('annotation', data.db_id)]
+ del nodeMap[('annotation', data.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(data, doc, childNode)
+ elif data.vtType == 'function':
+ if nodeMap.has_key(('function', data.db_id)):
+ childNode = nodeMap[('function', data.db_id)]
+ del nodeMap[('function', data.db_id)]
+ else:
+ childNode = doc.createElement('function')
+ node.appendChild(childNode)
+ self.getDao('function').toXML(data, doc, childNode)
+ elif data.vtType == 'connection':
+ if nodeMap.has_key(('connection', data.db_id)):
+ childNode = nodeMap[('connection', data.db_id)]
+ del nodeMap[('connection', data.db_id)]
+ else:
+ childNode = doc.createElement('connection')
+ node.appendChild(childNode)
+ self.getDao('connection').toXML(data, doc, childNode)
+ elif data.vtType == 'port':
+ if nodeMap.has_key(('port', data.db_id)):
+ childNode = nodeMap[('port', data.db_id)]
+ del nodeMap[('port', data.db_id)]
+ else:
+ childNode = doc.createElement('port')
+ node.appendChild(childNode)
+ self.getDao('port').toXML(data, doc, childNode)
+ elif data.vtType == 'parameter':
+ if nodeMap.has_key(('parameter', data.db_id)):
+ childNode = nodeMap[('parameter', data.db_id)]
+ del nodeMap[('parameter', data.db_id)]
+ else:
+ childNode = doc.createElement('parameter')
+ node.appendChild(childNode)
+ self.getDao('parameter').toXML(data, doc, childNode)
+ elif data.vtType == 'portSpec':
+ if nodeMap.has_key(('portSpec', data.db_id)):
+ childNode = nodeMap[('portSpec', data.db_id)]
+ del nodeMap[('portSpec', data.db_id)]
+ else:
+ childNode = doc.createElement('portSpec')
+ node.appendChild(childNode)
+ self.getDao('portSpec').toXML(data, doc, childNode)
+ elif data.vtType == 'abstractionRef':
+ if nodeMap.has_key(('abstractionRef', data.db_id)):
+ childNode = nodeMap[('abstractionRef', data.db_id)]
+ del nodeMap[('abstractionRef', data.db_id)]
+ else:
+ childNode = doc.createElement('abstractionRef')
+ node.appendChild(childNode)
+ self.getDao('abstractionRef').toXML(data, doc, childNode)
+ elif data.vtType == 'other':
+ if nodeMap.has_key(('other', data.db_id)):
+ childNode = nodeMap[('other', data.db_id)]
+ del nodeMap[('other', data.db_id)]
+ else:
+ childNode = doc.createElement('other')
+ node.appendChild(childNode)
+ self.getDao('other').toXML(data, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'parameter':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ pos = self.convertFromStr(self.getAttribute(node, 'pos'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ type = self.convertFromStr(self.getAttribute(node, 'type'), 'str')
+ val = self.convertFromStr(self.getAttribute(node, 'val'), 'str')
+ alias = self.convertFromStr(self.getAttribute(node, 'alias'), 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, doc, node):
+ if node is None:
+ node = doc.createElement('parameter')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(parameter.db_id, 'long'))
+ node.setAttribute('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.setAttribute('name',self.convertToStr(parameter.db_name, 'str'))
+ node.setAttribute('type',self.convertToStr(parameter.db_type, 'str'))
+ node.setAttribute('val',self.convertToStr(parameter.db_val, 'str'))
+ node.setAttribute('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'connection':
+ return None
+
+ ports = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'port':
+ port = self.getDao('port').fromXML(child)
+ ports.append(port)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, doc, node):
+ if node is None:
+ node = doc.createElement('connection')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(connection.db_id, 'long'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ if nodeMap.has_key(('port', port.db_id)):
+ childNode = nodeMap[('port', port.db_id)]
+ del nodeMap[('port', port.db_id)]
+ else:
+ childNode = doc.createElement('port')
+ node.appendChild(childNode)
+ self.getDao('port').toXML(port, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'action':
+ return None
+
+ operations = []
+
+ annotations = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ prevId = self.convertFromStr(self.getAttribute(node, 'prevId'), 'long')
+ date = self.convertFromStr(self.getAttribute(node, 'date'), 'datetime')
+ user = self.convertFromStr(self.getAttribute(node, 'user'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'annotation':
+ annotation = self.getDao('annotation').fromXML(child)
+ annotations[annotation.db_id] = annotation
+ elif child.nodeName == 'add':
+ operation = self.getDao('add').fromXML(child)
+ operations.append(operation)
+ elif child.nodeName == 'delete':
+ operation = self.getDao('delete').fromXML(child)
+ operations.append(operation)
+ elif child.nodeName == 'change':
+ operation = self.getDao('change').fromXML(child)
+ operations.append(operation)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBAction(id=id,
+ prevId=prevId,
+ date=date,
+ user=user,
+ annotations=annotations,
+ operations=operations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, doc, node):
+ if node is None:
+ node = doc.createElement('action')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(action.db_id, 'long'))
+ node.setAttribute('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.setAttribute('date',self.convertToStr(action.db_date, 'datetime'))
+ node.setAttribute('user',self.convertToStr(action.db_user, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations.itervalues():
+ if nodeMap.has_key(('annotation', annotation.db_id)):
+ childNode = nodeMap[('annotation', annotation.db_id)]
+ del nodeMap[('annotation', annotation.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(annotation, doc, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ if nodeMap.has_key(('add', operation.db_id)):
+ childNode = nodeMap[('add', operation.db_id)]
+ del nodeMap[('add', operation.db_id)]
+ else:
+ childNode = doc.createElement('add')
+ node.appendChild(childNode)
+ self.getDao('add').toXML(operation, doc, childNode)
+ elif operation.vtType == 'delete':
+ if nodeMap.has_key(('delete', operation.db_id)):
+ childNode = nodeMap[('delete', operation.db_id)]
+ del nodeMap[('delete', operation.db_id)]
+ else:
+ childNode = doc.createElement('delete')
+ node.appendChild(childNode)
+ self.getDao('delete').toXML(operation, doc, childNode)
+ elif operation.vtType == 'change':
+ if nodeMap.has_key(('change', operation.db_id)):
+ childNode = nodeMap[('change', operation.db_id)]
+ del nodeMap[('change', operation.db_id)]
+ else:
+ childNode = doc.createElement('change')
+ node.appendChild(childNode)
+ self.getDao('change').toXML(operation, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'delete':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ what = self.convertFromStr(self.getAttribute(node, 'what'), 'str')
+ objectId = self.convertFromStr(self.getAttribute(node, 'objectId'), 'long')
+ parentObjId = self.convertFromStr(self.getAttribute(node, 'parentObjId'), 'long')
+ parentObjType = self.convertFromStr(self.getAttribute(node, 'parentObjType'), 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, doc, node):
+ if node is None:
+ node = doc.createElement('delete')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(delete.db_id, 'long'))
+ node.setAttribute('what',self.convertToStr(delete.db_what, 'str'))
+ node.setAttribute('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.setAttribute('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.setAttribute('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'vistrail':
+ return None
+
+ actions = {}
+ tags = {}
+ abstractions = {}
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ version = self.convertFromStr(self.getAttribute(node, 'version'), 'str')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ dbHost = self.convertFromStr(self.getAttribute(node, 'dbHost'), 'str')
+ dbPort = self.convertFromStr(self.getAttribute(node, 'dbPort'), 'int')
+ dbName = self.convertFromStr(self.getAttribute(node, 'dbName'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'action':
+ action = self.getDao('action').fromXML(child)
+ actions[action.db_id] = action
+ elif child.nodeName == 'tag':
+ tag = self.getDao('tag').fromXML(child)
+ tags[tag.db_id] = tag
+ elif child.nodeName == 'abstraction':
+ abstraction = self.getDao('abstraction').fromXML(child)
+ abstractions[abstraction.db_id] = abstraction
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ dbHost=dbHost,
+ dbPort=dbPort,
+ dbName=dbName,
+ actions=actions,
+ tags=tags,
+ abstractions=abstractions)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, doc, node):
+ if node is None:
+ node = doc.createElement('vistrail')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.setAttribute('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.setAttribute('name',self.convertToStr(vistrail.db_name, 'str'))
+ node.setAttribute('dbHost',self.convertToStr(vistrail.db_dbHost, 'str'))
+ node.setAttribute('dbPort',self.convertToStr(vistrail.db_dbPort, 'int'))
+ node.setAttribute('dbName',self.convertToStr(vistrail.db_dbName, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions.itervalues():
+ if nodeMap.has_key(('action', action.db_id)):
+ childNode = nodeMap[('action', action.db_id)]
+ del nodeMap[('action', action.db_id)]
+ else:
+ childNode = doc.createElement('action')
+ node.appendChild(childNode)
+ self.getDao('action').toXML(action, doc, childNode)
+ tags = vistrail.db_tags
+ for tag in tags.itervalues():
+ if nodeMap.has_key(('tag', tag.db_id)):
+ childNode = nodeMap[('tag', tag.db_id)]
+ del nodeMap[('tag', tag.db_id)]
+ else:
+ childNode = doc.createElement('tag')
+ node.appendChild(childNode)
+ self.getDao('tag').toXML(tag, doc, childNode)
+ abstractions = vistrail.db_abstractions
+ for abstraction in abstractions.itervalues():
+ if nodeMap.has_key(('abstraction', abstraction.db_id)):
+ childNode = nodeMap[('abstraction', abstraction.db_id)]
+ del nodeMap[('abstraction', abstraction.db_id)]
+ else:
+ childNode = doc.createElement('abstraction')
+ node.appendChild(childNode)
+ self.getDao('abstraction').toXML(abstraction, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'moduleExec':
+ return None
+
+ annotations = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ ts_start = self.convertFromStr(self.getAttribute(node, 'tsStart'), 'datetime')
+ ts_end = self.convertFromStr(self.getAttribute(node, 'tsEnd'), 'datetime')
+ module_id = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ module_name = self.convertFromStr(self.getAttribute(node, 'moduleName'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'annotation':
+ annotation = self.getDao('annotation').fromXML(child)
+ annotations.append(annotation)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ # node.removeChild(child)
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ module_id=module_id,
+ module_name=module_name,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, doc, node):
+ if node is None:
+ node = doc.createElement('moduleExec')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.setAttribute('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.setAttribute('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.setAttribute('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.setAttribute('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ if nodeMap.has_key(('annotation', annotation.db_id)):
+ childNode = nodeMap[('annotation', annotation.db_id)]
+ del nodeMap[('annotation', annotation.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(annotation, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v0_6_0/persistence/xml/io.py b/vistrails/db/versions/v0_6_0/persistence/xml/io.py
new file mode 100644
index 0000000..4b5116f
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/persistence/xml/io.py
@@ -0,0 +1,95 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.parsers.expat import ExpatError
+import xml.dom.minidom
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_6_0 import version as my_version
+
+def parse_xml_file(filename):
+ try:
+ return xml.dom.minidom.parse(filename)
+ except xml.parsers.expat.ExpatError, e:
+ msg = 'XML parse error at line %s, col %s: %s' % \
+ (e.lineno, e.offset, e.code)
+ raise VistrailsDBException(msg)
+
+def write_xml_file(filename, dom, prettyprint=True):
+ output = open(filename, 'w')
+ if prettyprint:
+ dom.writexml(output, '',' ','\n')
+ else:
+ dom.writexml(output)
+ output.close()
+
+def read_xml_object(vtType, node, dao_list):
+ return dao_list[vtType].fromXML(node)
+
+def write_xml_object(obj, dom, dao_list, node=None):
+ res_node = dao_list[obj.vtType].toXML(obj, dom, node)
+ return res_node
+
+def open_from_xml(filename, vtType, dao_list):
+ """open_from_xml(filename) -> DBVistrail"""
+ dom = parse_xml_file(filename)
+ vistrail = read_xml_object(vtType, dom.documentElement, dao_list)
+ dom.unlink()
+ return vistrail
+
+def save_to_xml(obj, filename, dao_list):
+ dom = xml.dom.minidom.getDOMImplementation().createDocument(None, None,
+ None)
+ root = write_xml_object(obj, dom, dao_list)
+ dom.appendChild(root)
+ if obj.vtType == 'vistrail':
+ root.setAttribute('version', my_version)
+ root.setAttribute('xmlns:xsi',
+ 'http://www.w3.org/2001/XMLSchema-instance')
+ root.setAttribute('xsi:schemaLocation',
+ 'http://www.vistrails.org/vistrail.xsd')
+ write_xml_file(filename, dom)
+ dom.unlink()
+
+def serialize(object, dao_list):
+ dom = xml.dom.minidom.getDOMImplementation().createDocument(None, None,
+ None)
+ root = write_xml_object(object, dom, dao_list)
+ dom.appendChild(root)
+ return dom.toxml()
+
+def unserialize(str, obj_type):
+ dom = xml.dom.minidom.parseString(str)
+ return read_xml_object(obj_type, dom.documentElement, dao_list)
+
diff --git a/vistrails/db/versions/v0_6_0/persistence/xml/xml_dao.py b/vistrails/db/versions/v0_6_0/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..955c01a
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/persistence/xml/xml_dao.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v0_6_0/schemas/sql/vistrails.sql b/vistrails/db/versions/v0_6_0/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..05eeb79
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/schemas/sql/vistrails.sql
@@ -0,0 +1,242 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(22),
+ type varchar(255),
+ spec varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ package varchar(511),
+ version varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ sig varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE log_tbl(
+ id int,
+ vt_id int
+);
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ module_exec_id int
+);
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+);
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ name varchar(255),
+ log_id int,
+ vt_id int
+);
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE abstraction(
+ id int,
+ name varchar(255),
+ vt_id int
+);
+
+CREATE TABLE workflow(
+ id int,
+ name varchar(255),
+ vt_id int
+);
+
+CREATE TABLE abstraction_ref(
+ id int,
+ abstraction_id int,
+ version int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+);
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ user varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+);
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ version char(16),
+ name varchar(255)
+);
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ module_id int,
+ module_name varchar(255),
+ machine_id int,
+ wf_exec_id int,
+ vt_id int
+);
+
diff --git a/vistrails/db/versions/v0_6_0/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v0_6_0/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..4540fbb
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,37 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, tag, port, log_tbl, machine, add_tbl, other, location, workflow_exec, function, abstraction, workflow, abstraction_ref, annotation, change_tbl, parameter, connection_tbl, action, delete_tbl, vistrail, module_exec
diff --git a/vistrails/db/versions/v0_6_0/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_6_0/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..9471940
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/schemas/xml/vistrail.xsd
@@ -0,0 +1,227 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="dbHost" type="xs:string"/>
+ <xs:attribute name="dbPort" type="xs:int"/>
+ <xs:attribute name="dbName" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="user" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="sig" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstractionRef">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="abstractionId" type="xs:int"/>
+ <xs:attribute name="version" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_6_0/specs/abstraction.xml b/vistrails/db/versions/v0_6_0/specs/abstraction.xml
new file mode 100644
index 0000000..6f76c61
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/abstraction.xml
@@ -0,0 +1,65 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="action" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="hash" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="vistrail" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/abstractionRef.xml b/vistrails/db/versions/v0_6_0/specs/abstractionRef.xml
new file mode 100644
index 0000000..5645c3d
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/abstractionRef.xml
@@ -0,0 +1,78 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstractionRef">
+ <layout>
+ <xml name="abstractionRef" nodeType="xs:element"/>
+ <sql table="abstraction_ref"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_id" type="long">
+ <xml name="abstractionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/action.xml b/vistrails/db/versions/v0_6_0/specs/action.xml
new file mode 100644
index 0000000..d9c259f
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/action.xml
@@ -0,0 +1,100 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="annotation" type="hash" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/add.xml b/vistrails/db/versions/v0_6_0/specs/add.xml
new file mode 100644
index 0000000..7cbca5c
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/add.xml
@@ -0,0 +1,110 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/annotation.xml b/vistrails/db/versions/v0_6_0/specs/annotation.xml
new file mode 100644
index 0000000..19e9a54
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/annotation.xml
@@ -0,0 +1,93 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/change.xml b/vistrails/db/versions/v0_6_0/specs/change.xml
new file mode 100644
index 0000000..54b348f
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/change.xml
@@ -0,0 +1,115 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/connection.xml b/vistrails/db/versions/v0_6_0/specs/connection.xml
new file mode 100644
index 0000000..b559fab
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/connection.xml
@@ -0,0 +1,74 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/delete.xml b/vistrails/db/versions/v0_6_0/specs/delete.xml
new file mode 100644
index 0000000..9df9273
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/delete.xml
@@ -0,0 +1,77 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/function.xml b/vistrails/db/versions/v0_6_0/specs/function.xml
new file mode 100644
index 0000000..8254645
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/function.xml
@@ -0,0 +1,83 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/location.xml b/vistrails/db/versions/v0_6_0/specs/location.xml
new file mode 100644
index 0000000..6e56055
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/location.xml
@@ -0,0 +1,80 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_6_0/specs/log.xml b/vistrails/db/versions/v0_6_0/specs/log.xml
new file mode 100644
index 0000000..c2554e3
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/log.xml
@@ -0,0 +1,62 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="hash"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="hash"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/machine.xml b/vistrails/db/versions/v0_6_0/specs/machine.xml
new file mode 100644
index 0000000..dea813d
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/machine.xml
@@ -0,0 +1,85 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="long" mapping="one-to-many">
+ <sql column="module_exec_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/module.xml b/vistrails/db/versions/v0_6_0/specs/module.xml
new file mode 100644
index 0000000..3a89cf8
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/module.xml
@@ -0,0 +1,107 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="hash" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="hash" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/module_exec.xml b/vistrails/db/versions/v0_6_0/specs/module_exec.xml
new file mode 100644
index 0000000..465407b
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/module_exec.xml
@@ -0,0 +1,86 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="machine" name="machine_id" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="machine_id" type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/other.xml b/vistrails/db/versions/v0_6_0/specs/other.xml
new file mode 100644
index 0000000..40e1388
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/other.xml
@@ -0,0 +1,79 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/parameter.xml b/vistrails/db/versions/v0_6_0/specs/parameter.xml
new file mode 100644
index 0000000..78f6cf7
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/parameter.xml
@@ -0,0 +1,94 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/port.xml b/vistrails/db/versions/v0_6_0/specs/port.xml
new file mode 100644
index 0000000..2a369ff
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/port.xml
@@ -0,0 +1,90 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="sig" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/portSpec.xml b/vistrails/db/versions/v0_6_0/specs/portSpec.xml
new file mode 100644
index 0000000..e42a5f0
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/portSpec.xml
@@ -0,0 +1,84 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(22)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/tag.xml b/vistrails/db/versions/v0_6_0/specs/tag.xml
new file mode 100644
index 0000000..f8412b9
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/tag.xml
@@ -0,0 +1,71 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/vistrail.xml b/vistrails/db/versions/v0_6_0/specs/vistrail.xml
new file mode 100644
index 0000000..4f139cb
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/vistrail.xml
@@ -0,0 +1,81 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="vt_id"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="dbHost" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="dbPort" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="dbName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property ref="true" object="action" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="hash" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="abstraction" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_6_0/specs/workflow.xml b/vistrails/db/versions/v0_6_0/specs/workflow.xml
new file mode 100644
index 0000000..486e3f8
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/workflow.xml
@@ -0,0 +1,79 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="module" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="connection" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="abstractionRef" type="hash"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_6_0/specs/workflow_exec.xml b/vistrails/db/versions/v0_6_0/specs/workflow_exec.xml
new file mode 100644
index 0000000..6944ede
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/specs/workflow_exec.xml
@@ -0,0 +1,106 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="hash" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_6_0/translate/__init__.py b/vistrails/db/versions/v0_6_0/translate/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_6_0/translate/v0_3_1.py b/vistrails/db/versions/v0_6_0/translate/v0_3_1.py
new file mode 100644
index 0000000..27f5a80
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/translate/v0_3_1.py
@@ -0,0 +1,716 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import sys
+import copy
+from datetime import datetime
+from time import strptime
+
+from vistrails.core.data_structures.graph import Graph
+from vistrails.db.versions.v0_6_0.domain import DBVistrail, DBAction, DBTag, DBModule, \
+ DBConnection, DBPortSpec, DBFunction, DBParameter, DBLocation, DBAdd, \
+ DBChange, DBDelete, DBAnnotation, DBPort
+
+def convertDate(date):
+ if date is not None and date != '':
+ return datetime(*strptime(date, '%d %b %Y %H:%M:%S')[0:6])
+ return datetime(1900, 1, 1)
+
+def translateVistrail(_vistrail):
+ vistrail = DBVistrail()
+ id_scope = vistrail.idScope
+ for _action in _vistrail.db_get_actions():
+# print 'translating action %s' % _action.db_time
+ functionName = 'translate%s%sAction' % \
+ (_action.db_what[0].upper(), _action.db_what[1:])
+ thisModule = sys.modules[__name__]
+ action = getattr(thisModule, functionName)(_action, id_scope)
+ vistrail.db_add_action(action)
+ for _tag in _vistrail.db_get_tags():
+ tag = DBTag(id=_tag.db_time,
+ name=_tag.db_name)
+ vistrail.db_add_tag(tag)
+
+ convertIds(vistrail)
+# for action in vistrail.getActions():
+# print '%s %s' % (action.id, action.operations)
+ vistrail.db_version = '0.6.0'
+ return vistrail
+
+def createAction(_action, operations, id_scope):
+ annotations = {}
+ if _action.db_notes is not None and _action.db_notes.strip() != '':
+ annotations['notes'] = DBAnnotation(id=id_scope.getNewId(DBAnnotation.vtType),
+ key='notes',
+ value=_action.db_notes.strip(),
+ )
+ return DBAction(id=_action.db_time,
+ prevId=_action.db_parent,
+ date=convertDate(_action.db_date),
+ user=_action.db_user,
+ operations=operations,
+ annotations=annotations,
+ )
+
+def translateAddModuleAction(_action, id_scope):
+ operations = []
+ for _module in _action.db_datas:
+ # note that we're just blindly setting all cache tags to 1 since
+ # v0.3.1 didn't really switch this
+ module = DBModule(id=_module.db_id,
+ name=_module.db_name,
+ cache=1,
+ location=DBLocation(id=_module.db_id,
+ x=_module.db_x,
+ y=_module.db_y))
+ module.db_location.relative = False
+ operation = DBAdd(id=_action.db_time,
+ what='module',
+ objectId=_module.db_id,
+ data=module)
+ operations.append(operation)
+
+ return createAction(_action, operations, id_scope)
+
+def translateAddConnectionAction(_action, id_scope):
+ operations = []
+ for _connection in _action.db_datas:
+ source = DBPort(id=_connection.db_id,
+ type='source',
+ moduleId=_connection.db_sourceId,
+ moduleName=_connection.db_sourceModule,
+ sig=_connection.db_sourcePort)
+ destination = DBPort(id=_connection.db_id,
+ type='destination',
+ moduleId=_connection.db_destinationId,
+ moduleName=_connection.db_destinationModule,
+ sig=_connection.db_destinationPort)
+ connection = DBConnection(id=_connection.db_id,
+ ports=[source, destination])
+ operation = DBAdd(id=_action.db_time,
+ what='connection',
+ objectId=_connection.db_id,
+ data=connection)
+ operations.append(operation)
+
+ return createAction(_action, operations, id_scope)
+
+def translateChangeParameterAction(_action, id_scope):
+ operations = []
+ for _set in _action.db_datas:
+ parameter = DBParameter(id=_set.db_parameterId,
+ pos=_set.db_parameterId,
+ name=_set.db_parameter,
+ alias=_set.db_alias,
+ val=_set.db_value,
+ type=_set.db_type)
+ function = DBFunction(id=_set.db_functionId,
+ pos=_set.db_functionId,
+ name=_set.db_function,
+ parameters=[parameter])
+ operation = DBChange(id=_action.db_time,
+ what='function',
+ oldObjId=_set.db_functionId,
+ parentObjId=_set.db_moduleId,
+ parentObjType='module',
+ data=function)
+ operations.append(operation)
+
+ return createAction(_action, operations, id_scope)
+
+def translateAddModulePortAction(_action, id_scope):
+ operations = []
+ for _portSpec in _action.db_datas:
+ # ids need to be checked
+ portSpec = DBPortSpec(id=_portSpec.db_moduleId,
+ name=_portSpec.db_portName,
+ type=_portSpec.db_portType,
+ spec=_portSpec.db_portSpec)
+ operation = DBAdd(id=_action.db_time,
+ what='portSpec',
+ objectId=(_portSpec.db_portName,
+ _portSpec.db_portType),
+ parentObjId=_portSpec.db_moduleId,
+ parentObjType='module',
+ data=portSpec)
+ operations.append(operation)
+
+ return createAction(_action, operations, id_scope)
+
+def translateChangeAnnotationAction(_action, id_scope):
+ operations = []
+ for _annotation in _action.db_datas:
+ if _annotation.db_key.strip() != '' or \
+ _annotation.db_value.strip() != '':
+ annotation = DBAnnotation(id=-1,
+ key=_annotation.db_key,
+ value=_annotation.db_value)
+ operation = DBChange(id=_action.db_time,
+ what='annotation',
+ oldObjId=_annotation.db_key,
+ parentObjId=_annotation.db_moduleId,
+ parentObjType='module',
+ data=annotation)
+ operations.append(operation)
+
+ return createAction(_action, operations, id_scope)
+
+def translateDeleteModuleAction(_action, id_scope):
+ operations = []
+ for _module in _action.db_datas:
+ operation = DBDelete(id=_action.db_time,
+ what='module',
+ objectId=_module.db_moduleId)
+ operations.append(operation)
+
+ return createAction(_action, operations, id_scope)
+
+def translateDeleteConnectionAction(_action, id_scope):
+ operations = []
+ for _connection in _action.db_datas:
+ operation = DBDelete(id=_action.db_time,
+ what='connection',
+ objectId=_connection.db_connectionId)
+ operations.append(operation)
+
+ return createAction(_action, operations, id_scope)
+
+def translateDeleteFunctionAction(_action, id_scope):
+ operations = []
+ for _function in _action.db_datas:
+ operation = DBDelete(id=_action.db_time,
+ what='function',
+ objectId=_function.db_functionId,
+ parentObjId=_function.db_moduleId,
+ parentObjType='module')
+ operations.append(operation)
+
+ return createAction(_action, operations, id_scope)
+
+def translateDeleteAnnotationAction(_action, id_scope):
+ operations = []
+ for _annotation in _action.db_datas:
+ operation = DBDelete(id=_action.db_time,
+ what='annotation',
+ objectId=_annotation.db_key)
+ operations.append(operation)
+
+ return createAction(_action, operations, id_scope)
+
+def translateDeleteModulePortAction(_action, id_scope):
+ operations = []
+ for _portSpec in _action.db_datas:
+ operation = DBDelete(id=_action.db_time,
+ what='portSpec',
+ objectId=(_portSpec.db_portName,
+ _portSpec.db_portType),
+ parentObjId=_portSpec.db_moduleId,
+ parentObjType='module')
+ operations.append(operation)
+
+ return createAction(_action, operations, id_scope)
+
+def translateMoveModuleAction(_action, id_scope):
+ operations = []
+ for _location in _action.db_datas:
+ location = DBLocation(id=_location.db_id,
+ x=_location.db_dx,
+ y=_location.db_dy)
+ location.relative = True
+
+ operation = DBChange(id=_action.db_time,
+ what='location',
+ oldObjId=_location.db_id,
+ parentObjId=_location.db_id,
+ parentObjType='module',
+ data=location)
+ operations.append(operation)
+
+ return createAction(_action, operations, id_scope)
+
+### UPDATE IDS ###
+
+def convertIds(vistrail):
+ actions = vistrail.db_get_actions()
+ actions.sort(key=lambda x: x.db_id)
+ objectDict = {}
+# refDict = {'objectDict': objectDict}
+
+ graph = Graph()
+ for action in actions:
+ graph.add_vertex(action.db_id)
+ graph.add_edge(action.db_prevId, action.db_id)
+
+ def convertAction(actionId):
+# print 'converting %s' % actionId
+ if actionId == 0:
+ return
+ allOps = []
+ action = vistrail.db_get_action(actionId)
+# objectDict = refDict['objectDict']
+# if action.actionType == 'delete' or action.actionType == 'change':
+# action.objectDict = copy.deepcopy(objectDict)
+# else:
+# action.objectDict = objectDict
+ for operation in action.db_get_operations():
+ allOps.extend(convertOperation(vistrail,
+ objectDict,
+ operation.vtType,
+ operation))
+ action.db_operations = allOps
+
+ def removeObjects(actionId):
+ if actionId == 0:
+ return
+# print "removeObjects(%s)" % actionId
+ action = vistrail.db_get_action(actionId)
+
+ # need to reverse ops here
+ reverseOps = action.db_get_operations()
+ reverseOps.reverse()
+ for operation in reverseOps:
+ parentList = getTypeIdList(operation)
+ removeObject(operation.db_what,
+ operation.db_oldId,
+ objectDict,
+ parentList[:-1])
+ reverseOps.reverse()
+
+
+ graph.dfs(enter_vertex=convertAction,
+ leave_vertex=removeObjects)
+
+def getTypeIdList(operation):
+ if operation.db_what in ('module', 'connection'):
+ return [(operation.db_what, operation.db_oldId)]
+ elif operation.db_what in \
+ ('function', 'portSpec', 'location', 'annotation'):
+ return [('module', operation.db_oldParentId),
+ (operation.db_what, operation.db_oldId)]
+ elif operation.db_what in ('port'):
+ return [('connection', operation.db_oldParentId),
+ (operation.db_what, operation.db_oldId)]
+ elif operation.db_what in ('parameter'):
+ return [('module', operation.db_moduleId),
+ ('function', operation.db_oldParentId),
+ ('parameter', operation.db_oldId)]
+ else:
+ print "unknown type: '%s'" % operation.db_what
+ return [(operation.db_what, operation.db_oldId)]
+
+def getOldId(object):
+ if object.vtType == 'annotation':
+ return object.db_key
+ elif object.vtType == 'port':
+ return object.db_type
+ elif object.vtType == 'portSpec':
+ return (object.db_name, object.db_type)
+ else:
+ return object.getPrimaryKey()
+
+def getChildren(object):
+ childList = []
+ if object.vtType == 'module':
+ childList = object.db_get_functions() + \
+ object.db_get_portSpecs() + \
+ object.db_get_annotations()
+ childList.append(object.db_location)
+ object.db_functions = []
+ object.db_portSpecs = {}
+ object.db_annotations = {}
+ object.db_location = None
+ elif object.vtType == 'connection':
+ childList = object.db_get_ports()
+ object.db_ports = []
+ elif object.vtType == 'function':
+ childList = object.db_get_parameters()
+ object.db_parameters = []
+ return childList
+
+def captureObject(object, objectDict, newId, parentList):
+
+# print "capturing %s" % object
+ currentDict = objectDict
+ for key in parentList:
+ (objType, objId) = key
+# (currentId, newDict, _) = currentDict[(objType, objId)]
+# currentDict = newDict
+ (objList, curIdx) = currentDict[(objType, objId)]
+ currentDict = objList[curIdx][1]
+ oldId = getOldId(object)
+# print "capture: %s %s" % (object.vtType, oldId)
+# currentDict[(object.vtType, oldId)] = (newId, {}, object)
+ if not currentDict.has_key((object.vtType, oldId)):
+ currentDict[(object.vtType, oldId)] = ([], -1)
+ (curList, curIdx) = currentDict[(object.vtType, oldId)]
+ curList.append((newId, {}, object, curIdx))
+ currentDict[(object.vtType, oldId)] = (curList, len(curList) - 1)
+
+def captureDelete(objType, objId, objectDict, parentList):
+ currentDict = objectDict
+ for (aType, aId) in parentList:
+# (currentId, newDict, _) = currentDict[(objType, objId)]
+# currentDict = newDict
+ (objList, curIdx) = currentDict[(aType, aId)]
+ currentDict = objList[curIdx][1]
+
+# print "captureDelete: %s %s" % (objType, objId)
+ if not currentDict.has_key((objType, objId)):
+ raise Exception("invalid delete")
+ (curList, curIdx) = currentDict[(objType, objId)]
+ curList.append((-1, {}, None, curIdx))
+ currentDict[(objType, objId)] = (curList, len(curList) - 1)
+
+def removeObject(oldObjType, oldId, objectDict, parentList):
+# print '%s %s' % (oldObjType, oldId)
+# print objectDict
+# print parentList
+
+ try:
+ currentDict = objectDict
+ for key in parentList:
+ (objType, objId) = key
+# (currentId, newDict, _) = currentDict[(objType, objId)]
+# currentDict = newDict
+ (objList, objIdx) = currentDict[(objType, objId)]
+ currentDict = objList[objIdx][1]
+# print "remove: %s %s" % (oldObjType, oldId)
+ (curList, curIdx) = currentDict[(oldObjType, oldId)]
+# print "ok"
+ newIdx = curList[curIdx][3]
+# del curList[curIdx]
+ currentDict[(oldObjType, oldId)] = (curList, newIdx)
+ except KeyError:
+ print "cannot remove (%s, %s)" % (oldObjType, oldId)
+ print parentList
+ print objList
+ print "index: %s" % objIdx
+
+def findNewId(typeIdList, objectDict):
+ try:
+ currentDict = objectDict
+ for key in typeIdList:
+# (currentId, currentDict, currentObj) = currentDict[key]
+ (objList, curIdx) = currentDict[key]
+ if curIdx == -1:
+ return (None, None)
+ (currentId, currentDict, currentObj, _) = objList[curIdx]
+ if currentId == -1:
+ return (None, None)
+ return (currentId, currentObj)
+ except KeyError:
+ pass
+ return (None, None)
+
+def getChildList(typeIdList, objectDict):
+ try:
+ currentDict = objectDict
+ for (objType, objOldId) in typeIdList:
+# (currentId, currentDict, _) = currentDict[(objType, objOldId)]
+ (objList, curIdx) = currentDict[(objType, objOldId)]
+ if curIdx == -1:
+ return {}
+ currentDict = objList[curIdx][1]
+ return currentDict
+ except KeyError:
+ pass
+ return {}
+
+def createOperation(actionType, objId, objType, parentId, parentType,
+ object=None):
+ if actionType == 'add':
+ operation = DBAdd(what=objType,
+ objectId=objId,
+ parentObjId=parentId,
+ parentObjType=parentType,
+ data=object)
+
+ elif actionType == 'change':
+ operation = DBChange(what=objType,
+ oldObjId=objId,
+ parentObjId=parentId,
+ parentObjType=parentType,
+ data=object)
+ elif actionType == 'delete':
+ operation = DBDelete(what=objType,
+ objectId=objId,
+ parentObjId=parentId,
+ parentObjType=parentType)
+ else:
+ msg = "Cannot find actionType='%s'" % actionType
+ raise Exception(msg)
+
+ return operation
+
+def convertChangeToAdd(operation):
+ return DBAdd(what=operation.db_what,
+ objectId=operation.db_newObjId,
+ parentObjId=operation.db_parentObjId,
+ parentObjType=operation.db_parentObjType,
+ data=operation.db_data)
+
+def convertOperation(vistrail, objectDict, actionType, operation):
+ newOps = []
+ if actionType == 'add':
+ object = operation.db_data
+ if object.vtType == 'parameter' and object.db_pos == -1:
+ return newOps
+ operation.db_oldId = operation.db_objectId
+ if operation.db_what == 'annotation':
+ operation.db_oldId = object.db_key
+ elif operation.db_what == 'port':
+ operation.db_oldId = object.db_type
+ operation.db_oldParentId = operation.db_parentObjId
+ parentList = getTypeIdList(operation)
+
+
+ newId = vistrail.idScope.getNewId(object.vtType)
+ captureObject(object, objectDict, newId, parentList[:-1])
+ operation.db_objectId = newId
+ oldId = object.getPrimaryKey()
+ if object.vtType == 'annotation':
+ oldId = object.db_key
+ elif object.vtType == 'port':
+ oldId = object.db_type
+ if hasattr(object, 'db_id'):
+ object.db_id = newId
+
+ # set parent ids correctly...
+ operation.db_id = vistrail.idScope.getNewId('operation')
+ if operation.db_parentObjId is not None:
+ oldParentObjId = operation.db_parentObjId
+ operation.db_parentObjId = findNewId(parentList[:-1], objectDict)[0]
+ if object.vtType == 'port':
+ object.db_moduleId = \
+ findNewId([('module', object.db_moduleId)], objectDict)[0]
+# if object.vtType == 'connection':
+# for port in object.db_ports.itervalues():
+# port.db_moduleId = \
+# findNewId([('module', port.db_moduleId)], objectDict)[0]
+
+ newOps.append(operation)
+
+ # set child operations
+ children = getChildren(object)
+ for child in children:
+ # hack to get around fact that location ids are wrong
+ if child.vtType == 'location':
+ child.db_id = oldId
+ newOp = createOperation('add',
+ child.getPrimaryKey(),
+ child.vtType,
+ oldId,
+ object.vtType,
+ child)
+
+ # hack to get moduleId at parameter level
+ if child.vtType == 'parameter':
+ newOp.db_moduleId = oldParentObjId
+ newOps.extend(convertOperation(vistrail,
+ objectDict,
+ 'add',
+ newOp))
+ newOp.db_parentObjId = newId
+ elif actionType == 'change':
+ object = operation.db_data
+ if object.vtType == 'parameter' and object.db_pos == -1:
+ return newOps
+ operation.db_oldId = operation.db_oldObjId
+ if operation.db_what == 'annotation':
+ operation.db_oldId = object.db_key
+ elif operation.db_what == 'port':
+ operation.db_oldId = object.db_type
+ operation.db_oldParentId = operation.db_parentObjId
+ parentList = getTypeIdList(operation)
+
+ # need to get changed id as new id if have one
+ (foundId, foundObj) = findNewId(parentList, objectDict)
+ if foundId is not None:
+ if foundObj.vtType == 'function' and \
+ foundObj.db_pos == object.db_pos and \
+ foundObj.db_name == object.db_name:
+ # don't create new function, convert parameter
+ for parameter in object.db_parameters:
+ newOp = createOperation('change',
+ parameter.getPrimaryKey(),
+ parameter.vtType,
+ object.getPrimaryKey(),
+ object.vtType,
+ parameter)
+ newOp.db_moduleId = operation.db_parentObjId
+ newOps.extend(convertOperation(vistrail,
+ objectDict,
+ 'change',
+ newOp))
+ newOp.db_parentObjId = foundId
+ return newOps
+ else:
+ if foundObj.vtType == 'location' and object.relative == True:
+ object.db_x += foundObj.db_x
+ object.db_y += foundObj.db_y
+ object.relative = False
+ # get new id for new object
+ newId = vistrail.idScope.getNewId(object.vtType)
+ operation.db_oldObjId = foundId
+ operation.db_newObjId = newId
+ else:
+ # get new id for new object
+ newId = vistrail.idScope.getNewId(object.vtType)
+ operation.db_oldObjId = -1
+ operation.db_newObjId = newId
+ anOldId = operation.db_oldId
+ anOldParentId = operation.db_parentObjId
+ if hasattr(operation,'db_moduleId'):
+ aModuleId = operation.db_moduleId
+ else:
+ aModuleId = None
+ operation = convertChangeToAdd(operation)
+ operation.db_oldId = anOldId
+ operation.db_oldParentId = operation.db_parentObjId
+ operation.db_moduleId = aModuleId
+
+ # need to do child deletes first
+ childDict = getChildList(parentList, objectDict)
+ for k,v in childDict.items():
+ (objType, objId) = k
+# (newId, newDict) = v
+# print 'creating delete for %s' % objType
+ newOp = createOperation('delete',
+ objId,
+ objType,
+ object.getPrimaryKey(),
+ object.vtType)
+ # hack to get moduleId at parameter level
+ if objType == 'parameter':
+ newOp.db_moduleId = operation.db_parentObjId
+ newOps.extend(convertOperation(vistrail,
+ objectDict,
+ 'delete',
+ newOp))
+ newOp.db_parentObjId = newId
+ # don't reverse -- ordering is correct
+ # newOps.reverse()
+
+ # set new object id
+ captureObject(object, objectDict, newId, parentList[:-1])
+# operation.db_objectId = newId
+ oldId = object.getPrimaryKey()
+ if object.vtType == 'annotation':
+ oldId = object.db_key
+ elif object.vtType == 'port':
+ oldId = object.db_type
+ if hasattr(object, 'db_id'):
+ object.db_id = newId
+
+ # set parent ids correctly...
+ operation.db_id = vistrail.idScope.getNewId('operation')
+ if operation.db_parentObjId is not None:
+ oldParentObjId = operation.db_parentObjId
+ operation.db_parentObjId = findNewId(parentList[:-1], objectDict)[0]
+ if object.vtType == 'port':
+ object.db_moduleId = \
+ findNewId([('module', object.db_moduleId)], objectDict)[0]
+# if object.vtType == 'connection':
+# for port in object.db_ports.itervalues():
+# port.db_moduleId = \
+# findNewId([('module', port.db_moduleId)], objectDict)[0]
+ newOps.append(operation)
+
+ # set child operations
+ children = getChildren(operation.db_data)
+ for child in children:
+# print 'creating add for %s' % child.vtType
+ newOp = createOperation('add',
+ child.getPrimaryKey(),
+ child.vtType,
+ oldId,
+ object.vtType,
+ child)
+ # hack to get moduleId at parameter level
+ if child.vtType == 'parameter':
+ newOp.db_moduleId = oldParentObjId
+ newOps.extend(convertOperation(vistrail,
+ objectDict,
+ 'add',
+ newOp))
+ newOp.db_parentObjId = newId
+ elif actionType == 'delete':
+ operation.db_oldId = operation.db_objectId
+# if operation.db_what == 'annotation':
+# operation.db_oldId = object.db_key
+# elif operation.db_what == 'port':
+# operation.db_oldId = object.db_type
+ operation.db_oldParentId = operation.db_parentObjId
+ parentList = getTypeIdList(operation)
+
+ # get new id for delete operation
+ (newId, _) = findNewId(parentList, objectDict)
+# print 'found new id: %s' % newId
+ if newId is None:
+ msg = "Cannot find id: %s" % parentList
+ print msg
+# raise Exception(msg)
+ return []
+
+ # need to do child deletes first
+ childDict = getChildList(parentList, objectDict)
+ for k,v in childDict.items():
+ (objType, objId) = k
+# (newId, newDict) = v
+ newOp = createOperation('delete',
+ objId,
+ objType,
+ operation.db_objectId,
+ operation.db_what)
+ # hack to get moduleId at parameter level
+ if objType == 'parameter':
+ newOp.db_moduleId = operation.db_parentObjId
+ newOps.extend(convertOperation(vistrail,
+ objectDict,
+ 'delete',
+ newOp))
+ newOp.db_parentObjId = newId
+# newOps.reverse()
+
+ captureDelete(operation.db_what, operation.db_objectId, objectDict,
+ parentList[:-1])
+ operation.db_objectId = newId
+
+ # set parent ids correctly
+ operation.db_id = vistrail.idScope.getNewId('operation')
+ if operation.db_parentObjId is not None:
+ operation.db_parentObjId = findNewId(parentList[:-1], objectDict)[0]
+ newOps.append(operation)
+
+ return newOps
diff --git a/vistrails/db/versions/v0_6_0/translate/v0_5_0.py b/vistrails/db/versions/v0_6_0/translate/v0_5_0.py
new file mode 100644
index 0000000..c267ab2
--- /dev/null
+++ b/vistrails/db/versions/v0_6_0/translate/v0_5_0.py
@@ -0,0 +1,121 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v0_6_0.domain import DBVistrail, DBAction, DBTag, DBModule, \
+ DBConnection, DBPortSpec, DBFunction, DBParameter, DBLocation, DBAdd, \
+ DBChange, DBDelete, DBAnnotation, DBPort
+
+def translateVistrail(_vistrail):
+ # FIXME should this be a deepcopy?
+ vistrail = DBVistrail()
+
+ for _action in _vistrail.db_actions.itervalues():
+ ops = []
+ for op in _action.db_operations:
+ if op.vtType == 'add':
+ data = convert_data(op.db_data)
+ ops.append(DBAdd(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'change':
+ data = convert_data(op.db_data)
+ ops.append(DBChange(id=op.db_id,
+ what=op.db_what,
+ oldObjId=op.db_oldObjId,
+ newObjId=op.db_newObjId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'delete':
+ ops.append(DBDelete(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType))
+ action = DBAction(id=_action.db_id,
+ prevId=_action.db_prevId,
+ date=_action.db_date,
+ user=_action.db_user,
+ operations=ops)
+ vistrail.db_add_action(action)
+
+ for _tag in _vistrail.db_tags.itervalues():
+ tag = DBTag(id=_tag.db_time,
+ name=_tag.db_name)
+ vistrail.db_add_tag(tag)
+
+ vistrail.db_version = '0.6.0'
+ return vistrail
+
+def convert_data(child):
+ if child.vtType == 'module':
+ return DBModule(id=child.db_id,
+ cache=child.db_cache,
+ name=child.db_name)
+ elif child.vtType == 'connection':
+ return DBConnection(id=child.db_id)
+ elif child.vtType == 'portSpec':
+ return DBPortSpec(id=child.db_id,
+ name=child.db_name,
+ type=child.db_type,
+ spec=child.db_spec)
+ elif child.vtType == 'function':
+ return DBFunction(id=child.db_id,
+ pos=child.db_pos,
+ name=child.db_name)
+ elif child.vtType == 'parameter':
+ return DBParameter(id=child.db_id,
+ pos=child.db_pos,
+ name=child.db_name,
+ type=child.db_type,
+ val=child.db_val,
+ alias=child.db_alias)
+ elif child.vtType == 'location':
+ return DBLocation(id=child.db_id,
+ x=child.db_x,
+ y=child.db_y)
+ elif child.vtType == 'annotation':
+ return DBAnnotation(id=child.db_id,
+ key=child.db_key,
+ value=child.db_value)
+ elif child.vtType == 'port':
+ return DBPort(id=child.db_id,
+ type=child.db_type,
+ moduleId=child.db_moduleId,
+ moduleName=child.db_moduleName,
+ sig=child.db_sig)
diff --git a/vistrails/db/versions/v0_7_0/__init__.py b/vistrails/db/versions/v0_7_0/__init__.py
new file mode 100644
index 0000000..98fe4b0
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.7.0'
diff --git a/vistrails/db/versions/v0_7_0/domain/__init__.py b/vistrails/db/versions/v0_7_0/domain/__init__.py
new file mode 100644
index 0000000..f8bbb47
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/domain/__init__.py
@@ -0,0 +1,40 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from workflow import DBWorkflow
+from vistrail import DBVistrail
+from abstraction import DBAbstraction
+from id_scope import IdScope
diff --git a/vistrails/db/versions/v0_7_0/domain/abstraction.py b/vistrails/db/versions/v0_7_0/domain/abstraction.py
new file mode 100644
index 0000000..5972a93
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/domain/abstraction.py
@@ -0,0 +1,54 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+from auto_gen import DBAbstraction as _DBAbstraction
+from id_scope import IdScope
+
+class DBAbstraction(_DBAbstraction):
+ def __init__(self, *args, **kwargs):
+ _DBAbstraction.__init__(self, *args, **kwargs)
+ self.idScope = IdScope()
+ self.idScope.setBeginId('action', 1)
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBAbstraction.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBAbstraction
+ # need to go through and reset the index to the copied objects
+ cp.idScope = copy.copy(self.idScope)
+ return cp
diff --git a/vistrails/db/versions/v0_7_0/domain/auto_gen.py b/vistrails/db/versions/v0_7_0/domain/auto_gen.py
new file mode 100644
index 0000000..ee3f826
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/domain/auto_gen.py
@@ -0,0 +1,4137 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, spec=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_type = type
+ self.__db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBPortSpec()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_type = self.db_type
+ cp.db_spec = self.db_spec
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_type = self.db_type
+ cp.db_spec = self.db_spec
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_spec(self):
+ return self.__db_spec
+ def __set_db_spec(self, spec):
+ self.__db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self.__db_spec = spec
+ def db_change_spec(self, spec):
+ self.__db_spec = spec
+ def db_delete_spec(self, spec):
+ self.__db_spec = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, abstraction=None, name=None, package=None, version=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self.__db_id = id
+ self.__db_cache = cache
+ self.__db_abstraction = abstraction
+ self.__db_name = name
+ self.__db_package = package
+ self.__db_version = version
+ self.__db_location = location
+ self.db_functions_id_index = {}
+ if functions is None:
+ self.__db_functions = []
+ else:
+ self.__db_functions = functions
+ for v in self.__db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self.__db_portSpecs = []
+ else:
+ self.__db_portSpecs = portSpecs
+ for v in self.__db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[v.db_name] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBModule()
+ cp.db_id = self.db_id
+ cp.db_cache = self.db_cache
+ cp.db_abstraction = self.db_abstraction
+ cp.db_name = self.db_name
+ cp.db_package = self.db_package
+ cp.db_version = self.db_version
+ cp.db_location = self.db_location
+ if self.db_functions is None:
+ cp.db_functions = None
+ else:
+ cp.db_functions = [copy.copy(v) for v in self.db_functions]
+ for v in cp.__db_functions:
+ cp.db_functions_id_index[v.db_id] = v
+ if self.db_annotations is None:
+ cp.db_annotations = None
+ else:
+ cp.db_annotations = [copy.copy(v) for v in self.db_annotations]
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.db_annotations_key_index[v.db_key] = v
+ if self.db_portSpecs is None:
+ cp.db_portSpecs = None
+ else:
+ cp.db_portSpecs = [copy.copy(v) for v in self.db_portSpecs]
+ for v in cp.__db_portSpecs:
+ cp.db_portSpecs_id_index[v.db_id] = v
+ cp.db_portSpecs_name_index[v.db_name] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule()
+ cp.db_id = self.db_id
+ cp.db_cache = self.db_cache
+ cp.db_abstraction = self.db_abstraction
+ cp.db_name = self.db_name
+ cp.db_package = self.db_package
+ cp.db_version = self.db_version
+ if self.db_location is not None:
+ cp.db_location = self.db_location.do_copy(new_ids, id_scope, id_remap)
+ if self.db_functions is None:
+ cp.db_functions = []
+ else:
+ cp.db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_functions]
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+ if self.db_portSpecs is None:
+ cp.db_portSpecs = []
+ else:
+ cp.db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_functions:
+ cp.db_functions_id_index[v.db_id] = v
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.db_annotations_key_index[v.db_key] = v
+ for v in cp.__db_portSpecs:
+ cp.db_portSpecs_id_index[v.db_id] = v
+ cp.db_portSpecs_name_index[v.db_name] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_location is not None:
+ children.extend(self.db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_location is not None and self.db_location.has_changes():
+ return True
+ for child in self.db_functions:
+ if child.has_changes():
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ for child in self.db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_cache(self):
+ return self.__db_cache
+ def __set_db_cache(self, cache):
+ self.__db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self.__db_cache = cache
+ def db_change_cache(self, cache):
+ self.__db_cache = cache
+ def db_delete_cache(self, cache):
+ self.__db_cache = None
+
+ def __get_db_abstraction(self):
+ return self.__db_abstraction
+ def __set_db_abstraction(self, abstraction):
+ self.__db_abstraction = abstraction
+ self.is_dirty = True
+ db_abstraction = property(__get_db_abstraction, __set_db_abstraction)
+ def db_add_abstraction(self, abstraction):
+ self.__db_abstraction = abstraction
+ def db_change_abstraction(self, abstraction):
+ self.__db_abstraction = abstraction
+ def db_delete_abstraction(self, abstraction):
+ self.__db_abstraction = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_package(self):
+ return self.__db_package
+ def __set_db_package(self, package):
+ self.__db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self.__db_package = package
+ def db_change_package(self, package):
+ self.__db_package = package
+ def db_delete_package(self, package):
+ self.__db_package = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_location(self):
+ return self.__db_location
+ def __set_db_location(self, location):
+ self.__db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self.__db_location = location
+ def db_change_location(self, location):
+ self.__db_location = location
+ def db_delete_location(self, location):
+ self.__db_location = None
+
+ def __get_db_functions(self):
+ return self.__db_functions
+ def __set_db_functions(self, functions):
+ self.__db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self.__db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self.__db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ self.__db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self.__db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ del self.__db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == key:
+ return self.__db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return self.db_functions_id_index.has_key(key)
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return self.db_annotations_key_index.has_key(key)
+
+ def __get_db_portSpecs(self):
+ return self.__db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self.__db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self.__db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self.__db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[portSpec.db_name] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == portSpec.db_id:
+ self.__db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self.__db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[portSpec.db_name] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == portSpec.db_id:
+ del self.__db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[portSpec.db_name]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == key:
+ return self.__db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return self.db_portSpecs_id_index.has_key(key)
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return self.db_portSpecs_name_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBTag()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and id_remap.has_key(('action', self.db_id)):
+ cp.db_id = id_remap[('action', self.db_id)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, name=None, spec=None):
+ self.__db_id = id
+ self.__db_type = type
+ self.__db_moduleId = moduleId
+ self.__db_moduleName = moduleName
+ self.__db_name = name
+ self.__db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBPort()
+ cp.db_id = self.db_id
+ cp.db_type = self.db_type
+ cp.db_moduleId = self.db_moduleId
+ cp.db_moduleName = self.db_moduleName
+ cp.db_name = self.db_name
+ cp.db_spec = self.db_spec
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort()
+ cp.db_id = self.db_id
+ cp.db_type = self.db_type
+ cp.db_moduleId = self.db_moduleId
+ cp.db_moduleName = self.db_moduleName
+ cp.db_name = self.db_name
+ cp.db_spec = self.db_spec
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_moduleId') and id_remap.has_key(('module', self.db_moduleId)):
+ cp.db_moduleId = id_remap[('module', self.db_moduleId)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self.__db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self.__db_moduleName = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_spec(self):
+ return self.__db_spec
+ def __set_db_spec(self, spec):
+ self.__db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self.__db_spec = spec
+ def db_change_spec(self, spec):
+ self.__db_spec = spec
+ def db_delete_spec(self, spec):
+ self.__db_spec = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, workflow_execs=None, machines=None):
+ self.__db_id = id
+ self.db_workflow_execs_id_index = {}
+ if workflow_execs is None:
+ self.__db_workflow_execs = []
+ else:
+ self.__db_workflow_execs = workflow_execs
+ for v in self.__db_workflow_execs:
+ self.db_workflow_execs_id_index[v.db_id] = v
+ self.db_machines_id_index = {}
+ if machines is None:
+ self.__db_machines = []
+ else:
+ self.__db_machines = machines
+ for v in self.__db_machines:
+ self.db_machines_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBLog()
+ cp.db_id = self.db_id
+ if self.db_workflow_execs is None:
+ cp.db_workflow_execs = None
+ else:
+ cp.db_workflow_execs = [copy.copy(v) for v in self.db_workflow_execs]
+ for v in cp.__db_workflow_execs:
+ cp.db_workflow_execs_id_index[v.db_id] = v
+ if self.db_machines is None:
+ cp.db_machines = None
+ else:
+ cp.db_machines = [copy.copy(v) for v in self.db_machines]
+ for v in cp.__db_machines:
+ cp.db_machines_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog()
+ cp.db_id = self.db_id
+ if self.db_workflow_execs is None:
+ cp.db_workflow_execs = []
+ else:
+ cp.db_workflow_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_workflow_execs]
+ if self.db_machines is None:
+ cp.db_machines = []
+ else:
+ cp.db_machines = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_machines]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_workflow_execs:
+ cp.db_workflow_execs_id_index[v.db_id] = v
+ for v in cp.__db_machines:
+ cp.db_machines_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_workflow_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self.db_machines:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_workflow_execs:
+ if child.has_changes():
+ return True
+ for child in self.db_machines:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_workflow_execs(self):
+ return self.__db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self.__db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self.__db_workflow_execs
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self.__db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_workflow_execs)):
+ if self.__db_workflow_execs[i].db_id == workflow_exec.db_id:
+ self.__db_workflow_execs[i] = workflow_exec
+ found = True
+ break
+ if not found:
+ self.__db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_workflow_execs)):
+ if self.__db_workflow_execs[i].db_id == workflow_exec.db_id:
+ del self.__db_workflow_execs[i]
+ break
+ del self.db_workflow_execs_id_index[workflow_exec.db_id]
+ def db_get_workflow_exec(self, key):
+ for i in xrange(len(self.__db_workflow_execs)):
+ if self.__db_workflow_execs[i].db_id == key:
+ return self.__db_workflow_execs[i]
+ return None
+ def db_get_workflow_exec_by_id(self, key):
+ return self.db_workflow_execs_id_index[key]
+ def db_has_workflow_exec_with_id(self, key):
+ return self.db_workflow_execs_id_index.has_key(key)
+
+ def __get_db_machines(self):
+ return self.__db_machines
+ def __set_db_machines(self, machines):
+ self.__db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self.__db_machines
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self.__db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_machines)):
+ if self.__db_machines[i].db_id == machine.db_id:
+ self.__db_machines[i] = machine
+ found = True
+ break
+ if not found:
+ self.__db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_machines)):
+ if self.__db_machines[i].db_id == machine.db_id:
+ del self.__db_machines[i]
+ break
+ del self.db_machines_id_index[machine.db_id]
+ def db_get_machine(self, key):
+ for i in xrange(len(self.__db_machines)):
+ if self.__db_machines[i].db_id == key:
+ return self.__db_machines[i]
+ return None
+ def db_get_machine_by_id(self, key):
+ return self.db_machines_id_index[key]
+ def db_has_machine_with_id(self, key):
+ return self.db_machines_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None, module_execs=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_os = os
+ self.__db_architecture = architecture
+ self.__db_processor = processor
+ self.__db_ram = ram
+ self.db_module_execs_id_index = {}
+ if module_execs is None:
+ self.__db_module_execs = []
+ else:
+ self.__db_module_execs = module_execs
+ for v in self.__db_module_execs:
+ self.db_module_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBMachine()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_os = self.db_os
+ cp.db_architecture = self.db_architecture
+ cp.db_processor = self.db_processor
+ cp.db_ram = self.db_ram
+ if self.db_module_execs is None:
+ cp.db_module_execs = None
+ else:
+ cp.db_module_execs = [copy.copy(v) for v in self.db_module_execs]
+ for v in cp.__db_module_execs:
+ cp.db_module_execs_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_os = self.db_os
+ cp.db_architecture = self.db_architecture
+ cp.db_processor = self.db_processor
+ cp.db_ram = self.db_ram
+ if self.db_module_execs is None:
+ cp.db_module_execs = []
+ else:
+ cp.db_module_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_module_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_module_execs:
+ cp.db_module_execs_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_module_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_os(self):
+ return self.__db_os
+ def __set_db_os(self, os):
+ self.__db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self.__db_os = os
+ def db_change_os(self, os):
+ self.__db_os = os
+ def db_delete_os(self, os):
+ self.__db_os = None
+
+ def __get_db_architecture(self):
+ return self.__db_architecture
+ def __set_db_architecture(self, architecture):
+ self.__db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self.__db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self.__db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self.__db_architecture = None
+
+ def __get_db_processor(self):
+ return self.__db_processor
+ def __set_db_processor(self, processor):
+ self.__db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self.__db_processor = processor
+ def db_change_processor(self, processor):
+ self.__db_processor = processor
+ def db_delete_processor(self, processor):
+ self.__db_processor = None
+
+ def __get_db_ram(self):
+ return self.__db_ram
+ def __set_db_ram(self, ram):
+ self.__db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self.__db_ram = ram
+ def db_change_ram(self, ram):
+ self.__db_ram = ram
+ def db_delete_ram(self, ram):
+ self.__db_ram = None
+
+ def __get_db_module_execs(self):
+ return self.__db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self.__db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self.__db_module_execs
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self.__db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ self.__db_module_execs[i] = module_exec
+ found = True
+ break
+ if not found:
+ self.__db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ del self.__db_module_execs[i]
+ break
+ del self.db_module_execs_id_index[module_exec.db_id]
+ def db_get_module_exec(self, key):
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == key:
+ return self.__db_module_execs[i]
+ return None
+ def db_get_module_exec_by_id(self, key):
+ return self.db_module_execs_id_index[key]
+ def db_has_module_exec_with_id(self, key):
+ return self.db_module_execs_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None, data=None):
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_objectId = objectId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.__db_data = data
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBAdd()
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_objectId = self.db_objectId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+ cp.db_data = self.db_data
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd()
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_objectId = self.db_objectId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+ if self.db_data is not None:
+ cp.db_data = self.db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and id_remap.has_key((self.db_what, self.db_objectId)):
+ cp.db_objectId = id_remap[(self.db_what, self.db_objectId)]
+ if hasattr(self, 'db_parentObjId') and id_remap.has_key((self.db_parentObjType, self.db_parentObjId)):
+ cp.db_parentObjId = id_remap[(self.db_parentObjType, self.db_parentObjId)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_data is not None:
+ children.extend(self.db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_data is not None and self.db_data.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_objectId(self):
+ return self.__db_objectId
+ def __set_db_objectId(self, objectId):
+ self.__db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self.__db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def __get_db_data(self):
+ return self.__db_data
+ def __set_db_data(self, data):
+ self.__db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self.__db_data = data
+ def db_change_data(self, data):
+ self.__db_data = data
+ def db_delete_data(self, data):
+ self.__db_data = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self.__db_id = id
+ self.__db_key = key
+ self.__db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBOther()
+ cp.db_id = self.db_id
+ cp.db_key = self.db_key
+ cp.db_value = self.db_value
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOther()
+ cp.db_id = self.db_id
+ cp.db_key = self.db_key
+ cp.db_value = self.db_value
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self.__db_id = id
+ self.__db_x = x
+ self.__db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBLocation()
+ cp.db_id = self.db_id
+ cp.db_x = self.db_x
+ cp.db_y = self.db_y
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation()
+ cp.db_id = self.db_id
+ cp.db_x = self.db_x
+ cp.db_y = self.db_y
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_x(self):
+ return self.__db_x
+ def __set_db_x(self, x):
+ self.__db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self.__db_x = x
+ def db_change_x(self, x):
+ self.__db_x = x
+ def db_delete_x(self, x):
+ self.__db_x = None
+
+ def __get_db_y(self):
+ return self.__db_y
+ def __set_db_y(self, y):
+ self.__db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self.__db_y = y
+ def db_change_y(self, y):
+ self.__db_y = y
+ def db_delete_y(self, y):
+ self.__db_y = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, id=None, user=None, ip=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, name=None, module_execs=None):
+ self.__db_id = id
+ self.__db_user = user
+ self.__db_ip = ip
+ self.__db_vt_version = vt_version
+ self.__db_ts_start = ts_start
+ self.__db_ts_end = ts_end
+ self.__db_parent_id = parent_id
+ self.__db_parent_type = parent_type
+ self.__db_parent_version = parent_version
+ self.__db_name = name
+ self.db_module_execs_id_index = {}
+ if module_execs is None:
+ self.__db_module_execs = []
+ else:
+ self.__db_module_execs = module_execs
+ for v in self.__db_module_execs:
+ self.db_module_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBWorkflowExec()
+ cp.db_id = self.db_id
+ cp.db_user = self.db_user
+ cp.db_ip = self.db_ip
+ cp.db_vt_version = self.db_vt_version
+ cp.db_ts_start = self.db_ts_start
+ cp.db_ts_end = self.db_ts_end
+ cp.db_parent_id = self.db_parent_id
+ cp.db_parent_type = self.db_parent_type
+ cp.db_parent_version = self.db_parent_version
+ cp.db_name = self.db_name
+ if self.db_module_execs is None:
+ cp.db_module_execs = None
+ else:
+ cp.db_module_execs = [copy.copy(v) for v in self.db_module_execs]
+ for v in cp.__db_module_execs:
+ cp.db_module_execs_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec()
+ cp.db_id = self.db_id
+ cp.db_user = self.db_user
+ cp.db_ip = self.db_ip
+ cp.db_vt_version = self.db_vt_version
+ cp.db_ts_start = self.db_ts_start
+ cp.db_ts_end = self.db_ts_end
+ cp.db_parent_id = self.db_parent_id
+ cp.db_parent_type = self.db_parent_type
+ cp.db_parent_version = self.db_parent_version
+ cp.db_name = self.db_name
+ if self.db_module_execs is None:
+ cp.db_module_execs = []
+ else:
+ cp.db_module_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_module_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_module_execs:
+ cp.db_module_execs_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_module_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_user(self):
+ return self.__db_user
+ def __set_db_user(self, user):
+ self.__db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self.__db_user = user
+ def db_change_user(self, user):
+ self.__db_user = user
+ def db_delete_user(self, user):
+ self.__db_user = None
+
+ def __get_db_ip(self):
+ return self.__db_ip
+ def __set_db_ip(self, ip):
+ self.__db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self.__db_ip = ip
+ def db_change_ip(self, ip):
+ self.__db_ip = ip
+ def db_delete_ip(self, ip):
+ self.__db_ip = None
+
+ def __get_db_vt_version(self):
+ return self.__db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self.__db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self.__db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self.__db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self.__db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self.__db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self.__db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self.__db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self.__db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self.__db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self.__db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self.__db_parent_version = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_module_execs(self):
+ return self.__db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self.__db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self.__db_module_execs
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self.__db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ self.__db_module_execs[i] = module_exec
+ found = True
+ break
+ if not found:
+ self.__db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ del self.__db_module_execs[i]
+ break
+ del self.db_module_execs_id_index[module_exec.db_id]
+ def db_get_module_exec(self, key):
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == key:
+ return self.__db_module_execs[i]
+ return None
+ def db_get_module_exec_by_id(self, key):
+ return self.db_module_execs_id_index[key]
+ def db_has_module_exec_with_id(self, key):
+ return self.db_module_execs_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self.__db_id = id
+ self.__db_pos = pos
+ self.__db_name = name
+ self.db_parameters_id_index = {}
+ if parameters is None:
+ self.__db_parameters = []
+ else:
+ self.__db_parameters = parameters
+ for v in self.__db_parameters:
+ self.db_parameters_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBFunction()
+ cp.db_id = self.db_id
+ cp.db_pos = self.db_pos
+ cp.db_name = self.db_name
+ if self.db_parameters is None:
+ cp.db_parameters = None
+ else:
+ cp.db_parameters = [copy.copy(v) for v in self.db_parameters]
+ for v in cp.__db_parameters:
+ cp.db_parameters_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction()
+ cp.db_id = self.db_id
+ cp.db_pos = self.db_pos
+ cp.db_name = self.db_name
+ if self.db_parameters is None:
+ cp.db_parameters = []
+ else:
+ cp.db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_parameters:
+ cp.db_parameters_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_pos(self):
+ return self.__db_pos
+ def __set_db_pos(self, pos):
+ self.__db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self.__db_pos = pos
+ def db_change_pos(self, pos):
+ self.__db_pos = pos
+ def db_delete_pos(self, pos):
+ self.__db_pos = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_parameters(self):
+ return self.__db_parameters
+ def __set_db_parameters(self, parameters):
+ self.__db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self.__db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self.__db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == parameter.db_id:
+ self.__db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self.__db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == parameter.db_id:
+ del self.__db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter.db_id]
+ def db_get_parameter(self, key):
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == key:
+ return self.__db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return self.db_parameters_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, name=None, actions=None, tags=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.db_actions_id_index = {}
+ if actions is None:
+ self.__db_actions = []
+ else:
+ self.__db_actions = actions
+ for v in self.__db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self.__db_tags = []
+ else:
+ self.__db_tags = tags
+ for v in self.__db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBAbstraction()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ if self.db_actions is None:
+ cp.db_actions = None
+ else:
+ cp.db_actions = [copy.copy(v) for v in self.db_actions]
+ for v in cp.__db_actions:
+ cp.db_actions_id_index[v.db_id] = v
+ if self.db_tags is None:
+ cp.db_tags = None
+ else:
+ cp.db_tags = [copy.copy(v) for v in self.db_tags]
+ for v in cp.__db_tags:
+ cp.db_tags_id_index[v.db_id] = v
+ cp.db_tags_name_index[v.db_name] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ if self.db_actions is None:
+ cp.db_actions = []
+ else:
+ cp.db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_actions]
+ if self.db_tags is None:
+ cp.db_tags = []
+ else:
+ cp.db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_tags]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp.__db_actions:
+ cp.db_actions_id_index[v.db_id] = v
+ for v in cp.__db_tags:
+ cp.db_tags_id_index[v.db_id] = v
+ cp.db_tags_name_index[v.db_name] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_actions:
+ if child.has_changes():
+ return True
+ for child in self.db_tags:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_actions(self):
+ return self.__db_actions
+ def __set_db_actions(self, actions):
+ self.__db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self.__db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ self.__db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ del self.__db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == key:
+ return self.__db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return self.db_actions_id_index.has_key(key)
+
+ def __get_db_tags(self):
+ return self.__db_tags
+ def __set_db_tags(self, tags):
+ self.__db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self.__db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ self.__db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ del self.__db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == key:
+ return self.__db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return self.db_tags_id_index.has_key(key)
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return self.db_tags_name_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, id=None, name=None, modules=None, connections=None, annotations=None, others=None, abstractionRefs=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.db_modules_id_index = {}
+ if modules is None:
+ self.__db_modules = []
+ else:
+ self.__db_modules = modules
+ for v in self.__db_modules:
+ self.db_modules_id_index[v.db_id] = v
+ self.db_connections_id_index = {}
+ if connections is None:
+ self.__db_connections = []
+ else:
+ self.__db_connections = connections
+ for v in self.__db_connections:
+ self.db_connections_id_index[v.db_id] = v
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_others_id_index = {}
+ if others is None:
+ self.__db_others = []
+ else:
+ self.__db_others = others
+ for v in self.__db_others:
+ self.db_others_id_index[v.db_id] = v
+ self.db_abstractionRefs_id_index = {}
+ if abstractionRefs is None:
+ self.__db_abstractionRefs = []
+ else:
+ self.__db_abstractionRefs = abstractionRefs
+ for v in self.__db_abstractionRefs:
+ self.db_abstractionRefs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBWorkflow()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ if self.db_modules is None:
+ cp.db_modules = None
+ else:
+ cp.db_modules = [copy.copy(v) for v in self.db_modules]
+ for v in cp.__db_modules:
+ cp.db_modules_id_index[v.db_id] = v
+ if self.db_connections is None:
+ cp.db_connections = None
+ else:
+ cp.db_connections = [copy.copy(v) for v in self.db_connections]
+ for v in cp.__db_connections:
+ cp.db_connections_id_index[v.db_id] = v
+ if self.db_annotations is None:
+ cp.db_annotations = None
+ else:
+ cp.db_annotations = [copy.copy(v) for v in self.db_annotations]
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ if self.db_others is None:
+ cp.db_others = None
+ else:
+ cp.db_others = [copy.copy(v) for v in self.db_others]
+ for v in cp.__db_others:
+ cp.db_others_id_index[v.db_id] = v
+ if self.db_abstractionRefs is None:
+ cp.db_abstractionRefs = None
+ else:
+ cp.db_abstractionRefs = [copy.copy(v) for v in self.db_abstractionRefs]
+ for v in cp.__db_abstractionRefs:
+ cp.db_abstractionRefs_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ if self.db_modules is None:
+ cp.db_modules = []
+ else:
+ cp.db_modules = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_modules]
+ if self.db_connections is None:
+ cp.db_connections = []
+ else:
+ cp.db_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_connections]
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+ if self.db_others is None:
+ cp.db_others = []
+ else:
+ cp.db_others = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_others]
+ if self.db_abstractionRefs is None:
+ cp.db_abstractionRefs = []
+ else:
+ cp.db_abstractionRefs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_abstractionRefs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_modules:
+ cp.db_modules_id_index[v.db_id] = v
+ for v in cp.__db_connections:
+ cp.db_connections_id_index[v.db_id] = v
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ for v in cp.__db_others:
+ cp.db_others_id_index[v.db_id] = v
+ for v in cp.__db_abstractionRefs:
+ cp.db_abstractionRefs_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_modules:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module(child)
+ to_del = []
+ for child in self.db_connections:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_connection(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_other(child)
+ to_del = []
+ for child in self.db_abstractionRefs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_abstractionRef(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_modules:
+ if child.has_changes():
+ return True
+ for child in self.db_connections:
+ if child.has_changes():
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ for child in self.db_others:
+ if child.has_changes():
+ return True
+ for child in self.db_abstractionRefs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_modules(self):
+ return self.__db_modules
+ def __set_db_modules(self, modules):
+ self.__db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self.__db_modules
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self.__db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_modules)):
+ if self.__db_modules[i].db_id == module.db_id:
+ self.__db_modules[i] = module
+ found = True
+ break
+ if not found:
+ self.__db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_modules)):
+ if self.__db_modules[i].db_id == module.db_id:
+ del self.__db_modules[i]
+ break
+ del self.db_modules_id_index[module.db_id]
+ def db_get_module(self, key):
+ for i in xrange(len(self.__db_modules)):
+ if self.__db_modules[i].db_id == key:
+ return self.__db_modules[i]
+ return None
+ def db_get_module_by_id(self, key):
+ return self.db_modules_id_index[key]
+ def db_has_module_with_id(self, key):
+ return self.db_modules_id_index.has_key(key)
+
+ def __get_db_connections(self):
+ return self.__db_connections
+ def __set_db_connections(self, connections):
+ self.__db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self.__db_connections
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self.__db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_connections)):
+ if self.__db_connections[i].db_id == connection.db_id:
+ self.__db_connections[i] = connection
+ found = True
+ break
+ if not found:
+ self.__db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_connections)):
+ if self.__db_connections[i].db_id == connection.db_id:
+ del self.__db_connections[i]
+ break
+ del self.db_connections_id_index[connection.db_id]
+ def db_get_connection(self, key):
+ for i in xrange(len(self.__db_connections)):
+ if self.__db_connections[i].db_id == key:
+ return self.__db_connections[i]
+ return None
+ def db_get_connection_by_id(self, key):
+ return self.db_connections_id_index[key]
+ def db_has_connection_with_id(self, key):
+ return self.db_connections_id_index.has_key(key)
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+
+ def __get_db_others(self):
+ return self.__db_others
+ def __set_db_others(self, others):
+ self.__db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self.__db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self.__db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == other.db_id:
+ self.__db_others[i] = other
+ found = True
+ break
+ if not found:
+ self.__db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == other.db_id:
+ del self.__db_others[i]
+ break
+ del self.db_others_id_index[other.db_id]
+ def db_get_other(self, key):
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == key:
+ return self.__db_others[i]
+ return None
+ def db_get_other_by_id(self, key):
+ return self.db_others_id_index[key]
+ def db_has_other_with_id(self, key):
+ return self.db_others_id_index.has_key(key)
+
+ def __get_db_abstractionRefs(self):
+ return self.__db_abstractionRefs
+ def __set_db_abstractionRefs(self, abstractionRefs):
+ self.__db_abstractionRefs = abstractionRefs
+ self.is_dirty = True
+ db_abstractionRefs = property(__get_db_abstractionRefs, __set_db_abstractionRefs)
+ def db_get_abstractionRefs(self):
+ return self.__db_abstractionRefs
+ def db_add_abstractionRef(self, abstractionRef):
+ self.is_dirty = True
+ self.__db_abstractionRefs.append(abstractionRef)
+ self.db_abstractionRefs_id_index[abstractionRef.db_id] = abstractionRef
+ def db_change_abstractionRef(self, abstractionRef):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_abstractionRefs)):
+ if self.__db_abstractionRefs[i].db_id == abstractionRef.db_id:
+ self.__db_abstractionRefs[i] = abstractionRef
+ found = True
+ break
+ if not found:
+ self.__db_abstractionRefs.append(abstractionRef)
+ self.db_abstractionRefs_id_index[abstractionRef.db_id] = abstractionRef
+ def db_delete_abstractionRef(self, abstractionRef):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_abstractionRefs)):
+ if self.__db_abstractionRefs[i].db_id == abstractionRef.db_id:
+ del self.__db_abstractionRefs[i]
+ break
+ del self.db_abstractionRefs_id_index[abstractionRef.db_id]
+ def db_get_abstractionRef(self, key):
+ for i in xrange(len(self.__db_abstractionRefs)):
+ if self.__db_abstractionRefs[i].db_id == key:
+ return self.__db_abstractionRefs[i]
+ return None
+ def db_get_abstractionRef_by_id(self, key):
+ return self.db_abstractionRefs_id_index[key]
+ def db_has_abstractionRef_with_id(self, key):
+ return self.db_abstractionRefs_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAbstractionRef(object):
+
+ vtType = 'abstractionRef'
+
+ def __init__(self, id=None, abstraction_id=None, version=None, location=None):
+ self.__db_id = id
+ self.__db_abstraction_id = abstraction_id
+ self.__db_version = version
+ self.__db_location = location
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBAbstractionRef()
+ cp.db_id = self.db_id
+ cp.db_abstraction_id = self.db_abstraction_id
+ cp.db_version = self.db_version
+ cp.db_location = self.db_location
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstractionRef()
+ cp.db_id = self.db_id
+ cp.db_abstraction_id = self.db_abstraction_id
+ cp.db_version = self.db_version
+ if self.db_location is not None:
+ cp.db_location = self.db_location.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_location is not None:
+ children.extend(self.db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_location = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_location is not None and self.db_location.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_abstraction_id(self):
+ return self.__db_abstraction_id
+ def __set_db_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ self.is_dirty = True
+ db_abstraction_id = property(__get_db_abstraction_id, __set_db_abstraction_id)
+ def db_add_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ def db_change_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ def db_delete_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_location(self):
+ return self.__db_location
+ def __set_db_location(self, location):
+ self.__db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self.__db_location = location
+ def db_change_location(self, location):
+ self.__db_location = location
+ def db_delete_location(self, location):
+ self.__db_location = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self.__db_id = id
+ self.__db_key = key
+ self.__db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBAnnotation()
+ cp.db_id = self.db_id
+ cp.db_key = self.db_key
+ cp.db_value = self.db_value
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation()
+ cp.db_id = self.db_id
+ cp.db_key = self.db_key
+ cp.db_value = self.db_value
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None, data=None):
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_oldObjId = oldObjId
+ self.__db_newObjId = newObjId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.__db_data = data
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBChange()
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_oldObjId = self.db_oldObjId
+ cp.db_newObjId = self.db_newObjId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+ cp.db_data = self.db_data
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange()
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_oldObjId = self.db_oldObjId
+ cp.db_newObjId = self.db_newObjId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+ if self.db_data is not None:
+ cp.db_data = self.db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_oldObjId') and id_remap.has_key((self.db_what, self.db_oldObjId)):
+ cp.db_oldObjId = id_remap[(self.db_what, self.db_oldObjId)]
+ if hasattr(self, 'db_newObjId') and id_remap.has_key((self.db_what, self.db_newObjId)):
+ cp.db_newObjId = id_remap[(self.db_what, self.db_newObjId)]
+ if hasattr(self, 'db_parentObjId') and id_remap.has_key((self.db_parentObjType, self.db_parentObjId)):
+ cp.db_parentObjId = id_remap[(self.db_parentObjType, self.db_parentObjId)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_data is not None:
+ children.extend(self.db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_data is not None and self.db_data.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_oldObjId(self):
+ return self.__db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self.__db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self.__db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self.__db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def __get_db_data(self):
+ return self.__db_data
+ def __set_db_data(self, data):
+ self.__db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self.__db_data = data
+ def db_change_data(self, data):
+ self.__db_data = data
+ def db_delete_data(self, data):
+ self.__db_data = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self.__db_id = id
+ self.__db_pos = pos
+ self.__db_name = name
+ self.__db_type = type
+ self.__db_val = val
+ self.__db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBParameter()
+ cp.db_id = self.db_id
+ cp.db_pos = self.db_pos
+ cp.db_name = self.db_name
+ cp.db_type = self.db_type
+ cp.db_val = self.db_val
+ cp.db_alias = self.db_alias
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter()
+ cp.db_id = self.db_id
+ cp.db_pos = self.db_pos
+ cp.db_name = self.db_name
+ cp.db_type = self.db_type
+ cp.db_val = self.db_val
+ cp.db_alias = self.db_alias
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_pos(self):
+ return self.__db_pos
+ def __set_db_pos(self, pos):
+ self.__db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self.__db_pos = pos
+ def db_change_pos(self, pos):
+ self.__db_pos = pos
+ def db_delete_pos(self, pos):
+ self.__db_pos = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_val(self):
+ return self.__db_val
+ def __set_db_val(self, val):
+ self.__db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self.__db_val = val
+ def db_change_val(self, val):
+ self.__db_val = val
+ def db_delete_val(self, val):
+ self.__db_val = None
+
+ def __get_db_alias(self):
+ return self.__db_alias
+ def __set_db_alias(self, alias):
+ self.__db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self.__db_alias = alias
+ def db_change_alias(self, alias):
+ self.__db_alias = alias
+ def db_delete_alias(self, alias):
+ self.__db_alias = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self.__db_id = id
+ self.db_ports_id_index = {}
+ self.db_ports_type_index = {}
+ if ports is None:
+ self.__db_ports = []
+ else:
+ self.__db_ports = ports
+ for v in self.__db_ports:
+ self.db_ports_id_index[v.db_id] = v
+ self.db_ports_type_index[v.db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBConnection()
+ cp.db_id = self.db_id
+ if self.db_ports is None:
+ cp.db_ports = None
+ else:
+ cp.db_ports = [copy.copy(v) for v in self.db_ports]
+ for v in cp.__db_ports:
+ cp.db_ports_id_index[v.db_id] = v
+ cp.db_ports_type_index[v.db_type] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection()
+ cp.db_id = self.db_id
+ if self.db_ports is None:
+ cp.db_ports = []
+ else:
+ cp.db_ports = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_ports]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_ports:
+ cp.db_ports_id_index[v.db_id] = v
+ cp.db_ports_type_index[v.db_type] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_ports(self):
+ return self.__db_ports
+ def __set_db_ports(self, ports):
+ self.__db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self.__db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self.__db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == port.db_id:
+ self.__db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self.__db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == port.db_id:
+ del self.__db_ports[i]
+ break
+ del self.db_ports_id_index[port.db_id]
+ del self.db_ports_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == key:
+ return self.__db_ports[i]
+ return None
+ def db_get_port_by_id(self, key):
+ return self.db_ports_id_index[key]
+ def db_has_port_with_id(self, key):
+ return self.db_ports_id_index.has_key(key)
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return self.db_ports_type_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, id=None, prevId=None, date=None, session=None, user=None, prune=None, annotations=None, operations=None):
+ self.__db_id = id
+ self.__db_prevId = prevId
+ self.__db_date = date
+ self.__db_session = session
+ self.__db_user = user
+ self.__db_prune = prune
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_operations_id_index = {}
+ if operations is None:
+ self.__db_operations = []
+ else:
+ self.__db_operations = operations
+ for v in self.__db_operations:
+ self.db_operations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBAction()
+ cp.db_id = self.db_id
+ cp.db_prevId = self.db_prevId
+ cp.db_date = self.db_date
+ cp.db_session = self.db_session
+ cp.db_user = self.db_user
+ cp.db_prune = self.db_prune
+ if self.db_annotations is None:
+ cp.db_annotations = None
+ else:
+ cp.db_annotations = [copy.copy(v) for v in self.db_annotations]
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.db_annotations_key_index[v.db_key] = v
+ if self.db_operations is None:
+ cp.db_operations = None
+ else:
+ cp.db_operations = [copy.copy(v) for v in self.db_operations]
+ for v in cp.__db_operations:
+ cp.db_operations_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction()
+ cp.db_id = self.db_id
+ cp.db_prevId = self.db_prevId
+ cp.db_date = self.db_date
+ cp.db_session = self.db_session
+ cp.db_user = self.db_user
+ cp.db_prune = self.db_prune
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+ if self.db_operations is None:
+ cp.db_operations = []
+ else:
+ cp.db_operations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_operations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.db_annotations_key_index[v.db_key] = v
+ for v in cp.__db_operations:
+ cp.db_operations_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_operations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ for child in self.db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_prevId(self):
+ return self.__db_prevId
+ def __set_db_prevId(self, prevId):
+ self.__db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self.__db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self.__db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self.__db_prevId = None
+
+ def __get_db_date(self):
+ return self.__db_date
+ def __set_db_date(self, date):
+ self.__db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self.__db_date = date
+ def db_change_date(self, date):
+ self.__db_date = date
+ def db_delete_date(self, date):
+ self.__db_date = None
+
+ def __get_db_session(self):
+ return self.__db_session
+ def __set_db_session(self, session):
+ self.__db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self.__db_session = session
+ def db_change_session(self, session):
+ self.__db_session = session
+ def db_delete_session(self, session):
+ self.__db_session = None
+
+ def __get_db_user(self):
+ return self.__db_user
+ def __set_db_user(self, user):
+ self.__db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self.__db_user = user
+ def db_change_user(self, user):
+ self.__db_user = user
+ def db_delete_user(self, user):
+ self.__db_user = None
+
+ def __get_db_prune(self):
+ return self.__db_prune
+ def __set_db_prune(self, prune):
+ self.__db_prune = prune
+ self.is_dirty = True
+ db_prune = property(__get_db_prune, __set_db_prune)
+ def db_add_prune(self, prune):
+ self.__db_prune = prune
+ def db_change_prune(self, prune):
+ self.__db_prune = prune
+ def db_delete_prune(self, prune):
+ self.__db_prune = None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return self.db_annotations_key_index.has_key(key)
+
+ def __get_db_operations(self):
+ return self.__db_operations
+ def __set_db_operations(self, operations):
+ self.__db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self.__db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self.__db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == operation.db_id:
+ self.__db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self.__db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == operation.db_id:
+ del self.__db_operations[i]
+ break
+ del self.db_operations_id_index[operation.db_id]
+ def db_get_operation(self, key):
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == key:
+ return self.__db_operations[i]
+ return None
+ def db_get_operation_by_id(self, key):
+ return self.db_operations_id_index[key]
+ def db_has_operation_with_id(self, key):
+ return self.db_operations_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_objectId = objectId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBDelete()
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_objectId = self.db_objectId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete()
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_objectId = self.db_objectId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and id_remap.has_key((self.db_what, self.db_objectId)):
+ cp.db_objectId = id_remap[(self.db_what, self.db_objectId)]
+ if hasattr(self, 'db_parentObjId') and id_remap.has_key((self.db_parentObjType, self.db_parentObjId)):
+ cp.db_parentObjId = id_remap[(self.db_parentObjType, self.db_parentObjId)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_objectId(self):
+ return self.__db_objectId
+ def __set_db_objectId(self, objectId):
+ self.__db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self.__db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, version=None, name=None, dbHost=None, dbPort=None, dbName=None, actions=None, tags=None, abstractions=None):
+ self.__db_id = id
+ self.__db_version = version
+ self.__db_name = name
+ self.__db_dbHost = dbHost
+ self.__db_dbPort = dbPort
+ self.__db_dbName = dbName
+ self.db_actions_id_index = {}
+ if actions is None:
+ self.__db_actions = []
+ else:
+ self.__db_actions = actions
+ for v in self.__db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self.__db_tags = []
+ else:
+ self.__db_tags = tags
+ for v in self.__db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.db_abstractions_id_index = {}
+ if abstractions is None:
+ self.__db_abstractions = []
+ else:
+ self.__db_abstractions = abstractions
+ for v in self.__db_abstractions:
+ self.db_abstractions_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBVistrail()
+ cp.db_id = self.db_id
+ cp.db_version = self.db_version
+ cp.db_name = self.db_name
+ cp.db_dbHost = self.db_dbHost
+ cp.db_dbPort = self.db_dbPort
+ cp.db_dbName = self.db_dbName
+ if self.db_actions is None:
+ cp.db_actions = None
+ else:
+ cp.db_actions = [copy.copy(v) for v in self.db_actions]
+ for v in cp.__db_actions:
+ cp.db_actions_id_index[v.db_id] = v
+ if self.db_tags is None:
+ cp.db_tags = None
+ else:
+ cp.db_tags = [copy.copy(v) for v in self.db_tags]
+ for v in cp.__db_tags:
+ cp.db_tags_id_index[v.db_id] = v
+ cp.db_tags_name_index[v.db_name] = v
+ if self.db_abstractions is None:
+ cp.db_abstractions = None
+ else:
+ cp.db_abstractions = [copy.copy(v) for v in self.db_abstractions]
+ for v in cp.__db_abstractions:
+ cp.db_abstractions_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail()
+ cp.db_id = self.db_id
+ cp.db_version = self.db_version
+ cp.db_name = self.db_name
+ cp.db_dbHost = self.db_dbHost
+ cp.db_dbPort = self.db_dbPort
+ cp.db_dbName = self.db_dbName
+ if self.db_actions is None:
+ cp.db_actions = []
+ else:
+ cp.db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_actions]
+ if self.db_tags is None:
+ cp.db_tags = []
+ else:
+ cp.db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_tags]
+ if self.db_abstractions is None:
+ cp.db_abstractions = []
+ else:
+ cp.db_abstractions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_abstractions]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp.__db_actions:
+ cp.db_actions_id_index[v.db_id] = v
+ for v in cp.__db_tags:
+ cp.db_tags_id_index[v.db_id] = v
+ cp.db_tags_name_index[v.db_name] = v
+ for v in cp.__db_abstractions:
+ cp.db_abstractions_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self.db_abstractions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_abstraction(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_actions:
+ if child.has_changes():
+ return True
+ for child in self.db_tags:
+ if child.has_changes():
+ return True
+ for child in self.db_abstractions:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_dbHost(self):
+ return self.__db_dbHost
+ def __set_db_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ self.is_dirty = True
+ db_dbHost = property(__get_db_dbHost, __set_db_dbHost)
+ def db_add_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ def db_change_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ def db_delete_dbHost(self, dbHost):
+ self.__db_dbHost = None
+
+ def __get_db_dbPort(self):
+ return self.__db_dbPort
+ def __set_db_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ self.is_dirty = True
+ db_dbPort = property(__get_db_dbPort, __set_db_dbPort)
+ def db_add_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ def db_change_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ def db_delete_dbPort(self, dbPort):
+ self.__db_dbPort = None
+
+ def __get_db_dbName(self):
+ return self.__db_dbName
+ def __set_db_dbName(self, dbName):
+ self.__db_dbName = dbName
+ self.is_dirty = True
+ db_dbName = property(__get_db_dbName, __set_db_dbName)
+ def db_add_dbName(self, dbName):
+ self.__db_dbName = dbName
+ def db_change_dbName(self, dbName):
+ self.__db_dbName = dbName
+ def db_delete_dbName(self, dbName):
+ self.__db_dbName = None
+
+ def __get_db_actions(self):
+ return self.__db_actions
+ def __set_db_actions(self, actions):
+ self.__db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self.__db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ self.__db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ del self.__db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == key:
+ return self.__db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return self.db_actions_id_index.has_key(key)
+
+ def __get_db_tags(self):
+ return self.__db_tags
+ def __set_db_tags(self, tags):
+ self.__db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self.__db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ self.__db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ del self.__db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == key:
+ return self.__db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return self.db_tags_id_index.has_key(key)
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return self.db_tags_name_index.has_key(key)
+
+ def __get_db_abstractions(self):
+ return self.__db_abstractions
+ def __set_db_abstractions(self, abstractions):
+ self.__db_abstractions = abstractions
+ self.is_dirty = True
+ db_abstractions = property(__get_db_abstractions, __set_db_abstractions)
+ def db_get_abstractions(self):
+ return self.__db_abstractions
+ def db_add_abstraction(self, abstraction):
+ self.is_dirty = True
+ self.__db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_change_abstraction(self, abstraction):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == abstraction.db_id:
+ self.__db_abstractions[i] = abstraction
+ found = True
+ break
+ if not found:
+ self.__db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_delete_abstraction(self, abstraction):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == abstraction.db_id:
+ del self.__db_abstractions[i]
+ break
+ del self.db_abstractions_id_index[abstraction.db_id]
+ def db_get_abstraction(self, key):
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == key:
+ return self.__db_abstractions[i]
+ return None
+ def db_get_abstraction_by_id(self, key):
+ return self.db_abstractions_id_index[key]
+ def db_has_abstraction_with_id(self, key):
+ return self.db_abstractions_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, module_id=None, module_name=None, annotations=None):
+ self.__db_id = id
+ self.__db_ts_start = ts_start
+ self.__db_ts_end = ts_end
+ self.__db_module_id = module_id
+ self.__db_module_name = module_name
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ cp = DBModuleExec()
+ cp.db_id = self.db_id
+ cp.db_ts_start = self.db_ts_start
+ cp.db_ts_end = self.db_ts_end
+ cp.db_module_id = self.db_module_id
+ cp.db_module_name = self.db_module_name
+ if self.db_annotations is None:
+ cp.db_annotations = None
+ else:
+ cp.db_annotations = [copy.copy(v) for v in self.db_annotations]
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec()
+ cp.db_id = self.db_id
+ cp.db_ts_start = self.db_ts_start
+ cp.db_ts_end = self.db_ts_end
+ cp.db_module_id = self.db_module_id
+ cp.db_module_name = self.db_module_name
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and id_remap.has_key(('module', self.db_module_id)):
+ cp.db_module_id = id_remap[('module', self.db_module_id)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_ts_start(self):
+ return self.__db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self.__db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self.__db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self.__db_ts_end = None
+
+ def __get_db_module_id(self):
+ return self.__db_module_id
+ def __set_db_module_id(self, module_id):
+ self.__db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self.__db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self.__db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self.__db_module_id = None
+
+ def __get_db_module_name(self):
+ return self.__db_module_name
+ def __set_db_module_name(self, module_name):
+ self.__db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self.__db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self.__db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self.__db_module_name = None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
diff --git a/vistrails/db/versions/v0_7_0/domain/id_scope.py b/vistrails/db/versions/v0_7_0/domain/id_scope.py
new file mode 100644
index 0000000..c510efa
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/domain/id_scope.py
@@ -0,0 +1,76 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L, remap=None):
+ self.ids = {}
+ self.beginId = beginId
+ if remap is None:
+ self.remap = {}
+ else:
+ self.remap = remap
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ cp.remap = copy.copy(self.remap)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ if self.remap.has_key(objType):
+ objType = self.remap[objType]
+ if self.ids.has_key(objType):
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ else:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ if self.remap.has_key(objType):
+ objType = self.remap[objType]
+ if not self.ids.has_key(objType) or self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ if self.remap.has_key(objType):
+ objType = self.remap[objType]
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v0_7_0/domain/vistrail.py b/vistrails/db/versions/v0_7_0/domain/vistrail.py
new file mode 100644
index 0000000..4fdb6e2
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/domain/vistrail.py
@@ -0,0 +1,46 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBVistrail as _DBVistrail
+from auto_gen import DBAdd, DBChange, DBDelete
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAdd.vtType: 'operation',
+ DBChange.vtType: 'operation',
+ DBDelete.vtType: 'operation'})
+ self.idScope.setBeginId('action', 1)
diff --git a/vistrails/db/versions/v0_7_0/domain/workflow.py b/vistrails/db/versions/v0_7_0/domain/workflow.py
new file mode 100644
index 0000000..20dacf1
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/domain/workflow.py
@@ -0,0 +1,122 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1)
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.objects = {}
+ for (child, _, _) in cp.db_children():
+ cp.addToIndex(child)
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ def addToIndex(self, object):
+ self.objects[(object.vtType, object.getPrimaryKey())] = object
+
+ def deleteFromIndex(self, object):
+ del self.objects[(object.vtType, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_get_object(self, type, id):
+ return self.objects[(type, id)]
+
+ def db_add_object(self, object, parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_add_%s' % object.vtType
+ objCopy = copy.copy(object)
+ getattr(parentObj, funname)(objCopy)
+ self.addToIndex(objCopy)
+
+ def db_change_object(self, object, parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_change_%s' % object.vtType
+ objCopy = copy.copy(object)
+ getattr(parentObj, funname)(objCopy)
+ self.addToIndex(objCopy)
+
+ def db_delete_object(self, objId, objType,
+ parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_get_%s' % objType
+ try:
+ object = getattr(parentObj, funname)(objId)
+ except AttributeError:
+ attr_name = 'db_%s' % objType
+ object = getattr(parentObj, attr_name)
+ funname = 'db_delete_%s' % objType
+ getattr(parentObj, funname)(object)
+ self.deleteFromIndex(object)
diff --git a/vistrails/db/versions/v0_7_0/persistence/__init__.py b/vistrails/db/versions/v0_7_0/persistence/__init__.py
new file mode 100644
index 0000000..0a10c9d
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/persistence/__init__.py
@@ -0,0 +1,55 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+import xml.io
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ return xml.io.open_from_xml(filename, vtType, self['xml'])
+
+ def save_to_xml(self, obj, filename):
+ xml.io.save_to_xml(obj, filename, self['xml'])
+
+ def serialize(self, obj):
+ return xml.io.serialize(obj, self['xml'])
+
+ def unserialize(self, str, type):
+ return xml.io.unserialize(str, type, self['xml'])
diff --git a/vistrails/db/versions/v0_7_0/persistence/sql/__init__.py b/vistrails/db/versions/v0_7_0/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_7_0/persistence/sql/auto_gen.py b/vistrails/db/versions/v0_7_0/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..9b987f0
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/persistence/sql/auto_gen.py
@@ -0,0 +1,4104 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v0_7_0.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(22)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[4], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[5], 'long', 'int')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ spec=spec,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_vistrailId = vistrailId
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(22)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'type', 'spec', 'id']
+ table = 'port_spec'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(22)')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[3], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ portSpec = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ spec=spec)
+ portSpec.is_dirty = False
+ list.append(portSpec)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'port_spec'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(22)')
+ if obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'cache', 'abstraction', 'name', 'package', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ abstraction = self.convertFromDB(row[2], 'long', 'int')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ abstraction=abstraction,
+ name=name,
+ package=package,
+ version=version,
+ id=id)
+ module.db_parentType = parentType
+ module.db_vistrailId = vistrailId
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'abstraction', 'name', 'package', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_abstraction') and obj.db_abstraction is not None:
+ columnMap['abstraction'] = \
+ self.convertToDB(obj.db_abstraction, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['cache', 'abstraction', 'name', 'package', 'version', 'id']
+ table = 'module'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ cache = self.convertFromDB(row[0], 'int', 'int')
+ abstraction = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[3], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('location').fromSQL(db, None, foreignKey, globalProps)
+ if len(res) > 0:
+ location = res[0]
+ else:
+ location = None
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('function').fromSQL(db, None, foreignKey, globalProps)
+ functions = res
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ annotations = res
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('portSpec').fromSQL(db, None, foreignKey, globalProps)
+ portSpecs = res
+
+ module = DBModule(id=id,
+ cache=cache,
+ abstraction=abstraction,
+ name=name,
+ package=package,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ module.is_dirty = False
+ list.append(module)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'module'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if obj.db_abstraction is not None:
+ columnMap['abstraction'] = \
+ self.convertToDB(obj.db_abstraction, 'long', 'int')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ child = obj.db_location
+ if child is not None:
+ self.getDao('location').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_functions:
+ self.getDao('function').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_annotations:
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('module','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_portSpecs:
+ self.getDao('portSpec').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[3], 'long', 'int')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_parentType = parentType
+ tag.db_vistrailId = vistrailId
+ tag.db_parent = parent
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_tag(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'tag'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'id']
+ table = 'tag'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[1], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ tag = DBTag(id=id,
+ name=name)
+ tag.is_dirty = False
+ list.append(tag)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'tag'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec,
+ id=id)
+ port.db_parentType = parentType
+ port.db_vistrailId = vistrailId
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['type', 'moduleId', 'moduleName', 'name', 'spec', 'id']
+ table = 'port'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ type = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[1], 'long', 'int')
+ moduleName = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[4], 'str', 'varchar(4095)')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ port = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec)
+ port.is_dirty = False
+ list.append(port)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'port'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(4095)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'vt_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ vistrailId = self.convertFromDB(row[1], 'long', 'int')
+
+ log = DBLog(id=id)
+ log.db_vistrailId = vistrailId
+ log.is_dirty = False
+ res[('log', id)] = log
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'vt_id']
+ table = 'log_tbl'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_workflow_execs:
+ child.db_log = obj.db_id
+ for child in obj.db_machines:
+ child.db_log = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['id']
+ table = 'log_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ foreignKey = {'log_id': keyStr}
+ res = self.getDao('workflow_exec').fromSQL(db, None, foreignKey, globalProps)
+ workflow_execs = res
+
+ foreignKey = {'log_id': keyStr}
+ res = self.getDao('machine').fromSQL(db, None, foreignKey, globalProps)
+ machines = res
+
+ log = DBLog(id=id,
+ workflow_execs=workflow_execs,
+ machines=machines)
+ log.is_dirty = False
+ list.append(log)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'log_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ foreignKey = {'log_id': keyStr}
+ for child in obj.db_workflow_execs:
+ self.getDao('workflow_exec').toSQL(db, child, foreignKey, globalProps)
+
+ foreignKey = {'log_id': keyStr}
+ for child in obj.db_machines:
+ self.getDao('machine').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'module_exec_id']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ module_execs = self.convertFromDB(row[8], 'long', 'int')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'module_exec_id']
+ table = 'machine'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_module_exec') and obj.db_module_exec is not None:
+ columnMap['module_exec_id'] = \
+ self.convertToDB(obj.db_module_execs, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_module_execs:
+ child.db_machine_id = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'os', 'architecture', 'processor', 'ram', 'id']
+ table = 'machine'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[4], 'int', 'int')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ foreignKey = {'machine_id': keyStr}
+ res = self.getDao('module_exec').fromSQL(db, None, foreignKey, globalProps)
+ module_execs = res
+
+ machine = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ module_execs=module_execs)
+ machine.is_dirty = False
+ list.append(machine)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'machine'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ foreignKey = {'machine_id': keyStr}
+ for child in obj.db_module_execs:
+ self.getDao('module_exec').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_vistrailId = vistrailId
+ add.is_dirty = False
+ res[('add', id)] = add
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'add_tbl'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['what', 'object_id', 'par_obj_id', 'par_obj_type', 'id']
+ table = 'add_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ what = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[1], 'long', 'int')
+ parentObjId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjType = self.convertFromDB(row[3], 'str', 'char(16)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ data = None
+ if what == 'module':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('module').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'location':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('location').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'annotation':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'function':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('function').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'connection':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('connection').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'port':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('port').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'parameter':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('parameter').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'portSpec':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('portSpec').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'abstractionRef':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('abstractionRef').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'other':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('other').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+
+ add = DBAdd(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ add.is_dirty = False
+ list.append(add)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'add_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ child = obj.db_data
+ if child.vtType == 'module':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('module').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'location':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('location').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'annotation':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'function':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('function').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'connection':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('connection').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'port':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('port').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'parameter':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('parameter').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'portSpec':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('portSpec').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'abstractionRef':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('abstractionRef').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'other':
+ discStr = self.convertToDB('add','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('other').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'okey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_vistrailId = vistrailId
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['okey', 'value', 'id']
+ table = 'other'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ key = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ other = DBOther(id=id,
+ key=key,
+ value=value)
+ other.is_dirty = False
+ list.append(other)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'other'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'x', 'y', 'parent_type', 'vt_id', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_vistrailId = vistrailId
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'vt_id', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['x', 'y', 'id']
+ table = 'location'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ x = self.convertFromDB(row[0], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ location = DBLocation(id=id,
+ x=x,
+ y=y)
+ location.is_dirty = False
+ list.append(location)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'location'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'log_id', 'vt_id']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ vt_version = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[4], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[5], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[6], 'long', 'int')
+ parent_type = self.convertFromDB(row[7], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[8], 'long', 'int')
+ name = self.convertFromDB(row[9], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[10], 'long', 'int')
+ vistrailId = self.convertFromDB(row[11], 'long', 'int')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_vistrailId = vistrailId
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'log_id', 'vt_id']
+ table = 'workflow_exec'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_module_execs:
+ child.db_workflow_exec = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'id']
+ table = 'workflow_exec'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ user = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vt_version = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[3], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[4], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[5], 'long', 'int')
+ parent_type = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[7], 'long', 'int')
+ name = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[9], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ foreignKey = {'wf_exec_id': keyStr}
+ res = self.getDao('module_exec').fromSQL(db, None, foreignKey, globalProps)
+ module_execs = res
+
+ workflow_exec = DBWorkflowExec(id=id,
+ user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ module_execs=module_execs)
+ workflow_exec.is_dirty = False
+ list.append(workflow_exec)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'workflow_exec'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ foreignKey = {'wf_exec_id': keyStr}
+ for child in obj.db_module_execs:
+ self.getDao('module_exec').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'pos', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_vistrailId = vistrailId
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['pos', 'name', 'id']
+ table = 'function'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ pos = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('function','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('parameter').fromSQL(db, None, foreignKey, globalProps)
+ parameters = res
+
+ function = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ function.is_dirty = False
+ list.append(function)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'function'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('function','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_parameters:
+ self.getDao('parameter').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'name', 'vt_id']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[2], 'long', 'int')
+
+ abstraction = DBAbstraction(name=name,
+ id=id)
+ abstraction.db_vistrail = vistrail
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_abstraction(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'vt_id']
+ table = 'abstraction'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_actions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'id']
+ table = 'abstraction'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[1], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('abstraction','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('action').fromSQL(db, None, foreignKey, globalProps)
+ actions = res
+
+ discStr = self.convertToDB('abstraction','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('tag').fromSQL(db, None, foreignKey, globalProps)
+ tags = res
+
+ abstraction = DBAbstraction(id=id,
+ name=name,
+ actions=actions,
+ tags=tags)
+ abstraction.is_dirty = False
+ list.append(abstraction)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'abstraction'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('abstraction','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_actions:
+ self.getDao('action').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('abstraction','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_tags:
+ self.getDao('tag').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'name', 'vt_id']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrailId = self.convertFromDB(row[2], 'long', 'int')
+
+ workflow = DBWorkflow(name=name,
+ id=id)
+ workflow.db_vistrailId = vistrailId
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'vt_id']
+ table = 'workflow'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_modules:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_connections:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_abstractionRefs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['name', 'id']
+ table = 'workflow'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[1], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('module').fromSQL(db, None, foreignKey, globalProps)
+ modules = res
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('connection').fromSQL(db, None, foreignKey, globalProps)
+ connections = res
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ annotations = res
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('other').fromSQL(db, None, foreignKey, globalProps)
+ others = res
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('abstractionRef').fromSQL(db, None, foreignKey, globalProps)
+ abstractionRefs = res
+
+ workflow = DBWorkflow(id=id,
+ name=name,
+ modules=modules,
+ connections=connections,
+ annotations=annotations,
+ others=others,
+ abstractionRefs=abstractionRefs)
+ workflow.is_dirty = False
+ list.append(workflow)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'workflow'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_modules:
+ self.getDao('module').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_connections:
+ self.getDao('connection').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_annotations:
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_others:
+ self.getDao('other').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('workflow','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_abstractionRefs:
+ self.getDao('abstractionRef').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBAbstractionRefSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'abstraction_id', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ abstraction_id = self.convertFromDB(row[1], 'long', 'int')
+ version = self.convertFromDB(row[2], 'long', 'int')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ abstractionRef = DBAbstractionRef(abstraction_id=abstraction_id,
+ version=version,
+ id=id)
+ abstractionRef.db_parentType = parentType
+ abstractionRef.db_vistrailId = vistrailId
+ abstractionRef.db_parent = parent
+ abstractionRef.is_dirty = False
+ res[('abstractionRef', id)] = abstractionRef
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_abstractionRef(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'abstraction_id', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_abstraction_id') and obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['abstraction_id', 'version', 'id']
+ table = 'abstraction_ref'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ abstraction_id = self.convertFromDB(row[0], 'long', 'int')
+ version = self.convertFromDB(row[1], 'long', 'int')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('abstractionRef','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('location').fromSQL(db, None, foreignKey, globalProps)
+ if len(res) > 0:
+ location = res[0]
+ else:
+ location = None
+
+ abstractionRef = DBAbstractionRef(id=id,
+ abstraction_id=abstraction_id,
+ version=version,
+ location=location)
+ abstractionRef.is_dirty = False
+ list.append(abstractionRef)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'abstraction_ref'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'long', 'int')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('abstractionRef','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ child = obj.db_location
+ if child is not None:
+ self.getDao('location').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'akey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_vistrailId = vistrailId
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['akey', 'value', 'id']
+ table = 'annotation'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ key = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[1], 'str', 'varchar(8191)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ annotation = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ annotation.is_dirty = False
+ list.append(annotation)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'annotation'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_vistrailId = vistrailId
+ change.is_dirty = False
+ res[('change', id)] = change
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'change_tbl'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'id']
+ table = 'change_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ what = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[1], 'long', 'int')
+ newObjId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ data = None
+ if what == 'module':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('module').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'location':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('location').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'annotation':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'function':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('function').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'connection':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('connection').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'port':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('port').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'parameter':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('parameter').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'portSpec':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('portSpec').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'abstractionRef':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('abstractionRef').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+ elif what == 'other':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('other').fromSQL(db, None, foreignKey, globalProps)
+ data = res[0]
+
+ change = DBChange(id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ change.is_dirty = False
+ list.append(change)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'change_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ child = obj.db_data
+ if child.vtType == 'module':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('module').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'location':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('location').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'annotation':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'function':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('function').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'connection':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('connection').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'port':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('port').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'parameter':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('parameter').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'portSpec':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('portSpec').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'abstractionRef':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('abstractionRef').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'other':
+ discStr = self.convertToDB('change','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ self.getDao('other').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'vt_id', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_vistrailId = vistrailId
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'vt_id', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['pos', 'name', 'type', 'val', 'alias', 'id']
+ table = 'parameter'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ pos = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[3], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ parameter = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ parameter.is_dirty = False
+ list.append(parameter)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'parameter'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'parent_type', 'vt_id', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[2], 'long', 'int')
+ parent = self.convertFromDB(row[3], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_vistrailId = vistrailId
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'vt_id', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['id']
+ table = 'connection_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('connection','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('port').fromSQL(db, None, foreignKey, globalProps)
+ ports = res
+
+ connection = DBConnection(id=id,
+ ports=ports)
+ connection.is_dirty = False
+ list.append(connection)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'connection_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('connection','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_ports:
+ self.getDao('port').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_type', 'vt_id', 'parent_id']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'str', 'varchar(1023)')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ prune = self.convertFromDB(row[5], 'int', 'int')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ id=id)
+ action.db_parentType = parentType
+ action.db_vistrailId = vistrailId
+ action.db_parent = parent
+ action.is_dirty = False
+ res[('action', id)] = action
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_action(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_type', 'vt_id', 'parent_id']
+ table = 'action'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_prune') and obj.db_prune is not None:
+ columnMap['prune'] = \
+ self.convertToDB(obj.db_prune, 'int', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['prev_id', 'date', 'session', 'user', 'prune', 'id']
+ table = 'action'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ prevId = self.convertFromDB(row[0], 'long', 'int')
+ date = self.convertFromDB(row[1], 'datetime', 'datetime')
+ session = self.convertFromDB(row[2], 'str', 'varchar(1023)')
+ user = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ prune = self.convertFromDB(row[4], 'int', 'int')
+ id = self.convertFromDB(row[5], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('action','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ annotations = res
+
+ operations = []
+
+ foreignKey = {'action_id': keyStr}
+ res = self.getDao('add').fromSQL(db, None, foreignKey, globalProps)
+ operations.extend(res)
+
+ foreignKey = {'action_id': keyStr}
+ res = self.getDao('delete').fromSQL(db, None, foreignKey, globalProps)
+ operations.extend(res)
+
+ foreignKey = {'action_id': keyStr}
+ res = self.getDao('change').fromSQL(db, None, foreignKey, globalProps)
+ operations.extend(res)
+
+ action = DBAction(id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ annotations=annotations,
+ operations=operations)
+ action.is_dirty = False
+ list.append(action)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'action'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'str', 'varchar(1023)')
+ if obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if obj.db_prune is not None:
+ columnMap['prune'] = \
+ self.convertToDB(obj.db_prune, 'int', 'int')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('action','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_annotations:
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+
+ for child in obj.db_operations:
+ if child.vtType == 'add':
+ foreignKey = {'action_id' : keyStr}
+ self.getDao('add').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'delete':
+ foreignKey = {'action_id' : keyStr}
+ self.getDao('delete').toSQL(db, child, foreignKey, globalProps)
+ elif child.vtType == 'change':
+ foreignKey = {'action_id' : keyStr}
+ self.getDao('change').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_vistrailId = vistrailId
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'delete_tbl'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['what', 'object_id', 'par_obj_id', 'par_obj_type', 'id']
+ table = 'delete_tbl'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ what = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[1], 'long', 'int')
+ parentObjId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjType = self.convertFromDB(row[3], 'str', 'char(16)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ delete = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ delete.is_dirty = False
+ list.append(delete)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'delete_tbl'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'version', 'name']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['vt_id'] = self.convertToDB(id, 'long', 'int')
+ version = self.convertFromDB(row[1], 'str', 'char(16)')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+
+ vistrail = DBVistrail(version=version,
+ name=name,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'version', 'name']
+ table = 'vistrail'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ global_props['vt_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_actions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_abstractions:
+ child.db_vistrail = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['version', 'name', 'id']
+ table = 'vistrail'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ version = self.convertFromDB(row[0], 'str', 'char(16)')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[2], 'long', 'int')
+ if globalProps is None:
+ globalProps = {}
+ globalProps['vt_id'] = self.convertToDB(id, 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('vistrail','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('action').fromSQL(db, None, foreignKey, globalProps)
+ actions = res
+
+ discStr = self.convertToDB('vistrail','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('tag').fromSQL(db, None, foreignKey, globalProps)
+ tags = res
+
+ foreignKey = {'vt_id': keyStr}
+ res = self.getDao('abstraction').fromSQL(db, None, foreignKey, globalProps)
+ abstractions = res
+
+ vistrail = DBVistrail(id=id,
+ version=version,
+ name=name,
+ actions=actions,
+ tags=tags,
+ abstractions=abstractions)
+ vistrail.is_dirty = False
+ list.append(vistrail)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'vistrail'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ if obj.db_id is not None:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if globalProps is None:
+ globalProps = {}
+ globalProps['vt_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+
+ discStr = self.convertToDB('vistrail','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_actions:
+ self.getDao('action').toSQL(db, child, foreignKey, globalProps)
+
+ discStr = self.convertToDB('vistrail','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_tags:
+ self.getDao('tag').toSQL(db, child, foreignKey, globalProps)
+
+ foreignKey = {'vt_id': keyStr}
+ for child in obj.db_abstractions:
+ self.getDao('abstraction').toSQL(db, child, foreignKey, globalProps)
+
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props):
+ columns = ['id', 'ts_start', 'ts_end', 'module_id', 'module_name', 'machine_id', 'wf_exec_id', 'vt_id']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ module_id = self.convertFromDB(row[3], 'long', 'int')
+ module_name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ machine_id = self.convertFromDB(row[5], 'long', 'int')
+ workflow_exec = self.convertFromDB(row[6], 'long', 'int')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ module_id=module_id,
+ module_name=module_name,
+ id=id)
+ module_exec.db_machine_id = machine_id
+ module_exec.db_workflow_exec = workflow_exec
+ module_exec.db_vistrailId = vistrailId
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('machine', obj.db_machine_id)]
+ p.db_add_module_exec(obj)
+ p = all_objects[('workflow_exec', obj.db_workflow_exec)]
+ p.db_add_module_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'module_id', 'module_name', 'machine_id', 'wf_exec_id', 'vt_id']
+ table = 'module_exec'
+ whereMap = {}
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_workflow_exec') and obj.db_workflow_exec is not None:
+ columnMap['wf_exec_id'] = \
+ self.convertToDB(obj.db_workflow_exec, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def fromSQL(self, db, id=None, foreignKey=None, globalProps=None):
+ columns = ['ts_start', 'ts_end', 'module_id', 'module_name', 'id']
+ table = 'module_exec'
+ whereMap = {}
+ orderBy = 'id'
+
+ if id is not None:
+ keyStr = self.convertToDB(id, 'long', 'int')
+ whereMap['id'] = keyStr
+ elif foreignKey is not None:
+ whereMap.update(foreignKey)
+ elif globalProps is None:
+ print '***ERROR: need to specify id or foreign key info'
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy)
+ data = self.executeSQL(db, dbCommand, True)
+ list = []
+ for row in data:
+ ts_start = self.convertFromDB(row[0], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[1], 'datetime', 'datetime')
+ module_id = self.convertFromDB(row[2], 'long', 'int')
+ module_name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ id = self.convertFromDB(row[4], 'long', 'int')
+ keyStr = self.convertToDB(id,'long','int')
+
+ discStr = self.convertToDB('module_exec','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ res = self.getDao('annotation').fromSQL(db, None, foreignKey, globalProps)
+ annotations = res
+
+ module_exec = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ module_id=module_id,
+ module_name=module_name,
+ annotations=annotations)
+ module_exec.is_dirty = False
+ list.append(module_exec)
+
+ return list
+
+ def toSQL(self, db, obj, foreignKey=None, globalProps=None):
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if obj.is_dirty:
+ columns = ['id']
+ table = 'module_exec'
+ whereMap = {}
+ columnMap = {}
+
+ whereMap['id'] = keyStr
+ if globalProps is not None:
+ whereMap.update(globalProps)
+ if obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if foreignKey is not None:
+ columnMap.update(foreignKey)
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap)
+ data = self.executeSQL(db, dbCommand, True)
+ if len(data) <= 0:
+ columnMap['id'] = keyStr
+ if globalProps is not None:
+ columnMap.update(globalProps)
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+
+ discStr = self.convertToDB('module_exec','str','char(16)')
+ foreignKey = {'parent_id' : keyStr, 'parent_type': discStr}
+ for child in obj.db_annotations:
+ self.getDao('annotation').toSQL(db, child, foreignKey, globalProps)
+
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefSQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v0_7_0/persistence/sql/sql_dao.py b/vistrails/db/versions/v0_7_0/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..7f92a24
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/persistence/sql/sql_dao.py
@@ -0,0 +1,141 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return "'" + str(value).replace("'", "''") + "'"
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ return str(value)
+ elif type == 'int':
+ return str(value)
+ elif type == 'date':
+ return "'" + value.isoformat() + "'"
+ elif type == 'datetime':
+ return "'" + value.strftime('%Y-%m-%d %H:%M:%S') + "'"
+ else:
+ return str(value)
+
+ return "''"
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ return dbCommand
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ valueStr = ', '.join(values)
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s)""" % \
+ (table, columnStr, valueStr)
+ return dbCommand
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ setStr += '%s %s = %s' % (comma, column, value)
+ comma = ','
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """UPDATE %s SET %s WHERE %s""" % \
+ (table, setStr, whereStr)
+ return dbCommand
+
+ def executeSQL(self, db, dbCommand, isFetch):
+ print 'db: %s' % dbCommand
+ data = None
+ cursor = db.cursor()
+ cursor.execute(dbCommand)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ cursor.close()
+ return data
diff --git a/vistrails/db/versions/v0_7_0/persistence/xml/__init__.py b/vistrails/db/versions/v0_7_0/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_7_0/persistence/xml/auto_gen.py b/vistrails/db/versions/v0_7_0/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..623548b
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/persistence/xml/auto_gen.py
@@ -0,0 +1,1778 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from xml_dao import XMLDAO
+from vistrails.db.versions.v0_7_0.domain import *
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'portSpec':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ type = self.convertFromStr(self.getAttribute(node, 'type'), 'str')
+ spec = self.convertFromStr(self.getAttribute(node, 'spec'), 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, doc, node):
+ if node is None:
+ node = doc.createElement('portSpec')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.setAttribute('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.setAttribute('spec',self.convertToStr(portSpec.db_spec, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'module':
+ return None
+
+ functions = []
+ annotations = []
+ portSpecs = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ cache = self.convertFromStr(self.getAttribute(node, 'cache'), 'int')
+ abstraction = self.convertFromStr(self.getAttribute(node, 'abstraction'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ package = self.convertFromStr(self.getAttribute(node, 'package'), 'str')
+ version = self.convertFromStr(self.getAttribute(node, 'version'), 'str')
+
+ location = None
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'location':
+ location = self.getDao('location').fromXML(child)
+ elif child.nodeName == 'function':
+ function = self.getDao('function').fromXML(child)
+ functions.append(function)
+ elif child.nodeName == 'annotation':
+ annotation = self.getDao('annotation').fromXML(child)
+ annotations.append(annotation)
+ elif child.nodeName == 'portSpec':
+ portSpec = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(portSpec)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBModule(id=id,
+ cache=cache,
+ abstraction=abstraction,
+ name=name,
+ package=package,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, doc, node):
+ if node is None:
+ node = doc.createElement('module')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(module.db_id, 'long'))
+ node.setAttribute('cache',self.convertToStr(module.db_cache, 'int'))
+ node.setAttribute('abstraction',self.convertToStr(module.db_abstraction, 'long'))
+ node.setAttribute('name',self.convertToStr(module.db_name, 'str'))
+ node.setAttribute('package',self.convertToStr(module.db_package, 'str'))
+ node.setAttribute('version',self.convertToStr(module.db_version, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ if nodeMap.has_key(('location', location.db_id)):
+ childNode = nodeMap[('location', location.db_id)]
+ del nodeMap[('location', location.db_id)]
+ else:
+ childNode = doc.createElement('location')
+ node.appendChild(childNode)
+ self.getDao('location').toXML(location, doc, childNode)
+ functions = module.db_functions
+ for function in functions:
+ if nodeMap.has_key(('function', function.db_id)):
+ childNode = nodeMap[('function', function.db_id)]
+ del nodeMap[('function', function.db_id)]
+ else:
+ childNode = doc.createElement('function')
+ node.appendChild(childNode)
+ self.getDao('function').toXML(function, doc, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations:
+ if nodeMap.has_key(('annotation', annotation.db_id)):
+ childNode = nodeMap[('annotation', annotation.db_id)]
+ del nodeMap[('annotation', annotation.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(annotation, doc, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ if nodeMap.has_key(('portSpec', portSpec.db_id)):
+ childNode = nodeMap[('portSpec', portSpec.db_id)]
+ del nodeMap[('portSpec', portSpec.db_id)]
+ else:
+ childNode = doc.createElement('portSpec')
+ node.appendChild(childNode)
+ self.getDao('portSpec').toXML(portSpec, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'tag':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, doc, node):
+ if node is None:
+ node = doc.createElement('tag')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(tag.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'port':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ type = self.convertFromStr(self.getAttribute(node, 'type'), 'str')
+ moduleId = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ moduleName = self.convertFromStr(self.getAttribute(node, 'moduleName'), 'str')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ spec = self.convertFromStr(self.getAttribute(node, 'spec'), 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, doc, node):
+ if node is None:
+ node = doc.createElement('port')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(port.db_id, 'long'))
+ node.setAttribute('type',self.convertToStr(port.db_type, 'str'))
+ node.setAttribute('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.setAttribute('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.setAttribute('name',self.convertToStr(port.db_name, 'str'))
+ node.setAttribute('spec',self.convertToStr(port.db_spec, 'str'))
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'log':
+ return None
+
+ workflow_execs = []
+ machines = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'workflowExec':
+ workflow_exec = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs.append(workflow_exec)
+ elif child.nodeName == 'machine':
+ machine = self.getDao('machine').fromXML(child)
+ machines.append(machine)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBLog(id=id,
+ workflow_execs=workflow_execs,
+ machines=machines)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, doc, node):
+ if node is None:
+ node = doc.createElement('log')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(log.db_id, 'long'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs:
+ if nodeMap.has_key(('workflow_exec', workflow_exec.db_id)):
+ childNode = nodeMap[('workflow_exec', workflow_exec.db_id)]
+ del nodeMap[('workflow_exec', workflow_exec.db_id)]
+ else:
+ childNode = doc.createElement('workflow_exec')
+ node.appendChild(childNode)
+ self.getDao('workflow_exec').toXML(workflow_exec, doc, childNode)
+ machines = log.db_machines
+ for machine in machines:
+ if nodeMap.has_key(('machine', machine.db_id)):
+ childNode = nodeMap[('machine', machine.db_id)]
+ del nodeMap[('machine', machine.db_id)]
+ else:
+ childNode = doc.createElement('machine')
+ node.appendChild(childNode)
+ self.getDao('machine').toXML(machine, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'machine':
+ return None
+
+ module_execs = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ os = self.convertFromStr(self.getAttribute(node, 'os'), 'str')
+ architecture = self.convertFromStr(self.getAttribute(node, 'architecture'), 'str')
+ processor = self.convertFromStr(self.getAttribute(node, 'processor'), 'str')
+ ram = self.convertFromStr(self.getAttribute(node, 'ram'), 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ module_execs=module_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, doc, node):
+ if node is None:
+ node = doc.createElement('machine')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(machine.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(machine.db_name, 'str'))
+ node.setAttribute('os',self.convertToStr(machine.db_os, 'str'))
+ node.setAttribute('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.setAttribute('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.setAttribute('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'add':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ what = self.convertFromStr(self.getAttribute(node, 'what'), 'str')
+ objectId = self.convertFromStr(self.getAttribute(node, 'objectId'), 'long')
+ parentObjId = self.convertFromStr(self.getAttribute(node, 'parentObjId'), 'long')
+ parentObjType = self.convertFromStr(self.getAttribute(node, 'parentObjType'), 'str')
+
+ data = None
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'module':
+ data = self.getDao('module').fromXML(child)
+ elif child.nodeName == 'location':
+ data = self.getDao('location').fromXML(child)
+ elif child.nodeName == 'annotation':
+ data = self.getDao('annotation').fromXML(child)
+ elif child.nodeName == 'function':
+ data = self.getDao('function').fromXML(child)
+ elif child.nodeName == 'connection':
+ data = self.getDao('connection').fromXML(child)
+ elif child.nodeName == 'port':
+ data = self.getDao('port').fromXML(child)
+ elif child.nodeName == 'parameter':
+ data = self.getDao('parameter').fromXML(child)
+ elif child.nodeName == 'portSpec':
+ data = self.getDao('portSpec').fromXML(child)
+ elif child.nodeName == 'abstractionRef':
+ data = self.getDao('abstractionRef').fromXML(child)
+ elif child.nodeName == 'other':
+ data = self.getDao('other').fromXML(child)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBAdd(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, doc, node):
+ if node is None:
+ node = doc.createElement('add')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(add.db_id, 'long'))
+ node.setAttribute('what',self.convertToStr(add.db_what, 'str'))
+ node.setAttribute('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.setAttribute('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.setAttribute('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ data = add.db_data
+ if data.vtType == 'module':
+ if nodeMap.has_key(('module', data.db_id)):
+ childNode = nodeMap[('module', data.db_id)]
+ del nodeMap[('module', data.db_id)]
+ else:
+ childNode = doc.createElement('module')
+ node.appendChild(childNode)
+ self.getDao('module').toXML(data, doc, childNode)
+ elif data.vtType == 'location':
+ if nodeMap.has_key(('location', data.db_id)):
+ childNode = nodeMap[('location', data.db_id)]
+ del nodeMap[('location', data.db_id)]
+ else:
+ childNode = doc.createElement('location')
+ node.appendChild(childNode)
+ self.getDao('location').toXML(data, doc, childNode)
+ elif data.vtType == 'annotation':
+ if nodeMap.has_key(('annotation', data.db_id)):
+ childNode = nodeMap[('annotation', data.db_id)]
+ del nodeMap[('annotation', data.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(data, doc, childNode)
+ elif data.vtType == 'function':
+ if nodeMap.has_key(('function', data.db_id)):
+ childNode = nodeMap[('function', data.db_id)]
+ del nodeMap[('function', data.db_id)]
+ else:
+ childNode = doc.createElement('function')
+ node.appendChild(childNode)
+ self.getDao('function').toXML(data, doc, childNode)
+ elif data.vtType == 'connection':
+ if nodeMap.has_key(('connection', data.db_id)):
+ childNode = nodeMap[('connection', data.db_id)]
+ del nodeMap[('connection', data.db_id)]
+ else:
+ childNode = doc.createElement('connection')
+ node.appendChild(childNode)
+ self.getDao('connection').toXML(data, doc, childNode)
+ elif data.vtType == 'port':
+ if nodeMap.has_key(('port', data.db_id)):
+ childNode = nodeMap[('port', data.db_id)]
+ del nodeMap[('port', data.db_id)]
+ else:
+ childNode = doc.createElement('port')
+ node.appendChild(childNode)
+ self.getDao('port').toXML(data, doc, childNode)
+ elif data.vtType == 'parameter':
+ if nodeMap.has_key(('parameter', data.db_id)):
+ childNode = nodeMap[('parameter', data.db_id)]
+ del nodeMap[('parameter', data.db_id)]
+ else:
+ childNode = doc.createElement('parameter')
+ node.appendChild(childNode)
+ self.getDao('parameter').toXML(data, doc, childNode)
+ elif data.vtType == 'portSpec':
+ if nodeMap.has_key(('portSpec', data.db_id)):
+ childNode = nodeMap[('portSpec', data.db_id)]
+ del nodeMap[('portSpec', data.db_id)]
+ else:
+ childNode = doc.createElement('portSpec')
+ node.appendChild(childNode)
+ self.getDao('portSpec').toXML(data, doc, childNode)
+ elif data.vtType == 'abstractionRef':
+ if nodeMap.has_key(('abstractionRef', data.db_id)):
+ childNode = nodeMap[('abstractionRef', data.db_id)]
+ del nodeMap[('abstractionRef', data.db_id)]
+ else:
+ childNode = doc.createElement('abstractionRef')
+ node.appendChild(childNode)
+ self.getDao('abstractionRef').toXML(data, doc, childNode)
+ elif data.vtType == 'other':
+ if nodeMap.has_key(('other', data.db_id)):
+ childNode = nodeMap[('other', data.db_id)]
+ del nodeMap[('other', data.db_id)]
+ else:
+ childNode = doc.createElement('other')
+ node.appendChild(childNode)
+ self.getDao('other').toXML(data, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'other':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ key = self.convertFromStr(self.getAttribute(node, 'key'), 'str')
+
+ value = None
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'value':
+ value = self.convertFromStr(child.firstChild.nodeValue,'str')
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, doc, node):
+ if node is None:
+ node = doc.createElement('other')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(other.db_id, 'long'))
+ node.setAttribute('key',self.convertToStr(other.db_key, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ if other.db_value is not None:
+ child = other.db_value
+ if nodeMap.has_key(('value',child.db_id)):
+ childNode = nodeMap[('value',child.db_id)]
+ del nodeMap[('value', child.db_id)]
+ textNode = childNode.firstChild
+ textNode.replaceWholeText(self.convertToStr(child, 'str'))
+ else:
+ childNode = doc.createElement('value')
+ node.appendChild(childNode)
+ textNode = doc.createTextNode(self.convertToStr(child, 'str'))
+ childNode.appendChild(textNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'location':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ x = self.convertFromStr(self.getAttribute(node, 'x'), 'float')
+ y = self.convertFromStr(self.getAttribute(node, 'y'), 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, doc, node):
+ if node is None:
+ node = doc.createElement('location')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(location.db_id, 'long'))
+ node.setAttribute('x',self.convertToStr(location.db_x, 'float'))
+ node.setAttribute('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'workflowExec':
+ return None
+
+ module_execs = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ user = self.convertFromStr(self.getAttribute(node, 'user'), 'str')
+ ip = self.convertFromStr(self.getAttribute(node, 'ip'), 'str')
+ vt_version = self.convertFromStr(self.getAttribute(node, 'vtVersion'), 'str')
+ ts_start = self.convertFromStr(self.getAttribute(node, 'tsStart'), 'datetime')
+ ts_end = self.convertFromStr(self.getAttribute(node, 'tsEnd'), 'datetime')
+ parent_id = self.convertFromStr(self.getAttribute(node, 'parentId'), 'long')
+ parent_type = self.convertFromStr(self.getAttribute(node, 'parentType'), 'str')
+ parent_version = self.convertFromStr(self.getAttribute(node, 'parentVersion'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'moduleExec':
+ module_exec = self.getDao('module_exec').fromXML(child)
+ module_execs.append(module_exec)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBWorkflowExec(id=id,
+ user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ module_execs=module_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, doc, node):
+ if node is None:
+ node = doc.createElement('workflowExec')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.setAttribute('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.setAttribute('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.setAttribute('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.setAttribute('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.setAttribute('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.setAttribute('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.setAttribute('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.setAttribute('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.setAttribute('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ module_execs = workflow_exec.db_module_execs
+ for module_exec in module_execs:
+ if nodeMap.has_key(('module_exec', module_exec.db_id)):
+ childNode = nodeMap[('module_exec', module_exec.db_id)]
+ del nodeMap[('module_exec', module_exec.db_id)]
+ else:
+ childNode = doc.createElement('module_exec')
+ node.appendChild(childNode)
+ self.getDao('module_exec').toXML(module_exec, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'function':
+ return None
+
+ parameters = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ pos = self.convertFromStr(self.getAttribute(node, 'pos'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'parameter':
+ parameter = self.getDao('parameter').fromXML(child)
+ parameters.append(parameter)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, doc, node):
+ if node is None:
+ node = doc.createElement('function')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(function.db_id, 'long'))
+ node.setAttribute('pos',self.convertToStr(function.db_pos, 'long'))
+ node.setAttribute('name',self.convertToStr(function.db_name, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ if nodeMap.has_key(('parameter', parameter.db_id)):
+ childNode = nodeMap[('parameter', parameter.db_id)]
+ del nodeMap[('parameter', parameter.db_id)]
+ else:
+ childNode = doc.createElement('parameter')
+ node.appendChild(childNode)
+ self.getDao('parameter').toXML(parameter, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'abstraction':
+ return None
+
+ actions = []
+ tags = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'action':
+ action = self.getDao('action').fromXML(child)
+ actions.append(action)
+ elif child.nodeName == 'tag':
+ tag = self.getDao('tag').fromXML(child)
+ tags.append(tag)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBAbstraction(id=id,
+ name=name,
+ actions=actions,
+ tags=tags)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, doc, node):
+ if node is None:
+ node = doc.createElement('abstraction')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(abstraction.db_name, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ actions = abstraction.db_actions
+ for action in actions:
+ if nodeMap.has_key(('action', action.db_id)):
+ childNode = nodeMap[('action', action.db_id)]
+ del nodeMap[('action', action.db_id)]
+ else:
+ childNode = doc.createElement('action')
+ node.appendChild(childNode)
+ self.getDao('action').toXML(action, doc, childNode)
+ tags = abstraction.db_tags
+ for tag in tags:
+ if nodeMap.has_key(('tag', tag.db_id)):
+ childNode = nodeMap[('tag', tag.db_id)]
+ del nodeMap[('tag', tag.db_id)]
+ else:
+ childNode = doc.createElement('tag')
+ node.appendChild(childNode)
+ self.getDao('tag').toXML(tag, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'workflow':
+ return None
+
+ modules = []
+ connections = []
+ annotations = []
+ others = []
+ abstractionRefs = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'module':
+ module = self.getDao('module').fromXML(child)
+ modules.append(module)
+ elif child.nodeName == 'connection':
+ connection = self.getDao('connection').fromXML(child)
+ connections.append(connection)
+ elif child.nodeName == 'annotation':
+ annotation = self.getDao('annotation').fromXML(child)
+ annotations.append(annotation)
+ elif child.nodeName == 'other':
+ other = self.getDao('other').fromXML(child)
+ others.append(other)
+ elif child.nodeName == 'abstractionRef':
+ abstractionRef = self.getDao('abstractionRef').fromXML(child)
+ abstractionRefs.append(abstractionRef)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBWorkflow(id=id,
+ name=name,
+ modules=modules,
+ connections=connections,
+ annotations=annotations,
+ others=others,
+ abstractionRefs=abstractionRefs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, doc, node):
+ if node is None:
+ node = doc.createElement('workflow')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(workflow.db_id, 'long'))
+ node.setAttribute('name',self.convertToStr(workflow.db_name, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ modules = workflow.db_modules
+ for module in modules:
+ if nodeMap.has_key(('module', module.db_id)):
+ childNode = nodeMap[('module', module.db_id)]
+ del nodeMap[('module', module.db_id)]
+ else:
+ childNode = doc.createElement('module')
+ node.appendChild(childNode)
+ self.getDao('module').toXML(module, doc, childNode)
+ connections = workflow.db_connections
+ for connection in connections:
+ if nodeMap.has_key(('connection', connection.db_id)):
+ childNode = nodeMap[('connection', connection.db_id)]
+ del nodeMap[('connection', connection.db_id)]
+ else:
+ childNode = doc.createElement('connection')
+ node.appendChild(childNode)
+ self.getDao('connection').toXML(connection, doc, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ if nodeMap.has_key(('annotation', annotation.db_id)):
+ childNode = nodeMap[('annotation', annotation.db_id)]
+ del nodeMap[('annotation', annotation.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(annotation, doc, childNode)
+ others = workflow.db_others
+ for other in others:
+ if nodeMap.has_key(('other', other.db_id)):
+ childNode = nodeMap[('other', other.db_id)]
+ del nodeMap[('other', other.db_id)]
+ else:
+ childNode = doc.createElement('other')
+ node.appendChild(childNode)
+ self.getDao('other').toXML(other, doc, childNode)
+ abstractionRefs = workflow.db_abstractionRefs
+ for abstractionRef in abstractionRefs:
+ if nodeMap.has_key(('abstractionRef', abstractionRef.db_id)):
+ childNode = nodeMap[('abstractionRef', abstractionRef.db_id)]
+ del nodeMap[('abstractionRef', abstractionRef.db_id)]
+ else:
+ childNode = doc.createElement('abstractionRef')
+ node.appendChild(childNode)
+ self.getDao('abstractionRef').toXML(abstractionRef, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBAbstractionRefXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'abstractionRef':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ abstraction_id = self.convertFromStr(self.getAttribute(node, 'abstractionId'), 'long')
+ version = self.convertFromStr(self.getAttribute(node, 'version'), 'long')
+
+ location = None
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'location':
+ location = self.getDao('location').fromXML(child)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBAbstractionRef(id=id,
+ abstraction_id=abstraction_id,
+ version=version,
+ location=location)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstractionRef, doc, node):
+ if node is None:
+ node = doc.createElement('abstractionRef')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(abstractionRef.db_id, 'long'))
+ node.setAttribute('abstractionId',self.convertToStr(abstractionRef.db_abstraction_id, 'long'))
+ node.setAttribute('version',self.convertToStr(abstractionRef.db_version, 'long'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ location = abstractionRef.db_location
+ if location is not None:
+ if nodeMap.has_key(('location', location.db_id)):
+ childNode = nodeMap[('location', location.db_id)]
+ del nodeMap[('location', location.db_id)]
+ else:
+ childNode = doc.createElement('location')
+ node.appendChild(childNode)
+ self.getDao('location').toXML(location, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'annotation':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ key = self.convertFromStr(self.getAttribute(node, 'key'), 'str')
+ value = self.convertFromStr(self.getAttribute(node, 'value'), 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, doc, node):
+ if node is None:
+ node = doc.createElement('annotation')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(annotation.db_id, 'long'))
+ node.setAttribute('key',self.convertToStr(annotation.db_key, 'str'))
+ node.setAttribute('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'change':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ what = self.convertFromStr(self.getAttribute(node, 'what'), 'str')
+ oldObjId = self.convertFromStr(self.getAttribute(node, 'oldObjId'), 'long')
+ newObjId = self.convertFromStr(self.getAttribute(node, 'newObjId'), 'long')
+ parentObjId = self.convertFromStr(self.getAttribute(node, 'parentObjId'), 'long')
+ parentObjType = self.convertFromStr(self.getAttribute(node, 'parentObjType'), 'str')
+
+ data = None
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'module':
+ data = self.getDao('module').fromXML(child)
+ elif child.nodeName == 'location':
+ data = self.getDao('location').fromXML(child)
+ elif child.nodeName == 'annotation':
+ data = self.getDao('annotation').fromXML(child)
+ elif child.nodeName == 'function':
+ data = self.getDao('function').fromXML(child)
+ elif child.nodeName == 'connection':
+ data = self.getDao('connection').fromXML(child)
+ elif child.nodeName == 'port':
+ data = self.getDao('port').fromXML(child)
+ elif child.nodeName == 'parameter':
+ data = self.getDao('parameter').fromXML(child)
+ elif child.nodeName == 'portSpec':
+ data = self.getDao('portSpec').fromXML(child)
+ elif child.nodeName == 'abstractionRef':
+ data = self.getDao('abstractionRef').fromXML(child)
+ elif child.nodeName == 'other':
+ data = self.getDao('other').fromXML(child)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBChange(id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, doc, node):
+ if node is None:
+ node = doc.createElement('change')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(change.db_id, 'long'))
+ node.setAttribute('what',self.convertToStr(change.db_what, 'str'))
+ node.setAttribute('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.setAttribute('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.setAttribute('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.setAttribute('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ data = change.db_data
+ if data.vtType == 'module':
+ if nodeMap.has_key(('module', data.db_id)):
+ childNode = nodeMap[('module', data.db_id)]
+ del nodeMap[('module', data.db_id)]
+ else:
+ childNode = doc.createElement('module')
+ node.appendChild(childNode)
+ self.getDao('module').toXML(data, doc, childNode)
+ elif data.vtType == 'location':
+ if nodeMap.has_key(('location', data.db_id)):
+ childNode = nodeMap[('location', data.db_id)]
+ del nodeMap[('location', data.db_id)]
+ else:
+ childNode = doc.createElement('location')
+ node.appendChild(childNode)
+ self.getDao('location').toXML(data, doc, childNode)
+ elif data.vtType == 'annotation':
+ if nodeMap.has_key(('annotation', data.db_id)):
+ childNode = nodeMap[('annotation', data.db_id)]
+ del nodeMap[('annotation', data.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(data, doc, childNode)
+ elif data.vtType == 'function':
+ if nodeMap.has_key(('function', data.db_id)):
+ childNode = nodeMap[('function', data.db_id)]
+ del nodeMap[('function', data.db_id)]
+ else:
+ childNode = doc.createElement('function')
+ node.appendChild(childNode)
+ self.getDao('function').toXML(data, doc, childNode)
+ elif data.vtType == 'connection':
+ if nodeMap.has_key(('connection', data.db_id)):
+ childNode = nodeMap[('connection', data.db_id)]
+ del nodeMap[('connection', data.db_id)]
+ else:
+ childNode = doc.createElement('connection')
+ node.appendChild(childNode)
+ self.getDao('connection').toXML(data, doc, childNode)
+ elif data.vtType == 'port':
+ if nodeMap.has_key(('port', data.db_id)):
+ childNode = nodeMap[('port', data.db_id)]
+ del nodeMap[('port', data.db_id)]
+ else:
+ childNode = doc.createElement('port')
+ node.appendChild(childNode)
+ self.getDao('port').toXML(data, doc, childNode)
+ elif data.vtType == 'parameter':
+ if nodeMap.has_key(('parameter', data.db_id)):
+ childNode = nodeMap[('parameter', data.db_id)]
+ del nodeMap[('parameter', data.db_id)]
+ else:
+ childNode = doc.createElement('parameter')
+ node.appendChild(childNode)
+ self.getDao('parameter').toXML(data, doc, childNode)
+ elif data.vtType == 'portSpec':
+ if nodeMap.has_key(('portSpec', data.db_id)):
+ childNode = nodeMap[('portSpec', data.db_id)]
+ del nodeMap[('portSpec', data.db_id)]
+ else:
+ childNode = doc.createElement('portSpec')
+ node.appendChild(childNode)
+ self.getDao('portSpec').toXML(data, doc, childNode)
+ elif data.vtType == 'abstractionRef':
+ if nodeMap.has_key(('abstractionRef', data.db_id)):
+ childNode = nodeMap[('abstractionRef', data.db_id)]
+ del nodeMap[('abstractionRef', data.db_id)]
+ else:
+ childNode = doc.createElement('abstractionRef')
+ node.appendChild(childNode)
+ self.getDao('abstractionRef').toXML(data, doc, childNode)
+ elif data.vtType == 'other':
+ if nodeMap.has_key(('other', data.db_id)):
+ childNode = nodeMap[('other', data.db_id)]
+ del nodeMap[('other', data.db_id)]
+ else:
+ childNode = doc.createElement('other')
+ node.appendChild(childNode)
+ self.getDao('other').toXML(data, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'parameter':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ pos = self.convertFromStr(self.getAttribute(node, 'pos'), 'long')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ type = self.convertFromStr(self.getAttribute(node, 'type'), 'str')
+ val = self.convertFromStr(self.getAttribute(node, 'val'), 'str')
+ alias = self.convertFromStr(self.getAttribute(node, 'alias'), 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, doc, node):
+ if node is None:
+ node = doc.createElement('parameter')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(parameter.db_id, 'long'))
+ node.setAttribute('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.setAttribute('name',self.convertToStr(parameter.db_name, 'str'))
+ node.setAttribute('type',self.convertToStr(parameter.db_type, 'str'))
+ node.setAttribute('val',self.convertToStr(parameter.db_val, 'str'))
+ node.setAttribute('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'connection':
+ return None
+
+ ports = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'port':
+ port = self.getDao('port').fromXML(child)
+ ports.append(port)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, doc, node):
+ if node is None:
+ node = doc.createElement('connection')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(connection.db_id, 'long'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ if nodeMap.has_key(('port', port.db_id)):
+ childNode = nodeMap[('port', port.db_id)]
+ del nodeMap[('port', port.db_id)]
+ else:
+ childNode = doc.createElement('port')
+ node.appendChild(childNode)
+ self.getDao('port').toXML(port, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'action':
+ return None
+
+ annotations = []
+ operations = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ prevId = self.convertFromStr(self.getAttribute(node, 'prevId'), 'long')
+ date = self.convertFromStr(self.getAttribute(node, 'date'), 'datetime')
+ session = self.convertFromStr(self.getAttribute(node, 'session'), 'str')
+ user = self.convertFromStr(self.getAttribute(node, 'user'), 'str')
+ prune = self.convertFromStr(self.getAttribute(node, 'prune'), 'int')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'annotation':
+ annotation = self.getDao('annotation').fromXML(child)
+ annotations.append(annotation)
+ elif child.nodeName == 'add':
+ operation = self.getDao('add').fromXML(child)
+ operations.append(operation)
+ elif child.nodeName == 'delete':
+ operation = self.getDao('delete').fromXML(child)
+ operations.append(operation)
+ elif child.nodeName == 'change':
+ operation = self.getDao('change').fromXML(child)
+ operations.append(operation)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBAction(id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ annotations=annotations,
+ operations=operations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, doc, node):
+ if node is None:
+ node = doc.createElement('action')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(action.db_id, 'long'))
+ node.setAttribute('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.setAttribute('date',self.convertToStr(action.db_date, 'datetime'))
+ node.setAttribute('session',self.convertToStr(action.db_session, 'str'))
+ node.setAttribute('user',self.convertToStr(action.db_user, 'str'))
+ node.setAttribute('prune',self.convertToStr(action.db_prune, 'int'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations:
+ if nodeMap.has_key(('annotation', annotation.db_id)):
+ childNode = nodeMap[('annotation', annotation.db_id)]
+ del nodeMap[('annotation', annotation.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(annotation, doc, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ if nodeMap.has_key(('add', operation.db_id)):
+ childNode = nodeMap[('add', operation.db_id)]
+ del nodeMap[('add', operation.db_id)]
+ else:
+ childNode = doc.createElement('add')
+ node.appendChild(childNode)
+ self.getDao('add').toXML(operation, doc, childNode)
+ elif operation.vtType == 'delete':
+ if nodeMap.has_key(('delete', operation.db_id)):
+ childNode = nodeMap[('delete', operation.db_id)]
+ del nodeMap[('delete', operation.db_id)]
+ else:
+ childNode = doc.createElement('delete')
+ node.appendChild(childNode)
+ self.getDao('delete').toXML(operation, doc, childNode)
+ elif operation.vtType == 'change':
+ if nodeMap.has_key(('change', operation.db_id)):
+ childNode = nodeMap[('change', operation.db_id)]
+ del nodeMap[('change', operation.db_id)]
+ else:
+ childNode = doc.createElement('change')
+ node.appendChild(childNode)
+ self.getDao('change').toXML(operation, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'delete':
+ return None
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ what = self.convertFromStr(self.getAttribute(node, 'what'), 'str')
+ objectId = self.convertFromStr(self.getAttribute(node, 'objectId'), 'long')
+ parentObjId = self.convertFromStr(self.getAttribute(node, 'parentObjId'), 'long')
+ parentObjType = self.convertFromStr(self.getAttribute(node, 'parentObjType'), 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, doc, node):
+ if node is None:
+ node = doc.createElement('delete')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(delete.db_id, 'long'))
+ node.setAttribute('what',self.convertToStr(delete.db_what, 'str'))
+ node.setAttribute('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.setAttribute('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.setAttribute('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'vistrail':
+ return None
+
+ actions = []
+ tags = []
+ abstractions = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ version = self.convertFromStr(self.getAttribute(node, 'version'), 'str')
+ name = self.convertFromStr(self.getAttribute(node, 'name'), 'str')
+ dbHost = self.convertFromStr(self.getAttribute(node, 'dbHost'), 'str')
+ dbPort = self.convertFromStr(self.getAttribute(node, 'dbPort'), 'int')
+ dbName = self.convertFromStr(self.getAttribute(node, 'dbName'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'action':
+ action = self.getDao('action').fromXML(child)
+ actions.append(action)
+ elif child.nodeName == 'tag':
+ tag = self.getDao('tag').fromXML(child)
+ tags.append(tag)
+ elif child.nodeName == 'abstraction':
+ abstraction = self.getDao('abstraction').fromXML(child)
+ abstractions.append(abstraction)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ dbHost=dbHost,
+ dbPort=dbPort,
+ dbName=dbName,
+ actions=actions,
+ tags=tags,
+ abstractions=abstractions)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, doc, node):
+ if node is None:
+ node = doc.createElement('vistrail')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.setAttribute('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.setAttribute('name',self.convertToStr(vistrail.db_name, 'str'))
+ node.setAttribute('dbHost',self.convertToStr(vistrail.db_dbHost, 'str'))
+ node.setAttribute('dbPort',self.convertToStr(vistrail.db_dbPort, 'int'))
+ node.setAttribute('dbName',self.convertToStr(vistrail.db_dbName, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions:
+ if nodeMap.has_key(('action', action.db_id)):
+ childNode = nodeMap[('action', action.db_id)]
+ del nodeMap[('action', action.db_id)]
+ else:
+ childNode = doc.createElement('action')
+ node.appendChild(childNode)
+ self.getDao('action').toXML(action, doc, childNode)
+ tags = vistrail.db_tags
+ for tag in tags:
+ if nodeMap.has_key(('tag', tag.db_id)):
+ childNode = nodeMap[('tag', tag.db_id)]
+ del nodeMap[('tag', tag.db_id)]
+ else:
+ childNode = doc.createElement('tag')
+ node.appendChild(childNode)
+ self.getDao('tag').toXML(tag, doc, childNode)
+ abstractions = vistrail.db_abstractions
+ for abstraction in abstractions:
+ if nodeMap.has_key(('abstraction', abstraction.db_id)):
+ childNode = nodeMap[('abstraction', abstraction.db_id)]
+ del nodeMap[('abstraction', abstraction.db_id)]
+ else:
+ childNode = doc.createElement('abstraction')
+ node.appendChild(childNode)
+ self.getDao('abstraction').toXML(abstraction, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.nodeName != 'moduleExec':
+ return None
+
+ annotations = []
+
+ # read attributes
+ id = self.convertFromStr(self.getAttribute(node, 'id'), 'long')
+ ts_start = self.convertFromStr(self.getAttribute(node, 'tsStart'), 'datetime')
+ ts_end = self.convertFromStr(self.getAttribute(node, 'tsEnd'), 'datetime')
+ module_id = self.convertFromStr(self.getAttribute(node, 'moduleId'), 'long')
+ module_name = self.convertFromStr(self.getAttribute(node, 'moduleName'), 'str')
+
+
+ # read children
+ for child in list(node.childNodes):
+ if child.nodeName == 'annotation':
+ annotation = self.getDao('annotation').fromXML(child)
+ annotations.append(annotation)
+ elif child.nodeType == child.TEXT_NODE and child.nodeValue.strip() == '':
+ pass
+ elif child.nodeType != child.TEXT_NODE:
+ print '*** ERROR *** nodeName = %s' % child.nodeName
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ module_id=module_id,
+ module_name=module_name,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, doc, node):
+ if node is None:
+ node = doc.createElement('moduleExec')
+
+ # set attributes
+ node.setAttribute('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.setAttribute('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.setAttribute('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.setAttribute('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.setAttribute('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+
+ # load DOM node map
+ nodeMap = {}
+ for childNode in node.childNodes:
+ if childNode.nodeType == childNode.ELEMENT_NODE and self.hasAttribute(childNode, 'id'):
+ nodeId = self.convertFromStr(self.getAttribute(childNode, 'id'), 'long')
+ nodeMap[(childNode.nodeName, nodeId)] = childNode
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ if nodeMap.has_key(('annotation', annotation.db_id)):
+ childNode = nodeMap[('annotation', annotation.db_id)]
+ del nodeMap[('annotation', annotation.db_id)]
+ else:
+ childNode = doc.createElement('annotation')
+ node.appendChild(childNode)
+ self.getDao('annotation').toXML(annotation, doc, childNode)
+
+ # delete nodes not around anymore
+ for childNode in nodeMap.itervalues():
+ childNode.parentNode.removeChild(childNode)
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v0_7_0/persistence/xml/io.py b/vistrails/db/versions/v0_7_0/persistence/xml/io.py
new file mode 100644
index 0000000..f01beb5
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/persistence/xml/io.py
@@ -0,0 +1,95 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.parsers.expat import ExpatError
+import xml.dom.minidom
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_7_0 import version as my_version
+
+def parse_xml_file(filename):
+ try:
+ return xml.dom.minidom.parse(filename)
+ except xml.parsers.expat.ExpatError, e:
+ msg = 'XML parse error at line %s, col %s: %s' % \
+ (e.lineno, e.offset, e.code)
+ raise VistrailsDBException(msg)
+
+def write_xml_file(filename, dom, prettyprint=True):
+ output = open(filename, 'w')
+ if prettyprint:
+ dom.writexml(output, '',' ','\n')
+ else:
+ dom.writexml(output)
+ output.close()
+
+def read_xml_object(vtType, node, dao_list):
+ return dao_list[vtType].fromXML(node)
+
+def write_xml_object(obj, dom, dao_list, node=None):
+ res_node = dao_list[obj.vtType].toXML(obj, dom, node)
+ return res_node
+
+def open_from_xml(filename, vtType, dao_list):
+ """open_from_xml(filename) -> DBVistrail"""
+ dom = parse_xml_file(filename)
+ vistrail = read_xml_object(vtType, dom.documentElement, dao_list)
+ dom.unlink()
+ return vistrail
+
+def save_to_xml(obj, filename, dao_list):
+ dom = xml.dom.minidom.getDOMImplementation().createDocument(None, None,
+ None)
+ root = write_xml_object(obj, dom, dao_list)
+ dom.appendChild(root)
+ if obj.vtType == 'vistrail':
+ root.setAttribute('version', my_version)
+ root.setAttribute('xmlns:xsi',
+ 'http://www.w3.org/2001/XMLSchema-instance')
+ root.setAttribute('xsi:schemaLocation',
+ 'http://www.vistrails.org/vistrail.xsd')
+ write_xml_file(filename, dom)
+ dom.unlink()
+
+def serialize(object, dao_list):
+ dom = xml.dom.minidom.getDOMImplementation().createDocument(None, None,
+ None)
+ root = write_xml_object(object, dom, dao_list)
+ dom.appendChild(root)
+ return dom.toxml()
+
+def unserialize(str, obj_type):
+ dom = xml.dom.minidom.parseString(str)
+ return read_xml_object(obj_type, dom.documentElement, dao_list)
+
diff --git a/vistrails/db/versions/v0_7_0/persistence/xml/xml_dao.py b/vistrails/db/versions/v0_7_0/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..955c01a
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/persistence/xml/xml_dao.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v0_7_0/schemas/sql/vistrails.sql b/vistrails/db/versions/v0_7_0/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..494b6b3
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/schemas/sql/vistrails.sql
@@ -0,0 +1,246 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(22),
+ type varchar(255),
+ spec varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ abstraction int,
+ name varchar(255),
+ package varchar(511),
+ version varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ spec varchar(4095),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE log_tbl(
+ id int,
+ vt_id int
+);
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ module_exec_id int
+);
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+);
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ name varchar(255),
+ log_id int,
+ vt_id int
+);
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE abstraction(
+ id int,
+ name varchar(255),
+ vt_id int
+);
+
+CREATE TABLE workflow(
+ id int,
+ name varchar(255),
+ vt_id int
+);
+
+CREATE TABLE abstraction_ref(
+ id int,
+ abstraction_id int,
+ version int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+);
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session varchar(1023),
+ user varchar(255),
+ prune int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+);
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+);
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ version char(16),
+ name varchar(255)
+);
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ module_id int,
+ module_name varchar(255),
+ machine_id int,
+ wf_exec_id int,
+ vt_id int
+);
+
diff --git a/vistrails/db/versions/v0_7_0/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v0_7_0/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..a4fd64c
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,38 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, tag, port, log_tbl, machine, add_tbl, other, location, workflow_exec, function, abstraction, workflow, abstraction_ref, annotation, change_tbl, parameter, connection_tbl, action, delete_tbl, vistrail, module_exec
diff --git a/vistrails/db/versions/v0_7_0/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_7_0/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..2f84013
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/schemas/xml/vistrail.xsd
@@ -0,0 +1,234 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="dbHost" type="xs:string"/>
+ <xs:attribute name="dbPort" type="xs:int"/>
+ <xs:attribute name="dbName" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:string"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="prune" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="abstraction" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstractionRef">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="abstractionId" type="xs:int"/>
+ <xs:attribute name="version" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_7_0/specs/abstraction.xml b/vistrails/db/versions/v0_7_0/specs/abstraction.xml
new file mode 100644
index 0000000..3cbb63a
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/abstraction.xml
@@ -0,0 +1,65 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="vistrail" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/abstractionRef.xml b/vistrails/db/versions/v0_7_0/specs/abstractionRef.xml
new file mode 100644
index 0000000..9cf4d55
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/abstractionRef.xml
@@ -0,0 +1,82 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstractionRef">
+ <layout>
+ <xml name="abstractionRef" nodeType="xs:element"/>
+ <sql table="abstraction_ref"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_id" type="long">
+ <xml name="abstractionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/action.xml b/vistrails/db/versions/v0_7_0/specs/action.xml
new file mode 100644
index 0000000..1c7d3c5
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/action.xml
@@ -0,0 +1,110 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="prune" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/add.xml b/vistrails/db/versions/v0_7_0/specs/add.xml
new file mode 100644
index 0000000..11f560c
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/add.xml
@@ -0,0 +1,111 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/annotation.xml b/vistrails/db/versions/v0_7_0/specs/annotation.xml
new file mode 100644
index 0000000..19e9a54
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/annotation.xml
@@ -0,0 +1,93 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/change.xml b/vistrails/db/versions/v0_7_0/specs/change.xml
new file mode 100644
index 0000000..8135c18
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/change.xml
@@ -0,0 +1,116 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/connection.xml b/vistrails/db/versions/v0_7_0/specs/connection.xml
new file mode 100644
index 0000000..b559fab
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/connection.xml
@@ -0,0 +1,74 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/delete.xml b/vistrails/db/versions/v0_7_0/specs/delete.xml
new file mode 100644
index 0000000..abcdfdb
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/delete.xml
@@ -0,0 +1,78 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/function.xml b/vistrails/db/versions/v0_7_0/specs/function.xml
new file mode 100644
index 0000000..8254645
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/function.xml
@@ -0,0 +1,83 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/location.xml b/vistrails/db/versions/v0_7_0/specs/location.xml
new file mode 100644
index 0000000..99c62f7
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/location.xml
@@ -0,0 +1,83 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_7_0/specs/log.xml b/vistrails/db/versions/v0_7_0/specs/log.xml
new file mode 100644
index 0000000..ca8720e
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/log.xml
@@ -0,0 +1,62 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/machine.xml b/vistrails/db/versions/v0_7_0/specs/machine.xml
new file mode 100644
index 0000000..dea813d
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/machine.xml
@@ -0,0 +1,85 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="long" mapping="one-to-many">
+ <sql column="module_exec_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/module.xml b/vistrails/db/versions/v0_7_0/specs/module.xml
new file mode 100644
index 0000000..263ba14
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/module.xml
@@ -0,0 +1,112 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/module_exec.xml b/vistrails/db/versions/v0_7_0/specs/module_exec.xml
new file mode 100644
index 0000000..465407b
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/module_exec.xml
@@ -0,0 +1,86 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="machine" name="machine_id" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="machine_id" type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/other.xml b/vistrails/db/versions/v0_7_0/specs/other.xml
new file mode 100644
index 0000000..40e1388
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/other.xml
@@ -0,0 +1,79 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/parameter.xml b/vistrails/db/versions/v0_7_0/specs/parameter.xml
new file mode 100644
index 0000000..78f6cf7
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/parameter.xml
@@ -0,0 +1,94 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/port.xml b/vistrails/db/versions/v0_7_0/specs/port.xml
new file mode 100644
index 0000000..94f7671
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/port.xml
@@ -0,0 +1,95 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/portSpec.xml b/vistrails/db/versions/v0_7_0/specs/portSpec.xml
new file mode 100644
index 0000000..e42a5f0
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/portSpec.xml
@@ -0,0 +1,84 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(22)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/tag.xml b/vistrails/db/versions/v0_7_0/specs/tag.xml
new file mode 100644
index 0000000..f8412b9
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/tag.xml
@@ -0,0 +1,71 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/vistrail.xml b/vistrails/db/versions/v0_7_0/specs/vistrail.xml
new file mode 100644
index 0000000..b7b98d7
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/vistrail.xml
@@ -0,0 +1,81 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="vt_id"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="dbHost" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="dbPort" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="dbName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="abstraction" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_7_0/specs/workflow.xml b/vistrails/db/versions/v0_7_0/specs/workflow.xml
new file mode 100644
index 0000000..b420aa0
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/workflow.xml
@@ -0,0 +1,79 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="module" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="abstractionRef" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_7_0/specs/workflow_exec.xml b/vistrails/db/versions/v0_7_0/specs/workflow_exec.xml
new file mode 100644
index 0000000..b616623
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/specs/workflow_exec.xml
@@ -0,0 +1,106 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_7_0/translate/__init__.py b/vistrails/db/versions/v0_7_0/translate/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_7_0/translate/v0_6_0.py b/vistrails/db/versions/v0_7_0/translate/v0_6_0.py
new file mode 100644
index 0000000..ea4d612
--- /dev/null
+++ b/vistrails/db/versions/v0_7_0/translate/v0_6_0.py
@@ -0,0 +1,218 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v0_7_0.domain import DBVistrail, DBAction, DBTag, DBModule, \
+ DBConnection, DBPortSpec, DBFunction, DBParameter, DBLocation, DBAdd, \
+ DBChange, DBDelete, DBAnnotation, DBPort
+
+def translateVistrail(_vistrail):
+ vistrail = DBVistrail()
+
+ for _action in _vistrail.db_actions.itervalues():
+ ops = []
+ for op in _action.db_operations:
+ if op.vtType == 'add':
+ data = convert_data(op.db_data, op.db_parentObjType,
+ op.db_parentObjId)
+ ops.append(DBAdd(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'change':
+ data = convert_data(op.db_data, op.db_parentObjType,
+ op.db_parentObjId)
+ ops.append(DBChange(id=op.db_id,
+ what=op.db_what,
+ oldObjId=op.db_oldObjId,
+ newObjId=op.db_newObjId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'delete':
+ ops.append(DBDelete(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType))
+ action = DBAction(id=_action.db_id,
+ prevId=_action.db_prevId,
+ date=_action.db_date,
+ user=_action.db_user,
+ operations=ops,
+ annotations=_action.db_annotations.values())
+ vistrail.db_add_action(action)
+
+ for _tag in _vistrail.db_tags.itervalues():
+ tag = DBTag(id=_tag.db_id,
+ name=_tag.db_name)
+ vistrail.db_add_tag(tag)
+
+ vistrail.db_version = '0.7.0'
+ return vistrail
+
+module_map = {}
+translate_ports = {'SetInputConnection': {None: 'SetInputConnection0'},
+ 'GetOutputPort': {None: 'GetOutputPort0'},
+ 'SetRenderWindow': {None: 'SetVTKCell'},
+ 'SetInteractorStyle': {None: 'InteractorStyle'},
+ 'ResetCamera': {None: 'ResetCamera'},
+ 'AddPoint': {None: 'AddPoint_1'},
+ 'AddRGBPoint': {None: 'AddRGBPoint_1'},
+ 'AddHSVPoint': {None: 'AddHSVPoint_1'},
+ 'AddInput': {None: 'AddInput',
+ 'vtkXYPlotActor': 'AddInput_2'},
+ 'SetInput': {None: 'SetInput',
+ 'vtkPolyDataNormals': 'SetInput_1',
+ 'vtkGlyph3D': 'SetInput_1',
+ 'vtkDelaunay2D': 'SetInput_1',
+ 'vtkDelaunay3D': 'SetInput_1',
+ 'vtkWarpVector': 'SetInput_1',
+ 'vtkContourFilter': 'SetInput_1',
+ 'vtkTubeFilter': 'SetInput_1',
+ 'vtkThresholdPoints': 'SetInput_1',
+ 'vtkProbeFilter': 'SetInput_1',
+ 'vtkTriangleFilter': 'SetInput_1',
+ 'vtkBandedPolyDataContourFilter': \
+ 'SetInput_1',
+ 'vtkWarpScalar': 'SetInput_1'},
+ 'SetSourceConnection': {None: 'SetSourceConnection',
+ 'vtkGlyph3D': \
+ 'SetSourceConnection_2'},
+ 'AddFunction': {None: 'AddFunction',
+ ('vtkImplicitSum', 'vtkPlane'): \
+ 'AddFunction_2',
+ ('vtkImplicitSum', 'Tuple'): \
+ 'AddFunction_1'},
+ 'SetColor': {None: 'SetColor',
+ ('vtkVolumeProperty',
+ 'vtkColorTransferFunction'): \
+ 'SetColor_4',
+ ('vtkVolumeProperty',
+ 'vtkPiecewiseFunction'): \
+ 'SetColor_2'},
+ 'SetScalarOpacity': {None: 'SetScalarOpacity',
+ 'vtkVolumeProperty': \
+ 'SetScalarOpacity_2'},
+ 'SetGradientOpacity': {None: 'SetGradientOpacity',
+ 'vtkVolumeProperty':
+ 'SetGradientOpacity_2'},
+ 'SetSource': {None: 'SetSource',
+ 'vtkGlyph3D': 'SetSource_1'},
+ }
+
+def translate_vtk(module_id, port_name, specs=None):
+ global module_map
+ if port_name in translate_ports:
+ if module_id in module_map:
+ (module_name, module_pkg) = module_map[module_id]
+ if module_pkg != 'edu.utah.sci.vistrails.vtk':
+ return port_name
+ if module_name in translate_ports[port_name]:
+ port_name = translate_ports[port_name][module_name]
+ elif (module_name, specs) in translate_ports[port_name]:
+ port_name = translate_ports[port_name][(module_name, specs)]
+ else:
+ port_name = translate_ports[port_name][None]
+ return port_name
+
+def convert_data(child, parent_type, parent_id):
+ from vistrails.core.vistrail.port_spec import PortSpec
+ from vistrails.core.modules.module_registry import get_module_registry
+ global module_map, translate_ports
+
+ registry = get_module_registry()
+ if child.vtType == 'module':
+ descriptor = registry.get_descriptor_from_name_only(child.db_name)
+ package = descriptor.identifier
+ module_map[child.db_id] = (child.db_name, package)
+ return DBModule(id=child.db_id,
+ cache=child.db_cache,
+ abstraction=0,
+ name=child.db_name,
+ package=package)
+ elif child.vtType == 'connection':
+ return DBConnection(id=child.db_id)
+ elif child.vtType == 'portSpec':
+ return DBPortSpec(id=child.db_id,
+ name=child.db_name,
+ type=child.db_type,
+ spec=child.db_spec)
+ elif child.vtType == 'function':
+ if parent_type == 'module':
+ name = translate_vtk(parent_id, child.db_name)
+ else:
+ name = child.db_name
+ return DBFunction(id=child.db_id,
+ pos=child.db_pos,
+ name=name)
+ elif child.vtType == 'parameter':
+ return DBParameter(id=child.db_id,
+ pos=child.db_pos,
+ name=child.db_name,
+ type=child.db_type,
+ val=child.db_val,
+ alias=child.db_alias)
+ elif child.vtType == 'location':
+ return DBLocation(id=child.db_id,
+ x=child.db_x,
+ y=child.db_y)
+ elif child.vtType == 'annotation':
+ return DBAnnotation(id=child.db_id,
+ key=child.db_key,
+ value=child.db_value)
+ elif child.vtType == 'port':
+ sig = child.db_sig
+ if '(' in sig and ')' in sig:
+ name = sig[:sig.find('(')]
+ specs = sig[sig.find('(')+1:sig.find(')')]
+ name = translate_vtk(child.db_moduleId, name, specs)
+
+ new_specs = []
+ for spec_name in specs.split(','):
+ descriptor = registry.get_descriptor_from_name_only(spec_name)
+ spec_str = descriptor.identifier + ':' + spec_name
+ new_specs.append(spec_str)
+ spec = '(' + ','.join(new_specs) + ')'
+ else:
+ name = sig
+ spec = ''
+ return DBPort(id=child.db_id,
+ type=child.db_type,
+ moduleId=child.db_moduleId,
+ moduleName=child.db_moduleName,
+ name=name,
+ spec=spec)
diff --git a/vistrails/db/versions/v0_8_0/__init__.py b/vistrails/db/versions/v0_8_0/__init__.py
new file mode 100644
index 0000000..692e9d5
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.8.0'
diff --git a/vistrails/db/versions/v0_8_0/domain/__init__.py b/vistrails/db/versions/v0_8_0/domain/__init__.py
new file mode 100644
index 0000000..f8bbb47
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/domain/__init__.py
@@ -0,0 +1,40 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from workflow import DBWorkflow
+from vistrail import DBVistrail
+from abstraction import DBAbstraction
+from id_scope import IdScope
diff --git a/vistrails/db/versions/v0_8_0/domain/abstraction.py b/vistrails/db/versions/v0_8_0/domain/abstraction.py
new file mode 100644
index 0000000..5972a93
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/domain/abstraction.py
@@ -0,0 +1,54 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+from auto_gen import DBAbstraction as _DBAbstraction
+from id_scope import IdScope
+
+class DBAbstraction(_DBAbstraction):
+ def __init__(self, *args, **kwargs):
+ _DBAbstraction.__init__(self, *args, **kwargs)
+ self.idScope = IdScope()
+ self.idScope.setBeginId('action', 1)
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBAbstraction.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBAbstraction
+ # need to go through and reset the index to the copied objects
+ cp.idScope = copy.copy(self.idScope)
+ return cp
diff --git a/vistrails/db/versions/v0_8_0/domain/auto_gen.py b/vistrails/db/versions/v0_8_0/domain/auto_gen.py
new file mode 100644
index 0000000..b17a214
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/domain/auto_gen.py
@@ -0,0 +1,4209 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, spec=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_type = type
+ self.__db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPortSpec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_type = self.db_type
+ cp.db_spec = self.db_spec
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_spec(self):
+ return self.__db_spec
+ def __set_db_spec(self, spec):
+ self.__db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self.__db_spec = spec
+ def db_change_spec(self, spec):
+ self.__db_spec = spec
+ def db_delete_spec(self, spec):
+ self.__db_spec = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, package=None, version=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self.__db_id = id
+ self.__db_cache = cache
+ self.__db_name = name
+ self.__db_package = package
+ self.__db_version = version
+ self.db_deleted_location = []
+ self.__db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self.__db_functions = []
+ else:
+ self.__db_functions = functions
+ for v in self.__db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self.__db_portSpecs = []
+ else:
+ self.__db_portSpecs = portSpecs
+ for v in self.__db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModule.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule()
+ cp.db_id = self.db_id
+ cp.db_cache = self.db_cache
+ cp.db_name = self.db_name
+ cp.db_package = self.db_package
+ cp.db_version = self.db_version
+ if self.db_location is not None:
+ cp.db_location = self.db_location.do_copy(new_ids, id_scope, id_remap)
+ if self.db_functions is None:
+ cp.db_functions = []
+ else:
+ cp.db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_functions]
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+ if self.db_portSpecs is None:
+ cp.db_portSpecs = []
+ else:
+ cp.db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_functions:
+ cp.db_functions_id_index[v.db_id] = v
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.db_annotations_key_index[v.db_key] = v
+ for v in cp.__db_portSpecs:
+ cp.db_portSpecs_id_index[v.db_id] = v
+ cp.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_location is not None:
+ children.extend(self.db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_location is not None and self.db_location.has_changes():
+ return True
+ for child in self.db_functions:
+ if child.has_changes():
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ for child in self.db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_cache(self):
+ return self.__db_cache
+ def __set_db_cache(self, cache):
+ self.__db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self.__db_cache = cache
+ def db_change_cache(self, cache):
+ self.__db_cache = cache
+ def db_delete_cache(self, cache):
+ self.__db_cache = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_package(self):
+ return self.__db_package
+ def __set_db_package(self, package):
+ self.__db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self.__db_package = package
+ def db_change_package(self, package):
+ self.__db_package = package
+ def db_delete_package(self, package):
+ self.__db_package = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_location(self):
+ return self.__db_location
+ def __set_db_location(self, location):
+ self.__db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self.__db_location = location
+ def db_change_location(self, location):
+ self.__db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self.__db_location)
+ self.__db_location = None
+
+ def __get_db_functions(self):
+ return self.__db_functions
+ def __set_db_functions(self, functions):
+ self.__db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self.__db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self.__db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ self.__db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self.__db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ if not self.__db_functions[i].is_new:
+ self.db_deleted_functions.append(self.__db_functions[i])
+ del self.__db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == key:
+ return self.__db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return self.db_functions_id_index.has_key(key)
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ if not self.__db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self.__db_annotations[i])
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return self.db_annotations_key_index.has_key(key)
+
+ def __get_db_portSpecs(self):
+ return self.__db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self.__db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self.__db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self.__db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == portSpec.db_id:
+ self.__db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self.__db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == portSpec.db_id:
+ if not self.__db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self.__db_portSpecs[i])
+ del self.__db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == key:
+ return self.__db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return self.db_portSpecs_id_index.has_key(key)
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return self.db_portSpecs_name_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBTag.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and id_remap.has_key(('action', self.db_id)):
+ cp.db_id = id_remap[('action', self.db_id)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, name=None, spec=None):
+ self.__db_id = id
+ self.__db_type = type
+ self.__db_moduleId = moduleId
+ self.__db_moduleName = moduleName
+ self.__db_name = name
+ self.__db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPort.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort()
+ cp.__db_id = self.__db_id
+ cp.__db_type = self.__db_type
+ cp.__db_moduleId = self.__db_moduleId
+ cp.__db_moduleName = self.__db_moduleName
+ cp.__db_name = self.__db_name
+ cp.__db_spec = self.__db_spec
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_moduleId') and id_remap.has_key(('module', self.db_moduleId)):
+ cp.db_moduleId = id_remap[('module', self.db_moduleId)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self.__db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self.__db_moduleName = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_spec(self):
+ return self.__db_spec
+ def __set_db_spec(self, spec):
+ self.__db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self.__db_spec = spec
+ def db_change_spec(self, spec):
+ self.__db_spec = spec
+ def db_delete_spec(self, spec):
+ self.__db_spec = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, workflow_execs=None, machines=None):
+ self.__db_id = id
+ self.db_deleted_workflow_execs = []
+ self.db_workflow_execs_id_index = {}
+ if workflow_execs is None:
+ self.__db_workflow_execs = []
+ else:
+ self.__db_workflow_execs = workflow_execs
+ for v in self.__db_workflow_execs:
+ self.db_workflow_execs_id_index[v.db_id] = v
+ self.db_deleted_machines = []
+ self.db_machines_id_index = {}
+ if machines is None:
+ self.__db_machines = []
+ else:
+ self.__db_machines = machines
+ for v in self.__db_machines:
+ self.db_machines_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog()
+ cp.db_id = self.db_id
+ if self.db_workflow_execs is None:
+ cp.db_workflow_execs = []
+ else:
+ cp.db_workflow_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_workflow_execs]
+ if self.db_machines is None:
+ cp.db_machines = []
+ else:
+ cp.db_machines = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_machines]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_workflow_execs:
+ cp.db_workflow_execs_id_index[v.db_id] = v
+ for v in cp.__db_machines:
+ cp.db_machines_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_workflow_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self.db_machines:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow_execs)
+ children.extend(self.db_deleted_machines)
+ if remove:
+ self.db_deleted_workflow_execs = []
+ self.db_deleted_machines = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_workflow_execs:
+ if child.has_changes():
+ return True
+ for child in self.db_machines:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_workflow_execs(self):
+ return self.__db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self.__db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self.__db_workflow_execs
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self.__db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_workflow_execs)):
+ if self.__db_workflow_execs[i].db_id == workflow_exec.db_id:
+ self.__db_workflow_execs[i] = workflow_exec
+ found = True
+ break
+ if not found:
+ self.__db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_workflow_execs)):
+ if self.__db_workflow_execs[i].db_id == workflow_exec.db_id:
+ if not self.__db_workflow_execs[i].is_new:
+ self.db_deleted_workflow_execs.append(self.__db_workflow_execs[i])
+ del self.__db_workflow_execs[i]
+ break
+ del self.db_workflow_execs_id_index[workflow_exec.db_id]
+ def db_get_workflow_exec(self, key):
+ for i in xrange(len(self.__db_workflow_execs)):
+ if self.__db_workflow_execs[i].db_id == key:
+ return self.__db_workflow_execs[i]
+ return None
+ def db_get_workflow_exec_by_id(self, key):
+ return self.db_workflow_execs_id_index[key]
+ def db_has_workflow_exec_with_id(self, key):
+ return self.db_workflow_execs_id_index.has_key(key)
+
+ def __get_db_machines(self):
+ return self.__db_machines
+ def __set_db_machines(self, machines):
+ self.__db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self.__db_machines
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self.__db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_machines)):
+ if self.__db_machines[i].db_id == machine.db_id:
+ self.__db_machines[i] = machine
+ found = True
+ break
+ if not found:
+ self.__db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_machines)):
+ if self.__db_machines[i].db_id == machine.db_id:
+ if not self.__db_machines[i].is_new:
+ self.db_deleted_machines.append(self.__db_machines[i])
+ del self.__db_machines[i]
+ break
+ del self.db_machines_id_index[machine.db_id]
+ def db_get_machine(self, key):
+ for i in xrange(len(self.__db_machines)):
+ if self.__db_machines[i].db_id == key:
+ return self.__db_machines[i]
+ return None
+ def db_get_machine_by_id(self, key):
+ return self.db_machines_id_index[key]
+ def db_has_machine_with_id(self, key):
+ return self.db_machines_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None, module_execs=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_os = os
+ self.__db_architecture = architecture
+ self.__db_processor = processor
+ self.__db_ram = ram
+ self.db_deleted_module_execs = []
+ self.db_module_execs_id_index = {}
+ if module_execs is None:
+ self.__db_module_execs = []
+ else:
+ self.__db_module_execs = module_execs
+ for v in self.__db_module_execs:
+ self.db_module_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMachine.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_os = self.db_os
+ cp.db_architecture = self.db_architecture
+ cp.db_processor = self.db_processor
+ cp.db_ram = self.db_ram
+ if self.db_module_execs is None:
+ cp.db_module_execs = []
+ else:
+ cp.db_module_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_module_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_module_execs:
+ cp.db_module_execs_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_execs)
+ if remove:
+ self.db_deleted_module_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_module_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_os(self):
+ return self.__db_os
+ def __set_db_os(self, os):
+ self.__db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self.__db_os = os
+ def db_change_os(self, os):
+ self.__db_os = os
+ def db_delete_os(self, os):
+ self.__db_os = None
+
+ def __get_db_architecture(self):
+ return self.__db_architecture
+ def __set_db_architecture(self, architecture):
+ self.__db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self.__db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self.__db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self.__db_architecture = None
+
+ def __get_db_processor(self):
+ return self.__db_processor
+ def __set_db_processor(self, processor):
+ self.__db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self.__db_processor = processor
+ def db_change_processor(self, processor):
+ self.__db_processor = processor
+ def db_delete_processor(self, processor):
+ self.__db_processor = None
+
+ def __get_db_ram(self):
+ return self.__db_ram
+ def __set_db_ram(self, ram):
+ self.__db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self.__db_ram = ram
+ def db_change_ram(self, ram):
+ self.__db_ram = ram
+ def db_delete_ram(self, ram):
+ self.__db_ram = None
+
+ def __get_db_module_execs(self):
+ return self.__db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self.__db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self.__db_module_execs
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self.__db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ self.__db_module_execs[i] = module_exec
+ found = True
+ break
+ if not found:
+ self.__db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ if not self.__db_module_execs[i].is_new:
+ self.db_deleted_module_execs.append(self.__db_module_execs[i])
+ del self.__db_module_execs[i]
+ break
+ del self.db_module_execs_id_index[module_exec.db_id]
+ def db_get_module_exec(self, key):
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == key:
+ return self.__db_module_execs[i]
+ return None
+ def db_get_module_exec_by_id(self, key):
+ return self.db_module_execs_id_index[key]
+ def db_has_module_exec_with_id(self, key):
+ return self.db_module_execs_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, data=None, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self.__db_data = data
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_objectId = objectId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAdd.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd()
+ if self.db_data is not None:
+ cp.db_data = self.db_data.do_copy(new_ids, id_scope, id_remap)
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_objectId = self.db_objectId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and id_remap.has_key((self.db_what, self.db_objectId)):
+ cp.db_objectId = id_remap[(self.db_what, self.db_objectId)]
+ if hasattr(self, 'db_parentObjId') and id_remap.has_key((self.db_parentObjType, self.db_parentObjId)):
+ cp.db_parentObjId = id_remap[(self.db_parentObjType, self.db_parentObjId)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_data is not None:
+ children.extend(self.db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_data is not None and self.db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self.__db_data
+ def __set_db_data(self, data):
+ self.__db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self.__db_data = data
+ def db_change_data(self, data):
+ self.__db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self.__db_data)
+ self.__db_data = None
+
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_objectId(self):
+ return self.__db_objectId
+ def __set_db_objectId(self, objectId):
+ self.__db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self.__db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self.__db_id = id
+ self.__db_key = key
+ self.__db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOther.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOther()
+ cp.db_id = self.db_id
+ cp.db_key = self.db_key
+ cp.db_value = self.db_value
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self.__db_id = id
+ self.__db_x = x
+ self.__db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLocation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation()
+ cp.db_id = self.db_id
+ cp.db_x = self.db_x
+ cp.db_y = self.db_y
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_x(self):
+ return self.__db_x
+ def __set_db_x(self, x):
+ self.__db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self.__db_x = x
+ def db_change_x(self, x):
+ self.__db_x = x
+ def db_delete_x(self, x):
+ self.__db_x = None
+
+ def __get_db_y(self):
+ return self.__db_y
+ def __set_db_y(self, y):
+ self.__db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self.__db_y = y
+ def db_change_y(self, y):
+ self.__db_y = y
+ def db_delete_y(self, y):
+ self.__db_y = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, id=None, user=None, ip=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, name=None, module_execs=None):
+ self.__db_id = id
+ self.__db_user = user
+ self.__db_ip = ip
+ self.__db_vt_version = vt_version
+ self.__db_ts_start = ts_start
+ self.__db_ts_end = ts_end
+ self.__db_parent_id = parent_id
+ self.__db_parent_type = parent_type
+ self.__db_parent_version = parent_version
+ self.__db_name = name
+ self.db_deleted_module_execs = []
+ self.db_module_execs_id_index = {}
+ if module_execs is None:
+ self.__db_module_execs = []
+ else:
+ self.__db_module_execs = module_execs
+ for v in self.__db_module_execs:
+ self.db_module_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflowExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec()
+ cp.db_id = self.db_id
+ cp.db_user = self.db_user
+ cp.db_ip = self.db_ip
+ cp.db_vt_version = self.db_vt_version
+ cp.db_ts_start = self.db_ts_start
+ cp.db_ts_end = self.db_ts_end
+ cp.db_parent_id = self.db_parent_id
+ cp.db_parent_type = self.db_parent_type
+ cp.db_parent_version = self.db_parent_version
+ cp.db_name = self.db_name
+ if self.db_module_execs is None:
+ cp.db_module_execs = []
+ else:
+ cp.db_module_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_module_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_module_execs:
+ cp.db_module_execs_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_execs)
+ if remove:
+ self.db_deleted_module_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_module_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_user(self):
+ return self.__db_user
+ def __set_db_user(self, user):
+ self.__db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self.__db_user = user
+ def db_change_user(self, user):
+ self.__db_user = user
+ def db_delete_user(self, user):
+ self.__db_user = None
+
+ def __get_db_ip(self):
+ return self.__db_ip
+ def __set_db_ip(self, ip):
+ self.__db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self.__db_ip = ip
+ def db_change_ip(self, ip):
+ self.__db_ip = ip
+ def db_delete_ip(self, ip):
+ self.__db_ip = None
+
+ def __get_db_vt_version(self):
+ return self.__db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self.__db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self.__db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self.__db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self.__db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self.__db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self.__db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self.__db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self.__db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self.__db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self.__db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self.__db_parent_version = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_module_execs(self):
+ return self.__db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self.__db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self.__db_module_execs
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self.__db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ self.__db_module_execs[i] = module_exec
+ found = True
+ break
+ if not found:
+ self.__db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ if not self.__db_module_execs[i].is_new:
+ self.db_deleted_module_execs.append(self.__db_module_execs[i])
+ del self.__db_module_execs[i]
+ break
+ del self.db_module_execs_id_index[module_exec.db_id]
+ def db_get_module_exec(self, key):
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == key:
+ return self.__db_module_execs[i]
+ return None
+ def db_get_module_exec_by_id(self, key):
+ return self.db_module_execs_id_index[key]
+ def db_has_module_exec_with_id(self, key):
+ return self.db_module_execs_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self.__db_id = id
+ self.__db_pos = pos
+ self.__db_name = name
+ self.db_deleted_parameters = []
+ self.db_parameters_id_index = {}
+ if parameters is None:
+ self.__db_parameters = []
+ else:
+ self.__db_parameters = parameters
+ for v in self.__db_parameters:
+ self.db_parameters_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction()
+ cp.db_id = self.db_id
+ cp.db_pos = self.db_pos
+ cp.db_name = self.db_name
+ if self.db_parameters is None:
+ cp.db_parameters = []
+ else:
+ cp.db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_parameters:
+ cp.db_parameters_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_parameters)
+ if remove:
+ self.db_deleted_parameters = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_pos(self):
+ return self.__db_pos
+ def __set_db_pos(self, pos):
+ self.__db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self.__db_pos = pos
+ def db_change_pos(self, pos):
+ self.__db_pos = pos
+ def db_delete_pos(self, pos):
+ self.__db_pos = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_parameters(self):
+ return self.__db_parameters
+ def __set_db_parameters(self, parameters):
+ self.__db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self.__db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self.__db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == parameter.db_id:
+ self.__db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self.__db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == parameter.db_id:
+ if not self.__db_parameters[i].is_new:
+ self.db_deleted_parameters.append(self.__db_parameters[i])
+ del self.__db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter.db_id]
+ def db_get_parameter(self, key):
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == key:
+ return self.__db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return self.db_parameters_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, name=None, actions=None, tags=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self.__db_actions = []
+ else:
+ self.__db_actions = actions
+ for v in self.__db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self.__db_tags = []
+ else:
+ self.__db_tags = tags
+ for v in self.__db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ if self.db_actions is None:
+ cp.db_actions = []
+ else:
+ cp.db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_actions]
+ if self.db_tags is None:
+ cp.db_tags = []
+ else:
+ cp.db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_tags]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp.__db_actions:
+ cp.db_actions_id_index[v.db_id] = v
+ for v in cp.__db_tags:
+ cp.db_tags_id_index[v.db_id] = v
+ cp.db_tags_name_index[v.db_name] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_actions:
+ if child.has_changes():
+ return True
+ for child in self.db_tags:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_actions(self):
+ return self.__db_actions
+ def __set_db_actions(self, actions):
+ self.__db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self.__db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ self.__db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ if not self.__db_actions[i].is_new:
+ self.db_deleted_actions.append(self.__db_actions[i])
+ del self.__db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == key:
+ return self.__db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return self.db_actions_id_index.has_key(key)
+
+ def __get_db_tags(self):
+ return self.__db_tags
+ def __set_db_tags(self, tags):
+ self.__db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self.__db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ self.__db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ if not self.__db_tags[i].is_new:
+ self.db_deleted_tags.append(self.__db_tags[i])
+ del self.__db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == key:
+ return self.__db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return self.db_tags_id_index.has_key(key)
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return self.db_tags_name_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, modules=None, id=None, name=None, connections=None, annotations=None, others=None):
+ self.db_deleted_modules = []
+ self.db_modules_id_index = {}
+ if modules is None:
+ self.__db_modules = []
+ else:
+ self.__db_modules = modules
+ for v in self.__db_modules:
+ self.db_modules_id_index[v.db_id] = v
+ self.__db_id = id
+ self.__db_name = name
+ self.db_deleted_connections = []
+ self.db_connections_id_index = {}
+ if connections is None:
+ self.__db_connections = []
+ else:
+ self.__db_connections = connections
+ for v in self.__db_connections:
+ self.db_connections_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_others = []
+ self.db_others_id_index = {}
+ if others is None:
+ self.__db_others = []
+ else:
+ self.__db_others = others
+ for v in self.__db_others:
+ self.db_others_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow()
+ if self.db_modules is None:
+ cp.db_modules = []
+ else:
+ cp.db_modules = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_modules]
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ if self.db_connections is None:
+ cp.db_connections = []
+ else:
+ cp.db_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_connections]
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+ if self.db_others is None:
+ cp.db_others = []
+ else:
+ cp.db_others = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_others]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_modules:
+ cp.db_modules_id_index[v.db_id] = v
+ for v in cp.__db_connections:
+ cp.db_connections_id_index[v.db_id] = v
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ for v in cp.__db_others:
+ cp.db_others_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_connections:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_connection(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_other(child)
+ to_del = []
+ for child in self.db_modules:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_connections)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_others)
+ children.extend(self.db_deleted_modules)
+ if remove:
+ self.db_deleted_connections = []
+ self.db_deleted_annotations = []
+ self.db_deleted_others = []
+ self.db_deleted_modules = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_connections:
+ if child.has_changes():
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ for child in self.db_others:
+ if child.has_changes():
+ return True
+ for child in self.db_modules:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_modules(self):
+ return self.__db_modules
+ def __set_db_modules(self, modules):
+ self.__db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self.__db_modules
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self.__db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_modules)):
+ if self.__db_modules[i].db_id == module.db_id:
+ self.__db_modules[i] = module
+ found = True
+ break
+ if not found:
+ self.__db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_modules)):
+ if self.__db_modules[i].db_id == module.db_id:
+ if not self.__db_modules[i].is_new:
+ self.db_deleted_modules.append(self.__db_modules[i])
+ del self.__db_modules[i]
+ break
+ del self.db_modules_id_index[module.db_id]
+ def db_get_module(self, key):
+ for i in xrange(len(self.__db_modules)):
+ if self.__db_modules[i].db_id == key:
+ return self.__db_modules[i]
+ return None
+ def db_get_module_by_id(self, key):
+ return self.db_modules_id_index[key]
+ def db_has_module_with_id(self, key):
+ return self.db_modules_id_index.has_key(key)
+
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_connections(self):
+ return self.__db_connections
+ def __set_db_connections(self, connections):
+ self.__db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self.__db_connections
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self.__db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_connections)):
+ if self.__db_connections[i].db_id == connection.db_id:
+ self.__db_connections[i] = connection
+ found = True
+ break
+ if not found:
+ self.__db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_connections)):
+ if self.__db_connections[i].db_id == connection.db_id:
+ if not self.__db_connections[i].is_new:
+ self.db_deleted_connections.append(self.__db_connections[i])
+ del self.__db_connections[i]
+ break
+ del self.db_connections_id_index[connection.db_id]
+ def db_get_connection(self, key):
+ for i in xrange(len(self.__db_connections)):
+ if self.__db_connections[i].db_id == key:
+ return self.__db_connections[i]
+ return None
+ def db_get_connection_by_id(self, key):
+ return self.db_connections_id_index[key]
+ def db_has_connection_with_id(self, key):
+ return self.db_connections_id_index.has_key(key)
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ if not self.__db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self.__db_annotations[i])
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+
+ def __get_db_others(self):
+ return self.__db_others
+ def __set_db_others(self, others):
+ self.__db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self.__db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self.__db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == other.db_id:
+ self.__db_others[i] = other
+ found = True
+ break
+ if not found:
+ self.__db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == other.db_id:
+ if not self.__db_others[i].is_new:
+ self.db_deleted_others.append(self.__db_others[i])
+ del self.__db_others[i]
+ break
+ del self.db_others_id_index[other.db_id]
+ def db_get_other(self, key):
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == key:
+ return self.__db_others[i]
+ return None
+ def db_get_other_by_id(self, key):
+ return self.db_others_id_index[key]
+ def db_has_other_with_id(self, key):
+ return self.db_others_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAbstractionRef(object):
+
+ vtType = 'abstractionRef'
+
+ def __init__(self, id=None, name=None, cache=None, abstraction_id=None, version=None, location=None, functions=None, annotations=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_cache = cache
+ self.__db_abstraction_id = abstraction_id
+ self.__db_version = version
+ self.db_deleted_location = []
+ self.__db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self.__db_functions = []
+ else:
+ self.__db_functions = functions
+ for v in self.__db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstractionRef.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstractionRef()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_cache = self.db_cache
+ cp.db_abstraction_id = self.db_abstraction_id
+ cp.db_version = self.db_version
+ if self.db_location is not None:
+ cp.db_location = self.db_location.do_copy(new_ids, id_scope, id_remap)
+ if self.db_functions is None:
+ cp.db_functions = []
+ else:
+ cp.db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_functions]
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_functions:
+ cp.db_functions_id_index[v.db_id] = v
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_location is not None:
+ children.extend(self.db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_location is not None and self.db_location.has_changes():
+ return True
+ for child in self.db_functions:
+ if child.has_changes():
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_cache(self):
+ return self.__db_cache
+ def __set_db_cache(self, cache):
+ self.__db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self.__db_cache = cache
+ def db_change_cache(self, cache):
+ self.__db_cache = cache
+ def db_delete_cache(self, cache):
+ self.__db_cache = None
+
+ def __get_db_abstraction_id(self):
+ return self.__db_abstraction_id
+ def __set_db_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ self.is_dirty = True
+ db_abstraction_id = property(__get_db_abstraction_id, __set_db_abstraction_id)
+ def db_add_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ def db_change_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ def db_delete_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_location(self):
+ return self.__db_location
+ def __set_db_location(self, location):
+ self.__db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self.__db_location = location
+ def db_change_location(self, location):
+ self.__db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self.__db_location)
+ self.__db_location = None
+
+ def __get_db_functions(self):
+ return self.__db_functions
+ def __set_db_functions(self, functions):
+ self.__db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self.__db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self.__db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ self.__db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self.__db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ if not self.__db_functions[i].is_new:
+ self.db_deleted_functions.append(self.__db_functions[i])
+ del self.__db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == key:
+ return self.__db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return self.db_functions_id_index.has_key(key)
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ if not self.__db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self.__db_annotations[i])
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self.__db_id = id
+ self.__db_key = key
+ self.__db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation()
+ cp.db_id = self.db_id
+ cp.db_key = self.db_key
+ cp.db_value = self.db_value
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, data=None, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self.__db_data = data
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_oldObjId = oldObjId
+ self.__db_newObjId = newObjId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBChange.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange()
+ if self.db_data is not None:
+ cp.db_data = self.db_data.do_copy(new_ids, id_scope, id_remap)
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_oldObjId = self.db_oldObjId
+ cp.db_newObjId = self.db_newObjId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_oldObjId') and id_remap.has_key((self.db_what, self.db_oldObjId)):
+ cp.db_oldObjId = id_remap[(self.db_what, self.db_oldObjId)]
+ if hasattr(self, 'db_newObjId') and id_remap.has_key((self.db_what, self.db_newObjId)):
+ cp.db_newObjId = id_remap[(self.db_what, self.db_newObjId)]
+ if hasattr(self, 'db_parentObjId') and id_remap.has_key((self.db_parentObjType, self.db_parentObjId)):
+ cp.db_parentObjId = id_remap[(self.db_parentObjType, self.db_parentObjId)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_data is not None:
+ children.extend(self.db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_data is not None and self.db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self.__db_data
+ def __set_db_data(self, data):
+ self.__db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self.__db_data = data
+ def db_change_data(self, data):
+ self.__db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self.__db_data)
+ self.__db_data = None
+
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_oldObjId(self):
+ return self.__db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self.__db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self.__db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self.__db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self.__db_id = id
+ self.__db_pos = pos
+ self.__db_name = name
+ self.__db_type = type
+ self.__db_val = val
+ self.__db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBParameter.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter()
+ cp.db_id = self.db_id
+ cp.db_pos = self.db_pos
+ cp.db_name = self.db_name
+ cp.db_type = self.db_type
+ cp.db_val = self.db_val
+ cp.db_alias = self.db_alias
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_pos(self):
+ return self.__db_pos
+ def __set_db_pos(self, pos):
+ self.__db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self.__db_pos = pos
+ def db_change_pos(self, pos):
+ self.__db_pos = pos
+ def db_delete_pos(self, pos):
+ self.__db_pos = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_val(self):
+ return self.__db_val
+ def __set_db_val(self, val):
+ self.__db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self.__db_val = val
+ def db_change_val(self, val):
+ self.__db_val = val
+ def db_delete_val(self, val):
+ self.__db_val = None
+
+ def __get_db_alias(self):
+ return self.__db_alias
+ def __set_db_alias(self, alias):
+ self.__db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self.__db_alias = alias
+ def db_change_alias(self, alias):
+ self.__db_alias = alias
+ def db_delete_alias(self, alias):
+ self.__db_alias = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self.__db_id = id
+ self.db_deleted_ports = []
+ self.db_ports_id_index = {}
+ self.db_ports_type_index = {}
+ if ports is None:
+ self.__db_ports = []
+ else:
+ self.__db_ports = ports
+ for v in self.__db_ports:
+ self.db_ports_id_index[v.db_id] = v
+ self.db_ports_type_index[v.db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBConnection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection()
+ cp.db_id = self.db_id
+ if self.db_ports is None:
+ cp.db_ports = []
+ else:
+ cp.db_ports = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_ports]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_ports:
+ cp.db_ports_id_index[v.db_id] = v
+ cp.db_ports_type_index[v.db_type] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_ports)
+ if remove:
+ self.db_deleted_ports = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_ports(self):
+ return self.__db_ports
+ def __set_db_ports(self, ports):
+ self.__db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self.__db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self.__db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == port.db_id:
+ self.__db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self.__db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == port.db_id:
+ if not self.__db_ports[i].is_new:
+ self.db_deleted_ports.append(self.__db_ports[i])
+ del self.__db_ports[i]
+ break
+ del self.db_ports_id_index[port.db_id]
+ del self.db_ports_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == key:
+ return self.__db_ports[i]
+ return None
+ def db_get_port_by_id(self, key):
+ return self.db_ports_id_index[key]
+ def db_has_port_with_id(self, key):
+ return self.db_ports_id_index.has_key(key)
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return self.db_ports_type_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, operations=None, id=None, prevId=None, date=None, session=None, user=None, prune=None, annotations=None):
+ self.db_deleted_operations = []
+ self.db_operations_id_index = {}
+ if operations is None:
+ self.__db_operations = []
+ else:
+ self.__db_operations = operations
+ for v in self.__db_operations:
+ self.db_operations_id_index[v.db_id] = v
+ self.__db_id = id
+ self.__db_prevId = prevId
+ self.__db_date = date
+ self.__db_session = session
+ self.__db_user = user
+ self.__db_prune = prune
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction()
+ if self.db_operations is None:
+ cp.db_operations = []
+ else:
+ cp.db_operations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_operations]
+ cp.db_id = self.db_id
+ cp.db_prevId = self.db_prevId
+ cp.db_date = self.db_date
+ cp.db_session = self.db_session
+ cp.db_user = self.db_user
+ cp.db_prune = self.db_prune
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_operations:
+ cp.db_operations_id_index[v.db_id] = v
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.db_annotations_key_index[v.db_key] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_operations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_operations)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_operations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ for child in self.db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_operations(self):
+ return self.__db_operations
+ def __set_db_operations(self, operations):
+ self.__db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self.__db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self.__db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == operation.db_id:
+ self.__db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self.__db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == operation.db_id:
+ if not self.__db_operations[i].is_new:
+ self.db_deleted_operations.append(self.__db_operations[i])
+ del self.__db_operations[i]
+ break
+ del self.db_operations_id_index[operation.db_id]
+ def db_get_operation(self, key):
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == key:
+ return self.__db_operations[i]
+ return None
+ def db_get_operation_by_id(self, key):
+ return self.db_operations_id_index[key]
+ def db_has_operation_with_id(self, key):
+ return self.db_operations_id_index.has_key(key)
+
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_prevId(self):
+ return self.__db_prevId
+ def __set_db_prevId(self, prevId):
+ self.__db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self.__db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self.__db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self.__db_prevId = None
+
+ def __get_db_date(self):
+ return self.__db_date
+ def __set_db_date(self, date):
+ self.__db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self.__db_date = date
+ def db_change_date(self, date):
+ self.__db_date = date
+ def db_delete_date(self, date):
+ self.__db_date = None
+
+ def __get_db_session(self):
+ return self.__db_session
+ def __set_db_session(self, session):
+ self.__db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self.__db_session = session
+ def db_change_session(self, session):
+ self.__db_session = session
+ def db_delete_session(self, session):
+ self.__db_session = None
+
+ def __get_db_user(self):
+ return self.__db_user
+ def __set_db_user(self, user):
+ self.__db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self.__db_user = user
+ def db_change_user(self, user):
+ self.__db_user = user
+ def db_delete_user(self, user):
+ self.__db_user = None
+
+ def __get_db_prune(self):
+ return self.__db_prune
+ def __set_db_prune(self, prune):
+ self.__db_prune = prune
+ self.is_dirty = True
+ db_prune = property(__get_db_prune, __set_db_prune)
+ def db_add_prune(self, prune):
+ self.__db_prune = prune
+ def db_change_prune(self, prune):
+ self.__db_prune = prune
+ def db_delete_prune(self, prune):
+ self.__db_prune = None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ if not self.__db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self.__db_annotations[i])
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return self.db_annotations_key_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_objectId = objectId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBDelete.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete()
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_objectId = self.db_objectId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and id_remap.has_key((self.db_what, self.db_objectId)):
+ cp.db_objectId = id_remap[(self.db_what, self.db_objectId)]
+ if hasattr(self, 'db_parentObjId') and id_remap.has_key((self.db_parentObjType, self.db_parentObjId)):
+ cp.db_parentObjId = id_remap[(self.db_parentObjType, self.db_parentObjId)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_objectId(self):
+ return self.__db_objectId
+ def __set_db_objectId(self, objectId):
+ self.__db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self.__db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, version=None, name=None, last_modified=None, dbHost=None, dbPort=None, dbName=None, actions=None, tags=None, abstractions=None):
+ self.__db_id = id
+ self.__db_version = version
+ self.__db_name = name
+ self.__db_last_modified = last_modified
+ self.__db_dbHost = dbHost
+ self.__db_dbPort = dbPort
+ self.__db_dbName = dbName
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self.__db_actions = []
+ else:
+ self.__db_actions = actions
+ for v in self.__db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self.__db_tags = []
+ else:
+ self.__db_tags = tags
+ for v in self.__db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.db_deleted_abstractions = []
+ self.db_abstractions_id_index = {}
+ if abstractions is None:
+ self.__db_abstractions = []
+ else:
+ self.__db_abstractions = abstractions
+ for v in self.__db_abstractions:
+ self.db_abstractions_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail()
+ cp.db_id = self.db_id
+ cp.db_version = self.db_version
+ cp.db_name = self.db_name
+ cp.db_last_modified = self.db_last_modified
+ cp.db_dbHost = self.db_dbHost
+ cp.db_dbPort = self.db_dbPort
+ cp.db_dbName = self.db_dbName
+ if self.db_actions is None:
+ cp.db_actions = []
+ else:
+ cp.db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_actions]
+ if self.db_tags is None:
+ cp.db_tags = []
+ else:
+ cp.db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_tags]
+ if self.db_abstractions is None:
+ cp.db_abstractions = []
+ else:
+ cp.db_abstractions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_abstractions]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp.__db_actions:
+ cp.db_actions_id_index[v.db_id] = v
+ for v in cp.__db_tags:
+ cp.db_tags_id_index[v.db_id] = v
+ cp.db_tags_name_index[v.db_name] = v
+ for v in cp.__db_abstractions:
+ cp.db_abstractions_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self.db_abstractions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_abstraction(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ children.extend(self.db_deleted_abstractions)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ self.db_deleted_abstractions = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_actions:
+ if child.has_changes():
+ return True
+ for child in self.db_tags:
+ if child.has_changes():
+ return True
+ for child in self.db_abstractions:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_last_modified(self):
+ return self.__db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self.__db_last_modified = None
+
+ def __get_db_dbHost(self):
+ return self.__db_dbHost
+ def __set_db_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ self.is_dirty = True
+ db_dbHost = property(__get_db_dbHost, __set_db_dbHost)
+ def db_add_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ def db_change_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ def db_delete_dbHost(self, dbHost):
+ self.__db_dbHost = None
+
+ def __get_db_dbPort(self):
+ return self.__db_dbPort
+ def __set_db_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ self.is_dirty = True
+ db_dbPort = property(__get_db_dbPort, __set_db_dbPort)
+ def db_add_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ def db_change_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ def db_delete_dbPort(self, dbPort):
+ self.__db_dbPort = None
+
+ def __get_db_dbName(self):
+ return self.__db_dbName
+ def __set_db_dbName(self, dbName):
+ self.__db_dbName = dbName
+ self.is_dirty = True
+ db_dbName = property(__get_db_dbName, __set_db_dbName)
+ def db_add_dbName(self, dbName):
+ self.__db_dbName = dbName
+ def db_change_dbName(self, dbName):
+ self.__db_dbName = dbName
+ def db_delete_dbName(self, dbName):
+ self.__db_dbName = None
+
+ def __get_db_actions(self):
+ return self.__db_actions
+ def __set_db_actions(self, actions):
+ self.__db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self.__db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ self.__db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ if not self.__db_actions[i].is_new:
+ self.db_deleted_actions.append(self.__db_actions[i])
+ del self.__db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == key:
+ return self.__db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return self.db_actions_id_index.has_key(key)
+
+ def __get_db_tags(self):
+ return self.__db_tags
+ def __set_db_tags(self, tags):
+ self.__db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self.__db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ self.__db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ if not self.__db_tags[i].is_new:
+ self.db_deleted_tags.append(self.__db_tags[i])
+ del self.__db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == key:
+ return self.__db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return self.db_tags_id_index.has_key(key)
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return self.db_tags_name_index.has_key(key)
+
+ def __get_db_abstractions(self):
+ return self.__db_abstractions
+ def __set_db_abstractions(self, abstractions):
+ self.__db_abstractions = abstractions
+ self.is_dirty = True
+ db_abstractions = property(__get_db_abstractions, __set_db_abstractions)
+ def db_get_abstractions(self):
+ return self.__db_abstractions
+ def db_add_abstraction(self, abstraction):
+ self.is_dirty = True
+ self.__db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_change_abstraction(self, abstraction):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == abstraction.db_id:
+ self.__db_abstractions[i] = abstraction
+ found = True
+ break
+ if not found:
+ self.__db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_delete_abstraction(self, abstraction):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == abstraction.db_id:
+ if not self.__db_abstractions[i].is_new:
+ self.db_deleted_abstractions.append(self.__db_abstractions[i])
+ del self.__db_abstractions[i]
+ break
+ del self.db_abstractions_id_index[abstraction.db_id]
+ def db_get_abstraction(self, key):
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == key:
+ return self.__db_abstractions[i]
+ return None
+ def db_get_abstraction_by_id(self, key):
+ return self.db_abstractions_id_index[key]
+ def db_has_abstraction_with_id(self, key):
+ return self.db_abstractions_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, module_id=None, module_name=None, annotations=None):
+ self.__db_id = id
+ self.__db_ts_start = ts_start
+ self.__db_ts_end = ts_end
+ self.__db_module_id = module_id
+ self.__db_module_name = module_name
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec()
+ cp.db_id = self.db_id
+ cp.db_ts_start = self.db_ts_start
+ cp.db_ts_end = self.db_ts_end
+ cp.db_module_id = self.db_module_id
+ cp.db_module_name = self.db_module_name
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and id_remap.has_key(('module', self.db_module_id)):
+ cp.db_module_id = id_remap[('module', self.db_module_id)]
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_ts_start(self):
+ return self.__db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self.__db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self.__db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self.__db_ts_end = None
+
+ def __get_db_module_id(self):
+ return self.__db_module_id
+ def __set_db_module_id(self, module_id):
+ self.__db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self.__db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self.__db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self.__db_module_id = None
+
+ def __get_db_module_name(self):
+ return self.__db_module_name
+ def __set_db_module_name(self, module_name):
+ self.__db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self.__db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self.__db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self.__db_module_name = None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ if not self.__db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self.__db_annotations[i])
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
diff --git a/vistrails/db/versions/v0_8_0/domain/id_scope.py b/vistrails/db/versions/v0_8_0/domain/id_scope.py
new file mode 100644
index 0000000..c510efa
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/domain/id_scope.py
@@ -0,0 +1,76 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L, remap=None):
+ self.ids = {}
+ self.beginId = beginId
+ if remap is None:
+ self.remap = {}
+ else:
+ self.remap = remap
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ cp.remap = copy.copy(self.remap)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ if self.remap.has_key(objType):
+ objType = self.remap[objType]
+ if self.ids.has_key(objType):
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ else:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ if self.remap.has_key(objType):
+ objType = self.remap[objType]
+ if not self.ids.has_key(objType) or self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ if self.remap.has_key(objType):
+ objType = self.remap[objType]
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v0_8_0/domain/vistrail.py b/vistrails/db/versions/v0_8_0/domain/vistrail.py
new file mode 100644
index 0000000..9c9b23c
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/domain/vistrail.py
@@ -0,0 +1,48 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBVistrail as _DBVistrail
+from auto_gen import DBAdd, DBChange, DBDelete, DBAbstractionRef, DBModule
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAdd.vtType: 'operation',
+ DBChange.vtType: 'operation',
+ DBDelete.vtType: 'operation',
+ DBAbstractionRef.vtType: DBModule.vtType})
+
+ self.idScope.setBeginId('action', 1)
diff --git a/vistrails/db/versions/v0_8_0/domain/workflow.py b/vistrails/db/versions/v0_8_0/domain/workflow.py
new file mode 100644
index 0000000..2a8f059
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/domain/workflow.py
@@ -0,0 +1,126 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1)
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.objects = {}
+ for (child, _, _) in cp.db_children():
+ cp.addToIndex(child)
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ def addToIndex(self, object):
+ self.objects[(object.vtType, object.getPrimaryKey())] = object
+
+ def deleteFromIndex(self, object):
+ del self.objects[(object.vtType, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_print_objects(self):
+ for k,v in self.objects.iteritems():
+ print '%s: %s' % (k, v)
+
+ def db_get_object(self, type, id):
+ return self.objects[(type, id)]
+
+ def db_add_object(self, object, parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_add_%s' % object.vtType
+ objCopy = copy.copy(object)
+ getattr(parentObj, funname)(objCopy)
+ self.addToIndex(objCopy)
+
+ def db_change_object(self, object, parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_change_%s' % object.vtType
+ objCopy = copy.copy(object)
+ getattr(parentObj, funname)(objCopy)
+ self.addToIndex(objCopy)
+
+ def db_delete_object(self, objId, objType,
+ parentObjType=None, parentObjId=None):
+ if parentObjType is None or parentObjId is None:
+ parentObj = self
+ else:
+ try:
+ parentObj = self.objects[(parentObjType, parentObjId)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parentObjType, parentObjId)
+ raise Exception(msg)
+ funname = 'db_get_%s' % objType
+ try:
+ object = getattr(parentObj, funname)(objId)
+ except AttributeError:
+ attr_name = 'db_%s' % objType
+ object = getattr(parentObj, attr_name)
+ funname = 'db_delete_%s' % objType
+ getattr(parentObj, funname)(object)
+ self.deleteFromIndex(object)
diff --git a/vistrails/db/versions/v0_8_0/persistence/__init__.py b/vistrails/db/versions/v0_8_0/persistence/__init__.py
new file mode 100644
index 0000000..37eacf9
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/persistence/__init__.py
@@ -0,0 +1,92 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+from vistrails.core.system import get_elementtree_library
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_8_0 import version as my_version
+
+ElementTree = get_elementtree_library()
+
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def parse_xml_file(self, filename):
+ return ElementTree.parse(filename)
+
+ def write_xml_file(self, filename, tree):
+ tree.write(filename)
+
+ def read_xml_object(self, vtType, node):
+ return self['xml'][vtType].fromXML(node)
+
+ def write_xml_object(self, obj, node=None):
+ res_node = self['xml'][obj.vtType].toXML(obj, node)
+ return res_node
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ """open_from_xml(filename) -> DBVistrail"""
+ if tree is None:
+ tree = self.parse_xml_file(filename)
+ vistrail = self.read_xml_object(vtType, tree.getroot())
+ return vistrail
+
+ def save_to_xml(self, obj, filename):
+ """save_to_xml(obj, filename: str) -> None
+
+ """
+ root = self.write_xml_object(obj)
+ root.set('version', my_version)
+ root.set('xmlns:xsi', 'http://www.w3.org/2001/XMLSchema-instance')
+ root.set('xsi:schemaLocation', 'http://www.vistrails.org/vistrail.xsd')
+ tree = ElementTree.ElementTree(root)
+ self.write_xml_file(filename, tree)
+
+ def serialize(self, object):
+ root = self.write_xml_object(object)
+ return ElementTree.tostring(root)
+
+ def unserialize(self, str, obj_type):
+ try:
+ root = ElementTree.fromstring(str)
+ return self.read_xml_object(obj_type, root)
+ except SyntaxError, e:
+ msg = "Invalid VisTrails serialized object %s" % str
+ raise VistrailsDBException(msg)
+ return None
diff --git a/vistrails/db/versions/v0_8_0/persistence/sql/__init__.py b/vistrails/db/versions/v0_8_0/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_8_0/persistence/sql/auto_gen.py b/vistrails/db/versions/v0_8_0/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..a8c910c
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/persistence/sql/auto_gen.py
@@ -0,0 +1,2332 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v0_8_0.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(22)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[4], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[5], 'long', 'int')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ spec=spec,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_vistrailId = vistrailId
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(22)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'package', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[3], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[5], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ parent = self.convertFromDB(row[7], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ package=package,
+ version=version,
+ id=id)
+ module.db_parentType = parentType
+ module.db_vistrailId = vistrailId
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'package', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[3], 'long', 'int')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_parentType = parentType
+ tag.db_vistrailId = vistrailId
+ tag.db_parent = parent
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_tag(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec,
+ id=id)
+ port.db_parentType = parentType
+ port.db_vistrailId = vistrailId
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'vt_id', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'vt_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ vistrailId = self.convertFromDB(row[1], 'long', 'int')
+
+ log = DBLog(id=id)
+ log.db_vistrailId = vistrailId
+ log.is_dirty = False
+ res[('log', id)] = log
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'vt_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_workflow_execs:
+ child.db_log = obj.db_id
+ for child in obj.db_machines:
+ child.db_log = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'module_exec_id']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ module_execs = self.convertFromDB(row[8], 'long', 'int')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'module_exec_id']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_module_exec') and obj.db_module_exec is not None:
+ columnMap['module_exec_id'] = \
+ self.convertToDB(obj.db_module_execs, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_module_execs:
+ child.db_machine_id = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_vistrailId = vistrailId
+ add.is_dirty = False
+ res[('add', id)] = add
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_vistrailId = vistrailId
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'vt_id', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_vistrailId = vistrailId
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'vt_id', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'log_id', 'vt_id']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ vt_version = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[4], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[5], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[6], 'long', 'int')
+ parent_type = self.convertFromDB(row[7], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[8], 'long', 'int')
+ name = self.convertFromDB(row[9], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[10], 'long', 'int')
+ vistrailId = self.convertFromDB(row[11], 'long', 'int')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_vistrailId = vistrailId
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'log_id', 'vt_id']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_module_execs:
+ child.db_workflow_exec = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_vistrailId = vistrailId
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'vt_id', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'vt_id']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[2], 'long', 'int')
+
+ abstraction = DBAbstraction(name=name,
+ id=id)
+ abstraction.db_vistrail = vistrail
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_abstraction(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'vt_id']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_actions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'vt_id']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrailId = self.convertFromDB(row[2], 'long', 'int')
+
+ workflow = DBWorkflow(name=name,
+ id=id)
+ workflow.db_vistrailId = vistrailId
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'vt_id']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_connections:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_modules:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionRefSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'cache', 'abstraction_id', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(1023)')
+ cache = self.convertFromDB(row[2], 'int', 'int')
+ abstraction_id = self.convertFromDB(row[3], 'long', 'int')
+ version = self.convertFromDB(row[4], 'long', 'int')
+ parentType = self.convertFromDB(row[5], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ parent = self.convertFromDB(row[7], 'long', 'long')
+
+ abstractionRef = DBAbstractionRef(cache=cache,
+ abstraction_id=abstraction_id,
+ version=version,
+ id=id)
+ abstractionRef.db_parentType = parentType
+ abstractionRef.db_vistrailId = vistrailId
+ abstractionRef.db_parent = parent
+ abstractionRef.is_dirty = False
+ res[('abstractionRef', id)] = abstractionRef
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'cache', 'abstraction_id', 'version', 'parent_type', 'vt_id', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_abstraction_id') and obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction_ref'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[4], 'long', 'int')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_vistrailId = vistrailId
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'vt_id', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_vistrailId = vistrailId
+ change.is_dirty = False
+ res[('change', id)] = change
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'vt_id', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_vistrailId = vistrailId
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'vt_id', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'vt_id', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[2], 'long', 'int')
+ parent = self.convertFromDB(row[3], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_vistrailId = vistrailId
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'vt_id', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_type', 'vt_id', 'parent_id']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'str', 'varchar(1023)')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ prune = self.convertFromDB(row[5], 'int', 'int')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ id=id)
+ action.db_parentType = parentType
+ action.db_vistrailId = vistrailId
+ action.db_parent = parent
+ action.is_dirty = False
+ res[('action', id)] = action
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_action(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_type', 'vt_id', 'parent_id']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_prune') and obj.db_prune is not None:
+ columnMap['prune'] = \
+ self.convertToDB(obj.db_prune, 'int', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_vistrailId = vistrailId
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'vt_id']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['vt_id'] = self.convertToDB(id, 'long', 'int')
+ version = self.convertFromDB(row[1], 'str', 'char(16)')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[3], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ global_props['vt_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_actions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_abstractions:
+ child.db_vistrail = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'module_id', 'module_name', 'machine_id', 'wf_exec_id', 'vt_id']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ module_id = self.convertFromDB(row[3], 'long', 'int')
+ module_name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ machine_id = self.convertFromDB(row[5], 'long', 'int')
+ workflow_exec = self.convertFromDB(row[6], 'long', 'int')
+ vistrailId = self.convertFromDB(row[7], 'long', 'int')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ module_id=module_id,
+ module_name=module_name,
+ id=id)
+ module_exec.db_machine_id = machine_id
+ module_exec.db_workflow_exec = workflow_exec
+ module_exec.db_vistrailId = vistrailId
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('machine', obj.db_machine_id)]
+ p.db_add_module_exec(obj)
+ p = all_objects[('workflow_exec', obj.db_workflow_exec)]
+ p.db_add_module_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'module_id', 'module_name', 'machine_id', 'wf_exec_id', 'vt_id']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_workflow_exec') and obj.db_workflow_exec is not None:
+ columnMap['wf_exec_id'] = \
+ self.convertToDB(obj.db_workflow_exec, 'long', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefSQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v0_8_0/persistence/sql/sql_dao.py b/vistrails/db/versions/v0_8_0/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..c54eb03
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/persistence/sql/sql_dao.py
@@ -0,0 +1,165 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return "'" + str(value).replace("'", "''") + "'"
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ return str(value)
+ elif type == 'int':
+ return str(value)
+ elif type == 'date':
+ return "'" + value.isoformat() + "'"
+ elif type == 'datetime':
+ return "'" + value.strftime('%Y-%m-%d %H:%M:%S') + "'"
+ else:
+ return str(value)
+
+ return "''"
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None,
+ forUpdate=False):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ if forUpdate:
+ dbCommand += " FOR UPDATE"
+ dbCommand += ";"
+ return dbCommand
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ valueStr = ', '.join(values)
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s);""" % \
+ (table, columnStr, valueStr)
+ return dbCommand
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ setStr += '%s %s = %s' % (comma, column, value)
+ comma = ','
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """UPDATE %s SET %s WHERE %s;""" % \
+ (table, setStr, whereStr)
+ return dbCommand
+
+ def createSQLDelete(self, table, whereMap):
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND '
+ dbCommand = """DELETE FROM %s WHERE %s;""" % \
+ (table, whereStr)
+ return dbCommand
+
+ def executeSQL(self, db, dbCommand, isFetch):
+ # print 'db: %s' % dbCommand
+ data = None
+ cursor = db.cursor()
+ cursor.execute(dbCommand)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ cursor.close()
+ return data
+
+ def start_transaction(self, db):
+ db.begin()
+
+ def commit_transaction(self, db):
+ db.commit()
+
+ def rollback_transaction(self, db):
+ db.rollback()
diff --git a/vistrails/db/versions/v0_8_0/persistence/xml/__init__.py b/vistrails/db/versions/v0_8_0/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_8_0/persistence/xml/auto_gen.py b/vistrails/db/versions/v0_8_0/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..1c4a266
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/persistence/xml/auto_gen.py
@@ -0,0 +1,1531 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from vistrails.core.system import get_elementtree_library
+
+from xml_dao import XMLDAO
+from vistrails.db.versions.v0_8_0.domain import *
+
+ElementTree = get_elementtree_library()
+
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'portSpec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('spec', None)
+ spec = self.convertFromStr(data, 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, node=None):
+ if node is None:
+ node = ElementTree.Element('portSpec')
+
+ # set attributes
+ node.set('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.set('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.set('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.set('spec',self.convertToStr(portSpec.db_spec, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'module':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ package=package,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, node=None):
+ if node is None:
+ node = ElementTree.Element('module')
+
+ # set attributes
+ node.set('id',self.convertToStr(module.db_id, 'long'))
+ node.set('cache',self.convertToStr(module.db_cache, 'int'))
+ node.set('name',self.convertToStr(module.db_name, 'str'))
+ node.set('package',self.convertToStr(module.db_package, 'str'))
+ node.set('version',self.convertToStr(module.db_version, 'str'))
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = module.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'tag':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, node=None):
+ if node is None:
+ node = ElementTree.Element('tag')
+
+ # set attributes
+ node.set('id',self.convertToStr(tag.db_id, 'long'))
+ node.set('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'port':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('moduleId', None)
+ moduleId = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ moduleName = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('spec', None)
+ spec = self.convertFromStr(data, 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, node=None):
+ if node is None:
+ node = ElementTree.Element('port')
+
+ # set attributes
+ node.set('id',self.convertToStr(port.db_id, 'long'))
+ node.set('type',self.convertToStr(port.db_type, 'str'))
+ node.set('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.set('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.set('name',self.convertToStr(port.db_name, 'str'))
+ node.set('spec',self.convertToStr(port.db_spec, 'str'))
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'log':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+
+ workflow_execs = []
+ machines = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'workflowExec':
+ _data = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs.append(_data)
+ elif child.tag == 'machine':
+ _data = self.getDao('machine').fromXML(child)
+ machines.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLog(id=id,
+ workflow_execs=workflow_execs,
+ machines=machines)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, node=None):
+ if node is None:
+ node = ElementTree.Element('log')
+
+ # set attributes
+ node.set('id',self.convertToStr(log.db_id, 'long'))
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs:
+ childNode = ElementTree.SubElement(node, 'workflow_exec')
+ self.getDao('workflow_exec').toXML(workflow_exec, childNode)
+ machines = log.db_machines
+ for machine in machines:
+ childNode = ElementTree.SubElement(node, 'machine')
+ self.getDao('machine').toXML(machine, childNode)
+
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'machine':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('os', None)
+ os = self.convertFromStr(data, 'str')
+ data = node.get('architecture', None)
+ architecture = self.convertFromStr(data, 'str')
+ data = node.get('processor', None)
+ processor = self.convertFromStr(data, 'str')
+ data = node.get('ram', None)
+ ram = self.convertFromStr(data, 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, node=None):
+ if node is None:
+ node = ElementTree.Element('machine')
+
+ # set attributes
+ node.set('id',self.convertToStr(machine.db_id, 'long'))
+ node.set('name',self.convertToStr(machine.db_name, 'str'))
+ node.set('os',self.convertToStr(machine.db_os, 'str'))
+ node.set('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.set('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.set('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'add':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAdd(data=data,
+ id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, node=None):
+ if node is None:
+ node = ElementTree.Element('add')
+
+ # set attributes
+ node.set('id',self.convertToStr(add.db_id, 'long'))
+ node.set('what',self.convertToStr(add.db_what, 'str'))
+ node.set('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # set elements
+ data = add.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'other':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'value':
+ _data = self.convertFromStr(child.text,'')
+ value = _data
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, node=None):
+ if node is None:
+ node = ElementTree.Element('other')
+
+ # set attributes
+ node.set('id',self.convertToStr(other.db_id, 'long'))
+ node.set('key',self.convertToStr(other.db_key, 'str'))
+
+ # set elements
+
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'location':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('x', None)
+ x = self.convertFromStr(data, 'float')
+ data = node.get('y', None)
+ y = self.convertFromStr(data, 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, node=None):
+ if node is None:
+ node = ElementTree.Element('location')
+
+ # set attributes
+ node.set('id',self.convertToStr(location.db_id, 'long'))
+ node.set('x',self.convertToStr(location.db_x, 'float'))
+ node.set('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflowExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('ip', None)
+ ip = self.convertFromStr(data, 'str')
+ data = node.get('vtVersion', None)
+ vt_version = self.convertFromStr(data, 'str')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('parentId', None)
+ parent_id = self.convertFromStr(data, 'long')
+ data = node.get('parentType', None)
+ parent_type = self.convertFromStr(data, 'str')
+ data = node.get('parentVersion', None)
+ parent_version = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ module_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ module_execs.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflowExec(id=id,
+ user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ module_execs=module_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('workflowExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.set('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.set('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.set('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.set('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.set('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.set('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.set('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.set('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # set elements
+ module_execs = workflow_exec.db_module_execs
+ for module_exec in module_execs:
+ childNode = ElementTree.SubElement(node, 'module_exec')
+ self.getDao('module_exec').toXML(module_exec, childNode)
+
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'function':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ parameters = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ parameters.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, node=None):
+ if node is None:
+ node = ElementTree.Element('function')
+
+ # set attributes
+ node.set('id',self.convertToStr(function.db_id, 'long'))
+ node.set('pos',self.convertToStr(function.db_pos, 'long'))
+ node.set('name',self.convertToStr(function.db_name, 'str'))
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(parameter, childNode)
+
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'abstraction':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child.tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstraction(id=id,
+ name=name,
+ actions=actions,
+ tags=tags)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, node=None):
+ if node is None:
+ node = ElementTree.Element('abstraction')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.set('name',self.convertToStr(abstraction.db_name, 'str'))
+
+ # set elements
+ actions = abstraction.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = abstraction.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflow':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ connections = []
+ annotations = []
+ others = []
+ modules = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ connections.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ others.append(_data)
+ elif child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ modules.append(_data)
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ modules.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflow(modules=modules,
+ id=id,
+ name=name,
+ connections=connections,
+ annotations=annotations,
+ others=others)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, node=None):
+ if node is None:
+ node = ElementTree.Element('workflow')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow.db_id, 'long'))
+ node.set('name',self.convertToStr(workflow.db_name, 'str'))
+
+ # set elements
+ connections = workflow.db_connections
+ for connection in connections:
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(connection, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ others = workflow.db_others
+ for other in others:
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(other, childNode)
+ modules = workflow.db_modules
+ for module in modules:
+ if module.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(module, childNode)
+ elif module.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(module, childNode)
+
+ return node
+
+class DBAbstractionRefXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'abstractionRef':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('abstractionId', None)
+ abstraction_id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'long')
+
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstractionRef(id=id,
+ name=name,
+ cache=cache,
+ abstraction_id=abstraction_id,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstractionRef, node=None):
+ if node is None:
+ node = ElementTree.Element('abstractionRef')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstractionRef.db_id, 'long'))
+ node.set('name',self.convertToStr(abstractionRef.db_name, 'str'))
+ node.set('cache',self.convertToStr(abstractionRef.db_cache, 'int'))
+ node.set('abstractionId',self.convertToStr(abstractionRef.db_abstraction_id, 'long'))
+ node.set('version',self.convertToStr(abstractionRef.db_version, 'long'))
+
+ # set elements
+ location = abstractionRef.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = abstractionRef.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = abstractionRef.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'annotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, node=None):
+ if node is None:
+ node = ElementTree.Element('annotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(annotation.db_id, 'long'))
+ node.set('key',self.convertToStr(annotation.db_key, 'str'))
+ node.set('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'change':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('oldObjId', None)
+ oldObjId = self.convertFromStr(data, 'long')
+ data = node.get('newObjId', None)
+ newObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBChange(data=data,
+ id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, node=None):
+ if node is None:
+ node = ElementTree.Element('change')
+
+ # set attributes
+ node.set('id',self.convertToStr(change.db_id, 'long'))
+ node.set('what',self.convertToStr(change.db_what, 'str'))
+ node.set('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.set('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.set('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # set elements
+ data = change.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'parameter':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('val', None)
+ val = self.convertFromStr(data, 'str')
+ data = node.get('alias', None)
+ alias = self.convertFromStr(data, 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, node=None):
+ if node is None:
+ node = ElementTree.Element('parameter')
+
+ # set attributes
+ node.set('id',self.convertToStr(parameter.db_id, 'long'))
+ node.set('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.set('name',self.convertToStr(parameter.db_name, 'str'))
+ node.set('type',self.convertToStr(parameter.db_type, 'str'))
+ node.set('val',self.convertToStr(parameter.db_val, 'str'))
+ node.set('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'connection':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+
+ ports = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ ports.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, node=None):
+ if node is None:
+ node = ElementTree.Element('connection')
+
+ # set attributes
+ node.set('id',self.convertToStr(connection.db_id, 'long'))
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(port, childNode)
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'action':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('prevId', None)
+ prevId = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'str')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('prune', None)
+ prune = self.convertFromStr(data, 'int')
+
+ annotations = []
+ operations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'add':
+ _data = self.getDao('add').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'delete':
+ _data = self.getDao('delete').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'change':
+ _data = self.getDao('change').fromXML(child)
+ operations.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAction(operations=operations,
+ id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, node=None):
+ if node is None:
+ node = ElementTree.Element('action')
+
+ # set attributes
+ node.set('id',self.convertToStr(action.db_id, 'long'))
+ node.set('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.set('date',self.convertToStr(action.db_date, 'datetime'))
+ node.set('session',self.convertToStr(action.db_session, 'str'))
+ node.set('user',self.convertToStr(action.db_user, 'str'))
+ node.set('prune',self.convertToStr(action.db_prune, 'int'))
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ childNode = ElementTree.SubElement(node, 'add')
+ self.getDao('add').toXML(operation, childNode)
+ elif operation.vtType == 'delete':
+ childNode = ElementTree.SubElement(node, 'delete')
+ self.getDao('delete').toXML(operation, childNode)
+ elif operation.vtType == 'change':
+ childNode = ElementTree.SubElement(node, 'change')
+ self.getDao('change').toXML(operation, childNode)
+
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'delete':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, node=None):
+ if node is None:
+ node = ElementTree.Element('delete')
+
+ # set attributes
+ node.set('id',self.convertToStr(delete.db_id, 'long'))
+ node.set('what',self.convertToStr(delete.db_what, 'str'))
+ node.set('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'vistrail':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('dbHost', None)
+ dbHost = self.convertFromStr(data, 'str')
+ data = node.get('dbPort', None)
+ dbPort = self.convertFromStr(data, 'int')
+ data = node.get('dbName', None)
+ dbName = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+ abstractions = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child.tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ abstractions.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ dbHost=dbHost,
+ dbPort=dbPort,
+ dbName=dbName,
+ actions=actions,
+ tags=tags,
+ abstractions=abstractions)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, node=None):
+ if node is None:
+ node = ElementTree.Element('vistrail')
+
+ # set attributes
+ node.set('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.set('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.set('name',self.convertToStr(vistrail.db_name, 'str'))
+ node.set('dbHost',self.convertToStr(vistrail.db_dbHost, 'str'))
+ node.set('dbPort',self.convertToStr(vistrail.db_dbPort, 'int'))
+ node.set('dbName',self.convertToStr(vistrail.db_dbName, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = vistrail.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+ abstractions = vistrail.db_abstractions
+ for abstraction in abstractions:
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(abstraction, childNode)
+
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'moduleExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ module_name = self.convertFromStr(data, 'str')
+
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ module_id=module_id,
+ module_name=module_name,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.set('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.set('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v0_8_0/persistence/xml/xml_dao.py b/vistrails/db/versions/v0_8_0/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..955c01a
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/persistence/xml/xml_dao.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v0_8_0/schemas/sql/vistrails.sql b/vistrails/db/versions/v0_8_0/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..bbb4a0c
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/schemas/sql/vistrails.sql
@@ -0,0 +1,249 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(22),
+ type varchar(255),
+ spec varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ package varchar(511),
+ version varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ spec varchar(4095),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int,
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ module_exec_id int
+) engine=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ name varchar(255),
+ log_id int,
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction(
+ id int,
+ name varchar(255),
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE workflow(
+ id int,
+ name varchar(255),
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction_ref(
+ id int,
+ name varchar(1023),
+ cache int,
+ abstraction_id int,
+ version int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session varchar(1023),
+ user varchar(255),
+ prune int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ module_id int,
+ module_name varchar(255),
+ machine_id int,
+ wf_exec_id int,
+ vt_id int
+) engine=InnoDB;
+
diff --git a/vistrails/db/versions/v0_8_0/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v0_8_0/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..a4fd64c
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,38 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, tag, port, log_tbl, machine, add_tbl, other, location, workflow_exec, function, abstraction, workflow, abstraction_ref, annotation, change_tbl, parameter, connection_tbl, action, delete_tbl, vistrail, module_exec
diff --git a/vistrails/db/versions/v0_8_0/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_8_0/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..276a2c0
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/schemas/xml/vistrail.xsd
@@ -0,0 +1,237 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="dbHost" type="xs:string"/>
+ <xs:attribute name="dbPort" type="xs:int"/>
+ <xs:attribute name="dbName" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:string"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="prune" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstractionRef">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="abstractionId" type="xs:int"/>
+ <xs:attribute name="version" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_8_0/specs/abstraction.xml b/vistrails/db/versions/v0_8_0/specs/abstraction.xml
new file mode 100644
index 0000000..3cbb63a
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/abstraction.xml
@@ -0,0 +1,65 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="vistrail" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/abstractionRef.xml b/vistrails/db/versions/v0_8_0/specs/abstractionRef.xml
new file mode 100644
index 0000000..46b61ba
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/abstractionRef.xml
@@ -0,0 +1,100 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstractionRef">
+ <layout>
+ <xml name="abstractionRef" nodeType="xs:element"/>
+ <sql table="abstraction_ref"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml name="cache" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_id" type="long">
+ <xml name="abstractionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/action.xml b/vistrails/db/versions/v0_8_0/specs/action.xml
new file mode 100644
index 0000000..1c7d3c5
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/action.xml
@@ -0,0 +1,110 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="prune" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/add.xml b/vistrails/db/versions/v0_8_0/specs/add.xml
new file mode 100644
index 0000000..11f560c
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/add.xml
@@ -0,0 +1,111 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/annotation.xml b/vistrails/db/versions/v0_8_0/specs/annotation.xml
new file mode 100644
index 0000000..ba8194f
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/annotation.xml
@@ -0,0 +1,97 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/change.xml b/vistrails/db/versions/v0_8_0/specs/change.xml
new file mode 100644
index 0000000..8135c18
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/change.xml
@@ -0,0 +1,116 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/connection.xml b/vistrails/db/versions/v0_8_0/specs/connection.xml
new file mode 100644
index 0000000..b559fab
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/connection.xml
@@ -0,0 +1,74 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/delete.xml b/vistrails/db/versions/v0_8_0/specs/delete.xml
new file mode 100644
index 0000000..abcdfdb
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/delete.xml
@@ -0,0 +1,78 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/function.xml b/vistrails/db/versions/v0_8_0/specs/function.xml
new file mode 100644
index 0000000..a95590d
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/function.xml
@@ -0,0 +1,86 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/location.xml b/vistrails/db/versions/v0_8_0/specs/location.xml
new file mode 100644
index 0000000..99c62f7
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/location.xml
@@ -0,0 +1,83 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_8_0/specs/log.xml b/vistrails/db/versions/v0_8_0/specs/log.xml
new file mode 100644
index 0000000..ca8720e
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/log.xml
@@ -0,0 +1,62 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/machine.xml b/vistrails/db/versions/v0_8_0/specs/machine.xml
new file mode 100644
index 0000000..dea813d
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/machine.xml
@@ -0,0 +1,85 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="long" mapping="one-to-many">
+ <sql column="module_exec_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/module.xml b/vistrails/db/versions/v0_8_0/specs/module.xml
new file mode 100644
index 0000000..fc9ed2a
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/module.xml
@@ -0,0 +1,107 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/module_exec.xml b/vistrails/db/versions/v0_8_0/specs/module_exec.xml
new file mode 100644
index 0000000..465407b
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/module_exec.xml
@@ -0,0 +1,86 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="machine" name="machine_id" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="machine_id" type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/other.xml b/vistrails/db/versions/v0_8_0/specs/other.xml
new file mode 100644
index 0000000..40e1388
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/other.xml
@@ -0,0 +1,79 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/parameter.xml b/vistrails/db/versions/v0_8_0/specs/parameter.xml
new file mode 100644
index 0000000..78f6cf7
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/parameter.xml
@@ -0,0 +1,94 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/port.xml b/vistrails/db/versions/v0_8_0/specs/port.xml
new file mode 100644
index 0000000..94f7671
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/port.xml
@@ -0,0 +1,95 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/portSpec.xml b/vistrails/db/versions/v0_8_0/specs/portSpec.xml
new file mode 100644
index 0000000..e42a5f0
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/portSpec.xml
@@ -0,0 +1,84 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(22)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/tag.xml b/vistrails/db/versions/v0_8_0/specs/tag.xml
new file mode 100644
index 0000000..f8412b9
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/tag.xml
@@ -0,0 +1,71 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/vistrail.xml b/vistrails/db/versions/v0_8_0/specs/vistrail.xml
new file mode 100644
index 0000000..ccbd34c
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/vistrail.xml
@@ -0,0 +1,85 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="vt_id"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property name="dbHost" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="dbPort" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="dbName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="abstraction" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_8_0/specs/workflow.xml b/vistrails/db/versions/v0_8_0/specs/workflow.xml
new file mode 100644
index 0000000..56189f1
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/workflow.xml
@@ -0,0 +1,80 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstractionRef" ref="true" object="abstractionRef">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_8_0/specs/workflow_exec.xml b/vistrails/db/versions/v0_8_0/specs/workflow_exec.xml
new file mode 100644
index 0000000..b616623
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/specs/workflow_exec.xml
@@ -0,0 +1,106 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_0/translate/__init__.py b/vistrails/db/versions/v0_8_0/translate/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_8_0/translate/v0_7_0.py b/vistrails/db/versions/v0_8_0/translate/v0_7_0.py
new file mode 100644
index 0000000..67ade06
--- /dev/null
+++ b/vistrails/db/versions/v0_8_0/translate/v0_7_0.py
@@ -0,0 +1,128 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v0_8_0.domain import DBVistrail, DBAction, DBTag, DBModule, \
+ DBConnection, DBPortSpec, DBFunction, DBParameter, DBLocation, DBAdd, \
+ DBChange, DBDelete, DBAnnotation, DBPort
+
+def translateVistrail(_vistrail):
+ vistrail = DBVistrail()
+
+ for _action in _vistrail.db_actions:
+ ops = []
+ for op in _action.db_operations:
+ if op.vtType == 'add':
+ data = convert_data(op.db_data)
+ ops.append(DBAdd(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'change':
+ data = convert_data(op.db_data)
+ ops.append(DBChange(id=op.db_id,
+ what=op.db_what,
+ oldObjId=op.db_oldObjId,
+ newObjId=op.db_newObjId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'delete':
+ ops.append(DBDelete(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType))
+ annotations = []
+ for annotation in _action.db_annotations:
+ annotations.append(DBAnnotation(id=annotation.db_id,
+ key=annotation.db_key,
+ value=annotation.db_value))
+ action = DBAction(id=_action.db_id,
+ prevId=_action.db_prevId,
+ date=_action.db_date,
+ user=_action.db_user,
+ operations=ops,
+ annotations=annotations)
+ vistrail.db_add_action(action)
+
+ for _tag in _vistrail.db_tags:
+ tag = DBTag(id=_tag.db_id,
+ name=_tag.db_name)
+ vistrail.db_add_tag(tag)
+
+ vistrail.db_version = '0.8.0'
+ return vistrail
+
+def convert_data(child):
+ if child.vtType == 'module':
+ return DBModule(id=child.db_id,
+ cache=child.db_cache,
+ name=child.db_name,
+ package=child.db_package)
+ elif child.vtType == 'connection':
+ return DBConnection(id=child.db_id)
+ elif child.vtType == 'portSpec':
+ return DBPortSpec(id=child.db_id,
+ name=child.db_name,
+ type=child.db_type,
+ spec=child.db_spec)
+ elif child.vtType == 'function':
+ return DBFunction(id=child.db_id,
+ pos=child.db_pos,
+ name=child.db_name)
+ elif child.vtType == 'parameter':
+ return DBParameter(id=child.db_id,
+ pos=child.db_pos,
+ name=child.db_name,
+ type=child.db_type,
+ val=child.db_val,
+ alias=child.db_alias)
+ elif child.vtType == 'location':
+ return DBLocation(id=child.db_id,
+ x=child.db_x,
+ y=child.db_y)
+ elif child.vtType == 'annotation':
+ return DBAnnotation(id=child.db_id,
+ key=child.db_key,
+ value=child.db_value)
+ elif child.vtType == 'port':
+ return DBPort(id=child.db_id,
+ type=child.db_type,
+ moduleId=child.db_moduleId,
+ moduleName=child.db_moduleName,
+ name=child.db_name,
+ spec=child.db_spec)
diff --git a/vistrails/db/versions/v0_8_1/__init__.py b/vistrails/db/versions/v0_8_1/__init__.py
new file mode 100644
index 0000000..f5dd2ba
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.8.1'
diff --git a/vistrails/db/versions/v0_8_1/domain/__init__.py b/vistrails/db/versions/v0_8_1/domain/__init__.py
new file mode 100644
index 0000000..5537997
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/domain/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.versions.v0_8_0.domain import *
diff --git a/vistrails/db/versions/v0_8_1/persistence/__init__.py b/vistrails/db/versions/v0_8_1/persistence/__init__.py
new file mode 100644
index 0000000..b24b280
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/persistence/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.versions.v0_8_0.persistence import DAOList
diff --git a/vistrails/db/versions/v0_8_1/schemas/sql/vistrails.sql b/vistrails/db/versions/v0_8_1/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..bbb4a0c
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/schemas/sql/vistrails.sql
@@ -0,0 +1,249 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(22),
+ type varchar(255),
+ spec varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ package varchar(511),
+ version varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ spec varchar(4095),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int,
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ module_exec_id int
+) engine=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ name varchar(255),
+ log_id int,
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction(
+ id int,
+ name varchar(255),
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE workflow(
+ id int,
+ name varchar(255),
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction_ref(
+ id int,
+ name varchar(1023),
+ cache int,
+ abstraction_id int,
+ version int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session varchar(1023),
+ user varchar(255),
+ prune int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+) engine=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ module_id int,
+ module_name varchar(255),
+ machine_id int,
+ wf_exec_id int,
+ vt_id int
+) engine=InnoDB;
+
diff --git a/vistrails/db/versions/v0_8_1/schemas/sql/vistrails.sql.bkp b/vistrails/db/versions/v0_8_1/schemas/sql/vistrails.sql.bkp
new file mode 100644
index 0000000..4f11895
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/schemas/sql/vistrails.sql.bkp
@@ -0,0 +1,248 @@
+--#############################################################################
+--
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: vistrails at sci.utah.edu
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(22),
+ type varchar(255),
+ spec varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ package varchar(511),
+ version varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ spec varchar(4095),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int,
+ vt_id int
+) type=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ module_exec_id int
+) type=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+) type=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ name varchar(255),
+ log_id int,
+ vt_id int
+) type=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE abstraction(
+ id int,
+ name varchar(255),
+ vt_id int
+) type=InnoDB;
+
+CREATE TABLE workflow(
+ id int,
+ name varchar(255),
+ vt_id int
+) type=InnoDB;
+
+CREATE TABLE abstraction_ref(
+ id int,
+ name varchar(1023),
+ cache int,
+ abstraction_id int,
+ version int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+) type=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session varchar(1023),
+ user varchar(255),
+ prune int,
+ parent_type char(16),
+ vt_id int,
+ parent_id int
+) type=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ vt_id int
+) type=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) type=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ module_id int,
+ module_name varchar(255),
+ machine_id int,
+ wf_exec_id int,
+ vt_id int
+) type=InnoDB;
+
diff --git a/vistrails/db/versions/v0_8_1/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v0_8_1/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..a4fd64c
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,38 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, tag, port, log_tbl, machine, add_tbl, other, location, workflow_exec, function, abstraction, workflow, abstraction_ref, annotation, change_tbl, parameter, connection_tbl, action, delete_tbl, vistrail, module_exec
diff --git a/vistrails/db/versions/v0_8_1/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_8_1/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..276a2c0
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/schemas/xml/vistrail.xsd
@@ -0,0 +1,237 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="dbHost" type="xs:string"/>
+ <xs:attribute name="dbPort" type="xs:int"/>
+ <xs:attribute name="dbName" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:string"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="prune" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstractionRef">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="abstractionId" type="xs:int"/>
+ <xs:attribute name="version" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_8_1/specs/abstraction.xml b/vistrails/db/versions/v0_8_1/specs/abstraction.xml
new file mode 100644
index 0000000..3cbb63a
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/abstraction.xml
@@ -0,0 +1,65 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="vistrail" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/abstractionRef.xml b/vistrails/db/versions/v0_8_1/specs/abstractionRef.xml
new file mode 100644
index 0000000..46b61ba
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/abstractionRef.xml
@@ -0,0 +1,100 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstractionRef">
+ <layout>
+ <xml name="abstractionRef" nodeType="xs:element"/>
+ <sql table="abstraction_ref"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml name="cache" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_id" type="long">
+ <xml name="abstractionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/action.xml b/vistrails/db/versions/v0_8_1/specs/action.xml
new file mode 100644
index 0000000..1c7d3c5
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/action.xml
@@ -0,0 +1,110 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="prune" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/add.xml b/vistrails/db/versions/v0_8_1/specs/add.xml
new file mode 100644
index 0000000..11f560c
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/add.xml
@@ -0,0 +1,111 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/annotation.xml b/vistrails/db/versions/v0_8_1/specs/annotation.xml
new file mode 100644
index 0000000..ba8194f
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/annotation.xml
@@ -0,0 +1,97 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/change.xml b/vistrails/db/versions/v0_8_1/specs/change.xml
new file mode 100644
index 0000000..8135c18
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/change.xml
@@ -0,0 +1,116 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/connection.xml b/vistrails/db/versions/v0_8_1/specs/connection.xml
new file mode 100644
index 0000000..b559fab
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/connection.xml
@@ -0,0 +1,74 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/delete.xml b/vistrails/db/versions/v0_8_1/specs/delete.xml
new file mode 100644
index 0000000..abcdfdb
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/delete.xml
@@ -0,0 +1,78 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/function.xml b/vistrails/db/versions/v0_8_1/specs/function.xml
new file mode 100644
index 0000000..a95590d
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/function.xml
@@ -0,0 +1,86 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/location.xml b/vistrails/db/versions/v0_8_1/specs/location.xml
new file mode 100644
index 0000000..99c62f7
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/location.xml
@@ -0,0 +1,83 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_8_1/specs/log.xml b/vistrails/db/versions/v0_8_1/specs/log.xml
new file mode 100644
index 0000000..ca8720e
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/log.xml
@@ -0,0 +1,62 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/machine.xml b/vistrails/db/versions/v0_8_1/specs/machine.xml
new file mode 100644
index 0000000..dea813d
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/machine.xml
@@ -0,0 +1,85 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="long" mapping="one-to-many">
+ <sql column="module_exec_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/module.xml b/vistrails/db/versions/v0_8_1/specs/module.xml
new file mode 100644
index 0000000..fc9ed2a
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/module.xml
@@ -0,0 +1,107 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/module_exec.xml b/vistrails/db/versions/v0_8_1/specs/module_exec.xml
new file mode 100644
index 0000000..465407b
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/module_exec.xml
@@ -0,0 +1,86 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="machine" name="machine_id" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="machine_id" type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/other.xml b/vistrails/db/versions/v0_8_1/specs/other.xml
new file mode 100644
index 0000000..40e1388
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/other.xml
@@ -0,0 +1,79 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/parameter.xml b/vistrails/db/versions/v0_8_1/specs/parameter.xml
new file mode 100644
index 0000000..78f6cf7
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/parameter.xml
@@ -0,0 +1,94 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/port.xml b/vistrails/db/versions/v0_8_1/specs/port.xml
new file mode 100644
index 0000000..94f7671
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/port.xml
@@ -0,0 +1,95 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/portSpec.xml b/vistrails/db/versions/v0_8_1/specs/portSpec.xml
new file mode 100644
index 0000000..e42a5f0
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/portSpec.xml
@@ -0,0 +1,84 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(22)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/tag.xml b/vistrails/db/versions/v0_8_1/specs/tag.xml
new file mode 100644
index 0000000..f8412b9
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/tag.xml
@@ -0,0 +1,71 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/vistrail.xml b/vistrails/db/versions/v0_8_1/specs/vistrail.xml
new file mode 100644
index 0000000..ccbd34c
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/vistrail.xml
@@ -0,0 +1,85 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="vt_id"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property name="dbHost" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="dbPort" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="dbName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="abstraction" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_8_1/specs/workflow.xml b/vistrails/db/versions/v0_8_1/specs/workflow.xml
new file mode 100644
index 0000000..56189f1
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/workflow.xml
@@ -0,0 +1,80 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstractionRef" ref="true" object="abstractionRef">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_8_1/specs/workflow_exec.xml b/vistrails/db/versions/v0_8_1/specs/workflow_exec.xml
new file mode 100644
index 0000000..b616623
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/specs/workflow_exec.xml
@@ -0,0 +1,106 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_8_1/translate/__init__.py b/vistrails/db/versions/v0_8_1/translate/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_8_1/translate/v0_8_0.py b/vistrails/db/versions/v0_8_1/translate/v0_8_0.py
new file mode 100644
index 0000000..c007351
--- /dev/null
+++ b/vistrails/db/versions/v0_8_1/translate/v0_8_0.py
@@ -0,0 +1,84 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_8_0.domain import DBAdd, DBAnnotation, DBChange, DBDelete
+
+# two step process
+# 1. remap all the old "notes" so that they exist in the id scope
+# 2. remap all the annotations that were numbered correctly
+# note that for 2, we don't need to worry about uniqueness -- they are unique
+# but step 1 may have taken some of their ids...
+
+def translateVistrail(vistrail):
+ id_remap = {}
+ for action in vistrail.db_get_actions():
+ # don't need to change key idx since none of that changes
+ new_action_idx = {}
+ for annotation in action.db_get_annotations():
+ annotation.db_id = vistrail.idScope.getNewId(DBAnnotation.vtType)
+ new_action_idx[annotation.db_id] = annotation
+ action.db_annotations_id_index = new_action_idx
+
+ for operation in action.db_get_operations():
+ # never have annotations as parent objs so
+ # don't have to worry about those ids
+ if operation.db_what == DBAnnotation.vtType:
+ if operation.vtType == 'add':
+ new_id = vistrail.idScope.getNewId(DBAnnotation.vtType)
+ old_id = operation.db_objectId
+ operation.db_objectId = new_id
+ operation.db_data.db_id = new_id
+ id_remap[old_id] = new_id
+ elif operation.vtType == 'change':
+ changed_id = operation.db_oldObjId
+ if id_remap.has_key(changed_id):
+ operation.db_oldObjId = id_remap[changed_id]
+ else:
+ raise VistrailsDBException('cannot translate')
+
+ new_id = vistrail.idScope.getNewId(DBAnnotation.vtType)
+ old_id = operation.db_newObjId
+ operation.db_newObjId = new_id
+ operation.db_data.db_id = new_id
+ id_remap[old_id] = new_id
+ elif operation.vtType == 'delete':
+ old_id = operation.db_objectId
+ if id_remap.has_key(old_id):
+ operation.db_objectId = id_remap[old_id]
+ else:
+ raise VistrailsDBException('cannot translate')
+
+ vistrail.db_version = '0.8.1'
+ return vistrail
diff --git a/vistrails/db/versions/v0_9_0/__init__.py b/vistrails/db/versions/v0_9_0/__init__.py
new file mode 100644
index 0000000..e8a8036
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.9.0'
diff --git a/vistrails/db/versions/v0_9_0/domain/__init__.py b/vistrails/db/versions/v0_9_0/domain/__init__.py
new file mode 100644
index 0000000..1fd287d
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/domain/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from workflow import DBWorkflow
+from vistrail import DBVistrail
+from abstraction import DBAbstraction
+from log import DBLog
+from id_scope import IdScope
diff --git a/vistrails/db/versions/v0_9_0/domain/abstraction.py b/vistrails/db/versions/v0_9_0/domain/abstraction.py
new file mode 100644
index 0000000..6c3ecb5
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/domain/abstraction.py
@@ -0,0 +1,55 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+from auto_gen import DBAbstraction as _DBAbstraction
+from auto_gen import DBAbstractionRef, DBModule
+from id_scope import IdScope
+
+class DBAbstraction(_DBAbstraction):
+ def __init__(self, *args, **kwargs):
+ _DBAbstraction.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAbstractionRef.vtType: DBModule.vtType})
+ self.idScope.setBeginId('action', 1)
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBAbstraction.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBAbstraction
+ # need to go through and reset the index to the copied objects
+ cp.idScope = copy.copy(self.idScope)
+ return cp
diff --git a/vistrails/db/versions/v0_9_0/domain/auto_gen.py b/vistrails/db/versions/v0_9_0/domain/auto_gen.py
new file mode 100644
index 0000000..bfc1313
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/domain/auto_gen.py
@@ -0,0 +1,4458 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, spec=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_type = type
+ self.__db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPortSpec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_type = self.db_type
+ cp.db_spec = self.db_spec
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_spec(self):
+ return self.__db_spec
+ def __set_db_spec(self, spec):
+ self.__db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self.__db_spec = spec
+ def db_change_spec(self, spec):
+ self.__db_spec = spec
+ def db_delete_spec(self, spec):
+ self.__db_spec = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self.__db_id = id
+ self.__db_cache = cache
+ self.__db_name = name
+ self.__db_package = package
+ self.__db_version = version
+ self.__db_tag = tag
+ self.db_deleted_location = []
+ self.__db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self.__db_functions = []
+ else:
+ self.__db_functions = functions
+ for v in self.__db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self.__db_portSpecs = []
+ else:
+ self.__db_portSpecs = portSpecs
+ for v in self.__db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModule.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule()
+ cp.db_id = self.db_id
+ cp.db_cache = self.db_cache
+ cp.db_name = self.db_name
+ cp.db_package = self.db_package
+ cp.db_version = self.db_version
+ cp.db_tag = self.db_tag
+ if self.db_location is not None:
+ cp.db_location = self.db_location.do_copy(new_ids, id_scope, id_remap)
+ if self.db_functions is None:
+ cp.db_functions = []
+ else:
+ cp.db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_functions]
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+ if self.db_portSpecs is None:
+ cp.db_portSpecs = []
+ else:
+ cp.db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp.__db_functions:
+ cp.db_functions_id_index[v.db_id] = v
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.db_annotations_key_index[v.db_key] = v
+ for v in cp.__db_portSpecs:
+ cp.db_portSpecs_id_index[v.db_id] = v
+ cp.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_location is not None:
+ children.extend(self.db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_location is not None and self.db_location.has_changes():
+ return True
+ for child in self.db_functions:
+ if child.has_changes():
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ for child in self.db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_cache(self):
+ return self.__db_cache
+ def __set_db_cache(self, cache):
+ self.__db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self.__db_cache = cache
+ def db_change_cache(self, cache):
+ self.__db_cache = cache
+ def db_delete_cache(self, cache):
+ self.__db_cache = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_package(self):
+ return self.__db_package
+ def __set_db_package(self, package):
+ self.__db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self.__db_package = package
+ def db_change_package(self, package):
+ self.__db_package = package
+ def db_delete_package(self, package):
+ self.__db_package = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_tag(self):
+ return self.__db_tag
+ def __set_db_tag(self, tag):
+ self.__db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self.__db_tag = tag
+ def db_change_tag(self, tag):
+ self.__db_tag = tag
+ def db_delete_tag(self, tag):
+ self.__db_tag = None
+
+ def __get_db_location(self):
+ return self.__db_location
+ def __set_db_location(self, location):
+ self.__db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self.__db_location = location
+ def db_change_location(self, location):
+ self.__db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self.__db_location)
+ self.__db_location = None
+
+ def __get_db_functions(self):
+ return self.__db_functions
+ def __set_db_functions(self, functions):
+ self.__db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self.__db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self.__db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ self.__db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self.__db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ if not self.__db_functions[i].is_new:
+ self.db_deleted_functions.append(self.__db_functions[i])
+ del self.__db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == key:
+ return self.__db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return self.db_functions_id_index.has_key(key)
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ if not self.__db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self.__db_annotations[i])
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return self.db_annotations_key_index.has_key(key)
+
+ def __get_db_portSpecs(self):
+ return self.__db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self.__db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self.__db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self.__db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == portSpec.db_id:
+ self.__db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self.__db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == portSpec.db_id:
+ if not self.__db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self.__db_portSpecs[i])
+ del self.__db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self.__db_portSpecs)):
+ if self.__db_portSpecs[i].db_id == key:
+ return self.__db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return self.db_portSpecs_id_index.has_key(key)
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return self.db_portSpecs_name_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBTag.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and id_remap.has_key(('action', self.db_id)):
+ cp.db_id = id_remap[('action', self.db_id)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, name=None, spec=None):
+ self.__db_id = id
+ self.__db_type = type
+ self.__db_moduleId = moduleId
+ self.__db_moduleName = moduleName
+ self.__db_name = name
+ self.__db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPort.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort()
+ cp.db_id = self.db_id
+ cp.db_type = self.db_type
+ cp.db_moduleId = self.db_moduleId
+ cp.db_moduleName = self.db_moduleName
+ cp.db_name = self.db_name
+ cp.db_spec = self.db_spec
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_moduleId') and id_remap.has_key(('module', self.db_moduleId)):
+ cp.db_moduleId = id_remap[('module', self.db_moduleId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_moduleId(self):
+ return self.__db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self.__db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self.__db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self.__db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self.__db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self.__db_moduleName = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_spec(self):
+ return self.__db_spec
+ def __set_db_spec(self, spec):
+ self.__db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self.__db_spec = spec
+ def db_change_spec(self, spec):
+ self.__db_spec = spec
+ def db_delete_spec(self, spec):
+ self.__db_spec = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, workflow_execs=None, machines=None, vistrail_id=None):
+ self.__db_id = id
+ self.__db_entity_type = entity_type
+ self.__db_version = version
+ self.__db_name = name
+ self.__db_last_modified = last_modified
+ self.db_deleted_workflow_execs = []
+ self.db_workflow_execs_id_index = {}
+ if workflow_execs is None:
+ self.__db_workflow_execs = []
+ else:
+ self.__db_workflow_execs = workflow_execs
+ for v in self.__db_workflow_execs:
+ self.db_workflow_execs_id_index[v.db_id] = v
+ self.db_deleted_machines = []
+ self.db_machines_id_index = {}
+ if machines is None:
+ self.__db_machines = []
+ else:
+ self.__db_machines = machines
+ for v in self.__db_machines:
+ self.db_machines_id_index[v.db_id] = v
+ self.__db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog()
+ cp.db_id = self.db_id
+ cp.db_entity_type = self.db_entity_type
+ cp.db_version = self.db_version
+ cp.db_name = self.db_name
+ cp.db_last_modified = self.db_last_modified
+ if self.db_workflow_execs is None:
+ cp.db_workflow_execs = []
+ else:
+ cp.db_workflow_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_workflow_execs]
+ if self.db_machines is None:
+ cp.db_machines = []
+ else:
+ cp.db_machines = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_machines]
+ cp.db_vistrail_id = self.db_vistrail_id
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and id_remap.has_key(('vistrail', self.db_vistrail_id)):
+ cp.db_vistrail_id = id_remap[('vistrail', self.db_vistrail_id)]
+
+ # recreate indices and set flags
+ for v in cp.__db_workflow_execs:
+ cp.db_workflow_execs_id_index[v.db_id] = v
+ for v in cp.__db_machines:
+ cp.db_machines_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_workflow_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self.db_machines:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow_execs)
+ children.extend(self.db_deleted_machines)
+ if remove:
+ self.db_deleted_workflow_execs = []
+ self.db_deleted_machines = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_workflow_execs:
+ if child.has_changes():
+ return True
+ for child in self.db_machines:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_entity_type(self):
+ return self.__db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self.__db_entity_type = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_last_modified(self):
+ return self.__db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self.__db_last_modified = None
+
+ def __get_db_workflow_execs(self):
+ return self.__db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self.__db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self.__db_workflow_execs
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self.__db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_workflow_execs)):
+ if self.__db_workflow_execs[i].db_id == workflow_exec.db_id:
+ self.__db_workflow_execs[i] = workflow_exec
+ found = True
+ break
+ if not found:
+ self.__db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_workflow_execs)):
+ if self.__db_workflow_execs[i].db_id == workflow_exec.db_id:
+ if not self.__db_workflow_execs[i].is_new:
+ self.db_deleted_workflow_execs.append(self.__db_workflow_execs[i])
+ del self.__db_workflow_execs[i]
+ break
+ del self.db_workflow_execs_id_index[workflow_exec.db_id]
+ def db_get_workflow_exec(self, key):
+ for i in xrange(len(self.__db_workflow_execs)):
+ if self.__db_workflow_execs[i].db_id == key:
+ return self.__db_workflow_execs[i]
+ return None
+ def db_get_workflow_exec_by_id(self, key):
+ return self.db_workflow_execs_id_index[key]
+ def db_has_workflow_exec_with_id(self, key):
+ return self.db_workflow_execs_id_index.has_key(key)
+
+ def __get_db_machines(self):
+ return self.__db_machines
+ def __set_db_machines(self, machines):
+ self.__db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self.__db_machines
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self.__db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_machines)):
+ if self.__db_machines[i].db_id == machine.db_id:
+ self.__db_machines[i] = machine
+ found = True
+ break
+ if not found:
+ self.__db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_machines)):
+ if self.__db_machines[i].db_id == machine.db_id:
+ if not self.__db_machines[i].is_new:
+ self.db_deleted_machines.append(self.__db_machines[i])
+ del self.__db_machines[i]
+ break
+ del self.db_machines_id_index[machine.db_id]
+ def db_get_machine(self, key):
+ for i in xrange(len(self.__db_machines)):
+ if self.__db_machines[i].db_id == key:
+ return self.__db_machines[i]
+ return None
+ def db_get_machine_by_id(self, key):
+ return self.db_machines_id_index[key]
+ def db_has_machine_with_id(self, key):
+ return self.db_machines_id_index.has_key(key)
+
+ def __get_db_vistrail_id(self):
+ return self.__db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self.__db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self.__db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self.__db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self.__db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_os = os
+ self.__db_architecture = architecture
+ self.__db_processor = processor
+ self.__db_ram = ram
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMachine.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_os = self.db_os
+ cp.db_architecture = self.db_architecture
+ cp.db_processor = self.db_processor
+ cp.db_ram = self.db_ram
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and id_remap.has_key(('vistrail', self.db_vistrailId)):
+ cp.db_vistrailId = id_remap[('vistrail', self.db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_os(self):
+ return self.__db_os
+ def __set_db_os(self, os):
+ self.__db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self.__db_os = os
+ def db_change_os(self, os):
+ self.__db_os = os
+ def db_delete_os(self, os):
+ self.__db_os = None
+
+ def __get_db_architecture(self):
+ return self.__db_architecture
+ def __set_db_architecture(self, architecture):
+ self.__db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self.__db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self.__db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self.__db_architecture = None
+
+ def __get_db_processor(self):
+ return self.__db_processor
+ def __set_db_processor(self, processor):
+ self.__db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self.__db_processor = processor
+ def db_change_processor(self, processor):
+ self.__db_processor = processor
+ def db_delete_processor(self, processor):
+ self.__db_processor = None
+
+ def __get_db_ram(self):
+ return self.__db_ram
+ def __set_db_ram(self, ram):
+ self.__db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self.__db_ram = ram
+ def db_change_ram(self, ram):
+ self.__db_ram = ram
+ def db_delete_ram(self, ram):
+ self.__db_ram = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, data=None, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self.__db_data = data
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_objectId = objectId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAdd.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd()
+ if self.db_data is not None:
+ cp.db_data = self.db_data.do_copy(new_ids, id_scope, id_remap)
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_objectId = self.db_objectId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and id_remap.has_key((self.db_what, self.db_objectId)):
+ cp.db_objectId = id_remap[(self.db_what, self.db_objectId)]
+ if hasattr(self, 'db_parentObjId') and id_remap.has_key((self.db_parentObjType, self.db_parentObjId)):
+ cp.db_parentObjId = id_remap[(self.db_parentObjType, self.db_parentObjId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_data is not None:
+ children.extend(self.db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_data is not None and self.db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self.__db_data
+ def __set_db_data(self, data):
+ self.__db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self.__db_data = data
+ def db_change_data(self, data):
+ self.__db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self.__db_data)
+ self.__db_data = None
+
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_objectId(self):
+ return self.__db_objectId
+ def __set_db_objectId(self, objectId):
+ self.__db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self.__db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self.__db_id = id
+ self.__db_key = key
+ self.__db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOther.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOther()
+ cp.db_id = self.db_id
+ cp.db_key = self.db_key
+ cp.db_value = self.db_value
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self.__db_id = id
+ self.__db_x = x
+ self.__db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLocation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation()
+ cp.db_id = self.db_id
+ cp.db_x = self.db_x
+ cp.db_y = self.db_y
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_x(self):
+ return self.__db_x
+ def __set_db_x(self, x):
+ self.__db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self.__db_x = x
+ def db_change_x(self, x):
+ self.__db_x = x
+ def db_delete_x(self, x):
+ self.__db_x = None
+
+ def __get_db_y(self):
+ return self.__db_y
+ def __set_db_y(self, y):
+ self.__db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self.__db_y = y
+ def db_change_y(self, y):
+ self.__db_y = y
+ def db_delete_y(self, y):
+ self.__db_y = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, id=None, user=None, ip=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, name=None, module_execs=None):
+ self.__db_id = id
+ self.__db_user = user
+ self.__db_ip = ip
+ self.__db_vt_version = vt_version
+ self.__db_ts_start = ts_start
+ self.__db_ts_end = ts_end
+ self.__db_parent_id = parent_id
+ self.__db_parent_type = parent_type
+ self.__db_parent_version = parent_version
+ self.__db_name = name
+ self.db_deleted_module_execs = []
+ self.db_module_execs_id_index = {}
+ if module_execs is None:
+ self.__db_module_execs = []
+ else:
+ self.__db_module_execs = module_execs
+ for v in self.__db_module_execs:
+ self.db_module_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflowExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec()
+ cp.db_id = self.db_id
+ cp.db_user = self.db_user
+ cp.db_ip = self.db_ip
+ cp.db_vt_version = self.db_vt_version
+ cp.db_ts_start = self.db_ts_start
+ cp.db_ts_end = self.db_ts_end
+ cp.db_parent_id = self.db_parent_id
+ cp.db_parent_type = self.db_parent_type
+ cp.db_parent_version = self.db_parent_version
+ cp.db_name = self.db_name
+ if self.db_module_execs is None:
+ cp.db_module_execs = []
+ else:
+ cp.db_module_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_module_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp.__db_module_execs:
+ cp.db_module_execs_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_execs)
+ if remove:
+ self.db_deleted_module_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_module_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_user(self):
+ return self.__db_user
+ def __set_db_user(self, user):
+ self.__db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self.__db_user = user
+ def db_change_user(self, user):
+ self.__db_user = user
+ def db_delete_user(self, user):
+ self.__db_user = None
+
+ def __get_db_ip(self):
+ return self.__db_ip
+ def __set_db_ip(self, ip):
+ self.__db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self.__db_ip = ip
+ def db_change_ip(self, ip):
+ self.__db_ip = ip
+ def db_delete_ip(self, ip):
+ self.__db_ip = None
+
+ def __get_db_vt_version(self):
+ return self.__db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self.__db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self.__db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self.__db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self.__db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self.__db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self.__db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self.__db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self.__db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self.__db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self.__db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self.__db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self.__db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self.__db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self.__db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self.__db_parent_version = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_module_execs(self):
+ return self.__db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self.__db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self.__db_module_execs
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self.__db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ self.__db_module_execs[i] = module_exec
+ found = True
+ break
+ if not found:
+ self.__db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == module_exec.db_id:
+ if not self.__db_module_execs[i].is_new:
+ self.db_deleted_module_execs.append(self.__db_module_execs[i])
+ del self.__db_module_execs[i]
+ break
+ del self.db_module_execs_id_index[module_exec.db_id]
+ def db_get_module_exec(self, key):
+ for i in xrange(len(self.__db_module_execs)):
+ if self.__db_module_execs[i].db_id == key:
+ return self.__db_module_execs[i]
+ return None
+ def db_get_module_exec_by_id(self, key):
+ return self.db_module_execs_id_index[key]
+ def db_has_module_exec_with_id(self, key):
+ return self.db_module_execs_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self.__db_id = id
+ self.__db_pos = pos
+ self.__db_name = name
+ self.db_deleted_parameters = []
+ self.db_parameters_id_index = {}
+ if parameters is None:
+ self.__db_parameters = []
+ else:
+ self.__db_parameters = parameters
+ for v in self.__db_parameters:
+ self.db_parameters_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction()
+ cp.db_id = self.db_id
+ cp.db_pos = self.db_pos
+ cp.db_name = self.db_name
+ if self.db_parameters is None:
+ cp.db_parameters = []
+ else:
+ cp.db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp.__db_parameters:
+ cp.db_parameters_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_parameters)
+ if remove:
+ self.db_deleted_parameters = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_pos(self):
+ return self.__db_pos
+ def __set_db_pos(self, pos):
+ self.__db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self.__db_pos = pos
+ def db_change_pos(self, pos):
+ self.__db_pos = pos
+ def db_delete_pos(self, pos):
+ self.__db_pos = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_parameters(self):
+ return self.__db_parameters
+ def __set_db_parameters(self, parameters):
+ self.__db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self.__db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self.__db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == parameter.db_id:
+ self.__db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self.__db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == parameter.db_id:
+ if not self.__db_parameters[i].is_new:
+ self.db_deleted_parameters.append(self.__db_parameters[i])
+ del self.__db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter.db_id]
+ def db_get_parameter(self, key):
+ for i in xrange(len(self.__db_parameters)):
+ if self.__db_parameters[i].db_id == key:
+ return self.__db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return self.db_parameters_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, entity_type=None, name=None, last_modified=None, actions=None, tags=None):
+ self.__db_id = id
+ self.__db_entity_type = entity_type
+ self.__db_name = name
+ self.__db_last_modified = last_modified
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self.__db_actions = []
+ else:
+ self.__db_actions = actions
+ for v in self.__db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self.__db_tags = []
+ else:
+ self.__db_tags = tags
+ for v in self.__db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction()
+ cp.db_id = self.db_id
+ cp.db_entity_type = self.db_entity_type
+ cp.db_name = self.db_name
+ cp.db_last_modified = self.db_last_modified
+ if self.db_actions is None:
+ cp.db_actions = []
+ else:
+ cp.db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_actions]
+ if self.db_tags is None:
+ cp.db_tags = []
+ else:
+ cp.db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_tags]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp.__db_actions:
+ cp.db_actions_id_index[v.db_id] = v
+ for v in cp.__db_tags:
+ cp.db_tags_id_index[v.db_id] = v
+ cp.db_tags_name_index[v.db_name] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_actions:
+ if child.has_changes():
+ return True
+ for child in self.db_tags:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_entity_type(self):
+ return self.__db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self.__db_entity_type = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_last_modified(self):
+ return self.__db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self.__db_last_modified = None
+
+ def __get_db_actions(self):
+ return self.__db_actions
+ def __set_db_actions(self, actions):
+ self.__db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self.__db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ self.__db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ if not self.__db_actions[i].is_new:
+ self.db_deleted_actions.append(self.__db_actions[i])
+ del self.__db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == key:
+ return self.__db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return self.db_actions_id_index.has_key(key)
+
+ def __get_db_tags(self):
+ return self.__db_tags
+ def __set_db_tags(self, tags):
+ self.__db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self.__db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ self.__db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ if not self.__db_tags[i].is_new:
+ self.db_deleted_tags.append(self.__db_tags[i])
+ del self.__db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == key:
+ return self.__db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return self.db_tags_id_index.has_key(key)
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return self.db_tags_name_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, modules=None, id=None, entity_type=None, name=None, version=None, last_modified=None, connections=None, annotations=None, abstractions=None, others=None, vistrail_id=None):
+ self.db_deleted_modules = []
+ self.db_modules_id_index = {}
+ if modules is None:
+ self.__db_modules = []
+ else:
+ self.__db_modules = modules
+ for v in self.__db_modules:
+ self.db_modules_id_index[v.db_id] = v
+ self.__db_id = id
+ self.__db_entity_type = entity_type
+ self.__db_name = name
+ self.__db_version = version
+ self.__db_last_modified = last_modified
+ self.db_deleted_connections = []
+ self.db_connections_id_index = {}
+ if connections is None:
+ self.__db_connections = []
+ else:
+ self.__db_connections = connections
+ for v in self.__db_connections:
+ self.db_connections_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_abstractions = []
+ self.db_abstractions_id_index = {}
+ if abstractions is None:
+ self.__db_abstractions = []
+ else:
+ self.__db_abstractions = abstractions
+ for v in self.__db_abstractions:
+ self.db_abstractions_id_index[v.db_id] = v
+ self.db_deleted_others = []
+ self.db_others_id_index = {}
+ if others is None:
+ self.__db_others = []
+ else:
+ self.__db_others = others
+ for v in self.__db_others:
+ self.db_others_id_index[v.db_id] = v
+ self.__db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow()
+ if self.db_modules is None:
+ cp.db_modules = []
+ else:
+ cp.db_modules = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_modules]
+ cp.db_id = self.db_id
+ cp.db_entity_type = self.db_entity_type
+ cp.db_name = self.db_name
+ cp.db_version = self.db_version
+ cp.db_last_modified = self.db_last_modified
+ if self.db_connections is None:
+ cp.db_connections = []
+ else:
+ cp.db_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_connections]
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+ if self.db_abstractions is None:
+ cp.db_abstractions = []
+ else:
+ cp.db_abstractions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_abstractions]
+ if self.db_others is None:
+ cp.db_others = []
+ else:
+ cp.db_others = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_others]
+ cp.db_vistrail_id = self.db_vistrail_id
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and id_remap.has_key(('vistrail', self.db_vistrail_id)):
+ cp.db_vistrail_id = id_remap[('vistrail', self.db_vistrail_id)]
+
+ # recreate indices and set flags
+ for v in cp.__db_modules:
+ cp.db_modules_id_index[v.db_id] = v
+ for v in cp.__db_connections:
+ cp.db_connections_id_index[v.db_id] = v
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ for v in cp.__db_abstractions:
+ cp.db_abstractions_id_index[v.db_id] = v
+ for v in cp.__db_others:
+ cp.db_others_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_connections:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_connection(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_abstractions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_abstraction(child)
+ to_del = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_other(child)
+ to_del = []
+ for child in self.db_modules:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_connections)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_abstractions)
+ children.extend(self.db_deleted_others)
+ children.extend(self.db_deleted_modules)
+ if remove:
+ self.db_deleted_connections = []
+ self.db_deleted_annotations = []
+ self.db_deleted_abstractions = []
+ self.db_deleted_others = []
+ self.db_deleted_modules = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_connections:
+ if child.has_changes():
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ for child in self.db_abstractions:
+ if child.has_changes():
+ return True
+ for child in self.db_others:
+ if child.has_changes():
+ return True
+ for child in self.db_modules:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_modules(self):
+ return self.__db_modules
+ def __set_db_modules(self, modules):
+ self.__db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self.__db_modules
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self.__db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_modules)):
+ if self.__db_modules[i].db_id == module.db_id:
+ self.__db_modules[i] = module
+ found = True
+ break
+ if not found:
+ self.__db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_modules)):
+ if self.__db_modules[i].db_id == module.db_id:
+ if not self.__db_modules[i].is_new:
+ self.db_deleted_modules.append(self.__db_modules[i])
+ del self.__db_modules[i]
+ break
+ del self.db_modules_id_index[module.db_id]
+ def db_get_module(self, key):
+ for i in xrange(len(self.__db_modules)):
+ if self.__db_modules[i].db_id == key:
+ return self.__db_modules[i]
+ return None
+ def db_get_module_by_id(self, key):
+ return self.db_modules_id_index[key]
+ def db_has_module_with_id(self, key):
+ return self.db_modules_id_index.has_key(key)
+
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_entity_type(self):
+ return self.__db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self.__db_entity_type = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_last_modified(self):
+ return self.__db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self.__db_last_modified = None
+
+ def __get_db_connections(self):
+ return self.__db_connections
+ def __set_db_connections(self, connections):
+ self.__db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self.__db_connections
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self.__db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_connections)):
+ if self.__db_connections[i].db_id == connection.db_id:
+ self.__db_connections[i] = connection
+ found = True
+ break
+ if not found:
+ self.__db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_connections)):
+ if self.__db_connections[i].db_id == connection.db_id:
+ if not self.__db_connections[i].is_new:
+ self.db_deleted_connections.append(self.__db_connections[i])
+ del self.__db_connections[i]
+ break
+ del self.db_connections_id_index[connection.db_id]
+ def db_get_connection(self, key):
+ for i in xrange(len(self.__db_connections)):
+ if self.__db_connections[i].db_id == key:
+ return self.__db_connections[i]
+ return None
+ def db_get_connection_by_id(self, key):
+ return self.db_connections_id_index[key]
+ def db_has_connection_with_id(self, key):
+ return self.db_connections_id_index.has_key(key)
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ if not self.__db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self.__db_annotations[i])
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+
+ def __get_db_abstractions(self):
+ return self.__db_abstractions
+ def __set_db_abstractions(self, abstractions):
+ self.__db_abstractions = abstractions
+ self.is_dirty = True
+ db_abstractions = property(__get_db_abstractions, __set_db_abstractions)
+ def db_get_abstractions(self):
+ return self.__db_abstractions
+ def db_add_abstraction(self, abstraction):
+ self.is_dirty = True
+ self.__db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_change_abstraction(self, abstraction):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == abstraction.db_id:
+ self.__db_abstractions[i] = abstraction
+ found = True
+ break
+ if not found:
+ self.__db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_delete_abstraction(self, abstraction):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == abstraction.db_id:
+ if not self.__db_abstractions[i].is_new:
+ self.db_deleted_abstractions.append(self.__db_abstractions[i])
+ del self.__db_abstractions[i]
+ break
+ del self.db_abstractions_id_index[abstraction.db_id]
+ def db_get_abstraction(self, key):
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == key:
+ return self.__db_abstractions[i]
+ return None
+ def db_get_abstraction_by_id(self, key):
+ return self.db_abstractions_id_index[key]
+ def db_has_abstraction_with_id(self, key):
+ return self.db_abstractions_id_index.has_key(key)
+
+ def __get_db_others(self):
+ return self.__db_others
+ def __set_db_others(self, others):
+ self.__db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self.__db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self.__db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == other.db_id:
+ self.__db_others[i] = other
+ found = True
+ break
+ if not found:
+ self.__db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == other.db_id:
+ if not self.__db_others[i].is_new:
+ self.db_deleted_others.append(self.__db_others[i])
+ del self.__db_others[i]
+ break
+ del self.db_others_id_index[other.db_id]
+ def db_get_other(self, key):
+ for i in xrange(len(self.__db_others)):
+ if self.__db_others[i].db_id == key:
+ return self.__db_others[i]
+ return None
+ def db_get_other_by_id(self, key):
+ return self.db_others_id_index[key]
+ def db_has_other_with_id(self, key):
+ return self.db_others_id_index.has_key(key)
+
+ def __get_db_vistrail_id(self):
+ return self.__db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self.__db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self.__db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self.__db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self.__db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAbstractionRef(object):
+
+ vtType = 'abstractionRef'
+
+ def __init__(self, id=None, name=None, cache=None, abstraction_id=None, version=None, location=None, functions=None, annotations=None):
+ self.__db_id = id
+ self.__db_name = name
+ self.__db_cache = cache
+ self.__db_abstraction_id = abstraction_id
+ self.__db_version = version
+ self.db_deleted_location = []
+ self.__db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self.__db_functions = []
+ else:
+ self.__db_functions = functions
+ for v in self.__db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstractionRef.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstractionRef()
+ cp.db_id = self.db_id
+ cp.db_name = self.db_name
+ cp.db_cache = self.db_cache
+ cp.db_abstraction_id = self.db_abstraction_id
+ cp.db_version = self.db_version
+ if self.db_location is not None:
+ cp.db_location = self.db_location.do_copy(new_ids, id_scope, id_remap)
+ if self.db_functions is None:
+ cp.db_functions = []
+ else:
+ cp.db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_functions]
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_abstraction_id') and id_remap.has_key(('abstraction', self.db_abstraction_id)):
+ cp.db_abstraction_id = id_remap[('abstraction', self.db_abstraction_id)]
+
+ # recreate indices and set flags
+ for v in cp.__db_functions:
+ cp.db_functions_id_index[v.db_id] = v
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.db_annotations_key_index[v.db_key] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_location is not None:
+ children.extend(self.db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_location is not None and self.db_location.has_changes():
+ return True
+ for child in self.db_functions:
+ if child.has_changes():
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_cache(self):
+ return self.__db_cache
+ def __set_db_cache(self, cache):
+ self.__db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self.__db_cache = cache
+ def db_change_cache(self, cache):
+ self.__db_cache = cache
+ def db_delete_cache(self, cache):
+ self.__db_cache = None
+
+ def __get_db_abstraction_id(self):
+ return self.__db_abstraction_id
+ def __set_db_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ self.is_dirty = True
+ db_abstraction_id = property(__get_db_abstraction_id, __set_db_abstraction_id)
+ def db_add_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ def db_change_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ def db_delete_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_location(self):
+ return self.__db_location
+ def __set_db_location(self, location):
+ self.__db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self.__db_location = location
+ def db_change_location(self, location):
+ self.__db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self.__db_location)
+ self.__db_location = None
+
+ def __get_db_functions(self):
+ return self.__db_functions
+ def __set_db_functions(self, functions):
+ self.__db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self.__db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self.__db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ self.__db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self.__db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == function.db_id:
+ if not self.__db_functions[i].is_new:
+ self.db_deleted_functions.append(self.__db_functions[i])
+ del self.__db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self.__db_functions)):
+ if self.__db_functions[i].db_id == key:
+ return self.__db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return self.db_functions_id_index.has_key(key)
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ if not self.__db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self.__db_annotations[i])
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return self.db_annotations_key_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self.__db_id = id
+ self.__db_key = key
+ self.__db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation()
+ cp.db_id = self.db_id
+ cp.db_key = self.db_key
+ cp.db_value = self.db_value
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_key(self):
+ return self.__db_key
+ def __set_db_key(self, key):
+ self.__db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self.__db_key = key
+ def db_change_key(self, key):
+ self.__db_key = key
+ def db_delete_key(self, key):
+ self.__db_key = None
+
+ def __get_db_value(self):
+ return self.__db_value
+ def __set_db_value(self, value):
+ self.__db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self.__db_value = value
+ def db_change_value(self, value):
+ self.__db_value = value
+ def db_delete_value(self, value):
+ self.__db_value = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, data=None, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self.__db_data = data
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_oldObjId = oldObjId
+ self.__db_newObjId = newObjId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBChange.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange()
+ if self.db_data is not None:
+ cp.db_data = self.db_data.do_copy(new_ids, id_scope, id_remap)
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_oldObjId = self.db_oldObjId
+ cp.db_newObjId = self.db_newObjId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_oldObjId') and id_remap.has_key((self.db_what, self.db_oldObjId)):
+ cp.db_oldObjId = id_remap[(self.db_what, self.db_oldObjId)]
+ if hasattr(self, 'db_newObjId') and id_remap.has_key((self.db_what, self.db_newObjId)):
+ cp.db_newObjId = id_remap[(self.db_what, self.db_newObjId)]
+ if hasattr(self, 'db_parentObjId') and id_remap.has_key((self.db_parentObjType, self.db_parentObjId)):
+ cp.db_parentObjId = id_remap[(self.db_parentObjType, self.db_parentObjId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self.db_data is not None:
+ children.extend(self.db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self.db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self.db_data is not None and self.db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self.__db_data
+ def __set_db_data(self, data):
+ self.__db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self.__db_data = data
+ def db_change_data(self, data):
+ self.__db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self.__db_data)
+ self.__db_data = None
+
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_oldObjId(self):
+ return self.__db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self.__db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self.__db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self.__db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self.__db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self.__db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self.__db_id = id
+ self.__db_pos = pos
+ self.__db_name = name
+ self.__db_type = type
+ self.__db_val = val
+ self.__db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBParameter.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter()
+ cp.db_id = self.db_id
+ cp.db_pos = self.db_pos
+ cp.db_name = self.db_name
+ cp.db_type = self.db_type
+ cp.db_val = self.db_val
+ cp.db_alias = self.db_alias
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_pos(self):
+ return self.__db_pos
+ def __set_db_pos(self, pos):
+ self.__db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self.__db_pos = pos
+ def db_change_pos(self, pos):
+ self.__db_pos = pos
+ def db_delete_pos(self, pos):
+ self.__db_pos = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_type(self):
+ return self.__db_type
+ def __set_db_type(self, type):
+ self.__db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self.__db_type = type
+ def db_change_type(self, type):
+ self.__db_type = type
+ def db_delete_type(self, type):
+ self.__db_type = None
+
+ def __get_db_val(self):
+ return self.__db_val
+ def __set_db_val(self, val):
+ self.__db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self.__db_val = val
+ def db_change_val(self, val):
+ self.__db_val = val
+ def db_delete_val(self, val):
+ self.__db_val = None
+
+ def __get_db_alias(self):
+ return self.__db_alias
+ def __set_db_alias(self, alias):
+ self.__db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self.__db_alias = alias
+ def db_change_alias(self, alias):
+ self.__db_alias = alias
+ def db_delete_alias(self, alias):
+ self.__db_alias = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self.__db_id = id
+ self.db_deleted_ports = []
+ self.db_ports_id_index = {}
+ self.db_ports_type_index = {}
+ if ports is None:
+ self.__db_ports = []
+ else:
+ self.__db_ports = ports
+ for v in self.__db_ports:
+ self.db_ports_id_index[v.db_id] = v
+ self.db_ports_type_index[v.db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBConnection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection()
+ cp.db_id = self.db_id
+ if self.db_ports is None:
+ cp.db_ports = []
+ else:
+ cp.db_ports = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_ports]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp.__db_ports:
+ cp.db_ports_id_index[v.db_id] = v
+ cp.db_ports_type_index[v.db_type] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_ports)
+ if remove:
+ self.db_deleted_ports = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_ports(self):
+ return self.__db_ports
+ def __set_db_ports(self, ports):
+ self.__db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self.__db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self.__db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == port.db_id:
+ self.__db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self.__db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == port.db_id:
+ if not self.__db_ports[i].is_new:
+ self.db_deleted_ports.append(self.__db_ports[i])
+ del self.__db_ports[i]
+ break
+ del self.db_ports_id_index[port.db_id]
+ del self.db_ports_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self.__db_ports)):
+ if self.__db_ports[i].db_id == key:
+ return self.__db_ports[i]
+ return None
+ def db_get_port_by_id(self, key):
+ return self.db_ports_id_index[key]
+ def db_has_port_with_id(self, key):
+ return self.db_ports_id_index.has_key(key)
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return self.db_ports_type_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, operations=None, id=None, prevId=None, date=None, session=None, user=None, prune=None, annotations=None):
+ self.db_deleted_operations = []
+ self.db_operations_id_index = {}
+ if operations is None:
+ self.__db_operations = []
+ else:
+ self.__db_operations = operations
+ for v in self.__db_operations:
+ self.db_operations_id_index[v.db_id] = v
+ self.__db_id = id
+ self.__db_prevId = prevId
+ self.__db_date = date
+ self.__db_session = session
+ self.__db_user = user
+ self.__db_prune = prune
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction()
+ if self.db_operations is None:
+ cp.db_operations = []
+ else:
+ cp.db_operations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_operations]
+ cp.db_id = self.db_id
+ cp.db_prevId = self.db_prevId
+ cp.db_date = self.db_date
+ cp.db_session = self.db_session
+ cp.db_user = self.db_user
+ cp.db_prune = self.db_prune
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp.__db_operations:
+ cp.db_operations_id_index[v.db_id] = v
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.db_annotations_key_index[v.db_key] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_operations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_operations)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_operations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ for child in self.db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_operations(self):
+ return self.__db_operations
+ def __set_db_operations(self, operations):
+ self.__db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self.__db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self.__db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == operation.db_id:
+ self.__db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self.__db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == operation.db_id:
+ if not self.__db_operations[i].is_new:
+ self.db_deleted_operations.append(self.__db_operations[i])
+ del self.__db_operations[i]
+ break
+ del self.db_operations_id_index[operation.db_id]
+ def db_get_operation(self, key):
+ for i in xrange(len(self.__db_operations)):
+ if self.__db_operations[i].db_id == key:
+ return self.__db_operations[i]
+ return None
+ def db_get_operation_by_id(self, key):
+ return self.db_operations_id_index[key]
+ def db_has_operation_with_id(self, key):
+ return self.db_operations_id_index.has_key(key)
+
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_prevId(self):
+ return self.__db_prevId
+ def __set_db_prevId(self, prevId):
+ self.__db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self.__db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self.__db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self.__db_prevId = None
+
+ def __get_db_date(self):
+ return self.__db_date
+ def __set_db_date(self, date):
+ self.__db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self.__db_date = date
+ def db_change_date(self, date):
+ self.__db_date = date
+ def db_delete_date(self, date):
+ self.__db_date = None
+
+ def __get_db_session(self):
+ return self.__db_session
+ def __set_db_session(self, session):
+ self.__db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self.__db_session = session
+ def db_change_session(self, session):
+ self.__db_session = session
+ def db_delete_session(self, session):
+ self.__db_session = None
+
+ def __get_db_user(self):
+ return self.__db_user
+ def __set_db_user(self, user):
+ self.__db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self.__db_user = user
+ def db_change_user(self, user):
+ self.__db_user = user
+ def db_delete_user(self, user):
+ self.__db_user = None
+
+ def __get_db_prune(self):
+ return self.__db_prune
+ def __set_db_prune(self, prune):
+ self.__db_prune = prune
+ self.is_dirty = True
+ db_prune = property(__get_db_prune, __set_db_prune)
+ def db_add_prune(self, prune):
+ self.__db_prune = prune
+ def db_change_prune(self, prune):
+ self.__db_prune = prune
+ def db_delete_prune(self, prune):
+ self.__db_prune = None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ if not self.__db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self.__db_annotations[i])
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return self.db_annotations_key_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.__db_id = id
+ self.__db_what = what
+ self.__db_objectId = objectId
+ self.__db_parentObjId = parentObjId
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBDelete.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete()
+ cp.db_id = self.db_id
+ cp.db_what = self.db_what
+ cp.db_objectId = self.db_objectId
+ cp.db_parentObjId = self.db_parentObjId
+ cp.db_parentObjType = self.db_parentObjType
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and id_remap.has_key((self.db_what, self.db_objectId)):
+ cp.db_objectId = id_remap[(self.db_what, self.db_objectId)]
+ if hasattr(self, 'db_parentObjId') and id_remap.has_key((self.db_parentObjType, self.db_parentObjId)):
+ cp.db_parentObjId = id_remap[(self.db_parentObjType, self.db_parentObjId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_what(self):
+ return self.__db_what
+ def __set_db_what(self, what):
+ self.__db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self.__db_what = what
+ def db_change_what(self, what):
+ self.__db_what = what
+ def db_delete_what(self, what):
+ self.__db_what = None
+
+ def __get_db_objectId(self):
+ return self.__db_objectId
+ def __set_db_objectId(self, objectId):
+ self.__db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self.__db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self.__db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self.__db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self.__db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self.__db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self.__db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self.__db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self.__db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, dbHost=None, dbPort=None, dbName=None, actions=None, tags=None, abstractions=None):
+ self.__db_id = id
+ self.__db_entity_type = entity_type
+ self.__db_version = version
+ self.__db_name = name
+ self.__db_last_modified = last_modified
+ self.__db_dbHost = dbHost
+ self.__db_dbPort = dbPort
+ self.__db_dbName = dbName
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self.__db_actions = []
+ else:
+ self.__db_actions = actions
+ for v in self.__db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self.__db_tags = []
+ else:
+ self.__db_tags = tags
+ for v in self.__db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.db_deleted_abstractions = []
+ self.db_abstractions_id_index = {}
+ if abstractions is None:
+ self.__db_abstractions = []
+ else:
+ self.__db_abstractions = abstractions
+ for v in self.__db_abstractions:
+ self.db_abstractions_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail()
+ cp.db_id = self.db_id
+ cp.db_entity_type = self.db_entity_type
+ cp.db_version = self.db_version
+ cp.db_name = self.db_name
+ cp.db_last_modified = self.db_last_modified
+ cp.db_dbHost = self.db_dbHost
+ cp.db_dbPort = self.db_dbPort
+ cp.db_dbName = self.db_dbName
+ if self.db_actions is None:
+ cp.db_actions = []
+ else:
+ cp.db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_actions]
+ if self.db_tags is None:
+ cp.db_tags = []
+ else:
+ cp.db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_tags]
+ if self.db_abstractions is None:
+ cp.db_abstractions = []
+ else:
+ cp.db_abstractions = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_abstractions]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp.__db_actions:
+ cp.db_actions_id_index[v.db_id] = v
+ for v in cp.__db_tags:
+ cp.db_tags_id_index[v.db_id] = v
+ cp.db_tags_name_index[v.db_name] = v
+ for v in cp.__db_abstractions:
+ cp.db_abstractions_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self.db_abstractions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_abstraction(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ children.extend(self.db_deleted_abstractions)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ self.db_deleted_abstractions = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_actions:
+ if child.has_changes():
+ return True
+ for child in self.db_tags:
+ if child.has_changes():
+ return True
+ for child in self.db_abstractions:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_entity_type(self):
+ return self.__db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self.__db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self.__db_entity_type = None
+
+ def __get_db_version(self):
+ return self.__db_version
+ def __set_db_version(self, version):
+ self.__db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self.__db_version = version
+ def db_change_version(self, version):
+ self.__db_version = version
+ def db_delete_version(self, version):
+ self.__db_version = None
+
+ def __get_db_name(self):
+ return self.__db_name
+ def __set_db_name(self, name):
+ self.__db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self.__db_name = name
+ def db_change_name(self, name):
+ self.__db_name = name
+ def db_delete_name(self, name):
+ self.__db_name = None
+
+ def __get_db_last_modified(self):
+ return self.__db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self.__db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self.__db_last_modified = None
+
+ def __get_db_dbHost(self):
+ return self.__db_dbHost
+ def __set_db_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ self.is_dirty = True
+ db_dbHost = property(__get_db_dbHost, __set_db_dbHost)
+ def db_add_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ def db_change_dbHost(self, dbHost):
+ self.__db_dbHost = dbHost
+ def db_delete_dbHost(self, dbHost):
+ self.__db_dbHost = None
+
+ def __get_db_dbPort(self):
+ return self.__db_dbPort
+ def __set_db_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ self.is_dirty = True
+ db_dbPort = property(__get_db_dbPort, __set_db_dbPort)
+ def db_add_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ def db_change_dbPort(self, dbPort):
+ self.__db_dbPort = dbPort
+ def db_delete_dbPort(self, dbPort):
+ self.__db_dbPort = None
+
+ def __get_db_dbName(self):
+ return self.__db_dbName
+ def __set_db_dbName(self, dbName):
+ self.__db_dbName = dbName
+ self.is_dirty = True
+ db_dbName = property(__get_db_dbName, __set_db_dbName)
+ def db_add_dbName(self, dbName):
+ self.__db_dbName = dbName
+ def db_change_dbName(self, dbName):
+ self.__db_dbName = dbName
+ def db_delete_dbName(self, dbName):
+ self.__db_dbName = None
+
+ def __get_db_actions(self):
+ return self.__db_actions
+ def __set_db_actions(self, actions):
+ self.__db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self.__db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ self.__db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self.__db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == action.db_id:
+ if not self.__db_actions[i].is_new:
+ self.db_deleted_actions.append(self.__db_actions[i])
+ del self.__db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self.__db_actions)):
+ if self.__db_actions[i].db_id == key:
+ return self.__db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return self.db_actions_id_index.has_key(key)
+
+ def __get_db_tags(self):
+ return self.__db_tags
+ def __set_db_tags(self, tags):
+ self.__db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self.__db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ self.__db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self.__db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == tag.db_id:
+ if not self.__db_tags[i].is_new:
+ self.db_deleted_tags.append(self.__db_tags[i])
+ del self.__db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self.__db_tags)):
+ if self.__db_tags[i].db_id == key:
+ return self.__db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return self.db_tags_id_index.has_key(key)
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return self.db_tags_name_index.has_key(key)
+
+ def __get_db_abstractions(self):
+ return self.__db_abstractions
+ def __set_db_abstractions(self, abstractions):
+ self.__db_abstractions = abstractions
+ self.is_dirty = True
+ db_abstractions = property(__get_db_abstractions, __set_db_abstractions)
+ def db_get_abstractions(self):
+ return self.__db_abstractions
+ def db_add_abstraction(self, abstraction):
+ self.is_dirty = True
+ self.__db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_change_abstraction(self, abstraction):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == abstraction.db_id:
+ self.__db_abstractions[i] = abstraction
+ found = True
+ break
+ if not found:
+ self.__db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_delete_abstraction(self, abstraction):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == abstraction.db_id:
+ if not self.__db_abstractions[i].is_new:
+ self.db_deleted_abstractions.append(self.__db_abstractions[i])
+ del self.__db_abstractions[i]
+ break
+ del self.db_abstractions_id_index[abstraction.db_id]
+ def db_get_abstraction(self, key):
+ for i in xrange(len(self.__db_abstractions)):
+ if self.__db_abstractions[i].db_id == key:
+ return self.__db_abstractions[i]
+ return None
+ def db_get_abstraction_by_id(self, key):
+ return self.db_abstractions_id_index[key]
+ def db_has_abstraction_with_id(self, key):
+ return self.db_abstractions_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, module_name=None, completed=None, abstraction_id=None, abstraction_version=None, machine_id=None, annotations=None):
+ self.__db_id = id
+ self.__db_ts_start = ts_start
+ self.__db_ts_end = ts_end
+ self.__db_cached = cached
+ self.__db_module_id = module_id
+ self.__db_module_name = module_name
+ self.__db_completed = completed
+ self.__db_abstraction_id = abstraction_id
+ self.__db_abstraction_version = abstraction_version
+ self.__db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self.__db_annotations = []
+ else:
+ self.__db_annotations = annotations
+ for v in self.__db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec()
+ cp.db_id = self.db_id
+ cp.db_ts_start = self.db_ts_start
+ cp.db_ts_end = self.db_ts_end
+ cp.db_cached = self.db_cached
+ cp.db_module_id = self.db_module_id
+ cp.db_module_name = self.db_module_name
+ cp.db_completed = self.db_completed
+ cp.db_abstraction_id = self.db_abstraction_id
+ cp.db_abstraction_version = self.db_abstraction_version
+ cp.db_machine_id = self.db_machine_id
+ if self.db_annotations is None:
+ cp.db_annotations = []
+ else:
+ cp.db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self.db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if id_scope.remap.has_key(self.vtType):
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and id_remap.has_key(('module', self.db_module_id)):
+ cp.db_module_id = id_remap[('module', self.db_module_id)]
+ if hasattr(self, 'db_machine_id') and id_remap.has_key(('machine', self.db_machine_id)):
+ cp.db_machine_id = id_remap[('machine', self.db_machine_id)]
+
+ # recreate indices and set flags
+ for v in cp.__db_annotations:
+ cp.db_annotations_id_index[v.db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self.db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self.__db_id
+ def __set_db_id(self, id):
+ self.__db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self.__db_id = id
+ def db_change_id(self, id):
+ self.__db_id = id
+ def db_delete_id(self, id):
+ self.__db_id = None
+
+ def __get_db_ts_start(self):
+ return self.__db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self.__db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self.__db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self.__db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self.__db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self.__db_ts_end = None
+
+ def __get_db_cached(self):
+ return self.__db_cached
+ def __set_db_cached(self, cached):
+ self.__db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self.__db_cached = cached
+ def db_change_cached(self, cached):
+ self.__db_cached = cached
+ def db_delete_cached(self, cached):
+ self.__db_cached = None
+
+ def __get_db_module_id(self):
+ return self.__db_module_id
+ def __set_db_module_id(self, module_id):
+ self.__db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self.__db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self.__db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self.__db_module_id = None
+
+ def __get_db_module_name(self):
+ return self.__db_module_name
+ def __set_db_module_name(self, module_name):
+ self.__db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self.__db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self.__db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self.__db_module_name = None
+
+ def __get_db_completed(self):
+ return self.__db_completed
+ def __set_db_completed(self, completed):
+ self.__db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self.__db_completed = completed
+ def db_change_completed(self, completed):
+ self.__db_completed = completed
+ def db_delete_completed(self, completed):
+ self.__db_completed = None
+
+ def __get_db_abstraction_id(self):
+ return self.__db_abstraction_id
+ def __set_db_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ self.is_dirty = True
+ db_abstraction_id = property(__get_db_abstraction_id, __set_db_abstraction_id)
+ def db_add_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ def db_change_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = abstraction_id
+ def db_delete_abstraction_id(self, abstraction_id):
+ self.__db_abstraction_id = None
+
+ def __get_db_abstraction_version(self):
+ return self.__db_abstraction_version
+ def __set_db_abstraction_version(self, abstraction_version):
+ self.__db_abstraction_version = abstraction_version
+ self.is_dirty = True
+ db_abstraction_version = property(__get_db_abstraction_version, __set_db_abstraction_version)
+ def db_add_abstraction_version(self, abstraction_version):
+ self.__db_abstraction_version = abstraction_version
+ def db_change_abstraction_version(self, abstraction_version):
+ self.__db_abstraction_version = abstraction_version
+ def db_delete_abstraction_version(self, abstraction_version):
+ self.__db_abstraction_version = None
+
+ def __get_db_machine_id(self):
+ return self.__db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self.__db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self.__db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self.__db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self.__db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self.__db_annotations
+ def __set_db_annotations(self, annotations):
+ self.__db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self.__db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ self.__db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self.__db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == annotation.db_id:
+ if not self.__db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self.__db_annotations[i])
+ del self.__db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self.__db_annotations)):
+ if self.__db_annotations[i].db_id == key:
+ return self.__db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return self.db_annotations_id_index.has_key(key)
+
+ def getPrimaryKey(self):
+ return self.__db_id
+
diff --git a/vistrails/db/versions/v0_9_0/domain/id_scope.py b/vistrails/db/versions/v0_9_0/domain/id_scope.py
new file mode 100644
index 0000000..c510efa
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/domain/id_scope.py
@@ -0,0 +1,76 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L, remap=None):
+ self.ids = {}
+ self.beginId = beginId
+ if remap is None:
+ self.remap = {}
+ else:
+ self.remap = remap
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ cp.remap = copy.copy(self.remap)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ if self.remap.has_key(objType):
+ objType = self.remap[objType]
+ if self.ids.has_key(objType):
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ else:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ if self.remap.has_key(objType):
+ objType = self.remap[objType]
+ if not self.ids.has_key(objType) or self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ if self.remap.has_key(objType):
+ objType = self.remap[objType]
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v0_9_0/domain/log.py b/vistrails/db/versions/v0_9_0/domain/log.py
new file mode 100644
index 0000000..5f56556
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/domain/log.py
@@ -0,0 +1,55 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBLog as _DBLog
+from auto_gen import DBAbstractionRef, DBModule
+from id_scope import IdScope
+
+import copy
+
+class DBLog(_DBLog):
+
+ def __init__(self, *args, **kwargs):
+ _DBLog.__init__(self, *args, **kwargs)
+ self.id_scope = IdScope(1,
+ {DBAbstractionRef.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBLog.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBLog
+ cp.id_scope = copy.copy(self.id_scope)
diff --git a/vistrails/db/versions/v0_9_0/domain/vistrail.py b/vistrails/db/versions/v0_9_0/domain/vistrail.py
new file mode 100644
index 0000000..8edc340
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/domain/vistrail.py
@@ -0,0 +1,64 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBVistrail as _DBVistrail
+from auto_gen import DBAdd, DBChange, DBDelete, DBAbstractionRef, DBModule
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAdd.vtType: 'operation',
+ DBChange.vtType: 'operation',
+ DBDelete.vtType: 'operation',
+ DBAbstractionRef.vtType: DBModule.vtType})
+
+ self.idScope.setBeginId('action', 1)
+ self.db_objects = {}
+
+ def db_add_object(self, obj):
+ self.db_objects[(obj.vtType, obj.db_id)] = obj
+
+ def db_get_object(self, type, id):
+ return self.db_objects.get((type, id), None)
+
+ def db_update_object(self, obj, **kwargs):
+ # want to swap out old object with a new version
+ # need this for updating aliases...
+ # hack it using setattr...
+ real_obj = self.db_objects[(obj.vtType, obj.db_id)]
+ for (k, v) in kwargs.iteritems():
+ if hasattr(real_obj, k):
+ setattr(real_obj, k, v)
diff --git a/vistrails/db/versions/v0_9_0/domain/workflow.py b/vistrails/db/versions/v0_9_0/domain/workflow.py
new file mode 100644
index 0000000..04db38e
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/domain/workflow.py
@@ -0,0 +1,155 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from auto_gen import DBAbstractionRef, DBModule
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1,
+ {DBAbstractionRef.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.objects = {}
+ for (child, _, _) in cp.db_children():
+ cp.add_to_index(child)
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ def add_to_index(self, object):
+ if object.vtType == 'abstractionRef':
+ obj_type = 'module'
+ else:
+ obj_type = object.vtType
+ self.objects[(obj_type, object.getPrimaryKey())] = object
+
+ def delete_from_index(self, object):
+ if object.vtType == 'abstractionRef':
+ obj_type = 'module'
+ else:
+ obj_type = object.vtType
+ del self.objects[(obj_type, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_print_objects(self):
+ for k,v in self.objects.iteritems():
+ print '%s: %s' % (k, v)
+
+ def db_has_object(self, type, id):
+ return self.objects.has_key((type, id))
+
+ def db_get_object(self, type, id):
+ return self.objects[(type, id)]
+
+ def db_add_object(self, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == 'abstractionRef':
+ parent_obj_type = 'module'
+ if self.objects.has_key((parent_obj_type, parent_obj_id)):
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ else:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if object.vtType == 'abstractionRef':
+ obj_type = 'module'
+ else:
+ obj_type = object.vtType
+ funname = 'db_add_%s' % obj_type
+ obj_copy = copy.copy(object)
+ getattr(parent_obj, funname)(obj_copy)
+ self.add_to_index(obj_copy)
+
+ def db_change_object(self, old_id, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == 'abstractionRef':
+ parent_obj_type = 'module'
+ if self.objects.has_key((parent_obj_type, parent_obj_id)):
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ else:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+
+ self.db_delete_object(old_id, object.vtType, None, None, parent_obj)
+ self.db_add_object(object, None, None, parent_obj)
+
+ def db_delete_object(self, obj_id, obj_type, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == 'abstractionRef':
+ parent_obj_type = 'module'
+ if self.objects.has_key((parent_obj_type, parent_obj_id)):
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ else:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if obj_type == 'abstractionRef':
+ obj_type = 'module'
+ funname = 'db_get_%s' % obj_type
+ if hasattr(parent_obj, funname):
+ object = getattr(parent_obj, funname)(obj_id)
+ else:
+ attr_name = 'db_%s' % obj_type
+ object = getattr(parent_obj, attr_name)
+ funname = 'db_delete_%s' % obj_type
+ getattr(parent_obj, funname)(object)
+ self.delete_from_index(object)
diff --git a/vistrails/db/versions/v0_9_0/persistence/__init__.py b/vistrails/db/versions/v0_9_0/persistence/__init__.py
new file mode 100644
index 0000000..5fc0ad4
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/persistence/__init__.py
@@ -0,0 +1,98 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+from vistrails.core.system import get_elementtree_library
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_9_0 import version as my_version
+
+ElementTree = get_elementtree_library()
+
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def parse_xml_file(self, filename):
+ return ElementTree.parse(filename)
+
+ def write_xml_file(self, filename, tree):
+ tree.write(filename)
+
+ def read_xml_object(self, vtType, node):
+ return self['xml'][vtType].fromXML(node)
+
+ def write_xml_object(self, obj, node=None):
+ res_node = self['xml'][obj.vtType].toXML(obj, node)
+ return res_node
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ """open_from_xml(filename) -> DBVistrail"""
+ if tree is None:
+ tree = self.parse_xml_file(filename)
+ vistrail = self.read_xml_object(vtType, tree.getroot())
+ return vistrail
+
+ def save_to_xml(self, obj, filename, tags):
+ """save_to_xml(obj : object, filename: str, tags: dict) -> None
+
+ """
+ root = self.write_xml_object(obj)
+ root.set('version', my_version)
+ for k, v in tags.iteritems():
+ root.set(k, v)
+ tree = ElementTree.ElementTree(root)
+ self.write_xml_file(filename, tree)
+
+ def open_from_db(self, db_connection, vtType, id, lock=False):
+ pass
+
+ def save_to_db(self, db_connection, obj, doCopy=False):
+ pass
+
+ def serialize(self, object):
+ root = self.write_xml_object(object)
+ return ElementTree.tostring(root)
+
+ def unserialize(self, str, obj_type):
+ try:
+ root = ElementTree.fromstring(str)
+ return self.read_xml_object(obj_type, root)
+ except SyntaxError, e:
+ msg = "Invalid VisTrails serialized object %s" % str
+ raise VistrailsDBException(msg)
+ return None
diff --git a/vistrails/db/versions/v0_9_0/persistence/sql/__init__.py b/vistrails/db/versions/v0_9_0/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_9_0/persistence/sql/auto_gen.py b/vistrails/db/versions/v0_9_0/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..50d5fcd
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/persistence/sql/auto_gen.py
@@ -0,0 +1,2525 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v0_9_0.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(22)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[4], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[5], 'long', 'int')
+ entity_type = self.convertFromDB(row[6], 'str', 'char(16)')
+ parent = self.convertFromDB(row[7], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ spec=spec,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_entity_id = entity_id
+ portSpec.db_entity_type = entity_type
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(22)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[3], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ module.db_parentType = parentType
+ module.db_entity_id = entity_id
+ module.db_entity_type = entity_type
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_parentType = parentType
+ tag.db_entity_id = entity_id
+ tag.db_entity_type = entity_type
+ tag.db_parent = parent
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_tag(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec,
+ id=id)
+ port.db_parentType = parentType
+ port.db_entity_id = entity_id
+ port.db_entity_type = entity_type
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ log = DBLog(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ log.is_dirty = False
+ res[('log', id)] = log
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_workflow_execs:
+ child.db_log = obj.db_id
+ for child in obj.db_machines:
+ child.db_log = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.db_entity_id = entity_id
+ machine.db_entity_type = entity_type
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_entity_id = entity_id
+ add.db_entity_type = entity_type
+ add.is_dirty = False
+ res[('add', id)] = add
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_entity_id = entity_id
+ other.db_entity_type = entity_type
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_entity_id = entity_id
+ location.db_entity_type = entity_type
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ vt_version = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[4], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[5], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[6], 'long', 'int')
+ parent_type = self.convertFromDB(row[7], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[8], 'long', 'int')
+ name = self.convertFromDB(row[9], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[10], 'long', 'int')
+ entity_id = self.convertFromDB(row[11], 'long', 'int')
+ entity_type = self.convertFromDB(row[12], 'str', 'char(16)')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_entity_id = entity_id
+ workflow_exec.db_entity_type = entity_type
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_module_execs:
+ child.db_workflow_exec = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_entity_id = entity_id
+ function.db_entity_type = entity_type
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'name', 'last_modified']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[3], 'datetime', 'datetime')
+
+ abstraction = DBAbstraction(entity_type=entity_type,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'name', 'last_modified']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_actions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[3], 'str', 'char(16)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ workflow = DBWorkflow(entity_type=entity_type,
+ name=name,
+ version=version,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_connections:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_modules:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionRefSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'cache', 'abstraction_id', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(1023)')
+ cache = self.convertFromDB(row[2], 'int', 'int')
+ abstraction_id = self.convertFromDB(row[3], 'long', 'int')
+ version = self.convertFromDB(row[4], 'long', 'int')
+ parentType = self.convertFromDB(row[5], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ abstractionRef = DBAbstractionRef(name=name,
+ cache=cache,
+ abstraction_id=abstraction_id,
+ version=version,
+ id=id)
+ abstractionRef.db_parentType = parentType
+ abstractionRef.db_entity_id = entity_id
+ abstractionRef.db_entity_type = entity_type
+ abstractionRef.db_parent = parent
+ abstractionRef.is_dirty = False
+ res[('abstractionRef', id)] = abstractionRef
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'cache', 'abstraction_id', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_abstraction_id') and obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction_ref'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_entity_id = entity_id
+ annotation.db_entity_type = entity_type
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_entity_id = entity_id
+ change.db_entity_type = entity_type
+ change.is_dirty = False
+ res[('change', id)] = change
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_entity_id = entity_id
+ parameter.db_entity_type = entity_type
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[2], 'long', 'int')
+ entity_type = self.convertFromDB(row[3], 'str', 'char(16)')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_entity_id = entity_id
+ connection.db_entity_type = entity_type
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'str', 'varchar(1023)')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ prune = self.convertFromDB(row[5], 'int', 'int')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ id=id)
+ action.db_parentType = parentType
+ action.db_entity_id = entity_id
+ action.db_entity_type = entity_type
+ action.db_parent = parent
+ action.is_dirty = False
+ res[('action', id)] = action
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_action(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_prune') and obj.db_prune is not None:
+ columnMap['prune'] = \
+ self.convertToDB(obj.db_prune, 'int', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_entity_id = entity_id
+ delete.db_entity_type = entity_type
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_actions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'abstraction_id', 'abstraction_version', 'machine_id', 'wf_exec_id', 'entity_id', 'entity_type']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ module_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[6], 'int', 'int')
+ abstraction_id = self.convertFromDB(row[7], 'long', 'int')
+ abstraction_version = self.convertFromDB(row[8], 'long', 'int')
+ machine_id = self.convertFromDB(row[9], 'long', 'int')
+ workflow_exec = self.convertFromDB(row[10], 'long', 'int')
+ entity_id = self.convertFromDB(row[11], 'long', 'int')
+ entity_type = self.convertFromDB(row[12], 'str', 'char(16)')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ abstraction_id=abstraction_id,
+ abstraction_version=abstraction_version,
+ machine_id=machine_id,
+ id=id)
+ module_exec.db_workflow_exec = workflow_exec
+ module_exec.db_entity_id = entity_id
+ module_exec.db_entity_type = entity_type
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('workflow_exec', obj.db_workflow_exec)]
+ p.db_add_module_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'abstraction_id', 'abstraction_version', 'machine_id', 'wf_exec_id', 'entity_id', 'entity_type']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_abstraction_id') and obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if hasattr(obj, 'db_abstraction_version') and obj.db_abstraction_version is not None:
+ columnMap['abstraction_version'] = \
+ self.convertToDB(obj.db_abstraction_version, 'long', 'int')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_workflow_exec') and obj.db_workflow_exec is not None:
+ columnMap['wf_exec_id'] = \
+ self.convertToDB(obj.db_workflow_exec, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefSQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v0_9_0/persistence/sql/sql_dao.py b/vistrails/db/versions/v0_9_0/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..c54eb03
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/persistence/sql/sql_dao.py
@@ -0,0 +1,165 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return "'" + str(value).replace("'", "''") + "'"
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ return str(value)
+ elif type == 'int':
+ return str(value)
+ elif type == 'date':
+ return "'" + value.isoformat() + "'"
+ elif type == 'datetime':
+ return "'" + value.strftime('%Y-%m-%d %H:%M:%S') + "'"
+ else:
+ return str(value)
+
+ return "''"
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None,
+ forUpdate=False):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ if forUpdate:
+ dbCommand += " FOR UPDATE"
+ dbCommand += ";"
+ return dbCommand
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ valueStr = ', '.join(values)
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s);""" % \
+ (table, columnStr, valueStr)
+ return dbCommand
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ setStr += '%s %s = %s' % (comma, column, value)
+ comma = ','
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """UPDATE %s SET %s WHERE %s;""" % \
+ (table, setStr, whereStr)
+ return dbCommand
+
+ def createSQLDelete(self, table, whereMap):
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND '
+ dbCommand = """DELETE FROM %s WHERE %s;""" % \
+ (table, whereStr)
+ return dbCommand
+
+ def executeSQL(self, db, dbCommand, isFetch):
+ # print 'db: %s' % dbCommand
+ data = None
+ cursor = db.cursor()
+ cursor.execute(dbCommand)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ cursor.close()
+ return data
+
+ def start_transaction(self, db):
+ db.begin()
+
+ def commit_transaction(self, db):
+ db.commit()
+
+ def rollback_transaction(self, db):
+ db.rollback()
diff --git a/vistrails/db/versions/v0_9_0/persistence/xml/__init__.py b/vistrails/db/versions/v0_9_0/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_9_0/persistence/xml/auto_gen.py b/vistrails/db/versions/v0_9_0/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..c939ec8
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/persistence/xml/auto_gen.py
@@ -0,0 +1,1584 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from vistrails.core.system import get_elementtree_library
+
+from xml_dao import XMLDAO
+from vistrails.db.versions.v0_9_0.domain import *
+
+ElementTree = get_elementtree_library()
+
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'portSpec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('spec', None)
+ spec = self.convertFromStr(data, 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, node=None):
+ if node is None:
+ node = ElementTree.Element('portSpec')
+
+ # set attributes
+ node.set('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.set('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.set('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.set('spec',self.convertToStr(portSpec.db_spec, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'module':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, node=None):
+ if node is None:
+ node = ElementTree.Element('module')
+
+ # set attributes
+ node.set('id',self.convertToStr(module.db_id, 'long'))
+ node.set('cache',self.convertToStr(module.db_cache, 'int'))
+ node.set('name',self.convertToStr(module.db_name, 'str'))
+ node.set('package',self.convertToStr(module.db_package, 'str'))
+ node.set('version',self.convertToStr(module.db_version, 'str'))
+ node.set('tag',self.convertToStr(module.db_tag, 'str'))
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = module.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'tag':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, node=None):
+ if node is None:
+ node = ElementTree.Element('tag')
+
+ # set attributes
+ node.set('id',self.convertToStr(tag.db_id, 'long'))
+ node.set('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'port':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('moduleId', None)
+ moduleId = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ moduleName = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('spec', None)
+ spec = self.convertFromStr(data, 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, node=None):
+ if node is None:
+ node = ElementTree.Element('port')
+
+ # set attributes
+ node.set('id',self.convertToStr(port.db_id, 'long'))
+ node.set('type',self.convertToStr(port.db_type, 'str'))
+ node.set('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.set('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.set('name',self.convertToStr(port.db_name, 'str'))
+ node.set('spec',self.convertToStr(port.db_spec, 'str'))
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'log':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ workflow_execs = []
+ machines = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'workflowExec':
+ _data = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs.append(_data)
+ elif child.tag == 'machine':
+ _data = self.getDao('machine').fromXML(child)
+ machines.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLog(id=id,
+ version=version,
+ name=name,
+ workflow_execs=workflow_execs,
+ machines=machines,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, node=None):
+ if node is None:
+ node = ElementTree.Element('log')
+
+ # set attributes
+ node.set('id',self.convertToStr(log.db_id, 'long'))
+ node.set('version',self.convertToStr(log.db_version, 'str'))
+ node.set('name',self.convertToStr(log.db_name, 'str'))
+ node.set('vistrail_id',self.convertToStr(log.db_vistrail_id, 'long'))
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs:
+ childNode = ElementTree.SubElement(node, 'workflow_exec')
+ self.getDao('workflow_exec').toXML(workflow_exec, childNode)
+ machines = log.db_machines
+ for machine in machines:
+ childNode = ElementTree.SubElement(node, 'machine')
+ self.getDao('machine').toXML(machine, childNode)
+
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'machine':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('os', None)
+ os = self.convertFromStr(data, 'str')
+ data = node.get('architecture', None)
+ architecture = self.convertFromStr(data, 'str')
+ data = node.get('processor', None)
+ processor = self.convertFromStr(data, 'str')
+ data = node.get('ram', None)
+ ram = self.convertFromStr(data, 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, node=None):
+ if node is None:
+ node = ElementTree.Element('machine')
+
+ # set attributes
+ node.set('id',self.convertToStr(machine.db_id, 'long'))
+ node.set('name',self.convertToStr(machine.db_name, 'str'))
+ node.set('os',self.convertToStr(machine.db_os, 'str'))
+ node.set('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.set('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.set('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'add':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAdd(data=data,
+ id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, node=None):
+ if node is None:
+ node = ElementTree.Element('add')
+
+ # set attributes
+ node.set('id',self.convertToStr(add.db_id, 'long'))
+ node.set('what',self.convertToStr(add.db_what, 'str'))
+ node.set('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # set elements
+ data = add.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'other':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'value':
+ _data = self.convertFromStr(child.text,'')
+ value = _data
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, node=None):
+ if node is None:
+ node = ElementTree.Element('other')
+
+ # set attributes
+ node.set('id',self.convertToStr(other.db_id, 'long'))
+ node.set('key',self.convertToStr(other.db_key, 'str'))
+
+ # set elements
+
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'location':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('x', None)
+ x = self.convertFromStr(data, 'float')
+ data = node.get('y', None)
+ y = self.convertFromStr(data, 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, node=None):
+ if node is None:
+ node = ElementTree.Element('location')
+
+ # set attributes
+ node.set('id',self.convertToStr(location.db_id, 'long'))
+ node.set('x',self.convertToStr(location.db_x, 'float'))
+ node.set('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflowExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('ip', None)
+ ip = self.convertFromStr(data, 'str')
+ data = node.get('vtVersion', None)
+ vt_version = self.convertFromStr(data, 'str')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('parentId', None)
+ parent_id = self.convertFromStr(data, 'long')
+ data = node.get('parentType', None)
+ parent_type = self.convertFromStr(data, 'str')
+ data = node.get('parentVersion', None)
+ parent_version = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ module_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ module_execs.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflowExec(id=id,
+ user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ module_execs=module_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('workflowExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.set('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.set('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.set('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.set('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.set('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.set('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.set('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.set('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # set elements
+ module_execs = workflow_exec.db_module_execs
+ for module_exec in module_execs:
+ childNode = ElementTree.SubElement(node, 'module_exec')
+ self.getDao('module_exec').toXML(module_exec, childNode)
+
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'function':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ parameters = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ parameters.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, node=None):
+ if node is None:
+ node = ElementTree.Element('function')
+
+ # set attributes
+ node.set('id',self.convertToStr(function.db_id, 'long'))
+ node.set('pos',self.convertToStr(function.db_pos, 'long'))
+ node.set('name',self.convertToStr(function.db_name, 'str'))
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(parameter, childNode)
+
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'abstraction':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child.tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstraction(id=id,
+ name=name,
+ actions=actions,
+ tags=tags)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, node=None):
+ if node is None:
+ node = ElementTree.Element('abstraction')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.set('name',self.convertToStr(abstraction.db_name, 'str'))
+
+ # set elements
+ actions = abstraction.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = abstraction.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflow':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ connections = []
+ annotations = []
+ abstractions = []
+ others = []
+ modules = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ connections.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ abstractions.append(_data)
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ others.append(_data)
+ elif child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ modules.append(_data)
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ modules.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflow(modules=modules,
+ id=id,
+ name=name,
+ version=version,
+ connections=connections,
+ annotations=annotations,
+ abstractions=abstractions,
+ others=others,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, node=None):
+ if node is None:
+ node = ElementTree.Element('workflow')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow.db_id, 'long'))
+ node.set('name',self.convertToStr(workflow.db_name, 'str'))
+ node.set('version',self.convertToStr(workflow.db_version, 'str'))
+ node.set('vistrail_id',self.convertToStr(workflow.db_vistrail_id, 'long'))
+
+ # set elements
+ connections = workflow.db_connections
+ for connection in connections:
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(connection, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ abstractions = workflow.db_abstractions
+ for abstraction in abstractions:
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(abstraction, childNode)
+ others = workflow.db_others
+ for other in others:
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(other, childNode)
+ modules = workflow.db_modules
+ for module in modules:
+ if module.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(module, childNode)
+ elif module.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(module, childNode)
+
+ return node
+
+class DBAbstractionRefXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'abstractionRef':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('abstractionId', None)
+ abstraction_id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'long')
+
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstractionRef(id=id,
+ name=name,
+ cache=cache,
+ abstraction_id=abstraction_id,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstractionRef, node=None):
+ if node is None:
+ node = ElementTree.Element('abstractionRef')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstractionRef.db_id, 'long'))
+ node.set('name',self.convertToStr(abstractionRef.db_name, 'str'))
+ node.set('cache',self.convertToStr(abstractionRef.db_cache, 'int'))
+ node.set('abstractionId',self.convertToStr(abstractionRef.db_abstraction_id, 'long'))
+ node.set('version',self.convertToStr(abstractionRef.db_version, 'long'))
+
+ # set elements
+ location = abstractionRef.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = abstractionRef.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = abstractionRef.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'annotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, node=None):
+ if node is None:
+ node = ElementTree.Element('annotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(annotation.db_id, 'long'))
+ node.set('key',self.convertToStr(annotation.db_key, 'str'))
+ node.set('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'change':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('oldObjId', None)
+ oldObjId = self.convertFromStr(data, 'long')
+ data = node.get('newObjId', None)
+ newObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBChange(data=data,
+ id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, node=None):
+ if node is None:
+ node = ElementTree.Element('change')
+
+ # set attributes
+ node.set('id',self.convertToStr(change.db_id, 'long'))
+ node.set('what',self.convertToStr(change.db_what, 'str'))
+ node.set('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.set('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.set('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # set elements
+ data = change.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'parameter':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('val', None)
+ val = self.convertFromStr(data, 'str')
+ data = node.get('alias', None)
+ alias = self.convertFromStr(data, 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, node=None):
+ if node is None:
+ node = ElementTree.Element('parameter')
+
+ # set attributes
+ node.set('id',self.convertToStr(parameter.db_id, 'long'))
+ node.set('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.set('name',self.convertToStr(parameter.db_name, 'str'))
+ node.set('type',self.convertToStr(parameter.db_type, 'str'))
+ node.set('val',self.convertToStr(parameter.db_val, 'str'))
+ node.set('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'connection':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+
+ ports = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ ports.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, node=None):
+ if node is None:
+ node = ElementTree.Element('connection')
+
+ # set attributes
+ node.set('id',self.convertToStr(connection.db_id, 'long'))
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(port, childNode)
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'action':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('prevId', None)
+ prevId = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'str')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('prune', None)
+ prune = self.convertFromStr(data, 'int')
+
+ annotations = []
+ operations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'add':
+ _data = self.getDao('add').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'delete':
+ _data = self.getDao('delete').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'change':
+ _data = self.getDao('change').fromXML(child)
+ operations.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAction(operations=operations,
+ id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, node=None):
+ if node is None:
+ node = ElementTree.Element('action')
+
+ # set attributes
+ node.set('id',self.convertToStr(action.db_id, 'long'))
+ node.set('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.set('date',self.convertToStr(action.db_date, 'datetime'))
+ node.set('session',self.convertToStr(action.db_session, 'str'))
+ node.set('user',self.convertToStr(action.db_user, 'str'))
+ node.set('prune',self.convertToStr(action.db_prune, 'int'))
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ childNode = ElementTree.SubElement(node, 'add')
+ self.getDao('add').toXML(operation, childNode)
+ elif operation.vtType == 'delete':
+ childNode = ElementTree.SubElement(node, 'delete')
+ self.getDao('delete').toXML(operation, childNode)
+ elif operation.vtType == 'change':
+ childNode = ElementTree.SubElement(node, 'change')
+ self.getDao('change').toXML(operation, childNode)
+
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'delete':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, node=None):
+ if node is None:
+ node = ElementTree.Element('delete')
+
+ # set attributes
+ node.set('id',self.convertToStr(delete.db_id, 'long'))
+ node.set('what',self.convertToStr(delete.db_what, 'str'))
+ node.set('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'vistrail':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('dbHost', None)
+ dbHost = self.convertFromStr(data, 'str')
+ data = node.get('dbPort', None)
+ dbPort = self.convertFromStr(data, 'int')
+ data = node.get('dbName', None)
+ dbName = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+ abstractions = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child.tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ abstractions.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ dbHost=dbHost,
+ dbPort=dbPort,
+ dbName=dbName,
+ actions=actions,
+ tags=tags,
+ abstractions=abstractions)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, node=None):
+ if node is None:
+ node = ElementTree.Element('vistrail')
+
+ # set attributes
+ node.set('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.set('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.set('name',self.convertToStr(vistrail.db_name, 'str'))
+ node.set('dbHost',self.convertToStr(vistrail.db_dbHost, 'str'))
+ node.set('dbPort',self.convertToStr(vistrail.db_dbPort, 'int'))
+ node.set('dbName',self.convertToStr(vistrail.db_dbName, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = vistrail.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+ abstractions = vistrail.db_abstractions
+ for abstraction in abstractions:
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(abstraction, childNode)
+
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'moduleExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ module_name = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('abstraction_id', None)
+ abstraction_id = self.convertFromStr(data, 'long')
+ data = node.get('abstraction_version', None)
+ abstraction_version = self.convertFromStr(data, 'long')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ abstraction_id=abstraction_id,
+ abstraction_version=abstraction_version,
+ machine_id=machine_id,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(module_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.set('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+ node.set('completed',self.convertToStr(module_exec.db_completed, 'int'))
+ node.set('abstraction_id',self.convertToStr(module_exec.db_abstraction_id, 'long'))
+ node.set('abstraction_version',self.convertToStr(module_exec.db_abstraction_version, 'long'))
+ node.set('machine_id',self.convertToStr(module_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v0_9_0/persistence/xml/xml_dao.py b/vistrails/db/versions/v0_9_0/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..955c01a
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/persistence/xml/xml_dao.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v0_9_0/schemas/sql/vistrails.sql b/vistrails/db/versions/v0_9_0/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..e4ad867
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/schemas/sql/vistrails.sql
@@ -0,0 +1,281 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(22),
+ type varchar(255),
+ spec varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ spec varchar(4095),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime,
+ vistrail_id int
+) engine=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ name varchar(255),
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE workflow(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ name varchar(255),
+ version char(16),
+ last_modified datetime,
+ vistrail_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction_ref(
+ id int,
+ name varchar(1023),
+ cache int,
+ abstraction_id int,
+ version int,
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session varchar(1023),
+ user varchar(255),
+ prune int,
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ module_name varchar(255),
+ completed int,
+ abstraction_id int,
+ abstraction_version int,
+ machine_id int,
+ wf_exec_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
diff --git a/vistrails/db/versions/v0_9_0/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v0_9_0/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..a4fd64c
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,38 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, tag, port, log_tbl, machine, add_tbl, other, location, workflow_exec, function, abstraction, workflow, abstraction_ref, annotation, change_tbl, parameter, connection_tbl, action, delete_tbl, vistrail, module_exec
diff --git a/vistrails/db/versions/v0_9_0/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_9_0/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..a6c8708
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/schemas/xml/vistrail.xsd
@@ -0,0 +1,238 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="dbHost" type="xs:string"/>
+ <xs:attribute name="dbPort" type="xs:int"/>
+ <xs:attribute name="dbName" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:string"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="prune" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstractionRef">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="abstractionId" type="xs:int"/>
+ <xs:attribute name="version" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_9_0/specs/abstraction.xml b/vistrails/db/versions/v0_9_0/specs/abstraction.xml
new file mode 100644
index 0000000..aa63aee
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/abstraction.xml
@@ -0,0 +1,69 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/abstractionRef.xml b/vistrails/db/versions/v0_9_0/specs/abstractionRef.xml
new file mode 100644
index 0000000..f92f174
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/abstractionRef.xml
@@ -0,0 +1,106 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstractionRef">
+ <layout>
+ <xml name="abstractionRef" nodeType="xs:element"/>
+ <sql table="abstraction_ref"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml name="cache" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_id" type="long" foreignKey="true"
+ object="abstraction">
+ <xml name="abstractionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/action.xml b/vistrails/db/versions/v0_9_0/specs/action.xml
new file mode 100644
index 0000000..e1048ab
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/action.xml
@@ -0,0 +1,113 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="prune" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/add.xml b/vistrails/db/versions/v0_9_0/specs/add.xml
new file mode 100644
index 0000000..0236869
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/add.xml
@@ -0,0 +1,114 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/annotation.xml b/vistrails/db/versions/v0_9_0/specs/annotation.xml
new file mode 100644
index 0000000..ccf678f
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/annotation.xml
@@ -0,0 +1,100 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/change.xml b/vistrails/db/versions/v0_9_0/specs/change.xml
new file mode 100644
index 0000000..92cff57
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/change.xml
@@ -0,0 +1,119 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/connection.xml b/vistrails/db/versions/v0_9_0/specs/connection.xml
new file mode 100644
index 0000000..2f6cefd
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/connection.xml
@@ -0,0 +1,77 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/delete.xml b/vistrails/db/versions/v0_9_0/specs/delete.xml
new file mode 100644
index 0000000..86d8855
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/delete.xml
@@ -0,0 +1,81 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/function.xml b/vistrails/db/versions/v0_9_0/specs/function.xml
new file mode 100644
index 0000000..61f349f
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/function.xml
@@ -0,0 +1,89 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/location.xml b/vistrails/db/versions/v0_9_0/specs/location.xml
new file mode 100644
index 0000000..2a7ea61
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/location.xml
@@ -0,0 +1,86 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_9_0/specs/log.xml b/vistrails/db/versions/v0_9_0/specs/log.xml
new file mode 100644
index 0000000..adb6466
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/log.xml
@@ -0,0 +1,80 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/machine.xml b/vistrails/db/versions/v0_9_0/specs/machine.xml
new file mode 100644
index 0000000..2cf9416
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/machine.xml
@@ -0,0 +1,90 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/module.xml b/vistrails/db/versions/v0_9_0/specs/module.xml
new file mode 100644
index 0000000..05f8454
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/module.xml
@@ -0,0 +1,115 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/module_exec.xml b/vistrails/db/versions/v0_9_0/specs/module_exec.xml
new file mode 100644
index 0000000..8b86b73
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/module_exec.xml
@@ -0,0 +1,109 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_id" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/other.xml b/vistrails/db/versions/v0_9_0/specs/other.xml
new file mode 100644
index 0000000..a87b179
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/other.xml
@@ -0,0 +1,82 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/parameter.xml b/vistrails/db/versions/v0_9_0/specs/parameter.xml
new file mode 100644
index 0000000..0a3a4b4
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/parameter.xml
@@ -0,0 +1,97 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/port.xml b/vistrails/db/versions/v0_9_0/specs/port.xml
new file mode 100644
index 0000000..9073a77
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/port.xml
@@ -0,0 +1,98 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/portSpec.xml b/vistrails/db/versions/v0_9_0/specs/portSpec.xml
new file mode 100644
index 0000000..bc52103
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/portSpec.xml
@@ -0,0 +1,87 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(22)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/tag.xml b/vistrails/db/versions/v0_9_0/specs/tag.xml
new file mode 100644
index 0000000..a5c380d
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/tag.xml
@@ -0,0 +1,75 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/vistrail.xml b/vistrails/db/versions/v0_9_0/specs/vistrail.xml
new file mode 100644
index 0000000..a97310b
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/vistrail.xml
@@ -0,0 +1,89 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property name="dbHost" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="dbPort" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="dbName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="abstraction" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_9_0/specs/workflow.xml b/vistrails/db/versions/v0_9_0/specs/workflow.xml
new file mode 100644
index 0000000..61523ba
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/workflow.xml
@@ -0,0 +1,98 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstractionRef" ref="true" object="abstractionRef">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <!-- only need for copy/paste for no sql bindings -->
+ <property ref="true" object="abstraction" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_9_0/specs/workflow_exec.xml b/vistrails/db/versions/v0_9_0/specs/workflow_exec.xml
new file mode 100644
index 0000000..d20253c
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/specs/workflow_exec.xml
@@ -0,0 +1,109 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_0/translate/__init__.py b/vistrails/db/versions/v0_9_0/translate/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_9_0/translate/v0_8_1.py b/vistrails/db/versions/v0_9_0/translate/v0_8_1.py
new file mode 100644
index 0000000..23b811e
--- /dev/null
+++ b/vistrails/db/versions/v0_9_0/translate/v0_8_1.py
@@ -0,0 +1,135 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v0_9_0.domain import DBVistrail, DBAction, DBTag, DBModule, \
+ DBConnection, DBPortSpec, DBFunction, DBParameter, DBLocation, DBAdd, \
+ DBChange, DBDelete, DBAnnotation, DBPort, DBAbstractionRef
+
+def translateVistrail(_vistrail):
+ vistrail = DBVistrail()
+
+ for _action in _vistrail.db_actions:
+ ops = []
+ for op in _action.db_operations:
+ if op.vtType == 'add':
+ data = convert_data(op.db_data)
+ ops.append(DBAdd(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'change':
+ data = convert_data(op.db_data)
+ ops.append(DBChange(id=op.db_id,
+ what=op.db_what,
+ oldObjId=op.db_oldObjId,
+ newObjId=op.db_newObjId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'delete':
+ ops.append(DBDelete(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType))
+ annotations = []
+ for annotation in _action.db_annotations:
+ annotations.append(DBAnnotation(id=annotation.db_id,
+ key=annotation.db_key,
+ value=annotation.db_value))
+ action = DBAction(id=_action.db_id,
+ prevId=_action.db_prevId,
+ date=_action.db_date,
+ user=_action.db_user,
+ prune=_action.db_prune,
+ operations=ops,
+ annotations=annotations)
+ vistrail.db_add_action(action)
+
+ for _tag in _vistrail.db_tags:
+ tag = DBTag(id=_tag.db_id,
+ name=_tag.db_name)
+ vistrail.db_add_tag(tag)
+
+ vistrail.db_version = '0.9.0'
+ return vistrail
+
+def convert_data(child):
+ if child.vtType == 'module':
+ return DBModule(id=child.db_id,
+ cache=child.db_cache,
+ name=child.db_name,
+ package=child.db_package)
+ elif child.vtType == 'abstractionRef':
+ return DBAbstractionRef(id=child.db_id,
+ name=child.db_name,
+ cache=child.db_cache,
+ abstraction_id=child.db_abstraction_id,
+ version=child.db_version)
+ elif child.vtType == 'connection':
+ return DBConnection(id=child.db_id)
+ elif child.vtType == 'portSpec':
+ return DBPortSpec(id=child.db_id,
+ name=child.db_name,
+ type=child.db_type,
+ spec=child.db_spec)
+ elif child.vtType == 'function':
+ return DBFunction(id=child.db_id,
+ pos=child.db_pos,
+ name=child.db_name)
+ elif child.vtType == 'parameter':
+ return DBParameter(id=child.db_id,
+ pos=child.db_pos,
+ name=child.db_name,
+ type=child.db_type,
+ val=child.db_val,
+ alias=child.db_alias)
+ elif child.vtType == 'location':
+ return DBLocation(id=child.db_id,
+ x=child.db_x,
+ y=child.db_y)
+ elif child.vtType == 'annotation':
+ return DBAnnotation(id=child.db_id,
+ key=child.db_key,
+ value=child.db_value)
+ elif child.vtType == 'port':
+ return DBPort(id=child.db_id,
+ type=child.db_type,
+ moduleId=child.db_moduleId,
+ moduleName=child.db_moduleName,
+ name=child.db_name,
+ spec=child.db_spec)
diff --git a/vistrails/db/versions/v0_9_1/__init__.py b/vistrails/db/versions/v0_9_1/__init__.py
new file mode 100644
index 0000000..b324ecf
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.9.1'
diff --git a/vistrails/db/versions/v0_9_1/domain/__init__.py b/vistrails/db/versions/v0_9_1/domain/__init__.py
new file mode 100644
index 0000000..1fd287d
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/domain/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from workflow import DBWorkflow
+from vistrail import DBVistrail
+from abstraction import DBAbstraction
+from log import DBLog
+from id_scope import IdScope
diff --git a/vistrails/db/versions/v0_9_1/domain/abstraction.py b/vistrails/db/versions/v0_9_1/domain/abstraction.py
new file mode 100644
index 0000000..6c3ecb5
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/domain/abstraction.py
@@ -0,0 +1,55 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+from auto_gen import DBAbstraction as _DBAbstraction
+from auto_gen import DBAbstractionRef, DBModule
+from id_scope import IdScope
+
+class DBAbstraction(_DBAbstraction):
+ def __init__(self, *args, **kwargs):
+ _DBAbstraction.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAbstractionRef.vtType: DBModule.vtType})
+ self.idScope.setBeginId('action', 1)
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBAbstraction.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBAbstraction
+ # need to go through and reset the index to the copied objects
+ cp.idScope = copy.copy(self.idScope)
+ return cp
diff --git a/vistrails/db/versions/v0_9_1/domain/auto_gen.py b/vistrails/db/versions/v0_9_1/domain/auto_gen.py
new file mode 100644
index 0000000..c1e54b5
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/domain/auto_gen.py
@@ -0,0 +1,4809 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, spec=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_type = type
+ self._db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPortSpec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec(self._db_id,
+ self._db_name,
+ self._db_type,
+ self._db_spec)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_spec(self):
+ return self._db_spec
+ def __set_db_spec(self, spec):
+ self._db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self._db_spec = spec
+ def db_change_spec(self, spec):
+ self._db_spec = spec
+ def db_delete_spec(self, spec):
+ self._db_spec = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v._db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v._db_id] = v
+ self.db_annotations_key_index[v._db_key] = v
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v._db_id] = v
+ self.db_portSpecs_name_index[(v._db_name,v._db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModule.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule(self._db_id,
+ self._db_cache,
+ self._db_name,
+ self._db_namespace,
+ self._db_package,
+ self._db_version,
+ self._db_tag)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v._db_id, v) for v in cp._db_functions)
+ for v in cp._db_annotations:
+ cp.db_annotations_id_index[v._db_id] = v
+ cp.db_annotations_key_index[v._db_key] = v
+ for v in cp._db_portSpecs:
+ cp.db_portSpecs_id_index[v._db_id] = v
+ cp.db_portSpecs_name_index[(v._db_name,v._db_type)] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self._db_id), orphan))
+ for child in self._db_functions:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ for child in self._db_annotations:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ for child in self._db_portSpecs:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ for child in self._db_functions[:]:
+ self.db_delete_function(child)
+ for child in self._db_annotations[:]:
+ self.db_delete_annotation(child)
+ for child in self._db_portSpecs[:]:
+ self.db_delete_portSpec(child)
+ self._db_location = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function._db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i]._db_id == function._db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function._db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i]._db_id == function._db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function._db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i]._db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ self.db_annotations_key_index[annotation._db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ self.db_annotations_key_index[annotation._db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation._db_id]
+ del self.db_annotations_key_index[annotation._db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec._db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec._db_name,portSpec._db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i]._db_id == portSpec._db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec._db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec._db_name,portSpec._db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i]._db_id == portSpec._db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec._db_id]
+ del self.db_portSpecs_name_index[(portSpec._db_name,portSpec._db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i]._db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self._db_id = id
+ self._db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBTag.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag(self._db_id,
+ self._db_name)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+ if hasattr(self, 'db_id') and ('action', self._db_id) in id_remap:
+ cp._db_id = id_remap[('action', self._db_id)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = [(self, parent[0], parent[1])]
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, name=None, spec=None):
+ self._db_id = id
+ self._db_type = type
+ self._db_moduleId = moduleId
+ self._db_moduleName = moduleName
+ self._db_name = name
+ self._db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPort.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort(self._db_id,
+ self._db_type,
+ self._db_moduleId,
+ self._db_moduleName,
+ self._db_name,
+ self._db_spec)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+ if hasattr(self, 'db_moduleId') and ('module', self._db_moduleId) in id_remap:
+ cp._db_moduleId = id_remap[('module', self._db_moduleId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = [(self, parent[0], parent[1])]
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_moduleId(self):
+ return self._db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self._db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self._db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self._db_moduleName = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_spec(self):
+ return self._db_spec
+ def __set_db_spec(self, spec):
+ self._db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self._db_spec = spec
+ def db_change_spec(self, spec):
+ self._db_spec = spec
+ def db_delete_spec(self, spec):
+ self._db_spec = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBGroup(object):
+
+ vtType = 'group'
+
+ def __init__(self, id=None, workflow=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self.db_deleted_workflow = []
+ self._db_workflow = workflow
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v._db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v._db_id] = v
+ self.db_annotations_key_index[v._db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroup.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroup(self._db_id,
+ self._db_workflow and self._db_workflow.do_copy(new_ids, id_scope, id_remap),
+ self._db_cache,
+ self._db_name,
+ self._db_namespace,
+ self._db_package,
+ self._db_version,
+ self._db_tag)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v._db_id, v) for v in cp._db_functions)
+ for v in cp._db_annotations:
+ cp.db_annotations_id_index[v._db_id] = v
+ cp.db_annotations_key_index[v._db_key] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self._db_id), orphan))
+ for child in self._db_functions:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ for child in self._db_annotations:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ self._db_location = None
+ for child in self._db_functions[:]:
+ self.db_delete_function(child)
+ for child in self._db_annotations[:]:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow)
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_workflow = []
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_workflow is not None and self._db_workflow.has_changes():
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_workflow(self):
+ return self._db_workflow
+ def __set_db_workflow(self, workflow):
+ self._db_workflow = workflow
+ self.is_dirty = True
+ db_workflow = property(__get_db_workflow, __set_db_workflow)
+ def db_add_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_change_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_delete_workflow(self, workflow):
+ if not self.is_new:
+ self.db_deleted_workflow.append(self._db_workflow)
+ self._db_workflow = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function._db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i]._db_id == function._db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function._db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i]._db_id == function._db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function._db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i]._db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ self.db_annotations_key_index[annotation._db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ self.db_annotations_key_index[annotation._db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation._db_id]
+ del self.db_annotations_key_index[annotation._db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, workflow_execs=None, machines=None, vistrail_id=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_workflow_execs = []
+ self.db_workflow_execs_id_index = {}
+ if workflow_execs is None:
+ self._db_workflow_execs = []
+ else:
+ self._db_workflow_execs = workflow_execs
+ for v in self._db_workflow_execs:
+ self.db_workflow_execs_id_index[v._db_id] = v
+ self.db_deleted_machines = []
+ self.db_machines_id_index = {}
+ if machines is None:
+ self._db_machines = []
+ else:
+ self._db_machines = machines
+ for v in self._db_machines:
+ self.db_machines_id_index[v._db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog(self._db_id,
+ self._db_entity_type,
+ self._db_version,
+ self._db_name,
+ self._db_last_modified)
+ if self._db_workflow_execs is None:
+ cp._db_workflow_execs = []
+ else:
+ cp._db_workflow_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_workflow_execs]
+ if self._db_machines is None:
+ cp._db_machines = []
+ else:
+ cp._db_machines = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_machines]
+ cp._db_vistrail_id = self._db_vistrail_id
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ for v in cp._db_workflow_execs:
+ cp.db_workflow_execs_id_index[v._db_id] = v
+ for v in cp._db_machines:
+ cp.db_machines_id_index[v._db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self._db_workflow_execs:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self._db_machines:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self._db_deleted_workflow_execs)
+ children.extend(self._db_deleted_machines)
+ if remove:
+ self.db_deleted_workflow_execs = []
+ self.db_deleted_machines = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_workflow_execs:
+ if child.has_changes():
+ return True
+ for child in self._db_machines:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_workflow_execs(self):
+ return self._db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self._db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self._db_workflow_execs
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec._db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i]._db_id == workflow_exec._db_id:
+ self._db_workflow_execs[i] = workflow_exec
+ found = True
+ break
+ if not found:
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec._db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i]._db_id == workflow_exec._db_id:
+ if not self._db_workflow_execs[i].is_new:
+ self.db_deleted_workflow_execs.append(self._db_workflow_execs[i])
+ del self._db_workflow_execs[i]
+ break
+ del self.db_workflow_execs_id_index[workflow_exec._db_id]
+ def db_get_workflow_exec(self, key):
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i]._db_id == key:
+ return self._db_workflow_execs[i]
+ return None
+ def db_get_workflow_exec_by_id(self, key):
+ return self.db_workflow_execs_id_index[key]
+ def db_has_workflow_exec_with_id(self, key):
+ return key in self.db_workflow_execs_id_index
+
+ def __get_db_machines(self):
+ return self._db_machines
+ def __set_db_machines(self, machines):
+ self._db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self._db_machines
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine._db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i]._db_id == machine._db_id:
+ self._db_machines[i] = machine
+ found = True
+ break
+ if not found:
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine._db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i]._db_id == machine._db_id:
+ if not self._db_machines[i].is_new:
+ self.db_deleted_machines.append(self._db_machines[i])
+ del self._db_machines[i]
+ break
+ del self.db_machines_id_index[machine._db_id]
+ def db_get_machine(self, key):
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i]._db_id == key:
+ return self._db_machines[i]
+ return None
+ def db_get_machine_by_id(self, key):
+ return self.db_machines_id_index[key]
+ def db_has_machine_with_id(self, key):
+ return key in self.db_machines_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_os = os
+ self._db_architecture = architecture
+ self._db_processor = processor
+ self._db_ram = ram
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMachine.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine(self._db_id,
+ self._db_name,
+ self._db_os,
+ self._db_architecture,
+ self._db_processor,
+ self._db_ram)
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+ if hasattr(self, 'db_vistrailId') and ('vistrail', self._db_vistrailId) in id_remap:
+ cp._db_vistrailId = id_remap[('vistrail', self._db_vistrailId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_os(self):
+ return self._db_os
+ def __set_db_os(self, os):
+ self._db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self._db_os = os
+ def db_change_os(self, os):
+ self._db_os = os
+ def db_delete_os(self, os):
+ self._db_os = None
+
+ def __get_db_architecture(self):
+ return self._db_architecture
+ def __set_db_architecture(self, architecture):
+ self._db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self._db_architecture = None
+
+ def __get_db_processor(self):
+ return self._db_processor
+ def __set_db_processor(self, processor):
+ self._db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self._db_processor = processor
+ def db_change_processor(self, processor):
+ self._db_processor = processor
+ def db_delete_processor(self, processor):
+ self._db_processor = None
+
+ def __get_db_ram(self):
+ return self._db_ram
+ def __set_db_ram(self, ram):
+ self._db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self._db_ram = ram
+ def db_change_ram(self, ram):
+ self._db_ram = ram
+ def db_delete_ram(self, ram):
+ self._db_ram = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, data=None, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAdd.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd(self._db_data and self._db_data.do_copy(new_ids, id_scope, id_remap),
+ self._db_id,
+ self._db_what,
+ self._db_objectId,
+ self._db_parentObjId,
+ self._db_parentObjType)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOther.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOther(self._db_id,
+ self._db_key,
+ self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self._db_id = id
+ self._db_x = x
+ self._db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLocation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation(self._db_id,
+ self._db_x,
+ self._db_y)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = [(self, parent[0], parent[1])]
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_x(self):
+ return self._db_x
+ def __set_db_x(self, x):
+ self._db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self._db_x = x
+ def db_change_x(self, x):
+ self._db_x = x
+ def db_delete_x(self, x):
+ self._db_x = None
+
+ def __get_db_y(self):
+ return self._db_y
+ def __set_db_y(self, y):
+ self._db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self._db_y = y
+ def db_change_y(self, y):
+ self._db_y = y
+ def db_delete_y(self, y):
+ self._db_y = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self._db_type = type
+ self._db_val = val
+ self._db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBParameter.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter(self._db_id,
+ self._db_pos,
+ self._db_name,
+ self._db_type,
+ self._db_val,
+ self._db_alias)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = [(self, parent[0], parent[1])]
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_val(self):
+ return self._db_val
+ def __set_db_val(self, val):
+ self._db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self._db_val = val
+ def db_change_val(self, val):
+ self._db_val = val
+ def db_delete_val(self, val):
+ self._db_val = None
+
+ def __get_db_alias(self):
+ return self._db_alias
+ def __set_db_alias(self, alias):
+ self._db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self._db_alias = alias
+ def db_change_alias(self, alias):
+ self._db_alias = alias
+ def db_delete_alias(self, alias):
+ self._db_alias = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self.db_deleted_parameters = []
+ if parameters is None:
+ self._db_parameters = []
+ self.db_parameters_id_index = {}
+ else:
+ self._db_parameters = parameters
+ self.db_parameters_id_index = dict((v._db_id, v)
+ for v in
+ self._db_parameters)
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction(self._db_id,
+ self._db_pos,
+ self._db_name)
+ if self._db_parameters is None:
+ cp._db_parameters = []
+ else:
+ cp._db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_parameters_id_index = dict((v._db_id, v)
+ for v in
+ cp._db_parameters)
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ for child in self._db_parameters:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ for child in self._db_parameters[:]:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_parameters)
+ if remove:
+ self.db_deleted_parameters = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_parameters(self):
+ return self._db_parameters
+ def __set_db_parameters(self, parameters):
+ self._db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self._db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter._db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i]._db_id == parameter._db_id:
+ self._db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter._db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i]._db_id == parameter._db_id:
+ if not self._db_parameters[i].is_new:
+ self.db_deleted_parameters.append(self._db_parameters[i])
+ del self._db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter._db_id]
+ def db_get_parameter(self, key):
+ try:
+ return self.db_parameters_id_index[key]
+ except KeyError:
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i]._db_id == key:
+ return self._db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return key in self.db_parameters_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, entity_type=None, name=None, last_modified=None, actions=None, tags=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self._db_actions = []
+ else:
+ self._db_actions = actions
+ for v in self._db_actions:
+ self.db_actions_id_index[v._db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self._db_tags = []
+ else:
+ self._db_tags = tags
+ for v in self._db_tags:
+ self.db_tags_id_index[v._db_id] = v
+ self.db_tags_name_index[v._db_name] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction(self._db_id,
+ self._db_entity_type,
+ self._db_name,
+ self._db_last_modified)
+ if self._db_actions is None:
+ cp._db_actions = []
+ else:
+ cp._db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actions]
+ if self._db_tags is None:
+ cp._db_tags = []
+ else:
+ cp._db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_tags]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp._db_actions:
+ cp.db_actions_id_index[v._db_id] = v
+ for v in cp._db_tags:
+ cp.db_tags_id_index[v._db_id] = v
+ cp.db_tags_name_index[v._db_name] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self._db_actions:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self._db_tags:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_actions:
+ if child.has_changes():
+ return True
+ for child in self._db_tags:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_actions(self):
+ return self._db_actions
+ def __set_db_actions(self, actions):
+ self._db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self._db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self._db_actions.append(action)
+ self.db_actions_id_index[action._db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i]._db_id == action._db_id:
+ self._db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self._db_actions.append(action)
+ self.db_actions_id_index[action._db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i]._db_id == action._db_id:
+ if not self._db_actions[i].is_new:
+ self.db_deleted_actions.append(self._db_actions[i])
+ del self._db_actions[i]
+ break
+ del self.db_actions_id_index[action._db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i]._db_id == key:
+ return self._db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return key in self.db_actions_id_index
+
+ def __get_db_tags(self):
+ return self._db_tags
+ def __set_db_tags(self, tags):
+ self._db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self._db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag._db_id] = tag
+ self.db_tags_name_index[tag._db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i]._db_id == tag._db_id:
+ self._db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag._db_id] = tag
+ self.db_tags_name_index[tag._db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i]._db_id == tag._db_id:
+ if not self._db_tags[i].is_new:
+ self.db_deleted_tags.append(self._db_tags[i])
+ del self._db_tags[i]
+ break
+ del self.db_tags_id_index[tag._db_id]
+ del self.db_tags_name_index[tag._db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i]._db_id == key:
+ return self._db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return key in self.db_tags_id_index
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return key in self.db_tags_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, modules=None, id=None, entity_type=None, name=None, version=None, last_modified=None, connections=None, annotations=None, abstractions=None, others=None, vistrail_id=None):
+ self.db_deleted_modules = []
+ self.db_modules_id_index = {}
+ self.db_modules_inverted_id_index = {}
+ if modules is None:
+ self._db_modules = []
+ else:
+ self._db_modules = modules
+ for i, v in enumerate(self._db_modules):
+ self.db_modules_id_index[v._db_id] = v
+ self.db_modules_inverted_id_index[v._db_id] = i
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_name = name
+ self._db_version = version
+ self._db_last_modified = last_modified
+ self.db_deleted_connections = []
+ self.db_connections_id_index = {}
+ self.db_connections_inverted_id_index = {}
+ if connections is None:
+ self._db_connections = []
+ else:
+ self._db_connections = connections
+ for i, v in enumerate(self._db_connections):
+ self.db_connections_id_index[v._db_id] = v
+ self.db_connections_inverted_id_index[v._db_id] = i
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v._db_id] = v
+ self.db_deleted_abstractions = []
+ self.db_abstractions_id_index = {}
+ if abstractions is None:
+ self._db_abstractions = []
+ else:
+ self._db_abstractions = abstractions
+ for v in self._db_abstractions:
+ self.db_abstractions_id_index[v._db_id] = v
+ self.db_deleted_others = []
+ self.db_others_id_index = {}
+ if others is None:
+ self._db_others = []
+ else:
+ self._db_others = others
+ for v in self._db_others:
+ self.db_others_id_index[v._db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow()
+ if self._db_modules is None:
+ cp._db_modules = []
+ else:
+ cp._db_modules = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_modules]
+ cp._db_id = self._db_id
+ cp._db_entity_type = self._db_entity_type
+ cp._db_name = self._db_name
+ cp._db_version = self._db_version
+ cp._db_last_modified = self._db_last_modified
+ if self._db_connections is None:
+ cp._db_connections = []
+ else:
+ cp._db_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_connections]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_abstractions is None:
+ cp._db_abstractions = []
+ else:
+ cp._db_abstractions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_abstractions]
+ if self._db_others is None:
+ cp._db_others = []
+ else:
+ cp._db_others = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_others]
+ cp._db_vistrail_id = self._db_vistrail_id
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ for i, v in enumerate(cp._db_modules):
+ cp.db_modules_id_index[v._db_id] = v
+ cp.db_modules_inverted_id_index[v._db_id] = i
+ for i, v in enumerate(cp._db_connections):
+ cp.db_connections_id_index[v._db_id] = v
+ cp.db_connections_inverted_id_index[v._db_id] = i
+ for v in cp._db_annotations:
+ cp.db_annotations_id_index[v._db_id] = v
+ for v in cp._db_abstractions:
+ cp.db_abstractions_id_index[v._db_id] = v
+ for v in cp._db_others:
+ cp.db_others_id_index[v._db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ for child in self._db_connections:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ for child in self._db_annotations:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ for child in self._db_abstractions:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ for child in self._db_others:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ for child in self._db_modules:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ for child in self._db_connections[:]:
+ self.db_delete_connection(child)
+ for child in self._db_annotations[:]:
+ self.db_delete_annotation(child)
+ for child in self._db_abstractions[:]:
+ self.db_delete_abstraction(child)
+ for child in self._db_others[:]:
+ self.db_delete_other(child)
+ for child in self._db_modules[:]:
+ self.db_delete_module(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_connections)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_abstractions)
+ children.extend(self.db_deleted_others)
+ children.extend(self.db_deleted_modules)
+ if remove:
+ self.db_deleted_connections = []
+ self.db_deleted_annotations = []
+ self.db_deleted_abstractions = []
+ self.db_deleted_others = []
+ self.db_deleted_modules = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_connections:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_abstractions:
+ if child.has_changes():
+ return True
+ for child in self._db_others:
+ if child.has_changes():
+ return True
+ for child in self._db_modules:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_modules(self):
+ return self._db_modules
+ def __set_db_modules(self, modules):
+ self._db_modules = modules
+ # FIXME INDICES?
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self._db_modules
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self.db_modules_inverted_id_index[module._db_id] = len(self._db_modules)
+ self._db_modules.append(module)
+ self.db_modules_id_index[module._db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ try:
+ i = self.db_modules_inverted_id_index[module._db_id]
+ except KeyError:
+ found = False
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i]._db_id == module._db_id:
+ found = True
+ break
+ if not found:
+ self.db_add_module(module)
+ return
+ self._db_modules[i] = module
+ self.db_modules_id_index[module._db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ try:
+ i = self.db_modules_inverted_id_index[module._db_id]
+ except KeyError:
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i]._db_id == module._db_id:
+ break
+ if not self._db_modules[i].is_new:
+ self.db_deleted_modules.append(self._db_modules[i])
+ # update inverted index because things got pulled back on the _db_modules list
+ for m in self._db_modules[i+1:]:
+ self.db_modules_inverted_id_index[m._db_id] -= 1
+ del self._db_modules[i]
+ del self.db_modules_id_index[module._db_id]
+ del self.db_modules_inverted_id_index[module._db_id]
+ def db_get_module(self, key):
+ try:
+ return self.db_modules_id_index[key]
+ except KeyError:
+ for module in self._db_modules:
+ if module._db_id == key:
+ return module
+ return None
+ def db_get_module_by_id(self, key):
+ return self.db_modules_id_index[key]
+ def db_has_module_with_id(self, key):
+ return key in self.db_modules_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_connections(self):
+ return self._db_connections
+ def __set_db_connections(self, connections):
+ self._db_connections = connections
+ # FIXME INDICES?
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self._db_connections
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self.db_connections_inverted_id_index[connection._db_id] = len(self._db_connections)
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection._db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ try:
+ i = self.db_connections_inverted_id_index[connection._db_id]
+ except KeyError:
+ found = False
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i]._db_id == connection._db_id:
+ self._db_connections[i] = connection
+ found = True
+ break
+ if not found:
+ self.db_add_connection(connection)
+ return
+ self._db_connections[i] = connection
+ self.db_connections_id_index[connection._db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ try:
+ i = self.db_connections_inverted_id_index[connection._db_id]
+ except KeyError:
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i]._db_id == connection._db_id:
+ break
+ if not self._db_connections[i].is_new:
+ self.db_deleted_connections.append(self._db_connections[i])
+ # update inverted index because things got pulled back on the _db_connections list
+ for conn in self._db_connections[i+1:]:
+ self.db_connections_inverted_id_index[conn._db_id] -= 1
+ del self._db_connections[i]
+ del self.db_connections_id_index[connection._db_id]
+ del self.db_connections_inverted_id_index[connection._db_id]
+
+ def db_get_connection(self, key):
+ try:
+ return self.db_connections_id_index[key]
+ except KeyError:
+ for connection in self._db_connections:
+ if connection._db_id == key:
+ return connection
+ return None
+ def db_get_connection_by_id(self, key):
+ return self.db_connections_id_index[key]
+ def db_has_connection_with_id(self, key):
+ return key in self.db_connections_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation._db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_abstractions(self):
+ return self._db_abstractions
+ def __set_db_abstractions(self, abstractions):
+ self._db_abstractions = abstractions
+ self.is_dirty = True
+ db_abstractions = property(__get_db_abstractions, __set_db_abstractions)
+ def db_get_abstractions(self):
+ return self._db_abstractions
+ def db_add_abstraction(self, abstraction):
+ self.is_dirty = True
+ self._db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction._db_id] = abstraction
+ def db_change_abstraction(self, abstraction):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i]._db_id == abstraction._db_id:
+ self._db_abstractions[i] = abstraction
+ found = True
+ break
+ if not found:
+ self._db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction._db_id] = abstraction
+ def db_delete_abstraction(self, abstraction):
+ self.is_dirty = True
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i]._db_id == abstraction._db_id:
+ if not self._db_abstractions[i].is_new:
+ self.db_deleted_abstractions.append(self._db_abstractions[i])
+ del self._db_abstractions[i]
+ break
+ del self.db_abstractions_id_index[abstraction._db_id]
+ def db_get_abstraction(self, key):
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i]._db_id == key:
+ return self._db_abstractions[i]
+ return None
+ def db_get_abstraction_by_id(self, key):
+ return self.db_abstractions_id_index[key]
+ def db_has_abstraction_with_id(self, key):
+ return key in self.db_abstractions_id_index
+
+ def __get_db_others(self):
+ return self._db_others
+ def __set_db_others(self, others):
+ self._db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self._db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self._db_others.append(other)
+ self.db_others_id_index[other._db_id] = other
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i]._db_id == other._db_id:
+ self._db_others[i] = other
+ found = True
+ break
+ if not found:
+ self._db_others.append(other)
+ self.db_others_id_index[other._db_id] = other
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i]._db_id == other._db_id:
+ if not self._db_others[i].is_new:
+ self.db_deleted_others.append(self._db_others[i])
+ del self._db_others[i]
+ break
+ del self.db_others_id_index[other._db_id]
+ def db_get_other(self, key):
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i]._db_id == key:
+ return self._db_others[i]
+ return None
+ def db_get_other_by_id(self, key):
+ return self.db_others_id_index[key]
+ def db_has_other_with_id(self, key):
+ return key in self.db_others_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAbstractionRef(object):
+
+ vtType = 'abstractionRef'
+
+ def __init__(self, id=None, name=None, cache=None, abstraction_id=None, version=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_cache = cache
+ self._db_abstraction_id = abstraction_id
+ self._db_version = version
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v._db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v._db_id] = v
+ self.db_annotations_key_index[v._db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstractionRef.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstractionRef()
+ cp._db_id = self._db_id
+ cp._db_name = self._db_name
+ cp._db_cache = self._db_cache
+ cp._db_abstraction_id = self._db_abstraction_id
+ cp._db_version = self._db_version
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+ if hasattr(self, 'db_abstraction_id') and ('abstraction', self._db_abstraction_id) in id_remap:
+ cp._db_abstraction_id = id_remap[('abstraction', self._db_abstraction_id)]
+
+ # recreate indices and set flags
+ for v in cp._db_functions:
+ cp.db_functions_id_index[v._db_id] = v
+ for v in cp._db_annotations:
+ cp.db_annotations_id_index[v._db_id] = v
+ cp.db_annotations_key_index[v._db_key] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self._db_functions:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self._db_annotations:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_abstraction_id(self):
+ return self._db_abstraction_id
+ def __set_db_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ self.is_dirty = True
+ db_abstraction_id = property(__get_db_abstraction_id, __set_db_abstraction_id)
+ def db_add_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_change_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_delete_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function._db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i]._db_id == function._db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function._db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i]._db_id == function._db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function._db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i]._db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ self.db_annotations_key_index[annotation._db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ self.db_annotations_key_index[annotation._db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation._db_id]
+ del self.db_annotations_key_index[annotation._db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation()
+ cp._db_id = self._db_id
+ cp._db_key = self._db_key
+ cp._db_value = self._db_value
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, data=None, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_oldObjId = oldObjId
+ self._db_newObjId = newObjId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBChange.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange()
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+ cp._db_id = self._db_id
+ cp._db_what = self._db_what
+ cp._db_oldObjId = self._db_oldObjId
+ cp._db_newObjId = self._db_newObjId
+ cp._db_parentObjId = self._db_parentObjId
+ cp._db_parentObjType = self._db_parentObjType
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+ if hasattr(self, 'db_oldObjId') and (self._db_what, self._db_oldObjId) in id_remap:
+ cp._db_oldObjId = id_remap[(self._db_what, self._db_oldObjId)]
+ if hasattr(self, 'db_newObjId') and (self._db_what, self._db_newObjId) in id_remap:
+ cp._db_newObjId = id_remap[(self._db_what, self._db_newObjId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_oldObjId(self):
+ return self._db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self._db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self._db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self._db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, id=None, user=None, ip=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, name=None, module_execs=None):
+ self._db_id = id
+ self._db_user = user
+ self._db_ip = ip
+ self._db_vt_version = vt_version
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_parent_id = parent_id
+ self._db_parent_type = parent_type
+ self._db_parent_version = parent_version
+ self._db_name = name
+ self.db_deleted_module_execs = []
+ self.db_module_execs_id_index = {}
+ if module_execs is None:
+ self._db_module_execs = []
+ else:
+ self._db_module_execs = module_execs
+ for v in self._db_module_execs:
+ self.db_module_execs_id_index[v._db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflowExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec()
+ cp._db_id = self._db_id
+ cp._db_user = self._db_user
+ cp._db_ip = self._db_ip
+ cp._db_vt_version = self._db_vt_version
+ cp._db_ts_start = self._db_ts_start
+ cp._db_ts_end = self._db_ts_end
+ cp._db_parent_id = self._db_parent_id
+ cp._db_parent_type = self._db_parent_type
+ cp._db_parent_version = self._db_parent_version
+ cp._db_name = self._db_name
+ if self._db_module_execs is None:
+ cp._db_module_execs = []
+ else:
+ cp._db_module_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_module_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp._db_module_execs:
+ cp.db_module_execs_id_index[v._db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self._db_module_execs:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_execs)
+ if remove:
+ self.db_deleted_module_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_module_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_ip(self):
+ return self._db_ip
+ def __set_db_ip(self, ip):
+ self._db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self._db_ip = ip
+ def db_change_ip(self, ip):
+ self._db_ip = ip
+ def db_delete_ip(self, ip):
+ self._db_ip = None
+
+ def __get_db_vt_version(self):
+ return self._db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self._db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self._db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self._db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self._db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self._db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self._db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self._db_parent_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_module_execs(self):
+ return self._db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self._db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self._db_module_execs
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self._db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec._db_id] = module_exec
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i]._db_id == module_exec._db_id:
+ self._db_module_execs[i] = module_exec
+ found = True
+ break
+ if not found:
+ self._db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec._db_id] = module_exec
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i]._db_id == module_exec._db_id:
+ if not self._db_module_execs[i].is_new:
+ self.db_deleted_module_execs.append(self._db_module_execs[i])
+ del self._db_module_execs[i]
+ break
+ del self.db_module_execs_id_index[module_exec._db_id]
+ def db_get_module_exec(self, key):
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i]._db_id == key:
+ return self._db_module_execs[i]
+ return None
+ def db_get_module_exec_by_id(self, key):
+ return self.db_module_execs_id_index[key]
+ def db_has_module_exec_with_id(self, key):
+ return key in self.db_module_execs_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self._db_id = id
+ self.db_deleted_ports = []
+ self.db_ports_id_index = {}
+ self.db_ports_type_index = {}
+ if ports is None:
+ self._db_ports = []
+ else:
+ self._db_ports = ports
+ for v in self._db_ports:
+ self.db_ports_id_index[v._db_id] = v
+ self.db_ports_type_index[v._db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBConnection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection()
+ cp._db_id = self._db_id
+ if self._db_ports is None:
+ cp._db_ports = []
+ else:
+ cp._db_ports = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ports]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp._db_ports:
+ cp.db_ports_id_index[v._db_id] = v
+ cp.db_ports_type_index[v._db_type] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self._db_ports:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ for child in self._db_ports[:]:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_ports)
+ if remove:
+ self.db_deleted_ports = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ports(self):
+ return self._db_ports
+ def __set_db_ports(self, ports):
+ self._db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self._db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self._db_ports.append(port)
+ self.db_ports_id_index[port._db_id] = port
+ self.db_ports_type_index[port._db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i]._db_id == port._db_id:
+ self._db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self._db_ports.append(port)
+ self.db_ports_id_index[port._db_id] = port
+ self.db_ports_type_index[port._db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i]._db_id == port._db_id:
+ if not self._db_ports[i].is_new:
+ self.db_deleted_ports.append(self._db_ports[i])
+ del self._db_ports[i]
+ break
+ del self.db_ports_id_index[port._db_id]
+ del self.db_ports_type_index[port._db_type]
+ def db_get_port(self, key):
+ try:
+ return self.db_ports_id_index[key]
+ except KeyError:
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i]._db_id == key:
+ return self._db_ports[i]
+ return None
+ def db_get_port_by_id(self, key):
+ return self.db_ports_id_index[key]
+ def db_has_port_with_id(self, key):
+ return key in self.db_ports_id_index
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return key in self.db_ports_type_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, operations=None, id=None, prevId=None, date=None, session=None, user=None, prune=None, annotations=None):
+ self.db_deleted_operations = []
+ self.db_operations_id_index = {}
+ if operations is None:
+ self._db_operations = []
+ else:
+ self._db_operations = operations
+ for v in self._db_operations:
+ self.db_operations_id_index[v._db_id] = v
+ self._db_id = id
+ self._db_prevId = prevId
+ self._db_date = date
+ self._db_session = session
+ self._db_user = user
+ self._db_prune = prune
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v._db_id] = v
+ self.db_annotations_key_index[v._db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction()
+ if self._db_operations is None:
+ cp._db_operations = []
+ else:
+ cp._db_operations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_operations]
+ cp._db_id = self._db_id
+ cp._db_prevId = self._db_prevId
+ cp._db_date = self._db_date
+ cp._db_session = self._db_session
+ cp._db_user = self._db_user
+ cp._db_prune = self._db_prune
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp._db_operations:
+ cp.db_operations_id_index[v._db_id] = v
+ for v in cp._db_annotations:
+ cp.db_annotations_id_index[v._db_id] = v
+ cp.db_annotations_key_index[v._db_key] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self._db_annotations:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self._db_operations:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_operations)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_operations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_operations(self):
+ return self._db_operations
+ def __set_db_operations(self, operations):
+ self._db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self._db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation._db_id] = operation
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i]._db_id == operation._db_id:
+ self._db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation._db_id] = operation
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i]._db_id == operation._db_id:
+ if not self._db_operations[i].is_new:
+ self.db_deleted_operations.append(self._db_operations[i])
+ del self._db_operations[i]
+ break
+ del self.db_operations_id_index[operation._db_id]
+ def db_get_operation(self, key):
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i]._db_id == key:
+ return self._db_operations[i]
+ return None
+ def db_get_operation_by_id(self, key):
+ return self.db_operations_id_index[key]
+ def db_has_operation_with_id(self, key):
+ return key in self.db_operations_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_prevId(self):
+ return self._db_prevId
+ def __set_db_prevId(self, prevId):
+ self._db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self._db_prevId = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_prune(self):
+ return self._db_prune
+ def __set_db_prune(self, prune):
+ self._db_prune = prune
+ self.is_dirty = True
+ db_prune = property(__get_db_prune, __set_db_prune)
+ def db_add_prune(self, prune):
+ self._db_prune = prune
+ def db_change_prune(self, prune):
+ self._db_prune = prune
+ def db_delete_prune(self, prune):
+ self._db_prune = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ self.db_annotations_key_index[annotation._db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ self.db_annotations_key_index[annotation._db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation._db_id]
+ del self.db_annotations_key_index[annotation._db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBDelete.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete()
+ cp._db_id = self._db_id
+ cp._db_what = self._db_what
+ cp._db_objectId = self._db_objectId
+ cp._db_parentObjId = self._db_parentObjId
+ cp._db_parentObjType = self._db_parentObjType
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, dbHost=None, dbPort=None, dbName=None, actions=None, tags=None, abstractions=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self._db_dbHost = dbHost
+ self._db_dbPort = dbPort
+ self._db_dbName = dbName
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self._db_actions = []
+ else:
+ self._db_actions = actions
+ for v in self._db_actions:
+ self.db_actions_id_index[v._db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self._db_tags = []
+ else:
+ self._db_tags = tags
+ for v in self._db_tags:
+ self.db_tags_id_index[v._db_id] = v
+ self.db_tags_name_index[v._db_name] = v
+ self.db_deleted_abstractions = []
+ self.db_abstractions_id_index = {}
+ if abstractions is None:
+ self._db_abstractions = []
+ else:
+ self._db_abstractions = abstractions
+ for v in self._db_abstractions:
+ self.db_abstractions_id_index[v._db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail()
+ cp._db_id = self._db_id
+ cp._db_entity_type = self._db_entity_type
+ cp._db_version = self._db_version
+ cp._db_name = self._db_name
+ cp._db_last_modified = self._db_last_modified
+ cp._db_dbHost = self._db_dbHost
+ cp._db_dbPort = self._db_dbPort
+ cp._db_dbName = self._db_dbName
+ if self._db_actions is None:
+ cp._db_actions = []
+ else:
+ cp._db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actions]
+ if self._db_tags is None:
+ cp._db_tags = []
+ else:
+ cp._db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_tags]
+ if self._db_abstractions is None:
+ cp._db_abstractions = []
+ else:
+ cp._db_abstractions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_abstractions]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+
+ # recreate indices and set flags
+ for v in cp._db_actions:
+ cp.db_actions_id_index[v._db_id] = v
+ for v in cp._db_tags:
+ cp.db_tags_id_index[v._db_id] = v
+ cp.db_tags_name_index[v._db_name] = v
+ for v in cp._db_abstractions:
+ cp.db_abstractions_id_index[v._db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self._db_actions:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self._db_tags:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self._db_abstractions:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_abstraction(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ children.extend(self.db_deleted_abstractions)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ self.db_deleted_abstractions = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_actions:
+ if child.has_changes():
+ return True
+ for child in self._db_tags:
+ if child.has_changes():
+ return True
+ for child in self._db_abstractions:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_dbHost(self):
+ return self._db_dbHost
+ def __set_db_dbHost(self, dbHost):
+ self._db_dbHost = dbHost
+ self.is_dirty = True
+ db_dbHost = property(__get_db_dbHost, __set_db_dbHost)
+ def db_add_dbHost(self, dbHost):
+ self._db_dbHost = dbHost
+ def db_change_dbHost(self, dbHost):
+ self._db_dbHost = dbHost
+ def db_delete_dbHost(self, dbHost):
+ self._db_dbHost = None
+
+ def __get_db_dbPort(self):
+ return self._db_dbPort
+ def __set_db_dbPort(self, dbPort):
+ self._db_dbPort = dbPort
+ self.is_dirty = True
+ db_dbPort = property(__get_db_dbPort, __set_db_dbPort)
+ def db_add_dbPort(self, dbPort):
+ self._db_dbPort = dbPort
+ def db_change_dbPort(self, dbPort):
+ self._db_dbPort = dbPort
+ def db_delete_dbPort(self, dbPort):
+ self._db_dbPort = None
+
+ def __get_db_dbName(self):
+ return self._db_dbName
+ def __set_db_dbName(self, dbName):
+ self._db_dbName = dbName
+ self.is_dirty = True
+ db_dbName = property(__get_db_dbName, __set_db_dbName)
+ def db_add_dbName(self, dbName):
+ self._db_dbName = dbName
+ def db_change_dbName(self, dbName):
+ self._db_dbName = dbName
+ def db_delete_dbName(self, dbName):
+ self._db_dbName = None
+
+ def __get_db_actions(self):
+ return self._db_actions
+ def __set_db_actions(self, actions):
+ self._db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self._db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self._db_actions.append(action)
+ self.db_actions_id_index[action._db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i]._db_id == action._db_id:
+ self._db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self._db_actions.append(action)
+ self.db_actions_id_index[action._db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i]._db_id == action._db_id:
+ if not self._db_actions[i].is_new:
+ self.db_deleted_actions.append(self._db_actions[i])
+ del self._db_actions[i]
+ break
+ del self.db_actions_id_index[action._db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i]._db_id == key:
+ return self._db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return key in self.db_actions_id_index
+
+ def __get_db_tags(self):
+ return self._db_tags
+ def __set_db_tags(self, tags):
+ self._db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self._db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag._db_id] = tag
+ self.db_tags_name_index[tag._db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i]._db_id == tag._db_id:
+ self._db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag._db_id] = tag
+ self.db_tags_name_index[tag._db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i]._db_id == tag._db_id:
+ if not self._db_tags[i].is_new:
+ self.db_deleted_tags.append(self._db_tags[i])
+ del self._db_tags[i]
+ break
+ del self.db_tags_id_index[tag._db_id]
+ del self.db_tags_name_index[tag._db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i]._db_id == key:
+ return self._db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return key in self.db_tags_id_index
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return key in self.db_tags_name_index
+
+ def __get_db_abstractions(self):
+ return self._db_abstractions
+ def __set_db_abstractions(self, abstractions):
+ self._db_abstractions = abstractions
+ self.is_dirty = True
+ db_abstractions = property(__get_db_abstractions, __set_db_abstractions)
+ def db_get_abstractions(self):
+ return self._db_abstractions
+ def db_add_abstraction(self, abstraction):
+ self.is_dirty = True
+ self._db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction._db_id] = abstraction
+ def db_change_abstraction(self, abstraction):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i]._db_id == abstraction._db_id:
+ self._db_abstractions[i] = abstraction
+ found = True
+ break
+ if not found:
+ self._db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction._db_id] = abstraction
+ def db_delete_abstraction(self, abstraction):
+ self.is_dirty = True
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i]._db_id == abstraction._db_id:
+ if not self._db_abstractions[i].is_new:
+ self.db_deleted_abstractions.append(self._db_abstractions[i])
+ del self._db_abstractions[i]
+ break
+ del self.db_abstractions_id_index[abstraction._db_id]
+ def db_get_abstraction(self, key):
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i]._db_id == key:
+ return self._db_abstractions[i]
+ return None
+ def db_get_abstraction_by_id(self, key):
+ return self.db_abstractions_id_index[key]
+ def db_has_abstraction_with_id(self, key):
+ return key in self.db_abstractions_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, module_name=None, completed=None, abstraction_id=None, abstraction_version=None, machine_id=None, annotations=None):
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_module_name = module_name
+ self._db_completed = completed
+ self._db_abstraction_id = abstraction_id
+ self._db_abstraction_version = abstraction_version
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v._db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec()
+ cp._db_id = self._db_id
+ cp._db_ts_start = self._db_ts_start
+ cp._db_ts_end = self._db_ts_end
+ cp._db_cached = self._db_cached
+ cp._db_module_id = self._db_module_id
+ cp._db_module_name = self._db_module_name
+ cp._db_completed = self._db_completed
+ cp._db_abstraction_id = self._db_abstraction_id
+ cp._db_abstraction_version = self._db_abstraction_version
+ cp._db_machine_id = self._db_machine_id
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self._db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self._db_id)] = new_id
+ cp._db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ for v in cp._db_annotations:
+ cp.db_annotations_id_index[v._db_id] = v
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self._db_annotations:
+ children.extend(child.db_children((self.vtType, self._db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_module_name(self):
+ return self._db_module_name
+ def __set_db_module_name(self, module_name):
+ self._db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self._db_module_name = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_abstraction_id(self):
+ return self._db_abstraction_id
+ def __set_db_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ self.is_dirty = True
+ db_abstraction_id = property(__get_db_abstraction_id, __set_db_abstraction_id)
+ def db_add_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_change_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_delete_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = None
+
+ def __get_db_abstraction_version(self):
+ return self._db_abstraction_version
+ def __set_db_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ self.is_dirty = True
+ db_abstraction_version = property(__get_db_abstraction_version, __set_db_abstraction_version)
+ def db_add_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ def db_change_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ def db_delete_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation._db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == annotation._db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation._db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i]._db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
diff --git a/vistrails/db/versions/v0_9_1/domain/id_scope.py b/vistrails/db/versions/v0_9_1/domain/id_scope.py
new file mode 100644
index 0000000..0e07f02
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/domain/id_scope.py
@@ -0,0 +1,85 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L, remap=None):
+ self.ids = {}
+ self.beginId = beginId
+ if remap is None:
+ self.remap = {}
+ else:
+ self.remap = remap
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ cp.remap = copy.copy(self.remap)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ except KeyError:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ if self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+ except KeyError:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v0_9_1/domain/log.py b/vistrails/db/versions/v0_9_1/domain/log.py
new file mode 100644
index 0000000..5f56556
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/domain/log.py
@@ -0,0 +1,55 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBLog as _DBLog
+from auto_gen import DBAbstractionRef, DBModule
+from id_scope import IdScope
+
+import copy
+
+class DBLog(_DBLog):
+
+ def __init__(self, *args, **kwargs):
+ _DBLog.__init__(self, *args, **kwargs)
+ self.id_scope = IdScope(1,
+ {DBAbstractionRef.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBLog.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBLog
+ cp.id_scope = copy.copy(self.id_scope)
diff --git a/vistrails/db/versions/v0_9_1/domain/vistrail.py b/vistrails/db/versions/v0_9_1/domain/vistrail.py
new file mode 100644
index 0000000..fe0f902
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/domain/vistrail.py
@@ -0,0 +1,66 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBVistrail as _DBVistrail
+from auto_gen import DBAdd, DBChange, DBDelete, DBAbstractionRef, DBGroup, \
+ DBModule
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAdd.vtType: 'operation',
+ DBChange.vtType: 'operation',
+ DBDelete.vtType: 'operation',
+ DBAbstractionRef.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ self.idScope.setBeginId('action', 1)
+ self.db_objects = {}
+
+ def db_add_object(self, obj):
+ self.db_objects[(obj.vtType, obj.db_id)] = obj
+
+ def db_get_object(self, type, id):
+ return self.db_objects.get((type, id), None)
+
+ def db_update_object(self, obj, **kwargs):
+ # want to swap out old object with a new version
+ # need this for updating aliases...
+ # hack it using setattr...
+ real_obj = self.db_objects[(obj.vtType, obj.db_id)]
+ for (k, v) in kwargs.iteritems():
+ if hasattr(real_obj, k):
+ setattr(real_obj, k, v)
diff --git a/vistrails/db/versions/v0_9_1/domain/workflow.py b/vistrails/db/versions/v0_9_1/domain/workflow.py
new file mode 100644
index 0000000..cb1f6fe
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/domain/workflow.py
@@ -0,0 +1,158 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from auto_gen import DBAbstractionRef, DBModule, DBGroup
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1,
+ {DBAbstractionRef.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.build_index()
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ _vtTypeMap = {'abstractionRef': 'module', 'group': 'module'}
+
+ def build_index(self):
+ g = self._vtTypeMap.get
+ self.objects = dict(((g(o.vtType, o.vtType), o._db_id), o)
+ for (o,_,_) in self.db_children())
+
+ def add_to_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ self.objects[(obj_type, object.getPrimaryKey())] = object
+
+ def delete_from_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ del self.objects[(obj_type, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_print_objects(self):
+ for k,v in self.objects.iteritems():
+ print '%s: %s' % (k, v)
+
+ def db_has_object(self, type, id):
+ return (type, id) in self.objects
+
+ def db_get_object(self, type, id):
+ return self.objects[(type, id)]
+
+ def db_add_object(self, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == 'abstractionRef' or \
+ parent_obj_type == 'group':
+ parent_obj_type = 'module'
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if object.vtType == 'abstractionRef' or object.vtType == 'group':
+ obj_type = 'module'
+ else:
+ obj_type = object.vtType
+ funname = 'db_add_' + obj_type
+ obj_copy = copy.copy(object)
+ getattr(parent_obj, funname)(obj_copy)
+ self.add_to_index(obj_copy)
+
+ def db_change_object(self, old_id, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == 'abstractionRef' or \
+ parent_obj_type == 'group':
+ parent_obj_type = 'module'
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+
+ self.db_delete_object(old_id, object.vtType, None, None, parent_obj)
+ self.db_add_object(object, None, None, parent_obj)
+
+ def db_delete_object(self, obj_id, obj_type, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == 'abstractionRef' or \
+ parent_obj_type == 'group':
+ parent_obj_type = 'module'
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if obj_type == 'abstractionRef' or obj_type == 'group':
+ obj_type = 'module'
+ funname = 'db_get_' + obj_type
+ if hasattr(parent_obj, funname):
+ object = getattr(parent_obj, funname)(obj_id)
+ else:
+ attr_name = 'db_' + obj_type
+ object = getattr(parent_obj, attr_name)
+ funname = 'db_delete_' + obj_type
+ getattr(parent_obj, funname)(object)
+ self.delete_from_index(object)
diff --git a/vistrails/db/versions/v0_9_1/persistence/__init__.py b/vistrails/db/versions/v0_9_1/persistence/__init__.py
new file mode 100644
index 0000000..d727263
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/persistence/__init__.py
@@ -0,0 +1,95 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+from vistrails.core.system import get_elementtree_library
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_9_1 import version as my_version
+
+ElementTree = get_elementtree_library()
+
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def parse_xml_file(self, filename):
+ return ElementTree.parse(filename)
+
+ def write_xml_file(self, filename, tree):
+ tree.write(filename)
+
+ def read_xml_object(self, vtType, node):
+ return self['xml'][vtType].fromXML(node)
+
+ def write_xml_object(self, obj, node=None):
+ res_node = self['xml'][obj.vtType].toXML(obj, node)
+ return res_node
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ """open_from_xml(filename) -> DBVistrail"""
+ if tree is None:
+ tree = self.parse_xml_file(filename)
+ vistrail = self.read_xml_object(vtType, tree.getroot())
+ return vistrail
+
+ def save_to_xml(self, obj, filename, tags, version=None):
+ """save_to_xml(obj : object, filename: str, tags: dict,
+ version: str) -> None
+
+ """
+ root = self.write_xml_object(obj)
+ if version is None:
+ version = my_version
+ root.set('version', version)
+ for k, v in tags.iteritems():
+ root.set(k, v)
+ tree = ElementTree.ElementTree(root)
+ self.write_xml_file(filename, tree)
+
+ def serialize(self, object):
+ root = self.write_xml_object(object)
+ return ElementTree.tostring(root)
+
+ def unserialize(self, str, obj_type):
+ try:
+ root = ElementTree.fromstring(str)
+ return self.read_xml_object(obj_type, root)
+ except SyntaxError, e:
+ msg = "Invalid VisTrails serialized object %s" % str
+ raise VistrailsDBException(msg)
+ return None
diff --git a/vistrails/db/versions/v0_9_1/persistence/sql/__init__.py b/vistrails/db/versions/v0_9_1/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_9_1/persistence/sql/auto_gen.py b/vistrails/db/versions/v0_9_1/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..d64a45e
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/persistence/sql/auto_gen.py
@@ -0,0 +1,2693 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v0_9_1.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(22)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[4], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[5], 'long', 'int')
+ entity_type = self.convertFromDB(row[6], 'str', 'char(16)')
+ parent = self.convertFromDB(row[7], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ spec=spec,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_entity_id = entity_id
+ portSpec.db_entity_type = entity_type
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(22)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ module.db_parentType = parentType
+ module.db_entity_id = entity_id
+ module.db_entity_type = entity_type
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_parentType = parentType
+ tag.db_entity_id = entity_id
+ tag.db_entity_type = entity_type
+ tag.db_parent = parent
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_tag(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec,
+ id=id)
+ port.db_parentType = parentType
+ port.db_entity_id = entity_id
+ port.db_entity_type = entity_type
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ group = DBGroup(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ group.db_parentType = parentType
+ group.db_entity_id = entity_id
+ group.db_entity_type = entity_type
+ group.db_parent = parent
+ group.is_dirty = False
+ res[('group', id)] = group
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_parent(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_workflow is not None:
+ child = obj.db_workflow
+ child.db_parent = obj.db_id
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ log = DBLog(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ log.is_dirty = False
+ res[('log', id)] = log
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_workflow_execs:
+ child.db_log = obj.db_id
+ for child in obj.db_machines:
+ child.db_log = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.db_entity_id = entity_id
+ machine.db_entity_type = entity_type
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_entity_id = entity_id
+ add.db_entity_type = entity_type
+ add.is_dirty = False
+ res[('add', id)] = add
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_entity_id = entity_id
+ other.db_entity_type = entity_type
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_entity_id = entity_id
+ location.db_entity_type = entity_type
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_entity_id = entity_id
+ parameter.db_entity_type = entity_type
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_entity_id = entity_id
+ function.db_entity_type = entity_type
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'name', 'last_modified']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[3], 'datetime', 'datetime')
+
+ abstraction = DBAbstraction(entity_type=entity_type,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'name', 'last_modified']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_actions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id', 'parent_type']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_id = self.convertFromDB(row[1], 'long', 'int')
+ entity_type = self.convertFromDB(row[2], 'str', 'char(16)')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'char(16)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[6], 'long', 'int')
+ parent = self.convertFromDB(row[7], 'long', 'int')
+ parentType = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ workflow = DBWorkflow(entity_type=entity_type,
+ name=name,
+ version=version,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ workflow.db_entity_id = entity_id
+ workflow.db_parent = parent
+ workflow.db_parentType = parentType
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_workflow(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id', 'parent_type']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_connections:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_modules:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionRefSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'cache', 'abstraction_id', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(1023)')
+ cache = self.convertFromDB(row[2], 'int', 'int')
+ abstraction_id = self.convertFromDB(row[3], 'long', 'int')
+ version = self.convertFromDB(row[4], 'long', 'int')
+ parentType = self.convertFromDB(row[5], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ abstractionRef = DBAbstractionRef(name=name,
+ cache=cache,
+ abstraction_id=abstraction_id,
+ version=version,
+ id=id)
+ abstractionRef.db_parentType = parentType
+ abstractionRef.db_entity_id = entity_id
+ abstractionRef.db_entity_type = entity_type
+ abstractionRef.db_parent = parent
+ abstractionRef.is_dirty = False
+ res[('abstractionRef', id)] = abstractionRef
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'cache', 'abstraction_id', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_abstraction_id') and obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction_ref'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_entity_id = entity_id
+ annotation.db_entity_type = entity_type
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_entity_id = entity_id
+ change.db_entity_type = entity_type
+ change.is_dirty = False
+ res[('change', id)] = change
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ vt_version = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[4], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[5], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[6], 'long', 'int')
+ parent_type = self.convertFromDB(row[7], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[8], 'long', 'int')
+ name = self.convertFromDB(row[9], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[10], 'long', 'int')
+ entity_id = self.convertFromDB(row[11], 'long', 'int')
+ entity_type = self.convertFromDB(row[12], 'str', 'char(16)')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_entity_id = entity_id
+ workflow_exec.db_entity_type = entity_type
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_module_execs:
+ child.db_workflow_exec = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[2], 'long', 'int')
+ entity_type = self.convertFromDB(row[3], 'str', 'char(16)')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_entity_id = entity_id
+ connection.db_entity_type = entity_type
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'str', 'varchar(1023)')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ prune = self.convertFromDB(row[5], 'int', 'int')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ id=id)
+ action.db_parentType = parentType
+ action.db_entity_id = entity_id
+ action.db_entity_type = entity_type
+ action.db_parent = parent
+ action.is_dirty = False
+ res[('action', id)] = action
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_action(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_prune') and obj.db_prune is not None:
+ columnMap['prune'] = \
+ self.convertToDB(obj.db_prune, 'int', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_entity_id = entity_id
+ delete.db_entity_type = entity_type
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ if not global_props.has_key('entity_id'):
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ if not global_props.has_key('entity_type'):
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_actions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'abstraction_id', 'abstraction_version', 'machine_id', 'wf_exec_id', 'entity_id', 'entity_type']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ module_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[6], 'int', 'int')
+ abstraction_id = self.convertFromDB(row[7], 'long', 'int')
+ abstraction_version = self.convertFromDB(row[8], 'long', 'int')
+ machine_id = self.convertFromDB(row[9], 'long', 'int')
+ workflow_exec = self.convertFromDB(row[10], 'long', 'int')
+ entity_id = self.convertFromDB(row[11], 'long', 'int')
+ entity_type = self.convertFromDB(row[12], 'str', 'char(16)')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ abstraction_id=abstraction_id,
+ abstraction_version=abstraction_version,
+ machine_id=machine_id,
+ id=id)
+ module_exec.db_workflow_exec = workflow_exec
+ module_exec.db_entity_id = entity_id
+ module_exec.db_entity_type = entity_type
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ p = all_objects[('workflow_exec', obj.db_workflow_exec)]
+ p.db_add_module_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'abstraction_id', 'abstraction_version', 'machine_id', 'wf_exec_id', 'entity_id', 'entity_type']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_abstraction_id') and obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if hasattr(obj, 'db_abstraction_version') and obj.db_abstraction_version is not None:
+ columnMap['abstraction_version'] = \
+ self.convertToDB(obj.db_abstraction_version, 'long', 'int')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_workflow_exec') and obj.db_workflow_exec is not None:
+ columnMap['wf_exec_id'] = \
+ self.convertToDB(obj.db_workflow_exec, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefSQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v0_9_1/persistence/sql/sql_dao.py b/vistrails/db/versions/v0_9_1/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..c54eb03
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/persistence/sql/sql_dao.py
@@ -0,0 +1,165 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return "'" + str(value).replace("'", "''") + "'"
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ return str(value)
+ elif type == 'int':
+ return str(value)
+ elif type == 'date':
+ return "'" + value.isoformat() + "'"
+ elif type == 'datetime':
+ return "'" + value.strftime('%Y-%m-%d %H:%M:%S') + "'"
+ else:
+ return str(value)
+
+ return "''"
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None,
+ forUpdate=False):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ if forUpdate:
+ dbCommand += " FOR UPDATE"
+ dbCommand += ";"
+ return dbCommand
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ valueStr = ', '.join(values)
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s);""" % \
+ (table, columnStr, valueStr)
+ return dbCommand
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ setStr += '%s %s = %s' % (comma, column, value)
+ comma = ','
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND'
+ dbCommand = """UPDATE %s SET %s WHERE %s;""" % \
+ (table, setStr, whereStr)
+ return dbCommand
+
+ def createSQLDelete(self, table, whereMap):
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %s' % \
+ (whereClause, column, value)
+ whereClause = ' AND '
+ dbCommand = """DELETE FROM %s WHERE %s;""" % \
+ (table, whereStr)
+ return dbCommand
+
+ def executeSQL(self, db, dbCommand, isFetch):
+ # print 'db: %s' % dbCommand
+ data = None
+ cursor = db.cursor()
+ cursor.execute(dbCommand)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ cursor.close()
+ return data
+
+ def start_transaction(self, db):
+ db.begin()
+
+ def commit_transaction(self, db):
+ db.commit()
+
+ def rollback_transaction(self, db):
+ db.rollback()
diff --git a/vistrails/db/versions/v0_9_1/persistence/xml/__init__.py b/vistrails/db/versions/v0_9_1/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_9_1/persistence/xml/auto_gen.py b/vistrails/db/versions/v0_9_1/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..e31a2bf
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/persistence/xml/auto_gen.py
@@ -0,0 +1,1707 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from vistrails.core.system import get_elementtree_library
+
+from xml_dao import XMLDAO
+from vistrails.db.versions.v0_9_1.domain import *
+
+ElementTree = get_elementtree_library()
+
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'portSpec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('spec', None)
+ spec = self.convertFromStr(data, 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, node=None):
+ if node is None:
+ node = ElementTree.Element('portSpec')
+
+ # set attributes
+ node.set('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.set('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.set('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.set('spec',self.convertToStr(portSpec.db_spec, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'module':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, node=None):
+ if node is None:
+ node = ElementTree.Element('module')
+
+ # set attributes
+ node.set('id',self.convertToStr(module.db_id, 'long'))
+ node.set('cache',self.convertToStr(module.db_cache, 'int'))
+ node.set('name',self.convertToStr(module.db_name, 'str'))
+ node.set('namespace',self.convertToStr(module.db_namespace, 'str'))
+ node.set('package',self.convertToStr(module.db_package, 'str'))
+ node.set('version',self.convertToStr(module.db_version, 'str'))
+ node.set('tag',self.convertToStr(module.db_tag, 'str'))
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = module.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'tag':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, node=None):
+ if node is None:
+ node = ElementTree.Element('tag')
+
+ # set attributes
+ node.set('id',self.convertToStr(tag.db_id, 'long'))
+ node.set('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'port':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('moduleId', None)
+ moduleId = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ moduleName = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('spec', None)
+ spec = self.convertFromStr(data, 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, node=None):
+ if node is None:
+ node = ElementTree.Element('port')
+
+ # set attributes
+ node.set('id',self.convertToStr(port.db_id, 'long'))
+ node.set('type',self.convertToStr(port.db_type, 'str'))
+ node.set('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.set('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.set('name',self.convertToStr(port.db_name, 'str'))
+ node.set('spec',self.convertToStr(port.db_spec, 'str'))
+
+ return node
+
+class DBGroupXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'group':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ workflow = None
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'workflow':
+ _data = self.getDao('workflow').fromXML(child)
+ workflow = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroup(id=id,
+ workflow=workflow,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group, node=None):
+ if node is None:
+ node = ElementTree.Element('group')
+
+ # set attributes
+ node.set('id',self.convertToStr(group.db_id, 'long'))
+ node.set('cache',self.convertToStr(group.db_cache, 'int'))
+ node.set('name',self.convertToStr(group.db_name, 'str'))
+ node.set('namespace',self.convertToStr(group.db_namespace, 'str'))
+ node.set('package',self.convertToStr(group.db_package, 'str'))
+ node.set('version',self.convertToStr(group.db_version, 'str'))
+ node.set('tag',self.convertToStr(group.db_tag, 'str'))
+
+ # set elements
+ workflow = group.db_workflow
+ if workflow is not None:
+ childNode = ElementTree.SubElement(node, 'workflow')
+ self.getDao('workflow').toXML(workflow, childNode)
+ location = group.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = group.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = group.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'log':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ workflow_execs = []
+ machines = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'workflowExec':
+ _data = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs.append(_data)
+ elif child.tag == 'machine':
+ _data = self.getDao('machine').fromXML(child)
+ machines.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLog(id=id,
+ version=version,
+ name=name,
+ workflow_execs=workflow_execs,
+ machines=machines,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, node=None):
+ if node is None:
+ node = ElementTree.Element('log')
+
+ # set attributes
+ node.set('id',self.convertToStr(log.db_id, 'long'))
+ node.set('version',self.convertToStr(log.db_version, 'str'))
+ node.set('name',self.convertToStr(log.db_name, 'str'))
+ node.set('vistrail_id',self.convertToStr(log.db_vistrail_id, 'long'))
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs:
+ childNode = ElementTree.SubElement(node, 'workflow_exec')
+ self.getDao('workflow_exec').toXML(workflow_exec, childNode)
+ machines = log.db_machines
+ for machine in machines:
+ childNode = ElementTree.SubElement(node, 'machine')
+ self.getDao('machine').toXML(machine, childNode)
+
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'machine':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('os', None)
+ os = self.convertFromStr(data, 'str')
+ data = node.get('architecture', None)
+ architecture = self.convertFromStr(data, 'str')
+ data = node.get('processor', None)
+ processor = self.convertFromStr(data, 'str')
+ data = node.get('ram', None)
+ ram = self.convertFromStr(data, 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, node=None):
+ if node is None:
+ node = ElementTree.Element('machine')
+
+ # set attributes
+ node.set('id',self.convertToStr(machine.db_id, 'long'))
+ node.set('name',self.convertToStr(machine.db_name, 'str'))
+ node.set('os',self.convertToStr(machine.db_os, 'str'))
+ node.set('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.set('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.set('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'add':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ data = _data
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAdd(data=data,
+ id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, node=None):
+ if node is None:
+ node = ElementTree.Element('add')
+
+ # set attributes
+ node.set('id',self.convertToStr(add.db_id, 'long'))
+ node.set('what',self.convertToStr(add.db_what, 'str'))
+ node.set('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # set elements
+ data = add.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'other':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'value':
+ _data = self.convertFromStr(child.text,'')
+ value = _data
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, node=None):
+ if node is None:
+ node = ElementTree.Element('other')
+
+ # set attributes
+ node.set('id',self.convertToStr(other.db_id, 'long'))
+ node.set('key',self.convertToStr(other.db_key, 'str'))
+
+ # set elements
+
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'location':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('x', None)
+ x = self.convertFromStr(data, 'float')
+ data = node.get('y', None)
+ y = self.convertFromStr(data, 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, node=None):
+ if node is None:
+ node = ElementTree.Element('location')
+
+ # set attributes
+ node.set('id',self.convertToStr(location.db_id, 'long'))
+ node.set('x',self.convertToStr(location.db_x, 'float'))
+ node.set('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'parameter':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('val', None)
+ val = self.convertFromStr(data, 'str')
+ data = node.get('alias', None)
+ alias = self.convertFromStr(data, 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, node=None):
+ if node is None:
+ node = ElementTree.Element('parameter')
+
+ # set attributes
+ node.set('id',self.convertToStr(parameter.db_id, 'long'))
+ node.set('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.set('name',self.convertToStr(parameter.db_name, 'str'))
+ node.set('type',self.convertToStr(parameter.db_type, 'str'))
+ node.set('val',self.convertToStr(parameter.db_val, 'str'))
+ node.set('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'function':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ parameters = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ parameters.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, node=None):
+ if node is None:
+ node = ElementTree.Element('function')
+
+ # set attributes
+ node.set('id',self.convertToStr(function.db_id, 'long'))
+ node.set('pos',self.convertToStr(function.db_pos, 'long'))
+ node.set('name',self.convertToStr(function.db_name, 'str'))
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(parameter, childNode)
+
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'abstraction':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child.tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstraction(id=id,
+ name=name,
+ actions=actions,
+ tags=tags)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, node=None):
+ if node is None:
+ node = ElementTree.Element('abstraction')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.set('name',self.convertToStr(abstraction.db_name, 'str'))
+
+ # set elements
+ actions = abstraction.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = abstraction.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflow':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ connections = []
+ annotations = []
+ abstractions = []
+ others = []
+ modules = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ connections.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ abstractions.append(_data)
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ others.append(_data)
+ elif child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ modules.append(_data)
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ modules.append(_data)
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ modules.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflow(modules=modules,
+ id=id,
+ name=name,
+ version=version,
+ connections=connections,
+ annotations=annotations,
+ abstractions=abstractions,
+ others=others,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, node=None):
+ if node is None:
+ node = ElementTree.Element('workflow')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow.db_id, 'long'))
+ node.set('name',self.convertToStr(workflow.db_name, 'str'))
+ node.set('version',self.convertToStr(workflow.db_version, 'str'))
+ node.set('vistrail_id',self.convertToStr(workflow.db_vistrail_id, 'long'))
+
+ # set elements
+ connections = workflow.db_connections
+ for connection in connections:
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(connection, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ abstractions = workflow.db_abstractions
+ for abstraction in abstractions:
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(abstraction, childNode)
+ others = workflow.db_others
+ for other in others:
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(other, childNode)
+ modules = workflow.db_modules
+ for module in modules:
+ if module.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(module, childNode)
+ elif module.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(module, childNode)
+ elif module.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(module, childNode)
+
+ return node
+
+class DBAbstractionRefXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'abstractionRef':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('abstractionId', None)
+ abstraction_id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'long')
+
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstractionRef(id=id,
+ name=name,
+ cache=cache,
+ abstraction_id=abstraction_id,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstractionRef, node=None):
+ if node is None:
+ node = ElementTree.Element('abstractionRef')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstractionRef.db_id, 'long'))
+ node.set('name',self.convertToStr(abstractionRef.db_name, 'str'))
+ node.set('cache',self.convertToStr(abstractionRef.db_cache, 'int'))
+ node.set('abstractionId',self.convertToStr(abstractionRef.db_abstraction_id, 'long'))
+ node.set('version',self.convertToStr(abstractionRef.db_version, 'long'))
+
+ # set elements
+ location = abstractionRef.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = abstractionRef.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = abstractionRef.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'annotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, node=None):
+ if node is None:
+ node = ElementTree.Element('annotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(annotation.db_id, 'long'))
+ node.set('key',self.convertToStr(annotation.db_key, 'str'))
+ node.set('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'change':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('oldObjId', None)
+ oldObjId = self.convertFromStr(data, 'long')
+ data = node.get('newObjId', None)
+ newObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ data = _data
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBChange(data=data,
+ id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, node=None):
+ if node is None:
+ node = ElementTree.Element('change')
+
+ # set attributes
+ node.set('id',self.convertToStr(change.db_id, 'long'))
+ node.set('what',self.convertToStr(change.db_what, 'str'))
+ node.set('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.set('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.set('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # set elements
+ data = change.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflowExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('ip', None)
+ ip = self.convertFromStr(data, 'str')
+ data = node.get('vtVersion', None)
+ vt_version = self.convertFromStr(data, 'str')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('parentId', None)
+ parent_id = self.convertFromStr(data, 'long')
+ data = node.get('parentType', None)
+ parent_type = self.convertFromStr(data, 'str')
+ data = node.get('parentVersion', None)
+ parent_version = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ module_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ module_execs.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflowExec(id=id,
+ user=user,
+ ip=ip,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ name=name,
+ module_execs=module_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('workflowExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.set('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.set('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.set('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.set('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.set('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.set('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.set('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.set('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # set elements
+ module_execs = workflow_exec.db_module_execs
+ for module_exec in module_execs:
+ childNode = ElementTree.SubElement(node, 'module_exec')
+ self.getDao('module_exec').toXML(module_exec, childNode)
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'connection':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+
+ ports = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ ports.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, node=None):
+ if node is None:
+ node = ElementTree.Element('connection')
+
+ # set attributes
+ node.set('id',self.convertToStr(connection.db_id, 'long'))
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(port, childNode)
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'action':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('prevId', None)
+ prevId = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'str')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('prune', None)
+ prune = self.convertFromStr(data, 'int')
+
+ annotations = []
+ operations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'add':
+ _data = self.getDao('add').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'delete':
+ _data = self.getDao('delete').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'change':
+ _data = self.getDao('change').fromXML(child)
+ operations.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAction(operations=operations,
+ id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, node=None):
+ if node is None:
+ node = ElementTree.Element('action')
+
+ # set attributes
+ node.set('id',self.convertToStr(action.db_id, 'long'))
+ node.set('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.set('date',self.convertToStr(action.db_date, 'datetime'))
+ node.set('session',self.convertToStr(action.db_session, 'str'))
+ node.set('user',self.convertToStr(action.db_user, 'str'))
+ node.set('prune',self.convertToStr(action.db_prune, 'int'))
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ childNode = ElementTree.SubElement(node, 'add')
+ self.getDao('add').toXML(operation, childNode)
+ elif operation.vtType == 'delete':
+ childNode = ElementTree.SubElement(node, 'delete')
+ self.getDao('delete').toXML(operation, childNode)
+ elif operation.vtType == 'change':
+ childNode = ElementTree.SubElement(node, 'change')
+ self.getDao('change').toXML(operation, childNode)
+
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'delete':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, node=None):
+ if node is None:
+ node = ElementTree.Element('delete')
+
+ # set attributes
+ node.set('id',self.convertToStr(delete.db_id, 'long'))
+ node.set('what',self.convertToStr(delete.db_what, 'str'))
+ node.set('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'vistrail':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('dbHost', None)
+ dbHost = self.convertFromStr(data, 'str')
+ data = node.get('dbPort', None)
+ dbPort = self.convertFromStr(data, 'int')
+ data = node.get('dbName', None)
+ dbName = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+ abstractions = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child.tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ abstractions.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ dbHost=dbHost,
+ dbPort=dbPort,
+ dbName=dbName,
+ actions=actions,
+ tags=tags,
+ abstractions=abstractions)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, node=None):
+ if node is None:
+ node = ElementTree.Element('vistrail')
+
+ # set attributes
+ node.set('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.set('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.set('name',self.convertToStr(vistrail.db_name, 'str'))
+ node.set('dbHost',self.convertToStr(vistrail.db_dbHost, 'str'))
+ node.set('dbPort',self.convertToStr(vistrail.db_dbPort, 'int'))
+ node.set('dbName',self.convertToStr(vistrail.db_dbName, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = vistrail.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+ abstractions = vistrail.db_abstractions
+ for abstraction in abstractions:
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(abstraction, childNode)
+
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'moduleExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ module_name = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('abstraction_id', None)
+ abstraction_id = self.convertFromStr(data, 'long')
+ data = node.get('abstraction_version', None)
+ abstraction_version = self.convertFromStr(data, 'long')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ abstraction_id=abstraction_id,
+ abstraction_version=abstraction_version,
+ machine_id=machine_id,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(module_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.set('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+ node.set('completed',self.convertToStr(module_exec.db_completed, 'int'))
+ node.set('abstraction_id',self.convertToStr(module_exec.db_abstraction_id, 'long'))
+ node.set('abstraction_version',self.convertToStr(module_exec.db_abstraction_version, 'long'))
+ node.set('machine_id',self.convertToStr(module_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v0_9_1/persistence/xml/xml_dao.py b/vistrails/db/versions/v0_9_1/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..955c01a
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/persistence/xml/xml_dao.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v0_9_1/schemas/sql/vistrails.sql b/vistrails/db/versions/v0_9_1/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..1e45703
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/schemas/sql/vistrails.sql
@@ -0,0 +1,298 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(22),
+ type varchar(255),
+ spec varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ spec varchar(4095),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE group_tbl(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime,
+ vistrail_id int
+) engine=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE workflow(
+ id int not null auto_increment primary key,
+ entity_id int,
+ entity_type char(16),
+ name varchar(255),
+ version char(16),
+ last_modified datetime,
+ vistrail_id int,
+ parent_id int,
+ parent_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE abstraction_ref(
+ id int,
+ name varchar(1023),
+ cache int,
+ abstraction_id int,
+ version int,
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ name varchar(255),
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session varchar(1023),
+ user varchar(255),
+ prune int,
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ module_name varchar(255),
+ completed int,
+ abstraction_id int,
+ abstraction_version int,
+ machine_id int,
+ wf_exec_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
diff --git a/vistrails/db/versions/v0_9_1/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v0_9_1/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..3cb6da4
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,38 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, tag, port, group_tbl, log_tbl, machine, add_tbl, other, location, parameter, function, abstraction, workflow, abstraction_ref, annotation, change_tbl, workflow_exec, connection_tbl, action, delete_tbl, vistrail, module_exec
diff --git a/vistrails/db/versions/v0_9_1/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_9_1/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..22bdf2a
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/schemas/xml/vistrail.xsd
@@ -0,0 +1,277 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="dbHost" type="xs:string"/>
+ <xs:attribute name="dbPort" type="xs:int"/>
+ <xs:attribute name="dbName" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:string"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="prune" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstractionRef">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="abstractionId" type="xs:int"/>
+ <xs:attribute name="version" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="group">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="workflow" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="workflow">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_9_1/schemas/xml/vtlink.xsd b/vistrails/db/versions/v0_9_1/schemas/xml/vtlink.xsd
new file mode 100644
index 0000000..e1ec5d0
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/schemas/xml/vtlink.xsd
@@ -0,0 +1,52 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0" encoding="UTF-8"?>
+
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
+<xs:element name="vtlink">
+<xs:complexType>
+<xs:attribute name="host" type="xs:string"></xs:attribute>
+<xs:attribute name="database" type="xs:string"></xs:attribute>
+<xs:attribute name="port" type="xs:int"></xs:attribute>
+<xs:attribute name="vtid" type="xs:int"></xs:attribute>
+<xs:attribute name="version" type="xs:int"></xs:attribute>
+<xs:attribute name="tag" type="xs:string"></xs:attribute>
+<xs:attribute name="execute" type="xs:boolean"></xs:attribute>
+<xs:attribute name="showSpreadsheetOnly" type="xs:boolean"></xs:attribute>
+</xs:complexType>
+</xs:element>
+
+</xs:schema>
diff --git a/vistrails/db/versions/v0_9_1/specs/abstraction.xml b/vistrails/db/versions/v0_9_1/specs/abstraction.xml
new file mode 100644
index 0000000..aa63aee
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/abstraction.xml
@@ -0,0 +1,69 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/abstractionRef.xml b/vistrails/db/versions/v0_9_1/specs/abstractionRef.xml
new file mode 100644
index 0000000..f92f174
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/abstractionRef.xml
@@ -0,0 +1,106 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="abstractionRef">
+ <layout>
+ <xml name="abstractionRef" nodeType="xs:element"/>
+ <sql table="abstraction_ref"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml name="cache" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_id" type="long" foreignKey="true"
+ object="abstraction">
+ <xml name="abstractionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/action.xml b/vistrails/db/versions/v0_9_1/specs/action.xml
new file mode 100644
index 0000000..e1048ab
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/action.xml
@@ -0,0 +1,113 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="prune" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/add.xml b/vistrails/db/versions/v0_9_1/specs/add.xml
new file mode 100644
index 0000000..20c1cc6
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/add.xml
@@ -0,0 +1,117 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/annotation.xml b/vistrails/db/versions/v0_9_1/specs/annotation.xml
new file mode 100644
index 0000000..49323ec
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/annotation.xml
@@ -0,0 +1,104 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/change.xml b/vistrails/db/versions/v0_9_1/specs/change.xml
new file mode 100644
index 0000000..e24ac1d
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/change.xml
@@ -0,0 +1,122 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/connection.xml b/vistrails/db/versions/v0_9_1/specs/connection.xml
new file mode 100644
index 0000000..2f6cefd
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/connection.xml
@@ -0,0 +1,77 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/delete.xml b/vistrails/db/versions/v0_9_1/specs/delete.xml
new file mode 100644
index 0000000..86d8855
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/delete.xml
@@ -0,0 +1,81 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/function.xml b/vistrails/db/versions/v0_9_1/specs/function.xml
new file mode 100644
index 0000000..02710b2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/function.xml
@@ -0,0 +1,92 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/group.xml b/vistrails/db/versions/v0_9_1/specs/group.xml
new file mode 100644
index 0000000..f275b60
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/group.xml
@@ -0,0 +1,120 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="group" parentClass="module">
+ <layout>
+ <xml name="group" nodeType="xs:element"/>
+ <sql table="group_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow" type="object" mapping="one-to-one"
+ expand="false">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/location.xml b/vistrails/db/versions/v0_9_1/specs/location.xml
new file mode 100644
index 0000000..6fd8c11
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/location.xml
@@ -0,0 +1,89 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
+
diff --git a/vistrails/db/versions/v0_9_1/specs/log.xml b/vistrails/db/versions/v0_9_1/specs/log.xml
new file mode 100644
index 0000000..adb6466
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/log.xml
@@ -0,0 +1,80 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/machine.xml b/vistrails/db/versions/v0_9_1/specs/machine.xml
new file mode 100644
index 0000000..2cf9416
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/machine.xml
@@ -0,0 +1,90 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/module.xml b/vistrails/db/versions/v0_9_1/specs/module.xml
new file mode 100644
index 0000000..0c70031
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/module.xml
@@ -0,0 +1,120 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/module_exec.xml b/vistrails/db/versions/v0_9_1/specs/module_exec.xml
new file mode 100644
index 0000000..8b86b73
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/module_exec.xml
@@ -0,0 +1,109 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_id" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/other.xml b/vistrails/db/versions/v0_9_1/specs/other.xml
new file mode 100644
index 0000000..a87b179
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/other.xml
@@ -0,0 +1,82 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/parameter.xml b/vistrails/db/versions/v0_9_1/specs/parameter.xml
new file mode 100644
index 0000000..0a3a4b4
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/parameter.xml
@@ -0,0 +1,97 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/port.xml b/vistrails/db/versions/v0_9_1/specs/port.xml
new file mode 100644
index 0000000..9073a77
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/port.xml
@@ -0,0 +1,98 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/portSpec.xml b/vistrails/db/versions/v0_9_1/specs/portSpec.xml
new file mode 100644
index 0000000..bc52103
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/portSpec.xml
@@ -0,0 +1,87 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(22)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/tag.xml b/vistrails/db/versions/v0_9_1/specs/tag.xml
new file mode 100644
index 0000000..a5c380d
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/tag.xml
@@ -0,0 +1,75 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/vistrail.xml b/vistrails/db/versions/v0_9_1/specs/vistrail.xml
new file mode 100644
index 0000000..a97310b
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/vistrail.xml
@@ -0,0 +1,89 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property name="dbHost" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="dbPort" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ </property>
+
+ <property name="dbName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="abstraction" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+</object>
diff --git a/vistrails/db/versions/v0_9_1/specs/workflow.xml b/vistrails/db/versions/v0_9_1/specs/workflow.xml
new file mode 100644
index 0000000..1601ddb
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/workflow.xml
@@ -0,0 +1,113 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstractionRef" ref="true" object="abstractionRef">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group" ref="true" object="group">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <!-- only need for copy/paste for no sql bindings -->
+ <property ref="true" object="abstraction" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent" ref="true" object="group" type="long" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+</object>
+
diff --git a/vistrails/db/versions/v0_9_1/specs/workflow_exec.xml b/vistrails/db/versions/v0_9_1/specs/workflow_exec.xml
new file mode 100644
index 0000000..d20253c
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/specs/workflow_exec.xml
@@ -0,0 +1,109 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+</object>
diff --git a/vistrails/db/versions/v0_9_1/translate/__init__.py b/vistrails/db/versions/v0_9_1/translate/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_9_1/translate/v0_9_0.py b/vistrails/db/versions/v0_9_1/translate/v0_9_0.py
new file mode 100644
index 0000000..668247e
--- /dev/null
+++ b/vistrails/db/versions/v0_9_1/translate/v0_9_0.py
@@ -0,0 +1,142 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v0_9_1.domain import DBVistrail, DBAction, DBTag, DBModule, \
+ DBConnection, DBPortSpec, DBFunction, DBParameter, DBLocation, DBAdd, \
+ DBChange, DBDelete, DBAnnotation, DBPort, DBAbstractionRef, DBGroup
+
+def translateVistrail(_vistrail):
+ vistrail = DBVistrail()
+
+ for _action in _vistrail.db_actions:
+ ops = []
+ for op in _action.db_operations:
+ if op.vtType == 'add':
+ data = convert_data(op.db_data)
+ ops.append(DBAdd(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'change':
+ data = convert_data(op.db_data)
+ ops.append(DBChange(id=op.db_id,
+ what=op.db_what,
+ oldObjId=op.db_oldObjId,
+ newObjId=op.db_newObjId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'delete':
+ ops.append(DBDelete(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType))
+ annotations = []
+ for annotation in _action.db_annotations:
+ annotations.append(DBAnnotation(id=annotation.db_id,
+ key=annotation.db_key,
+ value=annotation.db_value))
+ action = DBAction(id=_action.db_id,
+ prevId=_action.db_prevId,
+ date=_action.db_date,
+ user=_action.db_user,
+ prune=_action.db_prune,
+ operations=ops,
+ annotations=annotations)
+ vistrail.db_add_action(action)
+
+ for _tag in _vistrail.db_tags:
+ tag = DBTag(id=_tag.db_id,
+ name=_tag.db_name)
+ vistrail.db_add_tag(tag)
+
+ vistrail.db_version = '0.9.1'
+ return vistrail
+
+def convert_data(child):
+ if child.vtType == 'module':
+ name_str = child.db_name
+ if name_str.rfind('|') != -1:
+ (namespace, name) = name_str.rsplit('|',1)
+ else:
+ name = name_str
+ namespace = None
+ return DBModule(id=child.db_id,
+ cache=child.db_cache,
+ name=name,
+ namespace=namespace,
+ package=child.db_package)
+ elif child.vtType == 'abstractionRef':
+ return DBAbstractionRef(id=child.db_id,
+ name=child.db_name,
+ cache=child.db_cache,
+ abstraction_id=child.db_abstraction_id,
+ version=child.db_version)
+ elif child.vtType == 'connection':
+ return DBConnection(id=child.db_id)
+ elif child.vtType == 'portSpec':
+ return DBPortSpec(id=child.db_id,
+ name=child.db_name,
+ type=child.db_type,
+ spec=child.db_spec)
+ elif child.vtType == 'function':
+ return DBFunction(id=child.db_id,
+ pos=child.db_pos,
+ name=child.db_name)
+ elif child.vtType == 'parameter':
+ return DBParameter(id=child.db_id,
+ pos=child.db_pos,
+ name=child.db_name,
+ type=child.db_type,
+ val=child.db_val,
+ alias=child.db_alias)
+ elif child.vtType == 'location':
+ return DBLocation(id=child.db_id,
+ x=child.db_x,
+ y=child.db_y)
+ elif child.vtType == 'annotation':
+ return DBAnnotation(id=child.db_id,
+ key=child.db_key,
+ value=child.db_value)
+ elif child.vtType == 'port':
+ return DBPort(id=child.db_id,
+ type=child.db_type,
+ moduleId=child.db_moduleId,
+ moduleName=child.db_moduleName,
+ name=child.db_name,
+ spec=child.db_spec)
diff --git a/vistrails/db/versions/v0_9_2/__init__.py b/vistrails/db/versions/v0_9_2/__init__.py
new file mode 100644
index 0000000..75bdbf3
--- /dev/null
+++ b/vistrails/db/versions/v0_9_2/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.9.2'
diff --git a/vistrails/db/versions/v0_9_2/domain/__init__.py b/vistrails/db/versions/v0_9_2/domain/__init__.py
new file mode 100644
index 0000000..057dce6
--- /dev/null
+++ b/vistrails/db/versions/v0_9_2/domain/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.versions.v0_9_1.domain import *
diff --git a/vistrails/db/versions/v0_9_2/persistence/__init__.py b/vistrails/db/versions/v0_9_2/persistence/__init__.py
new file mode 100644
index 0000000..533a33e
--- /dev/null
+++ b/vistrails/db/versions/v0_9_2/persistence/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.versions.v0_9_1.persistence import DAOList
diff --git a/vistrails/db/versions/v0_9_2/translate/__init__.py b/vistrails/db/versions/v0_9_2/translate/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_9_2/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_9_2/translate/v0_9_1.py b/vistrails/db/versions/v0_9_2/translate/v0_9_1.py
new file mode 100644
index 0000000..a5b0d4c
--- /dev/null
+++ b/vistrails/db/versions/v0_9_2/translate/v0_9_1.py
@@ -0,0 +1,48 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_9_1.domain import DBAdd, DBAnnotation, DBChange, DBDelete
+
+def translateVistrail(vistrail):
+ id_remap = {}
+ for action in vistrail.db_get_actions():
+ for annotation in action.db_get_annotations():
+ if annotation.db_key == 'notes':
+ del action.db_annotations_key_index['notes']
+ annotation.db_key = '__notes__'
+ action.db_annotations_key_index['__notes__'] = annotation
+
+ vistrail.db_version = '0.9.2'
+ return vistrail
diff --git a/vistrails/db/versions/v0_9_3/__init__.py b/vistrails/db/versions/v0_9_3/__init__.py
new file mode 100644
index 0000000..e628fc0
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.9.3'
diff --git a/vistrails/db/versions/v0_9_3/domain/__init__.py b/vistrails/db/versions/v0_9_3/domain/__init__.py
new file mode 100644
index 0000000..1fd287d
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/domain/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from workflow import DBWorkflow
+from vistrail import DBVistrail
+from abstraction import DBAbstraction
+from log import DBLog
+from id_scope import IdScope
diff --git a/vistrails/db/versions/v0_9_3/domain/abstraction.py b/vistrails/db/versions/v0_9_3/domain/abstraction.py
new file mode 100644
index 0000000..6c3ecb5
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/domain/abstraction.py
@@ -0,0 +1,55 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+from auto_gen import DBAbstraction as _DBAbstraction
+from auto_gen import DBAbstractionRef, DBModule
+from id_scope import IdScope
+
+class DBAbstraction(_DBAbstraction):
+ def __init__(self, *args, **kwargs):
+ _DBAbstraction.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAbstractionRef.vtType: DBModule.vtType})
+ self.idScope.setBeginId('action', 1)
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBAbstraction.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBAbstraction
+ # need to go through and reset the index to the copied objects
+ cp.idScope = copy.copy(self.idScope)
+ return cp
diff --git a/vistrails/db/versions/v0_9_3/domain/auto_gen.py b/vistrails/db/versions/v0_9_3/domain/auto_gen.py
new file mode 100644
index 0000000..87512da
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/domain/auto_gen.py
@@ -0,0 +1,6369 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, spec=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_type = type
+ self._db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPortSpec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec(id=self._db_id,
+ name=self._db_name,
+ type=self._db_type,
+ spec=self._db_spec)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPortSpec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'spec' in class_dict:
+ res = class_dict['spec'](old_obj, trans_dict)
+ new_obj.db_spec = res
+ elif hasattr(old_obj, 'db_spec') and old_obj.db_spec is not None:
+ new_obj.db_spec = old_obj.db_spec
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_spec(self):
+ return self._db_spec
+ def __set_db_spec(self, spec):
+ self._db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self._db_spec = spec
+ def db_change_spec(self, spec):
+ self._db_spec = spec
+ def db_delete_spec(self, spec):
+ self._db_spec = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModule.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ tag=self._db_tag)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModule()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self._db_id = id
+ self._db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBTag.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag(id=self._db_id,
+ name=self._db_name)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('action', self._db_id) in id_remap:
+ cp._db_id = id_remap[('action', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBTag()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, name=None, spec=None):
+ self._db_id = id
+ self._db_type = type
+ self._db_moduleId = moduleId
+ self._db_moduleName = moduleName
+ self._db_name = name
+ self._db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPort.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort(id=self._db_id,
+ type=self._db_type,
+ moduleId=self._db_moduleId,
+ moduleName=self._db_moduleName,
+ name=self._db_name,
+ spec=self._db_spec)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_moduleId') and ('module', self._db_moduleId) in id_remap:
+ cp._db_moduleId = id_remap[('module', self._db_moduleId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPort()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'moduleId' in class_dict:
+ res = class_dict['moduleId'](old_obj, trans_dict)
+ new_obj.db_moduleId = res
+ elif hasattr(old_obj, 'db_moduleId') and old_obj.db_moduleId is not None:
+ new_obj.db_moduleId = old_obj.db_moduleId
+ if 'moduleName' in class_dict:
+ res = class_dict['moduleName'](old_obj, trans_dict)
+ new_obj.db_moduleName = res
+ elif hasattr(old_obj, 'db_moduleName') and old_obj.db_moduleName is not None:
+ new_obj.db_moduleName = old_obj.db_moduleName
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'spec' in class_dict:
+ res = class_dict['spec'](old_obj, trans_dict)
+ new_obj.db_spec = res
+ elif hasattr(old_obj, 'db_spec') and old_obj.db_spec is not None:
+ new_obj.db_spec = old_obj.db_spec
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_moduleId(self):
+ return self._db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self._db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self._db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self._db_moduleName = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_spec(self):
+ return self._db_spec
+ def __set_db_spec(self, spec):
+ self._db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self._db_spec = spec
+ def db_change_spec(self, spec):
+ self._db_spec = spec
+ def db_delete_spec(self, spec):
+ self._db_spec = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBGroup(object):
+
+ vtType = 'group'
+
+ def __init__(self, id=None, workflow=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self.db_deleted_workflow = []
+ self._db_workflow = workflow
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroup.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroup(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ tag=self._db_tag)
+ if self._db_workflow is not None:
+ cp._db_workflow = self._db_workflow.do_copy()
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroup()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'workflow' in class_dict:
+ res = class_dict['workflow'](old_obj, trans_dict)
+ new_obj.db_workflow = res
+ elif hasattr(old_obj, 'db_workflow') and old_obj.db_workflow is not None:
+ obj = old_obj.db_workflow
+ new_obj.db_add_workflow(DBWorkflow.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow') and hasattr(new_obj, 'db_deleted_workflow'):
+ for obj in old_obj.db_deleted_workflow:
+ n_obj = DBWorkflow.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow.append(n_obj)
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow)
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_workflow = []
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_workflow is not None and self._db_workflow.has_changes():
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_workflow(self):
+ return self._db_workflow
+ def __set_db_workflow(self, workflow):
+ self._db_workflow = workflow
+ self.is_dirty = True
+ db_workflow = property(__get_db_workflow, __set_db_workflow)
+ def db_add_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_change_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_delete_workflow(self, workflow):
+ if not self.is_new:
+ self.db_deleted_workflow.append(self._db_workflow)
+ self._db_workflow = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, workflow_execs=None, machines=None, vistrail_id=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_workflow_execs = []
+ self.db_workflow_execs_id_index = {}
+ if workflow_execs is None:
+ self._db_workflow_execs = []
+ else:
+ self._db_workflow_execs = workflow_execs
+ for v in self._db_workflow_execs:
+ self.db_workflow_execs_id_index[v.db_id] = v
+ self.db_deleted_machines = []
+ self.db_machines_id_index = {}
+ if machines is None:
+ self._db_machines = []
+ else:
+ self._db_machines = machines
+ for v in self._db_machines:
+ self.db_machines_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_workflow_execs is None:
+ cp._db_workflow_execs = []
+ else:
+ cp._db_workflow_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_workflow_execs]
+ if self._db_machines is None:
+ cp._db_machines = []
+ else:
+ cp._db_machines = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_machines]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_workflow_execs_id_index = dict((v.db_id, v) for v in cp._db_workflow_execs)
+ cp.db_machines_id_index = dict((v.db_id, v) for v in cp._db_machines)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'workflow_execs' in class_dict:
+ res = class_dict['workflow_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_workflow_exec(obj)
+ elif hasattr(old_obj, 'db_workflow_execs') and old_obj.db_workflow_execs is not None:
+ for obj in old_obj.db_workflow_execs:
+ new_obj.db_add_workflow_exec(DBWorkflowExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow_execs') and hasattr(new_obj, 'db_deleted_workflow_execs'):
+ for obj in old_obj.db_deleted_workflow_execs:
+ n_obj = DBWorkflowExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow_execs.append(n_obj)
+ if 'machines' in class_dict:
+ res = class_dict['machines'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_machine(obj)
+ elif hasattr(old_obj, 'db_machines') and old_obj.db_machines is not None:
+ for obj in old_obj.db_machines:
+ new_obj.db_add_machine(DBMachine.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_machines') and hasattr(new_obj, 'db_deleted_machines'):
+ for obj in old_obj.db_deleted_machines:
+ n_obj = DBMachine.update_version(obj, trans_dict)
+ new_obj.db_deleted_machines.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_workflow_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self.db_machines:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow_execs)
+ children.extend(self.db_deleted_machines)
+ if remove:
+ self.db_deleted_workflow_execs = []
+ self.db_deleted_machines = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_workflow_execs:
+ if child.has_changes():
+ return True
+ for child in self._db_machines:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_workflow_execs(self):
+ return self._db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self._db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self._db_workflow_execs
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ self._db_workflow_execs[i] = workflow_exec
+ found = True
+ break
+ if not found:
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ if not self._db_workflow_execs[i].is_new:
+ self.db_deleted_workflow_execs.append(self._db_workflow_execs[i])
+ del self._db_workflow_execs[i]
+ break
+ del self.db_workflow_execs_id_index[workflow_exec.db_id]
+ def db_get_workflow_exec(self, key):
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == key:
+ return self._db_workflow_execs[i]
+ return None
+ def db_get_workflow_exec_by_id(self, key):
+ return self.db_workflow_execs_id_index[key]
+ def db_has_workflow_exec_with_id(self, key):
+ return key in self.db_workflow_execs_id_index
+
+ def __get_db_machines(self):
+ return self._db_machines
+ def __set_db_machines(self, machines):
+ self._db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self._db_machines
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ self._db_machines[i] = machine
+ found = True
+ break
+ if not found:
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ if not self._db_machines[i].is_new:
+ self.db_deleted_machines.append(self._db_machines[i])
+ del self._db_machines[i]
+ break
+ del self.db_machines_id_index[machine.db_id]
+ def db_get_machine(self, key):
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == key:
+ return self._db_machines[i]
+ return None
+ def db_get_machine_by_id(self, key):
+ return self.db_machines_id_index[key]
+ def db_has_machine_with_id(self, key):
+ return key in self.db_machines_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_os = os
+ self._db_architecture = architecture
+ self._db_processor = processor
+ self._db_ram = ram
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMachine.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine(id=self._db_id,
+ name=self._db_name,
+ os=self._db_os,
+ architecture=self._db_architecture,
+ processor=self._db_processor,
+ ram=self._db_ram)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and ('vistrail', self._db_vistrailId) in id_remap:
+ cp._db_vistrailId = id_remap[('vistrail', self._db_vistrailId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMachine()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'os' in class_dict:
+ res = class_dict['os'](old_obj, trans_dict)
+ new_obj.db_os = res
+ elif hasattr(old_obj, 'db_os') and old_obj.db_os is not None:
+ new_obj.db_os = old_obj.db_os
+ if 'architecture' in class_dict:
+ res = class_dict['architecture'](old_obj, trans_dict)
+ new_obj.db_architecture = res
+ elif hasattr(old_obj, 'db_architecture') and old_obj.db_architecture is not None:
+ new_obj.db_architecture = old_obj.db_architecture
+ if 'processor' in class_dict:
+ res = class_dict['processor'](old_obj, trans_dict)
+ new_obj.db_processor = res
+ elif hasattr(old_obj, 'db_processor') and old_obj.db_processor is not None:
+ new_obj.db_processor = old_obj.db_processor
+ if 'ram' in class_dict:
+ res = class_dict['ram'](old_obj, trans_dict)
+ new_obj.db_ram = res
+ elif hasattr(old_obj, 'db_ram') and old_obj.db_ram is not None:
+ new_obj.db_ram = old_obj.db_ram
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_os(self):
+ return self._db_os
+ def __set_db_os(self, os):
+ self._db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self._db_os = os
+ def db_change_os(self, os):
+ self._db_os = os
+ def db_delete_os(self, os):
+ self._db_os = None
+
+ def __get_db_architecture(self):
+ return self._db_architecture
+ def __set_db_architecture(self, architecture):
+ self._db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self._db_architecture = None
+
+ def __get_db_processor(self):
+ return self._db_processor
+ def __set_db_processor(self, processor):
+ self._db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self._db_processor = processor
+ def db_change_processor(self, processor):
+ self._db_processor = processor
+ def db_delete_processor(self, processor):
+ self._db_processor = None
+
+ def __get_db_ram(self):
+ return self._db_ram
+ def __set_db_ram(self, ram):
+ self._db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self._db_ram = ram
+ def db_change_ram(self, ram):
+ self._db_ram = ram
+ def db_delete_ram(self, ram):
+ self._db_ram = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, data=None, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAdd.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAdd()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstractionRef':
+ new_obj.db_add_data(DBAbstractionRef.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstractionRef':
+ n_obj = DBAbstractionRef.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOther.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOther(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOther()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self._db_id = id
+ self._db_x = x
+ self._db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLocation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation(id=self._db_id,
+ x=self._db_x,
+ y=self._db_y)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLocation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'x' in class_dict:
+ res = class_dict['x'](old_obj, trans_dict)
+ new_obj.db_x = res
+ elif hasattr(old_obj, 'db_x') and old_obj.db_x is not None:
+ new_obj.db_x = old_obj.db_x
+ if 'y' in class_dict:
+ res = class_dict['y'](old_obj, trans_dict)
+ new_obj.db_y = res
+ elif hasattr(old_obj, 'db_y') and old_obj.db_y is not None:
+ new_obj.db_y = old_obj.db_y
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_x(self):
+ return self._db_x
+ def __set_db_x(self, x):
+ self._db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self._db_x = x
+ def db_change_x(self, x):
+ self._db_x = x
+ def db_delete_x(self, x):
+ self._db_x = None
+
+ def __get_db_y(self):
+ return self._db_y
+ def __set_db_y(self, y):
+ self._db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self._db_y = y
+ def db_change_y(self, y):
+ self._db_y = y
+ def db_delete_y(self, y):
+ self._db_y = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self._db_type = type
+ self._db_val = val
+ self._db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBParameter.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name,
+ type=self._db_type,
+ val=self._db_val,
+ alias=self._db_alias)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBParameter()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'val' in class_dict:
+ res = class_dict['val'](old_obj, trans_dict)
+ new_obj.db_val = res
+ elif hasattr(old_obj, 'db_val') and old_obj.db_val is not None:
+ new_obj.db_val = old_obj.db_val
+ if 'alias' in class_dict:
+ res = class_dict['alias'](old_obj, trans_dict)
+ new_obj.db_alias = res
+ elif hasattr(old_obj, 'db_alias') and old_obj.db_alias is not None:
+ new_obj.db_alias = old_obj.db_alias
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_val(self):
+ return self._db_val
+ def __set_db_val(self, val):
+ self._db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self._db_val = val
+ def db_change_val(self, val):
+ self._db_val = val
+ def db_delete_val(self, val):
+ self._db_val = None
+
+ def __get_db_alias(self):
+ return self._db_alias
+ def __set_db_alias(self, alias):
+ self._db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self._db_alias = alias
+ def db_change_alias(self, alias):
+ self._db_alias = alias
+ def db_delete_alias(self, alias):
+ self._db_alias = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBPluginData(object):
+
+ vtType = 'plugin_data'
+
+ def __init__(self, id=None, data=None):
+ self._db_id = id
+ self._db_data = data
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPluginData.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPluginData(id=self._db_id,
+ data=self._db_data)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPluginData()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ new_obj.db_data = old_obj.db_data
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ self._db_data = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self.db_deleted_parameters = []
+ self.db_parameters_id_index = {}
+ if parameters is None:
+ self._db_parameters = []
+ else:
+ self._db_parameters = parameters
+ for v in self._db_parameters:
+ self.db_parameters_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name)
+ if self._db_parameters is None:
+ cp._db_parameters = []
+ else:
+ cp._db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_parameters_id_index = dict((v.db_id, v) for v in cp._db_parameters)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBFunction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'parameters' in class_dict:
+ res = class_dict['parameters'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_parameter(obj)
+ elif hasattr(old_obj, 'db_parameters') and old_obj.db_parameters is not None:
+ for obj in old_obj.db_parameters:
+ new_obj.db_add_parameter(DBParameter.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_parameters') and hasattr(new_obj, 'db_deleted_parameters'):
+ for obj in old_obj.db_deleted_parameters:
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_parameters.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_parameters)
+ if remove:
+ self.db_deleted_parameters = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_parameters(self):
+ return self._db_parameters
+ def __set_db_parameters(self, parameters):
+ self._db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self._db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ self._db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ if not self._db_parameters[i].is_new:
+ self.db_deleted_parameters.append(self._db_parameters[i])
+ del self._db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter.db_id]
+ def db_get_parameter(self, key):
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == key:
+ return self._db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return key in self.db_parameters_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, entity_type=None, name=None, last_modified=None, actions=None, tags=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self._db_actions = []
+ else:
+ self._db_actions = actions
+ for v in self._db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self._db_tags = []
+ else:
+ self._db_tags = tags
+ for v in self._db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction(id=self._db_id,
+ entity_type=self._db_entity_type,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_actions is None:
+ cp._db_actions = []
+ else:
+ cp._db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actions]
+ if self._db_tags is None:
+ cp._db_tags = []
+ else:
+ cp._db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_tags]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_actions_id_index = dict((v.db_id, v) for v in cp._db_actions)
+ cp.db_tags_id_index = dict((v.db_id, v) for v in cp._db_tags)
+ cp.db_tags_name_index = dict((v.db_name, v) for v in cp._db_tags)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAbstraction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'actions' in class_dict:
+ res = class_dict['actions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_action(obj)
+ elif hasattr(old_obj, 'db_actions') and old_obj.db_actions is not None:
+ for obj in old_obj.db_actions:
+ new_obj.db_add_action(DBAction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actions') and hasattr(new_obj, 'db_deleted_actions'):
+ for obj in old_obj.db_deleted_actions:
+ n_obj = DBAction.update_version(obj, trans_dict)
+ new_obj.db_deleted_actions.append(n_obj)
+ if 'tags' in class_dict:
+ res = class_dict['tags'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_tag(obj)
+ elif hasattr(old_obj, 'db_tags') and old_obj.db_tags is not None:
+ for obj in old_obj.db_tags:
+ new_obj.db_add_tag(DBTag.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_tags') and hasattr(new_obj, 'db_deleted_tags'):
+ for obj in old_obj.db_deleted_tags:
+ n_obj = DBTag.update_version(obj, trans_dict)
+ new_obj.db_deleted_tags.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_actions:
+ if child.has_changes():
+ return True
+ for child in self._db_tags:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_actions(self):
+ return self._db_actions
+ def __set_db_actions(self, actions):
+ self._db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self._db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ self._db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ if not self._db_actions[i].is_new:
+ self.db_deleted_actions.append(self._db_actions[i])
+ del self._db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == key:
+ return self._db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return key in self.db_actions_id_index
+
+ def __get_db_tags(self):
+ return self._db_tags
+ def __set_db_tags(self, tags):
+ self._db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self._db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ self._db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ if not self._db_tags[i].is_new:
+ self.db_deleted_tags.append(self._db_tags[i])
+ del self._db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == key:
+ return self._db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return key in self.db_tags_id_index
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return key in self.db_tags_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, modules=None, id=None, entity_type=None, name=None, version=None, last_modified=None, connections=None, annotations=None, abstractions=None, plugin_datas=None, others=None, vistrail_id=None):
+ self.db_deleted_modules = []
+ self.db_modules_id_index = {}
+ if modules is None:
+ self._db_modules = []
+ else:
+ self._db_modules = modules
+ for v in self._db_modules:
+ self.db_modules_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_name = name
+ self._db_version = version
+ self._db_last_modified = last_modified
+ self.db_deleted_connections = []
+ self.db_connections_id_index = {}
+ if connections is None:
+ self._db_connections = []
+ else:
+ self._db_connections = connections
+ for v in self._db_connections:
+ self.db_connections_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_abstractions = []
+ self.db_abstractions_id_index = {}
+ if abstractions is None:
+ self._db_abstractions = []
+ else:
+ self._db_abstractions = abstractions
+ for v in self._db_abstractions:
+ self.db_abstractions_id_index[v.db_id] = v
+ self.db_deleted_plugin_datas = []
+ self.db_plugin_datas_id_index = {}
+ if plugin_datas is None:
+ self._db_plugin_datas = []
+ else:
+ self._db_plugin_datas = plugin_datas
+ for v in self._db_plugin_datas:
+ self.db_plugin_datas_id_index[v.db_id] = v
+ self.db_deleted_others = []
+ self.db_others_id_index = {}
+ if others is None:
+ self._db_others = []
+ else:
+ self._db_others = others
+ for v in self._db_others:
+ self.db_others_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow(id=self._db_id,
+ entity_type=self._db_entity_type,
+ name=self._db_name,
+ version=self._db_version,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_modules is None:
+ cp._db_modules = []
+ else:
+ cp._db_modules = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_modules]
+ if self._db_connections is None:
+ cp._db_connections = []
+ else:
+ cp._db_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_connections]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_abstractions is None:
+ cp._db_abstractions = []
+ else:
+ cp._db_abstractions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_abstractions]
+ if self._db_plugin_datas is None:
+ cp._db_plugin_datas = []
+ else:
+ cp._db_plugin_datas = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_plugin_datas]
+ if self._db_others is None:
+ cp._db_others = []
+ else:
+ cp._db_others = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_others]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_modules_id_index = dict((v.db_id, v) for v in cp._db_modules)
+ cp.db_connections_id_index = dict((v.db_id, v) for v in cp._db_connections)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_abstractions_id_index = dict((v.db_id, v) for v in cp._db_abstractions)
+ cp.db_plugin_datas_id_index = dict((v.db_id, v) for v in cp._db_plugin_datas)
+ cp.db_others_id_index = dict((v.db_id, v) for v in cp._db_others)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'modules' in class_dict:
+ res = class_dict['modules'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module(obj)
+ elif hasattr(old_obj, 'db_modules') and old_obj.db_modules is not None:
+ for obj in old_obj.db_modules:
+ if obj.vtType == 'module':
+ new_obj.db_add_module(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstractionRef':
+ new_obj.db_add_module(DBAbstractionRef.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_module(DBGroup.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_modules') and hasattr(new_obj, 'db_deleted_modules'):
+ for obj in old_obj.db_deleted_modules:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'abstractionRef':
+ n_obj = DBAbstractionRef.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'connections' in class_dict:
+ res = class_dict['connections'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_connection(obj)
+ elif hasattr(old_obj, 'db_connections') and old_obj.db_connections is not None:
+ for obj in old_obj.db_connections:
+ new_obj.db_add_connection(DBConnection.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_connections') and hasattr(new_obj, 'db_deleted_connections'):
+ for obj in old_obj.db_deleted_connections:
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_connections.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'abstractions' in class_dict:
+ res = class_dict['abstractions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_abstraction(obj)
+ elif hasattr(old_obj, 'db_abstractions') and old_obj.db_abstractions is not None:
+ for obj in old_obj.db_abstractions:
+ new_obj.db_add_abstraction(DBAbstraction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_abstractions') and hasattr(new_obj, 'db_deleted_abstractions'):
+ for obj in old_obj.db_deleted_abstractions:
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_abstractions.append(n_obj)
+ if 'plugin_datas' in class_dict:
+ res = class_dict['plugin_datas'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_plugin_data(obj)
+ elif hasattr(old_obj, 'db_plugin_datas') and old_obj.db_plugin_datas is not None:
+ for obj in old_obj.db_plugin_datas:
+ new_obj.db_add_plugin_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_plugin_datas') and hasattr(new_obj, 'db_deleted_plugin_datas'):
+ for obj in old_obj.db_deleted_plugin_datas:
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_plugin_datas.append(n_obj)
+ if 'others' in class_dict:
+ res = class_dict['others'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_other(obj)
+ elif hasattr(old_obj, 'db_others') and old_obj.db_others is not None:
+ for obj in old_obj.db_others:
+ new_obj.db_add_other(DBOther.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_others') and hasattr(new_obj, 'db_deleted_others'):
+ for obj in old_obj.db_deleted_others:
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_others.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_connections:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_connection(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_abstractions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_abstraction(child)
+ to_del = []
+ for child in self.db_plugin_datas:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_plugin_data(child)
+ to_del = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_other(child)
+ to_del = []
+ for child in self.db_modules:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_connections)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_abstractions)
+ children.extend(self.db_deleted_plugin_datas)
+ children.extend(self.db_deleted_others)
+ children.extend(self.db_deleted_modules)
+ if remove:
+ self.db_deleted_connections = []
+ self.db_deleted_annotations = []
+ self.db_deleted_abstractions = []
+ self.db_deleted_plugin_datas = []
+ self.db_deleted_others = []
+ self.db_deleted_modules = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_connections:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_abstractions:
+ if child.has_changes():
+ return True
+ for child in self._db_plugin_datas:
+ if child.has_changes():
+ return True
+ for child in self._db_others:
+ if child.has_changes():
+ return True
+ for child in self._db_modules:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_modules(self):
+ return self._db_modules
+ def __set_db_modules(self, modules):
+ self._db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self._db_modules
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ self._db_modules[i] = module
+ found = True
+ break
+ if not found:
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ if not self._db_modules[i].is_new:
+ self.db_deleted_modules.append(self._db_modules[i])
+ del self._db_modules[i]
+ break
+ del self.db_modules_id_index[module.db_id]
+ def db_get_module(self, key):
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == key:
+ return self._db_modules[i]
+ return None
+ def db_get_module_by_id(self, key):
+ return self.db_modules_id_index[key]
+ def db_has_module_with_id(self, key):
+ return key in self.db_modules_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_connections(self):
+ return self._db_connections
+ def __set_db_connections(self, connections):
+ self._db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self._db_connections
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ self._db_connections[i] = connection
+ found = True
+ break
+ if not found:
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ if not self._db_connections[i].is_new:
+ self.db_deleted_connections.append(self._db_connections[i])
+ del self._db_connections[i]
+ break
+ del self.db_connections_id_index[connection.db_id]
+ def db_get_connection(self, key):
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == key:
+ return self._db_connections[i]
+ return None
+ def db_get_connection_by_id(self, key):
+ return self.db_connections_id_index[key]
+ def db_has_connection_with_id(self, key):
+ return key in self.db_connections_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_abstractions(self):
+ return self._db_abstractions
+ def __set_db_abstractions(self, abstractions):
+ self._db_abstractions = abstractions
+ self.is_dirty = True
+ db_abstractions = property(__get_db_abstractions, __set_db_abstractions)
+ def db_get_abstractions(self):
+ return self._db_abstractions
+ def db_add_abstraction(self, abstraction):
+ self.is_dirty = True
+ self._db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_change_abstraction(self, abstraction):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i].db_id == abstraction.db_id:
+ self._db_abstractions[i] = abstraction
+ found = True
+ break
+ if not found:
+ self._db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_delete_abstraction(self, abstraction):
+ self.is_dirty = True
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i].db_id == abstraction.db_id:
+ if not self._db_abstractions[i].is_new:
+ self.db_deleted_abstractions.append(self._db_abstractions[i])
+ del self._db_abstractions[i]
+ break
+ del self.db_abstractions_id_index[abstraction.db_id]
+ def db_get_abstraction(self, key):
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i].db_id == key:
+ return self._db_abstractions[i]
+ return None
+ def db_get_abstraction_by_id(self, key):
+ return self.db_abstractions_id_index[key]
+ def db_has_abstraction_with_id(self, key):
+ return key in self.db_abstractions_id_index
+
+ def __get_db_plugin_datas(self):
+ return self._db_plugin_datas
+ def __set_db_plugin_datas(self, plugin_datas):
+ self._db_plugin_datas = plugin_datas
+ self.is_dirty = True
+ db_plugin_datas = property(__get_db_plugin_datas, __set_db_plugin_datas)
+ def db_get_plugin_datas(self):
+ return self._db_plugin_datas
+ def db_add_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_change_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ self._db_plugin_datas[i] = plugin_data
+ found = True
+ break
+ if not found:
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_delete_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ if not self._db_plugin_datas[i].is_new:
+ self.db_deleted_plugin_datas.append(self._db_plugin_datas[i])
+ del self._db_plugin_datas[i]
+ break
+ del self.db_plugin_datas_id_index[plugin_data.db_id]
+ def db_get_plugin_data(self, key):
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == key:
+ return self._db_plugin_datas[i]
+ return None
+ def db_get_plugin_data_by_id(self, key):
+ return self.db_plugin_datas_id_index[key]
+ def db_has_plugin_data_with_id(self, key):
+ return key in self.db_plugin_datas_id_index
+
+ def __get_db_others(self):
+ return self._db_others
+ def __set_db_others(self, others):
+ self._db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self._db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ self._db_others[i] = other
+ found = True
+ break
+ if not found:
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ if not self._db_others[i].is_new:
+ self.db_deleted_others.append(self._db_others[i])
+ del self._db_others[i]
+ break
+ del self.db_others_id_index[other.db_id]
+ def db_get_other(self, key):
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == key:
+ return self._db_others[i]
+ return None
+ def db_get_other_by_id(self, key):
+ return self.db_others_id_index[key]
+ def db_has_other_with_id(self, key):
+ return key in self.db_others_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAbstractionRef(object):
+
+ vtType = 'abstractionRef'
+
+ def __init__(self, id=None, name=None, cache=None, abstraction_id=None, version=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_cache = cache
+ self._db_abstraction_id = abstraction_id
+ self._db_version = version
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstractionRef.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstractionRef(id=self._db_id,
+ name=self._db_name,
+ cache=self._db_cache,
+ abstraction_id=self._db_abstraction_id,
+ version=self._db_version)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_abstraction_id') and ('abstraction', self._db_abstraction_id) in id_remap:
+ cp._db_abstraction_id = id_remap[('abstraction', self._db_abstraction_id)]
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAbstractionRef()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'abstraction_id' in class_dict:
+ res = class_dict['abstraction_id'](old_obj, trans_dict)
+ new_obj.db_abstraction_id = res
+ elif hasattr(old_obj, 'db_abstraction_id') and old_obj.db_abstraction_id is not None:
+ new_obj.db_abstraction_id = old_obj.db_abstraction_id
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_abstraction_id(self):
+ return self._db_abstraction_id
+ def __set_db_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ self.is_dirty = True
+ db_abstraction_id = property(__get_db_abstraction_id, __set_db_abstraction_id)
+ def db_add_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_change_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_delete_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAnnotation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, data=None, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_oldObjId = oldObjId
+ self._db_newObjId = newObjId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBChange.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange(id=self._db_id,
+ what=self._db_what,
+ oldObjId=self._db_oldObjId,
+ newObjId=self._db_newObjId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_oldObjId') and (self._db_what, self._db_oldObjId) in id_remap:
+ cp._db_oldObjId = id_remap[(self._db_what, self._db_oldObjId)]
+ if hasattr(self, 'db_newObjId') and (self._db_what, self._db_newObjId) in id_remap:
+ cp._db_newObjId = id_remap[(self._db_what, self._db_newObjId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBChange()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstractionRef':
+ new_obj.db_add_data(DBAbstractionRef.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstractionRef':
+ n_obj = DBAbstractionRef.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'oldObjId' in class_dict:
+ res = class_dict['oldObjId'](old_obj, trans_dict)
+ new_obj.db_oldObjId = res
+ elif hasattr(old_obj, 'db_oldObjId') and old_obj.db_oldObjId is not None:
+ new_obj.db_oldObjId = old_obj.db_oldObjId
+ if 'newObjId' in class_dict:
+ res = class_dict['newObjId'](old_obj, trans_dict)
+ new_obj.db_newObjId = res
+ elif hasattr(old_obj, 'db_newObjId') and old_obj.db_newObjId is not None:
+ new_obj.db_newObjId = old_obj.db_newObjId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_oldObjId(self):
+ return self._db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self._db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self._db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self._db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, id=None, user=None, ip=None, session=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, completed=None, name=None, module_execs=None):
+ self._db_id = id
+ self._db_user = user
+ self._db_ip = ip
+ self._db_session = session
+ self._db_vt_version = vt_version
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_parent_id = parent_id
+ self._db_parent_type = parent_type
+ self._db_parent_version = parent_version
+ self._db_completed = completed
+ self._db_name = name
+ self.db_deleted_module_execs = []
+ self.db_module_execs_id_index = {}
+ if module_execs is None:
+ self._db_module_execs = []
+ else:
+ self._db_module_execs = module_execs
+ for v in self._db_module_execs:
+ self.db_module_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflowExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec(id=self._db_id,
+ user=self._db_user,
+ ip=self._db_ip,
+ session=self._db_session,
+ vt_version=self._db_vt_version,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ parent_id=self._db_parent_id,
+ parent_type=self._db_parent_type,
+ parent_version=self._db_parent_version,
+ completed=self._db_completed,
+ name=self._db_name)
+ if self._db_module_execs is None:
+ cp._db_module_execs = []
+ else:
+ cp._db_module_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_module_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_module_execs_id_index = dict((v.db_id, v) for v in cp._db_module_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflowExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'ip' in class_dict:
+ res = class_dict['ip'](old_obj, trans_dict)
+ new_obj.db_ip = res
+ elif hasattr(old_obj, 'db_ip') and old_obj.db_ip is not None:
+ new_obj.db_ip = old_obj.db_ip
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'vt_version' in class_dict:
+ res = class_dict['vt_version'](old_obj, trans_dict)
+ new_obj.db_vt_version = res
+ elif hasattr(old_obj, 'db_vt_version') and old_obj.db_vt_version is not None:
+ new_obj.db_vt_version = old_obj.db_vt_version
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'parent_id' in class_dict:
+ res = class_dict['parent_id'](old_obj, trans_dict)
+ new_obj.db_parent_id = res
+ elif hasattr(old_obj, 'db_parent_id') and old_obj.db_parent_id is not None:
+ new_obj.db_parent_id = old_obj.db_parent_id
+ if 'parent_type' in class_dict:
+ res = class_dict['parent_type'](old_obj, trans_dict)
+ new_obj.db_parent_type = res
+ elif hasattr(old_obj, 'db_parent_type') and old_obj.db_parent_type is not None:
+ new_obj.db_parent_type = old_obj.db_parent_type
+ if 'parent_version' in class_dict:
+ res = class_dict['parent_version'](old_obj, trans_dict)
+ new_obj.db_parent_version = res
+ elif hasattr(old_obj, 'db_parent_version') and old_obj.db_parent_version is not None:
+ new_obj.db_parent_version = old_obj.db_parent_version
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'module_execs' in class_dict:
+ res = class_dict['module_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module_exec(obj)
+ elif hasattr(old_obj, 'db_module_execs') and old_obj.db_module_execs is not None:
+ for obj in old_obj.db_module_execs:
+ new_obj.db_add_module_exec(DBModuleExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_module_execs') and hasattr(new_obj, 'db_deleted_module_execs'):
+ for obj in old_obj.db_deleted_module_execs:
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_module_execs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_execs)
+ if remove:
+ self.db_deleted_module_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_module_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_ip(self):
+ return self._db_ip
+ def __set_db_ip(self, ip):
+ self._db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self._db_ip = ip
+ def db_change_ip(self, ip):
+ self._db_ip = ip
+ def db_delete_ip(self, ip):
+ self._db_ip = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_vt_version(self):
+ return self._db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self._db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self._db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self._db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self._db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self._db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self._db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self._db_parent_version = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_module_execs(self):
+ return self._db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self._db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self._db_module_execs
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self._db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == module_exec.db_id:
+ self._db_module_execs[i] = module_exec
+ found = True
+ break
+ if not found:
+ self._db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == module_exec.db_id:
+ if not self._db_module_execs[i].is_new:
+ self.db_deleted_module_execs.append(self._db_module_execs[i])
+ del self._db_module_execs[i]
+ break
+ del self.db_module_execs_id_index[module_exec.db_id]
+ def db_get_module_exec(self, key):
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == key:
+ return self._db_module_execs[i]
+ return None
+ def db_get_module_exec_by_id(self, key):
+ return self.db_module_execs_id_index[key]
+ def db_has_module_exec_with_id(self, key):
+ return key in self.db_module_execs_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self._db_id = id
+ self.db_deleted_ports = []
+ self.db_ports_id_index = {}
+ self.db_ports_type_index = {}
+ if ports is None:
+ self._db_ports = []
+ else:
+ self._db_ports = ports
+ for v in self._db_ports:
+ self.db_ports_id_index[v.db_id] = v
+ self.db_ports_type_index[v.db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBConnection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection(id=self._db_id)
+ if self._db_ports is None:
+ cp._db_ports = []
+ else:
+ cp._db_ports = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ports]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_ports_id_index = dict((v.db_id, v) for v in cp._db_ports)
+ cp.db_ports_type_index = dict((v.db_type, v) for v in cp._db_ports)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBConnection()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ports' in class_dict:
+ res = class_dict['ports'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_port(obj)
+ elif hasattr(old_obj, 'db_ports') and old_obj.db_ports is not None:
+ for obj in old_obj.db_ports:
+ new_obj.db_add_port(DBPort.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_ports') and hasattr(new_obj, 'db_deleted_ports'):
+ for obj in old_obj.db_deleted_ports:
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_ports.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_ports)
+ if remove:
+ self.db_deleted_ports = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ports(self):
+ return self._db_ports
+ def __set_db_ports(self, ports):
+ self._db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self._db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ self._db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ if not self._db_ports[i].is_new:
+ self.db_deleted_ports.append(self._db_ports[i])
+ del self._db_ports[i]
+ break
+ del self.db_ports_id_index[port.db_id]
+ del self.db_ports_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == key:
+ return self._db_ports[i]
+ return None
+ def db_get_port_by_id(self, key):
+ return self.db_ports_id_index[key]
+ def db_has_port_with_id(self, key):
+ return key in self.db_ports_id_index
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return key in self.db_ports_type_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, operations=None, id=None, prevId=None, date=None, session=None, user=None, prune=None, annotations=None):
+ self.db_deleted_operations = []
+ self.db_operations_id_index = {}
+ if operations is None:
+ self._db_operations = []
+ else:
+ self._db_operations = operations
+ for v in self._db_operations:
+ self.db_operations_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_prevId = prevId
+ self._db_date = date
+ self._db_session = session
+ self._db_user = user
+ self._db_prune = prune
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction(id=self._db_id,
+ prevId=self._db_prevId,
+ date=self._db_date,
+ session=self._db_session,
+ user=self._db_user,
+ prune=self._db_prune)
+ if self._db_operations is None:
+ cp._db_operations = []
+ else:
+ cp._db_operations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_operations]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prevId') and ('action', self._db_prevId) in id_remap:
+ cp._db_prevId = id_remap[('action', self._db_prevId)]
+
+ # recreate indices and set flags
+ cp.db_operations_id_index = dict((v.db_id, v) for v in cp._db_operations)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'operations' in class_dict:
+ res = class_dict['operations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_operation(obj)
+ elif hasattr(old_obj, 'db_operations') and old_obj.db_operations is not None:
+ for obj in old_obj.db_operations:
+ if obj.vtType == 'add':
+ new_obj.db_add_operation(DBAdd.update_version(obj, trans_dict))
+ elif obj.vtType == 'delete':
+ new_obj.db_add_operation(DBDelete.update_version(obj, trans_dict))
+ elif obj.vtType == 'change':
+ new_obj.db_add_operation(DBChange.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_operations') and hasattr(new_obj, 'db_deleted_operations'):
+ for obj in old_obj.db_deleted_operations:
+ if obj.vtType == 'add':
+ n_obj = DBAdd.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'delete':
+ n_obj = DBDelete.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'change':
+ n_obj = DBChange.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'prevId' in class_dict:
+ res = class_dict['prevId'](old_obj, trans_dict)
+ new_obj.db_prevId = res
+ elif hasattr(old_obj, 'db_prevId') and old_obj.db_prevId is not None:
+ new_obj.db_prevId = old_obj.db_prevId
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'prune' in class_dict:
+ res = class_dict['prune'](old_obj, trans_dict)
+ new_obj.db_prune = res
+ elif hasattr(old_obj, 'db_prune') and old_obj.db_prune is not None:
+ new_obj.db_prune = old_obj.db_prune
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_operations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_operations)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_operations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_operations(self):
+ return self._db_operations
+ def __set_db_operations(self, operations):
+ self._db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self._db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ self._db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ if not self._db_operations[i].is_new:
+ self.db_deleted_operations.append(self._db_operations[i])
+ del self._db_operations[i]
+ break
+ del self.db_operations_id_index[operation.db_id]
+ def db_get_operation(self, key):
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == key:
+ return self._db_operations[i]
+ return None
+ def db_get_operation_by_id(self, key):
+ return self.db_operations_id_index[key]
+ def db_has_operation_with_id(self, key):
+ return key in self.db_operations_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_prevId(self):
+ return self._db_prevId
+ def __set_db_prevId(self, prevId):
+ self._db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self._db_prevId = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_prune(self):
+ return self._db_prune
+ def __set_db_prune(self, prune):
+ self._db_prune = prune
+ self.is_dirty = True
+ db_prune = property(__get_db_prune, __set_db_prune)
+ def db_add_prune(self, prune):
+ self._db_prune = prune
+ def db_change_prune(self, prune):
+ self._db_prune = prune
+ def db_delete_prune(self, prune):
+ self._db_prune = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBDelete.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBDelete()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, actions=None, tags=None, annotations=None, abstractions=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self._db_actions = []
+ else:
+ self._db_actions = actions
+ for v in self._db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self._db_tags = []
+ else:
+ self._db_tags = tags
+ for v in self._db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_abstractions = []
+ self.db_abstractions_id_index = {}
+ if abstractions is None:
+ self._db_abstractions = []
+ else:
+ self._db_abstractions = abstractions
+ for v in self._db_abstractions:
+ self.db_abstractions_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_actions is None:
+ cp._db_actions = []
+ else:
+ cp._db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actions]
+ if self._db_tags is None:
+ cp._db_tags = []
+ else:
+ cp._db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_tags]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_abstractions is None:
+ cp._db_abstractions = []
+ else:
+ cp._db_abstractions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_abstractions]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_actions_id_index = dict((v.db_id, v) for v in cp._db_actions)
+ cp.db_tags_id_index = dict((v.db_id, v) for v in cp._db_tags)
+ cp.db_tags_name_index = dict((v.db_name, v) for v in cp._db_tags)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ cp.db_abstractions_id_index = dict((v.db_id, v) for v in cp._db_abstractions)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'actions' in class_dict:
+ res = class_dict['actions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_action(obj)
+ elif hasattr(old_obj, 'db_actions') and old_obj.db_actions is not None:
+ for obj in old_obj.db_actions:
+ new_obj.db_add_action(DBAction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actions') and hasattr(new_obj, 'db_deleted_actions'):
+ for obj in old_obj.db_deleted_actions:
+ n_obj = DBAction.update_version(obj, trans_dict)
+ new_obj.db_deleted_actions.append(n_obj)
+ if 'tags' in class_dict:
+ res = class_dict['tags'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_tag(obj)
+ elif hasattr(old_obj, 'db_tags') and old_obj.db_tags is not None:
+ for obj in old_obj.db_tags:
+ new_obj.db_add_tag(DBTag.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_tags') and hasattr(new_obj, 'db_deleted_tags'):
+ for obj in old_obj.db_deleted_tags:
+ n_obj = DBTag.update_version(obj, trans_dict)
+ new_obj.db_deleted_tags.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'abstractions' in class_dict:
+ res = class_dict['abstractions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_abstraction(obj)
+ elif hasattr(old_obj, 'db_abstractions') and old_obj.db_abstractions is not None:
+ for obj in old_obj.db_abstractions:
+ new_obj.db_add_abstraction(DBAbstraction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_abstractions') and hasattr(new_obj, 'db_deleted_abstractions'):
+ for obj in old_obj.db_deleted_abstractions:
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_abstractions.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_abstractions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_abstraction(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_abstractions)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ self.db_deleted_annotations = []
+ self.db_deleted_abstractions = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_actions:
+ if child.has_changes():
+ return True
+ for child in self._db_tags:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_abstractions:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_actions(self):
+ return self._db_actions
+ def __set_db_actions(self, actions):
+ self._db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self._db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ self._db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ if not self._db_actions[i].is_new:
+ self.db_deleted_actions.append(self._db_actions[i])
+ del self._db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == key:
+ return self._db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return key in self.db_actions_id_index
+
+ def __get_db_tags(self):
+ return self._db_tags
+ def __set_db_tags(self, tags):
+ self._db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self._db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ self._db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ if not self._db_tags[i].is_new:
+ self.db_deleted_tags.append(self._db_tags[i])
+ del self._db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == key:
+ return self._db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return key in self.db_tags_id_index
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return key in self.db_tags_name_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_abstractions(self):
+ return self._db_abstractions
+ def __set_db_abstractions(self, abstractions):
+ self._db_abstractions = abstractions
+ self.is_dirty = True
+ db_abstractions = property(__get_db_abstractions, __set_db_abstractions)
+ def db_get_abstractions(self):
+ return self._db_abstractions
+ def db_add_abstraction(self, abstraction):
+ self.is_dirty = True
+ self._db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_change_abstraction(self, abstraction):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i].db_id == abstraction.db_id:
+ self._db_abstractions[i] = abstraction
+ found = True
+ break
+ if not found:
+ self._db_abstractions.append(abstraction)
+ self.db_abstractions_id_index[abstraction.db_id] = abstraction
+ def db_delete_abstraction(self, abstraction):
+ self.is_dirty = True
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i].db_id == abstraction.db_id:
+ if not self._db_abstractions[i].is_new:
+ self.db_deleted_abstractions.append(self._db_abstractions[i])
+ del self._db_abstractions[i]
+ break
+ del self.db_abstractions_id_index[abstraction.db_id]
+ def db_get_abstraction(self, key):
+ for i in xrange(len(self._db_abstractions)):
+ if self._db_abstractions[i].db_id == key:
+ return self._db_abstractions[i]
+ return None
+ def db_get_abstraction_by_id(self, key):
+ return self.db_abstractions_id_index[key]
+ def db_has_abstraction_with_id(self, key):
+ return key in self.db_abstractions_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, module_name=None, completed=None, error=None, abstraction_id=None, abstraction_version=None, machine_id=None, annotations=None):
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_module_name = module_name
+ self._db_completed = completed
+ self._db_error = error
+ self._db_abstraction_id = abstraction_id
+ self._db_abstraction_version = abstraction_version
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ module_name=self._db_module_name,
+ completed=self._db_completed,
+ error=self._db_error,
+ abstraction_id=self._db_abstraction_id,
+ abstraction_version=self._db_abstraction_version,
+ machine_id=self._db_machine_id)
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'module_name' in class_dict:
+ res = class_dict['module_name'](old_obj, trans_dict)
+ new_obj.db_module_name = res
+ elif hasattr(old_obj, 'db_module_name') and old_obj.db_module_name is not None:
+ new_obj.db_module_name = old_obj.db_module_name
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'abstraction_id' in class_dict:
+ res = class_dict['abstraction_id'](old_obj, trans_dict)
+ new_obj.db_abstraction_id = res
+ elif hasattr(old_obj, 'db_abstraction_id') and old_obj.db_abstraction_id is not None:
+ new_obj.db_abstraction_id = old_obj.db_abstraction_id
+ if 'abstraction_version' in class_dict:
+ res = class_dict['abstraction_version'](old_obj, trans_dict)
+ new_obj.db_abstraction_version = res
+ elif hasattr(old_obj, 'db_abstraction_version') and old_obj.db_abstraction_version is not None:
+ new_obj.db_abstraction_version = old_obj.db_abstraction_version
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_module_name(self):
+ return self._db_module_name
+ def __set_db_module_name(self, module_name):
+ self._db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self._db_module_name = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_abstraction_id(self):
+ return self._db_abstraction_id
+ def __set_db_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ self.is_dirty = True
+ db_abstraction_id = property(__get_db_abstraction_id, __set_db_abstraction_id)
+ def db_add_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_change_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_delete_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = None
+
+ def __get_db_abstraction_version(self):
+ return self._db_abstraction_version
+ def __set_db_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ self.is_dirty = True
+ db_abstraction_version = property(__get_db_abstraction_version, __set_db_abstraction_version)
+ def db_add_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ def db_change_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ def db_delete_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
diff --git a/vistrails/db/versions/v0_9_3/domain/id_scope.py b/vistrails/db/versions/v0_9_3/domain/id_scope.py
new file mode 100644
index 0000000..0e07f02
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/domain/id_scope.py
@@ -0,0 +1,85 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L, remap=None):
+ self.ids = {}
+ self.beginId = beginId
+ if remap is None:
+ self.remap = {}
+ else:
+ self.remap = remap
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ cp.remap = copy.copy(self.remap)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ except KeyError:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ if self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+ except KeyError:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v0_9_3/domain/log.py b/vistrails/db/versions/v0_9_3/domain/log.py
new file mode 100644
index 0000000..effb9f1
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/domain/log.py
@@ -0,0 +1,68 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBLog as _DBLog
+from auto_gen import DBAbstractionRef, DBModule
+from id_scope import IdScope
+
+import copy
+
+class DBLog(_DBLog):
+
+ def __init__(self, *args, **kwargs):
+ _DBLog.__init__(self, *args, **kwargs)
+ self.id_scope = IdScope(1,
+ {DBAbstractionRef.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBLog.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBLog
+ cp.id_scope = copy.copy(self.id_scope)
+
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ new_obj = _DBLog.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
diff --git a/vistrails/db/versions/v0_9_3/domain/vistrail.py b/vistrails/db/versions/v0_9_3/domain/vistrail.py
new file mode 100644
index 0000000..22eb0ab
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/domain/vistrail.py
@@ -0,0 +1,127 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from auto_gen import DBVistrail as _DBVistrail
+from auto_gen import DBAdd, DBChange, DBDelete, DBAbstractionRef, DBGroup, \
+ DBModule
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAdd.vtType: 'operation',
+ DBChange.vtType: 'operation',
+ DBDelete.vtType: 'operation',
+ DBAbstractionRef.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ self.idScope.setBeginId('action', 1)
+ self.db_objects = {}
+
+ # keep a reference to the current logging information here
+ self.log_filename = None
+ self.log = None
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBVistrail.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBVistrail
+
+ cp.idScope = copy.copy(self.idScope)
+ cp.db_objects = copy.copy(self.db_objects)
+ cp.log_filename = self.log_filename
+ if self.log is not None:
+ cp.log = copy.copy(self.log)
+ else:
+ cp.log = None
+
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ new_obj = _DBVistrail.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ if hasattr(old_obj, 'log_filename'):
+ new_obj.log_filename = old_obj.log_filename
+ if hasattr(old_obj, 'log'):
+ new_obj.log = old_obj.log
+ return new_obj
+
+ def update_id_scope(self):
+ def getOldObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_oldObjId
+ return operation.db_objectId
+
+ def getNewObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_newObjId
+ return operation.db_objectId
+
+ for action in self.db_actions:
+ self.idScope.updateBeginId('action', action.db_id+1)
+ if action.db_session is not None:
+ self.idScope.updateBeginId('session', action.db_session + 1)
+ for operation in action.db_operations:
+ self.idScope.updateBeginId('operation', operation.db_id+1)
+ if operation.vtType == 'add' or operation.vtType == 'change':
+ # update ids of data
+ self.idScope.updateBeginId(operation.db_what,
+ getNewObjId(operation)+1)
+ if operation.db_data is None:
+ if operation.vtType == 'change':
+ operation.db_objectId = operation.db_oldObjId
+ self.db_add_object(operation.db_data)
+ for annotation in action.db_annotations:
+ self.idScope.updateBeginId('annotation', annotation.db_id+1)
+
+ def db_add_object(self, obj):
+ self.db_objects[(obj.vtType, obj.db_id)] = obj
+
+ def db_get_object(self, type, id):
+ return self.db_objects.get((type, id), None)
+
+ def db_update_object(self, obj, **kwargs):
+ # want to swap out old object with a new version
+ # need this for updating aliases...
+ # hack it using setattr...
+ real_obj = self.db_objects[(obj.vtType, obj.db_id)]
+ for (k, v) in kwargs.iteritems():
+ if hasattr(real_obj, k):
+ setattr(real_obj, k, v)
diff --git a/vistrails/db/versions/v0_9_3/domain/workflow.py b/vistrails/db/versions/v0_9_3/domain/workflow.py
new file mode 100644
index 0000000..cfe0dca
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/domain/workflow.py
@@ -0,0 +1,170 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from auto_gen import DBAbstractionRef, DBModule, DBGroup
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1,
+ {DBAbstractionRef.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.build_index()
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ new_obj = _DBWorkflow.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ new_obj.build_index()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
+
+ _vtTypeMap = {'abstractionRef': 'module', 'group': 'module'}
+
+ def build_index(self):
+ g = self._vtTypeMap.get
+ self.objects = dict(((g(o.vtType, o.vtType), o._db_id), o)
+ for (o,_,_) in self.db_children())
+
+ def add_to_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ self.objects[(obj_type, object.getPrimaryKey())] = object
+
+ def delete_from_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ del self.objects[(obj_type, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_print_objects(self):
+ for k,v in self.objects.iteritems():
+ print '%s: %s' % (k, v)
+
+ def db_has_object(self, type, id):
+ return (type, id) in self.objects
+
+ def db_get_object(self, type, id):
+ return self.objects[(type, id)]
+
+ def db_add_object(self, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == 'abstractionRef' or \
+ parent_obj_type == 'group':
+ parent_obj_type = 'module'
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if object.vtType == 'abstractionRef' or object.vtType == 'group':
+ obj_type = 'module'
+ else:
+ obj_type = object.vtType
+ funname = 'db_add_' + obj_type
+ obj_copy = copy.copy(object)
+ getattr(parent_obj, funname)(obj_copy)
+ self.add_to_index(obj_copy)
+
+ def db_change_object(self, old_id, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == 'abstractionRef' or \
+ parent_obj_type == 'group':
+ parent_obj_type = 'module'
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+
+ self.db_delete_object(old_id, object.vtType, None, None, parent_obj)
+ self.db_add_object(object, None, None, parent_obj)
+
+ def db_delete_object(self, obj_id, obj_type, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == 'abstractionRef' or \
+ parent_obj_type == 'group':
+ parent_obj_type = 'module'
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if obj_type == 'abstractionRef' or obj_type == 'group':
+ obj_type = 'module'
+ funname = 'db_get_' + obj_type
+ if hasattr(parent_obj, funname):
+ object = getattr(parent_obj, funname)(obj_id)
+ else:
+ attr_name = 'db_' + obj_type
+ object = getattr(parent_obj, attr_name)
+ funname = 'db_delete_' + obj_type
+ getattr(parent_obj, funname)(object)
+ self.delete_from_index(object)
diff --git a/vistrails/db/versions/v0_9_3/persistence/__init__.py b/vistrails/db/versions/v0_9_3/persistence/__init__.py
new file mode 100644
index 0000000..ce764d5
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/persistence/__init__.py
@@ -0,0 +1,204 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+from vistrails.core.system import get_elementtree_library
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_9_3 import version as my_version
+from vistrails.db.versions.v0_9_3.domain import DBVistrail, DBWorkflow, DBLog, \
+ DBAbstraction, DBGroup
+
+ElementTree = get_elementtree_library()
+
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def parse_xml_file(self, filename):
+ return ElementTree.parse(filename)
+
+ def write_xml_file(self, filename, tree):
+ tree.write(filename)
+
+ def read_xml_object(self, vtType, node):
+ return self['xml'][vtType].fromXML(node)
+
+ def write_xml_object(self, obj, node=None):
+ res_node = self['xml'][obj.vtType].toXML(obj, node)
+ return res_node
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ """open_from_xml(filename) -> DBVistrail"""
+ if tree is None:
+ tree = self.parse_xml_file(filename)
+ vistrail = self.read_xml_object(vtType, tree.getroot())
+ return vistrail
+
+ def save_to_xml(self, obj, filename, tags, version=None):
+ """save_to_xml(obj : object, filename: str, tags: dict,
+ version: str) -> None
+
+ """
+ root = self.write_xml_object(obj)
+ if version is None:
+ version = my_version
+ root.set('version', version)
+ for k, v in tags.iteritems():
+ root.set(k, v)
+ tree = ElementTree.ElementTree(root)
+ self.write_xml_file(filename, tree)
+
+ def open_from_db(self, db_connection, vtType, id, lock=False):
+ all_objects = {}
+ global_props = {'id': id}
+ # print global_props
+ res_objects = self['sql'][vtType].get_sql_columns(db_connection,
+ global_props,
+ lock)
+
+ if len(res_objects) > 1:
+ raise VistrailsDBException("More than object of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+ elif len(res_objects) <= 0:
+ raise VistrailsDBException("No objects of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+
+ all_objects.update(res_objects)
+ res = res_objects.values()[0]
+ del global_props['id']
+
+ for dao in self['sql'].itervalues():
+ if (dao == self['sql'][DBVistrail.vtType] or
+ # dao == self['sql'][DBWorkflow.vtType] or
+ dao == self['sql'][DBLog.vtType] or
+ dao == self['sql'][DBAbstraction.vtType]):
+ continue
+ current_objs = dao.get_sql_columns(db_connection, global_props,
+ lock)
+ if dao == self['sql'][DBWorkflow.vtType]:
+ for key, obj in current_objs.iteritems():
+ if key[0] == vtType and key[1] == id:
+ continue
+ elif key[0] == DBWorkflow.vtType:
+ res_obj = self.open_from_db(db_connection, key[0],
+ key[1], lock)
+ res_dict = {}
+ res_dict[(res_obj.vtType, res_obj.db_id)] = res_obj
+ all_objects.update(res_dict)
+ else:
+ all_objects.update(current_objs)
+
+ for key, obj in all_objects.iteritems():
+ if key[0] == vtType and key[1] == id:
+ continue
+ self['sql'][obj.vtType].from_sql_fast(obj, all_objects)
+ for obj in all_objects.itervalues():
+ obj.is_dirty = False
+ obj.is_new = False
+ return res
+
+ def save_to_db(self, db_connection, obj, do_copy=False, global_props=None):
+ if do_copy and obj.db_id is not None:
+ obj.db_id = None
+
+ children = obj.db_children() # forSQL=True)
+ children.reverse()
+ if global_props is None:
+ global_props = {'entity_type': obj.vtType}
+ # print 'global_props:', global_props
+
+ # assumes not deleting entire thing
+ (child, _, _) = children[0]
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ global_props = {'entity_id': child.db_id,
+ 'entity_type': child.vtType}
+
+ if not do_copy:
+ for (child, _, _) in children:
+ for c in child.db_deleted_children(True):
+ self['sql'][c.vtType].delete_sql_column(db_connection,
+ c,
+ global_props)
+
+ (child, _, _) = children.pop(0)
+ child.is_dirty = False
+ child.is_new = False
+ for (child, _, _) in children:
+ # print "child:", child.vtType, child.db_id
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ # print '*** entity_type:', global_props['entity_type']
+ self.save_to_db(db_connection, child.db_workflow,
+ do_copy,
+ {'entity_id': global_props['entity_id'],
+ 'entity_type': \
+ global_props['entity_type']}
+ )
+
+ child.is_dirty = False
+ child.is_new = False
+
+ def serialize(self, object):
+ root = self.write_xml_object(object)
+ return ElementTree.tostring(root)
+
+ def unserialize(self, str, obj_type):
+ def set_dirty(obj):
+ for child, _, _ in obj.db_children():
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ set_dirty(child.db_workflow)
+ child.is_dirty = True
+ child.is_new = True
+ try:
+ root = ElementTree.fromstring(str)
+ obj = self.read_xml_object(obj_type, root)
+ set_dirty(obj)
+ return obj
+ except SyntaxError, e:
+ msg = "Invalid VisTrails serialized object %s" % str
+ raise VistrailsDBException(msg)
+ return None
diff --git a/vistrails/db/versions/v0_9_3/persistence/sql/__init__.py b/vistrails/db/versions/v0_9_3/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_9_3/persistence/sql/auto_gen.py b/vistrails/db/versions/v0_9_3/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..e6ffdd4
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/persistence/sql/auto_gen.py
@@ -0,0 +1,2811 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v0_9_3.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port_spec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(22)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[4], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[5], 'long', 'int')
+ entity_type = self.convertFromDB(row[6], 'str', 'char(16)')
+ parent = self.convertFromDB(row[7], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ spec=spec,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_entity_id = entity_id
+ portSpec.db_entity_type = entity_type
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(22)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ module.db_parentType = parentType
+ module.db_entity_id = entity_id
+ module.db_entity_type = entity_type
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'tag'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_parentType = parentType
+ tag.db_entity_id = entity_id
+ tag.db_entity_type = entity_type
+ tag.db_parent = parent
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_tag(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec,
+ id=id)
+ port.db_parentType = parentType
+ port.db_entity_id = entity_id
+ port.db_entity_type = entity_type
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ group = DBGroup(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ group.db_parentType = parentType
+ group.db_entity_id = entity_id
+ group.db_entity_type = entity_type
+ group.db_parent = parent
+ group.is_dirty = False
+ res[('group', id)] = group
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_workflow is not None:
+ child = obj.db_workflow
+ child.db_parent = obj.db_id
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'log_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ log = DBLog(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ log.is_dirty = False
+ res[('log', id)] = log
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_workflow_execs:
+ child.db_log = obj.db_id
+ for child in obj.db_machines:
+ child.db_log = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'machine'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.db_entity_id = entity_id
+ machine.db_entity_type = entity_type
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'add_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_entity_id = entity_id
+ add.db_entity_type = entity_type
+ add.is_dirty = False
+ res[('add', id)] = add
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'other'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_entity_id = entity_id
+ other.db_entity_type = entity_type
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'location'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_entity_id = entity_id
+ location.db_entity_type = entity_type
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'parameter'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_entity_id = entity_id
+ parameter.db_entity_type = entity_type
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPluginDataSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'plugin_data'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ data = self.convertFromDB(row[1], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ plugin_data = DBPluginData(data=data,
+ id=id)
+ plugin_data.db_parentType = parentType
+ plugin_data.db_entity_id = entity_id
+ plugin_data.db_entity_type = entity_type
+ plugin_data.db_parent = parent
+ plugin_data.is_dirty = False
+ res[('plugin_data', id)] = plugin_data
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_plugin_data(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_data') and obj.db_data is not None:
+ columnMap['data'] = \
+ self.convertToDB(obj.db_data, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'function'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_entity_id = entity_id
+ function.db_entity_type = entity_type
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'abstraction'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'name', 'last_modified']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[3], 'datetime', 'datetime')
+
+ abstraction = DBAbstraction(entity_type=entity_type,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'name', 'last_modified']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_actions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id', 'parent_type']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_id = self.convertFromDB(row[1], 'long', 'int')
+ entity_type = self.convertFromDB(row[2], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'char(16)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[6], 'long', 'int')
+ parent = self.convertFromDB(row[7], 'long', 'int')
+ parentType = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ workflow = DBWorkflow(entity_type=entity_type,
+ name=name,
+ version=version,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ workflow.db_entity_id = entity_id
+ workflow.db_parent = parent
+ workflow.db_parentType = parentType
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('group', obj.db_parent) in all_objects:
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_workflow(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id', 'parent_type']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_connections:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_plugin_datas:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_modules:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionRefSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'abstraction_ref'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'cache', 'abstraction_id', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(1023)')
+ cache = self.convertFromDB(row[2], 'int', 'int')
+ abstraction_id = self.convertFromDB(row[3], 'long', 'int')
+ version = self.convertFromDB(row[4], 'long', 'int')
+ parentType = self.convertFromDB(row[5], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ abstractionRef = DBAbstractionRef(name=name,
+ cache=cache,
+ abstraction_id=abstraction_id,
+ version=version,
+ id=id)
+ abstractionRef.db_parentType = parentType
+ abstractionRef.db_entity_id = entity_id
+ abstractionRef.db_entity_type = entity_type
+ abstractionRef.db_parent = parent
+ abstractionRef.is_dirty = False
+ res[('abstractionRef', id)] = abstractionRef
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'cache', 'abstraction_id', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction_ref'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_abstraction_id') and obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction_ref'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'annotation'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_entity_id = entity_id
+ annotation.db_entity_type = entity_type
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'abstractionRef':
+ p = all_objects[('abstractionRef', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'change_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_entity_id = entity_id
+ change.db_entity_type = entity_type
+ change.is_dirty = False
+ res[('change', id)] = change
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ vt_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[5], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[6], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[7], 'long', 'int')
+ parent_type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[9], 'long', 'int')
+ completed = self.convertFromDB(row[10], 'int', 'int')
+ name = self.convertFromDB(row[11], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[12], 'long', 'int')
+ entity_id = self.convertFromDB(row[13], 'long', 'int')
+ entity_type = self.convertFromDB(row[14], 'str', 'char(16)')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_entity_id = entity_id
+ workflow_exec.db_entity_type = entity_type
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_module_execs:
+ child.db_workflow_exec = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'connection_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[2], 'long', 'int')
+ entity_type = self.convertFromDB(row[3], 'str', 'char(16)')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_entity_id = entity_id
+ connection.db_entity_type = entity_type
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'action'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ prune = self.convertFromDB(row[5], 'int', 'int')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ id=id)
+ action.db_parentType = parentType
+ action.db_entity_id = entity_id
+ action.db_entity_type = entity_type
+ action.db_parent = parent
+ action.is_dirty = False
+ res[('action', id)] = action
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_action(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_prune') and obj.db_prune is not None:
+ columnMap['prune'] = \
+ self.convertToDB(obj.db_prune, 'int', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'delete_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_entity_id = entity_id
+ delete.db_entity_type = entity_type
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'vistrail'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_actions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_tags:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'abstraction_id', 'abstraction_version', 'machine_id', 'wf_exec_id', 'entity_id', 'entity_type']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ module_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[6], 'int', 'int')
+ error = self.convertFromDB(row[7], 'str', 'varchar(1023)')
+ abstraction_id = self.convertFromDB(row[8], 'long', 'int')
+ abstraction_version = self.convertFromDB(row[9], 'long', 'int')
+ machine_id = self.convertFromDB(row[10], 'long', 'int')
+ workflow_exec = self.convertFromDB(row[11], 'long', 'int')
+ entity_id = self.convertFromDB(row[12], 'long', 'int')
+ entity_type = self.convertFromDB(row[13], 'str', 'char(16)')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ abstraction_id=abstraction_id,
+ abstraction_version=abstraction_version,
+ machine_id=machine_id,
+ id=id)
+ module_exec.db_workflow_exec = workflow_exec
+ module_exec.db_entity_id = entity_id
+ module_exec.db_entity_type = entity_type
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('workflow_exec', obj.db_workflow_exec) in all_objects:
+ p = all_objects[('workflow_exec', obj.db_workflow_exec)]
+ p.db_add_module_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'abstraction_id', 'abstraction_version', 'machine_id', 'wf_exec_id', 'entity_id', 'entity_type']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_abstraction_id') and obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if hasattr(obj, 'db_abstraction_version') and obj.db_abstraction_version is not None:
+ columnMap['abstraction_version'] = \
+ self.convertToDB(obj.db_abstraction_version, 'long', 'int')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_workflow_exec') and obj.db_workflow_exec is not None:
+ columnMap['wf_exec_id'] = \
+ self.convertToDB(obj.db_workflow_exec, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefSQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v0_9_3/persistence/sql/sql_dao.py b/vistrails/db/versions/v0_9_3/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..ad01dc5
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/persistence/sql/sql_dao.py
@@ -0,0 +1,183 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+from vistrails.db import VistrailsDBException
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ # return "'" + str(value).replace("'", "''") + "'"
+ return str(value)
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ return str(value)
+ elif type == 'int':
+ return str(value)
+ elif type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+
+ return None
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None,
+ forUpdate=False):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % \
+ (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ if forUpdate:
+ dbCommand += " FOR UPDATE"
+ dbCommand += ";"
+ return (dbCommand, tuple(values))
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ # valueStr = '%s, '.join(values)
+ valueStr = ''
+ if len(values) > 1:
+ valueStr = '%s,' * (len(values) - 1) + '%s'
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s);""" % \
+ (table, columnStr, valueStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ values = []
+ for column, value in columnMap.iteritems():
+# if value is None:
+# value = 'NULL'
+ setStr += '%s%s = %%s' % (comma, column)
+ comma = ', '
+ values.append(value)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """UPDATE %s SET %s WHERE %s;""" % \
+ (table, setStr, whereStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLDelete(self, table, whereMap):
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """DELETE FROM %s WHERE %s;""" % \
+ (table, whereStr)
+ return (dbCommand, tuple(values))
+
+ def executeSQL(self, db, cmd_tuple, isFetch):
+ dbCommand, values = cmd_tuple
+ # print 'db: %s' % dbCommand
+ # print 'values:', values
+ data = None
+ cursor = db.cursor()
+ try:
+ cursor.execute(dbCommand, values)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ except Exception, e:
+ raise VistrailsDBException('Command "%s" with values "%s" '
+ 'failed: %s' % (dbCommand, values, e))
+ finally:
+ cursor.close()
+ return data
+
+ def start_transaction(self, db):
+ db.begin()
+
+ def commit_transaction(self, db):
+ db.commit()
+
+ def rollback_transaction(self, db):
+ db.rollback()
diff --git a/vistrails/db/versions/v0_9_3/persistence/xml/__init__.py b/vistrails/db/versions/v0_9_3/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_9_3/persistence/xml/auto_gen.py b/vistrails/db/versions/v0_9_3/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..e491b17
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/persistence/xml/auto_gen.py
@@ -0,0 +1,1774 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from vistrails.core.system import get_elementtree_library
+
+from xml_dao import XMLDAO
+from vistrails.db.versions.v0_9_3.domain import *
+
+ElementTree = get_elementtree_library()
+
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'portSpec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('spec', None)
+ spec = self.convertFromStr(data, 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, node=None):
+ if node is None:
+ node = ElementTree.Element('portSpec')
+
+ # set attributes
+ node.set('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.set('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.set('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.set('spec',self.convertToStr(portSpec.db_spec, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'module':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, node=None):
+ if node is None:
+ node = ElementTree.Element('module')
+
+ # set attributes
+ node.set('id',self.convertToStr(module.db_id, 'long'))
+ node.set('cache',self.convertToStr(module.db_cache, 'int'))
+ node.set('name',self.convertToStr(module.db_name, 'str'))
+ node.set('namespace',self.convertToStr(module.db_namespace, 'str'))
+ node.set('package',self.convertToStr(module.db_package, 'str'))
+ node.set('version',self.convertToStr(module.db_version, 'str'))
+ node.set('tag',self.convertToStr(module.db_tag, 'str'))
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = module.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'tag':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, node=None):
+ if node is None:
+ node = ElementTree.Element('tag')
+
+ # set attributes
+ node.set('id',self.convertToStr(tag.db_id, 'long'))
+ node.set('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'port':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('moduleId', None)
+ moduleId = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ moduleName = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('spec', None)
+ spec = self.convertFromStr(data, 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, node=None):
+ if node is None:
+ node = ElementTree.Element('port')
+
+ # set attributes
+ node.set('id',self.convertToStr(port.db_id, 'long'))
+ node.set('type',self.convertToStr(port.db_type, 'str'))
+ node.set('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.set('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.set('name',self.convertToStr(port.db_name, 'str'))
+ node.set('spec',self.convertToStr(port.db_spec, 'str'))
+
+ return node
+
+class DBGroupXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'group':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ workflow = None
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'workflow':
+ _data = self.getDao('workflow').fromXML(child)
+ workflow = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroup(id=id,
+ workflow=workflow,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group, node=None):
+ if node is None:
+ node = ElementTree.Element('group')
+
+ # set attributes
+ node.set('id',self.convertToStr(group.db_id, 'long'))
+ node.set('cache',self.convertToStr(group.db_cache, 'int'))
+ node.set('name',self.convertToStr(group.db_name, 'str'))
+ node.set('namespace',self.convertToStr(group.db_namespace, 'str'))
+ node.set('package',self.convertToStr(group.db_package, 'str'))
+ node.set('version',self.convertToStr(group.db_version, 'str'))
+ node.set('tag',self.convertToStr(group.db_tag, 'str'))
+
+ # set elements
+ workflow = group.db_workflow
+ if workflow is not None:
+ childNode = ElementTree.SubElement(node, 'workflow')
+ self.getDao('workflow').toXML(workflow, childNode)
+ location = group.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = group.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = group.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'log':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ workflow_execs = []
+ machines = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'workflowExec':
+ _data = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs.append(_data)
+ elif child.tag == 'machine':
+ _data = self.getDao('machine').fromXML(child)
+ machines.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLog(id=id,
+ version=version,
+ name=name,
+ workflow_execs=workflow_execs,
+ machines=machines,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, node=None):
+ if node is None:
+ node = ElementTree.Element('log')
+
+ # set attributes
+ node.set('id',self.convertToStr(log.db_id, 'long'))
+ node.set('version',self.convertToStr(log.db_version, 'str'))
+ node.set('name',self.convertToStr(log.db_name, 'str'))
+ node.set('vistrail_id',self.convertToStr(log.db_vistrail_id, 'long'))
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs:
+ childNode = ElementTree.SubElement(node, 'workflow_exec')
+ self.getDao('workflow_exec').toXML(workflow_exec, childNode)
+ machines = log.db_machines
+ for machine in machines:
+ childNode = ElementTree.SubElement(node, 'machine')
+ self.getDao('machine').toXML(machine, childNode)
+
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'machine':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('os', None)
+ os = self.convertFromStr(data, 'str')
+ data = node.get('architecture', None)
+ architecture = self.convertFromStr(data, 'str')
+ data = node.get('processor', None)
+ processor = self.convertFromStr(data, 'str')
+ data = node.get('ram', None)
+ ram = self.convertFromStr(data, 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, node=None):
+ if node is None:
+ node = ElementTree.Element('machine')
+
+ # set attributes
+ node.set('id',self.convertToStr(machine.db_id, 'long'))
+ node.set('name',self.convertToStr(machine.db_name, 'str'))
+ node.set('os',self.convertToStr(machine.db_os, 'str'))
+ node.set('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.set('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.set('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'add':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ data = _data
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAdd(data=data,
+ id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, node=None):
+ if node is None:
+ node = ElementTree.Element('add')
+
+ # set attributes
+ node.set('id',self.convertToStr(add.db_id, 'long'))
+ node.set('what',self.convertToStr(add.db_what, 'str'))
+ node.set('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # set elements
+ data = add.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'other':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'value':
+ _data = self.convertFromStr(child.text,'')
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, node=None):
+ if node is None:
+ node = ElementTree.Element('other')
+
+ # set attributes
+ node.set('id',self.convertToStr(other.db_id, 'long'))
+ node.set('key',self.convertToStr(other.db_key, 'str'))
+
+ # set elements
+
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'location':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('x', None)
+ x = self.convertFromStr(data, 'float')
+ data = node.get('y', None)
+ y = self.convertFromStr(data, 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, node=None):
+ if node is None:
+ node = ElementTree.Element('location')
+
+ # set attributes
+ node.set('id',self.convertToStr(location.db_id, 'long'))
+ node.set('x',self.convertToStr(location.db_x, 'float'))
+ node.set('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'parameter':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('val', None)
+ val = self.convertFromStr(data, 'str')
+ data = node.get('alias', None)
+ alias = self.convertFromStr(data, 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, node=None):
+ if node is None:
+ node = ElementTree.Element('parameter')
+
+ # set attributes
+ node.set('id',self.convertToStr(parameter.db_id, 'long'))
+ node.set('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.set('name',self.convertToStr(parameter.db_name, 'str'))
+ node.set('type',self.convertToStr(parameter.db_type, 'str'))
+ node.set('val',self.convertToStr(parameter.db_val, 'str'))
+ node.set('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBPluginDataXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'plugin_data':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('data', None)
+ data = self.convertFromStr(data, 'str')
+
+ obj = DBPluginData(id=id,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, plugin_data, node=None):
+ if node is None:
+ node = ElementTree.Element('plugin_data')
+
+ # set attributes
+ node.set('id',self.convertToStr(plugin_data.db_id, 'long'))
+ node.set('data',self.convertToStr(plugin_data.db_data, 'str'))
+
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'function':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ parameters = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ parameters.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, node=None):
+ if node is None:
+ node = ElementTree.Element('function')
+
+ # set attributes
+ node.set('id',self.convertToStr(function.db_id, 'long'))
+ node.set('pos',self.convertToStr(function.db_pos, 'long'))
+ node.set('name',self.convertToStr(function.db_name, 'str'))
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(parameter, childNode)
+
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'abstraction':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child.tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstraction(id=id,
+ name=name,
+ actions=actions,
+ tags=tags)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, node=None):
+ if node is None:
+ node = ElementTree.Element('abstraction')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.set('name',self.convertToStr(abstraction.db_name, 'str'))
+
+ # set elements
+ actions = abstraction.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = abstraction.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflow':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ connections = []
+ annotations = []
+ abstractions = []
+ plugin_datas = []
+ others = []
+ modules = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ connections.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ abstractions.append(_data)
+ elif child.tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ plugin_datas.append(_data)
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ others.append(_data)
+ elif child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ modules.append(_data)
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ modules.append(_data)
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ modules.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflow(modules=modules,
+ id=id,
+ name=name,
+ version=version,
+ connections=connections,
+ annotations=annotations,
+ abstractions=abstractions,
+ plugin_datas=plugin_datas,
+ others=others,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, node=None):
+ if node is None:
+ node = ElementTree.Element('workflow')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow.db_id, 'long'))
+ node.set('name',self.convertToStr(workflow.db_name, 'str'))
+ node.set('version',self.convertToStr(workflow.db_version, 'str'))
+ node.set('vistrail_id',self.convertToStr(workflow.db_vistrail_id, 'long'))
+
+ # set elements
+ connections = workflow.db_connections
+ for connection in connections:
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(connection, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ abstractions = workflow.db_abstractions
+ for abstraction in abstractions:
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(abstraction, childNode)
+ plugin_datas = workflow.db_plugin_datas
+ for plugin_data in plugin_datas:
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(plugin_data, childNode)
+ others = workflow.db_others
+ for other in others:
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(other, childNode)
+ modules = workflow.db_modules
+ for module in modules:
+ if module.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(module, childNode)
+ elif module.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(module, childNode)
+ elif module.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(module, childNode)
+
+ return node
+
+class DBAbstractionRefXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'abstractionRef':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('abstractionId', None)
+ abstraction_id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'long')
+
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstractionRef(id=id,
+ name=name,
+ cache=cache,
+ abstraction_id=abstraction_id,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstractionRef, node=None):
+ if node is None:
+ node = ElementTree.Element('abstractionRef')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstractionRef.db_id, 'long'))
+ node.set('name',self.convertToStr(abstractionRef.db_name, 'str'))
+ node.set('cache',self.convertToStr(abstractionRef.db_cache, 'int'))
+ node.set('abstractionId',self.convertToStr(abstractionRef.db_abstraction_id, 'long'))
+ node.set('version',self.convertToStr(abstractionRef.db_version, 'long'))
+
+ # set elements
+ location = abstractionRef.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = abstractionRef.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = abstractionRef.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'annotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, node=None):
+ if node is None:
+ node = ElementTree.Element('annotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(annotation.db_id, 'long'))
+ node.set('key',self.convertToStr(annotation.db_key, 'str'))
+ node.set('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'change':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('oldObjId', None)
+ oldObjId = self.convertFromStr(data, 'long')
+ data = node.get('newObjId', None)
+ newObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstractionRef':
+ _data = self.getDao('abstractionRef').fromXML(child)
+ data = _data
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBChange(data=data,
+ id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, node=None):
+ if node is None:
+ node = ElementTree.Element('change')
+
+ # set attributes
+ node.set('id',self.convertToStr(change.db_id, 'long'))
+ node.set('what',self.convertToStr(change.db_what, 'str'))
+ node.set('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.set('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.set('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # set elements
+ data = change.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstractionRef':
+ childNode = ElementTree.SubElement(node, 'abstractionRef')
+ self.getDao('abstractionRef').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflowExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('ip', None)
+ ip = self.convertFromStr(data, 'str')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('vtVersion', None)
+ vt_version = self.convertFromStr(data, 'str')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('parentId', None)
+ parent_id = self.convertFromStr(data, 'long')
+ data = node.get('parentType', None)
+ parent_type = self.convertFromStr(data, 'str')
+ data = node.get('parentVersion', None)
+ parent_version = self.convertFromStr(data, 'long')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ module_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module_exec':
+ child.tag = 'moduleExec'
+ if child.tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ module_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflowExec(id=id,
+ user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ module_execs=module_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('workflowExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.set('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.set('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.set('session',self.convertToStr(workflow_exec.db_session, 'long'))
+ node.set('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.set('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.set('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.set('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.set('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.set('completed',self.convertToStr(workflow_exec.db_completed, 'int'))
+ node.set('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # set elements
+ module_execs = workflow_exec.db_module_execs
+ for module_exec in module_execs:
+ childNode = ElementTree.SubElement(node, 'module_exec')
+ self.getDao('module_exec').toXML(module_exec, childNode)
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'connection':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+
+ ports = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ ports.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, node=None):
+ if node is None:
+ node = ElementTree.Element('connection')
+
+ # set attributes
+ node.set('id',self.convertToStr(connection.db_id, 'long'))
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(port, childNode)
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'action':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('prevId', None)
+ prevId = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('prune', None)
+ prune = self.convertFromStr(data, 'int')
+
+ annotations = []
+ operations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'add':
+ _data = self.getDao('add').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'delete':
+ _data = self.getDao('delete').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'change':
+ _data = self.getDao('change').fromXML(child)
+ operations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAction(operations=operations,
+ id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, node=None):
+ if node is None:
+ node = ElementTree.Element('action')
+
+ # set attributes
+ node.set('id',self.convertToStr(action.db_id, 'long'))
+ node.set('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.set('date',self.convertToStr(action.db_date, 'datetime'))
+ node.set('session',self.convertToStr(action.db_session, 'long'))
+ node.set('user',self.convertToStr(action.db_user, 'str'))
+ node.set('prune',self.convertToStr(action.db_prune, 'int'))
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ childNode = ElementTree.SubElement(node, 'add')
+ self.getDao('add').toXML(operation, childNode)
+ elif operation.vtType == 'delete':
+ childNode = ElementTree.SubElement(node, 'delete')
+ self.getDao('delete').toXML(operation, childNode)
+ elif operation.vtType == 'change':
+ childNode = ElementTree.SubElement(node, 'change')
+ self.getDao('change').toXML(operation, childNode)
+
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'delete':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, node=None):
+ if node is None:
+ node = ElementTree.Element('delete')
+
+ # set attributes
+ node.set('id',self.convertToStr(delete.db_id, 'long'))
+ node.set('what',self.convertToStr(delete.db_what, 'str'))
+ node.set('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'vistrail':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+ annotations = []
+ abstractions = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child.tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ abstractions.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ actions=actions,
+ tags=tags,
+ annotations=annotations,
+ abstractions=abstractions)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, node=None):
+ if node is None:
+ node = ElementTree.Element('vistrail')
+
+ # set attributes
+ node.set('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.set('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.set('name',self.convertToStr(vistrail.db_name, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = vistrail.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+ annotations = vistrail.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ abstractions = vistrail.db_abstractions
+ for abstraction in abstractions:
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(abstraction, childNode)
+
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'moduleExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ module_name = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('abstraction_id', None)
+ abstraction_id = self.convertFromStr(data, 'long')
+ data = node.get('abstraction_version', None)
+ abstraction_version = self.convertFromStr(data, 'long')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ abstraction_id=abstraction_id,
+ abstraction_version=abstraction_version,
+ machine_id=machine_id,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(module_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.set('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+ node.set('completed',self.convertToStr(module_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(module_exec.db_error, 'str'))
+ node.set('abstraction_id',self.convertToStr(module_exec.db_abstraction_id, 'long'))
+ node.set('abstraction_version',self.convertToStr(module_exec.db_abstraction_version, 'long'))
+ node.set('machine_id',self.convertToStr(module_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'abstractionRef' not in self:
+ self['abstractionRef'] = DBAbstractionRefXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v0_9_3/persistence/xml/xml_dao.py b/vistrails/db/versions/v0_9_3/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..955c01a
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/persistence/xml/xml_dao.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v0_9_3/schemas/sql/vistrails.sql b/vistrails/db/versions/v0_9_3/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..633e54e
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/schemas/sql/vistrails.sql
@@ -0,0 +1,311 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(22),
+ type varchar(255),
+ spec varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ spec varchar(4095),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE group_tbl(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime,
+ vistrail_id int
+) engine=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE plugin_data(
+ id int,
+ data varchar(8191),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE workflow(
+ id int not null auto_increment primary key,
+ entity_id int,
+ entity_type char(16),
+ name varchar(255),
+ version char(16),
+ last_modified datetime,
+ vistrail_id int,
+ parent_id int,
+ parent_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE abstraction_ref(
+ id int,
+ name varchar(1023),
+ cache int,
+ abstraction_id int,
+ version int,
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ session int,
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ completed int,
+ name varchar(255),
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session int,
+ user varchar(255),
+ prune int,
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ module_name varchar(255),
+ completed int,
+ error varchar(1023),
+ abstraction_id int,
+ abstraction_version int,
+ machine_id int,
+ wf_exec_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
diff --git a/vistrails/db/versions/v0_9_3/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v0_9_3/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..fa131e2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,38 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, tag, port, group_tbl, log_tbl, machine, add_tbl, other, location, parameter, plugin_data, function, abstraction, workflow, abstraction_ref, annotation, change_tbl, workflow_exec, connection_tbl, action, delete_tbl, vistrail, module_exec;
diff --git a/vistrails/db/versions/v0_9_3/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_9_3/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..911ca0a
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/schemas/xml/vistrail.xsd
@@ -0,0 +1,285 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="prune" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstractionRef">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="abstractionId" type="xs:int"/>
+ <xs:attribute name="version" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="group">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="workflow" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plugin_data">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="workflow">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstractionRef" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_9_3/specs/all.xml b/vistrails/db/versions/v0_9_3/specs/all.xml
new file mode 100644
index 0000000..9adece8
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/specs/all.xml
@@ -0,0 +1,1652 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<objects>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ABSTRACTION +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ABSTRACTIONREF ++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="abstractionRef">
+ <layout>
+ <xml name="abstractionRef" nodeType="xs:element"/>
+ <sql table="abstraction_ref"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml name="cache" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_id" type="long" foreignKey="true"
+ object="abstraction">
+ <xml name="abstractionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ACTION ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long" foreignKey="true" object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="prune" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ADD +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ANNOTATION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CHANGE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstractionRef" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CONNECTION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- DELETE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- FUNCTION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group" parentClass="module">
+ <layout>
+ <xml name="group" nodeType="xs:element"/>
+ <sql table="group_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow" type="object" mapping="one-to-one"
+ expand="false">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOCATION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstractionRef">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MACHINE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_EXEC +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="abstraction_id" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OTHER +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PARAMETER +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PLUGIN DATA +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="plugin_data">
+ <layout>
+ <xml name="plugin_data" nodeType="xs:element"/>
+ <sql table="plugin_data"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="data" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORT ++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORTSPEC ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(22)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- TAG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" discriminator="parentType" type="long" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" type="long" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" type="long" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VISTRAIL ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="abstraction" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstractionRef" ref="true" object="abstractionRef">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group" ref="true" object="group">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <!-- only need for copy/paste so no sql bindings -->
+ <property ref="true" object="abstraction" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="plugin_data" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent" ref="true" object="group" type="long" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW_EXEC +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+</objects>
diff --git a/vistrails/db/versions/v0_9_3/translate/__init__.py b/vistrails/db/versions/v0_9_3/translate/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/db/versions/v0_9_3/translate/v0_9_1.py b/vistrails/db/versions/v0_9_3/translate/v0_9_1.py
new file mode 100644
index 0000000..437b595
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/translate/v0_9_1.py
@@ -0,0 +1,86 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v0_9_3.domain import DBVistrail, DBAction, DBTag, DBModule, \
+ DBConnection, DBPortSpec, DBFunction, DBParameter, DBLocation, DBAdd, \
+ DBChange, DBDelete, DBAnnotation, DBPort, DBAbstractionRef, DBGroup, \
+ DBWorkflow, DBLog
+
+def translateVistrail(_vistrail):
+ def update_key(old_obj, translate_dict):
+ return '__notes__'
+
+ def update_annotation(old_obj, translate_dict):
+ new_dict = {'DBAnnotation': {'key': update_key}}
+ new_list = []
+ for annotation in old_obj.db_annotations:
+ if annotation.db_key == 'notes':
+ new_list.append(DBAnnotation.update_version(annotation,
+ new_dict))
+ else:
+ new_list.append(DBAnnotation.update_version(annotation,
+ {}))
+ return new_list
+
+ def update_session(old_obj, translate_dict):
+ if not old_obj.db_session:
+ session = None
+ else:
+ session = long(old_obj.db_session)
+ return session
+
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+
+ translate_dict = {'DBAction': {'annotations': update_annotation,
+ 'session': update_session},
+ 'DBGroup': {'workflow': update_workflow}}
+ # pass DBVistrail because domain contains enriched version of the auto_gen
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict)
+ vistrail.db_version = '0.9.3'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBGroup': {'workflow': update_workflow}}
+ workflow = update_workflow(_workflow, translate_dict)
+ workflow.db_version = '0.9.3'
+ return workflow
+
+def translateLog(_log):
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '0.9.3'
+ return log
diff --git a/vistrails/db/versions/v0_9_3/translate/v0_9_2.py b/vistrails/db/versions/v0_9_3/translate/v0_9_2.py
new file mode 100644
index 0000000..848c2ab
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/translate/v0_9_2.py
@@ -0,0 +1,155 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v0_9_3.domain import DBVistrail, DBAction, DBTag, DBModule, \
+ DBConnection, DBPortSpec, DBFunction, DBParameter, DBLocation, DBAdd, \
+ DBChange, DBDelete, DBAnnotation, DBPort, DBAbstractionRef, DBGroup
+
+def translateVistrail(_vistrail):
+ vistrail = DBVistrail()
+
+ for _action in _vistrail.db_actions:
+ ops = []
+ for op in _action.db_operations:
+ if op.vtType == 'add':
+ data = convert_data(op.db_data)
+ ops.append(DBAdd(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'change':
+ data = convert_data(op.db_data)
+ ops.append(DBChange(id=op.db_id,
+ what=op.db_what,
+ oldObjId=op.db_oldObjId,
+ newObjId=op.db_newObjId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType,
+ data=data))
+ elif op.vtType == 'delete':
+ ops.append(DBDelete(id=op.db_id,
+ what=op.db_what,
+ objectId=op.db_objectId,
+ parentObjId=op.db_parentObjId,
+ parentObjType=op.db_parentObjType))
+ annotations = []
+ for annotation in _action.db_annotations:
+ annotations.append(DBAnnotation(id=annotation.db_id,
+ key=annotation.db_key,
+ value=annotation.db_value))
+ session = _action.db_session
+ if not session:
+ session = None
+ else:
+ session = long(_action.db_session)
+
+ action = DBAction(id=_action.db_id,
+ prevId=_action.db_prevId,
+ date=_action.db_date,
+ user=_action.db_user,
+ prune=_action.db_prune,
+ session=session,
+ operations=ops,
+ annotations=annotations)
+ vistrail.db_add_action(action)
+
+ for _tag in _vistrail.db_tags:
+ tag = DBTag(id=_tag.db_id,
+ name=_tag.db_name)
+ vistrail.db_add_tag(tag)
+
+ vistrail.db_version = '0.9.3'
+ return vistrail
+
+def convert_data(child):
+ if child.vtType == 'module':
+ return DBModule(id=child.db_id,
+ cache=child.db_cache,
+ name=child.db_name,
+ namespace=child.db_namespace,
+ package=child.db_package,
+ version=child.db_version,
+ tag=child.db_tag)
+ elif child.vtType == 'abstractionRef':
+ return DBAbstractionRef(id=child.db_id,
+ name=child.db_name,
+ cache=child.db_cache,
+ abstraction_id=child.db_abstraction_id,
+ version=child.db_version)
+ elif child.vtType == 'connection':
+ return DBConnection(id=child.db_id)
+ elif child.vtType == 'portSpec':
+ return DBPortSpec(id=child.db_id,
+ name=child.db_name,
+ type=child.db_type,
+ spec=child.db_spec)
+ elif child.vtType == 'function':
+ return DBFunction(id=child.db_id,
+ pos=child.db_pos,
+ name=child.db_name)
+ elif child.vtType == 'parameter':
+ return DBParameter(id=child.db_id,
+ pos=child.db_pos,
+ name=child.db_name,
+ type=child.db_type,
+ val=child.db_val,
+ alias=child.db_alias)
+ elif child.vtType == 'location':
+ return DBLocation(id=child.db_id,
+ x=child.db_x,
+ y=child.db_y)
+ elif child.vtType == 'annotation':
+ return DBAnnotation(id=child.db_id,
+ key=child.db_key,
+ value=child.db_value)
+ elif child.vtType == 'port':
+ return DBPort(id=child.db_id,
+ type=child.db_type,
+ moduleId=child.db_moduleId,
+ moduleName=child.db_moduleName,
+ name=child.db_name,
+ spec=child.db_spec)
+ elif child.vtType == 'group':
+ return DBGroup(id=child.db_id,
+ workflow=child.db_workflow,
+ cache=child.db_cache,
+ name=child.db_name,
+ namespace=child.db_namespace,
+ package=child.db_package,
+ version=child.db_version,
+ tag=child.db_tag)
+
diff --git a/vistrails/db/versions/v0_9_3/translate/v0_9_4.py b/vistrails/db/versions/v0_9_3/translate/v0_9_4.py
new file mode 100644
index 0000000..7a32422
--- /dev/null
+++ b/vistrails/db/versions/v0_9_3/translate/v0_9_4.py
@@ -0,0 +1,113 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.versions.v0_9_3.domain import DBVistrail, DBWorkflow, DBLog, \
+ DBAbstractionRef, DBAdd, DBChange, DBDelete, DBAbstractionRef, DBGroup, \
+ DBModule
+
+def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow,
+ translate_dict, DBWorkflow())
+
+def update_modules(old_obj, trans_dict):
+ new_modules = []
+ for obj in old_obj.db_modules:
+ if obj.vtType == 'module':
+ new_modules.append(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_modules.append(DBAbstractionRef.update_version(obj,
+ trans_dict))
+ elif obj.vtType == 'group':
+ new_modules.append(DBGroup.update_version(obj, trans_dict))
+ return new_modules
+
+def translateVistrail(_vistrail):
+ def update_operations(old_obj, trans_dict):
+ def update_abstraction(old_obj, trans_dict):
+ def get_version(old_obj, trans_dict):
+ return long(old_obj.db_internal_version)
+ new_dict = {'DBAbstractionRef': {'version': get_version}}
+ new_dict.update(trans_dict)
+ return DBAbstractionRef.update_version(old_obj.db_data, new_dict)
+ new_ops = []
+ for obj in old_obj.db_operations:
+ if obj.vtType == 'add':
+ if obj.db_what == 'abstraction':
+ trans_dict['DBAdd'] = {'data': update_abstraction}
+ new_op = DBAdd.update_version(obj, trans_dict)
+ new_op.db_what = 'abstractionRef'
+ new_ops.append(new_op)
+ del trans_dict['DBAdd']
+ else:
+ new_op = DBAdd.update_version(obj, trans_dict)
+ if obj.db_parentObjType == 'abstraction':
+ new_op.db_parentObjType = 'abstractionRef'
+ new_ops.append(new_op)
+ elif obj.vtType == 'delete':
+ new_ops.append(DBDelete.update_version(obj, trans_dict))
+ elif obj.vtType == 'change':
+ if obj.db_what == 'abstraction':
+ trans_dict['DBChange'] = {'data': update_abstraction}
+ new_op = DBChange.update_version(obj, trans_dict)
+ new_op.db_what = 'abstractionRef'
+ new_ops.append(new_op)
+ del trans_dict['DBChange']
+ else:
+ new_op = DBChange.update_version(obj, trans_dict)
+ if obj.db_parentObjType == 'abstraction':
+ new_op.db_parentObjType = 'abstractionRef'
+ new_ops.append(new_op)
+ return new_ops
+
+ translate_dict = {'DBGroup': {'workflow': update_workflow},
+ 'DBAction': {'operations': update_operations},
+ 'DBWorkflow': {'modules': update_modules}}
+ # pass DBVistrail because domain contains enriched version of the auto_gen
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict)
+ vistrail.db_version = '0.9.3'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ translate_dict = {'DBGroup': {'workflow': update_workflow},
+ 'DBWorkflow': {'modules': update_modules}}
+ workflow = DBWorkflow.update_version(_workflow, translate_dict)
+ workflow.db_version = '0.9.3'
+ return workflow
+
+def translateLog(_log):
+ translate_dict = {}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '0.9.3'
+ return log
+
diff --git a/vistrails/db/versions/v0_9_4/__init__.py b/vistrails/db/versions/v0_9_4/__init__.py
new file mode 100644
index 0000000..5cf1ec6
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.9.4'
diff --git a/vistrails/db/versions/v0_9_4/domain/__init__.py b/vistrails/db/versions/v0_9_4/domain/__init__.py
new file mode 100644
index 0000000..370b564
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/domain/__init__.py
@@ -0,0 +1,40 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from workflow import DBWorkflow
+from vistrail import DBVistrail
+from log import DBLog
+from id_scope import IdScope
diff --git a/vistrails/db/versions/v0_9_4/domain/auto_gen.py b/vistrails/db/versions/v0_9_4/domain/auto_gen.py
new file mode 100644
index 0000000..7a9a33c
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/domain/auto_gen.py
@@ -0,0 +1,5971 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, spec=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_type = type
+ self._db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPortSpec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec(id=self._db_id,
+ name=self._db_name,
+ type=self._db_type,
+ spec=self._db_spec)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPortSpec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'spec' in class_dict:
+ res = class_dict['spec'](old_obj, trans_dict)
+ new_obj.db_spec = res
+ elif hasattr(old_obj, 'db_spec') and old_obj.db_spec is not None:
+ new_obj.db_spec = old_obj.db_spec
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_spec(self):
+ return self._db_spec
+ def __set_db_spec(self, spec):
+ self._db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self._db_spec = spec
+ def db_change_spec(self, spec):
+ self._db_spec = spec
+ def db_delete_spec(self, spec):
+ self._db_spec = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModule.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ tag=self._db_tag)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModule()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self._db_id = id
+ self._db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBTag.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag(id=self._db_id,
+ name=self._db_name)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('action', self._db_id) in id_remap:
+ cp._db_id = id_remap[('action', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBTag()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, name=None, spec=None):
+ self._db_id = id
+ self._db_type = type
+ self._db_moduleId = moduleId
+ self._db_moduleName = moduleName
+ self._db_name = name
+ self._db_spec = spec
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPort.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort(id=self._db_id,
+ type=self._db_type,
+ moduleId=self._db_moduleId,
+ moduleName=self._db_moduleName,
+ name=self._db_name,
+ spec=self._db_spec)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_moduleId') and ('module', self._db_moduleId) in id_remap:
+ cp._db_moduleId = id_remap[('module', self._db_moduleId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPort()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'moduleId' in class_dict:
+ res = class_dict['moduleId'](old_obj, trans_dict)
+ new_obj.db_moduleId = res
+ elif hasattr(old_obj, 'db_moduleId') and old_obj.db_moduleId is not None:
+ new_obj.db_moduleId = old_obj.db_moduleId
+ if 'moduleName' in class_dict:
+ res = class_dict['moduleName'](old_obj, trans_dict)
+ new_obj.db_moduleName = res
+ elif hasattr(old_obj, 'db_moduleName') and old_obj.db_moduleName is not None:
+ new_obj.db_moduleName = old_obj.db_moduleName
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'spec' in class_dict:
+ res = class_dict['spec'](old_obj, trans_dict)
+ new_obj.db_spec = res
+ elif hasattr(old_obj, 'db_spec') and old_obj.db_spec is not None:
+ new_obj.db_spec = old_obj.db_spec
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_moduleId(self):
+ return self._db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self._db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self._db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self._db_moduleName = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_spec(self):
+ return self._db_spec
+ def __set_db_spec(self, spec):
+ self._db_spec = spec
+ self.is_dirty = True
+ db_spec = property(__get_db_spec, __set_db_spec)
+ def db_add_spec(self, spec):
+ self._db_spec = spec
+ def db_change_spec(self, spec):
+ self._db_spec = spec
+ def db_delete_spec(self, spec):
+ self._db_spec = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBGroup(object):
+
+ vtType = 'group'
+
+ def __init__(self, id=None, workflow=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self.db_deleted_workflow = []
+ self._db_workflow = workflow
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroup.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroup(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ tag=self._db_tag)
+ if self._db_workflow is not None:
+ cp._db_workflow = self._db_workflow.do_copy()
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroup()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'workflow' in class_dict:
+ res = class_dict['workflow'](old_obj, trans_dict)
+ new_obj.db_workflow = res
+ elif hasattr(old_obj, 'db_workflow') and old_obj.db_workflow is not None:
+ obj = old_obj.db_workflow
+ new_obj.db_add_workflow(DBWorkflow.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow') and hasattr(new_obj, 'db_deleted_workflow'):
+ for obj in old_obj.db_deleted_workflow:
+ n_obj = DBWorkflow.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow.append(n_obj)
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow)
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_workflow = []
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_workflow is not None and self._db_workflow.has_changes():
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_workflow(self):
+ return self._db_workflow
+ def __set_db_workflow(self, workflow):
+ self._db_workflow = workflow
+ self.is_dirty = True
+ db_workflow = property(__get_db_workflow, __set_db_workflow)
+ def db_add_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_change_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_delete_workflow(self, workflow):
+ if not self.is_new:
+ self.db_deleted_workflow.append(self._db_workflow)
+ self._db_workflow = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, workflow_execs=None, machines=None, vistrail_id=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_workflow_execs = []
+ self.db_workflow_execs_id_index = {}
+ if workflow_execs is None:
+ self._db_workflow_execs = []
+ else:
+ self._db_workflow_execs = workflow_execs
+ for v in self._db_workflow_execs:
+ self.db_workflow_execs_id_index[v.db_id] = v
+ self.db_deleted_machines = []
+ self.db_machines_id_index = {}
+ if machines is None:
+ self._db_machines = []
+ else:
+ self._db_machines = machines
+ for v in self._db_machines:
+ self.db_machines_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_workflow_execs is None:
+ cp._db_workflow_execs = []
+ else:
+ cp._db_workflow_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_workflow_execs]
+ if self._db_machines is None:
+ cp._db_machines = []
+ else:
+ cp._db_machines = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_machines]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_workflow_execs_id_index = dict((v.db_id, v) for v in cp._db_workflow_execs)
+ cp.db_machines_id_index = dict((v.db_id, v) for v in cp._db_machines)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'workflow_execs' in class_dict:
+ res = class_dict['workflow_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_workflow_exec(obj)
+ elif hasattr(old_obj, 'db_workflow_execs') and old_obj.db_workflow_execs is not None:
+ for obj in old_obj.db_workflow_execs:
+ new_obj.db_add_workflow_exec(DBWorkflowExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow_execs') and hasattr(new_obj, 'db_deleted_workflow_execs'):
+ for obj in old_obj.db_deleted_workflow_execs:
+ n_obj = DBWorkflowExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow_execs.append(n_obj)
+ if 'machines' in class_dict:
+ res = class_dict['machines'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_machine(obj)
+ elif hasattr(old_obj, 'db_machines') and old_obj.db_machines is not None:
+ for obj in old_obj.db_machines:
+ new_obj.db_add_machine(DBMachine.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_machines') and hasattr(new_obj, 'db_deleted_machines'):
+ for obj in old_obj.db_deleted_machines:
+ n_obj = DBMachine.update_version(obj, trans_dict)
+ new_obj.db_deleted_machines.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_workflow_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self.db_machines:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow_execs)
+ children.extend(self.db_deleted_machines)
+ if remove:
+ self.db_deleted_workflow_execs = []
+ self.db_deleted_machines = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_workflow_execs:
+ if child.has_changes():
+ return True
+ for child in self._db_machines:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_workflow_execs(self):
+ return self._db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self._db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self._db_workflow_execs
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ self._db_workflow_execs[i] = workflow_exec
+ found = True
+ break
+ if not found:
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ if not self._db_workflow_execs[i].is_new:
+ self.db_deleted_workflow_execs.append(self._db_workflow_execs[i])
+ del self._db_workflow_execs[i]
+ break
+ del self.db_workflow_execs_id_index[workflow_exec.db_id]
+ def db_get_workflow_exec(self, key):
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == key:
+ return self._db_workflow_execs[i]
+ return None
+ def db_get_workflow_exec_by_id(self, key):
+ return self.db_workflow_execs_id_index[key]
+ def db_has_workflow_exec_with_id(self, key):
+ return key in self.db_workflow_execs_id_index
+
+ def __get_db_machines(self):
+ return self._db_machines
+ def __set_db_machines(self, machines):
+ self._db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self._db_machines
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ self._db_machines[i] = machine
+ found = True
+ break
+ if not found:
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ if not self._db_machines[i].is_new:
+ self.db_deleted_machines.append(self._db_machines[i])
+ del self._db_machines[i]
+ break
+ del self.db_machines_id_index[machine.db_id]
+ def db_get_machine(self, key):
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == key:
+ return self._db_machines[i]
+ return None
+ def db_get_machine_by_id(self, key):
+ return self.db_machines_id_index[key]
+ def db_has_machine_with_id(self, key):
+ return key in self.db_machines_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_os = os
+ self._db_architecture = architecture
+ self._db_processor = processor
+ self._db_ram = ram
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMachine.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine(id=self._db_id,
+ name=self._db_name,
+ os=self._db_os,
+ architecture=self._db_architecture,
+ processor=self._db_processor,
+ ram=self._db_ram)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and ('vistrail', self._db_vistrailId) in id_remap:
+ cp._db_vistrailId = id_remap[('vistrail', self._db_vistrailId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMachine()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'os' in class_dict:
+ res = class_dict['os'](old_obj, trans_dict)
+ new_obj.db_os = res
+ elif hasattr(old_obj, 'db_os') and old_obj.db_os is not None:
+ new_obj.db_os = old_obj.db_os
+ if 'architecture' in class_dict:
+ res = class_dict['architecture'](old_obj, trans_dict)
+ new_obj.db_architecture = res
+ elif hasattr(old_obj, 'db_architecture') and old_obj.db_architecture is not None:
+ new_obj.db_architecture = old_obj.db_architecture
+ if 'processor' in class_dict:
+ res = class_dict['processor'](old_obj, trans_dict)
+ new_obj.db_processor = res
+ elif hasattr(old_obj, 'db_processor') and old_obj.db_processor is not None:
+ new_obj.db_processor = old_obj.db_processor
+ if 'ram' in class_dict:
+ res = class_dict['ram'](old_obj, trans_dict)
+ new_obj.db_ram = res
+ elif hasattr(old_obj, 'db_ram') and old_obj.db_ram is not None:
+ new_obj.db_ram = old_obj.db_ram
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_os(self):
+ return self._db_os
+ def __set_db_os(self, os):
+ self._db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self._db_os = os
+ def db_change_os(self, os):
+ self._db_os = os
+ def db_delete_os(self, os):
+ self._db_os = None
+
+ def __get_db_architecture(self):
+ return self._db_architecture
+ def __set_db_architecture(self, architecture):
+ self._db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self._db_architecture = None
+
+ def __get_db_processor(self):
+ return self._db_processor
+ def __set_db_processor(self, processor):
+ self._db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self._db_processor = processor
+ def db_change_processor(self, processor):
+ self._db_processor = processor
+ def db_delete_processor(self, processor):
+ self._db_processor = None
+
+ def __get_db_ram(self):
+ return self._db_ram
+ def __set_db_ram(self, ram):
+ self._db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self._db_ram = ram
+ def db_change_ram(self, ram):
+ self._db_ram = ram
+ def db_delete_ram(self, ram):
+ self._db_ram = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, data=None, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAdd.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAdd()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOther.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOther(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOther()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self._db_id = id
+ self._db_x = x
+ self._db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLocation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation(id=self._db_id,
+ x=self._db_x,
+ y=self._db_y)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLocation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'x' in class_dict:
+ res = class_dict['x'](old_obj, trans_dict)
+ new_obj.db_x = res
+ elif hasattr(old_obj, 'db_x') and old_obj.db_x is not None:
+ new_obj.db_x = old_obj.db_x
+ if 'y' in class_dict:
+ res = class_dict['y'](old_obj, trans_dict)
+ new_obj.db_y = res
+ elif hasattr(old_obj, 'db_y') and old_obj.db_y is not None:
+ new_obj.db_y = old_obj.db_y
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_x(self):
+ return self._db_x
+ def __set_db_x(self, x):
+ self._db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self._db_x = x
+ def db_change_x(self, x):
+ self._db_x = x
+ def db_delete_x(self, x):
+ self._db_x = None
+
+ def __get_db_y(self):
+ return self._db_y
+ def __set_db_y(self, y):
+ self._db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self._db_y = y
+ def db_change_y(self, y):
+ self._db_y = y
+ def db_delete_y(self, y):
+ self._db_y = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self._db_type = type
+ self._db_val = val
+ self._db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBParameter.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name,
+ type=self._db_type,
+ val=self._db_val,
+ alias=self._db_alias)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBParameter()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'val' in class_dict:
+ res = class_dict['val'](old_obj, trans_dict)
+ new_obj.db_val = res
+ elif hasattr(old_obj, 'db_val') and old_obj.db_val is not None:
+ new_obj.db_val = old_obj.db_val
+ if 'alias' in class_dict:
+ res = class_dict['alias'](old_obj, trans_dict)
+ new_obj.db_alias = res
+ elif hasattr(old_obj, 'db_alias') and old_obj.db_alias is not None:
+ new_obj.db_alias = old_obj.db_alias
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_val(self):
+ return self._db_val
+ def __set_db_val(self, val):
+ self._db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self._db_val = val
+ def db_change_val(self, val):
+ self._db_val = val
+ def db_delete_val(self, val):
+ self._db_val = None
+
+ def __get_db_alias(self):
+ return self._db_alias
+ def __set_db_alias(self, alias):
+ self._db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self._db_alias = alias
+ def db_change_alias(self, alias):
+ self._db_alias = alias
+ def db_delete_alias(self, alias):
+ self._db_alias = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBPluginData(object):
+
+ vtType = 'plugin_data'
+
+ def __init__(self, id=None, data=None):
+ self._db_id = id
+ self._db_data = data
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPluginData.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPluginData(id=self._db_id,
+ data=self._db_data)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPluginData()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ new_obj.db_data = old_obj.db_data
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ self._db_data = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self.db_deleted_parameters = []
+ self.db_parameters_id_index = {}
+ if parameters is None:
+ self._db_parameters = []
+ else:
+ self._db_parameters = parameters
+ for v in self._db_parameters:
+ self.db_parameters_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name)
+ if self._db_parameters is None:
+ cp._db_parameters = []
+ else:
+ cp._db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_parameters_id_index = dict((v.db_id, v) for v in cp._db_parameters)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBFunction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'parameters' in class_dict:
+ res = class_dict['parameters'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_parameter(obj)
+ elif hasattr(old_obj, 'db_parameters') and old_obj.db_parameters is not None:
+ for obj in old_obj.db_parameters:
+ new_obj.db_add_parameter(DBParameter.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_parameters') and hasattr(new_obj, 'db_deleted_parameters'):
+ for obj in old_obj.db_deleted_parameters:
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_parameters.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_parameters)
+ if remove:
+ self.db_deleted_parameters = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_parameters(self):
+ return self._db_parameters
+ def __set_db_parameters(self, parameters):
+ self._db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self._db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ self._db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ if not self._db_parameters[i].is_new:
+ self.db_deleted_parameters.append(self._db_parameters[i])
+ del self._db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter.db_id]
+ def db_get_parameter(self, key):
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == key:
+ return self._db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return key in self.db_parameters_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, internal_version=None, tag=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_internal_version = internal_version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ internal_version=self._db_internal_version,
+ tag=self._db_tag)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAbstraction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'internal_version' in class_dict:
+ res = class_dict['internal_version'](old_obj, trans_dict)
+ new_obj.db_internal_version = res
+ elif hasattr(old_obj, 'db_internal_version') and old_obj.db_internal_version is not None:
+ new_obj.db_internal_version = old_obj.db_internal_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_internal_version(self):
+ return self._db_internal_version
+ def __set_db_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ self.is_dirty = True
+ db_internal_version = property(__get_db_internal_version, __set_db_internal_version)
+ def db_add_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_change_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_delete_internal_version(self, internal_version):
+ self._db_internal_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, modules=None, id=None, entity_type=None, name=None, version=None, last_modified=None, connections=None, annotations=None, plugin_datas=None, others=None, vistrail_id=None):
+ self.db_deleted_modules = []
+ self.db_modules_id_index = {}
+ if modules is None:
+ self._db_modules = []
+ else:
+ self._db_modules = modules
+ for v in self._db_modules:
+ self.db_modules_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_name = name
+ self._db_version = version
+ self._db_last_modified = last_modified
+ self.db_deleted_connections = []
+ self.db_connections_id_index = {}
+ if connections is None:
+ self._db_connections = []
+ else:
+ self._db_connections = connections
+ for v in self._db_connections:
+ self.db_connections_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_plugin_datas = []
+ self.db_plugin_datas_id_index = {}
+ if plugin_datas is None:
+ self._db_plugin_datas = []
+ else:
+ self._db_plugin_datas = plugin_datas
+ for v in self._db_plugin_datas:
+ self.db_plugin_datas_id_index[v.db_id] = v
+ self.db_deleted_others = []
+ self.db_others_id_index = {}
+ if others is None:
+ self._db_others = []
+ else:
+ self._db_others = others
+ for v in self._db_others:
+ self.db_others_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow(id=self._db_id,
+ entity_type=self._db_entity_type,
+ name=self._db_name,
+ version=self._db_version,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_modules is None:
+ cp._db_modules = []
+ else:
+ cp._db_modules = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_modules]
+ if self._db_connections is None:
+ cp._db_connections = []
+ else:
+ cp._db_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_connections]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_plugin_datas is None:
+ cp._db_plugin_datas = []
+ else:
+ cp._db_plugin_datas = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_plugin_datas]
+ if self._db_others is None:
+ cp._db_others = []
+ else:
+ cp._db_others = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_others]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_modules_id_index = dict((v.db_id, v) for v in cp._db_modules)
+ cp.db_connections_id_index = dict((v.db_id, v) for v in cp._db_connections)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_plugin_datas_id_index = dict((v.db_id, v) for v in cp._db_plugin_datas)
+ cp.db_others_id_index = dict((v.db_id, v) for v in cp._db_others)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'modules' in class_dict:
+ res = class_dict['modules'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module(obj)
+ elif hasattr(old_obj, 'db_modules') and old_obj.db_modules is not None:
+ for obj in old_obj.db_modules:
+ if obj.vtType == 'module':
+ new_obj.db_add_module(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_module(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_module(DBGroup.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_modules') and hasattr(new_obj, 'db_deleted_modules'):
+ for obj in old_obj.db_deleted_modules:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'connections' in class_dict:
+ res = class_dict['connections'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_connection(obj)
+ elif hasattr(old_obj, 'db_connections') and old_obj.db_connections is not None:
+ for obj in old_obj.db_connections:
+ new_obj.db_add_connection(DBConnection.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_connections') and hasattr(new_obj, 'db_deleted_connections'):
+ for obj in old_obj.db_deleted_connections:
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_connections.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'plugin_datas' in class_dict:
+ res = class_dict['plugin_datas'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_plugin_data(obj)
+ elif hasattr(old_obj, 'db_plugin_datas') and old_obj.db_plugin_datas is not None:
+ for obj in old_obj.db_plugin_datas:
+ new_obj.db_add_plugin_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_plugin_datas') and hasattr(new_obj, 'db_deleted_plugin_datas'):
+ for obj in old_obj.db_deleted_plugin_datas:
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_plugin_datas.append(n_obj)
+ if 'others' in class_dict:
+ res = class_dict['others'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_other(obj)
+ elif hasattr(old_obj, 'db_others') and old_obj.db_others is not None:
+ for obj in old_obj.db_others:
+ new_obj.db_add_other(DBOther.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_others') and hasattr(new_obj, 'db_deleted_others'):
+ for obj in old_obj.db_deleted_others:
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_others.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_connections:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_connection(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_plugin_datas:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_plugin_data(child)
+ to_del = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_other(child)
+ to_del = []
+ for child in self.db_modules:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_connections)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_plugin_datas)
+ children.extend(self.db_deleted_others)
+ children.extend(self.db_deleted_modules)
+ if remove:
+ self.db_deleted_connections = []
+ self.db_deleted_annotations = []
+ self.db_deleted_plugin_datas = []
+ self.db_deleted_others = []
+ self.db_deleted_modules = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_connections:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_plugin_datas:
+ if child.has_changes():
+ return True
+ for child in self._db_others:
+ if child.has_changes():
+ return True
+ for child in self._db_modules:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_modules(self):
+ return self._db_modules
+ def __set_db_modules(self, modules):
+ self._db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self._db_modules
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ self._db_modules[i] = module
+ found = True
+ break
+ if not found:
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ if not self._db_modules[i].is_new:
+ self.db_deleted_modules.append(self._db_modules[i])
+ del self._db_modules[i]
+ break
+ del self.db_modules_id_index[module.db_id]
+ def db_get_module(self, key):
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == key:
+ return self._db_modules[i]
+ return None
+ def db_get_module_by_id(self, key):
+ return self.db_modules_id_index[key]
+ def db_has_module_with_id(self, key):
+ return key in self.db_modules_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_connections(self):
+ return self._db_connections
+ def __set_db_connections(self, connections):
+ self._db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self._db_connections
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ self._db_connections[i] = connection
+ found = True
+ break
+ if not found:
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ if not self._db_connections[i].is_new:
+ self.db_deleted_connections.append(self._db_connections[i])
+ del self._db_connections[i]
+ break
+ del self.db_connections_id_index[connection.db_id]
+ def db_get_connection(self, key):
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == key:
+ return self._db_connections[i]
+ return None
+ def db_get_connection_by_id(self, key):
+ return self.db_connections_id_index[key]
+ def db_has_connection_with_id(self, key):
+ return key in self.db_connections_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_plugin_datas(self):
+ return self._db_plugin_datas
+ def __set_db_plugin_datas(self, plugin_datas):
+ self._db_plugin_datas = plugin_datas
+ self.is_dirty = True
+ db_plugin_datas = property(__get_db_plugin_datas, __set_db_plugin_datas)
+ def db_get_plugin_datas(self):
+ return self._db_plugin_datas
+ def db_add_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_change_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ self._db_plugin_datas[i] = plugin_data
+ found = True
+ break
+ if not found:
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_delete_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ if not self._db_plugin_datas[i].is_new:
+ self.db_deleted_plugin_datas.append(self._db_plugin_datas[i])
+ del self._db_plugin_datas[i]
+ break
+ del self.db_plugin_datas_id_index[plugin_data.db_id]
+ def db_get_plugin_data(self, key):
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == key:
+ return self._db_plugin_datas[i]
+ return None
+ def db_get_plugin_data_by_id(self, key):
+ return self.db_plugin_datas_id_index[key]
+ def db_has_plugin_data_with_id(self, key):
+ return key in self.db_plugin_datas_id_index
+
+ def __get_db_others(self):
+ return self._db_others
+ def __set_db_others(self, others):
+ self._db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self._db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ self._db_others[i] = other
+ found = True
+ break
+ if not found:
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ if not self._db_others[i].is_new:
+ self.db_deleted_others.append(self._db_others[i])
+ del self._db_others[i]
+ break
+ del self.db_others_id_index[other.db_id]
+ def db_get_other(self, key):
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == key:
+ return self._db_others[i]
+ return None
+ def db_get_other_by_id(self, key):
+ return self.db_others_id_index[key]
+ def db_has_other_with_id(self, key):
+ return key in self.db_others_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAnnotation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, data=None, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_oldObjId = oldObjId
+ self._db_newObjId = newObjId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBChange.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange(id=self._db_id,
+ what=self._db_what,
+ oldObjId=self._db_oldObjId,
+ newObjId=self._db_newObjId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_oldObjId') and (self._db_what, self._db_oldObjId) in id_remap:
+ cp._db_oldObjId = id_remap[(self._db_what, self._db_oldObjId)]
+ if hasattr(self, 'db_newObjId') and (self._db_what, self._db_newObjId) in id_remap:
+ cp._db_newObjId = id_remap[(self._db_what, self._db_newObjId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBChange()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'oldObjId' in class_dict:
+ res = class_dict['oldObjId'](old_obj, trans_dict)
+ new_obj.db_oldObjId = res
+ elif hasattr(old_obj, 'db_oldObjId') and old_obj.db_oldObjId is not None:
+ new_obj.db_oldObjId = old_obj.db_oldObjId
+ if 'newObjId' in class_dict:
+ res = class_dict['newObjId'](old_obj, trans_dict)
+ new_obj.db_newObjId = res
+ elif hasattr(old_obj, 'db_newObjId') and old_obj.db_newObjId is not None:
+ new_obj.db_newObjId = old_obj.db_newObjId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_oldObjId(self):
+ return self._db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self._db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self._db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self._db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, id=None, user=None, ip=None, session=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, completed=None, name=None, module_execs=None):
+ self._db_id = id
+ self._db_user = user
+ self._db_ip = ip
+ self._db_session = session
+ self._db_vt_version = vt_version
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_parent_id = parent_id
+ self._db_parent_type = parent_type
+ self._db_parent_version = parent_version
+ self._db_completed = completed
+ self._db_name = name
+ self.db_deleted_module_execs = []
+ self.db_module_execs_id_index = {}
+ if module_execs is None:
+ self._db_module_execs = []
+ else:
+ self._db_module_execs = module_execs
+ for v in self._db_module_execs:
+ self.db_module_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflowExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec(id=self._db_id,
+ user=self._db_user,
+ ip=self._db_ip,
+ session=self._db_session,
+ vt_version=self._db_vt_version,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ parent_id=self._db_parent_id,
+ parent_type=self._db_parent_type,
+ parent_version=self._db_parent_version,
+ completed=self._db_completed,
+ name=self._db_name)
+ if self._db_module_execs is None:
+ cp._db_module_execs = []
+ else:
+ cp._db_module_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_module_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_module_execs_id_index = dict((v.db_id, v) for v in cp._db_module_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflowExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'ip' in class_dict:
+ res = class_dict['ip'](old_obj, trans_dict)
+ new_obj.db_ip = res
+ elif hasattr(old_obj, 'db_ip') and old_obj.db_ip is not None:
+ new_obj.db_ip = old_obj.db_ip
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'vt_version' in class_dict:
+ res = class_dict['vt_version'](old_obj, trans_dict)
+ new_obj.db_vt_version = res
+ elif hasattr(old_obj, 'db_vt_version') and old_obj.db_vt_version is not None:
+ new_obj.db_vt_version = old_obj.db_vt_version
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'parent_id' in class_dict:
+ res = class_dict['parent_id'](old_obj, trans_dict)
+ new_obj.db_parent_id = res
+ elif hasattr(old_obj, 'db_parent_id') and old_obj.db_parent_id is not None:
+ new_obj.db_parent_id = old_obj.db_parent_id
+ if 'parent_type' in class_dict:
+ res = class_dict['parent_type'](old_obj, trans_dict)
+ new_obj.db_parent_type = res
+ elif hasattr(old_obj, 'db_parent_type') and old_obj.db_parent_type is not None:
+ new_obj.db_parent_type = old_obj.db_parent_type
+ if 'parent_version' in class_dict:
+ res = class_dict['parent_version'](old_obj, trans_dict)
+ new_obj.db_parent_version = res
+ elif hasattr(old_obj, 'db_parent_version') and old_obj.db_parent_version is not None:
+ new_obj.db_parent_version = old_obj.db_parent_version
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'module_execs' in class_dict:
+ res = class_dict['module_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module_exec(obj)
+ elif hasattr(old_obj, 'db_module_execs') and old_obj.db_module_execs is not None:
+ for obj in old_obj.db_module_execs:
+ new_obj.db_add_module_exec(DBModuleExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_module_execs') and hasattr(new_obj, 'db_deleted_module_execs'):
+ for obj in old_obj.db_deleted_module_execs:
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_module_execs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_execs)
+ if remove:
+ self.db_deleted_module_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_module_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_ip(self):
+ return self._db_ip
+ def __set_db_ip(self, ip):
+ self._db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self._db_ip = ip
+ def db_change_ip(self, ip):
+ self._db_ip = ip
+ def db_delete_ip(self, ip):
+ self._db_ip = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_vt_version(self):
+ return self._db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self._db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self._db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self._db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self._db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self._db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self._db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self._db_parent_version = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_module_execs(self):
+ return self._db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self._db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self._db_module_execs
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self._db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == module_exec.db_id:
+ self._db_module_execs[i] = module_exec
+ found = True
+ break
+ if not found:
+ self._db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == module_exec.db_id:
+ if not self._db_module_execs[i].is_new:
+ self.db_deleted_module_execs.append(self._db_module_execs[i])
+ del self._db_module_execs[i]
+ break
+ del self.db_module_execs_id_index[module_exec.db_id]
+ def db_get_module_exec(self, key):
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == key:
+ return self._db_module_execs[i]
+ return None
+ def db_get_module_exec_by_id(self, key):
+ return self.db_module_execs_id_index[key]
+ def db_has_module_exec_with_id(self, key):
+ return key in self.db_module_execs_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self._db_id = id
+ self.db_deleted_ports = []
+ self.db_ports_id_index = {}
+ self.db_ports_type_index = {}
+ if ports is None:
+ self._db_ports = []
+ else:
+ self._db_ports = ports
+ for v in self._db_ports:
+ self.db_ports_id_index[v.db_id] = v
+ self.db_ports_type_index[v.db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBConnection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection(id=self._db_id)
+ if self._db_ports is None:
+ cp._db_ports = []
+ else:
+ cp._db_ports = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ports]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_ports_id_index = dict((v.db_id, v) for v in cp._db_ports)
+ cp.db_ports_type_index = dict((v.db_type, v) for v in cp._db_ports)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBConnection()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ports' in class_dict:
+ res = class_dict['ports'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_port(obj)
+ elif hasattr(old_obj, 'db_ports') and old_obj.db_ports is not None:
+ for obj in old_obj.db_ports:
+ new_obj.db_add_port(DBPort.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_ports') and hasattr(new_obj, 'db_deleted_ports'):
+ for obj in old_obj.db_deleted_ports:
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_ports.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_ports)
+ if remove:
+ self.db_deleted_ports = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ports(self):
+ return self._db_ports
+ def __set_db_ports(self, ports):
+ self._db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self._db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ self._db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ if not self._db_ports[i].is_new:
+ self.db_deleted_ports.append(self._db_ports[i])
+ del self._db_ports[i]
+ break
+ del self.db_ports_id_index[port.db_id]
+ del self.db_ports_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == key:
+ return self._db_ports[i]
+ return None
+ def db_get_port_by_id(self, key):
+ return self.db_ports_id_index[key]
+ def db_has_port_with_id(self, key):
+ return key in self.db_ports_id_index
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return key in self.db_ports_type_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, operations=None, id=None, prevId=None, date=None, session=None, user=None, prune=None, annotations=None):
+ self.db_deleted_operations = []
+ self.db_operations_id_index = {}
+ if operations is None:
+ self._db_operations = []
+ else:
+ self._db_operations = operations
+ for v in self._db_operations:
+ self.db_operations_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_prevId = prevId
+ self._db_date = date
+ self._db_session = session
+ self._db_user = user
+ self._db_prune = prune
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction(id=self._db_id,
+ prevId=self._db_prevId,
+ date=self._db_date,
+ session=self._db_session,
+ user=self._db_user,
+ prune=self._db_prune)
+ if self._db_operations is None:
+ cp._db_operations = []
+ else:
+ cp._db_operations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_operations]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prevId') and ('action', self._db_prevId) in id_remap:
+ cp._db_prevId = id_remap[('action', self._db_prevId)]
+
+ # recreate indices and set flags
+ cp.db_operations_id_index = dict((v.db_id, v) for v in cp._db_operations)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'operations' in class_dict:
+ res = class_dict['operations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_operation(obj)
+ elif hasattr(old_obj, 'db_operations') and old_obj.db_operations is not None:
+ for obj in old_obj.db_operations:
+ if obj.vtType == 'add':
+ new_obj.db_add_operation(DBAdd.update_version(obj, trans_dict))
+ elif obj.vtType == 'delete':
+ new_obj.db_add_operation(DBDelete.update_version(obj, trans_dict))
+ elif obj.vtType == 'change':
+ new_obj.db_add_operation(DBChange.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_operations') and hasattr(new_obj, 'db_deleted_operations'):
+ for obj in old_obj.db_deleted_operations:
+ if obj.vtType == 'add':
+ n_obj = DBAdd.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'delete':
+ n_obj = DBDelete.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'change':
+ n_obj = DBChange.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'prevId' in class_dict:
+ res = class_dict['prevId'](old_obj, trans_dict)
+ new_obj.db_prevId = res
+ elif hasattr(old_obj, 'db_prevId') and old_obj.db_prevId is not None:
+ new_obj.db_prevId = old_obj.db_prevId
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'prune' in class_dict:
+ res = class_dict['prune'](old_obj, trans_dict)
+ new_obj.db_prune = res
+ elif hasattr(old_obj, 'db_prune') and old_obj.db_prune is not None:
+ new_obj.db_prune = old_obj.db_prune
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_operations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_operations)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_operations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_operations(self):
+ return self._db_operations
+ def __set_db_operations(self, operations):
+ self._db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self._db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ self._db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ if not self._db_operations[i].is_new:
+ self.db_deleted_operations.append(self._db_operations[i])
+ del self._db_operations[i]
+ break
+ del self.db_operations_id_index[operation.db_id]
+ def db_get_operation(self, key):
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == key:
+ return self._db_operations[i]
+ return None
+ def db_get_operation_by_id(self, key):
+ return self.db_operations_id_index[key]
+ def db_has_operation_with_id(self, key):
+ return key in self.db_operations_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_prevId(self):
+ return self._db_prevId
+ def __set_db_prevId(self, prevId):
+ self._db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self._db_prevId = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_prune(self):
+ return self._db_prune
+ def __set_db_prune(self, prune):
+ self._db_prune = prune
+ self.is_dirty = True
+ db_prune = property(__get_db_prune, __set_db_prune)
+ def db_add_prune(self, prune):
+ self._db_prune = prune
+ def db_change_prune(self, prune):
+ self._db_prune = prune
+ def db_delete_prune(self, prune):
+ self._db_prune = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBDelete.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBDelete()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, actions=None, tags=None, annotations=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self._db_actions = []
+ else:
+ self._db_actions = actions
+ for v in self._db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self._db_tags = []
+ else:
+ self._db_tags = tags
+ for v in self._db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_actions is None:
+ cp._db_actions = []
+ else:
+ cp._db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actions]
+ if self._db_tags is None:
+ cp._db_tags = []
+ else:
+ cp._db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_tags]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_actions_id_index = dict((v.db_id, v) for v in cp._db_actions)
+ cp.db_tags_id_index = dict((v.db_id, v) for v in cp._db_tags)
+ cp.db_tags_name_index = dict((v.db_name, v) for v in cp._db_tags)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'actions' in class_dict:
+ res = class_dict['actions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_action(obj)
+ elif hasattr(old_obj, 'db_actions') and old_obj.db_actions is not None:
+ for obj in old_obj.db_actions:
+ new_obj.db_add_action(DBAction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actions') and hasattr(new_obj, 'db_deleted_actions'):
+ for obj in old_obj.db_deleted_actions:
+ n_obj = DBAction.update_version(obj, trans_dict)
+ new_obj.db_deleted_actions.append(n_obj)
+ if 'tags' in class_dict:
+ res = class_dict['tags'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_tag(obj)
+ elif hasattr(old_obj, 'db_tags') and old_obj.db_tags is not None:
+ for obj in old_obj.db_tags:
+ new_obj.db_add_tag(DBTag.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_tags') and hasattr(new_obj, 'db_deleted_tags'):
+ for obj in old_obj.db_deleted_tags:
+ n_obj = DBTag.update_version(obj, trans_dict)
+ new_obj.db_deleted_tags.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_actions:
+ if child.has_changes():
+ return True
+ for child in self._db_tags:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_actions(self):
+ return self._db_actions
+ def __set_db_actions(self, actions):
+ self._db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self._db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ self._db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ if not self._db_actions[i].is_new:
+ self.db_deleted_actions.append(self._db_actions[i])
+ del self._db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == key:
+ return self._db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return key in self.db_actions_id_index
+
+ def __get_db_tags(self):
+ return self._db_tags
+ def __set_db_tags(self, tags):
+ self._db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self._db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ self._db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ if not self._db_tags[i].is_new:
+ self.db_deleted_tags.append(self._db_tags[i])
+ del self._db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == key:
+ return self._db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return key in self.db_tags_id_index
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return key in self.db_tags_name_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, module_name=None, completed=None, error=None, abstraction_id=None, abstraction_version=None, machine_id=None, annotations=None):
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_module_name = module_name
+ self._db_completed = completed
+ self._db_error = error
+ self._db_abstraction_id = abstraction_id
+ self._db_abstraction_version = abstraction_version
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ module_name=self._db_module_name,
+ completed=self._db_completed,
+ error=self._db_error,
+ abstraction_id=self._db_abstraction_id,
+ abstraction_version=self._db_abstraction_version,
+ machine_id=self._db_machine_id)
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'module_name' in class_dict:
+ res = class_dict['module_name'](old_obj, trans_dict)
+ new_obj.db_module_name = res
+ elif hasattr(old_obj, 'db_module_name') and old_obj.db_module_name is not None:
+ new_obj.db_module_name = old_obj.db_module_name
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'abstraction_id' in class_dict:
+ res = class_dict['abstraction_id'](old_obj, trans_dict)
+ new_obj.db_abstraction_id = res
+ elif hasattr(old_obj, 'db_abstraction_id') and old_obj.db_abstraction_id is not None:
+ new_obj.db_abstraction_id = old_obj.db_abstraction_id
+ if 'abstraction_version' in class_dict:
+ res = class_dict['abstraction_version'](old_obj, trans_dict)
+ new_obj.db_abstraction_version = res
+ elif hasattr(old_obj, 'db_abstraction_version') and old_obj.db_abstraction_version is not None:
+ new_obj.db_abstraction_version = old_obj.db_abstraction_version
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_module_name(self):
+ return self._db_module_name
+ def __set_db_module_name(self, module_name):
+ self._db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self._db_module_name = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_abstraction_id(self):
+ return self._db_abstraction_id
+ def __set_db_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ self.is_dirty = True
+ db_abstraction_id = property(__get_db_abstraction_id, __set_db_abstraction_id)
+ def db_add_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_change_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_delete_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = None
+
+ def __get_db_abstraction_version(self):
+ return self._db_abstraction_version
+ def __set_db_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ self.is_dirty = True
+ db_abstraction_version = property(__get_db_abstraction_version, __set_db_abstraction_version)
+ def db_add_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ def db_change_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ def db_delete_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
diff --git a/vistrails/db/versions/v0_9_4/domain/id_scope.py b/vistrails/db/versions/v0_9_4/domain/id_scope.py
new file mode 100644
index 0000000..0e07f02
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/domain/id_scope.py
@@ -0,0 +1,85 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L, remap=None):
+ self.ids = {}
+ self.beginId = beginId
+ if remap is None:
+ self.remap = {}
+ else:
+ self.remap = remap
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ cp.remap = copy.copy(self.remap)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ except KeyError:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ if self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+ except KeyError:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v0_9_4/domain/log.py b/vistrails/db/versions/v0_9_4/domain/log.py
new file mode 100644
index 0000000..0328b80
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/domain/log.py
@@ -0,0 +1,69 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBLog as _DBLog
+from auto_gen import DBAbstraction, DBModule, DBGroup
+from id_scope import IdScope
+
+import copy
+
+class DBLog(_DBLog):
+
+ def __init__(self, *args, **kwargs):
+ _DBLog.__init__(self, *args, **kwargs)
+ self.id_scope = IdScope(1,
+ {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBLog.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBLog
+ cp.id_scope = copy.copy(self.id_scope)
+
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ new_obj = _DBLog.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
diff --git a/vistrails/db/versions/v0_9_4/domain/vistrail.py b/vistrails/db/versions/v0_9_4/domain/vistrail.py
new file mode 100644
index 0000000..eaac9d4
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/domain/vistrail.py
@@ -0,0 +1,127 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from auto_gen import DBVistrail as _DBVistrail
+from auto_gen import DBAdd, DBChange, DBDelete, DBAbstraction, DBGroup, \
+ DBModule
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAdd.vtType: 'operation',
+ DBChange.vtType: 'operation',
+ DBDelete.vtType: 'operation',
+ DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ self.idScope.setBeginId('action', 1)
+ self.db_objects = {}
+
+ # keep a reference to the current logging information here
+ self.log_filename = None
+ self.log = None
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBVistrail.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBVistrail
+
+ cp.idScope = copy.copy(self.idScope)
+ cp.db_objects = copy.copy(self.db_objects)
+ cp.log_filename = self.log_filename
+ if self.log is not None:
+ cp.log = copy.copy(self.log)
+ else:
+ cp.log = None
+
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ new_obj = _DBVistrail.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ if hasattr(old_obj, 'log_filename'):
+ new_obj.log_filename = old_obj.log_filename
+ if hasattr(old_obj, 'log'):
+ new_obj.log = old_obj.log
+ return new_obj
+
+ def update_id_scope(self):
+ def getOldObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_oldObjId
+ return operation.db_objectId
+
+ def getNewObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_newObjId
+ return operation.db_objectId
+
+ for action in self.db_actions:
+ self.idScope.updateBeginId('action', action.db_id+1)
+ if action.db_session is not None:
+ self.idScope.updateBeginId('session', action.db_session + 1)
+ for operation in action.db_operations:
+ self.idScope.updateBeginId('operation', operation.db_id+1)
+ if operation.vtType == 'add' or operation.vtType == 'change':
+ # update ids of data
+ self.idScope.updateBeginId(operation.db_what,
+ getNewObjId(operation)+1)
+ if operation.db_data is None:
+ if operation.vtType == 'change':
+ operation.db_objectId = operation.db_oldObjId
+ self.db_add_object(operation.db_data)
+ for annotation in action.db_annotations:
+ self.idScope.updateBeginId('annotation', annotation.db_id+1)
+
+ def db_add_object(self, obj):
+ self.db_objects[(obj.vtType, obj.db_id)] = obj
+
+ def db_get_object(self, type, id):
+ return self.db_objects.get((type, id), None)
+
+ def db_update_object(self, obj, **kwargs):
+ # want to swap out old object with a new version
+ # need this for updating aliases...
+ # hack it using setattr...
+ real_obj = self.db_objects[(obj.vtType, obj.db_id)]
+ for (k, v) in kwargs.iteritems():
+ if hasattr(real_obj, k):
+ setattr(real_obj, k, v)
diff --git a/vistrails/db/versions/v0_9_4/domain/workflow.py b/vistrails/db/versions/v0_9_4/domain/workflow.py
new file mode 100644
index 0000000..af484e6
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/domain/workflow.py
@@ -0,0 +1,172 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from auto_gen import DBAbstraction, DBModule, DBGroup
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1,
+ {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.build_index()
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ new_obj = _DBWorkflow.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ new_obj.build_index()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
+
+ _vtTypeMap = {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType}
+
+ def build_index(self):
+ g = self._vtTypeMap.get
+ self.objects = dict(((g(o.vtType, o.vtType), o._db_id), o)
+ for (o,_,_) in self.db_children())
+
+ def add_to_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ self.objects[(obj_type, object.getPrimaryKey())] = object
+
+ def delete_from_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ del self.objects[(obj_type, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_print_objects(self):
+ for k,v in self.objects.iteritems():
+ print '%s: %s' % (k, v)
+
+ def db_has_object(self, type, id):
+ return (type, id) in self.objects
+
+ def db_get_object(self, type, id):
+ return self.objects[(type, id)]
+
+ def db_add_object(self, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if object.vtType == DBAbstraction.vtType or \
+ object.vtType == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ else:
+ obj_type = object.vtType
+ funname = 'db_add_' + obj_type
+ obj_copy = copy.copy(object)
+ getattr(parent_obj, funname)(obj_copy)
+ self.add_to_index(obj_copy)
+
+ def db_change_object(self, old_id, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+
+ self.db_delete_object(old_id, object.vtType, None, None, parent_obj)
+ self.db_add_object(object, None, None, parent_obj)
+
+ def db_delete_object(self, obj_id, obj_type, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if obj_type == DBAbstraction.vtType or obj_type == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ funname = 'db_get_' + obj_type
+ if hasattr(parent_obj, funname):
+ object = getattr(parent_obj, funname)(obj_id)
+ else:
+ attr_name = 'db_' + obj_type
+ object = getattr(parent_obj, attr_name)
+ funname = 'db_delete_' + obj_type
+ getattr(parent_obj, funname)(object)
+ self.delete_from_index(object)
diff --git a/vistrails/db/versions/v0_9_4/persistence/__init__.py b/vistrails/db/versions/v0_9_4/persistence/__init__.py
new file mode 100644
index 0000000..d0234ba
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/persistence/__init__.py
@@ -0,0 +1,204 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+from vistrails.core.system import get_elementtree_library
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_9_4 import version as my_version
+from vistrails.db.versions.v0_9_4.domain import DBVistrail, DBWorkflow, DBLog, \
+ DBAbstraction, DBGroup
+
+ElementTree = get_elementtree_library()
+
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def parse_xml_file(self, filename):
+ return ElementTree.parse(filename)
+
+ def write_xml_file(self, filename, tree):
+ tree.write(filename)
+
+ def read_xml_object(self, vtType, node):
+ return self['xml'][vtType].fromXML(node)
+
+ def write_xml_object(self, obj, node=None):
+ res_node = self['xml'][obj.vtType].toXML(obj, node)
+ return res_node
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ """open_from_xml(filename) -> DBVistrail"""
+ if tree is None:
+ tree = self.parse_xml_file(filename)
+ vistrail = self.read_xml_object(vtType, tree.getroot())
+ return vistrail
+
+ def save_to_xml(self, obj, filename, tags, version=None):
+ """save_to_xml(obj : object, filename: str, tags: dict,
+ version: str) -> None
+
+ """
+ root = self.write_xml_object(obj)
+ if version is None:
+ version = my_version
+ root.set('version', version)
+ for k, v in tags.iteritems():
+ root.set(k, v)
+ tree = ElementTree.ElementTree(root)
+ self.write_xml_file(filename, tree)
+
+ def open_from_db(self, db_connection, vtType, id, lock=False):
+ all_objects = {}
+ global_props = {'id': id}
+ # print global_props
+ res_objects = self['sql'][vtType].get_sql_columns(db_connection,
+ global_props,
+ lock)
+
+ if len(res_objects) > 1:
+ raise VistrailsDBException("More than object of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+ elif len(res_objects) <= 0:
+ raise VistrailsDBException("No objects of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+
+ all_objects.update(res_objects)
+ res = res_objects.values()[0]
+ del global_props['id']
+
+ for dao in self['sql'].itervalues():
+ if (dao == self['sql'][DBVistrail.vtType] or
+ # dao == self['sql'][DBWorkflow.vtType] or
+ dao == self['sql'][DBLog.vtType] or
+ dao == self['sql'][DBAbstraction.vtType]):
+ continue
+ current_objs = dao.get_sql_columns(db_connection, global_props,
+ lock)
+ if dao == self['sql'][DBWorkflow.vtType]:
+ for key, obj in current_objs.iteritems():
+ if key[0] == vtType and key[1] == id:
+ continue
+ elif key[0] == DBWorkflow.vtType:
+ res_obj = self.open_from_db(db_connection, key[0],
+ key[1], lock)
+ res_dict = {}
+ res_dict[(res_obj.db_id, res_obj.vtType)] = res_obj
+ all_objects.update(res_dict)
+ else:
+ all_objects.update(current_objs)
+
+ for key, obj in all_objects.iteritems():
+ if key[0] == vtType and key[1] == id:
+ continue
+ self['sql'][obj.vtType].from_sql_fast(obj, all_objects)
+ for obj in all_objects.itervalues():
+ obj.is_dirty = False
+ obj.is_new = False
+ return res
+
+ def save_to_db(self, db_connection, obj, do_copy=False, global_props=None):
+ if do_copy and obj.db_id is not None:
+ obj.db_id = None
+
+ children = obj.db_children() # forSQL=True)
+ children.reverse()
+ if global_props is None:
+ global_props = {'entity_type': obj.vtType}
+ # print 'global_props:', global_props
+
+ # assumes not deleting entire thing
+ (child, _, _) = children[0]
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ global_props = {'entity_id': child.db_id,
+ 'entity_type': child.vtType}
+
+ if not do_copy:
+ for (child, _, _) in children:
+ for c in child.db_deleted_children(True):
+ self['sql'][c.vtType].delete_sql_column(db_connection,
+ c,
+ global_props)
+
+ (child, _, _) = children.pop(0)
+ child.is_dirty = False
+ child.is_new = False
+ for (child, _, _) in children:
+ # print "child:", child.vtType, child.db_id
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ # print '*** entity_type:', global_props['entity_type']
+ self.save_to_db(db_connection, child.db_workflow,
+ do_copy,
+ {'entity_id': global_props['entity_id'],
+ 'entity_type': \
+ global_props['entity_type']}
+ )
+
+ child.is_dirty = False
+ child.is_new = False
+
+ def serialize(self, object):
+ root = self.write_xml_object(object)
+ return ElementTree.tostring(root)
+
+ def unserialize(self, str, obj_type):
+ def set_dirty(obj):
+ for child, _, _ in obj.db_children():
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ set_dirty(child.db_workflow)
+ child.is_dirty = True
+ child.is_new = True
+ try:
+ root = ElementTree.fromstring(str)
+ obj = self.read_xml_object(obj_type, root)
+ set_dirty(obj)
+ return obj
+ except SyntaxError, e:
+ msg = "Invalid VisTrails serialized object %s" % str
+ raise VistrailsDBException(msg)
+ return None
diff --git a/vistrails/db/versions/v0_9_4/persistence/sql/__init__.py b/vistrails/db/versions/v0_9_4/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_9_4/persistence/sql/auto_gen.py b/vistrails/db/versions/v0_9_4/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..96b999b
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/persistence/sql/auto_gen.py
@@ -0,0 +1,2712 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v0_9_4.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port_spec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(22)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[4], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[5], 'long', 'int')
+ entity_type = self.convertFromDB(row[6], 'str', 'char(16)')
+ parent = self.convertFromDB(row[7], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ spec=spec,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_entity_id = entity_id
+ portSpec.db_entity_type = entity_type
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(22)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ module.db_parentType = parentType
+ module.db_entity_id = entity_id
+ module.db_entity_type = entity_type
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'tag'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[2], 'long', 'int')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_vistrail = vistrail
+ tag.db_entity_id = entity_id
+ tag.db_entity_type = entity_type
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ spec = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec,
+ id=id)
+ port.db_parentType = parentType
+ port.db_entity_id = entity_id
+ port.db_entity_type = entity_type
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'spec', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_spec') and obj.db_spec is not None:
+ columnMap['spec'] = \
+ self.convertToDB(obj.db_spec, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ group = DBGroup(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ group.db_parentType = parentType
+ group.db_entity_id = entity_id
+ group.db_entity_type = entity_type
+ group.db_parent = parent
+ group.is_dirty = False
+ res[('group', id)] = group
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_workflow is not None:
+ child = obj.db_workflow
+ child.db_parent = obj.db_id
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'log_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ log = DBLog(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ log.is_dirty = False
+ res[('log', id)] = log
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_workflow_execs:
+ child.db_log = obj.db_id
+ for child in obj.db_machines:
+ child.db_log = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'machine'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.db_entity_id = entity_id
+ machine.db_entity_type = entity_type
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'add_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_entity_id = entity_id
+ add.db_entity_type = entity_type
+ add.is_dirty = False
+ res[('add', id)] = add
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'other'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_entity_id = entity_id
+ other.db_entity_type = entity_type
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'location'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_entity_id = entity_id
+ location.db_entity_type = entity_type
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'parameter'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_entity_id = entity_id
+ parameter.db_entity_type = entity_type
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPluginDataSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'plugin_data'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ data = self.convertFromDB(row[1], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ plugin_data = DBPluginData(data=data,
+ id=id)
+ plugin_data.db_parentType = parentType
+ plugin_data.db_entity_id = entity_id
+ plugin_data.db_entity_type = entity_type
+ plugin_data.db_parent = parent
+ plugin_data.is_dirty = False
+ res[('plugin_data', id)] = plugin_data
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_plugin_data(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_data') and obj.db_data is not None:
+ columnMap['data'] = \
+ self.convertToDB(obj.db_data, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'function'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_entity_id = entity_id
+ function.db_entity_type = entity_type
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'abstraction'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ internal_version = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[7], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[8], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[9], 'long', 'int')
+ entity_type = self.convertFromDB(row[10], 'str', 'char(16)')
+ parent = self.convertFromDB(row[11], 'long', 'long')
+
+ abstraction = DBAbstraction(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ tag=tag,
+ id=id)
+ abstraction.db_parentType = parentType
+ abstraction.db_entity_id = entity_id
+ abstraction.db_entity_type = entity_type
+ abstraction.db_parent = parent
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_internal_version') and obj.db_internal_version is not None:
+ columnMap['internal_version'] = \
+ self.convertToDB(obj.db_internal_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id', 'parent_type']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_id = self.convertFromDB(row[1], 'long', 'int')
+ entity_type = self.convertFromDB(row[2], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'char(16)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[6], 'long', 'int')
+ parent = self.convertFromDB(row[7], 'long', 'int')
+ parentType = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ workflow = DBWorkflow(entity_type=entity_type,
+ name=name,
+ version=version,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ workflow.db_entity_id = entity_id
+ workflow.db_parent = parent
+ workflow.db_parentType = parentType
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('group', obj.db_parent) in all_objects:
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_workflow(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id', 'parent_type']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_connections:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_plugin_datas:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_modules:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'annotation'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_entity_id = entity_id
+ annotation.db_entity_type = entity_type
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'change_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_entity_id = entity_id
+ change.db_entity_type = entity_type
+ change.is_dirty = False
+ res[('change', id)] = change
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ vt_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[5], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[6], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[7], 'long', 'int')
+ parent_type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[9], 'long', 'int')
+ completed = self.convertFromDB(row[10], 'int', 'int')
+ name = self.convertFromDB(row[11], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[12], 'long', 'int')
+ entity_id = self.convertFromDB(row[13], 'long', 'int')
+ entity_type = self.convertFromDB(row[14], 'str', 'char(16)')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_entity_id = entity_id
+ workflow_exec.db_entity_type = entity_type
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_module_execs:
+ child.db_workflow_exec = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'connection_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(16)')
+ entity_id = self.convertFromDB(row[2], 'long', 'int')
+ entity_type = self.convertFromDB(row[3], 'str', 'char(16)')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_entity_id = entity_id
+ connection.db_entity_type = entity_type
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(16)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'action'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ prune = self.convertFromDB(row[5], 'int', 'int')
+ vistrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ id=id)
+ action.db_vistrail = vistrail
+ action.db_entity_id = entity_id
+ action.db_entity_type = entity_type
+ action.is_dirty = False
+ res[('action', id)] = action
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_prune') and obj.db_prune is not None:
+ columnMap['prune'] = \
+ self.convertToDB(obj.db_prune, 'int', 'int')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'delete_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_entity_id = entity_id
+ delete.db_entity_type = entity_type
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'vistrail'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_actions:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_tags:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'abstraction_id', 'abstraction_version', 'machine_id', 'wf_exec_id', 'entity_id', 'entity_type']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ module_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[6], 'int', 'int')
+ error = self.convertFromDB(row[7], 'str', 'varchar(1023)')
+ abstraction_id = self.convertFromDB(row[8], 'long', 'int')
+ abstraction_version = self.convertFromDB(row[9], 'long', 'int')
+ machine_id = self.convertFromDB(row[10], 'long', 'int')
+ workflow_exec = self.convertFromDB(row[11], 'long', 'int')
+ entity_id = self.convertFromDB(row[12], 'long', 'int')
+ entity_type = self.convertFromDB(row[13], 'str', 'char(16)')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ abstraction_id=abstraction_id,
+ abstraction_version=abstraction_version,
+ machine_id=machine_id,
+ id=id)
+ module_exec.db_workflow_exec = workflow_exec
+ module_exec.db_entity_id = entity_id
+ module_exec.db_entity_type = entity_type
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('workflow_exec', obj.db_workflow_exec) in all_objects:
+ p = all_objects[('workflow_exec', obj.db_workflow_exec)]
+ p.db_add_module_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'abstraction_id', 'abstraction_version', 'machine_id', 'wf_exec_id', 'entity_id', 'entity_type']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_abstraction_id') and obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if hasattr(obj, 'db_abstraction_version') and obj.db_abstraction_version is not None:
+ columnMap['abstraction_version'] = \
+ self.convertToDB(obj.db_abstraction_version, 'long', 'int')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_workflow_exec') and obj.db_workflow_exec is not None:
+ columnMap['wf_exec_id'] = \
+ self.convertToDB(obj.db_workflow_exec, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v0_9_4/persistence/sql/sql_dao.py b/vistrails/db/versions/v0_9_4/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..ad01dc5
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/persistence/sql/sql_dao.py
@@ -0,0 +1,183 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+from vistrails.db import VistrailsDBException
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ # return "'" + str(value).replace("'", "''") + "'"
+ return str(value)
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ return str(value)
+ elif type == 'int':
+ return str(value)
+ elif type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+
+ return None
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None,
+ forUpdate=False):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % \
+ (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ if forUpdate:
+ dbCommand += " FOR UPDATE"
+ dbCommand += ";"
+ return (dbCommand, tuple(values))
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ # valueStr = '%s, '.join(values)
+ valueStr = ''
+ if len(values) > 1:
+ valueStr = '%s,' * (len(values) - 1) + '%s'
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s);""" % \
+ (table, columnStr, valueStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ values = []
+ for column, value in columnMap.iteritems():
+# if value is None:
+# value = 'NULL'
+ setStr += '%s%s = %%s' % (comma, column)
+ comma = ', '
+ values.append(value)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """UPDATE %s SET %s WHERE %s;""" % \
+ (table, setStr, whereStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLDelete(self, table, whereMap):
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """DELETE FROM %s WHERE %s;""" % \
+ (table, whereStr)
+ return (dbCommand, tuple(values))
+
+ def executeSQL(self, db, cmd_tuple, isFetch):
+ dbCommand, values = cmd_tuple
+ # print 'db: %s' % dbCommand
+ # print 'values:', values
+ data = None
+ cursor = db.cursor()
+ try:
+ cursor.execute(dbCommand, values)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ except Exception, e:
+ raise VistrailsDBException('Command "%s" with values "%s" '
+ 'failed: %s' % (dbCommand, values, e))
+ finally:
+ cursor.close()
+ return data
+
+ def start_transaction(self, db):
+ db.begin()
+
+ def commit_transaction(self, db):
+ db.commit()
+
+ def rollback_transaction(self, db):
+ db.rollback()
diff --git a/vistrails/db/versions/v0_9_4/persistence/xml/__init__.py b/vistrails/db/versions/v0_9_4/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_9_4/persistence/xml/auto_gen.py b/vistrails/db/versions/v0_9_4/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..7f93e6c
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/persistence/xml/auto_gen.py
@@ -0,0 +1,1703 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from vistrails.core.system import get_elementtree_library
+
+from xml_dao import XMLDAO
+from vistrails.db.versions.v0_9_4.domain import *
+
+ElementTree = get_elementtree_library()
+
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'portSpec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('spec', None)
+ spec = self.convertFromStr(data, 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, node=None):
+ if node is None:
+ node = ElementTree.Element('portSpec')
+
+ # set attributes
+ node.set('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.set('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.set('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.set('spec',self.convertToStr(portSpec.db_spec, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'module':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, node=None):
+ if node is None:
+ node = ElementTree.Element('module')
+
+ # set attributes
+ node.set('id',self.convertToStr(module.db_id, 'long'))
+ node.set('cache',self.convertToStr(module.db_cache, 'int'))
+ node.set('name',self.convertToStr(module.db_name, 'str'))
+ node.set('namespace',self.convertToStr(module.db_namespace, 'str'))
+ node.set('package',self.convertToStr(module.db_package, 'str'))
+ node.set('version',self.convertToStr(module.db_version, 'str'))
+ node.set('tag',self.convertToStr(module.db_tag, 'str'))
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = module.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'tag':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, node=None):
+ if node is None:
+ node = ElementTree.Element('tag')
+
+ # set attributes
+ node.set('id',self.convertToStr(tag.db_id, 'long'))
+ node.set('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'port':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('moduleId', None)
+ moduleId = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ moduleName = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('spec', None)
+ spec = self.convertFromStr(data, 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ spec=spec)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, node=None):
+ if node is None:
+ node = ElementTree.Element('port')
+
+ # set attributes
+ node.set('id',self.convertToStr(port.db_id, 'long'))
+ node.set('type',self.convertToStr(port.db_type, 'str'))
+ node.set('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.set('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.set('name',self.convertToStr(port.db_name, 'str'))
+ node.set('spec',self.convertToStr(port.db_spec, 'str'))
+
+ return node
+
+class DBGroupXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'group':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ workflow = None
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'workflow':
+ _data = self.getDao('workflow').fromXML(child)
+ workflow = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroup(id=id,
+ workflow=workflow,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group, node=None):
+ if node is None:
+ node = ElementTree.Element('group')
+
+ # set attributes
+ node.set('id',self.convertToStr(group.db_id, 'long'))
+ node.set('cache',self.convertToStr(group.db_cache, 'int'))
+ node.set('name',self.convertToStr(group.db_name, 'str'))
+ node.set('namespace',self.convertToStr(group.db_namespace, 'str'))
+ node.set('package',self.convertToStr(group.db_package, 'str'))
+ node.set('version',self.convertToStr(group.db_version, 'str'))
+ node.set('tag',self.convertToStr(group.db_tag, 'str'))
+
+ # set elements
+ workflow = group.db_workflow
+ if workflow is not None:
+ childNode = ElementTree.SubElement(node, 'workflow')
+ self.getDao('workflow').toXML(workflow, childNode)
+ location = group.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = group.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = group.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'log':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ workflow_execs = []
+ machines = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'workflowExec':
+ _data = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs.append(_data)
+ elif child.tag == 'machine':
+ _data = self.getDao('machine').fromXML(child)
+ machines.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLog(id=id,
+ version=version,
+ name=name,
+ workflow_execs=workflow_execs,
+ machines=machines,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, node=None):
+ if node is None:
+ node = ElementTree.Element('log')
+
+ # set attributes
+ node.set('id',self.convertToStr(log.db_id, 'long'))
+ node.set('version',self.convertToStr(log.db_version, 'str'))
+ node.set('name',self.convertToStr(log.db_name, 'str'))
+ node.set('vistrail_id',self.convertToStr(log.db_vistrail_id, 'long'))
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs:
+ childNode = ElementTree.SubElement(node, 'workflow_exec')
+ self.getDao('workflow_exec').toXML(workflow_exec, childNode)
+ machines = log.db_machines
+ for machine in machines:
+ childNode = ElementTree.SubElement(node, 'machine')
+ self.getDao('machine').toXML(machine, childNode)
+
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'machine':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('os', None)
+ os = self.convertFromStr(data, 'str')
+ data = node.get('architecture', None)
+ architecture = self.convertFromStr(data, 'str')
+ data = node.get('processor', None)
+ processor = self.convertFromStr(data, 'str')
+ data = node.get('ram', None)
+ ram = self.convertFromStr(data, 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, node=None):
+ if node is None:
+ node = ElementTree.Element('machine')
+
+ # set attributes
+ node.set('id',self.convertToStr(machine.db_id, 'long'))
+ node.set('name',self.convertToStr(machine.db_name, 'str'))
+ node.set('os',self.convertToStr(machine.db_os, 'str'))
+ node.set('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.set('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.set('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'add':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAdd(data=data,
+ id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, node=None):
+ if node is None:
+ node = ElementTree.Element('add')
+
+ # set attributes
+ node.set('id',self.convertToStr(add.db_id, 'long'))
+ node.set('what',self.convertToStr(add.db_what, 'str'))
+ node.set('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # set elements
+ data = add.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'other':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'value':
+ _data = self.convertFromStr(child.text,'')
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, node=None):
+ if node is None:
+ node = ElementTree.Element('other')
+
+ # set attributes
+ node.set('id',self.convertToStr(other.db_id, 'long'))
+ node.set('key',self.convertToStr(other.db_key, 'str'))
+
+ # set elements
+
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'location':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('x', None)
+ x = self.convertFromStr(data, 'float')
+ data = node.get('y', None)
+ y = self.convertFromStr(data, 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, node=None):
+ if node is None:
+ node = ElementTree.Element('location')
+
+ # set attributes
+ node.set('id',self.convertToStr(location.db_id, 'long'))
+ node.set('x',self.convertToStr(location.db_x, 'float'))
+ node.set('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'parameter':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('val', None)
+ val = self.convertFromStr(data, 'str')
+ data = node.get('alias', None)
+ alias = self.convertFromStr(data, 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, node=None):
+ if node is None:
+ node = ElementTree.Element('parameter')
+
+ # set attributes
+ node.set('id',self.convertToStr(parameter.db_id, 'long'))
+ node.set('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.set('name',self.convertToStr(parameter.db_name, 'str'))
+ node.set('type',self.convertToStr(parameter.db_type, 'str'))
+ node.set('val',self.convertToStr(parameter.db_val, 'str'))
+ node.set('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBPluginDataXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'plugin_data':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('data', None)
+ data = self.convertFromStr(data, 'str')
+
+ obj = DBPluginData(id=id,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, plugin_data, node=None):
+ if node is None:
+ node = ElementTree.Element('plugin_data')
+
+ # set attributes
+ node.set('id',self.convertToStr(plugin_data.db_id, 'long'))
+ node.set('data',self.convertToStr(plugin_data.db_data, 'str'))
+
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'function':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ parameters = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ parameters.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, node=None):
+ if node is None:
+ node = ElementTree.Element('function')
+
+ # set attributes
+ node.set('id',self.convertToStr(function.db_id, 'long'))
+ node.set('pos',self.convertToStr(function.db_pos, 'long'))
+ node.set('name',self.convertToStr(function.db_name, 'str'))
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(parameter, childNode)
+
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'abstraction':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('internalVersion', None)
+ internal_version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstraction(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, node=None):
+ if node is None:
+ node = ElementTree.Element('abstraction')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.set('cache',self.convertToStr(abstraction.db_cache, 'int'))
+ node.set('name',self.convertToStr(abstraction.db_name, 'str'))
+ node.set('namespace',self.convertToStr(abstraction.db_namespace, 'str'))
+ node.set('package',self.convertToStr(abstraction.db_package, 'str'))
+ node.set('version',self.convertToStr(abstraction.db_version, 'str'))
+ node.set('internalVersion',self.convertToStr(abstraction.db_internal_version, 'str'))
+ node.set('tag',self.convertToStr(abstraction.db_tag, 'str'))
+
+ # set elements
+ location = abstraction.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = abstraction.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = abstraction.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflow':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ connections = []
+ annotations = []
+ plugin_datas = []
+ others = []
+ modules = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ connections.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ plugin_datas.append(_data)
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ others.append(_data)
+ elif child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ modules.append(_data)
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ modules.append(_data)
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ modules.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflow(modules=modules,
+ id=id,
+ name=name,
+ version=version,
+ connections=connections,
+ annotations=annotations,
+ plugin_datas=plugin_datas,
+ others=others,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, node=None):
+ if node is None:
+ node = ElementTree.Element('workflow')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow.db_id, 'long'))
+ node.set('name',self.convertToStr(workflow.db_name, 'str'))
+ node.set('version',self.convertToStr(workflow.db_version, 'str'))
+ node.set('vistrail_id',self.convertToStr(workflow.db_vistrail_id, 'long'))
+
+ # set elements
+ connections = workflow.db_connections
+ for connection in connections:
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(connection, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ plugin_datas = workflow.db_plugin_datas
+ for plugin_data in plugin_datas:
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(plugin_data, childNode)
+ others = workflow.db_others
+ for other in others:
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(other, childNode)
+ modules = workflow.db_modules
+ for module in modules:
+ if module.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(module, childNode)
+ elif module.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(module, childNode)
+ elif module.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(module, childNode)
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'annotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, node=None):
+ if node is None:
+ node = ElementTree.Element('annotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(annotation.db_id, 'long'))
+ node.set('key',self.convertToStr(annotation.db_key, 'str'))
+ node.set('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'change':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('oldObjId', None)
+ oldObjId = self.convertFromStr(data, 'long')
+ data = node.get('newObjId', None)
+ newObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBChange(data=data,
+ id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, node=None):
+ if node is None:
+ node = ElementTree.Element('change')
+
+ # set attributes
+ node.set('id',self.convertToStr(change.db_id, 'long'))
+ node.set('what',self.convertToStr(change.db_what, 'str'))
+ node.set('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.set('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.set('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # set elements
+ data = change.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflowExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('ip', None)
+ ip = self.convertFromStr(data, 'str')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('vtVersion', None)
+ vt_version = self.convertFromStr(data, 'str')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('parentId', None)
+ parent_id = self.convertFromStr(data, 'long')
+ data = node.get('parentType', None)
+ parent_type = self.convertFromStr(data, 'str')
+ data = node.get('parentVersion', None)
+ parent_version = self.convertFromStr(data, 'long')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ module_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ module_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflowExec(id=id,
+ user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ module_execs=module_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('workflowExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.set('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.set('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.set('session',self.convertToStr(workflow_exec.db_session, 'long'))
+ node.set('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.set('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.set('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.set('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.set('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.set('completed',self.convertToStr(workflow_exec.db_completed, 'int'))
+ node.set('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # set elements
+ module_execs = workflow_exec.db_module_execs
+ for module_exec in module_execs:
+ childNode = ElementTree.SubElement(node, 'module_exec')
+ self.getDao('module_exec').toXML(module_exec, childNode)
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'connection':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+
+ ports = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ ports.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, node=None):
+ if node is None:
+ node = ElementTree.Element('connection')
+
+ # set attributes
+ node.set('id',self.convertToStr(connection.db_id, 'long'))
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(port, childNode)
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'action':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('prevId', None)
+ prevId = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('prune', None)
+ prune = self.convertFromStr(data, 'int')
+
+ annotations = []
+ operations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'add':
+ _data = self.getDao('add').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'delete':
+ _data = self.getDao('delete').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'change':
+ _data = self.getDao('change').fromXML(child)
+ operations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAction(operations=operations,
+ id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, node=None):
+ if node is None:
+ node = ElementTree.Element('action')
+
+ # set attributes
+ node.set('id',self.convertToStr(action.db_id, 'long'))
+ node.set('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.set('date',self.convertToStr(action.db_date, 'datetime'))
+ node.set('session',self.convertToStr(action.db_session, 'long'))
+ node.set('user',self.convertToStr(action.db_user, 'str'))
+ node.set('prune',self.convertToStr(action.db_prune, 'int'))
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ childNode = ElementTree.SubElement(node, 'add')
+ self.getDao('add').toXML(operation, childNode)
+ elif operation.vtType == 'delete':
+ childNode = ElementTree.SubElement(node, 'delete')
+ self.getDao('delete').toXML(operation, childNode)
+ elif operation.vtType == 'change':
+ childNode = ElementTree.SubElement(node, 'change')
+ self.getDao('change').toXML(operation, childNode)
+
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'delete':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, node=None):
+ if node is None:
+ node = ElementTree.Element('delete')
+
+ # set attributes
+ node.set('id',self.convertToStr(delete.db_id, 'long'))
+ node.set('what',self.convertToStr(delete.db_what, 'str'))
+ node.set('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'vistrail':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child.tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ actions=actions,
+ tags=tags,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, node=None):
+ if node is None:
+ node = ElementTree.Element('vistrail')
+
+ # set attributes
+ node.set('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.set('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.set('name',self.convertToStr(vistrail.db_name, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = vistrail.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+ annotations = vistrail.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'moduleExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ module_name = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('abstraction_id', None)
+ abstraction_id = self.convertFromStr(data, 'long')
+ data = node.get('abstraction_version', None)
+ abstraction_version = self.convertFromStr(data, 'long')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ abstraction_id=abstraction_id,
+ abstraction_version=abstraction_version,
+ machine_id=machine_id,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(module_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.set('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+ node.set('completed',self.convertToStr(module_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(module_exec.db_error, 'str'))
+ node.set('abstraction_id',self.convertToStr(module_exec.db_abstraction_id, 'long'))
+ node.set('abstraction_version',self.convertToStr(module_exec.db_abstraction_version, 'long'))
+ node.set('machine_id',self.convertToStr(module_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v0_9_4/persistence/xml/xml_dao.py b/vistrails/db/versions/v0_9_4/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..955c01a
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/persistence/xml/xml_dao.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v0_9_4/schemas/sql/vistrails.sql b/vistrails/db/versions/v0_9_4/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..3cb4dc2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/schemas/sql/vistrails.sql
@@ -0,0 +1,305 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(22),
+ type varchar(255),
+ spec varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ spec varchar(4095),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE group_tbl(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime,
+ vistrail_id int
+) engine=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE plugin_data(
+ id int,
+ data varchar(8191),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ internal_version varchar(255),
+ tag varchar(255),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE workflow(
+ id int not null auto_increment primary key,
+ entity_id int,
+ entity_type char(16),
+ name varchar(255),
+ version char(16),
+ last_modified datetime,
+ vistrail_id int,
+ parent_id int,
+ parent_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ session int,
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ completed int,
+ name varchar(255),
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(16),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session int,
+ user varchar(255),
+ prune int,
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ module_name varchar(255),
+ completed int,
+ error varchar(1023),
+ abstraction_id int,
+ abstraction_version int,
+ machine_id int,
+ wf_exec_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
diff --git a/vistrails/db/versions/v0_9_4/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v0_9_4/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..6b29819
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,38 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, tag, port, group_tbl, log_tbl, machine, add_tbl, other, location, parameter, plugin_data, function, abstraction, workflow, annotation, change_tbl, workflow_exec, connection_tbl, action, delete_tbl, vistrail, module_exec;
diff --git a/vistrails/db/versions/v0_9_4/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_9_4/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..42ceda0
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/schemas/xml/vistrail.xsd
@@ -0,0 +1,276 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="prune" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="spec" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="internalVersion" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="group">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="workflow" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plugin_data">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="workflow">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_9_4/specs/all.xml b/vistrails/db/versions/v0_9_4/specs/all.xml
new file mode 100644
index 0000000..c1863b0
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/specs/all.xml
@@ -0,0 +1,1601 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<objects>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ABSTRACTION +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="internal_version" type="str">
+ <xml name="internalVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ACTION ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long" foreignKey="true" object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="prune" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="vistrail" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ADD +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ANNOTATION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CHANGE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CONNECTION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- DELETE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- FUNCTION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group" parentClass="module">
+ <layout>
+ <xml name="group" nodeType="xs:element"/>
+ <sql table="group_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow" type="object" mapping="one-to-one"
+ expand="false">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOCATION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MACHINE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_EXEC +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="abstraction_id" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OTHER +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PARAMETER +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PLUGIN DATA +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="plugin_data">
+ <layout>
+ <xml name="plugin_data" nodeType="xs:element"/>
+ <sql table="plugin_data"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="data" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORT ++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORTSPEC ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(22)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="spec" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- TAG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VISTRAIL ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstraction" ref="true" object="abstraction">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group" ref="true" object="group">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="plugin_data" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent" ref="true" object="group" type="long" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW_EXEC +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+</objects>
diff --git a/vistrails/db/versions/v0_9_4/translate/__init__.py b/vistrails/db/versions/v0_9_4/translate/__init__.py
new file mode 100644
index 0000000..5cf1ec6
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.9.4'
diff --git a/vistrails/db/versions/v0_9_4/translate/v0_9_3.py b/vistrails/db/versions/v0_9_4/translate/v0_9_3.py
new file mode 100644
index 0000000..8bde2da
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/translate/v0_9_3.py
@@ -0,0 +1,117 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v0_9_4.domain import DBVistrail, DBAction, DBTag, DBModule, \
+ DBConnection, DBPortSpec, DBFunction, DBParameter, DBLocation, DBAdd, \
+ DBChange, DBDelete, DBAnnotation, DBPort, DBGroup, \
+ DBWorkflow, DBLog, DBAbstraction
+
+def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow,
+ translate_dict, DBWorkflow())
+
+def update_modules(old_obj, trans_dict):
+ new_modules = []
+ for obj in old_obj.db_modules:
+ if obj.vtType == 'module':
+ new_modules.append(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstractionRef':
+ new_modules.append(DBAbstraction.update_version(obj,
+ trans_dict))
+ elif obj.vtType == 'group':
+ new_modules.append(DBGroup.update_version(obj, trans_dict))
+ return new_modules
+
+def translateVistrail(_vistrail):
+ def update_operations(old_obj, trans_dict):
+ def update_abstractionRef(old_obj, trans_dict):
+ def get_internal_version(old_obj, trans_dict):
+ return str(old_obj.db_version)
+ def get_version(old_obj, trans_dict):
+ return ''
+ new_dict = {'DBAbstraction':
+ {'internal_version': get_internal_version,
+ 'version': get_version}}
+ new_dict.update(trans_dict)
+ return DBAbstraction.update_version(old_obj.db_data, new_dict)
+ new_ops = []
+ for obj in old_obj.db_operations:
+ if obj.vtType == 'add':
+ if obj.db_what == 'abstractionRef':
+ trans_dict['DBAdd'] = {'data': update_abstractionRef}
+ new_op = DBAdd.update_version(obj, trans_dict)
+ new_op.db_what = 'abstraction'
+ new_ops.append(new_op)
+ del trans_dict['DBAdd']
+ else:
+ new_op = DBAdd.update_version(obj, trans_dict)
+ if obj.db_parentObjType == 'abstractionRef':
+ new_op.db_parentObjType = 'abstraction'
+ new_ops.append(new_op)
+ elif obj.vtType == 'delete':
+ new_ops.append(DBDelete.update_version(obj, trans_dict))
+ elif obj.vtType == 'change':
+ if obj.db_what == 'abstractionRef':
+ trans_dict['DBChange'] = {'data': update_abstractionRef}
+ new_op = DBChange.update_version(obj, trans_dict)
+ new_op.db_what = 'abstraction'
+ new_ops.append(new_op)
+ del trans_dict['DBChange']
+ else:
+ new_op = DBChange.update_version(obj, trans_dict)
+ if obj.db_parentObjType == 'abstractionRef':
+ new_op.db_parentObjType = 'abstraction'
+ new_ops.append(new_op)
+ return new_ops
+
+ translate_dict = {'DBGroup': {'workflow': update_workflow},
+ 'DBAction': {'operations': update_operations},
+ 'DBWorkflow': {'modules': update_modules}}
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict)
+ vistrail.db_version = '0.9.4'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ translate_dict = {'DBGroup': {'workflow': update_workflow},
+ 'DBWorkflow': {'modules': update_modules}}
+ workflow = DBWorkflow.update_version(_workflow, translate_dict)
+ workflow.db_version = '0.9.4'
+ return workflow
+
+def translateLog(_log):
+ translate_dict = {}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '0.9.4'
+ return log
diff --git a/vistrails/db/versions/v0_9_4/translate/v0_9_5.py b/vistrails/db/versions/v0_9_4/translate/v0_9_5.py
new file mode 100644
index 0000000..46837d4
--- /dev/null
+++ b/vistrails/db/versions/v0_9_4/translate/v0_9_5.py
@@ -0,0 +1,87 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.core import debug
+from vistrails.db.versions.v0_9_4.domain import DBVistrail, DBWorkflow, DBLog, DBGroup, DBModuleExec
+
+def translateVistrail(_vistrail):
+ def update_port_spec_spec(new_obj, translate_dict):
+ return new_obj.db_sigstring
+ def update_port_spec(new_obj, translate_dict):
+ return new_obj.db_signature
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+
+ translate_dict = {'DBPortSpec': {'spec': update_port_spec_spec},
+ 'DBPort': {'spec': update_port_spec},
+ 'DBGroup': {'workflow': update_workflow}}
+
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict)
+ vistrail.db_version = '0.9.4'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ def update_port_spec_spec(new_obj, translate_dict):
+ return new_obj.db_sigstring
+ def update_port_spec(new_obj, translate_dict):
+ return new_obj.db_signature
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+
+ translate_dict = {'DBPortSpec': {'spec': update_port_spec_spec},
+ 'DBPort': {'spec': update_port_spec},
+ 'DBGroup': {'workflow': update_workflow}}
+
+ workflow = DBWorkflow.update_version(_workflow, translate_dict)
+ workflow.db_version = '0.9.4'
+ return workflow
+
+def translateLog(_log):
+ def update_module_execs(old_obj, translate_dict):
+ new_module_execs = []
+ for obj in old_obj.db_items:
+ if obj.vtType == 'module_exec':
+ new_module_execs.append(DBModuleExec.update_version(obj,
+ translate_dict))
+ elif obj.vtType == 'group_exec':
+ # cannot handle group execs
+ debug.warning('Cannot translate group exec')
+ elif obj.vtType == 'loop_exec':
+ debug.warning('Cannot translate loop exec')
+ return new_module_execs
+ translate_dict = {'DBWorkflowExec': {'module_execs': update_module_execs}}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '0.9.4'
+ return log
diff --git a/vistrails/db/versions/v0_9_5/__init__.py b/vistrails/db/versions/v0_9_5/__init__.py
new file mode 100644
index 0000000..89c7f9a
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.9.5'
diff --git a/vistrails/db/versions/v0_9_5/domain/__init__.py b/vistrails/db/versions/v0_9_5/domain/__init__.py
new file mode 100644
index 0000000..a8208f6
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/domain/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from registry import DBRegistry
+from workflow import DBWorkflow
+from vistrail import DBVistrail
+from log import DBLog
+from id_scope import IdScope
diff --git a/vistrails/db/versions/v0_9_5/domain/auto_gen.py b/vistrails/db/versions/v0_9_5/domain/auto_gen.py
new file mode 100644
index 0000000..c78266f
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/domain/auto_gen.py
@@ -0,0 +1,7786 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, optional=None, sort_key=None, sigstring=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_type = type
+ self._db_optional = optional
+ self._db_sort_key = sort_key
+ self._db_sigstring = sigstring
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPortSpec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec(id=self._db_id,
+ name=self._db_name,
+ type=self._db_type,
+ optional=self._db_optional,
+ sort_key=self._db_sort_key,
+ sigstring=self._db_sigstring)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPortSpec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'optional' in class_dict:
+ res = class_dict['optional'](old_obj, trans_dict)
+ new_obj.db_optional = res
+ elif hasattr(old_obj, 'db_optional') and old_obj.db_optional is not None:
+ new_obj.db_optional = old_obj.db_optional
+ if 'sort_key' in class_dict:
+ res = class_dict['sort_key'](old_obj, trans_dict)
+ new_obj.db_sort_key = res
+ elif hasattr(old_obj, 'db_sort_key') and old_obj.db_sort_key is not None:
+ new_obj.db_sort_key = old_obj.db_sort_key
+ if 'sigstring' in class_dict:
+ res = class_dict['sigstring'](old_obj, trans_dict)
+ new_obj.db_sigstring = res
+ elif hasattr(old_obj, 'db_sigstring') and old_obj.db_sigstring is not None:
+ new_obj.db_sigstring = old_obj.db_sigstring
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_optional(self):
+ return self._db_optional
+ def __set_db_optional(self, optional):
+ self._db_optional = optional
+ self.is_dirty = True
+ db_optional = property(__get_db_optional, __set_db_optional)
+ def db_add_optional(self, optional):
+ self._db_optional = optional
+ def db_change_optional(self, optional):
+ self._db_optional = optional
+ def db_delete_optional(self, optional):
+ self._db_optional = None
+
+ def __get_db_sort_key(self):
+ return self._db_sort_key
+ def __set_db_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ self.is_dirty = True
+ db_sort_key = property(__get_db_sort_key, __set_db_sort_key)
+ def db_add_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ def db_change_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ def db_delete_sort_key(self, sort_key):
+ self._db_sort_key = None
+
+ def __get_db_sigstring(self):
+ return self._db_sigstring
+ def __set_db_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ self.is_dirty = True
+ db_sigstring = property(__get_db_sigstring, __set_db_sigstring)
+ def db_add_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ def db_change_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ def db_delete_sigstring(self, sigstring):
+ self._db_sigstring = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModule.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ tag=self._db_tag)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModule()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleDescriptor(object):
+
+ vtType = 'module_descriptor'
+
+ def __init__(self, id=None, name=None, package=None, namespace=None, version=None, base_descriptor_id=None, portSpecs=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_package = package
+ self._db_namespace = namespace
+ self._db_version = version
+ self._db_base_descriptor_id = base_descriptor_id
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleDescriptor.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleDescriptor(id=self._db_id,
+ name=self._db_name,
+ package=self._db_package,
+ namespace=self._db_namespace,
+ version=self._db_version,
+ base_descriptor_id=self._db_base_descriptor_id)
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_base_descriptor_id') and ('module_descriptor', self._db_base_descriptor_id) in id_remap:
+ cp._db_base_descriptor_id = id_remap[('module_descriptor', self._db_base_descriptor_id)]
+
+ # recreate indices and set flags
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleDescriptor()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'base_descriptor_id' in class_dict:
+ res = class_dict['base_descriptor_id'](old_obj, trans_dict)
+ new_obj.db_base_descriptor_id = res
+ elif hasattr(old_obj, 'db_base_descriptor_id') and old_obj.db_base_descriptor_id is not None:
+ new_obj.db_base_descriptor_id = old_obj.db_base_descriptor_id
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_base_descriptor_id(self):
+ return self._db_base_descriptor_id
+ def __set_db_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ self.is_dirty = True
+ db_base_descriptor_id = property(__get_db_base_descriptor_id, __set_db_base_descriptor_id)
+ def db_add_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ def db_change_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ def db_delete_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = None
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self._db_id = id
+ self._db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBTag.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag(id=self._db_id,
+ name=self._db_name)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('action', self._db_id) in id_remap:
+ cp._db_id = id_remap[('action', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBTag()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, name=None, signature=None):
+ self._db_id = id
+ self._db_type = type
+ self._db_moduleId = moduleId
+ self._db_moduleName = moduleName
+ self._db_name = name
+ self._db_signature = signature
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPort.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort(id=self._db_id,
+ type=self._db_type,
+ moduleId=self._db_moduleId,
+ moduleName=self._db_moduleName,
+ name=self._db_name,
+ signature=self._db_signature)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_moduleId') and ('module', self._db_moduleId) in id_remap:
+ cp._db_moduleId = id_remap[('module', self._db_moduleId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPort()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'moduleId' in class_dict:
+ res = class_dict['moduleId'](old_obj, trans_dict)
+ new_obj.db_moduleId = res
+ elif hasattr(old_obj, 'db_moduleId') and old_obj.db_moduleId is not None:
+ new_obj.db_moduleId = old_obj.db_moduleId
+ if 'moduleName' in class_dict:
+ res = class_dict['moduleName'](old_obj, trans_dict)
+ new_obj.db_moduleName = res
+ elif hasattr(old_obj, 'db_moduleName') and old_obj.db_moduleName is not None:
+ new_obj.db_moduleName = old_obj.db_moduleName
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'signature' in class_dict:
+ res = class_dict['signature'](old_obj, trans_dict)
+ new_obj.db_signature = res
+ elif hasattr(old_obj, 'db_signature') and old_obj.db_signature is not None:
+ new_obj.db_signature = old_obj.db_signature
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_moduleId(self):
+ return self._db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self._db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self._db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self._db_moduleName = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_signature(self):
+ return self._db_signature
+ def __set_db_signature(self, signature):
+ self._db_signature = signature
+ self.is_dirty = True
+ db_signature = property(__get_db_signature, __set_db_signature)
+ def db_add_signature(self, signature):
+ self._db_signature = signature
+ def db_change_signature(self, signature):
+ self._db_signature = signature
+ def db_delete_signature(self, signature):
+ self._db_signature = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBGroup(object):
+
+ vtType = 'group'
+
+ def __init__(self, id=None, workflow=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self.db_deleted_workflow = []
+ self._db_workflow = workflow
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroup.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroup(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ tag=self._db_tag)
+ if self._db_workflow is not None:
+ cp._db_workflow = self._db_workflow.do_copy()
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroup()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'workflow' in class_dict:
+ res = class_dict['workflow'](old_obj, trans_dict)
+ new_obj.db_workflow = res
+ elif hasattr(old_obj, 'db_workflow') and old_obj.db_workflow is not None:
+ obj = old_obj.db_workflow
+ new_obj.db_add_workflow(DBWorkflow.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow') and hasattr(new_obj, 'db_deleted_workflow'):
+ for obj in old_obj.db_deleted_workflow:
+ n_obj = DBWorkflow.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow.append(n_obj)
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow)
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_workflow = []
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_workflow is not None and self._db_workflow.has_changes():
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_workflow(self):
+ return self._db_workflow
+ def __set_db_workflow(self, workflow):
+ self._db_workflow = workflow
+ self.is_dirty = True
+ db_workflow = property(__get_db_workflow, __set_db_workflow)
+ def db_add_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_change_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_delete_workflow(self, workflow):
+ if not self.is_new:
+ self.db_deleted_workflow.append(self._db_workflow)
+ self._db_workflow = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, workflow_execs=None, machines=None, vistrail_id=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_workflow_execs = []
+ self.db_workflow_execs_id_index = {}
+ if workflow_execs is None:
+ self._db_workflow_execs = []
+ else:
+ self._db_workflow_execs = workflow_execs
+ for v in self._db_workflow_execs:
+ self.db_workflow_execs_id_index[v.db_id] = v
+ self.db_deleted_machines = []
+ self.db_machines_id_index = {}
+ if machines is None:
+ self._db_machines = []
+ else:
+ self._db_machines = machines
+ for v in self._db_machines:
+ self.db_machines_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_workflow_execs is None:
+ cp._db_workflow_execs = []
+ else:
+ cp._db_workflow_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_workflow_execs]
+ if self._db_machines is None:
+ cp._db_machines = []
+ else:
+ cp._db_machines = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_machines]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_workflow_execs_id_index = dict((v.db_id, v) for v in cp._db_workflow_execs)
+ cp.db_machines_id_index = dict((v.db_id, v) for v in cp._db_machines)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'workflow_execs' in class_dict:
+ res = class_dict['workflow_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_workflow_exec(obj)
+ elif hasattr(old_obj, 'db_workflow_execs') and old_obj.db_workflow_execs is not None:
+ for obj in old_obj.db_workflow_execs:
+ new_obj.db_add_workflow_exec(DBWorkflowExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow_execs') and hasattr(new_obj, 'db_deleted_workflow_execs'):
+ for obj in old_obj.db_deleted_workflow_execs:
+ n_obj = DBWorkflowExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow_execs.append(n_obj)
+ if 'machines' in class_dict:
+ res = class_dict['machines'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_machine(obj)
+ elif hasattr(old_obj, 'db_machines') and old_obj.db_machines is not None:
+ for obj in old_obj.db_machines:
+ new_obj.db_add_machine(DBMachine.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_machines') and hasattr(new_obj, 'db_deleted_machines'):
+ for obj in old_obj.db_deleted_machines:
+ n_obj = DBMachine.update_version(obj, trans_dict)
+ new_obj.db_deleted_machines.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_workflow_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self.db_machines:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow_execs)
+ children.extend(self.db_deleted_machines)
+ if remove:
+ self.db_deleted_workflow_execs = []
+ self.db_deleted_machines = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_workflow_execs:
+ if child.has_changes():
+ return True
+ for child in self._db_machines:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_workflow_execs(self):
+ return self._db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self._db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self._db_workflow_execs
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ self._db_workflow_execs[i] = workflow_exec
+ found = True
+ break
+ if not found:
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ if not self._db_workflow_execs[i].is_new:
+ self.db_deleted_workflow_execs.append(self._db_workflow_execs[i])
+ del self._db_workflow_execs[i]
+ break
+ del self.db_workflow_execs_id_index[workflow_exec.db_id]
+ def db_get_workflow_exec(self, key):
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == key:
+ return self._db_workflow_execs[i]
+ return None
+ def db_get_workflow_exec_by_id(self, key):
+ return self.db_workflow_execs_id_index[key]
+ def db_has_workflow_exec_with_id(self, key):
+ return key in self.db_workflow_execs_id_index
+
+ def __get_db_machines(self):
+ return self._db_machines
+ def __set_db_machines(self, machines):
+ self._db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self._db_machines
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ self._db_machines[i] = machine
+ found = True
+ break
+ if not found:
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ if not self._db_machines[i].is_new:
+ self.db_deleted_machines.append(self._db_machines[i])
+ del self._db_machines[i]
+ break
+ del self.db_machines_id_index[machine.db_id]
+ def db_get_machine(self, key):
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == key:
+ return self._db_machines[i]
+ return None
+ def db_get_machine_by_id(self, key):
+ return self.db_machines_id_index[key]
+ def db_has_machine_with_id(self, key):
+ return key in self.db_machines_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_os = os
+ self._db_architecture = architecture
+ self._db_processor = processor
+ self._db_ram = ram
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMachine.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine(id=self._db_id,
+ name=self._db_name,
+ os=self._db_os,
+ architecture=self._db_architecture,
+ processor=self._db_processor,
+ ram=self._db_ram)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and ('vistrail', self._db_vistrailId) in id_remap:
+ cp._db_vistrailId = id_remap[('vistrail', self._db_vistrailId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMachine()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'os' in class_dict:
+ res = class_dict['os'](old_obj, trans_dict)
+ new_obj.db_os = res
+ elif hasattr(old_obj, 'db_os') and old_obj.db_os is not None:
+ new_obj.db_os = old_obj.db_os
+ if 'architecture' in class_dict:
+ res = class_dict['architecture'](old_obj, trans_dict)
+ new_obj.db_architecture = res
+ elif hasattr(old_obj, 'db_architecture') and old_obj.db_architecture is not None:
+ new_obj.db_architecture = old_obj.db_architecture
+ if 'processor' in class_dict:
+ res = class_dict['processor'](old_obj, trans_dict)
+ new_obj.db_processor = res
+ elif hasattr(old_obj, 'db_processor') and old_obj.db_processor is not None:
+ new_obj.db_processor = old_obj.db_processor
+ if 'ram' in class_dict:
+ res = class_dict['ram'](old_obj, trans_dict)
+ new_obj.db_ram = res
+ elif hasattr(old_obj, 'db_ram') and old_obj.db_ram is not None:
+ new_obj.db_ram = old_obj.db_ram
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_os(self):
+ return self._db_os
+ def __set_db_os(self, os):
+ self._db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self._db_os = os
+ def db_change_os(self, os):
+ self._db_os = os
+ def db_delete_os(self, os):
+ self._db_os = None
+
+ def __get_db_architecture(self):
+ return self._db_architecture
+ def __set_db_architecture(self, architecture):
+ self._db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self._db_architecture = None
+
+ def __get_db_processor(self):
+ return self._db_processor
+ def __set_db_processor(self, processor):
+ self._db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self._db_processor = processor
+ def db_change_processor(self, processor):
+ self._db_processor = processor
+ def db_delete_processor(self, processor):
+ self._db_processor = None
+
+ def __get_db_ram(self):
+ return self._db_ram
+ def __set_db_ram(self, ram):
+ self._db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self._db_ram = ram
+ def db_change_ram(self, ram):
+ self._db_ram = ram
+ def db_delete_ram(self, ram):
+ self._db_ram = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, data=None, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAdd.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAdd()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOther.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOther(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOther()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self._db_id = id
+ self._db_x = x
+ self._db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLocation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation(id=self._db_id,
+ x=self._db_x,
+ y=self._db_y)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLocation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'x' in class_dict:
+ res = class_dict['x'](old_obj, trans_dict)
+ new_obj.db_x = res
+ elif hasattr(old_obj, 'db_x') and old_obj.db_x is not None:
+ new_obj.db_x = old_obj.db_x
+ if 'y' in class_dict:
+ res = class_dict['y'](old_obj, trans_dict)
+ new_obj.db_y = res
+ elif hasattr(old_obj, 'db_y') and old_obj.db_y is not None:
+ new_obj.db_y = old_obj.db_y
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_x(self):
+ return self._db_x
+ def __set_db_x(self, x):
+ self._db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self._db_x = x
+ def db_change_x(self, x):
+ self._db_x = x
+ def db_delete_x(self, x):
+ self._db_x = None
+
+ def __get_db_y(self):
+ return self._db_y
+ def __set_db_y(self, y):
+ self._db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self._db_y = y
+ def db_change_y(self, y):
+ self._db_y = y
+ def db_delete_y(self, y):
+ self._db_y = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self._db_type = type
+ self._db_val = val
+ self._db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBParameter.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name,
+ type=self._db_type,
+ val=self._db_val,
+ alias=self._db_alias)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBParameter()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'val' in class_dict:
+ res = class_dict['val'](old_obj, trans_dict)
+ new_obj.db_val = res
+ elif hasattr(old_obj, 'db_val') and old_obj.db_val is not None:
+ new_obj.db_val = old_obj.db_val
+ if 'alias' in class_dict:
+ res = class_dict['alias'](old_obj, trans_dict)
+ new_obj.db_alias = res
+ elif hasattr(old_obj, 'db_alias') and old_obj.db_alias is not None:
+ new_obj.db_alias = old_obj.db_alias
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_val(self):
+ return self._db_val
+ def __set_db_val(self, val):
+ self._db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self._db_val = val
+ def db_change_val(self, val):
+ self._db_val = val
+ def db_delete_val(self, val):
+ self._db_val = None
+
+ def __get_db_alias(self):
+ return self._db_alias
+ def __set_db_alias(self, alias):
+ self._db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self._db_alias = alias
+ def db_change_alias(self, alias):
+ self._db_alias = alias
+ def db_delete_alias(self, alias):
+ self._db_alias = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBPluginData(object):
+
+ vtType = 'plugin_data'
+
+ def __init__(self, id=None, data=None):
+ self._db_id = id
+ self._db_data = data
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPluginData.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPluginData(id=self._db_id,
+ data=self._db_data)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPluginData()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ new_obj.db_data = old_obj.db_data
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ self._db_data = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self.db_deleted_parameters = []
+ self.db_parameters_id_index = {}
+ if parameters is None:
+ self._db_parameters = []
+ else:
+ self._db_parameters = parameters
+ for v in self._db_parameters:
+ self.db_parameters_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name)
+ if self._db_parameters is None:
+ cp._db_parameters = []
+ else:
+ cp._db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_parameters_id_index = dict((v.db_id, v) for v in cp._db_parameters)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBFunction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'parameters' in class_dict:
+ res = class_dict['parameters'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_parameter(obj)
+ elif hasattr(old_obj, 'db_parameters') and old_obj.db_parameters is not None:
+ for obj in old_obj.db_parameters:
+ new_obj.db_add_parameter(DBParameter.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_parameters') and hasattr(new_obj, 'db_deleted_parameters'):
+ for obj in old_obj.db_deleted_parameters:
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_parameters.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_parameters)
+ if remove:
+ self.db_deleted_parameters = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_parameters(self):
+ return self._db_parameters
+ def __set_db_parameters(self, parameters):
+ self._db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self._db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ self._db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ if not self._db_parameters[i].is_new:
+ self.db_deleted_parameters.append(self._db_parameters[i])
+ del self._db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter.db_id]
+ def db_get_parameter(self, key):
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == key:
+ return self._db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return key in self.db_parameters_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, internal_version=None, tag=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_internal_version = internal_version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ internal_version=self._db_internal_version,
+ tag=self._db_tag)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAbstraction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'internal_version' in class_dict:
+ res = class_dict['internal_version'](old_obj, trans_dict)
+ new_obj.db_internal_version = res
+ elif hasattr(old_obj, 'db_internal_version') and old_obj.db_internal_version is not None:
+ new_obj.db_internal_version = old_obj.db_internal_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_internal_version(self):
+ return self._db_internal_version
+ def __set_db_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ self.is_dirty = True
+ db_internal_version = property(__get_db_internal_version, __set_db_internal_version)
+ def db_add_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_change_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_delete_internal_version(self, internal_version):
+ self._db_internal_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, modules=None, id=None, entity_type=None, name=None, version=None, last_modified=None, connections=None, annotations=None, plugin_datas=None, others=None, vistrail_id=None):
+ self.db_deleted_modules = []
+ self.db_modules_id_index = {}
+ if modules is None:
+ self._db_modules = []
+ else:
+ self._db_modules = modules
+ for v in self._db_modules:
+ self.db_modules_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_name = name
+ self._db_version = version
+ self._db_last_modified = last_modified
+ self.db_deleted_connections = []
+ self.db_connections_id_index = {}
+ if connections is None:
+ self._db_connections = []
+ else:
+ self._db_connections = connections
+ for v in self._db_connections:
+ self.db_connections_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_plugin_datas = []
+ self.db_plugin_datas_id_index = {}
+ if plugin_datas is None:
+ self._db_plugin_datas = []
+ else:
+ self._db_plugin_datas = plugin_datas
+ for v in self._db_plugin_datas:
+ self.db_plugin_datas_id_index[v.db_id] = v
+ self.db_deleted_others = []
+ self.db_others_id_index = {}
+ if others is None:
+ self._db_others = []
+ else:
+ self._db_others = others
+ for v in self._db_others:
+ self.db_others_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow(id=self._db_id,
+ entity_type=self._db_entity_type,
+ name=self._db_name,
+ version=self._db_version,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_modules is None:
+ cp._db_modules = []
+ else:
+ cp._db_modules = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_modules]
+ if self._db_connections is None:
+ cp._db_connections = []
+ else:
+ cp._db_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_connections]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_plugin_datas is None:
+ cp._db_plugin_datas = []
+ else:
+ cp._db_plugin_datas = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_plugin_datas]
+ if self._db_others is None:
+ cp._db_others = []
+ else:
+ cp._db_others = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_others]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_modules_id_index = dict((v.db_id, v) for v in cp._db_modules)
+ cp.db_connections_id_index = dict((v.db_id, v) for v in cp._db_connections)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_plugin_datas_id_index = dict((v.db_id, v) for v in cp._db_plugin_datas)
+ cp.db_others_id_index = dict((v.db_id, v) for v in cp._db_others)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'modules' in class_dict:
+ res = class_dict['modules'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module(obj)
+ elif hasattr(old_obj, 'db_modules') and old_obj.db_modules is not None:
+ for obj in old_obj.db_modules:
+ if obj.vtType == 'module':
+ new_obj.db_add_module(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_module(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_module(DBGroup.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_modules') and hasattr(new_obj, 'db_deleted_modules'):
+ for obj in old_obj.db_deleted_modules:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'connections' in class_dict:
+ res = class_dict['connections'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_connection(obj)
+ elif hasattr(old_obj, 'db_connections') and old_obj.db_connections is not None:
+ for obj in old_obj.db_connections:
+ new_obj.db_add_connection(DBConnection.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_connections') and hasattr(new_obj, 'db_deleted_connections'):
+ for obj in old_obj.db_deleted_connections:
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_connections.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'plugin_datas' in class_dict:
+ res = class_dict['plugin_datas'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_plugin_data(obj)
+ elif hasattr(old_obj, 'db_plugin_datas') and old_obj.db_plugin_datas is not None:
+ for obj in old_obj.db_plugin_datas:
+ new_obj.db_add_plugin_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_plugin_datas') and hasattr(new_obj, 'db_deleted_plugin_datas'):
+ for obj in old_obj.db_deleted_plugin_datas:
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_plugin_datas.append(n_obj)
+ if 'others' in class_dict:
+ res = class_dict['others'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_other(obj)
+ elif hasattr(old_obj, 'db_others') and old_obj.db_others is not None:
+ for obj in old_obj.db_others:
+ new_obj.db_add_other(DBOther.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_others') and hasattr(new_obj, 'db_deleted_others'):
+ for obj in old_obj.db_deleted_others:
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_others.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_connections:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_connection(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_plugin_datas:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_plugin_data(child)
+ to_del = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_other(child)
+ to_del = []
+ for child in self.db_modules:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_connections)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_plugin_datas)
+ children.extend(self.db_deleted_others)
+ children.extend(self.db_deleted_modules)
+ if remove:
+ self.db_deleted_connections = []
+ self.db_deleted_annotations = []
+ self.db_deleted_plugin_datas = []
+ self.db_deleted_others = []
+ self.db_deleted_modules = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_connections:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_plugin_datas:
+ if child.has_changes():
+ return True
+ for child in self._db_others:
+ if child.has_changes():
+ return True
+ for child in self._db_modules:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_modules(self):
+ return self._db_modules
+ def __set_db_modules(self, modules):
+ self._db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self._db_modules
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ self._db_modules[i] = module
+ found = True
+ break
+ if not found:
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ if not self._db_modules[i].is_new:
+ self.db_deleted_modules.append(self._db_modules[i])
+ del self._db_modules[i]
+ break
+ del self.db_modules_id_index[module.db_id]
+ def db_get_module(self, key):
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == key:
+ return self._db_modules[i]
+ return None
+ def db_get_module_by_id(self, key):
+ return self.db_modules_id_index[key]
+ def db_has_module_with_id(self, key):
+ return key in self.db_modules_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_connections(self):
+ return self._db_connections
+ def __set_db_connections(self, connections):
+ self._db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self._db_connections
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ self._db_connections[i] = connection
+ found = True
+ break
+ if not found:
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ if not self._db_connections[i].is_new:
+ self.db_deleted_connections.append(self._db_connections[i])
+ del self._db_connections[i]
+ break
+ del self.db_connections_id_index[connection.db_id]
+ def db_get_connection(self, key):
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == key:
+ return self._db_connections[i]
+ return None
+ def db_get_connection_by_id(self, key):
+ return self.db_connections_id_index[key]
+ def db_has_connection_with_id(self, key):
+ return key in self.db_connections_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_plugin_datas(self):
+ return self._db_plugin_datas
+ def __set_db_plugin_datas(self, plugin_datas):
+ self._db_plugin_datas = plugin_datas
+ self.is_dirty = True
+ db_plugin_datas = property(__get_db_plugin_datas, __set_db_plugin_datas)
+ def db_get_plugin_datas(self):
+ return self._db_plugin_datas
+ def db_add_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_change_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ self._db_plugin_datas[i] = plugin_data
+ found = True
+ break
+ if not found:
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_delete_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ if not self._db_plugin_datas[i].is_new:
+ self.db_deleted_plugin_datas.append(self._db_plugin_datas[i])
+ del self._db_plugin_datas[i]
+ break
+ del self.db_plugin_datas_id_index[plugin_data.db_id]
+ def db_get_plugin_data(self, key):
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == key:
+ return self._db_plugin_datas[i]
+ return None
+ def db_get_plugin_data_by_id(self, key):
+ return self.db_plugin_datas_id_index[key]
+ def db_has_plugin_data_with_id(self, key):
+ return key in self.db_plugin_datas_id_index
+
+ def __get_db_others(self):
+ return self._db_others
+ def __set_db_others(self, others):
+ self._db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self._db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ self._db_others[i] = other
+ found = True
+ break
+ if not found:
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ if not self._db_others[i].is_new:
+ self.db_deleted_others.append(self._db_others[i])
+ del self._db_others[i]
+ break
+ del self.db_others_id_index[other.db_id]
+ def db_get_other(self, key):
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == key:
+ return self._db_others[i]
+ return None
+ def db_get_other_by_id(self, key):
+ return self.db_others_id_index[key]
+ def db_has_other_with_id(self, key):
+ return key in self.db_others_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBRegistry(object):
+
+ vtType = 'registry'
+
+ def __init__(self, id=None, entity_type=None, version=None, root_descriptor_id=None, name=None, last_modified=None, packages=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_root_descriptor_id = root_descriptor_id
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_packages = []
+ self.db_packages_id_index = {}
+ self.db_packages_identifier_index = {}
+ if packages is None:
+ self._db_packages = []
+ else:
+ self._db_packages = packages
+ for v in self._db_packages:
+ self.db_packages_id_index[v.db_id] = v
+ self.db_packages_identifier_index[(v.db_identifier,v.db_version)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBRegistry.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBRegistry(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ root_descriptor_id=self._db_root_descriptor_id,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_packages is None:
+ cp._db_packages = []
+ else:
+ cp._db_packages = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_packages]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_root_descriptor_id') and ('module_descriptor', self._db_root_descriptor_id) in id_remap:
+ cp._db_root_descriptor_id = id_remap[('module_descriptor', self._db_root_descriptor_id)]
+
+ # recreate indices and set flags
+ cp.db_packages_id_index = dict((v.db_id, v) for v in cp._db_packages)
+ cp.db_packages_identifier_index = dict(((v.db_identifier,v.db_version), v) for v in cp._db_packages)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRegistry()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'root_descriptor_id' in class_dict:
+ res = class_dict['root_descriptor_id'](old_obj, trans_dict)
+ new_obj.db_root_descriptor_id = res
+ elif hasattr(old_obj, 'db_root_descriptor_id') and old_obj.db_root_descriptor_id is not None:
+ new_obj.db_root_descriptor_id = old_obj.db_root_descriptor_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'packages' in class_dict:
+ res = class_dict['packages'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_package(obj)
+ elif hasattr(old_obj, 'db_packages') and old_obj.db_packages is not None:
+ for obj in old_obj.db_packages:
+ new_obj.db_add_package(DBPackage.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_packages') and hasattr(new_obj, 'db_deleted_packages'):
+ for obj in old_obj.db_deleted_packages:
+ n_obj = DBPackage.update_version(obj, trans_dict)
+ new_obj.db_deleted_packages.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_packages:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_package(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_packages)
+ if remove:
+ self.db_deleted_packages = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_packages:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_root_descriptor_id(self):
+ return self._db_root_descriptor_id
+ def __set_db_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ self.is_dirty = True
+ db_root_descriptor_id = property(__get_db_root_descriptor_id, __set_db_root_descriptor_id)
+ def db_add_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ def db_change_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ def db_delete_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_packages(self):
+ return self._db_packages
+ def __set_db_packages(self, packages):
+ self._db_packages = packages
+ self.is_dirty = True
+ db_packages = property(__get_db_packages, __set_db_packages)
+ def db_get_packages(self):
+ return self._db_packages
+ def db_add_package(self, package):
+ self.is_dirty = True
+ self._db_packages.append(package)
+ self.db_packages_id_index[package.db_id] = package
+ self.db_packages_identifier_index[(package.db_identifier,package.db_version)] = package
+ def db_change_package(self, package):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == package.db_id:
+ self._db_packages[i] = package
+ found = True
+ break
+ if not found:
+ self._db_packages.append(package)
+ self.db_packages_id_index[package.db_id] = package
+ self.db_packages_identifier_index[(package.db_identifier,package.db_version)] = package
+ def db_delete_package(self, package):
+ self.is_dirty = True
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == package.db_id:
+ if not self._db_packages[i].is_new:
+ self.db_deleted_packages.append(self._db_packages[i])
+ del self._db_packages[i]
+ break
+ del self.db_packages_id_index[package.db_id]
+ del self.db_packages_identifier_index[(package.db_identifier,package.db_version)]
+ def db_get_package(self, key):
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == key:
+ return self._db_packages[i]
+ return None
+ def db_get_package_by_id(self, key):
+ return self.db_packages_id_index[key]
+ def db_has_package_with_id(self, key):
+ return key in self.db_packages_id_index
+ def db_get_package_by_identifier(self, key):
+ return self.db_packages_identifier_index[key]
+ def db_has_package_with_identifier(self, key):
+ return key in self.db_packages_identifier_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAnnotation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, data=None, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_oldObjId = oldObjId
+ self._db_newObjId = newObjId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBChange.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange(id=self._db_id,
+ what=self._db_what,
+ oldObjId=self._db_oldObjId,
+ newObjId=self._db_newObjId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_oldObjId') and (self._db_what, self._db_oldObjId) in id_remap:
+ cp._db_oldObjId = id_remap[(self._db_what, self._db_oldObjId)]
+ if hasattr(self, 'db_newObjId') and (self._db_what, self._db_newObjId) in id_remap:
+ cp._db_newObjId = id_remap[(self._db_what, self._db_newObjId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBChange()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'oldObjId' in class_dict:
+ res = class_dict['oldObjId'](old_obj, trans_dict)
+ new_obj.db_oldObjId = res
+ elif hasattr(old_obj, 'db_oldObjId') and old_obj.db_oldObjId is not None:
+ new_obj.db_oldObjId = old_obj.db_oldObjId
+ if 'newObjId' in class_dict:
+ res = class_dict['newObjId'](old_obj, trans_dict)
+ new_obj.db_newObjId = res
+ elif hasattr(old_obj, 'db_newObjId') and old_obj.db_newObjId is not None:
+ new_obj.db_newObjId = old_obj.db_newObjId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_oldObjId(self):
+ return self._db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self._db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self._db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self._db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBGroupExec(object):
+
+ vtType = 'group_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, group_name=None, group_type=None, completed=None, error=None, machine_id=None, annotations=None, loop_execs=None, module_execs=None, group_execs=None):
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_group_name = group_name
+ self._db_group_type = group_type
+ self._db_completed = completed
+ self._db_error = error
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_loop_execs = []
+ self.db_loop_execs_id_index = {}
+ if loop_execs is None:
+ self._db_loop_execs = []
+ else:
+ self._db_loop_execs = loop_execs
+ for v in self._db_loop_execs:
+ self.db_loop_execs_id_index[v.db_id] = v
+ self.db_deleted_module_execs = []
+ self.db_module_execs_id_index = {}
+ if module_execs is None:
+ self._db_module_execs = []
+ else:
+ self._db_module_execs = module_execs
+ for v in self._db_module_execs:
+ self.db_module_execs_id_index[v.db_id] = v
+ self.db_deleted_group_execs = []
+ self.db_group_execs_id_index = {}
+ if group_execs is None:
+ self._db_group_execs = []
+ else:
+ self._db_group_execs = group_execs
+ for v in self._db_group_execs:
+ self.db_group_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroupExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroupExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ group_name=self._db_group_name,
+ group_type=self._db_group_type,
+ completed=self._db_completed,
+ error=self._db_error,
+ machine_id=self._db_machine_id)
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_loop_execs is None:
+ cp._db_loop_execs = []
+ else:
+ cp._db_loop_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_loop_execs]
+ if self._db_module_execs is None:
+ cp._db_module_execs = []
+ else:
+ cp._db_module_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_module_execs]
+ if self._db_group_execs is None:
+ cp._db_group_execs = []
+ else:
+ cp._db_group_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_group_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_loop_execs_id_index = dict((v.db_id, v) for v in cp._db_loop_execs)
+ cp.db_module_execs_id_index = dict((v.db_id, v) for v in cp._db_module_execs)
+ cp.db_group_execs_id_index = dict((v.db_id, v) for v in cp._db_group_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroupExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'group_name' in class_dict:
+ res = class_dict['group_name'](old_obj, trans_dict)
+ new_obj.db_group_name = res
+ elif hasattr(old_obj, 'db_group_name') and old_obj.db_group_name is not None:
+ new_obj.db_group_name = old_obj.db_group_name
+ if 'group_type' in class_dict:
+ res = class_dict['group_type'](old_obj, trans_dict)
+ new_obj.db_group_type = res
+ elif hasattr(old_obj, 'db_group_type') and old_obj.db_group_type is not None:
+ new_obj.db_group_type = old_obj.db_group_type
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'loop_execs' in class_dict:
+ res = class_dict['loop_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_loop_exec(obj)
+ elif hasattr(old_obj, 'db_loop_execs') and old_obj.db_loop_execs is not None:
+ for obj in old_obj.db_loop_execs:
+ new_obj.db_add_loop_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_loop_execs') and hasattr(new_obj, 'db_deleted_loop_execs'):
+ for obj in old_obj.db_deleted_loop_execs:
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_loop_execs.append(n_obj)
+ if 'module_execs' in class_dict:
+ res = class_dict['module_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module_exec(obj)
+ elif hasattr(old_obj, 'db_module_execs') and old_obj.db_module_execs is not None:
+ for obj in old_obj.db_module_execs:
+ new_obj.db_add_module_exec(DBModuleExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_module_execs') and hasattr(new_obj, 'db_deleted_module_execs'):
+ for obj in old_obj.db_deleted_module_execs:
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_module_execs.append(n_obj)
+ if 'group_execs' in class_dict:
+ res = class_dict['group_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_group_exec(obj)
+ elif hasattr(old_obj, 'db_group_execs') and old_obj.db_group_execs is not None:
+ for obj in old_obj.db_group_execs:
+ new_obj.db_add_group_exec(DBGroupExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_group_execs') and hasattr(new_obj, 'db_deleted_group_execs'):
+ for obj in old_obj.db_deleted_group_execs:
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_group_execs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_loop_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_loop_exec(child)
+ to_del = []
+ for child in self.db_module_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ to_del = []
+ for child in self.db_group_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_group_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_loop_execs)
+ children.extend(self.db_deleted_module_execs)
+ children.extend(self.db_deleted_group_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_loop_execs = []
+ self.db_deleted_module_execs = []
+ self.db_deleted_group_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_loop_execs:
+ if child.has_changes():
+ return True
+ for child in self._db_module_execs:
+ if child.has_changes():
+ return True
+ for child in self._db_group_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_group_name(self):
+ return self._db_group_name
+ def __set_db_group_name(self, group_name):
+ self._db_group_name = group_name
+ self.is_dirty = True
+ db_group_name = property(__get_db_group_name, __set_db_group_name)
+ def db_add_group_name(self, group_name):
+ self._db_group_name = group_name
+ def db_change_group_name(self, group_name):
+ self._db_group_name = group_name
+ def db_delete_group_name(self, group_name):
+ self._db_group_name = None
+
+ def __get_db_group_type(self):
+ return self._db_group_type
+ def __set_db_group_type(self, group_type):
+ self._db_group_type = group_type
+ self.is_dirty = True
+ db_group_type = property(__get_db_group_type, __set_db_group_type)
+ def db_add_group_type(self, group_type):
+ self._db_group_type = group_type
+ def db_change_group_type(self, group_type):
+ self._db_group_type = group_type
+ def db_delete_group_type(self, group_type):
+ self._db_group_type = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_loop_execs(self):
+ return self._db_loop_execs
+ def __set_db_loop_execs(self, loop_execs):
+ self._db_loop_execs = loop_execs
+ self.is_dirty = True
+ db_loop_execs = property(__get_db_loop_execs, __set_db_loop_execs)
+ def db_get_loop_execs(self):
+ return self._db_loop_execs
+ def db_add_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_change_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ self._db_loop_execs[i] = loop_exec
+ found = True
+ break
+ if not found:
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_delete_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ if not self._db_loop_execs[i].is_new:
+ self.db_deleted_loop_execs.append(self._db_loop_execs[i])
+ del self._db_loop_execs[i]
+ break
+ del self.db_loop_execs_id_index[loop_exec.db_id]
+ def db_get_loop_exec(self, key):
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == key:
+ return self._db_loop_execs[i]
+ return None
+ def db_get_loop_exec_by_id(self, key):
+ return self.db_loop_execs_id_index[key]
+ def db_has_loop_exec_with_id(self, key):
+ return key in self.db_loop_execs_id_index
+
+ def __get_db_module_execs(self):
+ return self._db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self._db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self._db_module_execs
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self._db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == module_exec.db_id:
+ self._db_module_execs[i] = module_exec
+ found = True
+ break
+ if not found:
+ self._db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == module_exec.db_id:
+ if not self._db_module_execs[i].is_new:
+ self.db_deleted_module_execs.append(self._db_module_execs[i])
+ del self._db_module_execs[i]
+ break
+ del self.db_module_execs_id_index[module_exec.db_id]
+ def db_get_module_exec(self, key):
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == key:
+ return self._db_module_execs[i]
+ return None
+ def db_get_module_exec_by_id(self, key):
+ return self.db_module_execs_id_index[key]
+ def db_has_module_exec_with_id(self, key):
+ return key in self.db_module_execs_id_index
+
+ def __get_db_group_execs(self):
+ return self._db_group_execs
+ def __set_db_group_execs(self, group_execs):
+ self._db_group_execs = group_execs
+ self.is_dirty = True
+ db_group_execs = property(__get_db_group_execs, __set_db_group_execs)
+ def db_get_group_execs(self):
+ return self._db_group_execs
+ def db_add_group_exec(self, group_exec):
+ self.is_dirty = True
+ self._db_group_execs.append(group_exec)
+ self.db_group_execs_id_index[group_exec.db_id] = group_exec
+ def db_change_group_exec(self, group_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_group_execs)):
+ if self._db_group_execs[i].db_id == group_exec.db_id:
+ self._db_group_execs[i] = group_exec
+ found = True
+ break
+ if not found:
+ self._db_group_execs.append(group_exec)
+ self.db_group_execs_id_index[group_exec.db_id] = group_exec
+ def db_delete_group_exec(self, group_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_group_execs)):
+ if self._db_group_execs[i].db_id == group_exec.db_id:
+ if not self._db_group_execs[i].is_new:
+ self.db_deleted_group_execs.append(self._db_group_execs[i])
+ del self._db_group_execs[i]
+ break
+ del self.db_group_execs_id_index[group_exec.db_id]
+ def db_get_group_exec(self, key):
+ for i in xrange(len(self._db_group_execs)):
+ if self._db_group_execs[i].db_id == key:
+ return self._db_group_execs[i]
+ return None
+ def db_get_group_exec_by_id(self, key):
+ return self.db_group_execs_id_index[key]
+ def db_has_group_exec_with_id(self, key):
+ return key in self.db_group_execs_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBPackage(object):
+
+ vtType = 'package'
+
+ def __init__(self, id=None, name=None, identifier=None, codepath=None, load_configuration=None, version=None, description=None, module_descriptors=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_identifier = identifier
+ self._db_codepath = codepath
+ self._db_load_configuration = load_configuration
+ self._db_version = version
+ self._db_description = description
+ self.db_deleted_module_descriptors = []
+ self.db_module_descriptors_id_index = {}
+ self.db_module_descriptors_name_index = {}
+ if module_descriptors is None:
+ self._db_module_descriptors = []
+ else:
+ self._db_module_descriptors = module_descriptors
+ for v in self._db_module_descriptors:
+ self.db_module_descriptors_id_index[v.db_id] = v
+ self.db_module_descriptors_name_index[(v.db_name,v.db_namespace,v.db_version)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPackage.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPackage(id=self._db_id,
+ name=self._db_name,
+ identifier=self._db_identifier,
+ codepath=self._db_codepath,
+ load_configuration=self._db_load_configuration,
+ version=self._db_version,
+ description=self._db_description)
+ if self._db_module_descriptors is None:
+ cp._db_module_descriptors = []
+ else:
+ cp._db_module_descriptors = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_module_descriptors]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_module_descriptors_id_index = dict((v.db_id, v) for v in cp._db_module_descriptors)
+ cp.db_module_descriptors_name_index = dict(((v.db_name,v.db_namespace,v.db_version), v) for v in cp._db_module_descriptors)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPackage()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'identifier' in class_dict:
+ res = class_dict['identifier'](old_obj, trans_dict)
+ new_obj.db_identifier = res
+ elif hasattr(old_obj, 'db_identifier') and old_obj.db_identifier is not None:
+ new_obj.db_identifier = old_obj.db_identifier
+ if 'codepath' in class_dict:
+ res = class_dict['codepath'](old_obj, trans_dict)
+ new_obj.db_codepath = res
+ elif hasattr(old_obj, 'db_codepath') and old_obj.db_codepath is not None:
+ new_obj.db_codepath = old_obj.db_codepath
+ if 'load_configuration' in class_dict:
+ res = class_dict['load_configuration'](old_obj, trans_dict)
+ new_obj.db_load_configuration = res
+ elif hasattr(old_obj, 'db_load_configuration') and old_obj.db_load_configuration is not None:
+ new_obj.db_load_configuration = old_obj.db_load_configuration
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'description' in class_dict:
+ res = class_dict['description'](old_obj, trans_dict)
+ new_obj.db_description = res
+ elif hasattr(old_obj, 'db_description') and old_obj.db_description is not None:
+ new_obj.db_description = old_obj.db_description
+ if 'module_descriptors' in class_dict:
+ res = class_dict['module_descriptors'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module_descriptor(obj)
+ elif hasattr(old_obj, 'db_module_descriptors') and old_obj.db_module_descriptors is not None:
+ for obj in old_obj.db_module_descriptors:
+ new_obj.db_add_module_descriptor(DBModuleDescriptor.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_module_descriptors') and hasattr(new_obj, 'db_deleted_module_descriptors'):
+ for obj in old_obj.db_deleted_module_descriptors:
+ n_obj = DBModuleDescriptor.update_version(obj, trans_dict)
+ new_obj.db_deleted_module_descriptors.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_descriptors:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_descriptor(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_descriptors)
+ if remove:
+ self.db_deleted_module_descriptors = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_module_descriptors:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_identifier(self):
+ return self._db_identifier
+ def __set_db_identifier(self, identifier):
+ self._db_identifier = identifier
+ self.is_dirty = True
+ db_identifier = property(__get_db_identifier, __set_db_identifier)
+ def db_add_identifier(self, identifier):
+ self._db_identifier = identifier
+ def db_change_identifier(self, identifier):
+ self._db_identifier = identifier
+ def db_delete_identifier(self, identifier):
+ self._db_identifier = None
+
+ def __get_db_codepath(self):
+ return self._db_codepath
+ def __set_db_codepath(self, codepath):
+ self._db_codepath = codepath
+ self.is_dirty = True
+ db_codepath = property(__get_db_codepath, __set_db_codepath)
+ def db_add_codepath(self, codepath):
+ self._db_codepath = codepath
+ def db_change_codepath(self, codepath):
+ self._db_codepath = codepath
+ def db_delete_codepath(self, codepath):
+ self._db_codepath = None
+
+ def __get_db_load_configuration(self):
+ return self._db_load_configuration
+ def __set_db_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ self.is_dirty = True
+ db_load_configuration = property(__get_db_load_configuration, __set_db_load_configuration)
+ def db_add_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ def db_change_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ def db_delete_load_configuration(self, load_configuration):
+ self._db_load_configuration = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_description(self):
+ return self._db_description
+ def __set_db_description(self, description):
+ self._db_description = description
+ self.is_dirty = True
+ db_description = property(__get_db_description, __set_db_description)
+ def db_add_description(self, description):
+ self._db_description = description
+ def db_change_description(self, description):
+ self._db_description = description
+ def db_delete_description(self, description):
+ self._db_description = None
+
+ def __get_db_module_descriptors(self):
+ return self._db_module_descriptors
+ def __set_db_module_descriptors(self, module_descriptors):
+ self._db_module_descriptors = module_descriptors
+ self.is_dirty = True
+ db_module_descriptors = property(__get_db_module_descriptors, __set_db_module_descriptors)
+ def db_get_module_descriptors(self):
+ return self._db_module_descriptors
+ def db_add_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ self._db_module_descriptors.append(module_descriptor)
+ self.db_module_descriptors_id_index[module_descriptor.db_id] = module_descriptor
+ self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)] = module_descriptor
+ def db_change_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == module_descriptor.db_id:
+ self._db_module_descriptors[i] = module_descriptor
+ found = True
+ break
+ if not found:
+ self._db_module_descriptors.append(module_descriptor)
+ self.db_module_descriptors_id_index[module_descriptor.db_id] = module_descriptor
+ self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)] = module_descriptor
+ def db_delete_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == module_descriptor.db_id:
+ if not self._db_module_descriptors[i].is_new:
+ self.db_deleted_module_descriptors.append(self._db_module_descriptors[i])
+ del self._db_module_descriptors[i]
+ break
+ del self.db_module_descriptors_id_index[module_descriptor.db_id]
+ del self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)]
+ def db_get_module_descriptor(self, key):
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == key:
+ return self._db_module_descriptors[i]
+ return None
+ def db_get_module_descriptor_by_id(self, key):
+ return self.db_module_descriptors_id_index[key]
+ def db_has_module_descriptor_with_id(self, key):
+ return key in self.db_module_descriptors_id_index
+ def db_get_module_descriptor_by_name(self, key):
+ return self.db_module_descriptors_name_index[key]
+ def db_has_module_descriptor_with_name(self, key):
+ return key in self.db_module_descriptors_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, items=None, id=None, user=None, ip=None, session=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, completed=None, name=None):
+ self.db_deleted_items = []
+ self.db_items_id_index = {}
+ if items is None:
+ self._db_items = []
+ else:
+ self._db_items = items
+ for v in self._db_items:
+ self.db_items_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_user = user
+ self._db_ip = ip
+ self._db_session = session
+ self._db_vt_version = vt_version
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_parent_id = parent_id
+ self._db_parent_type = parent_type
+ self._db_parent_version = parent_version
+ self._db_completed = completed
+ self._db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflowExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec(id=self._db_id,
+ user=self._db_user,
+ ip=self._db_ip,
+ session=self._db_session,
+ vt_version=self._db_vt_version,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ parent_id=self._db_parent_id,
+ parent_type=self._db_parent_type,
+ parent_version=self._db_parent_version,
+ completed=self._db_completed,
+ name=self._db_name)
+ if self._db_items is None:
+ cp._db_items = []
+ else:
+ cp._db_items = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_items]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_items_id_index = dict((v.db_id, v) for v in cp._db_items)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflowExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'items' in class_dict:
+ res = class_dict['items'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item(obj)
+ elif hasattr(old_obj, 'db_items') and old_obj.db_items is not None:
+ for obj in old_obj.db_items:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item(DBGroupExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_items') and hasattr(new_obj, 'db_deleted_items'):
+ for obj in old_obj.db_deleted_items:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_items.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_items.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'ip' in class_dict:
+ res = class_dict['ip'](old_obj, trans_dict)
+ new_obj.db_ip = res
+ elif hasattr(old_obj, 'db_ip') and old_obj.db_ip is not None:
+ new_obj.db_ip = old_obj.db_ip
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'vt_version' in class_dict:
+ res = class_dict['vt_version'](old_obj, trans_dict)
+ new_obj.db_vt_version = res
+ elif hasattr(old_obj, 'db_vt_version') and old_obj.db_vt_version is not None:
+ new_obj.db_vt_version = old_obj.db_vt_version
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'parent_id' in class_dict:
+ res = class_dict['parent_id'](old_obj, trans_dict)
+ new_obj.db_parent_id = res
+ elif hasattr(old_obj, 'db_parent_id') and old_obj.db_parent_id is not None:
+ new_obj.db_parent_id = old_obj.db_parent_id
+ if 'parent_type' in class_dict:
+ res = class_dict['parent_type'](old_obj, trans_dict)
+ new_obj.db_parent_type = res
+ elif hasattr(old_obj, 'db_parent_type') and old_obj.db_parent_type is not None:
+ new_obj.db_parent_type = old_obj.db_parent_type
+ if 'parent_version' in class_dict:
+ res = class_dict['parent_version'](old_obj, trans_dict)
+ new_obj.db_parent_version = res
+ elif hasattr(old_obj, 'db_parent_version') and old_obj.db_parent_version is not None:
+ new_obj.db_parent_version = old_obj.db_parent_version
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_items:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_items)
+ if remove:
+ self.db_deleted_items = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_items:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_items(self):
+ return self._db_items
+ def __set_db_items(self, items):
+ self._db_items = items
+ self.is_dirty = True
+ db_items = property(__get_db_items, __set_db_items)
+ def db_get_items(self):
+ return self._db_items
+ def db_add_item(self, item):
+ self.is_dirty = True
+ self._db_items.append(item)
+ self.db_items_id_index[item.db_id] = item
+ def db_change_item(self, item):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_items)):
+ if self._db_items[i].db_id == item.db_id:
+ self._db_items[i] = item
+ found = True
+ break
+ if not found:
+ self._db_items.append(item)
+ self.db_items_id_index[item.db_id] = item
+ def db_delete_item(self, item):
+ self.is_dirty = True
+ for i in xrange(len(self._db_items)):
+ if self._db_items[i].db_id == item.db_id:
+ if not self._db_items[i].is_new:
+ self.db_deleted_items.append(self._db_items[i])
+ del self._db_items[i]
+ break
+ del self.db_items_id_index[item.db_id]
+ def db_get_item(self, key):
+ for i in xrange(len(self._db_items)):
+ if self._db_items[i].db_id == key:
+ return self._db_items[i]
+ return None
+ def db_get_item_by_id(self, key):
+ return self.db_items_id_index[key]
+ def db_has_item_with_id(self, key):
+ return key in self.db_items_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_ip(self):
+ return self._db_ip
+ def __set_db_ip(self, ip):
+ self._db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self._db_ip = ip
+ def db_change_ip(self, ip):
+ self._db_ip = ip
+ def db_delete_ip(self, ip):
+ self._db_ip = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_vt_version(self):
+ return self._db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self._db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self._db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self._db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self._db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self._db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self._db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self._db_parent_version = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLoopExec(object):
+
+ vtType = 'loop_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, completed=None, error=None, module_execs=None, group_execs=None):
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_completed = completed
+ self._db_error = error
+ self.db_deleted_module_execs = []
+ self.db_module_execs_id_index = {}
+ if module_execs is None:
+ self._db_module_execs = []
+ else:
+ self._db_module_execs = module_execs
+ for v in self._db_module_execs:
+ self.db_module_execs_id_index[v.db_id] = v
+ self.db_deleted_group_execs = []
+ self.db_group_execs_id_index = {}
+ if group_execs is None:
+ self._db_group_execs = []
+ else:
+ self._db_group_execs = group_execs
+ for v in self._db_group_execs:
+ self.db_group_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLoopExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLoopExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ completed=self._db_completed,
+ error=self._db_error)
+ if self._db_module_execs is None:
+ cp._db_module_execs = []
+ else:
+ cp._db_module_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_module_execs]
+ if self._db_group_execs is None:
+ cp._db_group_execs = []
+ else:
+ cp._db_group_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_group_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_module_execs_id_index = dict((v.db_id, v) for v in cp._db_module_execs)
+ cp.db_group_execs_id_index = dict((v.db_id, v) for v in cp._db_group_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLoopExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'module_execs' in class_dict:
+ res = class_dict['module_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module_exec(obj)
+ elif hasattr(old_obj, 'db_module_execs') and old_obj.db_module_execs is not None:
+ for obj in old_obj.db_module_execs:
+ new_obj.db_add_module_exec(DBModuleExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_module_execs') and hasattr(new_obj, 'db_deleted_module_execs'):
+ for obj in old_obj.db_deleted_module_execs:
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_module_execs.append(n_obj)
+ if 'group_execs' in class_dict:
+ res = class_dict['group_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_group_exec(obj)
+ elif hasattr(old_obj, 'db_group_execs') and old_obj.db_group_execs is not None:
+ for obj in old_obj.db_group_execs:
+ new_obj.db_add_group_exec(DBGroupExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_group_execs') and hasattr(new_obj, 'db_deleted_group_execs'):
+ for obj in old_obj.db_deleted_group_execs:
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_group_execs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_exec(child)
+ to_del = []
+ for child in self.db_group_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_group_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_execs)
+ children.extend(self.db_deleted_group_execs)
+ if remove:
+ self.db_deleted_module_execs = []
+ self.db_deleted_group_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_module_execs:
+ if child.has_changes():
+ return True
+ for child in self._db_group_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_module_execs(self):
+ return self._db_module_execs
+ def __set_db_module_execs(self, module_execs):
+ self._db_module_execs = module_execs
+ self.is_dirty = True
+ db_module_execs = property(__get_db_module_execs, __set_db_module_execs)
+ def db_get_module_execs(self):
+ return self._db_module_execs
+ def db_add_module_exec(self, module_exec):
+ self.is_dirty = True
+ self._db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_change_module_exec(self, module_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == module_exec.db_id:
+ self._db_module_execs[i] = module_exec
+ found = True
+ break
+ if not found:
+ self._db_module_execs.append(module_exec)
+ self.db_module_execs_id_index[module_exec.db_id] = module_exec
+ def db_delete_module_exec(self, module_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == module_exec.db_id:
+ if not self._db_module_execs[i].is_new:
+ self.db_deleted_module_execs.append(self._db_module_execs[i])
+ del self._db_module_execs[i]
+ break
+ del self.db_module_execs_id_index[module_exec.db_id]
+ def db_get_module_exec(self, key):
+ for i in xrange(len(self._db_module_execs)):
+ if self._db_module_execs[i].db_id == key:
+ return self._db_module_execs[i]
+ return None
+ def db_get_module_exec_by_id(self, key):
+ return self.db_module_execs_id_index[key]
+ def db_has_module_exec_with_id(self, key):
+ return key in self.db_module_execs_id_index
+
+ def __get_db_group_execs(self):
+ return self._db_group_execs
+ def __set_db_group_execs(self, group_execs):
+ self._db_group_execs = group_execs
+ self.is_dirty = True
+ db_group_execs = property(__get_db_group_execs, __set_db_group_execs)
+ def db_get_group_execs(self):
+ return self._db_group_execs
+ def db_add_group_exec(self, group_exec):
+ self.is_dirty = True
+ self._db_group_execs.append(group_exec)
+ self.db_group_execs_id_index[group_exec.db_id] = group_exec
+ def db_change_group_exec(self, group_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_group_execs)):
+ if self._db_group_execs[i].db_id == group_exec.db_id:
+ self._db_group_execs[i] = group_exec
+ found = True
+ break
+ if not found:
+ self._db_group_execs.append(group_exec)
+ self.db_group_execs_id_index[group_exec.db_id] = group_exec
+ def db_delete_group_exec(self, group_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_group_execs)):
+ if self._db_group_execs[i].db_id == group_exec.db_id:
+ if not self._db_group_execs[i].is_new:
+ self.db_deleted_group_execs.append(self._db_group_execs[i])
+ del self._db_group_execs[i]
+ break
+ del self.db_group_execs_id_index[group_exec.db_id]
+ def db_get_group_exec(self, key):
+ for i in xrange(len(self._db_group_execs)):
+ if self._db_group_execs[i].db_id == key:
+ return self._db_group_execs[i]
+ return None
+ def db_get_group_exec_by_id(self, key):
+ return self.db_group_execs_id_index[key]
+ def db_has_group_exec_with_id(self, key):
+ return key in self.db_group_execs_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self._db_id = id
+ self.db_deleted_ports = []
+ self.db_ports_id_index = {}
+ self.db_ports_type_index = {}
+ if ports is None:
+ self._db_ports = []
+ else:
+ self._db_ports = ports
+ for v in self._db_ports:
+ self.db_ports_id_index[v.db_id] = v
+ self.db_ports_type_index[v.db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBConnection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection(id=self._db_id)
+ if self._db_ports is None:
+ cp._db_ports = []
+ else:
+ cp._db_ports = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ports]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_ports_id_index = dict((v.db_id, v) for v in cp._db_ports)
+ cp.db_ports_type_index = dict((v.db_type, v) for v in cp._db_ports)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBConnection()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ports' in class_dict:
+ res = class_dict['ports'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_port(obj)
+ elif hasattr(old_obj, 'db_ports') and old_obj.db_ports is not None:
+ for obj in old_obj.db_ports:
+ new_obj.db_add_port(DBPort.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_ports') and hasattr(new_obj, 'db_deleted_ports'):
+ for obj in old_obj.db_deleted_ports:
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_ports.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_ports)
+ if remove:
+ self.db_deleted_ports = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ports(self):
+ return self._db_ports
+ def __set_db_ports(self, ports):
+ self._db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self._db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ self._db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ if not self._db_ports[i].is_new:
+ self.db_deleted_ports.append(self._db_ports[i])
+ del self._db_ports[i]
+ break
+ del self.db_ports_id_index[port.db_id]
+ del self.db_ports_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == key:
+ return self._db_ports[i]
+ return None
+ def db_get_port_by_id(self, key):
+ return self.db_ports_id_index[key]
+ def db_has_port_with_id(self, key):
+ return key in self.db_ports_id_index
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return key in self.db_ports_type_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, operations=None, id=None, prevId=None, date=None, session=None, user=None, prune=None, annotations=None):
+ self.db_deleted_operations = []
+ self.db_operations_id_index = {}
+ if operations is None:
+ self._db_operations = []
+ else:
+ self._db_operations = operations
+ for v in self._db_operations:
+ self.db_operations_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_prevId = prevId
+ self._db_date = date
+ self._db_session = session
+ self._db_user = user
+ self._db_prune = prune
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction(id=self._db_id,
+ prevId=self._db_prevId,
+ date=self._db_date,
+ session=self._db_session,
+ user=self._db_user,
+ prune=self._db_prune)
+ if self._db_operations is None:
+ cp._db_operations = []
+ else:
+ cp._db_operations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_operations]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prevId') and ('action', self._db_prevId) in id_remap:
+ cp._db_prevId = id_remap[('action', self._db_prevId)]
+
+ # recreate indices and set flags
+ cp.db_operations_id_index = dict((v.db_id, v) for v in cp._db_operations)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'operations' in class_dict:
+ res = class_dict['operations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_operation(obj)
+ elif hasattr(old_obj, 'db_operations') and old_obj.db_operations is not None:
+ for obj in old_obj.db_operations:
+ if obj.vtType == 'add':
+ new_obj.db_add_operation(DBAdd.update_version(obj, trans_dict))
+ elif obj.vtType == 'delete':
+ new_obj.db_add_operation(DBDelete.update_version(obj, trans_dict))
+ elif obj.vtType == 'change':
+ new_obj.db_add_operation(DBChange.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_operations') and hasattr(new_obj, 'db_deleted_operations'):
+ for obj in old_obj.db_deleted_operations:
+ if obj.vtType == 'add':
+ n_obj = DBAdd.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'delete':
+ n_obj = DBDelete.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'change':
+ n_obj = DBChange.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'prevId' in class_dict:
+ res = class_dict['prevId'](old_obj, trans_dict)
+ new_obj.db_prevId = res
+ elif hasattr(old_obj, 'db_prevId') and old_obj.db_prevId is not None:
+ new_obj.db_prevId = old_obj.db_prevId
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'prune' in class_dict:
+ res = class_dict['prune'](old_obj, trans_dict)
+ new_obj.db_prune = res
+ elif hasattr(old_obj, 'db_prune') and old_obj.db_prune is not None:
+ new_obj.db_prune = old_obj.db_prune
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_operations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_operations)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_operations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_operations(self):
+ return self._db_operations
+ def __set_db_operations(self, operations):
+ self._db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self._db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ self._db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ if not self._db_operations[i].is_new:
+ self.db_deleted_operations.append(self._db_operations[i])
+ del self._db_operations[i]
+ break
+ del self.db_operations_id_index[operation.db_id]
+ def db_get_operation(self, key):
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == key:
+ return self._db_operations[i]
+ return None
+ def db_get_operation_by_id(self, key):
+ return self.db_operations_id_index[key]
+ def db_has_operation_with_id(self, key):
+ return key in self.db_operations_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_prevId(self):
+ return self._db_prevId
+ def __set_db_prevId(self, prevId):
+ self._db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self._db_prevId = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_prune(self):
+ return self._db_prune
+ def __set_db_prune(self, prune):
+ self._db_prune = prune
+ self.is_dirty = True
+ db_prune = property(__get_db_prune, __set_db_prune)
+ def db_add_prune(self, prune):
+ self._db_prune = prune
+ def db_change_prune(self, prune):
+ self._db_prune = prune
+ def db_delete_prune(self, prune):
+ self._db_prune = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBDelete.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBDelete()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, actions=None, tags=None, annotations=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self._db_actions = []
+ else:
+ self._db_actions = actions
+ for v in self._db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self._db_tags = []
+ else:
+ self._db_tags = tags
+ for v in self._db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_actions is None:
+ cp._db_actions = []
+ else:
+ cp._db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actions]
+ if self._db_tags is None:
+ cp._db_tags = []
+ else:
+ cp._db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_tags]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_actions_id_index = dict((v.db_id, v) for v in cp._db_actions)
+ cp.db_tags_id_index = dict((v.db_id, v) for v in cp._db_tags)
+ cp.db_tags_name_index = dict((v.db_name, v) for v in cp._db_tags)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'actions' in class_dict:
+ res = class_dict['actions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_action(obj)
+ elif hasattr(old_obj, 'db_actions') and old_obj.db_actions is not None:
+ for obj in old_obj.db_actions:
+ new_obj.db_add_action(DBAction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actions') and hasattr(new_obj, 'db_deleted_actions'):
+ for obj in old_obj.db_deleted_actions:
+ n_obj = DBAction.update_version(obj, trans_dict)
+ new_obj.db_deleted_actions.append(n_obj)
+ if 'tags' in class_dict:
+ res = class_dict['tags'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_tag(obj)
+ elif hasattr(old_obj, 'db_tags') and old_obj.db_tags is not None:
+ for obj in old_obj.db_tags:
+ new_obj.db_add_tag(DBTag.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_tags') and hasattr(new_obj, 'db_deleted_tags'):
+ for obj in old_obj.db_deleted_tags:
+ n_obj = DBTag.update_version(obj, trans_dict)
+ new_obj.db_deleted_tags.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_actions:
+ if child.has_changes():
+ return True
+ for child in self._db_tags:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_actions(self):
+ return self._db_actions
+ def __set_db_actions(self, actions):
+ self._db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self._db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ self._db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ if not self._db_actions[i].is_new:
+ self.db_deleted_actions.append(self._db_actions[i])
+ del self._db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == key:
+ return self._db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return key in self.db_actions_id_index
+
+ def __get_db_tags(self):
+ return self._db_tags
+ def __set_db_tags(self, tags):
+ self._db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self._db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ self._db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ if not self._db_tags[i].is_new:
+ self.db_deleted_tags.append(self._db_tags[i])
+ del self._db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == key:
+ return self._db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return key in self.db_tags_id_index
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return key in self.db_tags_name_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, module_name=None, completed=None, error=None, abstraction_id=None, abstraction_version=None, machine_id=None, annotations=None, loop_execs=None):
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_module_name = module_name
+ self._db_completed = completed
+ self._db_error = error
+ self._db_abstraction_id = abstraction_id
+ self._db_abstraction_version = abstraction_version
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_loop_execs = []
+ self.db_loop_execs_id_index = {}
+ if loop_execs is None:
+ self._db_loop_execs = []
+ else:
+ self._db_loop_execs = loop_execs
+ for v in self._db_loop_execs:
+ self.db_loop_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ module_name=self._db_module_name,
+ completed=self._db_completed,
+ error=self._db_error,
+ abstraction_id=self._db_abstraction_id,
+ abstraction_version=self._db_abstraction_version,
+ machine_id=self._db_machine_id)
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_loop_execs is None:
+ cp._db_loop_execs = []
+ else:
+ cp._db_loop_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_loop_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_loop_execs_id_index = dict((v.db_id, v) for v in cp._db_loop_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'module_name' in class_dict:
+ res = class_dict['module_name'](old_obj, trans_dict)
+ new_obj.db_module_name = res
+ elif hasattr(old_obj, 'db_module_name') and old_obj.db_module_name is not None:
+ new_obj.db_module_name = old_obj.db_module_name
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'abstraction_id' in class_dict:
+ res = class_dict['abstraction_id'](old_obj, trans_dict)
+ new_obj.db_abstraction_id = res
+ elif hasattr(old_obj, 'db_abstraction_id') and old_obj.db_abstraction_id is not None:
+ new_obj.db_abstraction_id = old_obj.db_abstraction_id
+ if 'abstraction_version' in class_dict:
+ res = class_dict['abstraction_version'](old_obj, trans_dict)
+ new_obj.db_abstraction_version = res
+ elif hasattr(old_obj, 'db_abstraction_version') and old_obj.db_abstraction_version is not None:
+ new_obj.db_abstraction_version = old_obj.db_abstraction_version
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'loop_execs' in class_dict:
+ res = class_dict['loop_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_loop_exec(obj)
+ elif hasattr(old_obj, 'db_loop_execs') and old_obj.db_loop_execs is not None:
+ for obj in old_obj.db_loop_execs:
+ new_obj.db_add_loop_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_loop_execs') and hasattr(new_obj, 'db_deleted_loop_execs'):
+ for obj in old_obj.db_deleted_loop_execs:
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_loop_execs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_loop_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_loop_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_loop_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_loop_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_loop_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_module_name(self):
+ return self._db_module_name
+ def __set_db_module_name(self, module_name):
+ self._db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self._db_module_name = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_abstraction_id(self):
+ return self._db_abstraction_id
+ def __set_db_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ self.is_dirty = True
+ db_abstraction_id = property(__get_db_abstraction_id, __set_db_abstraction_id)
+ def db_add_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_change_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = abstraction_id
+ def db_delete_abstraction_id(self, abstraction_id):
+ self._db_abstraction_id = None
+
+ def __get_db_abstraction_version(self):
+ return self._db_abstraction_version
+ def __set_db_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ self.is_dirty = True
+ db_abstraction_version = property(__get_db_abstraction_version, __set_db_abstraction_version)
+ def db_add_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ def db_change_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = abstraction_version
+ def db_delete_abstraction_version(self, abstraction_version):
+ self._db_abstraction_version = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_loop_execs(self):
+ return self._db_loop_execs
+ def __set_db_loop_execs(self, loop_execs):
+ self._db_loop_execs = loop_execs
+ self.is_dirty = True
+ db_loop_execs = property(__get_db_loop_execs, __set_db_loop_execs)
+ def db_get_loop_execs(self):
+ return self._db_loop_execs
+ def db_add_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_change_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ self._db_loop_execs[i] = loop_exec
+ found = True
+ break
+ if not found:
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_delete_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ if not self._db_loop_execs[i].is_new:
+ self.db_deleted_loop_execs.append(self._db_loop_execs[i])
+ del self._db_loop_execs[i]
+ break
+ del self.db_loop_execs_id_index[loop_exec.db_id]
+ def db_get_loop_exec(self, key):
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == key:
+ return self._db_loop_execs[i]
+ return None
+ def db_get_loop_exec_by_id(self, key):
+ return self.db_loop_execs_id_index[key]
+ def db_has_loop_exec_with_id(self, key):
+ return key in self.db_loop_execs_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
diff --git a/vistrails/db/versions/v0_9_5/domain/id_scope.py b/vistrails/db/versions/v0_9_5/domain/id_scope.py
new file mode 100644
index 0000000..0e07f02
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/domain/id_scope.py
@@ -0,0 +1,85 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L, remap=None):
+ self.ids = {}
+ self.beginId = beginId
+ if remap is None:
+ self.remap = {}
+ else:
+ self.remap = remap
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ cp.remap = copy.copy(self.remap)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ except KeyError:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ if self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+ except KeyError:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v0_9_5/domain/log.py b/vistrails/db/versions/v0_9_5/domain/log.py
new file mode 100644
index 0000000..0328b80
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/domain/log.py
@@ -0,0 +1,69 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBLog as _DBLog
+from auto_gen import DBAbstraction, DBModule, DBGroup
+from id_scope import IdScope
+
+import copy
+
+class DBLog(_DBLog):
+
+ def __init__(self, *args, **kwargs):
+ _DBLog.__init__(self, *args, **kwargs)
+ self.id_scope = IdScope(1,
+ {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBLog.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBLog
+ cp.id_scope = copy.copy(self.id_scope)
+
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ new_obj = _DBLog.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
diff --git a/vistrails/db/versions/v0_9_5/domain/registry.py b/vistrails/db/versions/v0_9_5/domain/registry.py
new file mode 100644
index 0000000..70e47ab
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/domain/registry.py
@@ -0,0 +1,61 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBRegistry as _DBRegistry, DBPackage, DBModuleDescriptor, \
+ DBPortSpec
+from id_scope import IdScope
+
+class DBRegistry(_DBRegistry):
+ def __init__(self, *args, **kwargs):
+ _DBRegistry.__init__(self, *args, **kwargs)
+ self.idScope = IdScope()
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRegistry()
+ new_obj = _DBRegistry.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ for package in self.db_packages:
+ self.idScope.updateBeginId(DBPackage.vtType, package.db_id+1)
+ for descriptor in package.db_module_descriptors:
+ self.idScope.updateBeginId(DBModuleDescriptor.vtType,
+ descriptor.db_id+1)
+ for port_spec in descriptor.db_portSpecs:
+ self.idScope.updateBeginId(DBPortSpec.vtType,
+ port_spec.db_id+1)
diff --git a/vistrails/db/versions/v0_9_5/domain/vistrail.py b/vistrails/db/versions/v0_9_5/domain/vistrail.py
new file mode 100644
index 0000000..a007a32
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/domain/vistrail.py
@@ -0,0 +1,127 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from auto_gen import DBVistrail as _DBVistrail
+from auto_gen import DBAdd, DBChange, DBDelete, DBAbstraction, DBGroup, \
+ DBModule
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAdd.vtType: 'operation',
+ DBChange.vtType: 'operation',
+ DBDelete.vtType: 'operation',
+ DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ self.idScope.setBeginId('action', 1)
+ self.db_objects = {}
+
+ # keep a reference to the current logging information here
+ self.db_log_filename = None
+ self.log = None
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBVistrail.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBVistrail
+
+ cp.idScope = copy.copy(self.idScope)
+ cp.db_objects = copy.copy(self.db_objects)
+ cp.db_log_filename = self.db_log_filename
+ if self.log is not None:
+ cp.log = copy.copy(self.log)
+ else:
+ cp.log = None
+
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ new_obj = _DBVistrail.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ if hasattr(old_obj, 'db_log_filename'):
+ new_obj.db_log_filename = old_obj.db_log_filename
+ if hasattr(old_obj, 'log'):
+ new_obj.log = old_obj.log
+ return new_obj
+
+ def update_id_scope(self):
+ def getOldObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_oldObjId
+ return operation.db_objectId
+
+ def getNewObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_newObjId
+ return operation.db_objectId
+
+ for action in self.db_actions:
+ self.idScope.updateBeginId('action', action.db_id+1)
+ if action.db_session is not None:
+ self.idScope.updateBeginId('session', action.db_session + 1)
+ for operation in action.db_operations:
+ self.idScope.updateBeginId('operation', operation.db_id+1)
+ if operation.vtType == 'add' or operation.vtType == 'change':
+ # update ids of data
+ self.idScope.updateBeginId(operation.db_what,
+ getNewObjId(operation)+1)
+ if operation.db_data is None:
+ if operation.vtType == 'change':
+ operation.db_objectId = operation.db_oldObjId
+ self.db_add_object(operation.db_data)
+ for annotation in action.db_annotations:
+ self.idScope.updateBeginId('annotation', annotation.db_id+1)
+
+ def db_add_object(self, obj):
+ self.db_objects[(obj.vtType, obj.db_id)] = obj
+
+ def db_get_object(self, type, id):
+ return self.db_objects.get((type, id), None)
+
+ def db_update_object(self, obj, **kwargs):
+ # want to swap out old object with a new version
+ # need this for updating aliases...
+ # hack it using setattr...
+ real_obj = self.db_objects[(obj.vtType, obj.db_id)]
+ for (k, v) in kwargs.iteritems():
+ if hasattr(real_obj, k):
+ setattr(real_obj, k, v)
diff --git a/vistrails/db/versions/v0_9_5/domain/workflow.py b/vistrails/db/versions/v0_9_5/domain/workflow.py
new file mode 100644
index 0000000..af484e6
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/domain/workflow.py
@@ -0,0 +1,172 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from auto_gen import DBAbstraction, DBModule, DBGroup
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1,
+ {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.build_index()
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ new_obj = _DBWorkflow.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ new_obj.build_index()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
+
+ _vtTypeMap = {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType}
+
+ def build_index(self):
+ g = self._vtTypeMap.get
+ self.objects = dict(((g(o.vtType, o.vtType), o._db_id), o)
+ for (o,_,_) in self.db_children())
+
+ def add_to_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ self.objects[(obj_type, object.getPrimaryKey())] = object
+
+ def delete_from_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ del self.objects[(obj_type, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_print_objects(self):
+ for k,v in self.objects.iteritems():
+ print '%s: %s' % (k, v)
+
+ def db_has_object(self, type, id):
+ return (type, id) in self.objects
+
+ def db_get_object(self, type, id):
+ return self.objects[(type, id)]
+
+ def db_add_object(self, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if object.vtType == DBAbstraction.vtType or \
+ object.vtType == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ else:
+ obj_type = object.vtType
+ funname = 'db_add_' + obj_type
+ obj_copy = copy.copy(object)
+ getattr(parent_obj, funname)(obj_copy)
+ self.add_to_index(obj_copy)
+
+ def db_change_object(self, old_id, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+
+ self.db_delete_object(old_id, object.vtType, None, None, parent_obj)
+ self.db_add_object(object, None, None, parent_obj)
+
+ def db_delete_object(self, obj_id, obj_type, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if obj_type == DBAbstraction.vtType or obj_type == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ funname = 'db_get_' + obj_type
+ if hasattr(parent_obj, funname):
+ object = getattr(parent_obj, funname)(obj_id)
+ else:
+ attr_name = 'db_' + obj_type
+ object = getattr(parent_obj, attr_name)
+ funname = 'db_delete_' + obj_type
+ getattr(parent_obj, funname)(object)
+ self.delete_from_index(object)
diff --git a/vistrails/db/versions/v0_9_5/persistence/__init__.py b/vistrails/db/versions/v0_9_5/persistence/__init__.py
new file mode 100644
index 0000000..d005047
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/persistence/__init__.py
@@ -0,0 +1,230 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+from vistrails.core.system import get_elementtree_library
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v0_9_5 import version as my_version
+from vistrails.db.versions.v0_9_5.domain import DBGroup, DBWorkflow, DBVistrail, DBLog, \
+ DBRegistry
+
+ElementTree = get_elementtree_library()
+
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def parse_xml_file(self, filename):
+ return ElementTree.parse(filename)
+
+ def write_xml_file(self, filename, tree):
+ def indent(elem, level=0):
+ i = "\n" + level*" "
+ if len(elem):
+ if not elem.text or not elem.text.strip():
+ elem.text = i + " "
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ for elem in elem:
+ indent(elem, level+1)
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ else:
+ if level and (not elem.tail or not elem.tail.strip()):
+ elem.tail = i
+ indent(tree.getroot())
+ tree.write(filename)
+
+ def read_xml_object(self, vtType, node):
+ return self['xml'][vtType].fromXML(node)
+
+ def write_xml_object(self, obj, node=None):
+ res_node = self['xml'][obj.vtType].toXML(obj, node)
+ return res_node
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ """open_from_xml(filename) -> DBVistrail"""
+ if tree is None:
+ tree = self.parse_xml_file(filename)
+ vistrail = self.read_xml_object(vtType, tree.getroot())
+ return vistrail
+
+ def save_to_xml(self, obj, filename, tags, version=None):
+ """save_to_xml(obj : object, filename: str, tags: dict,
+ version: str) -> None
+
+ """
+ root = self.write_xml_object(obj)
+ if version is None:
+ version = my_version
+ root.set('version', version)
+ for k, v in tags.iteritems():
+ root.set(k, v)
+ tree = ElementTree.ElementTree(root)
+ self.write_xml_file(filename, tree)
+
+ def open_from_db(self, db_connection, vtType, id=None, lock=False,
+ global_props=None):
+ all_objects = {}
+ if global_props is None:
+ global_props = {}
+ if id is not None:
+ global_props['id'] = id
+ # print global_props
+ res_objects = self['sql'][vtType].get_sql_columns(db_connection,
+ global_props,
+ lock)
+ if len(res_objects) > 1:
+ raise VistrailsDBException("More than object of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+ elif len(res_objects) <= 0:
+ raise VistrailsDBException("No objects of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+
+ all_objects.update(res_objects)
+ res = res_objects.values()[0]
+ global_props = {'entity_id': res.db_id,
+ 'entity_type': res.vtType}
+
+ for dao_type, dao in self['sql'].iteritems():
+ if (dao_type == DBVistrail.vtType or
+ dao_type == DBWorkflow.vtType or
+ dao_type == DBLog.vtType or
+ dao_type == DBRegistry.vtType):
+ continue
+
+ current_objs = dao.get_sql_columns(db_connection, global_props,
+ lock)
+ all_objects.update(current_objs)
+
+ if dao_type == DBGroup.vtType:
+ for key, obj in current_objs.iteritems():
+ new_props = {'parent_id': key[1],
+ 'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ res_obj = self.open_from_db(db_connection,
+ DBWorkflow.vtType,
+ None, lock, new_props)
+ res_dict = {}
+ res_dict[(res_obj.vtType, res_obj.db_id)] = res_obj
+ all_objects.update(res_dict)
+
+ for key, obj in all_objects.iteritems():
+ if key[0] == vtType and key[1] == id:
+ continue
+ self['sql'][obj.vtType].from_sql_fast(obj, all_objects)
+ for obj in all_objects.itervalues():
+ obj.is_dirty = False
+ obj.is_new = False
+
+ return res
+
+ def save_to_db(self, db_connection, obj, do_copy=False, global_props=None):
+ if do_copy and obj.db_id is not None:
+ obj.db_id = None
+
+ children = obj.db_children()
+ children.reverse()
+ if global_props is None:
+ global_props = {'entity_type': obj.vtType}
+ # print 'global_props:', global_props
+
+ # assumes not deleting entire thing
+ child = children[0][0]
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ global_props = {'entity_id': child.db_id,
+ 'entity_type': child.vtType}
+
+ # do deletes
+ if not do_copy:
+ for (child, _, _) in children:
+ for c in child.db_deleted_children(True):
+ self['sql'][c.vtType].delete_sql_column(db_connection,
+ c,
+ global_props)
+
+ child = children.pop(0)[0]
+ child.is_dirty = False
+ child.is_new = False
+
+ # process remaining children
+ for (child, _, _) in children:
+ # print "child:", child.vtType, child.db_id
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ # print '*** entity_type:', global_props['entity_type']
+ new_props = {'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ is_dirty = child.db_workflow.is_dirty
+ child.db_workflow.db_entity_type = DBWorkflow.vtType
+ child.db_workflow.is_dirty = is_dirty
+ self.save_to_db(db_connection, child.db_workflow, do_copy,
+ new_props)
+
+ child.is_dirty = False
+ child.is_new = False
+
+ def serialize(self, object):
+ root = self.write_xml_object(object)
+ return ElementTree.tostring(root)
+
+ def unserialize(self, str, obj_type):
+ def set_dirty(obj):
+ for child, _, _ in obj.db_children():
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ set_dirty(child.db_workflow)
+ child.is_dirty = True
+ child.is_new = True
+ try:
+ root = ElementTree.fromstring(str)
+ obj = self.read_xml_object(obj_type, root)
+ set_dirty(obj)
+ return obj
+ except SyntaxError, e:
+ msg = "Invalid VisTrails serialized object %s" % str
+ raise VistrailsDBException(msg)
+ return None
diff --git a/vistrails/db/versions/v0_9_5/persistence/sql/__init__.py b/vistrails/db/versions/v0_9_5/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_9_5/persistence/sql/auto_gen.py b/vistrails/db/versions/v0_9_5/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..4fec1b4
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/persistence/sql/auto_gen.py
@@ -0,0 +1,3340 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v0_9_5.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port_spec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'sigstring', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ optional = self.convertFromDB(row[3], 'int', 'int')
+ sort_key = self.convertFromDB(row[4], 'int', 'int')
+ sigstring = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ sigstring=sigstring,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_entity_id = entity_id
+ portSpec.db_entity_type = entity_type
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'module_descriptor':
+ p = all_objects[('module_descriptor', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'sigstring', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_optional') and obj.db_optional is not None:
+ columnMap['optional'] = \
+ self.convertToDB(obj.db_optional, 'int', 'int')
+ if hasattr(obj, 'db_sort_key') and obj.db_sort_key is not None:
+ columnMap['sort_key'] = \
+ self.convertToDB(obj.db_sort_key, 'int', 'int')
+ if hasattr(obj, 'db_sigstring') and obj.db_sigstring is not None:
+ columnMap['sigstring'] = \
+ self.convertToDB(obj.db_sigstring, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ module.db_parentType = parentType
+ module.db_entity_id = entity_id
+ module.db_entity_type = entity_type
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleDescriptorSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_descriptor'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'package', 'namespace', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ base_descriptor_id = self.convertFromDB(row[5], 'long', 'int')
+ package = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ module_descriptor = DBModuleDescriptor(name=name,
+ package=package,
+ namespace=namespace,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ id=id)
+ module_descriptor.db_package = package
+ module_descriptor.db_entity_id = entity_id
+ module_descriptor.db_entity_type = entity_type
+ module_descriptor.is_dirty = False
+ res[('module_descriptor', id)] = module_descriptor
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('package', obj.db_package) in all_objects:
+ p = all_objects[('package', obj.db_package)]
+ p.db_add_module_descriptor(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'package', 'namespace', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_base_descriptor_id') and obj.db_base_descriptor_id is not None:
+ columnMap['base_descriptor_id'] = \
+ self.convertToDB(obj.db_base_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_package, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'tag'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[2], 'long', 'int')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_vistrail = vistrail
+ tag.db_entity_id = entity_id
+ tag.db_entity_type = entity_type
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ signature = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature,
+ id=id)
+ port.db_parentType = parentType
+ port.db_entity_id = entity_id
+ port.db_entity_type = entity_type
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_signature') and obj.db_signature is not None:
+ columnMap['signature'] = \
+ self.convertToDB(obj.db_signature, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ group = DBGroup(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ group.db_parentType = parentType
+ group.db_entity_id = entity_id
+ group.db_entity_type = entity_type
+ group.db_parent = parent
+ group.is_dirty = False
+ res[('group', id)] = group
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_workflow is not None:
+ child = obj.db_workflow
+ child.db_group = obj.db_id
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'log_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ log = DBLog(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ log.is_dirty = False
+ res[('log', id)] = log
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_workflow_execs:
+ child.db_log = obj.db_id
+ for child in obj.db_machines:
+ child.db_log = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'machine'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.db_entity_id = entity_id
+ machine.db_entity_type = entity_type
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'add_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_entity_id = entity_id
+ add.db_entity_type = entity_type
+ add.is_dirty = False
+ res[('add', id)] = add
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'other'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_entity_id = entity_id
+ other.db_entity_type = entity_type
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'location'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_entity_id = entity_id
+ location.db_entity_type = entity_type
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'parameter'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_entity_id = entity_id
+ parameter.db_entity_type = entity_type
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPluginDataSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'plugin_data'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ data = self.convertFromDB(row[1], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ plugin_data = DBPluginData(data=data,
+ id=id)
+ plugin_data.db_parentType = parentType
+ plugin_data.db_entity_id = entity_id
+ plugin_data.db_entity_type = entity_type
+ plugin_data.db_parent = parent
+ plugin_data.is_dirty = False
+ res[('plugin_data', id)] = plugin_data
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_plugin_data(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_data') and obj.db_data is not None:
+ columnMap['data'] = \
+ self.convertToDB(obj.db_data, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'function'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_entity_id = entity_id
+ function.db_entity_type = entity_type
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'abstraction'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ internal_version = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[7], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[8], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[9], 'long', 'int')
+ entity_type = self.convertFromDB(row[10], 'str', 'char(16)')
+ parent = self.convertFromDB(row[11], 'long', 'long')
+
+ abstraction = DBAbstraction(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ tag=tag,
+ id=id)
+ abstraction.db_parentType = parentType
+ abstraction.db_entity_id = entity_id
+ abstraction.db_entity_type = entity_type
+ abstraction.db_parent = parent
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_internal_version') and obj.db_internal_version is not None:
+ columnMap['internal_version'] = \
+ self.convertToDB(obj.db_internal_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_id = self.convertFromDB(row[1], 'long', 'int')
+ entity_type = self.convertFromDB(row[2], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'char(16)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[6], 'long', 'int')
+ group = self.convertFromDB(row[7], 'long', 'int')
+
+ workflow = DBWorkflow(entity_type=entity_type,
+ name=name,
+ version=version,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ workflow.db_entity_id = entity_id
+ workflow.db_group = group
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('group', obj.db_group) in all_objects:
+ p = all_objects[('group', obj.db_group)]
+ p.db_add_workflow(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ if hasattr(obj, 'db_group') and obj.db_group is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_group, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_connections:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_plugin_datas:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_modules:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBRegistrySQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'registry'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ root_descriptor_id = self.convertFromDB(row[3], 'long', 'int')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+
+ registry = DBRegistry(entity_type=entity_type,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ registry.is_dirty = False
+ res[('registry', id)] = registry
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_root_descriptor_id') and obj.db_root_descriptor_id is not None:
+ columnMap['root_descriptor_id'] = \
+ self.convertToDB(obj.db_root_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_packages:
+ child.db_registry = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'annotation'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_entity_id = entity_id
+ annotation.db_entity_type = entity_type
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'change_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_entity_id = entity_id
+ change.db_entity_type = entity_type
+ change.is_dirty = False
+ res[('change', id)] = change
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ group_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ group_type = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[7], 'int', 'int')
+ error = self.convertFromDB(row[8], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[9], 'long', 'int')
+ parentType = self.convertFromDB(row[10], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[11], 'long', 'int')
+ entity_type = self.convertFromDB(row[12], 'str', 'char(16)')
+ parent = self.convertFromDB(row[13], 'long', 'long')
+
+ group_exec = DBGroupExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ group_exec.db_parentType = parentType
+ group_exec.db_entity_id = entity_id
+ group_exec.db_entity_type = entity_type
+ group_exec.db_parent = parent
+ group_exec.is_dirty = False
+ res[('group_exec', id)] = group_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_group_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_group_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_group_name') and obj.db_group_name is not None:
+ columnMap['group_name'] = \
+ self.convertToDB(obj.db_group_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_group_type') and obj.db_group_type is not None:
+ columnMap['group_type'] = \
+ self.convertToDB(obj.db_group_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_loop_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_module_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_group_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPackageSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'package'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ identifier = self.convertFromDB(row[2], 'str', 'varchar(1023)')
+ codepath = self.convertFromDB(row[3], 'str', 'varchar(1023)')
+ load_configuration = self.convertFromDB(row[4], 'int', 'int')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ description = self.convertFromDB(row[6], 'str', 'varchar(1023)')
+ registry = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ package = DBPackage(name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ id=id)
+ package.db_registry = registry
+ package.db_entity_id = entity_id
+ package.db_entity_type = entity_type
+ package.is_dirty = False
+ res[('package', id)] = package
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('registry', obj.db_registry) in all_objects:
+ p = all_objects[('registry', obj.db_registry)]
+ p.db_add_package(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_identifier') and obj.db_identifier is not None:
+ columnMap['identifier'] = \
+ self.convertToDB(obj.db_identifier, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_codepath') and obj.db_codepath is not None:
+ columnMap['codepath'] = \
+ self.convertToDB(obj.db_codepath, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_load_configuration') and obj.db_load_configuration is not None:
+ columnMap['load_configuration'] = \
+ self.convertToDB(obj.db_load_configuration, 'int', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_description') and obj.db_description is not None:
+ columnMap['description'] = \
+ self.convertToDB(obj.db_description, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_registry') and obj.db_registry is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_registry, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_module_descriptors:
+ child.db_package = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ vt_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[5], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[6], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[7], 'long', 'int')
+ parent_type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[9], 'long', 'int')
+ completed = self.convertFromDB(row[10], 'int', 'int')
+ name = self.convertFromDB(row[11], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[12], 'long', 'int')
+ entity_id = self.convertFromDB(row[13], 'long', 'int')
+ entity_type = self.convertFromDB(row[14], 'str', 'char(16)')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_entity_id = entity_id
+ workflow_exec.db_entity_type = entity_type
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_items:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLoopExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'loop_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ completed = self.convertFromDB(row[3], 'int', 'int')
+ error = self.convertFromDB(row[4], 'str', 'varchar(1023)')
+ parentType = self.convertFromDB(row[5], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+ parent = self.convertFromDB(row[8], 'long', 'long')
+
+ loop_exec = DBLoopExec(ts_start=ts_start,
+ ts_end=ts_end,
+ completed=completed,
+ error=error,
+ id=id)
+ loop_exec.db_parentType = parentType
+ loop_exec.db_entity_id = entity_id
+ loop_exec.db_entity_type = entity_type
+ loop_exec.db_parent = parent
+ loop_exec.is_dirty = False
+ res[('loop_exec', id)] = loop_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_loop_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_loop_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_module_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_group_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'connection_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[2], 'long', 'int')
+ entity_type = self.convertFromDB(row[3], 'str', 'char(16)')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_entity_id = entity_id
+ connection.db_entity_type = entity_type
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'action'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ prune = self.convertFromDB(row[5], 'int', 'int')
+ vistrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ id=id)
+ action.db_vistrail = vistrail
+ action.db_entity_id = entity_id
+ action.db_entity_type = entity_type
+ action.is_dirty = False
+ res[('action', id)] = action
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_prune') and obj.db_prune is not None:
+ columnMap['prune'] = \
+ self.convertToDB(obj.db_prune, 'int', 'int')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'delete_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_entity_id = entity_id
+ delete.db_entity_type = entity_type
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'vistrail'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_actions:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_tags:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'abstraction_id', 'abstraction_version', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ module_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[6], 'int', 'int')
+ error = self.convertFromDB(row[7], 'str', 'varchar(1023)')
+ abstraction_id = self.convertFromDB(row[8], 'long', 'int')
+ abstraction_version = self.convertFromDB(row[9], 'long', 'int')
+ machine_id = self.convertFromDB(row[10], 'long', 'int')
+ parentType = self.convertFromDB(row[11], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[12], 'long', 'int')
+ entity_type = self.convertFromDB(row[13], 'str', 'char(16)')
+ parent = self.convertFromDB(row[14], 'long', 'long')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ abstraction_id=abstraction_id,
+ abstraction_version=abstraction_version,
+ machine_id=machine_id,
+ id=id)
+ module_exec.db_parentType = parentType
+ module_exec.db_entity_id = entity_id
+ module_exec.db_entity_type = entity_type
+ module_exec.db_parent = parent
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_module_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_module_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'abstraction_id', 'abstraction_version', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_abstraction_id') and obj.db_abstraction_id is not None:
+ columnMap['abstraction_id'] = \
+ self.convertToDB(obj.db_abstraction_id, 'long', 'int')
+ if hasattr(obj, 'db_abstraction_version') and obj.db_abstraction_version is not None:
+ columnMap['abstraction_version'] = \
+ self.convertToDB(obj.db_abstraction_version, 'long', 'int')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_loop_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'module_descriptor' not in self:
+ self['module_descriptor'] = DBModuleDescriptorSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'registry' not in self:
+ self['registry'] = DBRegistrySQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'group_exec' not in self:
+ self['group_exec'] = DBGroupExecSQLDAOBase(self)
+ if 'package' not in self:
+ self['package'] = DBPackageSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'loop_exec' not in self:
+ self['loop_exec'] = DBLoopExecSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v0_9_5/persistence/sql/sql_dao.py b/vistrails/db/versions/v0_9_5/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..ad01dc5
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/persistence/sql/sql_dao.py
@@ -0,0 +1,183 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+from vistrails.db import VistrailsDBException
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ # return "'" + str(value).replace("'", "''") + "'"
+ return str(value)
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ return str(value)
+ elif type == 'int':
+ return str(value)
+ elif type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+
+ return None
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None,
+ forUpdate=False):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % \
+ (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ if forUpdate:
+ dbCommand += " FOR UPDATE"
+ dbCommand += ";"
+ return (dbCommand, tuple(values))
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ # valueStr = '%s, '.join(values)
+ valueStr = ''
+ if len(values) > 1:
+ valueStr = '%s,' * (len(values) - 1) + '%s'
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s);""" % \
+ (table, columnStr, valueStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ values = []
+ for column, value in columnMap.iteritems():
+# if value is None:
+# value = 'NULL'
+ setStr += '%s%s = %%s' % (comma, column)
+ comma = ', '
+ values.append(value)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """UPDATE %s SET %s WHERE %s;""" % \
+ (table, setStr, whereStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLDelete(self, table, whereMap):
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """DELETE FROM %s WHERE %s;""" % \
+ (table, whereStr)
+ return (dbCommand, tuple(values))
+
+ def executeSQL(self, db, cmd_tuple, isFetch):
+ dbCommand, values = cmd_tuple
+ # print 'db: %s' % dbCommand
+ # print 'values:', values
+ data = None
+ cursor = db.cursor()
+ try:
+ cursor.execute(dbCommand, values)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ except Exception, e:
+ raise VistrailsDBException('Command "%s" with values "%s" '
+ 'failed: %s' % (dbCommand, values, e))
+ finally:
+ cursor.close()
+ return data
+
+ def start_transaction(self, db):
+ db.begin()
+
+ def commit_transaction(self, db):
+ db.commit()
+
+ def rollback_transaction(self, db):
+ db.rollback()
diff --git a/vistrails/db/versions/v0_9_5/persistence/xml/__init__.py b/vistrails/db/versions/v0_9_5/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v0_9_5/persistence/xml/auto_gen.py b/vistrails/db/versions/v0_9_5/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..016e5fa
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/persistence/xml/auto_gen.py
@@ -0,0 +1,2117 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from vistrails.core.system import get_elementtree_library
+
+from xml_dao import XMLDAO
+from vistrails.db.versions.v0_9_5.domain import *
+
+ElementTree = get_elementtree_library()
+
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'portSpec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('optional', None)
+ optional = self.convertFromStr(data, 'int')
+ data = node.get('sortKey', None)
+ sort_key = self.convertFromStr(data, 'int')
+ data = node.get('sigstring', None)
+ sigstring = self.convertFromStr(data, 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ sigstring=sigstring)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, node=None):
+ if node is None:
+ node = ElementTree.Element('portSpec')
+
+ # set attributes
+ node.set('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.set('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.set('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.set('optional',self.convertToStr(portSpec.db_optional, 'int'))
+ node.set('sortKey',self.convertToStr(portSpec.db_sort_key, 'int'))
+ node.set('sigstring',self.convertToStr(portSpec.db_sigstring, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'module':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, node=None):
+ if node is None:
+ node = ElementTree.Element('module')
+
+ # set attributes
+ node.set('id',self.convertToStr(module.db_id, 'long'))
+ node.set('cache',self.convertToStr(module.db_cache, 'int'))
+ node.set('name',self.convertToStr(module.db_name, 'str'))
+ node.set('namespace',self.convertToStr(module.db_namespace, 'str'))
+ node.set('package',self.convertToStr(module.db_package, 'str'))
+ node.set('version',self.convertToStr(module.db_version, 'str'))
+ node.set('tag',self.convertToStr(module.db_tag, 'str'))
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = module.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBModuleDescriptorXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'moduleDescriptor':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('baseDescriptorId', None)
+ base_descriptor_id = self.convertFromStr(data, 'long')
+
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleDescriptor(id=id,
+ name=name,
+ package=package,
+ namespace=namespace,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_descriptor, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleDescriptor')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_descriptor.db_id, 'long'))
+ node.set('name',self.convertToStr(module_descriptor.db_name, 'str'))
+ node.set('package',self.convertToStr(module_descriptor.db_package, 'str'))
+ node.set('namespace',self.convertToStr(module_descriptor.db_namespace, 'str'))
+ node.set('version',self.convertToStr(module_descriptor.db_version, 'str'))
+ node.set('baseDescriptorId',self.convertToStr(module_descriptor.db_base_descriptor_id, 'long'))
+
+ # set elements
+ portSpecs = module_descriptor.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'tag':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, node=None):
+ if node is None:
+ node = ElementTree.Element('tag')
+
+ # set attributes
+ node.set('id',self.convertToStr(tag.db_id, 'long'))
+ node.set('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'port':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('moduleId', None)
+ moduleId = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ moduleName = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('signature', None)
+ signature = self.convertFromStr(data, 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, node=None):
+ if node is None:
+ node = ElementTree.Element('port')
+
+ # set attributes
+ node.set('id',self.convertToStr(port.db_id, 'long'))
+ node.set('type',self.convertToStr(port.db_type, 'str'))
+ node.set('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.set('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.set('name',self.convertToStr(port.db_name, 'str'))
+ node.set('signature',self.convertToStr(port.db_signature, 'str'))
+
+ return node
+
+class DBGroupXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'group':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ workflow = None
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'workflow':
+ _data = self.getDao('workflow').fromXML(child)
+ workflow = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroup(id=id,
+ workflow=workflow,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group, node=None):
+ if node is None:
+ node = ElementTree.Element('group')
+
+ # set attributes
+ node.set('id',self.convertToStr(group.db_id, 'long'))
+ node.set('cache',self.convertToStr(group.db_cache, 'int'))
+ node.set('name',self.convertToStr(group.db_name, 'str'))
+ node.set('namespace',self.convertToStr(group.db_namespace, 'str'))
+ node.set('package',self.convertToStr(group.db_package, 'str'))
+ node.set('version',self.convertToStr(group.db_version, 'str'))
+ node.set('tag',self.convertToStr(group.db_tag, 'str'))
+
+ # set elements
+ workflow = group.db_workflow
+ if workflow is not None:
+ childNode = ElementTree.SubElement(node, 'workflow')
+ self.getDao('workflow').toXML(workflow, childNode)
+ location = group.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = group.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = group.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'log':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ workflow_execs = []
+ machines = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'workflowExec':
+ _data = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs.append(_data)
+ elif child.tag == 'machine':
+ _data = self.getDao('machine').fromXML(child)
+ machines.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLog(id=id,
+ version=version,
+ name=name,
+ workflow_execs=workflow_execs,
+ machines=machines,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, node=None):
+ if node is None:
+ node = ElementTree.Element('log')
+
+ # set attributes
+ node.set('id',self.convertToStr(log.db_id, 'long'))
+ node.set('version',self.convertToStr(log.db_version, 'str'))
+ node.set('name',self.convertToStr(log.db_name, 'str'))
+ node.set('vistrail_id',self.convertToStr(log.db_vistrail_id, 'long'))
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs:
+ childNode = ElementTree.SubElement(node, 'workflowExec')
+ self.getDao('workflow_exec').toXML(workflow_exec, childNode)
+ machines = log.db_machines
+ for machine in machines:
+ childNode = ElementTree.SubElement(node, 'machine')
+ self.getDao('machine').toXML(machine, childNode)
+
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'machine':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('os', None)
+ os = self.convertFromStr(data, 'str')
+ data = node.get('architecture', None)
+ architecture = self.convertFromStr(data, 'str')
+ data = node.get('processor', None)
+ processor = self.convertFromStr(data, 'str')
+ data = node.get('ram', None)
+ ram = self.convertFromStr(data, 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, node=None):
+ if node is None:
+ node = ElementTree.Element('machine')
+
+ # set attributes
+ node.set('id',self.convertToStr(machine.db_id, 'long'))
+ node.set('name',self.convertToStr(machine.db_name, 'str'))
+ node.set('os',self.convertToStr(machine.db_os, 'str'))
+ node.set('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.set('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.set('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'add':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAdd(data=data,
+ id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, node=None):
+ if node is None:
+ node = ElementTree.Element('add')
+
+ # set attributes
+ node.set('id',self.convertToStr(add.db_id, 'long'))
+ node.set('what',self.convertToStr(add.db_what, 'str'))
+ node.set('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # set elements
+ data = add.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'other':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'value':
+ _data = self.convertFromStr(child.text,'')
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, node=None):
+ if node is None:
+ node = ElementTree.Element('other')
+
+ # set attributes
+ node.set('id',self.convertToStr(other.db_id, 'long'))
+ node.set('key',self.convertToStr(other.db_key, 'str'))
+
+ # set elements
+
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'location':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('x', None)
+ x = self.convertFromStr(data, 'float')
+ data = node.get('y', None)
+ y = self.convertFromStr(data, 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, node=None):
+ if node is None:
+ node = ElementTree.Element('location')
+
+ # set attributes
+ node.set('id',self.convertToStr(location.db_id, 'long'))
+ node.set('x',self.convertToStr(location.db_x, 'float'))
+ node.set('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'parameter':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('val', None)
+ val = self.convertFromStr(data, 'str')
+ data = node.get('alias', None)
+ alias = self.convertFromStr(data, 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, node=None):
+ if node is None:
+ node = ElementTree.Element('parameter')
+
+ # set attributes
+ node.set('id',self.convertToStr(parameter.db_id, 'long'))
+ node.set('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.set('name',self.convertToStr(parameter.db_name, 'str'))
+ node.set('type',self.convertToStr(parameter.db_type, 'str'))
+ node.set('val',self.convertToStr(parameter.db_val, 'str'))
+ node.set('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBPluginDataXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'plugin_data':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('data', None)
+ data = self.convertFromStr(data, 'str')
+
+ obj = DBPluginData(id=id,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, plugin_data, node=None):
+ if node is None:
+ node = ElementTree.Element('plugin_data')
+
+ # set attributes
+ node.set('id',self.convertToStr(plugin_data.db_id, 'long'))
+ node.set('data',self.convertToStr(plugin_data.db_data, 'str'))
+
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'function':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ parameters = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ parameters.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, node=None):
+ if node is None:
+ node = ElementTree.Element('function')
+
+ # set attributes
+ node.set('id',self.convertToStr(function.db_id, 'long'))
+ node.set('pos',self.convertToStr(function.db_pos, 'long'))
+ node.set('name',self.convertToStr(function.db_name, 'str'))
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(parameter, childNode)
+
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'abstraction':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('internalVersion', None)
+ internal_version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstraction(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, node=None):
+ if node is None:
+ node = ElementTree.Element('abstraction')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.set('cache',self.convertToStr(abstraction.db_cache, 'int'))
+ node.set('name',self.convertToStr(abstraction.db_name, 'str'))
+ node.set('namespace',self.convertToStr(abstraction.db_namespace, 'str'))
+ node.set('package',self.convertToStr(abstraction.db_package, 'str'))
+ node.set('version',self.convertToStr(abstraction.db_version, 'str'))
+ node.set('internalVersion',self.convertToStr(abstraction.db_internal_version, 'str'))
+ node.set('tag',self.convertToStr(abstraction.db_tag, 'str'))
+
+ # set elements
+ location = abstraction.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = abstraction.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = abstraction.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflow':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ connections = []
+ annotations = []
+ plugin_datas = []
+ others = []
+ modules = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ connections.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ plugin_datas.append(_data)
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ others.append(_data)
+ elif child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ modules.append(_data)
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ modules.append(_data)
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ modules.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflow(modules=modules,
+ id=id,
+ name=name,
+ version=version,
+ connections=connections,
+ annotations=annotations,
+ plugin_datas=plugin_datas,
+ others=others,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, node=None):
+ if node is None:
+ node = ElementTree.Element('workflow')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow.db_id, 'long'))
+ node.set('name',self.convertToStr(workflow.db_name, 'str'))
+ node.set('version',self.convertToStr(workflow.db_version, 'str'))
+ node.set('vistrail_id',self.convertToStr(workflow.db_vistrail_id, 'long'))
+
+ # set elements
+ connections = workflow.db_connections
+ for connection in connections:
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(connection, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ plugin_datas = workflow.db_plugin_datas
+ for plugin_data in plugin_datas:
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(plugin_data, childNode)
+ others = workflow.db_others
+ for other in others:
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(other, childNode)
+ modules = workflow.db_modules
+ for module in modules:
+ if module.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(module, childNode)
+ elif module.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(module, childNode)
+ elif module.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(module, childNode)
+
+ return node
+
+class DBRegistryXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'registry':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('rootDescriptorId', None)
+ root_descriptor_id = self.convertFromStr(data, 'long')
+
+ packages = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'package':
+ _data = self.getDao('package').fromXML(child)
+ packages.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBRegistry(id=id,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ packages=packages)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, registry, node=None):
+ if node is None:
+ node = ElementTree.Element('registry')
+
+ # set attributes
+ node.set('id',self.convertToStr(registry.db_id, 'long'))
+ node.set('version',self.convertToStr(registry.db_version, 'str'))
+ node.set('rootDescriptorId',self.convertToStr(registry.db_root_descriptor_id, 'long'))
+
+ # set elements
+ packages = registry.db_packages
+ for package in packages:
+ childNode = ElementTree.SubElement(node, 'package')
+ self.getDao('package').toXML(package, childNode)
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'annotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, node=None):
+ if node is None:
+ node = ElementTree.Element('annotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(annotation.db_id, 'long'))
+ node.set('key',self.convertToStr(annotation.db_key, 'str'))
+ node.set('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'change':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('oldObjId', None)
+ oldObjId = self.convertFromStr(data, 'long')
+ data = node.get('newObjId', None)
+ newObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child.tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child.tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child.tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child.tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child.tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child.tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child.tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child.tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child.tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBChange(data=data,
+ id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, node=None):
+ if node is None:
+ node = ElementTree.Element('change')
+
+ # set attributes
+ node.set('id',self.convertToStr(change.db_id, 'long'))
+ node.set('what',self.convertToStr(change.db_what, 'str'))
+ node.set('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.set('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.set('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # set elements
+ data = change.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBGroupExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'groupExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('groupName', None)
+ group_name = self.convertFromStr(data, 'str')
+ data = node.get('groupType', None)
+ group_type = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+ loop_execs = []
+ module_execs = []
+ group_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ loop_execs.append(_data)
+ elif child.tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ module_execs.append(_data)
+ elif child.tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ group_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroupExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ annotations=annotations,
+ loop_execs=loop_execs,
+ module_execs=module_execs,
+ group_execs=group_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('groupExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(group_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(group_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(group_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(group_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(group_exec.db_module_id, 'long'))
+ node.set('groupName',self.convertToStr(group_exec.db_group_name, 'str'))
+ node.set('groupType',self.convertToStr(group_exec.db_group_type, 'str'))
+ node.set('completed',self.convertToStr(group_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(group_exec.db_error, 'str'))
+ node.set('machine_id',self.convertToStr(group_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = group_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ loop_execs = group_exec.db_loop_execs
+ for loop_exec in loop_execs:
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(loop_exec, childNode)
+ module_execs = group_exec.db_module_execs
+ for module_exec in module_execs:
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(module_exec, childNode)
+ group_execs = group_exec.db_group_execs
+ for group_exec in group_execs:
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(group_exec, childNode)
+
+ return node
+
+class DBPackageXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'package':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('identifier', None)
+ identifier = self.convertFromStr(data, 'str')
+ data = node.get('codepath', None)
+ codepath = self.convertFromStr(data, 'str')
+ data = node.get('loadConfiguration', None)
+ load_configuration = self.convertFromStr(data, 'int')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('description', None)
+ description = self.convertFromStr(data, 'str')
+
+ module_descriptors = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'moduleDescriptor':
+ _data = self.getDao('module_descriptor').fromXML(child)
+ module_descriptors.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBPackage(id=id,
+ name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ module_descriptors=module_descriptors)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, package, node=None):
+ if node is None:
+ node = ElementTree.Element('package')
+
+ # set attributes
+ node.set('id',self.convertToStr(package.db_id, 'long'))
+ node.set('name',self.convertToStr(package.db_name, 'str'))
+ node.set('identifier',self.convertToStr(package.db_identifier, 'str'))
+ node.set('codepath',self.convertToStr(package.db_codepath, 'str'))
+ node.set('loadConfiguration',self.convertToStr(package.db_load_configuration, 'int'))
+ node.set('version',self.convertToStr(package.db_version, 'str'))
+ node.set('description',self.convertToStr(package.db_description, 'str'))
+
+ # set elements
+ module_descriptors = package.db_module_descriptors
+ for module_descriptor in module_descriptors:
+ childNode = ElementTree.SubElement(node, 'moduleDescriptor')
+ self.getDao('module_descriptor').toXML(module_descriptor, childNode)
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'workflowExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('ip', None)
+ ip = self.convertFromStr(data, 'str')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('vtVersion', None)
+ vt_version = self.convertFromStr(data, 'str')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('parentId', None)
+ parent_id = self.convertFromStr(data, 'long')
+ data = node.get('parentType', None)
+ parent_type = self.convertFromStr(data, 'str')
+ data = node.get('parentVersion', None)
+ parent_version = self.convertFromStr(data, 'long')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ items = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ items.append(_data)
+ elif child.tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ items.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflowExec(items=items,
+ id=id,
+ user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('workflowExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.set('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.set('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.set('session',self.convertToStr(workflow_exec.db_session, 'long'))
+ node.set('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.set('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.set('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.set('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.set('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.set('completed',self.convertToStr(workflow_exec.db_completed, 'int'))
+ node.set('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # set elements
+ items = workflow_exec.db_items
+ for item in items:
+ if item.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item, childNode)
+ elif item.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item, childNode)
+
+ return node
+
+class DBLoopExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'loopExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+
+ module_execs = []
+ group_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ module_execs.append(_data)
+ elif child.tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ group_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLoopExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ completed=completed,
+ error=error,
+ module_execs=module_execs,
+ group_execs=group_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, loop_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('loopExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(loop_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(loop_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(loop_exec.db_ts_end, 'datetime'))
+ node.set('completed',self.convertToStr(loop_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(loop_exec.db_error, 'str'))
+
+ # set elements
+ module_execs = loop_exec.db_module_execs
+ for module_exec in module_execs:
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(module_exec, childNode)
+ group_execs = loop_exec.db_group_execs
+ for group_exec in group_execs:
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(group_exec, childNode)
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'connection':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+
+ ports = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ ports.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, node=None):
+ if node is None:
+ node = ElementTree.Element('connection')
+
+ # set attributes
+ node.set('id',self.convertToStr(connection.db_id, 'long'))
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(port, childNode)
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'action':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('prevId', None)
+ prevId = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('prune', None)
+ prune = self.convertFromStr(data, 'int')
+
+ annotations = []
+ operations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'add':
+ _data = self.getDao('add').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'delete':
+ _data = self.getDao('delete').fromXML(child)
+ operations.append(_data)
+ elif child.tag == 'change':
+ _data = self.getDao('change').fromXML(child)
+ operations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAction(operations=operations,
+ id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, node=None):
+ if node is None:
+ node = ElementTree.Element('action')
+
+ # set attributes
+ node.set('id',self.convertToStr(action.db_id, 'long'))
+ node.set('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.set('date',self.convertToStr(action.db_date, 'datetime'))
+ node.set('session',self.convertToStr(action.db_session, 'long'))
+ node.set('user',self.convertToStr(action.db_user, 'str'))
+ node.set('prune',self.convertToStr(action.db_prune, 'int'))
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ childNode = ElementTree.SubElement(node, 'add')
+ self.getDao('add').toXML(operation, childNode)
+ elif operation.vtType == 'delete':
+ childNode = ElementTree.SubElement(node, 'delete')
+ self.getDao('delete').toXML(operation, childNode)
+ elif operation.vtType == 'change':
+ childNode = ElementTree.SubElement(node, 'change')
+ self.getDao('change').toXML(operation, childNode)
+
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'delete':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, node=None):
+ if node is None:
+ node = ElementTree.Element('delete')
+
+ # set attributes
+ node.set('id',self.convertToStr(delete.db_id, 'long'))
+ node.set('what',self.convertToStr(delete.db_what, 'str'))
+ node.set('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'vistrail':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child.tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ actions=actions,
+ tags=tags,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, node=None):
+ if node is None:
+ node = ElementTree.Element('vistrail')
+
+ # set attributes
+ node.set('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.set('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.set('name',self.convertToStr(vistrail.db_name, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = vistrail.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+ annotations = vistrail.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag != 'moduleExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ module_name = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('abstraction_id', None)
+ abstraction_id = self.convertFromStr(data, 'long')
+ data = node.get('abstraction_version', None)
+ abstraction_version = self.convertFromStr(data, 'long')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+ loop_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ loop_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ abstraction_id=abstraction_id,
+ abstraction_version=abstraction_version,
+ machine_id=machine_id,
+ annotations=annotations,
+ loop_execs=loop_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(module_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.set('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+ node.set('completed',self.convertToStr(module_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(module_exec.db_error, 'str'))
+ node.set('abstraction_id',self.convertToStr(module_exec.db_abstraction_id, 'long'))
+ node.set('abstraction_version',self.convertToStr(module_exec.db_abstraction_version, 'long'))
+ node.set('machine_id',self.convertToStr(module_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ loop_execs = module_exec.db_loop_execs
+ for loop_exec in loop_execs:
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(loop_exec, childNode)
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'module_descriptor' not in self:
+ self['module_descriptor'] = DBModuleDescriptorXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'registry' not in self:
+ self['registry'] = DBRegistryXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'group_exec' not in self:
+ self['group_exec'] = DBGroupExecXMLDAOBase(self)
+ if 'package' not in self:
+ self['package'] = DBPackageXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'loop_exec' not in self:
+ self['loop_exec'] = DBLoopExecXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v0_9_5/persistence/xml/xml_dao.py b/vistrails/db/versions/v0_9_5/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..955c01a
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/persistence/xml/xml_dao.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v0_9_5/schemas/sql/vistrails.sql b/vistrails/db/versions/v0_9_5/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..2019bdc
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/schemas/sql/vistrails.sql
@@ -0,0 +1,373 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+CREATE TABLE `vistrails_version`(`version` char(16)) engine=InnoDB;
+INSERT INTO `vistrails_version`(`version`) VALUES ('0.9.5');
+
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(255),
+ type varchar(255),
+ optional int,
+ sort_key int,
+ sigstring varchar(4095),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module_descriptor(
+ id int,
+ name varchar(255),
+ package varchar(255),
+ namespace varchar(255),
+ version varchar(255),
+ base_descriptor_id int,
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ signature varchar(4095),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE group_tbl(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime,
+ vistrail_id int
+) engine=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE plugin_data(
+ id int,
+ data varchar(8191),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ internal_version varchar(255),
+ tag varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE workflow(
+ id int not null auto_increment primary key,
+ entity_id int,
+ entity_type char(16),
+ name varchar(255),
+ version char(16),
+ last_modified datetime,
+ vistrail_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE registry(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ root_descriptor_id int,
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE group_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ group_name varchar(255),
+ group_type varchar(255),
+ completed int,
+ error varchar(1023),
+ machine_id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE package(
+ id int not null auto_increment primary key,
+ name varchar(255),
+ identifier varchar(1023),
+ codepath varchar(1023),
+ load_configuration int,
+ version varchar(255),
+ description varchar(1023),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ session int,
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ completed int,
+ name varchar(255),
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE loop_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ completed int,
+ error varchar(1023),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session int,
+ user varchar(255),
+ prune int,
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ module_name varchar(255),
+ completed int,
+ error varchar(1023),
+ abstraction_id int,
+ abstraction_version int,
+ machine_id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
diff --git a/vistrails/db/versions/v0_9_5/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v0_9_5/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..558226e
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,40 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+DROP TABLE IF EXISTS `vistrails_version`;
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, module_descriptor, tag, port, group_tbl, log_tbl, machine, add_tbl, other, location, parameter, plugin_data, function, abstraction, workflow, registry, annotation, change_tbl, group_exec, package, workflow_exec, loop_exec, connection_tbl, action, delete_tbl, vistrail, module_exec;
diff --git a/vistrails/db/versions/v0_9_5/schemas/xml/vistrail.xsd b/vistrails/db/versions/v0_9_5/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..51f02b3
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/schemas/xml/vistrail.xsd
@@ -0,0 +1,278 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="prune" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="signature" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="optional" type="xs:int"/>
+ <xs:attribute name="sortKey" type="xs:int"/>
+ <xs:attribute name="sigstring" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="internalVersion" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="group">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="workflow" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plugin_data">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="workflow">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v0_9_5/specs/all.xml b/vistrails/db/versions/v0_9_5/specs/all.xml
new file mode 100644
index 0000000..d7b5e5a
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/specs/all.xml
@@ -0,0 +1,2017 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<objects>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ABSTRACTION +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="internal_version" type="str">
+ <xml name="internalVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ACTION ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long" foreignKey="true" object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="prune" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="vistrail" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ADD +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ANNOTATION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CHANGE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CONNECTION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- DELETE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- FUNCTION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group" parentClass="module">
+ <layout>
+ <xml name="group" nodeType="xs:element"/>
+ <sql table="group_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow" type="object" mapping="one-to-one"
+ expand="false">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOCATION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MACHINE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOOP_EXEC +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="loop_exec">
+ <layout>
+ <xml name="loopExec" nodeType="xs:element"/>
+ <sql table="loop_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <!--<property name="input" type="str">
+ <xml name="input" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>-->
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP_EXEC ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group_exec">
+ <layout>
+ <xml name="groupExec" nodeType="xs:element"/>
+ <sql table="group_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="group_name" type="str">
+ <xml name="groupName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="group_type" type="str">
+ <xml name="groupType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <!--<property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>-->
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_EXEC +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="abstraction_id" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="abstraction_version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OTHER +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PARAMETER +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PLUGIN DATA +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="plugin_data">
+ <layout>
+ <xml name="plugin_data" nodeType="xs:element"/>
+ <sql table="plugin_data"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="data" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORT ++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="signature" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORTSPEC ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="optional" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="sort_key" type="int">
+ <xml name="sortKey" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="sigstring" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="module_descriptor">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_DESCRIPTOR +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_descriptor">
+ <layout>
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ <sql table="module_descriptor"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="base_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="baseDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="package" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ <!--
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="registry">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="package">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+ -->
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PACKAGE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="package">
+ <layout>
+ <xml name="package" nodeType="xs:element"/>
+ <sql table="package"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="identifier" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="codepath" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="load_configuration" type="int">
+ <xml name="loadConfiguration" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="description" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property ref="true" object="module_descriptor" type="list"
+ mapping="one-to-many" index="name:namespace:version">
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="registry" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REGISTRY ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="registry">
+ <layout>
+ <xml name="registry" nodeType="xs:element"/>
+ <sql table="registry"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="root_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="rootDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <!-- <xml nodeType="xs:attribute" type="xs:string"/> -->
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="package" type="list"
+ mapping="one-to-many" index="identifier:version">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- TAG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VISTRAIL ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstraction" ref="true" object="abstraction">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group" ref="true" object="group">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="plugin_data" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="group" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW_EXEC +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <choice name="item" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+</objects>
diff --git a/vistrails/db/versions/v0_9_5/translate/__init__.py b/vistrails/db/versions/v0_9_5/translate/__init__.py
new file mode 100644
index 0000000..89c7f9a
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '0.9.5'
diff --git a/vistrails/db/versions/v0_9_5/translate/v0_9_4.py b/vistrails/db/versions/v0_9_5/translate/v0_9_4.py
new file mode 100644
index 0000000..0ed2be6
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/translate/v0_9_4.py
@@ -0,0 +1,99 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v0_9_5.domain import DBVistrail, DBWorkflow, DBLog, \
+ DBRegistry, DBModuleExec
+
+def translateVistrail(_vistrail):
+ def update_signature(old_obj, translate_dict):
+ return old_obj.db_spec
+ def update_optional(old_obj, translate_dict):
+ return 0
+ def update_sort_key(old_obj, translate_dict):
+ return -1
+ def update_sigstring(old_obj, translate_dict):
+ return old_obj.db_spec
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+
+ translate_dict = {'DBPortSpec': {'sigstring': update_sigstring,
+ 'optional': update_optional,
+ 'sort_key': update_sort_key},
+ 'DBPort': {'signature': update_signature},
+ 'DBGroup': {'workflow': update_workflow}}
+
+ # pass DBVistrail because domain contains enriched version of the auto_gen
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict)
+ vistrail.db_version = '0.9.5'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ def update_signature(old_obj, translate_dict):
+ return old_obj.db_spec
+ def update_optional(old_obj, translate_dict):
+ return 0
+ def update_sort_key(old_obj, translate_dict):
+ return -1
+ def update_sigstring(old_obj, translate_dict):
+ return old_obj.db_spec
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+
+ translate_dict = {'DBPortSpec': {'sigstring': update_sigstring,
+ 'optional': update_optional,
+ 'sort_key': update_sort_key},
+ 'DBPort': {'signature': update_signature},
+ 'DBGroup': {'workflow': update_workflow}}
+
+ workflow = DBWorkflow.update_version(_workflow, translate_dict)
+ workflow.db_version = '0.9.5'
+ return workflow
+
+def translateLog(_log):
+ def update_items(old_obj, translate_dict):
+ new_items = []
+ for obj in old_obj.db_module_execs:
+ new_items.append(DBModuleExec.update_version(obj, translate_dict))
+ return new_items
+ translate_dict = {'DBWorkflowExec': {'items': update_items}}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '0.9.5'
+ return log
+
+def translateRegistry(_registry):
+ translate_dict = {}
+ registry = DBRegistry.update_version(_registry, translate_dict)
+ registry.db_version = '0.9.5'
+ return registry
diff --git a/vistrails/db/versions/v0_9_5/translate/v1_0_0.py b/vistrails/db/versions/v0_9_5/translate/v1_0_0.py
new file mode 100644
index 0000000..fe40509
--- /dev/null
+++ b/vistrails/db/versions/v0_9_5/translate/v1_0_0.py
@@ -0,0 +1,113 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.core import debug
+
+from vistrails.db.versions.v0_9_5.domain import DBVistrail, DBWorkflow, DBLog, \
+ DBRegistry, DBModuleExec, DBGroupExec
+
+def translateVistrail(_vistrail):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBGroup': {'workflow': update_workflow}}
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict)
+ vistrail.db_version = '0.9.5'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBGroup': {'workflow': update_workflow}}
+ workflow = DBWorkflow.update_version(_workflow, translate_dict)
+ workflow.db_version = '0.9.5'
+ return workflow
+
+def translateLog(_log):
+ def update_items(old_obj, translate_dict):
+ new_items = []
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_items.append(DBModuleExec.update_version(obj, translate_dict))
+ elif obj.vtType == 'group_exec':
+ new_items.append(DBGroupExec.update_version(obj, translate_dict))
+ elif obj.vtType == 'loop_exec':
+ new_items.append(DBLoopExec.update_version(obj, translate_dict))
+
+ return new_items
+
+ def update_exec_items(which, old_obj, translate_dict, catch_loops=False):
+ new_items = []
+ for obj in old_obj.db_item_execs:
+ if catch_loops and obj.vtType == 'loop_exec':
+ debug.warning("Cannot translate loop_exec inside of loop_exec")
+ if obj.vtType == which:
+ if obj.vtType == 'module_exec':
+ new_items.append(DBModuleExec.update_version(obj, translate_dict))
+ elif obj.vtType == 'group_exec':
+ new_items.append(DBGroupExec.update_version(obj, translate_dict))
+ elif obj.vtType == 'loop_exec':
+ new_items.append(DBLoopExec.update_version(obj, translate_dict))
+ return new_items
+
+ def update_group_module_execs(old_obj, translate_dict):
+ return update_exec_items('module_exec', old_obj, translate_dict)
+
+ def update_group_group_execs(old_obj, translate_dict):
+ return update_exec_items('group_exec', old_obj, translate_dict)
+
+ def update_group_loop_execs(old_obj, translate_dict):
+ return update_exec_items('loop_exec', old_obj, translate_dict)
+
+ def update_loop_module_execs(old_obj, translate_dict):
+ return update_exec_tems('module_exec', old_obj, translate_dict, True)
+
+ def update_loop_group_execs(old_obj, translate_dict):
+ return update_exec_items('group_exec', old_obj, translate_dict)
+
+ translate_dict = {'DBWorkflowExec': {'items': update_items},
+ 'DBGroupExec': {'group_execs': update_group_group_execs,
+ 'module_execs': update_group_module_execs,
+ 'loop_execs': update_group_loop_execs},
+ 'DBLoopExec': {'group_execs': update_loop_group_execs,
+ 'module_execs': update_loop_module_execs}}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '0.9.5'
+ return log
+
+def translateRegistry(_registry):
+ translate_dict = {}
+ registry = DBRegistry.update_version(_registry, translate_dict)
+ registry.db_version = '0.9.5'
+ return registry
diff --git a/vistrails/db/versions/v1_0_0/__init__.py b/vistrails/db/versions/v1_0_0/__init__.py
new file mode 100644
index 0000000..85cbe3f
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '1.0.0'
diff --git a/vistrails/db/versions/v1_0_0/domain/__init__.py b/vistrails/db/versions/v1_0_0/domain/__init__.py
new file mode 100644
index 0000000..a8208f6
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/domain/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from registry import DBRegistry
+from workflow import DBWorkflow
+from vistrail import DBVistrail
+from log import DBLog
+from id_scope import IdScope
diff --git a/vistrails/db/versions/v1_0_0/domain/auto_gen.py b/vistrails/db/versions/v1_0_0/domain/auto_gen.py
new file mode 100644
index 0000000..c2aa908
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/domain/auto_gen.py
@@ -0,0 +1,11387 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBOpmProcessIdEffect(object):
+
+ vtType = 'opm_process_id_effect'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessIdEffect.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessIdEffect(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_process', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_process', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessIdEffect()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBOpmWasGeneratedBy(object):
+
+ vtType = 'opm_was_generated_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasGeneratedBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasGeneratedBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasGeneratedBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmArtifactIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmArtifactIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmProcessIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmProcessIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBOpmAccounts(object):
+
+ vtType = 'opm_accounts'
+
+ def __init__(self, accounts=None, opm_overlapss=None):
+ self.db_deleted_accounts = []
+ self.db_accounts_id_index = {}
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ for v in self._db_accounts:
+ self.db_accounts_id_index[v.db_id] = v
+ self.db_deleted_opm_overlapss = []
+ if opm_overlapss is None:
+ self._db_opm_overlapss = []
+ else:
+ self._db_opm_overlapss = opm_overlapss
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccounts.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccounts()
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_overlapss is None:
+ cp._db_opm_overlapss = []
+ else:
+ cp._db_opm_overlapss = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_overlapss]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_accounts_id_index = dict((v.db_id, v) for v in cp._db_accounts)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccounts()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccount.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccount.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_overlapss' in class_dict:
+ res = class_dict['opm_overlapss'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_overlaps(obj)
+ elif hasattr(old_obj, 'db_opm_overlapss') and old_obj.db_opm_overlapss is not None:
+ for obj in old_obj.db_opm_overlapss:
+ new_obj.db_add_opm_overlaps(DBOpmOverlaps.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_overlapss') and hasattr(new_obj, 'db_deleted_opm_overlapss'):
+ for obj in old_obj.db_deleted_opm_overlapss:
+ n_obj = DBOpmOverlaps.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_overlapss.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_overlapss:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_overlaps(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_overlapss)
+ if remove:
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_overlapss = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_overlapss:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ self.db_accounts_id_index[account.db_id] = account
+ def db_change_account(self, account):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == account.db_id:
+ self._db_accounts[i] = account
+ found = True
+ break
+ if not found:
+ self._db_accounts.append(account)
+ self.db_accounts_id_index[account.db_id] = account
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == account.db_id:
+ if not self._db_accounts[i].is_new:
+ self.db_deleted_accounts.append(self._db_accounts[i])
+ del self._db_accounts[i]
+ break
+ del self.db_accounts_id_index[account.db_id]
+ def db_get_account(self, key):
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == key:
+ return self._db_accounts[i]
+ return None
+ def db_get_account_by_id(self, key):
+ return self.db_accounts_id_index[key]
+ def db_has_account_with_id(self, key):
+ return key in self.db_accounts_id_index
+
+ def __get_db_opm_overlapss(self):
+ return self._db_opm_overlapss
+ def __set_db_opm_overlapss(self, opm_overlapss):
+ self._db_opm_overlapss = opm_overlapss
+ self.is_dirty = True
+ db_opm_overlapss = property(__get_db_opm_overlapss, __set_db_opm_overlapss)
+ def db_get_opm_overlapss(self):
+ return self._db_opm_overlapss
+ def db_add_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ self._db_opm_overlapss.append(opm_overlaps)
+ def db_change_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ self._db_opm_overlapss.append(opm_overlaps)
+ def db_delete_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_overlaps(self, key):
+ return None
+
+
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, optional=None, sort_key=None, sigstring=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_type = type
+ self._db_optional = optional
+ self._db_sort_key = sort_key
+ self._db_sigstring = sigstring
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPortSpec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec(id=self._db_id,
+ name=self._db_name,
+ type=self._db_type,
+ optional=self._db_optional,
+ sort_key=self._db_sort_key,
+ sigstring=self._db_sigstring)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPortSpec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'optional' in class_dict:
+ res = class_dict['optional'](old_obj, trans_dict)
+ new_obj.db_optional = res
+ elif hasattr(old_obj, 'db_optional') and old_obj.db_optional is not None:
+ new_obj.db_optional = old_obj.db_optional
+ if 'sort_key' in class_dict:
+ res = class_dict['sort_key'](old_obj, trans_dict)
+ new_obj.db_sort_key = res
+ elif hasattr(old_obj, 'db_sort_key') and old_obj.db_sort_key is not None:
+ new_obj.db_sort_key = old_obj.db_sort_key
+ if 'sigstring' in class_dict:
+ res = class_dict['sigstring'](old_obj, trans_dict)
+ new_obj.db_sigstring = res
+ elif hasattr(old_obj, 'db_sigstring') and old_obj.db_sigstring is not None:
+ new_obj.db_sigstring = old_obj.db_sigstring
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_optional(self):
+ return self._db_optional
+ def __set_db_optional(self, optional):
+ self._db_optional = optional
+ self.is_dirty = True
+ db_optional = property(__get_db_optional, __set_db_optional)
+ def db_add_optional(self, optional):
+ self._db_optional = optional
+ def db_change_optional(self, optional):
+ self._db_optional = optional
+ def db_delete_optional(self, optional):
+ self._db_optional = None
+
+ def __get_db_sort_key(self):
+ return self._db_sort_key
+ def __set_db_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ self.is_dirty = True
+ db_sort_key = property(__get_db_sort_key, __set_db_sort_key)
+ def db_add_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ def db_change_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ def db_delete_sort_key(self, sort_key):
+ self._db_sort_key = None
+
+ def __get_db_sigstring(self):
+ return self._db_sigstring
+ def __set_db_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ self.is_dirty = True
+ db_sigstring = property(__get_db_sigstring, __set_db_sigstring)
+ def db_add_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ def db_change_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ def db_delete_sigstring(self, sigstring):
+ self._db_sigstring = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModule.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ tag=self._db_tag)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModule()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleDescriptor(object):
+
+ vtType = 'module_descriptor'
+
+ def __init__(self, id=None, name=None, package=None, namespace=None, version=None, base_descriptor_id=None, portSpecs=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_package = package
+ self._db_namespace = namespace
+ self._db_version = version
+ self._db_base_descriptor_id = base_descriptor_id
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleDescriptor.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleDescriptor(id=self._db_id,
+ name=self._db_name,
+ package=self._db_package,
+ namespace=self._db_namespace,
+ version=self._db_version,
+ base_descriptor_id=self._db_base_descriptor_id)
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_base_descriptor_id') and ('module_descriptor', self._db_base_descriptor_id) in id_remap:
+ cp._db_base_descriptor_id = id_remap[('module_descriptor', self._db_base_descriptor_id)]
+
+ # recreate indices and set flags
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleDescriptor()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'base_descriptor_id' in class_dict:
+ res = class_dict['base_descriptor_id'](old_obj, trans_dict)
+ new_obj.db_base_descriptor_id = res
+ elif hasattr(old_obj, 'db_base_descriptor_id') and old_obj.db_base_descriptor_id is not None:
+ new_obj.db_base_descriptor_id = old_obj.db_base_descriptor_id
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_base_descriptor_id(self):
+ return self._db_base_descriptor_id
+ def __set_db_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ self.is_dirty = True
+ db_base_descriptor_id = property(__get_db_base_descriptor_id, __set_db_base_descriptor_id)
+ def db_add_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ def db_change_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ def db_delete_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = None
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self._db_id = id
+ self._db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBTag.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag(id=self._db_id,
+ name=self._db_name)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('action', self._db_id) in id_remap:
+ cp._db_id = id_remap[('action', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBTag()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmRole(object):
+
+ vtType = 'opm_role'
+
+ def __init__(self, value=None):
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmRole.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmRole(value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmRole()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+
+
+class DBOpmProcesses(object):
+
+ vtType = 'opm_processes'
+
+ def __init__(self, processs=None):
+ self.db_deleted_processs = []
+ self.db_processs_id_index = {}
+ if processs is None:
+ self._db_processs = []
+ else:
+ self._db_processs = processs
+ for v in self._db_processs:
+ self.db_processs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcesses.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcesses()
+ if self._db_processs is None:
+ cp._db_processs = []
+ else:
+ cp._db_processs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_processs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_processs_id_index = dict((v.db_id, v) for v in cp._db_processs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcesses()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'processs' in class_dict:
+ res = class_dict['processs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_process(obj)
+ elif hasattr(old_obj, 'db_processs') and old_obj.db_processs is not None:
+ for obj in old_obj.db_processs:
+ new_obj.db_add_process(DBOpmProcess.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_processs') and hasattr(new_obj, 'db_deleted_processs'):
+ for obj in old_obj.db_deleted_processs:
+ n_obj = DBOpmProcess.update_version(obj, trans_dict)
+ new_obj.db_deleted_processs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_processs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_process(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_processs)
+ if remove:
+ self.db_deleted_processs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_processs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_processs(self):
+ return self._db_processs
+ def __set_db_processs(self, processs):
+ self._db_processs = processs
+ self.is_dirty = True
+ db_processs = property(__get_db_processs, __set_db_processs)
+ def db_get_processs(self):
+ return self._db_processs
+ def db_add_process(self, process):
+ self.is_dirty = True
+ self._db_processs.append(process)
+ self.db_processs_id_index[process.db_id] = process
+ def db_change_process(self, process):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == process.db_id:
+ self._db_processs[i] = process
+ found = True
+ break
+ if not found:
+ self._db_processs.append(process)
+ self.db_processs_id_index[process.db_id] = process
+ def db_delete_process(self, process):
+ self.is_dirty = True
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == process.db_id:
+ if not self._db_processs[i].is_new:
+ self.db_deleted_processs.append(self._db_processs[i])
+ del self._db_processs[i]
+ break
+ del self.db_processs_id_index[process.db_id]
+ def db_get_process(self, key):
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == key:
+ return self._db_processs[i]
+ return None
+ def db_get_process_by_id(self, key):
+ return self.db_processs_id_index[key]
+ def db_has_process_with_id(self, key):
+ return key in self.db_processs_id_index
+
+
+
+class DBOpmAccountId(object):
+
+ vtType = 'opm_account_id'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccountId.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccountId(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_account', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_account', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccountId()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, name=None, signature=None):
+ self._db_id = id
+ self._db_type = type
+ self._db_moduleId = moduleId
+ self._db_moduleName = moduleName
+ self._db_name = name
+ self._db_signature = signature
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPort.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort(id=self._db_id,
+ type=self._db_type,
+ moduleId=self._db_moduleId,
+ moduleName=self._db_moduleName,
+ name=self._db_name,
+ signature=self._db_signature)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_moduleId') and ('module', self._db_moduleId) in id_remap:
+ cp._db_moduleId = id_remap[('module', self._db_moduleId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPort()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'moduleId' in class_dict:
+ res = class_dict['moduleId'](old_obj, trans_dict)
+ new_obj.db_moduleId = res
+ elif hasattr(old_obj, 'db_moduleId') and old_obj.db_moduleId is not None:
+ new_obj.db_moduleId = old_obj.db_moduleId
+ if 'moduleName' in class_dict:
+ res = class_dict['moduleName'](old_obj, trans_dict)
+ new_obj.db_moduleName = res
+ elif hasattr(old_obj, 'db_moduleName') and old_obj.db_moduleName is not None:
+ new_obj.db_moduleName = old_obj.db_moduleName
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'signature' in class_dict:
+ res = class_dict['signature'](old_obj, trans_dict)
+ new_obj.db_signature = res
+ elif hasattr(old_obj, 'db_signature') and old_obj.db_signature is not None:
+ new_obj.db_signature = old_obj.db_signature
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_moduleId(self):
+ return self._db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self._db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self._db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self._db_moduleName = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_signature(self):
+ return self._db_signature
+ def __set_db_signature(self, signature):
+ self._db_signature = signature
+ self.is_dirty = True
+ db_signature = property(__get_db_signature, __set_db_signature)
+ def db_add_signature(self, signature):
+ self._db_signature = signature
+ def db_change_signature(self, signature):
+ self._db_signature = signature
+ def db_delete_signature(self, signature):
+ self._db_signature = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmArtifact(object):
+
+ vtType = 'opm_artifact'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self.db_deleted_value = []
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifact.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifact(id=self._db_id)
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifact()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ new_obj.db_add_value(DBOpmArtifactValue.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ n_obj = DBOpmArtifactValue.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_value = []
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBGroup(object):
+
+ vtType = 'group'
+
+ def __init__(self, id=None, workflow=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self.db_deleted_workflow = []
+ self._db_workflow = workflow
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroup.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroup(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ tag=self._db_tag)
+ if self._db_workflow is not None:
+ cp._db_workflow = self._db_workflow.do_copy()
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroup()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'workflow' in class_dict:
+ res = class_dict['workflow'](old_obj, trans_dict)
+ new_obj.db_workflow = res
+ elif hasattr(old_obj, 'db_workflow') and old_obj.db_workflow is not None:
+ obj = old_obj.db_workflow
+ new_obj.db_add_workflow(DBWorkflow.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow') and hasattr(new_obj, 'db_deleted_workflow'):
+ for obj in old_obj.db_deleted_workflow:
+ n_obj = DBWorkflow.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow.append(n_obj)
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow)
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_workflow = []
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_workflow is not None and self._db_workflow.has_changes():
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_workflow(self):
+ return self._db_workflow
+ def __set_db_workflow(self, workflow):
+ self._db_workflow = workflow
+ self.is_dirty = True
+ db_workflow = property(__get_db_workflow, __set_db_workflow)
+ def db_add_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_change_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_delete_workflow(self, workflow):
+ if not self.is_new:
+ self.db_deleted_workflow.append(self._db_workflow)
+ self._db_workflow = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, workflow_execs=None, machines=None, vistrail_id=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_workflow_execs = []
+ self.db_workflow_execs_id_index = {}
+ if workflow_execs is None:
+ self._db_workflow_execs = []
+ else:
+ self._db_workflow_execs = workflow_execs
+ for v in self._db_workflow_execs:
+ self.db_workflow_execs_id_index[v.db_id] = v
+ self.db_deleted_machines = []
+ self.db_machines_id_index = {}
+ if machines is None:
+ self._db_machines = []
+ else:
+ self._db_machines = machines
+ for v in self._db_machines:
+ self.db_machines_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_workflow_execs is None:
+ cp._db_workflow_execs = []
+ else:
+ cp._db_workflow_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_workflow_execs]
+ if self._db_machines is None:
+ cp._db_machines = []
+ else:
+ cp._db_machines = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_machines]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_workflow_execs_id_index = dict((v.db_id, v) for v in cp._db_workflow_execs)
+ cp.db_machines_id_index = dict((v.db_id, v) for v in cp._db_machines)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'workflow_execs' in class_dict:
+ res = class_dict['workflow_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_workflow_exec(obj)
+ elif hasattr(old_obj, 'db_workflow_execs') and old_obj.db_workflow_execs is not None:
+ for obj in old_obj.db_workflow_execs:
+ new_obj.db_add_workflow_exec(DBWorkflowExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow_execs') and hasattr(new_obj, 'db_deleted_workflow_execs'):
+ for obj in old_obj.db_deleted_workflow_execs:
+ n_obj = DBWorkflowExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow_execs.append(n_obj)
+ if 'machines' in class_dict:
+ res = class_dict['machines'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_machine(obj)
+ elif hasattr(old_obj, 'db_machines') and old_obj.db_machines is not None:
+ for obj in old_obj.db_machines:
+ new_obj.db_add_machine(DBMachine.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_machines') and hasattr(new_obj, 'db_deleted_machines'):
+ for obj in old_obj.db_deleted_machines:
+ n_obj = DBMachine.update_version(obj, trans_dict)
+ new_obj.db_deleted_machines.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_workflow_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self.db_machines:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow_execs)
+ children.extend(self.db_deleted_machines)
+ if remove:
+ self.db_deleted_workflow_execs = []
+ self.db_deleted_machines = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_workflow_execs:
+ if child.has_changes():
+ return True
+ for child in self._db_machines:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_workflow_execs(self):
+ return self._db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self._db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self._db_workflow_execs
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ self._db_workflow_execs[i] = workflow_exec
+ found = True
+ break
+ if not found:
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ if not self._db_workflow_execs[i].is_new:
+ self.db_deleted_workflow_execs.append(self._db_workflow_execs[i])
+ del self._db_workflow_execs[i]
+ break
+ del self.db_workflow_execs_id_index[workflow_exec.db_id]
+ def db_get_workflow_exec(self, key):
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == key:
+ return self._db_workflow_execs[i]
+ return None
+ def db_get_workflow_exec_by_id(self, key):
+ return self.db_workflow_execs_id_index[key]
+ def db_has_workflow_exec_with_id(self, key):
+ return key in self.db_workflow_execs_id_index
+
+ def __get_db_machines(self):
+ return self._db_machines
+ def __set_db_machines(self, machines):
+ self._db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self._db_machines
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ self._db_machines[i] = machine
+ found = True
+ break
+ if not found:
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ if not self._db_machines[i].is_new:
+ self.db_deleted_machines.append(self._db_machines[i])
+ del self._db_machines[i]
+ break
+ del self.db_machines_id_index[machine.db_id]
+ def db_get_machine(self, key):
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == key:
+ return self._db_machines[i]
+ return None
+ def db_get_machine_by_id(self, key):
+ return self.db_machines_id_index[key]
+ def db_has_machine_with_id(self, key):
+ return key in self.db_machines_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmAgents(object):
+
+ vtType = 'opm_agents'
+
+ def __init__(self, agents=None):
+ self.db_deleted_agents = []
+ self.db_agents_id_index = {}
+ if agents is None:
+ self._db_agents = []
+ else:
+ self._db_agents = agents
+ for v in self._db_agents:
+ self.db_agents_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgents.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgents()
+ if self._db_agents is None:
+ cp._db_agents = []
+ else:
+ cp._db_agents = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_agents]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_agents_id_index = dict((v.db_id, v) for v in cp._db_agents)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgents()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'agents' in class_dict:
+ res = class_dict['agents'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_agent(obj)
+ elif hasattr(old_obj, 'db_agents') and old_obj.db_agents is not None:
+ for obj in old_obj.db_agents:
+ new_obj.db_add_agent(DBOpmAgent.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_agents') and hasattr(new_obj, 'db_deleted_agents'):
+ for obj in old_obj.db_deleted_agents:
+ n_obj = DBOpmAgent.update_version(obj, trans_dict)
+ new_obj.db_deleted_agents.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_agents:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_agent(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_agents)
+ if remove:
+ self.db_deleted_agents = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_agents:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_agents(self):
+ return self._db_agents
+ def __set_db_agents(self, agents):
+ self._db_agents = agents
+ self.is_dirty = True
+ db_agents = property(__get_db_agents, __set_db_agents)
+ def db_get_agents(self):
+ return self._db_agents
+ def db_add_agent(self, agent):
+ self.is_dirty = True
+ self._db_agents.append(agent)
+ self.db_agents_id_index[agent.db_id] = agent
+ def db_change_agent(self, agent):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == agent.db_id:
+ self._db_agents[i] = agent
+ found = True
+ break
+ if not found:
+ self._db_agents.append(agent)
+ self.db_agents_id_index[agent.db_id] = agent
+ def db_delete_agent(self, agent):
+ self.is_dirty = True
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == agent.db_id:
+ if not self._db_agents[i].is_new:
+ self.db_deleted_agents.append(self._db_agents[i])
+ del self._db_agents[i]
+ break
+ del self.db_agents_id_index[agent.db_id]
+ def db_get_agent(self, key):
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == key:
+ return self._db_agents[i]
+ return None
+ def db_get_agent_by_id(self, key):
+ return self.db_agents_id_index[key]
+ def db_has_agent_with_id(self, key):
+ return key in self.db_agents_id_index
+
+
+
+class DBOpmProcessIdCause(object):
+
+ vtType = 'opm_process_id_cause'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessIdCause.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessIdCause(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_process', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_process', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessIdCause()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_os = os
+ self._db_architecture = architecture
+ self._db_processor = processor
+ self._db_ram = ram
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMachine.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine(id=self._db_id,
+ name=self._db_name,
+ os=self._db_os,
+ architecture=self._db_architecture,
+ processor=self._db_processor,
+ ram=self._db_ram)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and ('vistrail', self._db_vistrailId) in id_remap:
+ cp._db_vistrailId = id_remap[('vistrail', self._db_vistrailId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMachine()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'os' in class_dict:
+ res = class_dict['os'](old_obj, trans_dict)
+ new_obj.db_os = res
+ elif hasattr(old_obj, 'db_os') and old_obj.db_os is not None:
+ new_obj.db_os = old_obj.db_os
+ if 'architecture' in class_dict:
+ res = class_dict['architecture'](old_obj, trans_dict)
+ new_obj.db_architecture = res
+ elif hasattr(old_obj, 'db_architecture') and old_obj.db_architecture is not None:
+ new_obj.db_architecture = old_obj.db_architecture
+ if 'processor' in class_dict:
+ res = class_dict['processor'](old_obj, trans_dict)
+ new_obj.db_processor = res
+ elif hasattr(old_obj, 'db_processor') and old_obj.db_processor is not None:
+ new_obj.db_processor = old_obj.db_processor
+ if 'ram' in class_dict:
+ res = class_dict['ram'](old_obj, trans_dict)
+ new_obj.db_ram = res
+ elif hasattr(old_obj, 'db_ram') and old_obj.db_ram is not None:
+ new_obj.db_ram = old_obj.db_ram
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_os(self):
+ return self._db_os
+ def __set_db_os(self, os):
+ self._db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self._db_os = os
+ def db_change_os(self, os):
+ self._db_os = os
+ def db_delete_os(self, os):
+ self._db_os = None
+
+ def __get_db_architecture(self):
+ return self._db_architecture
+ def __set_db_architecture(self, architecture):
+ self._db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self._db_architecture = None
+
+ def __get_db_processor(self):
+ return self._db_processor
+ def __set_db_processor(self, processor):
+ self._db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self._db_processor = processor
+ def db_change_processor(self, processor):
+ self._db_processor = processor
+ def db_delete_processor(self, processor):
+ self._db_processor = None
+
+ def __get_db_ram(self):
+ return self._db_ram
+ def __set_db_ram(self, ram):
+ self._db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self._db_ram = ram
+ def db_change_ram(self, ram):
+ self._db_ram = ram
+ def db_delete_ram(self, ram):
+ self._db_ram = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, data=None, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAdd.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAdd()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOther.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOther(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOther()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self._db_id = id
+ self._db_x = x
+ self._db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLocation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation(id=self._db_id,
+ x=self._db_x,
+ y=self._db_y)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLocation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'x' in class_dict:
+ res = class_dict['x'](old_obj, trans_dict)
+ new_obj.db_x = res
+ elif hasattr(old_obj, 'db_x') and old_obj.db_x is not None:
+ new_obj.db_x = old_obj.db_x
+ if 'y' in class_dict:
+ res = class_dict['y'](old_obj, trans_dict)
+ new_obj.db_y = res
+ elif hasattr(old_obj, 'db_y') and old_obj.db_y is not None:
+ new_obj.db_y = old_obj.db_y
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_x(self):
+ return self._db_x
+ def __set_db_x(self, x):
+ self._db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self._db_x = x
+ def db_change_x(self, x):
+ self._db_x = x
+ def db_delete_x(self, x):
+ self._db_x = None
+
+ def __get_db_y(self):
+ return self._db_y
+ def __set_db_y(self, y):
+ self._db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self._db_y = y
+ def db_change_y(self, y):
+ self._db_y = y
+ def db_delete_y(self, y):
+ self._db_y = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmOverlaps(object):
+
+ vtType = 'opm_overlaps'
+
+ def __init__(self, opm_account_ids=None):
+ self.db_deleted_opm_account_ids = []
+ if opm_account_ids is None:
+ self._db_opm_account_ids = []
+ else:
+ self._db_opm_account_ids = opm_account_ids
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmOverlaps.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmOverlaps()
+ if self._db_opm_account_ids is None:
+ cp._db_opm_account_ids = []
+ else:
+ cp._db_opm_account_ids = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_account_ids]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmOverlaps()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'opm_account_ids' in class_dict:
+ res = class_dict['opm_account_ids'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_account_id(obj)
+ elif hasattr(old_obj, 'db_opm_account_ids') and old_obj.db_opm_account_ids is not None:
+ for obj in old_obj.db_opm_account_ids:
+ new_obj.db_add_opm_account_id(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_account_ids') and hasattr(new_obj, 'db_deleted_opm_account_ids'):
+ for obj in old_obj.db_deleted_opm_account_ids:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_account_ids.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_opm_account_ids:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_account_id(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_opm_account_ids)
+ if remove:
+ self.db_deleted_opm_account_ids = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_opm_account_ids:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_opm_account_ids(self):
+ return self._db_opm_account_ids
+ def __set_db_opm_account_ids(self, opm_account_ids):
+ self._db_opm_account_ids = opm_account_ids
+ self.is_dirty = True
+ db_opm_account_ids = property(__get_db_opm_account_ids, __set_db_opm_account_ids)
+ def db_get_opm_account_ids(self):
+ return self._db_opm_account_ids
+ def db_add_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ self._db_opm_account_ids.append(opm_account_id)
+ def db_change_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ self._db_opm_account_ids.append(opm_account_id)
+ def db_delete_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_account_id(self, key):
+ return None
+
+
+
+class DBOpmArtifacts(object):
+
+ vtType = 'opm_artifacts'
+
+ def __init__(self, artifacts=None):
+ self.db_deleted_artifacts = []
+ self.db_artifacts_id_index = {}
+ if artifacts is None:
+ self._db_artifacts = []
+ else:
+ self._db_artifacts = artifacts
+ for v in self._db_artifacts:
+ self.db_artifacts_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifacts.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifacts()
+ if self._db_artifacts is None:
+ cp._db_artifacts = []
+ else:
+ cp._db_artifacts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_artifacts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_artifacts_id_index = dict((v.db_id, v) for v in cp._db_artifacts)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifacts()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'artifacts' in class_dict:
+ res = class_dict['artifacts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_artifact(obj)
+ elif hasattr(old_obj, 'db_artifacts') and old_obj.db_artifacts is not None:
+ for obj in old_obj.db_artifacts:
+ new_obj.db_add_artifact(DBOpmArtifact.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_artifacts') and hasattr(new_obj, 'db_deleted_artifacts'):
+ for obj in old_obj.db_deleted_artifacts:
+ n_obj = DBOpmArtifact.update_version(obj, trans_dict)
+ new_obj.db_deleted_artifacts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_artifacts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_artifact(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_artifacts)
+ if remove:
+ self.db_deleted_artifacts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_artifacts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_artifacts(self):
+ return self._db_artifacts
+ def __set_db_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ self.is_dirty = True
+ db_artifacts = property(__get_db_artifacts, __set_db_artifacts)
+ def db_get_artifacts(self):
+ return self._db_artifacts
+ def db_add_artifact(self, artifact):
+ self.is_dirty = True
+ self._db_artifacts.append(artifact)
+ self.db_artifacts_id_index[artifact.db_id] = artifact
+ def db_change_artifact(self, artifact):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == artifact.db_id:
+ self._db_artifacts[i] = artifact
+ found = True
+ break
+ if not found:
+ self._db_artifacts.append(artifact)
+ self.db_artifacts_id_index[artifact.db_id] = artifact
+ def db_delete_artifact(self, artifact):
+ self.is_dirty = True
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == artifact.db_id:
+ if not self._db_artifacts[i].is_new:
+ self.db_deleted_artifacts.append(self._db_artifacts[i])
+ del self._db_artifacts[i]
+ break
+ del self.db_artifacts_id_index[artifact.db_id]
+ def db_get_artifact(self, key):
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == key:
+ return self._db_artifacts[i]
+ return None
+ def db_get_artifact_by_id(self, key):
+ return self.db_artifacts_id_index[key]
+ def db_has_artifact_with_id(self, key):
+ return key in self.db_artifacts_id_index
+
+
+
+class DBOpmDependencies(object):
+
+ vtType = 'opm_dependencies'
+
+ def __init__(self, dependencys=None):
+ self.db_deleted_dependencys = []
+ if dependencys is None:
+ self._db_dependencys = []
+ else:
+ self._db_dependencys = dependencys
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmDependencies.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmDependencies()
+ if self._db_dependencys is None:
+ cp._db_dependencys = []
+ else:
+ cp._db_dependencys = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_dependencys]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmDependencies()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'dependencys' in class_dict:
+ res = class_dict['dependencys'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_dependency(obj)
+ elif hasattr(old_obj, 'db_dependencys') and old_obj.db_dependencys is not None:
+ for obj in old_obj.db_dependencys:
+ if obj.vtType == 'opm_used':
+ new_obj.db_add_dependency(DBOpmUsed.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_generated_by':
+ new_obj.db_add_dependency(DBOpmWasGeneratedBy.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_triggered_by':
+ new_obj.db_add_dependency(DBOpmWasTriggeredBy.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_derived_from':
+ new_obj.db_add_dependency(DBOpmWasDerivedFrom.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_controlled_by':
+ new_obj.db_add_dependency(DBOpmWasControlledBy.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_dependencys') and hasattr(new_obj, 'db_deleted_dependencys'):
+ for obj in old_obj.db_deleted_dependencys:
+ if obj.vtType == 'opm_used':
+ n_obj = DBOpmUsed.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_generated_by':
+ n_obj = DBOpmWasGeneratedBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_triggered_by':
+ n_obj = DBOpmWasTriggeredBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_derived_from':
+ n_obj = DBOpmWasDerivedFrom.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_controlled_by':
+ n_obj = DBOpmWasControlledBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_dependencys:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_dependency(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_dependencys)
+ if remove:
+ self.db_deleted_dependencys = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_dependencys:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_dependencys(self):
+ return self._db_dependencys
+ def __set_db_dependencys(self, dependencys):
+ self._db_dependencys = dependencys
+ self.is_dirty = True
+ db_dependencys = property(__get_db_dependencys, __set_db_dependencys)
+ def db_get_dependencys(self):
+ return self._db_dependencys
+ def db_add_dependency(self, dependency):
+ self.is_dirty = True
+ self._db_dependencys.append(dependency)
+ def db_change_dependency(self, dependency):
+ self.is_dirty = True
+ self._db_dependencys.append(dependency)
+ def db_delete_dependency(self, dependency):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_dependency(self, key):
+ return None
+
+
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self._db_type = type
+ self._db_val = val
+ self._db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBParameter.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name,
+ type=self._db_type,
+ val=self._db_val,
+ alias=self._db_alias)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBParameter()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'val' in class_dict:
+ res = class_dict['val'](old_obj, trans_dict)
+ new_obj.db_val = res
+ elif hasattr(old_obj, 'db_val') and old_obj.db_val is not None:
+ new_obj.db_val = old_obj.db_val
+ if 'alias' in class_dict:
+ res = class_dict['alias'](old_obj, trans_dict)
+ new_obj.db_alias = res
+ elif hasattr(old_obj, 'db_alias') and old_obj.db_alias is not None:
+ new_obj.db_alias = old_obj.db_alias
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_val(self):
+ return self._db_val
+ def __set_db_val(self, val):
+ self._db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self._db_val = val
+ def db_change_val(self, val):
+ self._db_val = val
+ def db_delete_val(self, val):
+ self._db_val = None
+
+ def __get_db_alias(self):
+ return self._db_alias
+ def __set_db_alias(self, alias):
+ self._db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self._db_alias = alias
+ def db_change_alias(self, alias):
+ self._db_alias = alias
+ def db_delete_alias(self, alias):
+ self._db_alias = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmUsed(object):
+
+ vtType = 'opm_used'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmUsed.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmUsed()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmUsed()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmArtifactIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmArtifactIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBPluginData(object):
+
+ vtType = 'plugin_data'
+
+ def __init__(self, id=None, data=None):
+ self._db_id = id
+ self._db_data = data
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPluginData.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPluginData(id=self._db_id,
+ data=self._db_data)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPluginData()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ new_obj.db_data = old_obj.db_data
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ self._db_data = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self.db_deleted_parameters = []
+ self.db_parameters_id_index = {}
+ if parameters is None:
+ self._db_parameters = []
+ else:
+ self._db_parameters = parameters
+ for v in self._db_parameters:
+ self.db_parameters_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name)
+ if self._db_parameters is None:
+ cp._db_parameters = []
+ else:
+ cp._db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_parameters_id_index = dict((v.db_id, v) for v in cp._db_parameters)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBFunction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'parameters' in class_dict:
+ res = class_dict['parameters'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_parameter(obj)
+ elif hasattr(old_obj, 'db_parameters') and old_obj.db_parameters is not None:
+ for obj in old_obj.db_parameters:
+ new_obj.db_add_parameter(DBParameter.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_parameters') and hasattr(new_obj, 'db_deleted_parameters'):
+ for obj in old_obj.db_deleted_parameters:
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_parameters.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_parameters)
+ if remove:
+ self.db_deleted_parameters = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_parameters(self):
+ return self._db_parameters
+ def __set_db_parameters(self, parameters):
+ self._db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self._db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ self._db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ if not self._db_parameters[i].is_new:
+ self.db_deleted_parameters.append(self._db_parameters[i])
+ del self._db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter.db_id]
+ def db_get_parameter(self, key):
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == key:
+ return self._db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return key in self.db_parameters_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, internal_version=None, tag=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_internal_version = internal_version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ internal_version=self._db_internal_version,
+ tag=self._db_tag)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAbstraction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'internal_version' in class_dict:
+ res = class_dict['internal_version'](old_obj, trans_dict)
+ new_obj.db_internal_version = res
+ elif hasattr(old_obj, 'db_internal_version') and old_obj.db_internal_version is not None:
+ new_obj.db_internal_version = old_obj.db_internal_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_internal_version(self):
+ return self._db_internal_version
+ def __set_db_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ self.is_dirty = True
+ db_internal_version = property(__get_db_internal_version, __set_db_internal_version)
+ def db_add_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_change_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_delete_internal_version(self, internal_version):
+ self._db_internal_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, modules=None, id=None, entity_type=None, name=None, version=None, last_modified=None, connections=None, annotations=None, plugin_datas=None, others=None, vistrail_id=None):
+ self.db_deleted_modules = []
+ self.db_modules_id_index = {}
+ if modules is None:
+ self._db_modules = []
+ else:
+ self._db_modules = modules
+ for v in self._db_modules:
+ self.db_modules_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_name = name
+ self._db_version = version
+ self._db_last_modified = last_modified
+ self.db_deleted_connections = []
+ self.db_connections_id_index = {}
+ if connections is None:
+ self._db_connections = []
+ else:
+ self._db_connections = connections
+ for v in self._db_connections:
+ self.db_connections_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_plugin_datas = []
+ self.db_plugin_datas_id_index = {}
+ if plugin_datas is None:
+ self._db_plugin_datas = []
+ else:
+ self._db_plugin_datas = plugin_datas
+ for v in self._db_plugin_datas:
+ self.db_plugin_datas_id_index[v.db_id] = v
+ self.db_deleted_others = []
+ self.db_others_id_index = {}
+ if others is None:
+ self._db_others = []
+ else:
+ self._db_others = others
+ for v in self._db_others:
+ self.db_others_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow(id=self._db_id,
+ entity_type=self._db_entity_type,
+ name=self._db_name,
+ version=self._db_version,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_modules is None:
+ cp._db_modules = []
+ else:
+ cp._db_modules = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_modules]
+ if self._db_connections is None:
+ cp._db_connections = []
+ else:
+ cp._db_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_connections]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_plugin_datas is None:
+ cp._db_plugin_datas = []
+ else:
+ cp._db_plugin_datas = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_plugin_datas]
+ if self._db_others is None:
+ cp._db_others = []
+ else:
+ cp._db_others = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_others]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_modules_id_index = dict((v.db_id, v) for v in cp._db_modules)
+ cp.db_connections_id_index = dict((v.db_id, v) for v in cp._db_connections)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_plugin_datas_id_index = dict((v.db_id, v) for v in cp._db_plugin_datas)
+ cp.db_others_id_index = dict((v.db_id, v) for v in cp._db_others)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'modules' in class_dict:
+ res = class_dict['modules'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module(obj)
+ elif hasattr(old_obj, 'db_modules') and old_obj.db_modules is not None:
+ for obj in old_obj.db_modules:
+ if obj.vtType == 'module':
+ new_obj.db_add_module(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_module(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_module(DBGroup.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_modules') and hasattr(new_obj, 'db_deleted_modules'):
+ for obj in old_obj.db_deleted_modules:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'connections' in class_dict:
+ res = class_dict['connections'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_connection(obj)
+ elif hasattr(old_obj, 'db_connections') and old_obj.db_connections is not None:
+ for obj in old_obj.db_connections:
+ new_obj.db_add_connection(DBConnection.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_connections') and hasattr(new_obj, 'db_deleted_connections'):
+ for obj in old_obj.db_deleted_connections:
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_connections.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'plugin_datas' in class_dict:
+ res = class_dict['plugin_datas'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_plugin_data(obj)
+ elif hasattr(old_obj, 'db_plugin_datas') and old_obj.db_plugin_datas is not None:
+ for obj in old_obj.db_plugin_datas:
+ new_obj.db_add_plugin_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_plugin_datas') and hasattr(new_obj, 'db_deleted_plugin_datas'):
+ for obj in old_obj.db_deleted_plugin_datas:
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_plugin_datas.append(n_obj)
+ if 'others' in class_dict:
+ res = class_dict['others'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_other(obj)
+ elif hasattr(old_obj, 'db_others') and old_obj.db_others is not None:
+ for obj in old_obj.db_others:
+ new_obj.db_add_other(DBOther.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_others') and hasattr(new_obj, 'db_deleted_others'):
+ for obj in old_obj.db_deleted_others:
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_others.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_connections:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_connection(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_plugin_datas:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_plugin_data(child)
+ to_del = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_other(child)
+ to_del = []
+ for child in self.db_modules:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_connections)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_plugin_datas)
+ children.extend(self.db_deleted_others)
+ children.extend(self.db_deleted_modules)
+ if remove:
+ self.db_deleted_connections = []
+ self.db_deleted_annotations = []
+ self.db_deleted_plugin_datas = []
+ self.db_deleted_others = []
+ self.db_deleted_modules = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_connections:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_plugin_datas:
+ if child.has_changes():
+ return True
+ for child in self._db_others:
+ if child.has_changes():
+ return True
+ for child in self._db_modules:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_modules(self):
+ return self._db_modules
+ def __set_db_modules(self, modules):
+ self._db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self._db_modules
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ self._db_modules[i] = module
+ found = True
+ break
+ if not found:
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ if not self._db_modules[i].is_new:
+ self.db_deleted_modules.append(self._db_modules[i])
+ del self._db_modules[i]
+ break
+ del self.db_modules_id_index[module.db_id]
+ def db_get_module(self, key):
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == key:
+ return self._db_modules[i]
+ return None
+ def db_get_module_by_id(self, key):
+ return self.db_modules_id_index[key]
+ def db_has_module_with_id(self, key):
+ return key in self.db_modules_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_connections(self):
+ return self._db_connections
+ def __set_db_connections(self, connections):
+ self._db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self._db_connections
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ self._db_connections[i] = connection
+ found = True
+ break
+ if not found:
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ if not self._db_connections[i].is_new:
+ self.db_deleted_connections.append(self._db_connections[i])
+ del self._db_connections[i]
+ break
+ del self.db_connections_id_index[connection.db_id]
+ def db_get_connection(self, key):
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == key:
+ return self._db_connections[i]
+ return None
+ def db_get_connection_by_id(self, key):
+ return self.db_connections_id_index[key]
+ def db_has_connection_with_id(self, key):
+ return key in self.db_connections_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_plugin_datas(self):
+ return self._db_plugin_datas
+ def __set_db_plugin_datas(self, plugin_datas):
+ self._db_plugin_datas = plugin_datas
+ self.is_dirty = True
+ db_plugin_datas = property(__get_db_plugin_datas, __set_db_plugin_datas)
+ def db_get_plugin_datas(self):
+ return self._db_plugin_datas
+ def db_add_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_change_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ self._db_plugin_datas[i] = plugin_data
+ found = True
+ break
+ if not found:
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_delete_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ if not self._db_plugin_datas[i].is_new:
+ self.db_deleted_plugin_datas.append(self._db_plugin_datas[i])
+ del self._db_plugin_datas[i]
+ break
+ del self.db_plugin_datas_id_index[plugin_data.db_id]
+ def db_get_plugin_data(self, key):
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == key:
+ return self._db_plugin_datas[i]
+ return None
+ def db_get_plugin_data_by_id(self, key):
+ return self.db_plugin_datas_id_index[key]
+ def db_has_plugin_data_with_id(self, key):
+ return key in self.db_plugin_datas_id_index
+
+ def __get_db_others(self):
+ return self._db_others
+ def __set_db_others(self, others):
+ self._db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self._db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ self._db_others[i] = other
+ found = True
+ break
+ if not found:
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ if not self._db_others[i].is_new:
+ self.db_deleted_others.append(self._db_others[i])
+ del self._db_others[i]
+ break
+ del self.db_others_id_index[other.db_id]
+ def db_get_other(self, key):
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == key:
+ return self._db_others[i]
+ return None
+ def db_get_other_by_id(self, key):
+ return self.db_others_id_index[key]
+ def db_has_other_with_id(self, key):
+ return key in self.db_others_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmArtifactIdCause(object):
+
+ vtType = 'opm_artifact_id_cause'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactIdCause.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactIdCause(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_artifact', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_artifact', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactIdCause()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBOpmArtifactValue(object):
+
+ vtType = 'opm_artifact_value'
+
+ def __init__(self, value=None):
+ self.db_deleted_value = []
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactValue.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactValue()
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactValue()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ if obj.vtType == 'portSpec':
+ new_obj.db_add_value(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_value(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ if obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ if remove:
+ self.db_deleted_value = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+
+
+class DBOpmArtifactIdEffect(object):
+
+ vtType = 'opm_artifact_id_effect'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactIdEffect.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactIdEffect(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_artifact', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_artifact', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactIdEffect()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBOpmGraph(object):
+
+ vtType = 'opm_graph'
+
+ def __init__(self, accounts=None, processes=None, artifacts=None, agents=None, dependencies=None):
+ self.db_deleted_accounts = []
+ self._db_accounts = accounts
+ self.db_deleted_processes = []
+ self._db_processes = processes
+ self.db_deleted_artifacts = []
+ self._db_artifacts = artifacts
+ self.db_deleted_agents = []
+ self._db_agents = agents
+ self.db_deleted_dependencies = []
+ self._db_dependencies = dependencies
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmGraph.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmGraph()
+ if self._db_accounts is not None:
+ cp._db_accounts = self._db_accounts.do_copy(new_ids, id_scope, id_remap)
+ if self._db_processes is not None:
+ cp._db_processes = self._db_processes.do_copy(new_ids, id_scope, id_remap)
+ if self._db_artifacts is not None:
+ cp._db_artifacts = self._db_artifacts.do_copy(new_ids, id_scope, id_remap)
+ if self._db_agents is not None:
+ cp._db_agents = self._db_agents.do_copy(new_ids, id_scope, id_remap)
+ if self._db_dependencies is not None:
+ cp._db_dependencies = self._db_dependencies.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmGraph()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ new_obj.db_accounts = res
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ obj = old_obj.db_accounts
+ new_obj.db_add_accounts(DBOpmAccounts.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccounts.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'processes' in class_dict:
+ res = class_dict['processes'](old_obj, trans_dict)
+ new_obj.db_processes = res
+ elif hasattr(old_obj, 'db_processes') and old_obj.db_processes is not None:
+ obj = old_obj.db_processes
+ new_obj.db_add_processes(DBOpmProcesses.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_processes') and hasattr(new_obj, 'db_deleted_processes'):
+ for obj in old_obj.db_deleted_processes:
+ n_obj = DBOpmProcesses.update_version(obj, trans_dict)
+ new_obj.db_deleted_processes.append(n_obj)
+ if 'artifacts' in class_dict:
+ res = class_dict['artifacts'](old_obj, trans_dict)
+ new_obj.db_artifacts = res
+ elif hasattr(old_obj, 'db_artifacts') and old_obj.db_artifacts is not None:
+ obj = old_obj.db_artifacts
+ new_obj.db_add_artifacts(DBOpmArtifacts.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_artifacts') and hasattr(new_obj, 'db_deleted_artifacts'):
+ for obj in old_obj.db_deleted_artifacts:
+ n_obj = DBOpmArtifacts.update_version(obj, trans_dict)
+ new_obj.db_deleted_artifacts.append(n_obj)
+ if 'agents' in class_dict:
+ res = class_dict['agents'](old_obj, trans_dict)
+ new_obj.db_agents = res
+ elif hasattr(old_obj, 'db_agents') and old_obj.db_agents is not None:
+ obj = old_obj.db_agents
+ new_obj.db_add_agents(DBOpmAgents.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_agents') and hasattr(new_obj, 'db_deleted_agents'):
+ for obj in old_obj.db_deleted_agents:
+ n_obj = DBOpmAgents.update_version(obj, trans_dict)
+ new_obj.db_deleted_agents.append(n_obj)
+ if 'dependencies' in class_dict:
+ res = class_dict['dependencies'](old_obj, trans_dict)
+ new_obj.db_dependencies = res
+ elif hasattr(old_obj, 'db_dependencies') and old_obj.db_dependencies is not None:
+ obj = old_obj.db_dependencies
+ new_obj.db_add_dependencies(DBOpmDependencies.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_dependencies') and hasattr(new_obj, 'db_deleted_dependencies'):
+ for obj in old_obj.db_deleted_dependencies:
+ n_obj = DBOpmDependencies.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencies.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_accounts is not None:
+ children.extend(self._db_accounts.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_accounts = None
+ if self._db_processes is not None:
+ children.extend(self._db_processes.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_processes = None
+ if self._db_artifacts is not None:
+ children.extend(self._db_artifacts.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_artifacts = None
+ if self._db_agents is not None:
+ children.extend(self._db_agents.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_agents = None
+ if self._db_dependencies is not None:
+ children.extend(self._db_dependencies.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_dependencies = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_processes)
+ children.extend(self.db_deleted_artifacts)
+ children.extend(self.db_deleted_agents)
+ children.extend(self.db_deleted_dependencies)
+ if remove:
+ self.db_deleted_accounts = []
+ self.db_deleted_processes = []
+ self.db_deleted_artifacts = []
+ self.db_deleted_agents = []
+ self.db_deleted_dependencies = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_accounts is not None and self._db_accounts.has_changes():
+ return True
+ if self._db_processes is not None and self._db_processes.has_changes():
+ return True
+ if self._db_artifacts is not None and self._db_artifacts.has_changes():
+ return True
+ if self._db_agents is not None and self._db_agents.has_changes():
+ return True
+ if self._db_dependencies is not None and self._db_dependencies.has_changes():
+ return True
+ return False
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_add_accounts(self, accounts):
+ self._db_accounts = accounts
+ def db_change_accounts(self, accounts):
+ self._db_accounts = accounts
+ def db_delete_accounts(self, accounts):
+ if not self.is_new:
+ self.db_deleted_accounts.append(self._db_accounts)
+ self._db_accounts = None
+
+ def __get_db_processes(self):
+ return self._db_processes
+ def __set_db_processes(self, processes):
+ self._db_processes = processes
+ self.is_dirty = True
+ db_processes = property(__get_db_processes, __set_db_processes)
+ def db_add_processes(self, processes):
+ self._db_processes = processes
+ def db_change_processes(self, processes):
+ self._db_processes = processes
+ def db_delete_processes(self, processes):
+ if not self.is_new:
+ self.db_deleted_processes.append(self._db_processes)
+ self._db_processes = None
+
+ def __get_db_artifacts(self):
+ return self._db_artifacts
+ def __set_db_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ self.is_dirty = True
+ db_artifacts = property(__get_db_artifacts, __set_db_artifacts)
+ def db_add_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ def db_change_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ def db_delete_artifacts(self, artifacts):
+ if not self.is_new:
+ self.db_deleted_artifacts.append(self._db_artifacts)
+ self._db_artifacts = None
+
+ def __get_db_agents(self):
+ return self._db_agents
+ def __set_db_agents(self, agents):
+ self._db_agents = agents
+ self.is_dirty = True
+ db_agents = property(__get_db_agents, __set_db_agents)
+ def db_add_agents(self, agents):
+ self._db_agents = agents
+ def db_change_agents(self, agents):
+ self._db_agents = agents
+ def db_delete_agents(self, agents):
+ if not self.is_new:
+ self.db_deleted_agents.append(self._db_agents)
+ self._db_agents = None
+
+ def __get_db_dependencies(self):
+ return self._db_dependencies
+ def __set_db_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ self.is_dirty = True
+ db_dependencies = property(__get_db_dependencies, __set_db_dependencies)
+ def db_add_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ def db_change_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ def db_delete_dependencies(self, dependencies):
+ if not self.is_new:
+ self.db_deleted_dependencies.append(self._db_dependencies)
+ self._db_dependencies = None
+
+
+
+class DBRegistry(object):
+
+ vtType = 'registry'
+
+ def __init__(self, id=None, entity_type=None, version=None, root_descriptor_id=None, name=None, last_modified=None, packages=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_root_descriptor_id = root_descriptor_id
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_packages = []
+ self.db_packages_id_index = {}
+ self.db_packages_identifier_index = {}
+ if packages is None:
+ self._db_packages = []
+ else:
+ self._db_packages = packages
+ for v in self._db_packages:
+ self.db_packages_id_index[v.db_id] = v
+ self.db_packages_identifier_index[(v.db_identifier,v.db_version)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBRegistry.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBRegistry(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ root_descriptor_id=self._db_root_descriptor_id,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_packages is None:
+ cp._db_packages = []
+ else:
+ cp._db_packages = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_packages]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_root_descriptor_id') and ('module_descriptor', self._db_root_descriptor_id) in id_remap:
+ cp._db_root_descriptor_id = id_remap[('module_descriptor', self._db_root_descriptor_id)]
+
+ # recreate indices and set flags
+ cp.db_packages_id_index = dict((v.db_id, v) for v in cp._db_packages)
+ cp.db_packages_identifier_index = dict(((v.db_identifier,v.db_version), v) for v in cp._db_packages)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRegistry()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'root_descriptor_id' in class_dict:
+ res = class_dict['root_descriptor_id'](old_obj, trans_dict)
+ new_obj.db_root_descriptor_id = res
+ elif hasattr(old_obj, 'db_root_descriptor_id') and old_obj.db_root_descriptor_id is not None:
+ new_obj.db_root_descriptor_id = old_obj.db_root_descriptor_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'packages' in class_dict:
+ res = class_dict['packages'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_package(obj)
+ elif hasattr(old_obj, 'db_packages') and old_obj.db_packages is not None:
+ for obj in old_obj.db_packages:
+ new_obj.db_add_package(DBPackage.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_packages') and hasattr(new_obj, 'db_deleted_packages'):
+ for obj in old_obj.db_deleted_packages:
+ n_obj = DBPackage.update_version(obj, trans_dict)
+ new_obj.db_deleted_packages.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_packages:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_package(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_packages)
+ if remove:
+ self.db_deleted_packages = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_packages:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_root_descriptor_id(self):
+ return self._db_root_descriptor_id
+ def __set_db_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ self.is_dirty = True
+ db_root_descriptor_id = property(__get_db_root_descriptor_id, __set_db_root_descriptor_id)
+ def db_add_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ def db_change_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ def db_delete_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_packages(self):
+ return self._db_packages
+ def __set_db_packages(self, packages):
+ self._db_packages = packages
+ self.is_dirty = True
+ db_packages = property(__get_db_packages, __set_db_packages)
+ def db_get_packages(self):
+ return self._db_packages
+ def db_add_package(self, package):
+ self.is_dirty = True
+ self._db_packages.append(package)
+ self.db_packages_id_index[package.db_id] = package
+ self.db_packages_identifier_index[(package.db_identifier,package.db_version)] = package
+ def db_change_package(self, package):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == package.db_id:
+ self._db_packages[i] = package
+ found = True
+ break
+ if not found:
+ self._db_packages.append(package)
+ self.db_packages_id_index[package.db_id] = package
+ self.db_packages_identifier_index[(package.db_identifier,package.db_version)] = package
+ def db_delete_package(self, package):
+ self.is_dirty = True
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == package.db_id:
+ if not self._db_packages[i].is_new:
+ self.db_deleted_packages.append(self._db_packages[i])
+ del self._db_packages[i]
+ break
+ del self.db_packages_id_index[package.db_id]
+ del self.db_packages_identifier_index[(package.db_identifier,package.db_version)]
+ def db_get_package(self, key):
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == key:
+ return self._db_packages[i]
+ return None
+ def db_get_package_by_id(self, key):
+ return self.db_packages_id_index[key]
+ def db_has_package_with_id(self, key):
+ return key in self.db_packages_id_index
+ def db_get_package_by_identifier(self, key):
+ return self.db_packages_identifier_index[key]
+ def db_has_package_with_identifier(self, key):
+ return key in self.db_packages_identifier_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmAccount(object):
+
+ vtType = 'opm_account'
+
+ def __init__(self, id=None, value=None):
+ self._db_id = id
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccount.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccount(id=self._db_id,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccount()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAnnotation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, data=None, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_oldObjId = oldObjId
+ self._db_newObjId = newObjId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBChange.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange(id=self._db_id,
+ what=self._db_what,
+ oldObjId=self._db_oldObjId,
+ newObjId=self._db_newObjId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_oldObjId') and (self._db_what, self._db_oldObjId) in id_remap:
+ cp._db_oldObjId = id_remap[(self._db_what, self._db_oldObjId)]
+ if hasattr(self, 'db_newObjId') and (self._db_what, self._db_newObjId) in id_remap:
+ cp._db_newObjId = id_remap[(self._db_what, self._db_newObjId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBChange()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'oldObjId' in class_dict:
+ res = class_dict['oldObjId'](old_obj, trans_dict)
+ new_obj.db_oldObjId = res
+ elif hasattr(old_obj, 'db_oldObjId') and old_obj.db_oldObjId is not None:
+ new_obj.db_oldObjId = old_obj.db_oldObjId
+ if 'newObjId' in class_dict:
+ res = class_dict['newObjId'](old_obj, trans_dict)
+ new_obj.db_newObjId = res
+ elif hasattr(old_obj, 'db_newObjId') and old_obj.db_newObjId is not None:
+ new_obj.db_newObjId = old_obj.db_newObjId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_oldObjId(self):
+ return self._db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self._db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self._db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self._db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmWasDerivedFrom(object):
+
+ vtType = 'opm_was_derived_from'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasDerivedFrom.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasDerivedFrom()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasDerivedFrom()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmArtifactIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmArtifactIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmArtifactIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmArtifactIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBOpmWasControlledBy(object):
+
+ vtType = 'opm_was_controlled_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, starts=None, ends=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_starts = []
+ if starts is None:
+ self._db_starts = []
+ else:
+ self._db_starts = starts
+ self.db_deleted_ends = []
+ if ends is None:
+ self._db_ends = []
+ else:
+ self._db_ends = ends
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasControlledBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasControlledBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_starts is None:
+ cp._db_starts = []
+ else:
+ cp._db_starts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_starts]
+ if self._db_ends is None:
+ cp._db_ends = []
+ else:
+ cp._db_ends = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ends]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasControlledBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmAgentId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmAgentId.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'starts' in class_dict:
+ res = class_dict['starts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_start(obj)
+ elif hasattr(old_obj, 'db_starts') and old_obj.db_starts is not None:
+ for obj in old_obj.db_starts:
+ new_obj.db_add_start(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_starts') and hasattr(new_obj, 'db_deleted_starts'):
+ for obj in old_obj.db_deleted_starts:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_starts.append(n_obj)
+ if 'ends' in class_dict:
+ res = class_dict['ends'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_end(obj)
+ elif hasattr(old_obj, 'db_ends') and old_obj.db_ends is not None:
+ for obj in old_obj.db_ends:
+ new_obj.db_add_end(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_ends') and hasattr(new_obj, 'db_deleted_ends'):
+ for obj in old_obj.db_deleted_ends:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_ends.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_starts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_start(child)
+ to_del = []
+ for child in self.db_ends:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_end(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_starts)
+ children.extend(self.db_deleted_ends)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_starts = []
+ self.db_deleted_ends = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_starts:
+ if child.has_changes():
+ return True
+ for child in self._db_ends:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_starts(self):
+ return self._db_starts
+ def __set_db_starts(self, starts):
+ self._db_starts = starts
+ self.is_dirty = True
+ db_starts = property(__get_db_starts, __set_db_starts)
+ def db_get_starts(self):
+ return self._db_starts
+ def db_add_start(self, start):
+ self.is_dirty = True
+ self._db_starts.append(start)
+ def db_change_start(self, start):
+ self.is_dirty = True
+ self._db_starts.append(start)
+ def db_delete_start(self, start):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_start(self, key):
+ return None
+
+ def __get_db_ends(self):
+ return self._db_ends
+ def __set_db_ends(self, ends):
+ self._db_ends = ends
+ self.is_dirty = True
+ db_ends = property(__get_db_ends, __set_db_ends)
+ def db_get_ends(self):
+ return self._db_ends
+ def db_add_end(self, end):
+ self.is_dirty = True
+ self._db_ends.append(end)
+ def db_change_end(self, end):
+ self.is_dirty = True
+ self._db_ends.append(end)
+ def db_delete_end(self, end):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_end(self, key):
+ return None
+
+
+
+class DBOpmAgentId(object):
+
+ vtType = 'opm_agent_id'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgentId.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgentId(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_agent', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_agent', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgentId()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBGroupExec(object):
+
+ vtType = 'group_exec'
+
+ def __init__(self, item_execs=None, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, group_name=None, group_type=None, completed=None, error=None, machine_id=None, annotations=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_group_name = group_name
+ self._db_group_type = group_type
+ self._db_completed = completed
+ self._db_error = error
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroupExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroupExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ group_name=self._db_group_name,
+ group_type=self._db_group_type,
+ completed=self._db_completed,
+ error=self._db_error,
+ machine_id=self._db_machine_id)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroupExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'group_name' in class_dict:
+ res = class_dict['group_name'](old_obj, trans_dict)
+ new_obj.db_group_name = res
+ elif hasattr(old_obj, 'db_group_name') and old_obj.db_group_name is not None:
+ new_obj.db_group_name = old_obj.db_group_name
+ if 'group_type' in class_dict:
+ res = class_dict['group_type'](old_obj, trans_dict)
+ new_obj.db_group_type = res
+ elif hasattr(old_obj, 'db_group_type') and old_obj.db_group_type is not None:
+ new_obj.db_group_type = old_obj.db_group_type
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_group_name(self):
+ return self._db_group_name
+ def __set_db_group_name(self, group_name):
+ self._db_group_name = group_name
+ self.is_dirty = True
+ db_group_name = property(__get_db_group_name, __set_db_group_name)
+ def db_add_group_name(self, group_name):
+ self._db_group_name = group_name
+ def db_change_group_name(self, group_name):
+ self._db_group_name = group_name
+ def db_delete_group_name(self, group_name):
+ self._db_group_name = None
+
+ def __get_db_group_type(self):
+ return self._db_group_type
+ def __set_db_group_type(self, group_type):
+ self._db_group_type = group_type
+ self.is_dirty = True
+ db_group_type = property(__get_db_group_type, __set_db_group_type)
+ def db_add_group_type(self, group_type):
+ self._db_group_type = group_type
+ def db_change_group_type(self, group_type):
+ self._db_group_type = group_type
+ def db_delete_group_type(self, group_type):
+ self._db_group_type = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmTime(object):
+
+ vtType = 'opm_time'
+
+ def __init__(self, no_later_than=None, no_earlier_than=None, clock_id=None):
+ self._db_no_later_than = no_later_than
+ self._db_no_earlier_than = no_earlier_than
+ self._db_clock_id = clock_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmTime.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmTime(no_later_than=self._db_no_later_than,
+ no_earlier_than=self._db_no_earlier_than,
+ clock_id=self._db_clock_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmTime()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'no_later_than' in class_dict:
+ res = class_dict['no_later_than'](old_obj, trans_dict)
+ new_obj.db_no_later_than = res
+ elif hasattr(old_obj, 'db_no_later_than') and old_obj.db_no_later_than is not None:
+ new_obj.db_no_later_than = old_obj.db_no_later_than
+ if 'no_earlier_than' in class_dict:
+ res = class_dict['no_earlier_than'](old_obj, trans_dict)
+ new_obj.db_no_earlier_than = res
+ elif hasattr(old_obj, 'db_no_earlier_than') and old_obj.db_no_earlier_than is not None:
+ new_obj.db_no_earlier_than = old_obj.db_no_earlier_than
+ if 'clock_id' in class_dict:
+ res = class_dict['clock_id'](old_obj, trans_dict)
+ new_obj.db_clock_id = res
+ elif hasattr(old_obj, 'db_clock_id') and old_obj.db_clock_id is not None:
+ new_obj.db_clock_id = old_obj.db_clock_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_no_later_than(self):
+ return self._db_no_later_than
+ def __set_db_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ self.is_dirty = True
+ db_no_later_than = property(__get_db_no_later_than, __set_db_no_later_than)
+ def db_add_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ def db_change_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ def db_delete_no_later_than(self, no_later_than):
+ self._db_no_later_than = None
+
+ def __get_db_no_earlier_than(self):
+ return self._db_no_earlier_than
+ def __set_db_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ self.is_dirty = True
+ db_no_earlier_than = property(__get_db_no_earlier_than, __set_db_no_earlier_than)
+ def db_add_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ def db_change_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ def db_delete_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = None
+
+ def __get_db_clock_id(self):
+ return self._db_clock_id
+ def __set_db_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ self.is_dirty = True
+ db_clock_id = property(__get_db_clock_id, __set_db_clock_id)
+ def db_add_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ def db_change_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ def db_delete_clock_id(self, clock_id):
+ self._db_clock_id = None
+
+
+
+class DBPackage(object):
+
+ vtType = 'package'
+
+ def __init__(self, id=None, name=None, identifier=None, codepath=None, load_configuration=None, version=None, description=None, module_descriptors=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_identifier = identifier
+ self._db_codepath = codepath
+ self._db_load_configuration = load_configuration
+ self._db_version = version
+ self._db_description = description
+ self.db_deleted_module_descriptors = []
+ self.db_module_descriptors_id_index = {}
+ self.db_module_descriptors_name_index = {}
+ if module_descriptors is None:
+ self._db_module_descriptors = []
+ else:
+ self._db_module_descriptors = module_descriptors
+ for v in self._db_module_descriptors:
+ self.db_module_descriptors_id_index[v.db_id] = v
+ self.db_module_descriptors_name_index[(v.db_name,v.db_namespace,v.db_version)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPackage.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPackage(id=self._db_id,
+ name=self._db_name,
+ identifier=self._db_identifier,
+ codepath=self._db_codepath,
+ load_configuration=self._db_load_configuration,
+ version=self._db_version,
+ description=self._db_description)
+ if self._db_module_descriptors is None:
+ cp._db_module_descriptors = []
+ else:
+ cp._db_module_descriptors = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_module_descriptors]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_module_descriptors_id_index = dict((v.db_id, v) for v in cp._db_module_descriptors)
+ cp.db_module_descriptors_name_index = dict(((v.db_name,v.db_namespace,v.db_version), v) for v in cp._db_module_descriptors)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPackage()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'identifier' in class_dict:
+ res = class_dict['identifier'](old_obj, trans_dict)
+ new_obj.db_identifier = res
+ elif hasattr(old_obj, 'db_identifier') and old_obj.db_identifier is not None:
+ new_obj.db_identifier = old_obj.db_identifier
+ if 'codepath' in class_dict:
+ res = class_dict['codepath'](old_obj, trans_dict)
+ new_obj.db_codepath = res
+ elif hasattr(old_obj, 'db_codepath') and old_obj.db_codepath is not None:
+ new_obj.db_codepath = old_obj.db_codepath
+ if 'load_configuration' in class_dict:
+ res = class_dict['load_configuration'](old_obj, trans_dict)
+ new_obj.db_load_configuration = res
+ elif hasattr(old_obj, 'db_load_configuration') and old_obj.db_load_configuration is not None:
+ new_obj.db_load_configuration = old_obj.db_load_configuration
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'description' in class_dict:
+ res = class_dict['description'](old_obj, trans_dict)
+ new_obj.db_description = res
+ elif hasattr(old_obj, 'db_description') and old_obj.db_description is not None:
+ new_obj.db_description = old_obj.db_description
+ if 'module_descriptors' in class_dict:
+ res = class_dict['module_descriptors'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module_descriptor(obj)
+ elif hasattr(old_obj, 'db_module_descriptors') and old_obj.db_module_descriptors is not None:
+ for obj in old_obj.db_module_descriptors:
+ new_obj.db_add_module_descriptor(DBModuleDescriptor.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_module_descriptors') and hasattr(new_obj, 'db_deleted_module_descriptors'):
+ for obj in old_obj.db_deleted_module_descriptors:
+ n_obj = DBModuleDescriptor.update_version(obj, trans_dict)
+ new_obj.db_deleted_module_descriptors.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_descriptors:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_descriptor(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_descriptors)
+ if remove:
+ self.db_deleted_module_descriptors = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_module_descriptors:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_identifier(self):
+ return self._db_identifier
+ def __set_db_identifier(self, identifier):
+ self._db_identifier = identifier
+ self.is_dirty = True
+ db_identifier = property(__get_db_identifier, __set_db_identifier)
+ def db_add_identifier(self, identifier):
+ self._db_identifier = identifier
+ def db_change_identifier(self, identifier):
+ self._db_identifier = identifier
+ def db_delete_identifier(self, identifier):
+ self._db_identifier = None
+
+ def __get_db_codepath(self):
+ return self._db_codepath
+ def __set_db_codepath(self, codepath):
+ self._db_codepath = codepath
+ self.is_dirty = True
+ db_codepath = property(__get_db_codepath, __set_db_codepath)
+ def db_add_codepath(self, codepath):
+ self._db_codepath = codepath
+ def db_change_codepath(self, codepath):
+ self._db_codepath = codepath
+ def db_delete_codepath(self, codepath):
+ self._db_codepath = None
+
+ def __get_db_load_configuration(self):
+ return self._db_load_configuration
+ def __set_db_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ self.is_dirty = True
+ db_load_configuration = property(__get_db_load_configuration, __set_db_load_configuration)
+ def db_add_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ def db_change_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ def db_delete_load_configuration(self, load_configuration):
+ self._db_load_configuration = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_description(self):
+ return self._db_description
+ def __set_db_description(self, description):
+ self._db_description = description
+ self.is_dirty = True
+ db_description = property(__get_db_description, __set_db_description)
+ def db_add_description(self, description):
+ self._db_description = description
+ def db_change_description(self, description):
+ self._db_description = description
+ def db_delete_description(self, description):
+ self._db_description = None
+
+ def __get_db_module_descriptors(self):
+ return self._db_module_descriptors
+ def __set_db_module_descriptors(self, module_descriptors):
+ self._db_module_descriptors = module_descriptors
+ self.is_dirty = True
+ db_module_descriptors = property(__get_db_module_descriptors, __set_db_module_descriptors)
+ def db_get_module_descriptors(self):
+ return self._db_module_descriptors
+ def db_add_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ self._db_module_descriptors.append(module_descriptor)
+ self.db_module_descriptors_id_index[module_descriptor.db_id] = module_descriptor
+ self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)] = module_descriptor
+ def db_change_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == module_descriptor.db_id:
+ self._db_module_descriptors[i] = module_descriptor
+ found = True
+ break
+ if not found:
+ self._db_module_descriptors.append(module_descriptor)
+ self.db_module_descriptors_id_index[module_descriptor.db_id] = module_descriptor
+ self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)] = module_descriptor
+ def db_delete_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == module_descriptor.db_id:
+ if not self._db_module_descriptors[i].is_new:
+ self.db_deleted_module_descriptors.append(self._db_module_descriptors[i])
+ del self._db_module_descriptors[i]
+ break
+ del self.db_module_descriptors_id_index[module_descriptor.db_id]
+ del self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)]
+ def db_get_module_descriptor(self, key):
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == key:
+ return self._db_module_descriptors[i]
+ return None
+ def db_get_module_descriptor_by_id(self, key):
+ return self.db_module_descriptors_id_index[key]
+ def db_has_module_descriptor_with_id(self, key):
+ return key in self.db_module_descriptors_id_index
+ def db_get_module_descriptor_by_name(self, key):
+ return self.db_module_descriptors_name_index[key]
+ def db_has_module_descriptor_with_name(self, key):
+ return key in self.db_module_descriptors_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, item_execs=None, id=None, user=None, ip=None, session=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, completed=None, name=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_user = user
+ self._db_ip = ip
+ self._db_session = session
+ self._db_vt_version = vt_version
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_parent_id = parent_id
+ self._db_parent_type = parent_type
+ self._db_parent_version = parent_version
+ self._db_completed = completed
+ self._db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflowExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec(id=self._db_id,
+ user=self._db_user,
+ ip=self._db_ip,
+ session=self._db_session,
+ vt_version=self._db_vt_version,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ parent_id=self._db_parent_id,
+ parent_type=self._db_parent_type,
+ parent_version=self._db_parent_version,
+ completed=self._db_completed,
+ name=self._db_name)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflowExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'ip' in class_dict:
+ res = class_dict['ip'](old_obj, trans_dict)
+ new_obj.db_ip = res
+ elif hasattr(old_obj, 'db_ip') and old_obj.db_ip is not None:
+ new_obj.db_ip = old_obj.db_ip
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'vt_version' in class_dict:
+ res = class_dict['vt_version'](old_obj, trans_dict)
+ new_obj.db_vt_version = res
+ elif hasattr(old_obj, 'db_vt_version') and old_obj.db_vt_version is not None:
+ new_obj.db_vt_version = old_obj.db_vt_version
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'parent_id' in class_dict:
+ res = class_dict['parent_id'](old_obj, trans_dict)
+ new_obj.db_parent_id = res
+ elif hasattr(old_obj, 'db_parent_id') and old_obj.db_parent_id is not None:
+ new_obj.db_parent_id = old_obj.db_parent_id
+ if 'parent_type' in class_dict:
+ res = class_dict['parent_type'](old_obj, trans_dict)
+ new_obj.db_parent_type = res
+ elif hasattr(old_obj, 'db_parent_type') and old_obj.db_parent_type is not None:
+ new_obj.db_parent_type = old_obj.db_parent_type
+ if 'parent_version' in class_dict:
+ res = class_dict['parent_version'](old_obj, trans_dict)
+ new_obj.db_parent_version = res
+ elif hasattr(old_obj, 'db_parent_version') and old_obj.db_parent_version is not None:
+ new_obj.db_parent_version = old_obj.db_parent_version
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_ip(self):
+ return self._db_ip
+ def __set_db_ip(self, ip):
+ self._db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self._db_ip = ip
+ def db_change_ip(self, ip):
+ self._db_ip = ip
+ def db_delete_ip(self, ip):
+ self._db_ip = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_vt_version(self):
+ return self._db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self._db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self._db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self._db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self._db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self._db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self._db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self._db_parent_version = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLoopExec(object):
+
+ vtType = 'loop_exec'
+
+ def __init__(self, item_execs=None, id=None, ts_start=None, ts_end=None, iteration=None, completed=None, error=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_iteration = iteration
+ self._db_completed = completed
+ self._db_error = error
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLoopExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLoopExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ iteration=self._db_iteration,
+ completed=self._db_completed,
+ error=self._db_error)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLoopExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'iteration' in class_dict:
+ res = class_dict['iteration'](old_obj, trans_dict)
+ new_obj.db_iteration = res
+ elif hasattr(old_obj, 'db_iteration') and old_obj.db_iteration is not None:
+ new_obj.db_iteration = old_obj.db_iteration
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_iteration(self):
+ return self._db_iteration
+ def __set_db_iteration(self, iteration):
+ self._db_iteration = iteration
+ self.is_dirty = True
+ db_iteration = property(__get_db_iteration, __set_db_iteration)
+ def db_add_iteration(self, iteration):
+ self._db_iteration = iteration
+ def db_change_iteration(self, iteration):
+ self._db_iteration = iteration
+ def db_delete_iteration(self, iteration):
+ self._db_iteration = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self._db_id = id
+ self.db_deleted_ports = []
+ self.db_ports_id_index = {}
+ self.db_ports_type_index = {}
+ if ports is None:
+ self._db_ports = []
+ else:
+ self._db_ports = ports
+ for v in self._db_ports:
+ self.db_ports_id_index[v.db_id] = v
+ self.db_ports_type_index[v.db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBConnection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection(id=self._db_id)
+ if self._db_ports is None:
+ cp._db_ports = []
+ else:
+ cp._db_ports = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ports]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_ports_id_index = dict((v.db_id, v) for v in cp._db_ports)
+ cp.db_ports_type_index = dict((v.db_type, v) for v in cp._db_ports)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBConnection()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ports' in class_dict:
+ res = class_dict['ports'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_port(obj)
+ elif hasattr(old_obj, 'db_ports') and old_obj.db_ports is not None:
+ for obj in old_obj.db_ports:
+ new_obj.db_add_port(DBPort.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_ports') and hasattr(new_obj, 'db_deleted_ports'):
+ for obj in old_obj.db_deleted_ports:
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_ports.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_ports)
+ if remove:
+ self.db_deleted_ports = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ports(self):
+ return self._db_ports
+ def __set_db_ports(self, ports):
+ self._db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self._db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ self._db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ if not self._db_ports[i].is_new:
+ self.db_deleted_ports.append(self._db_ports[i])
+ del self._db_ports[i]
+ break
+ del self.db_ports_id_index[port.db_id]
+ del self.db_ports_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == key:
+ return self._db_ports[i]
+ return None
+ def db_get_port_by_id(self, key):
+ return self.db_ports_id_index[key]
+ def db_has_port_with_id(self, key):
+ return key in self.db_ports_id_index
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return key in self.db_ports_type_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmProcess(object):
+
+ vtType = 'opm_process'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self.db_deleted_value = []
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcess.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcess(id=self._db_id)
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcess()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ new_obj.db_add_value(DBOpmProcessValue.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ n_obj = DBOpmProcessValue.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_value = []
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmWasTriggeredBy(object):
+
+ vtType = 'opm_was_triggered_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasTriggeredBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasTriggeredBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasTriggeredBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmProcessIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmProcessIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBOpmProcessValue(object):
+
+ vtType = 'opm_process_value'
+
+ def __init__(self, value=None):
+ self.db_deleted_value = []
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessValue.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessValue()
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessValue()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_value(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_value(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_value(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ if remove:
+ self.db_deleted_value = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, operations=None, id=None, prevId=None, date=None, session=None, user=None, prune=None, annotations=None):
+ self.db_deleted_operations = []
+ self.db_operations_id_index = {}
+ if operations is None:
+ self._db_operations = []
+ else:
+ self._db_operations = operations
+ for v in self._db_operations:
+ self.db_operations_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_prevId = prevId
+ self._db_date = date
+ self._db_session = session
+ self._db_user = user
+ self._db_prune = prune
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction(id=self._db_id,
+ prevId=self._db_prevId,
+ date=self._db_date,
+ session=self._db_session,
+ user=self._db_user,
+ prune=self._db_prune)
+ if self._db_operations is None:
+ cp._db_operations = []
+ else:
+ cp._db_operations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_operations]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prevId') and ('action', self._db_prevId) in id_remap:
+ cp._db_prevId = id_remap[('action', self._db_prevId)]
+
+ # recreate indices and set flags
+ cp.db_operations_id_index = dict((v.db_id, v) for v in cp._db_operations)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'operations' in class_dict:
+ res = class_dict['operations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_operation(obj)
+ elif hasattr(old_obj, 'db_operations') and old_obj.db_operations is not None:
+ for obj in old_obj.db_operations:
+ if obj.vtType == 'add':
+ new_obj.db_add_operation(DBAdd.update_version(obj, trans_dict))
+ elif obj.vtType == 'delete':
+ new_obj.db_add_operation(DBDelete.update_version(obj, trans_dict))
+ elif obj.vtType == 'change':
+ new_obj.db_add_operation(DBChange.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_operations') and hasattr(new_obj, 'db_deleted_operations'):
+ for obj in old_obj.db_deleted_operations:
+ if obj.vtType == 'add':
+ n_obj = DBAdd.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'delete':
+ n_obj = DBDelete.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'change':
+ n_obj = DBChange.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'prevId' in class_dict:
+ res = class_dict['prevId'](old_obj, trans_dict)
+ new_obj.db_prevId = res
+ elif hasattr(old_obj, 'db_prevId') and old_obj.db_prevId is not None:
+ new_obj.db_prevId = old_obj.db_prevId
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'prune' in class_dict:
+ res = class_dict['prune'](old_obj, trans_dict)
+ new_obj.db_prune = res
+ elif hasattr(old_obj, 'db_prune') and old_obj.db_prune is not None:
+ new_obj.db_prune = old_obj.db_prune
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_operations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_operations)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_operations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_operations(self):
+ return self._db_operations
+ def __set_db_operations(self, operations):
+ self._db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self._db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ self._db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ if not self._db_operations[i].is_new:
+ self.db_deleted_operations.append(self._db_operations[i])
+ del self._db_operations[i]
+ break
+ del self.db_operations_id_index[operation.db_id]
+ def db_get_operation(self, key):
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == key:
+ return self._db_operations[i]
+ return None
+ def db_get_operation_by_id(self, key):
+ return self.db_operations_id_index[key]
+ def db_has_operation_with_id(self, key):
+ return key in self.db_operations_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_prevId(self):
+ return self._db_prevId
+ def __set_db_prevId(self, prevId):
+ self._db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self._db_prevId = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_prune(self):
+ return self._db_prune
+ def __set_db_prune(self, prune):
+ self._db_prune = prune
+ self.is_dirty = True
+ db_prune = property(__get_db_prune, __set_db_prune)
+ def db_add_prune(self, prune):
+ self._db_prune = prune
+ def db_change_prune(self, prune):
+ self._db_prune = prune
+ def db_delete_prune(self, prune):
+ self._db_prune = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmAgent(object):
+
+ vtType = 'opm_agent'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgent.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgent(id=self._db_id,
+ value=self._db_value)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgent()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBDelete.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBDelete()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, actions=None, tags=None, annotations=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self._db_actions = []
+ else:
+ self._db_actions = actions
+ for v in self._db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self._db_tags = []
+ else:
+ self._db_tags = tags
+ for v in self._db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_actions is None:
+ cp._db_actions = []
+ else:
+ cp._db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actions]
+ if self._db_tags is None:
+ cp._db_tags = []
+ else:
+ cp._db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_tags]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_actions_id_index = dict((v.db_id, v) for v in cp._db_actions)
+ cp.db_tags_id_index = dict((v.db_id, v) for v in cp._db_tags)
+ cp.db_tags_name_index = dict((v.db_name, v) for v in cp._db_tags)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'actions' in class_dict:
+ res = class_dict['actions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_action(obj)
+ elif hasattr(old_obj, 'db_actions') and old_obj.db_actions is not None:
+ for obj in old_obj.db_actions:
+ new_obj.db_add_action(DBAction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actions') and hasattr(new_obj, 'db_deleted_actions'):
+ for obj in old_obj.db_deleted_actions:
+ n_obj = DBAction.update_version(obj, trans_dict)
+ new_obj.db_deleted_actions.append(n_obj)
+ if 'tags' in class_dict:
+ res = class_dict['tags'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_tag(obj)
+ elif hasattr(old_obj, 'db_tags') and old_obj.db_tags is not None:
+ for obj in old_obj.db_tags:
+ new_obj.db_add_tag(DBTag.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_tags') and hasattr(new_obj, 'db_deleted_tags'):
+ for obj in old_obj.db_deleted_tags:
+ n_obj = DBTag.update_version(obj, trans_dict)
+ new_obj.db_deleted_tags.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_actions:
+ if child.has_changes():
+ return True
+ for child in self._db_tags:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_actions(self):
+ return self._db_actions
+ def __set_db_actions(self, actions):
+ self._db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self._db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ self._db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ if not self._db_actions[i].is_new:
+ self.db_deleted_actions.append(self._db_actions[i])
+ del self._db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == key:
+ return self._db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return key in self.db_actions_id_index
+
+ def __get_db_tags(self):
+ return self._db_tags
+ def __set_db_tags(self, tags):
+ self._db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self._db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ self._db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ if not self._db_tags[i].is_new:
+ self.db_deleted_tags.append(self._db_tags[i])
+ del self._db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == key:
+ return self._db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return key in self.db_tags_id_index
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return key in self.db_tags_name_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, module_name=None, completed=None, error=None, machine_id=None, annotations=None, loop_execs=None):
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_module_name = module_name
+ self._db_completed = completed
+ self._db_error = error
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_loop_execs = []
+ self.db_loop_execs_id_index = {}
+ if loop_execs is None:
+ self._db_loop_execs = []
+ else:
+ self._db_loop_execs = loop_execs
+ for v in self._db_loop_execs:
+ self.db_loop_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ module_name=self._db_module_name,
+ completed=self._db_completed,
+ error=self._db_error,
+ machine_id=self._db_machine_id)
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_loop_execs is None:
+ cp._db_loop_execs = []
+ else:
+ cp._db_loop_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_loop_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_loop_execs_id_index = dict((v.db_id, v) for v in cp._db_loop_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'module_name' in class_dict:
+ res = class_dict['module_name'](old_obj, trans_dict)
+ new_obj.db_module_name = res
+ elif hasattr(old_obj, 'db_module_name') and old_obj.db_module_name is not None:
+ new_obj.db_module_name = old_obj.db_module_name
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'loop_execs' in class_dict:
+ res = class_dict['loop_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_loop_exec(obj)
+ elif hasattr(old_obj, 'db_loop_execs') and old_obj.db_loop_execs is not None:
+ for obj in old_obj.db_loop_execs:
+ new_obj.db_add_loop_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_loop_execs') and hasattr(new_obj, 'db_deleted_loop_execs'):
+ for obj in old_obj.db_deleted_loop_execs:
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_loop_execs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_loop_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_loop_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_loop_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_loop_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_loop_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_module_name(self):
+ return self._db_module_name
+ def __set_db_module_name(self, module_name):
+ self._db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self._db_module_name = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_loop_execs(self):
+ return self._db_loop_execs
+ def __set_db_loop_execs(self, loop_execs):
+ self._db_loop_execs = loop_execs
+ self.is_dirty = True
+ db_loop_execs = property(__get_db_loop_execs, __set_db_loop_execs)
+ def db_get_loop_execs(self):
+ return self._db_loop_execs
+ def db_add_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_change_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ self._db_loop_execs[i] = loop_exec
+ found = True
+ break
+ if not found:
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_delete_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ if not self._db_loop_execs[i].is_new:
+ self.db_deleted_loop_execs.append(self._db_loop_execs[i])
+ del self._db_loop_execs[i]
+ break
+ del self.db_loop_execs_id_index[loop_exec.db_id]
+ def db_get_loop_exec(self, key):
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == key:
+ return self._db_loop_execs[i]
+ return None
+ def db_get_loop_exec_by_id(self, key):
+ return self.db_loop_execs_id_index[key]
+ def db_has_loop_exec_with_id(self, key):
+ return key in self.db_loop_execs_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
diff --git a/vistrails/db/versions/v1_0_0/domain/id_scope.py b/vistrails/db/versions/v1_0_0/domain/id_scope.py
new file mode 100644
index 0000000..0e07f02
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/domain/id_scope.py
@@ -0,0 +1,85 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L, remap=None):
+ self.ids = {}
+ self.beginId = beginId
+ if remap is None:
+ self.remap = {}
+ else:
+ self.remap = remap
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ cp.remap = copy.copy(self.remap)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ except KeyError:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ if self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+ except KeyError:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v1_0_0/domain/log.py b/vistrails/db/versions/v1_0_0/domain/log.py
new file mode 100644
index 0000000..eedf100
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/domain/log.py
@@ -0,0 +1,72 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBLog as _DBLog
+from auto_gen import DBAbstraction, DBModule, DBGroup, DBLoopExec, \
+ DBGroupExec, DBModuleExec
+from id_scope import IdScope
+
+import copy
+
+class DBLog(_DBLog):
+
+ def __init__(self, *args, **kwargs):
+ _DBLog.__init__(self, *args, **kwargs)
+ self.id_scope = IdScope(1,
+ {DBLoopExec.vtType: 'item_exec',
+ DBModuleExec.vtType: 'item_exec',
+ DBGroupExec.vtType: 'item_exec',
+ DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBLog.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBLog
+ cp.id_scope = copy.copy(self.id_scope)
+ return cps
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ new_obj = _DBLog.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
diff --git a/vistrails/db/versions/v1_0_0/domain/registry.py b/vistrails/db/versions/v1_0_0/domain/registry.py
new file mode 100644
index 0000000..323ebbd
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/domain/registry.py
@@ -0,0 +1,63 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBRegistry as _DBRegistry, DBPackage, DBModuleDescriptor, \
+ DBPortSpec
+from id_scope import IdScope
+
+class DBRegistry(_DBRegistry):
+ def __init__(self, *args, **kwargs):
+ _DBRegistry.__init__(self, *args, **kwargs)
+ self.idScope = IdScope()
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRegistry()
+ new_obj = _DBRegistry.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ for package in self.db_packages:
+ self.idScope.updateBeginId(DBPackage.vtType, package.db_id+1)
+ for descriptor in package.db_module_descriptors:
+ self.idScope.updateBeginId(DBModuleDescriptor.vtType,
+ descriptor.db_id+1)
+ for port_spec in descriptor.db_portSpecs:
+ self.idScope.updateBeginId(DBPortSpec.vtType,
+ port_spec.db_id+1)
+
+
diff --git a/vistrails/db/versions/v1_0_0/domain/vistrail.py b/vistrails/db/versions/v1_0_0/domain/vistrail.py
new file mode 100644
index 0000000..8c4177e
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/domain/vistrail.py
@@ -0,0 +1,127 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from auto_gen import DBVistrail as _DBVistrail
+from auto_gen import DBAdd, DBChange, DBDelete, DBAbstraction, DBGroup, \
+ DBModule
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAdd.vtType: 'operation',
+ DBChange.vtType: 'operation',
+ DBDelete.vtType: 'operation',
+ DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ self.idScope.setBeginId('action', 1)
+ self.db_objects = {}
+
+ # keep a reference to the current logging information here
+ self.db_log_filename = None
+ self.log = None
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBVistrail.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBVistrail
+
+ cp.idScope = copy.copy(self.idScope)
+ cp.db_objects = copy.copy(self.db_objects)
+ cp.db_log_filename = self.db_log_filename
+ if self.log is not None:
+ cp.log = copy.copy(self.log)
+ else:
+ cp.log = None
+
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ new_obj = _DBVistrail.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ if hasattr(old_obj, 'db_log_filename'):
+ new_obj.db_log_filename = old_obj.db_log_filename
+ if hasattr(old_obj, 'log'):
+ new_obj.log = old_obj.log
+ return new_obj
+
+ def update_id_scope(self):
+ def getOldObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_oldObjId
+ return operation.db_objectId
+
+ def getNewObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_newObjId
+ return operation.db_objectId
+
+ for action in self.db_actions:
+ self.idScope.updateBeginId('action', action.db_id+1)
+ if action.db_session is not None:
+ self.idScope.updateBeginId('session', action.db_session + 1)
+ for operation in action.db_operations:
+ self.idScope.updateBeginId('operation', operation.db_id+1)
+ if operation.vtType == 'add' or operation.vtType == 'change':
+ # update ids of data
+ self.idScope.updateBeginId(operation.db_what,
+ getNewObjId(operation)+1)
+ if operation.db_data is None:
+ if operation.vtType == 'change':
+ operation.db_objectId = operation.db_oldObjId
+ self.db_add_object(operation.db_data)
+ for annotation in action.db_annotations:
+ self.idScope.updateBeginId('annotation', annotation.db_id+1)
+
+ def db_add_object(self, obj):
+ self.db_objects[(obj.vtType, obj.db_id)] = obj
+
+ def db_get_object(self, type, id):
+ return self.db_objects.get((type, id), None)
+
+ def db_update_object(self, obj, **kwargs):
+ # want to swap out old object with a new version
+ # need this for updating aliases...
+ # hack it using setattr...
+ real_obj = self.db_objects[(obj.vtType, obj.db_id)]
+ for (k, v) in kwargs.iteritems():
+ if hasattr(real_obj, k):
+ setattr(real_obj, k, v)
diff --git a/vistrails/db/versions/v1_0_0/domain/workflow.py b/vistrails/db/versions/v1_0_0/domain/workflow.py
new file mode 100644
index 0000000..af484e6
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/domain/workflow.py
@@ -0,0 +1,172 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from auto_gen import DBAbstraction, DBModule, DBGroup
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1,
+ {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.build_index()
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ new_obj = _DBWorkflow.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ new_obj.build_index()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
+
+ _vtTypeMap = {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType}
+
+ def build_index(self):
+ g = self._vtTypeMap.get
+ self.objects = dict(((g(o.vtType, o.vtType), o._db_id), o)
+ for (o,_,_) in self.db_children())
+
+ def add_to_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ self.objects[(obj_type, object.getPrimaryKey())] = object
+
+ def delete_from_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ del self.objects[(obj_type, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_print_objects(self):
+ for k,v in self.objects.iteritems():
+ print '%s: %s' % (k, v)
+
+ def db_has_object(self, type, id):
+ return (type, id) in self.objects
+
+ def db_get_object(self, type, id):
+ return self.objects[(type, id)]
+
+ def db_add_object(self, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if object.vtType == DBAbstraction.vtType or \
+ object.vtType == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ else:
+ obj_type = object.vtType
+ funname = 'db_add_' + obj_type
+ obj_copy = copy.copy(object)
+ getattr(parent_obj, funname)(obj_copy)
+ self.add_to_index(obj_copy)
+
+ def db_change_object(self, old_id, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+
+ self.db_delete_object(old_id, object.vtType, None, None, parent_obj)
+ self.db_add_object(object, None, None, parent_obj)
+
+ def db_delete_object(self, obj_id, obj_type, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if obj_type == DBAbstraction.vtType or obj_type == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ funname = 'db_get_' + obj_type
+ if hasattr(parent_obj, funname):
+ object = getattr(parent_obj, funname)(obj_id)
+ else:
+ attr_name = 'db_' + obj_type
+ object = getattr(parent_obj, attr_name)
+ funname = 'db_delete_' + obj_type
+ getattr(parent_obj, funname)(object)
+ self.delete_from_index(object)
diff --git a/vistrails/db/versions/v1_0_0/persistence/__init__.py b/vistrails/db/versions/v1_0_0/persistence/__init__.py
new file mode 100644
index 0000000..1144a31
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/persistence/__init__.py
@@ -0,0 +1,248 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+from vistrails.core.system import get_elementtree_library
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v1_0_0 import version as my_version
+from vistrails.db.versions.v1_0_0.domain import DBGroup, DBWorkflow, DBVistrail, DBLog, \
+ DBRegistry
+
+ElementTree = get_elementtree_library()
+
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def parse_xml_file(self, filename):
+ return ElementTree.parse(filename)
+
+ def write_xml_file(self, filename, tree):
+ def indent(elem, level=0):
+ i = "\n" + level*" "
+ if len(elem):
+ if not elem.text or not elem.text.strip():
+ elem.text = i + " "
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ for elem in elem:
+ indent(elem, level+1)
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ else:
+ if level and (not elem.tail or not elem.tail.strip()):
+ elem.tail = i
+ indent(tree.getroot())
+ tree.write(filename)
+
+ def read_xml_object(self, vtType, node):
+ return self['xml'][vtType].fromXML(node)
+
+ def write_xml_object(self, obj, node=None):
+ res_node = self['xml'][obj.vtType].toXML(obj, node)
+ return res_node
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ """open_from_xml(filename) -> DBVistrail"""
+ if tree is None:
+ tree = self.parse_xml_file(filename)
+ vistrail = self.read_xml_object(vtType, tree.getroot())
+ return vistrail
+
+ def save_to_xml(self, obj, filename, tags, version=None):
+ """save_to_xml(obj : object, filename: str, tags: dict,
+ version: str) -> None
+
+ """
+ root = self.write_xml_object(obj)
+ if version is None:
+ version = my_version
+ root.set('version', version)
+ for k, v in tags.iteritems():
+ root.set(k, v)
+ tree = ElementTree.ElementTree(root)
+ self.write_xml_file(filename, tree)
+
+ def open_from_db(self, db_connection, vtType, id=None, lock=False,
+ global_props=None):
+ all_objects = {}
+ if global_props is None:
+ global_props = {}
+ if id is not None:
+ global_props['id'] = id
+ # print global_props
+ res_objects = self['sql'][vtType].get_sql_columns(db_connection,
+ global_props,
+ lock)
+ if len(res_objects) > 1:
+ raise VistrailsDBException("More than object of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+ elif len(res_objects) <= 0:
+ raise VistrailsDBException("No objects of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+
+ all_objects.update(res_objects)
+ res = res_objects.values()[0]
+ global_props = {'entity_id': res.db_id,
+ 'entity_type': res.vtType}
+
+ for dao_type, dao in self['sql'].iteritems():
+ if (dao_type == DBVistrail.vtType or
+ dao_type == DBWorkflow.vtType or
+ dao_type == DBLog.vtType or
+ dao_type == DBRegistry.vtType):
+ continue
+
+ current_objs = dao.get_sql_columns(db_connection, global_props,
+ lock)
+ all_objects.update(current_objs)
+
+ if dao_type == DBGroup.vtType:
+ for key, obj in current_objs.iteritems():
+ new_props = {'parent_id': key[1],
+ 'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ res_obj = self.open_from_db(db_connection,
+ DBWorkflow.vtType,
+ None, lock, new_props)
+ res_dict = {}
+ res_dict[(res_obj.vtType, res_obj.db_id)] = res_obj
+ all_objects.update(res_dict)
+
+ for key, obj in all_objects.iteritems():
+ if key[0] == vtType and key[1] == id:
+ continue
+ self['sql'][obj.vtType].from_sql_fast(obj, all_objects)
+ for obj in all_objects.itervalues():
+ obj.is_dirty = False
+ obj.is_new = False
+
+ return res
+
+ def save_to_db(self, db_connection, obj, do_copy=False, global_props=None):
+ if do_copy and obj.db_id is not None:
+ obj.db_id = None
+
+ children = obj.db_children()
+ children.reverse()
+ if global_props is None:
+ global_props = {'entity_type': obj.vtType}
+ # print 'global_props:', global_props
+
+ # assumes not deleting entire thing
+ child = children[0][0]
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ global_props = {'entity_id': child.db_id,
+ 'entity_type': child.vtType}
+
+ # do deletes
+ if not do_copy:
+ for (child, _, _) in children:
+ for c in child.db_deleted_children(True):
+ self['sql'][c.vtType].delete_sql_column(db_connection,
+ c,
+ global_props)
+
+ child = children.pop(0)[0]
+ child.is_dirty = False
+ child.is_new = False
+
+ # process remaining children
+ for (child, _, _) in children:
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ # print '*** entity_type:', global_props['entity_type']
+ new_props = {'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ is_dirty = child.db_workflow.is_dirty
+ child.db_workflow.db_entity_type = DBWorkflow.vtType
+ child.db_workflow.is_dirty = is_dirty
+ self.save_to_db(db_connection, child.db_workflow, do_copy,
+ new_props)
+
+ child.is_dirty = False
+ child.is_new = False
+
+ def delete_from_db(self, db_connection, type, obj_id):
+ root_set = set([DBVistrail.vtType, DBWorkflow.vtType,
+ DBLog.vtType, DBRegistry.vtType])
+ if type not in root_set:
+ raise VistrailsDBException("Cannot delete entity of type '%s'" \
+ % type)
+
+ id_str = str(obj_id)
+ for (dao_type, dao) in self['sql'].iteritems():
+ if dao_type not in root_set:
+ db_cmd = \
+ self['sql'][type].createSQLDelete(dao.table,
+ {'entity_type': type,
+ 'entity_id': id_str})
+ self['sql'][type].executeSQL(db_connection, db_cmd, False)
+ db_cmd = self['sql'][type].createSQLDelete(self['sql'][type].table,
+ {'id': id_str})
+ self['sql'][type].executeSQL(db_connection, db_cmd, False)
+
+ def serialize(self, object):
+ root = self.write_xml_object(object)
+ return ElementTree.tostring(root)
+
+ def unserialize(self, str, obj_type):
+ def set_dirty(obj):
+ for child, _, _ in obj.db_children():
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ set_dirty(child.db_workflow)
+ child.is_dirty = True
+ child.is_new = True
+ try:
+ root = ElementTree.fromstring(str)
+ obj = self.read_xml_object(obj_type, root)
+ set_dirty(obj)
+ return obj
+ except SyntaxError, e:
+ msg = "Invalid VisTrails serialized object %s" % str
+ raise VistrailsDBException(msg)
+ return None
diff --git a/vistrails/db/versions/v1_0_0/persistence/sql/__init__.py b/vistrails/db/versions/v1_0_0/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v1_0_0/persistence/sql/auto_gen.py b/vistrails/db/versions/v1_0_0/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..34e919c
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/persistence/sql/auto_gen.py
@@ -0,0 +1,3332 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v1_0_0.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port_spec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'sigstring', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ optional = self.convertFromDB(row[3], 'int', 'int')
+ sort_key = self.convertFromDB(row[4], 'int', 'int')
+ sigstring = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ sigstring=sigstring,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_entity_id = entity_id
+ portSpec.db_entity_type = entity_type
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'module_descriptor':
+ p = all_objects[('module_descriptor', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'sigstring', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_optional') and obj.db_optional is not None:
+ columnMap['optional'] = \
+ self.convertToDB(obj.db_optional, 'int', 'int')
+ if hasattr(obj, 'db_sort_key') and obj.db_sort_key is not None:
+ columnMap['sort_key'] = \
+ self.convertToDB(obj.db_sort_key, 'int', 'int')
+ if hasattr(obj, 'db_sigstring') and obj.db_sigstring is not None:
+ columnMap['sigstring'] = \
+ self.convertToDB(obj.db_sigstring, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ module.db_parentType = parentType
+ module.db_entity_id = entity_id
+ module.db_entity_type = entity_type
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleDescriptorSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_descriptor'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'package', 'namespace', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ base_descriptor_id = self.convertFromDB(row[5], 'long', 'int')
+ package = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ module_descriptor = DBModuleDescriptor(name=name,
+ package=package,
+ namespace=namespace,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ id=id)
+ module_descriptor.db_package = package
+ module_descriptor.db_entity_id = entity_id
+ module_descriptor.db_entity_type = entity_type
+ module_descriptor.is_dirty = False
+ res[('module_descriptor', id)] = module_descriptor
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('package', obj.db_package) in all_objects:
+ p = all_objects[('package', obj.db_package)]
+ p.db_add_module_descriptor(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'package', 'namespace', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_base_descriptor_id') and obj.db_base_descriptor_id is not None:
+ columnMap['base_descriptor_id'] = \
+ self.convertToDB(obj.db_base_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_package, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'tag'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[2], 'long', 'int')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_vistrail = vistrail
+ tag.db_entity_id = entity_id
+ tag.db_entity_type = entity_type
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ signature = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature,
+ id=id)
+ port.db_parentType = parentType
+ port.db_entity_id = entity_id
+ port.db_entity_type = entity_type
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_signature') and obj.db_signature is not None:
+ columnMap['signature'] = \
+ self.convertToDB(obj.db_signature, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ group = DBGroup(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ group.db_parentType = parentType
+ group.db_entity_id = entity_id
+ group.db_entity_type = entity_type
+ group.db_parent = parent
+ group.is_dirty = False
+ res[('group', id)] = group
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_workflow is not None:
+ child = obj.db_workflow
+ child.db_group = obj.db_id
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'log_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ log = DBLog(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ log.is_dirty = False
+ res[('log', id)] = log
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_workflow_execs:
+ child.db_log = obj.db_id
+ for child in obj.db_machines:
+ child.db_log = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'machine'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.db_entity_id = entity_id
+ machine.db_entity_type = entity_type
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'add_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_entity_id = entity_id
+ add.db_entity_type = entity_type
+ add.is_dirty = False
+ res[('add', id)] = add
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'other'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_entity_id = entity_id
+ other.db_entity_type = entity_type
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'location'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_entity_id = entity_id
+ location.db_entity_type = entity_type
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'parameter'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_entity_id = entity_id
+ parameter.db_entity_type = entity_type
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPluginDataSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'plugin_data'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ data = self.convertFromDB(row[1], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ plugin_data = DBPluginData(data=data,
+ id=id)
+ plugin_data.db_parentType = parentType
+ plugin_data.db_entity_id = entity_id
+ plugin_data.db_entity_type = entity_type
+ plugin_data.db_parent = parent
+ plugin_data.is_dirty = False
+ res[('plugin_data', id)] = plugin_data
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_plugin_data(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_data') and obj.db_data is not None:
+ columnMap['data'] = \
+ self.convertToDB(obj.db_data, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'function'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_entity_id = entity_id
+ function.db_entity_type = entity_type
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'abstraction'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ internal_version = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[7], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[8], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[9], 'long', 'int')
+ entity_type = self.convertFromDB(row[10], 'str', 'char(16)')
+ parent = self.convertFromDB(row[11], 'long', 'long')
+
+ abstraction = DBAbstraction(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ tag=tag,
+ id=id)
+ abstraction.db_parentType = parentType
+ abstraction.db_entity_id = entity_id
+ abstraction.db_entity_type = entity_type
+ abstraction.db_parent = parent
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_internal_version') and obj.db_internal_version is not None:
+ columnMap['internal_version'] = \
+ self.convertToDB(obj.db_internal_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_id = self.convertFromDB(row[1], 'long', 'int')
+ entity_type = self.convertFromDB(row[2], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'char(16)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[6], 'long', 'int')
+ group = self.convertFromDB(row[7], 'long', 'int')
+
+ workflow = DBWorkflow(entity_type=entity_type,
+ name=name,
+ version=version,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ workflow.db_entity_id = entity_id
+ workflow.db_group = group
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('group', obj.db_group) in all_objects:
+ p = all_objects[('group', obj.db_group)]
+ p.db_add_workflow(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ if hasattr(obj, 'db_group') and obj.db_group is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_group, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_connections:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_plugin_datas:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_modules:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBRegistrySQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'registry'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ root_descriptor_id = self.convertFromDB(row[3], 'long', 'int')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+
+ registry = DBRegistry(entity_type=entity_type,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ registry.is_dirty = False
+ res[('registry', id)] = registry
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_root_descriptor_id') and obj.db_root_descriptor_id is not None:
+ columnMap['root_descriptor_id'] = \
+ self.convertToDB(obj.db_root_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_packages:
+ child.db_registry = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'annotation'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_entity_id = entity_id
+ annotation.db_entity_type = entity_type
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'change_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_entity_id = entity_id
+ change.db_entity_type = entity_type
+ change.is_dirty = False
+ res[('change', id)] = change
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ group_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ group_type = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[7], 'int', 'int')
+ error = self.convertFromDB(row[8], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[9], 'long', 'int')
+ parentType = self.convertFromDB(row[10], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[11], 'long', 'int')
+ entity_type = self.convertFromDB(row[12], 'str', 'char(16)')
+ parent = self.convertFromDB(row[13], 'long', 'long')
+
+ group_exec = DBGroupExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ group_exec.db_parentType = parentType
+ group_exec.db_entity_id = entity_id
+ group_exec.db_entity_type = entity_type
+ group_exec.db_parent = parent
+ group_exec.is_dirty = False
+ res[('group_exec', id)] = group_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_group_name') and obj.db_group_name is not None:
+ columnMap['group_name'] = \
+ self.convertToDB(obj.db_group_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_group_type') and obj.db_group_type is not None:
+ columnMap['group_type'] = \
+ self.convertToDB(obj.db_group_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPackageSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'package'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ identifier = self.convertFromDB(row[2], 'str', 'varchar(1023)')
+ codepath = self.convertFromDB(row[3], 'str', 'varchar(1023)')
+ load_configuration = self.convertFromDB(row[4], 'int', 'int')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ description = self.convertFromDB(row[6], 'str', 'varchar(1023)')
+ registry = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ package = DBPackage(name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ id=id)
+ package.db_registry = registry
+ package.db_entity_id = entity_id
+ package.db_entity_type = entity_type
+ package.is_dirty = False
+ res[('package', id)] = package
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('registry', obj.db_registry) in all_objects:
+ p = all_objects[('registry', obj.db_registry)]
+ p.db_add_package(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_identifier') and obj.db_identifier is not None:
+ columnMap['identifier'] = \
+ self.convertToDB(obj.db_identifier, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_codepath') and obj.db_codepath is not None:
+ columnMap['codepath'] = \
+ self.convertToDB(obj.db_codepath, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_load_configuration') and obj.db_load_configuration is not None:
+ columnMap['load_configuration'] = \
+ self.convertToDB(obj.db_load_configuration, 'int', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_description') and obj.db_description is not None:
+ columnMap['description'] = \
+ self.convertToDB(obj.db_description, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_registry') and obj.db_registry is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_registry, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_module_descriptors:
+ child.db_package = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ vt_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[5], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[6], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[7], 'long', 'int')
+ parent_type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[9], 'long', 'int')
+ completed = self.convertFromDB(row[10], 'int', 'int')
+ name = self.convertFromDB(row[11], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[12], 'long', 'int')
+ entity_id = self.convertFromDB(row[13], 'long', 'int')
+ entity_type = self.convertFromDB(row[14], 'str', 'char(16)')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_entity_id = entity_id
+ workflow_exec.db_entity_type = entity_type
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLoopExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'loop_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ iteration = self.convertFromDB(row[3], 'int', 'int')
+ completed = self.convertFromDB(row[4], 'int', 'int')
+ error = self.convertFromDB(row[5], 'str', 'varchar(1023)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ loop_exec = DBLoopExec(ts_start=ts_start,
+ ts_end=ts_end,
+ iteration=iteration,
+ completed=completed,
+ error=error,
+ id=id)
+ loop_exec.db_parentType = parentType
+ loop_exec.db_entity_id = entity_id
+ loop_exec.db_entity_type = entity_type
+ loop_exec.db_parent = parent
+ loop_exec.is_dirty = False
+ res[('loop_exec', id)] = loop_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_loop_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_iteration') and obj.db_iteration is not None:
+ columnMap['iteration'] = \
+ self.convertToDB(obj.db_iteration, 'int', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'connection_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[2], 'long', 'int')
+ entity_type = self.convertFromDB(row[3], 'str', 'char(16)')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_entity_id = entity_id
+ connection.db_entity_type = entity_type
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'action'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ prune = self.convertFromDB(row[5], 'int', 'int')
+ vistrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ id=id)
+ action.db_vistrail = vistrail
+ action.db_entity_id = entity_id
+ action.db_entity_type = entity_type
+ action.is_dirty = False
+ res[('action', id)] = action
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_prune') and obj.db_prune is not None:
+ columnMap['prune'] = \
+ self.convertToDB(obj.db_prune, 'int', 'int')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'delete_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_entity_id = entity_id
+ delete.db_entity_type = entity_type
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'vistrail'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_actions:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_tags:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ module_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[6], 'int', 'int')
+ error = self.convertFromDB(row[7], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[8], 'long', 'int')
+ parentType = self.convertFromDB(row[9], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[10], 'long', 'int')
+ entity_type = self.convertFromDB(row[11], 'str', 'char(16)')
+ parent = self.convertFromDB(row[12], 'long', 'long')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ module_exec.db_parentType = parentType
+ module_exec.db_entity_id = entity_id
+ module_exec.db_entity_type = entity_type
+ module_exec.db_parent = parent
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_loop_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'module_descriptor' not in self:
+ self['module_descriptor'] = DBModuleDescriptorSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'registry' not in self:
+ self['registry'] = DBRegistrySQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'group_exec' not in self:
+ self['group_exec'] = DBGroupExecSQLDAOBase(self)
+ if 'package' not in self:
+ self['package'] = DBPackageSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'loop_exec' not in self:
+ self['loop_exec'] = DBLoopExecSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v1_0_0/persistence/sql/sql_dao.py b/vistrails/db/versions/v1_0_0/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..ad01dc5
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/persistence/sql/sql_dao.py
@@ -0,0 +1,183 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+from vistrails.db import VistrailsDBException
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ # return "'" + str(value).replace("'", "''") + "'"
+ return str(value)
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ return str(value)
+ elif type == 'int':
+ return str(value)
+ elif type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+
+ return None
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None,
+ forUpdate=False):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % \
+ (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ if forUpdate:
+ dbCommand += " FOR UPDATE"
+ dbCommand += ";"
+ return (dbCommand, tuple(values))
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ # valueStr = '%s, '.join(values)
+ valueStr = ''
+ if len(values) > 1:
+ valueStr = '%s,' * (len(values) - 1) + '%s'
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s);""" % \
+ (table, columnStr, valueStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ values = []
+ for column, value in columnMap.iteritems():
+# if value is None:
+# value = 'NULL'
+ setStr += '%s%s = %%s' % (comma, column)
+ comma = ', '
+ values.append(value)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """UPDATE %s SET %s WHERE %s;""" % \
+ (table, setStr, whereStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLDelete(self, table, whereMap):
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """DELETE FROM %s WHERE %s;""" % \
+ (table, whereStr)
+ return (dbCommand, tuple(values))
+
+ def executeSQL(self, db, cmd_tuple, isFetch):
+ dbCommand, values = cmd_tuple
+ # print 'db: %s' % dbCommand
+ # print 'values:', values
+ data = None
+ cursor = db.cursor()
+ try:
+ cursor.execute(dbCommand, values)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ except Exception, e:
+ raise VistrailsDBException('Command "%s" with values "%s" '
+ 'failed: %s' % (dbCommand, values, e))
+ finally:
+ cursor.close()
+ return data
+
+ def start_transaction(self, db):
+ db.begin()
+
+ def commit_transaction(self, db):
+ db.commit()
+
+ def rollback_transaction(self, db):
+ db.rollback()
diff --git a/vistrails/db/versions/v1_0_0/persistence/xml/__init__.py b/vistrails/db/versions/v1_0_0/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v1_0_0/persistence/xml/auto_gen.py b/vistrails/db/versions/v1_0_0/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..d7fbe3c
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/persistence/xml/auto_gen.py
@@ -0,0 +1,3833 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from vistrails.core.system import get_elementtree_library
+
+from xml_dao import XMLDAO
+from vistrails.db.versions.v1_0_0.domain import *
+
+ElementTree = get_elementtree_library()
+
+
+class DBOpmProcessIdEffectXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'effect':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmProcessIdEffect(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_id_effect, node=None):
+ if node is None:
+ node = ElementTree.Element('effect')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process_id_effect.db_id, 'str'))
+
+ return node
+
+class DBOpmWasGeneratedByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasGeneratedBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_artifact_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_process_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasGeneratedBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_generated_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasGeneratedBy')
+
+ # set elements
+ effect = opm_was_generated_by.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_artifact_id_effect').toXML(effect, childNode)
+ role = opm_was_generated_by.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_generated_by.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_process_id_cause').toXML(cause, childNode)
+ accounts = opm_was_generated_by.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_generated_by.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBOpmAccountsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'accounts':
+ return None
+
+ accounts = []
+ opm_overlapss = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'account':
+ _data = self.getDao('opm_account').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'overlaps':
+ _data = self.getDao('opm_overlaps').fromXML(child)
+ opm_overlapss.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAccounts(accounts=accounts,
+ opm_overlapss=opm_overlapss)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_accounts, node=None):
+ if node is None:
+ node = ElementTree.Element('accounts')
+
+ # set elements
+ accounts = opm_accounts.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account').toXML(account, childNode)
+ opm_overlapss = opm_accounts.db_opm_overlapss
+ for opm_overlaps in opm_overlapss:
+ childNode = ElementTree.SubElement(node, 'overlaps')
+ self.getDao('opm_overlaps').toXML(opm_overlaps, childNode)
+
+ return node
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'portSpec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('optional', None)
+ optional = self.convertFromStr(data, 'int')
+ data = node.get('sortKey', None)
+ sort_key = self.convertFromStr(data, 'int')
+ data = node.get('sigstring', None)
+ sigstring = self.convertFromStr(data, 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ sigstring=sigstring)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, node=None):
+ if node is None:
+ node = ElementTree.Element('portSpec')
+
+ # set attributes
+ node.set('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.set('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.set('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.set('optional',self.convertToStr(portSpec.db_optional, 'int'))
+ node.set('sortKey',self.convertToStr(portSpec.db_sort_key, 'int'))
+ node.set('sigstring',self.convertToStr(portSpec.db_sigstring, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'module':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, node=None):
+ if node is None:
+ node = ElementTree.Element('module')
+
+ # set attributes
+ node.set('id',self.convertToStr(module.db_id, 'long'))
+ node.set('cache',self.convertToStr(module.db_cache, 'int'))
+ node.set('name',self.convertToStr(module.db_name, 'str'))
+ node.set('namespace',self.convertToStr(module.db_namespace, 'str'))
+ node.set('package',self.convertToStr(module.db_package, 'str'))
+ node.set('version',self.convertToStr(module.db_version, 'str'))
+ node.set('tag',self.convertToStr(module.db_tag, 'str'))
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = module.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBModuleDescriptorXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'moduleDescriptor':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('baseDescriptorId', None)
+ base_descriptor_id = self.convertFromStr(data, 'long')
+
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleDescriptor(id=id,
+ name=name,
+ package=package,
+ namespace=namespace,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_descriptor, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleDescriptor')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_descriptor.db_id, 'long'))
+ node.set('name',self.convertToStr(module_descriptor.db_name, 'str'))
+ node.set('package',self.convertToStr(module_descriptor.db_package, 'str'))
+ node.set('namespace',self.convertToStr(module_descriptor.db_namespace, 'str'))
+ node.set('version',self.convertToStr(module_descriptor.db_version, 'str'))
+ node.set('baseDescriptorId',self.convertToStr(module_descriptor.db_base_descriptor_id, 'long'))
+
+ # set elements
+ portSpecs = module_descriptor.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'tag':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, node=None):
+ if node is None:
+ node = ElementTree.Element('tag')
+
+ # set attributes
+ node.set('id',self.convertToStr(tag.db_id, 'long'))
+ node.set('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBOpmRoleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'role':
+ return None
+
+ # read attributes
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBOpmRole(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_role, node=None):
+ if node is None:
+ node = ElementTree.Element('role')
+
+ # set attributes
+ node.set('value',self.convertToStr(opm_role.db_value, 'str'))
+
+ return node
+
+class DBOpmProcessesXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'processes':
+ return None
+
+ processs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'process':
+ _data = self.getDao('opm_process').fromXML(child)
+ processs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcesses(processs=processs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_processes, node=None):
+ if node is None:
+ node = ElementTree.Element('processes')
+
+ # set elements
+ processs = opm_processes.db_processs
+ for process in processs:
+ childNode = ElementTree.SubElement(node, 'process')
+ self.getDao('opm_process').toXML(process, childNode)
+
+ return node
+
+class DBOpmAccountIdXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'account':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmAccountId(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_account_id, node=None):
+ if node is None:
+ node = ElementTree.Element('account')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_account_id.db_id, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'port':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('moduleId', None)
+ moduleId = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ moduleName = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('signature', None)
+ signature = self.convertFromStr(data, 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, node=None):
+ if node is None:
+ node = ElementTree.Element('port')
+
+ # set attributes
+ node.set('id',self.convertToStr(port.db_id, 'long'))
+ node.set('type',self.convertToStr(port.db_type, 'str'))
+ node.set('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.set('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.set('name',self.convertToStr(port.db_name, 'str'))
+ node.set('signature',self.convertToStr(port.db_signature, 'str'))
+
+ return node
+
+class DBOpmArtifactXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'artifact':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.getDao('opm_artifact_value').fromXML(child)
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifact(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact, node=None):
+ if node is None:
+ node = ElementTree.Element('artifact')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact.db_id, 'str'))
+
+ # set elements
+ value = opm_artifact.db_value
+ if value is not None:
+ childNode = ElementTree.SubElement(node, 'value')
+ self.getDao('opm_artifact_value').toXML(value, childNode)
+ accounts = opm_artifact.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBGroupXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'group':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ workflow = None
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'workflow':
+ _data = self.getDao('workflow').fromXML(child)
+ workflow = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroup(id=id,
+ workflow=workflow,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group, node=None):
+ if node is None:
+ node = ElementTree.Element('group')
+
+ # set attributes
+ node.set('id',self.convertToStr(group.db_id, 'long'))
+ node.set('cache',self.convertToStr(group.db_cache, 'int'))
+ node.set('name',self.convertToStr(group.db_name, 'str'))
+ node.set('namespace',self.convertToStr(group.db_namespace, 'str'))
+ node.set('package',self.convertToStr(group.db_package, 'str'))
+ node.set('version',self.convertToStr(group.db_version, 'str'))
+ node.set('tag',self.convertToStr(group.db_tag, 'str'))
+
+ # set elements
+ workflow = group.db_workflow
+ if workflow is not None:
+ childNode = ElementTree.SubElement(node, 'workflow')
+ self.getDao('workflow').toXML(workflow, childNode)
+ location = group.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = group.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = group.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'log':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ workflow_execs = []
+ machines = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'workflowExec':
+ _data = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs.append(_data)
+ elif child_tag == 'machine':
+ _data = self.getDao('machine').fromXML(child)
+ machines.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLog(id=id,
+ version=version,
+ name=name,
+ workflow_execs=workflow_execs,
+ machines=machines,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, node=None):
+ if node is None:
+ node = ElementTree.Element('log')
+
+ # set attributes
+ node.set('id',self.convertToStr(log.db_id, 'long'))
+ node.set('version',self.convertToStr(log.db_version, 'str'))
+ node.set('name',self.convertToStr(log.db_name, 'str'))
+ node.set('vistrail_id',self.convertToStr(log.db_vistrail_id, 'long'))
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs:
+ childNode = ElementTree.SubElement(node, 'workflowExec')
+ self.getDao('workflow_exec').toXML(workflow_exec, childNode)
+ machines = log.db_machines
+ for machine in machines:
+ childNode = ElementTree.SubElement(node, 'machine')
+ self.getDao('machine').toXML(machine, childNode)
+
+ return node
+
+class DBOpmAgentsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agents':
+ return None
+
+ agents = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'agent':
+ _data = self.getDao('opm_agent').fromXML(child)
+ agents.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAgents(agents=agents)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agents, node=None):
+ if node is None:
+ node = ElementTree.Element('agents')
+
+ # set elements
+ agents = opm_agents.db_agents
+ for agent in agents:
+ childNode = ElementTree.SubElement(node, 'agent')
+ self.getDao('opm_agent').toXML(agent, childNode)
+
+ return node
+
+class DBOpmProcessIdCauseXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'cause':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmProcessIdCause(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_id_cause, node=None):
+ if node is None:
+ node = ElementTree.Element('cause')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process_id_cause.db_id, 'str'))
+
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'machine':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('os', None)
+ os = self.convertFromStr(data, 'str')
+ data = node.get('architecture', None)
+ architecture = self.convertFromStr(data, 'str')
+ data = node.get('processor', None)
+ processor = self.convertFromStr(data, 'str')
+ data = node.get('ram', None)
+ ram = self.convertFromStr(data, 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, node=None):
+ if node is None:
+ node = ElementTree.Element('machine')
+
+ # set attributes
+ node.set('id',self.convertToStr(machine.db_id, 'long'))
+ node.set('name',self.convertToStr(machine.db_name, 'str'))
+ node.set('os',self.convertToStr(machine.db_os, 'str'))
+ node.set('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.set('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.set('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'add':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAdd(data=data,
+ id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, node=None):
+ if node is None:
+ node = ElementTree.Element('add')
+
+ # set attributes
+ node.set('id',self.convertToStr(add.db_id, 'long'))
+ node.set('what',self.convertToStr(add.db_what, 'str'))
+ node.set('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # set elements
+ data = add.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'other':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, node=None):
+ if node is None:
+ node = ElementTree.Element('other')
+
+ # set attributes
+ node.set('id',self.convertToStr(other.db_id, 'long'))
+ node.set('key',self.convertToStr(other.db_key, 'str'))
+
+ # set elements
+ value = other.db_value
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'location':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('x', None)
+ x = self.convertFromStr(data, 'float')
+ data = node.get('y', None)
+ y = self.convertFromStr(data, 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, node=None):
+ if node is None:
+ node = ElementTree.Element('location')
+
+ # set attributes
+ node.set('id',self.convertToStr(location.db_id, 'long'))
+ node.set('x',self.convertToStr(location.db_x, 'float'))
+ node.set('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBOpmOverlapsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'overlaps':
+ return None
+
+ opm_account_ids = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ opm_account_ids.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmOverlaps(opm_account_ids=opm_account_ids)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_overlaps, node=None):
+ if node is None:
+ node = ElementTree.Element('overlaps')
+
+ # set elements
+ opm_account_ids = opm_overlaps.db_opm_account_ids
+ for opm_account_id in opm_account_ids:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(opm_account_id, childNode)
+
+ return node
+
+class DBOpmArtifactsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'artifacts':
+ return None
+
+ artifacts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'artifact':
+ _data = self.getDao('opm_artifact').fromXML(child)
+ artifacts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifacts(artifacts=artifacts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifacts, node=None):
+ if node is None:
+ node = ElementTree.Element('artifacts')
+
+ # set elements
+ artifacts = opm_artifacts.db_artifacts
+ for artifact in artifacts:
+ childNode = ElementTree.SubElement(node, 'artifact')
+ self.getDao('opm_artifact').toXML(artifact, childNode)
+
+ return node
+
+class DBOpmDependenciesXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'causalDependencies':
+ return None
+
+ dependencys = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'used':
+ _data = self.getDao('opm_used').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasGeneratedBy':
+ _data = self.getDao('opm_was_generated_by').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasTriggeredBy':
+ _data = self.getDao('opm_was_triggered_by').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasDerivedFrom':
+ _data = self.getDao('opm_was_derived_from').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasControlledBy':
+ _data = self.getDao('opm_was_controlled_by').fromXML(child)
+ dependencys.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmDependencies(dependencys=dependencys)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_dependencies, node=None):
+ if node is None:
+ node = ElementTree.Element('causalDependencies')
+
+ # set elements
+ dependencys = opm_dependencies.db_dependencys
+ for dependency in dependencys:
+ if dependency.vtType == 'opm_used':
+ childNode = ElementTree.SubElement(node, 'used')
+ self.getDao('opm_used').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_generated_by':
+ childNode = ElementTree.SubElement(node, 'wasGeneratedBy')
+ self.getDao('opm_was_generated_by').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_triggered_by':
+ childNode = ElementTree.SubElement(node, 'wasTriggeredBy')
+ self.getDao('opm_was_triggered_by').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_derived_from':
+ childNode = ElementTree.SubElement(node, 'wasDerivedFrom')
+ self.getDao('opm_was_derived_from').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_controlled_by':
+ childNode = ElementTree.SubElement(node, 'wasControlledBy')
+ self.getDao('opm_was_controlled_by').toXML(dependency, childNode)
+
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'parameter':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('val', None)
+ val = self.convertFromStr(data, 'str')
+ data = node.get('alias', None)
+ alias = self.convertFromStr(data, 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, node=None):
+ if node is None:
+ node = ElementTree.Element('parameter')
+
+ # set attributes
+ node.set('id',self.convertToStr(parameter.db_id, 'long'))
+ node.set('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.set('name',self.convertToStr(parameter.db_name, 'str'))
+ node.set('type',self.convertToStr(parameter.db_type, 'str'))
+ node.set('val',self.convertToStr(parameter.db_val, 'str'))
+ node.set('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBOpmUsedXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'used':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_artifact_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmUsed(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_used, node=None):
+ if node is None:
+ node = ElementTree.Element('used')
+
+ # set elements
+ effect = opm_used.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_used.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_used.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_artifact_id_cause').toXML(cause, childNode)
+ accounts = opm_used.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_used.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBPluginDataXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'plugin_data':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('data', None)
+ data = self.convertFromStr(data, 'str')
+
+ obj = DBPluginData(id=id,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, plugin_data, node=None):
+ if node is None:
+ node = ElementTree.Element('plugin_data')
+
+ # set attributes
+ node.set('id',self.convertToStr(plugin_data.db_id, 'long'))
+ node.set('data',self.convertToStr(plugin_data.db_data, 'str'))
+
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'function':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ parameters = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ parameters.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, node=None):
+ if node is None:
+ node = ElementTree.Element('function')
+
+ # set attributes
+ node.set('id',self.convertToStr(function.db_id, 'long'))
+ node.set('pos',self.convertToStr(function.db_pos, 'long'))
+ node.set('name',self.convertToStr(function.db_name, 'str'))
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(parameter, childNode)
+
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'abstraction':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('internalVersion', None)
+ internal_version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstraction(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, node=None):
+ if node is None:
+ node = ElementTree.Element('abstraction')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.set('cache',self.convertToStr(abstraction.db_cache, 'int'))
+ node.set('name',self.convertToStr(abstraction.db_name, 'str'))
+ node.set('namespace',self.convertToStr(abstraction.db_namespace, 'str'))
+ node.set('package',self.convertToStr(abstraction.db_package, 'str'))
+ node.set('version',self.convertToStr(abstraction.db_version, 'str'))
+ node.set('internalVersion',self.convertToStr(abstraction.db_internal_version, 'str'))
+ node.set('tag',self.convertToStr(abstraction.db_tag, 'str'))
+
+ # set elements
+ location = abstraction.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = abstraction.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = abstraction.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'workflow':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ connections = []
+ annotations = []
+ plugin_datas = []
+ others = []
+ modules = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ connections.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ plugin_datas.append(_data)
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ others.append(_data)
+ elif child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ modules.append(_data)
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ modules.append(_data)
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ modules.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflow(modules=modules,
+ id=id,
+ name=name,
+ version=version,
+ connections=connections,
+ annotations=annotations,
+ plugin_datas=plugin_datas,
+ others=others,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, node=None):
+ if node is None:
+ node = ElementTree.Element('workflow')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow.db_id, 'long'))
+ node.set('name',self.convertToStr(workflow.db_name, 'str'))
+ node.set('version',self.convertToStr(workflow.db_version, 'str'))
+ node.set('vistrail_id',self.convertToStr(workflow.db_vistrail_id, 'long'))
+
+ # set elements
+ connections = workflow.db_connections
+ for connection in connections:
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(connection, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ plugin_datas = workflow.db_plugin_datas
+ for plugin_data in plugin_datas:
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(plugin_data, childNode)
+ others = workflow.db_others
+ for other in others:
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(other, childNode)
+ modules = workflow.db_modules
+ for module in modules:
+ if module.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(module, childNode)
+ elif module.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(module, childNode)
+ elif module.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(module, childNode)
+
+ return node
+
+class DBOpmArtifactIdCauseXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'cause':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmArtifactIdCause(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_id_cause, node=None):
+ if node is None:
+ node = ElementTree.Element('cause')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact_id_cause.db_id, 'str'))
+
+ return node
+
+class DBOpmArtifactValueXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'value':
+ return None
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ value = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifactValue(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_value, node=None):
+ if node is None:
+ node = ElementTree.Element('value')
+
+ # set elements
+ value = opm_artifact_value.db_value
+ if value is not None:
+ if value.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(value, childNode)
+ elif value.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(value, childNode)
+
+ return node
+
+class DBOpmArtifactIdEffectXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'effect':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmArtifactIdEffect(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_id_effect, node=None):
+ if node is None:
+ node = ElementTree.Element('effect')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact_id_effect.db_id, 'str'))
+
+ return node
+
+class DBOpmGraphXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'opmGraph':
+ return None
+
+ accounts = None
+ processes = None
+ artifacts = None
+ agents = None
+ dependencies = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'accounts':
+ _data = self.getDao('opm_accounts').fromXML(child)
+ accounts = _data
+ elif child_tag == 'processes':
+ _data = self.getDao('opm_processes').fromXML(child)
+ processes = _data
+ elif child_tag == 'artifacts':
+ _data = self.getDao('opm_artifacts').fromXML(child)
+ artifacts = _data
+ elif child_tag == 'agents':
+ _data = self.getDao('opm_agents').fromXML(child)
+ agents = _data
+ elif child_tag == 'causalDependencies':
+ _data = self.getDao('opm_dependencies').fromXML(child)
+ dependencies = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmGraph(accounts=accounts,
+ processes=processes,
+ artifacts=artifacts,
+ agents=agents,
+ dependencies=dependencies)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_graph, node=None):
+ if node is None:
+ node = ElementTree.Element('opmGraph')
+
+ # set elements
+ accounts = opm_graph.db_accounts
+ if accounts is not None:
+ childNode = ElementTree.SubElement(node, 'accounts')
+ self.getDao('opm_accounts').toXML(accounts, childNode)
+ processes = opm_graph.db_processes
+ if processes is not None:
+ childNode = ElementTree.SubElement(node, 'processes')
+ self.getDao('opm_processes').toXML(processes, childNode)
+ artifacts = opm_graph.db_artifacts
+ if artifacts is not None:
+ childNode = ElementTree.SubElement(node, 'artifacts')
+ self.getDao('opm_artifacts').toXML(artifacts, childNode)
+ agents = opm_graph.db_agents
+ if agents is not None:
+ childNode = ElementTree.SubElement(node, 'agents')
+ self.getDao('opm_agents').toXML(agents, childNode)
+ dependencies = opm_graph.db_dependencies
+ if dependencies is not None:
+ childNode = ElementTree.SubElement(node, 'causalDependencies')
+ self.getDao('opm_dependencies').toXML(dependencies, childNode)
+
+ return node
+
+class DBRegistryXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'registry':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('rootDescriptorId', None)
+ root_descriptor_id = self.convertFromStr(data, 'long')
+
+ packages = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'package':
+ _data = self.getDao('package').fromXML(child)
+ packages.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBRegistry(id=id,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ packages=packages)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, registry, node=None):
+ if node is None:
+ node = ElementTree.Element('registry')
+
+ # set attributes
+ node.set('id',self.convertToStr(registry.db_id, 'long'))
+ node.set('version',self.convertToStr(registry.db_version, 'str'))
+ node.set('rootDescriptorId',self.convertToStr(registry.db_root_descriptor_id, 'long'))
+
+ # set elements
+ packages = registry.db_packages
+ for package in packages:
+ childNode = ElementTree.SubElement(node, 'package')
+ self.getDao('package').toXML(package, childNode)
+
+ return node
+
+class DBOpmAccountXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'account':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAccount(id=id,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_account, node=None):
+ if node is None:
+ node = ElementTree.Element('account')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_account.db_id, 'str'))
+
+ # set elements
+ value = opm_account.db_value
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'annotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, node=None):
+ if node is None:
+ node = ElementTree.Element('annotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(annotation.db_id, 'long'))
+ node.set('key',self.convertToStr(annotation.db_key, 'str'))
+ node.set('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'change':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('oldObjId', None)
+ oldObjId = self.convertFromStr(data, 'long')
+ data = node.get('newObjId', None)
+ newObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBChange(data=data,
+ id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, node=None):
+ if node is None:
+ node = ElementTree.Element('change')
+
+ # set attributes
+ node.set('id',self.convertToStr(change.db_id, 'long'))
+ node.set('what',self.convertToStr(change.db_what, 'str'))
+ node.set('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.set('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.set('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # set elements
+ data = change.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBOpmWasDerivedFromXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasDerivedFrom':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_artifact_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_artifact_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasDerivedFrom(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_derived_from, node=None):
+ if node is None:
+ node = ElementTree.Element('wasDerivedFrom')
+
+ # set elements
+ effect = opm_was_derived_from.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_artifact_id_effect').toXML(effect, childNode)
+ role = opm_was_derived_from.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_derived_from.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_artifact_id_cause').toXML(cause, childNode)
+ accounts = opm_was_derived_from.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_derived_from.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBOpmWasControlledByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasControlledBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ starts = []
+ ends = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'agent':
+ _data = self.getDao('opm_agent_id').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ starts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ ends.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasControlledBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ starts=starts,
+ ends=ends)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_controlled_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasControlledBy')
+
+ # set elements
+ effect = opm_was_controlled_by.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_was_controlled_by.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_controlled_by.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'agent')
+ self.getDao('opm_agent_id').toXML(cause, childNode)
+ accounts = opm_was_controlled_by.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ starts = opm_was_controlled_by.db_starts
+ for start in starts:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(start, childNode)
+ ends = opm_was_controlled_by.db_ends
+ for end in ends:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(end, childNode)
+
+ return node
+
+class DBOpmAgentIdXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agent':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmAgentId(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agent_id, node=None):
+ if node is None:
+ node = ElementTree.Element('agent')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_agent_id.db_id, 'str'))
+
+ return node
+
+class DBGroupExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'groupExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('groupName', None)
+ group_name = self.convertFromStr(data, 'str')
+ data = node.get('groupType', None)
+ group_type = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroupExec(item_execs=item_execs,
+ id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('groupExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(group_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(group_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(group_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(group_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(group_exec.db_module_id, 'long'))
+ node.set('groupName',self.convertToStr(group_exec.db_group_name, 'str'))
+ node.set('groupType',self.convertToStr(group_exec.db_group_type, 'str'))
+ node.set('completed',self.convertToStr(group_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(group_exec.db_error, 'str'))
+ node.set('machine_id',self.convertToStr(group_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = group_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ item_execs = group_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBOpmTimeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'time':
+ return None
+
+ # read attributes
+ data = node.get('noLaterThan', None)
+ no_later_than = self.convertFromStr(data, 'datetime')
+ data = node.get('noEarlierThan', None)
+ no_earlier_than = self.convertFromStr(data, 'datetime')
+ data = node.get('clockId', None)
+ clock_id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmTime(no_later_than=no_later_than,
+ no_earlier_than=no_earlier_than,
+ clock_id=clock_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_time, node=None):
+ if node is None:
+ node = ElementTree.Element('time')
+
+ # set attributes
+ node.set('noLaterThan',self.convertToStr(opm_time.db_no_later_than, 'datetime'))
+ node.set('noEarlierThan',self.convertToStr(opm_time.db_no_earlier_than, 'datetime'))
+ node.set('clockId',self.convertToStr(opm_time.db_clock_id, 'str'))
+
+ return node
+
+class DBPackageXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'package':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('identifier', None)
+ identifier = self.convertFromStr(data, 'str')
+ data = node.get('codepath', None)
+ codepath = self.convertFromStr(data, 'str')
+ data = node.get('loadConfiguration', None)
+ load_configuration = self.convertFromStr(data, 'int')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('description', None)
+ description = self.convertFromStr(data, 'str')
+
+ module_descriptors = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleDescriptor':
+ _data = self.getDao('module_descriptor').fromXML(child)
+ module_descriptors.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBPackage(id=id,
+ name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ module_descriptors=module_descriptors)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, package, node=None):
+ if node is None:
+ node = ElementTree.Element('package')
+
+ # set attributes
+ node.set('id',self.convertToStr(package.db_id, 'long'))
+ node.set('name',self.convertToStr(package.db_name, 'str'))
+ node.set('identifier',self.convertToStr(package.db_identifier, 'str'))
+ node.set('codepath',self.convertToStr(package.db_codepath, 'str'))
+ node.set('loadConfiguration',self.convertToStr(package.db_load_configuration, 'int'))
+ node.set('version',self.convertToStr(package.db_version, 'str'))
+ node.set('description',self.convertToStr(package.db_description, 'str'))
+
+ # set elements
+ module_descriptors = package.db_module_descriptors
+ for module_descriptor in module_descriptors:
+ childNode = ElementTree.SubElement(node, 'moduleDescriptor')
+ self.getDao('module_descriptor').toXML(module_descriptor, childNode)
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'workflowExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('ip', None)
+ ip = self.convertFromStr(data, 'str')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('vtVersion', None)
+ vt_version = self.convertFromStr(data, 'str')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('parentId', None)
+ parent_id = self.convertFromStr(data, 'long')
+ data = node.get('parentType', None)
+ parent_type = self.convertFromStr(data, 'str')
+ data = node.get('parentVersion', None)
+ parent_version = self.convertFromStr(data, 'long')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflowExec(item_execs=item_execs,
+ id=id,
+ user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('workflowExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.set('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.set('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.set('session',self.convertToStr(workflow_exec.db_session, 'long'))
+ node.set('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.set('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.set('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.set('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.set('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.set('completed',self.convertToStr(workflow_exec.db_completed, 'int'))
+ node.set('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # set elements
+ item_execs = workflow_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBLoopExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'loopExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('iteration', None)
+ iteration = self.convertFromStr(data, 'int')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLoopExec(item_execs=item_execs,
+ id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ iteration=iteration,
+ completed=completed,
+ error=error)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, loop_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('loopExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(loop_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(loop_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(loop_exec.db_ts_end, 'datetime'))
+ node.set('iteration',self.convertToStr(loop_exec.db_iteration, 'int'))
+ node.set('completed',self.convertToStr(loop_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(loop_exec.db_error, 'str'))
+
+ # set elements
+ item_execs = loop_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'connection':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+
+ ports = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ ports.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, node=None):
+ if node is None:
+ node = ElementTree.Element('connection')
+
+ # set attributes
+ node.set('id',self.convertToStr(connection.db_id, 'long'))
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(port, childNode)
+
+ return node
+
+class DBOpmProcessXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'process':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.getDao('opm_process_value').fromXML(child)
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcess(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process, node=None):
+ if node is None:
+ node = ElementTree.Element('process')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process.db_id, 'str'))
+
+ # set elements
+ value = opm_process.db_value
+ if value is not None:
+ childNode = ElementTree.SubElement(node, 'value')
+ self.getDao('opm_process_value').toXML(value, childNode)
+ accounts = opm_process.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBOpmWasTriggeredByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasTriggeredBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_process_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasTriggeredBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_triggered_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasTriggeredBy')
+
+ # set elements
+ effect = opm_was_triggered_by.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_was_triggered_by.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_triggered_by.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_process_id_cause').toXML(cause, childNode)
+ accounts = opm_was_triggered_by.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_triggered_by.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBOpmProcessValueXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'value':
+ return None
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ value = _data
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ value = _data
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcessValue(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_value, node=None):
+ if node is None:
+ node = ElementTree.Element('value')
+
+ # set elements
+ value = opm_process_value.db_value
+ if value is not None:
+ if value.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(value, childNode)
+ elif value.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(value, childNode)
+ elif value.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(value, childNode)
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'action':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('prevId', None)
+ prevId = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('prune', None)
+ prune = self.convertFromStr(data, 'int')
+
+ annotations = []
+ operations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'add':
+ _data = self.getDao('add').fromXML(child)
+ operations.append(_data)
+ elif child_tag == 'delete':
+ _data = self.getDao('delete').fromXML(child)
+ operations.append(_data)
+ elif child_tag == 'change':
+ _data = self.getDao('change').fromXML(child)
+ operations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAction(operations=operations,
+ id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, node=None):
+ if node is None:
+ node = ElementTree.Element('action')
+
+ # set attributes
+ node.set('id',self.convertToStr(action.db_id, 'long'))
+ node.set('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.set('date',self.convertToStr(action.db_date, 'datetime'))
+ node.set('session',self.convertToStr(action.db_session, 'long'))
+ node.set('user',self.convertToStr(action.db_user, 'str'))
+ node.set('prune',self.convertToStr(action.db_prune, 'int'))
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ childNode = ElementTree.SubElement(node, 'add')
+ self.getDao('add').toXML(operation, childNode)
+ elif operation.vtType == 'delete':
+ childNode = ElementTree.SubElement(node, 'delete')
+ self.getDao('delete').toXML(operation, childNode)
+ elif operation.vtType == 'change':
+ childNode = ElementTree.SubElement(node, 'change')
+ self.getDao('change').toXML(operation, childNode)
+
+ return node
+
+class DBOpmAgentXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agent':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAgent(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agent, node=None):
+ if node is None:
+ node = ElementTree.Element('agent')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_agent.db_id, 'str'))
+
+ # set elements
+ value = opm_agent.db_value
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+ accounts = opm_agent.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'delete':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, node=None):
+ if node is None:
+ node = ElementTree.Element('delete')
+
+ # set attributes
+ node.set('id',self.convertToStr(delete.db_id, 'long'))
+ node.set('what',self.convertToStr(delete.db_what, 'str'))
+ node.set('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'vistrail':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child_tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ actions=actions,
+ tags=tags,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, node=None):
+ if node is None:
+ node = ElementTree.Element('vistrail')
+
+ # set attributes
+ node.set('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.set('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.set('name',self.convertToStr(vistrail.db_name, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = vistrail.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+ annotations = vistrail.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'moduleExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ module_name = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+ loop_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ loop_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ annotations=annotations,
+ loop_execs=loop_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(module_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.set('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+ node.set('completed',self.convertToStr(module_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(module_exec.db_error, 'str'))
+ node.set('machine_id',self.convertToStr(module_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ loop_execs = module_exec.db_loop_execs
+ for loop_exec in loop_execs:
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(loop_exec, childNode)
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'opm_process_id_effect' not in self:
+ self['opm_process_id_effect'] = DBOpmProcessIdEffectXMLDAOBase(self)
+ if 'opm_was_generated_by' not in self:
+ self['opm_was_generated_by'] = DBOpmWasGeneratedByXMLDAOBase(self)
+ if 'opm_accounts' not in self:
+ self['opm_accounts'] = DBOpmAccountsXMLDAOBase(self)
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'module_descriptor' not in self:
+ self['module_descriptor'] = DBModuleDescriptorXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'opm_role' not in self:
+ self['opm_role'] = DBOpmRoleXMLDAOBase(self)
+ if 'opm_processes' not in self:
+ self['opm_processes'] = DBOpmProcessesXMLDAOBase(self)
+ if 'opm_account_id' not in self:
+ self['opm_account_id'] = DBOpmAccountIdXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'opm_artifact' not in self:
+ self['opm_artifact'] = DBOpmArtifactXMLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'opm_agents' not in self:
+ self['opm_agents'] = DBOpmAgentsXMLDAOBase(self)
+ if 'opm_process_id_cause' not in self:
+ self['opm_process_id_cause'] = DBOpmProcessIdCauseXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'opm_overlaps' not in self:
+ self['opm_overlaps'] = DBOpmOverlapsXMLDAOBase(self)
+ if 'opm_artifacts' not in self:
+ self['opm_artifacts'] = DBOpmArtifactsXMLDAOBase(self)
+ if 'opm_dependencies' not in self:
+ self['opm_dependencies'] = DBOpmDependenciesXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'opm_used' not in self:
+ self['opm_used'] = DBOpmUsedXMLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'opm_artifact_id_cause' not in self:
+ self['opm_artifact_id_cause'] = DBOpmArtifactIdCauseXMLDAOBase(self)
+ if 'opm_artifact_value' not in self:
+ self['opm_artifact_value'] = DBOpmArtifactValueXMLDAOBase(self)
+ if 'opm_artifact_id_effect' not in self:
+ self['opm_artifact_id_effect'] = DBOpmArtifactIdEffectXMLDAOBase(self)
+ if 'opm_graph' not in self:
+ self['opm_graph'] = DBOpmGraphXMLDAOBase(self)
+ if 'registry' not in self:
+ self['registry'] = DBRegistryXMLDAOBase(self)
+ if 'opm_account' not in self:
+ self['opm_account'] = DBOpmAccountXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'opm_was_derived_from' not in self:
+ self['opm_was_derived_from'] = DBOpmWasDerivedFromXMLDAOBase(self)
+ if 'opm_was_controlled_by' not in self:
+ self['opm_was_controlled_by'] = DBOpmWasControlledByXMLDAOBase(self)
+ if 'opm_agent_id' not in self:
+ self['opm_agent_id'] = DBOpmAgentIdXMLDAOBase(self)
+ if 'group_exec' not in self:
+ self['group_exec'] = DBGroupExecXMLDAOBase(self)
+ if 'opm_time' not in self:
+ self['opm_time'] = DBOpmTimeXMLDAOBase(self)
+ if 'package' not in self:
+ self['package'] = DBPackageXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'loop_exec' not in self:
+ self['loop_exec'] = DBLoopExecXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'opm_process' not in self:
+ self['opm_process'] = DBOpmProcessXMLDAOBase(self)
+ if 'opm_was_triggered_by' not in self:
+ self['opm_was_triggered_by'] = DBOpmWasTriggeredByXMLDAOBase(self)
+ if 'opm_process_value' not in self:
+ self['opm_process_value'] = DBOpmProcessValueXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'opm_agent' not in self:
+ self['opm_agent'] = DBOpmAgentXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v1_0_0/persistence/xml/xml_dao.py b/vistrails/db/versions/v1_0_0/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..955c01a
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/persistence/xml/xml_dao.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v1_0_0/schemas/sql/vistrails.sql b/vistrails/db/versions/v1_0_0/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..b3f5adb
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/schemas/sql/vistrails.sql
@@ -0,0 +1,372 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+CREATE TABLE `vistrails_version`(`version` char(16)) engine=InnoDB;
+INSERT INTO `vistrails_version`(`version`) VALUES ('1.0.0');
+
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(255),
+ type varchar(255),
+ optional int,
+ sort_key int,
+ sigstring varchar(4095),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module_descriptor(
+ id int,
+ name varchar(255),
+ package varchar(255),
+ namespace varchar(255),
+ version varchar(255),
+ base_descriptor_id int,
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ signature varchar(4095),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE group_tbl(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime,
+ vistrail_id int
+) engine=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE plugin_data(
+ id int,
+ data varchar(8191),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ internal_version varchar(255),
+ tag varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE workflow(
+ id int not null auto_increment primary key,
+ entity_id int,
+ entity_type char(16),
+ name varchar(255),
+ version char(16),
+ last_modified datetime,
+ vistrail_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE registry(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ root_descriptor_id int,
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE group_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ group_name varchar(255),
+ group_type varchar(255),
+ completed int,
+ error varchar(1023),
+ machine_id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE package(
+ id int not null auto_increment primary key,
+ name varchar(255),
+ identifier varchar(1023),
+ codepath varchar(1023),
+ load_configuration int,
+ version varchar(255),
+ description varchar(1023),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ session int,
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ completed int,
+ name varchar(255),
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE loop_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ iteration int,
+ completed int,
+ error varchar(1023),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session int,
+ user varchar(255),
+ prune int,
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ module_name varchar(255),
+ completed int,
+ error varchar(1023),
+ machine_id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
diff --git a/vistrails/db/versions/v1_0_0/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v1_0_0/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..0a71def
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,40 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+DROP TABLE IF EXISTS `vistrails_version`;
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, module_descriptor, tag, port, group_tbl, log_tbl, machine, add_tbl, other, location, parameter, plugin_data, function, abstraction, workflow, registry, annotation, change_tbl, group_exec, package, workflow_exec, loop_exec, connection_tbl, action, delete_tbl, vistrail, module_exec
diff --git a/vistrails/db/versions/v1_0_0/schemas/xml/vistrail.xsd b/vistrails/db/versions/v1_0_0/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..51f02b3
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/schemas/xml/vistrail.xsd
@@ -0,0 +1,278 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="prune" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="signature" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="optional" type="xs:int"/>
+ <xs:attribute name="sortKey" type="xs:int"/>
+ <xs:attribute name="sigstring" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="internalVersion" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="group">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="workflow" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plugin_data">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="workflow">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v1_0_0/specs/all.xml b/vistrails/db/versions/v1_0_0/specs/all.xml
new file mode 100644
index 0000000..d9560c3
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/specs/all.xml
@@ -0,0 +1,2684 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<objects>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ABSTRACTION +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="internal_version" type="str">
+ <xml name="internalVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ACTION ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long" foreignKey="true" object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="prune" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="vistrail" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ADD +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ANNOTATION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CHANGE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CONNECTION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- DELETE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- FUNCTION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group" parentClass="module">
+ <layout>
+ <xml name="group" nodeType="xs:element"/>
+ <sql table="group_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow" type="object" mapping="one-to-one"
+ expand="false">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOCATION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MACHINE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOOP_EXEC +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="loop_exec">
+ <layout>
+ <xml name="loopExec" nodeType="xs:element"/>
+ <sql table="loop_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <!--<property name="input" type="str">
+ <xml name="input" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>-->
+
+ <property name="iteration" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP_EXEC ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group_exec">
+ <layout>
+ <xml name="groupExec" nodeType="xs:element"/>
+ <sql table="group_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="group_name" type="str">
+ <xml name="groupName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="group_type" type="str">
+ <xml name="groupType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <!--<property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>-->
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_EXEC +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OTHER +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PARAMETER +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PLUGIN DATA +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="plugin_data">
+ <layout>
+ <xml name="plugin_data" nodeType="xs:element"/>
+ <sql table="plugin_data"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="data" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORT ++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="signature" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORTSPEC ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="optional" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="sort_key" type="int">
+ <xml name="sortKey" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="sigstring" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="module_descriptor">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_DESCRIPTOR +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_descriptor">
+ <layout>
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ <sql table="module_descriptor"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="base_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="baseDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="package" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ <!--
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="registry">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="package">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+ -->
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PACKAGE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="package">
+ <layout>
+ <xml name="package" nodeType="xs:element"/>
+ <sql table="package"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="identifier" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="codepath" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="load_configuration" type="int">
+ <xml name="loadConfiguration" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="description" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property ref="true" object="module_descriptor" type="list"
+ mapping="one-to-many" index="name:namespace:version">
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="registry" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REGISTRY ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="registry">
+ <layout>
+ <xml name="registry" nodeType="xs:element"/>
+ <sql table="registry"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="root_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="rootDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <!-- <xml nodeType="xs:attribute" type="xs:string"/> -->
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="package" type="list"
+ mapping="one-to-many" index="identifier:version">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- TAG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VISTRAIL ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstraction" ref="true" object="abstraction">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group" ref="true" object="group">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="plugin_data" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="group" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW_EXEC +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_GRAPH +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_graph">
+ <layout>
+ <xml name="opmGraph" nodeType="xs:element"/>
+ <!-- <sql table="opm_graph"/> -->
+ </layout>
+
+ <property name="accounts" ref="true" object="opm_accounts"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="processes" ref="true" object="opm_processes"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="artifacts" ref="true" object="opm_artifacts"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="agents" ref="true" object="opm_agents"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="dependencies" ref="true" object="opm_dependencies"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNTS ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_accounts">
+ <layout>
+ <xml name="accounts" nodeType="xs:element"/>
+ <!-- <sql table="accounts"/> -->
+ </layout>
+
+ <property name="account" ref="true" object="opm_account" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="opm_overlaps" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNT +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_account">
+ <layout>
+ <xml name="account" nodeType="xs:element"/>
+ <!-- <sql table="account"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_OVERLAPS ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_overlaps">
+ <layout>
+ <xml name="overlaps" nodeType="xs:element"/>
+ <!-- <sql table="overlaps"/> -->
+ </layout>
+
+ <property ref="true" object="opm_account_id" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACTS +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifacts">
+ <layout>
+ <xml name="artifacts" nodeType="xs:element"/>
+ <!-- <sql table="artifacts"/> -->
+ </layout>
+
+ <property name="artifact" ref="true" object="opm_artifact" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_VALUE ++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_value">
+ <layout>
+ <xml name="value" nodeType="xs:element"/>
+ <!-- <sql table="artifact_value"/> -->
+ </layout>
+
+ <choice name="value" type="object" mapping="one-to-one">
+ <property ref="true" object="portSpec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact">
+ <layout>
+ <xml name="artifact" nodeType="xs:element"/>
+ <!-- <sql table="artifact"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" ref="true" object="opm_artifact_value" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESSES +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_processes">
+ <layout>
+ <xml name="processes" nodeType="xs:element"/>
+ <!-- <sql table="processes"/> -->
+ </layout>
+
+ <property name="process" ref="true" object="opm_process" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_VALUE +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_value">
+ <layout>
+ <xml name="value" nodeType="xs:element"/>
+ <!-- <sql table="process_value"/> -->
+ </layout>
+
+ <choice name="value" type="object" mapping="one-to-one">
+ <property ref="true" object="module_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process">
+ <layout>
+ <xml name="process" nodeType="xs:element"/>
+ <!-- <sql table="process"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" ref="true" object="opm_process_value" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENTS ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agents">
+ <layout>
+ <xml name="agents" nodeType="xs:element"/>
+ <!-- <sql table="agents"/> -->
+ </layout>
+
+ <property name="agent" ref="true" object="opm_agent" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENT +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agent">
+ <layout>
+ <xml name="agent" nodeType="xs:element"/>
+ <!-- <sql table="agent"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type=""/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_DEPENDENCIES ++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_dependencies">
+ <layout>
+ <xml name="causalDependencies" nodeType="xs:element"/>
+ <!-- <sql table="causal_dependencies"/> -->
+ </layout>
+
+ <choice name="dependency" type="list" mapping="one-to-many">
+ <property name="used" ref="true" object="opm_used">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_generated_by" ref="true"
+ object="opm_was_generated_by">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_triggered_by" ref="true"
+ object="opm_was_triggered_by">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_derived_from" ref="true"
+ object="opm_was_derived_from">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_controlled_by" ref="true"
+ object="opm_was_controlled_by">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_TIME ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_time">
+ <layout>
+ <xml name="time" nodeType="xs:element"/>
+ <!-- <sql table="time"/> -->
+ </layout>
+
+ <property name="no_later_than" type="datetime">
+ <xml name="noLaterThan" nodeType="xs:attribute" type="xs:dateTime"/>
+ <!-- <sql type="datetime"/> -->
+ </property>
+
+ <property name="no_earlier_than" type="datetime">
+ <xml name="noEarlierThan" nodeType="xs:attribute" type="xs:dateTime"/>
+ <!-- <sql type="datetime"/> -->
+ </property>
+
+ <property name="clock_id" type="str">
+ <xml name="clockId" nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNT_ID ++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_account_id">
+ <layout>
+ <xml name="account" nodeType="xs:element"/>
+ <!-- <sql table="account_id"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_account">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_ID_CAUSE ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_id_cause">
+ <layout>
+ <xml name="cause" nodeType="xs:element"/>
+ <!-- <sql table="process_id_cause"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_process">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_ID_EFFECT +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_id_effect">
+ <layout>
+ <xml name="effect" nodeType="xs:element"/>
+ <!-- <sql table="process_id_effect"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_process">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_ID_CAUSE +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_id_cause">
+ <layout>
+ <xml name="cause" nodeType="xs:element"/>
+ <!-- <sql table="artifact_id_cause"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_artifact">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_ID_EFFECT ++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_id_effect">
+ <layout>
+ <xml name="effect" nodeType="xs:element"/>
+ <!-- <sql table="artifact_id_effect"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_artifact">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENT_ID ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agent_id">
+ <layout>
+ <xml name="agent" nodeType="xs:element"/>
+ <!-- <sql table="agent_id"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_agent">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ROLE ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_role">
+ <layout>
+ <xml name="role" nodeType="xs:element"/>
+ <!-- <sql table="role"/> -->
+ </layout>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(4095)"/> -->
+ </property>
+ </object>
+
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_USED ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_used">
+ <layout>
+ <xml name="used" nodeType="xs:element"/>
+ <!-- <sql table="used"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_artifact_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_GENERATED_BY ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_generated_by">
+ <layout>
+ <xml name="wasGeneratedBy" nodeType="xs:element"/>
+ <!-- <sql table="was_generated_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_artifact_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_process_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_CONTROLLED_BY +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_controlled_by">
+ <layout>
+ <xml name="wasControlledBy" nodeType="xs:element"/>
+ <!-- <sql table="was_controlled_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_agent_id"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="start" ref="true" object="opm_time" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="end" ref="true" object="opm_time" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_DERIVED_FROM ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_derived_from">
+ <layout>
+ <xml name="wasDerivedFrom" nodeType="xs:element"/>
+ <!-- <sql table="was_derived_from"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_artifact_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_artifact_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_TRIGGERED_BY ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_triggered_by">
+ <layout>
+ <xml name="wasTriggeredBy" nodeType="xs:element"/>
+ <!-- <sql table="was_triggered_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_process_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+</objects>
diff --git a/vistrails/db/versions/v1_0_0/translate/__init__.py b/vistrails/db/versions/v1_0_0/translate/__init__.py
new file mode 100644
index 0000000..85cbe3f
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '1.0.0'
diff --git a/vistrails/db/versions/v1_0_0/translate/v0_9_5.py b/vistrails/db/versions/v1_0_0/translate/v0_9_5.py
new file mode 100644
index 0000000..71e3d60
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/translate/v0_9_5.py
@@ -0,0 +1,95 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v1_0_0.domain import DBVistrail, DBWorkflow, DBLog, \
+ DBRegistry, DBModuleExec, DBGroupExec, DBLoopExec, DBGroup
+
+def translateVistrail(_vistrail):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBGroup': {'workflow': update_workflow}}
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict)
+ vistrail.db_version = '1.0.0'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBGroup': {'workflow': update_workflow}}
+ workflow = DBWorkflow.update_version(_workflow, translate_dict)
+ workflow.db_version = '1.0.0'
+ return workflow
+
+def translateLog(_log):
+ def update_item_execs(old_obj, translate_dict):
+ new_item_execs = []
+ for obj in old_obj.db_items:
+ if obj.vtType == 'module_exec':
+ new_item_execs.append(DBModuleExec.update_version(obj, translate_dict))
+ elif obj.vtType == 'group_exec':
+ new_item_execs.append(DBGroupExec.update_version(obj, translate_dict))
+ elif obj.vtType == 'loop_exec':
+ new_item_execs.append(DBLoopExec.update_version(obj, translate_dict))
+ return new_item_execs
+
+ def update_sub_item_execs(old_obj, translate_dict, do_loop_execs=True):
+ new_item_execs = []
+ for obj in old_obj.db_module_execs:
+ new_item_execs.append(DBModuleExec.update_version(obj, translate_dict))
+ for obj in old_obj.db_group_execs:
+ new_item_execs.append(DBGroupExec.update_version(obj, translate_dict))
+ if do_loop_execs:
+ for obj in old_obj.db_loop_execs:
+ new_item_execs.append(DBLoopExec.update_version(obj, translate_dict))
+ return new_item_execs
+
+ def update_group_item_execs(old_obj, translate_dict):
+ return update_sub_item_execs(old_obj, translate_dict)
+
+ def update_loop_item_execs(old_obj, translate_dict):
+ return update_sub_item_execs(old_obj, translate_dict, False)
+
+ translate_dict = {'DBWorkflowExec': {'item_execs': update_item_execs},
+ 'DBGroupExec': {'item_execs': update_group_item_execs},
+ 'DBLoopExec': {'item_execs': update_loop_item_execs}}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '1.0.0'
+ return log
+
+def translateRegistry(_registry):
+ translate_dict = {}
+ registry = DBRegistry.update_version(_registry, translate_dict)
+ registry.db_version = '1.0.0'
+ return registry
diff --git a/vistrails/db/versions/v1_0_0/translate/v1_0_1.py b/vistrails/db/versions/v1_0_0/translate/v1_0_1.py
new file mode 100644
index 0000000..ab1aa8e
--- /dev/null
+++ b/vistrails/db/versions/v1_0_0/translate/v1_0_1.py
@@ -0,0 +1,65 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v1_0_0.domain import DBVistrail, DBWorkflow, DBLog, \
+ DBRegistry
+
+def translateVistrail(_vistrail):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBGroup': {'workflow': update_workflow}}
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict)
+ vistrail.db_version = '1.0.0'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBGroup': {'workflow': update_workflow}}
+ workflow = DBWorkflow.update_version(_workflow, translate_dict)
+ workflow.db_version = '1.0.0'
+ return workflow
+
+def translateLog(_log):
+ translate_dict = {}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '1.0.0'
+ return log
+
+def translateRegistry(_registry):
+ translate_dict = {}
+ registry = DBRegistry.update_version(_registry, translate_dict)
+ registry.db_version = '1.0.0'
+ return registry
diff --git a/vistrails/db/versions/v1_0_1/__init__.py b/vistrails/db/versions/v1_0_1/__init__.py
new file mode 100644
index 0000000..ecda317
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '1.0.1'
diff --git a/vistrails/db/versions/v1_0_1/domain/__init__.py b/vistrails/db/versions/v1_0_1/domain/__init__.py
new file mode 100644
index 0000000..a8208f6
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/domain/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from registry import DBRegistry
+from workflow import DBWorkflow
+from vistrail import DBVistrail
+from log import DBLog
+from id_scope import IdScope
diff --git a/vistrails/db/versions/v1_0_1/domain/auto_gen.py b/vistrails/db/versions/v1_0_1/domain/auto_gen.py
new file mode 100644
index 0000000..451d158
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/domain/auto_gen.py
@@ -0,0 +1,11447 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBOpmProcessIdEffect(object):
+
+ vtType = 'opm_process_id_effect'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessIdEffect.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessIdEffect(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_process', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_process', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessIdEffect()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBOpmWasGeneratedBy(object):
+
+ vtType = 'opm_was_generated_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasGeneratedBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasGeneratedBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasGeneratedBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmArtifactIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmArtifactIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmProcessIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmProcessIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBOpmAccounts(object):
+
+ vtType = 'opm_accounts'
+
+ def __init__(self, accounts=None, opm_overlapss=None):
+ self.db_deleted_accounts = []
+ self.db_accounts_id_index = {}
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ for v in self._db_accounts:
+ self.db_accounts_id_index[v.db_id] = v
+ self.db_deleted_opm_overlapss = []
+ if opm_overlapss is None:
+ self._db_opm_overlapss = []
+ else:
+ self._db_opm_overlapss = opm_overlapss
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccounts.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccounts()
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_overlapss is None:
+ cp._db_opm_overlapss = []
+ else:
+ cp._db_opm_overlapss = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_overlapss]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_accounts_id_index = dict((v.db_id, v) for v in cp._db_accounts)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccounts()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccount.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccount.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_overlapss' in class_dict:
+ res = class_dict['opm_overlapss'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_overlaps(obj)
+ elif hasattr(old_obj, 'db_opm_overlapss') and old_obj.db_opm_overlapss is not None:
+ for obj in old_obj.db_opm_overlapss:
+ new_obj.db_add_opm_overlaps(DBOpmOverlaps.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_overlapss') and hasattr(new_obj, 'db_deleted_opm_overlapss'):
+ for obj in old_obj.db_deleted_opm_overlapss:
+ n_obj = DBOpmOverlaps.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_overlapss.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_overlapss:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_overlaps(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_overlapss)
+ if remove:
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_overlapss = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_overlapss:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ self.db_accounts_id_index[account.db_id] = account
+ def db_change_account(self, account):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == account.db_id:
+ self._db_accounts[i] = account
+ found = True
+ break
+ if not found:
+ self._db_accounts.append(account)
+ self.db_accounts_id_index[account.db_id] = account
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == account.db_id:
+ if not self._db_accounts[i].is_new:
+ self.db_deleted_accounts.append(self._db_accounts[i])
+ del self._db_accounts[i]
+ break
+ del self.db_accounts_id_index[account.db_id]
+ def db_get_account(self, key):
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == key:
+ return self._db_accounts[i]
+ return None
+ def db_get_account_by_id(self, key):
+ return self.db_accounts_id_index[key]
+ def db_has_account_with_id(self, key):
+ return key in self.db_accounts_id_index
+
+ def __get_db_opm_overlapss(self):
+ return self._db_opm_overlapss
+ def __set_db_opm_overlapss(self, opm_overlapss):
+ self._db_opm_overlapss = opm_overlapss
+ self.is_dirty = True
+ db_opm_overlapss = property(__get_db_opm_overlapss, __set_db_opm_overlapss)
+ def db_get_opm_overlapss(self):
+ return self._db_opm_overlapss
+ def db_add_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ self._db_opm_overlapss.append(opm_overlaps)
+ def db_change_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ self._db_opm_overlapss.append(opm_overlaps)
+ def db_delete_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_overlaps(self, key):
+ return None
+
+
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, optional=None, sort_key=None, sigstring=None, labels=None, defaults=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_type = type
+ self._db_optional = optional
+ self._db_sort_key = sort_key
+ self._db_sigstring = sigstring
+ self._db_labels = labels
+ self._db_defaults = defaults
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPortSpec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec(id=self._db_id,
+ name=self._db_name,
+ type=self._db_type,
+ optional=self._db_optional,
+ sort_key=self._db_sort_key,
+ sigstring=self._db_sigstring,
+ labels=self._db_labels,
+ defaults=self._db_defaults)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPortSpec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'optional' in class_dict:
+ res = class_dict['optional'](old_obj, trans_dict)
+ new_obj.db_optional = res
+ elif hasattr(old_obj, 'db_optional') and old_obj.db_optional is not None:
+ new_obj.db_optional = old_obj.db_optional
+ if 'sort_key' in class_dict:
+ res = class_dict['sort_key'](old_obj, trans_dict)
+ new_obj.db_sort_key = res
+ elif hasattr(old_obj, 'db_sort_key') and old_obj.db_sort_key is not None:
+ new_obj.db_sort_key = old_obj.db_sort_key
+ if 'sigstring' in class_dict:
+ res = class_dict['sigstring'](old_obj, trans_dict)
+ new_obj.db_sigstring = res
+ elif hasattr(old_obj, 'db_sigstring') and old_obj.db_sigstring is not None:
+ new_obj.db_sigstring = old_obj.db_sigstring
+ if 'labels' in class_dict:
+ res = class_dict['labels'](old_obj, trans_dict)
+ new_obj.db_labels = res
+ elif hasattr(old_obj, 'db_labels') and old_obj.db_labels is not None:
+ new_obj.db_labels = old_obj.db_labels
+ if 'defaults' in class_dict:
+ res = class_dict['defaults'](old_obj, trans_dict)
+ new_obj.db_defaults = res
+ elif hasattr(old_obj, 'db_defaults') and old_obj.db_defaults is not None:
+ new_obj.db_defaults = old_obj.db_defaults
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_optional(self):
+ return self._db_optional
+ def __set_db_optional(self, optional):
+ self._db_optional = optional
+ self.is_dirty = True
+ db_optional = property(__get_db_optional, __set_db_optional)
+ def db_add_optional(self, optional):
+ self._db_optional = optional
+ def db_change_optional(self, optional):
+ self._db_optional = optional
+ def db_delete_optional(self, optional):
+ self._db_optional = None
+
+ def __get_db_sort_key(self):
+ return self._db_sort_key
+ def __set_db_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ self.is_dirty = True
+ db_sort_key = property(__get_db_sort_key, __set_db_sort_key)
+ def db_add_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ def db_change_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ def db_delete_sort_key(self, sort_key):
+ self._db_sort_key = None
+
+ def __get_db_sigstring(self):
+ return self._db_sigstring
+ def __set_db_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ self.is_dirty = True
+ db_sigstring = property(__get_db_sigstring, __set_db_sigstring)
+ def db_add_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ def db_change_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ def db_delete_sigstring(self, sigstring):
+ self._db_sigstring = None
+
+ def __get_db_labels(self):
+ return self._db_labels
+ def __set_db_labels(self, labels):
+ self._db_labels = labels
+ self.is_dirty = True
+ db_labels = property(__get_db_labels, __set_db_labels)
+ def db_add_labels(self, labels):
+ self._db_labels = labels
+ def db_change_labels(self, labels):
+ self._db_labels = labels
+ def db_delete_labels(self, labels):
+ self._db_labels = None
+
+ def __get_db_defaults(self):
+ return self._db_defaults
+ def __set_db_defaults(self, defaults):
+ self._db_defaults = defaults
+ self.is_dirty = True
+ db_defaults = property(__get_db_defaults, __set_db_defaults)
+ def db_add_defaults(self, defaults):
+ self._db_defaults = defaults
+ def db_change_defaults(self, defaults):
+ self._db_defaults = defaults
+ def db_delete_defaults(self, defaults):
+ self._db_defaults = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModule.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ tag=self._db_tag)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModule()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleDescriptor(object):
+
+ vtType = 'module_descriptor'
+
+ def __init__(self, id=None, name=None, package=None, namespace=None, package_version=None, version=None, base_descriptor_id=None, portSpecs=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_package = package
+ self._db_namespace = namespace
+ self._db_package_version = package_version
+ self._db_version = version
+ self._db_base_descriptor_id = base_descriptor_id
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleDescriptor.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleDescriptor(id=self._db_id,
+ name=self._db_name,
+ package=self._db_package,
+ namespace=self._db_namespace,
+ package_version=self._db_package_version,
+ version=self._db_version,
+ base_descriptor_id=self._db_base_descriptor_id)
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_base_descriptor_id') and ('module_descriptor', self._db_base_descriptor_id) in id_remap:
+ cp._db_base_descriptor_id = id_remap[('module_descriptor', self._db_base_descriptor_id)]
+
+ # recreate indices and set flags
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleDescriptor()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package_version' in class_dict:
+ res = class_dict['package_version'](old_obj, trans_dict)
+ new_obj.db_package_version = res
+ elif hasattr(old_obj, 'db_package_version') and old_obj.db_package_version is not None:
+ new_obj.db_package_version = old_obj.db_package_version
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'base_descriptor_id' in class_dict:
+ res = class_dict['base_descriptor_id'](old_obj, trans_dict)
+ new_obj.db_base_descriptor_id = res
+ elif hasattr(old_obj, 'db_base_descriptor_id') and old_obj.db_base_descriptor_id is not None:
+ new_obj.db_base_descriptor_id = old_obj.db_base_descriptor_id
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package_version(self):
+ return self._db_package_version
+ def __set_db_package_version(self, package_version):
+ self._db_package_version = package_version
+ self.is_dirty = True
+ db_package_version = property(__get_db_package_version, __set_db_package_version)
+ def db_add_package_version(self, package_version):
+ self._db_package_version = package_version
+ def db_change_package_version(self, package_version):
+ self._db_package_version = package_version
+ def db_delete_package_version(self, package_version):
+ self._db_package_version = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_base_descriptor_id(self):
+ return self._db_base_descriptor_id
+ def __set_db_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ self.is_dirty = True
+ db_base_descriptor_id = property(__get_db_base_descriptor_id, __set_db_base_descriptor_id)
+ def db_add_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ def db_change_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ def db_delete_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = None
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self._db_id = id
+ self._db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBTag.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag(id=self._db_id,
+ name=self._db_name)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('action', self._db_id) in id_remap:
+ cp._db_id = id_remap[('action', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBTag()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmRole(object):
+
+ vtType = 'opm_role'
+
+ def __init__(self, value=None):
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmRole.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmRole(value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmRole()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+
+
+class DBOpmProcesses(object):
+
+ vtType = 'opm_processes'
+
+ def __init__(self, processs=None):
+ self.db_deleted_processs = []
+ self.db_processs_id_index = {}
+ if processs is None:
+ self._db_processs = []
+ else:
+ self._db_processs = processs
+ for v in self._db_processs:
+ self.db_processs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcesses.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcesses()
+ if self._db_processs is None:
+ cp._db_processs = []
+ else:
+ cp._db_processs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_processs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_processs_id_index = dict((v.db_id, v) for v in cp._db_processs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcesses()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'processs' in class_dict:
+ res = class_dict['processs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_process(obj)
+ elif hasattr(old_obj, 'db_processs') and old_obj.db_processs is not None:
+ for obj in old_obj.db_processs:
+ new_obj.db_add_process(DBOpmProcess.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_processs') and hasattr(new_obj, 'db_deleted_processs'):
+ for obj in old_obj.db_deleted_processs:
+ n_obj = DBOpmProcess.update_version(obj, trans_dict)
+ new_obj.db_deleted_processs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_processs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_process(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_processs)
+ if remove:
+ self.db_deleted_processs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_processs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_processs(self):
+ return self._db_processs
+ def __set_db_processs(self, processs):
+ self._db_processs = processs
+ self.is_dirty = True
+ db_processs = property(__get_db_processs, __set_db_processs)
+ def db_get_processs(self):
+ return self._db_processs
+ def db_add_process(self, process):
+ self.is_dirty = True
+ self._db_processs.append(process)
+ self.db_processs_id_index[process.db_id] = process
+ def db_change_process(self, process):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == process.db_id:
+ self._db_processs[i] = process
+ found = True
+ break
+ if not found:
+ self._db_processs.append(process)
+ self.db_processs_id_index[process.db_id] = process
+ def db_delete_process(self, process):
+ self.is_dirty = True
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == process.db_id:
+ if not self._db_processs[i].is_new:
+ self.db_deleted_processs.append(self._db_processs[i])
+ del self._db_processs[i]
+ break
+ del self.db_processs_id_index[process.db_id]
+ def db_get_process(self, key):
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == key:
+ return self._db_processs[i]
+ return None
+ def db_get_process_by_id(self, key):
+ return self.db_processs_id_index[key]
+ def db_has_process_with_id(self, key):
+ return key in self.db_processs_id_index
+
+
+
+class DBOpmAccountId(object):
+
+ vtType = 'opm_account_id'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccountId.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccountId(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_account', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_account', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccountId()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, name=None, signature=None):
+ self._db_id = id
+ self._db_type = type
+ self._db_moduleId = moduleId
+ self._db_moduleName = moduleName
+ self._db_name = name
+ self._db_signature = signature
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPort.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort(id=self._db_id,
+ type=self._db_type,
+ moduleId=self._db_moduleId,
+ moduleName=self._db_moduleName,
+ name=self._db_name,
+ signature=self._db_signature)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_moduleId') and ('module', self._db_moduleId) in id_remap:
+ cp._db_moduleId = id_remap[('module', self._db_moduleId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPort()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'moduleId' in class_dict:
+ res = class_dict['moduleId'](old_obj, trans_dict)
+ new_obj.db_moduleId = res
+ elif hasattr(old_obj, 'db_moduleId') and old_obj.db_moduleId is not None:
+ new_obj.db_moduleId = old_obj.db_moduleId
+ if 'moduleName' in class_dict:
+ res = class_dict['moduleName'](old_obj, trans_dict)
+ new_obj.db_moduleName = res
+ elif hasattr(old_obj, 'db_moduleName') and old_obj.db_moduleName is not None:
+ new_obj.db_moduleName = old_obj.db_moduleName
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'signature' in class_dict:
+ res = class_dict['signature'](old_obj, trans_dict)
+ new_obj.db_signature = res
+ elif hasattr(old_obj, 'db_signature') and old_obj.db_signature is not None:
+ new_obj.db_signature = old_obj.db_signature
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_moduleId(self):
+ return self._db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self._db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self._db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self._db_moduleName = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_signature(self):
+ return self._db_signature
+ def __set_db_signature(self, signature):
+ self._db_signature = signature
+ self.is_dirty = True
+ db_signature = property(__get_db_signature, __set_db_signature)
+ def db_add_signature(self, signature):
+ self._db_signature = signature
+ def db_change_signature(self, signature):
+ self._db_signature = signature
+ def db_delete_signature(self, signature):
+ self._db_signature = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmArtifact(object):
+
+ vtType = 'opm_artifact'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self.db_deleted_value = []
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifact.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifact(id=self._db_id)
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifact()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ new_obj.db_add_value(DBOpmArtifactValue.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ n_obj = DBOpmArtifactValue.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_value = []
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBGroup(object):
+
+ vtType = 'group'
+
+ def __init__(self, id=None, workflow=None, cache=None, name=None, namespace=None, package=None, version=None, tag=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self.db_deleted_workflow = []
+ self._db_workflow = workflow
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroup.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroup(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ tag=self._db_tag)
+ if self._db_workflow is not None:
+ cp._db_workflow = self._db_workflow.do_copy()
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroup()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'workflow' in class_dict:
+ res = class_dict['workflow'](old_obj, trans_dict)
+ new_obj.db_workflow = res
+ elif hasattr(old_obj, 'db_workflow') and old_obj.db_workflow is not None:
+ obj = old_obj.db_workflow
+ new_obj.db_add_workflow(DBWorkflow.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow') and hasattr(new_obj, 'db_deleted_workflow'):
+ for obj in old_obj.db_deleted_workflow:
+ n_obj = DBWorkflow.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow.append(n_obj)
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow)
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_workflow = []
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_workflow is not None and self._db_workflow.has_changes():
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_workflow(self):
+ return self._db_workflow
+ def __set_db_workflow(self, workflow):
+ self._db_workflow = workflow
+ self.is_dirty = True
+ db_workflow = property(__get_db_workflow, __set_db_workflow)
+ def db_add_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_change_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_delete_workflow(self, workflow):
+ if not self.is_new:
+ self.db_deleted_workflow.append(self._db_workflow)
+ self._db_workflow = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, workflow_execs=None, machines=None, vistrail_id=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_workflow_execs = []
+ self.db_workflow_execs_id_index = {}
+ if workflow_execs is None:
+ self._db_workflow_execs = []
+ else:
+ self._db_workflow_execs = workflow_execs
+ for v in self._db_workflow_execs:
+ self.db_workflow_execs_id_index[v.db_id] = v
+ self.db_deleted_machines = []
+ self.db_machines_id_index = {}
+ if machines is None:
+ self._db_machines = []
+ else:
+ self._db_machines = machines
+ for v in self._db_machines:
+ self.db_machines_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_workflow_execs is None:
+ cp._db_workflow_execs = []
+ else:
+ cp._db_workflow_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_workflow_execs]
+ if self._db_machines is None:
+ cp._db_machines = []
+ else:
+ cp._db_machines = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_machines]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_workflow_execs_id_index = dict((v.db_id, v) for v in cp._db_workflow_execs)
+ cp.db_machines_id_index = dict((v.db_id, v) for v in cp._db_machines)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'workflow_execs' in class_dict:
+ res = class_dict['workflow_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_workflow_exec(obj)
+ elif hasattr(old_obj, 'db_workflow_execs') and old_obj.db_workflow_execs is not None:
+ for obj in old_obj.db_workflow_execs:
+ new_obj.db_add_workflow_exec(DBWorkflowExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow_execs') and hasattr(new_obj, 'db_deleted_workflow_execs'):
+ for obj in old_obj.db_deleted_workflow_execs:
+ n_obj = DBWorkflowExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow_execs.append(n_obj)
+ if 'machines' in class_dict:
+ res = class_dict['machines'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_machine(obj)
+ elif hasattr(old_obj, 'db_machines') and old_obj.db_machines is not None:
+ for obj in old_obj.db_machines:
+ new_obj.db_add_machine(DBMachine.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_machines') and hasattr(new_obj, 'db_deleted_machines'):
+ for obj in old_obj.db_deleted_machines:
+ n_obj = DBMachine.update_version(obj, trans_dict)
+ new_obj.db_deleted_machines.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_workflow_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self.db_machines:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow_execs)
+ children.extend(self.db_deleted_machines)
+ if remove:
+ self.db_deleted_workflow_execs = []
+ self.db_deleted_machines = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_workflow_execs:
+ if child.has_changes():
+ return True
+ for child in self._db_machines:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_workflow_execs(self):
+ return self._db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self._db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self._db_workflow_execs
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ self._db_workflow_execs[i] = workflow_exec
+ found = True
+ break
+ if not found:
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ if not self._db_workflow_execs[i].is_new:
+ self.db_deleted_workflow_execs.append(self._db_workflow_execs[i])
+ del self._db_workflow_execs[i]
+ break
+ del self.db_workflow_execs_id_index[workflow_exec.db_id]
+ def db_get_workflow_exec(self, key):
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == key:
+ return self._db_workflow_execs[i]
+ return None
+ def db_get_workflow_exec_by_id(self, key):
+ return self.db_workflow_execs_id_index[key]
+ def db_has_workflow_exec_with_id(self, key):
+ return key in self.db_workflow_execs_id_index
+
+ def __get_db_machines(self):
+ return self._db_machines
+ def __set_db_machines(self, machines):
+ self._db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self._db_machines
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ self._db_machines[i] = machine
+ found = True
+ break
+ if not found:
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ if not self._db_machines[i].is_new:
+ self.db_deleted_machines.append(self._db_machines[i])
+ del self._db_machines[i]
+ break
+ del self.db_machines_id_index[machine.db_id]
+ def db_get_machine(self, key):
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == key:
+ return self._db_machines[i]
+ return None
+ def db_get_machine_by_id(self, key):
+ return self.db_machines_id_index[key]
+ def db_has_machine_with_id(self, key):
+ return key in self.db_machines_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmAgents(object):
+
+ vtType = 'opm_agents'
+
+ def __init__(self, agents=None):
+ self.db_deleted_agents = []
+ self.db_agents_id_index = {}
+ if agents is None:
+ self._db_agents = []
+ else:
+ self._db_agents = agents
+ for v in self._db_agents:
+ self.db_agents_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgents.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgents()
+ if self._db_agents is None:
+ cp._db_agents = []
+ else:
+ cp._db_agents = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_agents]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_agents_id_index = dict((v.db_id, v) for v in cp._db_agents)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgents()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'agents' in class_dict:
+ res = class_dict['agents'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_agent(obj)
+ elif hasattr(old_obj, 'db_agents') and old_obj.db_agents is not None:
+ for obj in old_obj.db_agents:
+ new_obj.db_add_agent(DBOpmAgent.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_agents') and hasattr(new_obj, 'db_deleted_agents'):
+ for obj in old_obj.db_deleted_agents:
+ n_obj = DBOpmAgent.update_version(obj, trans_dict)
+ new_obj.db_deleted_agents.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_agents:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_agent(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_agents)
+ if remove:
+ self.db_deleted_agents = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_agents:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_agents(self):
+ return self._db_agents
+ def __set_db_agents(self, agents):
+ self._db_agents = agents
+ self.is_dirty = True
+ db_agents = property(__get_db_agents, __set_db_agents)
+ def db_get_agents(self):
+ return self._db_agents
+ def db_add_agent(self, agent):
+ self.is_dirty = True
+ self._db_agents.append(agent)
+ self.db_agents_id_index[agent.db_id] = agent
+ def db_change_agent(self, agent):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == agent.db_id:
+ self._db_agents[i] = agent
+ found = True
+ break
+ if not found:
+ self._db_agents.append(agent)
+ self.db_agents_id_index[agent.db_id] = agent
+ def db_delete_agent(self, agent):
+ self.is_dirty = True
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == agent.db_id:
+ if not self._db_agents[i].is_new:
+ self.db_deleted_agents.append(self._db_agents[i])
+ del self._db_agents[i]
+ break
+ del self.db_agents_id_index[agent.db_id]
+ def db_get_agent(self, key):
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == key:
+ return self._db_agents[i]
+ return None
+ def db_get_agent_by_id(self, key):
+ return self.db_agents_id_index[key]
+ def db_has_agent_with_id(self, key):
+ return key in self.db_agents_id_index
+
+
+
+class DBOpmProcessIdCause(object):
+
+ vtType = 'opm_process_id_cause'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessIdCause.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessIdCause(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_process', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_process', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessIdCause()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_os = os
+ self._db_architecture = architecture
+ self._db_processor = processor
+ self._db_ram = ram
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMachine.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine(id=self._db_id,
+ name=self._db_name,
+ os=self._db_os,
+ architecture=self._db_architecture,
+ processor=self._db_processor,
+ ram=self._db_ram)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and ('vistrail', self._db_vistrailId) in id_remap:
+ cp._db_vistrailId = id_remap[('vistrail', self._db_vistrailId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMachine()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'os' in class_dict:
+ res = class_dict['os'](old_obj, trans_dict)
+ new_obj.db_os = res
+ elif hasattr(old_obj, 'db_os') and old_obj.db_os is not None:
+ new_obj.db_os = old_obj.db_os
+ if 'architecture' in class_dict:
+ res = class_dict['architecture'](old_obj, trans_dict)
+ new_obj.db_architecture = res
+ elif hasattr(old_obj, 'db_architecture') and old_obj.db_architecture is not None:
+ new_obj.db_architecture = old_obj.db_architecture
+ if 'processor' in class_dict:
+ res = class_dict['processor'](old_obj, trans_dict)
+ new_obj.db_processor = res
+ elif hasattr(old_obj, 'db_processor') and old_obj.db_processor is not None:
+ new_obj.db_processor = old_obj.db_processor
+ if 'ram' in class_dict:
+ res = class_dict['ram'](old_obj, trans_dict)
+ new_obj.db_ram = res
+ elif hasattr(old_obj, 'db_ram') and old_obj.db_ram is not None:
+ new_obj.db_ram = old_obj.db_ram
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_os(self):
+ return self._db_os
+ def __set_db_os(self, os):
+ self._db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self._db_os = os
+ def db_change_os(self, os):
+ self._db_os = os
+ def db_delete_os(self, os):
+ self._db_os = None
+
+ def __get_db_architecture(self):
+ return self._db_architecture
+ def __set_db_architecture(self, architecture):
+ self._db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self._db_architecture = None
+
+ def __get_db_processor(self):
+ return self._db_processor
+ def __set_db_processor(self, processor):
+ self._db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self._db_processor = processor
+ def db_change_processor(self, processor):
+ self._db_processor = processor
+ def db_delete_processor(self, processor):
+ self._db_processor = None
+
+ def __get_db_ram(self):
+ return self._db_ram
+ def __set_db_ram(self, ram):
+ self._db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self._db_ram = ram
+ def db_change_ram(self, ram):
+ self._db_ram = ram
+ def db_delete_ram(self, ram):
+ self._db_ram = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, data=None, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAdd.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAdd()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOther.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOther(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOther()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self._db_id = id
+ self._db_x = x
+ self._db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLocation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation(id=self._db_id,
+ x=self._db_x,
+ y=self._db_y)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLocation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'x' in class_dict:
+ res = class_dict['x'](old_obj, trans_dict)
+ new_obj.db_x = res
+ elif hasattr(old_obj, 'db_x') and old_obj.db_x is not None:
+ new_obj.db_x = old_obj.db_x
+ if 'y' in class_dict:
+ res = class_dict['y'](old_obj, trans_dict)
+ new_obj.db_y = res
+ elif hasattr(old_obj, 'db_y') and old_obj.db_y is not None:
+ new_obj.db_y = old_obj.db_y
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_x(self):
+ return self._db_x
+ def __set_db_x(self, x):
+ self._db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self._db_x = x
+ def db_change_x(self, x):
+ self._db_x = x
+ def db_delete_x(self, x):
+ self._db_x = None
+
+ def __get_db_y(self):
+ return self._db_y
+ def __set_db_y(self, y):
+ self._db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self._db_y = y
+ def db_change_y(self, y):
+ self._db_y = y
+ def db_delete_y(self, y):
+ self._db_y = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmOverlaps(object):
+
+ vtType = 'opm_overlaps'
+
+ def __init__(self, opm_account_ids=None):
+ self.db_deleted_opm_account_ids = []
+ if opm_account_ids is None:
+ self._db_opm_account_ids = []
+ else:
+ self._db_opm_account_ids = opm_account_ids
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmOverlaps.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmOverlaps()
+ if self._db_opm_account_ids is None:
+ cp._db_opm_account_ids = []
+ else:
+ cp._db_opm_account_ids = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_account_ids]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmOverlaps()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'opm_account_ids' in class_dict:
+ res = class_dict['opm_account_ids'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_account_id(obj)
+ elif hasattr(old_obj, 'db_opm_account_ids') and old_obj.db_opm_account_ids is not None:
+ for obj in old_obj.db_opm_account_ids:
+ new_obj.db_add_opm_account_id(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_account_ids') and hasattr(new_obj, 'db_deleted_opm_account_ids'):
+ for obj in old_obj.db_deleted_opm_account_ids:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_account_ids.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_opm_account_ids:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_account_id(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_opm_account_ids)
+ if remove:
+ self.db_deleted_opm_account_ids = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_opm_account_ids:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_opm_account_ids(self):
+ return self._db_opm_account_ids
+ def __set_db_opm_account_ids(self, opm_account_ids):
+ self._db_opm_account_ids = opm_account_ids
+ self.is_dirty = True
+ db_opm_account_ids = property(__get_db_opm_account_ids, __set_db_opm_account_ids)
+ def db_get_opm_account_ids(self):
+ return self._db_opm_account_ids
+ def db_add_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ self._db_opm_account_ids.append(opm_account_id)
+ def db_change_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ self._db_opm_account_ids.append(opm_account_id)
+ def db_delete_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_account_id(self, key):
+ return None
+
+
+
+class DBOpmArtifacts(object):
+
+ vtType = 'opm_artifacts'
+
+ def __init__(self, artifacts=None):
+ self.db_deleted_artifacts = []
+ self.db_artifacts_id_index = {}
+ if artifacts is None:
+ self._db_artifacts = []
+ else:
+ self._db_artifacts = artifacts
+ for v in self._db_artifacts:
+ self.db_artifacts_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifacts.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifacts()
+ if self._db_artifacts is None:
+ cp._db_artifacts = []
+ else:
+ cp._db_artifacts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_artifacts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_artifacts_id_index = dict((v.db_id, v) for v in cp._db_artifacts)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifacts()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'artifacts' in class_dict:
+ res = class_dict['artifacts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_artifact(obj)
+ elif hasattr(old_obj, 'db_artifacts') and old_obj.db_artifacts is not None:
+ for obj in old_obj.db_artifacts:
+ new_obj.db_add_artifact(DBOpmArtifact.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_artifacts') and hasattr(new_obj, 'db_deleted_artifacts'):
+ for obj in old_obj.db_deleted_artifacts:
+ n_obj = DBOpmArtifact.update_version(obj, trans_dict)
+ new_obj.db_deleted_artifacts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_artifacts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_artifact(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_artifacts)
+ if remove:
+ self.db_deleted_artifacts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_artifacts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_artifacts(self):
+ return self._db_artifacts
+ def __set_db_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ self.is_dirty = True
+ db_artifacts = property(__get_db_artifacts, __set_db_artifacts)
+ def db_get_artifacts(self):
+ return self._db_artifacts
+ def db_add_artifact(self, artifact):
+ self.is_dirty = True
+ self._db_artifacts.append(artifact)
+ self.db_artifacts_id_index[artifact.db_id] = artifact
+ def db_change_artifact(self, artifact):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == artifact.db_id:
+ self._db_artifacts[i] = artifact
+ found = True
+ break
+ if not found:
+ self._db_artifacts.append(artifact)
+ self.db_artifacts_id_index[artifact.db_id] = artifact
+ def db_delete_artifact(self, artifact):
+ self.is_dirty = True
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == artifact.db_id:
+ if not self._db_artifacts[i].is_new:
+ self.db_deleted_artifacts.append(self._db_artifacts[i])
+ del self._db_artifacts[i]
+ break
+ del self.db_artifacts_id_index[artifact.db_id]
+ def db_get_artifact(self, key):
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == key:
+ return self._db_artifacts[i]
+ return None
+ def db_get_artifact_by_id(self, key):
+ return self.db_artifacts_id_index[key]
+ def db_has_artifact_with_id(self, key):
+ return key in self.db_artifacts_id_index
+
+
+
+class DBOpmDependencies(object):
+
+ vtType = 'opm_dependencies'
+
+ def __init__(self, dependencys=None):
+ self.db_deleted_dependencys = []
+ if dependencys is None:
+ self._db_dependencys = []
+ else:
+ self._db_dependencys = dependencys
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmDependencies.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmDependencies()
+ if self._db_dependencys is None:
+ cp._db_dependencys = []
+ else:
+ cp._db_dependencys = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_dependencys]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmDependencies()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'dependencys' in class_dict:
+ res = class_dict['dependencys'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_dependency(obj)
+ elif hasattr(old_obj, 'db_dependencys') and old_obj.db_dependencys is not None:
+ for obj in old_obj.db_dependencys:
+ if obj.vtType == 'opm_used':
+ new_obj.db_add_dependency(DBOpmUsed.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_generated_by':
+ new_obj.db_add_dependency(DBOpmWasGeneratedBy.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_triggered_by':
+ new_obj.db_add_dependency(DBOpmWasTriggeredBy.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_derived_from':
+ new_obj.db_add_dependency(DBOpmWasDerivedFrom.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_controlled_by':
+ new_obj.db_add_dependency(DBOpmWasControlledBy.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_dependencys') and hasattr(new_obj, 'db_deleted_dependencys'):
+ for obj in old_obj.db_deleted_dependencys:
+ if obj.vtType == 'opm_used':
+ n_obj = DBOpmUsed.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_generated_by':
+ n_obj = DBOpmWasGeneratedBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_triggered_by':
+ n_obj = DBOpmWasTriggeredBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_derived_from':
+ n_obj = DBOpmWasDerivedFrom.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_controlled_by':
+ n_obj = DBOpmWasControlledBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_dependencys:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_dependency(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_dependencys)
+ if remove:
+ self.db_deleted_dependencys = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_dependencys:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_dependencys(self):
+ return self._db_dependencys
+ def __set_db_dependencys(self, dependencys):
+ self._db_dependencys = dependencys
+ self.is_dirty = True
+ db_dependencys = property(__get_db_dependencys, __set_db_dependencys)
+ def db_get_dependencys(self):
+ return self._db_dependencys
+ def db_add_dependency(self, dependency):
+ self.is_dirty = True
+ self._db_dependencys.append(dependency)
+ def db_change_dependency(self, dependency):
+ self.is_dirty = True
+ self._db_dependencys.append(dependency)
+ def db_delete_dependency(self, dependency):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_dependency(self, key):
+ return None
+
+
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self._db_type = type
+ self._db_val = val
+ self._db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBParameter.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name,
+ type=self._db_type,
+ val=self._db_val,
+ alias=self._db_alias)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBParameter()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'val' in class_dict:
+ res = class_dict['val'](old_obj, trans_dict)
+ new_obj.db_val = res
+ elif hasattr(old_obj, 'db_val') and old_obj.db_val is not None:
+ new_obj.db_val = old_obj.db_val
+ if 'alias' in class_dict:
+ res = class_dict['alias'](old_obj, trans_dict)
+ new_obj.db_alias = res
+ elif hasattr(old_obj, 'db_alias') and old_obj.db_alias is not None:
+ new_obj.db_alias = old_obj.db_alias
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_val(self):
+ return self._db_val
+ def __set_db_val(self, val):
+ self._db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self._db_val = val
+ def db_change_val(self, val):
+ self._db_val = val
+ def db_delete_val(self, val):
+ self._db_val = None
+
+ def __get_db_alias(self):
+ return self._db_alias
+ def __set_db_alias(self, alias):
+ self._db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self._db_alias = alias
+ def db_change_alias(self, alias):
+ self._db_alias = alias
+ def db_delete_alias(self, alias):
+ self._db_alias = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmUsed(object):
+
+ vtType = 'opm_used'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmUsed.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmUsed()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmUsed()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmArtifactIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmArtifactIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBPluginData(object):
+
+ vtType = 'plugin_data'
+
+ def __init__(self, id=None, data=None):
+ self._db_id = id
+ self._db_data = data
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPluginData.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPluginData(id=self._db_id,
+ data=self._db_data)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPluginData()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ new_obj.db_data = old_obj.db_data
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ self._db_data = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self.db_deleted_parameters = []
+ self.db_parameters_id_index = {}
+ if parameters is None:
+ self._db_parameters = []
+ else:
+ self._db_parameters = parameters
+ for v in self._db_parameters:
+ self.db_parameters_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name)
+ if self._db_parameters is None:
+ cp._db_parameters = []
+ else:
+ cp._db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_parameters_id_index = dict((v.db_id, v) for v in cp._db_parameters)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBFunction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'parameters' in class_dict:
+ res = class_dict['parameters'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_parameter(obj)
+ elif hasattr(old_obj, 'db_parameters') and old_obj.db_parameters is not None:
+ for obj in old_obj.db_parameters:
+ new_obj.db_add_parameter(DBParameter.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_parameters') and hasattr(new_obj, 'db_deleted_parameters'):
+ for obj in old_obj.db_deleted_parameters:
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_parameters.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_parameters)
+ if remove:
+ self.db_deleted_parameters = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_parameters(self):
+ return self._db_parameters
+ def __set_db_parameters(self, parameters):
+ self._db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self._db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ self._db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ if not self._db_parameters[i].is_new:
+ self.db_deleted_parameters.append(self._db_parameters[i])
+ del self._db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter.db_id]
+ def db_get_parameter(self, key):
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == key:
+ return self._db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return key in self.db_parameters_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, internal_version=None, tag=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_internal_version = internal_version
+ self._db_tag = tag
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ internal_version=self._db_internal_version,
+ tag=self._db_tag)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAbstraction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'internal_version' in class_dict:
+ res = class_dict['internal_version'](old_obj, trans_dict)
+ new_obj.db_internal_version = res
+ elif hasattr(old_obj, 'db_internal_version') and old_obj.db_internal_version is not None:
+ new_obj.db_internal_version = old_obj.db_internal_version
+ if 'tag' in class_dict:
+ res = class_dict['tag'](old_obj, trans_dict)
+ new_obj.db_tag = res
+ elif hasattr(old_obj, 'db_tag') and old_obj.db_tag is not None:
+ new_obj.db_tag = old_obj.db_tag
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_internal_version(self):
+ return self._db_internal_version
+ def __set_db_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ self.is_dirty = True
+ db_internal_version = property(__get_db_internal_version, __set_db_internal_version)
+ def db_add_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_change_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_delete_internal_version(self, internal_version):
+ self._db_internal_version = None
+
+ def __get_db_tag(self):
+ return self._db_tag
+ def __set_db_tag(self, tag):
+ self._db_tag = tag
+ self.is_dirty = True
+ db_tag = property(__get_db_tag, __set_db_tag)
+ def db_add_tag(self, tag):
+ self._db_tag = tag
+ def db_change_tag(self, tag):
+ self._db_tag = tag
+ def db_delete_tag(self, tag):
+ self._db_tag = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, modules=None, id=None, entity_type=None, name=None, version=None, last_modified=None, connections=None, annotations=None, plugin_datas=None, others=None, vistrail_id=None):
+ self.db_deleted_modules = []
+ self.db_modules_id_index = {}
+ if modules is None:
+ self._db_modules = []
+ else:
+ self._db_modules = modules
+ for v in self._db_modules:
+ self.db_modules_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_name = name
+ self._db_version = version
+ self._db_last_modified = last_modified
+ self.db_deleted_connections = []
+ self.db_connections_id_index = {}
+ if connections is None:
+ self._db_connections = []
+ else:
+ self._db_connections = connections
+ for v in self._db_connections:
+ self.db_connections_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_plugin_datas = []
+ self.db_plugin_datas_id_index = {}
+ if plugin_datas is None:
+ self._db_plugin_datas = []
+ else:
+ self._db_plugin_datas = plugin_datas
+ for v in self._db_plugin_datas:
+ self.db_plugin_datas_id_index[v.db_id] = v
+ self.db_deleted_others = []
+ self.db_others_id_index = {}
+ if others is None:
+ self._db_others = []
+ else:
+ self._db_others = others
+ for v in self._db_others:
+ self.db_others_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow(id=self._db_id,
+ entity_type=self._db_entity_type,
+ name=self._db_name,
+ version=self._db_version,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_modules is None:
+ cp._db_modules = []
+ else:
+ cp._db_modules = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_modules]
+ if self._db_connections is None:
+ cp._db_connections = []
+ else:
+ cp._db_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_connections]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_plugin_datas is None:
+ cp._db_plugin_datas = []
+ else:
+ cp._db_plugin_datas = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_plugin_datas]
+ if self._db_others is None:
+ cp._db_others = []
+ else:
+ cp._db_others = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_others]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_modules_id_index = dict((v.db_id, v) for v in cp._db_modules)
+ cp.db_connections_id_index = dict((v.db_id, v) for v in cp._db_connections)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_plugin_datas_id_index = dict((v.db_id, v) for v in cp._db_plugin_datas)
+ cp.db_others_id_index = dict((v.db_id, v) for v in cp._db_others)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'modules' in class_dict:
+ res = class_dict['modules'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module(obj)
+ elif hasattr(old_obj, 'db_modules') and old_obj.db_modules is not None:
+ for obj in old_obj.db_modules:
+ if obj.vtType == 'module':
+ new_obj.db_add_module(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_module(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_module(DBGroup.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_modules') and hasattr(new_obj, 'db_deleted_modules'):
+ for obj in old_obj.db_deleted_modules:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'connections' in class_dict:
+ res = class_dict['connections'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_connection(obj)
+ elif hasattr(old_obj, 'db_connections') and old_obj.db_connections is not None:
+ for obj in old_obj.db_connections:
+ new_obj.db_add_connection(DBConnection.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_connections') and hasattr(new_obj, 'db_deleted_connections'):
+ for obj in old_obj.db_deleted_connections:
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_connections.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'plugin_datas' in class_dict:
+ res = class_dict['plugin_datas'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_plugin_data(obj)
+ elif hasattr(old_obj, 'db_plugin_datas') and old_obj.db_plugin_datas is not None:
+ for obj in old_obj.db_plugin_datas:
+ new_obj.db_add_plugin_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_plugin_datas') and hasattr(new_obj, 'db_deleted_plugin_datas'):
+ for obj in old_obj.db_deleted_plugin_datas:
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_plugin_datas.append(n_obj)
+ if 'others' in class_dict:
+ res = class_dict['others'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_other(obj)
+ elif hasattr(old_obj, 'db_others') and old_obj.db_others is not None:
+ for obj in old_obj.db_others:
+ new_obj.db_add_other(DBOther.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_others') and hasattr(new_obj, 'db_deleted_others'):
+ for obj in old_obj.db_deleted_others:
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_others.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_connections:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_connection(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_plugin_datas:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_plugin_data(child)
+ to_del = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_other(child)
+ to_del = []
+ for child in self.db_modules:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_connections)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_plugin_datas)
+ children.extend(self.db_deleted_others)
+ children.extend(self.db_deleted_modules)
+ if remove:
+ self.db_deleted_connections = []
+ self.db_deleted_annotations = []
+ self.db_deleted_plugin_datas = []
+ self.db_deleted_others = []
+ self.db_deleted_modules = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_connections:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_plugin_datas:
+ if child.has_changes():
+ return True
+ for child in self._db_others:
+ if child.has_changes():
+ return True
+ for child in self._db_modules:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_modules(self):
+ return self._db_modules
+ def __set_db_modules(self, modules):
+ self._db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self._db_modules
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ self._db_modules[i] = module
+ found = True
+ break
+ if not found:
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ if not self._db_modules[i].is_new:
+ self.db_deleted_modules.append(self._db_modules[i])
+ del self._db_modules[i]
+ break
+ del self.db_modules_id_index[module.db_id]
+ def db_get_module(self, key):
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == key:
+ return self._db_modules[i]
+ return None
+ def db_get_module_by_id(self, key):
+ return self.db_modules_id_index[key]
+ def db_has_module_with_id(self, key):
+ return key in self.db_modules_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_connections(self):
+ return self._db_connections
+ def __set_db_connections(self, connections):
+ self._db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self._db_connections
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ self._db_connections[i] = connection
+ found = True
+ break
+ if not found:
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ if not self._db_connections[i].is_new:
+ self.db_deleted_connections.append(self._db_connections[i])
+ del self._db_connections[i]
+ break
+ del self.db_connections_id_index[connection.db_id]
+ def db_get_connection(self, key):
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == key:
+ return self._db_connections[i]
+ return None
+ def db_get_connection_by_id(self, key):
+ return self.db_connections_id_index[key]
+ def db_has_connection_with_id(self, key):
+ return key in self.db_connections_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_plugin_datas(self):
+ return self._db_plugin_datas
+ def __set_db_plugin_datas(self, plugin_datas):
+ self._db_plugin_datas = plugin_datas
+ self.is_dirty = True
+ db_plugin_datas = property(__get_db_plugin_datas, __set_db_plugin_datas)
+ def db_get_plugin_datas(self):
+ return self._db_plugin_datas
+ def db_add_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_change_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ self._db_plugin_datas[i] = plugin_data
+ found = True
+ break
+ if not found:
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_delete_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ if not self._db_plugin_datas[i].is_new:
+ self.db_deleted_plugin_datas.append(self._db_plugin_datas[i])
+ del self._db_plugin_datas[i]
+ break
+ del self.db_plugin_datas_id_index[plugin_data.db_id]
+ def db_get_plugin_data(self, key):
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == key:
+ return self._db_plugin_datas[i]
+ return None
+ def db_get_plugin_data_by_id(self, key):
+ return self.db_plugin_datas_id_index[key]
+ def db_has_plugin_data_with_id(self, key):
+ return key in self.db_plugin_datas_id_index
+
+ def __get_db_others(self):
+ return self._db_others
+ def __set_db_others(self, others):
+ self._db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self._db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ self._db_others[i] = other
+ found = True
+ break
+ if not found:
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ if not self._db_others[i].is_new:
+ self.db_deleted_others.append(self._db_others[i])
+ del self._db_others[i]
+ break
+ del self.db_others_id_index[other.db_id]
+ def db_get_other(self, key):
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == key:
+ return self._db_others[i]
+ return None
+ def db_get_other_by_id(self, key):
+ return self.db_others_id_index[key]
+ def db_has_other_with_id(self, key):
+ return key in self.db_others_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmArtifactIdCause(object):
+
+ vtType = 'opm_artifact_id_cause'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactIdCause.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactIdCause(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_artifact', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_artifact', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactIdCause()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBOpmArtifactValue(object):
+
+ vtType = 'opm_artifact_value'
+
+ def __init__(self, value=None):
+ self.db_deleted_value = []
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactValue.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactValue()
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactValue()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ if obj.vtType == 'portSpec':
+ new_obj.db_add_value(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_value(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ if obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ if remove:
+ self.db_deleted_value = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+
+
+class DBOpmArtifactIdEffect(object):
+
+ vtType = 'opm_artifact_id_effect'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactIdEffect.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactIdEffect(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_artifact', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_artifact', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactIdEffect()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBOpmGraph(object):
+
+ vtType = 'opm_graph'
+
+ def __init__(self, accounts=None, processes=None, artifacts=None, agents=None, dependencies=None):
+ self.db_deleted_accounts = []
+ self._db_accounts = accounts
+ self.db_deleted_processes = []
+ self._db_processes = processes
+ self.db_deleted_artifacts = []
+ self._db_artifacts = artifacts
+ self.db_deleted_agents = []
+ self._db_agents = agents
+ self.db_deleted_dependencies = []
+ self._db_dependencies = dependencies
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmGraph.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmGraph()
+ if self._db_accounts is not None:
+ cp._db_accounts = self._db_accounts.do_copy(new_ids, id_scope, id_remap)
+ if self._db_processes is not None:
+ cp._db_processes = self._db_processes.do_copy(new_ids, id_scope, id_remap)
+ if self._db_artifacts is not None:
+ cp._db_artifacts = self._db_artifacts.do_copy(new_ids, id_scope, id_remap)
+ if self._db_agents is not None:
+ cp._db_agents = self._db_agents.do_copy(new_ids, id_scope, id_remap)
+ if self._db_dependencies is not None:
+ cp._db_dependencies = self._db_dependencies.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmGraph()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ new_obj.db_accounts = res
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ obj = old_obj.db_accounts
+ new_obj.db_add_accounts(DBOpmAccounts.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccounts.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'processes' in class_dict:
+ res = class_dict['processes'](old_obj, trans_dict)
+ new_obj.db_processes = res
+ elif hasattr(old_obj, 'db_processes') and old_obj.db_processes is not None:
+ obj = old_obj.db_processes
+ new_obj.db_add_processes(DBOpmProcesses.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_processes') and hasattr(new_obj, 'db_deleted_processes'):
+ for obj in old_obj.db_deleted_processes:
+ n_obj = DBOpmProcesses.update_version(obj, trans_dict)
+ new_obj.db_deleted_processes.append(n_obj)
+ if 'artifacts' in class_dict:
+ res = class_dict['artifacts'](old_obj, trans_dict)
+ new_obj.db_artifacts = res
+ elif hasattr(old_obj, 'db_artifacts') and old_obj.db_artifacts is not None:
+ obj = old_obj.db_artifacts
+ new_obj.db_add_artifacts(DBOpmArtifacts.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_artifacts') and hasattr(new_obj, 'db_deleted_artifacts'):
+ for obj in old_obj.db_deleted_artifacts:
+ n_obj = DBOpmArtifacts.update_version(obj, trans_dict)
+ new_obj.db_deleted_artifacts.append(n_obj)
+ if 'agents' in class_dict:
+ res = class_dict['agents'](old_obj, trans_dict)
+ new_obj.db_agents = res
+ elif hasattr(old_obj, 'db_agents') and old_obj.db_agents is not None:
+ obj = old_obj.db_agents
+ new_obj.db_add_agents(DBOpmAgents.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_agents') and hasattr(new_obj, 'db_deleted_agents'):
+ for obj in old_obj.db_deleted_agents:
+ n_obj = DBOpmAgents.update_version(obj, trans_dict)
+ new_obj.db_deleted_agents.append(n_obj)
+ if 'dependencies' in class_dict:
+ res = class_dict['dependencies'](old_obj, trans_dict)
+ new_obj.db_dependencies = res
+ elif hasattr(old_obj, 'db_dependencies') and old_obj.db_dependencies is not None:
+ obj = old_obj.db_dependencies
+ new_obj.db_add_dependencies(DBOpmDependencies.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_dependencies') and hasattr(new_obj, 'db_deleted_dependencies'):
+ for obj in old_obj.db_deleted_dependencies:
+ n_obj = DBOpmDependencies.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencies.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_accounts is not None:
+ children.extend(self._db_accounts.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_accounts = None
+ if self._db_processes is not None:
+ children.extend(self._db_processes.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_processes = None
+ if self._db_artifacts is not None:
+ children.extend(self._db_artifacts.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_artifacts = None
+ if self._db_agents is not None:
+ children.extend(self._db_agents.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_agents = None
+ if self._db_dependencies is not None:
+ children.extend(self._db_dependencies.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_dependencies = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_processes)
+ children.extend(self.db_deleted_artifacts)
+ children.extend(self.db_deleted_agents)
+ children.extend(self.db_deleted_dependencies)
+ if remove:
+ self.db_deleted_accounts = []
+ self.db_deleted_processes = []
+ self.db_deleted_artifacts = []
+ self.db_deleted_agents = []
+ self.db_deleted_dependencies = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_accounts is not None and self._db_accounts.has_changes():
+ return True
+ if self._db_processes is not None and self._db_processes.has_changes():
+ return True
+ if self._db_artifacts is not None and self._db_artifacts.has_changes():
+ return True
+ if self._db_agents is not None and self._db_agents.has_changes():
+ return True
+ if self._db_dependencies is not None and self._db_dependencies.has_changes():
+ return True
+ return False
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_add_accounts(self, accounts):
+ self._db_accounts = accounts
+ def db_change_accounts(self, accounts):
+ self._db_accounts = accounts
+ def db_delete_accounts(self, accounts):
+ if not self.is_new:
+ self.db_deleted_accounts.append(self._db_accounts)
+ self._db_accounts = None
+
+ def __get_db_processes(self):
+ return self._db_processes
+ def __set_db_processes(self, processes):
+ self._db_processes = processes
+ self.is_dirty = True
+ db_processes = property(__get_db_processes, __set_db_processes)
+ def db_add_processes(self, processes):
+ self._db_processes = processes
+ def db_change_processes(self, processes):
+ self._db_processes = processes
+ def db_delete_processes(self, processes):
+ if not self.is_new:
+ self.db_deleted_processes.append(self._db_processes)
+ self._db_processes = None
+
+ def __get_db_artifacts(self):
+ return self._db_artifacts
+ def __set_db_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ self.is_dirty = True
+ db_artifacts = property(__get_db_artifacts, __set_db_artifacts)
+ def db_add_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ def db_change_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ def db_delete_artifacts(self, artifacts):
+ if not self.is_new:
+ self.db_deleted_artifacts.append(self._db_artifacts)
+ self._db_artifacts = None
+
+ def __get_db_agents(self):
+ return self._db_agents
+ def __set_db_agents(self, agents):
+ self._db_agents = agents
+ self.is_dirty = True
+ db_agents = property(__get_db_agents, __set_db_agents)
+ def db_add_agents(self, agents):
+ self._db_agents = agents
+ def db_change_agents(self, agents):
+ self._db_agents = agents
+ def db_delete_agents(self, agents):
+ if not self.is_new:
+ self.db_deleted_agents.append(self._db_agents)
+ self._db_agents = None
+
+ def __get_db_dependencies(self):
+ return self._db_dependencies
+ def __set_db_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ self.is_dirty = True
+ db_dependencies = property(__get_db_dependencies, __set_db_dependencies)
+ def db_add_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ def db_change_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ def db_delete_dependencies(self, dependencies):
+ if not self.is_new:
+ self.db_deleted_dependencies.append(self._db_dependencies)
+ self._db_dependencies = None
+
+
+
+class DBRegistry(object):
+
+ vtType = 'registry'
+
+ def __init__(self, id=None, entity_type=None, version=None, root_descriptor_id=None, name=None, last_modified=None, packages=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_root_descriptor_id = root_descriptor_id
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_packages = []
+ self.db_packages_id_index = {}
+ self.db_packages_identifier_index = {}
+ if packages is None:
+ self._db_packages = []
+ else:
+ self._db_packages = packages
+ for v in self._db_packages:
+ self.db_packages_id_index[v.db_id] = v
+ self.db_packages_identifier_index[(v.db_identifier,v.db_version)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBRegistry.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBRegistry(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ root_descriptor_id=self._db_root_descriptor_id,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_packages is None:
+ cp._db_packages = []
+ else:
+ cp._db_packages = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_packages]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_root_descriptor_id') and ('module_descriptor', self._db_root_descriptor_id) in id_remap:
+ cp._db_root_descriptor_id = id_remap[('module_descriptor', self._db_root_descriptor_id)]
+
+ # recreate indices and set flags
+ cp.db_packages_id_index = dict((v.db_id, v) for v in cp._db_packages)
+ cp.db_packages_identifier_index = dict(((v.db_identifier,v.db_version), v) for v in cp._db_packages)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRegistry()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'root_descriptor_id' in class_dict:
+ res = class_dict['root_descriptor_id'](old_obj, trans_dict)
+ new_obj.db_root_descriptor_id = res
+ elif hasattr(old_obj, 'db_root_descriptor_id') and old_obj.db_root_descriptor_id is not None:
+ new_obj.db_root_descriptor_id = old_obj.db_root_descriptor_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'packages' in class_dict:
+ res = class_dict['packages'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_package(obj)
+ elif hasattr(old_obj, 'db_packages') and old_obj.db_packages is not None:
+ for obj in old_obj.db_packages:
+ new_obj.db_add_package(DBPackage.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_packages') and hasattr(new_obj, 'db_deleted_packages'):
+ for obj in old_obj.db_deleted_packages:
+ n_obj = DBPackage.update_version(obj, trans_dict)
+ new_obj.db_deleted_packages.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_packages:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_package(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_packages)
+ if remove:
+ self.db_deleted_packages = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_packages:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_root_descriptor_id(self):
+ return self._db_root_descriptor_id
+ def __set_db_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ self.is_dirty = True
+ db_root_descriptor_id = property(__get_db_root_descriptor_id, __set_db_root_descriptor_id)
+ def db_add_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ def db_change_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ def db_delete_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_packages(self):
+ return self._db_packages
+ def __set_db_packages(self, packages):
+ self._db_packages = packages
+ self.is_dirty = True
+ db_packages = property(__get_db_packages, __set_db_packages)
+ def db_get_packages(self):
+ return self._db_packages
+ def db_add_package(self, package):
+ self.is_dirty = True
+ self._db_packages.append(package)
+ self.db_packages_id_index[package.db_id] = package
+ self.db_packages_identifier_index[(package.db_identifier,package.db_version)] = package
+ def db_change_package(self, package):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == package.db_id:
+ self._db_packages[i] = package
+ found = True
+ break
+ if not found:
+ self._db_packages.append(package)
+ self.db_packages_id_index[package.db_id] = package
+ self.db_packages_identifier_index[(package.db_identifier,package.db_version)] = package
+ def db_delete_package(self, package):
+ self.is_dirty = True
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == package.db_id:
+ if not self._db_packages[i].is_new:
+ self.db_deleted_packages.append(self._db_packages[i])
+ del self._db_packages[i]
+ break
+ del self.db_packages_id_index[package.db_id]
+ del self.db_packages_identifier_index[(package.db_identifier,package.db_version)]
+ def db_get_package(self, key):
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == key:
+ return self._db_packages[i]
+ return None
+ def db_get_package_by_id(self, key):
+ return self.db_packages_id_index[key]
+ def db_has_package_with_id(self, key):
+ return key in self.db_packages_id_index
+ def db_get_package_by_identifier(self, key):
+ return self.db_packages_identifier_index[key]
+ def db_has_package_with_identifier(self, key):
+ return key in self.db_packages_identifier_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmAccount(object):
+
+ vtType = 'opm_account'
+
+ def __init__(self, id=None, value=None):
+ self._db_id = id
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccount.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccount(id=self._db_id,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccount()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAnnotation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, data=None, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_oldObjId = oldObjId
+ self._db_newObjId = newObjId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBChange.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange(id=self._db_id,
+ what=self._db_what,
+ oldObjId=self._db_oldObjId,
+ newObjId=self._db_newObjId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_oldObjId') and (self._db_what, self._db_oldObjId) in id_remap:
+ cp._db_oldObjId = id_remap[(self._db_what, self._db_oldObjId)]
+ if hasattr(self, 'db_newObjId') and (self._db_what, self._db_newObjId) in id_remap:
+ cp._db_newObjId = id_remap[(self._db_what, self._db_newObjId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBChange()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'oldObjId' in class_dict:
+ res = class_dict['oldObjId'](old_obj, trans_dict)
+ new_obj.db_oldObjId = res
+ elif hasattr(old_obj, 'db_oldObjId') and old_obj.db_oldObjId is not None:
+ new_obj.db_oldObjId = old_obj.db_oldObjId
+ if 'newObjId' in class_dict:
+ res = class_dict['newObjId'](old_obj, trans_dict)
+ new_obj.db_newObjId = res
+ elif hasattr(old_obj, 'db_newObjId') and old_obj.db_newObjId is not None:
+ new_obj.db_newObjId = old_obj.db_newObjId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_oldObjId(self):
+ return self._db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self._db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self._db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self._db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmWasDerivedFrom(object):
+
+ vtType = 'opm_was_derived_from'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasDerivedFrom.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasDerivedFrom()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasDerivedFrom()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmArtifactIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmArtifactIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmArtifactIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmArtifactIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBOpmWasControlledBy(object):
+
+ vtType = 'opm_was_controlled_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, starts=None, ends=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_starts = []
+ if starts is None:
+ self._db_starts = []
+ else:
+ self._db_starts = starts
+ self.db_deleted_ends = []
+ if ends is None:
+ self._db_ends = []
+ else:
+ self._db_ends = ends
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasControlledBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasControlledBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_starts is None:
+ cp._db_starts = []
+ else:
+ cp._db_starts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_starts]
+ if self._db_ends is None:
+ cp._db_ends = []
+ else:
+ cp._db_ends = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ends]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasControlledBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmAgentId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmAgentId.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'starts' in class_dict:
+ res = class_dict['starts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_start(obj)
+ elif hasattr(old_obj, 'db_starts') and old_obj.db_starts is not None:
+ for obj in old_obj.db_starts:
+ new_obj.db_add_start(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_starts') and hasattr(new_obj, 'db_deleted_starts'):
+ for obj in old_obj.db_deleted_starts:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_starts.append(n_obj)
+ if 'ends' in class_dict:
+ res = class_dict['ends'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_end(obj)
+ elif hasattr(old_obj, 'db_ends') and old_obj.db_ends is not None:
+ for obj in old_obj.db_ends:
+ new_obj.db_add_end(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_ends') and hasattr(new_obj, 'db_deleted_ends'):
+ for obj in old_obj.db_deleted_ends:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_ends.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_starts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_start(child)
+ to_del = []
+ for child in self.db_ends:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_end(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_starts)
+ children.extend(self.db_deleted_ends)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_starts = []
+ self.db_deleted_ends = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_starts:
+ if child.has_changes():
+ return True
+ for child in self._db_ends:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_starts(self):
+ return self._db_starts
+ def __set_db_starts(self, starts):
+ self._db_starts = starts
+ self.is_dirty = True
+ db_starts = property(__get_db_starts, __set_db_starts)
+ def db_get_starts(self):
+ return self._db_starts
+ def db_add_start(self, start):
+ self.is_dirty = True
+ self._db_starts.append(start)
+ def db_change_start(self, start):
+ self.is_dirty = True
+ self._db_starts.append(start)
+ def db_delete_start(self, start):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_start(self, key):
+ return None
+
+ def __get_db_ends(self):
+ return self._db_ends
+ def __set_db_ends(self, ends):
+ self._db_ends = ends
+ self.is_dirty = True
+ db_ends = property(__get_db_ends, __set_db_ends)
+ def db_get_ends(self):
+ return self._db_ends
+ def db_add_end(self, end):
+ self.is_dirty = True
+ self._db_ends.append(end)
+ def db_change_end(self, end):
+ self.is_dirty = True
+ self._db_ends.append(end)
+ def db_delete_end(self, end):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_end(self, key):
+ return None
+
+
+
+class DBOpmAgentId(object):
+
+ vtType = 'opm_agent_id'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgentId.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgentId(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_agent', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_agent', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgentId()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBGroupExec(object):
+
+ vtType = 'group_exec'
+
+ def __init__(self, item_execs=None, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, group_name=None, group_type=None, completed=None, error=None, machine_id=None, annotations=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_group_name = group_name
+ self._db_group_type = group_type
+ self._db_completed = completed
+ self._db_error = error
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroupExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroupExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ group_name=self._db_group_name,
+ group_type=self._db_group_type,
+ completed=self._db_completed,
+ error=self._db_error,
+ machine_id=self._db_machine_id)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroupExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'group_name' in class_dict:
+ res = class_dict['group_name'](old_obj, trans_dict)
+ new_obj.db_group_name = res
+ elif hasattr(old_obj, 'db_group_name') and old_obj.db_group_name is not None:
+ new_obj.db_group_name = old_obj.db_group_name
+ if 'group_type' in class_dict:
+ res = class_dict['group_type'](old_obj, trans_dict)
+ new_obj.db_group_type = res
+ elif hasattr(old_obj, 'db_group_type') and old_obj.db_group_type is not None:
+ new_obj.db_group_type = old_obj.db_group_type
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_group_name(self):
+ return self._db_group_name
+ def __set_db_group_name(self, group_name):
+ self._db_group_name = group_name
+ self.is_dirty = True
+ db_group_name = property(__get_db_group_name, __set_db_group_name)
+ def db_add_group_name(self, group_name):
+ self._db_group_name = group_name
+ def db_change_group_name(self, group_name):
+ self._db_group_name = group_name
+ def db_delete_group_name(self, group_name):
+ self._db_group_name = None
+
+ def __get_db_group_type(self):
+ return self._db_group_type
+ def __set_db_group_type(self, group_type):
+ self._db_group_type = group_type
+ self.is_dirty = True
+ db_group_type = property(__get_db_group_type, __set_db_group_type)
+ def db_add_group_type(self, group_type):
+ self._db_group_type = group_type
+ def db_change_group_type(self, group_type):
+ self._db_group_type = group_type
+ def db_delete_group_type(self, group_type):
+ self._db_group_type = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmTime(object):
+
+ vtType = 'opm_time'
+
+ def __init__(self, no_later_than=None, no_earlier_than=None, clock_id=None):
+ self._db_no_later_than = no_later_than
+ self._db_no_earlier_than = no_earlier_than
+ self._db_clock_id = clock_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmTime.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmTime(no_later_than=self._db_no_later_than,
+ no_earlier_than=self._db_no_earlier_than,
+ clock_id=self._db_clock_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmTime()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'no_later_than' in class_dict:
+ res = class_dict['no_later_than'](old_obj, trans_dict)
+ new_obj.db_no_later_than = res
+ elif hasattr(old_obj, 'db_no_later_than') and old_obj.db_no_later_than is not None:
+ new_obj.db_no_later_than = old_obj.db_no_later_than
+ if 'no_earlier_than' in class_dict:
+ res = class_dict['no_earlier_than'](old_obj, trans_dict)
+ new_obj.db_no_earlier_than = res
+ elif hasattr(old_obj, 'db_no_earlier_than') and old_obj.db_no_earlier_than is not None:
+ new_obj.db_no_earlier_than = old_obj.db_no_earlier_than
+ if 'clock_id' in class_dict:
+ res = class_dict['clock_id'](old_obj, trans_dict)
+ new_obj.db_clock_id = res
+ elif hasattr(old_obj, 'db_clock_id') and old_obj.db_clock_id is not None:
+ new_obj.db_clock_id = old_obj.db_clock_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_no_later_than(self):
+ return self._db_no_later_than
+ def __set_db_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ self.is_dirty = True
+ db_no_later_than = property(__get_db_no_later_than, __set_db_no_later_than)
+ def db_add_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ def db_change_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ def db_delete_no_later_than(self, no_later_than):
+ self._db_no_later_than = None
+
+ def __get_db_no_earlier_than(self):
+ return self._db_no_earlier_than
+ def __set_db_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ self.is_dirty = True
+ db_no_earlier_than = property(__get_db_no_earlier_than, __set_db_no_earlier_than)
+ def db_add_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ def db_change_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ def db_delete_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = None
+
+ def __get_db_clock_id(self):
+ return self._db_clock_id
+ def __set_db_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ self.is_dirty = True
+ db_clock_id = property(__get_db_clock_id, __set_db_clock_id)
+ def db_add_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ def db_change_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ def db_delete_clock_id(self, clock_id):
+ self._db_clock_id = None
+
+
+
+class DBPackage(object):
+
+ vtType = 'package'
+
+ def __init__(self, id=None, name=None, identifier=None, codepath=None, load_configuration=None, version=None, description=None, module_descriptors=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_identifier = identifier
+ self._db_codepath = codepath
+ self._db_load_configuration = load_configuration
+ self._db_version = version
+ self._db_description = description
+ self.db_deleted_module_descriptors = []
+ self.db_module_descriptors_id_index = {}
+ self.db_module_descriptors_name_index = {}
+ if module_descriptors is None:
+ self._db_module_descriptors = []
+ else:
+ self._db_module_descriptors = module_descriptors
+ for v in self._db_module_descriptors:
+ self.db_module_descriptors_id_index[v.db_id] = v
+ self.db_module_descriptors_name_index[(v.db_name,v.db_namespace,v.db_version)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPackage.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPackage(id=self._db_id,
+ name=self._db_name,
+ identifier=self._db_identifier,
+ codepath=self._db_codepath,
+ load_configuration=self._db_load_configuration,
+ version=self._db_version,
+ description=self._db_description)
+ if self._db_module_descriptors is None:
+ cp._db_module_descriptors = []
+ else:
+ cp._db_module_descriptors = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_module_descriptors]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_module_descriptors_id_index = dict((v.db_id, v) for v in cp._db_module_descriptors)
+ cp.db_module_descriptors_name_index = dict(((v.db_name,v.db_namespace,v.db_version), v) for v in cp._db_module_descriptors)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPackage()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'identifier' in class_dict:
+ res = class_dict['identifier'](old_obj, trans_dict)
+ new_obj.db_identifier = res
+ elif hasattr(old_obj, 'db_identifier') and old_obj.db_identifier is not None:
+ new_obj.db_identifier = old_obj.db_identifier
+ if 'codepath' in class_dict:
+ res = class_dict['codepath'](old_obj, trans_dict)
+ new_obj.db_codepath = res
+ elif hasattr(old_obj, 'db_codepath') and old_obj.db_codepath is not None:
+ new_obj.db_codepath = old_obj.db_codepath
+ if 'load_configuration' in class_dict:
+ res = class_dict['load_configuration'](old_obj, trans_dict)
+ new_obj.db_load_configuration = res
+ elif hasattr(old_obj, 'db_load_configuration') and old_obj.db_load_configuration is not None:
+ new_obj.db_load_configuration = old_obj.db_load_configuration
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'description' in class_dict:
+ res = class_dict['description'](old_obj, trans_dict)
+ new_obj.db_description = res
+ elif hasattr(old_obj, 'db_description') and old_obj.db_description is not None:
+ new_obj.db_description = old_obj.db_description
+ if 'module_descriptors' in class_dict:
+ res = class_dict['module_descriptors'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module_descriptor(obj)
+ elif hasattr(old_obj, 'db_module_descriptors') and old_obj.db_module_descriptors is not None:
+ for obj in old_obj.db_module_descriptors:
+ new_obj.db_add_module_descriptor(DBModuleDescriptor.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_module_descriptors') and hasattr(new_obj, 'db_deleted_module_descriptors'):
+ for obj in old_obj.db_deleted_module_descriptors:
+ n_obj = DBModuleDescriptor.update_version(obj, trans_dict)
+ new_obj.db_deleted_module_descriptors.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_descriptors:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_descriptor(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_descriptors)
+ if remove:
+ self.db_deleted_module_descriptors = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_module_descriptors:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_identifier(self):
+ return self._db_identifier
+ def __set_db_identifier(self, identifier):
+ self._db_identifier = identifier
+ self.is_dirty = True
+ db_identifier = property(__get_db_identifier, __set_db_identifier)
+ def db_add_identifier(self, identifier):
+ self._db_identifier = identifier
+ def db_change_identifier(self, identifier):
+ self._db_identifier = identifier
+ def db_delete_identifier(self, identifier):
+ self._db_identifier = None
+
+ def __get_db_codepath(self):
+ return self._db_codepath
+ def __set_db_codepath(self, codepath):
+ self._db_codepath = codepath
+ self.is_dirty = True
+ db_codepath = property(__get_db_codepath, __set_db_codepath)
+ def db_add_codepath(self, codepath):
+ self._db_codepath = codepath
+ def db_change_codepath(self, codepath):
+ self._db_codepath = codepath
+ def db_delete_codepath(self, codepath):
+ self._db_codepath = None
+
+ def __get_db_load_configuration(self):
+ return self._db_load_configuration
+ def __set_db_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ self.is_dirty = True
+ db_load_configuration = property(__get_db_load_configuration, __set_db_load_configuration)
+ def db_add_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ def db_change_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ def db_delete_load_configuration(self, load_configuration):
+ self._db_load_configuration = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_description(self):
+ return self._db_description
+ def __set_db_description(self, description):
+ self._db_description = description
+ self.is_dirty = True
+ db_description = property(__get_db_description, __set_db_description)
+ def db_add_description(self, description):
+ self._db_description = description
+ def db_change_description(self, description):
+ self._db_description = description
+ def db_delete_description(self, description):
+ self._db_description = None
+
+ def __get_db_module_descriptors(self):
+ return self._db_module_descriptors
+ def __set_db_module_descriptors(self, module_descriptors):
+ self._db_module_descriptors = module_descriptors
+ self.is_dirty = True
+ db_module_descriptors = property(__get_db_module_descriptors, __set_db_module_descriptors)
+ def db_get_module_descriptors(self):
+ return self._db_module_descriptors
+ def db_add_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ self._db_module_descriptors.append(module_descriptor)
+ self.db_module_descriptors_id_index[module_descriptor.db_id] = module_descriptor
+ self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)] = module_descriptor
+ def db_change_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == module_descriptor.db_id:
+ self._db_module_descriptors[i] = module_descriptor
+ found = True
+ break
+ if not found:
+ self._db_module_descriptors.append(module_descriptor)
+ self.db_module_descriptors_id_index[module_descriptor.db_id] = module_descriptor
+ self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)] = module_descriptor
+ def db_delete_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == module_descriptor.db_id:
+ if not self._db_module_descriptors[i].is_new:
+ self.db_deleted_module_descriptors.append(self._db_module_descriptors[i])
+ del self._db_module_descriptors[i]
+ break
+ del self.db_module_descriptors_id_index[module_descriptor.db_id]
+ del self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)]
+ def db_get_module_descriptor(self, key):
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == key:
+ return self._db_module_descriptors[i]
+ return None
+ def db_get_module_descriptor_by_id(self, key):
+ return self.db_module_descriptors_id_index[key]
+ def db_has_module_descriptor_with_id(self, key):
+ return key in self.db_module_descriptors_id_index
+ def db_get_module_descriptor_by_name(self, key):
+ return self.db_module_descriptors_name_index[key]
+ def db_has_module_descriptor_with_name(self, key):
+ return key in self.db_module_descriptors_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, item_execs=None, id=None, user=None, ip=None, session=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, completed=None, name=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_user = user
+ self._db_ip = ip
+ self._db_session = session
+ self._db_vt_version = vt_version
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_parent_id = parent_id
+ self._db_parent_type = parent_type
+ self._db_parent_version = parent_version
+ self._db_completed = completed
+ self._db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflowExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec(id=self._db_id,
+ user=self._db_user,
+ ip=self._db_ip,
+ session=self._db_session,
+ vt_version=self._db_vt_version,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ parent_id=self._db_parent_id,
+ parent_type=self._db_parent_type,
+ parent_version=self._db_parent_version,
+ completed=self._db_completed,
+ name=self._db_name)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflowExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'ip' in class_dict:
+ res = class_dict['ip'](old_obj, trans_dict)
+ new_obj.db_ip = res
+ elif hasattr(old_obj, 'db_ip') and old_obj.db_ip is not None:
+ new_obj.db_ip = old_obj.db_ip
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'vt_version' in class_dict:
+ res = class_dict['vt_version'](old_obj, trans_dict)
+ new_obj.db_vt_version = res
+ elif hasattr(old_obj, 'db_vt_version') and old_obj.db_vt_version is not None:
+ new_obj.db_vt_version = old_obj.db_vt_version
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'parent_id' in class_dict:
+ res = class_dict['parent_id'](old_obj, trans_dict)
+ new_obj.db_parent_id = res
+ elif hasattr(old_obj, 'db_parent_id') and old_obj.db_parent_id is not None:
+ new_obj.db_parent_id = old_obj.db_parent_id
+ if 'parent_type' in class_dict:
+ res = class_dict['parent_type'](old_obj, trans_dict)
+ new_obj.db_parent_type = res
+ elif hasattr(old_obj, 'db_parent_type') and old_obj.db_parent_type is not None:
+ new_obj.db_parent_type = old_obj.db_parent_type
+ if 'parent_version' in class_dict:
+ res = class_dict['parent_version'](old_obj, trans_dict)
+ new_obj.db_parent_version = res
+ elif hasattr(old_obj, 'db_parent_version') and old_obj.db_parent_version is not None:
+ new_obj.db_parent_version = old_obj.db_parent_version
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_ip(self):
+ return self._db_ip
+ def __set_db_ip(self, ip):
+ self._db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self._db_ip = ip
+ def db_change_ip(self, ip):
+ self._db_ip = ip
+ def db_delete_ip(self, ip):
+ self._db_ip = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_vt_version(self):
+ return self._db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self._db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self._db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self._db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self._db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self._db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self._db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self._db_parent_version = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLoopExec(object):
+
+ vtType = 'loop_exec'
+
+ def __init__(self, item_execs=None, id=None, ts_start=None, ts_end=None, iteration=None, completed=None, error=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_iteration = iteration
+ self._db_completed = completed
+ self._db_error = error
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLoopExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLoopExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ iteration=self._db_iteration,
+ completed=self._db_completed,
+ error=self._db_error)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLoopExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'iteration' in class_dict:
+ res = class_dict['iteration'](old_obj, trans_dict)
+ new_obj.db_iteration = res
+ elif hasattr(old_obj, 'db_iteration') and old_obj.db_iteration is not None:
+ new_obj.db_iteration = old_obj.db_iteration
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_iteration(self):
+ return self._db_iteration
+ def __set_db_iteration(self, iteration):
+ self._db_iteration = iteration
+ self.is_dirty = True
+ db_iteration = property(__get_db_iteration, __set_db_iteration)
+ def db_add_iteration(self, iteration):
+ self._db_iteration = iteration
+ def db_change_iteration(self, iteration):
+ self._db_iteration = iteration
+ def db_delete_iteration(self, iteration):
+ self._db_iteration = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self._db_id = id
+ self.db_deleted_ports = []
+ self.db_ports_id_index = {}
+ self.db_ports_type_index = {}
+ if ports is None:
+ self._db_ports = []
+ else:
+ self._db_ports = ports
+ for v in self._db_ports:
+ self.db_ports_id_index[v.db_id] = v
+ self.db_ports_type_index[v.db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBConnection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection(id=self._db_id)
+ if self._db_ports is None:
+ cp._db_ports = []
+ else:
+ cp._db_ports = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ports]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_ports_id_index = dict((v.db_id, v) for v in cp._db_ports)
+ cp.db_ports_type_index = dict((v.db_type, v) for v in cp._db_ports)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBConnection()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ports' in class_dict:
+ res = class_dict['ports'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_port(obj)
+ elif hasattr(old_obj, 'db_ports') and old_obj.db_ports is not None:
+ for obj in old_obj.db_ports:
+ new_obj.db_add_port(DBPort.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_ports') and hasattr(new_obj, 'db_deleted_ports'):
+ for obj in old_obj.db_deleted_ports:
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_ports.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_ports)
+ if remove:
+ self.db_deleted_ports = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ports(self):
+ return self._db_ports
+ def __set_db_ports(self, ports):
+ self._db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self._db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ self._db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ if not self._db_ports[i].is_new:
+ self.db_deleted_ports.append(self._db_ports[i])
+ del self._db_ports[i]
+ break
+ del self.db_ports_id_index[port.db_id]
+ del self.db_ports_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == key:
+ return self._db_ports[i]
+ return None
+ def db_get_port_by_id(self, key):
+ return self.db_ports_id_index[key]
+ def db_has_port_with_id(self, key):
+ return key in self.db_ports_id_index
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return key in self.db_ports_type_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmProcess(object):
+
+ vtType = 'opm_process'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self.db_deleted_value = []
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcess.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcess(id=self._db_id)
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcess()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ new_obj.db_add_value(DBOpmProcessValue.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ n_obj = DBOpmProcessValue.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_value = []
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmWasTriggeredBy(object):
+
+ vtType = 'opm_was_triggered_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasTriggeredBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasTriggeredBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasTriggeredBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmProcessIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmProcessIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBOpmProcessValue(object):
+
+ vtType = 'opm_process_value'
+
+ def __init__(self, value=None):
+ self.db_deleted_value = []
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessValue.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessValue()
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessValue()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_value(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_value(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_value(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ if remove:
+ self.db_deleted_value = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, operations=None, id=None, prevId=None, date=None, session=None, user=None, prune=None, annotations=None):
+ self.db_deleted_operations = []
+ self.db_operations_id_index = {}
+ if operations is None:
+ self._db_operations = []
+ else:
+ self._db_operations = operations
+ for v in self._db_operations:
+ self.db_operations_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_prevId = prevId
+ self._db_date = date
+ self._db_session = session
+ self._db_user = user
+ self._db_prune = prune
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction(id=self._db_id,
+ prevId=self._db_prevId,
+ date=self._db_date,
+ session=self._db_session,
+ user=self._db_user,
+ prune=self._db_prune)
+ if self._db_operations is None:
+ cp._db_operations = []
+ else:
+ cp._db_operations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_operations]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prevId') and ('action', self._db_prevId) in id_remap:
+ cp._db_prevId = id_remap[('action', self._db_prevId)]
+
+ # recreate indices and set flags
+ cp.db_operations_id_index = dict((v.db_id, v) for v in cp._db_operations)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'operations' in class_dict:
+ res = class_dict['operations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_operation(obj)
+ elif hasattr(old_obj, 'db_operations') and old_obj.db_operations is not None:
+ for obj in old_obj.db_operations:
+ if obj.vtType == 'add':
+ new_obj.db_add_operation(DBAdd.update_version(obj, trans_dict))
+ elif obj.vtType == 'delete':
+ new_obj.db_add_operation(DBDelete.update_version(obj, trans_dict))
+ elif obj.vtType == 'change':
+ new_obj.db_add_operation(DBChange.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_operations') and hasattr(new_obj, 'db_deleted_operations'):
+ for obj in old_obj.db_deleted_operations:
+ if obj.vtType == 'add':
+ n_obj = DBAdd.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'delete':
+ n_obj = DBDelete.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'change':
+ n_obj = DBChange.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'prevId' in class_dict:
+ res = class_dict['prevId'](old_obj, trans_dict)
+ new_obj.db_prevId = res
+ elif hasattr(old_obj, 'db_prevId') and old_obj.db_prevId is not None:
+ new_obj.db_prevId = old_obj.db_prevId
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'prune' in class_dict:
+ res = class_dict['prune'](old_obj, trans_dict)
+ new_obj.db_prune = res
+ elif hasattr(old_obj, 'db_prune') and old_obj.db_prune is not None:
+ new_obj.db_prune = old_obj.db_prune
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_operations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_operations)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_operations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_operations(self):
+ return self._db_operations
+ def __set_db_operations(self, operations):
+ self._db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self._db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ self._db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ if not self._db_operations[i].is_new:
+ self.db_deleted_operations.append(self._db_operations[i])
+ del self._db_operations[i]
+ break
+ del self.db_operations_id_index[operation.db_id]
+ def db_get_operation(self, key):
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == key:
+ return self._db_operations[i]
+ return None
+ def db_get_operation_by_id(self, key):
+ return self.db_operations_id_index[key]
+ def db_has_operation_with_id(self, key):
+ return key in self.db_operations_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_prevId(self):
+ return self._db_prevId
+ def __set_db_prevId(self, prevId):
+ self._db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self._db_prevId = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_prune(self):
+ return self._db_prune
+ def __set_db_prune(self, prune):
+ self._db_prune = prune
+ self.is_dirty = True
+ db_prune = property(__get_db_prune, __set_db_prune)
+ def db_add_prune(self, prune):
+ self._db_prune = prune
+ def db_change_prune(self, prune):
+ self._db_prune = prune
+ def db_delete_prune(self, prune):
+ self._db_prune = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmAgent(object):
+
+ vtType = 'opm_agent'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgent.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgent(id=self._db_id,
+ value=self._db_value)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgent()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBDelete.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBDelete()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, actions=None, tags=None, annotations=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self._db_actions = []
+ else:
+ self._db_actions = actions
+ for v in self._db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self._db_tags = []
+ else:
+ self._db_tags = tags
+ for v in self._db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_actions is None:
+ cp._db_actions = []
+ else:
+ cp._db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actions]
+ if self._db_tags is None:
+ cp._db_tags = []
+ else:
+ cp._db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_tags]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_actions_id_index = dict((v.db_id, v) for v in cp._db_actions)
+ cp.db_tags_id_index = dict((v.db_id, v) for v in cp._db_tags)
+ cp.db_tags_name_index = dict((v.db_name, v) for v in cp._db_tags)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'actions' in class_dict:
+ res = class_dict['actions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_action(obj)
+ elif hasattr(old_obj, 'db_actions') and old_obj.db_actions is not None:
+ for obj in old_obj.db_actions:
+ new_obj.db_add_action(DBAction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actions') and hasattr(new_obj, 'db_deleted_actions'):
+ for obj in old_obj.db_deleted_actions:
+ n_obj = DBAction.update_version(obj, trans_dict)
+ new_obj.db_deleted_actions.append(n_obj)
+ if 'tags' in class_dict:
+ res = class_dict['tags'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_tag(obj)
+ elif hasattr(old_obj, 'db_tags') and old_obj.db_tags is not None:
+ for obj in old_obj.db_tags:
+ new_obj.db_add_tag(DBTag.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_tags') and hasattr(new_obj, 'db_deleted_tags'):
+ for obj in old_obj.db_deleted_tags:
+ n_obj = DBTag.update_version(obj, trans_dict)
+ new_obj.db_deleted_tags.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_actions:
+ if child.has_changes():
+ return True
+ for child in self._db_tags:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_actions(self):
+ return self._db_actions
+ def __set_db_actions(self, actions):
+ self._db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self._db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ self._db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ if not self._db_actions[i].is_new:
+ self.db_deleted_actions.append(self._db_actions[i])
+ del self._db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == key:
+ return self._db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return key in self.db_actions_id_index
+
+ def __get_db_tags(self):
+ return self._db_tags
+ def __set_db_tags(self, tags):
+ self._db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self._db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ self._db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ if not self._db_tags[i].is_new:
+ self.db_deleted_tags.append(self._db_tags[i])
+ del self._db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == key:
+ return self._db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return key in self.db_tags_id_index
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return key in self.db_tags_name_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, module_name=None, completed=None, error=None, machine_id=None, annotations=None, loop_execs=None):
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_module_name = module_name
+ self._db_completed = completed
+ self._db_error = error
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_loop_execs = []
+ self.db_loop_execs_id_index = {}
+ if loop_execs is None:
+ self._db_loop_execs = []
+ else:
+ self._db_loop_execs = loop_execs
+ for v in self._db_loop_execs:
+ self.db_loop_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ module_name=self._db_module_name,
+ completed=self._db_completed,
+ error=self._db_error,
+ machine_id=self._db_machine_id)
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_loop_execs is None:
+ cp._db_loop_execs = []
+ else:
+ cp._db_loop_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_loop_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_loop_execs_id_index = dict((v.db_id, v) for v in cp._db_loop_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'module_name' in class_dict:
+ res = class_dict['module_name'](old_obj, trans_dict)
+ new_obj.db_module_name = res
+ elif hasattr(old_obj, 'db_module_name') and old_obj.db_module_name is not None:
+ new_obj.db_module_name = old_obj.db_module_name
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'loop_execs' in class_dict:
+ res = class_dict['loop_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_loop_exec(obj)
+ elif hasattr(old_obj, 'db_loop_execs') and old_obj.db_loop_execs is not None:
+ for obj in old_obj.db_loop_execs:
+ new_obj.db_add_loop_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_loop_execs') and hasattr(new_obj, 'db_deleted_loop_execs'):
+ for obj in old_obj.db_deleted_loop_execs:
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_loop_execs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_loop_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_loop_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_loop_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_loop_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_loop_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_module_name(self):
+ return self._db_module_name
+ def __set_db_module_name(self, module_name):
+ self._db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self._db_module_name = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_loop_execs(self):
+ return self._db_loop_execs
+ def __set_db_loop_execs(self, loop_execs):
+ self._db_loop_execs = loop_execs
+ self.is_dirty = True
+ db_loop_execs = property(__get_db_loop_execs, __set_db_loop_execs)
+ def db_get_loop_execs(self):
+ return self._db_loop_execs
+ def db_add_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_change_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ self._db_loop_execs[i] = loop_exec
+ found = True
+ break
+ if not found:
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_delete_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ if not self._db_loop_execs[i].is_new:
+ self.db_deleted_loop_execs.append(self._db_loop_execs[i])
+ del self._db_loop_execs[i]
+ break
+ del self.db_loop_execs_id_index[loop_exec.db_id]
+ def db_get_loop_exec(self, key):
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == key:
+ return self._db_loop_execs[i]
+ return None
+ def db_get_loop_exec_by_id(self, key):
+ return self.db_loop_execs_id_index[key]
+ def db_has_loop_exec_with_id(self, key):
+ return key in self.db_loop_execs_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
diff --git a/vistrails/db/versions/v1_0_1/domain/id_scope.py b/vistrails/db/versions/v1_0_1/domain/id_scope.py
new file mode 100644
index 0000000..0e07f02
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/domain/id_scope.py
@@ -0,0 +1,85 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L, remap=None):
+ self.ids = {}
+ self.beginId = beginId
+ if remap is None:
+ self.remap = {}
+ else:
+ self.remap = remap
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ cp.remap = copy.copy(self.remap)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ except KeyError:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ if self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+ except KeyError:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v1_0_1/domain/log.py b/vistrails/db/versions/v1_0_1/domain/log.py
new file mode 100644
index 0000000..a127726
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/domain/log.py
@@ -0,0 +1,72 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBLog as _DBLog
+from auto_gen import DBAbstraction, DBModule, DBGroup, DBLoopExec, \
+ DBGroupExec, DBModuleExec
+from id_scope import IdScope
+
+import copy
+
+class DBLog(_DBLog):
+
+ def __init__(self, *args, **kwargs):
+ _DBLog.__init__(self, *args, **kwargs)
+ self.id_scope = IdScope(1,
+ {DBLoopExec.vtType: 'item_exec',
+ DBModuleExec.vtType: 'item_exec',
+ DBGroupExec.vtType: 'item_exec',
+ DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBLog.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBLog
+ cp.id_scope = copy.copy(self.id_scope)
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ new_obj = _DBLog.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
diff --git a/vistrails/db/versions/v1_0_1/domain/registry.py b/vistrails/db/versions/v1_0_1/domain/registry.py
new file mode 100644
index 0000000..323ebbd
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/domain/registry.py
@@ -0,0 +1,63 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBRegistry as _DBRegistry, DBPackage, DBModuleDescriptor, \
+ DBPortSpec
+from id_scope import IdScope
+
+class DBRegistry(_DBRegistry):
+ def __init__(self, *args, **kwargs):
+ _DBRegistry.__init__(self, *args, **kwargs)
+ self.idScope = IdScope()
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRegistry()
+ new_obj = _DBRegistry.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ for package in self.db_packages:
+ self.idScope.updateBeginId(DBPackage.vtType, package.db_id+1)
+ for descriptor in package.db_module_descriptors:
+ self.idScope.updateBeginId(DBModuleDescriptor.vtType,
+ descriptor.db_id+1)
+ for port_spec in descriptor.db_portSpecs:
+ self.idScope.updateBeginId(DBPortSpec.vtType,
+ port_spec.db_id+1)
+
+
diff --git a/vistrails/db/versions/v1_0_1/domain/vistrail.py b/vistrails/db/versions/v1_0_1/domain/vistrail.py
new file mode 100644
index 0000000..c76edd7
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/domain/vistrail.py
@@ -0,0 +1,203 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+import hashlib
+from auto_gen import DBVistrail as _DBVistrail
+from auto_gen import DBAdd, DBChange, DBDelete, DBAbstraction, DBGroup, \
+ DBModule
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAdd.vtType: 'operation',
+ DBChange.vtType: 'operation',
+ DBDelete.vtType: 'operation',
+ DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ self.idScope.setBeginId('action', 1)
+ self.db_objects = {}
+
+ # keep a reference to the current logging information here
+ self.db_log_filename = None
+ self.log = None
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBVistrail.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBVistrail
+
+ cp.idScope = copy.copy(self.idScope)
+ cp.db_objects = copy.copy(self.db_objects)
+ cp.db_log_filename = self.db_log_filename
+ if self.log is not None:
+ cp.log = copy.copy(self.log)
+ else:
+ cp.log = None
+
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ new_obj = _DBVistrail.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ if hasattr(old_obj, 'db_log_filename'):
+ new_obj.db_log_filename = old_obj.db_log_filename
+ if hasattr(old_obj, 'log'):
+ new_obj.log = old_obj.log
+ return new_obj
+
+ def update_id_scope(self):
+ def getOldObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_oldObjId
+ return operation.db_objectId
+
+ def getNewObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_newObjId
+ return operation.db_objectId
+
+ for action in self.db_actions:
+ self.idScope.updateBeginId('action', action.db_id+1)
+ if action.db_session is not None:
+ self.idScope.updateBeginId('session', action.db_session + 1)
+ for operation in action.db_operations:
+ self.idScope.updateBeginId('operation', operation.db_id+1)
+ if operation.vtType == 'add' or operation.vtType == 'change':
+ # update ids of data
+ self.idScope.updateBeginId(operation.db_what,
+ getNewObjId(operation)+1)
+ if operation.db_data is None:
+ if operation.vtType == 'change':
+ operation.db_objectId = operation.db_oldObjId
+ self.db_add_object(operation.db_data)
+ for annotation in action.db_annotations:
+ self.idScope.updateBeginId('annotation', annotation.db_id+1)
+
+ def db_add_object(self, obj):
+ self.db_objects[(obj.vtType, obj.db_id)] = obj
+
+ def db_get_object(self, type, id):
+ return self.db_objects.get((type, id), None)
+
+ def db_update_object(self, obj, **kwargs):
+ # want to swap out old object with a new version
+ # need this for updating aliases...
+ # hack it using setattr...
+ real_obj = self.db_objects[(obj.vtType, obj.db_id)]
+ for (k, v) in kwargs.iteritems():
+ if hasattr(real_obj, k):
+ setattr(real_obj, k, v)
+
+ def update_checkout_version(self, app=''):
+ checkout_key = "__checkout_version_"
+ action_key = checkout_key + app
+ tag_key = action_key + '_taghash'
+ annotation_key = action_key + '_annotationhash'
+ action_annotation_key = action_key + '_actionannotationhash'
+
+ # delete previous checkout annotations
+ deletekeys = [action_key,tag_key,annotation_key,action_annotation_key]
+ for key in deletekeys:
+ while self.db_has_annotation_with_key(key):
+ a = self.db_get_annotation_by_key(key)
+ self.db_delete_annotation(a)
+
+ # annotation hash - requires annotations to be clean
+ value = self.hashAnnotations()
+ self.set_annotation(annotation_key, value)
+ # action annotation hash
+ value = self.hashActionAnnotations()
+ self.set_annotation(action_annotation_key, value)
+ # last action id hash
+ if len(self.db_actions) == 0:
+ value = 0
+ else:
+ value = max(v.db_id for v in self.db_actions)
+ self.set_annotation(action_key, value)
+ # tag hash
+ self.set_annotation(tag_key, self.hashTags())
+
+ def hashTags(self):
+ tagKeys = [tag.db_id for tag in self.db_tags]
+ tagKeys.sort()
+ m = hashlib.md5()
+ for k in tagKeys:
+ m.update(str(k))
+ m.update(self.db_get_tag_by_id(k).db_name)
+ return m.hexdigest()
+
+ def hashAnnotations(self):
+ annotations = {}
+ for annotation in self.db_annotations:
+ if annotation._db_key not in annotations:
+ annotations[annotation._db_key] = []
+ if annotation._db_value not in annotations[annotation._db_key]:
+ annotations[annotation._db_key].append(annotation._db_value)
+ keys = annotations.keys()
+ keys.sort()
+ m = hashlib.md5()
+ for k in keys:
+ m.update(k)
+ annotations[k].sort()
+ for v in annotations[k]:
+ m.update(v)
+ return m.hexdigest()
+
+ def hashActionAnnotations(self):
+ action_annotations = {}
+ for id, annotations in [[action.db_id, action.db_annotations] for action in self.db_actions]:
+ for annotation in annotations:
+ index = (str(id), annotation.db_key)
+ if index not in action_annotations:
+ action_annotations[index] = []
+ if annotation.db_value not in action_annotations[index]:
+ action_annotations[index].append(annotation.db_value)
+ keys = action_annotations.keys()
+ keys.sort()
+ m = hashlib.md5()
+ for k in keys:
+ m.update(k[0] + k[1])
+ action_annotations[k].sort()
+ for v in action_annotations[k]:
+ m.update(v)
+ return m.hexdigest()
diff --git a/vistrails/db/versions/v1_0_1/domain/workflow.py b/vistrails/db/versions/v1_0_1/domain/workflow.py
new file mode 100644
index 0000000..af484e6
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/domain/workflow.py
@@ -0,0 +1,172 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from auto_gen import DBAbstraction, DBModule, DBGroup
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1,
+ {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.build_index()
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ new_obj = _DBWorkflow.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ new_obj.build_index()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
+
+ _vtTypeMap = {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType}
+
+ def build_index(self):
+ g = self._vtTypeMap.get
+ self.objects = dict(((g(o.vtType, o.vtType), o._db_id), o)
+ for (o,_,_) in self.db_children())
+
+ def add_to_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ self.objects[(obj_type, object.getPrimaryKey())] = object
+
+ def delete_from_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ del self.objects[(obj_type, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_print_objects(self):
+ for k,v in self.objects.iteritems():
+ print '%s: %s' % (k, v)
+
+ def db_has_object(self, type, id):
+ return (type, id) in self.objects
+
+ def db_get_object(self, type, id):
+ return self.objects[(type, id)]
+
+ def db_add_object(self, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if object.vtType == DBAbstraction.vtType or \
+ object.vtType == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ else:
+ obj_type = object.vtType
+ funname = 'db_add_' + obj_type
+ obj_copy = copy.copy(object)
+ getattr(parent_obj, funname)(obj_copy)
+ self.add_to_index(obj_copy)
+
+ def db_change_object(self, old_id, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+
+ self.db_delete_object(old_id, object.vtType, None, None, parent_obj)
+ self.db_add_object(object, None, None, parent_obj)
+
+ def db_delete_object(self, obj_id, obj_type, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if obj_type == DBAbstraction.vtType or obj_type == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ funname = 'db_get_' + obj_type
+ if hasattr(parent_obj, funname):
+ object = getattr(parent_obj, funname)(obj_id)
+ else:
+ attr_name = 'db_' + obj_type
+ object = getattr(parent_obj, attr_name)
+ funname = 'db_delete_' + obj_type
+ getattr(parent_obj, funname)(object)
+ self.delete_from_index(object)
diff --git a/vistrails/db/versions/v1_0_1/persistence/__init__.py b/vistrails/db/versions/v1_0_1/persistence/__init__.py
new file mode 100644
index 0000000..f7c0477
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/persistence/__init__.py
@@ -0,0 +1,248 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+from vistrails.core.system import get_elementtree_library
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v1_0_1 import version as my_version
+from vistrails.db.versions.v1_0_1.domain import DBGroup, DBWorkflow, DBVistrail, DBLog, \
+ DBRegistry
+
+ElementTree = get_elementtree_library()
+
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def parse_xml_file(self, filename):
+ return ElementTree.parse(filename)
+
+ def write_xml_file(self, filename, tree):
+ def indent(elem, level=0):
+ i = "\n" + level*" "
+ if len(elem):
+ if not elem.text or not elem.text.strip():
+ elem.text = i + " "
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ for elem in elem:
+ indent(elem, level+1)
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ else:
+ if level and (not elem.tail or not elem.tail.strip()):
+ elem.tail = i
+ indent(tree.getroot())
+ tree.write(filename)
+
+ def read_xml_object(self, vtType, node):
+ return self['xml'][vtType].fromXML(node)
+
+ def write_xml_object(self, obj, node=None):
+ res_node = self['xml'][obj.vtType].toXML(obj, node)
+ return res_node
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ """open_from_xml(filename) -> DBVistrail"""
+ if tree is None:
+ tree = self.parse_xml_file(filename)
+ vistrail = self.read_xml_object(vtType, tree.getroot())
+ return vistrail
+
+ def save_to_xml(self, obj, filename, tags, version=None):
+ """save_to_xml(obj : object, filename: str, tags: dict,
+ version: str) -> None
+
+ """
+ root = self.write_xml_object(obj)
+ if version is None:
+ version = my_version
+ root.set('version', version)
+ for k, v in tags.iteritems():
+ root.set(k, v)
+ tree = ElementTree.ElementTree(root)
+ self.write_xml_file(filename, tree)
+
+ def open_from_db(self, db_connection, vtType, id=None, lock=False,
+ global_props=None):
+ all_objects = {}
+ if global_props is None:
+ global_props = {}
+ if id is not None:
+ global_props['id'] = id
+ # print global_props
+ res_objects = self['sql'][vtType].get_sql_columns(db_connection,
+ global_props,
+ lock)
+ if len(res_objects) > 1:
+ raise VistrailsDBException("More than object of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+ elif len(res_objects) <= 0:
+ raise VistrailsDBException("No objects of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+
+ all_objects.update(res_objects)
+ res = res_objects.values()[0]
+ global_props = {'entity_id': res.db_id,
+ 'entity_type': res.vtType}
+
+ for dao_type, dao in self['sql'].iteritems():
+ if (dao_type == DBVistrail.vtType or
+ dao_type == DBWorkflow.vtType or
+ dao_type == DBLog.vtType or
+ dao_type == DBRegistry.vtType):
+ continue
+
+ current_objs = dao.get_sql_columns(db_connection, global_props,
+ lock)
+ all_objects.update(current_objs)
+
+ if dao_type == DBGroup.vtType:
+ for key, obj in current_objs.iteritems():
+ new_props = {'parent_id': key[1],
+ 'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ res_obj = self.open_from_db(db_connection,
+ DBWorkflow.vtType,
+ None, lock, new_props)
+ res_dict = {}
+ res_dict[(res_obj.vtType, res_obj.db_id)] = res_obj
+ all_objects.update(res_dict)
+
+ for key, obj in all_objects.iteritems():
+ if key[0] == vtType and key[1] == id:
+ continue
+ self['sql'][obj.vtType].from_sql_fast(obj, all_objects)
+ for obj in all_objects.itervalues():
+ obj.is_dirty = False
+ obj.is_new = False
+
+ return res
+
+ def save_to_db(self, db_connection, obj, do_copy=False, global_props=None):
+ if do_copy and obj.db_id is not None:
+ obj.db_id = None
+
+ children = obj.db_children()
+ children.reverse()
+ if global_props is None:
+ global_props = {'entity_type': obj.vtType}
+ # print 'global_props:', global_props
+
+ # assumes not deleting entire thing
+ child = children[0][0]
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ global_props = {'entity_id': child.db_id,
+ 'entity_type': child.vtType}
+
+ # do deletes
+ if not do_copy:
+ for (child, _, _) in children:
+ for c in child.db_deleted_children(True):
+ self['sql'][c.vtType].delete_sql_column(db_connection,
+ c,
+ global_props)
+
+ child = children.pop(0)[0]
+ child.is_dirty = False
+ child.is_new = False
+
+ # process remaining children
+ for (child, _, _) in children:
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ # print '*** entity_type:', global_props['entity_type']
+ new_props = {'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ is_dirty = child.db_workflow.is_dirty
+ child.db_workflow.db_entity_type = DBWorkflow.vtType
+ child.db_workflow.is_dirty = is_dirty
+ self.save_to_db(db_connection, child.db_workflow, do_copy,
+ new_props)
+
+ child.is_dirty = False
+ child.is_new = False
+
+ def delete_from_db(self, db_connection, type, obj_id):
+ root_set = set([DBVistrail.vtType, DBWorkflow.vtType,
+ DBLog.vtType, DBRegistry.vtType])
+ if type not in root_set:
+ raise VistrailsDBException("Cannot delete entity of type '%s'" \
+ % type)
+
+ id_str = str(obj_id)
+ for (dao_type, dao) in self['sql'].iteritems():
+ if dao_type not in root_set:
+ db_cmd = \
+ self['sql'][type].createSQLDelete(dao.table,
+ {'entity_type': type,
+ 'entity_id': id_str})
+ self['sql'][type].executeSQL(db_connection, db_cmd, False)
+ db_cmd = self['sql'][type].createSQLDelete(self['sql'][type].table,
+ {'id': id_str})
+ self['sql'][type].executeSQL(db_connection, db_cmd, False)
+
+ def serialize(self, object):
+ root = self.write_xml_object(object)
+ return ElementTree.tostring(root)
+
+ def unserialize(self, str, obj_type):
+ def set_dirty(obj):
+ for child, _, _ in obj.db_children():
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ set_dirty(child.db_workflow)
+ child.is_dirty = True
+ child.is_new = True
+ try:
+ root = ElementTree.fromstring(str)
+ obj = self.read_xml_object(obj_type, root)
+ set_dirty(obj)
+ return obj
+ except SyntaxError, e:
+ msg = "Invalid VisTrails serialized object %s" % str
+ raise VistrailsDBException(msg)
+ return None
diff --git a/vistrails/db/versions/v1_0_1/persistence/sql/__init__.py b/vistrails/db/versions/v1_0_1/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v1_0_1/persistence/sql/auto_gen.py b/vistrails/db/versions/v1_0_1/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..a083843
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/persistence/sql/auto_gen.py
@@ -0,0 +1,3344 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v1_0_1.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port_spec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'sigstring', 'labels', 'defaults', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ optional = self.convertFromDB(row[3], 'int', 'int')
+ sort_key = self.convertFromDB(row[4], 'int', 'int')
+ sigstring = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ labels = self.convertFromDB(row[6], 'str', 'varchar(4095)')
+ defaults = self.convertFromDB(row[7], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[8], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[9], 'long', 'int')
+ entity_type = self.convertFromDB(row[10], 'str', 'char(16)')
+ parent = self.convertFromDB(row[11], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ sigstring=sigstring,
+ labels=labels,
+ defaults=defaults,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_entity_id = entity_id
+ portSpec.db_entity_type = entity_type
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'module_descriptor':
+ p = all_objects[('module_descriptor', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'sigstring', 'labels', 'defaults', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_optional') and obj.db_optional is not None:
+ columnMap['optional'] = \
+ self.convertToDB(obj.db_optional, 'int', 'int')
+ if hasattr(obj, 'db_sort_key') and obj.db_sort_key is not None:
+ columnMap['sort_key'] = \
+ self.convertToDB(obj.db_sort_key, 'int', 'int')
+ if hasattr(obj, 'db_sigstring') and obj.db_sigstring is not None:
+ columnMap['sigstring'] = \
+ self.convertToDB(obj.db_sigstring, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_labels') and obj.db_labels is not None:
+ columnMap['labels'] = \
+ self.convertToDB(obj.db_labels, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_defaults') and obj.db_defaults is not None:
+ columnMap['defaults'] = \
+ self.convertToDB(obj.db_defaults, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ module.db_parentType = parentType
+ module.db_entity_id = entity_id
+ module.db_entity_type = entity_type
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleDescriptorSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_descriptor'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'package', 'namespace', 'package_version', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ base_descriptor_id = self.convertFromDB(row[6], 'long', 'int')
+ package = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ module_descriptor = DBModuleDescriptor(name=name,
+ package=package,
+ namespace=namespace,
+ package_version=package_version,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ id=id)
+ module_descriptor.db_package = package
+ module_descriptor.db_entity_id = entity_id
+ module_descriptor.db_entity_type = entity_type
+ module_descriptor.is_dirty = False
+ res[('module_descriptor', id)] = module_descriptor
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('package', obj.db_package) in all_objects:
+ p = all_objects[('package', obj.db_package)]
+ p.db_add_module_descriptor(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'package', 'namespace', 'package_version', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package_version') and obj.db_package_version is not None:
+ columnMap['package_version'] = \
+ self.convertToDB(obj.db_package_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_base_descriptor_id') and obj.db_base_descriptor_id is not None:
+ columnMap['base_descriptor_id'] = \
+ self.convertToDB(obj.db_base_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_package, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'tag'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[2], 'long', 'int')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_vistrail = vistrail
+ tag.db_entity_id = entity_id
+ tag.db_entity_type = entity_type
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ signature = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature,
+ id=id)
+ port.db_parentType = parentType
+ port.db_entity_id = entity_id
+ port.db_entity_type = entity_type
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_signature') and obj.db_signature is not None:
+ columnMap['signature'] = \
+ self.convertToDB(obj.db_signature, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ group = DBGroup(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ id=id)
+ group.db_parentType = parentType
+ group.db_entity_id = entity_id
+ group.db_entity_type = entity_type
+ group.db_parent = parent
+ group.is_dirty = False
+ res[('group', id)] = group
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_workflow is not None:
+ child = obj.db_workflow
+ child.db_group = obj.db_id
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'log_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ log = DBLog(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ log.is_dirty = False
+ res[('log', id)] = log
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_workflow_execs:
+ child.db_log = obj.db_id
+ for child in obj.db_machines:
+ child.db_log = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'machine'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.db_entity_id = entity_id
+ machine.db_entity_type = entity_type
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'add_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_entity_id = entity_id
+ add.db_entity_type = entity_type
+ add.is_dirty = False
+ res[('add', id)] = add
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'other'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_entity_id = entity_id
+ other.db_entity_type = entity_type
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'location'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_entity_id = entity_id
+ location.db_entity_type = entity_type
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'parameter'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_entity_id = entity_id
+ parameter.db_entity_type = entity_type
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPluginDataSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'plugin_data'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ data = self.convertFromDB(row[1], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ plugin_data = DBPluginData(data=data,
+ id=id)
+ plugin_data.db_parentType = parentType
+ plugin_data.db_entity_id = entity_id
+ plugin_data.db_entity_type = entity_type
+ plugin_data.db_parent = parent
+ plugin_data.is_dirty = False
+ res[('plugin_data', id)] = plugin_data
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_plugin_data(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_data') and obj.db_data is not None:
+ columnMap['data'] = \
+ self.convertToDB(obj.db_data, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'function'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_entity_id = entity_id
+ function.db_entity_type = entity_type
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'abstraction'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ internal_version = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ tag = self.convertFromDB(row[7], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[8], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[9], 'long', 'int')
+ entity_type = self.convertFromDB(row[10], 'str', 'char(16)')
+ parent = self.convertFromDB(row[11], 'long', 'long')
+
+ abstraction = DBAbstraction(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ tag=tag,
+ id=id)
+ abstraction.db_parentType = parentType
+ abstraction.db_entity_id = entity_id
+ abstraction.db_entity_type = entity_type
+ abstraction.db_parent = parent
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'tag', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_internal_version') and obj.db_internal_version is not None:
+ columnMap['internal_version'] = \
+ self.convertToDB(obj.db_internal_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_tag') and obj.db_tag is not None:
+ columnMap['tag'] = \
+ self.convertToDB(obj.db_tag, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_id = self.convertFromDB(row[1], 'long', 'int')
+ entity_type = self.convertFromDB(row[2], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'char(16)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[6], 'long', 'int')
+ group = self.convertFromDB(row[7], 'long', 'int')
+
+ workflow = DBWorkflow(entity_type=entity_type,
+ name=name,
+ version=version,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ workflow.db_entity_id = entity_id
+ workflow.db_group = group
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('group', obj.db_group) in all_objects:
+ p = all_objects[('group', obj.db_group)]
+ p.db_add_workflow(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ if hasattr(obj, 'db_group') and obj.db_group is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_group, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_connections:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_plugin_datas:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_modules:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBRegistrySQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'registry'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ root_descriptor_id = self.convertFromDB(row[3], 'long', 'int')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+
+ registry = DBRegistry(entity_type=entity_type,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ registry.is_dirty = False
+ res[('registry', id)] = registry
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_root_descriptor_id') and obj.db_root_descriptor_id is not None:
+ columnMap['root_descriptor_id'] = \
+ self.convertToDB(obj.db_root_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_packages:
+ child.db_registry = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'annotation'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_entity_id = entity_id
+ annotation.db_entity_type = entity_type
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'change_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_entity_id = entity_id
+ change.db_entity_type = entity_type
+ change.is_dirty = False
+ res[('change', id)] = change
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ group_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ group_type = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[7], 'int', 'int')
+ error = self.convertFromDB(row[8], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[9], 'long', 'int')
+ parentType = self.convertFromDB(row[10], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[11], 'long', 'int')
+ entity_type = self.convertFromDB(row[12], 'str', 'char(16)')
+ parent = self.convertFromDB(row[13], 'long', 'long')
+
+ group_exec = DBGroupExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ group_exec.db_parentType = parentType
+ group_exec.db_entity_id = entity_id
+ group_exec.db_entity_type = entity_type
+ group_exec.db_parent = parent
+ group_exec.is_dirty = False
+ res[('group_exec', id)] = group_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_group_name') and obj.db_group_name is not None:
+ columnMap['group_name'] = \
+ self.convertToDB(obj.db_group_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_group_type') and obj.db_group_type is not None:
+ columnMap['group_type'] = \
+ self.convertToDB(obj.db_group_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPackageSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'package'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ identifier = self.convertFromDB(row[2], 'str', 'varchar(1023)')
+ codepath = self.convertFromDB(row[3], 'str', 'varchar(1023)')
+ load_configuration = self.convertFromDB(row[4], 'int', 'int')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ description = self.convertFromDB(row[6], 'str', 'varchar(1023)')
+ registry = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ package = DBPackage(name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ id=id)
+ package.db_registry = registry
+ package.db_entity_id = entity_id
+ package.db_entity_type = entity_type
+ package.is_dirty = False
+ res[('package', id)] = package
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('registry', obj.db_registry) in all_objects:
+ p = all_objects[('registry', obj.db_registry)]
+ p.db_add_package(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_identifier') and obj.db_identifier is not None:
+ columnMap['identifier'] = \
+ self.convertToDB(obj.db_identifier, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_codepath') and obj.db_codepath is not None:
+ columnMap['codepath'] = \
+ self.convertToDB(obj.db_codepath, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_load_configuration') and obj.db_load_configuration is not None:
+ columnMap['load_configuration'] = \
+ self.convertToDB(obj.db_load_configuration, 'int', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_description') and obj.db_description is not None:
+ columnMap['description'] = \
+ self.convertToDB(obj.db_description, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_registry') and obj.db_registry is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_registry, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_module_descriptors:
+ child.db_package = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ vt_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[5], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[6], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[7], 'long', 'int')
+ parent_type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[9], 'long', 'int')
+ completed = self.convertFromDB(row[10], 'int', 'int')
+ name = self.convertFromDB(row[11], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[12], 'long', 'int')
+ entity_id = self.convertFromDB(row[13], 'long', 'int')
+ entity_type = self.convertFromDB(row[14], 'str', 'char(16)')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_entity_id = entity_id
+ workflow_exec.db_entity_type = entity_type
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLoopExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'loop_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ iteration = self.convertFromDB(row[3], 'int', 'int')
+ completed = self.convertFromDB(row[4], 'int', 'int')
+ error = self.convertFromDB(row[5], 'str', 'varchar(1023)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ loop_exec = DBLoopExec(ts_start=ts_start,
+ ts_end=ts_end,
+ iteration=iteration,
+ completed=completed,
+ error=error,
+ id=id)
+ loop_exec.db_parentType = parentType
+ loop_exec.db_entity_id = entity_id
+ loop_exec.db_entity_type = entity_type
+ loop_exec.db_parent = parent
+ loop_exec.is_dirty = False
+ res[('loop_exec', id)] = loop_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_loop_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_iteration') and obj.db_iteration is not None:
+ columnMap['iteration'] = \
+ self.convertToDB(obj.db_iteration, 'int', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'connection_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[2], 'long', 'int')
+ entity_type = self.convertFromDB(row[3], 'str', 'char(16)')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_entity_id = entity_id
+ connection.db_entity_type = entity_type
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'action'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ prune = self.convertFromDB(row[5], 'int', 'int')
+ vistrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ id=id)
+ action.db_vistrail = vistrail
+ action.db_entity_id = entity_id
+ action.db_entity_type = entity_type
+ action.is_dirty = False
+ res[('action', id)] = action
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'prune', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_prune') and obj.db_prune is not None:
+ columnMap['prune'] = \
+ self.convertToDB(obj.db_prune, 'int', 'int')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'delete_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_entity_id = entity_id
+ delete.db_entity_type = entity_type
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'vistrail'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_actions:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_tags:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ module_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[6], 'int', 'int')
+ error = self.convertFromDB(row[7], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[8], 'long', 'int')
+ parentType = self.convertFromDB(row[9], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[10], 'long', 'int')
+ entity_type = self.convertFromDB(row[11], 'str', 'char(16)')
+ parent = self.convertFromDB(row[12], 'long', 'long')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ module_exec.db_parentType = parentType
+ module_exec.db_entity_id = entity_id
+ module_exec.db_entity_type = entity_type
+ module_exec.db_parent = parent
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_loop_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'module_descriptor' not in self:
+ self['module_descriptor'] = DBModuleDescriptorSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'registry' not in self:
+ self['registry'] = DBRegistrySQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'group_exec' not in self:
+ self['group_exec'] = DBGroupExecSQLDAOBase(self)
+ if 'package' not in self:
+ self['package'] = DBPackageSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'loop_exec' not in self:
+ self['loop_exec'] = DBLoopExecSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v1_0_1/persistence/sql/sql_dao.py b/vistrails/db/versions/v1_0_1/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..ad01dc5
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/persistence/sql/sql_dao.py
@@ -0,0 +1,183 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+from vistrails.db import VistrailsDBException
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ # return "'" + str(value).replace("'", "''") + "'"
+ return str(value)
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ return str(value)
+ elif type == 'int':
+ return str(value)
+ elif type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+
+ return None
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None,
+ forUpdate=False):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % \
+ (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ if forUpdate:
+ dbCommand += " FOR UPDATE"
+ dbCommand += ";"
+ return (dbCommand, tuple(values))
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ # valueStr = '%s, '.join(values)
+ valueStr = ''
+ if len(values) > 1:
+ valueStr = '%s,' * (len(values) - 1) + '%s'
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s);""" % \
+ (table, columnStr, valueStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ values = []
+ for column, value in columnMap.iteritems():
+# if value is None:
+# value = 'NULL'
+ setStr += '%s%s = %%s' % (comma, column)
+ comma = ', '
+ values.append(value)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """UPDATE %s SET %s WHERE %s;""" % \
+ (table, setStr, whereStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLDelete(self, table, whereMap):
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """DELETE FROM %s WHERE %s;""" % \
+ (table, whereStr)
+ return (dbCommand, tuple(values))
+
+ def executeSQL(self, db, cmd_tuple, isFetch):
+ dbCommand, values = cmd_tuple
+ # print 'db: %s' % dbCommand
+ # print 'values:', values
+ data = None
+ cursor = db.cursor()
+ try:
+ cursor.execute(dbCommand, values)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ except Exception, e:
+ raise VistrailsDBException('Command "%s" with values "%s" '
+ 'failed: %s' % (dbCommand, values, e))
+ finally:
+ cursor.close()
+ return data
+
+ def start_transaction(self, db):
+ db.begin()
+
+ def commit_transaction(self, db):
+ db.commit()
+
+ def rollback_transaction(self, db):
+ db.rollback()
diff --git a/vistrails/db/versions/v1_0_1/persistence/xml/__init__.py b/vistrails/db/versions/v1_0_1/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v1_0_1/persistence/xml/auto_gen.py b/vistrails/db/versions/v1_0_1/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..95973ad
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/persistence/xml/auto_gen.py
@@ -0,0 +1,3845 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from vistrails.core.system import get_elementtree_library
+
+from xml_dao import XMLDAO
+from vistrails.db.versions.v1_0_1.domain import *
+
+ElementTree = get_elementtree_library()
+
+
+class DBOpmProcessIdEffectXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'effect':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmProcessIdEffect(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_id_effect, node=None):
+ if node is None:
+ node = ElementTree.Element('effect')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process_id_effect.db_id, 'str'))
+
+ return node
+
+class DBOpmWasGeneratedByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasGeneratedBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_artifact_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_process_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasGeneratedBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_generated_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasGeneratedBy')
+
+ # set elements
+ effect = opm_was_generated_by.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_artifact_id_effect').toXML(effect, childNode)
+ role = opm_was_generated_by.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_generated_by.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_process_id_cause').toXML(cause, childNode)
+ accounts = opm_was_generated_by.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_generated_by.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBOpmAccountsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'accounts':
+ return None
+
+ accounts = []
+ opm_overlapss = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'account':
+ _data = self.getDao('opm_account').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'overlaps':
+ _data = self.getDao('opm_overlaps').fromXML(child)
+ opm_overlapss.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAccounts(accounts=accounts,
+ opm_overlapss=opm_overlapss)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_accounts, node=None):
+ if node is None:
+ node = ElementTree.Element('accounts')
+
+ # set elements
+ accounts = opm_accounts.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account').toXML(account, childNode)
+ opm_overlapss = opm_accounts.db_opm_overlapss
+ for opm_overlaps in opm_overlapss:
+ childNode = ElementTree.SubElement(node, 'overlaps')
+ self.getDao('opm_overlaps').toXML(opm_overlaps, childNode)
+
+ return node
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'portSpec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('optional', None)
+ optional = self.convertFromStr(data, 'int')
+ data = node.get('sortKey', None)
+ sort_key = self.convertFromStr(data, 'int')
+ data = node.get('sigstring', None)
+ sigstring = self.convertFromStr(data, 'str')
+ data = node.get('labels', None)
+ labels = self.convertFromStr(data, 'str')
+ data = node.get('defaults', None)
+ defaults = self.convertFromStr(data, 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ sigstring=sigstring,
+ labels=labels,
+ defaults=defaults)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, node=None):
+ if node is None:
+ node = ElementTree.Element('portSpec')
+
+ # set attributes
+ node.set('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.set('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.set('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.set('optional',self.convertToStr(portSpec.db_optional, 'int'))
+ node.set('sortKey',self.convertToStr(portSpec.db_sort_key, 'int'))
+ node.set('sigstring',self.convertToStr(portSpec.db_sigstring, 'str'))
+ node.set('labels',self.convertToStr(portSpec.db_labels, 'str'))
+ node.set('defaults',self.convertToStr(portSpec.db_defaults, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'module':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, node=None):
+ if node is None:
+ node = ElementTree.Element('module')
+
+ # set attributes
+ node.set('id',self.convertToStr(module.db_id, 'long'))
+ node.set('cache',self.convertToStr(module.db_cache, 'int'))
+ node.set('name',self.convertToStr(module.db_name, 'str'))
+ node.set('namespace',self.convertToStr(module.db_namespace, 'str'))
+ node.set('package',self.convertToStr(module.db_package, 'str'))
+ node.set('version',self.convertToStr(module.db_version, 'str'))
+ node.set('tag',self.convertToStr(module.db_tag, 'str'))
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = module.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBModuleDescriptorXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'moduleDescriptor':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('packageVersion', None)
+ package_version = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('baseDescriptorId', None)
+ base_descriptor_id = self.convertFromStr(data, 'long')
+
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleDescriptor(id=id,
+ name=name,
+ package=package,
+ namespace=namespace,
+ package_version=package_version,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_descriptor, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleDescriptor')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_descriptor.db_id, 'long'))
+ node.set('name',self.convertToStr(module_descriptor.db_name, 'str'))
+ node.set('package',self.convertToStr(module_descriptor.db_package, 'str'))
+ node.set('namespace',self.convertToStr(module_descriptor.db_namespace, 'str'))
+ node.set('packageVersion',self.convertToStr(module_descriptor.db_package_version, 'str'))
+ node.set('version',self.convertToStr(module_descriptor.db_version, 'str'))
+ node.set('baseDescriptorId',self.convertToStr(module_descriptor.db_base_descriptor_id, 'long'))
+
+ # set elements
+ portSpecs = module_descriptor.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'tag':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, node=None):
+ if node is None:
+ node = ElementTree.Element('tag')
+
+ # set attributes
+ node.set('id',self.convertToStr(tag.db_id, 'long'))
+ node.set('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBOpmRoleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'role':
+ return None
+
+ # read attributes
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBOpmRole(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_role, node=None):
+ if node is None:
+ node = ElementTree.Element('role')
+
+ # set attributes
+ node.set('value',self.convertToStr(opm_role.db_value, 'str'))
+
+ return node
+
+class DBOpmProcessesXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'processes':
+ return None
+
+ processs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'process':
+ _data = self.getDao('opm_process').fromXML(child)
+ processs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcesses(processs=processs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_processes, node=None):
+ if node is None:
+ node = ElementTree.Element('processes')
+
+ # set elements
+ processs = opm_processes.db_processs
+ for process in processs:
+ childNode = ElementTree.SubElement(node, 'process')
+ self.getDao('opm_process').toXML(process, childNode)
+
+ return node
+
+class DBOpmAccountIdXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'account':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmAccountId(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_account_id, node=None):
+ if node is None:
+ node = ElementTree.Element('account')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_account_id.db_id, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'port':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('moduleId', None)
+ moduleId = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ moduleName = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('signature', None)
+ signature = self.convertFromStr(data, 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, node=None):
+ if node is None:
+ node = ElementTree.Element('port')
+
+ # set attributes
+ node.set('id',self.convertToStr(port.db_id, 'long'))
+ node.set('type',self.convertToStr(port.db_type, 'str'))
+ node.set('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.set('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.set('name',self.convertToStr(port.db_name, 'str'))
+ node.set('signature',self.convertToStr(port.db_signature, 'str'))
+
+ return node
+
+class DBOpmArtifactXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'artifact':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.getDao('opm_artifact_value').fromXML(child)
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifact(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact, node=None):
+ if node is None:
+ node = ElementTree.Element('artifact')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact.db_id, 'str'))
+
+ # set elements
+ value = opm_artifact.db_value
+ if value is not None:
+ childNode = ElementTree.SubElement(node, 'value')
+ self.getDao('opm_artifact_value').toXML(value, childNode)
+ accounts = opm_artifact.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBGroupXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'group':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ workflow = None
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'workflow':
+ _data = self.getDao('workflow').fromXML(child)
+ workflow = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroup(id=id,
+ workflow=workflow,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group, node=None):
+ if node is None:
+ node = ElementTree.Element('group')
+
+ # set attributes
+ node.set('id',self.convertToStr(group.db_id, 'long'))
+ node.set('cache',self.convertToStr(group.db_cache, 'int'))
+ node.set('name',self.convertToStr(group.db_name, 'str'))
+ node.set('namespace',self.convertToStr(group.db_namespace, 'str'))
+ node.set('package',self.convertToStr(group.db_package, 'str'))
+ node.set('version',self.convertToStr(group.db_version, 'str'))
+ node.set('tag',self.convertToStr(group.db_tag, 'str'))
+
+ # set elements
+ workflow = group.db_workflow
+ if workflow is not None:
+ childNode = ElementTree.SubElement(node, 'workflow')
+ self.getDao('workflow').toXML(workflow, childNode)
+ location = group.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = group.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = group.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'log':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ workflow_execs = []
+ machines = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'workflowExec':
+ _data = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs.append(_data)
+ elif child_tag == 'machine':
+ _data = self.getDao('machine').fromXML(child)
+ machines.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLog(id=id,
+ version=version,
+ name=name,
+ workflow_execs=workflow_execs,
+ machines=machines,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, node=None):
+ if node is None:
+ node = ElementTree.Element('log')
+
+ # set attributes
+ node.set('id',self.convertToStr(log.db_id, 'long'))
+ node.set('version',self.convertToStr(log.db_version, 'str'))
+ node.set('name',self.convertToStr(log.db_name, 'str'))
+ node.set('vistrail_id',self.convertToStr(log.db_vistrail_id, 'long'))
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs:
+ childNode = ElementTree.SubElement(node, 'workflowExec')
+ self.getDao('workflow_exec').toXML(workflow_exec, childNode)
+ machines = log.db_machines
+ for machine in machines:
+ childNode = ElementTree.SubElement(node, 'machine')
+ self.getDao('machine').toXML(machine, childNode)
+
+ return node
+
+class DBOpmAgentsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agents':
+ return None
+
+ agents = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'agent':
+ _data = self.getDao('opm_agent').fromXML(child)
+ agents.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAgents(agents=agents)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agents, node=None):
+ if node is None:
+ node = ElementTree.Element('agents')
+
+ # set elements
+ agents = opm_agents.db_agents
+ for agent in agents:
+ childNode = ElementTree.SubElement(node, 'agent')
+ self.getDao('opm_agent').toXML(agent, childNode)
+
+ return node
+
+class DBOpmProcessIdCauseXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'cause':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmProcessIdCause(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_id_cause, node=None):
+ if node is None:
+ node = ElementTree.Element('cause')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process_id_cause.db_id, 'str'))
+
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'machine':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('os', None)
+ os = self.convertFromStr(data, 'str')
+ data = node.get('architecture', None)
+ architecture = self.convertFromStr(data, 'str')
+ data = node.get('processor', None)
+ processor = self.convertFromStr(data, 'str')
+ data = node.get('ram', None)
+ ram = self.convertFromStr(data, 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, node=None):
+ if node is None:
+ node = ElementTree.Element('machine')
+
+ # set attributes
+ node.set('id',self.convertToStr(machine.db_id, 'long'))
+ node.set('name',self.convertToStr(machine.db_name, 'str'))
+ node.set('os',self.convertToStr(machine.db_os, 'str'))
+ node.set('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.set('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.set('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'add':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAdd(data=data,
+ id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, node=None):
+ if node is None:
+ node = ElementTree.Element('add')
+
+ # set attributes
+ node.set('id',self.convertToStr(add.db_id, 'long'))
+ node.set('what',self.convertToStr(add.db_what, 'str'))
+ node.set('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # set elements
+ data = add.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'other':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, node=None):
+ if node is None:
+ node = ElementTree.Element('other')
+
+ # set attributes
+ node.set('id',self.convertToStr(other.db_id, 'long'))
+ node.set('key',self.convertToStr(other.db_key, 'str'))
+
+ # set elements
+ value = other.db_value
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'location':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('x', None)
+ x = self.convertFromStr(data, 'float')
+ data = node.get('y', None)
+ y = self.convertFromStr(data, 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, node=None):
+ if node is None:
+ node = ElementTree.Element('location')
+
+ # set attributes
+ node.set('id',self.convertToStr(location.db_id, 'long'))
+ node.set('x',self.convertToStr(location.db_x, 'float'))
+ node.set('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBOpmOverlapsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'overlaps':
+ return None
+
+ opm_account_ids = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ opm_account_ids.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmOverlaps(opm_account_ids=opm_account_ids)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_overlaps, node=None):
+ if node is None:
+ node = ElementTree.Element('overlaps')
+
+ # set elements
+ opm_account_ids = opm_overlaps.db_opm_account_ids
+ for opm_account_id in opm_account_ids:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(opm_account_id, childNode)
+
+ return node
+
+class DBOpmArtifactsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'artifacts':
+ return None
+
+ artifacts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'artifact':
+ _data = self.getDao('opm_artifact').fromXML(child)
+ artifacts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifacts(artifacts=artifacts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifacts, node=None):
+ if node is None:
+ node = ElementTree.Element('artifacts')
+
+ # set elements
+ artifacts = opm_artifacts.db_artifacts
+ for artifact in artifacts:
+ childNode = ElementTree.SubElement(node, 'artifact')
+ self.getDao('opm_artifact').toXML(artifact, childNode)
+
+ return node
+
+class DBOpmDependenciesXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'causalDependencies':
+ return None
+
+ dependencys = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'used':
+ _data = self.getDao('opm_used').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasGeneratedBy':
+ _data = self.getDao('opm_was_generated_by').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasTriggeredBy':
+ _data = self.getDao('opm_was_triggered_by').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasDerivedFrom':
+ _data = self.getDao('opm_was_derived_from').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasControlledBy':
+ _data = self.getDao('opm_was_controlled_by').fromXML(child)
+ dependencys.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmDependencies(dependencys=dependencys)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_dependencies, node=None):
+ if node is None:
+ node = ElementTree.Element('causalDependencies')
+
+ # set elements
+ dependencys = opm_dependencies.db_dependencys
+ for dependency in dependencys:
+ if dependency.vtType == 'opm_used':
+ childNode = ElementTree.SubElement(node, 'used')
+ self.getDao('opm_used').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_generated_by':
+ childNode = ElementTree.SubElement(node, 'wasGeneratedBy')
+ self.getDao('opm_was_generated_by').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_triggered_by':
+ childNode = ElementTree.SubElement(node, 'wasTriggeredBy')
+ self.getDao('opm_was_triggered_by').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_derived_from':
+ childNode = ElementTree.SubElement(node, 'wasDerivedFrom')
+ self.getDao('opm_was_derived_from').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_controlled_by':
+ childNode = ElementTree.SubElement(node, 'wasControlledBy')
+ self.getDao('opm_was_controlled_by').toXML(dependency, childNode)
+
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'parameter':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('val', None)
+ val = self.convertFromStr(data, 'str')
+ data = node.get('alias', None)
+ alias = self.convertFromStr(data, 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, node=None):
+ if node is None:
+ node = ElementTree.Element('parameter')
+
+ # set attributes
+ node.set('id',self.convertToStr(parameter.db_id, 'long'))
+ node.set('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.set('name',self.convertToStr(parameter.db_name, 'str'))
+ node.set('type',self.convertToStr(parameter.db_type, 'str'))
+ node.set('val',self.convertToStr(parameter.db_val, 'str'))
+ node.set('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBOpmUsedXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'used':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_artifact_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmUsed(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_used, node=None):
+ if node is None:
+ node = ElementTree.Element('used')
+
+ # set elements
+ effect = opm_used.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_used.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_used.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_artifact_id_cause').toXML(cause, childNode)
+ accounts = opm_used.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_used.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBPluginDataXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'plugin_data':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('data', None)
+ data = self.convertFromStr(data, 'str')
+
+ obj = DBPluginData(id=id,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, plugin_data, node=None):
+ if node is None:
+ node = ElementTree.Element('plugin_data')
+
+ # set attributes
+ node.set('id',self.convertToStr(plugin_data.db_id, 'long'))
+ node.set('data',self.convertToStr(plugin_data.db_data, 'str'))
+
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'function':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ parameters = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ parameters.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, node=None):
+ if node is None:
+ node = ElementTree.Element('function')
+
+ # set attributes
+ node.set('id',self.convertToStr(function.db_id, 'long'))
+ node.set('pos',self.convertToStr(function.db_pos, 'long'))
+ node.set('name',self.convertToStr(function.db_name, 'str'))
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(parameter, childNode)
+
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'abstraction':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('internalVersion', None)
+ internal_version = self.convertFromStr(data, 'str')
+ data = node.get('tag', None)
+ tag = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstraction(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ tag=tag,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, node=None):
+ if node is None:
+ node = ElementTree.Element('abstraction')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.set('cache',self.convertToStr(abstraction.db_cache, 'int'))
+ node.set('name',self.convertToStr(abstraction.db_name, 'str'))
+ node.set('namespace',self.convertToStr(abstraction.db_namespace, 'str'))
+ node.set('package',self.convertToStr(abstraction.db_package, 'str'))
+ node.set('version',self.convertToStr(abstraction.db_version, 'str'))
+ node.set('internalVersion',self.convertToStr(abstraction.db_internal_version, 'str'))
+ node.set('tag',self.convertToStr(abstraction.db_tag, 'str'))
+
+ # set elements
+ location = abstraction.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = abstraction.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = abstraction.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'workflow':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ connections = []
+ annotations = []
+ plugin_datas = []
+ others = []
+ modules = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ connections.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ plugin_datas.append(_data)
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ others.append(_data)
+ elif child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ modules.append(_data)
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ modules.append(_data)
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ modules.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflow(modules=modules,
+ id=id,
+ name=name,
+ version=version,
+ connections=connections,
+ annotations=annotations,
+ plugin_datas=plugin_datas,
+ others=others,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, node=None):
+ if node is None:
+ node = ElementTree.Element('workflow')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow.db_id, 'long'))
+ node.set('name',self.convertToStr(workflow.db_name, 'str'))
+ node.set('version',self.convertToStr(workflow.db_version, 'str'))
+ node.set('vistrail_id',self.convertToStr(workflow.db_vistrail_id, 'long'))
+
+ # set elements
+ connections = workflow.db_connections
+ for connection in connections:
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(connection, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ plugin_datas = workflow.db_plugin_datas
+ for plugin_data in plugin_datas:
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(plugin_data, childNode)
+ others = workflow.db_others
+ for other in others:
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(other, childNode)
+ modules = workflow.db_modules
+ for module in modules:
+ if module.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(module, childNode)
+ elif module.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(module, childNode)
+ elif module.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(module, childNode)
+
+ return node
+
+class DBOpmArtifactIdCauseXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'cause':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmArtifactIdCause(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_id_cause, node=None):
+ if node is None:
+ node = ElementTree.Element('cause')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact_id_cause.db_id, 'str'))
+
+ return node
+
+class DBOpmArtifactValueXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'value':
+ return None
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ value = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifactValue(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_value, node=None):
+ if node is None:
+ node = ElementTree.Element('value')
+
+ # set elements
+ value = opm_artifact_value.db_value
+ if value is not None:
+ if value.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(value, childNode)
+ elif value.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(value, childNode)
+
+ return node
+
+class DBOpmArtifactIdEffectXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'effect':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmArtifactIdEffect(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_id_effect, node=None):
+ if node is None:
+ node = ElementTree.Element('effect')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact_id_effect.db_id, 'str'))
+
+ return node
+
+class DBOpmGraphXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'opmGraph':
+ return None
+
+ accounts = None
+ processes = None
+ artifacts = None
+ agents = None
+ dependencies = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'accounts':
+ _data = self.getDao('opm_accounts').fromXML(child)
+ accounts = _data
+ elif child_tag == 'processes':
+ _data = self.getDao('opm_processes').fromXML(child)
+ processes = _data
+ elif child_tag == 'artifacts':
+ _data = self.getDao('opm_artifacts').fromXML(child)
+ artifacts = _data
+ elif child_tag == 'agents':
+ _data = self.getDao('opm_agents').fromXML(child)
+ agents = _data
+ elif child_tag == 'causalDependencies':
+ _data = self.getDao('opm_dependencies').fromXML(child)
+ dependencies = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmGraph(accounts=accounts,
+ processes=processes,
+ artifacts=artifacts,
+ agents=agents,
+ dependencies=dependencies)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_graph, node=None):
+ if node is None:
+ node = ElementTree.Element('opmGraph')
+
+ # set elements
+ accounts = opm_graph.db_accounts
+ if accounts is not None:
+ childNode = ElementTree.SubElement(node, 'accounts')
+ self.getDao('opm_accounts').toXML(accounts, childNode)
+ processes = opm_graph.db_processes
+ if processes is not None:
+ childNode = ElementTree.SubElement(node, 'processes')
+ self.getDao('opm_processes').toXML(processes, childNode)
+ artifacts = opm_graph.db_artifacts
+ if artifacts is not None:
+ childNode = ElementTree.SubElement(node, 'artifacts')
+ self.getDao('opm_artifacts').toXML(artifacts, childNode)
+ agents = opm_graph.db_agents
+ if agents is not None:
+ childNode = ElementTree.SubElement(node, 'agents')
+ self.getDao('opm_agents').toXML(agents, childNode)
+ dependencies = opm_graph.db_dependencies
+ if dependencies is not None:
+ childNode = ElementTree.SubElement(node, 'causalDependencies')
+ self.getDao('opm_dependencies').toXML(dependencies, childNode)
+
+ return node
+
+class DBRegistryXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'registry':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('rootDescriptorId', None)
+ root_descriptor_id = self.convertFromStr(data, 'long')
+
+ packages = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'package':
+ _data = self.getDao('package').fromXML(child)
+ packages.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBRegistry(id=id,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ packages=packages)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, registry, node=None):
+ if node is None:
+ node = ElementTree.Element('registry')
+
+ # set attributes
+ node.set('id',self.convertToStr(registry.db_id, 'long'))
+ node.set('version',self.convertToStr(registry.db_version, 'str'))
+ node.set('rootDescriptorId',self.convertToStr(registry.db_root_descriptor_id, 'long'))
+
+ # set elements
+ packages = registry.db_packages
+ for package in packages:
+ childNode = ElementTree.SubElement(node, 'package')
+ self.getDao('package').toXML(package, childNode)
+
+ return node
+
+class DBOpmAccountXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'account':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAccount(id=id,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_account, node=None):
+ if node is None:
+ node = ElementTree.Element('account')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_account.db_id, 'str'))
+
+ # set elements
+ value = opm_account.db_value
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'annotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, node=None):
+ if node is None:
+ node = ElementTree.Element('annotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(annotation.db_id, 'long'))
+ node.set('key',self.convertToStr(annotation.db_key, 'str'))
+ node.set('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'change':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('oldObjId', None)
+ oldObjId = self.convertFromStr(data, 'long')
+ data = node.get('newObjId', None)
+ newObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBChange(data=data,
+ id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, node=None):
+ if node is None:
+ node = ElementTree.Element('change')
+
+ # set attributes
+ node.set('id',self.convertToStr(change.db_id, 'long'))
+ node.set('what',self.convertToStr(change.db_what, 'str'))
+ node.set('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.set('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.set('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # set elements
+ data = change.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBOpmWasDerivedFromXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasDerivedFrom':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_artifact_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_artifact_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasDerivedFrom(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_derived_from, node=None):
+ if node is None:
+ node = ElementTree.Element('wasDerivedFrom')
+
+ # set elements
+ effect = opm_was_derived_from.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_artifact_id_effect').toXML(effect, childNode)
+ role = opm_was_derived_from.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_derived_from.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_artifact_id_cause').toXML(cause, childNode)
+ accounts = opm_was_derived_from.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_derived_from.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBOpmWasControlledByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasControlledBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ starts = []
+ ends = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'agent':
+ _data = self.getDao('opm_agent_id').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ starts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ ends.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasControlledBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ starts=starts,
+ ends=ends)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_controlled_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasControlledBy')
+
+ # set elements
+ effect = opm_was_controlled_by.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_was_controlled_by.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_controlled_by.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'agent')
+ self.getDao('opm_agent_id').toXML(cause, childNode)
+ accounts = opm_was_controlled_by.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ starts = opm_was_controlled_by.db_starts
+ for start in starts:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(start, childNode)
+ ends = opm_was_controlled_by.db_ends
+ for end in ends:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(end, childNode)
+
+ return node
+
+class DBOpmAgentIdXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agent':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmAgentId(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agent_id, node=None):
+ if node is None:
+ node = ElementTree.Element('agent')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_agent_id.db_id, 'str'))
+
+ return node
+
+class DBGroupExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'groupExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('groupName', None)
+ group_name = self.convertFromStr(data, 'str')
+ data = node.get('groupType', None)
+ group_type = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroupExec(item_execs=item_execs,
+ id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('groupExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(group_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(group_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(group_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(group_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(group_exec.db_module_id, 'long'))
+ node.set('groupName',self.convertToStr(group_exec.db_group_name, 'str'))
+ node.set('groupType',self.convertToStr(group_exec.db_group_type, 'str'))
+ node.set('completed',self.convertToStr(group_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(group_exec.db_error, 'str'))
+ node.set('machine_id',self.convertToStr(group_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = group_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ item_execs = group_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBOpmTimeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'time':
+ return None
+
+ # read attributes
+ data = node.get('noLaterThan', None)
+ no_later_than = self.convertFromStr(data, 'datetime')
+ data = node.get('noEarlierThan', None)
+ no_earlier_than = self.convertFromStr(data, 'datetime')
+ data = node.get('clockId', None)
+ clock_id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmTime(no_later_than=no_later_than,
+ no_earlier_than=no_earlier_than,
+ clock_id=clock_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_time, node=None):
+ if node is None:
+ node = ElementTree.Element('time')
+
+ # set attributes
+ node.set('noLaterThan',self.convertToStr(opm_time.db_no_later_than, 'datetime'))
+ node.set('noEarlierThan',self.convertToStr(opm_time.db_no_earlier_than, 'datetime'))
+ node.set('clockId',self.convertToStr(opm_time.db_clock_id, 'str'))
+
+ return node
+
+class DBPackageXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'package':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('identifier', None)
+ identifier = self.convertFromStr(data, 'str')
+ data = node.get('codepath', None)
+ codepath = self.convertFromStr(data, 'str')
+ data = node.get('loadConfiguration', None)
+ load_configuration = self.convertFromStr(data, 'int')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('description', None)
+ description = self.convertFromStr(data, 'str')
+
+ module_descriptors = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleDescriptor':
+ _data = self.getDao('module_descriptor').fromXML(child)
+ module_descriptors.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBPackage(id=id,
+ name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ module_descriptors=module_descriptors)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, package, node=None):
+ if node is None:
+ node = ElementTree.Element('package')
+
+ # set attributes
+ node.set('id',self.convertToStr(package.db_id, 'long'))
+ node.set('name',self.convertToStr(package.db_name, 'str'))
+ node.set('identifier',self.convertToStr(package.db_identifier, 'str'))
+ node.set('codepath',self.convertToStr(package.db_codepath, 'str'))
+ node.set('loadConfiguration',self.convertToStr(package.db_load_configuration, 'int'))
+ node.set('version',self.convertToStr(package.db_version, 'str'))
+ node.set('description',self.convertToStr(package.db_description, 'str'))
+
+ # set elements
+ module_descriptors = package.db_module_descriptors
+ for module_descriptor in module_descriptors:
+ childNode = ElementTree.SubElement(node, 'moduleDescriptor')
+ self.getDao('module_descriptor').toXML(module_descriptor, childNode)
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'workflowExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('ip', None)
+ ip = self.convertFromStr(data, 'str')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('vtVersion', None)
+ vt_version = self.convertFromStr(data, 'str')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('parentId', None)
+ parent_id = self.convertFromStr(data, 'long')
+ data = node.get('parentType', None)
+ parent_type = self.convertFromStr(data, 'str')
+ data = node.get('parentVersion', None)
+ parent_version = self.convertFromStr(data, 'long')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflowExec(item_execs=item_execs,
+ id=id,
+ user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('workflowExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.set('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.set('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.set('session',self.convertToStr(workflow_exec.db_session, 'long'))
+ node.set('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.set('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.set('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.set('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.set('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.set('completed',self.convertToStr(workflow_exec.db_completed, 'int'))
+ node.set('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # set elements
+ item_execs = workflow_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBLoopExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'loopExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('iteration', None)
+ iteration = self.convertFromStr(data, 'int')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLoopExec(item_execs=item_execs,
+ id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ iteration=iteration,
+ completed=completed,
+ error=error)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, loop_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('loopExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(loop_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(loop_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(loop_exec.db_ts_end, 'datetime'))
+ node.set('iteration',self.convertToStr(loop_exec.db_iteration, 'int'))
+ node.set('completed',self.convertToStr(loop_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(loop_exec.db_error, 'str'))
+
+ # set elements
+ item_execs = loop_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'connection':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+
+ ports = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ ports.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, node=None):
+ if node is None:
+ node = ElementTree.Element('connection')
+
+ # set attributes
+ node.set('id',self.convertToStr(connection.db_id, 'long'))
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(port, childNode)
+
+ return node
+
+class DBOpmProcessXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'process':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.getDao('opm_process_value').fromXML(child)
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcess(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process, node=None):
+ if node is None:
+ node = ElementTree.Element('process')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process.db_id, 'str'))
+
+ # set elements
+ value = opm_process.db_value
+ if value is not None:
+ childNode = ElementTree.SubElement(node, 'value')
+ self.getDao('opm_process_value').toXML(value, childNode)
+ accounts = opm_process.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBOpmWasTriggeredByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasTriggeredBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_process_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasTriggeredBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_triggered_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasTriggeredBy')
+
+ # set elements
+ effect = opm_was_triggered_by.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_was_triggered_by.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_triggered_by.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_process_id_cause').toXML(cause, childNode)
+ accounts = opm_was_triggered_by.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_triggered_by.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBOpmProcessValueXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'value':
+ return None
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ value = _data
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ value = _data
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcessValue(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_value, node=None):
+ if node is None:
+ node = ElementTree.Element('value')
+
+ # set elements
+ value = opm_process_value.db_value
+ if value is not None:
+ if value.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(value, childNode)
+ elif value.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(value, childNode)
+ elif value.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(value, childNode)
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'action':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('prevId', None)
+ prevId = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('prune', None)
+ prune = self.convertFromStr(data, 'int')
+
+ annotations = []
+ operations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'add':
+ _data = self.getDao('add').fromXML(child)
+ operations.append(_data)
+ elif child_tag == 'delete':
+ _data = self.getDao('delete').fromXML(child)
+ operations.append(_data)
+ elif child_tag == 'change':
+ _data = self.getDao('change').fromXML(child)
+ operations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAction(operations=operations,
+ id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ prune=prune,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, node=None):
+ if node is None:
+ node = ElementTree.Element('action')
+
+ # set attributes
+ node.set('id',self.convertToStr(action.db_id, 'long'))
+ node.set('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.set('date',self.convertToStr(action.db_date, 'datetime'))
+ node.set('session',self.convertToStr(action.db_session, 'long'))
+ node.set('user',self.convertToStr(action.db_user, 'str'))
+ node.set('prune',self.convertToStr(action.db_prune, 'int'))
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ childNode = ElementTree.SubElement(node, 'add')
+ self.getDao('add').toXML(operation, childNode)
+ elif operation.vtType == 'delete':
+ childNode = ElementTree.SubElement(node, 'delete')
+ self.getDao('delete').toXML(operation, childNode)
+ elif operation.vtType == 'change':
+ childNode = ElementTree.SubElement(node, 'change')
+ self.getDao('change').toXML(operation, childNode)
+
+ return node
+
+class DBOpmAgentXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agent':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAgent(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agent, node=None):
+ if node is None:
+ node = ElementTree.Element('agent')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_agent.db_id, 'str'))
+
+ # set elements
+ value = opm_agent.db_value
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+ accounts = opm_agent.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'delete':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, node=None):
+ if node is None:
+ node = ElementTree.Element('delete')
+
+ # set attributes
+ node.set('id',self.convertToStr(delete.db_id, 'long'))
+ node.set('what',self.convertToStr(delete.db_what, 'str'))
+ node.set('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'vistrail':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child_tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ actions=actions,
+ tags=tags,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, node=None):
+ if node is None:
+ node = ElementTree.Element('vistrail')
+
+ # set attributes
+ node.set('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.set('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.set('name',self.convertToStr(vistrail.db_name, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = vistrail.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+ annotations = vistrail.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'moduleExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ module_name = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+ loop_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ loop_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ annotations=annotations,
+ loop_execs=loop_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(module_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.set('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+ node.set('completed',self.convertToStr(module_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(module_exec.db_error, 'str'))
+ node.set('machine_id',self.convertToStr(module_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ loop_execs = module_exec.db_loop_execs
+ for loop_exec in loop_execs:
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(loop_exec, childNode)
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'opm_process_id_effect' not in self:
+ self['opm_process_id_effect'] = DBOpmProcessIdEffectXMLDAOBase(self)
+ if 'opm_was_generated_by' not in self:
+ self['opm_was_generated_by'] = DBOpmWasGeneratedByXMLDAOBase(self)
+ if 'opm_accounts' not in self:
+ self['opm_accounts'] = DBOpmAccountsXMLDAOBase(self)
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'module_descriptor' not in self:
+ self['module_descriptor'] = DBModuleDescriptorXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'opm_role' not in self:
+ self['opm_role'] = DBOpmRoleXMLDAOBase(self)
+ if 'opm_processes' not in self:
+ self['opm_processes'] = DBOpmProcessesXMLDAOBase(self)
+ if 'opm_account_id' not in self:
+ self['opm_account_id'] = DBOpmAccountIdXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'opm_artifact' not in self:
+ self['opm_artifact'] = DBOpmArtifactXMLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'opm_agents' not in self:
+ self['opm_agents'] = DBOpmAgentsXMLDAOBase(self)
+ if 'opm_process_id_cause' not in self:
+ self['opm_process_id_cause'] = DBOpmProcessIdCauseXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'opm_overlaps' not in self:
+ self['opm_overlaps'] = DBOpmOverlapsXMLDAOBase(self)
+ if 'opm_artifacts' not in self:
+ self['opm_artifacts'] = DBOpmArtifactsXMLDAOBase(self)
+ if 'opm_dependencies' not in self:
+ self['opm_dependencies'] = DBOpmDependenciesXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'opm_used' not in self:
+ self['opm_used'] = DBOpmUsedXMLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'opm_artifact_id_cause' not in self:
+ self['opm_artifact_id_cause'] = DBOpmArtifactIdCauseXMLDAOBase(self)
+ if 'opm_artifact_value' not in self:
+ self['opm_artifact_value'] = DBOpmArtifactValueXMLDAOBase(self)
+ if 'opm_artifact_id_effect' not in self:
+ self['opm_artifact_id_effect'] = DBOpmArtifactIdEffectXMLDAOBase(self)
+ if 'opm_graph' not in self:
+ self['opm_graph'] = DBOpmGraphXMLDAOBase(self)
+ if 'registry' not in self:
+ self['registry'] = DBRegistryXMLDAOBase(self)
+ if 'opm_account' not in self:
+ self['opm_account'] = DBOpmAccountXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'opm_was_derived_from' not in self:
+ self['opm_was_derived_from'] = DBOpmWasDerivedFromXMLDAOBase(self)
+ if 'opm_was_controlled_by' not in self:
+ self['opm_was_controlled_by'] = DBOpmWasControlledByXMLDAOBase(self)
+ if 'opm_agent_id' not in self:
+ self['opm_agent_id'] = DBOpmAgentIdXMLDAOBase(self)
+ if 'group_exec' not in self:
+ self['group_exec'] = DBGroupExecXMLDAOBase(self)
+ if 'opm_time' not in self:
+ self['opm_time'] = DBOpmTimeXMLDAOBase(self)
+ if 'package' not in self:
+ self['package'] = DBPackageXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'loop_exec' not in self:
+ self['loop_exec'] = DBLoopExecXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'opm_process' not in self:
+ self['opm_process'] = DBOpmProcessXMLDAOBase(self)
+ if 'opm_was_triggered_by' not in self:
+ self['opm_was_triggered_by'] = DBOpmWasTriggeredByXMLDAOBase(self)
+ if 'opm_process_value' not in self:
+ self['opm_process_value'] = DBOpmProcessValueXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'opm_agent' not in self:
+ self['opm_agent'] = DBOpmAgentXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v1_0_1/persistence/xml/xml_dao.py b/vistrails/db/versions/v1_0_1/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..955c01a
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/persistence/xml/xml_dao.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v1_0_1/schemas/sql/vistrails.sql b/vistrails/db/versions/v1_0_1/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..badb7af
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/schemas/sql/vistrails.sql
@@ -0,0 +1,382 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+CREATE TABLE `vistrails_version`(`version` char(16)) engine=InnoDB;
+INSERT INTO `vistrails_version`(`version`) VALUES ('1.0.1');
+
+CREATE TABLE thumbnail(
+ id int not null auto_increment primary key,
+ file_name varchar(255),
+ image_bytes mediumblob,
+ last_modified datetime
+) engine=InnoDB;
+
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(255),
+ type varchar(255),
+ optional int,
+ sort_key int,
+ sigstring varchar(4095),
+ labels varchar(4095),
+ defaults varchar(4095),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module_descriptor(
+ id int,
+ name varchar(255),
+ package varchar(255),
+ namespace varchar(255),
+ package_version varchar(255),
+ version varchar(255),
+ base_descriptor_id int,
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ signature varchar(4095),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE group_tbl(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ tag varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime,
+ vistrail_id int
+) engine=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE plugin_data(
+ id int,
+ data varchar(8191),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE abstraction(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ internal_version varchar(255),
+ tag varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE workflow(
+ id int not null auto_increment primary key,
+ entity_id int,
+ entity_type char(16),
+ name varchar(255),
+ version char(16),
+ last_modified datetime,
+ vistrail_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE registry(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ root_descriptor_id int,
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE group_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ group_name varchar(255),
+ group_type varchar(255),
+ completed int,
+ error varchar(1023),
+ machine_id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE package(
+ id int not null auto_increment primary key,
+ name varchar(255),
+ identifier varchar(1023),
+ codepath varchar(1023),
+ load_configuration int,
+ version varchar(255),
+ description varchar(1023),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ session int,
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ completed int,
+ name varchar(255),
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE loop_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ iteration int,
+ completed int,
+ error varchar(1023),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session int,
+ user varchar(255),
+ prune int,
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ module_name varchar(255),
+ completed int,
+ error varchar(1023),
+ machine_id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
diff --git a/vistrails/db/versions/v1_0_1/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v1_0_1/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..47043c1
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,42 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+DROP TABLE IF EXISTS `vistrails_version`;
+
+DROP TABLE IF EXISTS thumbnail;
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, module_descriptor, tag, port, group_tbl, log_tbl, machine, add_tbl, other, location, parameter, plugin_data, function, abstraction, workflow, registry, annotation, change_tbl, group_exec, package, workflow_exec, loop_exec, connection_tbl, action, delete_tbl, vistrail, module_exec;
diff --git a/vistrails/db/versions/v1_0_1/schemas/xml/vistrail.xsd b/vistrails/db/versions/v1_0_1/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..997f9da
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/schemas/xml/vistrail.xsd
@@ -0,0 +1,280 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="prune" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="signature" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="optional" type="xs:int"/>
+ <xs:attribute name="sortKey" type="xs:int"/>
+ <xs:attribute name="sigstring" type="xs:string"/>
+ <xs:attribute name="labels" type="xs:string"/>
+ <xs:attribute name="defaults" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="internalVersion" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="group">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="workflow" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="tag" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plugin_data">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="workflow">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v1_0_1/schemas/xml/vtlink.xsd b/vistrails/db/versions/v1_0_1/schemas/xml/vtlink.xsd
new file mode 100644
index 0000000..6ae8bca
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/schemas/xml/vtlink.xsd
@@ -0,0 +1,55 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0" encoding="UTF-8"?>
+
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
+<xs:element name="vtlink">
+<xs:complexType>
+<xs:attribute name="host" type="xs:string"></xs:attribute>
+<xs:attribute name="database" type="xs:string"></xs:attribute>
+<xs:attribute name="port" type="xs:int"></xs:attribute>
+<xs:attribute name="vtid" type="xs:int"></xs:attribute>
+<xs:attribute name="version" type="xs:int"></xs:attribute>
+<xs:attribute name="tag" type="xs:string"></xs:attribute>
+<xs:attribute name="url" type="xs:string"></xs:attribute>
+<xs:attribute name="vtcontent" type="xs:string"></xs:attribute>
+<xs:attribute name="execute" type="xs:boolean"></xs:attribute>
+<xs:attribute name="showSpreadsheetOnly" type="xs:boolean"></xs:attribute>
+<xs:attribute name="forceDB" type="xs:boolean"></xs:attribute>
+</xs:complexType>
+</xs:element>
+
+</xs:schema>
diff --git a/vistrails/db/versions/v1_0_1/specs/all.xml b/vistrails/db/versions/v1_0_1/specs/all.xml
new file mode 100644
index 0000000..60a5dba
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/specs/all.xml
@@ -0,0 +1,2699 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<objects>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ABSTRACTION +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="internal_version" type="str">
+ <xml name="internalVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ACTION ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long" foreignKey="true" object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="prune" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="vistrail" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ADD +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ANNOTATION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CHANGE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CONNECTION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- DELETE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- FUNCTION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group" parentClass="module">
+ <layout>
+ <xml name="group" nodeType="xs:element"/>
+ <sql table="group_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow" type="object" mapping="one-to-one"
+ expand="false">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOCATION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MACHINE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="tag" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOOP_EXEC +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="loop_exec">
+ <layout>
+ <xml name="loopExec" nodeType="xs:element"/>
+ <sql table="loop_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <!--<property name="input" type="str">
+ <xml name="input" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>-->
+
+ <property name="iteration" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP_EXEC ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group_exec">
+ <layout>
+ <xml name="groupExec" nodeType="xs:element"/>
+ <sql table="group_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="group_name" type="str">
+ <xml name="groupName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="group_type" type="str">
+ <xml name="groupType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <!--<property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>-->
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_EXEC +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OTHER +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PARAMETER +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PLUGIN DATA +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="plugin_data">
+ <layout>
+ <xml name="plugin_data" nodeType="xs:element"/>
+ <sql table="plugin_data"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="data" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORT ++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="signature" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORTSPEC ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="optional" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="sort_key" type="int">
+ <xml name="sortKey" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="sigstring" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="labels" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="defaults" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="module_descriptor">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_DESCRIPTOR +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_descriptor">
+ <layout>
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ <sql table="module_descriptor"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package_version" type="str">
+ <xml name="packageVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="base_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="baseDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="package" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ <!--
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="registry">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="package">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+ -->
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PACKAGE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="package">
+ <layout>
+ <xml name="package" nodeType="xs:element"/>
+ <sql table="package"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="identifier" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="codepath" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="load_configuration" type="int">
+ <xml name="loadConfiguration" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="description" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property ref="true" object="module_descriptor" type="list"
+ mapping="one-to-many" index="name:namespace:version">
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="registry" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REGISTRY ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="registry">
+ <layout>
+ <xml name="registry" nodeType="xs:element"/>
+ <sql table="registry"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="root_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="rootDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <!-- <xml nodeType="xs:attribute" type="xs:string"/> -->
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="package" type="list"
+ mapping="one-to-many" index="identifier:version">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- TAG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VISTRAIL ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstraction" ref="true" object="abstraction">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group" ref="true" object="group">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="plugin_data" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="group" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW_EXEC +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_GRAPH +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_graph">
+ <layout>
+ <xml name="opmGraph" nodeType="xs:element"/>
+ <!-- <sql table="opm_graph"/> -->
+ </layout>
+
+ <property name="accounts" ref="true" object="opm_accounts"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="processes" ref="true" object="opm_processes"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="artifacts" ref="true" object="opm_artifacts"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="agents" ref="true" object="opm_agents"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="dependencies" ref="true" object="opm_dependencies"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNTS ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_accounts">
+ <layout>
+ <xml name="accounts" nodeType="xs:element"/>
+ <!-- <sql table="accounts"/> -->
+ </layout>
+
+ <property name="account" ref="true" object="opm_account" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="opm_overlaps" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNT +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_account">
+ <layout>
+ <xml name="account" nodeType="xs:element"/>
+ <!-- <sql table="account"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_OVERLAPS ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_overlaps">
+ <layout>
+ <xml name="overlaps" nodeType="xs:element"/>
+ <!-- <sql table="overlaps"/> -->
+ </layout>
+
+ <property ref="true" object="opm_account_id" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACTS +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifacts">
+ <layout>
+ <xml name="artifacts" nodeType="xs:element"/>
+ <!-- <sql table="artifacts"/> -->
+ </layout>
+
+ <property name="artifact" ref="true" object="opm_artifact" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_VALUE ++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_value">
+ <layout>
+ <xml name="value" nodeType="xs:element"/>
+ <!-- <sql table="artifact_value"/> -->
+ </layout>
+
+ <choice name="value" type="object" mapping="one-to-one">
+ <property ref="true" object="portSpec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact">
+ <layout>
+ <xml name="artifact" nodeType="xs:element"/>
+ <!-- <sql table="artifact"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" ref="true" object="opm_artifact_value" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESSES +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_processes">
+ <layout>
+ <xml name="processes" nodeType="xs:element"/>
+ <!-- <sql table="processes"/> -->
+ </layout>
+
+ <property name="process" ref="true" object="opm_process" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_VALUE +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_value">
+ <layout>
+ <xml name="value" nodeType="xs:element"/>
+ <!-- <sql table="process_value"/> -->
+ </layout>
+
+ <choice name="value" type="object" mapping="one-to-one">
+ <property ref="true" object="module_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process">
+ <layout>
+ <xml name="process" nodeType="xs:element"/>
+ <!-- <sql table="process"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" ref="true" object="opm_process_value" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENTS ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agents">
+ <layout>
+ <xml name="agents" nodeType="xs:element"/>
+ <!-- <sql table="agents"/> -->
+ </layout>
+
+ <property name="agent" ref="true" object="opm_agent" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENT +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agent">
+ <layout>
+ <xml name="agent" nodeType="xs:element"/>
+ <!-- <sql table="agent"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type=""/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_DEPENDENCIES ++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_dependencies">
+ <layout>
+ <xml name="causalDependencies" nodeType="xs:element"/>
+ <!-- <sql table="causal_dependencies"/> -->
+ </layout>
+
+ <choice name="dependency" type="list" mapping="one-to-many">
+ <property name="used" ref="true" object="opm_used">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_generated_by" ref="true"
+ object="opm_was_generated_by">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_triggered_by" ref="true"
+ object="opm_was_triggered_by">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_derived_from" ref="true"
+ object="opm_was_derived_from">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_controlled_by" ref="true"
+ object="opm_was_controlled_by">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_TIME ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_time">
+ <layout>
+ <xml name="time" nodeType="xs:element"/>
+ <!-- <sql table="time"/> -->
+ </layout>
+
+ <property name="no_later_than" type="datetime">
+ <xml name="noLaterThan" nodeType="xs:attribute" type="xs:dateTime"/>
+ <!-- <sql type="datetime"/> -->
+ </property>
+
+ <property name="no_earlier_than" type="datetime">
+ <xml name="noEarlierThan" nodeType="xs:attribute" type="xs:dateTime"/>
+ <!-- <sql type="datetime"/> -->
+ </property>
+
+ <property name="clock_id" type="str">
+ <xml name="clockId" nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNT_ID ++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_account_id">
+ <layout>
+ <xml name="account" nodeType="xs:element"/>
+ <!-- <sql table="account_id"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_account">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_ID_CAUSE ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_id_cause">
+ <layout>
+ <xml name="cause" nodeType="xs:element"/>
+ <!-- <sql table="process_id_cause"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_process">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_ID_EFFECT +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_id_effect">
+ <layout>
+ <xml name="effect" nodeType="xs:element"/>
+ <!-- <sql table="process_id_effect"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_process">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_ID_CAUSE +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_id_cause">
+ <layout>
+ <xml name="cause" nodeType="xs:element"/>
+ <!-- <sql table="artifact_id_cause"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_artifact">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_ID_EFFECT ++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_id_effect">
+ <layout>
+ <xml name="effect" nodeType="xs:element"/>
+ <!-- <sql table="artifact_id_effect"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_artifact">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENT_ID ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agent_id">
+ <layout>
+ <xml name="agent" nodeType="xs:element"/>
+ <!-- <sql table="agent_id"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_agent">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ROLE ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_role">
+ <layout>
+ <xml name="role" nodeType="xs:element"/>
+ <!-- <sql table="role"/> -->
+ </layout>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(4095)"/> -->
+ </property>
+ </object>
+
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_USED ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_used">
+ <layout>
+ <xml name="used" nodeType="xs:element"/>
+ <!-- <sql table="used"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_artifact_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_GENERATED_BY ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_generated_by">
+ <layout>
+ <xml name="wasGeneratedBy" nodeType="xs:element"/>
+ <!-- <sql table="was_generated_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_artifact_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_process_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_CONTROLLED_BY +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_controlled_by">
+ <layout>
+ <xml name="wasControlledBy" nodeType="xs:element"/>
+ <!-- <sql table="was_controlled_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_agent_id"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="start" ref="true" object="opm_time" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="end" ref="true" object="opm_time" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_DERIVED_FROM ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_derived_from">
+ <layout>
+ <xml name="wasDerivedFrom" nodeType="xs:element"/>
+ <!-- <sql table="was_derived_from"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_artifact_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_artifact_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_TRIGGERED_BY ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_triggered_by">
+ <layout>
+ <xml name="wasTriggeredBy" nodeType="xs:element"/>
+ <!-- <sql table="was_triggered_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_process_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+</objects>
diff --git a/vistrails/db/versions/v1_0_1/translate/__init__.py b/vistrails/db/versions/v1_0_1/translate/__init__.py
new file mode 100644
index 0000000..ecda317
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '1.0.1'
diff --git a/vistrails/db/versions/v1_0_1/translate/v1_0_0.py b/vistrails/db/versions/v1_0_1/translate/v1_0_0.py
new file mode 100644
index 0000000..8cc7274
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/translate/v1_0_0.py
@@ -0,0 +1,80 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v1_0_1.domain import DBVistrail, DBWorkflow, DBLog, \
+ DBRegistry, DBModuleDescriptor, DBGroup
+
+def translateVistrail(_vistrail):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBGroup': {'workflow': update_workflow}}
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict)
+ vistrail.db_version = '1.0.1'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBGroup': {'workflow': update_workflow}}
+ workflow = DBWorkflow.update_version(_workflow, translate_dict)
+ workflow.db_version = '1.0.1'
+ return workflow
+
+def translateLog(_log):
+ translate_dict = {}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '1.0.1'
+ return log
+
+def translateRegistry(_registry):
+ def update_descriptors(old_obj, translate_dict):
+ def get_update_method(package_version):
+ def update_package_version(old_desc, t_dict):
+ return package_version
+ return update_package_version
+
+ descriptors = []
+ for descriptor in old_obj.db_module_descriptors:
+ new_t_dict = {'DBModuleDescriptor':
+ {'package_version': \
+ get_update_method(old_obj.db_version)}}
+ d = DBModuleDescriptor.update_version(descriptor, new_t_dict)
+ descriptors.append(d)
+ return descriptors
+
+ translate_dict = {'DBPackage': {'module_descriptors': update_descriptors}}
+ registry = DBRegistry.update_version(_registry, translate_dict)
+ registry.db_version = '1.0.1'
+ return registry
diff --git a/vistrails/db/versions/v1_0_1/translate/v1_0_2.py b/vistrails/db/versions/v1_0_1/translate/v1_0_2.py
new file mode 100644
index 0000000..6f16c1c
--- /dev/null
+++ b/vistrails/db/versions/v1_0_1/translate/v1_0_2.py
@@ -0,0 +1,193 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v1_0_1.domain import DBVistrail, DBWorkflow, DBLog, \
+ DBRegistry, DBGroup, DBTag, DBAnnotation, DBAction, IdScope
+
+def translateVistrail(_vistrail):
+ tag_annotations = {}
+ notes_annotations = {}
+ thumb_annotations = {}
+ upgrade_annotations = {}
+ prune_annotations = {}
+
+ del_tag_annotations = {}
+ del_notes_annotations = {}
+ del_thumb_annotations = {}
+ del_upgrade_annotations = {}
+ del_prune_annotations = {}
+
+ key_lists = {'__tag__': tag_annotations,
+ '__notes__': notes_annotations,
+ '__thumb__': thumb_annotations,
+ '__upgrade__': upgrade_annotations,
+ '__prune__': prune_annotations}
+
+ del_key_lists = {'__tag__': del_tag_annotations,
+ '__notes__': del_notes_annotations,
+ '__thumb__': del_thumb_annotations,
+ '__upgrade__': del_upgrade_annotations,
+ '__prune__': del_prune_annotations}
+
+ _vistrail.update_id_scope()
+ id_scope = _vistrail.idScope
+
+ def update_tags(old_obj, translate_dict):
+ new_tags = []
+ for (id, (_, tag, is_new, is_dirty)) in tag_annotations.iteritems():
+ new_tag = DBTag(id=id, name=tag)
+ new_tag.is_new = is_new
+ new_tag.is_dirty = is_dirty
+ new_tags.append(new_tag)
+ return new_tags
+
+ def update_prune(old_obj, translate_dict):
+ if old_obj.db_id in prune_annotations:
+ (_, prune_val, _, _) = prune_annotations[old_obj.db_id]
+ if prune_val == str(True):
+ return 1
+ elif prune_val == str(False):
+ return 0
+ return None
+
+ def update_annotations(old_obj, translate_dict):
+ new_annotations = [DBAnnotation.update_version(a, translate_dict)
+ for a in old_obj.db_annotations]
+ if old_obj.db_id in notes_annotations:
+ (id, notes, is_new, is_dirty) = notes_annotations[old_obj.db_id]
+ ann = DBAnnotation(id=id,
+ key='__notes__',
+ value=notes)
+ ann.is_new = is_new
+ ann.is_dirty = is_dirty
+ new_annotations.append(ann)
+ if old_obj.db_id in upgrade_annotations:
+ (id, upgrade, is_new, is_dirty) = \
+ upgrade_annotations[old_obj.db_id]
+ ann = DBAnnotation(id=id,
+ key='__upgrade__',
+ value=upgrade)
+ ann.is_new = is_new
+ ann.is_dirty = is_dirty
+ new_annotations.append(ann)
+ if old_obj.db_id in thumb_annotations:
+ (id, thumb, is_new, is_dirty) = thumb_annotations[old_obj.db_id]
+ ann = DBAnnotation(id=id,
+ key='__thumb__',
+ value=thumb)
+ ann.is_new = is_new
+ ann.is_dirty = is_dirty
+ new_annotations.append(ann)
+ return new_annotations
+
+ def update_actions(old_obj, translate_dict):
+ new_actions = []
+ for action in old_obj.db_actions:
+ if action.db_id in del_notes_annotations:
+ (id, notes, is_new, is_dirty) = \
+ del_notes_annotations[action.db_id]
+ ann = DBAnnotation(id=id,
+ key='__notes__',
+ value=notes)
+ ann.is_new = is_new
+ ann.is_dirty = is_dirty
+ action.db_deleted_annotations.append(ann)
+ if action.db_id in del_upgrade_annotations:
+ (id, upgrade, is_new, is_dirty) = \
+ del_upgrade_annotations[action.db_id]
+ ann = DBAnnotation(id=id,
+ key='__upgrade__',
+ value=upgrade)
+ ann.is_new = is_new
+ ann.is_dirty = is_dirty
+ action.db_deleted_annotations.append(ann)
+ if action.db_id in del_thumb_annotations:
+ (id, thumb, is_new, is_dirty) = \
+ del_thumb_annotations[action.db_id]
+ ann = DBAnnotation(id=id,
+ key='__thumb__',
+ value=thumb)
+ ann.is_new = is_new
+ ann.is_dirty = is_dirty
+ action.db_deleted_annotations.append(ann)
+ new_actions.append(DBAction.update_version(action, translate_dict))
+ return new_actions
+
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+
+ for a in _vistrail.db_actionAnnotations:
+ if a.db_key in key_lists:
+ key_lists[a.db_key][a.db_action_id] = \
+ (a.db_id, a.db_value, a.is_new, a.is_dirty)
+ for a in _vistrail.db_deleted_actionAnnotations:
+ if a.db_key in del_key_lists:
+ del_key_lists[a.db_key][a.db_action_id] = \
+ (a.db_id, a.db_value, a.is_new, a.is_dirty)
+
+ translate_dict = {'DBGroup': {'workflow': update_workflow},
+ 'DBVistrail': {'tags': update_tags,
+ 'actions': update_actions},
+ 'DBAction': {'annotations': update_annotations,
+ 'prune': update_prune}}
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict)
+ for (id, (_, tag, is_new, is_dirty)) in del_tag_annotations.iteritems():
+ new_tag = DBTag(id=id, name=tag)
+ new_tag.is_new = is_new
+ new_tag.is_dirty = is_dirty
+ vistrail.db_deleted_tags.append(new_tag)
+
+ vistrail.db_version = '1.0.1'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBGroup': {'workflow': update_workflow}}
+ workflow = DBWorkflow.update_version(_workflow, translate_dict)
+ workflow.db_version = '1.0.1'
+ return workflow
+
+def translateLog(_log):
+ translate_dict = {}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '1.0.1'
+ return log
+
+def translateRegistry(_registry):
+ translate_dict = {}
+ registry = DBRegistry.update_version(_registry, translate_dict)
+ registry.db_version = '1.0.1'
+ return registry
diff --git a/vistrails/db/versions/v1_0_2/__init__.py b/vistrails/db/versions/v1_0_2/__init__.py
new file mode 100644
index 0000000..0e024b6
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '1.0.2'
diff --git a/vistrails/db/versions/v1_0_2/domain/__init__.py b/vistrails/db/versions/v1_0_2/domain/__init__.py
new file mode 100644
index 0000000..a8208f6
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/domain/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from registry import DBRegistry
+from workflow import DBWorkflow
+from vistrail import DBVistrail
+from log import DBLog
+from id_scope import IdScope
diff --git a/vistrails/db/versions/v1_0_2/domain/auto_gen.py b/vistrails/db/versions/v1_0_2/domain/auto_gen.py
new file mode 100644
index 0000000..3934e4f
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/domain/auto_gen.py
@@ -0,0 +1,11719 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBOpmProcessIdEffect(object):
+
+ vtType = 'opm_process_id_effect'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessIdEffect.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessIdEffect(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_process', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_process', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessIdEffect()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBOpmWasGeneratedBy(object):
+
+ vtType = 'opm_was_generated_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasGeneratedBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasGeneratedBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasGeneratedBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmArtifactIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmArtifactIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmProcessIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmProcessIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBOpmAccounts(object):
+
+ vtType = 'opm_accounts'
+
+ def __init__(self, accounts=None, opm_overlapss=None):
+ self.db_deleted_accounts = []
+ self.db_accounts_id_index = {}
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ for v in self._db_accounts:
+ self.db_accounts_id_index[v.db_id] = v
+ self.db_deleted_opm_overlapss = []
+ if opm_overlapss is None:
+ self._db_opm_overlapss = []
+ else:
+ self._db_opm_overlapss = opm_overlapss
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccounts.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccounts()
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_overlapss is None:
+ cp._db_opm_overlapss = []
+ else:
+ cp._db_opm_overlapss = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_overlapss]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_accounts_id_index = dict((v.db_id, v) for v in cp._db_accounts)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccounts()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccount.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccount.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_overlapss' in class_dict:
+ res = class_dict['opm_overlapss'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_overlaps(obj)
+ elif hasattr(old_obj, 'db_opm_overlapss') and old_obj.db_opm_overlapss is not None:
+ for obj in old_obj.db_opm_overlapss:
+ new_obj.db_add_opm_overlaps(DBOpmOverlaps.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_overlapss') and hasattr(new_obj, 'db_deleted_opm_overlapss'):
+ for obj in old_obj.db_deleted_opm_overlapss:
+ n_obj = DBOpmOverlaps.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_overlapss.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_overlapss:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_overlaps(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_overlapss)
+ if remove:
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_overlapss = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_overlapss:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ self.db_accounts_id_index[account.db_id] = account
+ def db_change_account(self, account):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == account.db_id:
+ self._db_accounts[i] = account
+ found = True
+ break
+ if not found:
+ self._db_accounts.append(account)
+ self.db_accounts_id_index[account.db_id] = account
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == account.db_id:
+ if not self._db_accounts[i].is_new:
+ self.db_deleted_accounts.append(self._db_accounts[i])
+ del self._db_accounts[i]
+ break
+ del self.db_accounts_id_index[account.db_id]
+ def db_get_account(self, key):
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == key:
+ return self._db_accounts[i]
+ return None
+ def db_get_account_by_id(self, key):
+ return self.db_accounts_id_index[key]
+ def db_has_account_with_id(self, key):
+ return key in self.db_accounts_id_index
+
+ def __get_db_opm_overlapss(self):
+ return self._db_opm_overlapss
+ def __set_db_opm_overlapss(self, opm_overlapss):
+ self._db_opm_overlapss = opm_overlapss
+ self.is_dirty = True
+ db_opm_overlapss = property(__get_db_opm_overlapss, __set_db_opm_overlapss)
+ def db_get_opm_overlapss(self):
+ return self._db_opm_overlapss
+ def db_add_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ self._db_opm_overlapss.append(opm_overlaps)
+ def db_change_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ self._db_opm_overlapss.append(opm_overlaps)
+ def db_delete_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_overlaps(self, key):
+ return None
+
+
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, optional=None, sort_key=None, sigstring=None, labels=None, defaults=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_type = type
+ self._db_optional = optional
+ self._db_sort_key = sort_key
+ self._db_sigstring = sigstring
+ self._db_labels = labels
+ self._db_defaults = defaults
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPortSpec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec(id=self._db_id,
+ name=self._db_name,
+ type=self._db_type,
+ optional=self._db_optional,
+ sort_key=self._db_sort_key,
+ sigstring=self._db_sigstring,
+ labels=self._db_labels,
+ defaults=self._db_defaults)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPortSpec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'optional' in class_dict:
+ res = class_dict['optional'](old_obj, trans_dict)
+ new_obj.db_optional = res
+ elif hasattr(old_obj, 'db_optional') and old_obj.db_optional is not None:
+ new_obj.db_optional = old_obj.db_optional
+ if 'sort_key' in class_dict:
+ res = class_dict['sort_key'](old_obj, trans_dict)
+ new_obj.db_sort_key = res
+ elif hasattr(old_obj, 'db_sort_key') and old_obj.db_sort_key is not None:
+ new_obj.db_sort_key = old_obj.db_sort_key
+ if 'sigstring' in class_dict:
+ res = class_dict['sigstring'](old_obj, trans_dict)
+ new_obj.db_sigstring = res
+ elif hasattr(old_obj, 'db_sigstring') and old_obj.db_sigstring is not None:
+ new_obj.db_sigstring = old_obj.db_sigstring
+ if 'labels' in class_dict:
+ res = class_dict['labels'](old_obj, trans_dict)
+ new_obj.db_labels = res
+ elif hasattr(old_obj, 'db_labels') and old_obj.db_labels is not None:
+ new_obj.db_labels = old_obj.db_labels
+ if 'defaults' in class_dict:
+ res = class_dict['defaults'](old_obj, trans_dict)
+ new_obj.db_defaults = res
+ elif hasattr(old_obj, 'db_defaults') and old_obj.db_defaults is not None:
+ new_obj.db_defaults = old_obj.db_defaults
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_optional(self):
+ return self._db_optional
+ def __set_db_optional(self, optional):
+ self._db_optional = optional
+ self.is_dirty = True
+ db_optional = property(__get_db_optional, __set_db_optional)
+ def db_add_optional(self, optional):
+ self._db_optional = optional
+ def db_change_optional(self, optional):
+ self._db_optional = optional
+ def db_delete_optional(self, optional):
+ self._db_optional = None
+
+ def __get_db_sort_key(self):
+ return self._db_sort_key
+ def __set_db_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ self.is_dirty = True
+ db_sort_key = property(__get_db_sort_key, __set_db_sort_key)
+ def db_add_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ def db_change_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ def db_delete_sort_key(self, sort_key):
+ self._db_sort_key = None
+
+ def __get_db_sigstring(self):
+ return self._db_sigstring
+ def __set_db_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ self.is_dirty = True
+ db_sigstring = property(__get_db_sigstring, __set_db_sigstring)
+ def db_add_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ def db_change_sigstring(self, sigstring):
+ self._db_sigstring = sigstring
+ def db_delete_sigstring(self, sigstring):
+ self._db_sigstring = None
+
+ def __get_db_labels(self):
+ return self._db_labels
+ def __set_db_labels(self, labels):
+ self._db_labels = labels
+ self.is_dirty = True
+ db_labels = property(__get_db_labels, __set_db_labels)
+ def db_add_labels(self, labels):
+ self._db_labels = labels
+ def db_change_labels(self, labels):
+ self._db_labels = labels
+ def db_delete_labels(self, labels):
+ self._db_labels = None
+
+ def __get_db_defaults(self):
+ return self._db_defaults
+ def __set_db_defaults(self, defaults):
+ self._db_defaults = defaults
+ self.is_dirty = True
+ db_defaults = property(__get_db_defaults, __set_db_defaults)
+ def db_add_defaults(self, defaults):
+ self._db_defaults = defaults
+ def db_change_defaults(self, defaults):
+ self._db_defaults = defaults
+ def db_delete_defaults(self, defaults):
+ self._db_defaults = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModule.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModule()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleDescriptor(object):
+
+ vtType = 'module_descriptor'
+
+ def __init__(self, id=None, name=None, package=None, namespace=None, package_version=None, version=None, base_descriptor_id=None, portSpecs=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_package = package
+ self._db_namespace = namespace
+ self._db_package_version = package_version
+ self._db_version = version
+ self._db_base_descriptor_id = base_descriptor_id
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleDescriptor.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleDescriptor(id=self._db_id,
+ name=self._db_name,
+ package=self._db_package,
+ namespace=self._db_namespace,
+ package_version=self._db_package_version,
+ version=self._db_version,
+ base_descriptor_id=self._db_base_descriptor_id)
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_base_descriptor_id') and ('module_descriptor', self._db_base_descriptor_id) in id_remap:
+ cp._db_base_descriptor_id = id_remap[('module_descriptor', self._db_base_descriptor_id)]
+
+ # recreate indices and set flags
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleDescriptor()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package_version' in class_dict:
+ res = class_dict['package_version'](old_obj, trans_dict)
+ new_obj.db_package_version = res
+ elif hasattr(old_obj, 'db_package_version') and old_obj.db_package_version is not None:
+ new_obj.db_package_version = old_obj.db_package_version
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'base_descriptor_id' in class_dict:
+ res = class_dict['base_descriptor_id'](old_obj, trans_dict)
+ new_obj.db_base_descriptor_id = res
+ elif hasattr(old_obj, 'db_base_descriptor_id') and old_obj.db_base_descriptor_id is not None:
+ new_obj.db_base_descriptor_id = old_obj.db_base_descriptor_id
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package_version(self):
+ return self._db_package_version
+ def __set_db_package_version(self, package_version):
+ self._db_package_version = package_version
+ self.is_dirty = True
+ db_package_version = property(__get_db_package_version, __set_db_package_version)
+ def db_add_package_version(self, package_version):
+ self._db_package_version = package_version
+ def db_change_package_version(self, package_version):
+ self._db_package_version = package_version
+ def db_delete_package_version(self, package_version):
+ self._db_package_version = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_base_descriptor_id(self):
+ return self._db_base_descriptor_id
+ def __set_db_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ self.is_dirty = True
+ db_base_descriptor_id = property(__get_db_base_descriptor_id, __set_db_base_descriptor_id)
+ def db_add_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ def db_change_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ def db_delete_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = None
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self._db_id = id
+ self._db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBTag.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag(id=self._db_id,
+ name=self._db_name)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('action', self._db_id) in id_remap:
+ cp._db_id = id_remap[('action', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBTag()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmRole(object):
+
+ vtType = 'opm_role'
+
+ def __init__(self, value=None):
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmRole.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmRole(value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmRole()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+
+
+class DBOpmProcesses(object):
+
+ vtType = 'opm_processes'
+
+ def __init__(self, processs=None):
+ self.db_deleted_processs = []
+ self.db_processs_id_index = {}
+ if processs is None:
+ self._db_processs = []
+ else:
+ self._db_processs = processs
+ for v in self._db_processs:
+ self.db_processs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcesses.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcesses()
+ if self._db_processs is None:
+ cp._db_processs = []
+ else:
+ cp._db_processs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_processs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_processs_id_index = dict((v.db_id, v) for v in cp._db_processs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcesses()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'processs' in class_dict:
+ res = class_dict['processs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_process(obj)
+ elif hasattr(old_obj, 'db_processs') and old_obj.db_processs is not None:
+ for obj in old_obj.db_processs:
+ new_obj.db_add_process(DBOpmProcess.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_processs') and hasattr(new_obj, 'db_deleted_processs'):
+ for obj in old_obj.db_deleted_processs:
+ n_obj = DBOpmProcess.update_version(obj, trans_dict)
+ new_obj.db_deleted_processs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_processs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_process(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_processs)
+ if remove:
+ self.db_deleted_processs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_processs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_processs(self):
+ return self._db_processs
+ def __set_db_processs(self, processs):
+ self._db_processs = processs
+ self.is_dirty = True
+ db_processs = property(__get_db_processs, __set_db_processs)
+ def db_get_processs(self):
+ return self._db_processs
+ def db_add_process(self, process):
+ self.is_dirty = True
+ self._db_processs.append(process)
+ self.db_processs_id_index[process.db_id] = process
+ def db_change_process(self, process):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == process.db_id:
+ self._db_processs[i] = process
+ found = True
+ break
+ if not found:
+ self._db_processs.append(process)
+ self.db_processs_id_index[process.db_id] = process
+ def db_delete_process(self, process):
+ self.is_dirty = True
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == process.db_id:
+ if not self._db_processs[i].is_new:
+ self.db_deleted_processs.append(self._db_processs[i])
+ del self._db_processs[i]
+ break
+ del self.db_processs_id_index[process.db_id]
+ def db_get_process(self, key):
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == key:
+ return self._db_processs[i]
+ return None
+ def db_get_process_by_id(self, key):
+ return self.db_processs_id_index[key]
+ def db_has_process_with_id(self, key):
+ return key in self.db_processs_id_index
+
+
+
+class DBOpmAccountId(object):
+
+ vtType = 'opm_account_id'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccountId.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccountId(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_account', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_account', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccountId()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, name=None, signature=None):
+ self._db_id = id
+ self._db_type = type
+ self._db_moduleId = moduleId
+ self._db_moduleName = moduleName
+ self._db_name = name
+ self._db_signature = signature
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPort.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort(id=self._db_id,
+ type=self._db_type,
+ moduleId=self._db_moduleId,
+ moduleName=self._db_moduleName,
+ name=self._db_name,
+ signature=self._db_signature)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_moduleId') and ('module', self._db_moduleId) in id_remap:
+ cp._db_moduleId = id_remap[('module', self._db_moduleId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPort()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'moduleId' in class_dict:
+ res = class_dict['moduleId'](old_obj, trans_dict)
+ new_obj.db_moduleId = res
+ elif hasattr(old_obj, 'db_moduleId') and old_obj.db_moduleId is not None:
+ new_obj.db_moduleId = old_obj.db_moduleId
+ if 'moduleName' in class_dict:
+ res = class_dict['moduleName'](old_obj, trans_dict)
+ new_obj.db_moduleName = res
+ elif hasattr(old_obj, 'db_moduleName') and old_obj.db_moduleName is not None:
+ new_obj.db_moduleName = old_obj.db_moduleName
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'signature' in class_dict:
+ res = class_dict['signature'](old_obj, trans_dict)
+ new_obj.db_signature = res
+ elif hasattr(old_obj, 'db_signature') and old_obj.db_signature is not None:
+ new_obj.db_signature = old_obj.db_signature
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_moduleId(self):
+ return self._db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self._db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self._db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self._db_moduleName = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_signature(self):
+ return self._db_signature
+ def __set_db_signature(self, signature):
+ self._db_signature = signature
+ self.is_dirty = True
+ db_signature = property(__get_db_signature, __set_db_signature)
+ def db_add_signature(self, signature):
+ self._db_signature = signature
+ def db_change_signature(self, signature):
+ self._db_signature = signature
+ def db_delete_signature(self, signature):
+ self._db_signature = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmArtifact(object):
+
+ vtType = 'opm_artifact'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self.db_deleted_value = []
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifact.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifact(id=self._db_id)
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifact()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ new_obj.db_add_value(DBOpmArtifactValue.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ n_obj = DBOpmArtifactValue.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_value = []
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBGroup(object):
+
+ vtType = 'group'
+
+ def __init__(self, id=None, workflow=None, cache=None, name=None, namespace=None, package=None, version=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self.db_deleted_workflow = []
+ self._db_workflow = workflow
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroup.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroup(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version)
+ if self._db_workflow is not None:
+ cp._db_workflow = self._db_workflow.do_copy()
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroup()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'workflow' in class_dict:
+ res = class_dict['workflow'](old_obj, trans_dict)
+ new_obj.db_workflow = res
+ elif hasattr(old_obj, 'db_workflow') and old_obj.db_workflow is not None:
+ obj = old_obj.db_workflow
+ new_obj.db_add_workflow(DBWorkflow.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow') and hasattr(new_obj, 'db_deleted_workflow'):
+ for obj in old_obj.db_deleted_workflow:
+ n_obj = DBWorkflow.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow.append(n_obj)
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow)
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_workflow = []
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_workflow is not None and self._db_workflow.has_changes():
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_workflow(self):
+ return self._db_workflow
+ def __set_db_workflow(self, workflow):
+ self._db_workflow = workflow
+ self.is_dirty = True
+ db_workflow = property(__get_db_workflow, __set_db_workflow)
+ def db_add_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_change_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_delete_workflow(self, workflow):
+ if not self.is_new:
+ self.db_deleted_workflow.append(self._db_workflow)
+ self._db_workflow = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, workflow_execs=None, machines=None, vistrail_id=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_workflow_execs = []
+ self.db_workflow_execs_id_index = {}
+ if workflow_execs is None:
+ self._db_workflow_execs = []
+ else:
+ self._db_workflow_execs = workflow_execs
+ for v in self._db_workflow_execs:
+ self.db_workflow_execs_id_index[v.db_id] = v
+ self.db_deleted_machines = []
+ self.db_machines_id_index = {}
+ if machines is None:
+ self._db_machines = []
+ else:
+ self._db_machines = machines
+ for v in self._db_machines:
+ self.db_machines_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_workflow_execs is None:
+ cp._db_workflow_execs = []
+ else:
+ cp._db_workflow_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_workflow_execs]
+ if self._db_machines is None:
+ cp._db_machines = []
+ else:
+ cp._db_machines = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_machines]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_workflow_execs_id_index = dict((v.db_id, v) for v in cp._db_workflow_execs)
+ cp.db_machines_id_index = dict((v.db_id, v) for v in cp._db_machines)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'workflow_execs' in class_dict:
+ res = class_dict['workflow_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_workflow_exec(obj)
+ elif hasattr(old_obj, 'db_workflow_execs') and old_obj.db_workflow_execs is not None:
+ for obj in old_obj.db_workflow_execs:
+ new_obj.db_add_workflow_exec(DBWorkflowExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow_execs') and hasattr(new_obj, 'db_deleted_workflow_execs'):
+ for obj in old_obj.db_deleted_workflow_execs:
+ n_obj = DBWorkflowExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow_execs.append(n_obj)
+ if 'machines' in class_dict:
+ res = class_dict['machines'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_machine(obj)
+ elif hasattr(old_obj, 'db_machines') and old_obj.db_machines is not None:
+ for obj in old_obj.db_machines:
+ new_obj.db_add_machine(DBMachine.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_machines') and hasattr(new_obj, 'db_deleted_machines'):
+ for obj in old_obj.db_deleted_machines:
+ n_obj = DBMachine.update_version(obj, trans_dict)
+ new_obj.db_deleted_machines.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_workflow_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self.db_machines:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow_execs)
+ children.extend(self.db_deleted_machines)
+ if remove:
+ self.db_deleted_workflow_execs = []
+ self.db_deleted_machines = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_workflow_execs:
+ if child.has_changes():
+ return True
+ for child in self._db_machines:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_workflow_execs(self):
+ return self._db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self._db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self._db_workflow_execs
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ self._db_workflow_execs[i] = workflow_exec
+ found = True
+ break
+ if not found:
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ if not self._db_workflow_execs[i].is_new:
+ self.db_deleted_workflow_execs.append(self._db_workflow_execs[i])
+ del self._db_workflow_execs[i]
+ break
+ del self.db_workflow_execs_id_index[workflow_exec.db_id]
+ def db_get_workflow_exec(self, key):
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == key:
+ return self._db_workflow_execs[i]
+ return None
+ def db_get_workflow_exec_by_id(self, key):
+ return self.db_workflow_execs_id_index[key]
+ def db_has_workflow_exec_with_id(self, key):
+ return key in self.db_workflow_execs_id_index
+
+ def __get_db_machines(self):
+ return self._db_machines
+ def __set_db_machines(self, machines):
+ self._db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self._db_machines
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ self._db_machines[i] = machine
+ found = True
+ break
+ if not found:
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ if not self._db_machines[i].is_new:
+ self.db_deleted_machines.append(self._db_machines[i])
+ del self._db_machines[i]
+ break
+ del self.db_machines_id_index[machine.db_id]
+ def db_get_machine(self, key):
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == key:
+ return self._db_machines[i]
+ return None
+ def db_get_machine_by_id(self, key):
+ return self.db_machines_id_index[key]
+ def db_has_machine_with_id(self, key):
+ return key in self.db_machines_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmAgents(object):
+
+ vtType = 'opm_agents'
+
+ def __init__(self, agents=None):
+ self.db_deleted_agents = []
+ self.db_agents_id_index = {}
+ if agents is None:
+ self._db_agents = []
+ else:
+ self._db_agents = agents
+ for v in self._db_agents:
+ self.db_agents_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgents.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgents()
+ if self._db_agents is None:
+ cp._db_agents = []
+ else:
+ cp._db_agents = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_agents]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_agents_id_index = dict((v.db_id, v) for v in cp._db_agents)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgents()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'agents' in class_dict:
+ res = class_dict['agents'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_agent(obj)
+ elif hasattr(old_obj, 'db_agents') and old_obj.db_agents is not None:
+ for obj in old_obj.db_agents:
+ new_obj.db_add_agent(DBOpmAgent.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_agents') and hasattr(new_obj, 'db_deleted_agents'):
+ for obj in old_obj.db_deleted_agents:
+ n_obj = DBOpmAgent.update_version(obj, trans_dict)
+ new_obj.db_deleted_agents.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_agents:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_agent(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_agents)
+ if remove:
+ self.db_deleted_agents = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_agents:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_agents(self):
+ return self._db_agents
+ def __set_db_agents(self, agents):
+ self._db_agents = agents
+ self.is_dirty = True
+ db_agents = property(__get_db_agents, __set_db_agents)
+ def db_get_agents(self):
+ return self._db_agents
+ def db_add_agent(self, agent):
+ self.is_dirty = True
+ self._db_agents.append(agent)
+ self.db_agents_id_index[agent.db_id] = agent
+ def db_change_agent(self, agent):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == agent.db_id:
+ self._db_agents[i] = agent
+ found = True
+ break
+ if not found:
+ self._db_agents.append(agent)
+ self.db_agents_id_index[agent.db_id] = agent
+ def db_delete_agent(self, agent):
+ self.is_dirty = True
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == agent.db_id:
+ if not self._db_agents[i].is_new:
+ self.db_deleted_agents.append(self._db_agents[i])
+ del self._db_agents[i]
+ break
+ del self.db_agents_id_index[agent.db_id]
+ def db_get_agent(self, key):
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == key:
+ return self._db_agents[i]
+ return None
+ def db_get_agent_by_id(self, key):
+ return self.db_agents_id_index[key]
+ def db_has_agent_with_id(self, key):
+ return key in self.db_agents_id_index
+
+
+
+class DBOpmProcessIdCause(object):
+
+ vtType = 'opm_process_id_cause'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessIdCause.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessIdCause(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_process', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_process', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessIdCause()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_os = os
+ self._db_architecture = architecture
+ self._db_processor = processor
+ self._db_ram = ram
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMachine.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine(id=self._db_id,
+ name=self._db_name,
+ os=self._db_os,
+ architecture=self._db_architecture,
+ processor=self._db_processor,
+ ram=self._db_ram)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and ('vistrail', self._db_vistrailId) in id_remap:
+ cp._db_vistrailId = id_remap[('vistrail', self._db_vistrailId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMachine()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'os' in class_dict:
+ res = class_dict['os'](old_obj, trans_dict)
+ new_obj.db_os = res
+ elif hasattr(old_obj, 'db_os') and old_obj.db_os is not None:
+ new_obj.db_os = old_obj.db_os
+ if 'architecture' in class_dict:
+ res = class_dict['architecture'](old_obj, trans_dict)
+ new_obj.db_architecture = res
+ elif hasattr(old_obj, 'db_architecture') and old_obj.db_architecture is not None:
+ new_obj.db_architecture = old_obj.db_architecture
+ if 'processor' in class_dict:
+ res = class_dict['processor'](old_obj, trans_dict)
+ new_obj.db_processor = res
+ elif hasattr(old_obj, 'db_processor') and old_obj.db_processor is not None:
+ new_obj.db_processor = old_obj.db_processor
+ if 'ram' in class_dict:
+ res = class_dict['ram'](old_obj, trans_dict)
+ new_obj.db_ram = res
+ elif hasattr(old_obj, 'db_ram') and old_obj.db_ram is not None:
+ new_obj.db_ram = old_obj.db_ram
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_os(self):
+ return self._db_os
+ def __set_db_os(self, os):
+ self._db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self._db_os = os
+ def db_change_os(self, os):
+ self._db_os = os
+ def db_delete_os(self, os):
+ self._db_os = None
+
+ def __get_db_architecture(self):
+ return self._db_architecture
+ def __set_db_architecture(self, architecture):
+ self._db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self._db_architecture = None
+
+ def __get_db_processor(self):
+ return self._db_processor
+ def __set_db_processor(self, processor):
+ self._db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self._db_processor = processor
+ def db_change_processor(self, processor):
+ self._db_processor = processor
+ def db_delete_processor(self, processor):
+ self._db_processor = None
+
+ def __get_db_ram(self):
+ return self._db_ram
+ def __set_db_ram(self, ram):
+ self._db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self._db_ram = ram
+ def db_change_ram(self, ram):
+ self._db_ram = ram
+ def db_delete_ram(self, ram):
+ self._db_ram = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, data=None, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAdd.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAdd()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOther.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOther(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOther()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self._db_id = id
+ self._db_x = x
+ self._db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLocation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation(id=self._db_id,
+ x=self._db_x,
+ y=self._db_y)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLocation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'x' in class_dict:
+ res = class_dict['x'](old_obj, trans_dict)
+ new_obj.db_x = res
+ elif hasattr(old_obj, 'db_x') and old_obj.db_x is not None:
+ new_obj.db_x = old_obj.db_x
+ if 'y' in class_dict:
+ res = class_dict['y'](old_obj, trans_dict)
+ new_obj.db_y = res
+ elif hasattr(old_obj, 'db_y') and old_obj.db_y is not None:
+ new_obj.db_y = old_obj.db_y
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_x(self):
+ return self._db_x
+ def __set_db_x(self, x):
+ self._db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self._db_x = x
+ def db_change_x(self, x):
+ self._db_x = x
+ def db_delete_x(self, x):
+ self._db_x = None
+
+ def __get_db_y(self):
+ return self._db_y
+ def __set_db_y(self, y):
+ self._db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self._db_y = y
+ def db_change_y(self, y):
+ self._db_y = y
+ def db_delete_y(self, y):
+ self._db_y = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmOverlaps(object):
+
+ vtType = 'opm_overlaps'
+
+ def __init__(self, opm_account_ids=None):
+ self.db_deleted_opm_account_ids = []
+ if opm_account_ids is None:
+ self._db_opm_account_ids = []
+ else:
+ self._db_opm_account_ids = opm_account_ids
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmOverlaps.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmOverlaps()
+ if self._db_opm_account_ids is None:
+ cp._db_opm_account_ids = []
+ else:
+ cp._db_opm_account_ids = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_account_ids]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmOverlaps()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'opm_account_ids' in class_dict:
+ res = class_dict['opm_account_ids'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_account_id(obj)
+ elif hasattr(old_obj, 'db_opm_account_ids') and old_obj.db_opm_account_ids is not None:
+ for obj in old_obj.db_opm_account_ids:
+ new_obj.db_add_opm_account_id(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_account_ids') and hasattr(new_obj, 'db_deleted_opm_account_ids'):
+ for obj in old_obj.db_deleted_opm_account_ids:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_account_ids.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_opm_account_ids:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_account_id(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_opm_account_ids)
+ if remove:
+ self.db_deleted_opm_account_ids = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_opm_account_ids:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_opm_account_ids(self):
+ return self._db_opm_account_ids
+ def __set_db_opm_account_ids(self, opm_account_ids):
+ self._db_opm_account_ids = opm_account_ids
+ self.is_dirty = True
+ db_opm_account_ids = property(__get_db_opm_account_ids, __set_db_opm_account_ids)
+ def db_get_opm_account_ids(self):
+ return self._db_opm_account_ids
+ def db_add_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ self._db_opm_account_ids.append(opm_account_id)
+ def db_change_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ self._db_opm_account_ids.append(opm_account_id)
+ def db_delete_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_account_id(self, key):
+ return None
+
+
+
+class DBOpmArtifacts(object):
+
+ vtType = 'opm_artifacts'
+
+ def __init__(self, artifacts=None):
+ self.db_deleted_artifacts = []
+ self.db_artifacts_id_index = {}
+ if artifacts is None:
+ self._db_artifacts = []
+ else:
+ self._db_artifacts = artifacts
+ for v in self._db_artifacts:
+ self.db_artifacts_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifacts.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifacts()
+ if self._db_artifacts is None:
+ cp._db_artifacts = []
+ else:
+ cp._db_artifacts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_artifacts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_artifacts_id_index = dict((v.db_id, v) for v in cp._db_artifacts)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifacts()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'artifacts' in class_dict:
+ res = class_dict['artifacts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_artifact(obj)
+ elif hasattr(old_obj, 'db_artifacts') and old_obj.db_artifacts is not None:
+ for obj in old_obj.db_artifacts:
+ new_obj.db_add_artifact(DBOpmArtifact.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_artifacts') and hasattr(new_obj, 'db_deleted_artifacts'):
+ for obj in old_obj.db_deleted_artifacts:
+ n_obj = DBOpmArtifact.update_version(obj, trans_dict)
+ new_obj.db_deleted_artifacts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_artifacts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_artifact(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_artifacts)
+ if remove:
+ self.db_deleted_artifacts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_artifacts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_artifacts(self):
+ return self._db_artifacts
+ def __set_db_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ self.is_dirty = True
+ db_artifacts = property(__get_db_artifacts, __set_db_artifacts)
+ def db_get_artifacts(self):
+ return self._db_artifacts
+ def db_add_artifact(self, artifact):
+ self.is_dirty = True
+ self._db_artifacts.append(artifact)
+ self.db_artifacts_id_index[artifact.db_id] = artifact
+ def db_change_artifact(self, artifact):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == artifact.db_id:
+ self._db_artifacts[i] = artifact
+ found = True
+ break
+ if not found:
+ self._db_artifacts.append(artifact)
+ self.db_artifacts_id_index[artifact.db_id] = artifact
+ def db_delete_artifact(self, artifact):
+ self.is_dirty = True
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == artifact.db_id:
+ if not self._db_artifacts[i].is_new:
+ self.db_deleted_artifacts.append(self._db_artifacts[i])
+ del self._db_artifacts[i]
+ break
+ del self.db_artifacts_id_index[artifact.db_id]
+ def db_get_artifact(self, key):
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == key:
+ return self._db_artifacts[i]
+ return None
+ def db_get_artifact_by_id(self, key):
+ return self.db_artifacts_id_index[key]
+ def db_has_artifact_with_id(self, key):
+ return key in self.db_artifacts_id_index
+
+
+
+class DBOpmDependencies(object):
+
+ vtType = 'opm_dependencies'
+
+ def __init__(self, dependencys=None):
+ self.db_deleted_dependencys = []
+ if dependencys is None:
+ self._db_dependencys = []
+ else:
+ self._db_dependencys = dependencys
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmDependencies.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmDependencies()
+ if self._db_dependencys is None:
+ cp._db_dependencys = []
+ else:
+ cp._db_dependencys = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_dependencys]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmDependencies()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'dependencys' in class_dict:
+ res = class_dict['dependencys'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_dependency(obj)
+ elif hasattr(old_obj, 'db_dependencys') and old_obj.db_dependencys is not None:
+ for obj in old_obj.db_dependencys:
+ if obj.vtType == 'opm_used':
+ new_obj.db_add_dependency(DBOpmUsed.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_generated_by':
+ new_obj.db_add_dependency(DBOpmWasGeneratedBy.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_triggered_by':
+ new_obj.db_add_dependency(DBOpmWasTriggeredBy.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_derived_from':
+ new_obj.db_add_dependency(DBOpmWasDerivedFrom.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_controlled_by':
+ new_obj.db_add_dependency(DBOpmWasControlledBy.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_dependencys') and hasattr(new_obj, 'db_deleted_dependencys'):
+ for obj in old_obj.db_deleted_dependencys:
+ if obj.vtType == 'opm_used':
+ n_obj = DBOpmUsed.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_generated_by':
+ n_obj = DBOpmWasGeneratedBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_triggered_by':
+ n_obj = DBOpmWasTriggeredBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_derived_from':
+ n_obj = DBOpmWasDerivedFrom.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_controlled_by':
+ n_obj = DBOpmWasControlledBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_dependencys:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_dependency(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_dependencys)
+ if remove:
+ self.db_deleted_dependencys = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_dependencys:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_dependencys(self):
+ return self._db_dependencys
+ def __set_db_dependencys(self, dependencys):
+ self._db_dependencys = dependencys
+ self.is_dirty = True
+ db_dependencys = property(__get_db_dependencys, __set_db_dependencys)
+ def db_get_dependencys(self):
+ return self._db_dependencys
+ def db_add_dependency(self, dependency):
+ self.is_dirty = True
+ self._db_dependencys.append(dependency)
+ def db_change_dependency(self, dependency):
+ self.is_dirty = True
+ self._db_dependencys.append(dependency)
+ def db_delete_dependency(self, dependency):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_dependency(self, key):
+ return None
+
+
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self._db_type = type
+ self._db_val = val
+ self._db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBParameter.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name,
+ type=self._db_type,
+ val=self._db_val,
+ alias=self._db_alias)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBParameter()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'val' in class_dict:
+ res = class_dict['val'](old_obj, trans_dict)
+ new_obj.db_val = res
+ elif hasattr(old_obj, 'db_val') and old_obj.db_val is not None:
+ new_obj.db_val = old_obj.db_val
+ if 'alias' in class_dict:
+ res = class_dict['alias'](old_obj, trans_dict)
+ new_obj.db_alias = res
+ elif hasattr(old_obj, 'db_alias') and old_obj.db_alias is not None:
+ new_obj.db_alias = old_obj.db_alias
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_val(self):
+ return self._db_val
+ def __set_db_val(self, val):
+ self._db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self._db_val = val
+ def db_change_val(self, val):
+ self._db_val = val
+ def db_delete_val(self, val):
+ self._db_val = None
+
+ def __get_db_alias(self):
+ return self._db_alias
+ def __set_db_alias(self, alias):
+ self._db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self._db_alias = alias
+ def db_change_alias(self, alias):
+ self._db_alias = alias
+ def db_delete_alias(self, alias):
+ self._db_alias = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmUsed(object):
+
+ vtType = 'opm_used'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmUsed.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmUsed()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmUsed()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmArtifactIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmArtifactIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBPluginData(object):
+
+ vtType = 'plugin_data'
+
+ def __init__(self, id=None, data=None):
+ self._db_id = id
+ self._db_data = data
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPluginData.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPluginData(id=self._db_id,
+ data=self._db_data)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPluginData()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ new_obj.db_data = old_obj.db_data
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ self._db_data = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self.db_deleted_parameters = []
+ self.db_parameters_id_index = {}
+ if parameters is None:
+ self._db_parameters = []
+ else:
+ self._db_parameters = parameters
+ for v in self._db_parameters:
+ self.db_parameters_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name)
+ if self._db_parameters is None:
+ cp._db_parameters = []
+ else:
+ cp._db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_parameters_id_index = dict((v.db_id, v) for v in cp._db_parameters)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBFunction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'parameters' in class_dict:
+ res = class_dict['parameters'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_parameter(obj)
+ elif hasattr(old_obj, 'db_parameters') and old_obj.db_parameters is not None:
+ for obj in old_obj.db_parameters:
+ new_obj.db_add_parameter(DBParameter.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_parameters') and hasattr(new_obj, 'db_deleted_parameters'):
+ for obj in old_obj.db_deleted_parameters:
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_parameters.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_parameters)
+ if remove:
+ self.db_deleted_parameters = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_parameters(self):
+ return self._db_parameters
+ def __set_db_parameters(self, parameters):
+ self._db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self._db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ self._db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ if not self._db_parameters[i].is_new:
+ self.db_deleted_parameters.append(self._db_parameters[i])
+ del self._db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter.db_id]
+ def db_get_parameter(self, key):
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == key:
+ return self._db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return key in self.db_parameters_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBActionAnnotation(object):
+
+ vtType = 'actionAnnotation'
+
+ def __init__(self, id=None, key=None, value=None, action_id=None, date=None, user=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self._db_action_id = action_id
+ self._db_date = date
+ self._db_user = user
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBActionAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBActionAnnotation(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value,
+ action_id=self._db_action_id,
+ date=self._db_date,
+ user=self._db_user)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_action_id') and ('action', self._db_action_id) in id_remap:
+ cp._db_action_id = id_remap[('action', self._db_action_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBActionAnnotation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ if 'action_id' in class_dict:
+ res = class_dict['action_id'](old_obj, trans_dict)
+ new_obj.db_action_id = res
+ elif hasattr(old_obj, 'db_action_id') and old_obj.db_action_id is not None:
+ new_obj.db_action_id = old_obj.db_action_id
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def __get_db_action_id(self):
+ return self._db_action_id
+ def __set_db_action_id(self, action_id):
+ self._db_action_id = action_id
+ self.is_dirty = True
+ db_action_id = property(__get_db_action_id, __set_db_action_id)
+ def db_add_action_id(self, action_id):
+ self._db_action_id = action_id
+ def db_change_action_id(self, action_id):
+ self._db_action_id = action_id
+ def db_delete_action_id(self, action_id):
+ self._db_action_id = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, internal_version=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_internal_version = internal_version
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ internal_version=self._db_internal_version)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAbstraction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'internal_version' in class_dict:
+ res = class_dict['internal_version'](old_obj, trans_dict)
+ new_obj.db_internal_version = res
+ elif hasattr(old_obj, 'db_internal_version') and old_obj.db_internal_version is not None:
+ new_obj.db_internal_version = old_obj.db_internal_version
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_internal_version(self):
+ return self._db_internal_version
+ def __set_db_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ self.is_dirty = True
+ db_internal_version = property(__get_db_internal_version, __set_db_internal_version)
+ def db_add_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_change_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_delete_internal_version(self, internal_version):
+ self._db_internal_version = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, modules=None, id=None, entity_type=None, name=None, version=None, last_modified=None, connections=None, annotations=None, plugin_datas=None, others=None, vistrail_id=None):
+ self.db_deleted_modules = []
+ self.db_modules_id_index = {}
+ if modules is None:
+ self._db_modules = []
+ else:
+ self._db_modules = modules
+ for v in self._db_modules:
+ self.db_modules_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_name = name
+ self._db_version = version
+ self._db_last_modified = last_modified
+ self.db_deleted_connections = []
+ self.db_connections_id_index = {}
+ if connections is None:
+ self._db_connections = []
+ else:
+ self._db_connections = connections
+ for v in self._db_connections:
+ self.db_connections_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_plugin_datas = []
+ self.db_plugin_datas_id_index = {}
+ if plugin_datas is None:
+ self._db_plugin_datas = []
+ else:
+ self._db_plugin_datas = plugin_datas
+ for v in self._db_plugin_datas:
+ self.db_plugin_datas_id_index[v.db_id] = v
+ self.db_deleted_others = []
+ self.db_others_id_index = {}
+ if others is None:
+ self._db_others = []
+ else:
+ self._db_others = others
+ for v in self._db_others:
+ self.db_others_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow(id=self._db_id,
+ entity_type=self._db_entity_type,
+ name=self._db_name,
+ version=self._db_version,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_modules is None:
+ cp._db_modules = []
+ else:
+ cp._db_modules = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_modules]
+ if self._db_connections is None:
+ cp._db_connections = []
+ else:
+ cp._db_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_connections]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_plugin_datas is None:
+ cp._db_plugin_datas = []
+ else:
+ cp._db_plugin_datas = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_plugin_datas]
+ if self._db_others is None:
+ cp._db_others = []
+ else:
+ cp._db_others = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_others]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_modules_id_index = dict((v.db_id, v) for v in cp._db_modules)
+ cp.db_connections_id_index = dict((v.db_id, v) for v in cp._db_connections)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_plugin_datas_id_index = dict((v.db_id, v) for v in cp._db_plugin_datas)
+ cp.db_others_id_index = dict((v.db_id, v) for v in cp._db_others)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'modules' in class_dict:
+ res = class_dict['modules'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module(obj)
+ elif hasattr(old_obj, 'db_modules') and old_obj.db_modules is not None:
+ for obj in old_obj.db_modules:
+ if obj.vtType == 'module':
+ new_obj.db_add_module(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_module(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_module(DBGroup.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_modules') and hasattr(new_obj, 'db_deleted_modules'):
+ for obj in old_obj.db_deleted_modules:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'connections' in class_dict:
+ res = class_dict['connections'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_connection(obj)
+ elif hasattr(old_obj, 'db_connections') and old_obj.db_connections is not None:
+ for obj in old_obj.db_connections:
+ new_obj.db_add_connection(DBConnection.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_connections') and hasattr(new_obj, 'db_deleted_connections'):
+ for obj in old_obj.db_deleted_connections:
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_connections.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'plugin_datas' in class_dict:
+ res = class_dict['plugin_datas'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_plugin_data(obj)
+ elif hasattr(old_obj, 'db_plugin_datas') and old_obj.db_plugin_datas is not None:
+ for obj in old_obj.db_plugin_datas:
+ new_obj.db_add_plugin_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_plugin_datas') and hasattr(new_obj, 'db_deleted_plugin_datas'):
+ for obj in old_obj.db_deleted_plugin_datas:
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_plugin_datas.append(n_obj)
+ if 'others' in class_dict:
+ res = class_dict['others'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_other(obj)
+ elif hasattr(old_obj, 'db_others') and old_obj.db_others is not None:
+ for obj in old_obj.db_others:
+ new_obj.db_add_other(DBOther.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_others') and hasattr(new_obj, 'db_deleted_others'):
+ for obj in old_obj.db_deleted_others:
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_others.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_connections:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_connection(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_plugin_datas:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_plugin_data(child)
+ to_del = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_other(child)
+ to_del = []
+ for child in self.db_modules:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_connections)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_plugin_datas)
+ children.extend(self.db_deleted_others)
+ children.extend(self.db_deleted_modules)
+ if remove:
+ self.db_deleted_connections = []
+ self.db_deleted_annotations = []
+ self.db_deleted_plugin_datas = []
+ self.db_deleted_others = []
+ self.db_deleted_modules = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_connections:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_plugin_datas:
+ if child.has_changes():
+ return True
+ for child in self._db_others:
+ if child.has_changes():
+ return True
+ for child in self._db_modules:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_modules(self):
+ return self._db_modules
+ def __set_db_modules(self, modules):
+ self._db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self._db_modules
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ self._db_modules[i] = module
+ found = True
+ break
+ if not found:
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ if not self._db_modules[i].is_new:
+ self.db_deleted_modules.append(self._db_modules[i])
+ del self._db_modules[i]
+ break
+ del self.db_modules_id_index[module.db_id]
+ def db_get_module(self, key):
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == key:
+ return self._db_modules[i]
+ return None
+ def db_get_module_by_id(self, key):
+ return self.db_modules_id_index[key]
+ def db_has_module_with_id(self, key):
+ return key in self.db_modules_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_connections(self):
+ return self._db_connections
+ def __set_db_connections(self, connections):
+ self._db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self._db_connections
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ self._db_connections[i] = connection
+ found = True
+ break
+ if not found:
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ if not self._db_connections[i].is_new:
+ self.db_deleted_connections.append(self._db_connections[i])
+ del self._db_connections[i]
+ break
+ del self.db_connections_id_index[connection.db_id]
+ def db_get_connection(self, key):
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == key:
+ return self._db_connections[i]
+ return None
+ def db_get_connection_by_id(self, key):
+ return self.db_connections_id_index[key]
+ def db_has_connection_with_id(self, key):
+ return key in self.db_connections_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_plugin_datas(self):
+ return self._db_plugin_datas
+ def __set_db_plugin_datas(self, plugin_datas):
+ self._db_plugin_datas = plugin_datas
+ self.is_dirty = True
+ db_plugin_datas = property(__get_db_plugin_datas, __set_db_plugin_datas)
+ def db_get_plugin_datas(self):
+ return self._db_plugin_datas
+ def db_add_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_change_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ self._db_plugin_datas[i] = plugin_data
+ found = True
+ break
+ if not found:
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_delete_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ if not self._db_plugin_datas[i].is_new:
+ self.db_deleted_plugin_datas.append(self._db_plugin_datas[i])
+ del self._db_plugin_datas[i]
+ break
+ del self.db_plugin_datas_id_index[plugin_data.db_id]
+ def db_get_plugin_data(self, key):
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == key:
+ return self._db_plugin_datas[i]
+ return None
+ def db_get_plugin_data_by_id(self, key):
+ return self.db_plugin_datas_id_index[key]
+ def db_has_plugin_data_with_id(self, key):
+ return key in self.db_plugin_datas_id_index
+
+ def __get_db_others(self):
+ return self._db_others
+ def __set_db_others(self, others):
+ self._db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self._db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ self._db_others[i] = other
+ found = True
+ break
+ if not found:
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ if not self._db_others[i].is_new:
+ self.db_deleted_others.append(self._db_others[i])
+ del self._db_others[i]
+ break
+ del self.db_others_id_index[other.db_id]
+ def db_get_other(self, key):
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == key:
+ return self._db_others[i]
+ return None
+ def db_get_other_by_id(self, key):
+ return self.db_others_id_index[key]
+ def db_has_other_with_id(self, key):
+ return key in self.db_others_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmArtifactIdCause(object):
+
+ vtType = 'opm_artifact_id_cause'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactIdCause.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactIdCause(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_artifact', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_artifact', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactIdCause()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBOpmArtifactValue(object):
+
+ vtType = 'opm_artifact_value'
+
+ def __init__(self, value=None):
+ self.db_deleted_value = []
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactValue.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactValue()
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactValue()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ if obj.vtType == 'portSpec':
+ new_obj.db_add_value(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_value(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ if obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ if remove:
+ self.db_deleted_value = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+
+
+class DBOpmArtifactIdEffect(object):
+
+ vtType = 'opm_artifact_id_effect'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactIdEffect.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactIdEffect(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_artifact', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_artifact', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactIdEffect()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBOpmGraph(object):
+
+ vtType = 'opm_graph'
+
+ def __init__(self, accounts=None, processes=None, artifacts=None, agents=None, dependencies=None):
+ self.db_deleted_accounts = []
+ self._db_accounts = accounts
+ self.db_deleted_processes = []
+ self._db_processes = processes
+ self.db_deleted_artifacts = []
+ self._db_artifacts = artifacts
+ self.db_deleted_agents = []
+ self._db_agents = agents
+ self.db_deleted_dependencies = []
+ self._db_dependencies = dependencies
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmGraph.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmGraph()
+ if self._db_accounts is not None:
+ cp._db_accounts = self._db_accounts.do_copy(new_ids, id_scope, id_remap)
+ if self._db_processes is not None:
+ cp._db_processes = self._db_processes.do_copy(new_ids, id_scope, id_remap)
+ if self._db_artifacts is not None:
+ cp._db_artifacts = self._db_artifacts.do_copy(new_ids, id_scope, id_remap)
+ if self._db_agents is not None:
+ cp._db_agents = self._db_agents.do_copy(new_ids, id_scope, id_remap)
+ if self._db_dependencies is not None:
+ cp._db_dependencies = self._db_dependencies.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmGraph()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ new_obj.db_accounts = res
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ obj = old_obj.db_accounts
+ new_obj.db_add_accounts(DBOpmAccounts.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccounts.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'processes' in class_dict:
+ res = class_dict['processes'](old_obj, trans_dict)
+ new_obj.db_processes = res
+ elif hasattr(old_obj, 'db_processes') and old_obj.db_processes is not None:
+ obj = old_obj.db_processes
+ new_obj.db_add_processes(DBOpmProcesses.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_processes') and hasattr(new_obj, 'db_deleted_processes'):
+ for obj in old_obj.db_deleted_processes:
+ n_obj = DBOpmProcesses.update_version(obj, trans_dict)
+ new_obj.db_deleted_processes.append(n_obj)
+ if 'artifacts' in class_dict:
+ res = class_dict['artifacts'](old_obj, trans_dict)
+ new_obj.db_artifacts = res
+ elif hasattr(old_obj, 'db_artifacts') and old_obj.db_artifacts is not None:
+ obj = old_obj.db_artifacts
+ new_obj.db_add_artifacts(DBOpmArtifacts.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_artifacts') and hasattr(new_obj, 'db_deleted_artifacts'):
+ for obj in old_obj.db_deleted_artifacts:
+ n_obj = DBOpmArtifacts.update_version(obj, trans_dict)
+ new_obj.db_deleted_artifacts.append(n_obj)
+ if 'agents' in class_dict:
+ res = class_dict['agents'](old_obj, trans_dict)
+ new_obj.db_agents = res
+ elif hasattr(old_obj, 'db_agents') and old_obj.db_agents is not None:
+ obj = old_obj.db_agents
+ new_obj.db_add_agents(DBOpmAgents.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_agents') and hasattr(new_obj, 'db_deleted_agents'):
+ for obj in old_obj.db_deleted_agents:
+ n_obj = DBOpmAgents.update_version(obj, trans_dict)
+ new_obj.db_deleted_agents.append(n_obj)
+ if 'dependencies' in class_dict:
+ res = class_dict['dependencies'](old_obj, trans_dict)
+ new_obj.db_dependencies = res
+ elif hasattr(old_obj, 'db_dependencies') and old_obj.db_dependencies is not None:
+ obj = old_obj.db_dependencies
+ new_obj.db_add_dependencies(DBOpmDependencies.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_dependencies') and hasattr(new_obj, 'db_deleted_dependencies'):
+ for obj in old_obj.db_deleted_dependencies:
+ n_obj = DBOpmDependencies.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencies.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_accounts is not None:
+ children.extend(self._db_accounts.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_accounts = None
+ if self._db_processes is not None:
+ children.extend(self._db_processes.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_processes = None
+ if self._db_artifacts is not None:
+ children.extend(self._db_artifacts.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_artifacts = None
+ if self._db_agents is not None:
+ children.extend(self._db_agents.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_agents = None
+ if self._db_dependencies is not None:
+ children.extend(self._db_dependencies.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_dependencies = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_processes)
+ children.extend(self.db_deleted_artifacts)
+ children.extend(self.db_deleted_agents)
+ children.extend(self.db_deleted_dependencies)
+ if remove:
+ self.db_deleted_accounts = []
+ self.db_deleted_processes = []
+ self.db_deleted_artifacts = []
+ self.db_deleted_agents = []
+ self.db_deleted_dependencies = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_accounts is not None and self._db_accounts.has_changes():
+ return True
+ if self._db_processes is not None and self._db_processes.has_changes():
+ return True
+ if self._db_artifacts is not None and self._db_artifacts.has_changes():
+ return True
+ if self._db_agents is not None and self._db_agents.has_changes():
+ return True
+ if self._db_dependencies is not None and self._db_dependencies.has_changes():
+ return True
+ return False
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_add_accounts(self, accounts):
+ self._db_accounts = accounts
+ def db_change_accounts(self, accounts):
+ self._db_accounts = accounts
+ def db_delete_accounts(self, accounts):
+ if not self.is_new:
+ self.db_deleted_accounts.append(self._db_accounts)
+ self._db_accounts = None
+
+ def __get_db_processes(self):
+ return self._db_processes
+ def __set_db_processes(self, processes):
+ self._db_processes = processes
+ self.is_dirty = True
+ db_processes = property(__get_db_processes, __set_db_processes)
+ def db_add_processes(self, processes):
+ self._db_processes = processes
+ def db_change_processes(self, processes):
+ self._db_processes = processes
+ def db_delete_processes(self, processes):
+ if not self.is_new:
+ self.db_deleted_processes.append(self._db_processes)
+ self._db_processes = None
+
+ def __get_db_artifacts(self):
+ return self._db_artifacts
+ def __set_db_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ self.is_dirty = True
+ db_artifacts = property(__get_db_artifacts, __set_db_artifacts)
+ def db_add_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ def db_change_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ def db_delete_artifacts(self, artifacts):
+ if not self.is_new:
+ self.db_deleted_artifacts.append(self._db_artifacts)
+ self._db_artifacts = None
+
+ def __get_db_agents(self):
+ return self._db_agents
+ def __set_db_agents(self, agents):
+ self._db_agents = agents
+ self.is_dirty = True
+ db_agents = property(__get_db_agents, __set_db_agents)
+ def db_add_agents(self, agents):
+ self._db_agents = agents
+ def db_change_agents(self, agents):
+ self._db_agents = agents
+ def db_delete_agents(self, agents):
+ if not self.is_new:
+ self.db_deleted_agents.append(self._db_agents)
+ self._db_agents = None
+
+ def __get_db_dependencies(self):
+ return self._db_dependencies
+ def __set_db_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ self.is_dirty = True
+ db_dependencies = property(__get_db_dependencies, __set_db_dependencies)
+ def db_add_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ def db_change_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ def db_delete_dependencies(self, dependencies):
+ if not self.is_new:
+ self.db_deleted_dependencies.append(self._db_dependencies)
+ self._db_dependencies = None
+
+
+
+class DBRegistry(object):
+
+ vtType = 'registry'
+
+ def __init__(self, id=None, entity_type=None, version=None, root_descriptor_id=None, name=None, last_modified=None, packages=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_root_descriptor_id = root_descriptor_id
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_packages = []
+ self.db_packages_id_index = {}
+ self.db_packages_identifier_index = {}
+ if packages is None:
+ self._db_packages = []
+ else:
+ self._db_packages = packages
+ for v in self._db_packages:
+ self.db_packages_id_index[v.db_id] = v
+ self.db_packages_identifier_index[(v.db_identifier,v.db_version)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBRegistry.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBRegistry(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ root_descriptor_id=self._db_root_descriptor_id,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_packages is None:
+ cp._db_packages = []
+ else:
+ cp._db_packages = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_packages]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_root_descriptor_id') and ('module_descriptor', self._db_root_descriptor_id) in id_remap:
+ cp._db_root_descriptor_id = id_remap[('module_descriptor', self._db_root_descriptor_id)]
+
+ # recreate indices and set flags
+ cp.db_packages_id_index = dict((v.db_id, v) for v in cp._db_packages)
+ cp.db_packages_identifier_index = dict(((v.db_identifier,v.db_version), v) for v in cp._db_packages)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRegistry()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'root_descriptor_id' in class_dict:
+ res = class_dict['root_descriptor_id'](old_obj, trans_dict)
+ new_obj.db_root_descriptor_id = res
+ elif hasattr(old_obj, 'db_root_descriptor_id') and old_obj.db_root_descriptor_id is not None:
+ new_obj.db_root_descriptor_id = old_obj.db_root_descriptor_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'packages' in class_dict:
+ res = class_dict['packages'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_package(obj)
+ elif hasattr(old_obj, 'db_packages') and old_obj.db_packages is not None:
+ for obj in old_obj.db_packages:
+ new_obj.db_add_package(DBPackage.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_packages') and hasattr(new_obj, 'db_deleted_packages'):
+ for obj in old_obj.db_deleted_packages:
+ n_obj = DBPackage.update_version(obj, trans_dict)
+ new_obj.db_deleted_packages.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_packages:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_package(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_packages)
+ if remove:
+ self.db_deleted_packages = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_packages:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_root_descriptor_id(self):
+ return self._db_root_descriptor_id
+ def __set_db_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ self.is_dirty = True
+ db_root_descriptor_id = property(__get_db_root_descriptor_id, __set_db_root_descriptor_id)
+ def db_add_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ def db_change_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ def db_delete_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_packages(self):
+ return self._db_packages
+ def __set_db_packages(self, packages):
+ self._db_packages = packages
+ self.is_dirty = True
+ db_packages = property(__get_db_packages, __set_db_packages)
+ def db_get_packages(self):
+ return self._db_packages
+ def db_add_package(self, package):
+ self.is_dirty = True
+ self._db_packages.append(package)
+ self.db_packages_id_index[package.db_id] = package
+ self.db_packages_identifier_index[(package.db_identifier,package.db_version)] = package
+ def db_change_package(self, package):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == package.db_id:
+ self._db_packages[i] = package
+ found = True
+ break
+ if not found:
+ self._db_packages.append(package)
+ self.db_packages_id_index[package.db_id] = package
+ self.db_packages_identifier_index[(package.db_identifier,package.db_version)] = package
+ def db_delete_package(self, package):
+ self.is_dirty = True
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == package.db_id:
+ if not self._db_packages[i].is_new:
+ self.db_deleted_packages.append(self._db_packages[i])
+ del self._db_packages[i]
+ break
+ del self.db_packages_id_index[package.db_id]
+ del self.db_packages_identifier_index[(package.db_identifier,package.db_version)]
+ def db_get_package(self, key):
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == key:
+ return self._db_packages[i]
+ return None
+ def db_get_package_by_id(self, key):
+ return self.db_packages_id_index[key]
+ def db_has_package_with_id(self, key):
+ return key in self.db_packages_id_index
+ def db_get_package_by_identifier(self, key):
+ return self.db_packages_identifier_index[key]
+ def db_has_package_with_identifier(self, key):
+ return key in self.db_packages_identifier_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmAccount(object):
+
+ vtType = 'opm_account'
+
+ def __init__(self, id=None, value=None):
+ self._db_id = id
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccount.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccount(id=self._db_id,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccount()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAnnotation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, data=None, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_oldObjId = oldObjId
+ self._db_newObjId = newObjId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBChange.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange(id=self._db_id,
+ what=self._db_what,
+ oldObjId=self._db_oldObjId,
+ newObjId=self._db_newObjId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_oldObjId') and (self._db_what, self._db_oldObjId) in id_remap:
+ cp._db_oldObjId = id_remap[(self._db_what, self._db_oldObjId)]
+ if hasattr(self, 'db_newObjId') and (self._db_what, self._db_newObjId) in id_remap:
+ cp._db_newObjId = id_remap[(self._db_what, self._db_newObjId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBChange()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'oldObjId' in class_dict:
+ res = class_dict['oldObjId'](old_obj, trans_dict)
+ new_obj.db_oldObjId = res
+ elif hasattr(old_obj, 'db_oldObjId') and old_obj.db_oldObjId is not None:
+ new_obj.db_oldObjId = old_obj.db_oldObjId
+ if 'newObjId' in class_dict:
+ res = class_dict['newObjId'](old_obj, trans_dict)
+ new_obj.db_newObjId = res
+ elif hasattr(old_obj, 'db_newObjId') and old_obj.db_newObjId is not None:
+ new_obj.db_newObjId = old_obj.db_newObjId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_oldObjId(self):
+ return self._db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self._db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self._db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self._db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmWasDerivedFrom(object):
+
+ vtType = 'opm_was_derived_from'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasDerivedFrom.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasDerivedFrom()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasDerivedFrom()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmArtifactIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmArtifactIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmArtifactIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmArtifactIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBOpmWasControlledBy(object):
+
+ vtType = 'opm_was_controlled_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, starts=None, ends=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_starts = []
+ if starts is None:
+ self._db_starts = []
+ else:
+ self._db_starts = starts
+ self.db_deleted_ends = []
+ if ends is None:
+ self._db_ends = []
+ else:
+ self._db_ends = ends
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasControlledBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasControlledBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_starts is None:
+ cp._db_starts = []
+ else:
+ cp._db_starts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_starts]
+ if self._db_ends is None:
+ cp._db_ends = []
+ else:
+ cp._db_ends = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ends]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasControlledBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmAgentId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmAgentId.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'starts' in class_dict:
+ res = class_dict['starts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_start(obj)
+ elif hasattr(old_obj, 'db_starts') and old_obj.db_starts is not None:
+ for obj in old_obj.db_starts:
+ new_obj.db_add_start(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_starts') and hasattr(new_obj, 'db_deleted_starts'):
+ for obj in old_obj.db_deleted_starts:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_starts.append(n_obj)
+ if 'ends' in class_dict:
+ res = class_dict['ends'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_end(obj)
+ elif hasattr(old_obj, 'db_ends') and old_obj.db_ends is not None:
+ for obj in old_obj.db_ends:
+ new_obj.db_add_end(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_ends') and hasattr(new_obj, 'db_deleted_ends'):
+ for obj in old_obj.db_deleted_ends:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_ends.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_starts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_start(child)
+ to_del = []
+ for child in self.db_ends:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_end(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_starts)
+ children.extend(self.db_deleted_ends)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_starts = []
+ self.db_deleted_ends = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_starts:
+ if child.has_changes():
+ return True
+ for child in self._db_ends:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_starts(self):
+ return self._db_starts
+ def __set_db_starts(self, starts):
+ self._db_starts = starts
+ self.is_dirty = True
+ db_starts = property(__get_db_starts, __set_db_starts)
+ def db_get_starts(self):
+ return self._db_starts
+ def db_add_start(self, start):
+ self.is_dirty = True
+ self._db_starts.append(start)
+ def db_change_start(self, start):
+ self.is_dirty = True
+ self._db_starts.append(start)
+ def db_delete_start(self, start):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_start(self, key):
+ return None
+
+ def __get_db_ends(self):
+ return self._db_ends
+ def __set_db_ends(self, ends):
+ self._db_ends = ends
+ self.is_dirty = True
+ db_ends = property(__get_db_ends, __set_db_ends)
+ def db_get_ends(self):
+ return self._db_ends
+ def db_add_end(self, end):
+ self.is_dirty = True
+ self._db_ends.append(end)
+ def db_change_end(self, end):
+ self.is_dirty = True
+ self._db_ends.append(end)
+ def db_delete_end(self, end):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_end(self, key):
+ return None
+
+
+
+class DBOpmAgentId(object):
+
+ vtType = 'opm_agent_id'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgentId.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgentId(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_agent', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_agent', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgentId()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBGroupExec(object):
+
+ vtType = 'group_exec'
+
+ def __init__(self, item_execs=None, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, group_name=None, group_type=None, completed=None, error=None, machine_id=None, annotations=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_group_name = group_name
+ self._db_group_type = group_type
+ self._db_completed = completed
+ self._db_error = error
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroupExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroupExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ group_name=self._db_group_name,
+ group_type=self._db_group_type,
+ completed=self._db_completed,
+ error=self._db_error,
+ machine_id=self._db_machine_id)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroupExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'group_name' in class_dict:
+ res = class_dict['group_name'](old_obj, trans_dict)
+ new_obj.db_group_name = res
+ elif hasattr(old_obj, 'db_group_name') and old_obj.db_group_name is not None:
+ new_obj.db_group_name = old_obj.db_group_name
+ if 'group_type' in class_dict:
+ res = class_dict['group_type'](old_obj, trans_dict)
+ new_obj.db_group_type = res
+ elif hasattr(old_obj, 'db_group_type') and old_obj.db_group_type is not None:
+ new_obj.db_group_type = old_obj.db_group_type
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_group_name(self):
+ return self._db_group_name
+ def __set_db_group_name(self, group_name):
+ self._db_group_name = group_name
+ self.is_dirty = True
+ db_group_name = property(__get_db_group_name, __set_db_group_name)
+ def db_add_group_name(self, group_name):
+ self._db_group_name = group_name
+ def db_change_group_name(self, group_name):
+ self._db_group_name = group_name
+ def db_delete_group_name(self, group_name):
+ self._db_group_name = None
+
+ def __get_db_group_type(self):
+ return self._db_group_type
+ def __set_db_group_type(self, group_type):
+ self._db_group_type = group_type
+ self.is_dirty = True
+ db_group_type = property(__get_db_group_type, __set_db_group_type)
+ def db_add_group_type(self, group_type):
+ self._db_group_type = group_type
+ def db_change_group_type(self, group_type):
+ self._db_group_type = group_type
+ def db_delete_group_type(self, group_type):
+ self._db_group_type = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmTime(object):
+
+ vtType = 'opm_time'
+
+ def __init__(self, no_later_than=None, no_earlier_than=None, clock_id=None):
+ self._db_no_later_than = no_later_than
+ self._db_no_earlier_than = no_earlier_than
+ self._db_clock_id = clock_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmTime.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmTime(no_later_than=self._db_no_later_than,
+ no_earlier_than=self._db_no_earlier_than,
+ clock_id=self._db_clock_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmTime()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'no_later_than' in class_dict:
+ res = class_dict['no_later_than'](old_obj, trans_dict)
+ new_obj.db_no_later_than = res
+ elif hasattr(old_obj, 'db_no_later_than') and old_obj.db_no_later_than is not None:
+ new_obj.db_no_later_than = old_obj.db_no_later_than
+ if 'no_earlier_than' in class_dict:
+ res = class_dict['no_earlier_than'](old_obj, trans_dict)
+ new_obj.db_no_earlier_than = res
+ elif hasattr(old_obj, 'db_no_earlier_than') and old_obj.db_no_earlier_than is not None:
+ new_obj.db_no_earlier_than = old_obj.db_no_earlier_than
+ if 'clock_id' in class_dict:
+ res = class_dict['clock_id'](old_obj, trans_dict)
+ new_obj.db_clock_id = res
+ elif hasattr(old_obj, 'db_clock_id') and old_obj.db_clock_id is not None:
+ new_obj.db_clock_id = old_obj.db_clock_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_no_later_than(self):
+ return self._db_no_later_than
+ def __set_db_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ self.is_dirty = True
+ db_no_later_than = property(__get_db_no_later_than, __set_db_no_later_than)
+ def db_add_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ def db_change_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ def db_delete_no_later_than(self, no_later_than):
+ self._db_no_later_than = None
+
+ def __get_db_no_earlier_than(self):
+ return self._db_no_earlier_than
+ def __set_db_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ self.is_dirty = True
+ db_no_earlier_than = property(__get_db_no_earlier_than, __set_db_no_earlier_than)
+ def db_add_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ def db_change_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ def db_delete_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = None
+
+ def __get_db_clock_id(self):
+ return self._db_clock_id
+ def __set_db_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ self.is_dirty = True
+ db_clock_id = property(__get_db_clock_id, __set_db_clock_id)
+ def db_add_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ def db_change_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ def db_delete_clock_id(self, clock_id):
+ self._db_clock_id = None
+
+
+
+class DBPackage(object):
+
+ vtType = 'package'
+
+ def __init__(self, id=None, name=None, identifier=None, codepath=None, load_configuration=None, version=None, description=None, module_descriptors=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_identifier = identifier
+ self._db_codepath = codepath
+ self._db_load_configuration = load_configuration
+ self._db_version = version
+ self._db_description = description
+ self.db_deleted_module_descriptors = []
+ self.db_module_descriptors_id_index = {}
+ self.db_module_descriptors_name_index = {}
+ if module_descriptors is None:
+ self._db_module_descriptors = []
+ else:
+ self._db_module_descriptors = module_descriptors
+ for v in self._db_module_descriptors:
+ self.db_module_descriptors_id_index[v.db_id] = v
+ self.db_module_descriptors_name_index[(v.db_name,v.db_namespace,v.db_version)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPackage.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPackage(id=self._db_id,
+ name=self._db_name,
+ identifier=self._db_identifier,
+ codepath=self._db_codepath,
+ load_configuration=self._db_load_configuration,
+ version=self._db_version,
+ description=self._db_description)
+ if self._db_module_descriptors is None:
+ cp._db_module_descriptors = []
+ else:
+ cp._db_module_descriptors = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_module_descriptors]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_module_descriptors_id_index = dict((v.db_id, v) for v in cp._db_module_descriptors)
+ cp.db_module_descriptors_name_index = dict(((v.db_name,v.db_namespace,v.db_version), v) for v in cp._db_module_descriptors)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPackage()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'identifier' in class_dict:
+ res = class_dict['identifier'](old_obj, trans_dict)
+ new_obj.db_identifier = res
+ elif hasattr(old_obj, 'db_identifier') and old_obj.db_identifier is not None:
+ new_obj.db_identifier = old_obj.db_identifier
+ if 'codepath' in class_dict:
+ res = class_dict['codepath'](old_obj, trans_dict)
+ new_obj.db_codepath = res
+ elif hasattr(old_obj, 'db_codepath') and old_obj.db_codepath is not None:
+ new_obj.db_codepath = old_obj.db_codepath
+ if 'load_configuration' in class_dict:
+ res = class_dict['load_configuration'](old_obj, trans_dict)
+ new_obj.db_load_configuration = res
+ elif hasattr(old_obj, 'db_load_configuration') and old_obj.db_load_configuration is not None:
+ new_obj.db_load_configuration = old_obj.db_load_configuration
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'description' in class_dict:
+ res = class_dict['description'](old_obj, trans_dict)
+ new_obj.db_description = res
+ elif hasattr(old_obj, 'db_description') and old_obj.db_description is not None:
+ new_obj.db_description = old_obj.db_description
+ if 'module_descriptors' in class_dict:
+ res = class_dict['module_descriptors'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module_descriptor(obj)
+ elif hasattr(old_obj, 'db_module_descriptors') and old_obj.db_module_descriptors is not None:
+ for obj in old_obj.db_module_descriptors:
+ new_obj.db_add_module_descriptor(DBModuleDescriptor.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_module_descriptors') and hasattr(new_obj, 'db_deleted_module_descriptors'):
+ for obj in old_obj.db_deleted_module_descriptors:
+ n_obj = DBModuleDescriptor.update_version(obj, trans_dict)
+ new_obj.db_deleted_module_descriptors.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_module_descriptors:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_descriptor(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_descriptors)
+ if remove:
+ self.db_deleted_module_descriptors = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_module_descriptors:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_identifier(self):
+ return self._db_identifier
+ def __set_db_identifier(self, identifier):
+ self._db_identifier = identifier
+ self.is_dirty = True
+ db_identifier = property(__get_db_identifier, __set_db_identifier)
+ def db_add_identifier(self, identifier):
+ self._db_identifier = identifier
+ def db_change_identifier(self, identifier):
+ self._db_identifier = identifier
+ def db_delete_identifier(self, identifier):
+ self._db_identifier = None
+
+ def __get_db_codepath(self):
+ return self._db_codepath
+ def __set_db_codepath(self, codepath):
+ self._db_codepath = codepath
+ self.is_dirty = True
+ db_codepath = property(__get_db_codepath, __set_db_codepath)
+ def db_add_codepath(self, codepath):
+ self._db_codepath = codepath
+ def db_change_codepath(self, codepath):
+ self._db_codepath = codepath
+ def db_delete_codepath(self, codepath):
+ self._db_codepath = None
+
+ def __get_db_load_configuration(self):
+ return self._db_load_configuration
+ def __set_db_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ self.is_dirty = True
+ db_load_configuration = property(__get_db_load_configuration, __set_db_load_configuration)
+ def db_add_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ def db_change_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ def db_delete_load_configuration(self, load_configuration):
+ self._db_load_configuration = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_description(self):
+ return self._db_description
+ def __set_db_description(self, description):
+ self._db_description = description
+ self.is_dirty = True
+ db_description = property(__get_db_description, __set_db_description)
+ def db_add_description(self, description):
+ self._db_description = description
+ def db_change_description(self, description):
+ self._db_description = description
+ def db_delete_description(self, description):
+ self._db_description = None
+
+ def __get_db_module_descriptors(self):
+ return self._db_module_descriptors
+ def __set_db_module_descriptors(self, module_descriptors):
+ self._db_module_descriptors = module_descriptors
+ self.is_dirty = True
+ db_module_descriptors = property(__get_db_module_descriptors, __set_db_module_descriptors)
+ def db_get_module_descriptors(self):
+ return self._db_module_descriptors
+ def db_add_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ self._db_module_descriptors.append(module_descriptor)
+ self.db_module_descriptors_id_index[module_descriptor.db_id] = module_descriptor
+ self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)] = module_descriptor
+ def db_change_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == module_descriptor.db_id:
+ self._db_module_descriptors[i] = module_descriptor
+ found = True
+ break
+ if not found:
+ self._db_module_descriptors.append(module_descriptor)
+ self.db_module_descriptors_id_index[module_descriptor.db_id] = module_descriptor
+ self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)] = module_descriptor
+ def db_delete_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == module_descriptor.db_id:
+ if not self._db_module_descriptors[i].is_new:
+ self.db_deleted_module_descriptors.append(self._db_module_descriptors[i])
+ del self._db_module_descriptors[i]
+ break
+ del self.db_module_descriptors_id_index[module_descriptor.db_id]
+ del self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)]
+ def db_get_module_descriptor(self, key):
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == key:
+ return self._db_module_descriptors[i]
+ return None
+ def db_get_module_descriptor_by_id(self, key):
+ return self.db_module_descriptors_id_index[key]
+ def db_has_module_descriptor_with_id(self, key):
+ return key in self.db_module_descriptors_id_index
+ def db_get_module_descriptor_by_name(self, key):
+ return self.db_module_descriptors_name_index[key]
+ def db_has_module_descriptor_with_name(self, key):
+ return key in self.db_module_descriptors_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, item_execs=None, id=None, user=None, ip=None, session=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, completed=None, name=None, annotations=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_user = user
+ self._db_ip = ip
+ self._db_session = session
+ self._db_vt_version = vt_version
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_parent_id = parent_id
+ self._db_parent_type = parent_type
+ self._db_parent_version = parent_version
+ self._db_completed = completed
+ self._db_name = name
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflowExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec(id=self._db_id,
+ user=self._db_user,
+ ip=self._db_ip,
+ session=self._db_session,
+ vt_version=self._db_vt_version,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ parent_id=self._db_parent_id,
+ parent_type=self._db_parent_type,
+ parent_version=self._db_parent_version,
+ completed=self._db_completed,
+ name=self._db_name)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflowExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'ip' in class_dict:
+ res = class_dict['ip'](old_obj, trans_dict)
+ new_obj.db_ip = res
+ elif hasattr(old_obj, 'db_ip') and old_obj.db_ip is not None:
+ new_obj.db_ip = old_obj.db_ip
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'vt_version' in class_dict:
+ res = class_dict['vt_version'](old_obj, trans_dict)
+ new_obj.db_vt_version = res
+ elif hasattr(old_obj, 'db_vt_version') and old_obj.db_vt_version is not None:
+ new_obj.db_vt_version = old_obj.db_vt_version
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'parent_id' in class_dict:
+ res = class_dict['parent_id'](old_obj, trans_dict)
+ new_obj.db_parent_id = res
+ elif hasattr(old_obj, 'db_parent_id') and old_obj.db_parent_id is not None:
+ new_obj.db_parent_id = old_obj.db_parent_id
+ if 'parent_type' in class_dict:
+ res = class_dict['parent_type'](old_obj, trans_dict)
+ new_obj.db_parent_type = res
+ elif hasattr(old_obj, 'db_parent_type') and old_obj.db_parent_type is not None:
+ new_obj.db_parent_type = old_obj.db_parent_type
+ if 'parent_version' in class_dict:
+ res = class_dict['parent_version'](old_obj, trans_dict)
+ new_obj.db_parent_version = res
+ elif hasattr(old_obj, 'db_parent_version') and old_obj.db_parent_version is not None:
+ new_obj.db_parent_version = old_obj.db_parent_version
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_ip(self):
+ return self._db_ip
+ def __set_db_ip(self, ip):
+ self._db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self._db_ip = ip
+ def db_change_ip(self, ip):
+ self._db_ip = ip
+ def db_delete_ip(self, ip):
+ self._db_ip = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_vt_version(self):
+ return self._db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self._db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self._db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self._db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self._db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self._db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self._db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self._db_parent_version = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLoopExec(object):
+
+ vtType = 'loop_exec'
+
+ def __init__(self, item_execs=None, id=None, ts_start=None, ts_end=None, iteration=None, completed=None, error=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_iteration = iteration
+ self._db_completed = completed
+ self._db_error = error
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLoopExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLoopExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ iteration=self._db_iteration,
+ completed=self._db_completed,
+ error=self._db_error)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLoopExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'iteration' in class_dict:
+ res = class_dict['iteration'](old_obj, trans_dict)
+ new_obj.db_iteration = res
+ elif hasattr(old_obj, 'db_iteration') and old_obj.db_iteration is not None:
+ new_obj.db_iteration = old_obj.db_iteration
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_iteration(self):
+ return self._db_iteration
+ def __set_db_iteration(self, iteration):
+ self._db_iteration = iteration
+ self.is_dirty = True
+ db_iteration = property(__get_db_iteration, __set_db_iteration)
+ def db_add_iteration(self, iteration):
+ self._db_iteration = iteration
+ def db_change_iteration(self, iteration):
+ self._db_iteration = iteration
+ def db_delete_iteration(self, iteration):
+ self._db_iteration = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self._db_id = id
+ self.db_deleted_ports = []
+ self.db_ports_id_index = {}
+ self.db_ports_type_index = {}
+ if ports is None:
+ self._db_ports = []
+ else:
+ self._db_ports = ports
+ for v in self._db_ports:
+ self.db_ports_id_index[v.db_id] = v
+ self.db_ports_type_index[v.db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBConnection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection(id=self._db_id)
+ if self._db_ports is None:
+ cp._db_ports = []
+ else:
+ cp._db_ports = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ports]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_ports_id_index = dict((v.db_id, v) for v in cp._db_ports)
+ cp.db_ports_type_index = dict((v.db_type, v) for v in cp._db_ports)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBConnection()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ports' in class_dict:
+ res = class_dict['ports'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_port(obj)
+ elif hasattr(old_obj, 'db_ports') and old_obj.db_ports is not None:
+ for obj in old_obj.db_ports:
+ new_obj.db_add_port(DBPort.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_ports') and hasattr(new_obj, 'db_deleted_ports'):
+ for obj in old_obj.db_deleted_ports:
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_ports.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_ports)
+ if remove:
+ self.db_deleted_ports = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ports(self):
+ return self._db_ports
+ def __set_db_ports(self, ports):
+ self._db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self._db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ self._db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ if not self._db_ports[i].is_new:
+ self.db_deleted_ports.append(self._db_ports[i])
+ del self._db_ports[i]
+ break
+ del self.db_ports_id_index[port.db_id]
+ del self.db_ports_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == key:
+ return self._db_ports[i]
+ return None
+ def db_get_port_by_id(self, key):
+ return self.db_ports_id_index[key]
+ def db_has_port_with_id(self, key):
+ return key in self.db_ports_id_index
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return key in self.db_ports_type_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmProcess(object):
+
+ vtType = 'opm_process'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self.db_deleted_value = []
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcess.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcess(id=self._db_id)
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcess()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ new_obj.db_add_value(DBOpmProcessValue.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ n_obj = DBOpmProcessValue.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_value = []
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmWasTriggeredBy(object):
+
+ vtType = 'opm_was_triggered_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasTriggeredBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasTriggeredBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasTriggeredBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmProcessIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmProcessIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBOpmProcessValue(object):
+
+ vtType = 'opm_process_value'
+
+ def __init__(self, value=None):
+ self.db_deleted_value = []
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessValue.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessValue()
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessValue()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_value(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_value(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_value(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ self._db_value = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ if remove:
+ self.db_deleted_value = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, operations=None, id=None, prevId=None, date=None, session=None, user=None, annotations=None):
+ self.db_deleted_operations = []
+ self.db_operations_id_index = {}
+ if operations is None:
+ self._db_operations = []
+ else:
+ self._db_operations = operations
+ for v in self._db_operations:
+ self.db_operations_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_prevId = prevId
+ self._db_date = date
+ self._db_session = session
+ self._db_user = user
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction(id=self._db_id,
+ prevId=self._db_prevId,
+ date=self._db_date,
+ session=self._db_session,
+ user=self._db_user)
+ if self._db_operations is None:
+ cp._db_operations = []
+ else:
+ cp._db_operations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_operations]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prevId') and ('action', self._db_prevId) in id_remap:
+ cp._db_prevId = id_remap[('action', self._db_prevId)]
+
+ # recreate indices and set flags
+ cp.db_operations_id_index = dict((v.db_id, v) for v in cp._db_operations)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'operations' in class_dict:
+ res = class_dict['operations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_operation(obj)
+ elif hasattr(old_obj, 'db_operations') and old_obj.db_operations is not None:
+ for obj in old_obj.db_operations:
+ if obj.vtType == 'add':
+ new_obj.db_add_operation(DBAdd.update_version(obj, trans_dict))
+ elif obj.vtType == 'delete':
+ new_obj.db_add_operation(DBDelete.update_version(obj, trans_dict))
+ elif obj.vtType == 'change':
+ new_obj.db_add_operation(DBChange.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_operations') and hasattr(new_obj, 'db_deleted_operations'):
+ for obj in old_obj.db_deleted_operations:
+ if obj.vtType == 'add':
+ n_obj = DBAdd.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'delete':
+ n_obj = DBDelete.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'change':
+ n_obj = DBChange.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'prevId' in class_dict:
+ res = class_dict['prevId'](old_obj, trans_dict)
+ new_obj.db_prevId = res
+ elif hasattr(old_obj, 'db_prevId') and old_obj.db_prevId is not None:
+ new_obj.db_prevId = old_obj.db_prevId
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_operations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_operations)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_operations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_operations(self):
+ return self._db_operations
+ def __set_db_operations(self, operations):
+ self._db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self._db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ self._db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ if not self._db_operations[i].is_new:
+ self.db_deleted_operations.append(self._db_operations[i])
+ del self._db_operations[i]
+ break
+ del self.db_operations_id_index[operation.db_id]
+ def db_get_operation(self, key):
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == key:
+ return self._db_operations[i]
+ return None
+ def db_get_operation_by_id(self, key):
+ return self.db_operations_id_index[key]
+ def db_has_operation_with_id(self, key):
+ return key in self.db_operations_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_prevId(self):
+ return self._db_prevId
+ def __set_db_prevId(self, prevId):
+ self._db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self._db_prevId = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmAgent(object):
+
+ vtType = 'opm_agent'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgent.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgent(id=self._db_id,
+ value=self._db_value)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgent()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBDelete.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBDelete()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, actions=None, tags=None, annotations=None, actionAnnotations=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self._db_actions = []
+ else:
+ self._db_actions = actions
+ for v in self._db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self._db_tags = []
+ else:
+ self._db_tags = tags
+ for v in self._db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_actionAnnotations = []
+ self.db_actionAnnotations_id_index = {}
+ self.db_actionAnnotations_action_id_index = {}
+ self.db_actionAnnotations_key_index = {}
+ if actionAnnotations is None:
+ self._db_actionAnnotations = []
+ else:
+ self._db_actionAnnotations = actionAnnotations
+ for v in self._db_actionAnnotations:
+ self.db_actionAnnotations_id_index[v.db_id] = v
+ self.db_actionAnnotations_action_id_index[(v.db_action_id,v.db_key)] = v
+ self.db_actionAnnotations_key_index[(v.db_key,v.db_value)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_actions is None:
+ cp._db_actions = []
+ else:
+ cp._db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actions]
+ if self._db_tags is None:
+ cp._db_tags = []
+ else:
+ cp._db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_tags]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_actionAnnotations is None:
+ cp._db_actionAnnotations = []
+ else:
+ cp._db_actionAnnotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actionAnnotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_actions_id_index = dict((v.db_id, v) for v in cp._db_actions)
+ cp.db_tags_id_index = dict((v.db_id, v) for v in cp._db_tags)
+ cp.db_tags_name_index = dict((v.db_name, v) for v in cp._db_tags)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ cp.db_actionAnnotations_id_index = dict((v.db_id, v) for v in cp._db_actionAnnotations)
+ cp.db_actionAnnotations_action_id_index = dict(((v.db_action_id,v.db_key), v) for v in cp._db_actionAnnotations)
+ cp.db_actionAnnotations_key_index = dict(((v.db_key,v.db_value), v) for v in cp._db_actionAnnotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'actions' in class_dict:
+ res = class_dict['actions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_action(obj)
+ elif hasattr(old_obj, 'db_actions') and old_obj.db_actions is not None:
+ for obj in old_obj.db_actions:
+ new_obj.db_add_action(DBAction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actions') and hasattr(new_obj, 'db_deleted_actions'):
+ for obj in old_obj.db_deleted_actions:
+ n_obj = DBAction.update_version(obj, trans_dict)
+ new_obj.db_deleted_actions.append(n_obj)
+ if 'tags' in class_dict:
+ res = class_dict['tags'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_tag(obj)
+ elif hasattr(old_obj, 'db_tags') and old_obj.db_tags is not None:
+ for obj in old_obj.db_tags:
+ new_obj.db_add_tag(DBTag.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_tags') and hasattr(new_obj, 'db_deleted_tags'):
+ for obj in old_obj.db_deleted_tags:
+ n_obj = DBTag.update_version(obj, trans_dict)
+ new_obj.db_deleted_tags.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'actionAnnotations' in class_dict:
+ res = class_dict['actionAnnotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_actionAnnotation(obj)
+ elif hasattr(old_obj, 'db_actionAnnotations') and old_obj.db_actionAnnotations is not None:
+ for obj in old_obj.db_actionAnnotations:
+ new_obj.db_add_actionAnnotation(DBActionAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actionAnnotations') and hasattr(new_obj, 'db_deleted_actionAnnotations'):
+ for obj in old_obj.db_deleted_actionAnnotations:
+ n_obj = DBActionAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_actionAnnotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_actionAnnotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_actionAnnotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_actionAnnotations)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ self.db_deleted_annotations = []
+ self.db_deleted_actionAnnotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_actions:
+ if child.has_changes():
+ return True
+ for child in self._db_tags:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_actionAnnotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_actions(self):
+ return self._db_actions
+ def __set_db_actions(self, actions):
+ self._db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self._db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ self._db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ if not self._db_actions[i].is_new:
+ self.db_deleted_actions.append(self._db_actions[i])
+ del self._db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == key:
+ return self._db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return key in self.db_actions_id_index
+
+ def __get_db_tags(self):
+ return self._db_tags
+ def __set_db_tags(self, tags):
+ self._db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self._db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ self._db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ if not self._db_tags[i].is_new:
+ self.db_deleted_tags.append(self._db_tags[i])
+ del self._db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == key:
+ return self._db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return key in self.db_tags_id_index
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return key in self.db_tags_name_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_actionAnnotations(self):
+ return self._db_actionAnnotations
+ def __set_db_actionAnnotations(self, actionAnnotations):
+ self._db_actionAnnotations = actionAnnotations
+ self.is_dirty = True
+ db_actionAnnotations = property(__get_db_actionAnnotations, __set_db_actionAnnotations)
+ def db_get_actionAnnotations(self):
+ return self._db_actionAnnotations
+ def db_add_actionAnnotation(self, actionAnnotation):
+ self.is_dirty = True
+ self._db_actionAnnotations.append(actionAnnotation)
+ self.db_actionAnnotations_id_index[actionAnnotation.db_id] = actionAnnotation
+ self.db_actionAnnotations_action_id_index[(actionAnnotation.db_action_id,actionAnnotation.db_key)] = actionAnnotation
+ self.db_actionAnnotations_key_index[(actionAnnotation.db_key,actionAnnotation.db_value)] = actionAnnotation
+ def db_change_actionAnnotation(self, actionAnnotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actionAnnotations)):
+ if self._db_actionAnnotations[i].db_id == actionAnnotation.db_id:
+ self._db_actionAnnotations[i] = actionAnnotation
+ found = True
+ break
+ if not found:
+ self._db_actionAnnotations.append(actionAnnotation)
+ self.db_actionAnnotations_id_index[actionAnnotation.db_id] = actionAnnotation
+ self.db_actionAnnotations_action_id_index[(actionAnnotation.db_action_id,actionAnnotation.db_key)] = actionAnnotation
+ self.db_actionAnnotations_key_index[(actionAnnotation.db_key,actionAnnotation.db_value)] = actionAnnotation
+ def db_delete_actionAnnotation(self, actionAnnotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actionAnnotations)):
+ if self._db_actionAnnotations[i].db_id == actionAnnotation.db_id:
+ if not self._db_actionAnnotations[i].is_new:
+ self.db_deleted_actionAnnotations.append(self._db_actionAnnotations[i])
+ del self._db_actionAnnotations[i]
+ break
+ del self.db_actionAnnotations_id_index[actionAnnotation.db_id]
+ del self.db_actionAnnotations_action_id_index[(actionAnnotation.db_action_id,actionAnnotation.db_key)]
+ try:
+ del self.db_actionAnnotations_key_index[(actionAnnotation.db_key,actionAnnotation.db_value)]
+ except KeyError:
+ pass
+ def db_get_actionAnnotation(self, key):
+ for i in xrange(len(self._db_actionAnnotations)):
+ if self._db_actionAnnotations[i].db_id == key:
+ return self._db_actionAnnotations[i]
+ return None
+ def db_get_actionAnnotation_by_id(self, key):
+ return self.db_actionAnnotations_id_index[key]
+ def db_has_actionAnnotation_with_id(self, key):
+ return key in self.db_actionAnnotations_id_index
+ def db_get_actionAnnotation_by_action_id(self, key):
+ return self.db_actionAnnotations_action_id_index[key]
+ def db_has_actionAnnotation_with_action_id(self, key):
+ return key in self.db_actionAnnotations_action_id_index
+ def db_get_actionAnnotation_by_key(self, key):
+ return self.db_actionAnnotations_key_index[key]
+ def db_has_actionAnnotation_with_key(self, key):
+ return key in self.db_actionAnnotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, module_name=None, completed=None, error=None, machine_id=None, annotations=None, loop_execs=None):
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_module_name = module_name
+ self._db_completed = completed
+ self._db_error = error
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_loop_execs = []
+ self.db_loop_execs_id_index = {}
+ if loop_execs is None:
+ self._db_loop_execs = []
+ else:
+ self._db_loop_execs = loop_execs
+ for v in self._db_loop_execs:
+ self.db_loop_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ module_name=self._db_module_name,
+ completed=self._db_completed,
+ error=self._db_error,
+ machine_id=self._db_machine_id)
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_loop_execs is None:
+ cp._db_loop_execs = []
+ else:
+ cp._db_loop_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_loop_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_loop_execs_id_index = dict((v.db_id, v) for v in cp._db_loop_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'module_name' in class_dict:
+ res = class_dict['module_name'](old_obj, trans_dict)
+ new_obj.db_module_name = res
+ elif hasattr(old_obj, 'db_module_name') and old_obj.db_module_name is not None:
+ new_obj.db_module_name = old_obj.db_module_name
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'loop_execs' in class_dict:
+ res = class_dict['loop_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_loop_exec(obj)
+ elif hasattr(old_obj, 'db_loop_execs') and old_obj.db_loop_execs is not None:
+ for obj in old_obj.db_loop_execs:
+ new_obj.db_add_loop_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_loop_execs') and hasattr(new_obj, 'db_deleted_loop_execs'):
+ for obj in old_obj.db_deleted_loop_execs:
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_loop_execs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_loop_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_loop_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_loop_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_loop_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_loop_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_module_name(self):
+ return self._db_module_name
+ def __set_db_module_name(self, module_name):
+ self._db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self._db_module_name = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_loop_execs(self):
+ return self._db_loop_execs
+ def __set_db_loop_execs(self, loop_execs):
+ self._db_loop_execs = loop_execs
+ self.is_dirty = True
+ db_loop_execs = property(__get_db_loop_execs, __set_db_loop_execs)
+ def db_get_loop_execs(self):
+ return self._db_loop_execs
+ def db_add_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_change_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ self._db_loop_execs[i] = loop_exec
+ found = True
+ break
+ if not found:
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_delete_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ if not self._db_loop_execs[i].is_new:
+ self.db_deleted_loop_execs.append(self._db_loop_execs[i])
+ del self._db_loop_execs[i]
+ break
+ del self.db_loop_execs_id_index[loop_exec.db_id]
+ def db_get_loop_exec(self, key):
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == key:
+ return self._db_loop_execs[i]
+ return None
+ def db_get_loop_exec_by_id(self, key):
+ return self.db_loop_execs_id_index[key]
+ def db_has_loop_exec_with_id(self, key):
+ return key in self.db_loop_execs_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
diff --git a/vistrails/db/versions/v1_0_2/domain/id_scope.py b/vistrails/db/versions/v1_0_2/domain/id_scope.py
new file mode 100644
index 0000000..0e07f02
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/domain/id_scope.py
@@ -0,0 +1,85 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L, remap=None):
+ self.ids = {}
+ self.beginId = beginId
+ if remap is None:
+ self.remap = {}
+ else:
+ self.remap = remap
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ cp.remap = copy.copy(self.remap)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ except KeyError:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ if self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+ except KeyError:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v1_0_2/domain/log.py b/vistrails/db/versions/v1_0_2/domain/log.py
new file mode 100644
index 0000000..a127726
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/domain/log.py
@@ -0,0 +1,72 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBLog as _DBLog
+from auto_gen import DBAbstraction, DBModule, DBGroup, DBLoopExec, \
+ DBGroupExec, DBModuleExec
+from id_scope import IdScope
+
+import copy
+
+class DBLog(_DBLog):
+
+ def __init__(self, *args, **kwargs):
+ _DBLog.__init__(self, *args, **kwargs)
+ self.id_scope = IdScope(1,
+ {DBLoopExec.vtType: 'item_exec',
+ DBModuleExec.vtType: 'item_exec',
+ DBGroupExec.vtType: 'item_exec',
+ DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBLog.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBLog
+ cp.id_scope = copy.copy(self.id_scope)
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ new_obj = _DBLog.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
diff --git a/vistrails/db/versions/v1_0_2/domain/registry.py b/vistrails/db/versions/v1_0_2/domain/registry.py
new file mode 100644
index 0000000..323ebbd
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/domain/registry.py
@@ -0,0 +1,63 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBRegistry as _DBRegistry, DBPackage, DBModuleDescriptor, \
+ DBPortSpec
+from id_scope import IdScope
+
+class DBRegistry(_DBRegistry):
+ def __init__(self, *args, **kwargs):
+ _DBRegistry.__init__(self, *args, **kwargs)
+ self.idScope = IdScope()
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRegistry()
+ new_obj = _DBRegistry.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ for package in self.db_packages:
+ self.idScope.updateBeginId(DBPackage.vtType, package.db_id+1)
+ for descriptor in package.db_module_descriptors:
+ self.idScope.updateBeginId(DBModuleDescriptor.vtType,
+ descriptor.db_id+1)
+ for port_spec in descriptor.db_portSpecs:
+ self.idScope.updateBeginId(DBPortSpec.vtType,
+ port_spec.db_id+1)
+
+
diff --git a/vistrails/db/versions/v1_0_2/domain/vistrail.py b/vistrails/db/versions/v1_0_2/domain/vistrail.py
new file mode 100644
index 0000000..29962da
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/domain/vistrail.py
@@ -0,0 +1,216 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+import hashlib
+from auto_gen import DBVistrail as _DBVistrail
+from auto_gen import DBAdd, DBChange, DBDelete, DBAbstraction, DBGroup, \
+ DBModule, DBAnnotation, DBActionAnnotation
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAdd.vtType: 'operation',
+ DBChange.vtType: 'operation',
+ DBDelete.vtType: 'operation',
+ DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType,
+ DBActionAnnotation.vtType: \
+ DBAnnotation.vtType})
+
+ self.idScope.setBeginId('action', 1)
+ self.db_objects = {}
+
+ # keep a reference to the current logging information here
+ self.db_log_filename = None
+ self.log = None
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBVistrail.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBVistrail
+
+ cp.idScope = copy.copy(self.idScope)
+ cp.db_objects = copy.copy(self.db_objects)
+ cp.db_log_filename = self.db_log_filename
+ if self.log is not None:
+ cp.log = copy.copy(self.log)
+ else:
+ cp.log = None
+
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ new_obj = _DBVistrail.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ if hasattr(old_obj, 'db_log_filename'):
+ new_obj.db_log_filename = old_obj.db_log_filename
+ if hasattr(old_obj, 'log'):
+ new_obj.log = old_obj.log
+ return new_obj
+
+ def update_id_scope(self):
+ def getOldObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_oldObjId
+ return operation.db_objectId
+
+ def getNewObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_newObjId
+ return operation.db_objectId
+
+ for action in self.db_actions:
+ self.idScope.updateBeginId('action', action.db_id+1)
+ if action.db_session is not None:
+ self.idScope.updateBeginId('session', action.db_session + 1)
+ for operation in action.db_operations:
+ self.idScope.updateBeginId('operation', operation.db_id+1)
+ if operation.vtType == 'add' or operation.vtType == 'change':
+ # update ids of data
+ self.idScope.updateBeginId(operation.db_what,
+ getNewObjId(operation)+1)
+ if operation.db_data is None:
+ if operation.vtType == 'change':
+ operation.db_objectId = operation.db_oldObjId
+ self.db_add_object(operation.db_data)
+ for annotation in action.db_annotations:
+ self.idScope.updateBeginId('annotation', annotation.db_id+1)
+
+ for annotation in self.db_annotations:
+ self.idScope.updateBeginId('annotation', annotation.db_id+1)
+ for annotation in self.db_actionAnnotations:
+ self.idScope.updateBeginId('annotation', annotation.db_id+1)
+
+ def db_add_object(self, obj):
+ self.db_objects[(obj.vtType, obj.db_id)] = obj
+
+ def db_get_object(self, type, id):
+ return self.db_objects.get((type, id), None)
+
+ def db_update_object(self, obj, **kwargs):
+ # want to swap out old object with a new version
+ # need this for updating aliases...
+ # hack it using setattr...
+ real_obj = self.db_objects[(obj.vtType, obj.db_id)]
+ for (k, v) in kwargs.iteritems():
+ if hasattr(real_obj, k):
+ setattr(real_obj, k, v)
+
+ def update_checkout_version(self, app=''):
+ checkout_key = "__checkout_version_"
+ action_key = checkout_key + app
+ annotation_key = action_key + '_annotationhash'
+ action_annotation_key = action_key + '_actionannotationhash'
+
+ # delete previous checkout annotations
+ deletekeys = [action_key,annotation_key,action_annotation_key]
+ for key in deletekeys:
+ while self.db_has_annotation_with_key(key):
+ a = self.db_get_annotation_by_key(key)
+ self.db_delete_annotation(a)
+
+ # annotation hash - requires annotations to be clean
+ value = self.hashAnnotations()
+ if self.db_has_annotation_with_key(annotation_key):
+ annotation = self.db_get_annotation_by_key(annotation_key)
+ annotation.db_value = value
+ else:
+ annotation=DBAnnotation(self.idScope.getNewId(DBAnnotation.vtType),
+ annotation_key, value)
+ self.db_add_annotation(annotation)
+ # action annotation hash
+ value = self.hashActionAnnotations()
+ if self.db_has_annotation_with_key(action_annotation_key):
+ annotation = self.db_get_annotation_by_key(action_annotation_key)
+ annotation.db_value = value
+ else:
+ annotation=DBAnnotation(self.idScope.getNewId(DBAnnotation.vtType),
+ action_annotation_key, value)
+ self.db_add_annotation(annotation)
+ # last action id hash
+ if len(self.db_actions) == 0:
+ value = 0
+ else:
+ value = max(v.db_id for v in self.db_actions)
+ if self.db_has_annotation_with_key(action_key):
+ annotation = self.db_get_annotation_by_key(action_key)
+ annotation.db_value = str(value)
+ else:
+ annotation=DBAnnotation(self.idScope.getNewId(DBAnnotation.vtType),
+ action_key, str(value))
+ self.db_add_annotation(annotation)
+
+ def hashAnnotations(self):
+ annotations = {}
+ for annotation in self.db_annotations:
+ if annotation._db_key not in annotations:
+ annotations[annotation._db_key] = []
+ if annotation._db_value not in annotations[annotation._db_key]:
+ annotations[annotation._db_key].append(annotation._db_value)
+ keys = annotations.keys()
+ keys.sort()
+ m = hashlib.md5()
+ for k in keys:
+ m.update(str(k))
+ annotations[k].sort()
+ for v in annotations[k]:
+ m.update(str(v))
+ return m.hexdigest()
+
+ def hashActionAnnotations(self):
+ action_annotations = {}
+ for action_id, key, value in [[aa.db_action_id, aa.db_key,
+ aa.db_value] for aa in self.db_actionAnnotations]:
+ index = (str(action_id), key)
+ if index not in action_annotations:
+ action_annotations[index] = []
+ if value not in action_annotations[index]:
+ action_annotations[index].append(value)
+ keys = action_annotations.keys()
+ keys.sort()
+ m = hashlib.md5()
+ for k in keys:
+ m.update(k[0] + k[1])
+ action_annotations[k].sort()
+ for v in action_annotations[k]:
+ m.update(str(v))
+ return m.hexdigest()
diff --git a/vistrails/db/versions/v1_0_2/domain/workflow.py b/vistrails/db/versions/v1_0_2/domain/workflow.py
new file mode 100644
index 0000000..af484e6
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/domain/workflow.py
@@ -0,0 +1,172 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from auto_gen import DBAbstraction, DBModule, DBGroup
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1,
+ {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.build_index()
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ new_obj = _DBWorkflow.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ new_obj.build_index()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
+
+ _vtTypeMap = {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType}
+
+ def build_index(self):
+ g = self._vtTypeMap.get
+ self.objects = dict(((g(o.vtType, o.vtType), o._db_id), o)
+ for (o,_,_) in self.db_children())
+
+ def add_to_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ self.objects[(obj_type, object.getPrimaryKey())] = object
+
+ def delete_from_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ del self.objects[(obj_type, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_print_objects(self):
+ for k,v in self.objects.iteritems():
+ print '%s: %s' % (k, v)
+
+ def db_has_object(self, type, id):
+ return (type, id) in self.objects
+
+ def db_get_object(self, type, id):
+ return self.objects[(type, id)]
+
+ def db_add_object(self, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if object.vtType == DBAbstraction.vtType or \
+ object.vtType == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ else:
+ obj_type = object.vtType
+ funname = 'db_add_' + obj_type
+ obj_copy = copy.copy(object)
+ getattr(parent_obj, funname)(obj_copy)
+ self.add_to_index(obj_copy)
+
+ def db_change_object(self, old_id, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+
+ self.db_delete_object(old_id, object.vtType, None, None, parent_obj)
+ self.db_add_object(object, None, None, parent_obj)
+
+ def db_delete_object(self, obj_id, obj_type, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if obj_type == DBAbstraction.vtType or obj_type == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ funname = 'db_get_' + obj_type
+ if hasattr(parent_obj, funname):
+ object = getattr(parent_obj, funname)(obj_id)
+ else:
+ attr_name = 'db_' + obj_type
+ object = getattr(parent_obj, attr_name)
+ funname = 'db_delete_' + obj_type
+ getattr(parent_obj, funname)(object)
+ self.delete_from_index(object)
diff --git a/vistrails/db/versions/v1_0_2/persistence/__init__.py b/vistrails/db/versions/v1_0_2/persistence/__init__.py
new file mode 100644
index 0000000..d992cd3
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/persistence/__init__.py
@@ -0,0 +1,473 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+from vistrails.core.system import get_elementtree_library
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v1_0_2 import version as my_version
+from vistrails.db.versions.v1_0_2.domain import DBGroup, DBWorkflow, DBVistrail, DBLog, \
+ DBRegistry
+
+ElementTree = get_elementtree_library()
+
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def parse_xml_file(self, filename):
+ return ElementTree.parse(filename)
+
+ def write_xml_file(self, filename, tree):
+ def indent(elem, level=0):
+ i = "\n" + level*" "
+ if len(elem):
+ if not elem.text or not elem.text.strip():
+ elem.text = i + " "
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ for elem in elem:
+ indent(elem, level+1)
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ else:
+ if level and (not elem.tail or not elem.tail.strip()):
+ elem.tail = i
+ indent(tree.getroot())
+ tree.write(filename)
+
+ def read_xml_object(self, vtType, node):
+ return self['xml'][vtType].fromXML(node)
+
+ def write_xml_object(self, obj, node=None):
+ res_node = self['xml'][obj.vtType].toXML(obj, node)
+ return res_node
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ """open_from_xml(filename) -> DBVistrail"""
+ if tree is None:
+ tree = self.parse_xml_file(filename)
+ vistrail = self.read_xml_object(vtType, tree.getroot())
+ return vistrail
+
+ def save_to_xml(self, obj, filename, tags, version=None):
+ """save_to_xml(obj : object, filename: str, tags: dict,
+ version: str) -> None
+
+ """
+ root = self.write_xml_object(obj)
+ if version is None:
+ version = my_version
+ root.set('version', version)
+ for k, v in tags.iteritems():
+ root.set(k, v)
+ tree = ElementTree.ElementTree(root)
+ self.write_xml_file(filename, tree)
+
+ def open_from_db(self, db_connection, vtType, id=None, lock=False,
+ global_props=None):
+ all_objects = {}
+ if global_props is None:
+ global_props = {}
+ if id is not None:
+ global_props['id'] = id
+ # print global_props
+ res_objects = self['sql'][vtType].get_sql_columns(db_connection,
+ global_props,
+ lock)
+ if len(res_objects) > 1:
+ raise VistrailsDBException("More than object of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+ elif len(res_objects) <= 0:
+ raise VistrailsDBException("No objects of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+
+ all_objects.update(res_objects)
+ res = res_objects.values()[0]
+ global_props = {'entity_id': res.db_id,
+ 'entity_type': res.vtType}
+
+ # collect all commands so that they can be executed together
+ # daoList should contain (dao_type, dao, dbCommand) values
+ daoList = []
+ # dbCommandList should contain dbCommand values
+ dbCommandList = []
+
+ # generate SELECT statements
+ for dao_type, dao in self['sql'].iteritems():
+ if (dao_type == DBVistrail.vtType or
+ dao_type == DBWorkflow.vtType or
+ dao_type == DBLog.vtType or
+ dao_type == DBRegistry.vtType):
+ continue
+
+ daoList.append([dao_type, dao, None])
+ dbCommand = dao.get_sql_select(db_connection, global_props, lock)
+ dbCommandList.append(dbCommand)
+
+ # Exacute all select statements
+ results = self['sql'][vtType].executeSQLGroup(db_connection,
+ dbCommandList, True)
+
+ # add result to correct dao
+ for i in xrange(len(daoList)):
+ daoList[i][2] = results[i]
+
+ # process results
+ for dao_type, dao, data in daoList:
+ current_objs = dao.process_sql_columns(data, global_props)
+ all_objects.update(current_objs)
+
+ if dao_type == DBGroup.vtType:
+ for key, obj in current_objs.iteritems():
+ new_props = {'parent_id': key[1],
+ 'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ res_obj = self.open_from_db(db_connection,
+ DBWorkflow.vtType,
+ None, lock, new_props)
+ res_dict = {}
+ res_dict[(res_obj.vtType, res_obj.db_id)] = res_obj
+ all_objects.update(res_dict)
+
+ for key, obj in all_objects.iteritems():
+ if key[0] == vtType and key[1] == id:
+ continue
+ self['sql'][obj.vtType].from_sql_fast(obj, all_objects)
+ for obj in all_objects.itervalues():
+ obj.is_dirty = False
+ obj.is_new = False
+
+ return res
+
+ def open_many_from_db(self, db_connection, vtType, ids, lock=False):
+ """ Loads multiple objects. They need to be loaded as one single
+ multiple select statement command for performance reasons.
+ """
+
+ log_dao = self['sql'][vtType]
+ # loop through ids and build SELECT statements
+ selects = [log_dao.get_sql_select(db_connection, {'id': id}, lock)
+ for id in ids]
+ # Execute all SELECT statements for main objects
+ results = log_dao.executeSQLGroup(db_connection, selects, True)
+
+ # list of final objects
+ objects = []
+ # list of selects
+ selects = []
+ # list of children id:all_objects_dict
+ all_objects_dict = {}
+ # process each result and extract child SELECTS
+ # daoList should contain (id, dao_type, dao, result) values
+ daoList = []
+ # selects should contain dbCommand values
+ selects = []
+ global_props = {}
+ for id, data in zip(ids, results):
+ res_objects = log_dao.process_sql_columns(data, global_props)
+ if len(res_objects) > 1:
+ raise VistrailsDBException("More than object of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+ elif len(res_objects) <= 0:
+ raise VistrailsDBException("No objects of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+ all_objects = {}
+ all_objects_dict[id] = all_objects
+ all_objects.update(res_objects)
+ objects.append(res_objects.values()[0])
+ # collect all commands so that they can be executed together
+
+ # generate SELECT statements for children
+ for dao_type, dao in self['sql'].iteritems():
+ if (dao_type == DBVistrail.vtType or
+ dao_type == DBWorkflow.vtType or
+ dao_type == DBLog.vtType or
+ dao_type == DBRegistry.vtType):
+ continue
+
+ daoList.append([id, dao_type, dao, None])
+ dbCommand = dao.get_sql_select(db_connection, global_props, lock)
+ selects.append(dbCommand)
+
+ # Execute all child select statements
+ results = self['sql'][vtType].executeSQLGroup(db_connection,
+ selects, True)
+ for i in xrange(len(daoList)):
+ daoList[i][3] = results[i]
+
+ # process results
+ for id, dao_type, dao, data in daoList:
+ all_objects = all_objects_dict[id]
+ current_objs = dao.process_sql_columns(data, global_props)
+ all_objects.update(current_objs)
+
+ if dao_type == DBGroup.vtType:
+ for key, obj in current_objs.iteritems():
+ new_props = {'parent_id': key[1],
+ 'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ res_obj = self.open_from_db(db_connection,
+ DBWorkflow.vtType,
+ None, lock, new_props)
+ res_dict = {}
+ res_dict[(res_obj.vtType, res_obj.db_id)] = res_obj
+ all_objects.update(res_dict)
+
+
+ for id, all_objects in all_objects_dict.iteritems():
+ for key, obj in all_objects.iteritems():
+ if key[0] == vtType and key[1] == id:
+ continue
+ self['sql'][obj.vtType].from_sql_fast(obj, all_objects)
+ for id, dao_type, dao, data in daoList:
+ all_objects = all_objects_dict[id]
+ for obj in all_objects.itervalues():
+ obj.is_dirty = False
+ obj.is_new = False
+
+ return objects
+
+ def save_to_db(self, db_connection, obj, do_copy=False, global_props=None):
+ if do_copy == 'with_ids':
+ do_copy = True
+ elif do_copy and obj.db_id is not None:
+ obj.db_id = None
+
+ children = obj.db_children()
+ children.reverse()
+ if global_props is None:
+ global_props = {'entity_type': obj.vtType}
+ # print 'global_props:', global_props
+
+ # assumes not deleting entire thing
+ child = children[0][0]
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ global_props = {'entity_id': child.db_id,
+ 'entity_type': child.vtType}
+
+ # do deletes
+ if not do_copy:
+ for (child, _, _) in children:
+ for c in child.db_deleted_children(True):
+ self['sql'][c.vtType].delete_sql_column(db_connection,
+ c,
+ global_props)
+ child = children.pop(0)[0]
+ child.is_dirty = False
+ child.is_new = False
+
+ if not len(children):
+ return
+
+ # list of all children
+ dbCommandList = []
+ writtenChildren = []
+ # process remaining children
+ for (child, _, _) in children:
+ dbCommand = self['sql'][child.vtType].set_sql_command(
+ db_connection, child, global_props, do_copy)
+ if dbCommand is not None:
+ dbCommandList.append(dbCommand)
+ writtenChildren.append(child)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ # Execute all insert/update statements
+ results = self['sql'][children[0][0].vtType].executeSQLGroup(
+ db_connection,
+ dbCommandList, False)
+ resultDict = dict(zip(writtenChildren, results))
+ # process remaining children
+ for (child, _, _) in children:
+ if child in resultDict:
+ lastId = resultDict[child]
+ self['sql'][child.vtType].set_sql_process(child,
+ global_props,
+ lastId)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ # print '*** entity_type:', global_props['entity_type']
+ new_props = {'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ is_dirty = child.db_workflow.is_dirty
+ child.db_workflow.db_entity_type = DBWorkflow.vtType
+ child.db_workflow.is_dirty = is_dirty
+ self.save_to_db(db_connection, child.db_workflow, do_copy,
+ new_props)
+
+ def save_many_to_db(self, db_connection, objList, do_copy=False):
+ if do_copy == 'with_ids':
+ do_copy = True
+ if not len(objList):
+ return
+ childrenDict = {}
+ global_propsDict = {}
+ dbCommandList = []
+ writtenChildren = []
+ for obj in objList:
+ if do_copy and obj.db_id is not None:
+ obj.db_id = None
+
+ children = obj.db_children()
+ children.reverse()
+ global_props = {'entity_type': obj.vtType}
+
+ child = children[0][0]
+ dbCommand = self['sql'][child.vtType].set_sql_command(
+ db_connection, child, global_props, do_copy)
+ if dbCommand is not None:
+ dbCommandList.append(dbCommand)
+ writtenChildren.append(child)
+
+ childrenDict[child] = children
+ global_propsDict[child] = global_props
+
+ # Execute all insert/update statements for the main objects
+ results = self['sql'][children[0][0].vtType].executeSQLGroup(
+ db_connection,
+ dbCommandList, False)
+ resultDict = dict(zip(writtenChildren, results))
+ dbCommandList = []
+ writtenChildren = []
+ for child, children in childrenDict.iteritems():
+ # process objects
+ if child in resultDict:
+ lastId = resultDict[child]
+ self['sql'][child.vtType].set_sql_process(
+ child, global_propsDict[child], lastId)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ # process children
+ global_props = {'entity_id': child.db_id,
+ 'entity_type': child.vtType}
+ global_propsDict[child] = global_props
+ # do deletes
+ if not do_copy:
+ for (child, _, _) in childrenDict[child]:
+ for c in child.db_deleted_children(True):
+ self['sql'][c.vtType].delete_sql_column(db_connection,
+ c,
+ global_props)
+ child = children.pop(0)[0]
+ child.is_dirty = False
+ child.is_new = False
+
+ # list of all children
+ # process remaining children
+ for (child, _, _) in children:
+ dbCommand = self['sql'][child.vtType].set_sql_command(
+ db_connection, child, global_props, do_copy)
+ if dbCommand is not None:
+ dbCommandList.append(dbCommand)
+ writtenChildren.append(child)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ # Execute all child insert/update statements
+ results = self['sql'][children[0][0].vtType].executeSQLGroup(
+ db_connection,
+ dbCommandList, False)
+ resultDict = dict(zip(writtenChildren, results))
+
+ for child, children in childrenDict.iteritems():
+ global_props = global_propsDict[child]
+ # process remaining children
+ for (child, _, _) in children:
+ if child in resultDict:
+ lastId = resultDict[child]
+ self['sql'][child.vtType].set_sql_process(child,
+ global_props,
+ lastId)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ # print '*** entity_type:', global_props['entity_type']
+ new_props = {'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ is_dirty = child.db_workflow.is_dirty
+ child.db_workflow.db_entity_type = DBWorkflow.vtType
+ child.db_workflow.is_dirty = is_dirty
+ self.save_to_db(db_connection, child.db_workflow, do_copy,
+ new_props)
+
+ def delete_from_db(self, db_connection, type, obj_id):
+ root_set = set([DBVistrail.vtType, DBWorkflow.vtType,
+ DBLog.vtType, DBRegistry.vtType])
+ if type not in root_set:
+ raise VistrailsDBException("Cannot delete entity of type '%s'" \
+ % type)
+
+ id_str = str(obj_id)
+ for (dao_type, dao) in self['sql'].iteritems():
+ if dao_type not in root_set:
+ db_cmd = \
+ self['sql'][type].createSQLDelete(dao.table,
+ {'entity_type': type,
+ 'entity_id': id_str})
+ self['sql'][type].executeSQL(db_connection, db_cmd, False)
+ db_cmd = self['sql'][type].createSQLDelete(self['sql'][type].table,
+ {'id': id_str})
+ self['sql'][type].executeSQL(db_connection, db_cmd, False)
+
+ def serialize(self, object):
+ root = self.write_xml_object(object)
+ return ElementTree.tostring(root)
+
+ def unserialize(self, str, obj_type):
+ def set_dirty(obj):
+ for child, _, _ in obj.db_children():
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ set_dirty(child.db_workflow)
+ child.is_dirty = True
+ child.is_new = True
+ try:
+ root = ElementTree.fromstring(str)
+ obj = self.read_xml_object(obj_type, root)
+ set_dirty(obj)
+ return obj
+ except SyntaxError, e:
+ msg = "Invalid VisTrails serialized object %s" % str
+ raise VistrailsDBException(msg)
+ return None
diff --git a/vistrails/db/versions/v1_0_2/persistence/sql/__init__.py b/vistrails/db/versions/v1_0_2/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v1_0_2/persistence/sql/auto_gen.py b/vistrails/db/versions/v1_0_2/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..95ec735
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/persistence/sql/auto_gen.py
@@ -0,0 +1,5804 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from sql_dao import SQLDAO
+from vistrails.db.versions.v1_0_2.domain import *
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port_spec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'sigstring', 'labels', 'defaults', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ optional = self.convertFromDB(row[3], 'int', 'int')
+ sort_key = self.convertFromDB(row[4], 'int', 'int')
+ sigstring = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ labels = self.convertFromDB(row[6], 'str', 'varchar(4095)')
+ defaults = self.convertFromDB(row[7], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[8], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[9], 'long', 'int')
+ entity_type = self.convertFromDB(row[10], 'str', 'char(16)')
+ parent = self.convertFromDB(row[11], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ sigstring=sigstring,
+ labels=labels,
+ defaults=defaults,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_entity_id = entity_id
+ portSpec.db_entity_type = entity_type
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'sigstring', 'labels', 'defaults', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ optional = self.convertFromDB(row[3], 'int', 'int')
+ sort_key = self.convertFromDB(row[4], 'int', 'int')
+ sigstring = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ labels = self.convertFromDB(row[6], 'str', 'varchar(4095)')
+ defaults = self.convertFromDB(row[7], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[8], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[9], 'long', 'int')
+ entity_type = self.convertFromDB(row[10], 'str', 'char(16)')
+ parent = self.convertFromDB(row[11], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ sigstring=sigstring,
+ labels=labels,
+ defaults=defaults,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_entity_id = entity_id
+ portSpec.db_entity_type = entity_type
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'module_descriptor':
+ p = all_objects[('module_descriptor', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'sigstring', 'labels', 'defaults', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_optional') and obj.db_optional is not None:
+ columnMap['optional'] = \
+ self.convertToDB(obj.db_optional, 'int', 'int')
+ if hasattr(obj, 'db_sort_key') and obj.db_sort_key is not None:
+ columnMap['sort_key'] = \
+ self.convertToDB(obj.db_sort_key, 'int', 'int')
+ if hasattr(obj, 'db_sigstring') and obj.db_sigstring is not None:
+ columnMap['sigstring'] = \
+ self.convertToDB(obj.db_sigstring, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_labels') and obj.db_labels is not None:
+ columnMap['labels'] = \
+ self.convertToDB(obj.db_labels, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_defaults') and obj.db_defaults is not None:
+ columnMap['defaults'] = \
+ self.convertToDB(obj.db_defaults, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'sigstring', 'labels', 'defaults', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_optional') and obj.db_optional is not None:
+ columnMap['optional'] = \
+ self.convertToDB(obj.db_optional, 'int', 'int')
+ if hasattr(obj, 'db_sort_key') and obj.db_sort_key is not None:
+ columnMap['sort_key'] = \
+ self.convertToDB(obj.db_sort_key, 'int', 'int')
+ if hasattr(obj, 'db_sigstring') and obj.db_sigstring is not None:
+ columnMap['sigstring'] = \
+ self.convertToDB(obj.db_sigstring, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_labels') and obj.db_labels is not None:
+ columnMap['labels'] = \
+ self.convertToDB(obj.db_labels, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_defaults') and obj.db_defaults is not None:
+ columnMap['defaults'] = \
+ self.convertToDB(obj.db_defaults, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ id=id)
+ module.db_parentType = parentType
+ module.db_entity_id = entity_id
+ module.db_entity_type = entity_type
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ id=id)
+ module.db_parentType = parentType
+ module.db_entity_id = entity_id
+ module.db_entity_type = entity_type
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleDescriptorSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_descriptor'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'package', 'namespace', 'package_version', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ base_descriptor_id = self.convertFromDB(row[6], 'long', 'int')
+ package = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ module_descriptor = DBModuleDescriptor(name=name,
+ package=package,
+ namespace=namespace,
+ package_version=package_version,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ id=id)
+ module_descriptor.db_package = package
+ module_descriptor.db_entity_id = entity_id
+ module_descriptor.db_entity_type = entity_type
+ module_descriptor.is_dirty = False
+ res[('module_descriptor', id)] = module_descriptor
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'package', 'namespace', 'package_version', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ base_descriptor_id = self.convertFromDB(row[6], 'long', 'int')
+ package = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ module_descriptor = DBModuleDescriptor(name=name,
+ package=package,
+ namespace=namespace,
+ package_version=package_version,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ id=id)
+ module_descriptor.db_package = package
+ module_descriptor.db_entity_id = entity_id
+ module_descriptor.db_entity_type = entity_type
+ module_descriptor.is_dirty = False
+ res[('module_descriptor', id)] = module_descriptor
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('package', obj.db_package) in all_objects:
+ p = all_objects[('package', obj.db_package)]
+ p.db_add_module_descriptor(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'package', 'namespace', 'package_version', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package_version') and obj.db_package_version is not None:
+ columnMap['package_version'] = \
+ self.convertToDB(obj.db_package_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_base_descriptor_id') and obj.db_base_descriptor_id is not None:
+ columnMap['base_descriptor_id'] = \
+ self.convertToDB(obj.db_base_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_package, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'package', 'namespace', 'package_version', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package_version') and obj.db_package_version is not None:
+ columnMap['package_version'] = \
+ self.convertToDB(obj.db_package_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_base_descriptor_id') and obj.db_base_descriptor_id is not None:
+ columnMap['base_descriptor_id'] = \
+ self.convertToDB(obj.db_base_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_package, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'tag'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[2], 'long', 'int')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_vistrail = vistrail
+ tag.db_entity_id = entity_id
+ tag.db_entity_type = entity_type
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[2], 'long', 'int')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_vistrail = vistrail
+ tag.db_entity_id = entity_id
+ tag.db_entity_type = entity_type
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ signature = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature,
+ id=id)
+ port.db_parentType = parentType
+ port.db_entity_id = entity_id
+ port.db_entity_type = entity_type
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ signature = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature,
+ id=id)
+ port.db_parentType = parentType
+ port.db_entity_id = entity_id
+ port.db_entity_type = entity_type
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_signature') and obj.db_signature is not None:
+ columnMap['signature'] = \
+ self.convertToDB(obj.db_signature, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_signature') and obj.db_signature is not None:
+ columnMap['signature'] = \
+ self.convertToDB(obj.db_signature, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ group = DBGroup(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ id=id)
+ group.db_parentType = parentType
+ group.db_entity_id = entity_id
+ group.db_entity_type = entity_type
+ group.db_parent = parent
+ group.is_dirty = False
+ res[('group', id)] = group
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ group = DBGroup(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ id=id)
+ group.db_parentType = parentType
+ group.db_entity_id = entity_id
+ group.db_entity_type = entity_type
+ group.db_parent = parent
+ group.is_dirty = False
+ res[('group', id)] = group
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_workflow is not None:
+ child = obj.db_workflow
+ child.db_group = obj.db_id
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'log_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ log = DBLog(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ log.is_dirty = False
+ res[('log', id)] = log
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ log = DBLog(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ log.is_dirty = False
+ res[('log', id)] = log
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_workflow_execs:
+ child.db_log = obj.db_id
+ for child in obj.db_machines:
+ child.db_log = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'machine'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.db_entity_id = entity_id
+ machine.db_entity_type = entity_type
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'int')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.db_entity_id = entity_id
+ machine.db_entity_type = entity_type
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'int')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'add_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_entity_id = entity_id
+ add.db_entity_type = entity_type
+ add.is_dirty = False
+ res[('add', id)] = add
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_entity_id = entity_id
+ add.db_entity_type = entity_type
+ add.is_dirty = False
+ res[('add', id)] = add
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'other'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_entity_id = entity_id
+ other.db_entity_type = entity_type
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_entity_id = entity_id
+ other.db_entity_type = entity_type
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'location'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_entity_id = entity_id
+ location.db_entity_type = entity_type
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_entity_id = entity_id
+ location.db_entity_type = entity_type
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'parameter'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_entity_id = entity_id
+ parameter.db_entity_type = entity_type
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'varchar(8191)')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_entity_id = entity_id
+ parameter.db_entity_type = entity_type
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPluginDataSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'plugin_data'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ data = self.convertFromDB(row[1], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ plugin_data = DBPluginData(data=data,
+ id=id)
+ plugin_data.db_parentType = parentType
+ plugin_data.db_entity_id = entity_id
+ plugin_data.db_entity_type = entity_type
+ plugin_data.db_parent = parent
+ plugin_data.is_dirty = False
+ res[('plugin_data', id)] = plugin_data
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ data = self.convertFromDB(row[1], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ plugin_data = DBPluginData(data=data,
+ id=id)
+ plugin_data.db_parentType = parentType
+ plugin_data.db_entity_id = entity_id
+ plugin_data.db_entity_type = entity_type
+ plugin_data.db_parent = parent
+ plugin_data.is_dirty = False
+ res[('plugin_data', id)] = plugin_data
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_plugin_data(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_data') and obj.db_data is not None:
+ columnMap['data'] = \
+ self.convertToDB(obj.db_data, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_data') and obj.db_data is not None:
+ columnMap['data'] = \
+ self.convertToDB(obj.db_data, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'function'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_entity_id = entity_id
+ function.db_entity_type = entity_type
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_entity_id = entity_id
+ function.db_entity_type = entity_type
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'action_annotation'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action_annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ action_id = self.convertFromDB(row[3], 'long', 'int')
+ date = self.convertFromDB(row[4], 'datetime', 'datetime')
+ user = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ actionAnnotation = DBActionAnnotation(key=key,
+ value=value,
+ action_id=action_id,
+ date=date,
+ user=user,
+ id=id)
+ actionAnnotation.db_vistrail = vistrail
+ actionAnnotation.db_entity_id = entity_id
+ actionAnnotation.db_entity_type = entity_type
+ actionAnnotation.is_dirty = False
+ res[('actionAnnotation', id)] = actionAnnotation
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action_annotation'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ action_id = self.convertFromDB(row[3], 'long', 'int')
+ date = self.convertFromDB(row[4], 'datetime', 'datetime')
+ user = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ actionAnnotation = DBActionAnnotation(key=key,
+ value=value,
+ action_id=action_id,
+ date=date,
+ user=user,
+ id=id)
+ actionAnnotation.db_vistrail = vistrail
+ actionAnnotation.db_entity_id = entity_id
+ actionAnnotation.db_entity_type = entity_type
+ actionAnnotation.is_dirty = False
+ res[('actionAnnotation', id)] = actionAnnotation
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_actionAnnotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action_annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_action_id') and obj.db_action_id is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action_id, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action_annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_action_id') and obj.db_action_id is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action_id, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action_annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'abstraction'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ internal_version = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ abstraction = DBAbstraction(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ id=id)
+ abstraction.db_parentType = parentType
+ abstraction.db_entity_id = entity_id
+ abstraction.db_entity_type = entity_type
+ abstraction.db_parent = parent
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ internal_version = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ abstraction = DBAbstraction(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ id=id)
+ abstraction.db_parentType = parentType
+ abstraction.db_entity_id = entity_id
+ abstraction.db_entity_type = entity_type
+ abstraction.db_parent = parent
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_internal_version') and obj.db_internal_version is not None:
+ columnMap['internal_version'] = \
+ self.convertToDB(obj.db_internal_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_internal_version') and obj.db_internal_version is not None:
+ columnMap['internal_version'] = \
+ self.convertToDB(obj.db_internal_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_id = self.convertFromDB(row[1], 'long', 'int')
+ entity_type = self.convertFromDB(row[2], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'char(16)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[6], 'long', 'int')
+ group = self.convertFromDB(row[7], 'long', 'int')
+
+ workflow = DBWorkflow(entity_type=entity_type,
+ name=name,
+ version=version,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ workflow.db_entity_id = entity_id
+ workflow.db_group = group
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_id = self.convertFromDB(row[1], 'long', 'int')
+ entity_type = self.convertFromDB(row[2], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'char(16)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[6], 'long', 'int')
+ group = self.convertFromDB(row[7], 'long', 'int')
+
+ workflow = DBWorkflow(entity_type=entity_type,
+ name=name,
+ version=version,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ workflow.db_entity_id = entity_id
+ workflow.db_group = group
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('group', obj.db_group) in all_objects:
+ p = all_objects[('group', obj.db_group)]
+ p.db_add_workflow(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ if hasattr(obj, 'db_group') and obj.db_group is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_group, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ if hasattr(obj, 'db_group') and obj.db_group is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_group, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_connections:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_plugin_datas:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_modules:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBRegistrySQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'registry'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ root_descriptor_id = self.convertFromDB(row[3], 'long', 'int')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+
+ registry = DBRegistry(entity_type=entity_type,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ registry.is_dirty = False
+ res[('registry', id)] = registry
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ root_descriptor_id = self.convertFromDB(row[3], 'long', 'int')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+
+ registry = DBRegistry(entity_type=entity_type,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ registry.is_dirty = False
+ res[('registry', id)] = registry
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_root_descriptor_id') and obj.db_root_descriptor_id is not None:
+ columnMap['root_descriptor_id'] = \
+ self.convertToDB(obj.db_root_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_root_descriptor_id') and obj.db_root_descriptor_id is not None:
+ columnMap['root_descriptor_id'] = \
+ self.convertToDB(obj.db_root_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_packages:
+ child.db_registry = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'annotation'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_entity_id = entity_id
+ annotation.db_entity_type = entity_type
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_entity_id = entity_id
+ annotation.db_entity_type = entity_type
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'change_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_entity_id = entity_id
+ change.db_entity_type = entity_type
+ change.is_dirty = False
+ res[('change', id)] = change
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_entity_id = entity_id
+ change.db_entity_type = entity_type
+ change.is_dirty = False
+ res[('change', id)] = change
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ group_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ group_type = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[7], 'int', 'int')
+ error = self.convertFromDB(row[8], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[9], 'long', 'int')
+ parentType = self.convertFromDB(row[10], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[11], 'long', 'int')
+ entity_type = self.convertFromDB(row[12], 'str', 'char(16)')
+ parent = self.convertFromDB(row[13], 'long', 'long')
+
+ group_exec = DBGroupExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ group_exec.db_parentType = parentType
+ group_exec.db_entity_id = entity_id
+ group_exec.db_entity_type = entity_type
+ group_exec.db_parent = parent
+ group_exec.is_dirty = False
+ res[('group_exec', id)] = group_exec
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ group_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ group_type = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[7], 'int', 'int')
+ error = self.convertFromDB(row[8], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[9], 'long', 'int')
+ parentType = self.convertFromDB(row[10], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[11], 'long', 'int')
+ entity_type = self.convertFromDB(row[12], 'str', 'char(16)')
+ parent = self.convertFromDB(row[13], 'long', 'long')
+
+ group_exec = DBGroupExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ group_exec.db_parentType = parentType
+ group_exec.db_entity_id = entity_id
+ group_exec.db_entity_type = entity_type
+ group_exec.db_parent = parent
+ group_exec.is_dirty = False
+ res[('group_exec', id)] = group_exec
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_group_name') and obj.db_group_name is not None:
+ columnMap['group_name'] = \
+ self.convertToDB(obj.db_group_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_group_type') and obj.db_group_type is not None:
+ columnMap['group_type'] = \
+ self.convertToDB(obj.db_group_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_group_name') and obj.db_group_name is not None:
+ columnMap['group_name'] = \
+ self.convertToDB(obj.db_group_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_group_type') and obj.db_group_type is not None:
+ columnMap['group_type'] = \
+ self.convertToDB(obj.db_group_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPackageSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'package'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ identifier = self.convertFromDB(row[2], 'str', 'varchar(1023)')
+ codepath = self.convertFromDB(row[3], 'str', 'varchar(1023)')
+ load_configuration = self.convertFromDB(row[4], 'int', 'int')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ description = self.convertFromDB(row[6], 'str', 'varchar(1023)')
+ registry = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ package = DBPackage(name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ id=id)
+ package.db_registry = registry
+ package.db_entity_id = entity_id
+ package.db_entity_type = entity_type
+ package.is_dirty = False
+ res[('package', id)] = package
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ identifier = self.convertFromDB(row[2], 'str', 'varchar(1023)')
+ codepath = self.convertFromDB(row[3], 'str', 'varchar(1023)')
+ load_configuration = self.convertFromDB(row[4], 'int', 'int')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ description = self.convertFromDB(row[6], 'str', 'varchar(1023)')
+ registry = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ package = DBPackage(name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ id=id)
+ package.db_registry = registry
+ package.db_entity_id = entity_id
+ package.db_entity_type = entity_type
+ package.is_dirty = False
+ res[('package', id)] = package
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('registry', obj.db_registry) in all_objects:
+ p = all_objects[('registry', obj.db_registry)]
+ p.db_add_package(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_identifier') and obj.db_identifier is not None:
+ columnMap['identifier'] = \
+ self.convertToDB(obj.db_identifier, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_codepath') and obj.db_codepath is not None:
+ columnMap['codepath'] = \
+ self.convertToDB(obj.db_codepath, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_load_configuration') and obj.db_load_configuration is not None:
+ columnMap['load_configuration'] = \
+ self.convertToDB(obj.db_load_configuration, 'int', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_description') and obj.db_description is not None:
+ columnMap['description'] = \
+ self.convertToDB(obj.db_description, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_registry') and obj.db_registry is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_registry, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_identifier') and obj.db_identifier is not None:
+ columnMap['identifier'] = \
+ self.convertToDB(obj.db_identifier, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_codepath') and obj.db_codepath is not None:
+ columnMap['codepath'] = \
+ self.convertToDB(obj.db_codepath, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_load_configuration') and obj.db_load_configuration is not None:
+ columnMap['load_configuration'] = \
+ self.convertToDB(obj.db_load_configuration, 'int', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_description') and obj.db_description is not None:
+ columnMap['description'] = \
+ self.convertToDB(obj.db_description, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_registry') and obj.db_registry is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_registry, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_module_descriptors:
+ child.db_package = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ vt_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[5], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[6], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[7], 'long', 'int')
+ parent_type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[9], 'long', 'int')
+ completed = self.convertFromDB(row[10], 'int', 'int')
+ name = self.convertFromDB(row[11], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[12], 'long', 'int')
+ entity_id = self.convertFromDB(row[13], 'long', 'int')
+ entity_type = self.convertFromDB(row[14], 'str', 'char(16)')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_entity_id = entity_id
+ workflow_exec.db_entity_type = entity_type
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ vt_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[5], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[6], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[7], 'long', 'int')
+ parent_type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[9], 'long', 'int')
+ completed = self.convertFromDB(row[10], 'int', 'int')
+ name = self.convertFromDB(row[11], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[12], 'long', 'int')
+ entity_id = self.convertFromDB(row[13], 'long', 'int')
+ entity_type = self.convertFromDB(row[14], 'str', 'char(16)')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_entity_id = entity_id
+ workflow_exec.db_entity_type = entity_type
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLoopExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'loop_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ iteration = self.convertFromDB(row[3], 'int', 'int')
+ completed = self.convertFromDB(row[4], 'int', 'int')
+ error = self.convertFromDB(row[5], 'str', 'varchar(1023)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ loop_exec = DBLoopExec(ts_start=ts_start,
+ ts_end=ts_end,
+ iteration=iteration,
+ completed=completed,
+ error=error,
+ id=id)
+ loop_exec.db_parentType = parentType
+ loop_exec.db_entity_id = entity_id
+ loop_exec.db_entity_type = entity_type
+ loop_exec.db_parent = parent
+ loop_exec.is_dirty = False
+ res[('loop_exec', id)] = loop_exec
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ iteration = self.convertFromDB(row[3], 'int', 'int')
+ completed = self.convertFromDB(row[4], 'int', 'int')
+ error = self.convertFromDB(row[5], 'str', 'varchar(1023)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ loop_exec = DBLoopExec(ts_start=ts_start,
+ ts_end=ts_end,
+ iteration=iteration,
+ completed=completed,
+ error=error,
+ id=id)
+ loop_exec.db_parentType = parentType
+ loop_exec.db_entity_id = entity_id
+ loop_exec.db_entity_type = entity_type
+ loop_exec.db_parent = parent
+ loop_exec.is_dirty = False
+ res[('loop_exec', id)] = loop_exec
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_loop_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_iteration') and obj.db_iteration is not None:
+ columnMap['iteration'] = \
+ self.convertToDB(obj.db_iteration, 'int', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_iteration') and obj.db_iteration is not None:
+ columnMap['iteration'] = \
+ self.convertToDB(obj.db_iteration, 'int', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'connection_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[2], 'long', 'int')
+ entity_type = self.convertFromDB(row[3], 'str', 'char(16)')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_entity_id = entity_id
+ connection.db_entity_type = entity_type
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[2], 'long', 'int')
+ entity_type = self.convertFromDB(row[3], 'str', 'char(16)')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_entity_id = entity_id
+ connection.db_entity_type = entity_type
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'action'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ id=id)
+ action.db_vistrail = vistrail
+ action.db_entity_id = entity_id
+ action.db_entity_type = entity_type
+ action.is_dirty = False
+ res[('action', id)] = action
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ id=id)
+ action.db_vistrail = vistrail
+ action.db_entity_id = entity_id
+ action.db_entity_type = entity_type
+ action.is_dirty = False
+ res[('action', id)] = action
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'delete_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_entity_id = entity_id
+ delete.db_entity_type = entity_type
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_entity_id = entity_id
+ delete.db_entity_type = entity_type
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'vistrail'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_actions:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_tags:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_actionAnnotations:
+ child.db_vistrail = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ module_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[6], 'int', 'int')
+ error = self.convertFromDB(row[7], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[8], 'long', 'int')
+ parentType = self.convertFromDB(row[9], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[10], 'long', 'int')
+ entity_type = self.convertFromDB(row[11], 'str', 'char(16)')
+ parent = self.convertFromDB(row[12], 'long', 'long')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ module_exec.db_parentType = parentType
+ module_exec.db_entity_id = entity_id
+ module_exec.db_entity_type = entity_type
+ module_exec.db_parent = parent
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ module_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[6], 'int', 'int')
+ error = self.convertFromDB(row[7], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[8], 'long', 'int')
+ parentType = self.convertFromDB(row[9], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[10], 'long', 'int')
+ entity_type = self.convertFromDB(row[11], 'str', 'char(16)')
+ parent = self.convertFromDB(row[12], 'long', 'long')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ module_exec.db_parentType = parentType
+ module_exec.db_entity_id = entity_id
+ module_exec.db_entity_type = entity_type
+ module_exec.db_parent = parent
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_loop_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'module_descriptor' not in self:
+ self['module_descriptor'] = DBModuleDescriptorSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'actionAnnotation' not in self:
+ self['actionAnnotation'] = DBActionAnnotationSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'registry' not in self:
+ self['registry'] = DBRegistrySQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'group_exec' not in self:
+ self['group_exec'] = DBGroupExecSQLDAOBase(self)
+ if 'package' not in self:
+ self['package'] = DBPackageSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'loop_exec' not in self:
+ self['loop_exec'] = DBLoopExecSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v1_0_2/persistence/sql/sql_dao.py b/vistrails/db/versions/v1_0_2/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..eab1acc
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/persistence/sql/sql_dao.py
@@ -0,0 +1,259 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.services.io import get_db_lib
+from vistrails.core import debug
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertWarning(self, before, after, _from, to):
+ text = ["Value truncated when saving to database",
+ "%s truncated to %s\nwhile converting '%s' to '%s'"]
+ debug.warning(text[0], text[1] % (before, after, _from, to))
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ value = str(value)
+ if db_type.startswith('varchar'):
+ try:
+ length = int(db_type[8:-1])
+ if len(value) > length:
+ self.convertWarning(value, value[:length],
+ type, db_type)
+ value = value[:length]
+ except Exception, e:
+ pass
+ if db_type.startswith('char'):
+ try:
+ length = int(db_type[5:-1])
+ if len(value) > length:
+ self.convertWarning(value, value[:length],
+ type, db_type)
+ value = value[:length]
+ except Exception, e:
+ pass
+ # return "'" + str(value).replace("'", "''") + "'"
+ return value
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ # necessary to avoid conversion warnings in MySQL
+ if db_type.startswith('DECIMAL'):
+ try:
+ value="%%.%sf"%str(db_type[8:-1].split(',')[1])%value
+ except Exception, e:
+ pass
+ return str(value)
+ elif type == 'int':
+ # note: on 64-bit machines int:s are 64-bit
+ MIN_INT = -2147483648
+ MAX_INT = 2147483647
+ if db_type == 'int':
+ if int(value) < MIN_INT:
+ self.convertWarning(value, MIN_INT, type, db_type)
+ value = MIN_INT
+ if int(value) > MAX_INT:
+ self.convertWarning(value, MAX_INT, type, db_type)
+ value = MAX_INT
+ return str(value)
+ elif type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+
+ return None
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None,
+ forUpdate=False):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % \
+ (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ if forUpdate:
+ dbCommand += " FOR UPDATE"
+ dbCommand += ";"
+ return (dbCommand, tuple(values))
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ # valueStr = '%s, '.join(values)
+ valueStr = ''
+ if len(values) > 1:
+ valueStr = '%s,' * (len(values) - 1) + '%s'
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s);""" % \
+ (table, columnStr, valueStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ values = []
+ for column, value in columnMap.iteritems():
+# if value is None:
+# value = 'NULL'
+ setStr += '%s%s = %%s' % (comma, column)
+ comma = ', '
+ values.append(value)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """UPDATE %s SET %s WHERE %s;""" % \
+ (table, setStr, whereStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLDelete(self, table, whereMap):
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """DELETE FROM %s WHERE %s;""" % \
+ (table, whereStr)
+ return (dbCommand, tuple(values))
+
+ def executeSQL(self, db, cmd_tuple, isFetch):
+ dbCommand, values = cmd_tuple
+ # print 'db: %s' % dbCommand
+ # print 'values:', values
+ data = None
+ cursor = db.cursor()
+ try:
+ cursor.execute(dbCommand, values)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ except Exception, e:
+ raise VistrailsDBException('Command "%s" with values "%s" '
+ 'failed: %s' % (dbCommand, values, e))
+ finally:
+ cursor.close()
+ return data
+
+ def executeSQLGroup(self, db, dbCommandList, isFetch):
+ """ Executes a command consisting of multiple SELECT statements
+ It returns a list of results from the SELECT statements
+ """
+ data = []
+ # break up into bundles
+ BUNDLE_SIZE = 10000
+ num_commands = len(dbCommandList)
+ n = 0
+ while n<num_commands:
+ dbCommands = dbCommandList[n:(n+BUNDLE_SIZE)]
+ commandString = ''
+ for prepared, values in dbCommands:
+ command = prepared % \
+ db.escape(values, get_db_lib().converters.conversions)
+ commandString += command
+ cur = db.cursor()
+ try:
+ result = cur.execute(commandString)
+ while True:
+ r = cur.fetchall() if isFetch else cur.lastrowid
+ data.append(r)
+ next = cur.nextset()
+ if not next:
+ break
+ except Exception, e:
+ raise VistrailsDBException('Command failed: %s -- """ %s """' %
+ (e, commandString))
+ finally:
+ cur.close()
+
+ n += BUNDLE_SIZE
+ return data
+
+ def start_transaction(self, db):
+ db.begin()
+
+ def commit_transaction(self, db):
+ db.commit()
+
+ def rollback_transaction(self, db):
+ db.rollback()
diff --git a/vistrails/db/versions/v1_0_2/persistence/xml/__init__.py b/vistrails/db/versions/v1_0_2/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v1_0_2/persistence/xml/auto_gen.py b/vistrails/db/versions/v1_0_2/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..d17b767
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/persistence/xml/auto_gen.py
@@ -0,0 +1,3902 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+from vistrails.core.system import get_elementtree_library
+
+from xml_dao import XMLDAO
+from vistrails.db.versions.v1_0_2.domain import *
+
+ElementTree = get_elementtree_library()
+
+
+class DBOpmProcessIdEffectXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'effect':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmProcessIdEffect(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_id_effect, node=None):
+ if node is None:
+ node = ElementTree.Element('effect')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process_id_effect.db_id, 'str'))
+
+ return node
+
+class DBOpmWasGeneratedByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasGeneratedBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_artifact_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_process_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasGeneratedBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_generated_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasGeneratedBy')
+
+ # set elements
+ effect = opm_was_generated_by.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_artifact_id_effect').toXML(effect, childNode)
+ role = opm_was_generated_by.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_generated_by.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_process_id_cause').toXML(cause, childNode)
+ accounts = opm_was_generated_by.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_generated_by.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBOpmAccountsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'accounts':
+ return None
+
+ accounts = []
+ opm_overlapss = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'account':
+ _data = self.getDao('opm_account').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'overlaps':
+ _data = self.getDao('opm_overlaps').fromXML(child)
+ opm_overlapss.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAccounts(accounts=accounts,
+ opm_overlapss=opm_overlapss)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_accounts, node=None):
+ if node is None:
+ node = ElementTree.Element('accounts')
+
+ # set elements
+ accounts = opm_accounts.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account').toXML(account, childNode)
+ opm_overlapss = opm_accounts.db_opm_overlapss
+ for opm_overlaps in opm_overlapss:
+ childNode = ElementTree.SubElement(node, 'overlaps')
+ self.getDao('opm_overlaps').toXML(opm_overlaps, childNode)
+
+ return node
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'portSpec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('optional', None)
+ optional = self.convertFromStr(data, 'int')
+ data = node.get('sortKey', None)
+ sort_key = self.convertFromStr(data, 'int')
+ data = node.get('sigstring', None)
+ sigstring = self.convertFromStr(data, 'str')
+ data = node.get('labels', None)
+ labels = self.convertFromStr(data, 'str')
+ data = node.get('defaults', None)
+ defaults = self.convertFromStr(data, 'str')
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ sigstring=sigstring,
+ labels=labels,
+ defaults=defaults)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, node=None):
+ if node is None:
+ node = ElementTree.Element('portSpec')
+
+ # set attributes
+ node.set('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.set('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.set('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.set('optional',self.convertToStr(portSpec.db_optional, 'int'))
+ node.set('sortKey',self.convertToStr(portSpec.db_sort_key, 'int'))
+ node.set('sigstring',self.convertToStr(portSpec.db_sigstring, 'str'))
+ node.set('labels',self.convertToStr(portSpec.db_labels, 'str'))
+ node.set('defaults',self.convertToStr(portSpec.db_defaults, 'str'))
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'module':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, node=None):
+ if node is None:
+ node = ElementTree.Element('module')
+
+ # set attributes
+ node.set('id',self.convertToStr(module.db_id, 'long'))
+ node.set('cache',self.convertToStr(module.db_cache, 'int'))
+ node.set('name',self.convertToStr(module.db_name, 'str'))
+ node.set('namespace',self.convertToStr(module.db_namespace, 'str'))
+ node.set('package',self.convertToStr(module.db_package, 'str'))
+ node.set('version',self.convertToStr(module.db_version, 'str'))
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = module.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBModuleDescriptorXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'moduleDescriptor':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('packageVersion', None)
+ package_version = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('baseDescriptorId', None)
+ base_descriptor_id = self.convertFromStr(data, 'long')
+
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleDescriptor(id=id,
+ name=name,
+ package=package,
+ namespace=namespace,
+ package_version=package_version,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_descriptor, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleDescriptor')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_descriptor.db_id, 'long'))
+ node.set('name',self.convertToStr(module_descriptor.db_name, 'str'))
+ node.set('package',self.convertToStr(module_descriptor.db_package, 'str'))
+ node.set('namespace',self.convertToStr(module_descriptor.db_namespace, 'str'))
+ node.set('packageVersion',self.convertToStr(module_descriptor.db_package_version, 'str'))
+ node.set('version',self.convertToStr(module_descriptor.db_version, 'str'))
+ node.set('baseDescriptorId',self.convertToStr(module_descriptor.db_base_descriptor_id, 'long'))
+
+ # set elements
+ portSpecs = module_descriptor.db_portSpecs
+ for portSpec in portSpecs:
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'tag':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, node=None):
+ if node is None:
+ node = ElementTree.Element('tag')
+
+ # set attributes
+ node.set('id',self.convertToStr(tag.db_id, 'long'))
+ node.set('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBOpmRoleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'role':
+ return None
+
+ # read attributes
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBOpmRole(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_role, node=None):
+ if node is None:
+ node = ElementTree.Element('role')
+
+ # set attributes
+ node.set('value',self.convertToStr(opm_role.db_value, 'str'))
+
+ return node
+
+class DBOpmProcessesXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'processes':
+ return None
+
+ processs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'process':
+ _data = self.getDao('opm_process').fromXML(child)
+ processs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcesses(processs=processs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_processes, node=None):
+ if node is None:
+ node = ElementTree.Element('processes')
+
+ # set elements
+ processs = opm_processes.db_processs
+ for process in processs:
+ childNode = ElementTree.SubElement(node, 'process')
+ self.getDao('opm_process').toXML(process, childNode)
+
+ return node
+
+class DBOpmAccountIdXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'account':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmAccountId(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_account_id, node=None):
+ if node is None:
+ node = ElementTree.Element('account')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_account_id.db_id, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'port':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('moduleId', None)
+ moduleId = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ moduleName = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('signature', None)
+ signature = self.convertFromStr(data, 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, node=None):
+ if node is None:
+ node = ElementTree.Element('port')
+
+ # set attributes
+ node.set('id',self.convertToStr(port.db_id, 'long'))
+ node.set('type',self.convertToStr(port.db_type, 'str'))
+ node.set('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.set('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.set('name',self.convertToStr(port.db_name, 'str'))
+ node.set('signature',self.convertToStr(port.db_signature, 'str'))
+
+ return node
+
+class DBOpmArtifactXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'artifact':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.getDao('opm_artifact_value').fromXML(child)
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifact(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact, node=None):
+ if node is None:
+ node = ElementTree.Element('artifact')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact.db_id, 'str'))
+
+ # set elements
+ value = opm_artifact.db_value
+ if value is not None:
+ childNode = ElementTree.SubElement(node, 'value')
+ self.getDao('opm_artifact_value').toXML(value, childNode)
+ accounts = opm_artifact.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBGroupXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'group':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+
+ workflow = None
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'workflow':
+ _data = self.getDao('workflow').fromXML(child)
+ workflow = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroup(id=id,
+ workflow=workflow,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group, node=None):
+ if node is None:
+ node = ElementTree.Element('group')
+
+ # set attributes
+ node.set('id',self.convertToStr(group.db_id, 'long'))
+ node.set('cache',self.convertToStr(group.db_cache, 'int'))
+ node.set('name',self.convertToStr(group.db_name, 'str'))
+ node.set('namespace',self.convertToStr(group.db_namespace, 'str'))
+ node.set('package',self.convertToStr(group.db_package, 'str'))
+ node.set('version',self.convertToStr(group.db_version, 'str'))
+
+ # set elements
+ workflow = group.db_workflow
+ if workflow is not None:
+ childNode = ElementTree.SubElement(node, 'workflow')
+ self.getDao('workflow').toXML(workflow, childNode)
+ location = group.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = group.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = group.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'log':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ workflow_execs = []
+ machines = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'workflowExec':
+ _data = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs.append(_data)
+ elif child_tag == 'machine':
+ _data = self.getDao('machine').fromXML(child)
+ machines.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLog(id=id,
+ version=version,
+ name=name,
+ workflow_execs=workflow_execs,
+ machines=machines,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, node=None):
+ if node is None:
+ node = ElementTree.Element('log')
+
+ # set attributes
+ node.set('id',self.convertToStr(log.db_id, 'long'))
+ node.set('version',self.convertToStr(log.db_version, 'str'))
+ node.set('name',self.convertToStr(log.db_name, 'str'))
+ node.set('vistrail_id',self.convertToStr(log.db_vistrail_id, 'long'))
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs:
+ childNode = ElementTree.SubElement(node, 'workflowExec')
+ self.getDao('workflow_exec').toXML(workflow_exec, childNode)
+ machines = log.db_machines
+ for machine in machines:
+ childNode = ElementTree.SubElement(node, 'machine')
+ self.getDao('machine').toXML(machine, childNode)
+
+ return node
+
+class DBOpmAgentsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agents':
+ return None
+
+ agents = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'agent':
+ _data = self.getDao('opm_agent').fromXML(child)
+ agents.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAgents(agents=agents)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agents, node=None):
+ if node is None:
+ node = ElementTree.Element('agents')
+
+ # set elements
+ agents = opm_agents.db_agents
+ for agent in agents:
+ childNode = ElementTree.SubElement(node, 'agent')
+ self.getDao('opm_agent').toXML(agent, childNode)
+
+ return node
+
+class DBOpmProcessIdCauseXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'cause':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmProcessIdCause(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_id_cause, node=None):
+ if node is None:
+ node = ElementTree.Element('cause')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process_id_cause.db_id, 'str'))
+
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'machine':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('os', None)
+ os = self.convertFromStr(data, 'str')
+ data = node.get('architecture', None)
+ architecture = self.convertFromStr(data, 'str')
+ data = node.get('processor', None)
+ processor = self.convertFromStr(data, 'str')
+ data = node.get('ram', None)
+ ram = self.convertFromStr(data, 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, node=None):
+ if node is None:
+ node = ElementTree.Element('machine')
+
+ # set attributes
+ node.set('id',self.convertToStr(machine.db_id, 'long'))
+ node.set('name',self.convertToStr(machine.db_name, 'str'))
+ node.set('os',self.convertToStr(machine.db_os, 'str'))
+ node.set('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.set('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.set('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'add':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAdd(data=data,
+ id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, node=None):
+ if node is None:
+ node = ElementTree.Element('add')
+
+ # set attributes
+ node.set('id',self.convertToStr(add.db_id, 'long'))
+ node.set('what',self.convertToStr(add.db_what, 'str'))
+ node.set('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # set elements
+ data = add.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'other':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, node=None):
+ if node is None:
+ node = ElementTree.Element('other')
+
+ # set attributes
+ node.set('id',self.convertToStr(other.db_id, 'long'))
+ node.set('key',self.convertToStr(other.db_key, 'str'))
+
+ # set elements
+ value = other.db_value
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'location':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('x', None)
+ x = self.convertFromStr(data, 'float')
+ data = node.get('y', None)
+ y = self.convertFromStr(data, 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, node=None):
+ if node is None:
+ node = ElementTree.Element('location')
+
+ # set attributes
+ node.set('id',self.convertToStr(location.db_id, 'long'))
+ node.set('x',self.convertToStr(location.db_x, 'float'))
+ node.set('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBOpmOverlapsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'overlaps':
+ return None
+
+ opm_account_ids = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ opm_account_ids.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmOverlaps(opm_account_ids=opm_account_ids)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_overlaps, node=None):
+ if node is None:
+ node = ElementTree.Element('overlaps')
+
+ # set elements
+ opm_account_ids = opm_overlaps.db_opm_account_ids
+ for opm_account_id in opm_account_ids:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(opm_account_id, childNode)
+
+ return node
+
+class DBOpmArtifactsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'artifacts':
+ return None
+
+ artifacts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'artifact':
+ _data = self.getDao('opm_artifact').fromXML(child)
+ artifacts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifacts(artifacts=artifacts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifacts, node=None):
+ if node is None:
+ node = ElementTree.Element('artifacts')
+
+ # set elements
+ artifacts = opm_artifacts.db_artifacts
+ for artifact in artifacts:
+ childNode = ElementTree.SubElement(node, 'artifact')
+ self.getDao('opm_artifact').toXML(artifact, childNode)
+
+ return node
+
+class DBOpmDependenciesXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'causalDependencies':
+ return None
+
+ dependencys = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'used':
+ _data = self.getDao('opm_used').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasGeneratedBy':
+ _data = self.getDao('opm_was_generated_by').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasTriggeredBy':
+ _data = self.getDao('opm_was_triggered_by').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasDerivedFrom':
+ _data = self.getDao('opm_was_derived_from').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasControlledBy':
+ _data = self.getDao('opm_was_controlled_by').fromXML(child)
+ dependencys.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmDependencies(dependencys=dependencys)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_dependencies, node=None):
+ if node is None:
+ node = ElementTree.Element('causalDependencies')
+
+ # set elements
+ dependencys = opm_dependencies.db_dependencys
+ for dependency in dependencys:
+ if dependency.vtType == 'opm_used':
+ childNode = ElementTree.SubElement(node, 'used')
+ self.getDao('opm_used').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_generated_by':
+ childNode = ElementTree.SubElement(node, 'wasGeneratedBy')
+ self.getDao('opm_was_generated_by').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_triggered_by':
+ childNode = ElementTree.SubElement(node, 'wasTriggeredBy')
+ self.getDao('opm_was_triggered_by').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_derived_from':
+ childNode = ElementTree.SubElement(node, 'wasDerivedFrom')
+ self.getDao('opm_was_derived_from').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_controlled_by':
+ childNode = ElementTree.SubElement(node, 'wasControlledBy')
+ self.getDao('opm_was_controlled_by').toXML(dependency, childNode)
+
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'parameter':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('val', None)
+ val = self.convertFromStr(data, 'str')
+ data = node.get('alias', None)
+ alias = self.convertFromStr(data, 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, node=None):
+ if node is None:
+ node = ElementTree.Element('parameter')
+
+ # set attributes
+ node.set('id',self.convertToStr(parameter.db_id, 'long'))
+ node.set('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.set('name',self.convertToStr(parameter.db_name, 'str'))
+ node.set('type',self.convertToStr(parameter.db_type, 'str'))
+ node.set('val',self.convertToStr(parameter.db_val, 'str'))
+ node.set('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBOpmUsedXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'used':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_artifact_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmUsed(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_used, node=None):
+ if node is None:
+ node = ElementTree.Element('used')
+
+ # set elements
+ effect = opm_used.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_used.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_used.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_artifact_id_cause').toXML(cause, childNode)
+ accounts = opm_used.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_used.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBPluginDataXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'plugin_data':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('data', None)
+ data = self.convertFromStr(data, 'str')
+
+ obj = DBPluginData(id=id,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, plugin_data, node=None):
+ if node is None:
+ node = ElementTree.Element('plugin_data')
+
+ # set attributes
+ node.set('id',self.convertToStr(plugin_data.db_id, 'long'))
+ node.set('data',self.convertToStr(plugin_data.db_data, 'str'))
+
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'function':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ parameters = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ parameters.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, node=None):
+ if node is None:
+ node = ElementTree.Element('function')
+
+ # set attributes
+ node.set('id',self.convertToStr(function.db_id, 'long'))
+ node.set('pos',self.convertToStr(function.db_pos, 'long'))
+ node.set('name',self.convertToStr(function.db_name, 'str'))
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(parameter, childNode)
+
+ return node
+
+class DBActionAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'actionAnnotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+ data = node.get('actionId', None)
+ action_id = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+
+ obj = DBActionAnnotation(id=id,
+ key=key,
+ value=value,
+ action_id=action_id,
+ date=date,
+ user=user)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, actionAnnotation, node=None):
+ if node is None:
+ node = ElementTree.Element('actionAnnotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(actionAnnotation.db_id, 'long'))
+ node.set('key',self.convertToStr(actionAnnotation.db_key, 'str'))
+ node.set('value',self.convertToStr(actionAnnotation.db_value, 'str'))
+ node.set('actionId',self.convertToStr(actionAnnotation.db_action_id, 'long'))
+ node.set('date',self.convertToStr(actionAnnotation.db_date, 'datetime'))
+ node.set('user',self.convertToStr(actionAnnotation.db_user, 'str'))
+
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'abstraction':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('internalVersion', None)
+ internal_version = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstraction(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, node=None):
+ if node is None:
+ node = ElementTree.Element('abstraction')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.set('cache',self.convertToStr(abstraction.db_cache, 'int'))
+ node.set('name',self.convertToStr(abstraction.db_name, 'str'))
+ node.set('namespace',self.convertToStr(abstraction.db_namespace, 'str'))
+ node.set('package',self.convertToStr(abstraction.db_package, 'str'))
+ node.set('version',self.convertToStr(abstraction.db_version, 'str'))
+ node.set('internalVersion',self.convertToStr(abstraction.db_internal_version, 'str'))
+
+ # set elements
+ location = abstraction.db_location
+ if location is not None:
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = abstraction.db_functions
+ for function in functions:
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = abstraction.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'workflow':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ connections = []
+ annotations = []
+ plugin_datas = []
+ others = []
+ modules = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ connections.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ plugin_datas.append(_data)
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ others.append(_data)
+ elif child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ modules.append(_data)
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ modules.append(_data)
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ modules.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflow(modules=modules,
+ id=id,
+ name=name,
+ version=version,
+ connections=connections,
+ annotations=annotations,
+ plugin_datas=plugin_datas,
+ others=others,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, node=None):
+ if node is None:
+ node = ElementTree.Element('workflow')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow.db_id, 'long'))
+ node.set('name',self.convertToStr(workflow.db_name, 'str'))
+ node.set('version',self.convertToStr(workflow.db_version, 'str'))
+ node.set('vistrail_id',self.convertToStr(workflow.db_vistrail_id, 'long'))
+
+ # set elements
+ connections = workflow.db_connections
+ for connection in connections:
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(connection, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ plugin_datas = workflow.db_plugin_datas
+ for plugin_data in plugin_datas:
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(plugin_data, childNode)
+ others = workflow.db_others
+ for other in others:
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(other, childNode)
+ modules = workflow.db_modules
+ for module in modules:
+ if module.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(module, childNode)
+ elif module.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(module, childNode)
+ elif module.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(module, childNode)
+
+ return node
+
+class DBOpmArtifactIdCauseXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'cause':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmArtifactIdCause(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_id_cause, node=None):
+ if node is None:
+ node = ElementTree.Element('cause')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact_id_cause.db_id, 'str'))
+
+ return node
+
+class DBOpmArtifactValueXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'value':
+ return None
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ value = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifactValue(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_value, node=None):
+ if node is None:
+ node = ElementTree.Element('value')
+
+ # set elements
+ value = opm_artifact_value.db_value
+ if value is not None:
+ if value.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(value, childNode)
+ elif value.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(value, childNode)
+
+ return node
+
+class DBOpmArtifactIdEffectXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'effect':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmArtifactIdEffect(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_id_effect, node=None):
+ if node is None:
+ node = ElementTree.Element('effect')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact_id_effect.db_id, 'str'))
+
+ return node
+
+class DBOpmGraphXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'opmGraph':
+ return None
+
+ accounts = None
+ processes = None
+ artifacts = None
+ agents = None
+ dependencies = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'accounts':
+ _data = self.getDao('opm_accounts').fromXML(child)
+ accounts = _data
+ elif child_tag == 'processes':
+ _data = self.getDao('opm_processes').fromXML(child)
+ processes = _data
+ elif child_tag == 'artifacts':
+ _data = self.getDao('opm_artifacts').fromXML(child)
+ artifacts = _data
+ elif child_tag == 'agents':
+ _data = self.getDao('opm_agents').fromXML(child)
+ agents = _data
+ elif child_tag == 'causalDependencies':
+ _data = self.getDao('opm_dependencies').fromXML(child)
+ dependencies = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmGraph(accounts=accounts,
+ processes=processes,
+ artifacts=artifacts,
+ agents=agents,
+ dependencies=dependencies)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_graph, node=None):
+ if node is None:
+ node = ElementTree.Element('opmGraph')
+
+ # set elements
+ accounts = opm_graph.db_accounts
+ if accounts is not None:
+ childNode = ElementTree.SubElement(node, 'accounts')
+ self.getDao('opm_accounts').toXML(accounts, childNode)
+ processes = opm_graph.db_processes
+ if processes is not None:
+ childNode = ElementTree.SubElement(node, 'processes')
+ self.getDao('opm_processes').toXML(processes, childNode)
+ artifacts = opm_graph.db_artifacts
+ if artifacts is not None:
+ childNode = ElementTree.SubElement(node, 'artifacts')
+ self.getDao('opm_artifacts').toXML(artifacts, childNode)
+ agents = opm_graph.db_agents
+ if agents is not None:
+ childNode = ElementTree.SubElement(node, 'agents')
+ self.getDao('opm_agents').toXML(agents, childNode)
+ dependencies = opm_graph.db_dependencies
+ if dependencies is not None:
+ childNode = ElementTree.SubElement(node, 'causalDependencies')
+ self.getDao('opm_dependencies').toXML(dependencies, childNode)
+
+ return node
+
+class DBRegistryXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'registry':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('rootDescriptorId', None)
+ root_descriptor_id = self.convertFromStr(data, 'long')
+
+ packages = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'package':
+ _data = self.getDao('package').fromXML(child)
+ packages.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBRegistry(id=id,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ packages=packages)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, registry, node=None):
+ if node is None:
+ node = ElementTree.Element('registry')
+
+ # set attributes
+ node.set('id',self.convertToStr(registry.db_id, 'long'))
+ node.set('version',self.convertToStr(registry.db_version, 'str'))
+ node.set('rootDescriptorId',self.convertToStr(registry.db_root_descriptor_id, 'long'))
+
+ # set elements
+ packages = registry.db_packages
+ for package in packages:
+ childNode = ElementTree.SubElement(node, 'package')
+ self.getDao('package').toXML(package, childNode)
+
+ return node
+
+class DBOpmAccountXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'account':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAccount(id=id,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_account, node=None):
+ if node is None:
+ node = ElementTree.Element('account')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_account.db_id, 'str'))
+
+ # set elements
+ value = opm_account.db_value
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'annotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, node=None):
+ if node is None:
+ node = ElementTree.Element('annotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(annotation.db_id, 'long'))
+ node.set('key',self.convertToStr(annotation.db_key, 'str'))
+ node.set('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'change':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('oldObjId', None)
+ oldObjId = self.convertFromStr(data, 'long')
+ data = node.get('newObjId', None)
+ newObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBChange(data=data,
+ id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, node=None):
+ if node is None:
+ node = ElementTree.Element('change')
+
+ # set attributes
+ node.set('id',self.convertToStr(change.db_id, 'long'))
+ node.set('what',self.convertToStr(change.db_what, 'str'))
+ node.set('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.set('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.set('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # set elements
+ data = change.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBOpmWasDerivedFromXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasDerivedFrom':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_artifact_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_artifact_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasDerivedFrom(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_derived_from, node=None):
+ if node is None:
+ node = ElementTree.Element('wasDerivedFrom')
+
+ # set elements
+ effect = opm_was_derived_from.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_artifact_id_effect').toXML(effect, childNode)
+ role = opm_was_derived_from.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_derived_from.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_artifact_id_cause').toXML(cause, childNode)
+ accounts = opm_was_derived_from.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_derived_from.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBOpmWasControlledByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasControlledBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ starts = []
+ ends = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'agent':
+ _data = self.getDao('opm_agent_id').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ starts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ ends.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasControlledBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ starts=starts,
+ ends=ends)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_controlled_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasControlledBy')
+
+ # set elements
+ effect = opm_was_controlled_by.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_was_controlled_by.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_controlled_by.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'agent')
+ self.getDao('opm_agent_id').toXML(cause, childNode)
+ accounts = opm_was_controlled_by.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ starts = opm_was_controlled_by.db_starts
+ for start in starts:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(start, childNode)
+ ends = opm_was_controlled_by.db_ends
+ for end in ends:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(end, childNode)
+
+ return node
+
+class DBOpmAgentIdXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agent':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmAgentId(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agent_id, node=None):
+ if node is None:
+ node = ElementTree.Element('agent')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_agent_id.db_id, 'str'))
+
+ return node
+
+class DBGroupExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'groupExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('groupName', None)
+ group_name = self.convertFromStr(data, 'str')
+ data = node.get('groupType', None)
+ group_type = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroupExec(item_execs=item_execs,
+ id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('groupExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(group_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(group_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(group_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(group_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(group_exec.db_module_id, 'long'))
+ node.set('groupName',self.convertToStr(group_exec.db_group_name, 'str'))
+ node.set('groupType',self.convertToStr(group_exec.db_group_type, 'str'))
+ node.set('completed',self.convertToStr(group_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(group_exec.db_error, 'str'))
+ node.set('machine_id',self.convertToStr(group_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = group_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ item_execs = group_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBOpmTimeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'time':
+ return None
+
+ # read attributes
+ data = node.get('noLaterThan', None)
+ no_later_than = self.convertFromStr(data, 'datetime')
+ data = node.get('noEarlierThan', None)
+ no_earlier_than = self.convertFromStr(data, 'datetime')
+ data = node.get('clockId', None)
+ clock_id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmTime(no_later_than=no_later_than,
+ no_earlier_than=no_earlier_than,
+ clock_id=clock_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_time, node=None):
+ if node is None:
+ node = ElementTree.Element('time')
+
+ # set attributes
+ node.set('noLaterThan',self.convertToStr(opm_time.db_no_later_than, 'datetime'))
+ node.set('noEarlierThan',self.convertToStr(opm_time.db_no_earlier_than, 'datetime'))
+ node.set('clockId',self.convertToStr(opm_time.db_clock_id, 'str'))
+
+ return node
+
+class DBPackageXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'package':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('identifier', None)
+ identifier = self.convertFromStr(data, 'str')
+ data = node.get('codepath', None)
+ codepath = self.convertFromStr(data, 'str')
+ data = node.get('loadConfiguration', None)
+ load_configuration = self.convertFromStr(data, 'int')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('description', None)
+ description = self.convertFromStr(data, 'str')
+
+ module_descriptors = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleDescriptor':
+ _data = self.getDao('module_descriptor').fromXML(child)
+ module_descriptors.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBPackage(id=id,
+ name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ module_descriptors=module_descriptors)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, package, node=None):
+ if node is None:
+ node = ElementTree.Element('package')
+
+ # set attributes
+ node.set('id',self.convertToStr(package.db_id, 'long'))
+ node.set('name',self.convertToStr(package.db_name, 'str'))
+ node.set('identifier',self.convertToStr(package.db_identifier, 'str'))
+ node.set('codepath',self.convertToStr(package.db_codepath, 'str'))
+ node.set('loadConfiguration',self.convertToStr(package.db_load_configuration, 'int'))
+ node.set('version',self.convertToStr(package.db_version, 'str'))
+ node.set('description',self.convertToStr(package.db_description, 'str'))
+
+ # set elements
+ module_descriptors = package.db_module_descriptors
+ for module_descriptor in module_descriptors:
+ childNode = ElementTree.SubElement(node, 'moduleDescriptor')
+ self.getDao('module_descriptor').toXML(module_descriptor, childNode)
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'workflowExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('ip', None)
+ ip = self.convertFromStr(data, 'str')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('vtVersion', None)
+ vt_version = self.convertFromStr(data, 'str')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('parentId', None)
+ parent_id = self.convertFromStr(data, 'long')
+ data = node.get('parentType', None)
+ parent_type = self.convertFromStr(data, 'str')
+ data = node.get('parentVersion', None)
+ parent_version = self.convertFromStr(data, 'long')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ annotations = []
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflowExec(item_execs=item_execs,
+ id=id,
+ user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('workflowExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.set('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.set('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.set('session',self.convertToStr(workflow_exec.db_session, 'long'))
+ node.set('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.set('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.set('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.set('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.set('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.set('completed',self.convertToStr(workflow_exec.db_completed, 'int'))
+ node.set('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # set elements
+ annotations = workflow_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ item_execs = workflow_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBLoopExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'loopExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('iteration', None)
+ iteration = self.convertFromStr(data, 'int')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLoopExec(item_execs=item_execs,
+ id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ iteration=iteration,
+ completed=completed,
+ error=error)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, loop_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('loopExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(loop_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(loop_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(loop_exec.db_ts_end, 'datetime'))
+ node.set('iteration',self.convertToStr(loop_exec.db_iteration, 'int'))
+ node.set('completed',self.convertToStr(loop_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(loop_exec.db_error, 'str'))
+
+ # set elements
+ item_execs = loop_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'connection':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+
+ ports = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ ports.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, node=None):
+ if node is None:
+ node = ElementTree.Element('connection')
+
+ # set attributes
+ node.set('id',self.convertToStr(connection.db_id, 'long'))
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(port, childNode)
+
+ return node
+
+class DBOpmProcessXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'process':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.getDao('opm_process_value').fromXML(child)
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcess(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process, node=None):
+ if node is None:
+ node = ElementTree.Element('process')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process.db_id, 'str'))
+
+ # set elements
+ value = opm_process.db_value
+ if value is not None:
+ childNode = ElementTree.SubElement(node, 'value')
+ self.getDao('opm_process_value').toXML(value, childNode)
+ accounts = opm_process.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBOpmWasTriggeredByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasTriggeredBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_process_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasTriggeredBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_triggered_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasTriggeredBy')
+
+ # set elements
+ effect = opm_was_triggered_by.db_effect
+ if effect is not None:
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_was_triggered_by.db_role
+ if role is not None:
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_triggered_by.db_cause
+ if cause is not None:
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_process_id_cause').toXML(cause, childNode)
+ accounts = opm_was_triggered_by.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_triggered_by.db_opm_times
+ for opm_time in opm_times:
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBOpmProcessValueXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'value':
+ return None
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ value = _data
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ value = _data
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcessValue(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_value, node=None):
+ if node is None:
+ node = ElementTree.Element('value')
+
+ # set elements
+ value = opm_process_value.db_value
+ if value is not None:
+ if value.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(value, childNode)
+ elif value.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(value, childNode)
+ elif value.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(value, childNode)
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'action':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('prevId', None)
+ prevId = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+
+ annotations = []
+ operations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'add':
+ _data = self.getDao('add').fromXML(child)
+ operations.append(_data)
+ elif child_tag == 'delete':
+ _data = self.getDao('delete').fromXML(child)
+ operations.append(_data)
+ elif child_tag == 'change':
+ _data = self.getDao('change').fromXML(child)
+ operations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAction(operations=operations,
+ id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, node=None):
+ if node is None:
+ node = ElementTree.Element('action')
+
+ # set attributes
+ node.set('id',self.convertToStr(action.db_id, 'long'))
+ node.set('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.set('date',self.convertToStr(action.db_date, 'datetime'))
+ node.set('session',self.convertToStr(action.db_session, 'long'))
+ node.set('user',self.convertToStr(action.db_user, 'str'))
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ childNode = ElementTree.SubElement(node, 'add')
+ self.getDao('add').toXML(operation, childNode)
+ elif operation.vtType == 'delete':
+ childNode = ElementTree.SubElement(node, 'delete')
+ self.getDao('delete').toXML(operation, childNode)
+ elif operation.vtType == 'change':
+ childNode = ElementTree.SubElement(node, 'change')
+ self.getDao('change').toXML(operation, childNode)
+
+ return node
+
+class DBOpmAgentXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agent':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAgent(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agent, node=None):
+ if node is None:
+ node = ElementTree.Element('agent')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_agent.db_id, 'str'))
+
+ # set elements
+ value = opm_agent.db_value
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+ accounts = opm_agent.db_accounts
+ for account in accounts:
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'delete':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, node=None):
+ if node is None:
+ node = ElementTree.Element('delete')
+
+ # set attributes
+ node.set('id',self.convertToStr(delete.db_id, 'long'))
+ node.set('what',self.convertToStr(delete.db_what, 'str'))
+ node.set('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'vistrail':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+ annotations = []
+ actionAnnotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child_tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'actionAnnotation':
+ _data = self.getDao('actionAnnotation').fromXML(child)
+ actionAnnotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ actions=actions,
+ tags=tags,
+ annotations=annotations,
+ actionAnnotations=actionAnnotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, node=None):
+ if node is None:
+ node = ElementTree.Element('vistrail')
+
+ # set attributes
+ node.set('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.set('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.set('name',self.convertToStr(vistrail.db_name, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions:
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = vistrail.db_tags
+ for tag in tags:
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+ annotations = vistrail.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ actionAnnotations = vistrail.db_actionAnnotations
+ for actionAnnotation in actionAnnotations:
+ childNode = ElementTree.SubElement(node, 'actionAnnotation')
+ self.getDao('actionAnnotation').toXML(actionAnnotation, childNode)
+
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'moduleExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ module_name = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+ loop_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ loop_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ annotations=annotations,
+ loop_execs=loop_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(module_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.set('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+ node.set('completed',self.convertToStr(module_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(module_exec.db_error, 'str'))
+ node.set('machine_id',self.convertToStr(module_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ loop_execs = module_exec.db_loop_execs
+ for loop_exec in loop_execs:
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(loop_exec, childNode)
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'opm_process_id_effect' not in self:
+ self['opm_process_id_effect'] = DBOpmProcessIdEffectXMLDAOBase(self)
+ if 'opm_was_generated_by' not in self:
+ self['opm_was_generated_by'] = DBOpmWasGeneratedByXMLDAOBase(self)
+ if 'opm_accounts' not in self:
+ self['opm_accounts'] = DBOpmAccountsXMLDAOBase(self)
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'module_descriptor' not in self:
+ self['module_descriptor'] = DBModuleDescriptorXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'opm_role' not in self:
+ self['opm_role'] = DBOpmRoleXMLDAOBase(self)
+ if 'opm_processes' not in self:
+ self['opm_processes'] = DBOpmProcessesXMLDAOBase(self)
+ if 'opm_account_id' not in self:
+ self['opm_account_id'] = DBOpmAccountIdXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'opm_artifact' not in self:
+ self['opm_artifact'] = DBOpmArtifactXMLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'opm_agents' not in self:
+ self['opm_agents'] = DBOpmAgentsXMLDAOBase(self)
+ if 'opm_process_id_cause' not in self:
+ self['opm_process_id_cause'] = DBOpmProcessIdCauseXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'opm_overlaps' not in self:
+ self['opm_overlaps'] = DBOpmOverlapsXMLDAOBase(self)
+ if 'opm_artifacts' not in self:
+ self['opm_artifacts'] = DBOpmArtifactsXMLDAOBase(self)
+ if 'opm_dependencies' not in self:
+ self['opm_dependencies'] = DBOpmDependenciesXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'opm_used' not in self:
+ self['opm_used'] = DBOpmUsedXMLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'actionAnnotation' not in self:
+ self['actionAnnotation'] = DBActionAnnotationXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'opm_artifact_id_cause' not in self:
+ self['opm_artifact_id_cause'] = DBOpmArtifactIdCauseXMLDAOBase(self)
+ if 'opm_artifact_value' not in self:
+ self['opm_artifact_value'] = DBOpmArtifactValueXMLDAOBase(self)
+ if 'opm_artifact_id_effect' not in self:
+ self['opm_artifact_id_effect'] = DBOpmArtifactIdEffectXMLDAOBase(self)
+ if 'opm_graph' not in self:
+ self['opm_graph'] = DBOpmGraphXMLDAOBase(self)
+ if 'registry' not in self:
+ self['registry'] = DBRegistryXMLDAOBase(self)
+ if 'opm_account' not in self:
+ self['opm_account'] = DBOpmAccountXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'opm_was_derived_from' not in self:
+ self['opm_was_derived_from'] = DBOpmWasDerivedFromXMLDAOBase(self)
+ if 'opm_was_controlled_by' not in self:
+ self['opm_was_controlled_by'] = DBOpmWasControlledByXMLDAOBase(self)
+ if 'opm_agent_id' not in self:
+ self['opm_agent_id'] = DBOpmAgentIdXMLDAOBase(self)
+ if 'group_exec' not in self:
+ self['group_exec'] = DBGroupExecXMLDAOBase(self)
+ if 'opm_time' not in self:
+ self['opm_time'] = DBOpmTimeXMLDAOBase(self)
+ if 'package' not in self:
+ self['package'] = DBPackageXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'loop_exec' not in self:
+ self['loop_exec'] = DBLoopExecXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'opm_process' not in self:
+ self['opm_process'] = DBOpmProcessXMLDAOBase(self)
+ if 'opm_was_triggered_by' not in self:
+ self['opm_was_triggered_by'] = DBOpmWasTriggeredByXMLDAOBase(self)
+ if 'opm_process_value' not in self:
+ self['opm_process_value'] = DBOpmProcessValueXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'opm_agent' not in self:
+ self['opm_agent'] = DBOpmAgentXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v1_0_2/persistence/xml/xml_dao.py b/vistrails/db/versions/v1_0_2/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..c7a78ca
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/persistence/xml/xml_dao.py
@@ -0,0 +1,86 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ try:
+ return int(value)
+ except ValueError:
+ if 'False' == value:
+ return -1
+ else:
+ return 0
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v1_0_2/schemas/sql/vistrails.sql b/vistrails/db/versions/v1_0_2/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..a6e8e43
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/schemas/sql/vistrails.sql
@@ -0,0 +1,390 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+CREATE TABLE `vistrails_version`(`version` char(16)) engine=InnoDB;
+INSERT INTO `vistrails_version`(`version`) VALUES ('1.0.2');
+
+CREATE TABLE thumbnail(
+ id int not null auto_increment primary key,
+ file_name varchar(255),
+ image_bytes mediumblob,
+ last_modified datetime
+) engine=InnoDB;
+
+-- generated automatically by auto_dao.py
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(255),
+ type varchar(255),
+ optional int,
+ sort_key int,
+ sigstring varchar(4095),
+ labels varchar(4095),
+ defaults varchar(4095),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module_descriptor(
+ id int,
+ name varchar(255),
+ package varchar(255),
+ namespace varchar(255),
+ package_version varchar(255),
+ version varchar(255),
+ base_descriptor_id int,
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ signature varchar(4095),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE group_tbl(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime,
+ vistrail_id int
+) engine=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram int,
+ vt_id int,
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val varchar(8191),
+ alias varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE plugin_data(
+ id int,
+ data varchar(8191),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action_annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ action_id int,
+ date datetime,
+ user varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE abstraction(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ internal_version varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE workflow(
+ id int not null auto_increment primary key,
+ entity_id int,
+ entity_type char(16),
+ name varchar(255),
+ version char(16),
+ last_modified datetime,
+ vistrail_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE registry(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ root_descriptor_id int,
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE group_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ group_name varchar(255),
+ group_type varchar(255),
+ completed int,
+ error varchar(1023),
+ machine_id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE package(
+ id int not null auto_increment primary key,
+ name varchar(255),
+ identifier varchar(1023),
+ codepath varchar(1023),
+ load_configuration int,
+ version varchar(255),
+ description varchar(1023),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ session int,
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ completed int,
+ name varchar(255),
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE loop_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ iteration int,
+ completed int,
+ error varchar(1023),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session int,
+ user varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ module_name varchar(255),
+ completed int,
+ error varchar(1023),
+ machine_id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
diff --git a/vistrails/db/versions/v1_0_2/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v1_0_2/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..42c5b42
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,42 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+DROP TABLE IF EXISTS `vistrails_version`;
+
+DROP TABLE IF EXISTS thumbnail;
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS port_spec, module, module_descriptor, tag, port, group_tbl, log_tbl, machine, add_tbl, other, location, parameter, plugin_data, function, action_annotation, abstraction, workflow, registry, annotation, change_tbl, group_exec, package, workflow_exec, loop_exec, connection_tbl, action, delete_tbl, vistrail, module_exec;
diff --git a/vistrails/db/versions/v1_0_2/schemas/xml/log.xsd b/vistrails/db/versions/v1_0_2/schemas/xml/log.xsd
new file mode 100644
index 0000000..2f6a6af
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/schemas/xml/log.xsd
@@ -0,0 +1,146 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="log">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="workflow_exec" ref="workflowExec" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="machine" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="workflowExec">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element name="module_exec" ref="moduleExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="group_exec" ref="groupExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="loop_exec" ref="loopExec" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="ip" type="xs:string"/>
+ <xs:attribute name="session" type="xs:int"/>
+ <xs:attribute name="vtVersion" type="xs:string"/>
+ <xs:attribute name="tsStart" type="xs:dateTime"/>
+ <xs:attribute name="tsEnd" type="xs:dateTime"/>
+ <xs:attribute name="parentId" type="xs:int"/>
+ <xs:attribute name="parentType" type="xs:string"/>
+ <xs:attribute name="parentVersion" type="xs:int"/>
+ <xs:attribute name="completed" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="machine">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="os" type="xs:string"/>
+ <xs:attribute name="architecture" type="xs:string"/>
+ <xs:attribute name="processor" type="xs:string"/>
+ <xs:attribute name="ram" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="moduleExec">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="loop_exec" ref="loopExec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="tsStart" type="xs:dateTime"/>
+ <xs:attribute name="tsEnd" type="xs:dateTime"/>
+ <xs:attribute name="cached" type="xs:int"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="completed" type="xs:int"/>
+ <xs:attribute name="error" type="xs:string"/>
+ <xs:attribute name="machine_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="groupExec">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element name="module_exec" ref="moduleExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="group_exec" ref="groupExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="loop_exec" ref="loopExec" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="tsStart" type="xs:dateTime"/>
+ <xs:attribute name="tsEnd" type="xs:dateTime"/>
+ <xs:attribute name="cached" type="xs:int"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="groupName" type="xs:string"/>
+ <xs:attribute name="groupType" type="xs:string"/>
+ <xs:attribute name="completed" type="xs:int"/>
+ <xs:attribute name="error" type="xs:string"/>
+ <xs:attribute name="machine_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="loopExec">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element name="module_exec" ref="moduleExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="group_exec" ref="groupExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="loop_exec" ref="loopExec" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="tsStart" type="xs:dateTime"/>
+ <xs:attribute name="tsEnd" type="xs:dateTime"/>
+ <xs:attribute name="iteration" type="xs:int"/>
+ <xs:attribute name="completed" type="xs:int"/>
+ <xs:attribute name="error" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v1_0_2/schemas/xml/vistrail.xsd b/vistrails/db/versions/v1_0_2/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..5174ac7
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/schemas/xml/vistrail.xsd
@@ -0,0 +1,287 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="actionAnnotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="actionAnnotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ <xs:attribute name="actionId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="user" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="signature" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="optional" type="xs:int"/>
+ <xs:attribute name="sortKey" type="xs:int"/>
+ <xs:attribute name="sigstring" type="xs:string"/>
+ <xs:attribute name="labels" type="xs:string"/>
+ <xs:attribute name="defaults" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="internalVersion" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="group">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="workflow" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plugin_data">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="workflow">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v1_0_2/schemas/xml/vtlink.xsd b/vistrails/db/versions/v1_0_2/schemas/xml/vtlink.xsd
new file mode 100644
index 0000000..011b59c
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/schemas/xml/vtlink.xsd
@@ -0,0 +1,69 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0" encoding="UTF-8"?>
+
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
+<xs:element name="vtlink">
+<xs:complexType>
+<!-- if the vistrail is in a DB use host, database, port and vtid -->
+<xs:attribute name="host" type="xs:string"></xs:attribute>
+<xs:attribute name="database" type="xs:string"></xs:attribute>
+<xs:attribute name="port" type="xs:int"></xs:attribute>
+<xs:attribute name="vtid" type="xs:int"></xs:attribute>
+<!-- if the vistrail is a file use filename below -->
+<xs:attribute name="filename" type="xs:string"></xs:attribute>
+<!-- this is the workflow version -->
+<xs:attribute name="version" type="xs:int"></xs:attribute>
+<!-- this is the workflow tag -->
+<xs:attribute name="tag" type="xs:string"></xs:attribute>
+<xs:attribute name="url" type="xs:string"></xs:attribute>
+<!-- vtcontent can be a workflow in xml or a .vt file base64 encoded -->
+<xs:attribute name="vtcontent" type="xs:string"></xs:attribute>
+<!-- if execute is true the workflow will be executed -->
+<xs:attribute name="execute" type="xs:boolean"></xs:attribute>
+<!-- if showSpreadsheetOnly is True we will hide the builder -->
+<xs:attribute name="showSpreadsheetOnly" type="xs:boolean"></xs:attribute>
+<!-- if there's database information and a workflow is embedded, it will
+force loading from the db instead of using the emebedded version -->
+<xs:attribute name="forceDB" type="xs:boolean"></xs:attribute>
+<!-- if mashuptrail and mashupVersion are set, VisTrails will execute the
+mashup -->
+<xs:attribute name="mashuptrail" type="xs:string"></xs:attribute>
+<xs:attribute name="mashupVersion" type="xs:int"></xs:attribute>
+</xs:complexType>
+</xs:element>
+
+</xs:schema>
diff --git a/vistrails/db/versions/v1_0_2/schemas/xml/workflow.xsd b/vistrails/db/versions/v1_0_2/schemas/xml/workflow.xsd
new file mode 100644
index 0000000..9f7fbda
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/schemas/xml/workflow.xsd
@@ -0,0 +1,185 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="workflow">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plugin_data">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="internalVersion" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="group">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="workflow" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="signature" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="optional" type="xs:int"/>
+ <xs:attribute name="sortKey" type="xs:int"/>
+ <xs:attribute name="sigstring" type="xs:string"/>
+ <xs:attribute name="labels" type="xs:string"/>
+ <xs:attribute name="defaults" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v1_0_2/specs/all.xml b/vistrails/db/versions/v1_0_2/specs/all.xml
new file mode 100644
index 0000000..6fba3a2
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/specs/all.xml
@@ -0,0 +1,2746 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<objects>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ABSTRACTION +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="internal_version" type="str">
+ <xml name="internalVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ACTION ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long" foreignKey="true" object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="vistrail" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ADD +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ACTION_ANNOTATION +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="actionAnnotation">
+ <layout>
+ <xml nodeType="xs:element"/>
+ <sql table="action_annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="action_id" type="long" foreignKey="true" object="action">
+ <xml name="actionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ANNOTATION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="workflow_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CHANGE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CONNECTION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- DELETE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- FUNCTION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group" parentClass="module">
+ <layout>
+ <xml name="group" nodeType="xs:element"/>
+ <sql table="group_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow" type="object" mapping="one-to-one"
+ expand="false">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOCATION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MACHINE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOOP_EXEC +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="loop_exec">
+ <layout>
+ <xml name="loopExec" nodeType="xs:element"/>
+ <sql table="loop_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <!--<property name="input" type="str">
+ <xml name="input" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>-->
+
+ <property name="iteration" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP_EXEC ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group_exec">
+ <layout>
+ <xml name="groupExec" nodeType="xs:element"/>
+ <sql table="group_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="group_name" type="str">
+ <xml name="groupName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="group_type" type="str">
+ <xml name="groupType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <!--<property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>-->
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_EXEC +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OTHER +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PARAMETER +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PLUGIN DATA +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="plugin_data">
+ <layout>
+ <xml name="plugin_data" nodeType="xs:element"/>
+ <sql table="plugin_data"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="data" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORT ++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="signature" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORTSPEC ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="optional" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="sort_key" type="int">
+ <xml name="sortKey" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="sigstring" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="labels" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="defaults" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="module_descriptor">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_DESCRIPTOR +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_descriptor">
+ <layout>
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ <sql table="module_descriptor"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package_version" type="str">
+ <xml name="packageVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="base_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="baseDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="package" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ <!--
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="registry">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="package">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+ -->
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PACKAGE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="package">
+ <layout>
+ <xml name="package" nodeType="xs:element"/>
+ <sql table="package"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="identifier" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="codepath" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="load_configuration" type="int">
+ <xml name="loadConfiguration" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="description" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property ref="true" object="module_descriptor" type="list"
+ mapping="one-to-many" index="name:namespace:version">
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="registry" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REGISTRY ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="registry">
+ <layout>
+ <xml name="registry" nodeType="xs:element"/>
+ <sql table="registry"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="root_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="rootDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <!-- <xml nodeType="xs:attribute" type="xs:string"/> -->
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="package" type="list"
+ mapping="one-to-many" index="identifier:version">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- TAG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VISTRAIL ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="actionAnnotation" type="list"
+ mapping="one-to-many" index="action_id:key !key:value">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstraction" ref="true" object="abstraction">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group" ref="true" object="group">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="plugin_data" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="group" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW_EXEC +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_GRAPH +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_graph">
+ <layout>
+ <xml name="opmGraph" nodeType="xs:element"/>
+ <!-- <sql table="opm_graph"/> -->
+ </layout>
+
+ <property name="accounts" ref="true" object="opm_accounts"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="processes" ref="true" object="opm_processes"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="artifacts" ref="true" object="opm_artifacts"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="agents" ref="true" object="opm_agents"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="dependencies" ref="true" object="opm_dependencies"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNTS ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_accounts">
+ <layout>
+ <xml name="accounts" nodeType="xs:element"/>
+ <!-- <sql table="accounts"/> -->
+ </layout>
+
+ <property name="account" ref="true" object="opm_account" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="opm_overlaps" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNT +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_account">
+ <layout>
+ <xml name="account" nodeType="xs:element"/>
+ <!-- <sql table="account"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_OVERLAPS ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_overlaps">
+ <layout>
+ <xml name="overlaps" nodeType="xs:element"/>
+ <!-- <sql table="overlaps"/> -->
+ </layout>
+
+ <property ref="true" object="opm_account_id" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACTS +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifacts">
+ <layout>
+ <xml name="artifacts" nodeType="xs:element"/>
+ <!-- <sql table="artifacts"/> -->
+ </layout>
+
+ <property name="artifact" ref="true" object="opm_artifact" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_VALUE ++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_value">
+ <layout>
+ <xml name="value" nodeType="xs:element"/>
+ <!-- <sql table="artifact_value"/> -->
+ </layout>
+
+ <choice name="value" type="object" mapping="one-to-one">
+ <property ref="true" object="portSpec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact">
+ <layout>
+ <xml name="artifact" nodeType="xs:element"/>
+ <!-- <sql table="artifact"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" ref="true" object="opm_artifact_value" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESSES +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_processes">
+ <layout>
+ <xml name="processes" nodeType="xs:element"/>
+ <!-- <sql table="processes"/> -->
+ </layout>
+
+ <property name="process" ref="true" object="opm_process" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_VALUE +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_value">
+ <layout>
+ <xml name="value" nodeType="xs:element"/>
+ <!-- <sql table="process_value"/> -->
+ </layout>
+
+ <choice name="value" type="object" mapping="one-to-one">
+ <property ref="true" object="module_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process">
+ <layout>
+ <xml name="process" nodeType="xs:element"/>
+ <!-- <sql table="process"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" ref="true" object="opm_process_value" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENTS ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agents">
+ <layout>
+ <xml name="agents" nodeType="xs:element"/>
+ <!-- <sql table="agents"/> -->
+ </layout>
+
+ <property name="agent" ref="true" object="opm_agent" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENT +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agent">
+ <layout>
+ <xml name="agent" nodeType="xs:element"/>
+ <!-- <sql table="agent"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type=""/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_DEPENDENCIES ++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_dependencies">
+ <layout>
+ <xml name="causalDependencies" nodeType="xs:element"/>
+ <!-- <sql table="causal_dependencies"/> -->
+ </layout>
+
+ <choice name="dependency" type="list" mapping="one-to-many">
+ <property name="used" ref="true" object="opm_used">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_generated_by" ref="true"
+ object="opm_was_generated_by">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_triggered_by" ref="true"
+ object="opm_was_triggered_by">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_derived_from" ref="true"
+ object="opm_was_derived_from">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_controlled_by" ref="true"
+ object="opm_was_controlled_by">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_TIME ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_time">
+ <layout>
+ <xml name="time" nodeType="xs:element"/>
+ <!-- <sql table="time"/> -->
+ </layout>
+
+ <property name="no_later_than" type="datetime">
+ <xml name="noLaterThan" nodeType="xs:attribute" type="xs:dateTime"/>
+ <!-- <sql type="datetime"/> -->
+ </property>
+
+ <property name="no_earlier_than" type="datetime">
+ <xml name="noEarlierThan" nodeType="xs:attribute" type="xs:dateTime"/>
+ <!-- <sql type="datetime"/> -->
+ </property>
+
+ <property name="clock_id" type="str">
+ <xml name="clockId" nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNT_ID ++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_account_id">
+ <layout>
+ <xml name="account" nodeType="xs:element"/>
+ <!-- <sql table="account_id"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_account">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_ID_CAUSE ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_id_cause">
+ <layout>
+ <xml name="cause" nodeType="xs:element"/>
+ <!-- <sql table="process_id_cause"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_process">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_ID_EFFECT +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_id_effect">
+ <layout>
+ <xml name="effect" nodeType="xs:element"/>
+ <!-- <sql table="process_id_effect"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_process">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_ID_CAUSE +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_id_cause">
+ <layout>
+ <xml name="cause" nodeType="xs:element"/>
+ <!-- <sql table="artifact_id_cause"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_artifact">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_ID_EFFECT ++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_id_effect">
+ <layout>
+ <xml name="effect" nodeType="xs:element"/>
+ <!-- <sql table="artifact_id_effect"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_artifact">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENT_ID ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agent_id">
+ <layout>
+ <xml name="agent" nodeType="xs:element"/>
+ <!-- <sql table="agent_id"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_agent">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ROLE ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_role">
+ <layout>
+ <xml name="role" nodeType="xs:element"/>
+ <!-- <sql table="role"/> -->
+ </layout>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(4095)"/> -->
+ </property>
+ </object>
+
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_USED ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_used">
+ <layout>
+ <xml name="used" nodeType="xs:element"/>
+ <!-- <sql table="used"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_artifact_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_GENERATED_BY ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_generated_by">
+ <layout>
+ <xml name="wasGeneratedBy" nodeType="xs:element"/>
+ <!-- <sql table="was_generated_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_artifact_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_process_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_CONTROLLED_BY +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_controlled_by">
+ <layout>
+ <xml name="wasControlledBy" nodeType="xs:element"/>
+ <!-- <sql table="was_controlled_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_agent_id"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="start" ref="true" object="opm_time" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="end" ref="true" object="opm_time" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_DERIVED_FROM ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_derived_from">
+ <layout>
+ <xml name="wasDerivedFrom" nodeType="xs:element"/>
+ <!-- <sql table="was_derived_from"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_artifact_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_artifact_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_TRIGGERED_BY ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_triggered_by">
+ <layout>
+ <xml name="wasTriggeredBy" nodeType="xs:element"/>
+ <!-- <sql table="was_triggered_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_process_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+</objects>
diff --git a/vistrails/db/versions/v1_0_2/translate/__init__.py b/vistrails/db/versions/v1_0_2/translate/__init__.py
new file mode 100644
index 0000000..0e024b6
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '1.0.2'
diff --git a/vistrails/db/versions/v1_0_2/translate/v1_0_1.py b/vistrails/db/versions/v1_0_2/translate/v1_0_1.py
new file mode 100644
index 0000000..375c11f
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/translate/v1_0_1.py
@@ -0,0 +1,145 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+from vistrails.db.versions.v1_0_2.domain import DBVistrail, DBWorkflow, DBLog, \
+ DBRegistry, DBGroup, DBActionAnnotation, DBAnnotation, DBAction, IdScope
+
+def translateVistrail(_vistrail):
+ tag_annotations = []
+ notes_annotations = []
+ thumb_annotations = []
+ upgrade_annotations = []
+ prune_annotations = []
+
+ def update_type(old_obj, translate_dict):
+ if old_obj.db_type.find('|') >= 0:
+ [identifier, m_and_ns] = old_obj.db_type.split(':', 1)
+ # this second check is fragile but should be ok
+ if m_and_ns.find(':') == -1 or m_and_ns.startswith('http://'):
+ # need to move module name
+ try:
+ [namespace, module] = m_and_ns.rsplit('|', 1)
+ new_type = ':'.join([identifier, module, namespace])
+ return new_type
+ except Exception, e:
+ # just bail for now
+ print e
+ pass
+ return old_obj.db_type
+
+ def update_tags(old_obj, translate_dict):
+ for tag in old_obj.db_tags:
+ tag_annotations.append((tag.db_id, tag.db_name, None))
+ return []
+
+ def update_actions(old_obj, translate_dict):
+ new_actions = []
+ for action in old_obj.db_actions:
+ if action.db_prune == 1:
+ prune_annotations.append((action.db_id, str(True), None))
+ new_actions.append(DBAction.update_version(action, translate_dict))
+ return new_actions
+
+ def update_annotations(old_obj, translate_dict):
+ same_annotations = []
+ for annotation in old_obj.db_annotations:
+ if annotation.db_key == '__notes__':
+ notes_annotations.append((old_obj.db_id, annotation.db_value,
+ annotation.db_id))
+ elif annotation.db_key == '__thumb__':
+ thumb_annotations.append((old_obj.db_id, annotation.db_value,
+ annotation.db_id))
+ elif annotation.db_key == '__upgrade__':
+ upgrade_annotations.append((old_obj.db_id,
+ annotation.db_value,
+ annotation.db_id))
+ else:
+ same_annotations.append(
+ DBAnnotation.update_version(annotation, translate_dict))
+ return same_annotations
+
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+
+ translate_dict = {'DBGroup': {'workflow': update_workflow},
+ 'DBVistrail': {'tags': update_tags,
+ 'actions': update_actions},
+ 'DBAction': {'annotations': update_annotations},
+ 'DBParameter': {'type': update_type},
+ }
+ _vistrail.update_id_scope()
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict)
+
+ id_scope = vistrail.idScope
+ id_scope.setBeginId('annotation', _vistrail.idScope.getNewId('annotation'))
+ key_lists = {'__tag__': tag_annotations,
+ '__notes__': notes_annotations,
+ '__thumb__': thumb_annotations,
+ '__upgrade__': upgrade_annotations,
+ '__prune__': prune_annotations}
+ for key, annotations in key_lists.iteritems():
+ for action_id, value, new_id in annotations:
+ if new_id is None:
+ new_id = id_scope.getNewId(DBActionAnnotation.vtType)
+ annotation = DBActionAnnotation(id=new_id,
+ action_id=action_id,
+ key=key,
+ value=value)
+ annotation.is_new = False
+ annotation.is_dirty = False
+ vistrail.db_add_actionAnnotation(annotation)
+
+ vistrail.db_version = '1.0.2'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBGroup': {'workflow': update_workflow}}
+ workflow = DBWorkflow.update_version(_workflow, translate_dict)
+ workflow.db_version = '1.0.2'
+ return workflow
+
+def translateLog(_log):
+ translate_dict = {}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '1.0.2'
+ return log
+
+def translateRegistry(_registry):
+ translate_dict = {}
+ registry = DBRegistry.update_version(_registry, translate_dict)
+ registry.db_version = '1.0.2'
+ return registry
diff --git a/vistrails/db/versions/v1_0_2/translate/v1_0_3.py b/vistrails/db/versions/v1_0_2/translate/v1_0_3.py
new file mode 100644
index 0000000..d4d7a8c
--- /dev/null
+++ b/vistrails/db/versions/v1_0_2/translate/v1_0_3.py
@@ -0,0 +1,207 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.versions.v1_0_2.domain import DBVistrail, DBAnnotation, \
+ DBWorkflow, DBLog, DBRegistry, \
+ DBPortSpec, DBAdd, DBChange, DBDelete
+from vistrails.core import debug
+from vistrails.core.system import get_elementtree_library
+ElementTree = get_elementtree_library()
+
+import unittest
+
+id_scope = None
+
+def update_portSpec(old_obj, translate_dict):
+ global id_scope
+
+ sigs = []
+ defaults = []
+ labels = []
+ for psi in sorted(old_obj.db_portSpecItems, key=lambda x: x.db_pos):
+ sigs.append((psi.db_package, psi.db_module, psi.db_namespace))
+ defaults.append(psi.db_default)
+ labels.append(psi.db_label)
+ new_obj = DBPortSpec.update_version(old_obj, translate_dict)
+ sigstring = '(' + ','.join('%s:%s%s' %
+ (s[0], s[1], ":%s" % s[2] if s[2] else "")
+ for s in sigs) + ')'
+ new_obj.db_sigstring = sigstring
+ if all(not d for d in defaults):
+ new_obj.db_defaults = None
+ else:
+ new_obj.db_defaults = unicode(defaults)
+ if all(not label for label in labels):
+ new_obj.db_labels = None
+ else:
+ new_obj.db_labels = unicode(labels)
+
+ return new_obj
+
+def update_portSpecs(old_obj, translate_dict):
+ new_port_specs = []
+ for port_spec in old_obj.db_portSpecs:
+ new_port_specs.append(update_portSpec(port_spec, translate_dict))
+ return new_port_specs
+
+def update_portSpec_op(old_obj, translate_dict):
+ return update_portSpec(old_obj.db_data, translate_dict)
+
+def translateVistrail(_vistrail):
+ """ Translate new DBVistrailVariable based vistrail variables to old
+ annotation based type """
+ global id_scope
+
+ def update_workflow(old_obj, trans_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow,
+ trans_dict, DBWorkflow())
+
+ def update_operations(old_obj, trans_dict):
+ new_ops = []
+ for obj in old_obj.db_operations:
+ if obj.vtType == 'delete':
+ new_ops.append(DBDelete.update_version(obj, trans_dict))
+ elif obj.vtType == 'add':
+ if obj.db_what == 'portSpec':
+ trans_dict['DBAdd'] = {'data': update_portSpec_op}
+ new_op = DBAdd.update_version(obj, trans_dict)
+ new_ops.append(new_op)
+ del trans_dict['DBAdd']
+ else:
+ new_op = DBAdd.update_version(obj, trans_dict)
+ new_ops.append(new_op)
+ elif obj.vtType == 'change':
+ if obj.db_what == 'portSpec':
+ trans_dict['DBChange'] = {'data': update_portSpec_op}
+ new_op = DBChange.update_version(obj, trans_dict)
+ new_ops.append(new_op)
+ del trans_dict['DBChange']
+ else:
+ new_op = DBChange.update_version(obj, trans_dict)
+ new_ops.append(new_op)
+ return new_ops
+
+ vistrail = DBVistrail()
+ id_scope = vistrail.idScope
+
+ def update_annotations(old_obj, trans_dict):
+ new_annotations = []
+ for a in old_obj.db_annotations:
+ new_annotations.append(DBAnnotation.update_version(a,
+ translate_dict))
+ id_scope.updateBeginId(DBAnnotation.vtType, a.db_id)
+ vars = {}
+ for var in old_obj.db_vistrailVariables:
+ descriptor = (var.db_package, var.db_module, var.db_namespace)
+ vars[var.db_name] = (var.db_uuid, descriptor, var.db_value)
+ if vars:
+ new_id = id_scope.getNewId(DBAnnotation.vtType)
+ annotation = DBAnnotation(id=new_id, key='__vistrail_vars__',
+ value=str(vars))
+ new_annotations.append(annotation)
+
+ return new_annotations
+
+ translate_dict = {'DBModule': {'portSpecs': update_portSpecs},
+ 'DBModuleDescriptor': {'portSpecs': update_portSpecs},
+ 'DBAction': {'operations': update_operations},
+ 'DBGroup': {'workflow': update_workflow},
+ 'DBVistrail': {'annotations': update_annotations},
+ }
+
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict, vistrail)
+
+ if _vistrail.db_parameter_explorations:
+ debug.warning(("Vistrail contains %s parameter explorations that "
+ "cannot be converted") % len(_vistrail.db_parameter_explorations))
+
+ vistrail.db_version = '1.0.2'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBModule': {'portSpecs': update_portSpecs},
+ 'DBGroup': {'workflow': update_workflow}}
+ workflow = DBWorkflow.update_version(_workflow, translate_dict)
+
+ workflow.db_version = '1.0.2'
+ return workflow
+
+def translateLog(_log):
+ translate_dict = {}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '1.0.2'
+ return log
+
+def translateRegistry(_registry):
+ global id_scope
+ translate_dict = {'DBModuleDescriptor': {'portSpecs': update_portSpecs}}
+ registry = DBRegistry()
+ id_scope = registry.idScope
+ vistrail = DBRegistry.update_version(_registry, translate_dict, registry)
+ registry.db_version = '1.0.2'
+ return registry
+
+class TestTranslate(unittest.TestCase):
+ def testParamexp(self):
+ """test translating parameter explorations from 1.0.3 to 1.0.2"""
+ from vistrails.db.services.io import open_bundle_from_zip_xml
+ from vistrails.core.system import vistrails_root_directory
+ import os
+ (save_bundle, vt_save_dir) = open_bundle_from_zip_xml(DBVistrail.vtType, \
+ os.path.join(vistrails_root_directory(),
+ 'tests/resources/paramexp-1.0.3.vt'))
+ vistrail = translateVistrail(save_bundle.vistrail)
+ # paramexps cannot be downgraded but should produce a warning
+
+ def testVistrailvars(self):
+ """test translating vistrail variables from 1.0.3 to 1.0.2"""
+ from vistrails.db.services.io import open_bundle_from_zip_xml
+ from vistrails.core.system import vistrails_root_directory
+ import os
+ (save_bundle, vt_save_dir) = open_bundle_from_zip_xml(DBVistrail.vtType, \
+ os.path.join(vistrails_root_directory(),
+ 'tests/resources/visvar-1.0.3.vt'))
+ vistrail = translateVistrail(save_bundle.vistrail)
+ visvars = vistrail.db_annotations_key_index['__vistrail_vars__']
+ self.assertTrue(visvars.db_value)
+
+if __name__ == '__main__':
+ from vistrails.gui.application import start_application
+ v = start_application({'interactiveMode': False,
+ 'nologger': True,
+ 'singleInstance': False,
+ 'fixedSpreadsheetCells': True})
+ unittest.main()
diff --git a/vistrails/db/versions/v1_0_3/__init__.py b/vistrails/db/versions/v1_0_3/__init__.py
new file mode 100644
index 0000000..aee1abc
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '1.0.3'
diff --git a/vistrails/db/versions/v1_0_3/domain/__init__.py b/vistrails/db/versions/v1_0_3/domain/__init__.py
new file mode 100644
index 0000000..a8208f6
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/domain/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import *
+from registry import DBRegistry
+from workflow import DBWorkflow
+from vistrail import DBVistrail
+from log import DBLog
+from id_scope import IdScope
diff --git a/vistrails/db/versions/v1_0_3/domain/auto_gen.py b/vistrails/db/versions/v1_0_3/domain/auto_gen.py
new file mode 100644
index 0000000..57be93c
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/domain/auto_gen.py
@@ -0,0 +1,16928 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+import copy
+
+class DBOpmProcessIdEffect(object):
+
+ vtType = 'opm_process_id_effect'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessIdEffect.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessIdEffect(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_process', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_process', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessIdEffect()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBVistrailVariable(object):
+
+ vtType = 'vistrailVariable'
+
+ def __init__(self, name=None, uuid=None, package=None, module=None, namespace=None, value=None):
+ self._db_name = name
+ self._db_uuid = uuid
+ self._db_package = package
+ self._db_module = module
+ self._db_namespace = namespace
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVistrailVariable.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrailVariable(name=self._db_name,
+ uuid=self._db_uuid,
+ package=self._db_package,
+ module=self._db_module,
+ namespace=self._db_namespace,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrailVariable()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'uuid' in class_dict:
+ res = class_dict['uuid'](old_obj, trans_dict)
+ new_obj.db_uuid = res
+ elif hasattr(old_obj, 'db_uuid') and old_obj.db_uuid is not None:
+ new_obj.db_uuid = old_obj.db_uuid
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'module' in class_dict:
+ res = class_dict['module'](old_obj, trans_dict)
+ new_obj.db_module = res
+ elif hasattr(old_obj, 'db_module') and old_obj.db_module is not None:
+ new_obj.db_module = old_obj.db_module
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_uuid(self):
+ return self._db_uuid
+ def __set_db_uuid(self, uuid):
+ self._db_uuid = uuid
+ self.is_dirty = True
+ db_uuid = property(__get_db_uuid, __set_db_uuid)
+ def db_add_uuid(self, uuid):
+ self._db_uuid = uuid
+ def db_change_uuid(self, uuid):
+ self._db_uuid = uuid
+ def db_delete_uuid(self, uuid):
+ self._db_uuid = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_module(self):
+ return self._db_module
+ def __set_db_module(self, module):
+ self._db_module = module
+ self.is_dirty = True
+ db_module = property(__get_db_module, __set_db_module)
+ def db_add_module(self, module):
+ self._db_module = module
+ def db_change_module(self, module):
+ self._db_module = module
+ def db_delete_module(self, module):
+ self._db_module = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_name
+
+class DBProvAgent(object):
+
+ vtType = 'prov_agent'
+
+ def __init__(self, id=None, vt_id=None, prov_type=None, prov_label=None, vt_machine_os=None, vt_machine_architecture=None, vt_machine_processor=None, vt_machine_ram=None):
+ self._db_id = id
+ self._db_vt_id = vt_id
+ self._db_prov_type = prov_type
+ self._db_prov_label = prov_label
+ self._db_vt_machine_os = vt_machine_os
+ self._db_vt_machine_architecture = vt_machine_architecture
+ self._db_vt_machine_processor = vt_machine_processor
+ self._db_vt_machine_ram = vt_machine_ram
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBProvAgent.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBProvAgent(id=self._db_id,
+ vt_id=self._db_vt_id,
+ prov_type=self._db_prov_type,
+ prov_label=self._db_prov_label,
+ vt_machine_os=self._db_vt_machine_os,
+ vt_machine_architecture=self._db_vt_machine_architecture,
+ vt_machine_processor=self._db_vt_machine_processor,
+ vt_machine_ram=self._db_vt_machine_ram)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBProvAgent()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'vt_id' in class_dict:
+ res = class_dict['vt_id'](old_obj, trans_dict)
+ new_obj.db_vt_id = res
+ elif hasattr(old_obj, 'db_vt_id') and old_obj.db_vt_id is not None:
+ new_obj.db_vt_id = old_obj.db_vt_id
+ if 'prov_type' in class_dict:
+ res = class_dict['prov_type'](old_obj, trans_dict)
+ new_obj.db_prov_type = res
+ elif hasattr(old_obj, 'db_prov_type') and old_obj.db_prov_type is not None:
+ new_obj.db_prov_type = old_obj.db_prov_type
+ if 'prov_label' in class_dict:
+ res = class_dict['prov_label'](old_obj, trans_dict)
+ new_obj.db_prov_label = res
+ elif hasattr(old_obj, 'db_prov_label') and old_obj.db_prov_label is not None:
+ new_obj.db_prov_label = old_obj.db_prov_label
+ if 'vt_machine_os' in class_dict:
+ res = class_dict['vt_machine_os'](old_obj, trans_dict)
+ new_obj.db_vt_machine_os = res
+ elif hasattr(old_obj, 'db_vt_machine_os') and old_obj.db_vt_machine_os is not None:
+ new_obj.db_vt_machine_os = old_obj.db_vt_machine_os
+ if 'vt_machine_architecture' in class_dict:
+ res = class_dict['vt_machine_architecture'](old_obj, trans_dict)
+ new_obj.db_vt_machine_architecture = res
+ elif hasattr(old_obj, 'db_vt_machine_architecture') and old_obj.db_vt_machine_architecture is not None:
+ new_obj.db_vt_machine_architecture = old_obj.db_vt_machine_architecture
+ if 'vt_machine_processor' in class_dict:
+ res = class_dict['vt_machine_processor'](old_obj, trans_dict)
+ new_obj.db_vt_machine_processor = res
+ elif hasattr(old_obj, 'db_vt_machine_processor') and old_obj.db_vt_machine_processor is not None:
+ new_obj.db_vt_machine_processor = old_obj.db_vt_machine_processor
+ if 'vt_machine_ram' in class_dict:
+ res = class_dict['vt_machine_ram'](old_obj, trans_dict)
+ new_obj.db_vt_machine_ram = res
+ elif hasattr(old_obj, 'db_vt_machine_ram') and old_obj.db_vt_machine_ram is not None:
+ new_obj.db_vt_machine_ram = old_obj.db_vt_machine_ram
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_vt_id(self):
+ return self._db_vt_id
+ def __set_db_vt_id(self, vt_id):
+ self._db_vt_id = vt_id
+ self.is_dirty = True
+ db_vt_id = property(__get_db_vt_id, __set_db_vt_id)
+ def db_add_vt_id(self, vt_id):
+ self._db_vt_id = vt_id
+ def db_change_vt_id(self, vt_id):
+ self._db_vt_id = vt_id
+ def db_delete_vt_id(self, vt_id):
+ self._db_vt_id = None
+
+ def __get_db_prov_type(self):
+ return self._db_prov_type
+ def __set_db_prov_type(self, prov_type):
+ self._db_prov_type = prov_type
+ self.is_dirty = True
+ db_prov_type = property(__get_db_prov_type, __set_db_prov_type)
+ def db_add_prov_type(self, prov_type):
+ self._db_prov_type = prov_type
+ def db_change_prov_type(self, prov_type):
+ self._db_prov_type = prov_type
+ def db_delete_prov_type(self, prov_type):
+ self._db_prov_type = None
+
+ def __get_db_prov_label(self):
+ return self._db_prov_label
+ def __set_db_prov_label(self, prov_label):
+ self._db_prov_label = prov_label
+ self.is_dirty = True
+ db_prov_label = property(__get_db_prov_label, __set_db_prov_label)
+ def db_add_prov_label(self, prov_label):
+ self._db_prov_label = prov_label
+ def db_change_prov_label(self, prov_label):
+ self._db_prov_label = prov_label
+ def db_delete_prov_label(self, prov_label):
+ self._db_prov_label = None
+
+ def __get_db_vt_machine_os(self):
+ return self._db_vt_machine_os
+ def __set_db_vt_machine_os(self, vt_machine_os):
+ self._db_vt_machine_os = vt_machine_os
+ self.is_dirty = True
+ db_vt_machine_os = property(__get_db_vt_machine_os, __set_db_vt_machine_os)
+ def db_add_vt_machine_os(self, vt_machine_os):
+ self._db_vt_machine_os = vt_machine_os
+ def db_change_vt_machine_os(self, vt_machine_os):
+ self._db_vt_machine_os = vt_machine_os
+ def db_delete_vt_machine_os(self, vt_machine_os):
+ self._db_vt_machine_os = None
+
+ def __get_db_vt_machine_architecture(self):
+ return self._db_vt_machine_architecture
+ def __set_db_vt_machine_architecture(self, vt_machine_architecture):
+ self._db_vt_machine_architecture = vt_machine_architecture
+ self.is_dirty = True
+ db_vt_machine_architecture = property(__get_db_vt_machine_architecture, __set_db_vt_machine_architecture)
+ def db_add_vt_machine_architecture(self, vt_machine_architecture):
+ self._db_vt_machine_architecture = vt_machine_architecture
+ def db_change_vt_machine_architecture(self, vt_machine_architecture):
+ self._db_vt_machine_architecture = vt_machine_architecture
+ def db_delete_vt_machine_architecture(self, vt_machine_architecture):
+ self._db_vt_machine_architecture = None
+
+ def __get_db_vt_machine_processor(self):
+ return self._db_vt_machine_processor
+ def __set_db_vt_machine_processor(self, vt_machine_processor):
+ self._db_vt_machine_processor = vt_machine_processor
+ self.is_dirty = True
+ db_vt_machine_processor = property(__get_db_vt_machine_processor, __set_db_vt_machine_processor)
+ def db_add_vt_machine_processor(self, vt_machine_processor):
+ self._db_vt_machine_processor = vt_machine_processor
+ def db_change_vt_machine_processor(self, vt_machine_processor):
+ self._db_vt_machine_processor = vt_machine_processor
+ def db_delete_vt_machine_processor(self, vt_machine_processor):
+ self._db_vt_machine_processor = None
+
+ def __get_db_vt_machine_ram(self):
+ return self._db_vt_machine_ram
+ def __set_db_vt_machine_ram(self, vt_machine_ram):
+ self._db_vt_machine_ram = vt_machine_ram
+ self.is_dirty = True
+ db_vt_machine_ram = property(__get_db_vt_machine_ram, __set_db_vt_machine_ram)
+ def db_add_vt_machine_ram(self, vt_machine_ram):
+ self._db_vt_machine_ram = vt_machine_ram
+ def db_change_vt_machine_ram(self, vt_machine_ram):
+ self._db_vt_machine_ram = vt_machine_ram
+ def db_delete_vt_machine_ram(self, vt_machine_ram):
+ self._db_vt_machine_ram = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmWasGeneratedBy(object):
+
+ vtType = 'opm_was_generated_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasGeneratedBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasGeneratedBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasGeneratedBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmArtifactIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmArtifactIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmProcessIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmProcessIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBOpmAccounts(object):
+
+ vtType = 'opm_accounts'
+
+ def __init__(self, accounts=None, opm_overlapss=None):
+ self.db_deleted_accounts = []
+ self.db_accounts_id_index = {}
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ for v in self._db_accounts:
+ self.db_accounts_id_index[v.db_id] = v
+ self.db_deleted_opm_overlapss = []
+ if opm_overlapss is None:
+ self._db_opm_overlapss = []
+ else:
+ self._db_opm_overlapss = opm_overlapss
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccounts.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccounts()
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_overlapss is None:
+ cp._db_opm_overlapss = []
+ else:
+ cp._db_opm_overlapss = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_overlapss]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_accounts_id_index = dict((v.db_id, v) for v in cp._db_accounts)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccounts()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccount.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccount.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_overlapss' in class_dict:
+ res = class_dict['opm_overlapss'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_overlaps(obj)
+ elif hasattr(old_obj, 'db_opm_overlapss') and old_obj.db_opm_overlapss is not None:
+ for obj in old_obj.db_opm_overlapss:
+ new_obj.db_add_opm_overlaps(DBOpmOverlaps.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_overlapss') and hasattr(new_obj, 'db_deleted_opm_overlapss'):
+ for obj in old_obj.db_deleted_opm_overlapss:
+ n_obj = DBOpmOverlaps.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_overlapss.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_overlapss:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_overlaps(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_overlapss)
+ if remove:
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_overlapss = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_overlapss:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ self.db_accounts_id_index[account.db_id] = account
+ def db_change_account(self, account):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == account.db_id:
+ self._db_accounts[i] = account
+ found = True
+ break
+ if not found:
+ self._db_accounts.append(account)
+ self.db_accounts_id_index[account.db_id] = account
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == account.db_id:
+ if not self._db_accounts[i].is_new:
+ self.db_deleted_accounts.append(self._db_accounts[i])
+ del self._db_accounts[i]
+ break
+ del self.db_accounts_id_index[account.db_id]
+ def db_get_account(self, key):
+ for i in xrange(len(self._db_accounts)):
+ if self._db_accounts[i].db_id == key:
+ return self._db_accounts[i]
+ return None
+ def db_get_account_by_id(self, key):
+ return self.db_accounts_id_index[key]
+ def db_has_account_with_id(self, key):
+ return key in self.db_accounts_id_index
+
+ def __get_db_opm_overlapss(self):
+ return self._db_opm_overlapss
+ def __set_db_opm_overlapss(self, opm_overlapss):
+ self._db_opm_overlapss = opm_overlapss
+ self.is_dirty = True
+ db_opm_overlapss = property(__get_db_opm_overlapss, __set_db_opm_overlapss)
+ def db_get_opm_overlapss(self):
+ return self._db_opm_overlapss
+ def db_add_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ self._db_opm_overlapss.append(opm_overlaps)
+ def db_change_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ self._db_opm_overlapss.append(opm_overlaps)
+ def db_delete_opm_overlaps(self, opm_overlaps):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_overlaps(self, key):
+ return None
+
+
+
+class DBRefProvAgent(object):
+
+ vtType = 'ref_prov_agent'
+
+ def __init__(self, prov_ref=None):
+ self._db_prov_ref = prov_ref
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBRefProvAgent.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBRefProvAgent(prov_ref=self._db_prov_ref)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prov_ref') and ('prov_agent', self._db_prov_ref) in id_remap:
+ cp._db_prov_ref = id_remap[('prov_agent', self._db_prov_ref)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRefProvAgent()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'prov_ref' in class_dict:
+ res = class_dict['prov_ref'](old_obj, trans_dict)
+ new_obj.db_prov_ref = res
+ elif hasattr(old_obj, 'db_prov_ref') and old_obj.db_prov_ref is not None:
+ new_obj.db_prov_ref = old_obj.db_prov_ref
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_prov_ref(self):
+ return self._db_prov_ref
+ def __set_db_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ self.is_dirty = True
+ db_prov_ref = property(__get_db_prov_ref, __set_db_prov_ref)
+ def db_add_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ def db_change_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ def db_delete_prov_ref(self, prov_ref):
+ self._db_prov_ref = None
+
+
+
+class DBPortSpec(object):
+
+ vtType = 'portSpec'
+
+ def __init__(self, id=None, name=None, type=None, optional=None, sort_key=None, portSpecItems=None, min_conns=None, max_conns=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_type = type
+ self._db_optional = optional
+ self._db_sort_key = sort_key
+ self.db_deleted_portSpecItems = []
+ self.db_portSpecItems_id_index = {}
+ if portSpecItems is None:
+ self._db_portSpecItems = []
+ else:
+ self._db_portSpecItems = portSpecItems
+ for v in self._db_portSpecItems:
+ self.db_portSpecItems_id_index[v.db_id] = v
+ self._db_min_conns = min_conns
+ self._db_max_conns = max_conns
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPortSpec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpec(id=self._db_id,
+ name=self._db_name,
+ type=self._db_type,
+ optional=self._db_optional,
+ sort_key=self._db_sort_key,
+ min_conns=self._db_min_conns,
+ max_conns=self._db_max_conns)
+ if self._db_portSpecItems is None:
+ cp._db_portSpecItems = []
+ else:
+ cp._db_portSpecItems = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecItems]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_portSpecItems_id_index = dict((v.db_id, v) for v in cp._db_portSpecItems)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPortSpec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'optional' in class_dict:
+ res = class_dict['optional'](old_obj, trans_dict)
+ new_obj.db_optional = res
+ elif hasattr(old_obj, 'db_optional') and old_obj.db_optional is not None:
+ new_obj.db_optional = old_obj.db_optional
+ if 'sort_key' in class_dict:
+ res = class_dict['sort_key'](old_obj, trans_dict)
+ new_obj.db_sort_key = res
+ elif hasattr(old_obj, 'db_sort_key') and old_obj.db_sort_key is not None:
+ new_obj.db_sort_key = old_obj.db_sort_key
+ if 'portSpecItems' in class_dict:
+ res = class_dict['portSpecItems'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpecItem(obj)
+ elif hasattr(old_obj, 'db_portSpecItems') and old_obj.db_portSpecItems is not None:
+ for obj in old_obj.db_portSpecItems:
+ new_obj.db_add_portSpecItem(DBPortSpecItem.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecItems') and hasattr(new_obj, 'db_deleted_portSpecItems'):
+ for obj in old_obj.db_deleted_portSpecItems:
+ n_obj = DBPortSpecItem.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecItems.append(n_obj)
+ if 'min_conns' in class_dict:
+ res = class_dict['min_conns'](old_obj, trans_dict)
+ new_obj.db_min_conns = res
+ elif hasattr(old_obj, 'db_min_conns') and old_obj.db_min_conns is not None:
+ new_obj.db_min_conns = old_obj.db_min_conns
+ if 'max_conns' in class_dict:
+ res = class_dict['max_conns'](old_obj, trans_dict)
+ new_obj.db_max_conns = res
+ elif hasattr(old_obj, 'db_max_conns') and old_obj.db_max_conns is not None:
+ new_obj.db_max_conns = old_obj.db_max_conns
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if not for_action:
+ for child in self.db_portSpecItems:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_portSpecItems)
+ if remove:
+ self.db_deleted_portSpecItems = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_portSpecItems:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_optional(self):
+ return self._db_optional
+ def __set_db_optional(self, optional):
+ self._db_optional = optional
+ self.is_dirty = True
+ db_optional = property(__get_db_optional, __set_db_optional)
+ def db_add_optional(self, optional):
+ self._db_optional = optional
+ def db_change_optional(self, optional):
+ self._db_optional = optional
+ def db_delete_optional(self, optional):
+ self._db_optional = None
+
+ def __get_db_sort_key(self):
+ return self._db_sort_key
+ def __set_db_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ self.is_dirty = True
+ db_sort_key = property(__get_db_sort_key, __set_db_sort_key)
+ def db_add_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ def db_change_sort_key(self, sort_key):
+ self._db_sort_key = sort_key
+ def db_delete_sort_key(self, sort_key):
+ self._db_sort_key = None
+
+ def __get_db_portSpecItems(self):
+ return self._db_portSpecItems
+ def __set_db_portSpecItems(self, portSpecItems):
+ self._db_portSpecItems = portSpecItems
+ self.is_dirty = True
+ db_portSpecItems = property(__get_db_portSpecItems, __set_db_portSpecItems)
+ def db_get_portSpecItems(self):
+ return self._db_portSpecItems
+ def db_add_portSpecItem(self, portSpecItem):
+ self.is_dirty = True
+ self._db_portSpecItems.append(portSpecItem)
+ self.db_portSpecItems_id_index[portSpecItem.db_id] = portSpecItem
+ def db_change_portSpecItem(self, portSpecItem):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecItems)):
+ if self._db_portSpecItems[i].db_id == portSpecItem.db_id:
+ self._db_portSpecItems[i] = portSpecItem
+ found = True
+ break
+ if not found:
+ self._db_portSpecItems.append(portSpecItem)
+ self.db_portSpecItems_id_index[portSpecItem.db_id] = portSpecItem
+ def db_delete_portSpecItem(self, portSpecItem):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecItems)):
+ if self._db_portSpecItems[i].db_id == portSpecItem.db_id:
+ if not self._db_portSpecItems[i].is_new:
+ self.db_deleted_portSpecItems.append(self._db_portSpecItems[i])
+ del self._db_portSpecItems[i]
+ break
+ del self.db_portSpecItems_id_index[portSpecItem.db_id]
+ def db_get_portSpecItem(self, key):
+ for i in xrange(len(self._db_portSpecItems)):
+ if self._db_portSpecItems[i].db_id == key:
+ return self._db_portSpecItems[i]
+ return None
+ def db_get_portSpecItem_by_id(self, key):
+ return self.db_portSpecItems_id_index[key]
+ def db_has_portSpecItem_with_id(self, key):
+ return key in self.db_portSpecItems_id_index
+
+ def __get_db_min_conns(self):
+ return self._db_min_conns
+ def __set_db_min_conns(self, min_conns):
+ self._db_min_conns = min_conns
+ self.is_dirty = True
+ db_min_conns = property(__get_db_min_conns, __set_db_min_conns)
+ def db_add_min_conns(self, min_conns):
+ self._db_min_conns = min_conns
+ def db_change_min_conns(self, min_conns):
+ self._db_min_conns = min_conns
+ def db_delete_min_conns(self, min_conns):
+ self._db_min_conns = None
+
+ def __get_db_max_conns(self):
+ return self._db_max_conns
+ def __set_db_max_conns(self, max_conns):
+ self._db_max_conns = max_conns
+ self.is_dirty = True
+ db_max_conns = property(__get_db_max_conns, __set_db_max_conns)
+ def db_add_max_conns(self, max_conns):
+ self._db_max_conns = max_conns
+ def db_change_max_conns(self, max_conns):
+ self._db_max_conns = max_conns
+ def db_delete_max_conns(self, max_conns):
+ self._db_max_conns = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModule(object):
+
+ vtType = 'module'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, location=None, functions=None, annotations=None, portSpecs=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModule.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModule(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModule()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleDescriptor(object):
+
+ vtType = 'module_descriptor'
+
+ def __init__(self, id=None, name=None, package=None, namespace=None, package_version=None, version=None, base_descriptor_id=None, portSpecs=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_package = package
+ self._db_namespace = namespace
+ self._db_package_version = package_version
+ self._db_version = version
+ self._db_base_descriptor_id = base_descriptor_id
+ self.db_deleted_portSpecs = []
+ self.db_portSpecs_id_index = {}
+ self.db_portSpecs_name_index = {}
+ if portSpecs is None:
+ self._db_portSpecs = []
+ else:
+ self._db_portSpecs = portSpecs
+ for v in self._db_portSpecs:
+ self.db_portSpecs_id_index[v.db_id] = v
+ self.db_portSpecs_name_index[(v.db_name,v.db_type)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleDescriptor.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleDescriptor(id=self._db_id,
+ name=self._db_name,
+ package=self._db_package,
+ namespace=self._db_namespace,
+ package_version=self._db_package_version,
+ version=self._db_version,
+ base_descriptor_id=self._db_base_descriptor_id)
+ if self._db_portSpecs is None:
+ cp._db_portSpecs = []
+ else:
+ cp._db_portSpecs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_portSpecs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_base_descriptor_id') and ('module_descriptor', self._db_base_descriptor_id) in id_remap:
+ cp._db_base_descriptor_id = id_remap[('module_descriptor', self._db_base_descriptor_id)]
+
+ # recreate indices and set flags
+ cp.db_portSpecs_id_index = dict((v.db_id, v) for v in cp._db_portSpecs)
+ cp.db_portSpecs_name_index = dict(((v.db_name,v.db_type), v) for v in cp._db_portSpecs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleDescriptor()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package_version' in class_dict:
+ res = class_dict['package_version'](old_obj, trans_dict)
+ new_obj.db_package_version = res
+ elif hasattr(old_obj, 'db_package_version') and old_obj.db_package_version is not None:
+ new_obj.db_package_version = old_obj.db_package_version
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'base_descriptor_id' in class_dict:
+ res = class_dict['base_descriptor_id'](old_obj, trans_dict)
+ new_obj.db_base_descriptor_id = res
+ elif hasattr(old_obj, 'db_base_descriptor_id') and old_obj.db_base_descriptor_id is not None:
+ new_obj.db_base_descriptor_id = old_obj.db_base_descriptor_id
+ if 'portSpecs' in class_dict:
+ res = class_dict['portSpecs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_portSpec(obj)
+ elif hasattr(old_obj, 'db_portSpecs') and old_obj.db_portSpecs is not None:
+ for obj in old_obj.db_portSpecs:
+ new_obj.db_add_portSpec(DBPortSpec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_portSpecs') and hasattr(new_obj, 'db_deleted_portSpecs'):
+ for obj in old_obj.db_deleted_portSpecs:
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_portSpecs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_portSpecs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_portSpec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_portSpecs)
+ if remove:
+ self.db_deleted_portSpecs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_portSpecs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package_version(self):
+ return self._db_package_version
+ def __set_db_package_version(self, package_version):
+ self._db_package_version = package_version
+ self.is_dirty = True
+ db_package_version = property(__get_db_package_version, __set_db_package_version)
+ def db_add_package_version(self, package_version):
+ self._db_package_version = package_version
+ def db_change_package_version(self, package_version):
+ self._db_package_version = package_version
+ def db_delete_package_version(self, package_version):
+ self._db_package_version = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_base_descriptor_id(self):
+ return self._db_base_descriptor_id
+ def __set_db_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ self.is_dirty = True
+ db_base_descriptor_id = property(__get_db_base_descriptor_id, __set_db_base_descriptor_id)
+ def db_add_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ def db_change_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = base_descriptor_id
+ def db_delete_base_descriptor_id(self, base_descriptor_id):
+ self._db_base_descriptor_id = None
+
+ def __get_db_portSpecs(self):
+ return self._db_portSpecs
+ def __set_db_portSpecs(self, portSpecs):
+ self._db_portSpecs = portSpecs
+ self.is_dirty = True
+ db_portSpecs = property(__get_db_portSpecs, __set_db_portSpecs)
+ def db_get_portSpecs(self):
+ return self._db_portSpecs
+ def db_add_portSpec(self, portSpec):
+ self.is_dirty = True
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_change_portSpec(self, portSpec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ self._db_portSpecs[i] = portSpec
+ found = True
+ break
+ if not found:
+ self._db_portSpecs.append(portSpec)
+ self.db_portSpecs_id_index[portSpec.db_id] = portSpec
+ self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)] = portSpec
+ def db_delete_portSpec(self, portSpec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == portSpec.db_id:
+ if not self._db_portSpecs[i].is_new:
+ self.db_deleted_portSpecs.append(self._db_portSpecs[i])
+ del self._db_portSpecs[i]
+ break
+ del self.db_portSpecs_id_index[portSpec.db_id]
+ del self.db_portSpecs_name_index[(portSpec.db_name,portSpec.db_type)]
+ def db_get_portSpec(self, key):
+ for i in xrange(len(self._db_portSpecs)):
+ if self._db_portSpecs[i].db_id == key:
+ return self._db_portSpecs[i]
+ return None
+ def db_get_portSpec_by_id(self, key):
+ return self.db_portSpecs_id_index[key]
+ def db_has_portSpec_with_id(self, key):
+ return key in self.db_portSpecs_id_index
+ def db_get_portSpec_by_name(self, key):
+ return self.db_portSpecs_name_index[key]
+ def db_has_portSpec_with_name(self, key):
+ return key in self.db_portSpecs_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBTag(object):
+
+ vtType = 'tag'
+
+ def __init__(self, id=None, name=None):
+ self._db_id = id
+ self._db_name = name
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBTag.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBTag(id=self._db_id,
+ name=self._db_name)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('action', self._db_id) in id_remap:
+ cp._db_id = id_remap[('action', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBTag()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmRole(object):
+
+ vtType = 'opm_role'
+
+ def __init__(self, value=None):
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmRole.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmRole(value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmRole()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+
+
+class DBProvDocument(object):
+
+ vtType = 'prov_document'
+
+ def __init__(self, prov_entitys=None, prov_activitys=None, prov_agents=None, vt_connections=None, prov_usages=None, prov_generations=None, prov_associations=None):
+ self.db_deleted_prov_entitys = []
+ self.db_prov_entitys_id_index = {}
+ if prov_entitys is None:
+ self._db_prov_entitys = []
+ else:
+ self._db_prov_entitys = prov_entitys
+ for v in self._db_prov_entitys:
+ self.db_prov_entitys_id_index[v.db_id] = v
+ self.db_deleted_prov_activitys = []
+ self.db_prov_activitys_id_index = {}
+ if prov_activitys is None:
+ self._db_prov_activitys = []
+ else:
+ self._db_prov_activitys = prov_activitys
+ for v in self._db_prov_activitys:
+ self.db_prov_activitys_id_index[v.db_id] = v
+ self.db_deleted_prov_agents = []
+ self.db_prov_agents_id_index = {}
+ if prov_agents is None:
+ self._db_prov_agents = []
+ else:
+ self._db_prov_agents = prov_agents
+ for v in self._db_prov_agents:
+ self.db_prov_agents_id_index[v.db_id] = v
+ self.db_deleted_vt_connections = []
+ self.db_vt_connections_id_index = {}
+ if vt_connections is None:
+ self._db_vt_connections = []
+ else:
+ self._db_vt_connections = vt_connections
+ for v in self._db_vt_connections:
+ self.db_vt_connections_id_index[v.db_id] = v
+ self.db_deleted_prov_usages = []
+ if prov_usages is None:
+ self._db_prov_usages = []
+ else:
+ self._db_prov_usages = prov_usages
+ self.db_deleted_prov_generations = []
+ if prov_generations is None:
+ self._db_prov_generations = []
+ else:
+ self._db_prov_generations = prov_generations
+ self.db_deleted_prov_associations = []
+ if prov_associations is None:
+ self._db_prov_associations = []
+ else:
+ self._db_prov_associations = prov_associations
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBProvDocument.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBProvDocument()
+ if self._db_prov_entitys is None:
+ cp._db_prov_entitys = []
+ else:
+ cp._db_prov_entitys = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_prov_entitys]
+ if self._db_prov_activitys is None:
+ cp._db_prov_activitys = []
+ else:
+ cp._db_prov_activitys = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_prov_activitys]
+ if self._db_prov_agents is None:
+ cp._db_prov_agents = []
+ else:
+ cp._db_prov_agents = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_prov_agents]
+ if self._db_vt_connections is None:
+ cp._db_vt_connections = []
+ else:
+ cp._db_vt_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_vt_connections]
+ if self._db_prov_usages is None:
+ cp._db_prov_usages = []
+ else:
+ cp._db_prov_usages = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_prov_usages]
+ if self._db_prov_generations is None:
+ cp._db_prov_generations = []
+ else:
+ cp._db_prov_generations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_prov_generations]
+ if self._db_prov_associations is None:
+ cp._db_prov_associations = []
+ else:
+ cp._db_prov_associations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_prov_associations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_prov_entitys_id_index = dict((v.db_id, v) for v in cp._db_prov_entitys)
+ cp.db_prov_activitys_id_index = dict((v.db_id, v) for v in cp._db_prov_activitys)
+ cp.db_prov_agents_id_index = dict((v.db_id, v) for v in cp._db_prov_agents)
+ cp.db_vt_connections_id_index = dict((v.db_id, v) for v in cp._db_vt_connections)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBProvDocument()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'prov_entitys' in class_dict:
+ res = class_dict['prov_entitys'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_prov_entity(obj)
+ elif hasattr(old_obj, 'db_prov_entitys') and old_obj.db_prov_entitys is not None:
+ for obj in old_obj.db_prov_entitys:
+ new_obj.db_add_prov_entity(DBProvEntity.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_entitys') and hasattr(new_obj, 'db_deleted_prov_entitys'):
+ for obj in old_obj.db_deleted_prov_entitys:
+ n_obj = DBProvEntity.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_entitys.append(n_obj)
+ if 'prov_activitys' in class_dict:
+ res = class_dict['prov_activitys'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_prov_activity(obj)
+ elif hasattr(old_obj, 'db_prov_activitys') and old_obj.db_prov_activitys is not None:
+ for obj in old_obj.db_prov_activitys:
+ new_obj.db_add_prov_activity(DBProvActivity.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_activitys') and hasattr(new_obj, 'db_deleted_prov_activitys'):
+ for obj in old_obj.db_deleted_prov_activitys:
+ n_obj = DBProvActivity.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_activitys.append(n_obj)
+ if 'prov_agents' in class_dict:
+ res = class_dict['prov_agents'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_prov_agent(obj)
+ elif hasattr(old_obj, 'db_prov_agents') and old_obj.db_prov_agents is not None:
+ for obj in old_obj.db_prov_agents:
+ new_obj.db_add_prov_agent(DBProvAgent.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_agents') and hasattr(new_obj, 'db_deleted_prov_agents'):
+ for obj in old_obj.db_deleted_prov_agents:
+ n_obj = DBProvAgent.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_agents.append(n_obj)
+ if 'vt_connections' in class_dict:
+ res = class_dict['vt_connections'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_vt_connection(obj)
+ elif hasattr(old_obj, 'db_vt_connections') and old_obj.db_vt_connections is not None:
+ for obj in old_obj.db_vt_connections:
+ new_obj.db_add_vt_connection(DBVtConnection.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_vt_connections') and hasattr(new_obj, 'db_deleted_vt_connections'):
+ for obj in old_obj.db_deleted_vt_connections:
+ n_obj = DBVtConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_vt_connections.append(n_obj)
+ if 'prov_usages' in class_dict:
+ res = class_dict['prov_usages'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_prov_usage(obj)
+ elif hasattr(old_obj, 'db_prov_usages') and old_obj.db_prov_usages is not None:
+ for obj in old_obj.db_prov_usages:
+ new_obj.db_add_prov_usage(DBProvUsage.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_usages') and hasattr(new_obj, 'db_deleted_prov_usages'):
+ for obj in old_obj.db_deleted_prov_usages:
+ n_obj = DBProvUsage.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_usages.append(n_obj)
+ if 'prov_generations' in class_dict:
+ res = class_dict['prov_generations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_prov_generation(obj)
+ elif hasattr(old_obj, 'db_prov_generations') and old_obj.db_prov_generations is not None:
+ for obj in old_obj.db_prov_generations:
+ new_obj.db_add_prov_generation(DBProvGeneration.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_generations') and hasattr(new_obj, 'db_deleted_prov_generations'):
+ for obj in old_obj.db_deleted_prov_generations:
+ n_obj = DBProvGeneration.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_generations.append(n_obj)
+ if 'prov_associations' in class_dict:
+ res = class_dict['prov_associations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_prov_association(obj)
+ elif hasattr(old_obj, 'db_prov_associations') and old_obj.db_prov_associations is not None:
+ for obj in old_obj.db_prov_associations:
+ new_obj.db_add_prov_association(DBProvAssociation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_associations') and hasattr(new_obj, 'db_deleted_prov_associations'):
+ for obj in old_obj.db_deleted_prov_associations:
+ n_obj = DBProvAssociation.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_associations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_prov_entitys:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_prov_entity(child)
+ to_del = []
+ for child in self.db_prov_activitys:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_prov_activity(child)
+ to_del = []
+ for child in self.db_prov_agents:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_prov_agent(child)
+ to_del = []
+ for child in self.db_vt_connections:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_vt_connection(child)
+ to_del = []
+ for child in self.db_prov_usages:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_prov_usage(child)
+ to_del = []
+ for child in self.db_prov_generations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_prov_generation(child)
+ to_del = []
+ for child in self.db_prov_associations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_prov_association(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_prov_entitys)
+ children.extend(self.db_deleted_prov_activitys)
+ children.extend(self.db_deleted_prov_agents)
+ children.extend(self.db_deleted_vt_connections)
+ children.extend(self.db_deleted_prov_usages)
+ children.extend(self.db_deleted_prov_generations)
+ children.extend(self.db_deleted_prov_associations)
+ if remove:
+ self.db_deleted_prov_entitys = []
+ self.db_deleted_prov_activitys = []
+ self.db_deleted_prov_agents = []
+ self.db_deleted_vt_connections = []
+ self.db_deleted_prov_usages = []
+ self.db_deleted_prov_generations = []
+ self.db_deleted_prov_associations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_prov_entitys:
+ if child.has_changes():
+ return True
+ for child in self._db_prov_activitys:
+ if child.has_changes():
+ return True
+ for child in self._db_prov_agents:
+ if child.has_changes():
+ return True
+ for child in self._db_vt_connections:
+ if child.has_changes():
+ return True
+ for child in self._db_prov_usages:
+ if child.has_changes():
+ return True
+ for child in self._db_prov_generations:
+ if child.has_changes():
+ return True
+ for child in self._db_prov_associations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_prov_entitys(self):
+ return self._db_prov_entitys
+ def __set_db_prov_entitys(self, prov_entitys):
+ self._db_prov_entitys = prov_entitys
+ self.is_dirty = True
+ db_prov_entitys = property(__get_db_prov_entitys, __set_db_prov_entitys)
+ def db_get_prov_entitys(self):
+ return self._db_prov_entitys
+ def db_add_prov_entity(self, prov_entity):
+ self.is_dirty = True
+ self._db_prov_entitys.append(prov_entity)
+ self.db_prov_entitys_id_index[prov_entity.db_id] = prov_entity
+ def db_change_prov_entity(self, prov_entity):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_prov_entitys)):
+ if self._db_prov_entitys[i].db_id == prov_entity.db_id:
+ self._db_prov_entitys[i] = prov_entity
+ found = True
+ break
+ if not found:
+ self._db_prov_entitys.append(prov_entity)
+ self.db_prov_entitys_id_index[prov_entity.db_id] = prov_entity
+ def db_delete_prov_entity(self, prov_entity):
+ self.is_dirty = True
+ for i in xrange(len(self._db_prov_entitys)):
+ if self._db_prov_entitys[i].db_id == prov_entity.db_id:
+ if not self._db_prov_entitys[i].is_new:
+ self.db_deleted_prov_entitys.append(self._db_prov_entitys[i])
+ del self._db_prov_entitys[i]
+ break
+ del self.db_prov_entitys_id_index[prov_entity.db_id]
+ def db_get_prov_entity(self, key):
+ for i in xrange(len(self._db_prov_entitys)):
+ if self._db_prov_entitys[i].db_id == key:
+ return self._db_prov_entitys[i]
+ return None
+ def db_get_prov_entity_by_id(self, key):
+ return self.db_prov_entitys_id_index[key]
+ def db_has_prov_entity_with_id(self, key):
+ return key in self.db_prov_entitys_id_index
+
+ def __get_db_prov_activitys(self):
+ return self._db_prov_activitys
+ def __set_db_prov_activitys(self, prov_activitys):
+ self._db_prov_activitys = prov_activitys
+ self.is_dirty = True
+ db_prov_activitys = property(__get_db_prov_activitys, __set_db_prov_activitys)
+ def db_get_prov_activitys(self):
+ return self._db_prov_activitys
+ def db_add_prov_activity(self, prov_activity):
+ self.is_dirty = True
+ self._db_prov_activitys.append(prov_activity)
+ self.db_prov_activitys_id_index[prov_activity.db_id] = prov_activity
+ def db_change_prov_activity(self, prov_activity):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_prov_activitys)):
+ if self._db_prov_activitys[i].db_id == prov_activity.db_id:
+ self._db_prov_activitys[i] = prov_activity
+ found = True
+ break
+ if not found:
+ self._db_prov_activitys.append(prov_activity)
+ self.db_prov_activitys_id_index[prov_activity.db_id] = prov_activity
+ def db_delete_prov_activity(self, prov_activity):
+ self.is_dirty = True
+ for i in xrange(len(self._db_prov_activitys)):
+ if self._db_prov_activitys[i].db_id == prov_activity.db_id:
+ if not self._db_prov_activitys[i].is_new:
+ self.db_deleted_prov_activitys.append(self._db_prov_activitys[i])
+ del self._db_prov_activitys[i]
+ break
+ del self.db_prov_activitys_id_index[prov_activity.db_id]
+ def db_get_prov_activity(self, key):
+ for i in xrange(len(self._db_prov_activitys)):
+ if self._db_prov_activitys[i].db_id == key:
+ return self._db_prov_activitys[i]
+ return None
+ def db_get_prov_activity_by_id(self, key):
+ return self.db_prov_activitys_id_index[key]
+ def db_has_prov_activity_with_id(self, key):
+ return key in self.db_prov_activitys_id_index
+
+ def __get_db_prov_agents(self):
+ return self._db_prov_agents
+ def __set_db_prov_agents(self, prov_agents):
+ self._db_prov_agents = prov_agents
+ self.is_dirty = True
+ db_prov_agents = property(__get_db_prov_agents, __set_db_prov_agents)
+ def db_get_prov_agents(self):
+ return self._db_prov_agents
+ def db_add_prov_agent(self, prov_agent):
+ self.is_dirty = True
+ self._db_prov_agents.append(prov_agent)
+ self.db_prov_agents_id_index[prov_agent.db_id] = prov_agent
+ def db_change_prov_agent(self, prov_agent):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_prov_agents)):
+ if self._db_prov_agents[i].db_id == prov_agent.db_id:
+ self._db_prov_agents[i] = prov_agent
+ found = True
+ break
+ if not found:
+ self._db_prov_agents.append(prov_agent)
+ self.db_prov_agents_id_index[prov_agent.db_id] = prov_agent
+ def db_delete_prov_agent(self, prov_agent):
+ self.is_dirty = True
+ for i in xrange(len(self._db_prov_agents)):
+ if self._db_prov_agents[i].db_id == prov_agent.db_id:
+ if not self._db_prov_agents[i].is_new:
+ self.db_deleted_prov_agents.append(self._db_prov_agents[i])
+ del self._db_prov_agents[i]
+ break
+ del self.db_prov_agents_id_index[prov_agent.db_id]
+ def db_get_prov_agent(self, key):
+ for i in xrange(len(self._db_prov_agents)):
+ if self._db_prov_agents[i].db_id == key:
+ return self._db_prov_agents[i]
+ return None
+ def db_get_prov_agent_by_id(self, key):
+ return self.db_prov_agents_id_index[key]
+ def db_has_prov_agent_with_id(self, key):
+ return key in self.db_prov_agents_id_index
+
+ def __get_db_vt_connections(self):
+ return self._db_vt_connections
+ def __set_db_vt_connections(self, vt_connections):
+ self._db_vt_connections = vt_connections
+ self.is_dirty = True
+ db_vt_connections = property(__get_db_vt_connections, __set_db_vt_connections)
+ def db_get_vt_connections(self):
+ return self._db_vt_connections
+ def db_add_vt_connection(self, vt_connection):
+ self.is_dirty = True
+ self._db_vt_connections.append(vt_connection)
+ self.db_vt_connections_id_index[vt_connection.db_id] = vt_connection
+ def db_change_vt_connection(self, vt_connection):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_vt_connections)):
+ if self._db_vt_connections[i].db_id == vt_connection.db_id:
+ self._db_vt_connections[i] = vt_connection
+ found = True
+ break
+ if not found:
+ self._db_vt_connections.append(vt_connection)
+ self.db_vt_connections_id_index[vt_connection.db_id] = vt_connection
+ def db_delete_vt_connection(self, vt_connection):
+ self.is_dirty = True
+ for i in xrange(len(self._db_vt_connections)):
+ if self._db_vt_connections[i].db_id == vt_connection.db_id:
+ if not self._db_vt_connections[i].is_new:
+ self.db_deleted_vt_connections.append(self._db_vt_connections[i])
+ del self._db_vt_connections[i]
+ break
+ del self.db_vt_connections_id_index[vt_connection.db_id]
+ def db_get_vt_connection(self, key):
+ for i in xrange(len(self._db_vt_connections)):
+ if self._db_vt_connections[i].db_id == key:
+ return self._db_vt_connections[i]
+ return None
+ def db_get_vt_connection_by_id(self, key):
+ return self.db_vt_connections_id_index[key]
+ def db_has_vt_connection_with_id(self, key):
+ return key in self.db_vt_connections_id_index
+
+ def __get_db_prov_usages(self):
+ return self._db_prov_usages
+ def __set_db_prov_usages(self, prov_usages):
+ self._db_prov_usages = prov_usages
+ self.is_dirty = True
+ db_prov_usages = property(__get_db_prov_usages, __set_db_prov_usages)
+ def db_get_prov_usages(self):
+ return self._db_prov_usages
+ def db_add_prov_usage(self, prov_usage):
+ self.is_dirty = True
+ self._db_prov_usages.append(prov_usage)
+ def db_change_prov_usage(self, prov_usage):
+ self.is_dirty = True
+ self._db_prov_usages.append(prov_usage)
+ def db_delete_prov_usage(self, prov_usage):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_prov_usage(self, key):
+ return None
+
+ def __get_db_prov_generations(self):
+ return self._db_prov_generations
+ def __set_db_prov_generations(self, prov_generations):
+ self._db_prov_generations = prov_generations
+ self.is_dirty = True
+ db_prov_generations = property(__get_db_prov_generations, __set_db_prov_generations)
+ def db_get_prov_generations(self):
+ return self._db_prov_generations
+ def db_add_prov_generation(self, prov_generation):
+ self.is_dirty = True
+ self._db_prov_generations.append(prov_generation)
+ def db_change_prov_generation(self, prov_generation):
+ self.is_dirty = True
+ self._db_prov_generations.append(prov_generation)
+ def db_delete_prov_generation(self, prov_generation):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_prov_generation(self, key):
+ return None
+
+ def __get_db_prov_associations(self):
+ return self._db_prov_associations
+ def __set_db_prov_associations(self, prov_associations):
+ self._db_prov_associations = prov_associations
+ self.is_dirty = True
+ db_prov_associations = property(__get_db_prov_associations, __set_db_prov_associations)
+ def db_get_prov_associations(self):
+ return self._db_prov_associations
+ def db_add_prov_association(self, prov_association):
+ self.is_dirty = True
+ self._db_prov_associations.append(prov_association)
+ def db_change_prov_association(self, prov_association):
+ self.is_dirty = True
+ self._db_prov_associations.append(prov_association)
+ def db_delete_prov_association(self, prov_association):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_prov_association(self, key):
+ return None
+
+
+
+class DBOpmAccount(object):
+
+ vtType = 'opm_account'
+
+ def __init__(self, id=None, value=None):
+ self._db_id = id
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccount.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccount(id=self._db_id,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccount()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmProcesses(object):
+
+ vtType = 'opm_processes'
+
+ def __init__(self, processs=None):
+ self.db_deleted_processs = []
+ self.db_processs_id_index = {}
+ if processs is None:
+ self._db_processs = []
+ else:
+ self._db_processs = processs
+ for v in self._db_processs:
+ self.db_processs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcesses.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcesses()
+ if self._db_processs is None:
+ cp._db_processs = []
+ else:
+ cp._db_processs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_processs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_processs_id_index = dict((v.db_id, v) for v in cp._db_processs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcesses()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'processs' in class_dict:
+ res = class_dict['processs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_process(obj)
+ elif hasattr(old_obj, 'db_processs') and old_obj.db_processs is not None:
+ for obj in old_obj.db_processs:
+ new_obj.db_add_process(DBOpmProcess.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_processs') and hasattr(new_obj, 'db_deleted_processs'):
+ for obj in old_obj.db_deleted_processs:
+ n_obj = DBOpmProcess.update_version(obj, trans_dict)
+ new_obj.db_deleted_processs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_processs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_process(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_processs)
+ if remove:
+ self.db_deleted_processs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_processs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_processs(self):
+ return self._db_processs
+ def __set_db_processs(self, processs):
+ self._db_processs = processs
+ self.is_dirty = True
+ db_processs = property(__get_db_processs, __set_db_processs)
+ def db_get_processs(self):
+ return self._db_processs
+ def db_add_process(self, process):
+ self.is_dirty = True
+ self._db_processs.append(process)
+ self.db_processs_id_index[process.db_id] = process
+ def db_change_process(self, process):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == process.db_id:
+ self._db_processs[i] = process
+ found = True
+ break
+ if not found:
+ self._db_processs.append(process)
+ self.db_processs_id_index[process.db_id] = process
+ def db_delete_process(self, process):
+ self.is_dirty = True
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == process.db_id:
+ if not self._db_processs[i].is_new:
+ self.db_deleted_processs.append(self._db_processs[i])
+ del self._db_processs[i]
+ break
+ del self.db_processs_id_index[process.db_id]
+ def db_get_process(self, key):
+ for i in xrange(len(self._db_processs)):
+ if self._db_processs[i].db_id == key:
+ return self._db_processs[i]
+ return None
+ def db_get_process_by_id(self, key):
+ return self.db_processs_id_index[key]
+ def db_has_process_with_id(self, key):
+ return key in self.db_processs_id_index
+
+
+
+class DBRefProvActivity(object):
+
+ vtType = 'ref_prov_activity'
+
+ def __init__(self, prov_ref=None):
+ self._db_prov_ref = prov_ref
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBRefProvActivity.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBRefProvActivity(prov_ref=self._db_prov_ref)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prov_ref') and ('prov_activity', self._db_prov_ref) in id_remap:
+ cp._db_prov_ref = id_remap[('prov_activity', self._db_prov_ref)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRefProvActivity()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'prov_ref' in class_dict:
+ res = class_dict['prov_ref'](old_obj, trans_dict)
+ new_obj.db_prov_ref = res
+ elif hasattr(old_obj, 'db_prov_ref') and old_obj.db_prov_ref is not None:
+ new_obj.db_prov_ref = old_obj.db_prov_ref
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_prov_ref(self):
+ return self._db_prov_ref
+ def __set_db_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ self.is_dirty = True
+ db_prov_ref = property(__get_db_prov_ref, __set_db_prov_ref)
+ def db_add_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ def db_change_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ def db_delete_prov_ref(self, prov_ref):
+ self._db_prov_ref = None
+
+
+
+class DBOpmAccountId(object):
+
+ vtType = 'opm_account_id'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAccountId.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAccountId(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_account', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_account', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAccountId()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBPort(object):
+
+ vtType = 'port'
+
+ def __init__(self, id=None, type=None, moduleId=None, moduleName=None, name=None, signature=None):
+ self._db_id = id
+ self._db_type = type
+ self._db_moduleId = moduleId
+ self._db_moduleName = moduleName
+ self._db_name = name
+ self._db_signature = signature
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPort.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPort(id=self._db_id,
+ type=self._db_type,
+ moduleId=self._db_moduleId,
+ moduleName=self._db_moduleName,
+ name=self._db_name,
+ signature=self._db_signature)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_moduleId') and ('module', self._db_moduleId) in id_remap:
+ cp._db_moduleId = id_remap[('module', self._db_moduleId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPort()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'moduleId' in class_dict:
+ res = class_dict['moduleId'](old_obj, trans_dict)
+ new_obj.db_moduleId = res
+ elif hasattr(old_obj, 'db_moduleId') and old_obj.db_moduleId is not None:
+ new_obj.db_moduleId = old_obj.db_moduleId
+ if 'moduleName' in class_dict:
+ res = class_dict['moduleName'](old_obj, trans_dict)
+ new_obj.db_moduleName = res
+ elif hasattr(old_obj, 'db_moduleName') and old_obj.db_moduleName is not None:
+ new_obj.db_moduleName = old_obj.db_moduleName
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'signature' in class_dict:
+ res = class_dict['signature'](old_obj, trans_dict)
+ new_obj.db_signature = res
+ elif hasattr(old_obj, 'db_signature') and old_obj.db_signature is not None:
+ new_obj.db_signature = old_obj.db_signature
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_moduleId(self):
+ return self._db_moduleId
+ def __set_db_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ self.is_dirty = True
+ db_moduleId = property(__get_db_moduleId, __set_db_moduleId)
+ def db_add_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_change_moduleId(self, moduleId):
+ self._db_moduleId = moduleId
+ def db_delete_moduleId(self, moduleId):
+ self._db_moduleId = None
+
+ def __get_db_moduleName(self):
+ return self._db_moduleName
+ def __set_db_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ self.is_dirty = True
+ db_moduleName = property(__get_db_moduleName, __set_db_moduleName)
+ def db_add_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_change_moduleName(self, moduleName):
+ self._db_moduleName = moduleName
+ def db_delete_moduleName(self, moduleName):
+ self._db_moduleName = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_signature(self):
+ return self._db_signature
+ def __set_db_signature(self, signature):
+ self._db_signature = signature
+ self.is_dirty = True
+ db_signature = property(__get_db_signature, __set_db_signature)
+ def db_add_signature(self, signature):
+ self._db_signature = signature
+ def db_change_signature(self, signature):
+ self._db_signature = signature
+ def db_delete_signature(self, signature):
+ self._db_signature = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBRefProvPlan(object):
+
+ vtType = 'ref_prov_plan'
+
+ def __init__(self, prov_ref=None):
+ self._db_prov_ref = prov_ref
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBRefProvPlan.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBRefProvPlan(prov_ref=self._db_prov_ref)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prov_ref') and ('prov_entity', self._db_prov_ref) in id_remap:
+ cp._db_prov_ref = id_remap[('prov_entity', self._db_prov_ref)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRefProvPlan()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'prov_ref' in class_dict:
+ res = class_dict['prov_ref'](old_obj, trans_dict)
+ new_obj.db_prov_ref = res
+ elif hasattr(old_obj, 'db_prov_ref') and old_obj.db_prov_ref is not None:
+ new_obj.db_prov_ref = old_obj.db_prov_ref
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_prov_ref(self):
+ return self._db_prov_ref
+ def __set_db_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ self.is_dirty = True
+ db_prov_ref = property(__get_db_prov_ref, __set_db_prov_ref)
+ def db_add_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ def db_change_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ def db_delete_prov_ref(self, prov_ref):
+ self._db_prov_ref = None
+
+
+
+class DBOpmArtifact(object):
+
+ vtType = 'opm_artifact'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self.db_deleted_value = []
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifact.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifact(id=self._db_id)
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifact()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ new_obj.db_add_value(DBOpmArtifactValue.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ n_obj = DBOpmArtifactValue.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_value = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_value = []
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBGroup(object):
+
+ vtType = 'group'
+
+ def __init__(self, id=None, workflow=None, cache=None, name=None, namespace=None, package=None, version=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self.db_deleted_workflow = []
+ self._db_workflow = workflow
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroup.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroup(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version)
+ if self._db_workflow is not None:
+ cp._db_workflow = self._db_workflow.do_copy()
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroup()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'workflow' in class_dict:
+ res = class_dict['workflow'](old_obj, trans_dict)
+ new_obj.db_workflow = res
+ elif hasattr(old_obj, 'db_workflow') and old_obj.db_workflow is not None:
+ obj = old_obj.db_workflow
+ new_obj.db_add_workflow(DBWorkflow.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow') and hasattr(new_obj, 'db_deleted_workflow'):
+ for obj in old_obj.db_deleted_workflow:
+ n_obj = DBWorkflow.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow.append(n_obj)
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow)
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_workflow = []
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_workflow is not None and self._db_workflow.has_changes():
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_workflow(self):
+ return self._db_workflow
+ def __set_db_workflow(self, workflow):
+ self._db_workflow = workflow
+ self.is_dirty = True
+ db_workflow = property(__get_db_workflow, __set_db_workflow)
+ def db_add_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_change_workflow(self, workflow):
+ self._db_workflow = workflow
+ def db_delete_workflow(self, workflow):
+ if not self.is_new:
+ self.db_deleted_workflow.append(self._db_workflow)
+ self._db_workflow = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLog(object):
+
+ vtType = 'log'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, workflow_execs=None, machines=None, vistrail_id=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_workflow_execs = []
+ self.db_workflow_execs_id_index = {}
+ if workflow_execs is None:
+ self._db_workflow_execs = []
+ else:
+ self._db_workflow_execs = workflow_execs
+ for v in self._db_workflow_execs:
+ self.db_workflow_execs_id_index[v.db_id] = v
+ self.db_deleted_machines = []
+ self.db_machines_id_index = {}
+ if machines is None:
+ self._db_machines = []
+ else:
+ self._db_machines = machines
+ for v in self._db_machines:
+ self.db_machines_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLog(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_workflow_execs is None:
+ cp._db_workflow_execs = []
+ else:
+ cp._db_workflow_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_workflow_execs]
+ if self._db_machines is None:
+ cp._db_machines = []
+ else:
+ cp._db_machines = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_machines]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_workflow_execs_id_index = dict((v.db_id, v) for v in cp._db_workflow_execs)
+ cp.db_machines_id_index = dict((v.db_id, v) for v in cp._db_machines)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'workflow_execs' in class_dict:
+ res = class_dict['workflow_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_workflow_exec(obj)
+ elif hasattr(old_obj, 'db_workflow_execs') and old_obj.db_workflow_execs is not None:
+ for obj in old_obj.db_workflow_execs:
+ new_obj.db_add_workflow_exec(DBWorkflowExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_workflow_execs') and hasattr(new_obj, 'db_deleted_workflow_execs'):
+ for obj in old_obj.db_deleted_workflow_execs:
+ n_obj = DBWorkflowExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_workflow_execs.append(n_obj)
+ if 'machines' in class_dict:
+ res = class_dict['machines'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_machine(obj)
+ elif hasattr(old_obj, 'db_machines') and old_obj.db_machines is not None:
+ for obj in old_obj.db_machines:
+ new_obj.db_add_machine(DBMachine.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_machines') and hasattr(new_obj, 'db_deleted_machines'):
+ for obj in old_obj.db_deleted_machines:
+ n_obj = DBMachine.update_version(obj, trans_dict)
+ new_obj.db_deleted_machines.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_workflow_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_workflow_exec(child)
+ to_del = []
+ for child in self.db_machines:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_machine(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_workflow_execs)
+ children.extend(self.db_deleted_machines)
+ if remove:
+ self.db_deleted_workflow_execs = []
+ self.db_deleted_machines = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_workflow_execs:
+ if child.has_changes():
+ return True
+ for child in self._db_machines:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_workflow_execs(self):
+ return self._db_workflow_execs
+ def __set_db_workflow_execs(self, workflow_execs):
+ self._db_workflow_execs = workflow_execs
+ self.is_dirty = True
+ db_workflow_execs = property(__get_db_workflow_execs, __set_db_workflow_execs)
+ def db_get_workflow_execs(self):
+ return self._db_workflow_execs
+ def db_add_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_change_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ self._db_workflow_execs[i] = workflow_exec
+ found = True
+ break
+ if not found:
+ self._db_workflow_execs.append(workflow_exec)
+ self.db_workflow_execs_id_index[workflow_exec.db_id] = workflow_exec
+ def db_delete_workflow_exec(self, workflow_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == workflow_exec.db_id:
+ if not self._db_workflow_execs[i].is_new:
+ self.db_deleted_workflow_execs.append(self._db_workflow_execs[i])
+ del self._db_workflow_execs[i]
+ break
+ del self.db_workflow_execs_id_index[workflow_exec.db_id]
+ def db_get_workflow_exec(self, key):
+ for i in xrange(len(self._db_workflow_execs)):
+ if self._db_workflow_execs[i].db_id == key:
+ return self._db_workflow_execs[i]
+ return None
+ def db_get_workflow_exec_by_id(self, key):
+ return self.db_workflow_execs_id_index[key]
+ def db_has_workflow_exec_with_id(self, key):
+ return key in self.db_workflow_execs_id_index
+
+ def __get_db_machines(self):
+ return self._db_machines
+ def __set_db_machines(self, machines):
+ self._db_machines = machines
+ self.is_dirty = True
+ db_machines = property(__get_db_machines, __set_db_machines)
+ def db_get_machines(self):
+ return self._db_machines
+ def db_add_machine(self, machine):
+ self.is_dirty = True
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_change_machine(self, machine):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ self._db_machines[i] = machine
+ found = True
+ break
+ if not found:
+ self._db_machines.append(machine)
+ self.db_machines_id_index[machine.db_id] = machine
+ def db_delete_machine(self, machine):
+ self.is_dirty = True
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == machine.db_id:
+ if not self._db_machines[i].is_new:
+ self.db_deleted_machines.append(self._db_machines[i])
+ del self._db_machines[i]
+ break
+ del self.db_machines_id_index[machine.db_id]
+ def db_get_machine(self, key):
+ for i in xrange(len(self._db_machines)):
+ if self._db_machines[i].db_id == key:
+ return self._db_machines[i]
+ return None
+ def db_get_machine_by_id(self, key):
+ return self.db_machines_id_index[key]
+ def db_has_machine_with_id(self, key):
+ return key in self.db_machines_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBMashupAlias(object):
+
+ vtType = 'mashup_alias'
+
+ def __init__(self, id=None, name=None, component=None):
+ self._db_id = id
+ self._db_name = name
+ self.db_deleted_component = []
+ self._db_component = component
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMashupAlias.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMashupAlias(id=self._db_id,
+ name=self._db_name)
+ if self._db_component is not None:
+ cp._db_component = self._db_component.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMashupAlias()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'component' in class_dict:
+ res = class_dict['component'](old_obj, trans_dict)
+ new_obj.db_component = res
+ elif hasattr(old_obj, 'db_component') and old_obj.db_component is not None:
+ obj = old_obj.db_component
+ new_obj.db_add_component(DBMashupComponent.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_component') and hasattr(new_obj, 'db_deleted_component'):
+ for obj in old_obj.db_deleted_component:
+ n_obj = DBMashupComponent.update_version(obj, trans_dict)
+ new_obj.db_deleted_component.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_component is not None:
+ children.extend(self._db_component.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_component = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_component)
+ if remove:
+ self.db_deleted_component = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_component is not None and self._db_component.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_component(self):
+ return self._db_component
+ def __set_db_component(self, component):
+ self._db_component = component
+ self.is_dirty = True
+ db_component = property(__get_db_component, __set_db_component)
+ def db_add_component(self, component):
+ self._db_component = component
+ def db_change_component(self, component):
+ self._db_component = component
+ def db_delete_component(self, component):
+ if not self.is_new:
+ self.db_deleted_component.append(self._db_component)
+ self._db_component = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmAgents(object):
+
+ vtType = 'opm_agents'
+
+ def __init__(self, agents=None):
+ self.db_deleted_agents = []
+ self.db_agents_id_index = {}
+ if agents is None:
+ self._db_agents = []
+ else:
+ self._db_agents = agents
+ for v in self._db_agents:
+ self.db_agents_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgents.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgents()
+ if self._db_agents is None:
+ cp._db_agents = []
+ else:
+ cp._db_agents = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_agents]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_agents_id_index = dict((v.db_id, v) for v in cp._db_agents)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgents()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'agents' in class_dict:
+ res = class_dict['agents'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_agent(obj)
+ elif hasattr(old_obj, 'db_agents') and old_obj.db_agents is not None:
+ for obj in old_obj.db_agents:
+ new_obj.db_add_agent(DBOpmAgent.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_agents') and hasattr(new_obj, 'db_deleted_agents'):
+ for obj in old_obj.db_deleted_agents:
+ n_obj = DBOpmAgent.update_version(obj, trans_dict)
+ new_obj.db_deleted_agents.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_agents:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_agent(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_agents)
+ if remove:
+ self.db_deleted_agents = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_agents:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_agents(self):
+ return self._db_agents
+ def __set_db_agents(self, agents):
+ self._db_agents = agents
+ self.is_dirty = True
+ db_agents = property(__get_db_agents, __set_db_agents)
+ def db_get_agents(self):
+ return self._db_agents
+ def db_add_agent(self, agent):
+ self.is_dirty = True
+ self._db_agents.append(agent)
+ self.db_agents_id_index[agent.db_id] = agent
+ def db_change_agent(self, agent):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == agent.db_id:
+ self._db_agents[i] = agent
+ found = True
+ break
+ if not found:
+ self._db_agents.append(agent)
+ self.db_agents_id_index[agent.db_id] = agent
+ def db_delete_agent(self, agent):
+ self.is_dirty = True
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == agent.db_id:
+ if not self._db_agents[i].is_new:
+ self.db_deleted_agents.append(self._db_agents[i])
+ del self._db_agents[i]
+ break
+ del self.db_agents_id_index[agent.db_id]
+ def db_get_agent(self, key):
+ for i in xrange(len(self._db_agents)):
+ if self._db_agents[i].db_id == key:
+ return self._db_agents[i]
+ return None
+ def db_get_agent_by_id(self, key):
+ return self.db_agents_id_index[key]
+ def db_has_agent_with_id(self, key):
+ return key in self.db_agents_id_index
+
+
+
+class DBMashup(object):
+
+ vtType = 'mashup'
+
+ def __init__(self, id=None, name=None, version=None, aliases=None, type=None, vtid=None, layout=None, geometry=None, has_seq=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_version = version
+ self.db_deleted_aliases = []
+ self.db_aliases_id_index = {}
+ if aliases is None:
+ self._db_aliases = []
+ else:
+ self._db_aliases = aliases
+ for v in self._db_aliases:
+ self.db_aliases_id_index[v.db_id] = v
+ self._db_type = type
+ self._db_vtid = vtid
+ self._db_layout = layout
+ self._db_geometry = geometry
+ self._db_has_seq = has_seq
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMashup.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMashup(id=self._db_id,
+ name=self._db_name,
+ version=self._db_version,
+ type=self._db_type,
+ vtid=self._db_vtid,
+ layout=self._db_layout,
+ geometry=self._db_geometry,
+ has_seq=self._db_has_seq)
+ if self._db_aliases is None:
+ cp._db_aliases = []
+ else:
+ cp._db_aliases = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_aliases]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vtid') and ('vistrail', self._db_vtid) in id_remap:
+ cp._db_vtid = id_remap[('vistrail', self._db_vtid)]
+
+ # recreate indices and set flags
+ cp.db_aliases_id_index = dict((v.db_id, v) for v in cp._db_aliases)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMashup()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'aliases' in class_dict:
+ res = class_dict['aliases'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_alias(obj)
+ elif hasattr(old_obj, 'db_aliases') and old_obj.db_aliases is not None:
+ for obj in old_obj.db_aliases:
+ new_obj.db_add_alias(DBMashupAlias.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_aliases') and hasattr(new_obj, 'db_deleted_aliases'):
+ for obj in old_obj.db_deleted_aliases:
+ n_obj = DBMashupAlias.update_version(obj, trans_dict)
+ new_obj.db_deleted_aliases.append(n_obj)
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'vtid' in class_dict:
+ res = class_dict['vtid'](old_obj, trans_dict)
+ new_obj.db_vtid = res
+ elif hasattr(old_obj, 'db_vtid') and old_obj.db_vtid is not None:
+ new_obj.db_vtid = old_obj.db_vtid
+ if 'layout' in class_dict:
+ res = class_dict['layout'](old_obj, trans_dict)
+ new_obj.db_layout = res
+ elif hasattr(old_obj, 'db_layout') and old_obj.db_layout is not None:
+ new_obj.db_layout = old_obj.db_layout
+ if 'geometry' in class_dict:
+ res = class_dict['geometry'](old_obj, trans_dict)
+ new_obj.db_geometry = res
+ elif hasattr(old_obj, 'db_geometry') and old_obj.db_geometry is not None:
+ new_obj.db_geometry = old_obj.db_geometry
+ if 'has_seq' in class_dict:
+ res = class_dict['has_seq'](old_obj, trans_dict)
+ new_obj.db_has_seq = res
+ elif hasattr(old_obj, 'db_has_seq') and old_obj.db_has_seq is not None:
+ new_obj.db_has_seq = old_obj.db_has_seq
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_aliases:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_alias(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_aliases)
+ if remove:
+ self.db_deleted_aliases = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_aliases:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_aliases(self):
+ return self._db_aliases
+ def __set_db_aliases(self, aliases):
+ self._db_aliases = aliases
+ self.is_dirty = True
+ db_aliases = property(__get_db_aliases, __set_db_aliases)
+ def db_get_aliases(self):
+ return self._db_aliases
+ def db_add_alias(self, alias):
+ self.is_dirty = True
+ self._db_aliases.append(alias)
+ self.db_aliases_id_index[alias.db_id] = alias
+ def db_change_alias(self, alias):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_aliases)):
+ if self._db_aliases[i].db_id == alias.db_id:
+ self._db_aliases[i] = alias
+ found = True
+ break
+ if not found:
+ self._db_aliases.append(alias)
+ self.db_aliases_id_index[alias.db_id] = alias
+ def db_delete_alias(self, alias):
+ self.is_dirty = True
+ for i in xrange(len(self._db_aliases)):
+ if self._db_aliases[i].db_id == alias.db_id:
+ if not self._db_aliases[i].is_new:
+ self.db_deleted_aliases.append(self._db_aliases[i])
+ del self._db_aliases[i]
+ break
+ del self.db_aliases_id_index[alias.db_id]
+ def db_get_alias(self, key):
+ for i in xrange(len(self._db_aliases)):
+ if self._db_aliases[i].db_id == key:
+ return self._db_aliases[i]
+ return None
+ def db_get_alias_by_id(self, key):
+ return self.db_aliases_id_index[key]
+ def db_has_alias_with_id(self, key):
+ return key in self.db_aliases_id_index
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_vtid(self):
+ return self._db_vtid
+ def __set_db_vtid(self, vtid):
+ self._db_vtid = vtid
+ self.is_dirty = True
+ db_vtid = property(__get_db_vtid, __set_db_vtid)
+ def db_add_vtid(self, vtid):
+ self._db_vtid = vtid
+ def db_change_vtid(self, vtid):
+ self._db_vtid = vtid
+ def db_delete_vtid(self, vtid):
+ self._db_vtid = None
+
+ def __get_db_layout(self):
+ return self._db_layout
+ def __set_db_layout(self, layout):
+ self._db_layout = layout
+ self.is_dirty = True
+ db_layout = property(__get_db_layout, __set_db_layout)
+ def db_add_layout(self, layout):
+ self._db_layout = layout
+ def db_change_layout(self, layout):
+ self._db_layout = layout
+ def db_delete_layout(self, layout):
+ self._db_layout = None
+
+ def __get_db_geometry(self):
+ return self._db_geometry
+ def __set_db_geometry(self, geometry):
+ self._db_geometry = geometry
+ self.is_dirty = True
+ db_geometry = property(__get_db_geometry, __set_db_geometry)
+ def db_add_geometry(self, geometry):
+ self._db_geometry = geometry
+ def db_change_geometry(self, geometry):
+ self._db_geometry = geometry
+ def db_delete_geometry(self, geometry):
+ self._db_geometry = None
+
+ def __get_db_has_seq(self):
+ return self._db_has_seq
+ def __set_db_has_seq(self, has_seq):
+ self._db_has_seq = has_seq
+ self.is_dirty = True
+ db_has_seq = property(__get_db_has_seq, __set_db_has_seq)
+ def db_add_has_seq(self, has_seq):
+ self._db_has_seq = has_seq
+ def db_change_has_seq(self, has_seq):
+ self._db_has_seq = has_seq
+ def db_delete_has_seq(self, has_seq):
+ self._db_has_seq = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmProcessIdCause(object):
+
+ vtType = 'opm_process_id_cause'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessIdCause.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessIdCause(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_process', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_process', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessIdCause()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBProvGeneration(object):
+
+ vtType = 'prov_generation'
+
+ def __init__(self, prov_entity=None, prov_activity=None, prov_role=None):
+ self.db_deleted_prov_entity = []
+ self._db_prov_entity = prov_entity
+ self.db_deleted_prov_activity = []
+ self._db_prov_activity = prov_activity
+ self._db_prov_role = prov_role
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBProvGeneration.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBProvGeneration(prov_role=self._db_prov_role)
+ if self._db_prov_entity is not None:
+ cp._db_prov_entity = self._db_prov_entity.do_copy(new_ids, id_scope, id_remap)
+ if self._db_prov_activity is not None:
+ cp._db_prov_activity = self._db_prov_activity.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBProvGeneration()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'prov_entity' in class_dict:
+ res = class_dict['prov_entity'](old_obj, trans_dict)
+ new_obj.db_prov_entity = res
+ elif hasattr(old_obj, 'db_prov_entity') and old_obj.db_prov_entity is not None:
+ obj = old_obj.db_prov_entity
+ new_obj.db_add_prov_entity(DBRefProvEntity.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_entity') and hasattr(new_obj, 'db_deleted_prov_entity'):
+ for obj in old_obj.db_deleted_prov_entity:
+ n_obj = DBRefProvEntity.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_entity.append(n_obj)
+ if 'prov_activity' in class_dict:
+ res = class_dict['prov_activity'](old_obj, trans_dict)
+ new_obj.db_prov_activity = res
+ elif hasattr(old_obj, 'db_prov_activity') and old_obj.db_prov_activity is not None:
+ obj = old_obj.db_prov_activity
+ new_obj.db_add_prov_activity(DBRefProvActivity.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_activity') and hasattr(new_obj, 'db_deleted_prov_activity'):
+ for obj in old_obj.db_deleted_prov_activity:
+ n_obj = DBRefProvActivity.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_activity.append(n_obj)
+ if 'prov_role' in class_dict:
+ res = class_dict['prov_role'](old_obj, trans_dict)
+ new_obj.db_prov_role = res
+ elif hasattr(old_obj, 'db_prov_role') and old_obj.db_prov_role is not None:
+ new_obj.db_prov_role = old_obj.db_prov_role
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_prov_entity is not None:
+ children.extend(self._db_prov_entity.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_prov_entity = None
+ if self._db_prov_activity is not None:
+ children.extend(self._db_prov_activity.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_prov_activity = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_prov_entity)
+ children.extend(self.db_deleted_prov_activity)
+ if remove:
+ self.db_deleted_prov_entity = []
+ self.db_deleted_prov_activity = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_prov_entity is not None and self._db_prov_entity.has_changes():
+ return True
+ if self._db_prov_activity is not None and self._db_prov_activity.has_changes():
+ return True
+ return False
+ def __get_db_prov_entity(self):
+ return self._db_prov_entity
+ def __set_db_prov_entity(self, prov_entity):
+ self._db_prov_entity = prov_entity
+ self.is_dirty = True
+ db_prov_entity = property(__get_db_prov_entity, __set_db_prov_entity)
+ def db_add_prov_entity(self, prov_entity):
+ self._db_prov_entity = prov_entity
+ def db_change_prov_entity(self, prov_entity):
+ self._db_prov_entity = prov_entity
+ def db_delete_prov_entity(self, prov_entity):
+ if not self.is_new:
+ self.db_deleted_prov_entity.append(self._db_prov_entity)
+ self._db_prov_entity = None
+
+ def __get_db_prov_activity(self):
+ return self._db_prov_activity
+ def __set_db_prov_activity(self, prov_activity):
+ self._db_prov_activity = prov_activity
+ self.is_dirty = True
+ db_prov_activity = property(__get_db_prov_activity, __set_db_prov_activity)
+ def db_add_prov_activity(self, prov_activity):
+ self._db_prov_activity = prov_activity
+ def db_change_prov_activity(self, prov_activity):
+ self._db_prov_activity = prov_activity
+ def db_delete_prov_activity(self, prov_activity):
+ if not self.is_new:
+ self.db_deleted_prov_activity.append(self._db_prov_activity)
+ self._db_prov_activity = None
+
+ def __get_db_prov_role(self):
+ return self._db_prov_role
+ def __set_db_prov_role(self, prov_role):
+ self._db_prov_role = prov_role
+ self.is_dirty = True
+ db_prov_role = property(__get_db_prov_role, __set_db_prov_role)
+ def db_add_prov_role(self, prov_role):
+ self._db_prov_role = prov_role
+ def db_change_prov_role(self, prov_role):
+ self._db_prov_role = prov_role
+ def db_delete_prov_role(self, prov_role):
+ self._db_prov_role = None
+
+
+
+class DBPortSpecItem(object):
+
+ vtType = 'portSpecItem'
+
+ def __init__(self, id=None, pos=None, module=None, package=None, namespace=None, label=None, default=None, values=None, entry_type=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_module = module
+ self._db_package = package
+ self._db_namespace = namespace
+ self._db_label = label
+ self._db_default = default
+ self._db_values = values
+ self._db_entry_type = entry_type
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPortSpecItem.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPortSpecItem(id=self._db_id,
+ pos=self._db_pos,
+ module=self._db_module,
+ package=self._db_package,
+ namespace=self._db_namespace,
+ label=self._db_label,
+ default=self._db_default,
+ values=self._db_values,
+ entry_type=self._db_entry_type)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPortSpecItem()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'module' in class_dict:
+ res = class_dict['module'](old_obj, trans_dict)
+ new_obj.db_module = res
+ elif hasattr(old_obj, 'db_module') and old_obj.db_module is not None:
+ new_obj.db_module = old_obj.db_module
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'label' in class_dict:
+ res = class_dict['label'](old_obj, trans_dict)
+ new_obj.db_label = res
+ elif hasattr(old_obj, 'db_label') and old_obj.db_label is not None:
+ new_obj.db_label = old_obj.db_label
+ if 'default' in class_dict:
+ res = class_dict['default'](old_obj, trans_dict)
+ new_obj.db_default = res
+ elif hasattr(old_obj, 'db_default') and old_obj.db_default is not None:
+ new_obj.db_default = old_obj.db_default
+ if 'values' in class_dict:
+ res = class_dict['values'](old_obj, trans_dict)
+ new_obj.db_values = res
+ elif hasattr(old_obj, 'db_values') and old_obj.db_values is not None:
+ new_obj.db_values = old_obj.db_values
+ if 'entry_type' in class_dict:
+ res = class_dict['entry_type'](old_obj, trans_dict)
+ new_obj.db_entry_type = res
+ elif hasattr(old_obj, 'db_entry_type') and old_obj.db_entry_type is not None:
+ new_obj.db_entry_type = old_obj.db_entry_type
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_module(self):
+ return self._db_module
+ def __set_db_module(self, module):
+ self._db_module = module
+ self.is_dirty = True
+ db_module = property(__get_db_module, __set_db_module)
+ def db_add_module(self, module):
+ self._db_module = module
+ def db_change_module(self, module):
+ self._db_module = module
+ def db_delete_module(self, module):
+ self._db_module = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_label(self):
+ return self._db_label
+ def __set_db_label(self, label):
+ self._db_label = label
+ self.is_dirty = True
+ db_label = property(__get_db_label, __set_db_label)
+ def db_add_label(self, label):
+ self._db_label = label
+ def db_change_label(self, label):
+ self._db_label = label
+ def db_delete_label(self, label):
+ self._db_label = None
+
+ def __get_db_default(self):
+ return self._db_default
+ def __set_db_default(self, default):
+ self._db_default = default
+ self.is_dirty = True
+ db_default = property(__get_db_default, __set_db_default)
+ def db_add_default(self, default):
+ self._db_default = default
+ def db_change_default(self, default):
+ self._db_default = default
+ def db_delete_default(self, default):
+ self._db_default = None
+
+ def __get_db_values(self):
+ return self._db_values
+ def __set_db_values(self, values):
+ self._db_values = values
+ self.is_dirty = True
+ db_values = property(__get_db_values, __set_db_values)
+ def db_add_values(self, values):
+ self._db_values = values
+ def db_change_values(self, values):
+ self._db_values = values
+ def db_delete_values(self, values):
+ self._db_values = None
+
+ def __get_db_entry_type(self):
+ return self._db_entry_type
+ def __set_db_entry_type(self, entry_type):
+ self._db_entry_type = entry_type
+ self.is_dirty = True
+ db_entry_type = property(__get_db_entry_type, __set_db_entry_type)
+ def db_add_entry_type(self, entry_type):
+ self._db_entry_type = entry_type
+ def db_change_entry_type(self, entry_type):
+ self._db_entry_type = entry_type
+ def db_delete_entry_type(self, entry_type):
+ self._db_entry_type = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBMachine(object):
+
+ vtType = 'machine'
+
+ def __init__(self, id=None, name=None, os=None, architecture=None, processor=None, ram=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_os = os
+ self._db_architecture = architecture
+ self._db_processor = processor
+ self._db_ram = ram
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMachine.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMachine(id=self._db_id,
+ name=self._db_name,
+ os=self._db_os,
+ architecture=self._db_architecture,
+ processor=self._db_processor,
+ ram=self._db_ram)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrailId') and ('vistrail', self._db_vistrailId) in id_remap:
+ cp._db_vistrailId = id_remap[('vistrail', self._db_vistrailId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMachine()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'os' in class_dict:
+ res = class_dict['os'](old_obj, trans_dict)
+ new_obj.db_os = res
+ elif hasattr(old_obj, 'db_os') and old_obj.db_os is not None:
+ new_obj.db_os = old_obj.db_os
+ if 'architecture' in class_dict:
+ res = class_dict['architecture'](old_obj, trans_dict)
+ new_obj.db_architecture = res
+ elif hasattr(old_obj, 'db_architecture') and old_obj.db_architecture is not None:
+ new_obj.db_architecture = old_obj.db_architecture
+ if 'processor' in class_dict:
+ res = class_dict['processor'](old_obj, trans_dict)
+ new_obj.db_processor = res
+ elif hasattr(old_obj, 'db_processor') and old_obj.db_processor is not None:
+ new_obj.db_processor = old_obj.db_processor
+ if 'ram' in class_dict:
+ res = class_dict['ram'](old_obj, trans_dict)
+ new_obj.db_ram = res
+ elif hasattr(old_obj, 'db_ram') and old_obj.db_ram is not None:
+ new_obj.db_ram = old_obj.db_ram
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_os(self):
+ return self._db_os
+ def __set_db_os(self, os):
+ self._db_os = os
+ self.is_dirty = True
+ db_os = property(__get_db_os, __set_db_os)
+ def db_add_os(self, os):
+ self._db_os = os
+ def db_change_os(self, os):
+ self._db_os = os
+ def db_delete_os(self, os):
+ self._db_os = None
+
+ def __get_db_architecture(self):
+ return self._db_architecture
+ def __set_db_architecture(self, architecture):
+ self._db_architecture = architecture
+ self.is_dirty = True
+ db_architecture = property(__get_db_architecture, __set_db_architecture)
+ def db_add_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_change_architecture(self, architecture):
+ self._db_architecture = architecture
+ def db_delete_architecture(self, architecture):
+ self._db_architecture = None
+
+ def __get_db_processor(self):
+ return self._db_processor
+ def __set_db_processor(self, processor):
+ self._db_processor = processor
+ self.is_dirty = True
+ db_processor = property(__get_db_processor, __set_db_processor)
+ def db_add_processor(self, processor):
+ self._db_processor = processor
+ def db_change_processor(self, processor):
+ self._db_processor = processor
+ def db_delete_processor(self, processor):
+ self._db_processor = None
+
+ def __get_db_ram(self):
+ return self._db_ram
+ def __set_db_ram(self, ram):
+ self._db_ram = ram
+ self.is_dirty = True
+ db_ram = property(__get_db_ram, __set_db_ram)
+ def db_add_ram(self, ram):
+ self._db_ram = ram
+ def db_change_ram(self, ram):
+ self._db_ram = ram
+ def db_delete_ram(self, ram):
+ self._db_ram = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAdd(object):
+
+ vtType = 'add'
+
+ def __init__(self, data=None, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAdd.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAdd(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAdd()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOther(object):
+
+ vtType = 'other'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOther.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOther(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOther()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLocation(object):
+
+ vtType = 'location'
+
+ def __init__(self, id=None, x=None, y=None):
+ self._db_id = id
+ self._db_x = x
+ self._db_y = y
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLocation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLocation(id=self._db_id,
+ x=self._db_x,
+ y=self._db_y)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLocation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'x' in class_dict:
+ res = class_dict['x'](old_obj, trans_dict)
+ new_obj.db_x = res
+ elif hasattr(old_obj, 'db_x') and old_obj.db_x is not None:
+ new_obj.db_x = old_obj.db_x
+ if 'y' in class_dict:
+ res = class_dict['y'](old_obj, trans_dict)
+ new_obj.db_y = res
+ elif hasattr(old_obj, 'db_y') and old_obj.db_y is not None:
+ new_obj.db_y = old_obj.db_y
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_x(self):
+ return self._db_x
+ def __set_db_x(self, x):
+ self._db_x = x
+ self.is_dirty = True
+ db_x = property(__get_db_x, __set_db_x)
+ def db_add_x(self, x):
+ self._db_x = x
+ def db_change_x(self, x):
+ self._db_x = x
+ def db_delete_x(self, x):
+ self._db_x = None
+
+ def __get_db_y(self):
+ return self._db_y
+ def __set_db_y(self, y):
+ self._db_y = y
+ self.is_dirty = True
+ db_y = property(__get_db_y, __set_db_y)
+ def db_add_y(self, y):
+ self._db_y = y
+ def db_change_y(self, y):
+ self._db_y = y
+ def db_delete_y(self, y):
+ self._db_y = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmOverlaps(object):
+
+ vtType = 'opm_overlaps'
+
+ def __init__(self, opm_account_ids=None):
+ self.db_deleted_opm_account_ids = []
+ if opm_account_ids is None:
+ self._db_opm_account_ids = []
+ else:
+ self._db_opm_account_ids = opm_account_ids
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmOverlaps.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmOverlaps()
+ if self._db_opm_account_ids is None:
+ cp._db_opm_account_ids = []
+ else:
+ cp._db_opm_account_ids = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_account_ids]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmOverlaps()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'opm_account_ids' in class_dict:
+ res = class_dict['opm_account_ids'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_account_id(obj)
+ elif hasattr(old_obj, 'db_opm_account_ids') and old_obj.db_opm_account_ids is not None:
+ for obj in old_obj.db_opm_account_ids:
+ new_obj.db_add_opm_account_id(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_account_ids') and hasattr(new_obj, 'db_deleted_opm_account_ids'):
+ for obj in old_obj.db_deleted_opm_account_ids:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_account_ids.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_opm_account_ids:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_account_id(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_opm_account_ids)
+ if remove:
+ self.db_deleted_opm_account_ids = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_opm_account_ids:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_opm_account_ids(self):
+ return self._db_opm_account_ids
+ def __set_db_opm_account_ids(self, opm_account_ids):
+ self._db_opm_account_ids = opm_account_ids
+ self.is_dirty = True
+ db_opm_account_ids = property(__get_db_opm_account_ids, __set_db_opm_account_ids)
+ def db_get_opm_account_ids(self):
+ return self._db_opm_account_ids
+ def db_add_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ self._db_opm_account_ids.append(opm_account_id)
+ def db_change_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ self._db_opm_account_ids.append(opm_account_id)
+ def db_delete_opm_account_id(self, opm_account_id):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_account_id(self, key):
+ return None
+
+
+
+class DBPEParameter(object):
+
+ vtType = 'pe_parameter'
+
+ def __init__(self, id=None, pos=None, interpolator=None, value=None, dimension=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_interpolator = interpolator
+ self._db_value = value
+ self._db_dimension = dimension
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPEParameter.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPEParameter(id=self._db_id,
+ pos=self._db_pos,
+ interpolator=self._db_interpolator,
+ value=self._db_value,
+ dimension=self._db_dimension)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPEParameter()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'interpolator' in class_dict:
+ res = class_dict['interpolator'](old_obj, trans_dict)
+ new_obj.db_interpolator = res
+ elif hasattr(old_obj, 'db_interpolator') and old_obj.db_interpolator is not None:
+ new_obj.db_interpolator = old_obj.db_interpolator
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ if 'dimension' in class_dict:
+ res = class_dict['dimension'](old_obj, trans_dict)
+ new_obj.db_dimension = res
+ elif hasattr(old_obj, 'db_dimension') and old_obj.db_dimension is not None:
+ new_obj.db_dimension = old_obj.db_dimension
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_interpolator(self):
+ return self._db_interpolator
+ def __set_db_interpolator(self, interpolator):
+ self._db_interpolator = interpolator
+ self.is_dirty = True
+ db_interpolator = property(__get_db_interpolator, __set_db_interpolator)
+ def db_add_interpolator(self, interpolator):
+ self._db_interpolator = interpolator
+ def db_change_interpolator(self, interpolator):
+ self._db_interpolator = interpolator
+ def db_delete_interpolator(self, interpolator):
+ self._db_interpolator = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def __get_db_dimension(self):
+ return self._db_dimension
+ def __set_db_dimension(self, dimension):
+ self._db_dimension = dimension
+ self.is_dirty = True
+ db_dimension = property(__get_db_dimension, __set_db_dimension)
+ def db_add_dimension(self, dimension):
+ self._db_dimension = dimension
+ def db_change_dimension(self, dimension):
+ self._db_dimension = dimension
+ def db_delete_dimension(self, dimension):
+ self._db_dimension = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmDependencies(object):
+
+ vtType = 'opm_dependencies'
+
+ def __init__(self, dependencys=None):
+ self.db_deleted_dependencys = []
+ if dependencys is None:
+ self._db_dependencys = []
+ else:
+ self._db_dependencys = dependencys
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmDependencies.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmDependencies()
+ if self._db_dependencys is None:
+ cp._db_dependencys = []
+ else:
+ cp._db_dependencys = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_dependencys]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmDependencies()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'dependencys' in class_dict:
+ res = class_dict['dependencys'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_dependency(obj)
+ elif hasattr(old_obj, 'db_dependencys') and old_obj.db_dependencys is not None:
+ for obj in old_obj.db_dependencys:
+ if obj.vtType == 'opm_used':
+ new_obj.db_add_dependency(DBOpmUsed.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_generated_by':
+ new_obj.db_add_dependency(DBOpmWasGeneratedBy.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_triggered_by':
+ new_obj.db_add_dependency(DBOpmWasTriggeredBy.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_derived_from':
+ new_obj.db_add_dependency(DBOpmWasDerivedFrom.update_version(obj, trans_dict))
+ elif obj.vtType == 'opm_was_controlled_by':
+ new_obj.db_add_dependency(DBOpmWasControlledBy.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_dependencys') and hasattr(new_obj, 'db_deleted_dependencys'):
+ for obj in old_obj.db_deleted_dependencys:
+ if obj.vtType == 'opm_used':
+ n_obj = DBOpmUsed.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_generated_by':
+ n_obj = DBOpmWasGeneratedBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_triggered_by':
+ n_obj = DBOpmWasTriggeredBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_derived_from':
+ n_obj = DBOpmWasDerivedFrom.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ elif obj.vtType == 'opm_was_controlled_by':
+ n_obj = DBOpmWasControlledBy.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencys.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_dependencys:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_dependency(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_dependencys)
+ if remove:
+ self.db_deleted_dependencys = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_dependencys:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_dependencys(self):
+ return self._db_dependencys
+ def __set_db_dependencys(self, dependencys):
+ self._db_dependencys = dependencys
+ self.is_dirty = True
+ db_dependencys = property(__get_db_dependencys, __set_db_dependencys)
+ def db_get_dependencys(self):
+ return self._db_dependencys
+ def db_add_dependency(self, dependency):
+ self.is_dirty = True
+ self._db_dependencys.append(dependency)
+ def db_change_dependency(self, dependency):
+ self.is_dirty = True
+ self._db_dependencys.append(dependency)
+ def db_delete_dependency(self, dependency):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_dependency(self, key):
+ return None
+
+
+
+class DBParameter(object):
+
+ vtType = 'parameter'
+
+ def __init__(self, id=None, pos=None, name=None, type=None, val=None, alias=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self._db_type = type
+ self._db_val = val
+ self._db_alias = alias
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBParameter.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameter(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name,
+ type=self._db_type,
+ val=self._db_val,
+ alias=self._db_alias)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBParameter()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'val' in class_dict:
+ res = class_dict['val'](old_obj, trans_dict)
+ new_obj.db_val = res
+ elif hasattr(old_obj, 'db_val') and old_obj.db_val is not None:
+ new_obj.db_val = old_obj.db_val
+ if 'alias' in class_dict:
+ res = class_dict['alias'](old_obj, trans_dict)
+ new_obj.db_alias = res
+ elif hasattr(old_obj, 'db_alias') and old_obj.db_alias is not None:
+ new_obj.db_alias = old_obj.db_alias
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_val(self):
+ return self._db_val
+ def __set_db_val(self, val):
+ self._db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self._db_val = val
+ def db_change_val(self, val):
+ self._db_val = val
+ def db_delete_val(self, val):
+ self._db_val = None
+
+ def __get_db_alias(self):
+ return self._db_alias
+ def __set_db_alias(self, alias):
+ self._db_alias = alias
+ self.is_dirty = True
+ db_alias = property(__get_db_alias, __set_db_alias)
+ def db_add_alias(self, alias):
+ self._db_alias = alias
+ def db_change_alias(self, alias):
+ self._db_alias = alias
+ def db_delete_alias(self, alias):
+ self._db_alias = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmUsed(object):
+
+ vtType = 'opm_used'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmUsed.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmUsed()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmUsed()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmArtifactIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmArtifactIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBPluginData(object):
+
+ vtType = 'plugin_data'
+
+ def __init__(self, id=None, data=None):
+ self._db_id = id
+ self._db_data = data
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPluginData.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPluginData(id=self._db_id,
+ data=self._db_data)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPluginData()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ new_obj.db_data = old_obj.db_data
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ self._db_data = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBFunction(object):
+
+ vtType = 'function'
+
+ def __init__(self, id=None, pos=None, name=None, parameters=None):
+ self._db_id = id
+ self._db_pos = pos
+ self._db_name = name
+ self.db_deleted_parameters = []
+ self.db_parameters_id_index = {}
+ if parameters is None:
+ self._db_parameters = []
+ else:
+ self._db_parameters = parameters
+ for v in self._db_parameters:
+ self.db_parameters_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBFunction(id=self._db_id,
+ pos=self._db_pos,
+ name=self._db_name)
+ if self._db_parameters is None:
+ cp._db_parameters = []
+ else:
+ cp._db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_parameters_id_index = dict((v.db_id, v) for v in cp._db_parameters)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBFunction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'parameters' in class_dict:
+ res = class_dict['parameters'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_parameter(obj)
+ elif hasattr(old_obj, 'db_parameters') and old_obj.db_parameters is not None:
+ for obj in old_obj.db_parameters:
+ new_obj.db_add_parameter(DBParameter.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_parameters') and hasattr(new_obj, 'db_deleted_parameters'):
+ for obj in old_obj.db_deleted_parameters:
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_parameters.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_parameters)
+ if remove:
+ self.db_deleted_parameters = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_parameters(self):
+ return self._db_parameters
+ def __set_db_parameters(self, parameters):
+ self._db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self._db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ self._db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ if not self._db_parameters[i].is_new:
+ self.db_deleted_parameters.append(self._db_parameters[i])
+ del self._db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter.db_id]
+ def db_get_parameter(self, key):
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == key:
+ return self._db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return key in self.db_parameters_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBActionAnnotation(object):
+
+ vtType = 'actionAnnotation'
+
+ def __init__(self, id=None, key=None, value=None, action_id=None, date=None, user=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self._db_action_id = action_id
+ self._db_date = date
+ self._db_user = user
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBActionAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBActionAnnotation(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value,
+ action_id=self._db_action_id,
+ date=self._db_date,
+ user=self._db_user)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_action_id') and ('action', self._db_action_id) in id_remap:
+ cp._db_action_id = id_remap[('action', self._db_action_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBActionAnnotation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ if 'action_id' in class_dict:
+ res = class_dict['action_id'](old_obj, trans_dict)
+ new_obj.db_action_id = res
+ elif hasattr(old_obj, 'db_action_id') and old_obj.db_action_id is not None:
+ new_obj.db_action_id = old_obj.db_action_id
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def __get_db_action_id(self):
+ return self._db_action_id
+ def __set_db_action_id(self, action_id):
+ self._db_action_id = action_id
+ self.is_dirty = True
+ db_action_id = property(__get_db_action_id, __set_db_action_id)
+ def db_add_action_id(self, action_id):
+ self._db_action_id = action_id
+ def db_change_action_id(self, action_id):
+ self._db_action_id = action_id
+ def db_delete_action_id(self, action_id):
+ self._db_action_id = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAbstraction(object):
+
+ vtType = 'abstraction'
+
+ def __init__(self, id=None, cache=None, name=None, namespace=None, package=None, version=None, internal_version=None, location=None, functions=None, annotations=None):
+ self._db_id = id
+ self._db_cache = cache
+ self._db_name = name
+ self._db_namespace = namespace
+ self._db_package = package
+ self._db_version = version
+ self._db_internal_version = internal_version
+ self.db_deleted_location = []
+ self._db_location = location
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAbstraction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAbstraction(id=self._db_id,
+ cache=self._db_cache,
+ name=self._db_name,
+ namespace=self._db_namespace,
+ package=self._db_package,
+ version=self._db_version,
+ internal_version=self._db_internal_version)
+ if self._db_location is not None:
+ cp._db_location = self._db_location.do_copy(new_ids, id_scope, id_remap)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAbstraction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'cache' in class_dict:
+ res = class_dict['cache'](old_obj, trans_dict)
+ new_obj.db_cache = res
+ elif hasattr(old_obj, 'db_cache') and old_obj.db_cache is not None:
+ new_obj.db_cache = old_obj.db_cache
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'namespace' in class_dict:
+ res = class_dict['namespace'](old_obj, trans_dict)
+ new_obj.db_namespace = res
+ elif hasattr(old_obj, 'db_namespace') and old_obj.db_namespace is not None:
+ new_obj.db_namespace = old_obj.db_namespace
+ if 'package' in class_dict:
+ res = class_dict['package'](old_obj, trans_dict)
+ new_obj.db_package = res
+ elif hasattr(old_obj, 'db_package') and old_obj.db_package is not None:
+ new_obj.db_package = old_obj.db_package
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'internal_version' in class_dict:
+ res = class_dict['internal_version'](old_obj, trans_dict)
+ new_obj.db_internal_version = res
+ elif hasattr(old_obj, 'db_internal_version') and old_obj.db_internal_version is not None:
+ new_obj.db_internal_version = old_obj.db_internal_version
+ if 'location' in class_dict:
+ res = class_dict['location'](old_obj, trans_dict)
+ new_obj.db_location = res
+ elif hasattr(old_obj, 'db_location') and old_obj.db_location is not None:
+ obj = old_obj.db_location
+ new_obj.db_add_location(DBLocation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_location') and hasattr(new_obj, 'db_deleted_location'):
+ for obj in old_obj.db_deleted_location:
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_location.append(n_obj)
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_location is not None:
+ children.extend(self._db_location.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_location = None
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_location)
+ children.extend(self.db_deleted_functions)
+ children.extend(self.db_deleted_annotations)
+ if remove:
+ self.db_deleted_location = []
+ self.db_deleted_functions = []
+ self.db_deleted_annotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_location is not None and self._db_location.has_changes():
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_cache(self):
+ return self._db_cache
+ def __set_db_cache(self, cache):
+ self._db_cache = cache
+ self.is_dirty = True
+ db_cache = property(__get_db_cache, __set_db_cache)
+ def db_add_cache(self, cache):
+ self._db_cache = cache
+ def db_change_cache(self, cache):
+ self._db_cache = cache
+ def db_delete_cache(self, cache):
+ self._db_cache = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_namespace(self):
+ return self._db_namespace
+ def __set_db_namespace(self, namespace):
+ self._db_namespace = namespace
+ self.is_dirty = True
+ db_namespace = property(__get_db_namespace, __set_db_namespace)
+ def db_add_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_change_namespace(self, namespace):
+ self._db_namespace = namespace
+ def db_delete_namespace(self, namespace):
+ self._db_namespace = None
+
+ def __get_db_package(self):
+ return self._db_package
+ def __set_db_package(self, package):
+ self._db_package = package
+ self.is_dirty = True
+ db_package = property(__get_db_package, __set_db_package)
+ def db_add_package(self, package):
+ self._db_package = package
+ def db_change_package(self, package):
+ self._db_package = package
+ def db_delete_package(self, package):
+ self._db_package = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_internal_version(self):
+ return self._db_internal_version
+ def __set_db_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ self.is_dirty = True
+ db_internal_version = property(__get_db_internal_version, __set_db_internal_version)
+ def db_add_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_change_internal_version(self, internal_version):
+ self._db_internal_version = internal_version
+ def db_delete_internal_version(self, internal_version):
+ self._db_internal_version = None
+
+ def __get_db_location(self):
+ return self._db_location
+ def __set_db_location(self, location):
+ self._db_location = location
+ self.is_dirty = True
+ db_location = property(__get_db_location, __set_db_location)
+ def db_add_location(self, location):
+ self._db_location = location
+ def db_change_location(self, location):
+ self._db_location = location
+ def db_delete_location(self, location):
+ if not self.is_new:
+ self.db_deleted_location.append(self._db_location)
+ self._db_location = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflow(object):
+
+ vtType = 'workflow'
+
+ def __init__(self, modules=None, id=None, entity_type=None, name=None, version=None, last_modified=None, connections=None, annotations=None, plugin_datas=None, others=None, vistrail_id=None):
+ self.db_deleted_modules = []
+ self.db_modules_id_index = {}
+ if modules is None:
+ self._db_modules = []
+ else:
+ self._db_modules = modules
+ for v in self._db_modules:
+ self.db_modules_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_name = name
+ self._db_version = version
+ self._db_last_modified = last_modified
+ self.db_deleted_connections = []
+ self.db_connections_id_index = {}
+ if connections is None:
+ self._db_connections = []
+ else:
+ self._db_connections = connections
+ for v in self._db_connections:
+ self.db_connections_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_plugin_datas = []
+ self.db_plugin_datas_id_index = {}
+ if plugin_datas is None:
+ self._db_plugin_datas = []
+ else:
+ self._db_plugin_datas = plugin_datas
+ for v in self._db_plugin_datas:
+ self.db_plugin_datas_id_index[v.db_id] = v
+ self.db_deleted_others = []
+ self.db_others_id_index = {}
+ if others is None:
+ self._db_others = []
+ else:
+ self._db_others = others
+ for v in self._db_others:
+ self.db_others_id_index[v.db_id] = v
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflow(id=self._db_id,
+ entity_type=self._db_entity_type,
+ name=self._db_name,
+ version=self._db_version,
+ last_modified=self._db_last_modified,
+ vistrail_id=self._db_vistrail_id)
+ if self._db_modules is None:
+ cp._db_modules = []
+ else:
+ cp._db_modules = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_modules]
+ if self._db_connections is None:
+ cp._db_connections = []
+ else:
+ cp._db_connections = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_connections]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_plugin_datas is None:
+ cp._db_plugin_datas = []
+ else:
+ cp._db_plugin_datas = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_plugin_datas]
+ if self._db_others is None:
+ cp._db_others = []
+ else:
+ cp._db_others = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_others]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_vistrail_id') and ('vistrail', self._db_vistrail_id) in id_remap:
+ cp._db_vistrail_id = id_remap[('vistrail', self._db_vistrail_id)]
+
+ # recreate indices and set flags
+ cp.db_modules_id_index = dict((v.db_id, v) for v in cp._db_modules)
+ cp.db_connections_id_index = dict((v.db_id, v) for v in cp._db_connections)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_plugin_datas_id_index = dict((v.db_id, v) for v in cp._db_plugin_datas)
+ cp.db_others_id_index = dict((v.db_id, v) for v in cp._db_others)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'modules' in class_dict:
+ res = class_dict['modules'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module(obj)
+ elif hasattr(old_obj, 'db_modules') and old_obj.db_modules is not None:
+ for obj in old_obj.db_modules:
+ if obj.vtType == 'module':
+ new_obj.db_add_module(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_module(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_module(DBGroup.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_modules') and hasattr(new_obj, 'db_deleted_modules'):
+ for obj in old_obj.db_deleted_modules:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_modules.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'connections' in class_dict:
+ res = class_dict['connections'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_connection(obj)
+ elif hasattr(old_obj, 'db_connections') and old_obj.db_connections is not None:
+ for obj in old_obj.db_connections:
+ new_obj.db_add_connection(DBConnection.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_connections') and hasattr(new_obj, 'db_deleted_connections'):
+ for obj in old_obj.db_deleted_connections:
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_connections.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'plugin_datas' in class_dict:
+ res = class_dict['plugin_datas'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_plugin_data(obj)
+ elif hasattr(old_obj, 'db_plugin_datas') and old_obj.db_plugin_datas is not None:
+ for obj in old_obj.db_plugin_datas:
+ new_obj.db_add_plugin_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_plugin_datas') and hasattr(new_obj, 'db_deleted_plugin_datas'):
+ for obj in old_obj.db_deleted_plugin_datas:
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_plugin_datas.append(n_obj)
+ if 'others' in class_dict:
+ res = class_dict['others'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_other(obj)
+ elif hasattr(old_obj, 'db_others') and old_obj.db_others is not None:
+ for obj in old_obj.db_others:
+ new_obj.db_add_other(DBOther.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_others') and hasattr(new_obj, 'db_deleted_others'):
+ for obj in old_obj.db_deleted_others:
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_others.append(n_obj)
+ if 'vistrail_id' in class_dict:
+ res = class_dict['vistrail_id'](old_obj, trans_dict)
+ new_obj.db_vistrail_id = res
+ elif hasattr(old_obj, 'db_vistrail_id') and old_obj.db_vistrail_id is not None:
+ new_obj.db_vistrail_id = old_obj.db_vistrail_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_connections:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_connection(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_plugin_datas:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_plugin_data(child)
+ to_del = []
+ for child in self.db_others:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_other(child)
+ to_del = []
+ for child in self.db_modules:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_connections)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_plugin_datas)
+ children.extend(self.db_deleted_others)
+ children.extend(self.db_deleted_modules)
+ if remove:
+ self.db_deleted_connections = []
+ self.db_deleted_annotations = []
+ self.db_deleted_plugin_datas = []
+ self.db_deleted_others = []
+ self.db_deleted_modules = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_connections:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_plugin_datas:
+ if child.has_changes():
+ return True
+ for child in self._db_others:
+ if child.has_changes():
+ return True
+ for child in self._db_modules:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_modules(self):
+ return self._db_modules
+ def __set_db_modules(self, modules):
+ self._db_modules = modules
+ self.is_dirty = True
+ db_modules = property(__get_db_modules, __set_db_modules)
+ def db_get_modules(self):
+ return self._db_modules
+ def db_add_module(self, module):
+ self.is_dirty = True
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_change_module(self, module):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ self._db_modules[i] = module
+ found = True
+ break
+ if not found:
+ self._db_modules.append(module)
+ self.db_modules_id_index[module.db_id] = module
+ def db_delete_module(self, module):
+ self.is_dirty = True
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == module.db_id:
+ if not self._db_modules[i].is_new:
+ self.db_deleted_modules.append(self._db_modules[i])
+ del self._db_modules[i]
+ break
+ del self.db_modules_id_index[module.db_id]
+ def db_get_module(self, key):
+ for i in xrange(len(self._db_modules)):
+ if self._db_modules[i].db_id == key:
+ return self._db_modules[i]
+ return None
+ def db_get_module_by_id(self, key):
+ return self.db_modules_id_index[key]
+ def db_has_module_with_id(self, key):
+ return key in self.db_modules_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_connections(self):
+ return self._db_connections
+ def __set_db_connections(self, connections):
+ self._db_connections = connections
+ self.is_dirty = True
+ db_connections = property(__get_db_connections, __set_db_connections)
+ def db_get_connections(self):
+ return self._db_connections
+ def db_add_connection(self, connection):
+ self.is_dirty = True
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_change_connection(self, connection):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ self._db_connections[i] = connection
+ found = True
+ break
+ if not found:
+ self._db_connections.append(connection)
+ self.db_connections_id_index[connection.db_id] = connection
+ def db_delete_connection(self, connection):
+ self.is_dirty = True
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == connection.db_id:
+ if not self._db_connections[i].is_new:
+ self.db_deleted_connections.append(self._db_connections[i])
+ del self._db_connections[i]
+ break
+ del self.db_connections_id_index[connection.db_id]
+ def db_get_connection(self, key):
+ for i in xrange(len(self._db_connections)):
+ if self._db_connections[i].db_id == key:
+ return self._db_connections[i]
+ return None
+ def db_get_connection_by_id(self, key):
+ return self.db_connections_id_index[key]
+ def db_has_connection_with_id(self, key):
+ return key in self.db_connections_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_plugin_datas(self):
+ return self._db_plugin_datas
+ def __set_db_plugin_datas(self, plugin_datas):
+ self._db_plugin_datas = plugin_datas
+ self.is_dirty = True
+ db_plugin_datas = property(__get_db_plugin_datas, __set_db_plugin_datas)
+ def db_get_plugin_datas(self):
+ return self._db_plugin_datas
+ def db_add_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_change_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ self._db_plugin_datas[i] = plugin_data
+ found = True
+ break
+ if not found:
+ self._db_plugin_datas.append(plugin_data)
+ self.db_plugin_datas_id_index[plugin_data.db_id] = plugin_data
+ def db_delete_plugin_data(self, plugin_data):
+ self.is_dirty = True
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == plugin_data.db_id:
+ if not self._db_plugin_datas[i].is_new:
+ self.db_deleted_plugin_datas.append(self._db_plugin_datas[i])
+ del self._db_plugin_datas[i]
+ break
+ del self.db_plugin_datas_id_index[plugin_data.db_id]
+ def db_get_plugin_data(self, key):
+ for i in xrange(len(self._db_plugin_datas)):
+ if self._db_plugin_datas[i].db_id == key:
+ return self._db_plugin_datas[i]
+ return None
+ def db_get_plugin_data_by_id(self, key):
+ return self.db_plugin_datas_id_index[key]
+ def db_has_plugin_data_with_id(self, key):
+ return key in self.db_plugin_datas_id_index
+
+ def __get_db_others(self):
+ return self._db_others
+ def __set_db_others(self, others):
+ self._db_others = others
+ self.is_dirty = True
+ db_others = property(__get_db_others, __set_db_others)
+ def db_get_others(self):
+ return self._db_others
+ def db_add_other(self, other):
+ self.is_dirty = True
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_change_other(self, other):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ self._db_others[i] = other
+ found = True
+ break
+ if not found:
+ self._db_others.append(other)
+ self.db_others_id_index[other.db_id] = other
+ def db_delete_other(self, other):
+ self.is_dirty = True
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == other.db_id:
+ if not self._db_others[i].is_new:
+ self.db_deleted_others.append(self._db_others[i])
+ del self._db_others[i]
+ break
+ del self.db_others_id_index[other.db_id]
+ def db_get_other(self, key):
+ for i in xrange(len(self._db_others)):
+ if self._db_others[i].db_id == key:
+ return self._db_others[i]
+ return None
+ def db_get_other_by_id(self, key):
+ return self.db_others_id_index[key]
+ def db_has_other_with_id(self, key):
+ return key in self.db_others_id_index
+
+ def __get_db_vistrail_id(self):
+ return self._db_vistrail_id
+ def __set_db_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ self.is_dirty = True
+ db_vistrail_id = property(__get_db_vistrail_id, __set_db_vistrail_id)
+ def db_add_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_change_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = vistrail_id
+ def db_delete_vistrail_id(self, vistrail_id):
+ self._db_vistrail_id = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmArtifactIdCause(object):
+
+ vtType = 'opm_artifact_id_cause'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactIdCause.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactIdCause(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_artifact', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_artifact', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactIdCause()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBRefProvEntity(object):
+
+ vtType = 'ref_prov_entity'
+
+ def __init__(self, prov_ref=None):
+ self._db_prov_ref = prov_ref
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBRefProvEntity.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBRefProvEntity(prov_ref=self._db_prov_ref)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prov_ref') and ('prov_entity', self._db_prov_ref) in id_remap:
+ cp._db_prov_ref = id_remap[('prov_entity', self._db_prov_ref)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRefProvEntity()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'prov_ref' in class_dict:
+ res = class_dict['prov_ref'](old_obj, trans_dict)
+ new_obj.db_prov_ref = res
+ elif hasattr(old_obj, 'db_prov_ref') and old_obj.db_prov_ref is not None:
+ new_obj.db_prov_ref = old_obj.db_prov_ref
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_prov_ref(self):
+ return self._db_prov_ref
+ def __set_db_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ self.is_dirty = True
+ db_prov_ref = property(__get_db_prov_ref, __set_db_prov_ref)
+ def db_add_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ def db_change_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ def db_delete_prov_ref(self, prov_ref):
+ self._db_prov_ref = None
+
+
+
+class DBProvActivity(object):
+
+ vtType = 'prov_activity'
+
+ def __init__(self, id=None, startTime=None, endTime=None, vt_id=None, vt_type=None, vt_cached=None, vt_completed=None, vt_machine_id=None, vt_error=None, is_part_of=None):
+ self._db_id = id
+ self._db_startTime = startTime
+ self._db_endTime = endTime
+ self._db_vt_id = vt_id
+ self._db_vt_type = vt_type
+ self._db_vt_cached = vt_cached
+ self._db_vt_completed = vt_completed
+ self._db_vt_machine_id = vt_machine_id
+ self._db_vt_error = vt_error
+ self.db_deleted_is_part_of = []
+ self._db_is_part_of = is_part_of
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBProvActivity.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBProvActivity(id=self._db_id,
+ startTime=self._db_startTime,
+ endTime=self._db_endTime,
+ vt_id=self._db_vt_id,
+ vt_type=self._db_vt_type,
+ vt_cached=self._db_vt_cached,
+ vt_completed=self._db_vt_completed,
+ vt_machine_id=self._db_vt_machine_id,
+ vt_error=self._db_vt_error)
+ if self._db_is_part_of is not None:
+ cp._db_is_part_of = self._db_is_part_of.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBProvActivity()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'startTime' in class_dict:
+ res = class_dict['startTime'](old_obj, trans_dict)
+ new_obj.db_startTime = res
+ elif hasattr(old_obj, 'db_startTime') and old_obj.db_startTime is not None:
+ new_obj.db_startTime = old_obj.db_startTime
+ if 'endTime' in class_dict:
+ res = class_dict['endTime'](old_obj, trans_dict)
+ new_obj.db_endTime = res
+ elif hasattr(old_obj, 'db_endTime') and old_obj.db_endTime is not None:
+ new_obj.db_endTime = old_obj.db_endTime
+ if 'vt_id' in class_dict:
+ res = class_dict['vt_id'](old_obj, trans_dict)
+ new_obj.db_vt_id = res
+ elif hasattr(old_obj, 'db_vt_id') and old_obj.db_vt_id is not None:
+ new_obj.db_vt_id = old_obj.db_vt_id
+ if 'vt_type' in class_dict:
+ res = class_dict['vt_type'](old_obj, trans_dict)
+ new_obj.db_vt_type = res
+ elif hasattr(old_obj, 'db_vt_type') and old_obj.db_vt_type is not None:
+ new_obj.db_vt_type = old_obj.db_vt_type
+ if 'vt_cached' in class_dict:
+ res = class_dict['vt_cached'](old_obj, trans_dict)
+ new_obj.db_vt_cached = res
+ elif hasattr(old_obj, 'db_vt_cached') and old_obj.db_vt_cached is not None:
+ new_obj.db_vt_cached = old_obj.db_vt_cached
+ if 'vt_completed' in class_dict:
+ res = class_dict['vt_completed'](old_obj, trans_dict)
+ new_obj.db_vt_completed = res
+ elif hasattr(old_obj, 'db_vt_completed') and old_obj.db_vt_completed is not None:
+ new_obj.db_vt_completed = old_obj.db_vt_completed
+ if 'vt_machine_id' in class_dict:
+ res = class_dict['vt_machine_id'](old_obj, trans_dict)
+ new_obj.db_vt_machine_id = res
+ elif hasattr(old_obj, 'db_vt_machine_id') and old_obj.db_vt_machine_id is not None:
+ new_obj.db_vt_machine_id = old_obj.db_vt_machine_id
+ if 'vt_error' in class_dict:
+ res = class_dict['vt_error'](old_obj, trans_dict)
+ new_obj.db_vt_error = res
+ elif hasattr(old_obj, 'db_vt_error') and old_obj.db_vt_error is not None:
+ new_obj.db_vt_error = old_obj.db_vt_error
+ if 'is_part_of' in class_dict:
+ res = class_dict['is_part_of'](old_obj, trans_dict)
+ new_obj.db_is_part_of = res
+ elif hasattr(old_obj, 'db_is_part_of') and old_obj.db_is_part_of is not None:
+ obj = old_obj.db_is_part_of
+ new_obj.db_add_is_part_of(DBIsPartOf.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_is_part_of') and hasattr(new_obj, 'db_deleted_is_part_of'):
+ for obj in old_obj.db_deleted_is_part_of:
+ n_obj = DBIsPartOf.update_version(obj, trans_dict)
+ new_obj.db_deleted_is_part_of.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_is_part_of is not None:
+ children.extend(self._db_is_part_of.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_is_part_of = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_is_part_of)
+ if remove:
+ self.db_deleted_is_part_of = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_is_part_of is not None and self._db_is_part_of.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_startTime(self):
+ return self._db_startTime
+ def __set_db_startTime(self, startTime):
+ self._db_startTime = startTime
+ self.is_dirty = True
+ db_startTime = property(__get_db_startTime, __set_db_startTime)
+ def db_add_startTime(self, startTime):
+ self._db_startTime = startTime
+ def db_change_startTime(self, startTime):
+ self._db_startTime = startTime
+ def db_delete_startTime(self, startTime):
+ self._db_startTime = None
+
+ def __get_db_endTime(self):
+ return self._db_endTime
+ def __set_db_endTime(self, endTime):
+ self._db_endTime = endTime
+ self.is_dirty = True
+ db_endTime = property(__get_db_endTime, __set_db_endTime)
+ def db_add_endTime(self, endTime):
+ self._db_endTime = endTime
+ def db_change_endTime(self, endTime):
+ self._db_endTime = endTime
+ def db_delete_endTime(self, endTime):
+ self._db_endTime = None
+
+ def __get_db_vt_id(self):
+ return self._db_vt_id
+ def __set_db_vt_id(self, vt_id):
+ self._db_vt_id = vt_id
+ self.is_dirty = True
+ db_vt_id = property(__get_db_vt_id, __set_db_vt_id)
+ def db_add_vt_id(self, vt_id):
+ self._db_vt_id = vt_id
+ def db_change_vt_id(self, vt_id):
+ self._db_vt_id = vt_id
+ def db_delete_vt_id(self, vt_id):
+ self._db_vt_id = None
+
+ def __get_db_vt_type(self):
+ return self._db_vt_type
+ def __set_db_vt_type(self, vt_type):
+ self._db_vt_type = vt_type
+ self.is_dirty = True
+ db_vt_type = property(__get_db_vt_type, __set_db_vt_type)
+ def db_add_vt_type(self, vt_type):
+ self._db_vt_type = vt_type
+ def db_change_vt_type(self, vt_type):
+ self._db_vt_type = vt_type
+ def db_delete_vt_type(self, vt_type):
+ self._db_vt_type = None
+
+ def __get_db_vt_cached(self):
+ return self._db_vt_cached
+ def __set_db_vt_cached(self, vt_cached):
+ self._db_vt_cached = vt_cached
+ self.is_dirty = True
+ db_vt_cached = property(__get_db_vt_cached, __set_db_vt_cached)
+ def db_add_vt_cached(self, vt_cached):
+ self._db_vt_cached = vt_cached
+ def db_change_vt_cached(self, vt_cached):
+ self._db_vt_cached = vt_cached
+ def db_delete_vt_cached(self, vt_cached):
+ self._db_vt_cached = None
+
+ def __get_db_vt_completed(self):
+ return self._db_vt_completed
+ def __set_db_vt_completed(self, vt_completed):
+ self._db_vt_completed = vt_completed
+ self.is_dirty = True
+ db_vt_completed = property(__get_db_vt_completed, __set_db_vt_completed)
+ def db_add_vt_completed(self, vt_completed):
+ self._db_vt_completed = vt_completed
+ def db_change_vt_completed(self, vt_completed):
+ self._db_vt_completed = vt_completed
+ def db_delete_vt_completed(self, vt_completed):
+ self._db_vt_completed = None
+
+ def __get_db_vt_machine_id(self):
+ return self._db_vt_machine_id
+ def __set_db_vt_machine_id(self, vt_machine_id):
+ self._db_vt_machine_id = vt_machine_id
+ self.is_dirty = True
+ db_vt_machine_id = property(__get_db_vt_machine_id, __set_db_vt_machine_id)
+ def db_add_vt_machine_id(self, vt_machine_id):
+ self._db_vt_machine_id = vt_machine_id
+ def db_change_vt_machine_id(self, vt_machine_id):
+ self._db_vt_machine_id = vt_machine_id
+ def db_delete_vt_machine_id(self, vt_machine_id):
+ self._db_vt_machine_id = None
+
+ def __get_db_vt_error(self):
+ return self._db_vt_error
+ def __set_db_vt_error(self, vt_error):
+ self._db_vt_error = vt_error
+ self.is_dirty = True
+ db_vt_error = property(__get_db_vt_error, __set_db_vt_error)
+ def db_add_vt_error(self, vt_error):
+ self._db_vt_error = vt_error
+ def db_change_vt_error(self, vt_error):
+ self._db_vt_error = vt_error
+ def db_delete_vt_error(self, vt_error):
+ self._db_vt_error = None
+
+ def __get_db_is_part_of(self):
+ return self._db_is_part_of
+ def __set_db_is_part_of(self, is_part_of):
+ self._db_is_part_of = is_part_of
+ self.is_dirty = True
+ db_is_part_of = property(__get_db_is_part_of, __set_db_is_part_of)
+ def db_add_is_part_of(self, is_part_of):
+ self._db_is_part_of = is_part_of
+ def db_change_is_part_of(self, is_part_of):
+ self._db_is_part_of = is_part_of
+ def db_delete_is_part_of(self, is_part_of):
+ if not self.is_new:
+ self.db_deleted_is_part_of.append(self._db_is_part_of)
+ self._db_is_part_of = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBMashupAction(object):
+
+ vtType = 'mashup_action'
+
+ def __init__(self, id=None, prevId=None, date=None, user=None, mashup=None):
+ self._db_id = id
+ self._db_prevId = prevId
+ self._db_date = date
+ self._db_user = user
+ self.db_deleted_mashup = []
+ self._db_mashup = mashup
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMashupAction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMashupAction(id=self._db_id,
+ prevId=self._db_prevId,
+ date=self._db_date,
+ user=self._db_user)
+ if self._db_mashup is not None:
+ cp._db_mashup = self._db_mashup.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prevId') and ('mashup_action', self._db_prevId) in id_remap:
+ cp._db_prevId = id_remap[('mashup_action', self._db_prevId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMashupAction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'prevId' in class_dict:
+ res = class_dict['prevId'](old_obj, trans_dict)
+ new_obj.db_prevId = res
+ elif hasattr(old_obj, 'db_prevId') and old_obj.db_prevId is not None:
+ new_obj.db_prevId = old_obj.db_prevId
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'mashup' in class_dict:
+ res = class_dict['mashup'](old_obj, trans_dict)
+ new_obj.db_mashup = res
+ elif hasattr(old_obj, 'db_mashup') and old_obj.db_mashup is not None:
+ obj = old_obj.db_mashup
+ new_obj.db_add_mashup(DBMashup.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_mashup') and hasattr(new_obj, 'db_deleted_mashup'):
+ for obj in old_obj.db_deleted_mashup:
+ n_obj = DBMashup.update_version(obj, trans_dict)
+ new_obj.db_deleted_mashup.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_mashup is not None:
+ children.extend(self._db_mashup.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_mashup = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_mashup)
+ if remove:
+ self.db_deleted_mashup = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_mashup is not None and self._db_mashup.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_prevId(self):
+ return self._db_prevId
+ def __set_db_prevId(self, prevId):
+ self._db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self._db_prevId = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_mashup(self):
+ return self._db_mashup
+ def __set_db_mashup(self, mashup):
+ self._db_mashup = mashup
+ self.is_dirty = True
+ db_mashup = property(__get_db_mashup, __set_db_mashup)
+ def db_add_mashup(self, mashup):
+ self._db_mashup = mashup
+ def db_change_mashup(self, mashup):
+ self._db_mashup = mashup
+ def db_delete_mashup(self, mashup):
+ if not self.is_new:
+ self.db_deleted_mashup.append(self._db_mashup)
+ self._db_mashup = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBProvUsage(object):
+
+ vtType = 'prov_usage'
+
+ def __init__(self, prov_activity=None, prov_entity=None, prov_role=None):
+ self.db_deleted_prov_activity = []
+ self._db_prov_activity = prov_activity
+ self.db_deleted_prov_entity = []
+ self._db_prov_entity = prov_entity
+ self._db_prov_role = prov_role
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBProvUsage.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBProvUsage(prov_role=self._db_prov_role)
+ if self._db_prov_activity is not None:
+ cp._db_prov_activity = self._db_prov_activity.do_copy(new_ids, id_scope, id_remap)
+ if self._db_prov_entity is not None:
+ cp._db_prov_entity = self._db_prov_entity.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBProvUsage()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'prov_activity' in class_dict:
+ res = class_dict['prov_activity'](old_obj, trans_dict)
+ new_obj.db_prov_activity = res
+ elif hasattr(old_obj, 'db_prov_activity') and old_obj.db_prov_activity is not None:
+ obj = old_obj.db_prov_activity
+ new_obj.db_add_prov_activity(DBRefProvActivity.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_activity') and hasattr(new_obj, 'db_deleted_prov_activity'):
+ for obj in old_obj.db_deleted_prov_activity:
+ n_obj = DBRefProvActivity.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_activity.append(n_obj)
+ if 'prov_entity' in class_dict:
+ res = class_dict['prov_entity'](old_obj, trans_dict)
+ new_obj.db_prov_entity = res
+ elif hasattr(old_obj, 'db_prov_entity') and old_obj.db_prov_entity is not None:
+ obj = old_obj.db_prov_entity
+ new_obj.db_add_prov_entity(DBRefProvEntity.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_entity') and hasattr(new_obj, 'db_deleted_prov_entity'):
+ for obj in old_obj.db_deleted_prov_entity:
+ n_obj = DBRefProvEntity.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_entity.append(n_obj)
+ if 'prov_role' in class_dict:
+ res = class_dict['prov_role'](old_obj, trans_dict)
+ new_obj.db_prov_role = res
+ elif hasattr(old_obj, 'db_prov_role') and old_obj.db_prov_role is not None:
+ new_obj.db_prov_role = old_obj.db_prov_role
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_prov_activity is not None:
+ children.extend(self._db_prov_activity.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_prov_activity = None
+ if self._db_prov_entity is not None:
+ children.extend(self._db_prov_entity.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_prov_entity = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_prov_activity)
+ children.extend(self.db_deleted_prov_entity)
+ if remove:
+ self.db_deleted_prov_activity = []
+ self.db_deleted_prov_entity = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_prov_activity is not None and self._db_prov_activity.has_changes():
+ return True
+ if self._db_prov_entity is not None and self._db_prov_entity.has_changes():
+ return True
+ return False
+ def __get_db_prov_activity(self):
+ return self._db_prov_activity
+ def __set_db_prov_activity(self, prov_activity):
+ self._db_prov_activity = prov_activity
+ self.is_dirty = True
+ db_prov_activity = property(__get_db_prov_activity, __set_db_prov_activity)
+ def db_add_prov_activity(self, prov_activity):
+ self._db_prov_activity = prov_activity
+ def db_change_prov_activity(self, prov_activity):
+ self._db_prov_activity = prov_activity
+ def db_delete_prov_activity(self, prov_activity):
+ if not self.is_new:
+ self.db_deleted_prov_activity.append(self._db_prov_activity)
+ self._db_prov_activity = None
+
+ def __get_db_prov_entity(self):
+ return self._db_prov_entity
+ def __set_db_prov_entity(self, prov_entity):
+ self._db_prov_entity = prov_entity
+ self.is_dirty = True
+ db_prov_entity = property(__get_db_prov_entity, __set_db_prov_entity)
+ def db_add_prov_entity(self, prov_entity):
+ self._db_prov_entity = prov_entity
+ def db_change_prov_entity(self, prov_entity):
+ self._db_prov_entity = prov_entity
+ def db_delete_prov_entity(self, prov_entity):
+ if not self.is_new:
+ self.db_deleted_prov_entity.append(self._db_prov_entity)
+ self._db_prov_entity = None
+
+ def __get_db_prov_role(self):
+ return self._db_prov_role
+ def __set_db_prov_role(self, prov_role):
+ self._db_prov_role = prov_role
+ self.is_dirty = True
+ db_prov_role = property(__get_db_prov_role, __set_db_prov_role)
+ def db_add_prov_role(self, prov_role):
+ self._db_prov_role = prov_role
+ def db_change_prov_role(self, prov_role):
+ self._db_prov_role = prov_role
+ def db_delete_prov_role(self, prov_role):
+ self._db_prov_role = None
+
+
+
+class DBOpmArtifactValue(object):
+
+ vtType = 'opm_artifact_value'
+
+ def __init__(self, value=None):
+ self.db_deleted_value = []
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactValue.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactValue()
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactValue()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ if obj.vtType == 'portSpec':
+ new_obj.db_add_value(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_value(DBFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ if obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_value = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ if remove:
+ self.db_deleted_value = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+
+
+class DBOpmArtifactIdEffect(object):
+
+ vtType = 'opm_artifact_id_effect'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifactIdEffect.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifactIdEffect(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_artifact', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_artifact', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifactIdEffect()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBOpmGraph(object):
+
+ vtType = 'opm_graph'
+
+ def __init__(self, accounts=None, processes=None, artifacts=None, agents=None, dependencies=None):
+ self.db_deleted_accounts = []
+ self._db_accounts = accounts
+ self.db_deleted_processes = []
+ self._db_processes = processes
+ self.db_deleted_artifacts = []
+ self._db_artifacts = artifacts
+ self.db_deleted_agents = []
+ self._db_agents = agents
+ self.db_deleted_dependencies = []
+ self._db_dependencies = dependencies
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmGraph.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmGraph()
+ if self._db_accounts is not None:
+ cp._db_accounts = self._db_accounts.do_copy(new_ids, id_scope, id_remap)
+ if self._db_processes is not None:
+ cp._db_processes = self._db_processes.do_copy(new_ids, id_scope, id_remap)
+ if self._db_artifacts is not None:
+ cp._db_artifacts = self._db_artifacts.do_copy(new_ids, id_scope, id_remap)
+ if self._db_agents is not None:
+ cp._db_agents = self._db_agents.do_copy(new_ids, id_scope, id_remap)
+ if self._db_dependencies is not None:
+ cp._db_dependencies = self._db_dependencies.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmGraph()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ new_obj.db_accounts = res
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ obj = old_obj.db_accounts
+ new_obj.db_add_accounts(DBOpmAccounts.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccounts.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'processes' in class_dict:
+ res = class_dict['processes'](old_obj, trans_dict)
+ new_obj.db_processes = res
+ elif hasattr(old_obj, 'db_processes') and old_obj.db_processes is not None:
+ obj = old_obj.db_processes
+ new_obj.db_add_processes(DBOpmProcesses.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_processes') and hasattr(new_obj, 'db_deleted_processes'):
+ for obj in old_obj.db_deleted_processes:
+ n_obj = DBOpmProcesses.update_version(obj, trans_dict)
+ new_obj.db_deleted_processes.append(n_obj)
+ if 'artifacts' in class_dict:
+ res = class_dict['artifacts'](old_obj, trans_dict)
+ new_obj.db_artifacts = res
+ elif hasattr(old_obj, 'db_artifacts') and old_obj.db_artifacts is not None:
+ obj = old_obj.db_artifacts
+ new_obj.db_add_artifacts(DBOpmArtifacts.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_artifacts') and hasattr(new_obj, 'db_deleted_artifacts'):
+ for obj in old_obj.db_deleted_artifacts:
+ n_obj = DBOpmArtifacts.update_version(obj, trans_dict)
+ new_obj.db_deleted_artifacts.append(n_obj)
+ if 'agents' in class_dict:
+ res = class_dict['agents'](old_obj, trans_dict)
+ new_obj.db_agents = res
+ elif hasattr(old_obj, 'db_agents') and old_obj.db_agents is not None:
+ obj = old_obj.db_agents
+ new_obj.db_add_agents(DBOpmAgents.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_agents') and hasattr(new_obj, 'db_deleted_agents'):
+ for obj in old_obj.db_deleted_agents:
+ n_obj = DBOpmAgents.update_version(obj, trans_dict)
+ new_obj.db_deleted_agents.append(n_obj)
+ if 'dependencies' in class_dict:
+ res = class_dict['dependencies'](old_obj, trans_dict)
+ new_obj.db_dependencies = res
+ elif hasattr(old_obj, 'db_dependencies') and old_obj.db_dependencies is not None:
+ obj = old_obj.db_dependencies
+ new_obj.db_add_dependencies(DBOpmDependencies.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_dependencies') and hasattr(new_obj, 'db_deleted_dependencies'):
+ for obj in old_obj.db_deleted_dependencies:
+ n_obj = DBOpmDependencies.update_version(obj, trans_dict)
+ new_obj.db_deleted_dependencies.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_accounts is not None:
+ children.extend(self._db_accounts.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_accounts = None
+ if self._db_processes is not None:
+ children.extend(self._db_processes.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_processes = None
+ if self._db_artifacts is not None:
+ children.extend(self._db_artifacts.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_artifacts = None
+ if self._db_agents is not None:
+ children.extend(self._db_agents.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_agents = None
+ if self._db_dependencies is not None:
+ children.extend(self._db_dependencies.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_dependencies = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_processes)
+ children.extend(self.db_deleted_artifacts)
+ children.extend(self.db_deleted_agents)
+ children.extend(self.db_deleted_dependencies)
+ if remove:
+ self.db_deleted_accounts = []
+ self.db_deleted_processes = []
+ self.db_deleted_artifacts = []
+ self.db_deleted_agents = []
+ self.db_deleted_dependencies = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_accounts is not None and self._db_accounts.has_changes():
+ return True
+ if self._db_processes is not None and self._db_processes.has_changes():
+ return True
+ if self._db_artifacts is not None and self._db_artifacts.has_changes():
+ return True
+ if self._db_agents is not None and self._db_agents.has_changes():
+ return True
+ if self._db_dependencies is not None and self._db_dependencies.has_changes():
+ return True
+ return False
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_add_accounts(self, accounts):
+ self._db_accounts = accounts
+ def db_change_accounts(self, accounts):
+ self._db_accounts = accounts
+ def db_delete_accounts(self, accounts):
+ if not self.is_new:
+ self.db_deleted_accounts.append(self._db_accounts)
+ self._db_accounts = None
+
+ def __get_db_processes(self):
+ return self._db_processes
+ def __set_db_processes(self, processes):
+ self._db_processes = processes
+ self.is_dirty = True
+ db_processes = property(__get_db_processes, __set_db_processes)
+ def db_add_processes(self, processes):
+ self._db_processes = processes
+ def db_change_processes(self, processes):
+ self._db_processes = processes
+ def db_delete_processes(self, processes):
+ if not self.is_new:
+ self.db_deleted_processes.append(self._db_processes)
+ self._db_processes = None
+
+ def __get_db_artifacts(self):
+ return self._db_artifacts
+ def __set_db_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ self.is_dirty = True
+ db_artifacts = property(__get_db_artifacts, __set_db_artifacts)
+ def db_add_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ def db_change_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ def db_delete_artifacts(self, artifacts):
+ if not self.is_new:
+ self.db_deleted_artifacts.append(self._db_artifacts)
+ self._db_artifacts = None
+
+ def __get_db_agents(self):
+ return self._db_agents
+ def __set_db_agents(self, agents):
+ self._db_agents = agents
+ self.is_dirty = True
+ db_agents = property(__get_db_agents, __set_db_agents)
+ def db_add_agents(self, agents):
+ self._db_agents = agents
+ def db_change_agents(self, agents):
+ self._db_agents = agents
+ def db_delete_agents(self, agents):
+ if not self.is_new:
+ self.db_deleted_agents.append(self._db_agents)
+ self._db_agents = None
+
+ def __get_db_dependencies(self):
+ return self._db_dependencies
+ def __set_db_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ self.is_dirty = True
+ db_dependencies = property(__get_db_dependencies, __set_db_dependencies)
+ def db_add_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ def db_change_dependencies(self, dependencies):
+ self._db_dependencies = dependencies
+ def db_delete_dependencies(self, dependencies):
+ if not self.is_new:
+ self.db_deleted_dependencies.append(self._db_dependencies)
+ self._db_dependencies = None
+
+
+
+class DBMashuptrail(object):
+
+ vtType = 'mashuptrail'
+
+ def __init__(self, id=None, name=None, version=None, vtVersion=None, last_modified=None, actions=None, annotations=None, actionAnnotations=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_version = version
+ self._db_vtVersion = vtVersion
+ self._db_last_modified = last_modified
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self._db_actions = []
+ else:
+ self._db_actions = actions
+ for v in self._db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_actionAnnotations = []
+ self.db_actionAnnotations_id_index = {}
+ self.db_actionAnnotations_action_id_index = {}
+ self.db_actionAnnotations_key_index = {}
+ if actionAnnotations is None:
+ self._db_actionAnnotations = []
+ else:
+ self._db_actionAnnotations = actionAnnotations
+ for v in self._db_actionAnnotations:
+ self.db_actionAnnotations_id_index[v.db_id] = v
+ self.db_actionAnnotations_action_id_index[(v.db_action_id,v.db_key)] = v
+ self.db_actionAnnotations_key_index[(v.db_key,v.db_value)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMashuptrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMashuptrail(id=self._db_id,
+ name=self._db_name,
+ version=self._db_version,
+ vtVersion=self._db_vtVersion,
+ last_modified=self._db_last_modified)
+ if self._db_actions is None:
+ cp._db_actions = []
+ else:
+ cp._db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actions]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_actionAnnotations is None:
+ cp._db_actionAnnotations = []
+ else:
+ cp._db_actionAnnotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actionAnnotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_actions_id_index = dict((v.db_id, v) for v in cp._db_actions)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ cp.db_actionAnnotations_id_index = dict((v.db_id, v) for v in cp._db_actionAnnotations)
+ cp.db_actionAnnotations_action_id_index = dict(((v.db_action_id,v.db_key), v) for v in cp._db_actionAnnotations)
+ cp.db_actionAnnotations_key_index = dict(((v.db_key,v.db_value), v) for v in cp._db_actionAnnotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMashuptrail()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'vtVersion' in class_dict:
+ res = class_dict['vtVersion'](old_obj, trans_dict)
+ new_obj.db_vtVersion = res
+ elif hasattr(old_obj, 'db_vtVersion') and old_obj.db_vtVersion is not None:
+ new_obj.db_vtVersion = old_obj.db_vtVersion
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'actions' in class_dict:
+ res = class_dict['actions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_action(obj)
+ elif hasattr(old_obj, 'db_actions') and old_obj.db_actions is not None:
+ for obj in old_obj.db_actions:
+ new_obj.db_add_action(DBMashupAction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actions') and hasattr(new_obj, 'db_deleted_actions'):
+ for obj in old_obj.db_deleted_actions:
+ n_obj = DBMashupAction.update_version(obj, trans_dict)
+ new_obj.db_deleted_actions.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'actionAnnotations' in class_dict:
+ res = class_dict['actionAnnotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_actionAnnotation(obj)
+ elif hasattr(old_obj, 'db_actionAnnotations') and old_obj.db_actionAnnotations is not None:
+ for obj in old_obj.db_actionAnnotations:
+ new_obj.db_add_actionAnnotation(DBMashupActionAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actionAnnotations') and hasattr(new_obj, 'db_deleted_actionAnnotations'):
+ for obj in old_obj.db_deleted_actionAnnotations:
+ n_obj = DBMashupActionAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_actionAnnotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_actionAnnotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_actionAnnotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_actionAnnotations)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_annotations = []
+ self.db_deleted_actionAnnotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_actions:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_actionAnnotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_vtVersion(self):
+ return self._db_vtVersion
+ def __set_db_vtVersion(self, vtVersion):
+ self._db_vtVersion = vtVersion
+ self.is_dirty = True
+ db_vtVersion = property(__get_db_vtVersion, __set_db_vtVersion)
+ def db_add_vtVersion(self, vtVersion):
+ self._db_vtVersion = vtVersion
+ def db_change_vtVersion(self, vtVersion):
+ self._db_vtVersion = vtVersion
+ def db_delete_vtVersion(self, vtVersion):
+ self._db_vtVersion = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_actions(self):
+ return self._db_actions
+ def __set_db_actions(self, actions):
+ self._db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self._db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ self._db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ if not self._db_actions[i].is_new:
+ self.db_deleted_actions.append(self._db_actions[i])
+ del self._db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == key:
+ return self._db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return key in self.db_actions_id_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_actionAnnotations(self):
+ return self._db_actionAnnotations
+ def __set_db_actionAnnotations(self, actionAnnotations):
+ self._db_actionAnnotations = actionAnnotations
+ self.is_dirty = True
+ db_actionAnnotations = property(__get_db_actionAnnotations, __set_db_actionAnnotations)
+ def db_get_actionAnnotations(self):
+ return self._db_actionAnnotations
+ def db_add_actionAnnotation(self, actionAnnotation):
+ self.is_dirty = True
+ self._db_actionAnnotations.append(actionAnnotation)
+ self.db_actionAnnotations_id_index[actionAnnotation.db_id] = actionAnnotation
+ self.db_actionAnnotations_action_id_index[(actionAnnotation.db_action_id,actionAnnotation.db_key)] = actionAnnotation
+ self.db_actionAnnotations_key_index[(actionAnnotation.db_key,actionAnnotation.db_value)] = actionAnnotation
+ def db_change_actionAnnotation(self, actionAnnotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actionAnnotations)):
+ if self._db_actionAnnotations[i].db_id == actionAnnotation.db_id:
+ self._db_actionAnnotations[i] = actionAnnotation
+ found = True
+ break
+ if not found:
+ self._db_actionAnnotations.append(actionAnnotation)
+ self.db_actionAnnotations_id_index[actionAnnotation.db_id] = actionAnnotation
+ self.db_actionAnnotations_action_id_index[(actionAnnotation.db_action_id,actionAnnotation.db_key)] = actionAnnotation
+ self.db_actionAnnotations_key_index[(actionAnnotation.db_key,actionAnnotation.db_value)] = actionAnnotation
+ def db_delete_actionAnnotation(self, actionAnnotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actionAnnotations)):
+ if self._db_actionAnnotations[i].db_id == actionAnnotation.db_id:
+ if not self._db_actionAnnotations[i].is_new:
+ self.db_deleted_actionAnnotations.append(self._db_actionAnnotations[i])
+ del self._db_actionAnnotations[i]
+ break
+ del self.db_actionAnnotations_id_index[actionAnnotation.db_id]
+ del self.db_actionAnnotations_action_id_index[(actionAnnotation.db_action_id,actionAnnotation.db_key)]
+ try:
+ del self.db_actionAnnotations_key_index[(actionAnnotation.db_key,actionAnnotation.db_value)]
+ except KeyError:
+ pass
+ def db_get_actionAnnotation(self, key):
+ for i in xrange(len(self._db_actionAnnotations)):
+ if self._db_actionAnnotations[i].db_id == key:
+ return self._db_actionAnnotations[i]
+ return None
+ def db_get_actionAnnotation_by_id(self, key):
+ return self.db_actionAnnotations_id_index[key]
+ def db_has_actionAnnotation_with_id(self, key):
+ return key in self.db_actionAnnotations_id_index
+ def db_get_actionAnnotation_by_action_id(self, key):
+ return self.db_actionAnnotations_action_id_index[key]
+ def db_has_actionAnnotation_with_action_id(self, key):
+ return key in self.db_actionAnnotations_action_id_index
+ def db_get_actionAnnotation_by_key(self, key):
+ return self.db_actionAnnotations_key_index[key]
+ def db_has_actionAnnotation_with_key(self, key):
+ return key in self.db_actionAnnotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBRegistry(object):
+
+ vtType = 'registry'
+
+ def __init__(self, id=None, entity_type=None, version=None, root_descriptor_id=None, name=None, last_modified=None, packages=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_root_descriptor_id = root_descriptor_id
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_packages = []
+ self.db_packages_id_index = {}
+ self.db_packages_identifier_index = {}
+ if packages is None:
+ self._db_packages = []
+ else:
+ self._db_packages = packages
+ for v in self._db_packages:
+ self.db_packages_id_index[v.db_id] = v
+ self.db_packages_identifier_index[(v.db_identifier,v.db_version)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBRegistry.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBRegistry(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ root_descriptor_id=self._db_root_descriptor_id,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_packages is None:
+ cp._db_packages = []
+ else:
+ cp._db_packages = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_packages]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_root_descriptor_id') and ('module_descriptor', self._db_root_descriptor_id) in id_remap:
+ cp._db_root_descriptor_id = id_remap[('module_descriptor', self._db_root_descriptor_id)]
+
+ # recreate indices and set flags
+ cp.db_packages_id_index = dict((v.db_id, v) for v in cp._db_packages)
+ cp.db_packages_identifier_index = dict(((v.db_identifier,v.db_version), v) for v in cp._db_packages)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRegistry()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'root_descriptor_id' in class_dict:
+ res = class_dict['root_descriptor_id'](old_obj, trans_dict)
+ new_obj.db_root_descriptor_id = res
+ elif hasattr(old_obj, 'db_root_descriptor_id') and old_obj.db_root_descriptor_id is not None:
+ new_obj.db_root_descriptor_id = old_obj.db_root_descriptor_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'packages' in class_dict:
+ res = class_dict['packages'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_package(obj)
+ elif hasattr(old_obj, 'db_packages') and old_obj.db_packages is not None:
+ for obj in old_obj.db_packages:
+ new_obj.db_add_package(DBPackage.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_packages') and hasattr(new_obj, 'db_deleted_packages'):
+ for obj in old_obj.db_deleted_packages:
+ n_obj = DBPackage.update_version(obj, trans_dict)
+ new_obj.db_deleted_packages.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_packages:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_package(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_packages)
+ if remove:
+ self.db_deleted_packages = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_packages:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_root_descriptor_id(self):
+ return self._db_root_descriptor_id
+ def __set_db_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ self.is_dirty = True
+ db_root_descriptor_id = property(__get_db_root_descriptor_id, __set_db_root_descriptor_id)
+ def db_add_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ def db_change_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = root_descriptor_id
+ def db_delete_root_descriptor_id(self, root_descriptor_id):
+ self._db_root_descriptor_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_packages(self):
+ return self._db_packages
+ def __set_db_packages(self, packages):
+ self._db_packages = packages
+ self.is_dirty = True
+ db_packages = property(__get_db_packages, __set_db_packages)
+ def db_get_packages(self):
+ return self._db_packages
+ def db_add_package(self, package):
+ self.is_dirty = True
+ self._db_packages.append(package)
+ self.db_packages_id_index[package.db_id] = package
+ self.db_packages_identifier_index[(package.db_identifier,package.db_version)] = package
+ def db_change_package(self, package):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == package.db_id:
+ self._db_packages[i] = package
+ found = True
+ break
+ if not found:
+ self._db_packages.append(package)
+ self.db_packages_id_index[package.db_id] = package
+ self.db_packages_identifier_index[(package.db_identifier,package.db_version)] = package
+ def db_delete_package(self, package):
+ self.is_dirty = True
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == package.db_id:
+ if not self._db_packages[i].is_new:
+ self.db_deleted_packages.append(self._db_packages[i])
+ del self._db_packages[i]
+ break
+ del self.db_packages_id_index[package.db_id]
+ del self.db_packages_identifier_index[(package.db_identifier,package.db_version)]
+ def db_get_package(self, key):
+ for i in xrange(len(self._db_packages)):
+ if self._db_packages[i].db_id == key:
+ return self._db_packages[i]
+ return None
+ def db_get_package_by_id(self, key):
+ return self.db_packages_id_index[key]
+ def db_has_package_with_id(self, key):
+ return key in self.db_packages_id_index
+ def db_get_package_by_identifier(self, key):
+ return self.db_packages_identifier_index[key]
+ def db_has_package_with_identifier(self, key):
+ return key in self.db_packages_identifier_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBVtConnection(object):
+
+ vtType = 'vt_connection'
+
+ def __init__(self, id=None, vt_source=None, vt_dest=None, vt_source_port=None, vt_dest_port=None, vt_source_signature=None, vt_dest_signature=None):
+ self._db_id = id
+ self._db_vt_source = vt_source
+ self._db_vt_dest = vt_dest
+ self._db_vt_source_port = vt_source_port
+ self._db_vt_dest_port = vt_dest_port
+ self._db_vt_source_signature = vt_source_signature
+ self._db_vt_dest_signature = vt_dest_signature
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVtConnection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVtConnection(id=self._db_id,
+ vt_source=self._db_vt_source,
+ vt_dest=self._db_vt_dest,
+ vt_source_port=self._db_vt_source_port,
+ vt_dest_port=self._db_vt_dest_port,
+ vt_source_signature=self._db_vt_source_signature,
+ vt_dest_signature=self._db_vt_dest_signature)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVtConnection()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'vt_source' in class_dict:
+ res = class_dict['vt_source'](old_obj, trans_dict)
+ new_obj.db_vt_source = res
+ elif hasattr(old_obj, 'db_vt_source') and old_obj.db_vt_source is not None:
+ new_obj.db_vt_source = old_obj.db_vt_source
+ if 'vt_dest' in class_dict:
+ res = class_dict['vt_dest'](old_obj, trans_dict)
+ new_obj.db_vt_dest = res
+ elif hasattr(old_obj, 'db_vt_dest') and old_obj.db_vt_dest is not None:
+ new_obj.db_vt_dest = old_obj.db_vt_dest
+ if 'vt_source_port' in class_dict:
+ res = class_dict['vt_source_port'](old_obj, trans_dict)
+ new_obj.db_vt_source_port = res
+ elif hasattr(old_obj, 'db_vt_source_port') and old_obj.db_vt_source_port is not None:
+ new_obj.db_vt_source_port = old_obj.db_vt_source_port
+ if 'vt_dest_port' in class_dict:
+ res = class_dict['vt_dest_port'](old_obj, trans_dict)
+ new_obj.db_vt_dest_port = res
+ elif hasattr(old_obj, 'db_vt_dest_port') and old_obj.db_vt_dest_port is not None:
+ new_obj.db_vt_dest_port = old_obj.db_vt_dest_port
+ if 'vt_source_signature' in class_dict:
+ res = class_dict['vt_source_signature'](old_obj, trans_dict)
+ new_obj.db_vt_source_signature = res
+ elif hasattr(old_obj, 'db_vt_source_signature') and old_obj.db_vt_source_signature is not None:
+ new_obj.db_vt_source_signature = old_obj.db_vt_source_signature
+ if 'vt_dest_signature' in class_dict:
+ res = class_dict['vt_dest_signature'](old_obj, trans_dict)
+ new_obj.db_vt_dest_signature = res
+ elif hasattr(old_obj, 'db_vt_dest_signature') and old_obj.db_vt_dest_signature is not None:
+ new_obj.db_vt_dest_signature = old_obj.db_vt_dest_signature
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_vt_source(self):
+ return self._db_vt_source
+ def __set_db_vt_source(self, vt_source):
+ self._db_vt_source = vt_source
+ self.is_dirty = True
+ db_vt_source = property(__get_db_vt_source, __set_db_vt_source)
+ def db_add_vt_source(self, vt_source):
+ self._db_vt_source = vt_source
+ def db_change_vt_source(self, vt_source):
+ self._db_vt_source = vt_source
+ def db_delete_vt_source(self, vt_source):
+ self._db_vt_source = None
+
+ def __get_db_vt_dest(self):
+ return self._db_vt_dest
+ def __set_db_vt_dest(self, vt_dest):
+ self._db_vt_dest = vt_dest
+ self.is_dirty = True
+ db_vt_dest = property(__get_db_vt_dest, __set_db_vt_dest)
+ def db_add_vt_dest(self, vt_dest):
+ self._db_vt_dest = vt_dest
+ def db_change_vt_dest(self, vt_dest):
+ self._db_vt_dest = vt_dest
+ def db_delete_vt_dest(self, vt_dest):
+ self._db_vt_dest = None
+
+ def __get_db_vt_source_port(self):
+ return self._db_vt_source_port
+ def __set_db_vt_source_port(self, vt_source_port):
+ self._db_vt_source_port = vt_source_port
+ self.is_dirty = True
+ db_vt_source_port = property(__get_db_vt_source_port, __set_db_vt_source_port)
+ def db_add_vt_source_port(self, vt_source_port):
+ self._db_vt_source_port = vt_source_port
+ def db_change_vt_source_port(self, vt_source_port):
+ self._db_vt_source_port = vt_source_port
+ def db_delete_vt_source_port(self, vt_source_port):
+ self._db_vt_source_port = None
+
+ def __get_db_vt_dest_port(self):
+ return self._db_vt_dest_port
+ def __set_db_vt_dest_port(self, vt_dest_port):
+ self._db_vt_dest_port = vt_dest_port
+ self.is_dirty = True
+ db_vt_dest_port = property(__get_db_vt_dest_port, __set_db_vt_dest_port)
+ def db_add_vt_dest_port(self, vt_dest_port):
+ self._db_vt_dest_port = vt_dest_port
+ def db_change_vt_dest_port(self, vt_dest_port):
+ self._db_vt_dest_port = vt_dest_port
+ def db_delete_vt_dest_port(self, vt_dest_port):
+ self._db_vt_dest_port = None
+
+ def __get_db_vt_source_signature(self):
+ return self._db_vt_source_signature
+ def __set_db_vt_source_signature(self, vt_source_signature):
+ self._db_vt_source_signature = vt_source_signature
+ self.is_dirty = True
+ db_vt_source_signature = property(__get_db_vt_source_signature, __set_db_vt_source_signature)
+ def db_add_vt_source_signature(self, vt_source_signature):
+ self._db_vt_source_signature = vt_source_signature
+ def db_change_vt_source_signature(self, vt_source_signature):
+ self._db_vt_source_signature = vt_source_signature
+ def db_delete_vt_source_signature(self, vt_source_signature):
+ self._db_vt_source_signature = None
+
+ def __get_db_vt_dest_signature(self):
+ return self._db_vt_dest_signature
+ def __set_db_vt_dest_signature(self, vt_dest_signature):
+ self._db_vt_dest_signature = vt_dest_signature
+ self.is_dirty = True
+ db_vt_dest_signature = property(__get_db_vt_dest_signature, __set_db_vt_dest_signature)
+ def db_add_vt_dest_signature(self, vt_dest_signature):
+ self._db_vt_dest_signature = vt_dest_signature
+ def db_change_vt_dest_signature(self, vt_dest_signature):
+ self._db_vt_dest_signature = vt_dest_signature
+ def db_delete_vt_dest_signature(self, vt_dest_signature):
+ self._db_vt_dest_signature = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBMashupComponent(object):
+
+ vtType = 'mashup_component'
+
+ def __init__(self, id=None, vtid=None, vttype=None, vtparent_type=None, vtparent_id=None, vtpos=None, vtmid=None, pos=None, type=None, val=None, minVal=None, maxVal=None, stepSize=None, strvaluelist=None, widget=None, seq=None, parent=None):
+ self._db_id = id
+ self._db_vtid = vtid
+ self._db_vttype = vttype
+ self._db_vtparent_type = vtparent_type
+ self._db_vtparent_id = vtparent_id
+ self._db_vtpos = vtpos
+ self._db_vtmid = vtmid
+ self._db_pos = pos
+ self._db_type = type
+ self._db_val = val
+ self._db_minVal = minVal
+ self._db_maxVal = maxVal
+ self._db_stepSize = stepSize
+ self._db_strvaluelist = strvaluelist
+ self._db_widget = widget
+ self._db_seq = seq
+ self._db_parent = parent
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMashupComponent.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMashupComponent(id=self._db_id,
+ vtid=self._db_vtid,
+ vttype=self._db_vttype,
+ vtparent_type=self._db_vtparent_type,
+ vtparent_id=self._db_vtparent_id,
+ vtpos=self._db_vtpos,
+ vtmid=self._db_vtmid,
+ pos=self._db_pos,
+ type=self._db_type,
+ val=self._db_val,
+ minVal=self._db_minVal,
+ maxVal=self._db_maxVal,
+ stepSize=self._db_stepSize,
+ strvaluelist=self._db_strvaluelist,
+ widget=self._db_widget,
+ seq=self._db_seq,
+ parent=self._db_parent)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMashupComponent()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'vtid' in class_dict:
+ res = class_dict['vtid'](old_obj, trans_dict)
+ new_obj.db_vtid = res
+ elif hasattr(old_obj, 'db_vtid') and old_obj.db_vtid is not None:
+ new_obj.db_vtid = old_obj.db_vtid
+ if 'vttype' in class_dict:
+ res = class_dict['vttype'](old_obj, trans_dict)
+ new_obj.db_vttype = res
+ elif hasattr(old_obj, 'db_vttype') and old_obj.db_vttype is not None:
+ new_obj.db_vttype = old_obj.db_vttype
+ if 'vtparent_type' in class_dict:
+ res = class_dict['vtparent_type'](old_obj, trans_dict)
+ new_obj.db_vtparent_type = res
+ elif hasattr(old_obj, 'db_vtparent_type') and old_obj.db_vtparent_type is not None:
+ new_obj.db_vtparent_type = old_obj.db_vtparent_type
+ if 'vtparent_id' in class_dict:
+ res = class_dict['vtparent_id'](old_obj, trans_dict)
+ new_obj.db_vtparent_id = res
+ elif hasattr(old_obj, 'db_vtparent_id') and old_obj.db_vtparent_id is not None:
+ new_obj.db_vtparent_id = old_obj.db_vtparent_id
+ if 'vtpos' in class_dict:
+ res = class_dict['vtpos'](old_obj, trans_dict)
+ new_obj.db_vtpos = res
+ elif hasattr(old_obj, 'db_vtpos') and old_obj.db_vtpos is not None:
+ new_obj.db_vtpos = old_obj.db_vtpos
+ if 'vtmid' in class_dict:
+ res = class_dict['vtmid'](old_obj, trans_dict)
+ new_obj.db_vtmid = res
+ elif hasattr(old_obj, 'db_vtmid') and old_obj.db_vtmid is not None:
+ new_obj.db_vtmid = old_obj.db_vtmid
+ if 'pos' in class_dict:
+ res = class_dict['pos'](old_obj, trans_dict)
+ new_obj.db_pos = res
+ elif hasattr(old_obj, 'db_pos') and old_obj.db_pos is not None:
+ new_obj.db_pos = old_obj.db_pos
+ if 'type' in class_dict:
+ res = class_dict['type'](old_obj, trans_dict)
+ new_obj.db_type = res
+ elif hasattr(old_obj, 'db_type') and old_obj.db_type is not None:
+ new_obj.db_type = old_obj.db_type
+ if 'val' in class_dict:
+ res = class_dict['val'](old_obj, trans_dict)
+ new_obj.db_val = res
+ elif hasattr(old_obj, 'db_val') and old_obj.db_val is not None:
+ new_obj.db_val = old_obj.db_val
+ if 'minVal' in class_dict:
+ res = class_dict['minVal'](old_obj, trans_dict)
+ new_obj.db_minVal = res
+ elif hasattr(old_obj, 'db_minVal') and old_obj.db_minVal is not None:
+ new_obj.db_minVal = old_obj.db_minVal
+ if 'maxVal' in class_dict:
+ res = class_dict['maxVal'](old_obj, trans_dict)
+ new_obj.db_maxVal = res
+ elif hasattr(old_obj, 'db_maxVal') and old_obj.db_maxVal is not None:
+ new_obj.db_maxVal = old_obj.db_maxVal
+ if 'stepSize' in class_dict:
+ res = class_dict['stepSize'](old_obj, trans_dict)
+ new_obj.db_stepSize = res
+ elif hasattr(old_obj, 'db_stepSize') and old_obj.db_stepSize is not None:
+ new_obj.db_stepSize = old_obj.db_stepSize
+ if 'strvaluelist' in class_dict:
+ res = class_dict['strvaluelist'](old_obj, trans_dict)
+ new_obj.db_strvaluelist = res
+ elif hasattr(old_obj, 'db_strvaluelist') and old_obj.db_strvaluelist is not None:
+ new_obj.db_strvaluelist = old_obj.db_strvaluelist
+ if 'widget' in class_dict:
+ res = class_dict['widget'](old_obj, trans_dict)
+ new_obj.db_widget = res
+ elif hasattr(old_obj, 'db_widget') and old_obj.db_widget is not None:
+ new_obj.db_widget = old_obj.db_widget
+ if 'seq' in class_dict:
+ res = class_dict['seq'](old_obj, trans_dict)
+ new_obj.db_seq = res
+ elif hasattr(old_obj, 'db_seq') and old_obj.db_seq is not None:
+ new_obj.db_seq = old_obj.db_seq
+ if 'parent' in class_dict:
+ res = class_dict['parent'](old_obj, trans_dict)
+ new_obj.db_parent = res
+ elif hasattr(old_obj, 'db_parent') and old_obj.db_parent is not None:
+ new_obj.db_parent = old_obj.db_parent
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_vtid(self):
+ return self._db_vtid
+ def __set_db_vtid(self, vtid):
+ self._db_vtid = vtid
+ self.is_dirty = True
+ db_vtid = property(__get_db_vtid, __set_db_vtid)
+ def db_add_vtid(self, vtid):
+ self._db_vtid = vtid
+ def db_change_vtid(self, vtid):
+ self._db_vtid = vtid
+ def db_delete_vtid(self, vtid):
+ self._db_vtid = None
+
+ def __get_db_vttype(self):
+ return self._db_vttype
+ def __set_db_vttype(self, vttype):
+ self._db_vttype = vttype
+ self.is_dirty = True
+ db_vttype = property(__get_db_vttype, __set_db_vttype)
+ def db_add_vttype(self, vttype):
+ self._db_vttype = vttype
+ def db_change_vttype(self, vttype):
+ self._db_vttype = vttype
+ def db_delete_vttype(self, vttype):
+ self._db_vttype = None
+
+ def __get_db_vtparent_type(self):
+ return self._db_vtparent_type
+ def __set_db_vtparent_type(self, vtparent_type):
+ self._db_vtparent_type = vtparent_type
+ self.is_dirty = True
+ db_vtparent_type = property(__get_db_vtparent_type, __set_db_vtparent_type)
+ def db_add_vtparent_type(self, vtparent_type):
+ self._db_vtparent_type = vtparent_type
+ def db_change_vtparent_type(self, vtparent_type):
+ self._db_vtparent_type = vtparent_type
+ def db_delete_vtparent_type(self, vtparent_type):
+ self._db_vtparent_type = None
+
+ def __get_db_vtparent_id(self):
+ return self._db_vtparent_id
+ def __set_db_vtparent_id(self, vtparent_id):
+ self._db_vtparent_id = vtparent_id
+ self.is_dirty = True
+ db_vtparent_id = property(__get_db_vtparent_id, __set_db_vtparent_id)
+ def db_add_vtparent_id(self, vtparent_id):
+ self._db_vtparent_id = vtparent_id
+ def db_change_vtparent_id(self, vtparent_id):
+ self._db_vtparent_id = vtparent_id
+ def db_delete_vtparent_id(self, vtparent_id):
+ self._db_vtparent_id = None
+
+ def __get_db_vtpos(self):
+ return self._db_vtpos
+ def __set_db_vtpos(self, vtpos):
+ self._db_vtpos = vtpos
+ self.is_dirty = True
+ db_vtpos = property(__get_db_vtpos, __set_db_vtpos)
+ def db_add_vtpos(self, vtpos):
+ self._db_vtpos = vtpos
+ def db_change_vtpos(self, vtpos):
+ self._db_vtpos = vtpos
+ def db_delete_vtpos(self, vtpos):
+ self._db_vtpos = None
+
+ def __get_db_vtmid(self):
+ return self._db_vtmid
+ def __set_db_vtmid(self, vtmid):
+ self._db_vtmid = vtmid
+ self.is_dirty = True
+ db_vtmid = property(__get_db_vtmid, __set_db_vtmid)
+ def db_add_vtmid(self, vtmid):
+ self._db_vtmid = vtmid
+ def db_change_vtmid(self, vtmid):
+ self._db_vtmid = vtmid
+ def db_delete_vtmid(self, vtmid):
+ self._db_vtmid = None
+
+ def __get_db_pos(self):
+ return self._db_pos
+ def __set_db_pos(self, pos):
+ self._db_pos = pos
+ self.is_dirty = True
+ db_pos = property(__get_db_pos, __set_db_pos)
+ def db_add_pos(self, pos):
+ self._db_pos = pos
+ def db_change_pos(self, pos):
+ self._db_pos = pos
+ def db_delete_pos(self, pos):
+ self._db_pos = None
+
+ def __get_db_type(self):
+ return self._db_type
+ def __set_db_type(self, type):
+ self._db_type = type
+ self.is_dirty = True
+ db_type = property(__get_db_type, __set_db_type)
+ def db_add_type(self, type):
+ self._db_type = type
+ def db_change_type(self, type):
+ self._db_type = type
+ def db_delete_type(self, type):
+ self._db_type = None
+
+ def __get_db_val(self):
+ return self._db_val
+ def __set_db_val(self, val):
+ self._db_val = val
+ self.is_dirty = True
+ db_val = property(__get_db_val, __set_db_val)
+ def db_add_val(self, val):
+ self._db_val = val
+ def db_change_val(self, val):
+ self._db_val = val
+ def db_delete_val(self, val):
+ self._db_val = None
+
+ def __get_db_minVal(self):
+ return self._db_minVal
+ def __set_db_minVal(self, minVal):
+ self._db_minVal = minVal
+ self.is_dirty = True
+ db_minVal = property(__get_db_minVal, __set_db_minVal)
+ def db_add_minVal(self, minVal):
+ self._db_minVal = minVal
+ def db_change_minVal(self, minVal):
+ self._db_minVal = minVal
+ def db_delete_minVal(self, minVal):
+ self._db_minVal = None
+
+ def __get_db_maxVal(self):
+ return self._db_maxVal
+ def __set_db_maxVal(self, maxVal):
+ self._db_maxVal = maxVal
+ self.is_dirty = True
+ db_maxVal = property(__get_db_maxVal, __set_db_maxVal)
+ def db_add_maxVal(self, maxVal):
+ self._db_maxVal = maxVal
+ def db_change_maxVal(self, maxVal):
+ self._db_maxVal = maxVal
+ def db_delete_maxVal(self, maxVal):
+ self._db_maxVal = None
+
+ def __get_db_stepSize(self):
+ return self._db_stepSize
+ def __set_db_stepSize(self, stepSize):
+ self._db_stepSize = stepSize
+ self.is_dirty = True
+ db_stepSize = property(__get_db_stepSize, __set_db_stepSize)
+ def db_add_stepSize(self, stepSize):
+ self._db_stepSize = stepSize
+ def db_change_stepSize(self, stepSize):
+ self._db_stepSize = stepSize
+ def db_delete_stepSize(self, stepSize):
+ self._db_stepSize = None
+
+ def __get_db_strvaluelist(self):
+ return self._db_strvaluelist
+ def __set_db_strvaluelist(self, strvaluelist):
+ self._db_strvaluelist = strvaluelist
+ self.is_dirty = True
+ db_strvaluelist = property(__get_db_strvaluelist, __set_db_strvaluelist)
+ def db_add_strvaluelist(self, strvaluelist):
+ self._db_strvaluelist = strvaluelist
+ def db_change_strvaluelist(self, strvaluelist):
+ self._db_strvaluelist = strvaluelist
+ def db_delete_strvaluelist(self, strvaluelist):
+ self._db_strvaluelist = None
+
+ def __get_db_widget(self):
+ return self._db_widget
+ def __set_db_widget(self, widget):
+ self._db_widget = widget
+ self.is_dirty = True
+ db_widget = property(__get_db_widget, __set_db_widget)
+ def db_add_widget(self, widget):
+ self._db_widget = widget
+ def db_change_widget(self, widget):
+ self._db_widget = widget
+ def db_delete_widget(self, widget):
+ self._db_widget = None
+
+ def __get_db_seq(self):
+ return self._db_seq
+ def __set_db_seq(self, seq):
+ self._db_seq = seq
+ self.is_dirty = True
+ db_seq = property(__get_db_seq, __set_db_seq)
+ def db_add_seq(self, seq):
+ self._db_seq = seq
+ def db_change_seq(self, seq):
+ self._db_seq = seq
+ def db_delete_seq(self, seq):
+ self._db_seq = None
+
+ def __get_db_parent(self):
+ return self._db_parent
+ def __set_db_parent(self, parent):
+ self._db_parent = parent
+ self.is_dirty = True
+ db_parent = property(__get_db_parent, __set_db_parent)
+ def db_add_parent(self, parent):
+ self._db_parent = parent
+ def db_change_parent(self, parent):
+ self._db_parent = parent
+ def db_delete_parent(self, parent):
+ self._db_parent = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBProvEntity(object):
+
+ vtType = 'prov_entity'
+
+ def __init__(self, id=None, prov_type=None, prov_label=None, prov_value=None, vt_id=None, vt_type=None, vt_desc=None, vt_package=None, vt_version=None, vt_cache=None, vt_location_x=None, vt_location_y=None, is_part_of=None):
+ self._db_id = id
+ self._db_prov_type = prov_type
+ self._db_prov_label = prov_label
+ self._db_prov_value = prov_value
+ self._db_vt_id = vt_id
+ self._db_vt_type = vt_type
+ self._db_vt_desc = vt_desc
+ self._db_vt_package = vt_package
+ self._db_vt_version = vt_version
+ self._db_vt_cache = vt_cache
+ self._db_vt_location_x = vt_location_x
+ self._db_vt_location_y = vt_location_y
+ self.db_deleted_is_part_of = []
+ self._db_is_part_of = is_part_of
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBProvEntity.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBProvEntity(id=self._db_id,
+ prov_type=self._db_prov_type,
+ prov_label=self._db_prov_label,
+ prov_value=self._db_prov_value,
+ vt_id=self._db_vt_id,
+ vt_type=self._db_vt_type,
+ vt_desc=self._db_vt_desc,
+ vt_package=self._db_vt_package,
+ vt_version=self._db_vt_version,
+ vt_cache=self._db_vt_cache,
+ vt_location_x=self._db_vt_location_x,
+ vt_location_y=self._db_vt_location_y)
+ if self._db_is_part_of is not None:
+ cp._db_is_part_of = self._db_is_part_of.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBProvEntity()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'prov_type' in class_dict:
+ res = class_dict['prov_type'](old_obj, trans_dict)
+ new_obj.db_prov_type = res
+ elif hasattr(old_obj, 'db_prov_type') and old_obj.db_prov_type is not None:
+ new_obj.db_prov_type = old_obj.db_prov_type
+ if 'prov_label' in class_dict:
+ res = class_dict['prov_label'](old_obj, trans_dict)
+ new_obj.db_prov_label = res
+ elif hasattr(old_obj, 'db_prov_label') and old_obj.db_prov_label is not None:
+ new_obj.db_prov_label = old_obj.db_prov_label
+ if 'prov_value' in class_dict:
+ res = class_dict['prov_value'](old_obj, trans_dict)
+ new_obj.db_prov_value = res
+ elif hasattr(old_obj, 'db_prov_value') and old_obj.db_prov_value is not None:
+ new_obj.db_prov_value = old_obj.db_prov_value
+ if 'vt_id' in class_dict:
+ res = class_dict['vt_id'](old_obj, trans_dict)
+ new_obj.db_vt_id = res
+ elif hasattr(old_obj, 'db_vt_id') and old_obj.db_vt_id is not None:
+ new_obj.db_vt_id = old_obj.db_vt_id
+ if 'vt_type' in class_dict:
+ res = class_dict['vt_type'](old_obj, trans_dict)
+ new_obj.db_vt_type = res
+ elif hasattr(old_obj, 'db_vt_type') and old_obj.db_vt_type is not None:
+ new_obj.db_vt_type = old_obj.db_vt_type
+ if 'vt_desc' in class_dict:
+ res = class_dict['vt_desc'](old_obj, trans_dict)
+ new_obj.db_vt_desc = res
+ elif hasattr(old_obj, 'db_vt_desc') and old_obj.db_vt_desc is not None:
+ new_obj.db_vt_desc = old_obj.db_vt_desc
+ if 'vt_package' in class_dict:
+ res = class_dict['vt_package'](old_obj, trans_dict)
+ new_obj.db_vt_package = res
+ elif hasattr(old_obj, 'db_vt_package') and old_obj.db_vt_package is not None:
+ new_obj.db_vt_package = old_obj.db_vt_package
+ if 'vt_version' in class_dict:
+ res = class_dict['vt_version'](old_obj, trans_dict)
+ new_obj.db_vt_version = res
+ elif hasattr(old_obj, 'db_vt_version') and old_obj.db_vt_version is not None:
+ new_obj.db_vt_version = old_obj.db_vt_version
+ if 'vt_cache' in class_dict:
+ res = class_dict['vt_cache'](old_obj, trans_dict)
+ new_obj.db_vt_cache = res
+ elif hasattr(old_obj, 'db_vt_cache') and old_obj.db_vt_cache is not None:
+ new_obj.db_vt_cache = old_obj.db_vt_cache
+ if 'vt_location_x' in class_dict:
+ res = class_dict['vt_location_x'](old_obj, trans_dict)
+ new_obj.db_vt_location_x = res
+ elif hasattr(old_obj, 'db_vt_location_x') and old_obj.db_vt_location_x is not None:
+ new_obj.db_vt_location_x = old_obj.db_vt_location_x
+ if 'vt_location_y' in class_dict:
+ res = class_dict['vt_location_y'](old_obj, trans_dict)
+ new_obj.db_vt_location_y = res
+ elif hasattr(old_obj, 'db_vt_location_y') and old_obj.db_vt_location_y is not None:
+ new_obj.db_vt_location_y = old_obj.db_vt_location_y
+ if 'is_part_of' in class_dict:
+ res = class_dict['is_part_of'](old_obj, trans_dict)
+ new_obj.db_is_part_of = res
+ elif hasattr(old_obj, 'db_is_part_of') and old_obj.db_is_part_of is not None:
+ obj = old_obj.db_is_part_of
+ new_obj.db_add_is_part_of(DBIsPartOf.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_is_part_of') and hasattr(new_obj, 'db_deleted_is_part_of'):
+ for obj in old_obj.db_deleted_is_part_of:
+ n_obj = DBIsPartOf.update_version(obj, trans_dict)
+ new_obj.db_deleted_is_part_of.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_is_part_of is not None:
+ children.extend(self._db_is_part_of.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_is_part_of = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_is_part_of)
+ if remove:
+ self.db_deleted_is_part_of = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_is_part_of is not None and self._db_is_part_of.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_prov_type(self):
+ return self._db_prov_type
+ def __set_db_prov_type(self, prov_type):
+ self._db_prov_type = prov_type
+ self.is_dirty = True
+ db_prov_type = property(__get_db_prov_type, __set_db_prov_type)
+ def db_add_prov_type(self, prov_type):
+ self._db_prov_type = prov_type
+ def db_change_prov_type(self, prov_type):
+ self._db_prov_type = prov_type
+ def db_delete_prov_type(self, prov_type):
+ self._db_prov_type = None
+
+ def __get_db_prov_label(self):
+ return self._db_prov_label
+ def __set_db_prov_label(self, prov_label):
+ self._db_prov_label = prov_label
+ self.is_dirty = True
+ db_prov_label = property(__get_db_prov_label, __set_db_prov_label)
+ def db_add_prov_label(self, prov_label):
+ self._db_prov_label = prov_label
+ def db_change_prov_label(self, prov_label):
+ self._db_prov_label = prov_label
+ def db_delete_prov_label(self, prov_label):
+ self._db_prov_label = None
+
+ def __get_db_prov_value(self):
+ return self._db_prov_value
+ def __set_db_prov_value(self, prov_value):
+ self._db_prov_value = prov_value
+ self.is_dirty = True
+ db_prov_value = property(__get_db_prov_value, __set_db_prov_value)
+ def db_add_prov_value(self, prov_value):
+ self._db_prov_value = prov_value
+ def db_change_prov_value(self, prov_value):
+ self._db_prov_value = prov_value
+ def db_delete_prov_value(self, prov_value):
+ self._db_prov_value = None
+
+ def __get_db_vt_id(self):
+ return self._db_vt_id
+ def __set_db_vt_id(self, vt_id):
+ self._db_vt_id = vt_id
+ self.is_dirty = True
+ db_vt_id = property(__get_db_vt_id, __set_db_vt_id)
+ def db_add_vt_id(self, vt_id):
+ self._db_vt_id = vt_id
+ def db_change_vt_id(self, vt_id):
+ self._db_vt_id = vt_id
+ def db_delete_vt_id(self, vt_id):
+ self._db_vt_id = None
+
+ def __get_db_vt_type(self):
+ return self._db_vt_type
+ def __set_db_vt_type(self, vt_type):
+ self._db_vt_type = vt_type
+ self.is_dirty = True
+ db_vt_type = property(__get_db_vt_type, __set_db_vt_type)
+ def db_add_vt_type(self, vt_type):
+ self._db_vt_type = vt_type
+ def db_change_vt_type(self, vt_type):
+ self._db_vt_type = vt_type
+ def db_delete_vt_type(self, vt_type):
+ self._db_vt_type = None
+
+ def __get_db_vt_desc(self):
+ return self._db_vt_desc
+ def __set_db_vt_desc(self, vt_desc):
+ self._db_vt_desc = vt_desc
+ self.is_dirty = True
+ db_vt_desc = property(__get_db_vt_desc, __set_db_vt_desc)
+ def db_add_vt_desc(self, vt_desc):
+ self._db_vt_desc = vt_desc
+ def db_change_vt_desc(self, vt_desc):
+ self._db_vt_desc = vt_desc
+ def db_delete_vt_desc(self, vt_desc):
+ self._db_vt_desc = None
+
+ def __get_db_vt_package(self):
+ return self._db_vt_package
+ def __set_db_vt_package(self, vt_package):
+ self._db_vt_package = vt_package
+ self.is_dirty = True
+ db_vt_package = property(__get_db_vt_package, __set_db_vt_package)
+ def db_add_vt_package(self, vt_package):
+ self._db_vt_package = vt_package
+ def db_change_vt_package(self, vt_package):
+ self._db_vt_package = vt_package
+ def db_delete_vt_package(self, vt_package):
+ self._db_vt_package = None
+
+ def __get_db_vt_version(self):
+ return self._db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self._db_vt_version = None
+
+ def __get_db_vt_cache(self):
+ return self._db_vt_cache
+ def __set_db_vt_cache(self, vt_cache):
+ self._db_vt_cache = vt_cache
+ self.is_dirty = True
+ db_vt_cache = property(__get_db_vt_cache, __set_db_vt_cache)
+ def db_add_vt_cache(self, vt_cache):
+ self._db_vt_cache = vt_cache
+ def db_change_vt_cache(self, vt_cache):
+ self._db_vt_cache = vt_cache
+ def db_delete_vt_cache(self, vt_cache):
+ self._db_vt_cache = None
+
+ def __get_db_vt_location_x(self):
+ return self._db_vt_location_x
+ def __set_db_vt_location_x(self, vt_location_x):
+ self._db_vt_location_x = vt_location_x
+ self.is_dirty = True
+ db_vt_location_x = property(__get_db_vt_location_x, __set_db_vt_location_x)
+ def db_add_vt_location_x(self, vt_location_x):
+ self._db_vt_location_x = vt_location_x
+ def db_change_vt_location_x(self, vt_location_x):
+ self._db_vt_location_x = vt_location_x
+ def db_delete_vt_location_x(self, vt_location_x):
+ self._db_vt_location_x = None
+
+ def __get_db_vt_location_y(self):
+ return self._db_vt_location_y
+ def __set_db_vt_location_y(self, vt_location_y):
+ self._db_vt_location_y = vt_location_y
+ self.is_dirty = True
+ db_vt_location_y = property(__get_db_vt_location_y, __set_db_vt_location_y)
+ def db_add_vt_location_y(self, vt_location_y):
+ self._db_vt_location_y = vt_location_y
+ def db_change_vt_location_y(self, vt_location_y):
+ self._db_vt_location_y = vt_location_y
+ def db_delete_vt_location_y(self, vt_location_y):
+ self._db_vt_location_y = None
+
+ def __get_db_is_part_of(self):
+ return self._db_is_part_of
+ def __set_db_is_part_of(self, is_part_of):
+ self._db_is_part_of = is_part_of
+ self.is_dirty = True
+ db_is_part_of = property(__get_db_is_part_of, __set_db_is_part_of)
+ def db_add_is_part_of(self, is_part_of):
+ self._db_is_part_of = is_part_of
+ def db_change_is_part_of(self, is_part_of):
+ self._db_is_part_of = is_part_of
+ def db_delete_is_part_of(self, is_part_of):
+ if not self.is_new:
+ self.db_deleted_is_part_of.append(self._db_is_part_of)
+ self._db_is_part_of = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBAnnotation(object):
+
+ vtType = 'annotation'
+
+ def __init__(self, id=None, key=None, value=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAnnotation(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAnnotation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBChange(object):
+
+ vtType = 'change'
+
+ def __init__(self, data=None, id=None, what=None, oldObjId=None, newObjId=None, parentObjId=None, parentObjType=None):
+ self.db_deleted_data = []
+ self._db_data = data
+ self._db_id = id
+ self._db_what = what
+ self._db_oldObjId = oldObjId
+ self._db_newObjId = newObjId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBChange.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBChange(id=self._db_id,
+ what=self._db_what,
+ oldObjId=self._db_oldObjId,
+ newObjId=self._db_newObjId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+ if self._db_data is not None:
+ cp._db_data = self._db_data.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_oldObjId') and (self._db_what, self._db_oldObjId) in id_remap:
+ cp._db_oldObjId = id_remap[(self._db_what, self._db_oldObjId)]
+ if hasattr(self, 'db_newObjId') and (self._db_what, self._db_newObjId) in id_remap:
+ cp._db_newObjId = id_remap[(self._db_what, self._db_newObjId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBChange()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'data' in class_dict:
+ res = class_dict['data'](old_obj, trans_dict)
+ new_obj.db_data = res
+ elif hasattr(old_obj, 'db_data') and old_obj.db_data is not None:
+ obj = old_obj.db_data
+ if obj.vtType == 'module':
+ new_obj.db_add_data(DBModule.update_version(obj, trans_dict))
+ elif obj.vtType == 'location':
+ new_obj.db_add_data(DBLocation.update_version(obj, trans_dict))
+ elif obj.vtType == 'annotation':
+ new_obj.db_add_data(DBAnnotation.update_version(obj, trans_dict))
+ elif obj.vtType == 'function':
+ new_obj.db_add_data(DBFunction.update_version(obj, trans_dict))
+ elif obj.vtType == 'connection':
+ new_obj.db_add_data(DBConnection.update_version(obj, trans_dict))
+ elif obj.vtType == 'port':
+ new_obj.db_add_data(DBPort.update_version(obj, trans_dict))
+ elif obj.vtType == 'parameter':
+ new_obj.db_add_data(DBParameter.update_version(obj, trans_dict))
+ elif obj.vtType == 'portSpec':
+ new_obj.db_add_data(DBPortSpec.update_version(obj, trans_dict))
+ elif obj.vtType == 'abstraction':
+ new_obj.db_add_data(DBAbstraction.update_version(obj, trans_dict))
+ elif obj.vtType == 'group':
+ new_obj.db_add_data(DBGroup.update_version(obj, trans_dict))
+ elif obj.vtType == 'other':
+ new_obj.db_add_data(DBOther.update_version(obj, trans_dict))
+ elif obj.vtType == 'plugin_data':
+ new_obj.db_add_data(DBPluginData.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_data') and hasattr(new_obj, 'db_deleted_data'):
+ for obj in old_obj.db_deleted_data:
+ if obj.vtType == 'module':
+ n_obj = DBModule.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'location':
+ n_obj = DBLocation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'annotation':
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'function':
+ n_obj = DBFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'connection':
+ n_obj = DBConnection.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'port':
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'parameter':
+ n_obj = DBParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'portSpec':
+ n_obj = DBPortSpec.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'abstraction':
+ n_obj = DBAbstraction.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'group':
+ n_obj = DBGroup.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'other':
+ n_obj = DBOther.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ elif obj.vtType == 'plugin_data':
+ n_obj = DBPluginData.update_version(obj, trans_dict)
+ new_obj.db_deleted_data.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'oldObjId' in class_dict:
+ res = class_dict['oldObjId'](old_obj, trans_dict)
+ new_obj.db_oldObjId = res
+ elif hasattr(old_obj, 'db_oldObjId') and old_obj.db_oldObjId is not None:
+ new_obj.db_oldObjId = old_obj.db_oldObjId
+ if 'newObjId' in class_dict:
+ res = class_dict['newObjId'](old_obj, trans_dict)
+ new_obj.db_newObjId = res
+ elif hasattr(old_obj, 'db_newObjId') and old_obj.db_newObjId is not None:
+ new_obj.db_newObjId = old_obj.db_newObjId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_data is not None:
+ children.extend(self._db_data.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_data = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_data)
+ if remove:
+ self.db_deleted_data = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_data is not None and self._db_data.has_changes():
+ return True
+ return False
+ def __get_db_data(self):
+ return self._db_data
+ def __set_db_data(self, data):
+ self._db_data = data
+ self.is_dirty = True
+ db_data = property(__get_db_data, __set_db_data)
+ def db_add_data(self, data):
+ self._db_data = data
+ def db_change_data(self, data):
+ self._db_data = data
+ def db_delete_data(self, data):
+ if not self.is_new:
+ self.db_deleted_data.append(self._db_data)
+ self._db_data = None
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_oldObjId(self):
+ return self._db_oldObjId
+ def __set_db_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ self.is_dirty = True
+ db_oldObjId = property(__get_db_oldObjId, __set_db_oldObjId)
+ def db_add_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_change_oldObjId(self, oldObjId):
+ self._db_oldObjId = oldObjId
+ def db_delete_oldObjId(self, oldObjId):
+ self._db_oldObjId = None
+
+ def __get_db_newObjId(self):
+ return self._db_newObjId
+ def __set_db_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ self.is_dirty = True
+ db_newObjId = property(__get_db_newObjId, __set_db_newObjId)
+ def db_add_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_change_newObjId(self, newObjId):
+ self._db_newObjId = newObjId
+ def db_delete_newObjId(self, newObjId):
+ self._db_newObjId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmWasDerivedFrom(object):
+
+ vtType = 'opm_was_derived_from'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasDerivedFrom.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasDerivedFrom()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasDerivedFrom()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmArtifactIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmArtifactIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmArtifactIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmArtifactIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBOpmArtifacts(object):
+
+ vtType = 'opm_artifacts'
+
+ def __init__(self, artifacts=None):
+ self.db_deleted_artifacts = []
+ self.db_artifacts_id_index = {}
+ if artifacts is None:
+ self._db_artifacts = []
+ else:
+ self._db_artifacts = artifacts
+ for v in self._db_artifacts:
+ self.db_artifacts_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmArtifacts.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmArtifacts()
+ if self._db_artifacts is None:
+ cp._db_artifacts = []
+ else:
+ cp._db_artifacts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_artifacts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_artifacts_id_index = dict((v.db_id, v) for v in cp._db_artifacts)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmArtifacts()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'artifacts' in class_dict:
+ res = class_dict['artifacts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_artifact(obj)
+ elif hasattr(old_obj, 'db_artifacts') and old_obj.db_artifacts is not None:
+ for obj in old_obj.db_artifacts:
+ new_obj.db_add_artifact(DBOpmArtifact.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_artifacts') and hasattr(new_obj, 'db_deleted_artifacts'):
+ for obj in old_obj.db_deleted_artifacts:
+ n_obj = DBOpmArtifact.update_version(obj, trans_dict)
+ new_obj.db_deleted_artifacts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_artifacts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_artifact(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_artifacts)
+ if remove:
+ self.db_deleted_artifacts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_artifacts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_artifacts(self):
+ return self._db_artifacts
+ def __set_db_artifacts(self, artifacts):
+ self._db_artifacts = artifacts
+ self.is_dirty = True
+ db_artifacts = property(__get_db_artifacts, __set_db_artifacts)
+ def db_get_artifacts(self):
+ return self._db_artifacts
+ def db_add_artifact(self, artifact):
+ self.is_dirty = True
+ self._db_artifacts.append(artifact)
+ self.db_artifacts_id_index[artifact.db_id] = artifact
+ def db_change_artifact(self, artifact):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == artifact.db_id:
+ self._db_artifacts[i] = artifact
+ found = True
+ break
+ if not found:
+ self._db_artifacts.append(artifact)
+ self.db_artifacts_id_index[artifact.db_id] = artifact
+ def db_delete_artifact(self, artifact):
+ self.is_dirty = True
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == artifact.db_id:
+ if not self._db_artifacts[i].is_new:
+ self.db_deleted_artifacts.append(self._db_artifacts[i])
+ del self._db_artifacts[i]
+ break
+ del self.db_artifacts_id_index[artifact.db_id]
+ def db_get_artifact(self, key):
+ for i in xrange(len(self._db_artifacts)):
+ if self._db_artifacts[i].db_id == key:
+ return self._db_artifacts[i]
+ return None
+ def db_get_artifact_by_id(self, key):
+ return self.db_artifacts_id_index[key]
+ def db_has_artifact_with_id(self, key):
+ return key in self.db_artifacts_id_index
+
+
+
+class DBOpmWasControlledBy(object):
+
+ vtType = 'opm_was_controlled_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, starts=None, ends=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_starts = []
+ if starts is None:
+ self._db_starts = []
+ else:
+ self._db_starts = starts
+ self.db_deleted_ends = []
+ if ends is None:
+ self._db_ends = []
+ else:
+ self._db_ends = ends
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasControlledBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasControlledBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_starts is None:
+ cp._db_starts = []
+ else:
+ cp._db_starts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_starts]
+ if self._db_ends is None:
+ cp._db_ends = []
+ else:
+ cp._db_ends = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ends]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasControlledBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmAgentId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmAgentId.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'starts' in class_dict:
+ res = class_dict['starts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_start(obj)
+ elif hasattr(old_obj, 'db_starts') and old_obj.db_starts is not None:
+ for obj in old_obj.db_starts:
+ new_obj.db_add_start(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_starts') and hasattr(new_obj, 'db_deleted_starts'):
+ for obj in old_obj.db_deleted_starts:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_starts.append(n_obj)
+ if 'ends' in class_dict:
+ res = class_dict['ends'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_end(obj)
+ elif hasattr(old_obj, 'db_ends') and old_obj.db_ends is not None:
+ for obj in old_obj.db_ends:
+ new_obj.db_add_end(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_ends') and hasattr(new_obj, 'db_deleted_ends'):
+ for obj in old_obj.db_deleted_ends:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_ends.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_starts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_start(child)
+ to_del = []
+ for child in self.db_ends:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_end(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_starts)
+ children.extend(self.db_deleted_ends)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_starts = []
+ self.db_deleted_ends = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_starts:
+ if child.has_changes():
+ return True
+ for child in self._db_ends:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_starts(self):
+ return self._db_starts
+ def __set_db_starts(self, starts):
+ self._db_starts = starts
+ self.is_dirty = True
+ db_starts = property(__get_db_starts, __set_db_starts)
+ def db_get_starts(self):
+ return self._db_starts
+ def db_add_start(self, start):
+ self.is_dirty = True
+ self._db_starts.append(start)
+ def db_change_start(self, start):
+ self.is_dirty = True
+ self._db_starts.append(start)
+ def db_delete_start(self, start):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_start(self, key):
+ return None
+
+ def __get_db_ends(self):
+ return self._db_ends
+ def __set_db_ends(self, ends):
+ self._db_ends = ends
+ self.is_dirty = True
+ db_ends = property(__get_db_ends, __set_db_ends)
+ def db_get_ends(self):
+ return self._db_ends
+ def db_add_end(self, end):
+ self.is_dirty = True
+ self._db_ends.append(end)
+ def db_change_end(self, end):
+ self.is_dirty = True
+ self._db_ends.append(end)
+ def db_delete_end(self, end):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_end(self, key):
+ return None
+
+
+
+class DBOpmAgentId(object):
+
+ vtType = 'opm_agent_id'
+
+ def __init__(self, id=None):
+ self._db_id = id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgentId.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgentId(id=self._db_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_id') and ('opm_agent', self._db_id) in id_remap:
+ cp._db_id = id_remap[('opm_agent', self._db_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgentId()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+
+
+class DBGroupExec(object):
+
+ vtType = 'group_exec'
+
+ def __init__(self, item_execs=None, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, group_name=None, group_type=None, completed=None, error=None, machine_id=None, annotations=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_group_name = group_name
+ self._db_group_type = group_type
+ self._db_completed = completed
+ self._db_error = error
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBGroupExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBGroupExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ group_name=self._db_group_name,
+ group_type=self._db_group_type,
+ completed=self._db_completed,
+ error=self._db_error,
+ machine_id=self._db_machine_id)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBGroupExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'group_name' in class_dict:
+ res = class_dict['group_name'](old_obj, trans_dict)
+ new_obj.db_group_name = res
+ elif hasattr(old_obj, 'db_group_name') and old_obj.db_group_name is not None:
+ new_obj.db_group_name = old_obj.db_group_name
+ if 'group_type' in class_dict:
+ res = class_dict['group_type'](old_obj, trans_dict)
+ new_obj.db_group_type = res
+ elif hasattr(old_obj, 'db_group_type') and old_obj.db_group_type is not None:
+ new_obj.db_group_type = old_obj.db_group_type
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_group_name(self):
+ return self._db_group_name
+ def __set_db_group_name(self, group_name):
+ self._db_group_name = group_name
+ self.is_dirty = True
+ db_group_name = property(__get_db_group_name, __set_db_group_name)
+ def db_add_group_name(self, group_name):
+ self._db_group_name = group_name
+ def db_change_group_name(self, group_name):
+ self._db_group_name = group_name
+ def db_delete_group_name(self, group_name):
+ self._db_group_name = None
+
+ def __get_db_group_type(self):
+ return self._db_group_type
+ def __set_db_group_type(self, group_type):
+ self._db_group_type = group_type
+ self.is_dirty = True
+ db_group_type = property(__get_db_group_type, __set_db_group_type)
+ def db_add_group_type(self, group_type):
+ self._db_group_type = group_type
+ def db_change_group_type(self, group_type):
+ self._db_group_type = group_type
+ def db_delete_group_type(self, group_type):
+ self._db_group_type = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmTime(object):
+
+ vtType = 'opm_time'
+
+ def __init__(self, no_later_than=None, no_earlier_than=None, clock_id=None):
+ self._db_no_later_than = no_later_than
+ self._db_no_earlier_than = no_earlier_than
+ self._db_clock_id = clock_id
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmTime.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmTime(no_later_than=self._db_no_later_than,
+ no_earlier_than=self._db_no_earlier_than,
+ clock_id=self._db_clock_id)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmTime()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'no_later_than' in class_dict:
+ res = class_dict['no_later_than'](old_obj, trans_dict)
+ new_obj.db_no_later_than = res
+ elif hasattr(old_obj, 'db_no_later_than') and old_obj.db_no_later_than is not None:
+ new_obj.db_no_later_than = old_obj.db_no_later_than
+ if 'no_earlier_than' in class_dict:
+ res = class_dict['no_earlier_than'](old_obj, trans_dict)
+ new_obj.db_no_earlier_than = res
+ elif hasattr(old_obj, 'db_no_earlier_than') and old_obj.db_no_earlier_than is not None:
+ new_obj.db_no_earlier_than = old_obj.db_no_earlier_than
+ if 'clock_id' in class_dict:
+ res = class_dict['clock_id'](old_obj, trans_dict)
+ new_obj.db_clock_id = res
+ elif hasattr(old_obj, 'db_clock_id') and old_obj.db_clock_id is not None:
+ new_obj.db_clock_id = old_obj.db_clock_id
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_no_later_than(self):
+ return self._db_no_later_than
+ def __set_db_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ self.is_dirty = True
+ db_no_later_than = property(__get_db_no_later_than, __set_db_no_later_than)
+ def db_add_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ def db_change_no_later_than(self, no_later_than):
+ self._db_no_later_than = no_later_than
+ def db_delete_no_later_than(self, no_later_than):
+ self._db_no_later_than = None
+
+ def __get_db_no_earlier_than(self):
+ return self._db_no_earlier_than
+ def __set_db_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ self.is_dirty = True
+ db_no_earlier_than = property(__get_db_no_earlier_than, __set_db_no_earlier_than)
+ def db_add_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ def db_change_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = no_earlier_than
+ def db_delete_no_earlier_than(self, no_earlier_than):
+ self._db_no_earlier_than = None
+
+ def __get_db_clock_id(self):
+ return self._db_clock_id
+ def __set_db_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ self.is_dirty = True
+ db_clock_id = property(__get_db_clock_id, __set_db_clock_id)
+ def db_add_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ def db_change_clock_id(self, clock_id):
+ self._db_clock_id = clock_id
+ def db_delete_clock_id(self, clock_id):
+ self._db_clock_id = None
+
+
+
+class DBPackage(object):
+
+ vtType = 'package'
+
+ def __init__(self, id=None, name=None, identifier=None, codepath=None, load_configuration=None, version=None, description=None, module_descriptors=None):
+ self._db_id = id
+ self._db_name = name
+ self._db_identifier = identifier
+ self._db_codepath = codepath
+ self._db_load_configuration = load_configuration
+ self._db_version = version
+ self._db_description = description
+ self.db_deleted_module_descriptors = []
+ self.db_module_descriptors_id_index = {}
+ self.db_module_descriptors_name_index = {}
+ if module_descriptors is None:
+ self._db_module_descriptors = []
+ else:
+ self._db_module_descriptors = module_descriptors
+ for v in self._db_module_descriptors:
+ self.db_module_descriptors_id_index[v.db_id] = v
+ self.db_module_descriptors_name_index[(v.db_name,v.db_namespace,v.db_version)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPackage.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPackage(id=self._db_id,
+ name=self._db_name,
+ identifier=self._db_identifier,
+ codepath=self._db_codepath,
+ load_configuration=self._db_load_configuration,
+ version=self._db_version,
+ description=self._db_description)
+ if self._db_module_descriptors is None:
+ cp._db_module_descriptors = []
+ else:
+ cp._db_module_descriptors = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_module_descriptors]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_module_descriptors_id_index = dict((v.db_id, v) for v in cp._db_module_descriptors)
+ cp.db_module_descriptors_name_index = dict(((v.db_name,v.db_namespace,v.db_version), v) for v in cp._db_module_descriptors)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPackage()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'identifier' in class_dict:
+ res = class_dict['identifier'](old_obj, trans_dict)
+ new_obj.db_identifier = res
+ elif hasattr(old_obj, 'db_identifier') and old_obj.db_identifier is not None:
+ new_obj.db_identifier = old_obj.db_identifier
+ if 'codepath' in class_dict:
+ res = class_dict['codepath'](old_obj, trans_dict)
+ new_obj.db_codepath = res
+ elif hasattr(old_obj, 'db_codepath') and old_obj.db_codepath is not None:
+ new_obj.db_codepath = old_obj.db_codepath
+ if 'load_configuration' in class_dict:
+ res = class_dict['load_configuration'](old_obj, trans_dict)
+ new_obj.db_load_configuration = res
+ elif hasattr(old_obj, 'db_load_configuration') and old_obj.db_load_configuration is not None:
+ new_obj.db_load_configuration = old_obj.db_load_configuration
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'description' in class_dict:
+ res = class_dict['description'](old_obj, trans_dict)
+ new_obj.db_description = res
+ elif hasattr(old_obj, 'db_description') and old_obj.db_description is not None:
+ new_obj.db_description = old_obj.db_description
+ if 'module_descriptors' in class_dict:
+ res = class_dict['module_descriptors'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_module_descriptor(obj)
+ elif hasattr(old_obj, 'db_module_descriptors') and old_obj.db_module_descriptors is not None:
+ for obj in old_obj.db_module_descriptors:
+ new_obj.db_add_module_descriptor(DBModuleDescriptor.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_module_descriptors') and hasattr(new_obj, 'db_deleted_module_descriptors'):
+ for obj in old_obj.db_deleted_module_descriptors:
+ n_obj = DBModuleDescriptor.update_version(obj, trans_dict)
+ new_obj.db_deleted_module_descriptors.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_module_descriptors:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_module_descriptor(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_module_descriptors)
+ if remove:
+ self.db_deleted_module_descriptors = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_module_descriptors:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_identifier(self):
+ return self._db_identifier
+ def __set_db_identifier(self, identifier):
+ self._db_identifier = identifier
+ self.is_dirty = True
+ db_identifier = property(__get_db_identifier, __set_db_identifier)
+ def db_add_identifier(self, identifier):
+ self._db_identifier = identifier
+ def db_change_identifier(self, identifier):
+ self._db_identifier = identifier
+ def db_delete_identifier(self, identifier):
+ self._db_identifier = None
+
+ def __get_db_codepath(self):
+ return self._db_codepath
+ def __set_db_codepath(self, codepath):
+ self._db_codepath = codepath
+ self.is_dirty = True
+ db_codepath = property(__get_db_codepath, __set_db_codepath)
+ def db_add_codepath(self, codepath):
+ self._db_codepath = codepath
+ def db_change_codepath(self, codepath):
+ self._db_codepath = codepath
+ def db_delete_codepath(self, codepath):
+ self._db_codepath = None
+
+ def __get_db_load_configuration(self):
+ return self._db_load_configuration
+ def __set_db_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ self.is_dirty = True
+ db_load_configuration = property(__get_db_load_configuration, __set_db_load_configuration)
+ def db_add_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ def db_change_load_configuration(self, load_configuration):
+ self._db_load_configuration = load_configuration
+ def db_delete_load_configuration(self, load_configuration):
+ self._db_load_configuration = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_description(self):
+ return self._db_description
+ def __set_db_description(self, description):
+ self._db_description = description
+ self.is_dirty = True
+ db_description = property(__get_db_description, __set_db_description)
+ def db_add_description(self, description):
+ self._db_description = description
+ def db_change_description(self, description):
+ self._db_description = description
+ def db_delete_description(self, description):
+ self._db_description = None
+
+ def __get_db_module_descriptors(self):
+ return self._db_module_descriptors
+ def __set_db_module_descriptors(self, module_descriptors):
+ self._db_module_descriptors = module_descriptors
+ self.is_dirty = True
+ db_module_descriptors = property(__get_db_module_descriptors, __set_db_module_descriptors)
+ def db_get_module_descriptors(self):
+ return self._db_module_descriptors
+ def db_add_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ self._db_module_descriptors.append(module_descriptor)
+ self.db_module_descriptors_id_index[module_descriptor.db_id] = module_descriptor
+ self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)] = module_descriptor
+ def db_change_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == module_descriptor.db_id:
+ self._db_module_descriptors[i] = module_descriptor
+ found = True
+ break
+ if not found:
+ self._db_module_descriptors.append(module_descriptor)
+ self.db_module_descriptors_id_index[module_descriptor.db_id] = module_descriptor
+ self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)] = module_descriptor
+ def db_delete_module_descriptor(self, module_descriptor):
+ self.is_dirty = True
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == module_descriptor.db_id:
+ if not self._db_module_descriptors[i].is_new:
+ self.db_deleted_module_descriptors.append(self._db_module_descriptors[i])
+ del self._db_module_descriptors[i]
+ break
+ del self.db_module_descriptors_id_index[module_descriptor.db_id]
+ del self.db_module_descriptors_name_index[(module_descriptor.db_name,module_descriptor.db_namespace,module_descriptor.db_version)]
+ def db_get_module_descriptor(self, key):
+ for i in xrange(len(self._db_module_descriptors)):
+ if self._db_module_descriptors[i].db_id == key:
+ return self._db_module_descriptors[i]
+ return None
+ def db_get_module_descriptor_by_id(self, key):
+ return self.db_module_descriptors_id_index[key]
+ def db_has_module_descriptor_with_id(self, key):
+ return key in self.db_module_descriptors_id_index
+ def db_get_module_descriptor_by_name(self, key):
+ return self.db_module_descriptors_name_index[key]
+ def db_has_module_descriptor_with_name(self, key):
+ return key in self.db_module_descriptors_name_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBWorkflowExec(object):
+
+ vtType = 'workflow_exec'
+
+ def __init__(self, item_execs=None, id=None, user=None, ip=None, session=None, vt_version=None, ts_start=None, ts_end=None, parent_id=None, parent_type=None, parent_version=None, completed=None, name=None, annotations=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_user = user
+ self._db_ip = ip
+ self._db_session = session
+ self._db_vt_version = vt_version
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_parent_id = parent_id
+ self._db_parent_type = parent_type
+ self._db_parent_version = parent_version
+ self._db_completed = completed
+ self._db_name = name
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBWorkflowExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBWorkflowExec(id=self._db_id,
+ user=self._db_user,
+ ip=self._db_ip,
+ session=self._db_session,
+ vt_version=self._db_vt_version,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ parent_id=self._db_parent_id,
+ parent_type=self._db_parent_type,
+ parent_version=self._db_parent_version,
+ completed=self._db_completed,
+ name=self._db_name)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflowExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'ip' in class_dict:
+ res = class_dict['ip'](old_obj, trans_dict)
+ new_obj.db_ip = res
+ elif hasattr(old_obj, 'db_ip') and old_obj.db_ip is not None:
+ new_obj.db_ip = old_obj.db_ip
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'vt_version' in class_dict:
+ res = class_dict['vt_version'](old_obj, trans_dict)
+ new_obj.db_vt_version = res
+ elif hasattr(old_obj, 'db_vt_version') and old_obj.db_vt_version is not None:
+ new_obj.db_vt_version = old_obj.db_vt_version
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'parent_id' in class_dict:
+ res = class_dict['parent_id'](old_obj, trans_dict)
+ new_obj.db_parent_id = res
+ elif hasattr(old_obj, 'db_parent_id') and old_obj.db_parent_id is not None:
+ new_obj.db_parent_id = old_obj.db_parent_id
+ if 'parent_type' in class_dict:
+ res = class_dict['parent_type'](old_obj, trans_dict)
+ new_obj.db_parent_type = res
+ elif hasattr(old_obj, 'db_parent_type') and old_obj.db_parent_type is not None:
+ new_obj.db_parent_type = old_obj.db_parent_type
+ if 'parent_version' in class_dict:
+ res = class_dict['parent_version'](old_obj, trans_dict)
+ new_obj.db_parent_version = res
+ elif hasattr(old_obj, 'db_parent_version') and old_obj.db_parent_version is not None:
+ new_obj.db_parent_version = old_obj.db_parent_version
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_ip(self):
+ return self._db_ip
+ def __set_db_ip(self, ip):
+ self._db_ip = ip
+ self.is_dirty = True
+ db_ip = property(__get_db_ip, __set_db_ip)
+ def db_add_ip(self, ip):
+ self._db_ip = ip
+ def db_change_ip(self, ip):
+ self._db_ip = ip
+ def db_delete_ip(self, ip):
+ self._db_ip = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_vt_version(self):
+ return self._db_vt_version
+ def __set_db_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ self.is_dirty = True
+ db_vt_version = property(__get_db_vt_version, __set_db_vt_version)
+ def db_add_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_change_vt_version(self, vt_version):
+ self._db_vt_version = vt_version
+ def db_delete_vt_version(self, vt_version):
+ self._db_vt_version = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_parent_id(self):
+ return self._db_parent_id
+ def __set_db_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ self.is_dirty = True
+ db_parent_id = property(__get_db_parent_id, __set_db_parent_id)
+ def db_add_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_change_parent_id(self, parent_id):
+ self._db_parent_id = parent_id
+ def db_delete_parent_id(self, parent_id):
+ self._db_parent_id = None
+
+ def __get_db_parent_type(self):
+ return self._db_parent_type
+ def __set_db_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ self.is_dirty = True
+ db_parent_type = property(__get_db_parent_type, __set_db_parent_type)
+ def db_add_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_change_parent_type(self, parent_type):
+ self._db_parent_type = parent_type
+ def db_delete_parent_type(self, parent_type):
+ self._db_parent_type = None
+
+ def __get_db_parent_version(self):
+ return self._db_parent_version
+ def __set_db_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ self.is_dirty = True
+ db_parent_version = property(__get_db_parent_version, __set_db_parent_version)
+ def db_add_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_change_parent_version(self, parent_version):
+ self._db_parent_version = parent_version
+ def db_delete_parent_version(self, parent_version):
+ self._db_parent_version = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBParameterExploration(object):
+
+ vtType = 'parameter_exploration'
+
+ def __init__(self, id=None, action_id=None, name=None, date=None, user=None, dims=None, layout=None, functions=None):
+ self._db_id = id
+ self._db_action_id = action_id
+ self._db_name = name
+ self._db_date = date
+ self._db_user = user
+ self._db_dims = dims
+ self._db_layout = layout
+ self.db_deleted_functions = []
+ self.db_functions_id_index = {}
+ if functions is None:
+ self._db_functions = []
+ else:
+ self._db_functions = functions
+ for v in self._db_functions:
+ self.db_functions_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBParameterExploration.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBParameterExploration(id=self._db_id,
+ action_id=self._db_action_id,
+ name=self._db_name,
+ date=self._db_date,
+ user=self._db_user,
+ dims=self._db_dims,
+ layout=self._db_layout)
+ if self._db_functions is None:
+ cp._db_functions = []
+ else:
+ cp._db_functions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_functions]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_action_id') and ('action', self._db_action_id) in id_remap:
+ cp._db_action_id = id_remap[('action', self._db_action_id)]
+
+ # recreate indices and set flags
+ cp.db_functions_id_index = dict((v.db_id, v) for v in cp._db_functions)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBParameterExploration()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'action_id' in class_dict:
+ res = class_dict['action_id'](old_obj, trans_dict)
+ new_obj.db_action_id = res
+ elif hasattr(old_obj, 'db_action_id') and old_obj.db_action_id is not None:
+ new_obj.db_action_id = old_obj.db_action_id
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'dims' in class_dict:
+ res = class_dict['dims'](old_obj, trans_dict)
+ new_obj.db_dims = res
+ elif hasattr(old_obj, 'db_dims') and old_obj.db_dims is not None:
+ new_obj.db_dims = old_obj.db_dims
+ if 'layout' in class_dict:
+ res = class_dict['layout'](old_obj, trans_dict)
+ new_obj.db_layout = res
+ elif hasattr(old_obj, 'db_layout') and old_obj.db_layout is not None:
+ new_obj.db_layout = old_obj.db_layout
+ if 'functions' in class_dict:
+ res = class_dict['functions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_function(obj)
+ elif hasattr(old_obj, 'db_functions') and old_obj.db_functions is not None:
+ for obj in old_obj.db_functions:
+ new_obj.db_add_function(DBPEFunction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_functions') and hasattr(new_obj, 'db_deleted_functions'):
+ for obj in old_obj.db_deleted_functions:
+ n_obj = DBPEFunction.update_version(obj, trans_dict)
+ new_obj.db_deleted_functions.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_functions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_function(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_functions)
+ if remove:
+ self.db_deleted_functions = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_functions:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_action_id(self):
+ return self._db_action_id
+ def __set_db_action_id(self, action_id):
+ self._db_action_id = action_id
+ self.is_dirty = True
+ db_action_id = property(__get_db_action_id, __set_db_action_id)
+ def db_add_action_id(self, action_id):
+ self._db_action_id = action_id
+ def db_change_action_id(self, action_id):
+ self._db_action_id = action_id
+ def db_delete_action_id(self, action_id):
+ self._db_action_id = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_dims(self):
+ return self._db_dims
+ def __set_db_dims(self, dims):
+ self._db_dims = dims
+ self.is_dirty = True
+ db_dims = property(__get_db_dims, __set_db_dims)
+ def db_add_dims(self, dims):
+ self._db_dims = dims
+ def db_change_dims(self, dims):
+ self._db_dims = dims
+ def db_delete_dims(self, dims):
+ self._db_dims = None
+
+ def __get_db_layout(self):
+ return self._db_layout
+ def __set_db_layout(self, layout):
+ self._db_layout = layout
+ self.is_dirty = True
+ db_layout = property(__get_db_layout, __set_db_layout)
+ def db_add_layout(self, layout):
+ self._db_layout = layout
+ def db_change_layout(self, layout):
+ self._db_layout = layout
+ def db_delete_layout(self, layout):
+ self._db_layout = None
+
+ def __get_db_functions(self):
+ return self._db_functions
+ def __set_db_functions(self, functions):
+ self._db_functions = functions
+ self.is_dirty = True
+ db_functions = property(__get_db_functions, __set_db_functions)
+ def db_get_functions(self):
+ return self._db_functions
+ def db_add_function(self, function):
+ self.is_dirty = True
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_change_function(self, function):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ self._db_functions[i] = function
+ found = True
+ break
+ if not found:
+ self._db_functions.append(function)
+ self.db_functions_id_index[function.db_id] = function
+ def db_delete_function(self, function):
+ self.is_dirty = True
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == function.db_id:
+ if not self._db_functions[i].is_new:
+ self.db_deleted_functions.append(self._db_functions[i])
+ del self._db_functions[i]
+ break
+ del self.db_functions_id_index[function.db_id]
+ def db_get_function(self, key):
+ for i in xrange(len(self._db_functions)):
+ if self._db_functions[i].db_id == key:
+ return self._db_functions[i]
+ return None
+ def db_get_function_by_id(self, key):
+ return self.db_functions_id_index[key]
+ def db_has_function_with_id(self, key):
+ return key in self.db_functions_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBLoopExec(object):
+
+ vtType = 'loop_exec'
+
+ def __init__(self, item_execs=None, id=None, ts_start=None, ts_end=None, iteration=None, completed=None, error=None):
+ self.db_deleted_item_execs = []
+ self.db_item_execs_id_index = {}
+ if item_execs is None:
+ self._db_item_execs = []
+ else:
+ self._db_item_execs = item_execs
+ for v in self._db_item_execs:
+ self.db_item_execs_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_iteration = iteration
+ self._db_completed = completed
+ self._db_error = error
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBLoopExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBLoopExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ iteration=self._db_iteration,
+ completed=self._db_completed,
+ error=self._db_error)
+ if self._db_item_execs is None:
+ cp._db_item_execs = []
+ else:
+ cp._db_item_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_item_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_item_execs_id_index = dict((v.db_id, v) for v in cp._db_item_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLoopExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'item_execs' in class_dict:
+ res = class_dict['item_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_item_exec(obj)
+ elif hasattr(old_obj, 'db_item_execs') and old_obj.db_item_execs is not None:
+ for obj in old_obj.db_item_execs:
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_item_exec(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_item_exec(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_item_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_item_execs') and hasattr(new_obj, 'db_deleted_item_execs'):
+ for obj in old_obj.db_deleted_item_execs:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_item_execs.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'iteration' in class_dict:
+ res = class_dict['iteration'](old_obj, trans_dict)
+ new_obj.db_iteration = res
+ elif hasattr(old_obj, 'db_iteration') and old_obj.db_iteration is not None:
+ new_obj.db_iteration = old_obj.db_iteration
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_item_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_item_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_item_execs)
+ if remove:
+ self.db_deleted_item_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_item_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_item_execs(self):
+ return self._db_item_execs
+ def __set_db_item_execs(self, item_execs):
+ self._db_item_execs = item_execs
+ self.is_dirty = True
+ db_item_execs = property(__get_db_item_execs, __set_db_item_execs)
+ def db_get_item_execs(self):
+ return self._db_item_execs
+ def db_add_item_exec(self, item_exec):
+ self.is_dirty = True
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_change_item_exec(self, item_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ self._db_item_execs[i] = item_exec
+ found = True
+ break
+ if not found:
+ self._db_item_execs.append(item_exec)
+ self.db_item_execs_id_index[item_exec.db_id] = item_exec
+ def db_delete_item_exec(self, item_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == item_exec.db_id:
+ if not self._db_item_execs[i].is_new:
+ self.db_deleted_item_execs.append(self._db_item_execs[i])
+ del self._db_item_execs[i]
+ break
+ del self.db_item_execs_id_index[item_exec.db_id]
+ def db_get_item_exec(self, key):
+ for i in xrange(len(self._db_item_execs)):
+ if self._db_item_execs[i].db_id == key:
+ return self._db_item_execs[i]
+ return None
+ def db_get_item_exec_by_id(self, key):
+ return self.db_item_execs_id_index[key]
+ def db_has_item_exec_with_id(self, key):
+ return key in self.db_item_execs_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_iteration(self):
+ return self._db_iteration
+ def __set_db_iteration(self, iteration):
+ self._db_iteration = iteration
+ self.is_dirty = True
+ db_iteration = property(__get_db_iteration, __set_db_iteration)
+ def db_add_iteration(self, iteration):
+ self._db_iteration = iteration
+ def db_change_iteration(self, iteration):
+ self._db_iteration = iteration
+ def db_delete_iteration(self, iteration):
+ self._db_iteration = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmWasTriggeredBy(object):
+
+ vtType = 'opm_was_triggered_by'
+
+ def __init__(self, effect=None, role=None, cause=None, accounts=None, opm_times=None):
+ self.db_deleted_effect = []
+ self._db_effect = effect
+ self.db_deleted_role = []
+ self._db_role = role
+ self.db_deleted_cause = []
+ self._db_cause = cause
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.db_deleted_opm_times = []
+ if opm_times is None:
+ self._db_opm_times = []
+ else:
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmWasTriggeredBy.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmWasTriggeredBy()
+ if self._db_effect is not None:
+ cp._db_effect = self._db_effect.do_copy(new_ids, id_scope, id_remap)
+ if self._db_role is not None:
+ cp._db_role = self._db_role.do_copy(new_ids, id_scope, id_remap)
+ if self._db_cause is not None:
+ cp._db_cause = self._db_cause.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+ if self._db_opm_times is None:
+ cp._db_opm_times = []
+ else:
+ cp._db_opm_times = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_opm_times]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmWasTriggeredBy()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'effect' in class_dict:
+ res = class_dict['effect'](old_obj, trans_dict)
+ new_obj.db_effect = res
+ elif hasattr(old_obj, 'db_effect') and old_obj.db_effect is not None:
+ obj = old_obj.db_effect
+ new_obj.db_add_effect(DBOpmProcessIdEffect.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_effect') and hasattr(new_obj, 'db_deleted_effect'):
+ for obj in old_obj.db_deleted_effect:
+ n_obj = DBOpmProcessIdEffect.update_version(obj, trans_dict)
+ new_obj.db_deleted_effect.append(n_obj)
+ if 'role' in class_dict:
+ res = class_dict['role'](old_obj, trans_dict)
+ new_obj.db_role = res
+ elif hasattr(old_obj, 'db_role') and old_obj.db_role is not None:
+ obj = old_obj.db_role
+ new_obj.db_add_role(DBOpmRole.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_role') and hasattr(new_obj, 'db_deleted_role'):
+ for obj in old_obj.db_deleted_role:
+ n_obj = DBOpmRole.update_version(obj, trans_dict)
+ new_obj.db_deleted_role.append(n_obj)
+ if 'cause' in class_dict:
+ res = class_dict['cause'](old_obj, trans_dict)
+ new_obj.db_cause = res
+ elif hasattr(old_obj, 'db_cause') and old_obj.db_cause is not None:
+ obj = old_obj.db_cause
+ new_obj.db_add_cause(DBOpmProcessIdCause.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_cause') and hasattr(new_obj, 'db_deleted_cause'):
+ for obj in old_obj.db_deleted_cause:
+ n_obj = DBOpmProcessIdCause.update_version(obj, trans_dict)
+ new_obj.db_deleted_cause.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ if 'opm_times' in class_dict:
+ res = class_dict['opm_times'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_opm_time(obj)
+ elif hasattr(old_obj, 'db_opm_times') and old_obj.db_opm_times is not None:
+ for obj in old_obj.db_opm_times:
+ new_obj.db_add_opm_time(DBOpmTime.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_opm_times') and hasattr(new_obj, 'db_deleted_opm_times'):
+ for obj in old_obj.db_deleted_opm_times:
+ n_obj = DBOpmTime.update_version(obj, trans_dict)
+ new_obj.db_deleted_opm_times.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_effect is not None:
+ children.extend(self._db_effect.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_effect = None
+ if self._db_role is not None:
+ children.extend(self._db_role.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_role = None
+ if self._db_cause is not None:
+ children.extend(self._db_cause.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_cause = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ to_del = []
+ for child in self.db_opm_times:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_opm_time(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_effect)
+ children.extend(self.db_deleted_role)
+ children.extend(self.db_deleted_cause)
+ children.extend(self.db_deleted_accounts)
+ children.extend(self.db_deleted_opm_times)
+ if remove:
+ self.db_deleted_effect = []
+ self.db_deleted_role = []
+ self.db_deleted_cause = []
+ self.db_deleted_accounts = []
+ self.db_deleted_opm_times = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_effect is not None and self._db_effect.has_changes():
+ return True
+ if self._db_role is not None and self._db_role.has_changes():
+ return True
+ if self._db_cause is not None and self._db_cause.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ for child in self._db_opm_times:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_effect(self):
+ return self._db_effect
+ def __set_db_effect(self, effect):
+ self._db_effect = effect
+ self.is_dirty = True
+ db_effect = property(__get_db_effect, __set_db_effect)
+ def db_add_effect(self, effect):
+ self._db_effect = effect
+ def db_change_effect(self, effect):
+ self._db_effect = effect
+ def db_delete_effect(self, effect):
+ if not self.is_new:
+ self.db_deleted_effect.append(self._db_effect)
+ self._db_effect = None
+
+ def __get_db_role(self):
+ return self._db_role
+ def __set_db_role(self, role):
+ self._db_role = role
+ self.is_dirty = True
+ db_role = property(__get_db_role, __set_db_role)
+ def db_add_role(self, role):
+ self._db_role = role
+ def db_change_role(self, role):
+ self._db_role = role
+ def db_delete_role(self, role):
+ if not self.is_new:
+ self.db_deleted_role.append(self._db_role)
+ self._db_role = None
+
+ def __get_db_cause(self):
+ return self._db_cause
+ def __set_db_cause(self, cause):
+ self._db_cause = cause
+ self.is_dirty = True
+ db_cause = property(__get_db_cause, __set_db_cause)
+ def db_add_cause(self, cause):
+ self._db_cause = cause
+ def db_change_cause(self, cause):
+ self._db_cause = cause
+ def db_delete_cause(self, cause):
+ if not self.is_new:
+ self.db_deleted_cause.append(self._db_cause)
+ self._db_cause = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def __get_db_opm_times(self):
+ return self._db_opm_times
+ def __set_db_opm_times(self, opm_times):
+ self._db_opm_times = opm_times
+ self.is_dirty = True
+ db_opm_times = property(__get_db_opm_times, __set_db_opm_times)
+ def db_get_opm_times(self):
+ return self._db_opm_times
+ def db_add_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_change_opm_time(self, opm_time):
+ self.is_dirty = True
+ self._db_opm_times.append(opm_time)
+ def db_delete_opm_time(self, opm_time):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_opm_time(self, key):
+ return None
+
+
+
+class DBMashupActionAnnotation(object):
+
+ vtType = 'mashup_actionAnnotation'
+
+ def __init__(self, id=None, key=None, value=None, action_id=None, date=None, user=None):
+ self._db_id = id
+ self._db_key = key
+ self._db_value = value
+ self._db_action_id = action_id
+ self._db_date = date
+ self._db_user = user
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBMashupActionAnnotation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBMashupActionAnnotation(id=self._db_id,
+ key=self._db_key,
+ value=self._db_value,
+ action_id=self._db_action_id,
+ date=self._db_date,
+ user=self._db_user)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_action_id') and ('mashup_action', self._db_action_id) in id_remap:
+ cp._db_action_id = id_remap[('mashup_action', self._db_action_id)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBMashupActionAnnotation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'key' in class_dict:
+ res = class_dict['key'](old_obj, trans_dict)
+ new_obj.db_key = res
+ elif hasattr(old_obj, 'db_key') and old_obj.db_key is not None:
+ new_obj.db_key = old_obj.db_key
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ if 'action_id' in class_dict:
+ res = class_dict['action_id'](old_obj, trans_dict)
+ new_obj.db_action_id = res
+ elif hasattr(old_obj, 'db_action_id') and old_obj.db_action_id is not None:
+ new_obj.db_action_id = old_obj.db_action_id
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_key(self):
+ return self._db_key
+ def __set_db_key(self, key):
+ self._db_key = key
+ self.is_dirty = True
+ db_key = property(__get_db_key, __set_db_key)
+ def db_add_key(self, key):
+ self._db_key = key
+ def db_change_key(self, key):
+ self._db_key = key
+ def db_delete_key(self, key):
+ self._db_key = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def __get_db_action_id(self):
+ return self._db_action_id
+ def __set_db_action_id(self, action_id):
+ self._db_action_id = action_id
+ self.is_dirty = True
+ db_action_id = property(__get_db_action_id, __set_db_action_id)
+ def db_add_action_id(self, action_id):
+ self._db_action_id = action_id
+ def db_change_action_id(self, action_id):
+ self._db_action_id = action_id
+ def db_delete_action_id(self, action_id):
+ self._db_action_id = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBConnection(object):
+
+ vtType = 'connection'
+
+ def __init__(self, id=None, ports=None):
+ self._db_id = id
+ self.db_deleted_ports = []
+ self.db_ports_id_index = {}
+ self.db_ports_type_index = {}
+ if ports is None:
+ self._db_ports = []
+ else:
+ self._db_ports = ports
+ for v in self._db_ports:
+ self.db_ports_id_index[v.db_id] = v
+ self.db_ports_type_index[v.db_type] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBConnection.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBConnection(id=self._db_id)
+ if self._db_ports is None:
+ cp._db_ports = []
+ else:
+ cp._db_ports = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_ports]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_ports_id_index = dict((v.db_id, v) for v in cp._db_ports)
+ cp.db_ports_type_index = dict((v.db_type, v) for v in cp._db_ports)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBConnection()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ports' in class_dict:
+ res = class_dict['ports'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_port(obj)
+ elif hasattr(old_obj, 'db_ports') and old_obj.db_ports is not None:
+ for obj in old_obj.db_ports:
+ new_obj.db_add_port(DBPort.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_ports') and hasattr(new_obj, 'db_deleted_ports'):
+ for obj in old_obj.db_deleted_ports:
+ n_obj = DBPort.update_version(obj, trans_dict)
+ new_obj.db_deleted_ports.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_ports:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_port(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_ports)
+ if remove:
+ self.db_deleted_ports = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_ports:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ports(self):
+ return self._db_ports
+ def __set_db_ports(self, ports):
+ self._db_ports = ports
+ self.is_dirty = True
+ db_ports = property(__get_db_ports, __set_db_ports)
+ def db_get_ports(self):
+ return self._db_ports
+ def db_add_port(self, port):
+ self.is_dirty = True
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_change_port(self, port):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ self._db_ports[i] = port
+ found = True
+ break
+ if not found:
+ self._db_ports.append(port)
+ self.db_ports_id_index[port.db_id] = port
+ self.db_ports_type_index[port.db_type] = port
+ def db_delete_port(self, port):
+ self.is_dirty = True
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == port.db_id:
+ if not self._db_ports[i].is_new:
+ self.db_deleted_ports.append(self._db_ports[i])
+ del self._db_ports[i]
+ break
+ del self.db_ports_id_index[port.db_id]
+ del self.db_ports_type_index[port.db_type]
+ def db_get_port(self, key):
+ for i in xrange(len(self._db_ports)):
+ if self._db_ports[i].db_id == key:
+ return self._db_ports[i]
+ return None
+ def db_get_port_by_id(self, key):
+ return self.db_ports_id_index[key]
+ def db_has_port_with_id(self, key):
+ return key in self.db_ports_id_index
+ def db_get_port_by_type(self, key):
+ return self.db_ports_type_index[key]
+ def db_has_port_with_type(self, key):
+ return key in self.db_ports_type_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmProcess(object):
+
+ vtType = 'opm_process'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self.db_deleted_value = []
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcess.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcess(id=self._db_id)
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcess()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ new_obj.db_add_value(DBOpmProcessValue.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ n_obj = DBOpmProcessValue.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_value = None
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_value = []
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBIsPartOf(object):
+
+ vtType = 'is_part_of'
+
+ def __init__(self, prov_ref=None):
+ self._db_prov_ref = prov_ref
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBIsPartOf.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBIsPartOf(prov_ref=self._db_prov_ref)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBIsPartOf()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'prov_ref' in class_dict:
+ res = class_dict['prov_ref'](old_obj, trans_dict)
+ new_obj.db_prov_ref = res
+ elif hasattr(old_obj, 'db_prov_ref') and old_obj.db_prov_ref is not None:
+ new_obj.db_prov_ref = old_obj.db_prov_ref
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_prov_ref(self):
+ return self._db_prov_ref
+ def __set_db_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ self.is_dirty = True
+ db_prov_ref = property(__get_db_prov_ref, __set_db_prov_ref)
+ def db_add_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ def db_change_prov_ref(self, prov_ref):
+ self._db_prov_ref = prov_ref
+ def db_delete_prov_ref(self, prov_ref):
+ self._db_prov_ref = None
+
+
+
+class DBPEFunction(object):
+
+ vtType = 'pe_function'
+
+ def __init__(self, id=None, module_id=None, port_name=None, is_alias=None, parameters=None):
+ self._db_id = id
+ self._db_module_id = module_id
+ self._db_port_name = port_name
+ self._db_is_alias = is_alias
+ self.db_deleted_parameters = []
+ self.db_parameters_id_index = {}
+ if parameters is None:
+ self._db_parameters = []
+ else:
+ self._db_parameters = parameters
+ for v in self._db_parameters:
+ self.db_parameters_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBPEFunction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBPEFunction(id=self._db_id,
+ module_id=self._db_module_id,
+ port_name=self._db_port_name,
+ is_alias=self._db_is_alias)
+ if self._db_parameters is None:
+ cp._db_parameters = []
+ else:
+ cp._db_parameters = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_parameters]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+
+ # recreate indices and set flags
+ cp.db_parameters_id_index = dict((v.db_id, v) for v in cp._db_parameters)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBPEFunction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'port_name' in class_dict:
+ res = class_dict['port_name'](old_obj, trans_dict)
+ new_obj.db_port_name = res
+ elif hasattr(old_obj, 'db_port_name') and old_obj.db_port_name is not None:
+ new_obj.db_port_name = old_obj.db_port_name
+ if 'is_alias' in class_dict:
+ res = class_dict['is_alias'](old_obj, trans_dict)
+ new_obj.db_is_alias = res
+ elif hasattr(old_obj, 'db_is_alias') and old_obj.db_is_alias is not None:
+ new_obj.db_is_alias = old_obj.db_is_alias
+ if 'parameters' in class_dict:
+ res = class_dict['parameters'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_parameter(obj)
+ elif hasattr(old_obj, 'db_parameters') and old_obj.db_parameters is not None:
+ for obj in old_obj.db_parameters:
+ new_obj.db_add_parameter(DBPEParameter.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_parameters') and hasattr(new_obj, 'db_deleted_parameters'):
+ for obj in old_obj.db_deleted_parameters:
+ n_obj = DBPEParameter.update_version(obj, trans_dict)
+ new_obj.db_deleted_parameters.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_parameters:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_parameters)
+ if remove:
+ self.db_deleted_parameters = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_parameters:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_port_name(self):
+ return self._db_port_name
+ def __set_db_port_name(self, port_name):
+ self._db_port_name = port_name
+ self.is_dirty = True
+ db_port_name = property(__get_db_port_name, __set_db_port_name)
+ def db_add_port_name(self, port_name):
+ self._db_port_name = port_name
+ def db_change_port_name(self, port_name):
+ self._db_port_name = port_name
+ def db_delete_port_name(self, port_name):
+ self._db_port_name = None
+
+ def __get_db_is_alias(self):
+ return self._db_is_alias
+ def __set_db_is_alias(self, is_alias):
+ self._db_is_alias = is_alias
+ self.is_dirty = True
+ db_is_alias = property(__get_db_is_alias, __set_db_is_alias)
+ def db_add_is_alias(self, is_alias):
+ self._db_is_alias = is_alias
+ def db_change_is_alias(self, is_alias):
+ self._db_is_alias = is_alias
+ def db_delete_is_alias(self, is_alias):
+ self._db_is_alias = None
+
+ def __get_db_parameters(self):
+ return self._db_parameters
+ def __set_db_parameters(self, parameters):
+ self._db_parameters = parameters
+ self.is_dirty = True
+ db_parameters = property(__get_db_parameters, __set_db_parameters)
+ def db_get_parameters(self):
+ return self._db_parameters
+ def db_add_parameter(self, parameter):
+ self.is_dirty = True
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_change_parameter(self, parameter):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ self._db_parameters[i] = parameter
+ found = True
+ break
+ if not found:
+ self._db_parameters.append(parameter)
+ self.db_parameters_id_index[parameter.db_id] = parameter
+ def db_delete_parameter(self, parameter):
+ self.is_dirty = True
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == parameter.db_id:
+ if not self._db_parameters[i].is_new:
+ self.db_deleted_parameters.append(self._db_parameters[i])
+ del self._db_parameters[i]
+ break
+ del self.db_parameters_id_index[parameter.db_id]
+ def db_get_parameter(self, key):
+ for i in xrange(len(self._db_parameters)):
+ if self._db_parameters[i].db_id == key:
+ return self._db_parameters[i]
+ return None
+ def db_get_parameter_by_id(self, key):
+ return self.db_parameters_id_index[key]
+ def db_has_parameter_with_id(self, key):
+ return key in self.db_parameters_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmProcessValue(object):
+
+ vtType = 'opm_process_value'
+
+ def __init__(self, value=None):
+ self.db_deleted_value = []
+ self._db_value = value
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmProcessValue.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmProcessValue()
+ if self._db_value is not None:
+ cp._db_value = self._db_value.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmProcessValue()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ obj = old_obj.db_value
+ if obj.vtType == 'module_exec':
+ new_obj.db_add_value(DBModuleExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'group_exec':
+ new_obj.db_add_value(DBGroupExec.update_version(obj, trans_dict))
+ elif obj.vtType == 'loop_exec':
+ new_obj.db_add_value(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_value') and hasattr(new_obj, 'db_deleted_value'):
+ for obj in old_obj.db_deleted_value:
+ if obj.vtType == 'module_exec':
+ n_obj = DBModuleExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'group_exec':
+ n_obj = DBGroupExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ elif obj.vtType == 'loop_exec':
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_value.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_value is not None:
+ children.extend(self._db_value.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_value = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_value)
+ if remove:
+ self.db_deleted_value = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_value is not None and self._db_value.has_changes():
+ return True
+ return False
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ if not self.is_new:
+ self.db_deleted_value.append(self._db_value)
+ self._db_value = None
+
+
+
+class DBAction(object):
+
+ vtType = 'action'
+
+ def __init__(self, operations=None, id=None, prevId=None, date=None, session=None, user=None, annotations=None):
+ self.db_deleted_operations = []
+ self.db_operations_id_index = {}
+ if operations is None:
+ self._db_operations = []
+ else:
+ self._db_operations = operations
+ for v in self._db_operations:
+ self.db_operations_id_index[v.db_id] = v
+ self._db_id = id
+ self._db_prevId = prevId
+ self._db_date = date
+ self._db_session = session
+ self._db_user = user
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBAction.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBAction(id=self._db_id,
+ prevId=self._db_prevId,
+ date=self._db_date,
+ session=self._db_session,
+ user=self._db_user)
+ if self._db_operations is None:
+ cp._db_operations = []
+ else:
+ cp._db_operations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_operations]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_prevId') and ('action', self._db_prevId) in id_remap:
+ cp._db_prevId = id_remap[('action', self._db_prevId)]
+
+ # recreate indices and set flags
+ cp.db_operations_id_index = dict((v.db_id, v) for v in cp._db_operations)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBAction()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'operations' in class_dict:
+ res = class_dict['operations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_operation(obj)
+ elif hasattr(old_obj, 'db_operations') and old_obj.db_operations is not None:
+ for obj in old_obj.db_operations:
+ if obj.vtType == 'add':
+ new_obj.db_add_operation(DBAdd.update_version(obj, trans_dict))
+ elif obj.vtType == 'delete':
+ new_obj.db_add_operation(DBDelete.update_version(obj, trans_dict))
+ elif obj.vtType == 'change':
+ new_obj.db_add_operation(DBChange.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_operations') and hasattr(new_obj, 'db_deleted_operations'):
+ for obj in old_obj.db_deleted_operations:
+ if obj.vtType == 'add':
+ n_obj = DBAdd.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'delete':
+ n_obj = DBDelete.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ elif obj.vtType == 'change':
+ n_obj = DBChange.update_version(obj, trans_dict)
+ new_obj.db_deleted_operations.append(n_obj)
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'prevId' in class_dict:
+ res = class_dict['prevId'](old_obj, trans_dict)
+ new_obj.db_prevId = res
+ elif hasattr(old_obj, 'db_prevId') and old_obj.db_prevId is not None:
+ new_obj.db_prevId = old_obj.db_prevId
+ if 'date' in class_dict:
+ res = class_dict['date'](old_obj, trans_dict)
+ new_obj.db_date = res
+ elif hasattr(old_obj, 'db_date') and old_obj.db_date is not None:
+ new_obj.db_date = old_obj.db_date
+ if 'session' in class_dict:
+ res = class_dict['session'](old_obj, trans_dict)
+ new_obj.db_session = res
+ elif hasattr(old_obj, 'db_session') and old_obj.db_session is not None:
+ new_obj.db_session = old_obj.db_session
+ if 'user' in class_dict:
+ res = class_dict['user'](old_obj, trans_dict)
+ new_obj.db_user = res
+ elif hasattr(old_obj, 'db_user') and old_obj.db_user is not None:
+ new_obj.db_user = old_obj.db_user
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_operations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_operation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_operations)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_operations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_operations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_operations(self):
+ return self._db_operations
+ def __set_db_operations(self, operations):
+ self._db_operations = operations
+ self.is_dirty = True
+ db_operations = property(__get_db_operations, __set_db_operations)
+ def db_get_operations(self):
+ return self._db_operations
+ def db_add_operation(self, operation):
+ self.is_dirty = True
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_change_operation(self, operation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ self._db_operations[i] = operation
+ found = True
+ break
+ if not found:
+ self._db_operations.append(operation)
+ self.db_operations_id_index[operation.db_id] = operation
+ def db_delete_operation(self, operation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == operation.db_id:
+ if not self._db_operations[i].is_new:
+ self.db_deleted_operations.append(self._db_operations[i])
+ del self._db_operations[i]
+ break
+ del self.db_operations_id_index[operation.db_id]
+ def db_get_operation(self, key):
+ for i in xrange(len(self._db_operations)):
+ if self._db_operations[i].db_id == key:
+ return self._db_operations[i]
+ return None
+ def db_get_operation_by_id(self, key):
+ return self.db_operations_id_index[key]
+ def db_has_operation_with_id(self, key):
+ return key in self.db_operations_id_index
+
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_prevId(self):
+ return self._db_prevId
+ def __set_db_prevId(self, prevId):
+ self._db_prevId = prevId
+ self.is_dirty = True
+ db_prevId = property(__get_db_prevId, __set_db_prevId)
+ def db_add_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_change_prevId(self, prevId):
+ self._db_prevId = prevId
+ def db_delete_prevId(self, prevId):
+ self._db_prevId = None
+
+ def __get_db_date(self):
+ return self._db_date
+ def __set_db_date(self, date):
+ self._db_date = date
+ self.is_dirty = True
+ db_date = property(__get_db_date, __set_db_date)
+ def db_add_date(self, date):
+ self._db_date = date
+ def db_change_date(self, date):
+ self._db_date = date
+ def db_delete_date(self, date):
+ self._db_date = None
+
+ def __get_db_session(self):
+ return self._db_session
+ def __set_db_session(self, session):
+ self._db_session = session
+ self.is_dirty = True
+ db_session = property(__get_db_session, __set_db_session)
+ def db_add_session(self, session):
+ self._db_session = session
+ def db_change_session(self, session):
+ self._db_session = session
+ def db_delete_session(self, session):
+ self._db_session = None
+
+ def __get_db_user(self):
+ return self._db_user
+ def __set_db_user(self, user):
+ self._db_user = user
+ self.is_dirty = True
+ db_user = property(__get_db_user, __set_db_user)
+ def db_add_user(self, user):
+ self._db_user = user
+ def db_change_user(self, user):
+ self._db_user = user
+ def db_delete_user(self, user):
+ self._db_user = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBOpmAgent(object):
+
+ vtType = 'opm_agent'
+
+ def __init__(self, id=None, value=None, accounts=None):
+ self._db_id = id
+ self._db_value = value
+ self.db_deleted_accounts = []
+ if accounts is None:
+ self._db_accounts = []
+ else:
+ self._db_accounts = accounts
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBOpmAgent.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBOpmAgent(id=self._db_id,
+ value=self._db_value)
+ if self._db_accounts is None:
+ cp._db_accounts = []
+ else:
+ cp._db_accounts = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_accounts]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBOpmAgent()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'value' in class_dict:
+ res = class_dict['value'](old_obj, trans_dict)
+ new_obj.db_value = res
+ elif hasattr(old_obj, 'db_value') and old_obj.db_value is not None:
+ new_obj.db_value = old_obj.db_value
+ if 'accounts' in class_dict:
+ res = class_dict['accounts'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_account(obj)
+ elif hasattr(old_obj, 'db_accounts') and old_obj.db_accounts is not None:
+ for obj in old_obj.db_accounts:
+ new_obj.db_add_account(DBOpmAccountId.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_accounts') and hasattr(new_obj, 'db_deleted_accounts'):
+ for obj in old_obj.db_deleted_accounts:
+ n_obj = DBOpmAccountId.update_version(obj, trans_dict)
+ new_obj.db_deleted_accounts.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_accounts:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_account(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_accounts)
+ if remove:
+ self.db_deleted_accounts = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_accounts:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_value(self):
+ return self._db_value
+ def __set_db_value(self, value):
+ self._db_value = value
+ self.is_dirty = True
+ db_value = property(__get_db_value, __set_db_value)
+ def db_add_value(self, value):
+ self._db_value = value
+ def db_change_value(self, value):
+ self._db_value = value
+ def db_delete_value(self, value):
+ self._db_value = None
+
+ def __get_db_accounts(self):
+ return self._db_accounts
+ def __set_db_accounts(self, accounts):
+ self._db_accounts = accounts
+ self.is_dirty = True
+ db_accounts = property(__get_db_accounts, __set_db_accounts)
+ def db_get_accounts(self):
+ return self._db_accounts
+ def db_add_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_change_account(self, account):
+ self.is_dirty = True
+ self._db_accounts.append(account)
+ def db_delete_account(self, account):
+ self.is_dirty = True
+ raise Exception('Cannot delete a non-keyed object')
+ def db_get_account(self, key):
+ return None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBDelete(object):
+
+ vtType = 'delete'
+
+ def __init__(self, id=None, what=None, objectId=None, parentObjId=None, parentObjType=None):
+ self._db_id = id
+ self._db_what = what
+ self._db_objectId = objectId
+ self._db_parentObjId = parentObjId
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBDelete.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBDelete(id=self._db_id,
+ what=self._db_what,
+ objectId=self._db_objectId,
+ parentObjId=self._db_parentObjId,
+ parentObjType=self._db_parentObjType)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_objectId') and (self._db_what, self._db_objectId) in id_remap:
+ cp._db_objectId = id_remap[(self._db_what, self._db_objectId)]
+ if hasattr(self, 'db_parentObjId') and (self._db_parentObjType, self._db_parentObjId) in id_remap:
+ cp._db_parentObjId = id_remap[(self._db_parentObjType, self._db_parentObjId)]
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBDelete()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'what' in class_dict:
+ res = class_dict['what'](old_obj, trans_dict)
+ new_obj.db_what = res
+ elif hasattr(old_obj, 'db_what') and old_obj.db_what is not None:
+ new_obj.db_what = old_obj.db_what
+ if 'objectId' in class_dict:
+ res = class_dict['objectId'](old_obj, trans_dict)
+ new_obj.db_objectId = res
+ elif hasattr(old_obj, 'db_objectId') and old_obj.db_objectId is not None:
+ new_obj.db_objectId = old_obj.db_objectId
+ if 'parentObjId' in class_dict:
+ res = class_dict['parentObjId'](old_obj, trans_dict)
+ new_obj.db_parentObjId = res
+ elif hasattr(old_obj, 'db_parentObjId') and old_obj.db_parentObjId is not None:
+ new_obj.db_parentObjId = old_obj.db_parentObjId
+ if 'parentObjType' in class_dict:
+ res = class_dict['parentObjType'](old_obj, trans_dict)
+ new_obj.db_parentObjType = res
+ elif hasattr(old_obj, 'db_parentObjType') and old_obj.db_parentObjType is not None:
+ new_obj.db_parentObjType = old_obj.db_parentObjType
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ return [(self, parent[0], parent[1])]
+ def db_deleted_children(self, remove=False):
+ children = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_what(self):
+ return self._db_what
+ def __set_db_what(self, what):
+ self._db_what = what
+ self.is_dirty = True
+ db_what = property(__get_db_what, __set_db_what)
+ def db_add_what(self, what):
+ self._db_what = what
+ def db_change_what(self, what):
+ self._db_what = what
+ def db_delete_what(self, what):
+ self._db_what = None
+
+ def __get_db_objectId(self):
+ return self._db_objectId
+ def __set_db_objectId(self, objectId):
+ self._db_objectId = objectId
+ self.is_dirty = True
+ db_objectId = property(__get_db_objectId, __set_db_objectId)
+ def db_add_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_change_objectId(self, objectId):
+ self._db_objectId = objectId
+ def db_delete_objectId(self, objectId):
+ self._db_objectId = None
+
+ def __get_db_parentObjId(self):
+ return self._db_parentObjId
+ def __set_db_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ self.is_dirty = True
+ db_parentObjId = property(__get_db_parentObjId, __set_db_parentObjId)
+ def db_add_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_change_parentObjId(self, parentObjId):
+ self._db_parentObjId = parentObjId
+ def db_delete_parentObjId(self, parentObjId):
+ self._db_parentObjId = None
+
+ def __get_db_parentObjType(self):
+ return self._db_parentObjType
+ def __set_db_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ self.is_dirty = True
+ db_parentObjType = property(__get_db_parentObjType, __set_db_parentObjType)
+ def db_add_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_change_parentObjType(self, parentObjType):
+ self._db_parentObjType = parentObjType
+ def db_delete_parentObjType(self, parentObjType):
+ self._db_parentObjType = None
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBProvAssociation(object):
+
+ vtType = 'prov_association'
+
+ def __init__(self, prov_activity=None, prov_agent=None, prov_plan=None, prov_role=None):
+ self.db_deleted_prov_activity = []
+ self._db_prov_activity = prov_activity
+ self.db_deleted_prov_agent = []
+ self._db_prov_agent = prov_agent
+ self.db_deleted_prov_plan = []
+ self._db_prov_plan = prov_plan
+ self._db_prov_role = prov_role
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBProvAssociation.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBProvAssociation(prov_role=self._db_prov_role)
+ if self._db_prov_activity is not None:
+ cp._db_prov_activity = self._db_prov_activity.do_copy(new_ids, id_scope, id_remap)
+ if self._db_prov_agent is not None:
+ cp._db_prov_agent = self._db_prov_agent.do_copy(new_ids, id_scope, id_remap)
+ if self._db_prov_plan is not None:
+ cp._db_prov_plan = self._db_prov_plan.do_copy(new_ids, id_scope, id_remap)
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBProvAssociation()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'prov_activity' in class_dict:
+ res = class_dict['prov_activity'](old_obj, trans_dict)
+ new_obj.db_prov_activity = res
+ elif hasattr(old_obj, 'db_prov_activity') and old_obj.db_prov_activity is not None:
+ obj = old_obj.db_prov_activity
+ new_obj.db_add_prov_activity(DBRefProvActivity.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_activity') and hasattr(new_obj, 'db_deleted_prov_activity'):
+ for obj in old_obj.db_deleted_prov_activity:
+ n_obj = DBRefProvActivity.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_activity.append(n_obj)
+ if 'prov_agent' in class_dict:
+ res = class_dict['prov_agent'](old_obj, trans_dict)
+ new_obj.db_prov_agent = res
+ elif hasattr(old_obj, 'db_prov_agent') and old_obj.db_prov_agent is not None:
+ obj = old_obj.db_prov_agent
+ new_obj.db_add_prov_agent(DBRefProvAgent.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_agent') and hasattr(new_obj, 'db_deleted_prov_agent'):
+ for obj in old_obj.db_deleted_prov_agent:
+ n_obj = DBRefProvAgent.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_agent.append(n_obj)
+ if 'prov_plan' in class_dict:
+ res = class_dict['prov_plan'](old_obj, trans_dict)
+ new_obj.db_prov_plan = res
+ elif hasattr(old_obj, 'db_prov_plan') and old_obj.db_prov_plan is not None:
+ obj = old_obj.db_prov_plan
+ new_obj.db_add_prov_plan(DBRefProvPlan.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_prov_plan') and hasattr(new_obj, 'db_deleted_prov_plan'):
+ for obj in old_obj.db_deleted_prov_plan:
+ n_obj = DBRefProvPlan.update_version(obj, trans_dict)
+ new_obj.db_deleted_prov_plan.append(n_obj)
+ if 'prov_role' in class_dict:
+ res = class_dict['prov_role'](old_obj, trans_dict)
+ new_obj.db_prov_role = res
+ elif hasattr(old_obj, 'db_prov_role') and old_obj.db_prov_role is not None:
+ new_obj.db_prov_role = old_obj.db_prov_role
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ if self._db_prov_activity is not None:
+ children.extend(self._db_prov_activity.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_prov_activity = None
+ if self._db_prov_agent is not None:
+ children.extend(self._db_prov_agent.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_prov_agent = None
+ if self._db_prov_plan is not None:
+ children.extend(self._db_prov_plan.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ self._db_prov_plan = None
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_prov_activity)
+ children.extend(self.db_deleted_prov_agent)
+ children.extend(self.db_deleted_prov_plan)
+ if remove:
+ self.db_deleted_prov_activity = []
+ self.db_deleted_prov_agent = []
+ self.db_deleted_prov_plan = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ if self._db_prov_activity is not None and self._db_prov_activity.has_changes():
+ return True
+ if self._db_prov_agent is not None and self._db_prov_agent.has_changes():
+ return True
+ if self._db_prov_plan is not None and self._db_prov_plan.has_changes():
+ return True
+ return False
+ def __get_db_prov_activity(self):
+ return self._db_prov_activity
+ def __set_db_prov_activity(self, prov_activity):
+ self._db_prov_activity = prov_activity
+ self.is_dirty = True
+ db_prov_activity = property(__get_db_prov_activity, __set_db_prov_activity)
+ def db_add_prov_activity(self, prov_activity):
+ self._db_prov_activity = prov_activity
+ def db_change_prov_activity(self, prov_activity):
+ self._db_prov_activity = prov_activity
+ def db_delete_prov_activity(self, prov_activity):
+ if not self.is_new:
+ self.db_deleted_prov_activity.append(self._db_prov_activity)
+ self._db_prov_activity = None
+
+ def __get_db_prov_agent(self):
+ return self._db_prov_agent
+ def __set_db_prov_agent(self, prov_agent):
+ self._db_prov_agent = prov_agent
+ self.is_dirty = True
+ db_prov_agent = property(__get_db_prov_agent, __set_db_prov_agent)
+ def db_add_prov_agent(self, prov_agent):
+ self._db_prov_agent = prov_agent
+ def db_change_prov_agent(self, prov_agent):
+ self._db_prov_agent = prov_agent
+ def db_delete_prov_agent(self, prov_agent):
+ if not self.is_new:
+ self.db_deleted_prov_agent.append(self._db_prov_agent)
+ self._db_prov_agent = None
+
+ def __get_db_prov_plan(self):
+ return self._db_prov_plan
+ def __set_db_prov_plan(self, prov_plan):
+ self._db_prov_plan = prov_plan
+ self.is_dirty = True
+ db_prov_plan = property(__get_db_prov_plan, __set_db_prov_plan)
+ def db_add_prov_plan(self, prov_plan):
+ self._db_prov_plan = prov_plan
+ def db_change_prov_plan(self, prov_plan):
+ self._db_prov_plan = prov_plan
+ def db_delete_prov_plan(self, prov_plan):
+ if not self.is_new:
+ self.db_deleted_prov_plan.append(self._db_prov_plan)
+ self._db_prov_plan = None
+
+ def __get_db_prov_role(self):
+ return self._db_prov_role
+ def __set_db_prov_role(self, prov_role):
+ self._db_prov_role = prov_role
+ self.is_dirty = True
+ db_prov_role = property(__get_db_prov_role, __set_db_prov_role)
+ def db_add_prov_role(self, prov_role):
+ self._db_prov_role = prov_role
+ def db_change_prov_role(self, prov_role):
+ self._db_prov_role = prov_role
+ def db_delete_prov_role(self, prov_role):
+ self._db_prov_role = None
+
+
+
+class DBVistrail(object):
+
+ vtType = 'vistrail'
+
+ def __init__(self, id=None, entity_type=None, version=None, name=None, last_modified=None, actions=None, tags=None, annotations=None, vistrailVariables=None, parameter_explorations=None, actionAnnotations=None):
+ self._db_id = id
+ self._db_entity_type = entity_type
+ self._db_version = version
+ self._db_name = name
+ self._db_last_modified = last_modified
+ self.db_deleted_actions = []
+ self.db_actions_id_index = {}
+ if actions is None:
+ self._db_actions = []
+ else:
+ self._db_actions = actions
+ for v in self._db_actions:
+ self.db_actions_id_index[v.db_id] = v
+ self.db_deleted_tags = []
+ self.db_tags_id_index = {}
+ self.db_tags_name_index = {}
+ if tags is None:
+ self._db_tags = []
+ else:
+ self._db_tags = tags
+ for v in self._db_tags:
+ self.db_tags_id_index[v.db_id] = v
+ self.db_tags_name_index[v.db_name] = v
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ self.db_annotations_key_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_annotations_key_index[v.db_key] = v
+ self.db_deleted_vistrailVariables = []
+ self.db_vistrailVariables_name_index = {}
+ self.db_vistrailVariables_uuid_index = {}
+ if vistrailVariables is None:
+ self._db_vistrailVariables = []
+ else:
+ self._db_vistrailVariables = vistrailVariables
+ for v in self._db_vistrailVariables:
+ self.db_vistrailVariables_name_index[v.db_name] = v
+ self.db_vistrailVariables_uuid_index[v.db_uuid] = v
+ self.db_deleted_parameter_explorations = []
+ self.db_parameter_explorations_id_index = {}
+ if parameter_explorations is None:
+ self._db_parameter_explorations = []
+ else:
+ self._db_parameter_explorations = parameter_explorations
+ for v in self._db_parameter_explorations:
+ self.db_parameter_explorations_id_index[v.db_id] = v
+ self.db_deleted_actionAnnotations = []
+ self.db_actionAnnotations_id_index = {}
+ self.db_actionAnnotations_action_id_index = {}
+ self.db_actionAnnotations_key_index = {}
+ if actionAnnotations is None:
+ self._db_actionAnnotations = []
+ else:
+ self._db_actionAnnotations = actionAnnotations
+ for v in self._db_actionAnnotations:
+ self.db_actionAnnotations_id_index[v.db_id] = v
+ self.db_actionAnnotations_action_id_index[(v.db_action_id,v.db_key)] = v
+ self.db_actionAnnotations_key_index[(v.db_key,v.db_value)] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBVistrail(id=self._db_id,
+ entity_type=self._db_entity_type,
+ version=self._db_version,
+ name=self._db_name,
+ last_modified=self._db_last_modified)
+ if self._db_actions is None:
+ cp._db_actions = []
+ else:
+ cp._db_actions = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actions]
+ if self._db_tags is None:
+ cp._db_tags = []
+ else:
+ cp._db_tags = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_tags]
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_vistrailVariables is None:
+ cp._db_vistrailVariables = []
+ else:
+ cp._db_vistrailVariables = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_vistrailVariables]
+ if self._db_parameter_explorations is None:
+ cp._db_parameter_explorations = []
+ else:
+ cp._db_parameter_explorations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_parameter_explorations]
+ if self._db_actionAnnotations is None:
+ cp._db_actionAnnotations = []
+ else:
+ cp._db_actionAnnotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_actionAnnotations]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+
+ # recreate indices and set flags
+ cp.db_actions_id_index = dict((v.db_id, v) for v in cp._db_actions)
+ cp.db_tags_id_index = dict((v.db_id, v) for v in cp._db_tags)
+ cp.db_tags_name_index = dict((v.db_name, v) for v in cp._db_tags)
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_annotations_key_index = dict((v.db_key, v) for v in cp._db_annotations)
+ cp.db_vistrailVariables_name_index = dict((v.db_name, v) for v in cp._db_vistrailVariables)
+ cp.db_vistrailVariables_uuid_index = dict((v.db_uuid, v) for v in cp._db_vistrailVariables)
+ cp.db_parameter_explorations_id_index = dict((v.db_id, v) for v in cp._db_parameter_explorations)
+ cp.db_actionAnnotations_id_index = dict((v.db_id, v) for v in cp._db_actionAnnotations)
+ cp.db_actionAnnotations_action_id_index = dict(((v.db_action_id,v.db_key), v) for v in cp._db_actionAnnotations)
+ cp.db_actionAnnotations_key_index = dict(((v.db_key,v.db_value), v) for v in cp._db_actionAnnotations)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'entity_type' in class_dict:
+ res = class_dict['entity_type'](old_obj, trans_dict)
+ new_obj.db_entity_type = res
+ elif hasattr(old_obj, 'db_entity_type') and old_obj.db_entity_type is not None:
+ new_obj.db_entity_type = old_obj.db_entity_type
+ if 'version' in class_dict:
+ res = class_dict['version'](old_obj, trans_dict)
+ new_obj.db_version = res
+ elif hasattr(old_obj, 'db_version') and old_obj.db_version is not None:
+ new_obj.db_version = old_obj.db_version
+ if 'name' in class_dict:
+ res = class_dict['name'](old_obj, trans_dict)
+ new_obj.db_name = res
+ elif hasattr(old_obj, 'db_name') and old_obj.db_name is not None:
+ new_obj.db_name = old_obj.db_name
+ if 'last_modified' in class_dict:
+ res = class_dict['last_modified'](old_obj, trans_dict)
+ new_obj.db_last_modified = res
+ elif hasattr(old_obj, 'db_last_modified') and old_obj.db_last_modified is not None:
+ new_obj.db_last_modified = old_obj.db_last_modified
+ if 'actions' in class_dict:
+ res = class_dict['actions'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_action(obj)
+ elif hasattr(old_obj, 'db_actions') and old_obj.db_actions is not None:
+ for obj in old_obj.db_actions:
+ new_obj.db_add_action(DBAction.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actions') and hasattr(new_obj, 'db_deleted_actions'):
+ for obj in old_obj.db_deleted_actions:
+ n_obj = DBAction.update_version(obj, trans_dict)
+ new_obj.db_deleted_actions.append(n_obj)
+ if 'tags' in class_dict:
+ res = class_dict['tags'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_tag(obj)
+ elif hasattr(old_obj, 'db_tags') and old_obj.db_tags is not None:
+ for obj in old_obj.db_tags:
+ new_obj.db_add_tag(DBTag.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_tags') and hasattr(new_obj, 'db_deleted_tags'):
+ for obj in old_obj.db_deleted_tags:
+ n_obj = DBTag.update_version(obj, trans_dict)
+ new_obj.db_deleted_tags.append(n_obj)
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'vistrailVariables' in class_dict:
+ res = class_dict['vistrailVariables'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_vistrailVariable(obj)
+ elif hasattr(old_obj, 'db_vistrailVariables') and old_obj.db_vistrailVariables is not None:
+ for obj in old_obj.db_vistrailVariables:
+ new_obj.db_add_vistrailVariable(DBVistrailVariable.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_vistrailVariables') and hasattr(new_obj, 'db_deleted_vistrailVariables'):
+ for obj in old_obj.db_deleted_vistrailVariables:
+ n_obj = DBVistrailVariable.update_version(obj, trans_dict)
+ new_obj.db_deleted_vistrailVariables.append(n_obj)
+ if 'parameter_explorations' in class_dict:
+ res = class_dict['parameter_explorations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_parameter_exploration(obj)
+ elif hasattr(old_obj, 'db_parameter_explorations') and old_obj.db_parameter_explorations is not None:
+ for obj in old_obj.db_parameter_explorations:
+ new_obj.db_add_parameter_exploration(DBParameterExploration.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_parameter_explorations') and hasattr(new_obj, 'db_deleted_parameter_explorations'):
+ for obj in old_obj.db_deleted_parameter_explorations:
+ n_obj = DBParameterExploration.update_version(obj, trans_dict)
+ new_obj.db_deleted_parameter_explorations.append(n_obj)
+ if 'actionAnnotations' in class_dict:
+ res = class_dict['actionAnnotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_actionAnnotation(obj)
+ elif hasattr(old_obj, 'db_actionAnnotations') and old_obj.db_actionAnnotations is not None:
+ for obj in old_obj.db_actionAnnotations:
+ new_obj.db_add_actionAnnotation(DBActionAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_actionAnnotations') and hasattr(new_obj, 'db_deleted_actionAnnotations'):
+ for obj in old_obj.db_deleted_actionAnnotations:
+ n_obj = DBActionAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_actionAnnotations.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_actions:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_action(child)
+ to_del = []
+ for child in self.db_tags:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_tag(child)
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_vistrailVariables:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_vistrailVariable(child)
+ to_del = []
+ for child in self.db_parameter_explorations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_parameter_exploration(child)
+ to_del = []
+ for child in self.db_actionAnnotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_actionAnnotation(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_actions)
+ children.extend(self.db_deleted_tags)
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_vistrailVariables)
+ children.extend(self.db_deleted_parameter_explorations)
+ children.extend(self.db_deleted_actionAnnotations)
+ if remove:
+ self.db_deleted_actions = []
+ self.db_deleted_tags = []
+ self.db_deleted_annotations = []
+ self.db_deleted_vistrailVariables = []
+ self.db_deleted_parameter_explorations = []
+ self.db_deleted_actionAnnotations = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_actions:
+ if child.has_changes():
+ return True
+ for child in self._db_tags:
+ if child.has_changes():
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_vistrailVariables:
+ if child.has_changes():
+ return True
+ for child in self._db_parameter_explorations:
+ if child.has_changes():
+ return True
+ for child in self._db_actionAnnotations:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_entity_type(self):
+ return self._db_entity_type
+ def __set_db_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ self.is_dirty = True
+ db_entity_type = property(__get_db_entity_type, __set_db_entity_type)
+ def db_add_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_change_entity_type(self, entity_type):
+ self._db_entity_type = entity_type
+ def db_delete_entity_type(self, entity_type):
+ self._db_entity_type = None
+
+ def __get_db_version(self):
+ return self._db_version
+ def __set_db_version(self, version):
+ self._db_version = version
+ self.is_dirty = True
+ db_version = property(__get_db_version, __set_db_version)
+ def db_add_version(self, version):
+ self._db_version = version
+ def db_change_version(self, version):
+ self._db_version = version
+ def db_delete_version(self, version):
+ self._db_version = None
+
+ def __get_db_name(self):
+ return self._db_name
+ def __set_db_name(self, name):
+ self._db_name = name
+ self.is_dirty = True
+ db_name = property(__get_db_name, __set_db_name)
+ def db_add_name(self, name):
+ self._db_name = name
+ def db_change_name(self, name):
+ self._db_name = name
+ def db_delete_name(self, name):
+ self._db_name = None
+
+ def __get_db_last_modified(self):
+ return self._db_last_modified
+ def __set_db_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ self.is_dirty = True
+ db_last_modified = property(__get_db_last_modified, __set_db_last_modified)
+ def db_add_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_change_last_modified(self, last_modified):
+ self._db_last_modified = last_modified
+ def db_delete_last_modified(self, last_modified):
+ self._db_last_modified = None
+
+ def __get_db_actions(self):
+ return self._db_actions
+ def __set_db_actions(self, actions):
+ self._db_actions = actions
+ self.is_dirty = True
+ db_actions = property(__get_db_actions, __set_db_actions)
+ def db_get_actions(self):
+ return self._db_actions
+ def db_add_action(self, action):
+ self.is_dirty = True
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_change_action(self, action):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ self._db_actions[i] = action
+ found = True
+ break
+ if not found:
+ self._db_actions.append(action)
+ self.db_actions_id_index[action.db_id] = action
+ def db_delete_action(self, action):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == action.db_id:
+ if not self._db_actions[i].is_new:
+ self.db_deleted_actions.append(self._db_actions[i])
+ del self._db_actions[i]
+ break
+ del self.db_actions_id_index[action.db_id]
+ def db_get_action(self, key):
+ for i in xrange(len(self._db_actions)):
+ if self._db_actions[i].db_id == key:
+ return self._db_actions[i]
+ return None
+ def db_get_action_by_id(self, key):
+ return self.db_actions_id_index[key]
+ def db_has_action_with_id(self, key):
+ return key in self.db_actions_id_index
+
+ def __get_db_tags(self):
+ return self._db_tags
+ def __set_db_tags(self, tags):
+ self._db_tags = tags
+ self.is_dirty = True
+ db_tags = property(__get_db_tags, __set_db_tags)
+ def db_get_tags(self):
+ return self._db_tags
+ def db_add_tag(self, tag):
+ self.is_dirty = True
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_change_tag(self, tag):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ self._db_tags[i] = tag
+ found = True
+ break
+ if not found:
+ self._db_tags.append(tag)
+ self.db_tags_id_index[tag.db_id] = tag
+ self.db_tags_name_index[tag.db_name] = tag
+ def db_delete_tag(self, tag):
+ self.is_dirty = True
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == tag.db_id:
+ if not self._db_tags[i].is_new:
+ self.db_deleted_tags.append(self._db_tags[i])
+ del self._db_tags[i]
+ break
+ del self.db_tags_id_index[tag.db_id]
+ del self.db_tags_name_index[tag.db_name]
+ def db_get_tag(self, key):
+ for i in xrange(len(self._db_tags)):
+ if self._db_tags[i].db_id == key:
+ return self._db_tags[i]
+ return None
+ def db_get_tag_by_id(self, key):
+ return self.db_tags_id_index[key]
+ def db_has_tag_with_id(self, key):
+ return key in self.db_tags_id_index
+ def db_get_tag_by_name(self, key):
+ return self.db_tags_name_index[key]
+ def db_has_tag_with_name(self, key):
+ return key in self.db_tags_name_index
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ self.db_annotations_key_index[annotation.db_key] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ del self.db_annotations_key_index[annotation.db_key]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+ def db_get_annotation_by_key(self, key):
+ return self.db_annotations_key_index[key]
+ def db_has_annotation_with_key(self, key):
+ return key in self.db_annotations_key_index
+
+ def __get_db_vistrailVariables(self):
+ return self._db_vistrailVariables
+ def __set_db_vistrailVariables(self, vistrailVariables):
+ self._db_vistrailVariables = vistrailVariables
+ self.is_dirty = True
+ db_vistrailVariables = property(__get_db_vistrailVariables, __set_db_vistrailVariables)
+ def db_get_vistrailVariables(self):
+ return self._db_vistrailVariables
+ def db_add_vistrailVariable(self, vistrailVariable):
+ self.is_dirty = True
+ self._db_vistrailVariables.append(vistrailVariable)
+ self.db_vistrailVariables_name_index[vistrailVariable.db_name] = vistrailVariable
+ self.db_vistrailVariables_uuid_index[vistrailVariable.db_uuid] = vistrailVariable
+ def db_change_vistrailVariable(self, vistrailVariable):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_vistrailVariables)):
+ if self._db_vistrailVariables[i].db_name == vistrailVariable.db_name:
+ self._db_vistrailVariables[i] = vistrailVariable
+ found = True
+ break
+ if not found:
+ self._db_vistrailVariables.append(vistrailVariable)
+ self.db_vistrailVariables_name_index[vistrailVariable.db_name] = vistrailVariable
+ self.db_vistrailVariables_uuid_index[vistrailVariable.db_uuid] = vistrailVariable
+ def db_delete_vistrailVariable(self, vistrailVariable):
+ self.is_dirty = True
+ for i in xrange(len(self._db_vistrailVariables)):
+ if self._db_vistrailVariables[i].db_name == vistrailVariable.db_name:
+ if not self._db_vistrailVariables[i].is_new:
+ self.db_deleted_vistrailVariables.append(self._db_vistrailVariables[i])
+ del self._db_vistrailVariables[i]
+ break
+ del self.db_vistrailVariables_name_index[vistrailVariable.db_name]
+ del self.db_vistrailVariables_uuid_index[vistrailVariable.db_uuid]
+ def db_get_vistrailVariable(self, key):
+ for i in xrange(len(self._db_vistrailVariables)):
+ if self._db_vistrailVariables[i].db_name == key:
+ return self._db_vistrailVariables[i]
+ return None
+ def db_get_vistrailVariable_by_name(self, key):
+ return self.db_vistrailVariables_name_index[key]
+ def db_has_vistrailVariable_with_name(self, key):
+ return key in self.db_vistrailVariables_name_index
+ def db_get_vistrailVariable_by_uuid(self, key):
+ return self.db_vistrailVariables_uuid_index[key]
+ def db_has_vistrailVariable_with_uuid(self, key):
+ return key in self.db_vistrailVariables_uuid_index
+
+ def __get_db_parameter_explorations(self):
+ return self._db_parameter_explorations
+ def __set_db_parameter_explorations(self, parameter_explorations):
+ self._db_parameter_explorations = parameter_explorations
+ self.is_dirty = True
+ db_parameter_explorations = property(__get_db_parameter_explorations, __set_db_parameter_explorations)
+ def db_get_parameter_explorations(self):
+ return self._db_parameter_explorations
+ def db_add_parameter_exploration(self, parameter_exploration):
+ self.is_dirty = True
+ self._db_parameter_explorations.append(parameter_exploration)
+ self.db_parameter_explorations_id_index[parameter_exploration.db_id] = parameter_exploration
+ def db_change_parameter_exploration(self, parameter_exploration):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_parameter_explorations)):
+ if self._db_parameter_explorations[i].db_id == parameter_exploration.db_id:
+ self._db_parameter_explorations[i] = parameter_exploration
+ found = True
+ break
+ if not found:
+ self._db_parameter_explorations.append(parameter_exploration)
+ self.db_parameter_explorations_id_index[parameter_exploration.db_id] = parameter_exploration
+ def db_delete_parameter_exploration(self, parameter_exploration):
+ self.is_dirty = True
+ for i in xrange(len(self._db_parameter_explorations)):
+ if self._db_parameter_explorations[i].db_id == parameter_exploration.db_id:
+ if not self._db_parameter_explorations[i].is_new:
+ self.db_deleted_parameter_explorations.append(self._db_parameter_explorations[i])
+ del self._db_parameter_explorations[i]
+ break
+ del self.db_parameter_explorations_id_index[parameter_exploration.db_id]
+ def db_get_parameter_exploration(self, key):
+ for i in xrange(len(self._db_parameter_explorations)):
+ if self._db_parameter_explorations[i].db_id == key:
+ return self._db_parameter_explorations[i]
+ return None
+ def db_get_parameter_exploration_by_id(self, key):
+ return self.db_parameter_explorations_id_index[key]
+ def db_has_parameter_exploration_with_id(self, key):
+ return key in self.db_parameter_explorations_id_index
+
+ def __get_db_actionAnnotations(self):
+ return self._db_actionAnnotations
+ def __set_db_actionAnnotations(self, actionAnnotations):
+ self._db_actionAnnotations = actionAnnotations
+ self.is_dirty = True
+ db_actionAnnotations = property(__get_db_actionAnnotations, __set_db_actionAnnotations)
+ def db_get_actionAnnotations(self):
+ return self._db_actionAnnotations
+ def db_add_actionAnnotation(self, actionAnnotation):
+ self.is_dirty = True
+ self._db_actionAnnotations.append(actionAnnotation)
+ self.db_actionAnnotations_id_index[actionAnnotation.db_id] = actionAnnotation
+ self.db_actionAnnotations_action_id_index[(actionAnnotation.db_action_id,actionAnnotation.db_key)] = actionAnnotation
+ self.db_actionAnnotations_key_index[(actionAnnotation.db_key,actionAnnotation.db_value)] = actionAnnotation
+ def db_change_actionAnnotation(self, actionAnnotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_actionAnnotations)):
+ if self._db_actionAnnotations[i].db_id == actionAnnotation.db_id:
+ self._db_actionAnnotations[i] = actionAnnotation
+ found = True
+ break
+ if not found:
+ self._db_actionAnnotations.append(actionAnnotation)
+ self.db_actionAnnotations_id_index[actionAnnotation.db_id] = actionAnnotation
+ self.db_actionAnnotations_action_id_index[(actionAnnotation.db_action_id,actionAnnotation.db_key)] = actionAnnotation
+ self.db_actionAnnotations_key_index[(actionAnnotation.db_key,actionAnnotation.db_value)] = actionAnnotation
+ def db_delete_actionAnnotation(self, actionAnnotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_actionAnnotations)):
+ if self._db_actionAnnotations[i].db_id == actionAnnotation.db_id:
+ if not self._db_actionAnnotations[i].is_new:
+ self.db_deleted_actionAnnotations.append(self._db_actionAnnotations[i])
+ del self._db_actionAnnotations[i]
+ break
+ del self.db_actionAnnotations_id_index[actionAnnotation.db_id]
+ del self.db_actionAnnotations_action_id_index[(actionAnnotation.db_action_id,actionAnnotation.db_key)]
+ try:
+ del self.db_actionAnnotations_key_index[(actionAnnotation.db_key,actionAnnotation.db_value)]
+ except KeyError:
+ pass
+ def db_get_actionAnnotation(self, key):
+ for i in xrange(len(self._db_actionAnnotations)):
+ if self._db_actionAnnotations[i].db_id == key:
+ return self._db_actionAnnotations[i]
+ return None
+ def db_get_actionAnnotation_by_id(self, key):
+ return self.db_actionAnnotations_id_index[key]
+ def db_has_actionAnnotation_with_id(self, key):
+ return key in self.db_actionAnnotations_id_index
+ def db_get_actionAnnotation_by_action_id(self, key):
+ return self.db_actionAnnotations_action_id_index[key]
+ def db_has_actionAnnotation_with_action_id(self, key):
+ return key in self.db_actionAnnotations_action_id_index
+ def db_get_actionAnnotation_by_key(self, key):
+ return self.db_actionAnnotations_key_index[key]
+ def db_has_actionAnnotation_with_key(self, key):
+ return key in self.db_actionAnnotations_key_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
+class DBModuleExec(object):
+
+ vtType = 'module_exec'
+
+ def __init__(self, id=None, ts_start=None, ts_end=None, cached=None, module_id=None, module_name=None, completed=None, error=None, machine_id=None, annotations=None, loop_execs=None):
+ self._db_id = id
+ self._db_ts_start = ts_start
+ self._db_ts_end = ts_end
+ self._db_cached = cached
+ self._db_module_id = module_id
+ self._db_module_name = module_name
+ self._db_completed = completed
+ self._db_error = error
+ self._db_machine_id = machine_id
+ self.db_deleted_annotations = []
+ self.db_annotations_id_index = {}
+ if annotations is None:
+ self._db_annotations = []
+ else:
+ self._db_annotations = annotations
+ for v in self._db_annotations:
+ self.db_annotations_id_index[v.db_id] = v
+ self.db_deleted_loop_execs = []
+ self.db_loop_execs_id_index = {}
+ if loop_execs is None:
+ self._db_loop_execs = []
+ else:
+ self._db_loop_execs = loop_execs
+ for v in self._db_loop_execs:
+ self.db_loop_execs_id_index[v.db_id] = v
+ self.is_dirty = True
+ self.is_new = True
+
+ def __copy__(self):
+ return DBModuleExec.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = DBModuleExec(id=self._db_id,
+ ts_start=self._db_ts_start,
+ ts_end=self._db_ts_end,
+ cached=self._db_cached,
+ module_id=self._db_module_id,
+ module_name=self._db_module_name,
+ completed=self._db_completed,
+ error=self._db_error,
+ machine_id=self._db_machine_id)
+ if self._db_annotations is None:
+ cp._db_annotations = []
+ else:
+ cp._db_annotations = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_annotations]
+ if self._db_loop_execs is None:
+ cp._db_loop_execs = []
+ else:
+ cp._db_loop_execs = [v.do_copy(new_ids, id_scope, id_remap) for v in self._db_loop_execs]
+
+ # set new ids
+ if new_ids:
+ new_id = id_scope.getNewId(self.vtType)
+ if self.vtType in id_scope.remap:
+ id_remap[(id_scope.remap[self.vtType], self.db_id)] = new_id
+ else:
+ id_remap[(self.vtType, self.db_id)] = new_id
+ cp.db_id = new_id
+ if hasattr(self, 'db_module_id') and ('module', self._db_module_id) in id_remap:
+ cp._db_module_id = id_remap[('module', self._db_module_id)]
+ if hasattr(self, 'db_machine_id') and ('machine', self._db_machine_id) in id_remap:
+ cp._db_machine_id = id_remap[('machine', self._db_machine_id)]
+
+ # recreate indices and set flags
+ cp.db_annotations_id_index = dict((v.db_id, v) for v in cp._db_annotations)
+ cp.db_loop_execs_id_index = dict((v.db_id, v) for v in cp._db_loop_execs)
+ if not new_ids:
+ cp.is_dirty = self.is_dirty
+ cp.is_new = self.is_new
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBModuleExec()
+ class_dict = {}
+ if new_obj.__class__.__name__ in trans_dict:
+ class_dict = trans_dict[new_obj.__class__.__name__]
+ if 'id' in class_dict:
+ res = class_dict['id'](old_obj, trans_dict)
+ new_obj.db_id = res
+ elif hasattr(old_obj, 'db_id') and old_obj.db_id is not None:
+ new_obj.db_id = old_obj.db_id
+ if 'ts_start' in class_dict:
+ res = class_dict['ts_start'](old_obj, trans_dict)
+ new_obj.db_ts_start = res
+ elif hasattr(old_obj, 'db_ts_start') and old_obj.db_ts_start is not None:
+ new_obj.db_ts_start = old_obj.db_ts_start
+ if 'ts_end' in class_dict:
+ res = class_dict['ts_end'](old_obj, trans_dict)
+ new_obj.db_ts_end = res
+ elif hasattr(old_obj, 'db_ts_end') and old_obj.db_ts_end is not None:
+ new_obj.db_ts_end = old_obj.db_ts_end
+ if 'cached' in class_dict:
+ res = class_dict['cached'](old_obj, trans_dict)
+ new_obj.db_cached = res
+ elif hasattr(old_obj, 'db_cached') and old_obj.db_cached is not None:
+ new_obj.db_cached = old_obj.db_cached
+ if 'module_id' in class_dict:
+ res = class_dict['module_id'](old_obj, trans_dict)
+ new_obj.db_module_id = res
+ elif hasattr(old_obj, 'db_module_id') and old_obj.db_module_id is not None:
+ new_obj.db_module_id = old_obj.db_module_id
+ if 'module_name' in class_dict:
+ res = class_dict['module_name'](old_obj, trans_dict)
+ new_obj.db_module_name = res
+ elif hasattr(old_obj, 'db_module_name') and old_obj.db_module_name is not None:
+ new_obj.db_module_name = old_obj.db_module_name
+ if 'completed' in class_dict:
+ res = class_dict['completed'](old_obj, trans_dict)
+ new_obj.db_completed = res
+ elif hasattr(old_obj, 'db_completed') and old_obj.db_completed is not None:
+ new_obj.db_completed = old_obj.db_completed
+ if 'error' in class_dict:
+ res = class_dict['error'](old_obj, trans_dict)
+ new_obj.db_error = res
+ elif hasattr(old_obj, 'db_error') and old_obj.db_error is not None:
+ new_obj.db_error = old_obj.db_error
+ if 'machine_id' in class_dict:
+ res = class_dict['machine_id'](old_obj, trans_dict)
+ new_obj.db_machine_id = res
+ elif hasattr(old_obj, 'db_machine_id') and old_obj.db_machine_id is not None:
+ new_obj.db_machine_id = old_obj.db_machine_id
+ if 'annotations' in class_dict:
+ res = class_dict['annotations'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_annotation(obj)
+ elif hasattr(old_obj, 'db_annotations') and old_obj.db_annotations is not None:
+ for obj in old_obj.db_annotations:
+ new_obj.db_add_annotation(DBAnnotation.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_annotations') and hasattr(new_obj, 'db_deleted_annotations'):
+ for obj in old_obj.db_deleted_annotations:
+ n_obj = DBAnnotation.update_version(obj, trans_dict)
+ new_obj.db_deleted_annotations.append(n_obj)
+ if 'loop_execs' in class_dict:
+ res = class_dict['loop_execs'](old_obj, trans_dict)
+ for obj in res:
+ new_obj.db_add_loop_exec(obj)
+ elif hasattr(old_obj, 'db_loop_execs') and old_obj.db_loop_execs is not None:
+ for obj in old_obj.db_loop_execs:
+ new_obj.db_add_loop_exec(DBLoopExec.update_version(obj, trans_dict))
+ if hasattr(old_obj, 'db_deleted_loop_execs') and hasattr(new_obj, 'db_deleted_loop_execs'):
+ for obj in old_obj.db_deleted_loop_execs:
+ n_obj = DBLoopExec.update_version(obj, trans_dict)
+ new_obj.db_deleted_loop_execs.append(n_obj)
+ new_obj.is_new = old_obj.is_new
+ new_obj.is_dirty = old_obj.is_dirty
+ return new_obj
+
+ def db_children(self, parent=(None,None), orphan=False, for_action=False):
+ children = []
+ to_del = []
+ for child in self.db_annotations:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_annotation(child)
+ to_del = []
+ for child in self.db_loop_execs:
+ children.extend(child.db_children((self.vtType, self.db_id), orphan, for_action))
+ if orphan:
+ to_del.append(child)
+ for child in to_del:
+ self.db_delete_loop_exec(child)
+ children.append((self, parent[0], parent[1]))
+ return children
+ def db_deleted_children(self, remove=False):
+ children = []
+ children.extend(self.db_deleted_annotations)
+ children.extend(self.db_deleted_loop_execs)
+ if remove:
+ self.db_deleted_annotations = []
+ self.db_deleted_loop_execs = []
+ return children
+ def has_changes(self):
+ if self.is_dirty:
+ return True
+ for child in self._db_annotations:
+ if child.has_changes():
+ return True
+ for child in self._db_loop_execs:
+ if child.has_changes():
+ return True
+ return False
+ def __get_db_id(self):
+ return self._db_id
+ def __set_db_id(self, id):
+ self._db_id = id
+ self.is_dirty = True
+ db_id = property(__get_db_id, __set_db_id)
+ def db_add_id(self, id):
+ self._db_id = id
+ def db_change_id(self, id):
+ self._db_id = id
+ def db_delete_id(self, id):
+ self._db_id = None
+
+ def __get_db_ts_start(self):
+ return self._db_ts_start
+ def __set_db_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ self.is_dirty = True
+ db_ts_start = property(__get_db_ts_start, __set_db_ts_start)
+ def db_add_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_change_ts_start(self, ts_start):
+ self._db_ts_start = ts_start
+ def db_delete_ts_start(self, ts_start):
+ self._db_ts_start = None
+
+ def __get_db_ts_end(self):
+ return self._db_ts_end
+ def __set_db_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ self.is_dirty = True
+ db_ts_end = property(__get_db_ts_end, __set_db_ts_end)
+ def db_add_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_change_ts_end(self, ts_end):
+ self._db_ts_end = ts_end
+ def db_delete_ts_end(self, ts_end):
+ self._db_ts_end = None
+
+ def __get_db_cached(self):
+ return self._db_cached
+ def __set_db_cached(self, cached):
+ self._db_cached = cached
+ self.is_dirty = True
+ db_cached = property(__get_db_cached, __set_db_cached)
+ def db_add_cached(self, cached):
+ self._db_cached = cached
+ def db_change_cached(self, cached):
+ self._db_cached = cached
+ def db_delete_cached(self, cached):
+ self._db_cached = None
+
+ def __get_db_module_id(self):
+ return self._db_module_id
+ def __set_db_module_id(self, module_id):
+ self._db_module_id = module_id
+ self.is_dirty = True
+ db_module_id = property(__get_db_module_id, __set_db_module_id)
+ def db_add_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_change_module_id(self, module_id):
+ self._db_module_id = module_id
+ def db_delete_module_id(self, module_id):
+ self._db_module_id = None
+
+ def __get_db_module_name(self):
+ return self._db_module_name
+ def __set_db_module_name(self, module_name):
+ self._db_module_name = module_name
+ self.is_dirty = True
+ db_module_name = property(__get_db_module_name, __set_db_module_name)
+ def db_add_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_change_module_name(self, module_name):
+ self._db_module_name = module_name
+ def db_delete_module_name(self, module_name):
+ self._db_module_name = None
+
+ def __get_db_completed(self):
+ return self._db_completed
+ def __set_db_completed(self, completed):
+ self._db_completed = completed
+ self.is_dirty = True
+ db_completed = property(__get_db_completed, __set_db_completed)
+ def db_add_completed(self, completed):
+ self._db_completed = completed
+ def db_change_completed(self, completed):
+ self._db_completed = completed
+ def db_delete_completed(self, completed):
+ self._db_completed = None
+
+ def __get_db_error(self):
+ return self._db_error
+ def __set_db_error(self, error):
+ self._db_error = error
+ self.is_dirty = True
+ db_error = property(__get_db_error, __set_db_error)
+ def db_add_error(self, error):
+ self._db_error = error
+ def db_change_error(self, error):
+ self._db_error = error
+ def db_delete_error(self, error):
+ self._db_error = None
+
+ def __get_db_machine_id(self):
+ return self._db_machine_id
+ def __set_db_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ self.is_dirty = True
+ db_machine_id = property(__get_db_machine_id, __set_db_machine_id)
+ def db_add_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_change_machine_id(self, machine_id):
+ self._db_machine_id = machine_id
+ def db_delete_machine_id(self, machine_id):
+ self._db_machine_id = None
+
+ def __get_db_annotations(self):
+ return self._db_annotations
+ def __set_db_annotations(self, annotations):
+ self._db_annotations = annotations
+ self.is_dirty = True
+ db_annotations = property(__get_db_annotations, __set_db_annotations)
+ def db_get_annotations(self):
+ return self._db_annotations
+ def db_add_annotation(self, annotation):
+ self.is_dirty = True
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_change_annotation(self, annotation):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ self._db_annotations[i] = annotation
+ found = True
+ break
+ if not found:
+ self._db_annotations.append(annotation)
+ self.db_annotations_id_index[annotation.db_id] = annotation
+ def db_delete_annotation(self, annotation):
+ self.is_dirty = True
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == annotation.db_id:
+ if not self._db_annotations[i].is_new:
+ self.db_deleted_annotations.append(self._db_annotations[i])
+ del self._db_annotations[i]
+ break
+ del self.db_annotations_id_index[annotation.db_id]
+ def db_get_annotation(self, key):
+ for i in xrange(len(self._db_annotations)):
+ if self._db_annotations[i].db_id == key:
+ return self._db_annotations[i]
+ return None
+ def db_get_annotation_by_id(self, key):
+ return self.db_annotations_id_index[key]
+ def db_has_annotation_with_id(self, key):
+ return key in self.db_annotations_id_index
+
+ def __get_db_loop_execs(self):
+ return self._db_loop_execs
+ def __set_db_loop_execs(self, loop_execs):
+ self._db_loop_execs = loop_execs
+ self.is_dirty = True
+ db_loop_execs = property(__get_db_loop_execs, __set_db_loop_execs)
+ def db_get_loop_execs(self):
+ return self._db_loop_execs
+ def db_add_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_change_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ found = False
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ self._db_loop_execs[i] = loop_exec
+ found = True
+ break
+ if not found:
+ self._db_loop_execs.append(loop_exec)
+ self.db_loop_execs_id_index[loop_exec.db_id] = loop_exec
+ def db_delete_loop_exec(self, loop_exec):
+ self.is_dirty = True
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == loop_exec.db_id:
+ if not self._db_loop_execs[i].is_new:
+ self.db_deleted_loop_execs.append(self._db_loop_execs[i])
+ del self._db_loop_execs[i]
+ break
+ del self.db_loop_execs_id_index[loop_exec.db_id]
+ def db_get_loop_exec(self, key):
+ for i in xrange(len(self._db_loop_execs)):
+ if self._db_loop_execs[i].db_id == key:
+ return self._db_loop_execs[i]
+ return None
+ def db_get_loop_exec_by_id(self, key):
+ return self.db_loop_execs_id_index[key]
+ def db_has_loop_exec_with_id(self, key):
+ return key in self.db_loop_execs_id_index
+
+ def getPrimaryKey(self):
+ return self._db_id
+
diff --git a/vistrails/db/versions/v1_0_3/domain/id_scope.py b/vistrails/db/versions/v1_0_3/domain/id_scope.py
new file mode 100644
index 0000000..0e07f02
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/domain/id_scope.py
@@ -0,0 +1,85 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+
+class IdScope:
+ def __init__(self, beginId=0L, remap=None):
+ self.ids = {}
+ self.beginId = beginId
+ if remap is None:
+ self.remap = {}
+ else:
+ self.remap = remap
+
+ def __copy__(self):
+ cp = IdScope(beginId=self.beginId)
+ cp.ids = copy.copy(self.ids)
+ cp.remap = copy.copy(self.remap)
+ return cp
+
+ def __str__(self):
+ return str(self.ids)
+
+ def getNewId(self, objType):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ id = self.ids[objType]
+ self.ids[objType] += 1
+ return id
+ except KeyError:
+ self.ids[objType] = self.beginId + 1
+ return self.beginId
+
+ def updateBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ try:
+ if self.ids[objType] <= beginId:
+ self.ids[objType] = beginId
+ except KeyError:
+ self.ids[objType] = beginId
+
+ def setBeginId(self, objType, beginId):
+ try:
+ objType = self.remap[objType]
+ except KeyError:
+ pass
+ self.ids[objType] = beginId
diff --git a/vistrails/db/versions/v1_0_3/domain/log.py b/vistrails/db/versions/v1_0_3/domain/log.py
new file mode 100644
index 0000000..a127726
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/domain/log.py
@@ -0,0 +1,72 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBLog as _DBLog
+from auto_gen import DBAbstraction, DBModule, DBGroup, DBLoopExec, \
+ DBGroupExec, DBModuleExec
+from id_scope import IdScope
+
+import copy
+
+class DBLog(_DBLog):
+
+ def __init__(self, *args, **kwargs):
+ _DBLog.__init__(self, *args, **kwargs)
+ self.id_scope = IdScope(1,
+ {DBLoopExec.vtType: 'item_exec',
+ DBModuleExec.vtType: 'item_exec',
+ DBGroupExec.vtType: 'item_exec',
+ DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBLog.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBLog.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBLog
+ cp.id_scope = copy.copy(self.id_scope)
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBLog()
+ new_obj = _DBLog.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
diff --git a/vistrails/db/versions/v1_0_3/domain/registry.py b/vistrails/db/versions/v1_0_3/domain/registry.py
new file mode 100644
index 0000000..323ebbd
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/domain/registry.py
@@ -0,0 +1,63 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBRegistry as _DBRegistry, DBPackage, DBModuleDescriptor, \
+ DBPortSpec
+from id_scope import IdScope
+
+class DBRegistry(_DBRegistry):
+ def __init__(self, *args, **kwargs):
+ _DBRegistry.__init__(self, *args, **kwargs)
+ self.idScope = IdScope()
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBRegistry()
+ new_obj = _DBRegistry.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ return new_obj
+
+ def update_id_scope(self):
+ for package in self.db_packages:
+ self.idScope.updateBeginId(DBPackage.vtType, package.db_id+1)
+ for descriptor in package.db_module_descriptors:
+ self.idScope.updateBeginId(DBModuleDescriptor.vtType,
+ descriptor.db_id+1)
+ for port_spec in descriptor.db_portSpecs:
+ self.idScope.updateBeginId(DBPortSpec.vtType,
+ port_spec.db_id+1)
+
+
diff --git a/vistrails/db/versions/v1_0_3/domain/vistrail.py b/vistrails/db/versions/v1_0_3/domain/vistrail.py
new file mode 100644
index 0000000..4c1e5a2
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/domain/vistrail.py
@@ -0,0 +1,220 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import copy
+import hashlib
+from auto_gen import DBVistrail as _DBVistrail
+from auto_gen import DBAdd, DBChange, DBDelete, DBAbstraction, DBGroup, \
+ DBModule, DBAnnotation, DBActionAnnotation, DBParameterExploration
+from id_scope import IdScope
+
+class DBVistrail(_DBVistrail):
+ def __init__(self, *args, **kwargs):
+ _DBVistrail.__init__(self, *args, **kwargs)
+ self.idScope = IdScope(remap={DBAdd.vtType: 'operation',
+ DBChange.vtType: 'operation',
+ DBDelete.vtType: 'operation',
+ DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType,
+ DBActionAnnotation.vtType: \
+ DBAnnotation.vtType})
+
+ self.idScope.setBeginId('action', 1)
+ self.idScope.setBeginId(DBParameterExploration.vtType, 1)
+ self.db_objects = {}
+
+ # keep a reference to the current logging information here
+ self.db_log_filename = None
+ self.log = None
+
+ def __copy__(self):
+ return DBVistrail.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBVistrail.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBVistrail
+
+ cp.idScope = copy.copy(self.idScope)
+ cp.db_objects = copy.copy(self.db_objects)
+ cp.db_log_filename = self.db_log_filename
+ if self.log is not None:
+ cp.log = copy.copy(self.log)
+ else:
+ cp.log = None
+
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBVistrail()
+ new_obj = _DBVistrail.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ if hasattr(old_obj, 'db_log_filename'):
+ new_obj.db_log_filename = old_obj.db_log_filename
+ if hasattr(old_obj, 'log'):
+ new_obj.log = old_obj.log
+ return new_obj
+
+ def update_id_scope(self):
+ def getOldObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_oldObjId
+ return operation.db_objectId
+
+ def getNewObjId(operation):
+ if operation.vtType == 'change':
+ return operation.db_newObjId
+ return operation.db_objectId
+
+ for action in self.db_actions:
+ self.idScope.updateBeginId('action', action.db_id+1)
+ if action.db_session is not None:
+ self.idScope.updateBeginId('session', action.db_session + 1)
+ for operation in action.db_operations:
+ self.idScope.updateBeginId('operation', operation.db_id+1)
+ if operation.vtType == 'add' or operation.vtType == 'change':
+ # update ids of data
+ self.idScope.updateBeginId(operation.db_what,
+ getNewObjId(operation)+1)
+ if operation.db_data is None:
+ if operation.vtType == 'change':
+ operation.db_objectId = operation.db_oldObjId
+ self.db_add_object(operation.db_data)
+ for annotation in action.db_annotations:
+ self.idScope.updateBeginId('annotation', annotation.db_id+1)
+
+ for annotation in self.db_annotations:
+ self.idScope.updateBeginId('annotation', annotation.db_id+1)
+ for annotation in self.db_actionAnnotations:
+ self.idScope.updateBeginId('annotation', annotation.db_id+1)
+ for paramexp in self.db_parameter_explorations:
+ self.idScope.updateBeginId('parameter_exploration',
+ paramexp.db_id+1)
+
+ def db_add_object(self, obj):
+ self.db_objects[(obj.vtType, obj.db_id)] = obj
+
+ def db_get_object(self, type, id):
+ return self.db_objects.get((type, id), None)
+
+ def db_update_object(self, obj, **kwargs):
+ # want to swap out old object with a new version
+ # need this for updating aliases...
+ # hack it using setattr...
+ real_obj = self.db_objects[(obj.vtType, obj.db_id)]
+ for (k, v) in kwargs.iteritems():
+ if hasattr(real_obj, k):
+ setattr(real_obj, k, v)
+
+ def update_checkout_version(self, app=''):
+ checkout_key = "__checkout_version_"
+ action_key = checkout_key + app
+ annotation_key = action_key + '_annotationhash'
+ action_annotation_key = action_key + '_actionannotationhash'
+
+ # delete previous checkout annotations
+ deletekeys = [action_key,annotation_key,action_annotation_key]
+ for key in deletekeys:
+ while self.db_has_annotation_with_key(key):
+ a = self.db_get_annotation_by_key(key)
+ self.db_delete_annotation(a)
+
+ # annotation hash - requires annotations to be clean
+ value = self.hashAnnotations()
+ if self.db_has_annotation_with_key(annotation_key):
+ annotation = self.db_get_annotation_by_key(annotation_key)
+ annotation.db_value = value
+ else:
+ annotation=DBAnnotation(self.idScope.getNewId(DBAnnotation.vtType),
+ annotation_key, value)
+ self.db_add_annotation(annotation)
+ # action annotation hash
+ value = self.hashActionAnnotations()
+ if self.db_has_annotation_with_key(action_annotation_key):
+ annotation = self.db_get_annotation_by_key(action_annotation_key)
+ annotation.db_value = value
+ else:
+ annotation=DBAnnotation(self.idScope.getNewId(DBAnnotation.vtType),
+ action_annotation_key, value)
+ self.db_add_annotation(annotation)
+ # last action id hash
+ if len(self.db_actions) == 0:
+ value = 0
+ else:
+ value = max(v.db_id for v in self.db_actions)
+ if self.db_has_annotation_with_key(action_key):
+ annotation = self.db_get_annotation_by_key(action_key)
+ annotation.db_value = str(value)
+ else:
+ annotation=DBAnnotation(self.idScope.getNewId(DBAnnotation.vtType),
+ action_key, str(value))
+ self.db_add_annotation(annotation)
+
+ def hashAnnotations(self):
+ annotations = {}
+ for annotation in self.db_annotations:
+ if annotation._db_key not in annotations:
+ annotations[annotation._db_key] = []
+ if annotation._db_value not in annotations[annotation._db_key]:
+ annotations[annotation._db_key].append(annotation._db_value)
+ keys = annotations.keys()
+ keys.sort()
+ m = hashlib.md5()
+ for k in keys:
+ m.update(str(k))
+ annotations[k].sort()
+ for v in annotations[k]:
+ m.update(str(v))
+ return m.hexdigest()
+
+ def hashActionAnnotations(self):
+ action_annotations = {}
+ for action_id, key, value in [[aa.db_action_id, aa.db_key,
+ aa.db_value] for aa in self.db_actionAnnotations]:
+ index = (str(action_id), key)
+ if index not in action_annotations:
+ action_annotations[index] = []
+ if value not in action_annotations[index]:
+ action_annotations[index].append(value)
+ keys = action_annotations.keys()
+ keys.sort()
+ m = hashlib.md5()
+ for k in keys:
+ m.update(k[0] + k[1])
+ action_annotations[k].sort()
+ for v in action_annotations[k]:
+ m.update(str(v))
+ return m.hexdigest()
diff --git a/vistrails/db/versions/v1_0_3/domain/workflow.py b/vistrails/db/versions/v1_0_3/domain/workflow.py
new file mode 100644
index 0000000..af484e6
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/domain/workflow.py
@@ -0,0 +1,172 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from auto_gen import DBWorkflow as _DBWorkflow
+from auto_gen import DBAbstraction, DBModule, DBGroup
+from id_scope import IdScope
+
+import copy
+
+class DBWorkflow(_DBWorkflow):
+
+ def __init__(self, *args, **kwargs):
+ _DBWorkflow.__init__(self, *args, **kwargs)
+ self.objects = {}
+ self.tmp_id = IdScope(1,
+ {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType})
+
+ def __copy__(self):
+ return DBWorkflow.do_copy(self)
+
+ def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
+ cp = _DBWorkflow.do_copy(self, new_ids, id_scope, id_remap)
+ cp.__class__ = DBWorkflow
+ # need to go through and reset the index to the copied objects
+ cp.build_index()
+ cp.tmp_id = copy.copy(self.tmp_id)
+ return cp
+
+ @staticmethod
+ def update_version(old_obj, trans_dict, new_obj=None):
+ if new_obj is None:
+ new_obj = DBWorkflow()
+ new_obj = _DBWorkflow.update_version(old_obj, trans_dict, new_obj)
+ new_obj.update_id_scope()
+ new_obj.build_index()
+ return new_obj
+
+ def update_id_scope(self):
+ pass
+
+ _vtTypeMap = {DBAbstraction.vtType: DBModule.vtType,
+ DBGroup.vtType: DBModule.vtType}
+
+ def build_index(self):
+ g = self._vtTypeMap.get
+ self.objects = dict(((g(o.vtType, o.vtType), o._db_id), o)
+ for (o,_,_) in self.db_children())
+
+ def add_to_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ self.objects[(obj_type, object.getPrimaryKey())] = object
+
+ def delete_from_index(self, object):
+ obj_type = self._vtTypeMap.get(object.vtType, object.vtType)
+ del self.objects[(obj_type, object.getPrimaryKey())]
+
+ def capitalizeOne(self, str):
+ return str[0].upper() + str[1:]
+
+ def db_print_objects(self):
+ for k,v in self.objects.iteritems():
+ print '%s: %s' % (k, v)
+
+ def db_has_object(self, type, id):
+ return (type, id) in self.objects
+
+ def db_get_object(self, type, id):
+ return self.objects[(type, id)]
+
+ def db_add_object(self, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if object.vtType == DBAbstraction.vtType or \
+ object.vtType == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ else:
+ obj_type = object.vtType
+ funname = 'db_add_' + obj_type
+ obj_copy = copy.copy(object)
+ getattr(parent_obj, funname)(obj_copy)
+ self.add_to_index(obj_copy)
+
+ def db_change_object(self, old_id, object, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+
+ self.db_delete_object(old_id, object.vtType, None, None, parent_obj)
+ self.db_add_object(object, None, None, parent_obj)
+
+ def db_delete_object(self, obj_id, obj_type, parent_obj_type=None,
+ parent_obj_id=None, parent_obj=None):
+ if parent_obj is None:
+ if parent_obj_type is None or parent_obj_id is None:
+ parent_obj = self
+ else:
+ if parent_obj_type == DBAbstraction.vtType or \
+ parent_obj_type == DBGroup.vtType:
+ parent_obj_type = DBModule.vtType
+ try:
+ parent_obj = self.objects[(parent_obj_type, parent_obj_id)]
+ except KeyError:
+ msg = "Cannot find object of type '%s' with id '%s'" % \
+ (parent_obj_type, parent_obj_id)
+ raise Exception(msg)
+ if obj_type == DBAbstraction.vtType or obj_type == DBGroup.vtType:
+ obj_type = DBModule.vtType
+ funname = 'db_get_' + obj_type
+ if hasattr(parent_obj, funname):
+ object = getattr(parent_obj, funname)(obj_id)
+ else:
+ attr_name = 'db_' + obj_type
+ object = getattr(parent_obj, attr_name)
+ funname = 'db_delete_' + obj_type
+ getattr(parent_obj, funname)(object)
+ self.delete_from_index(object)
diff --git a/vistrails/db/versions/v1_0_3/persistence/__init__.py b/vistrails/db/versions/v1_0_3/persistence/__init__.py
new file mode 100644
index 0000000..0a7bec1
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/persistence/__init__.py
@@ -0,0 +1,472 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from xml.auto_gen import XMLDAOListBase
+from sql.auto_gen import SQLDAOListBase
+from vistrails.core.system import get_elementtree_library
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.versions.v1_0_3 import version as my_version
+from vistrails.db.versions.v1_0_3.domain import DBGroup, DBWorkflow, DBVistrail, DBLog, \
+ DBRegistry, DBMashuptrail
+
+root_set = set([DBVistrail.vtType, DBWorkflow.vtType,
+ DBLog.vtType, DBRegistry.vtType, DBMashuptrail.vtType])
+
+ElementTree = get_elementtree_library()
+
+
+class DAOList(dict):
+ def __init__(self):
+ self['xml'] = XMLDAOListBase()
+ self['sql'] = SQLDAOListBase()
+
+ def parse_xml_file(self, filename):
+ return ElementTree.parse(filename)
+
+ def write_xml_file(self, filename, tree):
+ def indent(elem, level=0):
+ i = "\n" + level*" "
+ if len(elem):
+ if not elem.text or not elem.text.strip():
+ elem.text = i + " "
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ for elem in elem:
+ indent(elem, level+1)
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ else:
+ if level and (not elem.tail or not elem.tail.strip()):
+ elem.tail = i
+ indent(tree.getroot())
+ tree.write(filename)
+
+ def read_xml_object(self, vtType, node):
+ return self['xml'][vtType].fromXML(node)
+
+ def write_xml_object(self, obj, node=None):
+ res_node = self['xml'][obj.vtType].toXML(obj, node)
+ return res_node
+
+ def open_from_xml(self, filename, vtType, tree=None):
+ """open_from_xml(filename) -> DBVistrail"""
+ if tree is None:
+ tree = self.parse_xml_file(filename)
+ vistrail = self.read_xml_object(vtType, tree.getroot())
+ return vistrail
+
+ def save_to_xml(self, obj, filename, tags, version=None):
+ """save_to_xml(obj : object, filename: str, tags: dict,
+ version: str) -> None
+
+ """
+ root = self.write_xml_object(obj)
+ if version is None:
+ version = my_version
+ root.set('version', version)
+ for k, v in tags.iteritems():
+ root.set(k, v)
+ tree = ElementTree.ElementTree(root)
+ self.write_xml_file(filename, tree)
+
+ def open_from_db(self, db_connection, vtType, id=None, lock=False,
+ global_props=None):
+ all_objects = {}
+ if global_props is None:
+ global_props = {}
+ if id is not None:
+ global_props['id'] = id
+ # global_props
+ res_objects = self['sql'][vtType].get_sql_columns(db_connection,
+ global_props,
+ lock)
+ if len(res_objects) > 1:
+ raise VistrailsDBException("More than object of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+ elif len(res_objects) <= 0:
+ raise VistrailsDBException("No objects of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+
+ all_objects.update(res_objects)
+ res = res_objects.values()[0]
+ global_props = {'entity_id': res.db_id,
+ 'entity_type': res.vtType}
+
+ # collect all commands so that they can be executed together
+ # daoList should contain (dao_type, dao, dbCommand) values
+ daoList = []
+ # dbCommandList should contain dbCommand values
+ dbCommandList = []
+
+ # generate SELECT statements
+ for dao_type, dao in self['sql'].iteritems():
+ if dao_type in root_set:
+ continue
+
+ daoList.append([dao_type, dao, None])
+ dbCommand = dao.get_sql_select(db_connection, global_props, lock)
+ dbCommandList.append(dbCommand)
+
+ # Exacute all select statements
+ results = self['sql'][vtType].executeSQLGroup(db_connection,
+ dbCommandList, True)
+
+ # add result to correct dao
+ for i in xrange(len(daoList)):
+ daoList[i][2] = results[i]
+
+ # process results
+ for dao_type, dao, data in daoList:
+ current_objs = dao.process_sql_columns(data, global_props)
+ all_objects.update(current_objs)
+
+ if dao_type == DBGroup.vtType:
+ for key, obj in current_objs.iteritems():
+ new_props = {'parent_id': key[1],
+ 'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ res_obj = self.open_from_db(db_connection,
+ DBWorkflow.vtType,
+ None, lock, new_props)
+ res_dict = {}
+ res_dict[(res_obj.vtType, res_obj.db_id)] = res_obj
+ all_objects.update(res_dict)
+
+ for key, obj in all_objects.iteritems():
+ if key[0] == vtType and key[1] == id:
+ continue
+ self['sql'][obj.vtType].from_sql_fast(obj, all_objects)
+ for obj in all_objects.itervalues():
+ obj.is_dirty = False
+ obj.is_new = False
+
+ return res
+
+ def open_many_from_db(self, db_connection, vtType, ids, lock=False):
+ """ Loads multiple objects. They need to be loaded as one single
+ multiple select statement command for performance reasons.
+ """
+
+ log_dao = self['sql'][vtType]
+ # loop through ids and build SELECT statements
+ selects = [log_dao.get_sql_select(db_connection, {'id': id}, lock)
+ for id in ids]
+ # Execute all SELECT statements for main objects
+ results = log_dao.executeSQLGroup(db_connection, selects, True)
+
+ # list of final objects
+ objects = []
+ # list of selects
+ selects = []
+ # list of children id:all_objects_dict
+ all_objects_dict = {}
+ # process each result and extract child SELECTS
+ # daoList should contain (id, dao_type, dao, result) values
+ daoList = []
+ # selects should contain dbCommand values
+ selects = []
+ global_props = {}
+ for id, data in zip(ids, results):
+ res_objects = log_dao.process_sql_columns(data, global_props)
+ if len(res_objects) > 1:
+ raise VistrailsDBException("More than object of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+ elif len(res_objects) <= 0:
+ raise VistrailsDBException("No objects of type '%s' and "
+ "id '%s' exist in the database" % \
+ (vtType, id))
+ all_objects = {}
+ all_objects_dict[id] = all_objects
+ all_objects.update(res_objects)
+ objects.append(res_objects.values()[0])
+ # collect all commands so that they can be executed together
+
+ # generate SELECT statements for children
+ for dao_type, dao in self['sql'].iteritems():
+ if dao_type in root_set:
+ continue
+
+ daoList.append([id, dao_type, dao, None])
+ dbCommand = dao.get_sql_select(db_connection, global_props, lock)
+ selects.append(dbCommand)
+
+ # Execute all child select statements
+ results = self['sql'][vtType].executeSQLGroup(db_connection,
+ selects, True)
+ for i in xrange(len(daoList)):
+ daoList[i][3] = results[i]
+
+ # process results
+ for id, dao_type, dao, data in daoList:
+ all_objects = all_objects_dict[id]
+ current_objs = dao.process_sql_columns(data, global_props)
+ all_objects.update(current_objs)
+
+ if dao_type == DBGroup.vtType:
+ for key, obj in current_objs.iteritems():
+ new_props = {'parent_id': key[1],
+ 'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ res_obj = self.open_from_db(db_connection,
+ DBWorkflow.vtType,
+ None, lock, new_props)
+ res_dict = {}
+ res_dict[(res_obj.vtType, res_obj.db_id)] = res_obj
+ all_objects.update(res_dict)
+
+
+ for id, all_objects in all_objects_dict.iteritems():
+ for key, obj in all_objects.iteritems():
+ if key[0] == vtType and key[1] == id:
+ continue
+ self['sql'][obj.vtType].from_sql_fast(obj, all_objects)
+ for id, dao_type, dao, data in daoList:
+ all_objects = all_objects_dict[id]
+ for obj in all_objects.itervalues():
+ obj.is_dirty = False
+ obj.is_new = False
+
+ return objects
+
+ def save_to_db(self, db_connection, obj, do_copy=False, global_props=None):
+ if do_copy == 'with_ids':
+ do_copy = True
+ elif do_copy and obj.db_id is not None:
+ obj.db_id = None
+
+ children = obj.db_children()
+ children.reverse()
+ if global_props is None:
+ global_props = {'entity_type': obj.vtType}
+ # print 'global_props:', global_props
+
+ # assumes not deleting entire thing
+ child = children[0][0]
+ self['sql'][child.vtType].set_sql_columns(db_connection, child,
+ global_props, do_copy)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ global_props = {'entity_id': child.db_id,
+ 'entity_type': child.vtType}
+
+ # do deletes
+ if not do_copy:
+ for (child, _, _) in children:
+ for c in child.db_deleted_children(True):
+ self['sql'][c.vtType].delete_sql_column(db_connection,
+ c,
+ global_props)
+ child = children.pop(0)[0]
+ child.is_dirty = False
+ child.is_new = False
+
+ if not len(children):
+ return
+
+ # list of all children
+ dbCommandList = []
+ writtenChildren = []
+ # process remaining children
+ for (child, _, _) in children:
+ dbCommand = self['sql'][child.vtType].set_sql_command(
+ db_connection, child, global_props, do_copy)
+ if dbCommand is not None:
+ dbCommandList.append(dbCommand)
+ writtenChildren.append(child)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ # Debug version of Execute all insert/update statements
+ #results = [self['sql'][children[0][0].vtType].executeSQL(
+ # db_connection, c, False) for c in dbCommandList]
+
+ # Execute all insert/update statements
+ results = self['sql'][children[0][0].vtType].executeSQLGroup(
+ db_connection,
+ dbCommandList, False)
+ resultDict = dict(zip(writtenChildren, results))
+ # process remaining children
+ for (child, _, _) in children:
+ if child in resultDict:
+ lastId = resultDict[child]
+ self['sql'][child.vtType].set_sql_process(child,
+ global_props,
+ lastId)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ # print '*** entity_type:', global_props['entity_type']
+ new_props = {'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ is_dirty = child.db_workflow.is_dirty
+ child.db_workflow.db_entity_type = DBWorkflow.vtType
+ child.db_workflow.is_dirty = is_dirty
+ self.save_to_db(db_connection, child.db_workflow, do_copy,
+ new_props)
+
+ def save_many_to_db(self, db_connection, objList, do_copy=False):
+ if do_copy == 'with_ids':
+ do_copy = True
+ if not len(objList):
+ return
+ childrenDict = {}
+ global_propsDict = {}
+ dbCommandList = []
+ writtenChildren = []
+ for obj in objList:
+ if do_copy and obj.db_id is not None:
+ obj.db_id = None
+
+ children = obj.db_children()
+ children.reverse()
+ global_props = {'entity_type': obj.vtType}
+
+ child = children[0][0]
+ dbCommand = self['sql'][child.vtType].set_sql_command(
+ db_connection, child, global_props, do_copy)
+ if dbCommand is not None:
+ dbCommandList.append(dbCommand)
+ writtenChildren.append(child)
+
+ childrenDict[child] = children
+ global_propsDict[child] = global_props
+
+ # Execute all insert/update statements for the main objects
+ results = self['sql'][children[0][0].vtType].executeSQLGroup(
+ db_connection,
+ dbCommandList, False)
+ resultDict = dict(zip(writtenChildren, results))
+ dbCommandList = []
+ writtenChildren = []
+ for child, children in childrenDict.iteritems():
+ # process objects
+ if child in resultDict:
+ lastId = resultDict[child]
+ self['sql'][child.vtType].set_sql_process(
+ child, global_propsDict[child], lastId)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ # process children
+ global_props = {'entity_id': child.db_id,
+ 'entity_type': child.vtType}
+ global_propsDict[child] = global_props
+ # do deletes
+ if not do_copy:
+ for (child, _, _) in childrenDict[child]:
+ for c in child.db_deleted_children(True):
+ self['sql'][c.vtType].delete_sql_column(db_connection,
+ c,
+ global_props)
+ child = children.pop(0)[0]
+ child.is_dirty = False
+ child.is_new = False
+
+ # list of all children
+ # process remaining children
+ for (child, _, _) in children:
+ dbCommand = self['sql'][child.vtType].set_sql_command(
+ db_connection, child, global_props, do_copy)
+ if dbCommand is not None:
+ dbCommandList.append(dbCommand)
+ writtenChildren.append(child)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+
+ # Execute all child insert/update statements
+ results = self['sql'][children[0][0].vtType].executeSQLGroup(
+ db_connection,
+ dbCommandList, False)
+ resultDict = dict(zip(writtenChildren, results))
+
+ for child, children in childrenDict.iteritems():
+ global_props = global_propsDict[child]
+ # process remaining children
+ for (child, _, _) in children:
+ if child in resultDict:
+ lastId = resultDict[child]
+ self['sql'][child.vtType].set_sql_process(child,
+ global_props,
+ lastId)
+ self['sql'][child.vtType].to_sql_fast(child, do_copy)
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ # print '*** entity_type:', global_props['entity_type']
+ new_props = {'entity_id': global_props['entity_id'],
+ 'entity_type': global_props['entity_type']}
+ is_dirty = child.db_workflow.is_dirty
+ child.db_workflow.db_entity_type = DBWorkflow.vtType
+ child.db_workflow.is_dirty = is_dirty
+ self.save_to_db(db_connection, child.db_workflow, do_copy,
+ new_props)
+
+ def delete_from_db(self, db_connection, type, obj_id):
+ if type not in root_set:
+ raise VistrailsDBException("Cannot delete entity of type '%s'" \
+ % type)
+
+ id_str = str(obj_id)
+ for (dao_type, dao) in self['sql'].iteritems():
+ if dao_type not in root_set:
+ db_cmd = \
+ self['sql'][type].createSQLDelete(dao.table,
+ {'entity_type': type,
+ 'entity_id': id_str})
+ self['sql'][type].executeSQL(db_connection, db_cmd, False)
+ db_cmd = self['sql'][type].createSQLDelete(self['sql'][type].table,
+ {'id': id_str})
+ self['sql'][type].executeSQL(db_connection, db_cmd, False)
+
+ def serialize(self, object):
+ root = self.write_xml_object(object)
+ return ElementTree.tostring(root)
+
+ def unserialize(self, str, obj_type):
+ def set_dirty(obj):
+ for child, _, _ in obj.db_children():
+ if child.vtType == DBGroup.vtType:
+ if child.db_workflow:
+ set_dirty(child.db_workflow)
+ child.is_dirty = True
+ child.is_new = True
+ try:
+ root = ElementTree.fromstring(str)
+ obj = self.read_xml_object(obj_type, root)
+ set_dirty(obj)
+ return obj
+ except SyntaxError, e:
+ msg = "Invalid VisTrails serialized object %s" % str
+ raise VistrailsDBException(msg)
+ return None
diff --git a/vistrails/db/versions/v1_0_3/persistence/sql/__init__.py b/vistrails/db/versions/v1_0_3/persistence/sql/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/persistence/sql/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v1_0_3/persistence/sql/auto_gen.py b/vistrails/db/versions/v1_0_3/persistence/sql/auto_gen.py
new file mode 100644
index 0000000..db939f3
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/persistence/sql/auto_gen.py
@@ -0,0 +1,7984 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+from sql_dao import SQLDAO
+from vistrails.db.versions.v1_0_3.domain import *
+
+class DBVistrailVariableSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'vistrail_variable'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['name', 'uuid', 'package', 'module', 'namespace', 'value', 'parent_id', 'entity_id', 'entity_type']
+ table = 'vistrail_variable'
+ whereMap = global_props
+ orderBy = 'name'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ uuid = self.convertFromDB(row[1], 'str', 'char(36)')
+ package = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ module = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[5], 'str', 'varchar(8191)')
+ vistrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ vistrailVariable = DBVistrailVariable(uuid=uuid,
+ package=package,
+ module=module,
+ namespace=namespace,
+ value=value,
+ name=name)
+ vistrailVariable.db_vistrail = vistrail
+ vistrailVariable.db_entity_id = entity_id
+ vistrailVariable.db_entity_type = entity_type
+ vistrailVariable.is_dirty = False
+ res[('vistrailVariable', name)] = vistrailVariable
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['name', 'uuid', 'package', 'module', 'namespace', 'value', 'parent_id', 'entity_id', 'entity_type']
+ table = 'vistrail_variable'
+ whereMap = global_props
+ orderBy = 'name'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ name = self.convertFromDB(row[0], 'str', 'varchar(255)')
+ uuid = self.convertFromDB(row[1], 'str', 'char(36)')
+ package = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ module = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[5], 'str', 'varchar(8191)')
+ vistrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ vistrailVariable = DBVistrailVariable(uuid=uuid,
+ package=package,
+ module=module,
+ namespace=namespace,
+ value=value,
+ name=name)
+ vistrailVariable.db_vistrail = vistrail
+ vistrailVariable.db_entity_id = entity_id
+ vistrailVariable.db_entity_type = entity_type
+ vistrailVariable.is_dirty = False
+ res[('vistrailVariable', name)] = vistrailVariable
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_vistrailVariable(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['name', 'uuid', 'package', 'module', 'namespace', 'value', 'parent_id', 'entity_id', 'entity_type']
+ table = 'vistrail_variable'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_name is not None:
+ keyStr = self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ whereMap['name'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_uuid') and obj.db_uuid is not None:
+ columnMap['uuid'] = \
+ self.convertToDB(obj.db_uuid, 'str', 'char(36)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_module') and obj.db_module is not None:
+ columnMap['module'] = \
+ self.convertToDB(obj.db_module, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['name', 'uuid', 'package', 'module', 'namespace', 'value', 'parent_id', 'entity_id', 'entity_type']
+ table = 'vistrail_variable'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_name is not None:
+ keyStr = self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ whereMap['name'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_uuid') and obj.db_uuid is not None:
+ columnMap['uuid'] = \
+ self.convertToDB(obj.db_uuid, 'str', 'char(36)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_module') and obj.db_module is not None:
+ columnMap['module'] = \
+ self.convertToDB(obj.db_module, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'vistrail_variable'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_name is not None:
+ keyStr = self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ whereMap['name'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSpecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port_spec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'min_conns', 'max_conns', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ optional = self.convertFromDB(row[3], 'int', 'int')
+ sort_key = self.convertFromDB(row[4], 'int', 'int')
+ min_conns = self.convertFromDB(row[5], 'int', 'int')
+ max_conns = self.convertFromDB(row[6], 'int', 'int')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ min_conns=min_conns,
+ max_conns=max_conns,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_entity_id = entity_id
+ portSpec.db_entity_type = entity_type
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'min_conns', 'max_conns', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ optional = self.convertFromDB(row[3], 'int', 'int')
+ sort_key = self.convertFromDB(row[4], 'int', 'int')
+ min_conns = self.convertFromDB(row[5], 'int', 'int')
+ max_conns = self.convertFromDB(row[6], 'int', 'int')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ portSpec = DBPortSpec(name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ min_conns=min_conns,
+ max_conns=max_conns,
+ id=id)
+ portSpec.db_parentType = parentType
+ portSpec.db_entity_id = entity_id
+ portSpec.db_entity_type = entity_type
+ portSpec.db_parent = parent
+ portSpec.is_dirty = False
+ res[('portSpec', id)] = portSpec
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'module_descriptor':
+ p = all_objects[('module_descriptor', obj.db_parent)]
+ p.db_add_portSpec(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'min_conns', 'max_conns', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_optional') and obj.db_optional is not None:
+ columnMap['optional'] = \
+ self.convertToDB(obj.db_optional, 'int', 'int')
+ if hasattr(obj, 'db_sort_key') and obj.db_sort_key is not None:
+ columnMap['sort_key'] = \
+ self.convertToDB(obj.db_sort_key, 'int', 'int')
+ if hasattr(obj, 'db_min_conns') and obj.db_min_conns is not None:
+ columnMap['min_conns'] = \
+ self.convertToDB(obj.db_min_conns, 'int', 'int')
+ if hasattr(obj, 'db_max_conns') and obj.db_max_conns is not None:
+ columnMap['max_conns'] = \
+ self.convertToDB(obj.db_max_conns, 'int', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'type', 'optional', 'sort_key', 'min_conns', 'max_conns', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_optional') and obj.db_optional is not None:
+ columnMap['optional'] = \
+ self.convertToDB(obj.db_optional, 'int', 'int')
+ if hasattr(obj, 'db_sort_key') and obj.db_sort_key is not None:
+ columnMap['sort_key'] = \
+ self.convertToDB(obj.db_sort_key, 'int', 'int')
+ if hasattr(obj, 'db_min_conns') and obj.db_min_conns is not None:
+ columnMap['min_conns'] = \
+ self.convertToDB(obj.db_min_conns, 'int', 'int')
+ if hasattr(obj, 'db_max_conns') and obj.db_max_conns is not None:
+ columnMap['max_conns'] = \
+ self.convertToDB(obj.db_max_conns, 'int', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_portSpecItems:
+ child.db_portSpec = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port_spec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ id=id)
+ module.db_parentType = parentType
+ module.db_entity_id = entity_id
+ module.db_entity_type = entity_type
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ module = DBModule(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ id=id)
+ module.db_parentType = parentType
+ module.db_entity_id = entity_id
+ module.db_entity_type = entity_type
+ module.db_parent = parent
+ module.is_dirty = False
+ res[('module', id)] = module
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleDescriptorSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_descriptor'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'package', 'namespace', 'package_version', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ base_descriptor_id = self.convertFromDB(row[6], 'long', 'int')
+ package = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ module_descriptor = DBModuleDescriptor(name=name,
+ package=package,
+ namespace=namespace,
+ package_version=package_version,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ id=id)
+ module_descriptor.db_package = package
+ module_descriptor.db_entity_id = entity_id
+ module_descriptor.db_entity_type = entity_type
+ module_descriptor.is_dirty = False
+ res[('module_descriptor', id)] = module_descriptor
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'package', 'namespace', 'package_version', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ base_descriptor_id = self.convertFromDB(row[6], 'long', 'int')
+ package = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ module_descriptor = DBModuleDescriptor(name=name,
+ package=package,
+ namespace=namespace,
+ package_version=package_version,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ id=id)
+ module_descriptor.db_package = package
+ module_descriptor.db_entity_id = entity_id
+ module_descriptor.db_entity_type = entity_type
+ module_descriptor.is_dirty = False
+ res[('module_descriptor', id)] = module_descriptor
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('package', obj.db_package) in all_objects:
+ p = all_objects[('package', obj.db_package)]
+ p.db_add_module_descriptor(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'package', 'namespace', 'package_version', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package_version') and obj.db_package_version is not None:
+ columnMap['package_version'] = \
+ self.convertToDB(obj.db_package_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_base_descriptor_id') and obj.db_base_descriptor_id is not None:
+ columnMap['base_descriptor_id'] = \
+ self.convertToDB(obj.db_base_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_package, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'package', 'namespace', 'package_version', 'version', 'base_descriptor_id', 'parent_id', 'entity_id', 'entity_type']
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package_version') and obj.db_package_version is not None:
+ columnMap['package_version'] = \
+ self.convertToDB(obj.db_package_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_base_descriptor_id') and obj.db_base_descriptor_id is not None:
+ columnMap['base_descriptor_id'] = \
+ self.convertToDB(obj.db_base_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_package, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_portSpecs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_descriptor'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBTagSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'tag'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[2], 'long', 'int')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_vistrail = vistrail
+ tag.db_entity_id = entity_id
+ tag.db_entity_type = entity_type
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[2], 'long', 'int')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+
+ tag = DBTag(name=name,
+ id=id)
+ tag.db_vistrail = vistrail
+ tag.db_entity_id = entity_id
+ tag.db_entity_type = entity_type
+ tag.is_dirty = False
+ res[('tag', id)] = tag
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_tag(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'tag'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ signature = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature,
+ id=id)
+ port.db_parentType = parentType
+ port.db_entity_id = entity_id
+ port.db_entity_type = entity_type
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ type = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ moduleId = self.convertFromDB(row[2], 'long', 'int')
+ moduleName = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ signature = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ port = DBPort(type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature,
+ id=id)
+ port.db_parentType = parentType
+ port.db_entity_id = entity_id
+ port.db_entity_type = entity_type
+ port.db_parent = parent
+ port.is_dirty = False
+ res[('port', id)] = port
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'connection':
+ p = all_objects[('connection', obj.db_parent)]
+ p.db_add_port(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_signature') and obj.db_signature is not None:
+ columnMap['signature'] = \
+ self.convertToDB(obj.db_signature, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'type', 'moduleId', 'moduleName', 'name', 'signature', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_moduleId') and obj.db_moduleId is not None:
+ columnMap['moduleId'] = \
+ self.convertToDB(obj.db_moduleId, 'long', 'int')
+ if hasattr(obj, 'db_moduleName') and obj.db_moduleName is not None:
+ columnMap['moduleName'] = \
+ self.convertToDB(obj.db_moduleName, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_signature') and obj.db_signature is not None:
+ columnMap['signature'] = \
+ self.convertToDB(obj.db_signature, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ group = DBGroup(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ id=id)
+ group.db_parentType = parentType
+ group.db_entity_id = entity_id
+ group.db_entity_type = entity_type
+ group.db_parent = parent
+ group.is_dirty = False
+ res[('group', id)] = group
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ group = DBGroup(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ id=id)
+ group.db_parentType = parentType
+ group.db_entity_id = entity_id
+ group.db_entity_type = entity_type
+ group.db_parent = parent
+ group.is_dirty = False
+ res[('group', id)] = group
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_workflow is not None:
+ child = obj.db_workflow
+ child.db_group = obj.db_id
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLogSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'log_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ log = DBLog(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ log.is_dirty = False
+ res[('log', id)] = log
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[5], 'long', 'int')
+
+ log = DBLog(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ log.is_dirty = False
+ res[('log', id)] = log
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified', 'vistrail_id']
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_workflow_execs:
+ child.db_log = obj.db_id
+ for child in obj.db_machines:
+ child.db_log = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'log_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMashupAliasSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'mashup_alias'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_alias'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ parent = self.convertFromDB(row[2], 'long', 'int')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+
+ mashup_alias = DBMashupAlias(name=name,
+ id=id)
+ mashup_alias.db_parent = parent
+ mashup_alias.db_entity_id = entity_id
+ mashup_alias.db_entity_type = entity_type
+ mashup_alias.is_dirty = False
+ res[('mashup_alias', id)] = mashup_alias
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_alias'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ parent = self.convertFromDB(row[2], 'long', 'int')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+
+ mashup_alias = DBMashupAlias(name=name,
+ id=id)
+ mashup_alias.db_parent = parent
+ mashup_alias.db_entity_id = entity_id
+ mashup_alias.db_entity_type = entity_type
+ mashup_alias.is_dirty = False
+ res[('mashup_alias', id)] = mashup_alias
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('mashup', obj.db_parent) in all_objects:
+ p = all_objects[('mashup', obj.db_parent)]
+ p.db_add_alias(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_alias'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_alias'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_component is not None:
+ child = obj.db_component
+ child.db_mashup_alias = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'mashup_alias'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMashupSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'mashup'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'version', 'type', 'vtid', 'layout', 'geometry', 'has_seq', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[2], 'long', 'int')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ vtid = self.convertFromDB(row[4], 'long', 'int')
+ layout = self.convertFromDB(row[5], 'str', 'mediumtext')
+ geometry = self.convertFromDB(row[6], 'str', 'mediumtext')
+ has_seq = self.convertFromDB(row[7], 'int', 'int')
+ parent = self.convertFromDB(row[8], 'long', 'int')
+ entity_id = self.convertFromDB(row[9], 'long', 'int')
+ entity_type = self.convertFromDB(row[10], 'str', 'char(16)')
+
+ mashup = DBMashup(name=name,
+ version=version,
+ type=type,
+ vtid=vtid,
+ layout=layout,
+ geometry=geometry,
+ has_seq=has_seq,
+ id=id)
+ mashup.db_parent = parent
+ mashup.db_entity_id = entity_id
+ mashup.db_entity_type = entity_type
+ mashup.is_dirty = False
+ res[('mashup', id)] = mashup
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'version', 'type', 'vtid', 'layout', 'geometry', 'has_seq', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[2], 'long', 'int')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ vtid = self.convertFromDB(row[4], 'long', 'int')
+ layout = self.convertFromDB(row[5], 'str', 'mediumtext')
+ geometry = self.convertFromDB(row[6], 'str', 'mediumtext')
+ has_seq = self.convertFromDB(row[7], 'int', 'int')
+ parent = self.convertFromDB(row[8], 'long', 'int')
+ entity_id = self.convertFromDB(row[9], 'long', 'int')
+ entity_type = self.convertFromDB(row[10], 'str', 'char(16)')
+
+ mashup = DBMashup(name=name,
+ version=version,
+ type=type,
+ vtid=vtid,
+ layout=layout,
+ geometry=geometry,
+ has_seq=has_seq,
+ id=id)
+ mashup.db_parent = parent
+ mashup.db_entity_id = entity_id
+ mashup.db_entity_type = entity_type
+ mashup.is_dirty = False
+ res[('mashup', id)] = mashup
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('mashup_action', obj.db_parent) in all_objects:
+ p = all_objects[('mashup_action', obj.db_parent)]
+ p.db_add_mashup(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'version', 'type', 'vtid', 'layout', 'geometry', 'has_seq', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vtid') and obj.db_vtid is not None:
+ columnMap['vtid'] = \
+ self.convertToDB(obj.db_vtid, 'long', 'int')
+ if hasattr(obj, 'db_layout') and obj.db_layout is not None:
+ columnMap['layout'] = \
+ self.convertToDB(obj.db_layout, 'str', 'mediumtext')
+ if hasattr(obj, 'db_geometry') and obj.db_geometry is not None:
+ columnMap['geometry'] = \
+ self.convertToDB(obj.db_geometry, 'str', 'mediumtext')
+ if hasattr(obj, 'db_has_seq') and obj.db_has_seq is not None:
+ columnMap['has_seq'] = \
+ self.convertToDB(obj.db_has_seq, 'int', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'version', 'type', 'vtid', 'layout', 'geometry', 'has_seq', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vtid') and obj.db_vtid is not None:
+ columnMap['vtid'] = \
+ self.convertToDB(obj.db_vtid, 'long', 'int')
+ if hasattr(obj, 'db_layout') and obj.db_layout is not None:
+ columnMap['layout'] = \
+ self.convertToDB(obj.db_layout, 'str', 'mediumtext')
+ if hasattr(obj, 'db_geometry') and obj.db_geometry is not None:
+ columnMap['geometry'] = \
+ self.convertToDB(obj.db_geometry, 'str', 'mediumtext')
+ if hasattr(obj, 'db_has_seq') and obj.db_has_seq is not None:
+ columnMap['has_seq'] = \
+ self.convertToDB(obj.db_has_seq, 'int', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_aliases:
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'mashup'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPortSpecItemSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'port_spec_item'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'module', 'package', 'namespace', 'label', '_default', '_values', 'entry_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'port_spec_item'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ module = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ label = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ default = self.convertFromDB(row[6], 'str', 'varchar(4095)')
+ values = self.convertFromDB(row[7], 'str', 'mediumtext')
+ entry_type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ portSpec = self.convertFromDB(row[9], 'long', 'int')
+ entity_id = self.convertFromDB(row[10], 'long', 'int')
+ entity_type = self.convertFromDB(row[11], 'str', 'char(16)')
+
+ portSpecItem = DBPortSpecItem(pos=pos,
+ module=module,
+ package=package,
+ namespace=namespace,
+ label=label,
+ default=default,
+ values=values,
+ entry_type=entry_type,
+ id=id)
+ portSpecItem.db_portSpec = portSpec
+ portSpecItem.db_entity_id = entity_id
+ portSpecItem.db_entity_type = entity_type
+ portSpecItem.is_dirty = False
+ res[('portSpecItem', id)] = portSpecItem
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'module', 'package', 'namespace', 'label', '_default', '_values', 'entry_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'port_spec_item'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ module = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ label = self.convertFromDB(row[5], 'str', 'varchar(4095)')
+ default = self.convertFromDB(row[6], 'str', 'varchar(4095)')
+ values = self.convertFromDB(row[7], 'str', 'mediumtext')
+ entry_type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ portSpec = self.convertFromDB(row[9], 'long', 'int')
+ entity_id = self.convertFromDB(row[10], 'long', 'int')
+ entity_type = self.convertFromDB(row[11], 'str', 'char(16)')
+
+ portSpecItem = DBPortSpecItem(pos=pos,
+ module=module,
+ package=package,
+ namespace=namespace,
+ label=label,
+ default=default,
+ values=values,
+ entry_type=entry_type,
+ id=id)
+ portSpecItem.db_portSpec = portSpec
+ portSpecItem.db_entity_id = entity_id
+ portSpecItem.db_entity_type = entity_type
+ portSpecItem.is_dirty = False
+ res[('portSpecItem', id)] = portSpecItem
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('portSpec', obj.db_portSpec) in all_objects:
+ p = all_objects[('portSpec', obj.db_portSpec)]
+ p.db_add_portSpecItem(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'module', 'package', 'namespace', 'label', '_default', '_values', 'entry_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'port_spec_item'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_module') and obj.db_module is not None:
+ columnMap['module'] = \
+ self.convertToDB(obj.db_module, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_label') and obj.db_label is not None:
+ columnMap['label'] = \
+ self.convertToDB(obj.db_label, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_default') and obj.db_default is not None:
+ columnMap['_default'] = \
+ self.convertToDB(obj.db_default, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_values') and obj.db_values is not None:
+ columnMap['_values'] = \
+ self.convertToDB(obj.db_values, 'str', 'mediumtext')
+ if hasattr(obj, 'db_entry_type') and obj.db_entry_type is not None:
+ columnMap['entry_type'] = \
+ self.convertToDB(obj.db_entry_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_portSpec') and obj.db_portSpec is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_portSpec, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'pos', 'module', 'package', 'namespace', 'label', '_default', '_values', 'entry_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'port_spec_item'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_module') and obj.db_module is not None:
+ columnMap['module'] = \
+ self.convertToDB(obj.db_module, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_label') and obj.db_label is not None:
+ columnMap['label'] = \
+ self.convertToDB(obj.db_label, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_default') and obj.db_default is not None:
+ columnMap['_default'] = \
+ self.convertToDB(obj.db_default, 'str', 'varchar(4095)')
+ if hasattr(obj, 'db_values') and obj.db_values is not None:
+ columnMap['_values'] = \
+ self.convertToDB(obj.db_values, 'str', 'mediumtext')
+ if hasattr(obj, 'db_entry_type') and obj.db_entry_type is not None:
+ columnMap['entry_type'] = \
+ self.convertToDB(obj.db_entry_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_portSpec') and obj.db_portSpec is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_portSpec, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'port_spec_item'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMachineSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'machine'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'bigint')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.db_entity_id = entity_id
+ machine.db_entity_type = entity_type
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ os = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ architecture = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ processor = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ram = self.convertFromDB(row[5], 'int', 'bigint')
+ vistrailId = self.convertFromDB(row[6], 'long', 'int')
+ log = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ machine = DBMachine(name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram,
+ id=id)
+ machine.db_vistrailId = vistrailId
+ machine.db_log = log
+ machine.db_entity_id = entity_id
+ machine.db_entity_type = entity_type
+ machine.is_dirty = False
+ res[('machine', id)] = machine
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_machine(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'bigint')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'os', 'architecture', 'processor', 'ram', 'vt_id', 'log_id', 'entity_id', 'entity_type']
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_os') and obj.db_os is not None:
+ columnMap['os'] = \
+ self.convertToDB(obj.db_os, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_architecture') and obj.db_architecture is not None:
+ columnMap['architecture'] = \
+ self.convertToDB(obj.db_architecture, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_processor') and obj.db_processor is not None:
+ columnMap['processor'] = \
+ self.convertToDB(obj.db_processor, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ram') and obj.db_ram is not None:
+ columnMap['ram'] = \
+ self.convertToDB(obj.db_ram, 'int', 'bigint')
+ if hasattr(obj, 'db_vistrailId') and obj.db_vistrailId is not None:
+ columnMap['vt_id'] = \
+ self.convertToDB(obj.db_vistrailId, 'long', 'int')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'machine'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAddSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'add_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_entity_id = entity_id
+ add.db_entity_type = entity_type
+ add.is_dirty = False
+ res[('add', id)] = add
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ add = DBAdd(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ add.db_action = action
+ add.db_entity_id = entity_id
+ add.db_entity_type = entity_type
+ add.is_dirty = False
+ res[('add', id)] = add
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'add_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBOtherSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'other'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_entity_id = entity_id
+ other.db_entity_type = entity_type
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ other = DBOther(key=key,
+ value=value,
+ id=id)
+ other.db_parentType = parentType
+ other.db_entity_id = entity_id
+ other.db_entity_type = entity_type
+ other.db_parent = parent
+ other.is_dirty = False
+ res[('other', id)] = other
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_other(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'okey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['okey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'other'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLocationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'location'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_entity_id = entity_id
+ location.db_entity_type = entity_type
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ x = self.convertFromDB(row[1], 'float', 'DECIMAL(18,12)')
+ y = self.convertFromDB(row[2], 'float', 'DECIMAL(18,12)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ location = DBLocation(x=x,
+ y=y,
+ id=id)
+ location.db_parentType = parentType
+ location.db_entity_id = entity_id
+ location.db_entity_type = entity_type
+ location.db_parent = parent
+ location.is_dirty = False
+ res[('location', id)] = location
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_location(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'x', 'y', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_x') and obj.db_x is not None:
+ columnMap['x'] = \
+ self.convertToDB(obj.db_x, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_y') and obj.db_y is not None:
+ columnMap['y'] = \
+ self.convertToDB(obj.db_y, 'float', 'DECIMAL(18,12)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'location'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPEParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'pe_parameter'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'interpolator', 'value', 'dimension', 'parent_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'pe_parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ interpolator = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[3], 'str', 'mediumtext')
+ dimension = self.convertFromDB(row[4], 'long', 'int')
+ parentType = self.convertFromDB(row[5], 'str', 'char(32)')
+ pe_function = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ pe_parameter = DBPEParameter(pos=pos,
+ interpolator=interpolator,
+ value=value,
+ dimension=dimension,
+ id=id)
+ pe_parameter.db_parentType = parentType
+ pe_parameter.db_pe_function = pe_function
+ pe_parameter.db_entity_id = entity_id
+ pe_parameter.db_entity_type = entity_type
+ pe_parameter.is_dirty = False
+ res[('pe_parameter', id)] = pe_parameter
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'interpolator', 'value', 'dimension', 'parent_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'pe_parameter'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ interpolator = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[3], 'str', 'mediumtext')
+ dimension = self.convertFromDB(row[4], 'long', 'int')
+ parentType = self.convertFromDB(row[5], 'str', 'char(32)')
+ pe_function = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ pe_parameter = DBPEParameter(pos=pos,
+ interpolator=interpolator,
+ value=value,
+ dimension=dimension,
+ id=id)
+ pe_parameter.db_parentType = parentType
+ pe_parameter.db_pe_function = pe_function
+ pe_parameter.db_entity_id = entity_id
+ pe_parameter.db_entity_type = entity_type
+ pe_parameter.is_dirty = False
+ res[('pe_parameter', id)] = pe_parameter
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('pe_function', obj.db_pe_function) in all_objects:
+ p = all_objects[('pe_function', obj.db_pe_function)]
+ p.db_add_parameter(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'interpolator', 'value', 'dimension', 'parent_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'pe_parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_interpolator') and obj.db_interpolator is not None:
+ columnMap['interpolator'] = \
+ self.convertToDB(obj.db_interpolator, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'mediumtext')
+ if hasattr(obj, 'db_dimension') and obj.db_dimension is not None:
+ columnMap['dimension'] = \
+ self.convertToDB(obj.db_dimension, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_pe_function') and obj.db_pe_function is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_pe_function, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'pos', 'interpolator', 'value', 'dimension', 'parent_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'pe_parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_interpolator') and obj.db_interpolator is not None:
+ columnMap['interpolator'] = \
+ self.convertToDB(obj.db_interpolator, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'mediumtext')
+ if hasattr(obj, 'db_dimension') and obj.db_dimension is not None:
+ columnMap['dimension'] = \
+ self.convertToDB(obj.db_dimension, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_pe_function') and obj.db_pe_function is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_pe_function, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'pe_parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBParameterSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'parameter'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'mediumtext')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_entity_id = entity_id
+ parameter.db_entity_type = entity_type
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ type = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[4], 'str', 'mediumtext')
+ alias = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ parameter = DBParameter(pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias,
+ id=id)
+ parameter.db_parentType = parentType
+ parameter.db_entity_id = entity_id
+ parameter.db_entity_type = entity_type
+ parameter.db_parent = parent
+ parameter.is_dirty = False
+ res[('parameter', id)] = parameter
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'function':
+ p = all_objects[('function', obj.db_parent)]
+ p.db_add_parameter(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'mediumtext')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'pos', 'name', 'type', 'val', 'alias', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'mediumtext')
+ if hasattr(obj, 'db_alias') and obj.db_alias is not None:
+ columnMap['alias'] = \
+ self.convertToDB(obj.db_alias, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'parameter'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPluginDataSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'plugin_data'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ data = self.convertFromDB(row[1], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ plugin_data = DBPluginData(data=data,
+ id=id)
+ plugin_data.db_parentType = parentType
+ plugin_data.db_entity_id = entity_id
+ plugin_data.db_entity_type = entity_type
+ plugin_data.db_parent = parent
+ plugin_data.is_dirty = False
+ res[('plugin_data', id)] = plugin_data
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ data = self.convertFromDB(row[1], 'str', 'varchar(8191)')
+ parentType = self.convertFromDB(row[2], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[3], 'long', 'int')
+ entity_type = self.convertFromDB(row[4], 'str', 'char(16)')
+ parent = self.convertFromDB(row[5], 'long', 'long')
+
+ plugin_data = DBPluginData(data=data,
+ id=id)
+ plugin_data.db_parentType = parentType
+ plugin_data.db_entity_id = entity_id
+ plugin_data.db_entity_type = entity_type
+ plugin_data.db_parent = parent
+ plugin_data.is_dirty = False
+ res[('plugin_data', id)] = plugin_data
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_plugin_data(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_data') and obj.db_data is not None:
+ columnMap['data'] = \
+ self.convertToDB(obj.db_data, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'data', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_data') and obj.db_data is not None:
+ columnMap['data'] = \
+ self.convertToDB(obj.db_data, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'plugin_data'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'function'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_entity_id = entity_id
+ function.db_entity_type = entity_type
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ pos = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ function = DBFunction(pos=pos,
+ name=name,
+ id=id)
+ function.db_parentType = parentType
+ function.db_entity_id = entity_id
+ function.db_entity_type = entity_type
+ function.db_parent = parent
+ function.is_dirty = False
+ res[('function', id)] = function
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_function(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'pos', 'name', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_parameters:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'action_annotation'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action_annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ action_id = self.convertFromDB(row[3], 'long', 'int')
+ date = self.convertFromDB(row[4], 'datetime', 'datetime')
+ user = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ actionAnnotation = DBActionAnnotation(key=key,
+ value=value,
+ action_id=action_id,
+ date=date,
+ user=user,
+ id=id)
+ actionAnnotation.db_vistrail = vistrail
+ actionAnnotation.db_entity_id = entity_id
+ actionAnnotation.db_entity_type = entity_type
+ actionAnnotation.is_dirty = False
+ res[('actionAnnotation', id)] = actionAnnotation
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action_annotation'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ action_id = self.convertFromDB(row[3], 'long', 'int')
+ date = self.convertFromDB(row[4], 'datetime', 'datetime')
+ user = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ actionAnnotation = DBActionAnnotation(key=key,
+ value=value,
+ action_id=action_id,
+ date=date,
+ user=user,
+ id=id)
+ actionAnnotation.db_vistrail = vistrail
+ actionAnnotation.db_entity_id = entity_id
+ actionAnnotation.db_entity_type = entity_type
+ actionAnnotation.is_dirty = False
+ res[('actionAnnotation', id)] = actionAnnotation
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_actionAnnotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action_annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_action_id') and obj.db_action_id is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action_id, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action_annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_action_id') and obj.db_action_id is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action_id, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action_annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAbstractionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'abstraction'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ internal_version = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ abstraction = DBAbstraction(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ id=id)
+ abstraction.db_parentType = parentType
+ abstraction.db_entity_id = entity_id
+ abstraction.db_entity_type = entity_type
+ abstraction.db_parent = parent
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ cache = self.convertFromDB(row[1], 'int', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ namespace = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ package = self.convertFromDB(row[4], 'str', 'varchar(511)')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ internal_version = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ parentType = self.convertFromDB(row[7], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+ parent = self.convertFromDB(row[10], 'long', 'long')
+
+ abstraction = DBAbstraction(cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ id=id)
+ abstraction.db_parentType = parentType
+ abstraction.db_entity_id = entity_id
+ abstraction.db_entity_type = entity_type
+ abstraction.db_parent = parent
+ abstraction.is_dirty = False
+ res[('abstraction', id)] = abstraction
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_module(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_internal_version') and obj.db_internal_version is not None:
+ columnMap['internal_version'] = \
+ self.convertToDB(obj.db_internal_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'cache', 'name', 'namespace', 'package', 'version', 'internal_version', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_cache') and obj.db_cache is not None:
+ columnMap['cache'] = \
+ self.convertToDB(obj.db_cache, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_namespace') and obj.db_namespace is not None:
+ columnMap['namespace'] = \
+ self.convertToDB(obj.db_namespace, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_package') and obj.db_package is not None:
+ columnMap['package'] = \
+ self.convertToDB(obj.db_package, 'str', 'varchar(511)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_internal_version') and obj.db_internal_version is not None:
+ columnMap['internal_version'] = \
+ self.convertToDB(obj.db_internal_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_location is not None:
+ child = obj.db_location
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_functions:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'abstraction'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_id = self.convertFromDB(row[1], 'long', 'int')
+ entity_type = self.convertFromDB(row[2], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'char(16)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[6], 'long', 'int')
+ group = self.convertFromDB(row[7], 'long', 'int')
+
+ workflow = DBWorkflow(entity_type=entity_type,
+ name=name,
+ version=version,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ workflow.db_entity_id = entity_id
+ workflow.db_group = group
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_id = self.convertFromDB(row[1], 'long', 'int')
+ entity_type = self.convertFromDB(row[2], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ version = self.convertFromDB(row[4], 'str', 'char(16)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+ vistrail_id = self.convertFromDB(row[6], 'long', 'int')
+ group = self.convertFromDB(row[7], 'long', 'int')
+
+ workflow = DBWorkflow(entity_type=entity_type,
+ name=name,
+ version=version,
+ last_modified=last_modified,
+ vistrail_id=vistrail_id,
+ id=id)
+ workflow.db_entity_id = entity_id
+ workflow.db_group = group
+ workflow.is_dirty = False
+ res[('workflow', id)] = workflow
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('group', obj.db_group) in all_objects:
+ p = all_objects[('group', obj.db_group)]
+ p.db_add_workflow(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ if hasattr(obj, 'db_group') and obj.db_group is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_group, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'entity_id', 'entity_type', 'name', 'version', 'last_modified', 'vistrail_id', 'parent_id']
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_vistrail_id') and obj.db_vistrail_id is not None:
+ columnMap['vistrail_id'] = \
+ self.convertToDB(obj.db_vistrail_id, 'long', 'int')
+ if hasattr(obj, 'db_group') and obj.db_group is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_group, 'long', 'int')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_connections:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_plugin_datas:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_others:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_modules:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMashupActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'mashup_action'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ user = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ mashuptrail = self.convertFromDB(row[4], 'long', 'int')
+ entity_id = self.convertFromDB(row[5], 'long', 'int')
+ entity_type = self.convertFromDB(row[6], 'str', 'char(16)')
+
+ mashup_action = DBMashupAction(prevId=prevId,
+ date=date,
+ user=user,
+ id=id)
+ mashup_action.db_mashuptrail = mashuptrail
+ mashup_action.db_entity_id = entity_id
+ mashup_action.db_entity_type = entity_type
+ mashup_action.is_dirty = False
+ res[('mashup_action', id)] = mashup_action
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_action'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ user = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ mashuptrail = self.convertFromDB(row[4], 'long', 'int')
+ entity_id = self.convertFromDB(row[5], 'long', 'int')
+ entity_type = self.convertFromDB(row[6], 'str', 'char(16)')
+
+ mashup_action = DBMashupAction(prevId=prevId,
+ date=date,
+ user=user,
+ id=id)
+ mashup_action.db_mashuptrail = mashuptrail
+ mashup_action.db_entity_id = entity_id
+ mashup_action.db_entity_type = entity_type
+ mashup_action.is_dirty = False
+ res[('mashup_action', id)] = mashup_action
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('mashuptrail', obj.db_mashuptrail) in all_objects:
+ p = all_objects[('mashuptrail', obj.db_mashuptrail)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_mashuptrail') and obj.db_mashuptrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_mashuptrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'prev_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_mashuptrail') and obj.db_mashuptrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_mashuptrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_mashup is not None:
+ child = obj.db_mashup
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'mashup_action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMashuptrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'mashuptrail'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'version', 'vt_version', 'last_modified', 'entity_type']
+ table = 'mashuptrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'char(36)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ vtVersion = self.convertFromDB(row[3], 'long', 'int')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+
+ mashuptrail = DBMashuptrail(name=name,
+ version=version,
+ vtVersion=vtVersion,
+ last_modified=last_modified,
+ id=id)
+ mashuptrail.db_entity_type = entity_type
+ mashuptrail.is_dirty = False
+ res[('mashuptrail', id)] = mashuptrail
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'version', 'vt_version', 'last_modified', 'entity_type']
+ table = 'mashuptrail'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'char(36)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ vtVersion = self.convertFromDB(row[3], 'long', 'int')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+
+ mashuptrail = DBMashuptrail(name=name,
+ version=version,
+ vtVersion=vtVersion,
+ last_modified=last_modified,
+ id=id)
+ mashuptrail.db_entity_type = entity_type
+ mashuptrail.is_dirty = False
+ res[('mashuptrail', id)] = mashuptrail
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'version', 'vt_version', 'last_modified', 'entity_type']
+ table = 'mashuptrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'char(36)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_vtVersion') and obj.db_vtVersion is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vtVersion, 'long', 'int')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'version', 'vt_version', 'last_modified', 'entity_type']
+ table = 'mashuptrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'char(36)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_vtVersion') and obj.db_vtVersion is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vtVersion, 'long', 'int')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_actions:
+ child.db_mashuptrail = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_actionAnnotations:
+ child.db_mashuptrail = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'mashuptrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBRegistrySQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'registry'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ root_descriptor_id = self.convertFromDB(row[3], 'long', 'int')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+
+ registry = DBRegistry(entity_type=entity_type,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ registry.is_dirty = False
+ res[('registry', id)] = registry
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ root_descriptor_id = self.convertFromDB(row[3], 'long', 'int')
+ name = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[5], 'datetime', 'datetime')
+
+ registry = DBRegistry(entity_type=entity_type,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ registry.is_dirty = False
+ res[('registry', id)] = registry
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_root_descriptor_id') and obj.db_root_descriptor_id is not None:
+ columnMap['root_descriptor_id'] = \
+ self.convertToDB(obj.db_root_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'entity_type', 'version', 'root_descriptor_id', 'name', 'last_modified']
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_root_descriptor_id') and obj.db_root_descriptor_id is not None:
+ columnMap['root_descriptor_id'] = \
+ self.convertToDB(obj.db_root_descriptor_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_packages:
+ child.db_registry = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'registry'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMashupComponentSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'mashup_component'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'vtid', 'vttype', 'vtparent_type', 'vtparent_id', 'vtpos', 'vtmid', 'pos', 'type', 'val', 'minVal', 'maxVal', 'stepSize', 'strvaluelist', 'widget', 'seq', 'parent', 'alias_id', 'entity_id', 'entity_type']
+ table = 'mashup_component'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ vtid = self.convertFromDB(row[1], 'long', 'int')
+ vttype = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ vtparent_type = self.convertFromDB(row[3], 'str', 'char(32)')
+ vtparent_id = self.convertFromDB(row[4], 'long', 'int')
+ vtpos = self.convertFromDB(row[5], 'long', 'int')
+ vtmid = self.convertFromDB(row[6], 'long', 'int')
+ pos = self.convertFromDB(row[7], 'long', 'int')
+ type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[9], 'str', 'mediumtext')
+ minVal = self.convertFromDB(row[10], 'str', 'varchar(255)')
+ maxVal = self.convertFromDB(row[11], 'str', 'varchar(255)')
+ stepSize = self.convertFromDB(row[12], 'str', 'varchar(255)')
+ strvaluelist = self.convertFromDB(row[13], 'str', 'mediumtext')
+ widget = self.convertFromDB(row[14], 'str', 'varchar(255)')
+ seq = self.convertFromDB(row[15], 'int', 'int')
+ parent = self.convertFromDB(row[16], 'str', 'varchar(255)')
+ mashup_alias = self.convertFromDB(row[17], 'long', 'int')
+ entity_id = self.convertFromDB(row[18], 'long', 'int')
+ entity_type = self.convertFromDB(row[19], 'str', 'char(16)')
+
+ mashup_component = DBMashupComponent(vtid=vtid,
+ vttype=vttype,
+ vtparent_type=vtparent_type,
+ vtparent_id=vtparent_id,
+ vtpos=vtpos,
+ vtmid=vtmid,
+ pos=pos,
+ type=type,
+ val=val,
+ minVal=minVal,
+ maxVal=maxVal,
+ stepSize=stepSize,
+ strvaluelist=strvaluelist,
+ widget=widget,
+ seq=seq,
+ parent=parent,
+ id=id)
+ mashup_component.db_mashup_alias = mashup_alias
+ mashup_component.db_entity_id = entity_id
+ mashup_component.db_entity_type = entity_type
+ mashup_component.is_dirty = False
+ res[('mashup_component', id)] = mashup_component
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'vtid', 'vttype', 'vtparent_type', 'vtparent_id', 'vtpos', 'vtmid', 'pos', 'type', 'val', 'minVal', 'maxVal', 'stepSize', 'strvaluelist', 'widget', 'seq', 'parent', 'alias_id', 'entity_id', 'entity_type']
+ table = 'mashup_component'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ vtid = self.convertFromDB(row[1], 'long', 'int')
+ vttype = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ vtparent_type = self.convertFromDB(row[3], 'str', 'char(32)')
+ vtparent_id = self.convertFromDB(row[4], 'long', 'int')
+ vtpos = self.convertFromDB(row[5], 'long', 'int')
+ vtmid = self.convertFromDB(row[6], 'long', 'int')
+ pos = self.convertFromDB(row[7], 'long', 'int')
+ type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ val = self.convertFromDB(row[9], 'str', 'mediumtext')
+ minVal = self.convertFromDB(row[10], 'str', 'varchar(255)')
+ maxVal = self.convertFromDB(row[11], 'str', 'varchar(255)')
+ stepSize = self.convertFromDB(row[12], 'str', 'varchar(255)')
+ strvaluelist = self.convertFromDB(row[13], 'str', 'mediumtext')
+ widget = self.convertFromDB(row[14], 'str', 'varchar(255)')
+ seq = self.convertFromDB(row[15], 'int', 'int')
+ parent = self.convertFromDB(row[16], 'str', 'varchar(255)')
+ mashup_alias = self.convertFromDB(row[17], 'long', 'int')
+ entity_id = self.convertFromDB(row[18], 'long', 'int')
+ entity_type = self.convertFromDB(row[19], 'str', 'char(16)')
+
+ mashup_component = DBMashupComponent(vtid=vtid,
+ vttype=vttype,
+ vtparent_type=vtparent_type,
+ vtparent_id=vtparent_id,
+ vtpos=vtpos,
+ vtmid=vtmid,
+ pos=pos,
+ type=type,
+ val=val,
+ minVal=minVal,
+ maxVal=maxVal,
+ stepSize=stepSize,
+ strvaluelist=strvaluelist,
+ widget=widget,
+ seq=seq,
+ parent=parent,
+ id=id)
+ mashup_component.db_mashup_alias = mashup_alias
+ mashup_component.db_entity_id = entity_id
+ mashup_component.db_entity_type = entity_type
+ mashup_component.is_dirty = False
+ res[('mashup_component', id)] = mashup_component
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('mashup_alias', obj.db_mashup_alias) in all_objects:
+ p = all_objects[('mashup_alias', obj.db_mashup_alias)]
+ p.db_add_component(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'vtid', 'vttype', 'vtparent_type', 'vtparent_id', 'vtpos', 'vtmid', 'pos', 'type', 'val', 'minVal', 'maxVal', 'stepSize', 'strvaluelist', 'widget', 'seq', 'parent', 'alias_id', 'entity_id', 'entity_type']
+ table = 'mashup_component'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_vtid') and obj.db_vtid is not None:
+ columnMap['vtid'] = \
+ self.convertToDB(obj.db_vtid, 'long', 'int')
+ if hasattr(obj, 'db_vttype') and obj.db_vttype is not None:
+ columnMap['vttype'] = \
+ self.convertToDB(obj.db_vttype, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vtparent_type') and obj.db_vtparent_type is not None:
+ columnMap['vtparent_type'] = \
+ self.convertToDB(obj.db_vtparent_type, 'str', 'char(32)')
+ if hasattr(obj, 'db_vtparent_id') and obj.db_vtparent_id is not None:
+ columnMap['vtparent_id'] = \
+ self.convertToDB(obj.db_vtparent_id, 'long', 'int')
+ if hasattr(obj, 'db_vtpos') and obj.db_vtpos is not None:
+ columnMap['vtpos'] = \
+ self.convertToDB(obj.db_vtpos, 'long', 'int')
+ if hasattr(obj, 'db_vtmid') and obj.db_vtmid is not None:
+ columnMap['vtmid'] = \
+ self.convertToDB(obj.db_vtmid, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'mediumtext')
+ if hasattr(obj, 'db_minVal') and obj.db_minVal is not None:
+ columnMap['minVal'] = \
+ self.convertToDB(obj.db_minVal, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_maxVal') and obj.db_maxVal is not None:
+ columnMap['maxVal'] = \
+ self.convertToDB(obj.db_maxVal, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_stepSize') and obj.db_stepSize is not None:
+ columnMap['stepSize'] = \
+ self.convertToDB(obj.db_stepSize, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_strvaluelist') and obj.db_strvaluelist is not None:
+ columnMap['strvaluelist'] = \
+ self.convertToDB(obj.db_strvaluelist, 'str', 'mediumtext')
+ if hasattr(obj, 'db_widget') and obj.db_widget is not None:
+ columnMap['widget'] = \
+ self.convertToDB(obj.db_widget, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_seq') and obj.db_seq is not None:
+ columnMap['seq'] = \
+ self.convertToDB(obj.db_seq, 'int', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent'] = \
+ self.convertToDB(obj.db_parent, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_mashup_alias') and obj.db_mashup_alias is not None:
+ columnMap['alias_id'] = \
+ self.convertToDB(obj.db_mashup_alias, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'vtid', 'vttype', 'vtparent_type', 'vtparent_id', 'vtpos', 'vtmid', 'pos', 'type', 'val', 'minVal', 'maxVal', 'stepSize', 'strvaluelist', 'widget', 'seq', 'parent', 'alias_id', 'entity_id', 'entity_type']
+ table = 'mashup_component'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_vtid') and obj.db_vtid is not None:
+ columnMap['vtid'] = \
+ self.convertToDB(obj.db_vtid, 'long', 'int')
+ if hasattr(obj, 'db_vttype') and obj.db_vttype is not None:
+ columnMap['vttype'] = \
+ self.convertToDB(obj.db_vttype, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vtparent_type') and obj.db_vtparent_type is not None:
+ columnMap['vtparent_type'] = \
+ self.convertToDB(obj.db_vtparent_type, 'str', 'char(32)')
+ if hasattr(obj, 'db_vtparent_id') and obj.db_vtparent_id is not None:
+ columnMap['vtparent_id'] = \
+ self.convertToDB(obj.db_vtparent_id, 'long', 'int')
+ if hasattr(obj, 'db_vtpos') and obj.db_vtpos is not None:
+ columnMap['vtpos'] = \
+ self.convertToDB(obj.db_vtpos, 'long', 'int')
+ if hasattr(obj, 'db_vtmid') and obj.db_vtmid is not None:
+ columnMap['vtmid'] = \
+ self.convertToDB(obj.db_vtmid, 'long', 'int')
+ if hasattr(obj, 'db_pos') and obj.db_pos is not None:
+ columnMap['pos'] = \
+ self.convertToDB(obj.db_pos, 'long', 'int')
+ if hasattr(obj, 'db_type') and obj.db_type is not None:
+ columnMap['type'] = \
+ self.convertToDB(obj.db_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_val') and obj.db_val is not None:
+ columnMap['val'] = \
+ self.convertToDB(obj.db_val, 'str', 'mediumtext')
+ if hasattr(obj, 'db_minVal') and obj.db_minVal is not None:
+ columnMap['minVal'] = \
+ self.convertToDB(obj.db_minVal, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_maxVal') and obj.db_maxVal is not None:
+ columnMap['maxVal'] = \
+ self.convertToDB(obj.db_maxVal, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_stepSize') and obj.db_stepSize is not None:
+ columnMap['stepSize'] = \
+ self.convertToDB(obj.db_stepSize, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_strvaluelist') and obj.db_strvaluelist is not None:
+ columnMap['strvaluelist'] = \
+ self.convertToDB(obj.db_strvaluelist, 'str', 'mediumtext')
+ if hasattr(obj, 'db_widget') and obj.db_widget is not None:
+ columnMap['widget'] = \
+ self.convertToDB(obj.db_widget, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_seq') and obj.db_seq is not None:
+ columnMap['seq'] = \
+ self.convertToDB(obj.db_seq, 'int', 'int')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent'] = \
+ self.convertToDB(obj.db_parent, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_mashup_alias') and obj.db_mashup_alias is not None:
+ columnMap['alias_id'] = \
+ self.convertToDB(obj.db_mashup_alias, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'mashup_component'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'annotation'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'mediumtext')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_entity_id = entity_id
+ annotation.db_entity_type = entity_type
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'mediumtext')
+ parentType = self.convertFromDB(row[3], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[4], 'long', 'int')
+ entity_type = self.convertFromDB(row[5], 'str', 'char(16)')
+ parent = self.convertFromDB(row[6], 'long', 'long')
+
+ annotation = DBAnnotation(key=key,
+ value=value,
+ id=id)
+ annotation.db_parentType = parentType
+ annotation.db_entity_id = entity_id
+ annotation.db_entity_type = entity_type
+ annotation.db_parent = parent
+ annotation.is_dirty = False
+ res[('annotation', id)] = annotation
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'vistrail':
+ p = all_objects[('vistrail', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module':
+ p = all_objects[('module', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'action':
+ p = all_objects[('action', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'abstraction':
+ p = all_objects[('abstraction', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'mashuptrail':
+ p = all_objects[('mashuptrail', obj.db_parent)]
+ p.db_add_annotation(obj)
+ elif obj.db_parentType == 'group':
+ p = all_objects[('group', obj.db_parent)]
+ p.db_add_annotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'mediumtext')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'akey', 'value', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'mediumtext')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBChangeSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'change_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_entity_id = entity_id
+ change.db_entity_type = entity_type
+ change.is_dirty = False
+ res[('change', id)] = change
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ oldObjId = self.convertFromDB(row[2], 'long', 'int')
+ newObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjId = self.convertFromDB(row[4], 'long', 'int')
+ parentObjType = self.convertFromDB(row[5], 'str', 'char(16)')
+ action = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ change = DBChange(what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ change.db_action = action
+ change.db_entity_id = entity_id
+ change.db_entity_type = entity_type
+ change.is_dirty = False
+ res[('change', id)] = change
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'what', 'old_obj_id', 'new_obj_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_oldObjId') and obj.db_oldObjId is not None:
+ columnMap['old_obj_id'] = \
+ self.convertToDB(obj.db_oldObjId, 'long', 'int')
+ if hasattr(obj, 'db_newObjId') and obj.db_newObjId is not None:
+ columnMap['new_obj_id'] = \
+ self.convertToDB(obj.db_newObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ if obj.db_data is not None:
+ child = obj.db_data
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'change_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBGroupExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'group_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ group_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ group_type = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[7], 'int', 'int')
+ error = self.convertFromDB(row[8], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[9], 'long', 'int')
+ parentType = self.convertFromDB(row[10], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[11], 'long', 'int')
+ entity_type = self.convertFromDB(row[12], 'str', 'char(16)')
+ parent = self.convertFromDB(row[13], 'long', 'long')
+
+ group_exec = DBGroupExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ group_exec.db_parentType = parentType
+ group_exec.db_entity_id = entity_id
+ group_exec.db_entity_type = entity_type
+ group_exec.db_parent = parent
+ group_exec.is_dirty = False
+ res[('group_exec', id)] = group_exec
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ group_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ group_type = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[7], 'int', 'int')
+ error = self.convertFromDB(row[8], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[9], 'long', 'int')
+ parentType = self.convertFromDB(row[10], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[11], 'long', 'int')
+ entity_type = self.convertFromDB(row[12], 'str', 'char(16)')
+ parent = self.convertFromDB(row[13], 'long', 'long')
+
+ group_exec = DBGroupExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ group_exec.db_parentType = parentType
+ group_exec.db_entity_id = entity_id
+ group_exec.db_entity_type = entity_type
+ group_exec.db_parent = parent
+ group_exec.is_dirty = False
+ res[('group_exec', id)] = group_exec
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_group_name') and obj.db_group_name is not None:
+ columnMap['group_name'] = \
+ self.convertToDB(obj.db_group_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_group_type') and obj.db_group_type is not None:
+ columnMap['group_type'] = \
+ self.convertToDB(obj.db_group_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'group_name', 'group_type', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_group_name') and obj.db_group_name is not None:
+ columnMap['group_name'] = \
+ self.convertToDB(obj.db_group_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_group_type') and obj.db_group_type is not None:
+ columnMap['group_type'] = \
+ self.convertToDB(obj.db_group_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'group_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPackageSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'package'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ identifier = self.convertFromDB(row[2], 'str', 'varchar(1023)')
+ codepath = self.convertFromDB(row[3], 'str', 'varchar(1023)')
+ load_configuration = self.convertFromDB(row[4], 'int', 'int')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ description = self.convertFromDB(row[6], 'str', 'varchar(1023)')
+ registry = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ package = DBPackage(name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ id=id)
+ package.db_registry = registry
+ package.db_entity_id = entity_id
+ package.db_entity_type = entity_type
+ package.is_dirty = False
+ res[('package', id)] = package
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ name = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ identifier = self.convertFromDB(row[2], 'str', 'varchar(1023)')
+ codepath = self.convertFromDB(row[3], 'str', 'varchar(1023)')
+ load_configuration = self.convertFromDB(row[4], 'int', 'int')
+ version = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ description = self.convertFromDB(row[6], 'str', 'varchar(1023)')
+ registry = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ package = DBPackage(name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ id=id)
+ package.db_registry = registry
+ package.db_entity_id = entity_id
+ package.db_entity_type = entity_type
+ package.is_dirty = False
+ res[('package', id)] = package
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('registry', obj.db_registry) in all_objects:
+ p = all_objects[('registry', obj.db_registry)]
+ p.db_add_package(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_identifier') and obj.db_identifier is not None:
+ columnMap['identifier'] = \
+ self.convertToDB(obj.db_identifier, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_codepath') and obj.db_codepath is not None:
+ columnMap['codepath'] = \
+ self.convertToDB(obj.db_codepath, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_load_configuration') and obj.db_load_configuration is not None:
+ columnMap['load_configuration'] = \
+ self.convertToDB(obj.db_load_configuration, 'int', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_description') and obj.db_description is not None:
+ columnMap['description'] = \
+ self.convertToDB(obj.db_description, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_registry') and obj.db_registry is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_registry, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'name', 'identifier', 'codepath', 'load_configuration', 'version', 'description', 'parent_id', 'entity_id', 'entity_type']
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_identifier') and obj.db_identifier is not None:
+ columnMap['identifier'] = \
+ self.convertToDB(obj.db_identifier, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_codepath') and obj.db_codepath is not None:
+ columnMap['codepath'] = \
+ self.convertToDB(obj.db_codepath, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_load_configuration') and obj.db_load_configuration is not None:
+ columnMap['load_configuration'] = \
+ self.convertToDB(obj.db_load_configuration, 'int', 'int')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_description') and obj.db_description is not None:
+ columnMap['description'] = \
+ self.convertToDB(obj.db_description, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_registry') and obj.db_registry is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_registry, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_module_descriptors:
+ child.db_package = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'package'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBWorkflowExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'workflow_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ vt_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[5], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[6], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[7], 'long', 'int')
+ parent_type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[9], 'long', 'int')
+ completed = self.convertFromDB(row[10], 'int', 'int')
+ name = self.convertFromDB(row[11], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[12], 'long', 'int')
+ entity_id = self.convertFromDB(row[13], 'long', 'int')
+ entity_type = self.convertFromDB(row[14], 'str', 'char(16)')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_entity_id = entity_id
+ workflow_exec.db_entity_type = entity_type
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ user = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ ip = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ vt_version = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ ts_start = self.convertFromDB(row[5], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[6], 'datetime', 'datetime')
+ parent_id = self.convertFromDB(row[7], 'long', 'int')
+ parent_type = self.convertFromDB(row[8], 'str', 'varchar(255)')
+ parent_version = self.convertFromDB(row[9], 'long', 'int')
+ completed = self.convertFromDB(row[10], 'int', 'int')
+ name = self.convertFromDB(row[11], 'str', 'varchar(255)')
+ log = self.convertFromDB(row[12], 'long', 'int')
+ entity_id = self.convertFromDB(row[13], 'long', 'int')
+ entity_type = self.convertFromDB(row[14], 'str', 'char(16)')
+
+ workflow_exec = DBWorkflowExec(user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ id=id)
+ workflow_exec.db_log = log
+ workflow_exec.db_entity_id = entity_id
+ workflow_exec.db_entity_type = entity_type
+ workflow_exec.is_dirty = False
+ res[('workflow_exec', id)] = workflow_exec
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('log', obj.db_log) in all_objects:
+ p = all_objects[('log', obj.db_log)]
+ p.db_add_workflow_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'user', 'ip', 'session', 'vt_version', 'ts_start', 'ts_end', 'parent_id', 'parent_type', 'parent_version', 'completed', 'name', 'log_id', 'entity_id', 'entity_type']
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ip') and obj.db_ip is not None:
+ columnMap['ip'] = \
+ self.convertToDB(obj.db_ip, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_vt_version') and obj.db_vt_version is not None:
+ columnMap['vt_version'] = \
+ self.convertToDB(obj.db_vt_version, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_parent_id') and obj.db_parent_id is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent_id, 'long', 'int')
+ if hasattr(obj, 'db_parent_type') and obj.db_parent_type is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parent_type, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_parent_version') and obj.db_parent_version is not None:
+ columnMap['parent_version'] = \
+ self.convertToDB(obj.db_parent_version, 'long', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_log') and obj.db_log is not None:
+ columnMap['log_id'] = \
+ self.convertToDB(obj.db_log, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'workflow_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBParameterExplorationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'parameter_exploration'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'action_id', 'name', 'date', 'user', 'dims', 'layout', 'parent_id', 'entity_id', 'entity_type']
+ table = 'parameter_exploration'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ action_id = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ date = self.convertFromDB(row[3], 'datetime', 'datetime')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ dims = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ layout = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ parameter_exploration = DBParameterExploration(action_id=action_id,
+ name=name,
+ date=date,
+ user=user,
+ dims=dims,
+ layout=layout,
+ id=id)
+ parameter_exploration.db_vistrail = vistrail
+ parameter_exploration.db_entity_id = entity_id
+ parameter_exploration.db_entity_type = entity_type
+ parameter_exploration.is_dirty = False
+ res[('parameter_exploration', id)] = parameter_exploration
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'action_id', 'name', 'date', 'user', 'dims', 'layout', 'parent_id', 'entity_id', 'entity_type']
+ table = 'parameter_exploration'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ action_id = self.convertFromDB(row[1], 'long', 'int')
+ name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ date = self.convertFromDB(row[3], 'datetime', 'datetime')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ dims = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ layout = self.convertFromDB(row[6], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[7], 'long', 'int')
+ entity_id = self.convertFromDB(row[8], 'long', 'int')
+ entity_type = self.convertFromDB(row[9], 'str', 'char(16)')
+
+ parameter_exploration = DBParameterExploration(action_id=action_id,
+ name=name,
+ date=date,
+ user=user,
+ dims=dims,
+ layout=layout,
+ id=id)
+ parameter_exploration.db_vistrail = vistrail
+ parameter_exploration.db_entity_id = entity_id
+ parameter_exploration.db_entity_type = entity_type
+ parameter_exploration.is_dirty = False
+ res[('parameter_exploration', id)] = parameter_exploration
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_parameter_exploration(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'action_id', 'name', 'date', 'user', 'dims', 'layout', 'parent_id', 'entity_id', 'entity_type']
+ table = 'parameter_exploration'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_action_id') and obj.db_action_id is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_dims') and obj.db_dims is not None:
+ columnMap['dims'] = \
+ self.convertToDB(obj.db_dims, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_layout') and obj.db_layout is not None:
+ columnMap['layout'] = \
+ self.convertToDB(obj.db_layout, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'action_id', 'name', 'date', 'user', 'dims', 'layout', 'parent_id', 'entity_id', 'entity_type']
+ table = 'parameter_exploration'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_action_id') and obj.db_action_id is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action_id, 'long', 'int')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_dims') and obj.db_dims is not None:
+ columnMap['dims'] = \
+ self.convertToDB(obj.db_dims, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_layout') and obj.db_layout is not None:
+ columnMap['layout'] = \
+ self.convertToDB(obj.db_layout, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_functions:
+ child.db_parameter_exploration = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'parameter_exploration'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBLoopExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'loop_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ iteration = self.convertFromDB(row[3], 'int', 'int')
+ completed = self.convertFromDB(row[4], 'int', 'int')
+ error = self.convertFromDB(row[5], 'str', 'varchar(1023)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ loop_exec = DBLoopExec(ts_start=ts_start,
+ ts_end=ts_end,
+ iteration=iteration,
+ completed=completed,
+ error=error,
+ id=id)
+ loop_exec.db_parentType = parentType
+ loop_exec.db_entity_id = entity_id
+ loop_exec.db_entity_type = entity_type
+ loop_exec.db_parent = parent
+ loop_exec.is_dirty = False
+ res[('loop_exec', id)] = loop_exec
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ iteration = self.convertFromDB(row[3], 'int', 'int')
+ completed = self.convertFromDB(row[4], 'int', 'int')
+ error = self.convertFromDB(row[5], 'str', 'varchar(1023)')
+ parentType = self.convertFromDB(row[6], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+ parent = self.convertFromDB(row[9], 'long', 'long')
+
+ loop_exec = DBLoopExec(ts_start=ts_start,
+ ts_end=ts_end,
+ iteration=iteration,
+ completed=completed,
+ error=error,
+ id=id)
+ loop_exec.db_parentType = parentType
+ loop_exec.db_entity_id = entity_id
+ loop_exec.db_entity_type = entity_type
+ loop_exec.db_parent = parent
+ loop_exec.is_dirty = False
+ res[('loop_exec', id)] = loop_exec
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'module_exec':
+ p = all_objects[('module_exec', obj.db_parent)]
+ p.db_add_loop_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_iteration') and obj.db_iteration is not None:
+ columnMap['iteration'] = \
+ self.convertToDB(obj.db_iteration, 'int', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'ts_start', 'ts_end', 'iteration', 'completed', 'error', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_iteration') and obj.db_iteration is not None:
+ columnMap['iteration'] = \
+ self.convertToDB(obj.db_iteration, 'int', 'int')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_item_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'loop_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBMashupActionAnnotationSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'mashup_action_annotation'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_action_annotation'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ action_id = self.convertFromDB(row[3], 'long', 'int')
+ date = self.convertFromDB(row[4], 'datetime', 'datetime')
+ user = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ mashuptrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ mashup_actionAnnotation = DBMashupActionAnnotation(key=key,
+ value=value,
+ action_id=action_id,
+ date=date,
+ user=user,
+ id=id)
+ mashup_actionAnnotation.db_mashuptrail = mashuptrail
+ mashup_actionAnnotation.db_entity_id = entity_id
+ mashup_actionAnnotation.db_entity_type = entity_type
+ mashup_actionAnnotation.is_dirty = False
+ res[('mashup_actionAnnotation', id)] = mashup_actionAnnotation
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_action_annotation'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ key = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ value = self.convertFromDB(row[2], 'str', 'varchar(8191)')
+ action_id = self.convertFromDB(row[3], 'long', 'int')
+ date = self.convertFromDB(row[4], 'datetime', 'datetime')
+ user = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ mashuptrail = self.convertFromDB(row[6], 'long', 'int')
+ entity_id = self.convertFromDB(row[7], 'long', 'int')
+ entity_type = self.convertFromDB(row[8], 'str', 'char(16)')
+
+ mashup_actionAnnotation = DBMashupActionAnnotation(key=key,
+ value=value,
+ action_id=action_id,
+ date=date,
+ user=user,
+ id=id)
+ mashup_actionAnnotation.db_mashuptrail = mashuptrail
+ mashup_actionAnnotation.db_entity_id = entity_id
+ mashup_actionAnnotation.db_entity_type = entity_type
+ mashup_actionAnnotation.is_dirty = False
+ res[('mashup_actionAnnotation', id)] = mashup_actionAnnotation
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('mashuptrail', obj.db_mashuptrail) in all_objects:
+ p = all_objects[('mashuptrail', obj.db_mashuptrail)]
+ p.db_add_actionAnnotation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_action_annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_action_id') and obj.db_action_id is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action_id, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_mashuptrail') and obj.db_mashuptrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_mashuptrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'akey', 'value', 'action_id', 'date', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'mashup_action_annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_key') and obj.db_key is not None:
+ columnMap['akey'] = \
+ self.convertToDB(obj.db_key, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_value') and obj.db_value is not None:
+ columnMap['value'] = \
+ self.convertToDB(obj.db_value, 'str', 'varchar(8191)')
+ if hasattr(obj, 'db_action_id') and obj.db_action_id is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action_id, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_mashuptrail') and obj.db_mashuptrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_mashuptrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'mashup_action_annotation'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBConnectionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'connection_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[2], 'long', 'int')
+ entity_type = self.convertFromDB(row[3], 'str', 'char(16)')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_entity_id = entity_id
+ connection.db_entity_type = entity_type
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ parentType = self.convertFromDB(row[1], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[2], 'long', 'int')
+ entity_type = self.convertFromDB(row[3], 'str', 'char(16)')
+ parent = self.convertFromDB(row[4], 'long', 'long')
+
+ connection = DBConnection(id=id)
+ connection.db_parentType = parentType
+ connection.db_entity_id = entity_id
+ connection.db_entity_type = entity_type
+ connection.db_parent = parent
+ connection.is_dirty = False
+ res[('connection', id)] = connection
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow':
+ p = all_objects[('workflow', obj.db_parent)]
+ p.db_add_connection(obj)
+ elif obj.db_parentType == 'add':
+ p = all_objects[('add', obj.db_parent)]
+ p.db_add_data(obj)
+ elif obj.db_parentType == 'change':
+ p = all_objects[('change', obj.db_parent)]
+ p.db_add_data(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_ports:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'connection_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBPEFunctionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'pe_function'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'module_id', 'port_name', 'is_alias', 'parent_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'pe_function'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ module_id = self.convertFromDB(row[1], 'long', 'int')
+ port_name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ is_alias = self.convertFromDB(row[3], 'long', 'int')
+ parentType = self.convertFromDB(row[4], 'str', 'char(32)')
+ parameter_exploration = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ pe_function = DBPEFunction(module_id=module_id,
+ port_name=port_name,
+ id=id)
+ pe_function.db_parentType = parentType
+ pe_function.db_parameter_exploration = parameter_exploration
+ pe_function.db_entity_id = entity_id
+ pe_function.db_entity_type = entity_type
+ pe_function.is_dirty = False
+ res[('pe_function', id)] = pe_function
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'module_id', 'port_name', 'is_alias', 'parent_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'pe_function'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ module_id = self.convertFromDB(row[1], 'long', 'int')
+ port_name = self.convertFromDB(row[2], 'str', 'varchar(255)')
+ is_alias = self.convertFromDB(row[3], 'long', 'int')
+ parentType = self.convertFromDB(row[4], 'str', 'char(32)')
+ parameter_exploration = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ pe_function = DBPEFunction(module_id=module_id,
+ port_name=port_name,
+ id=id)
+ pe_function.db_parentType = parentType
+ pe_function.db_parameter_exploration = parameter_exploration
+ pe_function.db_entity_id = entity_id
+ pe_function.db_entity_type = entity_type
+ pe_function.is_dirty = False
+ res[('pe_function', id)] = pe_function
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('parameter_exploration', obj.db_parameter_exploration) in all_objects:
+ p = all_objects[('parameter_exploration', obj.db_parameter_exploration)]
+ p.db_add_function(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'module_id', 'port_name', 'is_alias', 'parent_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'pe_function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_port_name') and obj.db_port_name is not None:
+ columnMap['port_name'] = \
+ self.convertToDB(obj.db_port_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_is_alias') and obj.db_is_alias is not None:
+ columnMap['is_alias'] = \
+ self.convertToDB(obj.db_is_alias, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_parameter_exploration') and obj.db_parameter_exploration is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parameter_exploration, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'module_id', 'port_name', 'is_alias', 'parent_type', 'parent_id', 'entity_id', 'entity_type']
+ table = 'pe_function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_port_name') and obj.db_port_name is not None:
+ columnMap['port_name'] = \
+ self.convertToDB(obj.db_port_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_is_alias') and obj.db_is_alias is not None:
+ columnMap['is_alias'] = \
+ self.convertToDB(obj.db_is_alias, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_parameter_exploration') and obj.db_parameter_exploration is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parameter_exploration, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_parameters:
+ child.db_pe_function = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'pe_function'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBActionSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'action'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ id=id)
+ action.db_vistrail = vistrail
+ action.db_entity_id = entity_id
+ action.db_entity_type = entity_type
+ action.is_dirty = False
+ res[('action', id)] = action
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ prevId = self.convertFromDB(row[1], 'long', 'int')
+ date = self.convertFromDB(row[2], 'datetime', 'datetime')
+ session = self.convertFromDB(row[3], 'long', 'int')
+ user = self.convertFromDB(row[4], 'str', 'varchar(255)')
+ vistrail = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ action = DBAction(prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ id=id)
+ action.db_vistrail = vistrail
+ action.db_entity_id = entity_id
+ action.db_entity_type = entity_type
+ action.is_dirty = False
+ res[('action', id)] = action
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('vistrail', obj.db_vistrail) in all_objects:
+ p = all_objects[('vistrail', obj.db_vistrail)]
+ p.db_add_action(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'prev_id', 'date', 'session', 'user', 'parent_id', 'entity_id', 'entity_type']
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_prevId') and obj.db_prevId is not None:
+ columnMap['prev_id'] = \
+ self.convertToDB(obj.db_prevId, 'long', 'int')
+ if hasattr(obj, 'db_date') and obj.db_date is not None:
+ columnMap['date'] = \
+ self.convertToDB(obj.db_date, 'datetime', 'datetime')
+ if hasattr(obj, 'db_session') and obj.db_session is not None:
+ columnMap['session'] = \
+ self.convertToDB(obj.db_session, 'long', 'int')
+ if hasattr(obj, 'db_user') and obj.db_user is not None:
+ columnMap['user'] = \
+ self.convertToDB(obj.db_user, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_vistrail') and obj.db_vistrail is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_vistrail, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_operations:
+ child.db_action = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'action'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBDeleteSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'delete_tbl'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_entity_id = entity_id
+ delete.db_entity_type = entity_type
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ what = self.convertFromDB(row[1], 'str', 'varchar(255)')
+ objectId = self.convertFromDB(row[2], 'long', 'int')
+ parentObjId = self.convertFromDB(row[3], 'long', 'int')
+ parentObjType = self.convertFromDB(row[4], 'str', 'char(16)')
+ action = self.convertFromDB(row[5], 'long', 'int')
+ entity_id = self.convertFromDB(row[6], 'long', 'int')
+ entity_type = self.convertFromDB(row[7], 'str', 'char(16)')
+
+ delete = DBDelete(what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType,
+ id=id)
+ delete.db_action = action
+ delete.db_entity_id = entity_id
+ delete.db_entity_type = entity_type
+ delete.is_dirty = False
+ res[('delete', id)] = delete
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if ('action', obj.db_action) in all_objects:
+ p = all_objects[('action', obj.db_action)]
+ p.db_add_operation(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'what', 'object_id', 'par_obj_id', 'par_obj_type', 'action_id', 'entity_id', 'entity_type']
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_what') and obj.db_what is not None:
+ columnMap['what'] = \
+ self.convertToDB(obj.db_what, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_objectId') and obj.db_objectId is not None:
+ columnMap['object_id'] = \
+ self.convertToDB(obj.db_objectId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjId') and obj.db_parentObjId is not None:
+ columnMap['par_obj_id'] = \
+ self.convertToDB(obj.db_parentObjId, 'long', 'int')
+ if hasattr(obj, 'db_parentObjType') and obj.db_parentObjType is not None:
+ columnMap['par_obj_type'] = \
+ self.convertToDB(obj.db_parentObjType, 'str', 'char(16)')
+ if hasattr(obj, 'db_action') and obj.db_action is not None:
+ columnMap['action_id'] = \
+ self.convertToDB(obj.db_action, 'long', 'int')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ pass
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'delete_tbl'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBVistrailSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'vistrail'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ global_props['entity_id'] = self.convertToDB(id, 'long', 'int')
+ entity_type = self.convertFromDB(row[1], 'str', 'char(16)')
+ global_props['entity_type'] = self.convertToDB(entity_type, 'str', 'char(16)')
+ version = self.convertFromDB(row[2], 'str', 'char(16)')
+ name = self.convertFromDB(row[3], 'str', 'varchar(255)')
+ last_modified = self.convertFromDB(row[4], 'datetime', 'datetime')
+
+ vistrail = DBVistrail(entity_type=entity_type,
+ version=version,
+ name=name,
+ last_modified=last_modified,
+ id=id)
+ vistrail.is_dirty = False
+ res[('vistrail', id)] = vistrail
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ pass
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'entity_type', 'version', 'name', 'last_modified']
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_version') and obj.db_version is not None:
+ columnMap['version'] = \
+ self.convertToDB(obj.db_version, 'str', 'char(16)')
+ if hasattr(obj, 'db_name') and obj.db_name is not None:
+ columnMap['name'] = \
+ self.convertToDB(obj.db_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_last_modified') and obj.db_last_modified is not None:
+ columnMap['last_modified'] = \
+ self.convertToDB(obj.db_last_modified, 'datetime', 'datetime')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ if obj.db_id is None:
+ obj.db_id = lastId
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ global_props['entity_type'] = self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ global_props['entity_id'] = self.convertToDB(obj.db_id, 'long', 'int')
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_actions:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_tags:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_vistrailVariables:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_parameter_explorations:
+ child.db_vistrail = obj.db_id
+ for child in obj.db_actionAnnotations:
+ child.db_vistrail = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'vistrail'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+class DBModuleExecSQLDAOBase(SQLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+ self.table = 'module_exec'
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def get_sql_columns(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+
+ dbCommand = self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+ data = self.executeSQL(db, dbCommand, True)
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ module_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[6], 'int', 'int')
+ error = self.convertFromDB(row[7], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[8], 'long', 'int')
+ parentType = self.convertFromDB(row[9], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[10], 'long', 'int')
+ entity_type = self.convertFromDB(row[11], 'str', 'char(16)')
+ parent = self.convertFromDB(row[12], 'long', 'long')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ module_exec.db_parentType = parentType
+ module_exec.db_entity_id = entity_id
+ module_exec.db_entity_type = entity_type
+ module_exec.db_parent = parent
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+ return res
+
+ def get_sql_select(self, db, global_props,lock=False):
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = global_props
+ orderBy = 'id'
+ return self.createSQLSelect(table, columns, whereMap, orderBy, lock)
+
+ def process_sql_columns(self, data, global_props):
+ res = {}
+ for row in data:
+ id = self.convertFromDB(row[0], 'long', 'int')
+ ts_start = self.convertFromDB(row[1], 'datetime', 'datetime')
+ ts_end = self.convertFromDB(row[2], 'datetime', 'datetime')
+ cached = self.convertFromDB(row[3], 'int', 'int')
+ module_id = self.convertFromDB(row[4], 'long', 'int')
+ module_name = self.convertFromDB(row[5], 'str', 'varchar(255)')
+ completed = self.convertFromDB(row[6], 'int', 'int')
+ error = self.convertFromDB(row[7], 'str', 'varchar(1023)')
+ machine_id = self.convertFromDB(row[8], 'long', 'int')
+ parentType = self.convertFromDB(row[9], 'str', 'char(32)')
+ entity_id = self.convertFromDB(row[10], 'long', 'int')
+ entity_type = self.convertFromDB(row[11], 'str', 'char(16)')
+ parent = self.convertFromDB(row[12], 'long', 'long')
+
+ module_exec = DBModuleExec(ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ id=id)
+ module_exec.db_parentType = parentType
+ module_exec.db_entity_id = entity_id
+ module_exec.db_entity_type = entity_type
+ module_exec.db_parent = parent
+ module_exec.is_dirty = False
+ res[('module_exec', id)] = module_exec
+ return res
+
+ def from_sql_fast(self, obj, all_objects):
+ if obj.db_parentType == 'workflow_exec':
+ p = all_objects[('workflow_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'group_exec':
+ p = all_objects[('group_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+ elif obj.db_parentType == 'loop_exec':
+ p = all_objects[('loop_exec', obj.db_parent)]
+ p.db_add_item_exec(obj)
+
+ def set_sql_columns(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ lastId = self.executeSQL(db, dbCommand, False)
+
+ def set_sql_command(self, db, obj, global_props, do_copy=True):
+ if not do_copy and not obj.is_dirty:
+ return None
+ columns = ['id', 'ts_start', 'ts_end', 'cached', 'module_id', 'module_name', 'completed', 'error', 'machine_id', 'parent_type', 'entity_id', 'entity_type', 'parent_id']
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ columnMap = {}
+ if hasattr(obj, 'db_id') and obj.db_id is not None:
+ columnMap['id'] = \
+ self.convertToDB(obj.db_id, 'long', 'int')
+ if hasattr(obj, 'db_ts_start') and obj.db_ts_start is not None:
+ columnMap['ts_start'] = \
+ self.convertToDB(obj.db_ts_start, 'datetime', 'datetime')
+ if hasattr(obj, 'db_ts_end') and obj.db_ts_end is not None:
+ columnMap['ts_end'] = \
+ self.convertToDB(obj.db_ts_end, 'datetime', 'datetime')
+ if hasattr(obj, 'db_cached') and obj.db_cached is not None:
+ columnMap['cached'] = \
+ self.convertToDB(obj.db_cached, 'int', 'int')
+ if hasattr(obj, 'db_module_id') and obj.db_module_id is not None:
+ columnMap['module_id'] = \
+ self.convertToDB(obj.db_module_id, 'long', 'int')
+ if hasattr(obj, 'db_module_name') and obj.db_module_name is not None:
+ columnMap['module_name'] = \
+ self.convertToDB(obj.db_module_name, 'str', 'varchar(255)')
+ if hasattr(obj, 'db_completed') and obj.db_completed is not None:
+ columnMap['completed'] = \
+ self.convertToDB(obj.db_completed, 'int', 'int')
+ if hasattr(obj, 'db_error') and obj.db_error is not None:
+ columnMap['error'] = \
+ self.convertToDB(obj.db_error, 'str', 'varchar(1023)')
+ if hasattr(obj, 'db_machine_id') and obj.db_machine_id is not None:
+ columnMap['machine_id'] = \
+ self.convertToDB(obj.db_machine_id, 'long', 'int')
+ if hasattr(obj, 'db_parentType') and obj.db_parentType is not None:
+ columnMap['parent_type'] = \
+ self.convertToDB(obj.db_parentType, 'str', 'char(32)')
+ if hasattr(obj, 'db_entity_id') and obj.db_entity_id is not None:
+ columnMap['entity_id'] = \
+ self.convertToDB(obj.db_entity_id, 'long', 'int')
+ if hasattr(obj, 'db_entity_type') and obj.db_entity_type is not None:
+ columnMap['entity_type'] = \
+ self.convertToDB(obj.db_entity_type, 'str', 'char(16)')
+ if hasattr(obj, 'db_parent') and obj.db_parent is not None:
+ columnMap['parent_id'] = \
+ self.convertToDB(obj.db_parent, 'long', 'long')
+ columnMap.update(global_props)
+
+ if obj.is_new or do_copy:
+ dbCommand = self.createSQLInsert(table, columnMap)
+ else:
+ dbCommand = self.createSQLUpdate(table, columnMap, whereMap)
+ return dbCommand
+
+ def set_sql_process(self, obj, global_props, lastId):
+ pass
+
+ def to_sql_fast(self, obj, do_copy=True):
+ for child in obj.db_annotations:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+ for child in obj.db_loop_execs:
+ child.db_parentType = obj.vtType
+ child.db_parent = obj.db_id
+
+ def delete_sql_column(self, db, obj, global_props):
+ table = 'module_exec'
+ whereMap = {}
+ whereMap.update(global_props)
+ if obj.db_id is not None:
+ keyStr = self.convertToDB(obj.db_id, 'long', 'int')
+ whereMap['id'] = keyStr
+ dbCommand = self.createSQLDelete(table, whereMap)
+ self.executeSQL(db, dbCommand, False)
+
+"""generated automatically by auto_dao.py"""
+
+class SQLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'vistrailVariable' not in self:
+ self['vistrailVariable'] = DBVistrailVariableSQLDAOBase(self)
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecSQLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleSQLDAOBase(self)
+ if 'module_descriptor' not in self:
+ self['module_descriptor'] = DBModuleDescriptorSQLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagSQLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortSQLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupSQLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogSQLDAOBase(self)
+ if 'mashup_alias' not in self:
+ self['mashup_alias'] = DBMashupAliasSQLDAOBase(self)
+ if 'mashup' not in self:
+ self['mashup'] = DBMashupSQLDAOBase(self)
+ if 'portSpecItem' not in self:
+ self['portSpecItem'] = DBPortSpecItemSQLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineSQLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddSQLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherSQLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationSQLDAOBase(self)
+ if 'pe_parameter' not in self:
+ self['pe_parameter'] = DBPEParameterSQLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterSQLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataSQLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionSQLDAOBase(self)
+ if 'actionAnnotation' not in self:
+ self['actionAnnotation'] = DBActionAnnotationSQLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionSQLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowSQLDAOBase(self)
+ if 'mashup_action' not in self:
+ self['mashup_action'] = DBMashupActionSQLDAOBase(self)
+ if 'mashuptrail' not in self:
+ self['mashuptrail'] = DBMashuptrailSQLDAOBase(self)
+ if 'registry' not in self:
+ self['registry'] = DBRegistrySQLDAOBase(self)
+ if 'mashup_component' not in self:
+ self['mashup_component'] = DBMashupComponentSQLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationSQLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeSQLDAOBase(self)
+ if 'group_exec' not in self:
+ self['group_exec'] = DBGroupExecSQLDAOBase(self)
+ if 'package' not in self:
+ self['package'] = DBPackageSQLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecSQLDAOBase(self)
+ if 'parameter_exploration' not in self:
+ self['parameter_exploration'] = DBParameterExplorationSQLDAOBase(self)
+ if 'loop_exec' not in self:
+ self['loop_exec'] = DBLoopExecSQLDAOBase(self)
+ if 'mashup_actionAnnotation' not in self:
+ self['mashup_actionAnnotation'] = DBMashupActionAnnotationSQLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionSQLDAOBase(self)
+ if 'pe_function' not in self:
+ self['pe_function'] = DBPEFunctionSQLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionSQLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteSQLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailSQLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecSQLDAOBase(self)
diff --git a/vistrails/db/versions/v1_0_3/persistence/sql/sql_dao.py b/vistrails/db/versions/v1_0_3/persistence/sql/sql_dao.py
new file mode 100644
index 0000000..eab1acc
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/persistence/sql/sql_dao.py
@@ -0,0 +1,259 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+from vistrails.db import VistrailsDBException
+from vistrails.db.services.io import get_db_lib
+from vistrails.core import debug
+
+class SQLDAO:
+ def __init__(self):
+ pass
+
+ def convertFromDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'date':
+ if db_type == 'date':
+ return value
+ else:
+ return date(*strptime(str(value), '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ if db_type == 'datetime':
+ return value
+ else:
+ return datetime(*strptime(str(value),
+ '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertWarning(self, before, after, _from, to):
+ text = ["Value truncated when saving to database",
+ "%s truncated to %s\nwhile converting '%s' to '%s'"]
+ debug.warning(text[0], text[1] % (before, after, _from, to))
+
+ def convertToDB(self, value, type, db_type):
+ if value is not None:
+ if type == 'str':
+ value = str(value)
+ if db_type.startswith('varchar'):
+ try:
+ length = int(db_type[8:-1])
+ if len(value) > length:
+ self.convertWarning(value, value[:length],
+ type, db_type)
+ value = value[:length]
+ except Exception, e:
+ pass
+ if db_type.startswith('char'):
+ try:
+ length = int(db_type[5:-1])
+ if len(value) > length:
+ self.convertWarning(value, value[:length],
+ type, db_type)
+ value = value[:length]
+ except Exception, e:
+ pass
+ # return "'" + str(value).replace("'", "''") + "'"
+ return value
+ elif type == 'long':
+ return str(value)
+ elif type == 'float':
+ # necessary to avoid conversion warnings in MySQL
+ if db_type.startswith('DECIMAL'):
+ try:
+ value="%%.%sf"%str(db_type[8:-1].split(',')[1])%value
+ except Exception, e:
+ pass
+ return str(value)
+ elif type == 'int':
+ # note: on 64-bit machines int:s are 64-bit
+ MIN_INT = -2147483648
+ MAX_INT = 2147483647
+ if db_type == 'int':
+ if int(value) < MIN_INT:
+ self.convertWarning(value, MIN_INT, type, db_type)
+ value = MIN_INT
+ if int(value) > MAX_INT:
+ self.convertWarning(value, MAX_INT, type, db_type)
+ value = MAX_INT
+ return str(value)
+ elif type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+
+ return None
+
+ def createSQLSelect(self, table, columns, whereMap, orderBy=None,
+ forUpdate=False):
+ columnStr = ', '.join(columns)
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % \
+ (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """SELECT %s FROM %s WHERE %s""" % \
+ (columnStr, table, whereStr)
+ if orderBy is not None:
+ dbCommand += " ORDER BY " + orderBy
+ if forUpdate:
+ dbCommand += " FOR UPDATE"
+ dbCommand += ";"
+ return (dbCommand, tuple(values))
+
+ def createSQLInsert(self, table, columnMap):
+ columns = []
+ values = []
+ for column, value in columnMap.iteritems():
+ if value is None:
+ value = 'NULL'
+ columns.append(column)
+ values.append(value)
+ columnStr = ', '.join(columns)
+ # valueStr = '%s, '.join(values)
+ valueStr = ''
+ if len(values) > 1:
+ valueStr = '%s,' * (len(values) - 1) + '%s'
+ dbCommand = """INSERT INTO %s(%s) VALUES (%s);""" % \
+ (table, columnStr, valueStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLUpdate(self, table, columnMap, whereMap):
+ setStr = ''
+ comma = ''
+ values = []
+ for column, value in columnMap.iteritems():
+# if value is None:
+# value = 'NULL'
+ setStr += '%s%s = %%s' % (comma, column)
+ comma = ', '
+ values.append(value)
+ whereStr = ''
+ whereClause = ''
+ for column, value in whereMap.iteritems():
+ whereStr += '%s%s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """UPDATE %s SET %s WHERE %s;""" % \
+ (table, setStr, whereStr)
+ return (dbCommand, tuple(values))
+
+ def createSQLDelete(self, table, whereMap):
+ whereStr = ''
+ whereClause = ''
+ values = []
+ for column, value in whereMap.iteritems():
+ whereStr += '%s %s = %%s' % (whereClause, column)
+ values.append(value)
+ whereClause = ' AND '
+ dbCommand = """DELETE FROM %s WHERE %s;""" % \
+ (table, whereStr)
+ return (dbCommand, tuple(values))
+
+ def executeSQL(self, db, cmd_tuple, isFetch):
+ dbCommand, values = cmd_tuple
+ # print 'db: %s' % dbCommand
+ # print 'values:', values
+ data = None
+ cursor = db.cursor()
+ try:
+ cursor.execute(dbCommand, values)
+ if isFetch:
+ data = cursor.fetchall()
+ else:
+ data = cursor.lastrowid
+ except Exception, e:
+ raise VistrailsDBException('Command "%s" with values "%s" '
+ 'failed: %s' % (dbCommand, values, e))
+ finally:
+ cursor.close()
+ return data
+
+ def executeSQLGroup(self, db, dbCommandList, isFetch):
+ """ Executes a command consisting of multiple SELECT statements
+ It returns a list of results from the SELECT statements
+ """
+ data = []
+ # break up into bundles
+ BUNDLE_SIZE = 10000
+ num_commands = len(dbCommandList)
+ n = 0
+ while n<num_commands:
+ dbCommands = dbCommandList[n:(n+BUNDLE_SIZE)]
+ commandString = ''
+ for prepared, values in dbCommands:
+ command = prepared % \
+ db.escape(values, get_db_lib().converters.conversions)
+ commandString += command
+ cur = db.cursor()
+ try:
+ result = cur.execute(commandString)
+ while True:
+ r = cur.fetchall() if isFetch else cur.lastrowid
+ data.append(r)
+ next = cur.nextset()
+ if not next:
+ break
+ except Exception, e:
+ raise VistrailsDBException('Command failed: %s -- """ %s """' %
+ (e, commandString))
+ finally:
+ cur.close()
+
+ n += BUNDLE_SIZE
+ return data
+
+ def start_transaction(self, db):
+ db.begin()
+
+ def commit_transaction(self, db):
+ db.commit()
+
+ def rollback_transaction(self, db):
+ db.rollback()
diff --git a/vistrails/db/versions/v1_0_3/persistence/xml/__init__.py b/vistrails/db/versions/v1_0_3/persistence/xml/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/persistence/xml/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/db/versions/v1_0_3/persistence/xml/auto_gen.py b/vistrails/db/versions/v1_0_3/persistence/xml/auto_gen.py
new file mode 100644
index 0000000..d1b6ebf
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/persistence/xml/auto_gen.py
@@ -0,0 +1,5822 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""generated automatically by auto_dao.py"""
+
+from vistrails.core.system import get_elementtree_library
+ElementTree = get_elementtree_library()
+
+from xml_dao import XMLDAO
+from vistrails.db.versions.v1_0_3.domain import *
+
+class DBOpmProcessIdEffectXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'effect':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmProcessIdEffect(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_id_effect, node=None):
+ if node is None:
+ node = ElementTree.Element('effect')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process_id_effect.db_id, 'str'))
+
+ return node
+
+class DBVistrailVariableXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'vistrailVariable':
+ return None
+
+ # read attributes
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('uuid', None)
+ uuid = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('module', None)
+ module = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBVistrailVariable(name=name,
+ uuid=uuid,
+ package=package,
+ module=module,
+ namespace=namespace,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrailVariable, node=None):
+ if node is None:
+ node = ElementTree.Element('vistrailVariable')
+
+ # set attributes
+ node.set('name',self.convertToStr(vistrailVariable.db_name, 'str'))
+ node.set('uuid',self.convertToStr(vistrailVariable.db_uuid, 'str'))
+ node.set('package',self.convertToStr(vistrailVariable.db_package, 'str'))
+ node.set('module',self.convertToStr(vistrailVariable.db_module, 'str'))
+ node.set('namespace',self.convertToStr(vistrailVariable.db_namespace, 'str'))
+ node.set('value',self.convertToStr(vistrailVariable.db_value, 'str'))
+
+ return node
+
+class DBProvAgentXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'prov:agent':
+ return None
+
+ # read attributes
+ data = node.get('prov:id', None)
+ id = self.convertFromStr(data, 'str')
+
+ vt_id = None
+ prov_type = None
+ prov_label = None
+ vt_machine_os = None
+ vt_machine_architecture = None
+ vt_machine_processor = None
+ vt_machine_ram = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'vt:id':
+ _data = self.convertFromStr(child.text,'str')
+ vt_id = _data
+ elif child_tag == 'prov:type':
+ _data = self.convertFromStr(child.text,'str')
+ prov_type = _data
+ elif child_tag == 'prov:label':
+ _data = self.convertFromStr(child.text,'str')
+ prov_label = _data
+ elif child_tag == 'vt:machine_os':
+ _data = self.convertFromStr(child.text,'str')
+ vt_machine_os = _data
+ elif child_tag == 'vt:machine_architecture':
+ _data = self.convertFromStr(child.text,'str')
+ vt_machine_architecture = _data
+ elif child_tag == 'vt:machine_processor':
+ _data = self.convertFromStr(child.text,'str')
+ vt_machine_processor = _data
+ elif child_tag == 'vt:machine_ram':
+ _data = self.convertFromStr(child.text,'str')
+ vt_machine_ram = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBProvAgent(id=id,
+ vt_id=vt_id,
+ prov_type=prov_type,
+ prov_label=prov_label,
+ vt_machine_os=vt_machine_os,
+ vt_machine_architecture=vt_machine_architecture,
+ vt_machine_processor=vt_machine_processor,
+ vt_machine_ram=vt_machine_ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, prov_agent, node=None):
+ if node is None:
+ node = ElementTree.Element('prov:agent')
+
+ # set attributes
+ node.set('prov:id',self.convertToStr(prov_agent.db_id, 'str'))
+
+ # set elements
+ vt_id = prov_agent.db_vt_id
+ if (vt_id is not None) and (vt_id != ""):
+ childNode = ElementTree.SubElement(node, 'vt:id')
+ childNode.text = self.convertToStr(vt_id, 'str')
+ prov_type = prov_agent.db_prov_type
+ if (prov_type is not None) and (prov_type != ""):
+ childNode = ElementTree.SubElement(node, 'prov:type')
+ childNode.text = self.convertToStr(prov_type, 'str')
+ prov_label = prov_agent.db_prov_label
+ if (prov_label is not None) and (prov_label != ""):
+ childNode = ElementTree.SubElement(node, 'prov:label')
+ childNode.text = self.convertToStr(prov_label, 'str')
+ vt_machine_os = prov_agent.db_vt_machine_os
+ if (vt_machine_os is not None) and (vt_machine_os != ""):
+ childNode = ElementTree.SubElement(node, 'vt:machine_os')
+ childNode.text = self.convertToStr(vt_machine_os, 'str')
+ vt_machine_architecture = prov_agent.db_vt_machine_architecture
+ if (vt_machine_architecture is not None) and (vt_machine_architecture != ""):
+ childNode = ElementTree.SubElement(node, 'vt:machine_architecture')
+ childNode.text = self.convertToStr(vt_machine_architecture, 'str')
+ vt_machine_processor = prov_agent.db_vt_machine_processor
+ if (vt_machine_processor is not None) and (vt_machine_processor != ""):
+ childNode = ElementTree.SubElement(node, 'vt:machine_processor')
+ childNode.text = self.convertToStr(vt_machine_processor, 'str')
+ vt_machine_ram = prov_agent.db_vt_machine_ram
+ if (vt_machine_ram is not None) and (vt_machine_ram != ""):
+ childNode = ElementTree.SubElement(node, 'vt:machine_ram')
+ childNode.text = self.convertToStr(vt_machine_ram, 'str')
+
+ return node
+
+class DBOpmWasGeneratedByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasGeneratedBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_artifact_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_process_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasGeneratedBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_generated_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasGeneratedBy')
+
+ # set elements
+ effect = opm_was_generated_by.db_effect
+ if effect is not None:
+ if (effect is not None) and (effect != ""):
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_artifact_id_effect').toXML(effect, childNode)
+ role = opm_was_generated_by.db_role
+ if role is not None:
+ if (role is not None) and (role != ""):
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_generated_by.db_cause
+ if cause is not None:
+ if (cause is not None) and (cause != ""):
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_process_id_cause').toXML(cause, childNode)
+ accounts = opm_was_generated_by.db_accounts
+ for account in accounts:
+ if (accounts is not None) and (accounts != ""):
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_generated_by.db_opm_times
+ for opm_time in opm_times:
+ if (opm_times is not None) and (opm_times != ""):
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBOpmAccountsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'accounts':
+ return None
+
+ accounts = []
+ opm_overlapss = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'account':
+ _data = self.getDao('opm_account').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'overlaps':
+ _data = self.getDao('opm_overlaps').fromXML(child)
+ opm_overlapss.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAccounts(accounts=accounts,
+ opm_overlapss=opm_overlapss)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_accounts, node=None):
+ if node is None:
+ node = ElementTree.Element('accounts')
+
+ # set elements
+ accounts = opm_accounts.db_accounts
+ for account in accounts:
+ if (accounts is not None) and (accounts != ""):
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account').toXML(account, childNode)
+ opm_overlapss = opm_accounts.db_opm_overlapss
+ for opm_overlaps in opm_overlapss:
+ if (opm_overlapss is not None) and (opm_overlapss != ""):
+ childNode = ElementTree.SubElement(node, 'overlaps')
+ self.getDao('opm_overlaps').toXML(opm_overlaps, childNode)
+
+ return node
+
+class DBRefProvAgentXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'prov:agent':
+ return None
+
+ # read attributes
+ data = node.get('prov:ref', None)
+ prov_ref = self.convertFromStr(data, 'str')
+
+ obj = DBRefProvAgent(prov_ref=prov_ref)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, ref_prov_agent, node=None):
+ if node is None:
+ node = ElementTree.Element('prov:agent')
+
+ # set attributes
+ node.set('prov:ref',self.convertToStr(ref_prov_agent.db_prov_ref, 'str'))
+
+ return node
+
+class DBPortSpecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'portSpec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('optional', None)
+ optional = self.convertFromStr(data, 'int')
+ data = node.get('sortKey', None)
+ sort_key = self.convertFromStr(data, 'int')
+ data = node.get('minConns', None)
+ min_conns = self.convertFromStr(data, 'int')
+ data = node.get('maxConns', None)
+ max_conns = self.convertFromStr(data, 'int')
+
+ portSpecItems = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'portSpecItem':
+ _data = self.getDao('portSpecItem').fromXML(child)
+ portSpecItems.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBPortSpec(id=id,
+ name=name,
+ type=type,
+ optional=optional,
+ sort_key=sort_key,
+ portSpecItems=portSpecItems,
+ min_conns=min_conns,
+ max_conns=max_conns)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpec, node=None):
+ if node is None:
+ node = ElementTree.Element('portSpec')
+
+ # set attributes
+ node.set('id',self.convertToStr(portSpec.db_id, 'long'))
+ node.set('name',self.convertToStr(portSpec.db_name, 'str'))
+ node.set('type',self.convertToStr(portSpec.db_type, 'str'))
+ node.set('optional',self.convertToStr(portSpec.db_optional, 'int'))
+ node.set('sortKey',self.convertToStr(portSpec.db_sort_key, 'int'))
+ node.set('minConns',self.convertToStr(portSpec.db_min_conns, 'int'))
+ node.set('maxConns',self.convertToStr(portSpec.db_max_conns, 'int'))
+
+ # set elements
+ portSpecItems = portSpec.db_portSpecItems
+ for portSpecItem in portSpecItems:
+ if (portSpecItems is not None) and (portSpecItems != ""):
+ childNode = ElementTree.SubElement(node, 'portSpecItem')
+ self.getDao('portSpecItem').toXML(portSpecItem, childNode)
+
+ return node
+
+class DBModuleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'module':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModule(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module, node=None):
+ if node is None:
+ node = ElementTree.Element('module')
+
+ # set attributes
+ node.set('id',self.convertToStr(module.db_id, 'long'))
+ node.set('cache',self.convertToStr(module.db_cache, 'int'))
+ node.set('name',self.convertToStr(module.db_name, 'str'))
+ node.set('namespace',self.convertToStr(module.db_namespace, 'str'))
+ node.set('package',self.convertToStr(module.db_package, 'str'))
+ node.set('version',self.convertToStr(module.db_version, 'str'))
+
+ # set elements
+ location = module.db_location
+ if location is not None:
+ if (location is not None) and (location != ""):
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = module.db_functions
+ for function in functions:
+ if (functions is not None) and (functions != ""):
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = module.db_annotations
+ for annotation in annotations:
+ if (annotations is not None) and (annotations != ""):
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ portSpecs = module.db_portSpecs
+ for portSpec in portSpecs:
+ if (portSpecs is not None) and (portSpecs != ""):
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBModuleDescriptorXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'moduleDescriptor':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('packageVersion', None)
+ package_version = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('baseDescriptorId', None)
+ base_descriptor_id = self.convertFromStr(data, 'long')
+
+ portSpecs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ portSpecs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleDescriptor(id=id,
+ name=name,
+ package=package,
+ namespace=namespace,
+ package_version=package_version,
+ version=version,
+ base_descriptor_id=base_descriptor_id,
+ portSpecs=portSpecs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_descriptor, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleDescriptor')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_descriptor.db_id, 'long'))
+ node.set('name',self.convertToStr(module_descriptor.db_name, 'str'))
+ node.set('package',self.convertToStr(module_descriptor.db_package, 'str'))
+ node.set('namespace',self.convertToStr(module_descriptor.db_namespace, 'str'))
+ node.set('packageVersion',self.convertToStr(module_descriptor.db_package_version, 'str'))
+ node.set('version',self.convertToStr(module_descriptor.db_version, 'str'))
+ node.set('baseDescriptorId',self.convertToStr(module_descriptor.db_base_descriptor_id, 'long'))
+
+ # set elements
+ portSpecs = module_descriptor.db_portSpecs
+ for portSpec in portSpecs:
+ if (portSpecs is not None) and (portSpecs != ""):
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(portSpec, childNode)
+
+ return node
+
+class DBTagXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'tag':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ obj = DBTag(id=id,
+ name=name)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, tag, node=None):
+ if node is None:
+ node = ElementTree.Element('tag')
+
+ # set attributes
+ node.set('id',self.convertToStr(tag.db_id, 'long'))
+ node.set('name',self.convertToStr(tag.db_name, 'str'))
+
+ return node
+
+class DBOpmRoleXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'role':
+ return None
+
+ # read attributes
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBOpmRole(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_role, node=None):
+ if node is None:
+ node = ElementTree.Element('role')
+
+ # set attributes
+ node.set('value',self.convertToStr(opm_role.db_value, 'str'))
+
+ return node
+
+class DBProvDocumentXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'prov:document':
+ return None
+
+ prov_entitys = []
+ prov_activitys = []
+ prov_agents = []
+ vt_connections = []
+ prov_usages = []
+ prov_generations = []
+ prov_associations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'prov:entity':
+ _data = self.getDao('prov_entity').fromXML(child)
+ prov_entitys.append(_data)
+ elif child_tag == 'prov:activity':
+ _data = self.getDao('prov_activity').fromXML(child)
+ prov_activitys.append(_data)
+ elif child_tag == 'prov:agent':
+ _data = self.getDao('prov_agent').fromXML(child)
+ prov_agents.append(_data)
+ elif child_tag == 'vt:connection':
+ _data = self.getDao('vt_connection').fromXML(child)
+ vt_connections.append(_data)
+ elif child_tag == 'prov:used':
+ _data = self.getDao('prov_usage').fromXML(child)
+ prov_usages.append(_data)
+ elif child_tag == 'prov:wasGeneratedBy':
+ _data = self.getDao('prov_generation').fromXML(child)
+ prov_generations.append(_data)
+ elif child_tag == 'prov:wasAssociatedWith':
+ _data = self.getDao('prov_association').fromXML(child)
+ prov_associations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBProvDocument(prov_entitys=prov_entitys,
+ prov_activitys=prov_activitys,
+ prov_agents=prov_agents,
+ vt_connections=vt_connections,
+ prov_usages=prov_usages,
+ prov_generations=prov_generations,
+ prov_associations=prov_associations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, prov_document, node=None):
+ if node is None:
+ node = ElementTree.Element('prov:document')
+
+ # set elements
+ prov_entitys = prov_document.db_prov_entitys
+ for prov_entity in prov_entitys:
+ if (prov_entitys is not None) and (prov_entitys != ""):
+ childNode = ElementTree.SubElement(node, 'prov:entity')
+ self.getDao('prov_entity').toXML(prov_entity, childNode)
+ prov_activitys = prov_document.db_prov_activitys
+ for prov_activity in prov_activitys:
+ if (prov_activitys is not None) and (prov_activitys != ""):
+ childNode = ElementTree.SubElement(node, 'prov:activity')
+ self.getDao('prov_activity').toXML(prov_activity, childNode)
+ prov_agents = prov_document.db_prov_agents
+ for prov_agent in prov_agents:
+ if (prov_agents is not None) and (prov_agents != ""):
+ childNode = ElementTree.SubElement(node, 'prov:agent')
+ self.getDao('prov_agent').toXML(prov_agent, childNode)
+ vt_connections = prov_document.db_vt_connections
+ for vt_connection in vt_connections:
+ if (vt_connections is not None) and (vt_connections != ""):
+ childNode = ElementTree.SubElement(node, 'vt:connection')
+ self.getDao('vt_connection').toXML(vt_connection, childNode)
+ prov_usages = prov_document.db_prov_usages
+ for prov_usage in prov_usages:
+ if (prov_usages is not None) and (prov_usages != ""):
+ childNode = ElementTree.SubElement(node, 'prov:used')
+ self.getDao('prov_usage').toXML(prov_usage, childNode)
+ prov_generations = prov_document.db_prov_generations
+ for prov_generation in prov_generations:
+ if (prov_generations is not None) and (prov_generations != ""):
+ childNode = ElementTree.SubElement(node, 'prov:wasGeneratedBy')
+ self.getDao('prov_generation').toXML(prov_generation, childNode)
+ prov_associations = prov_document.db_prov_associations
+ for prov_association in prov_associations:
+ if (prov_associations is not None) and (prov_associations != ""):
+ childNode = ElementTree.SubElement(node, 'prov:wasAssociatedWith')
+ self.getDao('prov_association').toXML(prov_association, childNode)
+
+ return node
+
+class DBOpmAccountXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'account':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAccount(id=id,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_account, node=None):
+ if node is None:
+ node = ElementTree.Element('account')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_account.db_id, 'str'))
+
+ # set elements
+ value = opm_account.db_value
+ if (value is not None) and (value != ""):
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+
+ return node
+
+class DBOpmProcessesXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'processes':
+ return None
+
+ processs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'process':
+ _data = self.getDao('opm_process').fromXML(child)
+ processs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcesses(processs=processs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_processes, node=None):
+ if node is None:
+ node = ElementTree.Element('processes')
+
+ # set elements
+ processs = opm_processes.db_processs
+ for process in processs:
+ if (processs is not None) and (processs != ""):
+ childNode = ElementTree.SubElement(node, 'process')
+ self.getDao('opm_process').toXML(process, childNode)
+
+ return node
+
+class DBRefProvActivityXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'prov:activity':
+ return None
+
+ # read attributes
+ data = node.get('prov:ref', None)
+ prov_ref = self.convertFromStr(data, 'str')
+
+ obj = DBRefProvActivity(prov_ref=prov_ref)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, ref_prov_activity, node=None):
+ if node is None:
+ node = ElementTree.Element('prov:activity')
+
+ # set attributes
+ node.set('prov:ref',self.convertToStr(ref_prov_activity.db_prov_ref, 'str'))
+
+ return node
+
+class DBOpmAccountIdXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'account':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmAccountId(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_account_id, node=None):
+ if node is None:
+ node = ElementTree.Element('account')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_account_id.db_id, 'str'))
+
+ return node
+
+class DBPortXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'port':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('moduleId', None)
+ moduleId = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ moduleName = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('signature', None)
+ signature = self.convertFromStr(data, 'str')
+
+ obj = DBPort(id=id,
+ type=type,
+ moduleId=moduleId,
+ moduleName=moduleName,
+ name=name,
+ signature=signature)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, port, node=None):
+ if node is None:
+ node = ElementTree.Element('port')
+
+ # set attributes
+ node.set('id',self.convertToStr(port.db_id, 'long'))
+ node.set('type',self.convertToStr(port.db_type, 'str'))
+ node.set('moduleId',self.convertToStr(port.db_moduleId, 'long'))
+ node.set('moduleName',self.convertToStr(port.db_moduleName, 'str'))
+ node.set('name',self.convertToStr(port.db_name, 'str'))
+ node.set('signature',self.convertToStr(port.db_signature, 'str'))
+
+ return node
+
+class DBRefProvPlanXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'prov:plan':
+ return None
+
+ # read attributes
+ data = node.get('prov:ref', None)
+ prov_ref = self.convertFromStr(data, 'str')
+
+ obj = DBRefProvPlan(prov_ref=prov_ref)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, ref_prov_plan, node=None):
+ if node is None:
+ node = ElementTree.Element('prov:plan')
+
+ # set attributes
+ node.set('prov:ref',self.convertToStr(ref_prov_plan.db_prov_ref, 'str'))
+
+ return node
+
+class DBOpmArtifactXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'artifact':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.getDao('opm_artifact_value').fromXML(child)
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifact(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact, node=None):
+ if node is None:
+ node = ElementTree.Element('artifact')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact.db_id, 'str'))
+
+ # set elements
+ value = opm_artifact.db_value
+ if value is not None:
+ if (value is not None) and (value != ""):
+ childNode = ElementTree.SubElement(node, 'value')
+ self.getDao('opm_artifact_value').toXML(value, childNode)
+ accounts = opm_artifact.db_accounts
+ for account in accounts:
+ if (accounts is not None) and (accounts != ""):
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBGroupXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'group':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+
+ workflow = None
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'workflow':
+ _data = self.getDao('workflow').fromXML(child)
+ workflow = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroup(id=id,
+ workflow=workflow,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group, node=None):
+ if node is None:
+ node = ElementTree.Element('group')
+
+ # set attributes
+ node.set('id',self.convertToStr(group.db_id, 'long'))
+ node.set('cache',self.convertToStr(group.db_cache, 'int'))
+ node.set('name',self.convertToStr(group.db_name, 'str'))
+ node.set('namespace',self.convertToStr(group.db_namespace, 'str'))
+ node.set('package',self.convertToStr(group.db_package, 'str'))
+ node.set('version',self.convertToStr(group.db_version, 'str'))
+
+ # set elements
+ workflow = group.db_workflow
+ if workflow is not None:
+ if (workflow is not None) and (workflow != ""):
+ childNode = ElementTree.SubElement(node, 'workflow')
+ self.getDao('workflow').toXML(workflow, childNode)
+ location = group.db_location
+ if location is not None:
+ if (location is not None) and (location != ""):
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = group.db_functions
+ for function in functions:
+ if (functions is not None) and (functions != ""):
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = group.db_annotations
+ for annotation in annotations:
+ if (annotations is not None) and (annotations != ""):
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBLogXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'log':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ workflow_execs = []
+ machines = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'workflowExec':
+ _data = self.getDao('workflow_exec').fromXML(child)
+ workflow_execs.append(_data)
+ elif child_tag == 'machine':
+ _data = self.getDao('machine').fromXML(child)
+ machines.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLog(id=id,
+ version=version,
+ name=name,
+ workflow_execs=workflow_execs,
+ machines=machines,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, log, node=None):
+ if node is None:
+ node = ElementTree.Element('log')
+
+ # set attributes
+ node.set('id',self.convertToStr(log.db_id, 'long'))
+ node.set('version',self.convertToStr(log.db_version, 'str'))
+ node.set('name',self.convertToStr(log.db_name, 'str'))
+ node.set('vistrail_id',self.convertToStr(log.db_vistrail_id, 'long'))
+
+ # set elements
+ workflow_execs = log.db_workflow_execs
+ for workflow_exec in workflow_execs:
+ if (workflow_execs is not None) and (workflow_execs != ""):
+ childNode = ElementTree.SubElement(node, 'workflowExec')
+ self.getDao('workflow_exec').toXML(workflow_exec, childNode)
+ machines = log.db_machines
+ for machine in machines:
+ if (machines is not None) and (machines != ""):
+ childNode = ElementTree.SubElement(node, 'machine')
+ self.getDao('machine').toXML(machine, childNode)
+
+ return node
+
+class DBMashupAliasXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'alias':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ component = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'component':
+ _data = self.getDao('mashup_component').fromXML(child)
+ component = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBMashupAlias(id=id,
+ name=name,
+ component=component)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, mashup_alias, node=None):
+ if node is None:
+ node = ElementTree.Element('alias')
+
+ # set attributes
+ node.set('id',self.convertToStr(mashup_alias.db_id, 'long'))
+ node.set('name',self.convertToStr(mashup_alias.db_name, 'str'))
+
+ # set elements
+ component = mashup_alias.db_component
+ if component is not None:
+ if (component is not None) and (component != ""):
+ childNode = ElementTree.SubElement(node, 'component')
+ self.getDao('mashup_component').toXML(component, childNode)
+
+ return node
+
+class DBOpmAgentsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agents':
+ return None
+
+ agents = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'agent':
+ _data = self.getDao('opm_agent').fromXML(child)
+ agents.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAgents(agents=agents)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agents, node=None):
+ if node is None:
+ node = ElementTree.Element('agents')
+
+ # set elements
+ agents = opm_agents.db_agents
+ for agent in agents:
+ if (agents is not None) and (agents != ""):
+ childNode = ElementTree.SubElement(node, 'agent')
+ self.getDao('opm_agent').toXML(agent, childNode)
+
+ return node
+
+class DBMashupXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'mashup':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('vtid', None)
+ vtid = self.convertFromStr(data, 'long')
+ data = node.get('has_seq', None)
+ has_seq = self.convertFromStr(data, 'int')
+
+ aliases = []
+ layout = None
+ geometry = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'alias':
+ _data = self.getDao('mashup_alias').fromXML(child)
+ aliases.append(_data)
+ elif child_tag == 'layout':
+ _data = self.convertFromStr(child.text,'str')
+ layout = _data
+ elif child_tag == 'geometry':
+ _data = self.convertFromStr(child.text,'str')
+ geometry = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBMashup(id=id,
+ name=name,
+ version=version,
+ aliases=aliases,
+ type=type,
+ vtid=vtid,
+ layout=layout,
+ geometry=geometry,
+ has_seq=has_seq)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, mashup, node=None):
+ if node is None:
+ node = ElementTree.Element('mashup')
+
+ # set attributes
+ node.set('id',self.convertToStr(mashup.db_id, 'long'))
+ node.set('name',self.convertToStr(mashup.db_name, 'str'))
+ node.set('version',self.convertToStr(mashup.db_version, 'long'))
+ node.set('type',self.convertToStr(mashup.db_type, 'str'))
+ node.set('vtid',self.convertToStr(mashup.db_vtid, 'long'))
+ node.set('has_seq',self.convertToStr(mashup.db_has_seq, 'int'))
+
+ # set elements
+ aliases = mashup.db_aliases
+ for alias in aliases:
+ if (aliases is not None) and (aliases != ""):
+ childNode = ElementTree.SubElement(node, 'alias')
+ self.getDao('mashup_alias').toXML(alias, childNode)
+ layout = mashup.db_layout
+ if (layout is not None) and (layout != ""):
+ childNode = ElementTree.SubElement(node, 'layout')
+ childNode.text = self.convertToStr(layout, 'str')
+ geometry = mashup.db_geometry
+ if (geometry is not None) and (geometry != ""):
+ childNode = ElementTree.SubElement(node, 'geometry')
+ childNode.text = self.convertToStr(geometry, 'str')
+
+ return node
+
+class DBOpmProcessIdCauseXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'cause':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmProcessIdCause(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_id_cause, node=None):
+ if node is None:
+ node = ElementTree.Element('cause')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process_id_cause.db_id, 'str'))
+
+ return node
+
+class DBProvGenerationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'prov:wasGeneratedBy':
+ return None
+
+ prov_entity = None
+ prov_activity = None
+ prov_role = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'prov:entity':
+ _data = self.getDao('ref_prov_entity').fromXML(child)
+ prov_entity = _data
+ elif child_tag == 'prov:activity':
+ _data = self.getDao('ref_prov_activity').fromXML(child)
+ prov_activity = _data
+ elif child_tag == 'prov:role':
+ _data = self.convertFromStr(child.text,'str')
+ prov_role = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBProvGeneration(prov_entity=prov_entity,
+ prov_activity=prov_activity,
+ prov_role=prov_role)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, prov_generation, node=None):
+ if node is None:
+ node = ElementTree.Element('prov:wasGeneratedBy')
+
+ # set elements
+ prov_entity = prov_generation.db_prov_entity
+ if prov_entity is not None:
+ if (prov_entity is not None) and (prov_entity != ""):
+ childNode = ElementTree.SubElement(node, 'prov:entity')
+ self.getDao('ref_prov_entity').toXML(prov_entity, childNode)
+ prov_activity = prov_generation.db_prov_activity
+ if prov_activity is not None:
+ if (prov_activity is not None) and (prov_activity != ""):
+ childNode = ElementTree.SubElement(node, 'prov:activity')
+ self.getDao('ref_prov_activity').toXML(prov_activity, childNode)
+ prov_role = prov_generation.db_prov_role
+ if (prov_role is not None) and (prov_role != ""):
+ childNode = ElementTree.SubElement(node, 'prov:role')
+ childNode.text = self.convertToStr(prov_role, 'str')
+
+ return node
+
+class DBPortSpecItemXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'portSpecItem':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('module', None)
+ module = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('label', None)
+ label = self.convertFromStr(data, 'str')
+ data = node.get('default', None)
+ default = self.convertFromStr(data, 'str')
+ data = node.get('values', None)
+ values = self.convertFromStr(data, 'str')
+ data = node.get('entryType', None)
+ entry_type = self.convertFromStr(data, 'str')
+
+ obj = DBPortSpecItem(id=id,
+ pos=pos,
+ module=module,
+ package=package,
+ namespace=namespace,
+ label=label,
+ default=default,
+ values=values,
+ entry_type=entry_type)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, portSpecItem, node=None):
+ if node is None:
+ node = ElementTree.Element('portSpecItem')
+
+ # set attributes
+ node.set('id',self.convertToStr(portSpecItem.db_id, 'long'))
+ node.set('pos',self.convertToStr(portSpecItem.db_pos, 'long'))
+ node.set('module',self.convertToStr(portSpecItem.db_module, 'str'))
+ node.set('package',self.convertToStr(portSpecItem.db_package, 'str'))
+ node.set('namespace',self.convertToStr(portSpecItem.db_namespace, 'str'))
+ node.set('label',self.convertToStr(portSpecItem.db_label, 'str'))
+ node.set('default',self.convertToStr(portSpecItem.db_default, 'str'))
+ node.set('values',self.convertToStr(portSpecItem.db_values, 'str'))
+ node.set('entryType',self.convertToStr(portSpecItem.db_entry_type, 'str'))
+
+ return node
+
+class DBMachineXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'machine':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('os', None)
+ os = self.convertFromStr(data, 'str')
+ data = node.get('architecture', None)
+ architecture = self.convertFromStr(data, 'str')
+ data = node.get('processor', None)
+ processor = self.convertFromStr(data, 'str')
+ data = node.get('ram', None)
+ ram = self.convertFromStr(data, 'int')
+
+ obj = DBMachine(id=id,
+ name=name,
+ os=os,
+ architecture=architecture,
+ processor=processor,
+ ram=ram)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, machine, node=None):
+ if node is None:
+ node = ElementTree.Element('machine')
+
+ # set attributes
+ node.set('id',self.convertToStr(machine.db_id, 'long'))
+ node.set('name',self.convertToStr(machine.db_name, 'str'))
+ node.set('os',self.convertToStr(machine.db_os, 'str'))
+ node.set('architecture',self.convertToStr(machine.db_architecture, 'str'))
+ node.set('processor',self.convertToStr(machine.db_processor, 'str'))
+ node.set('ram',self.convertToStr(machine.db_ram, 'int'))
+
+ return node
+
+class DBAddXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'add':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAdd(data=data,
+ id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, add, node=None):
+ if node is None:
+ node = ElementTree.Element('add')
+
+ # set attributes
+ node.set('id',self.convertToStr(add.db_id, 'long'))
+ node.set('what',self.convertToStr(add.db_what, 'str'))
+ node.set('objectId',self.convertToStr(add.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(add.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(add.db_parentObjType, 'str'))
+
+ # set elements
+ data = add.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBOtherXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'other':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOther(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, other, node=None):
+ if node is None:
+ node = ElementTree.Element('other')
+
+ # set attributes
+ node.set('id',self.convertToStr(other.db_id, 'long'))
+ node.set('key',self.convertToStr(other.db_key, 'str'))
+
+ # set elements
+ value = other.db_value
+ if (value is not None) and (value != ""):
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+
+ return node
+
+class DBLocationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'location':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('x', None)
+ x = self.convertFromStr(data, 'float')
+ data = node.get('y', None)
+ y = self.convertFromStr(data, 'float')
+
+ obj = DBLocation(id=id,
+ x=x,
+ y=y)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, location, node=None):
+ if node is None:
+ node = ElementTree.Element('location')
+
+ # set attributes
+ node.set('id',self.convertToStr(location.db_id, 'long'))
+ node.set('x',self.convertToStr(location.db_x, 'float'))
+ node.set('y',self.convertToStr(location.db_y, 'float'))
+
+ return node
+
+class DBOpmOverlapsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'overlaps':
+ return None
+
+ opm_account_ids = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ opm_account_ids.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmOverlaps(opm_account_ids=opm_account_ids)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_overlaps, node=None):
+ if node is None:
+ node = ElementTree.Element('overlaps')
+
+ # set elements
+ opm_account_ids = opm_overlaps.db_opm_account_ids
+ for opm_account_id in opm_account_ids:
+ if (opm_account_ids is not None) and (opm_account_ids != ""):
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(opm_account_id, childNode)
+
+ return node
+
+class DBPEParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'peParameter':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('interpolator', None)
+ interpolator = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+ data = node.get('dimension', None)
+ dimension = self.convertFromStr(data, 'long')
+
+ obj = DBPEParameter(id=id,
+ pos=pos,
+ interpolator=interpolator,
+ value=value,
+ dimension=dimension)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, pe_parameter, node=None):
+ if node is None:
+ node = ElementTree.Element('peParameter')
+
+ # set attributes
+ node.set('id',self.convertToStr(pe_parameter.db_id, 'long'))
+ node.set('pos',self.convertToStr(pe_parameter.db_pos, 'long'))
+ node.set('interpolator',self.convertToStr(pe_parameter.db_interpolator, 'str'))
+ node.set('value',self.convertToStr(pe_parameter.db_value, 'str'))
+ node.set('dimension',self.convertToStr(pe_parameter.db_dimension, 'long'))
+
+ return node
+
+class DBOpmDependenciesXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'causalDependencies':
+ return None
+
+ dependencys = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'used':
+ _data = self.getDao('opm_used').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasGeneratedBy':
+ _data = self.getDao('opm_was_generated_by').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasTriggeredBy':
+ _data = self.getDao('opm_was_triggered_by').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasDerivedFrom':
+ _data = self.getDao('opm_was_derived_from').fromXML(child)
+ dependencys.append(_data)
+ elif child_tag == 'wasControlledBy':
+ _data = self.getDao('opm_was_controlled_by').fromXML(child)
+ dependencys.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmDependencies(dependencys=dependencys)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_dependencies, node=None):
+ if node is None:
+ node = ElementTree.Element('causalDependencies')
+
+ # set elements
+ dependencys = opm_dependencies.db_dependencys
+ for dependency in dependencys:
+ if dependency.vtType == 'opm_used':
+ childNode = ElementTree.SubElement(node, 'used')
+ self.getDao('opm_used').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_generated_by':
+ childNode = ElementTree.SubElement(node, 'wasGeneratedBy')
+ self.getDao('opm_was_generated_by').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_triggered_by':
+ childNode = ElementTree.SubElement(node, 'wasTriggeredBy')
+ self.getDao('opm_was_triggered_by').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_derived_from':
+ childNode = ElementTree.SubElement(node, 'wasDerivedFrom')
+ self.getDao('opm_was_derived_from').toXML(dependency, childNode)
+ elif dependency.vtType == 'opm_was_controlled_by':
+ childNode = ElementTree.SubElement(node, 'wasControlledBy')
+ self.getDao('opm_was_controlled_by').toXML(dependency, childNode)
+
+ return node
+
+class DBParameterXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'parameter':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('val', None)
+ val = self.convertFromStr(data, 'str')
+ data = node.get('alias', None)
+ alias = self.convertFromStr(data, 'str')
+
+ obj = DBParameter(id=id,
+ pos=pos,
+ name=name,
+ type=type,
+ val=val,
+ alias=alias)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter, node=None):
+ if node is None:
+ node = ElementTree.Element('parameter')
+
+ # set attributes
+ node.set('id',self.convertToStr(parameter.db_id, 'long'))
+ node.set('pos',self.convertToStr(parameter.db_pos, 'long'))
+ node.set('name',self.convertToStr(parameter.db_name, 'str'))
+ node.set('type',self.convertToStr(parameter.db_type, 'str'))
+ node.set('val',self.convertToStr(parameter.db_val, 'str'))
+ node.set('alias',self.convertToStr(parameter.db_alias, 'str'))
+
+ return node
+
+class DBOpmUsedXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'used':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_artifact_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmUsed(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_used, node=None):
+ if node is None:
+ node = ElementTree.Element('used')
+
+ # set elements
+ effect = opm_used.db_effect
+ if effect is not None:
+ if (effect is not None) and (effect != ""):
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_used.db_role
+ if role is not None:
+ if (role is not None) and (role != ""):
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_used.db_cause
+ if cause is not None:
+ if (cause is not None) and (cause != ""):
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_artifact_id_cause').toXML(cause, childNode)
+ accounts = opm_used.db_accounts
+ for account in accounts:
+ if (accounts is not None) and (accounts != ""):
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_used.db_opm_times
+ for opm_time in opm_times:
+ if (opm_times is not None) and (opm_times != ""):
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBPluginDataXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'plugin_data':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('data', None)
+ data = self.convertFromStr(data, 'str')
+
+ obj = DBPluginData(id=id,
+ data=data)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, plugin_data, node=None):
+ if node is None:
+ node = ElementTree.Element('plugin_data')
+
+ # set attributes
+ node.set('id',self.convertToStr(plugin_data.db_id, 'long'))
+ node.set('data',self.convertToStr(plugin_data.db_data, 'str'))
+
+ return node
+
+class DBFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'function':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ parameters = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ parameters.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBFunction(id=id,
+ pos=pos,
+ name=name,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, function, node=None):
+ if node is None:
+ node = ElementTree.Element('function')
+
+ # set attributes
+ node.set('id',self.convertToStr(function.db_id, 'long'))
+ node.set('pos',self.convertToStr(function.db_pos, 'long'))
+ node.set('name',self.convertToStr(function.db_name, 'str'))
+
+ # set elements
+ parameters = function.db_parameters
+ for parameter in parameters:
+ if (parameters is not None) and (parameters != ""):
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(parameter, childNode)
+
+ return node
+
+class DBActionAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'actionAnnotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+ data = node.get('actionId', None)
+ action_id = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+
+ obj = DBActionAnnotation(id=id,
+ key=key,
+ value=value,
+ action_id=action_id,
+ date=date,
+ user=user)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, actionAnnotation, node=None):
+ if node is None:
+ node = ElementTree.Element('actionAnnotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(actionAnnotation.db_id, 'long'))
+ node.set('key',self.convertToStr(actionAnnotation.db_key, 'str'))
+ node.set('value',self.convertToStr(actionAnnotation.db_value, 'str'))
+ node.set('actionId',self.convertToStr(actionAnnotation.db_action_id, 'long'))
+ node.set('date',self.convertToStr(actionAnnotation.db_date, 'datetime'))
+ node.set('user',self.convertToStr(actionAnnotation.db_user, 'str'))
+
+ return node
+
+class DBAbstractionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'abstraction':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('cache', None)
+ cache = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('namespace', None)
+ namespace = self.convertFromStr(data, 'str')
+ data = node.get('package', None)
+ package = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('internalVersion', None)
+ internal_version = self.convertFromStr(data, 'str')
+
+ location = None
+ functions = []
+ annotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ location = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ functions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAbstraction(id=id,
+ cache=cache,
+ name=name,
+ namespace=namespace,
+ package=package,
+ version=version,
+ internal_version=internal_version,
+ location=location,
+ functions=functions,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, abstraction, node=None):
+ if node is None:
+ node = ElementTree.Element('abstraction')
+
+ # set attributes
+ node.set('id',self.convertToStr(abstraction.db_id, 'long'))
+ node.set('cache',self.convertToStr(abstraction.db_cache, 'int'))
+ node.set('name',self.convertToStr(abstraction.db_name, 'str'))
+ node.set('namespace',self.convertToStr(abstraction.db_namespace, 'str'))
+ node.set('package',self.convertToStr(abstraction.db_package, 'str'))
+ node.set('version',self.convertToStr(abstraction.db_version, 'str'))
+ node.set('internalVersion',self.convertToStr(abstraction.db_internal_version, 'str'))
+
+ # set elements
+ location = abstraction.db_location
+ if location is not None:
+ if (location is not None) and (location != ""):
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(location, childNode)
+ functions = abstraction.db_functions
+ for function in functions:
+ if (functions is not None) and (functions != ""):
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(function, childNode)
+ annotations = abstraction.db_annotations
+ for annotation in annotations:
+ if (annotations is not None) and (annotations != ""):
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+
+ return node
+
+class DBWorkflowXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'workflow':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('vistrail_id', None)
+ vistrail_id = self.convertFromStr(data, 'long')
+
+ connections = []
+ annotations = []
+ plugin_datas = []
+ others = []
+ modules = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ connections.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ plugin_datas.append(_data)
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ others.append(_data)
+ elif child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ modules.append(_data)
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ modules.append(_data)
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ modules.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflow(modules=modules,
+ id=id,
+ name=name,
+ version=version,
+ connections=connections,
+ annotations=annotations,
+ plugin_datas=plugin_datas,
+ others=others,
+ vistrail_id=vistrail_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow, node=None):
+ if node is None:
+ node = ElementTree.Element('workflow')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow.db_id, 'long'))
+ node.set('name',self.convertToStr(workflow.db_name, 'str'))
+ node.set('version',self.convertToStr(workflow.db_version, 'str'))
+ node.set('vistrail_id',self.convertToStr(workflow.db_vistrail_id, 'long'))
+
+ # set elements
+ connections = workflow.db_connections
+ for connection in connections:
+ if (connections is not None) and (connections != ""):
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(connection, childNode)
+ annotations = workflow.db_annotations
+ for annotation in annotations:
+ if (annotations is not None) and (annotations != ""):
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ plugin_datas = workflow.db_plugin_datas
+ for plugin_data in plugin_datas:
+ if (plugin_datas is not None) and (plugin_datas != ""):
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(plugin_data, childNode)
+ others = workflow.db_others
+ for other in others:
+ if (others is not None) and (others != ""):
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(other, childNode)
+ modules = workflow.db_modules
+ for module in modules:
+ if module.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(module, childNode)
+ elif module.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(module, childNode)
+ elif module.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(module, childNode)
+
+ return node
+
+class DBOpmArtifactIdCauseXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'cause':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmArtifactIdCause(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_id_cause, node=None):
+ if node is None:
+ node = ElementTree.Element('cause')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact_id_cause.db_id, 'str'))
+
+ return node
+
+class DBRefProvEntityXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'prov:entity':
+ return None
+
+ # read attributes
+ data = node.get('prov:ref', None)
+ prov_ref = self.convertFromStr(data, 'str')
+
+ obj = DBRefProvEntity(prov_ref=prov_ref)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, ref_prov_entity, node=None):
+ if node is None:
+ node = ElementTree.Element('prov:entity')
+
+ # set attributes
+ node.set('prov:ref',self.convertToStr(ref_prov_entity.db_prov_ref, 'str'))
+
+ return node
+
+class DBProvActivityXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'prov:activity':
+ return None
+
+ # read attributes
+ data = node.get('prov:id', None)
+ id = self.convertFromStr(data, 'str')
+
+ startTime = None
+ endTime = None
+ vt_id = None
+ vt_type = None
+ vt_cached = None
+ vt_completed = None
+ vt_machine_id = None
+ vt_error = None
+ is_part_of = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'prov:startTime':
+ _data = self.convertFromStr(child.text,'str')
+ startTime = _data
+ elif child_tag == 'prov:endTime':
+ _data = self.convertFromStr(child.text,'str')
+ endTime = _data
+ elif child_tag == 'vt:id':
+ _data = self.convertFromStr(child.text,'str')
+ vt_id = _data
+ elif child_tag == 'vt:type':
+ _data = self.convertFromStr(child.text,'str')
+ vt_type = _data
+ elif child_tag == 'vt:cached':
+ _data = self.convertFromStr(child.text,'str')
+ vt_cached = _data
+ elif child_tag == 'vt:completed':
+ _data = self.convertFromStr(child.text,'str')
+ vt_completed = _data
+ elif child_tag == 'vt:machine_id':
+ _data = self.convertFromStr(child.text,'str')
+ vt_machine_id = _data
+ elif child_tag == 'vt:error':
+ _data = self.convertFromStr(child.text,'str')
+ vt_error = _data
+ elif child_tag == 'dcterms:isPartOf':
+ _data = self.getDao('is_part_of').fromXML(child)
+ is_part_of = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBProvActivity(id=id,
+ startTime=startTime,
+ endTime=endTime,
+ vt_id=vt_id,
+ vt_type=vt_type,
+ vt_cached=vt_cached,
+ vt_completed=vt_completed,
+ vt_machine_id=vt_machine_id,
+ vt_error=vt_error,
+ is_part_of=is_part_of)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, prov_activity, node=None):
+ if node is None:
+ node = ElementTree.Element('prov:activity')
+
+ # set attributes
+ node.set('prov:id',self.convertToStr(prov_activity.db_id, 'str'))
+
+ # set elements
+ startTime = prov_activity.db_startTime
+ if (startTime is not None) and (startTime != ""):
+ childNode = ElementTree.SubElement(node, 'prov:startTime')
+ childNode.text = self.convertToStr(startTime, 'str')
+ endTime = prov_activity.db_endTime
+ if (endTime is not None) and (endTime != ""):
+ childNode = ElementTree.SubElement(node, 'prov:endTime')
+ childNode.text = self.convertToStr(endTime, 'str')
+ vt_id = prov_activity.db_vt_id
+ if (vt_id is not None) and (vt_id != ""):
+ childNode = ElementTree.SubElement(node, 'vt:id')
+ childNode.text = self.convertToStr(vt_id, 'str')
+ vt_type = prov_activity.db_vt_type
+ if (vt_type is not None) and (vt_type != ""):
+ childNode = ElementTree.SubElement(node, 'vt:type')
+ childNode.text = self.convertToStr(vt_type, 'str')
+ vt_cached = prov_activity.db_vt_cached
+ if (vt_cached is not None) and (vt_cached != ""):
+ childNode = ElementTree.SubElement(node, 'vt:cached')
+ childNode.text = self.convertToStr(vt_cached, 'str')
+ vt_completed = prov_activity.db_vt_completed
+ if (vt_completed is not None) and (vt_completed != ""):
+ childNode = ElementTree.SubElement(node, 'vt:completed')
+ childNode.text = self.convertToStr(vt_completed, 'str')
+ vt_machine_id = prov_activity.db_vt_machine_id
+ if (vt_machine_id is not None) and (vt_machine_id != ""):
+ childNode = ElementTree.SubElement(node, 'vt:machine_id')
+ childNode.text = self.convertToStr(vt_machine_id, 'str')
+ vt_error = prov_activity.db_vt_error
+ if (vt_error is not None) and (vt_error != ""):
+ childNode = ElementTree.SubElement(node, 'vt:error')
+ childNode.text = self.convertToStr(vt_error, 'str')
+ is_part_of = prov_activity.db_is_part_of
+ if is_part_of is not None:
+ if (is_part_of is not None) and (is_part_of != ""):
+ childNode = ElementTree.SubElement(node, 'dcterms:isPartOf')
+ self.getDao('is_part_of').toXML(is_part_of, childNode)
+
+ return node
+
+class DBMashupActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'action':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('prevId', None)
+ prevId = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+
+ mashup = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'mashup':
+ _data = self.getDao('mashup').fromXML(child)
+ mashup = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBMashupAction(id=id,
+ prevId=prevId,
+ date=date,
+ user=user,
+ mashup=mashup)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, mashup_action, node=None):
+ if node is None:
+ node = ElementTree.Element('action')
+
+ # set attributes
+ node.set('id',self.convertToStr(mashup_action.db_id, 'long'))
+ node.set('prevId',self.convertToStr(mashup_action.db_prevId, 'long'))
+ node.set('date',self.convertToStr(mashup_action.db_date, 'datetime'))
+ node.set('user',self.convertToStr(mashup_action.db_user, 'str'))
+
+ # set elements
+ mashup = mashup_action.db_mashup
+ if mashup is not None:
+ if (mashup is not None) and (mashup != ""):
+ childNode = ElementTree.SubElement(node, 'mashup')
+ self.getDao('mashup').toXML(mashup, childNode)
+
+ return node
+
+class DBProvUsageXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'prov:used':
+ return None
+
+ prov_activity = None
+ prov_entity = None
+ prov_role = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'prov:activity':
+ _data = self.getDao('ref_prov_activity').fromXML(child)
+ prov_activity = _data
+ elif child_tag == 'prov:entity':
+ _data = self.getDao('ref_prov_entity').fromXML(child)
+ prov_entity = _data
+ elif child_tag == 'prov:role':
+ _data = self.convertFromStr(child.text,'str')
+ prov_role = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBProvUsage(prov_activity=prov_activity,
+ prov_entity=prov_entity,
+ prov_role=prov_role)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, prov_usage, node=None):
+ if node is None:
+ node = ElementTree.Element('prov:used')
+
+ # set elements
+ prov_activity = prov_usage.db_prov_activity
+ if prov_activity is not None:
+ if (prov_activity is not None) and (prov_activity != ""):
+ childNode = ElementTree.SubElement(node, 'prov:activity')
+ self.getDao('ref_prov_activity').toXML(prov_activity, childNode)
+ prov_entity = prov_usage.db_prov_entity
+ if prov_entity is not None:
+ if (prov_entity is not None) and (prov_entity != ""):
+ childNode = ElementTree.SubElement(node, 'prov:entity')
+ self.getDao('ref_prov_entity').toXML(prov_entity, childNode)
+ prov_role = prov_usage.db_prov_role
+ if (prov_role is not None) and (prov_role != ""):
+ childNode = ElementTree.SubElement(node, 'prov:role')
+ childNode.text = self.convertToStr(prov_role, 'str')
+
+ return node
+
+class DBOpmArtifactValueXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'value':
+ return None
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ value = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifactValue(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_value, node=None):
+ if node is None:
+ node = ElementTree.Element('value')
+
+ # set elements
+ value = opm_artifact_value.db_value
+ if value is not None:
+ if value.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(value, childNode)
+ elif value.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(value, childNode)
+
+ return node
+
+class DBOpmArtifactIdEffectXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'effect':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmArtifactIdEffect(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifact_id_effect, node=None):
+ if node is None:
+ node = ElementTree.Element('effect')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_artifact_id_effect.db_id, 'str'))
+
+ return node
+
+class DBOpmGraphXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'opmGraph':
+ return None
+
+ accounts = None
+ processes = None
+ artifacts = None
+ agents = None
+ dependencies = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'accounts':
+ _data = self.getDao('opm_accounts').fromXML(child)
+ accounts = _data
+ elif child_tag == 'processes':
+ _data = self.getDao('opm_processes').fromXML(child)
+ processes = _data
+ elif child_tag == 'artifacts':
+ _data = self.getDao('opm_artifacts').fromXML(child)
+ artifacts = _data
+ elif child_tag == 'agents':
+ _data = self.getDao('opm_agents').fromXML(child)
+ agents = _data
+ elif child_tag == 'causalDependencies':
+ _data = self.getDao('opm_dependencies').fromXML(child)
+ dependencies = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmGraph(accounts=accounts,
+ processes=processes,
+ artifacts=artifacts,
+ agents=agents,
+ dependencies=dependencies)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_graph, node=None):
+ if node is None:
+ node = ElementTree.Element('opmGraph')
+
+ # set elements
+ accounts = opm_graph.db_accounts
+ if accounts is not None:
+ if (accounts is not None) and (accounts != ""):
+ childNode = ElementTree.SubElement(node, 'accounts')
+ self.getDao('opm_accounts').toXML(accounts, childNode)
+ processes = opm_graph.db_processes
+ if processes is not None:
+ if (processes is not None) and (processes != ""):
+ childNode = ElementTree.SubElement(node, 'processes')
+ self.getDao('opm_processes').toXML(processes, childNode)
+ artifacts = opm_graph.db_artifacts
+ if artifacts is not None:
+ if (artifacts is not None) and (artifacts != ""):
+ childNode = ElementTree.SubElement(node, 'artifacts')
+ self.getDao('opm_artifacts').toXML(artifacts, childNode)
+ agents = opm_graph.db_agents
+ if agents is not None:
+ if (agents is not None) and (agents != ""):
+ childNode = ElementTree.SubElement(node, 'agents')
+ self.getDao('opm_agents').toXML(agents, childNode)
+ dependencies = opm_graph.db_dependencies
+ if dependencies is not None:
+ if (dependencies is not None) and (dependencies != ""):
+ childNode = ElementTree.SubElement(node, 'causalDependencies')
+ self.getDao('opm_dependencies').toXML(dependencies, childNode)
+
+ return node
+
+class DBMashuptrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'mashuptrail':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('vtVersion', None)
+ vtVersion = self.convertFromStr(data, 'long')
+
+ actions = []
+ annotations = []
+ actionAnnotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'action':
+ _data = self.getDao('mashup_action').fromXML(child)
+ actions.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'actionAnnotation':
+ _data = self.getDao('mashup_actionAnnotation').fromXML(child)
+ actionAnnotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBMashuptrail(name=name,
+ version=version,
+ vtVersion=vtVersion,
+ actions=actions,
+ annotations=annotations,
+ actionAnnotations=actionAnnotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, mashuptrail, node=None):
+ if node is None:
+ node = ElementTree.Element('mashuptrail')
+
+ # set attributes
+ node.set('id',self.convertToStr(mashuptrail.db_name, 'str'))
+ node.set('version',self.convertToStr(mashuptrail.db_version, 'str'))
+ node.set('vtVersion',self.convertToStr(mashuptrail.db_vtVersion, 'long'))
+
+ # set elements
+ actions = mashuptrail.db_actions
+ for action in actions:
+ if (actions is not None) and (actions != ""):
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('mashup_action').toXML(action, childNode)
+ annotations = mashuptrail.db_annotations
+ for annotation in annotations:
+ if (annotations is not None) and (annotations != ""):
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ actionAnnotations = mashuptrail.db_actionAnnotations
+ for actionAnnotation in actionAnnotations:
+ if (actionAnnotations is not None) and (actionAnnotations != ""):
+ childNode = ElementTree.SubElement(node, 'actionAnnotation')
+ self.getDao('mashup_actionAnnotation').toXML(actionAnnotation, childNode)
+
+ return node
+
+class DBRegistryXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'registry':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('rootDescriptorId', None)
+ root_descriptor_id = self.convertFromStr(data, 'long')
+
+ packages = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'package':
+ _data = self.getDao('package').fromXML(child)
+ packages.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBRegistry(id=id,
+ version=version,
+ root_descriptor_id=root_descriptor_id,
+ packages=packages)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, registry, node=None):
+ if node is None:
+ node = ElementTree.Element('registry')
+
+ # set attributes
+ node.set('id',self.convertToStr(registry.db_id, 'long'))
+ node.set('version',self.convertToStr(registry.db_version, 'str'))
+ node.set('rootDescriptorId',self.convertToStr(registry.db_root_descriptor_id, 'long'))
+
+ # set elements
+ packages = registry.db_packages
+ for package in packages:
+ if (packages is not None) and (packages != ""):
+ childNode = ElementTree.SubElement(node, 'package')
+ self.getDao('package').toXML(package, childNode)
+
+ return node
+
+class DBVtConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'vt:connection':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ vt_source = None
+ vt_dest = None
+ vt_source_port = None
+ vt_dest_port = None
+ vt_source_signature = None
+ vt_dest_signature = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'vt:source':
+ _data = self.convertFromStr(child.text,'str')
+ vt_source = _data
+ elif child_tag == 'vt:dest':
+ _data = self.convertFromStr(child.text,'str')
+ vt_dest = _data
+ elif child_tag == 'vt:source_port':
+ _data = self.convertFromStr(child.text,'str')
+ vt_source_port = _data
+ elif child_tag == 'vt:dest_port':
+ _data = self.convertFromStr(child.text,'str')
+ vt_dest_port = _data
+ elif child_tag == 'vt:source_signature':
+ _data = self.convertFromStr(child.text,'str')
+ vt_source_signature = _data
+ elif child_tag == 'vt:dest_signature':
+ _data = self.convertFromStr(child.text,'str')
+ vt_dest_signature = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBVtConnection(id=id,
+ vt_source=vt_source,
+ vt_dest=vt_dest,
+ vt_source_port=vt_source_port,
+ vt_dest_port=vt_dest_port,
+ vt_source_signature=vt_source_signature,
+ vt_dest_signature=vt_dest_signature)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vt_connection, node=None):
+ if node is None:
+ node = ElementTree.Element('vt:connection')
+
+ # set attributes
+ node.set('id',self.convertToStr(vt_connection.db_id, 'str'))
+
+ # set elements
+ vt_source = vt_connection.db_vt_source
+ if (vt_source is not None) and (vt_source != ""):
+ childNode = ElementTree.SubElement(node, 'vt:source')
+ childNode.text = self.convertToStr(vt_source, 'str')
+ vt_dest = vt_connection.db_vt_dest
+ if (vt_dest is not None) and (vt_dest != ""):
+ childNode = ElementTree.SubElement(node, 'vt:dest')
+ childNode.text = self.convertToStr(vt_dest, 'str')
+ vt_source_port = vt_connection.db_vt_source_port
+ if (vt_source_port is not None) and (vt_source_port != ""):
+ childNode = ElementTree.SubElement(node, 'vt:source_port')
+ childNode.text = self.convertToStr(vt_source_port, 'str')
+ vt_dest_port = vt_connection.db_vt_dest_port
+ if (vt_dest_port is not None) and (vt_dest_port != ""):
+ childNode = ElementTree.SubElement(node, 'vt:dest_port')
+ childNode.text = self.convertToStr(vt_dest_port, 'str')
+ vt_source_signature = vt_connection.db_vt_source_signature
+ if (vt_source_signature is not None) and (vt_source_signature != ""):
+ childNode = ElementTree.SubElement(node, 'vt:source_signature')
+ childNode.text = self.convertToStr(vt_source_signature, 'str')
+ vt_dest_signature = vt_connection.db_vt_dest_signature
+ if (vt_dest_signature is not None) and (vt_dest_signature != ""):
+ childNode = ElementTree.SubElement(node, 'vt:dest_signature')
+ childNode.text = self.convertToStr(vt_dest_signature, 'str')
+
+ return node
+
+class DBMashupComponentXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'component':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('vtid', None)
+ vtid = self.convertFromStr(data, 'long')
+ data = node.get('vttype', None)
+ vttype = self.convertFromStr(data, 'str')
+ data = node.get('vtparent_type', None)
+ vtparent_type = self.convertFromStr(data, 'str')
+ data = node.get('vtparent_id', None)
+ vtparent_id = self.convertFromStr(data, 'long')
+ data = node.get('vtpos', None)
+ vtpos = self.convertFromStr(data, 'long')
+ data = node.get('vtmid', None)
+ vtmid = self.convertFromStr(data, 'long')
+ data = node.get('pos', None)
+ pos = self.convertFromStr(data, 'long')
+ data = node.get('type', None)
+ type = self.convertFromStr(data, 'str')
+ data = node.get('val', None)
+ val = self.convertFromStr(data, 'str')
+ data = node.get('minVal', None)
+ minVal = self.convertFromStr(data, 'str')
+ data = node.get('maxVal', None)
+ maxVal = self.convertFromStr(data, 'str')
+ data = node.get('stepSize', None)
+ stepSize = self.convertFromStr(data, 'str')
+ data = node.get('valueList', None)
+ strvaluelist = self.convertFromStr(data, 'str')
+ data = node.get('widget', None)
+ widget = self.convertFromStr(data, 'str')
+ data = node.get('seq', None)
+ seq = self.convertFromStr(data, 'int')
+ data = node.get('parent', None)
+ parent = self.convertFromStr(data, 'str')
+
+ obj = DBMashupComponent(id=id,
+ vtid=vtid,
+ vttype=vttype,
+ vtparent_type=vtparent_type,
+ vtparent_id=vtparent_id,
+ vtpos=vtpos,
+ vtmid=vtmid,
+ pos=pos,
+ type=type,
+ val=val,
+ minVal=minVal,
+ maxVal=maxVal,
+ stepSize=stepSize,
+ strvaluelist=strvaluelist,
+ widget=widget,
+ seq=seq,
+ parent=parent)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, mashup_component, node=None):
+ if node is None:
+ node = ElementTree.Element('component')
+
+ # set attributes
+ node.set('id',self.convertToStr(mashup_component.db_id, 'long'))
+ node.set('vtid',self.convertToStr(mashup_component.db_vtid, 'long'))
+ node.set('vttype',self.convertToStr(mashup_component.db_vttype, 'str'))
+ node.set('vtparent_type',self.convertToStr(mashup_component.db_vtparent_type, 'str'))
+ node.set('vtparent_id',self.convertToStr(mashup_component.db_vtparent_id, 'long'))
+ node.set('vtpos',self.convertToStr(mashup_component.db_vtpos, 'long'))
+ node.set('vtmid',self.convertToStr(mashup_component.db_vtmid, 'long'))
+ node.set('pos',self.convertToStr(mashup_component.db_pos, 'long'))
+ node.set('type',self.convertToStr(mashup_component.db_type, 'str'))
+ node.set('val',self.convertToStr(mashup_component.db_val, 'str'))
+ node.set('minVal',self.convertToStr(mashup_component.db_minVal, 'str'))
+ node.set('maxVal',self.convertToStr(mashup_component.db_maxVal, 'str'))
+ node.set('stepSize',self.convertToStr(mashup_component.db_stepSize, 'str'))
+ node.set('valueList',self.convertToStr(mashup_component.db_strvaluelist, 'str'))
+ node.set('widget',self.convertToStr(mashup_component.db_widget, 'str'))
+ node.set('seq',self.convertToStr(mashup_component.db_seq, 'int'))
+ node.set('parent',self.convertToStr(mashup_component.db_parent, 'str'))
+
+ return node
+
+class DBProvEntityXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'prov:entity':
+ return None
+
+ # read attributes
+ data = node.get('prov:id', None)
+ id = self.convertFromStr(data, 'str')
+
+ prov_type = None
+ prov_label = None
+ prov_value = None
+ vt_id = None
+ vt_type = None
+ vt_desc = None
+ vt_package = None
+ vt_version = None
+ vt_cache = None
+ vt_location_x = None
+ vt_location_y = None
+ is_part_of = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'prov:type':
+ _data = self.convertFromStr(child.text,'str')
+ prov_type = _data
+ elif child_tag == 'prov:label':
+ _data = self.convertFromStr(child.text,'str')
+ prov_label = _data
+ elif child_tag == 'prov:value':
+ _data = self.convertFromStr(child.text,'str')
+ prov_value = _data
+ elif child_tag == 'vt:id':
+ _data = self.convertFromStr(child.text,'str')
+ vt_id = _data
+ elif child_tag == 'vt:type':
+ _data = self.convertFromStr(child.text,'str')
+ vt_type = _data
+ elif child_tag == 'vt:desc':
+ _data = self.convertFromStr(child.text,'str')
+ vt_desc = _data
+ elif child_tag == 'vt:package':
+ _data = self.convertFromStr(child.text,'str')
+ vt_package = _data
+ elif child_tag == 'vt:version':
+ _data = self.convertFromStr(child.text,'str')
+ vt_version = _data
+ elif child_tag == 'vt:cache':
+ _data = self.convertFromStr(child.text,'str')
+ vt_cache = _data
+ elif child_tag == 'vt:location_x':
+ _data = self.convertFromStr(child.text,'str')
+ vt_location_x = _data
+ elif child_tag == 'vt:location_y':
+ _data = self.convertFromStr(child.text,'str')
+ vt_location_y = _data
+ elif child_tag == 'dcterms:isPartOf':
+ _data = self.getDao('is_part_of').fromXML(child)
+ is_part_of = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBProvEntity(id=id,
+ prov_type=prov_type,
+ prov_label=prov_label,
+ prov_value=prov_value,
+ vt_id=vt_id,
+ vt_type=vt_type,
+ vt_desc=vt_desc,
+ vt_package=vt_package,
+ vt_version=vt_version,
+ vt_cache=vt_cache,
+ vt_location_x=vt_location_x,
+ vt_location_y=vt_location_y,
+ is_part_of=is_part_of)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, prov_entity, node=None):
+ if node is None:
+ node = ElementTree.Element('prov:entity')
+
+ # set attributes
+ node.set('prov:id',self.convertToStr(prov_entity.db_id, 'str'))
+
+ # set elements
+ prov_type = prov_entity.db_prov_type
+ if (prov_type is not None) and (prov_type != ""):
+ childNode = ElementTree.SubElement(node, 'prov:type')
+ childNode.text = self.convertToStr(prov_type, 'str')
+ prov_label = prov_entity.db_prov_label
+ if (prov_label is not None) and (prov_label != ""):
+ childNode = ElementTree.SubElement(node, 'prov:label')
+ childNode.text = self.convertToStr(prov_label, 'str')
+ prov_value = prov_entity.db_prov_value
+ if (prov_value is not None) and (prov_value != ""):
+ childNode = ElementTree.SubElement(node, 'prov:value')
+ childNode.text = self.convertToStr(prov_value, 'str')
+ vt_id = prov_entity.db_vt_id
+ if (vt_id is not None) and (vt_id != ""):
+ childNode = ElementTree.SubElement(node, 'vt:id')
+ childNode.text = self.convertToStr(vt_id, 'str')
+ vt_type = prov_entity.db_vt_type
+ if (vt_type is not None) and (vt_type != ""):
+ childNode = ElementTree.SubElement(node, 'vt:type')
+ childNode.text = self.convertToStr(vt_type, 'str')
+ vt_desc = prov_entity.db_vt_desc
+ if (vt_desc is not None) and (vt_desc != ""):
+ childNode = ElementTree.SubElement(node, 'vt:desc')
+ childNode.text = self.convertToStr(vt_desc, 'str')
+ vt_package = prov_entity.db_vt_package
+ if (vt_package is not None) and (vt_package != ""):
+ childNode = ElementTree.SubElement(node, 'vt:package')
+ childNode.text = self.convertToStr(vt_package, 'str')
+ vt_version = prov_entity.db_vt_version
+ if (vt_version is not None) and (vt_version != ""):
+ childNode = ElementTree.SubElement(node, 'vt:version')
+ childNode.text = self.convertToStr(vt_version, 'str')
+ vt_cache = prov_entity.db_vt_cache
+ if (vt_cache is not None) and (vt_cache != ""):
+ childNode = ElementTree.SubElement(node, 'vt:cache')
+ childNode.text = self.convertToStr(vt_cache, 'str')
+ vt_location_x = prov_entity.db_vt_location_x
+ if (vt_location_x is not None) and (vt_location_x != ""):
+ childNode = ElementTree.SubElement(node, 'vt:location_x')
+ childNode.text = self.convertToStr(vt_location_x, 'str')
+ vt_location_y = prov_entity.db_vt_location_y
+ if (vt_location_y is not None) and (vt_location_y != ""):
+ childNode = ElementTree.SubElement(node, 'vt:location_y')
+ childNode.text = self.convertToStr(vt_location_y, 'str')
+ is_part_of = prov_entity.db_is_part_of
+ if is_part_of is not None:
+ if (is_part_of is not None) and (is_part_of != ""):
+ childNode = ElementTree.SubElement(node, 'dcterms:isPartOf')
+ self.getDao('is_part_of').toXML(is_part_of, childNode)
+
+ return node
+
+class DBAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'annotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+
+ obj = DBAnnotation(id=id,
+ key=key,
+ value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, annotation, node=None):
+ if node is None:
+ node = ElementTree.Element('annotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(annotation.db_id, 'long'))
+ node.set('key',self.convertToStr(annotation.db_key, 'str'))
+ node.set('value',self.convertToStr(annotation.db_value, 'str'))
+
+ return node
+
+class DBChangeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'change':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('oldObjId', None)
+ oldObjId = self.convertFromStr(data, 'long')
+ data = node.get('newObjId', None)
+ newObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ data = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'module':
+ _data = self.getDao('module').fromXML(child)
+ data = _data
+ elif child_tag == 'location':
+ _data = self.getDao('location').fromXML(child)
+ data = _data
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ data = _data
+ elif child_tag == 'function':
+ _data = self.getDao('function').fromXML(child)
+ data = _data
+ elif child_tag == 'connection':
+ _data = self.getDao('connection').fromXML(child)
+ data = _data
+ elif child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ data = _data
+ elif child_tag == 'parameter':
+ _data = self.getDao('parameter').fromXML(child)
+ data = _data
+ elif child_tag == 'portSpec':
+ _data = self.getDao('portSpec').fromXML(child)
+ data = _data
+ elif child_tag == 'abstraction':
+ _data = self.getDao('abstraction').fromXML(child)
+ data = _data
+ elif child_tag == 'group':
+ _data = self.getDao('group').fromXML(child)
+ data = _data
+ elif child_tag == 'other':
+ _data = self.getDao('other').fromXML(child)
+ data = _data
+ elif child_tag == 'plugin_data':
+ _data = self.getDao('plugin_data').fromXML(child)
+ data = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBChange(data=data,
+ id=id,
+ what=what,
+ oldObjId=oldObjId,
+ newObjId=newObjId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, change, node=None):
+ if node is None:
+ node = ElementTree.Element('change')
+
+ # set attributes
+ node.set('id',self.convertToStr(change.db_id, 'long'))
+ node.set('what',self.convertToStr(change.db_what, 'str'))
+ node.set('oldObjId',self.convertToStr(change.db_oldObjId, 'long'))
+ node.set('newObjId',self.convertToStr(change.db_newObjId, 'long'))
+ node.set('parentObjId',self.convertToStr(change.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(change.db_parentObjType, 'str'))
+
+ # set elements
+ data = change.db_data
+ if data is not None:
+ if data.vtType == 'module':
+ childNode = ElementTree.SubElement(node, 'module')
+ self.getDao('module').toXML(data, childNode)
+ elif data.vtType == 'location':
+ childNode = ElementTree.SubElement(node, 'location')
+ self.getDao('location').toXML(data, childNode)
+ elif data.vtType == 'annotation':
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(data, childNode)
+ elif data.vtType == 'function':
+ childNode = ElementTree.SubElement(node, 'function')
+ self.getDao('function').toXML(data, childNode)
+ elif data.vtType == 'connection':
+ childNode = ElementTree.SubElement(node, 'connection')
+ self.getDao('connection').toXML(data, childNode)
+ elif data.vtType == 'port':
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(data, childNode)
+ elif data.vtType == 'parameter':
+ childNode = ElementTree.SubElement(node, 'parameter')
+ self.getDao('parameter').toXML(data, childNode)
+ elif data.vtType == 'portSpec':
+ childNode = ElementTree.SubElement(node, 'portSpec')
+ self.getDao('portSpec').toXML(data, childNode)
+ elif data.vtType == 'abstraction':
+ childNode = ElementTree.SubElement(node, 'abstraction')
+ self.getDao('abstraction').toXML(data, childNode)
+ elif data.vtType == 'group':
+ childNode = ElementTree.SubElement(node, 'group')
+ self.getDao('group').toXML(data, childNode)
+ elif data.vtType == 'other':
+ childNode = ElementTree.SubElement(node, 'other')
+ self.getDao('other').toXML(data, childNode)
+ elif data.vtType == 'plugin_data':
+ childNode = ElementTree.SubElement(node, 'plugin_data')
+ self.getDao('plugin_data').toXML(data, childNode)
+
+ return node
+
+class DBOpmWasDerivedFromXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasDerivedFrom':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_artifact_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_artifact_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasDerivedFrom(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_derived_from, node=None):
+ if node is None:
+ node = ElementTree.Element('wasDerivedFrom')
+
+ # set elements
+ effect = opm_was_derived_from.db_effect
+ if effect is not None:
+ if (effect is not None) and (effect != ""):
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_artifact_id_effect').toXML(effect, childNode)
+ role = opm_was_derived_from.db_role
+ if role is not None:
+ if (role is not None) and (role != ""):
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_derived_from.db_cause
+ if cause is not None:
+ if (cause is not None) and (cause != ""):
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_artifact_id_cause').toXML(cause, childNode)
+ accounts = opm_was_derived_from.db_accounts
+ for account in accounts:
+ if (accounts is not None) and (accounts != ""):
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_derived_from.db_opm_times
+ for opm_time in opm_times:
+ if (opm_times is not None) and (opm_times != ""):
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBOpmArtifactsXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'artifacts':
+ return None
+
+ artifacts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'artifact':
+ _data = self.getDao('opm_artifact').fromXML(child)
+ artifacts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmArtifacts(artifacts=artifacts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_artifacts, node=None):
+ if node is None:
+ node = ElementTree.Element('artifacts')
+
+ # set elements
+ artifacts = opm_artifacts.db_artifacts
+ for artifact in artifacts:
+ if (artifacts is not None) and (artifacts != ""):
+ childNode = ElementTree.SubElement(node, 'artifact')
+ self.getDao('opm_artifact').toXML(artifact, childNode)
+
+ return node
+
+class DBOpmWasControlledByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasControlledBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ starts = []
+ ends = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'agent':
+ _data = self.getDao('opm_agent_id').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ starts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ ends.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasControlledBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ starts=starts,
+ ends=ends)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_controlled_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasControlledBy')
+
+ # set elements
+ effect = opm_was_controlled_by.db_effect
+ if effect is not None:
+ if (effect is not None) and (effect != ""):
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_was_controlled_by.db_role
+ if role is not None:
+ if (role is not None) and (role != ""):
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_controlled_by.db_cause
+ if cause is not None:
+ if (cause is not None) and (cause != ""):
+ childNode = ElementTree.SubElement(node, 'agent')
+ self.getDao('opm_agent_id').toXML(cause, childNode)
+ accounts = opm_was_controlled_by.db_accounts
+ for account in accounts:
+ if (accounts is not None) and (accounts != ""):
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ starts = opm_was_controlled_by.db_starts
+ for start in starts:
+ if (starts is not None) and (starts != ""):
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(start, childNode)
+ ends = opm_was_controlled_by.db_ends
+ for end in ends:
+ if (ends is not None) and (ends != ""):
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(end, childNode)
+
+ return node
+
+class DBOpmAgentIdXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agent':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmAgentId(id=id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agent_id, node=None):
+ if node is None:
+ node = ElementTree.Element('agent')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_agent_id.db_id, 'str'))
+
+ return node
+
+class DBGroupExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'groupExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('groupName', None)
+ group_name = self.convertFromStr(data, 'str')
+ data = node.get('groupType', None)
+ group_type = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBGroupExec(item_execs=item_execs,
+ id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ group_name=group_name,
+ group_type=group_type,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, group_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('groupExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(group_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(group_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(group_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(group_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(group_exec.db_module_id, 'long'))
+ node.set('groupName',self.convertToStr(group_exec.db_group_name, 'str'))
+ node.set('groupType',self.convertToStr(group_exec.db_group_type, 'str'))
+ node.set('completed',self.convertToStr(group_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(group_exec.db_error, 'str'))
+ node.set('machine_id',self.convertToStr(group_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = group_exec.db_annotations
+ for annotation in annotations:
+ if (annotations is not None) and (annotations != ""):
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ item_execs = group_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBOpmTimeXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'time':
+ return None
+
+ # read attributes
+ data = node.get('noLaterThan', None)
+ no_later_than = self.convertFromStr(data, 'datetime')
+ data = node.get('noEarlierThan', None)
+ no_earlier_than = self.convertFromStr(data, 'datetime')
+ data = node.get('clockId', None)
+ clock_id = self.convertFromStr(data, 'str')
+
+ obj = DBOpmTime(no_later_than=no_later_than,
+ no_earlier_than=no_earlier_than,
+ clock_id=clock_id)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_time, node=None):
+ if node is None:
+ node = ElementTree.Element('time')
+
+ # set attributes
+ node.set('noLaterThan',self.convertToStr(opm_time.db_no_later_than, 'datetime'))
+ node.set('noEarlierThan',self.convertToStr(opm_time.db_no_earlier_than, 'datetime'))
+ node.set('clockId',self.convertToStr(opm_time.db_clock_id, 'str'))
+
+ return node
+
+class DBPackageXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'package':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('identifier', None)
+ identifier = self.convertFromStr(data, 'str')
+ data = node.get('codepath', None)
+ codepath = self.convertFromStr(data, 'str')
+ data = node.get('loadConfiguration', None)
+ load_configuration = self.convertFromStr(data, 'int')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('description', None)
+ description = self.convertFromStr(data, 'str')
+
+ module_descriptors = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleDescriptor':
+ _data = self.getDao('module_descriptor').fromXML(child)
+ module_descriptors.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBPackage(id=id,
+ name=name,
+ identifier=identifier,
+ codepath=codepath,
+ load_configuration=load_configuration,
+ version=version,
+ description=description,
+ module_descriptors=module_descriptors)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, package, node=None):
+ if node is None:
+ node = ElementTree.Element('package')
+
+ # set attributes
+ node.set('id',self.convertToStr(package.db_id, 'long'))
+ node.set('name',self.convertToStr(package.db_name, 'str'))
+ node.set('identifier',self.convertToStr(package.db_identifier, 'str'))
+ node.set('codepath',self.convertToStr(package.db_codepath, 'str'))
+ node.set('loadConfiguration',self.convertToStr(package.db_load_configuration, 'int'))
+ node.set('version',self.convertToStr(package.db_version, 'str'))
+ node.set('description',self.convertToStr(package.db_description, 'str'))
+
+ # set elements
+ module_descriptors = package.db_module_descriptors
+ for module_descriptor in module_descriptors:
+ if (module_descriptors is not None) and (module_descriptors != ""):
+ childNode = ElementTree.SubElement(node, 'moduleDescriptor')
+ self.getDao('module_descriptor').toXML(module_descriptor, childNode)
+
+ return node
+
+class DBWorkflowExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'workflowExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('ip', None)
+ ip = self.convertFromStr(data, 'str')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('vtVersion', None)
+ vt_version = self.convertFromStr(data, 'str')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('parentId', None)
+ parent_id = self.convertFromStr(data, 'long')
+ data = node.get('parentType', None)
+ parent_type = self.convertFromStr(data, 'str')
+ data = node.get('parentVersion', None)
+ parent_version = self.convertFromStr(data, 'long')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ annotations = []
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBWorkflowExec(item_execs=item_execs,
+ id=id,
+ user=user,
+ ip=ip,
+ session=session,
+ vt_version=vt_version,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ parent_id=parent_id,
+ parent_type=parent_type,
+ parent_version=parent_version,
+ completed=completed,
+ name=name,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, workflow_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('workflowExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(workflow_exec.db_id, 'long'))
+ node.set('user',self.convertToStr(workflow_exec.db_user, 'str'))
+ node.set('ip',self.convertToStr(workflow_exec.db_ip, 'str'))
+ node.set('session',self.convertToStr(workflow_exec.db_session, 'long'))
+ node.set('vtVersion',self.convertToStr(workflow_exec.db_vt_version, 'str'))
+ node.set('tsStart',self.convertToStr(workflow_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(workflow_exec.db_ts_end, 'datetime'))
+ node.set('parentId',self.convertToStr(workflow_exec.db_parent_id, 'long'))
+ node.set('parentType',self.convertToStr(workflow_exec.db_parent_type, 'str'))
+ node.set('parentVersion',self.convertToStr(workflow_exec.db_parent_version, 'long'))
+ node.set('completed',self.convertToStr(workflow_exec.db_completed, 'int'))
+ node.set('name',self.convertToStr(workflow_exec.db_name, 'str'))
+
+ # set elements
+ annotations = workflow_exec.db_annotations
+ for annotation in annotations:
+ if (annotations is not None) and (annotations != ""):
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ item_execs = workflow_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBParameterExplorationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'parameterExploration':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('actionId', None)
+ action_id = self.convertFromStr(data, 'long')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+ data = node.get('dims', None)
+ dims = self.convertFromStr(data, 'str')
+ data = node.get('layout', None)
+ layout = self.convertFromStr(data, 'str')
+
+ functions = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'peFunction':
+ _data = self.getDao('pe_function').fromXML(child)
+ functions.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBParameterExploration(id=id,
+ action_id=action_id,
+ name=name,
+ user=user,
+ dims=dims,
+ layout=layout,
+ functions=functions)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, parameter_exploration, node=None):
+ if node is None:
+ node = ElementTree.Element('parameterExploration')
+
+ # set attributes
+ node.set('id',self.convertToStr(parameter_exploration.db_id, 'long'))
+ node.set('actionId',self.convertToStr(parameter_exploration.db_action_id, 'long'))
+ node.set('name',self.convertToStr(parameter_exploration.db_name, 'str'))
+ node.set('user',self.convertToStr(parameter_exploration.db_user, 'str'))
+ node.set('dims',self.convertToStr(parameter_exploration.db_dims, 'str'))
+ node.set('layout',self.convertToStr(parameter_exploration.db_layout, 'str'))
+
+ # set elements
+ functions = parameter_exploration.db_functions
+ for function in functions:
+ if (functions is not None) and (functions != ""):
+ childNode = ElementTree.SubElement(node, 'peFunction')
+ self.getDao('pe_function').toXML(function, childNode)
+
+ return node
+
+class DBLoopExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'loopExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('iteration', None)
+ iteration = self.convertFromStr(data, 'int')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+
+ item_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ item_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBLoopExec(item_execs=item_execs,
+ id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ iteration=iteration,
+ completed=completed,
+ error=error)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, loop_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('loopExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(loop_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(loop_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(loop_exec.db_ts_end, 'datetime'))
+ node.set('iteration',self.convertToStr(loop_exec.db_iteration, 'int'))
+ node.set('completed',self.convertToStr(loop_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(loop_exec.db_error, 'str'))
+
+ # set elements
+ item_execs = loop_exec.db_item_execs
+ for item_exec in item_execs:
+ if item_exec.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(item_exec, childNode)
+ elif item_exec.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(item_exec, childNode)
+
+ return node
+
+class DBOpmWasTriggeredByXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'wasTriggeredBy':
+ return None
+
+ effect = None
+ role = None
+ cause = None
+ accounts = []
+ opm_times = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'effect':
+ _data = self.getDao('opm_process_id_effect').fromXML(child)
+ effect = _data
+ elif child_tag == 'role':
+ _data = self.getDao('opm_role').fromXML(child)
+ role = _data
+ elif child_tag == 'cause':
+ _data = self.getDao('opm_process_id_cause').fromXML(child)
+ cause = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child_tag == 'time':
+ _data = self.getDao('opm_time').fromXML(child)
+ opm_times.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmWasTriggeredBy(effect=effect,
+ role=role,
+ cause=cause,
+ accounts=accounts,
+ opm_times=opm_times)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_was_triggered_by, node=None):
+ if node is None:
+ node = ElementTree.Element('wasTriggeredBy')
+
+ # set elements
+ effect = opm_was_triggered_by.db_effect
+ if effect is not None:
+ if (effect is not None) and (effect != ""):
+ childNode = ElementTree.SubElement(node, 'effect')
+ self.getDao('opm_process_id_effect').toXML(effect, childNode)
+ role = opm_was_triggered_by.db_role
+ if role is not None:
+ if (role is not None) and (role != ""):
+ childNode = ElementTree.SubElement(node, 'role')
+ self.getDao('opm_role').toXML(role, childNode)
+ cause = opm_was_triggered_by.db_cause
+ if cause is not None:
+ if (cause is not None) and (cause != ""):
+ childNode = ElementTree.SubElement(node, 'cause')
+ self.getDao('opm_process_id_cause').toXML(cause, childNode)
+ accounts = opm_was_triggered_by.db_accounts
+ for account in accounts:
+ if (accounts is not None) and (accounts != ""):
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+ opm_times = opm_was_triggered_by.db_opm_times
+ for opm_time in opm_times:
+ if (opm_times is not None) and (opm_times != ""):
+ childNode = ElementTree.SubElement(node, 'time')
+ self.getDao('opm_time').toXML(opm_time, childNode)
+
+ return node
+
+class DBMashupActionAnnotationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'actionAnnotation':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('key', None)
+ key = self.convertFromStr(data, 'str')
+ data = node.get('value', None)
+ value = self.convertFromStr(data, 'str')
+ data = node.get('action_id', None)
+ action_id = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+
+ obj = DBMashupActionAnnotation(id=id,
+ key=key,
+ value=value,
+ action_id=action_id,
+ date=date,
+ user=user)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, mashup_actionAnnotation, node=None):
+ if node is None:
+ node = ElementTree.Element('actionAnnotation')
+
+ # set attributes
+ node.set('id',self.convertToStr(mashup_actionAnnotation.db_id, 'long'))
+ node.set('key',self.convertToStr(mashup_actionAnnotation.db_key, 'str'))
+ node.set('value',self.convertToStr(mashup_actionAnnotation.db_value, 'str'))
+ node.set('action_id',self.convertToStr(mashup_actionAnnotation.db_action_id, 'long'))
+ node.set('date',self.convertToStr(mashup_actionAnnotation.db_date, 'datetime'))
+ node.set('user',self.convertToStr(mashup_actionAnnotation.db_user, 'str'))
+
+ return node
+
+class DBConnectionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'connection':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+
+ ports = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'port':
+ _data = self.getDao('port').fromXML(child)
+ ports.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBConnection(id=id,
+ ports=ports)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, connection, node=None):
+ if node is None:
+ node = ElementTree.Element('connection')
+
+ # set attributes
+ node.set('id',self.convertToStr(connection.db_id, 'long'))
+
+ # set elements
+ ports = connection.db_ports
+ for port in ports:
+ if (ports is not None) and (ports != ""):
+ childNode = ElementTree.SubElement(node, 'port')
+ self.getDao('port').toXML(port, childNode)
+
+ return node
+
+class DBOpmProcessXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'process':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.getDao('opm_process_value').fromXML(child)
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcess(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process, node=None):
+ if node is None:
+ node = ElementTree.Element('process')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_process.db_id, 'str'))
+
+ # set elements
+ value = opm_process.db_value
+ if value is not None:
+ if (value is not None) and (value != ""):
+ childNode = ElementTree.SubElement(node, 'value')
+ self.getDao('opm_process_value').toXML(value, childNode)
+ accounts = opm_process.db_accounts
+ for account in accounts:
+ if (accounts is not None) and (accounts != ""):
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBIsPartOfXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'dcterms:isPartOf':
+ return None
+
+ # read attributes
+ data = node.get('prov:ref', None)
+ prov_ref = self.convertFromStr(data, 'str')
+
+ obj = DBIsPartOf(prov_ref=prov_ref)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, is_part_of, node=None):
+ if node is None:
+ node = ElementTree.Element('dcterms:isPartOf')
+
+ # set attributes
+ node.set('prov:ref',self.convertToStr(is_part_of.db_prov_ref, 'str'))
+
+ return node
+
+class DBPEFunctionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'peFunction':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('port_name', None)
+ port_name = self.convertFromStr(data, 'str')
+ data = node.get('is_alias', None)
+ is_alias = self.convertFromStr(data, 'long')
+
+ parameters = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'peParameter':
+ _data = self.getDao('pe_parameter').fromXML(child)
+ parameters.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBPEFunction(id=id,
+ module_id=module_id,
+ port_name=port_name,
+ is_alias=is_alias,
+ parameters=parameters)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, pe_function, node=None):
+ if node is None:
+ node = ElementTree.Element('peFunction')
+
+ # set attributes
+ node.set('id',self.convertToStr(pe_function.db_id, 'long'))
+ node.set('moduleId',self.convertToStr(pe_function.db_module_id, 'long'))
+ node.set('port_name',self.convertToStr(pe_function.db_port_name, 'str'))
+ node.set('is_alias',self.convertToStr(pe_function.db_is_alias, 'long'))
+
+ # set elements
+ parameters = pe_function.db_parameters
+ for parameter in parameters:
+ if (parameters is not None) and (parameters != ""):
+ childNode = ElementTree.SubElement(node, 'peParameter')
+ self.getDao('pe_parameter').toXML(parameter, childNode)
+
+ return node
+
+class DBOpmProcessValueXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'value':
+ return None
+
+ value = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'moduleExec':
+ _data = self.getDao('module_exec').fromXML(child)
+ value = _data
+ elif child_tag == 'groupExec':
+ _data = self.getDao('group_exec').fromXML(child)
+ value = _data
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ value = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmProcessValue(value=value)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_process_value, node=None):
+ if node is None:
+ node = ElementTree.Element('value')
+
+ # set elements
+ value = opm_process_value.db_value
+ if value is not None:
+ if value.vtType == 'module_exec':
+ childNode = ElementTree.SubElement(node, 'moduleExec')
+ self.getDao('module_exec').toXML(value, childNode)
+ elif value.vtType == 'group_exec':
+ childNode = ElementTree.SubElement(node, 'groupExec')
+ self.getDao('group_exec').toXML(value, childNode)
+ elif value.vtType == 'loop_exec':
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(value, childNode)
+
+ return node
+
+class DBActionXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'action':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('prevId', None)
+ prevId = self.convertFromStr(data, 'long')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
+ data = node.get('session', None)
+ session = self.convertFromStr(data, 'long')
+ data = node.get('user', None)
+ user = self.convertFromStr(data, 'str')
+
+ annotations = []
+ operations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'add':
+ _data = self.getDao('add').fromXML(child)
+ operations.append(_data)
+ elif child_tag == 'delete':
+ _data = self.getDao('delete').fromXML(child)
+ operations.append(_data)
+ elif child_tag == 'change':
+ _data = self.getDao('change').fromXML(child)
+ operations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBAction(operations=operations,
+ id=id,
+ prevId=prevId,
+ date=date,
+ session=session,
+ user=user,
+ annotations=annotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, action, node=None):
+ if node is None:
+ node = ElementTree.Element('action')
+
+ # set attributes
+ node.set('id',self.convertToStr(action.db_id, 'long'))
+ node.set('prevId',self.convertToStr(action.db_prevId, 'long'))
+ node.set('date',self.convertToStr(action.db_date, 'datetime'))
+ node.set('session',self.convertToStr(action.db_session, 'long'))
+ node.set('user',self.convertToStr(action.db_user, 'str'))
+
+ # set elements
+ annotations = action.db_annotations
+ for annotation in annotations:
+ if (annotations is not None) and (annotations != ""):
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ operations = action.db_operations
+ for operation in operations:
+ if operation.vtType == 'add':
+ childNode = ElementTree.SubElement(node, 'add')
+ self.getDao('add').toXML(operation, childNode)
+ elif operation.vtType == 'delete':
+ childNode = ElementTree.SubElement(node, 'delete')
+ self.getDao('delete').toXML(operation, childNode)
+ elif operation.vtType == 'change':
+ childNode = ElementTree.SubElement(node, 'change')
+ self.getDao('change').toXML(operation, childNode)
+
+ return node
+
+class DBOpmAgentXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'agent':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'str')
+
+ value = None
+ accounts = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'value':
+ _data = self.convertFromStr(child.text,'str')
+ value = _data
+ elif child_tag == 'account':
+ _data = self.getDao('opm_account_id').fromXML(child)
+ accounts.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBOpmAgent(id=id,
+ value=value,
+ accounts=accounts)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, opm_agent, node=None):
+ if node is None:
+ node = ElementTree.Element('agent')
+
+ # set attributes
+ node.set('id',self.convertToStr(opm_agent.db_id, 'str'))
+
+ # set elements
+ value = opm_agent.db_value
+ if (value is not None) and (value != ""):
+ childNode = ElementTree.SubElement(node, 'value')
+ childNode.text = self.convertToStr(value, 'str')
+ accounts = opm_agent.db_accounts
+ for account in accounts:
+ if (accounts is not None) and (accounts != ""):
+ childNode = ElementTree.SubElement(node, 'account')
+ self.getDao('opm_account_id').toXML(account, childNode)
+
+ return node
+
+class DBDeleteXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'delete':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('what', None)
+ what = self.convertFromStr(data, 'str')
+ data = node.get('objectId', None)
+ objectId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjId', None)
+ parentObjId = self.convertFromStr(data, 'long')
+ data = node.get('parentObjType', None)
+ parentObjType = self.convertFromStr(data, 'str')
+
+ obj = DBDelete(id=id,
+ what=what,
+ objectId=objectId,
+ parentObjId=parentObjId,
+ parentObjType=parentObjType)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, delete, node=None):
+ if node is None:
+ node = ElementTree.Element('delete')
+
+ # set attributes
+ node.set('id',self.convertToStr(delete.db_id, 'long'))
+ node.set('what',self.convertToStr(delete.db_what, 'str'))
+ node.set('objectId',self.convertToStr(delete.db_objectId, 'long'))
+ node.set('parentObjId',self.convertToStr(delete.db_parentObjId, 'long'))
+ node.set('parentObjType',self.convertToStr(delete.db_parentObjType, 'str'))
+
+ return node
+
+class DBProvAssociationXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'prov:wasAssociatedWith':
+ return None
+
+ prov_activity = None
+ prov_agent = None
+ prov_plan = None
+ prov_role = None
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'prov:activity':
+ _data = self.getDao('ref_prov_activity').fromXML(child)
+ prov_activity = _data
+ elif child_tag == 'prov:agent':
+ _data = self.getDao('ref_prov_agent').fromXML(child)
+ prov_agent = _data
+ elif child_tag == 'prov:plan':
+ _data = self.getDao('ref_prov_plan').fromXML(child)
+ prov_plan = _data
+ elif child_tag == 'prov:role':
+ _data = self.convertFromStr(child.text,'str')
+ prov_role = _data
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBProvAssociation(prov_activity=prov_activity,
+ prov_agent=prov_agent,
+ prov_plan=prov_plan,
+ prov_role=prov_role)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, prov_association, node=None):
+ if node is None:
+ node = ElementTree.Element('prov:wasAssociatedWith')
+
+ # set elements
+ prov_activity = prov_association.db_prov_activity
+ if prov_activity is not None:
+ if (prov_activity is not None) and (prov_activity != ""):
+ childNode = ElementTree.SubElement(node, 'prov:activity')
+ self.getDao('ref_prov_activity').toXML(prov_activity, childNode)
+ prov_agent = prov_association.db_prov_agent
+ if prov_agent is not None:
+ if (prov_agent is not None) and (prov_agent != ""):
+ childNode = ElementTree.SubElement(node, 'prov:agent')
+ self.getDao('ref_prov_agent').toXML(prov_agent, childNode)
+ prov_plan = prov_association.db_prov_plan
+ if prov_plan is not None:
+ if (prov_plan is not None) and (prov_plan != ""):
+ childNode = ElementTree.SubElement(node, 'prov:plan')
+ self.getDao('ref_prov_plan').toXML(prov_plan, childNode)
+ prov_role = prov_association.db_prov_role
+ if (prov_role is not None) and (prov_role != ""):
+ childNode = ElementTree.SubElement(node, 'prov:role')
+ childNode.text = self.convertToStr(prov_role, 'str')
+
+ return node
+
+class DBVistrailXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'vistrail':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('version', None)
+ version = self.convertFromStr(data, 'str')
+ data = node.get('name', None)
+ name = self.convertFromStr(data, 'str')
+
+ actions = []
+ tags = []
+ annotations = []
+ vistrailVariables = []
+ parameter_explorations = []
+ actionAnnotations = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'action':
+ _data = self.getDao('action').fromXML(child)
+ actions.append(_data)
+ elif child_tag == 'tag':
+ _data = self.getDao('tag').fromXML(child)
+ tags.append(_data)
+ elif child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'vistrailVariable':
+ _data = self.getDao('vistrailVariable').fromXML(child)
+ vistrailVariables.append(_data)
+ elif child_tag == 'parameterExploration':
+ _data = self.getDao('parameter_exploration').fromXML(child)
+ parameter_explorations.append(_data)
+ elif child_tag == 'actionAnnotation':
+ _data = self.getDao('actionAnnotation').fromXML(child)
+ actionAnnotations.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBVistrail(id=id,
+ version=version,
+ name=name,
+ actions=actions,
+ tags=tags,
+ annotations=annotations,
+ vistrailVariables=vistrailVariables,
+ parameter_explorations=parameter_explorations,
+ actionAnnotations=actionAnnotations)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, vistrail, node=None):
+ if node is None:
+ node = ElementTree.Element('vistrail')
+
+ # set attributes
+ node.set('id',self.convertToStr(vistrail.db_id, 'long'))
+ node.set('version',self.convertToStr(vistrail.db_version, 'str'))
+ node.set('name',self.convertToStr(vistrail.db_name, 'str'))
+
+ # set elements
+ actions = vistrail.db_actions
+ for action in actions:
+ if (actions is not None) and (actions != ""):
+ childNode = ElementTree.SubElement(node, 'action')
+ self.getDao('action').toXML(action, childNode)
+ tags = vistrail.db_tags
+ for tag in tags:
+ if (tags is not None) and (tags != ""):
+ childNode = ElementTree.SubElement(node, 'tag')
+ self.getDao('tag').toXML(tag, childNode)
+ annotations = vistrail.db_annotations
+ for annotation in annotations:
+ if (annotations is not None) and (annotations != ""):
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ vistrailVariables = vistrail.db_vistrailVariables
+ for vistrailVariable in vistrailVariables:
+ if (vistrailVariables is not None) and (vistrailVariables != ""):
+ childNode = ElementTree.SubElement(node, 'vistrailVariable')
+ self.getDao('vistrailVariable').toXML(vistrailVariable, childNode)
+ parameter_explorations = vistrail.db_parameter_explorations
+ for parameter_exploration in parameter_explorations:
+ if (parameter_explorations is not None) and (parameter_explorations != ""):
+ childNode = ElementTree.SubElement(node, 'parameterExploration')
+ self.getDao('parameter_exploration').toXML(parameter_exploration, childNode)
+ actionAnnotations = vistrail.db_actionAnnotations
+ for actionAnnotation in actionAnnotations:
+ if (actionAnnotations is not None) and (actionAnnotations != ""):
+ childNode = ElementTree.SubElement(node, 'actionAnnotation')
+ self.getDao('actionAnnotation').toXML(actionAnnotation, childNode)
+
+ return node
+
+class DBModuleExecXMLDAOBase(XMLDAO):
+
+ def __init__(self, daoList):
+ self.daoList = daoList
+
+ def getDao(self, dao):
+ return self.daoList[dao]
+
+ def fromXML(self, node):
+ if node.tag[0] == "{":
+ node_tag = node.tag.split("}")[1]
+ else:
+ node_tag = node.tag
+ if node_tag != 'moduleExec':
+ return None
+
+ # read attributes
+ data = node.get('id', None)
+ id = self.convertFromStr(data, 'long')
+ data = node.get('tsStart', None)
+ ts_start = self.convertFromStr(data, 'datetime')
+ data = node.get('tsEnd', None)
+ ts_end = self.convertFromStr(data, 'datetime')
+ data = node.get('cached', None)
+ cached = self.convertFromStr(data, 'int')
+ data = node.get('moduleId', None)
+ module_id = self.convertFromStr(data, 'long')
+ data = node.get('moduleName', None)
+ module_name = self.convertFromStr(data, 'str')
+ data = node.get('completed', None)
+ completed = self.convertFromStr(data, 'int')
+ data = node.get('error', None)
+ error = self.convertFromStr(data, 'str')
+ data = node.get('machine_id', None)
+ machine_id = self.convertFromStr(data, 'long')
+
+ annotations = []
+ loop_execs = []
+
+ # read children
+ for child in node.getchildren():
+ if child.tag[0] == "{":
+ child_tag = child.tag.split("}")[1]
+ else:
+ child_tag = child.tag
+ if child_tag == 'annotation':
+ _data = self.getDao('annotation').fromXML(child)
+ annotations.append(_data)
+ elif child_tag == 'loopExec':
+ _data = self.getDao('loop_exec').fromXML(child)
+ loop_execs.append(_data)
+ elif child.text is None or child.text.strip() == '':
+ pass
+ else:
+ print '*** ERROR *** tag = %s' % child.tag
+
+ obj = DBModuleExec(id=id,
+ ts_start=ts_start,
+ ts_end=ts_end,
+ cached=cached,
+ module_id=module_id,
+ module_name=module_name,
+ completed=completed,
+ error=error,
+ machine_id=machine_id,
+ annotations=annotations,
+ loop_execs=loop_execs)
+ obj.is_dirty = False
+ return obj
+
+ def toXML(self, module_exec, node=None):
+ if node is None:
+ node = ElementTree.Element('moduleExec')
+
+ # set attributes
+ node.set('id',self.convertToStr(module_exec.db_id, 'long'))
+ node.set('tsStart',self.convertToStr(module_exec.db_ts_start, 'datetime'))
+ node.set('tsEnd',self.convertToStr(module_exec.db_ts_end, 'datetime'))
+ node.set('cached',self.convertToStr(module_exec.db_cached, 'int'))
+ node.set('moduleId',self.convertToStr(module_exec.db_module_id, 'long'))
+ node.set('moduleName',self.convertToStr(module_exec.db_module_name, 'str'))
+ node.set('completed',self.convertToStr(module_exec.db_completed, 'int'))
+ node.set('error',self.convertToStr(module_exec.db_error, 'str'))
+ node.set('machine_id',self.convertToStr(module_exec.db_machine_id, 'long'))
+
+ # set elements
+ annotations = module_exec.db_annotations
+ for annotation in annotations:
+ if (annotations is not None) and (annotations != ""):
+ childNode = ElementTree.SubElement(node, 'annotation')
+ self.getDao('annotation').toXML(annotation, childNode)
+ loop_execs = module_exec.db_loop_execs
+ for loop_exec in loop_execs:
+ if (loop_execs is not None) and (loop_execs != ""):
+ childNode = ElementTree.SubElement(node, 'loopExec')
+ self.getDao('loop_exec').toXML(loop_exec, childNode)
+
+ return node
+
+"""generated automatically by auto_dao.py"""
+
+class XMLDAOListBase(dict):
+
+ def __init__(self, daos=None):
+ if daos is not None:
+ dict.update(self, daos)
+
+ if 'opm_process_id_effect' not in self:
+ self['opm_process_id_effect'] = DBOpmProcessIdEffectXMLDAOBase(self)
+ if 'vistrailVariable' not in self:
+ self['vistrailVariable'] = DBVistrailVariableXMLDAOBase(self)
+ if 'prov_agent' not in self:
+ self['prov_agent'] = DBProvAgentXMLDAOBase(self)
+ if 'opm_was_generated_by' not in self:
+ self['opm_was_generated_by'] = DBOpmWasGeneratedByXMLDAOBase(self)
+ if 'opm_accounts' not in self:
+ self['opm_accounts'] = DBOpmAccountsXMLDAOBase(self)
+ if 'ref_prov_agent' not in self:
+ self['ref_prov_agent'] = DBRefProvAgentXMLDAOBase(self)
+ if 'portSpec' not in self:
+ self['portSpec'] = DBPortSpecXMLDAOBase(self)
+ if 'module' not in self:
+ self['module'] = DBModuleXMLDAOBase(self)
+ if 'module_descriptor' not in self:
+ self['module_descriptor'] = DBModuleDescriptorXMLDAOBase(self)
+ if 'tag' not in self:
+ self['tag'] = DBTagXMLDAOBase(self)
+ if 'opm_role' not in self:
+ self['opm_role'] = DBOpmRoleXMLDAOBase(self)
+ if 'prov_document' not in self:
+ self['prov_document'] = DBProvDocumentXMLDAOBase(self)
+ if 'opm_account' not in self:
+ self['opm_account'] = DBOpmAccountXMLDAOBase(self)
+ if 'opm_processes' not in self:
+ self['opm_processes'] = DBOpmProcessesXMLDAOBase(self)
+ if 'ref_prov_activity' not in self:
+ self['ref_prov_activity'] = DBRefProvActivityXMLDAOBase(self)
+ if 'opm_account_id' not in self:
+ self['opm_account_id'] = DBOpmAccountIdXMLDAOBase(self)
+ if 'port' not in self:
+ self['port'] = DBPortXMLDAOBase(self)
+ if 'ref_prov_plan' not in self:
+ self['ref_prov_plan'] = DBRefProvPlanXMLDAOBase(self)
+ if 'opm_artifact' not in self:
+ self['opm_artifact'] = DBOpmArtifactXMLDAOBase(self)
+ if 'group' not in self:
+ self['group'] = DBGroupXMLDAOBase(self)
+ if 'log' not in self:
+ self['log'] = DBLogXMLDAOBase(self)
+ if 'mashup_alias' not in self:
+ self['mashup_alias'] = DBMashupAliasXMLDAOBase(self)
+ if 'opm_agents' not in self:
+ self['opm_agents'] = DBOpmAgentsXMLDAOBase(self)
+ if 'mashup' not in self:
+ self['mashup'] = DBMashupXMLDAOBase(self)
+ if 'opm_process_id_cause' not in self:
+ self['opm_process_id_cause'] = DBOpmProcessIdCauseXMLDAOBase(self)
+ if 'prov_generation' not in self:
+ self['prov_generation'] = DBProvGenerationXMLDAOBase(self)
+ if 'portSpecItem' not in self:
+ self['portSpecItem'] = DBPortSpecItemXMLDAOBase(self)
+ if 'machine' not in self:
+ self['machine'] = DBMachineXMLDAOBase(self)
+ if 'add' not in self:
+ self['add'] = DBAddXMLDAOBase(self)
+ if 'other' not in self:
+ self['other'] = DBOtherXMLDAOBase(self)
+ if 'location' not in self:
+ self['location'] = DBLocationXMLDAOBase(self)
+ if 'opm_overlaps' not in self:
+ self['opm_overlaps'] = DBOpmOverlapsXMLDAOBase(self)
+ if 'pe_parameter' not in self:
+ self['pe_parameter'] = DBPEParameterXMLDAOBase(self)
+ if 'opm_dependencies' not in self:
+ self['opm_dependencies'] = DBOpmDependenciesXMLDAOBase(self)
+ if 'parameter' not in self:
+ self['parameter'] = DBParameterXMLDAOBase(self)
+ if 'opm_used' not in self:
+ self['opm_used'] = DBOpmUsedXMLDAOBase(self)
+ if 'plugin_data' not in self:
+ self['plugin_data'] = DBPluginDataXMLDAOBase(self)
+ if 'function' not in self:
+ self['function'] = DBFunctionXMLDAOBase(self)
+ if 'actionAnnotation' not in self:
+ self['actionAnnotation'] = DBActionAnnotationXMLDAOBase(self)
+ if 'abstraction' not in self:
+ self['abstraction'] = DBAbstractionXMLDAOBase(self)
+ if 'workflow' not in self:
+ self['workflow'] = DBWorkflowXMLDAOBase(self)
+ if 'opm_artifact_id_cause' not in self:
+ self['opm_artifact_id_cause'] = DBOpmArtifactIdCauseXMLDAOBase(self)
+ if 'ref_prov_entity' not in self:
+ self['ref_prov_entity'] = DBRefProvEntityXMLDAOBase(self)
+ if 'prov_activity' not in self:
+ self['prov_activity'] = DBProvActivityXMLDAOBase(self)
+ if 'mashup_action' not in self:
+ self['mashup_action'] = DBMashupActionXMLDAOBase(self)
+ if 'prov_usage' not in self:
+ self['prov_usage'] = DBProvUsageXMLDAOBase(self)
+ if 'opm_artifact_value' not in self:
+ self['opm_artifact_value'] = DBOpmArtifactValueXMLDAOBase(self)
+ if 'opm_artifact_id_effect' not in self:
+ self['opm_artifact_id_effect'] = DBOpmArtifactIdEffectXMLDAOBase(self)
+ if 'opm_graph' not in self:
+ self['opm_graph'] = DBOpmGraphXMLDAOBase(self)
+ if 'mashuptrail' not in self:
+ self['mashuptrail'] = DBMashuptrailXMLDAOBase(self)
+ if 'registry' not in self:
+ self['registry'] = DBRegistryXMLDAOBase(self)
+ if 'vt_connection' not in self:
+ self['vt_connection'] = DBVtConnectionXMLDAOBase(self)
+ if 'mashup_component' not in self:
+ self['mashup_component'] = DBMashupComponentXMLDAOBase(self)
+ if 'prov_entity' not in self:
+ self['prov_entity'] = DBProvEntityXMLDAOBase(self)
+ if 'annotation' not in self:
+ self['annotation'] = DBAnnotationXMLDAOBase(self)
+ if 'change' not in self:
+ self['change'] = DBChangeXMLDAOBase(self)
+ if 'opm_was_derived_from' not in self:
+ self['opm_was_derived_from'] = DBOpmWasDerivedFromXMLDAOBase(self)
+ if 'opm_artifacts' not in self:
+ self['opm_artifacts'] = DBOpmArtifactsXMLDAOBase(self)
+ if 'opm_was_controlled_by' not in self:
+ self['opm_was_controlled_by'] = DBOpmWasControlledByXMLDAOBase(self)
+ if 'opm_agent_id' not in self:
+ self['opm_agent_id'] = DBOpmAgentIdXMLDAOBase(self)
+ if 'group_exec' not in self:
+ self['group_exec'] = DBGroupExecXMLDAOBase(self)
+ if 'opm_time' not in self:
+ self['opm_time'] = DBOpmTimeXMLDAOBase(self)
+ if 'package' not in self:
+ self['package'] = DBPackageXMLDAOBase(self)
+ if 'workflow_exec' not in self:
+ self['workflow_exec'] = DBWorkflowExecXMLDAOBase(self)
+ if 'parameter_exploration' not in self:
+ self['parameter_exploration'] = DBParameterExplorationXMLDAOBase(self)
+ if 'loop_exec' not in self:
+ self['loop_exec'] = DBLoopExecXMLDAOBase(self)
+ if 'opm_was_triggered_by' not in self:
+ self['opm_was_triggered_by'] = DBOpmWasTriggeredByXMLDAOBase(self)
+ if 'mashup_actionAnnotation' not in self:
+ self['mashup_actionAnnotation'] = DBMashupActionAnnotationXMLDAOBase(self)
+ if 'connection' not in self:
+ self['connection'] = DBConnectionXMLDAOBase(self)
+ if 'opm_process' not in self:
+ self['opm_process'] = DBOpmProcessXMLDAOBase(self)
+ if 'is_part_of' not in self:
+ self['is_part_of'] = DBIsPartOfXMLDAOBase(self)
+ if 'pe_function' not in self:
+ self['pe_function'] = DBPEFunctionXMLDAOBase(self)
+ if 'opm_process_value' not in self:
+ self['opm_process_value'] = DBOpmProcessValueXMLDAOBase(self)
+ if 'action' not in self:
+ self['action'] = DBActionXMLDAOBase(self)
+ if 'opm_agent' not in self:
+ self['opm_agent'] = DBOpmAgentXMLDAOBase(self)
+ if 'delete' not in self:
+ self['delete'] = DBDeleteXMLDAOBase(self)
+ if 'prov_association' not in self:
+ self['prov_association'] = DBProvAssociationXMLDAOBase(self)
+ if 'vistrail' not in self:
+ self['vistrail'] = DBVistrailXMLDAOBase(self)
+ if 'module_exec' not in self:
+ self['module_exec'] = DBModuleExecXMLDAOBase(self)
diff --git a/vistrails/db/versions/v1_0_3/persistence/xml/xml_dao.py b/vistrails/db/versions/v1_0_3/persistence/xml/xml_dao.py
new file mode 100644
index 0000000..dea8449
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/persistence/xml/xml_dao.py
@@ -0,0 +1,89 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from datetime import date, datetime
+from time import strptime
+
+class XMLDAO:
+ def __init__(self):
+ pass
+
+ def hasAttribute(self, node, attr):
+ return node.hasAttribute(attr)
+
+ def getAttribute(self, node, attr):
+ try:
+ attribute = node.attributes.get(attr)
+ if attribute is not None:
+ return attribute.value
+ except KeyError:
+ pass
+ return None
+
+ def convertFromStr(self, value, type):
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ try:
+ return long(value)
+ except ValueError:
+ return -1
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ try:
+ return int(value)
+ except ValueError:
+ if 'False' == value:
+ return -1
+ else:
+ return 0
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ def convertToStr(self, value, type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
diff --git a/vistrails/db/versions/v1_0_3/schemas/sql/vistrails.sql b/vistrails/db/versions/v1_0_3/schemas/sql/vistrails.sql
new file mode 100644
index 0000000..b3031dd
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/schemas/sql/vistrails.sql
@@ -0,0 +1,528 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+CREATE TABLE `vistrails_version`(`version` char(16)) engine=InnoDB;
+INSERT INTO `vistrails_version`(`version`) VALUES ('1.0.3');
+
+CREATE TABLE thumbnail(
+ id int not null auto_increment primary key,
+ file_name varchar(255),
+ image_bytes mediumblob,
+ last_modified datetime
+) engine=InnoDB;
+
+-- generated automatically by auto_dao.py
+
+CREATE TABLE vistrail_variable(
+ name varchar(255),
+ uuid char(36),
+ package varchar(255),
+ module varchar(255),
+ namespace varchar(255),
+ value varchar(8191),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE port_spec(
+ id int,
+ name varchar(255),
+ type varchar(255),
+ optional int,
+ sort_key int,
+ min_conns int,
+ max_conns int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE module_descriptor(
+ id int,
+ name varchar(255),
+ package varchar(255),
+ namespace varchar(255),
+ package_version varchar(255),
+ version varchar(255),
+ base_descriptor_id int,
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE tag(
+ id int,
+ name varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE port(
+ id int,
+ type varchar(255),
+ moduleId int,
+ moduleName varchar(255),
+ name varchar(255),
+ signature varchar(4095),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE group_tbl(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE log_tbl(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime,
+ vistrail_id int
+) engine=InnoDB;
+
+CREATE TABLE mashup_alias(
+ id int,
+ name varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE mashup(
+ id int,
+ name varchar(255),
+ version int,
+ type varchar(255),
+ vtid int,
+ layout mediumtext,
+ geometry mediumtext,
+ has_seq int,
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE port_spec_item(
+ id int,
+ pos int,
+ module varchar(255),
+ package varchar(255),
+ namespace varchar(255),
+ label varchar(4095),
+ _default varchar(4095),
+ _values mediumtext,
+ entry_type varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE machine(
+ id int,
+ name varchar(255),
+ os varchar(255),
+ architecture varchar(255),
+ processor varchar(255),
+ ram bigint,
+ vt_id int,
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE add_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE other(
+ id int,
+ okey varchar(255),
+ value varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE location(
+ id int,
+ x DECIMAL(18,12),
+ y DECIMAL(18,12),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE pe_parameter(
+ id int,
+ pos int,
+ interpolator varchar(255),
+ value mediumtext,
+ dimension int,
+ parent_type char(32),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE parameter(
+ id int,
+ pos int,
+ name varchar(255),
+ type varchar(255),
+ val mediumtext,
+ alias varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE plugin_data(
+ id int,
+ data varchar(8191),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE function(
+ id int,
+ pos int,
+ name varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE action_annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ action_id int,
+ date datetime,
+ user varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE abstraction(
+ id int,
+ cache int,
+ name varchar(255),
+ namespace varchar(255),
+ package varchar(511),
+ version varchar(255),
+ internal_version varchar(255),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE workflow(
+ id int not null auto_increment primary key,
+ entity_id int,
+ entity_type char(16),
+ name varchar(255),
+ version char(16),
+ last_modified datetime,
+ vistrail_id int,
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE mashup_action(
+ id int,
+ prev_id int,
+ date datetime,
+ user varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE mashuptrail(
+ id int not null auto_increment primary key,
+ name char(36),
+ version char(16),
+ vt_version int,
+ last_modified datetime,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE registry(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ root_descriptor_id int,
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE mashup_component(
+ id int,
+ vtid int,
+ vttype varchar(255),
+ vtparent_type char(32),
+ vtparent_id int,
+ vtpos int,
+ vtmid int,
+ pos int,
+ type varchar(255),
+ val mediumtext,
+ minVal varchar(255),
+ maxVal varchar(255),
+ stepSize varchar(255),
+ strvaluelist mediumtext,
+ widget varchar(255),
+ seq int,
+ parent varchar(255),
+ alias_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE annotation(
+ id int,
+ akey varchar(255),
+ value mediumtext,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE change_tbl(
+ id int,
+ what varchar(255),
+ old_obj_id int,
+ new_obj_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE group_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ group_name varchar(255),
+ group_type varchar(255),
+ completed int,
+ error varchar(1023),
+ machine_id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE package(
+ id int not null auto_increment primary key,
+ name varchar(255),
+ identifier varchar(1023),
+ codepath varchar(1023),
+ load_configuration int,
+ version varchar(255),
+ description varchar(1023),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE workflow_exec(
+ id int,
+ user varchar(255),
+ ip varchar(255),
+ session int,
+ vt_version varchar(255),
+ ts_start datetime,
+ ts_end datetime,
+ parent_id int,
+ parent_type varchar(255),
+ parent_version int,
+ completed int,
+ name varchar(255),
+ log_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE parameter_exploration(
+ id int,
+ action_id int,
+ name varchar(255),
+ date datetime,
+ user varchar(255),
+ dims varchar(255),
+ layout varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE loop_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ iteration int,
+ completed int,
+ error varchar(1023),
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE mashup_action_annotation(
+ id int,
+ akey varchar(255),
+ value varchar(8191),
+ action_id int,
+ date datetime,
+ user varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE connection_tbl(
+ id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
+CREATE TABLE pe_function(
+ id int,
+ module_id int,
+ port_name varchar(255),
+ is_alias int,
+ parent_type char(32),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE action(
+ id int,
+ prev_id int,
+ date datetime,
+ session int,
+ user varchar(255),
+ parent_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE delete_tbl(
+ id int,
+ what varchar(255),
+ object_id int,
+ par_obj_id int,
+ par_obj_type char(16),
+ action_id int,
+ entity_id int,
+ entity_type char(16)
+) engine=InnoDB;
+
+CREATE TABLE vistrail(
+ id int not null auto_increment primary key,
+ entity_type char(16),
+ version char(16),
+ name varchar(255),
+ last_modified datetime
+) engine=InnoDB;
+
+CREATE TABLE module_exec(
+ id int,
+ ts_start datetime,
+ ts_end datetime,
+ cached int,
+ module_id int,
+ module_name varchar(255),
+ completed int,
+ error varchar(1023),
+ machine_id int,
+ parent_type char(32),
+ entity_id int,
+ entity_type char(16),
+ parent_id int
+) engine=InnoDB;
+
diff --git a/vistrails/db/versions/v1_0_3/schemas/sql/vistrails_drop.sql b/vistrails/db/versions/v1_0_3/schemas/sql/vistrails_drop.sql
new file mode 100644
index 0000000..5fc87bb
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/schemas/sql/vistrails_drop.sql
@@ -0,0 +1,42 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+DROP TABLE IF EXISTS `vistrails_version`;
+
+DROP TABLE IF EXISTS thumbnail;
+
+-- genereated automatically by generate.py
+
+DROP TABLE IF EXISTS vistrail_variable, port_spec, module, module_descriptor, tag, port, group_tbl, log_tbl, mashup_alias, mashup, port_spec_item, machine, add_tbl, other, location, pe_parameter, parameter, plugin_data, function, action_annotation, abstraction, workflow, mashup_action, mashuptrail, registry, mashup_component, annotation, change_tbl, group_exec, package, workflow_exec, parameter_exploration, loop_exec, mashup_action_annotation, connection_tbl, pe_function, action, delete_ [...]
diff --git a/vistrails/db/versions/v1_0_3/schemas/xml/log.xsd b/vistrails/db/versions/v1_0_3/schemas/xml/log.xsd
new file mode 100644
index 0000000..effdfa5
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/schemas/xml/log.xsd
@@ -0,0 +1,146 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="log">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="workflow_exec" ref="workflowExec" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="machine" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="workflowExec">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element name="module_exec" ref="moduleExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="group_exec" ref="groupExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="loop_exec" ref="loopExec" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="ip" type="xs:string"/>
+ <xs:attribute name="session" type="xs:int"/>
+ <xs:attribute name="vtVersion" type="xs:string"/>
+ <xs:attribute name="tsStart" type="xs:dateTime"/>
+ <xs:attribute name="tsEnd" type="xs:dateTime"/>
+ <xs:attribute name="parentId" type="xs:int"/>
+ <xs:attribute name="parentType" type="xs:string"/>
+ <xs:attribute name="parentVersion" type="xs:int"/>
+ <xs:attribute name="completed" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="machine">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="os" type="xs:string"/>
+ <xs:attribute name="architecture" type="xs:string"/>
+ <xs:attribute name="processor" type="xs:string"/>
+ <xs:attribute name="ram" type="xs:long"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="moduleExec">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="loop_exec" ref="loopExec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="tsStart" type="xs:dateTime"/>
+ <xs:attribute name="tsEnd" type="xs:dateTime"/>
+ <xs:attribute name="cached" type="xs:int"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="completed" type="xs:int"/>
+ <xs:attribute name="error" type="xs:string"/>
+ <xs:attribute name="machine_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="groupExec">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element name="module_exec" ref="moduleExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="group_exec" ref="groupExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="loop_exec" ref="loopExec" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="tsStart" type="xs:dateTime"/>
+ <xs:attribute name="tsEnd" type="xs:dateTime"/>
+ <xs:attribute name="cached" type="xs:int"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="groupName" type="xs:string"/>
+ <xs:attribute name="groupType" type="xs:string"/>
+ <xs:attribute name="completed" type="xs:int"/>
+ <xs:attribute name="error" type="xs:string"/>
+ <xs:attribute name="machine_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="loopExec">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element name="module_exec" ref="moduleExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="group_exec" ref="groupExec" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="loop_exec" ref="loopExec" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="tsStart" type="xs:dateTime"/>
+ <xs:attribute name="tsEnd" type="xs:dateTime"/>
+ <xs:attribute name="iteration" type="xs:int"/>
+ <xs:attribute name="completed" type="xs:int"/>
+ <xs:attribute name="error" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v1_0_3/schemas/xml/vistrail.xsd b/vistrails/db/versions/v1_0_3/schemas/xml/vistrail.xsd
new file mode 100644
index 0000000..29a043d
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/schemas/xml/vistrail.xsd
@@ -0,0 +1,347 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="vistrail">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="action" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="tag" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vistrailVariable" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="parameter_exploration" ref="parameterExploration" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="actionAnnotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="action">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="add" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="delete" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="change" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="prevId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="session" type="xs:int"/>
+ <xs:attribute name="user" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="tag">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="vistrailVariable">
+ <xs:complexType>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="uuid" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="module" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameterExploration">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="function" ref="peFunction" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="actionId" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="user" type="xs:string"/>
+ <xs:attribute name="dims" type="xs:string"/>
+ <xs:attribute name="layout" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="actionAnnotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ <xs:attribute name="actionId" type="xs:int"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
+ <xs:attribute name="user" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="add">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="delete">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="objectId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="change">
+ <xs:complexType>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="port" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="what" type="xs:string"/>
+ <xs:attribute name="oldObjId" type="xs:int"/>
+ <xs:attribute name="newObjId" type="xs:int"/>
+ <xs:attribute name="parentObjId" type="xs:int"/>
+ <xs:attribute name="parentObjType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="peFunction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="parameter" ref="peParameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="port_name" type="xs:string"/>
+ <xs:attribute name="is_alias" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="signature" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="portSpecItem" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="optional" type="xs:int"/>
+ <xs:attribute name="sortKey" type="xs:int"/>
+ <xs:attribute name="minConns" type="xs:int"/>
+ <xs:attribute name="maxConns" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="internalVersion" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="group">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="workflow" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plugin_data">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="peParameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="interpolator" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ <xs:attribute name="dimension" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpecItem">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="module" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="label" type="xs:string"/>
+ <xs:attribute name="default" type="xs:string"/>
+ <xs:attribute name="values" type="xs:string"/>
+ <xs:attribute name="entryType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="workflow">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v1_0_3/schemas/xml/vtlink.xsd b/vistrails/db/versions/v1_0_3/schemas/xml/vtlink.xsd
new file mode 100644
index 0000000..011b59c
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/schemas/xml/vtlink.xsd
@@ -0,0 +1,69 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<?xml version="1.0" encoding="UTF-8"?>
+
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
+<xs:element name="vtlink">
+<xs:complexType>
+<!-- if the vistrail is in a DB use host, database, port and vtid -->
+<xs:attribute name="host" type="xs:string"></xs:attribute>
+<xs:attribute name="database" type="xs:string"></xs:attribute>
+<xs:attribute name="port" type="xs:int"></xs:attribute>
+<xs:attribute name="vtid" type="xs:int"></xs:attribute>
+<!-- if the vistrail is a file use filename below -->
+<xs:attribute name="filename" type="xs:string"></xs:attribute>
+<!-- this is the workflow version -->
+<xs:attribute name="version" type="xs:int"></xs:attribute>
+<!-- this is the workflow tag -->
+<xs:attribute name="tag" type="xs:string"></xs:attribute>
+<xs:attribute name="url" type="xs:string"></xs:attribute>
+<!-- vtcontent can be a workflow in xml or a .vt file base64 encoded -->
+<xs:attribute name="vtcontent" type="xs:string"></xs:attribute>
+<!-- if execute is true the workflow will be executed -->
+<xs:attribute name="execute" type="xs:boolean"></xs:attribute>
+<!-- if showSpreadsheetOnly is True we will hide the builder -->
+<xs:attribute name="showSpreadsheetOnly" type="xs:boolean"></xs:attribute>
+<!-- if there's database information and a workflow is embedded, it will
+force loading from the db instead of using the emebedded version -->
+<xs:attribute name="forceDB" type="xs:boolean"></xs:attribute>
+<!-- if mashuptrail and mashupVersion are set, VisTrails will execute the
+mashup -->
+<xs:attribute name="mashuptrail" type="xs:string"></xs:attribute>
+<xs:attribute name="mashupVersion" type="xs:int"></xs:attribute>
+</xs:complexType>
+</xs:element>
+
+</xs:schema>
diff --git a/vistrails/db/versions/v1_0_3/schemas/xml/workflow.xsd b/vistrails/db/versions/v1_0_3/schemas/xml/workflow.xsd
new file mode 100644
index 0000000..840847f
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/schemas/xml/workflow.xsd
@@ -0,0 +1,200 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+
+<?xml version="1.0"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="workflow">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="connection" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="plugin_data" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="other" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:choice>
+ <xs:element ref="module" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="abstraction" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="group" minOccurs="0" maxOccurs="1"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="vistrail_id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="connection">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="port" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotation">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ <xs:attribute name="value" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plugin_data">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="other">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="value" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="key" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="module">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="portSpec" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="abstraction">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="internalVersion" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="group">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="workflow" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="location" minOccurs="0" maxOccurs="1"/>
+ <xs:element ref="function" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="cache" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="port">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="moduleId" type="xs:int"/>
+ <xs:attribute name="moduleName" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="signature" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="location">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="x" type="xs:float"/>
+ <xs:attribute name="y" type="xs:float"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="function">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="parameter" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpec">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="portSpecItem" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="optional" type="xs:int"/>
+ <xs:attribute name="sortKey" type="xs:int"/>
+ <xs:attribute name="minConns" type="xs:int"/>
+ <xs:attribute name="maxConns" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parameter">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+ <xs:attribute name="val" type="xs:string"/>
+ <xs:attribute name="alias" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="portSpecItem">
+ <xs:complexType>
+ <xs:attribute name="id" type="xs:int"/>
+ <xs:attribute name="pos" type="xs:int"/>
+ <xs:attribute name="module" type="xs:string"/>
+ <xs:attribute name="package" type="xs:string"/>
+ <xs:attribute name="namespace" type="xs:string"/>
+ <xs:attribute name="label" type="xs:string"/>
+ <xs:attribute name="default" type="xs:string"/>
+ <xs:attribute name="values" type="xs:string"/>
+ <xs:attribute name="entryType" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/vistrails/db/versions/v1_0_3/specs/all.xml b/vistrails/db/versions/v1_0_3/specs/all.xml
new file mode 100644
index 0000000..ab07b76
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/specs/all.xml
@@ -0,0 +1,3823 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<objects>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ABSTRACTION +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="abstraction">
+ <layout>
+ <xml name="abstraction" nodeType="xs:element"/>
+ <sql table="abstraction"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="internal_version" type="str">
+ <xml name="internalVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ACTION ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long" foreignKey="true" object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="operation" type="list" mapping="one-to-many">
+ <property name="add" ref="true" object="add">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="delete" ref="true" object="delete">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="change" ref="true" object="change">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="vistrail" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ADD +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="add">
+ <layout>
+ <xml name="add" nodeType="xs:element"/>
+ <sql table="add_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ACTION_ANNOTATION +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="actionAnnotation">
+ <layout>
+ <xml nodeType="xs:element"/>
+ <sql table="action_annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="action_id" type="long" foreignKey="true" object="action">
+ <xml name="actionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- ANNOTATION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="annotation">
+ <layout>
+ <xml name="annotation" nodeType="xs:element"/>
+ <sql table="annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="vistrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="workflow_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="action">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="mashuptrail">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VISTRAIL_VARIABLE +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vistrailVariable">
+ <layout>
+ <xml nodeType="xs:element"/>
+ <sql table="vistrail_variable"/>
+ </layout>
+
+ <property name="name" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="name" type="varchar(255)"/>
+ </property>
+
+ <property name="uuid" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="uuid" type="char(36)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="package" type="varchar(255)"/>
+ </property>
+
+ <property name="module" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="module" type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="namespace" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="value" type="varchar(8191)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CHANGE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="change">
+ <layout>
+ <xml name="change" nodeType="xs:element"/>
+ <sql table="change_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="oldObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="old_obj_id" type="int"/>
+ </property>
+
+ <property name="newObjId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="new_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <choice name="data" type="object" discriminator="what">
+ <property ref="true" object="module" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="location" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="annotation" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="function" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="connection" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="port" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="parameter" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="portSpec" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="abstraction" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="group" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="other" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ <property ref="true" object="plugin_data" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- CONNECTION ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="connection">
+ <layout>
+ <xml name="connection" nodeType="xs:element"/>
+ <sql table="connection_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="port" type="list" mapping="one-to-many"
+ index="type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- DELETE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="delete">
+ <layout>
+ <xml name="delete" nodeType="xs:element"/>
+ <sql table="delete_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="what" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="objectId" type="long" foreignKey="true" discriminator="what">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="object_id" type="int"/>
+ </property>
+
+ <property name="parentObjId" type="long" foreignKey="true"
+ discriminator="parentObjType">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="par_obj_id" type="int"/>
+ </property>
+
+ <property name="parentObjType" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="par_obj_type" type="char(16)"/>
+ </property>
+
+ <property name="action" type="long" ref="true" object="action"
+ mapping="many-to-one" inverse="true">
+ <sql column="action_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- FUNCTION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="function">
+ <layout>
+ <xml name="function" nodeType="xs:element"/>
+ <sql table="function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="parameter" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group" parentClass="module">
+ <layout>
+ <xml name="group" nodeType="xs:element"/>
+ <sql table="group_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="workflow" type="object" mapping="one-to-one"
+ expand="false">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOCATION ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="location">
+ <layout>
+ <xml name="location" nodeType="xs:element"/>
+ <sql table="location"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="x" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="y" type="float">
+ <xml nodeType="xs:attribute" type="xs:float"/>
+ <sql type="DECIMAL(18,12)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="abstraction">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="group">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="log">
+ <layout>
+ <xml name="log" nodeType="xs:element"/>
+ <sql table="log_tbl"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="workflow_exec" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="machine" cascade="false" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MACHINE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="machine">
+ <layout>
+ <xml name="machine" nodeType="xs:element"/>
+ <sql table="machine"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="os" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="architecture" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="processor" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ram" type="int">
+ <xml nodeType="xs:attribute" type="xs:long"/>
+ <sql type="bigint"/>
+ </property>
+
+ <property name="vistrailId" type="long" inverse="true"
+ foreignKey="true" object="vistrail">
+ <sql column="vt_id" type="int"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module">
+ <layout>
+ <xml name="module" nodeType="xs:element"/>
+ <sql table="module"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="cache" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(511)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="location" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- LOOP_EXEC +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="loop_exec">
+ <layout>
+ <xml name="loopExec" nodeType="xs:element"/>
+ <sql table="loop_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <!--<property name="input" type="str">
+ <xml name="input" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>-->
+
+ <property name="iteration" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="module_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- GROUP_EXEC ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="group_exec">
+ <layout>
+ <xml name="groupExec" nodeType="xs:element"/>
+ <sql table="group_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="group_name" type="str">
+ <xml name="groupName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="group_type" type="str">
+ <xml name="groupType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <!--<property ref="true" object="workflow_exec" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="wf_exec_id" type="int"/>
+ </property>-->
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_EXEC +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_exec">
+ <layout>
+ <xml name="moduleExec" nodeType="xs:element"/>
+ <sql table="module_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="cached" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql nodeType="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_name" type="str">
+ <xml name="moduleName" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="error" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="machine_id" type="long" foreignKey="true" object="machine">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OTHER +++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="other">
+ <layout>
+ <xml name="other" nodeType="xs:element"/>
+ <sql table="other"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="okey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PARAMETER +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="parameter">
+ <layout>
+ <xml name="parameter" nodeType="xs:element"/>
+ <sql table="parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="alias" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="function">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PLUGIN DATA +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="plugin_data">
+ <layout>
+ <xml name="plugin_data" nodeType="xs:element"/>
+ <sql table="plugin_data"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="data" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="workflow">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORT ++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="port">
+ <layout>
+ <xml name="port" nodeType="xs:element"/>
+ <sql table="port"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="moduleId" type="long" foreignKey="true" object="module">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="moduleName" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="signature" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="connection" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORTSPEC ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="portSpec">
+ <layout>
+ <xml name="portSpec" nodeType="xs:element"/>
+ <sql table="port_spec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="optional" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="sort_key" type="int">
+ <xml name="sortKey" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="portSpecItem" type="list"
+ mapping="one-to-many" expandAction="false">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="min_conns" type="int">
+ <xml name="minConns" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="max_conns" type="int">
+ <xml name="maxConns" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="module">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="module_descriptor">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="add">
+ <sql column="parent_id" type="int"/>
+ </property>
+ <property ref="true" object="change">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PORTSPECITEM ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="portSpecItem">
+ <layout>
+ <xml name="portSpecItem" nodeType="xs:element"/>
+ <sql table="port_spec_item"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="label" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(4095)"/>
+ </property>
+
+ <property name="default" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="_default" type="varchar(4095)"/>
+ </property>
+
+ <property name="values" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="_values" type="mediumtext"/>
+ </property>
+
+ <property name="entry_type" type="str">
+ <xml name="entryType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="portSpec" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MODULE_DESCRIPTOR +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="module_descriptor">
+ <layout>
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ <sql table="module_descriptor"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="namespace" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="package_version" type="str">
+ <xml name="packageVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="base_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="baseDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="portSpec" type="list" mapping="one-to-many"
+ index="name:type">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="package" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ <!--
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <choice name="parent" type="long" discriminator="parentType" inverse="true"
+ mapping="many-to-one">
+ <property ref="true" object="registry">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property ref="true" object="package">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </choice>
+ -->
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PACKAGE +++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="package">
+ <layout>
+ <xml name="package" nodeType="xs:element"/>
+ <sql table="package"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="identifier" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="codepath" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property name="load_configuration" type="int">
+ <xml name="loadConfiguration" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="description" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(1023)"/>
+ </property>
+
+ <property ref="true" object="module_descriptor" type="list"
+ mapping="one-to-many" index="name:namespace:version">
+ <xml name="moduleDescriptor" nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="registry" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REGISTRY ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="registry">
+ <layout>
+ <xml name="registry" nodeType="xs:element"/>
+ <sql table="registry"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="root_descriptor_id" type="long" foreignKey="true"
+ object="module_descriptor">
+ <xml name="rootDescriptorId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <!-- <xml nodeType="xs:attribute" type="xs:string"/> -->
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="package" type="list"
+ mapping="one-to-many" index="identifier:version">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- TAG +++++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="tag">
+ <layout>
+ <xml name="tag" nodeType="xs:element"/>
+ <sql table="tag"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true" foreignKey="true"
+ object="action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VISTRAIL ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vistrail">
+ <layout>
+ <xml name="vistrail" nodeType="xs:element"/>
+ <sql table="vistrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property ref="true" object="action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="tag" type="list" mapping="one-to-many"
+ index="name">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="vistrailVariable" type="list" mapping="one-to-many"
+ index="uuid">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="parameter_exploration" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="actionAnnotation" type="list"
+ mapping="one-to-many" index="action_id:key !key:value">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow">
+ <layout>
+ <xml name="workflow" nodeType="xs:element"/>
+ <sql table="workflow"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str">
+ <sql type="char(16)" global="true" globalName="entity_type"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <choice name="module" type="list" mapping="one-to-many">
+ <property name="module" ref="true" object="module">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="abstraction" ref="true" object="abstraction">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group" ref="true" object="group">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property ref="true" object="connection" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="plugin_data" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="other" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="vistrail_id" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" object="group" type="long" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- WORKFLOW_EXEC +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="workflow_exec">
+ <layout>
+ <xml name="workflowExec" nodeType="xs:element"/>
+ <sql table="workflow_exec"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ip" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="session" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="ts_start" type="datetime">
+ <xml name="tsStart" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="ts_end" type="datetime">
+ <xml name="tsEnd" nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="parent_id" type="long">
+ <xml name="parentId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent_type" type="str">
+ <xml name="parentType" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="parent_version" type="long">
+ <xml name="parentVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="completed" type="int">
+ <xml name="completed" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="log" type="long" mapping="many-to-one"
+ inverse="true">
+ <sql column="log_id" type="int"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <choice name="item_exec" type="list" mapping="one-to-many">
+ <property name="module_exec" ref="true" object="module_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="group_exec" ref="true" object="group_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="loop_exec" ref="true" object="loop_exec">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PE_PARAMETER ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="pe_parameter" className="DBPEParameter">
+ <layout>
+ <xml name="peParameter" nodeType="xs:element"/>
+ <sql table="pe_parameter"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="interpolator" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="dimension" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <property ref="true" type="long" object="pe_function" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PE_FUNCTION +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="pe_function" className="DBPEFunction">
+ <layout>
+ <xml name="peFunction" nodeType="xs:element"/>
+ <sql table="pe_function"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="module_id" type="long" foreignKey="true" object="module">
+ <xml name="moduleId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="port_name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="is_alias" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property ref="true" name="parameter" object="pe_parameter" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parentType" type="str" inverse="true">
+ <sql column="parent_type" type="char(32)"/>
+ </property>
+
+ <property ref="true" type="long" object="parameter_exploration"
+ inverse="true" mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PARAMETER_EXPLORATION +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="parameter_exploration">
+ <layout>
+ <xml name="parameterExploration" nodeType="xs:element"/>
+ <sql table="parameter_exploration"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="action_id" type="long" foreignKey="true" object="action">
+ <xml name="actionId" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="dims" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="layout" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" name="function" object="pe_function" type="list"
+ mapping="one-to-many" index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="vistrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MASHUP_ACTION +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="mashup_action">
+ <layout>
+ <xml name="action" nodeType="xs:element"/>
+ <sql table="mashup_action"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="prevId" type="long" foreignKey="true" object="mashup_action">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql column="prev_id" type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="mashup" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" type="long" object="mashuptrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--+++++++++++++++++++++++++++++-->
+ <!-- MASHUP_ACTION_ANNOTATION +++-->
+ <!--+++++++++++++++++++++++++++++-->
+
+ <object name="mashup_actionAnnotation">
+ <layout>
+ <xml name="actionAnnotation" nodeType="xs:element"/>
+ <sql table="mashup_action_annotation"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="key" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql column="akey" type="varchar(255)"/>
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(8191)"/>
+ </property>
+
+ <property name="action_id" type="long" foreignKey="true" object="mashup_action">
+ <xml name="action_id" nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
+ <sql type="datetime"/>
+ </property>
+
+ <property name="user" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" type="long" object="mashuptrail" inverse="true"
+ mapping="many-to-one">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MASHUPTRAIL +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="mashuptrail">
+ <layout>
+ <xml name="mashuptrail" nodeType="xs:element"/>
+ <sql table="mashuptrail"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <sql type="int" autoInc="true" global="true" globalName="entity_id"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml name="id" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(36)"/>
+ </property>
+
+ <property name="version" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(16)"/>
+ </property>
+
+ <property name="vtVersion" type="long">
+ <xml name="vtVersion" nodeType="xs:attribute" type="xs:int"/>
+ <sql column="vt_version" type="int"/>
+ </property>
+
+ <property name="last_modified" type="datetime">
+ <sql type="datetime"/>
+ </property>
+
+ <property name="action" ref="true" object="mashup_action" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="annotation" type="list" mapping="one-to-many"
+ index="key">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="actionAnnotation" ref="true" object="mashup_actionAnnotation" type="list"
+ mapping="one-to-many" index="action_id:key !key:value">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--+++++++++++++++++++++++++++++-->
+ <!-- MASHUP_ALIAS +++++++++++++++-->
+ <!--+++++++++++++++++++++++++++++-->
+
+ <object name="mashup_alias">
+ <layout>
+ <xml name="alias" nodeType="xs:element"/>
+ <sql table="mashup_alias"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="component" ref="true" object="mashup_component" type="object" mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="parent" ref="true" object="mashup" type="long"
+ mapping="many-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MASHUP_COMPONENT ++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="mashup_component">
+ <layout>
+ <xml name="component" nodeType="xs:element"/>
+ <sql table="mashup_component"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vtid" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vttype" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="vtparent_type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="char(32)"/>
+ </property>
+
+ <property name="vtparent_id" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vtpos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="vtmid" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="pos" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="val" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="minVal" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="maxVal" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="stepSize" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="strvaluelist" type="str">
+ <xml name="valueList" nodeType="xs:attribute" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="widget" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="seq" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property ref="true" object="mashup_alias" type="long" mapping="one-to-one"
+ inverse="true">
+ <sql column="alias_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- MASHUP ++++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="mashup">
+ <layout>
+ <xml name="mashup" nodeType="xs:element"/>
+ <sql table="mashup"/>
+ </layout>
+
+ <property name="id" type="long" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="name" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="version" type="long">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="alias" pluralName="aliases" type= "list" ref="true"
+ object="mashup_alias" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="type" type="str">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="varchar(255)"/>
+ </property>
+
+ <property name="vtid" type="long" foreignKey="true" object="vistrail">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="layout" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="geometry" type="str">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <sql type="mediumtext"/>
+ </property>
+
+ <property name="has_seq" type="int">
+ <xml nodeType="xs:attribute" type="xs:int"/>
+ <sql type="int"/>
+ </property>
+
+ <property name="parent" ref="true" object="mashup_action" type="long"
+ mapping="one-to-one" inverse="true">
+ <sql column="parent_id" type="int"/>
+ </property>
+
+ <property name="entity_id" type="long" inverse="true">
+ <sql type="int"/>
+ </property>
+
+ <property name="entity_type" type="str" inverse="true">
+ <sql type="char(16)"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_GRAPH +++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_graph">
+ <layout>
+ <xml name="opmGraph" nodeType="xs:element"/>
+ <!-- <sql table="opm_graph"/> -->
+ </layout>
+
+ <property name="accounts" ref="true" object="opm_accounts"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="processes" ref="true" object="opm_processes"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="artifacts" ref="true" object="opm_artifacts"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="agents" ref="true" object="opm_agents"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="dependencies" ref="true" object="opm_dependencies"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNTS ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_accounts">
+ <layout>
+ <xml name="accounts" nodeType="xs:element"/>
+ <!-- <sql table="accounts"/> -->
+ </layout>
+
+ <property name="account" ref="true" object="opm_account" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="opm_overlaps" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNT +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_account">
+ <layout>
+ <xml name="account" nodeType="xs:element"/>
+ <!-- <sql table="account"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_OVERLAPS ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_overlaps">
+ <layout>
+ <xml name="overlaps" nodeType="xs:element"/>
+ <!-- <sql table="overlaps"/> -->
+ </layout>
+
+ <property ref="true" object="opm_account_id" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACTS +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifacts">
+ <layout>
+ <xml name="artifacts" nodeType="xs:element"/>
+ <!-- <sql table="artifacts"/> -->
+ </layout>
+
+ <property name="artifact" ref="true" object="opm_artifact" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_VALUE ++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_value">
+ <layout>
+ <xml name="value" nodeType="xs:element"/>
+ <!-- <sql table="artifact_value"/> -->
+ </layout>
+
+ <choice name="value" type="object" mapping="one-to-one">
+ <property ref="true" object="portSpec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="function" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact">
+ <layout>
+ <xml name="artifact" nodeType="xs:element"/>
+ <!-- <sql table="artifact"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" ref="true" object="opm_artifact_value" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESSES +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_processes">
+ <layout>
+ <xml name="processes" nodeType="xs:element"/>
+ <!-- <sql table="processes"/> -->
+ </layout>
+
+ <property name="process" ref="true" object="opm_process" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_VALUE +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_value">
+ <layout>
+ <xml name="value" nodeType="xs:element"/>
+ <!-- <sql table="process_value"/> -->
+ </layout>
+
+ <choice name="value" type="object" mapping="one-to-one">
+ <property ref="true" object="module_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="group_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property ref="true" object="loop_exec" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process">
+ <layout>
+ <xml name="process" nodeType="xs:element"/>
+ <!-- <sql table="process"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" ref="true" object="opm_process_value" type="object"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENTS ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agents">
+ <layout>
+ <xml name="agents" nodeType="xs:element"/>
+ <!-- <sql table="agents"/> -->
+ </layout>
+
+ <property name="agent" ref="true" object="opm_agent" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENT +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agent">
+ <layout>
+ <xml name="agent" nodeType="xs:element"/>
+ <!-- <sql table="agent"/> -->
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type=""/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_DEPENDENCIES ++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_dependencies">
+ <layout>
+ <xml name="causalDependencies" nodeType="xs:element"/>
+ <!-- <sql table="causal_dependencies"/> -->
+ </layout>
+
+ <choice name="dependency" type="list" mapping="one-to-many">
+ <property name="used" ref="true" object="opm_used">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_generated_by" ref="true"
+ object="opm_was_generated_by">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_triggered_by" ref="true"
+ object="opm_was_triggered_by">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_derived_from" ref="true"
+ object="opm_was_derived_from">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="was_controlled_by" ref="true"
+ object="opm_was_controlled_by">
+ <xml nodeType="xs:element"/>
+ </property>
+ </choice>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_TIME ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_time">
+ <layout>
+ <xml name="time" nodeType="xs:element"/>
+ <!-- <sql table="time"/> -->
+ </layout>
+
+ <property name="no_later_than" type="datetime">
+ <xml name="noLaterThan" nodeType="xs:attribute" type="xs:dateTime"/>
+ <!-- <sql type="datetime"/> -->
+ </property>
+
+ <property name="no_earlier_than" type="datetime">
+ <xml name="noEarlierThan" nodeType="xs:attribute" type="xs:dateTime"/>
+ <!-- <sql type="datetime"/> -->
+ </property>
+
+ <property name="clock_id" type="str">
+ <xml name="clockId" nodeType="xs:attribute" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ACCOUNT_ID ++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_account_id">
+ <layout>
+ <xml name="account" nodeType="xs:element"/>
+ <!-- <sql table="account_id"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_account">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_ID_CAUSE ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_id_cause">
+ <layout>
+ <xml name="cause" nodeType="xs:element"/>
+ <!-- <sql table="process_id_cause"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_process">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_PROCESS_ID_EFFECT +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_process_id_effect">
+ <layout>
+ <xml name="effect" nodeType="xs:element"/>
+ <!-- <sql table="process_id_effect"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_process">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_ID_CAUSE +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_id_cause">
+ <layout>
+ <xml name="cause" nodeType="xs:element"/>
+ <!-- <sql table="artifact_id_cause"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_artifact">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ARTIFACT_ID_EFFECT ++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_artifact_id_effect">
+ <layout>
+ <xml name="effect" nodeType="xs:element"/>
+ <!-- <sql table="artifact_id_effect"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_artifact">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_AGENT_ID ++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_agent_id">
+ <layout>
+ <xml name="agent" nodeType="xs:element"/>
+ <!-- <sql table="agent_id"/> -->
+ </layout>
+
+ <property name="id" type="str" foreignKey="true" object="opm_agent">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_ROLE ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_role">
+ <layout>
+ <xml name="role" nodeType="xs:element"/>
+ <!-- <sql table="role"/> -->
+ </layout>
+
+ <property name="value" type="str">
+ <xml nodeType="xs:attribute"/>
+ <!-- <sql type="varchar(4095)"/> -->
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_USED ++++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_used">
+ <layout>
+ <xml name="used" nodeType="xs:element"/>
+ <!-- <sql table="used"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_artifact_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_GENERATED_BY ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_generated_by">
+ <layout>
+ <xml name="wasGeneratedBy" nodeType="xs:element"/>
+ <!-- <sql table="was_generated_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_artifact_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_process_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_CONTROLLED_BY +++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_controlled_by">
+ <layout>
+ <xml name="wasControlledBy" nodeType="xs:element"/>
+ <!-- <sql table="was_controlled_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_agent_id"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="start" ref="true" object="opm_time" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+
+ <property name="end" ref="true" object="opm_time" type="list"
+ mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_DERIVED_FROM ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_derived_from">
+ <layout>
+ <xml name="wasDerivedFrom" nodeType="xs:element"/>
+ <!-- <sql table="was_derived_from"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_artifact_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_artifact_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- OPM_WAS_TRIGGERED_BY ++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="opm_was_triggered_by">
+ <layout>
+ <xml name="wasTriggeredBy" nodeType="xs:element"/>
+ <!-- <sql table="was_triggered_by"/> -->
+ </layout>
+
+ <property name="effect" ref="true" object="opm_process_id_effect"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="role" ref="true" object="opm_role" type="str"
+ mapping="one-to-one">
+ <xml nodeType="xs:element"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="cause" ref="true" object="opm_process_id_cause"
+ type="str" mapping="one-to-one">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property name="account" ref="true" object="opm_account_id"
+ type="list" mapping="one-to-many">
+ <xml nodeType="xs:element" type="xs:string"/>
+ <!-- <sql type="varchar(255)"/> -->
+ </property>
+
+ <property ref="true" object="opm_time" type="list" mapping="one-to-many">
+ <xml nodeType="xs:element"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_DOCUMENT +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_document">
+ <layout>
+ <xml name="prov:document" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_entity" ref="true" object="prov_entity" type="list"
+ mapping="one-to-many">
+ <xml name="prov:entity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_activity" ref="true" object="prov_activity" type="list"
+ mapping="one-to-many">
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_agent" ref="true" object="prov_agent" type="list"
+ mapping="one-to-many">
+ <xml name="prov:agent" nodeType="xs:element"/>
+ </property>
+
+ <property name="vt_connection" ref="true" object="vt_connection" type="list"
+ mapping="one-to-many">
+ <xml name="vt:connection" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_usage" ref="true" object="prov_usage" type="list"
+ mapping="one-to-many">
+ <xml name="prov:used" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_generation" ref="true" object="prov_generation" type="list"
+ mapping="one-to-many">
+ <xml name="prov:wasGeneratedBy" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_association" ref="true" object="prov_association" type="list"
+ mapping="one-to-many">
+ <xml name="prov:wasAssociatedWith" nodeType="xs:element"/>
+ </property>
+
+ <!--<property name="vt_part" ref="true" object="vt_part" type="list"
+ mapping="one-to-many">
+ <xml name="vt:isPartOf" nodeType="xs:element"/>
+ </property>-->
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_ENTITY +++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_entity">
+ <layout>
+ <xml name="prov:entity" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml name="prov:id" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="prov_type" type="str">
+ <xml name="prov:type" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="prov_label" type="str">
+ <xml name="prov:label" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="prov_value" type="str">
+ <xml name="prov:value" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_id" type="str">
+ <xml name="vt:id" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_type" type="str">
+ <xml name="vt:type" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_desc" type="str">
+ <xml name="vt:desc" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_package" type="str">
+ <xml name="vt:package" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_version" type="str">
+ <xml name="vt:version" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_cache" type="str">
+ <xml name="vt:cache" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_location_x" type="str">
+ <xml name="vt:location_x" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_location_y" type="str">
+ <xml name="vt:location_y" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="is_part_of" ref="true" object="is_part_of" type="str">
+ <xml name="dcterms:isPartOf" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REF_PROV_ENTITY +++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="ref_prov_entity">
+ <layout>
+ <xml name="prov:entity" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_ref" type="str" foreignKey="true" object="prov_entity">
+ <xml name="prov:ref" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REF_PROV_PLAN +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="ref_prov_plan">
+ <layout>
+ <xml name="prov:plan" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_ref" type="str" foreignKey="true" object="prov_entity">
+ <xml name="prov:ref" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_ACTIVITY +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_activity">
+ <layout>
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml name="prov:id" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="startTime" type="str">
+ <xml name="prov:startTime" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="endTime" type="str">
+ <xml name="prov:endTime" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_id" type="str" primaryKey="true">
+ <xml name="vt:id" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_type" type="str">
+ <xml name="vt:type" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_cached" type="str">
+ <xml name="vt:cached" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_completed" type="str">
+ <xml name="vt:completed" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_machine_id" type="str">
+ <xml name="vt:machine_id" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_error" type="str">
+ <xml name="vt:error" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="is_part_of" ref="true" object="is_part_of" type="str">
+ <xml name="dcterms:isPartOf" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REF_PROV_ACTIVITY +++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="ref_prov_activity">
+ <layout>
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_ref" type="str" foreignKey="true" object="prov_activity">
+ <xml name="prov:ref" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_AGENT ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_agent">
+ <layout>
+ <xml name="prov:agent" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml name="prov:id" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="vt_id" type="str">
+ <xml name="vt:id" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="prov_type" type="str">
+ <xml name="prov:type" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="prov_label" type="str">
+ <xml name="prov:label" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_machine_os" type="str">
+ <xml name="vt:machine_os" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_machine_architecture" type="str">
+ <xml name="vt:machine_architecture" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_machine_processor" type="str">
+ <xml name="vt:machine_processor" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_machine_ram" type="str">
+ <xml name="vt:machine_ram" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- REF_PROV_AGENT ++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="ref_prov_agent">
+ <layout>
+ <xml name="prov:agent" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_ref" type="str" foreignKey="true" object="prov_agent">
+ <xml name="prov:ref" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- VT_CONNECTION +++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="vt_connection">
+ <layout>
+ <xml name="vt:connection" nodeType="xs:element"/>
+ </layout>
+
+ <property name="id" type="str" primaryKey="true">
+ <xml name="id" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+
+ <property name="vt_source" type="str">
+ <xml name="vt:source" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_dest" type="str">
+ <xml name="vt:dest" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_source_port" type="str">
+ <xml name="vt:source_port" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_dest_port" type="str">
+ <xml name="vt:dest_port" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_source_signature" type="str">
+ <xml name="vt:source_signature" nodeType="xs:element" type="xs:string"/>
+ </property>
+
+ <property name="vt_dest_signature" type="str">
+ <xml name="vt:dest_signature" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_USAGE ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_usage">
+ <layout>
+ <xml name="prov:used" nodeType="xs:element"/>
+ </layout>
+
+ <!--<property name="id" type="str" primaryKey="true">
+ <xml name="id" nodeType="xs:attribute" type="xs:string"/>
+ </property>-->
+
+ <property name="prov_activity" ref="true" object="ref_prov_activity" type="str">
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_entity" ref="true" object="ref_prov_entity" type="str">
+ <xml name="prov:entity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_role" type="str">
+ <xml name="prov:role" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_GENERATION +++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_generation">
+ <layout>
+ <xml name="prov:wasGeneratedBy" nodeType="xs:element"/>
+ </layout>
+
+ <!--<property name="id" type="str" primaryKey="true">
+ <xml name="id" nodeType="xs:attribute" type="xs:string"/>
+ </property>-->
+
+ <property name="prov_entity" ref="true" object="ref_prov_entity" type="str">
+ <xml name="prov:entity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_activity" ref="true" object="ref_prov_activity" type="str">
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_role" type="str">
+ <xml name="prov:role" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- PROV_ASSOCIATION ++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="prov_association">
+ <layout>
+ <xml name="prov:wasAssociatedWith" nodeType="xs:element"/>
+ </layout>
+
+ <!--<property name="id" type="str" primaryKey="true">
+ <xml name="id" nodeType="xs:attribute" type="xs:string"/>
+ </property>-->
+
+ <property name="prov_activity" ref="true" object="ref_prov_activity" type="str">
+ <xml name="prov:activity" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_agent" ref="true" object="ref_prov_agent" type="str">
+ <xml name="prov:agent" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_plan" ref="true" object="ref_prov_plan" type="str">
+ <xml name="prov:plan" nodeType="xs:element"/>
+ </property>
+
+ <property name="prov_role" type="str">
+ <xml name="prov:role" nodeType="xs:element" type="xs:string"/>
+ </property>
+ </object>
+
+ <!--++++++++++++++++++++++++++-->
+ <!-- IS_PART_OF ++++++++++++++-->
+ <!--++++++++++++++++++++++++++-->
+
+ <object name="is_part_of">
+ <layout>
+ <xml name="dcterms:isPartOf" nodeType="xs:element"/>
+ </layout>
+
+ <property name="prov_ref" type="str">
+ <xml name="prov:ref" nodeType="xs:attribute" type="xs:string"/>
+ </property>
+ </object>
+
+</objects>
diff --git a/vistrails/db/versions/v1_0_3/translate/__init__.py b/vistrails/db/versions/v1_0_3/translate/__init__.py
new file mode 100644
index 0000000..aee1abc
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/translate/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+version = '1.0.3'
diff --git a/vistrails/db/versions/v1_0_3/translate/v1_0_2.py b/vistrails/db/versions/v1_0_3/translate/v1_0_2.py
new file mode 100644
index 0000000..a16c5d1
--- /dev/null
+++ b/vistrails/db/versions/v1_0_3/translate/v1_0_2.py
@@ -0,0 +1,342 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.db.versions.v1_0_3.domain import DBVistrail, DBVistrailVariable, \
+ DBWorkflow, DBLog, DBRegistry, \
+ DBAdd, DBChange, DBDelete, \
+ DBPortSpec, DBPortSpecItem, \
+ DBParameterExploration, \
+ DBPEParameter, DBPEFunction, \
+ IdScope, DBAbstraction, \
+ DBModule, DBGroup, DBAnnotation, \
+ DBActionAnnotation
+
+from vistrails.db.services.vistrail import materializeWorkflow
+from xml.dom.minidom import parseString
+from itertools import izip
+
+import unittest
+
+id_scope = None
+
+def update_portSpec(old_obj, translate_dict):
+ global id_scope
+ sigstring = old_obj.db_sigstring
+ sigs = []
+ if sigstring and sigstring != '()':
+ for sig in sigstring[1:-1].split(','):
+ sigs.append(sig.split(':', 2))
+ # not great to use eval...
+ defaults = eval(old_obj.db_defaults) if old_obj.db_defaults else []
+ if isinstance(defaults, basestring):
+ defaults = (defaults,)
+ else:
+ try:
+ it = iter(defaults)
+ except TypeError:
+ defaults = (defaults,)
+ # not great to use eval...
+ labels = eval(old_obj.db_labels) if old_obj.db_labels else []
+ if isinstance(labels, basestring):
+ labels = (labels,)
+ else:
+ try:
+ it = iter(labels)
+ except TypeError:
+ labels = (labels,)
+ new_obj = DBPortSpec.update_version(old_obj, translate_dict)
+ total_len = len(sigs)
+ if len(defaults) < total_len:
+ defaults.extend("" for i in xrange(total_len-len(defaults)))
+ if len(labels) < total_len:
+ labels.extend("" for i in xrange(total_len-len(labels)))
+ for i, (sig, default, label) in enumerate(izip(sigs, defaults, labels)):
+ module = None
+ package = None
+ namespace = ''
+ if len(sig) == 1:
+ module = sig[0]
+ else:
+ package = sig[0]
+ module = sig[1]
+ if len(sig) > 2:
+ namespace = sig[2]
+ item = DBPortSpecItem(id=id_scope.getNewId(DBPortSpecItem.vtType),
+ pos=i,
+ module=module,
+ package=package,
+ namespace=namespace,
+ label=label,
+ default=default)
+ item.db_values = ''
+ item.db_entry_type = ''
+ new_obj.db_add_portSpecItem(item)
+ return new_obj
+
+def update_portSpecs(old_obj, translate_dict):
+ new_port_specs = []
+ for port_spec in old_obj.db_portSpecs:
+ new_port_specs.append(update_portSpec(port_spec, translate_dict))
+ return new_port_specs
+
+def update_portSpec_op(old_obj, translate_dict):
+ return update_portSpec(old_obj.db_data, translate_dict)
+
+def createParameterExploration(action_id, xmlString, vistrail):
+ if not xmlString:
+ return
+ # Parse/validate the xml
+
+ try:
+ striplen = len("<paramexps>")
+ xmlString = xmlString[striplen:-(striplen+1)].strip()
+ xmlDoc = parseString(xmlString).documentElement
+ except:
+ return None
+ # we need the pipeline to look up function/paramater id:s
+ pipeline = materializeWorkflow(vistrail, action_id)
+ # Populate parameter exploration window with stored functions and aliases
+ functions = []
+ for f in xmlDoc.getElementsByTagName('function'):
+ f_id = long(f.attributes['id'].value)
+ # we need to convert function id:s to (module_id, port_name)
+ module_id = None
+ f_name = None
+ for m in pipeline.db_modules:
+ for _f in m.db_functions:
+ if _f.db_id == f_id:
+ module_id = m.db_id
+ f_name = _f.db_name
+ continue
+ if not (module_id and f_name):
+ break
+ parameters = []
+ for p in f.getElementsByTagName('param'):
+ # we need to convert function id:s to (module_id, port_name)
+ p_id = long(p.attributes['id'].value)
+ p_pos = None
+ for m in pipeline.db_modules:
+ for _f in m.db_functions:
+ for _p in _f.db_parameters:
+ if _p.db_id == p_id:
+ p_pos = _p.db_pos
+ continue
+ if p_pos is None:
+ break
+ p_intType = str(p.attributes['interp'].value)
+ if p_intType in ['Linear Interpolation']:
+ p_min = str(p.attributes['min'].value)
+ p_max = str(p.attributes['max'].value)
+ value = "[%s, %s]" % (p_min, p_max)
+ if p_intType in ['RGB Interpolation', 'HSV Interpolation']:
+ p_min = str(p.attributes['min'].value)
+ p_max = str(p.attributes['max'].value)
+ value = '["%s", "%s"]' % (p_min, p_max)
+ elif p_intType == 'List':
+ value = str(p.attributes['values'].value)
+ elif p_intType == 'User-defined Function':
+ # Set function code
+ value = str(p.attributes['code'].value)
+ param = DBPEParameter(id=vistrail.idScope.getNewId(DBPEParameter.vtType),
+ pos=p_pos,
+ interpolator=p_intType,
+ value=value,
+ dimension=int(p.attributes['dim'].value))
+ parameters.append(param)
+ f_is_alias = (str(f.attributes['alias'].value) == 'True')
+ function = DBPEFunction(id=vistrail.idScope.getNewId(DBPEFunction.vtType),
+ module_id=module_id,
+ port_name=f_name,
+ is_alias=1 if f_is_alias else 0,
+ parameters=parameters)
+ functions.append(function)
+ pe = DBParameterExploration(id=vistrail.idScope.getNewId(DBParameterExploration.vtType),
+ action_id=action_id,
+ dims=str(xmlDoc.attributes['dims'].value),
+ layout=str(xmlDoc.attributes['layout'].value),
+ date=str(xmlDoc.attributes['date'].value),
+ functions = functions)
+ return pe
+
+
+def translateVistrail(_vistrail):
+ """ Translate old annotation based vistrail variables to new
+ DBVistrailVariable class """
+ global id_scope
+
+ new_vistrail_vars = []
+ new_param_exps = []
+
+ def update_workflow(old_obj, trans_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow,
+ trans_dict, DBWorkflow())
+
+ def update_operations(old_obj, trans_dict):
+ new_ops = []
+ for obj in old_obj.db_operations:
+ if obj.vtType == 'delete':
+ new_ops.append(DBDelete.update_version(obj, trans_dict))
+ elif obj.vtType == 'add':
+ if obj.db_what == 'portSpec':
+ trans_dict['DBAdd'] = {'data': update_portSpec_op}
+ new_op = DBAdd.update_version(obj, trans_dict)
+ new_ops.append(new_op)
+ del trans_dict['DBAdd']
+ else:
+ new_op = DBAdd.update_version(obj, trans_dict)
+ new_ops.append(new_op)
+ elif obj.vtType == 'change':
+ if obj.db_what == 'portSpec':
+ trans_dict['DBChange'] = {'data': update_portSpec_op}
+ new_op = DBChange.update_version(obj, trans_dict)
+ new_ops.append(new_op)
+ del trans_dict['DBChange']
+ else:
+ new_op = DBChange.update_version(obj, trans_dict)
+ new_ops.append(new_op)
+ return new_ops
+
+ def update_annotations(old_obj, trans_dict):
+ new_annotations = []
+ for a in old_obj.db_annotations:
+ if a.db_key == '__vistrail_vars__':
+ for name, data in dict(eval(a.db_value)).iteritems():
+ uuid, identifier, value = data
+ package, module, namespace = identifier
+ var = DBVistrailVariable(name, uuid, package, module,
+ namespace, value)
+ new_vistrail_vars.append(var)
+ else:
+ new_a = DBAnnotation.update_version(a, trans_dict)
+ new_annotations.append(new_a)
+
+ return new_annotations
+
+ def update_actionAnnotations(old_obj, trans_dict):
+ new_actionAnnotations = []
+ for aa in old_obj.db_actionAnnotations:
+ if aa.db_key == '__paramexp__':
+ pe = createParameterExploration(aa.db_action_id, aa.db_value,
+ vistrail)
+ new_param_exps.append(pe)
+ else:
+ new_aa = DBActionAnnotation.update_version(aa, trans_dict)
+ new_actionAnnotations.append(new_aa)
+ return new_actionAnnotations
+
+ translate_dict = {'DBModule': {'portSpecs': update_portSpecs},
+ 'DBModuleDescriptor': {'portSpecs': update_portSpecs},
+ 'DBAction': {'operations': update_operations},
+ 'DBGroup': {'workflow': update_workflow},
+ 'DBVistrail': {'annotations': update_annotations,
+ 'actionAnnotations': \
+ update_actionAnnotations}
+ }
+ vistrail = DBVistrail()
+ id_scope = vistrail.idScope
+ vistrail = DBVistrail.update_version(_vistrail, translate_dict, vistrail)
+ for v in new_vistrail_vars:
+ vistrail.db_add_vistrailVariable(v)
+ for pe in new_param_exps:
+ vistrail.db_add_parameter_exploration(pe)
+
+ vistrail.db_version = '1.0.3'
+ return vistrail
+
+def translateWorkflow(_workflow):
+ global id_scope
+ def update_workflow(old_obj, translate_dict):
+ return DBWorkflow.update_version(old_obj.db_workflow, translate_dict)
+ translate_dict = {'DBModule': {'portSpecs': update_portSpecs},
+ 'DBGroup': {'workflow': update_workflow}}
+
+ workflow = DBWorkflow()
+ id_scope = IdScope(remap={DBAbstraction.vtType: DBModule.vtType, DBGroup.vtType: DBModule.vtType})
+ workflow = DBWorkflow.update_version(_workflow, translate_dict, workflow)
+ workflow.db_version = '1.0.3'
+ return workflow
+
+def translateLog(_log):
+ translate_dict = {}
+ log = DBLog.update_version(_log, translate_dict)
+ log.db_version = '1.0.3'
+ return log
+
+def translateRegistry(_registry):
+ global id_scope
+ translate_dict = {'DBModuleDescriptor': {'portSpecs': update_portSpecs}}
+ registry = DBRegistry()
+ id_scope = registry.idScope
+ registry = DBRegistry.update_version(_registry, translate_dict, registry)
+ registry.db_version = '1.0.3'
+ return registry
+
+class TestTranslate(unittest.TestCase):
+ def testParamexp(self):
+ """test translating parameter explorations from 1.0.2 to 1.0.3"""
+ from vistrails.db.services.io import open_bundle_from_zip_xml
+ from vistrails.core.system import vistrails_root_directory
+ import os
+ (save_bundle, vt_save_dir) = open_bundle_from_zip_xml(DBVistrail.vtType, \
+ os.path.join(vistrails_root_directory(),
+ 'tests/resources/paramexp-1.0.2.vt'))
+ vistrail = translateVistrail(save_bundle.vistrail)
+ pes = vistrail.db_get_parameter_explorations()
+ self.assertEqual(len(pes), 1)
+ funs = pes[0].db_functions
+ self.assertEqual(set([f.db_port_name for f in funs]),
+ set(['SetCoefficients', 'SetBackgroundWidget']))
+ parameters = funs[0].db_parameters
+ self.assertEqual(len(parameters), 10)
+
+ def testVistrailvars(self):
+ """test translating vistrail variables from 1.0.2 to 1.0.3"""
+ from vistrails.db.services.io import open_bundle_from_zip_xml
+ from vistrails.core.system import vistrails_root_directory
+ import os
+ (save_bundle, vt_save_dir) = open_bundle_from_zip_xml(DBVistrail.vtType, \
+ os.path.join(vistrails_root_directory(),
+ 'tests/resources/visvar-1.0.2.vt'))
+ vistrail = translateVistrail(save_bundle.vistrail)
+ visvars = vistrail.db_vistrailVariables
+ self.assertEqual(len(visvars), 2)
+ self.assertNotEqual(visvars[0].db_name, visvars[1].db_name)
+
+if __name__ == '__main__':
+ from vistrails.gui.application import start_application
+ v = start_application({'interactiveMode': False,
+ 'nologger': True,
+ 'singleInstance': False,
+ 'fixedSpreadsheetCells': True})
+ unittest.main()
diff --git a/vistrails/gui/__init__.py b/vistrails/gui/__init__.py
new file mode 100644
index 0000000..fac3164
--- /dev/null
+++ b/vistrails/gui/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
diff --git a/vistrails/gui/application.py b/vistrails/gui/application.py
new file mode 100644
index 0000000..48a71d8
--- /dev/null
+++ b/vistrails/gui/application.py
@@ -0,0 +1,853 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This is the main application of vistrail, it will calls for
+initializations to the theme, packages and the builder...
+
+"""
+from PyQt4 import QtGui, QtCore, QtNetwork
+from vistrails.core.application import VistrailsApplicationInterface, \
+ get_vistrails_application, set_vistrails_application
+from vistrails.core import command_line
+from vistrails.core import debug
+from vistrails.core import system
+from vistrails.core.application import APP_SUCCESS, APP_FAIL, APP_DONE
+from vistrails.core.db.locator import FileLocator, DBLocator
+import vistrails.core.requirements
+from vistrails.db import VistrailsDBException
+import vistrails.db.services.io
+from vistrails.gui import qt
+import vistrails.gui.theme
+import os.path
+import getpass
+import re
+import sys
+
+################################################################################
+
+class VistrailsApplicationSingleton(VistrailsApplicationInterface,
+ QtGui.QApplication):
+ """
+ VistrailsApplicationSingleton is the singleton of the application,
+ there will be only one instance of the application during VisTrails
+
+ """
+
+ def __call__(self):
+ """ __call__() -> VistrailsApplicationSingleton
+ Return self for calling method
+
+ """
+ if not self._initialized and not self._is_running:
+ self.init()
+ return self
+
+ def __init__(self):
+ # font bugfix for Qt 4.8 and OS X 10.9
+ import platform
+ if platform.system()=='Darwin':
+ release = platform.mac_ver()[0].split('.')
+ if len(release)>=2 and int(release[0])*100+int(release[1])>=1009:
+ QtGui.QFont.insertSubstitution(".Lucida Grande UI", "Lucida Grande")
+ QtGui.QApplication.__init__(self, sys.argv)
+ VistrailsApplicationInterface.__init__(self)
+
+ if system.systemType in ['Darwin']:
+ self.installEventFilter(self)
+ self.builderWindow = None
+ # local notifications
+ self.window_notifications = {}
+ self.view_notifications = {}
+
+ if QtCore.QT_VERSION < 0x40200: # 0x40200 = 4.2.0
+ raise vistrails.core.requirements.MissingRequirement("Qt version >= 4.2")
+ self._is_running = False
+ self.shared_memory = None
+ self.local_server = None
+ self.setAttribute(QtCore.Qt.AA_DontShowIconsInMenus)
+ qt.allowQObjects()
+
+ def run_single_instance(self):
+ # code for single instance of the application
+ # based on the C++ solution available at
+ # http://wiki.qtcentre.org/index.php?title=SingleApplication
+ if QtCore.QT_VERSION >= 0x40400:
+ self.timeout = 600000
+ self._unique_key = os.path.join(system.home_directory(),
+ "vistrails-single-instance-check-%s"%getpass.getuser())
+ self.shared_memory = QtCore.QSharedMemory(self._unique_key)
+ self.local_server = None
+ if self.shared_memory.attach():
+ self._is_running = True
+
+ local_socket = QtNetwork.QLocalSocket(self)
+ local_socket.connectToServer(self._unique_key)
+ if not local_socket.waitForConnected(self.timeout):
+ debug.critical(
+ "Connection failed: %s\n"
+ "Removing socket" % (local_socket.errorString()))
+ try:
+ os.remove(self._unique_key)
+ except OSError, e:
+ debug.critical("Couldn't remove socket: %s (%s)" % (
+ self._unique_key, e))
+
+ else:
+ if self.found_another_instance_running(local_socket):
+ return APP_DONE # success, we should shut down
+ else:
+ return APP_FAIL # error, we should shut down
+
+ if not self.shared_memory.create(1):
+ debug.critical("Unable to create single instance "
+ "of vistrails application")
+ return
+ self.local_server = QtNetwork.QLocalServer(self)
+ self.connect(self.local_server, QtCore.SIGNAL("newConnection()"),
+ self.message_received)
+ if self.local_server.listen(self._unique_key):
+ debug.log("Listening on %s"%self.local_server.fullServerName())
+ else:
+ # This usually happens when vistrails have crashed
+ # Delete the key and try again
+ self.shared_memory.detach()
+ self.local_server.close()
+ if os.path.exists(self._unique_key):
+ os.remove(self._unique_key)
+
+ self.shared_memory = QtCore.QSharedMemory(self._unique_key)
+ self.local_server = None
+
+ if not self.shared_memory.create(1):
+ debug.critical("Unable to create single instance "
+ "of vistrails application")
+ return
+ self.local_server = QtNetwork.QLocalServer(self)
+ self.connect(self.local_server, QtCore.SIGNAL("newConnection()"),
+ self.message_received)
+ if self.local_server.listen(self._unique_key):
+ debug.log("Listening on %s"%self.local_server.fullServerName())
+ else:
+ debug.warning(
+ "Server is not listening. This means it "
+ "will not accept parameters from other "
+ "instances")
+
+ return None
+
+ def found_another_instance_running(self, local_socket):
+ debug.critical("Found another instance of VisTrails running")
+ msg = bytes(sys.argv[1:])
+ debug.critical("Will send parameters to main instance %s" % msg)
+ res = self.send_message(local_socket, msg)
+ if res is True:
+ debug.critical("Main instance succeeded")
+ return True
+ elif res is False:
+ return False
+ else:
+ debug.critical("Main instance reports: %s" % res)
+ return False
+
+ def init(self, optionsDict=None):
+ """ VistrailsApplicationSingleton(optionDict: dict)
+ -> VistrailsApplicationSingleton
+ Create the application with a dict of settings
+
+ """
+ vistrails.gui.theme.initializeCurrentTheme()
+ VistrailsApplicationInterface.init(self, optionsDict)
+
+ # singleInstance configuration
+ singleInstance = self.temp_configuration.check('singleInstance')
+ if singleInstance:
+ finished = self.run_single_instance()
+ if finished is not None:
+ return finished
+
+ interactive = self.temp_configuration.check('interactiveMode')
+ if interactive:
+ self.setIcon()
+ self.createWindows()
+ self.processEvents()
+
+ self.vistrailsStartup.init()
+ # ugly workaround for configuration initialization order issue
+ # If we go through the configuration too late,
+ # The window does not get maximized. If we do it too early,
+ # there are no created windows during spreadsheet initialization.
+ if interactive:
+ if self.temp_configuration.check('maximizeWindows'):
+ self.builderWindow.showMaximized()
+ if self.temp_configuration.check('dbDefault'):
+ self.builderWindow.setDBDefault(True)
+ self._python_environment = self.vistrailsStartup.get_python_environment()
+ self._initialized = True
+
+ # default handler installation
+ if system.systemType == 'Linux':
+ if not (self.temp_configuration.check('handlerDontAsk') or
+ self.configuration.check('handlerDontAsk')):
+ if not linux_default_application_set():
+ self.ask_update_default_application()
+
+ if interactive:
+ self.interactiveMode()
+ else:
+ r = self.noninteractiveMode()
+ return APP_SUCCESS if r is True else APP_FAIL
+ return APP_SUCCESS
+
+ def ask_update_default_application(self, dont_ask_checkbox=True):
+ dialog = QtGui.QDialog()
+ dialog.setWindowTitle(u"Install .vt .vtl handler")
+ layout = QtGui.QVBoxLayout()
+ dialog.setLayout(layout)
+ layout.addWidget(QtGui.QLabel(u"Install VisTrails as default handler "
+ u"to open .vt and .vtl files?"))
+ if dont_ask_checkbox:
+ dont_ask = QtGui.QCheckBox(u"Don't ask on startup")
+ dont_ask_setting = self.configuration.check('handlerDontAsk')
+ dont_ask.setChecked(dont_ask_setting)
+ layout.addWidget(dont_ask)
+ buttons = QtGui.QDialogButtonBox(
+ QtGui.QDialogButtonBox.Yes | QtGui.QDialogButtonBox.No)
+ layout.addWidget(buttons)
+ QtCore.QObject.connect(buttons, QtCore.SIGNAL('accepted()'),
+ dialog, QtCore.SLOT('accept()'))
+ QtCore.QObject.connect(buttons, QtCore.SIGNAL('rejected()'),
+ dialog, QtCore.SLOT('reject()'))
+
+ res = dialog.exec_()
+ if dont_ask_checkbox:
+ if dont_ask.isChecked() != dont_ask_setting:
+ self.configuration.handlerDontAsk = dont_ask.isChecked()
+ self.configuration.handlerDontAsk = dont_ask.isChecked()
+ if res != QtGui.QDialog.Accepted:
+ return False
+ if system.systemType == 'Linux':
+ if not linux_update_default_application():
+ QtGui.QMessageBox.warning(
+ None,
+ u"Install .vt .vtl handler",
+ u"Couldn't set VisTrails as default handler "
+ u"to open .vt and .vtl files")
+ return False
+ else:
+ QtGui.QMessageBox.warning(
+ None,
+ u"Install .vt .vtl handler",
+ u"Can't install a default handler on this platform")
+ return False
+ return True
+
+ def is_running_gui(self):
+ return True
+
+ def get_current_controller(self):
+ return self.builderWindow.get_current_controller()
+ get_controller = get_current_controller
+
+ def get_vistrail(self):
+ if self.get_controller():
+ return self.get_controller().vistrail
+ return None
+
+ def ensure_vistrail(self, locator):
+ view = self.builderWindow.ensureVistrail(locator)
+ if view is not None:
+ return view.controller
+ return None
+
+ def add_vistrail(self, *objs):
+ return self.builderWindow.add_vistrail(*objs)
+
+ def remove_vistrail(self, locator=None):
+ return self.builderWindow.remove_vistrail(locator)
+
+ def select_version(self, version):
+ return self.builderWindow.select_version(version)
+
+ def update_locator(self, old_locator, new_locator):
+ pass
+
+ def create_notification(self, notification_id, window=None, view=None):
+ if view is not None:
+ if view not in self.view_notifications:
+ self.view_notifications[view] = {}
+ notifications = self.view_notifications[view]
+ elif window is not None:
+ if window not in self.window_notifications:
+ self.window_notifications[window] = {}
+ notifications = self.window_notifications[window]
+ else:
+ notifications = self.notifications
+ if notification_id not in notifications:
+ notifications[notification_id] = set()
+ # else:
+ # print "already added notification", notification_id
+
+ def register_notification(self, notification_id, method, window=None,
+ view=None):
+ if view is not None:
+ if view not in self.view_notifications:
+ self.view_notifications[view] = {}
+ notifications = self.view_notifications[view]
+ #print '>>> LOCAL adding notification', notification_id, view, method
+ #print id(notifications), notifications
+ #for n, o in notifications.iteritems():
+ # print " ", n , "(%s)"%len(o)
+ # for m in o:
+ # print " ", m
+ elif window is not None:
+ if window not in self.window_notifications:
+ self.window_notifications[window] = {}
+ notifications = self.window_notifications[window]
+ else:
+ notifications = self.notifications
+ #print '>>> GLOBAL adding notification', notification_id, method
+ #print id(notifications), notifications
+ if notification_id not in notifications:
+ self.create_notification(notification_id, window, view)
+ notifications[notification_id].add(method)
+
+ def unregister_notification(self, notification_id, method, window=None,
+ view=None):
+ if view is not None:
+ if view in self.view_notifications:
+ notifications = self.view_notifications[view]
+ else:
+ notifications = {}
+ #print '>>> LOCAL remove notification', notification_id, view
+
+ #print id(notifications), notifications
+# for n, o in notifications.iteritems():
+# print " ", n , "(%s)"%len(o)
+# for m in o:
+# print " ", m
+ elif window is not None:
+ if window in self.window_notifications:
+ notifications = self.window_notifications[window]
+ else:
+ notifications = {}
+ else:
+ notifications = self.notifications
+ #print '>>> GLOBAL remove notification', notification_id, method
+ #print id(notifications), notifications
+ if notification_id in notifications:
+ notifications[notification_id].remove(method)
+
+ def send_notification(self, notification_id, *args):
+ # do global notifications
+ if notification_id in self.notifications:
+ for m in self.notifications[notification_id]:
+ try:
+ m(*args)
+ except Exception:
+ import traceback
+ traceback.print_exc()
+ notifications = {}
+
+ current_window = self.builderWindow
+
+ # do window notifications
+ if current_window in self.window_notifications:
+ notifications = self.window_notifications[current_window]
+
+ if notification_id in notifications:
+ for m in notifications[notification_id]:
+ try:
+ m(*args)
+ except Exception:
+ import traceback
+ traceback.print_exc()
+
+ if current_window is not None:
+ current_view = current_window.current_view
+ else:
+ current_view = None
+ # do local notifications
+ if current_view in self.view_notifications:
+ notifications = self.view_notifications[current_view]
+
+ if notification_id in notifications:
+ for m in notifications[notification_id]:
+ try:
+ m(*args)
+ except Exception:
+ import traceback
+ traceback.print_exc()
+
+ def showBuilderWindow(self):
+ # in some systems (Linux and Tiger) we need to make both calls
+ # so builderWindow is activated
+ self.setActiveWindow(self.builderWindow)
+ self.builderWindow.activateWindow()
+ self.builderWindow.show()
+ self.builderWindow.raise_()
+
+ def interactiveMode(self):
+ """ interactiveMode() -> None
+ Instantiate the GUI for interactive mode
+
+ """
+ if self.temp_configuration.check('showSplash'):
+ self.splashScreen.finish(self.builderWindow)
+ debug.DebugPrint.getInstance().register_splash(None)
+ self.splashScreen = None
+ # self.builderWindow.modulePalette.updateFromModuleRegistry()
+ # self.builderWindow.modulePalette.connect_registry_signals()
+ self.builderWindow.link_registry()
+
+ self.process_interactive_input()
+ if not self.temp_configuration.showSpreadsheetOnly:
+ self.showBuilderWindow()
+ else:
+ self.builderWindow.hide()
+ self.builderWindow.create_first_vistrail()
+ self.builderWindow.check_running_jobs()
+
+ def noninteractiveMode(self):
+ """ noninteractiveMode() -> None
+ Run the console in non-interactive mode
+
+ """
+ usedb = False
+ if self.temp_db_options.host:
+ usedb = True
+ passwd = ''
+ if usedb and self.temp_db_options.user:
+ if self.temp_db_options.user:
+ db_config = dict((x, self.temp_db_options.__dict__[x])
+ for x in ['host', 'port',
+ 'db', 'user'])
+ try:
+ vistrails.db.services.io.test_db_connection(db_config)
+ except VistrailsDBException:
+ passwd = \
+ getpass.getpass("Connecting to %s:%s. Password for user '%s':" % (
+ self.temp_db_options.host,
+ self.temp_db_options.db,
+ self.temp_db_options.user))
+ db_config['passwd'] = passwd
+ try:
+ vistrails.db.services.io.test_db_connection(db_config)
+ except VistrailsDBException:
+ debug.critical("Cannot login to database")
+ return False
+
+ if self.input:
+ w_list = []
+ vt_list = []
+ for filename in self.input:
+ f_name, version = self._parse_vtinfo(filename, not usedb)
+ if not f_name:
+ debug.critical("File not found: %s" % filename)
+ return False
+ if not usedb:
+ locator = FileLocator(os.path.abspath(f_name))
+ else:
+ locator = DBLocator(host=self.temp_db_options.host,
+ port=self.temp_db_options.port,
+ database=self.temp_db_options.db,
+ user=self.temp_db_options.user,
+ passwd=passwd,
+ obj_id=f_name,
+ obj_type=None,
+ connection_id=None)
+ if not locator.is_valid():
+ #here there is a problem: as we allow execution from
+ #command line with VisTrails already running, we need
+ #to update from the gui
+ if hasattr(self, 'builderWindow'):
+ ok = locator.update_from_gui(self.builderWindow)
+ else:
+ ok = locator.update_from_console()
+ if not ok:
+ debug.critical("Cannot login to database")
+ w_list.append((locator, version))
+ vt_list.append(locator)
+ import vistrails.core.console_mode
+ if self.temp_db_options.parameters == None:
+ self.temp_db_options.parameters = ''
+
+ errs = []
+ if self.temp_configuration.check('workflowGraph'):
+ workflow_graph = self.temp_configuration.workflowGraph
+ results = vistrails.core.console_mode.get_wf_graph(w_list, workflow_graph,
+ self.temp_configuration.spreadsheetDumpPDF)
+ for r in results:
+ if r[0] == False:
+ errs.append("Error generating workflow graph: %s" % \
+ r[1])
+ debug.critical("*** Error in get_wf_graph: %s" % r[1])
+
+ if self.temp_configuration.check('evolutionGraph'):
+ evolution_graph = self.temp_configuration.evolutionGraph
+ results = vistrails.core.console_mode.get_vt_graph(vt_list, evolution_graph,
+ self.temp_configuration.spreadsheetDumpPDF)
+ for r in results:
+ if r[0] == False:
+ errs.append("Error generating vistrail graph: %s" % \
+ r[1])
+ debug.critical("*** Error in get_vt_graph: %s" % r[1])
+
+ if self.temp_configuration.check('workflowInfo'):
+ workflow_info = self.temp_configuration.workflowInfo
+ else:
+ workflow_info = None
+
+ extra_info = None
+ if self.temp_configuration.check('spreadsheetDumpCells'):
+ extra_info = \
+ {'pathDumpCells': self.temp_configuration.spreadsheetDumpCells}
+ if self.temp_configuration.check('spreadsheetDumpPDF'):
+ if extra_info is None:
+ extra_info = {}
+ extra_info['pdf'] = self.temp_configuration.spreadsheetDumpPDF
+
+ if self.temp_configuration.check('parameterExploration'):
+ errs.extend(
+ vistrails.core.console_mode.run_parameter_explorations(
+ w_list, extra_info=extra_info))
+ else:
+ errs.extend(vistrails.core.console_mode.run(w_list,
+ self.temp_db_options.parameters,
+ workflow_info, update_vistrail=True,
+ extra_info=extra_info))
+ if len(errs) > 0:
+ for err in errs:
+ debug.critical("*** Error in %s:%s:%s -- %s" % err)
+ return [False, ["*** Error in %s:%s:%s -- %s" % err for err in errs]]
+ return True
+ else:
+ debug.warning("no input vistrails provided")
+ return True
+
+ def setIcon(self):
+ """ setIcon() -> None
+ Setup Vistrail Icon
+ """
+ self.setWindowIcon(vistrails.gui.theme.CurrentTheme.APPLICATION_ICON)
+
+ def setupSplashScreen(self):
+ """ setupSplashScreen() -> None
+ Create the splash-screen at startup
+
+ """
+ if self.temp_configuration.check('showSplash'):
+ splashPath = (system.vistrails_root_directory() +
+ "/gui/resources/images/vistrails_splash.png")
+ pixmap = QtGui.QPixmap(splashPath)
+ self.splashScreen = QtGui.QSplashScreen(pixmap, QtCore.Qt.WindowStaysOnTopHint)
+ self.splashScreen.setFont(vistrails.gui.theme.CurrentTheme.SPLASH_SCREEN_FONT)
+ debug.DebugPrint.getInstance().register_splash(self)
+ self.splashScreen.show()
+
+ def splashMessage(self, msg):
+ if hasattr(self, "splashScreen"):
+ self.splashScreen.showMessage(msg,
+ QtCore.Qt.AlignBottom|QtCore.Qt.AlignLeft,
+ QtCore.Qt.white)
+ self.processEvents()
+
+ def createWindows(self):
+ """ createWindows() -> None
+ Create and configure all GUI widgets including the builder
+
+ """
+ self.setupSplashScreen()
+
+ # This is so that we don't import too many things before we
+ # have to. Otherwise, requirements are checked too late.
+ # from gui.builder_window import QBuilderWindow
+ from vistrails.gui.vistrails_window import QVistrailsWindow
+
+ # self.builderWindow = QBuilderWindow()
+ self.builderWindow = QVistrailsWindow()
+ if not self.temp_configuration.showSpreadsheetOnly:
+ # self.builderWindow.show()
+ # self.setActiveWindow(self.builderWindow)
+ pass
+
+ def finishSession(self):
+ if QtCore.QT_VERSION >= 0x40400 and self.shared_memory is not None:
+ self.shared_memory.detach()
+ if self.local_server:
+ self.local_server.close()
+ if system.systemType in ['Darwin']:
+ self.removeEventFilter(self)
+ VistrailsApplicationInterface.finishSession(self)
+
+ def eventFilter(self, o, event):
+ """eventFilter(obj,event)-> boolean
+ This will filter all create events and will set on the WA_MacMetalStyle
+ attribute of a QWidget. It will also filter the FileOpen events on a Mac
+
+ """
+ metalstyle = self.temp_configuration.check('useMacBrushedMetalStyle')
+ if metalstyle:
+ if QtCore.QT_VERSION < 0x40500:
+ create_event = QtCore.QEvent.Create
+ mac_attribute = QtCore.Qt.WA_MacMetalStyle
+ else:
+ create_event = 15
+ mac_attribute = QtCore.Qt.WA_MacBrushedMetal
+ if (event.type() == create_event and
+ isinstance(o, QtGui.QWidget) and
+ not isinstance(o, QtGui.QSplashScreen) and
+ not (o.windowFlags() & QtCore.Qt.Popup)):
+ o.setAttribute(mac_attribute)
+ if event.type() == QtCore.QEvent.FileOpen:
+ self.input = [str(event.file())]
+ self.process_interactive_input()
+ return QtGui.QApplication.eventFilter(self,o,event)
+
+ def is_running(self):
+ return self._is_running
+
+ def message_received(self):
+ if QtCore.QT_VERSION >= 0x40400:
+ local_socket = self.local_server.nextPendingConnection()
+ if not local_socket.waitForReadyRead(self.timeout):
+ debug.critical("Read error: %s" %
+ local_socket.errorString())
+ return
+ byte_array = local_socket.readAll()
+ self.temp_db_options = None
+ self.temp_configuration.workflowGraph = None
+ self.temp_configuration.workflowInfo = None
+ self.temp_configuration.evolutionGraph = None
+ self.temp_configuration.spreadsheetDumpPDF = False
+ self.temp_configuration.spreadsheetDumpCells = None
+ self.temp_configuration.executeWorkflows = False
+ self.temp_configuration.interactiveMode = True
+
+ try:
+ result = self.parse_input_args_from_other_instance(str(byte_array))
+ except Exception, e:
+ import traceback
+ debug.critical("Unknown error: %s" % str(e))
+ result = traceback.format_exc()
+ if None == result:
+ result = True
+ if True == result:
+ result = "Command Completed"
+ elif False == result:
+ result = "Command Failed"
+ elif type(result) == list:
+ result = '\n'.join(result[1])
+ self.shared_memory.lock()
+ local_socket.write(bytes(result))
+ self.shared_memory.unlock()
+ if not local_socket.waitForBytesWritten(self.timeout):
+ debug.critical("Writing failed: %s" %
+ local_socket.errorString())
+ return
+ local_socket.disconnectFromServer()
+
+ def send_message(self, local_socket, message):
+ self.shared_memory.lock()
+ local_socket.write(message)
+ self.shared_memory.unlock()
+ if not local_socket.waitForBytesWritten(self.timeout):
+ debug.critical("Writing failed: %s" %
+ local_socket.errorString())
+ return False
+ if not local_socket.waitForReadyRead(self.timeout):
+ debug.critical("Read error: %s" %
+ local_socket.errorString())
+ return False
+ byte_array = local_socket.readAll()
+ result = str(byte_array)
+ debug.log("Other instance processed input (%s)"%result)
+ if result != 'Command Completed':
+ debug.critical(result)
+ else:
+ local_socket.disconnectFromServer()
+ return True
+ local_socket.disconnectFromServer()
+ return False
+
+ def parse_input_args_from_other_instance(self, msg):
+ options_re = re.compile(r"^(\[('([^'])*', ?)*'([^']*)'\])|(\[\s?\])$")
+ if options_re.match(msg):
+ #it's safe to eval as a list
+ args = eval(msg)
+ if isinstance(args, list):
+ #print "args from another instance %s"%args
+ try:
+ command_line.CommandLineParser.init_options(args)
+ except SystemExit:
+ debug.critical("Invalid options: %s" % ' '.join(args))
+ return False
+ self.readOptions()
+ interactive = self.temp_configuration.check('interactiveMode')
+ if interactive:
+ result = self.process_interactive_input()
+ if not self.temp_configuration.showSpreadsheetOnly:
+ # in some systems (Linux and Tiger) we need to make both calls
+ # so builderWindow is activated
+ self.builderWindow.raise_()
+ self.builderWindow.activateWindow()
+ return result
+ else:
+ return self.noninteractiveMode()
+ else:
+ debug.critical("Invalid string: %s" % msg)
+ else:
+ debug.critical("Invalid input: %s" % msg)
+ return False
+
+def linux_default_application_set():
+ """linux_default_application_set() -> True|False|None
+ For Linux - checks if a handler is set for .vt and .vtl files.
+ """
+ command = ['xdg-mime', 'query', 'filetype',
+ os.path.join(system.vistrails_examples_directory(),
+ 'terminator.vt')]
+ try:
+ output = []
+ result = system.execute_cmdline(command, output)
+ if result != 0:
+ # something is wrong, abort
+ debug.warning("Error checking mimetypes: %s" % output[0])
+ return None
+ except OSError, e:
+ debug.warning("Error checking mimetypes: %s" % e.message)
+ return None
+ if 'application/x-vistrails' == output[0].strip():
+ return True
+ return False
+
+def linux_update_default_application():
+ """ update_default_application() -> None
+ For Linux - checks if we should install vistrails as the default
+ application for .vt and .vtl files.
+ If replace is False, don't replace an existing handler.
+
+ Returns True if installation succeeded.
+ """
+ root = system.vistrails_root_directory()
+ home = os.path.expanduser('~')
+
+ # install mime type
+ command = ['xdg-mime', 'install',
+ os.path.join(system.vistrails_root_directory(),
+ 'gui/resources/vistrails-mime.xml')]
+ output = []
+ try:
+ result = system.execute_cmdline(command, output)
+ except OSError, e:
+ result = None
+ if result != 0:
+ debug.warning("Error running xdg-mime")
+ return False
+
+ command = ['update-mime-database', home + '/.local/share/mime']
+ output = []
+ try:
+ result = system.execute_cmdline(command, output)
+ except OSError, e:
+ result = None
+ if result != 0:
+ debug.warning("Error running update-mime-database")
+ return False
+
+ # install icon
+ command = ['xdg-icon-resource', 'install',
+ '--context', 'mimetypes',
+ '--size', '48',
+ os.path.join(system.vistrails_root_directory(),
+ 'gui/resources/images/vistrails_icon_small.png'),
+ 'application-x-vistrails']
+ output = []
+ try:
+ result = system.execute_cmdline(command, output)
+ except OSError, e:
+ result = None
+ if result != 0:
+ debug.warning("Error running xdg-icon-resource")
+ return True # the handler is set anyway
+
+ # install desktop file
+ dirs = [home + '/.local', home + '/.local/share',
+ home + '/.local/share/applications']
+
+ for d in dirs:
+ if not os.path.isdir(d):
+ os.mkdir(d)
+ desktop = """[Desktop Entry]
+Name=VisTrails
+Exec=python {root}/run.py %f
+Icon={root}/gui/resources/images/vistrails_icon_small.png
+Type=Application
+MimeType=application/x-vistrails
+""".format(root=root)
+ f = open(os.path.join(dirs[2], 'vistrails.desktop'), 'w')
+ f.write(desktop)
+ f.close()
+
+ command = ['update-desktop-database', dirs[2]]
+ output = []
+ try:
+ result = system.execute_cmdline(command, output)
+ except OSError, e:
+ result = None
+ if result != 0:
+ debug.warning("Error running update-desktop-database")
+ return True
+
+# The initialization must be explicitly signalled. Otherwise, any
+# modules importing vis_application will try to initialize the entire
+# app.
+def start_application(optionsDict=None):
+ """Initializes the application singleton."""
+ VistrailsApplication = get_vistrails_application()
+ if VistrailsApplication:
+ debug.critical("Application already started.")
+ return
+ VistrailsApplication = VistrailsApplicationSingleton()
+ set_vistrails_application(VistrailsApplication)
+ x = VistrailsApplication.init(optionsDict)
+ return x
+
+def stop_application():
+ """Stop and finalize the application singleton."""
+ VistrailsApplication = get_vistrails_application()
+ VistrailsApplication.finishSession()
+ VistrailsApplication.save_configuration()
+ VistrailsApplication.destroy()
+ VistrailsApplication.deleteLater()
+
diff --git a/vistrails/gui/application_server.py b/vistrails/gui/application_server.py
new file mode 100644
index 0000000..6acb922
--- /dev/null
+++ b/vistrails/gui/application_server.py
@@ -0,0 +1,2229 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This is the application for vistrails when running as a server. """
+import Queue
+import base64
+import hashlib
+import inspect
+import sys
+import logging
+import logging.handlers
+import os
+import re
+import shutil
+import subprocess
+import tempfile
+import time
+import traceback
+import urllib
+import xmlrpclib
+import ConfigParser
+
+from PyQt4 import QtGui, QtCore
+import SocketServer
+from SimpleXMLRPCServer import SimpleXMLRPCServer
+from datetime import date, datetime
+from time import strptime
+
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core.application import VistrailsApplicationInterface
+import vistrails.gui.theme
+import vistrails.core.application
+from vistrails.gui import qt
+from vistrails.core.db.locator import DBLocator, ZIPFileLocator, FileLocator
+from vistrails.core.db import io
+import vistrails.core.db.action
+
+from vistrails.core.utils import InstanceObject
+from vistrails.core.vistrail.vistrail import Vistrail
+from vistrails.core import command_line
+from vistrails.core import system
+from vistrails.core.modules.module_registry import get_module_registry as module_registry
+from vistrails.core import interpreter
+from vistrails.core.packagemanager import get_package_manager
+import vistrails.core.system
+import vistrails.db.services.io
+import gc
+
+import vistrails.core.requirements
+import vistrails.core.console_mode
+
+from vistrails.db.versions import currentVersion
+
+ElementTree = vistrails.core.system.get_elementtree_library()
+
+
+
+################################################################################
+class StoppableXMLRPCServer(SimpleXMLRPCServer):
+ """This class allows a server to be stopped by a external request"""
+ #accessList contains the list of ip addresses and hostnames that can send
+ #request to this server. Change this according to your server
+ global accessList
+
+ allow_reuse_address = True
+ def __init__(self, addr, logger):
+ self.logger = logger
+ SimpleXMLRPCServer.__init__(self, addr)
+
+ def serve_forever(self):
+ self.stop = False
+ while not self.stop:
+ self.handle_request()
+
+ def verify_request(self, request, client_address):
+ if client_address[0] in accessList:
+ self.logger.info("Request from %s allowed!"%str(client_address))
+ return 1
+ else:
+ self.logger.info("Request from %s denied!"%str(client_address))
+ return 0
+
+################################################################################
+
+class ThreadedXMLRPCServer(SocketServer.ThreadingMixIn,
+ StoppableXMLRPCServer): pass
+"""This is a multithreaded version of the RPC Server. For each request, the
+ server will spawn a thread. Notice that these threads cannot use any Qt
+ related objects because they won't be in the main thread."""
+################################################################################
+
+class RequestHandler(object):
+ """This class will handle all the requests sent to the server.
+ Add new methods here and they will be exposed through the XML-RPC interface
+ """
+ def __init__(self, logger, instances):
+ self.server_logger = logger
+ self.instances = instances
+ self.proxies_queue = None
+ self.instantiate_proxies()
+
+ #proxies
+ def instantiate_proxies(self):
+ """instantiate_proxies() -> None
+ If this server started other instances of VisTrails, this will create
+ the client proxies to connect to them.
+ """
+ if len(self.instances) > 0:
+ self.proxies_queue = Queue.Queue()
+ for uri in self.instances:
+ try:
+ proxy = xmlrpclib.ServerProxy(uri)
+ self.proxies_queue.put(proxy)
+ self.server_logger.info("Instantiated client for %s" % uri)
+ except Exception, e:
+ self.server_logger.error("Error when instantiating proxy %s" % uri)
+ self.server_logger.error(str(e))
+ #utils
+ def memory_usage(self):
+ """memory_usage() -> dict
+ Memory usage of the current process in kilobytes. We plan to
+ use this to clear cache on demand later.
+ I believe this works on Linux only.
+ """
+ status = None
+ result = {'peak': 0, 'rss': 0}
+ try:
+ # This will only work on systems with a /proc file system
+ # (like Linux).
+ status = open('/proc/self/status')
+ for line in status:
+ parts = line.split()
+ key = parts[0][2:-1].lower()
+ if key in result:
+ result[key] = int(parts[1])
+ finally:
+ if status is not None:
+ status.close()
+ return result
+
+ def path_exists_and_not_empty(self, path):
+ """path_exists_and_not_empty(path:str) -> boolean
+ Returns True if given path exists and it's not empty, otherwise returns
+ False.
+ """
+ if os.path.exists(path):
+ n = 0
+ for root, dirs, file_names in os.walk(path):
+ n += len(file_names)
+ if n > 0:
+ return True
+ return False
+
+ def try_ping(self):
+ return 1
+
+ #crowdlabs
+ def get_wf_modules(self, host, port, db_name, vt_id, version):
+ """get_wf_modules(host:str, port:int, db_name:str, vt_id:int,
+ version:int) -> (return_status, list of dict)
+ Returns a list of information about the modules used in a workflow
+ in a list of dictionaries. The dictionary has the following keys:
+ name, package, documentation.
+ """
+ self.server_logger.info("Request: get_wf_modules(%s,%s,%s,%s,%s)" % \
+ (host, port, db_name, vt_id, version))
+ try:
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+
+ v = locator.load().vistrail
+ p = v.getPipeline(long(version))
+
+ if p:
+ result = []
+ for module in p.module_list:
+ descriptor = module_registry().get_descriptor_by_name(
+ module.package,
+ module.name,
+ module.namespace)
+ documentation = descriptor.module_documentation(module)
+ result.append({'name':module.name,
+ 'package':module.package,
+ 'documentation':documentation})
+ return (result, 1)
+ else:
+ result = "Pipeline was not materialized"
+ self.server_logger.error(str(result))
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ result = str(e)
+ self.server_logger.error(result)
+ self.server_logger.error(traceback.format_exc())
+ return (result, 0)
+
+ def get_packages(self):
+ """get_packages()-> dict
+ This returns a dictionary with all the packages available in the
+ VisTrails registry.
+ The keys are the package identifier and for each identifier there's a
+ dictionary with modules and description.
+ """
+ self.server_logger.info("Request: get_packages()")
+ try:
+ package_dic = {}
+
+ for package in module_registry().package_list:
+ package_dic[package.identifier] = {}
+ package_dic[package.identifier]['modules'] = []
+ for module in package._db_module_descriptors:
+ documentation = inspect.getdoc(module.module)
+ if documentation:
+ documentation = re.sub('^ *\n', '', documentation.rstrip())
+ else:
+ documentation = "(No documentation available)"
+ package_dic[package.identifier]['modules'].append({'name':module.name,
+ 'package':module.package,
+ 'documentation':documentation})
+ package_dic[package.identifier]['description'] = \
+ package.description if package.description else "(No description available)"
+ return (package_dic, 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def get_server_packages(self, codepath=None, status=None):
+ """get_server_packages()-> dict
+ This returns a dictionary with all the packages to vistrails with status indicating wether it is loaded.
+ It is also possible to enable/disable a package by passing a package codepath and the desired status on/off
+ The keys are the package identifier.
+ """
+ self.server_logger.info("Request: get_server_packages()")
+
+ messages = []
+ if self.proxies_queue is not None:
+ # collect all proxies:
+ proxies = []
+ while len(proxies) < len(self.instances):
+ self.server_logger.info("Proxies: %s Instances: %s" % (len(proxies), len(self.instances)))
+ if self.proxies_queue.empty():
+ for p in proxies:
+ self.proxies_queue.put(p)
+ return [[[],
+ "Not all vistrail instances are free, please try again."], 1]
+ proxies.append(self.proxies_queue.get())
+ for proxy in proxies:
+ try:
+ if codepath and status is not None:
+ result, s = proxy.get_server_packages(codepath, status)
+ else:
+ result, s = proxy.get_server_packages()
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ if s == 0:
+ messages.append('An error occurred: %s' % result)
+ else:
+ messages.append(result[1])
+ self.proxies_queue.put(proxy)
+
+ try:
+ pkg_manager = get_package_manager()
+ message = ''
+ if codepath and status is not None:
+ if int(status):
+ # Try to enable package
+ try:
+ pkg_manager.late_enable_package(codepath)
+ message = "Successfully enabled package '%s'" % codepath
+ except Exception, e:
+ message = "Could not enable package '%s': %s %s" % \
+ (codepath, str(e), traceback.format_exc())
+ else:
+ # Try to disable package
+ if codepath in ["basic_modules", 'abstraction']:
+ message = "Package '%s' cannot be disabled" % codepath
+ elif not pkg_manager.can_be_disabled(
+ pkg_manager.get_package_by_codepath(codepath).identifier):
+ message = "Package '%s' cannot be disabled because other packages depends on it." % codepath
+ else:
+ try:
+ pkg_manager.remove_package(codepath)
+ message = "Successfully disabled package '%s'" % codepath
+ except Exception, e:
+ message = "Could not disable package '%s': %s %s" % \
+ (codepath, str(e), traceback.format_exc())
+ packages = []
+ enabled_pkgs = sorted(pkg_manager.enabled_package_list())
+ enabled_pkg_dict = dict([(pkg.codepath, pkg) for
+ pkg in enabled_pkgs])
+ for pkg in sorted([pkg.codepath for pkg in enabled_pkgs]):
+ packages.append([pkg, True])
+ available_pkg_names = [pkg for pkg in
+ sorted(pkg_manager.available_package_names_list())
+ if pkg not in enabled_pkg_dict]
+ for pkg in available_pkg_names:
+ packages.append([pkg, False])
+
+ if codepath and messages:
+ # we are the main instance so assemble messages
+ message = ''.join(["Main instance: %s" % message] + \
+ ["<br/>Instance %s: %s" % (i+1, m) for i, m in
+ zip(xrange(len(messages)), messages)])
+ return [[packages, message], 1]
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def add_vt_to_db(self, host, port, db_name, user, vt_filepath, filename,
+ repository_vt_id, repository_creator, is_local=True):
+ """add_vt_to_db(host:str, port:int, db_name:str, user:str,
+ vt_filepath:str(or datastream), filename:str,
+ repository_vt_id:int, repository_creator:str) ->
+ (return_status, int)
+ This will add a vistrail in vt_filepath to the the database. If running
+ on a remote machine, vt_filepath will contain vt file data stream.
+ Before adding it it will annotate the vistrail with the
+ repository_vt_id and repository_creator.
+
+ """
+ try:
+ if is_local:
+ locator = ZIPFileLocator(vt_filepath).load()
+ else:
+ # vt_filepath contains vt file datastream
+ # write to tmp file, read into FileLocator
+ # TODO: can we just read the file stream directly in?
+ (fd, fname) = tempfile.mkstemp(prefix='vt_tmp',
+ suffix='.vt')
+ os.close(fd)
+ try:
+ vt_file = open(fname, "wb")
+ vt_file.write(vt_filepath.data)
+ vt_file.close()
+ locator = ZIPFileLocator(fname).load()
+ finally:
+ os.unlink(fname)
+
+ # set some crowdlabs id info
+ if repository_vt_id != -1:
+ vistrail = locator.vistrail
+ vistrail.set_annotation('repository_vt_id', repository_vt_id)
+ vistrail.set_annotation('repository_creator', repository_creator)
+
+ db_locator = DBLocator(host=host, port=int(port), database=db_name,
+ name=filename, user=db_write_user, passwd=db_write_pass)
+ db_locator.save_as(locator)
+ return (db_locator.obj_id, 1)
+
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def merge_vt(self, host, port, db_name, user, new_vt_filepath,
+ old_db_vt_id, is_local=True):
+ """
+ Merge new_vt (new_vt_filepath) with current vt (old_db_vt_id)
+
+ new_vt_filepath is either filepath to vt, or datastream of vt,
+ depending on if the server is on a remote machine
+ """
+ self.server_logger.info("Request: merge_vt(%s,%s,%s,%s,%s,%s,%s)" % \
+ (host, port, db_name, user, new_vt_filepath,
+ old_db_vt_id, is_local))
+ try:
+ tmp_file = None
+ if is_local:
+ new_locator = ZIPFileLocator(new_vt_filepath)
+ else:
+ # vt_filepath contains vt file datastream
+ # write to tmp file, read into FileLocator
+ # TODO: can we just read the file stream directly in?
+ (fd, tmp_file) = tempfile.mkstemp(prefix='vt_tmp',
+ suffix='.vt')
+ os.close(fd)
+ vt_file = open(tmp_file, "wb")
+ vt_file.write(new_vt_filepath.data)
+ vt_file.close()
+ new_locator = ZIPFileLocator(tmp_file)
+
+ new_bundle = new_locator.load()
+ new_locator.save(new_bundle)
+ old_db_locator = DBLocator(host=host, port=int(port), database=db_name,
+ obj_id=int(old_db_vt_id), user=db_write_user, passwd=db_write_pass)
+ old_db_bundle = old_db_locator.load()
+ vistrails.db.services.vistrail.merge(old_db_bundle, new_bundle, 'vistrails')
+ old_db_locator.save(old_db_bundle)
+ new_locator.save(old_db_bundle)
+ if tmp_file is not None:
+ os.unlink(tmp_file)
+ return (1, 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def remove_vt_from_db(self, host, port, db_name, user, vt_id):
+ """remove_vt_from_db(host:str, port:int, db_name:str, user:str,
+ vt_id:int) -> (return_status, 0 or 1)
+ Remove a vistrail from the repository
+ """
+ config = {}
+ config['host'] = host
+ config['port'] = int(port)
+ config['db'] = db_name
+ config['user'] = db_write_user
+ config['passwd'] = db_write_pass
+ try:
+ conn = vistrails.db.services.io.open_db_connection(config)
+ vistrails.db.services.io.delete_entity_from_db(conn,'vistrail', vt_id)
+ vistrails.db.services.io.close_db_connection(conn)
+ return (1, 1)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ if conn:
+ vistrails.db.services.io.close_db_connection(conn)
+ return (str(e), 0)
+
+ def get_runnable_workflows(self, host, port, db_name, vt_id):
+ try:
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+ (vistrail, _, _, _) = io.load_vistrail(locator)
+
+ # get server packages
+ local_packages = [x.identifier for x in \
+ module_registry().package_list]
+
+ runnable_workflows = []
+ py_source_workflows = []
+ local_data_modules = ['File', 'FileSink', 'Path']
+
+ # find runnable workflows
+ for version_id, version_tag in vistrail.get_tagMap().iteritems():
+ pipeline = vistrail.getPipeline(version_id)
+ workflow_packages = set()
+ on_repo = True
+ has_python_source = False
+ for module in pipeline.module_list:
+ # count modules that use data unavailable to web repo
+ if module.name[-6:] == 'Reader' or \
+ module.name in local_data_modules:
+ has_accessible_data = False
+ for edge in pipeline.graph.edges_to(module.id):
+ # TODO check for RepoSync checksum param
+ if pipeline.modules[edge[0]].name in \
+ ['HTTPFile', 'RepoSync']:
+ has_accessible_data = True
+
+ if not has_accessible_data:
+ on_repo = False
+
+ elif module.name == "PythonSource":
+ has_python_source = True
+
+ # get packages used in tagged versions of this VisTrail
+ workflow_packages.add(module.package)
+
+ # ensure workflow doesn't use unsupported packages
+ if not filter(lambda p: p not in local_packages,
+ workflow_packages):
+ if has_python_source and on_repo and \
+ version_id not in py_source_workflows:
+ py_source_workflows.append(version_id)
+
+ elif not has_python_source and on_repo and \
+ version_id not in runnable_workflows:
+ runnable_workflows.append(version_id)
+
+ return ((runnable_workflows, py_source_workflows), 1)
+
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ return (str(e), 0)
+
+ #medleys
+
+ def executeMedley(self, xml_medley, extra_info=None):
+ self.server_logger.info("executeMedley request received")
+ try:
+ self.server_logger.info(xml_medley)
+ xml_string = xml_medley.replace('\\"','"')
+ root = ElementTree.fromstring(xml_string)
+ try:
+ medley = MedleySimpleGUI.from_xml(root)
+ except:
+ #even if this error occurred there's still a chance of
+ # recovering from it... (the server can find cached images)
+ self.server_logger.error("couldn't instantiate medley")
+
+ self.server_logger.debug("%s medley: %s"%(medley._type, medley._name))
+ result = ""
+ subdir = hashlib.sha224(xml_string).hexdigest()
+ path_to_images = \
+ os.path.join(media_dir, 'medleys/images', subdir)
+ if (not self.path_exists_and_not_empty(path_to_images) and
+ self.proxies_queue is not None):
+ #this server can send requests to other instances
+ proxy = self.proxies_queue.get()
+ try:
+ self.server_logger.info("Sending request to %s" % proxy)
+ if extra_info is not None:
+ result = proxy.executeMedley(xml_medley, extra_info)
+ else:
+ result = proxy.executeMedley(xml_medley)
+ self.proxies_queue.put(proxy)
+ self.server_logger.info("returning %s"% result)
+ return result
+ except Exception, e:
+ self.server_logger.error(str(e))
+ return (str(e), 0)
+
+ if extra_info is None:
+ extra_info = {}
+
+ if extra_info.has_key('pathDumpCells'):
+ if extra_info['pathDumpCells']:
+ extra_path = extra_info['pathDumpCells']
+ else:
+ extra_info['pathDumpCells'] = path_to_images
+
+ if not self.path_exists_and_not_empty(extra_info['pathDumpCells']):
+ if not os.path.exists(extra_info['pathDumpCells']):
+ os.mkdir(extra_info['pathDumpCells'])
+
+ if medley._type == 'vistrail':
+ locator = DBLocator(host=db_host,
+ port=3306,
+ database='vistrails',
+ user=db_write_user,
+ passwd=db_write_pass,
+ obj_id=medley._vtid,
+ obj_type=None,
+ connection_id=None)
+
+ workflow = medley._version
+ sequence = False
+ for (k,v) in medley._alias_list.iteritems():
+ if v._component._seq == True:
+ sequence = True
+ val = XMLObject.convert_from_str(v._component._minVal,
+ v._component._spec)
+ maxval = XMLObject.convert_from_str(v._component._maxVal,
+ v._component._spec)
+ #making sure the filenames are generated in order
+ mask = '%s'
+ if isinstance(maxval, (int, long)):
+ mask = '%0' + str(len(v._component._maxVal)) + 'd'
+
+ while val <= maxval:
+ s_alias = "%s=%s$&$" % (k,val)
+ for (k2,v2) in medley._alias_list.iteritems():
+ if k2 != k and v2._component._val != '':
+ s_alias += "%s=%s$&$" % (k2,v2._component._val)
+ if s_alias != '':
+ s_alias = s_alias[:-3]
+ self.server_logger.info("Aliases: %s" % s_alias)
+ try:
+ gc.collect()
+ results = \
+ vistrails.core.console_mode.run_and_get_results( \
+ [(locator,int(workflow))],
+ s_alias,
+ extra_info=extra_info)
+ self.server_logger.info("Memory usage: %s"% self.memory_usage())
+ interpreter.cached.CachedInterpreter.flush()
+ except Exception, e:
+ self.server_logger.error(str(e))
+ return (str(e), 0)
+ ok = True
+ for r in results:
+ (objs, errors, _) = (r.objects, r.errors, r.executed)
+ for e in errors.itervalues():
+ self.server_logger.error("Module failed: %s"% str(e))
+ for i in objs.iterkeys():
+ if errors.has_key(long(i)):
+ ok = False
+ result += str(errors[i])
+ if ok:
+ self.server_logger.info("renaming files")
+ for root, dirs, file_names in os.walk(extra_info['pathDumpCells']):
+ break
+ s = []
+ for f in file_names:
+ if f.lower().endswith(".png"):
+ fmask = "%s_"+mask+"%s"
+ os.renames(os.path.join(root,f),
+ os.path.join(root,"%s" % f[:-4],
+ fmask% (f[:-4],val,f[-4:])))
+ if val < maxval:
+ val += XMLObject.convert_from_str(v._component._stepSize,
+ v._component._spec)
+ if val > maxval:
+ val = maxval
+ else:
+ break
+
+ if not sequence:
+ s_alias = ''
+ for (k,v) in medley._alias_list.iteritems():
+ if v._component._val != '':
+ s_alias += "%s=%s$&$" % (k,v._component._val)
+ if s_alias != '':
+ s_alias = s_alias[:-3]
+ self.server_logger.info("Not sequence aliases: %s"% s_alias)
+ try:
+ results = \
+ vistrails.core.console_mode.run_and_get_results( \
+ [(locator,int(workflow))],
+ s_alias,
+ extra_info=extra_info)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ return (str(e), 0)
+ ok = True
+ for r in results:
+ (objs, errors, _) = (r.objects, r.errors, r.executed)
+ for e in errors.itervalues():
+ self.server_logger.error(str(e))
+ for i in objs.iterkeys():
+ if errors.has_key(long(i)):
+ ok = False
+ result += str(errors[i])
+
+ self.server_logger.info( "success? %s"% ok)
+
+ elif medley._type == 'visit':
+ cur_dir = os.getcwd()
+ os.chdir(self.temp_configuration.spreadsheetDumpCells)
+ if medley._id == 6:
+ session_file = 'crotamine.session'
+ elif medley._id == 7:
+ session_file = '1NTS.session'
+ else:
+ session_file = 'head.session'
+ session_file = '/server/code/visit/saved_sessions/' + session_file
+ self.server_logger.info("session_file: %s" % session_file)
+ ok = os.system('/server/code/visit/vistrails_plugin/visit/render-session.sh ' + \
+ session_file) == 0
+ self.server_logger.info( "success? %s" % ok)
+ os.chdir(cur_dir)
+ else:
+ self.server_logger.info("Found cached images.")
+ ok = True
+
+ if ok:
+ s = []
+ self.server_logger.info("images path: %s"%extra_info['pathDumpCells'])
+ for root, dirs, file_names in os.walk(extra_info['pathDumpCells']):
+ sub = []
+ #n = len(file_names)
+ #print "%s file(s) generated" % n
+ file_names.sort()
+ for f in file_names:
+ sub.append(os.path.join(root[root.find(subdir):],
+ f))
+ s.append(";".join(sub))
+ result = ":::".join(s)
+ # FIXME: copy images to extra_path
+ self.server_logger.info("returning %s" % result)
+ return (result, 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ return (str(e), 0)
+
+ #vistrails
+ def run_from_db(self, host, port, db_name, vt_id, path_to_figures,
+ version=None, pdf=False, vt_tag='', build_always=False,
+ parameters='', is_local=True):
+ self.server_logger.info("Request: run_vistrail_from_db(%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)" % \
+ (host, port, db_name, vt_id,
+ path_to_figures, version, pdf,
+ vt_tag, build_always, parameters, is_local))
+
+ self.server_logger.info("path_exists_and_not_empty? %s" % self.path_exists_and_not_empty(path_to_figures))
+ self.server_logger.info("build_always? %s" % build_always)
+ self.server_logger.info(str(self.proxies_queue))
+
+ if not is_local:
+ # use same hashing as on crowdlabs webserver
+ dest_version = "%s_%s_%d_%d_%d" % (host, db_name, int(port), int(vt_id), int(version))
+ dest_version = hashlib.sha1(dest_version).hexdigest()
+ path_to_figures = os.path.join(media_dir, "wf_execution", dest_version)
+
+ if ((not self.path_exists_and_not_empty(path_to_figures) or
+ build_always) and self.proxies_queue is not None):
+ self.server_logger.info("will forward request")
+ #this server can send requests to other instances
+ proxy = self.proxies_queue.get()
+ try:
+ self.server_logger.info("Sending request to %s" % proxy)
+ result = proxy.run_from_db(host, port, db_name, vt_id,
+ path_to_figures, version, pdf, vt_tag,
+ build_always, parameters, is_local)
+ self.proxies_queue.put(proxy)
+ self.server_logger.info("returning %s" % result)
+ return result
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ return (str(e), 0)
+
+ extra_info = {}
+ extra_info['pathDumpCells'] = path_to_figures
+ self.server_logger.debug(path_to_figures)
+ extra_info['pdf'] = pdf
+ self.server_logger.debug("pdf: %s" % pdf)
+ # execute workflow
+ ok = True
+ if (not self.path_exists_and_not_empty(extra_info['pathDumpCells'])
+ or build_always):
+ if os.path.exists(extra_info['pathDumpCells']):
+ shutil.rmtree(extra_info['pathDumpCells'])
+ os.mkdir(extra_info['pathDumpCells'])
+
+ result = ''
+ if vt_tag !='':
+ version = vt_tag;
+ try:
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_write_user,
+ passwd=db_write_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+ results = []
+ try:
+ results = \
+ vistrails.core.console_mode.run_and_get_results([(locator,
+ int(version))],
+ parameters,
+ update_vistrail=True,
+ extra_info=extra_info,
+ reason="Server Pipeline Execution")
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+ ok = True
+
+ for r in results:
+ (objs, errors, _) = (r.objects, r.errors, r.executed)
+
+ for i in objs.iterkeys():
+ if errors.has_key(i):
+ ok = False
+ result += str(errors[i])
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ if ok:
+ if is_local:
+ return (1, 1)
+ else:
+ # TODO pdf version
+ images = [im for im in os.listdir(path_to_figures) if im[-3:] == "png"]
+ results = {}
+ for image in images:
+ handler = open(os.path.join(path_to_figures, image), "rb")
+ image_data = handler.read()
+ handler.close()
+ results[image] = xmlrpclib.Binary(image_data)
+ return (results, 1)
+ else:
+ self.server_logger.error(result)
+ return (result, 0)
+
+ def get_package_list(self):
+ """ get_package_list() -> str
+ Returns a list of supported packages identifiers delimited by || """
+ self.server_logger.info("Request: get_package_list()")
+ try:
+ packages = [x.identifier for x in module_registry().package_list]
+ return (packages, 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def get_wf_datasets(self, host, port, db_name, vt_id, version):
+ self.server_logger.info("Request: get_wf_datasets(%s,%s,%s,%s,%s)" % \
+ (host, port, db_name, vt_id, version))
+ try:
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+
+ v = locator.load().vistrail
+ p = v.getPipeline(long(version))
+
+ if p:
+ result = []
+ for module in p.module_list:
+ if module.name == "RepoSync":
+ for function in module.functions:
+ if function.name == 'checksum':
+ result.append(function.parameters[0].value())
+ return (result, 1)
+ else:
+ result = "Pipeline was not materialized"
+ self.server_logger.error(result)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ result = str(e)
+ self.server_logger.error(result)
+ self.server_logger.error(traceback.format_exc())
+ return (result, 0)
+
+ def get_tag_version(self, host, port, db_name, vt_id, vt_tag):
+ self.server_logger.info("Request: get_tag_version(%s,%s,%s,%s,%s)" % \
+ (host, port, db_name, vt_id, vt_tag))
+ version = -1
+ try:
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+
+ (v, _ , _, _) = io.load_vistrail(locator)
+ if v.has_tag_str(vt_tag):
+ version = v.get_tag_str(vt_tag).action_id
+ self.server_logger.info("Answer: %s" % version)
+ return (version, 1)
+
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+
+ def get_vt_xml(self, host, port, db_name, vt_id):
+ self.server_logger.info("Request: get_vt_xml(%s,%s,%s,%s)" % \
+ (host, port, db_name, vt_id))
+ try:
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+
+ (v, _ , _, _) = io.load_vistrail(locator)
+ result = io.serialize(v)
+ return (result, 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def get_wf_xml(self, host, port, db_name, vt_id, version):
+ self.server_logger.info("Request: get_wf_xml(%s,%s,%s,%s,%s)" % \
+ (host, port, db_name, vt_id, version))
+ try:
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+
+ (v, _ , _, _) = io.load_vistrail(locator)
+ p = v.getPipeline(long(version))
+ if p:
+ result = io.serialize(p)
+ self.server_logger.info("success")
+ return (result, 1)
+ else:
+ result = "Pipeline was not materialized"
+ self.server_logger.info(result)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ result = str(e)
+ self.server_logger.error(result)
+ self.server_logger.error(traceback.format_exc())
+ return (result, 0)
+
+ def get_wf_graph_pdf(self, host, port, db_name, vt_id, version, is_local=True):
+ """get_wf_graph_pdf(host:str, port:int, db_name:str, vt_id:int,
+ version:int) -> str
+ Returns the relative url to the generated PDF
+ """
+ self.server_logger.info("get_wf_graph_pdf(%s,%s,%s,%s,%s) request received" % \
+ (host, port, db_name, vt_id, version))
+ try:
+ vt_id = long(vt_id)
+ version = long(version)
+ subdir = 'workflows'
+ filepath = os.path.join(media_dir, 'graphs', subdir)
+ base_fname = "graph_%s_%s.pdf" % (vt_id, version)
+ filename = os.path.join(filepath,base_fname)
+ if ((not os.path.exists(filepath) or
+ os.path.exists(filepath) and not os.path.exists(filename))
+ and self.proxies_queue is not None):
+ #this server can send requests to other instances
+ proxy = self.proxies_queue.get()
+ try:
+ result = proxy.get_wf_graph_pdf(host,port,db_name, vt_id, version, is_local)
+ self.proxies_queue.put(proxy)
+ self.server_logger.info("get_wf_graph_pdf returning %s"% result)
+ return result
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ if not os.path.exists(filepath):
+ os.mkdir(filepath)
+
+ if not os.path.exists(filename):
+ from vistrails.gui.vistrail_controller import VistrailController
+
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+
+ (v, abstractions , thumbnails, mashups) = io.load_vistrail(locator)
+ controller = VistrailController(v, locator, abstractions,
+ thumbnails, mashups)
+ controller.change_selected_version(version)
+ controller.updatePipelineScene()
+ controller.current_pipeline_scene.saveToPDF(filename)
+ else:
+ self.server_logger.info("found cached pdf: %s" % filename)
+
+ if is_local:
+ return (os.path.join(subdir,base_fname), 1)
+ else:
+ f = open(filename, 'rb')
+ contents = f.read()
+ f.close()
+ return (xmlrpclib.Binary(contents), 1)
+
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error("Error when saving pdf: %s" % str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def get_wf_graph_png(self, host, port, db_name, vt_id, version, is_local=True):
+ """get_wf_graph_png(host:str, port:int, db_name:str, vt_id:int,
+ version:int) -> str
+ Returns the relative url to the generated image
+ """
+ self.server_logger.info("get_wf_graph_png(%s,%s,%s,%s,%s) request received" % \
+ (host, port, db_name, vt_id, version))
+ try:
+ vt_id = long(vt_id)
+ version = long(version)
+ subdir = 'workflows'
+ filepath = os.path.join(media_dir, 'graphs', subdir)
+ base_fname = "graph_%s_%s.png" % (vt_id, version)
+ filename = os.path.join(filepath,base_fname)
+ if ((not os.path.exists(filepath) or
+ os.path.exists(filepath) and not os.path.exists(filename))
+ and self.proxies_queue is not None):
+ #this server can send requests to other instances
+ proxy = self.proxies_queue.get()
+ try:
+ self.server_logger.info("Sending request to %s" % proxy)
+ result = proxy.get_wf_graph_png(host, port, db_name, vt_id, version, is_local)
+ self.proxies_queue.put(proxy)
+ self.server_logger.info("returning %s" % result)
+ return result
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+ #if it gets here, this means that we will execute on this instance
+ if not os.path.exists(filepath):
+ os.mkdir(filepath)
+
+ if not os.path.exists(filename):
+ from vistrails.gui.vistrail_controller import VistrailController
+
+ locator = DBLocator(host=host,
+ port=port,
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+ (v, abstractions , thumbnails, mashups) = io.load_vistrail(locator)
+ controller = VistrailController(v, locator, abstractions,
+ thumbnails, mashups)
+ controller.change_selected_version(version)
+ controller.updatePipelineScene()
+ controller.current_pipeline_scene.saveToPNG(filename)
+ else:
+ self.server_logger.info("found cached image: %s" % filename)
+ if is_local:
+ return (os.path.join(subdir,base_fname), 1)
+ else:
+ f = open(filename, 'rb')
+ contents = f.read()
+ f.close()
+ return (xmlrpclib.Binary(contents), 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error("Error when saving png %s" % str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def _is_image_stale(self, filename, host, port, db_name, vt_id):
+ statinfo = os.stat(filename)
+ image_time = datetime.fromtimestamp(statinfo.st_mtime)
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+ vt_mod_time = locator.get_db_modification_time()
+ self.server_logger.info("image time: %s, vt time: %s"%(image_time,
+ vt_mod_time))
+ if image_time < vt_mod_time:
+ return True
+ else:
+ return False
+
+ def get_vt_graph_png(self, host, port, db_name, vt_id, is_local=True):
+ """get_vt_graph_png(host:str, port: str, db_name: str, vt_id:str) -> str
+ Returns the relative url of the generated image
+ """
+
+ self.server_logger.info("get_vt_graph_png(%s, %s, %s, %s)" % (host, port, db_name, vt_id))
+ try:
+ vt_id = long(vt_id)
+ subdir = 'vistrails'
+ filepath = os.path.join(media_dir, 'graphs', subdir)
+ base_fname = "graph_%s.png" % (vt_id)
+ filename = os.path.join(filepath,base_fname)
+ if ((not os.path.exists(filepath) or
+ (os.path.exists(filepath) and not os.path.exists(filename)) or
+ self._is_image_stale(filename, host, port, db_name, vt_id)) and
+ self.proxies_queue is not None):
+ #this server can send requests to other instances
+ proxy = self.proxies_queue.get()
+ try:
+ self.server_logger.info("Sending request to %s" % proxy)
+ result = proxy.get_vt_graph_png(host, port, db_name, vt_id, is_local)
+ self.proxies_queue.put(proxy)
+ self.server_logger.info("returning %s" % result)
+ return result
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ #if it gets here, this means that we will execute on this instance
+ if (not os.path.exists(filepath) or
+ (os.path.exists(filepath) and not os.path.exists(filename)) or
+ self._is_image_stale(filename, host, port, db_name, vt_id)):
+
+ from vistrails.gui.vistrail_controller import VistrailController
+
+ if os.path.exists(filepath):
+ shutil.rmtree(filepath)
+
+ os.mkdir(filepath)
+
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+ (v, abstractions , thumbnails, mashups) = io.load_vistrail(locator)
+ controller = VistrailController(v, locator, abstractions,
+ thumbnails, mashups)
+ from vistrails.gui.version_view import QVersionTreeView
+ version_view = QVersionTreeView()
+ version_view.scene().setupScene(controller)
+ version_view.scene().saveToPNG(filename)
+ del version_view
+ else:
+ self.server_logger.info("Found cached image: %s" % filename)
+ if is_local:
+ return (os.path.join(subdir,base_fname), 1)
+ else:
+ f = open(filename, 'rb')
+ contents = f.read()
+ f.close()
+ return (xmlrpclib.Binary(contents), 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error("Error when saving png: %s" % str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def get_vt_graph_pdf(self, host, port, db_name, vt_id, is_local=True):
+ """get_vt_graph_pdf(host:str, port: str, db_name: str, vt_id:str) -> str
+ Returns the relative url of the generated image
+ """
+
+ self.server_logger.info("get_vt_graph_pdf(%s, %s, %s, %s)" % (host, port, db_name, vt_id))
+ try:
+ vt_id = long(vt_id)
+ subdir = 'vistrails'
+ filepath = os.path.join(media_dir, 'graphs', subdir)
+ base_fname = "graph_%s.pdf" % (vt_id)
+ filename = os.path.join(filepath,base_fname)
+ if ((not os.path.exists(filepath) or
+ (os.path.exists(filepath) and not os.path.exists(filename)) or
+ self._is_image_stale(filename, host, port, db_name, vt_id)) and
+ self.proxies_queue is not None):
+ #this server can send requests to other instances
+ proxy = self.proxies_queue.get()
+ try:
+ self.server_logger.info("Sending request to %s" % proxy)
+ result = proxy.get_vt_graph_pdf(host, port, db_name, vt_id, is_local)
+ self.proxies_queue.put(proxy)
+ self.server_logger.info("returning %s" % result)
+ return result
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+
+ #if it gets here, this means that we will execute on this instance
+ if (not os.path.exists(filepath) or
+ (os.path.exists(filepath) and not os.path.exists(filename)) or
+ self._is_image_stale(filename, host, port, db_name, vt_id)):
+
+ from vistrails.gui.vistrail_controller import VistrailController
+
+ if os.path.exists(filepath):
+ shutil.rmtree(filepath)
+
+ os.mkdir(filepath)
+
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+ (v, abstractions , thumbnails, mashups) = io.load_vistrail(locator)
+ controller = VistrailController(v, locator, abstractions,
+ thumbnails, mashups)
+ from vistrails.gui.version_view import QVersionTreeView
+ version_view = QVersionTreeView()
+ version_view.scene().setupScene(controller)
+ version_view.scene().saveToPDF(filename)
+ del version_view
+ else:
+ self.server_logger.info("Found cached pdf: %s" % filename)
+ if is_local:
+ return (os.path.join(subdir,base_fname), 1)
+ else:
+ f = open(filename, 'rb')
+ contents = f.read()
+ f.close()
+ return (xmlrpclib.Binary(contents), 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error("Error when saving pdf: %s" % str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def get_vt_zip(self, host, port, db_name, vt_id):
+ """get_vt_zip(host:str, port: str, db_name: str, vt_id:str) -> str
+ Returns a .vt file encoded as base64 string
+ """
+
+ self.server_logger.info("Request: get_vt_zip(%s,%s,%s,%s)" % \
+ (host, port, db_name, vt_id))
+ try:
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+ save_bundle = locator.load()
+ #annotate the vistrail
+ save_bundle.vistrail.update_checkout_version('vistrails')
+ #create temporary file
+ (fd, name) = tempfile.mkstemp(prefix='vt_tmp',
+ suffix='.vt')
+ os.close(fd)
+ try:
+ fileLocator = FileLocator(name)
+ fileLocator.save(save_bundle)
+ contents = open(name).read()
+ result = base64.b64encode(contents)
+ finally:
+ os.unlink(name)
+ return (result, 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def get_wf_vt_zip(self, host, port, db_name, vt_id, version):
+ """get_wf_vt_zip(host:str, port:str, db_name:str, vt_id:str,
+ version:str) -> str
+ Returns a vt file containing the single workflow defined by version
+ encoded as base64 string
+
+ """
+ self.server_logger.info("Request: get_wf_vt_zip(%s,%s,%s,%s,%s)" % \
+ (host, port, db_name, vt_id, version))
+ try:
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+
+ (v, _ , _, _) = io.load_vistrail(locator)
+ p = v.getPipeline(long(version))
+ if p:
+ vistrail = Vistrail()
+ action_list = []
+ for module in p.module_list:
+ action_list.append(('add', module))
+ for connection in p.connection_list:
+ action_list.append(('add', connection))
+ action = vistrails.core.db.action.create_action(action_list)
+ vistrail.add_action(action, 0L)
+ vistrail.addTag("Imported workflow", action.id)
+ if not vistrail.db_version:
+ vistrail.db_version = currentVersion
+ pipxmlstr = io.serialize(vistrail)
+ result = base64.b64encode(pipxmlstr)
+ return (result, 1)
+ else:
+ result = "Error: Pipeline was not materialized"
+ self.server_logger.info(result)
+ return (result, 0)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.info(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def get_db_vt_list(self, host, port, db_name):
+ self.server_logger.info("Request: get_db_vistrail_list(%s,%s,%s)" % \
+ (host, port, db_name))
+ config = {}
+ config['host'] = host
+ config['port'] = int(port)
+ config['db'] = db_name
+ config['user'] = db_read_user
+ config['passwd'] = db_read_pass
+ try:
+ rows = io.get_db_vistrail_list(config)
+ self.server_logger.info("returning %s" % str(rows))
+ return (rows, 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ return (str(e), 0)
+
+ def get_db_vt_list_xml(self, host, port, db_name):
+ self.server_logger.info("Request: get_db_vistrail_list(%s,%s,%s)" % \
+ (host, port, db_name))
+ config = {}
+ config['host'] = host
+ config['port'] = int(port)
+ config['db'] = db_name
+ config['user'] = db_read_user
+ config['passwd'] = db_read_pass
+ try:
+ rows = io.get_db_vistrail_list(config)
+ result = '<vistrails>'
+ for (id, name, mod_time) in rows:
+ result += '<vistrail id="%s" name="%s" mod_time="%s" />'%(id,name,mod_time)
+ result += '</vistrails>'
+ return (result, 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+ def get_vt_tagged_versions(self, host, port, db_name, vt_id, is_local=True):
+ self.server_logger.info("Request: get_vt_tagged_versions(%s,%s,%s,%s,%s)" % \
+ (host, port, db_name, vt_id, is_local))
+ try:
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+
+ result = []
+ v = locator.load().vistrail
+ for elem, tag in v.get_tagMap().iteritems():
+ action_map = v.actionMap[long(elem)]
+ if v.get_thumbnail(elem):
+ thumbnail_fname = os.path.join(
+ get_vistrails_configuration().thumbs.cacheDirectory,
+ v.get_thumbnail(elem))
+ else:
+ thumbnail_fname = ""
+ if not thumbnail_fname or is_local:
+ result.append({'id': elem, 'name': tag,
+ 'notes': v.get_notes(elem) or '',
+ 'user':action_map.user or '',
+ 'date':action_map.date,
+ 'thumbnail': thumbnail_fname})
+ else:
+ handler = open(thumbnail_fname, "rb")
+ thumbnail_data = handler.read()
+ handler.close()
+ result.append({'id': elem, 'name': tag,
+ 'notes': v.get_notes(elem) or '',
+ 'user':action_map.user or '',
+ 'date':action_map.date,
+ 'thumbnail': xmlrpclib.Binary(thumbnail_data)})
+ return (result, 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ self.server_logger.error(str(e))
+ self.server_logger.error(traceback.format_exc())
+ return (str(e), 0)
+
+################################################################################
+# Some Medley code
+class XMLObject(object):
+ @staticmethod
+ def convert_from_str(value, type):
+ def bool_conv(x):
+ s = str(x).upper()
+ if s == 'TRUE':
+ return True
+ if s == 'FALSE':
+ return False
+
+ if value is not None:
+ if type == 'str':
+ return str(value)
+ elif value.strip() != '':
+ if type == 'long':
+ return long(value)
+ elif type == 'float':
+ return float(value)
+ elif type == 'int':
+ return int(value)
+ elif type == 'bool':
+ return bool_conv(value)
+ elif type == 'date':
+ return date(*strptime(value, '%Y-%m-%d')[0:3])
+ elif type == 'datetime':
+ return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
+ return None
+
+ @staticmethod
+ def convert_to_str(value,type):
+ if value is not None:
+ if type == 'date':
+ return value.isoformat()
+ elif type == 'datetime':
+ return value.strftime('%Y-%m-%d %H:%M:%S')
+ else:
+ return str(value)
+ return ''
+
+################################################################################
+
+class MedleySimpleGUI(XMLObject):
+ def __init__(self, id, name, vtid=None, version=None, alias_list=None,
+ t='vistrail', has_seq=None):
+ self._id = id
+ self._name = name
+ self._version = version
+ self._alias_list = alias_list
+ self._vtid = vtid
+ self._type = t
+
+ if has_seq == None:
+ self._has_seq = False
+ if isinstance(self._alias_list, dict):
+ for v in self._alias_list.itervalues():
+ if v._component._seq == True:
+ self._has_seq = True
+ else:
+ self._has_seq = has_seq
+
+ def to_xml(self, node=None):
+ """to_xml(node: ElementTree.Element) -> ElementTree.Element
+ writes itself to xml
+ """
+
+ if node is None:
+ node = ElementTree.Element('medley_simple_gui')
+
+ #set attributes
+ node.set('id', self.convert_to_str(self._id,'long'))
+ node.set('version', self.convert_to_str(self._version,'long'))
+ node.set('vtid', self.convert_to_str(self._vtid,'long'))
+ node.set('name', self.convert_to_str(self._name,'str'))
+ node.set('type', self.convert_to_str(self._type,'str'))
+ node.set('has_seq', self.convert_to_str(self._has_seq,'bool'))
+ for (k,v) in self._alias_list.iteritems():
+ child_ = ElementTree.SubElement(node, 'alias')
+ v.to_xml(child_)
+ return node
+
+ @staticmethod
+ def from_xml(node):
+ if node.tag != 'medley_simple_gui':
+ print "node.tag != 'medley_simple_gui'"
+ return None
+ #read attributes
+ data = node.get('id', None)
+ id = MedleySimpleGUI.convert_from_str(data, 'long')
+ data = node.get('name', None)
+ name = MedleySimpleGUI.convert_from_str(data, 'str')
+ data = node.get('version', None)
+ version = MedleySimpleGUI.convert_from_str(data, 'long')
+ data = node.get('vtid', None)
+ vtid = MedleySimpleGUI.convert_from_str(data, 'long')
+ data = node.get('type', None)
+ type = MedleySimpleGUI.convert_from_str(data, 'str')
+ data = node.get('has_seq', None)
+ seq = ComponentSimpleGUI.convert_from_str(data, 'bool')
+ alias_list = {}
+ for child in node.getchildren():
+ if child.tag == "alias":
+ alias = AliasSimpleGUI.from_xml(child)
+ alias_list[alias._name] = alias
+ return MedleySimpleGUI(id=id, name=name, vtid=vtid, version=version,
+ alias_list=alias_list, t=type, has_seq=seq)
+
+################################################################################
+
+class AliasSimpleGUI(XMLObject):
+ def __init__(self, id, name, component=None):
+ self._id = id
+ self._name = name
+ self._component = component
+
+ def to_xml(self, node=None):
+ """to_xml(node: ElementTree.Element) -> ElementTree.Element
+ writes itself to xml
+ """
+ if node is None:
+ node = ElementTree.Element('alias')
+
+ #set attributes
+ node.set('id', self.convert_to_str(self._id,'long'))
+ node.set('name', self.convert_to_str(self._name,'str'))
+ child_ = ElementTree.SubElement(node, 'component')
+ self._component.to_xml(child_)
+
+ return node
+
+ @staticmethod
+ def from_xml(node):
+ if node.tag != 'alias':
+ return None
+
+ #read attributes
+ data = node.get('id', None)
+ id = AliasSimpleGUI.convert_from_str(data, 'long')
+ data = node.get('name', None)
+ name = AliasSimpleGUI.convert_from_str(data, 'str')
+ for child in node.getchildren():
+ if child.tag == "component":
+ component = ComponentSimpleGUI.from_xml(child)
+ alias = AliasSimpleGUI(id,name,component)
+ return alias
+
+################################################################################
+
+class ComponentSimpleGUI(XMLObject):
+ def __init__(self, id, pos, ctype, spec, val=None, minVal=None, maxVal=None,
+ stepSize=None, strvalueList="", parent=None, seq=False,
+ widget="text"):
+ """ComponentSimpleGUI()
+ widget can be: text, slider, combobox, numericstepper, checkbox
+
+ """
+ self._id = id
+ self._pos = pos
+ self._spec = spec
+ self._ctype = ctype
+ self._val = val
+ self._minVal = minVal
+ self._maxVal = maxVal
+ self._stepSize = stepSize
+ self._strvaluelist = strvalueList
+ self._parent = parent
+ self._seq = seq
+ self._widget = widget
+
+ def _get_valuelist(self):
+ data = self._strvaluelist.split(',')
+ result = []
+ for d in data:
+ result.append(urllib.unquote_plus(d))
+ return result
+ def _set_valuelist(self, valuelist):
+ q = []
+ for v in valuelist:
+ q.append(urllib.quote_plus(v))
+ self._strvaluelist = ",".join(q)
+
+ _valueList = property(_get_valuelist,_set_valuelist)
+
+ def to_xml(self, node=None):
+ """to_xml(node: ElementTree.Element) -> ElementTree.Element
+ writes itself to xml
+ """
+ if node is None:
+ node = ElementTree.Element('component')
+
+ #set attributes
+ node.set('id', self.convert_to_str(self._id,'long'))
+ node.set('pos', self.convert_to_str(self._pos,'long'))
+ node.set('spec', self.convert_to_str(self._spec,'str'))
+ node.set('ctype', self.convert_to_str(self._ctype,'str'))
+ node.set('val', self.convert_to_str(self._val, 'str'))
+ node.set('minVal', self.convert_to_str(self._minVal,'str'))
+ node.set('maxVal', self.convert_to_str(self._maxVal,'str'))
+ node.set('stepSize', self.convert_to_str(self._stepSize,'str'))
+ node.set('valueList',self.convert_to_str(self._strvaluelist,'str'))
+ node.set('parent', self.convert_to_str(self._parent,'str'))
+ node.set('seq', self.convert_to_str(self._seq,'bool'))
+ node.set('widget',self.convert_to_str(self._widget,'str'))
+ return node
+
+ @staticmethod
+ def from_xml(node):
+ if node.tag != 'component':
+ return None
+
+ #read attributes
+ data = node.get('id', None)
+ id = ComponentSimpleGUI.convert_from_str(data, 'long')
+ data = node.get('pos', None)
+ pos = ComponentSimpleGUI.convert_from_str(data, 'long')
+ data = node.get('ctype', None)
+ ctype = ComponentSimpleGUI.convert_from_str(data, 'str')
+ data = node.get('spec', None)
+ spec = ComponentSimpleGUI.convert_from_str(data, 'str')
+ data = node.get('val', None)
+ val = ComponentSimpleGUI.convert_from_str(data, 'str')
+ val = val.replace("<", "<")
+ val = val.replace(">", ">")
+ val = val.replace("&","&")
+ data = node.get('minVal', None)
+ minVal = ComponentSimpleGUI.convert_from_str(data, 'str')
+ data = node.get('maxVal', None)
+ maxVal = ComponentSimpleGUI.convert_from_str(data, 'str')
+ data = node.get('stepSize', None)
+ stepSize = ComponentSimpleGUI.convert_from_str(data, 'str')
+ data = node.get('valueList', None)
+ values = ComponentSimpleGUI.convert_from_str(data, 'str')
+ values = values.replace("<", "<")
+ values = values.replace(">", ">")
+ values = values.replace("&","&")
+ data = node.get('parent', None)
+ parent = ComponentSimpleGUI.convert_from_str(data, 'str')
+ data = node.get('seq', None)
+ seq = ComponentSimpleGUI.convert_from_str(data, 'bool')
+ data = node.get('widget', None)
+ widget = ComponentSimpleGUI.convert_from_str(data, 'str')
+ component = ComponentSimpleGUI(id=id,
+ pos=pos,
+ ctype=ctype,
+ spec=spec,
+ val=val,
+ minVal=minVal,
+ maxVal=maxVal,
+ stepSize=stepSize,
+ strvalueList=values,
+ parent=parent,
+ seq=seq,
+ widget=widget)
+ return component
+
+################################################################################
+################################################################################
+
+class VistrailsServerSingleton(VistrailsApplicationInterface,
+ QtGui.QApplication):
+ """
+ VistrailsServerSingleton is the singleton of the application,
+ there will be only one instance of the application during VisTrails
+
+ """
+ def __call__(self):
+ """ __call__() -> VistrailsServerSingleton
+ Return self for calling method
+
+ """
+ if not self._initialized:
+ self.init()
+ return self
+
+ def __init__(self):
+ QtGui.QApplication.__init__(self, sys.argv)
+ VistrailsApplicationInterface.__init__(self)
+ if QtCore.QT_VERSION < 0x40200: # 0x40200 = 4.2.0
+ raise vistrails.core.requirements.MissingRequirement("Qt version >= 4.2")
+
+ self.rpcserver = None
+ self.pingserver = None
+ self.images_url = "http://vistrails.sci.utah.edu/medleys/images/"
+ self.temp_xml_rpc_options = InstanceObject(server=None,
+ port=None,
+ log_file=None)
+ qt.allowQObjects()
+
+ def is_running_gui(self):
+ return True
+
+ def make_logger(self, filename, label):
+ """self.make_logger(filename:str) -> logger. Creates a logging object to
+ be used for the server so we can log requests in file f."""
+ logger = logging.getLogger("VistrailsRPC[%s]"%label)
+ handler = logging.handlers.RotatingFileHandler(filename, maxBytes = 1024*1024,
+ backupCount=5)
+ handler.setFormatter(logging.Formatter('%(name)s - %(asctime)s %(levelname)-8s %(message)s'))
+ handler.setLevel(logging.DEBUG)
+ logger.setLevel(logging.DEBUG)
+ logger.addHandler(handler)
+ return logger
+
+ def load_config(self, filename):
+ """ Load in server parameters from config file.
+ If parameters are missing, write them in and raise error.
+ If file doesn't exist, create one and raise error. """
+
+ global accessList, db_host, db_read_user, db_read_pass, db_write_user, db_write_pass, media_dir, script_file, virtual_display
+ accessList = []
+ db_host = ''
+ db_read_user = ''
+ db_read_pass = ''
+ db_write_user = ''
+ db_write_pass = ''
+ media_dir = ''
+ script_file = ''
+ virtual_display = ''
+
+ config = ConfigParser.ConfigParser()
+ file_opened = config.read(filename)
+ has_changed = False
+
+ if not file_opened:
+ # new file to store default (empt) config
+ new_filename = os.path.join(system.vistrails_root_directory(), 'server.cfg')
+
+ # load or create access fields
+ if config.has_option("access", "permitted_addresses"):
+ read_accessList = config.get("access", "permitted_addresses")
+ accessList = [elem.strip() for elem in read_accessList.split(',')]
+ else:
+ if not config.has_section("access"):
+ config.add_section("access")
+ config.set("access", "permitted_addresses", "localhost,")
+ accessList = []
+ has_changed = True
+
+ # load or create database fields
+ if not config.has_section("database"):
+ config.add_section("database")
+ has_changed = True
+
+ if config.has_option("database", "host"):
+ db_host = config.get("database", "host")
+ else:
+ config.set("database", "host", "")
+ has_changed = True
+
+ if config.has_option("database", "read_user"):
+ db_read_user = config.get("database", "read_user")
+ else:
+ config.set("database", "read_user", "")
+ has_changed = True
+
+ if config.has_option("database", "read_password"):
+ db_read_pass = config.get("database", "read_password")
+ else:
+ config.set("database", "read_password", "")
+ has_changed = True
+
+ if config.has_option("database", "write_user"):
+ db_write_user = config.get("database", "write_user")
+ else:
+ config.set("database", "write_user", "")
+ has_changed = True
+
+ if config.has_option("database", "write_password"):
+ db_write_pass = config.get("database", "write_password")
+ else:
+ config.set("database", "write_password", "")
+ has_changed = True
+
+ if not config.has_section("media"):
+ config.add_section("media")
+ has_changed = True
+
+ if config.has_option("media", "media_dir"):
+ media_dir = config.get("media", "media_dir")
+ if not os.path.exists(media_dir):
+ raise ValueError("media_dir %s doesn't exist." % media_dir)
+
+ if not config.has_section("script"):
+ config.add_section("script")
+ has_changed = True
+
+ if config.has_option("script", "script_file"):
+ script_file = config.get("script", "script_file")
+ if not os.path.exists(script_file):
+ raise ValueError("script_file %s doesn't exist." % script_file)
+ else:
+ config.set("script", "script_file", "")
+ has_changed = True
+
+ if config.has_option("script", "virtual_display"):
+ virtual_display = config.get("script", "virtual_display")
+
+ if virtual_display == "":
+ virtual_display = "0"
+
+ # check if all required parameters are present
+ missing_req_fields = [y for (x,y) in ((db_host,"host"),
+ (db_read_user,"read_user"),
+ (db_write_user,"write_user"),
+ (media_dir,"media_dir"),
+ (script_file,"script_file"),
+ (accessList,"permission_addresses")) if not x]
+ if missing_req_fields:
+ self.server_logger.error(("Following required parameters where missing "
+ "from %s config file: %s ") % \
+ (filename, ", ".join(missing_req_fields)))
+ if not has_changed:
+ raise ValueError("Following required parameters where missing from %s config file: %s " %
+ (filename, ", ".join(missing_req_fields)))
+
+ if has_changed:
+ # save changes to passed config file
+ if file_opened:
+ config.write(open(filename, "wb"))
+ self.server_logger.error("Invalid config file, the missing fields have been "
+ "added to your config, please populate them")
+ raise RuntimeError("Invalid config file, the missing fields have been "
+ "added to your config, please populate them")
+ else:
+ # save changes to default config file
+ config.write(open(new_filename, "wb"))
+ self.server_logger.error("Config file %s doesn't exist. Creating new file at %s. "
+ "Please populated it with the correct values and use it" %
+ (filename, new_filename))
+ raise RuntimeError("Config file %s doesn't exist. Creating new file at %s. "
+ "Please populate it with the correct values and use it" %
+ (filename, new_filename))
+
+ def init(self, optionsDict=None):
+ """ init(optionDict: dict) -> boolean
+ Create the application with a dict of settings
+
+ """
+ VistrailsApplicationInterface.init(self,optionsDict)
+
+ self.vistrailsStartup.init()
+ self.server_logger = self.make_logger(self.temp_xml_rpc_options.log_file,
+ self.temp_xml_rpc_options.port)
+ self.load_config(self.temp_xml_rpc_options.config_file)
+ self.start_other_instances(self.temp_xml_rpc_options.instances)
+ self._python_environment = self.vistrailsStartup.get_python_environment()
+ self._initialized = True
+ return True
+
+ def start_other_instances(self, number):
+ global virtual_display, script_file
+ self.others = []
+ host = self.temp_xml_rpc_options.server
+ port = self.temp_xml_rpc_options.port
+ virt_disp = int(virtual_display)
+ for x in xrange(number):
+ port += 1 # each instance needs one port space for now
+ #later we might need 2 (normal requests and status requests)
+ virt_disp += 1
+ args = [script_file,":%s"%virt_disp,host,str(port),'0', '0']
+ try:
+ p = subprocess.Popen(args)
+ time.sleep(20)
+ self.others.append("http://%s:%s"%(host,port))
+ except Exception, e:
+ self.server_logger.error(("Couldn't start the instance on display:"
+ "%s port: %s") % (virtual_display, port))
+ self.server_logger.error(str(e))
+
+ def stop_other_instances(self):
+ script = os.path.join(system.vistrails_root_directory(), "stop_vistrails_server.py")
+ for o in self.others:
+ args = ['python', script, o]
+ try:
+ subprocess.Popen(args)
+ time.sleep(15)
+ except Exception, e:
+ self.server_logger.error("Couldn't stop instance: %s" % o)
+ self.server_logger.error(str(e))
+
+ def run_server(self):
+ """run_server() -> None
+ This will run forever until the server receives a quit request, done
+ via xml-rpc.
+ """
+
+ self.server_logger.info("Server is running on http://%s:%s"%(self.temp_xml_rpc_options.server,
+ self.temp_xml_rpc_options.port))
+ if self.temp_xml_rpc_options.multithread:
+ self.rpcserver = ThreadedXMLRPCServer((self.temp_xml_rpc_options.server,
+ self.temp_xml_rpc_options.port),
+ self.server_logger)
+ self.server_logger.info(" multithreaded instance")
+ else:
+ self.rpcserver = StoppableXMLRPCServer((self.temp_xml_rpc_options.server,
+ self.temp_xml_rpc_options.port),
+ self.server_logger)
+ """
+ self.pingserver = StoppableXMLRPCServer((self.temp_xml_rpc_options.server,
+ self.temp_xml_rpc_options.port-1),
+ self.server_logger)
+ """
+ self.server_logger.info(" singlethreaded instance")
+ #self.rpcserver.register_introspection_functions()
+ self.rpcserver.register_instance(RequestHandler(self.server_logger,
+ self.others))
+ if self.pingserver:
+ self.pingserver.register_instance(RequestHandler(self.server_logger, []))
+ self.server_logger.info("Status XML RPC Server is listening on http://%s:%s"% \
+ (self.temp_xml_rpc_options.server,
+ self.temp_xml_rpc_options.port-1))
+ self.pingserver.register_function(self.quit_server, "quit")
+ self.pingserver.serve_forever()
+ self.pingserver.serve_close()
+
+ self.rpcserver.register_function(self.quit_server, "quit")
+ self.server_logger.info("Vistrails XML RPC Server is listening on http://%s:%s"% \
+ (self.temp_xml_rpc_options.server,
+ self.temp_xml_rpc_options.port))
+ self.rpcserver.serve_forever()
+ self.rpcserver.server_close()
+ return 0
+
+ def quit_server(self):
+ result = "Vistrails XML RPC Server is quitting."
+ self.stop_other_instances()
+ self.server_logger.info(result)
+ self.rpcserver.stop = True
+ return result
+
+ def setupOptions(self, args=None):
+ """ setupOptions() -> None
+ Check and store all command-line arguments
+
+ """
+ add = command_line.CommandLineParser.add_option
+
+ add("-T", "--xml_rpc_server", action="store", dest="rpcserver",
+ help="hostname or ip address where this xml rpc server will work")
+ add("-R", "--xml_rpc_port", action="store", type="int", default=8080,
+ dest="rpcport", help="database port")
+ add("-L", "--xml_rpc_log_file", action="store", dest="rpclogfile",
+ default=os.path.join(system.vistrails_root_directory(),
+ 'rpcserver.log'),
+ help="log file for XML RPC server")
+ add("-O", "--xml_rpc_instances", action="store", type='int', default=0,
+ dest="rpcinstances",
+ help="number of other instances that vistrails should start")
+ add("-M", "--multithreaded", action="store_true",
+ default = None, dest='multithread',
+ help="server will start a thread for each request")
+ add("-C", "--config-file", action="store", dest = "rpcconfig",
+ default=os.path.join(system.vistrails_root_directory(),
+ 'server.cfg'),
+ help="config file for server connection options")
+ VistrailsApplicationInterface.setupOptions(self, args)
+
+ def readOptions(self):
+ """ readOptions() -> None
+ Read arguments from the command line
+
+ """
+ get = command_line.CommandLineParser().get_option
+ self.temp_xml_rpc_options = InstanceObject(server=get('rpcserver'),
+ port=get('rpcport'),
+ log_file=get('rpclogfile'),
+ instances=get('rpcinstances'),
+ multithread=get('multithread'),
+ config_file=get('rpcconfig'))
+ VistrailsApplicationInterface.readOptions(self)
+
+
+
+# The initialization must be explicitly signalled. Otherwise, any
+# modules importing vis_application will try to initialize the entire
+# app.
+def start_server(optionsDict=None):
+ """Initializes the application singleton."""
+ global VistrailsServer
+ if VistrailsServer:
+ print "Server already started."
+ return
+ VistrailsServer = VistrailsServerSingleton()
+ vistrails.gui.theme.initializeCurrentTheme()
+ vistrails.core.application.set_vistrails_application(VistrailsServer)
+ x = VistrailsServer.init(optionsDict)
+ if x == True:
+ return 0
+ else:
+ return 1
+
+VistrailsServer = None
+
+def stop_server():
+ """Stop and finalize the application singleton."""
+ global VistrailsServer
+ VistrailsServer.save_configuration()
+ VistrailsServer.destroy()
+ VistrailsServer.deleteLater()
diff --git a/vistrails/gui/base_view.py b/vistrails/gui/base_view.py
new file mode 100644
index 0000000..29fbcd5
--- /dev/null
+++ b/vistrails/gui/base_view.py
@@ -0,0 +1,114 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from PyQt4 import QtCore, QtGui
+
+class BaseView(object):
+ """ BaseView is the base class for the views in VisTrails.
+
+
+ """
+
+ def __init__(self):
+ self.controller = None
+ self.title = None
+ self.index = -1
+ self.tab_idx = -1
+
+ self.palette_layout = {}
+ self.set_default_layout()
+ self.action_links = {}
+ self.action_defaults = {}
+ BaseView.set_action_defaults(self)
+ self.set_action_defaults()
+ self.set_action_links()
+ self.detachable = False
+ self.vistrail_view = None
+
+ def set_default_layout(self):
+ raise NotImplementedError("Class must define the layout as self.palette_layout")
+
+ def set_palette_layout(self, layout):
+ self.palette_layout = layout
+
+ def set_action_links(self):
+ raise NotImplementedError("Class must define the action links")
+
+ def set_action_defaults(self):
+ self.action_defaults.update(
+ {'history' : [('setEnabled', False, True)],
+ 'search' : [('setEnabled', False, True)],
+ 'explore' : [('setEnabled', False, True)],
+ 'provenance' : [('setEnabled', False, True)],
+ 'mashup' : [('setEnabled', False, True)]
+ })
+
+ def set_title(self, title):
+ self.title = title
+
+ def get_title(self):
+ return self.title
+
+ def set_long_title(self, title):
+ self.long_title = title
+
+ def get_long_title(self):
+ return self.title
+
+ def get_index(self):
+ return self.index
+
+ def set_index(self, index):
+ self.index = index
+
+ def get_tab_idx(self):
+ return self.tab_idx
+
+ def set_tab_idx(self, tab_idx):
+ self.tab_idx = tab_idx
+
+ def set_controller(self, controller):
+ pass
+
+ def set_vistrail_view(self, view):
+ self.vistrail_view = view
+
+ def get_vistrail_view(self):
+ return self.vistrail_view
+
+ def changeEvent(self, event):
+ if event.type() == QtCore.QEvent.WindowTitleChange:
+ self.emit(QtCore.SIGNAL("windowTitleChanged"), self)
+ QtGui.QWidget.changeEvent(self, event)
diff --git a/vistrails/gui/bundles/__init__.py b/vistrails/gui/bundles/__init__.py
new file mode 100644
index 0000000..fac3164
--- /dev/null
+++ b/vistrails/gui/bundles/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
diff --git a/vistrails/gui/bundles/installbundle.py b/vistrails/gui/bundles/installbundle.py
new file mode 100644
index 0000000..a0e52de
--- /dev/null
+++ b/vistrails/gui/bundles/installbundle.py
@@ -0,0 +1,270 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Module with utilities to try and install a bundle if possible."""
+from vistrails.core import get_vistrails_application
+from vistrails.core.configuration import get_vistrails_configuration, \
+ get_vistrails_persistent_configuration
+from vistrails.core import debug
+from vistrails.core.system import get_executable_path
+from vistrails.core.system import vistrails_root_directory, systemType
+from vistrails.gui.bundles.utils import guess_system, guess_graphical_sudo
+import vistrails.gui.bundles.installbundle # this is on purpose
+import subprocess
+import sys
+
+##############################################################################
+
+def has_qt():
+ try:
+ import PyQt4.QtGui
+ return True
+ except ImportError:
+ return False
+
+pip_installed = True
+try:
+ import pip
+except ImportError:
+ pip_installed = False
+
+def hide_splash_if_necessary():
+ """Disables the splashscreen, otherwise it sits in front of windows.
+ """
+ app = get_vistrails_application()
+ if hasattr(app, 'splashScreen') and app.splashScreen:
+ app.splashScreen.hide()
+
+
+def shell_escape(arg):
+ return '"%s"' % arg.replace('\\', '\\\\').replace('"', '\\"')
+
+
+def run_install_command_as_root(graphical, cmd, args):
+ if isinstance(args, str):
+ cmd += ' %s' % shell_escape(args)
+ elif isinstance(args, list):
+ for package in args:
+ if not isinstance(package, str):
+ raise TypeError("Expected string or list of strings")
+ cmd += ' %s' % shell_escape(package)
+ else:
+ raise TypeError("Expected string or list of strings")
+
+ if graphical:
+ sucmd, escape = guess_graphical_sudo()
+ else:
+ debug.warning("VisTrails wants to install package(s) %r" %
+ args)
+ if get_executable_path('sudo'):
+ sucmd, escape = "sudo %s", False
+ elif systemType not in ['Darwin', 'Windows']:
+ sucmd, escape = "su -c %s", True
+ else:
+ sucmd, escape = '%s', False
+
+ if escape:
+ sucmd = sucmd % shell_escape(cmd)
+ else:
+ sucmd = sucmd % cmd
+
+ print "about to run: %s" % sucmd
+ p = subprocess.Popen(sucmd, stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ shell=True)
+ lines = []
+ try:
+ for line in iter(p.stdout.readline, ''):
+ print line,
+ lines.append(line)
+ except IOError, e:
+ print "Ignoring IOError:", str(e)
+ result = p.wait()
+
+ if result != 0:
+ debug.critical("Error running: %s" % cmd, ''.join(lines))
+
+ return result == 0 # 0 indicates success
+
+
+def linux_debian_install(package_name):
+ qt = has_qt()
+ try:
+ import apt
+ import apt_pkg
+ except ImportError:
+ qt = False
+ hide_splash_if_necessary()
+
+ if qt:
+ cmd = shell_escape(vistrails_root_directory() +
+ '/gui/bundles/linux_debian_install.py')
+ else:
+ cmd = '%s install -y' % ('aptitude'
+ if get_executable_path('aptitude')
+ else 'apt-get')
+
+ return run_install_command_as_root(qt, cmd, package_name)
+
+linux_ubuntu_install = linux_debian_install
+
+
+def linux_fedora_install(package_name):
+ qt = has_qt()
+ hide_splash_if_necessary()
+
+ if qt:
+ cmd = shell_escape(vistrails_root_directory() +
+ '/gui/bundles/linux_fedora_install.py')
+ else:
+ cmd = 'yum -y install'
+
+ return run_install_command_as_root(qt, cmd, package_name)
+
+
+def pip_install(package_name):
+ hide_splash_if_necessary()
+
+ if get_executable_path('pip'):
+ cmd = '%s install' % shell_escape(get_executable_path('pip'))
+ else:
+ cmd = shell_escape(sys.executable) + ' -m pip install'
+ return run_install_command_as_root(has_qt(), cmd, package_name)
+
+def show_question(which_files, has_distro_pkg, has_pip):
+ if has_qt():
+ from PyQt4 import QtCore, QtGui
+ if isinstance(which_files, str):
+ which_files = [which_files]
+ dialog = QtGui.QDialog()
+ dialog.setWindowTitle("Required packages missing")
+ layout = QtGui.QVBoxLayout()
+
+ label = QtGui.QLabel(
+ "One or more required packages are missing: %s. VisTrails can "
+ "automatically install them. If you click OK, VisTrails will "
+ "need administrator privileges, and you might be asked for "
+ "the administrator password." % (" ".join(which_files)))
+ label.setWordWrap(True)
+ layout.addWidget(label)
+
+ if pip_installed and has_pip:
+ use_pip = QtGui.QCheckBox("Use pip")
+ use_pip.setChecked(
+ not has_distro_pkg or (
+ has_pip and
+ getattr(get_vistrails_configuration(),
+ 'installBundlesWithPip')))
+ use_pip.setEnabled(has_distro_pkg and has_pip)
+ layout.addWidget(use_pip)
+
+ remember_align = QtGui.QHBoxLayout()
+ remember_align.addSpacing(20)
+ remember_pip = QtGui.QCheckBox("Remember my choice")
+ remember_pip.setChecked(False)
+ remember_pip.setEnabled(use_pip.isEnabled())
+ remember_align.addWidget(remember_pip)
+ layout.addLayout(remember_align)
+ elif has_pip:
+ label = QtGui.QLabel("pip package is available but pip is not installed")
+ layout.addWidget(label)
+ buttons = QtGui.QDialogButtonBox(
+ QtGui.QDialogButtonBox.Ok | QtGui.QDialogButtonBox.Cancel)
+ QtCore.QObject.connect(buttons, QtCore.SIGNAL('accepted()'),
+ dialog, QtCore.SLOT('accept()'))
+ QtCore.QObject.connect(buttons, QtCore.SIGNAL('rejected()'),
+ dialog, QtCore.SLOT('reject()'))
+ layout.addWidget(buttons)
+
+ dialog.setLayout(layout)
+ hide_splash_if_necessary()
+ if dialog.exec_() != QtGui.QDialog.Accepted:
+ return False
+ else:
+ if pip_installed and has_pip:
+ if remember_pip.isChecked():
+ setattr(get_vistrails_persistent_configuration(),
+ 'installBundlesWithPip',
+ use_pip.isChecked())
+
+ if use_pip.isChecked():
+ return 'pip'
+ return 'distro'
+ else:
+ print "\nRequired package missing"
+ print ("A required package is missing, but VisTrails can " +
+ "automatically install it. " +
+ "If you say Yes, VisTrails will need "+
+ "administrator privileges, and you" +
+ "might be asked for the administrator password.")
+ if has_distro_pkg:
+ print "(VisTrails will use your distribution's package manager)"
+ else:
+ print "(VisTrails will use the 'pip' installer)"
+ print "Give VisTrails permission to try to install package? (y/N)"
+ v = raw_input().upper()
+ if v == 'Y' or v == 'YES':
+ if has_distro_pkg:
+ return 'distro'
+ else:
+ return 'pip'
+
+
+def install(dependency_dictionary):
+ """Tries to install a bundle after a py_import() failed.."""
+
+ distro = guess_system()
+ files = (dependency_dictionary.get(distro) or
+ dependency_dictionary.get('pip'))
+ if not files:
+ return None
+ can_install = (('pip' in dependency_dictionary and pip_installed) or
+ distro in dependency_dictionary)
+ if can_install:
+ action = show_question(
+ files,
+ distro in dependency_dictionary,
+ 'pip' in dependency_dictionary)
+ if action == 'distro':
+ callable_ = getattr(vistrails.gui.bundles.installbundle,
+ distro.replace('-', '_') + '_install')
+ return callable_(files)
+ elif action == 'pip':
+ if not pip_installed:
+ debug.warning("Attempted to use pip, but it is not installed.")
+ return False
+ return pip_install(dependency_dictionary.get('pip'))
+ else:
+ return False
diff --git a/vistrails/gui/bundles/linux_debian_install.py b/vistrails/gui/bundles/linux_debian_install.py
new file mode 100755
index 0000000..3bfc8b9
--- /dev/null
+++ b/vistrails/gui/bundles/linux_debian_install.py
@@ -0,0 +1,255 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# Installs a package through APT, showing progress.
+import apt
+import apt_pkg
+import sys
+import time
+
+from apt_pkg import gettext as _
+from apt.progress.base import InstallProgress, OpProgress, AcquireProgress
+
+from PyQt4 import QtCore, QtGui
+
+if __name__ != '__main__':
+ import vistrails.tests
+ raise vistrails.tests.NotModule('This should not be imported as a module')
+
+
+package_name = sys.argv[1]
+
+##############################################################################
+
+class GuiOpProgress(OpProgress):
+ def __init__(self, pbar):
+ OpProgress.__init__(self)
+ self.pbar = pbar
+
+ def update(self, percent):
+ self.pbar.setValue(int(percent))
+ QtGui.qApp.processEvents()
+ OpProgress.update(self, percent)
+
+ def done(self):
+ OpProgress.done(self)
+
+class GUIAcquireProgress(AcquireProgress):
+ def __init__(self, pbar, status_label):
+ AcquireProgress.__init__(self)
+ self.pbar = pbar
+ self.status_label = status_label
+ self.percent = 0.0
+
+ def pulse(self, owner):
+ current_item = self.current_items + 1
+ if current_item > self.total_items:
+ current_item = self.total_items
+ if self.current_cps > 0:
+ text = (_("Downloading file %(current)li of %(total)li with "
+ "%(speed)s/s") % \
+ {"current": current_item,
+ "total": self.total_items,
+ "speed": apt_pkg.size_to_str(self.current_cps)})
+ else:
+ text = (_("Downloading file %(current)li of %(total)li") % \
+ {"current": current_item,
+ "total": self.total_items})
+ self.status_label.setText(text)
+ percent = (((self.current_bytes + self.current_items) * 100.0) /
+ float(self.total_bytes + self.total_items))
+ self.pbar.setValue(int(percent))
+ QtGui.qApp.processEvents()
+ return True
+
+ def start(self):
+ self.status_label.setText("Started downloading.")
+ QtGui.qApp.processEvents()
+
+ def stop(self):
+ self.status_label.setText("Finished downloading.")
+ QtGui.qApp.processEvents()
+
+ def done(self, item):
+ print "[Fetched] %s" % item.shortdesc
+ self.status_label.setText("[Fetched] %s" % item.shortdesc)
+ QtGui.qApp.processEvents()
+
+ def fail(self, item):
+ print "[Failed] %s" % item.shortdesc
+
+ def ims_hit(self, item):
+ print "[Hit] %s" % item.shortdesc
+ self.status_label.setText("[Hit] %s" % item.shortdesc)
+ QtGui.qApp.processEvents()
+
+ def media_change(self, media, drive):
+ print "[Waiting] Please insert media '%s' in drive '%s'" % (
+ media, drive)
+
+class GUIInstallProgress(InstallProgress):
+ def __init__(self, pbar, status_label):
+ InstallProgress.__init__(self)
+ self.pbar = pbar
+ self.status_label = status_label
+ self.last = 0.0
+
+ def status_change(self, pkg, percent, status):
+ if self.last >= percent:
+ return
+ self.status_label.setText(status)
+ self.pbar.setValue(int(percent))
+ self.last = percent
+ QtGui.qApp.processEvents()
+
+ def pulse(self):
+ QtGui.qApp.processEvents()
+ return InstallProgress.pulse(self)
+
+ def finish_update(self):
+ pass
+
+ def processing(self, pkg, stage):
+ print "starting '%s' stage for %s" % (stage, pkg)
+
+ def conffile(self,current,new):
+ print "WARNING: conffile prompt: %s %s" % (current, new)
+
+ def error(self, errorstr):
+ print "ERROR: got dpkg error: '%s'" % errorstr
+
+##############################################################################
+
+class Window(QtGui.QWidget):
+ def __init__(self, parent=None):
+ QtGui.QMainWindow.__init__(self, parent)
+
+ mainlayout = QtGui.QVBoxLayout()
+ self.setLayout(mainlayout)
+ desktop = QtGui.qApp.desktop()
+ geometry = desktop.screenGeometry(self)
+ h = 200
+ w = 300
+ self.setGeometry(geometry.left() + (geometry.width() - w)/2,
+ geometry.top() + (geometry.height() - h)/2,
+ w, h)
+ self.setWindowTitle('VisTrails APT interface')
+ lbl = QtGui.QLabel(self)
+ mainlayout.addWidget(lbl)
+ lbl.setText("VisTrails is about to install '%s'."
+ "Continue?" % package_name)
+ lbl.resize(self.width(), 150)
+ lbl.setAlignment(QtCore.Qt.AlignHCenter)
+ lbl.setWordWrap(True)
+ layout = QtGui.QHBoxLayout()
+ self.allowBtn = QtGui.QPushButton("Install")
+ self.denyBtn = QtGui.QPushButton("Cancel")
+ layout.addWidget(self.allowBtn)
+ layout.addWidget(self.denyBtn)
+ self.layout().addLayout(layout)
+
+ self.connect(self.allowBtn, QtCore.SIGNAL("clicked()"),
+ self.perform_install)
+ self.connect(self.denyBtn, QtCore.SIGNAL("clicked()"),
+ self.fail_quit)
+ pbarlayout = QtGui.QVBoxLayout()
+ pbar = QtGui.QProgressBar()
+ pbar.setMinimum(0)
+ pbar.setMaximum(100)
+ pbarlayout.addWidget(pbar)
+ self.layout().addLayout(pbarlayout)
+ pbar.show()
+ self.pbar = pbar
+ self.pbar.setValue(0)
+ self.status_label = QtGui.QLabel(self)
+ mainlayout.addWidget(self.status_label)
+ self.layout().addStretch()
+
+ self.op_progress = None #GuiOpProgress(self.pbar)
+ self.status_label.setText('Waiting for decision...')
+
+ def fail_quit(self):
+ sys.exit(-1)
+
+ def perform_install(self):
+ self.allowBtn.setEnabled(False)
+ self.denyBtn.setEnabled(False)
+
+ self.status_label.setText('Reading package cache')
+ QtGui.qApp.processEvents()
+ apt_pkg.init()
+ cache = apt.cache.Cache(self.op_progress)
+ pkg = None
+ try:
+ pkg = cache[package_name]
+ except KeyError:
+ self.status_label.setText('Package not found: updating cache')
+ QtGui.qApp.processEvents()
+ cache.update(self.op_progress)
+ try:
+ pkg = cache[package_name]
+ except KeyError:
+ self.show_quit('Package not found!')
+ if pkg.is_installed:
+ self.show_quit('Package already installed!', result=0)
+ self.status_label.setText('Marking for install')
+ pkg.mark_install()
+ self.status_label.setText('Installing')
+ QtGui.qApp.processEvents()
+ try:
+ aprogress = GUIAcquireProgress(self.pbar, self.status_label)
+ iprogress = GUIInstallProgress(self.pbar, self.status_label)
+ cache.commit(aprogress, iprogress)
+ except Exception:
+ import traceback; traceback.print_exc()
+ self.show_quit('Error installing package!')
+ print "Installation successful, back to VisTrails..."
+ self.show_quit("Success, exiting...", result=0)
+
+ def show_quit(self, message, t=2, result=1):
+ self.status_label.setText(message)
+ QtGui.qApp.processEvents()
+ time.sleep(t)
+ sys.exit(result)
+
+##############################################################################
+
+app = QtGui.QApplication(sys.argv)
+
+window = Window()
+window.show()
+app.exec_()
+sys.exit(0)
diff --git a/vistrails/gui/bundles/linux_fedora_install.py b/vistrails/gui/bundles/linux_fedora_install.py
new file mode 100755
index 0000000..a950763
--- /dev/null
+++ b/vistrails/gui/bundles/linux_fedora_install.py
@@ -0,0 +1,198 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# Installs a package through YUM
+
+# import yum
+# import apt_pkg
+# import sys, os
+# import copy
+# import time
+
+# package_name = sys.argv[1]
+
+# from apt.progress import InstallProgress
+# from apt.progress import FetchProgress
+
+# cache = apt.Cache(apt.progress.OpTextProgress())
+
+# try:
+# pkg = cache[package_name]
+# except KeyError:
+# sys.exit(1)
+
+# if pkg.isInstalled:
+# print "Package '%s' already installed" % package_name
+# sys.exit(0)
+
+
+# ##############################################################################
+
+# from PyQt4 import Qt, QtCore, QtGui
+
+# class GUIInstallProgress(InstallProgress):
+# def __init__(self, pbar, status_label):
+# apt.progress.InstallProgress.__init__(self)
+# self.pbar = pbar
+# self.status_label = status_label
+# self.last = 0.0
+# def updateInterface(self):
+# InstallProgress.updateInterface(self)
+# if self.last >= self.percent:
+# return
+# self.status_label.setText(self.status)
+# self.pbar.setValue(int(self.percent))
+# self.last = self.percent
+# QtGui.qApp.processEvents()
+# def pulse(self):
+# QtGui.qApp.processEvents()
+# return InstallProgress.pulse(self)
+# def conffile(self,current,new):
+# print "conffile prompt: %s %s" % (current,new)
+# def error(self, errorstr):
+# print "got dpkg error: '%s'" % errorstr
+
+# class GUIFetchProgress(FetchProgress):
+
+# def __init__(self, pbar, status_label):
+# apt.progress.FetchProgress.__init__(self)
+# self.pbar = pbar
+# self.status_label = status_label
+
+# def pulse(self):
+# FetchProgress.pulse(self)
+# if self.currentCPS > 0:
+# s = "%sB/s %s" % (apt_pkg.SizeToStr(int(self.currentCPS)),
+# apt_pkg.TimeToStr(int(self.eta)))
+# else:
+# s = "[Working..]"
+# self.status_label.setText(s)
+# self.pbar.setValue(int(self.percent))
+# QtGui.qApp.processEvents()
+# return True
+
+# def stop(self):
+# self.status_label.setText("Finished downloading.")
+# QtGui.qApp.processEvents()
+
+# def updateStatus(self, uri, descr, shortDescr, status):
+# if status != self.dlQueued:
+# print "\r%s %s" % (self.dlStatusStr[status], descr)
+
+
+# class Window(QtGui.QWidget):
+
+# def __init__(self, parent=None):
+# QtGui.QMainWindow.__init__(self, parent)
+
+# mainlayout = QtGui.QVBoxLayout()
+# self.setLayout(mainlayout)
+# desktop = QtGui.qApp.desktop()
+# print desktop.isVirtualDesktop()
+# geometry = desktop.screenGeometry(self)
+# h = 200
+# w = 300
+# self.setGeometry(geometry.left() + (geometry.width() - w)/2,
+# geometry.top() + (geometry.height() - h)/2,
+# w, h)
+# self.setWindowTitle('VisTrails APT interface')
+# lbl = QtGui.QLabel(self)
+# mainlayout.addWidget(lbl)
+# lbl.setText("VisTrails wants to use APT to install\
+# package '%s'. Do you want to allow this?" % package_name)
+# lbl.resize(self.width(), 150)
+# lbl.setAlignment(QtCore.Qt.AlignHCenter)
+# lbl.setWordWrap(True)
+# layout = QtGui.QHBoxLayout()
+# self.allowBtn = QtGui.QPushButton("Yes, allow")
+# self.denyBtn = QtGui.QPushButton("No, deny")
+# layout.addWidget(self.allowBtn)
+# layout.addWidget(self.denyBtn)
+# self.layout().addLayout(layout)
+
+# self.connect(self.allowBtn, QtCore.SIGNAL("clicked()"),
+# self.perform_install)
+# self.connect(self.denyBtn, QtCore.SIGNAL("clicked()"),
+# QtGui.qApp, QtCore.SLOT("quit()"))
+
+# pbarlayout = QtGui.QVBoxLayout()
+# pbar = QtGui.QProgressBar()
+# pbar.setMinimum(0)
+# pbar.setMaximum(100)
+# pbarlayout.addWidget(pbar)
+# self.layout().addLayout(pbarlayout)
+# pbar.show()
+# self.pbar = pbar
+# self.pbar.setValue(0)
+# self.status_label = QtGui.QLabel(self)
+# mainlayout.addWidget(self.status_label)
+# self.status_label.setText('Waiting for decision...')
+# self.layout().addStretch()
+
+# def perform_install(self):
+# pkg.markInstall()
+# self.allowBtn.setEnabled(False)
+# self.denyBtn.setEnabled(False)
+# fprogress = GUIFetchProgress(self.pbar, self.status_label)
+# iprogress = GUIInstallProgress(self.pbar, self.status_label)
+# try:
+# cache.commit(fprogress, iprogress)
+# except OSError, e:
+# pass
+# except Exception, e:
+
+# self._timeout = QtCore.QTimer()
+# self.connect(self._timeout, QtCore.SIGNAL("timeout()"),
+# QtGui.qApp, QtCore.SLOT("quit()"))
+# self._timeout.start(3000)
+# self.status_label.setText("Success, exiting in 3 seconds.")
+
+# app = QtGui.QApplication(sys.argv)
+
+# window = Window()
+# window.show()
+# print app.exec_()
+# sys.exit(0)
+import os
+import sys
+
+if __name__ != '__main__':
+ from vistrails.tests import NotModule
+ raise NotModule('This should not be imported as a module')
+
+sys.exit(os.system('yum -y install ' + ' '.join(sys.argv[1:])))
+
+################################################################################
diff --git a/vistrails/gui/bundles/utils.py b/vistrails/gui/bundles/utils.py
new file mode 100644
index 0000000..0209958
--- /dev/null
+++ b/vistrails/gui/bundles/utils.py
@@ -0,0 +1,150 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Utility functions for core.bundles"""
+from vistrails.core import debug
+import vistrails.core.system
+import os
+import platform
+import sys
+
+##############################################################################
+
+def guess_graphical_sudo():
+ """Tries to guess what to call to run a shell with elevated privileges.
+
+ Returns: (sudo, escape)
+ Where:
+ sudo is the command to be used to gain root privileges, it
+ should contain %s where the actual command will be inserted
+ escape is True if the rest of the line needs to be escaped
+ """
+ if sys.platform == 'win32':
+ return '%s', False
+ # sudo needs -E so that the Xauthority file is found and root can connect
+ # to the user's X server
+ if vistrails.core.system.executable_is_in_path('kdesudo'):
+ return 'kdesudo %s', True
+ elif vistrails.core.system.executable_is_in_path('kdesu'):
+ return 'kdesu %s', False
+ elif vistrails.core.system.executable_is_in_path('gksu'):
+ return 'gksu %s', False
+ elif (vistrails.core.system.executable_is_in_path('sudo') and
+ vistrails.core.system.executable_is_in_path('zenity')):
+ # This is a reasonably convoluted hack to only prompt for the password
+ # if user has not recently entered it
+ return ('((echo "" | sudo -v -S -p "") || '
+ '(zenity --entry --title "sudo password prompt" --text '
+ '"Please enter your password to give the system install '
+ 'authorization." --hide-text="" | sudo -v -S -p "")); '
+ 'sudo -E -S -p "" %s',
+ False)
+ # graphical sudo for osx
+ elif vistrails.core.system.executable_is_in_path('osascript'):
+ return "osascript -e " \
+ "'do shell script %s with administrator privileges'", True
+ else:
+ debug.warning("Could not find a graphical sudo-like command.")
+
+ if vistrails.core.system.get_executable_path('sudo'):
+ debug.warning("Will use regular sudo")
+ return "sudo -E %s", False
+ else:
+ debug.warning("Will use regular su")
+ return "su --preserve-environment -c %s", True
+
+##############################################################################
+
+class System_guesser(object):
+
+ def __init__(self):
+ self._callable_dict = {}
+
+ def add_test(self, test, system_name):
+ if self._callable_dict.has_key(system_name):
+ raise ValueError("test for '%s' already present." % system_name)
+ if system_name == 'UNKNOWN':
+ raise ValueError("Invalid system name")
+ assert isinstance(system_name, str)
+ self._callable_dict[system_name] = test
+
+ def guess_system(self):
+ for (name, callable_) in self._callable_dict.iteritems():
+ if callable_():
+ return name
+ else:
+ return 'UNKNOWN'
+
+_system_guesser = System_guesser()
+
+##############################################################################
+# System tests
+
+def _guess_suse():
+ try:
+ tokens = open('/etc/SuSE-release').readline()[-1].split()
+ return tokens[0] == 'SUSE'
+ except:
+ return False
+_system_guesser.add_test(_guess_suse, 'linux-suse')
+
+def _guess_ubuntu():
+ return platform.linux_distribution()[0]=='Ubuntu' or \
+ platform.linux_distribution()[0]=='LinuxMint'
+_system_guesser.add_test(_guess_ubuntu, 'linux-ubuntu')
+
+def _guess_debian():
+ return platform.linux_distribution()[0].lower() == 'debian'
+_system_guesser.add_test(_guess_debian, 'linux-debian')
+
+def _guess_fedora():
+ return os.path.isfile('/etc/fedora-release')
+_system_guesser.add_test(_guess_fedora, 'linux-fedora')
+
+def _guess_windows():
+ return vistrails.core.system.systemType == 'Windows'
+_system_guesser.add_test(_guess_windows, 'windows')
+
+##############################################################################
+
+def guess_system():
+ """guess_system will try to identify which system you're running. Result
+will be a string describing the system. This is more discriminating than
+Linux/OSX/Windows: We'll try to figure out whether you're running SuSE, Debian,
+Ubuntu, RedHat, fink, darwinports, etc.
+
+Currently, we only support SuSE, Debian, Ubuntu and Fedora. However, we only
+have actual bundle installing for Debian, Ubuntu and Fedora."""
+ return _system_guesser.guess_system()
diff --git a/vistrails/gui/collection/__init__.py b/vistrails/gui/collection/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/gui/collection/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/gui/collection/explorer.py b/vistrails/gui/collection/explorer.py
new file mode 100644
index 0000000..a02724e
--- /dev/null
+++ b/vistrails/gui/collection/explorer.py
@@ -0,0 +1,758 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core import debug
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.core.collection.search import SearchCompiler, SearchParseError
+from vistrails.core.db.locator import FileLocator, DBLocator
+from vistrails.core.system import default_connections_file
+from vistrails.core.external_connection import ExtConnectionList
+from vistrails.db import VistrailsDBException
+from vistrails.db.services.io import test_db_connection
+from vistrails.db.services.query import runLogQuery, runWorkflowQuery
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.open_db_window import QDBConnectionList, QConnectionDBSetupWindow
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+import vistrails.gui
+
+class QExplorerWindow(QtGui.QWidget, QVistrailsPaletteInterface):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+
+ self.layout = QtGui.QVBoxLayout()
+ self.layout.setContentsMargins(0, 0, 0, 0)
+
+ self.splitter = QtGui.QSplitter()
+ self.splitter.setContentsMargins(0, 0, 0, 0)
+ self.layout.addWidget(self.splitter)
+ self.connectionList = QDBConnectionList(self)
+ dbGrid = QtGui.QGridLayout(self)
+ dbGrid.setMargin(0)
+ dbGrid.setSpacing(0)
+ dbGrid.addWidget(self.connectionList, 2, 1, QtCore.Qt.AlignLeft)
+ self.addAct = QtGui.QAction("Add Database", self)
+ self.removeAct = QtGui.QAction("Remove Database", self)
+ self.addButton = QtGui.QToolButton()
+ self.addButton.setToolTip("Create a new database connection")
+ self.addButton.setDefaultAction(self.addAct)
+ self.addButton.setAutoRaise(True)
+ self.removeButton = QtGui.QToolButton()
+ self.removeButton.setToolTip("Remove the selected connection from list")
+ self.removeButton.setDefaultAction(self.removeAct)
+ self.removeButton.setAutoRaise(True)
+ self.removeButton.setEnabled(False)
+ panelButtonsLayout = QtGui.QHBoxLayout()
+ panelButtonsLayout.setMargin(0)
+ panelButtonsLayout.setSpacing(0)
+ panelButtonsLayout.addWidget(self.addButton)
+ panelButtonsLayout.addWidget(self.removeButton)
+ dbGrid.addLayout(panelButtonsLayout, 1, 1, QtCore.Qt.AlignLeft)
+ dbWidget = QDBWidget(parent, self.connectionList)
+ dbWidget.setLayout(dbGrid)
+ self.splitter.addWidget(dbWidget)
+ self.connect(self.addAct,
+ QtCore.SIGNAL('triggered()'),
+ self.showConnConfig)
+ self.connect(self.removeAct,
+ QtCore.SIGNAL('triggered()'),
+ self.connectionList.removeConnection)
+ self.connect(self.connectionList,
+ QtCore.SIGNAL('itemSelectionChanged()'),
+ self.updateEditButtons)
+ self.connect(self.connectionList,
+ QtCore.SIGNAL('itemSelectionChanged()'),
+ self.checkConnection)
+ self.tabView = QtGui.QTabWidget()
+ self.tabView.setContentsMargins(0, 0, 0, 0)
+ self.splitter.addWidget(self.tabView)
+# self.workflowSearch = WorkflowSearchWidget(self.connectionList)
+# self.tabView.addTab(self.workflowSearch, "Search for Workflows")
+ self.executionSearch = ExecutionSearchWidget(self.connectionList)
+ self.tabView.addTab(self.executionSearch, "Search for Workflow Executions")
+ self.setLayout(self.layout)
+ self.setWindowTitle('Provenance Browser')
+ self.resize(QtCore.QSize(800, 600))
+# self.workflowSearch.setup_results()
+ self.executionSearch.setup_results()
+
+ def showConnConfig(self, *args, **keywords):
+ return showConnConfig(self.connectionList, *args, **keywords)
+
+ def updateEditButtons(self):
+ """updateEditButtons() -> None
+ It will enable/disable the connections buttons according to the
+ selection
+
+ """
+ self.workflowSearch.setup_results()
+ self.executionSearch.setup_results()
+ id = self.connectionList.getCurrentItemId()
+ if id != -1:
+ self.removeButton.setEnabled(True)
+ else:
+ self.removeButton.setEnabled(False)
+
+ def checkConnection(self):
+ checkConnection(self.connectionList)
+
+
+ def getConnectionInfo(self, id):
+ return getConnectionInfo(self.connectionList, id)
+
+def showConnConfig(connectionList, *args, **keywords):
+ """showConnConfig(*args, **keywords) -> None
+ shows a window to configure the connection. The valid keywords
+ are defined in QConnectionDBSetupWindow.__init__()
+
+ """
+ dialog = QConnectionDBSetupWindow(**keywords)
+ if dialog.exec_() == QtGui.QDialog.Accepted:
+ config = {'id': int(dialog.id),
+ 'name': str(dialog.nameEdt.text()),
+ 'host': str(dialog.hostEdt.text()),
+ 'port': int(dialog.portEdt.value()),
+ 'user': str(dialog.userEdt.text()),
+ 'passwd': str(dialog.passwdEdt.text()),
+ 'db': str(dialog.databaseEdt.text())}
+ id = connectionList.setConnectionInfo(**config)
+ connectionList.setCurrentId(id)
+ return True
+ else:
+ return False
+
+def getConnectionInfo(connectionList, id):
+ """getConnectionInfo(connectionList: QDBConnectionList, id: int) -> dict
+ Returns info of ExtConnection """
+ conn = connectionList.get_connection(id)
+ key = str(conn.id) + "." + conn.name + "." + conn.host
+ passwd = DBLocator.keyChain.get_key(key)
+ if conn != None:
+ config = {'id': conn.id,
+ 'name': conn.name,
+ 'host': conn.host,
+ 'port': conn.port,
+ 'user': conn.user,
+ 'passwd': passwd,
+ 'db': conn.database}
+ else:
+ config = None
+ return config
+
+def checkConnection(connectionList):
+ """checkConnection() -> None
+ It will try if the connection works or if a password is necessary
+
+ """
+ conn_id = connectionList.getCurrentItemId()
+ if conn_id != -1:
+ conn = connectionList.get_connection(conn_id)
+ config = getConnectionInfo(connectionList, conn_id)
+ if config != None:
+ try:
+ config_name = config['name']
+ del config['name']
+ config_id = config['id']
+ del config['id']
+ test_db_connection(config)
+ except VistrailsDBException:
+ # assume connection is wrong
+ config['name'] = config_name
+ config['id'] = config_id
+ config["create"] = False
+ showConnConfig(connectionList, **config)
+
+class QDBWidget(QtGui.QWidget):
+ """ Custom widget for handling the showConnConfig """
+
+ def __init__(self, parent, connectionList):
+ QtGui.QWidget.__init__(self, parent)
+ self.connectionList = connectionList
+
+ def showConnConfig(self, *args, **keywords):
+ return showConnConfig(self.connectionList, *args, **keywords)
+
+class ExecutionSearchWidget(QtGui.QSplitter):
+ def __init__(self, connectionList):
+ QtGui.QSplitter.__init__(self)
+ self.connectionList = connectionList
+ self.conn = None
+ self.config = None
+ self.offset = 0
+ self.limit = 50
+ self.numRows = None
+ self.vistrail = None
+ self.version = None
+ self.fromTime = None
+ self.toTime = None
+ self.user = None
+ self.thumbs = None
+ self.completed = None
+ self.modules = []
+ self.setOrientation(QtCore.Qt.Vertical)
+ self.searchLayout = QtGui.QGridLayout()
+ self.vistrailEditCheckBox = QtGui.QCheckBox()
+ self.vistrailEditCheckBox.setToolTip('Check to enable this search option')
+ self.vistrailEdit = QtGui.QLineEdit()
+ self.searchLayout.addWidget(self.vistrailEditCheckBox, 0,0)
+ self.searchLayout.addWidget(QtGui.QLabel('Vistrail:'), 0,1)
+ self.searchLayout.addWidget(self.vistrailEdit, 0,2)
+ self.versionEditCheckBox = QtGui.QCheckBox()
+ self.versionEditCheckBox.setToolTip('Check to enable this search option')
+ self.versionEdit = QtGui.QLineEdit()
+ self.searchLayout.addWidget(self.versionEditCheckBox, 0,3)
+ self.searchLayout.addWidget(QtGui.QLabel('Version:'), 0,4)
+ self.searchLayout.addWidget(self.versionEdit, 0,5)
+ self.fromTimeEditCheckBox = QtGui.QCheckBox()
+ self.fromTimeEditCheckBox.setToolTip('Check to enable this search option')
+ self.fromTimeEdit = QtGui.QDateTimeEdit(QtCore.QDateTime.currentDateTime().addDays(-1))
+ self.fromTimeEdit.setDisplayFormat('yyyy-MM-d H:mm:ss')
+ self.fromTimeEdit.setCalendarPopup(True)
+ self.searchLayout.addWidget(self.fromTimeEditCheckBox, 1,0)
+ self.searchLayout.addWidget(QtGui.QLabel('From time:'), 1,1)
+ self.searchLayout.addWidget(self.fromTimeEdit, 1,2)
+ self.toTimeEditCheckBox = QtGui.QCheckBox()
+ self.toTimeEditCheckBox.setToolTip('Check to enable this search option')
+ self.toTimeEdit = QtGui.QDateTimeEdit(QtCore.QDateTime.currentDateTime())
+ self.toTimeEdit.setDisplayFormat('yyyy-MM-d H:mm:ss')
+ self.toTimeEdit.setCalendarPopup(True)
+ self.searchLayout.addWidget(self.toTimeEditCheckBox, 1,3)
+ self.searchLayout.addWidget(QtGui.QLabel('To time:'), 1,4)
+ self.searchLayout.addWidget(self.toTimeEdit, 1,5)
+ self.userEditCheckBox = QtGui.QCheckBox()
+ self.userEditCheckBox.setToolTip('Check to enable this search option')
+ self.userEdit = QtGui.QLineEdit()
+ self.searchLayout.addWidget(self.userEditCheckBox, 2,0)
+ self.searchLayout.addWidget(QtGui.QLabel('User:'), 2,1)
+ self.searchLayout.addWidget(self.userEdit, 2,2)
+ self.completedEditCheckBox = QtGui.QCheckBox()
+ self.completedEditCheckBox.setToolTip('Check to enable this search option')
+ self.completedEdit = QtGui.QComboBox()
+ self.completedEdit.addItems(['Yes', 'No', 'Error'])
+ self.searchLayout.addWidget(self.completedEditCheckBox, 2,3)
+ self.searchLayout.addWidget(QtGui.QLabel('Completed:'), 2,4)
+ self.searchLayout.addWidget(self.completedEdit, 2,5)
+
+ self.moduleEditCheckBox = QtGui.QCheckBox()
+ self.moduleEditCheckBox.setToolTip('Check to enable this search option')
+ self.moduleEdit = QtGui.QLineEdit()
+ self.moduleEdit.setToolTip('Add module names separated by ,\nResult type can be specified by using: ModuleName:Yes/No/Error')
+ self.searchLayout.addWidget(self.moduleEditCheckBox, 3,0)
+ self.searchLayout.addWidget(QtGui.QLabel('Modules:'), 3,1)
+ self.searchLayout.addWidget(self.moduleEdit, 3,2)
+ self.thumbsCheckBox = QtGui.QCheckBox()
+ self.thumbsCheckBox.setToolTip('Check to view result thumbnails (may be slow)')
+ self.searchLayout.addWidget(self.thumbsCheckBox, 3,3)
+ self.searchLayout.addWidget(QtGui.QLabel('View thumbs'), 3,4)
+ self.searchButton = QtGui.QPushButton("Search")
+ self.searchButton.setStatusTip("Search the database for executions")
+ self.searchLayout.addWidget(self.searchButton, 3, 5)
+ self.searchWidget = QtGui.QWidget()
+ self.searchWidget.setLayout(self.searchLayout)
+ self.addWidget(self.searchWidget)
+ self.itemView = QtGui.QTreeWidget(self.parent())
+ self.addWidget(self.itemView)
+ statusGrid = QtGui.QGridLayout()
+ statusGrid.setMargin(0)
+ statusGrid.setSpacing(0)
+ statusWidget = QtGui.QWidget()
+ statusWidget.setLayout(statusGrid)
+ self.addWidget(statusWidget)
+ self.setStretchFactor(0, 0)
+ self.setStretchFactor(1, 1)
+ self.setStretchFactor(2, 0)
+ statusLayout = QtGui.QHBoxLayout()
+ statusLayout.setSpacing(5)
+ statusGrid.addLayout(statusLayout, 2, 1, QtCore.Qt.AlignLeft)
+
+ self.prevButton = QtGui.QPushButton("Previous")
+ self.prevButton.setStatusTip("Show previous results")
+ self.prevButton.hide()
+ statusLayout.addWidget(self.prevButton)
+
+ self.nextButton = QtGui.QPushButton("Next")
+ self.nextButton.setStatusTip("Show next results")
+ self.nextButton.hide()
+ statusLayout.addWidget(self.nextButton)
+
+ self.statusText = QtGui.QLabel('No query specified')
+ statusLayout.addWidget(self.statusText)
+ self.connect(self.searchButton,
+ QtCore.SIGNAL('clicked()'),
+ self.newQuery)
+ self.connect(self.prevButton,
+ QtCore.SIGNAL('clicked()'),
+ self.gotoPrevious)
+ self.connect(self.nextButton,
+ QtCore.SIGNAL('clicked()'),
+ self.gotoNext)
+ self.connect(self.itemView,
+ QtCore.SIGNAL('itemDoubleClicked(QTreeWidgetItem *,int)'),
+ self.showItem)
+
+ def newQuery(self):
+ self.offset = 0
+ self.vistrail = None
+ if self.vistrailEditCheckBox.isChecked():
+ self.vistrail = str(self.vistrailEdit.text()).strip()
+ self.version = None
+ if self.versionEditCheckBox.isChecked():
+ self.version = str(self.versionEdit.text()).strip()
+ self.fromTime = None
+ if self.fromTimeEditCheckBox.isChecked():
+ self.fromTime = str(
+ self.fromTimeEdit.dateTime().toString('yyyy-MM-d H:mm:ss'))
+ self.toTime = None
+ if self.toTimeEditCheckBox.isChecked():
+ self.toTime = str(
+ self.toTimeEdit.dateTime().toString('yyyy-MM-d H:mm:ss'))
+ self.user = None
+ if self.userEditCheckBox.isChecked():
+ self.user = str(self.userEdit.text()).strip()
+ self.completed = None
+ if self.completedEditCheckBox.isChecked():
+ self.completed = str(self.completedEdit.currentText()).strip()
+ self.modules = []
+ if self.moduleEditCheckBox.isChecked():
+ # create list of [moduleType, completed] pairs
+ modules = str(self.moduleEdit.text()).strip()
+ for k in [i.strip() for i in modules.split(',')]:
+ v = k.split(':')
+ if len(v)>1:
+ self.modules.append((v[0].strip(), v[1].strip()))
+ else:
+ self.modules.append((v[0].strip(), None))
+ self.thumbs = self.thumbsCheckBox.isChecked()
+ conn_id = self.connectionList.getCurrentItemId()
+ self.conn = self.connectionList.get_connection(conn_id)
+ self.config = getConnectionInfo(self.connectionList, conn_id)
+
+ self.searchDatabase()
+
+ def searchDatabase(self):
+ self.statusText.setText("Running query...")
+ self.repaint()
+ # create connection
+ conn = self.conn
+ config = self.config
+ if conn.dbtype == 'MySQL':
+ #removing extra keyword arguments for MySQldb
+ config_name = config['name']
+ del config['name']
+ config_id = config['id']
+ del config['id']
+
+ wf_exec_list = runLogQuery(config,
+ vistrail=self.vistrail, version=self.version,
+ fromTime=self.fromTime, toTime=self.toTime,
+ user=self.user, completed=self.completed,
+ offset=self.offset, limit=self.limit,
+ modules=self.modules, thumbs=self.thumbs)
+ if 0 == self.offset:
+ wf_exec_list, self.numRows = wf_exec_list
+ if conn.dbtype == 'MySQL':
+ config['name'] = config_name
+ config['id'] = config_id
+ self.setup_results(wf_exec_list)
+ self.updateStatus()
+
+ def gotoPrevious(self):
+ self.offset = max(self.offset - self.limit, 0)
+ self.searchDatabase()
+
+ def gotoNext(self):
+ self.offset = min(self.offset + self.limit, self.numRows)
+ self.searchDatabase()
+
+ def updateStatus(self):
+ if self.offset > 0:
+ self.prevButton.show()
+ else:
+ self.prevButton.hide()
+ last = self.offset + self.limit
+ if last < self.numRows:
+ self.nextButton.show()
+ else:
+ self.nextButton.hide()
+ last = self.numRows
+ if self.numRows:
+ self.statusText.setText("Showing %s-%s out of %s results" %
+ (self.offset+1, last, self.numRows))
+ else:
+ self.statusText.setText("No matching results found")
+
+ def setup_results(self, wf_exec_list=[]):
+ self.itemView.clear()
+ self.itemView.setIconSize(QtCore.QSize(32,32))
+ columns = ['Vistrail', 'Version', 'Start time', 'End time', 'Completed']
+ self.itemView.setColumnCount(len(columns))
+ self.itemView.setHeaderLabels(columns)
+ self.itemView.setSortingEnabled(True)
+ for wf_exec in wf_exec_list:
+ item = QExecutionItem(wf_exec)
+ self.itemView.addTopLevelItem(item)
+ self.itemView.header().setResizeMode(4, QtGui.QHeaderView.ResizeToContents)
+ self.itemView.header().setResizeMode(3, QtGui.QHeaderView.ResizeToContents)
+ self.itemView.header().setResizeMode(2, QtGui.QHeaderView.ResizeToContents)
+ self.itemView.header().setResizeMode(1, QtGui.QHeaderView.Interactive)
+ self.itemView.header().setResizeMode(0, QtGui.QHeaderView.Interactive)
+ self.itemView.header().resizeSections(QtGui.QHeaderView.Stretch)
+ conn_id = self.connectionList.getCurrentItemId()
+ if conn_id < 0:
+ self.statusText.setText("Select a database")
+
+ def showItem(self, item, col):
+ (v_name, v_id, log_id, v_version, version_name, e_id,
+ ts_start, ts_end, user, completed, thumb) = item.wf_exec
+ config = self.config
+ locator = \
+ DBLocator(config['host'],
+ config['port'],
+ config['db'],
+ config['user'],
+ config['passwd'],
+ config['name'],
+ obj_id=v_id,
+ obj_type='vistrail',
+ workflow_exec=ts_start,
+ connection_id=config.get('id', None))
+ #print "url:", locator.to_url()
+ import vistrails.gui.application
+ app = vistrails.gui.application.get_vistrails_application()
+ open_vistrail = app.builderWindow.open_vistrail_without_prompt
+
+ workflow_exec = locator.kwargs.get('workflow_exec', None)
+ args = {}
+ if workflow_exec:
+ args['workflow_exec'] = workflow_exec
+ args['version'] = version_name if version_name else v_version
+ open_vistrail(locator, **args)
+
+class QExecutionItem(QtGui.QTreeWidgetItem):
+ def __init__(self, wf_exec, parent=None):
+ (v_name, v_id, log_id, v_version, version_name, e_id,
+ ts_start, ts_end, user, completed, thumb) = wf_exec
+ version = version_name if version_name else v_version
+ completed = {'-1':'Error', '0':'No', '1':'Yes'}.get(str(completed), 'Unknown')
+ labels = (str(v_name), str(version),
+ str(ts_start), str(ts_end), str(completed))
+ QtGui.QTreeWidgetItem.__init__(self, labels)
+ self.wf_exec = wf_exec
+ self.setToolTip(0, 'vistrail:%s version:%s log:%s wf_exec:%s user:%s' %
+ (v_id, v_version, log_id, e_id, user))
+ if thumb:
+ pixmap = QtGui.QPixmap()
+ pixmap.loadFromData(thumb)
+ self.setIcon(1, QtGui.QIcon(pixmap))
+ tooltip = """<img border=0 src="data:image/png;base64,%s">""" % thumb.encode('base64')
+ self.setToolTip(1, tooltip)
+
+ def __lt__(self, other):
+ sort_col = self.treeWidget().sortColumn()
+ if sort_col in set([1]):
+ try:
+ return int(self.text(sort_col)) < int(other.text(sort_col))
+ except ValueError:
+ pass
+ return QtGui.QTreeWidgetItem.__lt__(self, other)
+
+class WorkflowSearchWidget(QtGui.QSplitter):
+ def __init__(self, connectionList):
+ QtGui.QSplitter.__init__(self)
+ self.connectionList = connectionList
+ self.conn = None
+ self.config = None
+ self.offset = 0
+ self.limit = 50
+ self.numRows = None
+ self.vistrail = None
+ self.version = None
+ self.fromTime = None
+ self.toTime = None
+ self.user = None
+ self.thumbs = None
+ self.modules = []
+ self.setOrientation(QtCore.Qt.Vertical)
+ self.searchLayout = QtGui.QGridLayout()
+ self.vistrailEditCheckBox = QtGui.QCheckBox()
+ self.vistrailEditCheckBox.setToolTip('Check to enable this search option')
+ self.vistrailEdit = QtGui.QLineEdit()
+ self.searchLayout.addWidget(self.vistrailEditCheckBox, 0,0)
+ self.searchLayout.addWidget(QtGui.QLabel('Vistrail:'), 0,1)
+ self.searchLayout.addWidget(self.vistrailEdit, 0,2)
+ self.versionEditCheckBox = QtGui.QCheckBox()
+ self.versionEditCheckBox.setToolTip('Check to enable this search option')
+ self.versionEdit = QtGui.QLineEdit()
+ self.searchLayout.addWidget(self.versionEditCheckBox, 0,3)
+ self.searchLayout.addWidget(QtGui.QLabel('Version:'), 0,4)
+ self.searchLayout.addWidget(self.versionEdit, 0,5)
+ self.fromTimeEditCheckBox = QtGui.QCheckBox()
+ self.fromTimeEditCheckBox.setToolTip('Check to enable this search option')
+ self.fromTimeEdit = QtGui.QDateTimeEdit(QtCore.QDateTime.currentDateTime().addDays(-1))
+ self.fromTimeEdit.setDisplayFormat('yyyy-MM-d H:mm:ss')
+ self.fromTimeEdit.setCalendarPopup(True)
+ self.searchLayout.addWidget(self.fromTimeEditCheckBox, 1,0)
+ self.searchLayout.addWidget(QtGui.QLabel('From time:'), 1,1)
+ self.searchLayout.addWidget(self.fromTimeEdit, 1,2)
+ self.toTimeEditCheckBox = QtGui.QCheckBox()
+ self.toTimeEditCheckBox.setToolTip('Check to enable this search option')
+ self.toTimeEdit = QtGui.QDateTimeEdit(QtCore.QDateTime.currentDateTime())
+ self.toTimeEdit.setDisplayFormat('yyyy-MM-d H:mm:ss')
+ self.toTimeEdit.setCalendarPopup(True)
+ self.searchLayout.addWidget(self.toTimeEditCheckBox, 1,3)
+ self.searchLayout.addWidget(QtGui.QLabel('To time:'), 1,4)
+ self.searchLayout.addWidget(self.toTimeEdit, 1,5)
+ self.userEditCheckBox = QtGui.QCheckBox()
+ self.userEditCheckBox.setToolTip('Check to enable this search option')
+ self.userEdit = QtGui.QLineEdit()
+ self.searchLayout.addWidget(self.userEditCheckBox, 2,0)
+ self.searchLayout.addWidget(QtGui.QLabel('User:'), 2,1)
+ self.searchLayout.addWidget(self.userEdit, 2,2)
+
+ self.moduleEditCheckBox = QtGui.QCheckBox()
+ self.moduleEditCheckBox.setToolTip('Check to enable this search option')
+ self.moduleEdit = QtGui.QLineEdit()
+ self.moduleEdit.setToolTip('Add module names separated by ,\nConnected modules can be specified by using: ModuleA->ModuleB')
+ self.searchLayout.addWidget(self.moduleEditCheckBox, 3,0)
+ self.searchLayout.addWidget(QtGui.QLabel('Modules:'), 3,1)
+ self.searchLayout.addWidget(self.moduleEdit, 3,2)
+ self.thumbsCheckBox = QtGui.QCheckBox()
+ self.thumbsCheckBox.setToolTip('Check to view result thumbnails (may be slow)')
+ self.searchLayout.addWidget(self.thumbsCheckBox, 3,3)
+ self.searchLayout.addWidget(QtGui.QLabel('View thumbs'), 3,4)
+ self.searchButton = QtGui.QPushButton("Search")
+ self.searchButton.setStatusTip("Search the database for executions")
+ self.searchLayout.addWidget(self.searchButton, 3, 5)
+ self.searchWidget = QtGui.QWidget()
+ self.searchWidget.setLayout(self.searchLayout)
+ self.addWidget(self.searchWidget)
+ self.itemView = QtGui.QTreeWidget(self.parent())
+ self.addWidget(self.itemView)
+ statusGrid = QtGui.QGridLayout()
+ statusGrid.setMargin(0)
+ statusGrid.setSpacing(0)
+ statusWidget = QtGui.QWidget()
+ statusWidget.setLayout(statusGrid)
+ self.addWidget(statusWidget)
+ self.setStretchFactor(0, 0)
+ self.setStretchFactor(1, 1)
+ self.setStretchFactor(2, 0)
+ statusLayout = QtGui.QHBoxLayout()
+ statusLayout.setSpacing(5)
+ statusGrid.addLayout(statusLayout, 2, 1, QtCore.Qt.AlignLeft)
+
+ self.prevButton = QtGui.QPushButton("Previous")
+ self.prevButton.setStatusTip("Show previous results")
+ self.prevButton.hide()
+ statusLayout.addWidget(self.prevButton)
+
+ self.nextButton = QtGui.QPushButton("Next")
+ self.nextButton.setStatusTip("Show next results")
+ self.nextButton.hide()
+ statusLayout.addWidget(self.nextButton)
+
+ self.statusText = QtGui.QLabel('No query specified')
+ statusLayout.addWidget(self.statusText)
+ self.connect(self.searchButton,
+ QtCore.SIGNAL('clicked()'),
+ self.newQuery)
+ self.connect(self.prevButton,
+ QtCore.SIGNAL('clicked()'),
+ self.gotoPrevious)
+ self.connect(self.nextButton,
+ QtCore.SIGNAL('clicked()'),
+ self.gotoNext)
+ self.connect(self.itemView,
+ QtCore.SIGNAL('itemDoubleClicked(QTreeWidgetItem *,int)'),
+ self.showItem)
+
+ def newQuery(self):
+ self.offset = 0
+ self.vistrail = None
+ if self.vistrailEditCheckBox.isChecked():
+ self.vistrail = str(self.vistrailEdit.text()).strip()
+ self.version = None
+ if self.versionEditCheckBox.isChecked():
+ self.version = str(self.versionEdit.text()).strip()
+ self.fromTime = None
+ if self.fromTimeEditCheckBox.isChecked():
+ self.fromTime = str(
+ self.fromTimeEdit.dateTime().toString('yyyy-MM-d H:mm:ss'))
+ self.toTime = None
+ if self.toTimeEditCheckBox.isChecked():
+ self.toTime = str(
+ self.toTimeEdit.dateTime().toString('yyyy-MM-d H:mm:ss'))
+ self.user = None
+ if self.userEditCheckBox.isChecked():
+ self.user = str(self.userEdit.text()).strip()
+ self.modules = []
+ if self.moduleEditCheckBox.isChecked():
+ # create list of [moduleType, connected to previous] pairs
+ groups = str(self.moduleEdit.text()).strip()
+ groups = [i.strip() for i in groups.split(',')]
+ for group in [i.split('->') for i in groups]:
+ if len(group):
+ module = group.pop(0).strip()
+ if len(module):
+ self.modules.append((module, False))
+ while len(group):
+ module = group.pop(0).strip()
+ if len(module):
+ self.modules.append((module, True))
+ self.thumbs = self.thumbsCheckBox.isChecked()
+ conn_id = self.connectionList.getCurrentItemId()
+ self.conn = self.connectionList.get_connection(conn_id)
+ self.config = getConnectionInfo(self.connectionList, conn_id)
+
+ self.searchDatabase()
+
+ def searchDatabase(self):
+ self.statusText.setText("Running query...")
+ self.repaint()
+ # create connection
+ conn = self.conn
+ config = self.config
+ if conn.dbtype == 'MySQL':
+ #removing extra keyword arguments for MySQldb
+ config_name = config['name']
+ del config['name']
+ config_id = config['id']
+ del config['id']
+
+ workflow_list = runWorkflowQuery(config,
+ vistrail=self.vistrail, version=self.version,
+ fromTime=self.fromTime, toTime=self.toTime,
+ user=self.user,
+ offset=self.offset, limit=self.limit,
+ modules=self.modules,
+ thumbs=self.thumbs)
+ if 0 == self.offset:
+ workflow_list, self.numRows = workflow_list
+ if conn.dbtype == 'MySQL':
+ config['name'] = config_name
+ config['id'] = config_id
+ self.setup_results(workflow_list)
+ self.updateStatus()
+
+ def gotoPrevious(self):
+ self.offset = max(self.offset - self.limit, 0)
+ self.searchDatabase()
+
+ def gotoNext(self):
+ self.offset = min(self.offset + self.limit, self.numRows)
+ self.searchDatabase()
+
+ def updateStatus(self):
+ if self.offset > 0:
+ self.prevButton.show()
+ else:
+ self.prevButton.hide()
+ last = self.offset + self.limit
+ if last < self.numRows:
+ self.nextButton.show()
+ else:
+ self.nextButton.hide()
+ last = self.numRows
+ if self.numRows:
+ self.statusText.setText("Showing %s-%s out of %s results" %
+ (self.offset+1, last, self.numRows))
+ else:
+ self.statusText.setText("No matching results found")
+
+ def setup_results(self, workflow_list=[]):
+ self.itemView.clear()
+ self.itemView.setIconSize(QtCore.QSize(32,32))
+ columns = ['Vistrail', 'Version', 'Time', 'User']
+ self.itemView.setColumnCount(len(columns))
+ self.itemView.setHeaderLabels(columns)
+ self.itemView.setSortingEnabled(True)
+ for workflow in workflow_list:
+ item = QWorkflowItem(workflow)
+ self.itemView.addTopLevelItem(item)
+ self.itemView.header().setResizeMode(3, QtGui.QHeaderView.ResizeToContents)
+ self.itemView.header().setResizeMode(2, QtGui.QHeaderView.ResizeToContents)
+ self.itemView.header().setResizeMode(1, QtGui.QHeaderView.Interactive)
+ self.itemView.header().setResizeMode(0, QtGui.QHeaderView.Interactive)
+ self.itemView.header().resizeSections(QtGui.QHeaderView.Stretch)
+ conn_id = self.connectionList.getCurrentItemId()
+ if conn_id < 0:
+ self.statusText.setText("Select a database")
+
+ def showItem(self, item, col):
+ (v_name, v_id, v_version, version_name, time, user, thumb) = \
+ item.workflow
+ config = self.config
+ locator = \
+ DBLocator(config['host'],
+ config['port'],
+ config['db'],
+ config['user'],
+ config['passwd'],
+ config['name'],
+ obj_id=v_id,
+ obj_type='vistrail',
+ connection_id=config.get('id', None))
+ #print "url:", locator.to_url()
+ import vistrails.gui.application
+ app = vistrails.gui.application.get_vistrails_application()
+ open_vistrail = app.builderWindow.open_vistrail_without_prompt
+ args = {}
+ args['version'] = version_name if version_name else v_version
+ #print "args", args
+ open_vistrail(locator, **args)
+
+class QWorkflowItem(QtGui.QTreeWidgetItem):
+ def __init__(self, workflow, parent=None):
+ (v_name, v_id, v_version, version_name, time, user, thumb) = workflow
+ version = version_name if version_name else v_version
+ labels = (str(v_name), str(version), str(time), str(user))
+ QtGui.QTreeWidgetItem.__init__(self, labels)
+ self.workflow = workflow
+ self.setToolTip(0, 'vistrail:%s version:%s' % (v_id, v_version))
+ if thumb:
+ pixmap = QtGui.QPixmap()
+ pixmap.loadFromData(thumb)
+ self.setIcon(1, QtGui.QIcon(pixmap))
+ tooltip = """<img border=0 src="data:image/png;base64,%s">""" % thumb.encode('base64')
+ self.setToolTip(1, tooltip)
+
+ def __lt__(self, other):
+ sort_col = self.treeWidget().sortColumn()
+ if sort_col in set([1]):
+ try:
+ return int(self.text(sort_col)) < int(other.text(sort_col))
+ except ValueError:
+ pass
+ return QtGui.QTreeWidgetItem.__lt__(self, other)
diff --git a/vistrails/gui/collection/vis_log.py b/vistrails/gui/collection/vis_log.py
new file mode 100644
index 0000000..69cf5a4
--- /dev/null
+++ b/vistrails/gui/collection/vis_log.py
@@ -0,0 +1,582 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This modules builds a widget to visualize workflow execution logs """
+from PyQt4 import QtCore, QtGui
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.log.module_exec import ModuleExec
+from vistrails.core.log.group_exec import GroupExec
+from vistrails.core.log.loop_exec import LoopExec
+from vistrails.core.log.workflow_exec import WorkflowExec
+from vistrails.gui.pipeline_view import QPipelineView
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+from vistrails.gui.collection.workspace import QWorkspaceWindow
+from vistrails.core import system, debug
+import vistrails.core.db.io
+
+
+##############################################################################
+
+
+class QExecutionItem(QtGui.QTreeWidgetItem):
+ """
+ QExecutionListWidget is a widget containing a list of workflow executions.
+
+ """
+ def __init__(self, execution, parent=None):
+ QtGui.QTreeWidgetItem.__init__(self, parent)
+ self.execution = execution
+ execution.item = self
+
+ # find parent workflow or group
+ if parent is not None:
+ while (parent.parent() is not None and
+ not isinstance(parent.execution, GroupExec)):
+ parent = parent.parent()
+ self.wf_execution = parent.execution
+ else:
+ self.wf_execution = execution
+
+ if isinstance(execution, WorkflowExec):
+ for item_exec in execution.item_execs:
+ QExecutionItem(item_exec, self)
+ if execution.completed == -2:
+ brush = CurrentTheme.SUSPENDED_MODULE_BRUSH
+ elif execution.completed == 1:
+ brush = CurrentTheme.SUCCESS_MODULE_BRUSH
+ else:
+ brush = CurrentTheme.ERROR_MODULE_BRUSH
+
+ if execution.db_name:
+ self.setText(0, execution.db_name)
+ else:
+ self.setText(0, 'Version #%s' % execution.parent_version )
+ if isinstance(execution, ModuleExec):
+ for loop_exec in execution.loop_execs:
+ QExecutionItem(loop_exec, self)
+ if execution.completed == 1:
+ if execution.error:
+ brush = CurrentTheme.ERROR_MODULE_BRUSH
+ self.wf_execution.completed = -1
+ elif execution.cached:
+ brush = CurrentTheme.NOT_EXECUTED_MODULE_BRUSH
+ else:
+ brush = CurrentTheme.SUCCESS_MODULE_BRUSH
+ elif execution.completed == -2:
+ brush = CurrentTheme.SUSPENDED_MODULE_BRUSH
+ else:
+ brush = CurrentTheme.ERROR_MODULE_BRUSH
+ self.setText(0, '%s' % execution.module_name)
+ if isinstance(execution, GroupExec):
+ for item_exec in execution.item_execs:
+ QExecutionItem(item_exec, self)
+ if execution.completed == 1:
+ if execution.error:
+ self.wf_execution.completed = -1
+ brush = CurrentTheme.ERROR_MODULE_BRUSH
+ elif execution.cached:
+ brush = CurrentTheme.NOT_EXECUTED_MODULE_BRUSH
+ else:
+ brush = CurrentTheme.SUCCESS_MODULE_BRUSH
+ elif execution.completed == -2:
+ brush = CurrentTheme.SUSPENDED_MODULE_BRUSH
+ else:
+ brush = CurrentTheme.ERROR_MODULE_BRUSH
+ self.setText(0, 'Group')
+ if isinstance(execution, LoopExec):
+ for item_exec in execution.item_execs:
+ QExecutionItem(item_exec, self)
+ if execution.completed == 1:
+ if execution.error:
+ self.wf_execution.completed = -1
+ brush = CurrentTheme.ERROR_MODULE_BRUSH
+ else:
+ brush = CurrentTheme.SUCCESS_MODULE_BRUSH
+ elif execution.completed == -2:
+ brush = CurrentTheme.SUSPENDED_MODULE_BRUSH
+ else:
+ brush = CurrentTheme.ERROR_MODULE_BRUSH
+ self.setText(0, 'Loop #%s' % execution.db_iteration)
+ self.setText(1, '%s' % execution.ts_start)
+ self.setText(2, '%s' % execution.ts_end)
+ pixmap = QtGui.QPixmap(10,10)
+ pixmap.fill(brush.color())
+ icon = QtGui.QIcon(pixmap)
+ self.setIcon(0, icon)
+
+class QExecutionListWidget(QtGui.QTreeWidget):
+ """
+ QExecutionListWidget is a widget containing a list of workflow executions.
+
+ """
+ def __init__(self, parent=None):
+ QtGui.QTreeWidget.__init__(self, parent)
+ self.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
+ self.setColumnCount(3)
+ self.setHeaderLabels(['Pipeline', 'Start', 'End'])
+ self.sortByColumn(1, QtCore.Qt.AscendingOrder)
+ self.setSortingEnabled(True)
+
+ def set_log(self, log=None):
+ self.clear()
+ for execution in log:
+ self.addTopLevelItem(QExecutionItem(execution))
+
+ def add_workflow_exec(self, workflow_exec):
+ # mark as recent
+ workflow_exec.db_name = workflow_exec.db_name + '*' \
+ if workflow_exec.db_name \
+ else '%s*' % self.controller.get_pipeline_name(
+ workflow_exec.parent_version)
+
+ self.addTopLevelItem(QExecutionItem(workflow_exec))
+
+
+class QLegendBox(QtGui.QFrame):
+ """
+ QLegendBox is just a rectangular box with a solid color
+
+ """
+ def __init__(self, brush, size, parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QLegendBox(color: QBrush, size: (int,int), parent: QWidget,
+ f: WindowFlags) -> QLegendBox
+ Initialize the widget with a color and fixed size
+
+ """
+ QtGui.QFrame.__init__(self, parent, f)
+ self.setFrameStyle(QtGui.QFrame.Box | QtGui.QFrame.Plain)
+ self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
+ self.setAutoFillBackground(True)
+ palette = QtGui.QPalette(self.palette())
+ palette.setBrush(QtGui.QPalette.Window, brush)
+ self.setPalette(palette)
+ self.setFixedSize(*size)
+ if system.systemType in ['Darwin']:
+ #the mac's nice looking messes up with the colors
+ if QtCore.QT_VERSION < 0x40500:
+ self.setAttribute(QtCore.Qt.WA_MacMetalStyle, False)
+ else:
+ self.setAttribute(QtCore.Qt.WA_MacBrushedMetal, False)
+
+
+class QLegendWidget(QtGui.QWidget):
+ """
+ QLegendWindow contains a list of QLegendBox and its description
+
+ """
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.gridLayout = QtGui.QGridLayout(self)
+ self.gridLayout.setMargin(10)
+ self.gridLayout.setSpacing(10)
+ self.setFont(CurrentTheme.VISUAL_DIFF_LEGEND_FONT)
+
+ data = [[0, 0, "Successful", CurrentTheme.SUCCESS_MODULE_BRUSH],
+ [0, 1, "Error", CurrentTheme.ERROR_MODULE_BRUSH],
+ [0, 2, "Cached", CurrentTheme.NOT_EXECUTED_MODULE_BRUSH],
+ [1, 0, "Not executed", CurrentTheme.PERSISTENT_MODULE_BRUSH],
+ [1, 1, "Suspended", CurrentTheme.SUSPENDED_MODULE_BRUSH]]
+
+ for x, y, text, brush in data:
+ self.gridLayout.addWidget(
+ QLegendBox(brush, CurrentTheme.VISUAL_DIFF_LEGEND_SIZE, self),
+ x*2, y*2)
+ self.gridLayout.addWidget(QtGui.QLabel(text, self), x*2, y*2+1)
+
+class QLogDetails(QtGui.QWidget, QVistrailsPaletteInterface):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.execution = None
+ self.parentExecution = None
+ self.set_title("Log Details")
+ self.legend = QLegendWidget()
+ self.executionList = QExecutionListWidget()
+ self.executionList.setExpandsOnDoubleClick(False)
+ self.isDoubling = False
+ self.isUpdating = False
+ layout = QtGui.QVBoxLayout()
+
+ self.backButton = QtGui.QPushButton('Go back')
+ self.backButton.setToolTip("Go back to parent workflow")
+ layout.addWidget(self.backButton)
+ self.backButton.hide()
+
+ layout.addWidget(self.legend)
+ layout.addWidget(self.executionList)
+ self.detailsWidget = QtGui.QTextEdit()
+ layout.addWidget(self.detailsWidget)
+ self.setLayout(layout)
+ self.connect(self.executionList,
+ QtCore.SIGNAL("itemSelectionChanged()"),
+ self.set_execution)
+ self.connect(self.backButton,
+ QtCore.SIGNAL('clicked()'),
+ self.goBack)
+# self.connect(self.executionList, QtCore.SIGNAL(
+# "itemClicked(QTreeWidgetItem *, int)"),
+# self.singleClick)
+ self.connect(self.executionList, QtCore.SIGNAL(
+ "itemDoubleClicked(QTreeWidgetItem *, int)"),
+ self.doubleClick)
+ self.addButtonsToToolbar()
+
+ def addButtonsToToolbar(self):
+ # Add the open version action
+ self.openVersionAction = QtGui.QAction(
+ QtGui.QIcon.fromTheme('go-next'),
+ 'Go to this pipeline', None, triggered=self.openVersion)
+ self.toolWindow().toolbar.insertAction(self.toolWindow().pinAction,
+ self.openVersionAction)
+
+ def openVersion(self):
+ if not hasattr(self.parentExecution, 'item'):
+ return
+ version = self.parentExecution.item.wf_execution.parent_version
+ from vistrails.gui.vistrails_window import _app
+ _app.get_current_view().version_selected(version, True)
+ self.controller.recompute_terse_graph()
+ _app.get_current_view().version_view.select_current_version()
+ _app.get_current_view().version_view.scene().setupScene(self.controller)
+ _app.qactions['pipeline'].trigger()
+
+ def execution_updated(self):
+ for e in self.controller.log.workflow_execs:
+ if e not in self.log:
+ self.log[e] = e
+ wf_id = e.parent_version
+ tagMap = self.controller.vistrail.get_tagMap()
+ if wf_id in tagMap:
+ e.db_name = tagMap[wf_id]
+ self.executionList.add_workflow_exec(e)
+
+ def set_execution(self):
+ item = self.executionList.selectedItems()
+ if not item:
+ return
+ item = item[0]
+ if self.isDoubling:
+ self.isDoubling = False
+ return
+ if isinstance(item.wf_execution, GroupExec):
+ self.backButton.show()
+ else:
+ self.backButton.hide()
+ self.notify_app(item.wf_execution, item.execution)
+
+ def notify_app(self, wf_execution, execution):
+ # make sure it is only called once
+ if self.isUpdating:
+ return
+ self.isUpdating = True
+ from vistrails.gui.vistrails_window import _app
+ _app.notify("execution_changed", wf_execution, execution)
+ self.isUpdating = False
+
+ def set_controller(self, controller):
+ #print '@@@@ QLogDetails calling set_controller'
+ self.controller = controller
+ self.executionList.controller = self.controller
+ if not hasattr(self.controller, 'loaded_workflow_execs'):
+ self.controller.loaded_workflow_execs = {}
+ for e in self.controller.read_log().workflow_execs:
+ # set workflow names
+ e.db_name = controller.get_pipeline_name(e.parent_version)
+ self.controller.loaded_workflow_execs[e] = e
+ self.log = self.controller.loaded_workflow_execs
+ self.executionList.set_log(self.log)
+
+ def execution_changed(self, wf_execution, execution):
+ if not execution:
+ return
+ self.execution = execution
+ self.parentExecution = wf_execution
+ text = ''
+ if hasattr(execution, 'item') and \
+ not execution.item == self.executionList.currentItem():
+ self.executionList.setCurrentItem(execution.item)
+ if hasattr(execution, 'item'):
+ text += '%s\n' % execution.item.text(0)
+ text += 'Start: %s\n' % execution.ts_start
+ text += 'End: %s\n' % execution.ts_end
+ if hasattr(execution, 'user'):
+ text += 'User: %s\n' % execution.user
+ if hasattr(execution, 'cached'):
+ text += 'Cached: %s\n' % ("Yes" if execution.cached else 'No')
+ text += 'Completed: %s\n' % {'0':'No', '1':'Yes'}.get(
+ str(execution.completed), 'No')
+ if hasattr(execution, 'error') and execution.error:
+ text += 'Error: %s\n' % execution.error
+ annotations = execution.db_annotations \
+ if hasattr(execution, 'db_annotations') else []
+ if len(annotations):
+ text += '\n\nAnnotations:'
+ for annotation in annotations:
+ text += "\n %s: %s" % (annotation.key, annotation.value)
+ self.detailsWidget.setText(text)
+ self.update_selection()
+
+ def singleClick(self, item, col):
+ if self.isDoubling:
+ self.isDoubling = False
+ return
+ if isinstance(item.wf_execution, GroupExec):
+ self.backButton.show()
+ else:
+ self.backButton.hide()
+ self.notify_app(item.wf_execution, item.execution)
+
+ def doubleClick(self, item, col):
+ # only difference here is that we should show contents of GroupExecs
+ self.isDoubling = True
+ if isinstance(item.wf_execution, GroupExec):
+ self.backButton.show()
+ else:
+ self.backButton.hide()
+ if isinstance(item.execution, GroupExec):
+ # use itself as the workflow
+ self.notify_app(item.execution, item.execution)
+ else:
+ self.notify_app(item.wf_execution, item.execution)
+
+ def goBack(self):
+ if not isinstance(self.parentExecution, GroupExec):
+ self.backButton.hide()
+ self.notify_app(self.parentExecution.item.wf_execution,
+ self.parentExecution)
+
+ def update_selection(self):
+ if hasattr(self.execution, 'item') and \
+ not self.execution.item.isSelected():
+ self.execution.item.setSelected(True)
+
+class QLogView(QPipelineView):
+ def __init__(self, parent=None):
+ QPipelineView.__init__(self, parent)
+ self.setReadOnlyMode(True)
+ self.set_title("Provenance")
+ self.log = None
+ self.execution = None
+ self.parentExecution = None
+ self.isUpdating = False
+ # self.exec_to_wf_map = {}
+ # self.workflow_execs = []
+ # Hook shape selecting functions
+ self.connect(self.scene(), QtCore.SIGNAL("moduleSelected"),
+ self.moduleSelected)
+
+ def set_default_layout(self):
+ self.set_palette_layout({QtCore.Qt.RightDockWidgetArea: QLogDetails})
+
+ def set_action_links(self):
+ self.action_links = { }
+
+ def set_action_defaults(self):
+ self.action_defaults.update(
+ {'execute' : [('setEnabled', False, False)],
+ 'publishWeb': [('setEnabled', False, False)],
+ 'publishPaper': [('setEnabled', False, False)],
+ })
+
+ def notify_app(self, wf_execution, execution):
+ # make sure it is only called once
+ if self.isUpdating:
+ return
+ self.isUpdating = True
+ from vistrails.gui.vistrails_window import _app
+ _app.notify("execution_changed", wf_execution, execution)
+ self.isUpdating = False
+
+
+ def set_controller(self, controller):
+ QPipelineView.set_controller(self, controller)
+ #print "@@@ set_controller called", id(self.controller), len(self.controller.vistrail.actions)
+ if not hasattr(self.controller, 'loaded_workflow_execs'):
+ self.controller.loaded_workflow_execs = {}
+ for e in self.controller.read_log().workflow_execs:
+ # set workflow names
+ e.db_name = controller.get_pipeline_name(e.parent_version)
+ self.controller.loaded_workflow_execs[e] = e
+ self.log = self.controller.loaded_workflow_execs
+
+ def set_to_current(self):
+ self.controller.set_pipeline_view(self)
+
+ def version_changed(self):
+ pass
+
+ def moduleSelected(self, id, selectedItems):
+ """ moduleSelected(id: int, selectedItems: [QGraphicsItem]) -> None
+ """
+ if len(selectedItems)!=1 or id==-1:
+ if self.execution != self.parentExecution:
+ self.notify_app(self.parentExecution, self.parentExecution)
+# self.moduleUnselected()
+ return
+
+ item = selectedItems[0]
+ if hasattr(item,'execution') and item.execution:
+ if self.execution != item.execution:
+ item = self.scene().selectedItems()[0]
+ self.notify_app(self.parentExecution, item.execution)
+ elif self.execution != self.parentExecution:
+ self.notify_app(self.parentExecution, self.parentExecution)
+
+ def set_exec_by_id(self, exec_id):
+ if not self.log:
+ return False
+ try:
+ workflow_execs = [e for e in self.log
+ if e.id == int(str(exec_id))]
+ except ValueError:
+ return False
+ if len(workflow_execs):
+ self.notify_app(workflow_execs[0], workflow_execs[0])
+ return True
+ return False
+
+ def set_exec_by_date(self, exec_date):
+ if not self.log:
+ return False
+ workflow_execs = [e for e in self.log
+ if str(e.ts_start) == str(exec_date)]
+ if len(workflow_execs):
+ self.notify_app(workflow_execs[0], workflow_execs[0])
+ return True
+ return False
+
+ def get_execution_pipeline(self, execution):
+ """ Recursively finds pipeline through layers of groupExecs """
+ if isinstance(execution, WorkflowExec):
+ version = execution.parent_version
+ # change the current version to this as well
+
+ return self.controller.vistrail.getPipeline(version)
+ if isinstance(execution, GroupExec):
+ parent = execution.item.wf_execution
+ parent_pipeline = self.get_execution_pipeline(parent)
+ return parent_pipeline.db_get_module_by_id(
+ execution.db_module_id).pipeline
+
+ def execution_changed(self, wf_execution, execution):
+ self.execution = execution
+ if self.parentExecution != wf_execution:
+ self.parentExecution = wf_execution
+ self.pipeline = self.get_execution_pipeline(wf_execution)
+ self.update_pipeline()
+ self.update_selection()
+
+ # if idx < len(self.workflow_execs) and idx >= 0:
+ # self.execution = self.workflow_execs[idx]
+ # else:
+ # self.execution = None
+
+ # self.currentItem = self.workflow_execs[idx]
+ # self.execution = item.execution
+ # self.workflowExecution = item
+ # while self.workflowExecution.parent():
+ # self.workflowExecution = self.workflowExecution.parent()
+ # self.workflowExecution = self.workflowExecution.execution
+ # self.parentExecution = item
+ # while self.parentExecution.execution.__class__ not in \
+ # [WorkflowExec, LoopExec, GroupExec]:
+ # self.parentExecution = self.parentExecution.parent()
+ # self.parentExecution = self.parentExecution.execution
+ # self.showExecution()
+
+ def update_pipeline(self):
+ #print "ACTIONS!"
+ #print "#### controller", id(self.controller)
+ scene = self.scene()
+ scene.clearItems()
+ self.pipeline.validate(False)
+
+ module_execs = dict([(e.module_id, e)
+ for e in self.parentExecution.item_execs])
+ # controller = DummyController(self.pipeline)
+ scene.controller = self.controller
+ self.moduleItems = {}
+ for m_id in self.pipeline.modules:
+ module = self.pipeline.modules[m_id]
+ brush = CurrentTheme.PERSISTENT_MODULE_BRUSH
+ if m_id in module_execs:
+ e = module_execs[m_id]
+ if e.completed == 1:
+ if e.error:
+ brush = CurrentTheme.ERROR_MODULE_BRUSH
+ elif e.cached:
+ brush = CurrentTheme.NOT_EXECUTED_MODULE_BRUSH
+ else:
+ brush = CurrentTheme.SUCCESS_MODULE_BRUSH
+ elif e.completed == -2:
+ brush = CurrentTheme.SUSPENDED_MODULE_BRUSH
+ else:
+ brush = CurrentTheme.ERROR_MODULE_BRUSH
+ module.is_valid = True
+ item = scene.addModule(module, brush)
+ item.controller = self.controller
+ self.moduleItems[m_id] = item
+ if m_id in module_execs:
+ e = module_execs[m_id]
+ item.execution = e
+ e.module = item
+ else:
+ item.execution = None
+ connectionItems = []
+ for c in self.pipeline.connections.values():
+ connectionItems.append(scene.addConnection(c))
+
+ # Color Code connections
+ for c in connectionItems:
+ pen = QtGui.QPen(CurrentTheme.CONNECTION_PEN)
+ pen.setBrush(QtGui.QBrush(QtGui.QColor(0, 0, 0, 128+64)))
+ c.connectionPen = pen
+
+ scene.updateSceneBoundingRect()
+ scene.fitToView(self, True)
+
+ def update_selection(self):
+ # avoid module update signal
+ self.isUpdating = True
+ module = None
+ if (isinstance(self.execution, ModuleExec) or \
+ (isinstance(self.execution, GroupExec) and
+ self.execution == self.parentExecution)) and \
+ not self.execution.module.isSelected():
+ self.execution.module.setSelected(True)
+ module = self.execution.module
+ for m in self.scene().selectedItems():
+ if m.isSelected() and m != module:
+ m.setSelected(False)
+ self.isUpdating = False
diff --git a/vistrails/gui/collection/workspace.py b/vistrails/gui/collection/workspace.py
new file mode 100644
index 0000000..538d647
--- /dev/null
+++ b/vistrails/gui/collection/workspace.py
@@ -0,0 +1,1631 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+
+import glob
+from itertools import chain
+import os
+from datetime import datetime
+from time import strptime
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.core import debug
+from vistrails.core.collection import Collection, MashupEntity, ThumbnailEntity, \
+ VistrailEntity, WorkflowEntity, WorkflowExecEntity, ParameterExplorationEntity
+from vistrails.core.collection.search import SearchCompiler, SearchParseError
+from vistrails.core.db.locator import FileLocator
+from vistrails.db.services.locator import UntitledLocator
+from vistrails.gui.common_widgets import QToolWindowInterface, QToolWindow, QSearchBox
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.module_palette import QModuleTreeWidgetItemDelegate
+from vistrails.gui.vis_diff import QDiffView
+
+class QCollectionWidget(QtGui.QTreeWidget):
+ """ This is an abstract class that contains functions for handling
+ a core.collection.Collection object
+ a subclass should provide a view of the collection
+ """
+ def __init__(self, collection, parent=None):
+ QtGui.QTreeWidget.__init__(self, parent)
+ self.collection = collection
+ self.collection.add_listener(self)
+ self.setExpandsOnDoubleClick(False)
+ self.connect(self,
+ QtCore.SIGNAL('itemDoubleClicked(QTreeWidgetItem *, int)'),
+ self.item_selected)
+ self.setIconSize(QtCore.QSize(16,16))
+
+ def setup_widget(self, workspace=None):
+ """ Adds the items from the current workspace """
+ pass
+
+ def updated(self):
+ """ Called from the collection when committed """
+ self.setup_widget()
+
+ def run_search(self, search, items=None):
+ # FIXME only uses top level items
+ if items is None:
+ items = [self.topLevelItem(i)
+ for i in xrange(self.topLevelItemCount())]
+ for item in items:
+ if search.match(item.entity):
+ item.setHidden(False)
+ parent = item.parent()
+ while parent is not None:
+ if parent.isHidden():
+ parent.setHidden(False)
+ parent = parent.parent()
+ else:
+ item.setHidden(True)
+ self.run_search(search, [item.child(i)
+ for i in xrange(item.childCount())])
+
+ def reset_search(self, items=None):
+ if items is None:
+ items = [self.topLevelItem(i)
+ for i in xrange(self.topLevelItemCount())]
+ for item in items:
+ item.setHidden(False)
+ self.reset_search([item.child(i)
+ for i in xrange(item.childCount())])
+
+ def item_selected(self, widget_item, column):
+ #print 'item_selected'
+ locator = widget_item.entity.locator()
+ #print "locator", locator
+ import vistrails.gui.application
+# if not locator.is_valid():
+# debug.critical("Locator is not valid:" % locator.to_url())
+# return
+ app = vistrails.gui.application.get_vistrails_application()
+ open_vistrail = app.builderWindow.open_vistrail_without_prompt
+ args = {}
+ args['version'] = locator.kwargs.get('version_node', None) or \
+ locator.kwargs.get('version_tag', None)
+ if args['version']:
+ # set vistrail name
+ locator = widget_item.entity.parent.locator()
+ pass
+ #locator._name = widget_item.entity.parent.name
+
+ workflow_exec = locator.kwargs.get('workflow_exec', None)
+ if workflow_exec:
+ args['workflow_exec'] = workflow_exec
+ locator = widget_item.entity.parent.parent.locator()
+ locator.update_from_gui(self)
+ # set vistrail name
+ #locator._name = widget_item.entity.parent.parent.name
+
+ locator.update_from_gui(self)
+# print '*** opening'
+# print locator.to_url()
+# print locator.name
+# print '***'
+ open_vistrail(locator, **args)
+
+ def contextMenuEvent(self, event):
+ item = self.itemAt(event.pos())
+ menu = QtGui.QMenu(self)
+ if item:
+ # find top level
+ p = item
+ while p.parent():
+ p = p.parent()
+ act = QtGui.QAction("&Update", self)
+ act.setStatusTip("Update this object")
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ p.refresh_object)
+ menu.addAction(act)
+ act = QtGui.QAction("&Remove", self)
+ act.setStatusTip("Remove from this list")
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ p.remove_object)
+ menu.addAction(act)
+ act = QtGui.QAction("", self)
+ act.setSeparator(True)
+ menu.addAction(act)
+ act = QtGui.QAction("Check &All", self)
+ act.setStatusTip("Removes deleted files")
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ self.check_objects)
+ menu.addAction(act)
+ act = QtGui.QAction("Remove All", self)
+ act.setStatusTip("Removes all files")
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ self.remove_all)
+ menu.addAction(act)
+ act = QtGui.QAction("Add &File", self)
+ act.setStatusTip("Add specified vistrail file")
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ self.add_file)
+ menu.addAction(act)
+ act = QtGui.QAction("Add from &Directory", self)
+ act.setStatusTip("Add all vistrail files in a directory")
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ self.add_dir)
+ menu.addAction(act)
+ act = QtGui.QAction("", self)
+ act.setSeparator(True)
+ menu.addAction(act)
+ act = QtGui.QAction("Add a new Workspace", self)
+ act.setStatusTip("Create a new workspace")
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ self.add_workspace)
+ menu.addAction(act)
+ if self.collection.currentWorkspace != 'Default':
+ act = QtGui.QAction("Delete Workspace", self)
+ act.setStatusTip("Remove current workspace")
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ self.delete_workspace)
+ menu.addAction(act)
+ menu.exec_(event.globalPos())
+
+ def check_objects(self):
+ items = [self.topLevelItem(i)
+ for i in xrange(self.topLevelItemCount())]
+ for item in items:
+ item.entity.locator().update_from_gui(self)
+ if not self.collection.urlExists(item.entity.url):
+ self.collection.delete_entity(item.entity)
+ self.collection.commit()
+
+ def remove_all(self):
+ items = [self.topLevelItem(i)
+ for i in xrange(self.topLevelItemCount())]
+ for item in items:
+ self.collection.del_from_workspace(item.entity)
+ self.collection.commit()
+
+ def add_file(self):
+ s = QtGui.QFileDialog.getOpenFileName(
+ self, "Choose a file",
+ "", "Vistrail files (*.vt *.xml)");
+ if str(s):
+ locator = FileLocator(str(s))
+ url = locator.to_url()
+ entity = self.collection.updateVistrail(url)
+ # add to relevant workspace categories
+ self.collection.add_to_workspace(entity)
+ self.collection.commit()
+
+ def add_dir(self):
+ s = QtGui.QFileDialog.getExistingDirectory(
+ self, "Choose a directory",
+ "", QtGui.QFileDialog.ShowDirsOnly);
+ if str(s):
+ self.update_from_directory(str(s))
+
+ def update_from_directory(self, s):
+ filenames = glob.glob(os.path.join(s, '*.vt,*.xml'))
+
+ progress = QtGui.QProgressDialog('', '', 0, len(filenames))
+ progress.setWindowTitle('Adding files')
+ progress.setMinimumDuration(500)
+ progress.setWindowModality(QtCore.Qt.WindowModal)
+ i = 0
+ for filename in filenames:
+ progress.setValue(i)
+ progress.setLabelText(filename)
+ i += 1
+ try:
+ locator = FileLocator(filename)
+ url = locator.to_url()
+ entity = self.collection.updateVistrail(url)
+ self.collection.add_to_workspace(entity)
+ except:
+ debug.critical("Failed to add file '%s'" % filename)
+ progress.setValue(len(filenames))
+ self.collection.commit()
+
+ def add_workspace(self):
+ text, ok = QtGui.QInputDialog.getText(self, 'Create workspace',
+ 'Enter new workspace name:')
+ workspace = str(text).strip()
+ if ok and workspace != '':
+ self.collection.currentWorkspace = workspace
+ if workspace not in self.collection.workspaces:
+ self.collection.add_workspace(workspace)
+ self.collection.commit()
+ self.emit(QtCore.SIGNAL("workspaceListUpdated()"))
+
+ def delete_workspace(self):
+ if self.collection.currentWorkspace != 'Default':
+ self.collection.delete_workspace(self.collection.currentWorkspace)
+ self.collection.currentWorkspace = 'Default'
+ self.collection.commit()
+ self.emit(QtCore.SIGNAL("workspaceListUpdated()"))
+
+class QWorkspaceWidget(QCollectionWidget):
+ """ This class implements QCollectionWidget as a side bar browser widget
+ """
+ def __init__(self, collection, parent=None):
+ QCollectionWidget.__init__(self, collection, parent)
+ self.setColumnCount(1)
+ self.setHeaderHidden(True)
+
+ def setup_widget(self, workspace=None):
+ """ Adds the items from the current workspace """
+ while self.topLevelItemCount():
+ self.takeTopLevelItem(0)
+ if workspace:
+ self.collection.currentWorkspace = workspace
+ for entity in self.collection.workspaces[self.collection.currentWorkspace]:
+ item = QBrowserWidgetItem(entity, self)
+ self.addTopLevelItem(item)
+# if self.collection.currentWorkspace != 'Default':
+ self.setSortingEnabled(True)
+ self.sortItems(0, QtCore.Qt.AscendingOrder)
+
+class QWorkflowsItem(QtGui.QTreeWidgetItem):
+ def __init__(self, parent=None):
+ QtGui.QTreeWidgetItem.__init__(self, parent, ['Workflows'])
+
+class QMashupsItem(QtGui.QTreeWidgetItem):
+ def __init__(self, parent=None):
+ QtGui.QTreeWidgetItem.__init__(self, parent, ['Mashups'])
+
+class QParamExplorationsItem(QtGui.QTreeWidgetItem):
+ def __init__(self, parent=None):
+ QtGui.QTreeWidgetItem.__init__(self, parent, ['Parameter Explorations'])
+
+class QBrowserWidgetItem(QtGui.QTreeWidgetItem):
+ def __init__(self, entity, parent=None):
+ if not entity:
+ # assuming an unsaved item
+ QtGui.QTreeWidgetItem.__init__(self, parent)
+ self.tag_to_item = {}
+ self.workflowsItem = QWorkflowsItem()
+ self.addChild(self.workflowsItem)
+ self.mshp_to_item = {}
+ self.mashupsItem = QMashupsItem()
+ self.addChild(self.mashupsItem)
+ self.pe_to_item = {}
+ self.paramExplorationsItem = QParamExplorationsItem()
+ self.addChild(self.paramExplorationsItem)
+ self.setIcon(0, CurrentTheme.HISTORY_ICON)
+ return
+
+ # # old, esoteric code
+ #
+ # l = list(str(x) for x in entity.save())
+ # l.pop(0) # remove identifier
+ # type = l.pop(0)
+ # desc = l[5]
+ # if len(desc) > 20:
+ # l[5] = desc[:20] + '...'
+ klass = self.__class__
+ self.entity = entity
+ QtGui.QTreeWidgetItem.__init__(self, parent, [entity.name])
+ if entity.type_id == VistrailEntity.type_id:
+ # vistrail - create Workflows and Mashups item
+ self.workflowsItem = QWorkflowsItem()
+ self.addChild(self.workflowsItem)
+ self.mashupsItem = QMashupsItem()
+ self.addChild(self.mashupsItem)
+ self.mashupsItem.setHidden(True)
+ self.paramExplorationsItem = QParamExplorationsItem()
+ self.addChild(self.paramExplorationsItem)
+ self.paramExplorationsItem.setHidden(True)
+ self.setIcon(0, CurrentTheme.HISTORY_ICON)
+ self.tag_to_item = {}
+ self.mshp_to_item = {}
+ self.pe_to_item = {}
+ elif entity.type_id == WorkflowEntity.type_id:
+ self.setIcon(0, CurrentTheme.PIPELINE_ICON)
+ self.executionList = []
+ elif entity.type_id == WorkflowExecEntity.type_id:
+ self.setIcon(0, CurrentTheme.EXECUTE_PIPELINE_ICON)
+
+ tooltip = '<html>%s' % entity.url
+
+ for child in entity.children:
+ # l = child.save()
+ if child.type_id == ThumbnailEntity.type_id:
+ # is a thumbnail
+ # add to parent workflow item
+ cache = ThumbnailCache.getInstance()
+ path = cache.get_abs_name_entry(child.name)
+ if path:
+ pixmap = QtGui.QPixmap(path)
+ if pixmap and not pixmap.isNull():
+ self.setIcon(0, QtGui.QIcon(pixmap.scaled(16, 16)))
+ tooltip += """<br/><img border=0 src='%(path)s'/>
+ """ % {'path':path}
+ elif child.type_id == WorkflowEntity.type_id:
+ # is a pipeline
+ # only show tagged items
+ # Add to 'Workflows' item
+
+ if not child.name.startswith('Version #'):
+ childItem = QWorkflowEntityItem(child)
+ self.workflowsItem.addChild(childItem)
+ # keep list of tagged workflows
+ self.tag_to_item[child.name] = childItem
+ elif child.type_id == WorkflowExecEntity.type_id:
+ # is an execution
+ childItem = QWorkflowExecEntityItem(child)
+ # hidden by default
+ self.executionList.append(childItem)
+ self.addChild(childItem)
+ childItem.setHidden(True)
+ elif child.type_id == MashupEntity.type_id:
+ # is a mashup
+ childItem = QMashupEntityItem(child)
+ self.mashupsItem.addChild(childItem)
+ # keep list of tagged mashups
+ self.mshp_to_item[child.name] = childItem
+ elif child.type_id == ParameterExplorationEntity.type_id:
+ # is a parameter exploration
+ childItem = QParamExplorationEntityItem(child)
+ self.paramExplorationsItem.addChild(childItem)
+ # keep list of tagged pe:s
+ self.pe_to_item[child.url] = childItem
+ else:
+ self.addChild(QBrowserWidgetItem(child))
+ if entity.description:
+ tooltip += '<br/>%s' % entity.description
+ tooltip += '</html>'
+ self.setToolTip(0, tooltip)
+
+ #def __lt__(self, other):
+ # sort_col = self.treeWidget().sortColumn()
+ # if sort_col in set([4]):
+ # return int(self.text(sort_col)) < int(other.text(sort_col))
+ # elif sort_col in set([2,3]):
+ # return datetime(*strptime(str(self.text(sort_col)), '%d %b %Y %H:%M:%S')[0:6]) < datetime(*strptime(str(other.text(sort_col)), '%d %b %Y %H:%M:%S')[0:6])
+ # return QtGui.QTreeWidgetItem.__lt__(self, other)
+
+ def refresh_object(self):
+ Collection.getInstance().updateVistrail(self.entity.url)
+ Collection.getInstance().commit()
+
+ def remove_object(self):
+ Collection.getInstance().del_from_workspace(self.entity)
+ Collection.getInstance().commit()
+
+class QWorkflowEntityItem(QBrowserWidgetItem):
+ def get_vistrail(self):
+ parent = self.parent()
+ QVistrailEntityItem
+ while parent and type(parent) != QVistrailEntityItem:
+ parent = parent.parent()
+ return parent
+
+ def open_workflow(self):
+ self.treeWidget().item_selected(self, 0)
+
+ def open_workflow_in_new_tab(self):
+ self.get_vistrail().window.add_pipeline_view()
+ self.open_workflow()
+
+ def open_workflow_in_new_window(self):
+ self.open_workflow_in_new_tab()
+ self.get_vistrail().window.detach_view(
+ self.get_vistrail().window.tabs.currentIndex())
+
+class QWorkflowExecEntityItem(QBrowserWidgetItem):
+ pass
+
+class QMashupEntityItem(QBrowserWidgetItem):
+ def open_mashup(self):
+ self.treeWidget().open_mashup(self.entity)
+
+ def edit_mashup(self):
+ self.treeWidget().edit_mashup(self.entity)
+
+class QParamExplorationEntityItem(QBrowserWidgetItem):
+ pass
+
+class QExplorerWidget(QCollectionWidget):
+ """ This class implements QCollectionWidget as a full-screen explorer widget
+ """
+ def __init__(self, collection, parent=None):
+ QCollectionWidget.__init__(self, collection, parent)
+ self.setColumnCount(6)
+ self.setHeaderLabels(['name', 'user', 'mod_date', 'create_date', 'size', 'url'])
+
+ def setup_widget(self, workspace=None):
+ """ Adds the items from the current workspace """
+ self.clear()
+ if workspace:
+ self.collection.currentWorkspace = workspace
+ for entity in self.collection.workspaces[self.collection.currentWorkspace]:
+ item = QExplorerWidgetItem(entity)
+ self.addTopLevelItem(item)
+# if self.collection.currentWorkspace != 'Default':
+ self.setSortingEnabled(True)
+ self.sortItems(0, QtCore.Qt.AscendingOrder)
+
+class QExplorerWidgetItem(QtGui.QTreeWidgetItem):
+ def __init__(self, entity, parent=None):
+ l = list(str(x) for x in entity.save())
+ l.pop(0) # remove identifier
+ type = l.pop(0)
+ desc = l.pop(5)
+# l.pop(7)
+# if len(desc) > 20:
+# l[5] = desc[:20] + '...'
+ QtGui.QTreeWidgetItem.__init__(self, parent, l)
+ self.entity = entity
+ if type == '1':
+ self.setIcon(0, CurrentTheme.HISTORY_ICON)
+ elif type == '2':
+ self.setIcon(0, CurrentTheme.PIPELINE_ICON)
+ elif type == '3':
+ self.setIcon(0, CurrentTheme.EXECUTE_PIPELINE_ICON)
+
+ self.setToolTip(0, entity.url)
+
+ for child in entity.children:
+ l = child.save()
+ if l[1] == 4:
+ cache = ThumbnailCache.getInstance()
+ path = cache.get_abs_name_entry(l[2])
+ if path:
+ self.setIcon(0, QtGui.QIcon(path))
+ continue
+ else:
+ self.addChild(QExplorerWidgetItem(child))
+
+ def __lt__(self, other):
+ sort_col = self.treeWidget().sortColumn()
+ if sort_col in set([4]):
+ return int(self.text(sort_col)) < int(other.text(sort_col))
+ elif sort_col in set([2,3]):
+ return datetime(*strptime(str(self.text(sort_col)), '%d %b %Y %H:%M:%S')[0:6]) < datetime(*strptime(str(other.text(sort_col)), '%d %b %Y %H:%M:%S')[0:6])
+ return QtGui.QTreeWidgetItem.__lt__(self, other)
+
+ def refresh_object(self):
+ Collection.getInstance().updateVistrail(self.entity.url)
+ Collection.getInstance().commit()
+
+ def remove_object(self):
+ Collection.getInstance().del_from_workspace(self.entity)
+ Collection.getInstance().commit()
+
+class QWorkspaceWindow(QtGui.QWidget, QVistrailsPaletteInterface):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+
+# self.workspace_list = QtGui.QComboBox()
+# self.titleWidget = QtGui.QWidget()
+# self.titleLayout = QtGui.QHBoxLayout()
+# self.titleLayout.setMargin(0)
+# self.titleLayout.setSpacing(5)
+# self.titleLayout.addWidget(QtGui.QLabel('Project:'), 0)
+# self.titleLayout.addWidget(self.workspace_list, 1)
+# self.titleWidget.setLayout(self.titleLayout)
+# self.setTitleBarWidget(self.titleWidget)
+ self.setWindowTitle('Workspace')
+ # make it possible to ignore updates during updating of workspace list
+ self.updatingWorkspaceList = False
+# self.connect(self.workspace_list,
+# QtCore.SIGNAL("currentIndexChanged(QString)"),
+# self.workspace_changed)
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(0)
+ layout.setSpacing(5)
+# self.search_box = QSearchBox(True, False, self)
+# layout.addWidget(self.search_box)
+
+ self.collection = Collection.getInstance()
+
+ self.open_list = QVistrailList()
+ self.open_list.collection = self.collection
+ layout.addWidget(self.open_list)
+# layout.addWidget(self.titleWidget)
+
+# self.browser = QWorkspaceWidget(self.collection)
+# layout.addWidget(self.browser)
+# self.browser.setup_widget('Default')
+# self.connect(self.search_box, QtCore.SIGNAL('resetSearch()'),
+# self.reset_search)
+# self.connect(self.search_box, QtCore.SIGNAL('executeSearch(QString)'),
+# self.execute_search)
+# self.connect(self.search_box, QtCore.SIGNAL('refineMode(bool)'),
+# self.refine_mode)
+# self.connect(self.browser, QtCore.SIGNAL('workspaceListUpdated()'),
+# self.update_workspace_list)
+ self.setLayout(layout)
+# self.update_workspace_list()
+
+ self.addButtonsToToolbar()
+
+ def addButtonsToToolbar(self):
+ # button for toggling executions
+ self.execAction = QtGui.QAction(CurrentTheme.EXECUTE_PIPELINE_ICON,
+ "Show/hide workflow executions",
+ None,
+ triggered=self.showWorkflowExecutions)
+ self.execAction.setCheckable(True)
+ self.toolWindow().toolbar.insertAction(self.toolWindow().pinAction,
+ self.execAction)
+ # buttons for toggling list/tree views of workflows
+ self.listAction = QtGui.QAction(CurrentTheme.LIST_VIEW_ICON,
+ "View workflows in a list",
+ None,
+ triggered=self.viewAsList)
+ self.listAction.setCheckable(True)
+ self.listAction.setChecked(True)
+ self.treeAction = QtGui.QAction(CurrentTheme.TREE_VIEW_ICON,
+ "View workflows in a tree",
+ None,
+ triggered=self.viewAsTree)
+ self.treeAction.setCheckable(True)
+ self.workflowDisplayGroup = QtGui.QActionGroup(self)
+ self.workflowDisplayGroup.setExclusive(True)
+ self.workflowDisplayGroup.addAction(self.listAction)
+ self.workflowDisplayGroup.addAction(self.treeAction)
+ self.toolWindow().toolbar.insertAction(self.toolWindow().pinAction,
+ self.listAction)
+ self.toolWindow().toolbar.insertAction(self.toolWindow().pinAction,
+ self.treeAction)
+ # buttons for going to the search view to search all vistrails
+ self.searchAction = QtGui.QAction("Search", self.toolWindow().toolbar,
+ triggered=self.gotoSearch)
+ self.searchAction.searchMode = False
+ self.toolWindow().toolbar.insertAction(self.toolWindow().pinAction,
+ self.searchAction)
+
+ def state_changed(self, view):
+ self.open_list.state_changed(view)
+
+ def gotoSearch(self):
+ if self.searchAction.searchMode:
+ self.open_list.hide_search_results()
+ self.searchAction.searchMode = False
+ self.open_list.searchMode = False
+ self.searchAction.setText("Search")
+
+ from vistrails.gui.vistrails_window import _app
+ _app.notify('query_changed', None)
+ else:
+ from vistrails.gui.vistrails_window import _app
+ _app.qactions['search'].trigger()
+
+ def updateSearchResults(self, search=None, result_list=None):
+ if search is None:
+ self.gotoSearch()
+ elif not self.searchAction.searchMode:
+ self.open_list.show_search_results()
+ self.searchAction.searchMode = True
+ self.open_list.searchMode = True
+ self.searchAction.setText("Clear Search")
+ self.open_list.update_search_results(search, result_list)
+
+ def execution_updated(self):
+ self.open_list.execution_updated()
+
+ def showWorkflowExecutions(self, state):
+ """ toggle show executions on/off """
+ self.open_list.hideExecutions(not state)
+
+ def viewAsList(self):
+ """ Order workflow items as a flat list """
+ self.open_list.isTreeView = False
+ for i in xrange(self.open_list.openFilesItem.childCount()):
+ item = self.open_list.openFilesItem.child(i)
+ self.open_list.make_list(item)
+
+ def viewAsTree(self):
+ """ Order workflow items as a history tree """
+ self.open_list.isTreeView = True
+ for i in xrange(self.open_list.openFilesItem.childCount()):
+ item = self.open_list.openFilesItem.child(i)
+ self.open_list.make_tree(item)
+
+ def update_workspace_list(self):
+ """ Updates workspace list and highlights currentWorkspace
+ Keeps 'Recent files' on top
+ """
+ self.updatingWorkspaceList = True
+ self.workspace_list.clear()
+ self.workspace_list.addItem('Default')
+ if 'Default' == self.browser.collection.currentWorkspace:
+ self.workspace_list.setCurrentIndex(self.workspace_list.count()-1)
+ locations = self.browser.collection.workspaces.keys()
+
+ workspaces = [ l for l in locations \
+ if not l.startswith('file') and \
+ not l.startswith('db') and \
+ not l == 'Default']
+ workspaces.sort()
+ for w in workspaces:
+ self.workspace_list.addItem(w)
+ if w == self.browser.collection.currentWorkspace:
+ self.workspace_list.setCurrentIndex(self.workspace_list.count()-1)
+ self.updatingWorkspaceList = False
+
+ def workspace_changed(self, workspace):
+ if not self.updatingWorkspaceList:
+ self.browser.setup_widget(str(workspace))
+
+ def reset_search(self):
+ self.browser.reset_search()
+
+ def set_results(self, results):
+ pass
+
+ def execute_search(self, text):
+ s = str(text)
+ try:
+ search = SearchCompiler(s).searchStmt
+ except SearchParseError, e:
+ debug.warning("Search Parse Error", str(e))
+ search = None
+
+ self.browser.run_search(search)
+
+ def refine_mode(self, on):
+ pass
+
+ def change_vt_window(self, vistrail_window):
+ self.open_list.change_vt_window(vistrail_window)
+
+ def add_vt_window(self, vistrail_window):
+ self.open_list.add_vt_window(vistrail_window)
+
+ def remove_vt_window(self, vistrail_window):
+ self.open_list.remove_vt_window(vistrail_window)
+
+class QExplorerDialog(QToolWindow, QToolWindowInterface):
+ def __init__(self, parent=None):
+ QToolWindow.__init__(self, parent=parent)
+
+ self.widget = QtGui.QWidget()
+ self.setWidget(self.widget)
+ self.workspace_list = QtGui.QComboBox()
+ self.setTitleBarWidget(self.workspace_list)
+ # make it possible to ignore updates during updating of workspace list
+ self.updatingWorkspaceList = False
+ self.connect(self.workspace_list,
+ QtCore.SIGNAL("currentIndexChanged(QString)"),
+ self.workspace_changed)
+ layout = QtGui.QVBoxLayout()
+# layout.setMargin(0)
+# layout.setSpacing(5)
+ self.search_box = QSearchBox(True, False, self)
+ layout.addWidget(self.search_box)
+
+ self.collection = Collection.getInstance()
+ self.browser = QExplorerWidget(self.collection, self)
+ layout.addWidget(self.browser)
+ self.browser.setup_widget('Recent files')
+ self.connect(self.search_box, QtCore.SIGNAL('resetSearch()'),
+ self.reset_search)
+ self.connect(self.search_box, QtCore.SIGNAL('executeSearch(QString)'),
+ self.execute_search)
+ self.connect(self.search_box, QtCore.SIGNAL('refineMode(bool)'),
+ self.refine_mode)
+ self.connect(self.browser, QtCore.SIGNAL('workspaceListUpdated()'),
+ self.update_workspace_list)
+ self.widget.setLayout(layout)
+ self.update_workspace_list()
+
+ def update_workspace_list(self):
+ """ Updates workspace list and highlights currentWorkspace
+ Keeps 'Default' on top
+ """
+ self.updatingWorkspaceList = True
+ self.workspace_list.clear()
+ self.workspace_list.addItem('Default')
+ if 'Default' == self.browser.collection.currentWorkspace:
+ self.workspace_list.setCurrentIndex(self.workspace_list.count()-1)
+ sorted_workspaces = self.browser.collection.workspaces.keys()
+ if 'Default' in sorted_workspaces:
+ sorted_workspaces.remove('Default')
+ sorted_workspaces.sort()
+ for p in sorted_workspaces:
+ self.workspace_list.addItem(p)
+ if p == self.browser.collection.currentWorkspace:
+ self.workspace_list.setCurrentIndex(self.workspace_list.count()-1)
+ self.updatingWorkspaceList = False
+
+ def workspace_changed(self, workspace):
+ if not self.updatingWorkspaceList:
+ self.browser.setup_widget(str(workspace))
+
+ def reset_search(self):
+ self.browser.reset_search()
+
+ def set_results(self, results):
+ pass
+
+ def execute_search(self, text):
+ s = str(text)
+ try:
+ search = SearchCompiler(s).searchStmt
+ except SearchParseError, e:
+ debug.warning("Search Parse Error", str(e))
+ search = None
+
+ self.browser.run_search(search)
+
+ def refine_mode(self, on):
+ pass
+
+class QVistrailEntityItem(QBrowserWidgetItem):
+ def __init__(self, entity, window=None):
+ QBrowserWidgetItem.__init__(self, entity)
+ if window:
+ self.window = window
+ self.entity = entity
+ if not entity:
+ self.setText(0, self.window.get_name())
+ # make them draggable
+ self.setFlags(self.flags() | QtCore.Qt.ItemIsDragEnabled
+ | QtCore.Qt.ItemIsDropEnabled
+# | QtCore.Qt.ItemIsSelectable
+ )
+
+ def open_in_new_window(self):
+ if hasattr(self, "window"):
+ self.treeWidget().setSelected(self.window)
+ self.treeWidget().parent().emit(QtCore.SIGNAL("detachVistrail"),
+ self.window)
+
+ def open_workflow(self):
+ self.treeWidget().item_selected(self, 0)
+
+ def open_workflow_in_new_tab(self):
+ self.parent().parent().window.add_pipeline_view()
+ self.open_workflow()
+
+ def open_workflow_in_new_window(self):
+ self.open_workflow_in_new_tab()
+ self.parent().parent().window.detach_view(
+ self.parent().parent().window.tabs.currentIndex())
+
+ def open_parameter_exploration(self):
+ self.treeWidget().open_parameter_exploration(self.entity)
+
+class QVistrailListLatestItem(QtGui.QTreeWidgetItem):
+ def __init__(self):
+ QtGui.QTreeWidgetItem.__init__(self)
+ self.setIcon(0, CurrentTheme.PIPELINE_ICON)
+ self.setText(0, '(latest)')
+
+ def get_vistrail(self):
+ return self.parent().parent()
+
+ def open_workflow(self):
+ self.treeWidget().item_selected(self, 0)
+
+ def open_workflow_in_new_tab(self):
+ self.parent().parent().window.add_pipeline_view()
+ self.open_workflow()
+
+ def open_workflow_in_new_window(self):
+ self.open_workflow_in_new_tab()
+ self.parent().parent().window.detach_view(
+ self.parent().parent().window.tabs.currentIndex())
+
+class QVistrailList(QtGui.QTreeWidget):
+ def __init__(self, parent=None):
+ QtGui.QTreeWidget.__init__(self, parent)
+ self.searchMode = False
+ self.search = None
+ self.setColumnCount(1)
+ self.setHeaderHidden(True)
+ self.setSelectionMode(self.SingleSelection)
+ self.setSelectionBehavior(self.SelectItems)
+ self.setDragEnabled(True)
+ self.setAcceptDrops(True)
+ self.setDropIndicatorShown(True)
+ self.setExpandsOnDoubleClick(False)
+ self.setRootIsDecorated(False)
+
+ self.isTreeView = False
+ self.executionsHidden = True
+
+ self.collection = Collection.getInstance()
+ self.items = {}
+
+ self.delegate = QModuleTreeWidgetItemDelegate(self, self)
+ self.setItemDelegate(self.delegate)
+
+ self.openFilesItem = QtGui.QTreeWidgetItem(['Current Vistrails'])
+ self.addTopLevelItem(self.openFilesItem)
+
+ self.setup_closed_files()
+
+ self.openFilesItem.setExpanded(True)
+ self.closedFilesItem.setExpanded(True)
+
+ self.setSortingEnabled(True)
+ self.sortItems(0, QtCore.Qt.AscendingOrder)
+
+ self.connect(self,
+ QtCore.SIGNAL('itemDoubleClicked(QTreeWidgetItem *, int)'),
+ self.item_selected)
+
+ self.setIconSize(QtCore.QSize(16,16))
+
+ self.connect(self,
+ QtCore.SIGNAL('itemPressed(QTreeWidgetItem *,int)'),
+ self.onItemPressed)
+ self.updateHideExecutions()
+ self.connect_current_changed()
+
+ def setup_closed_files(self):
+ self.closedFilesItem = QtGui.QTreeWidgetItem(['My Vistrails'])
+ self.addTopLevelItem(self.closedFilesItem)
+ closed_entities = self.collection.workspaces['Default']
+ for entity in closed_entities:
+ if entity.url.startswith('file://'):
+ if not entity.locator().is_valid():
+ self.collection.del_from_workspace(entity)
+ self.collection.delete_entity(entity)
+ continue
+ item = QVistrailEntityItem(entity)
+ self.closedFilesItem.addChild(item)
+ item.mashupsItem.setHidden(not item.mashupsItem.childCount())
+ item.paramExplorationsItem.setHidden(
+ not item.paramExplorationsItem.childCount())
+
+ def connect_current_changed(self):
+ # using currentItemChanged makes sure a drag selects the dragged-from
+ # vistrail
+ self.connect(self,
+ QtCore.SIGNAL("currentItemChanged(QTreeWidgetItem*,"
+ "QTreeWidgetItem*)"),
+ self.item_changed)
+ # using item_clicked makes sure even selected items can be clicked
+ self.connect(self,
+ QtCore.SIGNAL("itemClicked(QTreeWidgetItem*,int)"),
+ self.item_changed)
+
+ def disconnect_current_changed(self):
+ self.disconnect(self,
+ QtCore.SIGNAL("currentItemChanged(QTreeWidgetItem*,"
+ "QTreeWidgetItem*)"),
+ self.item_changed)
+ self.disconnect(self,
+ QtCore.SIGNAL("itemClicked(QTreeWidgetItem*,int)"),
+ self.item_changed)
+
+ def show_search_results(self):
+ self.searchResultsItem = QtGui.QTreeWidgetItem(['Search Results'])
+ self.addTopLevelItem(self.searchResultsItem)
+ self.openFilesItem.setHidden(True)
+ self.closedFilesItem.setHidden(True)
+
+ def hide_search_results(self):
+ self.takeTopLevelItem(self.indexOfTopLevelItem(self.searchResultsItem))
+ self.openFilesItem.setHidden(False)
+ self.closedFilesItem.setHidden(False)
+
+ def update_search_results(self, search=None, result_list=None):
+ self.search = search
+ self.searchResultsItem.takeChildren()
+ if result_list is not None:
+ for entity in result_list:
+ item = QVistrailEntityItem(entity)
+ self.searchResultsItem.addChild(item)
+ item.setExpanded(True)
+ self.searchResultsItem.setExpanded(True)
+
+ def onItemPressed(self, item, column):
+ """ onItemPressed(item: QTreeWidgetItem, column: int) -> None
+ Expand/Collapse top-level item when the mouse is pressed
+
+ """
+ if item and item.parent() == None:
+ self.setItemExpanded(item, not self.isItemExpanded(item))
+
+ def search_result_selected(self, view, version):
+ # need to signal the query view to change its version and vistrail
+ from vistrails.gui.vistrails_window import _app
+ _app.change_view(view)
+ view.query_version_selected(self.search, version)
+
+ def item_selected(self, widget_item, column):
+ """ opens or displays the selected item if possible """
+ locator = None
+ entity = None
+ if hasattr(widget_item, 'entity') and widget_item.entity is not None:
+ entity = widget_item.entity
+ locator = entity.locator()
+ elif isinstance(widget_item, QVistrailListLatestItem) and \
+ hasattr(widget_item.parent().parent(), 'entity') and \
+ widget_item.parent().parent().entity is not None:
+ entity = widget_item.parent().parent().entity
+ locator = entity.locator()
+ elif not isinstance(widget_item, QVistrailListLatestItem):
+ # no valid item selected
+ return
+ from vistrails.gui.vistrails_window import _app
+ open_vistrail = _app.open_vistrail_without_prompt
+ set_current_locator = _app.set_current_locator
+
+ if not locator or isinstance(locator, UntitledLocator):
+ # assuming an unsaved vistrail - need to use view
+ vistrail_widget = widget_item
+ view = None
+ while view is None and vistrail_widget is not None:
+ if hasattr(vistrail_widget, 'window'):
+ view = vistrail_widget.window
+ break
+ elif (hasattr(vistrail_widget, 'entity') and
+ hasattr(vistrail_widget.entity, '_window')):
+ view = vistrail_widget.entity._window
+ break
+ vistrail_widget = vistrail_widget.parent()
+
+ if vistrail_widget == widget_item:
+ # do nothing - view is already selected
+ return
+ is_execution = False
+ version = None
+ if isinstance(widget_item, QVistrailListLatestItem):
+ version = view.controller.vistrail.get_latest_version()
+ elif hasattr(widget_item, 'entity'):
+ if hasattr(widget_item, 'executionList'):
+ version = widget_item.entity.name
+ else:
+ is_execution = True
+ version = widget_item.parent().entity.name
+ if not version:
+ # assume execution
+ version = str(widget_item.parent().text(0))
+ if isinstance(version, str):
+ try:
+ version = \
+ view.controller.vistrail.get_version_number(version)
+ except:
+ version = None
+ if self.searchMode:
+ self.search_result_selected(view, version)
+ else:
+ # _app.view_changed(view)
+ _app.change_view(view)
+ if version:
+ view.version_selected(version, True, double_click=True)
+
+ if is_execution:
+ _app.qactions['provenance'].trigger()
+ workflow_exec = widget_item.entity.name
+ view.log_view.set_exec_by_id(workflow_exec) or \
+ view.log_view.set_exec_by_date(workflow_exec)
+ return
+
+ args = {}
+ args['version'] = locator.kwargs.get('version_node', None) or \
+ locator.kwargs.get('version_tag', None)
+ args['parameterExploration']=locator.kwargs.get('parameterExploration',
+ None)
+ vistrail_widget = widget_item
+ vistrail_entity = entity
+ version = None
+ if args['version']:
+ vistrail_widget = widget_item.parent()
+ vistrail_entity = entity.parent
+ locator = vistrail_entity.locator()
+ version = args['version']
+
+ if args['parameterExploration']:
+ args['parameterExploration'] = int(args['parameterExploration'])
+ vistrail_widget = widget_item.parent().parent()
+ vistrail_entity = entity.parent
+ locator = vistrail_entity.locator()
+
+ workflow_exec = locator.kwargs.get('workflow_exec', None)
+ if workflow_exec:
+ args['workflow_exec'] = workflow_exec
+ vistrail_widget = widget_item.parent().parent()
+ vistrail_entity = entity.parent.parent
+ locator = vistrail_entity.locator()
+ locator.update_from_gui(self)
+ # set vistrail name
+ #locator._name = widget_item.entity.parent.parent.name
+
+ if isinstance(widget_item, QVistrailListLatestItem):
+ # find the latest item (max action id)
+ vistrail = widget_item.parent().parent().window.controller.vistrail
+ args['version'] = vistrail.get_latest_version()
+ version = vistrail.get_latest_version()
+ locator.update_from_gui(self)
+ if not locator.is_valid():
+ debug.critical("File not found: '%s'. Entry will be deleted." % locator.to_url())
+ vistrail_widget.parent().removeChild(vistrail_widget)
+ self.collection.delete_entity(vistrail_entity)
+ self.collection.commit()
+
+ view = _app.ensureVistrail(locator)
+ if self.searchMode:
+ self.search_result_selected(view, version)
+ else:
+ if view:
+ self.ensureNotDiffView()
+ open_vistrail(locator, **args)
+ if view is None or not view.is_abstraction:
+ set_current_locator(locator)
+ if view and isinstance(entity, MashupEntity):
+ # I am assuming that double-clicking a mashup, the user wants to
+ # run the mashup
+ # if it is doubele-clicked without the vistrail being open we
+ #should open the vistrail
+ self.open_mashup(entity)
+ if view and isinstance(entity, ParameterExplorationEntity):
+ # I am assuming that double-clicking a p.e., the user wants to
+ # run it
+ # if it is double-clicked without the vistrail being open we
+ #should open the vistrail
+ self.open_parameter_exploration(entity)
+
+ def ensureNotDiffView(self):
+ """ If current tab is a diff, create a new tab """
+ from vistrails.gui.vistrails_window import _app
+ view = _app.get_current_view()
+ tab = view.get_current_tab()
+ if isinstance(tab, QDiffView):
+ view.add_pipeline_view()
+
+ def open_mashup(self, entity):
+ """open_mashup(entity:MashupEntity) -> None
+ It will ask the Vistrail view to execute the mashup
+ """
+ self.ensureNotDiffView()
+ from vistrails.gui.vistrails_window import _app
+ _app.open_vistrail_without_prompt(entity.locator(),
+ execute_workflow=True)
+
+ def edit_mashup(self, entity):
+ """open_mashup(entity:MashupEntity) -> None
+ It will ask the Vistrail view to execute the mashup
+ """
+ from vistrails.gui.vistrails_window import _app
+ _app.open_vistrail_without_prompt(entity.locator())
+
+ def open_parameter_exploration(self, entity):
+ """open_parameter_exploration(entity:ParameterExplorationEntity) -> None
+ It will switch to the correct pipeline and pe, and open the pe
+ """
+ self.ensureNotDiffView()
+ from vistrails.gui.vistrails_window import _app
+ view = _app.get_current_view()
+ if view.controller.current_version != entity.pe.action_id:
+ view.version_selected(entity.pe.action_id, True)
+ if entity.pe != view.controller.current_parameter_exploration:
+ view.controller.current_parameter_exploration = entity.pe
+ view.pe_view.setParameterExploration(entity.pe)
+ _app.qactions['explore'].trigger()
+
+ def mimeData(self, itemList):
+ """ mimeData(itemList) -> None
+ Setup the mime data to contain itemList because Qt 4.2.2
+ implementation doesn't instantiate QTreeWidgetMimeData
+ anywhere as it's supposed to. It must have been a bug...
+
+ """
+ data = QtGui.QTreeWidget.mimeData(self, itemList)
+ data.items = itemList
+ return data
+
+ def dropEvent( self, event):
+ event.accept()
+ destination = self.itemAt(event.pos())
+ if not destination:
+ return
+ if isinstance(event.source(), QVistrailList):
+ data = event.mimeData()
+ if hasattr(data, 'items'):
+ assert len(data.items) == 1
+ source = data.items[0]
+ if not source or source == destination:
+ return
+
+ if hasattr(source, 'window') and hasattr(destination, 'window'):
+ # both are vistrails
+ self.merge_vistrails(source, destination)
+ elif (isinstance(source, QVistrailListLatestItem) or
+ hasattr(source, 'executionList')) and \
+ (isinstance(destination, QVistrailListLatestItem) or
+ hasattr(destination, 'executionList')):
+ # workflows can be from diff vistrails
+ self.visual_diff(source, destination)
+
+ def merge_vistrails(self, source, destination):
+ if source.window.controller.changed or destination.window.controller.changed:
+ text = ('Both Vistrails need to be saved before they can be merged.')
+ QtGui.QMessageBox.information(None, 'Cannot perform merge',
+ text, '&OK')
+ return
+ res = QtGui.QMessageBox.question(None, 'Merge the histories of these 2 vistrails into a new vistrail?',
+ source.window.get_name() + '\n' + destination.window.get_name(),
+ buttons=QtGui.QMessageBox.Yes,
+ defaultButton=QtGui.QMessageBox.No)
+ if res == QtGui.QMessageBox.Yes:
+ from vistrails.gui.vistrails_window import _app
+ _app.merge_vistrails(destination.window.controller, source.window.controller)
+
+ def visual_diff(self, source, destination):
+ source_parent = source.parent()
+ while not hasattr(source_parent, 'window'):
+ source_parent = source_parent.parent()
+ destination_parent = destination.parent()
+ while not hasattr(destination_parent, 'window'):
+ destination_parent = destination_parent.parent()
+ vistrail_1 = source_parent.window.controller.vistrail
+ vistrail_2 = destination_parent.window.controller.vistrail
+ if hasattr(source, 'entity'):
+ v1 = source.entity.locator().kwargs.get('version_node', None)
+ else:
+ v1 = vistrail_1.get_latest_version()
+ if hasattr(destination, 'entity'):
+ v2 = destination.entity.locator().kwargs.get('version_node', None)
+ else:
+ v2 = vistrail_2.get_latest_version()
+
+ # if we don't have the same vistrail, pass the second vistrail
+ if id(vistrail_1) == id(vistrail_2):
+ source_parent.window.diff_requested(v1, v2)
+ else:
+ source_parent.window.diff_requested(v1, v2, vistrail_2)
+
+ def hideExecutions(self, hidden):
+ self.executionsHidden = hidden
+ self.updateHideExecutions()
+
+ def updateHideExecutions(self):
+ for i in xrange(self.openFilesItem.childCount()):
+ vt = self.openFilesItem.child(i)
+ if not hasattr(vt, 'tag_to_item'):
+ continue
+ for item in vt.tag_to_item.itervalues():
+ if not hasattr(item, 'executionList'):
+ continue
+ for exec_item in item.executionList:
+ exec_item.setHidden(self.executionsHidden)
+ for i in xrange(self.closedFilesItem.childCount()):
+ vt = self.closedFilesItem.child(i)
+ if not hasattr(vt, 'tag_to_item'):
+ continue
+ for item in vt.tag_to_item.itervalues():
+ if not hasattr(item, 'executionList'):
+ continue
+ for exec_item in item.executionList:
+ exec_item.setHidden(self.executionsHidden)
+
+ def make_list(self, item):
+ """ construct a list from the tagged workflows in a loaded vistrail
+ """
+ self.setSortingEnabled(False)
+ if not (hasattr(item, 'tag_to_item') or hasattr(item, 'mshp_to_item')):
+ return
+ for tag, wf in item.tag_to_item.iteritems():
+ index = wf.parent().indexOfChild(wf)
+ wf = wf.parent().takeChild(index)
+ item.workflowsItem.addChild(wf)
+ self.updateHideExecutions()
+ self.setSortingEnabled(True)
+
+ def make_tree(self, item):
+ """ construct a tree from the tagged workflows in a loaded vistrail
+ """
+ self.setSortingEnabled(False)
+ if not hasattr(item, 'window'):
+ return
+ am = item.window.controller.vistrail.actionMap
+ tm = item.window.controller.vistrail.get_tagMap()
+ vm = dict((v,k) for k, v in tm.iteritems())
+ # loop through tagged workflows and add to parent workflow
+ if not hasattr(item, 'tag_to_item'):
+ return
+ for tag, wf in item.tag_to_item.iteritems():
+ if tag not in vm:
+ continue
+ # find parent
+ version = vm[tag]
+ action = am[version]
+ while action.parent in am:
+ action = am[action.parent]
+ if action.timestep in tm:
+ break
+ if action.timestep not in tm or action.timestep == version:
+ continue
+ parent_tag = tm[action.timestep]
+ if parent_tag in item.tag_to_item:
+ parent_wf = item.tag_to_item[parent_tag]
+ index = wf.parent().indexOfChild(wf)
+ wf = wf.parent().takeChild(index)
+ parent_wf.addChild(wf)
+ self.updateHideExecutions()
+ self.setSortingEnabled(True)
+
+
+ def state_changed(self, view):
+ """ update tags, mashups and parameter explorations """
+ # sometimes references to closed views trigger a state_changed event
+ if id(view) not in self.items:
+ return
+ item = self.items[id(view)]
+ entity = item.entity
+
+ (new_entity, was_updated) = \
+ entity.update_vistrail(view.controller.vistrail)
+ #if new_entity:
+ # Collection.getInstance().create_vistrail_entity(
+ # view.controller.vistrail)
+ # self.add_vt_window(view)
+ # return
+ if was_updated:
+ item.setText(0, entity.name)
+ (added_wfs, deleted_wfs) = entity.update_workflows()
+ (more_added_wfs, added_wf_execs) = entity.update_log()
+ (added_mshps, deleted_mshps) = entity.update_mashups()
+ (added_pes, deleted_pes) = entity.update_parameter_explorations()
+
+ for wf_entity in deleted_wfs:
+ assert(wf_entity.name in item.tag_to_item)
+ child = item.tag_to_item[wf_entity.name]
+ child_idx = child.parent().indexOfChild(child)
+ child.parent().takeChild(child_idx)
+ del item.tag_to_item[wf_entity.name]
+ for wf_entity in chain(added_wfs, more_added_wfs):
+ if not wf_entity.name.startswith('Version #'):
+ childItem = QWorkflowEntityItem(wf_entity)
+ item.workflowsItem.addChild(childItem)
+ item.tag_to_item[wf_entity.name] = childItem
+
+ for wf_exec_entity in added_wf_execs:
+ parent_version = wf_exec_entity.workflow_exec.parent_version
+ wf_entity = entity.wf_entity_map[parent_version]
+ if not wf_entity.name.startswith('Version #'):
+ assert(wf_entity.name in item.tag_to_item)
+ wf_item = item.tag_to_item[wf_entity.name]
+ child = QWorkflowExecEntityItem(wf_exec_entity)
+ wf_item.addChild(child)
+ wf_item.executionList.append(child)
+ self.updateHideExecutions()
+
+ for mshp_entity in deleted_mshps:
+ assert(mshp_entity.name in item.mshp_to_item)
+ child = item.mshp_to_item[mshp_entity.name]
+ child_idx = child.parent().indexOfChild(child)
+ child.parent().takeChild(child_idx)
+ del item.mshp_to_item[mshp_entity.name]
+ item.mashupsItem.setHidden(not len(item.mshp_to_item))
+ for mshp_entity in added_mshps:
+ childItem = QMashupEntityItem(mshp_entity)
+ item.mashupsItem.addChild(childItem)
+ item.mshp_to_item[mshp_entity.name] = childItem
+ item.mashupsItem.setHidden(not len(item.mshp_to_item))
+
+ for pe_entity in deleted_pes:
+ assert(pe_entity.url in item.pe_to_item)
+ child = item.pe_to_item[pe_entity.url]
+ child_idx = child.parent().indexOfChild(child)
+ child.parent().takeChild(child_idx)
+ del item.pe_to_item[pe_entity.url]
+ item.paramExplorationsItem.setHidden(not len(item.pe_to_item))
+ for pe_entity in added_pes:
+ childItem = QParamExplorationEntityItem(pe_entity)
+ item.paramExplorationsItem.addChild(childItem)
+ # keep list of tagged workflows
+ item.pe_to_item[pe_entity.url] = childItem
+ item.paramExplorationsItem.setHidden(not len(item.pe_to_item))
+
+ self.make_tree(item) if self.isTreeView else self.make_list(item)
+
+ def execution_updated(self):
+ """ Add new executions to workflow """
+ # get view and item
+ from vistrails.gui.vistrails_window import _app
+ view = _app.get_current_view()
+ if id(view) not in self.items:
+ return
+ item = self.items[id(view)]
+
+ entity = item.entity
+ entity.set_vistrail(view.controller.vistrail)
+ (added_wfs, added_wf_execs) = entity.update_log()
+ for wf_entity in added_wfs:
+ if not wf_entity.name.startswith('Version #'):
+ childItem = QWorkflowEntityItem(wf_entity)
+ item.workflowsItem.addChild(childItem)
+ # keep list of tagged workflows
+ item.tag_to_item[wf_entity.name] = childItem
+
+ for wf_exec_entity in added_wf_execs:
+ parent_version = wf_exec_entity.workflow_exec.parent_version
+ wf_entity = entity.wf_entity_map[parent_version]
+ if not wf_entity.name.startswith('Version #'):
+ assert(wf_entity.name in item.tag_to_item)
+ wf_item = item.tag_to_item[wf_entity.name]
+ child = QWorkflowExecEntityItem(wf_exec_entity)
+ wf_item.addChild(child)
+ wf_item.executionList.append(child)
+ self.updateHideExecutions()
+
+ def add_vt_window(self, vistrail_window):
+ locator = vistrail_window.controller.locator
+ entity = None
+ entity_was_none = False
+ item_reused = False
+ if locator:
+ entity = self.collection.fromUrl(locator.to_url())
+ if entity is None:
+ entity = VistrailEntity(vistrail_window.controller.vistrail)
+ entity_was_none = True
+
+ # remove item from recent list
+ for i in xrange(self.closedFilesItem.childCount()):
+ recent = self.closedFilesItem.child(i)
+ if entity and recent and recent.entity and \
+ recent.entity.url == entity.url:
+ self.setSelected(None)
+ index = self.closedFilesItem.indexOfChild(recent)
+ item = self.closedFilesItem.takeChild(index)
+ item = QVistrailEntityItem(entity, vistrail_window)
+ item.current_item = QVistrailListLatestItem()
+ item.workflowsItem.addChild(item.current_item)
+ if id(vistrail_window) in self.items:
+ # window already exists
+ old_item = self.items[id(vistrail_window)]
+ url = None
+ if old_item.entity is not None:
+ url = old_item.entity.url
+ # if there was a change in the locator, we need to remove the old
+ # item and put in the closed vistrails area
+
+ if url != vistrail_window.controller.locator.to_url():
+ self.remove_vt_window(vistrail_window)
+ else:
+ # we will reuse the item
+ if hasattr(item, 'entity'):
+ old_item.entity = item.entity
+ old_item.window = item.window
+ old_item.current_item = item.current_item
+ old_item.workflowsItem = item.workflowsItem
+ old_item.mashupsItem = item.mashupsItem
+ old_item.paramExplorationsItem = item.paramExplorationsItem
+ old_item.tag_to_item = item.tag_to_item
+ old_item.mshp_to_item = item.mshp_to_item
+ old_item.pe_to_item = item.pe_to_item
+ old_item.setText(0, item.text(0))
+ while old_item.childCount():
+ child = old_item.child(0)
+ index = old_item.indexOfChild(child)
+ old_item.takeChild(index)
+ while item.childCount():
+ child = item.child(0)
+ index = item.indexOfChild(child)
+ child = item.takeChild(index)
+ old_item.addChild(child)
+ item = old_item
+ item_reused = True
+
+ if not item_reused:
+ self.items[id(vistrail_window)] = item
+ if entity_was_none:
+ self.collection.add_temp_entity(entity)
+ entity.is_open = True
+ entity._window = vistrail_window
+ self.openFilesItem.addChild(item)
+ item.setExpanded(True)
+ item.workflowsItem.setExpanded(True)
+ item.mashupsItem.setExpanded(True)
+ item.paramExplorationsItem.setExpanded(True)
+ item.mashupsItem.setHidden(not item.mashupsItem.childCount())
+ item.paramExplorationsItem.setHidden(
+ not item.paramExplorationsItem.childCount())
+ self.make_tree(item) if self.isTreeView else self.make_list(item)
+ self.setSelected(vistrail_window)
+ self.updateHideExecutions()
+
+ def remove_vt_window(self, vistrail_window):
+ if id(vistrail_window) not in self.items:
+ return
+ self.setSelected(None)
+ item = self.items[id(vistrail_window)]
+ del self.items[id(vistrail_window)]
+ delattr(item, 'window')
+ index = self.openFilesItem.indexOfChild(item)
+ item = self.openFilesItem.takeChild(index)
+ url = None
+ if item.entity is not None:
+ item.entity.is_open = False
+ item.entity._window = None
+ url = item.entity.url
+ item.current_item.parent().removeChild(item.current_item)
+ # entity may have changed
+ entity = None
+ if url is None:
+ locator = vistrail_window.controller.locator
+ if locator and not isinstance(locator, UntitledLocator):
+ entity = self.collection.fromUrl(locator.to_url())
+ else:
+ entity = self.collection.fromUrl(url)
+
+ if entity and not self.collection.is_temp_entity(entity) and \
+ not vistrail_window.is_abstraction:
+ item = QVistrailEntityItem(entity)
+ self.make_tree(item) if self.isTreeView else self.make_list(item)
+ self.closedFilesItem.addChild(item)
+ item.setText(0, entity.name)
+ self.updateHideExecutions()
+
+ def change_vt_window(self, vistrail_window):
+ self.setSelected(vistrail_window)
+
+ def setSelected(self, view):
+ """ Highlights the vistrail item for the selected item"""
+ self.disconnect_current_changed()
+
+ def setBold(parent_item):
+ """ """
+ for i in xrange(parent_item.childCount()):
+ item = parent_item.child(i)
+ font = item.font(0)
+ window = item.window if hasattr(item, 'window') else None
+ font.setBold(view == window if window and view else False)
+ item.setFont(0, font)
+ if window:
+ item.setText(0, window.get_name())
+
+ if not self.openFilesItem.isHidden():
+ setBold(self.openFilesItem)
+ elif self.searchMode:
+ setBold(self.searchResultsItem)
+ self.connect_current_changed()
+
+ def item_changed(self, item, prev_item):
+ if not item:
+ return
+ vistrail = item
+ while not hasattr(vistrail, 'window'):
+ if not vistrail or not vistrail.parent:
+ # parent node
+ return
+ vistrail = vistrail.parent()
+ #print "*** item clicked", id(vistrail.window)
+
+ self.setSelected(vistrail.window)
+ self.parent().emit(QtCore.SIGNAL("vistrailChanged(PyQt_PyObject)"),
+ vistrail.window)
+
+ def keyPressEvent(self, event):
+ if event.key() in [QtCore.Qt.Key_Delete, QtCore.Qt.Key_Backspace]:
+ items = self.selectedItems()
+ if len(items) == 1:
+ item = items[0]
+ if item.parent() == self.openFilesItem:
+ # close current vistrail
+ from vistrails.gui.vistrails_window import _app
+ if hasattr(item, 'window'):
+ _app.close_vistrail(item.window)
+ else:
+ _app.close_vistrail()
+ elif item.parent() == self.closedFilesItem:
+ # remove from closed list
+ self.closedFilesItem.removeChild(item)
+ self.collection.del_from_workspace(item.entity)
+ self.collection.delete_entity(item.entity)
+ self.collection.commit()
+ elif isinstance(item,QParamExplorationEntityItem):
+ parent = item.parent()
+ while parent and not hasattr(parent, 'window'):
+ parent = parent.parent()
+ if parent:
+ # delete this parameter exploration
+ parent.window.controller.vistrail.delete_paramexp(
+ item.entity.pe)
+ parent.window.controller.set_changed(True)
+
+ else:
+ QtGui.QTreeWidget.keyPressEvent(self, event)
+
+ def contextMenuEvent(self, event):
+ item = self.itemAt(event.pos())
+ if isinstance(item, QVistrailEntityItem):
+ if item and self.openFilesItem.indexOfChild(item) == -1:
+ # vistrail is not open
+ return
+ # item is vistrail
+ menu = QtGui.QMenu(self)
+ act = QtGui.QAction("Open in New Window", self,
+ triggered=item.open_in_new_window)
+ act.setStatusTip("Open specified vistrail file in another window")
+ menu.addAction(act)
+ menu.exec_(event.globalPos())
+ elif (isinstance(item, QWorkflowEntityItem) or
+ isinstance(item, QVistrailListLatestItem)):
+ if item and self.openFilesItem.indexOfChild(item.get_vistrail()) == -1:
+ # vistrail is not open
+ return
+ # item is workflow
+ menu = QtGui.QMenu(self)
+ act = QtGui.QAction("Open", self,
+ triggered=item.open_workflow)
+ act.setStatusTip("Open specified workflow in this window")
+ menu.addAction(act)
+ act = QtGui.QAction("Open in new Tab", self,
+ triggered=item.open_workflow_in_new_tab)
+ act.setStatusTip("Open specified workflow in a new tab")
+ menu.addAction(act)
+ act = QtGui.QAction("Open in new Window", self,
+ triggered=item.open_workflow_in_new_window)
+ act.setStatusTip("Open specified workflow in a new window")
+ menu.addAction(act)
+ menu.exec_(event.globalPos())
+ elif isinstance(item,QMashupEntityItem):
+ if item and self.openFilesItem.indexOfChild(item.parent().parent()) == -1:
+ # vistrail is not open
+ return
+ # item is mashup
+ menu = QtGui.QMenu(self)
+ act = QtGui.QAction("Edit", self,
+ triggered=item.edit_mashup)
+ act.setStatusTip("Edit the mashup")
+ menu.addAction(act)
+ act = QtGui.QAction("Execute", self,
+ triggered=item.open_mashup)
+ act.setStatusTip("Execute the mashup")
+ menu.addAction(act)
+ menu.exec_(event.globalPos())
+
+if __name__ == '__main__':
+ import sys
+ sys.path.append('/vistrails/src/query/vistrails')
+ from vistrails.core.collection import Collection
+
+# vt_1 = load_vistrail(ZIPFileLocator('/vistrails/examples/spx.vt'))[0]
+# vt_2 = load_vistrail(DBLocator('vistrails.sci.utah.edu', 3306,
+# 'vistrails', 'vistrails', '8edLj4',
+# obj_id=9, obj_type='vistrail'))[0]
+
+ c = Collection('test.db')
+ # c.clear()
+ # e_1 = c.create_vistrail_entity(vt_1)
+ # e_2 = c.create_vistrail_entity(vt_2)
+
+ c.entities = {}
+ c.load_entities()
+
+ app = QtGui.QApplication(sys.argv)
+ widget = QBrowserWidget(c)
+ widget.setup_widget('Recent items')
+ widget.show()
+ sys.exit(app.exec_())
diff --git a/vistrails/gui/common_widgets.py b/vistrails/gui/common_widgets.py
new file mode 100644
index 0000000..228e489
--- /dev/null
+++ b/vistrails/gui/common_widgets.py
@@ -0,0 +1,833 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This common widgets using on the interface of VisTrails. These are
+only simple widgets in term of coding and additional features. It
+should have no interaction with VisTrail core"""
+from PyQt4 import QtCore, QtGui
+from PyQt4.QtCore import pyqtSlot, pyqtSignal
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.modules.constant_configuration import StandardConstantWidget
+from vistrails.core.system import systemType
+################################################################################
+
+class QToolWindow(QtGui.QDockWidget):
+ """
+ QToolWindow is a floating-dockable widget. It also keeps track of
+ its widget window title to update the tool window accordingly
+
+ """
+ def __init__(self, widget=None, parent=None):
+ """ QToolWindow(parent: QWidget) -> QToolWindow
+ Construct a floating, dockable widget
+
+ """
+ QtGui.QDockWidget.__init__(self, parent)
+ self.setFeatures(QtGui.QDockWidget.AllDockWidgetFeatures)
+ self.mwindow = QtGui.QMainWindow(self)
+ self.centralwidget = widget
+ self.mwindow.setWindowFlags(QtCore.Qt.Widget)
+ self.mwindow.setCentralWidget(widget)
+ self.setWidget(self.mwindow)
+ self.createToolBar()
+ if widget:
+ self.setWindowTitle(widget.windowTitle())
+ self.pinStatus = False
+ self.monitorWindowTitle(widget)
+
+ self.connect(self, QtCore.SIGNAL("topLevelChanged(bool)"),
+ self.setDefaultPinStatus)
+
+ def createToolBar(self):
+ self.toolbar = QtGui.QToolBar(self.mwindow)
+ self.pinButton = QtGui.QAction(CurrentTheme.UNPINNED_PALETTE_ICON,
+ "", self.toolbar,checkable=True,
+ checked=False,
+ toggled=self.pinStatusChanged)
+
+ self.pinButton.setToolTip("Pin this on the Tab Bar")
+ spacer = QtGui.QWidget()
+ spacer.setSizePolicy(QtGui.QSizePolicy.MinimumExpanding,
+ QtGui.QSizePolicy.Preferred)
+ self.toolbar.addWidget(spacer)
+ self.toolbar.addAction(self.pinButton)
+ self.pinAction = self.pinButton
+ self.toolbar.setFloatable(False)
+ self.toolbar.setMovable(False)
+ self.toolbar.setIconSize(QtCore.QSize(16,16))
+ self.mwindow.addToolBar(self.toolbar)
+
+ def setDefaultPinStatus(self, topLevel):
+ if topLevel:
+ self.setPinStatus(False)
+ self.pinButton.setEnabled(False)
+ else:
+ self.pinButton.setEnabled(True)
+
+ def pinStatusChanged(self, pinStatus):
+ self.pinStatus = pinStatus
+ self.updateButtonIcon(pinStatus)
+
+ def updateButtonIcon(self, on):
+ if on:
+ self.pinButton.setIcon(CurrentTheme.PINNED_PALETTE_ICON)
+ self.pinButton.setToolTip("Unpin this from the the Tab Bar")
+ else:
+ self.pinButton.setIcon(CurrentTheme.UNPINNED_PALETTE_ICON)
+ self.pinButton.setToolTip("Pin this on the Tab Bar")
+
+ def setPinStatus(self, pinStatus):
+ self.pinStatus = pinStatus
+ self.pinButton.setChecked(pinStatus)
+ self.updateButtonIcon(pinStatus)
+
+ def monitorWindowTitle(self, widget):
+ """ monitorWindowTitle(widget: QWidget) -> None
+ Watching window title changed on widget and use it as a window
+ title on this tool window
+
+ """
+ if widget:
+ widget.installEventFilter(self)
+
+ def eventFilter(self, object, event):
+ """ eventFilter(object: QObject, event: QEvent) -> bool
+ Filter window title change event to change the tool window title
+
+ """
+ if event.type()==QtCore.QEvent.WindowTitleChange:
+ self.setWindowTitle(object.windowTitle())
+ elif event.type()==QtCore.QEvent.Close:
+ object.removeEventFilter(self)
+ return QtGui.QDockWidget.eventFilter(self, object, event)
+ # return super(QToolWindow, self).eventFilter(object, event)
+
+
+class QToolWindowInterface(object):
+ """
+ QToolWindowInterface can be co-inherited in any class to allow the
+ inherited class to switch to be contained in a window
+
+ """
+ def toolWindow(self):
+ """ toolWindow() -> None
+ Return the tool window and set its parent to self.parent()
+ while having self as its contained widget
+
+ """
+ if not hasattr(self, '_toolWindow'):
+ self._toolWindow = QToolWindow(self, self.parent and self.parent())
+ elif self._toolWindow.centralwidget!=self:
+ self._toolWindow.window.setCentralWidget(self)
+ return self._toolWindow
+
+ def changeEvent(self, event):
+ """ changeEvent(event: QEvent) -> None
+ Make sure to update the tool parent when to match the widget's
+ real parent
+
+ """
+ if (event.type()==QtCore.QEvent.ParentChange and
+ hasattr(self, '_toolWindow')):
+ if self.parent()!=self._toolWindow:
+ self._toolWindow.setParent(self.parent())
+
+ def setToolWindowAcceptDrops(self, value):
+ self.toolWindow().setAcceptDrops(value)
+
+###############################################################################
+
+class QDockContainer(QtGui.QMainWindow):
+ """
+ QDockContainer is a window that can contain dock widgets while
+ still be contained in a tool window. It is just a straight
+ inheritance from QMainWindow
+
+ """
+ def __init__(self, parent=None):
+ """ QMainWindow(parent: QWidget) -> QMainWindow
+ Setup window to have its widget dockable everywhere
+
+ """
+ QtGui.QMainWindow.__init__(self, parent)
+ self.setDockNestingEnabled(True)
+
+###############################################################################
+
+class QSearchTreeWidget(QtGui.QTreeWidget):
+ """
+ QSearchTreeWidget is just a QTreeWidget with a support function to
+ refine itself when searching for some text
+
+ """
+ def __init__(self, parent=None):
+ """ QSearchTreeWidget(parent: QWidget) -> QSearchTreeWidget
+ Set up size policy and header
+
+ """
+ QtGui.QTreeWidget.__init__(self, parent)
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ self.setRootIsDecorated(True)
+ self.setDragEnabled(True)
+ self.flags = QtCore.Qt.ItemIsDragEnabled
+
+ self._search_was_empty = True
+
+ def searchItemName(self, name):
+ """ searchItemName(name: QString) -> None
+ Search and refine the module tree widget to contain only items
+ whose name is 'name'
+
+ """
+ matchedItems = []
+
+ def recursiveSetVisible(item, testFunction):
+ """ recursiveSetVisible
+ Pass through all items of a item
+
+ """
+ enabled = testFunction(item)
+
+ visible = enabled
+ child = item.child
+ for childIndex in xrange(item.childCount()):
+ visible |= recursiveSetVisible(child(childIndex),
+ testFunction)
+
+ # if item is hidden or has changed visibility
+ if not visible or (item.isHidden() != (not visible)):
+ item.setHidden(not visible)
+
+ if visible:
+ f = item.flags()
+ b = f & self.flags
+ if enabled:
+ if not b:
+ item.setFlags(f | self.flags)
+ elif b:
+ item.setFlags(f & ~self.flags)
+
+ return visible
+
+ if str(name)=='':
+ testFunction = lambda x: (not hasattr(x, 'is_hidden') or
+ not x.is_hidden)
+ if not self._search_was_empty:
+ self.collapseAll()
+ self._search_was_empty = True
+ else:
+ matchedItems = set(self.findItems(name,
+ QtCore.Qt.MatchContains |
+ QtCore.Qt.MatchWrap |
+ QtCore.Qt.MatchRecursive))
+ testFunction = matchedItems.__contains__
+ if self._search_was_empty:
+ self.expandAll()
+ self._search_was_empty = False
+ for itemIndex in xrange(self.topLevelItemCount()):
+ recursiveSetVisible(self.topLevelItem(itemIndex),
+ testFunction)
+
+ def mimeData(self, itemList):
+ """ mimeData(itemList) -> None
+ Setup the mime data to contain itemList because Qt 4.2.2
+ implementation doesn't instantiate QTreeWidgetMimeData
+ anywhere as it's supposed to. It must have been a bug...
+
+ """
+ data = QtGui.QTreeWidget.mimeData(self, itemList)
+ data.items = itemList
+ return data
+
+ def setMatchedFlags(self, flags):
+ """ setMatchedFlags(flags: QItemFlags) -> None Set the flags
+ for matched item in the search tree. Parents of matched node
+ will be visible with these flags off.
+
+ """
+ self.flags = flags
+
+class QSearchTreeWindow(QtGui.QWidget):
+ """
+ QSearchTreeWindow contains a search box on top of a tree widget
+ for easy search and refine. The subclass has to implement
+ createTreeWidget() method to return a tree widget that is also
+ needs to expose searchItemName method
+
+ """
+ def __init__(self, parent=None):
+ """ QSearchTreeWindow(parent: QWidget) -> QSearchTreeWindow
+ Intialize all GUI components
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self.setWindowTitle('Search Tree')
+
+ vLayout = QtGui.QVBoxLayout(self)
+ vLayout.setMargin(0)
+ vLayout.setSpacing(0)
+ self.setLayout(vLayout)
+
+ self.searchBox = QSearchBox(False, True, self)
+ vLayout.addWidget(self.searchBox)
+
+ self.treeWidget = self.createTreeWidget()
+ vLayout.addWidget(self.treeWidget)
+
+ self.connect(self.searchBox,
+ QtCore.SIGNAL('executeIncrementalSearch(QString)'),
+ self.treeWidget.searchItemName)
+ self.connect(self.searchBox,
+ QtCore.SIGNAL('executeSearch(QString)'),
+ self.treeWidget.searchItemName)
+ self.connect(self.searchBox,
+ QtCore.SIGNAL('resetSearch()'),
+ self.clearTreeWidget)
+
+ def clearTreeWidget(self):
+ """ clearTreeWidget():
+ Return the default search tree
+
+ """
+ self.treeWidget.searchItemName('')
+
+ def createTreeWidget(self):
+ """ createTreeWidget() -> QSearchTreeWidget
+ Return a default searchable tree widget
+
+ """
+ return QSearchTreeWidget(self)
+
+class QPromptWidget(QtGui.QLabel):
+ """
+ QPromptWidget is a widget that will display a prompt text when it
+ doesn't have any child visible, or else, it will disappear. This
+ is good for drag and drop prompt. The inheritance should call
+ setPromptText and showPrompt in appropriate time to show/hide the
+ prompt text
+ """
+ def __init__(self, parent=None):
+ """ QPromptWidget(parent: QWidget) -> QPromptWidget
+ Set up the font and alignment for the prompt
+
+ """
+ QtGui.QLabel.__init__(self, parent)
+ self.setAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
+ self.setWordWrap(True)
+ self.regularFont = self.font()
+ self.promptFont = QtGui.QFont(self.font())
+ self.promptFont.setItalic(True)
+ self.promptText = ''
+ self.promptVisible = False
+
+ def setPromptText(self, text):
+ """ setPromptText(text: str) -> None
+ Set the prompt text string
+
+ """
+ self.promptText = text
+
+ def showPrompt(self, show=True):
+ """ showPrompt(show: boolean) -> None
+ Show/Hide the prompt
+
+ """
+ if show!=self.promptVisible:
+ self.promptVisible = show
+ self.repaint(self.rect())
+
+ def showPromptByChildren(self):
+ """ showPromptByChildren()
+ Show/Hide the prompt based on the current state of children
+
+ """
+ if self.promptText=='':
+ self.showPrompt(False)
+ else:
+ self.showPrompt(self.layout()==None or
+ self.layout().count()==0)
+
+ def paintEvent(self, event):
+ """ paintEvent(event: QPaintEvent) -> None
+ Paint the prompt in the center if neccesary
+
+ """
+ if self.promptVisible:
+ painter = QtGui.QPainter(self)
+ painter.setFont(self.promptFont)
+ painter.drawText(self.rect(),
+ QtCore.Qt.AlignCenter | QtCore.Qt.TextWordWrap,
+ self.promptText)
+ painter.end()
+ QtGui.QLabel.paintEvent(self, event)
+ # super(QPromptWidget, self).paintEvent(event)
+
+class QStringEdit(QtGui.QFrame):
+ """
+ QStringEdit is a line edit that has an extra button to allow user
+ to use a file as the value
+
+ """
+ def __init__(self, parent=None):
+ """ QStringEdit(parent: QWidget) -> QStringEdit
+ Create a hbox layout to contain a line edit and a button
+
+ """
+ QtGui.QFrame.__init__(self, parent)
+ hLayout = QtGui.QHBoxLayout(self)
+ hLayout.setMargin(0)
+ hLayout.setSpacing(0)
+ self.setLayout(hLayout)
+
+ self.lineEdit = QtGui.QLineEdit()
+ self.lineEdit.setFrame(False)
+ self.lineEdit.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ hLayout.addWidget(self.lineEdit)
+ self.setFocusProxy(self.lineEdit)
+
+ self.fileButton = QtGui.QToolButton()
+ self.fileButton.setText('...')
+ self.fileButton.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Expanding)
+ self.fileButton.setFocusPolicy(QtCore.Qt.NoFocus)
+ self.fileButton.setAutoFillBackground(True)
+ self.connect(self.fileButton, QtCore.SIGNAL('clicked()'),
+ self.insertFileNameDialog)
+ hLayout.addWidget(self.fileButton)
+
+ def setText(self, text):
+ """ setText(text: QString) -> None
+ Overloaded function for setting the line edit text
+
+ """
+ self.lineEdit.setText(text)
+
+ def text(self):
+ """ text() -> QString
+ Overloaded function for getting the line edit text
+
+ """
+ return self.lineEdit.text()
+
+ def selectAll(self):
+ """ selectAll() -> None
+ Overloaded function for selecting all the text
+
+ """
+ self.lineEdit.selectAll()
+
+ def setFrame(self, frame):
+ """ setFrame(frame: bool) -> None
+ Show/Hide the frame of this widget
+
+ """
+ if frame:
+ self.setFrameStyle(QtGui.QFrame.StyledPanel |
+ QtGui.QFrame.Plain)
+ else:
+ self.setFrameStyle(QtGui.QFrame.NoFrame)
+
+ def insertFileNameDialog(self):
+ """ insertFileNameDialog() -> None
+ Allow user to insert a file name as a value to the string
+
+ """
+ fileName = QtGui.QFileDialog.getOpenFileName(self,
+ 'Use Filename '
+ 'as Value...',
+ self.text(),
+ 'All files '
+ '(*.*)')
+ if fileName:
+ self.setText(fileName)
+
+###############################################################################
+
+class MultiLineWidget(StandardConstantWidget):
+ def __init__(self, contents, contentType, parent=None):
+ """__init__(contents: str, contentType: str, parent: QWidget) ->
+ StandardConstantWidget
+ Initialize the line edit with its contents. Content type is limited
+ to 'int', 'float', and 'string'
+
+ """
+ StandardConstantWidget.__init__(self, parent)
+
+ def update_parent(self):
+ pass
+
+ def keyPressEvent(self, event):
+ """ keyPressEvent(event) -> None
+ If this is a string line edit, we can use Ctrl+Enter to enter
+ the file name
+
+ """
+ k = event.key()
+ s = event.modifiers()
+ if ((k == QtCore.Qt.Key_Enter or k == QtCore.Qt.Key_Return) and
+ s & QtCore.Qt.ShiftModifier):
+ event.accept()
+ if self.contentIsString and self.multiLines:
+ fileNames = QtGui.QFileDialog.getOpenFileNames(self,
+ 'Use Filename '
+ 'as Value...',
+ self.text(),
+ 'All files '
+ '(*.*)')
+ fileName = fileNames.join(',')
+ if fileName:
+ self.setText(fileName)
+ return
+ QtGui.QLineEdit.keyPressEvent(self,event)
+
+###############################################################################
+
+class QSearchEditBox(QtGui.QComboBox):
+ def __init__(self, incremental=True, parent=None):
+ QtGui.QComboBox.__init__(self, parent)
+ self.setEditable(True)
+ self.setInsertPolicy(QtGui.QComboBox.InsertAtTop)
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Fixed)
+ regexp = QtCore.QRegExp("\S.*")
+ self.setDuplicatesEnabled(False)
+ validator = QtGui.QRegExpValidator(regexp, self)
+ self.setValidator(validator)
+ self.addItem('Clear Recent Searches')
+ item = self.model().item(0, 0)
+ font = QtGui.QFont(item.font())
+ font.setItalic(True)
+ item.setFont(font)
+ self.is_incremental = incremental
+
+ def keyPressEvent(self, e):
+ if e.key() in (QtCore.Qt.Key_Return,QtCore.Qt.Key_Enter):
+ if self.currentText():
+ if not self.is_incremental:
+ self.emit(QtCore.SIGNAL('executeSearch(QString)'),
+ self.currentText())
+ self.insertItem(0, self.currentText())
+ else:
+ self.emit(QtCore.SIGNAL('resetText()'))
+ return
+ QtGui.QComboBox.keyPressEvent(self, e)
+
+###############################################################################
+
+class QSearchBox(QtGui.QWidget):
+ """
+ QSearchBox contains a search combo box with a clear button and
+ a search icon.
+
+ """
+ def __init__(self, refine=True, incremental=True, parent=None):
+ """ QSearchBox(parent: QWidget) -> QSearchBox
+ Intialize all GUI components
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self.setWindowTitle('Search')
+
+ hLayout = QtGui.QHBoxLayout(self)
+ hLayout.setMargin(0)
+ hLayout.setSpacing(2)
+ self.setLayout(hLayout)
+
+ self.searchEdit = QSearchEditBox(incremental, self)
+ #TODO: Add separator!
+ self.searchEdit.clearEditText()
+
+ if refine:
+ self.actionGroup = QtGui.QActionGroup(self)
+ self.searchAction = QtGui.QAction('Search', self)
+ self.searchAction.setCheckable(True)
+ self.actionGroup.addAction(self.searchAction)
+ self.refineAction = QtGui.QAction('Refine', self)
+ self.refineAction.setCheckable(True)
+ self.actionGroup.addAction(self.refineAction)
+ self.searchAction.setChecked(True)
+
+ self.searchMenu = QtGui.QMenu()
+ self.searchMenu.addAction(self.searchAction)
+ self.searchMenu.addAction(self.refineAction)
+
+ self.searchButton = QtGui.QToolButton(self)
+ self.searchButton.setIcon(CurrentTheme.QUERY_ARROW_ICON)
+ self.searchButton.setAutoRaise(True)
+ self.searchButton.setPopupMode(QtGui.QToolButton.InstantPopup)
+ self.searchButton.setMenu(self.searchMenu)
+ hLayout.addWidget(self.searchButton)
+ self.connect(self.searchAction, QtCore.SIGNAL('triggered()'),
+ self.searchMode)
+ self.connect(self.refineAction, QtCore.SIGNAL('triggered()'),
+ self.refineMode)
+ else:
+ self.searchLabel = QtGui.QLabel(self)
+ pix = CurrentTheme.QUERY_VIEW_ICON.pixmap(QtCore.QSize(16,16))
+ self.searchLabel.setPixmap(pix)
+ self.searchLabel.setAlignment(QtCore.Qt.AlignCenter)
+ self.searchLabel.setMargin(4)
+ hLayout.addWidget(self.searchLabel)
+
+ hLayout.addWidget(self.searchEdit)
+
+ self.resetButton = QtGui.QToolButton(self)
+ self.resetButton.setIcon(QtGui.QIcon(
+ self.style().standardPixmap(QtGui.QStyle.SP_DialogCloseButton)))
+ self.resetButton.setIconSize(QtCore.QSize(12,12))
+ self.resetButton.setAutoRaise(True)
+ self.resetButton.setEnabled(False)
+ hLayout.addWidget(self.resetButton)
+ self.manualResetEnabled = False
+
+ self.connect(self.resetButton, QtCore.SIGNAL('clicked()'),
+ self.resetSearch)
+ self.connect(self.searchEdit, QtCore.SIGNAL('activated(int)'),
+ self.executeSearch)
+ self.connect(self.searchEdit, QtCore.SIGNAL('resetText'),
+ self.resetSearch)
+ self.connect(self.searchEdit, QtCore.SIGNAL('executeSearch(QString)'),
+ self.executeTextSearch)
+ if incremental:
+ self.connect(self.searchEdit,
+ QtCore.SIGNAL('editTextChanged(QString)'),
+ self.executeIncrementalSearch)
+ else:
+ self.connect(self.searchEdit,
+ QtCore.SIGNAL('editTextChanged(QString)'),
+ self.resetToggle)
+
+ def resetSearch(self):
+ """
+ resetSearch() -> None
+ Emit a signal to clear the search.
+
+ """
+ self.searchEdit.clearEditText()
+ self.resetButton.setEnabled(False)
+ self.manualResetEnabled = False
+ self.emit(QtCore.SIGNAL('resetSearch()'))
+
+ def clearSearch(self):
+ """ clearSearch() -> None
+ Clear the edit text without emitting resetSearch() signal
+ This is for when the search is rest from the version view and
+ the signal are already taken care of
+
+ """
+ self.searchEdit.clearEditText()
+ self.resetButton.setEnabled(False)
+ self.manualResetEnabled = False
+
+ def searchMode(self):
+ """
+ searchMode() -> None
+
+ """
+ self.emit(QtCore.SIGNAL('refineMode(bool)'), False)
+
+ def refineMode(self):
+ """
+ refineMode() -> None
+
+ """
+ self.emit(QtCore.SIGNAL('refineMode(bool)'), True)
+
+ def resetToggle(self, text):
+ self.resetButton.setEnabled((str(text) != '') or
+ self.manualResetEnabled)
+
+ def executeIncrementalSearch(self, text):
+ """
+ executeIncrementalSearch(text: QString) -> None
+ The text is changing, so update the search.
+
+ """
+ self.resetButton.setEnabled((str(text)!='') or
+ self.manualResetEnabled)
+ self.emit(QtCore.SIGNAL('executeIncrementalSearch(QString)'), text)
+
+ def executeTextSearch(self, text):
+ self.emit(QtCore.SIGNAL('executeSearch(QString)'),
+ text)
+
+ def executeSearch(self, index):
+ """
+ executeSearch(index: int) -> None
+ The text is finished changing or a different item was selected.
+
+ """
+ count = self.searchEdit.count()
+ if index == count-1:
+ for i in xrange(count-1):
+ self.searchEdit.removeItem(0)
+ self.resetSearch()
+ else:
+ self.resetButton.setEnabled(True)
+ self.emit(QtCore.SIGNAL('executeSearch(QString)'),
+ self.searchEdit.currentText())
+
+ def getCurrentText(self):
+ return str(self.searchEdit.currentText())
+
+ def setManualResetEnabled(self, boolVal):
+ self.manualResetEnabled = boolVal
+ self.resetButton.setEnabled((self.getCurrentText() != '') or
+ self.manualResetEnabled)
+
+###############################################################################
+
+class QTabBarDetachButton(QtGui.QAbstractButton):
+ """QTabBarDetachButton is a special button to be added to a tab
+
+ """
+ def __init__(self, parent):
+ QtGui.QAbstractButton.__init__(self)
+ self.setFocusPolicy(QtCore.Qt.NoFocus)
+ self.setCursor(QtCore.Qt.ArrowCursor)
+ self.setToolTip("Detach Tab")
+ self.setIcon(CurrentTheme.DETACH_TAB_ICON)
+ self.activePixmap = self.icon().pixmap(self.sizeHint(),
+ mode=QtGui.QIcon.Active)
+ self.normalPixmap = self.icon().pixmap(self.sizeHint(),
+ mode=QtGui.QIcon.Normal)
+
+ self.resize(self.sizeHint())
+
+ def sizeHint(self):
+ self.ensurePolished()
+ size = QtCore.QSize()
+ if not self.icon().isNull():
+ iconSize = self.style().pixelMetric(QtGui.QStyle.PM_SmallIconSize,
+ None, self)
+ sz = self.icon().actualSize(QtCore.QSize(iconSize, iconSize))
+ size = max(sz.width(), sz.height())
+
+ return QtCore.QSize(size, size)
+
+ def enterEvent(self, event):
+ if self.isEnabled():
+ icon = QtGui.QIcon(self.activePixmap)
+ self.setIcon(icon)
+ self.update()
+ else:
+ icon = QtGui.QIcon(self.normalPixmap)
+ self.setIcon(icon)
+ QtGui.QAbstractButton.enterEvent(self, event)
+
+ def leaveEvent(self, event):
+ icon = QtGui.QIcon(self.normalPixmap)
+ self.setIcon(icon)
+ if self.isEnabled():
+ self.update()
+ QtGui.QAbstractButton.leaveEvent(self, event)
+
+ def closePosition(self):
+ tb = self.parent()
+ if isinstance(tb, QtGui.QTabBar):
+ close_position = self.style().styleHint(QtGui.QStyle.SH_TabBar_CloseButtonPosition,
+ None, tb)
+ return close_position
+ return -1
+
+ def otherPosition(self):
+ tb = self.parent()
+ if isinstance(tb, QtGui.QTabBar):
+ close_position = self.closePosition()
+ if close_position == QtGui.QTabBar.LeftSide:
+ position = QtGui.QTabBar.RightSide
+ else:
+ position = QtGui.QTabBar.LeftSide
+ return position
+ return -1
+
+ def paintEvent(self, event):
+ p = QtGui.QPainter(self)
+ opt = QtGui.QStyleOptionToolButton()
+ opt.init(self)
+ opt.state |= QtGui.QStyle.State_AutoRaise
+ if (self.isEnabled() and self.underMouse() and
+ not self.isChecked() and not self.isDown()):
+ opt.state |= QtGui.QStyle.State_Raised
+ if self.isChecked():
+ opt.state |= QtGui.QStyle.State_On
+ if self.isDown():
+ opt.state |= QtGui.QStyle.State_Sunken
+ tb = self.parent()
+ if isinstance(tb, QtGui.QTabBar):
+ index = tb.currentIndex()
+ position = self.otherPosition()
+ if tb.tabButton(index, position) == self:
+ opt.state |= QtGui.QStyle.State_Selected
+ opt.icon = self.icon()
+ opt.subControls = QtGui.QStyle.SC_None
+ opt.activeSubControls = QtGui.QStyle.SC_None
+ opt.features = QtGui.QStyleOptionToolButton.None
+ opt.arrowType = QtCore.Qt.NoArrow
+ size = self.style().pixelMetric(QtGui.QStyle.PM_SmallIconSize,
+ None, self)
+ opt.iconSize = QtCore.QSize(size,size)
+ self.style().drawComplexControl(QtGui.QStyle.CC_ToolButton, opt, p,
+ self)
+
+###############################################################################
+
+class QMouseTabBar(QtGui.QTabBar):
+ """QMouseTabBar is a QTabBar that emits a signal when a tab
+ receives a mouse event. For now only doubleclick events are
+ emitted."""
+ #signals
+ tabDoubleClicked = pyqtSignal(int,QtCore.QPoint)
+
+ def __init__(self, parent=None):
+ QtGui.QTabBar.__init__(self, parent)
+
+ def mouseDoubleClickEvent(self, event):
+ if event.button() == QtCore.Qt.LeftButton:
+ tab_idx = self.tabAt(event.pos())
+ if tab_idx != -1:
+ self.tabDoubleClicked.emit(tab_idx, event.pos())
+ QtGui.QTabBar.mouseDoubleClickEvent(self, event)
+
+###############################################################################
+
+class QDockPushButton(QtGui.QPushButton):
+ """QDockPushButton is a button to be used inside QDockWidgets. It will
+ set the minimum height on Mac so it looks nice on both Mac and Windows"""
+ def __init__(self, text, parent=None):
+ QtGui.QPushButton.__init__(self, text, parent)
+ if systemType in ['Darwin']:
+ self.setMinimumHeight(32)
diff --git a/vistrails/gui/configuration.py b/vistrails/gui/configuration.py
new file mode 100644
index 0000000..bd6ee61
--- /dev/null
+++ b/vistrails/gui/configuration.py
@@ -0,0 +1,979 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Widgets to display/edit configuration objects."""
+import os
+import os.path
+from PyQt4 import QtGui, QtCore
+
+from vistrails.core import debug
+from vistrails.core.configuration import ConfigurationObject, \
+ get_vistrails_configuration
+
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.gui.common_widgets import QSearchTreeWindow, QSearchTreeWidget
+from vistrails.gui.utils import YES_BUTTON, NO_BUTTON, show_question, show_warning
+
+import vistrails.core.system
+
+##############################################################################
+
+def bool_conv(st):
+ if st == 'True':
+ return True
+ elif st == 'False':
+ return False
+ else:
+ raise TypeError('Bogus value for bool_conv ' + str(st))
+
+class QConfigurationTreeWidgetItem(QtGui.QTreeWidgetItem):
+
+ def __init__(self, parent, obj, parent_obj, name, temp_obj, temp_parent_obj):
+ lst = [name]
+ t = type(obj)
+ if t == bool:
+ self._obj_type = bool_conv
+ else:
+ self._obj_type = t
+ self._parent_obj = parent_obj
+ self._temp_parent_obj = temp_parent_obj
+
+ self._name = name
+ if t == ConfigurationObject:
+ lst.extend(['', ''])
+ QtGui.QTreeWidgetItem.__init__(self, parent, lst)
+ self.setFlags(self.flags() & ~(QtCore.Qt.ItemIsDragEnabled |
+ QtCore.Qt.ItemIsSelectable ))
+ elif t == tuple and obj[0] is None and isinstance(obj[1], type):
+ self._obj_type = obj[1]
+ lst.extend(['', obj[1].__name__])
+ QtGui.QTreeWidgetItem.__init__(self, parent, lst)
+ self.setFlags((self.flags() & ~QtCore.Qt.ItemIsDragEnabled) |
+ QtCore.Qt.ItemIsEditable)
+ else:
+ lst.extend([str(obj), type(obj).__name__])
+ QtGui.QTreeWidgetItem.__init__(self, parent, lst)
+ self.setFlags((self.flags() & ~QtCore.Qt.ItemIsDragEnabled) |
+ QtCore.Qt.ItemIsEditable)
+
+ def change_value(self, new_value):
+ # if this is a parent ConfigurationObject, do nothing
+ if self._parent_obj and not self._obj_type == ConfigurationObject:
+ setattr(self._parent_obj, self._name, self._obj_type(new_value))
+ setattr(self._temp_parent_obj, self._name, self._obj_type(new_value))
+
+ def _get_name(self):
+ return self._name
+ name = property(_get_name)
+
+class QConfigurationTreeWidgetItemDelegate(QtGui.QItemDelegate):
+ """
+ QConfigurationTreeWidgetItemDelegate allows a custom editor for
+ each column of the QConfigurationTreeWidget
+ """
+
+ def createEditor(self, parent, option, index):
+ """ createEditor(parent: QWidget,
+ option: QStyleOptionViewItem,
+ index: QModelIndex) -> QWidget
+ Return the editing widget depending on columns
+
+ """
+ # We only allow users to edit the second column
+ if index.column()==1:
+ dataType = str(index.sibling(index.row(), 2).data())
+
+ # Create the editor based on dataType
+ if dataType=='int':
+ editor = QtGui.QLineEdit(parent)
+ editor.setValidator(QtGui.QIntValidator(parent))
+ elif dataType=='bool':
+ editor = QtGui.QComboBox(parent)
+ editor.addItem('True')
+ editor.addItem('False')
+ else:
+ editor = QtGui.QItemDelegate.createEditor(self, parent,
+ option, index)
+ return editor
+ return None
+
+ def setEditorData(self, editor, index):
+ """ setEditorData(editor: QWidget, index: QModelIndex) -> None
+ Set the editor to reflects data at index
+
+ """
+ if isinstance(editor, QtGui.QComboBox):
+ editor.setCurrentIndex(editor.findText(index.data()))
+ else:
+ QtGui.QItemDelegate.setEditorData(self, editor, index)
+
+ def setModelData(self, editor, model, index):
+ """ setModelData(editor: QStringEdit,
+ model: QAbstractItemModel,
+ index: QModelIndex) -> None
+ Set the text of the editor back to the item model
+
+ """
+ if isinstance(editor, QtGui.QComboBox):
+ model.setData(index, editor.currentText())
+ elif isinstance(editor, QtGui.QLineEdit):
+ model.setData(index, editor.text())
+ else:
+ # Should never get here
+ assert False
+
+
+class QConfigurationTreeWidget(QSearchTreeWidget):
+
+ def __init__(self, parent, persistent_config, temp_config):
+ QSearchTreeWidget.__init__(self, parent)
+ self.setMatchedFlags(QtCore.Qt.ItemIsEditable)
+ self.setColumnCount(3)
+ lst = ['Name', 'Value', 'Type']
+ self.setHeaderLabels(lst)
+ self.create_tree(persistent_config, temp_config)
+
+ def create_tree(self, persistent_config, temp_config):
+ def create_item(parent, obj, parent_obj, name, temp_obj, temp_parent_obj):
+ item = QConfigurationTreeWidgetItem(parent, obj, parent_obj,
+ name, temp_obj, temp_parent_obj)
+ if isinstance(obj, ConfigurationObject):
+ for key in sorted(obj.keys()):
+ create_item(item, getattr(obj, key), obj, key,
+ getattr(temp_obj, key), temp_obj)
+
+ # disconnect() and clear() are here because create_tree might
+ # also be called when an entirely new configuration object is set.
+
+ self.disconnect(self, QtCore.SIGNAL('itemChanged(QTreeWidgetItem *, int)'),
+ self.change_configuration)
+ self.clear()
+ self._configuration = persistent_config
+ self._temp_configuration = temp_config
+ create_item(self, self._configuration, None, 'configuration',
+ self._temp_configuration, None)
+
+ self.expandAll()
+ self.resizeColumnToContents(0)
+ self.connect(self,
+ QtCore.SIGNAL('itemChanged(QTreeWidgetItem *, int)'),
+ self.change_configuration)
+
+ def change_configuration(self, item, col):
+ if item.flags() & QtCore.Qt.ItemIsEditable:
+ new_value = self.indexFromItem(item, col).data()
+ item.change_value(new_value)
+ # option-specific code
+ if item._name == 'dbDefault':
+ # Update the state of the icons if changing between db and
+ # file support
+ dbState = getattr(get_vistrails_configuration(), 'dbDefault')
+ if new_value != dbState:
+ from vistrails.gui.vistrails_window import _app
+ _app.setDBDefault(dbState)
+
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ item, new_value)
+
+class QConfigurationTreeWindow(QSearchTreeWindow):
+
+ def __init__(self, parent, persistent_config, temp_config):
+ self._configuration_object = persistent_config
+ self._temp_configuration = temp_config
+ QSearchTreeWindow.__init__(self, parent)
+
+ def createTreeWidget(self):
+ self.setWindowTitle('Configuration')
+ treeWidget = QConfigurationTreeWidget(self, self._configuration_object,
+ self._temp_configuration)
+
+ # The delegate has to be around (self._delegate) to
+ # work, else the instance will be clean by Python...
+ self._delegate = QConfigurationTreeWidgetItemDelegate()
+ treeWidget.setItemDelegate(self._delegate)
+ return treeWidget
+
+
+class QConfigurationWidget(QtGui.QWidget):
+
+ def __init__(self, parent, persistent_config, temp_config, status_bar):
+ QtGui.QWidget.__init__(self, parent)
+ layout = QtGui.QVBoxLayout(self)
+ self.setLayout(layout)
+ self._status_bar = status_bar
+
+ self._tree = QConfigurationTreeWindow(self, persistent_config,
+ temp_config)
+ lbl = QtGui.QLabel("Set configuration variables for VisTrails here.", self)
+ layout.addWidget(lbl)
+ layout.addWidget(self._tree)
+
+ def configuration_changed(self, persistent_config, temp_config):
+ self._tree.treeWidget.create_tree(persistent_config, temp_config)
+
+class QGeneralConfiguration(QtGui.QWidget):
+ """
+ QGeneralConfiguration is a widget for showing a few general preferences
+ that can be set with widgets.
+
+ """
+ def __init__(self, parent, persistent_config, temp_config):
+ """
+ QGeneralConfiguration(parent: QWidget,
+ configuration_object: ConfigurationObject) -> None
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(10)
+ layout.setSpacing(10)
+ self.setLayout(layout)
+ self._configuration = None
+ self._temp_configuration = None
+ self.create_default_widgets(self, layout)
+ self.create_default_handler_button(self, layout)
+ self.create_other_widgets(self, layout)
+ self.update_state(persistent_config, temp_config)
+ self.connect_default_signals()
+ self.connect_other_signals()
+
+ def connect_default_signals(self):
+
+ # We need to connect only one of the radio buttons signal because
+ # only one of them will be checked at a time
+
+ #Auto save signals
+ self.connect(self._autosave_cb,
+ QtCore.SIGNAL('stateChanged(int)'),
+ self.temp_autosave_changed)
+ self.connect(self._autosave_always,
+ QtCore.SIGNAL('toggled(bool)'),
+ self.autosave_changed)
+
+ #Read and Write to database signals
+ self.connect(self._db_connect_cb,
+ QtCore.SIGNAL('stateChanged(int)'),
+ self.temp_db_connect_changed)
+ self.connect(self._db_connect_always,
+ QtCore.SIGNAL('toggled(bool)'),
+ self.db_connect_changed)
+
+ #Caching signals
+ self.connect(self._use_cache_cb,
+ QtCore.SIGNAL('stateChanged(int)'),
+ self.temp_use_cache_changed)
+ self.connect(self._use_cache_always,
+ QtCore.SIGNAL('toggled(bool)'),
+ self.use_cache_changed)
+
+ #Other signals
+ self.connect(self._splash_cb,
+ QtCore.SIGNAL('stateChanged(int)'),
+ self.splash_changed)
+ self.connect(self._maximize_cb,
+ QtCore.SIGNAL('stateChanged(int)'),
+ self.maximize_changed)
+ self.connect(self._multi_head_cb,
+ QtCore.SIGNAL('stateChanged(int)'),
+ self.multi_head_changed)
+
+ def connect_other_signals(self):
+ if vistrails.core.system.systemType in ['Darwin']:
+ self.connect(self._use_metal_style_cb,
+ QtCore.SIGNAL('stateChanged(int)'),
+ self.metalstyle_changed)
+
+ def create_default_widgets(self, parent, layout):
+ """create_default_widgets(parent: QWidget, layout: QLayout)-> None
+ Creates default widgets in parent
+
+ """
+ #Auto save
+ autosave_gb = QtGui.QGroupBox(parent)
+ autosave_gb.setTitle('Automatically save vistrails')
+ glayout = QtGui.QHBoxLayout()
+ parent._autosave_always = QtGui.QRadioButton("Always")
+ parent._autosave_never = QtGui.QRadioButton("Never")
+ parent._autosave_cb = QtGui.QCheckBox("Yes (for this session only)")
+ glayout.addWidget(parent._autosave_always)
+ glayout.addWidget(parent._autosave_never)
+ glayout.addWidget(parent._autosave_cb)
+ autosave_gb.setLayout(glayout)
+ layout.addWidget(autosave_gb)
+
+ #Read and Write to database
+ db_connect_gb = QtGui.QGroupBox(parent)
+ db_connect_gb.setTitle('Read/Write to database by default')
+ glayout = QtGui.QHBoxLayout()
+ parent._db_connect_always = QtGui.QRadioButton("Always")
+ parent._db_connect_never = QtGui.QRadioButton("Never")
+ parent._db_connect_cb = QtGui.QCheckBox("Yes (for this session only)")
+ glayout.addWidget(parent._db_connect_always)
+ glayout.addWidget(parent._db_connect_never)
+ glayout.addWidget(parent._db_connect_cb)
+ db_connect_gb.setLayout(glayout)
+ layout.addWidget(db_connect_gb)
+
+ #Caching
+ use_cache_gb = QtGui.QGroupBox(parent)
+ use_cache_gb.setTitle('Cache execution results')
+ glayout = QtGui.QHBoxLayout()
+ parent._use_cache_always = QtGui.QRadioButton("Always")
+ parent._use_cache_never = QtGui.QRadioButton("Never")
+ parent._use_cache_cb = QtGui.QCheckBox("Yes (for this session only)")
+ glayout.addWidget(parent._use_cache_always)
+ glayout.addWidget(parent._use_cache_never)
+ glayout.addWidget(parent._use_cache_cb)
+ use_cache_gb.setLayout(glayout)
+ layout.addWidget(use_cache_gb)
+
+ parent._splash_cb = QtGui.QCheckBox(parent)
+ parent._splash_cb.setText('Show splash dialog on startup*')
+ layout.addWidget(parent._splash_cb)
+
+ parent._maximize_cb = QtGui.QCheckBox(parent)
+ parent._maximize_cb.setText('Maximize windows on startup*')
+ layout.addWidget(parent._maximize_cb)
+
+ parent._multi_head_cb = QtGui.QCheckBox(parent)
+ parent._multi_head_cb.setText('Use multiple displays on startup*')
+ layout.addWidget(parent._multi_head_cb)
+
+ def create_default_handler_button(self, parent, layout):
+ if vistrails.core.system.systemType == 'Linux':
+ from vistrails.gui.application import linux_default_application_set
+ from vistrails.core.application import get_vistrails_application
+
+ group = QtGui.QGroupBox(u"Open .vt .vtl files with VisTrails")
+ layout.addWidget(group)
+ layout2 = QtGui.QHBoxLayout()
+ group.setLayout(layout2)
+
+ if linux_default_application_set():
+ label = u".vt .vtl has a handler set"
+ else:
+ label = u".vt .vtl has no handler"
+ self._handler_status = QtGui.QLabel(label)
+
+ def set_dont_ask(state):
+ self._configuration.handlerDontAsk = bool(state)
+ self._temp_configuration.handlerDontAsk = bool(state)
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ 'handlerDontAsk', bool(state))
+ self._handler_dont_ask = QtGui.QCheckBox(u"Don't ask at startup")
+ self.connect(self._handler_dont_ask,
+ QtCore.SIGNAL('stateChanged(int)'),
+ set_dont_ask)
+
+ def install():
+ app = get_vistrails_application()
+ if app.ask_update_default_application(False):
+ self._handler_status.setText(u".vt .vtl has a handler set")
+ install_button = QtGui.QPushButton(u"Install handler")
+ self.connect(install_button, QtCore.SIGNAL('clicked()'),
+ install)
+
+ layout2.addWidget(self._handler_status)
+ layout2.addWidget(self._handler_dont_ask)
+ layout2.addWidget(install_button)
+
+ def create_other_widgets(self, parent, layout):
+ """create_other_widgets(parent: QWidget, layout: QLayout)-> None
+ Creates system specific widgets in parent
+
+ """
+ if vistrails.core.system.systemType in ['Darwin']:
+ parent._use_metal_style_cb = QtGui.QCheckBox(parent)
+ parent._use_metal_style_cb.setText('Use brushed metal appearance*')
+ layout.addWidget(parent._use_metal_style_cb)
+
+ layout.addStretch()
+ label = QtGui.QLabel("* It requires restarting VisTrails for these \
+changes to take effect")
+ layout.addWidget(label)
+
+ def update_state(self, persistent_config, temp_config):
+ """ update_state(configuration: VistrailConfiguration) -> None
+
+ Update the dialog state based on a new configuration
+ """
+
+ self._configuration = persistent_config
+ self._temp_configuration = temp_config
+
+ #Autosave
+ if self._configuration.has('autosave'):
+ if self._configuration.autosave == True:
+ self._autosave_always.setChecked(True)
+ self._autosave_never.setChecked(False)
+ self._autosave_cb.setText("No (for this session only)")
+ self._autosave_cb.setChecked(
+ not self._temp_configuration.autosave)
+
+ else:
+ self._autosave_always.setChecked(False)
+ self._autosave_never.setChecked(True)
+ self._autosave_cb.setText("Yes (for this session only)")
+ self._autosave_cb.setChecked(self._temp_configuration.autosave)
+
+ #Read/Write from DB by default
+ if self._configuration.has('dbDefault'):
+ if self._configuration.dbDefault == True:
+ self._db_connect_always.setChecked(True)
+ self._db_connect_never.setChecked(False)
+ self._db_connect_cb.setText("No (for this session only)")
+ self._db_connect_cb.setChecked(
+ not self._temp_configuration.dbDefault)
+
+ else:
+ self._db_connect_always.setChecked(False)
+ self._db_connect_never.setChecked(True)
+ self._db_connect_cb.setText("Yes (for this session only)")
+ self._db_connect_cb.setChecked(
+ self._temp_configuration.dbDefault)
+ #Caching
+ if self._configuration.has('useCache'):
+ if self._configuration.useCache == True:
+ self._use_cache_always.setChecked(True)
+ self._use_cache_never.setChecked(False)
+ self._use_cache_cb.setText("No (for this session only)")
+ self._use_cache_cb.setChecked(
+ not self._temp_configuration.useCache)
+
+ else:
+ self._use_cache_always.setChecked(False)
+ self._use_cache_never.setChecked(True)
+ self._use_cache_cb.setText("Yes (for this session only)")
+ self._use_cache_cb.setChecked(self._temp_configuration.useCache)
+
+ if self._configuration.has('showSplash'):
+ self._splash_cb.setChecked(self._configuration.showSplash)
+ if self._configuration.has('maximizeWindows'):
+ self._maximize_cb.setChecked(self._configuration.maximizeWindows)
+ if self._configuration.has('multiHeads'):
+ self._multi_head_cb.setChecked(self._configuration.multiHeads)
+
+ #Default handler
+ if vistrails.core.system.systemType == 'Linux':
+ from vistrails.gui.application import \
+ linux_default_application_set, linux_update_default_application
+
+ if linux_default_application_set():
+ self._handler_status.setText(u".vt .vtl has a handler set")
+ else:
+ self._handler_status.setText(u".vt .vtl has no handler")
+
+ self._handler_dont_ask.setChecked(
+ self._configuration.check('handlerDontAsk'))
+
+ #other widgets
+ self.update_other_state()
+
+ def update_other_state(self):
+ """ update_state(configuration: VistrailConfiguration) -> None
+
+ Update the dialog state based on a new configuration
+ """
+ if vistrails.core.system.systemType in ['Darwin']:
+ self._use_metal_style_cb.setChecked(
+ self._configuration.check('useMacBrushedMetalStyle'))
+
+ def autosave_changed(self, on):
+ """ autosave_changed(on: bool) -> None
+
+ """
+ debug.log("auto_save_changed")
+ if self._autosave_always.isChecked() == True:
+ value = True
+ self._autosave_cb.setText("No (for this session only)")
+ self._autosave_cb.setChecked(False)
+ else:
+ value = False
+ self._autosave_cb.setText("Yes (for this session only)")
+ self._autosave_cb.setChecked(False)
+
+ self._configuration.autosave = value
+ self._temp_configuration.autosave = value
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, bool(on))
+
+ def temp_autosave_changed(self, on):
+ """ temp_autosave_changed(on: int) -> None
+
+ """
+ debug.log("temp_auto_save_changed")
+ value = bool(on)
+ if self._autosave_cb.text() == "No (for this session only)":
+ value = not bool(on)
+
+ self._temp_configuration.autosave = value
+
+ def db_connect_changed(self, on):
+ """ db_connect_changed(on: int) -> None
+
+ """
+ if self._db_connect_always.isChecked() == True:
+ value = True
+ self._db_connect_cb.setText("No (for this session only)")
+ self._db_connect_cb.setChecked(False)
+ else:
+ value = False
+ self._db_connect_cb.setText("Yes (for this session only)")
+ self._db_connect_cb.setChecked(False)
+
+ self._configuration.dbDefault = value
+ self._temp_configuration.dbDefault = value
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, bool(on))
+
+ def temp_db_connect_changed(self, on):
+ """ temp_db_connect_changed(on: int) -> None
+
+ """
+ debug.log("temp_db_connect_changed")
+ value = bool(on)
+ if self._db_connect_cb.text() == "No (for this session only)":
+ value = not bool(on)
+
+ self._temp_configuration.dbDefault = value
+
+ def use_cache_changed(self, on):
+ """ use_cache_changed(on: int) -> None
+
+ """
+ if self._use_cache_always.isChecked() == True:
+ value = True
+ self._use_cache_cb.setText("No (for this session only)")
+ self._use_cache_cb.setChecked(False)
+ else:
+ value = False
+ self._use_cache_cb.setText("Yes (for this session only)")
+ self._use_cache_cb.setChecked(False)
+
+ self._configuration.useCache = value
+ self._temp_configuration.useCache = value
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, bool(on))
+
+ def temp_use_cache_changed(self, on):
+ """ temp_use_cache_changed(on: int) -> None
+
+ """
+ debug.log("temp_use_cache_changed")
+ value = bool(on)
+ if self._use_cache_cb.text() == "No (for this session only)":
+ value = not bool(on)
+
+ self._temp_configuration.useCache = value
+
+ def splash_changed(self, on):
+ """ splash_changed(on: int) -> None
+
+ """
+ self._configuration.showSplash = bool(on)
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, bool(on))
+
+ def maximize_changed(self, on):
+ """ maximize_changed(on: int) -> None
+
+ """
+ self._configuration.maximizeWindows = bool(on)
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, bool(on))
+
+ def multi_head_changed(self, on):
+ """ multi_head_changed(on: int) -> None
+
+ """
+ self._configuration.multiHeads = bool(on)
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, bool(on))
+
+ def metalstyle_changed(self, on):
+ """ metalstyle_changed(on: int) -> None
+
+ """
+ self._configuration.useMacBrushedMetalStyle = bool(on)
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, bool(on))
+
+class QThumbnailConfiguration(QtGui.QWidget):
+ """
+ QThumbnailConfiguration is a widget for showing a few thumbnail related
+ preferences that can be set with widgets.
+
+ """
+ def __init__(self, parent, persistent_config, temp_config):
+ """
+ QThumbnailConfiguration(parent: QWidget,
+ configuration_object: ConfigurationObject) -> None
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self._configuration = None
+ self._temp_configuration = None
+ self._cache = ThumbnailCache.getInstance()
+ self.create_widgets()
+ self.update_state(persistent_config, temp_config)
+ self.connect_signals()
+
+ def create_widgets(self):
+ """create_widgets()-> None
+ Creates widgets
+
+ """
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(10)
+ layout.setSpacing(10)
+ self.setLayout(layout)
+
+ #Auto save
+ autosave_gb = QtGui.QGroupBox(self)
+ autosave_gb.setTitle('Automatically save thumbnails in .vt files')
+ glayout = QtGui.QHBoxLayout()
+ self._autosave_always = QtGui.QRadioButton("Always")
+ self._autosave_never = QtGui.QRadioButton("Never")
+ self._autosave_cb = QtGui.QCheckBox("Yes (for this session only)")
+ glayout.addWidget(self._autosave_always)
+ glayout.addWidget(self._autosave_never)
+ glayout.addWidget(self._autosave_cb)
+ autosave_gb.setLayout(glayout)
+ layout.addWidget(autosave_gb)
+
+ #Thumbnails for tagged versions only
+ tagsonly_gb = QtGui.QGroupBox(self)
+ tagsonly_gb.setTitle('Keep thumbnails of tagged versions only')
+ glayout = QtGui.QHBoxLayout()
+ self._tagsonly_always = QtGui.QRadioButton("Always")
+ self._tagsonly_never = QtGui.QRadioButton("Never")
+ self._tagsonly_cb = QtGui.QCheckBox("Yes (for this session only)")
+ glayout.addWidget(self._tagsonly_always)
+ glayout.addWidget(self._tagsonly_never)
+ glayout.addWidget(self._tagsonly_cb)
+ tagsonly_gb.setLayout(glayout)
+ layout.addWidget(tagsonly_gb)
+
+ #Show thumbnails on mouser hover events
+ mouse_hover_gb = QtGui.QGroupBox(self)
+ mouse_hover_gb.setTitle('Show thumbnails as tooltips on mouse \
+hovering tree nodes')
+ glayout = QtGui.QHBoxLayout()
+ self._mouse_hover_always = QtGui.QRadioButton("Always")
+ self._mouse_hover_never = QtGui.QRadioButton("Never")
+ self._mouse_hover_cb = QtGui.QCheckBox("Yes (for this session only)")
+ glayout.addWidget(self._mouse_hover_always)
+ glayout.addWidget(self._mouse_hover_never)
+ glayout.addWidget(self._mouse_hover_cb)
+ mouse_hover_gb.setLayout(glayout)
+ layout.addWidget(mouse_hover_gb)
+
+ hlayout = QtGui.QHBoxLayout()
+ cache_label = QtGui.QLabel(self)
+ cache_label.setText('Limit thumbnail cache size to ')
+
+ self._thumbs_cache_sb = QtGui.QSpinBox(self)
+ self._thumbs_cache_sb.setRange(10,128)
+ self._thumbs_cache_sb.setValue(10)
+ self._thumbs_cache_sb.setSuffix('MB')
+ self._thumbs_cache_sb.stepBy(5)
+
+ self._clear_thumbs_cache_btn = QtGui.QPushButton(self)
+ self._clear_thumbs_cache_btn.setText("Clear Cache")
+
+ hlayout.addWidget(cache_label)
+ hlayout.addWidget(self._thumbs_cache_sb)
+ hlayout.addWidget(self._clear_thumbs_cache_btn)
+ layout.addLayout(hlayout)
+
+ hlayout = QtGui.QHBoxLayout()
+ cache_label2 = QtGui.QLabel(self)
+ cache_label2.setText("Cache Directory:")
+ self._thumbs_cache_directory_edt = QtGui.QLineEdit(self)
+ self._thumbs_cache_directory_btn = QtGui.QPushButton("...", self)
+ hlayout.addWidget(cache_label2)
+ hlayout.addWidget(self._thumbs_cache_directory_edt)
+ hlayout.addWidget(self._thumbs_cache_directory_btn)
+ layout.addLayout(hlayout)
+ layout.addStretch()
+
+ def connect_signals(self):
+ # We need to connect only one of the radio buttons signal because
+ # only one of them will be checked at a time
+
+ #Auto save signals
+ self.connect(self._autosave_always,
+ QtCore.SIGNAL('toggled(bool)'),
+ self.autosave_changed)
+ self.connect(self._autosave_cb,
+ QtCore.SIGNAL('toggled(bool)'),
+ self.temp_autosave_changed)
+
+ #Thumbnails for tagged versions only signals
+ self.connect(self._tagsonly_always,
+ QtCore.SIGNAL('toggled(bool)'),
+ self.tagsonly_changed)
+ self.connect(self._tagsonly_cb,
+ QtCore.SIGNAL('stateChanged(int)'),
+ self.temp_tagsonly_changed)
+
+ #Show thumbnails on mouser hover events signals
+ self.connect(self._mouse_hover_always,
+ QtCore.SIGNAL('toggled(bool)'),
+ self.mouse_hover_changed)
+ self.connect(self._mouse_hover_cb,
+ QtCore.SIGNAL('stateChanged(int)'),
+ self.temp_mouse_hover_changed)
+
+ #Other widget signals
+ self.connect(self._thumbs_cache_sb,
+ QtCore.SIGNAL('valueChanged(int)'),
+ self.thumbs_cache_changed)
+ self.connect(self._clear_thumbs_cache_btn,
+ QtCore.SIGNAL('clicked()'),
+ self.clear_thumbs_cache_pressed)
+ self.connect(self._thumbs_cache_directory_edt,
+ QtCore.SIGNAL('editingFinished()'),
+ self.thumbs_cache_directory_changed)
+ self.connect(self._thumbs_cache_directory_btn,
+ QtCore.SIGNAL('clicked()'),
+ self.show_directory_chooser)
+
+ def update_state(self, persistent_config, temp_config):
+ """ update_state(persistent_config, temp_config: VistrailConfiguration)
+ -> None
+ Update the dialog state based on a new configuration
+
+ """
+ self._configuration = persistent_config
+ self._temp_configuration = temp_config
+ #Auto save
+ if self._configuration.has('thumbs'):
+ if self._configuration.thumbs.has('autoSave'):
+ if self._configuration.autosave == True:
+ self._autosave_always.setChecked(True)
+ self._autosave_never.setChecked(False)
+ self._autosave_cb.setText("No (for this session only)")
+ self._autosave_cb.setChecked(
+ not self._temp_configuration.thumbs.autoSave)
+
+ else:
+ self._autosave_always.setChecked(False)
+ self._autosave_never.setChecked(True)
+ self._autosave_cb.setText("Yes (for this session only)")
+ self._autosave_cb.setChecked(
+ self._temp_configuration.thumbs.autoSave)
+ #Thumbnails for tagged versions only
+ if self._configuration.thumbs.has('tagsOnly'):
+ if self._configuration.thumbs.tagsOnly == True:
+ self._tagsonly_always.setChecked(True)
+ self._tagsonly_never.setChecked(False)
+ self._tagsonly_cb.setText("No (for this session only)")
+ self._tagsonly_cb.setChecked(
+ not self._temp_configuration.thumbs.tagsOnly)
+
+ else:
+ self._tagsonly_always.setChecked(False)
+ self._tagsonly_never.setChecked(True)
+ self._tagsonly_cb.setText("Yes (for this session only)")
+ self._tagsonly_cb.setChecked(
+ self._temp_configuration.thumbs.tagsOnly)
+ #Show thumbnails on mouser hover events
+ if self._configuration.thumbs.has('mouseHover'):
+ if self._configuration.thumbs.mouseHover == True:
+ self._mouse_hover_always.setChecked(True)
+ self._mouse_hover_never.setChecked(False)
+ self._mouse_hover_cb.setText("No (for this session only)")
+ self._mouse_hover_cb.setChecked(
+ not self._temp_configuration.thumbs.mouseHover)
+
+ else:
+ self._mouse_hover_always.setChecked(False)
+ self._mouse_hover_never.setChecked(True)
+ self._mouse_hover_cb.setText("Yes (for this session only)")
+ self._mouse_hover_cb.setChecked(
+ self._temp_configuration.thumbs.mouseHover)
+ # Other widgets
+ if self._configuration.thumbs.has('cacheSize'):
+ self._thumbs_cache_sb.setValue(
+ self._configuration.thumbs.cacheSize)
+ if self._configuration.thumbs.has('cacheDirectory'):
+ self._thumbs_cache_directory_edt.setText(
+ self._configuration.thumbs.cacheDirectory)
+
+ def autosave_changed(self, on):
+ """ autosave_changed(on: bool) -> None
+
+ """
+ debug.log("thumbs_auto_save_changed")
+ if self._autosave_always.isChecked() == True:
+ value = True
+ self._autosave_cb.setText("No (for this session only)")
+ self._autosave_cb.setChecked(False)
+ else:
+ value = False
+ self._autosave_cb.setText("Yes (for this session only)")
+ self._autosave_cb.setChecked(False)
+
+ self._configuration.thumbs.autoSave = value
+ self._temp_configuration.thumbs.autoSave = value
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, bool(on))
+
+ def temp_autosave_changed(self, on):
+ """ temp_autosave_changed(on: int) -> None
+
+ """
+ debug.log("thumbs_temp_auto_save_changed")
+ value = bool(on)
+ if self._autosave_cb.text() == "No (for this session only)":
+ value = not bool(on)
+
+ self._temp_configuration.thumbs.autoSave = value
+
+ def tagsonly_changed(self, on):
+ """ tagsonly_changed(on: bool) -> None
+
+ """
+ debug.log("thumbs_tagsonly_changed")
+ if self._tagsonly_always.isChecked() == True:
+ value = True
+ self._tagsonly_cb.setText("No (for this session only)")
+ self._tagsonly_cb.setChecked(False)
+ else:
+ value = False
+ self._tagsonly_cb.setText("Yes (for this session only)")
+ self._tagsonly_cb.setChecked(False)
+
+ self._configuration.thumbs.tagsOnly = value
+ self._temp_configuration.thumbs.tagsOnly = value
+
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, bool(on))
+
+ def temp_tagsonly_changed(self, on):
+ """ temp_tagsonly_changed(on: int) -> None
+
+ """
+ debug.log("thumbs_temp_tagsonly_changed")
+ value = bool(on)
+ if self._tagsonly_cb.text() == "No (for this session only)":
+ value = not bool(on)
+
+ self._temp_configuration.thumbs.tagsOnly = value
+
+ def mouse_hover_changed(self, on):
+ """ mouse_hover_changed(on: bool) -> None
+
+ """
+ debug.log("thumbs_mouse_hover_changed")
+ if self._mouse_hover_always.isChecked() == True:
+ value = True
+ self._mouse_hover_cb.setText("No (for this session only)")
+ self._mouse_hover_cb.setChecked(False)
+ else:
+ value = False
+ self._mouse_hover_cb.setText("Yes (for this session only)")
+ self._mouse_hover_cb.setChecked(False)
+
+ self._configuration.thumbs.mouseHover = value
+ self._temp_configuration.thumbs.mouseHover = value
+
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, bool(on))
+
+ def temp_mouse_hover_changed(self, on):
+ """ temp_mouse_hover_changed(on: int) -> None
+
+ """
+ debug.log("thumbs_temp_mouse_hover_changed")
+ value = bool(on)
+ if self._mouse_hover_cb.text() == "No (for this session only)":
+ value = not bool(on)
+
+ self._temp_configuration.thumbs.mouseHover = value
+
+ def thumbs_cache_changed(self, v):
+ """ thumbs_cache_changed(v: int) -> None
+
+ """
+ self._configuration.thumbs.cacheSize = v
+ self._temp_configuration.thumbs.cacheSize = v
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, v)
+
+ def thumbs_cache_directory_changed(self):
+ """ thumbs_cache_changed(v: int) -> None
+
+ """
+ value = str(self._thumbs_cache_directory_edt.text())
+ old_folder = self._configuration.thumbs.cacheDirectory
+ if os.path.exists(value):
+ self._configuration.thumbs.cacheDirectory = value
+ self._temp_configuration.thumbs.cacheDirectory = value
+ self.emit(QtCore.SIGNAL('configuration_changed'),
+ None, value)
+ self._cache.move_cache_directory(old_folder,value)
+ else:
+ show_warning('VisTrails', 'The directory specified does not exist.')
+ self._thumbs_cache_directory_edt.setText(old_folder)
+
+ def show_directory_chooser(self):
+ """show_directory_chooser() -> None
+ Shows a dialog for choosing a directory
+
+ """
+ dir = QtGui.QFileDialog.getExistingDirectory(
+ self,
+ "Choose a new directory for storing thumbnail chache files",
+ "",
+ QtGui.QFileDialog.ShowDirsOnly)
+ if dir:
+ self._thumbs_cache_directory_edt.setText(dir)
+ self.thumbs_cache_directory_changed()
+
+ def clear_thumbs_cache_pressed(self):
+ """clear_thumbs_cache_pressed() -> None
+ Will delete all files in thumbs.cacheDirectory if user clicks yes
+
+ """
+ res = show_question('VisTrails',
+ "All files in %s will be removed. Are you sure? " % (
+ self._temp_configuration.thumbs.cacheDirectory),
+ buttons = [YES_BUTTON,NO_BUTTON],
+ default = NO_BUTTON)
+ if res == YES_BUTTON:
+ self._cache.clear()
+
diff --git a/vistrails/gui/controlflow_assist.py b/vistrails/gui/controlflow_assist.py
new file mode 100644
index 0000000..4662d2d
--- /dev/null
+++ b/vistrails/gui/controlflow_assist.py
@@ -0,0 +1,325 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This contains the dialog/logic for the Control Flow Assistant.
+
+QControlFlowAssistDialog
+"""
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core import debug
+from vistrails.core.modules.module_registry import MissingPackage
+from vistrails.core.packagemanager import get_package_manager
+from vistrails.gui.utils import show_info
+
+################################################################################
+
+class QControlFlowAssistDialog(QtGui.QDialog):
+ def __init__(self, parent, selected_module_ids, selected_connection_ids, scene):
+ """ QControlFlowAssistDialog(selected_module_ids: list,
+ selected_connection_ids: list,
+ scene: QGraphicsScene)
+ -> None
+ Creates the control flow assistant dialog
+
+ """
+
+ # FIXME do this here to avoid circular refs
+ from pipeline_view_select import QReadOnlyPortSelectPipelineView
+
+ QtGui.QDialog.__init__(self, parent)
+ self.module_ids = selected_module_ids
+ self.connection_ids = selected_connection_ids
+
+ self.setWindowTitle('Control Flow Assistant')
+ layout = QtGui.QVBoxLayout(self)
+ self.setLayout(layout)
+
+ # Add instruction label
+ self.instructionLabel = QtGui.QLabel('Select one or more Input Ports to receive Lists, and one Output Port to produce a List')
+ layout.addWidget(self.instructionLabel)
+
+ # Add pipeline view
+ self.pipelineView = QReadOnlyPortSelectPipelineView(self, scene, True, selected_module_ids)
+ self.controller = self.pipelineView.scene().controller
+ layout.addWidget(self.pipelineView)
+
+ self.enablePackage()
+
+ # Add ok/cancel buttons
+ buttonLayout = QtGui.QHBoxLayout()
+ buttonLayout.setMargin(5)
+ self.okButton = QtGui.QPushButton('&OK', self)
+ self.okButton.setAutoDefault(False)
+ self.okButton.setFixedWidth(100)
+ buttonLayout.addWidget(self.okButton)
+ self.cancelButton = QtGui.QPushButton('&Cancel', self)
+ self.cancelButton.setAutoDefault(False)
+ self.cancelButton.setShortcut('Esc')
+ self.cancelButton.setFixedWidth(100)
+ buttonLayout.addWidget(self.cancelButton)
+ layout.addLayout(buttonLayout)
+ self.connect(self.okButton, QtCore.SIGNAL('clicked(bool)'), self.okClicked)
+ self.connect(self.cancelButton, QtCore.SIGNAL('clicked(bool)'), self.close)
+
+ def enablePackage(self):
+ """ enablePackge() -> None
+ Tries to enable the controlflow package through the controller.
+ """
+ pm = get_package_manager()
+ cf_pkg_id = 'org.vistrails.vistrails.control_flow'
+ if not pm.has_package(cf_pkg_id):
+ dep_graph = pm.build_dependency_graph([cf_pkg_id])
+ if not self.controller.try_to_enable_package(cf_pkg_id, dep_graph):
+ raise MissingPackage(cf_pkg_id)
+
+ def getInputPortsInfo(self):
+ """ getInputPortsInfo() -> list
+ Gets a list of tuples from the selected input port (QGraphicsPortItem) objects
+ containing: (module, portspec, incoming_connections, halfwidth)
+
+ """
+ return [(gport.parentItem().module, gport.port, gport.controller.get_connections_to(gport.controller.current_pipeline, [gport.parentItem().module.id], gport.port.name), (gport.parentItem().boundingRect().right()-gport.parentItem().boundingRect().left())/2) for gport in self.pipelineView.getSelectedInputPorts()]
+
+ def getOutputPortsInfo(self):
+ """ getOutputPortsInfo() -> list
+ Gets a list of tuples from the selected output port (QGraphicsPortItem) objects
+ containing: (module, portspec, outgoing_connections, halfwidth)
+
+ """
+ return [(gport.parentItem().module, gport.port, gport.controller.get_connections_from(gport.controller.current_pipeline, [gport.parentItem().module.id], gport.port.name), (gport.parentItem().boundingRect().right()-gport.parentItem().boundingRect().left())/2) for gport in self.pipelineView.getSelectedOutputPorts()]
+
+ def okClicked(self):
+ """ okClicked() -> None
+ Verify selected ports and initiate control flow creation
+
+ """
+ try:
+ self.enablePackage()
+ except MissingPackage:
+ debug.critical("The controlflow package is not available")
+ return
+
+ # Verify that at least one input and one output have been chosen
+ input_ports_info = self.getInputPortsInfo()
+ output_ports_info = self.getOutputPortsInfo()
+ if len(input_ports_info) == 0:
+ show_info('No Input Ports Selected', 'No Input Ports have been selected. You must select at least one to proceed.')
+ elif len(output_ports_info) == 0:
+ show_info('No Output Port Selected', 'No Output Port has been selected. You must select one to proceed.')
+ else:
+ self.createControlFlow(input_ports_info, output_ports_info)
+ self.close()
+
+ def createControlFlow(self, input_ports_info, output_ports_info):
+ """ createControlFlow(input_ports_info: list,
+ output_ports_info: list)
+ -> None
+ Create a control flow from input and output port information.
+ input_ports_info is a list of tuples containing: (module, portspec, incoming_connections, halfwidth)
+ input_ports_info is a list of tuples containing: (module, portspec, outgoing_connections, halfwidth)
+
+ """
+ from vistrails.core.modules.basic_modules import identifier as bm_identifier
+ from vistrails.packages.controlflow import identifier as cf_identifier
+
+ io_modules = []
+ io_connections = []
+
+ # Create and connect InputPort for each of the inputs to force it to exist on group
+ offset = {}
+ [offset.__setitem__(module, halfwidth+65) for module, portspec, connections, halfwidth in input_ports_info]
+ for input_module, input_portspec, input_connections, halfwidth in input_ports_info:
+ # Remove function calls to selected input ports
+ try:
+ function_pos = [f.name for f in input_module.functions].index(input_portspec.name)
+ self.controller.delete_method(function_pos, input_module.id)
+ except:
+ pass
+ # Disconnect connections to selected input ports
+ for connection in input_connections:
+ self.connection_ids.remove(connection.id)
+ self.controller.delete_connection(connection.id)
+ group_inport_module = self.controller.add_module(input_module.location.x-offset[input_module], input_module.location.y, bm_identifier, 'InputPort')
+ io_modules.append(group_inport_module)
+ offset[input_module] += 130
+ for p in group_inport_module.sourcePorts():
+ if p.name == 'InternalPipe':
+ group_inport_conn = self.controller.add_connection(input_module.id, input_portspec, group_inport_module.id, p)
+ io_connections.append(group_inport_conn)
+ break
+
+ # Create and connect OutputPort for desired output to force it to exist on group
+ output_module, output_portspec, output_connections, halfwidth = output_ports_info[0]
+ # Disconnect connections to selected output port
+ for connection in output_connections:
+ self.connection_ids.remove(connection.id)
+ self.controller.delete_connection(connection.id)
+ group_outport_module = self.controller.add_module(output_module.location.x+halfwidth+75, output_module.location.y, bm_identifier, 'OutputPort')
+ io_modules.append(group_outport_module)
+ for p in group_outport_module.destinationPorts():
+ if p.name == 'InternalPipe':
+ group_outport_conn = self.controller.add_connection(output_module.id, output_portspec, group_outport_module.id, p)
+ io_connections.append(group_outport_conn)
+ break
+
+ # Create inner group from selected modules and their connections (plus newly created input/output connections)
+ inner_group = self.controller.create_group(self.module_ids + [m.id for m in io_modules], self.connection_ids + [c.id for c in io_connections])
+ self.controller.updatePipelineScene()
+ del io_modules[:]
+ del io_connections[:]
+ io_modules.append(inner_group)
+ io_connections.extend(self.controller.get_connections_to_and_from(self.controller.current_pipeline, [inner_group.id]))
+
+ # Add Map module
+ map_module = self.controller.add_module(inner_group.location.x-120, inner_group.location.y, cf_identifier, 'Map')
+ io_modules.append(map_module)
+
+ # Get group 'self' port object
+ for p in inner_group.sourcePorts():
+ if p.name == 'self':
+ inner_group_selfport = p
+ break
+
+ # Add PythonSource
+ py_source_module = self.controller.add_module(inner_group.location.x, inner_group.location.y+75, bm_identifier, 'PythonSource')
+ io_modules.append(py_source_module)
+ group_type = '('+bm_identifier+':Group)'
+ bool_type = '('+bm_identifier+':Boolean)'
+ list_type = '('+bm_identifier+':List)'
+ string_type = '('+bm_identifier+':String)'
+ base_input_ports = []
+ base_output_ports = [('output', 'InputList', list_type, 0),
+ ('output', 'InputPort', list_type, 1),
+ ('output', 'OutputPort', string_type, 2)]
+ add_input_ports = [('input', 'UseCartesianProduct', bool_type, 1),
+ ('input', 'UserDefinedInputList', list_type, 2)]
+ # Add List port to PythonSource module for each input port selected
+ sortkey = len(base_input_ports) + len(add_input_ports)
+ input_port_names_used = dict([(p[1], 1) for p in base_input_ports])
+ for input_module, input_portspec, input_connections, halfwidth in input_ports_info:
+ port_name = input_portspec.name
+ if port_name not in input_port_names_used:
+ input_port_names_used[port_name] = 1
+ else:
+ input_port_names_used[port_name] += 1
+ port_name += '_%d' % input_port_names_used[port_name]
+ add_input_ports.append(('input', port_name, list_type, sortkey))
+ sortkey += 1
+ # Generate the source
+ source_code = '''
+psrc_module = self.moduleInfo['pipeline'].modules[self.moduleInfo['moduleId']]
+input_ports = [p.name for p in psrc_module.input_port_specs if p.name not in ['UseCartesianProduct', 'UserDefinedInputList']]
+InputPort = input_ports
+OutputPort = '%s'
+custom_input_list = self.forceGetInputFromPort('UserDefinedInputList', [])
+if custom_input_list:
+ InputList = custom_input_list
+else:
+ cartesian_product = self.forceGetInputFromPort('UseCartesianProduct', False)
+ if cartesian_product:
+ input_lists = [self.getInputFromPort(input_ports[x]) for x in xrange(len(input_ports))]
+ InputList = [[]]
+ pools = map(tuple, input_lists)
+ for pool in pools:
+ InputList = [x+[y] for x in InputList for y in pool]
+ else:
+ # Dot Product
+ InputList = []
+ length = len(self.getInputFromPort(input_ports[0]))
+ if len(input_ports) > 1:
+ for p in input_ports[1:]:
+ if len(self.getInputFromPort(p)) != length:
+ fail('One or more of the input lists have different lengths.')
+ for x in xrange(length):
+ element_list = []
+ for p in input_ports:
+ element_list.append(self.getInputFromPort(p)[x])
+ InputList.append(element_list)
+ # Compact list format used when only one input port present
+ if len(input_ports) == 1:
+ InputList = [x[0] for x in InputList]
+print 'InputList: %%s' %% InputList
+''' % output_portspec.name
+ functions = [('source', [source_code])]
+ self.controller.update_ports_and_functions(py_source_module.id, [], base_input_ports + add_input_ports + base_output_ports, functions)
+
+ # Create connections to Map
+ map_module = self.controller.current_pipeline.modules[map_module.id]
+ py_source_module = self.controller.current_pipeline.modules[py_source_module.id]
+ psrc_inputlist = py_source_module.get_port_spec('InputList', 'output')
+ psrc_inputport = py_source_module.get_port_spec('InputPort', 'output')
+ psrc_outputport = py_source_module.get_port_spec('OutputPort', 'output')
+ for map_port in map_module.destinationPorts():
+ # Connect Group 'self' port to Map's FunctionPort
+ if map_port.name == 'FunctionPort':
+ map_conn = self.controller.add_connection(inner_group.id, inner_group_selfport, map_module.id, map_port)
+ # Connect PythonSource output ports to Map input ports
+ elif map_port.name == 'InputList':
+ map_conn = self.controller.add_connection(py_source_module.id, psrc_inputlist, map_module.id, map_port)
+ elif map_port.name == 'InputPort':
+ map_conn = self.controller.add_connection(py_source_module.id, psrc_inputport, map_module.id, map_port)
+ elif map_port.name == 'OutputPort':
+ map_conn = self.controller.add_connection(py_source_module.id, psrc_outputport, map_module.id, map_port)
+ io_connections.append(map_conn)
+
+ # Create and connect InputPort for each of the PythonSource inputs to force it to exist on group
+ offset = 165
+ for port_type, port_name, list_type, sortkey in add_input_ports:
+ group_inport_module = self.controller.add_module(py_source_module.location.x-offset, py_source_module.location.y+75, bm_identifier, 'InputPort')
+ if (port_type, port_name) in [('input', 'UseCartesianProduct'), ('input', 'UserDefinedInputList')]:
+ self.controller.update_ports_and_functions(group_inport_module.id, [], [], [('optional', [True])])
+ io_modules.append(group_inport_module)
+ offset += 130
+ input_portspec = py_source_module.get_port_spec(port_name, port_type)
+ for p in group_inport_module.sourcePorts():
+ if p.name == 'InternalPipe':
+ group_inport_conn = self.controller.add_connection(py_source_module.id, input_portspec, group_inport_module.id, p)
+ io_connections.append(group_inport_conn)
+ break
+
+ # Create and connect OutputPort from Map to force it to exist on group
+ group_outport_module = self.controller.add_module(map_module.location.x, map_module.location.y-75, bm_identifier, 'OutputPort')
+ io_modules.append(group_outport_module)
+ output_portspec = map_module.get_port_spec('Result', 'output')
+ for p in group_outport_module.destinationPorts():
+ if p.name == 'InternalPipe':
+ group_outport_conn = self.controller.add_connection(map_module.id, output_portspec, group_outport_module.id, p)
+ io_connections.append(group_outport_conn)
+ break
+
+ # Create outer group from PythonSource, Map, and inner Group, along with their connections and IO modules
+ outer_group = self.controller.create_group([m.id for m in io_modules], [c.id for c in io_connections])
+ self.controller.updatePipelineScene()
+
diff --git a/vistrails/gui/debug.py b/vistrails/gui/debug.py
new file mode 100644
index 0000000..cc67d13
--- /dev/null
+++ b/vistrails/gui/debug.py
@@ -0,0 +1,375 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import cgi
+import logging
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core.configuration import get_vistrails_configuration
+import vistrails.core.debug
+from vistrails.gui.application import get_vistrails_application
+from vistrails.gui.common_widgets import QDockPushButton
+from vistrails.gui.theme import CurrentTheme
+import vistrails.gui.utils
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+
+################################################################################
+
+
+class DebugView(QtGui.QWidget, QVistrailsPaletteInterface):
+ """ Class used for showing error messages and
+ debugging QT signals.
+
+ Example of usage:
+ import gui.debug
+ gui.debug.watch_signal(my_signal)
+ """
+ #Singleton technique
+ # _instance = None
+ # class DebugViewSingleton():
+ # def __call__(self, *args, **kw):
+ # if DebugView._instance is None:
+ # obj = DebugView(*args, **kw)
+ # DebugView._instance = obj
+ # return DebugView._instance
+
+ # getInstance = DebugViewSingleton()
+
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ ui = logging.StreamHandler(debugStream(self.write))
+ ui.setFormatter(logging.Formatter(
+ '%(levelname)s\n%(asctime)s\n%(message)s'))
+ ui.setLevel(logging.DEBUG)
+ vistrails.core.debug.DebugPrint.getInstance().logger.addHandler(ui)
+ self.setWindowTitle('VisTrails Messages')
+ layout = QtGui.QVBoxLayout()
+ self.setLayout(layout)
+
+ # top message filter buttons
+ filters = QtGui.QHBoxLayout()
+ layout.addLayout(filters)
+
+ filterLabel = QtGui.QLabel('Filter:')
+ filterLabel.setFixedWidth(40)
+ filters.addWidget(filterLabel)
+
+ self.levels = {}
+ for i, name in enumerate(('DEBUG', 'INFO', 'WARNING', 'CRITICAL')):
+ box = QtGui.QCheckBox(name, self)
+ box.setCheckable(True)
+ box.setChecked(name != 'DEBUG')
+ box.setStyleSheet(
+ 'color: %s;\n'
+ 'background-color: %s' % (
+ CurrentTheme.DEBUG_COLORS[name].name(),
+ CurrentTheme.DEBUG_FILTER_BACKGROUND_COLOR.name()))
+ self.connect(box, QtCore.SIGNAL('toggled(bool)'), self.refresh)
+ filters.addWidget(box)
+ self.levels[name] = box
+
+ filters.addStretch()
+
+ # message list
+ self.list = QtGui.QListWidget()
+ self.connect(self.list,
+ QtCore.SIGNAL('currentItemChanged(QListWidgetItem *, QListWidgetItem *)'),
+ self.showMessage)
+ layout.addWidget(self.list)
+
+ # message details field
+ self.text = QtGui.QTextEdit()
+ self.text.setReadOnly(True)
+ self.text.hide()
+ layout.addWidget(self.text)
+
+ # bottom buttons
+ buttons = QtGui.QGridLayout()
+ layout.addLayout(buttons)
+ leftbuttons = QtGui.QGridLayout()
+ buttons.addLayout(leftbuttons, 0, 0, QtCore.Qt.AlignLeft)
+ rightbuttons = QtGui.QGridLayout()
+ buttons.addLayout(rightbuttons, 0, 1, QtCore.Qt.AlignRight)
+
+ copy = QDockPushButton('Copy &Message', self)
+ copy.setToolTip('Copy selected message to clipboard')
+ copy.setFixedWidth(125)
+ rightbuttons.addWidget(copy, 0, 0)
+ self.connect(copy, QtCore.SIGNAL('clicked()'),
+ self.copyMessage)
+
+ copyAll = QDockPushButton('Copy &All', self)
+ copyAll.setToolTip('Copy all messages to clipboard (Can be a lot)')
+ copyAll.setFixedWidth(125)
+ rightbuttons.addWidget(copyAll, 0, 1)
+ self.connect(copyAll, QtCore.SIGNAL('clicked()'),
+ self.copyAll)
+ self.msg_box = None
+ self.itemQueue = []
+ self.resize(700, 400)
+
+ def refresh(self):
+ for i in xrange(self.list.count()):
+ item = self.list.item(i)
+ level = item.data(32).split('\n')[0]
+ self.list.setItemHidden(item, not self.levels[level].isChecked())
+
+ def copyMessage(self):
+ """ copy selected message to clipboard """
+ items = self.list.selectedItems()
+ if len(items)>0:
+ text = items[0].data(32)
+ get_vistrails_application().clipboard().setText(text)
+
+ def copyAll(self):
+ """ copy all messages to clipboard """
+ texts = []
+ for i in range(self.list.count()):
+ texts.append(self.list.item(i).data(32))
+ text = '\n'.join(texts)
+ get_vistrails_application().clipboard().setText(text)
+
+ def showMessage(self, item, olditem):
+ """ show item data in a messagebox """
+ s = item.data(32)
+ msgs = s.split('\n')
+ msgs = [cgi.escape(i) for i in msgs]
+ format = {'INFO': 'Message:',
+ 'WARNING': 'Warning message:',
+ 'CRITICAL': 'Critical message:'}
+
+ text = '<HTML><BODY BGCOLOR="#FFFFFF">'
+ text += '<H4>%s</H4>' % format.get(msgs[0], 'Message:')
+ text += '<H4>%s<br></H4>' % msgs[3]
+ text += '<table border="0">'
+ if len(msgs)>4:
+ text += '<tr><td> </td><td align=left>%s</td></tr>' % '<br>'.join(msgs[4:])
+ text += '<tr><td> </td><td> </td></tr>'
+ text += '<tr><td align=right><b>Time:</b></td><td>%s</td></tr>' % msgs[1]
+ text += '<tr><td align=right><b>Location:</b></td><td>%s</td></tr>' % msgs[2]
+ text += '</table></BODY></HTML>'
+
+ self.text.setHtml(text)
+ self.text.show()
+
+ def watch_signal(self, obj, sig):
+ """self.watch_signal(QObject, QSignal) -> None. Connects a debugging
+ call to a signal so that every time signal is emitted, it gets
+ registered on the log.
+ """
+ self.connect(obj, sig, self.__debugSignal)
+
+ def __debugSignal(self, *args):
+ """ Receives debug signal """
+ debug(str(args))
+
+ def updateMessageBox(self, item):
+ self.currentItem = item
+ msg_box = self.msg_box
+ # update messagebox with data from item
+ s = item.data(32)
+ msgs = s.split('\n')
+ if msgs[0] == "INFO":
+ msg_box.setIcon(QtGui.QMessageBox.Information)
+ msg_box.setWindowTitle("Information")
+ elif msgs[0] == "WARNING":
+ msg_box.setIcon(QtGui.QMessageBox.Warning)
+ msg_box.setWindowTitle("Warning")
+ elif msgs[0] == "CRITICAL":
+ msg_box.setIcon(QtGui.QMessageBox.Critical)
+ msg_box.setWindowTitle("Critical error")
+ msg_box.setText(msgs[3])
+
+ def showMessageBox(self, item):
+ """ Displays the current message in a messagebox
+ if a message is already shown the same message is shown again
+ but with a "next message"-button
+ """
+ msg_box = self.msg_box
+ if not msg_box or not msg_box.isVisible():
+ # create messagebox
+ # app segfaults if the handle to the old messagebox is removed
+ self.old_msg_box = msg_box
+ msg_box = QtGui.QMessageBox(self.parent())
+ self.msg_box = msg_box
+ msg_box.setStandardButtons(QtGui.QMessageBox.Ok)
+ msg_box.setDefaultButton(QtGui.QMessageBox.Ok)
+ msg_box.setEscapeButton(QtGui.QMessageBox.Ok)
+ msg_box.addButton('&Show Messages', msg_box.RejectRole)
+ self.manyButton = None
+ self.connect(msg_box,
+ QtCore.SIGNAL('buttonClicked(QAbstractButton *)'),
+ self.messageButtonClicked)
+ self.connect(msg_box,
+ QtCore.SIGNAL('rejected()'),
+ self.rejectMessage)
+ self.updateMessageBox(item)
+ else:
+ self.itemQueue.append(item)
+
+ # check queue
+ if self.itemQueue:
+ # need to set nextmessage-button
+ many = len(self.itemQueue)
+ text = '&Next Message (%s more)' % many
+ if not self.manyButton:
+ # create button
+ self.manyButton=QtGui.QPushButton(text)
+ msg_box.addButton(self.manyButton, msg_box.DestructiveRole)
+ else:
+ self.manyButton.setText(text)
+ else:
+ # remove button if it exist
+ if self.manyButton:
+ msg_box.removeButton(self.manyButton)
+ self.manyButton = None
+ if not msg_box.isVisible():
+ msg_box.show()
+ msg_box.resize(msg_box.sizeHint())
+ msg_box.updateGeometry()
+ msg_box.activateWindow()
+ msg_box.raise_()
+
+ def messageButtonClicked(self, button):
+ role = self.msg_box.buttonRole(button)
+ if role == self.msg_box.RejectRole:
+ self.itemQueue = []
+ self.set_visible(True)
+ self.list.setCurrentItem(self.currentItem)
+ self.list.scrollToItem(self.currentItem)
+ elif role == self.msg_box.DestructiveRole:
+ # show next message
+ item = self.itemQueue[0]
+ del self.itemQueue[0]
+ self.showMessageBox(item)
+ else:
+ self.itemQueue = []
+
+ def write(self, s):
+ """write(s) -> None
+ adds the string s to the message list and displays it
+ """
+ # adds the string s to the list and
+ s = s.strip()
+ msgs = s.split('\n')
+
+ if len(msgs)<=3:
+ msgs.append('Error logging message: invalid log format')
+ s += '\n' + msgs[3]
+ if not len(msgs[3].strip()):
+ msgs[3] = "Unknown Error"
+ s = '\n'.join(msgs)
+ text = msgs[3]
+ item = QtGui.QListWidgetItem(text)
+ item.setData(32, s)
+ item.setFlags(item.flags()&~QtCore.Qt.ItemIsEditable)
+ self.list.addItem(item)
+ item.setForeground(CurrentTheme.DEBUG_COLORS[msgs[0]])
+ self.list.setItemHidden(item, not self.levels[msgs[0]].isChecked())
+ alwaysShowDebugPopup = getattr(get_vistrails_configuration(),
+ 'alwaysShowDebugPopup',
+ False)
+ if msgs[0] == 'CRITICAL':
+ if self.isVisible() and not alwaysShowDebugPopup:
+ self.raise_()
+ self.activateWindow()
+ modal = get_vistrails_application().activeModalWidget()
+ if modal:
+ # need to beat modal window
+ self.showMessageBox(item)
+ else:
+ self.showMessageBox(item)
+
+ def closeEvent(self, e):
+ """closeEvent(e) -> None
+ Event handler called when the dialog is about to close."""
+ self.emit(QtCore.SIGNAL("messagesView(bool)"), False)
+
+ def showEvent(self, e):
+ """closeEvent(e) -> None
+ Event handler called when the dialog is about to close."""
+ self.emit(QtCore.SIGNAL("messagesView(bool)"), True)
+
+ def reject(self):
+ """ Captures Escape key and closes window correctly """
+ self.close()
+
+ def rejectMessage(self):
+ """ Captures Escape key and closes messageBox correctly """
+ self.itemQueue = []
+ self.msg_box.close()
+
+class debugStream(object):
+ def __init__(self, write):
+ self._write = write
+
+ def write(self, *args, **kwargs):
+ return self._write(*args, **kwargs)
+
+def watch_signal(obj, sig):
+ DebugView.getInstance().watch_signal(obj, sig)
+
+
+critical = vistrails.core.debug.critical
+warning = vistrails.core.debug.warning
+log = vistrails.core.debug.log
+debug = vistrails.core.debug.debug
+
+class TestDebugView(vistrails.gui.utils.TestVisTrailsGUI):
+
+ def test_messages(self):
+ debugview = DebugView.instance()
+ # test message types
+ examples = ["INFO\ntime\nplace\nShort test message\n"
+ "Full test message\nmulti-line",
+ "INFO\ntime\nplace\nShort test message only",
+ "INFO\ntime\nplace\n", # empty message
+ "INFO\ntime\nplace" # no message
+ ]
+ examples += ["%s\ntime\nplace\nShort test message\nFull test message"\
+ % m for m in ['INFO', 'WARNING', 'CRITICAL', 'DEBUG']]
+ for m in examples:
+ debugview.write(m)
+ item = debugview.list.item(debugview.list.count()-1)
+ debugview.showMessageBox(item)
+ # test message copying
+ debugview.copyMessage()
+ debugview.copyAll()
+ # test button toggling
+ debugview.levels['INFO'].setChecked(False)
+ debugview.levels['INFO'].setChecked(True)
+ debugview.levels['WARNING'].setChecked(False)
+ debugview.levels['WARNING'].setChecked(True)
+ debugview.levels['CRITICAL'].setChecked(False)
+ debugview.levels['CRITICAL'].setChecked(True)
diff --git a/vistrails/gui/debugger.py b/vistrails/gui/debugger.py
new file mode 100644
index 0000000..00d4a98
--- /dev/null
+++ b/vistrails/gui/debugger.py
@@ -0,0 +1,247 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtGui, QtCore
+import vistrails.core.system
+import copy
+import sys
+import time
+import os.path
+import vistrails.gui.application
+from vistrails.core.interpreter.default import get_default_interpreter
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+
+############################################################################
+
+class QDebugger(QtGui.QWidget, QVistrailsPaletteInterface):
+ """
+ This class provides a dockable interface to the debugger tree.
+ """
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent=parent)
+ self.app = vistrails.gui.application.get_vistrails_application()
+ self.inspector = QObjectInspector()
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(0)
+ layout.setSpacing(0)
+ layout.addWidget(self.inspector)
+ self.setLayout(layout)
+ # self.setTitleBarWidget(QtGui.QLabel("Debugger"))
+ self.setWindowTitle("Debugger")
+ self.controller = None
+ self.vistrails_interpreter = get_default_interpreter()
+ self.vistrails_interpreter.debugger = self
+
+ def set_controller(self, c):
+ """
+ set_controller(c) -> None
+ Set the current vistrails controller to be used by the debugger
+ """
+ self.controller = c
+ self.update()
+
+ def update_values(self):
+ """
+ update_vals() -> None
+ Update the debugger after an execution with any values that become
+ available on its input ports.
+ """
+ self.update(update_vals=True)
+
+ def update(self, update_vals=False):
+ """
+ update(update_vals=False) -> None
+ Update the debugger. If the update requires querying modules for input
+ changes, update_vals should be set to True
+ """
+ pipeline = self.controller.current_pipeline
+ if pipeline is None:
+ return
+
+ self.inspector.clear_modules()
+ for module in pipeline.module_list:
+ if module.is_breakpoint or module.is_watched:
+ self.inspector.add_module(module)
+ if update_vals:
+ (module_objects, _, _) = \
+ self.vistrails_interpreter.find_persistent_entities(pipeline)
+ for m_id in self.inspector.modules:
+ if m_id in module_objects and module_objects[m_id] is not None:
+ self.inspector.update_values(m_id, module_objects[m_id])
+ elif module_objects[m_id] is None:
+ edges = pipeline.graph.edges_to(m_id)
+ self.inspector.update_inputs(m_id, module_objects, edges,
+ pipeline.connections)
+
+ def closeEvent(self, e):
+ """closeEvent(e) -> None
+ Event handler called when the dialog is about to close."""
+ self.emit(QtCore.SIGNAL("debuggerHidden()"))
+
+###############################################################################
+# QObjectInspector
+
+class QObjectInspector(QtGui.QTreeWidget):
+ """
+ This class provides the ability to track and inspect breakpoints added to a pipeline.
+ It is meant to be embedded in the QDebugger object to allow debugging of workflows in
+ VisTrails
+ """
+ def __init__(self, parent=None):
+ QtGui.QTreeWidget.__init__(self, parent)
+ self.setColumnCount(2)
+ self.modules = {}
+
+ def clear_modules(self):
+ """
+ clear_modules() -> None
+ Clear the current list of module breakpoints
+ """
+ self.modules = {}
+ self.clear()
+
+ def add_module(self, m):
+ """
+ add_module(m : core.vistrail.module.Module) -> None
+ Add the give module, m, as a breakpoint.
+ """
+ # !!! This uses the core.vistrail.module.Module item
+ item = QDebugModuleItem(self)
+ item.setText(0, "%s (%d)" % (m.name, m.id))
+ item.setText(1, "Module Type")
+ self.modules[m.id] = item
+# self.add_dict(m, item)
+# self.add_ports(m, item, display_vals=get_vals)
+
+ def update_values(self, m_id, persistent_module):
+ """
+ update_values(m_id: long,
+ persistent_module : subclass of core.modules.vistrails_module.Module)
+ """
+ module_item = self.modules[m_id]
+ module_item.takeChildren()
+ self.add_dict(persistent_module, module_item)
+ self.add_ports(persistent_module, module_item, True)
+
+ def update_inputs(self, m_id, persistent_map, edges, connections):
+ input_ports = {}
+ for upstream_id, c_id in edges:
+ if upstream_id in persistent_map and \
+ persistent_map[upstream_id] is not None:
+ persistent_module = persistent_map[upstream_id]
+ connection = connections[c_id]
+ try:
+ output_port = \
+ persistent_module.get_output(connection.source.name)
+ input_ports[connection.destination.name] = output_port
+ except ModuleError:
+ input_ports[connection.destination.name] = None
+ if len(input_ports) > 0:
+ module_item = self.modules[m_id]
+ module_item.takeChildren()
+ inputs_item = QDebugModuleItem(module_item)
+ inputs_item.setText(0, "inputPorts")
+ inputs_item.setText(1, "")
+ for port_name, port_val in input_ports.iteritems():
+ self.create_port_item(port_name, port_val, True,
+ inputs_item)
+
+ def add_dict(self, m, parent_item):
+ """
+ add_dict(m, parent_item) -> None
+ Add the dictionary associated with module m to be displayed
+ as part of the debug information for that breakpoint.
+ """
+ dict_item = QDebugModuleItem(parent_item)
+ dict_item.setText(0, "__dict__")
+ dict_item.setText(1, "")
+ for k in m.__dict__.keys():
+ d_val = QDebugModuleItem(dict_item)
+ d_val.setText(0, str(k))
+ d_val.setText(1, str(m.__dict__[k]))
+
+
+ def create_port_item(self, port_name, port_value, display_vals=False,
+ parent=None):
+ p_item = QDebugModuleItem(parent)
+ p_item.setText(0, str(port_name))
+ if display_vals:
+ p_item.setText(1, str(port_value))
+ else:
+ typestr = str(port_val.__class__)
+ typestr = typestr.split('.')
+ typestr = typestr[len(typestr)-1]
+ typestr = typestr[0:len(typestr)-2]
+ p_item.setText(1, typestr)
+
+ def add_ports(self, m, parent_item, display_vals=False):
+ """
+ add_ports(m, item, display_vals=False) -> None
+ Add port information from module m to the item being displayed in the debugger.
+ If display_vals is True, fetch the appropriate values from the module's input ports.
+ """
+ inputs_item = QDebugModuleItem(parent_item)
+ inputs_item.setText(0, "inputPorts")
+ inputs_item.setText(1, "")
+ for port_name in m.inputPorts:
+ try:
+ port_val = m.getInputListFromPort(port_name)
+ if len(port_val) == 1:
+ port_val = port_val[0]
+ except ModuleError:
+ port_val = None
+ self.create_port_item(port_name, port_val, display_vals,
+ inputs_item)
+ outputs_item = QDebugModuleItem(parent_item)
+ outputs_item.setText(0, "outputPorts")
+ outputs_item.setText(1, "")
+ for port_name in m.outputPorts:
+ try:
+ port_val = m.get_output(port_name)
+ except ModuleError:
+ port_val = None
+ self.create_port_item(port_name, port_val, display_vals,
+ outputs_item)
+
+########################################################################
+# QDebugModuleItem
+
+class QDebugModuleItem(QtGui.QTreeWidgetItem):
+ """
+ This class provides a unique container for adding breakpoints in a workflow
+ to the debugger.
+ """
+ def __init__(self, parent=None):
+ QtGui.QTreeWidgetItem.__init__(self, parent)
+
diff --git a/vistrails/gui/extras/__init__.py b/vistrails/gui/extras/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/gui/extras/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/gui/extras/core/__init__.py b/vistrails/gui/extras/core/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/gui/extras/core/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/gui/extras/core/db/__init__.py b/vistrails/gui/extras/core/db/__init__.py
new file mode 100644
index 0000000..acfc9d2
--- /dev/null
+++ b/vistrails/gui/extras/core/db/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
\ No newline at end of file
diff --git a/vistrails/gui/extras/core/db/locator.py b/vistrails/gui/extras/core/db/locator.py
new file mode 100644
index 0000000..8413fd7
--- /dev/null
+++ b/vistrails/gui/extras/core/db/locator.py
@@ -0,0 +1,221 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.configuration import get_vistrails_persistent_configuration, \
+ get_vistrails_configuration
+from vistrails.gui.open_db_window import QOpenDBWindow, QConnectionDBSetupWindow
+from vistrails.core.db.locator import DBLocator, FileLocator
+from vistrails.db import VistrailsDBException
+from vistrails.core import debug
+import vistrails.db.services.io
+from PyQt4 import QtGui, QtCore
+import vistrails.core.system
+import os
+
+##############################################################################
+# DB dialogs
+
+def get_load_db_locator_from_gui(parent, obj_type):
+ config, obj_id, obj_name = QOpenDBWindow.getOpenDBObject(obj_type)
+ if config == {} or obj_id == -1:
+ return None
+ return DBLocator(config['host'],
+ config['port'],
+ config['db'],
+ config['user'],
+ config['passwd'],
+ obj_name,
+ obj_id=obj_id,
+ obj_type=obj_type,
+ connection_id=config.get('id', None))
+
+def get_save_db_locator_from_gui(parent, obj_type, locator=None):
+ config, name = QOpenDBWindow.getSaveDBObject(obj_type)
+ if config == {} or name == '':
+ return None
+ return DBLocator(config['host'],
+ config['port'],
+ config['db'],
+ config['user'],
+ config['passwd'],
+ name,
+ obj_id=None,
+ obj_type=obj_type,
+ connection_id=config.get('id', None))
+
+##############################################################################
+
+def get_db_connection_from_gui(parent, id, name, host, port, user, passwd,
+ database):
+ def show_dialog(parent, id, name, host, port, user,
+ passwd, databaseb, create):
+ dialog = QConnectionDBSetupWindow(parent, id, name, host, port, user,
+ passwd, database, create)
+ config = None
+ if dialog.exec_() == QtGui.QDialog.Accepted:
+ config = {'host': str(dialog.hostEdt.text()),
+ 'port': int(dialog.portEdt.value()),
+ 'user': unicode(dialog.userEdt.text()),
+ 'passwd': unicode(dialog.passwdEdt.text()),
+ 'db': str(dialog.databaseEdt.text())
+ }
+ try:
+ vistrails.db.services.io.test_db_connection(config)
+ config['succeeded'] = True
+ config['name'] = str(dialog.nameEdt.text())
+ config['id'] = dialog.id
+ except VistrailsDBException, e:
+ debug.critical('VisTrails DB Exception', str(e))
+ config['succeeded'] = False
+ return config
+ #check if the information is already there
+ dbwindow = QOpenDBWindow.getInstance()
+
+ config = dbwindow.connectionList.findConnectionInfo(host,port,database)
+
+ if config:
+ testconfig = dict(config)
+ del testconfig['id']
+ del testconfig['name']
+ try:
+ vistrails.db.services.io.test_db_connection(testconfig)
+ config['succeeded'] = True
+ except VistrailsDBException, e:
+ config = show_dialog(parent, config['id'],
+ config['name'], host, port, config['user'],
+ passwd, database, create = False)
+
+ elif config is None:
+ config = show_dialog(parent, -1,"",
+ host, port, user, passwd,
+ database, create = True)
+ if config['succeeded'] == True:
+ #add to connection list
+ dbwindow.connectionList.setConnectionInfo(**config)
+ return config
+
+##############################################################################
+# File dialogs
+
+suffix_map = {'vistrail': ['.vt', '.xml', '.vtl'],
+ 'workflow': ['.xml'],
+ 'log': ['.xml'],
+ 'registry': ['.xml'],
+ 'opm_graph': ['.xml'],
+ 'prov_document': ['.xml']
+ }
+
+def get_load_file_locator_from_gui(parent, obj_type):
+ suffixes = "*" + " *".join(suffix_map[obj_type])
+ fileName = QtGui.QFileDialog.getOpenFileName(
+ parent,
+ "Open %s..." % obj_type.capitalize(),
+ vistrails.core.system.vistrails_file_directory(),
+ "VisTrails files (%s)\nOther files (*)" % suffixes)
+ if not fileName:
+ return None
+ filename = os.path.abspath(str(QtCore.QFile.encodeName(fileName)))
+ dirName = os.path.dirname(filename)
+ setattr(get_vistrails_persistent_configuration(), 'fileDirectory', dirName)
+ setattr(get_vistrails_configuration(), 'fileDirectory', dirName)
+ vistrails.core.system.set_vistrails_file_directory(dirName)
+ return FileLocator(filename)
+
+def get_save_file_locator_from_gui(parent, obj_type, locator=None):
+ # Ignore current locator for now
+ # In the future, use locator to guide GUI for better starting directory
+
+ suffixes = "*" + " *".join(suffix_map[obj_type])
+ fileName = QtGui.QFileDialog.getSaveFileName(
+ parent,
+ "Save Vistrail...",
+ vistrails.core.system.vistrails_file_directory(),
+ filter="VisTrails files (%s)" % suffixes, # filetypes.strip()
+ options=QtGui.QFileDialog.DontConfirmOverwrite)
+ if not fileName:
+ return None
+ f = str(QtCore.QFile.encodeName(fileName))
+
+ # check for proper suffix
+ found_suffix = False
+ for suffix in suffix_map[obj_type]:
+ if f.endswith(suffix):
+ found_suffix = True
+ break
+ if not found_suffix:
+ if obj_type == 'vistrail':
+ f += get_vistrails_configuration().defaultFileType
+ else:
+ f += suffix_map[obj_type][0]
+
+ if os.path.isfile(f):
+ msg = QtGui.QMessageBox(QtGui.QMessageBox.Question,
+ "VisTrails",
+ "File exists. Overwrite?",
+ (QtGui.QMessageBox.Yes |
+ QtGui.QMessageBox.No),
+ parent)
+ if msg.exec_() == QtGui.QMessageBox.No:
+ return None
+ dirName = os.path.dirname(f)
+ setattr(get_vistrails_persistent_configuration(), 'fileDirectory', dirName)
+ setattr(get_vistrails_configuration(), 'fileDirectory', dirName)
+ vistrails.core.system.set_vistrails_file_directory(dirName)
+ return FileLocator(f)
+
+def get_autosave_prompt(parent):
+ """ get_autosave_prompt(parent: QWidget) -> bool
+
+ """
+ result = QtGui.QMessageBox.question(parent,
+ "AutoSave",
+ "Autosave data has been found.\nDo you want to open autosave data?",
+ QtGui.QMessageBox.Open,
+ QtGui.QMessageBox.Ignore)
+ return result == QtGui.QMessageBox.Open
+
+def ask_to_overwrite_file(parent=None, obj_type='vistrail'):
+ overwrite = True
+ fname = None
+ msg = QtGui.QMessageBox(QtGui.QMessageBox.Question,
+ "VisTrails",
+ "File exists and contains changes. Overwrite?",
+ (QtGui.QMessageBox.Yes | QtGui.QMessageBox.No),
+ parent)
+ if msg.exec_() == QtGui.QMessageBox.No:
+ overwrite = False
+ locator = get_save_file_locator_from_gui(parent, obj_type)
+ if locator:
+ fname = locator._name
+ return (overwrite, fname)
diff --git a/vistrails/gui/graphics_view.py b/vistrails/gui/graphics_view.py
new file mode 100644
index 0000000..5ea2abc
--- /dev/null
+++ b/vistrails/gui/graphics_view.py
@@ -0,0 +1,850 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This containing a subclassed QGraphicsView that allows
+zoom/pan/select inside the graphics view and supports PIP as well
+
+QInteractiveGraphicsScene
+QInteractiveGraphicsView
+QPIPGraphicsView
+"""
+from vistrails.core import debug
+from PyQt4 import QtCore, QtGui
+from vistrails.gui.theme import CurrentTheme
+from vistrails.core.configuration import get_vistrails_configuration
+import vistrails.core.system
+import math
+from vistrails.gui.qt import qt_super
+################################################################################
+
+class QGraphicsItemInterface(object):
+ """
+ QGraphicsItem will override the default QGraphicsItem mouseRelease
+ event to let it fires only 1 ItemSelectionChanged event. This is
+ due to the clearSelection() in
+ qgraphicsitem.cpp::QGrahpicsItem::mouseReleaseEvent
+
+ """
+ pass
+
+class QGraphicsRubberBandItem(QtGui.QGraphicsRectItem):
+ """
+ QGraphicsRubberBandItem try to replace QRubberBand to have a
+ unified look and feel on all platform. In the end, it mimics the
+ Windows look. It is just a rectangle with a 50% transparency
+
+ """
+ def paint(self, painter, option, widget=None):
+ """ paint(painter: QPainter, option: QStyleOptionGraphicsItem,
+ widget: QWidget) -> None
+ Peform actual painting of the rubber band
+
+ """
+ painter.setOpacity(0.5)
+ painter.fillRect(self.rect(),
+ CurrentTheme.SELECTION_BOX_BRUSH)
+ painter.setOpacity(1.0)
+ painter.setPen(CurrentTheme.SELECTION_BOX_PEN)
+ painter.drawRect(self.rect())
+
+class QInteractiveGraphicsScene(QtGui.QGraphicsScene):
+ """
+ QInteractiveGraphicsScene expands QGraphicsScene to allow panning
+ freely over the view are
+
+ """
+ def __init__(self, parent=None):
+ """ QInteractiveGraphicsScene(parent: QWidget)
+ -> QInteractiveGraphicsScene
+ Initialize the actual scene bounding rect
+ """
+ QtGui.QGraphicsScene.__init__(self, parent)
+ self.sceneBoundingRect = QtCore.QRectF()
+ self.multiSelecting = False
+
+ def updateSceneBoundingRect(self, keep_square=True):
+ """ updateSceneBoundingRect() -> None
+ Compute the actual bounding rect of all shapes, then update
+ the scene rect to be much wider for panning
+
+ """
+ self.sceneBoundingRect = QtCore.QRectF()
+ for item in self.items():
+ rect = item.sceneBoundingRect()
+ self.sceneBoundingRect = self.sceneBoundingRect.united(rect)
+
+ # Keep a minimum size
+ minWDiff = 0
+ minHDiff = 0
+ min = CurrentTheme.BOUNDING_RECT_MINIMUM
+ if self.sceneBoundingRect.width() < min:
+ minWDiff = min-self.sceneBoundingRect.width()
+ if self.sceneBoundingRect.height() < min:
+ minHDiff = min-self.sceneBoundingRect.height()
+ self.sceneBoundingRect.adjust(-minWDiff/2, -minHDiff/2,
+ minWDiff/2, minHDiff/2)
+
+ if keep_square:
+ diff = abs(self.sceneBoundingRect.width()-
+ self.sceneBoundingRect.height())
+ if self.sceneBoundingRect.width()<self.sceneBoundingRect.height():
+ self.sceneBoundingRect.adjust(-diff/2, 0, diff/2, 0)
+ else:
+ self.sceneBoundingRect.adjust(0, -diff/2, 0, diff/2)
+ panRect = self.sceneBoundingRect.adjusted(
+ -self.sceneBoundingRect.width()*100,
+ -self.sceneBoundingRect.height()*100,
+ self.sceneBoundingRect.width()*100,
+ self.sceneBoundingRect.height()*100)
+ if panRect.width()<1e-6 and panRect.height()<1e-6:
+ panRect = QtCore.QRectF(-1000,-1000,2000,2000)
+ self.setSceneRect(panRect)
+
+ # Reset cache
+ for view in self.views():
+ view.resetCachedContent()
+
+
+ def fitToView(self, view, recompute_bounding_rect=False):
+ """ fitToView(view: QGraphicsView,
+ recompute_bounding_rect=False) -> None
+ Adjust view to fit and center the whole scene. If recompute_bounding_rect is
+ False, does not recompute bounds, and instead uses previous one.
+
+ """
+ if recompute_bounding_rect:
+ self.updateSceneBoundingRect()
+ view.centerOn(self.sceneBoundingRect.center())
+ view.fitInView(self.sceneBoundingRect, QtCore.Qt.KeepAspectRatio)
+
+ def fitToAllViews(self, recompute_bounding_rect=False):
+ """ fitToAllViews(recompute_bounding_rect=False) -> None
+ Adjust all views using this scene to fit and center the whole scene
+
+ if recompute_bounding_rect is False, uses previous bounding rect.
+
+ """
+ if recompute_bounding_rect:
+ self.updateSceneBoundingRect()
+ for view in self.views():
+ self.fitToView(view, False)
+
+ def clearItems(self):
+ """ clearShapes() -> None
+ Remove and delete all items belonging to this scene
+
+ """
+ self.removeItems(self.items())
+
+ def removeItems(self, itemList):
+ """ removeItems(itemList: sequence of [QGraphicsItem]) -> None
+ Remove all items in itemList
+
+ """
+ for item in itemList:
+ if item.scene():
+ self.removeItem(item)
+
+ def saveToPDF(self, filename):
+ self.updateSceneBoundingRect(False)
+ printer = QtGui.QPrinter()
+ printer.setOutputFormat(QtGui.QPrinter.PdfFormat)
+ printer.setOutputFileName(filename)
+ b_rect = self.sceneBoundingRect
+ debug.debug("%sx%s" % (b_rect.width(), b_rect.height()))
+ printer.setPaperSize(QtCore.QSizeF(b_rect.width(), b_rect.height()),
+ QtGui.QPrinter.Point)
+ painter = QtGui.QPainter(printer)
+ brush = self.backgroundBrush()
+ self.setBackgroundBrush(QtGui.QBrush(QtGui.QColor(255,255,255)))
+ self.render(painter, QtCore.QRectF(), b_rect)
+ painter.end()
+ self.setBackgroundBrush(brush)
+
+ def saveToPNG(self, filename, width=None):
+ try:
+ self.updateSceneBoundingRect(False)
+ b_rect = QtCore.QRectF(self.sceneBoundingRect)
+ b_rect.setWidth(math.floor(b_rect.width()))
+ b_rect.setHeight(math.floor(b_rect.height()))
+ debug.debug("PNG bounding box %sx%s" % (b_rect.width(), b_rect.height()))
+ pixmap = QtGui.QPixmap(QtCore.QSize(int(math.floor(b_rect.width())),
+ int(math.floor(b_rect.height()))))
+ debug.debug("PNG pixmap size: %s"%str(pixmap.size()))
+ painter = QtGui.QPainter(pixmap)
+ painter.setRenderHint(QtGui.QPainter.Antialiasing)
+ brush = self.backgroundBrush()
+ self.setBackgroundBrush(QtGui.QBrush(QtGui.QColor(255,255,255)))
+ self.render(painter, QtCore.QRectF(), b_rect)
+ painter.end()
+ if width is not None:
+ pixmap = pixmap.scaledToWidth(width, QtCore.Qt.SmoothTransformation)
+ pixmap.save(filename)
+ self.setBackgroundBrush(brush)
+ except Exception, e:
+ debug.critical("Exception: %s"%str(e))
+
+class QInteractiveGraphicsView(QtGui.QGraphicsView):
+ """
+ QInteractiveGraphicsView is QGraphicsView with abilities to
+ zoom/span with right/mid click
+
+ """
+ def __init__(self, parent=None):
+ """ QInteractiveGraphicsView(parent: QWidget)
+ -> QInteractiveGraphicsView
+ Initialize the graphics view with interactive options
+
+ """
+ QtGui.QGraphicsView.__init__(self, parent)
+ self.setInteractive(True)
+# self.setCacheMode(QtGui.QGraphicsView.CacheBackground)
+ self.setResizeAnchor(QtGui.QGraphicsView.AnchorViewCenter)
+ self.setRenderHints (QtGui.QPainter.Antialiasing |
+ QtGui.QPainter.TextAntialiasing |
+ QtGui.QPainter.SmoothPixmapTransform)
+ self.scaleMax = 2000
+ self.scaleRatio = self.scaleMax/10
+ self.currentScale = self.scaleMax/2
+ self.startScroll = (0,0)
+ self.lastPos = QtCore.QPoint(0,0)
+ self.pipScene = None
+ self.pipFrame = None
+ self.resetButton = None
+ self.selectionBox = QGraphicsRubberBandItem(None)
+ self.startSelectingPos = None
+ self.setProperty('captureModifiers', 1)
+ self.defaultCursorState = 0
+ self.setCursorState(self.defaultCursorState)
+ self.canSelectBackground = True
+ self.canSelectRectangle = True
+
+ if QtCore.QT_VERSION >= 0x40600:
+ self.viewport().grabGesture(QtCore.Qt.PinchGesture)
+ self.gestureStartScale = None
+
+ conf = get_vistrails_configuration()
+ conf.subscribe('showScrollbars', self.setScrollbarPolicy)
+ self.setScrollbarPolicy('showScrollbars', conf.showScrollbars)
+
+ def setScrollbarPolicy(self, field, value):
+ if value:
+ self.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAsNeeded)
+ self.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAsNeeded)
+ else:
+ self.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ self.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+
+ def viewportEvent(self, event):
+ if QtCore.QT_VERSION >= 0x40600 and event.type() == QtCore.QEvent.Gesture:
+ pinch = event.gesture(QtCore.Qt.PinchGesture)
+ if pinch:
+ changeFlags = pinch.changeFlags()
+ if changeFlags & QtGui.QPinchGesture.ScaleFactorChanged:
+ if self.gestureStartScale is None:
+ self.gestureStartScale = self.currentScale
+ newScale = self.gestureStartScale * \
+ pinch.property("scaleFactor").toReal()[0]
+ # Clamp the scale
+ if newScale<0: newScale = 0
+ if newScale>self.scaleMax: newScale = self.scaleMax
+ self.currentScale = newScale
+ self.updateMatrix()
+ if pinch.state() == QtCore.Qt.GestureFinished:
+ self.gestureStartScale = None
+ return True
+ return QtGui.QGraphicsView.viewportEvent(self, event)
+
+ def modifiersPressed(self, modifiers):
+ """ modifiersPressed(modifiers: QtCore.Qt.KeyboardModifiers) -> None
+ Notification when one of the modifier keys has been pressed
+
+ """
+ self.validateCursorState(modifiers)
+
+ def modifiersReleased(self):
+ """ modifiersReleased() -> None
+ Notification when one of the modifier keys has been released
+
+ """
+ self.validateCursorState()
+
+ def findCursorState(self, modifiers=None):
+ """ findCursorState(modifiers: QtCore.Qt.KeyboardModifiers) -> None
+ Check the keyboard modifiers and return the cursor state
+
+ """
+ if not self.isActiveWindow():
+ return self.defaultCursorState
+ if modifiers==None:
+ modifiers = QtGui.QApplication.keyboardModifiers()
+ shift = modifiers & QtCore.Qt.ShiftModifier
+ alt = modifiers & QtCore.Qt.AltModifier
+ meta = modifiers & QtCore.Qt.MetaModifier or (alt and shift)
+ ctrl = modifiers & QtCore.Qt.ControlModifier
+ if shift and (not alt) and (not ctrl) and (not meta):
+ return 1
+ elif meta and (not ctrl):
+ return 2
+ else:
+ return self.defaultCursorState
+
+ def validateCursorState(self, modifiers=None):
+ """ validateCursorState(modifiers: QtCore.Qt.KeyboardModifiers) -> None
+ Check the keyboard modifiers to change the cursor shape correspondingly
+
+ """
+ self.setCursorState(self.findCursorState(modifiers))
+
+ def enterEvent(self, event):
+ """ enterEvent(event: QEnterEvent) -> None
+ Check the modifiers state when the mouse enter the
+ canvas. Then update the mouse functionality appropriately
+
+ """
+ self.validateCursorState()
+ return QtGui.QGraphicsView.enterEvent(self, event)
+ # super(QInteractiveGraphicsView, self).enterEvent(event)
+
+ def setCursorState(self, state):
+ """ setCursorState(state: int) -> None
+ Update the cursor shape
+
+ Keyword arguments:
+ state - 0: selecting (default)
+ 1: pan
+ 2: zoom
+ 3: panning
+
+ """
+ if state==0:
+ self.viewport().setCursor(CurrentTheme.SELECT_CURSOR)
+ elif state==1:
+ self.viewport().setCursor(CurrentTheme.OPEN_HAND_CURSOR)
+ elif state==2:
+ self.viewport().setCursor(CurrentTheme.ZOOM_CURSOR)
+ elif state==3:
+ self.viewport().setCursor(CurrentTheme.CLOSE_HAND_CURSOR)
+
+ def setDefaultCursorState(self, state):
+ """ setDefaultCursorState(state: int) -> None
+ Set the default cursor state when no modifier key is pressed
+
+ """
+ self.defaultCursorState = state
+ self.validateCursorState()
+
+ def translateButton(self, event):
+ """ translateButton(event: QInputEvent) -> None
+ Translate mouse button and modifiers into a virtual mouse button
+
+ """
+ if event.buttons() & QtCore.Qt.LeftButton:
+ state = self.findCursorState(event.modifiers())
+ state2Button = {0: QtCore.Qt.LeftButton,
+ 1: QtCore.Qt.MidButton,
+ 2: QtCore.Qt.RightButton}
+ if state2Button.has_key(state):
+ return state2Button[state]
+ return event.buttons()
+
+ def mousePressEvent(self, e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Handle mouse click event, use Qt rubber band for left-click
+ selection and prepare for zoom/pan on right/mid click
+
+ """
+ scenePos = self.mapToScene(e.pos())
+ item = self.scene().itemAt(scenePos)
+ buttons = self.translateButton(e)
+ if buttons == QtCore.Qt.LeftButton:
+ if item is None:
+ if self.scene():
+ self.scene().multiSelecting = True
+ self.scene().addItem(self.selectionBox)
+ self.selectionBox.setZValue(1000)
+
+ self.startSelectingPos = self.mapToScene(e.pos())
+ rect = QtCore.QRectF(self.startSelectingPos,
+ QtCore.QSizeF(0,0))
+ self.selectionBox.setRect(rect)
+ self.selectionBox.setVisible(self.canSelectRectangle)
+ else:
+ QtGui.QGraphicsView.mousePressEvent(self, e)
+ # super(QInteractiveGraphicsView, self).mousePressEvent(e)
+ else:
+ if buttons & QtCore.Qt.RightButton:
+ if item is None:
+ self.setCursorState(2)
+ self.computeScale()
+ else:
+ QtGui.QGraphicsView.mousePressEvent(self, e)
+ elif buttons & QtCore.Qt.MidButton:
+ self.setCursorState(3)
+ self.startScroll = (self.horizontalScrollBar().value(),
+ self.verticalScrollBar().value())
+ self.lastPos = QtCore.QPoint(QtGui.QCursor.pos())
+ self.setDragMode(QtGui.QGraphicsView.NoDrag)
+
+ def mouseMoveEvent(self, e):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Handle right click (zoom) and mid click (pan). This function
+ uses QCursor globalPos instead of e.globalX() and e.globalY()
+ because of their flaky values during transformation
+
+ """
+ self.setUpdatesEnabled(False)
+ buttons = self.translateButton(e)
+ if buttons == QtCore.Qt.LeftButton:
+ if self.startSelectingPos:
+ dis = self.mapToScene(e.pos())-self.startSelectingPos
+ rect = QtCore.QRectF(self.startSelectingPos,
+ QtCore.QSizeF(dis.x(), dis.y()))
+ self.selectionBox.prepareGeometryChange()
+ self.selectionBox.setRect(rect)
+ self.selectModules()
+ else:
+ QtGui.QGraphicsView.mouseMoveEvent(self, e)
+ # super(QInteractiveGraphicsView, self).mousePressEvent(e)
+ elif self.lastPos:
+ if buttons == QtCore.Qt.RightButton:
+ globalPos = QtGui.QCursor.pos()
+
+ # Set up new scale based on pixels moved
+ newScale = self.currentScale + globalPos.y() - self.lastPos.y()
+
+ # Clamp the scale
+ if newScale<0: newScale = 0
+ if newScale>self.scaleMax: newScale = self.scaleMax
+
+ # Update the scale and transformation matrix
+ self.currentScale = newScale
+ self.updateMatrix()
+
+ # Need to update last position
+ self.lastPos = QtCore.QPoint(globalPos)
+
+ elif buttons == QtCore.Qt.MidButton:
+ globalPos = QtGui.QCursor.pos()
+
+ # Just need to pan the scroll bar
+ self.horizontalScrollBar().setValue(self.startScroll[0] -
+ globalPos.x() +
+ self.lastPos.x())
+ self.verticalScrollBar().setValue(self.startScroll[1] -
+ globalPos.y() +
+ self.lastPos.y())
+ else:
+ self.validateCursorState(e.modifiers())
+ QtGui.QGraphicsView.mouseMoveEvent(self, e)
+ self.setUpdatesEnabled(True)
+
+ def mouseReleaseEvent(self, e):
+ """ mouseReleaseEvent(self, e: QMouseEvent) -> None
+ Mark box selecting as off
+ """
+ if self.startSelectingPos:
+ self.selectModules()
+ self.startSelectingPos = None
+ self.selectionBox.setVisible(False)
+ self.scene().removeItem(self.selectionBox)
+ self.scene().multiSelecting = False
+ self.lastPos = None
+ self.validateCursorState(e.modifiers())
+ self.setUpdatesEnabled(True)
+ QtGui.QGraphicsView.mouseReleaseEvent(self, e)
+ # super(QInteractiveGraphicsView, self).mouseReleaseEvent(e)
+
+ def mouseDoubleClickEvent(self, e):
+ """ mouseDoubleClickEvent(self, e: QMouseEvent) -> None
+ Try to avoid unselect if double-click on the background
+ """
+ if not self.canSelectBackground:
+ return
+ else:
+ qt_super(QInteractiveGraphicsView, self).mouseDoubleClickEvent(e)
+
+ def selectModules(self):
+ """ selectModules() -> None
+ Select all modules inside the self.selectionBox
+
+ """
+ if self.canSelectRectangle:
+ br = self.selectionBox.sceneBoundingRect()
+ else:
+ br = QtCore.QRectF(self.startSelectingPos,
+ self.startSelectingPos)
+ if not self.canSelectBackground:
+ items = self.scene().items(br)
+ if len(items)==0 or items==[self.selectionBox]:
+ return
+ path = QtGui.QPainterPath()
+ path.addRect(br)
+ self.scene().setSelectionArea(path)
+
+ def updateMatrix(self):
+ """ updateMatrix() -> None
+ Update the view matrix with the current scale
+
+ """
+ matrix = QtGui.QMatrix()
+ power = float(self.currentScale-self.scaleMax/2)/self.scaleRatio
+ scale = pow(2.0, power)
+ matrix.scale(scale, scale)
+ self.setMatrix(matrix)
+
+ def computeScale(self):
+ """ computeScale() -> None
+ Compute the current scale based on the view matrix
+
+ """
+ self.currentScale = (math.log(self.matrix().m11(), 2.0)*
+ self.scaleRatio + self.scaleMax/2)
+
+ def setPIPScene(self, scene):
+ """ setPIPScene(scene: QGraphicsScene) -> None
+ Set the Picture-In-Picture scene fo the current GraphicsView
+ to 'scene'
+
+ """
+ self.pipScene = scene
+
+ def setPIPEnabled(self, enabled=True):
+ """ setPIPEnabled(enabled: boolean) -> None
+ Enable/Disable PIP view
+
+ """
+ if self.pipScene:
+ if enabled:
+ if self.pipFrame==None:
+ self.pipFrame = QPIPGraphicsView(self)
+ self.pipFrame.graphicsView.setScene(self.pipScene)
+ self.pipFrame.move(self.width(), 0)
+ self.pipFrame.show()
+ self.pipFrame.updateGeometry()
+ elif self.pipFrame!=None:
+ self.pipFrame.hide()
+
+ def setQueryEnabled(self, enabled=True):
+ """ setQueryEnabled(enabled: bool) -> None
+ Enable/Disable the query reset button
+
+ """
+ if enabled:
+ if not self.resetButton:
+ self.resetButton = QResetQueryButton(self)
+ self.connect(self.resetButton,
+ QtCore.SIGNAL('resetQuery()'),
+ self.resetQuery)
+ self.resetButton.show()
+ self.resetButton.updateGeometry()
+ else:
+ if self.resetButton:
+ self.resetButton.hide()
+ self.scene().update()
+
+ def resetQuery(self):
+ """ resetQuery() -> None
+ pass the signal along
+
+ """
+ self.emit(QtCore.SIGNAL('resetQuery()'))
+
+ def resizeEvent(self, event):
+ """ resizeEvent(event: QResizeEvent) -> None
+ Make sure the pip frame is inside the graphics view
+ """
+ if self.pipFrame:
+ self.pipFrame.updateGeometry()
+ if self.resetButton:
+ self.resetButton.updateGeometry()
+ return QtGui.QGraphicsView.resizeEvent(self, event)
+ # super(QInteractiveGraphicsView, self).resizeEvent(event)
+
+ def zoomToFit(self):
+ self.scene().fitToView(self, True)
+
+ def zoomIn(self):
+ self.setUpdatesEnabled(False)
+ newScale = self.currentScale + 100.0
+
+ # Clamp the scale
+ if newScale<0: newScale = 0
+ if newScale>self.scaleMax: newScale = self.scaleMax
+
+ # Update the scale and transformation matrix
+ self.currentScale = newScale
+ self.updateMatrix()
+ self.setUpdatesEnabled(True)
+
+ def zoomOut(self):
+ self.setUpdatesEnabled(False)
+ newScale = self.currentScale - 100.0
+
+ # Clamp the scale
+ if newScale<0: newScale = 0
+ if newScale>self.scaleMax: newScale = self.scaleMax
+
+ # Update the scale and transformation matrix
+ self.currentScale = newScale
+ self.updateMatrix()
+ self.setUpdatesEnabled(True)
+
+ def sizeHint(self):
+ """ sizeHint(self) -> QSize
+ Return recommended size of the widget
+
+ """
+ return QtCore.QSize(512, 512)
+
+ def save_pdf(self, filename=None):
+ if filename is None:
+ fileName = QtGui.QFileDialog.getSaveFileName(self.window(),
+ "Save PDF...",
+ vistrails.core.system.vistrails_file_directory(),
+ "PDF files (*.pdf)")
+
+ if not fileName:
+ return None
+ f = str(fileName)
+ else:
+ f = str(filename)
+
+ self.scene().saveToPDF(f)
+
+ # Workaround for border aliasing on OSX
+ # However, it breaks things on Linux, because it
+ # makes zooming _extremely_ slow, so we check it
+ # before we run.
+ if vistrails.core.system.systemType == 'Darwin':
+ def setScene(self, scene):
+ """ setScene(scene: QGraphicsScene) -> None
+ Make sure the viewport background brush the same as the scene
+ one. This is only neccessary on the Mac to work around Qt/Mac
+ bug. We can remove this if any future release of Qt fixes
+ this.
+
+ """
+ QtGui.QGraphicsView.setScene(self, scene)
+ if self.scene():
+ palette = QtGui.QPalette(self.viewport().palette())
+ palette.setBrush(QtGui.QPalette.Base,
+ self.scene().backgroundBrush())
+ self.viewport().setPalette(palette)
+
+class QPIPGraphicsView(QtGui.QWidget):
+ """
+ QPIPGraphicsView is a tool window contain a
+ QInteractiveGraphicsView for PIP display
+
+ """
+ def __init__(self, parent=None):
+ """ QPIPGraphicsView(parent: QWidget) -> QPIPGraphicsView
+ Initialize a layout with some margin and a central widget
+ """
+ QtGui.QWidget.__init__(self, parent, QtCore.Qt.FramelessWindowHint)
+ self.setMouseTracking(True)
+ self.setAutoFillBackground(True)
+ self.palette().setColor(QtGui.QPalette.Base,
+ CurrentTheme.PIP_FRAME_COLOR)
+ self.setLayout(QtGui.QHBoxLayout(self))
+ self.layout().setMargin(CurrentTheme.PIP_OUT_FRAME_WIDTH)
+ self.graphicsView = QInteractiveGraphicsView()
+ self.layout().addWidget(self.graphicsView)
+ self.firstShow = True
+ self.anchorCorner = [QtCore.Qt.AlignRight, QtCore.Qt.AlignTop]
+
+ def sizeHint(self):
+ """ sizeHint(self) -> QSize
+ Return recommended size of the widget
+
+ """
+ return QtCore.QSize(*CurrentTheme.PIP_DEFAULT_SIZE)
+
+ def mousePressEvent(self, e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Capture mouse press event on the frame to move the widget
+
+ """
+ if e.buttons() & QtCore.Qt.LeftButton:
+ self.resizing = False
+ self.lastPos = QtCore.QPoint(e.globalX(), e.globalY())
+ gvRect = self.graphicsView.geometry()
+ if ((e.x()<gvRect.left() or e.x()>gvRect.right()) and
+ (e.y()<gvRect.top() or e.y()>gvRect.bottom())):
+ self.direction = [1,1]
+ if e.x()<gvRect.left():
+ self.direction[0] = -1
+ if e.y()<gvRect.top():
+ self.direction[1] = -1
+ self.resizing = True
+
+ def mouseMoveEvent(self, e):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Move widget as the mouse moving
+
+ """
+ if e.buttons() & QtCore.Qt.LeftButton:
+ (dx, dy) = (e.globalX()-self.lastPos.x(),
+ e.globalY()-self.lastPos.y())
+ parentGeometry = self.parent().geometry()
+ newGeometry = QtCore.QRect(self.geometry())
+ if self.resizing:
+ if self.direction[0]==1:
+ if newGeometry.right()+dx>parentGeometry.width()-1:
+ dx = parentGeometry.width()-1-newGeometry.right()
+ newGeometry.adjust(0, 0, dx, 0)
+ else:
+ if newGeometry.left()+dx<0:
+ dx = -newGeometry.left()
+ newGeometry.adjust(dx, 0, 0, 0)
+
+ if self.direction[1]==1:
+ if newGeometry.bottom()+dy>parentGeometry.height()-1:
+ dy = parentGeometry.height()-1-newGeometry.bottom()
+ newGeometry.adjust(0, 0, 0, dy)
+ else:
+ if newGeometry.top()+dy<0:
+ dy = -newGeometry.top()
+ newGeometry.adjust(0, dy, 0, 0)
+ else:
+ newGeometry.translate(dx, dy)
+ if (newGeometry.left()>0 and
+ newGeometry.right()<parentGeometry.width()-1):
+ self.anchorCorner[0] = None
+ if (newGeometry.top()>0 and
+ newGeometry.bottom()<parentGeometry.height()-1):
+ self.anchorCorner[1] = None
+ self.updateGeometry(newGeometry)
+ self.lastPos = QtCore.QPoint(e.globalX(), e.globalY())
+
+ def updateGeometry(self, newGeometry=None):
+ """ updateGeometry() -> None
+ Make sure the widget is inside the parent graphics view
+
+ """
+ parentGeometry = self.parent().geometry()
+ if newGeometry==None:
+ newGeometry = QtCore.QRect(self.geometry())
+
+ if self.anchorCorner[0]==None:
+ if newGeometry.left()<0:
+ newGeometry.moveLeft(0)
+ if newGeometry.right()>=parentGeometry.width():
+ newGeometry.moveRight(parentGeometry.width()-1)
+ if newGeometry.left()==0:
+ self.anchorCorner[0] = QtCore.Qt.AlignLeft
+ if newGeometry.right()==parentGeometry.width()-1:
+ self.anchorCorner[0] = QtCore.Qt.AlignRight
+ else:
+ if self.anchorCorner[0]==QtCore.Qt.AlignLeft:
+ newGeometry.moveLeft(0)
+ if self.anchorCorner[0]==QtCore.Qt.AlignRight:
+ newGeometry.moveRight(parentGeometry.width()-1)
+
+ if self.anchorCorner[1]==None:
+ if newGeometry.top()<0:
+ newGeometry.moveTop(0)
+ if newGeometry.bottom()>=parentGeometry.height():
+ newGeometry.moveBottom(parentGeometry.height()-1)
+ if newGeometry.top()==0:
+ self.anchorCorner[1] = QtCore.Qt.AlignTop
+ if newGeometry.bottom()==parentGeometry.height()-1:
+ self.anchorCorner[1] = QtCore.Qt.AlignBottom
+ else:
+ if self.anchorCorner[1]==QtCore.Qt.AlignTop:
+ newGeometry.moveTop(0)
+ if self.anchorCorner[1]==QtCore.Qt.AlignBottom:
+ newGeometry.moveBottom(parentGeometry.height()-1)
+
+ self.setGeometry(newGeometry)
+
+ def showEvent(self, event):
+ """ showEvent(event: QShowEvent) -> None
+ Fit the scene to view for the show event only
+
+ """
+ if self.firstShow:
+ self.firstShow = False
+ self.graphicsView.scene().fitToView(self.graphicsView, True)
+ return QtGui.QWidget.showEvent(self, event)
+ # super(QPIPGraphicsView, self).showEvent(event)
+
+ def enterEvent(self, event):
+ """ enterEvent(event: QEnterEvent) -> None
+ Show a larger frame when the mouse enter to facilitate
+ resizing
+
+ """
+ self.layout().setMargin(CurrentTheme.PIP_IN_FRAME_WIDTH)
+
+ def leaveEvent(self, event):
+ """ leaveEvent(event: QLeaveEvent) -> None
+ Show a smaller frame when the mouse exit the widget to get
+ more view
+
+ """
+ self.layout().setMargin(CurrentTheme.PIP_OUT_FRAME_WIDTH)
+
+
+class QResetQueryButton(QtGui.QLabel):
+ """
+
+ """
+ def __init__(self, parent=None):
+ QtGui.QLabel.__init__(self, parent)
+
+ self.setText('Reset Query')
+ self.setFrameStyle(QtGui.QFrame.StyledPanel)
+ self.setFrameShadow(QtGui.QFrame.Raised)
+ self.marginPad = 10
+
+ def mousePressEvent(self, e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Capture mouse press event on the frame to move the widget
+
+ """
+ if e.buttons() & QtCore.Qt.LeftButton:
+ self.setFrameShadow(QtGui.QFrame.Sunken)
+
+ def mouseReleaseEvent(self, e):
+ self.setFrameShadow(QtGui.QFrame.Raised)
+ self.emit(QtCore.SIGNAL('resetQuery()'))
+
+ def updateGeometry(self):
+ parentGeometry = self.parent().geometry()
+ self.move(self.marginPad,
+ parentGeometry.height()-self.height()-self.marginPad)
+
+
diff --git a/vistrails/gui/job_monitor.py b/vistrails/gui/job_monitor.py
new file mode 100644
index 0000000..5e61032
--- /dev/null
+++ b/vistrails/gui/job_monitor.py
@@ -0,0 +1,387 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core import debug, configuration
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+from vistrails.gui import theme
+from vistrails.core.db.locator import BaseLocator
+from vistrails.gui.common_widgets import QDockPushButton
+
+refresh_states = [('Off', 0), ('10 sec', 10),
+ ('1 min', 60), ('10 min', 600),
+ ('1 hour', 3600)]
+
+class QNumberValidator(QtGui.QIntValidator):
+ def validate(self, input, pos):
+ result = QtGui.QIntValidator.validate(self, input, pos)
+ if len(input) and result[0] == QtGui.QIntValidator.Intermediate:
+ return (QtGui.QIntValidator.Invalid, pos)
+ return result
+
+class QJobView(QtGui.QWidget, QVistrailsPaletteInterface):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+
+ self.timer_id = None
+
+ self.workflowItems = {}
+ self.layout = QtGui.QVBoxLayout()
+# self.layout.setContentsMargins(5, 5, 0, 0)
+
+ buttonsLayout = QtGui.QHBoxLayout()
+ #buttonsLayout.setMargin(5)
+ #buttonsLayout.setSpacing(5)
+ run_now = QDockPushButton("Check now")
+ run_now.setToolTip("Check all jobs now")
+ run_now.clicked.connect(self.timerEvent)
+ buttonsLayout.addWidget(run_now)
+ label = QtGui.QLabel('Refresh interval (seconds):')
+ buttonsLayout.addWidget(label)
+
+ self.interval = QtGui.QComboBox()
+ for text, seconds in refresh_states:
+ self.interval.addItem(text, seconds)
+ self.interval.editTextChanged.connect(self.set_refresh)
+ self.interval.setEditable(True)
+ self.interval.setCurrentIndex(self.interval.findText('10 min'))
+ self.interval.setCompleter(None)
+ self.interval.setValidator(QNumberValidator())
+ buttonsLayout.addWidget(self.interval)
+
+ self.autorun = QtGui.QCheckBox("Run When Ready")
+ self.autorun.setToolTip("Automatically re-execute the workflow when jobs have completed")
+ buttonsLayout.addWidget(self.autorun)
+
+ self.rerun = QtGui.QCheckBox("Run To Check")
+ self.rerun.setToolTip("Automatically re-execute workflows that does not provide a status check method")
+ buttonsLayout.addWidget(self.rerun)
+
+ buttonsLayout.addStretch(1)
+ self.layout.addLayout(buttonsLayout)
+
+ self.jobView = QtGui.QTreeWidget()
+ self.jobView.setContentsMargins(0, 0, 0, 0)
+ self.jobView.setColumnCount(2)
+ self.jobView.setHeaderLabels(['Job', 'Message'])
+ self.jobView.header().setResizeMode(0, QtGui.QHeaderView.ResizeToContents)
+ self.jobView.header().setResizeMode(1, QtGui.QHeaderView.Stretch)
+ self.jobView.setExpandsOnDoubleClick(False)
+ self.connect(self.jobView,
+ QtCore.SIGNAL('itemDoubleClicked(QTreeWidgetItem *, int)'),
+ self.item_selected)
+ self.layout.addWidget(self.jobView)
+
+ self.setLayout(self.layout)
+ self.setWindowTitle('Running Jobs')
+ self.resize(QtCore.QSize(800, 600))
+ self.updating_now = False
+
+
+ def set_refresh(self, refresh=0):
+ self.updating_now = True
+ refresh = str(refresh) if refresh else '0'
+ # changes the timer time
+ if refresh in dict(refresh_states):
+ refresh = dict(refresh_states)[refresh]
+ self.interval.setEditText(str(refresh))
+ else:
+ refresh = int(refresh)
+ if refresh:
+ if self.timer_id is not None:
+ self.killTimer(self.timer_id)
+ self.timer_id = self.startTimer(refresh*1000)
+ else:
+ if self.timer_id:
+ self.killTimer(self.timer_id)
+ self.timer_id = None
+ self.updating_now = False
+
+ def update_jobs(self):
+ # check all jobs
+ for workflow in self.workflowItems.values():
+ # jobs without a queue can also be checked
+ if not workflow.has_queue:
+ if self.rerun.isChecked():
+ workflow.execute()
+ continue
+ if workflow.workflowFinished:
+ continue
+ for job in workflow.jobs.itervalues():
+ if job.jobFinished:
+ continue
+ try:
+ # call queue
+ job.jobFinished = job.queue.finished()
+ # old version of BatchQ needs to call .val()
+ if not isinstance(job.jobFinished, bool):
+ job.jobFinished = job.jobFinished.val()
+ if job.jobFinished:
+ job.setText(1, "Finished")
+ except Exception, e:
+ debug.critical("Error checking job %s: %s" %
+ (workflow.name, str(e)))
+ if job.jobFinished:
+ job.setIcon(0, theme.get_current_theme().JOB_FINISHED)
+ workflow.countJobs()
+ workflow.workflowFinished = len(workflow.jobs) == \
+ sum(j.jobFinished for j in workflow.jobs.itervalues())
+ if workflow.workflowFinished:
+ workflow.setIcon(0, theme.get_current_theme().JOB_FINISHED)
+ workflow.setText(1, "Finished")
+ workflow.countJobs()
+ if workflow.workflowFinished:
+ if self.autorun.isChecked():
+ self.updating_now = False
+ workflow.execute()
+ self.updating_now = True
+ continue
+ ret = QtGui.QMessageBox.information(self, "Job Ready",
+ 'Pending Jobs in workflow "%s" have finished, '
+ 'continue execution now?' % workflow.name,
+ QtGui.QMessageBox.Ok, QtGui.QMessageBox.Cancel)
+ if ret == QtGui.QMessageBox.Ok:
+ self.updating_now = False
+ workflow.execute()
+ self.updating_now = True
+
+ def timerEvent(self, id=None):
+ if self.updating_now:
+ return
+ self.updating_now = True
+ self.update_jobs()
+ self.updating_now = False
+
+ def keyPressEvent(self, event):
+ if event.key() in [QtCore.Qt.Key_Delete, QtCore.Qt.Key_Backspace]:
+ items = self.jobView.selectedItems()
+ if len(items) == 1:
+ index = self.jobView.indexOfTopLevelItem(items[0])
+ if index>=0:
+ self.delete_job(items[0].controller, items[0].version)
+ else:
+ QtGui.QWidget.keyPressEvent(self, event)
+
+ def add_job(self, controller, error, prev='', workflow=None):
+ """ Adds job recursively """
+ added = False
+ if not prev:
+ if controller.vistrail.locator:
+ name = controller.vistrail.locator.short_name
+ else:
+ name = 'Untitled.vt'
+ version_id = controller.current_version
+ if (name, version_id) not in self.workflowItems:
+ workflow = QWorkflowItem(controller, error, self.jobView)
+ self.jobView.addTopLevelItem(workflow)
+ self.workflowItems[(name, version_id)] = workflow
+
+ # save job to configuration
+ if controller.vistrail.locator:
+ conf = configuration.get_vistrails_configuration()
+ if not conf.has('runningJobsList') or not conf.runningJobsList:
+ conf_jobs = []
+ else:
+ conf_jobs = conf.runningJobsList.split(';')
+ if not conf_jobs:
+ conf_jobs = []
+ url = controller.vistrail.locator.to_url()
+ if '?' in url:
+ url += '&workflow=%d' % version_id
+ else:
+ url += '?workflow=%d' % version_id
+ if not url in conf_jobs:
+ conf_jobs.append(str(url))
+ conf.runningJobsList = ';'.join(conf_jobs)
+ configuration.get_vistrails_persistent_configuration(
+ ).runningJobsList = conf.runningJobsList
+ else:
+ workflow = self.workflowItems[(name, version_id)]
+ job_name = ((prev+'.') if prev else '') + error.module.__class__.__name__
+
+ if not error.children:
+ if not error.queue:
+ # We allow jobs without queue objects, but they will
+ # have to be checked by re-executing the entire workflow
+ workflow.has_queue = False
+ workflow.setIcon(0, theme.get_current_theme().JOB_SCHEDULED)
+ workflow.setToolTip(0, 'To check this workflow it must be re-executed. Make sure "Run To Check" is checked.')
+
+ #return False
+ # remove any previous instance of this job, if name is shorter
+ if id(error) in workflow.jobs and \
+ len(job_name) > len(workflow.jobs[id(error)].text(0)):
+ workflow.takeChild(workflow.indexOfChild(
+ workflow.jobs[id(error)]))
+ del workflow.jobs[id(error)]
+ # if we did not keep an already existing job, add it
+ if id(error) not in workflow.jobs:
+ job = QJobItem(job_name, error)
+ workflow.addChild(job)
+ workflow.jobs[id(error)] = job
+ workflow.countJobs()
+ return True
+ else:
+ for child in error.children:
+ result = self.add_job(controller, child, job_name, workflow)
+ if result:
+ added = True
+ return added
+
+ def delete_job(self, controller, version_id=None, all=False):
+ if all:
+ for k in self.workflowItems.keys():
+ workflow = self.workflowItems[k]
+ if workflow.controller is controller:
+ self.jobView.takeTopLevelItem(
+ self.jobView.indexOfTopLevelItem(
+ self.workflowItems[k]))
+ del self.workflowItems[k]
+ return
+ if not version_id:
+ version_id = controller.current_version
+ if controller.locator:
+ conf = configuration.get_vistrails_configuration()
+ if not conf.has('runningJobsList') or not conf.runningJobsList:
+ conf_jobs = []
+ else:
+ conf_jobs = conf.runningJobsList.split(';')
+ if not conf_jobs:
+ conf_jobs = []
+ url = controller.locator.to_url()
+ if '?' in url:
+ url += '&workflow=%s' % version_id
+ else:
+ url += '?workflow=%s' % version_id
+ if url in conf_jobs:
+ conf_jobs.remove(url)
+ conf.runningJobsList = ';'.join(conf_jobs)
+ configuration.get_vistrails_persistent_configuration(
+ ).runningJobsList = conf.runningJobsList
+ name = controller.vistrail.locator.short_name
+ else:
+ name = 'Untitled.vt'
+ if (name, version_id) in self.workflowItems:
+ self.jobView.takeTopLevelItem(
+ self.jobView.indexOfTopLevelItem(
+ self.workflowItems[(name, version_id)]))
+ del self.workflowItems[(name, version_id)]
+
+ def item_selected(self, item):
+ if isinstance(item, QWorkflowItem):
+ item.goto()
+
+ def load_running_jobs(self):
+ conf = configuration.get_vistrails_configuration()
+ if conf.has('runningJobsList') and conf.runningJobsList:
+ for url in conf.runningJobsList.split(';'):
+ loc, version = url.split('?')
+ locator = BaseLocator.from_url(loc)
+ msgBox = QtGui.QMessageBox(QtGui.QMessageBox.Question,
+ "Running Job Found",
+ "Running Job Found:\n %s\n"
+ "Continue now?" % url)
+ msgBox.addButton("Later", msgBox.ActionRole)
+ delete = msgBox.addButton("Delete", msgBox.ActionRole)
+ yes = msgBox.addButton("Yes", msgBox.ActionRole)
+ msgBox.exec_()
+ if msgBox.clickedButton() == yes:
+ from vistrails.gui.vistrails_window import _app
+ _app.open_vistrail_without_prompt(locator,
+ int(version.split('=')[1]))
+ _app.get_current_view().execute()
+ if msgBox.clickedButton() == delete:
+ conf_jobs = conf.runningJobsList.split(';')
+ conf_jobs.remove(url)
+ conf.runningJobsList = ';'.join(conf_jobs)
+ configuration.get_vistrails_persistent_configuration(
+ ).runningJobsList = conf.runningJobsList
+ else:
+ conf.runningJobsList = ''
+ configuration.get_vistrails_persistent_configuration(
+ ).runningJobsList = conf.runningJobsList
+
+
+class QWorkflowItem(QtGui.QTreeWidgetItem):
+ """ The workflow that was suspended """
+ def __init__(self, controller, error, parent):
+ if controller.vistrail.locator:
+ self.name = "%s:%s" % (controller.vistrail.locator.short_name,
+ controller.get_pipeline_name())
+ else:
+ self.name = "Untitled.vt:%s" % controller.get_pipeline_name()
+
+ QtGui.QTreeWidgetItem.__init__(self, parent,
+ [self.name, error if isinstance(error, str) else error.msg])
+ self.setToolTip(0, "Double-Click to View Pipeline")
+ self.setToolTip(1, error if isinstance(error, str) else error.msg)
+
+ self.controller = controller
+ self.version = controller.current_version
+ self.has_queue = True
+ self.setIcon(0, theme.get_current_theme().JOB_CHECKING)
+ self.workflowFinished = False
+ self.jobs = {}
+ from vistrails.gui.vistrails_window import _app
+ self.view = _app.get_current_view()
+
+ def countJobs(self):
+ count = self.childCount()
+ finished = sum([self.child(i).jobFinished for i in xrange(count)])
+ self.setText(0, "%s (%s/%s)" % (self.name, finished, count))
+
+ def goto(self):
+ from vistrails.gui.vistrails_window import _app
+ _app.change_view(self.view)
+ self.view.version_selected(self.version, True, double_click=True)
+
+ def execute(self):
+ self.goto()
+ self.view.execute()
+
+class QJobItem(QtGui.QTreeWidgetItem):
+ """ The module that was suspended """
+ def __init__(self, name, error, parent=None):
+ QtGui.QTreeWidgetItem.__init__(self, parent, [name, error.msg])
+ self.setToolTip(1, error.msg)
+ self.queue = error.queue
+ if self.queue:
+ self.setIcon(0, theme.get_current_theme().JOB_CHECKING)
+ self.setToolTip(0, "This Job has a method to check if it has finished.")
+ else:
+ self.setIcon(0, theme.get_current_theme().JOB_SCHEDULED)
+ self.setToolTip(0, 'To check this job the workflow must be re-executed. Make sure "Run To Check" is checked.')
+ self.jobFinished = False
diff --git a/vistrails/gui/mashups/__init__.py b/vistrails/gui/mashups/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/gui/mashups/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/gui/mashups/alias_inspector.py b/vistrails/gui/mashups/alias_inspector.py
new file mode 100644
index 0000000..c017488
--- /dev/null
+++ b/vistrails/gui/mashups/alias_inspector.py
@@ -0,0 +1,759 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""This file contains the widget for displaying the properties panel for a
+selected alias in the list
+
+Classes defined in this file:
+
+QAliasInspector
+QAliasDetailsWidget
+QValuesListEditor
+QListEditDialog
+QListEditItemDelegate
+
+"""
+import copy
+from PyQt4 import QtCore, QtGui
+from PyQt4.QtCore import pyqtSignal, pyqtSlot
+from vistrails.core.mashup.alias import Alias
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.system import get_vistrails_basic_pkg_id
+from vistrails.gui.modules import get_widget_class
+from vistrails.gui.modules.constant_configuration import StandardConstantWidget
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.utils import show_warning
+################################################################################
+class QAliasInspector(QtGui.QScrollArea):
+ """
+ QAliasInspector is a widget to display the details of an alias.
+ """
+ #signals
+ aliasChanged = pyqtSignal(Alias)
+
+ def __init__(self, alias_list, parent=None):
+ QtGui.QScrollArea.__init__(self,parent)
+ self.setAcceptDrops(False)
+ self.setWidgetResizable(True)
+ self.vWidget = QAliasDetailsWidget(alias_list)
+ self.setWidget(self.vWidget)
+
+ #connecting signals
+ self.vWidget.aliasChanged.connect(self.aliasChanged)
+
+ def updateContents(self, alias_item=None, controller=None):
+ self.vWidget.updateContents(alias_item, controller)
+
+################################################################################
+class QAliasDetailsWidget(QtGui.QWidget):
+ #signals
+ aliasChanged = pyqtSignal(Alias)
+
+ def __init__(self, table, parent=None):
+ QtGui.QWidget.__init__(self,parent)
+ self.alias = None
+ self.table = table
+ self.createWidgets()
+ self.updateContents()
+
+ def createWidgets(self):
+ self.main_layout = QtGui.QVBoxLayout()
+ self.label = QtGui.QLabel("Alias Details")
+ self.main_layout.addWidget(self.label)
+
+ self.name_label = QtGui.QLabel("Name")
+ self.name_edit = QtGui.QLineEdit()
+ l1 = QtGui.QVBoxLayout()
+ l1.setContentsMargins(0, 11, 0, 0)
+ l1.setSpacing(3)
+ l1.addWidget(self.name_label)
+ l1.addWidget(self.name_edit)
+
+ self.order_label = QtGui.QLabel("Order")
+ self.order_spinbox = QtGui.QSpinBox()
+ self.order_spinbox.setRange(0,self.table.topLevelItemCount()-1)
+ if self.alias:
+ self.order_spinbox.setValue(self.alias.component.pos)
+ l2 = QtGui.QVBoxLayout()
+ l2.setContentsMargins(0, 11, 0, 0)
+ l2.setSpacing(3)
+ l2.addWidget(self.order_label)
+ l2.addWidget(self.order_spinbox)
+
+ l3 = QtGui.QHBoxLayout()
+ l3.addLayout(l1)
+ l3.addLayout(l2)
+ self.main_layout.addLayout(l3)
+
+ #Display Widget
+ self.dw_groupbox = QtGui.QGroupBox()
+ self.dw_groupbox.setFlat(True)
+ self.dw_label = QtGui.QLabel("Display Widget")
+ self.dw_combobox = QtGui.QComboBox()
+ self.dw_combobox.addItem("combobox")
+ self.dw_combobox.addItem("slider")
+ self.dw_combobox.addItem("numericstepper")
+
+ self.dw_layout = QtGui.QVBoxLayout()
+ self.dw_layout.setContentsMargins(0, 11, 0, 0)
+ self.dw_slider_layout = QtGui.QHBoxLayout()
+ self.dw_minval_label = QtGui.QLabel("Min Val")
+ self.dw_maxval_label = QtGui.QLabel("Max Val")
+ self.dw_stepsize_label = QtGui.QLabel("Step Size")
+ self.dw_minval_edit = QtGui.QLineEdit()
+ self.dw_maxval_edit = QtGui.QLineEdit()
+ self.dw_stepsize_edit = QtGui.QLineEdit()
+
+ l = QtGui.QVBoxLayout()
+ l.setMargin(0)
+ l.setSpacing(0)
+ l.addWidget(self.dw_minval_label)
+ l.addWidget(self.dw_minval_edit)
+ self.dw_slider_layout.addLayout(l)
+ l = QtGui.QVBoxLayout()
+ l.setMargin(0)
+ l.setSpacing(0)
+ l.addWidget(self.dw_maxval_label)
+ l.addWidget(self.dw_maxval_edit)
+ self.dw_slider_layout.addLayout(l)
+ l = QtGui.QVBoxLayout()
+ l.setMargin(0)
+ l.setSpacing(0)
+ l.addWidget(self.dw_stepsize_label)
+ l.addWidget(self.dw_stepsize_edit)
+ self.dw_slider_layout.addLayout(l)
+ self.dw_seq_toggle = QtGui.QCheckBox("Loop")
+ self.dw_seq_toggle.setToolTip("Enable option to loop through all steps")
+ self.dw_slider_layout.addWidget(self.dw_seq_toggle)
+ self.dw_layout.addWidget(self.dw_label)
+ self.dw_layout.addWidget(self.dw_combobox)
+ self.dw_layout.addLayout(self.dw_slider_layout)
+ self.dw_groupbox.setLayout(self.dw_layout)
+ self.toggle_dw_combobox(0)
+
+ #Default Value
+ self.dv_groupbox = QtGui.QGroupBox()
+ self.dv_groupbox.setFlat(True)
+ self.dv_label = QtGui.QLabel("Default Value")
+ self.dv_layout = QtGui.QVBoxLayout()
+ self.dv_layout.setContentsMargins(0, 11, 0, 0)
+ self.dv_layout.addWidget(self.dv_label)
+ self.dv_groupbox.setLayout(self.dv_layout)
+ self.dv_widget = None
+
+ #Values List
+ self.vl_groupbox = QtGui.QGroupBox()
+ self.vl_groupbox.setFlat(True)
+ self.vl_label = QtGui.QLabel("Values List")
+ self.vl_layout = QtGui.QVBoxLayout()
+ self.vl_layout.setContentsMargins(0, 11, 0, 0)
+ self.vl_layout.addWidget(self.vl_label)
+ self.vl_editor = None
+ self.vl_groupbox.setLayout(self.vl_layout)
+
+ self.main_layout.addWidget(self.dw_groupbox)
+ self.main_layout.addWidget(self.dv_groupbox)
+ self.main_layout.addWidget(self.vl_groupbox)
+ self.main_layout.addStretch(1)
+
+ self.deleteButton = QtGui.QPushButton("Delete Alias")
+ self.deleteButton.clicked.connect(self.table.removeCurrentAlias)
+ self.deleteButton.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed,
+ QtGui.QSizePolicy.Fixed))
+ self.main_layout.addWidget(self.deleteButton)
+
+ self.setLayout(self.main_layout)
+
+ #connect signals
+ self.plugSignals()
+
+ def plugSignals(self):
+ self.dw_combobox.currentIndexChanged.connect(self.toggle_dw_combobox)
+ self.name_edit.editingFinished.connect(self.nameChanged)
+ self.order_spinbox.valueChanged.connect(self.orderChanged)
+ self.dw_minval_edit.editingFinished.connect(self.minvalChanged)
+ self.dw_stepsize_edit.editingFinished.connect(self.stepsizeChanged)
+ self.dw_seq_toggle.clicked.connect(self.seqToggled)
+ self.dw_maxval_edit.editingFinished.connect(self.maxvalChanged)
+
+ def unplugSignals(self):
+ self.dw_combobox.currentIndexChanged.disconnect(self.toggle_dw_combobox)
+ self.name_edit.editingFinished.disconnect(self.nameChanged)
+ self.order_spinbox.valueChanged.disconnect(self.orderChanged)
+ self.dw_minval_edit.editingFinished.disconnect(self.minvalChanged)
+ self.dw_stepsize_edit.editingFinished.disconnect(self.stepsizeChanged)
+ self.dw_maxval_edit.editingFinished.disconnect(self.maxvalChanged)
+
+ def valuesListChanged(self):
+ self.aliasChanged.emit(self.alias)
+
+ @pyqtSlot()
+ def minvalChanged(self):
+ if self.alias:
+ old_minval = self.alias.component.minVal
+ new_minval = str(self.dw_minval_edit.text())
+ if old_minval == new_minval:
+ return
+ self.alias.component.minVal = new_minval
+ self.aliasChanged.emit(self.alias)
+
+ @pyqtSlot()
+ def maxvalChanged(self):
+ if self.alias:
+ old_maxval = self.alias.component.maxVal
+ new_maxval = str(self.dw_maxval_edit.text())
+ if old_maxval == new_maxval:
+ return
+ self.alias.component.maxVal = new_maxval
+ self.aliasChanged.emit(self.alias)
+
+ @pyqtSlot()
+ def stepsizeChanged(self):
+ if self.alias:
+ old_stepsize = self.alias.component.stepSize
+ new_stepsize = str(self.dw_stepsize_edit.text())
+ if old_stepsize == new_stepsize:
+ return
+ self.alias.component.stepSize = new_stepsize
+ self.aliasChanged.emit(self.alias)
+
+
+ @pyqtSlot()
+ def seqToggled(self):
+ if self.alias:
+ old_seq = self.alias.component.seq
+ new_seq = self.dw_seq_toggle.isChecked()
+ if old_seq == new_seq:
+ return
+ self.alias.component.seq = new_seq
+ self.aliasChanged.emit(self.alias)
+
+ @pyqtSlot()
+ def nameChanged(self):
+ old_alias = self.alias.name
+ new_alias = str(self.name_edit.text())
+ if old_alias == new_alias:
+ return
+ if new_alias in self.table.aliases.keys():
+ show_warning("Mashup",
+ """Label name %s already exists.
+Please type a different name. """ % new_alias)
+ self.name_edit.setText(old_alias)
+ self.name_edit.setFocus()
+ elif new_alias == '':
+ show_warning("Mashup",
+ """Variables with empty name are not allowed.
+Please type a unique name. """ % new_alias)
+ self.name_edit.setText(old_alias)
+ self.name_edit.setFocus()
+ else:
+ self.table.aliases[new_alias] = self.table.aliases[old_alias]
+ #self.table.alias_cache[new_alias] = self.table.alias_cache[old_alias]
+ del self.table.aliases[old_alias]
+ #del self.table.alias_cache[old_alias]
+ self.alias.name = new_alias
+ self.aliasChanged.emit(self.alias)
+
+ @pyqtSlot(int)
+ def orderChanged(self, neworder):
+ if self.alias.component.pos == neworder:
+ return
+ oldorder = self.alias.component.pos
+ self.alias.component.pos = neworder
+ self.table.moveItemToNewPos(oldorder, neworder)
+
+ @pyqtSlot(int)
+ def toggle_dw_combobox(self, index):
+ if index == 0:
+ self.show_dw_contents(False)
+ elif index in [1,2]:
+ self.show_dw_contents(True)
+ if self.alias and self.alias.component.type == "Integer":
+ self.set_int_validators()
+ elif self.alias and self.alias.component.type == "Float":
+ self.set_float_validators()
+ # show loop option for stepper
+ self.dw_seq_toggle.setVisible(index == 1)
+ if self.alias:
+ self.alias.component.widget = str(self.dw_combobox.currentText())
+ self.aliasChanged.emit(self.alias)
+
+ def set_int_validators(self):
+ validator = QtGui.QIntValidator(self)
+ self.dw_minval_edit.setValidator(validator)
+ self.dw_maxval_edit.setValidator(validator)
+ self.dw_stepsize_edit.setValidator(validator)
+
+ def set_float_validators(self):
+ validator = QtGui.QDoubleValidator(self)
+ self.dw_minval_edit.setValidator(validator)
+ self.dw_maxval_edit.setValidator(validator)
+ self.dw_stepsize_edit.setValidator(validator)
+
+ def show_dw_contents(self, on=True):
+ self.dw_minval_label.setVisible(on)
+ self.dw_minval_edit.setVisible(on)
+ self.dw_maxval_label.setVisible(on)
+ self.dw_maxval_edit.setVisible(on)
+ self.dw_stepsize_label.setVisible(on)
+ self.dw_stepsize_edit.setVisible(on)
+ self.dw_seq_toggle.setVisible(on)
+
+ def populate_dw_combobox(self):
+ self.dw_combobox.currentIndexChanged.disconnect(self.toggle_dw_combobox)
+ self.dw_combobox.clear()
+ if self.alias is not None:
+ self.dw_combobox.addItem("combobox")
+ if self.alias.component.type in ["Float", "Integer"]:
+ self.dw_combobox.addItem("slider")
+ self.dw_combobox.addItem("numericstepper")
+ self.dw_combobox.currentIndexChanged.connect(self.toggle_dw_combobox)
+
+ def updateContents(self, alias=None, controller=None):
+ self.alias = copy.copy(alias)
+ self.controller = controller
+ self.populate_dw_combobox()
+ self.unplugSignals()
+ if alias is not None and controller is not None:
+ self.name_edit.setText(self.alias.name)
+ #print "widget:", self.alias.component.widget
+ wtype = self.alias.component.widget
+ if wtype == 'text':
+ wtype = "combobox"
+ index = self.dw_combobox.findText(wtype)
+ if index < 0:
+ index = 0
+ self.dw_combobox.setCurrentIndex(index)
+ self.order_spinbox.setRange(0,self.table.topLevelItemCount()-1)
+ self.order_spinbox.setValue(self.alias.component.pos)
+
+ self.dw_minval_edit.setText(self.alias.component.minVal)
+ self.dw_maxval_edit.setText(self.alias.component.maxVal)
+ self.dw_stepsize_edit.setText(self.alias.component.stepSize)
+ self.dw_seq_toggle.setChecked(self.alias.component.seq)
+
+ if self.dw_combobox.currentIndex() == 0:
+ self.show_dw_contents(False)
+ else:
+ self.show_dw_contents(True)
+ # show loop option for stepper
+ self.dw_seq_toggle.setVisible(index == 1)
+
+ if self.dv_widget:
+ self.dv_layout.removeWidget(self.dv_widget)
+ self.disconnect(self.dv_widget,
+ QtCore.SIGNAL("contentsChanged"),
+ self.widgetContentsChanged)
+ self.dv_widget.deleteLater()
+
+ self.dv_widget = QAliasDetailsWidget.createAliasWidget(self.alias, self.controller, self)
+ self.dv_layout.addWidget(self.dv_widget)
+ self.connect(self.dv_widget,
+ QtCore.SIGNAL("contentsChanged"),
+ self.widgetContentsChanged)
+
+ if self.vl_editor:
+ self.vl_layout.removeWidget(self.vl_editor)
+ self.disconnect(self.vl_editor,
+ QtCore.SIGNAL("valuesChanged"),
+ self.valuesListChanged)
+ self.vl_editor.deleteLater()
+ self.vl_editor = None
+
+ self.vl_editor = QValuesListEditor(self.alias,self.controller)
+ self.vl_layout.addWidget(self.vl_editor)
+
+ #capturing widget changes to update alias
+ self.connect(self.vl_editor,
+ QtCore.SIGNAL("valuesChanged"),
+ self.valuesListChanged)
+ self.setEnabled(True)
+ else:
+ self.name_edit.setText("")
+
+ if self.dv_widget:
+ self.dv_layout.removeWidget(self.dv_widget)
+ self.disconnect(self.dv_widget,
+ QtCore.SIGNAL("contentsChanged"),
+ self.widgetContentsChanged)
+ self.dv_widget.deleteLater()
+ self.dv_widget = None
+
+ if self.vl_editor:
+ self.vl_layout.removeWidget(self.vl_editor)
+ self.disconnect(self.vl_editor,
+ QtCore.SIGNAL("valuesChanged"),
+ self.valuesListChanged)
+ self.vl_editor.deleteLater()
+ self.vl_editor = None
+
+ self.setEnabled(False)
+ self.plugSignals()
+
+ @staticmethod
+ def createAliasWidget(alias, controller, parent=None):
+ v = controller.vtController.vistrail
+ p = v.db_get_object(alias.component.vttype, alias.component.vtid)
+ if p.identifier == '':
+ idn = get_vistrails_basic_pkg_id()
+ else:
+ idn = p.identifier
+ reg = get_module_registry()
+ p_module = reg.get_module_by_name(idn, p.type, p.namespace)
+ widget_type = get_widget_class(p_module)
+ p.strValue = alias.component.val
+ return widget_type(p, parent)
+
+ def widgetContentsChanged(self, info):
+ self.alias.component.val = info[0].contents()
+ if self.alias.component.val not in self.alias.component.valueList:
+ self.alias.component.valueList.append(self.alias.component.val)
+ self.alias.component.valueList.sort()
+ self.vl_editor.alias_item_updated()
+ self.aliasChanged.emit(self.alias)
+
+################################################################################
+
+class QValuesListEditor(QtGui.QWidget):
+ """
+ QValuesListEditor is the actual widget allowing users to
+ enter a list of values
+
+ """
+ def __init__(self, alias, controller, parent=None):
+ """ QValuesListEditor(alias_item: AliasTableItem, parent: QWidget)
+ -> QValuesListEditor
+ Construct an edit box with a button for bringing up the dialog
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self._alias = alias
+ self.type = alias.component.type
+ self.controller = controller
+
+ hLayout = QtGui.QHBoxLayout(self)
+ hLayout.setMargin(0)
+ hLayout.setSpacing(0)
+ self.setLayout(hLayout)
+
+ self.listValues = QtGui.QLineEdit()
+
+ self.listValues.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Maximum)
+ self.alias_item_updated()
+
+ hLayout.addWidget(self.listValues)
+
+ self.connect(self.listValues, QtCore.SIGNAL('editingFinished()'),
+ self.values_were_edited)
+
+ inputButton = QtGui.QToolButton()
+ inputButton.setText('...')
+ self.connect(inputButton, QtCore.SIGNAL('clicked()'),
+ self.editListValues)
+ hLayout.addWidget(inputButton)
+
+ def alias_item_updated(self):
+ if self._alias.component.type not in ['Float', 'Integer']:
+ values = []
+ for v in self._alias.component.valueList:
+ values.append("'%s'"% v.replace("'", "\'"))
+
+ self.listValues.setText("[%s]" % ", ".join(values))
+ else:
+ self.listValues.setText('[%s]' % ", ".join(self._alias.component.valueList))
+ if self._alias.component.type in ['String','Integer','Float']:
+ self.listValues.setReadOnly(False)
+ else:
+ self.listValues.setReadOnly(True)
+ self.listValues.home(False)
+
+ def values_were_edited(self):
+ """values_were_edited(): None
+
+ Connected to self.listValues.textEdited.
+ Updates self._alias.valueList.
+
+ NB: Allowing the user to edit the LineEdit field directly is
+ not a very good idea, because we don't know what are the
+ syntactic rules for the translate_to_python() calls in
+ arbitrary classes. Right now, I'm assuming removing the
+ leading and trailing brackets and splitting on ',' is
+ enough. (in passing, The previous call to eval() is just
+ broken is a general scenario like we have now)
+
+ For example, this will break horribly if the user manually edits
+ a list of strings with commas in them."""
+
+ #print "values_were_edited"
+ new_text = self.listValues.text()
+ t = str(new_text)
+ if len(t) < 2:
+ self._alias.component.valueList = []
+ return
+ if not (t[0] == '[' and t[-1] == ']'):
+ self._alias.valueList = []
+ else:
+ self._alias.component.valueList = t[1:-1].split(',')
+ if self._alias.component.type not in ['Float', 'Integer']:
+ for i, val in enumerate(self._alias.component.valueList):
+ val = val.strip()
+ if len(val) >= 2 and \
+ ((val[0] == "'" and val[-1] == "'") or
+ (val[0] == '"' and val[-1] == '"')):
+ self._alias.component.valueList[i] = val.strip()[1:-1]
+
+ def editListValues(self):
+ """ editListValues() -> None
+ Show a dialog for editing the values
+
+ """
+ dialog = QListEditDialog(self._alias, self.controller, None)
+ if dialog.exec_() == QtGui.QDialog.Accepted:
+ values = dialog.getList()
+ #print values
+ self._alias.component.valueList = copy.copy(values)
+ self._str_values = [str(v) for v in values]
+ values2 = values
+ if self.type not in ['Float', 'Integer']:
+ values2 = ["'%s'" % v.replace("'", "\'")
+ for v in values]
+ self.listValues.setText('[%s]' % ', '.join(values2))
+ self.listValues.home(False)
+ self.emit(QtCore.SIGNAL("valuesChanged"))
+ dialog.deleteLater()
+
+##############################################################################
+
+class QListEditDialog(QtGui.QDialog):
+ """
+ QListEditDialog provides an interface for user to edit a list of
+ values and export to a string
+
+ """
+ def __init__(self, alias, controller, parent=None):
+ """ QListEditDialog(pType: str, strValues: list, parent: QWidget)
+ -> QListEditDialog
+ Parse values and setup the table
+
+ """
+ QtGui.QDialog.__init__(self, parent)
+ self._alias = alias
+ vLayout = QtGui.QVBoxLayout()
+ vLayout.setMargin(0)
+ vLayout.setSpacing(0)
+ self.controller = controller
+ self.setLayout(vLayout)
+
+ label = QtGui.QLabel("Please enter values in boxes below. "
+ "'Add' appends an empty value to the list. "
+ "And 'Del' removes the selected values.")
+ label.setMargin(5)
+ label.setWordWrap(True)
+ vLayout.addWidget(label)
+
+ self.table = QtGui.QTableWidget(0, 1, parent)
+ self.table.setHorizontalHeaderLabels(['Values'])
+ self.table.horizontalHeader().setStretchLastSection(True)
+ self.table.verticalHeader().setMovable(True)
+
+ self.delegate = QListEditItemDelegate(alias, controller)
+ self.table.setItemDelegate(self.delegate)
+ self.table.setSelectionMode(QtGui.QAbstractItemView.ExtendedSelection)
+ for v in alias.component.valueList:
+ self.addRow(v)
+ self.connect(self.table.verticalHeader(),
+ QtCore.SIGNAL('sectionMoved(int,int,int)'),
+ self.rowMoved)
+
+ vLayout.addWidget(self.table)
+
+ hLayout = QtGui.QHBoxLayout()
+ vLayout.addLayout(hLayout)
+
+ okButton = QtGui.QPushButton('&OK')
+ okButton.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+ self.connect(okButton, QtCore.SIGNAL('clicked()'), self.okButtonPressed)
+ hLayout.addWidget(okButton)
+
+ cancelButton = QtGui.QPushButton('&Cancel')
+ cancelButton.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+ self.connect(cancelButton, QtCore.SIGNAL('clicked()'), self.reject)
+ hLayout.addWidget(cancelButton)
+
+ addButton = QtGui.QPushButton('&Add')
+ addButton.setIcon(CurrentTheme.ADD_STRING_ICON)
+ addButton.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+ self.connect(addButton, QtCore.SIGNAL('clicked()'), self.addRow)
+ hLayout.addWidget(addButton)
+
+ removeButton = QtGui.QPushButton('&Del')
+ removeButton.setIcon(QtGui.QIcon(
+ self.style().standardPixmap(QtGui.QStyle.SP_DialogCancelButton)))
+ removeButton.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+ self.connect(removeButton, QtCore.SIGNAL('clicked()'),
+ self.removeSelection)
+ hLayout.addWidget(removeButton)
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+ Return the recommended size for the widget
+
+ """
+ return QtCore.QSize(256, 384)
+
+ def okButtonPressed(self):
+ """ okButtonPressed() -> None
+ Make sure to commit the editor data before accepting
+
+ """
+ self.table.itemDelegate().finishEditing()
+ self.accept()
+
+ def getList(self):
+ """ getList() -> list of str values
+ Return a list of values
+
+ """
+ result = []
+ for i in xrange(self.table.rowCount()):
+ logicalIndex = self.table.verticalHeader().logicalIndex(i)
+ value = self.table.cellWidget(logicalIndex, 0).contents()
+ result.append(str(value))
+ return result
+
+ def rowMoved(self, row, old, new):
+ """ rowMove(row: int, old: int, new: int) -> None
+ Renumber the vertical header labels when row moved
+
+ """
+ vHeader = self.table.verticalHeader()
+ labels = []
+ for i in xrange(self.table.rowCount()):
+ labels.append(str(vHeader.visualIndex(i)+1))
+ self.table.setVerticalHeaderLabels(labels)
+
+ def addRow(self, text=''):
+ """ addRow(text: str) -> QListStringEdit
+ Add an extra row to the end of the table
+
+ """
+ self.table.setRowCount(self.table.rowCount()+1)
+ alias = copy.copy(self._alias)
+ alias.component.val = text
+ widget = \
+ QAliasDetailsWidget.createAliasWidget(alias, self.controller, None)
+ if not isinstance(widget, StandardConstantWidget):
+ item = QtGui.QTableWidgetItem()
+ else:
+ item = QtGui.QTableWidgetItem(text)
+ row = self.table.rowCount()-1
+
+ self.table.setItem(row, 0, item)
+ self.table.setCellWidget(row,
+ 0,
+ widget)
+ h = widget.sizeHint().height()
+ self.table.setRowHeight(row,h)
+
+ def removeSelection(self):
+ """ removeSelection() -> None
+ Remove selected rows on the table
+
+ """
+ for item in self.table.selectedItems():
+ self.table.removeRow(item.row())
+
+##############################################################################
+
+class QListEditItemDelegate(QtGui.QItemDelegate):
+ """
+ QListEditItemDelegate sets up the editor for the QListEditDialog
+ table
+
+ """
+
+ def __init__(self, alias_item, controller, parent=None):
+ """ QListEditItemDelegate(parent: QWidget) -> QListEditItemDelegate
+ Store the uncommit editor for commit later
+
+ """
+ QtGui.QItemDelegate.__init__(self, parent)
+ self.controller = controller
+ self.alias_item = alias_item
+ self.editor = None
+
+ def createEditor(self, parent, option, index):
+ """ createEditor(parent: QWidget,
+ option: QStyleOptionViewItem,
+ index: QModelIndex) -> QStringEdit
+ Return the editor widget for the index
+
+ """
+ self.editor = QAliasDetailsWidget.createAliasWidget(self.alias_item,
+ self.controller,
+ parent)
+ #print "editor created"
+ return self.editor
+
+ def updateEditorGeometry(self, editor, option, index):
+ """ updateEditorGeometry(editor: QStringEdit,
+ option: QStyleOptionViewItem,
+ index: QModelIndex) -> None
+ Update the geometry of the editor based on the style option
+
+ """
+ editor.setGeometry(option.rect)
+
+ def setModelData(self, editor, model, index):
+ """ setModelData(editor: QStringEdit,
+ model: QAbstractItemModel,
+ index: QModelIndex) -> None
+ Set the text of the editor back to the item model
+
+ """
+ model.setData(index, editor.contents())
+ self.editor = None
+
+ def finishEditing(self):
+ #print "finishEditing"
+ if self.editor:
+ self.emit(QtCore.SIGNAL('commitData(QWidget*)'), self.editor)
+
+##############################################################################
diff --git a/vistrails/gui/mashups/alias_list.py b/vistrails/gui/mashups/alias_list.py
new file mode 100644
index 0000000..98e3e3a
--- /dev/null
+++ b/vistrails/gui/mashups/alias_list.py
@@ -0,0 +1,352 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+""" This file contains widgets for displaying a list of aliases.
+
+Classes defined in this file:
+
+QAliasListPanel
+QAliasListItem
+QAliasList
+
+"""
+import copy
+from PyQt4 import QtCore, QtGui
+from PyQt4.QtCore import pyqtSlot, pyqtSignal
+
+
+from vistrails.core.data_structures.bijectivedict import Bidict
+from vistrails.core.mashup.alias import Alias
+from vistrails.gui.base_view import BaseView
+from vistrails.gui.mashups.alias_inspector import QAliasInspector
+from vistrails.gui.utils import show_question, YES_BUTTON, NO_BUTTON
+
+###############################################################################
+class QAliasListPanel(QtGui.QWidget, BaseView):
+ """
+ QAliasListPanel shows list of aliases in pipeline.
+
+ """
+ #signals
+ highlightModule = pyqtSignal(int)
+ aliasesChanged = pyqtSignal()
+ aliasChanged = pyqtSignal(Alias)
+ aliasRemoved = pyqtSignal(str)
+
+ def __init__(self, controller=None, parent=None):
+ """ QAliasListPanel(controller: MashupController,
+ parent: QWidget) -> QAliasListPanel
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self.controller = None
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ layout = QtGui.QVBoxLayout()
+ self.aliases = QAliasList(controller, self)
+ self.inspector = QAliasInspector(self.aliases)
+ self.updateController(controller)
+ self.setLayout(layout)
+ #self.layout().setMargin(0)
+ #self.layout().setSpacing(1)
+ self.splitter = QtGui.QSplitter()
+ layout.addWidget(self.splitter)
+ self.splitter.setOrientation(QtCore.Qt.Vertical)
+ self.splitter.addWidget(self.aliases)
+ self.splitter.addWidget(self.inspector)
+ self.splitter.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ self.splitter.setStretchFactor(0,0)
+ self.splitter.setStretchFactor(1,1)
+
+ #connecting signals
+ self.aliases.itemSelectionChanged.connect(self.updateInspector)
+ self.aliases.highlightModule.connect(self.highlightModule)
+ self.aliases.aliasUpdated.connect(self.updateAlias)
+ self.aliases.aliasRemoved.connect(self.aliasRemoved)
+
+ self.inspector.aliasChanged.connect(self.updateAlias)
+
+ def updateController(self, controller, other_dict=None):
+ if self.controller:
+ self.aliasRemoved.disconnect(self.controller.removeAlias)
+ self.aliasChanged.disconnect(self.controller.updateAlias)
+ self.controller = controller
+ if self.controller:
+ self.aliases.controller = self.controller
+ if (self.controller.currentMashup.alias_list and
+ len(self.controller.currentMashup.alias_list) > 0):
+ self.aliases.populateFromMashup(self.controller)
+ else:
+ self.aliases.clear()
+ self.aliasRemoved.connect(self.controller.removeAlias)
+ self.aliasChanged.connect(self.controller.updateAlias)
+
+ def updateVersion(self, versionId):
+ #print "AliasPanel.updateVersion "
+ if self.controller:
+ if (self.controller.currentMashup.alias_list and
+ len(self.controller.currentMashup.alias_list) > 0):
+ self.aliases.populateFromMashup(self.controller)
+ else:
+ self.aliases.clear()
+
+ @pyqtSlot()
+ def updateInspector(self):
+ if len(self.aliases.selectedItems()) == 1:
+ item = self.aliases.selectedItems()[0]
+ self.inspector.updateContents(item.alias, self.controller)
+ else:
+ self.inspector.updateContents()
+
+ @pyqtSlot(Alias)
+ def updateAlias(self, alias):
+ #make sure the module is highlighted in the pipeline view
+ # or method_drop box is empty
+ self.aliasChanged.emit(alias)
+ self.aliasesChanged.emit()
+
+ def set_default_layout(self):
+ from vistrails.gui.mashups.mashups_inspector import QMashupsInspector
+ from vistrails.gui.mashups.alias_parameter_view import QAliasParameterView
+ self.set_palette_layout(
+ {QtCore.Qt.LeftDockWidgetArea: QMashupsInspector,
+ QtCore.Qt.RightDockWidgetArea: QAliasParameterView,
+ })
+
+ def set_action_links(self):
+ self.action_links = \
+ {
+ }
+
+###############################################################################
+
+class QAliasList(QtGui.QTreeWidget):
+ """
+ QAliasList just inherits from QListView to have a customized
+ list and items
+
+ """
+ #signals
+ aliasUpdated = pyqtSignal(Alias)
+ aliasRemoved = pyqtSignal(str)
+ highlightModule = pyqtSignal(int)
+
+ def __init__(self, controller, panel, parent=None):
+ """ QAliasList(parent: QWidget) -> QAliasTable
+
+ """
+ QtGui.QTreeWidget.__init__(self, parent)
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ self.setRootIsDecorated(False)
+ self.panel = panel
+ self.aliases = Bidict()
+ self.alias_widgets = {}
+ self.controller = controller
+ self.header().setStretchLastSection(True)
+ self.setHeaderLabels(["Position", "Name", "Type"])
+ self.itemSelectionChanged.connect(self.setPreviousSelected)
+ self.connect(self,
+ QtCore.SIGNAL("currentItemChanged(QTreeWidgetItem*,QTreeWidgetItem*)"),
+ self.currentAliasChanged)
+ self.previousSelected = -1
+
+ @pyqtSlot()
+ def setPreviousSelected(self):
+ if len(self.selectedItems()) == 1:
+ item = self.selectedItems()[0]
+ self.previousSelected = self.indexOfTopLevelItem(item)
+ else:
+ self.previousSelected = -1
+
+ def processCellChanges(self, row, col):
+ """ processCellChanges(row: int, col: int) -> None
+ Event handler for capturing when the contents in a cell changes
+
+ """
+ item = self.item(row, col)
+ if col == 0:
+ old_alias = item.alias.alias
+ new_alias = str(item.text())
+ if new_alias in self.aliases.keys():
+ QtGui.QMessageBox.warning(self,
+ "VisMashup",
+ """Label name %s already exists.
+ Please type a different name. """ %
+ new_alias)
+ item.setText(old_alias)
+ return
+ elif new_alias == '':
+ del self.aliases[old_alias]
+ wdgt = self.cellWidget(row, 1)
+ del self.alias_widgets[wdgt]
+ item.alias.alias = ''
+ self.removeRow(row)
+ wdgt.deleteLater()
+ self.updateRowNumbers()
+ else:
+ self.aliases[new_alias] = self.aliases[old_alias]
+ del self.aliases[old_alias]
+ item.alias.alias = new_alias
+
+ elif col == 1:
+ wdgt = self.cellWidget(row,col)
+ if wdgt is not None:
+ item.alias.value = wdgt.contents()
+ self.aliasUpdated.emit(item.alias)
+
+ def currentAliasChanged(self, current, previous):
+ if current:
+ if ((previous is not None and current.alias != previous.alias) or
+ previous is None):
+ self.highlightModule.emit(current.alias.component.vtmid)
+ else:
+ self.highlightModule.emit(-1)
+
+ def _getOtherParameterInfo(self, pipeline, id, ptype):
+ parameter = pipeline.db_get_object(ptype,id)
+ return (parameter.type, parameter.strValue, 1, parameter.pos)
+
+ def createAliasItem(self, alias):
+ """ createAliasRow( alias: core.mashup.Alias) -> AliasItem
+ Creates a row in the list
+
+ """
+
+ alias.pos = self.topLevelItemCount()
+ labels = [str(alias.component.pos), str(alias.name), \
+ str(alias.component.type)]
+ item = QAliasListItem(self, alias, labels)
+ item.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable )
+
+ return alias
+
+ def populateFromMashup(self, mashupController):
+ #print "populateFromMashup ", self , self.previousSelected
+ if self.controller != mashupController:
+ self.controller = mashupController
+ self.itemSelectionChanged.disconnect(self.setPreviousSelected)
+ self.aliases = {}
+ self.alias_cache = {}
+ self.alias_widgets = {}
+ self.clear()
+ mashup = self.controller.currentMashup
+ if len(mashup.alias_list) > 0:
+ for alias in mashup.alias_list:
+ alias = self.createAliasItem(copy.copy(alias))
+ self.aliases[alias.name] = alias
+
+ if self.previousSelected > -1:
+ if self.previousSelected >= self.topLevelItemCount():
+ self.previousSelected = self.topLevelItemCount()-1
+ item = self.topLevelItem(self.previousSelected)
+ self.setItemSelected(item, True)
+ self.setCurrentItem(item)
+ self.itemSelectionChanged.connect(self.setPreviousSelected)
+
+ def updatePosNumbers(self):
+ new_order = []
+ for idx in range(self.topLevelItemCount()):
+ item = self.topLevelItem(idx)
+ new_order.append(item.alias.component.pos)
+ item.setText(0,str(idx))
+ return new_order
+
+ def moveItemToNewPos(self, old, new):
+ """moveItemToNewPos(old:int, new:int) -> None
+ Move item from pos old to pos new
+
+ """
+ self.itemSelectionChanged.disconnect(self.panel.updateInspector)
+ item = self.takeTopLevelItem(old)
+ self.insertTopLevelItem(new,item)
+ self.clearSelection()
+ new_order = self.updatePosNumbers()
+ self.setItemSelected(item, True)
+ self.itemSelectionChanged.connect(self.panel.updateInspector)
+ self.controller.reorderAliases(new_order)
+
+ def keyPressEvent(self, event):
+ """ keyPressEvent(event: QKeyEvent) -> None
+ Capture 'Del', 'Backspace' for deleting aliases
+
+ """
+ if (event.key() in [QtCore.Qt.Key_Backspace, QtCore.Qt.Key_Delete]):
+ self.removeCurrentAlias()
+
+ @pyqtSlot(bool)
+ def removeCurrentAlias(self, checked=False):
+ item = self.currentItem()
+ if not item:
+ return
+ name = item.alias.name
+ # item will get recreated after question dialog shows so keep only index
+ pos = self.indexOfTopLevelItem(item)
+ res = show_question("Mashups",
+ "Are you sure do you want to remove '%s' from the mashup?"%name,
+ [YES_BUTTON, NO_BUTTON], NO_BUTTON)
+ if res == YES_BUTTON:
+ self.previousSelected = pos
+ self.takeTopLevelItem(pos)
+ del self.aliases[name]
+
+ self.updatePosNumbers()
+ if pos >= self.topLevelItemCount() - 1:
+ pos = self.topLevelItemCount() - 1
+ self.previousSelected = pos
+ if pos != -1:
+ new_item = self.topLevelItem(pos)
+ self.setCurrentItem(new_item)
+ self.setItemSelected(new_item, True)
+ self.aliasRemoved.emit(name)
+################################################################################
+
+class QAliasListItem (QtGui.QTreeWidgetItem):
+ """
+ QAliasListtItem represents alias on QAliasList
+
+ """
+ def __init__(self, parent, alias, labels):
+ """ QAliasListItem(alias: AliasItem, labels: string):
+ Create a new item with alias and text
+
+ """
+ QtGui.QTreeWidgetItem.__init__(self, parent, labels)
+ self.alias = alias
+
+###############################################################################
+
+
diff --git a/vistrails/gui/mashups/alias_parameter_view.py b/vistrails/gui/mashups/alias_parameter_view.py
new file mode 100644
index 0000000..888b254
--- /dev/null
+++ b/vistrails/gui/mashups/alias_parameter_view.py
@@ -0,0 +1,389 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+""" The file describes the parameter tree view that allows changing the alias
+of parameters
+
+QAliasParameterView
+"""
+from PyQt4 import QtCore, QtGui
+from PyQt4.QtCore import pyqtSignal, pyqtSlot
+from vistrails.core.inspector import PipelineInspector
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.gui.common_widgets import QSearchTreeWindow, QSearchTreeWidget
+from vistrails.gui.paramexplore.pe_pipeline import QAnnotatedPipelineView
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+from vistrails.gui.theme import CurrentTheme
+from vistrails.core.utils import InstanceObject
+
+################################################################################
+class QAliasParameterView(QtGui.QWidget, QVistrailsPaletteInterface):
+
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.set_title("Mashup Pipeline")
+ layout = QtGui.QVBoxLayout()
+ self.parameter_panel = QAliasParameterPanel()
+ font = QtGui.QFont("Arial", 11, QtGui.QFont.Normal)
+ font.setItalic(True)
+ label = QtGui.QLabel("Double-click a parameter to change alias")
+ label.setFont(font)
+ param_group = QtGui.QGroupBox(self.parameter_panel.windowTitle())
+ g_layout = QtGui.QVBoxLayout()
+ g_layout.setMargin(0)
+ g_layout.setSpacing(2)
+ g_layout.addWidget(label)
+ g_layout.addWidget(self.parameter_panel)
+ param_group.setLayout(g_layout)
+ layout.addWidget(param_group)
+
+ self.pipeline_view = QAnnotatedPipelineView()
+ self.pipeline_view.setReadOnlyMode(True)
+ p_view_group = QtGui.QGroupBox(self.pipeline_view.windowTitle())
+ g_layout = QtGui.QVBoxLayout()
+ g_layout.setMargin(0)
+ g_layout.setSpacing(0)
+ g_layout.addWidget(self.pipeline_view)
+ p_view_group.setLayout(g_layout)
+ layout.addWidget(p_view_group)
+ self.setLayout(layout)
+
+ self.parameter_panel.treeWidget.aliasChanged.connect(self.aliasChanged)
+
+ def updateMshpController(self, mshpController):
+ from vistrails.gui.vistrails_window import _app
+ self.mshpController = mshpController
+ self.parameter_panel.set_pipeline(
+ self.mshpController.vtPipeline)
+ self.pipeline_view.set_controller(self.mshpController.vtController)
+ self.mshpController.vtController.current_pipeline_view = \
+ self.pipeline_view
+ self.pipeline_view.scene().current_pipeline = self.mshpController.vtPipeline
+ self.mshpController.vtController.current_pipeline = self.mshpController.vtPipeline
+
+ #print "**** should update mashup pipeline view "
+
+ #self.pipeline_view.scene().setupScene(self.mshpController.vtPipeline)
+ self.pipeline_view.scene().clear()
+ self.pipeline_view.version_changed()
+ self.pipeline_view.zoomToFit()
+ self.pipeline_view.updateAnnotatedIds(
+ self.mshpController.vtPipeline)
+ #_app.notify('mashup_pipeline_view_set')
+
+ def updateMshpVersion(self, version):
+ #print "will update alias param view"
+ self.parameter_panel.set_pipeline(
+ self.mshpController.vtPipeline)
+ self.pipeline_view.version_changed()
+
+ def zoomToFit(self):
+ if self.pipeline_view:
+ self.pipeline_view.zoomToFit()
+
+ def aliasChanged(self, param):
+ from vistrails.gui.vistrails_window import _app
+ _app.notify('alias_changed', param)
+
+################################################################################
+
+class QAliasParameterPanel(QSearchTreeWindow):
+ """
+ QAliasParameterPanel is a special widget for displaying methods and
+ parameters inside a pipeline that allow changing aliases
+
+ """
+ def createTreeWidget(self):
+ """ createTreeWidget() -> QModuleTreeWidget
+ Return the search tree widget for this window
+
+ """
+ self.setWindowTitle("Parameter Aliases")
+ return QAliasParameterTreeWidget(self)
+
+ def set_pipeline(self, pipeline):
+ self.pipeline = pipeline
+ self.treeWidget.updateFromPipeline(pipeline)
+
+################################################################################
+class QAliasParameterTreeWidget(QSearchTreeWidget):
+ """
+ QAliasParameterTreeWidget is a subclass of QSearchTreeWidget to display all
+ Vistrails Module
+
+ """
+ #signals
+ aliasChanged = pyqtSignal(InstanceObject)
+
+ def __init__(self, parent=None):
+ """ QAliasParameterTreeWidget(parent: QWidget) -> QParameterTreeWidget
+ Set up size policy and header
+
+ """
+ QSearchTreeWidget.__init__(self, parent)
+ self.header().hide()
+ self.setRootIsDecorated(False)
+ self.delegate = QAliasParameterTreeWidgetItemDelegate(self, self)
+ self.setItemDelegate(self.delegate)
+ self.aliasNames = []
+ self.itemDoubleClicked.connect(self.changeAlias)
+ def updateFromPipeline(self, pipeline):
+ """ updateFromPipeline(pipeline: Pipeline) -> None
+ Read the list of aliases and parameters from the pipeline
+
+ """
+ self.clear()
+ if not pipeline:
+ return
+
+ # Update the aliases
+# if len(pipeline.aliases)>0:
+# aliasRoot = QParameterTreeWidgetItem(None, self, ['Aliases'])
+# aliasRoot.setFlags(QtCore.Qt.ItemIsEnabled,
+# )
+# for (alias, info) in pipeline.aliases.iteritems():
+# ptype, pId, parentType, parentId, _ = info
+# parameter = pipeline.db_get_object(ptype, pId)
+# v = parameter.strValue
+# aType = parameter.type
+# aIdentifier = parameter.identifier
+# aNamespace = parameter.namespace
+# label = ['%s = %s' % (alias, v)]
+# pInfo = InstanceObject(type=aType,
+# identifier=aIdentifier,
+# namespace=aNamespace,
+# value=v,
+# id=pId,
+# dbtype=ptype,
+# parent_dbtype=parentType,
+# parent_id=parentId,
+# is_alias=True)
+# aliasItem = QParameterTreeWidgetItem((alias, [pInfo]),
+# aliasRoot, label)
+# aliasRoot.setExpanded(True)
+
+ # Now go through all modules and functions
+ self.aliasNames = pipeline.aliases.keys()
+ inspector = PipelineInspector()
+ inspector.inspect_ambiguous_modules(pipeline)
+ sortedModules = sorted(pipeline.modules.iteritems(),
+ key=lambda item: item[1].name)
+ for mId, module in sortedModules:
+ if len(module.functions)>0:
+ mLabel = [module.name]
+ moduleItem = None
+ for fId in xrange(len(module.functions)):
+ function = module.functions[fId]
+ if len(function.params)==0: continue
+ if moduleItem==None:
+ if inspector.annotated_modules.has_key(mId):
+ annotatedId = inspector.annotated_modules[mId]
+ moduleItem = QAliasParameterTreeWidgetItem(annotatedId,
+ self, mLabel)
+ else:
+ moduleItem = QAliasParameterTreeWidgetItem(None,
+ self, mLabel)
+ #v = ', '.join([p.strValue for p in function.params])
+ label = ['%s'%function.name]
+
+ pList = [InstanceObject(type=function.params[pId].type,
+ identifier=function.params[pId].identifier,
+ namespace=function.params[pId].namespace,
+ value=function.params[pId].strValue,
+ id=function.params[pId].real_id,
+ dbtype=ModuleParam.vtType,
+ parent_dbtype=function.vtType,
+ parent_id=function.real_id,
+ alias=function.params[pId].alias,
+ mId=mId)
+ for pId in xrange(len(function.params))]
+ mName = module.name
+ if moduleItem.parameter!=None:
+ mName += '(%d)' % moduleItem.parameter
+ fName = '%s :: %s' % (mName, function.name)
+ mItem = QAliasParameterTreeWidgetItem((fName, pList),
+ moduleItem,
+ label)
+ if moduleItem:
+ moduleItem.setExpanded(True)
+
+ @pyqtSlot(QtGui.QTreeWidgetItem, int)
+ def changeAlias(self, item, column ):
+ """ itemClicked(item: , column: int) -> None
+ If mouse click on the item, show up a dialog to change/add
+ the alias name
+
+ """
+ if isinstance(item.parameter, InstanceObject):
+ (text, ok) = QtGui.QInputDialog.getText(self,
+ 'Set Parameter Alias',
+ 'Enter the parameter alias',
+ QtGui.QLineEdit.Normal,
+ item.parameter.alias)
+ while ok and str(text) in self.aliasNames:
+ msg =" This alias is already being used.\
+ Please enter a different parameter alias "
+ (text, ok) = QtGui.QInputDialog.getText(self,
+ 'Set Parameter Alias',
+ msg,
+ QtGui.QLineEdit.Normal,
+ text)
+ if ok and item.parameter.alias != str(text):
+ item.parameter.alias = str(text)
+ item.updateAlias()
+ self.aliasChanged.emit(item.parameter)
+
+
+
+class QAliasParameterTreeWidgetItemDelegate(QtGui.QItemDelegate):
+ """
+ QAliasParameterTreeWidgetItemDelegate will override the original
+ QTreeWidget paint function to draw buttons for top-level item
+ similar to QtDesigner. This mimics
+ Qt/tools/designer/src/lib/shared/sheet_delegate, which is only a
+ private class from QtDesigned.
+
+ """
+ def __init__(self, view, parent):
+ """ QParameterTreeWidgetItemDelegate(view: QTreeView,
+ parent: QWidget)
+ -> QParameterTreeWidgetItemDelegate
+ Create the item delegate given the tree view
+
+ """
+ QtGui.QItemDelegate.__init__(self, parent)
+ self.treeView = view
+
+ def paint(self, painter, option, index):
+ """ painter(painter: QPainter, option QStyleOptionViewItem,
+ index: QModelIndex) -> None
+ Repaint the top-level item to have a button-look style
+
+ """
+ model = index.model()
+ if (model.parent(index).isValid()==False or
+ model.parent(index).parent().isValid()==False):
+ style = self.treeView.style()
+ r = option.rect
+ textrect = QtCore.QRect(r.left() + 10,
+ r.top(),
+ r.width() - 10,
+ r.height())
+ font = painter.font()
+ font.setBold(True)
+ painter.setFont(font)
+ text = option.fontMetrics.elidedText(
+ model.data(index, QtCore.Qt.DisplayRole),
+ QtCore.Qt.ElideMiddle,
+ textrect.width()-10)
+ style.drawItemText(painter,
+ textrect,
+ QtCore.Qt.AlignLeft,
+ option.palette,
+ self.treeView.isEnabled(),
+ text)
+ painter.setPen(QtGui.QPen(QtCore.Qt.black))
+ fm = QtGui.QFontMetrics(font)
+ size = fm.size(QtCore.Qt.TextSingleLine, text)
+ #painter.drawLine(textrect.left()-5,
+ # textrect.bottom()-1,
+ # textrect.left()+size.width()+5,
+ # textrect.bottom()-1)
+
+ annotatedId = model.data(index, QtCore.Qt.UserRole+1)
+ if annotatedId:
+ idRect = QtCore.QRect(
+ QtCore.QPoint(textrect.left()+size.width()+5,
+ textrect.top()),
+ textrect.bottomRight())
+ QAnnotatedPipelineView.drawId(painter, idRect,
+ annotatedId,
+ QtCore.Qt.AlignLeft |
+ QtCore.Qt.AlignVCenter)
+ else:
+ QtGui.QItemDelegate.paint(self, painter, option, index)
+
+ def sizeHint(self, option, index):
+ """ sizeHint(option: QStyleOptionViewItem, index: QModelIndex) -> None
+ Take into account the size of the top-level button
+
+ """
+ return (QtGui.QItemDelegate.sizeHint(self, option, index) +
+ QtCore.QSize(2, 2))
+
+
+class QAliasParameterTreeWidgetItem(QtGui.QTreeWidgetItem):
+ """
+ QParameterTreeWidgetItem represents module on QParameterTreeWidget
+
+ """
+ def __init__(self, info, parent, labelList):
+ """ QAliasParameterTreeWidgetItem(info: (str, []),
+ parent: QTreeWidgetItem
+ labelList: string)
+ -> QParameterTreeWidget
+
+ Create a new tree widget item with a specific parent and
+ labels. info describing a set of parameters as follow:
+ (name, [InstanceObject]):
+ name = Name of the parameter set (alias or function)
+ If this item is a top-level item, info can either be None or
+ an integer specifying the annotated id of this module
+
+ """
+ self.parameter = info
+ QtGui.QTreeWidgetItem.__init__(self, parent, labelList)
+ if isinstance(self.parameter, int):
+ self.setData(0, QtCore.Qt.UserRole+1, self.parameter)
+ elif isinstance(self.parameter, tuple):
+ for param in self.parameter[1]:
+ label = ['']
+ item = QAliasParameterTreeWidgetItem(param, self, label)
+ item.setFlags(QtCore.Qt.ItemIsEnabled|
+ QtCore.Qt.ItemIsSelectable)
+ item.updateAlias()
+ self.setExpanded(True)
+
+ def updateAlias(self):
+ if isinstance(self.parameter, InstanceObject):
+ if self.parameter.alias != '':
+ self.setText(0,'%s(%s):%s'%(self.parameter.alias,
+ self.parameter.type,
+ self.parameter.value))
+ self.setIcon(0,CurrentTheme.MASHUP_ALIAS_ICON)
+ else:
+ self.setText(0,'%s:%s'%(self.parameter.type,
+ self.parameter.value))
+ self.setIcon(0,QtGui.QIcon())
diff --git a/vistrails/gui/mashups/controller.py b/vistrails/gui/mashups/controller.py
new file mode 100644
index 0000000..17a12b0
--- /dev/null
+++ b/vistrails/gui/mashups/controller.py
@@ -0,0 +1,87 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4.QtCore import QObject, pyqtSignal, pyqtSlot
+
+from vistrails.core.mashup.controller import MashupController as BaseController
+from vistrails.core.mashup.alias import Alias
+from vistrails.gui.utils import show_warning
+
+class MashupController(BaseController, QObject):
+ #signals
+ stateChanged = pyqtSignal()
+ versionChanged = pyqtSignal(int)
+
+ def __init__(self, originalController, vt_controller, vt_version, mshptrail=None):
+ QObject.__init__(self)
+ BaseController.__init__(self, originalController, vt_controller, vt_version, mshptrail)
+ self.name = ''
+ self.currentMashupView = None
+
+ def setChanged(self, on):
+ BaseController.setChanged(self, on)
+ self.stateChanged.emit()
+
+ def setCurrentVersion(self, version, quiet=True):
+ BaseController.setCurrentVersion(self, version)
+ if not quiet:
+ self.stateChanged.emit()
+ self.versionChanged.emit(version)
+
+ def updateCurrentTag(self, name):
+ if BaseController.updateCurrentTag(self, name) == False:
+ show_warning('Name Exists',
+ "There is already another version named '%s'.\n"
+ "Please enter a different one." % name)
+ return False
+ else:
+ return True
+
+ @pyqtSlot(str)
+ def removeAlias(self, name):
+ BaseController.removeAlias(self, name)
+
+ @pyqtSlot(Alias)
+ def updateAlias(self, alias):
+ BaseController.updateAlias(self, alias)
+
+ def moveTag(self, from_version, to_version, name):
+ BaseController.moveTag(self, from_version, to_version, name)
+ self.stateChanged.emit()
+
+ def execute(self, params):
+ from vistrails.gui.vistrails_window import _app
+ result = BaseController.execute(self, params)
+ _app.notify('execution_updated')
+ return result
\ No newline at end of file
diff --git a/vistrails/gui/mashups/mashup_app.py b/vistrails/gui/mashups/mashup_app.py
new file mode 100644
index 0000000..6f8bf17
--- /dev/null
+++ b/vistrails/gui/mashups/mashup_app.py
@@ -0,0 +1,624 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+from PyQt4.QtCore import pyqtSignal
+
+from vistrails.gui.mashups.mashups_widgets import (QAliasSliderWidget, QDropDownWidget,
+ QAliasNumericStepperWidget)
+from vistrails.gui.utils import show_warning, TestVisTrailsGUI
+
+spreadsheet = __import__('vistrails.packages.spreadsheet', globals(), locals(),
+ ['spreadsheet_controller'], -1)
+spreadsheetController = spreadsheet.spreadsheet_controller.spreadsheetController
+
+
+class QMashupAppMainWindow(QtGui.QMainWindow):
+ #signals
+ appWasClosed = pyqtSignal(QtGui.QMainWindow)
+
+ def __init__(self, parent=None, vistrail_view=None, dumpcells=False,
+ controller=None, version=-1):
+ """ QMashupAppMainWindow()
+ Initialize an app window from a mashup.
+
+ """
+ # Constructing the main widget
+ QtGui.QMainWindow.__init__(self, parent)
+ self.vtkCells = []
+ self.setStatusBar(QtGui.QStatusBar(self))
+
+ # Central widget
+ centralWidget = QtGui.QWidget()
+ self.mainLayout = QtGui.QVBoxLayout()
+ self.mainLayout.setMargin(0)
+ self.mainLayout.setSpacing(5)
+ centralWidget.setLayout(self.mainLayout)
+ self.setCentralWidget(centralWidget)
+ self.numberOfCells = 0
+ self.is_executing = False
+ self.sequenceOption = False
+ self.steps = []
+ self.isLooping = False
+ #self.resize(100,100)
+ self.dumpcells = dumpcells
+ self.view = vistrail_view
+ if controller:
+ self.controller = controller
+ self.mshptrail = controller.mshptrail
+ if version == -1:
+ self.currentMashup = self.controller.currentMashup
+ else:
+ self.currentMashup = self.mshptrail.getMashup(version)
+ self.setWindowTitle('%s Mashup'%self.controller.getMashupName(version))
+ else:
+ self.setWindowTitle('Mashup')
+
+ # Assign "hidden" shortcut
+ self.editingModeAct = QtGui.QAction("Chang&e Layout",
+ self, shortcut="Ctrl+E",
+ statusTip="Change the layout of the widgets",
+ triggered=self.toggleEditingMode)
+ #self.editingModeShortcut = QtGui.QShortcut(QtGui.QKeySequence('Ctrl+E'), self)
+ #self.connect(self.editingModeShortcut, QtCore.SIGNAL('activated()'),
+ # self.toggleEditingMode)
+ self.editing = False
+ # Constructing alias controls
+ self.controlDocks = []
+ # Show here to make sure XDisplay info is correct (for VTKCell)
+ self.show()
+
+ spreadsheetController.setEchoMode(True)
+ #will run to get Spreadsheet Cell events
+ (cellEvents, errors) = self.runAndGetCellEvents(useDefaultValues=True)
+ if cellEvents:
+ self.numberOfCells = len(cellEvents)
+ self.initCells(cellEvents)
+ if len(errors) > 0:
+ show_warning("VisTrails::Mashup Preview",
+ "There was a problem executing the pipeline: %s." %
+ errors)
+ # Construct the controllers for aliases
+ self.controlDocks = {}
+ self.cellControls = {}
+ self.aliasWidgets = {}
+ self.initControls()
+
+ if self.currentMashup.layout != None:
+ self.restoreState(QtCore.QByteArray.fromPercentEncoding(
+ QtCore.QByteArray(self.currentMashup.layout)))
+
+ if self.currentMashup.geometry != None:
+ self.restoreGeometry(QtCore.QByteArray.fromPercentEncoding(
+ QtCore.QByteArray(self.currentMashup.geometry)))
+ else:
+ self.resize(self.sizeHint())
+
+ # Constructing buttons
+ buttonDock = QCustomDockWidget('Control Buttons', self)
+ buttonWidget = QtGui.QWidget(buttonDock)
+ buttonWidget.setSizePolicy(QtGui.QSizePolicy.Preferred,
+ QtGui.QSizePolicy.Preferred)
+ buttonLayout = QtGui.QGridLayout()
+ buttonWidget.setLayout(buttonLayout)
+ buttonLayout.setMargin(5)
+ self.cb_auto_update = QtGui.QCheckBox("Turn on auto-update",
+ self.centralWidget())
+ self.cb_auto_update.setChecked(False)
+ self.cb_loop_sequence = QtGui.QCheckBox("Render all steps in '%s'" % \
+ (self.sequenceOption.alias.name if self.sequenceOption else 'None'),
+ self.centralWidget())
+ self.cb_loop_sequence.setChecked(False)
+ self.cb_loop_sequence.setVisible(self.sequenceOption is not False)
+ self.cb_loop_sequence.setToolTip(
+ "Render each step of this stepper for fast switching")
+ self.cb_loop_int = QtGui.QCheckBox("Interactive Steps",
+ self.centralWidget())
+ self.cb_loop_int.setChecked(False)
+ self.cb_loop_int.setVisible(False)
+ self.cb_loop_int.setToolTip(
+ "Show complete result of each step instead of static images")
+ self.cb_loop_sequence.clicked.connect(self.cb_loop_int.setVisible)
+ self.cb_keep_camera = QtGui.QCheckBox("Keep camera position",
+ self.centralWidget())
+ self.cb_keep_camera.setChecked(True)
+ self.connect(self.cb_auto_update,
+ QtCore.SIGNAL("stateChanged(int)"),
+ self.auto_update_changed)
+ self.connect(self.cb_loop_int,
+ QtCore.SIGNAL("stateChanged(int)"),
+ self.loop_int_changed)
+ self.loopButton = QtGui.QPushButton("&Loop", self.centralWidget())
+ self.loopButton.setToolTip("Loop automatically through steps")
+ self.loopButton.setCheckable(True)
+ self.loopButton.setVisible(self.sequenceOption is not False)
+ self.updateButton = QtGui.QPushButton("&Update", self.centralWidget())
+ if self.dumpcells:
+ self.quitButton = QtGui.QPushButton("&Save", self.centralWidget())
+ self.connect(self.quitButton,
+ QtCore.SIGNAL('clicked(bool)'),
+ self.saveAndExport)
+ else:
+ self.quitButton = QtGui.QPushButton("&Quit", self.centralWidget())
+ self.connect(self.quitButton,
+ QtCore.SIGNAL('clicked(bool)'),
+ self.close)
+ buttonLayout.setColumnStretch(0, 1)
+ if self.sequenceOption:
+ sequenceLayout = QtGui.QHBoxLayout()
+ sequenceLayout.setMargin(5)
+ sequenceLayout.addWidget(self.cb_loop_int)
+ sequenceLayout.addWidget(self.cb_loop_sequence)
+ buttonLayout.addLayout(sequenceLayout, 0, 0, QtCore.Qt.AlignRight)
+ buttonLayout.addWidget(self.cb_auto_update, 0, 1, QtCore.Qt.AlignLeft)
+ buttonLayout.addWidget(self.cb_keep_camera, 0, 2, 1, 2, QtCore.Qt.AlignLeft)
+ if self.sequenceOption:
+ buttonLayout.addWidget(self.loopButton, 1, 1, QtCore.Qt.AlignRight)
+ self.loopButton.setEnabled(False)
+ buttonLayout.addWidget(self.updateButton, 1, 2, QtCore.Qt.AlignRight)
+ buttonLayout.addWidget(self.quitButton, 1, 3, QtCore.Qt.AlignRight)
+ self.connect(self.updateButton,
+ QtCore.SIGNAL('clicked(bool)'),
+ self.updateButtonClick)
+ if self.sequenceOption:
+ self.connect(self.loopButton,
+ QtCore.SIGNAL('clicked(bool)'),
+ self.loopButtonClick)
+ buttonDock.setWidget(buttonWidget)
+ self.addDockWidget(QtCore.Qt.BottomDockWidgetArea, buttonDock)
+ self.controlDocks["__buttons__"] = buttonDock
+
+ self.saveAllAct = QtGui.QAction("S&ave Combined", self,
+ shortcut=QtGui.QKeySequence.SelectAll,
+ statusTip="Save combined images to disk",
+ triggered=self.saveAllEvent)
+ self.saveAct = QtGui.QAction("&Save Each", self,
+ shortcut=QtGui.QKeySequence.Save,
+ statusTip="Save separate images to disk",
+ triggered=self.saveEventAction)
+ self.showBuilderAct = QtGui.QAction("VisTrails Main Window", self,
+ statusTip="Show VisTrails Main Window",
+ triggered=self.showBuilderWindow)
+ self.createMenus()
+ self.lastExportPath = ''
+
+ def createMenus(self):
+ self.fileMenu = self.menuBar().addMenu("&File")
+ self.fileMenu.addAction(self.saveAct)
+ self.fileMenu.addAction(self.saveAllAct)
+
+ self.viewMenu = self.menuBar().addMenu("&View")
+ self.viewMenu.addAction(self.editingModeAct)
+
+ self.windowMenu = self.menuBar().addMenu("&Window")
+ self.windowMenu.addAction(self.showBuilderAct)
+
+ def runAndGetCellEvents(self, useDefaultValues=False):
+ spreadsheetController.setEchoMode(True)
+ #will run to get Spreadsheet Cell events
+ cellEvents = []
+ errors = []
+ try:
+ (res, errors) = self.run(useDefaultValues)
+ if res:
+ cellEvents = spreadsheetController.getEchoCellEvents()
+ except Exception, e:
+ import traceback
+ print "Executing pipeline failed:", str(e), traceback.format_exc()
+ finally:
+ spreadsheetController.setEchoMode(False)
+
+ return (cellEvents, errors)
+
+ def updateCells(self, info=None):
+ # check if we should create a sequence
+ if self.cb_loop_sequence.isChecked():
+ return self.updateCellsLoop(info)
+ self.is_executing = True
+ (cellEvents, errors) = self.runAndGetCellEvents()
+ self.is_executing = False
+ if len(cellEvents) != self.numberOfCells:
+ raise RuntimeError(
+ "The number of cells has changed (unexpectedly) "
+ "(%d vs. %d)!\n"
+ "Pipeline results: %s" % (len(cellEvents),
+ self.numberOfCells,
+ errors))
+ #self.SaveCamera()
+ for i in xrange(self.numberOfCells):
+ camera = []
+ if (hasattr(self.cellWidgets[i],"getRendererList") and
+ self.cb_keep_camera.isChecked()):
+ for ren in self.cellWidgets[i].getRendererList():
+ camera.append(ren.GetActiveCamera())
+ self.cellWidgets[i].updateContents(cellEvents[i].inputPorts, camera)
+ #self.cellWidgets[i].updateContents(cellEvents[i].inputPorts)
+ else:
+ self.cellWidgets[i].updateContents(cellEvents[i].inputPorts)
+
+ def updateCellsLoop(self, info=None):
+ """ Run workflow for each step in the loop sequence and collect results.
+ """
+ interactive = self.cb_loop_int.isChecked()
+ slider = self.sequenceOption.value
+ if info and info[1][0] == slider:
+ # User is moving the slider, so we use the existing result
+ if interactive:
+ if slider.value() < len(self.steps):
+ self.updateRenderedCells(slider.value())
+ else:
+ for i in xrange(self.numberOfCells):
+ self.cellWidgets[i].setPlayerFrame(slider.value())
+ return
+
+ if not interactive:
+ for i in xrange(self.numberOfCells):
+ self.cellWidgets[i].clearHistory()
+
+ self.is_executing = True
+ self.steps = []
+ old_value = slider.value()
+ value = slider.minimum()
+ slider.setValue(value)
+
+ while True:
+ (cellEvents, errors) = self.runAndGetCellEvents()
+ if len(cellEvents) != self.numberOfCells:
+ raise RuntimeError(
+ "The number of cells has changed (unexpectedly) "
+ "(%d vs. %d)!\n"
+ "Pipeline results: %s" % (len(cellEvents),
+ self.numberOfCells,
+ errors))
+ if interactive:
+ self.steps.append([])
+ else:
+ self.steps = [[]]
+ for i in xrange(self.numberOfCells):
+ self.steps[-1].append(cellEvents[i].inputPorts)
+
+ # show the result
+ self.updateRenderedCells(value if interactive else 0)
+ self.is_executing = True
+
+ if value >= slider.maximum():
+ break
+ value += slider.singleStep()
+ slider.setValue(value)
+ self.is_executing = False
+ slider.setValue(old_value)
+ self.loopButton.setEnabled(True)
+
+ def updateRenderedCells(self, value):
+ """ Show the cell specified by slider info
+ """
+ self.is_executing = True
+ for i in xrange(self.numberOfCells):
+ camera = []
+ if (hasattr(self.cellWidgets[i],"getRendererList") and
+ self.cb_keep_camera.isChecked()):
+ for ren in self.cellWidgets[i].getRendererList():
+ camera.append(ren.GetActiveCamera())
+ self.cellWidgets[i].updateContents(self.steps[value][i], camera)
+ else:
+ self.cellWidgets[i].updateContents(self.steps[value][i])
+ self.is_executing = False
+
+ def updateButtonClick(self):
+ self.updateButton.setEnabled(False)
+ try:
+ self.updateCells()
+ finally:
+ self.updateButton.setEnabled(True)
+
+ def loopButtonClick(self, toggled):
+ self.updateButton.setEnabled(not toggled)
+ self.cb_loop_int.setEnabled(not toggled)
+ self.cb_loop_sequence.setEnabled(not toggled)
+ self.cb_auto_update.setEnabled(not toggled)
+ if self.cb_loop_int.isChecked():
+ if toggled:
+ if self.isLooping:
+ self.killTimer(self.isLooping)
+ self.isLooping = self.startTimer(200)
+ elif self.isLooping:
+ self.killTimer(self.isLooping)
+ self.isLooping = None
+ else:
+ for cell in self.cellWidgets:
+ if toggled:
+ cell.startPlayer()
+ else:
+ cell.stopPlayer()
+
+
+ def timerEvent(self, event):
+ if self.steps:
+ stepper = self.sequenceOption.value
+ if stepper.value() == stepper.maximum():
+ stepper.setValue(stepper.minimum())
+ else:
+ stepper.setValue(stepper.value() + stepper.singleStep())
+ if stepper.value() >= len(self.steps):
+ self.loopButton.setChecked(False)
+ return
+
+ for i in xrange(self.numberOfCells):
+ self.cellWidgets[i].setAnimationEnabled(False)
+
+ self.updateRenderedCells(stepper.value())
+
+ for i in xrange(self.numberOfCells):
+ self.cellWidgets[i].setAnimationEnabled(True)
+
+ def toggleEditingMode(self):
+ if len(self.controlDocks) > 0:
+ for dock in self.controlDocks.itervalues():
+ dock.toggleTitleBar()
+ self.editing = not self.editing
+ if not self.editing:
+ self.saveSettings()
+
+ def saveSettings(self):
+ layout = self.saveState().toPercentEncoding()
+ geom = self.saveGeometry().toPercentEncoding()
+
+ self.currentMashup.layout = layout
+ self.currentMashup.geometry = geom
+
+ self.controller.setChanged(True)
+
+ #self.controller.writeMashuptrail()
+
+ def closeEvent(self, event):
+ self.saveSettings()
+ self.appWasClosed.emit(self)
+ event.accept()
+
+ def auto_update_changed(self, state):
+ if state == QtCore.Qt.Unchecked:
+ self.updateButton.setEnabled(True)
+ self.cb_loop_int.setEnabled(True)
+ self.cb_loop_sequence.setEnabled(True)
+ self.loopButton.setEnabled(True)
+ if self.cb_loop_sequence.isChecked() and not self.cb_loop_int.isChecked():
+ for i in xrange(self.numberOfCells):
+ cell = self.cellWidgets[i]
+ cell._player.hide()
+ cell.show()
+
+ elif state == QtCore.Qt.Checked:
+ self.updateButton.setEnabled(False)
+ self.cb_loop_int.setEnabled(False)
+ self.cb_loop_sequence.setEnabled(False)
+ self.loopButton.setEnabled(False)
+ if self.cb_loop_sequence.isChecked() and not self.cb_loop_int.isChecked():
+ for i in xrange(self.numberOfCells):
+ cell = self.cellWidgets[i]
+ cell._player.setParent(cell.parent())
+ cell._player.setGeometry(cell.geometry())
+ self.cellWidgets[i].setPlayerFrame(self.sequenceOption.value.value())
+ cell._player.raise_()
+ cell._player.show()
+ cell.hide()
+
+ def loop_int_changed(self, state):
+ self.loopButton.setEnabled(False)
+
+ def saveAll(self):
+ for w in self.widgets:
+ w.saveAll(self.dumpcells)
+
+ def saveEach(self):
+ for w in self.widgets:
+ w.saveEach(self.dumpcells, self.frameNo)
+
+ def saveEventAction(self, checked):
+ self.saveEvent()
+
+ def saveEvent(self, folder=None):
+ if folder == None:
+ folder = QtGui.QFileDialog.getExistingDirectory(self,
+ "Save images to...",
+ self.lastExportPath,
+ QtGui.QFileDialog.ShowDirsOnly)
+ if folder:
+ self.dumpcells = str(folder)
+ self.saveEach()
+ self.lastExportPath = str(folder)
+
+ def saveAllEvent(self, folder=None):
+ if folder == None:
+ folder = QtGui.QFileDialog.getExistingDirectory(self,
+ "Save images to...",
+ self.lastExportPath,
+ QtGui.QFileDialog.ShowDirsOnly)
+ if folder:
+ self.dumpcells = str(folder)
+ self.saveAll()
+ self.lastExportPath
+
+ def saveAndExport(self, clicked=True):
+ self.saveAll()
+
+ def initCells(self, cellEvents):
+ cellLayout = QtGui.QHBoxLayout()
+ self.mainLayout.addLayout(cellLayout, self.numberOfCells * 2)
+ self.cellWidgets = []
+ vtkCells = []
+ for event in cellEvents:
+ cellWidget = event.cellType(self.centralWidget())
+ if event.cellType.__name__ == 'QVTKWidget':
+ vtkCells.append(cellWidget)
+ cellWidget.updateContents(event.inputPorts)
+ cellWidget.show()
+ cellWidget.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ cellWidget.setMinimumSize(300, 100)
+ cellLayout.addWidget(cellWidget)
+ self.cellWidgets.append(cellWidget)
+ def getSelectedCellWidgets():
+ return vtkCells
+ for cellWidget in self.vtkCells:
+ cellWidget.getSelectedCellWidgets = getSelectedCellWidgets
+
+ def initControls(self):
+ if len(self.currentMashup.alias_list) == 0:
+ return
+
+ #Constructing alias controls
+ self.controlDocks = {}
+ self.cellControls = {}
+ self.toolbuttons = {}
+
+ row = 0
+ for alias in self.currentMashup.alias_list:
+ dock = QCustomDockWidget(alias.name, #"Control for '%s'" % aliasName,
+ self)
+ vtparam = self.controller.getVistrailParam(alias)
+
+ if alias.component.widget == 'slider':
+ aliasWidget = QAliasSliderWidget(alias, vtparam, dock)
+ # enables looping of
+ if alias.component.seq:
+ self.sequenceOption = aliasWidget
+
+
+ elif alias.component.widget == 'numericstepper':
+ aliasWidget = QAliasNumericStepperWidget(alias, vtparam, dock)
+ else:
+ aliasWidget = QDropDownWidget(alias, vtparam, dock)
+
+ aliasWidget.setSizePolicy(QtGui.QSizePolicy.Preferred,
+ QtGui.QSizePolicy.Maximum)
+ self.connect(aliasWidget,
+ QtCore.SIGNAL("contentsChanged"),
+ self.widget_changed)
+
+ dock.setWidget(aliasWidget)
+ self.addDockWidget(QtCore.Qt.RightDockWidgetArea, dock)
+ self.controlDocks[alias.name] = dock
+ self.cellControls[alias.name] = aliasWidget.value
+ row += 1
+ self.aliasWidgets[alias.name] = aliasWidget
+
+ # Added a stretch space
+ stretchDock = QCustomDockWidget('Stretch Space', self)
+ stretch = QtGui.QWidget()
+ stretch.setLayout(QtGui.QVBoxLayout())
+ stretch.layout().addStretch()
+ stretchDock.setWidget(stretch)
+ self.addDockWidget(QtCore.Qt.RightDockWidgetArea, stretchDock)
+ self.controlDocks["_stretch_"] = stretchDock
+
+ def widget_changed(self, info):
+ if self.cb_auto_update.isChecked() and not self.is_executing:
+ self.updateCells(info)
+
+
+ def run(self, useDefaultValues=False):
+
+ # Building the list of parameter values
+ params = []
+ if useDefaultValues:
+ for alias in self.currentMashup.alias_list:
+ params.append((alias.component.vttype, alias.component.vtid,
+ alias.component.val))
+ else:
+ for (aliasName, edit) in self.cellControls.iteritems():
+ alias = self.currentMashup.getAliasByName(aliasName)
+ if hasattr(edit, 'contents'):
+ val = str(edit.contents())
+ else:
+ val =str(edit.text())
+ params.append((alias.component.vttype, alias.component.vtid,
+ val))
+ results = self.controller.execute(params)[0]
+ result = results[0]
+ (objs, errors, executed) = (result.objects, result.errors,
+ result.executed)
+ if len(errors) > 0:
+ print '=== ERROR EXECUTING PIPELINE ==='
+ print errors
+ return (False, errors)
+ return (True, [])
+
+ def showBuilderWindow(self):
+ from vistrails.gui.vistrails_window import _app
+ _app.show()
+
+class QCustomDockWidget(QtGui.QDockWidget):
+ def __init__(self, title, parent=None):
+ QtGui.QDockWidget.__init__(self, title, parent)
+ self.setObjectName(title)
+ self.setFeatures(QtGui.QDockWidget.DockWidgetClosable |
+ QtGui.QDockWidget.DockWidgetMovable)
+ self.emptyTitleBar = QtGui.QWidget()
+ self.titleBarVisible = True
+ self.hideTitleBar()
+
+ def showTitleBar(self):
+ self.titleBarVisible = True
+ self.setFeatures(QtGui.QDockWidget.DockWidgetClosable |
+ QtGui.QDockWidget.DockWidgetMovable)
+ self.setMaximumHeight(524287)
+ self.setTitleBarWidget(None)
+
+ def hideTitleBar(self):
+ self.titleBarVisible = False
+ self.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)
+ self.setTitleBarWidget(self.emptyTitleBar)
+
+ def toggleTitleBar(self):
+ if self.titleBarVisible:
+ self.hideTitleBar()
+ else:
+ self.showTitleBar()
+
+################################################################################
+# Testing
+
+
+class TestMashupApp(TestVisTrailsGUI):
+
+ def test_load_mashup(self):
+ import vistrails.core.system
+ filename = (vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/spx_loop.vt')
+ view = vistrails.api.open_vistrail_from_file(filename)
+ id = "d5026457-de6c-11e2-b074-3c07543dba07"
+ mashup = view.get_mashup_from_mashuptrail_id(id, "loop")
+ view.open_mashup(mashup)
+ mashup = view.get_mashup_from_mashuptrail_id(id, "no loop")
+ view.open_mashup(mashup)
diff --git a/vistrails/gui/mashups/mashup_view.py b/vistrails/gui/mashups/mashup_view.py
new file mode 100644
index 0000000..29a3367
--- /dev/null
+++ b/vistrails/gui/mashups/mashup_view.py
@@ -0,0 +1,401 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+from PyQt4.QtCore import pyqtSignal, pyqtSlot
+from vistrails.core.data_structures.bijectivedict import Bidict
+from vistrails.gui.base_view import BaseView
+from vistrails.gui.mashups.mashups_manager import MashupsManager
+from vistrails.gui.mashups.alias_list import QAliasListPanel
+from vistrails.gui.utils import show_question, YES_BUTTON, NO_BUTTON, CANCEL_BUTTON
+
+class QMashupView(QtGui.QMainWindow, BaseView):
+ #signals
+ #mashupChanged = pyqtSignal()
+
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ QtGui.QMainWindow.__init__(self, parent, f)
+ BaseView.__init__(self)
+ self.set_title("Mashup")
+
+ self.controller = None
+ self.mshpController = None
+ self.createActions()
+ #Setting up a toolbar
+ self.createToolBar()
+ self.tab_to_stack_idx = {}
+ self.button_to_tab_idx = Bidict()
+ widget = QtGui.QWidget(self)
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(0)
+ layout.setSpacing(0)
+ self.tabBar = QtGui.QTabBar(self)
+ self.tabBar.setDocumentMode(True)
+ self.tabBar.setTabsClosable(False)
+ self.tabBar.setExpanding(False)
+ self.tabBar.currentChanged.connect(self.switchTab)
+ self.stack = QtGui.QStackedWidget(self)
+ layout.addWidget(self.tabBar)
+ layout.addWidget(self.stack)
+ widget.setLayout(layout)
+ self.setCentralWidget(widget)
+ self.createAliasPanelTab()
+ widget.setVisible(True)
+ #self.createPipelineTab()
+ self.setWindowTitle("Mashup Builder")
+ self.vtversion = -1
+ self.manager = MashupsManager.getInstance()
+
+ def set_default_layout(self):
+ from vistrails.gui.mashups.mashups_inspector import QMashupsInspector
+ from vistrails.gui.mashups.alias_parameter_view import QAliasParameterView
+ self.set_palette_layout(
+ {QtCore.Qt.LeftDockWidgetArea: QMashupsInspector,
+ QtCore.Qt.RightDockWidgetArea: QAliasParameterView,
+ })
+
+ def set_action_links(self):
+ self.action_links = \
+ {
+ }
+
+ def set_action_defaults(self):
+ self.action_defaults['execute'] = [('setEnabled', False, False)]
+
+ def set_controller(self, controller):
+ """set_controller(controller:VistrailController) -> None
+ This will set vistrail controller"""
+ if controller == self.controller:
+ return
+# if self.controller is not None:
+# self.disconnect(self.controller,
+# QtCore.SIGNAL('versionWasChanged'),
+# self.versionChanged)
+ self.controller = controller
+# if self.controller:
+# self.connect(self.controller,
+# QtCore.SIGNAL('versionWasChanged'),
+# self.versionChanged)
+ #print " *** mashup view set vtController: ", controller
+
+ def versionChanged(self, version):
+ window = self.window()
+ self.vtversion = version
+ if self.vtversion > -1:
+ window.qactions['mashup'].setEnabled(True)
+ else:
+ window.qactions['mashup'].setEnabled(False)
+ #print " *** mashup view versionChanged ", self.vtversion
+
+ def controllerChanged(self, controller):
+ if controller is self.controller:
+ return
+ from vistrails.gui.vistrails_window import _app
+ self.set_controller(controller)
+ self.versionChanged(self.controller.current_version)
+ if _app.get_current_tab() == self:
+ self.updateView()
+
+ def updateView(self):
+ from vistrails.gui.vistrails_window import _app
+ if self.vtversion > 0:
+ if self.mshpController is not None:
+ try:
+ self.mshpController.versionChanged.disconnect(self.mshpVersionChanged)
+ self.mshpController.stateChanged.disconnect(self.mshpStateChanged)
+ if self.mshpController.vtController is not None:
+ self.disconnect(self.mshpController.vtController,
+ QtCore.SIGNAL('vistrailChanged()'),
+ self.mshpControllerVistrailChanged)
+ except Exception, e:
+ print str(e)
+ self.controller.flush_delayed_actions()
+ self.vtversion = self.controller.current_version
+ self.mshpController = self.manager.createMashupController(self.controller,
+ self.vtversion)
+ #self.pipelineTab.set_controller(self.mshpController.vtController)
+ #self.pipelineTab.set_to_current()
+ self.mshpController.vtController.change_selected_version(self.vtversion)
+ self.connect(self.mshpController.vtController,
+ QtCore.SIGNAL('vistrailChanged()'),
+ self.mshpControllerVistrailChanged)
+ self.mshpController.versionChanged.connect(self.mshpVersionChanged)
+ self.mshpController.stateChanged.connect(self.mshpStateChanged)
+ self.aliasPanel.updateController(self.mshpController)
+ self.clearPreviewTabs()
+ _app.notify('mshpcontroller_changed', self.mshpController)
+
+ def createActions(self):
+ self.saveAction = QtGui.QAction("Tag", self,
+ triggered=self.saveTriggered)
+ self.saveAction.setToolTip("Tag current mashup")
+ self.saveAction.setEnabled(False)
+ self.previewAction = QtGui.QAction("Preview", self,
+ triggered=self.previewTriggered,
+ checkable=False)
+ self.previewAction.setToolTip("Preview current mashup")
+
+ def createToolBar(self):
+ self.toolbar = QtGui.QToolBar(self)
+
+ self.toolbar.addAction(self.previewAction)
+ self.toolbar.addSeparator()
+ self.toolbar.addAction(self.saveAction)
+ self.addToolBar(self.toolbar)
+
+ def createAliasPanelTab(self):
+ self.aliasPanel = QAliasListPanel(parent=self)
+
+ idx = self.stack.addWidget(self.aliasPanel)
+ self.aliasPanel.set_index(idx)
+ tab_idx = self.tabBar.addTab("Aliases")
+ self.aliasPanel.set_tab_idx(tab_idx)
+ self.tab_to_stack_idx[tab_idx] = idx
+
+ def createPreviewTab(self, version):
+
+ previewTab = QMashupViewTab(self.mshpController, version)
+# self.refreshButton = QtGui.QPushButton("Refresh", self)
+# self.refreshButton.setFlat(True)
+# self.refreshButton.setEnabled(False)
+# self.refreshButton.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed,
+# QtGui.QSizePolicy.Fixed))
+ previewApp = self.manager.createMashupApp(self.controller,
+ self.mshpController.mshptrail,
+ version)
+ previewApp.appWasClosed.connect(self.previewTabWasClosed)
+
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(0)
+ layout.setSpacing(5)
+ #layout.addWidget(self.refreshButton, QtCore.Qt.AlignLeft)
+ layout.addWidget(previewApp)
+ previewTab.setLayout(layout)
+ idx = self.stack.addWidget(previewTab)
+ previewTab.set_index(idx)
+ tab_idx = self.tabBar.addTab("Preview: %s"%self.mshpController.getMashupName(version))
+ previewTab.set_tab_idx(tab_idx)
+ self.tab_to_stack_idx[tab_idx] = idx
+ closeButton = QMashupViewCloseButton(self.tabBar)
+ closeSide = self.tabBar.style().styleHint(
+ QtGui.QStyle.SH_TabBar_CloseButtonPosition,
+ None, self.tabBar)
+ closeButton.clicked.connect(self.closePreviewTab)
+ self.tabBar.setTabButton(tab_idx, closeSide, closeButton)
+ self.button_to_tab_idx[closeButton] = tab_idx
+ self.tabBar.setCurrentIndex(tab_idx)
+
+ @pyqtSlot()
+ def closePreviewTab(self):
+ closeButton = self.sender()
+ tab_idx = self.button_to_tab_idx[closeButton]
+ self.tabBar.removeTab(tab_idx)
+ stack_idx = self.tab_to_stack_idx[tab_idx]
+ if stack_idx >= 0:
+ self.stack.removeWidget(self.stack.widget(stack_idx))
+ del self.button_to_tab_idx[closeButton]
+ self.updateIndexes(tab_idx, stack_idx)
+
+ def previewTabWasClosed(self, previewApp):
+ previewTab = previewApp.parent()
+ tab_idx = previewTab.get_tab_idx()
+ stack_idx = self.tab_to_stack_idx[tab_idx]
+ if previewTab == self.stack.widget(stack_idx):
+ #this means the quit button was pressed
+ closeButton = self.button_to_tab_idx.inverse[tab_idx]
+ self.tabBar.removeTab(tab_idx)
+ self.stack.removeWidget(self.stack.widget(stack_idx))
+ del self.button_to_tab_idx[closeButton]
+ self.updateIndexes(tab_idx, stack_idx)
+
+ def updateIndexes(self, rm_tab_idx, rm_stack_idx):
+ for (b,tab_idx) in self.button_to_tab_idx.iteritems():
+ if tab_idx > rm_tab_idx:
+ self.button_to_tab_idx[b] -= 1
+ for idx in range(self.stack.count()):
+ if idx >= rm_stack_idx:
+ view = self.stack.widget(idx)
+ view.set_index(idx)
+ view.set_tab_idx(view.tab_idx-1)
+
+ def clearPreviewTabs(self):
+ tab_idx = self.tabBar.count()-1
+ while self.tabBar.count() > 1:
+ idx = self.tab_to_stack_idx[tab_idx]
+ if isinstance(self.stack.widget(idx), QMashupViewTab):
+ self.tabBar.removeTab(tab_idx)
+ if idx >= 0:
+ self.stack.removeWidget(self.stack.widget(idx))
+ tab_idx -= 1
+
+ @pyqtSlot(int)
+ def switchTab(self, index):
+ try:
+ self.stack.setCurrentIndex(self.tab_to_stack_idx[index])
+ except KeyError:
+ pass
+
+ def previewTriggered(self):
+ self.createPreviewTab(self.mshpController.currentVersion)
+
+ def saveTriggered(self):
+ (pid, pname) = self.mshpController.findFirstTaggedParent(self.mshpController.currentVersion)
+ if pid >= 1:
+ res = show_question("VisTrails::Mashups",
+ """You've decided to keep a modified version of '%s'.
+Would you like to update it (this will move the tag to the current version)?
+Click on No to create a new tag.""" %pname,
+ [CANCEL_BUTTON, YES_BUTTON, NO_BUTTON], 0)
+ if res == YES_BUTTON:
+ #move tag
+ self.mshpController.moveTag(pid,
+ self.mshpController.currentVersion,
+ pname)
+ elif res == NO_BUTTON:
+ # show createNewtag dialog
+ tag_exists = True
+ ok = True
+ while ok and tag_exists:
+ (text, ok) = QtGui.QInputDialog.getText(self, "VisTrails::Mashups",
+ "Enter a new tag:",
+ text="")
+ if ok and text:
+ tag = str(text)
+ if self.mshpController.updateCurrentTag(tag):
+ tag_exists = False
+
+ def mshpControllerVistrailChanged(self):
+ #print "*** vistrailChanged mashup view ", self.mshpController.vtController.current_version
+ pipeline = self.mshpController.vtController.current_pipeline
+ self.mshpController.updateAliasesFromPipeline(pipeline)
+
+ def mshpVersionChanged(self, versionId):
+ from vistrails.gui.vistrails_window import _app
+ #print "*** mshpVersionChanged ", versionId
+ self.aliasPanel.updateVersion(versionId)
+ if not self.mshpController.versionHasTag(versionId):
+ self.saveAction.setEnabled(True)
+ else:
+ self.saveAction.setEnabled(False)
+ _app.notify('mshpversion_changed', versionId)
+
+ def mshpStateChanged(self):
+ for idx in range(self.stack.count()):
+ view = self.stack.widget(idx)
+ if isinstance(view, QMashupViewTab):
+ tab_idx = view.tab_idx
+ self.tabBar.setTabText(tab_idx,
+ "Preview: %s"%self.mshpController.getMashupName(view.version))
+
+ def aliasChanged(self, param):
+ #print "mashupView aliasChanged", param
+ self.mshpController.updateAliasFromParam(param)
+
+###############################################################################
+
+class QMashupViewTab(QtGui.QWidget, BaseView):
+ def __init__(self, mshpController, version, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ BaseView.__init__(self)
+ self.mshpController = mshpController
+ self.version = version
+
+ def set_default_layout(self):
+ from vistrails.gui.mashups.mashups_inspector import QMashupsInspector
+ from vistrails.gui.mashups.alias_parameter_view import QAliasParameterView
+ self.set_palette_layout(
+ {QtCore.Qt.LeftDockWidgetArea: QMashupsInspector,
+ QtCore.Qt.RightDockWidgetArea: QAliasParameterView,
+ })
+
+ def set_action_links(self):
+ self.action_links = \
+ {
+ }
+
+ def set_action_defaults(self):
+ self.action_defaults = \
+ {#'execute' : [('setEnabled', False, False)],
+ }
+
+###############################################################################
+
+class QMashupViewCloseButton(QtGui.QAbstractButton):
+ def __init__(self, parent):
+ QtGui.QAbstractButton.__init__(self)
+ self.setFocusPolicy(QtCore.Qt.NoFocus)
+ self.setCursor(QtCore.Qt.ArrowCursor)
+ self.setToolTip("Close Tab")
+ self.resize(self.sizeHint())
+
+ def sizeHint(self):
+ self.ensurePolished()
+ width = self.style().pixelMetric(QtGui.QStyle.PM_TabCloseIndicatorWidth,
+ None, self)
+ height = self.style().pixelMetric(QtGui.QStyle.PM_TabCloseIndicatorHeight,
+ None, self)
+ return QtCore.QSize(width, height)
+
+ def enterEvent(self, event):
+ if self.isEnabled():
+ self.update()
+ QtGui.QAbstractButton.enterEvent(self, event)
+
+ def leaveEvent(self, event):
+ if self.isEnabled():
+ self.update()
+ QtGui.QAbstractButton.leaveEvent(self, event)
+
+ def paintEvent(self, event):
+ p = QtGui.QPainter(self)
+ opt = QtGui.QStyleOption()
+ opt.init(self)
+ opt.state |= QtGui.QStyle.State_AutoRaise
+ if (self.isEnabled() and self.underMouse() and
+ not self.isChecked() and not self.isDown()):
+ opt.state |= QtGui.QStyle.State_Raised
+ if self.isChecked():
+ opt.state |= QtGui.QStyle.State_On
+ if self.isDown():
+ opt.state |= QtGui.QStyle.State_Sunken
+ tb = self.parent()
+ if isinstance(tb, QtGui.QTabBar):
+ index = tb.currentIndex()
+ position = self.style().styleHint(QtGui.QStyle.SH_TabBar_CloseButtonPosition,
+ None, tb)
+ if tb.tabButton(index, position) == self:
+ opt.state |= QtGui.QStyle.State_Selected
+ self.style().drawPrimitive(QtGui.QStyle.PE_IndicatorTabClose, opt, p,
+ self)
+
diff --git a/vistrails/gui/mashups/mashups_inspector.py b/vistrails/gui/mashups/mashups_inspector.py
new file mode 100644
index 0000000..2590210
--- /dev/null
+++ b/vistrails/gui/mashups/mashups_inspector.py
@@ -0,0 +1,408 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+from PyQt4.QtCore import pyqtSignal, pyqtSlot
+import vistrails.core.system
+from vistrails.gui.common_widgets import QDockPushButton
+from vistrails.gui.mashups.mashups_manager import MashupsManager
+from vistrails.gui.utils import show_warning
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+
+class QMashupsInspector(QtGui.QFrame, QVistrailsPaletteInterface):
+ """
+ QMashupsInspector is a widget with tabs showing properties of the selected
+ mashuptrail. It contains a list of tagged mashups, and when a mashup is
+ selected, it shows the list of aliases in the mashup.
+
+ """
+ #signals
+ mashupChanged = pyqtSignal()
+ def __init__(self, controller=None, parent=None):
+ """ QMashupsInspector(controller: MashupController,
+ parent: QWidget) -> QMashupsInspector
+
+ """
+ QtGui.QFrame.__init__(self, parent)
+ QVistrailsPaletteInterface.__init__(self)
+ #print "****** Inspector INIT"
+ self.set_title("Mashups Inspector")
+ self.setFrameStyle(QtGui.QFrame.Panel|QtGui.QFrame.Sunken)
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+
+ #ok, this will store the original vistrail controller
+ self.controller = controller
+ self.mshpController = None #MashupController
+ self.manager = MashupsManager.getInstance()
+
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(2)
+ layout.setSpacing(3)
+ self.workflowLabel = QtGui.QLabel("Workflow: ")
+ layout.addWidget(self.workflowLabel)
+ self.mashupsList = QMashupsListPanel(parent=self)
+ listLabel = QtGui.QLabel("Available Mashups:")
+ layout.addWidget(listLabel)
+ layout.addWidget(self.mashupsList)
+
+ self.mashupInspector = QMashupProp(parent=self)
+ inspector_group = QtGui.QGroupBox("Mashup properties")
+ g_layout = QtGui.QVBoxLayout()
+ g_layout.setMargin(1)
+ g_layout.setSpacing(3)
+ g_layout.addWidget(self.mashupInspector)
+ inspector_group.setLayout(g_layout)
+ layout.addWidget(inspector_group)
+ self.setLayout(layout)
+
+ def updateVistrailController(self, controller):
+ self.controller = controller
+ #print " *** Mashup Inspector: controller changed ", controller
+
+ def updateVistrailVersion(self, version):
+ if self.controller:
+ self.vt_version = version
+
+ #print " *** Mashup Inspector: version changed ", version
+
+ def updateMshpController(self, mshpController):
+ #print " **** updateMshpController", mshpController
+ if (self.mshpController is not None and
+ self.mshpController != mshpController):
+ self.mshpController.stateChanged.disconnect(self.stateChanged)
+ self.mshpController = mshpController
+ self.workflowLabel.setText(
+ "Workflow: <b>%s</b>"%self.mshpController.getVistrailWorkflowTag())
+ self.mshpController.stateChanged.connect(self.stateChanged)
+ self.mashupInspector.updateController(mshpController)
+ self.mashupsList.updateController(mshpController)
+
+ def updateMshpVersion(self, version):
+ pass
+ #print "updateMshpVersion", version
+
+ def stateChanged(self):
+ versionId = self.mshpController.currentVersion
+ self.mashupInspector.updateVersion(versionId)
+ self.mashupsList.stateChanged()
+
+################################################################################
+
+class QMashupProp(QtGui.QWidget):
+ def __init__(self, controller=None, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.controller = controller
+ self.versionNumber = -1
+ vLayout = QtGui.QVBoxLayout()
+ vLayout.setMargin(0)
+ vLayout.setSpacing(5)
+ self.setLayout(vLayout)
+ gLayout = QtGui.QGridLayout()
+ gLayout.setMargin(0)
+ gLayout.setSpacing(5)
+ gLayout.setColumnMinimumWidth(1,5)
+ gLayout.setRowMinimumHeight(0,24)
+ gLayout.setRowMinimumHeight(1,24)
+ gLayout.setRowMinimumHeight(2,24)
+ gLayout.setRowMinimumHeight(3,24)
+ vLayout.addLayout(gLayout)
+
+ #vtVersionLabel = QtGui.QLabel('Workflow:', self)
+ #gLayout.addWidget(vtVersionLabel, 0, 0, 1, 1)
+
+ #self.vtVersionEdit = QtGui.QLabel('', self)
+ #gLayout.addWidget(self.vtVersionEdit, 0, 2, 1, 1)
+
+ tagLabel = QtGui.QLabel('Mashup Tag:', self)
+ gLayout.addWidget(tagLabel, 0, 0, 1, 1)
+
+ editLayout = QtGui.QHBoxLayout()
+ editLayout.setMargin(0)
+ editLayout.setSpacing(2)
+ self.tagEdit = QtGui.QLineEdit()
+ tagLabel.setBuddy(self.tagEdit)
+ editLayout.addWidget(self.tagEdit)
+ self.tagEdit.setEnabled(False)
+
+ self.tagReset = QtGui.QToolButton(self)
+ self.tagReset.setIcon(QtGui.QIcon(
+ self.style().standardPixmap(QtGui.QStyle.SP_DialogCloseButton)))
+ self.tagReset.setIconSize(QtCore.QSize(12,12))
+ self.tagReset.setAutoRaise(True)
+ self.tagReset.setEnabled(False)
+ editLayout.addWidget(self.tagReset)
+
+ gLayout.addLayout(editLayout, 0, 2, 1, 1)
+
+ userLabel = QtGui.QLabel('User:', self)
+ gLayout.addWidget(userLabel, 1, 0, 1, 1)
+
+ self.userEdit = QtGui.QLabel('', self)
+ gLayout.addWidget(self.userEdit, 1, 2, 1, 1)
+
+ dateLabel = QtGui.QLabel('Date:', self)
+ gLayout.addWidget(dateLabel, 2, 0, 1, 1)
+
+ self.dateEdit = QtGui.QLabel('', self)
+ gLayout.addWidget(self.dateEdit, 2, 2, 1, 1)
+
+ self.btnExport = QDockPushButton("Export...")
+ gLayout.addWidget(self.btnExport, 3,0,1,3, QtCore.Qt.AlignHCenter)
+
+ vLayout.addStretch()
+
+ self.connect(self.tagEdit, QtCore.SIGNAL('editingFinished()'),
+ self.tagFinished)
+ self.connect(self.tagEdit, QtCore.SIGNAL('textChanged(QString)'),
+ self.tagChanged)
+ self.connect(self.tagReset, QtCore.SIGNAL('clicked()'),
+ self.tagCleared)
+ self.connect(self.btnExport, QtCore.SIGNAL("clicked()"),
+ self.exportMashupGUI)
+
+ def updateController(self, mshpController):
+ self.controller = mshpController
+
+ #print "QMashupProp.updateController ", self.controller, self.controller.currentVersion
+ if self.controller and self.controller.currentVersion > -1:
+ self.versionNumber = self.controller.currentVersion
+ self.tagEdit.setText(self.controller.mshptrail.getTagForActionId(
+ self.controller.currentVersion))
+ self.tagEdit.setEnabled(True)
+ action = self.controller.mshptrail.actionMap[self.controller.currentVersion]
+ self.userEdit.setText(action.user)
+ self.dateEdit.setText(action.date)
+ #self.vtEdit.setText(self.controller.getVistrailName())
+ #self.vtVersionEdit.setText(self.controller.getVistrailWorkflowTag())
+ return
+ else:
+ self.tagEdit.setEnabled(False)
+ self.tagReset.setEnabled(False)
+ self.tagEdit.setText('')
+ self.userEdit.setText('')
+ self.dateEdit.setText('')
+ #self.vtEdit.setText('')
+ #self.vtVersionEdit.setText('')
+
+ def updateVersion(self, versionNumber):
+ self.versionNumber = versionNumber
+ if self.controller and self.versionNumber > -1:
+ tagtext = self.controller.mshptrail.getTagForActionId(
+ self.versionNumber)
+ #print "updateVersion", versionNumber, tagtext
+ self.tagEdit.setText(tagtext)
+ action = self.controller.mshptrail.actionMap[self.versionNumber]
+ self.userEdit.setText(action.user)
+ self.dateEdit.setText(action.date)
+ #self.vtEdit.setText(self.controller.getVistrailName())
+ #self.vtVersionEdit.setText(self.controller.getVistrailWorkflowTag())
+ else:
+ self.tagEdit.setEnabled(False)
+ self.tagReset.setEnabled(False)
+ self.tagEdit.setText('')
+ self.userEdit.setText('')
+ self.dateEdit.setText('')
+ #self.vtEdit.setText('')
+ #self.vtVersionEdit.setText('')
+
+ def tagFinished(self):
+ """ tagFinished() -> None
+ Update the new tag to mashup
+
+ """
+ if self.controller:
+ name = self.controller.mshptrail.getTagForActionId(self.versionNumber)
+ currentText = str(self.tagEdit.text())
+ if name != currentText:
+ #print "will update current tag", currentText
+ self.controller.updateCurrentTag(currentText)
+
+
+ def tagChanged(self, text):
+ """ tagChanged(text: QString) -> None
+ Update the button state if there is text
+
+ """
+ self.tagReset.setEnabled(text != '')
+
+ def tagCleared(self):
+ """ tagCleared() -> None
+ Remove the tag
+
+ """
+ self.tagEdit.setText('')
+ self.tagFinished()
+
+ def exportMashupGUI(self):
+ if self.controller:
+ dialog = QMashupExportDialog(self)
+ if dialog.exec_() == QtGui.QDialog.Accepted:
+ result = dialog.btnPressed
+ fileName = QtGui.QFileDialog.getSaveFileName(
+ self,
+ "Export Mashup...",
+ vistrails.core.system.vistrails_file_directory(),
+ "VisTrail link files (*.vtl)")
+ if fileName:
+ filename = str(fileName)
+ res = MashupsManager.exportMashup(filename,
+ self.controller.originalController,
+ self.controller.mshptrail,
+ self.controller.currentVersion,
+ result)
+ if not res:
+ show_warning('VisTrails - Exporting Mashup',
+ 'There was an error and the mashup could not be exported.')
+
+################################################################################
+
+class QMashupsListPanel(QtGui.QWidget):
+ def __init__(self, controller=None, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.controller = controller
+ self.mashupsList = QtGui.QListWidget()
+ self.mashupsList.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
+ self.mashupsList.itemSelectionChanged.connect(self.changeSelection)
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(0)
+ layout.setSpacing(5)
+ layout.addWidget(self.mashupsList)
+ self.setLayout(layout)
+
+ def updateController(self, mshpController):
+ self.controller = mshpController
+ self.stateChanged()
+
+ def stateChanged(self):
+ self.mashupsList.itemSelectionChanged.disconnect(self.changeSelection)
+ self.mashupsList.clear()
+ if self.controller:
+ self.tagMap = self.controller.mshptrail.getTagMap()
+ currentTag = self.controller.getCurrentTag()
+ tags = self.tagMap.keys()
+ latestversion = self.controller.mshptrail.getLatestVersion()
+ if not self.controller.versionHasTag(latestversion):
+ item = QMashupListPanelItem("<latest>",
+ latestversion,
+ self.mashupsList)
+ if latestversion == self.controller.currentVersion:
+ item.setSelected(True)
+
+ if len(tags) > 0:
+ tags.sort()
+ for tag in tags:
+ item = QMashupListPanelItem(str(tag),
+ self.tagMap[tag],
+ self.mashupsList)
+ if tag == currentTag:
+ item.setSelected(True)
+
+ self.mashupsList.itemSelectionChanged.connect(self.changeSelection)
+
+ @pyqtSlot()
+ def changeSelection(self):
+ items = self.mashupsList.selectedItems()
+ if len(items) == 1:
+ version = items[0].version
+ if version != self.controller.currentVersion:
+ self.controller.setCurrentVersion(version, quiet=False)
+
+ def selectMashup(self, name):
+ itemlist = self.mashupsList.findItems(name,
+ QtCore.Qt.MatchExactly)
+ if len(itemlist) == 1:
+ item = itemlist[0]
+ self.mashupsList.setCurrentItem(item)
+
+################################################################################
+
+class QMashupListPanelItem(QtGui.QListWidgetItem):
+ def __init__(self, tag, version, parent=None):
+ QtGui.QListWidgetItem.__init__(self, tag, parent)
+ self.tag = tag
+ self.version = version
+
+################################################################################
+
+class QMashupExportDialog(QtGui.QDialog):
+ FULLTREE = 0
+ MINIMAL = 1
+ LINK = 2
+ def __init__(self, parent=None):
+ QtGui.QDialog.__init__(self, parent)
+ self.setWindowTitle('VisTrails - Exporting Mashup')
+ dlgLayout = QtGui.QVBoxLayout()
+ gb = QtGui.QGroupBox("This will export the mashup as a file:")
+ gblayout = QtGui.QVBoxLayout()
+ self.rbMinimal = QtGui.QRadioButton("Include only this mashup\
+ and its original workflow")
+ self.rbMinimal.setChecked(True)
+ self.rbFullTree = QtGui.QRadioButton("Include full tree (this will also\
+ include other mashups)")
+ self.rbLink = QtGui.QRadioButton("As a link (this will work only on\
+ this machine)")
+ gblayout.addWidget(self.rbMinimal)
+ gblayout.addWidget(self.rbFullTree)
+ gblayout.addWidget(self.rbLink)
+ gb.setLayout(gblayout)
+
+ btnOk = QtGui.QPushButton("OK")
+ btnCancel = QtGui.QPushButton("Cancel")
+ btnLayout = QtGui.QHBoxLayout()
+ btnLayout.addStretch()
+ btnLayout.addWidget(btnOk)
+ btnLayout.addWidget(btnCancel)
+ btnLayout.addStretch()
+
+ dlgLayout.addWidget(gb)
+ dlgLayout.addLayout(btnLayout)
+ self.setLayout(dlgLayout)
+
+ self.btnPressed = -1
+ self.connect(btnOk, QtCore.SIGNAL("clicked()"), self.btnOkPressed)
+ self.connect(btnCancel, QtCore.SIGNAL("clicked()"), self.btnCancelPressed)
+
+ def btnOkPressed(self):
+ if self.rbFullTree.isChecked():
+ self.btnPressed = self.FULLTREE
+ elif self.rbMinimal.isChecked():
+ self.btnPressed = self.MINIMAL
+ elif self.rbLink.isChecked():
+ self.btnPressed = self.LINK
+ self.accept()
+
+ def btnCancelPressed(self):
+ self.btnPressed = -1
+ self.reject()
\ No newline at end of file
diff --git a/vistrails/gui/mashups/mashups_manager.py b/vistrails/gui/mashups/mashups_manager.py
new file mode 100644
index 0000000..80df3e4
--- /dev/null
+++ b/vistrails/gui/mashups/mashups_manager.py
@@ -0,0 +1,450 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import base64
+import copy
+import os
+import tempfile
+import uuid
+from PyQt4 import QtCore, QtGui
+from vistrails.gui.vistrail_controller import VistrailController
+import vistrails.core.db.action
+from vistrails.core.vistrail.controller import VistrailController as BaseVistrailController
+from vistrails.gui.mashups.controller import MashupController
+from vistrails.core.mashup.mashup_trail import Mashuptrail
+from vistrails.core.mashup.mashup import Mashup
+from vistrails.core.utils import DummyView
+from vistrails.core.vistrail.vistrail import Vistrail
+from vistrails.db.services.locator import DBLocator
+from vistrails.core.db.locator import FileLocator
+import vistrails.core.system
+from vistrails.db.domain import IdScope
+from vistrails.core.system import get_elementtree_library
+from vistrails.db.services import io
+from vistrails.db.versions import currentVersion
+
+ElementTree = get_elementtree_library()
+
+############################################################################
+
+class MashupsManager(object):
+ _instance = None
+ class MashupsManagerSingleton(object):
+ def __call__(self, *args, **kw):
+ if MashupsManager._instance is None:
+ obj = MashupsManager(*args, **kw)
+ MashupsManager._instance = obj
+ return MashupsManager._instance
+
+ getInstance = MashupsManagerSingleton()
+
+ def __init__(self):
+ if not MashupsManager._instance:
+ MashupsManager._instance = self
+ else:
+ raise RuntimeError, 'Only one instance of MashupsManager is allowed'
+
+ def createMashupController(self, vt_controller, version, view=DummyView()):
+ #print "Manager creating mashup controller ", vt_controller, version
+ newvt_controller = MashupsManager.copyVistrailController(vt_controller,
+ view)
+ mashuptrail = \
+ MashupsManager.getMashuptrailforVersionInVistrailController(vt_controller,
+ version)
+ if mashuptrail is None:
+ (p_mashuptrail, p_version) = \
+ MashupsManager.findClosestParentMashuptrail(vt_controller,
+ version)
+ id_scope = IdScope(1L)
+ if p_mashuptrail is not None:
+ version_name = vt_controller.get_pipeline_name(p_version)
+ (res, mshpv) = MashupsManager.showFoundMashupsDialog(p_mashuptrail,
+ version_name)
+ if res in ['Copy', 'Move']:
+ pipeline = newvt_controller.vistrail.getPipeline(version)
+ if res == 'Copy':
+ # we will copy the mashup from the parent trail and
+ # validate it to the current pipeline before adding
+ # to the current mashup trail
+ mashuptrail = Mashuptrail(self.getNewMashuptrailId(),
+ version, id_scope)
+ p_mashup = p_mashuptrail.getMashup(mshpv)
+ mashup = p_mashup.do_copy()
+ mashup.id_scope = id_scope
+ mashup.version = version
+ mashup.validateForPipeline(pipeline)
+ currVersion = mashuptrail.addVersion(
+ parent_id=mashuptrail.getLatestVersion(),
+ mashup=mashup,
+ user=vistrails.core.system.current_user(),
+ date=vistrails.core.system.current_time())
+ mashuptrail.currentVersion = currVersion
+ mashuptrail.updateIdScope()
+ p_tag = p_mashuptrail.getTagForActionId(mshpv)
+ if p_tag == '':
+ tag = "<latest>"
+ tag = "Copy from %s"%p_tag
+ MashupsManager.addMashuptrailtoVistrailController(vt_controller,
+ mashuptrail)
+
+ elif res == 'Move':
+ # we will move the parent trail and validate all mashups
+ # for the current pipeline to make sure they will be
+ # executable for the current version
+
+ mashuptrail = p_mashuptrail
+ currVersion = mashuptrail.getLatestVersion()
+ mashuptrail.currentVersion = currVersion
+ mashuptrail.validateMashupsForPipeline(version, pipeline)
+ tag = None
+
+ mashuptrail.vtVersion = version
+ mshpController = MashupController(vt_controller,
+ newvt_controller,
+ version, mashuptrail)
+ mshpController.setCurrentVersion(mashuptrail.currentVersion)
+ # this is to make sure the pipeline displayed in the mashup
+ # view is consistent with the list of aliases in the central
+ # panel
+ mshpController.updatePipelineAliasesFromCurrentMashup()
+ if tag is not None:
+ mshpController.updateCurrentTag(tag)
+ return mshpController
+
+ mashuptrail = Mashuptrail(self.getNewMashuptrailId(), version,
+ id_scope)
+ pipeline = newvt_controller.vistrail.getPipeline(version)
+ id = id_scope.getNewId('mashup')
+ mashup = Mashup(id=id, name="mashup%s"%id, vtid=vt_controller.locator,
+ version=version)
+ mashup.loadAliasesFromPipeline(pipeline, id_scope)
+ currVersion = mashuptrail.addVersion(parent_id=mashuptrail.getLatestVersion(),
+ mashup=mashup,
+ user=vistrails.core.system.current_user(),
+ date=vistrails.core.system.current_time())
+
+ mashuptrail.currentVersion = currVersion
+
+ MashupsManager.addMashuptrailtoVistrailController(vt_controller,
+ mashuptrail)
+ mshpController = MashupController(vt_controller,
+ newvt_controller,
+ version, mashuptrail)
+ mshpController.setCurrentVersion(mashuptrail.currentVersion)
+ if mshpController.currentVersion == 1L:
+ mshpController.updateCurrentTag("ROOT")
+ else:
+ #print "----> found mashuptrail ", mashuptrail.currentVersion
+ mshpController = MashupController(vt_controller,
+ newvt_controller,
+ version, mashuptrail)
+ mshpController.setCurrentVersion(mashuptrail.currentVersion)
+ mshpController.updatePipelineAliasesFromCurrentMashup()
+
+ return mshpController
+
+ @staticmethod
+ def getNewMashuptrailId():
+ return uuid.uuid1()
+
+ @staticmethod
+ def copyVistrailController(vt_controller, view=DummyView()):
+ vistrail = vt_controller.vistrail
+ newvt_controller = VistrailController(vistrail, None,
+ pipeline_view=view)
+ current_log = vt_controller.log
+ newvt_controller.log = current_log
+ newvt_controller.disable_autosave()
+ return newvt_controller
+
+ @staticmethod
+ def copyBaseVistrailController(vt_controller):
+ vistrail = vt_controller.vistrail
+ newvt_controller = BaseVistrailController(vistrail, None)
+ current_log = vt_controller.log
+ newvt_controller.log = current_log
+ # DAK: why does the base version copy the _mashups but the non-base
+ # version doesn't??
+ for m in vt_controller._mashups:
+ newvt_controller._mashups.append(copy.copy(m))
+ return newvt_controller
+
+ @staticmethod
+ def getMashuptrailforVersionInVistrailController(controller, version):
+ #print version, controller
+ res = None
+ if hasattr(controller, "_mashups"):
+ for mashuptrail in controller._mashups:
+ #print mashuptrail.vtVersion
+ if mashuptrail.vtVersion == version:
+ return mashuptrail
+ return res
+
+ @staticmethod
+ def findClosestParentMashuptrail(vt_controller, version):
+ res = None
+ mashuptrails = {}
+ if hasattr(vt_controller, "_mashups"):
+ for mashuptrail in vt_controller._mashups:
+ #print mashuptrail.vtVersion
+ mashuptrails[mashuptrail.vtVersion] = mashuptrail
+ action_map = vt_controller.vistrail.actionMap
+ if version > 0 and len(mashuptrails) > 0:
+ v = action_map[version].parent
+ while True:
+ if v in mashuptrails or v <= 0:
+ if v in mashuptrails:
+ res = mashuptrails[v]
+ else:
+ res = None
+ return (res, v)
+ v = action_map[v].parent
+ return (res, -1)
+
+ @staticmethod
+ def showFoundMashupsDialog(mashup_trail, version_name, parent=None):
+ class FoundMashupDialog(QtGui.QDialog):
+
+ def __init__(self, mashup_trail, version_name, parent=None):
+ QtGui.QDialog.__init__(self, parent)
+ self.setWindowTitle('VisTrails - Mashup')
+ dlgLayout = QtGui.QVBoxLayout()
+ str_label = "VisTrails found mashup(s) already created in parent %s."
+ label = QtGui.QLabel(str_label%str(version_name))
+ label.setWordWrap(True)
+ gb = QtGui.QGroupBox("What would you like to do?")
+ gblayout = QtGui.QVBoxLayout()
+
+ self.btnNew = QtGui.QRadioButton("Create new mashup (starting from current pipeline's aliases)")
+ self.btnNew.setChecked(True)
+ self.btnCopy = QtGui.QRadioButton("Copy selected mashup (aliases will be merged)")
+ self.btnMove = QtGui.QRadioButton("Move all mashups to current pipeline")
+ self.mashupsList = QtGui.QListWidget()
+ self.mashupsList.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
+ self.mashupsList.setMaximumSize(100, 120)
+ self.mashupsList.setEnabled(False)
+ self.setMashupsList(mashup_trail)
+
+ hlayout = QtGui.QHBoxLayout()
+ hlayout.setMargin(5)
+ hlayout.setSpacing(5)
+ hlayout.addWidget(self.mashupsList)
+ hlayout.addStretch()
+
+ gblayout.addWidget(self.btnNew)
+ gblayout.addWidget(self.btnMove)
+ gblayout.addWidget(self.btnCopy)
+ gblayout.addLayout(hlayout)
+
+ gb.setLayout(gblayout)
+ btnOk = QtGui.QPushButton("OK")
+ btnLayout = QtGui.QHBoxLayout()
+ btnLayout.addStretch()
+ btnLayout.addWidget(btnOk)
+ btnLayout.addStretch()
+ self.btnPressed = 0
+ self.mashup_version = -1
+
+ dlgLayout.addWidget(label)
+ dlgLayout.addWidget(gb)
+ dlgLayout.addLayout(btnLayout)
+ self.setLayout(dlgLayout)
+ self.connect(self.btnCopy, QtCore.SIGNAL("toggled(bool)"),
+ self.mashupsList.setEnabled)
+ self.connect(btnOk, QtCore.SIGNAL("clicked()"),
+ self.btnOkPressed)
+
+ def btnOkPressed(self):
+ if self.btnNew.isChecked():
+ self.btnPressed = 'New'
+ elif self.btnMove.isChecked():
+ self.btnPressed = 'Move'
+ elif self.btnCopy.isChecked():
+ self.btnPressed = 'Copy'
+ self.mashup_version = self.getMashupVersion()
+ self.accept()
+
+ def setMashupsList(self, mshptrail):
+ from vistrails.gui.mashups.mashups_inspector import QMashupListPanelItem
+ self.mashupsList.clear()
+ tagMap = mshptrail.getTagMap()
+ tags = tagMap.keys()
+ latestversion = mshptrail.getLatestVersion()
+ item_selected = False
+ if not mshptrail.hasTagForActionId(latestversion):
+ item = QMashupListPanelItem("<latest>",
+ latestversion,
+ self.mashupsList)
+ item.setSelected(True)
+ item_selected = True
+ if len(tags) > 0:
+ tags.sort()
+ i = 0
+ for tag in tags:
+ item = QMashupListPanelItem(str(tag),
+ tagMap[tag],
+ self.mashupsList)
+ if i == 0 and not item_selected:
+ item.setSelected(True)
+ i+=1
+
+ def getMashupVersion(self):
+ items = self.mashupsList.selectedItems()
+ if len(items) == 1:
+ return items[0].version
+
+ dialog = FoundMashupDialog(mashup_trail, version_name, parent)
+ if dialog.exec_() == QtGui.QDialog.Accepted:
+ return (dialog.btnPressed,dialog.mashup_version)
+ else:
+ return ('New', -1)
+
+ @staticmethod
+ def addMashuptrailtoVistrailController(controller, mashuptrail):
+ controller._mashups.append(mashuptrail)
+ controller.set_changed(True)
+
+ @staticmethod
+ def createMashupApp(vtcontroller, mashuptrail, version):
+ from vistrails.gui.mashups.mashup_app import QMashupAppMainWindow
+ vistrail_view = vtcontroller.vistrail_view
+ vtVersion = mashuptrail.vtVersion
+ view = DummyView()
+ view.scene().current_pipeline = vtcontroller.vistrail.getPipeline(vtVersion)
+ view.scene().current_pipeline.validate()
+ new_vtcontroller = MashupsManager.copyBaseVistrailController(vtcontroller)
+ new_vtcontroller.change_selected_version(vtVersion)
+ mshpController = MashupController(vtcontroller,
+ new_vtcontroller,
+ vtVersion, mashuptrail)
+ mshpController.setCurrentVersion(version)
+ app = QMashupAppMainWindow(parent=None,
+ vistrail_view=vistrail_view,
+ controller=mshpController,
+ version=version)
+ return app
+
+ @staticmethod
+ def exportMashup(filename, vtcontroller, mashuptrail, mashupversion, etype):
+ """exportMashup(filename: str, vtcontroller: VistrailController,
+ mashuptrail: Mashuptrail, type: int) -> bool
+ where etype is
+ 0: include full tree
+ 1: include only workflow and mashup identified by version
+ 2: as a link, it will point to a local file.
+ """
+ result = False
+ if vtcontroller is not None and mashuptrail is not None:
+ locator = vtcontroller.locator
+ version = mashuptrail.vtVersion
+
+ node = ElementTree.Element('vtlink')
+
+ if isinstance(locator, DBLocator):
+ node.set('host', str(locator.host))
+ node.set('port', str(locator.port))
+ node.set('database', str(locator.db))
+ node.set('vtid', str(locator.obj_id))
+ else:
+ node.set('filename', str(locator.name))
+
+ node.set('version', str(version))
+ node.set('execute', "True")
+ node.set('forceDB', "False")
+ node.set('showSpreadsheetOnly', "True")
+ node.set('mashuptrail', str(mashuptrail.id))
+ node.set('mashupVersion', str(mashupversion))
+
+ if etype in [0,1]:
+ if etype == 1: #minimal
+ pip = vtcontroller.vistrail.getPipeline(version)
+ vistrail = Vistrail()
+ id_remap = {}
+ action = vistrails.core.db.action.create_paste_action(pip,
+ vistrail.idScope,
+ id_remap)
+ vistrail.add_action(action, 0L, 0)
+
+ tag = vtcontroller.vistrail.get_tag(version)
+ if tag is None:
+ tag = "Imported workflow"
+ vistrail.addTag(tag, action.id)
+ node.set('version', str(action.id))
+ id_scope = IdScope(1L)
+ newmashuptrail = Mashuptrail(
+ MashupsManager.getNewMashuptrailId(),
+ action.id,
+ id_scope)
+
+ maction = mashuptrail.actionMap[mashupversion]
+ mtag = mashuptrail.getTagForActionId(mashupversion)
+ newmashup = copy.copy(maction.mashup)
+ newmashup.remapPipelineObjects(id_remap)
+ currVersion = newmashuptrail.addVersion(
+ newmashuptrail.getLatestVersion(),
+ newmashup, maction.user,
+ maction.date)
+ newmashuptrail.currentVersion = currVersion
+ newmashuptrail.changeTag(currVersion, mtag, maction.user,
+ maction.date)
+ newvtcontroller = BaseVistrailController(vistrail, None)
+ MashupsManager.addMashuptrailtoVistrailController(newvtcontroller,
+ newmashuptrail)
+ node.set('mashuptrail', str(newmashuptrail.id))
+ node.set('mashupVersion', str(newmashuptrail.currentVersion))
+ else:
+ vistrail = vtcontroller.vistrail
+ newvtcontroller = MashupsManager.copyBaseVistrailController(vtcontroller)
+
+ #create temporary file
+ (fd, name) = tempfile.mkstemp(prefix='vt_tmp',
+ suffix='.vt')
+ os.close(fd)
+ try:
+ fileLocator = FileLocator(name)
+ newvtcontroller.write_vistrail(fileLocator)
+ contents = open(name).read()
+ vtcontent = base64.b64encode(contents)
+ finally:
+ os.unlink(name)
+ #if not vistrail.db_version:
+ # vistrail.db_version = currentVersion
+ node.set('vtcontent',vtcontent)
+
+ xmlstring = ElementTree.tostring(node)
+ file_ = open(filename,'w')
+ file_.write(xmlstring)
+ file_.close()
+ result = True
+ return result
diff --git a/vistrails/gui/mashups/mashups_widgets.py b/vistrails/gui/mashups/mashups_widgets.py
new file mode 100644
index 0000000..ff7c002
--- /dev/null
+++ b/vistrails/gui/mashups/mashups_widgets.py
@@ -0,0 +1,387 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+from vistrails.core.system import get_vistrails_basic_pkg_id
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.modules import get_widget_class
+from vistrails.gui.modules.constant_configuration import ConstantWidgetMixin, \
+ StandardConstantWidget
+from vistrails.core.modules.module_registry import get_module_registry
+
+class QAliasSliderWidget(QtGui.QWidget):
+ def __init__(self, alias, vtparam, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.alias = alias
+ self.vtparam = vtparam
+ self.palette().setColor(QtGui.QPalette.Window,
+ CurrentTheme.METHOD_SELECT_COLOR)
+ label = QtGui.QLabel(alias.name)
+ label.font().setBold(True)
+ self.value = QSliderWidget(param=vtparam, parent=self)
+ self.value.setRange(alias.component.minVal, alias.component.maxVal)
+ self.value.setSingleStep(alias.component.stepSize)
+ self.value.setContents(self.alias.component.val)
+
+ self.connect(self.value,
+ QtCore.SIGNAL("contentsChanged"),
+ self.contents_changed)
+
+ hbox = QtGui.QHBoxLayout()
+ hbox.setMargin(8)
+ hbox.addWidget(label)
+ hbox.addWidget(self.value)
+ self.setLayout(hbox)
+
+ def contents_changed(self, info):
+ #print "drop down emitting"
+ self.emit(QtCore.SIGNAL('contentsChanged'), (self, info))
+
+ def focusInEvent(self, event):
+ self.emit(QtCore.SIGNAL("receivedfocus"), self)
+
+ def focusOutEvent(self, event):
+ self.emit(QtCore.SIGNAL("removedfocus"), self)
+
+###############################################################################
+
+class QSliderWidget(ConstantWidgetMixin, QtGui.QSlider):
+ def __init__(self, param, parent=None):
+ QtGui.QSlider.__init__(self, QtCore.Qt.Horizontal, parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ assert param.type in['Integer', 'Float']
+ self.sliderType = int if param.type == 'Integer' else float
+ assert param.identifier == get_vistrails_basic_pkg_id()
+
+ self.connect(self, QtCore.SIGNAL('valueChanged(int)'),self.change_val)
+ QtGui.QSlider.setSingleStep(self, 1)
+ QtGui.QSlider.setPageStep(self, 5)
+ self.floatMinVal = 0.0
+ self.floatMaxVal = 1.0
+ self.floatStepSize = 1
+ self.numSteps = 1
+ self.setContents(param.strValue)
+ self.setTickPosition(QtGui.QSlider.TicksAbove)
+
+ def contents(self):
+ floatVal = float(self.value()) * self.floatStepSize + self.floatMinVal
+ return self.sliderType(floatVal)
+
+ def setContents(self, strValue, silent=True):
+ """ encodes a number to a scaled integer """
+ if strValue:
+ value = strValue
+ else:
+ value = "0.0"
+ floatVal = float(value)
+ value = int((floatVal-self.floatMinVal)/self.floatStepSize)
+ self.setValue(int(value))
+ self.setToolTip("%g" % floatVal)
+
+ if not silent:
+ self.update_parent()
+
+ def change_val(self, newval):
+ """ decodes a scaled integer to the correct number """
+ floatVal = float(newval) * self.floatStepSize + self.floatMinVal
+ self.setToolTip("%g" % floatVal)
+ self.update_parent()
+
+ def setRange(self, minVal, maxVal):
+ self.floatMinVal = float(minVal)
+ self.floatMaxVal = float(maxVal)
+ QtGui.QSlider.setRange(self, 0, 1)
+ self.setSingleStep(self.floatStepSize)
+
+ def setSingleStep(self, stepSize):
+ """ stepSize tells the step between values. We need to calculate the
+ number of steps """
+ self.floatStepSize = float(stepSize)
+ self.numSteps = int((self.floatMaxVal - self.floatMinVal)/self.floatStepSize)
+ QtGui.QSlider.setRange(self, 0, self.numSteps)
+
+
+###############################################################################
+
+class QAliasNumericStepperWidget(QtGui.QWidget):
+ def __init__(self, alias, vtparam, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.alias = alias
+ self.vtparam = vtparam
+ self.palette().setColor(QtGui.QPalette.Window,
+ CurrentTheme.METHOD_SELECT_COLOR)
+ label = QtGui.QLabel(alias.name)
+ label.font().setBold(True)
+ if self.alias.component.type == "Integer":
+ self.value = QNumericStepperIntegerWidget(param=vtparam,
+ parent=self)
+ self.value.setRange(int(alias.component.minVal),
+ int(alias.component.maxVal))
+ self.value.setSingleStep(int(alias.component.stepSize))
+ self.value.setContents(self.alias.component.val)
+ elif self.alias.component.type == "Float":
+ self.value = QNumericStepperFloatWidget(param=vtparam,
+ parent=self)
+ self.value.setRange(float(alias.component.minVal),
+ float(alias.component.maxVal))
+ self.value.setSingleStep(float(alias.component.stepSize))
+ self.value.setContents(self.alias.component.val)
+
+ self.connect(self.value,
+ QtCore.SIGNAL("contentsChanged"),
+ self.contents_changed)
+
+ hbox = QtGui.QHBoxLayout()
+ hbox.setMargin(8)
+ hbox.addWidget(label)
+ hbox.addWidget(self.value)
+ self.setLayout(hbox)
+
+ def contents_changed(self, info):
+ #print "drop down emitting"
+ self.emit(QtCore.SIGNAL('contentsChanged'), (self, info))
+
+ def focusInEvent(self, event):
+ self.emit(QtCore.SIGNAL("receivedfocus"), self)
+
+ def focusOutEvent(self, event):
+ self.emit(QtCore.SIGNAL("removedfocus"), self)
+
+###############################################################################
+class QNumericStepperIntegerWidget(ConstantWidgetMixin, QtGui.QSpinBox):
+ def __init__(self, param, parent=None):
+ QtGui.QSpinBox.__init__(self, parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ assert param.type == 'Integer'
+ assert param.identifier == get_vistrails_basic_pkg_id()
+
+ self.connect(self, QtCore.SIGNAL('valueChanged(int)'),
+ self.change_val)
+ self.setContents(param.strValue)
+
+ def contents(self):
+ return self.value()
+
+ def setContents(self, strValue, silent=True):
+ if strValue:
+ value = strValue
+ else:
+ value = "0"
+ self.setValue(int(value))
+
+ if not silent:
+ self.update_parent()
+
+ def change_val(self, newval):
+ self.update_parent()
+###############################################################################
+
+class QNumericStepperFloatWidget(ConstantWidgetMixin, QtGui.QDoubleSpinBox):
+ def __init__(self, param, parent=None):
+ QtGui.QDoubleSpinBox.__init__(self, parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ assert param.type == 'Float'
+ assert param.identifier == get_vistrails_basic_pkg_id()
+
+ self.connect(self, QtCore.SIGNAL('valueChanged(double)'),
+ self.change_val)
+ self.setContents(param.strValue)
+
+ def contents(self):
+ return self.value()
+
+ def setContents(self, strValue, silent=True):
+ if strValue:
+ value = strValue
+ else:
+ value = "0"
+ self.setValue(float(value))
+
+ if not silent:
+ self.update_parent()
+
+ def change_val(self, newval):
+ self.update_parent()
+
+###############################################################################
+
+class QDropDownWidget(QtGui.QWidget):
+ def __init__(self, alias, vtparam, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.alias = alias
+ self.vtparam = vtparam
+ self.palette().setColor(QtGui.QPalette.Window,
+ CurrentTheme.METHOD_SELECT_COLOR)
+ label = QtGui.QLabel(alias.name)
+ label.font().setBold(True)
+ self.value = self.createAliasWidget(val=self.alias.component.val,
+ parent=self)
+ self.connect(self.value,
+ QtCore.SIGNAL("contentsChanged"),
+ self.contents_changed)
+ self.dropdownbtn = QtGui.QToolButton(self)
+ self.dropdownbtn.setArrowType(QtCore.Qt.DownArrow)
+ self.dropdownbtn.setAutoRaise(True)
+
+ #menu button
+ self.createMenu()
+ self.dropdownbtn.setPopupMode(QtGui.QToolButton.InstantPopup)
+
+ hbox = QtGui.QHBoxLayout()
+ hbox.setMargin(8)
+ hbox.addWidget(label)
+ hbox.addWidget(self.value)
+ hbox.addWidget(self.dropdownbtn)
+ self.setLayout(hbox)
+
+ def createMenu(self):
+ self.menu = QMenuValue(self)
+ self.menu.setSizePolicy(QtGui.QSizePolicy.Preferred,
+ QtGui.QSizePolicy.Maximum)
+ mbox = QtGui.QVBoxLayout()
+ mbox.setSpacing(1)
+ mbox.setMargin(2)
+ self.menu_widgets = {}
+ valuelist = self.alias.component.valueList
+
+ for v in valuelist:
+ hbox = QtGui.QHBoxLayout()
+ rb = QMenuRadioButton()
+ rb.setChecked(False)
+ vw = self.createMenuAliasWidget(val=v, parent=self)
+ vw.setSizePolicy(QtGui.QSizePolicy.Preferred,
+ QtGui.QSizePolicy.Maximum)
+ vw.setReadOnly(True)
+
+ self.menu_widgets[rb] = vw
+ hbox.addWidget(rb)
+ hbox.addWidget(vw)
+ mbox.addLayout(hbox)
+
+ self.connect(rb,
+ QtCore.SIGNAL("clicked(bool)"),
+ self.menu.hide)
+ self.connect(vw,
+ QtCore.SIGNAL("clicked(bool)"),
+ rb.setChecked)
+ self.menu.setLayout(mbox)
+ self.dropdownbtn.setMenu(self.menu)
+
+ #there's a bug on a mac that causes the menu to be always displayed
+ #where it was shown for the first time... We need to ensure
+ #the right position.
+ self.connect(self.menu,
+ QtCore.SIGNAL("aboutToShow()"),
+ self.ensure_menu_position)
+ self.connect(self.menu,
+ QtCore.SIGNAL("aboutToHide()"),
+ self.value_selected)
+
+ def contents_changed(self, info):
+ #print "drop down emitting"
+ self.emit(QtCore.SIGNAL('contentsChanged'), (self, info))
+
+ def ensure_menu_position(self):
+ #print self.dropdownbtn.pos(),
+ newpos = QtCore.QPoint(self.dropdownbtn.pos().x(),
+ self.dropdownbtn.pos().y() + self.dropdownbtn.frameSize().height())
+ self.menu.move(self.mapToGlobal(newpos))
+ #print self.menu.pos()
+
+ def createAliasWidget(self, val=None, parent=None):
+ if self.vtparam.identifier == '':
+ idn = get_vistrails_basic_pkg_id()
+ else:
+ idn = self.vtparam.identifier
+ reg = get_module_registry()
+ p_module = reg.get_module_by_name(idn, self.vtparam.type,
+ self.vtparam.namespace)
+ widget_type = get_widget_class(p_module)
+ if val:
+ self.vtparam.strValue = val
+ return widget_type(self.vtparam, parent)
+
+ def createMenuAliasWidget(self, val=None, parent=None):
+ widget = self.createAliasWidget(val)
+ return QMenuValueItem(widget, parent)
+
+ def value_selected(self):
+ #print "value_selected", self.menu.pos()
+ for rb, vw in self.menu_widgets.iteritems():
+ if rb.isChecked():
+ self.value.setContents(vw.contents(), silent=False)
+ vw.setFocus()
+ rb.setChecked(False)
+ self.menu.hide()
+ break
+
+ def focusInEvent(self, event):
+ self.emit(QtCore.SIGNAL("receivedfocus"), self)
+
+ def focusOutEvent(self, event):
+ self.emit(QtCore.SIGNAL("removedfocus"), self)
+
+class QMenuRadioButton(QtGui.QRadioButton):
+ def focusInEvent(self, event):
+ self.setChecked(True)
+ #self.emit(QtCore.SIGNAL("clicked(bool)"), True)
+ QtGui.QRadioButton.focusInEvent(self, event)
+
+class QMenuValue(QtGui.QMenu):
+ def mousePressEvent(self, e):
+ vw = self.childAt(e.pos())
+ while vw is not None and not isinstance(vw, QMenuValueItem):
+ vw = vw.parent()
+ if vw is not None:
+ vw.emit(QtCore.SIGNAL("clicked(bool)"), True)
+ QtGui.QMenu.mousePressEvent(self, e)
+
+class QMenuValueItem(QtGui.QWidget):
+ def __init__(self, widget, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.widget = widget
+ vlayout = QtGui.QVBoxLayout()
+ vlayout.setMargin(0)
+ vlayout.setSpacing(0)
+ vlayout.addWidget(self.widget)
+ self.setLayout(vlayout)
+
+ def setReadOnly(self, on):
+ self.setEnabled(not on)
+
+ def contents(self):
+ return self.widget.contents()
+
+ def mousePressEvent(self, e):
+ self.emit(QtCore.SIGNAL("clicked(bool)"), True)
diff --git a/vistrails/gui/merge_gui.py b/vistrails/gui/merge_gui.py
new file mode 100644
index 0000000..49ee8a1
--- /dev/null
+++ b/vistrails/gui/merge_gui.py
@@ -0,0 +1,322 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtGui, QtCore
+import os
+import vistrails.api
+
+CHOICE_OTHER_ALL = 0
+CHOICE_OTHER = 1
+CHOICE_RESOLVED = 2
+CHOICE_OWN = 3
+CHOICE_OWN_ALL = 4
+
+class resolve_tags(QtGui.QWidget):
+ def __init__(self, a, b, text, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+
+ self.value = 4
+ self.a = a
+ self.b = b
+ self.text = text
+
+ self.initUI()
+
+ def initUI(self):
+
+ self.setWindowTitle("Tag conflict!")
+ self.move(250, 200)
+
+ # main layout
+ vbox = QtGui.QVBoxLayout()
+ self.setLayout(vbox)
+
+ # info boxes
+ hbox = QtGui.QHBoxLayout()
+ vbox.addLayout(hbox)
+
+ otherLabel = QtGui.QLabel(self)
+ otherLabel.setAlignment(QtCore.Qt.AlignHCenter)
+ otherLabel.setText("Other version")
+ hbox.addWidget(otherLabel)
+
+ ownLabel = QtGui.QLabel(self)
+ ownLabel.setAlignment(QtCore.Qt.AlignHCenter)
+ ownLabel.setText("Your version")
+ hbox.addWidget(ownLabel)
+
+ # tags
+ self.tedit = QtGui.QLineEdit(self.text)
+ self.tedit.setAlignment(QtCore.Qt.AlignHCenter)
+ vbox.addWidget(self.tedit)
+
+ # info boxes
+ hbox = QtGui.QHBoxLayout()
+ vbox.addLayout(hbox)
+
+ # info boxes
+ vbox1 = QtGui.QVBoxLayout()
+ vbox1.setAlignment(QtCore.Qt.AlignHCenter)
+ hbox.addLayout(vbox1)
+ userLabel = QtGui.QLabel(self)
+ userLabel.setText("User: " + self.a.db_user)
+ vbox1.addWidget(userLabel)
+ timeLabel = QtGui.QLabel(self)
+ timeLabel.setText("Time: " + str(self.a.db_date))
+ vbox1.addWidget(timeLabel)
+
+ vbox2 = QtGui.QVBoxLayout()
+ vbox2.setAlignment(QtCore.Qt.AlignHCenter)
+ hbox.addLayout(vbox2)
+ userLabel = QtGui.QLabel(self)
+ userLabel.setText("User: " + self.b.db_user)
+ vbox2.addWidget(userLabel)
+ timeLabel = QtGui.QLabel(self)
+ timeLabel.setText("Time: " + str(self.b.db_date))
+ vbox2.addWidget(timeLabel)
+
+ buttons = QtGui.QHBoxLayout()
+ vbox.addLayout(buttons)
+
+ self.otherAll = QtGui.QPushButton('Keep other (for all)', self)
+ self.connect(self.otherAll, QtCore.SIGNAL('clicked()'), self.setOtherAll)
+ buttons.addWidget(self.otherAll)
+ self.other = QtGui.QPushButton('Keep other', self)
+ self.connect(self.other, QtCore.SIGNAL('clicked()'), self.setOther)
+ buttons.addWidget(self.other)
+ self.resolve = QtGui.QPushButton('Resolved', self)
+ self.connect(self.resolve, QtCore.SIGNAL('clicked()'), self.setResolved)
+ buttons.addWidget(self.resolve)
+ self.own = QtGui.QPushButton('Keep yours', self)
+ self.connect(self.own, QtCore.SIGNAL('clicked()'), self.setOwn)
+ buttons.addWidget(self.own)
+ self.ownAll = QtGui.QPushButton('Keep yours (for all)', self)
+ self.connect(self.ownAll, QtCore.SIGNAL('clicked()'), self.setOwnAll)
+ buttons.addWidget(self.ownAll)
+
+ def setOtherAll(self):
+ self.value = CHOICE_OTHER_ALL
+ self.close()
+ def setOther(self):
+ self.value = CHOICE_OTHER
+ self.close()
+ def setResolved(self):
+ self.value = CHOICE_RESOLVED
+ self.text = str(self.tedit.text())
+ self.close()
+ def setOwn(self):
+ self.value = CHOICE_OWN
+ self.close()
+ def setOwnAll(self):
+ self.value = CHOICE_OWN_ALL
+ self.close()
+
+class resolve_notes(QtGui.QWidget):
+ def __init__(self, a, b, text, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+
+ self.value = 4
+ self.a = a
+ self.b = b
+ self.text = text
+
+ self.initUI()
+
+ def initUI(self):
+
+ self.setWindowTitle("Notes conflict!")
+ self.move(250, 200)
+
+ # main layout
+ vbox = QtGui.QVBoxLayout()
+ self.setLayout(vbox)
+
+ # thumbs layout
+ self.tedit = QtGui.QTextEdit(self.text)
+ vbox.addWidget(self.tedit)
+
+ buttons = QtGui.QHBoxLayout()
+ vbox.addLayout(buttons)
+
+ self.otherAll = QtGui.QPushButton('Keep other (for all)', self)
+ self.connect(self.otherAll, QtCore.SIGNAL('clicked()'), self.setOtherAll)
+ buttons.addWidget(self.otherAll)
+ self.other = QtGui.QPushButton('Keep other', self)
+ self.connect(self.other, QtCore.SIGNAL('clicked()'), self.setOther)
+ buttons.addWidget(self.other)
+ self.resolve = QtGui.QPushButton('Resolved', self)
+ self.connect(self.resolve, QtCore.SIGNAL('clicked()'), self.setResolved)
+ buttons.addWidget(self.resolve)
+ self.own = QtGui.QPushButton('Keep yours', self)
+ self.connect(self.own, QtCore.SIGNAL('clicked()'), self.setOwn)
+ buttons.addWidget(self.own)
+ self.ownAll = QtGui.QPushButton('Keep yours (for all)', self)
+ self.connect(self.ownAll, QtCore.SIGNAL('clicked()'), self.setOwnAll)
+ buttons.addWidget(self.ownAll)
+
+ def setOtherAll(self):
+ self.value = CHOICE_OTHER_ALL
+ self.close()
+ def setOther(self):
+ self.value = CHOICE_OTHER
+ self.close()
+ def setResolved(self):
+ self.value = CHOICE_RESOLVED
+ self.text = str(self.tedit.toHtml())
+ self.close()
+ def setOwn(self):
+ self.value = CHOICE_OWN
+ self.close()
+ def setOwnAll(self):
+ self.value = CHOICE_OWN_ALL
+ self.close()
+
+class resolve_thumbs(QtGui.QWidget):
+ def __init__(self, a, b, old_tmp_dir, new_tmp_dir, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+
+ self.value = 4
+ self.a = a
+ self.b = b
+
+ self.old_tmp_dir = old_tmp_dir
+ self.new_tmp_dir = new_tmp_dir
+ self.initUI()
+
+ def initUI(self):
+
+ self.setWindowTitle("Thumbnail conflict!")
+ self.move(250, 200)
+
+ # main layout
+ vbox = QtGui.QVBoxLayout()
+ self.setLayout(vbox)
+
+ # thumbs layout
+ hbox = QtGui.QHBoxLayout()
+ vbox.addLayout(hbox)
+
+ other = QtGui.QVBoxLayout()
+ hbox.addLayout(other)
+ otherLabel = QtGui.QLabel(self)
+ otherLabel.setText("Other version")
+ other.addWidget(otherLabel)
+ path = os.path.join(self.old_tmp_dir, 'thumbs', self.a.db_value)
+ pixmap = QtGui.QPixmap(path)
+ thumb1 = QtGui.QLabel(self)
+ thumb1.setPixmap(pixmap)
+ other.addWidget(thumb1)
+ userLabel = QtGui.QLabel(self)
+ userLabel.setText("User: " + self.a.db_user)
+ other.addWidget(userLabel)
+ timeLabel = QtGui.QLabel(self)
+ timeLabel.setText("Time: " + str(self.a.db_date))
+ other.addWidget(timeLabel)
+
+ own = QtGui.QVBoxLayout()
+ hbox.addLayout(own)
+ ownLabel = QtGui.QLabel(self)
+ ownLabel.setText("Your version")
+ own.addWidget(ownLabel)
+ path = os.path.join(self.old_tmp_dir, 'thumbs', self.b.db_value)
+ pixmap = QtGui.QPixmap(path)
+ thumb2 = QtGui.QLabel(self)
+ thumb2.setPixmap(pixmap)
+ own.addWidget(thumb2)
+ userLabel = QtGui.QLabel(self)
+ userLabel.setText("User: " + self.b.db_user)
+ own.addWidget(userLabel)
+ timeLabel = QtGui.QLabel(self)
+ timeLabel.setText("Time: " + str(self.b.db_date))
+ own.addWidget(timeLabel)
+
+ buttons = QtGui.QHBoxLayout()
+ vbox.addLayout(buttons)
+
+ self.otherAll = QtGui.QPushButton('Keep other (for all)', self)
+ self.connect(self.otherAll, QtCore.SIGNAL('clicked()'), self.setOtherAll)
+ buttons.addWidget(self.otherAll)
+ self.other = QtGui.QPushButton('Keep other', self)
+ self.connect(self.other, QtCore.SIGNAL('clicked()'), self.setOther)
+ buttons.addWidget(self.other)
+ self.own = QtGui.QPushButton('Keep yours', self)
+ self.connect(self.own, QtCore.SIGNAL('clicked()'), self.setOwn)
+ buttons.addWidget(self.own)
+ self.ownAll = QtGui.QPushButton('Keep yours (for all)', self)
+ self.connect(self.ownAll, QtCore.SIGNAL('clicked()'), self.setOwnAll)
+ buttons.addWidget(self.ownAll)
+
+ def setOtherAll(self):
+ self.value = CHOICE_OTHER_ALL
+ self.close()
+ def setOther(self):
+ self.value = CHOICE_OTHER
+ self.close()
+ def setOwn(self):
+ self.value = CHOICE_OWN
+ self.close()
+ def setOwnAll(self):
+ self.value = CHOICE_OWN_ALL
+ self.close()
+
+class MergeGUI:
+ @staticmethod
+ def resolveTags(a, b, text):
+ exm = resolve_tags(a, b, text)
+ exm.show()
+ app = vistrails.api.get_builder_window()
+ if not app:
+ app = QtGui.QApplication([])
+ app.exec_()
+ return exm.value, exm.text
+
+ @staticmethod
+ def resolveNotes(a, b, text):
+ exm = resolve_notes(a, b, text)
+ exm.show()
+ app = vistrails.api.get_builder_window()
+ if not app:
+ app = QtGui.QApplication([])
+ app.exec_()
+ return exm.value, exm.text
+
+ @staticmethod
+ def resolveThumbs(a, b, old_tmp_dir, new_tmp_dir):
+ exm = resolve_thumbs(a, b, old_tmp_dir, new_tmp_dir)
+ exm.show()
+ app = vistrails.api.get_builder_window()
+ if not app:
+ app = QtGui.QApplication([])
+ app.exec_()
+ return exm.value
diff --git a/vistrails/gui/module_annotation.py b/vistrails/gui/module_annotation.py
new file mode 100644
index 0000000..fb6ec4a
--- /dev/null
+++ b/vistrails/gui/module_annotation.py
@@ -0,0 +1,295 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file contains a dialog and widgets related to the module annotation
+displaying a list of all pairs (key,value) for a module
+
+QKeyValueDelegate
+QModuleAnnotation
+QModuleAnnotationTable
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.gui.common_widgets import QToolWindowInterface
+from vistrails.core import debug
+
+################################################################################
+
+class QModuleAnnotation(QtGui.QDialog):
+ """
+ QModuleAnnotation is a dialog for annotating modules
+
+ """
+ def __init__(self, module, controller, parent=None):
+ """
+ QModuleAnnotation(module: Module, controller: VistrailController)
+ -> None
+
+ """
+ QtGui.QDialog.__init__(self, parent)
+ self.module = module
+ self.controller = controller
+ self.setModal(True)
+ self.setWindowTitle('Module Annotations')
+ self.setLayout(QtGui.QVBoxLayout())
+ self.layout().setMargin(0)
+ self.layout().setSpacing(0)
+ self.scrollArea = QtGui.QScrollArea(self)
+ self.layout().addWidget(self.scrollArea)
+ self.scrollArea.setFrameStyle(QtGui.QFrame.NoFrame)
+ self.annotationTable = QModuleAnnotationTable(self.module,
+ self.controller,
+ self)
+ self.scrollArea.setWidget(self.annotationTable)
+ self.scrollArea.setWidgetResizable(True)
+ self.buttonLayout = QtGui.QHBoxLayout()
+ self.buttonLayout.setMargin(5)
+ self.closeButton = QtGui.QPushButton('Close', self)
+ self.closeButton.setFixedWidth(100)
+ self.buttonLayout.addWidget(self.closeButton)
+ self.closeButton.setShortcut('Esc')
+ self.layout().addLayout(self.buttonLayout)
+ self.connect(self.closeButton, QtCore.SIGNAL('clicked(bool)'), self.close)
+
+
+class QModuleAnnotationTable(QtGui.QTableWidget):
+ """
+ QModuleAnnotationTable is a table widget that can be dock inside a
+ window. It has two columns for key and value pairs to view/edit at
+ run-time
+
+ """
+ def __init__(self, module=None, controller=None, parent=None):
+ """ QModuleAnnotationTable(module: Module, controller:
+ VistrailController, parent: QWidget) -> QModuleAnnotationTable
+ Construct the 1x2 table
+
+ """
+ QtGui.QTableWidget.__init__(self, 1, 2, parent)
+ self.read_only = False
+ self.setHorizontalHeaderLabels(['Key', 'Value'])
+ self.horizontalHeader().setResizeMode(QtGui.QHeaderView.Interactive)
+ self.horizontalHeader().setMovable(False)
+ self.horizontalHeader().setStretchLastSection(True)
+ self.setSortingEnabled(True)
+ self.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
+ self.verticalHeader().hide()
+ self.delegate = QKeyValueDelegate(self)
+ self.setItemDelegate(self.delegate)
+ self.module = module
+ self.controller = controller
+ self.updateLocked = False
+ self.updateModule()
+
+ def set_controller(self, controller):
+ self.controller = controller
+
+ def setReadOnly(self, read_only):
+ if read_only != self.read_only:
+ self.read_only = read_only
+ self.setEnabled(not read_only and self.module is not None)
+
+ def updateModule(self, module=None):
+ """ updateModule() -> None
+ Update the widget to view the module annotations
+ """
+
+ self.module = module
+ self.setSortingEnabled(False)
+ if self.updateLocked: return
+ self.clearContents()
+ self.setRowCount(0)
+ if self.module:
+ self.setRowCount(len(self.module.annotations)+1)
+ curRow = 0
+ for annotation in self.module.annotations:
+ if annotation.key == '__desc__':
+ # We don't display the '__desc__' annotation in the list
+ # anymore. If it's present we decrease the rowcount by 1
+ self.setRowCount(len(self.module.annotations))
+ else:
+ self.setItem(curRow, 0, QtGui.QTableWidgetItem(annotation.key))
+ item = QtGui.QTableWidgetItem(annotation.value)
+ self.setItem(curRow, 1, item)
+ curRow += 1
+ self.setEnabled(not self.read_only)
+ else:
+ self.setRowCount(1)
+ self.setEnabled(False)
+ self.setItem(self.rowCount()-1, 0, QtGui.QTableWidgetItem(''))
+ self.setItem(self.rowCount()-1, 1, QtGui.QTableWidgetItem(''))
+ self.setSortingEnabled(True)
+
+ def makeItemBold(self, index):
+ """ makeItemBold(index: QModelIndex) -> None
+ Make the item at index to have a bold face
+
+ """
+ oldFont = QtGui.QFont(self.model().data(index, QtCore.Qt.FontRole))
+ oldFont.setBold(True)
+ oldFont.setPointSize(20)
+ self.model().setData(index, oldFont, QtCore.Qt.FontRole)
+
+ def lockUpdate(self):
+ """ lockUpdate() -> None
+ Do not allow updateModule()
+
+ """
+ self.updateLocked = True
+
+ def unlockUpdate(self):
+ """ unlockUpdate() -> None
+ Allow updateModule()
+
+ """
+ self.updateLocked = False
+
+ def addRow(self):
+ """ addRow() -> None
+ Adds a new empty row to the table
+
+ """
+ self.setSortingEnabled(False)
+ self.resizeRowsToContents()
+ self.insertRow(self.rowCount())
+ self.setItem(self.rowCount()-1, 0,
+ QtGui.QTableWidgetItem(''))
+ self.setItem(self.rowCount()-1, 1,
+ QtGui.QTableWidgetItem(''))
+ self.setSortingEnabled(False)
+
+ def editNextAvailableCell(self):
+ item = self.item(self.rowCount()-1, 0)
+ self.editItem(item)
+
+class QKeyValueDelegate(QtGui.QItemDelegate):
+ """
+ QKeyValueDelegate tries to create a special control widget
+ providing a simple interface for adding/deleting module
+ annotations
+
+ """
+
+ def __init__(self, table):
+ """ QKeyValueDelegate(table: QModuleAnnotationTable) -> QKeyValueDelegate
+ Save a reference to table and perform a default initialization
+
+ """
+ self.table = table
+ QtGui.QItemDelegate.__init__(self, None)
+
+ def setEditorData(self, editor, index):
+ """ setEditorData(editor: QWidget, index: QModelIndex) -> None
+ Set the current item (at index) data into editor for editting
+
+ """
+ text = index.data(QtCore.Qt.DisplayRole)
+ editor.setText(text)
+
+ def setModelData(self, editor, model, index):
+ """ setModelData(editor: QWidget, model: QAbstractItemModel,
+ index: QModelIndex) -> None
+ Assign the value of the editor back into the model and emit a
+ signal to update vistrail
+
+ """
+ text = str(editor.text())
+ row = index.row()
+ col = index.column()
+ keyItem = self.table.item(row, 0)
+ if keyItem:
+ key = str(keyItem.text())
+ else:
+ key = ''
+
+ valueItem = self.table.item(row, 1)
+ if valueItem:
+ value = str(valueItem.text())
+ else:
+ value = ''
+
+ if col==0:
+ if text=='' and row<self.table.rowCount()-1:
+ self.table.removeRow(row)
+ if self.table.controller and self.table.module:
+ self.table.lockUpdate()
+ self.table.controller.delete_annotation(key,
+ self.table.module.id)
+ self.table.unlockUpdate()
+ return
+ if text!='' and text!=key:
+ if (self.table.module and
+ self.table.module.has_annotation_with_key(text)):
+ if text == '__desc__':
+ QtGui.QMessageBox.information(None,
+ "VisTrails",
+ 'Please use "Set Module Label..." menu option'
+ ' to set the label for this module.')
+ else:
+ QtGui.QMessageBox.information(None,
+ "VisTrails",
+ text + ' already exists in '
+ 'the annotations.')
+ return
+
+ if col==1 and key=='':
+ QtGui.QMessageBox.information(None,
+ "VisTrails",
+ "Must provide a key first.")
+ return
+
+
+ if col==0 and key=='' and text!='' and value!='':
+ self.table.addRow()
+
+ if col==1:
+ if text!=value:
+ if self.table.controller and self.table.module:
+ self.table.lockUpdate()
+ self.table.controller.add_annotation((key, text),
+ self.table.module.id)
+ self.table.unlockUpdate()
+ if row == self.table.rowCount()-1:
+ self.table.addRow()
+
+ elif text!='' and self.table.controller and self.table.module:
+ moduleId = self.table.module.id
+ self.table.lockUpdate()
+ self.table.controller.previousModuleIds = [moduleId]
+ if key!=text and key!='':
+ self.table.controller.delete_annotation(key, moduleId)
+ self.table.controller.add_annotation((text, value),
+ moduleId)
+ self.table.unlockUpdate()
+
+ model.setData(index, text)
diff --git a/vistrails/gui/module_configuration.py b/vistrails/gui/module_configuration.py
new file mode 100644
index 0000000..b34f4c3
--- /dev/null
+++ b/vistrails/gui/module_configuration.py
@@ -0,0 +1,193 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file describe the module configuration box that is displayed when
+the user selects a module's "Edit Configuration"
+
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core.modules.module_registry import get_module_registry, \
+ ModuleRegistryException
+from vistrails.gui.modules.module_configure import DefaultModuleConfigurationWidget
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+
+################################################################################
+
+class QConfigurationWidget(QtGui.QWidget):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.setLayout(QtGui.QVBoxLayout())
+ self.widget = None
+ #self.setFocusPolicy(QtCore.Qt.StrongFocus)
+
+ def setUpWidget(self, widget):
+ self.widget = widget
+ self.layout().addWidget(self.widget)
+
+ def clear(self):
+ """ clear() -> None
+ Clear and delete widget in the layout
+
+ """
+ if self.widget:
+ self.widget.setVisible(False)
+ self.layout().removeWidget(self.widget)
+ self.widget.deleteLater()
+ self.widget = None
+
+ def askToSaveChanges(self):
+ if self.widget:
+ return self.widget.askToSaveChanges()
+
+ def activate(self):
+ if self.widget:
+ self.widget.activate()
+
+################################################################################
+
+class QModuleConfiguration(QtGui.QScrollArea, QVistrailsPaletteInterface):
+ def __init__(self, parent=None, scene=None):
+ """QModuleConfiguration(parent: QWidget) -> QModuleConfiguration
+ Initialize widget constraints
+
+ """
+ QtGui.QScrollArea.__init__(self, parent)
+ self.setWindowFlags(self.windowFlags() | QtCore.Qt.WindowStaysOnTopHint)
+ self.setWindowTitle('Module Configuration')
+ self.setWidgetResizable(True)
+ self.confWidget = QConfigurationWidget()
+ self.setWidget(self.confWidget)
+ self.module = None
+ self.controller = None
+ self.scene = scene
+ self.updateLocked = False
+ self.hasChanges = False
+
+ def set_controller(self, controller):
+ self.controller = controller
+ self.scene = controller.current_pipeline_scene
+
+ selected_ids = self.scene.get_selected_module_ids()
+ modules = [controller.current_pipeline.modules[i]
+ for i in selected_ids]
+ if len(modules) == 1:
+ self.updateModule(modules[0])
+ else:
+ self.updateModule(None)
+
+ def updateModule(self, module):
+ if self.updateLocked: return
+ self.check_need_save_changes()
+ self.module = module
+ self.confWidget.setUpdatesEnabled(False)
+ self.confWidget.setVisible(False)
+ self.confWidget.clear()
+ if module and self.controller:
+ # if module.has_annotation_with_key('__desc__'):
+ # label = module.get_annotation_by_key('__desc__').value.strip()
+ # title = '%s (%s) Module Configuration'%(label,
+ # module.name)
+ # else:
+ # title = '%s Module Configuration'%module.name
+ # self.setWindowTitle(title)
+ registry = get_module_registry()
+ getter = registry.get_configuration_widget
+ widgetType = None
+ try:
+ widgetType = \
+ getter(module.package, module.name, module.namespace)
+ except ModuleRegistryException:
+ pass
+ if not widgetType:
+ widgetType = DefaultModuleConfigurationWidget
+ widget = widgetType(module, self.controller)
+
+ self.confWidget.setUpWidget(widget)
+ self.connect(widget, QtCore.SIGNAL("doneConfigure"),
+ self.configureDone)
+ self.connect(widget, QtCore.SIGNAL("stateChanged"),
+ self.stateChanged)
+ self.confWidget.setUpdatesEnabled(True)
+ self.confWidget.setVisible(True)
+ self.hasChanges = False
+ # we need to reset the title in case there were changes
+ self.setWindowTitle("Module Configuration")
+
+ def configureDone(self):
+ from vistrails.gui.vistrails_window import _app
+ self.emit(QtCore.SIGNAL('doneConfigure'), self.module.id)
+ _app.notify('module_done_configure', self.module.id)
+
+ def stateChanged(self):
+ self.hasChanges = self.confWidget.widget.state_changed
+ # self.setWindowModified seems not to work here
+ # self.setWindowModified(self.hasChanges)
+ title = str(self.windowTitle())
+ if self.hasChanges:
+ if not title.endswith("*"):
+ self.setWindowTitle(title + "*")
+ else:
+ if title.endswith("*"):
+ self.setWindowTitle(title[:-1])
+
+ def lockUpdate(self):
+ """ lockUpdate() -> None
+ Do not allow updateModule()
+
+ """
+ self.updateLocked = True
+
+ def unlockUpdate(self):
+ """ unlockUpdate() -> None
+ Allow updateModule()
+
+ """
+ self.updateLocked = False
+
+ def closeEvent(self, event):
+ self.confWidget.askToSaveChanges()
+ event.accept()
+
+ def activate(self):
+ if self.isVisible() == False:
+ # self.toolWindow().show()
+ self.show()
+ self.activateWindow()
+ self.confWidget.activate()
+
+ def check_need_save_changes(self):
+ if self.confWidget:
+ self.lockUpdate()
+ self.confWidget.askToSaveChanges()
+ self.unlockUpdate()
diff --git a/vistrails/gui/module_documentation.py b/vistrails/gui/module_documentation.py
new file mode 100644
index 0000000..ef5df24
--- /dev/null
+++ b/vistrails/gui/module_documentation.py
@@ -0,0 +1,113 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file contains a dialog and widgets related to the module documentation
+dialog, which displays the available documentation for a given VisTrails module.
+
+QModuleDocumentation
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core.modules.module_registry import ModuleRegistryException
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+
+################################################################################
+
+class QModuleDocumentation(QtGui.QDialog, QVistrailsPaletteInterface):
+ """
+ QModuleDocumentation is a dialog for showing module documentation. duh.
+
+ """
+ def __init__(self, parent=None):
+ """
+ QModuleAnnotation(parent)
+ -> None
+
+ """
+ QtGui.QDialog.__init__(self, parent)
+ # self.setModal(True)
+ self.setWindowTitle("Module Documentation")
+ self.setLayout(QtGui.QVBoxLayout())
+ # self.layout().addStrut()
+ self.name_label = QtGui.QLabel("")
+ self.layout().addWidget(self.name_label)
+ self.package_label = QtGui.QLabel("")
+ self.layout().addWidget(self.package_label)
+ # self.closeButton = QtGui.QPushButton('Ok', self)
+ self.textEdit = QtGui.QTextEdit(self)
+ self.layout().addWidget(self.textEdit, 1)
+ self.textEdit.setReadOnly(True)
+ self.textEdit.setTextCursor(QtGui.QTextCursor(self.textEdit.document()))
+ # self.layout().addWidget(self.closeButton)
+ # self.connect(self.closeButton, QtCore.SIGNAL('clicked(bool)'),
+ # self.close)
+ # self.closeButton.setShortcut('Enter')
+
+ self.update_descriptor()
+
+ def set_controller(self, controller):
+ scene = controller.current_pipeline_scene
+ selected_ids = scene.get_selected_module_ids()
+ modules = [controller.current_pipeline.modules[i]
+ for i in selected_ids]
+ if len(modules) == 1:
+ self.update_module(modules[0])
+ else:
+ self.update_module(None)
+
+ def update_module(self, module=None):
+ descriptor = None
+ try:
+ if module and module.module_descriptor:
+ descriptor = module.module_descriptor
+ except ModuleRegistryException:
+ pass
+ self.update_descriptor(descriptor, module)
+
+ def update_descriptor(self, descriptor=None, module=None):
+ if descriptor is None:
+ # self.setWindowTitle("Module Documentation")
+ self.name_label.setText("Module name:")
+ self.package_label.setText("Module package:")
+ self.textEdit.setText("")
+ else:
+ # self.setWindowTitle('%s Documentation' % descriptor.name)
+ self.name_label.setText("Module name: %s" % descriptor.name)
+ self.package_label.setText("Module package: %s" % \
+ descriptor.module_package())
+ self.textEdit.setText(descriptor.module_documentation(module))
+
+ def activate(self):
+ if self.isVisible() == False:
+ self.show()
+ self.activateWindow()
diff --git a/vistrails/gui/module_info.py b/vistrails/gui/module_info.py
new file mode 100644
index 0000000..b35c1a7
--- /dev/null
+++ b/vistrails/gui/module_info.py
@@ -0,0 +1,211 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core.utils import versions_increasing
+from vistrails.gui.common_widgets import QDockPushButton
+from vistrails.gui.module_annotation import QModuleAnnotationTable
+from vistrails.gui.ports_pane import PortsList
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+
+class QModuleInfo(QtGui.QWidget, QVistrailsPaletteInterface):
+ def __init__(self, parent=None, flags=QtCore.Qt.Widget):
+ QtGui.QWidget.__init__(self, parent, flags)
+ self.build_widget()
+ self.controller = None
+ self.module = None
+ self.pipeline_view = None # pipeline_view
+ self.read_only = False
+ self.is_updating = False
+
+ def build_widget(self):
+ name_label = QtGui.QLabel("Name:")
+ self.name_edit = QtGui.QLineEdit()
+ self.connect(self.name_edit, QtCore.SIGNAL('editingFinished()'),
+ self.name_editing_finished)
+ self.name_edit.setMinimumSize(50, 22)
+ type_label = QtGui.QLabel("Type:")
+ self.type_edit = QtGui.QLabel("")
+ # self.type_edit.setReadOnly(True)
+ package_label = QtGui.QLabel("Package:")
+ self.package_edit = QtGui.QLabel("")
+ # self.package_edit.setReadOnly(True)
+ id = QtGui.QLabel("Id:")
+ self.module_id = QtGui.QLabel("")
+ # self.module_id.setReadOnly(True)
+ self.configure_button = QDockPushButton("Configure")
+ self.connect(self.configure_button, QtCore.SIGNAL('clicked()'),
+ self.configure)
+ self.doc_button = QDockPushButton("Documentation")
+ self.connect(self.doc_button, QtCore.SIGNAL('clicked()'),
+ self.documentation)
+
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(2)
+ layout.setSpacing(4)
+ def add_line(left, right):
+ h_layout = QtGui.QHBoxLayout()
+ h_layout.setMargin(2)
+ h_layout.setSpacing(2)
+ h_layout.setAlignment(QtCore.Qt.AlignLeft)
+ h_layout.addWidget(left)
+ h_layout.addWidget(right)
+ h_widget = QtGui.QWidget()
+ h_widget.setLayout(h_layout)
+ h_widget.setSizePolicy(QtGui.QSizePolicy.Ignored,
+ QtGui.QSizePolicy.Preferred)
+ layout.addWidget(h_widget)
+ add_line(name_label, self.name_edit)
+ add_line(type_label, self.type_edit)
+ add_line(package_label, self.package_edit)
+ add_line(id, self.module_id)
+ h_layout = QtGui.QHBoxLayout()
+ h_layout.setMargin(2)
+ h_layout.setSpacing(5)
+ h_layout.setAlignment(QtCore.Qt.AlignCenter)
+ h_layout.addWidget(self.configure_button)
+ h_layout.addWidget(self.doc_button)
+ layout.addLayout(h_layout)
+
+ self.tab_widget = QtGui.QTabWidget()
+ # this causes a crash when undocking the palette in Mac OS X
+ # see https://bugreports.qt-project.org/browse/QTBUG-16851
+ # self.tab_widget.setDocumentMode(True)
+ self.input_ports_list = PortsList('input')
+ self.tab_widget.addTab(self.input_ports_list, 'Inputs')
+ self.output_ports_list = PortsList('output')
+ self.tab_widget.addTab(self.output_ports_list, 'Outputs')
+ self.ports_lists = [self.input_ports_list,
+ self.output_ports_list]
+ self.annotations = QModuleAnnotationTable()
+ self.tab_widget.addTab(self.annotations, 'Annotations')
+ layout.addWidget(self.tab_widget, 1)
+
+ layout.setAlignment(QtCore.Qt.AlignTop)
+ self.setLayout(layout)
+ self.setWindowTitle('Module Information')
+
+ def setReadOnly(self, read_only):
+ if read_only != self.read_only:
+ self.read_only = read_only
+ for widget in self.ports_lists + [self.annotations]:
+ widget.setReadOnly(read_only)
+
+ def set_controller(self, controller):
+ self.controller = controller
+ for ports_list in self.ports_lists:
+ ports_list.set_controller(controller)
+ self.annotations.set_controller(controller)
+
+ scene = self.controller.current_pipeline_scene
+ selected_ids = scene.get_selected_module_ids()
+ modules = [self.controller.current_pipeline.modules[i]
+ for i in selected_ids]
+ if len(modules) == 1:
+ self.update_module(modules[0])
+ else:
+ self.update_module(None)
+
+ def update_module(self, module=None):
+ self.module = module
+ for ports_list in self.ports_lists:
+ ports_list.update_module(module)
+ self.annotations.updateModule(module)
+
+ if module is None:
+ self.name_edit.setText("")
+ if not versions_increasing(QtCore.QT_VERSION_STR, '4.7.0'):
+ self.name_edit.setPlaceholderText("")
+ # self.name_edit.setEnabled(False)
+ self.type_edit.setText("")
+ # self.type_edit.setEnabled(False)
+ self.package_edit.setText("")
+ self.module_id.setText("")
+ else:
+ if module.has_annotation_with_key('__desc__'):
+ label = module.get_annotation_by_key('__desc__').value.strip()
+ else:
+ label = ''
+ self.name_edit.setText(label)
+ if not label and not versions_increasing(QtCore.QT_VERSION_STR,
+ '4.7.0'):
+ self.name_edit.setPlaceholderText(self.module.name)
+
+ # self.name_edit.setEnabled(True)
+ self.type_edit.setText(self.module.name)
+ # self.type_edit.setEnabled(True)
+ self.package_edit.setText(self.module.package)
+ # self.package_edit.setEnabled(True)
+ self.module_id.setText('%d' % self.module.id)
+ # self.module_id.setEnabled(True)
+
+ def name_editing_finished(self):
+ # updating module may trigger a second call so we check for that
+ if self.is_updating or self.module is None:
+ return
+ try:
+ self.is_updating = True
+ old_text = ''
+ if self.module.has_annotation_with_key('__desc__'):
+ old_text = self.module.get_annotation_by_key('__desc__').value
+ new_text = str(self.name_edit.text()).strip()
+ if not new_text:
+ if old_text:
+ self.controller.delete_annotation('__desc__',
+ self.module.id)
+ elif old_text != new_text:
+ self.controller.add_annotation(('__desc__', new_text),
+ self.module.id)
+ scene = self.controller.current_pipeline_scene
+ scene.recreate_module(self.controller.current_pipeline,
+ self.module.id)
+ finally:
+ self.is_updating = False
+
+ def configure(self):
+ from vistrails.gui.vistrails_window import _app
+ _app.configure_module()
+
+ def documentation(self):
+ from vistrails.gui.vistrails_window import _app
+ _app.show_documentation()
+
+ def update_entry_klass(self, entry_klass):
+ self.input_ports_list.set_entry_klass(entry_klass)
+
+ def show_annotations(self):
+ if self.module is not None:
+ self.tab_widget.setCurrentWidget(self.annotations)
+ self.annotations.editNextAvailableCell()
diff --git a/vistrails/gui/module_palette.py b/vistrails/gui/module_palette.py
new file mode 100644
index 0000000..36668f0
--- /dev/null
+++ b/vistrails/gui/module_palette.py
@@ -0,0 +1,544 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file contains widgets related to the module palette
+displaying a list of all modules in Vistrails
+
+QModulePalette
+QModuleTreeWidget
+QModuleTreeWidgetItem
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core import get_vistrails_application
+from vistrails.core import debug
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.system import systemType
+from vistrails.core.utils import VistrailsInternalError
+from vistrails.gui.common_widgets import (QSearchTreeWindow,
+ QSearchTreeWidget)
+from vistrails.gui.module_documentation import QModuleDocumentation
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+import weakref
+
+################################################################################
+
+class QModulePalette(QSearchTreeWindow, QVistrailsPaletteInterface):
+ """
+ QModulePalette just inherits from QSearchTreeWindow to have its
+ own type of tree widget
+
+ """
+ def __init__(self, parent=None):
+ QSearchTreeWindow.__init__(self, parent)
+ self.setContentsMargins(0,5,0,0)
+ self.packages = {}
+ self.namespaces = {}
+ self.addButtonsToToolBar()
+
+ def addButtonsToToolBar(self):
+ self.expandAction = QtGui.QAction(CurrentTheme.EXPAND_ALL_ICON,
+ "Expand All", self.toolWindow().toolbar,
+ triggered=self.expandAll)
+
+ self.collapseAction = QtGui.QAction(CurrentTheme.COLLAPSE_ALL_ICON,
+ "Collapse All", self.toolWindow().toolbar,
+ triggered=self.collapseAll)
+ self.toolWindow().toolbar.insertAction(self.toolWindow().pinAction,
+ self.collapseAction)
+ self.toolWindow().toolbar.insertAction(self.toolWindow().pinAction,
+ self.expandAction)
+
+ def expandAll(self):
+ self.treeWidget.expandAll()
+
+ def collapseAll(self):
+ self.treeWidget.collapseAll()
+
+ def link_registry(self):
+ self.updateFromModuleRegistry()
+ self.connect_registry_signals()
+
+
+ def connect_registry_signals(self):
+ app = get_vistrails_application()
+ app.register_notification("reg_new_module", self.newModule)
+ app.register_notification("reg_new_package", self.newPackage)
+ app.register_notification("reg_deleted_module", self.deletedModule)
+ app.register_notification("reg_deleted_package", self.deletedPackage)
+ app.register_notification("reg_show_module", self.showModule)
+ app.register_notification("reg_hide_module", self.hideModule)
+ app.register_notification("reg_module_updated", self.switchDescriptors)
+
+ # registry = get_module_registry()
+ # self.connect(registry.signals, registry.signals.new_package_signal,
+ # self.newPackage)
+ # self.connect(registry.signals, registry.signals.new_module_signal,
+ # self.newModule)
+ # self.connect(registry.signals, registry.signals.deleted_module_signal,
+ # self.deletedModule)
+ # self.connect(registry.signals, registry.signals.deleted_package_signal,
+ # self.deletedPackage)
+ # self.connect(registry.signals, registry.signals.show_module_signal,
+ # self.showModule)
+ # self.connect(registry.signals, registry.signals.hide_module_signal,
+ # self.hideModule)
+ # self.connect(registry.signals, registry.signals.module_updated_signal,
+ # self.switchDescriptors)
+
+ def createTreeWidget(self):
+ """ createTreeWidget() -> QModuleTreeWidget
+ Return the search tree widget for this window
+
+ """
+ self.setWindowTitle('Modules')
+ return QModuleTreeWidget(self)
+
+ def findModule(self, descriptor):
+ moduleName = descriptor.name
+
+ items = [x for x in
+ self.treeWidget.findItems(moduleName,
+ QtCore.Qt.MatchExactly |
+ QtCore.Qt.MatchWrap |
+ QtCore.Qt.MatchRecursive)
+ if not x.is_top_level() and x.descriptor == descriptor]
+ if len(items) <> 1:
+ raise VistrailsInternalError("Expected one item (%s), got %d: %s" %
+ (moduleName,
+ len(items),
+ ";".join(x.descriptor.name
+ for x in items)))
+ item = items[0]
+ return item
+
+ def showModule(self, descriptor):
+ item = self.findModule(descriptor)
+ item.setHidden(False)
+
+ def hideModule(self, descriptor):
+ item = self.findModule(descriptor)
+ item.setHidden(True)
+
+ def switchDescriptors(self, old_descriptor, new_descriptor):
+ old_item = self.findModule(old_descriptor)
+ new_item = self.findModule(new_descriptor)
+ old_item.set_descriptor(new_descriptor)
+ new_item.set_descriptor(old_descriptor)
+
+ def deletedModule(self, descriptor):
+ """ deletedModule(descriptor: core.modules.module_registry.ModuleDescriptor)
+ A module has been removed from VisTrails
+
+ """
+ if descriptor.module_abstract():
+ # skip abstract and hidden modules, they're not in the tree
+ return
+
+ item = self.findModule(descriptor)
+ parent = item.parent()
+ parent.takeChild(parent.indexOfChild(item))
+ del item.descriptor
+
+ def deletedPackage(self, package):
+ """ deletedPackage(package):
+ A package has been deleted from VisTrails
+ """
+ item = self.packages[package.identifier]()
+ index = self.treeWidget.indexOfTopLevelItem(item)
+ self.treeWidget.takeTopLevelItem(index)
+ del self.packages[package.identifier]
+
+ def newPackage(self, package_identifier, prepend=False):
+ # prepend places at the front of the list of packages,
+ # by default adds to the end of the list of packages
+ # Right now the list is sorted so prepend has no effect
+ if package_identifier in self.packages:
+ return self.packages[package_identifier]
+ registry = get_module_registry()
+ package_name = registry.packages[package_identifier].name
+ package_item = \
+ QPackageTreeWidgetItem(None, [package_name])
+ self.packages[package_identifier] = weakref.ref(package_item)
+ if prepend:
+ self.treeWidget.insertTopLevelItem(0, package_item)
+ else:
+ self.treeWidget.addTopLevelItem(package_item)
+ return package_item
+
+ def newModule(self, descriptor, recurse=False):
+ """ newModule(descriptor: core.modules.module_registry.ModuleDescriptor)
+ A new module has been added to VisTrails
+
+ """
+ if not descriptor.module_abstract(): # and not descriptor.is_hidden:
+ # skip abstract modules, they're no longer in the tree
+
+ # NB: only looks for toplevel matches
+ package_identifier = descriptor.ghost_identifier or descriptor.identifier
+ if package_identifier not in self.packages:
+ package_item = self.newPackage(package_identifier, True)
+ else:
+ package_item = self.packages[package_identifier]()
+
+ if descriptor.ghost_namespace is not None:
+ namespace = descriptor.ghost_namespace
+ else:
+ namespace = descriptor.namespace
+ if descriptor.namespace_hidden or not namespace:
+ parent_item = package_item
+ else:
+ parent_item = \
+ package_item.get_namespace(namespace.split('|'))
+
+ item = QModuleTreeWidgetItem(descriptor, parent_item,
+ [descriptor.name],
+ descriptor.is_hidden)
+ if descriptor.is_hidden:
+ item.setHidden(True)
+ if recurse:
+ for child in descriptor.children:
+ self.newModule(child, recurse)
+
+ def updateFromModuleRegistry(self):
+ """ updateFromModuleRegistry(packageName: str) -> None
+ Setup this tree widget to show modules currently inside
+ module_registry.registry
+
+ """
+
+ self.treeWidget.setSortingEnabled(False)
+ registry = get_module_registry()
+ for package in registry.package_list:
+ self.newPackage(package.identifier)
+ self.newModule(registry.root_descriptor, True)
+ self.treeWidget.sortByColumn(0, QtCore.Qt.AscendingOrder)
+ self.treeWidget.setSortingEnabled(True)
+# self.treeWidget.expandAll()
+
+ def sizeHint(self):
+ return QtCore.QSize(256, 760)
+
+class QModuleTreeWidget(QSearchTreeWidget):
+ """
+ QModuleTreeWidget is a subclass of QSearchTreeWidget to display all
+ Vistrails Module
+
+ """
+ def __init__(self, parent=None):
+ """ QModuleTreeWidget(parent: QWidget) -> QModuleTreeWidget
+ Set up size policy and header
+
+ """
+ QSearchTreeWidget.__init__(self, parent)
+ self.header().hide()
+ self.setRootIsDecorated(False)
+ self.delegate = QModuleTreeWidgetItemDelegate(self, self)
+ self.setItemDelegate(self.delegate)
+ self.connect(self,
+ QtCore.SIGNAL('itemPressed(QTreeWidgetItem *,int)'),
+ self.onItemPressed)
+
+ def onItemPressed(self, item, column):
+ """ onItemPressed(item: QTreeWidgetItem, column: int) -> None
+ Expand/Collapse top-level item when the mouse is pressed
+
+ """
+ if item and item.parent() == None:
+ self.setItemExpanded(item, not self.isItemExpanded(item))
+
+ def contextMenuEvent(self, event):
+ # Just dispatches the menu event to the widget item
+ item = self.itemAt(event.pos())
+ if item:
+ # find top level
+ p = item
+ while p.parent():
+ p = p.parent()
+ # get package identifier
+ identifiers = [i for i, j in self.parent().packages.iteritems()
+ if j == weakref.ref(p)]
+ if identifiers:
+ try:
+ identifier = identifiers[0]
+ registry = get_module_registry()
+ package = registry.packages[identifier]
+ if package.has_contextMenuName():
+ name = package.contextMenuName(str(item.text(0)))
+ if name:
+ act = QtGui.QAction(name, self)
+ act.setStatusTip(name)
+ def callMenu():
+ if package.has_callContextMenu():
+ name = package.callContextMenu(str(item.text(0)))
+
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ callMenu)
+ menu = QtGui.QMenu(self)
+ menu.addAction(act)
+ menu.exec_(event.globalPos())
+ return
+ except Exception, e:
+ debug.warning("Got exception trying to display %s's "
+ "context menu in the palette: %s: %s" % (
+ package.name,
+ type(e).__name__, ', '.join(e.args)))
+
+ item.contextMenuEvent(event, self)
+
+ def startDrag(self, actions):
+ indexes = self.selectedIndexes()
+ if len(indexes) > 0:
+ mime_data = self.model().mimeData(indexes)
+ drag = QtGui.QDrag(self)
+ drag.setMimeData(mime_data)
+ item = mime_data.items[0]
+
+ app = get_vistrails_application()
+ pipeline_view = app.builderWindow.get_current_controller().current_pipeline_view
+ if hasattr(pipeline_view.scene(), 'add_tmp_module'):
+ module_item = \
+ pipeline_view.scene().add_tmp_module(item.descriptor)
+ pixmap = pipeline_view.paintModuleToPixmap(module_item)
+
+ drag.setPixmap(pixmap)
+ drag.setHotSpot(QtCore.QPoint(pixmap.width()/2,
+ pixmap.height()/2))
+ drag.exec_(actions)
+ pipeline_view.scene().delete_tmp_module()
+
+
+class QModuleTreeWidgetItemDelegate(QtGui.QItemDelegate):
+ """
+ QModuleTreeWidgetItemDelegate will override the original
+ QTreeWidget paint function to draw buttons for top-level item
+ similar to QtDesigner. This mimics
+ Qt/tools/designer/src/lib/shared/sheet_delegate, which is only a
+ private class from QtDesigned.
+
+ """
+ def __init__(self, view, parent):
+ """ QModuleTreeWidgetItemDelegate(view: QTreeView,
+ parent: QWidget)
+ -> QModuleTreeWidgetItemDelegate
+ Create the item delegate given the tree view
+
+ """
+ QtGui.QItemDelegate.__init__(self, parent)
+ self.treeView = view
+ self.isMac = systemType in ['Darwin']
+
+ def paint(self, painter, option, index):
+ """ painter(painter: QPainter, option QStyleOptionViewItem,
+ index: QModelIndex) -> None
+ Repaint the top-level item to have a button-look style
+
+ """
+ model = index.model()
+ if not model.parent(index).isValid():
+ buttonOption = QtGui.QStyleOptionButton()
+ buttonOption.state = option.state
+ if self.isMac:
+ buttonOption.state |= QtGui.QStyle.State_Raised
+ buttonOption.state &= ~QtGui.QStyle.State_HasFocus
+
+ buttonOption.rect = option.rect
+ buttonOption.palette = option.palette
+ buttonOption.features = QtGui.QStyleOptionButton.None
+
+ style = self.treeView.style()
+
+ style.drawControl(QtGui.QStyle.CE_PushButton,
+ buttonOption,
+ painter,
+ self.treeView)
+
+ branchOption = QtGui.QStyleOption()
+ i = 9 ### hardcoded in qcommonstyle.cpp
+ r = option.rect
+ branchOption.rect = QtCore.QRect(r.left() + i / 2,
+ r.top() + (r.height() - i) / 2,
+ i, i)
+ branchOption.palette = option.palette
+ branchOption.state = QtGui.QStyle.State_Children
+
+ if self.treeView.isExpanded(index):
+ branchOption.state |= QtGui.QStyle.State_Open
+
+ style.drawPrimitive(QtGui.QStyle.PE_IndicatorBranch,
+ branchOption,
+ painter, self.treeView)
+
+ textrect = QtCore.QRect(r.left() + i * 2,
+ r.top(),
+ r.width() - ((5 * i) / 2),
+ r.height())
+ text = option.fontMetrics.elidedText(
+ model.data(index,
+ QtCore.Qt.DisplayRole),
+ QtCore.Qt.ElideMiddle,
+ textrect.width())
+ style.drawItemText(painter,
+ textrect,
+ QtCore.Qt.AlignCenter,
+ option.palette,
+ self.treeView.isEnabled(),
+ text)
+ else:
+ QtGui.QItemDelegate.paint(self, painter, option, index)
+
+ def sizeHint(self, option, index):
+ """ sizeHint(option: QStyleOptionViewItem, index: QModelIndex) -> None
+ Take into account the size of the top-level button
+
+ """
+ return (QtGui.QItemDelegate.sizeHint(self, option, index) +
+ QtCore.QSize(2, 2))
+
+
+
+class QModuleTreeWidgetItem(QtGui.QTreeWidgetItem):
+ """
+ QModuleTreeWidgetItem represents module on QModuleTreeWidget
+
+ """
+
+ def __init__(self, descriptor, parent, labelList, is_hidden):
+ """ QModuleTreeWidgetItem(descriptor: ModuleDescriptor
+ (or None for top-level),
+ parent: QTreeWidgetItem
+ labelList: string)
+ -> QModuleTreeWidget
+ Create a new tree widget item with a specific parent and
+ labels
+
+ """
+ QtGui.QTreeWidgetItem.__init__(self, parent, labelList)
+ self.set_descriptor(descriptor)
+
+ # Real flags store the widget's flags prior to masking related
+ # to abstract modules, etc.
+ self._real_flags = self.flags()
+
+ # This is necessary since we override setFlags
+ self.setFlags(self._real_flags)
+
+ self.is_hidden = is_hidden
+
+ def added_input_port(self):
+ self.setFlags(self._real_flags)
+
+ def added_output_port(self):
+ self.setFlags(self._real_flags)
+
+ def setFlags(self, flags):
+ self._real_flags = flags
+ d = self.descriptor
+ if d is None:
+ # toplevel moduletree widgets are never draggable
+ flags = flags & ~QtCore.Qt.ItemIsDragEnabled
+ elif d.module_abstract():
+ # moduletree widgets for abstract modules are never
+ # draggable or enabled
+ flags = flags & ~(QtCore.Qt.ItemIsDragEnabled |
+ QtCore.Qt.ItemIsSelectable)
+ QtGui.QTreeWidgetItem.setFlags(self, flags)
+
+ def is_top_level(self):
+ return self.descriptor is None
+
+ def contextMenuEvent(self, event, widget):
+ if self.is_top_level():
+ return
+ menu = QtGui.QMenu(widget)
+ act = QtGui.QAction("View Documentation", widget)
+ act.setStatusTip("View module documentation")
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ self.view_documentation)
+ menu.addAction(act)
+ if self.descriptor.package == 'local.abstractions':
+ act = QtGui.QAction("Edit Subworkflow", widget)
+ act.setStatusTip("Edit this Subworkflow")
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ self.edit_subworkflow)
+ menu.addAction(act)
+ menu.exec_(event.globalPos())
+
+ def view_documentation(self):
+ from vistrails_window import _app
+ _app.show_documentation()
+ widget = QModuleDocumentation.instance()
+ widget.update_descriptor(self.descriptor)
+
+ def edit_subworkflow(self):
+ from vistrails_window import _app
+ filename = self.descriptor.module.vt_fname
+ _app.openAbstraction(filename)
+
+ def set_descriptor(self, descriptor):
+ self.descriptor = descriptor
+ if descriptor:
+ descriptor.set_widget(self)
+
+class QNamespaceTreeWidgetItem(QModuleTreeWidgetItem):
+ def __init__(self, parent, labelList):
+ QModuleTreeWidgetItem.__init__(self, None, parent, labelList, False)
+ self.setFlags(self.flags() & ~QtCore.Qt.ItemIsDragEnabled)
+ self.namespaces = {}
+
+ def get_namespace(self, namespace_items):
+ if len(namespace_items) <= 0:
+ return self
+ namespace_item = namespace_items.pop(0)
+ if namespace_item in self.namespaces and self.namespaces[namespace_item]():
+ item = self.namespaces[namespace_item]()
+ else:
+ item = QNamespaceTreeWidgetItem(self, [namespace_item])
+ self.namespaces[namespace_item] = weakref.ref(item)
+ return item.get_namespace(namespace_items)
+
+ def takeChild(self, index):
+ child = self.child(index)
+ if hasattr(self, "namespaces"):
+ if str(child.text(0)) in self.namespaces:
+ del self.namespaces[str(child.text(0))]
+ QModuleTreeWidgetItem.takeChild(self, index)
+ if self.childCount() < 1 and self.parent():
+ self.parent().takeChild(self.parent().indexOfChild(self))
+
+class QPackageTreeWidgetItem(QNamespaceTreeWidgetItem):
+ pass
diff --git a/vistrails/gui/modules/__init__.py b/vistrails/gui/modules/__init__.py
new file mode 100644
index 0000000..e2481ce
--- /dev/null
+++ b/vistrails/gui/modules/__init__.py
@@ -0,0 +1,63 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from constant_configuration import StandardConstantWidgetBase
+from query_configuration import BaseQueryWidget
+
+def get_widget_class(module_klass):
+ klass = module_klass.get_widget_class()
+ if klass is None:
+ return StandardConstantWidgetBase
+ if isinstance(klass, tuple):
+ (path, klass_name) = klass
+ module = __import__(path, globals(), locals(), [klass_name])
+ return getattr(module, klass_name)
+ return klass
+
+def get_query_widget_class(module_klass):
+ klass = module_klass.get_query_widget_class()
+ if klass is None:
+ class DefaultQueryWidget(BaseQueryWidget):
+ def __init__(self, param, parent=None):
+ BaseQueryWidget.__init__(self, get_widget_class(module_klass),
+ ["==", "!="],
+ param, parent)
+ return DefaultQueryWidget
+ if isinstance(klass, tuple):
+ (path, klass_name) = klass
+ module = __import__(path, globals(), locals(), [klass_name])
+ return getattr(module, klass_name)
+ return klass
+
diff --git a/vistrails/gui/modules/constant_configuration.py b/vistrails/gui/modules/constant_configuration.py
new file mode 100644
index 0000000..88d517a
--- /dev/null
+++ b/vistrails/gui/modules/constant_configuration.py
@@ -0,0 +1,775 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file specifies the configuration widget for Constant
+modules. Please notice that this is different from the module configuration
+widget described in module_configure.py. We present a Color constant to be
+used as a template for creating a configuration widget for other custom
+constants.
+
+"""
+
+from PyQt4 import QtCore, QtGui
+from vistrails.core.utils import any, expression, versions_increasing
+from vistrails.core import system
+from vistrails.gui.theme import CurrentTheme
+
+############################################################################
+
+def setPlaceholderTextCompat(self, value):
+ """ Qt pre 4.7.0 does not have setPlaceholderText
+ """
+ if versions_increasing(QtCore.QT_VERSION_STR, '4.7.0'):
+ self.setText(value)
+ else:
+ self.setPlaceholderText(value)
+
+class ConstantWidgetMixin(object):
+
+ def __init__(self, contents=None):
+ self._last_contents = contents
+
+ def update_parent(self):
+ newContents = self.contents()
+ if newContents != self._last_contents:
+ if self.parent() and hasattr(self.parent(), 'updateMethod'):
+ self.parent().updateMethod()
+ self._last_contents = newContents
+ self.emit(QtCore.SIGNAL('contentsChanged'), (self, newContents))
+
+ def setDefault(self, strValue):
+ pass
+
+class StandardConstantWidgetBase(ConstantWidgetMixin):
+ """
+ StandardConstantWidget is a basic widget to be used
+ to edit int/float/string values in VisTrails.
+
+ When creating your own widget, you can subclass from this widget if you
+ need only a QLineEdit or use your own QT widget. There are two things you
+ need to pay attention to:
+
+ 1) Re-implement the contents() method so we can get the current value
+ stored in the widget.
+
+ 2) When the user is done with configuration, make sure to call
+ update_parent() so VisTrails can pass that information to the Provenance
+ System. In this example we do that on focusOutEvent and when the user
+ presses the return key.
+
+ """
+ def __new__(cls, *args, **kwargs):
+ param = None
+ if len(args) > 0:
+ param = args[0]
+ if 'param' in kwargs:
+ param = kwargs['param']
+ if param is None:
+ raise ValueError("Must pass param as first argument.")
+ if param.port_spec_item and param.port_spec_item.entry_type and \
+ param.port_spec_item.entry_type.startswith("enum"):
+ return StandardConstantEnumWidget.__new__(StandardConstantEnumWidget, *args, **kwargs)
+ return StandardConstantWidget.__new__(StandardConstantWidget, *args, **kwargs)
+
+ def __init__(self, param, parent=None):
+ """__init__(param: core.vistrail.module_param.ModuleParam,
+ parent: QWidget)
+
+ Initialize the line edit with its contents. Content type is limited
+ to 'int', 'float', and 'string'
+
+ """
+
+ psi = param.port_spec_item
+ if param.strValue:
+ value = param.strValue
+ elif psi and psi.default:
+ value = psi.default
+ else:
+ value = param.strValue
+ ConstantWidgetMixin.__init__(self, value)
+
+ # assert param.namespace == None
+ # assert param.identifier == 'org.vistrails.vistrails.basic'
+ if psi and psi.default:
+ self.setDefault(psi.default)
+ contents = param.strValue
+ contentType = param.type
+ if contents: # do not replace old default value with empty value
+ self.setText(contents)
+ self._contentType = contentType
+
+ def setDefault(self, default):
+ # Implement this in a subclass!
+ pass
+
+ def contents(self):
+ """contents() -> str
+ Re-implement this method to make sure that it will return a string
+ representation of the value that it will be passed to the module
+ As this is a QLineEdit, we just call text()
+
+ """
+ self.update_text()
+ return str(self.text())
+
+ def setContents(self, strValue, silent=True):
+ """setContents(strValue: str) -> None
+ Re-implement this method so the widget can change its value after
+ constructed. If silent is False, it will propagate the event back
+ to the parent.
+ As this is a QLineEdit, we just call setText(strValue)
+ """
+ self.setText(strValue)
+ self.update_text()
+ if not silent:
+ self.update_parent()
+
+ def update_text(self):
+ """ update_text() -> None
+ Update the text to the result of the evaluation
+
+ """
+ # FIXME: eval should pretty much never be used
+ base = expression.evaluate_expressions(self.text())
+ if self._contentType == 'String':
+ self.setText(base)
+ else:
+ try:
+ self.setText(str(eval(str(base), None, None)))
+ except:
+ self.setText(base)
+
+
+class StandardConstantWidget(QtGui.QLineEdit, StandardConstantWidgetBase):
+ def __init__(self, param, parent=None):
+ QtGui.QLineEdit.__init__(self, parent)
+ StandardConstantWidgetBase.__init__(self, param, parent)
+ self.connect(self,
+ QtCore.SIGNAL('returnPressed()'),
+ self.update_parent)
+
+ def setDefault(self, value):
+ setPlaceholderTextCompat(self, value)
+
+ def sizeHint(self):
+ metrics = QtGui.QFontMetrics(self.font())
+ width = min(metrics.width(self.text())+10,70)
+ return QtCore.QSize(width,
+ metrics.height()+6)
+
+ def minimumSizeHint(self):
+ return self.sizeHint()
+
+ ###########################################################################
+ # event handlers
+
+ def focusInEvent(self, event):
+ """ focusInEvent(event: QEvent) -> None
+ Pass the event to the parent
+
+ """
+ self._contents = str(self.text())
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+ QtGui.QLineEdit.focusInEvent(self, event)
+
+ def focusOutEvent(self, event):
+ self.update_parent()
+ QtGui.QLineEdit.focusOutEvent(self, event)
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+
+
+class BaseStringWidget(object): # < virtual QtGui.QWidget
+ def focusInEvent(self, event):
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+ super(BaseStringWidget, self).focusInEvent(event)
+
+ def focusOutEvent(self, event):
+ self.parent().update_parent()
+ super(BaseStringWidget, self).focusOutEvent(event)
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+
+
+class SingleLineStringWidget(BaseStringWidget, QtGui.QLineEdit):
+ def __init__(self, parent, contents="", default=""):
+ QtGui.QLineEdit.__init__(self, contents, parent)
+ self.setDefault(default)
+
+ self.connect(self,
+ QtCore.SIGNAL('returnPressed()'),
+ parent.update_parent)
+
+ def setContents(self, contents):
+ self.setText(expression.evaluate_expressions(contents))
+
+ def contents(self):
+ contents = expression.evaluate_expressions(unicode(self.text()))
+ self.setText(contents)
+ return contents
+
+ def setDefault(self, value):
+ setPlaceholderTextCompat(self, value)
+
+ def sizeHint(self):
+ metrics = QtGui.QFontMetrics(self.font())
+ width = min(metrics.width(self.text()) + 10, 70)
+ return QtCore.QSize(width,
+ metrics.height() + 6)
+
+ def minimumSizeHint(self):
+ return self.sizeHint()
+
+
+class MultiLineStringWidget(BaseStringWidget, QtGui.QTextEdit):
+ def __init__(self, parent, contents="", default=""):
+ QtGui.QTextEdit.__init__(self, parent)
+ self.setPlainText(contents)
+ self.setAcceptRichText(False)
+ self.setDefault(default)
+
+ def setContents(self, contents):
+ self.setPlainText(expression.evaluate_expressions(contents))
+
+ def contents(self):
+ contents = expression.evaluate_expressions(unicode(self.toPlainText()))
+ self.setPlainText(contents)
+ return contents
+
+ def setDefault(self, value):
+ pass # TODO : some magic will be required for this
+
+ def sizeHint(self):
+ metrics = QtGui.QFontMetrics(self.font())
+ width = 70
+ return QtCore.QSize(width,
+ (metrics.height() + 1) * 3 + 5)
+
+ def minimumSizeHint(self):
+ return self.sizeHint()
+
+
+class StringWidget(QtGui.QWidget, ConstantWidgetMixin):
+ def __new__(cls, *args, **kwargs):
+ param = None
+ if len(args) > 0:
+ param = args[0]
+ if 'param' in kwargs:
+ param = kwargs['param']
+ if param is None:
+ raise ValueError("Must pass param as first argument.")
+ if param.port_spec_item and param.port_spec_item.entry_type and \
+ param.port_spec_item.entry_type.startswith("enum"):
+ # StandardConstantEnumWidget is not related to StringWidget, so
+ # we have to call __init__ as well before returning
+ # That's why there's no __new__ here
+ return StandardConstantEnumWidget(*args, **kwargs)
+ return QtGui.QWidget.__new__(cls, *args, **kwargs)
+
+ def __init__(self, param, parent=None):
+ QtGui.QWidget.__init__(self)
+ self.setLayout(QtGui.QHBoxLayout())
+ self.layout().setMargin(5)
+ self.layout().setSpacing(5)
+
+ self._widget = None
+ self._multiline = None
+ self._default = ""
+
+ self._button = QtGui.QToolButton()
+ self._button.setIcon(CurrentTheme.MULTILINE_STRING_ICON)
+ self._button.setIconSize(QtCore.QSize(12, 12))
+ self._button.setToolTip("Toggle multi-line editor")
+ self._button.setAutoRaise(True)
+ self._button.setSizePolicy(QtGui.QSizePolicy(
+ QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed))
+ self._button.setCheckable(True)
+ self.connect(self._button, QtCore.SIGNAL('toggled(bool)'),
+ self.switch_multiline)
+ self.layout().addWidget(self._button)
+
+ psi = param.port_spec_item
+ if param.strValue:
+ value = param.strValue
+ elif psi and psi.default:
+ value = psi.default
+ else:
+ value = param.strValue
+ ConstantWidgetMixin.__init__(self, value)
+
+ # assert param.namespace == None
+ # assert param.identifier == 'edu.utah.sci.vistrails.basic'
+ if psi and psi.default:
+ self.setDefault(psi.default)
+ contents = param.strValue
+ self.setContents(contents)
+
+ def switch_multiline(self, multiline):
+ if multiline != self._multiline:
+ # Doing multiline -> not multiline while the widget contains
+ # line-returns is weird but won't cause loss of data, so I'm not
+ # explicitely disabling it
+ # Not that the multiline widget will pop up again next time if the
+ # user doesn't change the contents
+ self.setContents(self.contents(), multiline=multiline)
+
+ def setDefault(self, value):
+ self._default = value
+ if self._widget is not None:
+ self._widget.setDefault(value)
+
+ def contents(self):
+ return self._widget.contents()
+
+ def setContents(self, strValue, silent=True, multiline=None):
+ if multiline is None:
+ multiline = '\n' in strValue
+ if self._multiline is not multiline:
+ self._multiline = multiline
+ if self._widget is not None:
+ self._widget.deleteLater()
+ if not multiline:
+ self._widget = SingleLineStringWidget(self,
+ strValue, self._default)
+ else:
+ self._widget = MultiLineStringWidget(self,
+ strValue, self._default)
+ self._button.setChecked(multiline)
+ self.layout().insertWidget(0, self._widget)
+ self.updateGeometry()
+ else:
+ self._widget.setContents(strValue)
+
+ if not silent:
+ self.update_parent()
+
+ def changeEvent(self, event):
+ """ Hide button when in read-only mode
+
+ """
+ if event.type() == QtCore.QEvent.EnabledChange:
+ self._button.setVisible(self.isEnabled())
+ return QtGui.QWidget.changeEvent(self, event)
+
+ ###########################################################################
+ # event handlers
+
+ def focusInEvent(self, event):
+ #self._contents = str(self.contents())
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+ super(StringWidget, self).focusInEvent(event)
+
+ def focusOutEvent(self, event):
+ self.update_parent()
+ super(StringWidget, self).focusOutEvent(event)
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+
+
+class StandardConstantEnumWidget(QtGui.QComboBox, StandardConstantWidgetBase):
+ def __init__(self, param, parent=None):
+ QtGui.QComboBox.__init__(self, parent)
+ psi = param.port_spec_item
+ if psi and psi.entry_type == 'enumFree':
+ self.setEditable(True)
+ self.setInsertPolicy(QtGui.QComboBox.NoInsert)
+ self.connect(self.lineEdit(),
+ QtCore.SIGNAL('returnPressed()'),
+ self.update_parent)
+ self.addItems(psi.values)
+ if psi and (psi.entry_type == "enumEmpty" or
+ psi.entry_type == 'enumFree'):
+ self.setCurrentIndex(-1)
+ StandardConstantWidgetBase.__init__(self, param, parent)
+ self.connect(self,
+ QtCore.SIGNAL('currentIndexChanged(int)'),
+ self.update_parent)
+
+ def text(self):
+ return self.currentText()
+
+ def setText(self, text):
+ idx = self.findText(text)
+ if idx > -1:
+ self.setCurrentIndex(idx)
+ if self.isEditable():
+ self.lineEdit().setText(text)
+ elif self.isEditable():
+ self.lineEdit().setText(text)
+
+ def setDefault(self, value):
+ idx = self.findText(value)
+ if idx > -1:
+ self.setCurrentIndex(idx)
+ if self.isEditable():
+ setPlaceholderTextCompat(self.lineEdit(), value)
+ elif self.isEditable():
+ setPlaceholderTextCompat(self.lineEdit(), value)
+
+
+ ###########################################################################
+ # event handlers
+
+ def focusInEvent(self, event):
+ """ focusInEvent(event: QEvent) -> None
+ Pass the event to the parent
+
+ """
+ self._contents = str(self.text())
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+ QtGui.QComboBox.focusInEvent(self, event)
+
+ def focusOutEvent(self, event):
+ self.update_parent()
+ QtGui.QComboBox.focusOutEvent(self, event)
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+
+
+###############################################################################
+# File Constant Widgets
+
+class PathChooserToolButton(QtGui.QToolButton):
+ """
+ PathChooserToolButton is a toolbar button that opens a browser for
+ paths. The lineEdit is updated with the pathname that is selected.
+
+ """
+ def __init__(self, parent=None, lineEdit=None, toolTip=None):
+ """
+ PathChooserToolButton(parent: QWidget,
+ lineEdit: StandardConstantWidget) ->
+ PathChooserToolButton
+
+ """
+ QtGui.QToolButton.__init__(self, parent)
+ self.setIcon(QtGui.QIcon(
+ self.style().standardPixmap(QtGui.QStyle.SP_DirOpenIcon)))
+ self.setIconSize(QtCore.QSize(12,12))
+ if toolTip is None:
+ toolTip = 'Open a file chooser'
+ self.setToolTip(toolTip)
+ self.setAutoRaise(True)
+ self.lineEdit = lineEdit
+ self.connect(self,
+ QtCore.SIGNAL('clicked()'),
+ self.runDialog)
+
+ def setPath(self, path):
+ """
+ setPath() -> None
+
+ """
+ if self.lineEdit and path:
+ self.lineEdit.setText(path)
+ self.lineEdit.update_parent()
+ self.parent().update_parent()
+
+ def openChooser(self):
+ text = self.lineEdit.text() or system.vistrails_data_directory()
+ return QtGui.QFileDialog.getOpenFileName(self,
+ 'Use Filename '
+ 'as Value...',
+ text,
+ 'All files '
+ '(*.*)')
+
+ def runDialog(self):
+ path = self.openChooser()
+ self.setPath(path)
+
+class PathChooserWidget(QtGui.QWidget, ConstantWidgetMixin):
+ """
+ PathChooserWidget is a widget containing a line edit and a button that
+ opens a browser for paths. The lineEdit is updated with the pathname that is
+ selected.
+
+ """
+ def __init__(self, param, parent=None):
+ """__init__(param: core.vistrail.module_param.ModuleParam,
+ parent: QWidget)
+ Initializes the line edit with contents
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ layout = QtGui.QHBoxLayout()
+ self.line_edit = StandardConstantWidget(param, self)
+ self.browse_button = self.create_browse_button()
+ layout.setMargin(5)
+ layout.setSpacing(5)
+ layout.addWidget(self.line_edit)
+ layout.addWidget(self.browse_button)
+ self.setLayout(layout)
+
+ def create_browse_button(self):
+ return PathChooserToolButton(self, self.line_edit)
+
+ def updateMethod(self):
+ if self.parent() and hasattr(self.parent(), 'updateMethod'):
+ self.parent().updateMethod()
+
+ def contents(self):
+ """contents() -> str
+ Return the contents of the line_edit
+
+ """
+ return self.line_edit.contents()
+
+ def setContents(self, strValue, silent=True):
+ """setContents(strValue: str) -> None
+ Updates the contents of the line_edit
+ """
+ self.line_edit.setContents(strValue, silent)
+ if not silent:
+ self.update_parent()
+
+
+ def focusInEvent(self, event):
+ """ focusInEvent(event: QEvent) -> None
+ Pass the event to the parent
+
+ """
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+ QtGui.QWidget.focusInEvent(self, event)
+
+ def focusOutEvent(self, event):
+ self.update_parent()
+ QtGui.QWidget.focusOutEvent(self, event)
+ if self.parent():
+ QtCore.QCoreApplication.sendEvent(self.parent(), event)
+
+class FileChooserToolButton(PathChooserToolButton):
+ def __init__(self, parent=None, lineEdit=None):
+ PathChooserToolButton.__init__(self, parent, lineEdit,
+ "Open a file chooser")
+
+ def openChooser(self):
+ text = self.lineEdit.text() or system.vistrails_data_directory()
+ return QtGui.QFileDialog.getOpenFileName(self,
+ 'Use Filename '
+ 'as Value...',
+ text,
+ 'All files '
+ '(*.*)')
+
+class FileChooserWidget(PathChooserWidget):
+ def create_browse_button(self):
+ return FileChooserToolButton(self, self.line_edit)
+
+
+class DirectoryChooserToolButton(PathChooserToolButton):
+ def __init__(self, parent=None, lineEdit=None):
+ PathChooserToolButton.__init__(self, parent, lineEdit,
+ "Open a directory chooser")
+
+ def openChooser(self):
+ text = self.lineEdit.text() or system.vistrails_data_directory()
+ return QtGui.QFileDialog.getExistingDirectory(self,
+ 'Use Directory '
+ 'as Value...',
+ text)
+
+class DirectoryChooserWidget(PathChooserWidget):
+ def create_browse_button(self):
+ return DirectoryChooserToolButton(self, self.line_edit)
+
+class OutputPathChooserToolButton(PathChooserToolButton):
+ def __init__(self, parent=None, lineEdit=None):
+ PathChooserToolButton.__init__(self, parent, lineEdit,
+ "Open a path chooser")
+
+ def openChooser(self):
+ text = self.lineEdit.text() or system.vistrails_data_directory()
+ return QtGui.QFileDialog.getSaveFileName(self,
+ 'Save Path',
+ text,
+ 'All files (*.*)')
+
+class OutputPathChooserWidget(PathChooserWidget):
+ def create_browse_button(self):
+ return OutputPathChooserToolButton(self, self.line_edit)
+
+class BooleanWidget(QtGui.QCheckBox, ConstantWidgetMixin):
+
+ _values = ['True', 'False']
+ _states = [QtCore.Qt.Checked, QtCore.Qt.Unchecked]
+
+ def __init__(self, param, parent=None):
+ """__init__(param: core.vistrail.module_param.ModuleParam,
+ parent: QWidget)
+ Initializes the line edit with contents
+ """
+ QtGui.QCheckBox.__init__(self, parent)
+
+ psi = param.port_spec_item
+ if param.strValue:
+ value = param.strValue
+ elif psi and psi.default:
+ value = psi.default
+ else:
+ value = param.strValue
+ ConstantWidgetMixin.__init__(self, value)
+
+ if psi and psi.default:
+ self.setDefault(psi.default)
+ if param.strValue:
+ self.setContents(param.strValue)
+
+ self._silent= False
+ self.connect(self, QtCore.SIGNAL('stateChanged(int)'),
+ self.change_state)
+
+ def contents(self):
+ return self._values[self._states.index(self.checkState())]
+
+ def setContents(self, strValue, silent=True):
+ if not strValue:
+ return
+
+ assert strValue in self._values
+ if silent:
+ self._silent = True
+ self.setCheckState(self._states[self._values.index(strValue)])
+ if not silent:
+ self.update_parent()
+ self._silent = False
+
+ def setDefault(self, strValue):
+ self.setContents(strValue)
+
+ def change_state(self, state):
+ if not self._silent:
+ self.update_parent()
+
+###############################################################################
+# Constant Color widgets
+
+class ColorChooserButton(QtGui.QPushButton):
+ def __init__(self, parent=None):
+ QtGui.QPushButton.__init__(self, parent)
+ # self.setFrameStyle(QtGui.QFrame.Box | QtGui.QFrame.Plain)
+ # self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
+ self.setFlat(True)
+ self.setAutoFillBackground(True)
+ self.setColor(QtGui.QColor(255,255,255))
+ self.setFixedSize(30,22)
+ if system.systemType == 'Darwin':
+ #the mac's nice look messes up with the colors
+ self.setAttribute(QtCore.Qt.WA_MacMetalStyle, False)
+ self.clicked.connect(self.openChooser)
+
+ def setColor(self, qcolor, silent=True):
+ self.qcolor = qcolor
+ self.setStyleSheet("border: 1px solid black; "
+ "background-color: rgb(%d, %d, %d);" %
+ (qcolor.red(), qcolor.green(), qcolor.blue()))
+ self.repaint()
+ if not silent:
+ self.emit(QtCore.SIGNAL("color_selected"))
+
+ def sizeHint(self):
+ return QtCore.QSize(24,24)
+
+ def openChooser(self):
+ """
+ openChooser() -> None
+
+ """
+ color = QtGui.QColorDialog.getColor(self.qcolor, self.parent())
+ if color.isValid():
+ self.setColor(color, silent=False)
+ else:
+ self.setColor(self.qcolor)
+
+
+class ColorWidget(QtGui.QWidget, ConstantWidgetMixin):
+ def __init__(self, param, parent=None):
+ """__init__(param: core.vistrail.module_param.ModuleParam,
+ parent: QWidget)
+ """
+ psi = param.port_spec_item
+ if not param.strValue and psi and psi.default:
+ contents = psi.default
+ self._is_default = True
+ else:
+ contents = param.strValue
+ self._is_default = not contents
+ QtGui.QWidget.__init__(self, parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ layout = QtGui.QHBoxLayout()
+ self.color_indicator = ColorChooserButton(self)
+ self.connect(self.color_indicator,
+ QtCore.SIGNAL("color_selected"),
+ self.update_parent)
+ self._last_contents = contents
+ layout.setMargin(5)
+ layout.setSpacing(5)
+ layout.addWidget(self.color_indicator)
+ layout.addStretch(1)
+ self.setLayout(layout)
+ self.setContents(contents)
+
+ def contents(self):
+ """contents() -> str
+ Return the string representation of color_indicator
+
+ """
+ return "%s,%s,%s" % (self.color_indicator.qcolor.redF(),
+ self.color_indicator.qcolor.greenF(),
+ self.color_indicator.qcolor.blueF())
+
+ def setContents(self, strValue, silent=True):
+ """setContents(strValue: str) -> None
+ Updates the color_indicator to display the color in strValue
+
+ """
+ if strValue != '':
+ color = strValue.split(',')
+ qcolor = QtGui.QColor(float(color[0])*255,
+ float(color[1])*255,
+ float(color[2])*255)
+ self.color_indicator.setColor(qcolor, silent)
+ self._is_default = False
+
+ def setDefault(self, strValue):
+ if self._is_default:
+ self.setContents(strValue, True)
+ self._is_default = True
diff --git a/vistrails/gui/modules/list_configuration.py b/vistrails/gui/modules/list_configuration.py
new file mode 100644
index 0000000..6b8cd75
--- /dev/null
+++ b/vistrails/gui/modules/list_configuration.py
@@ -0,0 +1,132 @@
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core.system import get_vistrails_basic_pkg_id
+from vistrails.gui.modules.module_configure import StandardModuleConfigurationWidget
+
+class ListConfigurationWidget(StandardModuleConfigurationWidget):
+ """
+ Configuration widget allowing to choose the number of ports.
+
+ This is used to build a List from several modules while ensuring a given
+ order. If no particular ordering is needed, connecting multiple ports to
+ the 'head' input ports should be sufficient.
+
+ """
+ def __init__(self, module, controller, parent=None):
+ """ ListConfigurationWidget(module: Module,
+ controller: VistrailController,
+ parent: QWidget)
+ -> TupleConfigurationWidget
+
+ Let StandardModuleConfigurationWidget constructor store the
+ controller/module object from the builder and set up the
+ configuration widget.
+ After StandardModuleConfigurationWidget constructor, all of
+ these will be available:
+ self.module : the Module object int the pipeline
+ self.controller: the current vistrail controller
+
+ """
+ StandardModuleConfigurationWidget.__init__(self, module,
+ controller, parent)
+
+ # Give it a nice window title
+ self.setWindowTitle("List Configuration")
+
+ # Add an empty vertical layout
+ centralLayout = QtGui.QVBoxLayout()
+ centralLayout.setMargin(0)
+ centralLayout.setSpacing(0)
+ self.setLayout(centralLayout)
+
+ # Add the configuration widget
+ config_layout = QtGui.QFormLayout()
+ self.number = QtGui.QSpinBox()
+ self.number.setValue(self.countAdditionalPorts())
+ self.connect(self.number, QtCore.SIGNAL('valueChanged(int)'),
+ lambda r: self.updateState())
+ config_layout.addRow("Number of additional connections:", self.number)
+ centralLayout.addLayout(config_layout)
+
+ self.createButtons()
+
+ def activate(self):
+ self.number.focusWidget(QtCore.Qt.ActiveWindowFocusReason)
+
+ def createButtons(self):
+ """ createButtons() -> None
+ Create and connect signals to Ok & Cancel button
+
+ """
+ self.buttonLayout = QtGui.QHBoxLayout()
+ self.buttonLayout.setMargin(5)
+ self.saveButton = QtGui.QPushButton("&Save", self)
+ self.saveButton.setFixedWidth(100)
+ self.saveButton.setEnabled(False)
+ self.buttonLayout.addWidget(self.saveButton)
+ self.resetButton = QtGui.QPushButton("&Reset", self)
+ self.resetButton.setFixedWidth(100)
+ self.resetButton.setEnabled(False)
+ self.buttonLayout.addWidget(self.resetButton)
+ self.layout().addLayout(self.buttonLayout)
+ self.connect(self.saveButton, QtCore.SIGNAL('clicked(bool)'),
+ self.saveTriggered)
+ self.connect(self.resetButton, QtCore.SIGNAL('clicked(bool)'),
+ self.resetTriggered)
+
+ def saveTriggered(self, checked = False):
+ """ saveTriggered(checked: bool) -> None
+ Update vistrail controller and module when the user click Ok
+
+ """
+ if self.updateVistrail():
+ self.saveButton.setEnabled(False)
+ self.resetButton.setEnabled(False)
+ self.state_changed = False
+ self.emit(QtCore.SIGNAL('stateChanged'))
+ self.emit(QtCore.SIGNAL('doneConfigure'), self.module.id)
+
+ def closeEvent(self, event):
+ self.askToSaveChanges()
+ event.accept()
+
+ def updateVistrail(self):
+ """ updateVistrail() -> None
+ Update Vistrail to contain changes in the port table
+
+ """
+ requested = self.number.value()
+ current = self.countAdditionalPorts()
+
+ if requested == current:
+ # Nothing changed
+ return
+
+ if requested > current:
+ sigstring = '(%s:Module)' % get_vistrails_basic_pkg_id()
+ add_ports = [('input', 'item%d' % i, sigstring, -1)
+ for i in xrange(current, requested)]
+ self.controller.update_ports(self.module.id, [], add_ports)
+ elif requested < current:
+ delete_ports = [('input', p.name) for p in self.module.input_port_specs[requested-current:]]
+ self.controller.update_ports(self.module.id, delete_ports, [])
+ return True
+
+ def countAdditionalPorts(self):
+ return len(self.module.input_port_specs)
+
+ def resetTriggered(self, checked = False):
+ self.number.setValue(self.countAdditionalPorts())
+ self.saveButton.setEnabled(False)
+ self.resetButton.setEnabled(False)
+ self.state_changed = False
+ self.emit(QtCore.SIGNAL('stateChanged'))
+
+ def updateState(self):
+ if not self.hasFocus():
+ self.setFocus(QtCore.Qt.TabFocusReason)
+ self.saveButton.setEnabled(True)
+ self.resetButton.setEnabled(True)
+ if not self.state_changed:
+ self.state_changed = True
+ self.emit(QtCore.SIGNAL('stateChanged'))
diff --git a/vistrails/gui/modules/module_configure.py b/vistrails/gui/modules/module_configure.py
new file mode 100644
index 0000000..686533e
--- /dev/null
+++ b/vistrails/gui/modules/module_configure.py
@@ -0,0 +1,272 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+from vistrails.core.utils import VistrailsInternalError
+from vistrails.core.vistrail.port import PortEndPoint
+from vistrails.gui.utils import show_question, SAVE_BUTTON, DISCARD_BUTTON
+from vistrails.gui.common_widgets import QPromptWidget
+
+class StandardModuleConfigurationWidget(QtGui.QWidget):
+
+ def __init__(self, module, controller, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.module = module
+ self.controller = controller
+ self.state_changed = False
+
+ def activate(self):
+ #reimplement this to set the focus to a certain widget when activated
+ pass
+
+ def askToSaveChanges(self):
+ if self.state_changed:
+ message = ('Configuration panel contains unsaved changes. '
+ 'Do you want to save changes before proceeding?' )
+ res = show_question('VisTrails',
+ message,
+ buttons = [SAVE_BUTTON, DISCARD_BUTTON])
+ if res == SAVE_BUTTON:
+ self.saveTriggered()
+ return True
+ else:
+ self.resetTriggered()
+ return False
+
+ def saveTriggered(self):
+ msg = "Must implement saveTriggered in subclass"
+ raise VistrailsInternalError(msg)
+
+ def resetTriggered(self):
+ msg = "Must implement saveTriggered in subclass"
+ raise VistrailsInternalError(msg)
+
+class DefaultModuleConfigurationWidget(StandardModuleConfigurationWidget):
+ def __init__(self, module, controller, parent=None):
+ StandardModuleConfigurationWidget.__init__(self, module, controller,
+ parent)
+ self.prompt = QPromptWidget()
+ self.prompt.setPromptText("Please use the visibility icon (an eye) in"
+ " the Module Information panel to show or"
+ " hide a port.")
+ layout = QtGui.QVBoxLayout()
+ layout.addWidget(self.prompt)
+ self.setLayout(layout)
+ self.prompt.showPrompt()
+
+ def saveTriggered(self):
+ pass
+
+ def resetTriggered(self):
+ pass
+
+class _DefaultModuleConfigurationWidget(StandardModuleConfigurationWidget):
+ """ This is the Default ModuleConfigurationWidget that shows a list of
+ ports to be enabled or disabled """
+ def __init__(self, module, controller, parent=None):
+ StandardModuleConfigurationWidget.__init__(self, module, controller,
+ parent)
+
+ self.setLayout(QtGui.QVBoxLayout())
+ self.layout().setMargin(0)
+ self.layout().setSpacing(0)
+ self.scrollArea = QtGui.QScrollArea(self)
+ self.layout().addWidget(self.scrollArea)
+ self.scrollArea.setFrameStyle(QtGui.QFrame.NoFrame)
+ self.listContainer = QtGui.QWidget(self.scrollArea)
+ self.listContainer.setLayout(QtGui.QGridLayout(self.listContainer))
+ self.listContainer.setFocusPolicy(QtCore.Qt.WheelFocus)
+ self.inputPorts = self.module.destinationPorts()
+ self.inputDict = {}
+ self.outputPorts = self.module.sourcePorts()
+ self.outputDict = {}
+ self.constructList()
+ self.buttonLayout = QtGui.QHBoxLayout()
+ self.buttonLayout.setMargin(5)
+ self.saveButton = QtGui.QPushButton('&Save', self)
+ self.saveButton.setFixedWidth(100)
+ self.saveButton.setEnabled(False)
+ self.buttonLayout.addWidget(self.saveButton)
+ self.resetButton = QtGui.QPushButton('&Reset', self)
+ self.resetButton.setFixedWidth(100)
+ self.resetButton.setEnabled(False)
+ self.buttonLayout.addWidget(self.resetButton)
+
+ self.layout().addLayout(self.buttonLayout)
+ self.connect(self.saveButton, QtCore.SIGNAL('clicked(bool)'),
+ self.saveTriggered)
+ self.connect(self.resetButton, QtCore.SIGNAL('clicked(bool)'),
+ self.resetTriggered)
+ self.setMouseTracking(True)
+ self.setFocusPolicy(QtCore.Qt.WheelFocus)
+ self.adjustSize()
+# self.mouseOver = False
+ self.state_changed = False
+
+ ###########################################################################
+ # Focus event handlers
+ # There is something wrong with focus on this widget, because I couldn't
+ # get it to work with just self.setFocusPolicy() and reimplementing
+ # focusOutEvent. No focus events were being generated at all
+ # I had to force calling setFocus(reason) when something changed
+ # and as this was also generating focusOutEvents when it shouldn't.
+ # So I also had to force to emit focusOutEvent only when the mouse is not
+ # over this panel.
+ # I already spent a lot of time trying fix and I couldn't.
+ # If anybody has the time to fix this, please do it. (Emanuele)
+ #
+ # DAK -- seems to be ok when in the palette window...
+
+# def focusOutEvent(self, event):
+# #self.askToSaveChanges()
+# QtGui.QWidget.focusOutEvent(self, event)
+#
+# def enterEvent(self, event):
+# self.mouseOver = True
+#
+# def leaveEvent(self, event):
+# self.mouseOver = False
+
+ def checkBoxFromPort(self, port, input_=False):
+ checkBox = QtGui.QCheckBox(port.name)
+ if input_:
+ port_visible = port.name in self.module.visible_input_ports
+ else:
+ port_visible = port.name in self.module.visible_output_ports
+ if not port.optional or port_visible:
+ checkBox.setCheckState(QtCore.Qt.Checked)
+ else:
+ checkBox.setCheckState(QtCore.Qt.Unchecked)
+ if not port.optional or (input_ and port.sigstring=='()'):
+ checkBox.setEnabled(False)
+ return checkBox
+
+ def constructList(self):
+ label = QtGui.QLabel('Input Ports')
+ label.setAlignment(QtCore.Qt.AlignHCenter)
+ label.font().setBold(True)
+ label.font().setPointSize(12)
+ self.listContainer.layout().addWidget(label, 0, 0)
+ label = QtGui.QLabel('Output Ports')
+ label.setAlignment(QtCore.Qt.AlignHCenter)
+ label.font().setBold(True)
+ label.font().setPointSize(12)
+ self.listContainer.layout().addWidget(label, 0, 1)
+
+ for i in xrange(len(self.inputPorts)):
+ port = self.inputPorts[i]
+ checkBox = self.checkBoxFromPort(port, True)
+ checkBox.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.connect(checkBox, QtCore.SIGNAL("stateChanged(int)"),
+ self.updateState)
+ self.inputDict[port.name] = checkBox
+ self.listContainer.layout().addWidget(checkBox, i+1, 0)
+
+ for i in xrange(len(self.outputPorts)):
+ port = self.outputPorts[i]
+ checkBox = self.checkBoxFromPort(port)
+ checkBox.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.connect(checkBox, QtCore.SIGNAL("stateChanged(int)"),
+ self.updateState)
+ self.outputDict[port.name] = checkBox
+ self.listContainer.layout().addWidget(checkBox, i+1, 1)
+
+ self.listContainer.adjustSize()
+ self.listContainer.setFixedHeight(self.listContainer.height())
+ self.scrollArea.setWidget(self.listContainer)
+ self.scrollArea.setWidgetResizable(True)
+
+ def sizeHint(self):
+ return QtCore.QSize(384, 512)
+
+ def saveTriggered(self, checked = False):
+ for port in self.inputPorts:
+ if (port.optional and
+ self.inputDict[port.name].checkState()==QtCore.Qt.Checked):
+ self.module.visible_input_ports.add(port.name)
+ else:
+ self.module.visible_input_ports.discard(port.name)
+
+ for port in self.outputPorts:
+ if (port.optional and
+ self.outputDict[port.name].checkState()==QtCore.Qt.Checked):
+ self.module.visible_output_ports.add(port.name)
+ else:
+ self.module.visible_output_ports.discard(port.name)
+ self.saveButton.setEnabled(False)
+ self.resetButton.setEnabled(False)
+ self.state_changed = False
+ self.emit(QtCore.SIGNAL("stateChanged"))
+ self.emit(QtCore.SIGNAL('doneConfigure'), self.module.id)
+
+ def closeEvent(self, event):
+ self.askToSaveChanges()
+ event.accept()
+
+ def resetTriggered(self):
+ self.setFocus(QtCore.Qt.MouseFocusReason)
+ self.setUpdatesEnabled(False)
+ for i in xrange(len(self.inputPorts)):
+ port = self.inputPorts[i]
+ entry = (PortEndPoint.Destination, port.name)
+ checkBox = self.inputDict[port.name]
+ if not port.optional or entry in self.module.portVisible:
+ checkBox.setCheckState(QtCore.Qt.Checked)
+ else:
+ checkBox.setCheckState(QtCore.Qt.Unchecked)
+ if not port.optional or port.sigstring=='()':
+ checkBox.setEnabled(False)
+ for i in xrange(len(self.outputPorts)):
+ port = self.outputPorts[i]
+ entry = (PortEndPoint.Source, port.name)
+ checkBox = self.outputDict[port.name]
+ if not port.optional or entry in self.module.portVisible:
+ checkBox.setCheckState(QtCore.Qt.Checked)
+ else:
+ checkBox.setCheckState(QtCore.Qt.Unchecked)
+ if not port.optional:
+ checkBox.setEnabled(False)
+ self.setUpdatesEnabled(True)
+ self.saveButton.setEnabled(False)
+ self.resetButton.setEnabled(False)
+ self.state_changed = False
+ self.emit(QtCore.SIGNAL("stateChanged"))
+
+ def updateState(self, state):
+ self.setFocus(QtCore.Qt.MouseFocusReason)
+ self.saveButton.setEnabled(True)
+ self.resetButton.setEnabled(True)
+ if not self.state_changed:
+ self.state_changed = True
+ self.emit(QtCore.SIGNAL("stateChanged"))
diff --git a/vistrails/gui/modules/paramexplore.py b/vistrails/gui/modules/paramexplore.py
new file mode 100644
index 0000000..4c130e5
--- /dev/null
+++ b/vistrails/gui/modules/paramexplore.py
@@ -0,0 +1,798 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file provides the basic infrastructure for extensible parameter
+exploration. This allows user-defined constants to be used as dimensions
+in parameter exploration, provided the user implements the appropriate
+API in the classes.
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core.modules.basic_modules import Color
+from vistrails.core.modules.paramexplore import IntegerLinearInterpolator, \
+ FloatLinearInterpolator, RGBColorInterpolator, HSVColorInterpolator
+
+from vistrails.gui.common_widgets import QStringEdit
+from vistrails.gui.modules.constant_configuration import ColorChooserButton
+from vistrails.gui.modules.python_source_configure import PythonEditor
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.utils import show_warning
+from vistrails.core.utils import all, unimplemented
+
+##############################################################################
+
+def get_param_explore_widget_list(module_klass):
+ widget_list = []
+ klass_list = module_klass.get_param_explore_widget_list()
+ for klass in klass_list:
+ if klass is None:
+ pass
+ elif isinstance(klass, tuple):
+ (path, klass_name) = klass
+ module = __import__(path, globals(), locals(), [klass_name])
+ widget_list.append(getattr(module, klass_name))
+ else:
+ widget_list.append(klass)
+ return widget_list
+
+class QParameterEditor(QtGui.QWidget):
+ """
+ QParameterEditor specifies the method used for interpolating
+ parameter values. It suppports Linear Interpolation, List and
+ User-define function.
+
+ """
+ def __init__(self, param_info, size, parent=None):
+ """ QParameterEditor(param_info: ParameterInfo,
+ size: int, parent=None: QWidget) -> QParameterEditor
+ Put a stacked widget and a popup button
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self._param_info = param_info
+ self.type = param_info.spec.descriptor.name
+ self.defaultValue = param_info.value
+
+ hLayout = QtGui.QHBoxLayout(self)
+ hLayout.setMargin(0)
+ hLayout.setSpacing(0)
+ self.setLayout(hLayout)
+
+ module = param_info.spec.descriptor.module
+
+ self.stackedEditors = QtGui.QStackedWidget()
+ self.stackedEditors.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Maximum)
+ self._exploration_widgets = []
+
+ def add_exploration_widget(wd):
+ self._exploration_widgets.append(wd)
+ self.stackedEditors.addWidget(wd)
+
+ for widget_class in get_param_explore_widget_list(module):
+ new_widget = widget_class(param_info, size)
+ add_exploration_widget(new_widget)
+
+ add_exploration_widget(QListInterpolationEditor(param_info, size))
+ add_exploration_widget(QUserFunctionEditor(param_info, size))
+
+ hLayout.addWidget(self.stackedEditors)
+
+ self.selector = QParameterEditorSelector(param_info, self._exploration_widgets)
+ self.connect(self.selector.actionGroup,
+ QtCore.SIGNAL('triggered(QAction*)'),
+ self.changeInterpolator)
+ hLayout.addWidget(self.selector)
+ self.selector.initAction()
+
+ def changeInterpolator(self, action):
+ """ changeInterpolator(action: QAction) -> None
+ Bring the correct interpolation editing widget to front in the
+ stacked widget
+
+ """
+ widgetIdx = action.data()
+ if widgetIdx < self.stackedEditors.count():
+ self.stackedEditors.setCurrentIndex(widgetIdx)
+
+ def selectInterpolator(self, type):
+ """ selectInterpolator(type: string) -> None
+ Programatically (without requiring a user action) selects
+ the interpolator specified by the name 'type'. If no
+ matching 'type' is found, no action is taken.
+
+ """
+ types = [widget.exploration_name for widget in self._exploration_widgets]
+ if type in types:
+ type_idx = types.index(type)
+ self.selector._actions[type_idx].trigger()
+
+class QParameterEditorSelector(QtGui.QToolButton):
+ """
+ QParameterEditorSelector is a button with a down arrow allowing
+ users to select which type of interpolator he/she wants to use
+
+ """
+ def __init__(self, param_info, widget_list, parent=None):
+ """ QParameterEditorSelector(param_info: ParameterInfo,
+ widget_list: list of widgets that conform to the parameter
+ exploration widget interface.
+ """
+ QtGui.QToolButton.__init__(self, parent)
+ self._param_info = param_info
+ self.type = param_info.spec.descriptor.name
+ self.setAutoRaise(True)
+ self.setToolButtonStyle(QtCore.Qt.ToolButtonTextOnly)
+ self.setPopupMode(QtGui.QToolButton.InstantPopup)
+
+ self.setText(unichr(0x25bc)) # Down triangle
+
+ self.actionGroup = QtGui.QActionGroup(self)
+
+ self._actions = []
+ for widget in widget_list:
+ action = QtGui.QAction(widget.exploration_name, self.actionGroup)
+ self._actions.append(action)
+
+ aId = 0
+ for action in self.actionGroup.actions():
+ action.setCheckable(True)
+ action.setData(aId)
+ aId += 1
+
+ menu = QtGui.QMenu(self)
+ menu.addActions(self.actionGroup.actions())
+ self.setMenu(menu)
+
+ def initAction(self):
+ """ initAction() -> None
+ Select the first choice of selector based on self.type
+
+ """
+ self._actions[0].trigger()
+
+##############################################################################
+
+class BasePEWidget(object):
+ def get_value(self):
+ unimplemented()
+ def set_value(self):
+ unimplemented()
+
+class QIntegerLineEdit(QtGui.QLineEdit, BasePEWidget):
+ def __init__(self, param_info, parent=None):
+ QtGui.QLineEdit.__init__(self, param_info.value, parent)
+ self.setValidator(QtGui.QIntValidator(self))
+ def get_value(self):
+ return int(str(self.text()))
+ def set_value(self, str_value):
+ self.setText(str_value)
+
+class QFloatLineEdit(QtGui.QLineEdit, BasePEWidget):
+ def __init__(self, param_info, parent=None):
+ QtGui.QLineEdit.__init__(self, param_info.value, parent)
+ self.setValidator(QtGui.QDoubleValidator(self))
+ def get_value(self):
+ return float(str(self.text()))
+ def set_value(self, str_value):
+ self.setText(str_value)
+##############################################################################
+
+def make_interpolator(widget_class, interpolator_class, name):
+ class InterpolationEditor(QtGui.QWidget):
+ """
+ QLinearInterpolationEditor is the actual widget allowing users to
+ edit his/her linear interpolation parameters.
+
+ """
+ def __init__(self, param_info, size, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self._param_info = param_info
+ self.type = param_info.spec.descriptor.name
+
+ hLayout = QtGui.QHBoxLayout(self)
+ hLayout.setMargin(0)
+ hLayout.setSpacing(0)
+ self.setLayout(hLayout)
+
+ self.fromEdit = widget_class(param_info)
+ hLayout.addWidget(self.fromEdit)
+
+ hLayout.addSpacing(5)
+
+ rightArrow = QtGui.QLabel()
+ pixmap = self.style().standardPixmap(QtGui.QStyle.SP_ArrowRight)
+ rightArrow.setPixmap(CurrentTheme.RIGHT_ARROW_PIXMAP)
+ hLayout.addWidget(rightArrow)
+
+ hLayout.addSpacing(5)
+
+ self.toEdit = widget_class(param_info)
+ hLayout.addWidget(self.toEdit)
+ self.exploration_name = name
+
+ def get_values(self, size):
+ """ get_values(size: int) -> tuple
+ Return the interpolated list containing 'size' values
+
+ """
+ begin = self.fromEdit.get_value()
+ end = self.toEdit.get_value()
+ lerp = interpolator_class(begin, end, size)
+ return lerp.get_values()
+ return InterpolationEditor
+
+FloatExploreWidget = make_interpolator(QFloatLineEdit,
+ FloatLinearInterpolator,
+ 'Linear Interpolation')
+IntegerExploreWidget = make_interpolator(QIntegerLineEdit,
+ IntegerLinearInterpolator,
+ 'Linear Interpolation')
+
+class PEColorChooserButton(ColorChooserButton, BasePEWidget):
+
+ def __init__(self, param_info, parent=None):
+ ColorChooserButton.__init__(self, parent)
+ try:
+ r,g,b = [int(float(i) * 255) for i in param_info.value.split(',')]
+ except ValueError:
+ r,g,b = (0.0, 0.0, 0.0)
+ self.setColor(QtGui.QColor(r,g,b))
+ self.setFixedHeight(22)
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Fixed)
+
+ def get_value(self):
+ return Color.to_string(self.qcolor.redF(),
+ self.qcolor.greenF(),
+ self.qcolor.blueF())
+
+ def set_value(self, str_value):
+ color = str_value.split(',')
+ qcolor = QtGui.QColor(float(color[0])*255,
+ float(color[1])*255,
+ float(color[2])*255)
+ self.setColor(qcolor)
+
+RGBExploreWidget = make_interpolator(PEColorChooserButton,
+ RGBColorInterpolator,
+ 'RGB Interpolation')
+HSVExploreWidget = make_interpolator(PEColorChooserButton,
+ HSVColorInterpolator,
+ 'HSV Interpolation')
+
+##############################################################################
+
+class QListInterpolationEditor(QtGui.QWidget):
+ """
+ QListInterpolationEditor is the actual widget allowing users to
+ enter a list of values for interpolation
+
+ """
+ def __init__(self, param_info, size, parent=None):
+ """ QListInterpolationEditor(param_info: ParameterInfo, parent: QWidget)
+ -> QListInterpolationEditor
+ Construct an edit box with a button for bringing up the dialog
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self._param_info = param_info
+ self.type = param_info.spec.descriptor.name
+
+ hLayout = QtGui.QHBoxLayout(self)
+ hLayout.setMargin(0)
+ hLayout.setSpacing(0)
+ self.setLayout(hLayout)
+
+ self.listValues = QtGui.QLineEdit()
+ if self.type=='String':
+ self.listValues.setText("['%s']" % param_info.value.replace("'", "\'"))
+ else:
+ self.listValues.setText('[%s]' % param_info.value)
+ self.listValues.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Maximum)
+ self.listValues.home(False)
+ hLayout.addWidget(self.listValues)
+
+ self.connect(self.listValues, QtCore.SIGNAL('textEdited(QString)'),
+ self.values_were_edited)
+
+ inputButton = QtGui.QToolButton()
+ inputButton.setText('...')
+ self.connect(inputButton, QtCore.SIGNAL('clicked()'),
+ self.editListValues)
+ hLayout.addWidget(inputButton)
+ self.exploration_name = 'List'
+ self._str_values = [param_info.value]
+
+ def values_were_edited(self, new_text):
+ """values_were_edited(new_text): None
+
+ Connected to self.listValues.textEdited. Updates self._str_values.
+
+ NB: Allowing the user to edit the LineEdit field directly is
+ not a very good idea, because we don't know what are the
+ syntactic rules for the translate_to_python() calls in
+ arbitrary classes. Right now, I'm assuming removing the
+ leading and trailing brackets and splitting on ',' is
+ enough. (in passing, The previous call to eval() is just
+ broken is a general scenario like we have now)
+
+ For example, this will break horribly if the user manually edits
+ a list of strings with commas in them."""
+
+ t = str(new_text)
+ if len(t) < 2:
+ self._str_values = []
+ return
+ if not (t[0] == '[' and t[-1] == ']'):
+ self._str_values = []
+ else:
+ self._str_values = t[1:-1].split(',')
+ if self._param_info.spec.descriptor.name=='String':
+ for i, val in enumerate(self._str_values):
+ val = val.strip()
+ if len(val) >= 2 and \
+ ((val[0] == "'" and val[-1] == "'") or
+ (val[0] == '"' and val[-1] == '"')):
+ self._str_values[i] = val.strip()[1:-1]
+
+ def get_values(self, count):
+ """ get_values(count) -> []
+ Convert the list values into a list
+
+ count should be an integer with the expected size of the list (given
+ by the dimension 'size' in the exploration)
+
+ """
+
+ param_info = self._param_info
+ module = param_info.spec.descriptor.module
+ result = [module.translate_to_python(m)
+ for m in self._str_values]
+ if len(result) != count:
+ show_warning('Inconsistent Size',
+ 'One of the <i>%s</i>\'s list '
+ 'interpolated '
+ 'values has a different '
+ 'size from the step count. '
+ 'Expected %d, got %d instead. '
+ 'Parameter Exploration aborted.'
+ % (self.type, count, len(result)))
+ return None
+ return result
+
+ def editListValues(self):
+ """ editListValues() -> None
+ Show a dialog for editing the values
+
+ """
+ dialog = QListEditDialog(self.type, self._str_values, None)
+ if dialog.exec_() == QtGui.QDialog.Accepted:
+ values = dialog.getList()
+ self._str_values = [str(v) for v in values]
+ if self.type == 'String':
+ values = ["'%s'" % v.replace("'", "\'")
+ for v in values]
+ self.listValues.setText('[%s]' % ', '.join(values))
+ self.listValues.home(False)
+ dialog.deleteLater()
+
+##############################################################################
+
+class QListEditDialog(QtGui.QDialog):
+ """
+ QListEditDialog provides an interface for user to edit a list of
+ values and export to a string
+
+ """
+ def __init__(self, pType, strValues, parent=None):
+ """ QListEditDialog(pType: str, strValues: list, parent: QWidget)
+ -> QListEditDialog
+ Parse values and setup the table
+
+ """
+ QtGui.QDialog.__init__(self, parent)
+ self.pType = pType
+ vLayout = QtGui.QVBoxLayout()
+ vLayout.setMargin(0)
+ vLayout.setSpacing(0)
+ self.setLayout(vLayout)
+
+ label = QtGui.QLabel("Please enter values in boxes below. Drag "
+ "rows up and down to arrange your list values. "
+ "'Add' appends an empty value to the list. "
+ "And 'Del' removes the selected values.")
+ label.setMargin(5)
+ label.setWordWrap(True)
+ vLayout.addWidget(label)
+
+ self.table = QtGui.QTableWidget(0, 1, parent)
+ self.table.setHorizontalHeaderLabels(['Values'])
+ self.table.horizontalHeader().setStretchLastSection(True)
+ self.table.verticalHeader().setMovable(True)
+ self.table.verticalHeader().setResizeMode(
+ QtGui.QHeaderView.ResizeToContents)
+ self.delegate = QListEditItemDelegate()
+ self.table.setItemDelegate(self.delegate)
+ self.table.setSelectionMode(QtGui.QAbstractItemView.ExtendedSelection)
+ for v in strValues:
+ self.addRow(v)
+ self.connect(self.table.verticalHeader(),
+ QtCore.SIGNAL('sectionMoved(int,int,int)'),
+ self.rowMoved)
+ vLayout.addWidget(self.table)
+
+ hLayout = QtGui.QHBoxLayout()
+ vLayout.addLayout(hLayout)
+
+ okButton = QtGui.QPushButton('&OK')
+ okButton.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+ self.connect(okButton, QtCore.SIGNAL('clicked()'), self.okButtonPressed)
+ hLayout.addWidget(okButton)
+
+ cancelButton = QtGui.QPushButton('&Cancel')
+ cancelButton.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+ self.connect(cancelButton, QtCore.SIGNAL('clicked()'), self.reject)
+ hLayout.addWidget(cancelButton)
+
+ addButton = QtGui.QPushButton('&Add')
+ addButton.setIcon(CurrentTheme.ADD_STRING_ICON)
+ addButton.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+ self.connect(addButton, QtCore.SIGNAL('clicked()'), self.addRow)
+ hLayout.addWidget(addButton)
+
+ removeButton = QtGui.QPushButton('&Del')
+ removeButton.setIcon(QtGui.QIcon(
+ self.style().standardPixmap(QtGui.QStyle.SP_DialogCancelButton)))
+ removeButton.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+ self.connect(removeButton, QtCore.SIGNAL('clicked()'),
+ self.removeSelection)
+ hLayout.addWidget(removeButton)
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+ Return the recommended size for the widget
+
+ """
+ return QtCore.QSize(256, 384)
+
+ def okButtonPressed(self):
+ """ okButtonPressed() -> None
+ Make sure to commit the editor data before accepting
+
+ """
+ self.table.itemDelegate().finishEditing()
+ self.accept()
+
+ def getList(self):
+ """ getList() -> list of str values
+ Return a list of values
+
+ """
+ result = []
+ for i in xrange(self.table.rowCount()):
+ logicalIndex = self.table.verticalHeader().logicalIndex(i)
+ value = self.table.item(logicalIndex, 0).text()
+ result.append(str(value))
+ return result
+
+ def rowMoved(self, row, old, new):
+ """ rowMove(row: int, old: int, new: int) -> None
+ Renumber the vertical header labels when row moved
+
+ """
+ vHeader = self.table.verticalHeader()
+ labels = []
+ for i in xrange(self.table.rowCount()):
+ labels.append(str(vHeader.visualIndex(i)+1))
+ self.table.setVerticalHeaderLabels(labels)
+
+ def addRow(self, text=None):
+ """ addRow(text: str) -> QListStringEdit
+ Add an extra row to the end of the table
+
+ """
+ self.table.setRowCount(self.table.rowCount()+1)
+ if text:
+ item = QtGui.QTableWidgetItem(text)
+ else:
+ item = QtGui.QTableWidgetItem()
+ row = self.table.rowCount()-1
+ self.table.setItem(row, 0, item)
+
+ def removeSelection(self):
+ """ removeSelection() -> None
+ Remove selected rows on the table
+
+ """
+ for item in self.table.selectedItems():
+ self.table.removeRow(item.row())
+
+##############################################################################
+
+class QListEditItemDelegate(QtGui.QItemDelegate):
+ """
+ QListEditItemDelegate sets up the editor for the QListEditDialog
+ table
+
+ """
+
+ def __init__(self, parent=None):
+ """ QListEditItemDelegate(parent: QWidget) -> QListEditItemDelegate
+ Store the uncommit editor for commit later
+
+ """
+ QtGui.QItemDelegate.__init__(self, parent)
+ self.editor = None
+
+ def createEditor(self, parent, option, index):
+ """ createEditor(parent: QWidget,
+ option: QStyleOptionViewItem,
+ index: QModelIndex) -> QStringEdit
+ Return the editor widget for the index
+
+ """
+ self.editor = QStringEdit(parent)
+ return self.editor
+
+ def setEditorData(self, editor, index):
+ """ setEditorData(editor: QWidget, index: QModelIndex) -> None
+ Set the editor to reflects data at index
+
+ """
+ editor.setText(index.data())
+ editor.selectAll()
+
+ def updateEditorGeometry(self, editor, option, index):
+ """ updateEditorGeometry(editor: QStringEdit,
+ option: QStyleOptionViewItem,
+ index: QModelIndex) -> None
+ Update the geometry of the editor based on the style option
+
+ """
+ editor.setGeometry(option.rect)
+
+ def setModelData(self, editor, model, index):
+ """ setModelData(editor: QStringEdit,
+ model: QAbstractItemModel,
+ index: QModelIndex) -> None
+ Set the text of the editor back to the item model
+
+ """
+ model.setData(index, editor.text())
+ self.editor = None
+
+ def finishEditing(self):
+ if self.editor:
+ self.emit(QtCore.SIGNAL('commitData(QWidget*)'), self.editor)
+
+##############################################################################
+
+class QUserFunctionEditor(QtGui.QFrame):
+ """
+ QUserFunctionEditor shows user-defined interpolation function
+
+ """
+ def __init__(self, param_info, size, parent=None):
+ """ QUserFunctionEditor(param_info: ParameterInfo, parent: QWidget)
+ -> QUserFunctionEditor
+ Create a read-only line edit widget and a button for
+ customizing the user-defined function
+
+ """
+ QtGui.QFrame.__init__(self, parent)
+ self.setFrameStyle(QtGui.QFrame.Box | QtGui.QFrame.Sunken)
+ self.size = -1
+ self._param_info = param_info
+ self.type = param_info.spec.descriptor.name
+ self.defaultValue = param_info.value
+ self.function = self.defaultFunction()
+
+ hLayout = QtGui.QHBoxLayout(self)
+ hLayout.setMargin(0)
+ hLayout.setSpacing(0)
+ self.setLayout(hLayout)
+
+ hLayout.addSpacing(2)
+ self.label = QtGui.QLabel()
+ hLayout.addWidget(self.label)
+
+ self.listValues = QtGui.QLineEdit()
+ self.listValues.setFrame(False)
+ self.listValues.palette().setBrush(QtGui.QPalette.Base,
+ QtGui.QBrush(QtCore.Qt.NoBrush))
+ self.listValues.setReadOnly(True)
+ self.listValues.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Maximum)
+ self.listValues.home(False)
+ hLayout.addWidget(self.listValues)
+
+ self.size_was_updated(size)
+
+ inputButton = QtGui.QToolButton()
+ inputButton.setText('...')
+ self.connect(inputButton, QtCore.SIGNAL('clicked()'),
+ self.editFunction)
+ hLayout.addWidget(inputButton)
+ self.exploration_name = 'User-defined Function'
+
+ def defaultFunction(self):
+ """ defaultFunction() -> str
+ Return the default function definition
+
+ """
+ if self.type=='String':
+ quote = '"'
+ else:
+ quote = ''
+ return 'def value(i):\n """ value(i: int) -> value\n'\
+ ' Returns the i-th value\n'\
+ ' i is from 0 to <step count>-1.\n'\
+ ' If this function has an error, the value will be\n'\
+ ' the default constant value\n'\
+ ' """\n'\
+ ' # Define your function here\n'
+
+ def get_values(self, count):
+ """ get_values() -> []
+ Convert the user define function into a list. Size specifies the size
+ request.
+
+ """
+ param_info = self._param_info
+ module = param_info.spec.descriptor.module
+ def get():
+ import code
+ values = []
+ d = {}
+ try:
+ exec(self.function) in {}, d
+ except Exception, e:
+ return [module.default_value] * count
+ def evaluate(i):
+ try:
+ v = d['value'](i)
+ if v == None:
+ return module.default_value
+ return v
+ except Exception, e:
+ return str(e)
+ return [evaluate(i) for i in xrange(self.size)]
+ result = get()
+
+ if not all(module.validate(x) for x in result):
+ show_warning('Failed Validation',
+ 'One of the <i>%s</i>\'s user defined '
+ 'functions has failed validation, '
+ 'which usually means it generated a '
+ 'value of a type different '
+ 'than that specified by the '
+ 'parameter. Parameter Exploration '
+ 'aborted.' % param_info.spec.descriptor.name)
+ return None
+ return result
+
+
+ def getValuesString(self):
+ """ getValuesString() -> str
+ Return a string representation of the parameter list
+
+ """
+ r = self.get_values(self.size)
+ if r is None:
+ return '{ERROR}'
+ else:
+ return '{%s}' % ','.join([str(v) for v in r])
+
+ def editFunction(self):
+ """ editFunction() -> None
+ Pop up a dialog for editing user-defined function
+
+ """
+ dialog = QUserFunctionDialog(self.function)
+ if dialog.exec_()==QtGui.QDialog.Accepted:
+ self.function = str(dialog.editor.toPlainText())
+ self.listValues.setText(self.getValuesString())
+ dialog.deleteLater()
+
+ def size_was_updated(self, size):
+ """ size_was_updated(size: int) -> None
+
+ This is called whenever the size of the interpolation is changed.
+ Values are re-calculated."""
+ if size!=self.size:
+ self.size = size
+ htmlText = '<html><big>ƒ</big>(n) <b>:</b> ' \
+ '[0,%d) → </html>' % size
+ self.label.setText(htmlText)
+ self.listValues.setText(self.getValuesString())
+
+##############################################################################
+
+class QUserFunctionDialog(QtGui.QDialog):
+ """
+ QUserFunctionDialog provides an interface for user to edit a
+ python function
+
+ """
+ def __init__(self, function, parent=None):
+ """ QUserFunctionDialog(function: str, parent: QWidget)
+ -> QUserFunctionDialog
+ Set up a python source editor
+
+ """
+ QtGui.QDialog.__init__(self, parent)
+ vLayout = QtGui.QVBoxLayout()
+ vLayout.setMargin(0)
+ vLayout.setSpacing(0)
+ self.setLayout(vLayout)
+ self.setWindowTitle('User-defined Function')
+
+ label = QtGui.QLabel("Please define your function below. This "
+ "'value(i)' function will be iteratively called "
+ "for <step count> numbers. For each step, "
+ "it should return a value of parameter type.")
+ label.setMargin(5)
+ label.setWordWrap(True)
+ vLayout.addWidget(label)
+
+ self.editor = PythonEditor(self)
+ self.editor.setPlainText(function)
+ vLayout.addWidget(self.editor)
+
+ hLayout = QtGui.QHBoxLayout()
+ vLayout.addLayout(hLayout)
+
+ okButton = QtGui.QPushButton('&OK')
+ okButton.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+ self.connect(okButton, QtCore.SIGNAL('clicked()'), self.accept)
+ hLayout.addWidget(okButton)
+
+ cancelButton = QtGui.QPushButton('&Cancel')
+ cancelButton.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+ self.connect(cancelButton, QtCore.SIGNAL('clicked()'), self.reject)
+ hLayout.addWidget(cancelButton)
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+ Return the recommended size for the widget
+
+ """
+ return QtCore.QSize(512, 512)
diff --git a/vistrails/gui/modules/python_source_configure.py b/vistrails/gui/modules/python_source_configure.py
new file mode 100644
index 0000000..45546af
--- /dev/null
+++ b/vistrails/gui/modules/python_source_configure.py
@@ -0,0 +1,244 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.bundles.pyimport import py_import
+import vistrails.core.requirements
+from vistrails.gui.modules.source_configure import SourceConfigurationWidget
+from PyQt4 import QtCore, QtGui
+from vistrails.gui.theme import CurrentTheme
+
+class PythonHighlighter(QtGui.QSyntaxHighlighter):
+ def __init__( self, document ):
+ QtGui.QSyntaxHighlighter.__init__( self, document )
+ self.rules = []
+
+ keywordFormat = QtGui.QTextCharFormat()
+ keywordFormat.setForeground(QtCore.Qt.blue)
+ self.rules += [(r"\b%s\b"%w, keywordFormat, -1, -1, False)
+ for w in ["def","from",
+ "import","for","in",
+ "while","True","None",
+ "False","pass","return",
+ "self","tuple","list",
+ "print","if","else",
+ "elif","len","string"
+ "assert","try","except",
+ "exec", "break", "continue",
+ "not", "and", "or", "as",
+ "type", "int", "float",
+ ]]
+
+ defclassFormat = QtGui.QTextCharFormat()
+ defclassFormat.setForeground(QtCore.Qt.blue)
+ self.rules += [(r"\bclass\b\s*(\w+)", defclassFormat, -1, -1, False)]
+
+ commentFormat = QtGui.QTextCharFormat()
+ commentFormat.setFontItalic(True)
+ commentFormat.setForeground(QtCore.Qt.darkGreen)
+ self.rules += [(r"#[^\n]*", commentFormat, -1, -1, False)]
+
+ literalFormat = QtGui.QTextCharFormat()
+ literalFormat.setForeground(QtGui.QColor(65, 105, 225)) #royalblue
+ self.rules += [
+ # Whole docstring
+ (r"'''.*'''", literalFormat, -1, -1, True),
+ (r'""".*"""', literalFormat, -1, -1, True),
+ # Hanging docstring (single quote)
+ (r"'''.*$", literalFormat, -1, 2, False),
+ (r"^.*'''", literalFormat, 2, -1, True),
+ (r"^.*$", literalFormat, 2, 2, False),
+ # Hanging docstring (double quote)
+ (r'""".*$', literalFormat, -1, 3, False),
+ (r'^.*"""', literalFormat, 3, -1, True),
+ (r'^.*$', literalFormat, 3, 3, False),
+ # Whole string
+ (r"'[^']*'", literalFormat, -1, -1, False),
+ (r'"[^"]*"', literalFormat, -1, -1, False),
+ # Hanging string (single quote)
+ (r"'[^']*$", literalFormat, -1, 0, False),
+ (r"^[^']*$", literalFormat, 0, 0, False),
+ (r"^[^']*'", literalFormat, 0, -1, False),
+ # Hanging string (double quotes)
+ (r'"[^"]*$', literalFormat, -1, 1, False),
+ (r'^[^"]*$', literalFormat, 1, 1, False),
+ (r'^[^"]*"', literalFormat, 1, -1, False),
+ ]
+
+ def highlightBlock(self, text):
+ baseFormat = self.format(0)
+ prevState = self.previousBlockState()
+ self.setCurrentBlockState(prevState)
+ shift = 0
+ while True:
+ matchedRule = (None, -1, -1, -1, -1)
+ for rule in self.rules:
+ if rule[2]==self.currentBlockState():
+ RE = QtCore.QRegExp(rule[0])
+ RE.setMinimal(rule[4])
+ pos = RE.indexIn(text, shift)
+ if (pos!=-1 and (matchedRule[0]==None or pos<matchedRule[1]) and
+ RE.matchedLength()>0):
+ matchedRule = (rule[1], pos, RE.matchedLength(), rule[3])
+ if matchedRule[0]!=None:
+ self.setFormat(matchedRule[1], matchedRule[2], matchedRule[0])
+ self.setCurrentBlockState(matchedRule[3])
+ shift = matchedRule[1]+matchedRule[2]
+ else:
+ break
+
+def PythonEditor(parent=None):
+ try:
+ py_import('PyQt4.Qsci', {'linux-ubuntu': 'python-qscintilla2'})
+ except ImportError:
+ return OldPythonEditor(parent)
+ else:
+ return NewPythonEditor(parent)
+
+def NewPythonEditor(parent):
+ vistrails.core.requirements.require_python_module('PyQt4.Qsci')
+ from PyQt4.Qsci import QsciScintilla, QsciLexerPython
+ class _PythonEditor(QsciScintilla):
+
+ def __init__(self, parent=None):
+ QsciScintilla.__init__(self, parent)
+ ## set the default font of the editor
+ ## and take the same font for line numbers
+ font = CurrentTheme.PYTHON_SOURCE_EDITOR_FONT
+ self.setFont(font)
+ fm = QtGui.QFontMetrics(font)
+
+ ## Line numbers
+ # conventionally, margin 0 is for line numbers
+ self.setMarginWidth(0, fm.width( "0000" ) + 4)
+ self.setMarginLineNumbers(0, True)
+
+ self.setAutoIndent(True)
+
+ ## Edge Mode shows a red vetical bar at 80 chars
+ self.setEdgeMode(QsciScintilla.EdgeLine)
+ self.setEdgeColumn(80)
+ self.setEdgeColor(QtGui.QColor("#CCCCCC"))
+
+ ## Folding visual : we will use boxes
+ self.setFolding(QsciScintilla.BoxedTreeFoldStyle)
+
+ ## Braces matching
+ self.setBraceMatching(QsciScintilla.SloppyBraceMatch)
+
+ ## Editing line color
+ # self.setCaretLineVisible(True)
+ # self.setCaretLineBackgroundColor(QtGui.QColor("#CDA869"))
+
+
+ ## Margins colors
+ # line numbers margin
+ self.setMarginsBackgroundColor(QtGui.QColor("#FFFFFF"))
+ self.setMarginsForegroundColor(QtGui.QColor("#000000"))
+
+ # folding margin colors (foreground,background)
+ self.setFoldMarginColors(QtGui.QColor("#DDDDDD"),QtGui.QColor("#DDDDDD"))
+ # do not use tabs
+ self.setIndentationsUseTabs(False)
+ self.setTabWidth(4)
+ self.setTabIndents(True)
+
+ ## Choose a lexer
+ lexer = QsciLexerPython()
+ lexer.setDefaultFont(font)
+ lexer.setFont(font)
+ self.setLexer(lexer)
+
+ # set autocompletion
+ self.setAutoCompletionThreshold(2)
+ self.setAutoCompletionSource(QsciScintilla.AcsDocument)
+ self.setAutoCompletionCaseSensitivity(True)
+ self.setAutoCompletionReplaceWord(True)
+ self.setAutoCompletionFillupsEnabled(True)
+
+ def setPlainText(self, text):
+ """ setPlainText(text: str) -> None
+ redirect to setText
+
+ """
+ self.setText(text)
+
+ def toPlainText(self):
+ """ setPlainText(text: str) -> None
+ redirect to self.text()
+
+ """
+ return self.text()
+
+# def focusOutEvent(self, event):
+# if self.parent():
+# QtCore.QCoreApplication.sendEvent(self.parent(), event)
+# QsciScintilla.focusOutEvent(self, event)
+
+ return _PythonEditor(parent)
+
+class OldPythonEditor(QtGui.QTextEdit):
+
+ def __init__(self, parent=None):
+ QtGui.QTextEdit.__init__(self, parent)
+ self.setLineWrapMode(QtGui.QTextEdit.NoWrap)
+ self.formatChanged(None)
+ self.setCursorWidth(8)
+ self.highlighter = PythonHighlighter(self.document())
+ self.connect(self,
+ QtCore.SIGNAL('currentCharFormatChanged(QTextCharFormat)'),
+ self.formatChanged)
+
+ def formatChanged(self, f):
+ self.setFont(CurrentTheme.PYTHON_SOURCE_EDITOR_FONT)
+
+ def keyPressEvent(self, event):
+ """ keyPressEvent(event: QKeyEvent) -> Nont
+ Handle tab with 4 spaces
+
+ """
+ if event.key()==QtCore.Qt.Key_Tab:
+ self.insertPlainText(' ')
+ else:
+ # super(PythonEditor, self).keyPressEvent(event)
+ QtGui.QTextEdit.keyPressEvent(self, event)
+
+# def focusOutEvent(self, event):
+# if self.parent():
+# QtCore.QCoreApplication.sendEvent(self.parent(), event)
+# QtGui.QTextEdit.focusOutEvent(self, event)
+
+class PythonSourceConfigurationWidget(SourceConfigurationWidget):
+ def __init__(self, module, controller, parent=None):
+ SourceConfigurationWidget.__init__(self, module, controller,
+ PythonEditor, True, True, parent)
diff --git a/vistrails/gui/modules/query_configuration.py b/vistrails/gui/modules/query_configuration.py
new file mode 100644
index 0000000..bab5610
--- /dev/null
+++ b/vistrails/gui/modules/query_configuration.py
@@ -0,0 +1,146 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: vistrails at sci.utah.edu
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+from vistrails.core.utils import any, expression
+from vistrails.core import system
+
+from constant_configuration import StandardConstantWidget, ColorWidget
+
+############################################################################
+
+class QueryWidgetMixin(object):
+
+ def __init__(self, contents=None, query_method=None):
+ self._last_contents = contents
+ self._last_query_method = query_method
+
+ # updateMethod intercepts calls from a child widget like the
+ # contents_widget
+ def updateMethod(self):
+ self.update_parent()
+
+ def update_parent(self):
+ new_contents = self.contents()
+ new_query_method = self.query_method()
+ if (new_contents != self._last_contents or
+ new_query_method != self._last_query_method):
+ if self.parent() and hasattr(self.parent(), 'updateMethod'):
+ self.parent().updateMethod()
+ self._last_contents = new_contents
+ self._last_query_method = new_query_method
+ self.emit(QtCore.SIGNAL('contentsChanged'), (self,new_contents))
+
+class BaseQueryWidget(QtGui.QWidget, QueryWidgetMixin):
+ def __init__(self, contents_klass, query_methods, param, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ QueryWidgetMixin.__init__(self, param.strValue, param.queryMethod)
+
+ contents = param.strValue
+ queryMethod = param.queryMethod
+
+ layout = QtGui.QHBoxLayout()
+ self.op_button = QtGui.QToolButton()
+ self.op_button.setPopupMode(QtGui.QToolButton.InstantPopup)
+ self.op_button.setArrowType(QtCore.Qt.NoArrow)
+ action_group = QtGui.QActionGroup(self.op_button)
+ actions = []
+ checked_exists = False
+ for method in query_methods:
+ action = QtGui.QAction(method, self)
+ action.setCheckable(True)
+ action_group.addAction(action)
+ if method == queryMethod:
+ action.setChecked(True)
+ checked_exists = True
+ actions.append(action)
+ if not checked_exists:
+ actions[0].setChecked(True)
+ self._last_query_method = str(actions[0].text())
+
+ menu = QtGui.QMenu(self.op_button)
+ menu.addActions(actions)
+ self.op_button.setMenu(menu)
+ self.op_button.setText(action_group.checkedAction().text())
+
+ self.contents_widget = contents_klass(param)
+ self.contents_widget.setContents(contents)
+
+ layout.setMargin(0)
+ layout.setSpacing(0)
+ layout.addWidget(self.op_button)
+ layout.addWidget(self.contents_widget)
+ self.setLayout(layout)
+
+ self.connect(self.op_button, QtCore.SIGNAL('triggered(QAction*)'),
+ self.update_action)
+
+ def contents(self):
+ return self.contents_widget.contents()
+
+ def setContents(self, strValue, silent=True):
+ self.contents_widget.setContents(strValue)
+ if not silent:
+ self.update_parent()
+
+ def update_action(self, action):
+ self.op_button.setText(action.text())
+ self.update_parent()
+
+ def query_method(self):
+ for action in self.op_button.menu().actions():
+ if action.isChecked():
+ return str(action.text())
+
+class StandardQueryWidget(BaseQueryWidget):
+ def __init__(self, param, parent=None):
+ BaseQueryWidget.__init__(self, StandardConstantWidget, ["==", "!="],
+ param, parent)
+
+class StringQueryWidget(StandardQueryWidget):
+ def __init__(self, param, parent=None):
+ BaseQueryWidget.__init__(self, StandardConstantWidget,
+ ["*[]*", "==", "=~"],
+ param, parent)
+
+class NumericQueryWidget(StandardQueryWidget):
+ def __init__(self, param, parent=None):
+ BaseQueryWidget.__init__(self, StandardConstantWidget,
+ ["==", "<", ">", "<=", ">="],
+ param, parent)
+
+class ColorQueryWidget(StandardQueryWidget):
+ def __init__(self, param, parent=None):
+ BaseQueryWidget.__init__(self, ColorWidget, ["2.3", "5", "10", "50"],
+ param, parent)
diff --git a/vistrails/gui/modules/resources/__init__.py b/vistrails/gui/modules/resources/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/gui/modules/resources/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
diff --git a/vistrails/gui/modules/resources/colorconfig_rc.py b/vistrails/gui/modules/resources/colorconfig_rc.py
new file mode 100644
index 0000000..eda280c
--- /dev/null
+++ b/vistrails/gui/modules/resources/colorconfig_rc.py
@@ -0,0 +1,1850 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# Resource object code
+#
+# Created: Thu Oct 5 21:38:17 2006
+# by: The Resource Compiler for PyQt (Qt v4.1.3)
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore
+
+qt_resource_data = b"\
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+"
+
+qt_resource_name = b"\
+\x00\x0e\
+\x07\xd2\x76\x07\
+\x00\x63\
+\x00\x6f\x00\x6c\x00\x6f\x00\x72\x00\x77\x00\x68\x00\x65\x00\x65\x00\x6c\x00\x2e\x00\x70\x00\x6e\x00\x67\
+"
+
+qt_resource_struct = b"\
+\x00\x00\x00\x00\x00\x02\x00\x00\x00\x01\x00\x00\x00\x01\
+\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\
+"
+
+def qInitResources():
+ QtCore.qRegisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+def qCleanupResources():
+ QtCore.qUnregisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+qInitResources()
diff --git a/vistrails/gui/modules/source_configure.py b/vistrails/gui/modules/source_configure.py
new file mode 100644
index 0000000..46ffa62
--- /dev/null
+++ b/vistrails/gui/modules/source_configure.py
@@ -0,0 +1,413 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+from vistrails.core import system, debug
+from vistrails.core.utils import PortAlreadyExists
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.gui.modules.module_configure import StandardModuleConfigurationWidget
+from vistrails.gui.modules.tuple_configuration import PortTableConfigurationWidget, \
+ PortTable
+from vistrails.gui.theme import CurrentTheme
+import urllib
+
+class SourceEditor(QtGui.QTextEdit):
+
+ def __init__(self, parent=None):
+ QtGui.QTextEdit.__init__(self, parent)
+ self.setLineWrapMode(QtGui.QTextEdit.NoWrap)
+ self.formatChanged(None)
+ self.setCursorWidth(8)
+ self.connect(self,
+ QtCore.SIGNAL('currentCharFormatChanged(QTextCharFormat)'),
+ self.formatChanged)
+
+ self.setFocusPolicy(QtCore.Qt.WheelFocus)
+
+ def formatChanged(self, f):
+ self.setFont(CurrentTheme.PYTHON_SOURCE_EDITOR_FONT)
+
+# def focusOutEvent(self, event):
+# if self.parent():
+# QtCore.QCoreApplication.sendEvent(self.parent(), event)
+# QtGui.QTextEdit.focusOutEvent(self, event)
+
+class SourceWidget(PortTableConfigurationWidget):
+ def __init__(self, module, controller, editor_class=None,
+ has_inputs=True, has_outputs=True, parent=None,
+ encode=True, portName='source'):
+ PortTableConfigurationWidget.__init__(self, module, controller, parent)
+ if editor_class is None:
+ editor_class = SourceEditor
+ self.codeEditor = editor_class(parent)
+ self.setWindowTitle('%s Configuration' % module.name)
+ self.setLayout(QtGui.QVBoxLayout())
+ self.layout().setMargin(0)
+ self.layout().setSpacing(0)
+ self.has_inputs = has_inputs
+ self.has_outputs = has_outputs
+ self.sourcePortName = portName
+ self.sourceEncode = encode
+ self.createPortTable(has_inputs, has_outputs)
+ self.setupEditor()
+ self.adjustSize()
+
+ def createPortTable(self, has_inputs=True, has_outputs=True):
+ if has_inputs:
+ self.inputPortTable = PortTable(self)
+ labels = ["Input Port Name", "Type"]
+ self.inputPortTable.setHorizontalHeaderLabels(labels)
+ self.inputPortTable.initializePorts(self.module.input_port_specs)
+ self.layout().addWidget(self.inputPortTable)
+ if has_outputs:
+ self.outputPortTable = PortTable(self)
+ labels = ["Output Port Name", "Type"]
+ self.outputPortTable.setHorizontalHeaderLabels(labels)
+ self.outputPortTable.initializePorts(self.module.output_port_specs,
+ True)
+ self.layout().addWidget(self.outputPortTable)
+ if has_inputs and has_outputs:
+ self.performPortConnection(self.connect)
+ if has_inputs:
+ self.inputPortTable.fixGeometry()
+ if has_outputs:
+ self.outputPortTable.fixGeometry()
+
+ def initializeCode(self):
+ self.codeEditor.clear()
+ fid = self.findSourceFunction()
+ code = None
+ # Get code from a function
+ if fid!=-1:
+ f = self.module.functions[fid]
+ code = f.params[0].strValue
+ # Get code from the default on the port
+ else:
+ port = self.module.get_port_spec(self.sourcePortName, 'input')
+ if port.defaults:
+ code, = port.defaults
+ if code is not None:
+ if self.sourceEncode:
+ code = urllib.unquote(code)
+ self.codeEditor.setPlainText(code)
+ if self.codeEditor.__class__.__name__ not in ['_PythonEditor', '_TextEditor']:
+ self.codeEditor.document().setModified(False)
+ else:
+ self.codeEditor.setModified(False)
+ self.codeEditor.setFocus()
+
+ def findSourceFunction(self):
+ fid = -1
+ for i in xrange(self.module.getNumFunctions()):
+ if self.module.functions[i].name==self.sourcePortName:
+ fid = i
+ break
+ return fid
+
+ def setupEditor(self):
+ self.initializeCode()
+ self.layout().addWidget(self.codeEditor, 1)
+
+ self.cursorLabel = QtGui.QLabel()
+ self.layout().addWidget(self.cursorLabel)
+ if self.codeEditor.__class__.__name__ not in ['_PythonEditor', '_TextEditor']:
+ self.connect(self.codeEditor,
+ QtCore.SIGNAL('cursorPositionChanged()'),
+ self.updateCursorLabel)
+ else:
+ self.connect(self.codeEditor,
+ QtCore.SIGNAL('cursorPositionChanged(int, int)'),
+ self.updateCursorLabel)
+ self.updateCursorLabel()
+
+ def updateCursorLabel(self, x=0, y=0):
+ if self.codeEditor.__class__.__name__ not in ['_PythonEditor', '_TextEditor']:
+ cursor = self.codeEditor.textCursor()
+ x = cursor.blockNumber()
+ y = cursor.columnNumber()
+
+ self.cursorLabel.setText('Line: %d / Col: %d' % (x+1, y+1))
+
+ def sizeHint(self):
+ return QtCore.QSize(512, 512)
+
+ def performPortConnection(self, operation):
+ operation(self.inputPortTable.horizontalHeader(),
+ QtCore.SIGNAL('sectionResized(int,int,int)'),
+ self.portTableResize)
+ operation(self.outputPortTable.horizontalHeader(),
+ QtCore.SIGNAL('sectionResized(int,int,int)'),
+ self.portTableResize)
+
+ def portTableResize(self, logicalIndex, oldSize, newSize):
+ self.performPortConnection(self.disconnect)
+ if self.inputPortTable.horizontalHeader().sectionSize(logicalIndex)!=newSize:
+ self.inputPortTable.horizontalHeader().resizeSection(logicalIndex,newSize)
+ if self.outputPortTable.horizontalHeader().sectionSize(logicalIndex)!=newSize:
+ self.outputPortTable.horizontalHeader().resizeSection(logicalIndex,newSize)
+ self.performPortConnection(self.connect)
+
+ def activate(self):
+ self.codeEditor.setFocus(QtCore.Qt.MouseFocusReason)
+
+class SourceViewerWidget(SourceWidget):
+ def __init__(self, module, controller, editor_class=None,
+ has_inputs=True, has_outputs=True, parent=None,
+ encode=True, portName='source'):
+ SourceWidget.__init__(self, module, controller, editor_class,
+ has_inputs, has_outputs, parent, encode,
+ portName)
+ self.codeEditor.setReadOnly(True)
+ self.createCloseButton()
+ self.setWindowTitle('%s Configuration (Read-Only)' % module.name)
+ self.setWindowFlags(QtCore.Qt.Window)
+ self.adjustSize()
+
+ def createPortTable(self, has_inputs=True, has_outputs=True):
+ if has_inputs:
+ self.inputPortTable = QtGui.QTableWidget(1, 2, self)
+ labels = ["Input Port Name", "Type"]
+ self.inputPortTable.horizontalHeader().setResizeMode(QtGui.QHeaderView.Interactive)
+ self.inputPortTable.horizontalHeader().setMovable(False)
+ self.inputPortTable.horizontalHeader().setStretchLastSection(True)
+ self.inputPortTable.setHorizontalHeaderLabels(labels)
+ self.initializePorts(self.inputPortTable,
+ self.module.input_port_specs)
+ self.layout().addWidget(self.inputPortTable)
+ if has_outputs:
+ self.outputPortTable = QtGui.QTableWidget(1, 2, self)
+ labels = ["Output Port Name", "Type"]
+ self.outputPortTable.horizontalHeader().setResizeMode(QtGui.QHeaderView.Interactive)
+ self.outputPortTable.horizontalHeader().setMovable(False)
+ self.outputPortTable.horizontalHeader().setStretchLastSection(True)
+
+ self.outputPortTable.setHorizontalHeaderLabels(labels)
+ self.initializePorts(self.outputPortTable,
+ self.module.output_port_specs, True)
+ self.layout().addWidget(self.outputPortTable)
+ if has_inputs and has_outputs:
+ self.performPortConnection(self.connect)
+
+ if has_inputs:
+ self.fixTableGeometry(self.inputPortTable)
+ if has_outputs:
+ self.fixTableGeometry(self.outputPortTable)
+
+ def initializePorts(self, table, port_specs, reverse_order=False):
+ if reverse_order:
+ port_specs_iter = reversed(port_specs)
+ else:
+ port_specs_iter = port_specs
+ for p in port_specs_iter:
+ row = table.rowCount()-1
+ sigstring = p.sigstring[1:-1]
+ siglist = sigstring.split(':')
+ short_name = "%s (%s)" % (siglist[1], siglist[0])
+ item = QtGui.QTableWidgetItem(p.name)
+ item.setFlags(QtCore.Qt.ItemIsSelectable|QtCore.Qt.ItemIsEnabled)
+ table.setItem(row, 0, item)
+ item = QtGui.QTableWidgetItem(short_name)
+ item.setFlags(QtCore.Qt.ItemIsSelectable|QtCore.Qt.ItemIsEnabled)
+ table.setItem(row, 1, item)
+ table.setRowCount(table.rowCount()+1)
+
+ def fixTableGeometry(self, table):
+ rect = table.visualRect(table.model().index(table.rowCount()-1,
+ table.columnCount()-1))
+ table.setFixedHeight(table.horizontalHeader().height()+
+ rect.y()+rect.height()+1)
+ def createCloseButton(self):
+ hboxlayout = QtGui.QHBoxLayout()
+ self.closeButton = QtGui.QPushButton("Close")
+ self.connect(self.closeButton, QtCore.SIGNAL("clicked()"),
+ self.closeWidget)
+ hboxlayout.addStretch()
+ hboxlayout.addWidget(self.closeButton)
+ hboxlayout.addStretch()
+ self.layout().addLayout(hboxlayout)
+
+ def closeWidget(self):
+ self.emit(QtCore.SIGNAL("widgetClosed"))
+ self.close()
+
+class SourceConfigurationWidget(SourceWidget):
+
+ def __init__(self, module, controller, editor_class=None,
+ has_inputs=True, has_outputs=True, parent=None,
+ encode=True, portName='source'):
+ SourceWidget.__init__(self, module, controller, editor_class,
+ has_inputs, has_outputs, parent, encode,
+ portName)
+ self.detached_windows = []
+ self.createButtons()
+ #connect signals
+ if has_inputs:
+ self.connect(self.inputPortTable, QtCore.SIGNAL("contentsChanged"),
+ self.updateState)
+ if has_outputs:
+ self.connect(self.outputPortTable, QtCore.SIGNAL("contentsChanged"),
+ self.updateState)
+ self.connect(self.codeEditor, QtCore.SIGNAL("textChanged()"),
+ self.updateState)
+ self.adjustSize()
+ self.setMouseTracking(True)
+ self.mouseOver = False
+
+ def enterEvent(self, event):
+ self.mouseOver = True
+
+ def leaveEvent(self, event):
+ self.mouseOver = False
+
+ def createButtons(self):
+ """ createButtons() -> None
+ Create and connect signals to Save & Reset button
+
+ """
+ self.buttonLayout = QtGui.QHBoxLayout()
+ self.buttonLayout.setMargin(5)
+ self.detachButton = QtGui.QPushButton("Show read-only window")
+ self.buttonLayout.addWidget(self.detachButton)
+ self.buttonLayout.addStretch()
+ self.saveButton = QtGui.QPushButton('&Save', self)
+ self.saveButton.setFixedWidth(100)
+ self.saveButton.setEnabled(False)
+ self.buttonLayout.addWidget(self.saveButton)
+ self.resetButton = QtGui.QPushButton('&Reset', self)
+ self.resetButton.setFixedWidth(100)
+ self.resetButton.setEnabled(False)
+ self.buttonLayout.addSpacing(10)
+ self.buttonLayout.addWidget(self.resetButton)
+ self.layout().addLayout(self.buttonLayout)
+ self.connect(self.detachButton, QtCore.SIGNAL("clicked()"),
+ self.detachReadOnlyWindow)
+ self.connect(self.saveButton, QtCore.SIGNAL('clicked(bool)'),
+ self.saveTriggered)
+ self.connect(self.resetButton, QtCore.SIGNAL('clicked(bool)'),
+ self.resetTriggered)
+
+ def detachReadOnlyWindow(self):
+ from vistrails.gui.vistrails_window import _app
+ widget = SourceViewerWidget(self.module, self.controller,
+ type(self.codeEditor),
+ self.has_inputs, self.has_outputs,
+ None, self.sourceEncode,
+ self.sourcePortName)
+ window = QtGui.QMainWindow()
+ window.setCentralWidget(widget)
+ window.setWindowTitle(widget.windowTitle())
+ self.connect(widget, QtCore.SIGNAL("widgetClosed"),
+ window.close)
+ widget.setVisible(True)
+ _app.palette_window.windows.append(window)
+ window.show()
+
+ def updateVistrail(self):
+ """updateVistrail() -> None
+ Update vistrail to contain changes to the python source
+
+ """
+ deleted_ports = []
+ added_ports = []
+ if self.has_inputs:
+ (input_deleted_ports, input_added_ports) = \
+ self.getPortDiff('input', self.inputPortTable)
+ deleted_ports.extend(input_deleted_ports)
+ added_ports.extend(input_added_ports)
+ if self.has_outputs:
+ (output_deleted_ports, output_added_ports) = \
+ self.getPortDiff('output', self.outputPortTable)
+ deleted_ports.extend(output_deleted_ports)
+ added_ports.extend(output_added_ports)
+
+ functions = []
+ modified = False
+ if self.codeEditor.__class__.__name__ not in ['_PythonEditor', '_TextEditor']:
+ modified = self.codeEditor.document().isModified()
+ else:
+ modified = self.codeEditor.isModified()
+
+ if (self.codeEditor is not None and modified):
+ try:
+ code = str(self.codeEditor.toPlainText())
+ except UnicodeEncodeError, e:
+ debug.critical('Source Code Editor does not support non-ascii characters', str(e))
+ return False
+ if self.sourceEncode:
+ code = urllib.quote(code)
+ functions.append((self.sourcePortName, [code]))
+ if len(deleted_ports) + len(added_ports) + len(functions) == 0:
+ # nothing changed
+ return True
+ try:
+ self.controller.update_ports_and_functions(self.module.id,
+ deleted_ports,
+ added_ports,
+ functions)
+ except PortAlreadyExists, e:
+ debug.critical('Port Already Exists %s' % str(e))
+ return False
+ return True
+
+ def resetTriggered(self, checked = False):
+ if self.has_inputs:
+ self.inputPortTable.clearContents()
+ self.inputPortTable.setRowCount(1)
+ self.inputPortTable.initializePorts(self.module.input_port_specs)
+ self.inputPortTable.fixGeometry()
+ if self.has_outputs:
+ self.outputPortTable.clearContents()
+ self.outputPortTable.setRowCount(1)
+ self.outputPortTable.initializePorts(self.module.output_port_specs,
+ True)
+ self.outputPortTable.fixGeometry()
+
+ self.initializeCode()
+ self.saveButton.setEnabled(False)
+ self.resetButton.setEnabled(False)
+ self.state_changed = False
+ self.emit(QtCore.SIGNAL("stateChanged"))
+
+ def updateState(self):
+ self.saveButton.setEnabled(True)
+ self.resetButton.setEnabled(True)
+ if not self.state_changed:
+ self.state_changed = True
+ self.emit(QtCore.SIGNAL("stateChanged"))
+
+# def focusOutEvent(self, event):
+ #if not self.mouseOver:
+ # self.askToSaveChanges()
+# QtGui.QWidget.focusOutEvent(self, event)
diff --git a/vistrails/gui/modules/string_configure.py b/vistrails/gui/modules/string_configure.py
new file mode 100644
index 0000000..059ef5e
--- /dev/null
+++ b/vistrails/gui/modules/string_configure.py
@@ -0,0 +1,154 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.bundles.pyimport import py_import
+import vistrails.core.requirements
+from vistrails.gui.modules.source_configure import SourceConfigurationWidget
+from PyQt4 import QtCore, QtGui
+from vistrails.gui.theme import CurrentTheme
+
+def TextEditor(parent=None):
+ try:
+ py_import('PyQt4.Qsci', {'linux-ubuntu': 'python-qscintilla2'})
+ except ImportError:
+ return OldTextEditor(parent)
+ else:
+ return NewTextEditor(parent)
+
+def NewTextEditor(parent):
+ vistrails.core.requirements.require_python_module('PyQt4.Qsci')
+ from PyQt4.Qsci import QsciScintilla
+ class _TextEditor(QsciScintilla):
+
+ def __init__(self, parent=None):
+ QsciScintilla.__init__(self, parent)
+ ## set the default font of the editor
+ ## and take the same font for line numbers
+ font = CurrentTheme.PYTHON_SOURCE_EDITOR_FONT
+ self.setFont(font)
+ fm = QtGui.QFontMetrics(font)
+
+ ## Line numbers
+ # conventionally, margin 0 is for line numbers
+ self.setMarginWidth(0, fm.width( "0000" ) + 4)
+ self.setMarginLineNumbers(0, True)
+
+ self.setAutoIndent(True)
+
+ ## Edge Mode shows a red vetical bar at 80 chars
+ self.setEdgeMode(QsciScintilla.EdgeLine)
+ self.setEdgeColumn(80)
+ self.setEdgeColor(QtGui.QColor("#CCCCCC"))
+
+ ## Folding visual : we will use boxes
+ self.setFolding(QsciScintilla.BoxedTreeFoldStyle)
+
+ ## Braces matching
+ self.setBraceMatching(QsciScintilla.SloppyBraceMatch)
+
+ ## Editing line color
+ # self.setCaretLineVisible(True)
+ # self.setCaretLineBackgroundColor(QtGui.QColor("#CDA869"))
+
+
+ ## Margins colors
+ # line numbers margin
+ self.setMarginsBackgroundColor(QtGui.QColor("#FFFFFF"))
+ self.setMarginsForegroundColor(QtGui.QColor("#000000"))
+
+ # folding margin colors (foreground,background)
+ self.setFoldMarginColors(QtGui.QColor("#DDDDDD"),QtGui.QColor("#DDDDDD"))
+ # do not use tabs
+ self.setIndentationsUseTabs(False)
+ self.setTabWidth(4)
+ self.setTabIndents(True)
+
+ # set autocompletion
+ self.setAutoCompletionThreshold(2)
+ self.setAutoCompletionSource(QsciScintilla.AcsDocument)
+ self.setAutoCompletionCaseSensitivity(True)
+ self.setAutoCompletionReplaceWord(True)
+ self.setAutoCompletionFillupsEnabled(True)
+
+ def setPlainText(self, text):
+ """ setPlainText(text: str) -> None
+ redirect to setText
+
+ """
+ self.setText(text)
+
+ def toPlainText(self):
+ """ setPlainText(text: str) -> None
+ redirect to self.text()
+
+ """
+ text = self.text()
+ return text.replace('\r', '\n')
+
+# def focusOutEvent(self, event):
+# if self.parent():
+# QtCore.QCoreApplication.sendEvent(self.parent(), event)
+# QsciScintilla.focusOutEvent(self, event)
+
+ return _TextEditor(parent)
+
+class OldTextEditor(QtGui.QTextEdit):
+
+ def __init__(self, parent=None):
+ QtGui.QTextEdit.__init__(self, parent)
+ self.setLineWrapMode(QtGui.QTextEdit.NoWrap)
+ self.formatChanged(None)
+ self.setCursorWidth(8)
+ self.connect(self,
+ QtCore.SIGNAL('currentCharFormatChanged(QTextCharFormat)'),
+ self.formatChanged)
+
+ def formatChanged(self, f):
+ self.setFont(CurrentTheme.PYTHON_SOURCE_EDITOR_FONT)
+
+ def keyPressEvent(self, event):
+ """ keyPressEvent(event: QKeyEvent) -> Nont
+ Handle tab with 4 spaces
+
+ """
+ if event.key()==QtCore.Qt.Key_Tab:
+ self.insertPlainText(' ')
+ else:
+ # super(PythonEditor, self).keyPressEvent(event)
+ QtGui.QTextEdit.keyPressEvent(self, event)
+
+class TextConfigurationWidget(SourceConfigurationWidget):
+ def __init__(self, module, controller, parent=None):
+ SourceConfigurationWidget.__init__(self, module, controller,
+ TextEditor, False, False, parent, False, portName='value')
diff --git a/vistrails/gui/modules/tuple_configuration.py b/vistrails/gui/modules/tuple_configuration.py
new file mode 100644
index 0000000..7e42352
--- /dev/null
+++ b/vistrails/gui/modules/tuple_configuration.py
@@ -0,0 +1,578 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file specifies the configuration widget for Tuple
+module. This should be used as a template for creating a configuration
+for other modules. The widget here should inherit from
+vistrails.gui.modules.module_configure.StandardModuleConfigurationWidget,
+which is also a QWidget.
+
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core import debug
+from vistrails.core.utils import VistrailsInternalError
+from vistrails.core.modules.module_registry import get_module_registry, \
+ ModuleRegistryException
+from vistrails.core.system import get_vistrails_basic_pkg_id
+from vistrails.core.utils import PortAlreadyExists
+from vistrails.gui.modules.module_configure import StandardModuleConfigurationWidget
+from vistrails.gui.utils import show_question, SAVE_BUTTON, DISCARD_BUTTON
+
+############################################################################
+
+class PortTable(QtGui.QTableWidget):
+ def __init__(self, parent=None):
+ QtGui.QTableWidget.__init__(self,1,2,parent)
+ self.horizontalHeader().setResizeMode(QtGui.QHeaderView.Interactive)
+ self.horizontalHeader().setMovable(False)
+ self.horizontalHeader().setStretchLastSection(True)
+ self.setSelectionMode(QtGui.QAbstractItemView.NoSelection)
+ self.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ self.delegate = PortTableItemDelegate(self)
+ self.setItemDelegate(self.delegate)
+ self.setFrameStyle(QtGui.QFrame.NoFrame)
+ self.connect(self.model(),
+ QtCore.SIGNAL('dataChanged(QModelIndex,QModelIndex)'),
+ self.handleDataChanged)
+ self.connect(self.delegate, QtCore.SIGNAL("modelDataChanged"),
+ self, QtCore.SIGNAL("contentsChanged"))
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ #self.setMouseTracking(True)
+ #self.mouseOver = False
+
+ def sizeHint(self):
+ return QtCore.QSize()
+
+ def fixGeometry(self):
+ rect = self.visualRect(self.model().index(self.rowCount()-1,
+ self.columnCount()-1))
+ self.setFixedHeight(self.horizontalHeader().height()+
+ rect.y()+rect.height()+1)
+
+ def handleDataChanged(self, topLeft, bottomRight):
+ if topLeft.column()==0:
+ text = str(self.model().data(topLeft, QtCore.Qt.DisplayRole))
+ changedGeometry = False
+ if text!='' and topLeft.row()==self.rowCount()-1:
+ self.setRowCount(self.rowCount()+1)
+ changedGeometry = True
+ if text=='' and topLeft.row()<self.rowCount()-1:
+ self.removeRow(topLeft.row())
+ changedGeometry = True
+ if changedGeometry:
+ self.fixGeometry()
+ self.emit(QtCore.SIGNAL("contentsChanged"))
+
+ def initializePorts(self, port_specs, reverse_order=False):
+ self.disconnect(self.model(),
+ QtCore.SIGNAL('dataChanged(QModelIndex,QModelIndex)'),
+ self.handleDataChanged)
+ if reverse_order:
+ port_specs_iter = reversed(port_specs)
+ else:
+ port_specs_iter = port_specs
+ for p in port_specs_iter:
+ model = self.model()
+ sigstring = p.sigstring[1:-1]
+ siglist = sigstring.split(':')
+ short_name = "%s (%s)" % (siglist[1], siglist[0])
+ model.setData(model.index(self.rowCount()-1, 1),
+ sigstring,
+ QtCore.Qt.UserRole)
+ model.setData(model.index(self.rowCount()-1, 1),
+ short_name,
+ QtCore.Qt.DisplayRole)
+ model.setData(model.index(self.rowCount()-1, 0),
+ p.name,
+ QtCore.Qt.DisplayRole)
+ self.setRowCount(self.rowCount()+1)
+ self.connect(self.model(),
+ QtCore.SIGNAL('dataChanged(QModelIndex,QModelIndex)'),
+ self.handleDataChanged)
+
+ def getPorts(self):
+ ports = []
+ model = self.model()
+ for i in xrange(self.rowCount()):
+ name = model.data(model.index(i, 0),
+ QtCore.Qt.DisplayRole)
+ sigstring = model.data(model.index(i, 1),
+ QtCore.Qt.UserRole)
+ if name is not None and sigstring is not None:
+ ports.append((name, '(%s)' % sigstring, i))
+ return ports
+
+# def focusOutEvent(self, event):
+# if self.parent():
+# QtCore.QCoreApplication.sendEvent(self.parent(), event)
+# QtGui.QTableWidget.focusOutEvent(self, event)
+
+
+class CompletingComboBox(QtGui.QComboBox):
+ def __init__(self, parent):
+ QtGui.QComboBox.__init__(self, parent)
+ self.setEditable(True)
+ self.setInsertPolicy(QtGui.QComboBox.NoInsert)
+ self._last_good_index = -1
+
+ def select_default_item(self, initial_idx):
+ self.setCurrentIndex(initial_idx)
+ self._last_good_index = initial_idx
+
+ def validate_input(self):
+ invalid = (self.currentIndex() == -1 or
+ self.itemData(self.currentIndex()) == '')
+ completion = self.completer().currentCompletion()
+ if completion:
+ idx = self.findText(completion)
+ if idx:
+ invalid = False
+ self.setCurrentIndex(idx)
+ if invalid and self._last_good_index != -1:
+ self.setCurrentIndex(self._last_good_index)
+ elif invalid:
+ self.setEditText('')
+ else:
+ self._last_good_index = self.currentIndex()
+ self.setEditText(self.itemText(self.currentIndex()))
+
+
+class PortTableItemDelegate(QtGui.QItemDelegate):
+
+ def createEditor(self, parent, option, index):
+ registry = get_module_registry()
+ if index.column()==1: #Port type
+ combo = CompletingComboBox(parent)
+ # FIXME just use descriptors here!!
+ variant_desc = registry.get_descriptor_by_name(
+ get_vistrails_basic_pkg_id(), 'Variant')
+ for _, pkg in sorted(registry.packages.iteritems()):
+ pkg_item = QtGui.QStandardItem("----- %s -----" % pkg.name)
+ pkg_item.setData('', QtCore.Qt.UserRole)
+ pkg_item.setFlags(pkg_item.flags() & ~(
+ QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable))
+ font = pkg_item.font()
+ font.setBold(True)
+ pkg_item.setFont(font)
+ combo.model().appendRow(pkg_item)
+ for _, descriptor in sorted(pkg.descriptors.iteritems()):
+ if descriptor is variant_desc:
+ variant_index = combo.count()
+ combo.addItem("%s (%s)" % (descriptor.name,
+ descriptor.identifier),
+ descriptor.sigstring)
+
+ combo.select_default_item(variant_index)
+ return combo
+ else:
+ return QtGui.QItemDelegate.createEditor(self, parent, option, index)
+
+ def setEditorData(self, editor, index):
+ if index.column()==1:
+ data = index.model().data(index, QtCore.Qt.UserRole)
+ editor.setCurrentIndex(editor.findData(data))
+ else:
+ QtGui.QItemDelegate.setEditorData(self, editor, index)
+
+ def setModelData(self, editor, model, index):
+ if index.column()==1:
+ editor.validate_input()
+ model.setData(index, editor.itemData(editor.currentIndex()),
+ QtCore.Qt.UserRole)
+ model.setData(index, editor.currentText(),
+ QtCore.Qt.DisplayRole)
+ else:
+ QtGui.QItemDelegate.setModelData(self, editor, model, index)
+ self.emit(QtCore.SIGNAL("modelDataChanged"))
+
+############################################################################
+
+class PortTableConfigurationWidget(StandardModuleConfigurationWidget):
+ """
+ PortTableConfigurationWidget is the configuration widget for a
+ tuple-like module, we want to build an interface for specifying a
+ number of input (output) ports and the type of each port. Then
+ compose (decompose) a tuple of those input as a result.
+
+ When subclassing StandardModuleConfigurationWidget, there are
+ only two things we need to care about:
+
+ 1) The builder will provide the VistrailController (through the
+ constructor) associated with the pipeline the module is in. The
+ configuration widget can use the controller to change the
+ current vistrail such as delete connections, add/delete module
+ port...
+
+ 2) The builder also provide the current Module object (through the
+ constructor) of the module. This is the instance of the module
+ in the pipeline. Changes to this Module object usually will not
+ result a new version in the current Vistrail. Such changes are
+ change the visibility of input/output ports on the builder,
+ change module color.
+
+ Each module has a local set of input and output ports that may
+ change, unlike those stored by the global registry. The same
+ module can have different types of input ports at two different
+ time in the same vistrail.
+
+ That's it, the rest of the widget will be just like a regular Qt
+ widget.
+
+ """
+ def __init__(self, module, controller, parent=None):
+ """ PortTableConfigurationWidget(module: Module,
+ controller: VistrailController,
+ parent: QWidget)
+ -> PortTableConfigurationWidget
+ Let StandardModuleConfigurationWidget constructor store the
+ controller/module object from the builder and set up the
+ configuration widget.
+ After StandardModuleConfigurationWidget constructor, all of
+ these will be available:
+ self.module : the Module object int the pipeline
+ self.controller: the current vistrail controller
+
+ """
+ StandardModuleConfigurationWidget.__init__(self, module,
+ controller, parent)
+
+ def updateVistrail(self):
+ msg = "Must implement updateVistrail in subclass"
+ raise VistrailsInternalError(msg)
+
+ def createButtons(self):
+ """ createButtons() -> None
+ Create and connect signals to Ok & Cancel button
+
+ """
+ self.buttonLayout = QtGui.QHBoxLayout()
+ self.buttonLayout.setMargin(5)
+ self.saveButton = QtGui.QPushButton('&Save', self)
+ self.saveButton.setFixedWidth(100)
+ self.saveButton.setEnabled(False)
+ self.buttonLayout.addWidget(self.saveButton)
+ self.resetButton = QtGui.QPushButton('&Reset', self)
+ self.resetButton.setFixedWidth(100)
+ self.resetButton.setEnabled(False)
+ self.buttonLayout.addWidget(self.resetButton)
+ self.layout().addLayout(self.buttonLayout)
+ self.connect(self.saveButton, QtCore.SIGNAL('clicked(bool)'),
+ self.saveTriggered)
+ self.connect(self.resetButton, QtCore.SIGNAL('clicked(bool)'),
+ self.resetTriggered)
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+ Return the recommended size of the configuration window
+
+ """
+ return QtCore.QSize(512, 256)
+
+ def saveTriggered(self, checked = False):
+ """ saveTriggered(checked: bool) -> None
+ Update vistrail controller and module when the user click Ok
+
+ """
+ if self.updateVistrail():
+ self.saveButton.setEnabled(False)
+ self.resetButton.setEnabled(False)
+ self.state_changed = False
+ self.emit(QtCore.SIGNAL("stateChanged"))
+ self.emit(QtCore.SIGNAL('doneConfigure'), self.module.id)
+
+ def resetTriggered(self, checked = False):
+ self.state_changed = False
+
+ def closeEvent(self, event):
+ self.askToSaveChanges()
+ event.accept()
+
+ def getRegistryPorts(self, registry, type):
+ if not registry:
+ return []
+ if type == 'input':
+ getter = registry.destination_ports_from_descriptor
+ elif type == 'output':
+ getter = registry.source_ports_from_descriptor
+ else:
+ raise VistrailsInternalError("Unrecognized port type '%s'", type)
+
+ ports = []
+ try:
+ ports = [(p.name, p.sigstring)
+ for p in getter(self.module.module_descriptor)]
+ except ModuleRegistryException:
+ pass
+ return ports
+
+ def registryChanges(self, old_ports, new_ports):
+ deleted_ports = [p for p in old_ports if p not in new_ports]
+ added_ports = [p for p in new_ports if p not in old_ports]
+ return (deleted_ports, added_ports)
+
+ def getPortDiff(self, p_type, port_table):
+ if p_type == 'input':
+ old_ports = [(p.name, p.sigstring, p.sort_key)
+ for p in self.module.input_port_specs]
+ elif p_type == 'output':
+ old_ports = [(p.name, p.sigstring, p.sort_key)
+ for p in self.module.output_port_specs]
+ else:
+ old_ports = []
+ # old_ports = self.getRegistryPorts(self.module.registry, p_type)
+ new_ports = port_table.getPorts()
+ (deleted_ports, added_ports) = \
+ self.registryChanges(old_ports, new_ports)
+ deleted_ports = [(p_type,) + p for p in deleted_ports]
+ added_ports = [(p_type,) + p for p in added_ports]
+ return (deleted_ports, added_ports)
+
+class TupleConfigurationWidget(PortTableConfigurationWidget):
+ def __init__(self, module, controller, parent=None):
+ """ TupleConfigurationWidget(module: Module,
+ controller: VistrailController,
+ parent: QWidget)
+ -> TupleConfigurationWidget
+
+ Let StandardModuleConfigurationWidget constructor store the
+ controller/module object from the builder and set up the
+ configuration widget.
+ After StandardModuleConfigurationWidget constructor, all of
+ these will be available:
+ self.module : the Module object int the pipeline
+ self.controller: the current vistrail controller
+
+ """
+ PortTableConfigurationWidget.__init__(self, module,
+ controller, parent)
+
+ # Give it a nice window title
+ self.setWindowTitle('Tuple Configuration')
+
+ # Add an empty vertical layout
+ centralLayout = QtGui.QVBoxLayout()
+ centralLayout.setMargin(0)
+ centralLayout.setSpacing(0)
+ self.setLayout(centralLayout)
+
+ # Then add a PortTable to our configuration widget
+ self.portTable = PortTable(self)
+ self.portTable.setHorizontalHeaderLabels(
+ ['Input Port Name', 'Type'])
+
+ # We know that the Tuple module initially doesn't have any
+ # input port, we just use the local registry to see what ports
+ # it has at the time of configuration.
+ self.portTable.initializePorts(self.module.input_port_specs)
+ self.portTable.fixGeometry()
+ centralLayout.addWidget(self.portTable)
+
+ # We need a padded widget to take all vertical white space away
+ paddedWidget = QtGui.QWidget(self)
+ paddedWidget.setSizePolicy(QtGui.QSizePolicy.Ignored,
+ QtGui.QSizePolicy.Expanding)
+ centralLayout.addWidget(paddedWidget, 1)
+
+ # Then we definitely need a Save & Reset button
+ self.createButtons()
+
+ #Connect signals
+ self.connect(self.portTable, QtCore.SIGNAL("contentsChanged"),
+ self.updateState)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ #self.setMouseTracking(True)
+ #self.mouseOver = False
+#
+# def enterEvent(self, event):
+# self.mouseOver = True
+#
+# def leaveEvent(self, event):
+# self.mouseOver = False
+
+
+ def updateVistrail(self):
+ """ updateVistrail() -> None
+ Update Vistrail to contain changes in the port table
+
+ """
+ (deleted_ports, added_ports) = self.getPortDiff('input', self.portTable)
+ if len(deleted_ports) + len(added_ports) == 0:
+ # nothing changed
+ return
+ current_ports = self.portTable.getPorts()
+ # note that the sigstring and sort_key for deletion doesn't matter
+ deleted_ports.append(('output', 'value'))
+ if len(current_ports) > 0:
+ spec = "(" + ','.join(p[1][1:-1] for p in current_ports) + ")"
+ added_ports.append(('output', 'value', spec, -1))
+ try:
+ self.controller.update_ports(self.module.id, deleted_ports,
+ added_ports)
+ except PortAlreadyExists, e:
+ debug.critical('Port Already Exists %s' % str(e))
+ return False
+ return True
+
+ def resetTriggered(self, checked = False):
+ self.portTable.clearContents()
+ self.portTable.setRowCount(1)
+ self.portTable.initializePorts(self.module.input_port_specs)
+ self.portTable.fixGeometry()
+ self.saveButton.setEnabled(False)
+ self.resetButton.setEnabled(False)
+ self.state_changed = False
+ self.emit(QtCore.SIGNAL("stateChanged"))
+
+ def updateState(self):
+ if not self.hasFocus():
+ self.setFocus(QtCore.Qt.TabFocusReason)
+ self.saveButton.setEnabled(True)
+ self.resetButton.setEnabled(True)
+ if not self.state_changed:
+ self.state_changed = True
+ self.emit(QtCore.SIGNAL("stateChanged"))
+
+# def focusOutEvent(self, event):
+ #if not self.mouseOver:
+ # self.askToSaveChanges()
+# QtGui.QWidget.focusOutEvent(self, event)
+
+class UntupleConfigurationWidget(PortTableConfigurationWidget):
+ def __init__(self, module, controller, parent=None):
+ """ UntupleConfigurationWidget(module: Module,
+ controller: VistrailController,
+ parent: QWidget)
+ -> UntupleConfigurationWidget
+ Let StandardModuleConfigurationWidget constructor store the
+ controller/module object from the builder and set up the
+ configuration widget.
+ After StandardModuleConfigurationWidget constructor, all of
+ these will be available:
+ self.module : the Module object int the pipeline
+ self.controller: the current vistrail controller
+
+ """
+ PortTableConfigurationWidget.__init__(self, module,
+ controller, parent)
+
+ # Give it a nice window title
+ self.setWindowTitle('Untuple Configuration')
+
+ # Add an empty vertical layout
+ centralLayout = QtGui.QVBoxLayout()
+ centralLayout.setMargin(0)
+ centralLayout.setSpacing(0)
+ self.setLayout(centralLayout)
+
+ # Then add a PortTable to our configuration widget
+ self.portTable = PortTable(self)
+ self.portTable.setHorizontalHeaderLabels(
+ ['Output Port Name', 'Type'])
+
+ # We know that the Tuple module initially doesn't have any
+ # input port, we just use the local registry to see what ports
+ # it has at the time of configuration.
+ self.portTable.initializePorts(self.module.output_port_specs, True)
+ self.portTable.fixGeometry()
+ centralLayout.addWidget(self.portTable)
+
+ # We need a padded widget to take all vertical white space away
+ paddedWidget = QtGui.QWidget(self)
+ paddedWidget.setSizePolicy(QtGui.QSizePolicy.Ignored,
+ QtGui.QSizePolicy.Expanding)
+ centralLayout.addWidget(paddedWidget, 1)
+
+ # Then we definitely need a Save & Reset button
+ self.createButtons()
+
+ #Connect signals
+ self.connect(self.portTable, QtCore.SIGNAL("contentsChanged"),
+ self.updateState)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ #self.setMouseTracking(True)
+ #self.mouseOver = False
+
+ def updateVistrail(self):
+ """ updateVistrail() -> None
+ Update Vistrail to contain changes in the port table
+
+ """
+ (deleted_ports, added_ports) = self.getPortDiff('output',
+ self.portTable)
+ if len(deleted_ports) + len(added_ports) == 0:
+ # nothing changed
+ return
+ current_ports = self.portTable.getPorts()
+ # note that the sigstring for deletion doesn't matter
+ deleted_ports.append(('input', 'value'))
+ if len(current_ports) > 0:
+ spec = "(" + ','.join(p[1][1:-1] for p in current_ports) + ")"
+ added_ports.append(('input', 'value', spec, -1))
+ try:
+ self.controller.update_ports(self.module.id, deleted_ports,
+ added_ports)
+ except PortAlreadyExists, e:
+ debug.critical('Port Already Exists %s' % str(e))
+ return False
+ return True
+
+ def updateState(self):
+ if not self.hasFocus():
+ self.setFocus(QtCore.Qt.TabFocusReason)
+ self.saveButton.setEnabled(True)
+ self.resetButton.setEnabled(True)
+ if not self.state_changed:
+ self.state_changed = True
+ self.emit(QtCore.SIGNAL("stateChanged"))
+
+# def focusOutEvent(self, event):
+# #if not self.mouseOver:
+# # self.askToSaveChanges()
+# QtGui.QWidget.focusOutEvent(self, event)
+#
+# def enterEvent(self, event):
+# self.mouseOver = True
+#
+# def leaveEvent(self, event):
+# self.mouseOver = False
+
+ def resetTriggered(self, checked = False):
+ self.portTable.clearContents()
+ self.portTable.setRowCount(1)
+ self.portTable.initializePorts(self.module.input_port_specs)
+ self.portTable.fixGeometry()
+ self.saveButton.setEnabled(False)
+ self.resetButton.setEnabled(False)
+ self.state_changed = False
+ self.emit(QtCore.SIGNAL("stateChanged"))
diff --git a/vistrails/gui/open_db_window.py b/vistrails/gui/open_db_window.py
new file mode 100644
index 0000000..3a03b49
--- /dev/null
+++ b/vistrails/gui/open_db_window.py
@@ -0,0 +1,775 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" File for the window used when opening VisTrails objects from the database
+
+QOpenDBWindow
+QDBConnectionList
+QDBConnectionListItem
+QDBObjectList
+QDBObjectListItem
+QConnectionDBSetupWindow
+
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.db import VistrailsDBException
+import vistrails.db.services.io
+from vistrails.core.external_connection import ExtConnectionList, DBConnection
+from vistrails.core.db.locator import DBLocator
+from vistrails.core.system import default_connections_file
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.utils import show_info, show_warning, show_question, \
+NO_BUTTON, YES_BUTTON
+from vistrails.core import debug
+
+class QOpenDBWindow(QtGui.QDialog):
+ """
+ QOpenDBWindow is a dialog containing two panels. the left panel shows all
+ the stored database connections and the right paanel shows the vistrails
+ available on the selected database connection.
+
+ """
+ _instance = None
+ def __init__(self, parent=None):
+ """ __init__(parent: QWidget) -> QOpenDBWindow
+ Construct the dialog with the two panels
+
+ """
+ QtGui.QDialog.__init__(self,parent)
+ self.setWindowTitle("Choose a vistrail")
+ self.save = False
+ mainLayout = QtGui.QVBoxLayout()
+ panelsLayout = QtGui.QGridLayout()
+
+ self.createActions()
+ self.saveasLayout = QtGui.QHBoxLayout()
+ self.saveasLabel = QtGui.QLabel("Save As:")
+ self.saveasEdt = QtGui.QLineEdit("")
+ self.saveasEdt.setFixedWidth(200)
+ self.saveasEdt.setSizePolicy(QtGui.QSizePolicy.Fixed,
+ QtGui.QSizePolicy.Fixed)
+ self.saveasLayout.addWidget(self.saveasLabel)
+ self.saveasLayout.addWidget(self.saveasEdt)
+ self.saveasLabel.setVisible(False)
+ self.saveasEdt.setVisible(False)
+ self.connectionList = QDBConnectionList(self)
+ self.objectList = QDBObjectList(self)
+
+ dbLabel = QtGui.QLabel("Databases:")
+ self.vtLabel = QtGui.QLabel("Vistrails: ")
+
+ panelsLayout.addWidget(dbLabel,0,0,1,1)
+ panelsLayout.setColumnMinimumWidth(1,10)
+ panelsLayout.addWidget(self.vtLabel,0,2,1,2)
+ panelsLayout.addWidget(self.connectionList,1,0,1,1)
+ panelsLayout.addWidget(self.objectList,1,2,1,2)
+
+ self.addButton = QtGui.QToolButton()
+ self.addButton.setDefaultAction(self.addAct)
+ self.addButton.setAutoRaise(True)
+
+ self.removeButton = QtGui.QToolButton()
+ self.removeButton.setDefaultAction(self.removeAct)
+ self.removeButton.setAutoRaise(True)
+ self.removeButton.setEnabled(False)
+
+ panelButtonsLayout = QtGui.QHBoxLayout()
+ panelButtonsLayout.setMargin(0)
+ panelButtonsLayout.setSpacing(0)
+ panelButtonsLayout.addWidget(self.addButton)
+ panelButtonsLayout.addWidget(self.removeButton)
+ panelsLayout.addLayout(panelButtonsLayout,2,0,1,1,
+ QtCore.Qt.AlignLeft)
+ buttonsLayout = QtGui.QHBoxLayout()
+ self.cancelButton = QtGui.QPushButton('Cancel')
+ self.cancelButton.setAutoDefault(False)
+ self.openButton = QtGui.QPushButton('Open')
+ self.openButton.setEnabled(False)
+ self.openButton.setAutoDefault(True)
+
+ buttonsLayout.addStretch(1)
+ buttonsLayout.addWidget(self.cancelButton)
+ buttonsLayout.addWidget(self.openButton)
+
+ mainLayout.addLayout(self.saveasLayout)
+ mainLayout.addLayout(panelsLayout)
+ mainLayout.addLayout(buttonsLayout)
+ mainLayout.setAlignment(self.saveasLayout, QtCore.Qt.AlignHCenter)
+ self.setLayout(mainLayout)
+ self.connectSignals()
+ QOpenDBWindow._instance = self
+
+ def createActions(self):
+ """ createActions() -> None
+ Create actions related to context menu
+
+ """
+ self.addAct = QtGui.QAction("+", self)
+ self.addAct.setStatusTip("Create a new connection")
+ self.removeAct = QtGui.QAction("-", self)
+ self.removeAct.setStatusTip("Remove the selected connection from list")
+
+ def showEvent(self, e):
+ """showEvent(e: QShowEvent) -> None
+ If the use doesn't have any connection set up, we will ask him
+ to create one.
+
+ """
+ if self.connectionList.count() == 0:
+ text = "You don't seem to have any connection available. \
+Would you like to create one?"
+ res = show_question('Vistrails',
+ text,
+ [NO_BUTTON, YES_BUTTON],
+ NO_BUTTON)
+ if res == YES_BUTTON:
+ self.showConnConfig()
+ else:
+ self.updateDBObjectsList()
+
+ def connectSignals(self):
+ """ connectSignals() -> None
+ Map signals between GUI components
+
+ """
+ self.connect(self.cancelButton,
+ QtCore.SIGNAL('clicked()'),
+ self.reject)
+ self.connect(self.openButton,
+ QtCore.SIGNAL('clicked()'),
+ self.accept)
+ self.connect(self.addAct,
+ QtCore.SIGNAL('triggered()'),
+ self.showConnConfig)
+ self.connect(self.removeAct,
+ QtCore.SIGNAL('triggered()'),
+ self.connectionList.removeConnection)
+ self.connect(self.connectionList,
+ QtCore.SIGNAL('itemSelectionChanged()'),
+ self.updateDBObjectsList)
+ self.connect(self.connectionList,
+ QtCore.SIGNAL('itemSelectionChanged()'),
+ self.updateButtons)
+ self.connect(self.connectionList,
+ QtCore.SIGNAL("reloadConnections"),
+ self.updateDBObjectsList)
+ self.connect(self.objectList,
+ QtCore.SIGNAL('itemSelectionChanged()'),
+ self.updateButtons)
+ self.connect(self.saveasEdt,
+ QtCore.SIGNAL('textChanged(QString)'),
+ self.updateButtons)
+ self.connect(self.objectList,
+ QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'),
+ self.accept)
+
+ def updateDBObjectsList(self):
+ """ updateDBObjectsList() -> None
+ It reloads the vistrails object list for the selected connection.
+ If nothing is selected, it will clear the list.
+
+ """
+ conn = self.connectionList.getCurrentItemId()
+ try:
+ self.objectList.updateContents(conn)
+ except VistrailsDBException, e:
+ self.connectionList.setCurrentItem(None)
+ self.updateEditButtons(conn)
+
+ def updateButtons(self):
+ """updateButtons() -> None
+ It will enable the open button if a vistrail is selected or in case
+ of saving a vistrail, if a connection is selected and the name is valid
+
+ """
+ vtlist = self.objectList
+ if not self.save:
+ if len(vtlist.selectedItems()) > 0:
+ self.openButton.setEnabled(True)
+ else:
+ self.openButton.setEnabled(False)
+ else:
+ if (len(self.connectionList.selectedItems()) > 0 and
+ self.saveasEdt.text() != '' and
+ len(vtlist.findItems(self.saveasEdt.text(),
+ QtCore.Qt.MatchFixedString)) == 0):
+ self.openButton.setEnabled(True)
+ else:
+ self.openButton.setEnabled(False)
+
+ def updateEditButtons(self, id):
+ """updateEditButtons(id: int) -> None
+ It will enable/disable the connections buttons according to the
+ selection
+
+ """
+ if id != -1:
+ self.removeButton.setEnabled(True)
+ else:
+ self.removeButton.setEnabled(False)
+
+ def showConnConfig(self, *args, **keywords):
+ """showConnConfig(*args, **keywords) -> None
+ shows a window to configure the connection. The valid keywords
+ are defined in QConnectionDBSetupWindow.__init__()
+
+ """
+ keywords["parent"] = self
+
+ dialog = QConnectionDBSetupWindow(**keywords)
+ if dialog.exec_() == QtGui.QDialog.Accepted:
+ config = {'id': int(dialog.id),
+ 'name': str(dialog.nameEdt.text()),
+ 'host': str(dialog.hostEdt.text()),
+ 'port': int(dialog.portEdt.value()),
+ 'user': str(dialog.userEdt.text()),
+ 'passwd': str(dialog.passwdEdt.text()),
+ 'db': str(dialog.databaseEdt.text())}
+ id = self.connectionList.setConnectionInfo(**config)
+ self.connectionList.setCurrentId(id)
+ return True
+ else:
+ return False
+
+ def prepareForOpening(self, obj_type):
+ """prepareForOpening() -> None
+ It will prepare the dialog to be a Open Dialog
+
+ """
+ self.setWindowTitle("Choose a %s" % obj_type.capitalize())
+ if obj_type != 'vistrail':
+ self.vtLabel.text = 'VisTrails %ss' % obj_type.capitalize()
+ else:
+ self.vtLabel.text = 'Vistrails'
+ self.save = False
+ self.objectList.obj_type = obj_type
+ self.objectList.setEnabled(True)
+ self.saveasLabel.setVisible(False)
+ self.saveasEdt.setVisible(False)
+ self.openButton.setEnabled(False)
+ self.openButton.setText("Open")
+
+ def prepareForSaving(self, obj_type):
+ """prepareForSaving() -> None
+ It will prepare the dialog to be a save as dialog
+
+ """
+ self.setWindowTitle("Save %s..." % obj_type.capitalize())
+ if obj_type != 'vistrail':
+ self.vtLabel.text = 'VisTrails %ss' % obj_type.capitalize()
+ else:
+ self.vtLabel.text = 'Vistrails'
+ self.save = True
+ self.objectList.obj_type = obj_type
+ self.objectList.setEnabled(False)
+ self.saveasLabel.setVisible(True)
+ self.saveasEdt.setVisible(True)
+ self.openButton.setText("Save")
+ self.openButton.setEnabled(False)
+
+ @staticmethod
+ def getInstance():
+ """getInstance() -> QOpenDBWindow
+ Returns the current instance of the QOpenDBWindow
+
+ """
+ if QOpenDBWindow._instance is None:
+ QOpenDBWindow._instance = QOpenDBWindow()
+ return QOpenDBWindow._instance
+
+ @staticmethod
+ def getOpenDBObject(obj_type):
+ """getOpenDBObject(obj_type : str) -> (dict,int)
+ Creates a dialog for opening a vistrails object from the database.
+ It will return the selected connection configuration information and
+ the object id.
+
+ """
+ if QOpenDBWindow._instance:
+ dlg = QOpenDBWindow._instance
+ else:
+ dlg = QOpenDBWindow()
+
+ dlg.prepareForOpening(obj_type)
+
+ if dlg.exec_() == QtGui.QDialog.Accepted:
+ return (dlg.connectionList.getCurrentConnConfig(),
+ dlg.objectList.currentItem().id,
+ dlg.objectList.currentItem().name)
+ else:
+ return({},-1,'')
+
+ @staticmethod
+ def getSaveDBObject(obj_type):
+ """getSaveDBObject(obj_type : str) -> (dict, str)
+ Creates a dialog for saving a vistrails object to the database.
+ It will return the selected connection configuration information
+ and the object name
+
+ """
+ if QOpenDBWindow._instance:
+ dlg = QOpenDBWindow._instance
+ else:
+ dlg = QOpenDBWindow()
+
+ dlg.prepareForSaving(obj_type)
+
+ if dlg.exec_() == QtGui.QDialog.Accepted:
+ return (dlg.connectionList.getCurrentConnConfig(),
+ str(dlg.saveasEdt.text()).strip(' \n\t'))
+ else:
+ return({},'')
+
+################################################################################
+
+class QDBConnectionList(QtGui.QListWidget):
+ """
+ QDBConnection list is a widget to show the available databases
+
+ """
+ def __init__(self, parent=None):
+ QtGui.QListWidget.__init__(self,parent)
+ self.__list = ExtConnectionList.getInstance(default_connections_file())
+ self.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
+ self.setIconSize(QtCore.QSize(32,32))
+ self.loadConnections()
+ self.editAct = QtGui.QAction("Edit", self)
+ self.editAct.setStatusTip("Edit the selected connection")
+ self.connect(self.editAct,
+ QtCore.SIGNAL("triggered()"),
+ self.editConnection)
+
+ def getCurrentItemId(self):
+ """getCurrentItemId() -> int
+ Returns the id of the selected item. If there is no item selected,
+ it will return -1.
+
+ """
+ item = None
+ if len(self.selectedItems()) > 0:
+ item = self.selectedItems()[0]
+ if item != None:
+ return int(item.id)
+ else:
+ return -1
+
+ def contextMenuEvent(self, e):
+ """contextMenuEvent(e: QContextMenuEvent) -> None
+ Shows a popup menu for the connection
+
+ """
+ item = self.currentItem()
+ if item:
+ menu = QtGui.QMenu()
+ menu.addAction(self.editAct)
+ menu.exec_(e.globalPos())
+
+ def editConnection(self):
+ """editConnection() -> None
+ Method called to edit a connection. It will get the information
+ from the selected connection and show the dialog so the user can
+ update the fields
+
+ """
+ conn_id = self.getCurrentItemId()
+ config = self.getConnectionInfo(conn_id)
+ if config != None:
+ config["create"] = False
+ self.parent().showConnConfig(**config)
+
+ def updateGUI(self):
+ """updateGUI() -> None
+ Update GUI list to be consistent with the the list of connections
+
+ """
+ self.clear()
+ for (id, c) in self.__list.items():
+ cItem = QDBConnectionListItem(CurrentTheme.DB_ICON,
+ int(id),
+ str(c.name))
+ self.addItem(cItem)
+ self.emit(QtCore.SIGNAL("reloadConnections"))
+
+ def loadConnections(self):
+ """loadConnections() -> None
+ Loads the internal connections and updates the GUI
+
+ """
+ self.__list.clear()
+ self.__list.load_connections()
+ self.updateGUI()
+
+ def getConnectionInfo(self, id):
+ """getConnectionInfo(id: int) -> dict
+ Returns info of ExtConnection """
+ conn = self.__list.get_connection(id)
+ key = str(conn.id) + "." + conn.name + "." + conn.host
+ passwd = DBLocator.keyChain.get_key(key)
+ if conn != None:
+ config = {'id': conn.id,
+ 'name': conn.name,
+ 'host': conn.host,
+ 'port': conn.port,
+ 'user': conn.user,
+ 'passwd': passwd,
+ 'db': conn.database}
+ else:
+ config = None
+ return config
+
+ def findConnectionInfo(self, host, port, db):
+ """findConnection(host:str, port: int, db: str) -> dict
+ Returns complete info of a connection with the given parameters
+
+ """
+ id = self.__list.find_db_connection(host,port,db)
+ if id != -1:
+ return self.getConnectionInfo(id)
+ else:
+ return None
+
+ def removeConnection(self):
+ """removeConnection() -> None
+ Removes the selected connection
+
+ """
+ id = self.getCurrentItemId()
+ self.takeItem(self.currentRow())
+ self.__list.remove_connection(id)
+
+ def get_connection(self, id):
+ """get_connection() -> None
+ Returns the selected connection
+
+ """
+ return self.__list.get_connection(id)
+
+ def setConnectionInfo(self, *args, **kwargs):
+ """setConnectionInfo(id: int, name: str, host: str, port:int,
+ user:str, passwd:str, db:str) -> None
+ If the connection exists it will update it, else it will add it
+
+ """
+ if kwargs.has_key("id"):
+ id = kwargs["id"]
+ if kwargs.has_key("name"):
+ name = kwargs["name"]
+ if kwargs.has_key("host"):
+ host = kwargs["host"]
+ if kwargs.has_key("port"):
+ port = kwargs["port"]
+ if kwargs.has_key("user"):
+ user = kwargs["user"]
+ if kwargs.has_key("passwd"):
+ passwd = kwargs["passwd"]
+ if kwargs.has_key("db"):
+ db = kwargs["db"]
+
+ conn = DBConnection(id=id,
+ name=name,
+ host=host,
+ port=port,
+ user=user,
+ passwd='',
+ database=db,
+ dbtype='MySQL')
+
+ if self.__list.has_connection(id):
+ self.__list.set_connection(id,conn)
+ else:
+ if conn.id == -1:
+ conn.id = self.__list.get_fresh_id()
+ self.__list.add_connection(conn)
+ self.updateGUI()
+ key = str(conn.id) + "." + conn.name + "." + conn.host
+ DBLocator.keyChain.set_key(key,passwd)
+ return conn.id
+
+ def setCurrentId(self, id):
+ """setCurrentId(id: int) -> None
+ set the connection with id 'id' to be the current selected connection
+
+ """
+ conn = self.__list.get_connection(id)
+
+ for i in self.findItems(conn.name, QtCore.Qt.MatchFixedString):
+ if i.id == id:
+ self.setCurrentItem(i)
+ break
+ self.emit(QtCore.SIGNAL("reloadConnections"), id)
+
+ def getCurrentConnConfig(self):
+ """getCurrentConnConfig() -> dict
+ Return dictionary of parameters of the current connection to pass
+ to MySQLdb
+
+ """
+ conn_id = self.currentItem().id
+ conn = self.__list.get_connection(conn_id)
+ config = self.getConnectionInfo(conn_id)
+ if conn.dbtype == 'MySQL':
+ #removing extra keyword arguments for MySQldb
+ del config['name']
+ return config
+
+ def getDBObjectList(self, conn_id, obj_type):
+ """getDBObjectList(conn_id: int, obj_type : str) -> list
+ Returns list of vistrails objects
+
+ """
+ conn = self.__list.get_connection(conn_id)
+ config = self.getConnectionInfo(conn_id)
+ if conn.dbtype == 'MySQL':
+ #removing extra keyword arguments for MySQldb
+ config_name = config['name']
+ del config['name']
+ config_id = config['id']
+ del config['id']
+ vt_list = vistrails.db.services.io.get_db_object_list(config, obj_type)
+ if conn.dbtype == 'MySQL':
+ config['name'] = config_name
+ config['id'] = config_id
+ return vt_list
+
+################################################################################
+
+class QDBConnectionListItem(QtGui.QListWidgetItem):
+
+ def __init__(self, icon, id, text, parent=None):
+ """__init__(icon: QIcon, id: int, text: QString, parent: QListWidget)
+ -> QDBConnectionListItem
+ Creates an item with id
+
+ """
+ QtGui.QListWidgetItem.__init__(self,icon, text, parent)
+ self.id = id
+
+################################################################################
+
+class QDBObjectList(QtGui.QListWidget):
+ """
+ QDBObjectList is a widget to show the vistrails available in the selected
+ database
+
+ """
+ def __init__(self, parent=None, obj_type='vistrail'):
+ QtGui.QListWidget.__init__(self, parent)
+ self.obj_type = obj_type
+
+ def updateContents(self, conn_id=-1):
+ """updateContents(connection_id: int) -> None
+ Reloads vistrails from the given connection
+
+ """
+ self.clear()
+ if conn_id != -1:
+ parent = self.parent()
+ try:
+ objs = parent.connectionList.getDBObjectList(int(conn_id),
+ self.obj_type)
+
+ for (id,obj,date) in objs:
+ item = QDBObjectListItem(CurrentTheme.FILE_ICON,
+ int(id),
+ str(obj),
+ str(date))
+ self.addItem(item)
+ except VistrailsDBException, e:
+ #show connection setup
+ error = str(e)
+ if "Couldn't get list of vistrails objects" in error:
+ debug.critical('An error has occurred', error)
+ raise e
+ config = parent.connectionList.getConnectionInfo(int(conn_id))
+ if config != None:
+ config["create"] = False
+ if not parent.showConnConfig(**config):
+ raise e
+ else:
+ raise e
+
+################################################################################
+
+class QDBObjectListItem(QtGui.QListWidgetItem):
+
+ def __init__(self, icon, id, name, date, parent=None):
+ """__init__(icon: QIcon, id: int, name: QString,
+ date: QString, user: QString, parent: QListWidget)
+ -> QDBObjectListItem
+ Creates an item with id
+
+ """
+ QtGui.QListWidgetItem.__init__(self, icon, name, parent)
+ self.id = id
+ self.name = name
+ self.date = date
+ self.setToolTip("Last Modified on %s" % date)
+
+################################################################################
+
+class QConnectionDBSetupWindow(QtGui.QDialog):
+ """
+ QConnectionDBSetupWindow is a dialog for creating a DB connection.
+
+ """
+ def __init__(self, parent=None, id=-1, name ='', host="", port=3306,
+ user="", passwd="", db="", create=True):
+ """ __init__(parent: QWidget, id: int, name: str, host:str, port:int,
+ user:str, passwd:str, db:str, create:Boolean)
+ -> QConnectionDBSetupWindow
+ Construct the dialog with the information provided
+ create tells if the caption of the button is Create or Update
+
+ """
+ QtGui.QDialog.__init__(self,parent)
+ if create:
+ self.setWindowTitle("Create a new connection")
+ else:
+ self.setWindowTitle("Update a connection")
+
+ mainLayout = QtGui.QVBoxLayout()
+ infoLayout = QtGui.QGridLayout()
+ self.id = id
+ nameLabel = QtGui.QLabel("Save as Connection Name:", self)
+ self.nameEdt = QtGui.QLineEdit(name, self)
+ hostLabel = QtGui.QLabel("Server Hostname:", self)
+ self.hostEdt = QtGui.QLineEdit(host, self)
+ portLabel = QtGui.QLabel("Port:", self)
+ self.portEdt = QtGui.QSpinBox(self)
+ self.portEdt.setMaximum(65535)
+ self.portEdt.setValue(port)
+ userLabel = QtGui.QLabel("Username:", self)
+ self.userEdt = QtGui.QLineEdit(user, self)
+ passwdLabel = QtGui.QLabel("Password:", self)
+ self.passwdEdt = QtGui.QLineEdit(passwd,self)
+ self.passwdEdt.setEchoMode(QtGui.QLineEdit.Password)
+ self.passwdEdt.setToolTip("For your protection, your "
+ "password will not be saved.")
+ databaseLabel = QtGui.QLabel("Database:", self)
+ self.databaseEdt = QtGui.QLineEdit(db,self)
+ mainLayout.addLayout(infoLayout)
+ infoLayout.addWidget(nameLabel,0,0,1,1)
+ infoLayout.addWidget(self.nameEdt,0,1,1,1)
+ infoLayout.addWidget(hostLabel,1,0,1,1)
+ infoLayout.addWidget(self.hostEdt,1,1,1,1)
+ infoLayout.addWidget(portLabel,1,2,1,1)
+ infoLayout.addWidget(self.portEdt,1,3,1,1)
+ infoLayout.addWidget(userLabel,2,0,1,1)
+ infoLayout.addWidget(self.userEdt,2,1,1,3)
+ infoLayout.addWidget(passwdLabel,3,0,1,1)
+ infoLayout.addWidget(self.passwdEdt,3,1,1,3)
+ infoLayout.addWidget(databaseLabel,4,0,1,1)
+ infoLayout.addWidget(self.databaseEdt,4,1,1,3)
+
+ buttonsLayout = QtGui.QHBoxLayout()
+ if create:
+ caption = 'Create'
+ else:
+ caption = 'Update'
+ self.createButton = QtGui.QPushButton(caption, self)
+ self.createButton.setDefault(True)
+ self.cancelButton = QtGui.QPushButton('Cancel', self)
+ self.testButton = QtGui.QPushButton('Test', self)
+
+ buttonsLayout.addStretch(1)
+ buttonsLayout.addWidget(self.cancelButton)
+ buttonsLayout.addWidget(self.testButton)
+ buttonsLayout.addWidget(self.createButton)
+
+ mainLayout.addLayout(buttonsLayout)
+
+ self.setLayout(mainLayout)
+ self.connectSignals()
+ self.updateButtons()
+
+ def connectSignals(self):
+ """ connectSignals() -> None
+ Map signals between GUI components
+
+ """
+ self.connect(self.cancelButton,
+ QtCore.SIGNAL('clicked()'),
+ self.reject)
+ self.connect(self.createButton,
+ QtCore.SIGNAL('clicked()'),
+ self.accept)
+ self.connect(self.testButton,
+ QtCore.SIGNAL('clicked()'),
+ self.testConnection)
+ self.connect(self.nameEdt,
+ QtCore.SIGNAL('textChanged(QString)'),
+ self.updateButtons)
+ self.connect(self.hostEdt,
+ QtCore.SIGNAL('textChanged(QString)'),
+ self.updateButtons)
+ self.connect(self.userEdt,
+ QtCore.SIGNAL('textChanged(QString)'),
+ self.updateButtons)
+ self.connect(self.passwdEdt,
+ QtCore.SIGNAL('textChanged(QString)'),
+ self.updateButtons)
+ self.connect(self.databaseEdt,
+ QtCore.SIGNAL('textChanged(QString)'),
+ self.updateButtons)
+ self.connect(self.portEdt,
+ QtCore.SIGNAL('valueChanged(int)'),
+ self.updateButtons)
+
+ def testConnection(self):
+ """testConnection() -> None """
+ config = {'host': str(self.hostEdt.text()),
+ 'port': int(self.portEdt.value()),
+ 'user': str(self.userEdt.text()),
+ 'passwd': str(self.passwdEdt.text()),
+ 'db': str(self.databaseEdt.text())}
+ try:
+ vistrails.db.services.io.test_db_connection(config)
+ show_info('Vistrails',"Connection succeeded!")
+
+ except Exception, e:
+ debug.critical('An error has occurred', str(e))
+
+ def updateButtons(self):
+ """updateButtons() -> None
+ enables button if there's enough information in the dialog
+
+ """
+ if (self.nameEdt.text() != "" and
+ self.hostEdt.text() != "" and
+ self.portEdt.value() != 0 and
+ self.userEdt.text() != "" and
+ self.databaseEdt.text() != ""):
+ self.createButton.setEnabled(True)
+ else:
+ self.createButton.setEnabled(False)
diff --git a/vistrails/gui/paramexplore/__init__.py b/vistrails/gui/paramexplore/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/gui/paramexplore/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/gui/paramexplore/param_view.py b/vistrails/gui/paramexplore/param_view.py
new file mode 100644
index 0000000..2f51b34
--- /dev/null
+++ b/vistrails/gui/paramexplore/param_view.py
@@ -0,0 +1,410 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" The file describes the parameter tree view
+
+QParameterView
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core.inspector import PipelineInspector
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.modules.basic_modules import Constant
+from vistrails.gui.common_widgets import QSearchTreeWindow, QSearchTreeWidget
+from vistrails.gui.paramexplore.pe_pipeline import QAnnotatedPipelineView
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+from vistrails.core.utils import InstanceObject
+from vistrails.core.debug import debug
+
+################################################################################
+
+class ParameterInfo(InstanceObject):
+ # ParameterInfo(type=,
+ # identifier=,
+ # namespace=,
+ # value=,
+ # id=,
+ # dbtype=,
+ # parent_dbtype=,
+ # parent_id=,
+ # is_alias=)
+ #new: ParameterInfo(module_id=,
+ # name=,
+ # pos=,
+ # value=,
+ # spec=,
+ # is_alias=)
+ pass
+
+################################################################################
+
+class QParameterView(QtGui.QWidget, QVistrailsPaletteInterface):
+ """
+ QParameterView contains the parameter exploration properties and the
+ parameter palette
+
+ """
+ def __init__(self, controller=None, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.set_title('Pipeline Methods')
+
+ self.controller = controller
+ vLayout = QtGui.QVBoxLayout()
+ vLayout.setMargin(0)
+ vLayout.setSpacing(5)
+ self.setLayout(vLayout)
+
+ self.toggleUnsetParameters = QtGui.QCheckBox('Show Unset Parameters')
+ vLayout.addWidget(self.toggleUnsetParameters, 0, QtCore.Qt.AlignRight)
+
+ self.parameterWidget = QParameterWidget()
+ vLayout.addWidget(self.parameterWidget)
+ self.treeWidget = self.parameterWidget.treeWidget
+
+ self.pipeline_view = QAnnotatedPipelineView()
+ vLayout.addWidget(self.pipeline_view)
+
+ vLayout.setStretch(0,0)
+ vLayout.setStretch(1,1)
+ vLayout.setStretch(2,0)
+
+ self.connect(self.toggleUnsetParameters, QtCore.SIGNAL("toggled(bool)"),
+ self.parameterWidget.treeWidget.toggleUnsetParameters)
+
+ def set_controller(self, controller):
+ self.controller = controller
+ self.set_pipeline(self.controller.current_pipeline)
+ self.pipeline_view.setScene(self.controller.current_pipeline_scene)
+
+ def set_pipeline(self, pipeline):
+ self.pipeline = pipeline
+ self.parameterWidget.set_pipeline(pipeline, self.controller)
+ self.pipeline_view.updateAnnotatedIds(pipeline)
+
+class QParameterWidget(QSearchTreeWindow):
+ """
+ QParameterWidget is a special widget for displaying aliases and
+ parameters inside a pipeline
+
+ """
+ def createTreeWidget(self):
+ """ createTreeWidget() -> QModuleTreeWidget
+ Return the search tree widget for this window
+
+ """
+ treeWidget = QParameterTreeWidget(self)
+ return treeWidget
+
+ def set_pipeline(self, pipeline, controller):
+ self.pipeline = pipeline
+ self.treeWidget.updateFromPipeline(pipeline, controller)
+
+
+class QParameterTreeWidget(QSearchTreeWidget):
+ """
+ QParameterTreeWidget is a subclass of QSearchTreeWidget to display all
+ Vistrails Module
+
+ """
+ def __init__(self, parent=None):
+ """ QParameterTreeWidget(parent: QWidget) -> QParameterTreeWidget
+ Set up size policy and header
+
+ """
+ QSearchTreeWidget.__init__(self, parent)
+ self.header().hide()
+ self.setRootIsDecorated(False)
+ self.delegate = QParameterTreeWidgetItemDelegate(self, self)
+ self.setItemDelegate(self.delegate)
+ self.showUnsetParameters = False
+
+ def updateFromPipeline(self, pipeline, controller):
+ """ updateFromPipeline(pipeline: Pipeline) -> None
+ Read the list of aliases and parameters from the pipeline
+
+ """
+ self.clear()
+ if not pipeline:
+ return
+
+ # Update the aliases
+ if len(pipeline.aliases)>0:
+ aliasRoot = QParameterTreeWidgetItem(None, self, ['Aliases'])
+ aliasRoot.setFlags(QtCore.Qt.ItemIsEnabled)
+ for (alias, info) in pipeline.aliases.iteritems():
+ ptype, pId, parentType, parentId, mId = info
+ parameter = pipeline.db_get_object(ptype, pId)
+ function = pipeline.db_get_object(parentType, parentId)
+ v = parameter.strValue
+ port_spec = function.get_spec('input')
+ port_spec_item = port_spec.port_spec_items[parameter.pos]
+ label = ['%s = %s' % (alias, v)]
+ pInfo = ParameterInfo(module_id=mId,
+ name=function.name,
+ pos=parameter.pos,
+ value=v,
+ spec=port_spec_item,
+ is_alias=True)
+ aliasItem = QParameterTreeWidgetItem((alias, [pInfo]),
+ aliasRoot, label)
+ aliasRoot.setExpanded(True)
+
+ vistrailVarsRoot = QParameterTreeWidgetItem(None, self,
+ ['Vistrail Variables'])
+ vistrailVarsRoot.setHidden(True)
+
+ # Now go through all modules and functions
+
+ inspector = PipelineInspector()
+ inspector.inspect_ambiguous_modules(pipeline)
+ sortedModules = sorted(pipeline.modules.iteritems(),
+ key=lambda item: item[1].name)
+
+ reg = get_module_registry()
+
+ for mId, module in sortedModules:
+ if module.is_vistrail_var():
+ vistrailVarsRoot.setHidden(False)
+ vistrailVarsRoot.setExpanded(True)
+ port_spec = module.get_port_spec('value', 'input')
+ if not port_spec:
+ debug.critical("Not port_spec for value in module %s" % module)
+ continue
+ port_spec_items = port_spec.port_spec_items
+
+ vv = controller.get_vistrail_variable_by_uuid(
+ module.get_vistrail_var())
+
+ label = ['%s = %s' % (vv.name, vv.value)]
+ pList = [ParameterInfo(module_id=mId,
+ name=port_spec.name,
+ pos=port_spec.port_spec_items[pId].pos,
+ value="",
+ spec=port_spec.port_spec_items[pId],
+ is_alias=False)
+ for pId in xrange(len(port_spec.port_spec_items))]
+ mItem = QParameterTreeWidgetItem((vv.name, pList),
+ vistrailVarsRoot,
+ label)
+ continue
+
+ function_names = {}
+ # Add existing parameters
+ mLabel = [module.name]
+ moduleItem = None
+ if len(module.functions)>0:
+ for fId in xrange(len(module.functions)):
+ function = module.functions[fId]
+ function_names[function.name] = function
+ if len(function.params)==0: continue
+ if moduleItem==None:
+ if inspector.annotated_modules.has_key(mId):
+ annotatedId = inspector.annotated_modules[mId]
+ moduleItem = QParameterTreeWidgetItem(annotatedId,
+ self, mLabel)
+ else:
+ moduleItem = QParameterTreeWidgetItem(None,
+ self, mLabel)
+ v = ', '.join([p.strValue for p in function.params])
+ label = ['%s(%s)' % (function.name, v)]
+
+ try:
+ port_spec = function.get_spec('input')
+ except Exception, e:
+ debug.critical("get_spec failed: %s %s %s" % \
+ (module, function, function.sigstring))
+ continue
+ port_spec_items = port_spec.port_spec_items
+ pList = [ParameterInfo(module_id=mId,
+ name=function.name,
+ pos=function.params[pId].pos,
+ value=function.params[pId].strValue,
+ spec=port_spec_items[pId],
+ is_alias=False)
+ for pId in xrange(len(function.params))]
+ mName = module.name
+ if moduleItem.parameter!=None:
+ mName += '(%d)' % moduleItem.parameter
+ fName = '%s :: %s' % (mName, function.name)
+ mItem = QParameterTreeWidgetItem((fName, pList),
+ moduleItem,
+ label)
+ # Add available parameters
+ if module.is_valid:
+ for port_spec in module.destinationPorts():
+ if (port_spec.name in function_names or
+ not port_spec.is_valid or
+ not len(port_spec.port_spec_items) or
+ not reg.is_constant(port_spec)):
+ # The function already exists or is empty
+ # or contains non-constant modules
+ continue
+ if moduleItem==None:
+ if inspector.annotated_modules.has_key(mId):
+ annotatedId = inspector.annotated_modules[mId]
+ moduleItem = QParameterTreeWidgetItem(annotatedId,
+ self,
+ mLabel,
+ False)
+ else:
+ moduleItem = QParameterTreeWidgetItem(None, self,
+ mLabel, False)
+ v = ', '.join([p.module for p in port_spec.port_spec_items])
+ label = ['%s(%s)' % (port_spec.name, v)]
+ pList = [ParameterInfo(module_id=mId,
+ name=port_spec.name,
+ pos=port_spec.port_spec_items[pId].pos,
+ value="",
+ spec=port_spec.port_spec_items[pId],
+ is_alias=False)
+ for pId in xrange(len(port_spec.port_spec_items))]
+ mName = module.name
+ if moduleItem.parameter!=None:
+ mName += '(%d)' % moduleItem.parameter
+ fName = '%s :: %s' % (mName, port_spec.name)
+ mItem = QParameterTreeWidgetItem((fName, pList),
+ moduleItem,
+ label, False)
+ if moduleItem:
+ moduleItem.setExpanded(True)
+ self.toggleUnsetParameters(self.showUnsetParameters)
+
+ def toggleUnsetParameters(self, state):
+ self.showUnsetParameters = state
+ for item in self.findItems("*", QtCore.Qt.MatchWildcard | QtCore.Qt.MatchRecursive):
+ if not item.isSet:
+ item.setHidden(not state)
+
+class QParameterTreeWidgetItemDelegate(QtGui.QItemDelegate):
+ """
+ QParameterTreeWidgetItemDelegate will override the original
+ QTreeWidget paint function to draw buttons for top-level item
+ similar to QtDesigner. This mimics
+ Qt/tools/designer/src/lib/shared/sheet_delegate, which is only a
+ private class from QtDesigned.
+
+ """
+ def __init__(self, view, parent):
+ """ QParameterTreeWidgetItemDelegate(view: QTreeView,
+ parent: QWidget)
+ -> QParameterTreeWidgetItemDelegate
+ Create the item delegate given the tree view
+
+ """
+ QtGui.QItemDelegate.__init__(self, parent)
+ self.treeView = view
+
+ def paint(self, painter, option, index):
+ """ painter(painter: QPainter, option QStyleOptionViewItem,
+ index: QModelIndex) -> None
+ Repaint the top-level item to have a button-look style
+
+ """
+ model = index.model()
+ if model.parent(index).isValid()==False:
+ style = self.treeView.style()
+ r = option.rect
+ textrect = QtCore.QRect(r.left() + 10,
+ r.top(),
+ r.width() - 10,
+ r.height())
+ font = painter.font()
+ font.setBold(True)
+ painter.setFont(font)
+ text = option.fontMetrics.elidedText(
+ model.data(index, QtCore.Qt.DisplayRole),
+ QtCore.Qt.ElideMiddle,
+ textrect.width()-10)
+ style.drawItemText(painter,
+ textrect,
+ QtCore.Qt.AlignLeft,
+ option.palette,
+ self.treeView.isEnabled(),
+ text)
+ painter.setPen(QtGui.QPen(QtCore.Qt.black))
+ fm = QtGui.QFontMetrics(font)
+ size = fm.size(QtCore.Qt.TextSingleLine, text)
+ painter.drawLine(textrect.left()-5,
+ textrect.bottom()-1,
+ textrect.left()+size.width()+5,
+ textrect.bottom()-1)
+
+ annotatedId = model.data(index, QtCore.Qt.UserRole+1)
+ if annotatedId:
+ idRect = QtCore.QRect(
+ QtCore.QPoint(textrect.left()+size.width()+5,
+ textrect.top()),
+ textrect.bottomRight())
+ QAnnotatedPipelineView.drawId(painter, idRect,
+ annotatedId,
+ QtCore.Qt.AlignLeft |
+ QtCore.Qt.AlignVCenter)
+ else:
+ QtGui.QItemDelegate.paint(self, painter, option, index)
+
+ def sizeHint(self, option, index):
+ """ sizeHint(option: QStyleOptionViewItem, index: QModelIndex) -> None
+ Take into account the size of the top-level button
+
+ """
+ return (QtGui.QItemDelegate.sizeHint(self, option, index) +
+ QtCore.QSize(2, 2))
+
+
+class QParameterTreeWidgetItem(QtGui.QTreeWidgetItem):
+ """
+ QParameterTreeWidgetItem represents module on QParameterTreeWidget
+
+ """
+ def __init__(self, info, parent, labelList, isSet=True):
+ """ QParameterTreeWidgetItem(info: (str, []),
+ parent: QTreeWidgetItem
+ labelList: string,
+ isSet: bool)
+ -> QParameterTreeWidget
+
+ Create a new tree widget item with a specific parent and
+ labels. info describing a set of paramters as follow:
+ (name, [ParameterInfo]):
+ name = Name of the parameter set (alias or function)
+ If this item is a top-level item, info can either be None or
+ an integer specifying the annotated id of this module
+ isSet indicates if it represents a set or unset parameter
+ """
+ self.parameter = info
+ QtGui.QTreeWidgetItem.__init__(self, parent, labelList)
+ if isinstance(self.parameter, int):
+ self.setData(0, QtCore.Qt.UserRole+1,
+ self.parameter)
+ self.isSet = isSet
+
diff --git a/vistrails/gui/paramexplore/pe_inspector.py b/vistrails/gui/paramexplore/pe_inspector.py
new file mode 100644
index 0000000..c2e4c3a
--- /dev/null
+++ b/vistrails/gui/paramexplore/pe_inspector.py
@@ -0,0 +1,291 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtGui, QtCore
+
+from vistrails.gui.paramexplore.virtual_cell import QVirtualCellWindow
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+from vistrails.gui.theme import CurrentTheme
+from pe_view import QParamExploreView
+
+import weakref
+
+class QParamExploreInspector(QtGui.QWidget, QVistrailsPaletteInterface):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.set_title("Explore Inspector")
+
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(2)
+ layout.setSpacing(3)
+
+ self.pe_properties = QParamExpProperties()
+ p_prop_group = QtGui.QGroupBox(self.pe_properties.windowTitle())
+ g_layout = QtGui.QVBoxLayout()
+ g_layout.setMargin(0)
+ g_layout.setSpacing(0)
+ g_layout.addWidget(self.pe_properties)
+ p_prop_group.setLayout(g_layout)
+ layout.addWidget(p_prop_group)
+ self.virtual_cell = QVirtualCellWindow()
+ v_cell_group = QtGui.QGroupBox(self.virtual_cell.windowTitle())
+ g_layout = QtGui.QVBoxLayout()
+ g_layout.setMargin(0)
+ g_layout.setSpacing(0)
+ g_layout.addWidget(self.virtual_cell)
+ v_cell_group.setLayout(g_layout)
+ layout.addWidget(v_cell_group)
+ self.setLayout(layout)
+ self.addButtonsToToolbar()
+
+ def addButtonsToToolbar(self):
+ # Add the back/forward exploration buttons
+ self.versionsLabel = QtGui.QLabel('Exploration: 0/0')
+ self.toolWindow().toolbar.insertWidget(self.toolWindow().pinAction,
+ self.versionsLabel)
+ self.pe_properties.versionsLabel = weakref.proxy(self.versionsLabel)
+ self.backAction = QtGui.QAction(
+ QtGui.QIcon(CurrentTheme.LEFT_ARROW_PIXMAP),
+ 'Go to Previous Exploration', None, triggered=self.backPressed)
+ self.toolWindow().toolbar.insertAction(self.toolWindow().pinAction,
+ self.backAction)
+ self.pe_properties.backAction = weakref.proxy(self.backAction)
+ self.forwardAction = QtGui.QAction(
+ QtGui.QIcon(CurrentTheme.RIGHT_ARROW_PIXMAP),
+ 'Got to Next Exploration', None, triggered=self.forwardPressed)
+ self.toolWindow().toolbar.insertAction(self.toolWindow().pinAction,
+ self.forwardAction)
+ self.pe_properties.forwardAction = weakref.proxy(self.forwardAction)
+
+ def set_controller(self, controller):
+ self.controller = controller
+ self.pe_properties.updateController(controller)
+ self.set_pipeline(self.controller.current_pipeline)
+
+ def set_pipeline(self, pipeline):
+ self.pipeline = pipeline
+ self.virtual_cell.updateVirtualCell(pipeline)
+ self.stateChanged()
+
+ def stateChanged(self):
+ self.pe_properties.updateVersion()
+
+ def set_exploration(self, pe = None):
+ self.stateChanged()
+
+ def backPressed(self):
+ self.pe_properties.goBack()
+
+ def forwardPressed(self):
+ self.pe_properties.goForward()
+
+
+class QParamExpProperties(QtGui.QWidget):
+ def __init__(self, controller=None, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.controller = controller
+ self.versionNumber = -1
+ self.versionsLabel = None
+ self.backAction = None
+ self.forwardAction = None
+ vLayout = QtGui.QVBoxLayout()
+ self.setLayout(vLayout)
+ vLayout.setMargin(3)
+ vLayout.setSpacing(3)
+ gLayout = QtGui.QGridLayout()
+ gLayout.setColumnMinimumWidth(1,5)
+ gLayout.setRowMinimumHeight(0,24)
+ gLayout.setRowMinimumHeight(1,24)
+ gLayout.setRowMinimumHeight(2,24)
+ gLayout.setRowMinimumHeight(3,24)
+ vLayout.addLayout(gLayout)
+ gLayout.setMargin(3)
+ gLayout.setSpacing(3)
+
+ #vtVersionLabel = QtGui.QLabel('Workflow:', self)
+ #gLayout.addWidget(vtVersionLabel, 0, 0, 1, 1)
+
+ #self.vtVersionEdit = QtGui.QLabel('', self)
+ #gLayout.addWidget(self.vtVersionEdit, 0, 2, 1, 1)
+
+ tagLabel = QtGui.QLabel('Exploration Tag:', self)
+ gLayout.addWidget(tagLabel, 0, 0, 1, 1)
+
+ editLayout = QtGui.QHBoxLayout()
+ self.tagEdit = QtGui.QLineEdit()
+ tagLabel.setBuddy(self.tagEdit)
+ editLayout.addWidget(self.tagEdit)
+ self.tagEdit.setEnabled(False)
+
+ self.tagReset = QtGui.QToolButton(self)
+ self.tagReset.setIcon(QtGui.QIcon(
+ self.style().standardPixmap(QtGui.QStyle.SP_DialogCloseButton)))
+ self.tagReset.setIconSize(QtCore.QSize(12,12))
+ self.tagReset.setAutoRaise(True)
+ self.tagReset.setEnabled(False)
+ editLayout.addWidget(self.tagReset)
+
+ gLayout.addLayout(editLayout, 0, 2, 1, 1)
+
+ userLabel = QtGui.QLabel('User:', self)
+ gLayout.addWidget(userLabel, 1, 0, 1, 1)
+
+ self.userEdit = QtGui.QLabel('', self)
+ gLayout.addWidget(self.userEdit, 1, 2, 1, 1)
+
+ dateLabel = QtGui.QLabel('Date:', self)
+ gLayout.addWidget(dateLabel, 2, 0, 1, 1)
+
+ self.dateEdit = QtGui.QLabel('', self)
+ gLayout.addWidget(self.dateEdit, 2, 2, 1, 1)
+
+ self.connect(self.tagEdit, QtCore.SIGNAL('editingFinished()'),
+ self.tagFinished)
+ self.connect(self.tagEdit, QtCore.SIGNAL('textChanged(QString)'),
+ self.tagChanged)
+ self.connect(self.tagReset, QtCore.SIGNAL('clicked()'),
+ self.tagCleared)
+
+ def updateController(self, controller):
+ self.controller = controller
+
+ def updateVersion(self):
+ self.pe = None
+ if self.controller:
+ # Check if version changed
+ version_changed = False
+ if self.controller.current_parameter_exploration and \
+ self.controller.current_parameter_exploration.action_id !=\
+ self.controller.current_version:
+ # we need to remove it
+ version_changed = True
+ self.controller.current_parameter_exploration=None
+
+ if not self.controller.current_parameter_exploration and \
+ self.controller.vistrail.has_paramexp(
+ self.controller.current_version):
+ version_changed = True
+ # load latest version
+ self.controller.current_parameter_exploration = \
+ self.controller.vistrail.get_paramexp(
+ self.controller.current_version)
+
+ if version_changed:
+ from vistrails.gui.vistrails_window import _app
+ _app.notify('exploration_changed')
+ return
+
+ self.pe = self.controller.current_parameter_exploration
+ if self.controller and self.pe:
+ # get all pe for this action
+ self.peDict = dict([(pe.id, pe) for pe in
+ self.controller.vistrail.parameter_explorations
+ if pe.action_id==self.pe.action_id])
+ count = len(self.peDict)
+ ids = self.peDict.keys()
+ ids.sort()
+ index = ids.index(self.pe.id) + 1
+
+ text = 'Exploration: %s/%s' % (index, count)
+ self.versionsLabel.setText(text)
+ self.backAction.setEnabled(index>1)
+ self.forwardAction.setEnabled(index<count)
+ self.tagEdit.setEnabled(True)
+ self.tagReset.setEnabled(True)
+ self.tagEdit.setText(self.pe.name or "")
+ self.userEdit.setText(self.pe.user or "")
+ self.dateEdit.setText(self.pe.date or "")
+ else:
+ self.versionsLabel.setText('Exploration: 0/0')
+ self.backAction.setEnabled(False)
+ self.forwardAction.setEnabled(False)
+ self.tagEdit.setEnabled(False)
+ self.tagReset.setEnabled(False)
+ self.tagEdit.setText('')
+ self.userEdit.setText('')
+ self.dateEdit.setText('')
+
+ def tagFinished(self):
+ """ tagFinished() -> None
+ Update the new tag to pe
+
+ """
+ if self.pe:
+ currentText = str(self.tagEdit.text())
+ if self.pe.name != currentText and \
+ not self.controller.vistrail.has_named_paramexp(currentText):
+ #print "will update current tag", currentText
+ self.pe.name = currentText
+ self.controller.set_changed(True)
+ else:
+ self.tagEdit.setText(self.pe.name)
+
+ def tagChanged(self, text):
+ """ tagChanged(text: QString) -> None
+ Update the button state if there is text
+
+ """
+ self.tagReset.setEnabled(text != '')
+
+ def tagCleared(self):
+ """ tagCleared() -> None
+ Remove the tag
+
+ """
+ self.tagEdit.setText('')
+ self.tagFinished()
+
+ def goBack(self):
+ """ Goes to the previous PE for this pipeline"""
+ ids = self.peDict.keys()
+ ids.sort()
+ index = ids.index(self.pe.id)
+ if index>0:
+ pe = self.peDict[ids[index-1]]
+ self.controller.current_parameter_exploration = pe
+ from vistrails.gui.vistrails_window import _app
+ _app.notify('exploration_changed')
+
+
+ def goForward(self):
+ """ Goes to the next PE for this pipeline"""
+ count = len(self.peDict)
+ ids = self.peDict.keys()
+ ids.sort()
+ index = ids.index(self.pe.id)
+ if index<count-1:
+ pe = self.peDict[ids[index+1]]
+ self.controller.current_parameter_exploration = pe
+ from vistrails.gui.vistrails_window import _app
+ _app.notify('exploration_changed')
diff --git a/vistrails/gui/paramexplore/pe_pipeline.py b/vistrails/gui/paramexplore/pe_pipeline.py
new file mode 100644
index 0000000..951e042
--- /dev/null
+++ b/vistrails/gui/paramexplore/pe_pipeline.py
@@ -0,0 +1,131 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This containing a subclassed QGraphicsView that allows View the
+pipeline in a specific way in the parameter exploration window
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core.inspector import PipelineInspector
+from vistrails.gui.common_widgets import QToolWindowInterface
+from vistrails.gui.pipeline_view import QPipelineView, QGraphicsModuleItem
+from vistrails.gui.theme import CurrentTheme
+
+################################################################################
+class QAnnotatedPipelineView(QPipelineView, QToolWindowInterface):
+ """
+ QAnnotatedPipelineView subclass QPipelineView to perform some overlay
+ marking on a pipeline view
+
+ """
+ def __init__(self, parent=None):
+ """ QPipelineView(parent: QWidget) -> QPipelineView
+ Initialize the graphics view and its properties
+
+ """
+ QPipelineView.__init__(self, parent)
+ self.setWindowTitle('Annotated Pipeline')
+ self.inspector = PipelineInspector()
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+ Prefer the view not so large
+
+ """
+ return QtCore.QSize(256, 256)
+
+ def paintEvent(self, event):
+ """ paintEvent(event: QPaintEvent) -> None
+ Paint an overlay annotation on spreadsheet cell modules
+
+ """
+ QPipelineView.paintEvent(self, event)
+ # super(QAnnotatedPipelineView, self).paintEvent(event)
+ if self.scene():
+ painter = QtGui.QPainter(self.viewport())
+ for mId, annotatedId in \
+ self.inspector.annotated_modules.iteritems():
+ if mId not in self.scene().modules:
+ # faulty annotated_modules entry
+ continue
+ item = self.scene().modules[mId]
+ br = item.sceneBoundingRect()
+ rect = QtCore.QRect(self.mapFromScene(br.topLeft()),
+ self.mapFromScene(br.bottomRight()))
+ QAnnotatedPipelineView.drawId(painter, rect, annotatedId)
+ painter.end()
+
+ def updateAnnotatedIds(self, pipeline):
+ """ updateAnnotatedIds(pipeline: Pipeline) -> None
+ Re-inspect the pipeline to get annotated ids
+
+ """
+ if pipeline and self.scene():
+ self.inspector.inspect_ambiguous_modules(pipeline)
+ self.scene().fitToView(self)
+
+ @staticmethod
+ def drawId(painter, rect, id, align=QtCore.Qt.AlignCenter):
+ """ drawId(painter: QPainter, rect: QRect, id: int,
+ align: QtCore.Qt.Align) -> None
+ Draw the rounded id number on a rectangular area
+
+ """
+ painter.save()
+ painter.setRenderHints(QtGui.QPainter.Antialiasing)
+ painter.setPen(CurrentTheme.ANNOTATED_ID_BRUSH.color())
+ painter.setBrush(CurrentTheme.ANNOTATED_ID_BRUSH)
+ font = QtGui.QFont()
+ font.setStyleStrategy(QtGui.QFont.ForceOutline)
+ font.setBold(True)
+ painter.setFont(font)
+ fm = QtGui.QFontMetrics(font)
+ size = fm.size(QtCore.Qt.TextSingleLine, str(id))
+ size = max(size.width(), size.height())
+
+ x = rect.left()
+ if align & QtCore.Qt.AlignHCenter:
+ x = rect.left() + rect.width()/2-size/2
+ if align & QtCore.Qt.AlignRight:
+ x = rect.left() + rect.width()-size
+ y = rect.top()
+ if align & QtCore.Qt.AlignVCenter:
+ y = rect.top() + rect.height()/2-size/2
+ if align & QtCore.Qt.AlignBottom:
+ y = rect.top() + rect.height()-size
+
+ newRect = QtCore.QRect(x, y, size, size)
+ painter.drawEllipse(newRect)
+ painter.setPen(CurrentTheme.ANNOTATED_ID_PEN)
+ painter.drawText(newRect, QtCore.Qt.AlignCenter, str(id))
+ painter.restore()
diff --git a/vistrails/gui/paramexplore/pe_tab.py b/vistrails/gui/paramexplore/pe_tab.py
new file mode 100644
index 0000000..2fd6e48
--- /dev/null
+++ b/vistrails/gui/paramexplore/pe_tab.py
@@ -0,0 +1,337 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" The file describes the parameter exploration tab for VisTrails
+
+QParameterExplorationTab
+"""
+from PyQt4 import QtCore, QtGui
+from xml.dom.minidom import parseString
+from xml.sax.saxutils import escape
+from vistrails.core import debug
+from vistrails.core.interpreter.default import get_default_interpreter
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.param_explore import ActionBasedParameterExploration
+from vistrails.core.system import current_time, get_vistrails_default_pkg_prefix
+from vistrails.gui.common_widgets import QDockContainer, QToolWindowInterface
+from vistrails.gui.paramexplore.pe_table import QParameterExplorationWidget, QParameterSetEditor
+from vistrails.gui.paramexplore.virtual_cell import QVirtualCellWindow
+from vistrails.gui.paramexplore.param_view import QParameterView
+from vistrails.gui.paramexplore.pe_pipeline import QAnnotatedPipelineView
+
+################################################################################
+
+class QParameterExplorationTab(QDockContainer, QToolWindowInterface):
+ """
+ QParameterExplorationTab is a tab containing different widgets
+ related to parameter exploration
+
+ """
+ explorationId = 0
+
+ def __init__(self, parent=None):
+ """ QParameterExplorationTab(parent: QWidget)
+ -> QParameterExplorationTab
+ Make it a main window with dockable area and a
+ QParameterExplorationTable
+
+ """
+ QDockContainer.__init__(self, parent)
+ self.setWindowTitle('Parameter Exploration')
+ self.toolWindow().setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)
+ self.toolWindow().hide()
+
+ self.peWidget = QParameterExplorationWidget()
+ self.setCentralWidget(self.peWidget)
+ self.connect(self.peWidget.table,
+ QtCore.SIGNAL('exploreChange(bool)'),
+ self.exploreChange)
+
+ self.paramView = QParameterView(self)
+ self.addDockWidget(QtCore.Qt.RightDockWidgetArea,
+ self.paramView.toolWindow())
+
+ self.annotatedPipelineView = QAnnotatedPipelineView(self)
+ self.addDockWidget(QtCore.Qt.RightDockWidgetArea,
+ self.annotatedPipelineView.toolWindow())
+
+ self.virtualCell = QVirtualCellWindow(self)
+ self.addDockWidget(QtCore.Qt.RightDockWidgetArea,
+ self.virtualCell.toolWindow())
+
+ self.controller = None
+ self.currentVersion = -1
+
+ def addViewActionsToMenu(self, menu):
+ """addViewActionsToMenu(menu: QMenu) -> None
+ Add toggle view actions to menu
+
+ """
+ menu.addAction(self.paramView.toolWindow().toggleViewAction())
+ menu.addAction(self.annotatedPipelineView.toolWindow().toggleViewAction())
+ menu.addAction(self.virtualCell.toolWindow().toggleViewAction())
+
+ def removeViewActionsFromMenu(self, menu):
+ """removeViewActionsFromMenu(menu: QMenu) -> None
+ Remove toggle view actions from menu
+
+ """
+ menu.removeAction(self.paramView.toolWindow().toggleViewAction())
+ menu.removeAction(self.annotatedPipelineView.toolWindow().toggleViewAction())
+ menu.removeAction(self.virtualCell.toolWindow().toggleViewAction())
+
+ def setController(self, controller):
+ """ setController(controller: VistrailController) -> None
+ Assign a controller to the parameter exploration tab
+
+ """
+ self.controller = controller
+
+ def getParameterExploration(self):
+ """ getParameterExploration() -> string
+ Generates an XML string that represents the current
+ parameter exploration, and which can be loaded with
+ setParameterExploration().
+
+ """
+ # Construct xml for persisting parameter exploration
+ escape_dict = { "'":"'", '"':'"', '\n':'
' }
+ timestamp = current_time().strftime('%Y-%m-%d %H:%M:%S')
+ # TODO: For now, we use the timestamp as the 'name' - Later, we should set 'name' based on a UI input field
+ xml = '\t<paramexp dims="%s" layout="%s" date="%s" name="%s">' % (str(self.peWidget.table.label.getCounts()), str(self.virtualCell.getConfiguration()[2]), timestamp, timestamp)
+ for i in xrange(self.peWidget.table.layout().count()):
+ pEditor = self.peWidget.table.layout().itemAt(i).widget()
+ if pEditor and isinstance(pEditor, QParameterSetEditor):
+ firstParam = True
+ for paramWidget in pEditor.paramWidgets:
+ paramInfo = paramWidget.param
+ interpolator = paramWidget.editor.stackedEditors.currentWidget()
+ intType = interpolator.exploration_name
+ # Write function tag prior to the first parameter of the function
+ if firstParam:
+ xml += '\n\t\t<function id="%s" alias="%s" name="%s">' % (paramInfo.parent_id, paramInfo.is_alias, pEditor.info[0])
+ firstParam = False
+ # Write parameter tag
+ xml += '\n\t\t\t<param id="%s" dim="%s" interp="%s"' % (paramInfo.id, paramWidget.getDimension(), intType)
+ if intType == 'Linear Interpolation':
+ xml += ' min="%s" max="%s"' % (interpolator.fromEdit.get_value(), interpolator.toEdit.get_value())
+ elif intType == 'List':
+ xml += ' values="%s"' % escape(str(interpolator._str_values), escape_dict)
+ elif intType == 'User-defined Function':
+ xml += ' code="%s"' % escape(interpolator.function, escape_dict)
+ xml += '/>'
+ xml += '\n\t\t</function>'
+ xml += '\n\t</paramexp>'
+ return xml
+
+ def setParameterExploration(self, xmlString):
+ """ setParameterExploration(xmlString: string) -> None
+ Sets the current parameter exploration to the one
+ defined by 'xmlString'.
+
+ """
+ if not xmlString:
+ return
+ # Parse/validate the xml
+ try:
+ xmlDoc = parseString(xmlString).documentElement
+ except:
+ debug.critical("Parameter Exploration load failed because of "
+ "invalid XML:\n\n%s" % xmlString)
+ return
+ # Set the exploration dimensions
+ dims = eval(str(xmlDoc.attributes['dims'].value))
+ self.peWidget.table.label.setCounts(dims)
+ # Set the virtual cell layout
+ layout = eval(str(xmlDoc.attributes['layout'].value))
+ self.virtualCell.setConfiguration(layout)
+ # Populate parameter exploration window with stored functions and aliases
+ for f in xmlDoc.getElementsByTagName('function'):
+ # Retrieve function attributes
+ f_id = long(f.attributes['id'].value)
+ f_name = str(f.attributes['name'].value)
+ f_is_alias = (str(f.attributes['alias'].value) == 'True')
+ # Search the parameter treeWidget for this function and add it directly
+ newEditor = None
+ for tidx in xrange(self.paramView.treeWidget.topLevelItemCount()):
+ moduleItem = self.paramView.treeWidget.topLevelItem(tidx)
+ for cidx in xrange(moduleItem.childCount()):
+ paramInfo = moduleItem.child(cidx).parameter
+ name, params = paramInfo
+ if params[0].parent_id == f_id and params[0].is_alias == f_is_alias:
+ newEditor = self.peWidget.table.addParameter(paramInfo)
+ # Retrieve params for this function and set their values in the UI
+ if newEditor:
+ for p in f.getElementsByTagName('param'):
+ # Locate the param in the newly added param editor and set values
+ p_id = long(p.attributes['id'].value)
+ for paramWidget in newEditor.paramWidgets:
+ if paramWidget.param.id == p_id:
+ # Set Parameter Dimension (radio button)
+ p_dim = int(p.attributes['dim'].value)
+ paramWidget.setDimension(p_dim)
+ # Set Interpolator Type (dropdown list)
+ p_intType = str(p.attributes['interp'].value)
+ paramWidget.editor.selectInterpolator(p_intType)
+ # Set Interpolator Value(s)
+ interpolator = paramWidget.editor.stackedEditors.currentWidget()
+ if p_intType == 'Linear Interpolation':
+ # Set min/max
+ p_min = str(p.attributes['min'].value)
+ p_max = str(p.attributes['max'].value)
+ interpolator.fromEdit.setText(p_min)
+ interpolator.toEdit.setText(p_max)
+ elif p_intType == 'List':
+ p_values = str(p.attributes['values'].value)
+ # Set internal list structure
+ interpolator._str_values = eval(p_values)
+ # Update UI list
+ if interpolator.type == 'String':
+ interpolator.listValues.setText(p_values)
+ else:
+ interpolator.listValues.setText(p_values.replace("'", "").replace('"', ''))
+ elif p_intType == 'User-defined Function':
+ # Set function code
+ p_code = str(p.attributes['code'].value)
+ interpolator.function = p_code
+
+ def showEvent(self, event):
+ """ showEvent(event: QShowEvent) -> None
+ Update the tab when it is shown
+
+ """
+ if self.currentVersion!=self.controller.current_version:
+ self.currentVersion = self.controller.current_version
+ # Update the virtual cell
+ pipeline = self.controller.current_pipeline
+ self.virtualCell.updateVirtualCell(pipeline)
+
+ # Now we need to inspect the parameter list
+ self.paramView.treeWidget.updateFromPipeline(pipeline)
+
+ # Update the annotated ids
+ self.annotatedPipelineView.updateAnnotatedIds(pipeline)
+
+ # Update the parameter exploration table
+ self.peWidget.updatePipeline(pipeline)
+
+ # Update the UI with the most recent parameter exploration
+ # TODO: For now, we just strip the root tags since there's only one
+ # exploration - Later we should parse the root tree and select
+ # the active exploration based on date, or user choice
+ xmlString = self.controller.vistrail.get_paramexp(self.currentVersion)
+ if xmlString is not None:
+ striplen = len("<paramexps>")
+ xmlString = xmlString[striplen:-(striplen+1)].strip()
+ self.setParameterExploration(xmlString)
+
+ def performParameterExploration(self):
+ """ performParameterExploration() -> None
+ Perform the exploration by collecting a list of actions
+ corresponding to each dimension
+
+ """
+ registry = get_module_registry()
+ actions = self.peWidget.table.collectParameterActions()
+ spreadsheet_pkg = '%s.spreadsheet' % get_vistrails_default_pkg_prefix()
+ # Set the annotation to persist the parameter exploration
+ # TODO: For now, we just replace the existing exploration - Later we should append them.
+ xmlString = "<paramexps>\n" + self.getParameterExploration() + "\n</paramexps>"
+ self.controller.vistrail.set_paramexp(self.currentVersion, xmlString)
+ self.controller.set_changed(True)
+
+ if self.controller.current_pipeline and actions:
+ explorer = ActionBasedParameterExploration()
+ (pipelines, performedActions) = explorer.explore(
+ self.controller.current_pipeline, actions)
+
+ dim = [max(1, len(a)) for a in actions]
+ if (registry.has_module(spreadsheet_pkg, 'CellLocation') and
+ registry.has_module(spreadsheet_pkg, 'SheetReference')):
+ modifiedPipelines = self.virtualCell.positionPipelines(
+ 'PE#%d %s' % (QParameterExplorationTab.explorationId,
+ self.controller.name),
+ dim[2], dim[1], dim[0], pipelines, self.controller)
+ else:
+ modifiedPipelines = pipelines
+
+ mCount = []
+ for p in modifiedPipelines:
+ if len(mCount)==0:
+ mCount.append(0)
+ else:
+ mCount.append(len(p.modules)+mCount[len(mCount)-1])
+
+ # Now execute the pipelines
+ totalProgress = sum([len(p.modules) for p in modifiedPipelines])
+ progress = QtGui.QProgressDialog('Performing Parameter '
+ 'Exploration...',
+ '&Cancel',
+ 0, totalProgress)
+ progress.setWindowTitle('Parameter Exploration')
+ progress.setWindowModality(QtCore.Qt.WindowModal)
+ progress.show()
+
+ QParameterExplorationTab.explorationId += 1
+ interpreter = get_default_interpreter()
+ for pi in xrange(len(modifiedPipelines)):
+ progress.setValue(mCount[pi])
+ QtCore.QCoreApplication.processEvents()
+ if progress.wasCanceled():
+ break
+ def moduleExecuted(objId):
+ if not progress.wasCanceled():
+ #progress.setValue(progress.value()+1)
+ #the call above was crashing when used by multithreaded
+ #code, replacing with the call below (thanks to Terence
+ #for submitting this fix).
+ QtCore.QMetaObject.invokeMethod(progress, "setValue",
+ QtCore.Q_ARG(int,progress.value()+1))
+ QtCore.QCoreApplication.processEvents()
+ kwargs = {'locator': self.controller.locator,
+ 'current_version': self.controller.current_version,
+ 'view': self.controller.current_pipeline_scene,
+ 'module_executed_hook': [moduleExecuted],
+ 'reason': 'Parameter Exploration',
+ 'actions': performedActions[pi],
+ }
+ interpreter.execute(modifiedPipelines[pi], **kwargs)
+ progress.setValue(totalProgress)
+
+ def exploreChange(self, notEmpty):
+ """ exploreChange(notEmpty: bool) -> None
+ echo the signal
+
+ """
+ self.emit(QtCore.SIGNAL('exploreChange(bool)'), notEmpty)
diff --git a/vistrails/gui/paramexplore/pe_table.py b/vistrails/gui/paramexplore/pe_table.py
new file mode 100644
index 0000000..786778e
--- /dev/null
+++ b/vistrails/gui/paramexplore/pe_table.py
@@ -0,0 +1,1015 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from getpass import getuser
+
+from PyQt4 import QtCore, QtGui
+from xml.dom.minidom import parseString
+from xml.sax.saxutils import escape, unescape
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.common_widgets import QPromptWidget
+from vistrails.gui.modules.paramexplore import QParameterEditor
+from vistrails.gui.paramexplore.param_view import QParameterTreeWidget
+from vistrails.gui.utils import show_warning
+from vistrails.core import debug
+from vistrails.core.modules.basic_modules import Constant
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.system import current_time
+from vistrails.core.paramexplore.param import PEParam
+from vistrails.core.paramexplore.function import PEFunction
+from vistrails.core.vistrail.module import Module as VistrailModule
+from vistrails.core.paramexplore.paramexplore import ParameterExploration
+import vistrails.core.db.action
+
+""" The file describes the parameter exploration table for VisTrails
+
+QParameterExplorationTable
+"""
+
+
+################################################################################
+class QParameterExplorationWidget(QtGui.QScrollArea):
+ """
+ QParameterExplorationWidget is a place holder for
+ QParameterExplorationTable
+
+ is a grid layout widget having 4 comlumns corresponding to 4
+ dimensions of exploration. It accept method/alias drops and can be
+ fully configured onto any dimension. For each parameter, 3
+ different approach can be chosen to assign the value of that
+ parameter during the exploration: linear interpolation (for int,
+ float), list (for int, float, string and boolean) and user-define
+ function (for int, float, string and boolean)
+
+ """
+ def __init__(self, parent=None):
+ """ QParameterExplorationWidget(parent: QWidget)
+ -> QParameterExplorationWidget
+ Put the QParameterExplorationTable as a main widget
+
+ """
+ QtGui.QScrollArea.__init__(self, parent)
+ self.setAcceptDrops(True)
+ self.setWidgetResizable(True)
+ self.table = QParameterExplorationTable()
+ self.setWidget(self.table)
+
+ def dragEnterEvent(self, event):
+ """ dragEnterEvent(event: QDragEnterEvent) -> None
+ Set to accept drops from the parameter list
+
+ """
+ if isinstance(event.source(), QParameterTreeWidget):
+ data = event.mimeData()
+ if hasattr(data, 'items'):
+ event.accept()
+ return
+ event.ignore()
+
+ def dropEvent(self, event):
+ """ dropEvent(event: QDragMoveEvent) -> None
+ Accept drop event to add a new method
+
+ """
+ if isinstance(event.source(), QParameterTreeWidget):
+ data = event.mimeData()
+ if hasattr(data, 'items'):
+ event.accept()
+ self.setFocus()
+ for item in data.items:
+ self.table.addParameter(item.parameter)
+ vsb = self.verticalScrollBar()
+ vsb.setValue(vsb.maximum())
+
+ def updatePipeline(self, pipeline):
+ """ updatePipeline(pipeline: Pipeline) -> None
+ Assign a pipeline to the table
+
+ """
+ self.table.setPipeline(pipeline)
+ # Update the UI with the most recent parameter exploration
+ if self.controller:
+ currentVersion = self.controller.current_version
+ pe = self.controller.vistrail.get_paramexp(currentVersion)
+ self.controller.current_parameter_exploration = pe
+ self.setParameterExploration(pe)
+
+ def getParameterExplorationOld(self):
+ """ getParameterExploration() -> string
+ Generates an XML string that represents the current
+ parameter exploration, and which can be loaded with
+ setParameterExploration().
+
+ """
+ # Construct xml for persisting parameter exploration
+ escape_dict = { "'":"'", '"':'"', '\n':'
' }
+ timestamp = current_time().strftime('%Y-%m-%d %H:%M:%S')
+ palette = self.get_palette()
+ # TODO: For now, we use the timestamp as the 'name' - Later, we should set 'name' based on a UI input field
+ xml = '\t<paramexp dims="%s" layout="%s" date="%s" name="%s">' % (str(self.table.label.getCounts()), str(palette.virtual_cell.getConfiguration()[2]), timestamp, timestamp)
+ for i in xrange(self.table.layout().count()):
+ pEditor = self.table.layout().itemAt(i).widget()
+ if pEditor and isinstance(pEditor, QParameterSetEditor):
+ firstParam = True
+ for paramWidget in pEditor.paramWidgets:
+ paramInfo = paramWidget.param
+ interpolator = paramWidget.editor.stackedEditors.currentWidget()
+ intType = interpolator.exploration_name
+ # Write function tag prior to the first parameter of the function
+ if firstParam:
+ xml += '\n\t\t<function id="%s" alias="%s" name="%s">' % (paramInfo.parent_id, paramInfo.is_alias, pEditor.info[0])
+ firstParam = False
+ # Write parameter tag
+ xml += '\n\t\t\t<param id="%s" dim="%s" interp="%s"' % (paramInfo.id, paramWidget.getDimension(), intType)
+ if intType in ['Linear Interpolation', 'RGB Interpolation',
+ 'HSV Interpolation']:
+ xml += ' min="%s" max="%s"' % (interpolator.fromEdit.get_value(), interpolator.toEdit.get_value())
+ elif intType == 'List':
+ xml += ' values="%s"' % escape(str(interpolator._str_values), escape_dict)
+ elif intType == 'User-defined Function':
+ xml += ' code="%s"' % escape(interpolator.function, escape_dict)
+ xml += '/>'
+ xml += '\n\t\t</function>'
+ xml += '\n\t</paramexp>'
+ return xml
+
+ def getParameterExploration(self):
+ """ getParameterExploration() -> ParameterExploration
+ Generates a ParameterExploration object hat represents the current
+ parameter exploration, and which can be loaded with
+ setParameterExploration().
+
+ """
+ # Construct xml for persisting parameter exploration
+ escape_dict = { "'":"'", '"':'"', '\n':'
' }
+ palette = self.get_palette()
+ id_scope = self.controller.id_scope
+ functions = []
+ for i in xrange(self.table.layout().count()):
+ pEditor = self.table.layout().itemAt(i).widget()
+ if pEditor and isinstance(pEditor, QParameterSetEditor):
+ function = None
+ firstParam = True
+ for paramWidget in pEditor.paramWidgets:
+ paramInfo = paramWidget.param
+ interpolator = paramWidget.editor.stackedEditors.currentWidget()
+ intType = interpolator.exploration_name
+ # Write function tag prior to the first parameter of the function
+ if firstParam:
+ function = PEFunction(id=id_scope.getNewId(PEFunction.vtType),
+ module_id=paramInfo.module_id,
+ port_name=paramInfo.name,
+ is_alias = 1 if paramInfo.is_alias else 0)
+ firstParam = False
+
+ if intType in ['Linear Interpolation', 'RGB Interpolation',
+ 'HSV Interpolation']:
+ value = '["%s", "%s"]' % (interpolator.fromEdit.get_value(),
+ interpolator.toEdit.get_value())
+ elif intType == 'List':
+ value = '%s' % escape(str(interpolator._str_values), escape_dict)
+ elif intType == 'User-defined Function':
+ value ='%s' % escape(interpolator.function, escape_dict)
+ # Write parameter tag
+ param = PEParam(id=id_scope.getNewId(PEParam.vtType),
+ pos=paramInfo.pos,
+ interpolator=intType,
+ value=value,
+ dimension=paramWidget.getDimension())
+ function.addParameter(param)
+ functions.append(function)
+ pe = ParameterExploration(dims=str(self.table.label.getCounts()),
+ layout=repr(palette.virtual_cell.getConfiguration()[2]),
+ date=current_time().strftime('%Y-%m-%d %H:%M:%S'),
+ user=getuser(),
+ functions=functions)
+ return pe
+
+ def setParameterExploration(self, pe, update_inspector=True):
+ """ setParameterExploration(pe: ParameterExploration) -> None
+ Sets the current parameter exploration to the one defined by pe
+
+ """
+ self.table.clear()
+ palette = self.get_palette()
+ if update_inspector:
+ palette.stateChanged()
+ if not pe:
+ return
+ unescape_dict = { "'":"'", '"':'"', '
':'\n' }
+ paramView = self.get_param_view()
+ # Set the exploration dimensions
+ self.table.label.setCounts(pe.dims)
+ # Set the virtual cell layout
+ palette.virtual_cell.setConfiguration(pe.layout)
+ # Populate parameter exploration window with stored functions and aliases
+ for f in pe.functions:
+ # Search the parameter treeWidget for this function and add it directly
+ newEditor = None
+ for tidx in xrange(paramView.treeWidget.topLevelItemCount()):
+ moduleItem = paramView.treeWidget.topLevelItem(tidx)
+ for cidx in xrange(moduleItem.childCount()):
+ paramInfo = moduleItem.child(cidx).parameter
+ name, params = paramInfo
+ if params[0].module_id == f.module_id and \
+ params[0].name == f.port_name and \
+ params[0].is_alias == f.is_alias:
+ newEditor = self.table.addParameter(paramInfo)
+
+ # Retrieve params for this function and set their values in the UI
+ if newEditor:
+ for p in f.parameters:
+ # Locate the param in the newly added param editor and set values
+ for paramWidget in newEditor.paramWidgets:
+ if paramWidget.param.pos == p.pos:
+ # Set Parameter Dimension (radio button)
+ paramWidget.setDimension(p.dimension)
+ # Set Interpolator Type (dropdown list)
+ paramWidget.editor.selectInterpolator(p.interpolator)
+ # Set Interpolator Value(s)
+ interpolator = paramWidget.editor.stackedEditors.currentWidget()
+ if p.interpolator in ['Linear Interpolation',
+ 'RGB Interpolation',
+ 'HSV Interpolation']:
+ try:
+ # Set min/max
+ i_range = eval('%s' % unescape(p.value,
+ unescape_dict))
+ p_min = str(i_range[0])
+ p_max =str(i_range[1])
+ interpolator.fromEdit.set_value(p_min)
+ interpolator.toEdit.set_value(p_max)
+ except:
+ pass
+ elif p.interpolator == 'List':
+ p_values = '%s' % unescape(p.value,
+ unescape_dict)
+ # Set internal list structure
+ interpolator._str_values = eval(p_values)
+ # Update UI list
+ if interpolator.type == 'String':
+ interpolator.listValues.setText(p_values)
+ else:
+ interpolator.listValues.setText(
+ p_values.replace("'","").replace('"',''))
+ elif p.interpolator == 'User-defined Function':
+ # Set function code
+ interpolator.function = '%s' % unescape(
+ str(p.value), unescape_dict)
+
+ def setParameterExplorationOld(self, xmlString):
+ """ setParameterExploration(xmlString: string) -> None
+ Sets the current parameter exploration to the one
+ defined by 'xmlString'.
+
+ """
+ if not xmlString:
+ return
+ # Parse/validate the xml
+ try:
+ xmlDoc = parseString(xmlString).documentElement
+ except:
+ debug.critical("Parameter Exploration load failed because of "
+ "invalid XML:\n\n%s" % xmlString)
+ return
+ palette = self.get_palette()
+ paramView = self.get_param_view()
+ # Set the exploration dimensions
+ dims = eval(str(xmlDoc.attributes['dims'].value))
+ self.table.label.setCounts(dims)
+ # Set the virtual cell layout
+ layout = eval(str(xmlDoc.attributes['layout'].value))
+ palette.virtual_cell.setConfiguration(layout)
+ # Populate parameter exploration window with stored functions and aliases
+ for f in xmlDoc.getElementsByTagName('function'):
+ # Retrieve function attributes
+ f_id = long(f.attributes['id'].value)
+ f_name = str(f.attributes['name'].value)
+ f_is_alias = (str(f.attributes['alias'].value) == 'True')
+ # Search the parameter treeWidget for this function and add it directly
+ newEditor = None
+ for tidx in xrange(paramView.treeWidget.topLevelItemCount()):
+ moduleItem = paramView.treeWidget.topLevelItem(tidx)
+ for cidx in xrange(moduleItem.childCount()):
+ paramInfo = moduleItem.child(cidx).parameter
+ name, params = paramInfo
+ if params[0].parent_id == f_id and params[0].is_alias == f_is_alias:
+ newEditor = self.table.addParameter(paramInfo)
+ # Retrieve params for this function and set their values in the UI
+ if newEditor:
+ for p in f.getElementsByTagName('param'):
+ # Locate the param in the newly added param editor and set values
+ p_id = long(p.attributes['id'].value)
+ for paramWidget in newEditor.paramWidgets:
+ if paramWidget.param.id == p_id:
+ # Set Parameter Dimension (radio button)
+ p_dim = int(p.attributes['dim'].value)
+ paramWidget.setDimension(p_dim)
+ # Set Interpolator Type (dropdown list)
+ p_intType = str(p.attributes['interp'].value)
+ paramWidget.editor.selectInterpolator(p_intType)
+ # Set Interpolator Value(s)
+ interpolator = paramWidget.editor.stackedEditors.currentWidget()
+ if p_intType in ['Linear Interpolation', 'RGB Interpolation',
+ 'HSV Interpolation']:
+ try:
+ # Set min/max
+ p_min = str(p.attributes['min'].value)
+ p_max = str(p.attributes['max'].value)
+ interpolator.fromEdit.set_value(p_min)
+ interpolator.toEdit.set_value(p_max)
+ except:
+ pass
+ elif p_intType == 'List':
+ p_values = str(p.attributes['values'].value)
+ # Set internal list structure
+ interpolator._str_values = eval(p_values)
+ # Update UI list
+ if interpolator.type == 'String':
+ interpolator.listValues.setText(p_values)
+ else:
+ interpolator.listValues.setText(p_values.replace("'", "").replace('"', ''))
+ elif p_intType == 'User-defined Function':
+ # Set function code
+ p_code = str(p.attributes['code'].value)
+ interpolator.function = p_code
+
+ def get_palette(self):
+ from vistrails.gui.paramexplore.pe_inspector import QParamExploreInspector
+ return QParamExploreInspector.instance()
+
+ def get_param_view(self):
+ from vistrails.gui.paramexplore.param_view import QParameterView
+ return QParameterView.instance()
+
+class QParameterExplorationTable(QPromptWidget):
+ """
+ QParameterExplorationTable is a grid layout widget having 4
+ comlumns corresponding to 4 dimensions of exploration. It accept
+ method/alias drops and can be fully configured onto any
+ dimension. For each parameter, 3 different approach can be chosen
+ to assign the value of that parameter during the exploration:
+ linear interpolation (for int, float), list (for int, float,
+ string and boolean) and user-define function (for int, float,
+ string and boolean)
+
+ """
+ def __init__(self, parent=None):
+ """ QParameterExplorationTable(parent: QWidget)
+ -> QParameterExplorationTable
+ Create an grid layout and accept drops
+
+ """
+ QPromptWidget.__init__(self, parent)
+ self.pipeline = None
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ self.setPromptText('Drag aliases/parameters here for a parameter '
+ 'exploration')
+ self.showPrompt()
+
+ vLayout = QtGui.QVBoxLayout(self)
+ vLayout.setSpacing(0)
+ vLayout.setMargin(0)
+ vLayout.setAlignment(QtCore.Qt.AlignTop)
+ self.setLayout(vLayout)
+
+ self.label = QDimensionLabel()
+
+ for labelIcon in self.label.labelIcons:
+ self.connect(labelIcon.countWidget,
+ QtCore.SIGNAL('editingFinished()'),
+ self.updateWidgets)
+ vLayout.addWidget(self.label)
+
+ for i in xrange(2):
+ hBar = QtGui.QFrame()
+ hBar.setFrameStyle(QtGui.QFrame.HLine | QtGui.QFrame.Sunken)
+ vLayout.addWidget(hBar)
+ self._parameterCount = 0
+
+ def addParameter(self, paramInfo):
+ """ addParameter(paramInfo: (str, [ParameterInfo]) -> None
+ Add a parameter to the table. The parameter info is specified
+ in QParameterTreeWidgetItem
+
+ """
+ # Check to see paramInfo is not a subset of some other parameter set
+ params = paramInfo[1]
+ for i in xrange(self.layout().count()):
+ pEditor = self.layout().itemAt(i).widget()
+ if pEditor and isinstance(pEditor, QParameterSetEditor):
+ subset = True
+ for p in params:
+ if not (p in pEditor.info[1]):
+ subset = False
+ break
+ if subset:
+ show_warning('Parameter Exists',
+ 'The parameter you are trying to add is '
+ 'already in the list.')
+ return
+ self.showPrompt(False)
+ newEditor = QParameterSetEditor(paramInfo, self)
+
+ # Make sure to disable all duplicated parameter
+ for p in xrange(len(params)):
+ for i in xrange(self.layout().count()):
+ pEditor = self.layout().itemAt(i).widget()
+ if pEditor and isinstance(pEditor, QParameterSetEditor):
+ if params[p] in pEditor.info[1]:
+ widget = newEditor.paramWidgets[p]
+ widget.setDimension(4)
+ widget.setDuplicate(True)
+ widget.setEnabled(False)
+ break
+
+ self.layout().addWidget(newEditor)
+ newEditor.show()
+ self.setMinimumHeight(self.layout().minimumSize().height())
+ self.emit(QtCore.SIGNAL('exploreChange(bool)'), self.layout().count() > 3)
+ return newEditor
+
+ def removeParameter(self, ps):
+ """ removeParameterSet(ps: QParameterSetEditor) -> None
+ Remove a parameter set from the table and validate the rest
+
+ """
+ self.layout().removeWidget(ps)
+ # Restore disabled parameter
+ for i in xrange(self.layout().count()):
+ pEditor = self.layout().itemAt(i).widget()
+ if pEditor and isinstance(pEditor, QParameterSetEditor):
+ for p in xrange(len(pEditor.info[1])):
+ param = pEditor.info[1][p]
+ widget = pEditor.paramWidgets[p]
+ if (param in ps.info[1] and (not widget.isEnabled())):
+ widget.setDimension(0)
+ widget.setDuplicate(False)
+ widget.setEnabled(True)
+ break
+ self.showPrompt(self.layout().count()<=3)
+ self.emit(QtCore.SIGNAL('exploreChange(bool)'), self.layout().count() > 3)
+
+ def updateWidgets(self):
+ """ updateWidgets() -> None
+ Update all widgets to reflect the step count
+
+ """
+ # Go through all possible parameter widgets
+ counts = self.label.getCounts()
+ for i in xrange(self.layout().count()):
+ pEditor = self.layout().itemAt(i).widget()
+ if pEditor and isinstance(pEditor, QParameterSetEditor):
+ for paramWidget in pEditor.paramWidgets:
+ dim = paramWidget.getDimension()
+ if dim in [0, 1, 2, 3]:
+ se = paramWidget.editor.stackedEditors
+ # Notifies editor widgets of size update
+ for i in xrange(se.count()):
+ wd = se.widget(i)
+ if hasattr(wd, 'size_was_updated'):
+ wd.size_was_updated(counts[dim])
+
+ def clear(self):
+ """ clear() -> None
+ Clear all widgets
+
+ """
+ for i in reversed(range(self.layout().count())):
+ pEditor = self.layout().itemAt(i).widget()
+ if pEditor and isinstance(pEditor, QParameterSetEditor):
+ pEditor.table = None
+ self.layout().removeWidget(pEditor)
+ pEditor.hide()
+ pEditor.deleteLater()
+ self.label.resetCounts()
+ self.showPrompt()
+ self.emit(QtCore.SIGNAL('exploreChange(bool)'), self.layout().count() > 3)
+
+ def setPipeline(self, pipeline):
+ """ setPipeline(pipeline: Pipeline) -> None
+ Assign a pipeline to the current table
+
+ """
+ if pipeline:
+ to_be_deleted = []
+ for i in xrange(self.layout().count()):
+ pEditor = self.layout().itemAt(i).widget()
+ if pEditor and isinstance(pEditor, QParameterSetEditor):
+ for param in pEditor.info[1]:
+ # We no longer require the parameter to exist
+ # we check if the module still exists
+ if not pipeline.db_has_object(VistrailModule.vtType,
+ param.module_id):
+ to_be_deleted.append(pEditor)
+ for pEditor in to_be_deleted:
+ pEditor.removeSelf()
+ else:
+ self.clear()
+ self.pipeline = pipeline
+ self.label.setEnabled(self.pipeline!=None)
+
+ def collectParameterActions(self):
+ """ collectParameterActions() -> list
+ Return a list of action lists corresponding to each dimension
+
+ """
+ if not self.pipeline:
+ return None
+
+ reg = get_module_registry()
+ parameterValues = [[], [], [], []]
+ counts = self.label.getCounts()
+ for i in xrange(self.layout().count()):
+ pEditor = self.layout().itemAt(i).widget()
+ if pEditor and isinstance(pEditor, QParameterSetEditor):
+ for paramWidget in pEditor.paramWidgets:
+ editor = paramWidget.editor
+ interpolator = editor.stackedEditors.currentWidget()
+ paramInfo = paramWidget.param
+ dim = paramWidget.getDimension()
+ if dim in [0, 1, 2, 3]:
+ count = counts[dim]
+ values = interpolator.get_values(count)
+ if not values:
+ return None
+ pId = paramInfo.id
+ pType = paramInfo.dbtype
+ parentType = paramInfo.parent_dbtype
+ parentId = paramInfo.parent_id
+ function = self.pipeline.db_get_object(parentType,
+ parentId)
+ fName = function.name
+ old_param = self.pipeline.db_get_object(pType,pId)
+ pName = old_param.name
+ pAlias = old_param.alias
+ pIdentifier = old_param.identifier
+ actions = []
+ tmp_id = -1L
+ for v in values:
+ getter = reg.get_descriptor_by_name
+ desc = getter(paramInfo.identifier,
+ paramInfo.type,
+ paramInfo.namespace)
+ if not isinstance(v, str):
+ str_value = desc.module.translate_to_string(v)
+ else:
+ str_value = v
+ new_param = ModuleParam(id=tmp_id,
+ pos=old_param.pos,
+ name=pName,
+ alias=pAlias,
+ val=str_value,
+ type=paramInfo.type,
+ identifier=pIdentifier
+ )
+ action_spec = ('change', old_param, new_param,
+ parentType, function.real_id)
+ action = vistrails.core.db.action.create_action([action_spec])
+ actions.append(action)
+ parameterValues[dim].append(actions)
+ tmp_id -= 1
+ return [zip(*p) for p in parameterValues]
+
+class QDimensionLabel(QtGui.QWidget):
+ """
+ QDimensionLabel represents a horizontal header item of the
+ parameter window. It has 4 small icons represents the dimensions
+ and a Skip label. It represents a group box.
+
+ """
+ def __init__(self, parent=None):
+ """ QDimensionLabel(parent: QWidget) -> None
+ Initialize icons and labels
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self.setAutoFillBackground(True)
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Maximum)
+
+ hLayout = QtGui.QHBoxLayout(self)
+ hLayout.setMargin(0)
+ hLayout.setSpacing(0)
+ self.setLayout(hLayout)
+
+ self.params = QDimensionLabelText('Parameters')
+ hLayout.addWidget(self.params)
+ self.params.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ hLayout.addWidget(QDimensionLabelSeparator())
+
+ pixes = [CurrentTheme.EXPLORE_COLUMN_PIXMAP,
+ CurrentTheme.EXPLORE_ROW_PIXMAP,
+ CurrentTheme.EXPLORE_SHEET_PIXMAP,
+ CurrentTheme.EXPLORE_TIME_PIXMAP]
+ self.labelIcons = []
+ for pix in pixes:
+ labelIcon = QDimensionLabelIcon(pix)
+ hLayout.addWidget(labelIcon)
+ self.labelIcons.append(labelIcon)
+ hLayout.addWidget(QDimensionLabelSeparator())
+
+ hLayout.addWidget(QDimensionLabelIcon(CurrentTheme.EXPLORE_SKIP_PIXMAP,
+ False))
+
+ def getCounts(self):
+ """ getCounts() -> [int]
+ Return a list of 4 ints denoting the step count desired for
+ each dimension
+
+ """
+ return [l.countWidget.value() for l in self.labelIcons]
+
+ def setCounts(self, counts):
+ """ setCounts(counts:list) -> None
+ Set the 4 step counts for each dimension from a list of 4 ints
+
+ """
+ dim = len(self.getCounts())
+ if len(counts) != dim:
+ return
+ for i in xrange(0, dim):
+ self.labelIcons[i].countWidget.setValue(counts[i])
+
+ def resetCounts(self):
+ """ resetCounts() -> None
+ Reset all counts to 1
+
+ """
+ for l in self.labelIcons:
+ l.countWidget.setValue(1)
+
+class QDimensionSpinBox(QtGui.QSpinBox):
+ """
+ QDimensionSpinBox is just an overrided spin box that will also emit
+ 'editingFinished()' signal when the user interact with mouse
+
+ """
+ def mouseReleaseEvent(self, event):
+ """ mouseReleaseEvent(event: QMouseEvent) -> None
+ Emit 'editingFinished()' signal when the user release a mouse button
+
+ """
+ QtGui.QSpinBox.mouseReleaseEvent(self, event)
+ # super(QDimensionSpinBox, self).mouseReleaseEvent(event)
+ self.emit(QtCore.SIGNAL("editingFinished()"))
+
+class QDimensionLabelIcon(QtGui.QWidget):
+ """
+ QDimensionLabelIcon describes those icons staying on the header
+ view of the table
+
+ """
+ def __init__(self, pix, hasCount = True, parent=None):
+ """ QDimensionalLabelIcon(pix: QPixmap, hasCount: bool, parent: QWidget)
+ -> QDimensionalLabelIcon
+ Using size 32x32 and a margin of 2
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(0)
+ layout.setSpacing(0)
+ self.setLayout(layout)
+
+ label = QtGui.QLabel()
+ label.setAlignment(QtCore.Qt.AlignCenter)
+ label.setPixmap(pix.scaled(32, 32, QtCore.Qt.KeepAspectRatio,
+ QtCore.Qt.SmoothTransformation))
+ layout.addWidget(label)
+
+ if hasCount:
+ self.countWidget = QDimensionSpinBox()
+ self.countWidget.setFixedWidth(32)
+ self.countWidget.setRange(1, 10000000)
+ self.countWidget.setAlignment(QtCore.Qt.AlignRight)
+ self.countWidget.setFrame(False)
+ pal = QtGui.QPalette(self.countWidget.lineEdit().palette())
+ pal.setBrush(QtGui.QPalette.Base,
+ QtGui.QBrush(QtCore.Qt.NoBrush))
+ self.countWidget.lineEdit().setPalette(pal)
+ layout.addWidget(self.countWidget)
+
+ self.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+
+class QDimensionLabelText(QtGui.QWidget):
+ """
+ QDimensionLabelText describes those texts staying on the header
+ view of the table. It also has a button to perform exploration
+
+ """
+ def __init__(self, text, parent=None):
+ """ QDimensionalLabelText(text: str, parent: QWidget)
+ -> QDimensionalLabelText
+ Putting the text bold in the center
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ hLayout = QtGui.QHBoxLayout()
+ self.setLayout(hLayout)
+
+ hLayout.addStretch()
+
+ hLayout.addWidget(QtGui.QLabel('<b>Parameters</b>'))
+
+ hLayout.addStretch()
+
+
+class QDimensionLabelSeparator(QtGui.QFrame):
+ """
+ QDimensionLabelSeparator is acting as a vertical separator which
+ has an appropriate style to go with the QDimensionalLabel
+
+ """
+ def __init__(self, parent=None):
+ """ QDimensionalLabelSeparator(parent: QWidget)
+ -> QDimensionalLabelSeparator
+ Make sure the frame only has a width of 2
+
+ """
+ QtGui.QFrame.__init__(self, parent)
+ self.setFrameStyle(QtGui.QFrame.Panel | QtGui.QFrame.Sunken)
+ self.setFixedWidth(2)
+
+class QParameterSetEditor(QtGui.QWidget):
+ """
+ QParameterSetEditor is a widget controlling a set of
+ parameters. The set can contain a single parameter (aliases) or
+ multiple of them (module methods).
+
+ """
+ def __init__(self, info, table=None, parent=None):
+ """ QParameterSetEditor(info: paraminfo,
+ table: QParameterExplorationTable,
+ parent: QWidget)
+ -> QParameterSetEditor
+ Construct a parameter editing widget based on the paraminfo
+ (described in QParameterTreeWidgetItem)
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self.info = info
+ self.table = table
+ (name, paramList) = info
+ if table:
+ size = table.label.getCounts()[0]
+ else:
+ size = 1
+
+ vLayout = QtGui.QVBoxLayout(self)
+ vLayout.setMargin(0)
+ vLayout.setSpacing(0)
+ self.setLayout(vLayout)
+
+ label = QParameterSetLabel(name)
+ self.connect(label.removeButton, QtCore.SIGNAL('clicked()'),
+ self.removeSelf)
+ vLayout.addWidget(label)
+
+ self.paramWidgets = []
+ for param in paramList:
+ paramWidget = QParameterWidget(param, size)
+ vLayout.addWidget(paramWidget)
+ self.paramWidgets.append(paramWidget)
+
+ vLayout.addSpacing(10)
+
+ hBar = QtGui.QFrame()
+ hBar.setFrameStyle(QtGui.QFrame.HLine | QtGui.QFrame.Sunken)
+ vLayout.addWidget(hBar)
+
+ def removeSelf(self):
+ """ removeSelf() -> None
+ Remove itself out of the parent layout()
+
+ """
+ if self.table:
+ self.table.removeParameter(self)
+ self.table = None
+ self.close()
+ self.deleteLater()
+
+class QParameterSetLabel(QtGui.QWidget):
+ """
+ QParameterSetLabel is the label bar showing at the top of the
+ parameter set editor. It also has a Remove button to remove the
+ parameter
+
+ """
+ def __init__(self, text, parent=None):
+ """ QParameterSetLabel(text: str, parent: QWidget) -> QParameterSetLabel
+ Init a label and a button
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ hLayout = QtGui.QHBoxLayout(self)
+ hLayout.setMargin(0)
+ hLayout.setSpacing(0)
+ self.setLayout(hLayout)
+
+ hLayout.addSpacing(5)
+
+ label = QtGui.QLabel(text)
+ font = QtGui.QFont(label.font())
+ font.setBold(True)
+ label.setFont(font)
+ hLayout.addWidget(label)
+
+ hLayout.addSpacing(5)
+
+ self.removeButton = QtGui.QToolButton()
+ self.removeButton.setAutoRaise(True)
+ self.removeButton.setIcon(QtGui.QIcon(
+ self.style().standardPixmap(QtGui.QStyle.SP_DialogCloseButton)))
+ self.removeButton.setIconSize(QtCore.QSize(12, 12))
+ self.removeButton.setFixedWidth(16)
+ hLayout.addWidget(self.removeButton)
+
+ hLayout.addStretch()
+
+class QParameterWidget(QtGui.QWidget):
+ """
+ QParameterWidget is a row widget containing a label, a parameter
+ editor and a radio group.
+
+ """
+ def __init__(self, param, size, parent=None):
+ """ QParameterWidget(param: ParameterInfo, size: int, parent: QWidget)
+ -> QParameterWidget
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self.param = param
+ self.prevWidget = 0
+
+ hLayout = QtGui.QHBoxLayout(self)
+ hLayout.setMargin(0)
+ hLayout.setSpacing(0)
+ self.setLayout(hLayout)
+
+ hLayout.addSpacing(5+16+5)
+
+ self.label = QtGui.QLabel(param.spec.module)
+ self.label.setFixedWidth(50)
+ hLayout.addWidget(self.label)
+
+ registry = get_module_registry()
+ module = param.spec.descriptor.module
+ assert issubclass(module, Constant)
+
+ self.editor = QParameterEditor(param, size)
+ hLayout.addWidget(self.editor)
+
+ self.selector = QDimensionSelector()
+ self.connect(self.selector.radioButtons[4],
+ QtCore.SIGNAL('toggled(bool)'),
+ self.disableParameter)
+ hLayout.addWidget(self.selector)
+
+ def getDimension(self):
+ """ getDimension() -> int
+ Return a number 0-4 indicating which radio button is
+ selected. If none is selected (should not be in this case),
+ return -1
+
+ """
+ for i in xrange(5):
+ if self.selector.radioButtons[i].isChecked():
+ return i
+ return -1
+
+ def disableParameter(self, disabled=True):
+ """ disableParameter(disabled: bool) -> None
+ Disable/Enable this parameter when disabled is True/False
+
+ """
+ self.label.setEnabled(not disabled)
+ self.editor.setEnabled(not disabled)
+
+ def setDimension(self, dim):
+ """ setDimension(dim: int) -> None
+ Select a dimension for this parameter
+
+ """
+ if dim in xrange(5):
+ self.selector.radioButtons[dim].setChecked(True)
+
+ def setDuplicate(self, duplicate):
+ """ setDuplicate(duplicate: True) -> None
+ Set if this parameter is a duplicate parameter
+
+ """
+ if duplicate:
+ self.prevWidget = self.editor.stackedEditors.currentIndex()
+ self.editor.stackedEditors.setCurrentIndex(3)
+ else:
+ self.editor.stackedEditors.setCurrentIndex(self.prevWidget)
+
+class QDimensionSelector(QtGui.QWidget):
+ """
+ QDimensionSelector provides 5 radio buttons to select dimension of
+ exploration or just skipping it.
+
+ """
+ def __init__(self, parent=None):
+ """ QDimensionSelector(parent: QWidget) -> QDimensionSelector
+ Initialize the horizontal layout and set the width to be fixed
+ equal to the QDimensionLabel
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+
+ hLayout = QtGui.QHBoxLayout(self)
+ hLayout.setMargin(0)
+ hLayout.setSpacing(0)
+ self.setLayout(hLayout)
+
+ self.radioButtons = []
+ for i in xrange(5):
+ hLayout.addSpacing(2)
+ button = QDimensionRadioButton()
+ self.radioButtons.append(button)
+ button.setFixedWidth(32)
+ hLayout.addWidget(button)
+ self.radioButtons[0].setChecked(True)
+
+class QDimensionRadioButton(QtGui.QRadioButton):
+ """
+ QDimensionRadioButton is a replacement of QRadioButton with
+ simpler appearance. We just need to override the paint event
+
+ """
+ def paintEvent(self, event):
+ """ paintEvent(event: QPaintEvent) -> None
+ Draw an outer circle and another solid one in side
+
+ """
+ painter = QtGui.QPainter(self)
+ painter.setRenderHint(QtGui.QPainter.Antialiasing)
+ painter.setPen(self.palette().color(QtGui.QPalette.Dark))
+ painter.setBrush(QtCore.Qt.NoBrush)
+ l = min(self.width()-2, self.height()-2, 12)
+ r = QtCore.QRect(0, 0, l, l)
+ r.moveCenter(self.rect().center())
+ painter.drawEllipse(r)
+
+ if self.isChecked():
+ r.adjust(3, 3, -3, -3)
+ painter.setPen(QtCore.Qt.NoPen)
+ painter.setBrush(self.palette().color(QtGui.QPalette.WindowText))
+ painter.drawEllipse(r)
+
+ painter.end()
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+ Force toggling the radio button
+
+ """
+ self.click()
+
+################################################################################
+
+if __name__=="__main__":
+ import sys
+ import vistrails.gui.theme
+ app = QtGui.QApplication(sys.argv)
+ vistrails.gui.theme.initializeCurrentTheme()
+ vc = QDimensionLabel(CurrentTheme.EXPLORE_SHEET_PIXMAP, 'Hello World')
+ vc.show()
+ sys.exit(app.exec_())
diff --git a/vistrails/gui/paramexplore/pe_view.py b/vistrails/gui/paramexplore/pe_view.py
new file mode 100644
index 0000000..04a88e5
--- /dev/null
+++ b/vistrails/gui/paramexplore/pe_view.py
@@ -0,0 +1,135 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.gui.base_view import BaseView
+from vistrails.gui.paramexplore.pe_table import QParameterExplorationWidget
+from vistrails.gui.theme import CurrentTheme
+from vistrails.core import debug
+
+class QParamExploreView(QParameterExplorationWidget, BaseView):
+ explorationId = 0
+
+ def __init__(self, parent=None):
+ QParameterExplorationWidget.__init__(self, parent)
+ BaseView.__init__(self)
+
+ self.set_title("Explore")
+ self.connect(self.table,
+ QtCore.SIGNAL('exploreChange(bool)'),
+ self.exploreChange)
+
+ def set_controller(self, controller):
+ if self.controller == controller:
+ return
+ self.controller = controller
+ self.set_exploration()
+
+ def updatePipeline(self, pipeline):
+ name = self.controller.get_pipeline_name()
+ self.set_title("Explore: %s" % name)
+
+ def set_exploration(self, pe=None):
+ if not pe:
+ pe = self.controller.current_parameter_exploration
+ self.setParameterExploration(pe)
+
+ def set_default_layout(self):
+ from vistrails.gui.paramexplore.pe_inspector import QParamExploreInspector
+ from vistrails.gui.paramexplore.param_view import QParameterView
+ self.set_palette_layout(
+ {QtCore.Qt.LeftDockWidgetArea: QParamExploreInspector,
+ QtCore.Qt.RightDockWidgetArea: QParameterView,
+ })
+
+ def set_action_links(self):
+ self.action_links = \
+ {
+ 'execute': ('explore_changed', self.explore_non_empty),
+ }
+
+ def set_action_defaults(self):
+ self.action_defaults.update(
+ { 'execute': [('setEnabled', True, self.set_execute_action),
+ ('setIcon', False, CurrentTheme.EXECUTE_EXPLORE_ICON),
+ ('setToolTip', False, 'Execute the parameter exploration')],
+ 'publishWeb': [('setEnabled', False, False)],
+ 'publishPaper': [('setEnabled', False, False)],
+ })
+
+ def set_execute_action(self):
+ if self.controller and self.controller.vistrail:
+ versionId = self.controller.current_version
+ return self.controller.vistrail.get_paramexp(versionId) != None
+ return False
+
+ def explore_non_empty(self, on):
+ return on
+
+ def exploreChange(self, on):
+ from vistrails.gui.vistrails_window import _app
+ _app.notify('explore_changed', on)
+
+ def execute(self):
+ """ execute() -> None
+ Perform the exploration by collecting a list of actions
+ corresponding to each dimension
+
+ """
+ # persist the parameter exploration
+ pe = self.getParameterExploration()
+ pe.action_id = self.controller.current_version
+
+ # check if pe has changed
+ changed = False
+ if not self.controller.current_parameter_exploration or \
+ pe != self.controller.current_parameter_exploration:
+ changed = True
+ pe.name = ''
+ self.controller.current_parameter_exploration = pe
+ self.controller.vistrail.add_paramexp(pe)
+ self.controller.set_changed(True)
+ else:
+ pe = self.controller.current_parameter_exploration
+
+ errors = self.controller.executeParameterExploration(pe,
+ self.get_param_view().pipeline_view.scene())
+ if errors:
+ errors = '\n'.join(['Position %s: %s' % (error[0], error[1]) for error in errors])
+ debug.critical("Parameter Exploration Execution had errors", errors)
+ if changed:
+ from vistrails.gui.vistrails_window import _app
+ _app.notify('exploration_changed')
diff --git a/vistrails/gui/paramexplore/virtual_cell.py b/vistrails/gui/paramexplore/virtual_cell.py
new file mode 100644
index 0000000..ec515e6
--- /dev/null
+++ b/vistrails/gui/paramexplore/virtual_cell.py
@@ -0,0 +1,673 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file describe the virtual cell layout widget used in
+Parameter Exploration Tab """
+from PyQt4 import QtCore, QtGui
+from vistrails.core.inspector import PipelineInspector
+from vistrails.gui.common_widgets import QToolWindowInterface
+from vistrails.gui.paramexplore.pe_pipeline import QAnnotatedPipelineView
+from vistrails.gui.theme import CurrentTheme
+import copy
+import os.path
+
+# FIXME broke this as Actions have been changed around
+#
+# from core.vistrail.action import AddModuleAction, AddConnectionAction, \
+# DeleteConnectionAction, ChangeParameterAction
+
+###############################################################################
+
+def split_camel_case(text):
+ if not text:
+ return u''
+ lines = []
+ # State machine!
+ # empty?
+ # initial ------------------------>
+ # | \ return empty
+ # | \
+ # | \
+ # | \
+ # | \
+ # U | mark L \ mark
+ # | \
+ # \/ L \/
+ # 1 ---------------> 2 ----\
+ # / /\ |\ / |\ | L
+ # / | \ U / \___/
+ # / | \-----------
+ # | | emit, mark
+ # | |
+ # U | L | emit -1
+ # | | mark -1
+ # | /
+ # | /
+ # \/ /
+ # 3 ----\
+ # |\ | U
+ # \___/
+ #
+ state = 0
+ for i, c in enumerate(text):
+ u = c.isupper()
+ if state == 1:
+ state = 3 if u else 2
+ elif state == 2 and u:
+ state = 1
+ lines.append(text[mark:i])
+ mark = i
+ elif state == 3 and not u:
+ lines.append(text[mark:i-1])
+ mark = i-1
+ state = 1
+ elif state == 0:
+ state = 1 if u else 2
+ mark = i
+ lines.append(text[mark:])
+
+ return u'\n'.join(lines)
+
+###############################################################################
+
+def decodeConfiguration(pipeline, cells):
+ """ decodeConfiguration(pipeline: Pipeline,
+ cells: configuration) -> decoded cells
+ Convert cells of type [{(type,id): (row, column)}) to
+ (mId, row, col) in a particular pipeline
+
+ """
+ decodedCells = []
+ inspector = PipelineInspector()
+ inspector.inspect_spreadsheet_cells(pipeline)
+ inspector.inspect_ambiguous_modules(pipeline)
+ orig_pipeline = pipeline
+
+ for id_list in inspector.spreadsheet_cells:
+ pipeline = orig_pipeline
+ id_iter = iter(id_list)
+ m = pipeline.modules[id_iter.next()]
+ m_id = m.id
+ for m_id in id_iter:
+ pipeline = m.pipeline
+ m = pipeline.modules[m_id]
+ name = m.name
+
+ if len(id_list) == 1 and m_id in inspector.annotated_modules:
+ idx = inspector.annotated_modules[m_id]
+ elif tuple(id_list) in inspector.annotated_modules:
+ idx = inspector.annotated_modules[tuple(id_list)]
+ else:
+ idx = -1
+ (vRow, vCol) = cells[(name, idx)]
+ if len(id_list) == 1:
+ decodedCells.append((m_id, vRow, vCol))
+ else:
+ decodedCells.append((tuple(id_list), vRow, vCol))
+ return decodedCells
+
+def positionPipelines(sheetPrefix, sheetCount, rowCount, colCount,
+ pipelines, cells, controller):
+ """ _positionPipelines(sheetPrefix: str, sheetCount: int, rowCount: int,
+ colCount: int, pipelines: list of Pipeline,
+ cells: List, controller: VistrailCintroller)
+ -> list of Pipelines
+ Apply the virtual cell location to a list of pipelines in a
+ parameter exploration given that pipelines has multiple chunk
+ of sheetCount x rowCount x colCount cells
+
+ """
+
+ # at this point, we know that we have the spreadsheet loaded
+ from vistrails.packages.spreadsheet.spreadsheet_execute import \
+ assignPipelineCellLocations
+
+ modifiedPipelines = []
+ pipelinePositions = []
+ for pId in xrange(len(pipelines)):
+ root_pipeline = copy.copy(pipelines[pId])
+ col = pId % colCount
+ row = (pId / colCount) % rowCount
+ sheet = (pId / (colCount*rowCount)) % sheetCount
+
+ decodedCells = decodeConfiguration(root_pipeline, cells)
+ vRCount = (max(c[1] for c in decodedCells) + 1) if len(decodedCells) else 1
+ vCCount = (max(c[2] for c in decodedCells) + 1) if len(decodedCells) else 1
+ # still need to go through each separately
+ for (id_list, vRow, vCol) in decodedCells:
+ sheet_name = "%s %d" % (sheetPrefix, sheet)
+ min_row_count = rowCount * vRCount
+ min_col_count = colCount * vCCount
+ real_row = row*vRCount+vRow+1
+ real_col = col*vCCount+vCol+1
+ root_pipeline = \
+ assignPipelineCellLocations(root_pipeline, sheet_name,
+ real_row, real_col,
+ [id_list], min_row_count,
+ min_col_count)
+
+ modifiedPipelines.append(root_pipeline)
+ pipelinePositions.append((row, col, sheet))
+ return modifiedPipelines, pipelinePositions
+
+def assembleThumbnails(images, name, background='#000000'):
+ """ assembleThumbnails(images {(sheet, row, col):filename}, name: 'str',
+ background: str)"""
+
+ bgcolor = QtGui.QColor()
+ bgcolor.setNamedColor(background)
+ maxRow = max(i[0] for i in images) + 1
+ maxCol = max(i[1] for i in images) + 1
+ maxSheet = max(i[2] for i in images) + 1
+
+ w = h = 0
+ sizeX = sizeY = 0
+ sheets = []
+ painter = QtGui.QPainter()
+
+ # paint thumbnails on correct positions
+ for pos, filename in images.iteritems():
+ row, col, sheet = pos
+
+ if not os.path.exists(filename + '.png'):
+ continue
+ pixmap = QtGui.QPixmap(filename)
+
+ # use first pixmap to calculate spreadsheet size
+ # this assumes all pixmaps have same size
+ if not w:
+ w, h = pixmap.width(), pixmap.height()
+ sizeX = w*maxCol
+ sizeY = h*maxRow
+ # init sheets with correct background
+ for i in xrange(maxSheet):
+ _sheet = QtGui.QPixmap(sizeX, sizeY)
+ sheets.append(_sheet)
+ painter.begin(_sheet)
+ painter.fillRect(0, 0, sizeX, sizeY, bgcolor)
+ painter.end()
+
+ sheet = sheets[sheet]
+ painter.begin(sheet)
+ painter.drawPixmap(col*w, h*row, w, h, pixmap.scaled(w, h,
+ transformMode=QtCore.Qt.SmoothTransformation))
+ painter.end()
+ # draw spreadsheet grid
+ #painter.setPen(QtCore.Qt.black)
+ #for x in xrange(rows+1):
+ # painter.drawLine(x*h-0.01, 0, x*h-0.01, size)
+ #for y in xrange(cols+1):
+ # painter.drawLine(0, y*w-0.01, size, y*w-0.01)
+ #self.setIcon(0, QtGui.QIcon(pic))
+
+ for i in xrange(len(sheets)):
+ sheet = sheets[i]
+ filename = '%s_%s.png' % (name, i)
+ sheet.save(filename)
+
+class QVirtualCellWindow(QtGui.QFrame, QToolWindowInterface):
+ """
+ QVirtualCellWindow contains a caption, a virtual cell
+ configuration
+
+ """
+ def __init__(self, parent=None):
+ """ QVirtualCellWindow(parent: QWidget) -> QVirtualCellWindow
+ Initialize the widget
+
+ """
+ QtGui.QFrame.__init__(self, parent)
+ self.setFrameShape(QtGui.QFrame.StyledPanel)
+ self.setWindowTitle('Spreadsheet Virtual Cell')
+ vLayout = QtGui.QVBoxLayout(self)
+ vLayout.setMargin(2)
+ vLayout.setSpacing(0)
+ self.setLayout(vLayout)
+
+ label = QtGui.QLabel('Arrange the cell(s) below to construct'
+ ' a virtual cell')
+ font = QtGui.QFont(label.font())
+ label.setFont(font)
+ label.setWordWrap(True)
+ vLayout.addWidget(label)
+
+ hLayout = QtGui.QVBoxLayout()
+ hLayout.setMargin(0)
+ hLayout.setSpacing(0)
+ vLayout.addLayout(hLayout)
+ self.config = QVirtualCellConfiguration()
+ self.config.setSizePolicy(QtGui.QSizePolicy.Maximum,
+ QtGui.QSizePolicy.Maximum)
+ hLayout.addWidget(self.config)
+ hPadWidget = QtGui.QWidget()
+ hLayout.addWidget(hPadWidget)
+ hPadWidget.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Ignored)
+
+ vPadWidget = QtGui.QWidget()
+ vLayout.addWidget(vPadWidget)
+ vPadWidget.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+
+ self.inspector = PipelineInspector()
+ self.pipeline = None
+
+ def updateVirtualCell(self, pipeline):
+ """ updateVirtualCell(pipeline: QPipeline) -> None
+ Setup the virtual cells given a pipeline
+
+ """
+ self.pipeline = pipeline
+ if self.pipeline and self.pipeline.is_valid:
+ self.inspector.inspect_spreadsheet_cells(self.pipeline)
+ self.inspector.inspect_ambiguous_modules(self.pipeline)
+ cells = []
+ for id_list in self.inspector.spreadsheet_cells:
+ pipeline = self.pipeline
+ id_iter = iter(id_list)
+ m = pipeline.modules[id_iter.next()]
+ m_id = m.id
+ for m_id in id_iter:
+ pipeline = m.pipeline
+ m = pipeline.modules[m_id]
+
+ name = m.name
+ if len(id_list) == 1 and \
+ m_id in self.inspector.annotated_modules:
+ cells.append((name, self.inspector.annotated_modules[m_id]))
+ elif tuple(id_list) in self.inspector.annotated_modules:
+ cells.append((name, self.inspector.annotated_modules[ \
+ tuple(id_list)]))
+ else:
+ cells.append((name, -1))
+ self.config.configVirtualCells(cells)
+ else:
+
+ self.config.clear()
+
+ def getConfiguration(self):
+ """ getConfiguration() -> info (see below)
+ Return the current configuration of the virtual cell. The
+ information is:
+ info = (rowCount, columnCount,
+ {(type,id): (row, column)})
+ """
+ return self.config.getConfiguration()
+
+ def setConfiguration(self, info):
+ """ setConfiguration(info) -> None (see below)
+ Set the configuration of the virtual cell. The
+ information is:
+ info = {(type, id): (row, column)}
+ or
+ info = (rowCount, columnCount,
+ {(type, id): (row, column)})
+ The second form is allowed so that the output of
+ getConfiguration could be passed directly to
+ setConfiguration (the dimensions aren't used).
+ """
+ self.config.setConfiguration(info)
+
+class QVirtualCellConfiguration(QtGui.QWidget):
+ """
+ QVirtualCellConfiguration is a widget provide a virtual layout of
+ the spreadsheet cell. Given a number of cells want to layout, it
+ will let users interactively select where to put a cell in a table
+ layout to construct a virtual cell out of that.
+
+ """
+ def __init__(self, parent=None):
+ """ QVirtualCellConfiguration(parent: QWidget)
+ -> QVirtualCellConfiguration
+ Initialize the widget
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self.rowCount = 1
+ self.colCount = 1
+ gridLayout = QtGui.QGridLayout(self)
+ gridLayout.setSpacing(0)
+ self.setLayout(gridLayout)
+ label = QVirtualCellLabel('')
+ self.layout().addWidget(label, 0, 0, 1, 1, QtCore.Qt.AlignCenter)
+ self.cells = [[label]]
+ self.numCell = 1
+
+ def clear(self):
+ """ clear() -> None
+ Remove and delete all widgets in self.gridLayout
+
+ """
+ while True:
+ item = self.layout().takeAt(0)
+ if item==None:
+ break
+ self.disconnect(item.widget(),
+ QtCore.SIGNAL('finishedDragAndDrop'),
+ self.compressCells)
+ item.widget().deleteLater()
+ del item
+ self.cells = []
+ self.numCell = 0
+
+ def configVirtualCells(self, cells):
+ """ configVirtualCells(cells: [(str, int)]) -> None
+ Given a list of cell types and ids, this will clear old
+ configuration and start a fresh one.
+
+ """
+ self.clear()
+ self.numCell = len(cells)
+ row = []
+ for i in xrange(self.numCell):
+ label = QVirtualCellLabel(*cells[i])
+ row.append(label)
+ self.layout().addWidget(label, 0, i, 1, 1, QtCore.Qt.AlignCenter)
+ self.connect(label, QtCore.SIGNAL('finishedDragAndDrop'),
+ self.compressCells)
+ self.cells.append(row)
+
+ for r in xrange(self.numCell-1):
+ row = []
+ for c in xrange(self.numCell):
+ label = QVirtualCellLabel()
+ row.append(label)
+ self.layout().addWidget(label, r+1, c, 1, 1,
+ QtCore.Qt.AlignCenter)
+ self.connect(label, QtCore.SIGNAL('finishedDragAndDrop'),
+ self.compressCells)
+ self.cells.append(row)
+
+ def compressCells(self):
+ """ compressCells() -> None
+ Eliminate all blank cells
+
+ """
+ # Check row by row first
+ visibleRows = []
+ for r in xrange(self.numCell):
+ row = self.cells[r]
+ hasRealCell = [True for label in row if label.type]!=[]
+ if hasRealCell:
+ visibleRows.append(r)
+
+ # Move rows up
+ for i in xrange(len(visibleRows)):
+ for c in xrange(self.numCell):
+ label = self.cells[visibleRows[i]][c]
+ if label.type==None:
+ label.type = ''
+ self.cells[i][c].setCellData(label.type, label.id)
+
+ # Now check column by column
+ visibleCols = []
+ for c in xrange(self.numCell):
+ hasRealCell = [True
+ for r in xrange(self.numCell)
+ if self.cells[r][c].type]!=[]
+ if hasRealCell:
+ visibleCols.append(c)
+
+ # Move columns left
+ for i in xrange(len(visibleCols)):
+ for r in xrange(self.numCell):
+ label = self.cells[r][visibleCols[i]]
+ if label.type==None:
+ label.type = ''
+ self.cells[r][i].setCellData(label.type, label.id)
+
+ # Clear redundant rows
+ for i in xrange(self.numCell-len(visibleRows)):
+ for label in self.cells[i+len(visibleRows)]:
+ label.setCellData(None, -1)
+
+ # Clear redundant columns
+ for i in xrange(self.numCell-len(visibleCols)):
+ for r in xrange(self.numCell):
+ self.cells[r][i+len(visibleCols)].setCellData(None, -1)
+
+ def getConfiguration(self):
+ """ getConfiguration() -> info (see below)
+ Return the current configuration of the virtual cell. The
+ information is:
+ info = (rowCount, columnCount,
+ {(type, id): (row, column)})
+ """
+ result = {}
+ rCount = 0
+ cCount = 0
+ for r in xrange(self.numCell):
+ for c in xrange(self.numCell):
+ cell = self.cells[r][c]
+ if cell.type:
+ result[(cell.type, cell.id)] = (r, c)
+ if r+1>rCount: rCount = r+1
+ if c+1>cCount: cCount = c+1
+ return (rCount, cCount, result)
+
+ def setConfiguration(self, info):
+ """ setConfiguration(info) -> None (see below)
+ Set the configuration of the virtual cell. The
+ information is:
+ info = {(type, id): (row, column)}
+ or
+ info = (rowCount, columnCount,
+ {(type, id): (row, column)})
+ The second form is allowed so that the output of
+ getConfiguration could be passed directly to
+ setConfiguration (the dimensions aren't used).
+ """
+ if isinstance(info, dict):
+ result = info
+ else:
+ rCount, cCount, result = info
+ # Reset the layout of the virtual cell to default state
+ config_cells = []
+ for cell_type, cell_id in result.iterkeys():
+ config_cells.append((cell_type, cell_id))
+ self.configVirtualCells(config_cells)
+ # Unset the 0th row types/ids, since they're auto-set for the default state
+ for c in xrange(len(config_cells)):
+ self.cells[0][c].setCellData('', -1)
+ # Set the new types/ids
+ for cell_type, cell_id in config_cells:
+ row, col = result[(cell_type, cell_id)]
+ self.cells[row][col].setCellData(cell_type, cell_id)
+ # Compress to properly reset newly empty cells
+ self.compressCells()
+
+class QVirtualCellLabel(QtGui.QLabel):
+ """
+ QVirtualCellLabel is a label represent a cell inside a cell. It
+ has rounded shape with a caption text
+
+ """
+ def __init__(self, label=None, id=-1, parent=None):
+ """ QVirtualCellLabel(text: QString, id: int,
+ parent: QWidget)
+ -> QVirtualCellLabel
+ Construct the label image
+
+ """
+ QtGui.QLabel.__init__(self, parent)
+ self.setMargin(2)
+ self.cellType = None
+ self.setCellData(label, id)
+ self.setAcceptDrops(True)
+ self.setFrameStyle(QtGui.QFrame.Panel)
+ self.palette().setColor(QtGui.QPalette.WindowText,
+ CurrentTheme.HOVER_SELECT_COLOR)
+
+ def setCellData(self, cellType, cellId):
+ """ setCellData(cellType: str, cellId: int) -> None Create an
+ image based on the cell type and id. Then assign it to the
+ label. If cellType is None, the cell will be drawn with
+ transparent background. If cellType is '', the cell will be
+ drawn with the caption 'Empty'. Otherwise, the cell will be
+ drawn with white background containing cellType as caption and
+ a small rounded shape on the lower right painted with cellId
+
+ """
+ self.type = cellType
+ self.id = cellId
+ size = QtCore.QSize(*CurrentTheme.VIRTUAL_CELL_LABEL_SIZE)
+ image = QtGui.QImage(size.width() + 12,
+ size.height()+ 12,
+ QtGui.QImage.Format_ARGB32_Premultiplied)
+ image.fill(0)
+
+ font = QtGui.QFont()
+ font.setStyleStrategy(QtGui.QFont.ForceOutline)
+ painter = QtGui.QPainter()
+ painter.begin(image)
+ painter.setRenderHint(QtGui.QPainter.Antialiasing)
+ if self.type==None:
+ painter.setPen(QtCore.Qt.NoPen)
+ painter.setBrush(QtCore.Qt.NoBrush)
+ else:
+ if self.type=='':
+ painter.setPen(QtCore.Qt.gray)
+ painter.setBrush(QtCore.Qt.NoBrush)
+ else:
+ painter.setPen(QtCore.Qt.black)
+ painter.setBrush(QtCore.Qt.lightGray)
+ painter.drawRoundRect(QtCore.QRectF(0.5, 0.5, image.width()-1,
+ image.height()-1), 25, 25)
+
+ painter.setFont(font)
+ if self.type!=None:
+ painter.drawText(QtCore.QRect(QtCore.QPoint(6, 6), size),
+ QtCore.Qt.AlignCenter | QtCore.Qt.TextWrapAnywhere,
+ split_camel_case(self.type))
+ # Draw the lower right corner number if there is an id
+ if self.id>=0 and self.type:
+ QAnnotatedPipelineView.drawId(painter, image.rect(), self.id,
+ QtCore.Qt.AlignRight |
+ QtCore.Qt.AlignBottom)
+
+ painter.end()
+
+ self.setPixmap(QtGui.QPixmap.fromImage(image))
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+ Start the drag and drop when the user click on the label
+
+ """
+ if self.type:
+ mimeData = QtCore.QMimeData()
+ mimeData.cellData = (self.type, self.id)
+
+ drag = QtGui.QDrag(self)
+ drag.setMimeData(mimeData)
+ drag.setHotSpot(self.pixmap().rect().center())
+ drag.setPixmap(self.pixmap())
+
+ self.setCellData('', -1)
+
+ drag.start(QtCore.Qt.MoveAction)
+ if mimeData.cellData!=('', -1):
+ self.setCellData(*mimeData.cellData)
+ self.emit(QtCore.SIGNAL('finishedDragAndDrop'))
+
+ def dragEnterEvent(self, event):
+ """ dragEnterEvent(event: QDragEnterEvent) -> None
+ Set to accept drops from the other cell info
+
+ """
+ mimeData = event.mimeData()
+ if hasattr(mimeData, 'cellData'):
+ event.setDropAction(QtCore.Qt.MoveAction)
+ event.accept()
+ self.highlight()
+ else:
+ event.ignore()
+
+ def dropEvent(self, event):
+ """ dropEvent(event: QDragMoveEvent) -> None
+ Accept drop event to set the current cell
+
+ """
+ mimeData = event.mimeData()
+ if hasattr(mimeData, 'cellData'):
+ event.setDropAction(QtCore.Qt.MoveAction)
+ event.accept()
+ if (self.type,self.id)!=(mimeData.cellData[0],mimeData.cellData[1]):
+ oldCellData = (self.type, self.id)
+ self.setCellData(*mimeData.cellData)
+ mimeData.cellData = oldCellData
+ else:
+ event.ignore()
+ self.highlight(False)
+
+ def dragLeaveEvent(self, event):
+ """ dragLeaveEvent(event: QDragLeaveEvent) -> None
+ Un highlight the current cell
+
+ """
+ self.highlight(False)
+
+ def highlight(self, on=True):
+ """ highlight(on: bool) -> None
+ Highlight the cell as if being selected
+
+ """
+ if on:
+ self.setFrameStyle(QtGui.QFrame.Panel | QtGui.QFrame.Plain)
+ else:
+ self.setFrameStyle(QtGui.QFrame.Panel)
+
+###############################################################################
+
+import unittest
+
+class TestCamelCase(unittest.TestCase):
+ def test_simple(self):
+ self.assertEqual(split_camel_case('camelCaseH'), 'camel\nCase\nH')
+ self.assertEqual(split_camel_case('CamelCase'), 'Camel\nCase')
+
+ def test_long(self):
+ self.assertEqual(split_camel_case('parseHTML'), 'parse\nHTML')
+ self.assertEqual(split_camel_case('HTMLParser'), 'HTML\nParser')
+ self.assertEqual(split_camel_case('vHTMLParser'), 'v\nHTML\nParser')
+
+if __name__=="__main__":
+ import sys
+ import vistrails.gui.theme
+ app = QtGui.QApplication(sys.argv)
+ vistrails.gui.theme.initializeCurrentTheme()
+ vc = QVirtualCellConfiguration()
+ vc.configVirtualCells(['VTKCell', 'ImageViewerCell', 'RichTextCell'])
+ vc.show()
+ sys.exit(app.exec_())
diff --git a/vistrails/gui/pipeline_view.py b/vistrails/gui/pipeline_view.py
new file mode 100644
index 0000000..53e1214
--- /dev/null
+++ b/vistrails/gui/pipeline_view.py
@@ -0,0 +1,3405 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This is a QGraphicsView for pipeline view, it also holds different
+types of graphics items that are only available in the pipeline
+view. It only handles GUI-related actions, the rest of the
+functionalities are implemented at somewhere else,
+e.g. core.vistrails
+
+QGraphicsConnectionItem
+QGraphicsPortItem
+QGraphicsConfigureItem
+QGraphicsModuleItem
+QPipelineScene
+QPipelineView
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core import debug
+from vistrails.core.db.action import create_action
+from vistrails.core.system import systemType
+from vistrails.core.modules.module_registry import get_module_registry, \
+ ModuleRegistryException, MissingPackage
+from vistrails.core.system import get_vistrails_basic_pkg_id
+from vistrails.core.vistrail.location import Location
+from vistrails.core.vistrail.module import Module
+from vistrails.core.vistrail.port import PortEndPoint
+from vistrails.core.vistrail.port_spec import PortSpec
+from vistrails.core.interpreter.base import AbortExecution
+from vistrails.core.interpreter.default import get_default_interpreter
+from vistrails.gui.base_view import BaseView
+from vistrails.gui.controlflow_assist import QControlFlowAssistDialog
+from vistrails.gui.graphics_view import (QInteractiveGraphicsScene,
+ QInteractiveGraphicsView,
+ QGraphicsItemInterface)
+from vistrails.gui.module_info import QModuleInfo
+from vistrails.gui.module_palette import QModuleTreeWidget
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.utils import getBuilderWindow
+from vistrails.gui.variable_dropbox import QDragVariableLabel
+
+import copy
+import math
+import operator
+
+import vistrails.api
+import vistrails.gui.utils
+
+##############################################################################
+# 2008-06-24 cscheid
+#
+# - Profiling has shown that calling setPen and setBrush takes a longer
+# time than we expected. Watch out for that in the future.
+
+##############################################################################
+# QAbstractGraphicsPortItem
+
+class QAbstractGraphicsPortItem(QtGui.QAbstractGraphicsShapeItem):
+ """
+ QAbstractGraphicsPortItem represents a port shape drawing on top
+ (a child) of QGraphicsModuleItem, it must be implemented by a
+ specific qgraphicsitem type.
+
+ """
+ def __init__(self, port, x, y, ghosted=False, parent=None):
+ """ QAbstractGraphicsPortItem(port: PortSpec,
+ x: float,
+ y: float,
+ ghosted: bool,
+ parent: QGraphicsItem)
+ -> QAbstractGraphicsPortItem
+ Create the shape, initialize its pen and brush accordingly
+
+ """
+ # local lookups are faster than global lookups..
+ self._rect = CurrentTheme.PORT_RECT.translated(x,y)
+ QtGui.QAbstractGraphicsShapeItem.__init__(self, parent)
+ self.setZValue(1)
+ self.setFlags(QtGui.QGraphicsItem.ItemIsSelectable)
+ self.controller = None
+ self.port = port
+ self.dragging = False
+ self.tmp_connection_item = None
+
+ self.vistrail_vars = {}
+ self.removeVarActions = []
+
+ if port is not None:
+ self._min_conns = port.min_conns
+ self._max_conns = port.max_conns
+ self.optional = port.optional
+ else:
+ self._min_conns = 0
+ self._max_conns = -1
+ self.optional = False
+ self._connected = 0
+ self._selected = False
+ self.ghosted = ghosted
+ self.invalid = False
+ self.setPainterState()
+
+ self.updateToolTip()
+ self.updateActions()
+
+ def getRect(self):
+ return self._rect
+
+ def boundingRect(self):
+ return self._boundingRect
+
+ def computeBoundingRect(self):
+ halfpw = self.pen().widthF() / 2
+ self._boundingRect = self.getRect().adjusted(-halfpw, -halfpw,
+ halfpw, halfpw)
+
+ def getPosition(self):
+ return self.sceneBoundingRect().center()
+
+ def setPainterState(self):
+ if self._selected:
+ self._pen_color = CurrentTheme.PORT_PEN_COLOR_SELECTED
+ elif self.ghosted:
+ self._pen_color = CurrentTheme.PORT_PEN_COLOR_GHOSTED
+ # self.setPen(CurrentTheme.GHOSTED_PORT_PEN)
+ self.setBrush(CurrentTheme.GHOSTED_PORT_BRUSH)
+ elif self.invalid:
+ self._pen_color = CurrentTheme.PORT_PEN_COLOR_INVALID
+ # self.setPen(CurrentTheme.INVALID_PORT_PEN)
+ self.setBrush(CurrentTheme.INVALID_PORT_BRUSH)
+ elif self._max_conns >= 0 and self._connected >= self._max_conns:
+ self._pen_color = CurrentTheme.PORT_PEN_COLOR_FULL
+ self.setBrush(CurrentTheme.PORT_BRUSH)
+ else:
+ self._pen_color = CurrentTheme.PORT_PEN_COLOR_NORMAL
+ # self.setPen(CurrentTheme.PORT_PEN)
+ self.setBrush(CurrentTheme.PORT_BRUSH)
+ if self.brush() == CurrentTheme.PORT_BRUSH:
+ if self._connected > 0:
+ self.setBrush(CurrentTheme.PORT_CONNECTED_BRUSH)
+ elif self._connected < self._min_conns:
+ self.setBrush(CurrentTheme.PORT_MANDATORY_BRUSH)
+ if self._selected:
+ self._pen_width = CurrentTheme.PORT_PEN_WIDTH_SELECTED
+ elif self._min_conns > 0 and self._connected < self._min_conns:
+ self._pen_width = CurrentTheme.PORT_PEN_WIDTH_MANDATORY
+ else:
+ self._pen_width = CurrentTheme.PORT_PEN_WIDTH_NORMAL
+ self.setPen(CurrentTheme.PORT_PENS[(self._pen_color,
+ self._pen_width)])
+ self.computeBoundingRect()
+
+ def setGhosted(self, ghosted):
+ """ setGhosted(ghosted: True) -> None
+ Set this link to be ghosted or not
+
+ """
+ if self.ghosted <> ghosted:
+ self.ghosted = ghosted
+ self.setPainterState()
+
+ def setInvalid(self, invalid):
+ if self.invalid != invalid:
+ self.invalid = invalid
+ self.setPainterState()
+
+ def setOptional(self, optional):
+ if self.optional != optional:
+ self.optional = optional
+ self.setPainterState()
+
+ def setSelected(self, selected):
+ # QtGui.QAbstractGraphicsShapeItem.setSelected(self, selected)
+ if self._selected != selected:
+ self._selected = selected
+ self.setPainterState()
+
+ def disconnect(self):
+ self._connected -= 1
+ # print "disconnecting", self._connected, self._min_conns, self._max_conns
+ if self._connected == 0 or self._connected+1 == self._min_conns or \
+ (self._max_conns >= 0 and self._connected+1 == self._max_conns):
+ self.setPainterState()
+
+ def connect(self):
+ self._connected += 1
+ # print "connecting", self._connected, self._min_conns, self._max_conns
+ if self._connected == 1 or self._connected == self._min_conns or \
+ (self._max_conns >= 0 and self._connected == self._max_conns):
+ self.setPainterState()
+
+ def draw(self, painter, option, widget=None):
+ raise NotImplementedError("Must implement draw method")
+
+ def paint(self, painter, option, widget=None):
+ painter.setPen(self.pen())
+ painter.setBrush(self.brush())
+ self.draw(painter, option, widget)
+
+ def addVistrailVar(self, vistrail_var):
+ self.vistrail_vars[vistrail_var.uuid] = vistrail_var
+ self.updateActions()
+ self.updateToolTip()
+
+ def deleteVistrailVar(self, var_uuid):
+ del self.vistrail_vars[var_uuid]
+ self.updateActions()
+ self.updateToolTip()
+
+ def deleteAllVistrailVars(self):
+ self.vistrail_vars = {}
+ self.updateActions()
+ self.updateToolTip()
+
+ def updateToolTip(self):
+ tooltip = ""
+ if (self.port is not None and self.port.is_valid and
+ hasattr(self.port, 'toolTip')):
+ tooltip = self.port.toolTip()
+ for vistrail_var in self.vistrail_vars.itervalues():
+ tooltip += '\nConnected to vistrail var "%s"' % vistrail_var.name
+ self.setToolTip(tooltip)
+
+ def contextMenuEvent(self, event):
+ if len(self.removeVarActions) > 0:
+ menu = QtGui.QMenu()
+ for (action, _) in self.removeVarActions:
+ menu.addAction(action)
+ menu.exec_(event.screenPos())
+ event.accept()
+
+ def updateActions(self):
+ def gen_action(var_uuid):
+ def remove_action():
+ self.removeVar(var_uuid)
+ return remove_action
+
+ for (action, callback) in self.removeVarActions:
+ action.disconnect(action, QtCore.SIGNAL("triggered()"), callback)
+ self.removeVarActions = []
+ if len(self.vistrail_vars) > 1:
+ removeAllVarsAct = \
+ QtGui.QAction("Disconnect all vistrail variables",
+ self.scene())
+ removeAllVarsAct.setStatusTip("Disconnects all vistrail"
+ " variables from the port")
+ QtCore.QObject.connect(removeAllVarsAct,
+ QtCore.SIGNAL("triggered()"),
+ self.removeAllVars)
+ self.removeVarActions.append((removeAllVarsAct, self.removeAllVars))
+ for vistrail_var in sorted(self.vistrail_vars.itervalues(),
+ key=lambda x: x.name):
+ removeVarAction = QtGui.QAction('Disconnect vistrail var "%s"' % \
+ vistrail_var.name, self.scene())
+ removeVarAction.setStatusTip('Disconnects vistrail variable "%s"'
+ ' from the port' % vistrail_var.name)
+ callback = gen_action(vistrail_var.uuid)
+ QtCore.QObject.connect(removeVarAction,
+ QtCore.SIGNAL("triggered()"),
+ callback)
+ self.removeVarActions.append((removeVarAction, callback))
+
+ def removeVar(self, var_uuid):
+ (to_delete_modules, to_delete_conns) = \
+ self.controller.get_disconnect_vistrail_vars( \
+ self.parentItem().module, self.port.name, var_uuid)
+ for conn in to_delete_conns:
+ self.scene().remove_connection(conn.id)
+ for module in to_delete_modules:
+ self.scene().remove_module(module.id)
+ self.deleteVistrailVar(var_uuid)
+ self.controller.disconnect_vistrail_vars(to_delete_modules,
+ to_delete_conns)
+
+
+ def removeAllVars(self):
+ # Get all connections to vistrail variables for this port
+ (to_delete_modules, to_delete_conns) = \
+ self.controller.get_disconnect_vistrail_vars( \
+ self.parentItem().module, self.port.name)
+ for conn in to_delete_conns:
+ self.scene().remove_connection(conn.id)
+ for module in to_delete_modules:
+ self.scene().remove_module(module.id)
+ self.deleteAllVistrailVars()
+ self.controller.disconnect_vistrail_vars(to_delete_modules,
+ to_delete_conns)
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+ Prepare for dragging a connection
+
+ """
+ if (self.controller and event.buttons() & QtCore.Qt.LeftButton
+ and not self.scene().read_only_mode):
+ self.dragging = True
+ self.setSelected(True)
+ event.accept()
+ QtGui.QAbstractGraphicsShapeItem.mousePressEvent(self, event)
+
+ def mouseReleaseEvent(self, event):
+ """ mouseReleaseEvent(event: QMouseEvent) -> None
+ Apply the connection
+
+ """
+ if self.tmp_connection_item:
+ if self.tmp_connection_item.snapPortItem is not None:
+ self.scene().addConnectionFromTmp(self.tmp_connection_item,
+ self.parentItem().module,
+ self.port.type == "output")
+ self.tmp_connection_item.disconnect(True)
+ self.scene().removeItem(self.tmp_connection_item)
+ self.tmp_connection_item = None
+ self.dragging = False
+ self.setSelected(False)
+ QtGui.QAbstractGraphicsShapeItem.mouseReleaseEvent(self, event)
+
+ def mouseMoveEvent(self, event):
+ """ mouseMoveEvent(event: QMouseEvent) -> None
+ Change the connection
+
+ """
+ if self.dragging:
+ if not self.tmp_connection_item:
+ z_val = max(self.controller.current_pipeline.modules) + 1
+ self.tmp_connection_item = QGraphicsTmpConnItem(self, z_val,
+ True)
+ self.scene().addItem(self.tmp_connection_item)
+ self.tmp_connection_item.setCurrentPos(event.scenePos())
+ snapPort = None
+ snapModule = self.scene().findModuleUnder(event.scenePos())
+ converters = []
+ if snapModule and snapModule != self.parentItem():
+ if self.port.type == 'output':
+ portMatch = self.scene().findPortMatch(
+ [self], snapModule.inputPorts.values(),
+ fixed_out_pos=event.scenePos(),
+ allow_conversion=True, out_converters=converters)
+ if portMatch[1] is not None:
+ snapPort = portMatch[1]
+ elif self.port.type == 'input':
+ portMatch = self.scene().findPortMatch(
+ snapModule.outputPorts.values(), [self],
+ fixed_in_pos=event.scenePos(),
+ allow_conversion=True, out_converters=converters)
+ if portMatch[0] is not None:
+ snapPort = portMatch[0]
+ self.tmp_connection_item.setSnapPort(snapPort)
+ if snapPort:
+ tooltip = self.tmp_connection_item.snapPortItem.toolTip()
+ if converters:
+ tooltip = ('<strong>conversion required</strong><br/>\n'
+ '%s' % tooltip)
+ QtGui.QToolTip.showText(event.screenPos(), tooltip)
+ else:
+ QtGui.QToolTip.hideText()
+ self.tmp_connection_item.setConverting(snapPort and converters)
+ QtGui.QAbstractGraphicsShapeItem.mouseMoveEvent(self, event)
+
+ def findSnappedPort(self, pos):
+ """ findSnappedPort(pos: QPoint) -> Port
+ Search all ports of the module under mouse cursor (if any) to
+ find the closest matched port
+
+ """
+ # FIXME don't hardcode input/output strings...
+ snapModule = self.scene().findModuleUnder(pos)
+ if snapModule and snapModule!=self.parentItem():
+ if self.port.type == 'output':
+ return snapModule.getDestPort(pos, self.port)
+ elif self.port.type == 'input':
+ return snapModule.getSourcePort(pos, self.port)
+ else:
+ return None
+
+ def itemChange(self, change, value):
+ """ itemChange(change: GraphicsItemChange, value: value) -> value
+ Do not allow port to be selected
+
+ """
+ if change==QtGui.QGraphicsItem.ItemSelectedChange and value:
+ return False
+ return QtGui.QAbstractGraphicsShapeItem.itemChange(self, change, value)
+
+##############################################################################
+# QGraphicsPortItem
+
+class QGraphicsPortRectItem(QAbstractGraphicsPortItem):
+ def draw(self, painter, option, widget=None):
+ painter.drawRect(self.getRect())
+
+class QGraphicsPortEllipseItem(QAbstractGraphicsPortItem):
+ def draw(self, painter, option, widget=None):
+ painter.drawEllipse(self.getRect())
+
+class QGraphicsPortTriangleItem(QAbstractGraphicsPortItem):
+ def __init__(self, *args, **kwargs):
+ if 'angle' in kwargs:
+ angle = kwargs['angle']
+ del kwargs['angle']
+ else:
+ angle = 0
+
+ QAbstractGraphicsPortItem.__init__(self, *args, **kwargs)
+ angle = angle % 360
+ if angle not in set([0,90,180,270]):
+ raise ValueError("Triangle item limited to angles 0,90,180,270.")
+ rect = self.getRect()
+ if angle == 0 or angle == 180:
+ width = rect.width()
+ height = width * math.sqrt(3)/2.0
+ if height > rect.height():
+ height = rect.height()
+ width = height * 2.0/math.sqrt(3)
+ else:
+ height = rect.height()
+ width = height * math.sqrt(3)/2.0
+ if width > rect.width():
+ width = rect.width()
+ height = width * 2.0/math.sqrt(3)
+ left_x = (rect.width() - width)/2.0 + rect.x()
+ right_x = (rect.width() + width) / 2.0 + rect.x()
+ mid_x = rect.width() / 2.0 + rect.x()
+ top_y = (rect.height() - height)/2.0 + rect.y()
+ bot_y = (rect.height() + height)/2.0 + rect.y()
+ mid_y = rect.height() / 2.0 + rect.y()
+ if angle == 0:
+ self._polygon = QtGui.QPolygonF([QtCore.QPointF(left_x, bot_y),
+ QtCore.QPointF(mid_x, top_y),
+ QtCore.QPointF(right_x, bot_y)])
+ elif angle == 90:
+ self._polygon = QtGui.QPolygonF([QtCore.QPointF(left_x, bot_y),
+ QtCore.QPointF(left_x, top_y),
+ QtCore.QPointF(right_x, mid_y)])
+ elif angle == 180:
+ self._polygon = QtGui.QPolygonF([QtCore.QPointF(left_x, top_y),
+ QtCore.QPointF(right_x, top_y),
+ QtCore.QPointF(mid_x, bot_y)])
+ elif angle == 270:
+ self._polygon = QtGui.QPolygonF([QtCore.QPointF(left_x, mid_y),
+ QtCore.QPointF(right_x, top_y),
+ QtCore.QPointF(right_x, bot_y)])
+
+ def draw(self, painter, option, widget=None):
+ painter.drawConvexPolygon(self._polygon)
+
+class QGraphicsPortPolygonItem(QAbstractGraphicsPortItem):
+ def __init__(self, *args, **kwargs):
+ if 'points' in kwargs:
+ points = kwargs['points']
+ del kwargs['points']
+ else:
+ points = None
+ if points is None or len(points) < 3:
+ raise ValueError("Must have at least three points")
+ QAbstractGraphicsPortItem.__init__(self, *args, **kwargs)
+ rect = self.getRect()
+ new_points = []
+ for p in points:
+ if p[0] is None:
+ x = rect.x() + rect.width()
+ elif p[0] != 0 and p[0] != 1 and p[0] > 0 and p[0] < 1:
+ x = rect.x() + rect.width() * p[0]
+ elif p[0] < 0:
+ x = rect.x() + rect.width() + p[0]
+ else:
+ x = rect.x() + p[0]
+ if p[1] is None:
+ y = rect.y() + rect.height()
+ elif p[1] != 0 and p[1] != 1 and p[1] > 0 and p[1] < 1:
+ y = rect.y() + rect.height() * p[1]
+ elif p[1] < 0:
+ y = rect.y() + rect.height() + p[1]
+ else:
+ y = rect.y() + p[1]
+
+ print "adding point", x, y
+ if x < rect.x():
+ x = rect.x()
+ elif x > (rect.x() + rect.width()):
+ x = rect.x() + rect.width()
+ if y < rect.y():
+ y = rect.y()
+ elif y > (rect.y() + rect.height()):
+ y = rect.y() + rect.height()
+ print "Adding point", x, y
+ new_points.append(QtCore.QPointF(x,y))
+ self._polygon = QtGui.QPolygonF(new_points)
+
+ def draw(self, painter, option, widget=None):
+ painter.drawPolygon(self._polygon)
+
+class QGraphicsPortDiamondItem(QGraphicsPortPolygonItem):
+ def __init__(self, *args, **kwargs):
+ kwargs['points'] = [(0, 0.5), (0.5, 0.999999),
+ (0.999999, 0.5), (0.5, 0)]
+ QGraphicsPortPolygonItem.__init__(self, *args, **kwargs)
+
+################################################################################
+# QGraphicsConfigureItem
+
+class QGraphicsConfigureItem(QtGui.QGraphicsPolygonItem):
+ """
+ QGraphicsConfigureItem is a small triangle shape drawing on top (a child)
+ of QGraphicsModuleItem
+
+ """
+ def __init__(self, parent=None, scene=None):
+ """ QGraphicsConfigureItem(parent: QGraphicsItem, scene: QGraphicsScene)
+ -> QGraphicsConfigureItem
+ Create the shape, initialize its pen and brush accordingly
+
+ """
+ _pen = CurrentTheme.CONFIGURE_PEN
+ _brush = CurrentTheme.CONFIGURE_BRUSH
+ _shape = CurrentTheme.CONFIGURE_SHAPE
+ QtGui.QGraphicsPolygonItem.__init__(self, _shape, parent, scene)
+ self.setZValue(1)
+ self.setPen(_pen)
+ self.setBrush(_brush)
+ self.ghosted = False
+ self.controller = None
+ self.moduleId = None
+ self.is_breakpoint = False
+ self.createActions()
+
+ def setGhosted(self, ghosted):
+ """ setGhosted(ghosted: Bool) -> None
+ Set this link to be ghosted or not
+
+ """
+ if ghosted <> self.ghosted:
+ self.ghosted = ghosted
+ if ghosted:
+ self.setPen(CurrentTheme.GHOSTED_CONFIGURE_PEN)
+ self.setBrush(CurrentTheme.GHOSTED_CONFIGURE_BRUSH)
+ else:
+ self.setPen(CurrentTheme.CONFIGURE_PEN)
+ self.setBrush(CurrentTheme.CONFIGURE_BRUSH)
+
+ def setBreakpoint(self, breakpoint):
+ if self.is_breakpoint != breakpoint:
+ if breakpoint:
+ self.setBreakpointAct.setText("Remove Breakpoint")
+ self.setBreakpointAct.setStatusTip("Remove Breakpoint")
+ else:
+ self.setBreakpointAct.setText("Set Breakpoint")
+ self.setBreakpointAct.setStatusTip("Set Breakpoint")
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+ Open the context menu
+
+ """
+ self.scene().clearSelection()
+ self.parentItem().setSelected(True)
+ self.contextMenuEvent(event)
+ event.accept()
+ self.ungrabMouse()
+
+ def contextMenuEvent(self, event):
+ """contextMenuEvent(event: QGraphicsSceneContextMenuEvent) -> None
+ Captures context menu event.
+
+ """
+ module = self.controller.current_pipeline.modules[self.moduleId]
+ menu = QtGui.QMenu()
+ menu.addAction(self.configureAct)
+ menu.addAction(self.annotateAct)
+ menu.addAction(self.viewDocumentationAct)
+ menu.addAction(self.changeModuleLabelAct)
+ menu.addAction(self.setBreakpointAct)
+ menu.addAction(self.setWatchedAct)
+ menu.addAction(self.runModuleAct)
+ menu.addAction(self.setErrorAct)
+ if module.is_abstraction() and not module.is_latest_version():
+ menu.addAction(self.upgradeAbstractionAct)
+ menu.exec_(event.screenPos())
+
+ def createActions(self):
+ """ createActions() -> None
+ Create actions related to context menu
+
+ """
+ self.configureAct = QtGui.QAction("Edit Configuration\tCtrl+E", self.scene())
+ self.configureAct.setStatusTip("Edit the Configure of the module")
+ QtCore.QObject.connect(self.configureAct,
+ QtCore.SIGNAL("triggered()"),
+ self.configure)
+ self.annotateAct = QtGui.QAction("Annotate", self.scene())
+ self.annotateAct.setStatusTip("Annotate the module")
+ QtCore.QObject.connect(self.annotateAct,
+ QtCore.SIGNAL("triggered()"),
+ self.annotate)
+ self.viewDocumentationAct = QtGui.QAction("View Documentation", self.scene())
+ self.viewDocumentationAct.setStatusTip("View module documentation")
+ QtCore.QObject.connect(self.viewDocumentationAct,
+ QtCore.SIGNAL("triggered()"),
+ self.viewDocumentation)
+ self.changeModuleLabelAct = QtGui.QAction("Set Module Label...", self.scene())
+ self.changeModuleLabelAct.setStatusTip("Set or remove module label")
+ QtCore.QObject.connect(self.changeModuleLabelAct,
+ QtCore.SIGNAL("triggered()"),
+ self.changeModuleLabel)
+ self.setBreakpointAct = QtGui.QAction("Set Breakpoint", self.scene())
+ self.setBreakpointAct.setStatusTip("Set Breakpoint")
+ QtCore.QObject.connect(self.setBreakpointAct,
+ QtCore.SIGNAL("triggered()"),
+ self.set_breakpoint)
+ self.setWatchedAct = QtGui.QAction("Watch Module", self.scene())
+ self.setWatchedAct.setStatusTip("Watch Module")
+ QtCore.QObject.connect(self.setWatchedAct,
+ QtCore.SIGNAL("triggered()"),
+ self.set_watched)
+ self.runModuleAct = QtGui.QAction("Run this module", self.scene())
+ self.runModuleAct.setStatusTip("Run this module")
+ QtCore.QObject.connect(self.runModuleAct,
+ QtCore.SIGNAL("triggered()"),
+ self.run_module)
+ self.setErrorAct = QtGui.QAction("Show Error", self.scene())
+ self.setErrorAct.setStatusTip("Show Error")
+ QtCore.QObject.connect(self.setErrorAct,
+ QtCore.SIGNAL("triggered()"),
+ self.set_error)
+ self.upgradeAbstractionAct = QtGui.QAction("Upgrade Module", self.scene())
+ self.upgradeAbstractionAct.setStatusTip("Upgrade the subworkflow module")
+ QtCore.QObject.connect(self.upgradeAbstractionAct,
+ QtCore.SIGNAL("triggered()"),
+ self.upgradeAbstraction)
+
+ def run_module(self):
+ self.scene().parent().execute(target=self.moduleId)
+
+ def set_breakpoint(self):
+ """ set_breakpoint() -> None
+ Sets this module as a breakpoint for execution
+ """
+ if self.moduleId >= 0:
+ self.scene().toggle_breakpoint(self.moduleId)
+ self.setBreakpoint(not self.is_breakpoint)
+ debug = get_default_interpreter().debugger
+ if debug:
+ debug.update()
+
+ def set_watched(self):
+ if self.moduleId >= 0:
+ self.scene().toggle_watched(self.moduleId)
+ debug = get_default_interpreter().debugger
+ if debug:
+ debug.update()
+
+ def set_error(self):
+ if self.moduleId >= 0:
+ self.scene().print_error(self.moduleId)
+
+ def configure(self):
+ """ configure() -> None
+ Open the modal configuration window
+ """
+ if self.moduleId>=0:
+ self.scene().open_configure_window(self.moduleId)
+
+ def annotate(self):
+ """ anotate() -> None
+ Open the annotations window
+ """
+ if self.moduleId>=0:
+ self.scene().open_annotations_window(self.moduleId)
+
+ def viewDocumentation(self):
+ """ viewDocumentation() -> None
+ Show the documentation for the module
+ """
+ assert self.moduleId >= 0
+ self.scene().open_documentation_window(self.moduleId)
+
+ def changeModuleLabel(self):
+ """ changeModuleLabel() -> None
+ Show the module label configuration widget
+ """
+ if self.moduleId>=0:
+ self.scene().open_module_label_window(self.moduleId)
+
+ def upgradeAbstraction(self):
+ """ upgradeAbstraction() -> None
+ Upgrade the abstraction to the latest version
+ """
+ if self.moduleId>=0:
+ (connections_preserved, missing_ports) = self.controller.upgrade_abstraction_module(self.moduleId, test_only=True)
+ upgrade_fail_prompt = getattr(get_vistrails_configuration(), 'upgradeModuleFailPrompt', True)
+ do_upgrade = True
+ if not connections_preserved and upgrade_fail_prompt:
+ ports_msg = '\n'.join([" - %s port '%s'" % (p[0].capitalize(), p[1]) for p in missing_ports])
+ r = QtGui.QMessageBox.question(getBuilderWindow(), 'Modify Pipeline',
+ 'Upgrading this module will change the pipeline because the following ports no longer exist in the upgraded module:\n\n'
+ + ports_msg +
+ '\n\nIf you proceed, function calls or connections to these ports will no longer exist and the pipeline may not execute properly.\n\n'
+ 'Are you sure you want to proceed?',
+ QtGui.QMessageBox.Yes | QtGui.QMessageBox.No,
+ QtGui.QMessageBox.No)
+ do_upgrade = (r==QtGui.QMessageBox.Yes)
+ if do_upgrade:
+ self.controller.upgrade_abstraction_module(self.moduleId)
+ self.scene().setupScene(self.controller.current_pipeline)
+ self.controller.invalidate_version_tree()
+
+class QGraphicsTmpConnItem(QtGui.QGraphicsLineItem):
+ def __init__(self, startPortItem, zValue=1, alwaysDraw=False, parent=None):
+ QtGui.QGraphicsLineItem.__init__(self, parent)
+ self.startPortItem = startPortItem
+ self.setPen(CurrentTheme.CONNECTION_SELECTED_PEN)
+ self.setZValue(zValue)
+ self.snapPortItem = None
+ self.alwaysDraw = alwaysDraw
+ self.currentPos = None
+
+ def updateLine(self):
+ if self.startPortItem is not None:
+ if self.snapPortItem is not None:
+ self.prepareGeometryChange()
+ self.setLine(QtCore.QLineF(self.startPortItem.getPosition(),
+ self.snapPortItem.getPosition()))
+ return
+ elif self.alwaysDraw and self.currentPos is not None:
+ self.prepareGeometryChange()
+ self.setLine(QtCore.QLineF(self.startPortItem.getPosition(),
+ self.currentPos))
+ return
+ self.disconnect()
+
+ def setStartPort(self, port):
+ self.startPortItem = port
+ self.updateLine()
+
+ def setSnapPort(self, port):
+ self.snapPortItem = port
+ self.updateLine()
+
+ def setCurrentPos(self, pos):
+ self.currentPos = pos
+ self.updateLine()
+
+ def disconnect(self, override=False):
+ if (not self.alwaysDraw or override) and self.startPortItem:
+ self.startPortItem.setSelected(False)
+ if self.snapPortItem:
+ self.snapPortItem.setSelected(False)
+
+ def hide(self):
+ self.disconnect(True)
+ QtGui.QGraphicsLineItem.hide(self)
+
+ def setConverting(self, converting):
+ if converting:
+ self.setPen(CurrentTheme.CONNECTION_SELECTED_CONVERTING_PEN)
+ else:
+ self.setPen(CurrentTheme.CONNECTION_SELECTED_PEN)
+
+##############################################################################
+# QGraphicsConnectionItem
+
+class QGraphicsConnectionItem(QGraphicsItemInterface,
+ QtGui.QGraphicsPathItem):
+ """
+ QGraphicsConnectionItem is a connection shape connecting two port items
+
+ """
+
+ def __init__(self,
+ srcPortItem, dstPortItem,
+ srcModule, dstModule,
+ connection,
+ parent=None):
+ """ QGraphicsConnectionItem(
+ srcPortItem, dstPortItem: QAbstractGraphicsPortItem
+ srcModule, dstModule: QGraphicsModuleItem
+ connection: core.vistrail.connection.Connection
+ parent: QGraphicsItem
+ ) -> QGraphicsConnectionItem
+ Create the shape, initialize its pen and brush accordingly
+
+ """
+ path = self.create_path(srcPortItem.getPosition(),
+ dstPortItem.getPosition())
+ QtGui.QGraphicsPathItem.__init__(self, path, parent)
+ self.setFlags(QtGui.QGraphicsItem.ItemIsSelectable)
+ # Bump it slightly higher than the highest module
+ self.setZValue(max(srcModule.id,
+ dstModule.id) + 0.1)
+ self.srcPortItem = srcPortItem
+ self.dstPortItem = dstPortItem
+ self.connectionPen = CurrentTheme.CONNECTION_PEN
+ self.connectingModules = (srcModule, dstModule)
+ self.ghosted = False
+ self.connection = connection
+ self.id = connection.id
+ # Keep a flag for changing selection state during module selection
+ self.useSelectionRules = True
+
+ def setGhosted(self, ghosted):
+ """ setGhosted(ghosted: True) -> None
+ Set this link to be ghosted or not
+
+ """
+ self.ghosted = ghosted
+ if ghosted:
+ self.connectionPen = CurrentTheme.GHOSTED_CONNECTION_PEN
+ else:
+ self.connectionPen = CurrentTheme.CONNECTION_PEN
+
+ def set_custom_brush(self, brush):
+ self.connectionPen = QtGui.QPen(CurrentTheme.CONNECTION_PEN)
+ self.connectionPen.setBrush(brush)
+
+ def paint(self, painter, option, widget=None):
+ """ paint(painter: QPainter, option: QStyleOptionGraphicsItem,
+ widget: QWidget) -> None
+ Peform actual painting of the connection
+
+ """
+ if self.isSelected():
+ painter.setPen(CurrentTheme.CONNECTION_SELECTED_PEN)
+ else:
+ painter.setPen(self.connectionPen)
+ painter.drawPath(self.path())
+
+ def setupConnection(self, startPos, endPos):
+ path = self.create_path(startPos, endPos)
+ self.setPath(path)
+
+ def create_path(self, startPos, endPos):
+ self.startPos = startPos
+ self.endPos = endPos
+
+ dx = abs(self.endPos.x() - self.startPos.x())
+ dy = (self.startPos.y() - self.endPos.y())
+
+ # This is reasonably ugly logic to get reasonably nice
+ # curves. Here goes: we use a cubic bezier p0,p1,p2,p3, where:
+
+ # p0 is the source port center
+ # p3 is the destination port center
+ # p1 is a control point displaced vertically from p0
+ # p2 is a control point displaced vertically from p3
+
+ # We want most curves to be "straight": they shouldn't bend
+ # much. However, we want "inverted" connections (connections
+ # that go against the natural up-down flow) to bend a little
+ # as they go out of the ports. So the logic is:
+
+ # As dy/dx -> oo, we want the control point displacement to go
+ # to max(dy/2, m) (m is described below)
+
+ # As dy/dx -> 0, we want the control point displacement to go
+ # to m
+
+ # As dy/dx -> -oo, we want the control point displacement to go
+ # to max(-dy/2, m)
+
+ # On points away from infinity, we want some smooth transition.
+ # I'm using f(x) = 2/pi arctan (x) as the mapping, since:
+
+ # f(-oo) = -1
+ # f(0) = 0
+ # f(oo) = 1
+
+ # m is the monotonicity breakdown point: this is the minimum
+ # displacement when dy/dx is low
+ m = float(CurrentTheme.MODULE_LABEL_MARGIN[0]) * 3.0
+
+ # positive_d and negative_d are the displacements when dy/dx is
+ # large positive and large negative
+ positive_d = max(m/3.0, dy / 2.0)
+ negative_d = max(m/3.0, -dy / 4.0)
+
+ if dx == 0.0:
+ v = 0.0
+ else:
+ w = math.atan(dy/dx) * (2 / math.pi)
+ if w < 0:
+ w = -w
+ v = w * negative_d + (1.0 - w) * m
+ else:
+ v = w * positive_d + (1.0 - w) * m
+
+ displacement = QtCore.QPointF(0.0, v)
+ self._control_1 = startPos + displacement
+ # !!! MAC OS X BUG !!!
+ # the difference between startPos.y and control_1.y cannot be
+ # equal to the difference between control_2.y and endPos.y
+ self._control_2 = self.endPos - displacement + QtCore.QPointF(0.0, 1e-11)
+ # self._control_2 = endPos - displacement
+
+
+ path = QtGui.QPainterPath(self.startPos)
+ path.cubicTo(self._control_1, self._control_2, self.endPos)
+ return path
+
+ def itemChange(self, change, value):
+ """ itemChange(change: GraphicsItemChange, value: value) -> value
+ If modules are selected, only allow connections between
+ selected modules
+
+ """
+ # Selection rules to be used only when a module isn't forcing
+ # the update
+ if (change==QtGui.QGraphicsItem.ItemSelectedChange and
+ self.useSelectionRules):
+ # Check for a selected module
+ selectedItems = self.scene().selectedItems()
+ selectedModules = False
+ for item in selectedItems:
+ if isinstance(item, QGraphicsModuleItem):
+ selectedModules = True
+ break
+ if selectedModules:
+ # Don't allow a connection between selected
+ # modules to be deselected
+ if (self.connectingModules[0].isSelected() and
+ self.connectingModules[1].isSelected()):
+ if not value:
+ return True
+ # Don't allow a connection to be selected if
+ # it is not between selected modules
+ else:
+ if value:
+ return False
+ self.useSelectionRules = True
+ return QtGui.QGraphicsPathItem.itemChange(self, change, value)
+
+##############################################################################
+# QGraphicsModuleItem
+
+class QGraphicsModuleItem(QGraphicsItemInterface, QtGui.QGraphicsItem):
+ """
+ QGraphicsModuleItem knows how to draw a Vistrail Module into the
+ pipeline view. It is usually a rectangular shape with a bold text
+ in the center. It also has its input/output port shapes as its
+ children. Another remark is that connections are also children of
+ module shapes. Each connection belongs to its source module
+ ('output port' end of the connection)
+
+ """
+ def __init__(self, parent=None, scene=None):
+ """ QGraphicsModuleItem(parent: QGraphicsItem, scene: QGraphicsScene)
+ -> QGraphicsModuleItem
+ Create the shape, initialize its pen and brush accordingly
+
+ """
+ QtGui.QGraphicsItem.__init__(self, parent, scene)
+ self.paddedRect = QtCore.QRectF()
+ if QtCore.QT_VERSION >= 0x40600:
+ #Qt 4.6 specific flags
+ self.setFlags(QtGui.QGraphicsItem.ItemIsSelectable |
+ QtGui.QGraphicsItem.ItemIsMovable |
+ QtGui.QGraphicsItem.ItemSendsGeometryChanges)
+ else:
+ self.setFlags(QtGui.QGraphicsItem.ItemIsSelectable |
+ QtGui.QGraphicsItem.ItemIsMovable)
+ self.setZValue(0)
+ self.labelFont = CurrentTheme.MODULE_FONT
+ self.labelFontMetric = CurrentTheme.MODULE_FONT_METRIC
+ self.descFont = CurrentTheme.MODULE_DESC_FONT
+ self.descFontMetric = CurrentTheme.MODULE_DESC_FONT_METRIC
+ self.modulePen = CurrentTheme.MODULE_PEN
+ self.moduleBrush = CurrentTheme.MODULE_BRUSH
+ self.labelPen = CurrentTheme.MODULE_LABEL_PEN
+ self.customBrush = None
+ self.statusBrush = None
+ self.labelRect = QtCore.QRectF()
+ self.descRect = QtCore.QRectF()
+ self.abstRect = QtCore.QRectF()
+ self.id = -1
+ self.label = ''
+ self.description = ''
+ self.inputPorts = {}
+ self.outputPorts = {}
+ self.controller = None
+ self.module = None
+ self.ghosted = False
+ self.invalid = False
+ self._module_shape = None
+ self._original_module_shape = None
+ self._old_connection_ids = None
+ self.errorTrace = None
+ self.is_breakpoint = False
+ self._needs_state_updated = True
+ self.progress = 0.0
+ self.progressBrush = CurrentTheme.SUCCESS_MODULE_BRUSH
+ self.connectionItems = {}
+ self._cur_function_names = set()
+ self.handlePositionChanges = True
+
+ def moduleHasChanged(self, core_module):
+ def module_text_has_changed(m1, m2):
+ m1_has = '__desc__' in m1.db_annotations_key_index
+ if m1_has != ('__desc__' in m2.db_annotations_key_index):
+ return True
+ if (m1_has and
+ # m2_has, since m1_has and previous condition
+ m1.db_annotations_key_index['__desc__'].value.strip()!=
+ m2.db_annotations_key_index['__desc__'].value.strip()):
+ return True
+ return False
+
+ # def module_functions_have_changed(m1, m2):
+ # f1_names = set([f.name for f in m1.functions])
+ # f2_names = set([f.name for f in m2.functions])
+ # return (len(f1_names ^ f2_names) > 0)
+
+ if self.scenePos().x() != core_module.center.x or \
+ -self.scenePos().y() != core_module.center.y:
+ return True
+ elif module_text_has_changed(self.module, core_module):
+ return True
+ # elif module_functions_have_changed(self.module, core_module):
+ # return True
+ else:
+ # Check for changed ports
+ # _db_name because this shows up in the profile.
+ cip = sorted([x.key_no_id() for x in self.inputPorts])
+ cop = sorted([x.key_no_id() for x in self.outputPorts])
+ d = PortEndPoint.Destination
+ s = PortEndPoint.Source
+ pv = core_module.portVisible
+ new_ip = []
+ new_op = []
+ try:
+ new_ip = sorted([x.key_no_id()
+ for x in core_module.destinationPorts()
+ if (not x.optional or (d, x._db_name) in pv)])
+ new_op = sorted([x.key_no_id()
+ for x in core_module.sourcePorts()
+ if (not x.optional or (s, x._db_name) in pv)])
+ except ModuleRegistryException, e:
+ debug.critical("MODULE REGISTRY EXCEPTION: %s" % e)
+ if cip <> new_ip or cop <> new_op:
+ return True
+ return False
+
+ def moduleFunctionsHaveChanged(self, core_module):
+ m1 = self.module
+ m2 = core_module
+ f1_names = set([f.name for f in m1.functions])
+ f2_names = set([f.name for f in m2.functions])
+ return (len(f1_names ^ f2_names) > 0)
+
+ def update_function_ports(self, core_module=None):
+ if core_module is None:
+ core_module = self.module
+ added_functions = set(f.name for f in self.module.functions)
+ deleted_functions = set()
+ self._cur_function_names = copy.copy(added_functions)
+ else:
+ before_names = self._cur_function_names
+ after_names = set([f.name for f in core_module.functions])
+ # print "before_names:", before_names
+ # print "after_names:", after_names
+ added_functions = after_names - before_names
+ deleted_functions = before_names - after_names
+ self._cur_function_names = copy.copy(after_names)
+
+ # print "added_functions:", added_functions
+ # print "deleted_functions:", deleted_functions
+ if len(deleted_functions) > 0:
+ for function_name in deleted_functions:
+ try:
+ r_spec = self.module.get_port_spec(function_name, 'input')
+ f_spec = PortSpec(id=-1,
+ name=function_name,
+ type=PortSpec.port_type_map['input'],
+ sigstring=r_spec.sigstring)
+ item = self.getInputPortItem(f_spec)
+ if item is not None:
+ item.disconnect()
+ except:
+ # import traceback
+ # traceback.print_exc()
+ pass
+
+ if len(added_functions) > 0:
+ for function in core_module.functions:
+ if function.name not in added_functions:
+ continue
+ added_functions.remove(function.name)
+ f_spec = PortSpec(id=-1,
+ name=function.name,
+ type=PortSpec.port_type_map['input'],
+ sigstring=function.sigstring)
+ item = self.getInputPortItem(f_spec)
+ if item is not None:
+ item.connect()
+
+ self.module = core_module
+
+ def setProgress(self, progress):
+ self.progress = progress
+
+ def computeBoundingRect(self):
+ """ computeBoundingRect() -> None
+ Adjust the module size according to the text size
+
+ """
+ labelRect = self.labelFontMetric.boundingRect(self.label)
+ if self.description:
+ self.description = '(' + self.description + ')'
+ descRect = self.descFontMetric.boundingRect(self.description)
+ # adjust labelRect in case descRect is wider
+ labelRect = labelRect.united(descRect)
+ descRect.adjust(0, 0, 0, CurrentTheme.MODULE_PORT_MARGIN[3])
+ else:
+ descRect = QtCore.QRectF(0, 0, 0, 0)
+
+ labelRect.translate(-labelRect.center().x(), -labelRect.center().y())
+ self.paddedRect = QtCore.QRectF(
+ labelRect.adjusted(-CurrentTheme.MODULE_LABEL_MARGIN[0],
+ -CurrentTheme.MODULE_LABEL_MARGIN[1]
+ -descRect.height()/2,
+ CurrentTheme.MODULE_LABEL_MARGIN[2],
+ CurrentTheme.MODULE_LABEL_MARGIN[3]
+ +descRect.height()/2))
+
+ self.labelRect = QtCore.QRectF(
+ self.paddedRect.left(),
+ -(labelRect.height()+descRect.height())/2,
+ self.paddedRect.width(),
+ labelRect.height())
+ self.descRect = QtCore.QRectF(
+ self.paddedRect.left(),
+ self.labelRect.bottom(),
+ self.paddedRect.width(),
+ descRect.height())
+ self.abstRect = QtCore.QRectF(
+ self.paddedRect.left(),
+ -self.labelRect.top()-CurrentTheme.MODULE_PORT_MARGIN[3],
+ labelRect.left()-self.paddedRect.left(),
+ self.paddedRect.bottom()+self.labelRect.top())
+
+ def boundingRect(self):
+ """ boundingRect() -> QRectF
+ Returns the bounding box of the module
+
+ """
+ try:
+ r = self.paddedRect.adjusted(-2, -2, 2, 2)
+ except:
+ r = QtCore.QRectF()
+ return r
+
+ def setPainterState(self, is_selected=None):
+ if is_selected is None:
+ is_selected = self.isSelected()
+ if is_selected:
+ self.modulePen = CurrentTheme.MODULE_SELECTED_PEN
+ self.labelPen = CurrentTheme.MODULE_LABEL_SELECTED_PEN
+ elif self.is_breakpoint:
+ self.modulePen = CurrentTheme.BREAKPOINT_MODULE_PEN
+ self.labelPen = CurrentTheme.BREAKPOINT_MODULE_LABEL_PEN
+ elif self.ghosted:
+ self.modulePen = CurrentTheme.GHOSTED_MODULE_PEN
+ self.labelPen = CurrentTheme.GHOSTED_MODULE_LABEL_PEN
+ elif self.invalid:
+ self.modulePen = CurrentTheme.INVALID_MODULE_PEN
+ self.labelPen = CurrentTheme.INVALID_MODULE_LABEL_PEN
+ else:
+ self.labelPen = CurrentTheme.MODULE_LABEL_PEN
+ if self.module is not None and self.module.is_abstraction():
+ self.modulePen = CurrentTheme.ABSTRACTION_PEN
+ elif self.module is not None and self.module.is_group():
+ self.modulePen = CurrentTheme.GROUP_PEN
+ else:
+ self.modulePen = CurrentTheme.MODULE_PEN
+
+ if self.statusBrush:
+ self.moduleBrush = self.statusBrush
+ elif self.customBrush:
+ self.moduleBrush = self.customBrush
+ elif self.is_breakpoint:
+ self.moduleBrush = CurrentTheme.BREAKPOINT_MODULE_BRUSH
+ elif self.ghosted:
+ self.moduleBrush = CurrentTheme.GHOSTED_MODULE_BRUSH
+ elif self.invalid:
+ self.moduleBrush = CurrentTheme.INVALID_MODULE_BRUSH
+ else:
+ self.moduleBrush = CurrentTheme.MODULE_BRUSH
+
+ def setGhosted(self, ghosted):
+ """ setGhosted(ghosted: True) -> None
+ Set this link to be ghosted or not
+
+ """
+ if self.ghosted != ghosted:
+ self.ghosted = ghosted
+ for port in self.inputPorts.itervalues():
+ port.setGhosted(ghosted)
+ for port in self.outputPorts.itervalues():
+ port.setGhosted(ghosted)
+ self._needs_state_udpated = True
+
+# if ghosted:
+# self.modulePen = CurrentTheme.GHOSTED_MODULE_PEN
+# self.moduleBrush = CurrentTheme.GHOSTED_MODULE_BRUSH
+# self.labelPen = CurrentTheme.GHOSTED_MODULE_LABEL_PEN
+# else:
+# self.modulePen = CurrentTheme.MODULE_PEN
+# self.moduleBrush = CurrentTheme.MODULE_BRUSH
+# self.labelPen = CurrentTheme.MODULE_LABEL_PEN
+
+ def setInvalid(self, invalid):
+ if self.invalid != invalid:
+ self.invalid = invalid
+ for port in self.inputPorts.itervalues():
+ port.setInvalid(invalid)
+ for port in self.outputPorts.itervalues():
+ port.setInvalid(invalid)
+ self._needs_state_updated = True
+
+ def setBreakpoint(self, breakpoint):
+ if self.is_breakpoint != breakpoint:
+ self.is_breakpoint = breakpoint
+ if breakpoint:
+ self._original_module_shape = self._module_shape
+ self.set_module_shape(self.create_shape_from_fringe(
+ CurrentTheme.BREAKPOINT_FRINGE))
+ else:
+ self._module_shape = self._original_module_shape
+ self._needs_state_updated = True
+
+# if breakpoint:
+# self.modulePen = CurrentTheme.BREAKPOINT_MODULE_PEN
+# self.moduleBrush = CurrentTheme.BREAKPOINT_MODULE_BRUSH
+# self.labelPen = CurrentTheme.BREAKPOINT_MODULE_LABEL_PEN
+
+ def set_module_shape(self, module_shape=None):
+ self._module_shape = module_shape
+ if self._module_shape is not None:
+ self.paddedRect = self._module_shape.boundingRect()
+
+ def set_custom_brush(self, brush):
+ self.customBrush = brush
+ self._needs_state_updated = True
+
+ def paint(self, painter, option, widget=None):
+ """ paint(painter: QPainter, option: QStyleOptionGraphicsItem,
+ widget: QWidget) -> None
+ Peform actual painting of the module
+
+ """
+ if self.progress>0.0:
+ width = (self.progress-1.0)*self.paddedRect.width()
+ progressRect = self.paddedRect.adjusted(0, 0, width, 0)
+
+ if self._needs_state_updated:
+ self.setPainterState()
+ self._needs_state_updated = False
+
+ # draw module shape
+ painter.setBrush(self.moduleBrush)
+ painter.setPen(self.modulePen)
+ if self._module_shape:
+ painter.drawPolygon(self._module_shape)
+ if self.progress>0.0:
+ painter.setClipRect(progressRect)
+ painter.setBrush(self.progressBrush)
+ painter.drawPolygon(self._module_shape)
+ painter.setClipping(False)
+ painter.drawPolyline(self._module_shape)
+ else:
+ painter.fillRect(self.paddedRect, painter.brush())
+ if self.progress>0.0:
+ painter.fillRect(progressRect, self.progressBrush)
+ painter.setBrush(QtCore.Qt.NoBrush)
+ painter.drawRect(self.paddedRect)
+
+ # draw module labels
+ painter.setPen(self.labelPen)
+ painter.setFont(self.labelFont)
+ painter.drawText(self.labelRect, QtCore.Qt.AlignCenter, self.label)
+ if self.module.is_abstraction() and not self.module.is_latest_version():
+ painter.drawText(self.abstRect, QtCore.Qt.AlignCenter, '!')
+ if self.descRect:
+ painter.setFont(self.descFont)
+ painter.drawText(self.descRect, QtCore.Qt.AlignCenter,
+ self.description)
+
+ def paintToPixmap(self, scale_x, scale_y):
+ bounding_rect = self.paddedRect.adjusted(-6,-6,6,6)
+ center_x = (bounding_rect.width() / 2.0) #* m.m11()
+ center_y = (bounding_rect.height() / 2.0) #* m.m22()
+ pixmap = QtGui.QPixmap(int(bounding_rect.width() * scale_x),
+ int(bounding_rect.height() * scale_y))
+ pixmap.fill(QtGui.QColor(255,255,255,0))
+ painter = QtGui.QPainter(pixmap)
+ painter.setOpacity(0.5)
+ painter.scale(scale_x, scale_y)
+ painter.setRenderHints(QtGui.QPainter.Antialiasing |
+ QtGui.QPainter.SmoothPixmapTransform)
+ painter.translate(center_x, center_y)
+ self.paint(painter, QtGui.QStyleOptionGraphicsItem())
+ for port in self.inputPorts.itervalues():
+ m = port.matrix()
+ painter.save()
+ painter.translate(m.dx(), m.dy())
+ port.paint(painter, QtGui.QStyleOptionGraphicsItem())
+ painter.restore()
+ for port in self.outputPorts.itervalues():
+ m = port.matrix()
+ painter.save()
+ painter.translate(m.dx(), m.dy())
+ port.paint(painter, QtGui.QStyleOptionGraphicsItem())
+ painter.restore()
+ painter.end()
+ return pixmap
+
+ def adjustWidthToMin(self, minWidth):
+ """ adjustWidthToContain(minWidth: int) -> None
+ Resize the module width to at least be minWidth
+
+ """
+ if minWidth>self.paddedRect.width():
+ diff = minWidth - self.paddedRect.width() + 1
+ self.paddedRect.adjust(-diff/2, 0, diff/2, 0)
+
+ def setupModule(self, module):
+ """ setupModule(module: Module) -> None
+ Set up the item to reflect the info in 'module'
+
+ """
+ # Update module info and visual
+ self.id = module.id
+ self.setZValue(float(self.id))
+ self.module = module
+ self.center = copy.copy(module.center)
+ if '__desc__' in module.db_annotations_key_index:
+ self.label = module.get_annotation_by_key('__desc__').value.strip()
+ self.description = module.label
+ else:
+ self.label = module.label
+ self.description = ''
+ self.setToolTip(self.description)
+ self.computeBoundingRect()
+ self.setPos(module.center.x, -module.center.y)
+
+ # Check to see which ports will be shown on the screen
+ # setupModule is in a hotpath, performance-wise, which is the
+ # reason for the strange ._db_name lookup - we're
+ # avoiding property calls
+ inputPorts = []
+ self.inputPorts = {}
+ visibleOptionalInputPorts = []
+ self.optionalInputPorts = []
+
+ outputPorts = []
+ self.outputPorts = {}
+ visibleOptionalOutputPorts = []
+ self.optionalOutputPorts = []
+
+ error = None
+ if module.is_valid:
+ try:
+ d = PortEndPoint.Destination
+ for p in module.destinationPorts():
+ if not p.optional:
+ inputPorts.append(p)
+ # elif (d, p.name) in module.portVisible:
+ elif p.name in module.visible_input_ports:
+ visibleOptionalInputPorts.append(p)
+ else:
+ self.optionalInputPorts.append(p)
+ inputPorts += visibleOptionalInputPorts
+
+ s = PortEndPoint.Source
+ for p in module.sourcePorts():
+ if not p.optional:
+ outputPorts.append(p)
+ # elif (s, p.name) in module.portVisible:
+ elif p.name in module.visible_output_ports:
+ visibleOptionalOutputPorts.append(p)
+ else:
+ self.optionalOutputPorts.append(p)
+ outputPorts += visibleOptionalOutputPorts
+ except ModuleRegistryException, e:
+ error = e
+
+ # Local dictionary lookups are faster than global ones..
+ t = CurrentTheme
+ (mpm0, mpm1, mpm2, mpm3) = t.MODULE_PORT_MARGIN
+
+ # Adjust the width to fit all ports
+ maxPortCount = max(len(inputPorts), len(outputPorts))
+ minWidth = (mpm0 +
+ t.PORT_WIDTH*maxPortCount +
+ t.MODULE_PORT_SPACE*(maxPortCount-1) +
+ mpm2 +
+ t.MODULE_PORT_PADDED_SPACE)
+ self.adjustWidthToMin(minWidth)
+
+ self.nextInputPortPos = [self.paddedRect.x() + mpm0,
+ self.paddedRect.y() + mpm1]
+ self.nextOutputPortPos = [self.paddedRect.right() - \
+ t.PORT_WIDTH - mpm2,
+ self.paddedRect.bottom() - \
+ t.PORT_HEIGHT - mpm3]
+
+ # Update input ports
+ [x, y] = self.nextInputPortPos
+ for port in inputPorts:
+ self.inputPorts[port] = self.createPortItem(port, x, y)
+ x += t.PORT_WIDTH + t.MODULE_PORT_SPACE
+ self.nextInputPortPos = [x,y]
+
+ # Update output ports
+ [x, y] = self.nextOutputPortPos
+ for port in outputPorts:
+ self.outputPorts[port] = self.createPortItem(port, x, y)
+ x -= t.PORT_WIDTH + t.MODULE_PORT_SPACE
+ self.nextOutputPortPos = [x, y]
+
+ # Add a configure button
+ y = self.paddedRect.y() + mpm1
+ x = (self.paddedRect.right() - t.CONFIGURE_WIDTH
+ - mpm2)
+ self.createConfigureItem(x, y)
+
+ if module.is_valid:
+ try:
+ # update module color and shape
+ descriptor = module.module_descriptor
+ # c = registry.get_module_color(module.package, module.name,
+ # module.namespace)
+ c = descriptor.module_color()
+ if c:
+ ic = [int(cl*255) for cl in c]
+ b = QtGui.QBrush(QtGui.QColor(ic[0], ic[1], ic[2]))
+ self.set_custom_brush(b)
+ # fringe = registry.get_module_fringe(module.package,
+ # module.name,
+ # module.namespace)
+ fringe = descriptor.module_fringe()
+ if fringe:
+ self.set_module_shape(self.create_shape_from_fringe(fringe))
+ except ModuleRegistryException, e:
+ error = e
+
+ self.update_function_ports()
+ else:
+ self.setInvalid(True)
+
+ def create_shape_from_fringe(self, fringe):
+ left_fringe, right_fringe = fringe
+ if left_fringe[0] != (0.0, 0.0):
+ left_fringe = [(0.0, 0.0)] + left_fringe
+ if left_fringe[-1] != (0.0, 1.0):
+ left_fringe = left_fringe + [(0.0, 1.0)]
+
+ if right_fringe[0] != (0.0, 0.0):
+ right_fringe = [(0.0, 0.0)] + right_fringe
+ if right_fringe[-1] != (0.0, 1.0):
+ right_fringe = right_fringe + [(0.0, 1.0)]
+
+ P = QtCore.QPointF
+ module_shape = QtGui.QPolygonF()
+ height = self.paddedRect.height()
+
+ # right side of shape
+ for (px, py) in right_fringe:
+ p = P(px, -py)
+ p *= height
+ p += self.paddedRect.bottomRight()
+ module_shape.append(p)
+
+ # left side of shape
+ for (px, py) in reversed(left_fringe):
+ p = P(px, -py)
+ p *= height
+ p += self.paddedRect.bottomLeft()
+ module_shape.append(p)
+ # close polygon
+ module_shape.append(module_shape[0])
+ return module_shape
+
+ def createPortItem(self, port, x, y):
+ """ createPortItem(port: Port, x: int, y: int) -> QGraphicsPortItem
+ Create a item from the port spec
+
+ """
+ # pts = [(0,2),(0,-2), (2,None), (-2,None),
+ # (None,-2), (None,2), (-2,0), (2,0)]
+ # pts = [(0,0.2), (0, 0.8), (0.2, None), (0.8, None),
+ # (None, 0.8), (None, 0.2), (0.8,0), (0.2, 0)]
+ # portShape = QGraphicsPortPolygonItem(x, y, self.ghosted, self,
+ # port.optional, port.min_conns,
+ # port.max_conns, points=pts)
+ # portShape = QGraphicsPortTriangleItem(x, y, self.ghosted, self,
+ # port.optional, port.min_conns,
+ # port.max_conns, angle=0)
+ # portShape = QGraphicsPortDiamondItem(x, y, self.ghosted, self,
+ # port.optional, port.min_conns,
+ # port.max_conns)
+
+ port_klass = QGraphicsPortRectItem
+ kwargs = {}
+ shape = port.shape()
+ if shape is not None:
+ if isinstance(shape, basestring):
+ if shape.startswith("triangle"):
+ port_klass = QGraphicsPortTriangleItem
+ try:
+ kwargs['angle'] = int(shape[8:])
+ except:
+ kwargs['angle'] = 0
+ elif shape == "diamond":
+ port_klass = QGraphicsPortDiamondItem
+ elif shape == "circle" or shape == "ellipse":
+ port_klass = QGraphicsPortEllipseItem
+ else:
+ is_iterable = False
+ try:
+ shape.__iter__()
+ is_iterable = True
+ port_klass = QGraphicsPortPolygonItem
+ kwargs['points'] = shape
+ except:
+ pass
+
+ portShape = port_klass(port, x, y, self.ghosted, self, **kwargs)
+ # portShape = QGraphicsPortRectItem(port, x, y, self.ghosted, self)
+
+ portShape.controller = self.controller
+ portShape.port = port
+ if not port.is_valid:
+ portShape.setInvalid(True)
+ return portShape
+
+ def createConfigureItem(self, x, y):
+ """ createConfigureItem(x: int, y: int) -> QGraphicsConfigureItem
+ Create a item from the configure spec
+
+ """
+ if self.module.is_valid:
+ configureShape = QGraphicsConfigureItem(self, self.scene())
+ configureShape.controller = self.controller
+ configureShape.moduleId = self.id
+ configureShape.setGhosted(self.ghosted)
+ configureShape.setBreakpoint(self.module.is_breakpoint)
+ configureShape.translate(x, y)
+ return configureShape
+ return None
+
+ def getPortItem(self, port, port_dict=None):
+ # print 'looking for port', port.name, port.type, port_type
+
+ registry = get_module_registry()
+
+ # if we haven't validated pipeline, don't try to use the registry
+ if self.module.is_valid:
+ # check enabled ports
+ for (p, item) in port_dict.iteritems():
+ if registry.port_and_port_spec_match(port, p):
+ return item
+
+ # FIXME Raise Error!
+ # else not available for some reason, just draw port and raise error?
+ # can also decide to use Variant/Module types
+ # or use types from the signature
+ # port_descs = port.descriptors()
+
+ # first, check if we've already added the port
+ for (p, item) in port_dict.iteritems():
+ if (PortSpec.port_type_map.inverse[port.type] == p.type and
+ port.name == p.name and
+ port.sigstring == p.sigstring):
+ return item
+
+ return None
+
+ def buildPortItem(self, port, port_dict, optional_ports, visible_ports,
+ next_pos, next_op, default_sig):
+ """buildPortItem(port: Port,
+ port_dict: {PortSpec: QGraphicsPortItem},
+ optional_ports: [PortSpec],
+ visible_ports: set(string),
+ next_pos: [float, float],
+ next_op: operator (operator.add, operator.sub),
+ default_sig: str
+ ) -> QPointF
+ Return the scene position of a port matched 'port' in port_dict
+
+ """
+ registry = get_module_registry()
+
+ # check optional ports
+ if self.module.is_valid:
+ for p in optional_ports:
+ if registry.port_and_port_spec_match(port, p):
+ item = self.createPortItem(p, *next_pos)
+ visible_ports.add(port.name)
+ port_dict[p] = item
+ next_pos[0] = next_op(next_pos[0],
+ (CurrentTheme.PORT_WIDTH +
+ CurrentTheme.MODULE_PORT_SPACE))
+ return item
+
+ debug.log("PORT SIG:" + port.signature)
+ if not port.signature or port.signature == '()':
+ # or len(port_descs) == 0:
+ sigstring = default_sig
+ else:
+ sigstring = port.signature
+ port_type = PortSpec.port_type_map.inverse[port.type]
+ names = []
+ for sig in sigstring[1:-1].split(','):
+ k = sig.split(':', 2)
+ if len(k) < 2:
+ names.append(k[0])
+ else:
+ names.append(k[1])
+ short_sigstring = '(' + ','.join(names) + ')'
+ tooltip = "%s port %s\n%s" % (port_type.capitalize(),
+ port.name,
+ short_sigstring)
+ new_spec = PortSpec(id=-1,
+ name=port.name,
+ type=port_type,
+ sigstring=sigstring,
+ tooltip=tooltip,
+ optional=True)
+
+ item = self.createPortItem(new_spec, *next_pos)
+ item.setInvalid(True)
+ port_dict[new_spec] = item
+ next_pos[0] = next_op(next_pos[0],
+ (CurrentTheme.PORT_WIDTH +
+ CurrentTheme.MODULE_PORT_SPACE))
+ return item
+
+ def getInputPortItem(self, port, do_create=False):
+ item = self.getPortItem(port, self.inputPorts)
+ if not item and do_create:
+ item = self.buildPortItem(port,
+ self.inputPorts,
+ self.optionalInputPorts,
+ self.module.visible_input_ports,
+ self.nextInputPortPos,
+ operator.add,
+ '(%s:Variant)' % \
+ get_vistrails_basic_pkg_id())
+ return item
+
+ def getOutputPortItem(self, port, do_create=False):
+ item = self.getPortItem(port, self.outputPorts)
+ if not item and do_create:
+ item = self.buildPortItem(port,
+ self.outputPorts,
+ self.optionalOutputPorts,
+ self.module.visible_output_ports,
+ self.nextOutputPortPos,
+ operator.sub,
+ '(%s:Module)' % \
+ get_vistrails_basic_pkg_id())
+ return item
+
+ def addConnectionItem(self, item):
+ self.connectionItems[item.connection.id] = item
+
+ def removeConnectionItem(self, item):
+ if item.connectingModules[0].id == self.module.id:
+ if item.srcPortItem is not None:
+ item.srcPortItem.disconnect()
+ if item.connectingModules[1].id == self.module.id:
+ if item.dstPortItem is not None:
+ item.dstPortItem.disconnect()
+ del self.connectionItems[item.connection.id]
+
+ # returns a dictionary of (id, connection) key-value pairs!
+ def dependingConnectionItems(self):
+ return self.connectionItems
+
+ # this is a generator that yields (connection, is_source [bool]) pairs
+ def dependingConnectionItemsWithDir(self):
+ for item in self.connectionItems.itervalues():
+ if item.connectingModules[0].id == self.id:
+ yield (item, False)
+ else:
+ yield (item, True)
+
+ def itemChange(self, change, value):
+ """ itemChange(change: GraphicsItemChange, value: value) -> value
+ Capture move event to also move the connections. Also unselect any
+ connections between unselected modules
+
+ """
+ # Move connections with modules
+ if change==QtGui.QGraphicsItem.ItemPositionChange and \
+ self.handlePositionChanges:
+ oldPos = self.pos()
+ newPos = value
+ dis = newPos - oldPos
+ for connectionItem, s in self.dependingConnectionItemsWithDir():
+ # If both modules are selected, both of them will
+ # trigger itemChange events.
+
+ # If we just add 'dis' to both connection endpoints, we'll
+ # end up moving each endpoint twice.
+
+ # But we also don't want to call setupConnection twice on these
+ # connections, so we ignore one of the endpoint dependencies and
+ # perform the change on the other one
+
+ (srcModule, dstModule) = connectionItem.connectingModules
+ start_s = srcModule.isSelected()
+ end_s = dstModule.isSelected()
+
+ if start_s and end_s and s:
+ continue
+
+ start = connectionItem.startPos
+ end = connectionItem.endPos
+
+ if start_s: start += dis
+ if end_s: end += dis
+
+ connectionItem.prepareGeometryChange()
+ connectionItem.setupConnection(start, end)
+ # Do not allow lone connections to be selected with modules.
+ # Also autoselect connections between selected modules. Thus the
+ # selection is always the subgraph
+ elif change==QtGui.QGraphicsItem.ItemSelectedHasChanged:
+ # Unselect any connections between modules that are not selected
+ for item in self.scene().selectedItems():
+ if isinstance(item,QGraphicsConnectionItem):
+ (srcModule, dstModule) = item.connectingModules
+ if (not srcModule.isSelected() or
+ not dstModule.isSelected()):
+ item.useSelectionRules = False
+ item.setSelected(False)
+ # Handle connections from self
+ for item in self.dependingConnectionItems().itervalues():
+ # Select any connections between self and other selected modules
+ (srcModule, dstModule) = item.connectingModules
+ if value:
+ if (srcModule==self and dstModule.isSelected() or
+ dstModule==self and srcModule.isSelected()):
+ # Because we are setting a state variable in the
+ # connection, do not make the change unless it is
+ # actually going to be performed
+ if not item.isSelected():
+ item.useSelectionRules = False
+ item.setSelected(True)
+ # Unselect any connections between self and other modules
+ else:
+ if item.isSelected():
+ item.useSelectionRules = False
+ item.setSelected(False)
+ # Capture only selected modules + or - self for selection signal
+ selectedItems = [m for m in self.scene().selectedItems()
+ if isinstance(m, QGraphicsModuleItem)]
+ #print "selectedItems", selectedItems
+ selectedId = -1
+ if len(selectedItems)==1:
+ selectedId = selectedItems[0].id
+ self.scene().emit(QtCore.SIGNAL('moduleSelected'),
+ selectedId, selectedItems)
+ self._needs_state_updated = True
+ return QtGui.QGraphicsItem.itemChange(self, change, value)
+
+def choose_converter(converters, parent=None):
+ """Chooses a converter among a list.
+ """
+ if len(converters) == 1:
+ return converters[0]
+
+ class ConverterItem(QtGui.QListWidgetItem):
+ def __init__(self, converter):
+ QtGui.QListWidgetItem.__init__(self, converter.name)
+ self.converter = converter
+
+ dialog = QtGui.QDialog(parent)
+ dialog.setWindowTitle("Automatic conversion")
+ layout = QtGui.QVBoxLayout()
+
+ label = QtGui.QLabel(
+ "You are connecting two incompatible ports, however there are "
+ "matching Converter modules. Please choose which Converter should "
+ "be inserted on this connection:")
+ label.setWordWrap(True)
+ layout.addWidget(label)
+ list_widget = QtGui.QListWidget()
+ list_widget.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
+ for converter in sorted(converters, key=lambda c: c.name):
+ list_widget.addItem(ConverterItem(converter))
+ layout.addWidget(list_widget)
+
+ buttons = QtGui.QDialogButtonBox(
+ QtGui.QDialogButtonBox.Ok | QtGui.QDialogButtonBox.Cancel,
+ QtCore.Qt.Horizontal)
+ QtCore.QObject.connect(buttons, QtCore.SIGNAL('accepted()'),
+ dialog, QtCore.SLOT('accept()'))
+ QtCore.QObject.connect(buttons, QtCore.SIGNAL('rejected()'),
+ dialog, QtCore.SLOT('reject()'))
+ layout.addWidget(buttons)
+
+ ok = buttons.button(QtGui.QDialogButtonBox.Ok)
+ ok.setEnabled(False)
+ QtCore.QObject.connect(
+ list_widget, QtCore.SIGNAL('itemSelectionChanged()'),
+ lambda: ok.setEnabled(True))
+
+ dialog.setLayout(layout)
+ if dialog.exec_() == QtGui.QDialog.Accepted:
+ return list_widget.selectedItems()[0].converter
+ else:
+ return None
+
+##############################################################################
+# QPipelineScene
+
+class QPipelineScene(QInteractiveGraphicsScene):
+ """
+ QPipelineScene inherits from QInteractiveGraphicsScene to keep track of the
+ pipeline scenes, i.e. modules, connections, selection
+
+ """
+
+ def __init__(self, parent=None):
+ """ QPipelineScene(parent: QWidget) -> QPipelineScene
+ Initialize the graphics scene with no shapes
+
+ """
+ QInteractiveGraphicsScene.__init__(self, parent)
+ self.setBackgroundBrush(CurrentTheme.PIPELINE_VIEW_BACKGROUND_BRUSH)
+ self.setSceneRect(QtCore.QRectF(-5000, -5000, 10000, 10000))
+ self.controller = None
+ self.modules = {}
+ self.connections = {}
+ self.noUpdate = False
+ self.installEventFilter(self)
+ self.pipeline_tab = None
+ self._old_module_ids = set()
+ self._old_connection_ids = set()
+ self._var_selected_port = None
+ self.pipeline = None
+ self.read_only_mode = False
+ self.current_pipeline = None
+ self.current_version = -1
+ self.progress = None
+
+ self.tmp_module_item = None
+ self.tmp_input_conn = None
+ self.tmp_output_conn = None
+
+ def addModule(self, module, moduleBrush=None):
+ """ addModule(module: Module, moduleBrush: QBrush) -> QGraphicsModuleItem
+ Add a module to the scene
+
+ """
+ moduleItem = QGraphicsModuleItem(None)
+ if self.controller and self.controller.search:
+ moduleQuery = (self.controller.current_version, module)
+ matched = self.controller.search.matchModule(*moduleQuery)
+ moduleItem.setGhosted(not matched)
+ moduleItem.controller = self.controller
+ moduleItem.setupModule(module)
+ moduleItem.setBreakpoint(module.is_breakpoint)
+ if moduleBrush:
+ moduleItem.set_custom_brush(moduleBrush)
+ self.addItem(moduleItem)
+ self.modules[module.id] = moduleItem
+ self._old_module_ids.add(module.id)
+ # Hide vistrail variable modules
+ if module.is_vistrail_var():
+ moduleItem.hide()
+
+ return moduleItem
+
+ def addConnection(self, connection, connectionBrush=None):
+ """ addConnection(connection: Connection) -> QGraphicsConnectionItem
+ Add a connection to the scene
+
+ """
+ srcModule = self.modules[connection.source.moduleId]
+ dstModule = self.modules[connection.destination.moduleId]
+ srcPortItem = srcModule.getOutputPortItem(connection.source, True)
+ dstPortItem = dstModule.getInputPortItem(connection.destination, True)
+ connectionItem = QGraphicsConnectionItem(srcPortItem, dstPortItem,
+ srcModule, dstModule,
+ connection)
+ srcPortItem.connect()
+ dstPortItem.connect()
+ connectionItem.id = connection.id
+ connectionItem.connection = connection
+ if connectionBrush:
+ connectionItem.set_custom_brush(connectionBrush)
+ self.addItem(connectionItem)
+ self.connections[connection.id] = connectionItem
+ self._old_connection_ids.add(connection.id)
+ srcModule.addConnectionItem(connectionItem)
+ dstModule.addConnectionItem(connectionItem)
+ if srcModule.module.is_vistrail_var():
+ connectionItem.hide()
+ var_uuid = srcModule.module.get_vistrail_var()
+ dstPortItem.addVistrailVar(
+ self.controller.get_vistrail_variable_by_uuid(var_uuid))
+ return connectionItem
+
+ def selected_subgraph(self):
+ """Returns the subgraph containing the selected modules and its
+ mutual connections.
+
+ """
+ items = self.selectedItems()
+ modules = [x.id
+ for x in items
+ if isinstance(x, QGraphicsModuleItem)]
+ return self.controller.current_pipeline.graph.subgraph(modules)
+
+# def contextMenuEvent(self, event):
+# selectedItems = self.selectedItems()
+# if len(selectedItems) == 0:
+# return QInteractiveGraphicsScene.contextMenuEvent(self, event)
+# else:
+# self._context_menu.exec_(event.screenPos())
+
+ def clear(self):
+ """ clear() -> None
+ Clear the whole scene
+
+ """
+ self.modules = {}
+ self.connections = {}
+ self._old_module_ids = set()
+ self._old_connection_ids = set()
+ self.unselect_all()
+ self.clearItems()
+
+ def remove_module(self, m_id):
+ """remove_module(m_id): None
+
+ Removes module from scene, updating appropriate data structures.
+
+ """
+ core_module = self.modules[m_id].module
+ if not core_module.has_annotation_with_key('__vistrail_var__'):
+ self.removeItem(self.modules[m_id])
+ del self.modules[m_id]
+ self._old_module_ids.remove(m_id)
+
+ def remove_connection(self, c_id):
+ """remove_connection(c_id): None
+
+ Removes connection from scene, updating appropriate data structures.
+
+ """
+ # if c_id in self.connections:
+ connItem = self.connections[c_id]
+ (srcModule, dstModule) = connItem.connectingModules
+ srcModule.removeConnectionItem(connItem)
+ dstModule.removeConnectionItem(connItem)
+ if not srcModule.module.has_annotation_with_key('__vistrail_var__'):
+ self.removeItem(self.connections[c_id])
+ del self.connections[c_id]
+ self._old_connection_ids.remove(c_id)
+
+
+ def recreate_module(self, pipeline, m_id):
+ """recreate_module(pipeline, m_id): None
+
+ Recreates a module on the scene."""
+ selected = self.modules[m_id].isSelected()
+
+ depending_connections = \
+ [c_id for c_id in self.modules[m_id].dependingConnectionItems()]
+ # old_depending_connections = self.modules[m_id]._old_connection_ids
+
+ #when configuring a python source, maybe connections were deleted
+ # but are not in the current pipeline. So we need to check the depending
+ # connections of the module just before the configure.
+ for c_id in depending_connections:
+ self.remove_connection(c_id)
+
+ self.remove_module(m_id)
+
+ self.addModule(pipeline.modules[m_id])
+ for c_id in depending_connections:
+ # only add back those connections that are in the pipeline
+ if c_id in pipeline.connections:
+ self.addConnection(pipeline.connections[c_id])
+
+ if selected:
+ self.modules[m_id].setSelected(True)
+
+ def update_module_functions(self, pipeline, m_id):
+ self.modules[m_id].update_function_ports(pipeline.modules[m_id])
+
+ def setupScene(self, pipeline):
+ """ setupScene(pipeline: Pipeline) -> None
+ Construct the scene to view a pipeline
+
+ """
+ old_pipeline = self.pipeline
+ self.pipeline = pipeline
+
+ if self.noUpdate: return
+ if (pipeline is None or
+ (old_pipeline and not old_pipeline.is_valid) or
+ (pipeline and not pipeline.is_valid)):
+ # clear things
+ self.clear()
+ if not pipeline: return
+
+ needReset = len(self.items())==0
+ try:
+ new_modules = set(pipeline.modules)
+ modules_to_be_added = new_modules - self._old_module_ids
+ modules_to_be_deleted = self._old_module_ids - new_modules
+ common_modules = new_modules.intersection(self._old_module_ids)
+
+ new_connections = set(pipeline.connections)
+ connections_to_be_added = new_connections - self._old_connection_ids
+ connections_to_be_deleted = self._old_connection_ids - new_connections
+ common_connections = new_connections.intersection(self._old_connection_ids)
+
+ # Check if connections to be added require
+ # optional ports in modules to be visible
+ for c_id in connections_to_be_added:
+ connection = pipeline.connections[c_id]
+ smid = connection.source.moduleId
+ s = connection.source.spec
+ if s and s.optional:
+ smm = pipeline.modules[smid]
+ smm.portVisible.add((PortEndPoint.Source,s.name))
+ dmid = connection.destination.moduleId
+ d = connection.destination.spec
+ if d and d.optional:
+ dmm = pipeline.modules[dmid]
+ dmm.portVisible.add((PortEndPoint.Destination,d.name))
+
+ # remove old connection shapes
+ for c_id in connections_to_be_deleted:
+ self.remove_connection(c_id)
+ # remove old module shapes
+ for m_id in modules_to_be_deleted:
+ self.remove_module(m_id)
+
+ selected_modules = []
+ # create new module shapes
+ for m_id in modules_to_be_added:
+ self.addModule(pipeline.modules[m_id])
+ if self.modules[m_id].isSelected():
+ selected_modules.append(m_id)
+
+ moved = set()
+ # Update common modules
+ for m_id in common_modules:
+ tm_item = self.modules[m_id]
+ tm = tm_item.module
+ nm = pipeline.modules[m_id]
+ if tm_item.moduleHasChanged(nm):
+ self.recreate_module(pipeline, m_id)
+ elif tm_item.moduleFunctionsHaveChanged(nm):
+ tm_item.update_function_ports(pipeline.modules[m_id])
+ if tm_item.isSelected():
+ selected_modules.append(m_id)
+ if self.controller and self.controller.search:
+ moduleQuery = (self.controller.current_version, nm)
+ matched = \
+ self.controller.search.matchModule(*moduleQuery)
+ tm_item.setGhosted(not matched)
+ else:
+ tm_item.setGhosted(False)
+ tm_item.setBreakpoint(nm.is_breakpoint)
+
+ # create new connection shapes
+ for c_id in connections_to_be_added:
+ self.addConnection(pipeline.connections[c_id])
+
+ # Update common connections
+ for c_id in common_connections:
+ connection = pipeline.connections[c_id]
+ pip_c = self.connections[c_id]
+ pip_c.connectingModules = (self.modules[connection.source.moduleId],
+ self.modules[connection.destination.moduleId])
+ (srcModule, dstModule) = pip_c.connectingModules
+
+ self._old_module_ids = new_modules
+ self._old_connection_ids = new_connections
+ self.unselect_all()
+ self.reset_module_colors()
+ for m_id in selected_modules:
+ self.modules[m_id].setSelected(True)
+ except ModuleRegistryException, e:
+ import traceback
+ traceback.print_exc()
+ views = self.views()
+ assert len(views) > 0
+ debug.critical("Missing package/module",
+ ("Package '%s' is missing (or module '%s' is not present " +
+ "in that package)") % (e._identifier, e._name))
+ self.clear()
+ self.controller.change_selected_version(0)
+
+ if needReset and len(self.items())>0:
+ self.fitToAllViews()
+
+ def findModuleUnder(self, pos):
+ """ findModuleUnder(pos: QPoint) -> QGraphicsItem
+ Search all items under pos and return the top-most module item if any
+
+ """
+ for item in self.items(pos):
+ if isinstance(item, QGraphicsModuleItem):
+ return item
+ return None
+
+ def findModulesNear(self, pos, where_mult):
+ rect = QtCore.QRectF(pos.x()-50+25*where_mult,
+ (pos.y()-50) + 50*where_mult,
+ 100, 100)
+ ### code to display target rectangle
+ #
+ # if where_mult < 0:
+ # if not hasattr(self, 'tmp_rect'):
+ # self.tmp_rect = QtGui.QGraphicsRectItem(rect)
+ # self.tmp_rect.setPen(QtGui.QColor("red"))
+ # self.addItem(self.tmp_rect)
+ # else:
+ # self.tmp_rect.setRect(rect)
+ # else:
+ # if not hasattr(self, 'tmp_rect2'):
+ # self.tmp_rect2 = QtGui.QGraphicsRectItem(rect)
+ # self.tmp_rect2.setPen(QtGui.QColor("red"))
+ # self.addItem(self.tmp_rect2)
+ # else:
+ # self.tmp_rect2.setRect(rect)
+
+ closest_item = None
+ min_dis = None
+ for item in self.items(rect):
+ if isinstance(item, QGraphicsModuleItem) and item.isVisible():
+ vector = item.scenePos() - pos
+ dis = vector.x() * vector.x() + vector.y() * vector.y()
+ if min_dis is None or dis < min_dis:
+ min_dis = dis
+ closest_item = item
+ return closest_item
+
+ def findPortsNear(self, pos, where_mult):
+ width = self.tmp_module_item.paddedRect.width() + 50
+ rect = QtCore.QRectF(pos.x()-width/2+25*where_mult,
+ pos.y()-50 + 50*where_mult,
+ width, 100)
+ ### code to display target rectangle
+ #
+ # rect = QtCore.QRectF(pos.x()-50+25*where_mult,
+ # (pos.y()-50) + 50*where_mult,
+ # 100, 100)
+ # if where_mult < 0:
+ # if not hasattr(self, 'tmp_rect'):
+ # self.tmp_rect = QtGui.QGraphicsRectItem(rect)
+ # self.tmp_rect.setPen(QtGui.QColor("red"))
+ # self.addItem(self.tmp_rect)
+ # else:
+ # self.tmp_rect.setRect(rect)
+ # else:
+ # if not hasattr(self, 'tmp_rect2'):
+ # self.tmp_rect2 = QtGui.QGraphicsRectItem(rect)
+ # self.tmp_rect2.setPen(QtGui.QColor("red"))
+ # self.addItem(self.tmp_rect2)
+ # else:
+ # self.tmp_rect2.setRect(rect)
+
+ # if not hasattr(self, 'tmp_rect'):
+ # self.tmp_rect = QtGui.QGraphicsRectItem(rect)
+ # self.tmp_rect.setPen(QtGui.QColor("red"))
+ # self.addItem(self.tmp_rect)
+ # else:
+ # self.tmp_rect.setRect(rect)
+ near_ports = []
+ for item in self.items(rect):
+ if isinstance(item, QAbstractGraphicsPortItem) and item.isVisible():
+ near_ports.append(item)
+ return near_ports
+
+ def findPortMatch(self, output_ports, input_ports, x_trans=0,
+ fixed_out_pos=None, fixed_in_pos=None,
+ allow_conversion=False, out_converters=None):
+ """findPortMatch(output_ports: list(QAbstractGraphicsPortItem),
+ input_ports: list(QAbstractGraphicsPortItem),
+ x_trans: int,
+ fixed_out_pos: QPointF | None,
+ fixed_in_pos: QPointF | None,
+ ) -> tuple(QAbstractGraphicsPortItem,
+ QAbstractGraphicsPortItem)
+ findPortMatch returns a port from output_ports and a port from
+ input_ports where the ports are compatible and the distance
+ between these ports is minimal with respect to compatible
+ ports
+
+ If allow_conversion is True, we also search for ports that are not
+ directly matched but can be connected if a Converter module is used. In
+ this case, we extend the optional 'out_converters' list with the
+ possible Converters' ModuleDescriptors.
+ """
+
+ reg = get_module_registry()
+ result = (None, None)
+ min_dis = None
+ selected_convs = None
+ for o_item in output_ports:
+ if o_item.invalid:
+ continue
+ for i_item in input_ports:
+ if i_item.invalid:
+ continue
+ convs = []
+ if reg.ports_can_connect(o_item.port, i_item.port,
+ allow_conversion=True,
+ out_converters=convs):
+ if fixed_out_pos is not None:
+ out_pos = fixed_out_pos
+ else:
+ out_pos = o_item.getPosition()
+ if fixed_in_pos is not None:
+ in_pos = fixed_in_pos
+ else:
+ in_pos = i_item.getPosition()
+ vector = (out_pos - in_pos)
+ dis = (vector.x()-x_trans)*(vector.x()-x_trans) + \
+ vector.y()*vector.y()
+ if result[0] is None or dis < min_dis:
+ min_dis = dis
+ result = (o_item, i_item)
+ selected_convs = convs
+ if selected_convs and out_converters is not None:
+ out_converters.extend(selected_convs)
+ return result
+
+ def updateTmpConnection(self, pos, tmp_connection_item, tmp_module_ports,
+ where_mult, order_f):
+ near_ports = self.findPortsNear(pos, where_mult)
+ if len(near_ports) > 0:
+ (src_item, dst_item) = \
+ self.findPortMatch(*order_f([near_ports,tmp_module_ports]),
+ x_trans=-50)
+ if src_item is not None:
+ if tmp_connection_item is None:
+ tmp_connection_item = QGraphicsTmpConnItem(dst_item, 1000)
+ self.addItem(tmp_connection_item)
+ # We are assuming the first view is the real pipeline view
+ v = self.views()[0]
+ tmp_connection_item.setStartPort(dst_item)
+ tmp_connection_item.setSnapPort(src_item)
+ tooltip = "%s %s\n -> %s %s" % (src_item.port.name,
+ src_item.port.short_sigstring,
+ dst_item.port.name,
+ dst_item.port.short_sigstring)
+ QtGui.QToolTip.showText(v.mapToGlobal(
+ v.mapFromScene((dst_item.getPosition() +
+ src_item.getPosition())/2.0)),
+ tooltip)
+ tmp_connection_item.show()
+ return tmp_connection_item
+
+ if tmp_connection_item is not None:
+ tmp_connection_item.hide()
+ QtGui.QToolTip.hideText()
+ return tmp_connection_item
+
+ def updateTmpInputConnection(self, pos):
+ self.tmp_input_conn = \
+ self.updateTmpConnection(pos, self.tmp_input_conn,
+ self.tmp_module_item.inputPorts.values(),
+ -1, lambda x: x)
+
+ def updateTmpOutputConnection(self, pos):
+ self.tmp_output_conn = \
+ self.updateTmpConnection(pos, self.tmp_output_conn,
+ self.tmp_module_item.outputPorts.values(),
+ 1, reversed)
+
+ def dragEnterEvent(self, event):
+ """ dragEnterEvent(event: QDragEnterEvent) -> None
+ Set to accept drops from the module palette
+
+ """
+ if (self.controller and (
+ isinstance(event.source(), QModuleTreeWidget) or
+ isinstance(event.source(), QDragVariableLabel))):
+ data = event.mimeData()
+ if not self.read_only_mode:
+ if hasattr(data, 'items'):
+ if self.tmp_module_item and \
+ get_vistrails_configuration().check('autoConnect'):
+ self.tmp_module_item.setPos(event.scenePos())
+ self.updateTmpInputConnection(event.scenePos())
+ self.updateTmpOutputConnection(event.scenePos())
+ event.accept()
+ return
+ elif hasattr(data, 'variableData'):
+ event.accept()
+ return
+ # Ignore if not accepted and returned by this point
+ event.ignore()
+
+ def dragMoveEvent(self, event):
+ """ dragMoveEvent(event: QDragMoveEvent) -> None
+ Set to accept drag move event from the module palette
+
+ """
+ if (self.controller and (
+ isinstance(event.source(), QModuleTreeWidget) or
+ isinstance(event.source(), QDragVariableLabel))):
+ data = event.mimeData()
+ if hasattr(data, 'items') and not self.read_only_mode:
+ if self.tmp_module_item and \
+ get_vistrails_configuration().check('autoConnect'):
+ self.tmp_module_item.setPos(event.scenePos())
+ self.updateTmpInputConnection(event.scenePos())
+ self.updateTmpOutputConnection(event.scenePos())
+ event.accept()
+ return
+ elif hasattr(data, 'variableData'):
+ # Find nearest suitable port
+ snapModule = self.findModuleUnder(event.scenePos())
+ nearest_port = None
+ if snapModule is not None:
+ tmp_port = QAbstractGraphicsPortItem(None, 0, 0)
+ tmp_port.port = data.variableData[0]
+ (_, nearest_port) = \
+ self.findPortMatch([tmp_port], \
+ snapModule.inputPorts.values(), \
+ fixed_out_pos=event.scenePos())
+ del tmp_port
+ # Unhighlight previous nearest port
+ if self._var_selected_port is not None:
+ self._var_selected_port.setSelected(False)
+ self._var_selected_port = nearest_port
+ # Highlight new nearest port
+ if nearest_port is not None:
+ nearest_port.setSelected(True)
+ QtGui.QToolTip.showText(event.screenPos(), nearest_port.toolTip())
+ event.accept()
+ return
+ else:
+ QtGui.QToolTip.hideText()
+ # Ignore if not accepted and returned by this point
+ if not systemType in ['Darwin']:
+ # Workaround: On a Mac, dropEvent isn't called if dragMoveEvent is ignored
+ event.ignore()
+
+ def dragLeaveEvent(self, event):
+ if (self.controller and isinstance(event.source(), QModuleTreeWidget)):
+ if self.tmp_output_conn:
+ self.tmp_output_conn.disconnect(True)
+ self.removeItem(self.tmp_output_conn)
+ self.tmp_output_conn = None
+ if self.tmp_input_conn:
+ self.tmp_input_conn.disconnect(True)
+ self.removeItem(self.tmp_input_conn)
+ self.tmp_input_conn = None
+ elif isinstance(event.source(), QDragVariableLabel):
+ data = event.mimeData()
+ if hasattr(data, 'variableData'):
+ if self._var_selected_port is not None:
+ self._var_selected_port.setPen(CurrentTheme.PORT_PEN)
+ self._var_selected_port = None
+ event.accept()
+
+ def unselect_all(self):
+ self.clearSelection()
+ if self.pipeline_tab:
+ self.pipeline_tab.moduleSelected(-1)
+
+ def createConnectionFromTmp(self, tmp_connection_item, module,
+ start_is_src=False):
+ if start_is_src:
+ src_port_item = tmp_connection_item.startPortItem
+ dst_port_item = tmp_connection_item.snapPortItem
+ else:
+ src_port_item = tmp_connection_item.snapPortItem
+ dst_port_item = tmp_connection_item.startPortItem
+
+ if src_port_item.parentItem().id < 0 or start_is_src:
+ src_module_id = module.id
+ dst_module_id = dst_port_item.parentItem().id
+ else:
+ src_module_id = src_port_item.parentItem().id
+ dst_module_id = module.id
+
+ reg = get_module_registry()
+
+ if reg.ports_can_connect(src_port_item.port, dst_port_item.port):
+ # Direct connection
+ conn = self.controller.add_connection(src_module_id,
+ src_port_item.port,
+ dst_module_id,
+ dst_port_item.port)
+ self.addConnection(conn)
+ else:
+ # Add a converter module
+ converters = reg.get_converters(src_port_item.port.descriptors(),
+ dst_port_item.port.descriptors())
+ converter = choose_converter(converters)
+ if converter is None:
+ return
+
+ src_pos = src_port_item.getPosition()
+ dst_pos = dst_port_item.getPosition()
+ mod_x = (src_pos.x() + dst_pos.x())/2.0
+ mod_y = (src_pos.y() + dst_pos.y())/2.0
+ mod = self.controller.create_module_from_descriptor(
+ converter,
+ x=mod_x,
+ y=-mod_y)
+ conn1 = self.controller.create_connection(
+ self.controller.current_pipeline.modules[src_module_id],
+ src_port_item.port,
+ mod,
+ 'in_value')
+ conn2 = self.controller.create_connection(
+ mod, 'out_value',
+ self.controller.current_pipeline.modules[dst_module_id],
+ dst_port_item.port)
+ operations = [('add', mod), ('add', conn1), ('add', conn2)]
+
+ action = create_action(operations)
+ self.controller.add_new_action(action)
+ self.controller.perform_action(action)
+
+ graphics_mod = self.addModule(mod)
+ graphics_mod.update()
+ self.addConnection(conn1)
+ self.addConnection(conn2)
+
+ def addConnectionFromTmp(self, tmp_connection_item, module, start_is_src):
+ self.createConnectionFromTmp(tmp_connection_item, module, start_is_src)
+ self.reset_module_colors()
+ self._old_connection_ids = \
+ set(self.controller.current_pipeline.connections)
+ self._old_module_ids = set(self.controller.current_pipeline.modules)
+
+ def add_module_event(self, event, data):
+ """Adds a new module from a drop event"""
+ item = data.items[0]
+ self.controller.reset_pipeline_view = False
+ self.noUpdate = True
+ internal_version = -1L
+ reg = get_module_registry()
+ if reg.is_abstraction(item.descriptor):
+ internal_version = item.descriptor.module.internal_version
+ adder = self.controller.add_module_from_descriptor
+ module = adder(item.descriptor,
+ event.scenePos().x(),
+ -event.scenePos().y(),
+ internal_version)
+ self.reset_module_colors()
+ graphics_item = self.addModule(module)
+ graphics_item.update()
+
+ if get_vistrails_configuration().check('autoConnect'):
+ if self.tmp_output_conn is not None:
+ if self.tmp_output_conn.isVisible():
+ self.createConnectionFromTmp(self.tmp_output_conn, module)
+ self.tmp_output_conn.disconnect()
+ self.removeItem(self.tmp_output_conn)
+ self.tmp_output_conn = None
+
+ if self.tmp_input_conn is not None:
+ if self.tmp_input_conn.isVisible():
+ self.createConnectionFromTmp(self.tmp_input_conn, module)
+ self.tmp_input_conn.disconnect()
+ self.removeItem(self.tmp_input_conn)
+ self.tmp_input_conn = None
+
+ self.unselect_all()
+ # Change selection
+ graphics_item.setSelected(True)
+
+ # controller changed pipeline: update ids
+ self._old_connection_ids = \
+ set(self.controller.current_pipeline.connections)
+ self._old_module_ids = set(self.controller.current_pipeline.modules)
+
+ # We are assuming the first view is the real pipeline view
+ self.views()[0].setFocus()
+
+ self.noUpdate = False
+
+ def add_tmp_module(self, desc):
+ self.noUpdate = True
+ self.tmp_module_item = QGraphicsModuleItem(None)
+ module = Module(id=-1,
+ name=desc.name,
+ package=desc.identifier,
+ location=Location(id=-1,x=0.0,y=0.0),
+ namespace=desc.namespace,
+ )
+ module.is_valid = True
+ self.tmp_module_item.setupModule(module)
+ self.addItem(self.tmp_module_item)
+ self.tmp_module_item.hide()
+ self.tmp_module_item.update()
+ self.noUpdate = False
+
+ return self.tmp_module_item
+
+ def delete_tmp_module(self):
+ if self.tmp_module_item is not None:
+ self.removeItem(self.tmp_module_item)
+ self.tmp_module_item = None
+
+ def dropEvent(self, event):
+ """ dropEvent(event: QDragMoveEvent) -> None
+ Accept drop event to add a new module
+
+ """
+ if (self.controller and (
+ isinstance(event.source(), QModuleTreeWidget) or
+ isinstance(event.source(), QDragVariableLabel))):
+ data = event.mimeData()
+ if hasattr(data, 'items') and not self.read_only_mode and \
+ self.controller.current_pipeline == self.current_pipeline:
+ assert len(data.items) == 1
+ self.add_module_event(event, data)
+ event.accept()
+ return
+ elif hasattr(data, 'variableData'):
+ if self._var_selected_port is not None:
+ # Unhighlight selected port and get var data
+ self._var_selected_port.setSelected(False)
+ output_portspec = data.variableData[0]
+ var_uuid = data.variableData[1]
+ var_name = data.variableData[2]
+ descriptor = output_portspec.descriptors()[0]
+ input_module = self._var_selected_port.parentItem().module
+ #input_portspec = self._var_selected_port.port
+ input_port = self._var_selected_port.port.name
+ m_pos_x = event.scenePos().x()
+ m_pos_y = -event.scenePos().y()
+
+ (new_conn, new_module) = \
+ self.controller.connect_vistrail_var(descriptor,
+ var_uuid,
+ input_module,
+ input_port,
+ m_pos_x,
+ m_pos_y)
+ if new_module is not None:
+ self.addModule(new_module)
+ if new_conn is not None:
+ self.addConnection(new_conn)
+ else:
+ msg = 'Vistrail Variable "%s" is already connected' \
+ ' to this port.' % var_name
+ QtGui.QMessageBox.information(None,
+ "Already Connected",
+ msg)
+ event.accept()
+ return
+ # Ignore if not accepted and returned by this point
+ event.ignore()
+
+ def delete_selected_items(self):
+ selectedItems = self.selectedItems()
+ if len(selectedItems)>0:
+ modules = []
+ module_ids = []
+ connection_ids = []
+ for it in selectedItems:
+ if isinstance(it, QGraphicsModuleItem):
+ modules.append(it)
+ module_ids.append(it.id)
+ elif isinstance(it, QGraphicsConnectionItem):
+ connection_ids.append(it.id)
+ if len(modules)>0:
+ self.noUpdate = True
+ dep_connection_ids = set()
+ for m in modules:
+ dep_connection_ids.update(
+ m.dependingConnectionItems().iterkeys())
+ # remove_connection updates the dependency list on the
+ # other side of connections, cannot use removeItem
+ for c_id in dep_connection_ids:
+ self.remove_connection(c_id)
+ for m_id in module_ids:
+ self.remove_module(m_id)
+ self.controller.delete_module_list(module_ids)
+ self.updateSceneBoundingRect()
+ self.reset_module_colors()
+ self.update()
+ self.noUpdate = False
+ # Notify that no module is selected
+ self.emit(QtCore.SIGNAL('moduleSelected'),
+ -1, selectedItems)
+ # Current pipeline changed, so we need to change the
+ # _old_*_ids. However, remove_module takes care of
+ # module ids, and the for loop above takes care of
+ # connection ids. So we don't need to call anything.
+ else:
+ for c_id in connection_ids:
+ self.remove_connection(c_id)
+ self.controller.reset_pipeline_view = False
+ self.controller.delete_connection_list(connection_ids)
+ self.reset_module_colors()
+ self.controller.reset_pipeline_view = True
+ # Current pipeline changed, so we need to change the
+ # _old_connection_ids. However, remove_connection
+ # above takes care of connection ids, so we don't need
+ # to call anything.
+
+ def keyPressEvent(self, event):
+ """ keyPressEvent(event: QKeyEvent) -> None
+ Capture 'Del', 'Backspace' for deleting modules.
+ Ctrl+C, Ctrl+V, Ctrl+A for copy, paste and select all
+
+ """
+ if (self.controller and
+ event.key() in [QtCore.Qt.Key_Backspace, QtCore.Qt.Key_Delete]):
+ if not self.read_only_mode:
+ self.delete_selected_items()
+ else:
+ QInteractiveGraphicsScene.keyPressEvent(self, event)
+ # super(QPipelineScene, self).keyPressEvent(event)
+
+ def get_selected_module_ids(self):
+ module_ids = []
+ for item in self.selectedItems():
+ if isinstance(item, QGraphicsModuleItem):
+ module_ids.append(item.module.id)
+ return module_ids
+
+ def get_selected_item_ids(self, dangling=False):
+ """get_selected_item_ids( self, dangling: bool) ->
+ (module_ids : list, connection_ids : list)
+ returns the list of selected modules and the connections
+ between them. If dangling is true, it includes connections
+ for which only one end point is selected, otherwise it only
+ includes connectiosn where both end points are selected
+
+ """
+ selectedItems = self.selectedItems()
+ if len(selectedItems) <= 0:
+ return None
+
+ connection_ids = {}
+ module_ids = {}
+ for item in selectedItems:
+ if isinstance(item, QGraphicsModuleItem):
+ module_ids[item.module.id] = 1
+ for item in selectedItems:
+ if isinstance(item, QGraphicsModuleItem):
+ for connItem in item.dependingConnectionItems().itervalues():
+ conn = connItem.connection
+ if not conn.id in connection_ids:
+ source_exists = conn.sourceId in module_ids
+ dest_exists = conn.destinationId in module_ids
+ if source_exists and dest_exists:
+ connection_ids[conn.id] = 1
+ elif dangling and (source_exists or dest_exists):
+ connection_ids[conn.id] = 1
+ return (module_ids.keys(), connection_ids.keys())
+
+ def group(self):
+ items = self.get_selected_item_ids(True)
+ if items is not None:
+ # self.clear()
+ self.controller.create_group(items[0], items[1])
+ self.setupScene(self.controller.current_pipeline)
+
+ def ungroup(self):
+ items = self.get_selected_item_ids(True)
+ if items is not None:
+ # self.clear()
+ self.controller.ungroup_set(items[0])
+ self.setupScene(self.controller.current_pipeline)
+
+ def layout(self):
+ if len(self.items()) <= 0:
+ return
+
+ def _func(module):
+ rect = self.modules[module.shortname].boundingRect()
+ return (rect.width(), rect.height())
+
+ selected = [self.modules[i].module for i in self.get_selected_module_ids()]
+ self.controller.layout_modules(selected,
+ module_size_func=_func)
+
+ def makeAbstraction(self):
+ items = self.get_selected_item_ids(True)
+ if items is not None:
+ # self.clear()
+ self.controller.create_abstraction_with_prompt(items[0], items[1])
+ self.setupScene(self.controller.current_pipeline)
+
+ def convertToAbstraction(self):
+ items = self.get_selected_item_ids(False)
+ if items is not None:
+ # self.clear()
+ self.controller.create_abstractions_from_groups(items[0])
+ self.setupScene(self.controller.current_pipeline)
+
+ def importAbstraction(self):
+ items = self.get_selected_item_ids(False)
+ if items is not None:
+ self.controller.import_abstractions(items[0])
+
+ def exportAbstraction(self):
+ items = self.get_selected_item_ids(False)
+ if items is not None:
+ self.controller.export_abstractions(items[0])
+
+ def copySelection(self):
+ """ copySelection() -> None
+ Copy the current selected modules into clipboard
+
+ """
+ items = self.get_selected_item_ids(False)
+ if items is not None:
+ cb = QtGui.QApplication.clipboard()
+ text = self.controller.copy_modules_and_connections(items[0],items[1])
+ cb.setText(text)
+
+ def pasteFromClipboard(self, center):
+ """ pasteFromClipboard(center: (float, float)) -> None
+ Paste modules/connections from the clipboard into this pipeline view
+
+ """
+ if self.controller and not self.read_only_mode:
+ cb = QtGui.QApplication.clipboard()
+ text = cb.text()
+ if text=='' or not text.startswith("<workflow"): return
+ ids = self.controller.paste_modules_and_connections(text, center)
+ self.setupScene(self.controller.current_pipeline)
+ self.reset_module_colors()
+ if len(ids) > 0:
+ self.unselect_all()
+ for moduleId in ids:
+ self.modules[moduleId].setSelected(True)
+
+ def event(self, e):
+ """ event(e: QEvent) -> None
+ Process the set module color events
+
+ """
+ if e.type()==QModuleStatusEvent.TYPE:
+ if e.moduleId>=0:
+ item = self.modules.get(e.moduleId, None)
+ if not item:
+ return True
+ item.setToolTip(e.toolTip)
+ item.errorTrace = e.errorTrace
+ statusMap = {
+ 0: CurrentTheme.SUCCESS_MODULE_BRUSH,
+ 1: CurrentTheme.ERROR_MODULE_BRUSH,
+ 2: CurrentTheme.NOT_EXECUTED_MODULE_BRUSH,
+ 3: CurrentTheme.ACTIVE_MODULE_BRUSH,
+ 4: CurrentTheme.COMPUTING_MODULE_BRUSH,
+ 6: CurrentTheme.PERSISTENT_MODULE_BRUSH,
+ 7: CurrentTheme.SUSPENDED_MODULE_BRUSH,
+ }
+ item.setProgress(e.progress)
+ if item.statusBrush is not None and e.status == 3:
+ # do not update, already in cache
+ pass
+ elif e.status in statusMap:
+ item.statusBrush = statusMap[e.status]
+ else:
+ item.statusBrush = None
+ item._needs_state_updated = True
+ item.update()
+ return True
+ return QInteractiveGraphicsScene.event(self, e)
+
+ def selectAll(self):
+ """ selectAll() -> None
+ Select all module items in the scene
+
+ """
+ for item in self.items():
+ if isinstance(item, QGraphicsModuleItem) or \
+ isinstance(item, QGraphicsConnectionItem):
+ item.setSelected(True)
+
+ def open_configure_window(self, id):
+ """ open_configure_window(int) -> None
+ Open the modal configuration window for module with given id
+ """
+ from vistrails.gui.vistrails_window import _app
+ _app.configure_module()
+
+ def perform_configure_done_actions(self, module_id):
+ if self.controller:
+ self.reset_module_colors()
+ self.flushMoveActions()
+ self.recreate_module(self.controller.current_pipeline, module_id)
+
+ def open_documentation_window(self, id):
+ """ open_documentation_window(int) -> None
+ Opens the modal module documentation window for module with given id
+ """
+ from vistrails.gui.vistrails_window import _app
+ _app.show_documentation()
+
+ def toggle_breakpoint(self, id):
+ """ toggle_breakpoint(int) -> None
+ Toggles the breakpoint attribute for the module with given id
+ """
+ if self.controller:
+ module = self.controller.current_pipeline.modules[id]
+ module.toggle_breakpoint()
+ self.recreate_module(self.controller.current_pipeline, id)
+
+ def toggle_watched(self, id):
+ if self.controller:
+ module = self.controller.current_pipeline.modules[id]
+ module.toggle_watched()
+
+ def print_error(self, id):
+ toolTip = str(self.modules[id].toolTip())
+ errorTrace = self.modules[id].errorTrace
+ if not toolTip and not errorTrace:
+ return
+ text = toolTip
+ if errorTrace and errorTrace.strip() != 'None':
+ text += '\n\n' + errorTrace
+ class StackPopup(QtGui.QDialog):
+ def __init__(self, errorTrace='', parent=None):
+ QtGui.QDialog.__init__(self, parent)
+ self.resize(700, 400)
+ self.setWindowTitle('Module Error')
+ layout = QtGui.QVBoxLayout()
+ self.setLayout(layout)
+ text = QtGui.QTextEdit('')
+ text.insertPlainText(errorTrace)
+ text.setReadOnly(True)
+ text.setLineWrapMode(QtGui.QTextEdit.NoWrap)
+ layout.addWidget(text)
+ close = QtGui.QPushButton('Close', self)
+ close.setFixedWidth(100)
+ layout.addWidget(close)
+ self.connect(close, QtCore.SIGNAL('clicked()'),
+ self, QtCore.SLOT('close()'))
+ sp = StackPopup(text)
+ sp.exec_()
+
+ def open_annotations_window(self, id):
+ """ open_annotations_window(int) -> None
+ Opens the modal annotations window for module with given id
+ """
+ if self.controller:
+ from vistrails.gui.module_info import QModuleInfo
+ module_info = QModuleInfo.instance()
+ module_info.show_annotations()
+
+ def open_module_label_window(self, id):
+ """ open_module_label_window(int) -> None
+ Opens the modal module label window for setting module label
+ """
+ if self.controller:
+ module = self.controller.current_pipeline.modules[id]
+ if module.has_annotation_with_key('__desc__'):
+ currentLabel = module.get_annotation_by_key('__desc__').value.strip()
+ else:
+ currentLabel = ''
+ (text, ok) = QtGui.QInputDialog.getText(None, 'Set Module Label',
+ 'Enter the module label',
+ QtGui.QLineEdit.Normal,
+ currentLabel)
+ if ok:
+ if not text:
+ if module.has_annotation_with_key('__desc__'):
+ self.controller.delete_annotation('__desc__', id)
+ self.recreate_module(self.controller.current_pipeline, id)
+ else:
+ self.controller.add_annotation(('__desc__', str(text)), id)
+ self.recreate_module(self.controller.current_pipeline, id)
+
+ ##########################################################################
+ # Execution reporting API
+
+ def cancel_progress(self):
+ """Checks if the user have canceled the execution and takes
+ appropriate action
+ """
+ if self.progress.wasCanceled():
+ if self.progress._progress_canceled:
+ # It has already been confirmed in a progress update
+ self.progress._progress_canceled = False
+ raise AbortExecution("Execution aborted by user")
+ r = QtGui.QMessageBox.question(self.parent(),
+ 'Execution Paused',
+ 'Are you sure you want to abort the execution?',
+ QtGui.QMessageBox.Yes | QtGui.QMessageBox.No,
+ QtGui.QMessageBox.No)
+ if r == QtGui.QMessageBox.Yes:
+ raise AbortExecution("Execution aborted by user")
+ else:
+ self.progress.goOn()
+
+ def set_module_success(self, moduleId):
+ """ set_module_success(moduleId: int) -> None
+ Post an event to the scene (self) for updating the module color
+
+ """
+ QtGui.QApplication.postEvent(self,
+ QModuleStatusEvent(moduleId, 0, ''))
+ QtCore.QCoreApplication.processEvents()
+
+ def set_module_error(self, moduleId, error, errorTrace=None):
+ """ set_module_error(moduleId: int, error: str) -> None
+ Post an event to the scene (self) for updating the module color
+
+ """
+ QtGui.QApplication.postEvent(self,
+ QModuleStatusEvent(moduleId, 1, error,
+ errorTrace = errorTrace))
+ QtCore.QCoreApplication.processEvents()
+
+ def set_module_not_executed(self, moduleId):
+ """ set_module_not_executed(moduleId: int) -> None
+ Post an event to the scene (self) for updating the module color
+
+ """
+ QtGui.QApplication.postEvent(self,
+ QModuleStatusEvent(moduleId, 2, ''))
+ QtCore.QCoreApplication.processEvents()
+
+ def set_module_active(self, moduleId):
+ """ set_module_active(moduleId: int) -> None
+ Post an event to the scene (self) for updating the module color
+
+ """
+ QtGui.QApplication.postEvent(self,
+ QModuleStatusEvent(moduleId, 3, ''))
+ QtCore.QCoreApplication.processEvents()
+
+ def set_module_computing(self, moduleId):
+ """ set_module_computing(moduleId: int) -> None
+ Post an event to the scene (self) for updating the module color
+
+ """
+ if self.progress:
+ self.cancel_progress()
+ self.progress.setValue(self.progress.value() + 1)
+ self.progress.setLabelText(self.controller.current_pipeline.get_module_by_id(moduleId).name)
+ QtGui.QApplication.postEvent(self,
+ QModuleStatusEvent(moduleId, 4, ''))
+ QtCore.QCoreApplication.processEvents()
+
+ def set_module_progress(self, moduleId, progress=0.0):
+ """ set_module_computing(moduleId: int, progress: float) -> None
+ Post an event to the scene (self) for updating the module color
+
+ """
+ if self.progress:
+ try:
+ self.cancel_progress()
+ except AbortExecution:
+ self.progress._progress_canceled = True
+ raise
+ QtGui.QApplication.postEvent(self,
+ QModuleStatusEvent(moduleId, 5,
+ '%d%% Completed' % int(progress*100),
+ progress))
+ QtCore.QCoreApplication.processEvents()
+
+ def set_module_persistent(self, moduleId):
+ QtGui.QApplication.postEvent(self,
+ QModuleStatusEvent(moduleId, 6, ''))
+ QtCore.QCoreApplication.processEvents()
+
+ def set_module_suspended(self, moduleId, error):
+ """ set_module_suspended(moduleId: int, error: str) -> None
+ Post an event to the scene (self) for updating the module color
+
+ """
+ msg = error if isinstance(error, str) else error.msg
+ text = "Module is suspended, reason: %s" % msg
+ QtGui.QApplication.postEvent(self,
+ QModuleStatusEvent(moduleId, 7, text))
+ QtCore.QCoreApplication.processEvents()
+ # add to suspended modules dialog
+ if isinstance(error, str):
+ return
+ from vistrails.gui.job_monitor import QJobView
+ jobView = QJobView.instance()
+ try:
+ result = jobView.add_job(self.controller, error)
+ if result:
+ jobView.set_visible(True)
+ except Exception, e:
+ import traceback
+ debug.critical("Error Monitoring Job: %s" % str(e), traceback.format_exc())
+
+ def reset_module_colors(self):
+ for module in self.modules.itervalues():
+ module.statusBrush = None
+ module._needs_state_updated = True
+
+ def hasMoveActions(self):
+ controller = self.controller
+ for (mId, item) in self.modules.iteritems():
+ module = controller.current_pipeline.modules[mId]
+ (dx,dy) = (item.scenePos().x(), -item.scenePos().y())
+ if (dx != module.center.x or dy != module.center.y):
+ return True
+ return False
+
+ def flushMoveActions(self):
+ """ flushMoveActions() -> None
+ Update all move actions into vistrail
+
+ """
+ controller = self.controller
+ moves = []
+ for (mId, item) in self.modules.iteritems():
+ module = controller.current_pipeline.modules[mId]
+ (dx,dy) = (item.scenePos().x(), -item.scenePos().y())
+ if (dx != module.center.x or dy != module.center.y):
+ moves.append((mId, dx, dy))
+ if len(moves)>0:
+ controller.quiet = True
+ controller.move_module_list(moves)
+ controller.quiet = False
+ return True
+ return False
+
+ def set_read_only_mode(self, on):
+ """set_read_only_mode(on: bool) -> None
+ This will prevent user to add/remove modules and connections."""
+ self.read_only_mode = on
+
+class QModuleStatusEvent(QtCore.QEvent):
+ """
+ QModuleStatusEvent is trying to handle thread-safe real-time
+ module updates in the scene through post-event
+
+ """
+ TYPE = QtCore.QEvent.Type(QtCore.QEvent.User)
+ def __init__(self, moduleId, status, toolTip, progress=0.0,
+ errorTrace=None):
+ """ QModuleStatusEvent(type: int) -> None
+ Initialize the specific event with the module status. Status 0
+ for success, 1 for error and 2 for not execute, 3 for active,
+ and 4 for computing
+
+ """
+ QtCore.QEvent.__init__(self, QModuleStatusEvent.TYPE)
+ self.moduleId = moduleId
+ self.status = status
+ self.toolTip = toolTip
+ self.progress = progress
+ self.errorTrace = errorTrace
+
+class QPipelineView(QInteractiveGraphicsView, BaseView):
+ """
+ QPipelineView inherits from QInteractiveGraphicsView that will
+ handle drawing of module, connection shapes and selecting
+ mechanism.
+
+ """
+
+ def __init__(self, parent=None):
+ """ QPipelineView(parent: QWidget) -> QPipelineView
+ Initialize the graphics view and its properties
+
+ """
+ QInteractiveGraphicsView.__init__(self, parent)
+ BaseView.__init__(self)
+ self.setScene(QPipelineScene(self))
+ self.set_title('Pipeline')
+ self.controller = None
+ self.detachable = True
+
+ def set_default_layout(self):
+ from vistrails.gui.module_palette import QModulePalette
+ from vistrails.gui.module_info import QModuleInfo
+ self.set_palette_layout(
+ {QtCore.Qt.LeftDockWidgetArea: QModulePalette,
+ QtCore.Qt.RightDockWidgetArea: QModuleInfo,
+ })
+
+ def set_action_links(self):
+ # FIXME execute should be tied to a pipleine_changed signal...
+ self.action_links = \
+ {'copy': ('module_changed', self.has_selected_modules),
+ 'paste': ('clipboard_changed', self.clipboard_non_empty),
+ 'layout': ('pipeline_changed', self.pipeline_non_empty),
+ 'group': ('module_changed', self.has_selected_modules),
+ 'ungroup': ('module_changed', self.has_selected_groups),
+ 'showGroup': ('module_changed', self.has_selected_group),
+ 'makeAbstraction': ('module_changed', self.has_selected_modules),
+ 'execute': ('pipeline_changed', self.pipeline_non_empty),
+ 'configureModule': ('module_changed', self.has_selected_module),
+ 'documentModule': ('module_changed', self.has_selected_module),
+ 'makeAbstraction': ('module_changed', self.has_selected_modules),
+ 'convertToAbstraction': ('module_changed',
+ self.has_selected_group),
+ 'editAbstraction': ('module_changed', self.has_selected_abs),
+ 'importAbstraction': ('module_changed', self.has_selected_abs),
+ 'exportAbstraction': ('module_changed', self.has_selected_abs),
+ 'publishWeb' : ('pipeline_changed', self.check_publish_db),
+ 'publishPaper' : ('pipeline_changed', self.pipeline_non_empty),
+ 'controlFlowAssist': ('pipeline_changed', self.pipeline_non_empty),
+ 'redo': ('version_changed', self.can_redo),
+ 'undo': ('version_changed', self.can_undo),
+ }
+
+ def can_redo(self, versionId):
+ return self.controller and self.controller.can_redo()
+
+ def can_undo(self, versionId):
+ return self.controller and self.controller.can_undo()
+
+ def set_action_defaults(self):
+ self.action_defaults.update(
+ { 'execute': [('setEnabled', True, self.set_execute_action),
+ ('setIcon', False, CurrentTheme.EXECUTE_PIPELINE_ICON),
+ ('setToolTip', False, 'Execute the current pipeline')],
+ })
+
+ def set_execute_action(self):
+ if self.controller:
+ return self.pipeline_non_empty(self.controller.current_pipeline)
+ return False
+
+ def execute(self, target=None):
+ # view.checkModuleConfigPanel()
+ # reset job view
+ from vistrails.gui.job_monitor import QJobView
+ jobView = QJobView.instance()
+ if jobView.updating_now:
+ debug.critical("Execution Aborted: Job Monitor is updating. Please wait a few seconds and try again.")
+ return
+ jobView.delete_job(self.controller)
+ jobView.updating_now = True
+
+ try:
+ modules = len(self.controller.current_pipeline.modules)
+ progress = ExecutionProgressDialog(modules)
+ self.scene().progress = progress
+ progress.show()
+
+ if target is not None:
+ self.controller.execute_current_workflow(
+ sinks=[target],
+ reason="Execute specific module")
+ else:
+ self.controller.execute_current_workflow()
+
+ progress.setValue(modules)
+ #progress.hide()
+ self.scene().progress = None
+ except Exception, e:
+ import traceback
+ debug.critical(str(e) or e.__class__.__name__,
+ traceback.format_exc())
+ finally:
+ self.scene().progress = None
+ jobView.updating_now = False
+ from vistrails.gui.vistrails_window import _app
+ _app.notify('execution_updated')
+
+ def publish_to_web(self):
+ from vistrails.gui.publishing import QVersionEmbed
+ panel = QVersionEmbed.instance()
+ panel.switchType('Wiki')
+ panel.set_visible(True)
+
+ def publish_to_paper(self):
+ from vistrails.gui.publishing import QVersionEmbed
+ panel = QVersionEmbed.instance()
+ panel.switchType('Latex')
+ panel.set_visible(True)
+
+ def check_publish_db(self, pipeline):
+ loc = self.controller.locator
+ result = False
+ if hasattr(loc,'host'):
+ result = True
+ return result and self.pipeline_non_empty(pipeline)
+
+ def has_selected_modules(self, module, only_one=False):
+ module_ids_len = len(self.scene().get_selected_module_ids())
+ #print ' module_ids_len:', module_ids_len
+ if only_one and module_ids_len != 1:
+ return False
+ return module_ids_len > 0
+
+ def has_selected_module(self, module):
+ #print 'calling has_selected_module'
+ return self.has_selected_modules(module, True)
+
+ def has_selected_groups(self, module, only_one=False):
+ module_ids = self.scene().get_selected_module_ids()
+ if len(module_ids) <= 0:
+ return False
+ if only_one and len(module_ids) != 1:
+ return False
+ for m_id in module_ids:
+ if not self.scene().current_pipeline.modules[m_id].is_group():
+ return False
+ return True
+
+ def has_selected_group(self, module):
+ return self.has_selected_groups(True)
+
+ def has_selected_abs(self, module):
+ module_ids = self.scene().get_selected_module_ids()
+ if len(module_ids) != 1:
+ return False
+ for m_id in module_ids:
+ if not self.scene().current_pipeline.modules[m_id].is_abstraction():
+ return False
+ return True
+
+ def clipboard_non_empty(self):
+ clipboard = QtGui.QApplication.clipboard()
+ clipboard_text = clipboard.text()
+ return bool(clipboard_text) #and \
+ # str(clipboard_text).startswith("<workflow")
+
+ def pipeline_non_empty(self, pipeline):
+ return pipeline is not None and len(pipeline.modules) > 0
+
+ def pasteFromClipboard(self):
+ center = self.mapToScene(self.width()/2.0, self.height()/2.0)
+ self.scene().pasteFromClipboard((center.x(), -center.y()))
+
+ def setQueryEnabled(self, on):
+ QInteractiveGraphicsView.setQueryEnabled(self, on)
+ if not self.scene().noUpdate and self.scene().controller:
+ self.scene().setupScene(self.scene().controller.current_pipeline)
+
+ def setReadOnlyMode(self, on):
+ self.scene().set_read_only_mode(on)
+
+ def set_title(self, title):
+ BaseView.set_title(self, title)
+ self.setWindowTitle(title)
+
+ def set_controller(self, controller):
+ oldController = self.controller
+ if oldController != controller:
+ if oldController != None:
+ # self.disconnect(oldController,
+ # QtCore.SIGNAL('versionWasChanged'),
+ # self.version_changed)
+ oldController.current_pipeline_view = None
+ self.controller = controller
+ self.scene().controller = controller
+ # self.connect(controller,
+ # QtCore.SIGNAL('versionWasChanged'),
+ # self.version_changed)
+ # self.module_info.set_controller(controller)
+ # self.moduleConfig.controller = controller
+ # controller.current_pipeline_view = self.scene()
+
+ def set_to_current(self):
+ QModuleInfo.instance().setReadOnly(self.scene().read_only_mode)
+ self.controller.set_pipeline_view(self)
+
+ def get_long_title(self):
+ pip_name = self.controller.get_pipeline_name()
+ vt_name = self.controller.name
+ self.long_title = "Pipeline %s from %s" % (pip_name,vt_name)
+ return self.long_title
+
+ def get_controller(self):
+ return self.controller
+
+ def version_changed(self):
+ self.scene().setupScene(self.controller.current_pipeline)
+
+ def run_control_flow_assist(self):
+ currentScene = self.scene()
+ if currentScene.controller:
+ selected_items = currentScene.get_selected_item_ids(True)
+ if selected_items is None:
+ selected_items = ([],[])
+ selected_module_ids = selected_items[0]
+ selected_connection_ids = selected_items[1]
+ if len(selected_module_ids) > 0:
+ try:
+ dialog = QControlFlowAssistDialog(
+ self,
+ selected_module_ids, selected_connection_ids,
+ currentScene)
+ except MissingPackage:
+ debug.critical("The controlflow package is not available")
+ else:
+ dialog.exec_()
+ else:
+ QtGui.QMessageBox.warning(
+ self,
+ 'No modules selected',
+ 'You must select at least one module to use the '
+ 'Control Flow Assistant')
+
+ def done_configure(self, mid):
+ self.scene().perform_configure_done_actions(mid)
+
+ def paintModuleToPixmap(self, module_item):
+ m = self.matrix()
+ return module_item.paintToPixmap(m.m11(), m.m22())
+
+class ExecutionProgressDialog(QtGui.QProgressDialog):
+ def __init__(self, modules):
+ QtGui.QProgressDialog.__init__(self, 'Executing Workflow',
+ '&Cancel',
+ 0, modules)
+ self.setWindowTitle('Executing')
+ self.setWindowModality(QtCore.Qt.WindowModal)
+ self._last_set_value = 0
+ self._progress_canceled = False
+
+ def setValue(self, value):
+ self._last_set_value = value
+ super(ExecutionProgressDialog, self).setValue(value)
+
+ def goOn(self):
+ self.reset()
+ self.show()
+ super(ExecutionProgressDialog, self).setValue(self._last_set_value)
+
+################################################################################
+# Testing
+
+
+class TestPipelineView(vistrails.gui.utils.TestVisTrailsGUI):
+
+ def test_quick_change_version_with_ports(self):
+ import vistrails.core.system
+ filename = (vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/triangle_count.vt')
+ view = vistrails.api.open_vistrail_from_file(filename)
+ vistrails.api.select_version(-1, view.controller)
+ vistrails.api.select_version('count + area', view.controller)
+ vistrails.api.select_version('writing to file', view.controller)
+
+ def test_change_version_with_common_connections(self):
+ import vistrails.core.system
+ filename = (vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/terminator.vt')
+ view = vistrails.api.open_vistrail_from_file(filename)
+ vistrails.api.select_version('Image Slices HW', view.controller)
+ vistrails.api.select_version('Combined Rendering HW', view.controller)
+
+ def test_switch_mode(self):
+ vistrails.api.switch_to_pipeline_view()
+ vistrails.api.switch_to_history_view()
+ vistrails.api.switch_to_query_view()
+ vistrails.api.switch_to_pipeline_view()
+ vistrails.api.switch_to_history_view()
+ vistrails.api.switch_to_query_view()
+
+ def test_group(self):
+ vistrails.api.new_vistrail()
+ basic_pkg = get_vistrails_basic_pkg_id()
+ m1 = vistrails.api.add_module(0, 0, basic_pkg, 'File', '')
+ m2 = vistrails.api.add_module(0, -100, basic_pkg, 'File', '')
+ m3 = vistrails.api.add_module(0, -100, basic_pkg, 'File', '')
+ r = vistrails.api.get_module_registry()
+ src = r.get_port_spec(basic_pkg, 'File', None, 'value_as_string',
+ 'output')
+ dst = r.get_port_spec(basic_pkg, 'File', None, 'name', 'input')
+# src = r.module_source_ports(True, basic_pkg, 'File', '')[1]
+# assert src.name == 'value_as_string'
+# dst = r.module_destination_ports(True, basic_pkg, 'File', '')[1]
+# assert dst.name == 'name'
+ vistrails.api.add_connection(m1.id, src, m2.id, dst)
+ vistrails.api.add_connection(m2.id, src, m3.id, dst)
+ vistrails.api.create_group([0, 1, 2], [0, 1])
+
diff --git a/vistrails/gui/pipeline_view_select.py b/vistrails/gui/pipeline_view_select.py
new file mode 100644
index 0000000..732ba69
--- /dev/null
+++ b/vistrails/gui/pipeline_view_select.py
@@ -0,0 +1,186 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This contains a customized pipeline view for read-only selection
+
+QReadOnlyPortSelectPipelineView
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.gui.pipeline_view import QGraphicsConfigureItem, QGraphicsModuleItem, \
+ QAbstractGraphicsPortItem, QPipelineScene, QPipelineView
+from vistrails.gui.theme import CurrentTheme
+
+class QReadOnlyPortSelectPipelineView(QPipelineView):
+ def __init__(self, parent, scene, single_output=False, include_module_ids=[]):
+ """ QReadOnlyPortSelectPipelineView(parent: QPipelineView,
+ scene: QGraphicsScene,
+ single_output: bool,
+ include_module_ids: list)
+ -> QReadOnlyPortSelectPipelineView
+ Create a read only pipeline view that only allows selection of ports from
+ the modules in include_module_ids. If single_output is True, only one
+ output port can be selected at a time.
+
+ """
+ QPipelineView.__init__(self, parent)
+ self.single_output = single_output
+ self._shown = False
+ self._selected_input_ports = []
+ self._selected_output_ports = []
+ # Create custom scene
+ scene_copy = QPipelineScene(self)
+ scene_copy.controller = scene.controller
+ scene_copy.setupScene(scene.pipeline)
+ scene_copy.selectAll()
+ if include_module_ids:
+ # Remove modules not in the include list and associated connections
+ sel_modules, sel_connections = scene_copy.get_selected_item_ids()
+ [scene_copy.remove_module(m_id) for m_id in sel_modules if m_id not in include_module_ids]
+ [scene_copy.remove_connection(c_id) for c_id in sel_connections if c_id not in scene_copy.get_selected_item_ids()[1]]
+ # Hide configure button on modules
+ for item in scene_copy.selectedItems():
+ if isinstance(item, QGraphicsModuleItem):
+ for c_item in item.childItems():
+ if isinstance(c_item, QGraphicsConfigureItem):
+ c_item.setVisible(False)
+ # Unselect everything and use the newly created scene
+ scene_copy.clearSelection()
+ scene_copy.updateSceneBoundingRect()
+ self.setScene(scene_copy)
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+ Toggle port selection
+
+ """
+ buttons = self.translateButton(event)
+ if buttons == QtCore.Qt.LeftButton:
+ scenePos = self.mapToScene(event.pos())
+ item = self.scene().itemAt(scenePos)
+ if isinstance(item, QAbstractGraphicsPortItem):
+ is_input = item.port.type == 'input'
+ if self.single_output and not is_input and len(self._selected_output_ports) > 0 and item != self._selected_output_ports[0]:
+ # Deselect current output port if another port selected in single output mode
+ self._selected_output_ports[0].setSelected(False)
+ del self._selected_output_ports[:]
+ if is_input:
+ port_set = self._selected_input_ports
+ else:
+ port_set = self._selected_output_ports
+ if item in port_set:
+ port_set.remove(item)
+ else:
+ port_set.append(item)
+ self._clicked_port = item
+ else:
+ self._clicked_port = None
+ event.accept()
+ else:
+ QPipelineView.mousePressEvent(self, event)
+
+ def mouseReleaseEvent(self, event):
+ """ mouseReleaseEvent(event: QMouseEvent) -> None
+ Update port highlighting
+
+ """
+ if event.button() == QtCore.Qt.LeftButton:
+ port = self._clicked_port
+ if port is not None:
+ port.setSelected(port in self._selected_input_ports or
+ port in self._selected_output_ports)
+ event.accept()
+ else:
+ QPipelineView.mouseReleaseEvent(self, event)
+
+ def mouseDoubleClickEvent(self, event):
+ """ mouseDoubleClickEvent(event: QMouseEvent) -> None
+ Disallow left button double clicks
+
+ """
+ buttons = self.translateButton(event)
+ if buttons == QtCore.Qt.LeftButton:
+ event.accept()
+ else:
+ QPipelineView.mouseDoubleClickEvent(self, event)
+
+ def mouseMoveEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+ Disallow left click and drag
+
+ """
+ buttons = self.translateButton(event)
+ if buttons == QtCore.Qt.LeftButton:
+ event.accept()
+ else:
+ QPipelineView.mouseMoveEvent(self, event)
+
+ def keyPressEvent(self, event):
+ """ keyPressEvent(event: QKeyEvent) -> None
+ Disallow key presses
+
+ """
+ event.accept()
+
+ def paintEvent(self, event):
+ """ paintEvent(event: QPaintEvent) -> None
+ Fit pipeline to view on first paint
+
+ """
+ if not self._shown:
+ self._shown = True
+ self.scene().fitToView(self)
+ QPipelineView.paintEvent(self, event)
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+ Set smaller pipeline view size
+
+ """
+ return QtCore.QSize(512, 512)
+
+ def getSelectedInputPorts(self):
+ """ getSelectedInputPorts() -> list
+ Get list of selected input port (QGraphicsPortItem) objects
+
+ """
+ return self._selected_input_ports
+
+ def getSelectedOutputPorts(self):
+ """ getSelectedOutputPorts() -> list
+ Get list of selected output port (QGraphicsPortItem) objects
+
+ """
+ return self._selected_output_ports
+
+
diff --git a/vistrails/gui/port_documentation.py b/vistrails/gui/port_documentation.py
new file mode 100644
index 0000000..a484fb4
--- /dev/null
+++ b/vistrails/gui/port_documentation.py
@@ -0,0 +1,89 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file contains a dialog and widgets related to the module documentation
+dialog, which displays the available documentation for a given VisTrails module.
+
+QMethodDocumentation
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core.vistrail.port import PortEndPoint
+from vistrails.core.utils import VistrailsInternalError
+
+class QPortDocumentation(QtGui.QDialog):
+ """
+ QPortDocumentation is a dialog for showing port documentation. duh.
+
+ """
+ def __init__(self, module, port_type, port_name, parent=None):
+ QtGui.QDialog.__init__(self, parent)
+
+ if not module.has_port_spec(port_name, port_type):
+ doc = None
+ else:
+ port_spec = module.get_port_spec(port_name, port_type)
+ doc = port_spec.docstring()
+ if doc is None:
+ descriptor = module.module_descriptor
+ # try the old method of accessing documentation
+ if port_type == 'output':
+ call_ = descriptor.module.provide_output_port_documentation
+ elif port_type == 'input':
+ call_ = descriptor.module.provide_input_port_documentation
+ else:
+ raise VistrailsInternalError("Invalid port type")
+ doc = call_(port_name)
+
+ self.setWindowTitle('Documentation for %s port %s in "%s"' %
+ (port_type, port_name, module.name))
+
+
+ layout = QtGui.QVBoxLayout()
+ layout.addStrut(600)
+ layout.addWidget(QtGui.QLabel("Port name: %s" % port_name))
+ layout.addWidget(QtGui.QLabel("Module name: %s" % module.name))
+ layout.addWidget(QtGui.QLabel("Module package: %s" % \
+ module.package))
+ self.textEdit = QtGui.QTextEdit(self)
+ layout.addWidget(self.textEdit, 1)
+ if doc:
+ self.textEdit.insertPlainText(doc)
+ else:
+ self.textEdit.insertPlainText("(Documentation not available)")
+ self.textEdit.setReadOnly(True)
+ self.textEdit.setTextCursor(QtGui.QTextCursor(self.textEdit.document()))
+ self.buttonBox = QtGui.QDialogButtonBox(QtGui.QDialogButtonBox.Ok)
+ layout.addWidget(self.buttonBox)
+ self.setLayout(layout)
+ self.connect(self.buttonBox, QtCore.SIGNAL('accepted()'), self.accept)
diff --git a/vistrails/gui/ports_pane.py b/vistrails/gui/ports_pane.py
new file mode 100644
index 0000000..5de8234
--- /dev/null
+++ b/vistrails/gui/ports_pane.py
@@ -0,0 +1,613 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+from itertools import izip
+import os
+
+from vistrails.core import debug
+from vistrails.core.modules.basic_modules import identifier as basic_identifier
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.modules.utils import create_port_spec_string
+from vistrails.core.vistrail.port_spec import PortSpec
+from vistrails.core.system import vistrails_root_directory
+from vistrails.gui.modules import get_widget_class
+from vistrails.gui.common_widgets import QToolWindowInterface
+from vistrails.gui.port_documentation import QPortDocumentation
+from vistrails.gui.theme import CurrentTheme
+
+class AliasLabel(QtGui.QLabel):
+ """
+ AliasLabel is a QLabel that supports hover actions similar
+ to a hot link
+ """
+ def __init__(self, alias='', text='', default_label='', parent=None):
+ """ AliasLabel(alias:str , text: str, default_label: str,
+ parent: QWidget) -> QHoverAliasLabel
+ Initialize the label with a text
+
+ """
+ QtGui.QLabel.__init__(self, parent)
+ self.alias = alias
+ self.caption = text
+ # catch None
+ if default_label:
+ self.default_label = default_label
+ else:
+ self.default_label = ""
+ self.updateText()
+ self.setAttribute(QtCore.Qt.WA_Hover)
+ self.setCursor(QtCore.Qt.PointingHandCursor)
+ self.setToolTip(alias)
+ self.palette().setColor(QtGui.QPalette.WindowText,
+ CurrentTheme.HOVER_DEFAULT_COLOR)
+
+ def updateText(self):
+ """ updateText() -> None
+ Update the label text to contain the alias name when appropriate
+
+ """
+ if self.alias != '':
+ self.setText(self.alias + ': ' + self.caption)
+ elif self.default_label != '':
+ self.setText(self.default_label + ': ' + self.caption)
+ else:
+ self.setText(self.caption)
+
+ def event(self, event):
+ """ event(event: QEvent) -> Event Result
+ Override to handle hover enter and leave events for hot links
+
+ """
+ if event.type()==QtCore.QEvent.HoverEnter:
+ self.palette().setColor(QtGui.QPalette.WindowText,
+ CurrentTheme.HOVER_SELECT_COLOR)
+ if event.type()==QtCore.QEvent.HoverLeave:
+ self.palette().setColor(QtGui.QPalette.WindowText,
+ CurrentTheme.HOVER_DEFAULT_COLOR)
+ return QtGui.QLabel.event(self, event)
+ # return super(QHoverAliasLabel, self).event(event)
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+ If mouse click on the label, show up a dialog to change/add
+ the alias name
+
+ """
+ if event.button()==QtCore.Qt.LeftButton:
+ (text, ok) = QtGui.QInputDialog.getText(self,
+ 'Set Parameter Alias',
+ 'Enter the parameter alias',
+ QtGui.QLineEdit.Normal,
+ self.alias)
+ while ok and self.parent().check_alias(str(text)):
+ msg =" This alias is already being used.\
+ Please enter a different parameter alias "
+ (text, ok) = QtGui.QInputDialog.getText(self,
+ 'Set Parameter Alias',
+ msg,
+ QtGui.QLineEdit.Normal,
+ text)
+ if ok and str(text)!=self.alias:
+ if not self.parent().check_alias(str(text)):
+ self.alias = str(text).strip()
+ self.updateText()
+ self.parent().updateMethod()
+
+class Parameter(object):
+ def __init__(self, desc):
+ self.type = desc.name
+ self.identifier = desc.identifier
+ self.namespace = None if not desc.namespace else desc.namespace
+ self.strValue = ''
+ self.alias = ''
+ self.queryMethod = None
+ self.port_spec_item = None
+ self.param_exists = False
+
+class ParameterEntry(QtGui.QTreeWidgetItem):
+ plus_icon = QtGui.QIcon(os.path.join(vistrails_root_directory(),
+ 'gui/resources/images/plus.png'))
+ minus_icon = QtGui.QIcon(os.path.join(vistrails_root_directory(),
+ 'gui/resources/images/minus.png'))
+ def __init__(self, port_spec, function=None, parent=None):
+ QtGui.QTreeWidgetItem.__init__(self, parent)
+ self.setFirstColumnSpanned(True)
+ self.port_spec = port_spec
+ self.function = function
+
+ def build_widget(self, widget_accessor, with_alias=True):
+ reg = get_module_registry()
+
+ # widget = QtGui.QDockWidget()
+ # widget.setFeatures(QtGui.QDockWidget.DockWidgetClosable |
+ # QtGui.QDockWidget.DockWidgetVerticalTitleBar)
+ widget = QtGui.QWidget()
+
+ h_layout = QtGui.QHBoxLayout()
+ h_layout.insertSpacing(0, 10)
+ h_layout.setMargin(2)
+ h_layout.setSpacing(2)
+
+ v_layout = QtGui.QVBoxLayout()
+ v_layout.setAlignment(QtCore.Qt.AlignVCenter)
+ delete_button = QtGui.QToolButton()
+ delete_button.setIconSize(QtCore.QSize(8,8))
+ delete_button.setIcon(ParameterEntry.minus_icon)
+ def delete_method():
+ if self.function is not None:
+ self.group_box.parent().parent().parent().delete_method(
+ self, self.port_spec.name, self.function.real_id)
+ else:
+ self.group_box.parent().parent().parent().delete_method(
+ self, self.port_spec.name, None)
+
+ QtCore.QObject.connect(delete_button, QtCore.SIGNAL("clicked()"),
+ delete_method)
+ v_layout.addWidget(delete_button)
+
+ add_button = QtGui.QToolButton()
+ add_button.setIcon(ParameterEntry.plus_icon)
+ add_button.setIconSize(QtCore.QSize(8,8))
+ def add_method():
+ self.group_box.parent().parent().parent().add_method(
+ self.port_spec.name)
+ QtCore.QObject.connect(add_button, QtCore.SIGNAL("clicked()"),
+ add_method)
+ v_layout.addWidget(add_button)
+ h_layout.addLayout(v_layout)
+
+ self.my_widgets = []
+ self.my_labels = []
+ self.group_box = QtGui.QGroupBox()
+ layout = QtGui.QGridLayout()
+ layout.setMargin(5)
+ layout.setSpacing(5)
+ layout.setColumnStretch(1,1)
+ self.group_box.setFocusPolicy(QtCore.Qt.ClickFocus)
+ self.group_box.setSizePolicy(QtGui.QSizePolicy.Preferred,
+ QtGui.QSizePolicy.Fixed)
+ self.group_box.palette().setColor(QtGui.QPalette.Window,
+ CurrentTheme.METHOD_SELECT_COLOR)
+
+ if self.function is not None:
+ params = self.function.parameters
+ else:
+ params = [None,] * len(self.port_spec.descriptors())
+
+ for i, (psi, param) in enumerate(izip(self.port_spec.port_spec_items,
+ params)):
+ widget_class = widget_accessor(psi.descriptor.module)
+ if param is not None:
+ obj = param
+ else:
+ obj = Parameter(psi.descriptor)
+ obj.port_spec_item = psi
+ if with_alias:
+ label = AliasLabel(obj.alias, obj.type, psi.label)
+ self.my_labels.append(label)
+ else:
+ label = QtGui.QLabel(obj.type)
+ param_widget = widget_class(obj, self.group_box)
+ self.my_widgets.append(param_widget)
+ layout.addWidget(label, i, 0)
+ layout.addWidget(param_widget, i, 1)
+
+ self.group_box.setLayout(layout)
+ def updateMethod():
+ if self.function is not None:
+ real_id = self.function.real_id
+ else:
+ real_id = -1
+ self.group_box.parent().parent().parent().update_method(
+ self, self.port_spec.name, self.my_widgets, self.my_labels, real_id)
+ def check_alias(name):
+ controller = self.group_box.parent().parent().parent().controller
+ if controller:
+ return controller.check_alias(name)
+ return False
+ self.group_box.updateMethod = updateMethod
+ self.group_box.check_alias = check_alias
+ h_layout.addWidget(self.group_box)
+ widget.setLayout(h_layout)
+ return widget
+
+ def get_widget(self):
+ return self.build_widget(get_widget_class, True)
+
+class PortItem(QtGui.QTreeWidgetItem):
+ null_icon = QtGui.QIcon()
+ eye_icon = QtGui.QIcon(os.path.join(vistrails_root_directory(),
+ 'gui/resources/images/eye.png'))
+ eye_disabled_icon = \
+ QtGui.QIcon(os.path.join(vistrails_root_directory(),
+ 'gui/resources/images/eye_gray.png'))
+ conn_icon = \
+ QtGui.QIcon(os.path.join(vistrails_root_directory(),
+ 'gui/resources/images/connection.png'))
+
+ def __init__(self, port_spec, is_connected, is_optional, is_visible,
+ parent=None):
+ QtGui.QTreeWidgetItem.__init__(self, parent)
+ # self.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled)
+ self.setFlags(QtCore.Qt.ItemIsEnabled)
+ # self.setCheckState(0, QtCore.Qt.Unchecked)
+ self.port_spec = port_spec
+ self.is_connected = is_connected
+ self.is_optional = is_optional
+ self.is_visible = is_visible
+ self.build_item(port_spec, is_connected, is_optional, is_visible)
+
+ def visible(self):
+ return not self.is_optional or self.is_visible
+
+ def set_visible(self, visible):
+ self.is_visible = visible
+ if visible:
+ self.setIcon(0, PortItem.eye_icon)
+ else:
+ self.setIcon(0, PortItem.null_icon)
+
+ def get_visible(self):
+ return self.visible_checkbox
+
+ def get_connected(self):
+ return self.connected_checkbox
+
+ def is_constant(self):
+ return (self.port_spec.is_valid and
+ get_module_registry().is_constant(self.port_spec))
+
+ def build_item(self, port_spec, is_connected, is_optional, is_visible):
+ if not is_optional:
+ self.setIcon(0, PortItem.eye_disabled_icon)
+ elif is_visible:
+ self.setIcon(0, PortItem.eye_icon)
+
+ if is_connected:
+ self.setIcon(1, PortItem.conn_icon)
+ self.setText(2, port_spec.name)
+
+ # if port_spec is not a method, make it gray
+ if not self.is_constant():
+ self.setForeground(2,
+ QtGui.QBrush(QtGui.QColor.fromRgb(128,128,128)))
+
+ self.visible_checkbox = QtGui.QCheckBox()
+ self.connected_checkbox = QtGui.QCheckBox()
+
+ def contextMenuEvent(self, event, widget):
+ if self.port_spec is None:
+ return
+ act = QtGui.QAction("View Documentation", widget)
+ act.setStatusTip("View method documentation")
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ self.view_documentation)
+ menu = QtGui.QMenu(widget)
+ menu.addAction(act)
+ menu.exec_(event.globalPos())
+
+ def view_documentation(self):
+ # descriptor = self.treeWidget().module.module_descriptor
+ module = self.treeWidget().module
+ port_type = self.treeWidget().port_type
+ widget = QPortDocumentation(module,
+ port_type,
+ self.port_spec.name)
+ widget.setAttribute(QtCore.Qt.WA_DeleteOnClose)
+ widget.exec_()
+
+class PortsList(QtGui.QTreeWidget):
+ def __init__(self, port_type, parent=None):
+ QtGui.QTreeWidget.__init__(self, parent)
+ self.port_type = port_type
+ self.setColumnCount(3)
+ self.setColumnWidth(0,24)
+ self.setColumnWidth(1,24)
+ self.setRootIsDecorated(False)
+ self.setIndentation(0)
+ self.setHeaderHidden(True)
+ self.connect(self, QtCore.SIGNAL("itemClicked(QTreeWidgetItem*, int)"),
+ self.item_clicked)
+ self.module = None
+ self.port_spec_items = {}
+ self.entry_klass = ParameterEntry
+
+ def setReadOnly(self, read_only):
+ self.setEnabled(not read_only)
+
+ def set_entry_klass(self, entry_klass):
+ self.entry_klass = entry_klass
+ self.update_module(self.module)
+
+ def update_module(self, module):
+ """ update_module(module: Module) -> None
+ Setup this tree widget to show functions of module
+
+ """
+ # this is strange but if you try to clear the widget when the focus is
+ # in one of the items (after setting a parameter for example),
+ # VisTrails crashes on a Mac (Emanuele) This is probably a Qt bug
+ w = QtGui.QApplication.focusWidget()
+ if self.isAncestorOf(w):
+ w.clearFocus()
+ self.clear()
+ self.module = module
+ self.port_spec_items = {}
+ self.function_map = {}
+ if module and module.is_valid:
+ reg = get_module_registry()
+ descriptor = module.module_descriptor
+ if self.port_type == 'input':
+ port_specs = module.destinationPorts()
+ connected_ports = module.connected_input_ports
+ visible_ports = module.visible_input_ports
+ elif self.port_type == 'output':
+ port_specs = module.sourcePorts()
+ connected_ports = module.connected_output_ports
+ visible_ports = module.visible_output_ports
+ else:
+ raise TypeError("Unknown port type: '%s'" % self.port_type)
+
+ for port_spec in sorted(port_specs, key=lambda x: x.name):
+ connected = port_spec.name in connected_ports and \
+ connected_ports[port_spec.name] > 0
+ item = PortItem(port_spec,
+ connected,
+ port_spec.optional,
+ port_spec.name in visible_ports)
+ self.addTopLevelItem(item)
+ self.port_spec_items[port_spec.name] = (port_spec, item)
+
+ if self.port_type == 'input':
+ for function in module.functions:
+ if not function.is_valid:
+ continue
+ port_spec, item = self.port_spec_items[function.name]
+ subitem = self.entry_klass(port_spec, function)
+ self.function_map[function.real_id] = subitem
+ item.addChild(subitem)
+ subitem.setFirstColumnSpanned(True)
+ self.setItemWidget(subitem, 0, subitem.get_widget())
+ item.setExpanded(True)
+
+ # self.setItemWidget(item, 0, item.get_visible())
+ # self.setItemWidget(item, 1, item.get_connected())
+
+ # i = QTreeWidgetItem(self)
+ # self.addTopLevelItem(i)
+ # i.setText(2, port_spec.name)
+ # visible_checkbox = QtGui.QCheckBox()
+ # self.setItemWidget(i, 0, visible_checkbox)
+ # connceted_checkbox = QtGui.QCheckBox()
+ # connected_checkbox.setEnabled(False)
+ # self.setItemWidget(i, 1, connected_checkbox)
+
+
+ # base_items = {}
+ # # Create the base widget item for each descriptor
+ # for descriptor in moduleHierarchy:
+ # baseName = descriptor.name
+ # base_package = descriptor.identifier
+ # baseItem = QMethodTreeWidgetItem(None,
+ # None,
+ # self,
+ # ([]
+ # << baseName
+ # << ''))
+ # base_items[descriptor] = baseItem
+
+ # method_specs = {}
+ # # do this in reverse to ensure proper overloading
+ # # !!! NOTE: we have to use ***all*** input ports !!!
+ # # because a subclass can overload a port with a
+ # # type that isn't a method
+ # for descriptor in reversed(moduleHierarchy):
+ # method_specs.update((name, (descriptor, spec))
+ # for name, spec in \
+ # registry.module_ports('input',
+ # descriptor))
+
+ # # add local registry last so that it takes precedence
+ # method_specs.update((spec.name, (descriptor, spec))
+ # for spec in module.port_spec_list
+ # if spec.type == 'input')
+
+ # for _, (desc, method_spec) in sorted(method_specs.iteritems()):
+ # if registry.is_method(method_spec):
+ # baseItem = base_items[desc]
+ # sig = method_spec.short_sigstring
+ # QMethodTreeWidgetItem(module,
+ # method_spec,
+ # baseItem,
+ # ([]
+ # << method_spec.name
+ # << sig))
+
+ # self.expandAll()
+ # self.resizeColumnToContents(2)
+ # show invalid module attributes
+ if module and not module.is_valid and self.port_type == 'input':
+ for function in module.functions:
+ if function.name in self.port_spec_items:
+ port_spec, item = self.port_spec_items[function.name]
+ else:
+ sigstring = create_port_spec_string(
+ [(basic_identifier, "String")
+ for i in xrange(len(function.parameters))])
+ port_spec = PortSpec(name=function.name, type='input',
+ sigstring=sigstring)
+ item = PortItem(port_spec, False, False, False)
+ self.addTopLevelItem(item)
+ self.port_spec_items[port_spec.name] = (port_spec, item)
+ subitem = self.entry_klass(port_spec, function)
+ self.function_map[function.real_id] = subitem
+ item.addChild(subitem)
+ subitem.setFirstColumnSpanned(True)
+ self.setItemWidget(subitem, 0, subitem.get_widget())
+ item.setExpanded(True)
+
+ def item_clicked(self, item, col):
+ if item.parent() is not None:
+ return
+
+ if self.port_type == 'input':
+ visible_ports = self.module.visible_input_ports
+ elif self.port_type == 'output':
+ visible_ports = self.module.visible_output_ports
+ else:
+ raise TypeError("Unknown port type: '%s'" % self.port_type)
+
+ if col == 0:
+ if item.is_optional:
+ item.set_visible(not item.is_visible)
+ if item.is_visible:
+ visible_ports.add(item.port_spec.name)
+ else:
+ visible_ports.discard(item.port_spec.name)
+ self.controller.flush_delayed_actions()
+ self.controller.current_pipeline_scene.recreate_module(
+ self.controller.current_pipeline, self.module.id)
+ if col == 2:
+ if item.isExpanded():
+ item.setExpanded(False)
+ elif item.childCount() > 0:
+ item.setExpanded(True)
+ elif item.childCount() == 0 and item.is_constant():
+ self.do_add_method(item.port_spec, item)
+
+ def set_controller(self, controller):
+ self.controller = controller
+
+ def update_method(self, subitem, port_name, widgets, labels, real_id=-1):
+ #print 'updateMethod called', port_name
+ if self.controller:
+ _, item = self.port_spec_items[port_name]
+ str_values = []
+ query_methods = []
+ for w in widgets:
+ str_values.append(str(w.contents()))
+ if hasattr(w, 'query_method'):
+ query_methods.append(w.query_method())
+ if real_id < 0:
+ should_replace = False
+ else:
+ should_replace = True
+ self.controller.update_function(self.module,
+ port_name,
+ str_values,
+ real_id,
+ [str(label.alias)
+ for label in labels],
+ query_methods,
+ should_replace)
+
+ # FIXME need to get the function set on the item somehow
+ # HACK for now
+ for function in self.module.functions:
+ if function.real_id not in self.function_map:
+ self.function_map[function.real_id] = subitem
+ subitem.function = function
+
+ # make the scene display the fact that we have a parameter
+ # by dimming the port
+ # self.controller.flush_delayed_actions()
+ self.controller.current_pipeline_scene.update_module_functions(
+ self.controller.current_pipeline, self.module.id)
+
+ def delete_method(self, subitem, port_name, real_id=None):
+ _, item = self.port_spec_items[port_name]
+ item.removeChild(subitem)
+
+ if real_id is not None and self.controller:
+ #print "got to delete"
+ self.controller.delete_function(real_id, self.module.id)
+
+ # make the scene display the fact that we have lost the
+ # parameter by undimming the port
+ # self.controller.flush_delayed_actions()
+ self.controller.current_pipeline_scene.update_module_functions(
+ self.controller.current_pipeline, self.module.id)
+
+ # how to delete items...x
+ # subitem.deleteLater()
+
+ def do_add_method(self, port_spec, item):
+ """do_add_method(port_spec: PortSpec,
+ item: PortItem) -> None
+
+ Displays a new method for the port.
+ """
+
+ subitem = self.entry_klass(port_spec)
+ item.addChild(subitem)
+ subitem.setFirstColumnSpanned(True)
+ self.setItemWidget(subitem, 0, subitem.get_widget())
+ item.setExpanded(True)
+ if len(port_spec.descriptors()) == 0:
+ self.update_method(subitem, port_spec.name, [], [])
+
+ def add_method(self, port_name):
+ port_spec, item = self.port_spec_items[port_name]
+ self.do_add_method(port_spec, item)
+
+ def contextMenuEvent(self, event):
+ # Just dispatches the menu event to the widget item
+ item = self.itemAt(event.pos())
+ if item:
+ item.contextMenuEvent(event, self)
+
+class QPortsPane(QtGui.QWidget, QToolWindowInterface):
+ def __init__(self, port_type, parent=None, flags=QtCore.Qt.Widget):
+ QtGui.QWidget.__init__(self, parent, flags)
+ self.port_type = port_type
+ self.build_widget()
+ self.controller = None
+
+ def build_widget(self):
+ self.tree_widget = PortsList(self.port_type)
+ layout = QtGui.QHBoxLayout()
+ layout.setMargin(0)
+ layout.addWidget(self.tree_widget)
+ self.setLayout(layout)
+ self.setWindowTitle('%s Ports' % self.port_type.capitalize())
+
+ def set_controller(self, controller):
+ self.controller = controller
+ self.tree_widget.set_controller(controller)
+
+ def update_module(self, module):
+ self.tree_widget.update_module(module)
+
diff --git a/vistrails/gui/preferences.py b/vistrails/gui/preferences.py
new file mode 100644
index 0000000..ed08003
--- /dev/null
+++ b/vistrails/gui/preferences.py
@@ -0,0 +1,696 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtGui, QtCore
+from vistrails.core import get_vistrails_application
+from vistrails.core.packagemanager import get_package_manager
+from vistrails.core.modules.package import Package
+from vistrails.core.utils import InvalidPipeline
+from vistrails.core.utils.uxml import (named_elements,
+ elements_filter, enter_named_element)
+from vistrails.gui.configuration import (QConfigurationWidget, QGeneralConfiguration,
+ QThumbnailConfiguration)
+from vistrails.gui.module_palette import QModulePalette
+from vistrails.gui.pipeline_view import QPipelineView
+from vistrails.core.configuration import get_vistrails_persistent_configuration, \
+ get_vistrails_configuration
+from vistrails.core import debug
+import os.path
+
+##############################################################################
+
+class QPackageConfigurationDialog(QtGui.QDialog):
+
+ def __init__(self, parent, package):
+ QtGui.QDialog.__init__(self, parent)
+
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+
+
+ self.setWindowTitle('Configuration for package "%s"' % package.name)
+ self._package = package
+ c = package.configuration
+ self._configuration_object = c
+ assert c is not None
+
+ layout = QtGui.QVBoxLayout(self)
+ self.setLayout(layout)
+ self._status_bar = QtGui.QStatusBar(self)
+
+ self._configuration_widget = QConfigurationWidget(self, c, c,
+ self._status_bar)
+ layout.addWidget(self._configuration_widget)
+
+ btns = (QtGui.QDialogButtonBox.Close |
+ QtGui.QDialogButtonBox.RestoreDefaults)
+ self._button_box = QtGui.QDialogButtonBox(btns,
+ QtCore.Qt.Horizontal,
+ self)
+ self.connect(self._button_box,
+ QtCore.SIGNAL('clicked(QAbstractButton *)'),
+ self.button_clicked)
+
+ self.connect(self._configuration_widget._tree.treeWidget,
+ QtCore.SIGNAL('configuration_changed'),
+ self.configuration_changed)
+
+ layout.addWidget(self._status_bar)
+ layout.addWidget(self._button_box)
+
+ def button_clicked(self, button):
+ role = self._button_box.buttonRole(button)
+ if role == QtGui.QDialogButtonBox.ResetRole:
+ txt = ("This will reset all configuration values of " +
+ "this package to their default values. Do you " +
+ "want to proceed?")
+ msg_box = QtGui.QMessageBox(QtGui.QMessageBox.Question,
+ "Really reset?", txt,
+ (QtGui.QMessageBox.Yes |
+ QtGui.QMessageBox.No))
+ if msg_box.exec_() == QtGui.QMessageBox.Yes:
+ self.reset_configuration()
+ else:
+ assert role == QtGui.QDialogButtonBox.RejectRole
+ self.close_dialog()
+
+ def reset_configuration(self):
+ self._package.reset_configuration()
+ conf = self._package.configuration
+ self._configuration_widget.configuration_changed(conf)
+
+ def close_dialog(self):
+ self.done(0)
+
+ def configuration_changed(self, item, new_value):
+ self._package.set_persistent_configuration()
+
+##############################################################################
+
+class QPackagesWidget(QtGui.QWidget):
+
+ # Signals that a package should be selected after the event loop updates (to remove old references)
+ select_package_after_update_signal = QtCore.SIGNAL("select_package_after_update_signal")
+
+ ##########################################################################
+ # Initialization
+
+ def __init__(self, parent, status_bar):
+ QtGui.QWidget.__init__(self, parent)
+ self._status_bar = status_bar
+
+ base_layout = QtGui.QHBoxLayout(self)
+
+ left = QtGui.QFrame(self)
+ right = QtGui.QFrame(self)
+
+ base_layout.addWidget(left)
+ base_layout.addWidget(right, 1)
+
+ ######################################################################
+ left_layout = QtGui.QVBoxLayout(left)
+ left_layout.addWidget(QtGui.QLabel("Disabled packages:", left))
+ self._available_packages_list = QtGui.QListWidget(left)
+ left_layout.addWidget(self._available_packages_list)
+ left_layout.addWidget(QtGui.QLabel("Enabled packages:", left))
+ self._enabled_packages_list = QtGui.QListWidget(left)
+ left_layout.addWidget(self._enabled_packages_list)
+ self.update_button = QtGui.QPushButton("Refresh Lists", left)
+ left_layout.addWidget(self.update_button, 0, QtCore.Qt.AlignLeft)
+
+ self.update_button.clicked.connect(self.populate_lists)
+
+ self.connect(self._available_packages_list,
+ QtCore.SIGNAL('itemSelectionChanged()'),
+ self.selected_available_list,
+ QtCore.Qt.QueuedConnection)
+
+ self.connect(self._enabled_packages_list,
+ QtCore.SIGNAL('itemSelectionChanged()'),
+ self.selected_enabled_list,
+ QtCore.Qt.QueuedConnection)
+
+ sm = QtGui.QAbstractItemView.SingleSelection
+ self._available_packages_list.setSelectionMode(sm)
+ self._enabled_packages_list.setSelectionMode(sm)
+
+
+ ######################################################################
+ right_layout = QtGui.QVBoxLayout(right)
+ info_frame = QtGui.QFrame(right)
+
+ info_layout = QtGui.QVBoxLayout(info_frame)
+ grid_frame = QtGui.QFrame(info_frame)
+ grid_frame.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+
+ info_layout.addWidget(grid_frame)
+ grid_layout = QtGui.QGridLayout(grid_frame)
+ l1 = QtGui.QLabel("Package Name:", grid_frame)
+ grid_layout.addWidget(l1, 0, 0)
+ l2 = QtGui.QLabel("Identifier:", grid_frame)
+ grid_layout.addWidget(l2, 1, 0)
+ l3 = QtGui.QLabel("Version:", grid_frame)
+ grid_layout.addWidget(l3, 2, 0)
+ l4 = QtGui.QLabel("Dependencies:", grid_frame)
+ grid_layout.addWidget(l4, 3, 0)
+ l5 = QtGui.QLabel("Reverse Dependencies:", grid_frame)
+ grid_layout.addWidget(l5, 4, 0)
+ l6 = QtGui.QLabel("Description:", grid_frame)
+ grid_layout.addWidget(l6, 5, 0)
+
+ self._name_label = QtGui.QLabel("", grid_frame)
+ grid_layout.addWidget(self._name_label, 0, 1)
+
+ self._identifier_label = QtGui.QLabel("", grid_frame)
+ grid_layout.addWidget(self._identifier_label, 1, 1)
+
+ self._version_label = QtGui.QLabel("", grid_frame)
+ grid_layout.addWidget(self._version_label, 2, 1)
+
+ self._dependencies_label = QtGui.QLabel("", grid_frame)
+ grid_layout.addWidget(self._dependencies_label, 3, 1)
+
+ self._reverse_dependencies_label = QtGui.QLabel("", grid_frame)
+ grid_layout.addWidget(self._reverse_dependencies_label, 4, 1)
+
+ self._description_label = QtGui.QLabel("", grid_frame)
+ grid_layout.addWidget(self._description_label, 5, 1)
+
+ for lbl in [l1, l2, l3, l4, l5, l6,
+ self._name_label,
+ self._version_label,
+ self._dependencies_label,
+ self._identifier_label,
+ self._reverse_dependencies_label,
+ self._description_label]:
+ lbl.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
+ lbl.setWordWrap(True)
+
+ grid_layout.setRowStretch(4, 1)
+ grid_layout.setColumnStretch(1, 1)
+
+ right_layout.addWidget(info_frame)
+
+ self._enable_button = QtGui.QPushButton("&Enable")
+ self._enable_button.setEnabled(False)
+ self.connect(self._enable_button,
+ QtCore.SIGNAL("clicked()"),
+ self.enable_current_package)
+ self._disable_button = QtGui.QPushButton("&Disable")
+ self._disable_button.setEnabled(False)
+ self.connect(self._disable_button,
+ QtCore.SIGNAL("clicked()"),
+ self.disable_current_package)
+ self._configure_button = QtGui.QPushButton("&Configure...")
+ self._configure_button.setEnabled(False)
+ self.connect(self._configure_button,
+ QtCore.SIGNAL("clicked()"),
+ self.configure_current_package)
+ self._reload_button = QtGui.QPushButton("&Reload")
+ self._reload_button.setEnabled(False)
+ self.connect(self._reload_button,
+ QtCore.SIGNAL("clicked()"),
+ self.reload_current_package)
+ button_box = QtGui.QDialogButtonBox()
+ button_box.addButton(self._enable_button, QtGui.QDialogButtonBox.ActionRole)
+ button_box.addButton(self._disable_button, QtGui.QDialogButtonBox.ActionRole)
+ button_box.addButton(self._configure_button, QtGui.QDialogButtonBox.ActionRole)
+ button_box.addButton(self._reload_button, QtGui.QDialogButtonBox.ActionRole)
+ right_layout.addWidget(button_box)
+
+ self.connect(self,
+ self.select_package_after_update_signal,
+ self.select_package_after_update_slot,
+ QtCore.Qt.QueuedConnection)
+
+ # pm = get_package_manager()
+ # self.connect(pm,
+ # pm.reloading_package_signal,
+ # self.reload_current_package_finisher,
+ # QtCore.Qt.QueuedConnection)
+ app = get_vistrails_application()
+ app.register_notification("pm_reloading_package",
+ self.reload_current_package_finisher)
+ app.register_notification("package_added", self.package_added)
+ app.register_notification("package_removed", self.package_removed)
+
+ self.populate_lists()
+
+ self._current_package = None
+
+ def populate_lists(self):
+ pkg_manager = get_package_manager()
+ enabled_pkgs = sorted(pkg_manager.enabled_package_list())
+ enabled_pkg_dict = dict([(pkg.codepath, pkg) for
+ pkg in enabled_pkgs])
+ self._enabled_packages_list.clear()
+ for pkg in enabled_pkgs:
+ self._enabled_packages_list.addItem(pkg.codepath)
+ self._enabled_packages_list.sortItems()
+ available_pkg_names = [pkg for pkg in
+ sorted(pkg_manager.available_package_names_list())
+ if pkg not in enabled_pkg_dict]
+ self._available_packages_list.clear()
+ for pkg in available_pkg_names:
+ self._available_packages_list.addItem(pkg)
+ self._available_packages_list.sortItems()
+
+ ##########################################################################
+
+ def enable_current_package(self):
+ av = self._available_packages_list
+ item = av.currentItem()
+ codepath = str(item.text())
+ pm = get_package_manager()
+
+ try:
+ new_deps = self._current_package.dependencies()
+ except Exception, e:
+ debug.critical("Failed getting dependencies of package %s, "
+ "so it will not be enabled" % \
+ self._current_package.name, str(e))
+ return
+ from vistrails.core.modules.basic_modules import identifier as basic_modules_identifier
+ if self._current_package.identifier != basic_modules_identifier:
+ new_deps.append(basic_modules_identifier)
+
+ try:
+ pm.check_dependencies(self._current_package, new_deps)
+ except Package.MissingDependency, e:
+ debug.critical("Missing dependencies", str(e))
+ else:
+ palette = QModulePalette.instance()
+ palette.setUpdatesEnabled(False)
+ try:
+ pm.late_enable_package(codepath)
+ except Package.InitializationFailed, e:
+ debug.critical("Initialization of package '%s' failed" %
+ codepath, str(e))
+ raise
+ finally:
+ palette.setUpdatesEnabled(True)
+ # the old code that used to be here to update the lists
+ # has been moved to package_added
+ self.invalidate_current_pipeline()
+
+ def disable_current_package(self):
+ inst = self._enabled_packages_list
+ item = inst.currentItem()
+ codepath = str(item.text())
+ pm = get_package_manager()
+
+ dependency_graph = pm.dependency_graph()
+ identifier = pm.get_package_by_codepath(codepath).identifier
+
+ if dependency_graph.in_degree(identifier) > 0:
+ rev_deps = dependency_graph.inverse_adjacency_list[identifier]
+ debug.critical("Missing dependency",
+ ("There are other packages that depend on this:\n %s" +
+ "Please disable those first.") % rev_deps)
+ else:
+ pm.late_disable_package(codepath)
+ self.invalidate_current_pipeline()
+ # the old code that used to be here to update the lists
+ # has been moved to package_removed
+
+ def configure_current_package(self):
+ dlg = QPackageConfigurationDialog(self, self._current_package)
+ dlg.exec_()
+
+ def reload_current_package(self):
+ # DISABLES the current package and all reverse dependencies
+ inst = self._enabled_packages_list
+ item = inst.currentItem()
+ pm = get_package_manager()
+ codepath = str(item.text())
+
+ palette = QModulePalette.instance()
+ palette.setUpdatesEnabled(False)
+ pm.reload_package_disable(codepath)
+
+ def reload_current_package_finisher(self, codepath, reverse_deps, prefix_dictionary):
+ # REENABLES the current package and all reverse dependencies
+ pm = get_package_manager()
+ try:
+ pm.reload_package_enable(reverse_deps, prefix_dictionary)
+ except Package.InitializationFailed, e:
+ debug.critical("Re-initialization of package '%s' failed" %
+ codepath, str(e))
+ raise
+ finally:
+ self.populate_lists()
+ palette = QModulePalette.instance()
+ palette.setUpdatesEnabled(True)
+ self.select_package_after_update(codepath)
+ self.invalidate_current_pipeline()
+
+ def package_added(self, codepath):
+ # package was added, we need to update list
+ av = self._available_packages_list
+ inst = self._enabled_packages_list
+ items = av.findItems(codepath, QtCore.Qt.MatchExactly)
+ if len(items) < 1:
+ # this is required for basic_modules and abstraction since
+ # they are not in available_package_names_list initially
+ self.populate_lists()
+ items = av.findItems(codepath, QtCore.Qt.MatchExactly)
+ for item in items:
+ pos = av.indexFromItem(item).row()
+ av.takeItem(pos)
+ inst.addItem(item)
+ inst.sortItems()
+ self.select_package_after_update(codepath)
+
+ def package_removed(self, codepath):
+ # package was removed, we need to update list
+ # if we run a late-enable with a prefix (console_mode_test),
+ # we don't actually have the package later
+ self.populate_lists()
+ self.select_package_after_update(codepath)
+
+ def select_package_after_update(self, codepath):
+ # Selecting the package causes self._current_package to be set,
+ # which reference prevents the package from being freed, so we
+ # queue it to select after the event loop completes.
+ self.emit(self.select_package_after_update_signal, codepath)
+
+ def select_package_after_update_slot(self, codepath):
+ inst = self._enabled_packages_list
+ av = self._available_packages_list
+ for item in av.findItems(codepath, QtCore.Qt.MatchExactly):
+ av.setCurrentItem(item)
+ for item in inst.findItems(codepath, QtCore.Qt.MatchExactly):
+ inst.setCurrentItem(item)
+
+ def set_buttons_to_enabled_package(self):
+ self._enable_button.setEnabled(False)
+ assert self._current_package
+ pm = get_package_manager()
+ from vistrails.core.modules.basic_modules import identifier as basic_modules_identifier
+ from vistrails.core.modules.abstraction import identifier as abstraction_identifier
+ is_not_basic_modules = (self._current_package.identifier != basic_modules_identifier)
+ is_not_abstraction = (self._current_package.identifier != abstraction_identifier)
+ can_disable = (pm.can_be_disabled(self._current_package.identifier) and
+ is_not_basic_modules and
+ is_not_abstraction)
+ self._disable_button.setEnabled(can_disable)
+ if not can_disable and is_not_basic_modules and is_not_abstraction:
+ msg = ("Module has reverse dependencies that must\n"+
+ "be first disabled.")
+ self._disable_button.setToolTip(msg)
+ else:
+ self._disable_button.setToolTip("")
+ conf = self._current_package.configuration is not None
+ self._configure_button.setEnabled(conf)
+ self._reload_button.setEnabled(is_not_basic_modules)
+
+ def set_buttons_to_available_package(self):
+ self._configure_button.setEnabled(False)
+ self._disable_button.setEnabled(False)
+ self._enable_button.setEnabled(True)
+ self._reload_button.setEnabled(False)
+
+ def set_package_information(self):
+ """Looks at current package and sets all labels (name,
+ dependencies, etc.) appropriately.
+
+ """
+ assert self._current_package
+ p = self._current_package
+
+ try:
+ p.load()
+ except Exception, e:
+ msg = 'ERROR: Could not load package.'
+ self._name_label.setText(msg)
+ self._version_label.setText(msg)
+ self._identifier_label.setText(msg)
+ self._dependencies_label.setText(msg)
+ self._description_label.setText(msg)
+ self._reverse_dependencies_label.setText(msg)
+ debug.critical('Cannot load package', str(e))
+ else:
+ self._name_label.setText(p.name)
+ try:
+ deps = ', '.join(str(d) for d in p.dependencies()) or \
+ 'No package dependencies.'
+ except Exception, e:
+ debug.critical("Failed getting dependencies of package %s "
+ "" % p.name, str(e))
+ deps = "ERROR: Failed getting dependencies"
+ try:
+ pm = get_package_manager()
+ reverse_deps = \
+ (', '.join(pm.reverse_dependencies(p.identifier)) or
+ 'No reverse dependencies.')
+ except KeyError:
+ reverse_deps = ("Reverse dependencies only " +
+ "available for enabled packages.")
+ self._identifier_label.setText(p.identifier)
+ self._version_label.setText(p.version)
+ self._dependencies_label.setText(deps)
+ self._description_label.setText(p.description)
+ self._reverse_dependencies_label.setText(reverse_deps)
+
+
+ ##########################################################################
+ # Signal handling
+
+ def selected_enabled_list(self):
+ item = self._enabled_packages_list.currentItem()
+ if item is None:
+ return # prevent back and forth looping when clearing selection
+ self._available_packages_list.setCurrentItem(None)
+ codepath = str(item.text())
+ pm = get_package_manager()
+ self._current_package = pm.get_package_by_codepath(codepath)
+ self.set_buttons_to_enabled_package()
+ # A delayed signal can result in the package already has been removed
+ if not pm.has_package(self._current_package.identifier):
+ return
+ self.set_package_information()
+ self._enabled_packages_list.setFocus()
+
+ def selected_available_list(self):
+ item = self._available_packages_list.currentItem()
+ if item is None:
+ return # prevent back and forth looping when clearing selection
+ self._enabled_packages_list.setCurrentItem(None)
+ codepath = str(item.text())
+ pm = get_package_manager()
+ self._current_package = pm.look_at_available_package(codepath)
+ self.set_buttons_to_available_package()
+ self.set_package_information()
+ self._available_packages_list.setFocus()
+
+ def invalidate_current_pipeline(self):
+ from vistrails.gui.vistrails_window import _app
+ _app.invalidate_pipelines()
+
+class QPreferencesDialog(QtGui.QDialog):
+
+ def __init__(self, parent):
+ QtGui.QDialog.__init__(self, parent)
+ self._status_bar = QtGui.QStatusBar(self)
+ self.setWindowTitle('VisTrails Preferences')
+ layout = QtGui.QHBoxLayout(self)
+ layout.setMargin(0)
+ layout.setSpacing(0)
+ self.setLayout(layout)
+
+ f = QtGui.QFrame()
+ layout.addWidget(f)
+
+ l = QtGui.QVBoxLayout(f)
+ f.setLayout(l)
+
+ self._tab_widget = QtGui.QTabWidget(f)
+ l.addWidget(self._tab_widget)
+ self._tab_widget.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+
+ self._general_tab = self.create_general_tab()
+ self._tab_widget.addTab(self._general_tab, 'General Configuration')
+
+ self._thumbs_tab = self.create_thumbs_tab()
+ self._tab_widget.addTab(self._thumbs_tab, 'Thumbnails Configuration')
+
+ self._packages_tab = self.create_packages_tab()
+ self._tab_widget.addTab(self._packages_tab, 'Module Packages')
+
+ self._configuration_tab = self.create_configuration_tab()
+ self._tab_widget.addTab(self._configuration_tab, 'Expert Configuration')
+
+ self._button_box = QtGui.QDialogButtonBox(QtGui.QDialogButtonBox.Close,
+ QtCore.Qt.Horizontal,
+ f)
+ self.connect(self._tab_widget,
+ QtCore.SIGNAL('currentChanged(int)'),
+ self.tab_changed)
+
+ self.connect(self._button_box,
+ QtCore.SIGNAL('clicked(QAbstractButton *)'),
+ self.close_dialog)
+
+ self.connect(self._configuration_tab._tree.treeWidget,
+ QtCore.SIGNAL('configuration_changed'),
+ self.configuration_changed)
+
+ self.connect(self._general_tab,
+ QtCore.SIGNAL('configuration_changed'),
+ self.configuration_changed)
+
+ self.connect(self._thumbs_tab,
+ QtCore.SIGNAL('configuration_changed'),
+ self.configuration_changed)
+
+ l.addWidget(self._button_box)
+ l.addWidget(self._status_bar)
+
+ def close_dialog(self):
+ self.done(0)
+
+ def create_general_tab(self):
+ """ create_general_tab() -> QGeneralConfiguration
+
+ """
+ return QGeneralConfiguration(self,
+ get_vistrails_persistent_configuration(),
+ get_vistrails_configuration())
+
+ def create_thumbs_tab(self):
+ """ create_thumbs_tab() -> QThumbnailConfiguration
+
+ """
+ return QThumbnailConfiguration(self,
+ get_vistrails_persistent_configuration(),
+ get_vistrails_configuration())
+
+ def create_configuration_tab(self):
+ return QConfigurationWidget(self,
+ get_vistrails_persistent_configuration(),
+ get_vistrails_configuration(),
+ self._status_bar)
+
+ def create_packages_tab(self):
+ return QPackagesWidget(self, self._status_bar)
+
+ def sizeHint(self):
+ return QtCore.QSize(800, 600)
+
+ def tab_changed(self, index):
+ """ tab_changed(index: int) -> None
+ Keep general and advanced configurations in sync
+
+ """
+ self._configuration_tab.configuration_changed(
+ get_vistrails_persistent_configuration(),
+ get_vistrails_configuration())
+ self._general_tab.update_state(
+ get_vistrails_persistent_configuration(),
+ get_vistrails_configuration())
+
+ def configuration_changed(self, item, new_value):
+ """ configuration_changed(item: QTreeWidgetItem *,
+ new_value: QString) -> None
+ Write the current session configuration to startup.xml.
+ Note: This is already happening on close to capture configuration
+ items that are not set in preferences. We are doing this here too, so
+ we guarantee the changes were saved before VisTrails crashes.
+
+ """
+ from PyQt4 import QtCore
+ from vistrails.gui.application import get_vistrails_application
+ get_vistrails_application().save_configuration()
+
+
+#############################################################################
+
+import unittest
+
+class TestPreferencesDialog(unittest.TestCase):
+ def test_remove_package(self):
+ """ Tests if the package really gets deleted, and that it gets
+ selected again in the available packages list.
+ """
+
+ pkg = "dialogs"
+ _app = get_vistrails_application()
+ builder = _app.builderWindow
+ builder.showPreferences()
+ prefs = builder.preferencesDialog
+ packages = prefs._packages_tab
+ prefs._tab_widget.setCurrentWidget(packages)
+
+ # check if package is loaded
+ av = packages._available_packages_list
+ for item in av.findItems(pkg, QtCore.Qt.MatchExactly):
+ av.setCurrentItem(item)
+ packages.enable_current_package()
+ QtCore.QCoreApplication.processEvents()
+
+ inst = packages._enabled_packages_list
+ for item in inst.findItems(pkg, QtCore.Qt.MatchExactly):
+ inst.setCurrentItem(item)
+ packages.disable_current_package()
+ QtCore.QCoreApplication.processEvents()
+
+ # force delayed calls
+ packages.populate_lists()
+ packages.select_package_after_update_slot(pkg)
+ QtCore.QCoreApplication.processEvents()
+
+ # This does not work because the selection is delayed
+ av = packages._available_packages_list
+ items = av.selectedItems()
+ self.assertEqual(len(items), 1, "No available items selected!")
+ self.assertEqual(items[0].text(), unicode(pkg),
+ "Wrong available item selected: %s" % items[0].text())
+ # check if configuration has been written correctly
+ startup = _app.vistrailsStartup
+ doc = startup.startup_dom().documentElement
+ disabledpackages = enter_named_element(doc, 'disabledpackages')
+ dpackage = None
+ for package_node in named_elements(disabledpackages, 'package'):
+ if str(package_node.attributes['name'].value) == pkg:
+ dpackage = package_node
+ self.assertIsNotNone(dpackage, "Removed package '%s' is not in unloaded packages list!" % pkg)
+
+ epackages = enter_named_element(doc, 'packages')
+ apackage = None
+ for package_node in named_elements(epackages, 'package'):
+ if str(package_node.attributes['name'].value) == pkg:
+ apackage = package_node
+ self.assertIsNone(apackage, "Removed package '%s' is still in loaded packages list!" % pkg)
diff --git a/vistrails/gui/publishing.py b/vistrails/gui/publishing.py
new file mode 100644
index 0000000..0f6edb1
--- /dev/null
+++ b/vistrails/gui/publishing.py
@@ -0,0 +1,857 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+import os
+
+from vistrails.core.db.locator import FileLocator, DBLocator, UntitledLocator
+from vistrails.core.publishing.parse_latex import parse_latex_file, \
+ parse_vt_command, build_vt_command
+from vistrails.gui.common_widgets import QDockPushButton
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+
+class QLatexFigureItem(QtGui.QListWidgetItem):
+ def __init__(self, opt_dict, parent=None):
+ QtGui.QListWidgetItem.__init__(self, parent)
+ self.opt_dict = opt_dict
+
+ def update_opt_dict(self, opt_dict):
+ self.opt_dict = opt_dict
+
+ def get_opt_dict(self):
+ return self.opt_dict
+
+
+class QLatexAssistant(QtGui.QWidget, QVistrailsPaletteInterface):
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ QtGui.QWidget.__init__(self, parent, f)
+
+ self.set_title("Export To LaTeX")
+
+ # add button to select tex source
+ # listview to select figure
+ # thumbnail display
+ # set figure specific options (show workflow, show execution, show
+ # set includegraphics options
+ source_label = QtGui.QLabel("LaTeX Source:")
+ self.source_edit = QtGui.QLineEdit()
+ source_selector = QDockPushButton("Select...")
+ # source_selector = QtGui.QToolButton()
+ # source_selector.setIcon(QtGui.QIcon(
+ # self.style().standardPixmap(QtGui.QStyle.SP_DirOpenIcon)))
+ # source_selector.setIconSize(QtCore.QSize(12,12))
+ source_selector.setToolTip("Open a file chooser")
+ # source_selector.setAutoRaise(True)
+ self.connect(source_selector,
+ QtCore.SIGNAL('clicked()'),
+ self.selectSource)
+
+ source_group = QtGui.QGroupBox("LaTeX Source")
+ s_layout = QtGui.QHBoxLayout()
+ s_layout.addWidget(source_label)
+ s_layout.addWidget(self.source_edit)
+ s_layout.addWidget(source_selector)
+ s_layout.setStretch(1,1)
+ source_group.setLayout(s_layout)
+
+ self.figure_list = QtGui.QListWidget()
+ self.figure_list.setSelectionMode(self.figure_list.SingleSelection)
+ self.preview_image = QtGui.QLabel()
+ self.preview_image.setScaledContents(False)
+ self.preview_image.setMinimumSize(240, 240)
+ add_figure = QDockPushButton("Add Figure")
+ delete_figure = QDockPushButton("Delete Figure")
+
+ self.connect(add_figure,
+ QtCore.SIGNAL("clicked()"),
+ self.addFigure)
+ self.connect(delete_figure,
+ QtCore.SIGNAL("clicked()"),
+ self.deleteFigure)
+ self.connect(self.figure_list,
+ QtCore.SIGNAL("itemSelectionChanged()"),
+ self.figureSelected)
+
+ figure_group = QtGui.QGroupBox("Figures")
+ figure_layout = QtGui.QGridLayout()
+ figure_layout.addWidget(self.figure_list,0,0,1,2)
+ figure_layout.addWidget(self.preview_image,0,2)
+ figure_layout.addWidget(add_figure,1,0,QtCore.Qt.AlignRight)
+ figure_layout.addWidget(delete_figure,1,1,QtCore.Qt.AlignRight)
+ figure_group.setLayout(figure_layout)
+
+ # figure type, vistrail reference (vt_locator), version (smart tag)
+ # use current version
+ self.figure_type = QtGui.QComboBox()
+ self.figure_type.setEditable(False)
+ # items = []
+ # items << "Workflow Results" << "Workflow Graph" << "History Tree Graph";
+ self.figure_type.addItems(["Workflow Results", "Workflow Graph",
+ "Version Tree"])
+ self.figure_ref = QtGui.QLineEdit()
+ version_label = QtGui.QLabel("Version:")
+ self.figure_version = QtGui.QLineEdit()
+ tag_label = QtGui.QLabel("Tag:")
+ self.figure_tag = QtGui.QComboBox()
+ self.figure_tag.setEditable(True)
+ self.figure_smart = QtGui.QCheckBox("Smart Tag")
+ current_button = QDockPushButton("Use Current")
+
+ self.connect(current_button, QtCore.SIGNAL("clicked()"),
+ self.useCurrent)
+
+ graphicx_label = QtGui.QLabel("Arguments for includegraphics:")
+ self.graphicx_edit = QtGui.QLineEdit()
+
+ self.def_group = QtGui.QGroupBox("Figure Definition")
+ def_layout = QtGui.QVBoxLayout()
+ def_h_layout = QtGui.QHBoxLayout()
+ def_h_layout.addWidget(self.figure_ref)
+ def_h_layout.addWidget(self.figure_type)
+ def_h_layout.setStretch(0,1)
+ def_layout.addLayout(def_h_layout)
+ def_h_layout = QtGui.QHBoxLayout()
+ def_h_layout.addWidget(version_label)
+ def_h_layout.addWidget(self.figure_version)
+ def_h_layout.addWidget(tag_label)
+ def_h_layout.addWidget(self.figure_tag)
+ def_h_layout.addWidget(self.figure_smart)
+ def_h_layout.addWidget(current_button)
+ def_h_layout.setStretch(3,1)
+ def_layout.addLayout(def_h_layout)
+ def_h_layout = QtGui.QHBoxLayout()
+ def_h_layout.addWidget(graphicx_label)
+ def_h_layout.addWidget(self.graphicx_edit)
+ def_h_layout.setStretch(1,1)
+ def_layout.addLayout(def_h_layout)
+ self.def_group.setLayout(def_layout)
+
+ self.chbPdf = QtGui.QCheckBox("As PDF")
+ self.chbCache = QtGui.QCheckBox("Cache Images")
+ self.chbLatexVTL = QtGui.QCheckBox("Include .vtl")
+
+ self.chbWorkflow = QtGui.QCheckBox("Include Workflow")
+ self.chbFullTree = QtGui.QCheckBox("Include Full Tree")
+ self.chbFullTree.setEnabled(False)
+ self.chbExecute = QtGui.QCheckBox("Execute Workflow")
+ self.chbSpreadsheet = QtGui.QCheckBox("Show Spreadsheet Only")
+
+ self.gbEmbedOpt = QtGui.QGroupBox("Embed Options")
+ gblayout = QtGui.QGridLayout()
+ gblayout.addWidget(self.chbPdf, 0, 0)
+ gblayout.addWidget(self.chbCache, 0, 1)
+ gblayout.addWidget(self.chbLatexVTL, 1, 0)
+ self.gbEmbedOpt.setLayout(gblayout)
+
+ self.gbDownOpt = QtGui.QGroupBox("Download Options")
+ gblayout = QtGui.QGridLayout()
+ gblayout.addWidget(self.chbWorkflow, 0, 0)
+ gblayout.addWidget(self.chbFullTree, 0, 1)
+ gblayout.addWidget(self.chbExecute, 1, 0)
+ gblayout.addWidget(self.chbSpreadsheet, 1, 1)
+ self.gbDownOpt.setLayout(gblayout)
+
+ revert_button = QDockPushButton("Revert...")
+ save_button = QDockPushButton("Save...")
+ save_button.setAutoDefault(True)
+
+ self.connect(save_button, QtCore.SIGNAL("clicked()"),
+ self.saveLatex)
+
+ main_layout = QtGui.QVBoxLayout()
+ main_layout.addWidget(source_group)
+ main_layout.addWidget(figure_group)
+ main_layout.addWidget(self.def_group)
+ main_h_layout = QtGui.QHBoxLayout()
+ main_h_layout.addWidget(self.gbEmbedOpt)
+ main_h_layout.addWidget(self.gbDownOpt)
+ main_layout.addLayout(main_h_layout)
+ main_h_layout = QtGui.QHBoxLayout()
+ main_h_layout.setAlignment(QtCore.Qt.AlignRight)
+ main_h_layout.addWidget(revert_button)
+ main_h_layout.addWidget(save_button)
+ main_layout.addLayout(main_h_layout)
+
+ self.setLayout(main_layout)
+
+ self.texts = None
+ self.selected_item = None
+
+ def selectSource(self):
+ fname = QtGui.QFileDialog.getOpenFileName(self,
+ 'Load LaTeX File...',
+ self.source_edit.text(),
+ 'LaTeX files (*.tex)')
+ if fname:
+ self.source_edit.setText(fname)
+ self.texts = parse_latex_file(fname)
+ for cmd_tuple in self.texts[1]:
+ if cmd_tuple:
+ opt_dict = parse_vt_command(*cmd_tuple)
+ item = QLatexFigureItem(opt_dict)
+ item.setText("Figure %d" % (self.figure_list.count() + 1))
+ self.figure_list.addItem(item)
+
+ def readImage(self, opt_dict):
+ if 'pdf' in opt_dict:
+ out_type = 'pdf'
+ else:
+ out_type = 'png'
+ if 'showtree' in opt_dict:
+ version_str = ''
+ else:
+ version_str = '_%s' % opt_dict['version']
+ if 'showworkflow' in opt_dict:
+ graph_str = '_graph'
+ else:
+ graph_str = ''
+
+ if 'filename' in opt_dict:
+ figure_name = "%s%s_%s%s" % (opt_dict['filename'], version_str,
+ out_type, graph_str)
+ else:
+ figure_name = "%s_%s_%s_%s%s_%s%s" % (opt_dict['host'],
+ opt_dict['db'],
+ opt_dict['port'],
+ opt_dict['vtid'],
+ version_str,
+ out_type,
+ graph_str)
+
+ source_dir = os.path.dirname(str(self.source_edit.text()))
+ path_to_figure = os.path.join(source_dir, 'vistrails_images',
+ figure_name)
+
+ #print 'LOOKING FOR %s' % path_to_figure
+ if os.path.exists(path_to_figure):
+ fnames = os.listdir(path_to_figure)
+ for fname in fnames:
+ #print "FOUND", fname
+ if fname.endswith('png'):
+ pixmap = QtGui.QPixmap(os.path.join(path_to_figure, fname))
+ if pixmap.width() > pixmap.height():
+ pixmap = pixmap.scaledToWidth(240,
+ QtCore.Qt.SmoothTransformation)
+ else:
+ pixmap = pixmap.scaledToHeight(240,
+ QtCore.Qt.SmoothTransformation)
+ self.preview_image.setPixmap(pixmap)
+
+
+ def doCheckLink(self, do_set=False, opt_dict=None):
+ check_links = {'pdf': self.chbPdf,
+ 'buildalways': (self.chbCache, True, True),
+ 'getvtl': self.chbLatexVTL,
+ 'execute': self.chbExecute,
+ 'showspreadsheetonly': self.chbSpreadsheet,
+ 'embedworkflow': self.chbWorkflow,
+ 'includefulltree': self.chbFullTree,
+ 'tag': self.figure_smart}
+
+ if opt_dict is None:
+ opt_dict = {}
+ for k, v in check_links.iteritems():
+ opt_set = k in opt_dict
+ if isinstance(v, tuple):
+ chb = v[0]
+ chb_default = v[1]
+ if len(v) > 2:
+ chb_rev = v[2]
+ else:
+ chb_rev = False
+ else:
+ chb = v
+ chb_rev = False
+ chb_default = False
+
+ if do_set:
+ if opt_set:
+ chb.setChecked(not chb_rev)
+ else:
+ chb.setChecked(chb_default)
+ else:
+ if not chb_rev and chb.isChecked():
+ opt_dict[k] = None
+ elif chb_rev and not chb.isChecked():
+ opt_dict[k] = None
+
+ return opt_dict
+
+ def setFigureInfo(self, opt_dict):
+ self.doCheckLink(True, opt_dict)
+
+ if 'showworkflow' in opt_dict:
+ self.figure_type.setCurrentIndex(1)
+ elif 'showtree' in opt_dict:
+ self.figure_type.setCurrentIndex(2)
+ else:
+ self.figure_type.setCurrentIndex(0)
+
+ if 'version' in opt_dict:
+ self.figure_version.setText(str(opt_dict['version']))
+ else:
+ self.figure_version.setText("")
+ if 'tag' in opt_dict:
+ self.figure_tag.setEditText(str(opt_dict['tag'])[1:-1])
+ else:
+ self.figure_tag.setEditText("")
+
+ if '_args' in opt_dict:
+ self.graphicx_edit.setText(opt_dict['_args'])
+
+ # build locator
+ if 'filename' in opt_dict:
+ # set using basedir of tex file
+ fname = opt_dict['filename']
+ if not os.path.isabs(fname):
+ source_dir = os.path.dirname(str(self.source_edit.text()))
+ #print 'source_dir:', str(self.source_edit.text()), source_dir
+ fname = os.path.join(source_dir, fname)
+
+ locator = FileLocator(fname)
+ elif 'host' in opt_dict:
+ if 'port' not in opt_dict:
+ opt_dict['port'] = '3306'
+ port = int(opt_dict['port'])
+ locator = DBLocator(opt_dict['host'], port,
+ opt_dict['db'], '', '',
+ obj_id=opt_dict['vtid'])
+ else:
+ locator = None
+ if locator is not None:
+ self.figure_ref.setText(locator.to_url())
+ else:
+ self.figure_ref.setText("")
+ self.figure_ref.locator = locator
+
+ self.readImage(opt_dict)
+
+ def getFigureInfo(self):
+ # return an opt_dict here...
+ opt_dict = self.doCheckLink(False)
+ if self.figure_type.currentIndex() == 1:
+ opt_dict['showworkflow'] = None
+ elif self.figure_type.currentIndex() == 2:
+ opt_dict['showtree'] = None
+
+ version_text = str(self.figure_version.text())
+ if version_text:
+ opt_dict['version'] = version_text
+ tag_text = str(self.figure_tag.currentText())
+ if self.figure_smart.isChecked() and tag_text:
+ opt_dict['tag'] = '{%s}' % tag_text
+
+ graphicx_text = str(self.graphicx_edit.text())
+ if graphicx_text:
+ opt_dict['_args'] = graphicx_text
+
+ locator = self.figure_ref.locator
+ if isinstance(locator, DBLocator):
+ opt_dict['host'] = locator.host
+ opt_dict['port'] = locator.port
+ opt_dict['db'] = locator.db
+ opt_dict['vtid'] = locator.obj_id
+ else:
+ fname = str(self.source_edit.text())
+ if os.path.dirname(fname) == os.path.dirname(locator.name):
+ # do relative
+ # FIXME do relative via a checkbox!
+ opt_dict['filename'] = os.path.basename(locator.name)
+ else:
+ opt_dict['filename'] = locator.name
+
+ return opt_dict
+
+ def figureSelected(self):
+ selected_items = self.figure_list.selectedItems()
+ if self.selected_item is not None:
+ self.selected_item.update_opt_dict(self.getFigureInfo())
+ #print "NEW OPTIONS:", self.selected_item.opt_dict
+ if len(selected_items) < 1:
+ self.gbEmbedOpt.setEnabled(False)
+ self.gbDownOpt.setEnabled(False)
+ self.def_group.setEnabled(False)
+ self.selected_item = None
+ else:
+ self.gbEmbedOpt.setEnabled(True)
+ self.gbDownOpt.setEnabled(True)
+ self.def_group.setEnabled(True)
+ item = selected_items[0]
+ #print "OPTIONS:", item.opt_dict
+ self.setFigureInfo(item.opt_dict)
+ self.selected_item = item
+
+ def addFigure(self):
+ item = QLatexFigureItem({})
+ item.setText("Figure %d" % (self.figure_list.count() + 1))
+ self.figure_list.addItem(item)
+
+ def deleteFigure(self):
+ selected_items = self.figure_list.selectedItems()
+ if len(selected_items) < 1:
+ return
+ idx = self.figure_list.row(selected_items[0])
+ self.figure_list.takeItem(idx)
+
+ def saveLatex(self):
+ fname = '/vistrails/src/git/extensions/latex/head2.tex'
+ f = open(fname, 'w')
+ raw_texts = self.texts[0]
+ figure_items = [self.figure_list.item(i)
+ for i in xrange(self.figure_list.count())]
+ for i in xrange(len(raw_texts)):
+ f.write(raw_texts[i])
+ if i < len(figure_items):
+ f.write(build_vt_command(figure_items[i].get_opt_dict()))
+ f.close()
+
+ def openVersion(self):
+ pass
+
+ def useCurrent(self):
+ pass
+
+class QVersionEmbed(QtGui.QWidget, QVistrailsPaletteInterface):
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ QtGui.QWidget.__init__(self, parent,
+ f | QtCore.Qt.Tool | QtCore.Qt.WindowStaysOnTopHint)
+ self.setWindowTitle('Publish Workflow')
+ self.setFocusPolicy(QtCore.Qt.ClickFocus)
+ self.versionNumber = None
+ self.versionTag = ''
+ label1 = QtGui.QLabel("Embed:")
+ self.cbcontent = QtGui.QComboBox()
+ self.cbcontent.setEditable(False)
+ items = ["Workflow Results", "Workflow Graph", "History Tree Graph"];
+ self.cbcontent.addItems(items)
+ label2 = QtGui.QLabel("In:")
+
+ self.cbtype = QtGui.QComboBox()
+ self.cbtype.setEditable(False)
+ items = ["Wiki", "Latex", "Shared Memory"];
+ self.cbtype.addItems(items)
+
+ self.controller = None
+ self.pptag = 'Image(s) from (%s,%s,%s,%s,%s)'
+
+ #options
+ self.gbEmbedOpt = QtGui.QGroupBox("Embed Options")
+ self.chbPdf = QtGui.QCheckBox("As PDF")
+ self.chbSmartTag = QtGui.QCheckBox("Smart Tag")
+ self.chbCache = QtGui.QCheckBox("Cache Images")
+ self.chbLatexVTL = QtGui.QCheckBox("Include .vtl")
+ self.chbLatexVTL.setEnabled(False)
+
+ gblayout = QtGui.QGridLayout()
+ gblayout.addWidget(self.chbPdf, 0, 0)
+ gblayout.addWidget(self.chbSmartTag, 0, 1)
+ gblayout.addWidget(self.chbCache, 1, 0)
+ gblayout.addWidget(self.chbLatexVTL, 1, 1)
+ self.gbEmbedOpt.setLayout(gblayout)
+
+ self.gbDownOpt = QtGui.QGroupBox("Download Options")
+ self.chbWorkflow = QtGui.QCheckBox("Include Workflow")
+ self.chbFullTree = QtGui.QCheckBox("Include Full Tree")
+ self.chbFullTree.setEnabled(False)
+ self.chbExecute = QtGui.QCheckBox("Execute Workflow")
+ self.chbSpreadsheet = QtGui.QCheckBox("Show Spreadsheet Only")
+
+ gblayout = QtGui.QGridLayout()
+ gblayout.addWidget(self.chbWorkflow, 0, 0)
+ gblayout.addWidget(self.chbFullTree, 0, 1)
+ gblayout.addWidget(self.chbExecute, 1, 0)
+ gblayout.addWidget(self.chbSpreadsheet, 1, 1)
+ self.gbDownOpt.setLayout(gblayout)
+
+ self.embededt = QtGui.QTextEdit(self)
+ self.embededt.setAcceptRichText(False)
+ self.embededt.setReadOnly(False)
+ # self.exportHtml = '<a href="export">Export...</a>'
+ # self.copyHtml = '<a href="copy">Copy to Clipboard</a>'
+ # self.copylabel = QtGui.QLabel(self.copyHtml)
+ # self.copylabel.setCursor(QtCore.Qt.PointingHandCursor)
+ self.copyButton = QtGui.QPushButton() # "Copy to Clipboard")
+ self.copyButton.setMinimumSize(50, 30)
+ self.link = "copy"
+
+ self.helpLabel = QtGui.QLabel()
+ # "After making your selection, "
+ # "click on 'Copy To Clipboard'. "
+ # "The code changes based on your "
+ # "selection.")
+ self.helpLabel.setWordWrap(True)
+
+ font = QtGui.QFont("Arial", 10, QtGui.QFont.Normal)
+ font.setItalic(True)
+ self.helpLabel.setFont(font)
+
+ layout = QtGui.QGridLayout()
+ layout.addWidget(label1,0,0)
+ layout.addWidget(self.cbcontent,0,1)
+ layout.addWidget(label2,1,0)
+ layout.addWidget(self.cbtype,1,1)
+ layout.addWidget(self.gbEmbedOpt,2,0,1,2)
+ layout.addWidget(self.gbDownOpt,3,0,1,2)
+ layout.addWidget(self.embededt,4,0,1,-1)
+ layout.addWidget(self.helpLabel,5,0,1,2)
+ layout.addWidget(self.copyButton,6,1,QtCore.Qt.AlignRight)
+
+ self.setLayout(layout)
+ self.changeEmbedType("Wiki")
+
+ #connect signals
+ self.connect(self.cbtype,
+ QtCore.SIGNAL("activated(const QString &)"),
+ self.changeEmbedType)
+
+ # self.connect(self.copylabel,
+ # QtCore.SIGNAL("linkActivated(const QString &)"),
+ # self.linkActivated)
+
+ self.connect(self.copyButton,
+ QtCore.SIGNAL("clicked()"),
+ self.copyClicked)
+
+ self.connect(self.cbcontent,
+ QtCore.SIGNAL("activated(const QString &)"),
+ self.changeOption)
+
+ optlist = [self.cbcontent,
+ self.chbPdf,
+ self.chbSmartTag,
+ self.chbCache,
+ self.chbLatexVTL,
+ self.chbWorkflow,
+ self.chbFullTree,
+ self.chbExecute,
+ self.chbSpreadsheet]
+ for cb in optlist:
+ self.connect(cb, QtCore.SIGNAL("toggled(bool)"),
+ self.changeOption)
+ #special cases
+ self.connect(self.chbWorkflow, QtCore.SIGNAL("toggled(bool)"),
+ self.changeIncludeWorkflow)
+ self.connect(self.chbSpreadsheet, QtCore.SIGNAL("toggled(bool)"),
+ self.changeShowSpreadsheet)
+ self.connect(self.chbExecute, QtCore.SIGNAL("toggled(bool)"),
+ self.changeExecute)
+ self.connect(self.cbcontent,
+ QtCore.SIGNAL("activated(const QString &)"),
+ self.changeContent)
+ self.connect(self.chbSmartTag, QtCore.SIGNAL("toggled(bool)"),
+ self.changeSmartTag)
+ self.connect(self.chbCache, QtCore.SIGNAL("toggled(bool)"),
+ self.changeCache)
+
+ def set_controller(self, controller):
+ self.controller = controller
+
+ def closeEvent(self,e):
+ """ closeEvent(e: QCloseEvent) -> None
+ Doesn't allow the Legend widget to close, but just hide
+ instead
+
+ """
+ e.ignore()
+ self.hide()
+
+ def focusInEvent(self, event):
+ if self.controller:
+ if self.controller.locator and \
+ not isinstance(self.controller.locator, UntitledLocator):
+ from vistrails.gui.vistrails_window import _app
+ _app.ensureVistrail(self.controller.locator)
+
+
+ def checkLocator(self):
+ """checkLocator() -> bool
+ Only vistrails on a database are allowed to embed a tag"""
+ result = False
+ if self.controller:
+ if self.controller.locator and \
+ not isinstance(self.controller.locator, UntitledLocator):
+ title = "Embed Options for %s"%self.controller.locator.name
+ self.setWindowTitle(title)
+ result = True
+ return result
+
+ def checkControllerStatus(self):
+ """checkControllerStatus() -> bool
+ this checks if the controller has saved the latest changes """
+ result = False
+ if self.controller:
+ result = not self.controller.changed
+ return result
+
+ def updateEmbedText(self):
+ ok = (self.checkLocator() and self.checkControllerStatus() and
+ self.versionNumber > 0)
+ self.embededt.setEnabled(ok)
+ self.copyButton.setEnabled(ok)
+ self.embededt.setText('')
+
+ if self.controller and self.versionNumber > 0:
+ if self.controller.locator and \
+ not isinstance(self.controller.locator, UntitledLocator) and \
+ not self.controller.changed:
+ loc = self.controller.locator
+ if hasattr(loc,'host'):
+ self.updateCbtype('db')
+ elif hasattr(loc, 'name'):
+ self.updateCbtype('file')
+
+ if self.versionTag != "":
+ self.chbSmartTag.setEnabled(True)
+ else:
+ self.chbSmartTag.setChecked(False)
+ self.chbSmartTag.setEnabled(False)
+
+ self.setEmbedText()
+ elif self.controller.changed:
+ self.embededt.setPlainText('You must save your vistrail to proceed')
+ else:
+ self.embededt.setPlainText('')
+
+ def setEmbedText(self):
+ #check options
+ options = {}
+ options['content'] = str(self.cbcontent.currentText())
+ options['pdf'] = self.chbPdf.isChecked()
+ options['smartTag'] = self.chbSmartTag.isChecked()
+ options['buildalways'] = not self.chbCache.isChecked()
+ options['includeWorkflow'] = self.chbWorkflow.isChecked()
+ options['includeFullTree'] = self.chbFullTree.isChecked()
+ options['execute'] = self.chbExecute.isChecked()
+ options['showspreadsheetonly'] = self.chbSpreadsheet.isChecked()
+
+ if str(self.cbtype.currentText()) == "Wiki":
+ text = self.buildWikiTag(options)
+ elif str(self.cbtype.currentText()) == "Latex":
+ options['getvtl'] = self.chbLatexVTL.isChecked()
+ text = self.buildLatexCommand(options)
+ elif str(self.cbtype.currentText()) == "Shared Memory":
+ text = self.pptag
+ self.embededt.setPlainText(text)
+
+ def updateVersion(self, versionNumber):
+ self.versionNumber = versionNumber
+ if versionNumber > 0:
+ self.versionTag = self.controller.vistrail.getVersionName(self.versionNumber)
+ self.updateEmbedText()
+
+ def copyClicked(self):
+ if self.link == 'copy':
+ clipboard = QtGui.QApplication.clipboard()
+ clipboard.setText(self.embededt.toPlainText())
+ elif self.link=='export':
+ app = QtCore.QCoreApplication.instance()
+ app.builderWindow.interactiveExportCurrentPipeline()
+
+ # def linkActivated(self, link):
+ # if link=='copy':
+ # clipboard = QtGui.QApplication.clipboard()
+ # clipboard.setText(self.embededt.toPlainText())
+ # elif link=='export':
+ # app = QtCore.QCoreApplication.instance()
+ # app.builderWindow.interactiveExportCurrentPipeline()
+
+ def switchType(self, text):
+ if text == 'Wiki':
+ index = 0
+ elif text == "Latex":
+ if self.cbtype.count() > 1:
+ index = 1
+ else:
+ index = 0
+ else:
+ index = 2
+ self.cbtype.setCurrentIndex(index)
+ self.changeEmbedType(text)
+
+ def changeEmbedType(self, text):
+ """changeEmbedType(text) -> None
+ This is called when the combobox is activated so the proper gui elements
+ are enabled.
+
+ """
+ if text!='Shared Memory':
+ # self.copylabel.setText(self.copyHtml)
+ self.link = 'copy'
+ self.copyButton.setText("Copy to Clipboard")
+ self.helpLabel.setText("After making your selections, "
+ "click on 'Copy To Clipboard'. "
+ "The code changes based on your "
+ "selections.")
+ else:
+ # self.copylabel.setText(self.exportHtml)
+ self.link = 'export'
+ self.copyButton.setText("Export...")
+ self.helpLabel.setText("After making your selections, "
+ "click 'Export...'. The code changes "
+ "based on your selections.")
+ self.chbLatexVTL.setEnabled(text == 'Latex')
+ self.chbPdf.setEnabled(text == 'Latex')
+ if self.controller is not None:
+ self.updateEmbedText()
+
+ def changeOption(self, value):
+ self.updateEmbedText()
+
+ def changeContent(self, text):
+ if text == "Workflow Results":
+ self.chbExecute.setEnabled(True)
+ self.chbSpreadsheet.setEnabled(True)
+ self.chbCache.setEnabled(True)
+ self.chbSmartTag.setEnabled(True)
+ else:
+ self.chbExecute.setChecked(False)
+ self.chbSpreadsheet.setChecked(False)
+ self.chbExecute.setEnabled(False)
+ self.chbSpreadsheet.setEnabled(False)
+ if text == "History Tree Graph":
+ self.chbCache.setChecked(False)
+ self.chbCache.setEnabled(False)
+ self.chbSmartTag.setChecked(False)
+ self.chbSmartTag.setEnabled(False)
+ else:
+ self.chbCache.setEnabled(True)
+ self.chbSmartTag.setEnabled(True)
+
+ def updateCbtype(self, type):
+ currentText = self.cbtype.currentText()
+ self.cbtype.clear()
+ items = []
+ if type == 'db':
+ items = ["Wiki", "Latex", "Shared Memory"]
+ elif type == 'file':
+ items = ["Latex"]
+ self.cbtype.addItems(items)
+ try:
+ index = items.index(currentText)
+ except ValueError:
+ index = -1
+ if index > 0:
+ self.cbtype.setCurrentIndex(index)
+ text = str(self.cbtype.currentText())
+ self.chbLatexVTL.setVisible(text == 'Latex')
+ self.chbPdf.setEnabled(text == 'Latex')
+
+ def buildLatexCommand(self, options):
+ text = '\\vistrail['
+ loc = self.controller.locator
+ if hasattr(loc, 'host'):
+ text += 'host=%s,\ndb=%s,\nport=%s,\nvtid=%s,\n'% (loc.host,
+ loc.db,
+ loc.port,
+ loc.obj_id)
+ else:
+ text += 'filename=%s,\n' % os.path.basename(loc.name)
+ if options['content'] != "History Tree Graph":
+ text += 'version=%s,\n'%self.versionNumber
+ if options['smartTag']:
+ text += 'tag={%s},\n'%self.versionTag
+ if options['pdf']:
+ text += 'pdf,\n'
+ if options['buildalways']:
+ text+= 'buildalways,\n'
+ if options['getvtl']:
+ text += 'getvtl,\n'
+ if options['includeWorkflow']:
+ text+= 'embedworkflow,\n'
+ if options['includeFullTree']:
+ text += 'includefulltree,\n'
+ if options['content'] == "Workflow Graph":
+ text += 'showworkflow,\n'
+ elif options['content'] == "History Tree Graph":
+ text += 'showtree,\n'
+ else:
+ if options['execute']:
+ text += 'execute,\n'
+ if options['showspreadsheetonly']:
+ text += 'showspreadsheetonly,\n'
+
+ text = text[0:-2] + "]{}"
+ return text
+
+ def buildWikiTag(self, options):
+ text = '<vistrail '
+ loc = self.controller.locator
+
+ text += 'host="%s" db="%s" port="%s" vtid="%s" '% (loc.host,
+ loc.db,
+ loc.port,
+ loc.obj_id)
+ if options['content'] != "History Tree Graph":
+ text += 'version="%s" '%self.versionNumber
+ if options['smartTag']:
+ text += 'tag="%s " '%self.versionTag
+ if options['buildalways']:
+ text+= 'buildalways="True" '
+ if options['includeWorkflow']:
+ text+= 'embedworkflow="True" '
+ if options['includeFullTree']:
+ text += 'includefulltree="True" '
+ if options['content'] == "Workflow Graph":
+ text += 'showworkflow="True" ' #"Workflow Results" << "Workflow Graph" << "History Tree Graph";
+ elif options['content'] == "History Tree Graph":
+ text += 'showtree="True" '
+ else:
+ if options['execute']:
+ text += 'execute="True" '
+ if options['showspreadsheetonly']:
+ text += 'showspreadsheetonly="True" '
+
+ text += "/>"
+ return text
+
+ def changeIncludeWorkflow(self,checked):
+ self.chbFullTree.setEnabled(checked)
+ if self.cbcontent.currentText() == "History Tree Graph":
+ self.chbFullTree.setChecked(checked)
+
+ def changeShowSpreadsheet(self, checked):
+ if checked:
+ self.chbExecute.setChecked(True)
+
+ def changeExecute(self, checked):
+ if not checked:
+ self.chbSpreadsheet.setChecked(False)
+
+ def changeSmartTag(self, checked):
+ if checked and self.cbtype.currentText() == 'Latex':
+ self.chbCache.setChecked(False)
+
+ def changeCache(self, checked):
+ if checked and self.cbtype.currentText() == 'Latex':
+ self.chbSmartTag.setChecked(False)
diff --git a/vistrails/gui/qt.py b/vistrails/gui/qt.py
new file mode 100644
index 0000000..3f8d217
--- /dev/null
+++ b/vistrails/gui/qt.py
@@ -0,0 +1,220 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""The only reason this module exists is to try to prevent QObjects
+from being created before a QApplication gets constructed. The problem
+with a QObject being constructed before a QApplication is that signals
+and slots do not get connected, leading to hard-to-spot bugs.
+
+Notice that there is no hard enforcement - if the client code does not
+ask for permission, nothing stops it from creating QObjects (which
+won't work correctly). Even worse, nothing stops a malicious object
+from setting okToCreateQObjects directly.
+
+As the python saying goes, 'we are all consenting adults here'."""
+
+import inspect
+from PyQt4 import QtGui, QtCore
+import types
+
+################################################################################
+
+class qt_super(object):
+
+ def __init__(self, class_, obj):
+ self._class = class_
+ self._obj = obj
+
+ def __getattr__(self, attr):
+ s = super(self._class, self._obj)
+ try:
+ return getattr(s, attr)
+ except AttributeError, e:
+ mro = type(self._obj).mro()
+ try:
+ ix = mro.index(self._class)
+ except ValueError:
+ raise TypeError("qt_super: obj must be an instance of class")
+
+ for class_ in mro[ix+1:]:
+ try:
+ unbound_meth = getattr(class_, attr)
+ return types.MethodType(unbound_meth, self._obj, class_)
+ except AttributeError:
+ pass
+ raise e
+
+################################################################################
+
+class DisallowedCaller(Exception):
+ """This expection is raised whenever a caller that's not privileged to
+allow QObject construction tries to do so."""
+ def __str__(self):
+ return "Caller is not allowed to call this function"
+
+class QApplicationNotYetCreated(Exception):
+ """This expection is raised whenever a function asks for permission to
+create a QObject but the QApplication has not granted it yet."""
+ def __str__(self):
+ return "QApplication has not been created yet"
+
+def allowQObjects():
+ """Allows subsequent QObject creation. The constructor for the
+QApplication-derived class must call this so that we know it's alright
+to start creating other QtCore.QObjects."""
+
+ # tries to check if caller is allowed to call this
+ caller = inspect.currentframe().f_back
+ d = caller.f_locals
+ if (not d.has_key('self') or
+ not isinstance(d['self'], QtCore.QCoreApplication)):
+ raise DisallowedCaller
+ global okToCreateQObjects
+ okToCreateQObjects = True
+
+def askForQObjectCreation():
+ """This function simply throws an exception if it is not yet ok
+to create QObjects."""
+ global okToCreateQObjects
+ if not okToCreateQObjects:
+ raise QApplicationNotYetCreated()
+
+global _appHolder
+_appHolder = None
+
+def createBogusQtGuiApp(argv=["bogus"]):
+ """createBogusQtGuiApp creates a bogus QtApplication so we can
+ create qobjects during test runs.
+ """
+ class BogusApplication(QtGui.QApplication):
+ def __init__(self):
+ QtGui.QApplication.__init__(self, argv)
+ allowQObjects()
+ global _appHolder
+ if QtGui.qApp:
+ _appHolder = QtGui.qApp
+ if not _appHolder:
+ _appHolder = BogusApplication()
+ return _appHolder
+
+def destroyBogusQtApp():
+ global _appHolder
+ del _appHolder
+
+def qt_version():
+ return [int(i)
+ for i in
+ QtCore.qVersion().split('.')]
+
+################################################################################
+
+okToCreateQObjects = False
+
+class SignalSet(object):
+
+ """SignalSet stores a list of (object, signal, method) that can be
+ all connected and disconnected simultaneously. This way, it's
+ harder to forget to disconnect one of many signals. Also, if the
+ SignalSet has already been plugged, it will signal an exception,
+ to avoid multiple connections."""
+
+ def __init__(self, owner, signalTripleList):
+ self.owner = owner
+ self.signalTripleList = signalTripleList
+ self.plugged = False
+
+ def plug(self):
+ if self.plugged:
+ raise ValueError("SignalSet %s is already plugged" % self)
+ for tupl in self.signalTripleList:
+ self.owner.connect(*tupl)
+ self.plugged = True
+
+ def unplug(self):
+ if not self.plugged:
+ return
+ for tupl in self.signalTripleList:
+ self.owner.disconnect(*tupl)
+ self.plugged = False
+
+
+################################################################################
+
+_oldConnect = QtCore.QObject.connect
+_oldDisconnect = QtCore.QObject.disconnect
+_oldEmit = QtCore.QObject.emit
+
+def _wrapConnect(callableObject):
+ """Returns a wrapped call to the old version of QtCore.QObject.connect"""
+ @staticmethod
+ def call(*args):
+ callableObject(*args)
+ _oldConnect(*args)
+ return call
+
+def _wrapDisconnect(callableObject):
+ """Returns a wrapped call to the old version of QtCore.QObject.disconnect"""
+ @staticmethod
+ def call(*args):
+ callableObject(*args)
+ _oldDisconnect(*args)
+ return call
+
+def enableSignalDebugging(**kwargs):
+ """Call this to enable Qt Signal debugging. This will trap all
+ connect, disconnect and emit calls. For example:
+
+ enableSignalDebugging(connectCall=callable1, disconnectCall=callable2,
+ emitCall=callable3)
+
+ will call callable1, 2 and 3 when the respective Qt methods are issued.
+ """
+
+ f = lambda *args: None
+ connectCall = kwargs.get('connectCall', f)
+ disconnectCall = kwargs.get('disconnectCall', f)
+ emitCall = kwargs.get('emitCall', f)
+
+ def printIt(msg):
+ def call(*args):
+ print msg, args
+ return call
+ QtCore.QObject.connect = _wrapConnect(connectCall)
+ QtCore.QObject.disconnect = _wrapDisconnect(disconnectCall)
+
+ def new_emit(self, *args):
+ emitCall(self, *args)
+ _oldEmit(self, *args)
+
+ QtCore.QObject.emit = new_emit
diff --git a/vistrails/gui/query_view.py b/vistrails/gui/query_view.py
new file mode 100644
index 0000000..0b09ef3
--- /dev/null
+++ b/vistrails/gui/query_view.py
@@ -0,0 +1,595 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core.collection import Collection
+from vistrails.core.collection.vistrail import VistrailEntity
+from vistrails.core.data_structures.bijectivedict import Bidict
+from vistrails.core.query.combined import CombinedSearch
+from vistrails.core.query.multiple import MultipleSearch
+from vistrails.core.query.version import SearchCompiler, SearchParseError, TrueSearch
+from vistrails.core.query.visual import VisualQuery
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.vistrail.vistrail import Vistrail
+
+from vistrails.gui.base_view import BaseView
+from vistrails.gui.common_widgets import QSearchBox
+from vistrails.gui.modules import get_query_widget_class
+from vistrails.gui.pipeline_view import QPipelineView
+from vistrails.gui.ports_pane import ParameterEntry
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.version_view import QVersionTreeView
+from vistrails.gui.vistrail_controller import VistrailController
+
+class QueryController(object):
+ LEVEL_ALL = 0
+ LEVEL_VISTRAIL = 1
+ LEVEL_WORKFLOW = 2
+
+ def __init__(self, query_view=None):
+ self.query_view = query_view
+ self.search = None
+ self.search_str = None
+ self.search_pipeline = None
+ self.search_level = 3
+ self.vt_controller = None
+ self.level = QueryController.LEVEL_VISTRAIL
+ self.workflow_version = None
+
+ def set_level(self, level):
+ self.query_view.query_box.setLevel(level)
+ self.level_changed(level)
+
+ def level_changed(self, level):
+ self.query_view.set_result_level(level)
+ if level >= QueryController.LEVEL_VISTRAIL and \
+ self.query_view.query_box.backButton.isEnabled():
+ self.query_view.query_box.editButton.setEnabled(True)
+ else:
+ self.query_view.query_box.editButton.setEnabled(False)
+ self.level = level
+
+ def set_query_view(self, query_view=None):
+ self.query_view = query_view
+
+ def set_vistrail_controller(self, vt_controller):
+ self.vt_controller = vt_controller
+
+ def set_search(self, search=None):
+ self.search = search
+ self.query_view.version_result_view.controller.search = search
+ self.query_view.workflow_result_view.controller.search = search
+
+ def run_search(self, search_str=None):
+ """ set_search(search_str: str) -> None
+ Change the currrent version tree search statement
+
+ """
+ search_pipeline = \
+ self.query_view.pipeline_view.scene().current_pipeline
+ if search_str is None:
+ search_str = self.query_view.query_box.getCurrentText()
+ self.query_view.update_controller()
+ if self.search is None or \
+ self.search.search_str != search_str or \
+ self.search.queryPipeline != search_pipeline or \
+ self.query_view.p_controller.changed or \
+ self.search_level > self.level:
+ self.search_str = search_str
+ self.search_pipeline = search_pipeline
+ self.search_level = self.level
+ # reset changed here
+ self.query_view.p_controller.set_changed(False)
+ vt_controller = self.query_view.vt_controller
+ current_vistrail = self.vt_controller.vistrail
+
+ def do_search(only_current_vistrail=False,
+ only_current_workflow=False):
+ entities_to_check = {}
+ open_col = Collection.getInstance()
+
+ for entity in open_col.get_current_entities():
+ if entity.type_id == VistrailEntity.type_id and \
+ entity.is_open:
+ controller = entity._window.controller
+ if only_current_vistrail and \
+ controller.vistrail != vt_controller.vistrail:
+ continue
+ if only_current_workflow:
+ versions_to_check = controller.current_version
+ else:
+ graph = controller._current_terse_graph
+ versions_to_check = set(graph.vertices.iterkeys())
+ entities_to_check[entity] = versions_to_check
+ self.set_search(MultipleSearch(search_str, search_pipeline,
+ entities_to_check))
+ self.search.run()
+ return self.search.getResultEntities()
+
+ if self.level == QueryController.LEVEL_VISTRAIL:
+ result_entities = do_search(True)
+ self.show_vistrail_matches()
+ elif self.level == QueryController.LEVEL_WORKFLOW:
+ self.search_level = QueryController.LEVEL_VISTRAIL
+ result_entities = do_search(True)
+ self.update_version_tree()
+ self.show_workflow_matches()
+ elif self.level == QueryController.LEVEL_ALL:
+ result_entities = do_search()
+ self.show_global_matches()
+
+ from vistrails.gui.vistrails_window import _app
+ _app.notify("search_changed", self.search, result_entities)
+ else:
+ self.query_view.set_to_result_mode()
+
+ def set_refine(self, refine):
+ """ set_refine(refine: bool) -> None
+ Set the refine state to True or False
+
+ """
+ self.query_view.version_result_view.controller.set_refine(refine)
+
+ def reset_search(self):
+ self.search = None
+ self.search_pipeline = None
+ self.query_view.pipeline_view.controller.change_selected_version(0)
+ self.query_view.pipeline_view.scene().setupScene(
+ self.query_view.pipeline_view.controller.current_pipeline)
+ self.query_view.set_to_search_mode()
+ self.query_view.query_box.searchBox.clearSearch()
+ self.query_view.vistrailChanged()
+
+ from vistrails.gui.vistrails_window import _app
+ _app.notify("search_changed", None, None)
+
+ def back_to_search(self):
+ self.query_view.set_to_search_mode()
+
+ def goto_edit(self):
+ # get the version info and send it to open_vistrail call
+ if self.level == QueryController.LEVEL_VISTRAIL:
+ from vistrails.gui.vistrails_window import _app
+ _app.qactions['history'].trigger()
+ elif self.level == QueryController.LEVEL_WORKFLOW:
+ from vistrails.gui.vistrails_window import _app
+ version = self.query_view.vt_controller.current_version
+ self.query_view.controller.change_selected_version(version, True)
+ _app.qactions['pipeline'].trigger()
+
+ def update_results(self):
+ if self.workflow_version != \
+ self.query_view.vt_controller.current_version:
+ result_view = self.query_view.workflow_result_view
+ result_view.scene().setupScene(
+ result_view.controller.current_pipeline)
+ result_view.scene().fitToView(result_view, True)
+ self.workflow_version = \
+ self.query_view.vt_controller.current_version
+
+ def update_version_tree(self):
+ result_view = self.query_view.version_result_view
+ if result_view.controller.refine:
+ result_view.controller.recompute_terse_graph()
+ result_view.controller.invalidate_version_tree()
+
+ def show_vistrail_matches(self, *args, **kwargs):
+ if self.level != QueryController.LEVEL_VISTRAIL:
+ self.set_level(QueryController.LEVEL_VISTRAIL)
+ self.query_view.set_to_result_mode()
+ result_view = self.query_view.version_result_view
+ if result_view.controller.refine:
+ result_view.controller.recompute_terse_graph()
+ result_view.controller.invalidate_version_tree(*args, **kwargs)
+
+ def show_workflow_matches(self):
+ if self.level != QueryController.LEVEL_WORKFLOW:
+ self.set_level(QueryController.LEVEL_WORKFLOW)
+ self.query_view.set_to_result_mode()
+ result_view = self.query_view.workflow_result_view
+ result_view.scene().setupScene(result_view.controller.current_pipeline)
+ result_view.scene().fitToView(result_view, True)
+
+ def show_global_matches(self):
+ if self.level != QueryController.LEVEL_ALL:
+ self.set_level(QueryController.LEVEL_ALL)
+ self.query_view.set_to_result_mode()
+
+ # def invalidate_version_tree(self, *args, **kwargs):
+ # self.query_view.set_to_result_mode()
+ # result_view = self.query_view.version_result_view
+ # result_view.controller.search = self.search
+ # result_view.controller.search_str = self.search_str
+ # result_view.controller.invalidate_version_tree(*args, **kwargs)
+
+ # def recompute_terse_graph(self, *args, **kwargs):
+ # self.query_view.set_to_result_mode()
+ # result_view = self.query_view.version_result_view
+ # result_view.controller.search = self.search
+ # result_view.controller.search_str = self.search_str
+ # result_view.controller.recompute_terse_graph(*args, **kwargs)
+
+
+class QQueryPipelineView(QPipelineView):
+ def __init__(self, parent=None):
+ QPipelineView.__init__(self, parent)
+ self.setBackgroundBrush(CurrentTheme.QUERY_BACKGROUND_BRUSH)
+ self.scene().current_pipeline = Pipeline()
+ self.query_controller = None
+
+ def set_query_controller(self, controller):
+ self.query_controller = controller
+
+ def execute(self):
+ self.query_controller.run_search(None)
+
+class QQueryResultGlobalView(QtGui.QWidget):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ layout = QtGui.QVBoxLayout()
+ label = QtGui.QLabel("See Workspace Window")
+ label.setAlignment(QtCore.Qt.AlignCenter)
+ layout.addWidget(label, QtCore.Qt.AlignCenter)
+ self.setLayout(layout)
+ # self.setBackgroundBrush(CurrentTheme.QUERY_RESULT_BACKGROUND_BRUSH)
+
+class QQueryResultVersionView(QVersionTreeView):
+ def __init__(self, parent=None):
+ QVersionTreeView.__init__(self, parent)
+ self.setBackgroundBrush(CurrentTheme.QUERY_RESULT_BACKGROUND_BRUSH)
+
+class QQueryResultWorkflowView(QPipelineView):
+ def __init__(self, parent=None):
+ QPipelineView.__init__(self, parent)
+ self.setBackgroundBrush(CurrentTheme.QUERY_RESULT_BACKGROUND_BRUSH)
+ self.scene().set_read_only_mode(True)
+
+class QQueryBox(QtGui.QWidget):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.build_widget()
+ self.controller = None
+
+ def set_controller(self, controller=None):
+ self.controller = controller
+
+ def build_widget(self):
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(4)
+ layout.setSpacing(2)
+ self.searchBox = QSearchBox(True, False, self)
+ layout.addWidget(self.searchBox)
+ radio_layout = QtGui.QHBoxLayout()
+ radio_layout.setSpacing(5)
+ radio_layout.setAlignment(QtCore.Qt.AlignLeft)
+ radio_layout.addWidget(QtGui.QLabel("Search:"))
+ searchAll = QtGui.QRadioButton("Open Vistrails")
+ searchCurrent = QtGui.QRadioButton("Current Vistrail")
+ searchWorkflow = QtGui.QRadioButton("Current Workflow")
+ self.level_group = QtGui.QButtonGroup()
+ self.level_group.addButton(searchAll)
+ self.level_group.addButton(searchCurrent)
+ self.level_group.addButton(searchWorkflow)
+ self.level_map = \
+ Bidict([(QueryController.LEVEL_ALL, searchAll),
+ (QueryController.LEVEL_VISTRAIL, searchCurrent),
+ (QueryController.LEVEL_WORKFLOW, searchWorkflow)])
+ radio_layout.addWidget(searchAll)
+ radio_layout.addWidget(searchCurrent)
+ radio_layout.addWidget(searchWorkflow)
+ searchCurrent.setChecked(True)
+
+ self.editButton = QtGui.QPushButton("Edit")
+ self.editButton.setEnabled(False)
+ self.backButton = QtGui.QPushButton("Back to Search")
+ self.backButton.setEnabled(False)
+ radio_layout.addStretch(1)
+ radio_layout.addWidget(self.editButton, 0, QtCore.Qt.AlignRight)
+ radio_layout.addWidget(self.backButton, 0, QtCore.Qt.AlignRight)
+ layout.addLayout(radio_layout)
+ self.setLayout(layout)
+
+ self.connect(self.searchBox, QtCore.SIGNAL('resetSearch()'),
+ self.resetSearch)
+ self.connect(self.searchBox, QtCore.SIGNAL('executeSearch(QString)'),
+ self.executeSearch)
+ self.connect(self.searchBox, QtCore.SIGNAL('refineMode(bool)'),
+ self.refineMode)
+ self.connect(self.backButton, QtCore.SIGNAL('clicked()'),
+ self.backToSearch)
+ self.connect(self.editButton, QtCore.SIGNAL('clicked()'),
+ self.doEdit)
+ self.connect(self.level_group,
+ QtCore.SIGNAL('buttonClicked(QAbstractButton*)'),
+ self.levelChanged)
+
+ def resetSearch(self, emit_signal=True):
+ """
+ resetSearch() -> None
+
+ """
+ if self.controller and emit_signal:
+ self.controller.reset_search()
+ self.emit(QtCore.SIGNAL('textQueryChange(bool)'), False)
+ else:
+ self.searchBox.clearSearch()
+
+ def backToSearch(self):
+ if self.controller:
+ self.controller.back_to_search()
+
+ def doEdit(self):
+ if self.controller:
+ self.controller.goto_edit()
+
+ def levelChanged(self, button):
+ self.controller.set_level(self.level_map.inverse[button])
+
+ def setLevel(self, level):
+ self.level_map[level].setChecked(True)
+
+ def executeSearch(self, text):
+ """
+ executeSearch(text: QString) -> None
+
+ """
+ s = str(text)
+ if self.controller:
+ self.controller.run_search(s)
+ # try:
+ # search = CombinedSearch(s,
+ # search = SearchCompiler(s).searchStmt
+ # except SearchParseError, e:
+ # debug.warning("Search Parse Error", str(e))
+ # search = None
+ # self.controller.set_search(search, s)
+ # self.emit(QtCore.SIGNAL('textQueryChange(bool)'), s!='')
+
+ def refineMode(self, on):
+ """
+ refineMode(on: bool) -> None
+
+ """
+ if self.controller:
+ self.controller.set_refine(on)
+
+ def getCurrentText(self):
+ return self.searchBox.getCurrentText()
+
+ def setManualResetEnabled(self, boolVal):
+ self.searchBox.setManualResetEnabled(boolVal)
+
+class QQueryView(QtGui.QWidget, BaseView):
+ VISUAL_SEARCH_VIEW = 0
+ GLOBAL_RESULT_VIEW = 1
+ VERSION_RESULT_VIEW = 2
+ WORKFLOW_RESULT_VIEW = 3
+
+ RESULT_LEVEL_MAP = \
+ Bidict([(QueryController.LEVEL_ALL, GLOBAL_RESULT_VIEW),
+ (QueryController.LEVEL_VISTRAIL, VERSION_RESULT_VIEW),
+ (QueryController.LEVEL_WORKFLOW, WORKFLOW_RESULT_VIEW)])
+
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ BaseView.__init__(self)
+ self.build_widget()
+ self.set_title("Search")
+
+ def set_controller(self, controller=None):
+ if self.controller:
+ self.disconnect(self.controller,
+ QtCore.SIGNAL('stateChanged'),
+ self.update_controller)
+ self.controller = controller
+ if controller:
+ self.connect(self.controller,
+ QtCore.SIGNAL('stateChanged'),
+ self.update_controller)
+ self.vt_controller.vistrail_view = self.version_result_view
+ self.vt_controller.current_pipeline_view = \
+ self.workflow_result_view
+ # self.vt_controller.vistrail_view.set_controller(self.vt_controller)
+ # FIXME Need to figure out how to deal with this !!!
+ self.vt_controller.set_vistrail(controller.vistrail, None,
+ set_log_on_vt=False)
+ self.vt_controller.change_selected_version(controller.current_version)
+ self.version_result_view.set_controller(self.vt_controller)
+ self.workflow_result_view.set_controller(self.vt_controller)
+ self.query_controller.set_vistrail_controller(controller)
+
+ def update_controller(self):
+ # FIXME Need to figure out how to deal with this !!!
+ self.vt_controller.set_vistrail(self.controller.vistrail, None,
+ set_log_on_vt=False)
+ self.vt_controller.change_selected_version(
+ self.controller.current_version)
+
+ def build_widget(self):
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(0)
+ layout.setSpacing(0)
+
+ self.query_controller = QueryController(self)
+ self.vt_controller = VistrailController(auto_save=False)
+ self.p_controller = VistrailController(Vistrail(), auto_save=False)
+
+ self.connect(self.p_controller,
+ QtCore.SIGNAL('vistrailChanged()'),
+ self.vistrailChanged)
+
+ self.query_box = QQueryBox()
+ self.query_box.set_controller(self.query_controller)
+ layout.addWidget(self.query_box)
+
+ self.stacked_widget = QtGui.QStackedWidget()
+ self.pipeline_view = QQueryPipelineView()
+ self.p_controller.current_pipeline_view = self.pipeline_view
+ self.pipeline_view.set_controller(self.p_controller)
+ self.pipeline_view.set_query_controller(self.query_controller)
+ QQueryView.VISUAL_SEARCH_VIEW = \
+ self.stacked_widget.addWidget(self.pipeline_view)
+ self.global_result_view = QQueryResultGlobalView()
+ QQueryView.GLOBAL_RESULT_VIEW = \
+ self.stacked_widget.addWidget(self.global_result_view)
+ self.version_result_view = QQueryResultVersionView()
+ self.connect(self.version_result_view.scene(),
+ QtCore.SIGNAL('versionSelected(int,bool,bool,bool,bool)'),
+ self.result_version_selected)
+ # self.version_result_view.set_controller(self.vt_controller)
+ QQueryView.VERSION_RESULT_VIEW = \
+ self.stacked_widget.addWidget(self.version_result_view)
+ self.workflow_result_view = QQueryResultWorkflowView()
+ # self.workflow_result_view.set_controller(self.vt_controller)
+ QQueryView.WORKFLOW_RESULT_VIEW = \
+ self.stacked_widget.addWidget(self.workflow_result_view)
+ self.stacked_widget.setCurrentWidget(self.pipeline_view)
+ layout.addWidget(self.stacked_widget)
+
+ self.setLayout(layout)
+ self.current_display = QQueryView.VISUAL_SEARCH_VIEW
+ self.current_result_view = QQueryView.VERSION_RESULT_VIEW
+
+ def set_default_layout(self):
+ from vistrails.gui.module_palette import QModulePalette
+ from vistrails.gui.module_info import QModuleInfo
+ self.set_palette_layout(
+ {QtCore.Qt.LeftDockWidgetArea: QModulePalette,
+ QtCore.Qt.RightDockWidgetArea: QModuleInfo,
+ })
+
+ def set_action_links(self):
+ self.action_links = \
+ { 'execute': ('query_pipeline_changed', self.set_execute_action) }
+
+ # also add other notification here...
+ from vistrails.gui.vistrails_window import _app
+ _app.register_notification('query_pipeline_changed',
+ self.set_reset_button)
+
+ def set_reset_button(self, pipeline):
+ self.query_box.setManualResetEnabled(self.pipeline_non_empty(pipeline))
+
+ def set_result_level(self, level):
+ view_idx = QQueryView.RESULT_LEVEL_MAP[level]
+ if self.current_display != QQueryView.VISUAL_SEARCH_VIEW:
+ self.set_display_view(view_idx)
+ self.current_result_view = view_idx
+ self.query_controller.update_results()
+
+ def set_to_search_mode(self):
+ self.set_display_view(QQueryView.VISUAL_SEARCH_VIEW)
+ self.query_box.backButton.setEnabled(False)
+ self.query_box.editButton.setEnabled(False)
+ self.set_reset_button(self.p_controller.current_pipeline)
+
+ from vistrails.gui.vistrails_window import _app
+ _app.notify('query_pipeline_changed',
+ self.p_controller.current_pipeline)
+
+ def set_to_result_mode(self):
+ self.set_display_view(self.current_result_view)
+ self.query_box.backButton.setEnabled(True)
+ if self.query_controller.level >= QueryController.LEVEL_VISTRAIL:
+ self.query_box.editButton.setEnabled(True)
+ self.query_box.setManualResetEnabled(True)
+
+ from vistrails.gui.vistrails_window import _app
+ _app.notify('query_pipeline_changed',
+ self.p_controller.current_pipeline)
+
+ def set_display_view(self, view_type):
+ self.current_display = view_type
+ self.stacked_widget.setCurrentIndex(view_type)
+
+ def get_current_view(self):
+ return self.stacked_widget.currentWidget()
+
+ def set_action_defaults(self):
+ self.action_defaults = \
+ {
+ 'execute': [('setEnabled', True, self.set_execute_action),
+ ('setIcon', False, CurrentTheme.VISUAL_QUERY_ICON),
+ ('setToolTip', False, 'Execute a visual query')],
+ 'publishWeb': [('setEnabled', False, False)],
+ 'publishPaper': [('setEnabled', False, False)],
+ }
+
+ def set_execute_action(self, pipeline=None):
+ if not self.vt_controller:
+ return False
+ if pipeline is None:
+ pipeline = self.p_controller.current_pipeline
+ if self.current_display == QQueryView.VISUAL_SEARCH_VIEW:
+ return self.pipeline_non_empty(pipeline)
+ return False
+
+ def pipeline_non_empty(self, pipeline):
+ return pipeline is not None and len(pipeline.modules) > 0
+
+ def vistrailChanged(self):
+ from vistrails.gui.vistrails_window import _app
+ self.p_controller.current_pipeline.ensure_connection_specs()
+ _app.notify('query_pipeline_changed', self.p_controller.current_pipeline)
+
+ def query_changed(self, query=None):
+ if query is None:
+ self.query_controller.reset_search()
+ # FIXME add support for changing the query to something specific
+
+ # DAK: removed this call as the query view maintains its own
+ # "current version"
+ # def version_changed(self, version_id):
+ # self.vt_controller.change_selected_version(version_id)
+ # self.version_result_view.select_current_version()
+ # self.query_controller.update_results()
+
+ def result_version_selected(self, version_id, by_click, do_validate=True,
+ from_root=False, double_click=False):
+ if by_click:
+ self.query_controller.search.setCurrentVistrail(
+ self.vt_controller.vistrail)
+ self.vt_controller.change_selected_version(version_id, by_click,
+ do_validate, from_root)
+ if double_click:
+ self.query_controller.set_level(QueryController.LEVEL_WORKFLOW)
+ self.query_controller.show_workflow_matches()
+
+class QueryEntry(ParameterEntry):
+ def __init__(self, port_spec, function=None, parent=None):
+ ParameterEntry.__init__(self, port_spec, function, parent)
+
+ def get_widget(self):
+ return self.build_widget(get_query_widget_class, False)
diff --git a/vistrails/gui/repository.py b/vistrails/gui/repository.py
new file mode 100644
index 0000000..a7f1419
--- /dev/null
+++ b/vistrails/gui/repository.py
@@ -0,0 +1,766 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""
+Dialog for web repository options
+Includes login and upload tabs
+"""
+from PyQt4 import QtGui, QtCore
+from vistrails.core.configuration import get_vistrails_configuration, get_vistrails_persistent_configuration
+from vistrails.core.repository.poster.encode import multipart_encode
+from vistrails.core.repository.poster.streaminghttp import register_openers
+from vistrails.core.vistrail.controller import VistrailController
+from vistrails.core.db.locator import ZIPFileLocator, FileLocator
+from vistrails.core.db.io import load_vistrail
+from vistrails.core import debug
+import urllib, urllib2, cookielib
+import os
+import tempfile
+import vistrails.api
+import json
+
+##############################################################################
+
+class QRepositoryPushWidget(QtGui.QWidget):
+ """ Tab that shows main repository options
+ Allows users to login and push VisTrails to the Repository """
+
+ def __init__(self, parent, status_bar, dialog):
+ QtGui.QWidget.__init__(self, parent)
+ self._status_bar = status_bar
+ self.dialog = dialog
+
+ base_layout = QtGui.QVBoxLayout(self)
+
+ top = QtGui.QFrame(self)
+ bottom = QtGui.QFrame(self)
+
+ base_layout.addWidget(top)
+ base_layout.addWidget(bottom, 1)
+
+ # TODO: this '/' check should probably be done in core/configuration.py
+ self.config = get_vistrails_configuration()
+ if self.config.webRepositoryURL[-1] == '/':
+ self.config.webRepositoryURL = self.config.webRepositoryURL[:-1]
+
+ # check if the web repository url has changed while logged in
+ if self.dialog.cookie_url and \
+ self.dialog.cookie_url != self.config.webRepositoryURL:
+ self.dialog.cookiejar = None
+
+
+
+ ######################################################################
+ # Detail Table
+ bottom_layout = QtGui.QVBoxLayout(bottom)
+ bottom_layout.setMargin(2)
+ bottom_layout.setSpacing(2)
+
+ # Show what workflows are unrunnble on the repository
+ # and for what reasons
+ self._unrunnable_table = QtGui.QTableWidget(0, 2, top)
+ self._unrunnable_table.horizontalHeader().setStretchLastSection(True)
+
+ bottom_layout.addWidget(self._unrunnable_table)
+
+ self._repository_status = {}
+
+ ######################################################################
+ # Push info
+ top_layout = QtGui.QVBoxLayout(top)
+
+ self._vistrail_status_label = QtGui.QLabel("")
+ self._vistrail_status_label.setWordWrap(True)
+ top_layout.addWidget(self._vistrail_status_label)
+
+ self.serverCombo = QtGui.QComboBox()
+ self.connect(self.serverCombo,
+ QtCore.SIGNAL("currentIndexChanged(int)"),
+ self.check_dependencies)
+ top_layout.addWidget(self.serverCombo)
+
+ """
+ self._default_perm_label = QtGui.QLabel("Default Global Permissions:")
+ top_layout.addWidget(self._default_perm_label)
+ self.perm_view = QtGui.QCheckBox("view")
+ self.perm_download = QtGui.QCheckBox("download")
+ self.perm_edit = QtGui.QCheckBox("edit")
+ top_layout.addWidget(self.perm_view)
+ top_layout.addWidget(self.perm_download)
+ top_layout.addWidget(self.perm_edit)
+ self.perm_view.setEnabled(True)
+ """
+
+ self.permission_gb = QtGui.QGroupBox(self)
+ self.permission_gb.setTitle("Default Global Permissions")
+ glayout = QtGui.QHBoxLayout()
+ self.perm_view = QtGui.QCheckBox("view")
+ self.perm_download = QtGui.QCheckBox("download")
+ self.perm_edit = QtGui.QCheckBox("edit")
+ glayout.addWidget(self.perm_view)
+ glayout.addWidget(self.perm_download)
+ glayout.addWidget(self.perm_edit)
+ self.perm_view.setChecked(True)
+ self.perm_download.setChecked(True)
+ self.permission_gb.setLayout(glayout)
+ top_layout.addWidget(self.permission_gb)
+
+ self._details_label = QtGui.QLabel("")
+ self._details_label.setWordWrap(True)
+ top_layout.addWidget(self._details_label)
+
+ for lbl in [self._details_label, self._vistrail_status_label]:
+ lbl.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
+ lbl.setWordWrap(True)
+
+ self._push_button = QtGui.QPushButton("&Push")
+ self._push_button.setEnabled(False)
+ self.connect(self._push_button,
+ QtCore.SIGNAL("clicked()"),
+ self.push_vistrail_to_repository)
+ self._branch_button = QtGui.QPushButton("&Branch")
+ self._branch_button.hide()
+ self.connect(self._branch_button,
+ QtCore.SIGNAL("clicked()"),
+ (lambda branching=True : self.push_vistrail_to_repository(branching)))
+ button_box = QtGui.QDialogButtonBox()
+ button_box.addButton(self._push_button,
+ QtGui.QDialogButtonBox.ActionRole)
+ button_box.addButton(self._branch_button,
+ QtGui.QDialogButtonBox.ActionRole)
+ bottom_layout.addWidget(button_box)
+
+ def populate_table(self):
+ self._unrunnable_table.clear()
+
+ # set horizontal headers
+ wf_title = QtGui.QTableWidgetItem('Workflow')
+ wf_title.setTextAlignment(QtCore.Qt.AlignCenter)
+ self._unrunnable_table.setHorizontalHeaderItem(0, wf_title)
+
+ detail_title = QtGui.QTableWidgetItem('Unsupported Modules/Packages')
+ detail_title.setTextAlignment(QtCore.Qt.AlignCenter)
+ self._unrunnable_table.setHorizontalHeaderItem(1, detail_title)
+
+ # populate table
+ count = 0
+ for wf in self._unrunnable_wfs.keys():
+ details = \
+ QtGui.QTableWidgetItem(', '.join(self._unrunnable_wfs[wf]))
+ details.setTextAlignment(QtCore.Qt.AlignCenter)
+
+ wf_item = QtGui.QTableWidgetItem(str(wf))
+ wf_item.setTextAlignment(QtCore.Qt.AlignCenter)
+
+ if count >= self._unrunnable_table.rowCount():
+ self._unrunnable_table.insertRow(count)
+ self._unrunnable_table.setItem(count, 0, wf_item)
+ self._unrunnable_table.setItem(count, 1, details)
+ count += 1
+
+ # delete vertical headers
+ for i in range(self._unrunnable_table.rowCount()):
+ self._unrunnable_table.setVerticalHeaderItem(i, QtGui.QTableWidgetItem())
+
+ def update_push_information(self):
+ """ display push information text in this widget """
+ self._vistrail_status_label.setText(self._repository_status['support_status'])
+ self._details_label.setText(self._repository_status['details'])
+
+
+ ##########################################################################
+ # Signal handling
+
+ def check_user_projects(self):
+ # are we logged in?
+ if not self.dialog.cookiejar:
+ self._repository_status['support_status'] = "Please login"
+ self._repository_status['details'] = ""
+ self.update_push_information()
+ self._push_button.setEnabled(False)
+ self._branch_button.setEnabled(False)
+ self._branch_button.hide()
+ else:
+ self._branch_button.setEnabled(False)
+ self._branch_button.hide()
+ server_url = "%s/projects/get_user_projects/" % \
+ self.config.webRepositoryURL
+ register_openers(cookiejar=self.dialog.cookiejar)
+ try:
+ request = urllib2.Request(server_url)
+ get_servers = urllib2.urlopen(request)
+ except urllib2.HTTPError, e:
+ self._repository_status['support_status'] = ""
+ self._repository_status['details'] = ""
+ if e.code == 500:
+ self._repository_status['support_status'] = \
+ ("Error checking user projects (server side issues)")
+ debug.critical("Error checking user projects (server side issues)")
+ else:
+ debug.critical(str(e))
+
+ self._push_button.setEnabled(False)
+ self.update_push_information()
+ return
+
+ servers = json.loads(get_servers.read())
+ if not self.serverCombo.count():
+ self.serverCombo.addItem("Please Select a Project", 0)
+ for prj, srvr in servers:
+ self.serverCombo.addItem("%s (%s)" % (prj, srvr), [prj, srvr])
+
+
+
+ def check_dependencies(self, index):
+ """
+ determines if current VisTrail will be
+ supported by the repository's VisTrail server
+ """
+
+ if not index: return
+
+ self._unrunnable_wfs = {}
+
+ # are we logged in?
+ if not self.dialog.cookiejar:
+ self._repository_status['support_status'] = "Please login"
+ self._repository_status['details'] = ""
+ self.update_push_information()
+ self._push_button.setEnabled(False)
+ self._branch_button.hide()
+ else:
+ self.repository_supports_vt = True
+ # get packages supported by VisTrails repository
+ server = self.serverCombo.itemData(index)[1]
+ packages_url = "%s/packages/supported_packages/%s" % \
+ (self.config.webRepositoryURL, server)
+
+
+ try:
+ get_supported_packages = urllib2.urlopen(url=packages_url)
+ except urllib2.HTTPError, e:
+ self._repository_status['support_status'] = ""
+ self._repository_status['details'] = ""
+ if e.code == 500:
+ self._repository_status['support_status'] = \
+ ("Error when checking dependencies (server side issues)")
+ debug.critical("Error when checking dependencies (server side issues)")
+ else:
+ debug.critical(str(e))
+
+ self._push_button.setEnabled(False)
+ self.update_push_information()
+ self.populate_table()
+ return
+ server_packages = json.loads(get_supported_packages.read())
+
+ # get local packages and local data modules
+ local_packages = []
+
+ self.local_data_modules = ['File', 'FileSink', 'Path']
+ self.unavailable_data = set()
+ self.unsupported_packages = set()
+ has_python_source = False
+
+ vistrail = vistrails.api.get_current_vistrail()
+
+ for version_id in vistrail.get_tagMap():
+ pipeline = vistrail.getPipeline(version_id)
+ tag = vistrail.get_tagMap()[version_id]
+ workflow_packages = []
+ for module in pipeline.module_list:
+ # count modules that use data unavailable to web repository
+ on_repo = False
+ if module.name[-6:] == 'Reader' or \
+ module.name in self.local_data_modules:
+ for edge in pipeline.graph.edges_to(module.id):
+ if pipeline.modules[edge[0]].name in ['HTTPFile',
+ 'RepoSync']:
+ on_repo = True
+
+ if not on_repo:
+ if tag not in self._unrunnable_wfs.keys():
+ self._unrunnable_wfs[tag] = []
+ self._unrunnable_wfs[tag].append(module.name)
+ self.unavailable_data.add(module.name)
+
+ if module.name == "PythonSource":
+ if tag not in self._unrunnable_wfs.keys():
+ self._unrunnable_wfs[tag] = []
+ self._unrunnable_wfs[tag].append(module.name)
+ has_python_source = True
+
+ # get all packages used in tagged versions of this workflow
+ if module.package not in workflow_packages:
+ workflow_packages.append(module.package)
+
+ # find unsupported packages
+ wf_unsupported_packages = filter((lambda p: p not in \
+ server_packages),
+ workflow_packages)
+ if wf_unsupported_packages:
+ if tag not in self._unrunnable_wfs.keys():
+ self._unrunnable_wfs[tag] = []
+ for package in wf_unsupported_packages:
+ self._unrunnable_wfs[tag].append(package)
+ self.unsupported_packages.add(package)
+
+ # display unsupported packages
+ self._repository_status['details'] = "Details:\n"
+ if self.unsupported_packages:
+ self.repository_supports_vt = False
+ self._repository_status['details'] += \
+ "Packages incompatible with web repository: %s\n\n" % \
+ (', '.join(self.unsupported_packages)[:-2])
+
+ # display unsupported data modules
+ if len(self.unavailable_data):
+ self.repository_supports_vt = False
+ self._repository_status['details'] += \
+ "Data sources not available on web repository: %s\n"%\
+ (', '.join(self.unavailable_data)[:-2])
+
+ if has_python_source:
+ self.repository_supports_vt = False
+ self._repository_status['details'] += \
+ ("This Vistrail contains PythonSource module(s) and "
+ "will have to be verified by admins before it can be "
+ "run on the web repository. You will be notified when"
+ " your workflows have been verfied")
+
+ self._repository_status['support_status'] = ""
+ controller = vistrails.api.get_current_controller()
+ if controller.vistrail.get_annotation('repository_vt_id'):
+ # Since repository_vt_id doesn't mirror crowdlabs vt id
+ # get the crowdlabs vt id for linkage
+ vt_url = "%s/vistrails/details/%s" % \
+ (self.config.webRepositoryURL,
+ controller.vistrail.get_annotation('repository_vt_id').value)
+ try:
+ request = urllib2.urlopen(url=vt_url)
+ # TODO: check project that vistrail is part of and notify user
+ # that branching will add it to a different project
+ if request.code == 200:
+ # the vistrail exists on the repository, setup merge settings
+ self.permission_gb.setTitle(("Default Global Permissions "
+ "(only applicable to branching):"))
+ self._push_button.setText("Commit changes")
+ self._branch_button.setEnabled(True)
+ self._branch_button.show()
+
+ vistrail_link = "%s/vistrails/details/%s" % \
+ (self.config.webRepositoryURL,
+ controller.vistrail.get_annotation('repository_vt_id').value)
+
+ self._repository_status['support_status'] = \
+ ("You are attempting to update this Vistrail: "
+ "<a href='%s'>%s</a>. This will possibly update your local version with changes from the web repository<br><br>") % \
+ (vistrail_link, vistrail_link)
+
+ except urllib2.HTTPError:
+ # the vistrail has *probably* been deleted or doesn't exist
+ # remove repository_vt_id annotation
+ repo_annotation = controller.vistrail.get_annotation('repository_vt_id')
+ if repo_annotation:
+ controller.vistrail.db_delete_annotation(repo_annotation)
+
+ if self.repository_supports_vt:
+ self._repository_status['support_status'] += \
+ ("All of this Vistrail's tagged versions are supported"
+ " by the Repository.")
+ else:
+ self._repository_status['support_status'] += \
+ ("This Vistrail contains packages or modules that are"
+ " not supported by the Repository.<br>"
+ "You may still upload the VisTrail but it will "
+ "not be run by the Repository.")
+
+
+ self._push_button.setEnabled(True)
+
+ self.update_push_information()
+ self.populate_table()
+
+ def push_vistrail_to_repository(self, branching=False):
+ """ uploads current VisTrail to web repository """
+
+ self._repository_status['details'] = "Pushing to repository..."
+ self._push_button.setEnabled(False)
+ self._branch_button.setEnabled(False)
+ self.update_push_information()
+ try:
+ # create temp file
+ (fd, filename) = tempfile.mkstemp(suffix='.vt', prefix='vt_tmp')
+ os.close(fd)
+
+ # writing tmp vt and switching back to orginal vt
+ locator = ZIPFileLocator(filename)
+ controller = vistrails.api.get_current_controller()
+ tmp_controller = VistrailController(controller.vistrail.do_copy(),
+ locator)
+ tmp_controller.changed = True
+ tmp_controller.write_vistrail(locator)
+
+ # check if this vt is from the repository
+ if controller.vistrail.get_annotation('repository_vt_id'):
+ repository_vt_id = controller.vistrail.get_annotation('repository_vt_id').value
+ else:
+ repository_vt_id = -1
+
+ # upload vistrail temp file to repository
+ register_openers(cookiejar=self.dialog.cookiejar)
+ project = self.serverCombo.itemData(self.serverCombo.currentIndex())[0]
+ if project == "Default": project = ""
+
+ params = {'vistrail_file': open(filename, 'rb'),
+ 'action': 'upload',
+ 'name': controller.locator.short_name,
+ 'repository_vt_id': repository_vt_id if not branching else -1,
+ 'is_runnable': not bool(len(self.unsupported_packages)+ \
+ len(self.local_data_modules)),
+ 'vt_id': 0,
+ 'branched_from': "" if not branching else repository_vt_id,
+ 'project': project,
+ 'everyone_can_view': self.perm_view.checkState(),
+ 'everyone_can_edit': self.perm_edit.checkState(),
+ 'everyone_can_download': self.perm_download.checkState()
+ }
+
+ upload_url = "%s/vistrails/remote_upload/" % \
+ self.config.webRepositoryURL
+
+ datagen, headers = multipart_encode(params)
+ request = urllib2.Request(upload_url, datagen, headers)
+ result = urllib2.urlopen(request)
+ updated_response = result.read()
+
+ os.unlink(filename)
+
+ if updated_response[:6] == "upload":
+ # No update, just upload
+ if result.code != 200:
+ self._repository_status['details'] = \
+ "Push to repository failed"
+ debug.critical("Push to repository failed (Please contact an administrator)")
+ else:
+ repository_vt_id = int(updated_response[8:])
+ controller.vistrail.set_annotation('repository_vt_id',
+ repository_vt_id)
+ controller.vistrail.set_annotation('repository_creator',
+ self.dialog.loginUser)
+ # ensure that the annotations get saved
+ controller.set_changed(True)
+ self._repository_status['details'] = \
+ "Push to repository was successful"
+ else:
+ # update, load updated vistrail
+ if result.code != 200:
+ self._repository_status['details'] = "Update Failed"
+ debug.critical("Update vistrail in web repository failed (Please contact an administrator)")
+ else:
+ debug.log("getting version from web")
+ # request file to download
+ download_url = "%s/vistrails/download/%s/" % \
+ (self.config.webRepositoryURL, updated_response)
+
+ request = urllib2.Request(download_url)
+ result = urllib2.urlopen(request)
+ updated_file = result.read()
+
+ # create temp file of updated vistrail
+ (fd, updated_filename) = tempfile.mkstemp(suffix='.vtl',
+ prefix='vtl_tmp')
+ os.close(fd)
+ updated_vt = open(updated_filename, 'w')
+ updated_vt.write(updated_file)
+ updated_vt.close()
+
+ # switch vistrails to updated one
+ controller = vistrails.api.get_current_controller()
+
+ updated_locator = FileLocator(updated_filename)
+
+ (up_vistrail, abstractions, thumbnails, mashups) = \
+ load_vistrail(updated_locator)
+
+ # FIXME need to figure out what to do with this !!!
+ controller.set_vistrail(up_vistrail,
+ controller.vistrail.locator,
+ abstractions, thumbnails, mashups)
+
+ # update version tree drawing
+ controller.recompute_terse_graph()
+ controller.invalidate_version_tree()
+
+ os.remove(updated_filename)
+ os.remove(updated_filename[:-1])
+
+ self._repository_status['details'] = \
+ "Update to repository was successful"
+
+ except Exception, e:
+ debug.critical("An error occurred", str(e))
+ self._repository_status['details'] = "An error occurred"
+ self.update_push_information()
+
+class QRepositoryLoginPopup(QtGui.QDialog):
+ """ Dialog that shows repository authentication """
+
+ def __init__(self, parent, status_bar, dialog):
+ QtGui.QDialog.__init__(self, parent)
+ self._status_bar = status_bar
+ self.dialog = dialog
+ self.dialog.cookiejar = None
+
+ self.config = get_vistrails_configuration()
+ # TODO: this '/' check should probably be done in core/configuration.py
+ if self.config.webRepositoryURL[-1] == '/':
+ self.config.webRepositoryURL = self.config.webRepositoryURL[:-1]
+
+ self.setWindowTitle('Log in to Web Repository')
+
+ grid_layout = QtGui.QGridLayout(self)
+ grid_layout.setSpacing(10)
+
+ l1 = QtGui.QLabel("Repository location: %s" % \
+ self.config.webRepositoryURL, self)
+ grid_layout.addWidget(l1, 0, 0, 1, 2)
+
+ l2 = QtGui.QLabel("Username:", self)
+ grid_layout.addWidget(l2, 1, 0)
+
+ if self.config.check('webRepositoryLogin'):
+ self.loginUser = QtGui.QLineEdit(self.config.webRepositoryLogin, self)
+ else:
+ self.loginUser = QtGui.QLineEdit("", self)
+
+ self.loginUser.setFixedWidth(200)
+ self.loginUser.setSizePolicy(QtGui.QSizePolicy.Fixed,
+ QtGui.QSizePolicy.Fixed)
+ grid_layout.addWidget(self.loginUser, 1, 1)
+
+ l3 = QtGui.QLabel("Password:", self)
+ grid_layout.addWidget(l3, 2, 0)
+
+ self.loginPassword = QtGui.QLineEdit("", self)
+ self.loginPassword.setEchoMode(2)
+ self.loginPassword.setFixedWidth(200)
+ self.loginPassword.setSizePolicy(QtGui.QSizePolicy.Fixed,
+ QtGui.QSizePolicy.Fixed)
+ grid_layout.addWidget(self.loginPassword, 2, 1)
+
+ self.saveLogin = QtGui.QCheckBox("Save username", self)
+ if self.config.check('webRepositoryLogin'):
+ self.saveLogin.setChecked(True)
+ grid_layout.addWidget(self.saveLogin, 3, 0)
+
+ self._login_status_label= QtGui.QLabel("", self)
+ grid_layout.addWidget(self._login_status_label, 4, 0)
+
+ self._login_button = QtGui.QPushButton("&Login", self)
+ self._cancel_button = QtGui.QPushButton("&Cancel", self)
+
+ self.connect(self._login_button,
+ QtCore.SIGNAL("clicked()"),
+ self.clicked_on_login)
+
+ self.connect(self._cancel_button,
+ QtCore.SIGNAL("clicked()"),
+ self.clicked_on_cancel)
+
+ button_box = QtGui.QDialogButtonBox()
+ button_box.addButton(self._login_button,
+ QtGui.QDialogButtonBox.ActionRole)
+ button_box.addButton(self._cancel_button,
+ QtGui.QDialogButtonBox.ActionRole)
+
+ grid_layout.addWidget(button_box, 5, 0)
+
+ for lbl in [l1, l2, l3, self.loginUser, self.loginPassword, self._login_status_label]:
+ lbl.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
+
+ grid_layout.setRowStretch(1, 1)
+ grid_layout.setColumnStretch(1, 1)
+
+ self.loginUser.setEnabled(True)
+ self.loginPassword.setEnabled(True)
+ self._login_button.setEnabled(True)
+ self.saveLogin.setEnabled(True)
+
+
+ if self.dialog.cookiejar and \
+ 'sessionid' in [cookie.name for cookie in self.dialog.cookiejar]:
+ self.loginUser.setEnabled(False)
+ self.loginPassword.setEnabled(False)
+ self._login_button.setEnabled(False)
+ self.saveLogin.setEnabled(False)
+
+ def show_login_information(self):
+ """ display/update login info text """
+ self._login_status_label.setText(self._login_status)
+
+
+ ##########################################################################
+ # Signal handling
+ def clicked_on_login(self):
+ """
+ Attempts to log into web repository
+ stores auth cookie for session
+ """
+ from vistrails.gui.application import get_vistrails_application
+
+ self.dialog.loginUser = self.loginUser.text()
+ params = urllib.urlencode({'username':self.dialog.loginUser,
+ 'password':self.loginPassword.text()})
+ self.dialog.cookiejar = cookielib.CookieJar()
+
+ # set base url used for cookie
+ self.dialog.cookie_url = self.config.webRepositoryURL
+
+ self.loginOpener = urllib2.build_opener(urllib2.HTTPCookieProcessor(self.dialog.cookiejar))
+
+ # FIXME doesn't use https
+ login_url = "%s/account/login/" % self.config.webRepositoryURL
+ request = urllib2.Request(login_url, params)
+ url = self.loginOpener.open(request)
+
+ # login failed
+ if not 'sessionid' in [cookie.name for cookie in self.dialog.cookiejar]:
+ debug.critical("Incorrect username or password")
+ self.dialog.cookiejar = None
+ else: # login successful
+
+ self._login_status = "login successful"
+
+ self.loginUser.setEnabled(False)
+ self.loginPassword.setEnabled(False)
+ self._login_button.setEnabled(False)
+ self.saveLogin.setEnabled(False)
+
+ # add association between VisTrails user and web repository user
+ if self.saveLogin.checkState():
+ if not (self.config.check('webRepositoryLogin') and self.config.webRepositoryLogin == self.loginUser.text()):
+ self.config.webRepositoryLogin = str(self.loginUser.text())
+ pers_config = get_vistrails_persistent_configuration()
+ pers_config.webRepositoryLogin = self.config.webRepositoryLogin
+ get_vistrails_application().save_configuration()
+
+ # remove association between VisTrails user and web repository user
+ else:
+ if self.config.check('webRepositoryLogin') and self.config.webRepositoryLogin:
+ self.config.webRepositoryLogin = ""
+ pers_config = get_vistrails_persistent_configuration()
+ pers_config.webRepositoryLogin = ""
+ get_vistrails_application().save_configuration()
+ self.close_dialog(0)
+
+ def clicked_on_cancel(self):
+ self.reject()
+
+ def close_dialog(self, status=0):
+ self.accept()
+
+class QRepositoryDialog(QtGui.QDialog):
+ """ Dialog that shows repository options """
+
+ cookiejar = None
+ cookie_url = None
+ loginUser = None
+ def __init__(self, parent):
+ QtGui.QDialog.__init__(self, parent)
+ self._status_bar = QtGui.QStatusBar(self)
+ self.setWindowTitle('Push vistrail to Web Repository')
+
+ l = QtGui.QVBoxLayout(self)
+ l.setMargin(0)
+ l.setSpacing(0)
+
+ widget = QtGui.QWidget(self)
+ user_layout = QtGui.QHBoxLayout(widget)
+ self._user_text = QtGui.QLabel('N/A')
+ user_layout.addWidget(self._user_text)
+ self._logout_button = QtGui.QPushButton('Log out')
+ #self._logout_button.setFixedWidth(100)
+ user_layout.addWidget(self._logout_button)
+ user_layout.addStretch(1)
+ l.addWidget(widget)
+ self._push_widget = QRepositoryPushWidget(self, self._status_bar,
+ self.__class__)
+ l.addWidget(self._push_widget)
+
+ self._button_box = QtGui.QDialogButtonBox(QtGui.QDialogButtonBox.Close,
+ QtCore.Qt.Horizontal,
+ self)
+
+ self.connect(self._button_box,
+ QtCore.SIGNAL('clicked(QAbstractButton *)'),
+ self.close_dialog)
+
+ self.connect(self._logout_button,
+ QtCore.SIGNAL('clicked()'),
+ self.clicked_on_logout)
+
+ l.addWidget(self._button_box)
+ l.addWidget(self._status_bar)
+
+ self.show_login_dialog()
+
+ self._push_widget.check_user_projects()
+
+ def clicked_on_logout(self):
+ """ Reset cookie and show login dialog """
+ self.cookiejar = None
+ self.show_login_dialog()
+
+ def show_login_dialog(self):
+ """ Prompt for login """
+ if not self.cookiejar:
+ loginDialog = QRepositoryLoginPopup(self, self._status_bar, self.__class__)
+ res = loginDialog.exec_()
+ if res == QtGui.QDialog.Rejected:
+ self.close_dialog()
+ return
+ self._user_text.setText('Logged in as: %s@%s' % (self.loginUser, self.cookie_url))
+ self._push_widget.check_user_projects()
+
+ def close_dialog(self):
+ self.done(0)
+
+ def tab_changed(self, index):
+ """ tab_changed(index: int) -> None """
+ if index == 1: # push tab
+ self._push_tab.check_user_projects()
+
+ def sizeHint(self):
+ return QtCore.QSize(800, 600)
diff --git a/vistrails/gui/requirements.py b/vistrails/gui/requirements.py
new file mode 100644
index 0000000..3b59180
--- /dev/null
+++ b/vistrails/gui/requirements.py
@@ -0,0 +1,61 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from vistrails.core.requirements import MissingRequirement, require_python_module
+import vistrails.gui.bundles.installbundle
+
+
+def setNewPyQtAPI():
+ import sip
+ # We now use the new PyQt API - IPython needs it
+ sip.setapi('QString', 2)
+ sip.setapi('QVariant', 2)
+
+
+def require_pyqt4_api2():
+ try:
+ require_python_module('sip')
+ setNewPyQtAPI()
+ require_python_module('PyQt4.QtGui')
+ require_python_module('PyQt4.QtOpenGL')
+ except MissingRequirement:
+ r = vistrails.gui.bundles.installbundle.install({
+ 'linux-debian': ['python-qt4', 'python-qt4-gl', 'python-qt4-sql'],
+ 'linux-ubuntu': ['python-qt4', 'python-qt4-gl', 'python-qt4-sql'],
+ 'linux-fedora': ['PyQt4'],
+ 'pip': ['PyQt<5.0']})
+ if not r:
+ raise
+ setNewPyQtAPI()
diff --git a/vistrails/gui/resources/__init__.py b/vistrails/gui/resources/__init__.py
new file mode 100644
index 0000000..cfd644b
--- /dev/null
+++ b/vistrails/gui/resources/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+pass
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diff --git a/vistrails/gui/resources/images/open_hand.png b/vistrails/gui/resources/images/open_hand.png
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diff --git a/vistrails/gui/resources/images/open_vistrail.png b/vistrails/gui/resources/images/open_vistrail.png
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diff --git a/vistrails/gui/resources/images/openfromdb.png b/vistrails/gui/resources/images/openfromdb.png
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diff --git a/vistrails/gui/resources/images/pan_icon.png b/vistrails/gui/resources/images/pan_icon.png
new file mode 100644
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diff --git a/vistrails/gui/resources/images/perform_pe.png b/vistrails/gui/resources/images/perform_pe.png
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diff --git a/vistrails/gui/resources/images/pinned.png b/vistrails/gui/resources/images/pinned.png
new file mode 100644
index 0000000..bc26347
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diff --git a/vistrails/gui/resources/images/pipeline.png b/vistrails/gui/resources/images/pipeline.png
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index 0000000..ac825e5
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diff --git a/vistrails/gui/resources/images/pipeline_bg.png b/vistrails/gui/resources/images/pipeline_bg.png
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index 0000000..a1f9d22
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diff --git a/vistrails/gui/resources/images/player_eject.png b/vistrails/gui/resources/images/player_eject.png
new file mode 100644
index 0000000..cd7d184
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diff --git a/vistrails/gui/resources/images/player_pause.png b/vistrails/gui/resources/images/player_pause.png
new file mode 100644
index 0000000..95fd2c2
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diff --git a/vistrails/gui/resources/images/player_play.png b/vistrails/gui/resources/images/player_play.png
new file mode 100644
index 0000000..1f7e5e3
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diff --git a/vistrails/gui/resources/images/plus.png b/vistrails/gui/resources/images/plus.png
new file mode 100644
index 0000000..c4b2097
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diff --git a/vistrails/gui/resources/images/query_bg.png b/vistrails/gui/resources/images/query_bg.png
new file mode 100644
index 0000000..5fa4580
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diff --git a/vistrails/gui/resources/images/redo.png b/vistrails/gui/resources/images/redo.png
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index 0000000..4020fd8
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diff --git a/vistrails/gui/resources/images/reload.png b/vistrails/gui/resources/images/reload.png
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diff --git a/vistrails/gui/resources/images/remove_param.png b/vistrails/gui/resources/images/remove_param.png
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diff --git a/vistrails/gui/resources/images/right.png b/vistrails/gui/resources/images/right.png
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diff --git a/vistrails/gui/resources/images/row.png b/vistrails/gui/resources/images/row.png
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diff --git a/vistrails/gui/resources/images/save_vistrail.png b/vistrails/gui/resources/images/save_vistrail.png
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index 0000000..2cbccf7
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diff --git a/vistrails/gui/resources/images/search.png b/vistrails/gui/resources/images/search.png
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index 0000000..2efb3cd
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diff --git a/vistrails/gui/resources/images/search_database.png b/vistrails/gui/resources/images/search_database.png
new file mode 100644
index 0000000..432fa12
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diff --git a/vistrails/gui/resources/images/select_icon.png b/vistrails/gui/resources/images/select_icon.png
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index 0000000..548bf3b
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diff --git a/vistrails/gui/resources/images/sheet.png b/vistrails/gui/resources/images/sheet.png
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index 0000000..ab5f26a
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diff --git a/vistrails/gui/resources/images/show_legends.png b/vistrails/gui/resources/images/show_legends.png
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diff --git a/vistrails/gui/resources/images/show_params.png b/vistrails/gui/resources/images/show_params.png
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diff --git a/vistrails/gui/resources/images/skip.png b/vistrails/gui/resources/images/skip.png
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index 0000000..c9addc8
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diff --git a/vistrails/gui/resources/images/tabbed_view.png b/vistrails/gui/resources/images/tabbed_view.png
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index 0000000..e3822e0
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diff --git a/vistrails/gui/resources/images/time.png b/vistrails/gui/resources/images/time.png
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index 0000000..7f487ef
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diff --git a/vistrails/gui/resources/images/tree_view.png b/vistrails/gui/resources/images/tree_view.png
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index 0000000..91c9db8
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diff --git a/vistrails/gui/resources/images/undo.png b/vistrails/gui/resources/images/undo.png
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index 0000000..ced68ac
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diff --git a/vistrails/gui/resources/images/unpinned.png b/vistrails/gui/resources/images/unpinned.png
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index 0000000..3dddd8f
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diff --git a/vistrails/gui/resources/images/up.png b/vistrails/gui/resources/images/up.png
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index 0000000..c38e165
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diff --git a/vistrails/gui/resources/images/ver_view.png b/vistrails/gui/resources/images/ver_view.png
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index 0000000..7eb56d4
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diff --git a/vistrails/gui/resources/images/version_bg.png b/vistrails/gui/resources/images/version_bg.png
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index 0000000..f9314d7
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diff --git a/vistrails/gui/resources/images/view-refresh.png b/vistrails/gui/resources/images/view-refresh.png
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index 0000000..606ea9e
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diff --git a/vistrails/gui/resources/images/view_fullscreen.png b/vistrails/gui/resources/images/view_fullscreen.png
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index 0000000..4972989
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diff --git a/vistrails/gui/resources/images/vistrails_icon.png b/vistrails/gui/resources/images/vistrails_icon.png
new file mode 100644
index 0000000..570a273
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diff --git a/vistrails/gui/resources/images/vistrails_icon_small.ico b/vistrails/gui/resources/images/vistrails_icon_small.ico
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index 0000000..3ac22c4
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diff --git a/vistrails/gui/resources/images/vistrails_icon_small.png b/vistrails/gui/resources/images/vistrails_icon_small.png
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index 0000000..7382873
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diff --git a/vistrails/gui/resources/images/vistrails_splash.png b/vistrails/gui/resources/images/vistrails_splash.png
new file mode 100644
index 0000000..87d44e6
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diff --git a/vistrails/gui/resources/images/visual_query.png b/vistrails/gui/resources/images/visual_query.png
new file mode 100644
index 0000000..0a1562a
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diff --git a/vistrails/gui/resources/images/zoom.png b/vistrails/gui/resources/images/zoom.png
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index 0000000..dae8fad
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diff --git a/vistrails/gui/resources/images/zoom_arrow_icon.png b/vistrails/gui/resources/images/zoom_arrow_icon.png
new file mode 100644
index 0000000..db4d1c4
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diff --git a/vistrails/gui/resources/images/zoom_icon.png b/vistrails/gui/resources/images/zoom_icon.png
new file mode 100644
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diff --git a/vistrails/gui/resources/macroicons.qrc b/vistrails/gui/resources/macroicons.qrc
new file mode 100644
index 0000000..f4fdd08
--- /dev/null
+++ b/vistrails/gui/resources/macroicons.qrc
@@ -0,0 +1,17 @@
+<!DOCTYPE RCC><RCC version="1.0">
+<qresource>
+ <file>images/macro.png</file>
+ <file>images/macro_info.png</file>
+ <file>images/macro_new.png</file>
+ <file>images/macro_pause.png</file>
+ <file>images/macro_play.png</file>
+ <file>images/macro_pause.png</file>
+ <file>images/macro_stop.png</file>
+ <file>images/macro_view.png</file>
+ <file>images/info.png</file>
+ <file>images/lightcheck.png</file>
+ <file>images/edit_add.png</file>
+ <file>images/down.png</file>
+ <file>images/up.png</file>
+</qresource>
+</RCC>
diff --git a/vistrails/gui/resources/macroicons_rc.py b/vistrails/gui/resources/macroicons_rc.py
new file mode 100644
index 0000000..b3a7f29
--- /dev/null
+++ b/vistrails/gui/resources/macroicons_rc.py
@@ -0,0 +1,1404 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# Resource object code
+#
+# Created: Wed Jun 14 12:55:01 2006
+# by: The Resource Compiler for PyQt (Qt v4.1.3)
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore
+
+qt_resource_data = b"\
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+\xdc\x69\x7a\xfe\x5f\x9a\xd1\xb8\xe4\x67\xe4\x0f\x62\x00\x00\x00\
+\x00\x49\x45\x4e\x44\xae\x42\x60\x82\
+"
+
+qt_resource_name = b"\
+\x00\x06\
+\x07\x03\x7d\xc3\
+\x00\x69\
+\x00\x6d\x00\x61\x00\x67\x00\x65\x00\x73\
+\x00\x0e\
+\x0b\x84\xe0\x07\
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+\x00\x08\
+\x04\xd2\x59\x47\
+\x00\x69\
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+\x00\x0e\
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+\x00\x0e\
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+\x00\x64\
+\x00\x6f\x00\x77\x00\x6e\x00\x2e\x00\x70\x00\x6e\x00\x67\
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+\x00\x75\
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+\x00\x0f\
+\x09\xbf\x57\xa7\
+\x00\x6d\
+\x00\x61\x00\x63\x00\x72\x00\x6f\x00\x5f\x00\x70\x00\x61\x00\x75\x00\x73\x00\x65\x00\x2e\x00\x70\x00\x6e\x00\x67\
+\x00\x0d\
+\x02\x3f\x7c\xc7\
+\x00\x6d\
+\x00\x61\x00\x63\x00\x72\x00\x6f\x00\x5f\x00\x6e\x00\x65\x00\x77\x00\x2e\x00\x70\x00\x6e\x00\x67\
+"
+
+qt_resource_struct = b"\
+\x00\x00\x00\x00\x00\x02\x00\x00\x00\x01\x00\x00\x00\x01\
+\x00\x00\x00\x00\x00\x02\x00\x00\x00\x0d\x00\x00\x00\x02\
+\x00\x00\x00\x4a\x00\x00\x00\x00\x00\x01\x00\x00\x0b\xac\
+\x00\x00\x01\x54\x00\x00\x00\x00\x00\x01\x00\x00\x46\xa3\
+\x00\x00\x00\x6c\x00\x00\x00\x00\x00\x01\x00\x00\x14\x84\
+\x00\x00\x00\xd8\x00\x00\x00\x00\x00\x01\x00\x00\x28\x97\
+\x00\x00\x00\x34\x00\x00\x00\x00\x00\x01\x00\x00\x07\x37\
+\x00\x00\x00\x8e\x00\x00\x00\x00\x00\x01\x00\x00\x19\xe3\
+\x00\x00\x00\xa4\x00\x00\x00\x00\x00\x01\x00\x00\x1d\x98\
+\x00\x00\x01\x30\x00\x00\x00\x00\x00\x01\x00\x00\x3f\x89\
+\x00\x00\x01\x30\x00\x00\x00\x00\x00\x01\x00\x00\x38\x6f\
+\x00\x00\x00\xfa\x00\x00\x00\x00\x00\x01\x00\x00\x2f\x84\
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+\x00\x00\x00\xb6\x00\x00\x00\x00\x00\x01\x00\x00\x21\x41\
+"
+
+def qInitResources():
+ QtCore.qRegisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+def qCleanupResources():
+ QtCore.qUnregisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+qInitResources()
diff --git a/vistrails/gui/resources/vistrails-mime.xml b/vistrails/gui/resources/vistrails-mime.xml
new file mode 100644
index 0000000..f19b2ef
--- /dev/null
+++ b/vistrails/gui/resources/vistrails-mime.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
+ <mime-type type="application/x-vistrails">
+
+ <comment>VisTrails</comment>
+
+ <glob pattern="*.vt"/>
+ <glob pattern="*.vtl"/>
+
+ </mime-type>
+</mime-info>
\ No newline at end of file
diff --git a/vistrails/gui/shell.py b/vistrails/gui/shell.py
new file mode 100644
index 0000000..27587c5
--- /dev/null
+++ b/vistrails/gui/shell.py
@@ -0,0 +1,965 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This module defines the following classes:
+ - QShellDialog
+ - QShell
+
+QShell is based on ideas and code from PyCute developed by Gerard Vermeulen.
+Used with the author's permission.
+More information on PyCute, visit:
+http://gerard.vermeulen.free.fr/html/pycute-intro.html
+
+"""
+from PyQt4 import QtGui, QtCore
+from code import InteractiveInterpreter
+import copy
+import sys
+import time
+import os.path
+
+import vistrails.api
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core.interpreter.default import get_default_interpreter
+import vistrails.core.modules.module_registry
+from vistrails.core.modules.utils import create_port_spec_string
+import vistrails.core.system
+from vistrails.core.vistrail.port_spec import PortSpec
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+from vistrails.core.utils import all
+
+################################################################################
+
+class QShellDialog(QtGui.QWidget, QVistrailsPaletteInterface):
+ """This class incorporates the QShell into a dockable widget for use in the
+ VisTrails environment"""
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent=parent)
+ #locals() returns the original dictionary, not a copy as
+ #the docs say
+ self.firstLocals = copy.copy(locals())
+ self.shell = QShell(self.firstLocals,None)
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(0)
+ layout.setSpacing(0)
+ layout.addWidget(self.shell)
+ self.setLayout(layout)
+ # self.setWidget(self.shell)
+ self.setWindowTitle(self.shell.windowTitle())
+ # self.setTitleBarWidget(QtGui.QLabel(self.shell.windowTitle()))
+ # self.monitorWindowTitle(self.shell)
+ self.vistrails_interpreter = get_default_interpreter()
+
+ def createMenu(self):
+ """createMenu() -> None
+ Creates a menu bar and adds it to the main layout.
+
+ """
+ self.newSessionAct = QtGui.QAction(self.tr("&Restart"),self)
+ self.newSessionAct.setShortcut(self.tr("Ctrl+R"))
+ self.connect(self.newSessionAct, QtCore.SIGNAL("triggered()"),
+ self.newSession)
+
+ self.saveSessionAct = QtGui.QAction(self.tr("&Save"), self)
+ self.saveSessionAct.setShortcut(self.tr("Ctrl+S"))
+ self.connect(self.saveSessionAct, QtCore.SIGNAL("triggered()"),
+ self.saveSession)
+
+ self.closeSessionAct = QtGui.QAction(self.tr("Close"), self)
+ self.closeSessionAct.setShortcut(self.tr("Ctrl+W"))
+ self.connect(self.closeSessionAct,QtCore.SIGNAL("triggered()"),
+ self.closeSession)
+
+ self.menuBar = QtGui.QMenuBar(self)
+ menu = self.menuBar.addMenu(self.tr("&Session"))
+ menu.addAction(self.newSessionAct)
+ menu.addAction(self.saveSessionAct)
+ menu.addAction(self.closeSessionAct)
+
+ self.layout().setMenuBar(self.menuBar)
+
+ def closeEvent(self, e):
+ """closeEvent(e) -> None
+ Event handler called when the dialog is about to close."""
+ self.closeSession()
+ self.emit(QtCore.SIGNAL("shellHidden()"))
+
+ def showEvent(self, e):
+ """showEvent(e) -> None
+ Event handler called when the dialog acquires focus
+
+ """
+ self.shell.show()
+
+ def closeSession(self):
+ """closeSession() -> None.
+ Hides the dialog instead of closing it, so the session continues open.
+
+ """
+ self.hide()
+
+ def newSession(self):
+ """newSession() -> None
+ Tells the shell to start a new session passing a copy of the original
+ locals dictionary.
+
+ """
+ self.shell.restart(copy.copy(self.firstLocals))
+
+ def saveSession(self):
+ """saveSession() -> None
+ Opens a File Save dialog and passes the filename to shell's saveSession.
+
+ """
+ default = 'visTrails' + '-' + time.strftime("%Y%m%d-%H%M.log")
+ default = os.path.join(vistrails.core.system.vistrails_file_directory(),default)
+ fileName = QtGui.QFileDialog.getSaveFileName(self,
+ "Save Session As..",
+ default,
+ "Log files (*.log)")
+ if not fileName:
+ return
+
+ self.shell.saveSession(str(fileName))
+
+ def visibility_changed(self, visible):
+ QVistrailsPaletteInterface.visibility_changed(self, visible)
+ if visible:
+ self.shell.show()
+ else:
+ self.shell.hide()
+
+##############################################################################
+# QShell
+
+
+class vistrails_port(object):
+ def __init__(self, vistrails_module, port_spec):
+ # print 'calling vistrails_port.__init__'
+ self._vistrails_module = vistrails_module
+ self._port_spec = port_spec
+
+ def __call__(self, *args, **kwargs):
+ if len(args) + len(kwargs) > 0:
+ self._vistrails_module._update_func(self._port_spec,
+ *args, **kwargs)
+ return None
+ return self
+
+class vistrails_module(object):
+ def __init__(self, *args, **kwargs):
+ if not hasattr(self, '_module'):
+ self._module = \
+ vistrails.api.add_module_from_descriptor(self._module_desc)
+ # FIXME if constant, we can use args
+ module_desc = self._module_desc
+ for attr_name, value in kwargs.iteritems():
+ self._process_attr_value(attr_name, value)
+
+ def _process_attr_value(self, attr_name, value):
+ if self._module.has_port_spec(attr_name, 'input'):
+ port_spec = self._module.get_port_spec(attr_name, 'input')
+
+ args = None
+ # FIXME want this to be any iterable
+ if isinstance(value, tuple):
+ args = value
+ else:
+ args = (value,)
+ self._update_func(port_spec, *args)
+ else:
+ raise AttributeError("type object '%s' has no "
+ "attribute '%s'" % \
+ (self.__class__.__name__,
+ attr_name))
+
+ def __getattr__(self, attr_name):
+ def create_port(port_spec):
+ return vistrails_port(self, port_spec)
+ try:
+ return self.__dict__[attr_name]
+ except KeyError:
+ if self._module.has_port_spec(attr_name, 'output'):
+ port_spec = \
+ self._module.get_port_spec(attr_name, 'output')
+ return create_port(port_spec)
+ elif self._module.has_port_spec(attr_name, 'input'):
+ port_spec = \
+ self._module.get_port_spec(attr_name, 'input')
+ return create_port(port_spec)
+ else:
+ raise AttributeError("type object '%s' has no "
+ "attribute '%s'" % \
+ (self.__class__.__name__,
+ attr_name))
+
+ def __setattr__(self, attr_name, value):
+ if attr_name.startswith('_'):
+ self.__dict__[attr_name] = value
+ else:
+ self._process_attr_value(attr_name, value)
+
+ def _update_func(self, port_spec, *args, **kwargs):
+ # print 'running _update_func', port_spec.name
+ # print args
+
+ if port_spec.type != 'input':
+ if self._module.has_port_spec(port_spec.name, 'input'):
+ port_spec = \
+ self._module.get_port_spec(port_spec.name, 'input')
+ else:
+ raise TypeError("cannot update an output port spec")
+
+ # FIXME deal with kwargs
+ num_ports = 0
+ num_params = 0
+ for value in args:
+ # print 'processing', type(value), value
+ if isinstance(value, vistrails_port):
+ # make connection to specified output port
+ # print 'updating port'
+ num_ports += 1
+ elif isinstance(value, vistrails_module):
+ # make connection to 'self' output port of value
+ # print 'updating module'
+ num_ports += 1
+ else:
+ # print 'update literal', type(value), value
+ num_params += 1
+ if num_ports > 1 or (num_ports == 1 and num_params > 0):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ tuple_desc = reg.get_descriptor_by_name(
+ vistrails.core.system.get_vistrails_basic_pkg_id(), 'Tuple')
+
+ d = {'_module_desc': tuple_desc,
+ '_package': self._package,}
+ tuple = type('module', (vistrails_module,), d)()
+
+ output_port_spec = PortSpec(id=-1,
+ name='value',
+ type='output',
+ sigstring=port_spec.sigstring)
+ vistrails.api.add_port_spec(tuple._module.id, output_port_spec)
+ self._update_func(port_spec, *[tuple.value()])
+ assert len(port_spec.descriptors()) == len(args)
+ for i, descriptor in enumerate(port_spec.descriptors()):
+ arg_name = 'arg%d' % i
+ sigstring = create_port_spec_string([descriptor.spec_tuple])
+ tuple_port_spec = PortSpec(id=-1,
+ name=arg_name,
+ type='input',
+ sigstring=sigstring)
+ vistrails.api.add_port_spec(tuple._module.id, tuple_port_spec)
+ tuple._process_attr_value(arg_name, args[i])
+
+
+ # create tuple object
+ pass
+ elif num_ports == 1:
+ other = args[0]
+ if isinstance(other, vistrails_port):
+ if other._port_spec.type != 'output':
+ other_module = other._vistrails_module._module
+ if other_module.has_port_spec(port_spec.name,
+ 'output'):
+ other_port_spec = \
+ other_module.get_port_spec(port_spec.name,
+ 'output')
+ else:
+ raise TypeError("cannot update an input "
+ "port spec")
+ else:
+ other_port_spec = other._port_spec
+
+ vistrails.api.add_connection(other._vistrails_module._module.id,
+ other_port_spec,
+ self._module.id,
+ port_spec)
+ elif isinstance(other, vistrails_module):
+ other_port_spec = \
+ other._module.get_port_spec('self', 'output')
+ vistrails.api.add_connection(other._module.id,
+ other_port_spec,
+ self._module.id,
+ port_spec)
+ else:
+ vistrails.api.change_parameter(self._module.id,
+ port_spec.name,
+ [str(x) for x in args])
+
+class QShell(QtGui.QTextEdit):
+ """This class embeds a python interperter in a QTextEdit Widget
+ It is based on PyCute developed by Gerard Vermeulen.
+
+ """
+ def __init__(self, locals=None, parent=None):
+ """Constructor.
+
+ The optional 'locals' argument specifies the dictionary in which code
+ will be executed; it defaults to a newly created dictionary with key
+ "__name__" set to "__console__" and key "__doc__" set to None.
+
+ The optional 'log' argument specifies the file in which the interpreter
+ session is to be logged.
+
+ The optional 'parent' argument specifies the parent widget. If no parent
+ widget has been specified, it is possible to exit the interpreter
+ by Ctrl-D.
+
+ """
+
+ QtGui.QTextEdit.__init__(self, parent)
+ self.setReadOnly(False)
+ self.setWindowTitle("Console")
+ # to exit the main interpreter by a Ctrl-D if QShell has no parent
+ if parent is None:
+ self.eofKey = QtCore.Qt.Key_D
+ else:
+ self.eofKey = None
+
+ # flag for knowing when selecting text
+ self.selectMode = False
+ self.interpreter = None
+ self.controller = None
+ # storing current state
+ #this is not working on mac
+ #self.prev_stdout = sys.stdout
+ #self.prev_stdin = sys.stdin
+ #self.prev_stderr = sys.stderr
+ # capture all interactive input/output
+ #sys.stdout = self
+ #sys.stderr = self
+ #sys.stdin = self
+
+ # user interface setup
+
+ self.setAcceptRichText(False)
+ self.setWordWrapMode(QtGui.QTextOption.WrapAnywhere)
+
+ conf = get_vistrails_configuration()
+ shell_conf = conf.shell
+ # font
+ font = QtGui.QFont(shell_conf.font_face, shell_conf.font_size)
+ font.setFixedPitch(1)
+ self.setFont(font)
+ self.reset(locals)
+
+ def load_package(self, pkg_name):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ package = reg.get_package_by_name(pkg_name)
+
+ def create_dict(modules, ns, m, mdesc):
+ md = {}
+ if len(ns) == 0:
+ d = {'_module_desc': mdesc,
+ '_package': pkg,}
+ modules[m] = type('module', (vistrails_module,), d)
+ else:
+ if ns[0] in modules:
+ md = create_dict(modules[ns[0]], ns[1:], m, mdesc)
+ else:
+ md = create_dict(md, ns[1:], m, mdesc)
+ modules[ns[0]] = md
+ return modules
+
+ def create_namespace_path(root, modules):
+ for k,v in modules.iteritems():
+ if isinstance(v, dict):
+ d = create_namespace_path(k,v)
+ modules[k] = d
+
+ if root is not None:
+ modules['_package'] = pkg
+ return type(root, (object,), modules)()
+ else:
+ return modules
+
+ def get_module_init(module_desc):
+ def init(self, *args, **kwargs):
+ self.__dict__['module'] = \
+ vistrails.api.add_module_from_descriptor(module_desc)
+ return init
+
+ def get_module(package):
+ def getter(self, attr_name):
+ desc_tuple = (attr_name, '')
+ if desc_tuple in package.descriptors:
+ module_desc = package.descriptors[desc_tuple]
+ d = {'_module_desc': module_desc,
+ '_package': self,}
+ return type('module', (vistrails_module,), d)
+ else:
+ raise AttributeError("type object '%s' has no attribute "
+ "'%s'" % (self.__class__.__name__,
+ attr_name))
+ return getter
+
+ d = {'__getattr__': get_module(package),}
+ pkg = type(package.name, (object,), d)()
+
+ modules = {}
+ for (m,ns) in package.descriptors:
+ module_desc = package.descriptors[(m,ns)]
+ modules = create_dict(modules, ns.split('|'), m, module_desc)
+
+ modules = create_namespace_path(None, modules)
+
+ for (k,v) in modules.iteritems():
+ setattr(pkg, k, v)
+ return pkg
+
+ def selected_modules(self):
+ shell_modules = []
+ modules = vistrails.api.get_selected_modules()
+ for module in modules:
+ d = {'_module': module}
+ shell_modules.append(type('module', (vistrails_module,), d)())
+ return shell_modules
+
+ def reset(self, locals):
+ """reset(locals) -> None
+ Reset shell preparing it for a new session.
+
+ """
+ locals['load_package'] = self.load_package
+ locals['selected_modules'] = self.selected_modules
+ if self.interpreter:
+ del self.interpreter
+ self.interpreter = InteractiveInterpreter(locals)
+
+ # last line + last incomplete lines
+ self.line = ''
+ self.lines = []
+ # the cursor position in the last line
+ self.point = 0
+ # flag: the interpreter needs more input to run the last lines.
+ self.more = 0
+ # flag: readline() is being used for e.g. raw_input() and input()
+ self.reading = 0
+ # history
+ self.history = []
+ self.pointer = 0
+ self.last = 0
+ # interpreter prompt.
+ if hasattr(sys, "ps1"):
+ sys.ps1
+ else:
+ sys.ps1 = ">>> "
+ if hasattr(sys, "ps2"):
+ sys.ps2
+ else:
+ sys.ps2 = "... "
+
+ # interpreter banner
+
+ self.write('VisTrails shell running Python %s on %s.\n' %
+ (sys.version, sys.platform))
+ self.write('Type "copyright", "credits" or "license"'
+ ' for more information on Python.\n')
+ self.write(sys.ps1)
+
+
+ def flush(self):
+ """flush() -> None.
+ Simulate stdin, stdout, and stderr.
+
+ """
+ pass
+
+ def isatty(self):
+ """isatty() -> int
+ Simulate stdin, stdout, and stderr.
+
+ """
+ return 1
+
+ def readline(self):
+ """readline() -> str
+
+ Simulate stdin, stdout, and stderr.
+
+ """
+ self.reading = 1
+ self.__clearLine()
+ cursor = self.textCursor()
+ cursor.movePosition(QtGui.QTextCursor.End)
+ self.setTextCursor(cursor)
+
+ while self.reading:
+ qApp.processOneEvent()
+ if len(self.line) == 0:
+ return '\n'
+ else:
+ return self.line
+
+ def write(self, text):
+ """write(text: str) -> None
+ Simulate stdin, stdout, and stderr.
+
+ """
+
+ cursor = self.textCursor()
+ cursor.movePosition(QtGui.QTextCursor.End)
+ cursor.clearSelection()
+ self.setTextCursor(cursor)
+ self.insertPlainText(text)
+ cursor = self.textCursor()
+ self.last = cursor.position()
+
+ def insertFromMimeData(self, source):
+ if source.hasText():
+ cursor = self.textCursor()
+ cursor.movePosition(QtGui.QTextCursor.End)
+ cursor.clearSelection()
+ self.setTextCursor(cursor)
+ self.__insertText(source.text())
+
+ def scroll_bar_at_bottom(self):
+ """Returns true if vertical bar exists and is at bottom, or if
+ vertical bar does not exist."""
+ bar = self.verticalScrollBar()
+ if not bar:
+ return True
+ return bar.value() == bar.maximum()
+
+ def __run(self):
+ """__run() -> None
+ Append the last line to the history list, let the interpreter execute
+ the last line(s), and clean up accounting for the interpreter results:
+ (1) the interpreter succeeds
+ (2) the interpreter fails, finds no errors and wants more line(s)
+ (3) the interpreter fails, finds errors and writes them to sys.stderr
+
+ """
+ cursor = self.textCursor()
+ cursor.movePosition(QtGui.QTextCursor.End)
+ self.setTextCursor(cursor)
+ # self.set_controller()
+ should_scroll = self.scroll_bar_at_bottom()
+ self.pointer = 0
+ self.history.append(self.line)
+ self.lines.append(self.line)
+ source = '\n'.join(self.lines)
+ self.write('\n')
+ self.more = self.interpreter.runsource(source)
+ if self.more:
+ self.write(sys.ps2)
+ else:
+ self.write(sys.ps1)
+ self.lines = []
+ self.__clearLine()
+ if should_scroll:
+ bar = self.verticalScrollBar()
+ if bar:
+ bar.setValue(bar.maximum())
+
+ def __clearLine(self):
+ """__clearLine() -> None
+ Clear input line buffer.
+
+ """
+ self.line = ""
+ self.point = 0
+
+ def __insertText(self, text):
+ """__insertText(text) -> None
+ Insert text at the current cursor position.
+
+ """
+ self.insertPlainText(text)
+ self.line = self.line[:self.point] + text + self.line[self.point:]
+ self.point += len(text)
+
+ # def add_pipeline(self, p):
+ # """
+ # add_pipeline(p) -> None
+ # Set the active pipeline in the command shell. This replaces the modules
+ # variable with the list of current active modules of the selected pipeline.
+ # """
+ # if self.controller:
+ # self.interpreter.active_pipeline = self.controller.current_pipeline
+ # else:
+ # self.interpreter.active_pipeline = p
+ # cmd = 'active_pipeline = self.shell.interpreter.active_pipeline'
+ # self.interpreter.runcode(cmd)
+ # cmd = 'modules = self.vistrails_interpreter.find_persistent_entities(active_pipeline)[0]'
+ # self.interpreter.runcode(cmd)
+
+ def set_controller(self, controller=None):
+ """set_controller(controller: VistrailController) -> None
+ Set the current VistrailController on the shell.
+ """
+ self.controller = controller
+ if controller:
+ self.interpreter.active_pipeline = self.controller.current_pipeline
+ cmd = 'active_pipeline = self.shell.interpreter.active_pipeline'
+ self.interpreter.runcode(cmd)
+ cmd = 'modules = self.vistrails_interpreter.' \
+ 'find_persistent_entities(active_pipeline)[0]'
+ self.interpreter.runcode(cmd)
+
+ # def set_pipeline(self):
+ # """set_active_pipeline() -> None
+ # Makes sure that the pipeline being displayed is present in the shell for
+ # direct inspection and manipulation
+ # """
+ # self.add_pipeline(None)
+
+ def keyPressEvent(self, e):
+ """keyPressEvent(e) -> None
+ Handle user input a key at a time.
+
+ Notice that text might come more than one keypress at a time
+ if user is a fast enough typist!
+
+ """
+ text = e.text()
+ key = e.key()
+
+ # NB: Sometimes len(str(text)) > 1!
+ if len(text) and all(ord(x) >= 32 and
+ ord(x) < 127
+ for x in str(text)):
+ # exit select mode and jump to end of text
+ cursor = self.textCursor()
+ if self.selectMode or cursor.hasSelection():
+ self.selectMode = False
+ cursor.movePosition(QtGui.QTextCursor.End)
+ cursor.clearSelection()
+ self.setTextCursor(cursor)
+ self.__insertText(text)
+ return
+
+ if e.modifiers() & QtCore.Qt.MetaModifier and key == self.eofKey:
+ self.parent().closeSession()
+
+ if e.modifiers() & QtCore.Qt.ControlModifier:
+ if key == QtCore.Qt.Key_C or key == QtCore.Qt.Key_Insert:
+ self.copy()
+ elif key == QtCore.Qt.Key_V:
+ cursor = self.textCursor()
+ cursor.movePosition(QtGui.QTextCursor.End)
+ cursor.clearSelection()
+ self.setTextCursor(cursor)
+ self.paste()
+ elif key == QtCore.Qt.Key_A:
+ self.selectAll()
+ self.selectMode = True
+ else:
+ e.ignore()
+ return
+
+ if e.modifiers() & QtCore.Qt.ShiftModifier:
+ if key == QtCore.Qt.Key_Insert:
+ cursor = self.textCursor()
+ cursor.movePosition(QtGui.QTextCursor.End)
+ cursor.clearSelection()
+ self.setTextCursor(cursor)
+ self.paste()
+ else:
+ e.ignore()
+ return
+
+ # exit select mode and jump to end of text
+ cursor = self.textCursor()
+ if self.selectMode or cursor.hasSelection():
+ self.selectMode = False
+ cursor.movePosition(QtGui.QTextCursor.End)
+ cursor.clearSelection()
+ self.setTextCursor(cursor)
+
+ if key == QtCore.Qt.Key_Backspace:
+ if self.point:
+ QtGui.QTextEdit.keyPressEvent(self, e)
+ self.point -= 1
+ self.line = self.line[:self.point] + self.line[self.point+1:]
+ elif key == QtCore.Qt.Key_Delete:
+ QtGui.QTextEdit.keyPressEvent(self, e)
+ self.line = self.line[:self.point] + self.line[self.point+1:]
+ elif key == QtCore.Qt.Key_Return or key == QtCore.Qt.Key_Enter:
+ if self.reading:
+ self.reading = 0
+ else:
+ self.__run()
+ elif key == QtCore.Qt.Key_Tab:
+ self.__insertText(text)
+ elif key == QtCore.Qt.Key_Left:
+ if self.point:
+ QtGui.QTextEdit.keyPressEvent(self, e)
+ self.point -= 1
+ elif key == QtCore.Qt.Key_Right:
+ if self.point < len(self.line):
+ QtGui.QTextEdit.keyPressEvent(self, e)
+ self.point += 1
+ elif key == QtCore.Qt.Key_Home:
+ cursor = self.textCursor()
+ cursor.movePosition(QtGui.QTextCursor.StartOfLine)
+ cursor.setPosition(cursor.position() + 4)
+ self.setTextCursor(cursor)
+ self.point = 0
+ elif key == QtCore.Qt.Key_End:
+ QtGui.QTextEdit.keyPressEvent(self, e)
+ self.point = len(self.line)
+ elif key == QtCore.Qt.Key_Up:
+ if len(self.history):
+ if self.pointer == 0:
+ self.pointer = len(self.history)
+ self.pointer -= 1
+ self.__recall()
+ elif key == QtCore.Qt.Key_Down:
+ if len(self.history):
+ self.pointer += 1
+ if self.pointer == len(self.history):
+ self.pointer = 0
+ self.__recall()
+ else:
+ e.ignore()
+
+ def __recall(self):
+ """__recall() -> None
+ Display the current item from the command history.
+
+ """
+ cursor = self.textCursor()
+ cursor.setPosition(self.last)
+
+ cursor.select(QtGui.QTextCursor.LineUnderCursor)
+
+ cursor.removeSelectedText()
+ self.setTextCursor(cursor)
+ self.insertPlainText(sys.ps1)
+ self.__clearLine()
+ self.__insertText(self.history[self.pointer])
+
+
+ def focusNextPrevChild(self, next):
+ """focusNextPrevChild(next) -> None
+ Suppress tabbing to the next window in multi-line commands.
+
+ """
+ if next and self.more:
+ return 0
+ return QtGui.QTextEdit.focusNextPrevChild(self, next)
+
+ def mousePressEvent(self, e):
+ """mousePressEvent(e) -> None
+ Keep the cursor after the last prompt.
+ """
+ if e.button() == QtCore.Qt.LeftButton:
+ self.selectMode = True
+ QtGui.QTextEdit.mousePressEvent(self, e)
+# cursor = self.textCursor()
+# cursor.movePosition(QtGui.QTextCursor.End)
+# self.setTextCursor(cursor)
+ return
+
+ def hide(self):
+ """suspend() -> None
+ Called when hiding the parent window in order to recover the previous
+ state.
+
+ """
+ #recovering the state
+ sys.stdout = sys.__stdout__
+ sys.stderr = sys.__stderr__
+ sys.stdin = sys.__stdin__
+
+ def show(self):
+ """show() -> None
+ Store previous state and starts capturing all interactive input and
+ output.
+
+ """
+ # capture all interactive input/output
+ sys.stdout = self
+ sys.stderr = self
+ sys.stdin = self
+ self.setFocus()
+
+ def saveSession(self, fileName):
+ """saveSession(fileName: str) -> None
+ Write its contents to a file """
+ output = open(str(fileName), 'w')
+ output.write(self.toPlainText())
+ output.close()
+
+ def restart(self, locals=None):
+ """restart(locals=None) -> None
+ Restart a new session
+
+ """
+ self.clear()
+ self.reset(locals)
+
+ def contentsContextMenuEvent(self,ev):
+ """
+ contentsContextMenuEvent(ev) -> None
+ Suppress the right button context menu.
+
+ """
+ return
+
+################################################################################
+
+def getIPythonDialog():
+ from IPython.qt.console.rich_ipython_widget import RichIPythonWidget
+ from IPython.qt.inprocess import QtInProcessKernelManager
+# from IPython.kernel.inprocess.ipkernel import InProcessKernel
+
+ km = QtInProcessKernelManager()
+ km.start_kernel()
+ kernel = km.kernel
+ kernel.gui = 'qt4'
+
+ kernel_client = km.client()
+ kernel_client.start_channels()
+
+ def stop():
+ kernel_client.stop_channels()
+ km.shutdown_kernel()
+
+ class IPythonDialog(RichIPythonWidget, QVistrailsPaletteInterface):
+ """This class incorporates an IPython shell into a dockable widget for use in the
+ VisTrails environment"""
+ def __init__(self, parent=None):
+ RichIPythonWidget.__init__(self, parent)
+ self.kernel_manager = km
+ self.kernel_client = kernel_client
+ self.exit_requested.connect(stop)
+ #locals() returns the original dictionary, not a copy as
+ #the docs say
+ # self.firstLocals = copy.copy(locals())
+ # self.shell = IPythonXXX(self.firstLocals,None)
+ # layout = QtGui.QVBoxLayout()
+ # layout.setMargin(0)
+ # layout.setSpacing(0)
+ # layout.addWidget(self.shell)
+ # self.setLayout(layout)
+ # self.setWidget(self.shell)
+ self.setWindowTitle("Console")
+ # self.setTitleBarWidget(QtGui.QLabel(self.shell.windowTitle()))
+ # self.monitorWindowTitle(self.shell)
+ self.vistrails_interpreter = get_default_interpreter()
+
+ def visibility_changed(self, visible):
+ QVistrailsPaletteInterface.visibility_changed(self, visible)
+ if visible:
+ self.show()
+ else:
+ self.hide()
+
+ def hide(self):
+ """suspend() -> None
+ Called when hiding the parent window in order to recover the previous
+ state.
+
+ """
+ #recovering the state
+ sys.stdout = sys.__stdout__
+ sys.stderr = sys.__stderr__
+ sys.stdin = sys.__stdin__
+ RichIPythonWidget.hide(self)
+
+ def show(self):
+ """show() -> None
+ Store previous state and starts capturing all interactive input and
+ output.
+
+ """
+ # capture all interactive input/output
+ sys.stdout = self
+ sys.stderr = self
+ sys.stdin = self
+ RichIPythonWidget.show(self)
+
+ def showEvent(self, e):
+ """showEvent(e) -> None
+ Event handler called when the dialog acquires focus
+
+ """
+ self.show()
+
+ def flush(self):
+ """flush() -> None.
+ Simulate stdin, stdout, and stderr.
+
+ """
+ pass
+
+ def isatty(self):
+ """isatty() -> int
+ Simulate stdin, stdout, and stderr.
+
+ """
+ return 1
+
+ def readline(self):
+ """readline() -> str
+
+ Simulate stdin, stdout, and stderr.
+
+ """
+ return ""
+
+ def write(self, text):
+ """write(text: str) -> None
+ Simulate stdin, stdout, and stderr.
+
+ """
+ self._append_plain_text(text, True)
+
+ return IPythonDialog
+
+#install_attempted = False
+#installed = vistrails.core.requirements.python_module_exists('IPython.frontend.qt')
+#if not installed and not install_attempted:
+# print "attempt to install"
+# install_attempted = True
+# from vistrails.core.bundles import installbundle
+# installed = installbundle.install({'linux-ubuntu': 'ipython-qtconsole'})
+#if installed:
+# print "installed!"
+# QShellDialog = getIPythonDialog()
+
+# This is tested with IPython 1.0.0 and its beta versions
+# TODO: Once IPython 1.0 is included in the distro we should add auto-install
+try:
+ from IPython.qt.inprocess import QtInProcessKernelManager
+ try:
+ QShellDialog = getIPythonDialog()
+ except Exception, e:
+ import traceback; traceback.print_exc()
+ print str(e)
+except:
+ pass
diff --git a/vistrails/gui/theme.py b/vistrails/gui/theme.py
new file mode 100644
index 0000000..9d7b878
--- /dev/null
+++ b/vistrails/gui/theme.py
@@ -0,0 +1,750 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""
+This module describes a theme structure for VisTrails GUI. It
+specifies colors, background images and other measurements
+"""
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core.utils.color import ColorByName
+from vistrails.core.theme import DefaultCoreTheme
+import vistrails.core.system
+
+import unittest
+import vistrails.gui.qt
+
+################################################################################
+
+def _create_configure_shape(w, h):
+ poly = QtGui.QPolygon(3)
+ poly.setPoint(0, 0, 0)
+ poly.setPoint(1, 0, h)
+ poly.setPoint(2, w, h/2)
+ return QtGui.QPolygonF(poly)
+
+
+class DefaultTheme(DefaultCoreTheme):
+ """
+ This is the default theme which contains color, images,
+ measurements, etc. for Vistrail. Other themes should derive from
+ this class and change appropriate values
+
+ """
+
+ def __init__(self):
+ """ DefaultTheme() -> DefaultTheme
+ This is for initializing all Qt objects
+
+ """
+ DefaultCoreTheme.__init__(self)
+ ######################
+ #### MEASUREMENTS ####
+
+ # Port shape
+ self.PORT_RECT = QtCore.QRectF(0, 0, self.PORT_WIDTH, self.PORT_HEIGHT)
+
+ # Configure button shape
+ self.CONFIGURE_SHAPE = _create_configure_shape(self.CONFIGURE_WIDTH,
+ self.CONFIGURE_HEIGHT)
+
+ #### BRUSH & PEN ####
+ # Background brush of the pipeline view
+ # self.PIPELINE_VIEW_BACKGROUND_BRUSH = QtGui.QBrush(
+ # QtGui.QImage(vistrails.core.system.vistrails_root_directory() +
+ # '/gui/resources/images/pipeline_bg.png'))
+ # #QtGui.QColor("white"))
+ # # Background brush of the version tree
+ # self.VERSION_TREE_BACKGROUND_BRUSH = QtGui.QBrush(
+ # QtGui.QImage(vistrails.core.system.vistrails_root_directory() +
+ # '/gui/resources/images/version_bg.png'))
+ # Background brush of the query pipeline view
+ # self.QUERY_BACKGROUND_BRUSH = QtGui.QBrush(
+ # QtGui.QImage(vistrails.core.system.vistrails_root_directory() +
+ # '/gui/resources/images/query_bg.png'))
+ self.PIPELINE_VIEW_BACKGROUND_BRUSH = QtGui.QBrush(
+ QtGui.QColor(128, 128, 128))
+ self.VERSION_TREE_BACKGROUND_BRUSH = QtGui.QBrush(
+ QtGui.QColor(240, 240, 240))
+ self.QUERY_BACKGROUND_BRUSH = QtGui.QBrush(
+ QtGui.QColor(119, 143, 159))
+ self.QUERY_RESULT_BACKGROUND_BRUSH = QtGui.QBrush(
+ QtGui.QColor(208, 226, 239))
+
+ # Pen to draw a module shape at regular state
+ self.MODULE_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('black')))), 2)
+ # Pen to draw a module shape when selected
+ self.MODULE_SELECTED_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('goldenrod_medium')))), 3)
+ # Brush and pen to draw a module label
+ self.MODULE_LABEL_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('black')))), 2)
+ self.MODULE_LABEL_SELECTED_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('black')))), 2)
+ # Brush to draw a module shape at different states
+ self.MODULE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('light_grey'))))
+ self.ERROR_MODULE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('salmon'))))
+ self.SUCCESS_MODULE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('mint'))))
+ self.ACTIVE_MODULE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('navajo_white'))))
+ self.COMPUTING_MODULE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('yellow'))))
+ self.NOT_EXECUTED_MODULE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('light_goldenrod'))))
+ self.PERSISTENT_MODULE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('slate_blue'))))
+ self.SUSPENDED_MODULE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('aureoline_yellow'))))
+
+ self.INVALID_MODULE_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(51, 51, 51, 255)), 2)
+ self.INVALID_MODULE_LABEL_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(51, 51, 51, 255)), 2)
+ self.INVALID_MODULE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(125, 92, 92, 255))
+
+ # Pen and brush for un-matched queried modules
+ self.GHOSTED_MODULE_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('dark_dim_grey')))), 2)
+ # Pen to draw module label when it is unmatched due to a query
+ self.GHOSTED_MODULE_LABEL_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('dark_dim_grey')))), 2)
+ self.GHOSTED_MODULE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('light_dim_grey'))))
+
+ # Pen and brush for breakpoint modules
+ self.BREAKPOINT_MODULE_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('dark_dim_grey')))), 2)
+ self.BREAKPOINT_MODULE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('light_dim_grey'))))
+ self.BREAKPOINT_MODULE_LABEL_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('dark_dim_grey')))), 2)
+
+ # Module pen styles
+ self.ABSTRACTION_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('black')))), 2,
+ QtCore.Qt.DotLine)
+ self.GROUP_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('black')))), 2,
+ QtCore.Qt.DashLine)
+
+ # Brush and pen to draw a port shape at regular state
+ self.PORT_PEN_WIDTH_MANDATORY = 'mandatory'
+ self.PORT_PEN_WIDTH_NORMAL = 'normal'
+ self.PORT_PEN_WIDTH_SELECTED = 'selected'
+ self.PORT_PEN_WIDTHS = {self.PORT_PEN_WIDTH_MANDATORY: 1.5,
+ self.PORT_PEN_WIDTH_NORMAL: 1.0,
+ self.PORT_PEN_WIDTH_SELECTED: 3.0}
+ self.PORT_PEN_COLOR_NORMAL = 'normal'
+ self.PORT_PEN_COLOR_FULL = 'full'
+ self.PORT_PEN_COLOR_INVALID = 'invalid'
+ self.PORT_PEN_COLOR_GHOSTED = 'ghosted'
+ self.PORT_PEN_COLOR_SELECTED = 'selected'
+ self.PORT_PEN_COLORS = \
+ {self.PORT_PEN_COLOR_NORMAL: \
+ QtGui.QColor(*(ColorByName.get_int('black'))),
+ self.PORT_PEN_COLOR_FULL: \
+ QtGui.QColor(*(ColorByName.get_int('dark_dim_grey'))),
+ self.PORT_PEN_COLOR_INVALID: QtGui.QColor(51, 51, 51, 255),
+ self.PORT_PEN_COLOR_GHOSTED: \
+ QtGui.QColor(*(ColorByName.get_int('dark_dim_grey'))),
+ self.PORT_PEN_COLOR_SELECTED: \
+ QtGui.QColor(*(ColorByName.get_int('goldenrod_medium')))
+ }
+
+ self.PORT_PENS = {}
+ for (color_type, color) in self.PORT_PEN_COLORS.iteritems():
+ for (width_type, width) in self.PORT_PEN_WIDTHS.iteritems():
+ self.PORT_PENS[(color_type, width_type)] = \
+ QtGui.QPen(QtGui.QBrush(color), width)
+
+ self.PORT_CONNECTED_BRUSH = QtGui.QBrush(
+ QtGui.QColor(0,0,0,60))
+ self.PORT_BRUSH = QtGui.QBrush(QtCore.Qt.NoBrush)
+ self.PORT_MANDATORY_BRUSH = QtGui.QBrush(QtGui.QColor(255,255,255,180))
+ self.GHOSTED_PORT_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('light_dim_grey'))))
+ self.INVALID_PORT_BRUSH = QtGui.QBrush(
+ QtGui.QColor(125, 92, 92, 255))
+
+ # Pen and brush for drawing the configure button
+ self.CONFIGURE_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('black')))), 1)
+ self.CONFIGURE_BRUSH= QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('black'))))
+
+ # Pen and brush for drawing the ghosted configure button
+ self.GHOSTED_CONFIGURE_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('dark_dim_grey')))), 2)
+ self.GHOSTED_CONFIGURE_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('dark_dim_grey'))))
+
+ # Brush and pen to draw connections
+ self.CONNECTION_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('black')))), 2)
+ self.CONNECTION_SELECTED_PEN = QtGui.QPen(
+ QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('goldenrod_medium')))),
+ 3,
+ QtCore.Qt.SolidLine)
+ self.CONNECTION_SELECTED_CONVERTING_PEN = QtGui.QPen(
+ QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('goldenrod_medium')))),
+ 3,
+ QtCore.Qt.DotLine)
+ self.CONNECTION_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('black'))))
+
+ # Pen for drawing while connecting any ghosted modules
+ self.GHOSTED_CONNECTION_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('dark_dim_grey')))), 2)
+
+ # Pen to draw version tree node
+ self.VERSION_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('black')))), 2)
+ self.GHOSTED_VERSION_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('light_grey')))), 2)
+ self.VERSION_SELECTED_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('goldenrod_medium')))), 4)
+
+ self.VERSION_LABEL_COLOR = \
+ QtGui.QColor(*(ColorByName.get_int('black')))
+ self.GHOSTED_VERSION_LABEL_COLOR = \
+ QtGui.QColor(*(ColorByName.get_int('light_grey')))
+
+ # Brush to draw version belongs to the current user
+ self.VERSION_USER_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('desatcornflower'))))
+ self.GHOSTED_VERSION_USER_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('very_light_grey'))))
+
+ # Brush to draw version belongs to the other users
+ self.VERSION_OTHER_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('melon'))))
+
+ # Brush and pen to draw a link between two versions
+ self.LINK_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('black')))), 1.5)
+ self.LINK_SELECTED_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('goldenrod_medium')))), 3)
+ self.GHOSTED_LINK_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('light_grey')))), 2)
+
+ # Selection box color
+ self.SELECTION_BOX_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*ColorByName.get_int('light_grey')))
+ self.SELECTION_BOX_PEN = QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*ColorByName.get_int('lamp_black'))), 1)
+
+ # Color of the version is being diff from in
+ self.VISUAL_DIFF_FROM_VERSION_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*ColorByName.get_int('melon')))
+
+ # Color of the version is being diff to in
+ self.VISUAL_DIFF_TO_VERSION_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*ColorByName.get_int('steel_blue_light')))
+
+ # Color of the paramter changed modules in Visual Diff
+ self.VISUAL_DIFF_PARAMETER_CHANGED_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*ColorByName.get_int('light_grey')))
+
+ # Color of the shared modules in Visual Diff
+ self.VISUAL_DIFF_SHARED_BRUSH = QtGui.QBrush(
+ QtGui.QColor(155, 155, 155, 255))
+
+ # Color of shared modules in Visual Diff matched by heuristic
+ self.VISUAL_DIFF_MATCH_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*ColorByName.get_int('white')))
+
+ # Color of partially shared modules in Visual Diff
+ self.VISUAL_DIFF_SUMMARY_BRUSH = QtGui.QBrush(
+ QtGui.QColor(*ColorByName.get_int('spring_green')))
+
+ # Pen & Brush of the circled id on the right corner of the
+ # virtual cell label
+ self.ANNOTATED_ID_PEN = QtGui.QPen(
+ QtCore.Qt.white)
+ self.ANNOTATED_ID_BRUSH = QtGui.QBrush(
+ QtGui.QColor(157, 0, 0, 255))
+
+ #### FONTS ####
+ # Font for module text
+ self.MODULE_FONT = QtGui.QFont("Arial", 14, QtGui.QFont.Bold)
+ self.MODULE_FONT_METRIC = QtGui.QFontMetrics(self.MODULE_FONT)
+ self.MODULE_DESC_FONT = QtGui.QFont("Arial", 12)
+ self.MODULE_DESC_FONT_METRIC = QtGui.QFontMetrics(self.MODULE_DESC_FONT)
+
+ # Font for version text
+ self.VERSION_FONT = QtGui.QFont("Arial", 15, QtGui.QFont.Bold)
+ self.VERSION_FONT_METRIC = QtGui.QFontMetrics(self.VERSION_FONT)
+ self.VERSION_DESCRIPTION_FONT = QtGui.QFont("Arial", 15, QtGui.QFont.Normal,
+ True)
+ self.VERSION_DESCRIPTION_FONT_METRIC = \
+ QtGui.QFontMetrics(self.VERSION_DESCRIPTION_FONT)
+ self.VERSION_PROPERTIES_FONT = QtGui.QFont("Arial", 12)
+ self.VERSION_PROPERTIES_FONT_METRIC = \
+ QtGui.QFontMetrics(self.VERSION_PROPERTIES_FONT)
+ self.VERSION_PROPERTIES_PEN = QtGui.QBrush(
+ QtGui.QColor(20, 100, 20, 255))
+
+
+ # Font showing on the Parameter Inspector window of Visual Diff
+ self.VISUAL_DIFF_PARAMETER_FONT = QtGui.QFont('Arial', 10)
+
+ # Font showing on the Legend window of Visual Diff
+ self.VISUAL_DIFF_LEGEND_FONT = QtGui.QFont('Arial', 9)
+
+ # Font for PythonSource
+ self.PYTHON_SOURCE_EDITOR_FONT = QtGui.QFont('Courier', 10,
+ QtGui.QFont.Normal)
+ # Font for Splash Screen messages
+ self.SPLASH_SCREEN_FONT = QtGui.QFont('Arial', 10,
+ QtGui.QFont.Normal)
+ #### ICONS & IMAGES ####
+ #The application disclaimer image
+ self.DISCLAIMER_IMAGE = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/disclaimer.png')
+ #The application icon
+ self.APPLICATION_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/vistrails_icon_small.png')
+
+ #The application pixmap
+ self.APPLICATION_PIXMAP = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/vistrails_icon_small.png')
+
+ # The execute icons in the first spot of vistrail view toolbar
+ self.EXECUTE_PIPELINE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/execute.png')
+ self.EXECUTE_EXPLORE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/execute_explore.png')
+
+ # The undo icons for the vistrail view toolbar
+ self.UNDO_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/undo.png')
+
+ # The redo icons for the vistrail view toolbar
+ self.REDO_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/redo.png')
+
+ # Icon to select the tabbed view
+ self.TABBED_VIEW_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/tabbed_view.png')
+
+ # Icon to select the horizontal split view
+ self.HORIZONTAL_VIEW_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/hor_view.png')
+
+ # Icon to select the vertical split view
+ self.VERTICAL_VIEW_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/ver_view.png')
+
+ # Icon to select the docking-style view
+ self.DOCK_VIEW_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/dock_view.png')
+
+ # Toolbar icon for creating a new Vistrail
+ self.NEW_VISTRAIL_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/new_vistrail.png')
+
+ # Toolbar icon for opening a vistrail
+ self.OPEN_VISTRAIL_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/open_vistrail.png')
+
+ #Toolbar icon for opening a vistrail from a database
+ self.OPEN_VISTRAIL_DB_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/openfromdb.png')
+
+ #Icon for database connections
+ self.DB_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/database.png')
+
+ #Icon for vistrails files
+ self.FILE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/file.png')
+
+ # Toolbar icon for save the current Vistrail
+ self.SAVE_VISTRAIL_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/save_vistrail.png')
+
+ # Toolbar icon for toggling console mode window
+ self.CONSOLE_MODE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/console.png')
+
+ # Background image of the Visual Diff pipeline view
+ self.VISUAL_DIFF_BACKGROUND_IMAGE = QtGui.QImage(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/pipeline_bg.png')
+
+ # Toolbar icon for showing the Parameter Inspector window
+ self.VISUAL_DIFF_SHOW_PARAM_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/show_params.png')
+
+ # Toolbar icon for showing the Legend window
+ self.VISUAL_DIFF_SHOW_LEGEND_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/show_legends.png')
+
+ # Toolbar icon for creating an analogy
+ self.VISUAL_DIFF_CREATE_ANALOGY_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/analogy.png')
+
+ # Toolbar icon for close button on the vistrail tabbar
+ self.VIEW_MANAGER_CLOSE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/closeview.png')
+
+ # Toolbar icon for the dock toolbutton on the splitted window
+ self.DOCK_BACK_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/dockback.png')
+
+ # Icon for adding string in the parameter exploration widget
+ self.ADD_STRING_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/edit_add.png')
+
+ # Icon for moving string up in the parameter exploration widget
+ self.UP_STRING_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/up.png')
+
+ # Icon for moving string up in the parameter exploration widget
+ self.DOWN_STRING_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/down.png')
+
+ # Icon for expand all/collapse all buttons in the Module Palette
+ self.EXPAND_ALL_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/expand_all.png')
+
+ self.COLLAPSE_ALL_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/collapse_all.png')
+
+ # Icons for tree/list view buttons in the Workspace
+ self.LIST_VIEW_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/list_view.png')
+
+ self.TREE_VIEW_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/tree_view.png')
+
+ # Toolbar icons for views
+ self.PIPELINE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/pipeline.png')
+ self.HISTORY_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/history.png')
+ self.QUERY_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/full_tree.png')
+ self.EXPLORE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/explore.png')
+ self.PROVENANCE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/search_database.png')
+
+ # Toolbar icon for visual query on a vistrail
+ self.VISUAL_QUERY_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/visual_query.png')
+
+ # Toolbar icon for viewing the whole version tree
+ self.VIEW_FULL_TREE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/full_tree.png')
+
+ # Toolbar icon for viewing the whole version tree
+ self.PERFORM_PARAMETER_EXPLORATION_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/perform_pe.png')
+
+ # Toolbar icon for dragging pixmap of VisDiff
+ self.VERSION_DRAG_PIXMAP = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/dragging.png')
+
+ #Tabbar icon for detach a tab
+ self.DETACH_TAB_ICON = QtGui.QIcon()
+ self.DETACH_TAB_ICON.addFile(vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/detach.png',
+ mode=QtGui.QIcon.Normal)
+ self.DETACH_TAB_ICON.addFile(vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/detach_on.png',
+ mode=QtGui.QIcon.Active)
+
+ #toolbutton icon for pin/unpin palette
+ self.PINNED_PALETTE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/pinned.png')
+ self.UNPINNED_PALETTE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/unpinned.png')
+ # Parameter Exploration Pixmaps
+ self.EXPLORE_COLUMN_PIXMAP = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/column.png')
+ self.EXPLORE_ROW_PIXMAP = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/row.png')
+ self.EXPLORE_SHEET_PIXMAP = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/sheet.png')
+ self.EXPLORE_TIME_PIXMAP = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/time.png')
+ self.EXPLORE_SKIP_PIXMAP = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/skip.png')
+ self.REMOVE_PARAM_PIXMAP = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/remove_param.png')
+ self.RIGHT_ARROW_PIXMAP = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/right.png')
+ self.LEFT_ARROW_PIXMAP = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/left.png')
+
+ # Cursor for zoom in/out graphics views
+ self.SELECT_CURSOR = QtGui.QCursor(QtCore.Qt.ArrowCursor)
+ self.OPEN_HAND_CURSOR = QtGui.QCursor(QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/open_hand.png'))
+ self.CLOSE_HAND_CURSOR = QtGui.QCursor(QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/close_hand.png'))
+ self.ZOOM_CURSOR = QtGui.QCursor(QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/zoom.png'))
+
+ # Cursor icon for zoom in/out graphics views
+ self.SELECT_ICON = QtGui.QIcon(QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/select_icon.png'))
+ self.PAN_ICON = QtGui.QIcon(QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/pan_icon.png'))
+ self.ZOOM_ICON = QtGui.QIcon(QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/zoom_icon.png'))
+
+ # Mashup Icons
+ self.EXECUTE_MASHUP_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/mashup_execute.png')
+ self.MASHUP_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/mashup_create.png')
+ self.MASHUP_ALIAS_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/alias.png')
+
+ # Job View Icons
+ self.JOB_SCHEDULED = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/appointment-new.png')
+ self.JOB_FINISHED = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/emblem-important.png')
+ self.JOB_CHECKING = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/view-refresh.png')
+
+ # Saved Queries icons
+ self.QUERY_VIEW_ICON = self.ZOOM_ICON
+ self.QUERY_ARROW_ICON = QtGui.QIcon(QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/zoom_arrow_icon.png'))
+ self.QUERY_EDIT_ICON = QtGui.QIcon(QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/edit.png'))
+
+ # Icon on the button to switch to single/multi line string edition
+ self.MULTILINE_STRING_ICON = QtGui.QIcon(QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/multiline_string_icon.png'))
+
+ #### COLORS ####
+ # Color for the PIP frame
+ self.PIP_FRAME_COLOR = QtGui.QColor(
+ *(ColorByName.get_int('yellow_light')))
+
+ # Color of selected methods in the modules method area
+ self.METHOD_SELECT_COLOR = QtGui.QColor(
+ *ColorByName.get_int('yellow_light'))
+
+ # Color of the hover/unhover alias labels
+ self.HOVER_DEFAULT_COLOR = QtGui.QColor(
+ *ColorByName.get_int('black'))
+ self.HOVER_SELECT_COLOR = QtGui.QColor(
+ *ColorByName.get_int('blue'))
+
+ # colors for debug messages
+ self.DEBUG_COLORS = {
+ 'DEBUG': QtGui.QColor("#777777"),
+ 'INFO': QtGui.QColor(QtCore.Qt.black),
+ 'WARNING': QtGui.QColor("#707000"),
+ 'CRITICAL': QtGui.QColor(QtCore.Qt.red),
+ }
+ class QTransparentColor(QtGui.QColor):
+ def name(self):
+ return 'transparent'
+ self.DEBUG_FILTER_BACKGROUND_COLOR = QTransparentColor("transparent")
+
+class MacTheme(DefaultTheme):
+ def __init__(self):
+
+ DefaultTheme.__init__(self)
+ #### ICONS & IMAGES ####
+ #The application icon
+ self.APPLICATION_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/vistrails_icon.png')
+
+ #The application pixmap
+ self.APPLICATION_PIXMAP = QtGui.QPixmap(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/vistrails_icon.png')
+
+ # Toolbar icon for close button on the vistrail tabbar
+ self.VIEW_MANAGER_CLOSE_ICON = QtGui.QIcon(
+ vistrails.core.system.vistrails_root_directory() +
+ '/gui/resources/images/mac/closetab.png')
+
+ #### FONTS ####
+ # Font for PythonSource
+ self.PYTHON_SOURCE_EDITOR_FONT = QtGui.QFont('Monaco', 11,
+ QtGui.QFont.Normal)
+
+ # Font for Splash Screen messages
+ self.SPLASH_SCREEN_FONT = QtGui.QFont('Helvetica', 10,
+ QtGui.QFont.Light)
+
+class LinuxTheme(DefaultTheme):
+ def __init__(self):
+ DefaultTheme.__init__(self)
+ #### FONTS ####
+ # Font for PythonSource
+ self.PYTHON_SOURCE_EDITOR_FONT = QtGui.QFont('Monospace', 10,
+ QtGui.QFont.Normal)
+
+class ThemeHolder(object):
+ """
+ ThemeHolder is a class holding a theme and exposed that theme
+ atrributes as attributes of itself. This is useful for global
+ import of the CurrentTheme variable
+
+ """
+ def __init__(self):
+ object.__init__(self)
+ self.theme = None
+
+ def setTheme(self, theme):
+ """ setTheme(theme: subclass of DefaultTheme) -> None
+ Set the current theme to theme
+
+ """
+ # This way, the lookups into the theme are much faster, since
+ # there's no function calls involved
+ self.__dict__.update(theme.__dict__)
+
+def get_current_theme():
+ """get_current_theme() -> subclass of DefaultTheme
+ Instantiates the theme according to the current platform """
+ if vistrails.core.system.systemType in ['Darwin']:
+ return MacTheme()
+ elif vistrails.core.system.systemType in ['Linux']:
+ return LinuxTheme()
+ else:
+ return DefaultTheme()
+
+def initializeCurrentTheme():
+ """ initializeCurrentTheme() -> None
+ Assign the current theme to the default theme
+
+ """
+ global CurrentTheme
+
+ CurrentTheme.setTheme(get_current_theme())
+
+global CurrentTheme
+CurrentTheme = ThemeHolder()
+
+################################################################################
+
+
+class TestPresetColor(unittest.TestCase):
+ """
+ A few simple tests to make sure Preset is working as expected
+
+ """
+ def setUp(self):
+ vistrails.gui.qt.createBogusQtGuiApp()
+
+ def testColorValues(self):
+ initializeCurrentTheme()
+ self.assertEquals(CurrentTheme.CONNECTION_CONTROL_POINTS,
+ 20)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/gui/utils.py b/vistrails/gui/utils.py
new file mode 100644
index 0000000..86edd6a
--- /dev/null
+++ b/vistrails/gui/utils.py
@@ -0,0 +1,243 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+""" Utilities for creating simple dialogs, notifications in Vistrails
+without exposing Qt codes """
+from PyQt4 import QtGui, QtCore
+from vistrails.gui.theme import CurrentTheme
+import vistrails.gui.theme
+from vistrails.core.system import systemType
+
+import unittest
+
+################################################################################
+
+OK_BUTTON = QtGui.QMessageBox.Ok
+OPEN_BUTTON = QtGui.QMessageBox.Open
+SAVE_BUTTON = QtGui.QMessageBox.Save
+CANCEL_BUTTON = QtGui.QMessageBox.Cancel
+CLOSE_BUTTON = QtGui.QMessageBox.Close
+DISCARD_BUTTON = QtGui.QMessageBox.Discard
+APPLY_BUTTON = QtGui.QMessageBox.Apply
+RESET_BUTTON = QtGui.QMessageBox.Reset
+RESTOREDEFAULTS_BUTTON = QtGui.QMessageBox.RestoreDefaults
+HELP_BUTTON = QtGui.QMessageBox.Help
+SAVEALL_BUTTON = QtGui.QMessageBox.SaveAll
+YES_BUTTON = QtGui.QMessageBox.Yes
+YESTOALL_BUTTON = QtGui.QMessageBox.YesToAll
+NO_BUTTON = QtGui.QMessageBox.No
+NOTOALL_BUTTON = QtGui.QMessageBox.NoToAll
+ABORT_BUTTON = QtGui.QMessageBox.Abort
+RETRY_BUTTON = QtGui.QMessageBox.Retry
+IGNORE_BUTTON = QtGui.QMessageBox.Ignore
+NOBUTTON_BUTTON = QtGui.QMessageBox.NoButton
+
+_buttons_captions_dict = { OK_BUTTON : "Ok",
+ OPEN_BUTTON : "Open",
+ SAVE_BUTTON : "Save",
+ CANCEL_BUTTON : "Cancel",
+ CLOSE_BUTTON : "Close",
+ DISCARD_BUTTON : "Discard",
+ APPLY_BUTTON : "Apply",
+ RESET_BUTTON : "Reset",
+ RESTOREDEFAULTS_BUTTON : "Restore Defaults",
+ HELP_BUTTON : "Help",
+ SAVEALL_BUTTON : "Save All",
+ YES_BUTTON : "Yes",
+ NO_BUTTON : "No",
+ NOTOALL_BUTTON : "No to All",
+ ABORT_BUTTON : "Abort",
+ RETRY_BUTTON : "Retry",
+ IGNORE_BUTTON : "Ignore",
+ NOBUTTON_BUTTON : ""}
+
+
+def show_warning(title, message):
+ """ show_warning(title: str, message: str) -> None
+ Show a warning message box with a specific title and contents
+ Deprecated, consider using core.debug instead!
+ """
+ if systemType not in ['Darwin']:
+ QtGui.QMessageBox.warning(None, title, message)
+ else:
+ show_custom(title,message)
+
+def show_info(title, message):
+ """ show_info(title: str, message: str) -> None
+ Show an information message box with a specific title and contents
+ Deprecated, consider using core.debug instead!
+ """
+ if systemType not in ['Darwin']:
+ QtGui.QMessageBox.information(None, title, message)
+ else:
+ show_custom(title,message)
+
+def show_question(title,
+ message,
+ buttons = [OK_BUTTON],
+ default = NOBUTTON_BUTTON):
+ """ show_question(title: str,
+ message: str,
+ buttons: list of buttons (defined above),
+ default: button (defined above)) -> button
+ Show a question message with a specific title, message and a set
+ of buttons defined by the list buttons. Default button is the
+ button that will take role when the user press 'Enter' without
+ selecting a button. The function returns the button that ends the
+ dialog.
+
+ """
+ qButtons = QtGui.QMessageBox.StandardButtons()
+ for button in buttons:
+ qButtons |= button
+ if systemType not in ['Darwin']:
+ return QtGui.QMessageBox.question(None, title, message,
+ qButtons, default)
+ else:
+ return show_custom(title,message,None,buttons)
+
+def build_custom_window(title, message, icon=None,
+ buttons = [OK_BUTTON], default=OK_BUTTON, escape=-1,
+ modal=True, parent=None):
+ """ show_custom(title: str,
+ message: str,
+ icon: QPixmap,
+ buttons: list of buttons (defined above),
+ default: str,
+ escape: str,
+ modal: bool,
+ parent: QWidget) -> QMessageBox
+ Build a custom dialog box.
+ Default is the button in buttons that will be clicked if
+ the user presses Enter. escape is the button in buttons
+ that will be clicked if Esc is pressed.
+ The function returns the index of the button that was pressed.
+
+ """
+ msgBox = QtGui.QMessageBox(parent)
+ abstractButtons = {}
+ for b in buttons:
+ msgBox.addButton(b)
+ abstractButtons[b] = msgBox.button(b)
+ if abstractButtons.has_key(default):
+ msgBox.setDefaultButton(abstractButtons[default])
+ if escape != -1:
+ msgBox.setEscapeButton(abstractButtons[escape])
+ msgBox.setWindowFlags(QtCore.Qt.SplashScreen | QtCore.Qt.WindowStaysOnTopHint)
+ if modal:
+ msgBox.setWindowModality(QtCore.Qt.ApplicationModal)
+ else:
+ msgBox.setWindowModality(QtCore.Qt.NonModal)
+ if icon:
+ msgBox.setIconPixmap(icon)
+ else:
+ pixmap = CurrentTheme.APPLICATION_PIXMAP.scaledToHeight(48)
+ msgBox.setIconPixmap(pixmap)
+
+ #mac doesn't show a window title
+ #we need to include the title as part of the message
+ if systemType not in ['Darwin']:
+ msgBox.setWindowTitle(title)
+ msgBox.setText(message)
+ else:
+ msgBox.setText("%s\n%s"%(title,
+ message))
+
+ qButtons = QtGui.QMessageBox.StandardButtons()
+ return msgBox
+
+def show_custom(title, message, icon=None,
+ buttons = [OK_BUTTON], default=OK_BUTTON, escape=-1):
+ """ show_custom(title: str,
+ message: str,
+ icon: QPixmap,
+ buttons: list of buttons (defined above),
+ default: str,
+ escape: str) -> int
+ Show a custom dialog box.
+ Default is the button in buttons that will be clicked if
+ the user presses Enter. escape is the button in buttons
+ that will be clicked if Esc is pressed.
+ The function returns the index of the button that was pressed.
+
+ """
+ msgBox = build_custom_window(title,message,icon,
+ buttons, default,escape)
+ return msgBox.exec_()
+
+def getBuilderWindow():
+ """ getBuilderWindow() -> QMainWindow
+ Return the current builder window of VisTrails if exists
+ """
+ try:
+ return QtCore.QCoreApplication.instance().builderWindow
+ except:
+ return None
+
+def getCurrentVersion():
+ """ getCurrentVersion() -> int
+ Return the current version on VisTrails, return -1 if the GUI is not available
+
+ """
+ builderWindow = getBuilderWindow()
+ if builderWindow!=None:
+ current_view = builderWindow.viewManager.currentWidget()
+ if current_view!=None:
+ return current_view.controller.current_version
+ return -1
+
+def initTheme():
+ return vistrails.gui.theme.initializeCurrentTheme()
+
+################################################################################
+# VisTrails GUI unit test class - setUp and teardown ensure no
+# vistrails are open
+
+
+class TestVisTrailsGUI(unittest.TestCase):
+
+ def _close_all(self):
+ import vistrails.api
+ # Close all open vistrails
+ vistrails.api.close_all_vistrails()
+
+ def setUp(self):
+ # we need to call twice because VisTrails will create a new vistrail
+ # by default if we are not closing the first vistrail.
+ self._close_all()
+ self._close_all()
+
+ def tearDown(self):
+ self._close_all()
diff --git a/vistrails/gui/variable_dropbox.py b/vistrails/gui/variable_dropbox.py
new file mode 100644
index 0000000..748df0d
--- /dev/null
+++ b/vistrails/gui/variable_dropbox.py
@@ -0,0 +1,510 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file contains widgets that can be used for dropping Constant class
+variables. It will construct an input form for the value.
+
+QVariableDropBox
+QVerticalWidget
+QVariableInputWidget
+QVariableInputForm
+QDragVariableLabel
+QHoverVariableLabel
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core import debug
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.modules import module_registry
+from vistrails.core.modules.basic_modules import Constant
+from vistrails.core.vistrail.vistrailvariable import VistrailVariable
+from vistrails.gui.common_widgets import QPromptWidget
+from vistrails.gui.modules import get_widget_class
+from vistrails.gui.modules.constant_configuration import StandardConstantWidget, \
+ FileChooserToolButton
+from vistrails.gui.module_palette import QModuleTreeWidget
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.utils import show_question, YES_BUTTON, NO_BUTTON
+import uuid
+
+################################################################################
+
+class QVariableDropBox(QtGui.QScrollArea):
+ """
+ QVariableDropBox is just a widget such that items that subclass
+ Constant from the module palette can be dropped into its client rect.
+ It then constructs an input form based on the type of handling widget
+
+ """
+ def __init__(self, parent=None):
+ """ QVariableDropBox(parent: QWidget) -> QVariableDropBox
+ Initialize widget constraints
+
+ """
+ QtGui.QScrollArea.__init__(self, parent)
+ self.setAcceptDrops(True)
+ self.setWidgetResizable(True)
+ self.vWidget = QVerticalWidget()
+ self.setWidget(self.vWidget)
+ self.updateLocked = False
+ self.controller = None
+
+ def dragEnterEvent(self, event):
+ """ dragEnterEvent(event: QDragEnterEvent) -> None
+ Set to accept drops from the module palette
+
+ """
+ if isinstance(event.source(), QModuleTreeWidget):
+ data = event.mimeData()
+ if hasattr(data, 'items'):
+ event.accept()
+ else:
+ event.ignore()
+
+ def dragMoveEvent(self, event):
+ """ dragMoveEvent(event: QDragMoveEvent) -> None
+ Set to accept drag move event from the module palette
+
+ """
+ if isinstance(event.source(), QModuleTreeWidget):
+ data = event.mimeData()
+ if hasattr(data, 'items'):
+ event.accept()
+
+ def dropEvent(self, event):
+ """ dropEvent(event: QDragMoveEvent) -> None
+ Accept drop event to add a new variable
+
+ """
+ if isinstance(event.source(), QModuleTreeWidget):
+ data = event.mimeData()
+ if hasattr(data, 'items'):
+ event.accept()
+ assert len(data.items) == 1
+ item = data.items[0]
+ if issubclass(item.descriptor.module, Constant):
+ if item.descriptor and self.controller:
+ self.lockUpdate()
+ (text, ok) = QtGui.QInputDialog.getText(self,
+ 'Set Variable Name',
+ 'Enter the variable name',
+ QtGui.QLineEdit.Normal,
+ '')
+ var_name = str(text).strip()
+ while ok and self.controller.check_vistrail_variable(var_name):
+ msg =" This variable name is already being used.\
+ Please enter a different variable name "
+ (text, ok) = QtGui.QInputDialog.getText(self,
+ 'Set Variable Name',
+ msg,
+ QtGui.QLineEdit.Normal,
+ text)
+ var_name = str(text).strip()
+ if ok:
+ self.vWidget.addVariable(str(uuid.uuid1()), var_name, item.descriptor)
+ self.scrollContentsBy(0, self.viewport().height())
+ self.unlockUpdate()
+ #self.emit(QtCore.SIGNAL("paramsAreaChanged"))
+
+ def updateController(self, controller):
+ """ updateController(controller: VistrailController) -> None
+ Construct input forms for a controller's variables
+
+ """
+ # we shouldn't do this whenver the controller changes...
+ if self.controller != controller:
+ self.controller = controller
+ if self.updateLocked: return
+ self.vWidget.clear()
+ if controller:
+ reg = module_registry.get_module_registry()
+ for var in [v for v in controller.vistrail.vistrail_vars]:
+ try:
+ descriptor = reg.get_descriptor_by_name(var.package,
+ var.module,
+ var.namespace)
+ except module_registry.ModuleRegistryException:
+ debug.critical("Missing Module Descriptor for vistrail"
+ " variable %s\nPackage: %s\nType: %s"
+ "\nNamespace: %s" % \
+ (var.name, var.package, var.module,
+ var.namespace))
+ continue
+ self.vWidget.addVariable(var.uuid, var.name, descriptor,
+ var.value)
+ self.vWidget.showPromptByChildren()
+ else:
+ self.vWidget.showPrompt(False)
+
+ def lockUpdate(self):
+ """ lockUpdate() -> None
+ Do not allow updateModule()
+
+ """
+ self.updateLocked = True
+
+ def unlockUpdate(self):
+ """ unlockUpdate() -> None
+ Allow updateModule()
+
+ """
+ self.updateLocked = False
+
+class QVerticalWidget(QPromptWidget):
+ """
+ QVerticalWidget is a widget holding other variable widgets
+ vertically
+
+ """
+ def __init__(self, parent=None):
+ """ QVerticalWidget(parent: QWidget) -> QVerticalWidget
+ Initialize with a vertical layout
+
+ """
+ QPromptWidget.__init__(self, parent)
+ self.setPromptText("Drag a constant from the Modules panel to create a variable")
+ self.setLayout(QtGui.QVBoxLayout())
+ self.layout().setMargin(0)
+ self.layout().setSpacing(5)
+ self.layout().setAlignment(QtCore.Qt.AlignTop)
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ self.setMinimumHeight(20)
+ self._variable_widgets = []
+
+ def addVariable(self, uuid, name, descriptor, value=''):
+ """ addVariable(uuid:str, name: str, descriptor: ModuleDescriptor, value: str) -> None
+ Add an input form for the variable
+
+ """
+ inputForm = QVariableInputWidget(uuid, name, descriptor, value, self)
+ self.connect(inputForm, QtCore.SIGNAL('deleted(QWidget*)'),
+ self.delete_form)
+ self.layout().addWidget(inputForm)
+ inputForm.show()
+ self.setMinimumHeight(self.layout().minimumSize().height())
+ self.showPrompt(False)
+ self._variable_widgets.append(inputForm)
+
+ def clear(self):
+ """ clear() -> None
+ Clear and delete all widgets in the layout
+
+ """
+ self.setEnabled(False)
+ for v in self._variable_widgets:
+ self.disconnect(v, QtCore.SIGNAL('deleted(QWidget*)'),
+ self.delete_form)
+ self.layout().removeWidget(v)
+ v.setParent(None)
+ v.deleteLater()
+ self._variable_widgets = []
+ self.setEnabled(True)
+
+ def delete_form(self, input_form):
+ self.disconnect(input_form, QtCore.SIGNAL('deleted(QWidget*)'),
+ self.delete_form)
+ var_name = input_form.var_name
+ variableBox = self.parent().parent()
+ self.layout().removeWidget(input_form)
+ self._variable_widgets.remove(input_form)
+ input_form.setParent(None)
+ input_form.deleteLater()
+ self.showPromptByChildren()
+
+ if variableBox.controller:
+ variableBox.lockUpdate()
+ variableBox.controller.set_vistrail_variable(var_name, None)
+ variableBox.unlockUpdate()
+ self.setMinimumHeight(self.layout().minimumSize().height())
+
+
+class QVariableInputWidget(QtGui.QDockWidget):
+ def __init__(self, uuid, name, descriptor, value='', parent=None):
+ QtGui.QDockWidget.__init__(self, parent)
+ self.var_uuid = uuid
+ self.var_name = name
+ self.descriptor = descriptor
+ self.setFeatures(QtGui.QDockWidget.DockWidgetClosable)
+ # Create group and titlebar widgets for input widget
+ self.group_box = QVariableInputForm(descriptor, value, self)
+ self.setWidget(self.group_box)
+ title_widget = QtGui.QWidget()
+ title_layout = QtGui.QHBoxLayout()
+ self.closeButton = QtGui.QToolButton()
+ self.closeButton.setAutoRaise(True)
+ self.closeButton.setIcon(QtGui.QIcon(self.style().standardPixmap(QtGui.QStyle.SP_TitleBarCloseButton)))
+ self.closeButton.setIconSize(QtCore.QSize(13, 13))
+ self.closeButton.setFixedWidth(16)
+ self.label = QHoverVariableLabel(name)
+ title_layout.addWidget(self.label)
+ title_layout.addWidget(self.closeButton)
+ title_widget.setLayout(title_layout)
+ self.setTitleBarWidget(title_widget)
+ self.connect(self.closeButton, QtCore.SIGNAL('clicked()'), self.close)
+
+ def renameVariable(self, var_name):
+ # First delete old var entry
+ variableBox = self.parent().parent().parent()
+ if variableBox.controller:
+ variableBox.lockUpdate()
+ variableBox.controller.set_vistrail_variable(self.var_name, None, False)
+ variableBox.unlockUpdate()
+ # Create var entry with new name, but keeping the same uuid
+ self.var_name = var_name
+ self.label.setText(var_name)
+ self.group_box.updateMethod()
+
+ def closeEvent(self, event):
+ choice = show_question('Delete %s?'%self.var_name,
+ 'Are you sure you want to permanently delete the VisTrail variable\
+ "%s"?\n\nNote: Any workflows using this variable will be left in an invalid state.'%self.var_name,
+ [NO_BUTTON,YES_BUTTON],
+ NO_BUTTON)
+ if choice == NO_BUTTON:
+ event.ignore()
+ return
+ self.emit(QtCore.SIGNAL('deleted(QWidget*)'), self)
+
+ def keyPressEvent(self, e):
+ if e.key() in [QtCore.Qt.Key_Delete, QtCore.Qt.Key_Backspace]:
+ self.close()
+ else:
+ QtGui.QDockWidget.keyPressEvent(self, e)
+
+ def check_variable(self, name):
+ """ check_variable(name: str) -> Boolean
+ Returns True if the vistrail already has the variable name
+
+ """
+ variableBox = self.parent().parent().parent()
+ if variableBox.controller:
+ return variableBox.controller.check_vistrail_variable(name)
+ return False
+
+class QVariableInputForm(QtGui.QGroupBox):
+ """
+ QVariableInputForm is a widget with multiple input lines depends on
+ the method signature
+
+ """
+ def __init__(self, descriptor, var_strValue="", parent=None):
+ """ QVariableInputForm(descriptor: ModuleDescriptor, var_strValue: str,
+ parent: QWidget) -> QVariableInputForm
+ Initialize with a vertical layout
+
+ """
+ QtGui.QGroupBox.__init__(self, parent)
+ self.setLayout(QtGui.QGridLayout())
+ self.layout().setMargin(5)
+ self.layout().setSpacing(5)
+ self.setFocusPolicy(QtCore.Qt.ClickFocus)
+ self.setSizePolicy(QtGui.QSizePolicy.Preferred,
+ QtGui.QSizePolicy.Fixed)
+ self.palette().setColor(QtGui.QPalette.Window,
+ CurrentTheme.METHOD_SELECT_COLOR)
+ # Create widget for editing variable
+ p = ModuleParam(type=descriptor.name, identifier=descriptor.identifier,
+ namespace=descriptor.namespace)
+ p.strValue = var_strValue
+ widget_type = get_widget_class(descriptor.module)
+ self.widget = widget_type(p, self)
+ self.label = QDragVariableLabel(p.type)
+ self.layout().addWidget(self.label, 0, 0)
+ self.layout().addWidget(self.widget, 0, 1)
+ self.updateMethod()
+
+ def focusInEvent(self, event):
+ """ gotFocus() -> None
+ Make sure the form painted as selected
+
+ """
+ self.setAutoFillBackground(True)
+
+ def focusOutEvent(self, event):
+ """ lostFocus() -> None
+ Make sure the form painted as non-selected and then
+ perform a parameter changes
+
+ """
+ self.setAutoFillBackground(False)
+
+ def updateMethod(self):
+ """ updateMethod() -> None
+ Update the variable values in vistrail controller
+
+ """
+ inputWidget = self.parent()
+ variableBox = inputWidget.parent().parent().parent()
+ if variableBox.controller:
+ variableBox.lockUpdate()
+ descriptor = inputWidget.descriptor
+ var = VistrailVariable(inputWidget.var_name, inputWidget.var_uuid,
+ descriptor.identifier, descriptor.name,
+ descriptor.namespace, str(self.widget.contents()))
+ variableBox.controller.set_vistrail_variable(inputWidget.var_name, var)
+ variableBox.unlockUpdate()
+
+class QDragVariableLabel(QtGui.QLabel):
+ """
+ QDragVariableLabel is a QLabel that can be dragged to connect
+ to an input port
+ """
+ def __init__(self, var_type='', parent=None):
+ """ QDragVariableLabel(var_type:str,
+ parent: QWidget) -> QDragVariableLabel
+ Initialize the label with a variable type
+
+ """
+ QtGui.QLabel.__init__(self, parent)
+ self.var_type = var_type
+ self.setText(var_type)
+ self.setAttribute(QtCore.Qt.WA_Hover)
+ self.setCursor(CurrentTheme.OPEN_HAND_CURSOR)
+ self.setToolTip('Drag to an input port')
+ self.palette().setColor(QtGui.QPalette.WindowText,
+ CurrentTheme.HOVER_DEFAULT_COLOR)
+
+ def event(self, event):
+ """ event(event: QEvent) -> Event Result
+ Override to handle hover enter and leave events for hot links
+
+ """
+ if event.type()==QtCore.QEvent.HoverEnter:
+ self.palette().setColor(QtGui.QPalette.WindowText,
+ CurrentTheme.HOVER_SELECT_COLOR)
+ if event.type()==QtCore.QEvent.HoverLeave:
+ self.palette().setColor(QtGui.QPalette.WindowText,
+ CurrentTheme.HOVER_DEFAULT_COLOR)
+ return QtGui.QLabel.event(self, event)
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+ If mouse click on the label, show up a dialog to change/add
+ the variable name
+
+ """
+ if event.button()==QtCore.Qt.LeftButton:
+ inputWidget = self.parent().parent()
+ var_name = inputWidget.var_name
+ var_uuid = inputWidget.var_uuid
+ # Create pixmap from variable name and type
+ drag_str = var_name + ' : ' + self.var_type
+ drag_label = QDragVariableLabel(drag_str)
+ drag_label.adjustSize()
+ painter = QtGui.QPainter()
+ font = QtGui.QFont()
+ size = drag_label.size()
+ image = QtGui.QImage(size.width()+4, size.height()+4, QtGui.QImage.Format_ARGB32_Premultiplied)
+ image.fill(0)
+ painter.begin(image)
+ painter.setPen(QtCore.Qt.NoPen)
+ painter.setBrush(self.palette().highlight())
+ painter.drawRect(QtCore.QRectF(0, 0, image.width(), image.height()))
+ painter.setFont(font)
+ painter.setPen(QtCore.Qt.black)
+ painter.drawText(QtCore.QRect(QtCore.QPoint(2,2), size), QtCore.Qt.AlignLeft | QtCore.Qt.TextSingleLine, drag_str)
+ painter.end()
+ pixmap = QtGui.QPixmap.fromImage(image)
+ # Create drag action
+ mimeData = QtCore.QMimeData()
+ portspec = inputWidget.descriptor.get_port_spec('value', 'output')
+ mimeData.variableData = (portspec, var_uuid, var_name)
+ drag = QtGui.QDrag(self)
+ drag.setMimeData(mimeData)
+ drag.setHotSpot(pixmap.rect().bottomRight())
+ drag.setPixmap(pixmap)
+ drag.start(QtCore.Qt.MoveAction)
+
+class QHoverVariableLabel(QtGui.QLabel):
+ """
+ QHoverVariableLabel is a QLabel that supports hover actions similar
+ to a hot link
+ """
+ def __init__(self, var_name='', parent=None):
+ """ QHoverVariableLabel(var_name:str,
+ parent: QWidget) -> QHoverVariableLabel
+ Initialize the label with a variable name
+
+ """
+ QtGui.QLabel.__init__(self, parent)
+ self.var_name = var_name
+ self.setText(var_name)
+ self.setAttribute(QtCore.Qt.WA_Hover)
+ self.setCursor(QtCore.Qt.PointingHandCursor)
+ self.setToolTip('Click to rename')
+ self.palette().setColor(QtGui.QPalette.WindowText,
+ CurrentTheme.HOVER_DEFAULT_COLOR)
+
+ def event(self, event):
+ """ event(event: QEvent) -> Event Result
+ Override to handle hover enter and leave events for hot links
+
+ """
+ if event.type()==QtCore.QEvent.HoverEnter:
+ self.palette().setColor(QtGui.QPalette.WindowText,
+ CurrentTheme.HOVER_SELECT_COLOR)
+ if event.type()==QtCore.QEvent.HoverLeave:
+ self.palette().setColor(QtGui.QPalette.WindowText,
+ CurrentTheme.HOVER_DEFAULT_COLOR)
+ return QtGui.QLabel.event(self, event)
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+ If mouse click on the label, show up a dialog to change/add
+ the variable name
+
+ """
+ if event.button()==QtCore.Qt.LeftButton:
+ inputWidget = self.parent().parent()
+ orig_var_name = inputWidget.var_name
+ (text, ok) = QtGui.QInputDialog.getText(self,
+ 'Set New Variable Name',
+ 'Enter the new variable name',
+ QtGui.QLineEdit.Normal,
+ orig_var_name)
+ var_name = str(text).strip()
+ while ok and self.parent().parent().check_variable(var_name):
+ msg =" This variable name is already being used.\
+ Please enter a different variable name "
+ (text, ok) = QtGui.QInputDialog.getText(self,
+ 'Set New Variable Name',
+ msg,
+ QtGui.QLineEdit.Normal,
+ text)
+ var_name = str(text).strip()
+ if ok and var_name != orig_var_name:
+ self.setText(var_name)
+ inputWidget.renameVariable(var_name)
+
diff --git a/vistrails/gui/version_prop.py b/vistrails/gui/version_prop.py
new file mode 100644
index 0000000..14da589
--- /dev/null
+++ b/vistrails/gui/version_prop.py
@@ -0,0 +1,817 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file describe a widget for keeping version notes,info and tag
+name
+
+QVersionProp
+QVersionNotes
+QVersionPropOverlay
+QExpandButton
+QNotesDialog
+QVersionThumbs
+QVersionMashups
+
+"""
+import re
+import os.path
+from PyQt4 import QtCore, QtGui
+from vistrails.core.query.version import SearchCompiler, SearchParseError, TrueSearch
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.common_widgets import QSearchBox
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+from vistrails.core.utils import all
+from vistrails.core import debug
+
+################################################################################
+
+class QVersionProp(QtGui.QWidget, QVistrailsPaletteInterface):
+ """
+ QVersionProp is a widget holding property of a version including
+ tagname and notes
+
+ """
+ def __init__(self, parent=None):
+ """ QVersionProp(parent: QWidget) -> QVersionProp
+ Initialize the main layout
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self.setWindowTitle('Properties')
+
+ vLayout = QtGui.QVBoxLayout()
+ vLayout.setMargin(2)
+ vLayout.setSpacing(2)
+ self.setLayout(vLayout)
+
+ gLayout = QtGui.QGridLayout()
+ gLayout.setMargin(2)
+ gLayout.setSpacing(5)
+ gLayout.setColumnMinimumWidth(1,5)
+ gLayout.setRowMinimumHeight(0,20)
+ gLayout.setRowMinimumHeight(1,20)
+ gLayout.setRowMinimumHeight(2,20)
+ gLayout.setRowMinimumHeight(3,20)
+ vLayout.addLayout(gLayout)
+
+ tagLabel = QtGui.QLabel('Tag:', self)
+ gLayout.addWidget(tagLabel, 0, 0, 1, 1)
+
+ editLayout = QtGui.QHBoxLayout()
+ editLayout.setMargin(2)
+ editLayout.setSpacing(2)
+ self.tagEdit = QtGui.QLineEdit()
+ tagLabel.setBuddy(self.tagEdit)
+ editLayout.addWidget(self.tagEdit)
+ self.tagEdit.setEnabled(False)
+ self.tagEdit.setMinimumHeight(22)
+
+ self.tagReset = QtGui.QToolButton(self)
+ self.tagReset.setIcon(QtGui.QIcon(
+ self.style().standardPixmap(QtGui.QStyle.SP_DialogCloseButton)))
+ self.tagReset.setIconSize(QtCore.QSize(12,12))
+ self.tagReset.setAutoRaise(True)
+ self.tagReset.setEnabled(False)
+ editLayout.addWidget(self.tagReset)
+
+ gLayout.addLayout(editLayout, 0, 2, 1, 1)
+
+ userLabel = QtGui.QLabel('User:', self)
+ gLayout.addWidget(userLabel, 1, 0, 1, 1)
+
+ self.userEdit = QtGui.QLabel('', self)
+ gLayout.addWidget(self.userEdit, 1, 2, 1, 1)
+
+ dateLabel = QtGui.QLabel('Date:', self)
+ gLayout.addWidget(dateLabel, 2, 0, 1, 1)
+
+ self.dateEdit = QtGui.QLabel('', self)
+ gLayout.addWidget(self.dateEdit, 2, 2, 1, 1)
+
+ idLabel = QtGui.QLabel('ID:', self)
+ gLayout.addWidget(idLabel, 3, 0, 1, 1)
+
+ self.idEdit = QtGui.QLabel('', self)
+ gLayout.addWidget(self.idEdit, 3, 2, 1, 1)
+
+ self.notesLabel = QtGui.QLabel('Notes:')
+ gLayout.addWidget(self.notesLabel, 4, 0, 1, 1)
+
+ self.versionNotes = QVersionNotes()
+ vLayout.addWidget(self.versionNotes)
+ self.versionNotes.setEnabled(False)
+
+ self.versionThumbs = QVersionThumbs()
+ vLayout.addWidget(self.versionThumbs)
+
+ self.versionMashups = QVersionMashups()
+ vLayout.addWidget(self.versionMashups)
+
+ self.connect(self.tagEdit, QtCore.SIGNAL('editingFinished()'),
+ self.tagFinished)
+ self.connect(self.tagEdit, QtCore.SIGNAL('textChanged(QString)'),
+ self.tagChanged)
+ self.connect(self.tagReset, QtCore.SIGNAL('clicked()'),
+ self.tagCleared)
+
+ self.controller = None
+ self.versionNumber = -1
+
+ def updateController(self, controller):
+ """ updateController(controller: VistrailController) -> None
+ Assign the controller to the property page
+
+ """
+ self.controller = controller
+ self.versionNotes.controller = controller
+ self.versionThumbs.controller = controller
+ self.versionMashups.controller = controller
+ self.updateVersion(controller.current_version)
+
+ def updateVersion(self, versionNumber):
+ """ updateVersion(versionNumber: int) -> None
+ Update the property page of the version
+
+ """
+ self.versionNumber = versionNumber
+ self.versionNotes.updateVersion(versionNumber)
+ self.versionThumbs.updateVersion(versionNumber)
+ self.versionMashups.updateVersion(versionNumber)
+ if self.controller:
+ if self.controller.vistrail.actionMap.has_key(versionNumber):
+ action = self.controller.vistrail.actionMap[versionNumber]
+ name = self.controller.vistrail.getVersionName(versionNumber)
+ self.tagEdit.setText(name)
+ self.userEdit.setText(action.user)
+ self.dateEdit.setText(action.date)
+ self.idEdit.setText(unicode(action.id))
+ self.tagEdit.setEnabled(True)
+ return
+ else:
+ self.tagEdit.setEnabled(False)
+ self.tagReset.setEnabled(False)
+
+ self.tagEdit.setText('')
+ self.userEdit.setText('')
+ self.dateEdit.setText('')
+ self.idEdit.setText('')
+
+
+ def tagFinished(self):
+ """ tagFinished() -> None
+ Update the new tag to vistrail
+
+ """
+ if self.controller:
+ name = self.controller.vistrail.getVersionName(self.versionNumber)
+ currentText = str(self.tagEdit.text())
+ if name != currentText:
+ self.controller.update_current_tag(currentText)
+
+ def tagChanged(self, text):
+ """ tagChanged(text: QString) -> None
+ Update the button state if there is text
+
+ """
+ self.tagReset.setEnabled(text != '')
+
+ def tagCleared(self):
+ """ tagCleared() -> None
+ Remove the tag
+
+ """
+ self.tagEdit.setText('')
+ self.tagFinished()
+
+class QVersionNotes(QtGui.QTextEdit):
+ """
+ QVersionNotes is text widget that update/change a version notes
+
+ """
+ def __init__(self, parent=None):
+ """ QVersionNotes(parent: QWidget) -> QVersionNotes
+ Initialize control variables
+
+ """
+ QtGui.QTextEdit.__init__(self, parent)
+ self.controller = None
+ self.versionNumber = -1
+ self.update_on_focus_out = True
+ self.setAcceptRichText(False)
+ # Reset text to black, for some reason it is grey by default on the mac
+ self.palette().setBrush(QtGui.QPalette.Text,
+ QtGui.QBrush(QtGui.QColor(0,0,0,255)))
+
+
+ def updateVersion(self, versionNumber):
+ """ updateVersion(versionNumber: int) -> None
+ Update the text to be the notes of the vistrail versionNumber
+
+ """
+ self.versionNumber = versionNumber
+ if self.controller:
+ if self.controller.vistrail.actionMap.has_key(versionNumber):
+ action = self.controller.vistrail.actionMap[versionNumber]
+ notes = self.controller.vistrail.get_notes(versionNumber)
+ if notes:
+ self.setHtml(notes)
+ # work around a strange bug where an empty new paragraph gets added every time
+ self.trim_first_paragraph()
+ else:
+ self.setHtml('')
+ self.setEnabled(True)
+ return
+ else:
+ self.setEnabled(False)
+ self.setPlainText('')
+
+ def commit_changes(self):
+ if self.controller and self.document().isModified():
+ self.controller.update_notes(str(self.toHtml()))
+
+ def reset_changes(self):
+ """ reset_changes() -> None
+
+ """
+ self.updateVersion(self.versionNumber)
+
+ def focusOutEvent(self, event):
+ """ focusOutEvent(event: QFocusEvent) -> None
+ Update the version notes if the text has been modified
+
+ """
+ if self.update_on_focus_out:
+ self.commit_changes()
+ QtGui.QTextEdit.focusOutEvent(self,event)
+
+ def trim_first_paragraph(self):
+ doc = self.document()
+ count = doc.blockCount()
+ cursor = QtGui.QTextCursor(doc)
+ cursor.select(QtGui.QTextCursor.LineUnderCursor)
+ sel = cursor.selection().toPlainText()
+ if all(c == ' ' for c in sel):
+ cursor.removeSelectedText()
+ cursor = QtGui.QTextCursor(doc)
+ cursor.deleteChar()
+
+
+################################################################################
+class QVersionPropOverlay(QtGui.QFrame):
+ """
+ QVersionPropOverlay is a transparent widget that sits on top of the version
+ view. It displays properties of a version: tag, user, date, and notes.
+
+ """
+ propagatingEvent = set([
+ QtCore.QEvent.MouseButtonDblClick,
+ QtCore.QEvent.MouseButtonPress,
+ QtCore.QEvent.MouseButtonRelease,
+ QtCore.QEvent.MouseMove,
+ QtCore.QEvent.Wheel,
+ ])
+ def __init__(self, parent=None, mouseWidget=None):
+ """ QVersionPropOverlay(parent: QWidget) -> QVersionPropOverlay
+ Setup layout
+
+ """
+ QtGui.QFrame.__init__(self, parent)
+ self.propagatingWidget = mouseWidget
+ self.palette = QtGui.QPalette()
+ self.palette.setColor(QtGui.QPalette.Base, QtGui.QColor(0,0,0,0))
+ self.setPalette(self.palette)
+ self.setAutoFillBackground(True)
+ self.setFrameStyle(QtGui.QFrame.NoFrame)
+ self.setFrameShadow(QtGui.QFrame.Plain)
+ self.layout = QtGui.QGridLayout()
+ self.layout.setVerticalSpacing(1)
+
+ self.tag_label = QtGui.QLabel()
+ self.tag_label.palette().setBrush(QtGui.QPalette.Text,
+ CurrentTheme.VERSION_PROPERTIES_PEN)
+ self.tag_label.setFont(CurrentTheme.VERSION_PROPERTIES_FONT)
+ self.tag_label.setText("Tag:")
+
+ self.tag = QtGui.QLabel()
+ self.tag.setFont(CurrentTheme.VERSION_PROPERTIES_FONT)
+
+ self.description_label = QtGui.QLabel()
+ self.description_label.palette().setBrush(QtGui.QPalette.Text,
+ CurrentTheme.VERSION_PROPERTIES_PEN)
+ self.description_label.setFont(CurrentTheme.VERSION_PROPERTIES_FONT)
+ self.description_label.setText("Action:")
+
+ self.description = QtGui.QLabel()
+ self.description.setFont(CurrentTheme.VERSION_PROPERTIES_FONT)
+
+ self.user_label = QtGui.QLabel()
+ self.user_label.palette().setBrush(QtGui.QPalette.Text,
+ CurrentTheme.VERSION_PROPERTIES_PEN)
+ self.user_label.setFont(CurrentTheme.VERSION_PROPERTIES_FONT)
+ self.user_label.setText("User:")
+
+ self.user = QtGui.QLabel()
+ self.user.setFont(CurrentTheme.VERSION_PROPERTIES_FONT)
+
+ self.date_label = QtGui.QLabel()
+ self.date_label.palette().setBrush(QtGui.QPalette.Text,
+ CurrentTheme.VERSION_PROPERTIES_PEN)
+ self.date_label.setFont(CurrentTheme.VERSION_PROPERTIES_FONT)
+ self.date_label.setText("Date:")
+
+ self.date = QtGui.QLabel()
+ self.date.setFont(CurrentTheme.VERSION_PROPERTIES_FONT)
+
+ self.notes_label = QtGui.QLabel()
+ self.notes_label.palette().setBrush(QtGui.QPalette.Text,
+ CurrentTheme.VERSION_PROPERTIES_PEN)
+ self.notes_label.setFont(CurrentTheme.VERSION_PROPERTIES_FONT)
+ self.notes_label.setText("Notes:")
+
+ self.notes = QtGui.QLabel()
+ self.notes.setTextFormat(QtCore.Qt.PlainText)
+ self.notes.setFont(CurrentTheme.VERSION_PROPERTIES_FONT)
+
+ self.notes_button = QExpandButton()
+ self.notes_button.hide()
+
+ self.notes_layout = QtGui.QHBoxLayout()
+ self.notes_layout.addWidget(self.notes)
+ self.notes_layout.addWidget(self.notes_button)
+ self.notes_layout.addStretch()
+
+ self.layout.addWidget(self.tag_label, 0, 0)
+ self.layout.addWidget(self.tag, 0, 1)
+ self.layout.addWidget(self.description_label, 1, 0)
+ self.layout.addWidget(self.description, 1, 1)
+ self.layout.addWidget(self.user_label, 2, 0)
+ self.layout.addWidget(self.user, 2, 1)
+ self.layout.addWidget(self.date_label, 3, 0)
+ self.layout.addWidget(self.date, 3, 1)
+ self.layout.addWidget(self.notes_label, 4, 0)
+ self.layout.addLayout(self.notes_layout, 4, 1)
+
+ self.layout.setColumnMinimumWidth(0,35)
+ self.layout.setColumnMinimumWidth(1,200)
+ self.layout.setContentsMargins(2,2,2,2)
+ self.layout.setColumnStretch(1,1)
+ self.setLayout(self.layout)
+ self.updateGeometry()
+ self.controller = None
+
+ self.notes_dialog = QNotesDialog(self)
+ self.notes_dialog.hide()
+
+ QtCore.QObject.connect(self.notes_button,
+ QtCore.SIGNAL("pressed()"),
+ self.openNotes)
+
+ def updateGeometry(self):
+ """ updateGeometry() -> None
+ Keep in upper left of screen
+
+ """
+ parentGeometry = self.parent().geometry()
+ self.pos_x = 4
+ self.pos_y = 4
+ self.move(self.pos_x, self.pos_y)
+
+ def updateController(self, controller):
+ """ updateController(controller: VistrailController) -> None
+ Assign the controller to the properties
+
+ """
+ self.controller = controller
+ self.notes_dialog.updateController(controller)
+
+ def updateVersion(self, versionNumber):
+ """ updateVersion(versionNumber: int) -> None
+ Update the text items
+
+ """
+ self.notes_dialog.updateVersion(versionNumber)
+ if self.controller:
+ if self.controller.vistrail.actionMap.has_key(versionNumber):
+ action = self.controller.vistrail.actionMap[versionNumber]
+ name = self.controller.vistrail.getVersionName(versionNumber)
+ description = self.controller.vistrail.get_description(versionNumber)
+ self.tag.setText(self.truncate(name))
+ self.description.setText(self.truncate(description))
+ self.user.setText(self.truncate(action.user))
+ self.date.setText(self.truncate(action.date))
+ notes = self.controller.vistrail.get_notes(action.id)
+ if notes:
+ s = self.convertHtmlToText(notes)
+ self.notes.setText(self.truncate(s))
+ else:
+ self.notes.setText('')
+ self.notes_button.show()
+ else:
+ self.tag.setText('')
+ self.description.setText('')
+ self.user.setText('')
+ self.date.setText('')
+ self.notes.setText('')
+ self.notes_button.hide()
+
+ def convertHtmlToText(self, str):
+ """ convertHtmlToText(str: QString) -> QString
+ Remove HTML tags and newlines
+
+ """
+ # Some text we want to ignore lives outside brackets in the header
+ str = re.sub(r"<head>.*</head>", r"", str)
+ # Remove all other tags
+ str = re.sub(r"<[^>]*>", r"", str)
+ # Remove newlines
+ str = re.sub(r"\n", r"", str)
+ return str
+
+ def truncate(self, str):
+ """ truncate(str: string) -> string
+ Shorten string to fit in smaller space
+
+ """
+ if len(str) > 24:
+ str = str[:22] + "..."
+ return str
+
+ def openNotes(self):
+ """ openNotes() -> None
+
+ Show notes dialog
+ """
+ self.notes_dialog.show()
+ self.notes_dialog.activateWindow()
+
+ def event(self, e):
+ """ Propagate all mouse events to the right widget """
+ if e.type() in self.propagatingEvent:
+ if self.propagatingWidget!=None:
+ QtCore.QCoreApplication.sendEvent(self.propagatingWidget, e)
+ return False
+ return QtGui.QFrame.event(self, e)
+
+################################################################################
+class QExpandButton(QtGui.QLabel):
+ """
+ A transparent button type with a + draw in
+ """
+ def __init__(self, parent=None):
+ """
+ QExpandButton(parent: QWidget) -> QExpandButton
+ """
+ QtGui.QLabel.__init__(self, parent)
+
+ self.drawButton(0)
+ self.setToolTip('Edit Notes')
+ self.setScaledContents(False)
+ self.setFrameShape(QtGui.QFrame.NoFrame)
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+
+ """
+ return QtCore.QSize(10,10)
+
+
+ def mousePressEvent(self, e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Capture mouse press event on the frame to move the widget
+
+ """
+ if e.buttons() & QtCore.Qt.LeftButton:
+ self.drawButton(1)
+
+ def mouseReleaseEvent(self, e):
+ self.drawButton(0)
+ self.emit(QtCore.SIGNAL('pressed()'))
+
+ def drawButton(self, down):
+ """ drawButton(down: bool) -> None
+ Custom draw function
+
+ """
+ self.picture = QtGui.QPicture()
+ painter = QtGui.QPainter()
+ painter.begin(self.picture)
+ painter.setRenderHints(QtGui.QPainter.Antialiasing, False)
+ pen = QtGui.QPen(QtCore.Qt.SolidLine)
+ pen.setWidth(1)
+ pen.setCapStyle(QtCore.Qt.RoundCap)
+ brush = QtGui.QBrush(QtCore.Qt.NoBrush)
+ if (down):
+ pen.setColor(QtGui.QColor(150,150,150,150))
+ else:
+ pen.setColor(QtGui.QColor(0,0,0,255))
+
+ painter.setPen(pen)
+ painter.setBrush(brush)
+ painter.drawRect(0,0,8,8)
+ painter.drawLine(QtCore.QLine(4,2,4,6))
+ painter.drawLine(QtCore.QLine(2,4,6,4))
+ painter.end()
+ self.setPicture(self.picture)
+
+################################################################################
+class QNotesDialog(QtGui.QDialog):
+ """
+ A small non-modal dialog with text entry to modify and view notes
+
+ """
+ def __init__(self, parent=None):
+ """
+ QNotesDialog(parent: QWidget) -> QNotesDialog
+
+ """
+ QtGui.QDialog.__init__(self, parent)
+ self.setModal(False)
+ self.notes = QVersionNotes(self)
+ self.notes.update_on_focus_out = False
+ layout = QtGui.QVBoxLayout(self)
+ layout.addWidget(self.notes)
+ layout.setMargin(0)
+
+ self.apply_button = QtGui.QPushButton('Apply', self)
+ self.apply_button.setDefault(False)
+ self.apply_button.setAutoDefault(False)
+ self.ok_button = QtGui.QPushButton('Ok', self)
+ self.ok_button.setDefault(False)
+ self.ok_button.setAutoDefault(False)
+ self.cancel_button = QtGui.QPushButton('Cancel', self)
+ self.cancel_button.setDefault(False)
+ self.cancel_button.setAutoDefault(False)
+ self.buttonLayout = QtGui.QHBoxLayout()
+ layout.addLayout(self.buttonLayout)
+ self.buttonLayout.addWidget(self.apply_button)
+ self.buttonLayout.addWidget(self.ok_button)
+ self.buttonLayout.addWidget(self.cancel_button)
+
+ self.setLayout(layout)
+ self.controller = None
+
+ QtCore.QObject.connect(self.apply_button,
+ QtCore.SIGNAL("released()"),
+ self.apply_pressed)
+
+ QtCore.QObject.connect(self.ok_button,
+ QtCore.SIGNAL("released()"),
+ self.ok_pressed)
+
+ QtCore.QObject.connect(self.cancel_button,
+ QtCore.SIGNAL("released()"),
+ self.cancel_pressed)
+ def apply_pressed(self):
+ """ apply_pressed() -> None
+
+ """
+ self.notes.commit_changes()
+
+ def ok_pressed(self):
+ """ ok_pressed() -> None
+
+ """
+ self.notes.commit_changes()
+ self.close()
+
+ def cancel_pressed(self):
+ """ cancel_pressed() -> None
+
+ """
+ self.notes.reset_changes()
+ self.close()
+
+ def updateController(self, controller):
+ """ updateController(controller: VistrailController) -> None
+
+ """
+ self.controller = controller
+ self.notes.controller = controller
+
+ def updateVersion(self, versionNumber):
+ """ updateVersion(versionNumber: int) -> None
+
+ """
+ self.notes.updateVersion(versionNumber)
+ if self.controller:
+ if self.controller.vistrail.actionMap.has_key(versionNumber):
+ name = self.controller.vistrail.getVersionName(versionNumber)
+ title = "Notes: "+name
+ self.setWindowTitle(title)
+ else:
+ self.setWindowTitle("Notes")
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+
+ """
+ return QtCore.QSize(250,200)
+
+################################################################################
+
+class QVersionThumbs(QtGui.QWidget):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.versionNumber = None
+ label = QtGui.QLabel("Preview:")
+ self.thumbs = QtGui.QLabel()
+ self.thumbs.setFrameShape(QtGui.QFrame.NoFrame)
+ self.scrollArea = QtGui.QScrollArea(self)
+ self.scrollArea.setFrameStyle(QtGui.QFrame.NoFrame)
+ self.scrollArea.setWidget(self.thumbs)
+ self.scrollArea.setWidgetResizable(True)
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(2)
+ layout.addWidget(label)
+ layout.addWidget(self.scrollArea)
+ self.setLayout(layout)
+ self.controller = None
+
+ def updateController(self, controller):
+ """ updateController(controller: VistrailController) -> None
+
+ """
+ self.controller = controller
+
+ def updateVersion(self, versionNumber):
+ """ updateVersion(versionNumber: int) -> None
+
+ """
+ if self.controller:
+ vistrail = self.controller.vistrail
+ if versionNumber in vistrail.actionMap.keys():
+ action = vistrail.actionMap[versionNumber]
+ if action and vistrail.has_thumbnail(action.id):
+ cache = ThumbnailCache.getInstance()
+ fname = cache.get_abs_name_entry(
+ vistrail.get_thumbnail(action.id))
+ if fname is not None:
+ pixmap = QtGui.QPixmap(fname)
+ self.thumbs.setPixmap(pixmap)
+ self.thumbs.adjustSize()
+ self.thumbs.setFrameShape(QtGui.QFrame.StyledPanel)
+ return
+
+ self.thumbs.setPixmap(QtGui.QPixmap())
+ self.thumbs.setFrameShape(QtGui.QFrame.NoFrame)
+
+################################################################################
+class QVersionMashups(QtGui.QWidget):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.versionNumber = None
+ self.controller = None
+ #label = QtGui.QLabel("Mashups:")
+ self.mashupsButton = QtGui.QToolButton()
+ self.mashupsButton.setText("Mashups")
+ self.mashupsButton.setPopupMode(QtGui.QToolButton.InstantPopup)
+ self.mashupsButton.setArrowType(QtCore.Qt.RightArrow)
+ self.mashupsButton.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
+
+# font = QtGui.QFont("Arial", 11, QtGui.QFont.Normal)
+# font.setItalic(True)
+# self.group = QtGui.QGroupBox()
+# helplabel = QtGui.QLabel("Double-click a mashup to execute it")
+# helplabel.setFont(font)
+# self.mashupsList = QtGui.QListWidget()
+# self.mashupsList.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
+# self.mashupsList.itemDoubleClicked.connect(self.mashupDoubleClicked)
+# glayout = QtGui.QVBoxLayout()
+# glayout.setMargin(2)
+# glayout.setSpacing(5)
+# #layout.addWidget(label)
+# glayout.addWidget(self.mashupsList)
+# glayout.addWidget(helplabel)
+# self.group.setLayout(glayout)
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(2)
+ layout.setSpacing(5)
+ #layout.addStretch()
+ layout.addWidget(self.mashupsButton)
+ #layout.addWidget(self.group)
+ self.setLayout(layout)
+ self.apps = {}
+ #self.group.setVisible(False)
+ #self.connect(self.mashupsButton, QtCore.SIGNAL("clicked(bool)"),
+ # self.showList)
+
+ def createMashupsMenu(self, tagMap):
+ tags = tagMap.keys()
+ self.mashupsButton.setText("Mashups (%s)"%str(len(tags)))
+ #latestversion = mtrail.getLatestVersion()
+ mashupsMenu = QtGui.QMenu(self)
+ if len(tags) > 0:
+ tags.sort()
+ for tag in tags:
+ action = QtGui.QAction(str(tag), self,
+ triggered=self.mashupSelected)
+ action.setData(tagMap[tag])
+ mashupsMenu.addAction(action)
+ self.mashupsButton.setEnabled(True)
+ return mashupsMenu
+
+# def showList(self, on):
+# self.group.setVisible(on)
+
+ def updateController(self, controller):
+ """ updateController(controller: VistrailController) -> None
+
+ """
+ self.controller = controller
+
+ def updateVersion(self, versionNumber):
+ """ updateVersion(versionNumber: int) -> None
+
+ """
+ #self.mashupsList.clear()
+
+ from vistrails.gui.mashups.mashups_manager import MashupsManager
+ from vistrails.gui.mashups.mashups_inspector import QMashupListPanelItem
+ getMshptrail = MashupsManager.getMashuptrailforVersionInVistrailController
+ if self.controller:
+ vistrail = self.controller.vistrail
+ if versionNumber in vistrail.actionMap.keys():
+ self.mtrail = getMshptrail(self.controller, versionNumber)
+ if self.mtrail:
+ tagMap = self.mtrail.getTagMap()
+ self.mashupsButton.setMenu(self.createMashupsMenu(tagMap))
+# tags = tagMap.keys()
+# self.mashupsButton.setText("Mashups (%s)"%str(len(tags)))
+# #latestversion = mtrail.getLatestVersion()
+# if len(tags) > 0:
+# tags.sort()
+# for tag in tags:
+# item = QMashupListPanelItem(str(tag),
+# tagMap[tag],
+# self.mashupsList)
+# self.mashupsButton.setEnabled(True)
+# else:
+# self.mashupsButton.setEnabled(False)
+ else:
+ self.mashupsButton.setText("Mashups (0)")
+ self.mashupsButton.setEnabled(False)
+ else:
+ self.mashupsButton.setText("Mashups (0)")
+ self.mashupsButton.setEnabled(False)
+ else:
+ self.mashupsButton.setText("Mashups (0)")
+ self.mashupsButton.setEnabled(False)
+
+ def mashupSelected(self):
+ action = self.sender()
+ version, ok = action.data()
+ self.openMashup(version)
+
+ def openMashup(self, version):
+ from vistrails.gui.mashups.mashups_manager import MashupsManager
+ item_key = (self.mtrail.id, version)
+ if self.apps.has_key(item_key):
+ app = self.apps[item_key]
+ if app:
+ app.activateWindow()
+ return
+
+ app = MashupsManager.createMashupApp(self.controller, self.mtrail,
+ version)
+ app.setAttribute(QtCore.Qt.WA_DeleteOnClose)
+ app.appWasClosed.connect(self.appWasClosed)
+ self.apps[item_key] = app
+ app.activateWindow()
+ app.raise_()
+
+ def appWasClosed(self, app):
+ for (k, a) in self.apps.iteritems():
+ if a == app:
+ self.apps[k] = None
diff --git a/vistrails/gui/version_view.py b/vistrails/gui/version_view.py
new file mode 100644
index 0000000..90784f5
--- /dev/null
+++ b/vistrails/gui/version_view.py
@@ -0,0 +1,1299 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This is a QGraphicsView for pipeline view, it also holds different
+types of graphics items that are only available in the pipeline
+view. It only handles GUI-related actions, the rest of the
+functionalities are implemented at somewhere else,
+e.g. core.vistrails
+
+QGraphicsLinkItem
+QGraphicsVersionTextItem
+QGraphicsVersionItem
+QVersionTreeScene
+QVersionTreeView
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core.system import systemType
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.gui.base_view import BaseView
+from vistrails.gui.graphics_view import (QInteractiveGraphicsScene,
+ QInteractiveGraphicsView,
+ QGraphicsItemInterface,
+ QGraphicsRubberBandItem)
+from vistrails.gui.qt import qt_super
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.version_prop import QVersionPropOverlay
+from vistrails.gui.vis_diff import QVisualDiff
+from vistrails.gui.collection.workspace import QParamExplorationEntityItem
+import vistrails.gui.utils
+import math
+
+
+################################################################################
+# QGraphicsLinkItem
+
+class QGraphicsLinkItem(QGraphicsItemInterface, QtGui.QGraphicsPolygonItem):
+ """
+ QGraphicsLinkItem is a connection shape connecting two versions
+
+ """
+ def __init__(self, parent=None, scene=None):
+ """ QGraphicsLinkItem(parent: QGraphicsItem,
+ scene: QGraphicsScene) -> QGraphicsLinkItem
+ Create the shape, initialize its pen and brush accordingly
+
+ """
+ QtGui.QGraphicsPolygonItem.__init__(self, parent, scene)
+ self.setFlags(QtGui.QGraphicsItem.ItemIsSelectable)
+ self.setZValue(0)
+ self.linkPen = CurrentTheme.LINK_PEN
+ self.ghosted = False
+
+ # cache link endpoints to improve performance on scene updates
+ self.c1 = None
+ self.c2 = None
+ self.expand = None
+ self.collapse = None
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+
+ """
+ qt_super(QGraphicsLinkItem, self).mousePressEvent(event)
+ self.setSelected(True)
+
+ def mouseReleaseEvent(self, event):
+ """ mouseReleaseEvent(event: QMouseEvent) -> None
+
+ """
+ qt_super(QGraphicsLinkItem, self).mouseReleaseEvent(event)
+ if self.expand:
+ self.scene().controller.expand_versions(self.startVersion, self.endVersion)
+ elif self.collapse:
+ self.scene().controller.collapse_versions(self.endVersion)
+ self.setSelected(False)
+
+ def setGhosted(self, ghosted):
+ """ setGhosted(ghosted: True) -> None
+ Set this link to be ghosted or not
+
+ """
+ if self.ghosted <> ghosted:
+ self.ghosted = ghosted
+ if ghosted:
+ self.linkPen = CurrentTheme.GHOSTED_LINK_PEN
+ else:
+ self.linkPen = CurrentTheme.LINK_PEN
+
+ def setupLink(self, v1, v2, expand=False, collapse=False):
+ """ setupLink(v1, v2: QGraphicsVersionItem, compact: bool) -> None
+ Setup a line connecting v1 and v2 items
+
+ """
+ self.startVersion = min(v1.id, v2.id)
+ self.endVersion = max(v1.id, v2.id)
+
+ c1 = v1.sceneBoundingRect().center()
+ c2 = v2.sceneBoundingRect().center()
+
+ # check if it is the same geometry
+ # improves performance on updates
+ if self.c1 != None and self.c2 != None and \
+ self.expand != None and self.collapse !=None:
+ isTheSame = self.c1 == c1 and \
+ self.c2 == c2 and \
+ self.expand == expand and \
+ self.collapse == collapse
+ if isTheSame:
+ return
+
+ # update current state
+ self.c1 = c1
+ self.c2 = c2
+ self.collapse = collapse
+ self.expand = expand
+
+ # Compute the line of the link and its normal line throught
+ # the midpoint
+ mainLine = QtCore.QLineF(c1, c2)
+ normalLine = mainLine.normalVector()
+ normalLine.setLength(CurrentTheme.LINK_SEGMENT_LENGTH)
+ dis = (mainLine.pointAt(0.5)-mainLine.p1()+
+ normalLine.p1()-normalLine.pointAt(0.5))
+ normalLine.translate(dis.x(), dis.y())
+
+ # Generate 2 segments along the main line and 3 segments along
+ # the normal line
+ if not self.collapse and not self.expand:
+ self.lines = [mainLine]
+ poly = QtGui.QPolygonF()
+ poly.append(self.lines[0].p1())
+ poly.append(self.lines[0].p2())
+ poly.append(self.lines[0].p1())
+ self.setPolygon(poly)
+ else:
+ self.lines = []
+
+ normalLine = mainLine.normalVector()
+ normalLine.setLength(CurrentTheme.LINK_SEGMENT_SQUARE_LENGTH)
+ dis = (mainLine.pointAt(0.5)-mainLine.p1()+
+ normalLine.p1()-normalLine.pointAt(0.5))
+ normalLine.translate(dis.x(), dis.y())
+
+ gapLine = QtCore.QLineF(mainLine)
+ gapLine.setLength(CurrentTheme.LINK_SEGMENT_SQUARE_LENGTH/2)
+ gapVector = gapLine.p2()-gapLine.p1()
+
+ # First segment along the main line
+ line = QtCore.QLineF(mainLine)
+ line.setLength(line.length()/2-CurrentTheme.LINK_SEGMENT_SQUARE_LENGTH/2)
+ self.lines.append(QtCore.QLineF(line))
+
+ # Second segment along the main line
+ line.translate(line.p2()-line.p1()+gapVector*2)
+ self.lines.append(QtCore.QLineF(line))
+
+ # First normal segment in front
+ line_t = QtCore.QLineF(normalLine)
+ line_t.translate(gapVector*(-1.0))
+ self.lines.append(QtCore.QLineF(line_t))
+
+ # Second normal segment in back
+ line_b = QtCore.QLineF(normalLine)
+ line_b.translate(gapVector)
+ self.lines.append(QtCore.QLineF(line_b))
+
+ # Left box
+ line = QtCore.QLineF(line_t.p1(),line_b.p1())
+ self.lines.append(QtCore.QLineF(line))
+
+ # Right box
+ line = QtCore.QLineF(line_t.p2(),line_b.p2())
+ self.lines.append(QtCore.QLineF(line))
+
+ # Horizontal plus
+ line_h = QtCore.QLineF(normalLine.pointAt(0.2),normalLine.pointAt(0.8))
+ self.lines.append(QtCore.QLineF(line_h))
+
+ if self.expand:
+ # Vertical plus
+ line = QtCore.QLineF(mainLine)
+ line.translate((line.p2()-line.p1())/2-gapVector)
+ line.setLength(CurrentTheme.LINK_SEGMENT_SQUARE_LENGTH)
+ line_v = QtCore.QLineF(line.pointAt(0.2), line.pointAt(0.8))
+ self.lines.append(QtCore.QLineF(line_v))
+
+ # Create the poly line for selection and redraw
+ poly = QtGui.QPolygonF()
+ poly.append(self.lines[0].p1())
+ poly.append(self.lines[2].p1())
+ poly.append(self.lines[3].p1())
+ poly.append(self.lines[1].p2())
+ poly.append(self.lines[3].p2())
+ poly.append(self.lines[2].p2())
+ poly.append(self.lines[0].p1())
+ self.setPolygon(poly)
+
+ self.setGhosted(v1.ghosted and v2.ghosted)
+
+ def paint(self, painter, option, widget=None):
+ """ paint(painter: QPainter, option: QStyleOptionGraphicsItem,
+ widget: QWidget) -> None
+ Peform actual painting of the link
+
+ """
+ if self.isSelected():
+ painter.setPen(CurrentTheme.LINK_SELECTED_PEN)
+ else:
+ painter.setPen(self.linkPen)
+ for line in self.lines:
+ painter.drawLine(line)
+
+ def itemChange(self, change, value):
+ """ itemChange(change: GraphicsItemChange, value: variant) -> variant
+ Do not allow link to be selected with version shape
+
+ """
+ if change==QtGui.QGraphicsItem.ItemSelectedChange and value:
+ return False
+ return QtGui.QGraphicsPolygonItem.itemChange(self, change, value)
+
+
+##############################################################################
+# QGraphicsVerstionTextItem
+
+class QGraphicsVersionTextItem(QGraphicsItemInterface, QtGui.QGraphicsTextItem):
+ """
+ QGraphicsVersionTextItem is an editable text item that appears on top of
+ a QGraphicsVersionItem to allow the tag to be changed
+
+ """
+ def __init__(self, parent=None, scene=None):
+ """ QGraphicsVersionTextItem(parent: QGraphicsVersionItem,
+ scene: QGraphicsScene) -> QGraphicsVersionTextItem
+
+ Create the shape, intialize its drawing style
+
+ """
+ QtGui.QGraphicsTextItem.__init__(self, parent, scene)
+ self.timer = None
+ self.isEditable = None
+ self.setEditable(False)
+ self.setFont(CurrentTheme.VERSION_FONT)
+ self.setTextWidth(CurrentTheme.VERSION_LABEL_MARGIN[0])
+ self.setDefaultTextColor(CurrentTheme.VERSION_LABEL_COLOR)
+ self.centerX = 0.0
+ self.centerY = 0.0
+ self.label = ''
+ self.isTag = True
+ self.updatingTag = False
+
+ def setEditable(self, editable=True):
+ if self.timer:
+ self.timer.stop()
+ self.timer = None
+ if editable == self.isEditable:
+ return
+ self.isEditable = editable
+ if editable:
+ self.setTextInteractionFlags(QtCore.Qt.TextEditorInteraction)
+ else:
+ if self.textCursor():
+ c = self.textCursor()
+ c.clearSelection()
+ self.setTextCursor(c)
+ self.setTextInteractionFlags(QtCore.Qt.NoTextInteraction)
+
+ def setEditableLater(self):
+ self.timer = QtCore.QTimer(self)
+ self.timer.setSingleShot(True)
+ self.connect(self.timer, QtCore.SIGNAL("timeout()"), self.setEditable)
+ self.timer.start(QtGui.QApplication.doubleClickInterval() + 5)
+
+ def setGhosted(self, ghosted):
+ if ghosted:
+ self.setDefaultTextColor(CurrentTheme.GHOSTED_VERSION_LABEL_COLOR)
+ else:
+ self.setDefaultTextColor(CurrentTheme.VERSION_LABEL_COLOR)
+
+ def changed(self, x, y, label, tag=True):
+ """ changed(x: float, y: float, label: str) -> None
+ Change the position and text label from outside the editor
+
+ """
+ if self.centerX <> x or self.centerY <> y or self.label <> label:
+ self.centerX = x
+ self.centerY = y
+ self.label = label
+ self.isTag = tag
+ if self.isTag:
+ self.setFont(CurrentTheme.VERSION_FONT)
+ else:
+ self.setFont(CurrentTheme.VERSION_DESCRIPTION_FONT)
+ self.reset()
+
+ def reset(self):
+ """ reset() -> None
+ Resets the text label, width, and positions to the stored values
+
+ """
+ self.setPlainText(self.label)
+ self.setEditable(False)
+ if (len(str(self.label)) > 0):
+ self.setTextWidth(-1)
+ else:
+ self.setTextWidth(CurrentTheme.VERSION_LABEL_MARGIN[0])
+
+ if self.isTag:
+ self.setFont(CurrentTheme.VERSION_FONT)
+ else:
+ self.setFont(CurrentTheme.VERSION_DESCRIPTION_FONT)
+ self.updatePos()
+ self.parentItem().updateWidthFromLabel()
+
+ def updatePos(self):
+ """ updatePos() -> None
+ Center the text, by default it uses the upper left corner
+
+ """
+ self.setPos(self.centerX-self.boundingRect().width()/2.0,
+ self.centerY-self.boundingRect().height()/2.0)
+
+ def keyPressEvent(self, event):
+ """ keyPressEvent(event: QEvent) -> None
+ Enter and Return keys signal a change in the label. Other keys
+ update the position and size of the parent ellipse during key entry.
+
+ """
+ if event.key() in [QtCore.Qt.Key_Enter, QtCore.Qt.Key_Return]:
+ self.updatingTag = True
+ if (self.label == str(self.toPlainText()) or
+ not self.scene().controller.update_current_tag(str(self.toPlainText()))):
+ self.reset()
+ self.updatingTag = False
+ event.ignore()
+ self.clearFocus()
+ return
+ qt_super(QGraphicsVersionTextItem, self).keyPressEvent(event)
+ if (len(str(self.toPlainText())) > 0):
+ self.setTextWidth(-1)
+ self.updatePos()
+ self.parentItem().updateWidthFromLabel()
+
+ def focusOutEvent(self, event):
+ """ focusOutEvent(event: QEvent) -> None
+ Update the tag if the text has changed
+
+ """
+ qt_super(QGraphicsVersionTextItem, self).focusOutEvent(event)
+ if not self.updatingTag and self.label != self.toPlainText():
+ self.updatingTag = True
+ if (self.label == str(self.toPlainText()) or
+ not self.scene().controller.update_current_tag(str(self.toPlainText()))):
+ self.reset()
+ self.updatingTag = False
+
+##############################################################################
+# QGraphicsVersionItem
+
+
+class QGraphicsVersionItem(QGraphicsItemInterface, QtGui.QGraphicsEllipseItem):
+ """
+ QGraphicsVersionItem is the version shape holding version id and
+ label
+
+ """
+ def __init__(self, parent=None, scene=None):
+ """ QGraphicsVersionItem(parent: QGraphicsItem, scene: QGraphicsScene)
+ -> QGraphicsVersionItem
+ Create the shape, initialize its pen and brush accordingly
+
+ """
+ QtGui.QGraphicsEllipseItem.__init__(self, parent, scene)
+ self.setZValue(1)
+ self.setAcceptDrops(True)
+ self.setFlags(QtGui.QGraphicsItem.ItemIsSelectable)
+ self._versionPenNormal = CurrentTheme.VERSION_PEN
+ self._versionPen = CurrentTheme.VERSION_PEN
+ self._versionBrush = CurrentTheme.VERSION_USER_BRUSH
+ self.id = -1
+ self.label = ''
+ self.descriptionLabel = ''
+ self.dragging = False
+ self.ghosted = False
+ self.updatePainterState()
+
+ # self.rank is a positive number that determines the
+ # saturation of the node. Two version nodes might have the
+ # same rank if they were created by different users
+ # self.max_rank is the maximum rank for that version class
+ self.rank = -1
+ self.max_rank = -1
+
+ # Editable text item that remains hidden unless the version is selected
+ self.text = QGraphicsVersionTextItem(self)
+
+ # Need a timer to start a drag to avoid stalls on QGraphicsView
+ self.dragTimer = QtCore.QTimer()
+ self.dragTimer.setSingleShot(True)
+ self.dragTimer.connect(self.dragTimer,
+ QtCore.SIGNAL('timeout()'),
+ self.startDrag)
+
+ self.dragPos = QtCore.QPoint()
+
+ def _get_versionPen(self):
+ return self._versionPen
+ def _set_versionPen(self, pen):
+ self._versionPen = pen
+ self.updatePainterState()
+ versionPen = property(_get_versionPen, _set_versionPen)
+
+ def _get_versionBrush(self):
+ return self._versionBrush
+ def _set_versionBrush(self, brush):
+ self._versionBrush = brush
+ self.updatePainterState()
+ versionBrush = property(_get_versionBrush, _set_versionBrush)
+
+ def itemChange(self, change, value):
+ if change == QtGui.QGraphicsItem.ItemSelectedHasChanged:
+ if self.isSelected():
+ self.versionPen = CurrentTheme.VERSION_SELECTED_PEN
+ self.text.setEditableLater()
+ else:
+ self.versionPen = self._versionPenNormal
+ self.text.setEditable(False)
+ self.updatePainterState()
+ return QtGui.QGraphicsItem.itemChange(self, change, value)
+
+ def setGhosted(self, ghosted=True):
+ """ setGhosted(ghosted: True) -> None
+ Set this version to be ghosted or not
+
+ """
+ if self.ghosted <> ghosted:
+ self.ghosted = ghosted
+ self.text.setGhosted(ghosted)
+ if ghosted:
+ self._versionPenNormal = CurrentTheme.GHOSTED_VERSION_PEN
+ self._versionBrush = CurrentTheme.GHOSTED_VERSION_USER_BRUSH
+ else:
+ self._versionPenNormal = CurrentTheme.VERSION_PEN
+ self._versionBrush = CurrentTheme.VERSION_USER_BRUSH
+ if not self.isSelected():
+ self._versionPen = self._versionPenNormal
+ self.updatePainterState()
+
+ def update_color(self, isThisUs, new_rank, new_max_rank, new_ghosted):
+ """ update_color(isThisUs: bool,
+ new_rank, new_max_rank: int) -> None
+
+ If necessary, update the colors of this version node based on
+ who owns the node and new ranks
+
+ NOTE: if username changes during execution, this might break.
+ """
+ if (new_rank == self.rank and new_max_rank == self.max_rank and
+ new_ghosted == self.ghosted):
+ # nothing changed
+ return
+ self.setGhosted(new_ghosted)
+ self.rank = new_rank
+ self.max_rank = new_max_rank
+ if not self.ghosted:
+ if isThisUs:
+ brush = CurrentTheme.VERSION_USER_BRUSH
+ else:
+ brush = CurrentTheme.VERSION_OTHER_BRUSH
+ sat = float(new_rank+1) / new_max_rank
+ (h, s, v, a) = brush.color().getHsvF()
+ newHsv = (h, s*sat, v+(1.0-v)*(1-sat), a)
+ self.versionBrush = QtGui.QBrush(QtGui.QColor.fromHsvF(*newHsv))
+
+ def setSaturation(self, isThisUser, sat):
+ """ setSaturation(isThisUser: bool, sat: float) -> None
+ Set the color of this version depending on whose is the user
+ and its saturation
+
+ """
+ if not self.ghosted:
+ if isThisUser:
+ brush = CurrentTheme.VERSION_USER_BRUSH
+ else:
+ brush = CurrentTheme.VERSION_OTHER_BRUSH
+
+ (h, s, v, a) = brush.color().getHsvF()
+ newHsv = (h, s*sat, v+(1.0-v)*(1-sat), a)
+ self.versionBrush = QtGui.QBrush(QtGui.QColor.fromHsvF(*newHsv))
+
+ def updateWidthFromLabel(self):
+ """ updateWidthFromLabel() -> None
+ Change the width of the ellipse based on a temporary change in the label
+
+ """
+ prevWidth = self.rect().width()
+ width = self.text.boundingRect().width() + \
+ CurrentTheme.VERSION_LABEL_MARGIN[0] - 4
+ r = self.rect()
+ r.setX(r.x()+(prevWidth-width)/2.0)
+ r.setWidth(width)
+ self.setRect(r)
+ self.update()
+
+ def setupVersion(self, node, action, tag, description):
+ """ setupPort(node: DotNode,
+ action: DBAction,
+ tag: str,
+ description: str) -> None
+ Update the version dimensions and id
+
+ """
+ # Lauro:
+ # what was this hacking??? the coordinates inside
+ # the input "node" should come to this point ready. This is
+ # not the point to do layout calculations (e.g. -node.p.y/2)
+
+ # Carlos:
+ # This is not layout as much as dealing with the way Qt
+ # specifies rectangles. Besides, moving this back here reduces
+ # code duplication, and allows customized behavior for
+ # subclasses.
+
+ rect = QtCore.QRectF(node.p.x-node.width/2.0,
+ node.p.y-node.height/2.0,
+ node.width,
+ node.height)
+ validLabel = True
+ if tag is None:
+ label = ''
+ validLabel=False
+ else:
+ label = tag
+
+ self.id = node.id
+ self.label = label
+ if description is None:
+ self.descriptionLabel = ''
+ else:
+ self.descriptionLabel = description
+ if validLabel:
+ textToDraw=self.label
+ else:
+ textToDraw=self.descriptionLabel
+
+ if (ThumbnailCache.getInstance().conf.mouseHover and
+ action and action.thumbnail is not None):
+ fname = ThumbnailCache.getInstance().get_abs_name_entry(action.thumbnail)
+ self.setToolTip('<img src="%s" height="128" border="1"/>'%fname)
+ else:
+ self.setToolTip('')
+ self.text.changed(node.p.x, node.p.y, textToDraw, validLabel)
+ self.setRect(rect)
+
+ def boundingRect(self):
+ """ boundingRect() -> QRectF
+ Add a padded space to avoid un-updated area
+ """
+ return self.rect().adjusted(-2, -2, 2, 2)
+
+ def paint(self, painter, option, widget=None):
+ option.state &= ~QtGui.QStyle.State_Selected
+ QtGui.QGraphicsEllipseItem.paint(self, painter, option, widget)
+
+ def updatePainterState(self):
+ self.setPen(self._versionPen)
+ self.setBrush(self._versionBrush)
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+ Start dragging a version to someplaces...
+
+ """
+ if event.button()==QtCore.Qt.LeftButton:
+ self.dragging = True
+ self.dragPos = QtCore.QPoint(event.screenPos())
+ return QtGui.QGraphicsEllipseItem.mousePressEvent(self, event)
+
+ def mouseMoveEvent(self, event):
+ """ mouseMoveEvent(event: QMouseEvent) -> None
+ Now set the timer preparing for dragging. Must use a timer in
+ junction with QDrag in order to avoid problem updates stall of
+ QGraphicsView, especially on Linux
+
+ """
+ if (self.dragging and
+ (event.screenPos()-self.dragPos).manhattanLength()>2):
+ self.dragging = False
+ #the timer has undesirable effects on Windows
+ if systemType not in ['Windows', 'Microsoft']:
+ self.dragTimer.start(1)
+ else:
+ self.startDrag()
+ QtGui.QGraphicsEllipseItem.mouseMoveEvent(self, event)
+ # super(QGraphicsVersionItem, self).mouseMoveEvent(event)
+
+ def startDrag(self):
+ """ startDrag() -> None
+ Start the drag of QDrag
+
+ """
+ data = QtCore.QMimeData()
+ data.versionId = self.id
+ data.controller = self.scene().controller
+ drag = QtGui.QDrag(self.scene().views()[0])
+ drag.setMimeData(data)
+ drag.setPixmap(CurrentTheme.VERSION_DRAG_PIXMAP)
+ drag.start()
+
+ def mouseReleaseEvent(self, event):
+ """ mouseReleaseEvent(event: QMouseEvent) -> None
+ Cancel the drag
+
+ """
+ self.dragging = False
+ QtGui.QGraphicsEllipseItem.mouseReleaseEvent(self, event)
+
+ def dragEnterEvent(self, event):
+ """ dragEnterEvent(event: QDragEnterEvent) -> None
+ Capture version-to-version drag-and-drop
+ Also capture parameter exploration assignment
+ """
+ data = event.mimeData()
+ if (hasattr(data, 'versionId') and
+ hasattr(data, 'controller') and
+ data.versionId!=self.id) or \
+ (hasattr(data, 'items') and
+ len(data.items) == 1 and
+ isinstance(data.items[0], QParamExplorationEntityItem)):
+ event.accept()
+ else:
+ event.ignore()
+
+ def dropEvent(self, event):
+ data = event.mimeData()
+ if (hasattr(data, 'versionId') and hasattr(data, 'controller') and
+ data.controller==self.scene().controller):
+ event.accept()
+ self.scene().emit(QtCore.SIGNAL('diffRequested(int,int)'),
+ data.versionId, self.id)
+ # visDiff = QVisualDiff(self.scene().controller.vistrail,
+ # data.versionId,
+ # self.id,
+ # self.scene().controller,
+ # self.scene().views()[0])
+ # visDiff.show()
+ elif (hasattr(data, 'items') and
+ len(data.items) == 1 and
+ isinstance(data.items[0], QParamExplorationEntityItem)):
+ # apply this parameter exploration to the new version, validate it and switch to PE view
+ from vistrails.gui.vistrails_window import _app
+ view = _app.get_current_view()
+ view.apply_parameter_exploration(self.id, data.items[0].entity.pe)
+ event.accept()
+ else:
+ event.ignore()
+
+ def perform_analogy(self):
+ sender = self.scene().sender()
+ analogy_name = str(sender.text())
+ # selectedItems = self.scene().selectedItems()
+ controller = self.scene().controller
+ print "calling perform analogy", analogy_name, self.id
+ # for item in selectedItems:
+ controller.perform_analogy(analogy_name, self.id)
+
+ def show_raw_pipeline(self):
+ self.scene().emit_selection = False
+ for item in self.scene().selectedItems():
+ item.setSelected(False)
+ self.setSelected(True)
+ self.scene().emit_selection = True
+ self.scene().emit(
+ QtCore.SIGNAL('versionSelected(int,bool,bool,bool,bool)'),
+ self.id, True, False, True, True)
+
+ def construct_from_root(self):
+ self.scene().emit_selection = False
+ for item in self.scene().selectedItems():
+ item.setSelected(False)
+ self.setSelected(True)
+ self.scene().emit_selection = True
+ self.scene().emit(
+ QtCore.SIGNAL('versionSelected(int,bool,bool,bool,bool)'),
+ self.id, True, True, True, True)
+
+ def contextMenuEvent(self, event):
+ """contextMenuEvent(event: QGraphicsSceneContextMenuEvent) -> None
+ Captures context menu event.
+
+ """
+ controller = self.scene().controller
+ menu = QtGui.QMenu()
+ raw_action = QtGui.QAction("Display raw pipeline", self.scene())
+ from_root_action = QtGui.QAction("Construct from root", self.scene())
+ QtCore.QObject.connect(raw_action,
+ QtCore.SIGNAL("triggered()"),
+ self.show_raw_pipeline)
+ QtCore.QObject.connect(from_root_action,
+ QtCore.SIGNAL("triggered()"),
+ self.construct_from_root)
+ menu.addAction(raw_action)
+ menu.addAction(from_root_action)
+ if len(controller.analogy) > 0:
+ analogies = QtGui.QMenu("Perform analogy...")
+ for title in sorted(controller.analogy.keys()):
+ act = QtGui.QAction(title, self.scene())
+ analogies.addAction(act)
+ QtCore.QObject.connect(act,
+ QtCore.SIGNAL("triggered()"),
+ self.perform_analogy)
+ menu.addMenu(analogies)
+ menu.exec_(event.screenPos())
+
+ def mouseDoubleClickEvent(self, event):
+ # QtGui.QGraphicsEllipseItem.mouseDoubleClickEvent(self, event)
+ event.accept()
+ self.scene().double_click(self.id)
+
+
+class QVersionTreeScene(QInteractiveGraphicsScene):
+ """
+ QVersionTree inherits from QInteractiveGraphicsScene to keep track
+ of the version scenes, i.e. versions, connections, etc.
+
+ """
+
+ def __init__(self, parent=None):
+ """ QVersionTree(parent: QWidget) -> QVersionTree
+ Initialize the graphics scene with no shapes
+
+ """
+ QInteractiveGraphicsScene.__init__(self, parent)
+ self.setBackgroundBrush(CurrentTheme.VERSION_TREE_BACKGROUND_BRUSH)
+ self.setSceneRect(QtCore.QRectF(-5000, -5000, 10000, 10000))
+ self.versions = {} # id -> version gui object
+ self.edges = {} # (sourceVersion, targetVersion) -> edge gui object
+ self.controller = None
+ self.fullGraph = None
+ self.timer = QtCore.QBasicTimer()
+ self.animation_step = 1
+ self.num_animation_steps = 1
+ self.emit_selection = True
+ self.select_by_click = True
+ self.connect(self, QtCore.SIGNAL("selectionChanged()"),
+ self.selectionChanged)
+
+ def addVersion(self, node, action, tag, description):
+ """ addModule(node, action: DBAction, tag: str, description: str)
+ -> None
+ Add a module to the scene.
+
+ """
+ versionShape = QGraphicsVersionItem(None)
+ versionShape.setupVersion(node, action, tag, description)
+ self.addItem(versionShape)
+ self.versions[node.id] = versionShape
+
+ def removeVersion(self, v):
+ """ addLink(v: integer) -> None
+ Remove version from scene and mapping
+
+ """
+ versionShape = self.versions[v]
+ self.removeItem(versionShape)
+ self.versions.pop(v)
+
+ def addLink(self, guiSource, guiTarget, expand, collapse):
+ """ addLink(v1, v2: QGraphicsVersionItem) -> None
+ Add a link to the scene
+
+ """
+ linkShape = QGraphicsLinkItem()
+ linkShape.setupLink(guiSource, guiTarget, expand, collapse)
+ self.addItem(linkShape)
+ self.edges[(guiSource.id, guiTarget.id)] = linkShape
+
+ def removeLink(self, source, target):
+ """ removeLink(v1, v2: integers) -> None
+ Remove link from scene and mapping
+
+ """
+ linkShape = self.edges[(source,target)]
+ self.removeItem(linkShape)
+ self.edges.pop((source, target))
+
+ def clear(self):
+ """ clear() -> None
+ Clear the whole scene
+
+ """
+ self.versions = {}
+ self.clearItems()
+
+ def adjust_version_colors(self, controller):
+ """ adjust_version_colors(controller: VistrailController) -> None
+ Based on the controller to set version colors
+
+ """
+ currentUser = controller.vistrail.getUser()
+ ranks = {}
+ ourMaxRank = 0
+ otherMaxRank = 0
+ am = controller.vistrail.actionMap
+ for nodeId in sorted(self.versions.keys()):
+ if nodeId!=0:
+ nodeUser = am[nodeId].user
+ if nodeUser==currentUser:
+ ranks[nodeId] = ourMaxRank
+ ourMaxRank += 1
+ else:
+ ranks[nodeId] = otherMaxRank
+ otherMaxRank += 1
+ for (nodeId, item) in self.versions.iteritems():
+ if nodeId == 0:
+ item.setGhosted(True)
+ continue
+ nodeUser = am[nodeId].user
+ if controller.search and nodeId!=0:
+ ghosted = not controller.search.match(controller.vistrail,
+ am[nodeId])
+ else:
+ ghosted = False
+
+ #item.setGhosted(ghosted) # we won't set it now so we can check if
+ # the state changed in update_color
+ if nodeUser==currentUser:
+ max_rank = ourMaxRank
+ else:
+ max_rank = otherMaxRank
+# max_rank = ourMaxRank if nodeUser==currentUser else otherMaxRank
+ item.update_color(nodeUser==currentUser,
+ ranks[nodeId],
+ max_rank, ghosted)
+ for (version_from, version_to), link in self.edges.iteritems():
+ if self.versions[version_from].ghosted and \
+ self.versions[version_to].ghosted:
+ link.setGhosted(True)
+ else:
+ link.setGhosted(False)
+
+ def update_scene_single_node_change(self, controller, old_version, new_version):
+ """ update_scene_single_node_change(controller: VistrailController,
+ old_version, new_version: int) -> None
+
+ Faster alternative to setup_scene when a single version is
+ changed. When this is called, we know that both old_version
+ and new_version don't have tags associated, so no layout
+ changes happen
+
+ """
+ # self.setupScene(controller)
+
+ # we need to call this every time because version ranks might
+ # change
+ self.adjust_version_colors(controller)
+
+ # update version item
+ v = self.versions[old_version]
+ old_desc = controller.vistrail.get_description(old_version)
+ new_desc = controller.vistrail.get_description(new_version)
+ if old_desc != new_desc:
+ v.descriptionLabel = new_desc
+ v.text.changed(v.text.centerX, v.text.centerY, new_desc, False)
+ v.updateWidthFromLabel()
+ self.versions[new_version] = v
+ del self.versions[old_version]
+ v.id = new_version
+
+ # update link items
+ dst = controller._current_terse_graph.edges_from(new_version)
+ for eto, _ in dst:
+ edge = self.edges[(old_version, eto)]
+ edge.setupLink(self.versions[new_version],
+ self.versions[eto],
+ self.fullGraph.parent(eto) != new_version,
+ False) # We shouldn't ever need a collapse here
+ self.edges[(new_version, eto)] = edge
+ del self.edges[(old_version, eto)]
+
+ src = controller._current_terse_graph.edges_to(new_version)
+ for efrom, _ in src:
+ edge = self.edges[(efrom, old_version)]
+ edge.setupLink(self.versions[efrom],
+ self.versions[new_version],
+ self.fullGraph.parent(new_version) != efrom,
+ False) # We shouldn't ever need a collapse here
+ self.edges[(efrom, new_version)] = edge
+ del self.edges[(efrom, old_version)]
+
+ def setupScene(self, controller, select_node=True):
+ """ setupScene(controller: VistrailController) -> None
+ Construct the scene to view a version tree
+
+ """
+ import time
+ t = time.clock()
+
+ tClearRefine = time.clock()
+
+ # Clean the previous scene
+ # self.clear()
+
+ self.select_by_click = False
+ self.controller = controller
+
+ # perform graph layout
+ (tree, self.fullGraph, layout) = \
+ controller.refine_graph(float(self.animation_step)/
+ float(self.num_animation_steps))
+
+ tClearRefine = time.clock() - tClearRefine
+
+ # compute nodes that should be removed
+ # O(n * (hashmap query key time)) on
+ # where n is the number of current
+ # nodes in the scene
+ removeNodeSet = set(i for i in self.versions
+ if not i in tree.vertices)
+
+ # compute edges to be removed
+ # O(n * (hashmap query key time))
+ # where n is the number of current
+ # edges in the scene
+ removeEdgeSet = set((s, t) for (s, t) in self.edges
+ if (s in removeNodeSet or
+ t in removeNodeSet or
+ not tree.has_edge(s, t)))
+
+ # loop on the nodes of the tree
+ vistrail = controller.vistrail
+ tm = vistrail.get_tagMap()
+ am = vistrail.actionMap
+ last_n = vistrail.getLastActions(controller.num_versions_always_shown)
+
+ self.emit_selection = False
+ for node in layout.nodes.itervalues():
+
+ # version id
+ v = node.id
+
+ # version tag
+ tag = tm.get(v, None)
+ action = am.get(v, None)
+ description = vistrail.get_description(v)
+
+ # if the version gui object already exists...
+ if v in self.versions:
+ versionShape = self.versions[v]
+ versionShape.setupVersion(node, action, tag, description)
+ else:
+ self.addVersion(node, action, tag, description)
+ if select_node:
+ self.versions[v].setSelected(v == controller.current_version)
+
+ self.emit_selection = True
+ self.selectionChanged()
+
+
+ # remove gui edges from scene
+ for (v1, v2) in removeEdgeSet:
+ self.removeLink(v1,v2)
+
+ # remove gui nodes from scene
+ for v in removeNodeSet:
+ self.removeVersion(v)
+
+ tCreate = time.clock()
+
+ # adjust the colors
+ self.adjust_version_colors(controller)
+
+ # Add or update links
+ for source in tree.vertices.iterkeys():
+ eFrom = tree.edges_from(source)
+ for (target, aux) in eFrom:
+ guiSource = self.versions[source]
+ guiTarget = self.versions[target]
+ sourceChildren = [to for (to, _) in
+ self.fullGraph.adjacency_list[source]
+ if (to in am) and not vistrail.is_pruned(to)]
+ targetChildren = [to for (to, _) in
+ self.fullGraph.adjacency_list[target]
+ if (to in am) and not vistrail.is_pruned(to)]
+ expand = self.fullGraph.parent(target)!=source
+ collapse = (self.fullGraph.parent(target)==source and # No in betweens
+ len(targetChildren) == 1 and # target is not a leaf or branch
+ target != controller.current_version and # target is not selected
+ target not in tm and # target has no tag
+ target not in last_n and # not one of the last n modules
+ (source in tm or # source has a tag
+ source == 0 or # source is root node
+ len(sourceChildren) > 1 or # source is branching node
+ source == controller.current_version)) # source is selected
+ if self.edges.has_key((source,target)):
+ linkShape = self.edges[(source,target)]
+ linkShape.setupLink(guiSource, guiTarget,
+ expand, collapse)
+ else:
+ #print "add link %d %d" % (source, target)
+ self.addLink(guiSource, guiTarget,
+ expand, collapse)
+
+ tCreate = time.clock() - tCreate
+
+ # Update bounding rects and fit to all view
+ tUpdate = time.clock()
+ if not self.controller.animate_layout:
+ self.updateSceneBoundingRect()
+ elif not self.timer.isActive():
+ self.timer.start(0, self)
+ tUpdate = time.clock() - tUpdate
+
+ self.select_by_click = True
+
+ t = time.clock() - t
+ # print "time in msec to setupScene total: %f refine %f layout %f create %f" % (t, tClearRefine, tCreate)
+
+ def timerEvent(self, event):
+ """ timerEvent(event: QTimerEvent) -> None
+
+ Start up a timer for animating tree drawing events
+ """
+ if event.timerId() == self.timer.timerId():
+ self.animation_step += 1
+ if self.animation_step >= self.num_animation_steps:
+ self.animation_step = 1
+ self.timer.stop()
+ self.controller.animate_layout = False
+ self.setupScene(self.controller)
+ self.update()
+ else:
+ qt_super(QVersionTreeScene, self).timerEvent(event)
+
+ def keyPressEvent(self, event):
+ """ keyPressEvent(event: QKeyEvent) -> None
+ Capture 'Del', 'Backspace' for pruning versions when not editing a tag
+
+ """
+ selectedItems = self.selectedItems()
+ versions = [item.id for item in selectedItems
+ if isinstance(item, QGraphicsVersionItem)
+ and not item.text.hasFocus()]
+ if (self.controller and len(versions)>0 and
+ event.key() in [QtCore.Qt.Key_Backspace, QtCore.Qt.Key_Delete]):
+ event.accept()
+ versions = [item.id for item in selectedItems]
+ res = vistrails.gui.utils.show_question("VisTrails",
+ "Are you sure that you want to "
+ "prune the selected version(s)?",
+ [vistrails.gui.utils.YES_BUTTON,
+ vistrails.gui.utils.NO_BUTTON],
+ vistrails.gui.utils.NO_BUTTON)
+ if res == vistrails.gui.utils.YES_BUTTON:
+ self.controller.prune_versions(versions)
+ else:
+ qt_super(QVersionTreeScene, self).keyPressEvent(event)
+
+ def selectionChanged(self):
+ if not self.emit_selection:
+ return
+
+ selected_items = self.selectedItems()
+ if len(selected_items) == 1:
+ # emit versionSelected selected_id
+ self.emit(QtCore.SIGNAL('versionSelected(int,bool,bool,bool,bool)'),
+ selected_items[0].id, self.select_by_click,
+ True, False, False)
+ else:
+ # emit versionSelected -1
+ for item in selected_items:
+ if item.text.isEditable:
+ item.text.setEditable(False)
+ self.emit(QtCore.SIGNAL('versionSelected(int,bool,bool,bool,bool)'),
+ -1, self.select_by_click, True, False, False)
+
+ if len(selected_items) == 2:
+ self.emit(
+ QtCore.SIGNAL('twoVersionsSelected(int, int)'),
+ selected_items[0].id, selected_items[1].id)
+
+ def double_click(self, version_id):
+ self.mouseGrabberItem().ungrabMouse()
+ self.emit(QtCore.SIGNAL('versionSelected(int,bool,bool,bool,bool)'),
+ version_id, self.select_by_click, True, False, True)
+
+class QVersionTreeView(QInteractiveGraphicsView, BaseView):
+ """
+ QVersionTreeView inherits from QInteractiveGraphicsView that will
+ handle drawing of versions layout output from Dotty
+
+ """
+
+ def __init__(self, parent=None):
+ """ QVersionTreeView(parent: QWidget) -> QVersionTreeView
+ Initialize the graphics view and its properties
+
+ """
+ QInteractiveGraphicsView.__init__(self, parent)
+ BaseView.__init__(self)
+ self.controller = None
+ self.set_title('Version Tree')
+ self.setScene(QVersionTreeScene(self))
+ self.versionProp = QVersionPropOverlay(self, self.viewport())
+ self.versionProp.hide()
+
+ def set_default_layout(self):
+ from vistrails.gui.collection.workspace import QWorkspaceWindow
+ from vistrails.gui.version_prop import QVersionProp
+ self.set_palette_layout(
+ {QtCore.Qt.LeftDockWidgetArea: QWorkspaceWindow,
+ QtCore.Qt.RightDockWidgetArea: QVersionProp,
+ })
+
+ def set_action_links(self):
+ self.action_links = \
+ {
+ 'publishWeb' : ('version_changed', self.check_publish_db),
+ 'publishPaper': ('version_changed', self.check_publish),
+ 'redo': ('version_changed', self.can_redo),
+ 'undo': ('version_changed', self.can_undo),
+ 'execute': ('pipeline_changed', self.can_execute)
+ }
+
+ def set_action_defaults(self):
+ self.action_defaults['execute'] = \
+ [('setEnabled', True, self.set_action_execute_default)]
+
+ def set_action_execute_default(self):
+ if self.controller:
+ if self.controller.current_pipeline:
+ return len(self.controller.current_pipeline.modules) > 0
+ return False
+
+ def check_publish_db(self, versionId):
+ loc = self.controller.locator
+ result = False
+ if hasattr(loc,'host'):
+ result = True
+ return result and self.check_publish(versionId)
+
+ def check_publish(self, versionId):
+ return versionId > 0
+
+ def can_redo(self, versionId):
+ return self.controller and self.controller.can_redo()
+
+ def can_undo(self, versionId):
+ return self.controller and self.controller.can_undo()
+
+ def can_execute(self, pipeline):
+ return pipeline is not None and len(pipeline.modules) > 0
+
+ def execute(self):
+ res = self.controller.execute_current_workflow()
+ from vistrails.gui.vistrails_window import _app
+ if len(res[0][0].errors) > 0:
+ _app.qactions['pipeline'].trigger()
+ _app.notify('execution_updated')
+
+ def publish_to_web(self):
+ from vistrails.gui.publishing import QVersionEmbed
+ panel = QVersionEmbed.instance()
+ panel.switchType('Wiki')
+ panel.set_visible(True)
+
+ def publish_to_paper(self):
+ from vistrails.gui.publishing import QVersionEmbed
+ panel = QVersionEmbed.instance()
+ panel.switchType('Latex')
+ panel.set_visible(True)
+
+ def selectModules(self):
+ """ selectModules() -> None
+ Overrides parent class to disable text items if you click on background
+
+ """
+ if self.canSelectRectangle:
+ br = self.selectionBox.sceneBoundingRect()
+ else:
+ br = QtCore.QRectF(self.startSelectingPos,
+ self.startSelectingPos)
+ items = self.scene().items(br)
+ if len(items)==0 or items==[self.selectionBox]:
+ for item in self.scene().selectedItems():
+ if isinstance(item, vistrails.gui.version_view.QGraphicsVersionItem):
+ item.text.clearFocus()
+ qt_super(QVersionTreeView, self).selectModules()
+
+ def set_title(self, title):
+ BaseView.set_title(self, title)
+ self.setWindowTitle(title)
+
+ def set_controller(self, controller):
+ oldController = self.controller
+ if oldController != controller:
+ if oldController != None:
+ self.disconnect(oldController,
+ QtCore.SIGNAL('vistrailChanged()'),
+ self.vistrailChanged)
+ self.disconnect(oldController,
+ QtCore.SIGNAL('invalidateSingleNodeInVersionTree'),
+ self.single_node_changed)
+ self.disconnect(oldController,
+ QtCore.SIGNAL('notesChanged()'),
+ self.notesChanged)
+ self.controller = controller
+ self.scene().controller = controller
+ self.connect(controller,
+ QtCore.SIGNAL('vistrailChanged()'),
+ self.vistrailChanged)
+ self.connect(controller,
+ QtCore.SIGNAL('invalidateSingleNodeInVersionTree'),
+ self.single_node_changed)
+ self.connect(controller,
+ QtCore.SIGNAL("notesChanged()"),
+ self.notesChanged)
+ if controller:
+ self.versionProp.updateController(controller)
+ self.scene().setupScene(controller)
+ # self.vistrailChanged()
+ # self.versionProp.updateController(controller)
+ # self.versionView.versionProp.updateController(controller)
+
+ def vistrailChanged(self):
+ """ vistrailChanged() -> None
+ An action was performed on the current vistrail
+
+ """
+ from vistrails.gui.vistrails_window import _app
+ select_node = True
+ if _app._previous_view and _app._previous_view.window() != self.window():
+ select_node = False
+ self.scene().setupScene(self.controller, select_node)
+ if self.controller and self.controller.reset_version_view:
+ self.scene().fitToAllViews()
+ if self.controller:
+ # self.versionProp.updateVersion(self.controller.current_version)
+ self.versionProp.updateVersion(self.controller.current_version)
+ self.emit(QtCore.SIGNAL("vistrailChanged()"))
+
+ def single_node_changed(self, old_version, new_version):
+ """ single_node_changed(old_version, new_version)
+ Handle single node change on version tree by not recomputing
+ entire scene.
+
+ """
+ self.scene().update_scene_single_node_change(self.controller,
+ old_version,
+ new_version)
+ if self.controller and self.controller.reset_version_view:
+ self.scene().fitToAllViews()
+ if self.controller:
+ # self.versionProp.updateVersion(self.controller.current_version)
+ self.versionProp.updateVersion(self.controller.current_version)
+ self.emit(QtCore.SIGNAL("vistrailChanged()"))
+
+ def notesChanged(self):
+ """ notesChanged() -> None
+ The notes for the current vistrail version changed
+
+ """
+ if self.controller:
+ self.versionProp.updateVersion(self.controller.current_version)
+
+ def select_current_version(self):
+ self.scene().setupScene(self.controller)
+################################################################################
diff --git a/vistrails/gui/view_manager.py b/vistrails/gui/view_manager.py
new file mode 100644
index 0000000..105488d
--- /dev/null
+++ b/vistrails/gui/view_manager.py
@@ -0,0 +1,903 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This holds a customized QTabWidget for controlling different
+vistrail views and tools
+
+QViewManager
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.utils import getBuilderWindow
+from vistrails.gui.vistrail_view import QVistrailView
+from vistrails.core import system, debug
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core.db.locator import FileLocator, XMLFileLocator, untitled_locator
+from vistrails.core.db.io import load_vistrail
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.core.log.log import Log
+from vistrails.core.log.opm_graph import OpmGraph
+from vistrails.core.collection import Collection
+import vistrails.core.system
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.vistrail.tag import Tag
+from vistrails.core.vistrail.vistrail import Vistrail
+from vistrails.core.modules.module_registry import ModuleRegistry, \
+ ModuleRegistryException
+import copy
+
+################################################################################
+class QDetachedView(QtGui.QStackedWidget):
+ """
+ QDetachedView is a stacked widget holding detached views
+ (e.g. Pipeline, History, etc) from the main view manager.
+
+ """
+
+ def __init__(self, title, parent=None):
+ """ QDetachedView(parent: QWidget) -> QDetachedView
+ Create an empty stacked widget
+
+ """
+ QtGui.QStackedWidget.__init__(self, parent)
+ self.title = title
+ self.setWindowTitle(self.title)
+
+ def sizeHint(self):
+ """ sizeHint() -> QRect
+ Return the recommended size of a detached view
+
+ """
+ return QtCore.QSize(800, 600)
+
+
+################################################################################
+class QViewManager(QtGui.QTabWidget):
+ """
+ QViewManager is a tabbed widget to containing multiple Vistrail
+ views. It takes care of emiting useful signals to the builder
+ window
+
+ """
+ def __init__(self, parent=None):
+ """ QViewManager(view: QVistrailView) -> QViewManager
+ Create an empty tab widget
+
+ """
+ QtGui.QTabWidget.__init__(self, parent)
+ self.closeButton = QtGui.QToolButton(self)
+ self.closeButton.setIcon(CurrentTheme.VIEW_MANAGER_CLOSE_ICON)
+ self.closeButton.setAutoRaise(True)
+ self.setCornerWidget(self.closeButton)
+ self.activeIndex = -1
+
+ self.connect(self, QtCore.SIGNAL('currentChanged(int)'),
+ self.currentChanged)
+ self.connect(self.closeButton, QtCore.SIGNAL('clicked()'),
+ self.closeVistrail)
+
+ self._views = {}
+ self.single_document_mode = False
+ self.pip_mode = True
+
+ self.createDetachedViews()
+
+ def createDetachedViews(self):
+ """ createDetachedViews() -> None
+ Create a set of QStackedWidget for displaying detached views
+ based on the input configuration
+
+ """
+ if getattr(get_vistrails_configuration(), 'detachHistoryView'):
+ self.historyView = QDetachedView('History View')
+ self.historyView.show()
+ else:
+ self.historyView = None
+
+ def set_single_document_mode(self, on):
+ """ set_single_document_mode(on: bool) -> None
+ Toggle single document interface
+
+ """
+ self.single_document_mode = on
+ if self.single_document_mode:
+ self.tabBar().hide()
+ else:
+ self.tabBar().show()
+
+ def add_vistrail_view(self, view):
+ """ add_vistrail_view(view: QVistrailView) -> None
+ Add a vistrail view to the tab, and connect to the right signals
+
+ """
+ self._views[view] = view.controller
+ if self.indexOf(view)!=-1:
+ return
+
+ if self.historyView!=None:
+ self.historyView.addWidget(view.versionTab)
+
+ view.installEventFilter(self)
+ self.connect(view.pipelineTab,
+ QtCore.SIGNAL('moduleSelectionChange'),
+ self.moduleSelectionChange)
+ self.connect(view,
+ QtCore.SIGNAL('versionSelectionChange'),
+ self.versionSelectionChange)
+ self.connect(view,
+ QtCore.SIGNAL('execStateChange()'),
+ self.execStateChange)
+ self.connect(view.versionTab,
+ QtCore.SIGNAL('vistrailChanged()'),
+ self.vistrailChanged)
+ self.connect(view.pipelineTab,
+ QtCore.SIGNAL('resetQuery()'),
+ self.resetQuery)
+ self.connect(view.versionTab,
+ QtCore.SIGNAL('resetQuery()'),
+ self.resetQuery)
+ self.connect(view.queryTab,
+ QtCore.SIGNAL('resetQuery()'),
+ self.resetQuery)
+
+ self.emit(QtCore.SIGNAL('vistrailViewAdded'), view)
+ self.addTab(view, view.windowTitle())
+ if self.count()==1:
+ self.emit(QtCore.SIGNAL('currentChanged(int)'), 0)
+
+ def removeVistrailView(self, view):
+ """ removeVistrailView(view: QVistrailView) -> None
+ Remove the current vistrail view and destroy it
+
+ """
+ if view:
+ del self._views[view]
+ view.removeEventFilter(self)
+ self.disconnect(view.pipelineTab,
+ QtCore.SIGNAL('moduleSelectionChange'),
+ self.moduleSelectionChange)
+ self.disconnect(view,
+ QtCore.SIGNAL('versionSelectionChange'),
+ self.versionSelectionChange)
+ self.disconnect(view.versionTab,
+ QtCore.SIGNAL('vistrailChanged()'),
+ self.vistrailChanged)
+
+ # FIXME move this elsewhere?
+ self.disconnect(view.versionTab.versionView.scene(),
+ QtCore.SIGNAL('selectionChanged()'),
+ view.versionTab.versionView.scene().selectionChanged)
+ self.emit(QtCore.SIGNAL('vistrailViewRemoved'), view)
+ index = self.indexOf(view)
+ if index !=-1:
+ if self.historyView:
+ self.historyView.removeWidget(self.historyView.widget(self.currentIndex()))
+ self.removeTab(self.currentIndex())
+ self.activeIndex = self.currentIndex()
+ view.controller.cleanup()
+ view.close()
+ view.deleteLater()
+
+ def moduleSelectionChange(self, selection):
+ """ moduleSelectionChange(selection: list[id]) -> None
+ Just echo the signal from the view
+
+ """
+ self.emit(QtCore.SIGNAL('moduleSelectionChange'), selection)
+
+ def versionSelectionChange(self, versionId):
+ """ versionSelectionChange(versionId: int) -> None
+ Just echo the signal from the view
+
+ """
+ self.emit(QtCore.SIGNAL('versionSelectionChange'), versionId)
+
+ def execStateChange(self):
+ """ execStateChange() -> None
+ Just echo the signal from the view
+
+ """
+ self.emit(QtCore.SIGNAL('execStateChange()'))
+
+ def vistrailChanged(self):
+ """ vistrailChanged() -> None
+ Just echo the signal from the view
+
+ """
+ self.emit(QtCore.SIGNAL('vistrailChanged()'))
+
+ def copySelection(self):
+ """ copySelection() -> None
+ Copy the current selected pipeline modules
+
+ """
+ vistrailView = self.currentWidget()
+ if vistrailView:
+ vistrailView.pipelineTab.pipelineView.scene().copySelection()
+
+ def group(self):
+ """group() -> None
+ Creates a group from the selected pipeline modules
+
+ """
+ vistrailView = self.currentWidget()
+ if vistrailView:
+ vistrailView.pipelineTab.pipelineView.scene().group()
+
+ def ungroup(self):
+ """ungroup() -> None
+ Ungroups selected pipeline modules
+
+ """
+ vistrailView = self.currentWidget()
+ if vistrailView:
+ vistrailView.pipelineTab.pipelineView.scene().ungroup()
+
+ def makeAbstraction(self):
+ vistrailView = self.currentWidget()
+ if vistrailView:
+ vistrailView.pipelineTab.pipelineView.scene().makeAbstraction()
+
+ def convertToAbstraction(self):
+ vistrailView = self.currentWidget()
+ if vistrailView:
+ vistrailView.pipelineTab.pipelineView.scene().convertToAbstraction()
+
+ def importAbstraction(self):
+ vistrailView = self.currentWidget()
+ if vistrailView:
+ vistrailView.pipelineTab.pipelineView.scene().importAbstraction()
+
+ def exportAbstraction(self):
+ vistrailView = self.currentWidget()
+ if vistrailView:
+ vistrailView.pipelineTab.pipelineView.scene().exportAbstraction()
+
+ def currentView(self):
+ """currentView() -> VistrailView. Returns the current vistrail view."""
+ return self.currentWidget()
+
+ def pasteToCurrentPipeline(self):
+ """ pasteToCurrentPipeline() -> None
+ Paste what is on the clipboard to the current pipeline
+
+ """
+ vistrailView = self.currentWidget()
+ if vistrailView:
+ vistrailView.pasteToCurrentTab()
+
+ def selectAllModules(self):
+ """ selectAllModules() -> None
+ Select all modules in the current view
+
+ """
+ vistrailView = self.currentWidget()
+ if vistrailView:
+ vistrailView.selectAll()
+
+ def canSelectAll(self):
+ """ canSelectAll() -> bool
+ Check to see if there is any module in the pipeline view to be
+ selected
+
+ """
+ vistrailView = self.currentWidget()
+ if vistrailView and vistrailView.controller.current_pipeline:
+ return len(vistrailView.controller.current_pipeline.modules)>0
+ return False
+
+ def redo(self):
+ """ redo() -> none
+ Performs a redo step.
+
+ """
+ vistrailView = self.currentWidget()
+ if not vistrailView:
+ return
+ new_version = vistrailView.redo()
+ self.emit(QtCore.SIGNAL('versionSelectionChange'), new_version)
+
+ def undo(self):
+ """ undo() -> None
+ Performs an undo step.
+
+ """
+ vistrailView = self.currentWidget()
+ if not vistrailView:
+ return
+ new_version = vistrailView.undo()
+ self.emit(QtCore.SIGNAL('versionSelectionChange'), new_version)
+
+ def newVistrail(self, recover_files=True):
+ """ newVistrail() -> (None or QVistrailView)
+ Create a new vistrail with no name. If user cancels process,
+ returns None.
+
+ FIXME: We should do the interactive parts separately.
+
+ """
+ if self.single_document_mode and self.currentView():
+ if not self.closeVistrail():
+ return None
+ if recover_files and untitled_locator().has_temporaries():
+ locator = copy.copy(untitled_locator())
+ else:
+ locator = None
+ try:
+ (vistrail, abstraction_files, thumbnail_files, _) = load_vistrail(locator)
+ except ModuleRegistryException, e:
+ debug.critical("Module registry error for %s" %
+ str(e.__class__.__name__), str(e))
+ except Exception, e:
+ debug.critical('An error has occurred', str(e))
+ raise
+ return self.set_vistrail_view(vistrail, locator, abstraction_files,
+ thumbnail_files)
+
+ def close_first_vistrail_if_necessary(self):
+ # Close first vistrail of no change was made
+ if not self._first_view:
+ return
+ vt = self._first_view.controller.vistrail
+ if vt.get_version_count() == 0:
+ self.closeVistrail(self._first_view)
+ self._first_view = None
+ else:
+ # We set it to none, since it's been changed, so
+ # we don't want to ever close it again.
+ self._first_view = None
+
+ def set_vistrail_view(self, vistrail, locator, abstraction_files=None,
+ thumbnail_files=None, version=None):
+ """set_vistrail_view(vistrail: Vistrail,
+ locator: VistrailLocator,
+ abstraction_files: list(str),
+ thumbnail_files: list(str),
+ version=None)
+ -> QVistrailView
+ Sets a new vistrail view for the vistrail object for the given version
+ if version is None, use the latest version
+ """
+
+ if isinstance(version, basestring):
+ try:
+ version = vistrail.get_version_number(version)
+ except:
+ version = None
+
+ vistrailView = QVistrailView()
+ vistrailView.set_vistrail(vistrail, locator, abstraction_files,
+ thumbnail_files)
+ self.add_vistrail_view(vistrailView)
+ self.setCurrentWidget(vistrailView)
+ vistrailView.setup_view(version)
+ vistrailView.setPIPMode(self.pip_mode)
+ self.versionSelectionChange(vistrailView.controller.current_version)
+ return vistrailView
+
+ def open_vistrail(self, locator, version=None, is_abstraction=False):
+ """open_vistrail(locator: Locator, version = None: int or str,
+ is_abstraction: bool)
+
+ opens a new vistrail from the given locator, selecting the
+ given version.
+
+ """
+ self.close_first_vistrail_if_necessary()
+ if self.single_document_mode and self.currentView():
+ self.closeVistrail()
+ view = self.ensureVistrail(locator)
+ if view:
+ if version is not None:
+ if isinstance(version, basestring):
+ try:
+ version = view.vistrail.get_version_number(version)
+ except:
+ version = None
+ if version is not None:
+ view.setup_view(version)
+ return view
+ try:
+ (vistrail, abstraction_files, thumbnail_files, _) = \
+ load_vistrail(locator, is_abstraction)
+ result = self.set_vistrail_view(vistrail, locator,
+ abstraction_files, thumbnail_files,
+ version)
+ # update collection
+ try:
+ vistrail.thumbnails = thumbnail_files
+ vistrail.abstractions = abstraction_files
+ collection = Collection.getInstance()
+ url = locator.to_url()
+ # create index if not exist
+ entity = collection.fromUrl(url)
+ if entity:
+ # find parent vistrail
+ while entity.parent:
+ entity = entity.parent
+ else:
+ entity = collection.updateVistrail(url, vistrail)
+ # add to relevant workspace categories
+ collection.add_to_workspace(entity)
+ collection.commit()
+ except Exception, e:
+ import traceback
+ debug.critical('Failed to index vistrail', str(e) + traceback.format_exc())
+ return result
+ except ModuleRegistryException, e:
+ debug.critical("Module registry error for %s" %
+ str(e.__class__.__name__), str(e))
+ except Exception, e:
+ import traceback
+ debug.critical('An error has occurred', str(e) + traceback.format_exc())
+ raise
+
+ def save_vistrail(self, locator_class,
+ vistrailView=None,
+ force_choose_locator=False):
+ """
+
+ force_choose_locator=True triggers 'save as' behavior
+ """
+ global bobo
+
+ if not vistrailView:
+ vistrailView = self.currentWidget()
+ vistrailView.flush_changes()
+ if vistrailView:
+ gui_get = locator_class.save_from_gui
+ # get a locator to write to
+ if force_choose_locator:
+ locator = gui_get(self, Vistrail.vtType,
+ vistrailView.controller.locator)
+ else:
+ locator = (vistrailView.controller.locator or
+ gui_get(self, Vistrail.vtType,
+ vistrailView.controller.locator))
+ if locator == untitled_locator():
+ locator = gui_get(self, Vistrail.vtType,
+ vistrailView.controller.locator)
+ # if couldn't get one, ignore the request
+ if not locator:
+ return False
+ # update collection
+ try:
+ vistrailView.controller.write_vistrail(locator)
+ except Exception, e:
+ debug.critical('An error has occurred', str(e))
+ raise
+ return False
+ try:
+ thumb_cache = ThumbnailCache.getInstance()
+ vistrailView.controller.vistrail.thumbnails = \
+ vistrailView.controller.find_thumbnails(
+ tags_only=thumb_cache.conf.tagsOnly)
+ vistrailView.controller.vistrail.abstractions = \
+ vistrailView.controller.find_abstractions(
+ vistrailView.controller.vistrail, True)
+
+ collection = Collection.getInstance()
+ url = locator.to_url()
+ # create index if not exist
+ entity = collection.fromUrl(url)
+ if entity:
+ # find parent vistrail
+ while entity.parent:
+ entity = entity.parent
+ else:
+ entity = collection.updateVistrail(url, vistrailView.controller.vistrail)
+ # add to relevant workspace categories
+ collection.add_to_workspace(entity)
+ collection.commit()
+ except Exception, e:
+ debug.critical('Failed to index vistrail', str(e))
+ return locator
+ return False
+
+ def open_workflow(self, locator, version=None):
+ self.close_first_vistrail_if_necessary()
+ if self.single_document_mode and self.currentView():
+ self.closeVistrail()
+
+ vistrail = Vistrail()
+ try:
+ if locator is not None:
+ workflow = locator.load(Pipeline)
+ action_list = []
+ for module in workflow.module_list:
+ action_list.append(('add', module))
+ for connection in workflow.connection_list:
+ action_list.append(('add', connection))
+ action = vistrails.core.db.action.create_action(action_list)
+ vistrail.add_action(action, 0L)
+ vistrail.update_id_scope()
+ vistrail.addTag("Imported workflow", action.id)
+ # FIXME might need different locator?
+ except ModuleRegistryException, e:
+ msg = ('Cannot find module "%s" in package "%s". '
+ 'Make sure package is '
+ 'enabled in the Preferences dialog.' % \
+ (e._name, e._identifier))
+ debug.critical(msg)
+ except Exception, e:
+ debug.critical('An error has occurred', str(e))
+ raise
+
+ return self.set_vistrail_view(vistrail, None)
+
+ # FIXME normalize workflow/log/registry!!!
+ def save_workflow(self, locator_class, force_choose_locator=True):
+ vistrailView = self.currentWidget()
+
+ if vistrailView:
+ vistrailView.flush_changes()
+ gui_get = locator_class.save_from_gui
+ if force_choose_locator:
+ locator = gui_get(self, Pipeline.vtType,
+ vistrailView.controller.locator)
+ else:
+ locator = (vistrailView.controller.locator or
+ gui_get(self, Pipeline.vtType,
+ vistrailView.controller.locator))
+ if locator == untitled_locator():
+ locator = gui_get(self, Pipeline.vtType,
+ vistrailView.controller.locator)
+ if not locator:
+ return False
+ vistrailView.controller.write_workflow(locator)
+ return True
+ return False
+
+ def save_log(self, locator_class, force_choose_locator=True):
+ vistrailView = self.currentWidget()
+
+ if vistrailView:
+ vistrailView.flush_changes()
+ gui_get = locator_class.save_from_gui
+ if force_choose_locator:
+ locator = gui_get(self, Log.vtType,
+ vistrailView.controller.locator)
+ else:
+ locator = (vistrailView.controller.locator or
+ gui_get(self, Log.vtType,
+ vistrailView.controller.locator))
+ if locator == untitled_locator():
+ locator = gui_get(self, Log.vtType,
+ vistrailView.controller.locator)
+ if not locator:
+ return False
+ vistrailView.controller.write_log(locator)
+ return True
+ return False
+
+ def save_registry(self, locator_class, force_choose_locator=True):
+ vistrailView = self.currentWidget()
+
+ if vistrailView:
+ vistrailView.flush_changes()
+ gui_get = locator_class.save_from_gui
+ if force_choose_locator:
+ locator = gui_get(self, ModuleRegistry.vtType,
+ vistrailView.controller.locator)
+ else:
+ locator = (vistrailView.controller.locator or
+ gui_get(self, ModuleRegistry.vtType,
+ vistrailView.controller.locator))
+ if locator == untitled_locator():
+ locator = gui_get(self, ModuleRegistry.vtType,
+ vistrailView.controller.locator)
+ if not locator:
+ return False
+ vistrailView.controller.write_registry(locator)
+ return True
+ return False
+
+ def save_opm(self, locator_class=XMLFileLocator,
+ force_choose_locator=True):
+ vistrailView = self.currentWidget()
+
+ if vistrailView:
+ vistrailView.flush_changes()
+ gui_get = locator_class.save_from_gui
+ if force_choose_locator:
+ locator = gui_get(self, OpmGraph.vtType,
+ vistrailView.controller.locator)
+ else:
+ locator = (vistrailView.controller.locator or
+ gui_get(self, OpmGraph.vtType,
+ vistrailView.controller.locator))
+ if locator == untitled_locator():
+ locator = gui_get(self, OpmGraph.vtType,
+ vistrailView.controller.locator)
+ if not locator:
+ return False
+ vistrailView.controller.write_opm(locator)
+ return True
+ return False
+
+ def export_stable(self, locator_class=XMLFileLocator,
+ force_choose_locator=True):
+ vistrailView = self.currentWidget()
+ vistrailView.flush_changes()
+
+ if vistrailView:
+ vistrailView.flush_changes()
+ gui_get = locator_class.save_from_gui
+ if force_choose_locator:
+ locator = gui_get(self, Vistrail.vtType,
+ vistrailView.controller.locator)
+ else:
+ locator = (vistrailView.controller.locator or
+ gui_get(self, Vistrail.vtType,
+ vistrailView.controller.locator))
+ if locator == untitled_locator():
+ locator = gui_get(self, Vistrail.vtType,
+ vistrailView.controller.locator)
+ if not locator:
+ return False
+ vistrailView.controller.write_vistrail(locator, '1.0.1')
+ return True
+ return False
+
+ def closeVistrail(self, vistrailView=None, quiet=False):
+ """ closeVistrail(vistrailView: QVistrailView, quiet: bool) -> bool
+ Close the current active vistrail
+
+ """
+ if not vistrailView:
+ vistrailView = self.currentWidget()
+ vistrailView.flush_changes()
+
+ if vistrailView:
+ if not quiet and vistrailView.controller.changed:
+ text = vistrailView.controller.name
+ if text=='':
+ text = 'Untitled%s'%vistrails.core.system.vistrails_default_file_type()
+ text = ('Vistrail ' +
+ QtCore.Qt.escape(text) +
+ ' contains unsaved changes.\n Do you want to '
+ 'save changes before closing it?')
+ res = QtGui.QMessageBox.information(getBuilderWindow(),
+ 'Vistrails',
+ text,
+ '&Save',
+ '&Discard',
+ 'Cancel',
+ 0,
+ 2)
+ else:
+ res = 1
+ locator = vistrailView.controller.locator
+ if res == 0:
+ if locator is None:
+ class_ = FileLocator()
+ else:
+ class_ = type(locator)
+ locator = self.save_vistrail(class_)
+ if not locator:
+ return False
+ elif res == 2:
+ return False
+
+ vistrailView.controller.close_vistrail(locator)
+ self.removeVistrailView(vistrailView)
+ if self.count()==0:
+ self.emit(QtCore.SIGNAL('currentVistrailChanged'), None)
+ self.emit(QtCore.SIGNAL('versionSelectionChange'), -1)
+ if vistrailView == self._first_view:
+ self._first_view = None
+ return True
+
+ def closeAllVistrails(self):
+ """ closeAllVistrails() -> bool
+ Attemps to close every single vistrail, return True if
+ everything is closed correctly
+
+ """
+ while self.count()>0:
+ if not self.closeVistrail():
+ return False
+ return True
+
+ def currentChanged(self, index):
+ """ currentChanged(index: int):
+ Emit signal saying a different vistrail has been chosen to the
+ builder
+
+ """
+ self.activeIndex = index
+ self.emit(QtCore.SIGNAL('currentVistrailChanged'),
+ self.currentWidget())
+ if index >= 0:
+ self.emit(QtCore.SIGNAL('versionSelectionChange'),
+ self.currentWidget().controller.current_version)
+ else:
+ self.emit(QtCore.SIGNAL('versionSelectionChange'),
+ -1)
+ if self.historyView:
+ self.historyView.setCurrentIndex(index)
+ if self.currentView()!=None:
+ self.historyView.setWindowTitle('History View - ' +
+ self.currentView().windowTitle())
+
+ def eventFilter(self, object, event):
+ """ eventFilter(object: QVistrailView, event: QEvent) -> None
+ Filter the window title change event for the view widget
+
+ """
+ if event.type()==QtCore.QEvent.WindowTitleChange:
+ if object==self.currentWidget():
+ self.setTabText(self.currentIndex(), object.windowTitle())
+ self.currentChanged(self.currentIndex())
+ return QtGui.QTabWidget.eventFilter(self, object, event)
+
+ def getCurrentVistrailFileName(self):
+ """ getCurrentVistrailFileName() -> str
+ Return the filename of the current vistrail or None if it
+ doesn't have one
+
+ """
+ vistrailView = self.currentWidget()
+ if vistrailView and vistrailView.controller.name!='':
+ return vistrailView.controller.name
+ else:
+ return None
+
+ def setPIPMode(self, on):
+ """ setPIPMode(on: Bool) -> None
+ Set the picture-in-picture mode for all views
+
+ """
+ self.pip_mode = on
+ for viewIndex in xrange(self.count()):
+ vistrailView = self.widget(viewIndex)
+ vistrailView.setPIPMode(on)
+
+ def setMethodsMode(self, on):
+ """ setMethodsMode(on: Bool) -> None
+ Turn the methods panel on/off for all views
+
+ """
+ for viewIndex in xrange(self.count()):
+ vistrailView = self.widget(viewIndex)
+ vistrailView.setMethodsMode(on)
+
+
+ def setSetMethodsMode(self, on):
+ """ setSetMethodsMode(on: Bool) -> None
+ Turn the set methods panel on/off for all views
+
+ """
+ for viewIndex in xrange(self.count()):
+ vistrailView = self.widget(viewIndex)
+ vistrailView.setSetMethodsMode(on)
+
+ def setPropertiesMode(self, on):
+ """ setPropertiesMode(on: Bool) -> None
+ Turn the properties panel on/off for all views
+
+ """
+ for viewIndex in xrange(self.count()):
+ vistrailView = self.widget(viewIndex)
+ vistrailView.setPropertiesMode(on)
+
+ def setPropertiesOverlayMode(self, on):
+ """ setPropertiesOverlayMode(on: Bool) -> None
+ Turn the properties overlay panel on/off for all views
+
+ """
+ for viewIndex in xrange(self.count()):
+ vistrailView = self.widget(viewIndex)
+ vistrailView.setPropertiesOverlayMode(on)
+
+ def setModuleConfigMode(self, on):
+ """ setModuleConfigMode(on: Bool) -> None
+ Turn the module configuration panel on/off for all views
+
+ """
+ for viewIndex in xrange(self.count()):
+ vistrailView = self.widget(viewIndex)
+ vistrailView.setModuleConfigMode(on)
+
+ def setVistrailVarsMode(self, on):
+ """ setVistrailVarsMode(on: Bool) -> None
+ Turn the vistrail variables panel on/off for all views
+
+ """
+ for viewIndex in xrange(self.count()):
+ vistrailView = self.widget(viewIndex)
+ vistrailView.setVistrailVarsMode(on)
+
+ def ensureVistrail(self, locator):
+ """ ensureVistrail(locator: VistrailLocator) -> QVistrailView
+ This will first find among the opened vistrails to see if
+ vistrails from locator has been opened. If not, it will return None.
+
+ """
+ for i in xrange(self.count()):
+ view = self.widget(i)
+ if view.controller.vistrail.locator == locator:
+ self.setCurrentWidget(view)
+ return view
+ return None
+
+ def set_first_view(self, view):
+ self._first_view = view
+
+ def viewModeChanged(self, mode):
+ """ viewModeChanged(mode: int) -> None
+
+ """
+ for viewIndex in xrange(self.count()):
+ vistrailView = self.widget(viewIndex)
+ if self.historyView!=None and mode>1:
+ vistrailView.viewModeChanged(mode-1)
+ else:
+ vistrailView.viewModeChanged(mode)
+
+ def changeCursor(self, mode):
+ """ changeCursor(mode: Int) -> None
+
+ """
+ for viewIndex in xrange(self.count()):
+ vistrailView = self.widget(viewIndex)
+ vistrailView.updateCursorState(mode)
+
+ def resetQuery(self):
+ """ resetQwuery() -> None
+
+ """
+ self.queryVistrail(False)
+
+ def queryVistrail(self, on=True):
+ """ queryVistrail(on: bool) -> None
+
+ """
+ self.currentView().setFocus(QtCore.Qt.MouseFocusReason)
+ self.currentView().queryVistrail(on)
+
+ def executeCurrentPipeline(self):
+ """ executeCurrentPipeline() -> None
+
+ """
+ self.currentView().setFocus(QtCore.Qt.MouseFocusReason)
+ self.currentView().checkModuleConfigPanel()
+ self.currentView().controller.execute_current_workflow()
+
+ def executeCurrentExploration(self):
+ """ executeCurrentExploration() -> None
+
+ """
+ self.currentView().setFocus(QtCore.Qt.MouseFocusReason)
+ self.currentView().executeParameterExploration()
diff --git a/vistrails/gui/vis_diff.py b/vistrails/gui/vis_diff.py
new file mode 100644
index 0000000..c89c548
--- /dev/null
+++ b/vistrails/gui/vis_diff.py
@@ -0,0 +1,1277 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This modules builds a widget to interact with vistrail diff
+operation """
+from PyQt4 import QtCore, QtGui
+from vistrails.core.system import get_vistrails_basic_pkg_id
+from vistrails.core.utils.color import ColorByName
+from vistrails.core.vistrail.abstraction import Abstraction
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.vistrail.port_spec import PortSpec
+from vistrails.gui.pipeline_view import QPipelineView
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.vistrail_controller import VistrailController
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+from vistrails.core import system, debug
+import vistrails.core.db.io
+
+import copy
+from itertools import chain
+
+################################################################################
+
+class QFunctionItemModel(QtGui.QStandardItemModel):
+ """
+ QFunctionItemModel is a item model that will allow item to be
+ show as a disabled one on the table
+
+ """
+ def __init__(self, row, col, parent=None):
+ """ QFunctionItemModel(row: int, col: int, parent: QWidget)
+ -> QFunctionItemModel
+ Initialize with a number of rows and columns
+
+ """
+ QtGui.QStandardItemModel.__init__(self, row, col, parent)
+ self.disabledRows = {}
+
+ def flags(self, index):
+ """ flags(index: QModelIndex) -> None
+ Return the current flags of the item with the index 'index'
+
+ """
+ if index.isValid() and self.disabledRows.has_key(index.row()):
+ return (QtCore.Qt.ItemIsDragEnabled | QtCore.Qt.ItemIsDropEnabled |
+ QtCore.Qt.ItemIsSelectable)
+ return QtGui.QStandardItemModel.flags(self,index)
+
+ def clearList(self):
+ """ clearList() -> None
+ Clear all items including the disabled ones
+
+ """
+ self.disabledRows = {}
+ self.removeRows(0,self.rowCount())
+
+ def disableRow(self,row):
+ """ disableRow(row: int) -> None
+ Disable a specific row on the table
+
+ """
+ self.disabledRows[row] = None
+
+class QParamTable(QtGui.QTableView):
+ """
+ QParamTable is a widget represents a diff between two version
+ as side-by-side comparisons
+
+ """
+ def __init__(self, v1Name=None, v2Name=None, parent=None):
+ """ QParamTable(v1Name: str, v2Name: str, parent: QWidget)
+ -> QParamTable
+ Initialize the table with two version names on the header view
+
+ """
+ QtGui.QTableView.__init__(self, parent)
+ itemModel = QFunctionItemModel(0, 2, self)
+ itemModel.setHeaderData(0, QtCore.Qt.Horizontal, v1Name)
+ itemModel.setHeaderData(1, QtCore.Qt.Horizontal, v2Name)
+ # self.setHorizontalHeaderLabels([v1Name, v2Name])
+ self.setModel(itemModel)
+ self.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
+ self.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
+ self.setEditTriggers(QtGui.QAbstractItemView.NoEditTriggers)
+ self.setFont(CurrentTheme.VISUAL_DIFF_PARAMETER_FONT)
+ self.horizontalHeader().setResizeMode(QtGui.QHeaderView.Stretch)
+
+ def set_names(self, v1_name, v2_name):
+ self.model().setHeaderData(0, QtCore.Qt.Horizontal, v1_name)
+ self.model().setHeaderData(1, QtCore.Qt.Horizontal, v2_name)
+ # self.setHorizontalHeaderLabels([v1_name, v2_name])
+
+class QParamInspector(QtGui.QWidget):
+ """
+ QParamInspector is a widget acting as an inspector vistrail modules
+ in diff mode. It consists of a function inspector and annotation
+ inspector
+
+ """
+ def __init__(self, v1Name='', v2Name='',
+ parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QParamInspector(v1Name: str, v2Name: str,
+ parent: QWidget, f: WindowFlags)
+ -> QParamInspector
+ Construct a widget containing tabs: Functions and Annotations,
+ each of them is in turn a table of two columns for two
+ corresponding versions.
+
+ """
+ QtGui.QWidget.__init__(self, parent, f | QtCore.Qt.Tool)
+ self.setWindowTitle('Parameter Inspector - None')
+ self.firstTime = True
+ self.boxLayout = QtGui.QVBoxLayout()
+ self.boxLayout.setMargin(0)
+ self.boxLayout.setSpacing(0)
+ self.tabWidget = QtGui.QTabWidget()
+ self.tabWidget.setTabPosition(QtGui.QTabWidget.North)
+ self.tabWidget.setTabShape(QtGui.QTabWidget.Triangular)
+ self.functionsTab = QParamTable(v1Name, v2Name)
+ self.tabWidget.addTab(self.functionsTab, 'Functions')
+# FIXME add annotation support back in
+# self.annotationsTab = QParamTable(v1Name, v2Name)
+# self.annotationsTab.horizontalHeader().setStretchLastSection(True)
+# self.tabWidget.addTab(self.annotationsTab, 'Annotations')
+ self.boxLayout.addWidget(self.tabWidget)
+ sizeGrip = QtGui.QSizeGrip(self)
+ self.boxLayout.addWidget(sizeGrip)
+ self.boxLayout.setAlignment(sizeGrip, QtCore.Qt.AlignRight)
+ self.setLayout(self.boxLayout)
+
+ def closeEvent(self, e):
+ """ closeEvent(e: QCloseEvent) -> None
+ Doesn't allow the QParamInspector widget to close, but just hide
+ instead
+
+ """
+ e.ignore()
+ self.parent().showInspectorAction.setChecked(False)
+
+
+class QLegendBox(QtGui.QFrame):
+ """
+ QLegendBox is just a rectangular box with a solid color
+
+ """
+ def __init__(self, brush, size, parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QLegendBox(color: QBrush, size: (int,int), parent: QWidget,
+ f: WindowFlags) -> QLegendBox
+ Initialize the widget with a color and fixed size
+
+ """
+ QtGui.QFrame.__init__(self, parent, f)
+ self.setFrameStyle(QtGui.QFrame.Box | QtGui.QFrame.Plain)
+ self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
+ self.setAutoFillBackground(True)
+ palette = QtGui.QPalette(self.palette())
+ palette.setBrush(QtGui.QPalette.Window, brush)
+ self.setPalette(palette)
+ self.setFixedSize(*size)
+ if system.systemType in ['Darwin']:
+ #the mac's nice looking messes up with the colors
+ if QtCore.QT_VERSION < 0x40500:
+ self.setAttribute(QtCore.Qt.WA_MacMetalStyle, False)
+ else:
+ self.setAttribute(QtCore.Qt.WA_MacBrushedMetal, False)
+
+
+class QLegendWindow(QtGui.QWidget):
+ """
+ QLegendWindow contains a list of QLegendBox and its description
+
+ """
+ def __init__(self, v1Name='', v2Name='', parent=None,
+ f=QtCore.Qt.WindowFlags()):
+ """ QLegendWindow(v1Name: str, v2Name: str,
+ parent: QWidget, f: WindowFlags)
+ -> QLegendWindow
+ Construct a window by default with 4 QLegendBox and 4 QLabels
+
+ """
+ QtGui.QWidget.__init__(self, parent, f | QtCore.Qt.Tool)
+ self.setWindowTitle('Visual Diff Legend')
+ self.firstTime = True
+ self.gridLayout = QtGui.QGridLayout(self)
+ self.gridLayout.setMargin(10)
+ self.gridLayout.setSpacing(10)
+ self.setFont(CurrentTheme.VISUAL_DIFF_LEGEND_FONT)
+
+ parent = self.parent()
+
+ self.legendV1Box = QLegendBox(
+ CurrentTheme.VISUAL_DIFF_FROM_VERSION_BRUSH,
+ CurrentTheme.VISUAL_DIFF_LEGEND_SIZE,
+ self)
+ self.gridLayout.addWidget(self.legendV1Box, 0, 0)
+ self.legendV1 = QtGui.QLabel(v1Name, self)
+ self.gridLayout.addWidget(self.legendV1, 0, 1)
+
+ self.legendV2Box = QLegendBox(
+ CurrentTheme.VISUAL_DIFF_TO_VERSION_BRUSH,
+ CurrentTheme.VISUAL_DIFF_LEGEND_SIZE,
+ self)
+ self.gridLayout.addWidget(self.legendV2Box, 1, 0)
+ self.legendV2 = QtGui.QLabel(v2Name, self)
+ self.gridLayout.addWidget(self.legendV2, 1, 1)
+
+ self.legendV12Box = QLegendBox(CurrentTheme.VISUAL_DIFF_SHARED_BRUSH,
+ CurrentTheme.VISUAL_DIFF_LEGEND_SIZE,
+ self)
+ self.gridLayout.addWidget(self.legendV12Box, 2, 0)
+ self.legendV12 = QtGui.QLabel("Shared", self)
+ self.gridLayout.addWidget(self.legendV12, 2, 1)
+
+ self.legendParamBox = QLegendBox(
+ CurrentTheme.VISUAL_DIFF_PARAMETER_CHANGED_BRUSH,
+ CurrentTheme.VISUAL_DIFF_LEGEND_SIZE,
+ self)
+ self.gridLayout.addWidget(self.legendParamBox,3,0)
+ self.legendParam = QtGui.QLabel("Parameter Changes", self)
+ self.gridLayout.addWidget(self.legendParam,3,1)
+
+ # self.legendMatchedBox = \
+ # QLegendBox(CurrentTheme.VISUAL_DIFF_MATCH_BRUSH,
+ # CurrentTheme.VISUAL_DIFF_LEGEND_SIZE,
+ # self)
+ # self.gridLayout.addWidget(self.legendMatchedBox, 4, 0)
+ # self.legendMatched = QtGui.QLabel("Matched", self)
+ # self.gridLayout.addWidget(self.legendMatched, 4, 1)
+
+ self.adjustSize()
+
+ def set_names(self, v1_name, v2_name):
+ self.legendV1.setText(v1_name)
+ self.legendV2.setText(v2_name)
+
+ def closeEvent(self,e):
+ """ closeEvent(e: QCloseEvent) -> None
+ Doesn't allow the Legend widget to close, but just hide
+ instead
+
+ """
+ e.ignore()
+ self.parent().showLegendsAction.setChecked(False)
+
+class QDiffProperties(QtGui.QWidget, QVistrailsPaletteInterface):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+
+ self.controller = None
+ self.set_title("Diff Properties")
+
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(0)
+ layout.setSpacing(0)
+ self.legend = QLegendWindow()
+ legend_group = QtGui.QGroupBox("Legend")
+ g_layout = QtGui.QVBoxLayout()
+ g_layout.setMargin(0)
+ g_layout.setSpacing(0)
+ g_layout.addWidget(self.legend)
+ legend_group.setLayout(g_layout)
+ layout.addWidget(legend_group)
+
+ self.params = QParamTable()
+ params_group = QtGui.QGroupBox("Parameter Changes")
+ g_layout = QtGui.QVBoxLayout()
+ g_layout.setMargin(0)
+ g_layout.setSpacing(0)
+ g_layout.addWidget(self.params)
+ params_group.setLayout(g_layout)
+ layout.addWidget(params_group)
+ self.setLayout(layout)
+ self.addButtonsToToolbar()
+
+ def addButtonsToToolbar(self):
+ # Add the create analogy action
+ self.createAnalogyAction = QtGui.QAction(
+ CurrentTheme.VISUAL_DIFF_CREATE_ANALOGY_ICON,
+ 'Create analogy', None, triggered=self.createAnalogy)
+ self.toolWindow().toolbar.insertAction(self.toolWindow().pinAction,
+ self.createAnalogyAction)
+ self.toolWindow().toolbar.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
+
+ def createAnalogy(self):
+ if not hasattr(self.controller, 'current_diff'):
+ return
+ ((vistrail_a, version_a), (vistrail_b, version_b)) = \
+ self.controller.current_diff_versions
+ # analogy only works on single vistrail
+ if not vistrail_a == vistrail_b:
+ return
+
+
+ default = 'from %s to %s' % (self.v1_name, self.v2_name)
+ (result, ok) = QtGui.QInputDialog.getText(None, "Enter Analogy Name",
+ "Name of analogy:",
+ QtGui.QLineEdit.Normal,
+ default)
+ if not ok:
+ return
+ result = str(result)
+ try:
+ self.controller.add_analogy(result, version_a, version_b)
+ except:
+ debug.critical("Analogy name already exists")
+
+ def set_diff(self):
+ if not hasattr(self.controller, 'current_diff'):
+ return
+ ((vistrail_a, version_a), (vistrail_b, version_b)) = \
+ self.controller.current_diff_versions
+ (p1, p2, v1Andv2, heuristicMatch, v1Only, v2Only, paramChanged) = \
+ self.controller.current_diff
+
+ # Set up the version name correctly
+ v1_name = vistrail_a.getVersionName(version_a)
+ if not v1_name:
+ v1_name = 'Version %d' % version_a
+ v2_name = vistrail_b.getVersionName(version_b)
+ if not v2_name:
+ v2_name = 'Version %d' % version_b
+
+ # Add vistrail name if necessary
+ if id(vistrail_a) != id(vistrail_b):
+ if vistrail_a.locator is not None:
+ v1_name = "%s : %s" % (vistrail_a.locator.short_name, v1_name)
+ else:
+ v1_name = "Vistrail A : %s" % v1_name
+ if vistrail_b.locator is not None:
+ v2_name = "%s : %s" % (vistrail_b.locator.short_name, v2_name)
+ else:
+ v2_name = "Vistrail B : %s" % v2_name
+
+ self.v1_name, self.v2_name = v1_name, v2_name
+
+ self.legend.set_names(v1_name, v2_name)
+ self.params.set_names(v1_name, v2_name)
+
+ def set_controller(self, controller=None):
+ self.controller = controller
+ self.set_diff()
+
+ def update_module(self, module=None):
+ """ moduleSelected(id: int, selectedItems: [QGraphicsItem]) -> None
+ When the user click on a module, display its parameter changes
+ in the Inspector
+
+ """
+ if module is None or not hasattr(self.controller, 'current_diff'):
+ self.params.model().clearList()
+ return
+
+ # Interprete the diff result and setup item models
+ (p1, p2, v1Andv2, heuristicMatch, v1Only, v2Only, paramChanged) = \
+ self.controller.current_diff
+
+ # # Set the window title
+ # if id>self.maxId1:
+ # self.inspector.setWindowTitle('Parameter Changes - %s' %
+ # p2.modules[id-self.maxId1-1].name)
+ # else:
+ # self.inspector.setWindowTitle('Parameter Changes - %s' %
+ # p1.modules[id].name)
+
+ # FIXME set the module name/package info?
+
+ # Clear the old inspector
+ param_model = self.params.model()
+ # annotations = self.inspector.annotationsTab.model()
+ param_model.clearList()
+ # annotations.clearList()
+
+ # Find the parameter changed module
+ matching = None
+ for ((m1id, m2id), paramMatching) in paramChanged:
+ if m1id == module.id:
+ #print "found match"
+ matching = paramMatching
+ break
+
+ #print "matching:", matching
+ # If the module has no parameter changed, just display nothing
+ if not matching:
+ return
+
+ # Else just layout the diff on a table
+ param_model.insertRows(0,len(matching))
+ currentRow = 0
+ for (f1, f2) in matching:
+ if f1[0]!=None:
+ param_model.setData(
+ param_model.index(currentRow, 0),
+ '%s(%s)' % (f1[0], ','.join(v[1] for v in f1[1])))
+ if f2[0]!=None:
+ param_model.setData(
+ param_model.index(currentRow, 1),
+ '%s(%s)' % (f2[0], ','.join(v[1] for v in f2[1])))
+ if f1==f2:
+ param_model.disableRow(currentRow)
+ currentRow += 1
+
+ self.params.resizeRowsToContents()
+ # self.inspector.annotationsTab.resizeRowsToContents()
+
+class QDiffView(QPipelineView):
+ def __init__(self, parent=None):
+ QPipelineView.__init__(self, parent)
+ self.set_title("Diff")
+ self.diff = None
+ self.diff_versions = None
+ self.controller = None
+ self.setReadOnlyMode(True)
+
+ def set_action_links(self):
+ self.action_links = \
+ {'copy': ('module_changed', self.has_selected_modules),
+ 'showGroup': ('module_changed', self.has_selected_group),
+ 'configureModule': ('module_changed', self.has_selected_module),
+ 'documentModule': ('module_changed', self.has_selected_module),
+ }
+
+ def set_action_defaults(self):
+ self.action_defaults.update(
+ {'execute' : [('setEnabled', False, False)],
+ 'history' : [('setEnabled', False, False)],
+ 'search' : [('setEnabled', False, False)],
+ 'explore' : [('setEnabled', False, False)],
+ 'provenance' : [('setEnabled', False, False)],
+ 'mashup' : [('setEnabled', False, False)]
+ })
+
+ def set_to_current(self):
+ self.controller.set_pipeline_view(self)
+ self.controller.current_diff = self.diff
+ self.controller.current_diff_versions = self.diff_versions
+
+ def set_default_layout(self):
+ from vistrails.gui.module_palette import QModulePalette
+ self.set_palette_layout(
+ {QtCore.Qt.LeftDockWidgetArea: QModulePalette,
+ QtCore.Qt.RightDockWidgetArea: QDiffProperties,
+ })
+
+ def version_changed(self):
+ pass
+
+ def set_controller(self, controller):
+ self.controller = controller
+ self.scene().controller = controller
+
+ def get_long_title(self):
+ return self.long_title
+
+ def set_diff_version_names(self):
+ ((vistrail_a, version_a), (vistrail_b, version_b)) = self.diff_versions
+
+ # Set up the version name correctly
+ v1_name = vistrail_a.getVersionName(version_a)
+ if not v1_name:
+ v1_name = 'Version %d' % version_a
+ v2_name = vistrail_b.getVersionName(version_b)
+ if not v2_name:
+ v2_name = 'Version %d' % version_b
+
+ # Add vistrail name if necessary
+ if id(vistrail_a) != id(vistrail_b):
+ if vistrail_a.locator is not None:
+ v1_name = "%s : %s" % (vistrail_a.locator.short_name, v1_name)
+ else:
+ v1_name = "Vistrail A : %s" % v1_name
+ if vistrail_b.locator is not None:
+ v2_name = "%s : %s" % (vistrail_b.locator.short_name, v2_name)
+ else:
+ v2_name = "Vistrail B : %s" % v2_name
+ title = "Diff: %s x %s"%(v1_name, v2_name)
+ else:
+ title = "Diff: %s x %s from %s" % (v1_name, v2_name,
+ self.vistrail_view.get_name())
+ self.v1_name = v1_name
+ self.v2_name = v2_name
+ self.set_long_title(title)
+
+ def set_diff(self, version_a, version_b, vistrail_b=None):
+ # Interprete the diff result
+ vistrail_a = self.controller.vistrail
+ if vistrail_b is None:
+ vistrail_b = self.controller.vistrail
+ self.diff_versions = ((vistrail_a, version_a),
+ (vistrail_b, version_b))
+ self.set_diff_version_names()
+ self.diff = vistrails.core.db.io.get_workflow_diff(*self.diff_versions)
+ # self.controller.vistrail.get_pipeline_diff(version_a, version_b)
+ (p1, p2, v1Andv2, heuristicMatch, v1Only, v2Only, paramChanged) = \
+ self.diff
+ # print " $$$ v1Andv2:", v1Andv2
+ # print " $$$ heuristicMatch:", heuristicMatch
+ # print " $$$ v1Only", v1Only
+ # print " $$$ v2Only", v2Only
+ # print " $$$ paramChanged", paramChanged
+ p1.validate(False)
+ p2.validate(False)
+ p_both = Pipeline()
+ # the abstraction map is the same for both p1 and p2
+ # p_both.set_abstraction_map(p1.abstraction_map)
+
+ scene = self.scene()
+ scene.clearItems()
+
+ basic_pkg = get_vistrails_basic_pkg_id()
+
+# # FIXME HACK: We will create a dummy object that looks like a
+# # controller so that the qgraphicsmoduleitems and the scene
+# # are happy. It will simply store the pipeline will all
+# # modules and connections of the diff, and know how to copy stuff
+# class DummyController(object):
+# def __init__(self, pip):
+# self.current_pipeline = pip
+# self.search = None
+# def copy_modules_and_connections(self, module_ids, connection_ids):
+# """copy_modules_and_connections(module_ids: [long],
+# connection_ids: [long]) -> str
+# Serializes a list of modules and connections
+# """
+
+# pipeline = Pipeline()
+# # pipeline.set_abstraction_map( \
+# # self.current_pipeline.abstraction_map)
+# for module_id in module_ids:
+# module = self.current_pipeline.modules[module_id]
+# # if module.vtType == Abstraction.vtType:
+# # abstraction = \
+# # pipeline.abstraction_map[module.abstraction_id]
+# # pipeline.add_abstraction(abstraction)
+# pipeline.add_module(module)
+# for connection_id in connection_ids:
+# connection = self.current_pipeline.connections[connection_id]
+# pipeline.add_connection(connection)
+# return core.db.io.serialize(pipeline)
+
+# controller = DummyController(p_both)
+# scene.controller = controller
+
+ # Find the max version id from v1 and start the adding process
+ self.maxId1 = 0
+ for m1id in p1.modules.keys():
+ if m1id>self.maxId1:
+ self.maxId1 = m1id
+ shiftId = self.maxId1 + 1
+
+ # First add all shared modules, just use v1 module id
+ sum1_x = 0.0
+ sum1_y = 0.0
+ sum2_x = 0.0
+ sum2_y = 0.0
+ for (m1id, m2id) in chain(v1Andv2, heuristicMatch):
+ # item = scene.addModule(p1.modules[m1id],
+ # CurrentTheme.VISUAL_DIFF_SHARED_BRUSH)
+ # item.controller = self.controller
+ # p_both.add_module(copy.copy(p1.modules[m1id]))
+ # sum1_x += p1.modules[m1id].location.x
+ # sum1_y += p1.modules[m1id].location.y
+ # sum2_x += p2.modules[m2id].location.x
+ # sum2_y += p2.modules[m2id].location.y
+ # for (m1id, m2id) in heuristicMatch:
+ m1 = p1.modules[m1id]
+ m2 = p2.modules[m2id]
+
+ sum1_x += p1.modules[m1id].location.x
+ sum1_y += p1.modules[m1id].location.y
+ sum2_x += p2.modules[m2id].location.x
+ sum2_y += p2.modules[m2id].location.y
+
+ #this is a hack for modules with a dynamic local registry.
+ #The problem arises when modules have the same name but different
+ #input/output ports. We just make sure that the module we add to
+ # the canvas has the ports from both modules, so we don't have
+ # addconnection errors.
+ port_specs = dict(((p.type, p.name), p) for p in m1.port_spec_list)
+ for p in m2.port_spec_list:
+ p_key = (p.type, p.name)
+ if not p_key in port_specs:
+ m1.add_port_spec(p)
+ elif port_specs[p_key] != p:
+ #if we add this port, we will get port overloading.
+ #To avoid this, just cast the current port to be of
+ # Module or Variant type.
+ old_port_spec = port_specs[p_key]
+ m1.delete_port_spec(old_port_spec)
+ if old_port_spec.type == 'input':
+ m_sig = '(%s:Module)' % basic_pkg
+ else:
+ m_sig = '(%s:Variant)' % basic_pkg
+ new_port_spec = PortSpec(id=old_port_spec.id,
+ name=old_port_spec.name,
+ type=old_port_spec.type,
+ sigstring=m_sig)
+ m1.add_port_spec(new_port_spec)
+
+ item = scene.addModule(p1.modules[m1id],
+ CurrentTheme.VISUAL_DIFF_SHARED_BRUSH)
+ # item = scene.addModule(p1.modules[m1id],
+ # CurrentTheme.VISUAL_DIFF_MATCH_BRUSH)
+ item.controller = self.controller
+ p_both.add_module(copy.copy(p1.modules[m1id]))
+
+ # Then add parameter changed version
+ for ((m1id, m2id), matching) in paramChanged:
+ m1 = p1.modules[m1id]
+ m2 = p2.modules[m2id]
+
+ sum1_x += p1.modules[m1id].location.x
+ sum1_y += p1.modules[m1id].location.y
+ sum2_x += p2.modules[m2id].location.x
+ sum2_y += p2.modules[m2id].location.y
+
+ #this is a hack for modules with a dynamic local registry.
+ #The problem arises when modules have the same name but different
+ #input/output ports. We just make sure that the module we add to
+ # the canvas has the ports from both modules, so we don't have
+ # addconnection errors.
+ port_specs = dict(((p.type, p.name), p) for p in m1.port_spec_list)
+ for p in m2.port_spec_list:
+ p_key = (p.type, p.name)
+ if not p_key in port_specs:
+ m1.add_port_spec(p)
+ elif port_specs[p_key] != p:
+ #if we add this port, we will get port overloading.
+ #To avoid this, just cast the current port to be of
+ # Module or Variant type.
+ old_port_spec = port_specs[p_key]
+ m1.delete_port_spec(old_port_spec)
+ if old_port_spec.type == 'input':
+ m_sig = '(%s:Module)' % basic_pkg
+ else:
+ m_sig = '(%s:Variant)' % basic_pkg
+ new_port_spec = PortSpec(id=old_port_spec.id,
+ name=old_port_spec.name,
+ type=old_port_spec.type,
+ sigstring=m_sig)
+ m1.add_port_spec(new_port_spec)
+
+ item = scene.addModule(p1.modules[m1id],
+ CurrentTheme.VISUAL_DIFF_PARAMETER_CHANGED_BRUSH)
+ item.controller = self.controller
+ p_both.add_module(copy.copy(p1.modules[m1id]))
+
+ total_len = len(v1Andv2) + + len(heuristicMatch) + len(paramChanged)
+ if total_len != 0:
+ avg1_x = sum1_x / total_len
+ avg1_y = sum1_y / total_len
+ avg2_x = sum2_x / total_len
+ avg2_y = sum2_y / total_len
+ else:
+ avg1_x = 0.0
+ avg1_y = 0.0
+ avg2_x = 0.0
+ avg2_y = 0.0
+# avg1_x = sum1_x / total_len if total_len != 0 else 0.0
+# avg1_y = sum1_y / total_len if total_len != 0 else 0.0
+# avg2_x = sum2_x / total_len if total_len != 0 else 0.0
+# avg2_y = sum2_y / total_len if total_len != 0 else 0.0
+
+ # Now add the ones only applicable for v1, still using v1 ids
+ for m1id in v1Only:
+ item = scene.addModule(p1.modules[m1id],
+ CurrentTheme.VISUAL_DIFF_FROM_VERSION_BRUSH)
+ item.controller = self.controller
+ p_both.add_module(copy.copy(p1.modules[m1id]))
+
+ # Now add the ones for v2 only but must shift the ids away from v1
+ for m2id in v2Only:
+ p2_module = copy.copy(p2.modules[m2id])
+ p2_module.id = m2id + shiftId
+ # p2.modules[m2id].id = m2id + shiftId
+ p2_module.location.x -= avg2_x - avg1_x
+ p2_module.location.y -= avg2_y - avg1_y
+ item = scene.addModule(p2_module, #p2.modules[m2id],
+ CurrentTheme.VISUAL_DIFF_TO_VERSION_BRUSH)
+ item.controller = self.controller
+ # p_both.add_module(copy.copy(p2.modules[m2id]))
+ p_both.add_module(p2_module)
+
+
+ # Create a mapping between share modules between v1 and v2
+ v1Tov2 = {}
+ v2Tov1 = {}
+ for (m1id, m2id) in v1Andv2:
+ v1Tov2[m1id] = m2id
+ v2Tov1[m2id] = m1id
+ for (m1id, m2id) in heuristicMatch:
+ v1Tov2[m1id] = m2id
+ v2Tov1[m2id] = m1id
+ for ((m1id, m2id), matching) in paramChanged:
+ v1Tov2[m1id] = m2id
+ v2Tov1[m2id] = m1id
+
+ # Next we're going to add connections, only connections of
+ # v2Only need to shift their ids
+ if p1.connections.keys():
+ connectionShift = max(p1.connections.keys())+1
+ else:
+ connectionShift = 0
+ allConnections = copy.copy(p1.connections)
+ sharedConnections = []
+ v2OnlyConnections = []
+ for (cid2, connection2) in copy.copy(p2.connections.items()):
+ if connection2.sourceId in v2Only:
+ connection2.sourceId += shiftId
+ else:
+ connection2.sourceId = v2Tov1[connection2.sourceId]
+
+ if connection2.destinationId in v2Only:
+ connection2.destinationId += shiftId
+ else:
+ connection2.destinationId = v2Tov1[connection2.destinationId]
+
+ # Is this connection also shared by p1?
+ shared = False
+ for (cid1, connection1) in p1.connections.items():
+ if (connection1.sourceId==connection2.sourceId and
+ connection1.destinationId==connection2.destinationId and
+ connection1.source.name==connection2.source.name and
+ connection1.destination.name==connection2.destination.name):
+ sharedConnections.append(cid1)
+ shared = True
+ break
+ if not shared:
+ allConnections[cid2+connectionShift] = connection2
+ connection2.id = cid2+connectionShift
+ v2OnlyConnections.append(cid2+connectionShift)
+
+ connectionItems = []
+ for c in allConnections.values():
+ p_both.add_connection(copy.copy(c))
+ connectionItems.append(scene.addConnection(c))
+
+ # Color Code connections
+ for c in connectionItems:
+ if c.id in sharedConnections:
+ pass
+ elif c.id in v2OnlyConnections:
+ pen = QtGui.QPen(CurrentTheme.CONNECTION_PEN)
+ pen.setBrush(CurrentTheme.VISUAL_DIFF_TO_VERSION_BRUSH)
+ c.connectionPen = pen
+ else:
+ pen = QtGui.QPen(CurrentTheme.CONNECTION_PEN)
+ pen.setBrush(CurrentTheme.VISUAL_DIFF_FROM_VERSION_BRUSH)
+ c.connectionPen = pen
+
+
+ scene.current_pipeline = p_both
+
+ scene.updateSceneBoundingRect()
+ scene.fitToView(self, True)
+
+class QVisualDiff(QtGui.QMainWindow):
+ """
+ QVisualDiff is a main widget for Visual Diff containing a GL
+ Widget to draw the pipeline
+
+ """
+ def __init__(self, vistrail, v1, v2,
+ controller,
+ parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QVisualDiff(vistrail: Vistrail, v1: str, v2: str,
+ parent: QWidget, f: WindowFlags) -> QVisualDiff
+ Initialize with all
+
+ """
+ # Set up the version name correctly
+ v1Name = vistrail.getVersionName(v1)
+ if not v1Name: v1Name = 'Version %d' % v1
+ v2Name = vistrail.getVersionName(v2)
+ if not v2Name: v2Name = 'Version %d' % v2
+
+ # Actually perform the diff and store its result
+ self.diff = vistrail.get_pipeline_diff(v1, v2)
+
+ self.v1_name = v1Name
+ self.v2_name = v2Name
+ self.v1 = v1
+ self.v2 = v2
+ self.controller = controller
+
+ # Create the top-level Visual Diff window
+ windowDecors = f | QtCore.Qt.Dialog |QtCore.Qt.WindowMaximizeButtonHint
+ QtGui.QMainWindow.__init__(self, parent)
+ self.setWindowTitle('Visual Diff - from %s to %s' % (v1Name, v2Name))
+ self.setMouseTracking(True)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding))
+ self.createPipelineView()
+ self.createToolBar()
+ self.createToolWindows(v1Name, v2Name)
+
+ self.installEventFilter(self)
+
+ def eventFilter(self, object, event):
+ if event.type() == QtCore.QEvent.ShortcutOverride and \
+ event.key() == QtCore.Qt.Key_W and \
+ event.modifiers() == QtCore.Qt.ControlModifier:
+ event.accept()
+ self.close()
+ return QtGui.QMainWindow.eventFilter(self, object, event)
+
+ def closeEvent(self, event):
+ self.inspector.close()
+ self.legendWindow.close()
+
+ def createPipelineView(self):
+ """ createPipelineView() -> None
+ Create a center pipeline view for Visual Diff and setup the
+ view based on the diff result self.diff
+
+ """
+ # Initialize the shape engine
+ self.pipelineView = QPipelineView()
+ self.setCentralWidget(self.pipelineView)
+
+ # Add all the shapes into the view
+ self.createDiffPipeline()
+
+ # Hook shape selecting functions
+ self.connect(self.pipelineView.scene(), QtCore.SIGNAL("moduleSelected"),
+ self.moduleSelected)
+
+ def createToolBar(self):
+ """ createToolBar() -> None
+ Create the default toolbar of Visual Diff window with two
+ buttons to toggle the Parameter Inspector and Legend window
+
+ """
+ # Initialize the Visual Diff toolbar
+ self.toolBar = self.addToolBar('Visual Diff Toolbar')
+ self.toolBar.setMovable(False)
+
+ # Add the Show Parameter Inspector action
+ self.showInspectorAction = self.toolBar.addAction(
+ CurrentTheme.VISUAL_DIFF_SHOW_PARAM_ICON,
+ 'Show Parameter Inspector window')
+ self.showInspectorAction.setCheckable(True)
+ self.connect(self.showInspectorAction, QtCore.SIGNAL("toggled(bool)"),
+ self.toggleShowInspector)
+
+ # Add the Show Legend window action
+ self.showLegendsAction = self.toolBar.addAction(
+ CurrentTheme.VISUAL_DIFF_SHOW_LEGEND_ICON,
+ 'Show Legends')
+ self.showLegendsAction.setCheckable(True)
+ self.connect(self.showLegendsAction, QtCore.SIGNAL("toggled(bool)"),
+ self.toggleShowLegend)
+
+ # Add the create analogy action
+ self.createAnalogyAction = self.toolBar.addAction(
+ CurrentTheme.VISUAL_DIFF_CREATE_ANALOGY_ICON,
+ 'Create analogy')
+ self.connect(self.createAnalogyAction, QtCore.SIGNAL("triggered()"),
+ self.createAnalogy)
+
+ def createAnalogy(self):
+ default = 'from %s to %s' % (self.v1_name, self.v2_name)
+ (result, ok) = QtGui.QInputDialog.getText(None, "Enter Analogy Name",
+ "Name of analogy:",
+ QtGui.QLineEdit.Normal,
+ default)
+ if not ok:
+ return
+ result = str(result)
+ try:
+ self.controller.add_analogy(result, self.v1, self.v2)
+ except:
+ debug.critical("Analogy name already exists")
+
+ def createToolWindows(self, v1Name, v2Name):
+ """ createToolWindows(v1Name: str, v2Name: str) -> None
+ Create Inspector and Legend window
+
+ """
+ self.inspector = QParamInspector(v1Name, v2Name, self)
+ self.inspector.resize(QtCore.QSize(
+ *CurrentTheme.VISUAL_DIFF_PARAMETER_WINDOW_SIZE))
+ self.legendWindow = QLegendWindow(v1Name, v2Name,self)
+
+ def moduleSelected(self, id, selectedItems):
+ """ moduleSelected(id: int, selectedItems: [QGraphicsItem]) -> None
+ When the user click on a module, display its parameter changes
+ in the Inspector
+
+ """
+ if len(selectedItems)!=1 or id==-1:
+ self.moduleUnselected()
+ return
+
+ # Interprete the diff result and setup item models
+ (p1, p2, v1Andv2, heuristicMatch, v1Only, v2Only, paramChanged) = \
+ self.diff
+
+ # Set the window title
+ if id>self.maxId1:
+ self.inspector.setWindowTitle('Parameter Changes - %s' %
+ p2.modules[id-self.maxId1-1].name)
+ else:
+ self.inspector.setWindowTitle('Parameter Changes - %s' %
+ p1.modules[id].name)
+
+ # Clear the old inspector
+ functions = self.inspector.functionsTab.model()
+# annotations = self.inspector.annotationsTab.model()
+ functions.clearList()
+# annotations.clearList()
+
+ # Find the parameter changed module
+ matching = None
+ for ((m1id, m2id), paramMatching) in paramChanged:
+ if m1id==id:
+ matching = paramMatching
+ break
+
+ # If the module has no parameter changed, just display nothing
+ if not matching:
+ return
+
+ # Else just layout the diff on a table
+ functions.insertRows(0,len(matching))
+ currentRow = 0
+ for (f1, f2) in matching:
+ if f1[0]!=None:
+ functions.setData(
+ functions.index(currentRow, 0),
+ '%s(%s)' % (f1[0], ','.join(v[1] for v in f1[1])))
+ if f2[0]!=None:
+ functions.setData(
+ functions.index(currentRow, 1),
+ '%s(%s)' % (f2[0], ','.join(v[1] for v in f2[1])))
+ if f1==f2:
+ functions.disableRow(currentRow)
+ currentRow += 1
+
+ self.inspector.functionsTab.resizeRowsToContents()
+# self.inspector.annotationsTab.resizeRowsToContents()
+
+ def moduleUnselected(self):
+ """ moduleUnselected() -> None
+ When a user selects nothing, make sure to display nothing as well
+
+ """
+# self.inspector.annotationsTab.model().clearList()
+ self.inspector.functionsTab.model().clearList()
+ self.inspector.setWindowTitle('Parameter Changes - None')
+
+ def toggleShowInspector(self):
+ """ toggleShowInspector() -> None
+ Show/Hide the inspector when toggle this button
+
+ """
+ if self.inspector.firstTime:
+ max_geom = QtGui.QApplication.desktop().screenGeometry(self)
+ if (self.frameSize().width() <
+ max_geom.width() - self.inspector.width()):
+ self.inspector.move(self.pos().x()+self.frameSize().width(),
+ self.pos().y())
+ else:
+ self.inspector.move(self.pos().x()+self.frameSize().width()-
+ self.inspector.frameSize().width(),
+ self.pos().y() +
+ self.legendWindow.frameSize().height())
+ self.inspector.firstTime = False
+ self.inspector.setVisible(self.showInspectorAction.isChecked())
+
+ def toggleShowLegend(self):
+ """ toggleShowLegend() -> None
+ Show/Hide the legend window when toggle this button
+
+ """
+ if self.legendWindow.firstTime:
+ self.legendWindow.move(self.pos().x()+self.frameSize().width()-
+ self.legendWindow.frameSize().width(),
+ self.pos().y())
+ self.legendWindow.setVisible(self.showLegendsAction.isChecked())
+ if self.legendWindow.firstTime:
+ self.legendWindow.firstTime = False
+ self.legendWindow.setFixedSize(self.legendWindow.size())
+
+ def createDiffPipeline(self):
+ """ createDiffPipeline() -> None
+ Actually walk through the self.diff result and add all modules
+ into the pipeline view
+
+ """
+
+ # Interprete the diff result
+ (p1, p2, v1Andv2, heuristicMatch, v1Only, v2Only, paramChanged) = \
+ self.diff
+ self.controller.validate(p1, False)
+ self.controller.validate(p2, False)
+ p_both = Pipeline()
+ # the abstraction map is the same for both p1 and p2
+ # p_both.set_abstraction_map(p1.abstraction_map)
+
+ scene = self.pipelineView.scene()
+ scene.clearItems()
+
+ basic_pkg = get_vistrails_basic_pkg_id()
+
+ # FIXME HACK: We will create a dummy object that looks like a
+ # controller so that the qgraphicsmoduleitems and the scene
+ # are happy. It will simply store the pipeline will all
+ # modules and connections of the diff, and know how to copy stuff
+ class DummyController(object):
+ def __init__(self, pip):
+ self.current_pipeline = pip
+ self.search = None
+ def copy_modules_and_connections(self, module_ids, connection_ids):
+ """copy_modules_and_connections(module_ids: [long],
+ connection_ids: [long]) -> str
+ Serializes a list of modules and connections
+ """
+
+ pipeline = Pipeline()
+# pipeline.set_abstraction_map( \
+# self.current_pipeline.abstraction_map)
+ for module_id in module_ids:
+ module = self.current_pipeline.modules[module_id]
+# if module.vtType == Abstraction.vtType:
+# abstraction = \
+# pipeline.abstraction_map[module.abstraction_id]
+# pipeline.add_abstraction(abstraction)
+ pipeline.add_module(module)
+ for connection_id in connection_ids:
+ connection = self.current_pipeline.connections[connection_id]
+ pipeline.add_connection(connection)
+ return vistrails.core.db.io.serialize(pipeline)
+
+ controller = DummyController(p_both)
+ scene.controller = controller
+
+ # Find the max version id from v1 and start the adding process
+ self.maxId1 = 0
+ for m1id in p1.modules.keys():
+ if m1id>self.maxId1:
+ self.maxId1 = m1id
+ shiftId = self.maxId1 + 1
+
+ # First add all shared modules, just use v1 module id
+ sum1_x = 0.0
+ sum1_y = 0.0
+ sum2_x = 0.0
+ sum2_y = 0.0
+ for (m1id, m2id) in v1Andv2:
+ item = scene.addModule(p1.modules[m1id],
+ CurrentTheme.VISUAL_DIFF_SHARED_BRUSH)
+ item.controller = controller
+ p_both.add_module(copy.copy(p1.modules[m1id]))
+ sum1_x += p1.modules[m1id].location.x
+ sum1_y += p1.modules[m1id].location.y
+ sum2_x += p2.modules[m2id].location.x
+ sum2_y += p2.modules[m2id].location.y
+ for (m1id, m2id) in heuristicMatch:
+ m1 = p1.modules[m1id]
+ m2 = p2.modules[m2id]
+
+ sum1_x += p1.modules[m1id].location.x
+ sum1_y += p1.modules[m1id].location.y
+ sum2_x += p2.modules[m2id].location.x
+ sum2_y += p2.modules[m2id].location.y
+
+ #this is a hack for modules with a dynamic local registry.
+ #The problem arises when modules have the same name but different
+ #input/output ports. We just make sure that the module we add to
+ # the canvas has the ports from both modules, so we don't have
+ # addconnection errors.
+ port_specs = dict(((p.type, p.name), p) for p in m1.port_spec_list)
+ for p in m2.port_spec_list:
+ p_key = (p.type, p.name)
+ if not p_key in port_specs:
+ m1.add_port_spec(p)
+ elif port_specs[p_key] != p:
+ #if we add this port, we will get port overloading.
+ #To avoid this, just cast the current port to be of
+ # Module or Variant type.
+ old_port_spec = port_specs[p_key]
+ m1.delete_port_spec(old_port_spec)
+ if old_port_spec.type == 'input':
+ m_sig = '(%s:Module)' % basic_pkg
+ else:
+ m_sig = '(%s:Variant)' % basic_pkg
+ new_port_spec = PortSpec(id=old_port_spec.id,
+ name=old_port_spec.name,
+ type=old_port_spec.type,
+ sigstring=m_sig)
+ m1.add_port_spec(new_port_spec)
+
+ item = scene.addModule(p1.modules[m1id],
+ CurrentTheme.VISUAL_DIFF_MATCH_BRUSH)
+ item.controller = controller
+ p_both.add_module(copy.copy(p1.modules[m1id]))
+
+ # Then add parameter changed version
+ for ((m1id, m2id), matching) in paramChanged:
+ m1 = p1.modules[m1id]
+ m2 = p2.modules[m2id]
+
+ sum1_x += p1.modules[m1id].location.x
+ sum1_y += p1.modules[m1id].location.y
+ sum2_x += p2.modules[m2id].location.x
+ sum2_y += p2.modules[m2id].location.y
+
+ #this is a hack for modules with a dynamic local registry.
+ #The problem arises when modules have the same name but different
+ #input/output ports. We just make sure that the module we add to
+ # the canvas has the ports from both modules, so we don't have
+ # addconnection errors.
+ port_specs = dict(((p.type, p.name), p) for p in m1.port_spec_list)
+ for p in m2.port_spec_list:
+ p_key = (p.type, p.name)
+ if not p_key in port_specs:
+ m1.add_port_spec(p)
+ elif port_specs[p_key] != p:
+ #if we add this port, we will get port overloading.
+ #To avoid this, just cast the current port to be of
+ # Module or Variant type.
+ old_port_spec = port_specs[p_key]
+ m1.delete_port_spec(old_port_spec)
+ if old_port_spec.type == 'input':
+ m_sig = '(%s:Module)' % basic_pkg
+ else:
+ m_sig = '(%s:Variant)' % basic_pkg
+ new_port_spec = PortSpec(id=old_port_spec.id,
+ name=old_port_spec.name,
+ type=old_port_spec.type,
+ sigstring=m_sig)
+ m1.add_port_spec(new_port_spec)
+
+ item = scene.addModule(p1.modules[m1id],
+ CurrentTheme.VISUAL_DIFF_PARAMETER_CHANGED_BRUSH)
+ item.controller = controller
+ p_both.add_module(copy.copy(p1.modules[m1id]))
+
+ total_len = len(v1Andv2) + + len(heuristicMatch) + len(paramChanged)
+ if total_len != 0:
+ avg1_x = sum1_x / total_len
+ avg1_y = sum1_y / total_len
+ avg2_x = sum2_x / total_len
+ avg2_y = sum2_y / total_len
+ else:
+ avg1_x = 0.0
+ avg1_y = 0.0
+ avg2_x = 0.0
+ avg2_y = 0.0
+# avg1_x = sum1_x / total_len if total_len != 0 else 0.0
+# avg1_y = sum1_y / total_len if total_len != 0 else 0.0
+# avg2_x = sum2_x / total_len if total_len != 0 else 0.0
+# avg2_y = sum2_y / total_len if total_len != 0 else 0.0
+
+ # Now add the ones only applicable for v1, still using v1 ids
+ for m1id in v1Only:
+ item = scene.addModule(p1.modules[m1id],
+ CurrentTheme.VISUAL_DIFF_FROM_VERSION_BRUSH)
+ item.controller = controller
+ p_both.add_module(copy.copy(p1.modules[m1id]))
+
+ # Now add the ones for v2 only but must shift the ids away from v1
+ for m2id in v2Only:
+ p2_module = copy.copy(p2.modules[m2id])
+ p2_module.id = m2id + shiftId
+ # p2.modules[m2id].id = m2id + shiftId
+ p2_module.location.x -= avg2_x - avg1_x
+ p2_module.location.y -= avg2_y - avg1_y
+ item = scene.addModule(p2_module, #p2.modules[m2id],
+ CurrentTheme.VISUAL_DIFF_TO_VERSION_BRUSH)
+ item.controller = controller
+ # p_both.add_module(copy.copy(p2.modules[m2id]))
+ p_both.add_module(p2_module)
+
+
+ # Create a mapping between share modules between v1 and v2
+ v1Tov2 = {}
+ v2Tov1 = {}
+ for (m1id, m2id) in v1Andv2:
+ v1Tov2[m1id] = m2id
+ v2Tov1[m2id] = m1id
+ for (m1id, m2id) in heuristicMatch:
+ v1Tov2[m1id] = m2id
+ v2Tov1[m2id] = m1id
+ for ((m1id, m2id), matching) in paramChanged:
+ v1Tov2[m1id] = m2id
+ v2Tov1[m2id] = m1id
+
+ # Next we're going to add connections, only connections of
+ # v2Only need to shift their ids
+ if p1.connections.keys():
+ connectionShift = max(p1.connections.keys())+1
+ else:
+ connectionShift = 0
+ allConnections = copy.copy(p1.connections)
+ sharedConnections = []
+ v2OnlyConnections = []
+ for (cid2, connection2) in copy.copy(p2.connections.items()):
+ if connection2.sourceId in v2Only:
+ connection2.sourceId += shiftId
+ else:
+ connection2.sourceId = v2Tov1[connection2.sourceId]
+
+ if connection2.destinationId in v2Only:
+ connection2.destinationId += shiftId
+ else:
+ connection2.destinationId = v2Tov1[connection2.destinationId]
+
+ # Is this connection also shared by p1?
+ shared = False
+ for (cid1, connection1) in p1.connections.items():
+ if (connection1.sourceId==connection2.sourceId and
+ connection1.destinationId==connection2.destinationId and
+ connection1.source.name==connection2.source.name and
+ connection1.destination.name==connection2.destination.name):
+ sharedConnections.append(cid1)
+ shared = True
+ break
+ if not shared:
+ allConnections[cid2+connectionShift] = connection2
+ connection2.id = cid2+connectionShift
+ v2OnlyConnections.append(cid2+connectionShift)
+
+ connectionItems = []
+ for c in allConnections.values():
+ p_both.add_connection(copy.copy(c))
+ connectionItems.append(scene.addConnection(c))
+
+ # Color Code connections
+ for c in connectionItems:
+ if c.id in sharedConnections:
+ pass
+ elif c.id in v2OnlyConnections:
+ pen = QtGui.QPen(CurrentTheme.CONNECTION_PEN)
+ pen.setBrush(CurrentTheme.VISUAL_DIFF_TO_VERSION_BRUSH)
+ c.connectionPen = pen
+ else:
+ pen = QtGui.QPen(CurrentTheme.CONNECTION_PEN)
+ pen.setBrush(CurrentTheme.VISUAL_DIFF_FROM_VERSION_BRUSH)
+ c.connectionPen = pen
+
+
+
+ scene.updateSceneBoundingRect()
+ scene.fitToView(self.pipelineView, True)
diff --git a/vistrails/gui/vistrail_controller.py b/vistrails/gui/vistrail_controller.py
new file mode 100644
index 0000000..c670e3d
--- /dev/null
+++ b/vistrails/gui/vistrail_controller.py
@@ -0,0 +1,1558 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+from vistrails.core.common import *
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core import debug
+import vistrails.core.db.action
+import vistrails.core.db.locator
+import vistrails.core.modules.vistrails_module
+from vistrails.core.utils import VistrailsInternalError, InvalidPipeline
+from vistrails.core.layout.version_tree_layout import VistrailsTreeLayoutLW
+from vistrails.core.log.opm_graph import OpmGraph
+from vistrails.core.log.prov_document import ProvDocument
+from vistrails.core.modules.abstraction import identifier as abstraction_pkg
+from vistrails.core.modules.module_registry import get_module_registry, MissingPort
+from vistrails.core.modules.package import Package
+from vistrails.core.packagemanager import PackageManager
+from vistrails.core.query.version import TrueSearch
+from vistrails.core.query.visual import VisualQuery
+from vistrails.core.param_explore import ActionBasedParameterExploration
+import vistrails.core.system
+
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.vistrail.controller import VistrailController as BaseController, \
+ vt_action
+from vistrails.core.vistrail.location import Location
+from vistrails.core.vistrail.module import Module
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.vistrail.port_spec import PortSpec
+from vistrails.core.vistrail.vistrail import Vistrail, TagExists
+from vistrails.core.interpreter.default import get_default_interpreter
+from vistrails.gui.pipeline_view import QPipelineView
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.utils import show_warning, show_question, YES_BUTTON, NO_BUTTON
+from vistrails.gui.version_prop import QVersionProp
+
+import vistrails.core.analogy
+import copy
+import os.path
+import math
+
+import unittest
+import vistrails.gui.utils
+import vistrails.api
+import os
+from vistrails.core.utils import DummyView
+
+################################################################################
+
+class VistrailController(QtCore.QObject, BaseController):
+ """
+ VistrailController is the class handling all action control in
+ VisTrails. It updates pipeline, vistrail and emit signals to
+ update the view
+
+ Signals emitted:
+
+ vistrailChanged(): emitted when the version tree needs to be
+ recreated (for example, a node was added/deleted or the layout
+ changed).
+
+ versionWasChanged(): emitted when the current version (the one
+ being displayed by the pipeline view) has changed.
+
+ searchChanged(): emitted when the search statement from the
+ version view has changed.
+
+ stateChanged(): stateChanged is called when a vistrail goes from
+ unsaved to saved or vice-versa.
+
+ notesChanged(): notesChanged is called when the version notes have
+ been updated
+
+ """
+
+ def __init__(self, vistrail=None, locator=None, abstractions=None,
+ thumbnails=None, mashups=None, pipeline_view=None,
+ id_scope=None, set_log_on_vt=True, auto_save=True, name=''):
+ """ VistrailController(vistrail: Vistrail,
+ locator: BaseLocator,
+ abstractions: [<filename strings>],
+ thumbnails: [<filename strings>],
+ mashups: [<filename strings>],
+ pipeline_view: QPipelineView
+ id_scope: IdScope,
+ set_log_on_vt: bool,
+ auto_save: bool,
+ name: str) -> VistrailController
+ Create a controller for a vistrail.
+
+ """
+
+ QtCore.QObject.__init__(self)
+
+ if pipeline_view is None:
+ self.current_pipeline_view = QPipelineView()
+ else:
+ self.current_pipeline_view = pipeline_view
+
+ self.vistrail_view = None
+ self.reset_pipeline_view = False
+ self.reset_version_view = True
+ self.quiet = False
+
+ self.analogy = {}
+ # if self._auto_save is True, an auto_saving timer will save a temporary
+ # file every 2 minutes
+ self._auto_save = auto_save
+ self.timer = None
+ if self._auto_save:
+ self.setup_timer()
+
+ self._previous_graph_layout = None
+
+ def width_f(text):
+ return CurrentTheme.VERSION_FONT_METRIC.width(text)
+ self._current_graph_layout = \
+ VistrailsTreeLayoutLW(width_f,
+ CurrentTheme.VERSION_FONT_METRIC.height(),
+ CurrentTheme.VERSION_LABEL_MARGIN[0],
+ CurrentTheme.VERSION_LABEL_MARGIN[1])
+ self.animate_layout = False
+ #this was moved to BaseController
+ #self.num_versions_always_shown = 1
+ BaseController.__init__(self, vistrail, locator, abstractions,
+ thumbnails, mashups, id_scope, set_log_on_vt,
+ auto_save)
+
+ def _get_current_pipeline_scene(self):
+ return self.current_pipeline_view.scene()
+ current_pipeline_scene = property(_get_current_pipeline_scene)
+
+ # just need to switch current_pipeline_view to update controller to
+ # new version and pipeline...
+ def _get_current_version(self):
+ if self.current_pipeline_view is None:
+ return -1
+ return self.current_pipeline_view.scene().current_version
+ def _set_current_version(self, version):
+ # print "set_current_version:", version, id(self.current_pipeline_view)
+ if self.current_pipeline_view is not None:
+ self.current_pipeline_view.scene().current_version = version
+ current_version = property(_get_current_version, _set_current_version)
+
+ def _get_current_pipeline(self):
+ if self.current_pipeline_view is None:
+ return None
+ return self.current_pipeline_view.scene().current_pipeline
+ def _set_current_pipeline(self, pipeline):
+ if self.current_pipeline_view is not None:
+ self.current_pipeline_view.scene().current_pipeline = pipeline
+ current_pipeline = property(_get_current_pipeline, _set_current_pipeline)
+
+ def set_pipeline_view(self, pipeline_view):
+ if self.current_pipeline_view is not None:
+ self.disconnect(self, QtCore.SIGNAL('versionWasChanged'),
+ self.current_pipeline_view.version_changed)
+ self.current_pipeline_view = pipeline_view
+ self.connect(self, QtCore.SIGNAL('versionWasChanged'),
+ self.current_pipeline_view.version_changed)
+
+ def setup_timer(self):
+ self.timer = QtCore.QTimer(self)
+ self.connect(self.timer, QtCore.SIGNAL("timeout()"), self.write_temporary)
+ self.timer.start(1000 * 60 * 2) # Save every two minutes
+
+ def stop_timer(self):
+ if self.timer:
+ self.disconnect(self.timer, QtCore.SIGNAL("timeout()"), self.write_temporary)
+ self.timer.stop()
+
+ ##########################################################################
+ # Signal vistrail relayout / redraw
+
+ def replace_unnamed_node_in_version_tree(self, old_version, new_version):
+ """method analogous to invalidate_version_tree but when only
+ a single unnamed node and links need to be updated. Much faster."""
+ self.reset_version_view = False
+ try:
+ self.emit(QtCore.SIGNAL('invalidateSingleNodeInVersionTree'),
+ old_version, new_version)
+ finally:
+ self.reset_version_view = True
+
+ def invalidate_version_tree(self, reset_version_view=True, animate_layout=False):
+ """ invalidate_version_tree(reset_version_tree: bool, animate_layout: bool) -> None
+
+ """
+ self.reset_version_view = reset_version_view
+ self.animate_layout = animate_layout
+ #FIXME: in the future, rename the signal
+ try:
+ self.emit(QtCore.SIGNAL('vistrailChanged()'))
+ finally:
+ self.reset_version_view = True
+
+ def has_move_actions(self):
+ return self.current_pipeline_scene.hasMoveActions()
+
+ def flush_move_actions(self):
+ return self.current_pipeline_scene.flushMoveActions()
+
+ ##########################################################################
+ # Pipeline View Methods
+
+ def updatePipelineScene(self):
+ self.current_pipeline_scene.setupScene(self.current_pipeline)
+
+ ##########################################################################
+ # Autosave
+
+ def enable_autosave(self):
+ self._auto_save = True
+
+ def disable_autosave(self):
+ self._auto_save = False
+
+ def get_locator(self):
+ from vistrails.gui.application import get_vistrails_application
+ if (self._auto_save and
+ get_vistrails_application().configuration.check('autosave')):
+ if self.locator is None:
+ raise ValueError("locator is None")
+ return self.locator
+ else:
+ return None
+
+ def cleanup(self):
+ locator = self.get_locator()
+ if locator:
+ locator.clean_temporaries()
+ if self._auto_save or self.timer:
+ self.stop_timer()
+ # close associated mashup apps
+ version_prop = QVersionProp.instance()
+ for app in version_prop.versionMashups.apps.values():
+ if app and app.view == self.vistrail_view:
+ app.close()
+
+
+ ##########################################################################
+ # Actions, etc
+
+ def perform_action(self, action, quiet=None):
+ """ performAction(action: Action, quiet=None) -> timestep
+
+ performs given action on current pipeline.
+
+ quiet and self.quiet control invalidation of version
+ tree. If quiet is set to any value, it overrides the field
+ value self.quiet.
+
+ If the value is True, then no invalidation happens (gui is not
+ updated.)
+
+ """
+ if action is not None:
+ BaseController.perform_action(self,action)
+
+ if quiet is None:
+ if not self.quiet:
+ self.invalidate_version_tree(False)
+ else:
+ if not quiet:
+ self.invalidate_version_tree(False)
+ return action.db_id
+ return None
+
+ def add_new_action(self, action, description=None):
+ """add_new_action(action) -> None
+
+ Call this function to add a new action to the vistrail being
+ controlled by the vistrailcontroller.
+
+ FIXME: In the future, this function should watch the vistrail
+ and get notified of the change.
+
+ """
+ if action is not None:
+ BaseController.add_new_action(self, action, description)
+ self.emit(QtCore.SIGNAL("new_action"), action)
+ self.recompute_terse_graph()
+
+ ##########################################################################
+
+ def add_module(self, x, y, identifier, name, namespace='',
+ internal_version=-1):
+ return BaseController.add_module(self, identifier, name, namespace, x, y,
+ internal_version)
+
+ def create_abstraction_with_prompt(self, module_ids, connection_ids,
+ name=""):
+ name = self.get_abstraction_name(name)
+ if name is None:
+ return
+ return self.create_abstraction(module_ids, connection_ids, name)
+
+ def update_notes(self, notes):
+ """
+ Parameters
+ ----------
+
+ - notes : 'string'
+
+ """
+ self.flush_delayed_actions()
+
+ if self.vistrail.set_notes(self.current_version, str(notes)):
+ self.emit(QtCore.SIGNAL('notesChanged()'))
+
+ ##########################################################################
+ # Workflow Execution
+
+ def execute_workflow_list(self, vistrails):
+ old_quiet = self.quiet
+ self.quiet = True
+ self.current_pipeline_scene.reset_module_colors()
+ self.current_pipeline_scene.update()
+ (results, changed) = BaseController.execute_workflow_list(self,
+ vistrails)
+ self.quiet = old_quiet
+ if changed:
+ self.invalidate_version_tree(False)
+ return (results, changed)
+
+ def execute_current_workflow(self, custom_aliases=None, custom_params=None,
+ reason='Pipeline Execution', sinks=None):
+ """ execute_current_workflow() -> None
+ Execute the current workflow (if exists)
+
+ """
+ self.flush_delayed_actions()
+ if self.current_pipeline:
+ locator = self.get_locator()
+ if locator:
+ locator.clean_temporaries()
+ locator.save_temporary(self.vistrail)
+ return self.execute_workflow_list([(self.locator,
+ self.current_version,
+ self.current_pipeline,
+ self.current_pipeline_scene,
+ custom_aliases,
+ custom_params,
+ reason,
+ sinks,
+ None)])
+ return ([], False)
+
+ def enable_missing_package(self, identifier, deps):
+ configuration = get_vistrails_configuration()
+ if getattr(configuration, 'enablePackagesSilently', False):
+ return True
+
+ msg = "VisTrails needs to enable package '%s'." % identifier
+ if len(deps) > 0:
+ msg += (" This will also enable the dependencies: %s."
+ " Do you want to enable these packages?") % str(deps)
+ else:
+ msg += " Do you want to enable this package?"
+ res = show_question('Enable package?',
+ msg,
+ [YES_BUTTON, NO_BUTTON],
+ YES_BUTTON)
+ if res == NO_BUTTON:
+# QtGui.QMessageBox.warning(get_vistrails_application().builderWindow,
+# 'Missing modules',
+# 'Some necessary modules will be missing.')
+ return False
+ return True
+
+ def install_missing_package(self, identifier):
+ res = show_question('Install package?',
+ "This pipeline contains a module"
+ " in package '%s', which"
+ " is not installed. Do you want to"
+ " install and enable that package?" % \
+ identifier, [YES_BUTTON, NO_BUTTON],
+ YES_BUTTON)
+ return res == YES_BUTTON
+
+ def change_selected_version(self, new_version, report_all_errors=True,
+ do_validate=True, from_root=False):
+ """change_selected_version(new_version: int,
+ report_all_errors: boolean,
+ do_validate: boolean,
+ from_root: boolean)
+
+ Change the current vistrail version into new_version and emit a
+ notification signal.
+
+ NB: in most situations, the following post-condition holds:
+
+ >>> controller.change_selected_version(v)
+ >>> assert v == controller.current_version
+
+ In some occasions, however, the controller will not be able to
+ switch to the desired version. One example where this can
+ happen is when the selected version has obsolete modules (that
+ is, the currently installed package for those modules has
+ module upgrades). In these cases, change_selected_version will
+ return a new version which corresponds to a workflow that was
+ created by the upgrading mechanism that packages can provide.
+
+ """
+
+ try:
+ self.do_version_switch(new_version, report_all_errors,
+ do_validate, from_root)
+ except InvalidPipeline, e:
+ from vistrails.gui.application import get_vistrails_application
+
+
+# def process_err(err):
+# if isinstance(err, Package.InitializationFailed):
+# QtGui.QMessageBox.critical(
+# get_vistrails_application().builderWindow,
+# 'Package load failed',
+# 'Package "%s" failed during initialization. '
+# 'Please contact the developer of that package '
+# 'and report a bug.' % err.package.name)
+# elif isinstance(err, MissingPackage):
+# QtGui.QMessageBox.critical(
+# get_vistrails_application().builderWindow,
+# 'Unavailable package',
+# 'Cannot find package "%s" in\n'
+# 'list of available packages. \n'
+# 'Please install it first.' % err._identifier)
+# elif issubclass(err.__class__, MissingPort):
+# msg = ('Cannot find %s port "%s" for module "%s" '
+# 'in loaded package "%s". A different package '
+# 'version might be necessary.') % \
+# (err._port_type, err._port_name,
+# err._module_name, err._package_name)
+# QtGui.QMessageBox.critical(
+# get_vistrails_application().builderWindow, 'Missing port',
+# msg)
+# else:
+# QtGui.QMessageBox.critical(
+# get_vistrails_application().builderWindow,
+# 'Invalid Pipeline', str(err))
+
+ # VisTrails will not raise upgrade exceptions unless
+ # configured to do so. To get the upgrade requests,
+ # configuration option upgradeModules must be set to True.
+
+ exception_set = e.get_exception_set()
+ if len(exception_set) > 0:
+# msg_box = QtGui.QMessageBox(get_vistrails_application().builderWindow)
+# msg_box.setIcon(QtGui.QMessageBox.Warning)
+# msg_box.setText("The current workflow could not be validated.")
+# msg_box.setInformativeText("Errors occurred when trying to "
+# "construct this workflow.")
+# msg_box.setStandardButtons(QtGui.QMessageBox.Ok)
+# msg_box.setDefaultButton(QtGui.QMessageBox.Ok)
+# msg_box.setDetailedText(str(e))
+# msg_box.exec_()
+ # text = "The current workflow could not be validated."
+ # debug.critical('%s\n%s' % (text, str(e)))
+ debug.critical(str(e))
+
+# print 'got to exception set'
+# # Process all errors as usual
+# if report_all_errors:
+# for exc in exception_set:
+# print 'processing', exc
+# process_err(exc)
+# else:
+# process_err(exception_set.__iter__().next())
+
+ except Exception, e:
+ import traceback
+ debug.critical('Unexpected Exception\n%s' % str(e),
+ traceback.format_exc())
+
+ # FIXME: this code breaks undo/redo, and seems to be ok with normal
+ # pipeline manipulations so I am leaving it commented out for now
+
+ # if not self._current_terse_graph or \
+ # new_version not in self._current_terse_graph.vertices:
+ # self.recompute_terse_graph()
+
+ self.emit(QtCore.SIGNAL('versionWasChanged'), self.current_version)
+
+ def set_search(self, search, text=''):
+ """ set_search(search: SearchStmt, text: str) -> None
+ Change the currrent version tree search statement
+
+ """
+ if self.search != search or self.search_str != text:
+ self.search = search
+ self.search_str = text
+ if self.search:
+ self.search.run(self.vistrail, '')
+ self.invalidate_version_tree(True)
+ if self.refine:
+ # need to recompute the graph because the refined items might
+ # have changed since last time
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(True)
+ else:
+ self.invalidate_version_tree(False)
+
+ self.emit(QtCore.SIGNAL('searchChanged'))
+
+ def set_refine(self, refine):
+ """ set_refine(refine: bool) -> None
+ Set the refine state to True or False
+
+ """
+ if self.refine!=refine:
+ self.refine = refine
+ # need to recompute the graph because the refined items might
+ # have changed since last time
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(True)
+
+ def set_full_tree(self, full):
+ """ set_full_tree(full: bool) -> None
+ Set if Vistrails should show a complete version tree or just a
+ terse tree
+
+ """
+ if full != self.full_tree:
+ self.full_tree = full
+ self.invalidate_version_tree(True)
+
+ def recompute_terse_graph(self):
+ BaseController.recompute_terse_graph(self)
+ self._previous_graph_layout = copy.deepcopy(self._current_graph_layout)
+ self._current_graph_layout.layout_from(self.vistrail,
+ self._current_terse_graph)
+
+ def refine_graph(self, step=1.0):
+ """ refine_graph(step: float in [0,1]) -> (Graph, Graph)
+ Refine the graph of the current vistrail based the search
+ status of the controller. It also return the full graph as a
+ reference
+
+ """
+ if self._current_full_graph is None:
+ self.recompute_terse_graph()
+
+ if not self.animate_layout:
+ return (self._current_terse_graph, self._current_full_graph,
+ self._current_graph_layout)
+
+ graph_layout = copy.deepcopy(self._current_graph_layout)
+ terse_graph = copy.deepcopy(self._current_terse_graph)
+ am = self.vistrail.actionMap
+ step = 1.0/(1.0+math.exp(-(step*12-6))) # use a logistic sigmoid function
+
+ # Adding nodes to tree
+ for (c_id, c_node) in self._current_graph_layout.nodes.iteritems():
+ if self._previous_graph_layout.nodes.has_key(c_id):
+ p_node = self._previous_graph_layout.nodes[c_id]
+ else:
+ p_id = c_id
+ # Find closest child of contained in both graphs
+ while not self._previous_graph_layout.nodes.has_key(p_id):
+ # Should always have exactly one child
+ p_id = [to for (to, _) in \
+ self._current_full_graph.adjacency_list[p_id]
+ if (to in am) and \
+ not self.vistrail.is_pruned(to)][0]
+ p_node = self._previous_graph_layout.nodes[p_id]
+
+ # Interpolate position
+ x = p_node.p.x - c_node.p.x
+ y = p_node.p.y - c_node.p.y
+ graph_layout.move_node(c_id, x*(1.0-step), y*(1.0-step))
+
+ # Removing nodes from tree
+ for (p_id, p_node) in self._previous_graph_layout.nodes.iteritems():
+ if not self._current_graph_layout.nodes.has_key(p_id):
+ # Find closest parent contained in both graphs
+ shared_parent = p_id
+ while (shared_parent > 0 and
+ shared_parent not in self._current_graph_layout.nodes):
+ shared_parent = \
+ self._current_full_graph.parent(shared_parent)
+
+ # Find closest child contained in both graphs
+ c_id = p_id
+ while not self._current_graph_layout.nodes.has_key(c_id):
+ # Should always have exactly one child
+ c_id = [to for (to, _) in \
+ self._current_full_graph.adjacency_list[c_id]
+ if (to in am) and \
+ not self.vistrail.is_pruned(to)][0]
+
+ # Don't show edge that skips the disappearing nodes
+ if terse_graph.has_edge(shared_parent, c_id):
+ terse_graph.delete_edge(shared_parent, c_id)
+
+ # Add the disappearing node to the graph and layout
+ c_node = copy.deepcopy(self._current_graph_layout.nodes[c_id])
+ c_node.id = p_id
+ graph_layout.add_node(p_id, c_node)
+ terse_graph.add_vertex(p_id)
+ p_parent = self._current_full_graph.parent(p_id)
+ if not terse_graph.has_edge(p_id, p_parent):
+ terse_graph.add_edge(p_parent, p_id)
+ p_child = p_id
+ while p_child not in self._current_graph_layout.nodes:
+ # Should always have exactly one child
+ p_child = [to for (to, _) in \
+ self._current_full_graph.adjacency_list[p_child]
+ if (to in am) and \
+ not self.vistrail.is_pruned(to)][0]
+ if not terse_graph.has_edge(p_id, p_child):
+ terse_graph.add_edge(p_id, p_child)
+
+ # Interpolate position
+ x = p_node.p.x - c_node.p.x
+ y = p_node.p.y - c_node.p.y
+ graph_layout.move_node(p_id, x*(1.0-step), y*(1.0-step))
+
+ return (terse_graph, self._current_full_graph,
+ graph_layout)
+
+ ##########################################################################
+ # undo/redo navigation
+
+ def _change_version_short_hop(self, new_version):
+ """_change_version_short_hop is used internally to
+ change versions when we're moving exactly one action up or down.
+ This allows a few optimizations that improve interactivity."""
+
+ if self.current_version <> new_version:
+ # Instead of recomputing the terse graph, simply update it
+
+ # There are two variables in play:
+ # a) whether or not the destination node is currently on the
+ # terse tree (it will certainly be after the move)
+ # b) whether or not the current node will be visible (it
+ # certainly is now, since it's the current one)
+
+ dest_node_in_terse_tree = new_version in self._current_terse_graph.vertices
+
+ current = self.current_version
+ tree = self.vistrail.tree.getVersionTree()
+ # same logic as recompute_terse_graph except for current
+ children_count = len([x for (x, _) in tree.adjacency_list[current]
+ if (x in self.vistrail.actionMap and
+ not self.vistrail.is_pruned(x))])
+ current_node_will_be_visible = \
+ (self.full_tree or
+ self.vistrail.has_tag(self.current_version) or
+ children_count <> 1)
+
+ self.change_selected_version(new_version)
+ # case 1:
+ if not dest_node_in_terse_tree and \
+ not current_node_will_be_visible and not current == 0:
+ # we're going from one boring node to another,
+ # so just rename the node on the terse graph
+ self._current_terse_graph.rename_vertex(current, new_version)
+ self.replace_unnamed_node_in_version_tree(current, new_version)
+ else:
+ # bail, for now
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(False)
+
+
+ def show_parent_version(self):
+ """ show_parent_version() -> None
+ Go back one from the current version and display it
+
+ """
+ # NOTE cscheid: Slight change in the logic under refined views:
+ # before r1185, undo would back up more than one action in the
+ # presence of non-matching refined nodes. That seems wrong. Undo
+ # should always move one step only.
+
+ prev = None
+ try:
+ prev = self._current_full_graph.parent(self.current_version)
+ except Graph.VertexHasNoParentError:
+ prev = 0
+
+ self._change_version_short_hop(prev)
+
+ def show_child_version(self, which_child):
+ """ show_child_version(which_child: int) -> None
+ Go forward one version and display it. This is used in redo.
+
+ ONLY CALL THIS FUNCTION IF which_child IS A CHILD OF self.current_version
+
+ """
+ self._change_version_short_hop(which_child)
+
+
+ def prune_versions(self, versions):
+ """ prune_versions(versions: list of version numbers) -> None
+ Prune all versions in 'versions' out of the view
+
+ """
+ # We need to go up-stream to the highest invisible node
+ current = self._current_terse_graph
+ if not current:
+ (current, full, layout) = self.refine_graph()
+ else:
+ full = self._current_full_graph
+ changed = False
+ new_current_version = None
+ for v in versions:
+ if v!=0: # not root
+ highest = v
+ while True:
+ p = full.parent(highest)
+ if p==-1:
+ break
+ if p in current.vertices:
+ break
+ highest = p
+ if highest!=0:
+ changed = True
+ if highest == self.current_version:
+ new_current_version = full.parent(highest)
+ self.vistrail.pruneVersion(highest)
+ if changed:
+ self.set_changed(True)
+ if new_current_version is not None:
+ self.change_selected_version(new_current_version)
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(False)
+
+ def hide_versions_below(self, v=None):
+ """ hide_versions_below(v: int) -> None
+ Hide all versions including and below v
+
+ """
+ if v is None:
+ v = self.current_version
+ full = self.vistrail.getVersionGraph()
+ x = [v]
+
+ am = self.vistrail.actionMap
+
+ changed = False
+
+ while 1:
+ try:
+ current=x.pop()
+ except IndexError:
+ break
+
+ children = [to for (to, _) in full.adjacency_list[current]
+ if (to in am) and \
+ not self.vistrail.is_pruned(to)]
+ self.vistrail.hideVersion(current)
+ changed = True
+
+ for child in children:
+ x.append(child)
+
+ if changed:
+ self.set_changed(True)
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(False, False)
+
+ def show_all_versions(self):
+ """ show_all_versions() -> None
+ Unprune (graft?) all pruned versions
+
+ """
+ full = self.vistrail.getVersionGraph()
+ am = self.vistrail.actionMap
+ for a in am.iterkeys():
+ self.vistrail.showVersion(a)
+ self.set_changed(True)
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(False, False)
+
+ def expand_versions(self, v1, v2):
+ """ expand_versions(v1: int, v2: int) -> None
+ Expand all versions between v1 and v2
+
+ """
+ full = self.vistrail.getVersionGraph()
+ changed = False
+ p = full.parent(v2)
+ while p>v1:
+ self.vistrail.expandVersion(p)
+ changed = True
+ p = full.parent(p)
+ if changed:
+ self.set_changed(True)
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(False, True)
+
+ def collapse_versions(self, v):
+ """ collapse_versions(v: int) -> None
+ Collapse all versions including and under version v until the next tag or branch
+
+ """
+ full = self.vistrail.getVersionGraph()
+ x = [v]
+
+ am = self.vistrail.actionMap
+ tm = self.vistrail.get_tagMap()
+
+ changed = False
+
+ while 1:
+ try:
+ current=x.pop()
+ except IndexError:
+ break
+
+ children = [to for (to, _) in full.adjacency_list[current]
+ if (to in am) and not self.vistrail.is_pruned(to)]
+ if len(children) > 1:
+ break;
+ self.vistrail.collapseVersion(current)
+ changed = True
+
+ for child in children:
+ if (not child in tm and # has no Tag
+ child != self.current_version): # not selected
+ x.append(child)
+
+ if changed:
+ self.set_changed(True)
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(False, True)
+
+ def expand_or_collapse_all_versions_below(self, v=None, expand=True):
+ """ expand_or_collapse_all_versions_below(v: int) -> None
+ Expand/Collapse all versions including and under version v
+
+ """
+ if v is None:
+ v = self.current_version
+
+ full = self.vistrail.getVersionGraph()
+ x = [v]
+
+ am = self.vistrail.actionMap
+
+ changed = False
+
+ while 1:
+ try:
+ current=x.pop()
+ except IndexError:
+ break
+
+ children = [to for (to, _) in full.adjacency_list[current]
+ if (to in am) and not self.vistrail.is_pruned(to)]
+ if expand:
+ self.vistrail.expandVersion(current)
+ else:
+ self.vistrail.collapseVersion(current)
+ changed = True
+
+ for child in children:
+ x.append(child)
+
+ if changed:
+ self.set_changed(True)
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(False, True)
+
+ def expand_all_versions_below(self, v=None):
+ self.expand_or_collapse_all_versions_below(v, True)
+
+ def collapse_all_versions_below(self, v=None):
+ self.expand_or_collapse_all_versions_below(v, False)
+
+ def collapse_all_versions(self):
+ """ collapse_all_versions() -> None
+ Collapse all expanded versions
+
+ """
+ am = self.vistrail.actionMap
+ for a in am.iterkeys():
+ self.vistrail.collapseVersion(a)
+ self.set_changed(True)
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(False, True)
+
+ def set_num_versions_always_shown(self, num):
+ """ set_num_versions_always_shown(num: int) -> None
+
+ """
+ if num <> self.num_versions_always_shown:
+ self.num_versions_always_shown = num
+ self.set_changed(True)
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(False)
+
+ def setSavedQueries(self, queries):
+ """ setSavedQueries(queries: list of (str, str, str)) -> None
+ Set the saved queries of a vistail
+
+ """
+ self.vistrail.setSavedQueries(queries)
+ self.set_changed(True)
+
+ def update_current_tag(self,tag):
+ """ update_current_tag(tag: str) -> Bool
+ Update the current vistrail tag and return success predicate
+
+ """
+ self.flush_delayed_actions()
+ try:
+ if self.vistrail.hasTag(self.current_version):
+ self.vistrail.changeTag(tag, self.current_version)
+ else:
+ self.vistrail.addTag(tag, self.current_version)
+ except TagExists:
+ show_warning('Name Exists',
+ "There is already another version named '%s'.\n"
+ "Please enter a different one." % tag)
+ return False
+ self.set_changed(True)
+ self.recompute_terse_graph()
+ self.invalidate_version_tree(False)
+ return True
+
+ def perform_param_changes(self, actions):
+ """perform_param_changes(actions) -> None
+
+ Performs a series of parameter change actions to the current version.
+
+ FIXME: this function seems to be called from a single place in
+ the spreadsheet cell code. Do we need it?
+ """
+ if len(actions) == 0:
+ return
+ for action in actions:
+ for operation in action.operations:
+ if operation.vtType == 'add' or operation.vtType == 'change':
+ if operation.new_obj_id < 0:
+ data = operation.data
+ new_id = self.vistrail.idScope.getNewId(data.vtType)
+ data.real_id = new_id
+ operation.new_obj_id = new_id
+ self.add_new_action(action)
+ self.perform_action(action, quiet=True)
+ self.set_changed(True)
+ self.invalidate_version_tree(False)
+
+ def get_pipeline_name(self, version=None):
+ if version == None:
+ version = self.current_version
+ return self.vistrail.get_pipeline_name(version)
+
+ ###########################################################################
+ # Clipboard, copy/paste
+
+ def get_selected_item_ids(self):
+ return self.current_pipeline_scene.get_selected_item_ids()
+
+ def copy_modules_and_connections(self, module_ids, connection_ids):
+ """copy_modules_and_connections(module_ids: [long],
+ connection_ids: [long]) -> str
+ Serializes a list of modules and connections
+ """
+ self.flush_delayed_actions()
+
+ def process_group(group):
+ # reset pipeline id for db
+ group.pipeline.id = None
+ # recurse
+ for module in group.pipeline.module_list:
+ if module.is_group():
+ process_group(module)
+
+ pipeline = Pipeline()
+ sum_x = 0.0
+ sum_y = 0.0
+ for module_id in module_ids:
+ module = self.current_pipeline.modules[module_id]
+ sum_x += module.location.x
+ sum_y += module.location.y
+ if module.is_group():
+ process_group(module)
+
+ center_x = sum_x / len(module_ids)
+ center_y = sum_y / len(module_ids)
+ for module_id in module_ids:
+ module = self.current_pipeline.modules[module_id]
+ module = module.do_copy()
+ module.location.x -= center_x
+ module.location.y -= center_y
+ pipeline.add_module(module)
+ for connection_id in connection_ids:
+ connection = self.current_pipeline.connections[connection_id]
+ pipeline.add_connection(connection)
+ return vistrails.core.db.io.serialize(pipeline)
+
+ def paste_modules_and_connections(self, str, center):
+ """ paste_modules_and_connections(str,
+ center: (float, float)) -> [id list]
+ Paste a list of modules and connections into the current pipeline.
+
+ Returns the list of module ids of added modules
+
+ """
+ def remove_duplicate_aliases(pip):
+ aliases = self.current_pipeline.aliases.keys()
+ for a in aliases:
+ if a in pip.aliases:
+ (type, oId, parentType, parentId, mid) = pip.aliases[a]
+ pip.remove_alias_by_name(a)
+ _mod = pip.modules[mid]
+ _fun = _mod.function_idx[parentId]
+ _par = _fun.parameter_idx[oId]
+ _par.alias = ''
+
+ self.flush_delayed_actions()
+ pipeline = vistrails.core.db.io.unserialize(str, Pipeline)
+ remove_duplicate_aliases(pipeline)
+
+ modules = []
+ connections = []
+ if pipeline:
+ def process_group(group):
+ # reset pipeline id for db
+ group.pipeline.id = None
+ # recurse
+ for module in group.pipeline.module_list:
+ if module.is_group():
+ process_group(module)
+
+ for module in pipeline.module_list:
+ module.location.x += center[0]
+ module.location.y += center[1]
+ if module.is_group():
+ process_group(module)
+
+ id_remap = {}
+ action = vistrails.core.db.action.create_paste_action(pipeline,
+ self.vistrail.idScope,
+ id_remap)
+
+ modules = [op.objectId
+ for op in action.operations
+ if (op.what == 'module' or
+ op.what == 'abstraction' or
+ op.what == 'group')]
+ connections = [op.objectId
+ for op in action.operations
+ if op.what == 'connection']
+
+ self.add_new_action(action)
+ self.vistrail.change_description("Paste", action.id)
+ self.perform_action(action)
+ self.validate(self.current_pipeline, False)
+ return modules
+
+ def get_abstraction_name(self, name="", check_exists=True):
+ name = self.do_abstraction_prompt(name)
+ if name is None:
+ return None
+ while name == "" or (check_exists and self.abstraction_exists(name)):
+ name = self.do_abstraction_prompt(name, name != "")
+ if name is None:
+ return None
+ return name
+
+ def do_abstraction_prompt(self, name="", exists=False):
+ if exists:
+ prompt = "'%s' already exists. Enter a new subworkflow name" % \
+ name
+ else:
+ prompt = 'Enter subworkflow name'
+
+ (text, ok) = QtGui.QInputDialog.getText(None,
+ 'Set SubWorkflow Name',
+ prompt,
+ QtGui.QLineEdit.Normal,
+ name)
+ if ok and text:
+ return str(text).strip().rstrip()
+ if not ok:
+ return None
+ return ""
+
+ def import_abstractions(self, abstraction_ids):
+ for abstraction_id in abstraction_ids:
+ abstraction = self.current_pipeline.modules[abstraction_id]
+ new_name = self.get_abstraction_name(abstraction.name)
+ if new_name:
+ self.import_abstraction(new_name,
+ abstraction.package,
+ abstraction.name,
+ abstraction.namespace,
+ abstraction.internal_version)
+
+ def do_export_prompt(self, title, prompt):
+ (text, ok) = QtGui.QInputDialog.getText(None,
+ title,
+ prompt,
+ QtGui.QLineEdit.Normal,
+ '')
+ if ok and not text:
+ return str(text).strip().rstrip()
+ return ''
+
+ def do_save_dir_prompt(self):
+ dialog = QtGui.QFileDialog.getExistingDirectory
+ dir_name = dialog(None, "Save Subworkflows...",
+ vistrails.core.system.vistrails_file_directory())
+ if dir_name:
+ return None
+ dir_name = os.path.abspath(str(dir_name))
+ setattr(get_vistrails_configuration(), 'fileDirectory', dir_name)
+ vistrails.core.system.set_vistrails_file_directory(dir_name)
+ return dir_name
+
+ def export_abstractions(self, abstraction_ids):
+ save_dir = self.do_save_dir_prompt()
+ if not save_dir:
+ return
+
+ def read_init(dir_name):
+ import imp
+ found_attrs = {}
+ found_lists = {}
+ attrs = ['identifier', 'name', 'version']
+ lists = ['_subworkflows', '_dependencies']
+ try:
+ (file, pathname, description) = \
+ imp.find_module(os.path.basename(dir_name),
+ [os.path.dirname(dir_name)])
+ module = imp.load_module(os.path.basename(dir_name), file,
+ pathname, description)
+ for attr in attrs:
+ if hasattr(module, attr):
+ found_attrs[attr] = getattr(module, attr)
+ for attr in lists:
+ if hasattr(module, attr):
+ found_lists[attr] = getattr(module, attr)
+ except Exception, e:
+ debug.critical("Exception: %s" % e)
+ pass
+ return (found_attrs, found_lists)
+
+ def write_init(save_dir, found_attrs, found_lists, attrs, lists):
+ init_file = os.path.join(save_dir, '__init__.py')
+ if os.path.exists(init_file):
+ f = open(init_file, 'a')
+ else:
+ f = open(init_file, 'w')
+ for attr, val in attrs.iteritems():
+ if attr not in found_attrs:
+ print >>f, "%s = '%s'" % (attr, val)
+ for attr, val_list in lists.iteritems():
+ if attr not in found_lists:
+ print >>f, "%s = %s" % (attr, str(val_list))
+ else:
+ diff_list = []
+ for val in val_list:
+ if val not in found_lists[attr]:
+ diff_list.append(val)
+ print >>f, '%s.extend(%s)' % (attr, str(diff_list))
+ f.close()
+
+ if os.path.exists(os.path.join(save_dir, '__init__.py')):
+ (found_attrs, found_lists) = read_init(save_dir)
+ else:
+ found_attrs = {}
+ found_lists = {}
+
+ if 'name' in found_attrs:
+ pkg_name = found_attrs['name']
+ else:
+ pkg_name = self.do_export_prompt("Target Package Name",
+ "Enter target package name")
+ if not pkg_name:
+ return
+
+ if 'identifier' in found_attrs:
+ pkg_identifier = found_attrs['identifier']
+ else:
+ pkg_identifier = self.do_export_prompt("Target Package Identifier",
+ "Enter target package "
+ "identifier (e.g. "
+ "org.place.user.package)")
+ if not pkg_identifier:
+ return
+
+ abstractions = []
+ for abstraction_id in abstraction_ids:
+ abstraction = self.current_pipeline.modules[abstraction_id]
+ if abstraction.is_abstraction() and \
+ abstraction.package == abstraction_pkg:
+ abstractions.append(abstraction)
+ [abstractions.extend(v) for v in self.find_abstractions(abstraction.vistrail).itervalues()]
+ pkg_subworkflows = []
+ pkg_dependencies = set()
+ for abstraction in abstractions:
+ new_name = self.get_abstraction_name(abstraction.name, False)
+ if not new_name:
+ break
+ (subworkflow, dependencies) = \
+ self.export_abstraction(new_name,
+ pkg_identifier,
+ save_dir,
+ abstraction.package,
+ abstraction.name,
+ abstraction.namespace,
+ str(abstraction.internal_version))
+ pkg_subworkflows.append(subworkflow)
+ pkg_dependencies.update(dependencies)
+
+ attrs = {'identifier': pkg_identifier,
+ 'name': pkg_name,
+ 'version': '0.0.1'}
+ lists = {'_subworkflows': pkg_subworkflows,
+ '_dependencies': list(pkg_dependencies)}
+ write_init(save_dir, found_attrs, found_lists, attrs, lists)
+
+ def set_changed(self, changed):
+ """ set_changed(changed: bool) -> None
+ Set the current state of changed and emit signal accordingly
+
+ """
+ BaseController.set_changed(self, changed)
+ if changed:
+ # FIXME: emit different signal in the future
+ self.emit(QtCore.SIGNAL('stateChanged'))
+
+ def set_file_name(self, file_name):
+ """ set_file_name(file_name: str) -> None
+ Change the controller file name
+
+ """
+ old_name = self.file_name
+ BaseController.set_file_name(self, file_name)
+ if old_name!=file_name:
+ self.emit(QtCore.SIGNAL('stateChanged'))
+
+ def write_vistrail(self, locator, version=None, export=False):
+ need_invalidate = BaseController.write_vistrail(self, locator,
+ version, export)
+ if need_invalidate and not export:
+ self.invalidate_version_tree(False)
+ self.set_changed(False)
+
+ def write_opm(self, locator):
+ if self.log:
+ if self.vistrail.db_log_filename is not None:
+ log = vistrails.core.db.io.merge_logs(self.log,
+ self.vistrail.db_log_filename)
+ else:
+ log = self.log
+ opm_graph = OpmGraph(log=log,
+ version=self.current_version,
+ workflow=self.current_pipeline,
+ registry=get_module_registry())
+ locator.save_as(opm_graph)
+
+ def write_prov(self, locator):
+ if self.log:
+ if self.vistrail.db_log_filename is not None:
+ log = vistrails.core.db.io.merge_logs(self.log,
+ self.vistrail.db_log_filename)
+ else:
+ log = self.log
+ prov_document = ProvDocument(log=log,
+ version=self.current_version,
+ workflow=self.current_pipeline,
+ registry=get_module_registry())
+ locator.save_as(prov_document)
+
+ def query_by_example(self, pipeline):
+ """ query_by_example(pipeline: Pipeline) -> None
+ Perform visual query on the current vistrail
+
+ """
+ if len(pipeline.modules)==0:
+ search = TrueSearch()
+ else:
+ if not self._current_terse_graph:
+ self.recompute_terse_graph()
+ versions_to_check = \
+ set(self._current_terse_graph.vertices.iterkeys())
+ search = VisualQuery(pipeline, versions_to_check)
+
+ self.set_search(search, '') # pipeline.dump_to_string())
+
+ ##########################################################################
+ # analogies
+
+ def add_analogy(self, analogy_name, version_from, version_to):
+ assert isinstance(analogy_name, str)
+ assert isinstance(version_from, (int, long))
+ assert isinstance(version_to, (int, long))
+ if analogy_name in self.analogy:
+ raise VistrailsInternalError("duplicated analogy name '%s'" %
+ analogy_name)
+ self.analogy[analogy_name] = (version_from, version_to)
+
+ def remove_analogy(self, analogy_name):
+ if analogy_name not in self.analogy:
+ raise VistrailsInternalError("missing analogy '%s'" %
+ analogy_name)
+ del self.analogy[analogy_name]
+
+ def perform_analogy(self, analogy_name, analogy_target):
+ if analogy_name not in self.analogy:
+ raise VistrailsInternalError("missing analogy '%s'" %
+ analogy_name)
+
+ # remove delayed actions since we're not necessarily using
+ # current_version
+ self._delayed_actions = []
+
+ (a, b) = self.analogy[analogy_name]
+ c = analogy_target
+ if self.current_version != c:
+ self.change_selected_version(c)
+
+ try:
+ pipeline_a = self.vistrail.getPipeline(a)
+ self.validate(pipeline_a)
+ except InvalidPipeline, e:
+ (_, pipeline_a) = \
+ self.handle_invalid_pipeline(e, a, Vistrail())
+ self._delayed_actions = []
+ try:
+ pipeline_c = self.vistrail.getPipeline(c)
+ self.validate(pipeline_c)
+ except InvalidPipeline, e:
+ (_, pipeline_c) = self.handle_invalid_pipeline(e, a, Vistrail())
+ self._delayed_actions = []
+
+ action = vistrails.core.analogy.perform_analogy_on_vistrail(self.vistrail,
+ a, b, c,
+ pipeline_a,
+ pipeline_c)
+ self.add_new_action(action)
+ self.vistrail.change_description("Analogy", action.id)
+ self.vistrail.change_analogy_info("(%s -> %s)(%s)" % (a, b, c),
+ action.id)
+
+ # make sure that the output from the analogy is as up-to-date
+ # as we can make it
+ self.change_selected_version(action.id, from_root=True)
+ self.flush_delayed_actions()
+ self.invalidate_version_tree()
+
+ def executeParameterExploration(self, pe, view=None, extra_info={}, showProgress=True):
+ """ execute(pe: ParameterExploration, view: QVistrailView,
+ extra_info: dict, showProgress: bool) -> None
+ Perform the exploration by collecting a list of actions
+ corresponding to each dimension
+
+ """
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ spreadsheet_pkg = '%s.spreadsheet' % \
+ vistrails.core.system.get_vistrails_default_pkg_prefix()
+ use_spreadsheet = reg.has_module(spreadsheet_pkg, 'CellLocation') and\
+ reg.has_module(spreadsheet_pkg, 'SheetReference')
+
+ if pe.action_id != self.current_version:
+ self.change_selected_version(pe.action_id)
+ actions, pre_actions, vistrail_vars = \
+ pe.collectParameterActions(self.current_pipeline)
+
+ if self.current_pipeline and actions:
+ explorer = ActionBasedParameterExploration()
+ (pipelines, performedActions) = explorer.explore(
+ self.current_pipeline, actions, pre_actions)
+
+ dim = [max(1, len(a)) for a in actions]
+ if use_spreadsheet:
+ from vistrails.gui.paramexplore.virtual_cell import positionPipelines, assembleThumbnails
+ from vistrails.gui.paramexplore.pe_view import QParamExploreView
+ modifiedPipelines, pipelinePositions = positionPipelines(
+ 'PE#%d %s' % (QParamExploreView.explorationId, self.name),
+ dim[2], dim[1], dim[0], pipelines, pe.layout, self)
+ QParamExploreView.explorationId += 1
+ else:
+ modifiedPipelines = pipelines
+
+ mCount = []
+ for p in modifiedPipelines:
+ if len(mCount)==0:
+ mCount.append(0)
+ else:
+ mCount.append(len(p.modules)+mCount[len(mCount)-1])
+
+ # Now execute the pipelines
+ if showProgress:
+ totalProgress = sum([len(p.modules) for p in modifiedPipelines])
+ progress = QtGui.QProgressDialog('Performing Parameter '
+ 'Exploration...',
+ '&Cancel',
+ 0, totalProgress)
+ progress.setWindowTitle('Parameter Exploration')
+ progress.setWindowModality(QtCore.Qt.WindowModal)
+ progress.show()
+
+ interpreter = get_default_interpreter()
+
+ images = {}
+ errors = []
+ for pi in xrange(len(modifiedPipelines)):
+ if showProgress:
+ progress.setValue(mCount[pi])
+ QtCore.QCoreApplication.processEvents()
+ if progress.wasCanceled():
+ break
+ def moduleExecuted(objId):
+ if not progress.wasCanceled():
+ progress.setValue(progress.value()+1)
+ QtCore.QCoreApplication.processEvents()
+ if use_spreadsheet:
+ name = os.path.splitext(self.name)[0] + \
+ ("_%s_%s_%s" % pipelinePositions[pi])
+ extra_info['nameDumpCells'] = name
+ if 'pathDumpCells' in extra_info:
+ images[pipelinePositions[pi]] = \
+ os.path.join(extra_info['pathDumpCells'], name)
+ kwargs = {'locator': self.locator,
+ 'current_version': self.current_version,
+ 'reason': 'Parameter Exploration',
+ 'actions': performedActions[pi],
+ 'extra_info': extra_info
+ }
+ if view:
+ kwargs['view'] = view
+ if showProgress:
+ kwargs['module_executed_hook'] = [moduleExecuted]
+ if self.get_vistrail_variables():
+ # remove vars used in pe
+ vars = dict([(v.uuid, v) for v in self.get_vistrail_variables()
+ if v.uuid not in vistrail_vars])
+ kwargs['vistrail_variables'] = lambda x: vars.get(x, None)
+ result = interpreter.execute(modifiedPipelines[pi], **kwargs)
+ for error in result.errors.itervalues():
+ if use_spreadsheet:
+ pp = pipelinePositions[pi]
+ errors.append(((pp[1], pp[0], pp[2]), error))
+ else:
+ errors.append(((0,0,0), error))
+
+ if showProgress:
+ progress.setValue(totalProgress)
+ if 'pathDumpCells' in extra_info:
+ filename = os.path.join(extra_info['pathDumpCells'],
+ os.path.splitext(self.name)[0])
+ assembleThumbnails(images, filename)
+ return errors
+
+################################################################################
+# Testing
+
+
+class TestVistrailController(vistrails.gui.utils.TestVisTrailsGUI):
+
+ # def test_add_module(self):
+ # v = api.new_vistrail()
+
+ def tearDown(self):
+ from vistrails.core.configuration import get_vistrails_configuration
+ vistrails.gui.utils.TestVisTrailsGUI.tearDown(self)
+
+ config = get_vistrails_configuration()
+ filename = os.path.join(config.abstractionsDirectory,
+ '__TestFloatList.xml')
+ if os.path.exists(filename):
+ os.remove(filename)
+
+ def test_create_functions(self):
+ controller = VistrailController(Vistrail(), None,
+ pipeline_view=DummyView(),
+ auto_save=False)
+ controller.change_selected_version(0L)
+ module = controller.add_module(0.0,0.0,
+ vistrails.core.system.get_vistrails_basic_pkg_id(),
+ 'ConcatenateString')
+ functions = [('str1', ['foo'], -1, True),
+ ('str2', ['bar'], -1, True)]
+ controller.update_functions(module, functions)
+
+ self.assertEquals(len(controller.current_pipeline.module_list), 1)
+ p_module = controller.current_pipeline.modules[module.id]
+ self.assertEquals(len(p_module.functions), 2)
+ self.assertEquals(p_module.functions[0].params[0].strValue, 'foo')
+ self.assertEquals(p_module.functions[1].params[0].strValue, 'bar')
+
+ # make sure updates work correctly
+ # also check that we can add more than one function w/ same name
+ # by passing False as should_replace
+ new_functions = [('str1', ['baz'], -1, True),
+ ('str2', ['foo'], -1, False),
+ ('str3', ['bar'], -1, False)]
+ controller.update_functions(p_module, new_functions)
+ self.assertEquals(len(p_module.functions), 4)
+
+ def test_abstraction_create(self):
+ from vistrails.core.db.locator import XMLFileLocator
+ import vistrails.core.db.io
+ from vistrails.core.configuration import get_vistrails_configuration
+ config = get_vistrails_configuration()
+ filename = os.path.join(config.abstractionsDirectory,
+ '__TestFloatList.xml')
+ locator = XMLFileLocator(vistrails.core.system.vistrails_root_directory() +
+ '/tests/resources/test_abstraction.xml')
+ v = locator.load()
+ controller = VistrailController(v, locator, pipeline_view=DummyView(),
+ auto_save=False)
+ # DAK: version is different because of upgrades
+ # controller.change_selected_version(9L)
+ controller.select_latest_version()
+ self.assertNotEqual(controller.current_pipeline, None)
+
+ # DAK: changed these because of upgrades...
+ # module_ids = [1, 2, 3]
+ # connection_ids = [1, 2, 3]
+ module_ids = [8, 10, 11]
+ #connection_ids = [6, 8, 9]
+ # TE: changed again because upgrades produced different id:s
+ # also saved upgrade in test_abstraction.xml
+ connection_ids = [13,14,15]
+ controller.create_abstraction(module_ids, connection_ids,
+ '__TestFloatList')
+ self.assert_(os.path.exists(filename))
diff --git a/vistrails/gui/vistrail_variables.py b/vistrails/gui/vistrail_variables.py
new file mode 100644
index 0000000..ad59c76
--- /dev/null
+++ b/vistrails/gui/vistrail_variables.py
@@ -0,0 +1,65 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file describes the vistrail variables box into which the user can
+drop constants from the module palette
+
+"""
+from PyQt4 import QtCore, QtGui
+from vistrails.gui.variable_dropbox import QVariableDropBox
+from vistrails.gui.common_widgets import QToolWindowInterface
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+
+################################################################################
+
+class QVistrailVariables(QVariableDropBox, QVistrailsPaletteInterface):
+ """
+ QVistrailVariables shows variables associated with a vistrail, and
+ supports drag/drop actions of constant items from the module palette
+
+ """
+ def __init__(self, parent=None):
+ """ QVistrailVariables(parent: QWidget) -> QVistrailVariables
+ Initialize widget constraints
+
+ """
+ QVariableDropBox.__init__(self, parent)
+ self.setWindowTitle('Vistrail Variables')
+ self.setToolWindowAcceptDrops(True)
+
+ def sizeHint(self):
+ """ sizeHint() -> None
+ """
+ return QtCore.QSize(self.size().width(), 300)
+
diff --git a/vistrails/gui/vistrail_view.py b/vistrails/gui/vistrail_view.py
new file mode 100644
index 0000000..b5cb0f3
--- /dev/null
+++ b/vistrails/gui/vistrail_view.py
@@ -0,0 +1,1295 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" The file describes a container widget consisting of a pipeline
+view and a version tree for each opened Vistrail """
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core import debug
+from vistrails.core.collection import Collection
+from vistrails.core.debug import critical
+from vistrails.core.data_structures.bijectivedict import Bidict
+from vistrails.core.system import vistrails_default_file_type
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.core.vistrail.vistrail import Vistrail
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.log.log import Log
+from vistrails.core.log.opm_graph import OpmGraph
+from vistrails.core.log.prov_document import ProvDocument
+from vistrails.core.db.locator import FileLocator, XMLFileLocator
+from vistrails.core.modules.module_registry import ModuleRegistry
+from vistrails.core.configuration import get_vistrails_configuration
+
+from vistrails.gui.collection.vis_log import QLogView
+from vistrails.gui.common_widgets import QMouseTabBar
+from vistrails.gui.pipeline_view import QPipelineView
+from vistrails.gui.version_view import QVersionTreeView
+from vistrails.gui.query_view import QQueryView
+from vistrails.gui.paramexplore.pe_view import QParamExploreView
+from vistrails.gui.vis_diff import QDiffView
+from vistrails.gui.paramexplore.param_view import QParameterView
+from vistrails.gui.vistrail_controller import VistrailController
+from vistrails.gui.mashups.mashup_view import QMashupView
+from vistrails.gui.ports_pane import ParameterEntry
+from vistrails.gui.query_view import QueryEntry
+
+################################################################################
+
+class QVistrailView(QtGui.QWidget):
+ """
+ QVistrailView is a widget containing four stacked widgets: Pipeline View,
+ Version Tree View, Query View and Parameter Exploration view
+ for manipulating vistrails.
+ """
+ def __init__(self, vistrail, locator=None, abstraction_files=None,
+ thumbnail_files=None, mashups=None, parent=None):
+ """ QVistrailView(parent: QWidget) -> QVistrailView
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+
+ layout = QtGui.QVBoxLayout(self)
+ layout.setMargin(0)
+ layout.setSpacing(0)
+ self.is_executing = False
+ self.is_abstraction = False
+ self.notifications = {}
+ self.tabs = QMouseTabBar(self)
+ self.tabs.setDocumentMode(True)
+ self.tabs.setTabsClosable(True)
+ self.tabs.setExpanding(False)
+ #self.tabs.setMovable(True)
+ self.tabs.hide()
+ self.tabs.tabDoubleClicked.connect(self.tabDoubleClicked)
+ layout.addWidget(self.tabs)
+ self.stack = QtGui.QStackedWidget(self)
+ layout.addWidget(self.stack)
+ self.setLayout(layout)
+
+ #this index is for pipeline/diff views
+ self.tab_to_stack_idx = {}
+ self.tab_state = {}
+ self.tab_to_view = {}
+ #self.button_to_tab_idx = Bidict()
+ self.detached_views = {}
+
+ # Create the initial views
+ self.version_view = None
+ pipeline_view = self.create_pipeline_view(set_controller=False)
+ self.version_view = self.create_version_view()
+ self.query_view = self.create_query_view()
+ self.pe_view = self.create_pe_view()
+ self.log_view = self.create_log_view()
+ self.mashup_view = self.create_mashup_view(False)
+
+ # Initialize the vistrail controller
+ self.locator = locator
+ self.controller = VistrailController(vistrail,
+ self.locator,
+ abstractions=abstraction_files,
+ thumbnails=thumbnail_files,
+ mashups=mashups,
+ pipeline_view=pipeline_view)
+
+ self.set_controller(self.controller)
+ pipeline_view.set_to_current()
+
+ self.tabs.setCurrentIndex(0)
+ self.current_tab = self.stack.setCurrentIndex(0)
+ self.pipeline_selected()
+ self.connect(self.tabs, QtCore.SIGNAL("currentChanged(int)"),
+ self.tab_changed)
+ self.connect(self.tabs, QtCore.SIGNAL("tabCloseRequested(int)"),
+ self.remove_view_by_index)
+
+ #self.view_changed()
+ #self.tab_changed(0)
+
+ self.connect(self.controller,
+ QtCore.SIGNAL('stateChanged'),
+ self.stateChanged)
+
+ from vistrails.gui.vistrails_window import _app
+ _app.register_notification("reg_new_abstraction",
+ self.controller.check_subworkflow_versions)
+ _app.register_notification("reg_deleted_abstraction",
+ self.controller.check_subworkflow_versions)
+
+ # self.controller = VistrailController()
+ # self.controller.vistrail_view = self
+ # self.connect(self.controller,
+ # QtCore.SIGNAL('stateChanged'),
+ # self.stateChanged)
+ # self.connect(self.controller,
+ # QtCore.SIGNAL('new_action'),
+ # self.new_action)
+
+ # # self.versionTab.versionView.scene()._vistrail_view = self
+ # self.connect(self.versionTab.versionView.scene(),
+ # QtCore.SIGNAL('versionSelected(int,bool,bool,bool)'),
+ # self.versionSelected,
+ # QtCore.Qt.QueuedConnection)
+
+ # self.connect(self.versionTab,
+ # QtCore.SIGNAL('twoVersionsSelected(int,int)'),
+ # self.twoVersionsSelected)
+ # self.connect(self.queryTab,
+ # QtCore.SIGNAL('queryPipelineChange'),
+ # self.queryPipelineChange)
+ # self.connect(self.peTab,
+ # QtCore.SIGNAL('exploreChange(bool)'),
+ # self.exploreChange)
+
+ # # We also keep track where this vistrail comes from
+ # # So we can save in the right place
+ # self.locator = None
+
+ # self.closeEventHandler = None
+
+ # # Keep the state of the execution button and menu items for the view
+ # self.execQueryEnabled = False
+ # self.execDiffEnabled = False
+ # self.execExploreEnabled = False
+ # self.execPipelineEnabled = False
+ # self.execDiffId1 = -1
+ # self.execDiffId2 = -1
+ if get_vistrails_configuration().detachHistoryView:
+ self.detach_history_view()
+
+ def get_notifications(self):
+ return self.notifications
+
+ def set_notification(self, notification_id, method):
+ if notification_id not in self.notifications:
+ self.notifications[notification_id] = []
+ self.notifications[notification_id].append(method)
+
+ def set_controller(self, controller):
+ self.controller = controller
+ self.controller.vistrail_view = self
+ for i in xrange(self.stack.count()):
+ view = self.stack.widget(i)
+ if hasattr(view, 'set_controller'):
+ view.set_controller(controller)
+
+ def get_controller(self):
+ return self.controller
+
+ def get_name(self):
+ title = self.controller.name
+ if title=='':
+ title = 'Untitled%s'%vistrails_default_file_type()
+ if self.controller.changed:
+ title += '*'
+ # self.setWindowTitle(title)
+ return title
+
+ def set_name(self):
+ title = self.get_name()
+ self.setWindowTitle(title)
+
+ def reset_version_view(self):
+ from vistrails.gui.vistrails_window import _app
+ if self.version_view is not None:
+ select_node = True
+ if _app._previous_view and _app._previous_view in self.detached_views:
+ select_node = False
+ self.version_view.scene().setupScene(self.controller, select_node)
+
+ def reset_tab_state(self):
+ try:
+ qaction = self.tab_state[self.tabs.currentIndex()]
+ qaction.trigger()
+ except:
+ pass
+
+ def reset_tab_view_to_current(self):
+ index = self.tabs.currentIndex()
+ view = self.stack.widget(self.tab_to_stack_idx[index])
+ #print "view changed: ", view
+ self.set_to_current(view)
+
+ def pipeline_selected(self):
+ from vistrails.gui.vistrails_window import _app
+ if hasattr(self.window(), 'qactions'):
+ window = self.window()
+ else:
+ window = _app
+ #print "PIPELINE"
+ self.stack.setCurrentIndex(
+ self.tab_to_stack_idx[self.tabs.currentIndex()])
+ self.tabs.setTabText(self.tabs.currentIndex(),
+ self.stack.currentWidget().get_title())
+ self.tab_state[self.tabs.currentIndex()] = window.qactions['pipeline']
+ self.tab_to_view[self.tabs.currentIndex()] = self.get_current_tab()
+
+ def pipeline_unselected(self):
+ #print "PIPELINE UN"
+ self.stack.setCurrentIndex(
+ self.tab_to_stack_idx[self.tabs.currentIndex()])
+ self.tabs.setTabText(self.tabs.currentIndex(),
+ self.stack.currentWidget().get_title())
+
+ def history_selected(self):
+ from vistrails.gui.vistrails_window import _app
+ if get_vistrails_configuration().detachHistoryView:
+ _app.history_view.raise_()
+ return
+ if hasattr(self.window(), 'qactions'):
+ window = self.window()
+ else:
+ window = _app
+ #print "VERSION"
+ self.stack.setCurrentIndex(self.stack.indexOf(self.version_view))
+ self.tabs.setTabText(self.tabs.currentIndex(), "History")
+ self.tab_state[self.tabs.currentIndex()] = window.qactions['history']
+ self.tab_to_view[self.tabs.currentIndex()] = self.get_current_tab()
+
+ def history_unselected(self):
+ #print "VERSION UN"
+ self.stack.setCurrentIndex(
+ self.tab_to_stack_idx[self.tabs.currentIndex()])
+ self.tabs.setTabText(self.tabs.currentIndex(),
+ self.stack.currentWidget().get_title())
+
+ def query_selected(self):
+ from vistrails.gui.vistrails_window import _app
+ if hasattr(self.window(), 'qactions'):
+ window = self.window()
+ else:
+ window = _app
+ #print "QUERY"
+ self.stack.setCurrentIndex(self.stack.indexOf(self.query_view))
+ self.tabs.setTabText(self.tabs.currentIndex(), "Search")
+ self.tab_state[self.tabs.currentIndex()] = window.qactions['search']
+ self.tab_to_view[self.tabs.currentIndex()] = self.get_current_tab()
+
+ def query_unselected(self):
+ #print "QUERY UN"
+ self.stack.setCurrentIndex(
+ self.tab_to_stack_idx[self.tabs.currentIndex()])
+ self.tabs.setTabText(self.tabs.currentIndex(),
+ self.stack.currentWidget().get_title())
+
+ def explore_selected(self):
+ from vistrails.gui.vistrails_window import _app
+ if hasattr(self.window(), 'qactions'):
+ window = self.window()
+ else:
+ window = _app
+ #print "EXPLORE"
+ self.stack.setCurrentIndex(self.stack.indexOf(self.pe_view))
+ self.tabs.setTabText(self.tabs.currentIndex(),
+ self.stack.currentWidget().get_title())
+ self.tab_state[self.tabs.currentIndex()] = window.qactions['explore']
+ self.tab_to_view[self.tabs.currentIndex()] = self.get_current_tab()
+
+ def explore_unselected(self):
+ #print "EXPLORE UN"
+ self.stack.setCurrentIndex(
+ self.tab_to_stack_idx[self.tabs.currentIndex()])
+ self.tabs.setTabText(self.tabs.currentIndex(),
+ self.stack.currentWidget().get_title())
+
+ def provenance_selected(self):
+ from vistrails.gui.vistrails_window import _app
+ if hasattr(self.window(), 'qactions'):
+ window = self.window()
+ else:
+ window = _app
+ #print "PROVENANCE"
+ self.stack.setCurrentIndex(self.stack.indexOf(self.log_view))
+ self.tabs.setTabText(self.tabs.currentIndex(), "Provenance")
+ self.tab_state[self.tabs.currentIndex()] = window.qactions['provenance']
+ self.tab_to_view[self.tabs.currentIndex()] = self.get_current_tab()
+
+ def provenance_unselected(self):
+ #print "PROVENANCE UN"
+ self.stack.setCurrentIndex(
+ self.tab_to_stack_idx[self.tabs.currentIndex()])
+ self.tabs.setTabText(self.tabs.currentIndex(),
+ self.stack.currentWidget().get_title())
+
+ def mashup_selected(self):
+ from vistrails.gui.vistrails_window import _app
+ if hasattr(self.window(), 'qactions'):
+ window = self.window()
+ else:
+ window = _app
+ #print "MASHUP"
+ #print self.stack.count(), self.stack.indexOf(self.mashup_view)
+ try:
+ self.stack.setCurrentIndex(self.stack.indexOf(self.mashup_view))
+ self.tabs.setTabText(self.tabs.currentIndex(), "Mashup")
+ self.tab_state[self.tabs.currentIndex()] = window.qactions['mashup']
+ self.mashup_view.updateView()
+ self.tab_to_view[self.tabs.currentIndex()] = self.get_current_tab()
+ except Exception, e:
+ print "EXCEPTION: ", str(e)
+ def mashup_unselected(self):
+ #print "MASHUP UN"
+ self.stack.setCurrentIndex(
+ self.tab_to_stack_idx[self.tabs.currentIndex()])
+ self.tabs.setTabText(self.tabs.currentIndex(),
+ self.stack.currentWidget().get_title())
+
+ def pipeline_change(self, checked):
+ if checked:
+ #print "PIPELINE SELECTED"
+ self.pipeline_selected()
+ else:
+ #print "PIPELINE UNSELECTED"
+ self.pipeline_unselected()
+ self.view_changed()
+
+ def history_change(self, checked):
+ from vistrails_window import _app
+ if checked:
+ #print "HISTORY SELECTED"
+ self.history_selected()
+ else:
+ #print "HISTORY UNSELECTED"
+ self.history_unselected()
+ self.view_changed()
+
+ def search_change(self, checked):
+ if checked:
+ self.query_selected()
+ else:
+ self.query_unselected()
+ self.view_changed()
+
+ def explore_change(self, checked):
+ if checked:
+ self.explore_selected()
+ else:
+ self.explore_unselected()
+ self.view_changed()
+
+ def provenance_change(self, checked):
+ if checked:
+ self.provenance_selected()
+ else:
+ self.provenance_unselected()
+ self.view_changed()
+
+ def mashup_change(self, checked):
+ if checked:
+ self.mashup_selected()
+ else:
+ self.mashup_unselected()
+ self.view_changed()
+
+ def show_group(self):
+ pipelineScene = self.controller.current_pipeline_scene
+ items = pipelineScene.get_selected_item_ids(True)
+ if items is not None:
+ for m_id in items[0]:
+ module = pipelineScene.current_pipeline.modules[m_id]
+ if module.is_group() or module.is_abstraction():
+ newPipelineView = self.add_pipeline_view(True)
+ newPipelineView.controller.current_pipeline_view = \
+ newPipelineView
+ module.pipeline.ensure_connection_specs()
+ newPipelineView.scene().setupScene(module.pipeline)
+ newPipelineView.scene().current_pipeline = module.pipeline
+
+ def create_view(self, klass, add_tab=True):
+ view = klass(self)
+ view.set_vistrail_view(self)
+ idx = self.stack.addWidget(view)
+ view.set_index(idx)
+ if add_tab:
+ tab_idx = self.tabs.addTab(view.get_title())
+ view.set_tab_idx(tab_idx)
+ self.tab_to_stack_idx[tab_idx] = idx
+ self.tab_to_view[tab_idx] = view
+ if self.isTabDetachable(tab_idx):
+ self.tabs.setTabToolTip(tab_idx, "Double-click to detach it")
+
+ self.connect(view, QtCore.SIGNAL("windowTitleChanged"),
+ self.view_title_changed)
+ if self.tabs.count() == 1:
+ #self.tabs.hide()
+ self.tabs.setTabsClosable(False)
+ else:
+ self.tabs.setTabsClosable(True)
+ self.updateTabsTooTip()
+ self.tabs.show()
+ return view
+
+ def detach_history_view(self):
+ from vistrails.gui.vistrails_window import _app
+ view = self.version_view
+ window = _app.history_view
+ self.version_index = window.stack.addWidget(view)
+ window.stack.setCurrentIndex(self.version_index)
+ window.view = view
+
+ def detach_view(self, tab_idx):
+ from vistrails.gui.vistrails_window import QBaseViewWindow
+ if self.tab_to_stack_idx.has_key(tab_idx):
+ stack_index = self.tab_to_stack_idx[tab_idx]
+ view = self.stack.widget(stack_index)
+ title = view.get_long_title()
+ self.remove_view_by_index(tab_idx)
+ window = QBaseViewWindow(view=view, parent=None)
+ view.set_title(title)
+ window.setWindowTitle(title)
+ self.connect(window, QtCore.SIGNAL("viewWasClosed"),
+ self.detachedViewWasClosed)
+ self.detached_views[view] = window
+ window.move(self.rect().center())
+ window.show()
+ else:
+ print "Error detach_view: ", tab_idx, self.tab_to_stack_idx
+
+ def isTabDetachable(self, index):
+ if self.tab_to_view.has_key(index):
+ return self.tabs.count() > 1 and self.tab_to_view[index].detachable
+ return False
+
+ def closeDetachedViews(self):
+ windows = self.detached_views.values()
+ for w in windows:
+ if w:
+ w.close()
+
+ def detachedViewWasClosed(self, view):
+ if self.controller.current_pipeline_view == view:
+ self.controller.current_pipeline_view = None
+ self.activateWindow()
+ self.reset_tab_view_to_current()
+ self.view_changed()
+ del self.detached_views[view]
+
+ def updateTabsTooTip(self):
+ for i in range(self.tabs.count()):
+ if self.isTabDetachable(i):
+ self.tabs.setTabToolTip(i, "Double-click to detach it")
+ else:
+ self.tabs.setTabToolTip(i, "")
+
+ def tabDoubleClicked(self, index, pos):
+ if self.isTabDetachable(index):
+ self.detach_view(index)
+
+ def view_title_changed(self, view):
+ if self.stack.currentWidget() == view:
+ self.tabs.setTabText(self.tabs.currentIndex(), view.windowTitle())
+
+ def update_indexes(self, rm_tab_idx, rm_stack_idx):
+ for (t,s) in self.tab_to_stack_idx.iteritems():
+ if s > rm_stack_idx:
+ self.tab_to_stack_idx[t] -= 1
+ tabs = self.tab_to_stack_idx.keys()
+ tabs.sort()
+ for t in tabs:
+ if t > rm_tab_idx:
+ self.tab_to_stack_idx[t-1] = self.tab_to_stack_idx[t]
+ self.tab_state[t-1] = self.tab_state[t]
+ del self.tab_to_stack_idx[tabs[-1]]
+ del self.tab_state[tabs[-1]]
+ for idx in range(self.stack.count()):
+ if idx >= rm_stack_idx:
+ view = self.get_tab(idx)
+ view.set_index(idx)
+ if view.tab_idx > rm_tab_idx:
+ view.set_tab_idx(view.tab_idx-1)
+
+ def remove_view_by_index(self, index):
+ self.disconnect(self.tabs, QtCore.SIGNAL("currentChanged(int)"),
+ self.tab_changed)
+ close_current = False
+ if index == self.tabs.currentIndex():
+ close_current = True
+ stack_idx = self.tab_to_stack_idx[index]
+ #print "\n\n >>>>> remove_view_by_index ", index, stack_idx, self.tabs.currentIndex()
+ self.tabs.removeTab(index)
+ del self.tab_to_view[index]
+ if stack_idx >= 0:
+ view = self.stack.widget(stack_idx)
+ self.disconnect(view, QtCore.SIGNAL("windowTitleChanged"),
+ self.view_title_changed)
+ self.stack.removeWidget(view)
+ self.update_indexes(index, stack_idx)
+ if self.tabs.count() == 1:
+ self.tabs.setTabsClosable(False)
+ self.updateTabsTooTip()
+ if close_current:
+ if index >= self.tabs.count():
+ new_index = index - 1
+ else:
+ new_index = index
+
+ self.tab_changed(new_index)
+ self.connect(self.tabs, QtCore.SIGNAL("currentChanged(int)"),
+ self.tab_changed)
+# self.tabs.setCurrentIndex(new_index)
+# print self.current_tab
+
+# self.view_changed()
+
+
+ def switch_to_tab(self, index):
+# if index < 0:
+# index = self.tabs.count() + index
+ self.tabs.setCurrentIndex(index)
+ self.tab_changed(index)
+
+ def get_current_tab(self, query_top_level=False):
+ window = QtGui.QApplication.activeWindow()
+ if window in self.detached_views.values():
+ return window.view
+ else:
+ #if none of the detached views is active we will assume that the
+ #window containing this vistrail has focus
+ widget = self.stack.currentWidget()
+ if not query_top_level and isinstance(widget, QQueryView):
+ widget = widget.get_current_view()
+ return widget
+
+ def get_current_outer_tab(self):
+ window = QtGui.QApplication.activeWindow()
+ if window in self.detached_views.values():
+ return window.view
+ else:
+ #if none of the detached views is active we will assume that the
+ #window containing this vistrail has focus
+ return self.stack.currentWidget()
+
+ def get_tab(self, stack_idx):
+ widget = self.stack.widget(stack_idx)
+ if isinstance(widget, QQueryView):
+ widget = widget.get_current_view()
+ return widget
+
+ def view_changed(self):
+ from vistrails.gui.vistrails_window import _app
+ _app.closeNotPinPalettes()
+ #view = self.stack.currentWidget()
+ view = self.get_current_outer_tab()
+ #print "changing tab from: ",self.current_tab, " to ", view
+ #print self.tab_to_stack_idx
+ if view != self.current_tab:
+ #print "!!unset_action_links of ", self.current_tab
+ _app.unset_action_links(self.current_tab)
+ self.current_tab = view
+# print "\n!! _app.notifications: "
+# for (k, v) in _app.notifications.iteritems():
+# print " ", k, " (%s) "%len(v)
+# for m in v:
+# print " ", m
+# print "\n!!set_action_defaults of ", self.current_tab
+ _app.set_action_defaults(self.current_tab)
+ #print "\n!!set_action_links of ", self.current_tab
+ _app.set_action_links(self.current_tab.action_links, self.current_tab,
+ self)
+
+ #else:
+ # print "tabs the same. do nothing"
+ self.showCurrentViewPalettes()
+ if isinstance(view, QQueryView):
+ _app.notify("controller_changed", view.p_controller)
+ _app.notify("entry_klass_changed", QueryEntry)
+ else:
+ _app.notify("entry_klass_changed", ParameterEntry)
+ _app.notify("controller_changed", self.controller)
+
+ if self.window().isActiveWindow():
+ if self.isTabDetachable(self.tabs.currentIndex()):
+ self.tabs.setTabToolTip(self.tabs.currentIndex(),
+ "Double-click to detach it")
+ else:
+ self.tabs.setTabToolTip(self.tabs.currentIndex(),
+ "")
+ if get_vistrails_configuration().detachHistoryView:
+ if hasattr(self.window(), 'qactions'):
+ _app = self.window()
+ _app.history_view.stack.setCurrentIndex(self.version_index)
+
+ def showCurrentViewPalettes(self):
+ current_tab = self.get_current_tab(True)
+ for dock_loc, palette_klass in current_tab.palette_layout.iteritems():
+ palette_instance = palette_klass.instance()
+ window = palette_instance.toolWindow().parentWidget()
+ if window:
+ current_loc = window.dockWidgetArea(palette_instance.toolWindow())
+ else:
+ current_loc = QtCore.Qt.NoDockWidgetArea
+ #print ">> P:", palette_instance.__class__.__name__, current_loc, \
+ # dock_loc
+
+ if current_loc == dock_loc:
+ # palette_instance.get_action().trigger()
+ palette_instance.set_visible(True)
+
+ def tab_changed(self, index):
+ #print 'raw tab_changed', index
+ if index < 0 or self.controller is None:
+ return
+
+ from vistrails.gui.vistrails_window import _app, QVistrailViewWindow
+
+ self.stack.setCurrentIndex(self.tab_to_stack_idx[index])
+ if isinstance(self.window(),QVistrailViewWindow):
+ window = self.window()
+ else:
+ window = _app
+ #print window
+ for action in window.view_action_group.actions():
+ action.setChecked(False)
+ self.selected_mode = None
+ action = None
+ if index in self.tab_state:
+ action = self.tab_state[index]
+ # if action is not None:
+ # print 'running toggle'
+ # action.toggle()
+ # action.setChecked(True)
+ else:
+ self.tab_state[index] = window.qactions['pipeline']
+ if action is not None:
+ action.setChecked(True)
+ # _app.view_triggered(action)
+
+ view = self.stack.widget(self.tab_to_stack_idx[index])
+ #print "view changed: ", view
+ self.set_to_current(view)
+
+ def set_to_current(self, view):
+ from vistrails.gui.vistrails_window import _app, QVistrailViewWindow
+ if isinstance(view, QDiffView):
+ view.set_to_current()
+ #print "view changed!", self.controller, \
+ # self.controller.current_version
+ _app.notify("controller_changed", self.controller)
+ self.reset_version_view()
+ elif isinstance(view, QLogView):
+ view.set_to_current()
+ #print "view changed!", self.controller, \
+ # self.controller.current_version
+ _app.notify("controller_changed", self.controller)
+ self.reset_version_view()
+ elif isinstance(view, QPipelineView):
+ #print "PIPELINE_VIEW NEW SCENE:", id(view.scene())
+
+ # need to set the controller's version, pipeline, view
+ # to this view...
+ # self.controller.current_version = view.current_version
+ # self.controller.current_pipeline = view.current_pipeline
+ view.set_to_current()
+ #print "view changed!", self.controller, \
+ # self.controller.current_version
+ real_view = self.stack.currentWidget()
+ if isinstance(real_view, QQueryView):
+ _app.notify("controller_changed", real_view.p_controller)
+ else:
+ _app.notify("controller_changed", self.controller)
+ self.reset_version_view()
+
+ def create_pipeline_view(self, read_only=False, set_controller=True):
+ view = self.create_view(QPipelineView)
+ view.setReadOnlyMode(read_only)
+ self.connect(view.scene(), QtCore.SIGNAL('moduleSelected'),
+ self.gen_module_selected(view))
+ if set_controller:
+ view.set_controller(self.controller)
+ view.set_to_current()
+ self.set_notification('module_done_configure', view.done_configure)
+ #self.switch_to_tab(view.tab_idx)
+ return view
+
+ def add_pipeline_view(self, read_only=False):
+ view = self.create_pipeline_view(read_only)
+ self.switch_to_tab(view.tab_idx)
+ return view
+
+ def create_version_view(self):
+ view = self.create_view(QVersionTreeView, False)
+ self.connect(view.scene(),
+ QtCore.SIGNAL('versionSelected(int,bool,bool,bool,bool)'),
+ self.version_selected)
+ self.connect(view.scene(),
+ QtCore.SIGNAL('diffRequested(int,int)'),
+ self.diff_requested)
+ return view
+
+ def create_query_view(self):
+ view = self.create_view(QQueryView, False)
+ self.connect(view.pipeline_view.scene(),
+ QtCore.SIGNAL('moduleSelected'),
+ self.gen_module_selected(view.pipeline_view))
+ # self.connect(view.version_result_view.scene(),
+ # QtCore.SIGNAL('versionSelected(int,bool,bool,bool,bool)'),
+ # self.version_selected)
+ # self.connect(view.version_result_view.scene(),
+ # QtCore.SIGNAL('diffRequested(int,int)'),
+ # self.diff_requested)
+ self.set_notification('query_changed', view.query_changed)
+ # DAK: removed this notification: query view has own version
+ # self.set_notification('version_changed', view.version_changed)
+ return view
+
+ def create_diff_view(self):
+ view = self.create_view(QDiffView)
+ self.connect(view.scene(), QtCore.SIGNAL('moduleSelected'),
+ self.gen_module_selected(view))
+ return view
+
+ def create_pe_view(self):
+ view = self.create_view(QParamExploreView, False)
+ self.set_notification('controller_changed', view.set_controller)
+ self.set_notification('pipeline_changed', view.updatePipeline)
+ self.set_notification('exploration_changed', view.set_exploration)
+ return view
+
+ def create_log_view(self):
+ from vistrails.gui.vistrails_window import _app
+ view = self.create_view(QLogView, False)
+ self.set_notification('execution_changed', view.execution_changed)
+ return view
+
+ def create_mashup_view(self, set_controller=True):
+ #print "******* create mashup view"
+ from vistrails.gui.vistrails_window import _app
+ view = self.create_view(QMashupView, False)
+ if set_controller:
+ view.set_controller(self.controller)
+ self.set_notification('controller_changed', view.controllerChanged)
+ self.set_notification('alias_changed', view.aliasChanged)
+ self.set_notification('version_changed', view.versionChanged)
+ return view
+
+ def gen_module_selected(self, view):
+ def module_selected(module_id, selection = []):
+ from vistrails.gui.vistrails_window import _app
+ pipeline = view.scene().current_pipeline
+ if pipeline is not None and module_id in pipeline.modules:
+ module = pipeline.modules[module_id]
+ _app.notify('module_changed', module)
+ else:
+ _app.notify('module_changed', None)
+ return module_selected
+
+ def version_selected(self, version_id, by_click, do_validate=True,
+ from_root=False, double_click=False):
+ from vistrails.gui.vistrails_window import _app
+ from vistrails.gui.vis_diff import QDiffView
+ if hasattr(self.window(), 'qactions'):
+ window = self.window()
+ else:
+ window = _app
+ #print 'got version selected:', version_id
+ if _app._focus_owner in self.detached_views.values():
+ view = _app._focus_owner.view
+ elif _app._previous_view in self.detached_views:
+ view = _app._previous_view
+ else:
+ view = self.stack.widget(
+ self.tab_to_stack_idx[self.tabs.currentIndex()])
+ if view and by_click:
+ self.controller.change_selected_version(version_id, True,
+ do_validate, from_root)
+
+ view.scene().fitToView(view, True)
+ if double_click:
+ # view = self.create_pipeline_view()
+ # view.set_controller(self.controller)
+ # view.set_to_current()
+ # self.tabs.setCurrentWidget(view.parent())
+ window.qactions['pipeline'].trigger()
+ self.controller.reset_redo_stack()
+ if view and not isinstance(view, QDiffView):
+ if view not in self.detached_views:
+ view.set_title("Pipeline: %s" %
+ self.controller.get_pipeline_name())
+ else:
+ view.set_title(view.get_long_title())
+ view.window().setWindowTitle(view.get_long_title())
+ _app.notify("version_changed", self.controller.current_version)
+ _app.notify("pipeline_changed", self.controller.current_pipeline)
+
+ def query_version_selected(self, search=None, version_id=None):
+ if version_id is None:
+ self.query_view.set_result_level(
+ self.query_view.query_controller.LEVEL_VISTRAIL)
+ self.query_view.query_controller.set_search(search)
+ else:
+ self.query_view.set_result_level(
+ self.query_view.query_controller.LEVEL_WORKFLOW)
+ self.query_view.query_controller.set_search(search)
+ self.query_view.result_version_selected(version_id, True,
+ double_click=True)
+
+ window = self.window()
+ window.qactions['search'].trigger()
+
+ def diff_requested(self, version_a, version_b, vistrail_b=None):
+ """diff_requested(self, id, id, Vistrail) -> None
+
+ Request a diff between two versions. If vistrail_b is
+ specified, the second version will be derived from that
+ vistrail instead of the common vistrail controlled by this
+ view.
+ """
+
+ view = self.create_diff_view()
+ view.set_controller(self.controller)
+ view.set_diff(version_a, version_b, vistrail_b)
+ self.switch_to_tab(view.tab_idx)
+ view.scene().fitToView(view, True)
+ self.view_changed()
+
+ def save_vistrail(self, locator_class, force_choose_locator=False, export=False):
+ """
+ force_choose_locator=True triggers 'save as' behavior
+ export=True does not update the current controller
+
+ """
+ locator = self.controller.locator
+ if locator_class is None:
+ if locator is not None:
+ locator_class = type(locator)
+ else:
+ debug.critical('Failed to save vistrail, unknown '
+ 'locator class.')
+
+ #print "CALLED SAVE VISTRAIL", locator_class
+
+ self.flush_changes()
+ gui_get = locator_class.save_from_gui
+ # get a locator to write to
+ if not locator or locator.is_untitled():
+ force_choose_locator = True
+ if force_choose_locator:
+ locator = gui_get(self, Vistrail.vtType,
+ self.controller.locator)
+ # if couldn't get one, ignore the request
+ if not locator:
+ return False
+ try:
+ self.controller.write_vistrail(locator, export=export)
+ except Exception, e:
+ import traceback
+ debug.critical('Failed to save vistrail: %s' % str(e),
+ traceback.format_exc())
+ raise
+ return False
+ if export:
+ return self.controller.locator
+
+ if not force_choose_locator:
+ from vistrails.gui.vistrails_window import _app
+ _app.view_changed(self)
+ _app.notify("vistrail_saved")
+ return locator
+ # update collection
+ try:
+ thumb_cache = ThumbnailCache.getInstance()
+ self.controller.vistrail.thumbnails = \
+ self.controller.find_thumbnails(
+ tags_only=thumb_cache.conf.tagsOnly)
+ self.controller.vistrail.abstractions = \
+ self.controller.find_abstractions(self.controller.vistrail,
+ True)
+ self.controller.vistrail.mashups = self.controller._mashups
+
+ collection = Collection.getInstance()
+ url = locator.to_url()
+ entity = collection.updateVistrail(url, self.controller.vistrail)
+ # add to relevant workspace categories
+ collection.add_to_workspace(entity)
+ collection.commit()
+ except Exception, e:
+ import traceback
+ debug.critical('Failed to index vistrail', traceback.format_exc())
+
+ from vistrails.gui.vistrails_window import _app
+ # update recent files menu items
+ if not self.is_abstraction:
+ _app.set_current_locator(locator)
+ _app.view_changed(self)
+ _app.notify("vistrail_saved")
+ # reload workspace entry
+ from vistrails.gui.collection.workspace import QWorkspaceWindow
+ QWorkspaceWindow.instance().add_vt_window(self)
+ return locator
+
+ def save_vistrail_as(self, locator_class):
+ #print "CALLED SAVE AS VISTRAIL", locator_class
+ self.save_vistrail(locator_class, force_choose_locator=True)
+
+ def export_vistrail(self, locator_class):
+ """ Exports vistrail without updating the current vistrail """
+ self.save_vistrail(locator_class, force_choose_locator=True, export=True)
+
+ def export_stable(self, locator_class=XMLFileLocator,
+ force_choose_locator=True):
+ """ save vistrail to previous stable version """
+ self.flush_changes()
+ gui_get = locator_class.save_from_gui
+ if force_choose_locator:
+ locator = gui_get(self, Vistrail.vtType,
+ self.controller.locator)
+ else:
+ locator = (self.controller.locator or
+ gui_get(self, Vistrail.vtType, self.controller.locator))
+ if locator is not None and locator.is_untitled():
+ locator = gui_get(self, Vistrail.vtType,
+ self.controller.locator)
+ if not locator:
+ return False
+ self.controller.write_vistrail(locator, '1.0.2', True)
+ return True
+
+
+
+ # FIXME normalize workflow/log/registry!!!
+ def save_workflow(self, locator_class, force_choose_locator=True):
+ self.flush_changes()
+ gui_get = locator_class.save_from_gui
+ if force_choose_locator:
+ locator = gui_get(self, Pipeline.vtType, self.controller.locator)
+ else:
+ locator = (self.controller.locator or
+ gui_get(self, Pipeline.vtType,
+ self.controller.locator))
+ if locator is not None and locator.is_untitled():
+ locator = gui_get(self, Pipeline.vtType, self.controller.locator)
+ if not locator:
+ return False
+ self.controller.write_workflow(locator)
+
+ def save_log(self, locator_class, force_choose_locator=True):
+ self.flush_changes()
+ gui_get = locator_class.save_from_gui
+ if force_choose_locator:
+ locator = gui_get(self, Log.vtType,
+ self.controller.locator)
+ else:
+ locator = (self.controller.locator or
+ gui_get(self, Log.vtType,
+ self.controller.locator))
+ if locator is not None and locator.is_untitled():
+ locator = gui_get(self, Log.vtType,
+ self.controller.locator)
+ if not locator:
+ return False
+ self.controller.write_log(locator)
+
+ def save_registry(self, locator_class, force_choose_locator=True):
+ self.flush_changes()
+ gui_get = locator_class.save_from_gui
+ if force_choose_locator:
+ locator = gui_get(self, ModuleRegistry.vtType,
+ self.controller.locator)
+ else:
+ locator = (self.controller.locator or
+ gui_get(self, ModuleRegistry.vtType,
+ self.controller.locator))
+ if locator is not None and locator.is_untitled():
+ locator = gui_get(self, ModuleRegistry.vtType,
+ self.controller.locator)
+ if not locator:
+ return False
+ self.controller.write_registry(locator)
+
+
+ def save_opm(self, locator_class=XMLFileLocator,
+ force_choose_locator=True):
+ self.flush_changes()
+ gui_get = locator_class.save_from_gui
+ if force_choose_locator:
+ locator = gui_get(self, OpmGraph.vtType,
+ self.controller.locator)
+ else:
+ locator = (self.controller.locator or
+ gui_get(self, OpmGraph.vtType,
+ self.controller.locator))
+ if locator is not None and locator.is_untitled():
+ locator = gui_get(self, OpmGraph.vtType,
+ self.controller.locator)
+ if not locator:
+ return False
+ self.controller.write_opm(locator)
+
+
+ def save_prov(self, locator_class=XMLFileLocator,
+ force_choose_locator=True):
+ self.flush_changes()
+ gui_get = locator_class.save_from_gui
+ if force_choose_locator:
+ locator = gui_get(self, ProvDocument.vtType,
+ self.controller.locator)
+ else:
+ locator = (self.controller.locator or
+ gui_get(self, ProvDocument.vtType,
+ self.controller.locator))
+ if locator is not None and locator.is_untitled():
+ locator = gui_get(self, ProvDocument.vtType,
+ self.controller.locator)
+ if not locator:
+ return False
+ self.controller.write_prov(locator)
+
+
+ def has_changes(self):
+ return self.controller.changed
+
+ def flush_changes(self):
+ """Flush changes in the vistrail before closing or saving.
+ """
+ # Quick workaround for notes focus out bug (ticket #182)
+ # There's probably a much better way to fix this.
+ from vistrails.gui.version_prop import QVersionProp
+ prop = QVersionProp.instance()
+ prop.versionNotes.commit_changes()
+
+ def execute(self):
+ # makes sure we are not already executing
+ if self.is_executing:
+ return
+ self.is_executing = True
+
+ view = self.get_current_tab()
+ try:
+ if hasattr(view, 'execute'):
+ view.setFocus(QtCore.Qt.MouseFocusReason)
+ view.execute()
+ finally:
+ self.is_executing = False
+
+ def publish_to_web(self):
+ view = self.get_current_tab()
+ if hasattr(view, 'publish_to_web'):
+ view.publish_to_web()
+
+ def publish_to_paper(self):
+ view = self.get_current_tab()
+ if hasattr(view, 'publish_to_paper'):
+ view.publish_to_paper()
+
+ def get_mashup_from_mashuptrail_id(self, mashuptrail_id, mashupVersion):
+ """get_mashup_from_mashuptrail_id(mashuptrail_id: int,
+ mashupVersion: int/str) -> None
+ It will find the matching mashuptrail and return the mashup
+ mashupVersion can be either version number or version tag
+
+ """
+ for mashuptrail in self.controller._mashups:
+ if str(mashuptrail.id) == mashuptrail_id:
+ try:
+ mashupVersion = int(mashupVersion)
+ except ValueError:
+ mashupVersion = mashuptrail.getTagMap()[mashupVersion]
+ mashup = mashuptrail.getMashup(mashupVersion)
+ return mashup
+ return None
+
+ def open_mashup(self, mashup):
+ """open_mashup(mashup: Mashup) -> None
+ It will switch to version view, select the corresponding node
+ and run the mashup """
+ from vistrails.gui.version_prop import QVersionProp
+ #first we will show the hisotry view and select the version that has
+ #this mashup
+ vt_version = mashup.version
+ window = self.window()
+ window.qactions['history'].trigger()
+ self.version_selected(vt_version, by_click=True)
+ self.version_view.select_current_version()
+ #then we will execute the mashup
+ version_prop = QVersionProp.instance()
+ version_prop.versionMashups.openMashup(mashup.id)
+
+ def edit_mashup(self, mashup):
+ """edit_mashup(mashup: Mashup) -> None
+ It will select the corresponding node, switch to mashup view,
+ and select mashup """
+ from vistrails.gui.mashups.mashups_inspector import QMashupsInspector
+ vt_version = mashup.version
+ window = self.window()
+ window.qactions['history'].trigger()
+ self.version_selected(vt_version, by_click=True)
+ self.version_view.select_current_version()
+ window.qactions['mashup'].trigger()
+ inspector = QMashupsInspector.instance()
+ inspector.mashupsList.selectMashup(mashup.name)
+
+ def open_parameter_exploration(self, pe_id):
+ pe = self.controller.vistrail.db_get_parameter_exploration_by_id(pe_id)
+ if not pe:
+ return
+ if self.controller.current_version != pe.action_id:
+ self.window().qactions['history'].trigger()
+ self.version_selected(pe.action_id, True)
+ self.version_view.select_current_version()
+ self.controller.current_parameter_exploration = pe
+ self.pe_view.setParameterExploration(pe)
+ self.window().qactions['explore'].trigger()
+
+ def apply_parameter_exploration(self, version, pe):
+ if not pe:
+ return
+ pe = pe.__copy__()
+ pe.action_id = version
+ if self.controller.current_version != version:
+ self.window().qactions['history'].trigger()
+ self.version_selected(version, True)
+ self.version_view.select_current_version()
+ #self.controller.current_parameter_exploration = pe
+ self.window().qactions['explore'].trigger()
+ self.pe_view.setParameterExploration(pe, False)
+ self.pe_view.table.setPipeline(self.controller.current_pipeline)
+
+ ##########################################################################
+ # Undo/redo
+
+ def set_pipeline_selection(self, old_action, new_action):
+ # need to check if anything on module changed or
+ # any connections changed
+ module_types = set(['module', 'group', 'abstraction'])
+ module_child_types = set(['function', 'parameter', 'location',
+ 'portSpec', 'annotation'])
+ conn_types = set(['connection'])
+ conn_child_types = set(['port'])
+
+ view = self.stack.currentWidget()
+ if not isinstance(view, QPipelineView):
+ return
+
+ pipeline_scene = view.scene()
+
+ if old_action is None:
+ old_action_id = 0
+ else:
+ old_action_id = old_action.id
+ if new_action is None:
+ new_action_id = 0
+ else:
+ new_action_id = new_action.id
+ action = self.controller.vistrail.general_action_chain(old_action_id,
+ new_action_id)
+
+ def module_change():
+ module_ids = set()
+ function_ids = set()
+ for op in action.operations:
+ if op.what in module_types and \
+ (op.vtType == 'change' or op.vtType == 'add'):
+ module_ids.add(op.objectId)
+ elif op.what in module_child_types and \
+ (op.vtType == 'change' or op.vtType == 'add' or
+ op.vtType == 'delete'):
+ if op.what == 'parameter':
+ function_ids.add(op.parentObjId)
+ else:
+ module_ids.add(op.parentObjId)
+ if len(function_ids) > 0:
+ for m_id, module in \
+ self.controller.current_pipeline.modules.iteritems():
+ to_discard = set()
+ for f_id in function_ids:
+ if module.has_function_with_real_id(f_id):
+ module_ids.add(m_id)
+ to_discard.add(f_id)
+ function_ids -= to_discard
+
+ for id in module_ids:
+ if id in pipeline_scene.modules:
+ pipeline_scene.modules[id].setSelected(True)
+
+ def connection_change():
+ conn_ids = set()
+ for op in action.operations:
+ if op.what in conn_types and \
+ (op.vtType == 'change' or op.vtType == 'add'):
+ conn_ids.add(op.objectId)
+ elif op.what in conn_child_types and \
+ (op.vtType == 'change' or op.vtType == 'add' or
+ op.vtType == 'delete'):
+ conn_ids.add(op.parentObjId)
+ for id in conn_ids:
+ if id in pipeline_scene.connections:
+ pipeline_scene.connections[id].setSelected(True)
+
+ module_change()
+ connection_change()
+
+ def undo(self):
+ (old_action, new_action) = self.controller.undo()
+ self.set_pipeline_selection(old_action, new_action)
+ if new_action is not None:
+ return new_action.id
+ return 0
+
+ def redo(self):
+ (old_action, new_action) = self.controller.redo()
+ self.set_pipeline_selection(old_action, new_action)
+ return new_action.id
+
+ def setVistrailVarsMode(self, on):
+ """ setVistrailVarsMode(on: bool) -> None
+ Set the vistrail variable panel state for the view
+
+ """
+ if on:
+ self.pipelineTab.vistrailVars.toolWindow().show()
+ else:
+ self.pipelineTab.vistrailVars.toolWindow().hide()
+
+ def stateChanged(self):
+ """ stateChanged() -> None
+ Handles 'stateChanged' signal from VistrailController """
+ from vistrails.gui.vistrails_window import _app
+ _app.notify("state_changed", self)
+ _app.state_changed(self)
+
+################################################################################
+# FIXME: There is a bug on VisTrails that shows up if you load terminator.vt,
+# open the image slices HW, undo about 300 times and then try to redo.
+# This should be a test here, as soon as we have an api for that.
+
+if __name__=="__main__":
+ # Initialize the Vistrails Application and Theme
+ import sys
+ from vistrails.gui import qt, theme
+ app = qt.createBogusQtGuiApp(sys.argv)
+ theme.initializeCurrentTheme()
+
+ # Now visually test QPipelineView
+ vv = QVistrailView(None)
+ vv.show()
+ sys.exit(app.exec_())
diff --git a/vistrails/gui/vistrails_palette.py b/vistrails/gui/vistrails_palette.py
new file mode 100644
index 0000000..abb47a6
--- /dev/null
+++ b/vistrails/gui/vistrails_palette.py
@@ -0,0 +1,122 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+from vistrails.gui.common_widgets import QToolWindowInterface
+
+class QVistrailsPaletteInterface(QToolWindowInterface):
+ def __init__(self):
+ QToolWindowInterface.__init__(self)
+ self.controller = None
+ self.title = None
+ self.p_id = None
+ self.main_window = None
+
+ @classmethod
+ def instance(klass):
+ if not hasattr(klass, '_instance'):
+ klass._instance = klass()
+ return klass._instance
+
+ def toolWindow(self):
+ tool_window = QToolWindowInterface.toolWindow(self)
+ return tool_window
+
+ def set_id(self, p_id):
+ self.p_id = p_id
+
+ def get_id(self):
+ return self.p_id
+
+ def set_title(self, title):
+ self.setWindowTitle(title)
+
+ def get_title(self):
+ return str(self.windowTitle())
+
+ def set_action(self, action):
+ self.action = action
+ self.connect(self.toolWindow(),
+ QtCore.SIGNAL("visibilityChanged(bool)"),
+ self.visibility_changed)
+
+ def get_action(self):
+ return self.action
+ # return self.toolWindow().toggleViewAction()
+
+ def get_action_tuple(self):
+ return (self.get_title(), self.get_title(),
+ {'checkable': True,
+ 'checked': self.toolWindow().isVisible(),
+ 'callback': self.set_visible})
+
+ def set_main_window(self, mw):
+ self.main_window = mw
+
+ def set_visible(self, enabled):
+ #print "set_visible ", self, enabled
+ if hasattr(self, 'main_window') and self.main_window is not None:
+ self.main_window.show()
+ self.main_window.raise_()
+
+ if enabled:
+ self.toolWindow().show()
+ self.toolWindow().raise_()
+
+ def set_pin_status(self, pin_status):
+ self.toolWindow().setPinStatus(pin_status)
+
+ def get_pin_status(self):
+ return self.toolWindow().pinStatus
+
+ def set_controller(self, controller):
+ self.controller = controller
+
+ def get_controller(self):
+ return self.controller
+
+ def set_module(self, module):
+ self.module = module
+
+ def get_module(self):
+ return self.module
+
+ def set_descriptor(self, descriptor):
+ self.descriptor = descriptor
+
+ def get_descriptor(self):
+ return self.descriptor
+
+ def visibility_changed(self, visible):
+ self.action.setChecked(visible)
diff --git a/vistrails/gui/vistrails_window.py b/vistrails/gui/vistrails_window.py
new file mode 100644
index 0000000..1ad99ce
--- /dev/null
+++ b/vistrails/gui/vistrails_window.py
@@ -0,0 +1,2695 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" The file describes a container widget consisting of a pipeline
+view and a version tree for each opened Vistrail """
+from PyQt4 import QtCore, QtGui
+import copy
+from itertools import izip
+import operator
+
+from vistrails.core import get_vistrails_application
+from vistrails.core.configuration import (get_vistrails_configuration,
+ get_vistrails_persistent_configuration)
+from vistrails.core.db.locator import FileLocator, XMLFileLocator, DBLocator, \
+ UntitledLocator
+from vistrails.core.db.io import load_vistrail
+from vistrails.core.interpreter.cached import CachedInterpreter
+from vistrails.core.modules.module_registry import ModuleRegistry, \
+ ModuleRegistryException
+from vistrails.core.recent_vistrails import RecentVistrailList
+import vistrails.core.system
+import vistrails.core.db.action
+from vistrails.core.packagemanager import get_package_manager
+from vistrails.core.system import vistrails_default_file_type
+from vistrails.core.vistrail.vistrail import Vistrail
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.thumbnails import ThumbnailCache
+from vistrails.core.collection import Collection
+from vistrails.core import debug
+
+from vistrails.gui.application import get_vistrails_application
+from vistrails.gui.preferences import QPreferencesDialog
+from vistrails.gui.base_view import BaseView
+from vistrails.gui.pipeline_view import QPipelineView
+from vistrails.gui.repository import QRepositoryDialog
+from vistrails.gui.theme import initializeCurrentTheme, CurrentTheme
+from vistrails.gui.utils import build_custom_window
+from vistrails.gui.vistrail_view import QVistrailView
+from vistrails.gui import merge_gui
+from vistrails.gui.vistrail_variables import QVistrailVariables
+from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
+from vistrails.gui.mashups.mashup_app import QMashupAppMainWindow
+from vistrails.gui.modules.constant_configuration import ConstantWidgetMixin
+from vistrails.gui.paramexplore.pe_view import QParamExploreView
+from vistrails.gui.mashups.alias_inspector import QAliasInspector
+from vistrails.gui.mashups.mashup_view import QMashupViewTab
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellWidget
+from vistrails.db.services.io import SaveBundle
+import vistrails.db.services.vistrail
+from vistrails.db import VistrailsDBException
+
+class QBaseViewWindow(QtGui.QMainWindow):
+ def __init__(self, view=None, parent=None, f=QtCore.Qt.WindowFlags()):
+ QtGui.QMainWindow.__init__(self, parent, f)
+
+ self.view = view
+
+ if self.view is not None:
+ self.setCentralWidget(view)
+ self.view.setVisible(True)
+
+ self.create_actions_and_toolbar()
+
+ def create_actions_and_toolbar(self):
+ self.create_actions()
+ self.init_toolbar()
+
+ def closeEvent(self, event):
+ self.emit(QtCore.SIGNAL("viewWasClosed"), self.view)
+ event.accept()
+
+ def init_toolbar(self):
+ pass
+
+ def get_current_view(self):
+ if self.view is None:
+ return None
+ return self.view.vistrail_view
+
+ def get_current_tab(self):
+ return self.view
+
+ def get_current_scene(self):
+ return self.get_current_tab().scene()
+
+ def get_current_controller(self):
+ if self.get_current_view() is None:
+ return None
+ return self.get_current_view().get_controller()
+
+ def process_list(self, action_list, parent, qactions, qmenus):
+ for data in action_list:
+ if data == "---":
+ if parent is not None:
+ parent.addSeparator()
+ continue
+ name, title, options = data
+ if isinstance(options, list):
+ # menu
+ if parent is not None:
+ qmenu = parent.addMenu(title)
+ qmenus[name] = qmenu
+ self.process_list(options, qmenu, qactions, qmenus)
+ else:
+ qaction = QtGui.QAction(title, self)
+ callback = None
+ if 'callback' in options:
+ callback = options['callback']
+ del options['callback']
+ for option, value in options.iteritems():
+ method = getattr(qaction, 'set%s' % \
+ option[0].capitalize() + \
+ option[1:])
+ method(value)
+ qactions[name] = qaction
+ if parent is not None:
+ parent.addAction(qaction)
+ if callback is not None:
+ if 'checkable' in options and \
+ options['checkable'] is True:
+ self.connect(qaction,
+ QtCore.SIGNAL("toggled(bool)"),
+ callback)
+ else:
+ self.connect(qaction, QtCore.SIGNAL("triggered()"),
+ callback)
+
+ def init_action_list(self):
+ global _app
+
+ self._actions = [("file", "&File",
+ [("export", "Export",
+ [('savePDF', "PDF...",
+ {'statusTip': "Save the current view to a PDF file",
+ 'enabled': True,
+ 'callback': _app.pass_through(self.get_current_tab,
+ 'save_pdf')}),
+ "---",
+ ('saveWorkflow', "Workflow To XML...",
+ {'statusTip': "Save the current workflow to a file",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'save_workflow',
+ FileLocator())}),
+ ('exportWorkflow', "Workflow to DB...",
+ {'statusTip': "Save the current workflow to a database",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'save_workflow',
+ DBLocator)})]),
+ "---",
+ ('close', "Close",
+ {'shortcut': QtGui.QKeySequence.Close,
+ 'statusTip': "Close the current window",
+ 'enabled': True,
+ 'callback': self.close})]),
+ ("edit", "&Edit",
+ [("undo", "Undo",
+ {'statusTip': "Undo the previous action",
+ 'shortcut': QtGui.QKeySequence.Undo,
+ 'callback': _app.pass_through(self.get_current_view,
+ 'undo'),
+ 'enabled': False}),
+ ("redo", "Redo",
+ {'statusTip': "Redo an undone action",
+ 'shortcut': QtGui.QKeySequence.Redo,
+ 'callback': _app.pass_through(self.get_current_view,
+ 'redo'),
+ 'enabled': False}),
+ "---",
+ ("copy", "Copy",
+ {'statusTip': "Copy the selected modules in the " \
+ "current pipeline view",
+ 'shortcut': QtGui.QKeySequence.Copy,
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_scene,
+ 'copySelection')}),
+ ("paste", "Paste",
+ {'statusTip': "Paste modules from the clipboard into " \
+ "the current pipeline view",
+ 'shortcut': QtGui.QKeySequence.Paste,
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_tab,
+ 'pasteFromClipboard')}),
+ ("selectAll", "Select All",
+ {'statusTip': "Select all modules in the current " \
+ "pipeline view",
+ 'enabled': True,
+ 'shortcut': QtGui.QKeySequence.SelectAll,
+ 'callback': _app.pass_through(self.get_current_scene,
+ 'selectAll')}),
+ "---",
+ ("controlFlowAssist", "Control Flow Assistant",
+ {'callback': _app.pass_through(self.get_current_tab,
+ 'run_control_flow_assist'),
+ 'statusTip': "Create a loop over the selected modules",
+ })]),
+ ("run", "&Workflow",
+ [("execute", "Execute",
+ {'icon': CurrentTheme.EXECUTE_PIPELINE_ICON,
+ 'shortcut': 'Ctrl+Return',
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_view,
+ 'execute')}),
+ ("stop_on_error", "Stop on first error",
+ {'checkable': True,
+ 'callback': _app.set_stop_on_error}),
+ ("flushCache", "Erase Cache Contents",
+ {'enabled': True,
+ 'callback': _app.flush_cache}),
+ "---",
+ ("layout", "Re-Layout",
+ {'statusTip': "Move all modules to create a clean " \
+ "layout for the workflow",
+ 'shortcut': 'Ctrl+L',
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_scene,
+ 'layout')}),
+ ("group", "Group",
+ {'statusTip': "Group the selected modules in the " \
+ "current pipeline view",
+ 'shortcut': 'Ctrl+G',
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_scene,
+ 'group')}),
+ ("ungroup", "Ungroup",
+ {'statusTip': "Ungroup the selected groups in the " \
+ "current pipeline view",
+ 'shortcut': 'Ctrl+Shift+G',
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_scene,
+ 'ungroup')}),
+ ("showGroup", "Show Pipeline",
+ {'statusTip': "Show the underlying pipeline for the " \
+ "selected group in the current pipeline view",
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_view,
+ 'show_group')}),
+ "---",
+ ("makeAbstraction", "Create Subworkflow",
+ {'statusTip': "Create a subworkflow from the selected " \
+ "modules",
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_scene,
+ 'makeAbstraction')}),
+ ("convertToAbstraction", "Convert to Subworkflow",
+ {'statusTip': "Convert selected group to a subworkflow",
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_scene,
+ 'convertToAbstraction')}),
+ ("editAbstraction", "Edit Subworkflow",
+ {'statusTip': "Edit a subworkflow",
+ 'enabled': False,
+ 'callback': _app.edit_abstraction}),
+ ("importAbstraction", "Import Subworkflow",
+ {'statusTip': "Import subworkflow from a vistrail to " \
+ "local subworkflows",
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_scene,
+ 'importAbstraction')}),
+ ("exportAbstraction", "Export Subworkflow",
+ {'statusTip': "Export subworkflow from local " \
+ "subworkflows for use in a package",
+ 'enabled': False,
+ 'callback': _app.pass_through(_app.get_current_scene,
+ 'exportAbstraction')}),
+ "---",
+ ("configureModule", "Configure Module...",
+ {'shortcut': "Ctrl+E",
+ 'enabled': False,
+ 'callback': _app.configure_module}),
+ ("documentModule", "Module Documentation...",
+ {'enabled': False,
+ 'callback': _app.show_documentation})]),
+ ("view", "&Views",
+ [("zoomToFit", "Zoom To Fit",
+ {'enabled': True,
+ 'shortcut': "Ctrl+R",
+ 'statusTip': "Fit current view to window",
+ 'callback': _app.pass_through(self.get_current_tab,
+ 'zoomToFit')}),
+ ("zoomIn", "Zoom In",
+ {'enabled': True,
+ 'shortcut': QtGui.QKeySequence.ZoomIn,
+ 'callback': _app.pass_through(self.get_current_tab,
+ 'zoomIn')}),
+ ("zoomOut", "Zoom Out",
+ {'enabled': True,
+ 'shortcut': QtGui.QKeySequence.ZoomOut,
+ 'callback': _app.pass_through(self.get_current_tab,
+ 'zoomOut')})]),
+ ("publish", "Publish",
+ [("publishPaper", "To Paper...",
+ {'enabled': True,
+ 'statusTip': \
+ "Embed workflow and results into a paper",
+ 'callback': _app.pass_through(self.get_current_view,
+ 'publish_to_paper')}),
+ ("publishWeb", "To Wiki...",
+ {'enabled': True,
+ 'statusTip': "Embed workflow in wiki",
+ 'callback' : _app.pass_through(self.get_current_view,
+ 'publish_to_web')}),
+ ("publishCrowdLabs", "To crowdLabs...",
+ {'enabled': True,
+ 'statusTip': "Publish workflows on crowdlabs.org",
+ 'callback': _app.publish_to_crowdlabs})]),
+ ("window", "Window",
+ []),
+ ("help", "Help",
+ [("help", "About VisTrails...",
+ {'callback': _app.showAboutMessage}),
+ ("checkUpdate", "Check for Updates",
+ {'callback': _app.showUpdatesMessage})])]
+
+ def create_actions(self):
+ self.init_action_list()
+
+ self.qactions = {}
+ self.qmenus = {}
+
+ menu_bar = self.menuBar()
+ #print 'menu_bar:', menu_bar
+ self.process_list(self._actions, menu_bar, self.qactions, self.qmenus)
+ #print 'done processing list'
+
+class QVistrailViewWindow(QBaseViewWindow):
+ def __init__(self, view=None, parent=None, f=QtCore.Qt.WindowFlags()):
+ QBaseViewWindow.__init__(self, view, parent, f)
+
+ self.setDocumentMode(True)
+ self.view = view
+
+ if self.view is not None:
+ self.setCentralWidget(view)
+ self.view.setVisible(True)
+ self.setWindowTitle('%s - VisTrails' % self.view.get_name())
+
+ def close_vistrail(self):
+ global _app
+ return _app.close_vistrail(self.view)
+
+ def closeEvent(self, event):
+ if not self.close_vistrail():
+ event.ignore()
+ else:
+ self.emit(QtCore.SIGNAL("window_closed"), self.view)
+ event.accept()
+
+ def get_current_controller(self):
+ return self.view.get_controller()
+
+ def get_current_view(self):
+ return self.view
+
+ def get_current_tab(self):
+ return self.view.get_current_tab()
+
+ def get_current_scene(self):
+ return self.get_current_tab().scene()
+
+ def init_toolbar(self):
+ def create_spacer():
+ spacer = QtGui.QWidget()
+ spacer.setSizePolicy(QtGui.QSizePolicy.MinimumExpanding,
+ QtGui.QSizePolicy.Preferred)
+ return spacer
+ def create_separator():
+ sep = QtGui.QWidget()
+ sep.setMinimumWidth(50)
+ return sep
+
+ self.selected_mode = None
+ self.toolbar = QtGui.QToolBar(self)
+
+ #left side
+ for action in [self.qactions[n]
+ for n in ['newVistrail', 'openFile', 'saveFile']]:
+ self.toolbar.addAction(action)
+
+ self.toolbar.addWidget(create_spacer())
+
+ #second group
+ self.view_action_group = QtGui.QActionGroup(self)
+ for action in [self.qactions[n]
+ for n in ['pipeline', 'history',
+ 'search', 'explore', 'provenance', 'mashup']]:
+ self.toolbar.addAction(action)
+ self.view_action_group.addAction(action)
+ self.toolbar.addWidget(create_separator())
+ # self.connect(self.view_action_group,
+ # QtCore.SIGNAL("triggered(QAction*)"),
+ # self.view_triggered)
+ #third group
+ for action in [self.qactions[n]
+ for n in ['execute']]:
+ self.toolbar.addAction(action)
+
+
+ self.toolbar.addWidget(create_spacer())
+ self.toolbar.addWidget(create_spacer())
+ self.toolbar.setToolButtonStyle(QtCore.Qt.ToolButtonTextUnderIcon)
+ self.addToolBar(self.toolbar)
+ self.setUnifiedTitleAndToolBarOnMac(True)
+
+ def set_title(self, title):
+ self.setWindowTitle('%s - VisTrails' % title)
+
+ def get_name(self):
+ return self.windowTitle()
+
+ def set_name(self):
+ if self.view:
+ self.set_title(self.view.get_name())
+ else:
+ self.set_title('(empty)')
+
+ def build_packages_menu_from_main_app(self):
+ global _app
+ if len(self._package_menu_items) == 0:
+ self.qmenus['packages'].menuAction().setEnabled(True)
+
+ for (pkg_id, d) in _app._package_menu_items.iteritems():
+ self._package_menu_items[pkg_id] = {}
+ for pkg_name,items in d['items']:
+ pkg_menu = self.qmenus['packages'].addMenu(str(pkg_name))
+ self._package_menu_items[pkg_id]['menu'] = pkg_menu
+ self._package_menu_items[pkg_id]['items'] = (pkg_name, items)
+ for item in items:
+ (name, callback) = item
+ action = QtGui.QAction(name, self,
+ triggered=callback)
+ pkg_menu.addAction(action)
+
+ def init_action_list(self):
+ global _app
+ # This keeps track of the menu items for each package
+ self._package_menu_items = {}
+
+ self.all_palette_actions = _app.create_palette_actions()
+ tools_actions = []
+ palette_actions = []
+ for a,p in self.all_palette_actions:
+ if p.toolWindow().window() == _app.palette_window:
+ tools_actions.append(a)
+ else:
+ palette_actions.append(a)
+
+ QBaseViewWindow.init_action_list(self)
+ #FIXME:
+ #The menus that are different from the base class' menus are being
+ # replaced in place. It would be much cleaner to create a function
+ # to add/replace a menu item of a menu.
+
+ self._actions[0] = ("file", "&File",
+ [('newVistrail', "&New",
+ {'icon': CurrentTheme.NEW_VISTRAIL_ICON,
+ 'shortcut': QtGui.QKeySequence.New,
+ 'statusTip': 'Create a new vistrail',
+ 'callback': _app.new_vistrail}),
+ ('openFile', "&Open",
+ {'icon': CurrentTheme.OPEN_VISTRAIL_ICON,
+ 'shortcut': QtGui.QKeySequence.Open,
+ 'statusTip': 'Open an existing vistrail from a file',
+ 'callback': _app.open_vistrail_default}),
+ ("openRecent", "Open Recent",
+ []),
+ ('saveFile', "&Save",
+ {'icon': CurrentTheme.SAVE_VISTRAIL_ICON,
+ 'shortcut': QtGui.QKeySequence.Save,
+ 'statusTip': "Save the current vistrail to a file",
+ 'enabled': False,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'save_vistrail')}),
+ ('saveFileAs', "Save as...",
+ {'shortcut': QtGui.QKeySequence.SaveAs,
+ 'statusTip': "Save the current vistrail to a " \
+ "different file location",
+ 'enabled': False,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'save_vistrail_as')}),
+ ('saveToOther', "Save To DB...",
+ {'statusTip': "Save the current vistrail to a " \
+ "database",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'save_vistrail_as',
+ reverse=True)}),
+ ('closeVistrail', "Close",
+ {'shortcut': QtGui.QKeySequence.Close,
+ 'statusTip': "Close the current vistrail",
+ 'enabled': False,
+ 'callback': _app.close_vistrail}),
+ "---",
+ ("import", "Import",
+ [('importFile', "From DB...",
+ {'icon': CurrentTheme.OPEN_VISTRAIL_DB_ICON,
+ 'statusTip': "Import an existing vistrail " \
+ "from a database",
+ 'callback': \
+ _app.import_vistrail_default}),
+ "---",
+ ('importWorkflow', "Workflow...",
+ {'statusTip': "Import a workflow from an XML file",
+ 'enabled': True,
+ 'callback': _app.import_workflow_default}),
+ ('importWorkflowDB', "Workflow from DB...",
+ {'statusTip': "Import a workflow from a database",
+ 'enabled': True,
+ 'callback': _app.import_workflow_from_db})]),
+ ("export", "Export",
+ [('exportFile', "To DB...",
+ {'statusTip': "Export the current vistrail to a " \
+ "database",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'export_vistrail',
+ reverse=True)}),
+ ('exportStable', "To Stable Version...",
+ {'statusTip': "Save vistrail as XML according to " \
+ "the older (stable) schema",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'export_stable')}),
+ "---",
+ ('savePDF', "PDF...",
+ {'statusTip': "Save the current view to a PDF file",
+ 'enabled': True,
+ 'callback': _app.pass_through(self.get_current_tab,
+ 'save_pdf')}),
+ "---",
+ ('saveWorkflow', "Workflow To XML...",
+ {'statusTip': "Save the current workflow to a file",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'save_workflow',
+ FileLocator())}),
+ ('exportWorkflow', "Workflow to DB...",
+ {'statusTip': "Save the current workflow to a database",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'save_workflow',
+ DBLocator)}),
+ "---",
+ ('saveOpm', "OPM XML...",
+ {'statusTip': "Save provenance according to the " \
+ "Open Provenance Model in XML",
+ 'enabled': True,
+ 'callback': _app.pass_through(self.get_current_view,
+ 'save_opm')}),
+ ('saveProv', "PROV Document...",
+ {'statusTip': "Saves provenance according to " \
+ "PROV-DM in XML",
+ 'enabled': True,
+ 'callback': _app.pass_through(self.get_current_view,
+ 'save_prov')}),
+ ('saveLog', "Log to XML...",
+ {'statusTip': "Save the execution log to a file",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'save_log',
+ FileLocator())}),
+ ('exportLog', "Log to DB...",
+ {'statusTip': "Save the execution log to a database",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'save_log',
+ DBLocator)}),
+ "---",
+ ('saveRegistry', "Registry to XML...",
+ {'statusTip': "Save the current registry to a file",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'save_registry',
+ FileLocator())}),
+ ('exportRegistry', "Registry to DB...",
+ {'statusTip': "Save the current registry to a database",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through_locator(self.get_current_view,
+ 'save_registry',
+ DBLocator)})]),
+ "---",
+ ('quitVistrails', "Quit",
+ {'shortcut': QtGui.QKeySequence.Quit,
+ 'statusTip': "Exit VisTrails",
+ 'callback': _app.quit})])
+
+ self._actions[1] = ("edit", "&Edit",
+ [("undo", "Undo",
+ {'statusTip': "Undo the previous action",
+ 'shortcut': QtGui.QKeySequence.Undo,
+ 'callback': _app.pass_through(self.get_current_view,
+ 'undo'),
+ 'enabled': False}),
+ ("redo", "Redo",
+ {'statusTip': "Redo an undone action",
+ 'shortcut': QtGui.QKeySequence.Redo,
+ 'callback': _app.pass_through(self.get_current_view,
+ 'redo'),
+ 'enabled': False}),
+ "---",
+ ("copy", "Copy",
+ {'statusTip': "Copy the selected modules in the " \
+ "current pipeline view",
+ 'shortcut': QtGui.QKeySequence.Copy,
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_scene,
+ 'copySelection')}),
+ ("paste", "Paste",
+ {'statusTip': "Paste modules from the clipboard into " \
+ "the current pipeline view",
+ 'shortcut': QtGui.QKeySequence.Paste,
+ 'enabled': False,
+ 'callback': _app.pass_through(self.get_current_tab,
+ 'pasteFromClipboard')}),
+ ("selectAll", "Select All",
+ {'statusTip': "Select all modules in the current " \
+ "pipeline view",
+ 'enabled': True,
+ 'shortcut': QtGui.QKeySequence.SelectAll,
+ 'callback': _app.pass_through(self.get_current_scene,
+ 'selectAll')}),
+ "---",
+ ("controlFlowAssist", "Control Flow Assistant",
+ {'callback': _app.pass_through(self.get_current_tab,
+ 'run_control_flow_assist'),
+ 'statusTip': "Create a loop over the selected modules",
+ }),
+ ("merge", "Merge with...",
+ []),
+ "---",
+ ("editPreferences", "Preferences...",
+ {'statusTip': "Edit system preferences",
+ 'enabled': True,
+ 'shortcut': QtGui.QKeySequence.Preferences,
+ 'callback': _app.showPreferences}),
+ ])
+ self._actions.insert(3, ("vistrail", "Vis&trail",
+ [("tag", "Tag...",
+ {'statusTip': "Tag the current pipeline",
+ 'shortcut': "Ctrl+Shift+T",
+ 'enabled': True,
+ 'callback': _app.add_tag}),
+ "---",
+ ("reLayout", "Re-Layout",
+ {'statusTip': "Re-layouts the version tree",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through(self.get_current_controller,
+ 'invalidate_version_tree')}),
+ ("expandBranch", "Expand Branch",
+ {'statusTip': "Expand all versions in the tree below " \
+ "the current version",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through(self.get_current_controller,
+ 'expand_all_versions_below')}),
+ ("collapseBranch", "Collapse Branch",
+ {'statusTip': "Collapse all expanded versions of the " \
+ "tree",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through(self.get_current_controller,
+ 'collapse_all_versions_below')}),
+ ("collapseAll", "Collapse All",
+ {'statusTip': "Collapse all expanded branches of the " \
+ "tree",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through(self.get_current_controller,
+ 'collapse_all_versions')}),
+ ("hideBranch", "Hide Branch",
+ {'statusTip': "Hide all versions in the tre including " \
+ "and below the current version",
+ 'enabled': True,
+ 'callback': \
+ _app.pass_through(self.get_current_controller,
+ 'hide_versions_below')}),
+ ("showAll", "Show All",
+ {'enabled': True,
+ 'statusTip': "Show all hidden versions",
+ 'callback': \
+ _app.pass_through(self.get_current_controller,
+ 'show_all_versions')})]))
+
+ self._actions[4] = ("view", "&Views",
+ [("newView", "New Pipeline View",
+ {'shortcut': QtGui.QKeySequence.AddTab,
+ 'enabled': True,
+ 'statusTip': "Create a new pipeline view",
+ 'callback': _app.pass_through(self.get_current_view,
+ 'add_pipeline_view')}),
+ ("newDiff", "New Visual Difference",
+ {'enabled': True,
+ 'statusTip': "Create a new visual difference for two" \
+ "pipelines",
+ 'callback': _app.new_diff}),
+ "---",
+ ("zoomToFit", "Zoom To Fit",
+ {'enabled': True,
+ 'shortcut': "Ctrl+R",
+ 'statusTip': "Fit current view to window",
+ 'callback': _app.pass_through(self.get_current_tab,
+ 'zoomToFit')}),
+ ("zoomIn", "Zoom In",
+ {'enabled': True,
+ 'shortcut': QtGui.QKeySequence.ZoomIn,
+ 'callback': _app.pass_through(self.get_current_tab,
+ 'zoomIn')}),
+ ("zoomOut", "Zoom Out",
+ {'enabled': True,
+ 'shortcut': QtGui.QKeySequence.ZoomOut,
+ 'callback': _app.pass_through(self.get_current_tab,
+ 'zoomOut')}),
+ "---",
+ ("pipeline", "Pipeline",
+ {'icon': CurrentTheme.PIPELINE_ICON,
+ 'checkable': True,
+ 'checked': True,
+ 'callback': \
+ _app.pass_through_bool(self.get_current_view,
+ 'pipeline_change')}),
+ ("history", "History",
+ {'icon': CurrentTheme.HISTORY_ICON,
+ 'checkable': True,
+ 'checked': False,
+ 'callback': \
+ _app.pass_through_bool(self.get_current_view,
+ 'history_change')}),
+ ("search", "Search",
+ {'icon': CurrentTheme.QUERY_ICON,
+ 'checkable': True,
+ 'checked': False,
+ 'callback': \
+ _app.pass_through_bool(self.get_current_view,
+ 'search_change')}),
+ ("explore", "Explore",
+ {'icon': CurrentTheme.EXPLORE_ICON,
+ 'checkable': True,
+ 'checked': False,
+ 'callback': \
+ _app.pass_through_bool(self.get_current_view,
+ 'explore_change')}),
+ ("provenance", "Provenance",
+ {'icon': CurrentTheme.PROVENANCE_ICON,
+ 'checkable': True,
+ 'checked': False,
+ 'callback': \
+ _app.pass_through_bool(self.get_current_view,
+ 'provenance_change')}),
+ ("mashup", "Mashup",
+ {'icon': CurrentTheme.MASHUP_ICON,
+ 'checkable': True,
+ 'checked': False,
+ 'enabled': False,
+ 'callback': \
+ _app.pass_through_bool(self.get_current_view,
+ 'mashup_change')}),
+ "---"] +
+ palette_actions +
+ ["---"] +
+ tools_actions +
+ ["---",
+ ("dockPalettes", "Dock Palettes",
+ {'enabled': True,
+ 'statusTip': "Dock palettes on active window",
+ 'callback': _app.dock_palettes})])
+ self._actions.insert(6, ("packages", "Packages",
+ []))
+
+ def create_actions(self):
+ """ createActions() -> None
+
+ Construct all menu/toolbar actions for window.
+
+ """
+ global _app
+
+ # format of each item in the list is:
+ # item: reference, title, options
+ # where options is either a list of subitems or
+ # a dictionary of options to be set for an action
+ # Also, "---" denotes a separator
+
+ is_main_window = False
+ if self == _app:
+ is_main_window = True
+
+ #global _global_menubar
+
+ # palettes = []
+ # palette_actions = []
+
+ self.init_action_list()
+
+ self.qactions = {}
+ self.qmenus = {}
+
+ #if is_main_window and core.system.systemType in ['Darwin']:
+ # menu_bar = QtGui.QMenuBar()
+ #_global_menubar = menu_bar
+ #else:
+ menu_bar = self.menuBar()
+ #print 'menu_bar:', menu_bar
+ self.process_list(self._actions, menu_bar, self.qactions, self.qmenus)
+ #print 'done processing list'
+
+ if is_main_window:
+ for action_tuple, palette in self.all_palette_actions:
+ palette.set_action(self.qactions[action_tuple[0]])
+ _app.connect_package_manager_signals()
+ else:
+ self.build_packages_menu_from_main_app()
+
+ self.qactions['stop_on_error'].setChecked(
+ getattr(get_vistrails_configuration(), 'stopOnError'))
+
+ # view_menu = self.qmenus["view"]
+ # for action_name, action in self.create_palette_actions():
+ # self.qactions[action_name] = action
+ # view_menu.addAction(action)
+
+class QVistrailsWindow(QVistrailViewWindow):
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ global _app
+ _app = self
+
+ QVistrailViewWindow.__init__(self, None, parent, f)
+
+ self.stack = QtGui.QStackedWidget()
+ self.vistrail_widgets = []
+ self.setCentralWidget(self.stack)
+ self.auto_view = True
+
+ self._focus_owner = None
+ self._previous_view = None
+ self._is_quitting = False
+ self._first_view = True
+ self.connect(QtGui.QApplication.clipboard(),
+ QtCore.SIGNAL('dataChanged()'),
+ self.clipboard_changed)
+ self.connect(QtGui.QApplication.instance(),
+ QtCore.SIGNAL("focusChanged(QWidget*,QWidget*)"),
+ self.applicationFocusChanged)
+
+ self.preferencesDialog = QPreferencesDialog(self)
+
+ # To track the current view we need to track all mouse clicks
+ builder = self
+ class FocusEvent(QtGui.QWidget):
+ def __init__(self):
+ QtGui.QWidget.__init__(self)
+ self.old_focus = None
+ self.vt_app = get_vistrails_application()
+ def eventFilter(self, object, event):
+ if event.type() == QtCore.QEvent.MouseButtonPress:
+ # object may be the old one when this window gets focus
+ object = self.vt_app.widgetAt(QtGui.QCursor.pos())
+ if object != self.old_focus:
+ builder.applicationFocusChanged(self.old_focus, object)
+ self.old_focus = object
+ return False
+ self.focusEvent = FocusEvent()
+ self.focusEvent.vt_app.installEventFilter(self.focusEvent)
+
+ if get_vistrails_configuration().detachHistoryView:
+ self.history_view = QBaseViewWindow(parent=None)
+ self.history_view.resize(800, 600)
+ from vistrails.gui.version_prop import QVersionProp
+ inst = QVersionProp.instance().toolWindow()
+ self.history_view.addDockWidget(QtCore.Qt.RightDockWidgetArea,inst)
+ self.history_view.stack = QtGui.QStackedWidget()
+ self.history_view.setCentralWidget(self.history_view.stack)
+ self.history_view.show()
+ self.history_view.move(self.rect().center())
+ self.history_view.setWindowTitle('Version Tree')
+
+ def create_actions_and_toolbar(self):
+ self.current_view = None
+ self.windows = {}
+ self.base_view_windows = {}
+ self.notifications = {}
+ self.view_notifications = {}
+ self.view_notifications[-1] = {}
+ self.action_links = {}
+ self.dbDefault = False
+
+ self.init_palettes()
+ self.create_menus()
+ self.setup_recent_vistrails()
+ self.init_toolbar()
+
+ def create_view(self, vistrail, locator, abstraction_files=None,
+ thumbnail_files=None, mashups=None):
+ view = QVistrailView(vistrail, locator, abstraction_files,
+ thumbnail_files, mashups)
+ self.vistrail_widgets.append(view)
+ index = self.stack.addWidget(view)
+ self.stack.setCurrentIndex(index)
+ self.view_notifications[view] = {}
+ for notification_id, method_list in \
+ view.get_notifications().iteritems():
+ for method in method_list:
+ self.register_notification(notification_id, method, True, view)
+ return view
+
+ def remove_view(self, view):
+ from vistrails.gui.collection.workspace import QWorkspaceWindow
+ if view not in self.windows:
+ if view in self.view_notifications:
+ del self.view_notifications[view]
+ self.stack.removeWidget(view)
+ else:
+ window = self.windows[view]
+ window.close()
+ QWorkspaceWindow.instance().remove_vt_window(view)
+ self.current_view = None
+
+ def view_triggered(self, action):
+ #print "VIEW_TRIGGERED", action
+ if self.selected_mode == action:
+ if action is not None:
+ #print "SETTING CHECKED FALSE"
+ action.setChecked(False)
+ self.selected_mode = None
+ else:
+ self.selected_mode = action
+ current_view = self.stack.currentWidget()
+ current_view.tab_state[current_view.tabs.currentIndex()] = \
+ self.selected_mode
+ current_view.view_changed()
+
+ def action_triggered(self, action):
+ if self.selected_mode is not None:
+ self.selected_mode.un_method()
+ if self.selected_mode != action:
+ self.selected_mode = action
+ if action is not None:
+ action.method()
+ elif self.selected_mode is not None:
+ self.selected_mode = None
+ action.setChecked(False)
+ current_view = self.stack.currentWidget()
+ current_view.tab_state[current_view.tabs.currentIndex()] = \
+ self.selected_mode
+ current_view.view_changed()
+
+ # enumeration for dock areas
+ (UPPER_LEFT_DOCK_AREA, LOWER_LEFT_DOCK_AREA, RIGHT_DOCK_AREA,
+ UTILITY_WINDOW_AREA) = range(4)
+ DOCK_AREA_MAP = {UPPER_LEFT_DOCK_AREA: QtCore.Qt.LeftDockWidgetArea,
+ LOWER_LEFT_DOCK_AREA: QtCore.Qt.LeftDockWidgetArea,
+ RIGHT_DOCK_AREA: QtCore.Qt.RightDockWidgetArea,
+ UTILITY_WINDOW_AREA: QtCore.Qt.NoDockWidgetArea}
+
+ def init_palettes(self):
+ # palettes are global!
+ from vistrails.gui.debug import DebugView
+ from vistrails.gui.job_monitor import QJobView
+ from vistrails.gui.debugger import QDebugger
+ from vistrails.gui.module_configuration import QModuleConfiguration
+ from vistrails.gui.module_documentation import QModuleDocumentation
+ from vistrails.gui.module_palette import QModulePalette
+ from vistrails.gui.module_info import QModuleInfo
+ from vistrails.gui.paramexplore.param_view import QParameterView
+ from vistrails.gui.paramexplore.pe_inspector import QParamExploreInspector
+ from vistrails.gui.shell import QShellDialog
+ from vistrails.gui.version_prop import QVersionProp
+ from vistrails.gui.vis_diff import QDiffProperties
+ from vistrails.gui.collection.explorer import QExplorerWindow
+ from vistrails.gui.collection.workspace import QWorkspaceWindow
+ from vistrails.gui.collection.vis_log import QLogDetails
+ from vistrails.gui.mashups.mashups_inspector import QMashupsInspector
+ from vistrails.gui.mashups.alias_parameter_view import QAliasParameterView
+ from vistrails.gui.publishing import QLatexAssistant, QVersionEmbed
+ self.palettes = []
+ self.palette_window = None
+
+ self.palette_layout = \
+ [(self.UPPER_LEFT_DOCK_AREA,
+ [((QWorkspaceWindow,True),
+ (('search_changed', 'updateSearchResults'),
+ ('execution_updated', 'execution_updated'),
+ ('state_changed', 'state_changed')))]),
+ (self.LOWER_LEFT_DOCK_AREA,
+ [(QModulePalette, True),
+ ((QParamExploreInspector, False),
+ (('pipeline_changed', 'set_pipeline'),
+ ('exploration_changed', 'set_exploration'),
+ ('controller_changed', 'set_controller'))),
+ ((QMashupsInspector, False),
+ (('controller_changed', 'updateVistrailController'),
+ ('mshpcontroller_changed', 'updateMshpController'),
+ ('mshpversion_changed', 'updateMshpVersion'),
+ ('version_changed', 'updateVistrailVersion')))]),
+ (self.RIGHT_DOCK_AREA,
+ [((QModuleInfo, True),
+ (('controller_changed', 'set_controller'),
+ ('module_changed', 'update_module'),
+ ('entry_klass_changed', 'update_entry_klass'))),
+ ((QVersionProp, True),
+ (('controller_changed', 'updateController'),
+ ('version_changed', 'updateVersion'))),
+ ((QDiffProperties, False),
+ (('controller_changed', 'set_controller'),
+ ('module_changed', 'update_module'))),
+ ((QParameterView, False),
+ (('controller_changed', 'set_controller'),
+ ('pipeline_changed', 'set_pipeline'))),
+ ((QLogDetails, False),
+ (('controller_changed', 'set_controller'),
+ ('execution_updated', 'execution_updated'),
+ ('execution_changed', 'execution_changed'))),
+ ((QAliasParameterView, False),
+ (('mshpcontroller_changed', 'updateMshpController'),
+ ('mshpversion_changed', 'updateMshpVersion'))),
+ ((QVistrailVariables, False),
+ (('controller_changed', 'updateController'),))]),
+ (self.UTILITY_WINDOW_AREA,
+ [((QModuleConfiguration, True),
+ (('controller_changed', 'set_controller'),
+ ('module_changed', 'updateModule'))),
+ ((QModuleDocumentation, True),
+ (('controller_changed', 'set_controller'),
+ ('module_changed', 'update_module'),
+ ('descriptor_changed', 'update_descriptor'))),
+ ((QShellDialog, True),
+ (('controller_changed', 'set_controller'),)),
+ ((QDebugger, True),
+ (('controller_changed', 'set_controller'),)),
+ (DebugView, True),
+ (QJobView, True),
+ (QExplorerWindow, True),
+# ((QLatexAssistant, True),
+# (('controller_changed', 'set_controller'),)),
+ ((QVersionEmbed, True),
+ (('controller_changed', 'set_controller'),
+ ('vistrail_saved', 'updateEmbedText'),
+ ('version_changed', 'updateVersion')))])]
+
+ left_added = None
+ self.palette_window = QPaletteMainWindow()
+ self.palette_window.setWindowTitle('VisTrails - Tools')
+ self.palette_window.setGeometry(200, 200, 768, 512)
+ self.palette_window.setDocumentMode(True)
+ for dock_area, p_group in self.palette_layout:
+ first_added = None
+ for p_klass in p_group:
+ notifications = []
+ if isinstance(p_klass, tuple):
+ p_klass, visible = p_klass
+ if isinstance(p_klass, tuple):
+ notifications = visible
+ p_klass, visible = p_klass
+ #print "generating instance", p_klass
+ palette = p_klass.instance()
+ #print 'palette:', palette
+ self.palettes.append(palette)
+ for n_tuple in notifications:
+ #print "n_tuple:", n_tuple
+ if isinstance(n_tuple, tuple):
+ if len(n_tuple) > 1:
+ n_id, method_name = n_tuple
+ else:
+ n_id = n_tuple[0]
+ method_name = n_tuple[0]
+ else:
+ n_id = n_tuple
+ method_name = n_tuple
+ method = getattr(palette, method_name)
+ self.register_notification(n_id, method)
+
+ # palette.toolWindow().show()
+ # palette.toolWindow().setFloating(True)
+ if dock_area != self.UTILITY_WINDOW_AREA:
+ palette.set_pin_status(visible)
+ qt_dock_area = self.DOCK_AREA_MAP[dock_area]
+ if first_added is None:
+ if qt_dock_area == QtCore.Qt.LeftDockWidgetArea and \
+ left_added is not None:
+ if dock_area == self.UPPER_LEFT_DOCK_AREA:
+ self.splitDockWidget(palette.toolWindow(),
+ left_added,
+ QtCore.Qt.Vertical)
+ else:
+ self.splitDockWidget(left_added,
+ palette.toolWindow(),
+ QtCore.Qt.Vertical)
+ else:
+ self.addDockWidget(qt_dock_area,
+ palette.toolWindow())
+ first_added = palette.toolWindow()
+ if qt_dock_area == QtCore.Qt.LeftDockWidgetArea and \
+ left_added is None:
+ left_added = first_added
+ else:
+ self.tabifyDockWidget(first_added, palette.toolWindow())
+ if not visible:
+ palette.toolWindow().close()
+ else:
+ self.palette_window.addPalette(palette)
+ palette.set_main_window(self.palette_window)
+
+ if self.palette_window:
+ self.palette_window.hide()
+
+ self.connect(QWorkspaceWindow.instance(),
+ QtCore.SIGNAL("vistrailChanged(PyQt_PyObject)"),
+ self.change_view)
+ self.connect(QWorkspaceWindow.instance(),
+ QtCore.SIGNAL("detachVistrail"),
+ self.detach_view)
+
+ def dock_palettes(self, window=None):
+ if not window:
+ window = QtGui.QApplication.activeWindow()
+ if window == self or window in self.windows.values():
+ left_first_added = None
+ right_first_added = None
+ for dock_area, p_group in self.palette_layout:
+ for p_klass in p_group:
+
+ if isinstance(p_klass, tuple):
+ p_klass, visible = p_klass
+ if isinstance(p_klass, tuple):
+ notifications = visible
+ p_klass, visible = p_klass
+ palette = p_klass.instance()
+ if dock_area == QtCore.Qt.RightDockWidgetArea:
+ pin_status = palette.get_pin_status()
+ palette.toolWindow().setParent(window)
+ if right_first_added is None:
+ window.addDockWidget(dock_area, palette.toolWindow())
+ right_first_added = palette.toolWindow()
+ else:
+ window.tabifyDockWidget(right_first_added, palette.toolWindow())
+ elif dock_area == QtCore.Qt.LeftDockWidgetArea:
+ pin_status = palette.get_pin_status()
+ palette.toolWindow().setParent(window)
+ if left_first_added is None:
+ window.addDockWidget(dock_area, palette.toolWindow())
+ left_first_added = palette.toolWindow()
+ else:
+ window.tabifyDockWidget(left_first_added, palette.toolWindow())
+ if not visible:
+ palette.toolWindow().close()
+ else:
+ palette.toolWindow().show()
+
+ def create_notification(self, notification_id, link_view=False, view=None):
+ vt_app = get_vistrails_application()
+ vt_app.create_notification(notification_id, self, view)
+ # if link_view:
+ # if view is not None:
+ # notifications = self.view_notifications[view]
+ # else:
+ # notifications = self.notifications
+ # if notification_id not in notifications:
+ # notifications[notification_id] = set()
+ # else:
+ # print "already added notification", notification_id
+
+ def register_notification(self, notification_id, method, link_view=False,
+ view=None):
+ vt_app = get_vistrails_application()
+ vt_app.register_notification(notification_id, method, self, view)
+ # if link_view:
+ # if view is not None:
+ # notifications = self.view_notifications[view]
+ # #print '>>> LOCAL adding notification', notification_id, view, method
+ # #print id(notifications), notifications
+ # #for n, o in notifications.iteritems():
+ # # print " ", n , "(%s)"%len(o)
+ # # for m in o:
+ # # print " ", m
+ # else:
+ # notifications = self.notifications
+ # #print '>>> GLOBAL adding notification', notification_id, method
+ # #print id(notifications), notifications
+ # if notification_id not in notifications:
+ # self.create_notification(notification_id, link_view, view)
+ # notifications[notification_id].add(method)
+
+ def unregister_notification(self, notification_id, method, link_view=False,
+ view=None):
+ vt_app = get_vistrails_application()
+ vt_app.unregister_notification(notification_id, method, self, view)
+
+# if link_view:
+# notifications = {}
+# if view in self.view_notifications:
+# notifications = self.view_notifications[view]
+# #print '>>> LOCAL remove notification', notification_id, view
+
+# #print id(notifications), notifications
+# # for n, o in notifications.iteritems():
+# # print " ", n , "(%s)"%len(o)
+# # for m in o:
+# # print " ", m
+# else:
+# notifications = self.notifications
+# #print '>>> GLOBAL remove notification', notification_id, method
+# #print id(notifications), notifications
+# if notification_id in notifications:
+# notifications[notification_id].remove(method)
+
+ def notify(self, notification_id, *args):
+ vt_app = get_vistrails_application()
+ vt_app.send_notification(notification_id, *args)
+
+ # # do global notifications
+ # if notification_id in self.notifications:
+ # print 'global notification ', notification_id
+ # for m in self.notifications[notification_id]:
+ # try:
+ # #print " m: ", m
+ # m(*args)
+ # except Exception, e:
+ # import traceback
+ # traceback.print_exc()
+ # notifications = {}
+ # # do local notifications
+ # if self.current_view in self.view_notifications:
+ # notifications = self.view_notifications[self.current_view]
+ # print 'local notification ', notification_id, self.current_view
+
+ # if notification_id in notifications:
+ # for m in notifications[notification_id]:
+ # try:
+ # #print " m: ", m
+ # m(*args)
+ # except Exception, e:
+ # import traceback
+ # traceback.print_exc()
+
+ def clipboard_changed(self):
+ self.notify("clipboard_changed")
+
+ def set_action_links(self, action_links, obj, view):
+ link_list = []
+ def get_method(_qaction, _check):
+ def do_check_and_set(*args, **kwargs):
+ _qaction.setEnabled(_check(*args, **kwargs))
+ return do_check_and_set
+ for action, (notification_id, check) in action_links.iteritems():
+ window = obj.window()
+ if isinstance(window, BaseView):
+ window = window.vistrail_view.window()
+ if action in window.qactions:
+ qaction = window.qactions[action]
+ method = get_method(qaction, check)
+ notification = (notification_id, method, True, view)
+ self.register_notification(*notification)
+ link_list.append(notification)
+ self.action_links[id(obj)] = link_list
+
+ def unset_action_links(self, obj):
+ if id(obj) in self.action_links:
+ for notification in self.action_links[id(obj)]:
+ self.unregister_notification(*notification)
+
+ def set_action_defaults(self, obj):
+ window = obj.window()
+ if isinstance(window, BaseView):
+ window = window.vistrail_view.window()
+ qactions = window.qactions
+ for action, mlist in obj.action_defaults.iteritems():
+ if action in qactions:
+ qaction = qactions[action]
+ for (method, is_callback, value) in mlist:
+ if is_callback:
+ getattr(qaction, method)(value())
+ else:
+ getattr(qaction, method)(value)
+
+ def set_name(self):
+ widget = self.stack.currentWidget()
+ if widget:
+ self.set_title(widget.get_name())
+ else:
+ self.set_title('(empty)')
+
+ # def action_triggered(self, action):
+ # if self.selected_mode is not None:
+ # self.selected_mode.un_method()
+ # if self.selected_mode != action:
+ # self.selected_mode = action
+ # if action is not None:
+ # action.method()
+ # elif self.selected_mode is not None:
+ # self.selected_mode = None
+ # action.setChecked(False)
+ # current_view = self.stack.currentWidget()
+ # current_view.tab_state[current_view.tabs.currentIndex()] = \
+ # self.selected_mode
+ # current_view.view_changed()
+
+ # def create_pass_actions(self):
+ # actions = ['history_selected', 'history_unselected',
+ # 'query_selected', 'query_unselected',
+ # 'explore_selected', 'explore_unselected']
+ # def create_action(action_str):
+ # def new_action():
+ # getattr(self.stack.currentWidget(), action_str)()
+ # return new_action
+ # for action_str in actions:
+ # method = create_action(action_str)
+ # setattr(self, action_str, method)
+
+ def sizeHint(self):
+ return QtCore.QSize(1280, 768)
+
+ def create_first_vistrail(self):
+ #print 'calling create_first_vistrail'
+ if self.get_current_view():
+ return
+ if not self.dbDefault:
+ untitled_temps = UntitledLocator.all_untitled_temporaries()
+ if len(untitled_temps) > 0:
+ if FileLocator.prompt_autosave(self):
+ for locator in untitled_temps:
+ self.open_vistrail(locator)
+ return
+ else:
+ for locator in untitled_temps:
+ locator.clean_temporaries()
+ self._first_view = None
+ self.new_vistrail(True)
+ self._first_view = self.get_current_view()
+
+ def change_view(self, view):
+ #print 'changing view', id(view), view
+ if isinstance(view, QVistrailView) or view is None:
+ if view and view not in self.windows:
+ if self.stack.currentWidget() != view:
+ self.stack.setCurrentWidget(view)
+ view.reset_tab_state()
+ self.view_changed(view)
+ if view and get_vistrails_configuration().detachHistoryView:
+ self.history_view.stack.setCurrentIndex(view.version_index)
+ self.history_view.view = view.controller
+ else:
+ debug.warning("change_view() got a wrong view type:'%s'"%view)
+
+ def detach_view(self, view):
+ if view not in self.windows:
+ index = self.stack.indexOf(view)
+ self.stack.removeWidget(view)
+ window = QVistrailViewWindow(view, parent=None)
+ self.windows[view] = window
+ self.connect(window, QtCore.SIGNAL("window_closed"),
+ self.window_closed)
+ window.qactions['history'].setChecked(True)
+ window.show()
+ # this is needed to make dropping modules work
+ self.dock_palettes(window)
+ self.dock_palettes(self)
+ self.view_changed(view)
+ else:
+ self.view_changed(view)
+
+ def attach_view(self, view=None):
+ if not view:
+ view = self.current_view
+ if view not in self.windows:
+ return
+ window = view.window()
+ self.disconnect(window, QtCore.SIGNAL("window_closed"),
+ self.window_closed)
+ self.stack.addWidget(view)
+ del self.windows[view]
+ # disable save_vistrail call
+ window.closeEvent = lambda event: event.accept()
+ window.close()
+ self.stack.setCurrentWidget(view)
+ self.view_changed(view)
+
+ def window_closed(self, view):
+ if view in self.windows:
+ del self.windows[view]
+
+ def view_changed(self, new_view):
+ """ Updates the controller when the view changes and
+ updates buttons when """
+ if self.current_view != new_view:
+ self.current_view = new_view
+ if new_view is not None:
+ self.notify('controller_changed', new_view.get_controller())
+ if new_view.current_tab:
+ self.set_action_defaults(new_view.current_tab)
+
+ if new_view is not None:
+ window = None
+ if new_view in self.windows:
+ window = self.windows[new_view]
+ if window is None:
+ if self.current_view.has_changes():
+ self.qactions['saveFile'].setEnabled(True)
+ # un-remember first view when it is changed
+ if self._first_view:
+ self._first_view = None
+ else:
+ self.qactions['saveFile'].setEnabled(False)
+ self.qactions['saveFileAs'].setEnabled(True)
+ self.qactions['closeVistrail'].setEnabled(True)
+ else:
+ window.set_name()
+ window.activateWindow()
+ window.raise_()
+ if self.current_view.has_changes():
+ window.qactions['saveFile'].setEnabled(True)
+ else:
+ window.qactions['saveFile'].setEnabled(False)
+ window.qactions['saveFileAs'].setEnabled(True)
+ window.qactions['closeVistrail'].setEnabled(True)
+ else:
+ self.qactions['saveFile'].setEnabled(False)
+ self.qactions['saveFileAs'].setEnabled(False)
+ self.qactions['closeVistrail'].setEnabled(False)
+
+ from vistrails.gui.collection.workspace import QWorkspaceWindow
+ QWorkspaceWindow.instance().change_vt_window(new_view)
+ self.update_merge_menu()
+ self.update_window_menu()
+ self.update_recent_vistrail_menu()
+ self.set_name()
+
+ def reset_toolbar_for_view(self, view):
+ if view:
+ window = view.window()
+ else:
+ window = self
+ for action in window.view_action_group.actions():
+ action.setChecked(False)
+
+ def state_changed(self, view):
+ """ state for the view changed so we need to update buttons"""
+ self.view_changed(view)
+
+ def new_vistrail(self, recover_files=False):
+ # if self.single_document_mode and self.currentView():
+ # if not self.closeVistrail():
+ # return None
+ self._first_view = None
+
+ locator = None
+ if recover_files:
+ untitled_temps = UntitledLocator.all_untitled_temporaries()
+ if len(untitled_temps) > 0:
+ # FIXME how do we choose which one? -- really should open all
+ locator = untitled_temps[0]
+
+ # try:
+ # (vistrail, abstraction_files, thumbnail_files) = load_vistrail(locator)
+ # except ModuleRegistryException, e:
+ # debug.critical("Module registry error for %s" %
+ # str(e.__class__.__name__), str(e))
+ # except Exception, e:
+ # debug.critical('An error has occurred', str(e))
+ # raise
+ # return self.set_vistrail_view(vistrail, locator, abstraction_files,
+ # thumbnail_files)
+
+ self.open_vistrail(locator)
+ self.qactions['pipeline'].trigger()
+
+ def close_first_vistrail_if_necessary(self):
+ # Close first vistrail of no change was made
+ if not self._first_view:
+ return
+ if self._first_view is True:
+ view = self.get_current_view()
+ if not view:
+ return
+ vt = view.controller.vistrail
+ else:
+ vt = self._first_view.controller.vistrail
+ if vt.get_version_count() == 0:
+ #print "closing first vistrail"
+ self.close_vistrail(self._first_view)
+ self._first_view = None
+ else:
+ # We set it to none, since it's been changed, so
+ # we don't want to ever close it again.
+ self._first_view = None
+
+ def ensureController(self, controller):
+ """ ensureController(locator: VistrailController) -> QVistrailView
+ This will first find among the opened vistrails to see if
+ controller is open. If not, it will try to open it if a locator exist.
+
+ This should be used when you have a controller and want to open the
+ associated vistrail
+ """
+ if controller is None:
+ return None
+ for i in xrange(self.stack.count()):
+ view = self.stack.widget(i)
+ if view.controller is controller:
+ self.change_view(view)
+ return view
+ for (view, window) in self.windows.iteritems():
+ if view.controller == controller:
+ window.activateWindow()
+ window.raise_()
+ return view
+ # try to open it
+ if controller.locator:
+ return self.open_vistrail(controller.locator)
+ return None
+
+ def getViewFromLocator(self, locator):
+ """ getViewFromLocator(locator: VistrailLocator) -> QVistrailView
+ This will find the view associated with the locator. If not, it will
+ return None.
+
+ """
+ if locator is None:
+ return None
+ for i in xrange(self.stack.count()):
+ view = self.stack.widget(i)
+ if view.controller.vistrail.locator == locator:
+ return view
+ for (view, window) in self.windows.iteritems():
+ if view.controller.vistrail.locator == locator:
+ return view
+ return None
+
+ def ensureVistrail(self, locator):
+ """ ensureVistrail(locator: VistrailLocator) -> QVistrailView
+ This will first find among the opened vistrails to see if
+ vistrails from locator has been opened. If not, it will return None.
+
+ """
+ if locator is None:
+ return None
+ for i in xrange(self.stack.count()):
+ view = self.stack.widget(i)
+ if view.controller.vistrail.locator == locator:
+ self.change_view(view)
+ return view
+ for (view, window) in self.windows.iteritems():
+ if view.controller.vistrail.locator == locator:
+ window.activateWindow()
+ window.raise_()
+ return view
+ return None
+
+ def add_vistrail(self, *objs):
+ view = self.create_view(*objs)
+ # view.is_abstraction = is_abstraction
+ self.view_changed(view)
+ self.reset_toolbar_for_view(view)
+ self.qactions['history'].trigger()
+ view.version_view.zoomToFit()
+ return view.controller
+
+ def remove_vistrail(self, locator):
+ for view in copy.copy(self.vistrail_widgets):
+ if view.controller.locator == locator:
+ from vistrails.gui.job_monitor import QJobView
+ jobView = QJobView.instance()
+ jobView.delete_job(view.controller, all=True)
+
+ view.closeDetachedViews()
+ self.remove_view(view)
+ self.vistrail_widgets.remove(view)
+ if view == self._first_view:
+ self._first_view = None
+ elif not self.stack.count() and not self._is_quitting and \
+ self.auto_view:
+ self.create_first_vistrail()
+ view = self.get_next_view()
+ self.change_view(view)
+
+ def select_version(self, version):
+ view = self.get_current_view()
+ if view is not None:
+ view.version_selected(version, True, double_click=True)
+ return True
+ return False
+
+ def open_vistrail(self, locator, version=None, is_abstraction=False):
+ """open_vistrail(locator: Locator, version = None: int or str,
+ is_abstraction: bool)
+
+ opens a new vistrail from the given locator, selecting the
+ given version.
+
+ """
+ old_view = self.getViewFromLocator(locator)
+ self.close_first_vistrail_if_necessary()
+
+ get_vistrails_application().open_vistrail(locator, version,
+ is_abstraction)
+ view = self.get_current_view()
+ view.is_abstraction = view.controller.is_abstraction
+ if not old_view:
+ # it was not already open
+ from vistrails.gui.collection.workspace import QWorkspaceWindow
+ QWorkspaceWindow.instance().add_vt_window(view)
+ return view
+
+ def open_vistrail_from_locator(self, locator_class):
+ """ open_vistrail(locator_class) -> None
+ Prompt user for information to get to a vistrail in different ways,
+ depending on the locator class given.
+ """
+ locator = locator_class.load_from_gui(self, Vistrail.vtType)
+ if locator:
+ if not self.getViewFromLocator(locator):
+ if locator.has_temporaries():
+ if not locator_class.prompt_autosave(self):
+ locator.clean_temporaries()
+ if hasattr(locator, '_vnode'):
+ version = locator._vnode
+ if hasattr(locator,'_vtag'):
+ # if a tag is set, it should be used instead of the
+ # version number
+ if locator._vtag != '':
+ version = locator._vtag
+ mashuptrail = None
+ mashupversion = None
+ execute = False
+ if hasattr(locator, '_mshptrail'):
+ mashuptrail = locator._mshptrail
+ if hasattr(locator, '_mshpversion'):
+ mashupversion = locator._mshpversion
+ if mashupversion:
+ execute = True
+ self.open_vistrail_without_prompt(locator, version,
+ mashuptrail=mashuptrail,
+ mashupVersion=mashupversion,
+ execute_workflow=execute)
+ self.set_current_locator(locator)
+
+ def executeParameterExploration(self, pe_id):
+ vistrail = self.current_view.controller.vistrail
+ try:
+ pe_id = int(pe_id)
+ pe = vistrail.get_paramexp(pe_id)
+ except ValueError:
+ pe= vistrail.get_named_paramexp(pe_id)
+ except Exception:
+ return
+ self.current_view.open_parameter_exploration(pe.id)
+ self.qactions['execute'].trigger()
+
+ def open_vistrail_without_prompt(self, locator, version=None,
+ execute_workflow=False,
+ is_abstraction=False, workflow_exec=None,
+ mashuptrail=None, mashupVersion=None,
+ parameterExploration=None):
+ """open_vistrail_without_prompt(locator_class, version: int or str,
+ execute_workflow: bool,
+ is_abstraction: bool) -> None
+ Open vistrail depending on the locator class given.
+ If a version is given, the workflow is shown on the Pipeline View.
+ If execute_workflow is True the workflow will be executed.
+ If is_abstraction is True, the vistrail is flagged as abstraction
+ If mashuptrail is not None and mashupVersion is not None, the mashup
+ will be executed.
+ If parameterExploration is not None, it will be opened.
+
+ """
+
+ # move additional information from locator to variables
+ if 'version_node' in locator.kwargs:
+ if locator.kwargs['version_node']:
+ version = locator.kwargs['version_node']
+ del locator.kwargs['version_node']
+ if 'version_tag' in locator.kwargs:
+ if locator.kwargs['version_tag']:
+ version = locator.kwargs['version_tag']
+ del locator.kwargs['version_tag']
+ if not parameterExploration:
+ if 'parameterExploration' in locator.kwargs:
+ parameterExploration = locator.kwargs['parameterExploration']
+ del locator.kwargs['parameterExploration']
+ if not mashuptrail:
+ if 'mashuptrail' in locator.kwargs:
+ mashuptrail = locator.kwargs['mashuptrail']
+ del locator.kwargs['mashuptrail']
+ if not mashupVersion:
+ if 'mashupVersion' in locator.kwargs:
+ mashupVersion = locator.kwargs['mashupVersion']
+ del locator.kwargs['mashupVersion']
+ if 'mashup' in locator.kwargs:
+ if not mashupVersion:
+ mashupVersion = locator.kwargs['mashup']
+ del locator.kwargs['mashup']
+
+ if not locator.is_valid():
+ ok = locator.update_from_gui(self)
+ else:
+ ok = True
+ if ok:
+ if locator and not self.getViewFromLocator(locator):
+ if locator.has_temporaries():
+ if not locator.prompt_autosave(self):
+ locator.clean_temporaries()
+ view = self.open_vistrail(locator, version, is_abstraction)
+ view.version_view.select_current_version()
+ conf = get_vistrails_configuration()
+ has_tag = len(view.controller.vistrail.get_tagMap()) > 0
+ if (not conf.check('showPipelineViewOnLoad')) and \
+ (conf.check('showHistoryViewOnLoad') or has_tag):
+ self.qactions['history'].trigger()
+
+ if version:
+ self.qactions['pipeline'].trigger()
+
+ if mashuptrail is not None and mashupVersion is not None:
+ mashup = view.get_mashup_from_mashuptrail_id(mashuptrail,
+ mashupVersion)
+ if execute_workflow:
+ view.open_mashup(mashup)
+ else:
+ view.edit_mashup(mashup)
+ elif parameterExploration is not None:
+ view.open_parameter_exploration(parameterExploration)
+ elif execute_workflow:
+ self.qactions['execute'].trigger()
+
+ # self.closeVistrailAction.setEnabled(True)
+ # self.saveFileAsAction.setEnabled(True)
+ # self.exportFileAction.setEnabled(True)
+ # self.vistrailMenu.menuAction().setEnabled(True)
+ # self.mergeMenu.menuAction().setEnabled(True)
+ # self.viewManager.changeCursor(self.interactionToolBar.cursorMode)
+ # if version:
+ # self.viewModeChanged(0)
+ # else:
+ # self.viewModeChanged(1)
+ if workflow_exec:
+ self.qactions['provenance'].trigger()
+ self.current_view.log_view.set_exec_by_id(workflow_exec) or \
+ self.current_view.log_view.set_exec_by_date(workflow_exec)
+
+ def open_vistrail_default(self):
+ """ open_vistrail_default() -> None
+ Opens a vistrail from the file/db
+
+ """
+ if self.dbDefault:
+ self.open_vistrail_from_locator(DBLocator)
+ else:
+ self.open_vistrail_from_locator(FileLocator())
+
+ def import_vistrail_default(self):
+ """ import_vistrail_default() -> None
+ Imports a vistrail from the file/db
+
+ """
+ if self.dbDefault:
+ self.open_vistrail_from_locator(FileLocator())
+ else:
+ self.open_vistrail_from_locator(DBLocator)
+
+ def import_workflow(self, locator_class):
+ locator = locator_class.load_from_gui(self, Pipeline.vtType)
+ if locator:
+ if not locator.is_valid():
+ ok = locator.update_from_gui(self, Pipeline.vtType)
+ else:
+ ok = True
+ if ok:
+ self.open_workflow(locator)
+
+ def import_workflow_default(self):
+ self.import_workflow(XMLFileLocator)
+
+ def import_workflow_from_db(self):
+ """ import_workflow_from_db() -> None
+ Imports a workflow from the db
+
+ """
+ self.import_workflow(DBLocator)
+
+ def open_workflow(self, locator):
+ self.close_first_vistrail_if_necessary()
+
+ get_vistrails_application().open_workflow(locator)
+
+ self.qactions['pipeline'].trigger()
+
+ def close_vistrail(self, current_view=None, quiet=False):
+ locator = None
+ if not current_view:
+ current_view = self.get_current_view()
+ if current_view:
+ locator = current_view.controller.locator
+
+ if not quiet and current_view and current_view.has_changes():
+ window = current_view.window()
+ name = current_view.controller.name
+ if name=='':
+ name = 'Untitled%s'%vistrails.core.system.vistrails_default_file_type()
+ text = ('Vistrail ' +
+ QtCore.Qt.escape(name) +
+ ' contains unsaved changes.\n Do you want to '
+ 'save changes before closing it?')
+ res = QtGui.QMessageBox.information(window,
+ 'Vistrails',
+ text,
+ '&Save',
+ '&Discard',
+ 'Cancel',
+ 0,
+ 2)
+ # Check if any unsaved workflow contains jobs
+ if res == 1:
+ vistrail = current_view.controller.vistrail
+ conf = get_vistrails_configuration()
+ if not conf.has('runningJobsList') or not conf.runningJobsList:
+ conf_jobs = []
+ else:
+ conf_jobs = conf.runningJobsList.split(';')
+ res2 = 0
+ for url in conf_jobs:
+ loc, version = url.split('?')
+ version = int(version.split('=')[1])
+ if loc != locator.to_url():
+ continue
+ action = vistrail.db_get_action_by_id(version)
+ if not action.is_dirty:
+ continue
+ if res2 == 1:
+ # already discarded
+ from vistrails.gui.job_monitor import QJobView
+ QJobView.instance().delete_job(
+ current_view.controller, version)
+ continue
+ text = ('Vistrail ' +
+ QtCore.Qt.escape(name) +
+ ' contains unsaved jobs.\n Do you want to '
+ 'save changes or discard the job(s)?')
+ res2 = QtGui.QMessageBox.information(window,
+ 'Vistrails',
+ text,
+ '&Save',
+ '&Discard',
+ 'Cancel',
+ 0,
+ 2)
+ if res2 == 0:
+ res = 0
+ break
+ elif res2 == 1:
+ from vistrails.gui.job_monitor import QJobView
+ QJobView.instance().delete_job(
+ current_view.controller, version)
+ elif res2 == 2:
+ return False
+ else:
+ res = 1
+
+ if res == 0:
+ if locator is None or locator.is_untitled():
+ class_ = FileLocator()
+ else:
+ class_ = type(locator)
+ locator = current_view.save_vistrail(class_)
+ if not locator:
+ return False
+ elif res == 2:
+ return False
+
+ if locator is not None:
+ get_vistrails_application().close_vistrail(locator, current_view.controller)
+ return True
+
+ def close_all_vistrails(self, quiet=False):
+ self.current_view = None
+ for view in [self.stack.widget(i) for i in xrange(self.stack.count())]:
+ if not self.close_vistrail(view, quiet=quiet):
+ return False
+ while len(self.windows) > 0:
+ window = self.windows.values()[0]
+ window.activateWindow()
+ window.raise_()
+ if not window.close():
+ return False
+ return True
+
+ def closeEvent(self, e):
+ """ closeEvent(e: QCloseEvent) -> None
+ Close the whole application when the builder is closed
+
+ """
+ if not self.quit():
+ e.ignore()
+
+ def quit(self):
+ self._is_quitting = True
+ if self.close_all_vistrails():
+ QtCore.QCoreApplication.quit()
+ # In case the quit() failed (when Qt doesn't have the main
+ # event loop), we have to return True still
+ return True
+ self._is_quitting = False
+ return False
+
+ def link_registry(self):
+ from vistrails.gui.module_palette import QModulePalette
+ QModulePalette.instance().link_registry()
+
+ def get_current_view(self):
+ # return the current global view
+ return self.current_view
+
+ def get_next_view(self):
+ # return an available view if one exist
+ # this can be used after closing a vistrail to get a new current one
+ if self.stack.count() > 0:
+ return self.stack.currentWidget()
+ else:
+ if len(self.windows) > 0:
+ return self.windows.iterkeys().next()
+ return None
+
+ def get_current_controller(self):
+ if self.get_current_view() is None:
+ return None
+ return self.get_current_view().get_controller()
+
+ def get_current_tab(self):
+ view = self.get_current_view()
+ if not view:
+ return None
+ return view.get_current_tab()
+
+ def get_current_scene(self):
+ return self.get_current_tab().scene()
+
+ def pass_through(self, accessor, method_name):
+ def method():
+ obj = accessor()
+ if obj is not None:
+ if hasattr(obj, method_name):
+ getattr(obj, method_name)()
+ return method
+
+ def pass_through_bool(self, accessor, method_name):
+ def method(checked):
+ obj = accessor()
+ if obj is not None:
+ getattr(obj, method_name)(checked)
+ return method
+
+ def pass_through_locator(self, accessor, method_name, locator_klass=None,
+ reverse=False):
+ def method():
+ obj = accessor()
+ obj_method = getattr(obj, method_name)
+ if locator_klass is not None:
+ obj_method(locator_klass)
+ elif self.dbDefault ^ reverse:
+ obj_method(DBLocator)
+ else:
+ obj_method(FileLocator())
+ return method
+
+ def create_menus(self):
+ self.create_actions()
+ # self.fileMenu = _menu_bar.addMenu('&File')
+ # self.newVistrailAction = QtGui.QAction('&New', self)
+ # self.newVistrailAction.setShortcut('Ctrl+N')
+ # self.newVistrailAction.setStatusTip('Create a new vistrail')
+ # self.openFileAction = QtGui.QAction('&Open', self)
+ # self.openFileAction.setShortcut('Ctrl+O')
+ # self.openFileAction.setStatusTip('Open an existing vistrail from '
+ # 'a file')
+
+ # self.fileMenu.addAction(self.newVistrailAction)
+ # self.fileMenu.addAction(self.openFileAction)
+
+ # trigger_actions = [(self.newVistrailAction, self.new_vistrail),
+ # (self.openFileAction, self.open_vistrail_default)]
+ # for (emitter, receiver) in trigger_actions:
+ # self.connect(emitter, QtCore.SIGNAL('triggered()'), receiver)
+
+
+ def create_palette_actions(self):
+ palette_actions = []
+ for palette in self.palettes:
+ # palette_actions.append((palette.get_title(), palette.get_action()))
+ palette_actions.append((palette.get_action_tuple(), palette))
+ palette_actions.sort()
+ return palette_actions
+
+ def connect_package_manager_signals(self):
+ """ connect_package_manager_signals()->None
+ Connect specific signals related to the package manager """
+ self.register_notification("pm_add_package_menu",
+ self.add_package_menu_items)
+ self.register_notification("pm_remove_package_menu",
+ self.remove_package_menu_items)
+ self.register_notification("pm_package_error_message",
+ self.show_package_error_message)
+ # pm = get_package_manager()
+ # self.connect(pm,
+ # pm.add_package_menu_signal,
+ # self.add_package_menu_items)
+ # self.connect(pm,
+ # pm.remove_package_menu_signal,
+ # self.remove_package_menu_items)
+ # self.connect(pm,
+ # pm.package_error_message_signal,
+ # self.show_package_error_message)
+
+ def add_package_menu_items(self, pkg_id, pkg_name, items):
+ """add_package_menu_items(pkg_id: str,pkg_name: str,items: list)->None
+ Add a pacckage menu entry with submenus defined by 'items' to
+ Packages menu.
+
+ """
+ if len(self._package_menu_items) == 0:
+ self.qmenus['packages'].menuAction().setEnabled(True)
+
+ # we don't support a menu hierarchy yet, only a flat list
+ # this can be added later
+ def update_menu(d, packagesMenu):
+ if pkg_id not in d:
+ pkg_menu = packagesMenu.addMenu(str(pkg_name))
+ d[pkg_id] = {}
+ d[pkg_id]['menu'] = pkg_menu
+ d[pkg_id]['items'] = []
+ else:
+ pkg_menu = d[pkg_id]['menu']
+ pkg_menu.clear()
+ d[pkg_id]['items'] = [(pkg_name,items)]
+
+ for item in items:
+ (name, callback) = item
+ action = QtGui.QAction(name,self,
+ triggered=callback)
+ pkg_menu.addAction(action)
+
+ update_menu(self._package_menu_items,self.qmenus['packages'])
+
+ for w in self.windows.values():
+ update_menu(w._package_menu_items, w.qmenus['packages'])
+
+ def remove_package_menu_items(self, pkg_id):
+ """remove_package_menu_items(pkg_id: str)-> None
+ removes all menu entries from the Packages Menu created by pkg_id """
+ def update_menu(items, menu):
+ if pkg_id in items:
+ pkg_menu = items[pkg_id]['menu']
+ del items[pkg_id]
+ pkg_menu.clear()
+ pkg_menu.deleteLater()
+ if len(items) == 0:
+ menu.menuAction().setEnabled(False)
+
+ update_menu(self._package_menu_items, self.qmenus['packages'])
+ for w in self.windows.values():
+ update_menu(w._package_menu_items, w.qmenus['packages'])
+
+ def show_package_error_message(self, pkg_id, pkg_name, msg):
+ """show_package_error_message(pkg_id: str, pkg_name: str, msg:str)->None
+ shows a message box with the message msg.
+ Because the way initialization is being set up, the messages will be
+ shown after the builder window is shown.
+
+ """
+ msgbox = build_custom_window("Package %s (%s) says:"%(pkg_name,pkg_id),
+ msg,
+ modal=True,
+ parent=self)
+ #we cannot call self.msgbox.exec_() or the initialization will hang
+ # creating a modal window and calling show() does not cause it to hang
+ # and forces the messages to be shown on top of the builder window after
+ # initialization
+ msgbox.show()
+
+ def showAboutMessage(self):
+ """showAboutMessage() -> None
+ Displays Application about message
+
+ """
+ class About(QtGui.QLabel):
+ def mousePressEvent(self, e):
+ self.emit(QtCore.SIGNAL("clicked()"))
+
+ dlg = QtGui.QDialog(self, QtCore.Qt.FramelessWindowHint)
+ layout = QtGui.QVBoxLayout()
+ layout.setMargin(0)
+ layout.setSpacing(0)
+ bgimage = About(dlg)
+ bgimage.setPixmap(CurrentTheme.DISCLAIMER_IMAGE)
+ layout.addWidget(bgimage)
+ dlg.setLayout(layout)
+ text = "<font color=\"white\"><b>%s</b></font>" % \
+ vistrails.core.system.short_about_string()
+ version = About(text, dlg)
+ version.setGeometry(11,20,450,30)
+ self.connect(bgimage,
+ QtCore.SIGNAL('clicked()'),
+ dlg,
+ QtCore.SLOT('accept()'))
+ self.connect(version,
+ QtCore.SIGNAL('clicked()'),
+ dlg,
+ QtCore.SLOT('accept()'))
+ dlg.setSizeGripEnabled(False)
+ dlg.exec_()
+
+ def showUpdatesMessage(self):
+ """ showUpdatesMessage() -> None
+ Displays Check for Updates message.
+ This queries vistrails.org for new VisTrails Versions
+
+ """
+
+ new_version_exists, version = vistrails.core.system.new_vistrails_release_exists()
+ if new_version_exists:
+ msg = 'Version %s of VisTrails is available at ' \
+ '<a href="%s">%s</a>' % \
+ (version, "http://www.vistrails.org/index.php/Downloads", \
+ "http://www.vistrails.org/index.php/Downloads")
+ else:
+ msg = "Your VisTrails installation is up-to-date."
+ QtGui.QMessageBox.information(self, "Check for VisTrails Updates",
+ msg)
+
+ def showRepositoryOptions(self):
+ """ Displays Repository Options for authentication and pushing VisTrail to Repository """
+ self.publish_to_crowdlabs()
+
+ def setDBDefault(self, dbState):
+ """ setDBDefault(on: bool) -> None
+ The preferences are set to turn on/off read/write from db instead of
+ file. Update the state accordingly.
+
+ """
+ self.dbDefault = dbState
+ if self.dbDefault:
+ openFileAction = self.qactions['openFile']
+ openFileAction.setIcon(CurrentTheme.OPEN_VISTRAIL_DB_ICON)
+ openFileAction.setStatusTip('Open an existing vistrail from '
+ 'a database')
+ importFileAction = self.qactions['importFile']
+ importFileAction.setIcon(CurrentTheme.OPEN_VISTRAIL_ICON)
+ importFileAction.setText('From XML File...')
+ importFileAction.setStatusTip('Import an existing vistrail '
+ 'from a file')
+ saveFileAction = self.qactions['saveFile']
+ saveFileAction.setStatusTip('Save the current vistrail '
+ 'to a database')
+ saveFileAsAction = self.qactions['saveFileAs']
+ saveFileAsAction.setStatusTip('Save the current vistrail to a '
+ 'different database location')
+ saveToOtherAction = self.qactions['saveToOther']
+ saveToOtherAction.setText('Save To File...')
+ saveToOtherAction.setStatusTip('Save the current vistrail to '
+ 'a file')
+ exportFileAction = self.qactions['exportFile']
+ exportFileAction.setText('To File...')
+ exportFileAction.setStatusTip('Export the current vistrail to '
+ 'a file')
+ else:
+ openFileAction = self.qactions['openFile']
+ openFileAction.setIcon(CurrentTheme.OPEN_VISTRAIL_ICON)
+ openFileAction.setStatusTip('Open an existing vistrail from '
+ 'a file')
+ importFileAction = self.qactions['importFile']
+ importFileAction.setIcon(CurrentTheme.OPEN_VISTRAIL_DB_ICON)
+ importFileAction.setText('From DB...')
+ importFileAction.setStatusTip('Import an existing vistrail '
+ 'from a database')
+ saveFileAction = self.qactions['saveFile']
+ saveFileAction.setStatusTip('Save the current vistrail '
+ 'to a file')
+ saveFileAsAction = self.qactions['saveFileAs']
+ saveFileAsAction.setStatusTip('Save the current vistrail to a '
+ 'different file location')
+ saveToOtherAction = self.qactions['saveToOther']
+ saveToOtherAction.setText('Save To DB...')
+ saveToOtherAction.setStatusTip('Save the current vistrail to '
+ 'a database')
+ exportFileAction = self.qactions['exportFile']
+ exportFileAction.setText('Export To DB...')
+ exportFileAction.setStatusTip('Export the current vistrail to '
+ 'a database')
+
+ def flush_cache(self):
+ CachedInterpreter.flush()
+
+ def set_stop_on_error(self, stop):
+ setattr(get_vistrails_persistent_configuration(), 'stopOnError', stop)
+ setattr(get_vistrails_configuration(), 'stopOnError', stop)
+
+ def showPreferences(self):
+ """showPreferences() -> None
+ Display Preferences dialog
+
+ """
+ self.preferencesDialog.show()
+
+ def new_diff(self):
+ selected_items = \
+ self.get_current_view().version_view.scene().selectedItems()
+ if len(selected_items) == 2:
+ selected_ids = [item.id for item in selected_items]
+ self.get_current_view().diff_requested(*selected_ids)
+
+ def setup_recent_vistrails(self):
+ conf = get_vistrails_configuration()
+ if conf.check('recentVistrailList'):
+ self.recentVistrailLocators = \
+ RecentVistrailList.unserialize(conf.recentVistrailList)
+ else:
+ self.recentVistrailLocators = RecentVistrailList()
+ conf.subscribe('maxRecentVistrails', self.max_recent_vistrails_changed)
+ self.update_recent_vistrail_actions()
+
+ def check_running_jobs(self):
+ from vistrails.gui.job_monitor import QJobView
+ QJobView.instance().load_running_jobs()
+
+ def open_recent_vistrail(self):
+ """ open_recent_vistrail() -> None
+ Opens a vistrail from Open Recent menu list
+
+ """
+ action = self.sender()
+ if action:
+ self.open_vistrail_without_prompt(action.locator)
+ self.set_current_locator(action.locator)
+
+ def update_recent_vistrail_menu(self):
+ #check if we have enough actions
+ def update_menu(openRecentMenu):
+ openRecentMenu.clear()
+ for i, locator in enumerate(self.recentVistrailLocators.locators):
+ action = QtGui.QAction(self)
+ self.connect(action, QtCore.SIGNAL("triggered()"),
+ self.open_recent_vistrail)
+ action.locator = locator
+ action.setText("&%d %s" % (i+1, locator.name))
+ openRecentMenu.addAction(action)
+ update_menu(self.qmenus['openRecent'])
+ for w in self.windows.values():
+ update_menu(w.qmenus['openRecent'])
+
+ def update_window_menu(self):
+ def compute_action_items():
+ actions = []
+ action = QtGui.QAction(
+ "Main Window", self,
+ triggered=lambda checked=False: self.activateWindow())
+ action.setCheckable(True)
+
+ base_view_windows = {}
+ if current_view == None or \
+ QtGui.QApplication.activeWindow() == self:
+ action.setChecked(True)
+ actions.append(action)
+ if current_view and current_view.window() == self:
+ for i in range(self.stack.count()):
+ view = self.stack.widget(i)
+ for dview, dw in current_view.detached_views.iteritems():
+ base_view_windows[dview] = dw
+ if len(self.windows) > 0:
+ windowactions = []
+ for view, w in self.windows.iteritems():
+ action = QtGui.QAction(view.get_name(), self,
+ triggered=lambda checked=False: w.activateWindow())
+ action.setCheckable(True)
+ if w == QtGui.QApplication.activeWindow():
+ action.setChecked(True)
+ windowactions.append(action)
+ for dview, dw in view.detached_views.iteritems():
+ base_view_windows[dview] = dw
+ actions.append(windowactions)
+ if len(base_view_windows) > 0:
+ base_view_actions = []
+ for view, w in base_view_windows.iteritems():
+ action = QtGui.QAction(w.windowTitle(), self,
+ triggered=lambda checked=False: w.activateWindow())
+ action.setCheckable(True)
+ if w == QtGui.QApplication.activeWindow():
+ action.setChecked(True)
+ base_view_actions.append(action)
+ actions.append(base_view_actions)
+ return actions
+
+ def update_menu(windowMenu):
+ actions = compute_action_items()
+ windowMenu.clear()
+ if len(actions) > 0:
+ windowMenu.addAction(actions[0])
+ if len(actions) > 1:
+ windowMenu.addSeparator()
+ for action in actions[1]:
+ windowMenu.addAction(action)
+ if len(actions) > 2:
+ windowMenu.addSeparator()
+ for action in actions[2]:
+ windowMenu.addAction(action)
+
+ current_view = self.get_current_view()
+ update_menu(self.qmenus['window'])
+ if current_view and current_view.window() == self:
+ for i in range(self.stack.count()):
+ view = self.stack.widget(i)
+ for dw in view.detached_views.values():
+ update_menu(dw.qmenus['window'])
+ for v, w in self.windows.iteritems():
+ update_menu(w.qmenus['window'])
+ for dw in v.detached_views.values():
+ update_menu(dw.qmenus['window'])
+
+ if current_view and current_view.window() in self.windows.values():
+ # add detach action
+ current_view.window().qmenus['window'].addSeparator()
+ action = QtGui.QAction(
+ "Re-attach Vistrail View", self,
+ triggered=lambda b=None: self.attach_view())
+ current_view.window().qmenus['window'].addAction(action)
+
+
+ def update_merge_menu(self):
+ #check if we have enough actions
+ def update_menu(mergeMenu):
+ mergeMenu.clear()
+ for i in xrange(self.stack.count()):
+ view = self.stack.widget(i)
+ # skip merge with self and not saved views
+ if view == self.current_view or not view.controller.vistrail.locator:
+ continue
+ action = QtGui.QAction(self)
+ self.connect(action, QtCore.SIGNAL("triggered()"),
+ self.merge_vistrail)
+ action.controller = view.controller
+ action.setText("%s" % view.controller.vistrail.locator.name)
+ mergeMenu.addAction(action)
+ for view, w in self.windows.iteritems():
+ # skip merge with self and not saved views
+ if view == self.current_view or not view.controller.vistrail.locator:
+ continue
+ action = QtGui.QAction(self)
+ self.connect(action, QtCore.SIGNAL("triggered()"),
+ self.merge_vistrail)
+ action.controller = view.controller
+ action.setText("%s" % view.controller.vistrail.locator.name)
+ mergeMenu.addAction(action)
+
+ update_menu(self.qmenus['merge'])
+ for w in self.windows.values():
+ update_menu(w.qmenus['merge'])
+
+ def update_recent_vistrail_actions(self):
+ maxRecentVistrails = \
+ int(get_vistrails_configuration().maxRecentVistrails)
+ self.recentVistrailLocators.ensure_no_more_than_max(maxRecentVistrails)
+ self.update_recent_vistrail_menu()
+
+ conf = get_vistrails_persistent_configuration()
+ tconf = get_vistrails_configuration()
+ conf.recentVistrailList = self.recentVistrailLocators.serialize()
+ tconf.recentVistrailList = conf.recentVistrailList
+ get_vistrails_application().save_configuration()
+
+ def set_current_locator(self, locator):
+ """ set_current_locator(locator: CoreLocator)
+ Updates the list of recent files in the gui and in the configuration
+
+ """
+ if locator:
+ self.recentVistrailLocators.add_locator(locator)
+ self.update_recent_vistrail_actions()
+
+ def max_recent_vistrails_changed(self, field, value):
+ """max_recent_vistrails_changed()-> obj
+ callback to create an object to be used as a subscriber when the
+ configuration changed.
+
+ """
+ self.update_recent_vistrail_actions()
+
+ def configure_module(self):
+ from vistrails.gui.module_configuration import QModuleConfiguration
+ action_name = QModuleConfiguration.instance().get_title()
+ if action_name[-1] == '*':
+ action_name = action_name[:-1]
+ # easy way to make sure that configuration window is raised
+ self.qactions[action_name].setChecked(False)
+ self.qactions[action_name].setChecked(True)
+
+ def show_documentation(self):
+ from vistrails.gui.module_documentation import QModuleDocumentation
+ action_name = QModuleDocumentation.instance().get_title()
+ # easy way to make sure that documentation window is raised
+ self.qactions[action_name].setChecked(False)
+ self.qactions[action_name].setChecked(True)
+
+# def show_group(self):
+# class DummyController(object):
+# def __init__(self, pip):
+# self.current_pipeline = pip
+# self.search = None
+# #FIXME: this should be delegated to QVistrailView
+# current_scene = self.get_current_scene()
+# selected_module_ids = current_scene.get_selected_module_ids()
+# if len(selected_module_ids) > 0:
+# for m_id in selected_module_ids:
+# module = current_scene.current_pipeline.modules[m_id]
+# if module.is_group() or module.is_abstraction():
+# pipelineView = QPipelineView()
+# controller = DummyController(module.pipeline)
+# pipelineView.controller = controller
+# pipelineMainWindow = QBaseViewWindow(pipelineView)
+# #pipelineMainWindow.setCentralWidget(pipelineView)
+# pipelineView.scene().controller = \
+# controller
+# controller.current_pipeline_view = \
+# pipelineView.scene()
+# module.pipeline.ensure_connection_specs()
+# pipelineView.scene().setupScene(module.pipeline)
+# pipelineView.scene().current_pipeline = module.pipeline
+# pipelineView.scene().fitToView(pipelineView, True)
+# pipelineView.show()
+# pipelineMainWindow.show()
+
+ def openAbstraction(self, filename):
+ locator = XMLFileLocator(filename)
+ self.open_vistrail_without_prompt(locator, None, False, True)
+
+ def edit_abstraction(self):
+ current_scene = self.get_current_tab().scene()
+ selected_module_ids = current_scene.get_selected_module_ids()
+ if len(selected_module_ids) > 0:
+ for m_id in selected_module_ids:
+ module = current_scene.current_pipeline.modules[m_id]
+ if module.is_abstraction():
+ from vistrails.core.modules.abstraction import identifier as \
+ abstraction_pkg
+ ann_get = module.vistrail.get_annotation
+ if module.package == abstraction_pkg and \
+ ann_get('__abstraction_descriptor_info__') is None:
+ desc = module.module_descriptor
+ filename = desc.module.vt_fname
+ self.openAbstraction(filename)
+ else:
+ debug.critical('Subworkflow is from a package and is '
+ 'read-only',
+ "This subworkflow is from a package and "
+ "cannot be modified. You can create an "
+ "editable copy in 'My Subworkflows' "
+ "using 'Edit->Import Subworkflow'")
+ def merge_vistrail(self):
+ action = self.sender()
+ if action:
+ self.merge_vistrails(self.current_view.controller, action.controller)
+
+ def merge_vistrails(self, c1, c2):
+ """ merge_vistrails(c1: VistrailController, c2: VistrailController) -> None
+ hamdle merge vistrail from 2 controller into new vistrail
+
+ """
+ thumb_cache = ThumbnailCache.getInstance()
+
+ l1 = c1.locator._name if c1.locator is not None else ''
+ t1 = c1.find_thumbnails(tags_only=thumb_cache.conf.tagsOnly) \
+ if thumb_cache.conf.autoSave else []
+ s1 = SaveBundle(c1.vistrail.vtType, c1.vistrail.do_copy(), c1.log, thumbnails=t1)
+
+ l2 = c2.locator._name if c2.locator is not None else ''
+ t2 = c2.find_thumbnails(tags_only=thumb_cache.conf.tagsOnly) \
+ if thumb_cache.conf.autoSave else []
+ s2 = SaveBundle(c2.vistrail.vtType, c2.vistrail, c2.log, thumbnails=t2)
+
+ vistrails.db.services.vistrail.merge(s1, s2, "", merge_gui, l1, l2)
+ vistrail = s1.vistrail
+ vistrail.locator = None
+ vistrail.set_defaults()
+ view = self.create_view(vistrail, None)
+ # FIXME need to figure out what to do with this !!!
+ view.controller.set_vistrail(vistrail, None, thumbnails=s1.thumbnails)
+ view.controller.set_changed(True)
+ self.view_changed(view)
+ self.reset_toolbar_for_view(view)
+ self.qactions['history'].trigger()
+ view.version_view.scene().fitToView(view.version_view, True)
+
+
+
+ def do_tag_prompt(self, name="", exists=False):
+ if exists:
+ prompt = "'%s' already exists. Enter a new tag" % name
+ else:
+ prompt = "Enter a tag"
+
+ (text, ok) = QtGui.QInputDialog.getText(None,
+ 'Tag Version',
+ prompt,
+ QtGui.QLineEdit.Normal,
+ name)
+ if ok and text:
+ return str(text).strip().rstrip()
+ if not ok:
+ return None
+ return ""
+
+ def add_tag(self, check_exists=True):
+ controller = self.get_current_controller()
+ vistrail = controller.vistrail
+ name = self.do_tag_prompt()
+ if name is None:
+ return None
+ while name == "" or (check_exists and vistrail.has_tag_str(name)):
+ name = self.do_tag_prompt(name, name != "")
+ if name is None:
+ return None
+ controller.update_current_tag(name)
+
+ def publish_to_crowdlabs(self):
+ dialog = QRepositoryDialog(self)
+ if QRepositoryDialog.cookiejar:
+ dialog.exec_()
+
+ def invalidate_pipelines(self):
+ """ invalidate_pipelines() -> None
+ Clears the cache and reloads the current pipelines in all views
+ This should be called when a module in the module registry
+ is changed/added/deleted
+ """
+
+ def reload_view(view):
+ view.version_selected(view.controller.current_version,
+ True, from_root=True)
+
+ for i in xrange(self.stack.count()):
+ view = self.stack.widget(i)
+ reload_view(view)
+ for view in self.windows:
+ reload_view(view)
+
+ def closeNotPinPalettes(self):
+ if (QtGui.QApplication.activeWindow() == self or
+ QtGui.QApplication.activeWindow() in self.windows.values()):
+ for p in self.palettes:
+ if p.toolWindow().window() == QtGui.QApplication.activeWindow():
+ if (p.toolWindow().isVisible() and
+ not p.toolWindow().isFloating() and not p.get_pin_status()):
+ p.toolWindow().close()
+
+ def applicationFocusChanged(self, old, current):
+ """ This method updates the current vistrail view when needed
+ Clicking a vistrail view selects it as the current unless clicking
+ in a vistrail palette widget which are global
+ """
+ if self._is_quitting:
+ return
+ # focus owner is used to prevent view update when re-clicking a detached view
+ focus_owner = self._focus_owner
+ self._focus_owner = None
+
+ vt_app = get_vistrails_application()
+ # sometimes the correct widget is not selected
+ current = vt_app.widgetAt(QtGui.QCursor.pos())
+
+ if current is not None:
+ owner = current.window()
+ #print "\n\n\n >>>>>> applicationfocuschanged"
+ #print "owner: ", owner, " current: ", current
+ def is_or_has_parent_of_types(widget, types):
+ while widget is not None:
+ for _type in types:
+ if isinstance(widget, _type):
+ return True
+ widget = widget.parent()
+ return False
+ allowed_widgets = [ConstantWidgetMixin,
+ QParamExploreView,
+ QAliasInspector,
+ QCellWidget,
+ QMashupViewTab,
+ QVistrailsPaletteInterface]
+ old_view = self.get_current_view()
+ view = None
+ if self.isAncestorOf(current):
+ view = self.stack.currentWidget()
+ elif owner in self.windows.values():
+ view = owner.get_current_view()
+ if view:
+ # owner is a vistrail view
+ if not is_or_has_parent_of_types(current, allowed_widgets):
+ # clicked in a valid view, so update it
+ #print "generating view_changed", view
+ self.change_view(view)
+ if view != old_view:
+ self.update_window_menu()
+ self._previous_view = self.current_view.current_tab
+ view.reset_tab_view_to_current()
+ view.view_changed()
+ return
+ if isinstance(owner, QBaseViewWindow):
+ # this is a pipeline view
+ self._focus_owner = owner
+ view = owner.get_current_view()
+ if (view and owner != focus_owner and
+ not is_or_has_parent_of_types(current, allowed_widgets)):
+ #print "generating view changed2", view
+ self.change_view(view)
+ if view != old_view:
+ self.update_window_menu()
+ self._previous_view = self.current_view.current_tab
+ view.set_to_current(owner.get_current_tab())
+ view.view_changed()
+_app = None
+#_global_menubar = None
+
+
+class QPaletteMainWindow(QtGui.QMainWindow):
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ QtGui.QMainWindow.__init__(self, parent, f)
+ self.palettes = []
+ self.windows = []
+
+ def addPalette(self, palette):
+ if palette not in self.palettes:
+ self.palettes.append(palette)
+ if len(self.palettes) == 1:
+ self.addDockWidget(QtCore.Qt.TopDockWidgetArea, palette.toolWindow())
+ else:
+ self.tabifyDockWidget(self.palettes[0].toolWindow(),
+ palette.toolWindow())
+ palette.toolWindow().close()
+
+ def closeDockedPalettes(self):
+ for p in self.palettes:
+ if (p.toolWindow().isVisible() and
+ not p.toolWindow().isFloating()):
+ p.toolWindow().close()
+
+ def closeEvent(self, event):
+ if not QtCore.QCoreApplication.closingDown():
+ self.closeDockedPalettes()
+ self.hide()
+ event.ignore()
+
+ def showEvent(self, event):
+ for p in self.palettes:
+ if (not p.toolWindow().isVisible() and
+ not p.toolWindow().isFloating() and p.get_pin_status()):
+ p.set_visible(True)
+
diff --git a/vistrails/index/__core.py b/vistrails/index/__core.py
new file mode 100644
index 0000000..dffedde
--- /dev/null
+++ b/vistrails/index/__core.py
@@ -0,0 +1,143 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This is the core classes for the general workflow model
+
+The structures can hold a description of a workflow and lists of operations.
+
+This file implements:
+ Annotation
+ Parameter
+ Module
+ Connection
+ Pipeline
+ Port
+ Operation
+ Service
+"""
+
+class Annotation:
+ """
+ annotation
+ """
+ def __init__(self, key='', value=''):
+ self.key = key
+ self.value = value
+ self.annotations = [] # list of annotations
+ def __eq__(self, other):
+ """ equal if keys are equal """
+ return self.key == other.key
+
+class Parameter:
+ """
+ module parameter
+ """
+ def __init__(self, name, value='', type=''):
+ self.name = name # parameter name
+ self.value = value # value
+ self.type = type # value type type/class (actually redundant)
+ self.annotations = [] # list of annotations
+
+class Module:
+ """
+ workflow module
+ """
+ def __init__(self, name = 'New', package = '',
+ version = '', type = 'Module'):
+ self.name = name # module name
+ self.package = package # package that the 'type' is in
+ self.version = version # version of the package
+ self.type = type # module type
+ self.annotations = [] # list of annotations
+ self.parameters = [] # list of parameters
+ self.up = [] # input modules (redundant)
+ self.down = [] # output modules (redundant)
+
+class Connection:
+ """
+ A connection between modules
+ """
+ def __init__(self, startModule=None, endModule=None, \
+ startPort='', endPort=''):
+ self.startModule = startModule # reference to startmodule
+ self.endModule = endModule # reference to endmodule
+ self.startPort = startPort
+ self.endPort = endPort
+ self.annotations = [] # list of annotations
+
+class Pipeline:
+ """
+ A representation of a pipeline
+ """
+ def __init__(self, name='', type='', version='', source=''):
+ self.name = name # textual representation of pipeline
+ self.source = source # location of source
+ self.type = type # source format
+ self.version = version # version of source format
+ self.modules = [] # list of modules
+ self.connections = [] # list of connections
+ self.annotations = [] # list of annotations
+
+outPort = False
+inPort = True
+class Port:
+ """
+ module port
+ """
+ def __init__(self, name, type=None, kind=inPort):
+ self.name = name # port name
+ self.type = type # port type/class
+ self.kind = kind # inPort/outPort
+ self.annotations = [] # list of annotations
+
+class Operation:
+ """
+ An operation
+ """
+ def __init__(self, name):
+ self.name = name # operation name
+ self.ports = [] # list of ports
+ self.annotations = [] # list of annotations
+
+class Service:
+ """
+ A service representation
+ """
+ def __init__(self, name='', source='', type='', version=''):
+ self.name = name # textual representation of pipeline
+ self.source = source # location of source
+ self.type = type # source format (namespace)
+ self.version = version # version of source format
+ self.operations = [] # list of operations
+ self.annotations = [] # list of annotations
diff --git a/vistrails/index/__init__.py b/vistrails/index/__init__.py
new file mode 100644
index 0000000..fac3164
--- /dev/null
+++ b/vistrails/index/__init__.py
@@ -0,0 +1,35 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
diff --git a/vistrails/index/indexworkflow.py b/vistrails/index/indexworkflow.py
new file mode 100755
index 0000000..00df65b
--- /dev/null
+++ b/vistrails/index/indexworkflow.py
@@ -0,0 +1,226 @@
+#!/usr/bin/python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import os
+import sys
+import urllib
+import hashlib
+import shutil
+import subprocess
+
+from lucene import FSDirectory, IndexWriter, StandardAnalyzer, initVM, CLASSPATH, Field, Document, Term, File
+
+from vistrailanalyzer import vistrailAnalyzer
+from __core import *
+from spec_io import spec
+
+lvm = initVM(CLASSPATH, maxheap='512m')
+
+location = "/server/index"
+
+class WorkflowIndexer:
+ store = None
+ writer = None
+ def __init__(self):
+ self.save = Field.Store.YES
+ self.ddict = dict()
+
+ lvm.attachCurrentThread()
+
+ if not WorkflowIndexer.store and not WorkflowIndexer.writer:
+ try:
+ # open lucene index
+ WorkflowIndexer.store = FSDirectory.open(File(location))
+ # if the index directory does not exist, create it.
+ WorkflowIndexer.writer = IndexWriter( WorkflowIndexer.store,
+ vistrailAnalyzer(), not len(WorkflowIndexer.store.list()))
+ except Exception, e:
+ print "EXCEPTION", e
+ self.close()
+ raise
+
+ def close(self):
+ if WorkflowIndexer.writer:
+ WorkflowIndexer.writer.commit()
+
+ def remove(self, id):
+ print "removing index for", id
+ spec.remove(id)
+ # Delete old versions
+ WorkflowIndexer.writer.deleteDocuments(
+ [Term('workflow_id', id)] )
+ print "done removing", id
+
+ def index_vt_wf(self, wf_info, pipeline):
+ # convert to general workflow model
+ wf = self.convert_vt_wf(pipeline)
+ wf.id = str(wf_info['crowdlabs_wf_id'])
+ # add meta information
+ wf.name = wf_info['name']
+ wf.annotations.append(Annotation("title", wf_info['name']))
+ wf.annotations.append(Annotation("user", wf_info['user']))
+#value.strftime('%Y-%m-%d %H:%M:%S')
+ wf.annotations.append(Annotation("date", wf_info['date']))
+ wf.annotations.append(Annotation("note", wf_info['description']))
+ if wf_info['thumbnail'] != '':
+ wf.annotations.append(Annotation("__thumb__", wf_info['thumbnail']))
+ return self.index_wf(wf)
+
+ def index_wf(self, wf):
+ # upload to database
+ print "uploading", wf.name
+ spec.add(wf)
+ # index workflow using lucene
+ print "indexing", wf.name
+ self.write_index(wf)
+ print "done indexing", wf.name
+
+ #
+ # Creates pickle workflow object from vistrails pipeline
+ #
+ def convert_vt_wf(self, wf):
+ pipeline = Pipeline("", "vistrail", wf.db_version, "")
+
+ # process modules
+ mdict = {}
+ for module in wf.db_modules:
+ name = module.db_name
+ for annotation in module.db_annotations:
+ if annotation.db_key == "__desc__":
+ name = annotation.db_value
+ m = Module(name, module.db_package, module.db_version, module.db_name)
+ m.id = module.db_id
+ mdict[m.id] = m
+ pipeline.modules.append(m)
+
+ # location x/y
+ m.annotations.append(Annotation('loc_x', str(module.db_location.db_x)))
+ m.annotations.append(Annotation('loc_y', str(module.db_location.db_y)))
+
+ # add functions
+ for function in module.db_functions:
+ name = function.db_name
+ for parameter in function.db_parameters:
+ value = urllib.unquote(parameter.db_val) # decode pythonsources
+ pos = str(parameter.db_pos)
+ name += ((':' + pos) if len(function.db_parameters)>1 else '')
+ m.parameters.append(Parameter(name, value, parameter.db_type))
+ # empty parameter
+ if len(function.db_parameters) == 0:
+ m.parameters.append(Parameter(name, '', ''))
+
+ for connection in wf.db_connections:
+ start = connection.db_get_port_by_type('source')
+ startModuleId = start.db_moduleId
+ end = connection.db_get_port_by_type('destination')
+ endModuleId = end.db_moduleId
+
+ # get the references
+ startModule = mdict[startModuleId] if startModuleId in mdict else None
+ endModule = mdict[endModuleId] if endModuleId in mdict else None
+
+ if startModule and endModule:
+ # redundant attribute: add a module chain for fast traversal
+ if startModule not in endModule.up:
+ endModule.up.append(startModule)
+ if endModule not in startModule.down:
+ startModule.down.append(endModule)
+ pipeline.connections.append(Connection(startModule, endModule,
+ start.db_name, end.db_name))
+ else:
+ print "A broken connection was found"
+ return pipeline
+
+ def adddd(self, k, v):
+ self.ddict[k] = self.ddict[k] + " " + v if self.ddict.has_key(k) else v
+
+ def write_index(self, workflow, property = False):
+ """
+ adds all keywords in workflow to the index at the specified location
+ types of the keywords can be preserved by setting (Property = True)
+ """
+ self.ddict = dict()
+ # name is used as id in this case
+ self.adddd("workflow_id", str(workflow.id))
+
+ self.adddd("text", workflow.id)
+ self.adddd("text", workflow.name)
+ # this is a key for the workflow
+ #adddd("workflow_source", workflow.source)
+ #self.adddd("text", workflow.source)
+ #adddd("workflow_type", workflow.type)
+ self.adddd("text", workflow.type)
+ # not very interesting
+ #d.add( Field("workflow_version", workflow.version, save, Field.Index.UN_TOKENIZED))
+ self.indexAnnotations(workflow.annotations, property)
+
+ for module in workflow.modules:
+ self.adddd("module_name" if property else "text", module.name)
+ self.adddd("package" if property else "text", module.package)
+ # not very interesting
+ #d.add( Field("package_version", module.version, save, Field.Index.UN_TOKENIZED))
+ self.adddd("module_type" if property else "text", module.type)
+ self.indexAnnotations(module.annotations, property)
+ for p in module.parameters:
+ self.adddd("parameter_name" if property else "text", p.name)
+ self.adddd("parameter_value" if property else "text", p.value)
+ self.adddd("parameter_type" if property else "text", p.type)
+ self.indexAnnotations(p.annotations, property)
+
+ for c in workflow.connections:
+ self.adddd("port_name" if property else "text", c.startPort)
+ self.adddd("port_name" if property else "text", c.endPort)
+ self.indexAnnotations(c.annotations, property)
+
+ d = Document()
+ for (k, v) in self.ddict.iteritems():
+ d.add(Field(k, v, self.save, Field.Index.TOKENIZED))
+
+ # Delete old versions
+ WorkflowIndexer.writer.deleteDocuments(
+ [Term('workflow_id', str(workflow.id))] )
+ # add new
+ WorkflowIndexer.writer.addDocument(d)
+
+ def indexAnnotations(self, annotations, p):
+ """
+ design choice: key and values are indexed separately,
+ it would be possible to index them as the same type
+ """
+ for annotation in annotations:
+ self.adddd("annotation_key" if p else "text", annotation.key)
+ self.adddd("annotation_value" if p else "text", annotation.value)
+ # annotations can be recursive
+ self.indexAnnotations(annotation.annotations, p)
diff --git a/vistrails/index/spec_io.py b/vistrails/index/spec_io.py
new file mode 100644
index 0000000..6f8d450
--- /dev/null
+++ b/vistrails/index/spec_io.py
@@ -0,0 +1,137 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import sys
+import cPickle
+import MySQLdb
+from __core import Pipeline
+
+DBHOST = 'localhost'
+DBUSER = 'specuser'
+DBPASS = 'specpass'
+DBDB = 'wfspec'
+
+class Spec:
+ def __init__(self):
+ try:
+ self.db = MySQLdb.connect(DBHOST, DBUSER, DBPASS, DBDB)
+ except MySQLdb.Error, e:
+ print "1Database Connection Error %d: %s" % (e.args[0], e.args[1])
+ sys.exit(1)
+ self.cursor = MySQLdb.cursors.DictCursor(self.db)
+
+ def _exec(self, command):
+ try:
+ self.cursor.execute(command)
+ except MySQLdb.Error, e:
+ try:
+ self.db = MySQLdb.connect(DBHOST, DBUSER, DBPASS, DBDB)
+ self.cursor = MySQLdb.cursors.DictCursor(self.db)
+ self.cursor.execute(command)
+ except MySQLdb.Error, e:
+ print "3Database Connection Error %d: %s"%(e.args[0],e.args[1])
+ sys.exit(1)
+ return self.cursor.fetchall()
+
+ def get(self, name):
+ """ Given a name - returns the specification as a pickle object """
+ command = "SELECT wf FROM single_spec WHERE name='%s'" % name
+ for r in self._exec(command):
+ wf = r['wf']
+ # change class of pickle object (core module not allowed)-UGLY hack
+ if wf[0:14] == '(iindex.__core':
+ wf = wf.replace('(iindex.__core\n', '(i__core\n')
+ return cPickle.loads(wf)
+ return None
+
+ def names(self):
+ """ returns all names in db """
+ command = "SELECT name FROM single_spec"
+ return [name['name'] for name in self._exec(command)]
+
+ def getIndex(self, name):
+ command = "SELECT paths FROM spec_index WHERE name='%s'" % name
+ for r in self._exec(command):
+ return cPickle.loads(r['paths'])
+
+ def add(self, wf):
+ """ Inserts name, wf to single_spec """
+ dump = cPickle.dumps(wf)
+ dump = MySQLdb.escape_string(dump)
+ command = "REPLACE INTO single_spec VALUES ('%s', '%s')"%(wf.id, dump)
+ self._exec(command)
+
+ def __del__(self):
+ self.cursor.close()
+ self.db.close()
+
+spec = Spec()
+
+idf = False
+def get_idf(module):
+ global idf
+ if not idf:
+ idf = cPickle.load(open("/server/crowdlabs/apps/vistrails/index/module.idf"))
+ return idf.get(module.type, 9.0)
+def getIDF(type):
+ global idf
+ if not idf:
+ idf = cPickle.load(open("/server/crowdlabs/apps/vistrails/index/module.idf"))
+ return idf.get(type, 9.0)
+
+idf2 = False
+def get2IDF(type):
+ global idf2
+ if not idf2:
+ idf2 = cPickle.load(open("2grams.idf"))
+ return idf2.get(type, 9.0)
+
+# right now actually just DF
+path_idf = False
+def getPathIDF(path):
+ global path_idf
+ if not path_idf:
+ path_idf = cPickle.load(open("idf.pi"))
+ return path_idf.get(path, 0)
+
+# right now actually just DF
+coIndex = False
+def getCoIndex(pair):
+ global coIndex
+ if not coIndex:
+ coIndex = cPickle.load(open("coindex.pi"))
+ return coIndex.get(pair, 1)
+
+
+
diff --git a/vistrails/index/vistrailanalyzer.py b/vistrails/index/vistrailanalyzer.py
new file mode 100644
index 0000000..303e92b
--- /dev/null
+++ b/vistrails/index/vistrailanalyzer.py
@@ -0,0 +1,116 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import re
+
+from lucene import *
+import lucene
+dir(lucene)
+
+class vistrailAnalyzer(PythonAnalyzer):
+
+ def tokenStream(self, fieldName, reader):
+
+ result = StandardTokenizer(reader)
+ result = StandardFilter(result)
+ result = vistrailFilter(result)
+ result = LowerCaseFilter(result)
+ result = PorterStemFilter(result)
+ result = StopFilter(result, StopAnalyzer.ENGLISH_STOP_WORDS)
+
+ return result
+
+class stemmingAnalyzer(PythonAnalyzer):
+
+ def tokenStream(self, fieldName, reader):
+
+ result = StandardTokenizer(reader)
+ result = StandardFilter(result)
+ result = LowerCaseFilter(result)
+ result = PorterStemFilter(result)
+ result = StopFilter(result, StopAnalyzer.ENGLISH_STOP_WORDS)
+
+ return result
+
+# patterns for splitting words into substrings
+patterns = [
+ # 32 char md5 sums
+ "[a-f0-9]{32}",
+ # '2D', '3D'
+ "2D", "3D",
+ # words beginning with capital letters
+ "[A-Z][a-z]+",
+ # capital letter sequence ending with a word that begins with a capital letter
+ "[A-Z]*(?=[A-Z][a-z])",
+ # capital letter sequence
+ "[A-Z]{2,}",
+ # non-capital letter sequence
+ "[a-z]{2,}" ]
+
+splitPattern = re.compile("|".join(patterns))
+
+class vistrailFilter(PythonTokenFilter):
+
+ TOKEN_TYPE_PART = "text"
+
+
+ def __init__(self, input):
+ super(vistrailFilter, self).__init__(input)
+ self.input = input
+ self.parts = [] # parts found for the current token
+ self.current = None
+
+ def next(self):
+ if self.parts:
+ # continue adding parts
+ part = self.parts.pop()
+ t = Token(part, self.current.startOffset(),
+ self.current.endOffset(), self.TOKEN_TYPE_PART)
+ t.setPositionIncrement(0)
+ return t
+ else:
+ # find parts
+ self.current = self.input.next()
+ if self.current is None:
+ return None
+ text = str(self.current.termText())
+ pattern = splitPattern.findall(text)
+ # remove single characters and duplicates
+ pattern = set([p for p in pattern if len(p)>1 and p != text])
+# if len(pattern) > 0:
+# print "vistrailFilter", text, "-->",','.join(pattern)
+ self.parts = pattern
+ return self.current
+
+
diff --git a/vistrails/packages/CLTools/README b/vistrails/packages/CLTools/README
new file mode 100644
index 0000000..79b82cc
--- /dev/null
+++ b/vistrails/packages/CLTools/README
@@ -0,0 +1,73 @@
+CLTools provide a way to wrap command line tools so that they can be used as modules in VisTrails.
+
+
+== Using the Wizard ==
+
+To launch the wizard run:
+python vistrails/package/CLTools/wizard.py
+
+The wizard enables you to create and edit a wrapper for a command line tool. You can create input/output ports or constant arguments and ports for stdin/stdout/stderr pipes. You can view and import flags from man and help pages.
+
+Files should be saved as {modulename}.clt in the directory .vistrails/CLTools/
+
+Supported flags:
+-c Import a command with arguments automatically
+example:
+create a wrapper for ls with two flags
+"python wizard.py -c ls -l -A"
+
+
+== Creating a standalone package ==
+
+1. Create a new directory in ".vistrails/userpackages/"
+2. Copy "__init__.py" and "init.py" from "vistrails/packages/CLTools" to the new directory.
+3. Update "name", "identifier", and "version" in "__init__.py" to the desired values
+4. Move all desired tools (*.clt files) to the new directory
+5. Test the new package
+
+
+== File Format ==
+
+The wrapper is stored as a JSON file with the following syntax:
+
+ROOT is a dict with the following possible keys:
+* command (required) - value is the command to execute like "cat" or "/home/tommy/cat"
+* stdin - handle stdin - value is a 3-list ["port name", CLASS, OPTIONDICT]
+* stdout - handle stdout - value is a 3-list ["port name", CLASS, OPTIONDICT]
+* stderr - handle stdout - value is a 3-list ["port name", CLASS, OPTIONDICT]
+* args - list of ordered arguments that can either be constants, inputs, or outputs. See ARG.
+* options - a dict of module options - see OPTIONDICT
+OPTIONDICT is a dict with module specific options
+recognized options are:
+std_using_files - connect files to pipes so that they need not be stored in memory. This is useful for large files but may be unsafe since it does not use subprocess.communicate
+ARG is a 4-list containing [TYPE, "name", KLASS, ARGOPTIONDICT]
+TYPE is one of:
+* input - create input port for this arg
+* output - create output port for this arg
+* constant - use "port name" directly as a constant string
+CLASS can either be "File", "String", "Flag", or "List". Unknown types are handled as "String". "Flag" is a boolean with the value specified by option "value". "List" is a list with subtype specified by option "type"
+ARGOPTIONDICT is a dict containing argument options. recognized options are:
+"type": "CLASS" - used by List-types to specify subtype.
+"flag": "name" - Append name as a constant before the specified argument. If type is "List" it is appended before each item
+"prefix": "name" - Append name as a prefix to the final argument. If it is also a list it is appended to each item.
+"required": "" - Makes the port always visible in VisTrails.
+
+
+== EXAMPLE ==
+
+wrap the command "cat" that takes 2 files as input named "first" and "second". Also take a list of files as input named "rest".
+Catch stdout as file, name it "combined".
+Catch stderr as string, name it "stderr".
+Show only "first" and "conbined" by default.
+
+{"command": "cat",
+"args": [["input", "first", "File", {"required":""}],
+ ["input", "second", "File", {}],
+ ["input", "rest", "List", {"type":"File"}]],
+"stdout": ["combined", "File", {"required":""}],
+"stderr": ["stderr", "String", {}]
+}
+
+Save as /home/{username}/.vistrails/CLTools/cat.clt
+Reload CLTools package in VisTrails. Test the new module.
+
diff --git a/vistrails/packages/CLTools/__init__.py b/vistrails/packages/CLTools/__init__.py
new file mode 100644
index 0000000..cf437f7
--- /dev/null
+++ b/vistrails/packages/CLTools/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This package provides a way to wrap command line tools into VisTrails modules
+"""
+from vistrails.core.configuration import ConfigurationObject
+
+from identifiers import *
+
+configuration = ConfigurationObject(env=(None, str))
diff --git a/vistrails/packages/CLTools/icons/document-new.png b/vistrails/packages/CLTools/icons/document-new.png
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diff --git a/vistrails/packages/CLTools/icons/document-open.png b/vistrails/packages/CLTools/icons/document-open.png
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diff --git a/vistrails/packages/CLTools/icons/document-save-as.png b/vistrails/packages/CLTools/icons/document-save-as.png
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diff --git a/vistrails/packages/CLTools/icons/document-save.png b/vistrails/packages/CLTools/icons/document-save.png
new file mode 100644
index 0000000..a94e0ea
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diff --git a/vistrails/packages/CLTools/icons/go-down.png b/vistrails/packages/CLTools/icons/go-down.png
new file mode 100644
index 0000000..af23788
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diff --git a/vistrails/packages/CLTools/icons/go-up.png b/vistrails/packages/CLTools/icons/go-up.png
new file mode 100644
index 0000000..b0a0cd7
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diff --git a/vistrails/packages/CLTools/icons/list-add.png b/vistrails/packages/CLTools/icons/list-add.png
new file mode 100644
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diff --git a/vistrails/packages/CLTools/icons/list-remove.png b/vistrails/packages/CLTools/icons/list-remove.png
new file mode 100644
index 0000000..45e5c2a
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diff --git a/vistrails/packages/CLTools/icons/view-refresh.png b/vistrails/packages/CLTools/icons/view-refresh.png
new file mode 100644
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diff --git a/vistrails/packages/CLTools/identifiers.py b/vistrails/packages/CLTools/identifiers.py
new file mode 100644
index 0000000..4b61931
--- /dev/null
+++ b/vistrails/packages/CLTools/identifiers.py
@@ -0,0 +1,4 @@
+name = 'CLTools'
+identifier = "org.vistrails.vistrails.cltools"
+version = "0.1.2"
+old_identifiers = ["edu.utah.sci.vistrails.cltools"]
diff --git a/vistrails/packages/CLTools/init.py b/vistrails/packages/CLTools/init.py
new file mode 100644
index 0000000..4e23521
--- /dev/null
+++ b/vistrails/packages/CLTools/init.py
@@ -0,0 +1,563 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED B Y THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import errno
+import json
+import os
+import shutil
+import subprocess
+import sys
+
+from vistrails.core.modules.vistrails_module import Module, ModuleError, IncompleteImplementation, new_module
+import vistrails.core.modules.module_registry
+from vistrails.core import debug
+from vistrails.core.packagemanager import get_package_manager
+import vistrails.core.system
+from vistrails.core.system import packages_directory, vistrails_root_directory
+
+import identifiers
+
+
+cl_tools = {}
+
+
+class CLTools(Module):
+ """ CLTools is the base Module.
+ We will create a SUDSWebService Module for each method published by
+ the web service.
+
+ """
+ def compute(self):
+ raise IncompleteImplementation
+
+
+SUFFIX = '.clt'
+DEFAULTFILESUFFIX = '.cld'
+
+
+def _eintr_retry_call(func, *args):
+ """Fixes OSErrors and IOErrors
+
+ From: http://code.google.com/p/seascope/source/detail?spec=svn8dbe5e23d41db673727ce90fd338e9a43f8877e8&name=8dbe5e23d41d&r=8dbe5e23d41db673727ce90fd338e9a43f8877e8
+ IOError added
+ """
+ while True:
+ try:
+ return func(*args)
+ except (OSError, IOError), e:
+ if e.errno == errno.EINTR:
+ continue
+ raise
+
+
+def add_tool(path):
+ # first create classes
+ tool_name = os.path.basename(path)
+ if not tool_name.endswith(SUFFIX):
+ return
+ (tool_name, _) = os.path.splitext(tool_name)
+
+ if tool_name in cl_tools:
+ debug.critical("Package CLTools already added: '%s'" % tool_name)
+ try:
+ conf = json.load(open(path))
+ except ValueError as exc:
+ debug.critical("Package CLTools could not parse '%s'" % path, exc)
+ return
+
+ def compute(self):
+ """ 1. read inputs
+ 2. call with inputs
+ 3. set outputs
+ """
+ # add all arguments as an unordered list
+ args = [self.conf['command']]
+ file_std = 'options' in self.conf and 'std_using_files' in self.conf['options']
+ setOutput = [] # (name, File) - set File contents as output for name
+ open_files = []
+ stdin = None
+ kwargs = {}
+ for type, name, klass, options in self.conf['args']:
+ type = type.lower()
+ klass = klass.lower()
+ if "constant" == type:
+ flag = 'flag' in options and options['flag']
+ if flag:
+ args.append(flag)
+ if name:
+ # if flag==name we assume user tried to name a constant
+ if not name == flag:
+ args.append('%s%s' % (options.get('prefix', ''), name))
+ elif "input" == type:
+ # handle multiple inputs
+ values = self.forceGetInputListFromPort(name)
+ if values and 'list' == klass:
+ values = values[0]
+ klass = options['type'].lower() \
+ if 'type' in options else 'string'
+ for value in values:
+ if 'flag' == klass:
+ if not value:
+ continue
+ if 'flag' in options and options['flag']:
+ value = options['flag']
+ else:
+ # use name as flag
+ value = name
+ elif 'file' == klass:
+ value = value.name
+ # check for flag and append file name
+ if not 'flag' == klass and 'flag' in options:
+ args.append(options['flag'])
+ value = '%s%s' % (options.get('prefix', ''),
+ value)
+ args.append(value)
+ elif "output" == type:
+ # output must be a filename but we may convert the result to a string
+ # create new file
+ file = self.interpreter.filePool.create_file(
+ suffix=options.get('suffix', DEFAULTFILESUFFIX))
+ fname = file.name
+ if 'prefix' in options:
+ fname = options['prefix'] + fname
+ if 'flag' in options:
+ args.append(options['flag'])
+ args.append(fname)
+ if "file" == klass:
+ self.setResult(name, file)
+ elif "string" == klass:
+ setOutput.append((name, file))
+ else:
+ raise ValueError
+ elif "inputoutput" == type:
+ # handle single file that is both input and output
+ value = self.getInputFromPort(name)
+
+ # create copy of infile to operate on
+ outfile = self.interpreter.filePool.create_file(
+ suffix=options.get('suffix', DEFAULTFILESUFFIX))
+ try:
+ shutil.copyfile(value.name, outfile.name)
+ except IOError, e:
+ raise ModuleError("Error copying file '%s': %s" %
+ (value.name, e))
+ value = '%s%s' % (options.get('prefix', ''), outfile.name)
+ # check for flag and append file name
+ if 'flag' in options:
+ args.append(options['flag'])
+ args.append(value)
+ self.setResult(name, outfile)
+ if "stdin" in self.conf:
+ name, type, options = self.conf["stdin"]
+ type = type.lower()
+ if self.hasInputFromPort(name):
+ value = self.getInputFromPort(name)
+ if "file" == type:
+ if file_std:
+ f = open(value.name, 'rb')
+ else:
+ f = open(value.name, 'rb')
+ stdin = f.read()
+ f.close()
+ elif "string" == type:
+ if file_std:
+ file = self.interpreter.filePool.create_file()
+ f = open(file.name, 'wb')
+ f.write(value)
+ f.close()
+ f = open(file.name, 'rb')
+ else:
+ stdin = value
+ else:
+ raise ValueError
+ if file_std:
+ open_files.append(f)
+ kwargs['stdin'] = f.fileno()
+ else:
+ kwargs['stdin'] = subprocess.PIPE
+ if "stdout" in self.conf:
+ if file_std:
+ name, type, options = self.conf["stdout"]
+ type = type.lower()
+ file = self.interpreter.filePool.create_file(
+ suffix=DEFAULTFILESUFFIX)
+ if "file" == type:
+ self.setResult(name, file)
+ elif "string" == type:
+ setOutput.append((name, file))
+ else:
+ raise ValueError
+ f = open(file.name, 'wb')
+ open_files.append(f)
+ kwargs['stdout'] = f.fileno()
+ else:
+ kwargs['stdout'] = subprocess.PIPE
+ if "stderr" in self.conf:
+ if file_std:
+ name, type, options = self.conf["stderr"]
+ type = type.lower()
+ file = self.interpreter.filePool.create_file(
+ suffix=DEFAULTFILESUFFIX)
+ if "file" == type:
+ self.setResult(name, file)
+ elif "string" == type:
+ setOutput.append((name, file))
+ else:
+ raise ValueError
+ f = open(file.name, 'wb')
+ open_files.append(f)
+ kwargs['stderr'] = f.fileno()
+ else:
+ kwargs['stderr'] = subprocess.PIPE
+
+ if "return_code" in self.conf:
+ return_code = self.forceGetInputFromPort(name)
+ else:
+ return_code = None
+
+ env = {}
+ # 0. add defaults
+ # 1. add from configuration
+ # 2. add from module env
+ # 3. add from env port
+ if configuration.check('env'):
+ try:
+ for var in configuration.env.split(";"):
+ key, value = var.split('=')
+ key = key.strip()
+ value = value.strip()
+ if key:
+ env[key] = value
+ except Exception, e:
+ raise ModuleError('Error parsing configuration env: %s' % e)
+
+ if 'options' in self.conf and 'env' in self.conf['options']:
+ try:
+ for var in self.conf['options']['env'].split(";"):
+ key, value = var.split('=')
+ key = key.strip()
+ value = value.strip()
+ if key:
+ env[key] = value
+ except Exception, e:
+ raise ModuleError('Error parsing module env: %s' % e)
+
+ if 'options' in self.conf and 'env_port' in self.conf['options']:
+ for e in self.forceGetInputListFromPort('env'):
+ try:
+ for var in e.split(';'):
+ if not var:
+ continue
+ key, value = var.split('=')
+ key = key.strip()
+ value = value.strip()
+ if key:
+ env[key] = value
+ except Exception, e:
+ raise ModuleError('Error parsing env port: %s' % e)
+
+ if env:
+ kwargs['env'] = dict(os.environ)
+ kwargs['env'].update(env)
+ # write to execution provenance
+ env = ';'.join(['%s=%s'%(k,v) for k,v in env.iteritems()])
+ self.annotate({'execution_env': env})
+
+ if 'dir' in self.conf:
+ kwargs['cwd'] = self.conf['dir']
+
+ process = subprocess.Popen(args, **kwargs)
+ if file_std:
+ process.wait()
+ else:
+ #if stdin:
+ # print "stdin:", len(stdin), stdin[:30]
+ stdout, stderr = _eintr_retry_call(process.communicate, stdin)
+ #stdout, stderr = process.communicate(stdin)
+ #if stdout:
+ # print "stdout:", len(stdout), stdout[:30]
+ #if stderr:
+ # print "stderr:", len(stderr), stderr[:30]
+
+ if return_code is not None:
+ if process.returncode != return_code:
+ raise ModuleError("Command returned %d (!= %d)" % (
+ process.returncode, return_code))
+ self.setResult('return_code', process.returncode)
+
+ for f in open_files:
+ f.close()
+
+ for name, file in setOutput:
+ f = open(file.name, 'rb')
+ self.setResult(name, f.read())
+ f.close()
+
+ if not file_std:
+ if stdout and "stdout" in self.conf:
+ name, type, options = self.conf["stdout"]
+ type = type.lower()
+ if "file" == type:
+ file = self.interpreter.filePool.create_file(
+ suffix=DEFAULTFILESUFFIX)
+ f = open(file.name, 'wb')
+ f.write(stdout)
+ f.close()
+ self.setResult(name, file)
+ elif "string" == type:
+ self.setResult(name, stdout)
+ else:
+ raise ValueError
+ if stderr and "stderr" in self.conf:
+ name, type, options = self.conf["stderr"]
+ type = type.lower()
+ if "file" == type:
+ file = self.interpreter.filePool.create_file(
+ suffix=DEFAULTFILESUFFIX)
+ f = open(file.name, 'wb')
+ f.write(stderr)
+ f.close()
+ self.setResult(name, file)
+ elif "string" == type:
+ self.setResult(name, stderr)
+ else:
+ raise ValueError
+
+
+ # create docstring
+ d = """This module is a wrapper for the command line tool '%s'""" % \
+ conf['command']
+ # create module
+ M = new_module(CLTools, tool_name,{"compute": compute,
+ "conf": conf,
+ "tool_name": tool_name,
+ "__doc__": d})
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ reg.add_module(M, package=identifiers.identifier,
+ package_version=identifiers.version)
+
+ def to_vt_type(s):
+ # add recognized types here - default is String
+ return '(basic:%s)' % \
+ {'file':'File', 'flag':'Boolean', 'list':'List',
+ 'float':'Float','integer':'Integer'
+ }.get(s.lower(), 'String')
+ # add module ports
+ if 'stdin' in conf:
+ name, type, options = conf['stdin']
+ optional = 'required' not in options
+ reg.add_input_port(M, name, to_vt_type(type), optional=optional)
+ if 'stdout' in conf:
+ name, type, options = conf['stdout']
+ optional = 'required' not in options
+ reg.add_output_port(M, name, to_vt_type(type), optional=optional)
+ if 'stderr' in conf:
+ name, type, options = conf['stderr']
+ optional = 'required' not in options
+ reg.add_output_port(M, name, to_vt_type(type), optional=optional)
+ if 'options' in conf and 'env_port' in conf['options']:
+ reg.add_input_port(M, 'env', to_vt_type('string'))
+ for type, name, klass, options in conf['args']:
+ optional = 'required' not in options
+ if 'input' == type.lower():
+ reg.add_input_port(M, name, to_vt_type(klass), optional=optional)
+ elif 'output' == type.lower():
+ reg.add_output_port(M, name, to_vt_type(klass), optional=optional)
+ elif 'inputoutput' == type.lower():
+ reg.add_input_port(M, name, to_vt_type('file'), optional=optional)
+ reg.add_output_port(M, name, to_vt_type('file'), optional=optional)
+ reg.add_output_port(M, 'return_code', to_vt_type('integer'))
+ cl_tools[tool_name] = M
+
+
+def initialize(*args, **keywords):
+ if "CLTools" == identifiers.name:
+ # this is the original package
+ location = os.path.join(vistrails.core.system.current_dot_vistrails(),
+ "CLTools")
+ # make sure dir exist
+ if not os.path.isdir(location):
+ try:
+ debug.log("Creating CLTools directory...")
+ os.mkdir(location)
+ except:
+ debug.critical("""Could not create CLTools directory. Make
+ sure '%s' does not exist and parent directory is writable""" % location)
+ sys.exit(1)
+ else:
+ # this is a standalone package so modules are placed in this directory
+ location = os.path.dirname(__file__)
+
+
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ reg.add_module(CLTools, abstract=True)
+ for path in os.listdir(location):
+ if path.endswith(SUFFIX):
+ try:
+ add_tool(os.path.join(location, path))
+ except Exception as exc:
+ import traceback
+ debug.critical("Package CLTools failed to create module "
+ "from '%s': %s" % (os.path.join(location, path), exc),
+ traceback.format_exc())
+
+
+def remove_all_scripts():
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ for tool_name in cl_tools.keys():
+ del cl_tools[tool_name]
+ reg.delete_module(identifiers.identifier, tool_name)
+
+def reload_scripts():
+ remove_all_scripts()
+ if "CLTools" == identifiers.name:
+ # this is the original package
+ location = os.path.join(vistrails.core.system.current_dot_vistrails(),
+ "CLTools")
+ # make sure dir exist
+ if not os.path.isdir(location):
+ try:
+ debug.log("Creating CLTools directory...")
+ os.mkdir(location)
+ except:
+ debug.critical("""Could not create CLTools directory. Make
+ sure '%s' does not exist and parent directory is writable""" % location)
+ sys.exit(1)
+ else:
+ # this is a standalone package so modules are placed in this directory
+ location = os.path.dirname(__file__)
+
+ for path in os.listdir(location):
+ if path.endswith(SUFFIX):
+ try:
+ add_tool(os.path.join(location, path))
+ except Exception as exc:
+ import traceback
+ debug.critical("Package CLTools failed to create module "
+ "from '%s': %s" % (os.path.join(location, path), exc),
+ traceback.format_exc())
+
+ from vistrails.core.interpreter.cached import CachedInterpreter
+ CachedInterpreter.clear_package(identifiers.identifier)
+
+ from vistrails.gui.vistrails_window import _app
+ _app.invalidate_pipelines()
+
+
+wizards_list = []
+
+def menu_items():
+ """menu_items() -> tuple of (str,function)
+ It returns a list of pairs containing text for the menu and a
+ callback function that will be executed when that menu item is selected.
+
+ """
+ # if wizard.py does not exist, assume it is a standalone package and abort
+ try:
+ from wizard import QCLToolsWizardWindow
+ except:
+ return
+ lst = []
+ if "CLTools" == identifiers.name:
+ def open_wizard():
+ window = QCLToolsWizardWindow(reload_scripts=reload_scripts)
+ wizards_list.append(window)
+ window.show()
+ lst.append(("Open Wizard", open_wizard))
+ lst.append(("Reload All Scripts", reload_scripts))
+ return tuple(lst)
+
+
+def finalize():
+ pass
+
+
+###############################################################################
+
+import unittest
+from vistrails.tests.utils import execute, intercept_results
+
+
+class TestCLTools(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ # first make sure CLTools is loaded
+ pm = get_package_manager()
+ if 'CLTools' not in pm._package_list:
+ pm.late_enable_package('CLTools')
+ remove_all_scripts()
+ cls.testdir = os.path.join(packages_directory(), 'CLTools', 'test_files')
+ cls._tools = {}
+ for name in os.listdir(cls.testdir):
+ if not name.endswith(SUFFIX):
+ continue
+ add_tool(os.path.join(cls.testdir, name))
+ toolname = os.path.splitext(name)[0]
+ cls._tools[toolname] = cl_tools[toolname]
+ cls._old_dir = os.getcwd()
+ os.chdir(vistrails_root_directory())
+
+ @classmethod
+ def tearDownClass(cls):
+ os.chdir(cls._old_dir)
+ reload_scripts()
+
+ def do_the_test(self, toolname):
+ with intercept_results(self._tools['intern_cltools_1'],
+ 'return_code', 'f_out', 'stdout') as (
+ return_code, f_out, stdout):
+ self.assertFalse(execute([
+ ('intern_cltools_1', 'org.vistrails.vistrails.cltools', [
+ ('f_in', [('File', self.testdir + '/test_1.cltest')]),
+ ('chars', [('List', '["a", "b", "c"]')]),
+ ('false', [('Boolean', 'False')]),
+ ('true', [('Boolean', 'True')]),
+ ('nb', [('Integer', '42')]),
+ ('stdin', [('String', 'some line\nignored')]),
+ ]),
+ ]))
+ self.assertEqual(return_code, [0])
+ self.assertEqual(f_out, ['ok\nmessage received'])
+ self.assertEqual(stdout, ['program output here'])
+
+ def test_with_pipes(self):
+ """Without std_using_files: use pipes instead of files.
+ """
+ self.do_the_test('intern_cltools_1')
+
+ def test_with_files(self):
+ """With std_using_files: use files instead of pipes.
+ """
+ self.do_the_test('intern_cltools_2')
diff --git a/vistrails/packages/CLTools/test_files/intern_cltools_1.clt b/vistrails/packages/CLTools/test_files/intern_cltools_1.clt
new file mode 100644
index 0000000..d2bf818
--- /dev/null
+++ b/vistrails/packages/CLTools/test_files/intern_cltools_1.clt
@@ -0,0 +1,78 @@
+{
+ "args": [
+ [
+ "constant",
+ "packages/CLTools/test_files/test_script_1.py",
+ "string",
+ {}
+ ],
+ [
+ "input",
+ "f_in",
+ "file",
+ {
+ "required": ""
+ }
+ ],
+ [
+ "output",
+ "f_out",
+ "string",
+ {
+ "required": "",
+ "suffix": ".cltest"
+ }
+ ],
+ [
+ "input",
+ "true",
+ "flag",
+ {
+ "flag": "-t",
+ "required": ""
+ }
+ ],
+ [
+ "input",
+ "false",
+ "flag",
+ {
+ "flag": "-f",
+ "required": ""
+ }
+ ],
+ [
+ "input",
+ "nb",
+ "integer",
+ {
+ "required": ""
+ }
+ ],
+ [
+ "input",
+ "chars",
+ "list",
+ {
+ "flag": "-l",
+ "required": "",
+ "type": "String"
+ }
+ ]
+ ],
+ "command": "python",
+ "stdin": [
+ "stdin",
+ "string",
+ {
+ "required": ""
+ }
+ ],
+ "stdout": [
+ "stdout",
+ "string",
+ {
+ "required": ""
+ }
+ ]
+}
\ No newline at end of file
diff --git a/vistrails/packages/CLTools/test_files/intern_cltools_2.clt b/vistrails/packages/CLTools/test_files/intern_cltools_2.clt
new file mode 100644
index 0000000..91cd2fd
--- /dev/null
+++ b/vistrails/packages/CLTools/test_files/intern_cltools_2.clt
@@ -0,0 +1,81 @@
+{
+ "args": [
+ [
+ "constant",
+ "packages/CLTools/test_files/test_script_1.py",
+ "string",
+ {}
+ ],
+ [
+ "input",
+ "f_in",
+ "file",
+ {
+ "required": ""
+ }
+ ],
+ [
+ "output",
+ "f_out",
+ "string",
+ {
+ "required": "",
+ "suffix": ".cltest"
+ }
+ ],
+ [
+ "input",
+ "true",
+ "flag",
+ {
+ "flag": "-t",
+ "required": ""
+ }
+ ],
+ [
+ "input",
+ "false",
+ "flag",
+ {
+ "flag": "-f",
+ "required": ""
+ }
+ ],
+ [
+ "input",
+ "nb",
+ "integer",
+ {
+ "required": ""
+ }
+ ],
+ [
+ "input",
+ "chars",
+ "list",
+ {
+ "flag": "-l",
+ "required": "",
+ "type": "String"
+ }
+ ]
+ ],
+ "command": "python",
+ "options": {
+ "std_using_files": ""
+ },
+ "stdin": [
+ "stdin",
+ "string",
+ {
+ "required": ""
+ }
+ ],
+ "stdout": [
+ "stdout",
+ "string",
+ {
+ "required": ""
+ }
+ ]
+}
\ No newline at end of file
diff --git a/vistrails/packages/CLTools/test_files/test_1.cltest b/vistrails/packages/CLTools/test_files/test_1.cltest
new file mode 100644
index 0000000..d54e5bc
--- /dev/null
+++ b/vistrails/packages/CLTools/test_files/test_1.cltest
@@ -0,0 +1,2 @@
+this is a
+test
\ No newline at end of file
diff --git a/vistrails/packages/CLTools/test_files/test_script_1.py b/vistrails/packages/CLTools/test_files/test_script_1.py
new file mode 100644
index 0000000..31a76c6
--- /dev/null
+++ b/vistrails/packages/CLTools/test_files/test_script_1.py
@@ -0,0 +1,42 @@
+import sys
+
+
+if __name__ == '__main__':
+ args = sys.argv[1:]
+
+ if len(args) != 10:
+ sys.stderr.write("Wrong number of parameters\n")
+ sys.exit(1)
+
+ fin = args.pop(0)
+ fout = args.pop(0)
+
+ if args != ['-t', '42', '-l', 'a', '-l', 'b', '-l', 'c']:
+ sys.stderr.write("Wrong parameters\n")
+ sys.exit(1)
+
+ stdin = sys.stdin.readline()
+ if stdin != 'some line\n':
+ sys.stderr.write("Wrong line on stdin\n")
+ sys.exit(1)
+
+ if not fin.endswith('.cltest'):
+ sys.stderr.write("Wrong extension for f_in '%s'\n" % fin)
+ sys.exit(1)
+
+ with open(fin, 'r') as fpin:
+ fcin = fpin.read()
+ if fcin != 'this is a\ntest':
+ sys.stderr.write("Wrong content in f_in '%s'\n" % fin)
+ sys.exit(1)
+
+ if not fout.endswith('.cltest'):
+ sys.stderr.write("Wrong extension for f_out '%s'\n" % fout)
+ sys.exit(1)
+
+ with open(fout, 'wb') as fpout:
+ fpout.write('ok\nmessage received')
+
+ sys.stdout.write("program output here")
+
+ sys.exit(0)
diff --git a/vistrails/packages/CLTools/wizard.py b/vistrails/packages/CLTools/wizard.py
new file mode 100644
index 0000000..41bc170
--- /dev/null
+++ b/vistrails/packages/CLTools/wizard.py
@@ -0,0 +1,1163 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+if __name__ == '__main__':
+ import sip
+ sip.setapi('QString', 2)
+ sip.setapi('QVariant', 2)
+
+import json
+import os
+import platform
+import string
+import subprocess
+import sys
+import threading
+from PyQt4 import QtCore, QtGui
+
+encode_list = [['\xe2\x80\x90', '-'],
+ ['\xe2\x80\x9d', '"'],
+ ['\xe2\x80\x9c', '"']]
+
+SUFFIX = '.clt'
+
+def default_dir():
+ systemType = platform.system()
+ if systemType in ['Windows', 'Microsoft']:
+ if len(os.environ['HOMEPATH']) == 0:
+ root = '\\'
+ else:
+ root = os.environ['HOMEDRIVE'] + os.environ['HOMEPATH']
+ else:
+ root = os.getenv('HOME')
+ default_dir = os.path.join(root, '.vistrails', 'CLTools')
+ if not os.path.exists(default_dir):
+ os.mkdir(default_dir)
+ return default_dir
+
+def quote_arg(arg):
+ arg = arg.replace('\\', '\\\\')
+ if '"' in arg or any(c in arg for c in string.whitespace):
+ return '"%s"' % arg.replace('"', '\\"')
+ else:
+ return arg
+
+# From: https://gist.github.com/kirpit/1306188
+class Command(object):
+ """
+ Enables to run subprocess commands in a different thread with TIMEOUT option.
+
+ Based on jcollado's solution:
+ http://stackoverflow.com/questions/1191374/subprocess-with-timeout/4825933#4825933
+ """
+ command = None
+ process = None
+ status = None
+ output, error = '', ''
+
+ def __init__(self, command):
+ self.command = command
+
+ def run(self, timeout=5, **kwargs):
+ """ Run a command then return: (status, output, error). """
+ def target(**kwargs):
+ try:
+ self.process = subprocess.Popen(self.command, **kwargs)
+ self.output, self.error = self.process.communicate()
+ self.status = self.process.returncode
+ except:
+ import traceback
+ self.error = traceback.format_exc()
+ self.status = -1
+ # default stdout and stderr
+ if 'stdout' not in kwargs:
+ kwargs['stdout'] = subprocess.PIPE
+ if 'stderr' not in kwargs:
+ kwargs['stderr'] = subprocess.PIPE
+ # thread
+ print "calling with kwargs", target, kwargs
+ thread = threading.Thread(target=target, kwargs=kwargs)
+ thread.start()
+ thread.join(timeout)
+ if thread.is_alive():
+ self.process.terminate()
+ thread.join()
+ return self.status, self.output, self.error
+
+class QCLToolsWizard(QtGui.QWidget):
+ def __init__(self, parent, reload_scripts=None):
+ QtGui.QWidget.__init__(self, parent)
+
+ self.vbox = QtGui.QVBoxLayout()
+ self.vbox.setContentsMargins(5,5,5,5)
+
+ self.setLayout(self.vbox)
+ self.setTitle()
+ self.file = None
+ self.conf = None
+ self.reload_scripts = reload_scripts
+
+ self.toolBar = QtGui.QToolBar()
+ self.layout().addWidget(self.toolBar)
+ self.newFileAction = QtGui.QAction(
+ self.get_icon('document-new'), 'New', self)
+ self.newFileAction.setToolTip('Start on a new Wrapper')
+ self.connect(self.newFileAction, QtCore.SIGNAL('triggered()'),
+ self.newFile)
+ self.toolBar.addAction(self.newFileAction)
+ self.openFileAction = QtGui.QAction(
+ self.get_icon('document-open'), 'Open', self)
+ self.openFileAction.setToolTip('Open an existing wrapper')
+ self.connect(self.openFileAction, QtCore.SIGNAL('triggered()'),
+ self.openFile)
+ self.toolBar.addAction(self.openFileAction)
+ self.saveFileAction = QtGui.QAction(
+ self.get_icon('document-save'), 'Save', self)
+ self.saveFileAction.setToolTip('Save wrapper')
+ self.connect(self.saveFileAction, QtCore.SIGNAL('triggered()'),
+ self.save)
+ self.toolBar.addAction(self.saveFileAction)
+ self.saveFileAsAction = QtGui.QAction(
+ self.get_icon('document-save-as'), 'Save As', self)
+ self.saveFileAsAction.setToolTip('Save wrapper as a new file')
+ self.connect(self.saveFileAsAction, QtCore.SIGNAL('triggered()'),
+ self.saveAs)
+ self.toolBar.addAction(self.saveFileAsAction)
+
+ if self.reload_scripts:
+ self.reloadAction = QtGui.QAction(
+ self.get_icon('view-refresh'), 'Refresh', self)
+ self.reloadAction.setToolTip('Save and Reload CLTools Modules in VisTrails')
+ self.connect(self.reloadAction, QtCore.SIGNAL('triggered()'),
+ self.refresh)
+ self.toolBar.addAction(self.reloadAction)
+
+ self.toolBar.addSeparator()
+ self.addAction = QtGui.QAction(
+ self.get_icon('list-add'), 'Add', self)
+ self.addAction.setToolTip('Add a new argument')
+ self.connect(self.addAction, QtCore.SIGNAL('triggered()'),
+ self.addArgument)
+ self.toolBar.addAction(self.addAction)
+ self.removeAction = QtGui.QAction(
+ self.get_icon('list-remove'), 'Remove', self)
+ self.removeAction.setToolTip('Remove the selected argument')
+ self.connect(self.removeAction, QtCore.SIGNAL('triggered()'),
+ self.removeArgument)
+ self.toolBar.addAction(self.removeAction)
+ self.upAction = QtGui.QAction(
+ self.get_icon('go-up'), 'Move up', self)
+ self.upAction.setToolTip('Move argument up one position')
+ self.connect(self.upAction, QtCore.SIGNAL('triggered()'),
+ self.moveUp)
+ self.toolBar.addAction(self.upAction)
+ self.downAction = QtGui.QAction(
+ self.get_icon('go-down'), 'Move down', self)
+ self.downAction.setToolTip('Move argument down one position')
+ self.connect(self.downAction, QtCore.SIGNAL('triggered()'),
+ self.moveDown)
+ self.toolBar.addAction(self.downAction)
+
+ self.toolBar.addSeparator()
+
+ self.showStdin = QtGui.QAction('stdin', self)
+ self.showStdin.setToolTip('Check to use standard input as an input port')
+ self.showStdin.setCheckable(True)
+ self.toolBar.addAction(self.showStdin)
+ self.showStdout = QtGui.QAction("stdout", self)
+ self.showStdout.setToolTip('Check to use standard output as an output port')
+ self.showStdout.setCheckable(True)
+ self.toolBar.addAction(self.showStdout)
+ self.showStderr = QtGui.QAction("stderr", self)
+ self.showStderr.setToolTip('Check to use standard error as an output port')
+ self.showStderr.setCheckable(True)
+ self.toolBar.addAction(self.showStderr)
+ self.envPort = QtGui.QAction("env", self)
+ self.envPort.setToolTip('Check to add the "env" input port for specifying environment variables')
+ self.envPort.setCheckable(True)
+ self.toolBar.addAction(self.envPort)
+
+ self.toolBar.addSeparator()
+
+ self.stdAsFiles = QtGui.QAction('std file processing', self)
+ self.stdAsFiles.setToolTip('Check to make pipes communicate using files instead of strings\nOnly useful when processing large files')
+ self.stdAsFiles.setCheckable(True)
+ self.toolBar.addAction(self.stdAsFiles)
+
+ self.toolBar.addSeparator()
+
+ self.previewPorts = QtGui.QAction('preview', self)
+ self.previewPorts.setToolTip('Check which ports will be available for this module')
+ self.connect(self.previewPorts, QtCore.SIGNAL('triggered()'),
+ self.preview_ports)
+ self.toolBar.addAction(self.previewPorts)
+
+
+ self.envOption = None
+
+ self.commandLayout = QtGui.QHBoxLayout()
+ self.commandLayout.setContentsMargins(5,5,5,5)
+ tooltip = 'The command to execute'
+ label = QtGui.QLabel("Command:")
+ label.setFixedWidth(80)
+ label.setToolTip(tooltip)
+ self.commandLayout.addWidget(label)
+ self.command = QtGui.QLineEdit()
+ self.command.setToolTip(tooltip)
+ self.commandLayout.addWidget(self.command)
+ tooltip = 'Sets directory to execute from. Leave blank to ignore.'
+ label = QtGui.QLabel("Directory:")
+ label.setToolTip(tooltip)
+ self.commandLayout.addWidget(label)
+ self.dir = QtGui.QLineEdit()
+ self.dir.setFixedWidth(140)
+ self.dir.setToolTip(tooltip)
+ self.commandLayout.addWidget(self.dir)
+ self.vbox.addLayout(self.commandLayout)
+
+ self.previewLayout = QtGui.QHBoxLayout()
+ self.previewLayout.setContentsMargins(5,5,5,5)
+ self.previewLayout.setAlignment(QtCore.Qt.AlignLeft)
+ tooltip = 'Shows what the command will look like when executed in the command line'
+ label = QtGui.QLabel("Preview:")
+ label.setToolTip(tooltip)
+ label.setFixedWidth(80)
+ self.previewLayout.addWidget(label)
+ self.preview = QtGui.QLabel()
+ self.preview.setToolTip(tooltip)
+ self.preview.setMaximumWidth(600)
+ self.previewLayout.addWidget(self.preview)
+ self.vbox.addLayout(self.previewLayout)
+
+ self.importLayout = QtGui.QHBoxLayout()
+ self.importLayout.setContentsMargins(5,5,5,5)
+ self.importLayout.setAlignment(QtCore.Qt.AlignLeft)
+ self.importLayout.addWidget(QtGui.QLabel("Man page:"))
+ self.viewManButton = QtGui.QPushButton("view")
+ self.viewManButton.setToolTip('View the man page for the current command')
+ self.connect(self.viewManButton, QtCore.SIGNAL('clicked()'),
+ self.viewManPage)
+ self.importLayout.addWidget(self.viewManButton)
+ self.importManButton = QtGui.QPushButton("import")
+ self.importManButton.setToolTip('Import arguments from the man page for the current command')
+ self.connect(self.importManButton, QtCore.SIGNAL('clicked()'),
+ self.generateFromManPage)
+ self.importLayout.addWidget(self.importManButton)
+
+ self.importLayout.addWidget(QtGui.QLabel("help page (-h):"))
+ self.viewHelpButton = QtGui.QPushButton("view")
+ self.viewHelpButton.setToolTip('View the help (-h) page for the current command')
+ self.connect(self.viewHelpButton, QtCore.SIGNAL('clicked()'),
+ self.viewHelpPage)
+ self.importLayout.addWidget(self.viewHelpButton)
+ self.importHelpButton = QtGui.QPushButton("import")
+ self.importHelpButton.setToolTip('Import arguments from the help (-h) page for the current command')
+ self.connect(self.importHelpButton, QtCore.SIGNAL('clicked()'),
+ self.generateFromHelpPage)
+ self.importLayout.addWidget(self.importHelpButton)
+
+ self.importLayout.addWidget(QtGui.QLabel("help page (--help):"))
+ self.viewHelpButton2 = QtGui.QPushButton("view")
+ self.viewHelpButton2.setToolTip('View the help (--help) page for the current command')
+ self.connect(self.viewHelpButton2, QtCore.SIGNAL('clicked()'),
+ self.viewHelpPage2)
+ self.importLayout.addWidget(self.viewHelpButton2)
+ self.importHelpButton2 = QtGui.QPushButton("import")
+ self.importHelpButton2.setToolTip('Import arguments from the help (--help) page for the current command')
+ self.connect(self.importHelpButton2, QtCore.SIGNAL('clicked()'),
+ self.generateFromHelpPage2)
+ self.importLayout.addWidget(self.importHelpButton2)
+ self.vbox.addLayout(self.importLayout)
+
+ self.stdinWidget = QArgWidget('stdin')
+ self.stdinGroup = QtGui.QGroupBox('Standard input')
+ self.stdinGroup.setLayout(QtGui.QHBoxLayout())
+ self.stdinGroup.layout().addWidget(self.stdinWidget)
+ self.layout().addWidget(self.stdinGroup)
+ self.stdinGroup.setVisible(False)
+ self.stdoutWidget = QArgWidget('stdout')
+ self.stdoutGroup = QtGui.QGroupBox('Standard output')
+ self.stdoutGroup.setLayout(QtGui.QHBoxLayout())
+ self.stdoutGroup.layout().addWidget(self.stdoutWidget)
+ self.layout().addWidget(self.stdoutGroup)
+ self.stdoutGroup.setVisible(False)
+ self.stderrWidget = QArgWidget('stderr')
+ self.stderrGroup = QtGui.QGroupBox('Standard error')
+ self.stderrGroup.setLayout(QtGui.QHBoxLayout())
+ self.stderrGroup.layout().addWidget(self.stderrWidget)
+ self.layout().addWidget(self.stderrGroup)
+ self.stderrGroup.setVisible(False)
+
+ self.connect(self.showStdin, QtCore.SIGNAL('toggled(bool)'),
+ self.stdinGroup.setVisible)
+ self.connect(self.showStdout, QtCore.SIGNAL('toggled(bool)'),
+ self.stdoutGroup.setVisible)
+ self.connect(self.showStderr, QtCore.SIGNAL('toggled(bool)'),
+ self.stderrGroup.setVisible)
+
+ self.argList = QtGui.QListWidget()
+ self.layout().addWidget(self.argList)
+
+ def get_icon(self, name):
+ return QtGui.QIcon(os.path.join(os.path.dirname(__file__),
+ "icons",
+ "%s.png" % name))
+ def setTitle(self, file=None):
+ self.parent().setWindowTitle("CLTools Wizard - " + (file if file else "untitled"))
+
+ def newFile(self):
+ self.conf = None
+ self.file = None
+ self.command.clear()
+ self.dir.clear()
+ self.showStdin.setChecked(False)
+ self.showStdout.setChecked(False)
+ self.showStderr.setChecked(False)
+ self.envPort.setChecked(False)
+ self.envOption = None
+ while self.argList.count():
+ item = self.argList.item(0)
+ itemWidget = self.argList.itemWidget(item)
+ itemWidget.setVisible(False)
+ itemWidget.setParent(None)
+ self.argList.removeItemWidget(item)
+ item.setHidden(True)
+ self.argList.takeItem(0)
+ self.argList.hide()
+ self.layout().takeAt(self.layout().indexOf(self.argList))
+ self.argList = QtGui.QListWidget()
+ self.layout().addWidget(self.argList)
+ self.stdAsFiles.setChecked(False)
+ self.setTitle()
+ self.generate_preview()
+
+ def openFile(self):
+ fileName = QtGui.QFileDialog.getOpenFileName(self,
+ "Open Wrapper",
+ self.file if self.file else default_dir(),
+ "Wrappers (*%s)" % SUFFIX)
+ if not fileName:
+ return
+ try:
+ conf = json.load(open(fileName))
+ except ValueError as exc:
+ print "Error opening Wrapper '%s': %s" % (fileName, exc)
+ return
+ self.newFile()
+ self.file = fileName
+ self.setTitle(self.file)
+ self.command.setText(conf.get('command', ''))
+ self.dir.setText(conf.get('dir', ''))
+ if 'stdin' in conf:
+ self.stdinWidget.fromList(conf['stdin'])
+ self.stdinGroup.setVisible('stdin' in conf)
+ self.showStdin.setChecked('stdin' in conf)
+ if 'stdout' in conf:
+ self.stdoutWidget.fromList(conf['stdout'])
+ self.stdoutGroup.setVisible('stdout' in conf)
+ self.showStdout.setChecked('stdout' in conf)
+ if 'stderr' in conf:
+ self.stderrWidget.fromList(conf['stderr'])
+ self.stderrGroup.setVisible('stderr' in conf)
+ self.showStderr.setChecked('stderr' in conf)
+ for argConf in conf.get('args', []):
+ arg = QArgWidget()
+ arg.fromList(argConf)
+ item = QtGui.QListWidgetItem()
+ item.setSizeHint(arg.sizeHint())
+ self.argList.addItem(item)
+ self.argList.setItemWidget(item, arg)
+ self.envPort.setChecked('options' in conf and
+ 'env_port' in conf['options'])
+ self.stdAsFiles.setChecked('options' in conf and
+ 'std_using_files' in conf['options'])
+ self.envOption = conf['options']['env'] \
+ if ('options' in conf and 'env' in conf['options']) else None
+ self.conf = conf
+ self.generate_preview()
+
+ def get_current_conf(self):
+ conf = {}
+ conf['command'] = self.command.text()
+ dir = self.dir.text()
+ if dir:
+ conf['dir'] = dir
+
+ if self.stdinGroup.isVisible():
+ conf['stdin'] = self.stdinWidget.toList()
+ if self.stdoutGroup.isVisible():
+ conf['stdout'] = self.stdoutWidget.toList()
+ if self.stderrGroup.isVisible():
+ conf['stderr'] = self.stderrWidget.toList()
+ args = []
+ for row in xrange(self.argList.count()):
+ arg = self.argList.itemWidget(self.argList.item(row))
+ args.append(arg.toList())
+ conf['args'] = args
+
+ options = {}
+ if self.stdAsFiles.isChecked():
+ options['std_using_files'] = ''
+ if self.envPort.isChecked():
+ options['env_port'] = ''
+ if self.envOption:
+ options['env'] = self.envOption
+ if options:
+ conf['options'] = options
+ return conf
+
+ def save(self):
+ if not self.file:
+ self.saveAs()
+ if not self.file:
+ return
+ self.conf = self.get_current_conf()
+ f = open(self.file, "w")
+ json.dump(self.conf, f, sort_keys=True, indent=4)
+ f.close()
+ self.generate_preview()
+
+ def saveAs(self):
+ fileName = QtGui.QFileDialog.getSaveFileName(self,
+ "Save Wrapper as",
+ self.file if self.file else default_dir(),
+ "Wrappers (*%s)" % SUFFIX)
+ if fileName:
+ self.file = fileName
+ if not self.file.endswith(SUFFIX):
+ self.file += SUFFIX
+ self.save()
+ self.setTitle(self.file)
+
+ def refresh(self):
+ self.save()
+ self.reload_scripts()
+
+ def generate_preview(self):
+ # generate preview from self.conf
+ c = self.get_current_conf()
+ if not c:
+ self.preview.setText('')
+ self.preview.setToolTip('')
+ return
+
+ text = ''
+
+ # show env as bash-style prefix
+ if 'options' in c:
+ o = c['options']
+ # env_port
+ if 'env_port' in o:
+ text += '<env_port>'
+ # env
+ if 'env' in o:
+ if text:
+ text += ' '
+ text += c['options']['env']
+ if text:
+ text += ' '
+
+ # command
+ text += c['command']
+
+ # args
+ if 'args' in c:
+ for type, name, klass, opts in c['args']:
+ type = type.lower()
+ klass = klass.lower()
+ text += ' '
+ if type == 'constant':
+ if 'flag' in opts:
+ text += opts['flag'] + ' '
+ text += quote_arg(name)
+ continue
+ if 'required' not in opts:
+ text += '['
+ if klass in 'list':
+ text += '{'
+ if 'flag' in opts:
+ text += opts['flag']
+ if klass != 'flag':
+ text += ' '
+ if 'prefix' in opts:
+ text += opts['prefix']
+ if type!='input' or klass != 'flag':
+ text += '<'
+ if klass == 'list':
+ text += opts['type'].lower() \
+ if ('type' in opts and opts['type']) else 'string'
+ elif type=='input' and klass == 'flag':
+ if 'flag' not in opts:
+ text += quote_arg(name)
+ elif type in ['output', 'inputoutput']:
+ text += 'file'
+ else:
+ text += klass
+ if type!='input' or klass != 'flag':
+ text += '>'
+ if klass == 'list':
+ text += '}'
+ if 'required' not in opts:
+ text += ']'
+
+ self.preview.setText(text)
+ self.preview.setToolTip(text)
+
+ def preview_ports(self):
+ # show dialog with the ports that this module will have
+ self.generate_preview()
+ conf = self.get_current_conf()
+ if not conf:
+ return
+
+ intext = []
+ outtext = []
+
+ if 'stdin' in conf:
+ name, type, options = conf['stdin']
+ optional = " (visible)" if "required" in options else ""
+ intext.append("%s: %s%s" % (name, type, optional))
+ if 'stdout' in conf:
+ name, type, options = conf['stdout']
+ optional = " (visible)" if "required" in options else ""
+ outtext.append("%s: %s%s" % (name, type, optional))
+ if 'stderr' in conf:
+ name, type, options = conf['stderr']
+ optional = " (visible)" if "required" in options else ""
+ outtext.append("%s: %s%s" % (name, type, optional))
+ if 'options' in conf and 'env_port' in conf['options']:
+ intext.append('env: String')
+ for type, name, klass, options in conf['args']:
+ optional = " (visible)" if "required" in options else ""
+ if 'input' == type.lower():
+ intext.append("%s: %s%s" % (name, klass, optional))
+ elif 'output' == type.lower():
+ outtext.append("%s: %s%s" % (name, klass, optional))
+ elif 'inputoutput' == type.lower():
+ intext.append("%s: %s%s" % (name, 'File', optional))
+ outtext.append("%s: %s%s" % (name, 'File', optional))
+
+ intext = ''.join(['Input %s. %s\n' % (i+1, t)
+ for i, t in zip(xrange(len(intext)), intext)])
+ outtext = ''.join(['Output %s. %s\n' % (i+1, t)
+ for i, t in zip(xrange(len(outtext)), outtext)])
+
+ self.helppageView = QManpageDialog("Module Ports for this Wrapper",
+ intext + "\n" + outtext, self)
+ self.helppageView.show()
+
+ def loadFromCommand(self, argv):
+ self.command.setText(argv[0])
+ pos = 0
+ for argName in argv[1:]:
+ arg = QArgWidget()
+ arg.guess(argName, pos)
+ pos += 1
+ item = QtGui.QListWidgetItem()
+ item.setSizeHint(arg.sizeHint())
+ self.argList.addItem(item)
+ self.argList.setItemWidget(item, arg)
+
+ def addArgument(self):
+ arg = QArgWidget()
+ item = QtGui.QListWidgetItem()
+ item.setSizeHint(arg.sizeHint())
+ self.argList.addItem(item)
+ self.argList.setItemWidget(item, arg)
+
+ def moveUp(self):
+ currentRow = self.argList.currentRow()
+ if currentRow < 1:
+ return
+ # moving widgets does not work so we just switch contents
+ w0 = self.argList.itemWidget(self.argList.item(currentRow-1))
+ w1 = self.argList.itemWidget(self.argList.item(currentRow))
+ arg0 = w0.toList()
+ arg1 = w1.toList()
+ w0.fromList(arg1)
+ w1.fromList(arg0)
+ self.argList.setCurrentRow(currentRow - 1)
+
+ def moveDown(self):
+ currentRow = self.argList.currentRow()
+ if currentRow<0 or currentRow>self.argList.count()-2:
+ return
+ # moving widgets does not work so we just switch contents
+ w1 = self.argList.itemWidget(self.argList.item(currentRow))
+ w2 = self.argList.itemWidget(self.argList.item(currentRow+1))
+ arg1 = w1.toList()
+ arg2 = w2.toList()
+ w1.fromList(arg2)
+ w2.fromList(arg1)
+ self.argList.setCurrentRow(currentRow + 1)
+
+ def removeArgument(self):
+ currentRow = self.argList.currentRow()
+ if currentRow<0:
+ return
+ self.argList.takeItem(currentRow)
+
+ def keyPressEvent(self, event):
+ if event.key() in [QtCore.Qt.Key_Delete, QtCore.Qt.Key_Backspace]:
+ self.removeArgument()
+ else:
+ QtGui.QWidget.keyPressEvent(self, event)
+
+ def parse(self, text):
+ """ parse(self, text)
+ parses the description of a command and extracts possible arguments
+ works on both man pages and help (-h) pages
+ """
+ lines = text.split('\n')
+ args = []
+ arg = None
+ for line in lines:
+ line = line.strip()
+ if len(line)>1 and line[0] == '-':
+ # make sure description is removed
+ flag = line.split(' ')[0].strip()
+ # use the last in the list of equal flags
+ #it is assumed to be most descriptive
+ flag = flag.split(',')[-1].strip()
+ # remove any special characters after flag
+ for i in ['=', '[', ' ']:
+ flag = flag.split(i)[0].strip()
+ # new arg (type, flag, description)
+ arg = ['Flag', flag, line]
+ if '=' in line: # assume string attribute with prefix
+ arg[0] = 'String'
+ args.append(arg)
+ elif arg:
+ if not line:
+ arg = None
+ else:
+ arg[2] += ' %s' % line.strip()
+ #print "args:"
+ #for arg in args:
+ # print arg
+ return args
+
+ def runProcess(self, args):
+ try:
+ command = Command(args)
+ status, text, stderr = command.run(stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ shell=True)
+ if not (text and len(text)):
+ text = stderr
+ if not (text and len(text)) or (text and text.startswith('No ')):
+ return None
+ # fix weird formatting
+ for a, b in encode_list:
+ text = text.replace(a, b)
+ return text
+ except:
+ return None
+
+ def generateFromManPage(self):
+ command = self.command.text()
+ if command == '':
+ return
+ text = self.runProcess(['-c', 'man %s | col -b' % command])
+ if not text:
+ QtGui.QMessageBox.warning(self, "Man page not found",
+ "For command '%s'" % command)
+ return
+ args = self.parse(text)
+ title = "Import arguments from man page for '%s'" % command
+ self.manpageImport = QManpageImport(title, args, self)
+ self.connect(self.manpageImport,
+ QtCore.SIGNAL("importArgs(PyQt_PyObject)"),
+ self.importArgs)
+ self.manpageImport.show()
+
+ def generateFromHelpPage(self):
+ command = self.command.text()
+ if command == '':
+ return
+ text = self.runProcess(['-c', command + ' -h'])
+ if not text:
+ QtGui.QMessageBox.warning(self, "Help page (-h) not found",
+ "For command '%s'" % command)
+ return
+ args = self.parse(text)
+
+ title = "Import arguments from help page (-h) for '%s'" % command
+ self.helppageImport = QManpageImport(title, args, self)
+ self.connect(self.helppageImport,
+ QtCore.SIGNAL("importArgs(PyQt_PyObject)"),
+ self.importArgs)
+ self.helppageImport.show()
+
+ def generateFromHelpPage2(self):
+ command = self.command.text()
+ if command == '':
+ return
+ text = self.runProcess(['-c', command + ' --help'])
+ if not text:
+ QtGui.QMessageBox.warning(self, "Help page (--help) not found",
+ "For command '%s'" % command)
+ return
+ args = self.parse(text)
+
+ title = "Import arguments from help page (--help) for '%s'" % command
+ self.helppageImport = QManpageImport(title, args, self)
+ self.connect(self.helppageImport,
+ QtCore.SIGNAL("importArgs(PyQt_PyObject)"),
+ self.importArgs)
+ self.helppageImport.show()
+
+ def viewManPage(self):
+ command = self.command.text()
+ if command == '':
+ return
+ text = self.runProcess(['-c', 'man %s | col -b' % command])
+ if not text:
+ QtGui.QMessageBox.warning(self, "Man page not found",
+ "For command '%s'" % command)
+ return
+ title = "man page for '%s'" % command
+ self.manpageView = QManpageDialog(title, text, self)
+ self.manpageView.show()
+
+ def viewHelpPage(self):
+ command = self.command.text()
+ if command == '':
+ return
+ text = self.runProcess(['-c', command + ' -h'])
+ if not text:
+ QtGui.QMessageBox.warning(self, "Help page (-h) not found",
+ "For command '%s'" % command)
+ return
+ title = "Help page for '%s'" % command
+ self.helppageView = QManpageDialog(title, text, self)
+ self.helppageView.show()
+
+ def viewHelpPage2(self):
+ command = self.command.text()
+ if command == '':
+ return
+ text = self.runProcess(['-c', command + ' --help'])
+ if not text:
+ QtGui.QMessageBox.warning(self, "Help page (--help) not found",
+ "For command '%s'" % command)
+ return
+ title = "Help page for '%s'" % command
+ self.helppageView = QManpageDialog(title, text, self)
+ self.helppageView.show()
+
+ def importArgs(self, args):
+ for arg in args:
+ item = QtGui.QListWidgetItem()
+ item.setSizeHint(arg.sizeHint())
+ self.argList.insertItem(0, item)
+ self.argList.setItemWidget(item, arg)
+
+class QArgWidget(QtGui.QWidget):
+ """ Widget for configuring an argument """
+ KLASSES = {
+ 'input': ['flag', 'file', 'string', 'integer', 'float', 'list'],
+ 'output': ['file', 'string'],
+ 'inputoutput': ['file'],
+ 'stdin': ['file', 'string'],
+ 'stdout': ['file', 'string'],
+ 'stderr': ['file', 'string'],
+ }
+ KLASSNAMES = {
+ 'flag': 'Boolean flag',
+ 'string': 'String',
+ 'integer': 'Integer',
+ 'float': 'Float',
+ 'file': 'File',
+ 'list': 'List',
+ }
+
+ TYPES = ['input', 'output', 'inputoutput', 'constant']
+ TYPENAMES = {
+ 'input': 'Input Port',
+ 'output': 'Output Port',
+ 'inputoutput': 'InputOutput Port',
+ 'constant': 'Constant',
+ }
+
+ def __init__(self, argtype='Input', name='untitled', klass='Flag', options={}, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.stdTypes = ['stdin', 'stdout', 'stderr']
+ self.stdLabels = ['Standard input', 'Standard output', 'Standard error']
+ self.stdDict = dict(zip(self.stdTypes, self.stdLabels))
+
+ self.argtype = argtype.lower()
+ self.name = name
+ self.klass = klass.lower()
+ self.options = options
+
+ layout = QtGui.QVBoxLayout()
+ self.setLayout(layout)
+
+ self.buildWidget()
+
+ def buildWidget(self):
+ layout = self.layout()
+ layout.setContentsMargins(2,2,2,2)
+ # remove any previous layout
+ layout1 = QtGui.QHBoxLayout()
+ layout1.setContentsMargins(2,2,2,2)
+ layout.addLayout(layout1)
+ if self.argtype not in self.stdTypes:
+ layout2 = QtGui.QHBoxLayout()
+ layout2.setContentsMargins(2,2,2,2)
+ layout.addLayout(layout2)
+ else:
+ layout2 = layout1
+ # type of argument
+ if self.argtype not in self.stdTypes:
+ self.typeList = QtGui.QComboBox()
+ self.typeDict = {}
+ for i, n in enumerate(self.TYPES):
+ self.typeList.addItem(self.TYPENAMES[n], n)
+ self.typeDict[n] = i
+ self.typeList.setCurrentIndex(self.typeDict.get(self.argtype, 0))
+ #label = QtGui.QLabel('Type:')
+ tt = "Select if argument will be an input port, output port, both, or a hidden constant. InputOutput's are always files."
+ #label.setToolTip(tt)
+ self.typeList.setToolTip(tt)
+ #layout1.addWidget(label)
+ layout1.addWidget(self.typeList)
+ else:
+ self.typeList = None
+ # type of port
+ self.klassList = QtGui.QComboBox()
+ klasses = self.KLASSES[self.argtype]
+ self.klassDict = {}
+ for i, n in enumerate(klasses):
+ self.klassList.addItem(self.KLASSNAMES[n], n)
+ self.klassDict[n] = i
+ self.klassList.setCurrentIndex(self.klassDict.get(self.klass, 0))
+ #label = QtGui.QLabel('Class:')
+ tt = 'Port Type. Can be String, Integer, Float, File or Boolean Flag. List means an input list of one of the other types. Only File and String should be used for output ports.'
+ self.klassList.setToolTip(tt)
+ #label.setToolTip(tt)
+ #layout1.addWidget(label)
+ layout1.addWidget(self.klassList)
+ # name of port
+ self.nameLine = QtGui.QLineEdit(self.name)
+ label = QtGui.QLabel('Name:')
+ tt = 'Name of the port, or the value for constants'
+ label.setToolTip(tt)
+ self.nameLine.setToolTip(tt)
+ layout1.addWidget(label)
+ layout1.addWidget(self.nameLine)
+ # options are different for each widget
+ if self.argtype not in self.stdTypes:
+ # all args can have flag
+ self.flag = QtGui.QLineEdit(self.options.get('flag', ''))
+ label = QtGui.QLabel('Flag:')
+ tt = 'a short-style flag before your input. Example: "-f" -> "-f yourinput"'
+ label.setToolTip(tt)
+ self.flag.setToolTip(tt)
+ self.flag.setFixedWidth(100)
+ layout1.addWidget(label)
+ layout1.addWidget(self.flag)
+
+ # all args can have prefix
+ self.prefix = QtGui.QLineEdit(self.options.get('prefix', ''))
+ label = QtGui.QLabel('Prefix:')
+ tt = 'a long-style prefix to your input. Example: "--X=" -> "--X=yourinput"'
+ label.setToolTip(tt)
+ self.prefix.setToolTip(tt)
+ layout1.addWidget(label)
+ layout1.addWidget(self.prefix)
+
+ # all can be required
+ self.required = QtGui.QCheckBox()
+ self.required.setChecked('required' in self.options)
+ label = QtGui.QLabel('Visible:')
+ tt = 'Check to make port always visible in VisTrails'
+ label.setToolTip(tt)
+ self.required.setToolTip(tt)
+ layout2.addWidget(label)
+ layout2.addWidget(self.required)
+
+ # subtype
+ self.subList = ['String', 'Integer', 'Float', 'File']
+ self.subDict = dict(zip(self.subList, xrange(len(self.subList))))
+ self.subDict.update(dict(zip([s.lower() for s in self.subList], xrange(len(self.subList)))))
+ self.subtype = QtGui.QComboBox()
+ self.subtype.addItems(self.subList)
+ self.subtype.setCurrentIndex(self.subDict.get(self.options.get('type', 'String'), 0))
+ self.listLabel = QtGui.QLabel('List type:')
+ self.subtype.setVisible(False)
+ tt = 'Choose type of values in List'
+ self.subtype.setToolTip(tt)
+ self.listLabel.setToolTip(tt)
+ layout2.addWidget(self.listLabel)
+ layout2.addWidget(self.subtype)
+ self.listLabel.setVisible(False)
+ self.subtype.setVisible(False)
+
+ # input files and inputoutput's can set file suffix
+ self.suffix = QtGui.QLineEdit(self.options.get('suffix', ''))
+ self.suffixLabel = QtGui.QLabel('File suffix:')
+ tt = 'Sets the specified file ending on the created file, like for example: ".txt"'
+ self.suffixLabel.setToolTip(tt)
+ self.suffix.setToolTip(tt)
+ self.suffix.setFixedWidth(50)
+ layout2.addWidget(self.suffixLabel)
+ layout2.addWidget(self.suffix)
+
+ self.typeChanged()
+ self.klassChanged()
+
+ # description
+ self.desc = QtGui.QLineEdit(self.options.get('desc', ''))
+ label = QtGui.QLabel('Description:')
+ tt = 'Add a helpful description of the port'
+ label.setToolTip(tt)
+ self.desc.setToolTip(tt)
+ layout2.addWidget(label)
+ layout2.addWidget(self.desc)
+
+ if self.argtype not in self.stdTypes:
+ self.connect(self.klassList, QtCore.SIGNAL('currentIndexChanged(int)'),
+ self.klassChanged)
+ self.connect(self.typeList, QtCore.SIGNAL('currentIndexChanged(int)'),
+ self.typeChanged)
+
+ def getValues(self):
+ """ get the values from the widgets and store them """
+ self.klass = self.klassList.itemData(self.klassList.currentIndex())
+ self.name = self.nameLine.text()
+ self.options = {}
+ if self.argtype not in self.stdTypes:
+ flag = self.flag.text()
+ if flag:
+ self.options['flag'] = flag
+ prefix = self.prefix.text()
+ if prefix:
+ self.options['prefix'] = prefix
+ desc = self.desc.text()
+ if desc:
+ self.options['desc'] = desc
+ if self.required.isChecked():
+ self.options['required'] = ''
+ if self.klass == 'list':
+ subtype = self.subtype.currentText()
+ if subtype:
+ self.options['type'] = subtype
+ type = self.argtype.lower()
+ suffix = self.suffix.text()
+ if (type == 'output' or type == 'inputoutput') and suffix:
+ self.options['suffix'] = suffix
+
+ def setValues(self):
+ if self.argtype not in self.stdTypes:
+ self.typeList.setCurrentIndex(self.typeDict.get(self.argtype, 0))
+ self.nameLine.setText(self.name)
+ self.klassList.setCurrentIndex(self.klassDict[self.klass])
+ if self.argtype not in self.stdTypes:
+ self.flag.setText(self.options.get('flag', ''))
+ self.prefix.setText(self.options.get('prefix', ''))
+ self.subtype.setCurrentIndex(self.subDict.get(self.options.get('type', 'String')))
+ self.subtype.setCurrentIndex(self.subDict.get(self.options.get('type', 'String'), 0))
+ self.required.setChecked('required' in self.options)
+ self.desc.setText(self.options.get('desc', ''))
+ type = self.argtype.lower()
+ if type == 'output' or type == 'inputoutput':
+ self.suffix.setText(self.options.get('suffix', ''))
+ self.typeChanged()
+ self.klassChanged()
+
+ def toList(self):
+ self.getValues()
+ if self.argtype not in self.stdTypes:
+ return [self.argtype, self.name, self.klass, self.options]
+ else:
+ return [self.name, self.klass, self.options]
+
+ def fromList(self, arg):
+ if self.argtype not in self.stdTypes:
+ self.argtype, self.name, self.klass, self.options = arg
+ else:
+ self.name, self.klass, self.options = arg
+ self.setValues()
+
+ def klassChanged(self, index=None):
+ if self.argtype in self.stdTypes:
+ return
+ klass = self.klassList.itemData(self.klassList.currentIndex())
+ self.listLabel.setVisible(klass == "list" and type == 'input')
+ self.subtype.setVisible(klass == "list" and type == 'input')
+
+ def typeChanged(self, index=None):
+ if self.argtype in self.stdTypes:
+ return
+ type = self.typeList.itemData(self.typeList.currentIndex())
+ if index is not None and type == self.argtype:
+ return
+ self.argtype = type
+ if type in ('constant', 'inputoutput'):
+ self.klassList.hide()
+ else:
+ self.klassList.show()
+ self.klassList.clear()
+ klasses = self.KLASSES[self.argtype]
+ self.klassDict = {}
+ for i, n in enumerate(klasses):
+ self.klassList.addItem(self.KLASSNAMES[n], n)
+ self.klassDict[n] = i
+ self.klassList.setCurrentIndex(self.klassDict.get(self.klass, 0))
+ self.suffixLabel.setVisible(type == 'output' or type == 'inputoutput')
+ self.suffix.setVisible(type == 'output' or type == 'inputoutput')
+
+ def guess(self, name, count=0):
+ """ add argument by guessing what the arg might be """
+ if '.' in name or '/' in name or '\\' in name: # guess file
+ self.fromList(['Input', 'file%s' % count, 'File',
+ {'desc':'"%s" guessed to be an Input file' % name}])
+ elif name.startswith('-'): # guess flag
+ self.fromList(['Input', 'flag%s' % name, 'Flag',
+ {'desc':'"%s" guessed to be a flag' % name,
+ 'flag':name}])
+ else: # guess string
+ self.fromList(['Input', 'input%s' % count, 'String',
+ {'desc':'"%s" guessed to be an input string' % name}])
+
+
+class QManpageDialog(QtGui.QDialog):
+ def __init__(self, title, text, parent=None):
+ QtGui.QDialog.__init__(self, parent)
+ self.setWindowTitle(title)
+ text = "<pre>%s</pre>" % text
+ self.textEdit = QtGui.QTextEdit(text)
+ self.textEdit.setReadOnly(True)
+ self.setLayout(QtGui.QHBoxLayout())
+ self.layout().addWidget(self.textEdit)
+ self.resize(800,600)
+
+class QManpageImport(QtGui.QDialog):
+ def __init__(self, title, args, parent=None):
+ QtGui.QDialog.__init__(self, parent)
+ self.setWindowTitle(title)
+ self.argLayout = QtGui.QVBoxLayout()
+ for arg in args:
+ if arg[0] == 'Flag':
+ w = QArgWidget(name=arg[1], options={'flag':arg[1],
+ 'desc':arg[2]})
+ else:
+ #if arg[0] == 'String':
+ w = QArgWidget(klass='String', name=arg[1],
+ options={'prefix':arg[1] + '=',
+ 'desc':arg[2]})
+ widgetLayout = QtGui.QHBoxLayout()
+ widgetLayout.addWidget(QtGui.QCheckBox())
+ widgetLayout.addWidget(w)
+ self.argLayout.addLayout(widgetLayout)
+ scroll = QtGui.QScrollArea()
+ w = QtGui.QWidget()
+ w.setLayout(self.argLayout)
+ scroll.setWidget(w)
+ scroll.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ scroll.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAsNeeded)
+ scroll.setWidgetResizable(True)
+ self.setLayout(QtGui.QVBoxLayout())
+ self.layout().addWidget(scroll)
+ layout2 = QtGui.QHBoxLayout()
+ self.layout().addLayout(layout2)
+ self.closeButton = QtGui.QPushButton('Close')
+ self.closeButton.setToolTip('Close this window')
+ self.connect(self.closeButton, QtCore.SIGNAL('clicked()'),
+ self.close)
+ layout2.addWidget(self.closeButton)
+ self.selectAllButton = QtGui.QPushButton('Select All')
+ self.selectAllButton.setToolTip('Select All arguments')
+ self.connect(self.selectAllButton, QtCore.SIGNAL('clicked()'),
+ self.selectAll)
+ layout2.addWidget(self.selectAllButton)
+ self.selectNoneButton = QtGui.QPushButton('Select None')
+ self.selectNoneButton.setToolTip('Unselect All arguments')
+ self.connect(self.selectNoneButton, QtCore.SIGNAL('clicked()'),
+ self.selectNone)
+ layout2.addWidget(self.selectNoneButton)
+ self.addSelectedButton = QtGui.QPushButton('Import Selected')
+ self.addSelectedButton.setToolTip('Import all selected arguments')
+ self.connect(self.addSelectedButton, QtCore.SIGNAL('clicked()'),
+ self.addSelected)
+ layout2.addWidget(self.addSelectedButton)
+ self.resize(800,600)
+
+ def selectAll(self):
+ for i in xrange(self.argLayout.count()):
+ w = self.argLayout.layout().itemAt(i)
+ w.layout().itemAt(0).widget().setChecked(True)
+
+ def selectNone(self):
+ for i in xrange(self.argLayout.count()):
+ w = self.argLayout.layout().itemAt(i)
+ w.layout().itemAt(0).widget().setChecked(False)
+
+ def addSelected(self):
+ # collect selected arguments and send through signal
+ args = []
+ remove_list = []
+ for i in xrange(self.argLayout.count()):
+ w = self.argLayout.layout().itemAt(i)
+ if w.layout().itemAt(0).widget().isChecked():
+ remove_list.append(w)
+ args.append(w.layout().itemAt(1).widget())
+ for w in remove_list:
+ w.layout().itemAt(0).widget().setChecked(False)
+ w.layout().itemAt(0).widget().hide()
+ w.layout().itemAt(1).widget().hide()
+ self.argLayout.removeItem(w)
+
+ self.emit(QtCore.SIGNAL('importArgs(PyQt_PyObject)'), args)
+
+class QCLToolsWizardWindow(QtGui.QMainWindow):
+
+ def __init__(self, parent=None, reload_scripts=None):
+ QtGui.QMainWindow.__init__(self, parent)
+ self.wizard = QCLToolsWizard(self, reload_scripts)
+ self.setCentralWidget(self.wizard)
+ self.setWindowTitle("CLTools Wizard")
+ self.resize(1000,600)
+
+if __name__ == "__main__":
+ app = QtGui.QApplication(sys.argv)
+ window = QCLToolsWizardWindow()
+ if len(sys.argv)>2 and sys.argv[1] == '-c':
+ # read command from command line
+ window.wizard.loadFromCommand(sys.argv[2:])
+ window.show()
+ app.exec_()
diff --git a/vistrails/packages/HTTP/__init__.py b/vistrails/packages/HTTP/__init__.py
new file mode 100644
index 0000000..c4046f3
--- /dev/null
+++ b/vistrails/packages/HTTP/__init__.py
@@ -0,0 +1,46 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""HTTP provides packages for HTTP-based file fetching. This provides
+a location-independent way of referring to files. This package uses a
+local cache of the files, inside the per-user VisTrails
+directory. This way, files that haven't been changed do not need
+downloading. The check is performed efficiently using the HTTP GET
+headers.
+"""
+
+identifier = 'org.vistrails.vistrails.http'
+name = 'HTTP'
+version = '0.9.1'
+old_identifiers = ['edu.utah.sci.vistrails.http']
diff --git a/vistrails/packages/HTTP/http_directory.py b/vistrails/packages/HTTP/http_directory.py
new file mode 100644
index 0000000..d24d492
--- /dev/null
+++ b/vistrails/packages/HTTP/http_directory.py
@@ -0,0 +1,175 @@
+# https://gist.github.com/remram44/6540454
+
+from HTMLParser import HTMLParser
+import urllib2
+import os
+import re
+
+
+re_url = re.compile(r'^(([a-zA-Z_-]+)://([^/]+))(/.*)?$')
+
+def resolve_link(link, url):
+ m = re_url.match(link)
+ if m is not None:
+ if not m.group(4):
+ # http://domain -> http://domain/
+ return link + '/'
+ else:
+ return link
+ elif link[0] == '/':
+ # /some/path
+ murl = re_url.match(url)
+ return murl.group(1) + link
+ else:
+ # relative/path
+ if url[-1] == '/':
+ return url + link
+ else:
+ return url + '/' + link
+
+
+class ListingParser(HTMLParser):
+ """Parses an HTML file and build a list of links.
+
+ Links are stored into the 'links' set. They are resolved into absolute
+ links.
+ """
+ def __init__(self, url):
+ HTMLParser.__init__(self)
+
+ if url[-1] != '/':
+ url += '/'
+ self.__url = url
+ self.links = set()
+
+ def handle_starttag(self, tag, attrs):
+ if tag == 'a':
+ for key, value in attrs:
+ if key == 'href':
+ if not value:
+ continue
+ value = resolve_link(value, self.__url)
+ self.links.add(value)
+ break
+
+
+def download_directory(url, target):
+ def mkdir():
+ if not mkdir.done:
+ try:
+ os.mkdir(target)
+ except OSError:
+ pass
+ mkdir.done = True
+ mkdir.done = False
+
+ response = urllib2.urlopen(url)
+
+ if response.info().type == 'text/html':
+ contents = response.read()
+
+ parser = ListingParser(url)
+ parser.feed(contents)
+ for link in parser.links:
+ link = resolve_link(link, url)
+ if link[-1] == '/':
+ link = link[:-1]
+ if not link.startswith(url):
+ continue
+ name = link.rsplit('/', 1)[1]
+ if '?' in name:
+ continue
+ mkdir()
+ download_directory(link, os.path.join(target, name))
+ if not mkdir.done:
+ # We didn't find anything to write inside this directory
+ # Maybe it's a HTML file?
+ if url[-1] != '/':
+ end = target[-5:].lower()
+ if not (end.endswith('.htm') or end.endswith('.html')):
+ target = target + '.html'
+ with open(target, 'wb') as fp:
+ fp.write(contents)
+ else:
+ buffer_size = 4096
+ with open(target, 'wb') as fp:
+ chunk = response.read(buffer_size)
+ while chunk:
+ fp.write(chunk)
+ chunk = response.read(buffer_size)
+
+
+###############################################################################
+
+import unittest
+
+
+class TestLinkResolution(unittest.TestCase):
+ def test_absolute_link(self):
+ self.assertEqual(
+ resolve_link('http://website.org/p/test.txt',
+ 'http://some/other/url'),
+ 'http://website.org/p/test.txt')
+ self.assertEqual(
+ resolve_link('http://website.org',
+ 'http://some/other/url'),
+ 'http://website.org/')
+
+ def test_absolute_path(self):
+ self.assertEqual(
+ resolve_link('/p/test.txt', 'http://some/url'),
+ 'http://some/p/test.txt')
+ self.assertEqual(
+ resolve_link('/p/test.txt', 'http://some/url/'),
+ 'http://some/p/test.txt')
+ self.assertEqual(
+ resolve_link('/p/test.txt', 'http://site'),
+ 'http://site/p/test.txt')
+ self.assertEqual(
+ resolve_link('/p/test.txt', 'http://site/'),
+ 'http://site/p/test.txt')
+
+ def test_relative_path(self):
+ self.assertEqual(
+ resolve_link('some/file', 'http://site/folder'),
+ 'http://site/folder/some/file')
+ self.assertEqual(
+ resolve_link('some/file', 'http://site/folder/'),
+ 'http://site/folder/some/file')
+ self.assertEqual(
+ resolve_link('some/dir/', 'http://site/folder'),
+ 'http://site/folder/some/dir/')
+
+
+class TestParser(unittest.TestCase):
+ def test_parse(self):
+ parser = ListingParser('http://a.remram.fr/test')
+ parser.feed("""
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN"><html><head><title>
+Index of /test</title></head><body><h1>Index of /test</h1><table><tr><th>
+<img src="/icons/blank.gif" alt="[ICO]"></th><th><a href="?C=N;O=D">Name</a>
+</th><th><a href="?C=M;O=A">Last modified</a></th><th><a href="?C=S;O=A">Size
+</a></th><th><a href="?C=D;O=A">Description</a></th></tr><tr><th colspan="5">
+<hr></th></tr><tr><td valign="top"><img src="/icons/back.gif" alt="[DIR]"></td>
+<td><a href="/">Parent Directory</a></td><td> </td><td align="right"> -
+</td><td> </td></tr><tr><td valign="top">
+<img src="/icons/unknown.gif" alt="[ ]"></td><td><a href="a">a</a></td>
+<td align="right">11-Sep-2013 15:46 </td><td align="right"> 3 </td><td>
+</td></tr><tr><td valign="top"><img src="/icons/unknown.gif" alt="[ ]"></td>
+<td><a href="/bb">bb</a></td><td align="right">11-Sep-2013 15:46 </td>
+<td align="right"> 3 </td><td> </td></tr><tr><td valign="top">
+<img src="/icons/folder.gif" alt="[DIR]"></td><td><a href="/cc/">cc/</a></td>
+<td align="right">11-Sep-2013 15:46 </td><td align="right"> - </td><td>
+</td></tr><tr><td valign="top"><img src="/icons/folder.gif" alt="[DIR]"></td>
+<td><a href="http://a.remram.fr/dd">dd/</a></td><td align="right">
+11-Sep-2013 15:46 </td><td align="right"> - </td><td> </td></tr><tr>
+<th colspan="5"><hr></th></tr></table></body></html>
+ """)
+ links = set(l for l in parser.links if '?' not in l)
+ self.assertEqual(links, set([
+ 'http://a.remram.fr/',
+ 'http://a.remram.fr/test/a',
+ 'http://a.remram.fr/bb',
+ 'http://a.remram.fr/cc/',
+ 'http://a.remram.fr/dd',
+ ]))
diff --git a/vistrails/packages/HTTP/init.py b/vistrails/packages/HTTP/init.py
new file mode 100644
index 0000000..bd89b7a
--- /dev/null
+++ b/vistrails/packages/HTTP/init.py
@@ -0,0 +1,539 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""HTTP provides packages for HTTP-based file fetching. This provides
+a location-independent way of referring to files. This package uses a
+local cache of the files, inside the per-user VisTrails
+directory. This way, files that haven't been changed do not need
+downloading. The check is performed efficiently using the HTTP GET
+headers.
+"""
+from vistrails.core.modules.vistrails_module import ModuleError
+from vistrails.core.configuration import get_vistrails_persistent_configuration
+from vistrails.gui.utils import show_warning
+from vistrails.core.modules.vistrails_module import Module
+import vistrails.core.modules.basic_modules
+import vistrails.core.modules.module_registry
+from vistrails.core import debug
+from vistrails.core.system import current_dot_vistrails
+import vistrails.gui.repository
+
+import datetime
+import email.utils
+import hashlib
+import os.path
+import sys
+import unittest
+import urllib
+import urllib2
+
+from vistrails.core.repository.poster.encode import multipart_encode
+from vistrails.core.repository.poster.streaminghttp import register_openers
+
+from vistrails.core.utils import DummyView
+
+from http_directory import download_directory
+
+# special file uploaders used to push files to repository
+
+package_directory = None
+
+###############################################################################
+
+class HTTPFile(Module):
+ """ Downloads file from URL """
+
+ def compute(self):
+ self.checkInputPort('url')
+ url = self.getInputFromPort("url")
+ (result, downloaded_file, local_filename) = self.download(url)
+ self.setResult("local_filename", local_filename)
+ if result == 2:
+ raise ModuleError(self, downloaded_file)
+ else:
+ self.setResult("file", downloaded_file)
+
+ def download(self, url):
+ """download(url:string) -> (result: int, downloaded_file: File,
+ local_filename:string)
+ Tries to download a file from url. It returns a tuple with:
+ result: 0 -> success
+ 1 -> couldn't download the file, but found a cached version
+ 2 -> failed (in this case downloaded_file will contain the
+ error message)
+ downloaded_file: The downloaded file or the error message in case it
+ failed
+
+ local_filename: the path to the local_filename
+
+ """
+
+ self._parse_url(url)
+
+ opener = urllib2.build_opener()
+
+ local_filename = self._local_filename(url)
+
+ # Get ETag from disk
+ try:
+ with open(local_filename + '.etag') as etag_file:
+ etag = etag_file.read()
+ except IOError:
+ etag = None
+
+ try:
+ request = urllib2.Request(url)
+ if etag is not None:
+ request.add_header(
+ 'If-None-Match',
+ etag)
+ try:
+ mtime = email.utils.formatdate(os.path.getmtime(local_filename),
+ usegmt=True)
+ request.add_header(
+ 'If-Modified-Since',
+ mtime)
+ except OSError:
+ pass
+ f1 = opener.open(request)
+ except urllib2.URLError, e:
+ if isinstance(e, urllib2.HTTPError) and e.code == 304:
+ # Not modified
+ result = vistrails.core.modules.basic_modules.File()
+ result.name = local_filename
+ return (0, result, local_filename)
+ if self._file_is_in_local_cache(local_filename):
+ debug.warning('A network error occurred. HTTPFile will use a '
+ 'cached version of the file')
+ result = vistrails.core.modules.basic_modules.File()
+ result.name = local_filename
+ return (1, result, local_filename)
+ else:
+ return (2, (str(e)), local_filename)
+ else:
+ try:
+ mod_header = f1.headers['last-modified']
+ except KeyError:
+ mod_header = None
+ try:
+ size_header = f1.headers['content-length']
+ if not size_header:
+ raise ValueError
+ size_header = int(size_header)
+ except ValueError:
+ size_header = None
+
+ result = vistrails.core.modules.basic_modules.File()
+ result.name = local_filename
+
+ if (not self._file_is_in_local_cache(local_filename) or
+ not mod_header or
+ self._is_outdated(mod_header, local_filename)):
+ try:
+ dl_size = 0
+ CHUNKSIZE = 4096
+ f2 = open(local_filename, 'wb')
+ while True:
+ if size_header is not None:
+ self.logging.update_progress(
+ self,
+ dl_size*1.0/size_header)
+ chunk = f1.read(CHUNKSIZE)
+ if not chunk:
+ break
+ dl_size += len(chunk)
+ f2.write(chunk)
+ f2.close()
+ f1.close()
+
+ except Exception, e:
+ try:
+ os.unlink(local_filename)
+ except OSError:
+ pass
+ return (2, ("Error retrieving URL: %s" % e), local_filename)
+ result.name = local_filename
+
+ # Save ETag
+ try:
+ etag = f1.headers['ETag']
+ except KeyError:
+ pass
+ else:
+ with open(local_filename + '.etag', 'w') as etag_file:
+ etag = etag_file.write(etag)
+
+ return (0, result, local_filename)
+
+ ##########################################################################
+
+ def _parse_url(self, url):
+ s = url.split('/')
+ try:
+ self.host = s[2]
+ self.filename = '/' + '/'.join(s[3:])
+ except:
+ raise ModuleError(self, "Malformed URL: %s" % url)
+
+ def _is_outdated(self, remoteHeader, localFile):
+ """Checks whether local file is outdated."""
+ local_time = \
+ datetime.datetime.utcfromtimestamp(os.path.getmtime(localFile))
+ try:
+ remote_time = datetime.datetime.strptime(remoteHeader,
+ "%a, %d %b %Y %H:%M:%S %Z")
+ except ValueError:
+ try:
+ remote_time = datetime.datetime.strptime(remoteHeader,
+ "%a, %d %B %Y %H:%M:%S %Z")
+ except ValueError:
+ # unable to parse last-modified header, download file again
+ debug.warning("Unable to parse Last-Modified header"
+ ", downloading file")
+ return True
+ return remote_time > local_time
+
+ def _file_is_in_local_cache(self, local_filename):
+ return os.path.isfile(local_filename)
+
+ def _local_filename(self, url):
+ return package_directory + '/' + urllib.quote_plus(url)
+
+
+class HTTPDirectory(Module):
+ """Downloads a whole directory recursively from a URL
+ """
+
+ def compute(self):
+ self.checkInputPort('url')
+ url = self.getInputFromPort('url')
+ local_path = self.download(url)
+ self.setResult('local_path', local_path)
+ local_dir = vistrails.core.modules.basic_modules.Directory()
+ local_dir.name = local_path
+ self.setResult('directory', local_dir)
+
+ def download(self, url):
+ local_path = self.interpreter.filePool.create_directory(
+ prefix='vt_http').name
+ download_directory(url, local_path)
+ return local_path
+
+
+class RepoSync(Module):
+ """ VisTrails Server version of RepoSync modules. Customized to play
+ nicely with crowdlabs. Needs refactoring.
+
+ RepoSync enables data to be synced with a online repository. The designated file
+ parameter will be uploaded to the repository on execution,
+ creating a new pipeline version that links to online repository data.
+ If the local file isn't available, then the online repository data is used.
+ """
+
+ def __init__(self):
+ Module.__init__(self)
+
+ config = get_vistrails_persistent_configuration()
+ if config.check('webRepositoryURL'):
+ self.base_url = config.webRepositoryURL
+ else:
+ raise ModuleError(self,
+ ("No webRepositoryURL value defined"
+ " in the Expert Configuration"))
+
+ # check if we are running in server mode
+ # this effects how the compute method functions
+ if config.check('isInServerMode'):
+ self.is_server = bool(config.isInServerMode)
+ else:
+ self.is_server = False
+
+ # TODO: this '/' check should probably be done in core/configuration.py
+ if self.base_url[-1] == '/':
+ self.base_url = self.base_url[:-1]
+
+ # used for invaliding cache when user isn't logged in to crowdLabs
+ # but wants to upload data
+ def invalidate_cache(self):
+ return False
+
+ def validate_cache(self):
+ return True
+
+ def _file_is_in_local_cache(self, local_filename):
+ return os.path.isfile(local_filename)
+
+ def checksum_lookup(self):
+ """ checks if the repository has the wanted data """
+
+ checksum_url = "%s/datasets/exists/%s/" % (self.base_url, self.checksum)
+ self.on_server = False
+ try:
+ check_dataset_on_repo = urllib2.urlopen(url=checksum_url)
+ self.up_to_date = True if \
+ check_dataset_on_repo.read() == 'uptodate' else False
+ self.on_server = True
+ except urllib2.HTTPError:
+ self.up_to_date = True
+
+ def data_sync(self):
+ """ downloads/uploads/uses the local file depending on availability """
+ self.checksum_lookup()
+
+ # local file not on repository, so upload
+ if not self.on_server and os.path.isfile(self.in_file.name):
+ cookiejar = vistrails.gui.repository.QRepositoryDialog.cookiejar
+ if cookiejar:
+ register_openers(cookiejar=cookiejar)
+
+ params = {'dataset_file': open(self.in_file.name, 'rb'),
+ 'name': self.in_file.name.split('/')[-1],
+ 'origin': 'vistrails',
+ 'checksum': self.checksum}
+
+ upload_url = "%s/datasets/upload/" % self.base_url
+
+ datagen, headers = multipart_encode(params)
+ request = urllib2.Request(upload_url, datagen, headers)
+ try:
+ result = urllib2.urlopen(request)
+ if result.code != 200:
+ show_warning("Upload Failure",
+ "Data failed to upload to repository")
+ # make temporarily uncachable
+ self.is_cacheable = self.invalidate_cache
+ else:
+ debug.warning("Push to repository was successful")
+ # make sure module caches
+ self.is_cacheable = self.validate_cache
+ except Exception, e:
+ show_warning("Upload Failure",
+ "Data failed to upload to repository")
+ # make temporarily uncachable
+ self.is_cacheable = self.invalidate_cache
+ debug.warning('RepoSync uploaded %s to the repository' % \
+ self.in_file.name)
+ else:
+ show_warning("Please login", ("You must be logged into the web"
+ " repository in order to upload "
+ "data. No data was synced"))
+ # make temporarily uncachable
+ self.is_cacheable = self.invalidate_cache
+
+ # use local data
+ self.setResult("file", self.in_file)
+ else:
+ # file on repository mirrors local file, so use local file
+ if self.up_to_date and os.path.isfile(self.in_file.name):
+ self.setResult("file", self.in_file)
+ else:
+ # local file not present or out of date, download or used cached
+ self.url = "%s/datasets/download/%s" % (self.base_url,
+ self.checksum)
+ local_filename = package_directory + '/' + \
+ urllib.quote_plus(self.url)
+ if not self._file_is_in_local_cache(local_filename):
+ # file not in cache, download.
+ try:
+ urllib.urlretrieve(self.url, local_filename)
+ except IOError, e:
+ raise ModuleError(self, ("Invalid URL: %s" % e))
+ out_file = vistrails.core.modules.basic_modules.File()
+ out_file.name = local_filename
+ debug.warning('RepoSync is using repository data')
+ self.setResult("file", out_file)
+
+
+ def compute(self):
+ # if server, grab local file using checksum id
+ if self.is_server:
+ self.checkInputPort('checksum')
+ self.checksum = self.getInputFromPort("checksum")
+ # get file path
+ path_url = "%s/datasets/path/%s/"%(self.base_url, self.checksum)
+ try:
+ dataset_path_request = urllib2.urlopen(url=path_url)
+ dataset_path = dataset_path_request.read()
+ except urllib2.HTTPError:
+ pass
+
+ if os.path.isfile(dataset_path):
+ out_file = vistrails.core.modules.basic_modules.File()
+ out_file.name = dataset_path
+ self.setResult("file", out_file)
+ else: # is client
+ self.checkInputPort('file')
+ self.in_file = self.getInputFromPort("file")
+ if os.path.isfile(self.in_file.name):
+ # do size check
+ size = os.path.getsize(self.in_file.name)
+ if size > 26214400:
+ show_warning("File is too large", ("file is larger than 25MB, "
+ "unable to sync with web repository"))
+ self.setResult("file", self.in_file)
+ else:
+ # compute checksum
+ f = open(self.in_file.name, 'r')
+ self.checksum = hashlib.sha1()
+ block = 1
+ while block:
+ block = f.read(128)
+ self.checksum.update(block)
+ f.close()
+ self.checksum = self.checksum.hexdigest()
+
+ # upload/download file
+ self.data_sync()
+
+ # set checksum param in module
+ if not self.hasInputFromPort('checksum'):
+ self.change_parameter('checksum', [self.checksum])
+
+ else:
+ # local file not present
+ if self.hasInputFromPort('checksum'):
+ self.checksum = self.getInputFromPort("checksum")
+
+ # download file
+ self.data_sync()
+
+def initialize(*args, **keywords):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ basic = vistrails.core.modules.basic_modules
+
+ reg.add_module(HTTPFile)
+ reg.add_input_port(HTTPFile, "url", (basic.String, 'URL'))
+ reg.add_output_port(HTTPFile, "file", (basic.File, 'local File object'))
+ reg.add_output_port(HTTPFile, "local_filename",
+ (basic.String, 'local filename'), optional=True)
+
+ reg.add_module(HTTPDirectory)
+ reg.add_input_port(HTTPDirectory, 'url', (basic.String, "URL"))
+ reg.add_output_port(HTTPDirectory, 'directory',
+ (basic.Directory, "local Directory object"))
+ reg.add_output_port(HTTPDirectory, 'local_path',
+ (basic.String, "local path"), optional=True)
+
+ reg.add_module(RepoSync)
+ reg.add_input_port(RepoSync, "file", (basic.File, 'File'))
+ reg.add_input_port(RepoSync, "checksum",
+ (basic.String, 'Checksum'), optional=True)
+ reg.add_output_port(RepoSync, "file", (basic.File,
+ 'Repository Synced File object'))
+ reg.add_output_port(RepoSync, "checksum",
+ (basic.String, 'Checksum'), optional=True)
+
+ global package_directory
+ dotVistrails = current_dot_vistrails()
+ package_directory = os.path.join(dotVistrails, "HTTP")
+
+ if not os.path.isdir(package_directory):
+ try:
+ debug.log("Creating HTTP package directory: %s" % package_directory)
+ os.mkdir(package_directory)
+ except:
+ debug.critical(("Create directory failed. Make sure '%s' does not"
+ " exist and parent directory is writable") %
+ package_directory)
+ sys.exit(1)
+
+##############################################################################
+
+
+class TestHTTPFile(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ from vistrails.core.packagemanager import get_package_manager
+ from vistrails.core.modules.module_registry import MissingPackage
+ pm = get_package_manager()
+ try:
+ pm.get_package('org.vistrails.vistrails.http')
+ except MissingPackage:
+ pm.late_enable_package('HTTP')
+
+ def testParseURL(self):
+ foo = HTTPFile()
+ foo._parse_url('http://www.sci.utah.edu/~cscheid/stuff/vtkdata-5.0.2.zip')
+ self.assertEquals(foo.host, 'www.sci.utah.edu')
+ self.assertEquals(foo.filename, '/~cscheid/stuff/vtkdata-5.0.2.zip')
+
+ def testIncorrectURL(self):
+ from vistrails.tests.utils import execute
+ self.assertTrue(execute([
+ ('HTTPFile', identifier, [
+ ('url', [('String', 'http://idbetthisdoesnotexistohrly')]),
+ ]),
+ ]))
+
+ def testIncorrectURL_2(self):
+ from vistrails.tests.utils import execute
+ self.assertTrue(execute([
+ ('HTTPFile', identifier, [
+ ('url', [('String', 'http://neitherodesthisohrly')]),
+ ]),
+ ]))
+
+class TestHTTPDirectory(unittest.TestCase):
+ def test_download(self):
+ url = 'http://www.vistrails.org/testing/httpdirectory/test/'
+
+ import shutil
+ import tempfile
+ testdir = tempfile.mkdtemp(prefix='vt_test_http_')
+ try:
+ download_directory(url, testdir)
+ files = {}
+ def addfiles(dirpath):
+ td = os.path.join(testdir, dirpath)
+ for name in os.listdir(td):
+ filename = os.path.join(testdir, dirpath, name)
+ dn = os.path.join(dirpath, name)
+ if os.path.isdir(filename):
+ addfiles(os.path.join(dirpath, name))
+ else:
+ with open(filename, 'rb') as f:
+ files[dn.replace(os.sep, '/')] = f.read()
+ addfiles('')
+ self.assertEqual(len(files), 4)
+ del files['f.html']
+ self.assertEqual(files, {
+ 'a': 'aa\n',
+ 'bb': 'bb\n',
+ 'cc/d': 'dd\n',
+ })
+ finally:
+ shutil.rmtree(testdir)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/vistrails/packages/ImageMagick/__init__.py b/vistrails/packages/ImageMagick/__init__.py
new file mode 100644
index 0000000..651420e
--- /dev/null
+++ b/vistrails/packages/ImageMagick/__init__.py
@@ -0,0 +1,48 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""ImageMagick package for VisTrails.
+
+This package defines a set of modules that perform some of the
+operations exposed by the ImageMagick package.
+
+"""
+from vistrails.core.configuration import ConfigurationObject
+
+identifier = 'org.vistrails.vistrails.imagemagick'
+name = 'ImageMagick'
+version = '0.9.5'
+old_identifiers = ['edu.utah.sci.vistrails.imagemagick']
+configuration = ConfigurationObject(quiet=False,
+ path=(None, str))
diff --git a/vistrails/packages/ImageMagick/init.py b/vistrails/packages/ImageMagick/init.py
new file mode 100644
index 0000000..c3393bd
--- /dev/null
+++ b/vistrails/packages/ImageMagick/init.py
@@ -0,0 +1,280 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+##############################################################################
+# Changes
+#
+# 20130827 (by Remi)
+# CombineRGBA can now also accept RGB
+# Factored code common between Convert and CombineRGBA
+# Removes 'geometry' and related ports from most modules, as they were
+# *already ignored* except by the Scale module
+#
+# 20090521 (by Emanuele)
+# Added path configuration option so imagemagick does not to be in the path
+# Removed ImageMagick presence check
+#
+# 20081002:
+# Added CombineRGBA to create image from channels.
+# Moved quiet to configuration
+# Fixed bug with GaussianBlur
+
+from vistrails.core import debug
+import vistrails.core.modules.basic_modules as basic
+import vistrails.core.modules.module_registry
+from vistrails.core.modules.vistrails_module import Module, ModuleError, \
+ new_module, IncompleteImplementation
+from vistrails.core.system import list2cmdline
+
+import os
+
+################################################################################
+
+class ImageMagick(Module):
+ """ImageMagick is the base Module for all Modules in the ImageMagick
+package. It simply defines some helper methods for subclasses."""
+
+ def compute(self):
+ raise IncompleteImplementation
+
+ def input_file_description(self):
+ """Returns a fully described name in the ImageMagick format.
+
+ For example, a file stored in PNG format may be described by:
+ - 'graphic.png' indicates the filename 'graphic.png', using the PNG
+ file format.
+ - 'png:graphic' indicates the filename 'graphic', still using the PNG
+ file format."""
+ i = self.getInputFromPort("input")
+ if self.hasInputFromPort('inputFormat'):
+ return self.getInputFromPort('inputFormat') + ':' + i.name
+ else:
+ return i.name
+
+ def create_output_file(self):
+ """Creates a File with the output format given by the
+outputFormat port."""
+ if self.hasInputFromPort('outputFormat'):
+ s = '.' + self.getInputFromPort('outputFormat')
+ return self.interpreter.filePool.create_file(suffix=s)
+ else:
+ return self.interpreter.filePool.create_file(suffix='.png')
+
+ def run(self, *args):
+ """run(*args), runs ImageMagick's 'convert' on a shell, passing all
+arguments to the program."""
+ path = None
+ if configuration.check('path'):
+ path = configuration.path
+ if path:
+ cmd = os.path.join(path,'convert')
+ else:
+ cmd = 'convert'
+ cmd = [cmd] + list(args)
+ cmdline = list2cmdline(cmd)
+ if not configuration.quiet:
+ debug.log(cmdline)
+ r = os.system(cmdline)
+ if r != 0:
+ raise ModuleError(self, "system call failed: %r" % cmdline)
+
+
+class Convert(ImageMagick):
+ """Convert is the base Module for VisTrails Modules in the ImageMagick
+package that transform a single input into a single output. Each subclass has
+a descriptive name of the operation it implements."""
+
+ def compute(self):
+ o = self.create_output_file()
+ i = self.input_file_description()
+ self.run(i, o.name)
+ self.setResult("output", o)
+
+
+class CombineRGBA(ImageMagick):
+ """Combines channels as separate images into a single RGBA file."""
+
+ def compute(self):
+ o = self.create_output_file()
+ r = self.getInputFromPort("r")
+ g = self.getInputFromPort("g")
+ b = self.getInputFromPort("b")
+ a = self.forceGetInputFromPort("a")
+
+ if a is not None:
+ self.run(r.name, g.name, b.name, a.name,
+ '-channel', 'RGBA',
+ '-combine', o.name)
+ else:
+ self.run(r.name, g.name, b.name,
+ '-channel', 'RGB',
+ '-combine', o.name)
+
+ self.setResult("output", o)
+
+
+class Scale(Convert):
+ """Scale rescales the input image to the given geometry description."""
+
+ def geometry_description(self):
+ """returns a string with the description of the geometry as
+indicated by the appropriate ports (geometry or width and height)"""
+ # if complete geometry is available, ignore rest
+ if self.hasInputFromPort("geometry"):
+ return self.getInputFromPort("geometry")
+ elif self.hasInputFromPort("width"):
+ w = self.getInputFromPort("width")
+ h = self.getInputFromPort("height")
+ return "'%sx%s'" % (w, h)
+ else:
+ raise ModuleError(self, "Needs geometry or width/height")
+
+ def compute(self):
+ o = self.create_output_file()
+ self.run(self.input_file_description(),
+ "-scale",
+ self.geometry_description(),
+ o.name)
+ self.setResult("output", o)
+
+
+class GaussianBlur(Convert):
+ """GaussianBlur convolves the image with a Gaussian filter of given radius
+and standard deviation."""
+
+ def compute(self):
+ (radius, sigma) = self.getInputFromPort('radiusSigma')
+ o = self.create_output_file()
+ self.run(self.input_file_description(),
+ "-blur",
+ "%sx%s" % (radius, sigma),
+ o.name)
+ self.setResult("output", o)
+
+
+no_param_options = [("Negate", "-negate",
+ """Negate performs the two's complement negation of the image."""
+ ),
+ ("EqualizeHistogram", "-equalize", None),
+ ("Enhance", "-enhance", None),
+ ("VerticalFlip", "-flip", None),
+ ("HorizontalFlip", "-flop", None),
+ ("FloydSteinbergDither", "-dither", None),
+ ("IncreaseContrast", "-contrast", None),
+ ("Despeckle", "-despeckle", None),
+ ("Normalize", "-normalize", None)]
+
+
+def no_param_options_method_dict(optionName):
+ """Creates a method dictionary for a module that takes no extra
+parameters. This dictionary will be used to dynamically create a
+VisTrails module."""
+
+ def compute(self):
+ o = self.create_output_file()
+ i = self.input_file_description()
+ self.run(i, optionName, o.name)
+ self.setResult("output", o)
+
+ return {'compute': compute}
+
+
+float_param_options = [("DetectEdges", "-edge", "radius", "filter radius"),
+ ("Emboss", "-emboss", "radius", "filter radius"),
+ ("GammaCorrect", "-gamma", "gamma", "gamma correction factor"),
+ ("MedianFilter", "-median", "radius", "filter radius")]
+
+def float_param_options_method_dict(optionName, portName):
+ """Creates a method dictionary for a module that has one port
+taking a floating-point value. This dictionary will be used to
+dynamically create a VisTrails module."""
+
+ def compute(self):
+ o = self.create_output_file()
+ optionValue = self.getInputFromPort(portName)
+ i = self.input_file_description()
+ self.run(i, optionName, str(optionValue), o.name)
+ self.setResult("output", o)
+
+ return {'compute': compute}
+
+
+
+################################################################################
+
+def initialize():
+ def parse_error_if_not_equal(s, expected):
+ if s != expected:
+ err = "Parse error on version line. Was expecting '%s', got '%s'"
+ raise RuntimeError(err % (s, expected))
+
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+
+ reg.add_module(ImageMagick, abstract=True)
+
+ reg.add_module(Convert)
+ reg.add_input_port(Convert, "input", (basic.File, 'the input file'))
+ reg.add_input_port(Convert, "inputFormat", (basic.String, 'coerce interpretation of file to this format'))
+ reg.add_output_port(Convert, "output", (basic.File, 'the output file'))
+ reg.add_input_port(Convert, "outputFormat", (basic.String, 'Force output to be of this format'))
+
+ for (name, opt, doc_string) in no_param_options:
+ m = new_module(Convert, name, no_param_options_method_dict(opt),
+ docstring=doc_string)
+ reg.add_module(m)
+
+ for (name, opt, paramName, paramComment) in float_param_options:
+ m = new_module(Convert, name, float_param_options_method_dict(opt, paramName))
+ reg.add_module(m)
+ reg.add_input_port(m, paramName, (basic.Float, paramComment))
+
+ reg.add_module(GaussianBlur)
+ reg.add_input_port(GaussianBlur, "radiusSigma", [(basic.Float, 'radius'), (basic.Float, 'sigma')])
+
+ reg.add_module(Scale)
+ reg.add_input_port(Scale, "geometry", (basic.String, 'ImageMagick geometry'))
+ reg.add_input_port(Scale, "width", (basic.String, 'width of the geometry for operation'))
+ reg.add_input_port(Scale, "height", (basic.String, 'height of the geometry for operation'))
+
+ reg.add_module(CombineRGBA)
+ reg.add_input_port(CombineRGBA, "r", basic.File)
+ reg.add_input_port(CombineRGBA, "g", basic.File)
+ reg.add_input_port(CombineRGBA, "b", basic.File)
+ reg.add_input_port(CombineRGBA, "a", basic.File, optional=True)
+ reg.add_input_port(CombineRGBA, "outputFormat", basic.String)
+ reg.add_output_port(CombineRGBA, "output", basic.File)
+
+################################################################################
+
diff --git a/vistrails/packages/JobSubmission/__init__.py b/vistrails/packages/JobSubmission/__init__.py
new file mode 100644
index 0000000..1f1fefb
--- /dev/null
+++ b/vistrails/packages/JobSubmission/__init__.py
@@ -0,0 +1,34 @@
+import sys
+import vistrails.core
+##
+# TODO list:
+# (V) 1) Write the JobInfo module
+# (V) 2) Make implement generator functionality
+# (V) 4) write generator and exporter functions
+# (V) 9) Move generators.py, exporters.py -> containers.py
+# (V) 10) auto_generated_types -> generator_definitions
+# (V) 11) Local file transfer fails when no visible files are present
+# 12) Qprint -> annotate
+# 13) Disconnect and kill process if queue exist
+# 14) Write the clean up and add it to run job
+# 15) There is an error with terminal selection
+
+
+## TODO:
+# 1) Fix the last things whatever they are
+# 9) Pull the git repository
+# 10) Add the package and update
+
+
+### TESTING
+# 1) Test collective operations
+# 2) check wether it uploads anything
+# 3) Try to see what happens when things are connected different from what you are supposed to do
+# 4) Test queue reusing - something tells me that this might fail
+version = '0.2'
+identifier = 'org.comp-phys.batchq'
+name = 'Job Submission'
+
+def package_requirements():
+ from vistrails.core.requirements import require_python_module
+ require_python_module('batchq')
diff --git a/vistrails/packages/JobSubmission/common_definitions.py b/vistrails/packages/JobSubmission/common_definitions.py
new file mode 100644
index 0000000..b1ede6d
--- /dev/null
+++ b/vistrails/packages/JobSubmission/common_definitions.py
@@ -0,0 +1,51 @@
+from batchq import queues
+from batchq.core.batch import BatchQ
+from batchq.queues import containers
+
+from vistrails.core.modules.basic_modules import File, Directory
+from vistrails.core.system import get_vistrails_basic_pkg_id
+
+###
+# Categories
+categories = {
+'basic_submission': 'Basic Submission',
+'job_collective_operations': "Collective operations",
+'low_level': "Low-level operations"
+}
+##
+# Helper functions
+name_formatter = lambda x: x
+capitalise = lambda x: x[0].upper() + x[1:].lower()
+remove_underscore = lambda j, name: j.join([capitalise(a) for a in name.split("_")])
+
+basic_pkg = get_vistrails_basic_pkg_id()
+type_conversion = {str:'(%s:String)' % basic_pkg, bool:'(%s:Boolean)' % basic_pkg, int:'(%s:Integer)' % basic_pkg, float:'(%s:Float)' % basic_pkg}
+
+batch_queue_list = [(a, getattr(queues,a)) for a in dir(queues) if isinstance(getattr(queues,a),type) and issubclass(getattr(queues,a),BatchQ) ]
+
+
+def create_directory(self, generator = None):
+ x = self.interpreter.filePool.create_directory()
+ return x.name
+
+def create_file(self, contents, generator = None):
+ ext=''
+ if not generator is None:
+ ext = generator.extension
+ f = self.interpreter.filePool.create_file(suffix=ext)
+ h = open(f.name,'w')
+ h.write(contents)
+ h.close()
+ return f, f.name
+
+def directory_wrapper(self, path, generator = None):
+ ret = Directory.translate_to_python(path)
+ return ret
+
+
+generator_definitions = { containers.DirectoryName:create_directory }
+
+exporter_definitions = { containers.TextFile: ('(%s:File)' % basic_pkg,
+ create_file),
+ containers.DirectoryName: ('(%s:Directory)' % basic_pkg,
+ directory_wrapper)}
diff --git a/vistrails/packages/JobSubmission/init.py b/vistrails/packages/JobSubmission/init.py
new file mode 100644
index 0000000..f2eb931
--- /dev/null
+++ b/vistrails/packages/JobSubmission/init.py
@@ -0,0 +1,315 @@
+from common_definitions import categories, capitalise, \
+ type_conversion, batch_queue_list, remove_underscore, name_formatter, \
+ generator_definitions, exporter_definitions
+from vistrails.core.modules.vistrails_module import Module, ModuleError, \
+ NotCacheable, InvalidOutput, ModuleSuspended
+from batchq.core.batch import BatchQ, Function, Property, FunctionMessage, \
+ Collection, Exportable
+from batchq.queues import NoHUP
+import copy
+from machine import module_definitions, Machine
+_modules = module_definitions
+
+
+
+#######################################
+## Creating queues/"machines"
+#######################################
+
+## Stores exportable properties
+## (property_name, vistrails_type, port visibility) for
+## each key = property_name
+exp_job_properties = {}
+
+## Stores all non-auto-generated
+## properties (property_name, vistrails type, port visibility)
+## for each key = property_name
+in_job_properties = {}
+
+## Stores property for each key = property_name
+job_properties = {}
+
+## Stores (property_name, vistrails type, generator)
+## for each key = property_name
+auto_job_properties = {}
+
+operations = {}
+operations_types = {}
+operations_highlevel = {}
+for queue_name, queue in batch_queue_list:
+
+ ## Generating queue classes
+ properties = []
+ for prop_name in dir(queue):
+ if isinstance(getattr(queue,prop_name), Property):
+ attr = getattr(queue,prop_name)
+
+ ## Properties which are machine dependent
+ if attr.verbose and attr.invariant:
+ properties.append( (prop_name,type_conversion[attr.type]) )
+
+ ## Properties which are job dependent
+ if not attr.password and not attr.invariant:
+ job_properties[prop_name] = attr
+
+ # Sorting auto generated fields
+ if attr.generator is None:
+ in_job_properties[prop_name] = (prop_name,
+ type_conversion[attr.type],
+ not attr.verbose)
+ elif attr.generator.type in generator_definitions:
+
+ auto_job_properties[prop_name] = (prop_name,
+ type_conversion[attr.type],
+ generator_definitions[attr.generator.type])
+
+ # Sorting exportable fields
+ if attr.exporter is None:
+ exp_job_properties[prop_name] = (prop_name,type_conversion[attr.type],
+ not attr.verbose)
+ else:
+ t, _ = exporter_definitions[attr.exporter.type]
+ exp_job_properties[prop_name] = (prop_name, t, not attr.verbose)
+
+ ## Definiting machines/queuing systems
+ members = { '_input_ports' : [('inherits',
+ '(org.comp-phys.batchq:Machine)',
+ True)] + properties,
+ 'queue_cls' : queue,
+ '_output_ports': [('machine',
+ '(org.comp-phys.batchq:Machine)')],
+ 'queue' : None
+ }
+
+ if hasattr(queue, "__descriptive_name__"):
+ descriptive_name = queue.__descriptive_name__
+ else:
+ descriptive_name = capitalise(queue_name)
+
+ cls = type(name_formatter(descriptive_name), (Machine,), members)
+
+ ## Extracing all functions from the queues - these will be used later
+ ## for module generation
+ functions = [(a,getattr(queue,a)) for a in dir(queue)
+ if isinstance(getattr(queue,a), Function) and
+ not a.startswith("_") and getattr(queue,a).enduser ]
+
+ for f, fnc in functions:
+ t = fnc.type
+ if not f in operations:
+ operations[f] = []
+ operations_types[f] = []
+ operations_highlevel[f] = False
+
+ operations[f].append(queue_name)
+ operations_highlevel[f] = operations_highlevel[f] or fnc.highlevel
+
+ if not t in operations_types[f]: operations_types[f].append(t)
+
+ _modules.append((cls,{'namespace':categories['basic_submission']}))
+
+functions = dict(functions)
+
+#######################################
+## Basic Job and Job creation module
+#######################################
+class Job(Machine):
+ pass
+_modules.append((Job, {'abstract':True}))
+
+
+def compute_jobpreparation(self):
+ mac = self.getInputFromPort("machine")
+ queue, cls = mac.queue, mac.queue_cls
+ kwargs = self.get_kwargs(cls)
+
+ for f, t, generator in auto_job_properties.itervalues():
+ kwargs[f] = generator(self)
+
+ self.queue = cls(queue, **kwargs)
+
+ self.setResult("job", self)
+
+dct = {'_input_ports' : [b for b in in_job_properties.itervalues()] \
+ + [('machine', '(org.comp-phys.batchq:Machine)'),],
+ '_output_ports' : [('job', '(org.comp-phys.batchq:Job)'),],
+ 'compute' : compute_jobpreparation
+ }
+
+PrepareJob = type(name_formatter("Prepare Job"), (Job,), dct)
+
+_modules += [(PrepareJob, {'namespace':categories['basic_submission']})]
+
+#######################################
+## Creating functions
+#######################################
+class JobOperation(NotCacheable,Module):
+ pass
+
+def joboperation_compute(self):
+ if self.hasInputFromPort("job"):
+ job = self.getInputFromPort('job')
+ queue = job.queue
+# print "TERMINAL ID", id(queue.terminal), id(queue.local_terminal)
+ self.anno_counter = 1
+ self.anno_dict = {}
+ def annotate(fncself, *args, **kwargs):
+ if len(args) == 1:
+ self.anno_dict.update( {"note%d"%self.anno_counter: args[0]} )
+ elif len(kwargs) == 0:
+ self.anno_dict.update( {"note%d"%self.anno_counter:" ".join(args)} )
+ else:
+ self.anno_dict.updateself.annotate( kwargs )
+ self.anno_counter +=1
+ return None
+ function = getattr(queue, self.function_name)
+ pnt = function.Qprint
+ function.Qprint = annotate
+ ret = function().val()
+ function.Qprint = pnt
+
+ ## TODO: annotate does not seem to work
+ self.annotate(self.anno_dict)
+
+ if isinstance(ret, FunctionMessage) and ret.code != 0:
+ raise ModuleSuspended(self, ret.message, queue) if ret.code > 0 \
+ else ModuleError(self,ret.message)
+
+ self.setResult("job", job)
+ self.setResult("result", ret)
+ self.setResult("string", str(ret))
+ self.setResult("operation", self)
+
+_modules+=[(JobOperation,{'abstract':True})]
+
+members = [ ('_input_ports', [('job', '(org.comp-phys.batchq:Job)'),] ),
+ ('_output_ports', [('job', '(org.comp-phys.batchq:Job)')] ),
+ ('compute', joboperation_compute)]
+
+low_level_functions = {}
+high_level_functions = {}
+high_level_modules = []
+for name in operations.iterkeys():
+ for t in operations_types[name]:
+ dct = dict(copy.deepcopy(members)+[('function_name',name)])
+ if not t is None and not t in [FunctionMessage]:
+ dct['_output_ports'].append( ('result', type_conversion[t]) )
+
+ # TODO: Multiple types yet to be implemented
+ ## append = "" if len(operations_types[name]) == 1 else capiltalise(str(t))
+ namespace = categories['low_level']
+
+ descriptive_name = remove_underscore(" ",name)
+ if t in [str,int, float, bool]:
+ if functions[name].exporter is None:
+ low_level_functions[name] = (name,type_conversion[t])
+ else:
+ tt, _ = exporter_definitions[functions[name].exporter.type]
+ low_level_functions[name] = (name,tt)
+
+ if t in [bool]:
+ descriptive_name = "Is" + remove_underscore("",name)
+ else:
+ descriptive_name = "Get" + remove_underscore("",name)
+
+ if not operations_highlevel[name]:
+ dct['_output_ports'].append( ('operation', '(org.comp-phys.batchq:JobOperation)') )
+ cls = ( type(name_formatter(descriptive_name),
+ (JobOperation,),dct),
+ {'namespace': namespace} )
+ _modules.append(cls)
+ else:
+ namespace = categories['basic_submission']
+ if t in type_conversion:
+ high_level_functions[name] = (name,type_conversion[t])
+ else:
+ high_level_functions[name] = (name,None)
+ high_level_modules.append((descriptive_name, dct, namespace))
+# namespace = categories['basic_submission']
+
+
+def jobinfo_compute(self):
+ job = self.getInputFromPort("job")
+ queue = job.queue
+ for function in self.queue_functions:
+ name = function[0]
+ function =getattr(queue, name)
+ ret =function().val()
+ if function.exporter is None:
+ self.setResult(name, ret)
+ else:
+ ## If the field is exported to a vistrails
+ ## type the conversion is done here
+ exporter = function.exporter
+ _, exp = exporter_definitions[exporter.type]
+ ret = function.exporter.as_str()
+ self.setResult(name, exp(self,ret))
+
+ for prop in self.queue_properties:
+ name = prop[0]
+ field = queue.fields[name]
+ ret = field.get()
+ if field.exporter is None:
+ self.setResult(name, ret)
+ else:
+ exporter = field.exporter
+ _, exp = exporter_definitions[exporter.type]
+
+ ret = exporter.as_str()
+ self.setResult(name, exp(self,ret))
+
+ self.setResult("job", job)
+
+
+queue_properties = [b for b in exp_job_properties.itervalues()]
+queue_functions = [b for b in low_level_functions.itervalues()]
+dct = {'_input_ports': [('job', '(org.comp-phys.batchq:Job)'),],
+ '_output_ports': queue_properties + queue_functions,
+ 'compute': jobinfo_compute,
+ 'queue_properties': queue_properties,
+ 'queue_functions': queue_functions}
+JobInfo = type(name_formatter("Job Info"), (NotCacheable,Job,), dct)
+
+_modules += [(JobInfo, {'namespace':categories['basic_submission']})]
+
+####
+# High-level function
+def highlevel_compute(self):
+ joboperation_compute(self)
+ jobinfo_compute(self)
+
+for descriptive_name, dct, namespace in high_level_modules:
+ dct['compute'] = highlevel_compute
+ dct['is_cacheable'] = lambda self: True
+ _modules.append((type(name_formatter(descriptive_name), (JobInfo,),dct), {'namespace': namespace} ))
+
+######
+## Creating collective operations
+class CollectiveOperation(NotCacheable,Module):
+ pass
+_modules.append((CollectiveOperation, {'abstract':True}))
+
+def collective_compute(self):
+ job = self.getInputFromPort('job')
+ operation = self.getInputFromPort('operation')
+ col = Collection()
+ col += job.queue
+
+ col2 = getattr(col, self.collection_name)()
+ rets = getattr(col2, operation.function_name)().as_list()
+ ## TODO: ad results
+ self.setResult('job', job)
+
+collective = dict([(name,getattr(Collection, name)) for name in dir(Collection) if isinstance(getattr(Collection, name),Exportable)])
+members = [ ('_input_ports', [('operation', '(org.comp-phys.batchq:JobOperation)'),('job', '(org.comp-phys.batchq:Job)')] ),
+ ('_output_ports', [('job', '(org.comp-phys.batchq:Job)')] ),
+ ('compute', collective_compute ),
+ ('collection_name', name)]
+namespace = categories['job_collective_operations']
+for name, func in collective.iteritems():
+ dct = dict(members)
+ _modules.append((type( "".join([capitalise(a) for a in name.split("_")]) , (CollectiveOperation,),dct),{'namespace':namespace} ))
+
+
+
+_modules = _modules
diff --git a/vistrails/packages/JobSubmission/machine.py b/vistrails/packages/JobSubmission/machine.py
new file mode 100644
index 0000000..b991a99
--- /dev/null
+++ b/vistrails/packages/JobSubmission/machine.py
@@ -0,0 +1,31 @@
+from vistrails.core.modules.vistrails_module import Module
+from batchq.core.batch import Property
+QUEUE_REGISTER = {}
+####
+# Machine definition
+class Machine(Module):
+ def get_kwargs(self, cls):
+
+ ret = dict([(a[0],self.getInputFromPort(a[0])) for a in self._input_ports if self.hasInputFromPort(a[0]) and a[0] in cls.__new_fields__ and isinstance(cls.__new_fields__[a[0]],Property)])
+ ret.update({'q_interact': False})
+ return ret
+
+ def compute(self):
+ global QUEUE_REGISTER
+ kwargs = self.get_kwargs(self.queue_cls)
+ inherits = self.getInputFromPort('inherits').queue if self.hasInputFromPort('inherits') else None
+
+# never disconnect because we want to check jobs later
+# if self.signature in QUEUE_REGISTER:
+# q = QUEUE_REGISTER[self.signature]
+# if hasattr(q, "disconnect"):
+# q.disconnect()
+
+
+ self.queue = self.queue_cls(**kwargs) if inherits is None else self.queue_cls(inherits, **kwargs)
+
+ QUEUE_REGISTER[str(self.signature)] = self.queue
+
+ self.setResult("machine", self)
+
+module_definitions = [(Machine,{'abstract':True})]
diff --git a/vistrails/packages/SUDSWebServices/__init__.py b/vistrails/packages/SUDSWebServices/__init__.py
new file mode 100644
index 0000000..4e37825
--- /dev/null
+++ b/vistrails/packages/SUDSWebServices/__init__.py
@@ -0,0 +1,72 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This package defines a set of methods to deal with web services.
+It requires suds library to be installed. Click on configure to add wsdl
+urls to the package (use a ; to separate the urls).
+"""
+from vistrails.core.configuration import ConfigurationObject
+import vistrails.core
+
+identifier = 'org.vistrails.vistrails.sudswebservices'
+name = 'SUDS Web Services'
+version = '0.1.2'
+old_identifiers = ['edu.utah.sci.vistrails.sudswebservices']
+configuration = ConfigurationObject(wsdlList=(None, str),
+ proxy_http=(None, str),
+ cache_days=(None, int))
+
+
+def can_handle_identifier(identifier):
+ """ This package handles packages where identifier starts with SUDS#
+ """
+ return identifier.startswith('SUDS#')
+
+def can_handle_vt_file(name):
+ """ This package handles file in zipped .vt files that ends with
+ "-wsdl-px"
+ They are cached web service instances
+ """
+ return name.endswith("-wsdl.px")
+
+#def package_dependencies():
+# return ['edu.utah.sci.vistrails.http']
+
+def package_requirements():
+ from vistrails.core.requirements import require_python_module
+ require_python_module('suds', {
+ 'pip': 'suds',
+ 'linux-debian': 'python-suds',
+ 'linux-ubuntu': 'python-suds',
+ 'linux-fedora': 'python-suds'})
diff --git a/vistrails/packages/SUDSWebServices/init.py b/vistrails/packages/SUDSWebServices/init.py
new file mode 100644
index 0000000..3851e99
--- /dev/null
+++ b/vistrails/packages/SUDSWebServices/init.py
@@ -0,0 +1,874 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import sys
+import os.path
+import shutil
+import hashlib
+import vistrails.core.system
+import vistrails.core.modules.module_registry
+import vistrails.core.modules.basic_modules
+import traceback
+from vistrails.core.packagemanager import get_package_manager
+from vistrails.core.modules.package import Package
+from vistrails.core.modules.vistrails_module import Module, ModuleError, new_module
+from vistrails.core.upgradeworkflow import UpgradeWorkflowHandler
+from vistrails.core import debug
+
+import suds
+
+
+package_cache = None
+
+webServicesDict = {}
+
+def toSignature(s):
+ """ transform wsdl address to valid package signature """
+ # cannot have ':' in package name
+ return 'SUDS#' + s.replace(':', '$')
+
+def toAddress(s):
+ """ transform package signature to valid wsdl address """
+ # look up address for a specific signature
+ return s[5:].replace('$', ':')
+
+###############################################################################
+
+wsdlSchemas = ['http://www.w3.org/2001/XMLSchema',
+ 'http://xml.apache.org/xml-soap',
+ 'http://schemas.xmlsoap.org/soap/encoding/']
+#Dictionary of primitive types
+#list extracted from http://www.w3.org/2001/XMLSchema
+wsdlTypesDict = { 'string' : vistrails.core.modules.basic_modules.String,
+ 'float': vistrails.core.modules.basic_modules.Float,
+ 'decimal': vistrails.core.modules.basic_modules.Float,
+ 'double': vistrails.core.modules.basic_modules.Float,
+ 'boolean': vistrails.core.modules.basic_modules.Boolean,
+ 'anyType': vistrails.core.modules.basic_modules.Variant,
+ 'anyURI': vistrails.core.modules.basic_modules.String,
+ 'DataHandler':vistrails.core.modules.basic_modules.String,
+ 'dateTime': vistrails.core.modules.basic_modules.String,
+ 'duration': vistrails.core.modules.basic_modules.String,
+ 'time': vistrails.core.modules.basic_modules.String,
+ 'date': vistrails.core.modules.basic_modules.String,
+ 'gYearMonth': vistrails.core.modules.basic_modules.String,
+ 'gYear': vistrails.core.modules.basic_modules.String,
+ 'gMonthDay': vistrails.core.modules.basic_modules.String,
+ 'gDay': vistrails.core.modules.basic_modules.String,
+ 'gMonth': vistrails.core.modules.basic_modules.String,
+ 'hexBinary': vistrails.core.modules.basic_modules.String,
+ 'base64': vistrails.core.modules.basic_modules.String,
+ 'base64Binary': vistrails.core.modules.basic_modules.String,
+ 'QName': vistrails.core.modules.basic_modules.String,
+ 'normalizedString': vistrails.core.modules.basic_modules.String,
+ 'token': vistrails.core.modules.basic_modules.String,
+ 'language': vistrails.core.modules.basic_modules.String,
+ 'IDREFS': vistrails.core.modules.basic_modules.String,
+ 'ENTITIES': vistrails.core.modules.basic_modules.String,
+ 'NMTOKEN': vistrails.core.modules.basic_modules.String,
+ 'NMTOKENS': vistrails.core.modules.basic_modules.String,
+ 'Name': vistrails.core.modules.basic_modules.String,
+ 'NCName': vistrails.core.modules.basic_modules.String,
+ 'ID': vistrails.core.modules.basic_modules.String,
+ 'IDREF': vistrails.core.modules.basic_modules.String,
+ 'ENTITY': vistrails.core.modules.basic_modules.String,
+ 'integer' : vistrails.core.modules.basic_modules.Integer,
+ 'nonPositiveInteger' : vistrails.core.modules.basic_modules.Integer,
+ 'negativeInteger' : vistrails.core.modules.basic_modules.Integer,
+ 'long' : vistrails.core.modules.basic_modules.Integer,
+ 'int' : vistrails.core.modules.basic_modules.Integer,
+ 'short' : vistrails.core.modules.basic_modules.Integer,
+ 'byte' : vistrails.core.modules.basic_modules.Integer,
+ 'nonNegativeInteger' : vistrails.core.modules.basic_modules.Integer,
+ 'unsignedLong' : vistrails.core.modules.basic_modules.Integer,
+ 'unsignedInt' : vistrails.core.modules.basic_modules.Integer,
+ 'unsignedShort' : vistrails.core.modules.basic_modules.Integer,
+ 'unsignedByte' : vistrails.core.modules.basic_modules.Integer,
+ 'positiveInteger' : vistrails.core.modules.basic_modules.Integer,
+ 'Array': vistrails.core.modules.basic_modules.List,
+
+ # soapenc types
+ 'arrayCoordinate': vistrails.core.modules.basic_modules.String,
+ 'Struct': vistrails.core.modules.basic_modules.String,
+ 'NOTATION': vistrails.core.modules.basic_modules.String
+ }
+
+def initialize(*args, **keywords):
+# import core.packagemanager
+ global webServicesDict
+ global package_cache
+
+ #Create a directory for the SUDSWebServices package
+ location = os.path.join(vistrails.core.system.current_dot_vistrails(),
+ "SUDSWebServices")
+ if not os.path.isdir(location):
+ try:
+ debug.log("Creating SUDS cache directory...")
+ os.mkdir(location)
+ except:
+ debug.critical(
+"""Could not create SUDS cache directory. Make sure
+'%s' does not exist and parent directory is writable""" % location)
+ sys.exit(1)
+ # the number of days to cache wsdl files
+ days = 1
+ if configuration.check("cache_days"):
+ days = configuration.cache_days
+ suds.client.ObjectCache.protocol = 0 # windows needs this
+ package_cache = suds.client.ObjectCache(location, days=days)
+
+ #reg = core.modules.module_registry.get_module_registry()
+ #reg.add_module(SUDSWebService, abstract=True)
+
+ wsdlList = []
+ if configuration.check('wsdlList'):
+ wsdlList = configuration.wsdlList.split(";")
+ else:
+ configuration.wsdlList = ''
+ for wsdl in wsdlList:
+ if not wsdl:
+ break
+ if not wsdl.startswith('http://'):
+ wsdl = 'http://' + wsdl
+ if wsdl in webServicesDict:
+ debug.warning('Duplicate WSDL entry: '+wsdl)
+ continue
+ s = Service(wsdl)
+ if s.service:
+ webServicesDict[wsdl] = s
+
+def finalize():
+ # unload service packages
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ for s in webServicesDict.itervalues():
+ if s.package:
+ reg.remove_package(s.package)
+
+class WSMethod:
+ """ A WSDL method
+ """
+ def __init__(self, qname=('','')):
+ self.qname = qname
+ "name: (typename, ns)"
+ self.inputs = {}
+ self.outputs = {}
+
+class WSElement:
+ """ A part of a WSDL type
+ """
+ def __init__(self, name='', type=('',''), optional=False, min=0,
+ max='unbounded', enum=False):
+ self.name = name
+ self.type = type
+ self.optional = optional
+ self.min = min
+ self.max = max
+ self.enum = enum
+
+class WSType:
+ """ A WSDL type definition
+ """
+ def __init__(self, qname=('',''), enum=False):
+ self.qname = qname
+ self.enum = enum
+ "name: WSElement"
+ self.parts = {}
+
+class Service:
+ def __init__(self, address):
+ """ Process WSDL and add all Types and Methods
+ """
+ self.address = address
+ self.signature = toSignature(self.address)
+ self.wsdlHash = '-1'
+ self.modules = []
+ self.package = None
+ debug.log("Installing Web Service from WSDL: %s"% address)
+
+ options = dict(cachingpolicy=1, cache=package_cache)
+
+ proxy_types = ['http']
+ for t in proxy_types:
+ key = 'proxy_%s'%t
+ if configuration.check(key):
+ proxy = getattr(configuration, key)
+ debug.log("Using proxy: %s" % proxy)
+ if len(proxy):
+ options['proxy'] = {t:proxy}
+ try:
+ self.service = suds.client.Client(address, **options)
+ self.backUpCache()
+ except Exception, e:
+ self.service = None
+ # We may be offline and the cache may have expired,
+ # try to use backup
+ if self.restoreFromBackup():
+ try:
+ self.service = suds.client.Client(address, **options)
+ except Exception, e:
+ self.service = None
+ debug.critical("Could not load WSDL: %s" % address,
+ str(e) + '\n' + str(traceback.format_exc()))
+ else:
+ debug.critical("Could not load WSDL: %s" % address,
+ str(e) + '\n' + str(traceback.format_exc()))
+ if self.service:
+ try:
+ self.createPackage()
+ self.setTypes()
+ self.setMethods()
+ self.createTypeClasses()
+ self.createMethodClasses()
+ except Exception, e:
+ debug.critical("Could not create Web Service: %s" % address,
+ str(e) + '\n' + str(traceback.format_exc()))
+ self.service = None
+ if self.wsdlHash == '-1':
+ # create empty package so that it can be reloaded/deleted
+ self.createFailedPackage()
+
+ def makeDictType(self, obj):
+ """ Create recursive dict from SUDS object
+ ignore attributes with None and empty dicts and handle lists
+ """
+ if not hasattr(obj,'__keylist__'):
+ return obj
+ if isinstance(obj, list):
+ p = [self.makeDictType(i) for i in obj if i is not None]
+ return [i for i in p if i is not None and i != {}]
+ d = {}
+ for o in obj.__keylist__:
+ e = getattr(obj, o)
+ if e is not None:
+ p = self.makeDictType(e)
+ if p is not None and p != {}:
+ d[str(o)] = self.makeDictType(e)
+ return d
+
+ def backUpCache(self):
+ """ We back up the cache for situations where the cache is expired and
+ the web service can not be reached. This allows working offline.
+ """
+ cached = os.path.join(package_cache.location,
+ "suds-%s-wsdl.px" % abs(hash(self.address)))
+ backup = os.path.join(package_cache.location,
+ "suds-%s-wsdl.px" % hashlib.md5(self.address
+ ).hexdigest())
+ if os.path.exists(cached):
+ shutil.copyfile(cached, backup)
+
+ def restoreFromBackup(self):
+ """ Restore from backup into cache with reset cache time"""
+ cached = os.path.join(package_cache.location,
+ "suds-%s-wsdl.px" % abs(hash(self.address)))
+ backup = os.path.join(package_cache.location,
+ "suds-%s-wsdl.px" % hashlib.md5(self.address
+ ).hexdigest())
+ if not os.path.exists(cached) and os.path.exists(backup):
+ shutil.copyfile(backup, cached)
+ return True
+ return False
+
+ def createPackage(self):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ if self.signature in reg.packages:
+ reg.remove_package(reg.packages[self.signature])
+
+ # create a document hash integer from the cached sax tree
+ # "name" is what suds use as the cache key
+ name = '%s-%s' % (abs(hash(self.address)), "wsdl")
+ wsdl = package_cache.get(name)
+ if not wsdl:
+ debug.critical("File not found in SUDS cache: '%s'" % name)
+ self.wsdlHash = '0'
+ return
+ self.wsdlHash = str(int(hashlib.md5(str(wsdl.root)).hexdigest(), 16))
+
+ package_id = reg.idScope.getNewId(Package.vtType)
+ package = Package(id=package_id,
+ load_configuration=False,
+ name="SUDS#" + self.address,
+ identifier=self.signature,
+ version=self.wsdlHash,
+ )
+ suds_package = reg.get_package_by_name(identifier)
+ package._module = suds_package.module
+ package._init_module = suds_package.init_module
+
+ self.package = package
+ reg.add_package(package)
+ reg.signals.emit_new_package(self.signature)
+
+ self.module = new_module(Module, str(self.signature))
+ reg.add_module(self.module, **{'package':self.signature,
+ 'package_version':self.wsdlHash,
+ 'abstract':True})
+
+ def createFailedPackage(self):
+ """ Failed package is created so that the user can remove
+ it manually using package submenu """
+ pm = get_package_manager()
+ if pm.has_package(self.signature):
+ # do nothing
+ return
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+
+ # create a document hash integer from the cached sax tree
+ # "name" is what suds use as the cache key
+ name = '%s-%s' % (abs(hash(self.address)), "wsdl")
+ self.wsdlHash = '0'
+
+ package_id = reg.idScope.getNewId(Package.vtType)
+ package = Package(id=package_id,
+ load_configuration=False,
+ name="SUDS#" + self.address,
+ identifier=self.signature,
+ version=self.wsdlHash,
+ )
+ suds_package = reg.get_package_by_name(identifier)
+ package._module = suds_package.module
+ package._init_module = suds_package.init_module
+ self.package = package
+ reg.add_package(package)
+ reg.signals.emit_new_package(self.signature)
+ self.module = new_module(Module, str(self.signature))
+ reg.add_module(self.module, **{'package':self.signature,
+ 'package_version':self.wsdlHash,
+ 'abstract':True})
+ self.service = -1
+
+ def setTypes(self):
+ """ Return dict containing all exposed types in the service
+ """
+ self.wstypes = {}
+ for sd in self.service.sd:
+ for type in sd.types:
+ type = type[0]
+ # ignore existing types and arrays
+ if type.qname[1] in wsdlSchemas or type.qname[0].startswith('Array'):
+ continue
+ qname = type.qname
+ wstype = WSType(qname, type.enum())
+ self.wstypes[qname] = wstype
+ # handle enums by adding a "value" port with the possible enums
+ if wstype.enum:
+ values = [i[0].name for i in type.children()]
+ wstype.parts["value"] = WSElement("value",
+ ('string', "http://www.w3.org/2001/XMLSchema"),
+ False, 1, 1, values)
+ continue
+ # add elements
+ for e in type.children():
+ e = e[0]
+ if e.type is None:
+ pass # probably empty type so just ignore
+ elif e.type[0].startswith('Array'):
+ qtype = ('Array', 'http://www.w3.org/2001/XMLSchema')
+ wstype.parts[e.name] = WSElement(e.name, qtype,
+ e.optional(), e.min, e.max)
+ else:
+ wstype.parts[e.name] = WSElement(e.name, e.type,
+ e.optional(), e.min, e.max)
+
+ def setMethods(self):
+ """ Return dict with methods in service
+ """
+ def isKnownType(qtype):
+ return not qtype or str(qtype[1]) in wsdlSchemas or \
+ qtype[0].startswith('Array') or qtype in self.wstypes
+
+ def getChildTypes(type):
+ schema = self.service.wsdl.schema
+ if type in schema.elements:
+ if schema.elements[type].type is not None:
+ return [(schema.elements[type].name, schema.elements[type].type)]
+ else:
+ return [(c[0].name, c[0].type) for c in schema.elements[type].children()]
+ elif type in schema.types:
+ return [(c[0].name, c[0].type) for c in schema.types[type].children()]
+ debug.critical("Could not resolve type in WSDL:" + str(type))
+ return []
+
+ def setMethod(m):
+ # create new method
+ wsm = WSMethod((m[0], self.address))
+ self.wsmethods[wsm.qname] = wsm
+ # process inputs
+ for param in m[1]:
+ name = param[0]
+ qtype = (param[1].resolve().name, param[1].resolve().namespace()[1])
+ qtype = (str(qtype[0]), str(qtype[1]))
+ if qtype is None:
+ qtype = param[1].element
+ qtype = (str(qtype[0]), str(qtype[1]))
+ if qtype is not None:
+ if qtype[0].startswith('Array'):
+ qtype = ('Array', 'http://www.w3.org/2001/XMLSchema')
+ wsm.inputs[name] = qtype
+ # process outputs - need to look recursively in wsdl
+ method = self.service.service.__getattr__(m[0])
+ for output in method.method.soap.output.body.parts:
+ # get schema definition of method
+ if output.type:
+ qtype = output.type
+ else:
+ element = self.service.wsdl.schema.elements[output.element]
+ qtype = element.type if element.type else output.element
+ # check that it exists
+ types = [(output.name, qtype)]
+ while qtype is not None and not isKnownType(qtype):
+ types = getChildTypes(qtype)
+ if len(types):
+ qtype = types[0][1]
+ else:
+ break
+ for name, qtype in types:
+ if qtype is not None:
+ if qtype[0].startswith('Array'):
+ qtype = ('Array', 'http://www.w3.org/2001/XMLSchema')
+ wsm.outputs[name] = qtype
+ # loop through services, ports, and methods
+ self.wsmethods = {}
+ for sd in self.service.sd:
+ for port in sd.ports:
+ for m in port[1]:
+ setMethod(m)
+
+ def createTypeClasses(self):
+ # first create classes
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ self.typeClasses = {}
+ for t in self.wstypes.itervalues():
+ def compute(self):
+ """ 1. use type input as object or create new
+ 2. add other inputs to obj
+ 3. set obj and parts as outputs
+ """
+ if self.wstype.enum:
+ # only makes sure the enum is one of the valid values
+ p = self.wstype.parts['value']
+ if self.hasInputFromPort(p.name):
+ obj = self.getInputFromPort(p.name)
+ else:
+ obj = p.enum[0] if len(p.enum) else ''
+ if self.hasInputFromPort('value'):
+ obj = self.getInputFromPort('value')
+ if obj not in p.enum:
+ raise ModuleError(self,
+ "'%s' is not one of the valid enums: %s" %
+ (obj, str(p.enum)) )
+ self.setResult(self.wstype.qname[0], obj)
+ self.setResult('value', obj)
+ return
+ if self.hasInputFromPort(self.wstype.qname[0]):
+ obj = self.getInputFromPort(self.wstype.qname[0])
+ else:
+ obj = {}
+ s = "{%s}%s"%(self.wstype.qname[1],self.wstype.qname[0])
+ try:
+ obj = self.service.service.factory.create(s)
+ except (suds.TypeNotFound, suds.BuildError):
+ raise ModuleError("Type not found: %s" % s)
+ for part in self.wstype.parts.itervalues():
+ #
+ if obj.__class__.__name__ == 'UberClass':
+ # UberClass is a placeholder and its value is assumed
+ # to be the correct attribute value
+ if len(self.wstype.parts) == 1:
+ setattr(obj, part.name, obj.value)
+ else:
+ # update each attribute
+ if hasattr(obj.value, part.name):
+ setattr(obj, part.name, getattr(obj.value, part.name))
+ if self.hasInputFromPort(part.name):
+ p = self.getInputFromPort(part.name)
+ if hasattr(obj, part.name):
+ setattr(obj, part.name, p)
+ else:
+ # do it anyway - assume attribute missing in template
+ setattr(obj, part.name, p)
+ if hasattr(obj, part.name):
+ #
+ res = getattr(obj, part.name)
+ self.setResult(part.name, res)
+ self.setResult(self.wstype.qname[0], obj)
+
+ # create docstring
+ parts = ", ".join([i.type[0]+' '+i.name for i in t.parts.itervalues()])
+ d = """This module was created using a wrapper for SUDS (fedorahosted.org/suds/)
+from the WSDL spec at:
+ %s
+It is a WSDL type with signature:
+ %s(%s)"""%(self.address, t.qname[0], parts)
+ M = new_module(self.module, str(t.qname[0]),{"compute":compute,
+ "wstype":t,
+ "service":self,
+ "__doc__":d})
+ self.typeClasses[t.qname] = M
+ reg.add_module(M, **{'namespace':'Types',
+ 'package':self.signature,
+ 'package_version':self.wsdlHash})
+
+ # then add ports
+ for t in self.wstypes:
+ wstype = self.wstypes[t]
+ # get type module
+ if t[1] in wsdlSchemas:
+ c = wsdlTypesDict[t[0]]
+ elif t in self.typeClasses:
+ c = self.typeClasses[t]
+ else:
+ debug.critical("Cannot find module for type: " + str(t))
+ continue
+ # add self ports
+ reg.add_input_port(self.typeClasses[t], t[0], c)
+ reg.add_output_port(self.typeClasses[t], t[0], c)
+ for p in wstype.parts:
+ part = wstype.parts[p]
+ # get type module
+ ptype = part.type
+ if part.max is not None and (part.max == 'unbounded' or int(part.max)>1):
+ # it can be multiple objects which means we need to make it a list
+ c = vistrails.core.modules.basic_modules.List
+ elif ptype[1] in wsdlSchemas:
+ c = wsdlTypesDict[ptype[0]]
+ elif ptype in self.typeClasses:
+ c = self.typeClasses[ptype]
+ else:
+ debug.critical("Cannot find module for type: " + str(ptype))
+ continue
+ # add as both input and output port
+ reg.add_input_port(self.typeClasses[t], p, c,
+ optional=part.optional)
+ reg.add_output_port(self.typeClasses[t], p, c,
+ optional=part.optional)
+
+ def createMethodClasses(self):
+ # register modules
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ self.methodClasses = {}
+ for m in self.wsmethods.itervalues():
+ def compute(self):
+ # create dict of inputs
+ cacheable = False
+ if self.hasInputFromPort('cacheable'):
+ cacheable = self.getInputFromPort('cacheable')
+ self.is_cacheable = lambda *args, **kwargs: cacheable
+ params = {}
+ mname = self.wsmethod.qname[0]
+ for name in self.wsmethod.inputs:
+ name = str(name)
+ if self.hasInputFromPort(name):
+ params[name] = self.getInputFromPort(name)
+ if params[name].__class__.__name__ == 'UberClass':
+ params[name] = params[name].value
+ params[name] = self.service.makeDictType(params[name])
+ try:
+ #import logging
+ #logging.basicConfig(level=logging.INFO)
+ #logging.getLogger('suds.client').setLevel(logging.DEBUG)
+ #print "params:", str(params)[:400]
+ #self.service.service.set_options(retxml = True)
+ #result = getattr(self.service.service.service, mname)(**params)
+ #print "result:", str(result)[:400]
+ #self.service.service.set_options(retxml = False)
+ result = getattr(self.service.service.service, mname)(**params)
+ except Exception, e:
+ raise ModuleError(self, "Error invoking method %s: %s"%(name, str(e)))
+ for name, qtype in self.wsmethod.outputs.iteritems():
+ if isinstance(result, list):
+ # if result is a list just set the output
+ self.setResult(name, result)
+ elif qtype[0] == 'Array':
+ # if result is a type but type is a list try to extract the correct element
+ if len(result.__keylist__):
+ self.setResult(name, getattr(result, result.__keylist__[0]))
+ else:
+ self.setResult(name, result)
+ elif result.__class__.__name__ == 'Text':
+ # only text returned so we assume each output wants all of it
+ self.setResult(name, str(result.trim()))
+ elif result.__class__.__name__ == qtype[0]:
+ # the return value is this type
+ self.setResult(name, result)
+ elif hasattr(result, name):
+ self.setResult(name, getattr(result, name))
+ else:
+ # nothing matches - assume it is an attribute of the correct class
+ class UberClass:
+ def __init__(self, value):
+ self.value = value
+ self.setResult(name, UberClass(result))
+
+ # create docstring
+ inputs = ", ".join([t[0]+' '+i for i,t in m.inputs.iteritems()])
+ outputs = ", ".join([t[0]+' '+o for o,t in m.outputs.iteritems()])
+ d = """This module was created using a wrapper for SUDS (fedorahosted.org/suds/)
+from the WSDL spec at:
+ %s
+It is a WSDL method with signature:
+ %s(%s)
+Outputs:
+ (%s)
+"""%(self.address, m.qname[0], inputs, outputs)
+
+ M = new_module(self.module, str(m.qname[0]), {"compute":compute,
+ "wsmethod":m,
+ "service":self,
+ "__doc__":d})
+ self.methodClasses[m.qname] = M
+ reg.add_module(M, **{'namespace':'Methods',
+ 'package':self.signature,
+ 'package_version':self.wsdlHash})
+ reg.add_input_port(self.methodClasses[m.qname], 'cacheable',
+ wsdlTypesDict['boolean'], optional=True)
+
+ # add ports
+ for p, ptype in m.inputs.iteritems():
+ if ptype[1] in wsdlSchemas:
+ c = wsdlTypesDict[ptype[0]]
+ elif ptype in self.typeClasses:
+ c = self.typeClasses[ptype]
+ else:
+ # use string as default
+ c = wsdlTypesDict['string']
+ reg.add_input_port(M, p, c)
+ for p, ptype in m.outputs.iteritems():
+ if ptype[1] in wsdlSchemas:
+ c = wsdlTypesDict[ptype[0]]
+ elif ptype in self.typeClasses:
+ c = self.typeClasses[ptype]
+ else:
+ # use string as default
+ c = wsdlTypesDict['string']
+ reg.add_output_port(M, p, c)
+
+def load_from_signature(signature):
+ """ Load wsdl from signature and return success status """
+ wsdl = toAddress(signature)
+ wsdlList = []
+ if configuration.check('wsdlList'):
+ wsdlList = configuration.wsdlList.split(";")
+ if not wsdl in wsdlList:
+ try:
+ service = Service(wsdl)
+ except:
+ return False
+ if not service.service:
+ return False
+ webServicesDict[wsdl] = service
+ wsdlList.append(wsdl)
+ configuration.wsdlList = ';'.join(wsdlList)
+ return True
+
+def handle_module_upgrade_request(controller, module_id, pipeline):
+ old_module = pipeline.modules[module_id]
+ # first check package
+ # v1.0 types:
+ if old_module.package == 'edu.utah.sci.vistrails.sudswebservices':
+ wsdl = old_module.namespace.split('|')[0]
+ namespace = old_module.namespace.split('|')[1]
+ else:
+ wsdl = toAddress(old_module.package)
+ namespace = old_module.namespace
+ name = old_module.name
+
+ wsdlList = []
+ if configuration.check('wsdlList'):
+ wsdlList = configuration.wsdlList.split(";")
+ if not wsdl in wsdlList:
+ service = Service(wsdl)
+ if not service.service:
+ return []
+ webServicesDict[wsdl] = service
+ wsdlList.append(wsdl)
+ configuration.wsdlList = ';'.join(wsdlList)
+
+ if old_module.package == 'edu.utah.sci.vistrails.sudswebservices':
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ new_descriptor = reg.get_descriptor_by_name(toSignature(wsdl), name,
+ namespace)
+ if not new_descriptor:
+ return []
+ try:
+ return UpgradeWorkflowHandler.replace_module(controller, pipeline,
+ module_id, new_descriptor)
+ except Exception, e:
+ import traceback
+ traceback.print_exc()
+ raise
+
+ return UpgradeWorkflowHandler.attempt_automatic_upgrade(controller,
+ pipeline,
+ module_id)
+
+def handle_missing_module(controller, module_id, pipeline):
+ global webServicesDict
+ global package_cache
+
+ def get_wsdl_from_namespace(m_namespace):
+ try:
+ wsdl = m_namespace.split("|")
+ return wsdl[0]
+ except:
+ return None
+
+ m = pipeline.modules[module_id]
+ if m.package == identifier:
+ # v1.0 old style
+ m_namespace = m.namespace
+ wsdl = get_wsdl_from_namespace(m_namespace)
+ else:
+ # v1.1 new style
+ wsdl = toAddress(m.package)
+
+ wsdlList = []
+ if configuration.check('wsdlList'):
+ wsdlList = configuration.wsdlList.split(";")
+ if wsdl in wsdlList:
+ # it is already loaded
+ return True
+
+ service = Service(wsdl)
+ if not service.service:
+ return False
+
+ webServicesDict[wsdl] = service
+ wsdlList.append(wsdl)
+ configuration.wsdlList = ';'.join(wsdlList)
+ return True
+
+def load_from_identifier(service_identifier):
+ """ Loads a web service from its package identifier """
+ global webServicesDict
+ global package_cache
+
+ wsdl = toAddress(service_identifier)
+
+ wsdlList = []
+ if configuration.check('wsdlList'):
+ wsdlList = configuration.wsdlList.split(";")
+ if wsdl in wsdlList:
+ # it is already loaded
+ return True
+
+ service = Service(wsdl)
+ if not service.service:
+ return False
+
+ webServicesDict[wsdl] = service
+ wsdlList.append(wsdl)
+ configuration.wsdlList = ';'.join(wsdlList)
+ return True
+
+def contextMenuName(signature):
+ """ Returns a context menu name that depends on the signature
+ should return None if no method is available
+ """
+ if signature == name:
+ return "Add Web Service"
+ elif signature.startswith('SUDS#'):
+ return "Remove this Web Service"
+ return None
+
+def saveVistrailFileHook(vistrail, temp_dir):
+ """ This is called when a vistrail is loaded
+ We should copy all used Web Services in temp_dir to .vistrails
+ """
+
+
+ packages = vistrail.get_used_packages()
+ # clear old files
+ for name in os.listdir(temp_dir):
+ if name.endswith("-wsdl.px"):
+ os.remove(os.path.join(temp_dir, name))
+
+ for package in packages:
+ if package.startswith("SUDS#"):
+ address = toAddress(package)
+ name = "suds-%s-wsdl.px" % hashlib.md5(address).hexdigest()
+ cached = os.path.join(package_cache.location, name)
+ vt_cached = os.path.join(temp_dir, name)
+ if os.path.exists(cached):
+ shutil.copyfile(cached, vt_cached)
+
+def loadVistrailFileHook(vistrail, temp_dir):
+ """ This is called when a vistrail is saved
+ We should copy all cached Web Services in vistrail to temp_dir
+ if they do not exist
+ """
+ for name in os.listdir(temp_dir):
+ src = os.path.join(temp_dir, name)
+ dest = os.path.join(package_cache.location, name)
+ if name.endswith("-wsdl.px") and not os.path.exists(dest):
+ shutil.copyfile(src, dest)
+
+def callContextMenu(signature):
+ global webServicesDict
+ if signature == name:
+ from PyQt4 import QtGui
+ wsdl, ret = QtGui.QInputDialog.getText(None, 'Add Web Service',
+ 'Enter the location of the WSDL:')
+ wsdl = str(wsdl)
+ if not wsdl:
+ return
+ if not wsdl.startswith('http://'):
+ wsdl = 'http://' + wsdl
+ if wsdl in webServicesDict:
+ debug.critical('WSDL already loaded: '+wsdl)
+ return
+ s = Service(wsdl)
+ if s.service:
+ webServicesDict[wsdl] = s
+ wsdlList = configuration.wsdlList.split(";")
+ wsdlList.append(wsdl)
+ configuration.wsdlList = ';'.join(wsdlList)
+ elif signature.startswith('SUDS#'):
+ address = toAddress(signature)
+ from PyQt4 import QtGui
+ res = QtGui.QMessageBox.question(None,
+ 'Remove the following web service from vistrails?',
+ address,
+ buttons=QtGui.QMessageBox.Yes,
+ defaultButton=QtGui.QMessageBox.No)
+ if res == QtGui.QMessageBox.Yes:
+ # Remove this Web Service
+ s = webServicesDict[address]
+ del webServicesDict[address]
+
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ reg.remove_package(s.package)
+ wsdlList = configuration.wsdlList.split(";")
+ wsdlList.remove(address)
+ configuration.wsdlList = ';'.join(wsdlList)
diff --git a/vistrails/packages/__init__.py b/vistrails/packages/__init__.py
new file mode 100644
index 0000000..cdc9214
--- /dev/null
+++ b/vistrails/packages/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# Nothing here on purpose
+pass
diff --git a/vistrails/packages/analytics/__init__.py b/vistrails/packages/analytics/__init__.py
new file mode 100644
index 0000000..e132e51
--- /dev/null
+++ b/vistrails/packages/analytics/__init__.py
@@ -0,0 +1,39 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+name = "VisTrails Analytics"
+identifier = "org.vistrails.vistrails.analytics"
+version = "0.0.2"
+old_identifiers = ["edu.utah.sci.vistrails.analytics"]
diff --git a/vistrails/packages/analytics/counts.vt b/vistrails/packages/analytics/counts.vt
new file mode 100644
index 0000000..4fa3750
Binary files /dev/null and b/vistrails/packages/analytics/counts.vt differ
diff --git a/vistrails/packages/analytics/executedWorkflows.vt b/vistrails/packages/analytics/executedWorkflows.vt
new file mode 100644
index 0000000..c77e5fd
Binary files /dev/null and b/vistrails/packages/analytics/executedWorkflows.vt differ
diff --git a/vistrails/packages/analytics/init.py b/vistrails/packages/analytics/init.py
new file mode 100644
index 0000000..520290e
--- /dev/null
+++ b/vistrails/packages/analytics/init.py
@@ -0,0 +1,180 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.modules.basic_modules import new_constant
+from vistrails.core.modules.vistrails_module import Module, ModuleError, ModuleConnector
+import vistrails.core.vistrail.vistrail
+import vistrails.core.log.log
+import vistrails.db.services.io
+
+
+class Vistrail(Module):
+ pass
+
+class Log(Module):
+ pass
+
+class ReadVistrail(Module):
+ _input_ports = [('file', '(basic:File)')]
+ _output_ports = [('vistrail','(Vistrail)'),
+ ('log', '(Log)')]
+
+ def read_vistrail(self, fname):
+ # open the .vt bundle specified by the filename "fname"
+ bundle = vistrails.db.services.io.open_vistrail_bundle_from_zip_xml(fname)[0]
+
+ # access the vistrail from the bundle
+ vistrail = bundle.vistrail
+
+ # convert the vistrail from a db object
+ vistrails.core.vistrail.vistrail.Vistrail.convert(vistrail)
+
+ return vistrail
+
+ def read_log(self, fname):
+ # open the .vt bundle specified by the filename "fname"
+ bundle = vistrails.db.services.io.open_vistrail_bundle_from_zip_xml(fname)[0]
+
+ # get the log filename
+ log_fname = bundle.vistrail.db_log_filename
+
+ if log_fname is not None:
+ # open the log
+ log = vistrails.db.services.io.open_log_from_xml(log_fname, True)
+
+ # convert the log from a db object
+ vistrails.core.log.log.Log.convert(log)
+ return log
+ if log_fname is None:
+ # throw error message
+ raise ModuleError(self, "No log file accessible")
+
+ return None
+
+ def compute(self):
+ fname = self.getInputFromPort('file').name
+ vistrail = self.read_vistrail(fname)
+ self.setResult('vistrail', vistrail)
+ fname = self.getInputFromPort('file').name
+ log = self.read_log(fname)
+ self.setResult('log', log)
+
+class CountActions(Module):
+ _input_ports = [('vistrail', '(Vistrail)')]
+ _output_ports = [('counts', '(basic:Dictionary)')]
+
+ def count_actions(self, vistrail):
+ # loop through the actionMap dictionary's (key, value) pairs in
+ # sorted order
+ Tally={}
+ for id, action in sorted(vistrail.actionMap.iteritems()):
+ # print action information
+ for action in action.operations:
+ # look for action(what) in dictionary
+ # if not there, create an entry with a sub dictionary containing the vtType
+ if action.what not in Tally:
+ Tally[action.what] = {action.vtType : 1}
+
+ # if is there, if subdictionray has the vtType key, update vtType count
+ elif Tally.has_key(action.what):
+ if Tally[action.what].has_key(action.vtType):
+ Tally[action.what][action.vtType] += 1
+ else:
+ Tally[action.what] = {action.vtType : 1}
+
+ # if is there, if subdictionary does not have vtType key, create entry
+ elif Tally.has_key(action.what) == none:
+ Tally[action.what] = {action.vtType : 1}
+ return Tally
+
+ def compute(self):
+ vistrail = self.getInputFromPort('vistrail')
+ Tally = self.count_actions(vistrail)
+ self.setResult('counts', Tally)
+
+class CountExecutedWorkflows(Module):
+ _input_ports = [('log', '(Log)')]
+ _output_ports = [('completed', '(basic:Dictionary)')]
+ def count_executed_workflows(self,log):
+ users={}
+ for workflow_exec in log.workflow_execs:
+ if workflow_exec.completed == 1:
+ if workflow_exec.user not in users:
+ users[workflow_exec.user] = 1
+ else:
+ users[workflow_exec.user] += 1
+ return users
+
+ def compute(self):
+ log = self.getInputFromPort('log')
+ users = self.count_executed_workflows(log)
+ self.setResult('completed', users)
+
+class TotalDays(Module):
+ _input_ports = [('vistrail','(Vistrail)')]
+ _output_ports = [('completed','(basic:Dictionary)')]
+ def calc_time(self, vistrail):
+ time = {}
+ totals = {}
+ for id,action in sorted(vistrail.actionMap.iteritems()):
+ if action.user not in time:
+ # action.date is a string representation
+ # action.db_date is the real python datetime object
+ time[action.user] = [action.db_date]
+ else:
+ time[action.user].append(action.db_date)
+
+ for user, time_list in time.iteritems():
+ max_time = max(time_list)
+ min_time = min(time_list)
+
+ # this is a timedelta object
+ # http://docs.python.org/library/datetime.html#timedelta-objects
+ time_delta = max_time - min_time
+
+ # .days returns the number of days in the time delta
+ totals[user] = time_delta.days + 1
+
+ return totals
+
+ def compute(self):
+ vistrail = self.getInputFromPort('vistrail')
+ totals = self.calc_time(vistrail)
+ self.setResult('completed', totals)
+
+#class TimevsTags(Module):
+ #Compare a few workflows to see how long the project took vs. how many tags were made
+ # pass
+
+_modules = [Vistrail, Log, ReadVistrail, CountActions, CountExecutedWorkflows, TotalDays]
diff --git a/vistrails/packages/analytics/times.vt b/vistrails/packages/analytics/times.vt
new file mode 100644
index 0000000..49e8bfb
Binary files /dev/null and b/vistrails/packages/analytics/times.vt differ
diff --git a/vistrails/packages/controlflow/__init__.py b/vistrails/packages/controlflow/__init__.py
new file mode 100644
index 0000000..2211a9b
--- /dev/null
+++ b/vistrails/packages/controlflow/__init__.py
@@ -0,0 +1,39 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+identifier="org.vistrails.vistrails.control_flow"
+name="Control Flow"
+version="0.2.3"
+old_identifiers = ["edu.utah.sci.vistrails.control_flow"]
diff --git a/vistrails/packages/controlflow/conditional.py b/vistrails/packages/controlflow/conditional.py
new file mode 100644
index 0000000..4494406
--- /dev/null
+++ b/vistrails/packages/controlflow/conditional.py
@@ -0,0 +1,119 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.modules.vistrails_module import Module, InvalidOutput, \
+ ModuleError
+import copy
+
+#################################################################################
+## If Operator
+
+class If(Module):
+ """
+ The If Module alows the user to choose the part of the workflow to be
+ executed through the use of a condition.
+ """
+
+ def updateUpstream(self):
+ """A modified version of the updateUpstream method."""
+
+ # everything is the same except that we don't update anything
+ # upstream of TruePort or FalsePort
+ excluded_ports = set(['TruePort', 'FalsePort', 'TrueOutputPorts',
+ 'FalseOutputPorts'])
+ for port_name, connector_list in self.inputPorts.iteritems():
+ if port_name not in excluded_ports:
+ for connector in connector_list:
+ connector.obj.update()
+ for port_name, connectorList in copy.copy(self.inputPorts.items()):
+ if port_name not in excluded_ports:
+ for connector in connectorList:
+ if connector.obj.get_output(connector.port) is \
+ InvalidOutput:
+ self.removeInputConnector(port_name, connector)
+
+ def compute(self):
+ """ The compute method for the If module."""
+
+ if not self.hasInputFromPort('Condition'):
+ raise ModuleError(self, 'Must set condition')
+ cond = self.getInputFromPort('Condition')
+
+ if cond:
+ port_name = 'TruePort'
+ output_ports_name = 'TrueOutputPorts'
+ else:
+ port_name = 'FalsePort'
+ output_ports_name = 'FalseOutputPorts'
+
+ if self.hasInputFromPort(output_ports_name):
+ for connector in self.inputPorts.get(output_ports_name):
+ connector.obj.update()
+
+ if not self.hasInputFromPort(port_name):
+ raise ModuleError(self, 'Must set ' + port_name)
+
+ for connector in self.inputPorts.get(port_name):
+ connector.obj.update()
+
+ if self.hasInputFromPort(output_ports_name):
+ output_ports = self.getInputFromPort(output_ports_name)
+ result = []
+ for output_port in output_ports:
+ result.append(connector.obj.get_output(output_port))
+
+ # FIXME can we just make this a list?
+ if len(output_ports) == 1:
+ self.setResult('Result', result[0])
+ else:
+ self.setResult('Result', result)
+
+#################################################################################
+## Default module
+
+class Default(Module):
+ """
+ The Default module allows the user to provide a default value.
+
+ This module can be put in the middle of a connection to provide a default
+ value from the Default port in case nothing is set on the Input port. This
+ is particularly useful when using subworkflows, with InputPort modules with
+ optional set to True.
+ """
+
+ def compute(self):
+ if self.hasInputFromPort('Input'):
+ self.setResult('Result', self.getInputFromPort('Input'))
+ else:
+ self.setResult('Result', self.getInputFromPort('Default'))
diff --git a/vistrails/packages/controlflow/fold.py b/vistrails/packages/controlflow/fold.py
new file mode 100644
index 0000000..1886011
--- /dev/null
+++ b/vistrails/packages/controlflow/fold.py
@@ -0,0 +1,308 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core import debug
+from vistrails.core.modules.vistrails_module import Module, ModuleError, \
+ ModuleConnector, InvalidOutput, ModuleSuspended
+from vistrails.core.modules.basic_modules import Boolean, String, Integer, \
+ Float, Constant, List
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.vistrail.port_spec import PortSpec
+
+import copy
+from itertools import izip
+
+###############################################################################
+## Fold Operator
+
+class Fold(Module):
+ """Fold is the base class for List-reducing modules.
+
+ It can be used to easily implement a module that takes a List and
+ aggregates its element one by one to get the final result, such as Sum.
+
+ To use it, create a subclass and override the setInitialValue() and
+ operation() methods.
+ """
+
+ def __init__(self):
+ Module.__init__(self)
+
+ def compute(self):
+ """The compute method for the Fold."""
+
+ self.setInitialValue()
+ self.partialResult = self.initialValue
+ self.elementResult = None
+
+ for element in self.getInputFromPort('InputList'):
+ self.element = element
+ self.operation()
+
+ if self.suspended:
+ raise ModuleSuspended(
+ self,
+ self.suspended,
+ children=self._module_suspended)
+ self.setResult('Result', self.partialResult)
+
+ def setInitialValue(self):
+ """This method defines the initial value of the Fold structure. It must
+ be defined before the operation() method."""
+
+ pass
+
+ def operation(self):
+ """This method defines the interaction between the current element of
+ the list and the previous iterations' result."""
+
+ pass
+
+###############################################################################
+
+class FoldWithModule(Fold):
+ """Implementation of Fold that uses another module as its operation.
+
+ This can be used to create structures like Map or Filter, where another
+ module will be called with each element of the list to retrieve something
+ that this module will use.
+ """
+
+ def __init__(self):
+ Fold.__init__(self)
+ self.is_looping_module = True
+
+ def updateUpstream(self):
+ """A modified version of the updateUpstream method."""
+
+ # everything is the same except that we don't update anything
+ # upstream of FunctionPort
+ for port_name, connector_list in self.inputPorts.iteritems():
+ if port_name == 'FunctionPort':
+ for connector in connector_list:
+ connector.obj.updateUpstream()
+ else:
+ for connector in connector_list:
+ connector.obj.update()
+ for port_name, connectorList in list(self.inputPorts.items()):
+ if port_name != 'FunctionPort':
+ for connector in connectorList:
+ if connector.obj.get_output(connector.port) is \
+ InvalidOutput:
+ self.removeInputConnector(port_name, connector)
+
+ def updateFunctionPort(self):
+ """
+ Function to be used inside the updateUsptream method of the
+ FoldWithModule module. It updates the modules connected to the
+ FunctionPort port.
+ """
+ nameInput = self.getInputFromPort('InputPort')
+ nameOutput = self.getInputFromPort('OutputPort')
+ rawInputList = self.getInputFromPort('InputList')
+
+ # Create inputList to always have iterable elements
+ # to simplify code
+ if len(nameInput) == 1:
+ element_is_iter = False
+ inputList = [[element] for element in rawInputList]
+ else:
+ element_is_iter = True
+ inputList = rawInputList
+ suspended = []
+ ## Update everything for each value inside the list
+ for i, element in enumerate(inputList):
+ self.logging.update_progress(self, float(i)/len(inputList))
+ if element_is_iter:
+ self.element = element
+ else:
+ self.element = element[0]
+ for connector in self.inputPorts.get('FunctionPort'):
+ module = copy.copy(connector.obj)
+
+ if not self.upToDate:
+ ## Type checking
+ if i == 0:
+ self.typeChecking(module, nameInput, inputList)
+
+ module.upToDate = False
+ module.computed = False
+
+ ## Setting information for logging stuff
+ module.is_looping = True
+ module.first_iteration = i == 0
+ module.last_iteration = i == len(inputList) - 1
+ module.loop_iteration = i
+
+ self.setInputValues(module, nameInput, element)
+
+ module.update()
+ if hasattr(module, 'suspended') and module.suspended:
+ suspended.append(module._module_suspended)
+ module.suspended = False
+ continue
+ ## Getting the result from the output port
+ if nameOutput not in module.outputPorts:
+ raise ModuleError(module,
+ 'Invalid output port: %s' % nameOutput)
+ self.elementResult = module.get_output(nameOutput)
+ self.operation()
+ if suspended:
+ self.suspended = "%d module(s) suspended: %s" % (
+ len(suspended), suspended[0].msg)
+ self._module_suspended = suspended
+
+ def setInputValues(self, module, inputPorts, elementList):
+ """
+ Function used to set a value inside 'module', given the input port(s).
+ """
+ for element, inputPort in izip(elementList, inputPorts):
+ ## Cleaning the previous connector...
+ if inputPort in module.inputPorts:
+ del module.inputPorts[inputPort]
+ new_connector = ModuleConnector(create_constant(element), 'value')
+ module.set_input_port(inputPort, new_connector)
+
+ def typeChecking(self, module, inputPorts, inputList):
+ """
+ Function used to check if the types of the input list element and of the
+ inputPort of 'module' match.
+ """
+ for elementList in inputList:
+ if len(elementList) != len(inputPorts):
+ raise ModuleError(self,
+ 'The number of input values and input ports '
+ 'are not the same.')
+ for element, inputPort in izip(elementList, inputPorts):
+ p_modules = module.moduleInfo['pipeline'].modules
+ p_module = p_modules[module.moduleInfo['moduleId']]
+ port_spec = p_module.get_port_spec(inputPort, 'input')
+ v_module = get_module(element, port_spec.signature)
+ if v_module is not None:
+ if not self.compare(port_spec, v_module, inputPort):
+ raise ModuleError(self,
+ 'The type of a list element does '
+ 'not match with the type of the '
+ 'port %s.' % inputPort)
+
+ del v_module
+ else:
+ break
+
+ def createSignature(self, v_module):
+ """
+ ` Function used to create a signature, given v_module, for a port spec.
+ """
+ if isinstance(v_module, tuple):
+ v_module_class = []
+ for module_ in v_module:
+ v_module_class.append(self.createSignature(module_))
+ return v_module_class
+ else:
+ return v_module
+
+ def compare(self, port_spec, v_module, port):
+ """
+ Function used to compare two port specs.
+ """
+ port_spec1 = port_spec
+
+ reg = get_module_registry()
+
+ v_module = self.createSignature(v_module)
+ port_spec2 = PortSpec(**{'signature': v_module})
+ matched = reg.are_specs_matched(port_spec2, port_spec1)
+
+ return matched
+
+ def compute(self):
+ """The compute method for the Fold."""
+
+ self.setInitialValue()
+ self.partialResult = self.initialValue
+ self.elementResult = None
+
+ self.updateFunctionPort()
+
+ if self.suspended:
+ raise ModuleSuspended(
+ self,
+ self.suspended,
+ children=self._module_suspended)
+ self.setResult('Result', self.partialResult)
+
+###############################################################################
+
+class NewConstant(Constant):
+ """
+ A new Constant module to be used inside the FoldWithModule module.
+ """
+ def setValue(self, v):
+ self.setResult("value", v)
+ self.upToDate = True
+
+def create_constant(value):
+ """
+ Creates a NewConstant module, to be used for the ModuleConnector.
+ """
+ constant = NewConstant()
+ constant.setValue(value)
+ return constant
+
+def get_module(value, signature):
+ """
+ Creates a module for value, in order to do the type checking.
+ """
+ if isinstance(value, Constant):
+ return type(value)
+ elif isinstance(value, bool):
+ return Boolean
+ elif isinstance(value, str):
+ return String
+ elif isinstance(value, int):
+ return Integer
+ elif isinstance(value, float):
+ return Float
+ elif isinstance(value, list):
+ return List
+ elif isinstance(value, tuple):
+ v_modules = ()
+ for element in xrange(len(value)):
+ v_modules += (get_module(value[element], signature[element]),)
+ return v_modules
+ else:
+ debug.warning("Could not identify the type of the list element.")
+ debug.warning("Type checking is not going to be done inside"
+ "FoldWithModule module.")
+ return None
diff --git a/vistrails/packages/controlflow/init.py b/vistrails/packages/controlflow/init.py
new file mode 100644
index 0000000..9055d59
--- /dev/null
+++ b/vistrails/packages/controlflow/init.py
@@ -0,0 +1,214 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.modules.vistrails_module import Module
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.modules.basic_modules import Boolean, String, Variant, \
+ List, Not, Integer, Float
+from vistrails.core.upgradeworkflow import UpgradeWorkflowHandler
+
+from fold import Fold, FoldWithModule
+from utils import Map, Filter, Sum, And, Or
+from conditional import If, Default
+from products import ElementwiseProduct, Dot, Cross, CartesianProduct
+from order import ExecuteInOrder
+from looping import For, While
+
+
+#################################################################################
+## An useful register function for control modules
+
+def registerControl(module, **kwargs):
+ """This function is used to register the control modules. In this way, all of
+ them will have the same style and shape."""
+
+ reg = get_module_registry()
+ reg.add_module(module,
+ moduleRightFringe=[(0.0,0.0),(0.25,0.5),(0.0,1.0)],
+ moduleLeftFringe=[(0.0,0.0),(0.0,1.0)],
+ **kwargs)
+
+#################################################################################
+
+def initialize(*args,**keywords):
+ reg = get_module_registry()
+
+ registerControl(Fold, abstract=True)
+ registerControl(FoldWithModule, abstract=True)
+ registerControl(Map)
+ registerControl(Filter)
+ registerControl(Sum)
+ registerControl(And)
+ registerControl(Or)
+ registerControl(If)
+ registerControl(Default)
+ registerControl(ExecuteInOrder)
+ registerControl(While)
+ registerControl(For)
+
+ reg.add_output_port(Or, 'Result', (Boolean, ""))
+ reg.add_output_port(And, 'Result', (Boolean, ""))
+
+ reg.add_input_port(Fold, 'InputList', (List, ""))
+ reg.add_output_port(Fold, 'Result', (Variant, ""))
+
+ reg.add_input_port(FoldWithModule, 'FunctionPort', (Module, ""))
+ reg.add_input_port(FoldWithModule, 'InputPort', (List, ""))
+ reg.add_input_port(FoldWithModule, 'OutputPort', (String, ""))
+
+ reg.add_input_port(If, 'Condition', (Boolean, ""))
+ reg.add_input_port(If, 'TruePort', (Module, ""))
+ reg.add_input_port(If, 'FalsePort', (Module, ""))
+ reg.add_input_port(If, 'TrueOutputPorts', (List, ""), optional=True)
+ reg.add_input_port(If, 'FalseOutputPorts', (List, ""), optional=True)
+ reg.add_output_port(If, 'Result', (Variant, ""))
+
+ reg.add_input_port(Default, 'Input', (Variant, ""))
+ reg.add_input_port(Default, 'Default', (Variant, ""))
+ reg.add_output_port(Default, 'Result', (Variant, ""))
+
+ reg.add_module(ElementwiseProduct)
+ reg.add_input_port(ElementwiseProduct, 'List1', (List, ""))
+ reg.add_input_port(ElementwiseProduct, 'List2', (List, ""))
+ reg.add_input_port(ElementwiseProduct, 'NumericalProduct', (Boolean, ""),
+ optional=True, defaults="['True']")
+ reg.add_output_port(ElementwiseProduct, 'Result', (List, ""))
+
+ reg.add_module(Dot)
+ reg.add_input_port(Dot, 'List1', (List, ""))
+ reg.add_input_port(Dot, 'List2', (List, ""))
+ reg.add_output_port(Dot, 'Result', (List, ""))
+
+ reg.add_module(Cross)
+ reg.add_input_port(Cross, 'List1', (List, ""))
+ reg.add_input_port(Cross, 'List2', (List, ""))
+ reg.add_output_port(Cross, 'Result', (List, ""))
+
+ reg.add_module(CartesianProduct)
+ reg.add_input_port(CartesianProduct, 'List1', (List, ""))
+ reg.add_input_port(CartesianProduct, 'List2', (List, ""))
+ reg.add_input_port(CartesianProduct, 'CombineTuple', (Boolean, ""),
+ optional=True, defaults="['True']")
+ reg.add_output_port(CartesianProduct, 'Result', (List, ""))
+
+ reg.add_input_port(ExecuteInOrder, 'module1', (Module, ""))
+ reg.add_input_port(ExecuteInOrder, 'module2', (Module, ""))
+
+ reg.add_input_port(While, 'FunctionPort', (Module, ""))
+ reg.add_input_port(While, 'OutputPort', (String, ""),
+ optional=True, defaults="['self']")
+ reg.add_input_port(While, 'ConditionPort', (String, ""))
+ reg.add_input_port(While, 'StateInputPorts', (List, ""),
+ optional=True)
+ reg.add_input_port(While, 'StateOutputPorts', (List, ""),
+ optional=True)
+ reg.add_input_port(While, 'MaxIterations', (Integer, ""),
+ optional=True, defaults="['20']")
+ reg.add_input_port(While, 'Delay', (Float, ""),
+ optional=True)
+ reg.add_output_port(While, 'Result', (Variant, ""))
+
+ reg.add_input_port(For, 'FunctionPort', (Module, ""))
+ reg.add_input_port(For, 'InputPort', (String, ""),
+ optional=True)
+ reg.add_input_port(For, 'OutputPort', (String, ""),
+ optional=True, defaults="['self']")
+ reg.add_input_port(For, 'LowerBound', (Integer, ""),
+ optional=True, defaults="['0']")
+ reg.add_input_port(For, 'HigherBound', (Integer, ""))
+ reg.add_output_port(For, 'Result', (List, ""))
+
+def handle_module_upgrade_request(controller, module_id, pipeline):
+ reg = get_module_registry()
+
+ # Product modules had a CombineTuple port, which has been replaced with
+ # NumericalProduct, with the opposite meaning
+ def product_change_connection(old_conn, new_module):
+ src_module = pipeline.modules[old_conn.source.moduleId]
+ new_x = (src_module.location.x + new_module.location.x) / 2.0
+ new_y = (src_module.location.y + new_module.location.y) / 2.0
+ Not_desc = reg.get_descriptor(Not)
+ not_mod = controller.create_module_from_descriptor(Not_desc,
+ new_x, new_y)
+ conn1 = UpgradeWorkflowHandler.create_new_connection(
+ controller,
+ src_module, old_conn.source,
+ not_mod, 'input')
+ conn2 = UpgradeWorkflowHandler.create_new_connection(
+ controller,
+ not_mod, 'value',
+ new_module, 'NumericalProduct')
+ return [('add', not_mod), ('add', conn1), ('add', conn2)]
+ def product_change_function(function, new_module):
+ parameter = function.parameters[0]
+ if parameter.value():
+ value = 'False'
+ else:
+ value = 'True'
+ return controller.update_function_ops(
+ new_module, 'NumericalProduct',
+ [value])
+
+ module_remap = {
+ 'ListOfElements': [
+ # Any 'ListOfElements' before 0.2.2 gets replaced with List
+ (None, '0.2.2', List, {}),
+ ],
+ 'Dot': [
+ # The Dot module in 0.2.1 was in fact ElementwiseProduct
+ (None, '0.2.2', ElementwiseProduct, {
+ 'dst_port_remap': {
+ 'List_1': 'List1',
+ 'List_2': 'List2',
+ 'CombineTuple': product_change_connection,
+ },
+ 'function_remap': {
+ 'CombineTuple': product_change_function,
+ },
+ }),
+ ],
+ 'Cross': [
+ (None, '0.2.2', CartesianProduct, {
+ 'dst_port_remap': {
+ 'List_1': 'List1',
+ 'List_2': 'List2',
+ },
+ }),
+ ],
+ }
+
+ return UpgradeWorkflowHandler.remap_module(controller,
+ module_id,
+ pipeline,
+ module_remap)
diff --git a/vistrails/packages/controlflow/looping.py b/vistrails/packages/controlflow/looping.py
new file mode 100644
index 0000000..8b945df
--- /dev/null
+++ b/vistrails/packages/controlflow/looping.py
@@ -0,0 +1,241 @@
+import copy
+from itertools import izip
+import time
+
+from vistrails.core.modules.vistrails_module import Module, InvalidOutput, \
+ ModuleSuspended, ModuleError, ModuleConnector
+
+from fold import create_constant
+
+
+class While(Module):
+ """
+ The While Module runs a module over and over until the condition port
+ is false. Then, it returns the result.
+ """
+
+ def __init__(self):
+ Module.__init__(self)
+ self.is_looping_module = True
+
+ def updateUpstream(self):
+ """A modified version of the updateUpstream method."""
+
+ # everything is the same except that we don't update the module on
+ # FunctionPort
+ for port_name, connector_list in self.inputPorts.iteritems():
+ if port_name == 'FunctionPort':
+ for connector in connector_list:
+ connector.obj.updateUpstream()
+ else:
+ for connector in connector_list:
+ connector.obj.update()
+ for port_name, connectorList in copy.copy(self.inputPorts.items()):
+ if port_name != 'FunctionPort':
+ for connector in connectorList:
+ if connector.obj.get_output(connector.port) is \
+ InvalidOutput:
+ self.removeInputConnector(port_name, connector)
+
+ def compute(self):
+ name_output = self.getInputFromPort('OutputPort')
+ name_condition = self.forceGetInputFromPort('ConditionPort')
+ name_state_input = self.forceGetInputFromPort('StateInputPorts')
+ name_state_output = self.forceGetInputFromPort('StateOutputPorts')
+ max_iterations = self.getInputFromPort('MaxIterations')
+ delay = self.forceGetInputFromPort('Delay')
+
+ if (name_condition is None and
+ not self.hasInputFromPort('MaxIterations')):
+ raise ModuleError(self,
+ "Please set MaxIterations or use ConditionPort")
+
+ if name_state_input or name_state_output:
+ if not name_state_input or not name_state_output:
+ raise ModuleError(self,
+ "Passing state between iterations requires "
+ "BOTH StateInputPorts and StateOutputPorts "
+ "to be set")
+ if len(name_state_input) != len(name_state_output):
+ raise ModuleError(self,
+ "StateInputPorts and StateOutputPorts need "
+ "to have the same number of ports "
+ "(got %d and %d)" % (len(name_state_input),
+ len(name_state_output)))
+
+ connectors = self.inputPorts.get('FunctionPort')
+ if len(connectors) != 1:
+ raise ModuleError(self,
+ "Multiple modules connected on FunctionPort")
+ module = copy.copy(connectors[0].obj)
+
+ state = None
+
+ for i in xrange(max_iterations):
+ if not self.upToDate:
+ module.upToDate = False
+ module.computed = False
+
+ # For logging
+ module.is_looping = True
+ module.first_iteration = i == 0
+ module.last_iteration = False
+ module.loop_iteration = i
+
+ # Set state on input ports
+ if i > 0 and name_state_input:
+ for value, port in izip(state, name_state_input):
+ if port in module.inputPorts:
+ del module.inputPorts[port]
+ new_connector = ModuleConnector(
+ create_constant(value),
+ 'value')
+ module.set_input_port(port, new_connector)
+
+ module.update()
+ if hasattr(module, 'suspended') and module.suspended:
+ raise ModuleSuspended(module._module_suspended)
+
+ if name_condition is not None:
+ if name_condition not in module.outputPorts:
+ raise ModuleError(
+ module,
+ "Invalid output port: %s" % name_condition)
+ if not module.get_output(name_condition):
+ break
+
+ if delay and i+1 != max_iterations:
+ time.sleep(delay)
+
+ # Get state on output ports
+ if name_state_output:
+ state = [module.get_output(port) for port in name_state_output]
+
+ if name_output not in module.outputPorts:
+ raise ModuleError(module,
+ "Invalid output port: %s" % name_output)
+ result = module.get_output(name_output)
+ self.setResult('Result', result)
+
+
+class For(Module):
+ """
+ The For Module runs a module with input from a range.
+ """
+
+ def __init__(self):
+ Module.__init__(self)
+ self.is_looping_module = True
+
+ def updateUpstream(self):
+ """A modified version of the updateUpstream method."""
+
+ # everything is the same except that we don't update the module on
+ # FunctionPort
+ for port_name, connector_list in self.inputPorts.iteritems():
+ if port_name == 'FunctionPort':
+ for connector in connector_list:
+ connector.obj.updateUpstream()
+ else:
+ for connector in connector_list:
+ connector.obj.update()
+ for port_name, connectorList in copy.copy(self.inputPorts.items()):
+ if port_name != 'FunctionPort':
+ for connector in connectorList:
+ if connector.obj.get_output(connector.port) is \
+ InvalidOutput:
+ self.removeInputConnector(port_name, connector)
+
+ def compute(self):
+ name_output = self.getInputFromPort('OutputPort') # or 'self'
+ name_input = self.forceGetInputFromPort('InputPort') # or None
+ lower_bound = self.getInputFromPort('LowerBound') # or 0
+ higher_bound = self.getInputFromPort('HigherBound') # required
+
+ connectors = self.inputPorts.get('FunctionPort')
+ if len(connectors) != 1:
+ raise ModuleError(self,
+ "Multiple modules connected on FunctionPort")
+
+ outputs = []
+ suspended = []
+ for i in xrange(lower_bound, higher_bound):
+ module = copy.copy(connectors[0].obj)
+
+ if not self.upToDate:
+ module.upToDate = False
+ module.computed = False
+
+ # For logging
+ module.is_looping = True
+ module.first_iteration = i == lower_bound
+ module.last_iteration = i+1 == higher_bound
+ module.loop_iteration = i - lower_bound
+
+ # Pass iteration number on input port
+ if name_input is not None:
+ if name_input in module.inputPorts:
+ del module.inputPorts[name_input]
+ new_connector = ModuleConnector(
+ create_constant(i),
+ 'value')
+ module.set_input_port(name_input, new_connector)
+
+ module.update()
+
+ if hasattr(module, 'suspended') and module.suspended:
+ suspended.append(module._module_suspended)
+ continue
+
+ if name_output not in module.outputPorts:
+ raise ModuleError(module,
+ "Invalid output port: %s" % name_output)
+ outputs.append(module.get_output(name_output))
+
+ if suspended:
+ self.suspended = "%d module(s) suspended: %s" % (
+ len(suspended), suspended[0].msg)
+ self._module_suspended = suspended
+ else:
+ self.setResult('Result', outputs)
+
+
+###############################################################################
+
+import unittest
+
+class TestWhile(unittest.TestCase):
+ def test_pythonsource(self):
+ import urllib2
+ source = ('o = i * 2\n'
+ "r = \"it's %d!!!\" % o\n"
+ 'go_on = o < 100')
+ source = urllib2.quote(source)
+ from vistrails.tests.utils import execute, intercept_result
+ with intercept_result(While, 'Result') as results:
+ self.assertFalse(execute([
+ ('PythonSource', 'org.vistrails.vistrails.basic', [
+ ('source', [('String', source)]),
+ ('i', [('Integer', '5')]),
+ ]),
+ ('While', 'org.vistrails.vistrails.control_flow', [
+ ('ConditionPort', [('String', 'go_on')]),
+ ('OutputPort', [('String', 'r')]),
+ ('StateInputPorts', [('List', "['i']")]),
+ ('StateOutputPorts', [('List', "['o']")]),
+ ]),
+ ],
+ [
+ (0, 'self', 1, 'FunctionPort'),
+ ],
+ add_port_specs=[
+ (0, 'input', 'i',
+ 'org.vistrails.vistrails.basic:Integer'),
+ (0, 'output', 'o',
+ 'org.vistrails.vistrails.basic:Integer'),
+ (0, 'output', 'r',
+ 'org.vistrails.vistrails.basic:String'),
+ (0, 'output', 'go_on',
+ 'org.vistrails.vistrails.basic:Boolean'),
+ ]))
+ self.assertEqual(results, ["it's 160!!!"])
diff --git a/vistrails/packages/controlflow/order.py b/vistrails/packages/controlflow/order.py
new file mode 100644
index 0000000..0f67878
--- /dev/null
+++ b/vistrails/packages/controlflow/order.py
@@ -0,0 +1,62 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.modules.vistrails_module import Module, InvalidOutput
+import copy
+
+##############################################################################
+## Order Operator
+
+class ExecuteInOrder(Module):
+ """
+ The Order Module alows the user to control which sink of a pair of
+ sinks ought to executed first. Connect the "self" port of each
+ sink to the corresponding port. Note that if you have more than
+ two sinks, you can string them together by using a string of Order
+ modules.
+ """
+
+ def updateUpstream(self):
+ # don't do update until compute!
+ pass
+
+ def compute(self):
+ # do updateUpstream as compute, but sort by key
+ for _, connectorList in sorted(self.inputPorts.iteritems()):
+ for connector in connectorList:
+ connector.obj.update()
+ for iport, connectorList in copy.copy(self.inputPorts.items()):
+ for connector in connectorList:
+ if connector.obj.get_output(connector.port) is InvalidOutput:
+ self.removeInputConnector(iport, connector)
diff --git a/vistrails/packages/controlflow/products.py b/vistrails/packages/controlflow/products.py
new file mode 100644
index 0000000..6bc74b1
--- /dev/null
+++ b/vistrails/packages/controlflow/products.py
@@ -0,0 +1,135 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import itertools
+
+from vistrails.core.modules.vistrails_module import Module, ModuleError
+
+#################################################################################
+## Products
+
+class ElementwiseProduct(Module):
+ """This module does the product of two lists.
+
+ If NumericalProduct is True, this will effectively compute the product of
+ each element, eg:
+ [1, 2, 3] x [3, -3, 1] = [3, -6, 3]
+ Else, it will make tuples, eg:
+ [1, 2, 3] x [3, -3, 1] = [(1, 3), (2, -3), (3, 1)]
+ """
+
+ def compute(self):
+ list1 = self.getInputFromPort('List1')
+ list2 = self.getInputFromPort('List2')
+ if len(list1) != len(list2):
+ raise ModuleError(self, "Both lists must have the same size.")
+
+ numerical = self.getInputFromPort('NumericalProduct')
+ if numerical:
+ result = [a*b for a, b in itertools.izip(list1, list2)]
+ else:
+ result = zip(list1, list2)
+
+ self.setResult('Result', result)
+
+
+class Dot(Module):
+ """This module produces a Dot product between two lists."""
+
+ def compute(self):
+ list1 = self.getInputFromPort("List1")
+ list2 = self.getInputFromPort("List2")
+ if len(list1) != len(list2):
+ raise ModuleError(self, 'Both lists must have the same size.')
+
+ result = sum(a*b for a, b in itertools.izip(list1, list2))
+
+ self.setResult("Result", result)
+
+
+class Cross(Module):
+ """This module produces a Cross product between two 3-D vectors."""
+
+ def compute(self):
+ list1 = self.getInputFromPort("List1")
+ list2 = self.getInputFromPort("List2")
+ if not (len(list1) == len(list2) == 3):
+ raise ModuleError(self, 'Both lists must have size 3.')
+
+ x1, y1, z1 = list1
+ x2, y2, z2 = list2
+
+ result = [y1*z2 - y2*z1,
+ z1*x2 - z2*x1,
+ x1*y2 - x2*y1]
+
+ self.setResult("Result", result)
+
+
+class CartesianProduct(Module):
+ """This module does the cartesian product of two lists.
+ """
+
+ def compute(self):
+ list1 = self.getInputFromPort("List1")
+ list2 = self.getInputFromPort("List2")
+ result = []
+ # If CombineTuple is not set or True, existing tuples will be
+ # concatenated instead of put inside a new tuple, eg:
+ # with CombineTuple (default):
+ # [(1, 2)], [3, 4] -> [(1, 2, 3), (1, 2, 4)]
+ # without:
+ # [(1, 2)], [3, 4] -> [((1, 2), 3), ((1, 2), 4)]
+ if not self.getInputFromPort('CombineTuple'):
+ for i in list1:
+ for j in list2:
+ tuple_ = (i, j)
+ result.append(tuple_)
+ else:
+ for i in list1:
+ for j in list2:
+ if isinstance(i, tuple) and isinstance(j, tuple):
+ tuple_ = i + j
+ result.append(tuple_)
+ elif isinstance(i, tuple) and not isinstance(j, tuple):
+ tuple_ = i + (j,)
+ result.append(tuple_)
+ elif not isinstance(i, tuple) and isinstance(j, tuple):
+ tuple_ = (i,) + j
+ result.append(tuple_)
+ else:
+ tuple_ = (i, j)
+ result.append(tuple_)
+
+ self.setResult("Result", result)
diff --git a/vistrails/packages/controlflow/utils.py b/vistrails/packages/controlflow/utils.py
new file mode 100644
index 0000000..8f5b6c8
--- /dev/null
+++ b/vistrails/packages/controlflow/utils.py
@@ -0,0 +1,116 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.modules.vistrails_module import ModuleError
+from fold import Fold, FoldWithModule
+
+#################################################################################
+## Some useful loop structures
+
+class Map(FoldWithModule):
+ """A Map module, that just appends the results in a list."""
+
+ def setInitialValue(self):
+ """Defining the initial value..."""
+
+ self.initialValue = []
+
+ def operation(self):
+ """Defining the operation..."""
+
+ self.partialResult.append(self.elementResult)
+
+
+class Filter(FoldWithModule):
+ """A Filter module, that returns in a list only the results that satisfy a
+ condition."""
+
+ def setInitialValue(self):
+ """Defining the initial value..."""
+
+ self.initialValue = []
+
+ def operation(self):
+ """Defining the operation..."""
+
+ if not isinstance(self.elementResult, bool):
+ raise ModuleError(self,'The function applied to the elements of the\
+list must return a boolean result.')
+
+ if self.elementResult:
+ self.partialResult.append(self.element)
+
+
+class Sum(Fold):
+ """A Sum module, that computes the sum of the elements in a list."""
+
+ def setInitialValue(self):
+ """Defining the initial value..."""
+
+ self.initialValue = 0
+
+ def operation(self):
+ """Defining the operation..."""
+
+ self.partialResult += self.element
+
+
+class And(Fold):
+ """An And module, that computes the And result among the elements
+ in a list."""
+
+ def setInitialValue(self):
+ """Defining the initial value..."""
+
+ self.initialValue = True
+
+ def operation(self):
+ """Defining the operation..."""
+
+ self.partialResult = self.partialResult and bool(self.element)
+
+
+class Or(Fold):
+ """An Or module, that computes the Or result among the elements
+ in a list."""
+
+ def setInitialValue(self):
+ """Defining the initial value..."""
+
+ self.initialValue = False
+
+ def operation(self):
+ """Defining the operation..."""
+
+ self.partialResult = self.partialResult or self.element
diff --git a/vistrails/packages/dialogs/__init__.py b/vistrails/packages/dialogs/__init__.py
new file mode 100644
index 0000000..16057bd
--- /dev/null
+++ b/vistrails/packages/dialogs/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""dialogs provides modules for user-based interaction on execution.
+Users can then enter file names, numbers, strings, etc."""
+
+identifier = 'org.vistrails.vistrails.dialogs'
+name = 'Dialogs'
+version = '0.9.1'
+old_identifiers = ['edu.utah.sci.vistrails.dialogs']
diff --git a/vistrails/packages/dialogs/init.py b/vistrails/packages/dialogs/init.py
new file mode 100644
index 0000000..53c4e9d
--- /dev/null
+++ b/vistrails/packages/dialogs/init.py
@@ -0,0 +1,110 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.modules.vistrails_module import Module, ModuleError
+import vistrails.core.modules
+import vistrails.core.modules.basic_modules
+import vistrails.core.modules.module_registry
+import vistrails.core.system
+import vistrails.gui.application
+from PyQt4 import QtCore, QtGui
+
+##############################################################################
+
+class Dialog(Module):
+ pass
+
+class TextDialog(Dialog):
+ password = False
+
+ def __init__(self, *args, **kwargs):
+ super(TextDialog,self).__init__(*args, **kwargs)
+ self.cacheable_dialog = False
+
+ def is_cacheable(self):
+ return self.cacheable_dialog
+
+ def compute(self):
+ if self.hasInputFromPort('title'):
+ title = self.getInputFromPort('title')
+ else:
+ title = 'VisTrails Dialog'
+ if self.hasInputFromPort('label'):
+ label = self.getInputFromPort('label')
+ else:
+ label = ''
+ if self.password:
+ label = 'Password'
+
+ if self.hasInputFromPort('default'):
+ default = self.getInputFromPort('default')
+ else:
+ default = ''
+
+ if self.hasInputFromPort('cacheable') and self.getInputFromPort('cacheable'):
+ self.cacheable_dialog = True
+ else:
+ self.cacheable_dialog = False
+
+ mode = QtGui.QLineEdit.Normal
+ if self.password:
+ mode = QtGui.QLineEdit.Password
+
+ (result, ok) = QtGui.QInputDialog.getText(None, title, label,
+ mode,
+ default)
+ if not ok:
+ raise ModuleError(self, "Canceled")
+ self.setResult('result', str(result))
+
+
+class PasswordDialog(TextDialog):
+ password = True
+
+
+##############################################################################
+
+def initialize(*args, **keywords):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ basic = vistrails.core.modules.basic_modules
+ reg.add_module(Dialog, abstract=True)
+ reg.add_module(TextDialog)
+
+ reg.add_input_port(TextDialog, "title", basic.String)
+ reg.add_input_port(TextDialog, "label", basic.String)
+ reg.add_input_port(TextDialog, "default", basic.String)
+ reg.add_input_port(TextDialog, "cacheable", basic.Boolean)
+ reg.add_output_port(TextDialog, "result", basic.String)
+
+ reg.add_module(PasswordDialog)
diff --git a/vistrails/packages/matplotlib/README b/vistrails/packages/matplotlib/README
new file mode 100644
index 0000000..e691d7a
--- /dev/null
+++ b/vistrails/packages/matplotlib/README
@@ -0,0 +1,94 @@
+This version of the matplotlib package seeks to make the features much
+more accessible in VisTrails. Previous versions required users to
+type code to generate figures, and this usually required reading
+external documentation. Because matplotlib has no standard way to
+determine all method and parameter specification automatically. We
+can, however, parse method declarations and the docutils documentation
+to infer many of the input types. While this generates much of the
+package specification, there are many pieces that are unknown without
+checking the documentation and/or code manually. To allow both
+automated generation and manual fixes to work, we use a multi-step process:
+
+(1) Automated Generation: based on documentation, method
+specifications, and heuristics, generate module and port
+specifications in XML.
+
+(2?) If a diff of previous edits exists (see step 3 & 4), apply it to
+the automated output.
+
+(3) Manual Fixes: Users then can manually edit the XML to fix and add
+extra information. They can also specify python code in the mixins.py
+file; this is nicer for editing than doing this in XML.
+
+(4) Difference Computation: Find and store the differences in the XML
+tree between the automated specs and the manual fixes. These
+differences are used in step (2).
+
+(5) Python Code Generation: Generate the VisTrails python wrapper code
+from the XML.
+
+This process is iterative as parsing heuristics may be updated and
+many manual fixes may be required. The update.py script wraps this
+entire process.
+
+== Automated Generation ==
+
+The automated generation scripts consist of a few techniques. First,
+for plotting functions, we can parse the function specification using
+python's inspect module, extracting argument names and defaults. For
+artists (lines, patches, rectangles), the matplotlib authors have
+tried to enforce property getters and setters, and they also have
+documentation standards where developers specify an "ACCEPTS:" clause
+which specifies what type of arguments the setters take. The
+ArtistInspector is tasked to grab this information. Second, the
+documentation is in docutils format which means we can run it through
+the docutils parser to find tables and definition lists which can be
+translated to variables and translation dictionaries (e.g. we can show
+a user "upper center" but translate it to 9 for matplotlib). In
+addition, we can search for certain keywords ("arguments") to find
+definition lists that likely correspond to ports. Finally, we can
+parse the call signatures which are sometimes present in the
+documentation using python's ast module.
+
+== XML Specification ==
+
+The most important piece in updating the specs is understanding the
+XML serialization. This serialization is a list of module specs which
+in turn have input and output port specs. Input port specs may have
+any number of alternate specs which represent alternative types for a
+single input argument; for example, the box() method's width may be a
+single scalar or a sequence of scalars. Output port specs are usually
+used to track internal outputs that permit customization; **they are
+not necessarily (nor often) associated with an actual output port**.
+Instead, if a boxplot command produces a dictionary of outputs (each a
+sequence of lines), the output port specs can specify how each artist
+may be customized (colors). This is usually done with an
+MplProperties subclass; the user adds the properties module as an
+input and the automated compute() method sets those properties on the
+artist objects output.
+
+== Mixin Code ==
+
+Users may specify blocks for the init, compute_before, compute_inner,
+and compute_after methods. This code is **copied** when the template
+is generated; mixins.py **is not imported** when the package is being
+used.
+
+== Shortcuts & Keywords ==
+
+-- When specifying alternate input port specs, users need only provide
+ the port_type field; everything else can be inferred from the
+ parent port spec.
+
+-- The output_type for a ModuleSpec should be one of "object",
+ "tuple", or "dict" if there is an output returned. Then, the
+ property_key for each output spec should be an integer for a tuple
+ and the key value for a dictionary.
+
+-- When specifying output port specs, name and compute_name are
+ defaulted using the arg setting
+
+-- The "__property__" output_type on an output port spec specifies
+ that this port is being used to identify an output of the plotting
+ command that can be customized according to the property_type
+ field.
diff --git a/vistrails/packages/matplotlib/__init__.py b/vistrails/packages/matplotlib/__init__.py
new file mode 100644
index 0000000..f432dda
--- /dev/null
+++ b/vistrails/packages/matplotlib/__init__.py
@@ -0,0 +1,63 @@
+###############################################################################
+##
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Matplotlib package for VisTrails.
+
+This package wrap Matplotlib to provide a plotting tool for
+VisTrails. We are going to use the 'Qt4Agg' backend of the library.
+
+"""
+
+from identifiers import *
+
+def package_dependencies():
+ import vistrails.core.packagemanager
+ manager = vistrails.core.packagemanager.get_package_manager()
+ if manager.has_package('org.vistrails.vistrails.spreadsheet'):
+ return ['org.vistrails.vistrails.spreadsheet']
+ else:
+ return []
+
+def package_requirements():
+ from vistrails.core.requirements import require_python_module
+ require_python_module('numpy', {
+ 'pip': 'numpy',
+ 'linux-debian': 'python-numpy',
+ 'linux-ubuntu': 'python-numpy',
+ 'linux-fedora': 'numpy'})
+ mpl_dict = {'pip': 'matplotlib',
+ 'linux-debian': 'python-matplotlib',
+ 'linux-ubuntu': 'python-matplotlib',
+ 'linux-fedora': 'python-matplotlib'}
+ require_python_module('matplotlib', mpl_dict)
+ require_python_module('pylab', mpl_dict)
diff --git a/vistrails/packages/matplotlib/artists.py b/vistrails/packages/matplotlib/artists.py
new file mode 100644
index 0000000..f167527
--- /dev/null
+++ b/vistrails/packages/matplotlib/artists.py
@@ -0,0 +1,3800 @@
+from vistrails.core.modules.vistrails_module import Module
+from bases import MplProperties
+import matplotlib.artist
+import matplotlib.cbook
+
+
+
+
+
+
+def translate_color(c):
+ return c.tuple
+
+def translate_MplLine2DProperties_marker(val):
+ translate_dict = {'caretright': 5, 'star': '*', 'point': '.', 'mathtext': '$...$', 'triangle_right': '>', 'tickup': 2, 'hexagon1': 'h', 'plus': '+', 'hline': '_', 'vline': '|', 'tickdown': 3, 'nothing': ' ', 'caretup': 6, 'caretleft': 4, 'pentagon': 'p', 'tri_left': '3', 'tickleft': 0, 'tickright': 1, 'tri_down': '1', 'thin_diamond': 'd', 'diamond': 'D', 'caretdown': 7, 'hexagon2': 'H', 'tri_up': '2', 'square': 's', 'x': 'x', 'triangle_down': 'v', 'triangle_up': '^', 'octagon': '8', [...]
+ return translate_dict[val]
+def translate_MplLine2DProperties_linestyle(val):
+ translate_dict = {'solid': '-', 'dashed': '--', 'dash_dot': '-.', 'dotted': ':', 'draw nothing': ''}
+ return translate_dict[val]
+def translate_MplAxesProperties_anchor(val):
+ translate_dict = {'right': 'E', 'Center': 'C', 'bottom right': 'SE', 'top right': 'NE', 'bottom': 'S', 'top left': 'NW', 'top': 'N', 'bottom left': 'SW', 'left': 'W'}
+ return translate_dict[val]
+
+class MplArtistProperties(MplProperties):
+ """
+ Abstract base class for someone who renders into a
+ :class:`FigureCanvas`.
+
+ """
+ _input_ports = [
+ ("picker", "basic:String",
+ {'optional': True, 'docstring': "Set the epsilon for picking used by this artist\n\npicker can be one of the following:\n\nNone: picking is disabled for this artist (default)\n\nA boolean: if True then picking will be enabled and the artist will fire a pick event if the mouse event is over the artist\n\nA float: if picker is a number it is interpreted as an epsilon tolerance in points and the artist will fire off an event if it's data is within epsilon of the mouse event. [...]
+ ("contains", "basic:String",
+ {'optional': True, 'docstring': 'Replace the contains test used by this artist. The new picker should be a callable function which determines whether the artist is hit by the mouse event:\n\nhit, props = picker(artist, mouseevent)\n\nIf the mouse event is over the artist, return hit = True and props is a dictionary of properties you want returned with the contains test.'}),
+ ("clip_on", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether artist uses clipping.'}),
+ ("agg_filter", "basic:String",
+ {'optional': True, 'docstring': 'set agg_filter fuction.'}),
+ ("visible", "basic:Boolean",
+ {'optional': True, 'docstring': "Set the artist's visiblity."}),
+ ("url", "basic:String",
+ {'optional': True, 'docstring': 'Sets the url for the artist'}),
+ ("transform", "basic:String",
+ {'optional': True, 'docstring': 'Set the :class:`~matplotlib.transforms.Transform` instance used by this artist.'}),
+ ("axes", "basic:String",
+ {'optional': True, 'docstring': 'Set the :class:`~matplotlib.axes.Axes` instance in which the artist resides, if any.'}),
+ ("clip_box", "basic:String",
+ {'optional': True, 'docstring': "Set the artist's clip :class:`~matplotlib.transforms.Bbox`."}),
+ ("clip_path", "basic:String",
+ {'optional': True, 'docstring': "Set the artist's clip path, which may be:\n\na :class:`~matplotlib.patches.Patch` (or subclass) instance\n\n\n\nNone, to remove the clipping path\n\nFor efficiency, if the path happens to be an axis-aligned rectangle, this method will set the clipping box to the corresponding rectangle and set the clipping path to None."}),
+ ("lod", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set Level of Detail on or off. If on, the artists may examine things like the pixel width of the axes and draw a subset of their contents accordingly'}),
+ ("label", "basic:String",
+ {'optional': True, 'docstring': 'Set the label to s for auto legend.'}),
+ ("rasterized", "basic:Boolean",
+ {'optional': True, 'docstring': "Force rasterized (bitmap) drawing in vector backend output.\n\nDefaults to None, which implies the backend's default behavior"}),
+ ("gid", "basic:String",
+ {'optional': True, 'docstring': 'Sets the (group) id for the artist'}),
+ ("zorder", "basic:String",
+ {'optional': True, 'docstring': 'Set the zorder for the artist. Artists with lower zorder values are drawn first.'}),
+ ("snap", "basic:String",
+ {'optional': True, 'docstring': 'Sets the snap setting which may be:\n\nTrue: snap vertices to the nearest pixel center\n\nFalse: leave vertices as-is\n\nNone: (auto) If the path contains only rectilinear line segments, round to the nearest pixel center\n\nOnly supported by the Agg and MacOSX backends.'}),
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'Set the alpha value used for blending - not supported on all backends.'}),
+ ("animated", "basic:Boolean",
+ {'optional': True, 'docstring': "Set the artist's animation state."}),
+ ("figure", "basic:String",
+ {'optional': True, 'docstring': 'Set the :class:`~matplotlib.figure.Figure` instance the artist belongs to.'}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplArtistProperties)")]
+
+ def __init__(self):
+ MplProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplProperties.compute(self)
+ if self.hasInputFromPort('picker'):
+ self.props['picker'] = self.getInputFromPort('picker')
+ if self.hasInputFromPort('contains'):
+ self.props['contains'] = self.getInputFromPort('contains')
+ if self.hasInputFromPort('clip_on'):
+ self.props['clip_on'] = self.getInputFromPort('clip_on')
+ if self.hasInputFromPort('agg_filter'):
+ self.props['agg_filter'] = self.getInputFromPort('agg_filter')
+ if self.hasInputFromPort('visible'):
+ self.props['visible'] = self.getInputFromPort('visible')
+ if self.hasInputFromPort('url'):
+ self.props['url'] = self.getInputFromPort('url')
+ if self.hasInputFromPort('transform'):
+ self.props['transform'] = self.getInputFromPort('transform')
+ if self.hasInputFromPort('axes'):
+ self.props['axes'] = self.getInputFromPort('axes')
+ if self.hasInputFromPort('clip_box'):
+ self.props['clip_box'] = self.getInputFromPort('clip_box')
+ if self.hasInputFromPort('clip_path'):
+ self.props['clip_path'] = self.getInputFromPort('clip_path')
+ if self.hasInputFromPort('lod'):
+ self.props['lod'] = self.getInputFromPort('lod')
+ if self.hasInputFromPort('label'):
+ self.props['label'] = self.getInputFromPort('label')
+ if self.hasInputFromPort('rasterized'):
+ self.props['rasterized'] = self.getInputFromPort('rasterized')
+ if self.hasInputFromPort('gid'):
+ self.props['gid'] = self.getInputFromPort('gid')
+ if self.hasInputFromPort('zorder'):
+ self.props['zorder'] = self.getInputFromPort('zorder')
+ if self.hasInputFromPort('snap'):
+ self.props['snap'] = self.getInputFromPort('snap')
+ if self.hasInputFromPort('alpha'):
+ self.props['alpha'] = self.getInputFromPort('alpha')
+ if self.hasInputFromPort('animated'):
+ self.props['animated'] = self.getInputFromPort('animated')
+ if self.hasInputFromPort('figure'):
+ self.props['figure'] = self.getInputFromPort('figure')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class Mpl_AxesImageBaseProperties(MplArtistProperties):
+ """None
+ """
+ _input_ports = [
+ ("origin", "basic:String",
+ {'optional': True}),
+ ("resample", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether or not image resampling is used'}),
+ ("norm", "basic:String",
+ {'optional': True}),
+ ("cmap", "basic:String",
+ {'optional': True}),
+ ("filternorm", "basic:String",
+ {'optional': True, 'docstring': 'Set whether the resize filter norms the weights -- see help for imshow'}),
+ ("ax", "basic:String",
+ {'optional': True}),
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'Set the alpha value used for blending - not supported on all backends'}),
+ ("array", "basic:String",
+ {'optional': True, 'docstring': 'Retained for backwards compatibility - use set_data instead'}),
+ ("data", "basic:String",
+ {'optional': True, 'docstring': 'Set the image array'}),
+ ("filterrad", "basic:Float",
+ {'optional': True, 'docstring': 'Set the resize filter radius only applicable to some interpolation schemes -- see help for imshow'}),
+ ("interpolation", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "Set the interpolation method the image uses when resizing.\n\nif None, use a value from rc setting. If 'none', the image is shown as is without interpolating. 'none' is only supported in agg, ps and pdf backends and will fall back to 'nearest' mode for other backends.", 'values': "[['nearest', 'bilinear', 'bicubic', 'spline16', 'spline36', 'hanning', 'hamming', 'hermite', 'kaiser', 'quadric', 'catrom', 'gaussian', 'bessel', 'mitch [...]
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(Mpl_AxesImageBaseProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('origin'):
+ self.constructor_props['origin'] = self.getInputFromPort('origin')
+ if self.hasInputFromPort('resample'):
+ self.props['resample'] = self.getInputFromPort('resample')
+ if self.hasInputFromPort('norm'):
+ self.constructor_props['norm'] = self.getInputFromPort('norm')
+ if self.hasInputFromPort('cmap'):
+ self.constructor_props['cmap'] = self.getInputFromPort('cmap')
+ if self.hasInputFromPort('filternorm'):
+ self.props['filternorm'] = self.getInputFromPort('filternorm')
+ if self.hasInputFromPort('ax'):
+ self.constructor_props['ax'] = self.getInputFromPort('ax')
+ if self.hasInputFromPort('alpha'):
+ self.props['alpha'] = self.getInputFromPort('alpha')
+ if self.hasInputFromPort('array'):
+ self.props['array'] = self.getInputFromPort('array')
+ if self.hasInputFromPort('data'):
+ self.props['data'] = self.getInputFromPort('data')
+ if self.hasInputFromPort('filterrad'):
+ self.props['filterrad'] = self.getInputFromPort('filterrad')
+ if self.hasInputFromPort('interpolation'):
+ self.props['interpolation'] = self.getInputFromPort('interpolation')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplAxesImageProperties(Mpl_AxesImageBaseProperties):
+ """None
+ """
+ _input_ports = [
+ ("origin", "basic:String",
+ {'optional': True}),
+ ("resample", "basic:Boolean",
+ {'optional': True, 'defaults': "['False']"}),
+ ("norm", "basic:String",
+ {'optional': True}),
+ ("cmap", "basic:String",
+ {'optional': True}),
+ ("filterrad", "basic:Float",
+ {'optional': True, 'defaults': "['4.0']"}),
+ ("extent", "basic:String",
+ {'optional': True, 'docstring': 'extent is data axes (left, right, bottom, top) for making image plots\n\nThis updates ax.dataLim, and, if autoscaling, sets viewLim to tightly fit the image, regardless of dataLim. Autoscaling state is not changed, so following this with ax.autoscale_view will redo the autoscaling in accord with dataLim.'}),
+ ("ax", "basic:String",
+ {'optional': True}),
+ ("filternorm", "basic:Integer",
+ {'optional': True, 'defaults': "['1']"}),
+ ("interpolation", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplAxesImageProperties)")]
+
+ def __init__(self):
+ Mpl_AxesImageBaseProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ Mpl_AxesImageBaseProperties.compute(self)
+ if self.hasInputFromPort('origin'):
+ self.constructor_props['origin'] = self.getInputFromPort('origin')
+ if self.hasInputFromPort('resample'):
+ self.constructor_props['resample'] = self.getInputFromPort('resample')
+ if self.hasInputFromPort('norm'):
+ self.constructor_props['norm'] = self.getInputFromPort('norm')
+ if self.hasInputFromPort('cmap'):
+ self.constructor_props['cmap'] = self.getInputFromPort('cmap')
+ if self.hasInputFromPort('filterrad'):
+ self.constructor_props['filterrad'] = self.getInputFromPort('filterrad')
+ if self.hasInputFromPort('extent'):
+ self.props['extent'] = self.getInputFromPort('extent')
+ if self.hasInputFromPort('ax'):
+ self.constructor_props['ax'] = self.getInputFromPort('ax')
+ if self.hasInputFromPort('filternorm'):
+ self.constructor_props['filternorm'] = self.getInputFromPort('filternorm')
+ if self.hasInputFromPort('interpolation'):
+ self.constructor_props['interpolation'] = self.getInputFromPort('interpolation')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplNonUniformImageProperties(MplAxesImageProperties):
+ """None
+ """
+ _input_ports = [
+ ("norm", "basic:String",
+ {'optional': True}),
+ ("cmap", "basic:String",
+ {'optional': True}),
+ ("filternorm", "basic:String",
+ {'optional': True}),
+ ("ax", "basic:String",
+ {'optional': True}),
+ ("array", "basic:String",
+ {'optional': True}),
+ ("data", "basic:String",
+ {'optional': True, 'docstring': 'Set the grid for the pixel centers, and the pixel values.'}),
+ ("filterrad", "basic:String",
+ {'optional': True}),
+ ("interpolation", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplNonUniformImageProperties)")]
+
+ def __init__(self):
+ MplAxesImageProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplAxesImageProperties.compute(self)
+ if self.hasInputFromPort('norm'):
+ self.props['norm'] = self.getInputFromPort('norm')
+ if self.hasInputFromPort('cmap'):
+ self.props['cmap'] = self.getInputFromPort('cmap')
+ if self.hasInputFromPort('filternorm'):
+ self.props['filternorm'] = self.getInputFromPort('filternorm')
+ if self.hasInputFromPort('ax'):
+ self.constructor_props['ax'] = self.getInputFromPort('ax')
+ if self.hasInputFromPort('array'):
+ self.props['array'] = self.getInputFromPort('array')
+ if self.hasInputFromPort('data'):
+ self.props['data'] = self.getInputFromPort('data')
+ if self.hasInputFromPort('filterrad'):
+ self.props['filterrad'] = self.getInputFromPort('filterrad')
+ if self.hasInputFromPort('interpolation'):
+ self.props['interpolation'] = self.getInputFromPort('interpolation')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplBboxImageProperties(Mpl_AxesImageBaseProperties):
+ """The Image class whose size is determined by the given bbox.
+ """
+ _input_ports = [
+ ("origin", "basic:String",
+ {'optional': True}),
+ ("interp_at_native", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("resample", "basic:Boolean",
+ {'optional': True, 'defaults': "['False']"}),
+ ("cmap", "basic:String",
+ {'optional': True}),
+ ("filternorm", "basic:Integer",
+ {'optional': True, 'defaults': "['1']"}),
+ ("norm", "basic:String",
+ {'optional': True}),
+ ("interpolation", "basic:String",
+ {'optional': True}),
+ ("filterrad", "basic:Float",
+ {'optional': True, 'defaults': "['4.0']"}),
+ ("bbox", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplBboxImageProperties)")]
+
+ def __init__(self):
+ Mpl_AxesImageBaseProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ Mpl_AxesImageBaseProperties.compute(self)
+ if self.hasInputFromPort('origin'):
+ self.constructor_props['origin'] = self.getInputFromPort('origin')
+ if self.hasInputFromPort('interp_at_native'):
+ self.constructor_props['interp_at_native'] = self.getInputFromPort('interp_at_native')
+ if self.hasInputFromPort('resample'):
+ self.constructor_props['resample'] = self.getInputFromPort('resample')
+ if self.hasInputFromPort('cmap'):
+ self.constructor_props['cmap'] = self.getInputFromPort('cmap')
+ if self.hasInputFromPort('filternorm'):
+ self.constructor_props['filternorm'] = self.getInputFromPort('filternorm')
+ if self.hasInputFromPort('norm'):
+ self.constructor_props['norm'] = self.getInputFromPort('norm')
+ if self.hasInputFromPort('interpolation'):
+ self.constructor_props['interpolation'] = self.getInputFromPort('interpolation')
+ if self.hasInputFromPort('filterrad'):
+ self.constructor_props['filterrad'] = self.getInputFromPort('filterrad')
+ if self.hasInputFromPort('bbox'):
+ self.constructor_props['bbox'] = self.getInputFromPort('bbox')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplPcolorImageProperties(MplArtistProperties):
+ """
+ Make a pcolor-style plot with an irregular rectangular grid.
+
+ This uses a variation of the original irregular image code,
+ and it is used by pcolorfast for the corresponding grid type.
+
+ """
+ _input_ports = [
+ ("A", "basic:String",
+ {'optional': True}),
+ ("ax", "basic:String",
+ {'optional': True}),
+ ("cmap", "basic:String",
+ {'optional': True}),
+ ("x", "basic:String",
+ {'optional': True}),
+ ("y", "basic:String",
+ {'optional': True}),
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'Set the alpha value used for blending - not supported on all backends'}),
+ ("array", "basic:String",
+ {'optional': True}),
+ ("data", "basic:String",
+ {'optional': True}),
+ ("norm", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplPcolorImageProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('A'):
+ self.constructor_props['A'] = self.getInputFromPort('A')
+ if self.hasInputFromPort('ax'):
+ self.constructor_props['ax'] = self.getInputFromPort('ax')
+ if self.hasInputFromPort('cmap'):
+ self.constructor_props['cmap'] = self.getInputFromPort('cmap')
+ if self.hasInputFromPort('x'):
+ self.constructor_props['x'] = self.getInputFromPort('x')
+ if self.hasInputFromPort('y'):
+ self.constructor_props['y'] = self.getInputFromPort('y')
+ if self.hasInputFromPort('alpha'):
+ self.props['alpha'] = self.getInputFromPort('alpha')
+ if self.hasInputFromPort('array'):
+ self.props['array'] = self.getInputFromPort('array')
+ if self.hasInputFromPort('data'):
+ self.props['data'] = self.getInputFromPort('data')
+ if self.hasInputFromPort('norm'):
+ self.constructor_props['norm'] = self.getInputFromPort('norm')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplFigureImageProperties(MplArtistProperties):
+ """None
+ """
+ _input_ports = [
+ ("origin", "basic:String",
+ {'optional': True}),
+ ("offsetx", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("offsety", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("cmap", "basic:String",
+ {'optional': True}),
+ ("fig", "basic:String",
+ {'optional': True}),
+ ("array", "basic:String",
+ {'optional': True, 'docstring': 'Deprecated; use set_data for consistency with other image types.'}),
+ ("data", "basic:String",
+ {'optional': True, 'docstring': 'Set the image array.'}),
+ ("norm", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplFigureImageProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('origin'):
+ self.constructor_props['origin'] = self.getInputFromPort('origin')
+ if self.hasInputFromPort('offsetx'):
+ self.constructor_props['offsetx'] = self.getInputFromPort('offsetx')
+ if self.hasInputFromPort('offsety'):
+ self.constructor_props['offsety'] = self.getInputFromPort('offsety')
+ if self.hasInputFromPort('cmap'):
+ self.constructor_props['cmap'] = self.getInputFromPort('cmap')
+ if self.hasInputFromPort('fig'):
+ self.constructor_props['fig'] = self.getInputFromPort('fig')
+ if self.hasInputFromPort('array'):
+ self.props['array'] = self.getInputFromPort('array')
+ if self.hasInputFromPort('data'):
+ self.props['data'] = self.getInputFromPort('data')
+ if self.hasInputFromPort('norm'):
+ self.constructor_props['norm'] = self.getInputFromPort('norm')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplCollectionProperties(MplArtistProperties):
+ """
+ Base class for Collections. Must be subclassed to be usable.
+
+ All properties in a collection must be sequences or scalars;
+ if scalars, they will be converted to sequences. The
+ property of the ith element of the collection is::
+
+ prop[i % len(props)]
+
+ Keyword arguments and default values:
+
+ * *edgecolors*: None
+ * *facecolors*: None
+ * *linewidths*: None
+ * *antialiaseds*: None
+ * *offsets*: None
+ * *transOffset*: transforms.IdentityTransform()
+ * *offset_position*: 'screen' (default) or 'data'
+ * *norm*: None (optional for
+ :class:`matplotlib.cm.ScalarMappable`)
+ * *cmap*: None (optional for
+ :class:`matplotlib.cm.ScalarMappable`)
+ * *hatch*: None
+
+ *offsets* and *transOffset* are used to translate the patch after
+ rendering (default no offsets). If offset_position is 'screen'
+ (default) the offset is applied after the master transform has
+ been applied, that is, the offsets are in screen coordinates. If
+ offset_position is 'data', the offset is applied before the master
+ transform, i.e., the offsets are in data coordinates.
+
+ If any of *edgecolors*, *facecolors*, *linewidths*, *antialiaseds*
+ are None, they default to their :data:`matplotlib.rcParams` patch
+ setting, in sequence form.
+
+ The use of :class:`~matplotlib.cm.ScalarMappable` is optional. If
+ the :class:`~matplotlib.cm.ScalarMappable` matrix _A is not None
+ (ie a call to set_array has been made), at draw time a call to
+ scalar mappable will be made to set the face colors.
+
+ """
+ _input_ports = [
+ ("transOffset", "basic:String",
+ {'optional': True}),
+ ("edgecolor", "basic:List",
+ {'optional': True, 'docstring': "Set the edgecolor(s) of the collection. c can be a matplotlib color arg (all patches have same color), or a sequence of rgba tuples; if it is a sequence the patches will cycle through the sequence.\n\nIf c is 'face', the edge color will always be the same as the face color. If it is 'none', the patch boundary will not be drawn."}),
+ ("offset_position", "basic:String",
+ {'optional': True, 'docstring': "Set how offsets are applied. If offset_position is 'screen' (default) the offset is applied after the master transform has been applied, that is, the offsets are in screen coordinates. If offset_position is 'data', the offset is applied before the master transform, i.e., the offsets are in data coordinates."}),
+ ("edgecolors", "basic:String",
+ {'optional': True}),
+ ("facecolor", "basic:List",
+ {'optional': True, 'docstring': "Set the facecolor(s) of the collection. c can be a matplotlib color arg (all patches have same color), or a sequence of rgba tuples; if it is a sequence the patches will cycle through the sequence.\n\nIf c is 'none', the patch will not be filled."}),
+ ("linestyles", "basic:String",
+ {'optional': True, 'defaults': "['solid']"}),
+ ("offsetsSequence", "basic:List",
+ {'optional': True, 'docstring': 'Set the offsets for the collection. offsets can be a scalar or a sequence.'}),
+ ("offsetsScalar", "basic:Float",
+ {'docstring': 'Set the offsets for the collection. offsets can be a scalar or a sequence.', 'optional': True}),
+ ("color", "basic:List",
+ {'optional': True, 'docstring': 'Set both the edgecolor and the facecolor. .. seealso:\n\n:meth:`set_facecolor`, :meth:`set_edgecolor` For setting the edge or face color individually.'}),
+ ("pickradius", "basic:String",
+ {'optional': True}),
+ ("antialiaseds", "basic:String",
+ {'optional': True}),
+ ("linewidths", "basic:String",
+ {'optional': True}),
+ ("cmap", "basic:String",
+ {'optional': True}),
+ ("antialiasedSequence", "basic:List",
+ {'optional': True, 'docstring': 'Set the antialiasing state for rendering.'}),
+ ("antialiasedScalar", "basic:Boolean",
+ {'docstring': 'Set the antialiasing state for rendering.', 'optional': True}),
+ ("urls", "basic:String",
+ {'optional': True}),
+ ("hatch", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the hatching pattern\n\nhatch can be one of:\n\n/ - diagonal hatching \\ - back diagonal | - vertical - - horizontal + - crossed x - crossed diagonal o - small circle O - large circle . - dots * - stars\n\nLetters can be combined, in which case all the specified hatchings are done. If same letter repeats, it increases the density of hatching of that pattern.\n\nHatching is supported in the PostScript, PDF, [...]
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'Set the alpha tranparencies of the collection. alpha must be a float or None.'}),
+ ("paths", "basic:String",
+ {'optional': True}),
+ ("linewidthSequence", "basic:List",
+ {'optional': True, 'docstring': 'Set the linewidth(s) for the collection. lw can be a scalar or a sequence; if it is a sequence the patches will cycle through the sequence'}),
+ ("linewidthScalar", "basic:Float",
+ {'docstring': 'Set the linewidth(s) for the collection. lw can be a scalar or a sequence; if it is a sequence the patches will cycle through the sequence', 'optional': True}),
+ ("linestyle", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the linestyle(s) for the collection.', 'values': "[['solid', ('dashed', 'dashdot', 'dotted'), '(offset, on-off-dash-seq)']]", 'optional': True}),
+ ("facecolors", "basic:String",
+ {'optional': True}),
+ ("norm", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplCollectionProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('transOffset'):
+ self.constructor_props['transOffset'] = self.getInputFromPort('transOffset')
+ if self.hasInputFromPort('edgecolor'):
+ self.props['edgecolor'] = self.getInputFromPort('edgecolor')
+ if self.hasInputFromPort('offset_position'):
+ self.props['offset_position'] = self.getInputFromPort('offset_position')
+ if self.hasInputFromPort('edgecolors'):
+ self.constructor_props['edgecolors'] = self.getInputFromPort('edgecolors')
+ if self.hasInputFromPort('facecolor'):
+ self.props['facecolor'] = self.getInputFromPort('facecolor')
+ if self.hasInputFromPort('linestyles'):
+ self.constructor_props['linestyles'] = self.getInputFromPort('linestyles')
+ if self.hasInputFromPort('offsetsSequence'):
+ self.props['offsets'] = self.getInputFromPort('offsetsSequence')
+ elif self.hasInputFromPort('offsetsScalar'):
+ self.props['offsets'] = self.getInputFromPort('offsetsScalar')
+ if self.hasInputFromPort('color'):
+ self.props['color'] = self.getInputFromPort('color')
+ if self.hasInputFromPort('pickradius'):
+ self.props['pickradius'] = self.getInputFromPort('pickradius')
+ if self.hasInputFromPort('antialiaseds'):
+ self.constructor_props['antialiaseds'] = self.getInputFromPort('antialiaseds')
+ if self.hasInputFromPort('linewidths'):
+ self.constructor_props['linewidths'] = self.getInputFromPort('linewidths')
+ if self.hasInputFromPort('cmap'):
+ self.constructor_props['cmap'] = self.getInputFromPort('cmap')
+ if self.hasInputFromPort('antialiasedSequence'):
+ self.props['antialiased'] = self.getInputFromPort('antialiasedSequence')
+ elif self.hasInputFromPort('antialiasedScalar'):
+ self.props['antialiased'] = self.getInputFromPort('antialiasedScalar')
+ if self.hasInputFromPort('urls'):
+ self.props['urls'] = self.getInputFromPort('urls')
+ if self.hasInputFromPort('hatch'):
+ self.props['hatch'] = self.getInputFromPort('hatch')
+ if self.hasInputFromPort('alpha'):
+ self.props['alpha'] = self.getInputFromPort('alpha')
+ if self.hasInputFromPort('paths'):
+ self.props['paths'] = self.getInputFromPort('paths')
+ if self.hasInputFromPort('linewidthSequence'):
+ self.props['linewidth'] = self.getInputFromPort('linewidthSequence')
+ elif self.hasInputFromPort('linewidthScalar'):
+ self.props['linewidth'] = self.getInputFromPort('linewidthScalar')
+ if self.hasInputFromPort('linestyle'):
+ self.props['linestyle'] = self.getInputFromPort('linestyle')
+ if self.hasInputFromPort('facecolors'):
+ self.constructor_props['facecolors'] = self.getInputFromPort('facecolors')
+ if self.hasInputFromPort('norm'):
+ self.constructor_props['norm'] = self.getInputFromPort('norm')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplPathCollectionProperties(MplCollectionProperties):
+ """
+ This is the most basic :class:`Collection` subclass.
+
+ """
+ _input_ports = [
+ ("paths", "basic:String",
+ {'optional': True}),
+ ("sizes", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplPathCollectionProperties)")]
+
+ def __init__(self):
+ MplCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplCollectionProperties.compute(self)
+ if self.hasInputFromPort('paths'):
+ self.props['paths'] = self.getInputFromPort('paths')
+ if self.hasInputFromPort('sizes'):
+ self.constructor_props['sizes'] = self.getInputFromPort('sizes')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplPolyCollectionProperties(MplCollectionProperties):
+ """None
+ """
+ _input_ports = [
+ ("paths", "basic:String",
+ {'optional': True, 'docstring': 'This allows one to delay initialization of the vertices.'}),
+ ("verts", "basic:String",
+ {'optional': True, 'docstring': 'This allows one to delay initialization of the vertices.'}),
+ ("closed", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("sizes", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplPolyCollectionProperties)")]
+
+ def __init__(self):
+ MplCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplCollectionProperties.compute(self)
+ if self.hasInputFromPort('paths'):
+ self.props['paths'] = self.getInputFromPort('paths')
+ if self.hasInputFromPort('verts'):
+ self.props['verts'] = self.getInputFromPort('verts')
+ if self.hasInputFromPort('closed'):
+ self.constructor_props['closed'] = self.getInputFromPort('closed')
+ if self.hasInputFromPort('sizes'):
+ self.constructor_props['sizes'] = self.getInputFromPort('sizes')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplBrokenBarHCollectionProperties(MplPolyCollectionProperties):
+ """
+ A collection of horizontal bars spanning *yrange* with a sequence of
+ *xranges*.
+
+ """
+ _input_ports = [
+ ("xranges", "basic:String",
+ {'optional': True}),
+ ("yrange", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplBrokenBarHCollectionProperties)")]
+
+ def __init__(self):
+ MplPolyCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPolyCollectionProperties.compute(self)
+ if self.hasInputFromPort('xranges'):
+ self.constructor_props['xranges'] = self.getInputFromPort('xranges')
+ if self.hasInputFromPort('yrange'):
+ self.constructor_props['yrange'] = self.getInputFromPort('yrange')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplRegularPolyCollectionProperties(MplCollectionProperties):
+ """Draw a collection of regular polygons with *numsides*.
+ """
+ _input_ports = [
+ ("numsides", "basic:String",
+ {'optional': True}),
+ ("rotation", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("sizes", "basic:String",
+ {'optional': True, 'defaults': "['(1,)']"}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplRegularPolyCollectionProperties)")]
+
+ def __init__(self):
+ MplCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplCollectionProperties.compute(self)
+ if self.hasInputFromPort('numsides'):
+ self.constructor_props['numsides'] = self.getInputFromPort('numsides')
+ if self.hasInputFromPort('rotation'):
+ self.constructor_props['rotation'] = self.getInputFromPort('rotation')
+ if self.hasInputFromPort('sizes'):
+ self.constructor_props['sizes'] = self.getInputFromPort('sizes')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplStarPolygonCollectionProperties(MplRegularPolyCollectionProperties):
+ """
+ Draw a collection of regular stars with *numsides* points.
+ """
+ _input_ports = [
+ ("numsides", "basic:String",
+ {'optional': True}),
+ ("rotation", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("sizes", "basic:String",
+ {'optional': True, 'defaults': "['(1,)']"}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplStarPolygonCollectionProperties)")]
+
+ def __init__(self):
+ MplRegularPolyCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplRegularPolyCollectionProperties.compute(self)
+ if self.hasInputFromPort('numsides'):
+ self.constructor_props['numsides'] = self.getInputFromPort('numsides')
+ if self.hasInputFromPort('rotation'):
+ self.constructor_props['rotation'] = self.getInputFromPort('rotation')
+ if self.hasInputFromPort('sizes'):
+ self.constructor_props['sizes'] = self.getInputFromPort('sizes')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplAsteriskPolygonCollectionProperties(MplRegularPolyCollectionProperties):
+ """
+ Draw a collection of regular asterisks with *numsides* points.
+ """
+ _input_ports = [
+ ("numsides", "basic:String",
+ {'optional': True}),
+ ("rotation", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("sizes", "basic:String",
+ {'optional': True, 'defaults': "['(1,)']"}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplAsteriskPolygonCollectionProperties)")]
+
+ def __init__(self):
+ MplRegularPolyCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplRegularPolyCollectionProperties.compute(self)
+ if self.hasInputFromPort('numsides'):
+ self.constructor_props['numsides'] = self.getInputFromPort('numsides')
+ if self.hasInputFromPort('rotation'):
+ self.constructor_props['rotation'] = self.getInputFromPort('rotation')
+ if self.hasInputFromPort('sizes'):
+ self.constructor_props['sizes'] = self.getInputFromPort('sizes')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplLineCollectionProperties(MplCollectionProperties):
+ """
+ All parameters must be sequences or scalars; if scalars, they will
+ be converted to sequences. The property of the ith line
+ segment is::
+
+ prop[i % len(props)]
+
+ i.e., the properties cycle if the ``len`` of props is less than the
+ number of segments.
+
+ """
+ _input_ports = [
+ ("paths", "basic:String",
+ {'optional': True}),
+ ("antialiaseds", "basic:String",
+ {'optional': True}),
+ ("linestyles", "basic:String",
+ {'optional': True, 'defaults': "['solid']"}),
+ ("offsets", "basic:String",
+ {'optional': True}),
+ ("color", "basic:List",
+ {'optional': True, 'docstring': 'Set the color(s) of the line collection. c can be a matplotlib color arg (all patches have same color), or a sequence or rgba tuples; if it is a sequence the patches will cycle through the sequence.'}),
+ ("segments", "basic:String",
+ {'optional': True}),
+ ("linewidths", "basic:String",
+ {'optional': True}),
+ ("colors", "basic:String",
+ {'optional': True}),
+ ("cmap", "basic:String",
+ {'optional': True}),
+ ("transOffset", "basic:String",
+ {'optional': True}),
+ ("verts", "basic:String",
+ {'optional': True}),
+ ("pickradius", "basic:Integer",
+ {'optional': True, 'defaults': "['5']"}),
+ ("norm", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplLineCollectionProperties)")]
+
+ def __init__(self):
+ MplCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplCollectionProperties.compute(self)
+ if self.hasInputFromPort('paths'):
+ self.props['paths'] = self.getInputFromPort('paths')
+ if self.hasInputFromPort('antialiaseds'):
+ self.constructor_props['antialiaseds'] = self.getInputFromPort('antialiaseds')
+ if self.hasInputFromPort('linestyles'):
+ self.constructor_props['linestyles'] = self.getInputFromPort('linestyles')
+ if self.hasInputFromPort('offsets'):
+ self.constructor_props['offsets'] = self.getInputFromPort('offsets')
+ if self.hasInputFromPort('color'):
+ self.props['color'] = self.getInputFromPort('color')
+ if self.hasInputFromPort('segments'):
+ self.props['segments'] = self.getInputFromPort('segments')
+ if self.hasInputFromPort('linewidths'):
+ self.constructor_props['linewidths'] = self.getInputFromPort('linewidths')
+ if self.hasInputFromPort('colors'):
+ self.constructor_props['colors'] = self.getInputFromPort('colors')
+ if self.hasInputFromPort('cmap'):
+ self.constructor_props['cmap'] = self.getInputFromPort('cmap')
+ if self.hasInputFromPort('transOffset'):
+ self.constructor_props['transOffset'] = self.getInputFromPort('transOffset')
+ if self.hasInputFromPort('verts'):
+ self.props['verts'] = self.getInputFromPort('verts')
+ if self.hasInputFromPort('pickradius'):
+ self.constructor_props['pickradius'] = self.getInputFromPort('pickradius')
+ if self.hasInputFromPort('norm'):
+ self.constructor_props['norm'] = self.getInputFromPort('norm')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplCircleCollectionProperties(MplCollectionProperties):
+ """
+ A collection of circles, drawn using splines.
+
+ """
+ _input_ports = [
+ ("sizes", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplCircleCollectionProperties)")]
+
+ def __init__(self):
+ MplCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplCollectionProperties.compute(self)
+ if self.hasInputFromPort('sizes'):
+ self.constructor_props['sizes'] = self.getInputFromPort('sizes')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplEllipseCollectionProperties(MplCollectionProperties):
+ """
+ A collection of ellipses, drawn using splines.
+
+ """
+ _input_ports = [
+ ("units", "basic:String",
+ {'optional': True, 'defaults': "['points']"}),
+ ("widths", "basic:String",
+ {'optional': True}),
+ ("angles", "basic:String",
+ {'optional': True}),
+ ("heights", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplEllipseCollectionProperties)")]
+
+ def __init__(self):
+ MplCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplCollectionProperties.compute(self)
+ if self.hasInputFromPort('units'):
+ self.constructor_props['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('widths'):
+ self.constructor_props['widths'] = self.getInputFromPort('widths')
+ if self.hasInputFromPort('angles'):
+ self.constructor_props['angles'] = self.getInputFromPort('angles')
+ if self.hasInputFromPort('heights'):
+ self.constructor_props['heights'] = self.getInputFromPort('heights')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplPatchCollectionProperties(MplCollectionProperties):
+ """
+ A generic collection of patches.
+
+ This makes it easier to assign a color map to a heterogeneous
+ collection of patches.
+
+ This also may improve plotting speed, since PatchCollection will
+ draw faster than a large number of patches.
+
+ """
+ _input_ports = [
+ ("paths", "basic:String",
+ {'optional': True}),
+ ("patches", "basic:String",
+ {'optional': True}),
+ ("match_original", "basic:Boolean",
+ {'optional': True, 'defaults': "['False']"}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplPatchCollectionProperties)")]
+
+ def __init__(self):
+ MplCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplCollectionProperties.compute(self)
+ if self.hasInputFromPort('paths'):
+ self.props['paths'] = self.getInputFromPort('paths')
+ if self.hasInputFromPort('patches'):
+ self.constructor_props['patches'] = self.getInputFromPort('patches')
+ if self.hasInputFromPort('match_original'):
+ self.constructor_props['match_original'] = self.getInputFromPort('match_original')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplTriMeshProperties(MplCollectionProperties):
+ """
+ Class for the efficient drawing of a triangular mesh using
+ Gouraud shading.
+
+ A triangular mesh is a :class:`~matplotlib.tri.Triangulation`
+ object.
+
+ """
+ _input_ports = [
+ ("triangulation", "basic:String",
+ {'optional': True}),
+ ("paths", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplTriMeshProperties)")]
+
+ def __init__(self):
+ MplCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplCollectionProperties.compute(self)
+ if self.hasInputFromPort('triangulation'):
+ self.constructor_props['triangulation'] = self.getInputFromPort('triangulation')
+ if self.hasInputFromPort('paths'):
+ self.props['paths'] = self.getInputFromPort('paths')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplQuadMeshProperties(MplCollectionProperties):
+ """
+ Class for the efficient drawing of a quadrilateral mesh.
+
+ A quadrilateral mesh consists of a grid of vertices. The
+ dimensions of this array are (*meshWidth* + 1, *meshHeight* +
+ 1). Each vertex in the mesh has a different set of "mesh
+ coordinates" representing its position in the topology of the
+ mesh. For any values (*m*, *n*) such that 0 <= *m* <= *meshWidth*
+ and 0 <= *n* <= *meshHeight*, the vertices at mesh coordinates
+ (*m*, *n*), (*m*, *n* + 1), (*m* + 1, *n* + 1), and (*m* + 1, *n*)
+ form one of the quadrilaterals in the mesh. There are thus
+ (*meshWidth* * *meshHeight*) quadrilaterals in the mesh. The mesh
+ need not be regular and the polygons need not be convex.
+
+ A quadrilateral mesh is represented by a (2 x ((*meshWidth* + 1) *
+ (*meshHeight* + 1))) numpy array *coordinates*, where each row is
+ the *x* and *y* coordinates of one of the vertices. To define the
+ function that maps from a data point to its corresponding color,
+ use the :meth:`set_cmap` method. Each of these arrays is indexed in
+ row-major order by the mesh coordinates of the vertex (or the mesh
+ coordinates of the lower left vertex, in the case of the
+ colors).
+
+ For example, the first entry in *coordinates* is the
+ coordinates of the vertex at mesh coordinates (0, 0), then the one
+ at (0, 1), then at (0, 2) .. (0, meshWidth), (1, 0), (1, 1), and
+ so on.
+
+ *shading* may be 'flat', or 'gouraud'
+
+ """
+ _input_ports = [
+ ("paths", "basic:String",
+ {'optional': True}),
+ ("meshWidth", "basic:String",
+ {'optional': True}),
+ ("coordinates", "basic:String",
+ {'optional': True}),
+ ("antialiased", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("shading", "basic:String",
+ {'optional': True, 'defaults': "['flat']"}),
+ ("meshHeight", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplQuadMeshProperties)")]
+
+ def __init__(self):
+ MplCollectionProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplCollectionProperties.compute(self)
+ if self.hasInputFromPort('paths'):
+ self.props['paths'] = self.getInputFromPort('paths')
+ if self.hasInputFromPort('meshWidth'):
+ self.constructor_props['meshWidth'] = self.getInputFromPort('meshWidth')
+ if self.hasInputFromPort('coordinates'):
+ self.constructor_props['coordinates'] = self.getInputFromPort('coordinates')
+ if self.hasInputFromPort('antialiased'):
+ self.constructor_props['antialiased'] = self.getInputFromPort('antialiased')
+ if self.hasInputFromPort('shading'):
+ self.constructor_props['shading'] = self.getInputFromPort('shading')
+ if self.hasInputFromPort('meshHeight'):
+ self.constructor_props['meshHeight'] = self.getInputFromPort('meshHeight')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplPatchProperties(MplArtistProperties):
+ """
+ A patch is a 2D artist with a face color and an edge color.
+
+ If any of *edgecolor*, *facecolor*, *linewidth*, or *antialiased*
+ are *None*, they default to their rc params setting.
+
+ """
+ _input_ports = [
+ ("edgecolor", "basic:Color",
+ {'optional': True, 'docstring': 'Set the patch edge color'}),
+ ("facecolor", "basic:Color",
+ {'optional': True, 'docstring': 'Set the patch face color'}),
+ ("path_effects", "basic:String",
+ {'optional': True, 'docstring': 'set path_effects, which should be a list of instances of matplotlib.patheffect._Base class or its derivatives.'}),
+ ("color", "basic:Color",
+ {'optional': True, 'docstring': 'Set both the edgecolor and the facecolor. .. seealso:\n\n:meth:`set_facecolor`, :meth:`set_edgecolor` For setting the edge or face color individually.'}),
+ ("antialiased", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether to use antialiased rendering'}),
+ ("hatch", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the hatching pattern\n\nhatch can be one of:\n\n/ - diagonal hatching \\ - back diagonal | - vertical - - horizontal + - crossed x - crossed diagonal o - small circle O - large circle . - dots * - stars\n\nLetters can be combined, in which case all the specified hatchings are done. If same letter repeats, it increases the density of hatching of that pattern.\n\nHatching is supported in the PostScript, PDF, [...]
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'Set the alpha tranparency of the patch.'}),
+ ("linewidth", "basic:Float",
+ {'optional': True, 'docstring': 'Set the patch linewidth in points'}),
+ ("linestyle", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the patch linestyle', 'values': "[['solid', 'dashed', 'dashdot', 'dotted']]", 'optional': True}),
+ ("fill", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether to fill the patch'}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplPatchProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('edgecolor'):
+ self.props['edgecolor'] = self.getInputFromPort('edgecolor')
+ self.props['edgecolor'] = translate_color(self.props['edgecolor'])
+ if self.hasInputFromPort('facecolor'):
+ self.props['facecolor'] = self.getInputFromPort('facecolor')
+ self.props['facecolor'] = translate_color(self.props['facecolor'])
+ if self.hasInputFromPort('path_effects'):
+ self.props['path_effects'] = self.getInputFromPort('path_effects')
+ if self.hasInputFromPort('color'):
+ self.props['color'] = self.getInputFromPort('color')
+ self.props['color'] = translate_color(self.props['color'])
+ if self.hasInputFromPort('antialiased'):
+ self.props['antialiased'] = self.getInputFromPort('antialiased')
+ if self.hasInputFromPort('hatch'):
+ self.props['hatch'] = self.getInputFromPort('hatch')
+ if self.hasInputFromPort('alpha'):
+ self.props['alpha'] = self.getInputFromPort('alpha')
+ if self.hasInputFromPort('linewidth'):
+ self.props['linewidth'] = self.getInputFromPort('linewidth')
+ if self.hasInputFromPort('linestyle'):
+ self.props['linestyle'] = self.getInputFromPort('linestyle')
+ if self.hasInputFromPort('fill'):
+ self.props['fill'] = self.getInputFromPort('fill')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplShadowProperties(MplPatchProperties):
+ """None
+ """
+ _input_ports = [
+ ("patch", "basic:String",
+ {'optional': True}),
+ ("props", "basic:String",
+ {'optional': True}),
+ ("oy", "basic:String",
+ {'optional': True}),
+ ("ox", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplShadowProperties)")]
+
+ def __init__(self):
+ MplPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPatchProperties.compute(self)
+ if self.hasInputFromPort('patch'):
+ self.constructor_props['patch'] = self.getInputFromPort('patch')
+ if self.hasInputFromPort('props'):
+ self.constructor_props['props'] = self.getInputFromPort('props')
+ if self.hasInputFromPort('oy'):
+ self.constructor_props['oy'] = self.getInputFromPort('oy')
+ if self.hasInputFromPort('ox'):
+ self.constructor_props['ox'] = self.getInputFromPort('ox')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplRectangleProperties(MplPatchProperties):
+ """
+ Draw a rectangle with lower left at *xy* = (*x*, *y*) with
+ specified *width* and *height*.
+
+ """
+ _input_ports = [
+ ("bounds", "basic:String",
+ {'optional': True, 'docstring': 'Set the bounds of the rectangle: l,b,w,h'}),
+ ("height", "basic:Float",
+ {'optional': True, 'docstring': 'Set the width rectangle'}),
+ ("width", "basic:Float",
+ {'optional': True, 'docstring': 'Set the width rectangle'}),
+ ("xy", "basic:List",
+ {'optional': True, 'docstring': 'Set the left and bottom coords of the rectangle'}),
+ ("y", "basic:Float",
+ {'optional': True, 'docstring': 'Set the bottom coord of the rectangle'}),
+ ("x", "basic:Float",
+ {'optional': True, 'docstring': 'Set the left coord of the rectangle'}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplRectangleProperties)")]
+
+ def __init__(self):
+ MplPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPatchProperties.compute(self)
+ if self.hasInputFromPort('bounds'):
+ self.props['bounds'] = self.getInputFromPort('bounds')
+ if self.hasInputFromPort('height'):
+ self.props['height'] = self.getInputFromPort('height')
+ if self.hasInputFromPort('width'):
+ self.props['width'] = self.getInputFromPort('width')
+ if self.hasInputFromPort('xy'):
+ self.props['xy'] = self.getInputFromPort('xy')
+ if self.hasInputFromPort('y'):
+ self.props['y'] = self.getInputFromPort('y')
+ if self.hasInputFromPort('x'):
+ self.props['x'] = self.getInputFromPort('x')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplRegularPolygonProperties(MplPatchProperties):
+ """
+ A regular polygon patch.
+
+ """
+ _input_ports = [
+ ("xy", "basic:String",
+ {'optional': True, 'docstring': 'A length 2 tuple (x, y) of the center.'}),
+ ("radius", "basic:Integer",
+ {'optional': True, 'docstring': 'The distance from the center to each of the vertices.', 'defaults': "['5']"}),
+ ("orientation", "basic:Integer",
+ {'optional': True, 'docstring': 'rotates the polygon (in radians).', 'defaults': "['0']"}),
+ ("numVertices", "basic:String",
+ {'optional': True, 'docstring': 'the number of vertices.'}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplRegularPolygonProperties)")]
+
+ def __init__(self):
+ MplPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPatchProperties.compute(self)
+ if self.hasInputFromPort('xy'):
+ self.constructor_props['xy'] = self.getInputFromPort('xy')
+ if self.hasInputFromPort('radius'):
+ self.constructor_props['radius'] = self.getInputFromPort('radius')
+ if self.hasInputFromPort('orientation'):
+ self.constructor_props['orientation'] = self.getInputFromPort('orientation')
+ if self.hasInputFromPort('numVertices'):
+ self.constructor_props['numVertices'] = self.getInputFromPort('numVertices')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplCirclePolygonProperties(MplRegularPolygonProperties):
+ """
+ A polygon-approximation of a circle patch.
+
+ """
+ _input_ports = [
+ ("radius", "basic:Integer",
+ {'optional': True, 'defaults': "['5']"}),
+ ("xy", "basic:String",
+ {'optional': True}),
+ ("resolution", "basic:Integer",
+ {'optional': True, 'defaults': "['20']"}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplCirclePolygonProperties)")]
+
+ def __init__(self):
+ MplRegularPolygonProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplRegularPolygonProperties.compute(self)
+ if self.hasInputFromPort('radius'):
+ self.constructor_props['radius'] = self.getInputFromPort('radius')
+ if self.hasInputFromPort('xy'):
+ self.constructor_props['xy'] = self.getInputFromPort('xy')
+ if self.hasInputFromPort('resolution'):
+ self.constructor_props['resolution'] = self.getInputFromPort('resolution')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplPathPatchProperties(MplPatchProperties):
+ """
+ A general polycurve path patch.
+
+ """
+ _input_ports = [
+ ("path", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplPathPatchProperties)")]
+
+ def __init__(self):
+ MplPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPatchProperties.compute(self)
+ if self.hasInputFromPort('path'):
+ self.constructor_props['path'] = self.getInputFromPort('path')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplPolygonProperties(MplPatchProperties):
+ """
+ A general polygon patch.
+
+ """
+ _input_ports = [
+ ("xy", "basic:String",
+ {'optional': True}),
+ ("closed", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplPolygonProperties)")]
+
+ def __init__(self):
+ MplPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPatchProperties.compute(self)
+ if self.hasInputFromPort('xy'):
+ self.props['xy'] = self.getInputFromPort('xy')
+ if self.hasInputFromPort('closed'):
+ self.props['closed'] = self.getInputFromPort('closed')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplFancyArrowProperties(MplPolygonProperties):
+ """
+ Like Arrow, but lets you set head width and head height independently.
+
+ """
+ _input_ports = [
+ ("length_includes_head", "basic:Boolean",
+ {'optional': True, 'defaults': "['False']"}),
+ ("head_length", "basic:String",
+ {'optional': True}),
+ ("head_width", "basic:String",
+ {'optional': True}),
+ ("width", "basic:Float",
+ {'optional': True, 'defaults': "['0.001']"}),
+ ("shape", "basic:String",
+ {'optional': True, 'defaults': "['full']"}),
+ ("dx", "basic:String",
+ {'optional': True}),
+ ("dy", "basic:String",
+ {'optional': True}),
+ ("y", "basic:String",
+ {'optional': True}),
+ ("x", "basic:String",
+ {'optional': True}),
+ ("head_starts_at_zero", "basic:Boolean",
+ {'optional': True, 'defaults': "['False']"}),
+ ("overhang", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplFancyArrowProperties)")]
+
+ def __init__(self):
+ MplPolygonProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPolygonProperties.compute(self)
+ if self.hasInputFromPort('length_includes_head'):
+ self.constructor_props['length_includes_head'] = self.getInputFromPort('length_includes_head')
+ if self.hasInputFromPort('head_length'):
+ self.constructor_props['head_length'] = self.getInputFromPort('head_length')
+ if self.hasInputFromPort('head_width'):
+ self.constructor_props['head_width'] = self.getInputFromPort('head_width')
+ if self.hasInputFromPort('width'):
+ self.constructor_props['width'] = self.getInputFromPort('width')
+ if self.hasInputFromPort('shape'):
+ self.constructor_props['shape'] = self.getInputFromPort('shape')
+ if self.hasInputFromPort('dx'):
+ self.constructor_props['dx'] = self.getInputFromPort('dx')
+ if self.hasInputFromPort('dy'):
+ self.constructor_props['dy'] = self.getInputFromPort('dy')
+ if self.hasInputFromPort('y'):
+ self.constructor_props['y'] = self.getInputFromPort('y')
+ if self.hasInputFromPort('x'):
+ self.constructor_props['x'] = self.getInputFromPort('x')
+ if self.hasInputFromPort('head_starts_at_zero'):
+ self.constructor_props['head_starts_at_zero'] = self.getInputFromPort('head_starts_at_zero')
+ if self.hasInputFromPort('overhang'):
+ self.constructor_props['overhang'] = self.getInputFromPort('overhang')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplWedgeProperties(MplPatchProperties):
+ """
+ Wedge shaped patch.
+
+ """
+ _input_ports = [
+ ("theta2", "basic:String",
+ {'optional': True}),
+ ("width", "basic:String",
+ {'optional': True}),
+ ("r", "basic:String",
+ {'optional': True}),
+ ("theta1", "basic:String",
+ {'optional': True}),
+ ("center", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplWedgeProperties)")]
+
+ def __init__(self):
+ MplPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPatchProperties.compute(self)
+ if self.hasInputFromPort('theta2'):
+ self.constructor_props['theta2'] = self.getInputFromPort('theta2')
+ if self.hasInputFromPort('width'):
+ self.constructor_props['width'] = self.getInputFromPort('width')
+ if self.hasInputFromPort('r'):
+ self.constructor_props['r'] = self.getInputFromPort('r')
+ if self.hasInputFromPort('theta1'):
+ self.constructor_props['theta1'] = self.getInputFromPort('theta1')
+ if self.hasInputFromPort('center'):
+ self.constructor_props['center'] = self.getInputFromPort('center')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplArrowProperties(MplPatchProperties):
+ """
+ An arrow patch.
+
+ """
+ _input_ports = [
+ ("y", "basic:String",
+ {'optional': True}),
+ ("x", "basic:String",
+ {'optional': True}),
+ ("dy", "basic:String",
+ {'optional': True}),
+ ("dx", "basic:String",
+ {'optional': True}),
+ ("width", "basic:Float",
+ {'optional': True, 'defaults': "['1.0']"}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplArrowProperties)")]
+
+ def __init__(self):
+ MplPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPatchProperties.compute(self)
+ if self.hasInputFromPort('y'):
+ self.constructor_props['y'] = self.getInputFromPort('y')
+ if self.hasInputFromPort('x'):
+ self.constructor_props['x'] = self.getInputFromPort('x')
+ if self.hasInputFromPort('dy'):
+ self.constructor_props['dy'] = self.getInputFromPort('dy')
+ if self.hasInputFromPort('dx'):
+ self.constructor_props['dx'] = self.getInputFromPort('dx')
+ if self.hasInputFromPort('width'):
+ self.constructor_props['width'] = self.getInputFromPort('width')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplYAArrowProperties(MplPatchProperties):
+ """
+ Yet another arrow class.
+
+ This is an arrow that is defined in display space and has a tip at
+ *x1*, *y1* and a base at *x2*, *y2*.
+
+ """
+ _input_ports = [
+ ("xytip", "basic:String",
+ {'optional': True, 'docstring': '(x, y) location of arrow tip'}),
+ ("headwidth", "basic:Integer",
+ {'optional': True, 'docstring': 'The width of the base of the arrow head in points', 'defaults': "['12']"}),
+ ("frac", "basic:Float",
+ {'optional': True, 'docstring': 'The fraction of the arrow length occupied by the head', 'defaults': "['0.1']"}),
+ ("figure", "basic:String",
+ {'optional': True, 'docstring': 'The :class:`~matplotlib.figure.Figure` instance (fig.dpi)'}),
+ ("xybase", "basic:String",
+ {'optional': True, 'docstring': '(x, y) location the arrow base mid point'}),
+ ("width", "basic:Integer",
+ {'optional': True, 'docstring': 'The width of the arrow in points', 'defaults': "['4']"}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplYAArrowProperties)")]
+
+ def __init__(self):
+ MplPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPatchProperties.compute(self)
+ if self.hasInputFromPort('xytip'):
+ self.constructor_props['xytip'] = self.getInputFromPort('xytip')
+ if self.hasInputFromPort('headwidth'):
+ self.constructor_props['headwidth'] = self.getInputFromPort('headwidth')
+ if self.hasInputFromPort('frac'):
+ self.constructor_props['frac'] = self.getInputFromPort('frac')
+ if self.hasInputFromPort('figure'):
+ self.constructor_props['figure'] = self.getInputFromPort('figure')
+ if self.hasInputFromPort('xybase'):
+ self.constructor_props['xybase'] = self.getInputFromPort('xybase')
+ if self.hasInputFromPort('width'):
+ self.constructor_props['width'] = self.getInputFromPort('width')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplEllipseProperties(MplPatchProperties):
+ """
+ A scale-free ellipse.
+
+ """
+ _input_ports = [
+ ("width", "basic:String",
+ {'optional': True}),
+ ("xy", "basic:String",
+ {'optional': True}),
+ ("angle", "basic:Float",
+ {'optional': True, 'defaults': "['0.0']"}),
+ ("height", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplEllipseProperties)")]
+
+ def __init__(self):
+ MplPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPatchProperties.compute(self)
+ if self.hasInputFromPort('width'):
+ self.constructor_props['width'] = self.getInputFromPort('width')
+ if self.hasInputFromPort('xy'):
+ self.constructor_props['xy'] = self.getInputFromPort('xy')
+ if self.hasInputFromPort('angle'):
+ self.constructor_props['angle'] = self.getInputFromPort('angle')
+ if self.hasInputFromPort('height'):
+ self.constructor_props['height'] = self.getInputFromPort('height')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplCircleProperties(MplEllipseProperties):
+ """
+ A circle patch.
+
+ """
+ _input_ports = [
+ ("xy", "basic:String",
+ {'optional': True}),
+ ("radius", "basic:Float",
+ {'optional': True, 'docstring': 'Set the radius of the circle'}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplCircleProperties)")]
+
+ def __init__(self):
+ MplEllipseProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplEllipseProperties.compute(self)
+ if self.hasInputFromPort('xy'):
+ self.constructor_props['xy'] = self.getInputFromPort('xy')
+ if self.hasInputFromPort('radius'):
+ self.props['radius'] = self.getInputFromPort('radius')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplArcProperties(MplEllipseProperties):
+ """
+ An elliptical arc. Because it performs various optimizations, it
+ can not be filled.
+
+ The arc must be used in an :class:`~matplotlib.axes.Axes`
+ instance---it can not be added directly to a
+ :class:`~matplotlib.figure.Figure`---because it is optimized to
+ only render the segments that are inside the axes bounding box
+ with high resolution.
+
+ """
+ _input_ports = [
+ ("theta2", "basic:Float",
+ {'optional': True, 'defaults': "['360.0']"}),
+ ("theta1", "basic:Float",
+ {'optional': True, 'defaults': "['0.0']"}),
+ ("angle", "basic:Float",
+ {'optional': True, 'defaults': "['0.0']"}),
+ ("height", "basic:String",
+ {'optional': True}),
+ ("width", "basic:String",
+ {'optional': True}),
+ ("xy", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplArcProperties)")]
+
+ def __init__(self):
+ MplEllipseProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplEllipseProperties.compute(self)
+ if self.hasInputFromPort('theta2'):
+ self.constructor_props['theta2'] = self.getInputFromPort('theta2')
+ if self.hasInputFromPort('theta1'):
+ self.constructor_props['theta1'] = self.getInputFromPort('theta1')
+ if self.hasInputFromPort('angle'):
+ self.constructor_props['angle'] = self.getInputFromPort('angle')
+ if self.hasInputFromPort('height'):
+ self.constructor_props['height'] = self.getInputFromPort('height')
+ if self.hasInputFromPort('width'):
+ self.constructor_props['width'] = self.getInputFromPort('width')
+ if self.hasInputFromPort('xy'):
+ self.constructor_props['xy'] = self.getInputFromPort('xy')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplFancyBboxPatchProperties(MplPatchProperties):
+ """
+ Draw a fancy box around a rectangle with lower left at *xy*=(*x*,
+ *y*) with specified width and height.
+
+ :class:`FancyBboxPatch` class is similar to :class:`Rectangle`
+ class, but it draws a fancy box around the rectangle. The
+ transformation of the rectangle box to the fancy box is delegated
+ to the :class:`BoxTransmuterBase` and its derived classes.
+
+
+ """
+ _input_ports = [
+ ("mutation_scale", "basic:Float",
+ {'optional': True, 'docstring': 'Set the mutation scale.'}),
+ ("bbox_transmuter", "basic:String",
+ {'optional': True}),
+ ("bounds", "basic:String",
+ {'optional': True, 'docstring': 'Set the bounds of the rectangle: l,b,w,h'}),
+ ("height", "basic:Float",
+ {'optional': True, 'docstring': 'Set the width rectangle'}),
+ ("width", "basic:Float",
+ {'optional': True, 'docstring': 'Set the width rectangle'}),
+ ("xy", "basic:String",
+ {'optional': True}),
+ ("boxstyle", "basic:String",
+ {'optional': True, 'docstring': 'Set the box style.\n\nboxstyle can be a string with boxstyle name with optional comma-separated attributes. Alternatively, the attrs can be provided as keywords:\n\nset_boxstyle("round,pad=0.2") set_boxstyle("round", pad=0.2)\n\nOld attrs simply are forgotten.\n\nWithout argument (or with boxstyle = None), it returns available box styles.'}),
+ ("mutation_aspect", "basic:Float",
+ {'optional': True, 'docstring': 'Set the aspect ratio of the bbox mutation.'}),
+ ("y", "basic:Float",
+ {'optional': True, 'docstring': 'Set the bottom coord of the rectangle'}),
+ ("x", "basic:Float",
+ {'optional': True, 'docstring': 'Set the left coord of the rectangle'}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplFancyBboxPatchProperties)")]
+
+ def __init__(self):
+ MplPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPatchProperties.compute(self)
+ if self.hasInputFromPort('mutation_scale'):
+ self.props['mutation_scale'] = self.getInputFromPort('mutation_scale')
+ if self.hasInputFromPort('bbox_transmuter'):
+ self.constructor_props['bbox_transmuter'] = self.getInputFromPort('bbox_transmuter')
+ if self.hasInputFromPort('bounds'):
+ self.props['bounds'] = self.getInputFromPort('bounds')
+ if self.hasInputFromPort('height'):
+ self.props['height'] = self.getInputFromPort('height')
+ if self.hasInputFromPort('width'):
+ self.props['width'] = self.getInputFromPort('width')
+ if self.hasInputFromPort('xy'):
+ self.constructor_props['xy'] = self.getInputFromPort('xy')
+ if self.hasInputFromPort('boxstyle'):
+ self.props['boxstyle'] = self.getInputFromPort('boxstyle')
+ if self.hasInputFromPort('mutation_aspect'):
+ self.props['mutation_aspect'] = self.getInputFromPort('mutation_aspect')
+ if self.hasInputFromPort('y'):
+ self.props['y'] = self.getInputFromPort('y')
+ if self.hasInputFromPort('x'):
+ self.props['x'] = self.getInputFromPort('x')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplFancyArrowPatchProperties(MplPatchProperties):
+ """
+ A fancy arrow patch. It draws an arrow using the :class:ArrowStyle.
+
+ """
+ _input_ports = [
+ ("connectionstyle", "basic:String",
+ {'optional': True, 'docstring': 'Set the connection style.\n\nOld attrs simply are forgotten.\n\nWithout argument (or with connectionstyle=None), return available styles as a list of strings.'}),
+ ("mutation_scale", "basic:Float",
+ {'optional': True, 'docstring': 'Set the mutation scale.'}),
+ ("arrowstyle", "basic:String",
+ {'optional': True, 'docstring': 'Set the arrow style.\n\nOld attrs simply are forgotten.\n\nWithout argument (or with arrowstyle=None), return available box styles as a list of strings.'}),
+ ("arrow_transmuter", "basic:String",
+ {'optional': True}),
+ ("positions", "basic:String",
+ {'optional': True}),
+ ("shrinkA", "basic:Float",
+ {'optional': True, 'defaults': "['2.0']"}),
+ ("posB", "basic:String",
+ {'optional': True}),
+ ("dpi_cor", "basic:String",
+ {'optional': True, 'docstring': 'dpi_cor is currently used for linewidth-related things and shink factor. Mutation scale is not affected by this.'}),
+ ("connector", "basic:String",
+ {'optional': True}),
+ ("path", "basic:String",
+ {'optional': True}),
+ ("shrinkB", "basic:Float",
+ {'optional': True, 'defaults': "['2.0']"}),
+ ("mutation_aspect", "basic:Float",
+ {'optional': True, 'docstring': 'Set the aspect ratio of the bbox mutation.'}),
+ ("patchA", "basic:String",
+ {'optional': True, 'docstring': 'set the begin patch.'}),
+ ("patchB", "basic:String",
+ {'optional': True, 'docstring': 'set the begin patch'}),
+ ("posA", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplFancyArrowPatchProperties)")]
+
+ def __init__(self):
+ MplPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplPatchProperties.compute(self)
+ if self.hasInputFromPort('connectionstyle'):
+ self.props['connectionstyle'] = self.getInputFromPort('connectionstyle')
+ if self.hasInputFromPort('mutation_scale'):
+ self.props['mutation_scale'] = self.getInputFromPort('mutation_scale')
+ if self.hasInputFromPort('arrowstyle'):
+ self.props['arrowstyle'] = self.getInputFromPort('arrowstyle')
+ if self.hasInputFromPort('arrow_transmuter'):
+ self.constructor_props['arrow_transmuter'] = self.getInputFromPort('arrow_transmuter')
+ if self.hasInputFromPort('positions'):
+ self.props['positions'] = self.getInputFromPort('positions')
+ if self.hasInputFromPort('shrinkA'):
+ self.constructor_props['shrinkA'] = self.getInputFromPort('shrinkA')
+ if self.hasInputFromPort('posB'):
+ self.constructor_props['posB'] = self.getInputFromPort('posB')
+ if self.hasInputFromPort('dpi_cor'):
+ self.props['dpi_cor'] = self.getInputFromPort('dpi_cor')
+ if self.hasInputFromPort('connector'):
+ self.constructor_props['connector'] = self.getInputFromPort('connector')
+ if self.hasInputFromPort('path'):
+ self.constructor_props['path'] = self.getInputFromPort('path')
+ if self.hasInputFromPort('shrinkB'):
+ self.constructor_props['shrinkB'] = self.getInputFromPort('shrinkB')
+ if self.hasInputFromPort('mutation_aspect'):
+ self.props['mutation_aspect'] = self.getInputFromPort('mutation_aspect')
+ if self.hasInputFromPort('patchA'):
+ self.props['patchA'] = self.getInputFromPort('patchA')
+ if self.hasInputFromPort('patchB'):
+ self.props['patchB'] = self.getInputFromPort('patchB')
+ if self.hasInputFromPort('posA'):
+ self.constructor_props['posA'] = self.getInputFromPort('posA')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplConnectionPatchProperties(MplFancyArrowPatchProperties):
+ """
+ A :class:`~matplotlib.patches.ConnectionPatch` class is to make
+ connecting lines between two points (possibly in different axes).
+
+ """
+ _input_ports = [
+ ("connectionstyle", "basic:String",
+ {'optional': True, 'docstring': 'the connection style', 'defaults': "['arc3']"}),
+ ("coordsA", "basic:String",
+ {'entry_types': "['enum']", 'values': "[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]", 'optional': True}),
+ ("arrowstyle", "basic:String",
+ {'optional': True, 'docstring': 'the arrow style', 'defaults': "['-']"}),
+ ("clip_on", "basic:Boolean",
+ {'optional': True, 'defaults': "['False']"}),
+ ("arrow_transmuter", "basic:String",
+ {'optional': True}),
+ ("axesA", "basic:String",
+ {'optional': True}),
+ ("axesB", "basic:String",
+ {'optional': True}),
+ ("annotation_clip", "basic:String",
+ {'optional': True, 'docstring': 'set annotation_clip attribute.\n\nNone: the self.xy will be checked only if xycoords is "data"'}),
+ ("dpi_cor", "basic:Float",
+ {'optional': True, 'defaults': "['1.0']"}),
+ ("connector", "basic:String",
+ {'optional': True}),
+ ("xyA", "basic:String",
+ {'optional': True}),
+ ("xyB", "basic:String",
+ {'optional': True}),
+ ("relpos", "basic:String",
+ {'optional': True, 'docstring': 'default is (0.5, 0.5)', 'defaults': "['(0.5']"}),
+ ("shrinkB", "basic:Float",
+ {'optional': True, 'docstring': 'default is 2 points', 'defaults': "['2']"}),
+ ("shrinkA", "basic:Float",
+ {'optional': True, 'docstring': 'default is 2 points', 'defaults': "['2']"}),
+ ("mutation_aspect", "basic:Integer",
+ {'optional': True, 'docstring': 'default is 1.', 'defaults': "['1']"}),
+ ("mutation_scale", "basic:String",
+ {'optional': True, 'docstring': 'default is text size (in points)', 'defaults': "['text']"}),
+ ("patchA", "basic:String",
+ {'optional': True, 'docstring': 'default is bounding box of the text', 'defaults': "['bounding']"}),
+ ("patchB", "basic:String",
+ {'optional': True, 'docstring': 'default is None'}),
+ ("coordsB", "basic:String",
+ {'entry_types': "['enum']", 'values': "[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]", 'optional': True}),
+ ("?", "basic:String",
+ {'optional': True, 'docstring': 'any key for :class:`matplotlib.patches.PathPatch`'}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplConnectionPatchProperties)")]
+
+ def __init__(self):
+ MplFancyArrowPatchProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplFancyArrowPatchProperties.compute(self)
+ if self.hasInputFromPort('connectionstyle'):
+ self.constructor_props['connectionstyle'] = self.getInputFromPort('connectionstyle')
+ if self.hasInputFromPort('coordsA'):
+ self.constructor_props['coordsA'] = self.getInputFromPort('coordsA')
+ if self.hasInputFromPort('arrowstyle'):
+ self.constructor_props['arrowstyle'] = self.getInputFromPort('arrowstyle')
+ if self.hasInputFromPort('clip_on'):
+ self.constructor_props['clip_on'] = self.getInputFromPort('clip_on')
+ if self.hasInputFromPort('arrow_transmuter'):
+ self.constructor_props['arrow_transmuter'] = self.getInputFromPort('arrow_transmuter')
+ if self.hasInputFromPort('axesA'):
+ self.constructor_props['axesA'] = self.getInputFromPort('axesA')
+ if self.hasInputFromPort('axesB'):
+ self.constructor_props['axesB'] = self.getInputFromPort('axesB')
+ if self.hasInputFromPort('annotation_clip'):
+ self.props['annotation_clip'] = self.getInputFromPort('annotation_clip')
+ if self.hasInputFromPort('dpi_cor'):
+ self.constructor_props['dpi_cor'] = self.getInputFromPort('dpi_cor')
+ if self.hasInputFromPort('connector'):
+ self.constructor_props['connector'] = self.getInputFromPort('connector')
+ if self.hasInputFromPort('xyA'):
+ self.constructor_props['xyA'] = self.getInputFromPort('xyA')
+ if self.hasInputFromPort('xyB'):
+ self.constructor_props['xyB'] = self.getInputFromPort('xyB')
+ if self.hasInputFromPort('relpos'):
+ self.constructor_props['relpos'] = self.getInputFromPort('relpos')
+ if self.hasInputFromPort('shrinkB'):
+ self.constructor_props['shrinkB'] = self.getInputFromPort('shrinkB')
+ if self.hasInputFromPort('shrinkA'):
+ self.constructor_props['shrinkA'] = self.getInputFromPort('shrinkA')
+ if self.hasInputFromPort('mutation_aspect'):
+ self.constructor_props['mutation_aspect'] = self.getInputFromPort('mutation_aspect')
+ if self.hasInputFromPort('mutation_scale'):
+ self.constructor_props['mutation_scale'] = self.getInputFromPort('mutation_scale')
+ if self.hasInputFromPort('patchA'):
+ self.constructor_props['patchA'] = self.getInputFromPort('patchA')
+ if self.hasInputFromPort('patchB'):
+ self.constructor_props['patchB'] = self.getInputFromPort('patchB')
+ if self.hasInputFromPort('coordsB'):
+ self.constructor_props['coordsB'] = self.getInputFromPort('coordsB')
+ if self.hasInputFromPort('?'):
+ self.constructor_props['?'] = self.getInputFromPort('?')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplLine2DProperties(MplArtistProperties):
+ """
+ A line - the line can have both a solid linestyle connecting all
+ the vertices, and a marker at each vertex. Additionally, the
+ drawing of the solid line is influenced by the drawstyle, eg one
+ can create "stepped" lines in various styles.
+
+
+
+ """
+ _input_ports = [
+ ("picker", "basic:Float",
+ {'optional': True, 'docstring': 'Sets the event picker details for the line.'}),
+ ("dash_capstyle", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the cap style for dashed linestyles', 'values': "[['butt', 'round', 'projecting']]", 'optional': True}),
+ ("color", "basic:Color",
+ {'optional': True, 'docstring': 'Set the color of the line'}),
+ ("markevery", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the markevery property to subsample the plot when using markers. Eg if markevery=5, every 5-th marker will be plotted. every can be', 'values': "[['(startind, stride)']]", 'optional': True}),
+ ("markeredgecolor", "basic:Color",
+ {'optional': True, 'docstring': 'Set the marker edge color'}),
+ ("marker", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the line marker\n\nThe marker can also be a tuple (numsides, style, angle), which will create a custom, regular symbol.\n\n\n\nFor backward compatibility, the form (verts, 0) is also accepted, but it is equivalent to just verts for giving a raw set of vertices that define the shape.', 'values': "[['caretdown', 'caretleft', 'caretright', 'caretup', 'circle', 'diamond', 'hexagon1', 'hexagon2', 'hline', 'nothing', 'octagon', 'pen [...]
+ ("markerfacecoloralt", "basic:Color",
+ {'optional': True, 'docstring': 'Set the alternate marker face color.'}),
+ ("linewidth", "basic:Float",
+ {'optional': True, 'docstring': 'Set the line width in points'}),
+ ("linestyle", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "Set the linestyle of the line (also accepts drawstyles)\n\n'steps' is equivalent to 'steps-pre' and is maintained for backward-compatibility.", 'values': "[['solid', 'dashed', 'dash_dot', 'dotted', 'draw nothing', 'draw nothing', 'draw nothing']]", 'optional': True}),
+ ("solid_joinstyle", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the join style for solid linestyles', 'values': "[['miter', 'round', 'bevel']]", 'optional': True}),
+ ("markerfacecolor", "basic:Color",
+ {'optional': True, 'docstring': 'Set the marker face color.'}),
+ ("axes", "basic:String",
+ {'optional': True, 'docstring': 'Set the :class:`~matplotlib.axes.Axes` instance in which the artist resides, if any.'}),
+ ("transform", "basic:String",
+ {'optional': True, 'docstring': 'set the Transformation instance used by this artist'}),
+ ("fillstyle", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "Set the marker fill style; 'full' means fill the whole marker. 'none' means no filling; other options are for half-filled markers.", 'values': "[['full', 'left', 'right', 'bottom', 'top', 'none']]", 'optional': True}),
+ ("markeredgewidth", "basic:Float",
+ {'optional': True, 'docstring': 'Set the marker edge width in points'}),
+ ("solid_capstyle", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the cap style for solid linestyles', 'values': "[['butt', 'round', 'projecting']]", 'optional': True}),
+ ("dashes", "basic:List",
+ {'optional': True, 'docstring': 'Set the dash sequence, sequence of dashes with on off ink in points. If seq is empty or if seq = (None, None), the linestyle will be set to solid.'}),
+ ("markersize", "basic:Float",
+ {'optional': True, 'docstring': 'Set the marker size in points'}),
+ ("antialiased", "basic:Boolean",
+ {'optional': True, 'docstring': 'True if line should be drawin with antialiased rendering'}),
+ ("xdata", "basic:String",
+ {'optional': True, 'docstring': 'Set the data np.array for x'}),
+ ("drawstyle", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "Set the drawstyle of the plot\n\n'default' connects the points with lines. The steps variants produce step-plots. 'steps' is equivalent to 'steps-pre' and is maintained for backward-compatibility.", 'values': "[['default', 'steps', 'steps-pre', 'steps-mid', 'steps-post']]", 'optional': True}),
+ ("data", "basic:String",
+ {'optional': True, 'docstring': 'Set the x and y data'}),
+ ("dash_joinstyle", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the join style for dashed linestyles', 'values': "[['miter', 'round', 'bevel']]", 'optional': True}),
+ ("pickradius", "basic:Float",
+ {'optional': True, 'docstring': 'Sets the pick radius used for containment tests'}),
+ ("ydata", "basic:String",
+ {'optional': True, 'docstring': 'Set the data np.array for y'}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplLine2DProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('picker'):
+ self.props['picker'] = self.getInputFromPort('picker')
+ if self.hasInputFromPort('dash_capstyle'):
+ self.props['dash_capstyle'] = self.getInputFromPort('dash_capstyle')
+ if self.hasInputFromPort('color'):
+ self.props['color'] = self.getInputFromPort('color')
+ self.props['color'] = translate_color(self.props['color'])
+ if self.hasInputFromPort('markevery'):
+ self.props['markevery'] = self.getInputFromPort('markevery')
+ if self.hasInputFromPort('markeredgecolor'):
+ self.props['markeredgecolor'] = self.getInputFromPort('markeredgecolor')
+ self.props['markeredgecolor'] = translate_color(self.props['markeredgecolor'])
+ if self.hasInputFromPort('marker'):
+ self.props['marker'] = self.getInputFromPort('marker')
+ self.props['marker'] = translate_MplLine2DProperties_marker(self.props['marker'])
+ if self.hasInputFromPort('markerfacecoloralt'):
+ self.props['markerfacecoloralt'] = self.getInputFromPort('markerfacecoloralt')
+ self.props['markerfacecoloralt'] = translate_color(self.props['markerfacecoloralt'])
+ if self.hasInputFromPort('linewidth'):
+ self.props['linewidth'] = self.getInputFromPort('linewidth')
+ if self.hasInputFromPort('linestyle'):
+ self.props['linestyle'] = self.getInputFromPort('linestyle')
+ self.props['linestyle'] = translate_MplLine2DProperties_linestyle(self.props['linestyle'])
+ if self.hasInputFromPort('solid_joinstyle'):
+ self.props['solid_joinstyle'] = self.getInputFromPort('solid_joinstyle')
+ if self.hasInputFromPort('markerfacecolor'):
+ self.props['markerfacecolor'] = self.getInputFromPort('markerfacecolor')
+ self.props['markerfacecolor'] = translate_color(self.props['markerfacecolor'])
+ if self.hasInputFromPort('axes'):
+ self.props['axes'] = self.getInputFromPort('axes')
+ if self.hasInputFromPort('transform'):
+ self.props['transform'] = self.getInputFromPort('transform')
+ if self.hasInputFromPort('fillstyle'):
+ self.props['fillstyle'] = self.getInputFromPort('fillstyle')
+ if self.hasInputFromPort('markeredgewidth'):
+ self.props['markeredgewidth'] = self.getInputFromPort('markeredgewidth')
+ if self.hasInputFromPort('solid_capstyle'):
+ self.props['solid_capstyle'] = self.getInputFromPort('solid_capstyle')
+ if self.hasInputFromPort('dashes'):
+ self.props['dashes'] = self.getInputFromPort('dashes')
+ if self.hasInputFromPort('markersize'):
+ self.props['markersize'] = self.getInputFromPort('markersize')
+ if self.hasInputFromPort('antialiased'):
+ self.props['antialiased'] = self.getInputFromPort('antialiased')
+ if self.hasInputFromPort('xdata'):
+ self.props['xdata'] = self.getInputFromPort('xdata')
+ if self.hasInputFromPort('drawstyle'):
+ self.props['drawstyle'] = self.getInputFromPort('drawstyle')
+ if self.hasInputFromPort('data'):
+ self.props['data'] = self.getInputFromPort('data')
+ if self.hasInputFromPort('dash_joinstyle'):
+ self.props['dash_joinstyle'] = self.getInputFromPort('dash_joinstyle')
+ if self.hasInputFromPort('pickradius'):
+ self.props['pickradius'] = self.getInputFromPort('pickradius')
+ if self.hasInputFromPort('ydata'):
+ self.props['ydata'] = self.getInputFromPort('ydata')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplTextProperties(MplArtistProperties):
+ """
+ Handle storing and drawing of text in window or data coordinates.
+
+ """
+ _input_ports = [
+ ("rotation_mode", "basic:String",
+ {'optional': True, 'docstring': 'set text rotation mode. If "anchor", the un-rotated text will first aligned according to their ha and va, and then will be rotated with the alignement reference point as a origin. If None (default), the text will be rotated first then will be aligned.'}),
+ ("style", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the font style.', 'values': "[['normal', 'italic', 'oblique']]", 'optional': True}),
+ ("linespacing", "basic:Float",
+ {'optional': True, 'docstring': 'Set the line spacing as a multiple of the font size. Default is 1.2.'}),
+ ("family", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the font family. May be either a single string, or a list of strings in decreasing priority. Each string may be either a real font name or a generic font class name. If the latter, the specific font names will be looked up in the :file:`matplotlibrc` file.', 'values': "[['FONTNAME', 'serif', 'sans-serif', 'cursive', 'fantasy', 'monospace']]", 'optional': True}),
+ ("x", "basic:Float",
+ {'optional': True, 'docstring': 'Set the x position of the text'}),
+ ("color", "basic:Color",
+ {'optional': True, 'docstring': 'Set the foreground color of the text'}),
+ ("text", "basic:String",
+ {'optional': True, 'docstring': 'Set the text string s\n\nIt may contain newlines (\\n) or math in LaTeX syntax.'}),
+ ("verticalalignment", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the vertical alignment', 'values': "[['center', 'top', 'bottom', 'baseline']]", 'optional': True}),
+ ("variant", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "Set the font variant, either 'normal' or 'small-caps'.", 'values': "[['normal', 'small-caps']]", 'optional': True}),
+ ("path_effects", "basic:String",
+ {'optional': True}),
+ ("weight", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the font weight.', 'values': "[['a numeric value in range 0-1000', 'ultralight', 'light', 'normal', 'regular', 'book', 'medium', 'roman', 'semibold', 'demibold', 'demi', 'bold', 'heavy', 'extra bold', 'black']]", 'optional': True}),
+ ("stretch", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the font stretch (horizontal condensation or expansion).', 'values': "[['a numeric value in range 0-1000', 'ultra-condensed', 'extra-condensed', 'condensed', 'semi-condensed', 'normal', 'semi-expanded', 'expanded', 'extra-expanded', 'ultra-expanded']]", 'optional': True}),
+ ("fontproperties", "basic:String",
+ {'optional': True, 'docstring': 'Set the font properties that control the text. fp must be a :class:`matplotlib.font_manager.FontProperties` object.'}),
+ ("horizontalalignment", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the horizontal alignment to one of', 'values': "[['center', 'right', 'left']]", 'optional': True}),
+ ("bbox", "basic:String",
+ {'optional': True, 'docstring': 'Draw a bounding box around self. rectprops are any settable properties for a rectangle, eg facecolor=\'red\', alpha=0.5.\n\nt.set_bbox(dict(facecolor=\'red\', alpha=0.5))\n\nIf rectprops has "boxstyle" key. A FancyBboxPatch is initialized with rectprops and will be drawn. The mutation scale of the FancyBboxPath is set to the fontsize.'}),
+ ("backgroundcolor", "basic:Color",
+ {'optional': True, 'docstring': 'Set the background color of the text by updating the bbox.'}),
+ ("position", "basic:String",
+ {'optional': True, 'docstring': 'Set the (x, y) position of the text'}),
+ ("y", "basic:Float",
+ {'optional': True, 'docstring': 'Set the y position of the text'}),
+ ("multialignment", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the alignment for multiple lines layout. The layout of the bounding box of all the lines is determined bu the horizontalalignment and verticalalignment properties, but the multiline text within that box can be', 'values': "[['left', 'right', 'center']]", 'optional': True}),
+ ("rotation", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the rotation of the text', 'values': "[['angle in degrees', 'vertical', 'horizontal']]", 'optional': True}),
+ ("size", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the font size. May be either a size string, relative to the default font size, or an absolute font size in points.', 'values': "[['size in points', 'xx-small', 'x-small', 'small', 'medium', 'large', 'x-large', 'xx-large']]", 'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplTextProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('rotation_mode'):
+ self.props['rotation_mode'] = self.getInputFromPort('rotation_mode')
+ if self.hasInputFromPort('style'):
+ self.props['style'] = self.getInputFromPort('style')
+ if self.hasInputFromPort('linespacing'):
+ self.props['linespacing'] = self.getInputFromPort('linespacing')
+ if self.hasInputFromPort('family'):
+ self.props['family'] = self.getInputFromPort('family')
+ if self.hasInputFromPort('x'):
+ self.props['x'] = self.getInputFromPort('x')
+ if self.hasInputFromPort('color'):
+ self.props['color'] = self.getInputFromPort('color')
+ self.props['color'] = translate_color(self.props['color'])
+ if self.hasInputFromPort('text'):
+ self.props['text'] = self.getInputFromPort('text')
+ if self.hasInputFromPort('verticalalignment'):
+ self.props['verticalalignment'] = self.getInputFromPort('verticalalignment')
+ if self.hasInputFromPort('variant'):
+ self.props['variant'] = self.getInputFromPort('variant')
+ if self.hasInputFromPort('path_effects'):
+ self.props['path_effects'] = self.getInputFromPort('path_effects')
+ if self.hasInputFromPort('weight'):
+ self.props['weight'] = self.getInputFromPort('weight')
+ if self.hasInputFromPort('stretch'):
+ self.props['stretch'] = self.getInputFromPort('stretch')
+ if self.hasInputFromPort('fontproperties'):
+ self.props['fontproperties'] = self.getInputFromPort('fontproperties')
+ if self.hasInputFromPort('horizontalalignment'):
+ self.props['horizontalalignment'] = self.getInputFromPort('horizontalalignment')
+ if self.hasInputFromPort('bbox'):
+ self.props['bbox'] = self.getInputFromPort('bbox')
+ if self.hasInputFromPort('backgroundcolor'):
+ self.props['backgroundcolor'] = self.getInputFromPort('backgroundcolor')
+ self.props['backgroundcolor'] = translate_color(self.props['backgroundcolor'])
+ if self.hasInputFromPort('position'):
+ self.props['position'] = self.getInputFromPort('position')
+ if self.hasInputFromPort('y'):
+ self.props['y'] = self.getInputFromPort('y')
+ if self.hasInputFromPort('multialignment'):
+ self.props['multialignment'] = self.getInputFromPort('multialignment')
+ if self.hasInputFromPort('rotation'):
+ self.props['rotation'] = self.getInputFromPort('rotation')
+ if self.hasInputFromPort('size'):
+ self.props['size'] = self.getInputFromPort('size')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplTextWithDashProperties(MplTextProperties):
+ """
+ This is basically a :class:`~matplotlib.text.Text` with a dash
+ (drawn with a :class:`~matplotlib.lines.Line2D`) before/after
+ it. It is intended to be a drop-in replacement for
+ :class:`~matplotlib.text.Text`, and should behave identically to
+ it when *dashlength* = 0.0.
+
+ The dash always comes between the point specified by
+ :meth:`~matplotlib.text.Text.set_position` and the text. When a
+ dash exists, the text alignment arguments (*horizontalalignment*,
+ *verticalalignment*) are ignored.
+
+ *dashlength* is the length of the dash in canvas units.
+ (default = 0.0).
+
+ *dashdirection* is one of 0 or 1, where 0 draws the dash after the
+ text and 1 before. (default = 0).
+
+ *dashrotation* specifies the rotation of the dash, and should
+ generally stay *None*. In this case
+ :meth:`~matplotlib.text.TextWithDash.get_dashrotation` returns
+ :meth:`~matplotlib.text.Text.get_rotation`. (I.e., the dash takes
+ its rotation from the text's rotation). Because the text center is
+ projected onto the dash, major deviations in the rotation cause
+ what may be considered visually unappealing results.
+ (default = *None*)
+
+ *dashpad* is a padding length to add (or subtract) space
+ between the text and the dash, in canvas units.
+ (default = 3)
+
+ *dashpush* "pushes" the dash and text away from the point
+ specified by :meth:`~matplotlib.text.Text.set_position` by the
+ amount in canvas units. (default = 0)
+
+ .. note::
+
+ The alignment of the two objects is based on the bounding box
+ of the :class:`~matplotlib.text.Text`, as obtained by
+ :meth:`~matplotlib.artist.Artist.get_window_extent`. This, in
+ turn, appears to depend on the font metrics as given by the
+ rendering backend. Hence the quality of the "centering" of the
+ label text with respect to the dash varies depending on the
+ backend used.
+
+ .. note::
+
+ I'm not sure that I got the
+ :meth:`~matplotlib.text.TextWithDash.get_window_extent` right,
+ or whether that's sufficient for providing the object bounding
+ box.
+
+
+ """
+ _input_ports = [
+ ("dashpush", "basic:Float",
+ {'optional': True, 'docstring': 'Set the "push" of the TextWithDash, which is the extra spacing between the beginning of the dash and the specified position.'}),
+ ("dashdirection", "basic:String",
+ {'optional': True, 'docstring': "Set the direction of the dash following the text. 1 is before the text and 0 is after. The default is 0, which is what you'd want for the typical case of ticks below and on the left of the figure."}),
+ ("linespacing", "basic:String",
+ {'optional': True}),
+ ("figure", "basic:String",
+ {'optional': True, 'docstring': 'Set the figure instance the artist belong to.'}),
+ ("color", "basic:String",
+ {'optional': True}),
+ ("text", "basic:String",
+ {'optional': True, 'defaults': "['']"}),
+ ("verticalalignment", "basic:String",
+ {'optional': True, 'defaults': "['center']"}),
+ ("dashpad", "basic:Float",
+ {'optional': True, 'docstring': 'Set the "pad" of the TextWithDash, which is the extra spacing between the dash and the text, in canvas units.'}),
+ ("dashrotation", "basic:Float",
+ {'optional': True, 'docstring': 'Set the rotation of the dash, in degrees'}),
+ ("transform", "basic:String",
+ {'optional': True, 'docstring': 'Set the :class:`matplotlib.transforms.Transform` instance used by this artist.'}),
+ ("fontproperties", "basic:String",
+ {'optional': True}),
+ ("multialignment", "basic:String",
+ {'optional': True}),
+ ("x", "basic:Float",
+ {'optional': True, 'docstring': 'Set the x position of the :class:`TextWithDash`.'}),
+ ("y", "basic:Float",
+ {'optional': True, 'docstring': 'Set the y position of the :class:`TextWithDash`.'}),
+ ("position", "basic:String",
+ {'optional': True, 'docstring': 'Set the (x, y) position of the :class:`TextWithDash`.'}),
+ ("dashlength", "basic:Float",
+ {'optional': True, 'docstring': 'Set the length of the dash.'}),
+ ("rotation", "basic:String",
+ {'optional': True}),
+ ("horizontalalignment", "basic:String",
+ {'optional': True, 'defaults': "['center']"}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplTextWithDashProperties)")]
+
+ def __init__(self):
+ MplTextProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplTextProperties.compute(self)
+ if self.hasInputFromPort('dashpush'):
+ self.props['dashpush'] = self.getInputFromPort('dashpush')
+ if self.hasInputFromPort('dashdirection'):
+ self.props['dashdirection'] = self.getInputFromPort('dashdirection')
+ if self.hasInputFromPort('linespacing'):
+ self.constructor_props['linespacing'] = self.getInputFromPort('linespacing')
+ if self.hasInputFromPort('figure'):
+ self.props['figure'] = self.getInputFromPort('figure')
+ if self.hasInputFromPort('color'):
+ self.constructor_props['color'] = self.getInputFromPort('color')
+ if self.hasInputFromPort('text'):
+ self.constructor_props['text'] = self.getInputFromPort('text')
+ if self.hasInputFromPort('verticalalignment'):
+ self.constructor_props['verticalalignment'] = self.getInputFromPort('verticalalignment')
+ if self.hasInputFromPort('dashpad'):
+ self.props['dashpad'] = self.getInputFromPort('dashpad')
+ if self.hasInputFromPort('dashrotation'):
+ self.props['dashrotation'] = self.getInputFromPort('dashrotation')
+ if self.hasInputFromPort('transform'):
+ self.props['transform'] = self.getInputFromPort('transform')
+ if self.hasInputFromPort('fontproperties'):
+ self.constructor_props['fontproperties'] = self.getInputFromPort('fontproperties')
+ if self.hasInputFromPort('multialignment'):
+ self.constructor_props['multialignment'] = self.getInputFromPort('multialignment')
+ if self.hasInputFromPort('x'):
+ self.props['x'] = self.getInputFromPort('x')
+ if self.hasInputFromPort('y'):
+ self.props['y'] = self.getInputFromPort('y')
+ if self.hasInputFromPort('position'):
+ self.props['position'] = self.getInputFromPort('position')
+ if self.hasInputFromPort('dashlength'):
+ self.props['dashlength'] = self.getInputFromPort('dashlength')
+ if self.hasInputFromPort('rotation'):
+ self.constructor_props['rotation'] = self.getInputFromPort('rotation')
+ if self.hasInputFromPort('horizontalalignment'):
+ self.constructor_props['horizontalalignment'] = self.getInputFromPort('horizontalalignment')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplTickProperties(MplArtistProperties):
+ """
+ Abstract base class for the axis ticks, grid lines and labels
+
+ 1 refers to the bottom of the plot for xticks and the left for yticks
+ 2 refers to the top of the plot for xticks and the right for yticks
+
+ Publicly accessible attributes:
+
+ :attr:`tick1line`
+ a Line2D instance
+
+ :attr:`tick2line`
+ a Line2D instance
+
+ :attr:`gridline`
+ a Line2D instance
+
+ :attr:`label1`
+ a Text instance
+
+ :attr:`label2`
+ a Text instance
+
+ :attr:`gridOn`
+ a boolean which determines whether to draw the tickline
+
+ :attr:`tick1On`
+ a boolean which determines whether to draw the 1st tickline
+
+ :attr:`tick2On`
+ a boolean which determines whether to draw the 2nd tickline
+
+ :attr:`label1On`
+ a boolean which determines whether to draw tick label
+
+ :attr:`label2On`
+ a boolean which determines whether to draw tick label
+
+
+ """
+ _input_ports = [
+ ("label1On", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("loc", "basic:String",
+ {'optional': True}),
+ ("major", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("label2On", "basic:Boolean",
+ {'optional': True, 'defaults': "['False']"}),
+ ("color", "basic:String",
+ {'optional': True}),
+ ("label1", "basic:String",
+ {'optional': True, 'docstring': 'Set the text of ticklabel'}),
+ ("label2", "basic:String",
+ {'optional': True, 'docstring': 'Set the text of ticklabel2'}),
+ ("axes", "basic:String",
+ {'optional': True}),
+ ("clip_path", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "Set the artist's clip path, which may be:\n\na :class:`~matplotlib.patches.Patch` (or subclass) instance\n\n\n\nNone, to remove the clipping path\n\nFor efficiency, if the path happens to be an axis-aligned rectangle, this method will set the clipping box to the corresponding rectangle and set the clipping path to None.", 'values': "[['(:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`)', ':class:`~ [...]
+ ("label", "basic:String",
+ {'optional': True, 'docstring': 'Set the text of ticklabel'}),
+ ("labelcolor", "basic:String",
+ {'optional': True}),
+ ("tickdir", "basic:String",
+ {'optional': True}),
+ ("pad", "basic:Float",
+ {'optional': True, 'docstring': 'Set the tick label pad in points'}),
+ ("gridOn", "basic:String",
+ {'optional': True}),
+ ("zorder", "basic:String",
+ {'optional': True}),
+ ("tick2On", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("labelsize", "basic:String",
+ {'optional': True}),
+ ("width", "basic:String",
+ {'optional': True}),
+ ("tick1On", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("size", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplTickProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('label1On'):
+ self.constructor_props['label1On'] = self.getInputFromPort('label1On')
+ if self.hasInputFromPort('loc'):
+ self.constructor_props['loc'] = self.getInputFromPort('loc')
+ if self.hasInputFromPort('major'):
+ self.constructor_props['major'] = self.getInputFromPort('major')
+ if self.hasInputFromPort('label2On'):
+ self.constructor_props['label2On'] = self.getInputFromPort('label2On')
+ if self.hasInputFromPort('color'):
+ self.constructor_props['color'] = self.getInputFromPort('color')
+ if self.hasInputFromPort('label1'):
+ self.props['label1'] = self.getInputFromPort('label1')
+ if self.hasInputFromPort('label2'):
+ self.props['label2'] = self.getInputFromPort('label2')
+ if self.hasInputFromPort('axes'):
+ self.constructor_props['axes'] = self.getInputFromPort('axes')
+ if self.hasInputFromPort('clip_path'):
+ self.props['clip_path'] = self.getInputFromPort('clip_path')
+ if self.hasInputFromPort('label'):
+ self.props['label'] = self.getInputFromPort('label')
+ if self.hasInputFromPort('labelcolor'):
+ self.constructor_props['labelcolor'] = self.getInputFromPort('labelcolor')
+ if self.hasInputFromPort('tickdir'):
+ self.constructor_props['tickdir'] = self.getInputFromPort('tickdir')
+ if self.hasInputFromPort('pad'):
+ self.props['pad'] = self.getInputFromPort('pad')
+ if self.hasInputFromPort('gridOn'):
+ self.constructor_props['gridOn'] = self.getInputFromPort('gridOn')
+ if self.hasInputFromPort('zorder'):
+ self.constructor_props['zorder'] = self.getInputFromPort('zorder')
+ if self.hasInputFromPort('tick2On'):
+ self.constructor_props['tick2On'] = self.getInputFromPort('tick2On')
+ if self.hasInputFromPort('labelsize'):
+ self.constructor_props['labelsize'] = self.getInputFromPort('labelsize')
+ if self.hasInputFromPort('width'):
+ self.constructor_props['width'] = self.getInputFromPort('width')
+ if self.hasInputFromPort('tick1On'):
+ self.constructor_props['tick1On'] = self.getInputFromPort('tick1On')
+ if self.hasInputFromPort('size'):
+ self.constructor_props['size'] = self.getInputFromPort('size')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplXTickProperties(MplTickProperties):
+ """
+ Contains all the Artists needed to make an x tick - the tick line,
+ the label text and the grid line
+
+ """
+ _input_ports = [
+ ("label1On", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("loc", "basic:String",
+ {'optional': True}),
+ ("major", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("label2On", "basic:Boolean",
+ {'optional': True, 'defaults': "['False']"}),
+ ("color", "basic:String",
+ {'optional': True}),
+ ("axes", "basic:String",
+ {'optional': True}),
+ ("label", "basic:String",
+ {'optional': True}),
+ ("labelcolor", "basic:String",
+ {'optional': True}),
+ ("tickdir", "basic:String",
+ {'optional': True}),
+ ("pad", "basic:String",
+ {'optional': True}),
+ ("gridOn", "basic:String",
+ {'optional': True}),
+ ("zorder", "basic:String",
+ {'optional': True}),
+ ("tick2On", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("labelsize", "basic:String",
+ {'optional': True}),
+ ("width", "basic:String",
+ {'optional': True}),
+ ("tick1On", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("size", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplXTickProperties)")]
+
+ def __init__(self):
+ MplTickProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplTickProperties.compute(self)
+ if self.hasInputFromPort('label1On'):
+ self.constructor_props['label1On'] = self.getInputFromPort('label1On')
+ if self.hasInputFromPort('loc'):
+ self.constructor_props['loc'] = self.getInputFromPort('loc')
+ if self.hasInputFromPort('major'):
+ self.constructor_props['major'] = self.getInputFromPort('major')
+ if self.hasInputFromPort('label2On'):
+ self.constructor_props['label2On'] = self.getInputFromPort('label2On')
+ if self.hasInputFromPort('color'):
+ self.constructor_props['color'] = self.getInputFromPort('color')
+ if self.hasInputFromPort('axes'):
+ self.constructor_props['axes'] = self.getInputFromPort('axes')
+ if self.hasInputFromPort('label'):
+ self.constructor_props['label'] = self.getInputFromPort('label')
+ if self.hasInputFromPort('labelcolor'):
+ self.constructor_props['labelcolor'] = self.getInputFromPort('labelcolor')
+ if self.hasInputFromPort('tickdir'):
+ self.constructor_props['tickdir'] = self.getInputFromPort('tickdir')
+ if self.hasInputFromPort('pad'):
+ self.constructor_props['pad'] = self.getInputFromPort('pad')
+ if self.hasInputFromPort('gridOn'):
+ self.constructor_props['gridOn'] = self.getInputFromPort('gridOn')
+ if self.hasInputFromPort('zorder'):
+ self.constructor_props['zorder'] = self.getInputFromPort('zorder')
+ if self.hasInputFromPort('tick2On'):
+ self.constructor_props['tick2On'] = self.getInputFromPort('tick2On')
+ if self.hasInputFromPort('labelsize'):
+ self.constructor_props['labelsize'] = self.getInputFromPort('labelsize')
+ if self.hasInputFromPort('width'):
+ self.constructor_props['width'] = self.getInputFromPort('width')
+ if self.hasInputFromPort('tick1On'):
+ self.constructor_props['tick1On'] = self.getInputFromPort('tick1On')
+ if self.hasInputFromPort('size'):
+ self.constructor_props['size'] = self.getInputFromPort('size')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplYTickProperties(MplTickProperties):
+ """
+ Contains all the Artists needed to make a Y tick - the tick line,
+ the label text and the grid line
+
+ """
+ _input_ports = [
+ ("label1On", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("loc", "basic:String",
+ {'optional': True}),
+ ("major", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("label2On", "basic:Boolean",
+ {'optional': True, 'defaults': "['False']"}),
+ ("color", "basic:String",
+ {'optional': True}),
+ ("axes", "basic:String",
+ {'optional': True}),
+ ("label", "basic:String",
+ {'optional': True}),
+ ("labelcolor", "basic:String",
+ {'optional': True}),
+ ("tickdir", "basic:String",
+ {'optional': True}),
+ ("pad", "basic:String",
+ {'optional': True}),
+ ("gridOn", "basic:String",
+ {'optional': True}),
+ ("zorder", "basic:String",
+ {'optional': True}),
+ ("tick2On", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("labelsize", "basic:String",
+ {'optional': True}),
+ ("width", "basic:String",
+ {'optional': True}),
+ ("tick1On", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("size", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplYTickProperties)")]
+
+ def __init__(self):
+ MplTickProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplTickProperties.compute(self)
+ if self.hasInputFromPort('label1On'):
+ self.constructor_props['label1On'] = self.getInputFromPort('label1On')
+ if self.hasInputFromPort('loc'):
+ self.constructor_props['loc'] = self.getInputFromPort('loc')
+ if self.hasInputFromPort('major'):
+ self.constructor_props['major'] = self.getInputFromPort('major')
+ if self.hasInputFromPort('label2On'):
+ self.constructor_props['label2On'] = self.getInputFromPort('label2On')
+ if self.hasInputFromPort('color'):
+ self.constructor_props['color'] = self.getInputFromPort('color')
+ if self.hasInputFromPort('axes'):
+ self.constructor_props['axes'] = self.getInputFromPort('axes')
+ if self.hasInputFromPort('label'):
+ self.constructor_props['label'] = self.getInputFromPort('label')
+ if self.hasInputFromPort('labelcolor'):
+ self.constructor_props['labelcolor'] = self.getInputFromPort('labelcolor')
+ if self.hasInputFromPort('tickdir'):
+ self.constructor_props['tickdir'] = self.getInputFromPort('tickdir')
+ if self.hasInputFromPort('pad'):
+ self.constructor_props['pad'] = self.getInputFromPort('pad')
+ if self.hasInputFromPort('gridOn'):
+ self.constructor_props['gridOn'] = self.getInputFromPort('gridOn')
+ if self.hasInputFromPort('zorder'):
+ self.constructor_props['zorder'] = self.getInputFromPort('zorder')
+ if self.hasInputFromPort('tick2On'):
+ self.constructor_props['tick2On'] = self.getInputFromPort('tick2On')
+ if self.hasInputFromPort('labelsize'):
+ self.constructor_props['labelsize'] = self.getInputFromPort('labelsize')
+ if self.hasInputFromPort('width'):
+ self.constructor_props['width'] = self.getInputFromPort('width')
+ if self.hasInputFromPort('tick1On'):
+ self.constructor_props['tick1On'] = self.getInputFromPort('tick1On')
+ if self.hasInputFromPort('size'):
+ self.constructor_props['size'] = self.getInputFromPort('size')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplAxisProperties(MplArtistProperties):
+ """
+ Public attributes
+
+ * :attr:`axes.transData` - transform data coords to display coords
+ * :attr:`axes.transAxes` - transform axis coords to display coords
+ * :attr:`labelpad` - number of points between the axis and its label
+
+ """
+ _input_ports = [
+ ("pickradius", "basic:String",
+ {'optional': True, 'docstring': 'Set the depth of the axis used by the picker'}),
+ ("minor_formatter", "basic:String",
+ {'optional': True, 'docstring': 'Set the formatter of the minor ticker'}),
+ ("smart_bounds", "basic:String",
+ {'optional': True, 'docstring': 'set the axis to have smart bounds'}),
+ ("ticksSequence", "basic:List",
+ {'optional': True, 'docstring': 'Set the locations of the tick marks from sequence ticks'}),
+ ("ticksScalar", "basic:Float",
+ {'docstring': 'Set the locations of the tick marks from sequence ticks', 'optional': True}),
+ ("axes", "basic:String",
+ {'optional': True}),
+ ("view_interval", "basic:String",
+ {'optional': True}),
+ ("major_locator", "basic:String",
+ {'optional': True, 'docstring': 'Set the locator of the major ticker'}),
+ ("major_formatter", "basic:String",
+ {'optional': True, 'docstring': 'Set the formatter of the major ticker'}),
+ ("ticklabelsSequence", "basic:List",
+ {'optional': True, 'docstring': 'Set the text values of the tick labels. Return a list of Text instances. Use kwarg minor=True to select minor ticks. All other kwargs are used to update the text object properties. As for get_ticklabels, label1 (left or bottom) is affected for a given tick only if its label1On attribute is True, and similarly for label2. The list of returned label text objects consists of all such label1 objects followed by all such label2 objects.\n\nTh [...]
+ ("ticklabelsScalar", "basic:String",
+ {'docstring': 'Set the text values of the tick labels. Return a list of Text instances. Use kwarg minor=True to select minor ticks. All other kwargs are used to update the text object properties. As for get_ticklabels, label1 (left or bottom) is affected for a given tick only if its label1On attribute is True, and similarly for label2. The list of returned label text objects consists of all such label1 objects followed by all such label2 objects.\n\nThe input ticklabels [...]
+ ("clip_path", "basic:String",
+ {'optional': True}),
+ ("minor_locator", "basic:String",
+ {'optional': True, 'docstring': 'Set the locator of the minor ticker'}),
+ ("default_intervals", "basic:String",
+ {'optional': True}),
+ ("scale", "basic:String",
+ {'optional': True}),
+ ("data_interval", "basic:String",
+ {'optional': True, 'docstring': 'set the axis data limits'}),
+ ("label_text", "basic:String",
+ {'optional': True, 'docstring': 'Sets the text value of the axis label'}),
+ ("label_coords", "basic:String",
+ {'optional': True, 'docstring': 'Set the coordinates of the label. By default, the x coordinate of the y label is determined by the tick label bounding boxes, but this can lead to poor alignment of multiple ylabels if there are multiple axes. Ditto for the y coodinate of the x label.\n\nYou can also specify the coordinate system of the label with the transform. If None, the default coordinate system will be the axes coordinate system (0,0) is (left,bottom), (0.5, 0.5) [...]
+ ("units", "basic:String",
+ {'optional': True, 'docstring': 'set the units for axis'}),
+ ("tick_params", "basic:String",
+ {'optional': True, 'docstring': 'Set appearance parameters for ticks and ticklabels.\n\nFor documentation of keyword arguments, see :meth:`matplotlib.axes.Axes.tick_params`.'}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplAxisProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('pickradius'):
+ self.props['pickradius'] = self.getInputFromPort('pickradius')
+ if self.hasInputFromPort('minor_formatter'):
+ self.props['minor_formatter'] = self.getInputFromPort('minor_formatter')
+ if self.hasInputFromPort('smart_bounds'):
+ self.props['smart_bounds'] = self.getInputFromPort('smart_bounds')
+ if self.hasInputFromPort('ticksSequence'):
+ self.props['ticks'] = self.getInputFromPort('ticksSequence')
+ elif self.hasInputFromPort('ticksScalar'):
+ self.props['ticks'] = self.getInputFromPort('ticksScalar')
+ if self.hasInputFromPort('axes'):
+ self.constructor_props['axes'] = self.getInputFromPort('axes')
+ if self.hasInputFromPort('view_interval'):
+ self.props['view_interval'] = self.getInputFromPort('view_interval')
+ if self.hasInputFromPort('major_locator'):
+ self.props['major_locator'] = self.getInputFromPort('major_locator')
+ if self.hasInputFromPort('major_formatter'):
+ self.props['major_formatter'] = self.getInputFromPort('major_formatter')
+ if self.hasInputFromPort('ticklabelsSequence'):
+ self.props['ticklabels'] = self.getInputFromPort('ticklabelsSequence')
+ elif self.hasInputFromPort('ticklabelsScalar'):
+ self.props['ticklabels'] = self.getInputFromPort('ticklabelsScalar')
+ if self.hasInputFromPort('clip_path'):
+ self.props['clip_path'] = self.getInputFromPort('clip_path')
+ if self.hasInputFromPort('minor_locator'):
+ self.props['minor_locator'] = self.getInputFromPort('minor_locator')
+ if self.hasInputFromPort('default_intervals'):
+ self.props['default_intervals'] = self.getInputFromPort('default_intervals')
+ if self.hasInputFromPort('scale'):
+ self.props['scale'] = self.getInputFromPort('scale')
+ if self.hasInputFromPort('data_interval'):
+ self.props['data_interval'] = self.getInputFromPort('data_interval')
+ if self.hasInputFromPort('label_text'):
+ self.props['label_text'] = self.getInputFromPort('label_text')
+ if self.hasInputFromPort('label_coords'):
+ self.props['label_coords'] = self.getInputFromPort('label_coords')
+ if self.hasInputFromPort('units'):
+ self.props['units'] = self.getInputFromPort('units')
+ if self.hasInputFromPort('tick_params'):
+ self.props['tick_params'] = self.getInputFromPort('tick_params')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplXAxisProperties(MplAxisProperties):
+ """None
+ """
+ _input_ports = [
+ ("view_interval", "basic:String",
+ {'optional': True, 'docstring': 'If ignore is False, the order of vmin, vmax does not matter; the original axis orientation will be preserved. In addition, the view limits can be expanded, but will not be reduced. This method is for mpl internal use; for normal use, see :meth:`~matplotlib.axes.Axes.set_xlim`.'}),
+ ("ticks_position", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "Set the ticks position (top, bottom, both, default or none) both sets the ticks to appear on both positions, but does not change the tick labels. 'default' resets the tick positions to the default: ticks on both positions, labels at bottom. 'none' can be used if you don't want any ticks. 'none' and 'both' affect only the ticks, not the labels.", 'values': "[['top', 'bottom', 'both', 'default', 'none']]", 'optional': True}),
+ ("axes", "basic:String",
+ {'optional': True}),
+ ("label_position", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the label position (top or bottom)', 'values': "[['top', 'bottom']]", 'optional': True}),
+ ("default_intervals", "basic:String",
+ {'optional': True, 'docstring': 'set the default limits for the axis interval if they are not mutated'}),
+ ("data_interval", "basic:String",
+ {'optional': True, 'docstring': 'set the axis data limits'}),
+ ("pickradius", "basic:Integer",
+ {'optional': True, 'defaults': "['15']"}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplXAxisProperties)")]
+
+ def __init__(self):
+ MplAxisProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplAxisProperties.compute(self)
+ if self.hasInputFromPort('view_interval'):
+ self.props['view_interval'] = self.getInputFromPort('view_interval')
+ if self.hasInputFromPort('ticks_position'):
+ self.props['ticks_position'] = self.getInputFromPort('ticks_position')
+ if self.hasInputFromPort('axes'):
+ self.constructor_props['axes'] = self.getInputFromPort('axes')
+ if self.hasInputFromPort('label_position'):
+ self.props['label_position'] = self.getInputFromPort('label_position')
+ if self.hasInputFromPort('default_intervals'):
+ self.props['default_intervals'] = self.getInputFromPort('default_intervals')
+ if self.hasInputFromPort('data_interval'):
+ self.props['data_interval'] = self.getInputFromPort('data_interval')
+ if self.hasInputFromPort('pickradius'):
+ self.constructor_props['pickradius'] = self.getInputFromPort('pickradius')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplYAxisProperties(MplAxisProperties):
+ """None
+ """
+ _input_ports = [
+ ("offset_position", "basic:String",
+ {'optional': True}),
+ ("view_interval", "basic:String",
+ {'optional': True, 'docstring': 'If ignore is False, the order of vmin, vmax does not matter; the original axis orientation will be preserved. In addition, the view limits can be expanded, but will not be reduced. This method is for mpl internal use; for normal use, see :meth:`~matplotlib.axes.Axes.set_ylim`.'}),
+ ("ticks_position", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "Set the ticks position (left, right, both, default or none) 'both' sets the ticks to appear on both positions, but does not change the tick labels. 'default' resets the tick positions to the default: ticks on both positions, labels at left. 'none' can be used if you don't want any ticks. 'none' and 'both' affect only the ticks, not the labels.", 'values': "[['left', 'right', 'both', 'default', 'none']]", 'optional': True}),
+ ("axes", "basic:String",
+ {'optional': True}),
+ ("label_position", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Set the label position (left or right)', 'values': "[['left', 'right']]", 'optional': True}),
+ ("default_intervals", "basic:String",
+ {'optional': True, 'docstring': 'set the default limits for the axis interval if they are not mutated'}),
+ ("data_interval", "basic:String",
+ {'optional': True, 'docstring': 'set the axis data limits'}),
+ ("pickradius", "basic:Integer",
+ {'optional': True, 'defaults': "['15']"}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplYAxisProperties)")]
+
+ def __init__(self):
+ MplAxisProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplAxisProperties.compute(self)
+ if self.hasInputFromPort('offset_position'):
+ self.props['offset_position'] = self.getInputFromPort('offset_position')
+ if self.hasInputFromPort('view_interval'):
+ self.props['view_interval'] = self.getInputFromPort('view_interval')
+ if self.hasInputFromPort('ticks_position'):
+ self.props['ticks_position'] = self.getInputFromPort('ticks_position')
+ if self.hasInputFromPort('axes'):
+ self.constructor_props['axes'] = self.getInputFromPort('axes')
+ if self.hasInputFromPort('label_position'):
+ self.props['label_position'] = self.getInputFromPort('label_position')
+ if self.hasInputFromPort('default_intervals'):
+ self.props['default_intervals'] = self.getInputFromPort('default_intervals')
+ if self.hasInputFromPort('data_interval'):
+ self.props['data_interval'] = self.getInputFromPort('data_interval')
+ if self.hasInputFromPort('pickradius'):
+ self.constructor_props['pickradius'] = self.getInputFromPort('pickradius')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplLegendProperties(MplArtistProperties):
+ """
+ Place a legend on the axes at location loc. Labels are a
+ sequence of strings and loc can be a string or an integer
+ specifying the legend location
+
+ The location codes are::
+
+ 'best' : 0, (only implemented for axis legends)
+ 'upper right' : 1,
+ 'upper left' : 2,
+ 'lower left' : 3,
+ 'lower right' : 4,
+ 'right' : 5,
+ 'center left' : 6,
+ 'center right' : 7,
+ 'lower center' : 8,
+ 'upper center' : 9,
+ 'center' : 10,
+
+ loc can be a tuple of the noramilzed coordinate values with
+ respect its parent.
+
+
+ """
+ _input_ports = [
+ ("fancybox", "basic:String",
+ {'optional': True}),
+ ("handlelength", "basic:String",
+ {'optional': True}),
+ ("labels", "basic:String",
+ {'optional': True}),
+ ("labelspacing", "basic:String",
+ {'optional': True}),
+ ("columnspacing", "basic:String",
+ {'optional': True}),
+ ("handletextpad", "basic:String",
+ {'optional': True}),
+ ("ncol", "basic:Integer",
+ {'optional': True, 'defaults': "['1']"}),
+ ("borderaxespad", "basic:String",
+ {'optional': True}),
+ ("loc", "basic:String",
+ {'optional': True}),
+ ("bbox_to_anchor", "basic:String",
+ {'optional': True, 'docstring': 'set the bbox that the legend will be anchored.\n\nbbox can be a BboxBase instance, a tuple of [left, bottom, width, height] in the given transform (normalized axes coordinate if None), or a tuple of [left, bottom] where the width and height will be assumed to be zero.'}),
+ ("title", "basic:String",
+ {'optional': True, 'docstring': 'set the legend title. Fontproperties can be optionally set with prop parameter.'}),
+ ("handletextsep", "basic:String",
+ {'optional': True}),
+ ("numpoints", "basic:String",
+ {'optional': True}),
+ ("prop", "basic:String",
+ {'optional': True}),
+ ("handles", "basic:String",
+ {'optional': True}),
+ ("pad", "basic:String",
+ {'optional': True}),
+ ("borderpad", "basic:String",
+ {'optional': True}),
+ ("parent", "basic:String",
+ {'optional': True}),
+ ("axespad", "basic:String",
+ {'optional': True}),
+ ("labelsep", "basic:String",
+ {'optional': True}),
+ ("frame_on", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether the legend box patch is drawn'}),
+ ("scatterpoints", "basic:Integer",
+ {'optional': True, 'defaults': "['3']"}),
+ ("fontsize", "basic:String",
+ {'optional': True}),
+ ("shadow", "basic:String",
+ {'optional': True}),
+ ("handler_map", "basic:String",
+ {'optional': True}),
+ ("handleheight", "basic:String",
+ {'optional': True}),
+ ("scatteryoffsets", "basic:String",
+ {'optional': True}),
+ ("markerscale", "basic:String",
+ {'optional': True}),
+ ("frameon", "basic:String",
+ {'optional': True}),
+ ("mode", "basic:String",
+ {'optional': True}),
+ ("handlelen", "basic:String",
+ {'optional': True}),
+ ("default_handler_map", "basic:String",
+ {'optional': True, 'docstring': 'A class method to set the default handler map.'}),
+ ("bbox_transform", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplLegendProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('fancybox'):
+ self.constructor_props['fancybox'] = self.getInputFromPort('fancybox')
+ if self.hasInputFromPort('handlelength'):
+ self.constructor_props['handlelength'] = self.getInputFromPort('handlelength')
+ if self.hasInputFromPort('labels'):
+ self.constructor_props['labels'] = self.getInputFromPort('labels')
+ if self.hasInputFromPort('labelspacing'):
+ self.constructor_props['labelspacing'] = self.getInputFromPort('labelspacing')
+ if self.hasInputFromPort('columnspacing'):
+ self.constructor_props['columnspacing'] = self.getInputFromPort('columnspacing')
+ if self.hasInputFromPort('handletextpad'):
+ self.constructor_props['handletextpad'] = self.getInputFromPort('handletextpad')
+ if self.hasInputFromPort('ncol'):
+ self.constructor_props['ncol'] = self.getInputFromPort('ncol')
+ if self.hasInputFromPort('borderaxespad'):
+ self.constructor_props['borderaxespad'] = self.getInputFromPort('borderaxespad')
+ if self.hasInputFromPort('loc'):
+ self.constructor_props['loc'] = self.getInputFromPort('loc')
+ if self.hasInputFromPort('bbox_to_anchor'):
+ self.props['bbox_to_anchor'] = self.getInputFromPort('bbox_to_anchor')
+ if self.hasInputFromPort('title'):
+ self.props['title'] = self.getInputFromPort('title')
+ if self.hasInputFromPort('handletextsep'):
+ self.constructor_props['handletextsep'] = self.getInputFromPort('handletextsep')
+ if self.hasInputFromPort('numpoints'):
+ self.constructor_props['numpoints'] = self.getInputFromPort('numpoints')
+ if self.hasInputFromPort('prop'):
+ self.constructor_props['prop'] = self.getInputFromPort('prop')
+ if self.hasInputFromPort('handles'):
+ self.constructor_props['handles'] = self.getInputFromPort('handles')
+ if self.hasInputFromPort('pad'):
+ self.constructor_props['pad'] = self.getInputFromPort('pad')
+ if self.hasInputFromPort('borderpad'):
+ self.constructor_props['borderpad'] = self.getInputFromPort('borderpad')
+ if self.hasInputFromPort('parent'):
+ self.constructor_props['parent'] = self.getInputFromPort('parent')
+ if self.hasInputFromPort('axespad'):
+ self.constructor_props['axespad'] = self.getInputFromPort('axespad')
+ if self.hasInputFromPort('labelsep'):
+ self.constructor_props['labelsep'] = self.getInputFromPort('labelsep')
+ if self.hasInputFromPort('frame_on'):
+ self.props['frame_on'] = self.getInputFromPort('frame_on')
+ if self.hasInputFromPort('scatterpoints'):
+ self.constructor_props['scatterpoints'] = self.getInputFromPort('scatterpoints')
+ if self.hasInputFromPort('fontsize'):
+ self.constructor_props['fontsize'] = self.getInputFromPort('fontsize')
+ if self.hasInputFromPort('shadow'):
+ self.constructor_props['shadow'] = self.getInputFromPort('shadow')
+ if self.hasInputFromPort('handler_map'):
+ self.constructor_props['handler_map'] = self.getInputFromPort('handler_map')
+ if self.hasInputFromPort('handleheight'):
+ self.constructor_props['handleheight'] = self.getInputFromPort('handleheight')
+ if self.hasInputFromPort('scatteryoffsets'):
+ self.constructor_props['scatteryoffsets'] = self.getInputFromPort('scatteryoffsets')
+ if self.hasInputFromPort('markerscale'):
+ self.constructor_props['markerscale'] = self.getInputFromPort('markerscale')
+ if self.hasInputFromPort('frameon'):
+ self.constructor_props['frameon'] = self.getInputFromPort('frameon')
+ if self.hasInputFromPort('mode'):
+ self.constructor_props['mode'] = self.getInputFromPort('mode')
+ if self.hasInputFromPort('handlelen'):
+ self.constructor_props['handlelen'] = self.getInputFromPort('handlelen')
+ if self.hasInputFromPort('default_handler_map'):
+ self.props['default_handler_map'] = self.getInputFromPort('default_handler_map')
+ if self.hasInputFromPort('bbox_transform'):
+ self.constructor_props['bbox_transform'] = self.getInputFromPort('bbox_transform')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplAxesProperties(MplArtistProperties):
+ """
+ The :class:`Axes` contains most of the figure elements:
+ :class:`~matplotlib.axis.Axis`, :class:`~matplotlib.axis.Tick`,
+ :class:`~matplotlib.lines.Line2D`, :class:`~matplotlib.text.Text`,
+ :class:`~matplotlib.patches.Polygon`, etc., and sets the
+ coordinate system.
+
+ The :class:`Axes` instance supports callbacks through a callbacks
+ attribute which is a :class:`~matplotlib.cbook.CallbackRegistry`
+ instance. The events you can connect to are 'xlim_changed' and
+ 'ylim_changed' and the callback will be called with func(*ax*)
+ where *ax* is the :class:`Axes` instance.
+
+ """
+ _input_ports = [
+ ("adjustable", "basic:String",
+ {'entry_types': "['enum']", 'values': "[['box', 'datalim', 'box-forced']]", 'optional': True}),
+ ("cursor_props", "basic:Float",
+ {'optional': True, 'docstring': 'Set the cursor property as:\n\nax.set_cursor_props(linewidth, color)\n\nor:\n\nax.set_cursor_props((linewidth, color))'}),
+ ("figure", "basic:String",
+ {'optional': True, 'docstring': 'Set the class:~matplotlib.axes.Axes figure\n\naccepts a class:~matplotlib.figure.Figure instance'}),
+ ("yscale", "basic:String",
+ {'optional': True, 'docstring': "Call signature:\n\nset_yscale(value)\n\nSet the scaling of the y-axis: 'linear' | 'log' | 'symlog' Different kwargs are accepted, depending on the scale: 'linear'\n\n'log'\n\n\n\n'symlog'"}),
+ ("navigate", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether the axes responds to navigation toolbar commands'}),
+ ("aspect", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "aspect\n\n\n\nadjustable\n\n\n\n'box' does not allow axes sharing, as this can cause unintended side effect. For cases when sharing axes is fine, use 'box-forced'.\n\nanchor", 'values': "[['auto', 'normal', 'equal', 'num']]", 'optional': True}),
+ ("axis_bgcolor", "basic:Color",
+ {'optional': True, 'docstring': 'set the axes background color'}),
+ ("ylimSequence", "basic:List",
+ {'optional': True, 'docstring': 'Call signature:\n\nset_ylim(self, *args, **kwargs):\n\nSet the data limits for the yaxis\n\nExamples:\n\nset_ylim((bottom, top)) set_ylim(bottom, top) set_ylim(bottom=1) # top unchanged set_ylim(top=1) # bottom unchanged\n\nKeyword arguments:\n\n\n\nNote, the bottom (formerly ymin) value may be greater than the top (formerly ymax). For example, suppose y is depth in the ocean. Then one might use:\n\nset_ylim(5000, 0)\n\nso 5000 m depth is [...]
+ ("ylimScalar", "basic:Float",
+ {'docstring': 'Call signature:\n\nset_ylim(self, *args, **kwargs):\n\nSet the data limits for the yaxis\n\nExamples:\n\nset_ylim((bottom, top)) set_ylim(bottom, top) set_ylim(bottom=1) # top unchanged set_ylim(top=1) # bottom unchanged\n\nKeyword arguments:\n\n\n\nNote, the bottom (formerly ymin) value may be greater than the top (formerly ymax). For example, suppose y is depth in the ocean. Then one might use:\n\nset_ylim(5000, 0)\n\nso 5000 m depth is at the bottom of th [...]
+ ("sharey", "basic:String",
+ {'optional': True}),
+ ("xlimSequence", "basic:List",
+ {'optional': True, 'docstring': 'Call signature:\n\nset_xlim(self, *args, **kwargs):\n\nSet the data limits for the xaxis\n\nExamples:\n\nset_xlim((left, right)) set_xlim(left, right) set_xlim(left=1) # right unchanged set_xlim(right=1) # left unchanged\n\nKeyword arguments:\n\n\n\nNote, the left (formerly xmin) value may be greater than the right (formerly xmax). For example, suppose x is years before present. Then one might use:\n\nset_ylim(5000, 0)\n\nso 5000 years ago [...]
+ ("xlimScalar", "basic:Float",
+ {'docstring': 'Call signature:\n\nset_xlim(self, *args, **kwargs):\n\nSet the data limits for the xaxis\n\nExamples:\n\nset_xlim((left, right)) set_xlim(left, right) set_xlim(left=1) # right unchanged set_xlim(right=1) # left unchanged\n\nKeyword arguments:\n\n\n\nNote, the left (formerly xmin) value may be greater than the right (formerly xmax). For example, suppose x is years before present. Then one might use:\n\nset_ylim(5000, 0)\n\nso 5000 years ago is on the left of [...]
+ ("axis_on", "basic:String",
+ {'optional': True, 'docstring': 'turn on the axis'}),
+ ("title", "basic:String",
+ {'optional': True, 'docstring': 'Call signature:\n\nset_title(label, fontdict=None, **kwargs):\n\nSet the title for the axes.'}),
+ ("axisbg", "basic:String",
+ {'optional': True}),
+ ("label", "basic:String",
+ {'optional': True, 'defaults': "['']"}),
+ ("xticks", "basic:List",
+ {'optional': True, 'docstring': 'Set the x ticks with list of ticks'}),
+ ("fig", "basic:String",
+ {'optional': True}),
+ ("ylabel", "basic:String",
+ {'optional': True, 'docstring': 'Call signature:\n\nset_ylabel(ylabel, fontdict=None, labelpad=None, **kwargs)\n\nSet the label for the yaxis\n\nlabelpad is the spacing in points between the label and the y-axis'}),
+ ("autoscalex_on", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether autoscaling for the x-axis is applied on plot commands'}),
+ ("rasterization_zorder", "basic:String",
+ {'optional': True, 'docstring': 'Set zorder value below which artists will be rasterized. Set to None to disable rasterizing of artists below a particular zorder.'}),
+ ("axes_locator", "basic:String",
+ {'optional': True, 'docstring': 'set axes_locator'}),
+ ("axisbelow", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether the axis ticks and gridlines are above or below most artists'}),
+ ("frame_on", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether the axes rectangle patch is drawn'}),
+ ("navigate_mode", "basic:String",
+ {'optional': True, 'docstring': 'Set the navigation toolbar button status;\n\nthis is not a user-API function.'}),
+ ("xscale", "basic:String",
+ {'optional': True, 'docstring': "Call signature:\n\nset_xscale(value)\n\nSet the scaling of the x-axis: 'linear' | 'log' | 'symlog' Different kwargs are accepted, depending on the scale: 'linear'\n\n'log'\n\n\n\n'symlog'"}),
+ ("axis_off", "basic:String",
+ {'optional': True, 'docstring': 'turn off the axis'}),
+ ("autoscale_on", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether autoscaling is applied on plot commands'}),
+ ("ybound", "basic:String",
+ {'optional': True, 'docstring': 'Set the lower and upper numerical bounds of the y-axis. This method will honor axes inversion regardless of parameter order. It will not change the _autoscaleYon attribute.'}),
+ ("rect", "basic:String",
+ {'optional': True}),
+ ("sharex", "basic:String",
+ {'optional': True}),
+ ("yticklabelsSequence", "basic:List",
+ {'optional': True, 'docstring': "Call signature:\n\nset_yticklabels(labels, fontdict=None, minor=False, **kwargs)\n\nSet the y tick labels with list of strings labels. Return a list of :class:`~matplotlib.text.Text` instances.\n\nkwargs set :class:`~matplotlib.text.Text` properties for the labels. Valid properties are\n\nagg_filter: unknown alpha: float (0.0 transparent through 1.0 opaque) animated: [True | False] axes: an :class:`~matplotlib.axes.Axes` instance backgrou [...]
+ ("yticklabelsScalar", "basic:String",
+ {'docstring': "Call signature:\n\nset_yticklabels(labels, fontdict=None, minor=False, **kwargs)\n\nSet the y tick labels with list of strings labels. Return a list of :class:`~matplotlib.text.Text` instances.\n\nkwargs set :class:`~matplotlib.text.Text` properties for the labels. Valid properties are\n\nagg_filter: unknown alpha: float (0.0 transparent through 1.0 opaque) animated: [True | False] axes: an :class:`~matplotlib.axes.Axes` instance backgroundcolor: any matplo [...]
+ ("autoscaley_on", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether autoscaling for the y-axis is applied on plot commands'}),
+ ("xmargin", "basic:Float",
+ {'optional': True, 'docstring': 'Set padding of X data limits prior to autoscaling.\n\nm times the data interval will be added to each end of that interval before it is used in autoscaling.'}),
+ ("color_cycle", "basic:Color",
+ {'optional': True, 'docstring': 'Set the color cycle for any future plot commands on this Axes.\n\nclist is a list of mpl color specifiers.'}),
+ ("frameon", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("xlabel", "basic:String",
+ {'optional': True, 'docstring': 'Call signature:\n\nset_xlabel(xlabel, fontdict=None, labelpad=None, **kwargs)\n\nSet the label for the xaxis.\n\nlabelpad is the spacing in points between the label and the x-axis'}),
+ ("xbound", "basic:String",
+ {'optional': True, 'docstring': 'Set the lower and upper numerical bounds of the x-axis. This method will honor axes inversion regardless of parameter order. It will not change the _autoscaleXon attribute.'}),
+ ("yticks", "basic:List",
+ {'optional': True, 'docstring': 'Set the y ticks with list of ticks Keyword arguments:'}),
+ ("ymargin", "basic:Float",
+ {'optional': True, 'docstring': 'Set padding of Y data limits prior to autoscaling.\n\nm times the data interval will be added to each end of that interval before it is used in autoscaling.'}),
+ ("position", "basic:String",
+ {'optional': True, 'docstring': 'Set the axes position with:\n\npos = [left, bottom, width, height]\n\nin relative 0,1 coords, or pos can be a :class:`~matplotlib.transforms.Bbox`\n\nThere are two position variables: one which is ultimately used, but which may be modified by :meth:`apply_aspect`, and a second which is the starting point for :meth:`apply_aspect`.'}),
+ ("anchor", "basic:String",
+ {'docstring': 'anchor', 'values': "[['Center', 'bottom left', 'bottom', 'bottom right', 'right', 'top right', 'top', 'top left', 'left']]", 'optional': True}),
+ ("xticklabelsSequence", "basic:List",
+ {'optional': True, 'docstring': "Call signature:\n\nset_xticklabels(labels, fontdict=None, minor=False, **kwargs)\n\nSet the xtick labels with list of strings labels. Return a list of axis text instances.\n\nkwargs set the :class:`~matplotlib.text.Text` properties. Valid properties are\n\nagg_filter: unknown alpha: float (0.0 transparent through 1.0 opaque) animated: [True | False] axes: an :class:`~matplotlib.axes.Axes` instance backgroundcolor: any matplotlib color bbox [...]
+ ("xticklabelsScalar", "basic:String",
+ {'docstring': "Call signature:\n\nset_xticklabels(labels, fontdict=None, minor=False, **kwargs)\n\nSet the xtick labels with list of strings labels. Return a list of axis text instances.\n\nkwargs set the :class:`~matplotlib.text.Text` properties. Valid properties are\n\nagg_filter: unknown alpha: float (0.0 transparent through 1.0 opaque) animated: [True | False] axes: an :class:`~matplotlib.axes.Axes` instance backgroundcolor: any matplotlib color bbox: rectangle prop di [...]
+ ("titleProperties", "MplTextProperties",
+ {}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplAxesProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('adjustable'):
+ self.props['adjustable'] = self.getInputFromPort('adjustable')
+ if self.hasInputFromPort('cursor_props'):
+ self.props['cursor_props'] = self.getInputFromPort('cursor_props')
+ if self.hasInputFromPort('figure'):
+ self.props['figure'] = self.getInputFromPort('figure')
+ if self.hasInputFromPort('yscale'):
+ self.props['yscale'] = self.getInputFromPort('yscale')
+ if self.hasInputFromPort('navigate'):
+ self.props['navigate'] = self.getInputFromPort('navigate')
+ if self.hasInputFromPort('aspect'):
+ self.props['aspect'] = self.getInputFromPort('aspect')
+ if self.hasInputFromPort('axis_bgcolor'):
+ self.props['axis_bgcolor'] = self.getInputFromPort('axis_bgcolor')
+ self.props['axis_bgcolor'] = translate_color(self.props['axis_bgcolor'])
+ if self.hasInputFromPort('ylimSequence'):
+ self.props['ylim'] = self.getInputFromPort('ylimSequence')
+ elif self.hasInputFromPort('ylimScalar'):
+ self.props['ylim'] = self.getInputFromPort('ylimScalar')
+ if self.hasInputFromPort('sharey'):
+ self.constructor_props['sharey'] = self.getInputFromPort('sharey')
+ if self.hasInputFromPort('xlimSequence'):
+ self.props['xlim'] = self.getInputFromPort('xlimSequence')
+ elif self.hasInputFromPort('xlimScalar'):
+ self.props['xlim'] = self.getInputFromPort('xlimScalar')
+ if self.hasInputFromPort('axis_on'):
+ self.props['axis_on'] = self.getInputFromPort('axis_on')
+ if self.hasInputFromPort('title'):
+ self.props['title'] = self.getInputFromPort('title')
+ if self.hasInputFromPort('axisbg'):
+ self.constructor_props['axisbg'] = self.getInputFromPort('axisbg')
+ if self.hasInputFromPort('label'):
+ self.constructor_props['label'] = self.getInputFromPort('label')
+ if self.hasInputFromPort('xticks'):
+ self.props['xticks'] = self.getInputFromPort('xticks')
+ if self.hasInputFromPort('fig'):
+ self.constructor_props['fig'] = self.getInputFromPort('fig')
+ if self.hasInputFromPort('ylabel'):
+ self.props['ylabel'] = self.getInputFromPort('ylabel')
+ if self.hasInputFromPort('autoscalex_on'):
+ self.props['autoscalex_on'] = self.getInputFromPort('autoscalex_on')
+ if self.hasInputFromPort('rasterization_zorder'):
+ self.props['rasterization_zorder'] = self.getInputFromPort('rasterization_zorder')
+ if self.hasInputFromPort('axes_locator'):
+ self.props['axes_locator'] = self.getInputFromPort('axes_locator')
+ if self.hasInputFromPort('axisbelow'):
+ self.props['axisbelow'] = self.getInputFromPort('axisbelow')
+ if self.hasInputFromPort('frame_on'):
+ self.props['frame_on'] = self.getInputFromPort('frame_on')
+ if self.hasInputFromPort('navigate_mode'):
+ self.props['navigate_mode'] = self.getInputFromPort('navigate_mode')
+ if self.hasInputFromPort('xscale'):
+ self.props['xscale'] = self.getInputFromPort('xscale')
+ if self.hasInputFromPort('axis_off'):
+ self.props['axis_off'] = self.getInputFromPort('axis_off')
+ if self.hasInputFromPort('autoscale_on'):
+ self.props['autoscale_on'] = self.getInputFromPort('autoscale_on')
+ if self.hasInputFromPort('ybound'):
+ self.props['ybound'] = self.getInputFromPort('ybound')
+ if self.hasInputFromPort('rect'):
+ self.constructor_props['rect'] = self.getInputFromPort('rect')
+ if self.hasInputFromPort('sharex'):
+ self.constructor_props['sharex'] = self.getInputFromPort('sharex')
+ if self.hasInputFromPort('yticklabelsSequence'):
+ self.props['yticklabels'] = self.getInputFromPort('yticklabelsSequence')
+ elif self.hasInputFromPort('yticklabelsScalar'):
+ self.props['yticklabels'] = self.getInputFromPort('yticklabelsScalar')
+ if self.hasInputFromPort('autoscaley_on'):
+ self.props['autoscaley_on'] = self.getInputFromPort('autoscaley_on')
+ if self.hasInputFromPort('xmargin'):
+ self.props['xmargin'] = self.getInputFromPort('xmargin')
+ if self.hasInputFromPort('color_cycle'):
+ self.props['color_cycle'] = self.getInputFromPort('color_cycle')
+ self.props['color_cycle'] = translate_color(self.props['color_cycle'])
+ if self.hasInputFromPort('frameon'):
+ self.constructor_props['frameon'] = self.getInputFromPort('frameon')
+ if self.hasInputFromPort('xlabel'):
+ self.props['xlabel'] = self.getInputFromPort('xlabel')
+ if self.hasInputFromPort('xbound'):
+ self.props['xbound'] = self.getInputFromPort('xbound')
+ if self.hasInputFromPort('yticks'):
+ self.props['yticks'] = self.getInputFromPort('yticks')
+ if self.hasInputFromPort('ymargin'):
+ self.props['ymargin'] = self.getInputFromPort('ymargin')
+ if self.hasInputFromPort('position'):
+ self.props['position'] = self.getInputFromPort('position')
+ if self.hasInputFromPort('anchor'):
+ self.props['anchor'] = self.getInputFromPort('anchor')
+ self.props['anchor'] = translate_MplAxesProperties_anchor(self.props['anchor'])
+ if self.hasInputFromPort('xticklabelsSequence'):
+ self.props['xticklabels'] = self.getInputFromPort('xticklabelsSequence')
+ elif self.hasInputFromPort('xticklabelsScalar'):
+ self.props['xticklabels'] = self.getInputFromPort('xticklabelsScalar')
+ if self.hasInputFromPort('titleProperties'):
+ self.sub_props['title'] = self.getInputFromPort('titleProperties')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+ if not matplotlib.cbook.iterable(objs):
+ objs = [objs]
+ else:
+ objs = matplotlib.cbook.flatten(objs)
+ for obj in objs:
+ if 'title' in self.sub_props:
+ self.sub_props['title'].update_props(obj.title)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplAxesSubplotProperties(MplAxesProperties):
+ """None
+ """
+ _input_ports = [
+ ("fig", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplAxesSubplotProperties)")]
+
+ def __init__(self):
+ MplAxesProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplAxesProperties.compute(self)
+ if self.hasInputFromPort('fig'):
+ self.constructor_props['fig'] = self.getInputFromPort('fig')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplFigureProperties(MplArtistProperties):
+ """
+ The Figure instance supports callbacks through a *callbacks*
+ attribute which is a :class:`matplotlib.cbook.CallbackRegistry`
+ instance. The events you can connect to are 'dpi_changed', and
+ the callback will be called with ``func(fig)`` where fig is the
+ :class:`Figure` instance.
+
+ *patch*
+ The figure patch is drawn by a
+ :class:`matplotlib.patches.Rectangle` instance
+
+ *suppressComposite*
+ For multiple figure images, the figure will make composite
+ images depending on the renderer option_image_nocomposite
+ function. If suppressComposite is True|False, this will
+ override the renderer.
+
+ """
+ _input_ports = [
+ ("edgecolor", "basic:Color",
+ {'optional': True, 'docstring': 'Set the edge color of the Figure rectangle'}),
+ ("canvas", "basic:String",
+ {'optional': True, 'docstring': 'Set the canvas the contains the figure'}),
+ ("facecolor", "basic:Color",
+ {'optional': True, 'docstring': 'Set the face color of the Figure rectangle'}),
+ ("size_inches", "basic:String",
+ {'optional': True, 'docstring': 'set_size_inches(w,h, forward=False)\n\nSet the figure size in inches\n\nUsage:\n\nfig.set_size_inches(w,h) # OR fig.set_size_inches((w,h) )\n\noptional kwarg forward=True will cause the canvas size to be automatically updated; eg you can resize the figure window from the shell'}),
+ ("figwidth", "basic:Float",
+ {'optional': True, 'docstring': 'Set the width of the figure in inches'}),
+ ("frameon", "basic:Boolean",
+ {'optional': True, 'docstring': 'Set whether the figure frame (background) is displayed or invisible'}),
+ ("subplotpars", "basic:String",
+ {'optional': True}),
+ ("figheight", "basic:Float",
+ {'optional': True, 'docstring': 'Set the height of the figure in inches'}),
+ ("figsize", "basic:String",
+ {'optional': True}),
+ ("linewidth", "basic:Float",
+ {'optional': True, 'defaults': "['0.0']"}),
+ ("tight_layout", "basic:Boolean",
+ {'optional': True, 'docstring': "Set whether :meth:`tight_layout` is used upon drawing. If None, the rcParams['figure.autolayout'] value will be set."}),
+ ("dpi", "basic:Float",
+ {'optional': True, 'docstring': 'Set the dots-per-inch of the figure'}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplFigureProperties)")]
+
+ def __init__(self):
+ MplArtistProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplArtistProperties.compute(self)
+ if self.hasInputFromPort('edgecolor'):
+ self.props['edgecolor'] = self.getInputFromPort('edgecolor')
+ self.props['edgecolor'] = translate_color(self.props['edgecolor'])
+ if self.hasInputFromPort('canvas'):
+ self.props['canvas'] = self.getInputFromPort('canvas')
+ if self.hasInputFromPort('facecolor'):
+ self.props['facecolor'] = self.getInputFromPort('facecolor')
+ self.props['facecolor'] = translate_color(self.props['facecolor'])
+ if self.hasInputFromPort('size_inches'):
+ self.props['size_inches'] = self.getInputFromPort('size_inches')
+ if self.hasInputFromPort('figwidth'):
+ self.props['figwidth'] = self.getInputFromPort('figwidth')
+ if self.hasInputFromPort('frameon'):
+ self.props['frameon'] = self.getInputFromPort('frameon')
+ if self.hasInputFromPort('subplotpars'):
+ self.constructor_props['subplotpars'] = self.getInputFromPort('subplotpars')
+ if self.hasInputFromPort('figheight'):
+ self.props['figheight'] = self.getInputFromPort('figheight')
+ if self.hasInputFromPort('figsize'):
+ self.constructor_props['figsize'] = self.getInputFromPort('figsize')
+ if self.hasInputFromPort('linewidth'):
+ self.constructor_props['linewidth'] = self.getInputFromPort('linewidth')
+ if self.hasInputFromPort('tight_layout'):
+ self.props['tight_layout'] = self.getInputFromPort('tight_layout')
+ if self.hasInputFromPort('dpi'):
+ self.props['dpi'] = self.getInputFromPort('dpi')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+class MplAnnotationProperties(MplTextProperties):
+ """
+ A :class:`~matplotlib.text.Text` class to make annotating things
+ in the figure, such as :class:`~matplotlib.figure.Figure`,
+ :class:`~matplotlib.axes.Axes`,
+ :class:`~matplotlib.patches.Rectangle`, etc., easier.
+
+ """
+ _input_ports = [
+ ("xycoords", "basic:String",
+ {'entry_types': "['enum']", 'values': "[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]", 'optional': True, 'defaults': "['data']"}),
+ ("figure", "basic:String",
+ {'optional': True}),
+ ("annotation_clip", "basic:String",
+ {'optional': True}),
+ ("xytext", "basic:String",
+ {'optional': True}),
+ ("s", "basic:String",
+ {'optional': True}),
+ ("xy", "basic:String",
+ {'optional': True}),
+ ("textcoords", "basic:String",
+ {'entry_types': "['enum']", 'values': "[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]", 'optional': True}),
+ ("arrowprops", "basic:String",
+ {'optional': True}),
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(MplAnnotationProperties)")]
+
+ def __init__(self):
+ MplTextProperties.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+
+ def compute(self):
+ MplTextProperties.compute(self)
+ if self.hasInputFromPort('xycoords'):
+ self.constructor_props['xycoords'] = self.getInputFromPort('xycoords')
+ if self.hasInputFromPort('figure'):
+ self.props['figure'] = self.getInputFromPort('figure')
+ if self.hasInputFromPort('annotation_clip'):
+ self.constructor_props['annotation_clip'] = self.getInputFromPort('annotation_clip')
+ if self.hasInputFromPort('xytext'):
+ self.constructor_props['xytext'] = self.getInputFromPort('xytext')
+ if self.hasInputFromPort('s'):
+ self.constructor_props['s'] = self.getInputFromPort('s')
+ if self.hasInputFromPort('xy'):
+ self.constructor_props['xy'] = self.getInputFromPort('xy')
+ if self.hasInputFromPort('textcoords'):
+ self.constructor_props['textcoords'] = self.getInputFromPort('textcoords')
+ if self.hasInputFromPort('arrowprops'):
+ self.constructor_props['arrowprops'] = self.getInputFromPort('arrowprops')
+
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+
+_modules = [
+ MplArtistProperties,
+ Mpl_AxesImageBaseProperties,
+ MplAxesImageProperties,
+ MplNonUniformImageProperties,
+ MplBboxImageProperties,
+ MplPcolorImageProperties,
+ MplFigureImageProperties,
+ MplCollectionProperties,
+ MplPathCollectionProperties,
+ MplPolyCollectionProperties,
+ MplBrokenBarHCollectionProperties,
+ MplRegularPolyCollectionProperties,
+ MplStarPolygonCollectionProperties,
+ MplAsteriskPolygonCollectionProperties,
+ MplLineCollectionProperties,
+ MplCircleCollectionProperties,
+ MplEllipseCollectionProperties,
+ MplPatchCollectionProperties,
+ MplTriMeshProperties,
+ MplQuadMeshProperties,
+ MplPatchProperties,
+ MplShadowProperties,
+ MplRectangleProperties,
+ MplRegularPolygonProperties,
+ MplCirclePolygonProperties,
+ MplPathPatchProperties,
+ MplPolygonProperties,
+ MplFancyArrowProperties,
+ MplWedgeProperties,
+ MplArrowProperties,
+ MplYAArrowProperties,
+ MplEllipseProperties,
+ MplCircleProperties,
+ MplArcProperties,
+ MplFancyBboxPatchProperties,
+ MplFancyArrowPatchProperties,
+ MplConnectionPatchProperties,
+ MplLine2DProperties,
+ MplTextProperties,
+ MplTextWithDashProperties,
+ MplTickProperties,
+ MplXTickProperties,
+ MplYTickProperties,
+ MplAxisProperties,
+ MplXAxisProperties,
+ MplYAxisProperties,
+ MplLegendProperties,
+ MplAxesProperties,
+ MplAxesSubplotProperties,
+ MplFigureProperties,
+ MplAnnotationProperties,
+]
diff --git a/vistrails/packages/matplotlib/artists_template.py.mako b/vistrails/packages/matplotlib/artists_template.py.mako
new file mode 100644
index 0000000..af51b1d
--- /dev/null
+++ b/vistrails/packages/matplotlib/artists_template.py.mako
@@ -0,0 +1,170 @@
+from vistrails.core.modules.vistrails_module import Module
+from bases import MplProperties
+import matplotlib.artist
+import matplotlib.cbook
+
+% if specs.custom_code:
+${specs.custom_code}
+% endif
+
+<%def name="get_props(t_ps)">\
+% if t_ps.constructor_arg:
+self.constructor_props['${t_ps.arg}']\
+% else:
+self.props['${t_ps.arg}']\
+% endif
+</%def>
+
+<%def name="do_translate(t_spec, t_ps, t_core_ps=None)">\
+<%
+if t_core_ps is None:
+ t_core_ps = t_ps
+%>\
+% if type(t_ps.translations) == dict:
+${get_props(t_core_ps)} = translate_${t_spec.name}_${t_ps.name}(${get_props(t_core_ps)})\
+% else:
+${get_props(t_core_ps)} = ${t_ps.translations}(${get_props(t_core_ps)})\
+% endif
+</%def>
+
+def translate_color(c):
+ return c.tuple
+
+% for spec in specs.module_specs:
+% for ps in spec.port_specs:
+% if ps.translations and type(ps.translations) == dict:
+def translate_${spec.name}_${ps.name}(val):
+ translate_dict = ${ps.translations}
+ return translate_dict[val]
+% endif
+% endfor
+% endfor
+
+% for spec in specs.module_specs:
+class ${spec.name}(${spec.superklass}):
+ """${spec.docstring}
+ """
+ _input_ports = [
+ % for ps in spec.port_specs:
+ % if not ps.hide:
+ ("${ps.name}", "${ps.get_port_type()}",
+ ${ps.get_port_attrs()}),
+ % for alt_ps in ps.alternate_specs:
+ ("${alt_ps.name}", "${alt_ps.get_port_type()}",
+ ${alt_ps.get_port_attrs()}),
+ % endfor
+ % endif
+ % endfor
+ % for ps in spec.output_port_specs:
+ % if ps.is_property():
+ ("${ps.name}", "${ps.get_property_type()}",
+ ${ps.get_port_attrs()}),
+ % endif
+ % endfor
+ ]
+
+ # no output ports except self
+ _output_ports = [("self", "(${spec.name})")]
+
+ def __init__(self):
+ ${spec.superklass}.__init__(self)
+ self.props = {}
+ self.constructor_props = {}
+ self.sub_props = {}
+ % if spec.get_init():
+ ${spec.get_init()}
+ % endif
+
+ def compute(self):
+ % if spec.get_compute_before():
+ ${spec.get_compute_before()}
+ % endif
+ ${spec.superklass}.compute(self)
+ % for ps in spec.port_specs:
+ % if not ps.hide and ps.in_kwargs:
+ % if ps.required:
+ % if ps.has_alternate_versions():
+ if self.hasInputFromPort('${ps.name}'):
+ ${get_props(ps)} = self.getInputFromPort('${ps.name}')
+ % if ps.translations:
+ ${do_translate(spec, ps)}
+ % endif
+ % for alt_ps in ps.alternate_specs:
+ elif self.hasInputFromPort('${alt_ps.name}'):
+ ${get_props(ps)} = self.getInputFromPort('${alt_ps.name}')
+ % if alt_ps.translations:
+ ${do_translate(spec, alt_ps, ps)}
+ % endif
+ % endfor
+ else:
+ raise ModuleError(self, 'Must set one of "${ps.name}", ' \
+ '${', '.join('"%s"' % alt_ps.name for alt_ps in ps.alternate_specs)}')
+ % else:
+ ${get_props(ps)} = self.getInputFromPort('${ps.name}')
+ % if ps.translations:
+ ${do_translate(spec, ps)}
+ % endif
+ % endif
+ ## self.props['${ps.arg}'] = self.getInputFromPort('${ps.name}')
+ ## % if ps.translations:
+ ## ${do_translate(spec, ps)}
+ ## % endif
+ % else:
+ if self.hasInputFromPort('${ps.name}'):
+ ${get_props(ps)} = self.getInputFromPort('${ps.name}')
+ % if ps.translations:
+ ${do_translate(spec, ps)}
+ % endif
+ % for alt_ps in ps.alternate_specs:
+ elif self.hasInputFromPort('${alt_ps.name}'):
+ ${get_props(ps)} = self.getInputFromPort('${alt_ps.name}')
+ % if alt_ps.translations:
+ ${do_translate(spec, alt_ps, ps)}
+ % endif
+ % endfor
+ ## if self.hasInputFromPort('${ps.name}'):
+ ## self.props['${ps.arg}'] = self.getInputFromPort('${ps.name}')
+ ## % if ps.translations:
+ ## ${do_translate(spec, ps)}
+ ## % endif
+ % endif
+ % endif
+ % endfor
+ % for ps in spec.output_port_specs:
+ % if ps.is_property():
+ if self.hasInputFromPort('${ps.name}'):
+ self.sub_props['${ps.arg}'] = self.getInputFromPort('${ps.name}')
+ % endif
+ % endfor
+
+ % if spec.get_compute_after():
+ ${spec.get_compute_after()}
+ % endif
+
+ def update_props(self, objs):
+ matplotlib.artist.setp(objs, **self.props)
+ % if any(ps.is_property() for ps in spec.output_port_specs):
+ if not matplotlib.cbook.iterable(objs):
+ objs = [objs]
+ else:
+ objs = matplotlib.cbook.flatten(objs)
+ for obj in objs:
+ % for ps in spec.output_port_specs:
+ % if ps.is_property():
+ if '${ps.arg}' in self.sub_props:
+ self.sub_props['${ps.arg}'].update_props(obj.${ps.compute_parent})
+ % endif
+ % endfor
+ % endif
+
+ def update_kwargs(self, kwargs):
+ kwargs.update(self.constructor_props)
+ kwargs.update(self.props)
+
+% endfor
+
+_modules = [
+% for spec in specs.module_specs:
+ ${spec.name},
+% endfor
+]
diff --git a/vistrails/packages/matplotlib/bases.py b/vistrails/packages/matplotlib/bases.py
new file mode 100644
index 0000000..92b7ea5
--- /dev/null
+++ b/vistrails/packages/matplotlib/bases.py
@@ -0,0 +1,291 @@
+###############################################################################
+##
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import pylab
+import urllib
+
+from vistrails.core.modules.basic_modules import CodeRunnerMixin
+from vistrails.core.modules.vistrails_module import Module, NotCacheable
+
+################################################################################
+
+class MplProperties(Module):
+ _output_ports = [("self", "(MplProperties)")]
+
+ def update_props(self, objs):
+ # must implement in subclass
+ pass
+
+
+#base class for 2D plots
+class MplPlot(NotCacheable, Module):
+ # _input_ports = [("subfigRow", "(edu.utah.sci.vistrails.basic:Integer)",
+ # {"defaults": ["1"]}),
+ # ("subfigCol", "(edu.utah.sci.vistrails.basic:Integer)",
+ # {"defaults": ["1"]})]
+ _output_ports = [("self", "(MplPlot)")]
+
+ def __init__(self):
+ Module.__init__(self)
+ # self.figInstance = None
+
+ # def set_fig(self, fig):
+ # self.figInstance = fig
+
+ # def get_fig(self):
+ # if self.figInstance is None:
+ # self.figInstance = pylab.figure()
+ # return self.figInstance
+
+ # def get_translation(self, port, val):
+ # '''doing translation for enum type of the input ports'''
+
+ # for klass in self.__class__.mro():
+ # if '_mpl_translations' in klass.__dict__ and \
+ # port in klass._mpl_translations:
+ # obj = klass._mpl_translations[port]
+ # if isinstance(obj, dict):
+ # if val in obj:
+ # return obj[val]
+ # else:
+ # raise ArtistException(
+ # "Value '%s' for input '%s' invalid." % (val, port))
+ # else:
+ # print "trying to call"
+ # return obj(val)
+ # return None
+
+ # def get_kwargs_except(self, listExcepts):
+ # ''' getting all the input ports except those ports listed inside listExcepts
+ # return format: {port_name:value,...}'''
+ # kwargs = {}
+ # for port in self.inputPorts:
+ # if port not in listExcepts:
+ # val = self.getInputFromPort(port)
+ # translation = self.get_translation(port, val)
+ # if translation is not None:
+ # kwargs[port] = translation
+ # else:
+ # kwargs[port] = val
+ # return kwargs
+
+class MplSource(CodeRunnerMixin, MplPlot):
+ """
+ MplSource is a module similar to PythonSource. The user can enter
+ Matplotlib code into this module. This will then get connected to
+ MplFigure to draw the figure. Please note that, codes entered in
+ this module should limit to subplot() scope only. Using
+ Figure-level commands, e.g. figure() or show(), the result will be
+ unknown
+
+ """
+ _input_ports = [('source', '(basic:String)')]
+
+ def compute(self):
+ """ compute() -> None
+ """
+ source = self.getInputFromPort('source')
+ s = ('from pylab import *\n' +
+ 'from numpy import *\n' +
+ urllib.unquote(source))
+
+ self.run_code(s, use_input=True, use_output=True)
+
+class MplFigure(Module):
+ # _input_ports = [("addPlot", "(MplPlot)"),
+ # ("numSubfigRows", "(edu.utah.sci.vistrails.basic:Integer)",
+ # {"defaults": ["1"]}),
+ # ("numSubfigCols", "(edu.utah.sci.vistrails.basic:Integer)",
+ # {"defaults": ["1"]}),
+ # ]
+ _input_ports = [("addPlot", "(MplPlot)"),
+ ("axesProperties", "(MplAxesProperties)"),
+ ("figureProperties", "(MplFigureProperties)"),
+ ("setLegend", "(MplLegend)")]
+
+ _output_ports = [("file", "(basic:File)"),
+ ("self", "(MplFigure)")]
+
+ def __init__(self):
+ Module.__init__(self)
+ self.figInstance = None
+
+ def updateUpstream(self):
+ if self.figInstance is None:
+ self.figInstance = pylab.figure()
+ pylab.hold(True)
+ Module.updateUpstream(self)
+
+ def compute(self):
+ plots = self.getInputListFromPort("addPlot")
+ # num_rows = self.getInputFromPort("numSubfigRows")
+ # if num_rows < 1:
+ # raise ModuleError(self, "numSubfigRows must be at least 1.")
+ # num_cols = self.getInputFromPort("numSubfigCols")
+ # if num_cols < 1:
+ # raise ModuleError(self, "numSubfigCols must be at least 1.")
+ # if len(plots) < 1:
+ # raise ModuleError(self, "Must add at least one plot to figure.")
+
+ # FIXME just take the fig instance from the first plot
+ # self.figInstance = plots[0].figInstance
+
+ if self.hasInputFromPort("figureProperties"):
+ figure_props = self.getInputFromPort("figureProperties")
+ figure_props.update_props(self.figInstance)
+ if self.hasInputFromPort("axesProperties"):
+ axes_props = self.getInputFromPort("axesProperties")
+ axes_props.update_props(self.figInstance.gca())
+ if self.hasInputFromPort("setLegend"):
+ legend = self.getInputFromPort("setLegend")
+ self.figInstance.gca().legend()
+
+ #FIXME write file out if File port is attached!
+
+ # if num_rows > 1 or num_cols > 1:
+ # # need to reconstruct plot...
+ # self.figInstance = pylab.figure()
+ # else:
+ # self.figInstance = plots[0].figInstance
+
+ # for plot in plots:
+ # p_axes = plot.get_fig().gca()
+ # print "DPI:", plot.get_fig().dpi
+ # for c in p_axes.collections:
+ # print "TRANSFORM:", c._transform
+ # print "DATALIM:", c.get_datalim(p_axes.transData)
+ # print "PREPARE POINTS:", c._prepare_points()
+
+ # self.figInstance = pylab.figure()
+ # axes = self.figInstance.gca()
+ # x0 = None
+ # x1 = None
+ # y0 = None
+ # y1 = None
+ # dataLim = None
+ # for plot in plots:
+ # p_axes = plot.get_fig().gca()
+ # dataLim = p_axes.dataLim.frozen()
+ # p_x0, p_x1 = p_axes.get_xlim()
+ # if x0 is None or p_x0 < x0:
+ # x0 = p_x0
+ # if x1 is None or p_x1 > x1:
+ # x1 = p_x1
+ # p_y0, p_y1 = p_axes.get_ylim()
+ # if y0 is None or p_y0 < y0:
+ # y0 = p_y0
+ # if y1 is None or p_y1 > y1:
+ # y1 = p_y1
+
+ # print x0, x1, y0, y1
+ # axes.set_xlim(x0, x1, emit=False, auto=None)
+ # axes.set_ylim(y0, y1, emit=False, auto=None)
+
+ # # axes.dataLim = dataLim
+ # # axes.ignore_existing_data_limits = False
+ # # axes.autoscale_view()
+
+ # for plot in plots:
+ # p_axes = plot.get_fig().gca()
+ # # axes.lines.extend(p_axes.lines)
+ # for line in p_axes.lines:
+ # print "adding line!"
+ # line = copy.copy(line)
+ # line._transformSet = False
+ # axes.add_line(line)
+ # # axes.patches.extend(p_axes.patches)
+ # for patch in p_axes.patches:
+ # print "adding patch!"
+ # patch = copy.copy(patch)
+ # patch._transformSet = False
+ # axes.add_patch(patch)
+ # axes.texts.extend(p_axes.texts)
+ # # axes.tables.extend(p_axes.tables)
+ # for table in p_axes.tables:
+ # table = copy.copy(table)
+ # table._transformSet = False
+ # axes.add_table(table)
+ # # axes.artists.extend(p_axes.artists)
+ # for artist in p_axes.artists:
+ # artist = copy.copy(artist)
+ # artist._transformSet = False
+ # axes.add_artist(artist)
+ # axes.images.extend(p_axes.images)
+ # # axes.collections.extend(p_axes.collections)
+ # for collection in p_axes.collections:
+ # print "adding collection!"
+ # # print "collection:", collection.__class__.__name__
+ # # print "datalim:", p_axes.dataLim
+ # # transOffset = axes.transData
+ # collection = copy.copy(collection)
+ # # collection._transformSet = False
+ # # print dir(mtransforms)
+ # collection.set_transform(mtransforms.IdentityTransform())
+ # collection._transOffset = axes.transData
+ # # collection._transformSet = False
+ # collection._label = None
+ # collection._clippath = None
+ # axes.add_collection(collection)
+ # # collection.set_transform(mtransforms.IdentityTransform())
+ # # axes.collections.append(collection)
+ # # axes.containers.extend(p_axes.containers)
+ # print "transFigure start:", self.figInstance.transFigure
+ # # axes.dataLim = dataLim
+ # # axes.ignore_existing_data_limits = False
+ # # print "datalim after:", axes.dataLim
+
+
+ # # print "DPI:", self.figInstance.dpi
+ # # for c in axes.collections:
+ # # print "TRANSFORM:", c._transform
+ # # print "DATALIM:", c.get_datalim(p_axes.transData)
+ # # print "PREPARE POINTS:", c._prepare_points()
+
+
+ self.setResult("self", self)
+
+class MplContourSet(Module):
+ pass
+
+class MplQuadContourSet(MplContourSet):
+ pass
+
+_modules = [(MplProperties, {'abstract': True}),
+ (MplPlot, {'abstract': True}),
+ (MplSource, {'configureWidgetType': \
+ ('vistrails.packages.matplotlib.widgets',
+ 'MplSourceConfigurationWidget')}),
+ MplFigure,
+ MplContourSet,
+ MplQuadContourSet]
diff --git a/vistrails/packages/matplotlib/diff.py b/vistrails/packages/matplotlib/diff.py
new file mode 100644
index 0000000..e5ddc9e
--- /dev/null
+++ b/vistrails/packages/matplotlib/diff.py
@@ -0,0 +1,354 @@
+import re
+from xml.etree import ElementTree as ET
+from specs import SpecList, ModuleSpec, InputPortSpec, OutputPortSpec, \
+ AlternatePortSpec
+
+def compute_ps_diff(root, in_ps_list, out_ps_list, code_ref, qualifier,
+ port=None):
+ if qualifier == "alternate":
+ if port is None:
+ raise ValueError("Must specify port with alternate")
+ out_port_specs = dict((ps.name, ps) for ps in out_ps_list)
+ in_port_specs = dict((ps.name, ps) for ps in in_ps_list)
+ else:
+ out_port_specs = dict((ps.arg, ps) for ps in out_ps_list)
+ in_port_specs = dict((ps.arg, ps) for ps in in_ps_list)
+
+ out_port_specs_set = set(out_port_specs.iterkeys())
+ in_port_specs_set = set(in_port_specs.iterkeys())
+
+ for arg in in_port_specs_set - out_port_specs_set:
+ # print 'argument "%s" of code reference "%s" removed' % \
+ # (arg, code_ref)
+ print "- %s.%s.%s" % (code_ref, qualifier, arg)
+ elt = ET.Element("deletePortSpec")
+ elt.set("code_ref", code_ref)
+ if qualifier == "alternate":
+ elt.set("port", port)
+ elt.set("altName", arg)
+ else:
+ elt.set("port", arg)
+ elt.set("type", qualifier)
+ root.append(elt)
+
+ for arg, out_ps in out_port_specs.iteritems():
+ if arg not in in_port_specs:
+ # print 'argument "%s" of code reference "%s" added' % \
+ # (arg, code_ref)
+ print "out_ps:", out_ps
+ print "+ %s.%s.%s %s" % (code_ref, qualifier, arg,
+ ET.tostring(out_ps.to_xml()))
+ elt = ET.Element("addPortSpec")
+ elt.set("code_ref", code_ref)
+ if qualifier == "alternate":
+ elt.set("port", port)
+ elt.set("altName", arg)
+ else:
+ elt.set("port", arg)
+ elt.set("type", qualifier)
+ subelt = ET.Element("value")
+ subelt.append(out_ps.to_xml())
+ elt.append(subelt)
+ root.append(elt)
+ continue
+
+ in_ps = in_port_specs[arg]
+
+ # attrs = ['name', 'port_type', 'docstring', 'hide', 'entry_types',
+ # 'values', 'defaults', 'translations']
+ if qualifier == "output":
+ attr_list = OutputPortSpec.attrs
+ elif qualifier == "input":
+ attr_list = InputPortSpec.attrs
+ elif qualifier == "alternate":
+ attr_list = AlternatePortSpec.attrs
+ else:
+ raise ValueError('Unknown port type "%s"' % qualifier)
+ for attr in attr_list:
+ in_val = getattr(in_ps, attr)
+ out_val = getattr(out_ps, attr)
+ if in_val != out_val:
+ # print '%s of argument "%s" changed from "%s" to "%s"' % \
+ # (attr, arg, in_val, out_val)
+ print "C %s.%s.%s.%s %s" % (code_ref, qualifier, arg, attr,
+ out_val)
+ elt = ET.Element("changePortSpec")
+ elt.set("code_ref", code_ref)
+ if qualifier == "alternate":
+ elt.set("port", port)
+ elt.set("altName", arg)
+ else:
+ elt.set("port", arg)
+ elt.set("type", qualifier)
+ elt.set("attr", attr)
+ subelt = ET.Element("value")
+ subelt.text = str(out_val)
+ elt.append(subelt)
+ root.append(elt)
+ # only do this for input right now
+ if qualifier == "input":
+ compute_ps_diff(root, in_ps.alternate_specs, out_ps.alternate_specs,
+ code_ref, "alternate", arg)
+
+def compute_diff(in_fname, out_fname, diff_fname):
+ in_specs = SpecList.read_from_xml(in_fname)
+ out_specs = SpecList.read_from_xml(out_fname)
+
+ in_refs = dict((spec.code_ref, spec) for spec in in_specs.module_specs)
+ out_refs = dict((spec.code_ref, spec) for spec in out_specs.module_specs)
+
+ in_refs_set = set(in_refs.iterkeys())
+ out_refs_set = set(out_refs.iterkeys())
+
+ root = ET.Element("diff")
+
+ if in_specs.custom_code != out_specs.custom_code:
+ elt = ET.Element("changeCustomCode")
+ subelt = ET.Element("value")
+ subelt.text = out_specs.custom_code
+ elt.append(subelt)
+ root.append(elt)
+
+ for ref in in_refs_set - out_refs_set:
+ # print 'code reference "%s" removed' % ref
+ print "- %s" % ref
+ elt = ET.Element("deleteModule")
+ elt.set("code_ref", ref)
+ root.append(elt)
+
+ for code_ref, out_spec in out_refs.iteritems():
+ # need to check port specs, which removed, which added
+ if code_ref not in in_refs:
+ # print 'code reference "%s" added' % code_ref
+ print "+ %s %s" % (ref, ET.tostring(out_spec.to_xml()))
+ elt = ET.Element("addModule")
+ elt.set("code_ref", ref)
+ subelt = ET.Element("value")
+ subelt.append(out_spec.to_xml())
+ elt.append(subelt)
+ root.append(elt)
+ continue
+
+ in_spec = in_refs[code_ref]
+
+ for attr in ModuleSpec.attrs:
+ in_val = getattr(in_spec, attr)
+ out_val = getattr(out_spec, attr)
+ if in_val != out_val:
+ print "C %s.%s %s" % (out_spec.code_ref, attr, out_val)
+ elt = ET.Element("changeModule")
+ elt.set("code_ref", out_spec.code_ref)
+ elt.set("attr", attr)
+ subelt = ET.Element("value")
+ subelt.text = str(out_val)
+ elt.append(subelt)
+ root.append(elt)
+
+ # if in_spec.name != out_spec.name:
+ # # print 'name of ref "%s" changed from "%s" to "%s"' % \
+ # # (out_spec.code_ref, in_spec.name, out_spec.name)
+ # print "C %s.name %s" % (out_spec.code_ref, out_spec.name)
+ # if in_spec.superklass != out_spec.superklass:
+ # print 'superclass of ref "%s" changed from "%s" to "%s"' % \
+ # (out_spec.code_ref, in_spec.superklass, out_spec.superklass)
+
+
+ compute_ps_diff(root, in_spec.port_specs, out_spec.port_specs,
+ code_ref, "input")
+ compute_ps_diff(root, in_spec.output_port_specs,
+ out_spec.output_port_specs,
+ code_ref, "output")
+ # out_port_specs = dict((ps.arg, ps) for ps in out_spec.port_specs)
+ # in_port_specs = dict((ps.arg, ps) for ps in in_spec.port_specs)
+
+ # out_port_specs_set = set(out_port_specs.iterkeys())
+ # in_port_specs_set = set(in_port_specs.iterkeys())
+
+ # for arg in in_port_specs_set - out_port_specs_set:
+ # # print 'argument "%s" of code reference "%s" removed' % \
+ # # (arg, code_ref)
+ # print "- %s.%s" % (code_ref, arg)
+
+ # for arg, out_ps in out_port_specs.iteritems():
+ # if arg not in in_port_specs:
+ # # print 'argument "%s" of code reference "%s" added' % \
+ # # (arg, code_ref)
+ # print "+ %s.%s" % (code_ref, arg)
+ # print ET.tostring(out_ps.to_xml())
+ # continue
+
+ # in_ps = in_port_specs[arg]
+
+ # # attrs = ['name', 'port_type', 'docstring', 'hide', 'entry_types',
+ # # 'values', 'defaults', 'translations']
+ # for attr in PortSpec.attrs:
+ # in_val = getattr(in_ps, attr)
+ # out_val = getattr(out_ps, attr)
+ # if in_val != out_val:
+ # # print '%s of argument "%s" changed from "%s" to "%s"' % \
+ # # (attr, arg, in_val, out_val)
+ # print "C %s.%s.%s %s" % (code_ref, arg, attr, out_val)
+
+ tree = ET.ElementTree(root)
+ def indent(elem, level=0):
+ i = "\n" + level*" "
+ if len(elem):
+ if not elem.text or not elem.text.strip():
+ elem.text = i + " "
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ for elem in elem:
+ indent(elem, level+1)
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ else:
+ if level and (not elem.tail or not elem.tail.strip()):
+ elem.tail = i
+ indent(tree.getroot())
+
+ tree.write(diff_fname)
+
+def apply_diff(in_fname, diff_fname, out_fname):
+ in_specs = SpecList.read_from_xml(in_fname)
+
+ in_refs = dict((spec.code_ref, (i, spec))
+ for i, spec in enumerate(in_specs.module_specs))
+ in_ips_refs = dict(((spec.code_ref, ps.arg), (i, ps))
+ for spec in in_specs.module_specs
+ for i, ps in enumerate(spec.port_specs))
+ in_ops_refs = dict(((spec.code_ref, ps.arg), (i, ps))
+ for spec in in_specs.module_specs
+ for i, ps in enumerate(spec.output_port_specs))
+ in_alt_refs = dict(((spec.code_ref, ps.arg, alt_ps.name), (i, ps))
+ for spec in in_specs.module_specs
+ for ps in spec.port_specs
+ for i, alt_ps in enumerate(ps.alternate_specs))
+
+ tree = ET.parse(diff_fname)
+ for elt in tree.getroot():
+ if elt.tag == "changeCustomCode":
+ val = elt.getchildren()[0].text
+ in_specs.custom_code = val
+ continue
+ code_ref = elt.get("code_ref")
+ m_spec = in_refs[code_ref][1]
+ port = elt.get("port", None)
+ if port:
+ port_type = elt.get("type")
+ if port_type == "alternate":
+ alt_name = elt.get("altName")
+ if elt.tag.startswith('delete'):
+ if port:
+ if port_type == "input":
+ idx = in_ips_refs[(code_ref, port)][0]
+ del m_spec.port_specs[idx]
+ elif port_type == 'output':
+ idx = in_ops_refs[(code_ref, port)][0]
+ del m_spec.output_port_specs[idx]
+ elif port_type == 'alternate':
+ ps = in_ips_refs[(code_ref, port)][1]
+ idx = in_alt_refs[(code_ref, port, alt_name)][0]
+ del ps.alternate_specs[idx]
+ else:
+ raise ValueError('Cannot access list of type "%s"' %
+ port_type)
+ else:
+ idx = in_refs[code_ref][0]
+ del in_specs.module_specs[idx]
+ elif elt.tag.startswith('add'):
+ for child in elt.getchildren():
+ if child.tag == 'value':
+ for subchild in child.getchildren():
+ value = subchild
+ if port:
+ if port_type == "input":
+ m_spec.port_specs.append(InputPortSpec.from_xml(value))
+ elif port_type == "output":
+ # print "VALUE:", ET.tostring(value)
+ m_spec.output_port_specs.append(
+ OutputPortSpec.from_xml(value))
+ elif port_type == "alternate":
+ ps = in_ips_refs[(code_ref, port)][1]
+ ps.alternate_specs.append(AlternatePortSpec.from_xml(value))
+ else:
+ raise ValueError('Cannot access list of type "%s"' %
+ port_type)
+ else:
+ in_specs.module_specs.append(ModuleSpec.from_xml(value))
+ elif elt.tag.startswith('change'):
+ attr = elt.get("attr")
+ for child in elt.getchildren():
+ if child.tag == 'value':
+ value = child.text
+ if port:
+ # KLUDGE to fix change from output_type to port_type
+ if attr == "output_type":
+ attr = "port_type"
+ if port_type == "input":
+ port_spec = in_ips_refs[(code_ref, port)][1]
+ setattr(port_spec, attr, value)
+ elif port_type == "output":
+ port_spec = in_ops_refs[(code_ref, port)][1]
+ setattr(port_spec, attr, value)
+ elif port_type == "alternate":
+ port_spec = in_alt_refs[(code_ref, port, alt_name)][1]
+ setattr(port_spec, attr, value)
+ else:
+ setattr(m_spec, attr, value)
+
+ # with f = open(diff_fname):
+ # f_iter = f.__iter__()
+ # for line in f_iter:
+ # line = line.strip()
+ # if not re.match("[+-C]", line):
+ # raise RuntimeError("Problem parsing line\n%s" % line)
+ # if line.startswith('-'):
+ # arr = line.split(' ', 1)
+ # prop = arr[1].split('.')
+ # if len(prop) < 2:
+ # idx = in_refs[prop[0]][0]
+ # del in_specs.module_specs[idx]
+ # else:
+ # m_specs = in_refs[prop[0]][1]
+ # if prop[1] == 'input':
+ # idx = in_ips_refs[prop[0], prop[2]][0]
+ # del m_specs.port_specs[idx]
+ # elif prop[1] == 'output':
+ # idx = in_ops_refs[prop[0], prop[2]][0]
+ # del m_specs.output_port_specs[idx]
+ # else:
+ # raise ValueError('Cannot access list of type "%s"' %
+ # prop[1])
+ # elif line.startswith('+'):
+ # arr = line.split(' ', 2)
+ # prop = arr[1].split('.')
+ # if len(prop) < 2:
+ # in_specs.module_specs.append(ModuleSpec.from_xml(arr[2]))
+
+ # line.split(' ', 2)
+
+ in_specs.write_to_xml(out_fname)
+
+def run_compute():
+ compute_diff("mpl_artists_raw.xml", "mpl_artists.xml",
+ "mpl_artists_diff.xml")
+ compute_diff("mpl_plots_raw.xml", "mpl_plots.xml", "mpl_plots_diff.xml")
+
+def run_apply():
+ apply_diff("mpl_artists_raw.xml", "mpl_artists_diff.xml", "mpl_artists.xml")
+ apply_diff("mpl_plots_raw.xml", "mpl_plots_diff.xml", "mpl_plots.xml")
+
+def usage():
+ print "Usage: %s %s [apply|compute]" % (sys.executable, sys.argv[0])
+
+if __name__ == '__main__':
+ import sys
+ if len(sys.argv) < 2:
+ usage()
+ elif sys.argv[1] == "apply":
+ run_apply()
+ elif sys.argv[1] == "compute":
+ run_compute()
+ else:
+ usage()
+
diff --git a/vistrails/packages/matplotlib/figure_cell.py b/vistrails/packages/matplotlib/figure_cell.py
new file mode 100644
index 0000000..5f4029b
--- /dev/null
+++ b/vistrails/packages/matplotlib/figure_cell.py
@@ -0,0 +1,294 @@
+###############################################################################
+##
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This file describe a new type of spreadsheet cell to embed
+Matplotlib viewer into our spreadsheet
+
+"""
+from PyQt4 import QtCore, QtGui
+import os
+
+import matplotlib
+import pylab
+from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg, NavigationToolbar2QT
+from matplotlib.backend_bases import NavigationToolbar2, FigureManagerBase
+
+from vistrails.packages.spreadsheet.basic_widgets import SpreadsheetCell
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+
+FigureCanvasQTAgg.DEBUG = True
+
+################################################################################
+
+class MplFigureCell(SpreadsheetCell):
+ """
+ MplFigureCell is a spreadsheet cell for displaying Figure from
+ Matplotlib
+
+ """
+ _input_ports = [("figure", "(MplFigure)")]
+
+ def compute(self):
+ """ compute() -> None
+ The class will take the figure manager and embed it into the spreadsheet
+
+ """
+ if self.hasInputFromPort('figure'):
+ fig = self.getInputFromPort('figure')
+ self.displayAndWait(MplFigureCellWidget, (fig, ))
+
+class MplFigureCellWidget(QCellWidget):
+ """
+ MplFigureCellWidget is the actual QWidget taking the FigureManager
+ as a child for displaying figures
+
+ """
+ def __init__(self, parent=None):
+ """ MplFigureCellWidget(parent: QWidget) -> MplFigureCellWidget
+ Initialize the widget with its central layout
+
+ """
+ QCellWidget.__init__(self, parent)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ centralLayout = QtGui.QVBoxLayout()
+ self.setLayout(centralLayout)
+ centralLayout.setMargin(0)
+ centralLayout.setSpacing(0)
+ # self.figManager = pylab.get_current_fig_manager()
+ # self.figManager = None
+ # self.figNumber = None
+ self.canvas = None
+ self.figure = None
+ self.figManager = None
+ self.toolBarType = MplFigureCellToolBar
+ self.mplToolbar = None
+
+ # def getFigManager(self):
+ # if self.figNumber is not None:
+ # pylab.figure(self.figNumber)
+ # return pylab.get_current_fig_manager()
+ # return None
+
+ # def getFigure(self):
+ # if self.figNumber is not None:
+ # return pylab.figure(self.figNumber)
+ # return None
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple) -> None
+ Update the widget contents based on the input data
+
+ """
+ (fig, ) = inputPorts
+ if not self.figure or self.figure.number != fig.figInstance.number:
+ if self.layout().count() > 0:
+ self.layout().removeWidget(self.canvas)
+
+ self.figure = fig.figInstance
+
+ # self.figure.set_size_inches(8.0,6.0)
+ self.canvas = FigureCanvasQTAgg(self.figure)
+ self.mplToolbar = MplNavigationToolbar(self.canvas, None)
+ self.canvas.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ # self.figManager = FigureManagerBase(self.canvas, self.figure.number)
+ self.layout().addWidget(self.canvas)
+
+ # Update the new figure canvas
+ # self.canvas.draw()
+ # self.layout().addWidget(self.getFigManager().window)
+
+ # Update the new figure canvas
+ # self.getFigManager().canvas.draw()
+
+ # # Replace the old one with the new one
+ # if newFigManager!=self.figManager:
+
+ # # Remove the old figure manager
+ # if self.figManager:
+ # self.figManager.window.hide()
+ # self.layout().removeWidget(self.figManager.window)
+
+ # # Add the new one in
+ # self.layout().addWidget(newFigManager.window)
+
+ # # Destroy the old one if possible
+ # if self.figManager:
+
+ # try:
+ # pylab.close(self.figManager.canvas.figure)
+ # # There is a bug in Matplotlib backend_qt4. It is a
+ # # wrong command for Qt4. Just ignore it and continue
+ # # to destroy the widget
+ # except:
+ # pass
+
+ # self.figManager.window.deleteLater()
+ # del self.figManager
+
+ # # Save back the manager
+ # self.figManager = newFigManager
+ # self.update()
+
+ def keyPressEvent(self, event):
+ print "KEY PRESS:", event.key()
+ self.canvas.keyPressEvent(event)
+
+ def keyReleaseEvent(self, event):
+ print "KEY RELEASE:", event.key()
+ self.canvas.keyReleaseEvent(event)
+
+ def deleteLater(self):
+ """ deleteLater() -> None
+ Overriding PyQt deleteLater to free up resources
+
+ """
+ # Destroy the old one if possible
+ if self.figure is not None:
+ # self.getFigManager().window.deleteLater()
+ print "pylab:", pylab
+ print "self.figure:", self.figure
+ pylab.close(self.figure)
+
+ # if self.figManager:
+
+ # try:
+ # pylab.close(self.figManager.canvas.figure)
+ # # There is a bug in Matplotlib backend_qt4. It is a
+ # # wrong command for Qt4. Just ignore it and continue
+ # # to destroy the widget
+ # except:
+ # pass
+
+ # self.figManager.window.deleteLater()
+ QCellWidget.deleteLater(self)
+
+ def grabWindowPixmap(self):
+ """ grabWindowPixmap() -> QPixmap
+ Widget special grabbing function
+
+ """
+ # pylab.figure(self.figNumber)
+ # figManager = pylab.get_current_fig_manager()
+ return QtGui.QPixmap.grabWidget(self.canvas)
+
+ def dumpToFile(self, filename):
+ previous_size = tuple(self.figure.get_size_inches())
+ self.figure.set_size_inches(8.0,6.0)
+ self.canvas.print_figure(filename)
+ self.figure.set_size_inches(previous_size[0],previous_size[1])
+ self.canvas.draw()
+
+ def saveToPDF(self, filename):
+ previous_size = tuple(self.figure.get_size_inches())
+ self.figure.set_size_inches(8.0,6.0)
+ self.canvas.print_figure(filename)
+ self.figure.set_size_inches(previous_size[0],previous_size[1])
+ self.canvas.draw()
+
+class MplNavigationToolbar(NavigationToolbar2QT):
+ # override a bunch of stuff here...
+ def __init__(self, canvas, parent):
+ self.canvas = canvas
+ NavigationToolbar2.__init__(self, canvas)
+
+ def _init_toolbar(self):
+ self.adj_window = None
+
+ def destroy(self):
+ pass
+
+ def pan(self, *args):
+ NavigationToolbar2.pan(self, *args)
+
+ def zoom(self, *args):
+ NavigationToolbar2.zoom(self, *args)
+
+ def set_message(self, s):
+ pass
+
+ def save_figure(self, *args):
+ pass
+
+ def set_history_buttons(self):
+ pass
+
+class MplFigureCellToolBar(QCellToolBar):
+ def createToolBar(self):
+ # can be copied from NavigationToolbar2QT... with checkable added
+ toolitems = (
+ ('Home', 'Reset original view', 'home.ppm', 'home', False),
+ ('Back', 'Back to previous view','back.ppm', 'back', False),
+ ('Forward', 'Forward to next view','forward.ppm', 'forward',
+ False),
+ # (None, None, None, None),
+ ('Pan', 'Pan axes with left mouse, zoom with right', 'move.ppm',
+ 'pan', True),
+ ('Zoom', 'Zoom to rectangle','zoom_to_rect.ppm', 'zoom', True),
+ # (None, None, None, None),
+ # ('Subplots', 'Configure subplots','subplots.png', 'configure_subplots'),
+ # ('Save', 'Save the figure','filesave.ppm', 'save_figure'),
+ )
+ icondir = os.path.join(matplotlib.rcParams[ 'datapath' ],'images')
+ exclusive_actions = {}
+ actions = {}
+ for (text, tooltip_text, image_file, callback, checkable) in toolitems:
+ icon = QtGui.QIcon(os.path.join(icondir, image_file))
+ action = QtGui.QAction(icon, text, self)
+ action.setStatusTip(tooltip_text)
+ # action.setToolTip(tooltip_text)
+ action.setCheckable(checkable)
+ # self.connect(action, QtCore.SIGNAL("triggered"),
+ # get_callback(callback))
+ actions[text] = action
+ if text == 'Pan' or text == 'Zoom':
+ exclusive_actions[text] = action
+
+ def get_callback(act, cb, txt):
+ print "CONSTRUCTING CALLBACK!", act, cb, txt
+ def callback():
+ print "GOT CALLBACK!!"
+ cellWidget = act.toolBar.getSnappedWidget()
+ print "CALLING callback", cb
+ getattr(cellWidget.mplToolbar, cb)()
+ if txt in exclusive_actions:
+ for t, a in exclusive_actions.iteritems():
+ if txt != t:
+ a.setChecked(False)
+ return callback
+
+
+ for (text, tooltip_text, image_file, callback, checkable) in toolitems:
+ action = actions[text]
+ action.triggeredSlot = get_callback(action, callback, text)
+ self.appendAction(action)
diff --git a/vistrails/packages/matplotlib/generate.py b/vistrails/packages/matplotlib/generate.py
new file mode 100644
index 0000000..346a0fa
--- /dev/null
+++ b/vistrails/packages/matplotlib/generate.py
@@ -0,0 +1,29 @@
+from mako.template import Template
+import sys
+from specs import SpecList
+
+def generate_from_specs(fname, out_fname, template_fname):
+ specs = SpecList.read_from_xml(fname)
+
+ template = Template(filename=template_fname,
+ module_directory='/tmp/mako')
+
+ f = open(out_fname, 'wb') # 'b' ensures that we always use LF line endings
+ f.write(template.render(specs=specs))
+ f.close()
+
+def run(which="all"):
+ if which == "all" or which == "plots":
+ generate_from_specs("mpl_plots.xml", "plots.py",
+ "plots_template.py.mako")
+ if which == "all" or which == "artists":
+ generate_from_specs("mpl_artists.xml", "artists.py",
+ "artists_template.py.mako")
+
+if __name__ == '__main__':
+ if len(sys.argv) <= 1:
+ run()
+ elif len(sys.argv) == 2:
+ run(sys.argv[1])
+ else:
+ raise TypeError("usage: python parse.py [all|artists|plots]")
diff --git a/vistrails/packages/matplotlib/identifiers.py b/vistrails/packages/matplotlib/identifiers.py
new file mode 100644
index 0000000..6da2f7c
--- /dev/null
+++ b/vistrails/packages/matplotlib/identifiers.py
@@ -0,0 +1,46 @@
+###############################################################################
+##
+## Copyright (C) 2011-2012, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Matplotlib package for VisTrails.
+
+This package wrap Matplotlib to provide a plotting tool for
+VisTrails. We are going to use the 'Qt4Agg' backend of the library.
+
+"""
+
+identifier = 'org.vistrails.vistrails.matplotlib'
+name = 'matplotlib'
+version = '1.0.1'
+old_identifiers = ['edu.utah.sci.vistrails.matplotlib',
+ 'org.vistrails.matplotlib.new']
diff --git a/vistrails/packages/matplotlib/init.py b/vistrails/packages/matplotlib/init.py
new file mode 100644
index 0000000..e465fe4
--- /dev/null
+++ b/vistrails/packages/matplotlib/init.py
@@ -0,0 +1,269 @@
+###############################################################################
+##
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import matplotlib
+matplotlib.use('Qt4Agg', warn=False)
+
+import vistrails.core.modules.module_registry
+import vistrails.core.db.action
+from vistrails.core.vistrail.module import Module
+from vistrails.core.vistrail.operation import AddOp
+
+from bases import _modules as _base_modules
+from plots import _modules as _plot_modules
+from artists import _modules as _artist_modules
+from identifiers import identifier
+
+################################################################################
+
+#list of modules to be displaced on matplotlib.new package
+_modules = _base_modules + _plot_modules + _artist_modules
+
+def initialize(*args, **kwargs):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ if reg.has_module('org.vistrails.vistrails.spreadsheet',
+ 'SpreadsheetCell'):
+ from figure_cell import MplFigureCell
+ _modules.append(MplFigureCell)
+
+def handle_module_upgrade_request(controller, module_id, pipeline):
+ from vistrails.core.upgradeworkflow import UpgradeWorkflowHandler
+ create_new_connection = UpgradeWorkflowHandler.create_new_connection
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+
+ def find_module_in_upgrade_action(action):
+ for op in action.operations:
+ if isinstance(op, AddOp):
+ if op.what == Module.vtType:
+ return op.data
+ return None
+
+ def find_inputs(m):
+ functions = {}
+ for f in m.functions:
+ if f.name not in functions:
+ functions[f.name] = [f]
+ else:
+ functions[f.name].append(f)
+ connections = {}
+ for edge in pipeline.graph.iter_edges_to(m.id):
+ c = pipeline.connections[edge[2]]
+ if c.destination.name not in connections:
+ connections[c.destination.name] = [c]
+ else:
+ connections[c.destination.name].append(c)
+ return (functions, connections)
+
+ def find_figure(m):
+ for edge in pipeline.graph.iter_edges_from(m.id):
+ to_m = pipeline.modules[edge[1]]
+ if to_m.name == 'MplFigure':
+ # !!! assume only a single down-stream MplFigure !!!
+ # may have old or new module...
+ if pipeline.connections[edge[2]].destination.name == 'addPlot':
+ return (to_m, None)
+ else:
+ return (to_m, edge)
+ return (None, None)
+
+ def attach_inputs(new_module, inputs, selected_inputs):
+ conns = []
+ for port_name in selected_inputs:
+ if port_name in inputs[0]:
+ for f in inputs[0][port_name]:
+ if len(f.parameters) > 0:
+ new_param_vals, aliases = zip(*[(p.strValue, p.alias)
+ for p in f.parameters])
+ else:
+ new_param_vals = []
+ aliases = []
+ new_f = controller.create_function(new_module,
+ port_name,
+ new_param_vals,
+ aliases)
+ new_module.add_function(new_f)
+ if port_name in inputs[1]:
+ for c in inputs[1][port_name]:
+ source_module = pipeline.modules[c.source.id]
+ new_conn = create_new_connection(controller,
+ source_module,
+ c.source,
+ new_module,
+ port_name)
+ conns.append(new_conn)
+ return conns
+
+ module = pipeline.modules[module_id]
+ to_properties = []
+ to_axes = []
+ old_figure = (None, None)
+ if module.name == 'MplScatterplot':
+ props_name = 'MplPathCollectionProperties'
+ props_input = 'pathCollectionProperties'
+ to_properties = ['facecolor']
+ to_axes = ['title', 'xlabel', 'ylabel']
+ inputs = find_inputs(module)
+ old_loc = module.location
+ old_figure = find_figure(module)
+ elif module.name == 'MplHistogram':
+ props_name = 'MplRectangleProperties'
+ props_input = 'rectangleProperties'
+ to_properties = ['facecolor']
+ to_axes = ['title', 'xlabel', 'ylabel']
+ inputs = find_inputs(module)
+ old_loc = module.location
+ old_figure = find_figure(module)
+
+ module_remap = {'MplPlot':
+ [(None, '1.0.0', 'MplSource',
+ {'dst_port_remap': {'source': 'source',
+ 'Hide Toolbar': None},
+ 'src_port_remap': {'source': 'self'}})],
+ 'MplFigure':
+ [(None, '1.0.0', None,
+ {'dst_port_remap': {'Script': 'addPlot'},
+ 'src_port_remap': {'FigureManager': 'self',
+ 'File': 'file'}})],
+ 'MplFigureCell':
+ [(None, '1.0.0', None,
+ {'dst_port_remap': {'FigureManager': 'figure'}})],
+ # we will delete parts of this but add back later
+ 'MplScatterplot':
+ [(None, '1.0.0', 'MplScatter',
+ {'dst_port_remap': {'xData': 'x',
+ 'yData': 'y',
+ 'facecolor': None,
+ 'title': None,
+ 'xlabel': None,
+ 'ylabel': None},
+ 'src_port_remap': {'source': 'self'}})],
+ 'MplHistogram':
+ [(None, '1.0.0', 'MplHist',
+ {'dst_port_remap': {'columnData': 'x',
+ 'bins': 'bins',
+ 'facecolor': None,
+ 'title': None,
+ 'xlabel': None,
+ 'ylabel': None},
+ 'src_port_remap': {'source': 'self'}})],
+ }
+
+ action_list = []
+ if old_figure[1] is not None and \
+ any(p in inputs[0] or p in inputs[1] for p in to_axes):
+ # need to remove the edge between plot and figure
+ pipeline.graph.delete_edge(*old_figure[1])
+ conn = pipeline.connections[old_figure[1][2]]
+ action = vistrails.core.db.action.create_action([('delete', conn)])
+ action_list.append(action)
+
+ normal_actions = UpgradeWorkflowHandler.remap_module(controller, module_id,
+ pipeline, module_remap)
+ action_list.extend(normal_actions)
+
+ more_ops = []
+ if any(p in inputs[0] or p in inputs[1] for p in to_properties):
+ # create props module
+ desc = reg.get_descriptor_by_name(identifier, props_name)
+ props_module = \
+ controller.create_module_from_descriptor(desc,
+ old_loc.x + 100,
+ old_loc.y + 100)
+ more_ops.append(('add', props_module))
+
+ # attach functions/connections
+ conns = attach_inputs(props_module, inputs, to_properties)
+ more_ops.extend([('add', c) for c in conns])
+
+ # attach into pipeline
+ new_plot_module = find_module_in_upgrade_action(normal_actions[0])
+ assert new_plot_module is not None
+ new_conn = create_new_connection(controller,
+ props_module,
+ 'self',
+ new_plot_module,
+ props_input)
+ more_ops.append(('add', new_conn))
+
+ if any(p in inputs[0] or p in inputs[1] for p in to_axes):
+ # create axes module
+ desc = reg.get_descriptor_by_name(identifier, "MplAxesProperties")
+ if old_figure[0] is not None:
+ old_loc = old_figure[0].location
+ axes_module = \
+ controller.create_module_from_descriptor(desc,
+ old_loc.x + 100,
+ old_loc.y + 100)
+ more_ops.append(('add', axes_module))
+
+ # attach functions/connections
+ conns = attach_inputs(axes_module, inputs, to_axes)
+ more_ops.extend([('add', c) for c in conns])
+
+ # attach axes properties to new figure
+ if old_figure[0] is not None and old_figure[1] is not None:
+ # remap figure
+ fig_action = UpgradeWorkflowHandler.remap_module(controller,
+ old_figure[0].id,
+ pipeline,
+ module_remap)
+ fig_module = find_module_in_upgrade_action(fig_action[0])
+ assert fig_module is not None
+ # add the removed edge back in
+ pipeline.graph.add_edge(*old_figure[1])
+ action_list.extend(fig_action)
+
+ new_plot_module = find_module_in_upgrade_action(normal_actions[0])
+ assert new_plot_module is not None
+ conn = create_new_connection(controller,
+ new_plot_module,
+ 'self',
+ fig_module,
+ 'addPlot')
+ action = vistrails.core.db.action.create_action([('add', conn)])
+ action_list.append(action)
+ else:
+ fig_module = old_figure[0]
+ new_conn = create_new_connection(controller,
+ axes_module,
+ 'self',
+ fig_module,
+ 'axesProperties')
+ more_ops.append(('add', new_conn))
+
+ # for action in action_list:
+ # for op in action.operations:
+ # print "@+>:", op
+ return action_list
+
diff --git a/vistrails/packages/matplotlib/mixins.py b/vistrails/packages/matplotlib/mixins.py
new file mode 100644
index 0000000..8da5801
--- /dev/null
+++ b/vistrails/packages/matplotlib/mixins.py
@@ -0,0 +1,62 @@
+class MplCorrBaseMixin(object):
+ def compute_after():
+ if 'usevlines' in kwargs and kwargs['usevlines']:
+ output = output + (output[2],)
+ else:
+ output = output + (None, None)
+
+class MplAcorrMixin(MplCorrBaseMixin):
+ pass
+
+class MplXcorrMixin(MplCorrBaseMixin):
+ pass
+
+class MplBoxplotMixin(object):
+ def compute_after():
+ if 'patch_artist' in kwargs and kwargs['patch_artist']:
+ output['boxPatches'] = output['boxes']
+ output['boxes'] = []
+ else:
+ output['boxPatches'] = []
+
+class MplContourBaseMixin(object):
+ def compute_before():
+ if self.hasInputFromPort("N") and self.hasInputFromPort("V"):
+ del args[-1]
+
+class MplContourMixin(MplContourBaseMixin):
+ def compute_inner():
+ contour_set = matplotlib.pyplot.contour(*args, **kwargs)
+ output = (contour_set, contour_set.collections)
+
+class MplContourfMixin(MplContourBaseMixin):
+ def compute_inner():
+ contour_set = matplotlib.pyplot.contourf(*args, **kwargs)
+ output = (contour_set, contour_set.collections)
+
+class MplPieMixin(object):
+ def compute_after():
+ if len(output) < 3:
+ output = output + ([],)
+
+class MplAnnotateMixin(object):
+ def compute_before():
+ if self.hasInputFromPort("fancyArrowProperties"):
+ kwargs['arrowprops'] = \
+ self.getInputFromPort("fancyArrowProperties").props
+ elif self.hasInputFromPort("arrowProperties"):
+ kwargs['arrowprops'] = \
+ self.getInputFromPort("arrowProperties").props
+
+class MplSpyMixin(object):
+ def compute_after():
+ if "marker" not in kwargs and "markersize" not in kwargs and \
+ not hasattr(kwargs["Z"], 'tocoo'):
+ output = (output, None)
+ else:
+ output = (None, output)
+
+class MplBarMixin(object):
+ def compute_before(self):
+ if not kwargs.has_key('left'):
+ kwargs['left'] = range(len(kwargs['height']))
diff --git a/vistrails/packages/matplotlib/mpl_artists.xml b/vistrails/packages/matplotlib/mpl_artists.xml
new file mode 100644
index 0000000..c97e605
--- /dev/null
+++ b/vistrails/packages/matplotlib/mpl_artists.xml
@@ -0,0 +1,1935 @@
+<specs>
+ <customCode />
+ <moduleSpec code_ref="matplotlib.artist.Artist" name="MplArtistProperties" superclass="MplProperties">
+ <docstring>
+ Abstract base class for someone who renders into a
+ :class:`FigureCanvas`.
+ </docstring>
+ <inputPortSpec arg="picker" name="picker">
+ <docstring>Set the epsilon for picking used by this artist
+
+picker can be one of the following:
+
+None: picking is disabled for this artist (default)
+
+A boolean: if True then picking will be enabled and the artist will fire a pick event if the mouse event is over the artist
+
+A float: if picker is a number it is interpreted as an epsilon tolerance in points and the artist will fire off an event if it's data is within epsilon of the mouse event. For some artists like lines and patch collections, the artist may provide additional data to the pick event that is generated, e.g. the indices of the data within epsilon of the pick event
+
+A function: if picker is callable, it is a user supplied function which determines whether the artist is hit by the mouse event:
+
+hit, props = picker(artist, mouseevent)
+
+to determine the hit test. if the mouse event is over the artist, return hit=True and props is a dictionary of properties you want added to the PickEvent attributes.</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ </inputPortSpec>
+ <inputPortSpec arg="contains" name="contains">
+ <docstring>Replace the contains test used by this artist. The new picker should be a callable function which determines whether the artist is hit by the mouse event:
+
+hit, props = picker(artist, mouseevent)
+
+If the mouse event is over the artist, return hit = True and props is a dictionary of properties you want returned with the contains test.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="clip_on" name="clip_on" port_type="basic:Boolean">
+ <docstring>Set whether artist uses clipping.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="agg_filter" name="agg_filter">
+ <docstring>set agg_filter fuction.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="visible" name="visible" port_type="basic:Boolean">
+ <docstring>Set the artist's visiblity.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="url" name="url" port_type="basic:String">
+ <docstring>Sets the url for the artist</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="transform" name="transform">
+ <docstring>Set the :class:`~matplotlib.transforms.Transform` instance used by this artist.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axes" name="axes">
+ <docstring>Set the :class:`~matplotlib.axes.Axes` instance in which the artist resides, if any.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="clip_box" name="clip_box">
+ <docstring>Set the artist's clip :class:`~matplotlib.transforms.Bbox`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="clip_path" name="clip_path" port_type="basic:String">
+ <docstring>Set the artist's clip path, which may be:
+
+a :class:`~matplotlib.patches.Patch` (or subclass) instance
+
+
+
+None, to remove the clipping path
+
+For efficiency, if the path happens to be an axis-aligned rectangle, this method will set the clipping box to the corresponding rectangle and set the clipping path to None.</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ </inputPortSpec>
+ <inputPortSpec arg="lod" name="lod" port_type="basic:Boolean">
+ <docstring>Set Level of Detail on or off. If on, the artists may examine things like the pixel width of the axes and draw a subset of their contents accordingly</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="label" name="label" port_type="basic:String">
+ <docstring>Set the label to s for auto legend.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rasterized" name="rasterized" port_type="basic:Boolean">
+ <docstring>Force rasterized (bitmap) drawing in vector backend output.
+
+Defaults to None, which implies the backend's default behavior</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="gid" name="gid" port_type="basic:String">
+ <docstring>Sets the (group) id for the artist</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="zorder" name="zorder">
+ <docstring>Set the zorder for the artist. Artists with lower zorder values are drawn first.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="snap" name="snap">
+ <docstring>Sets the snap setting which may be:
+
+True: snap vertices to the nearest pixel center
+
+False: leave vertices as-is
+
+None: (auto) If the path contains only rectilinear line segments, round to the nearest pixel center
+
+Only supported by the Agg and MacOSX backends.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>Set the alpha value used for blending - not supported on all backends.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="animated" name="animated" port_type="basic:Boolean">
+ <docstring>Set the artist's animation state.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="figure" name="figure">
+ <docstring>Set the :class:`~matplotlib.figure.Figure` instance the artist belongs to.</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image._AxesImageBase" name="Mpl_AxesImageBaseProperties" superclass="MplArtistProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="origin" arg_pos="4" constructor_arg="True" name="origin" />
+ <inputPortSpec arg="resample" name="resample" port_type="basic:Boolean">
+ <docstring>Set whether or not image resampling is used</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="2" constructor_arg="True" name="norm" />
+ <inputPortSpec arg="cmap" arg_pos="1" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="filternorm" name="filternorm">
+ <docstring>Set whether the resize filter norms the weights -- see help for imshow</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ax" arg_pos="0" constructor_arg="True" name="ax" />
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>Set the alpha value used for blending - not supported on all backends</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="array" name="array">
+ <docstring>Retained for backwards compatibility - use set_data instead</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="data" name="data">
+ <docstring>Set the image array</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="filterrad" name="filterrad" port_type="basic:Float">
+ <docstring>Set the resize filter radius only applicable to some interpolation schemes -- see help for imshow</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="interpolation" name="interpolation" port_type="basic:String">
+ <docstring>Set the interpolation method the image uses when resizing.
+
+if None, use a value from rc setting. If 'none', the image is shown as is without interpolating. 'none' is only supported in agg, ps and pdf backends and will fall back to 'nearest' mode for other backends.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['nearest', 'bilinear', 'bicubic', 'spline16', 'spline36', 'hanning', 'hamming', 'hermite', 'kaiser', 'quadric', 'catrom', 'gaussian', 'bessel', 'mitchell', 'sinc', 'lanczos', 'none', '']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image.AxesImage" name="MplAxesImageProperties" superclass="Mpl_AxesImageBaseProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="origin" arg_pos="4" constructor_arg="True" name="origin" />
+ <inputPortSpec arg="resample" arg_pos="8" constructor_arg="True" name="resample" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="2" constructor_arg="True" name="norm" />
+ <inputPortSpec arg="cmap" arg_pos="1" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="filterrad" arg_pos="7" constructor_arg="True" name="filterrad" port_type="basic:Float">
+ <defaults>['4.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="extent" name="extent">
+ <docstring>extent is data axes (left, right, bottom, top) for making image plots
+
+This updates ax.dataLim, and, if autoscaling, sets viewLim to tightly fit the image, regardless of dataLim. Autoscaling state is not changed, so following this with ax.autoscale_view will redo the autoscaling in accord with dataLim.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ax" arg_pos="0" constructor_arg="True" name="ax" />
+ <inputPortSpec arg="filternorm" arg_pos="6" constructor_arg="True" name="filternorm" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="interpolation" arg_pos="3" constructor_arg="True" name="interpolation" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image.NonUniformImage" name="MplNonUniformImageProperties" superclass="MplAxesImageProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="norm" name="norm" />
+ <inputPortSpec arg="cmap" name="cmap" />
+ <inputPortSpec arg="filternorm" name="filternorm" />
+ <inputPortSpec arg="ax" arg_pos="0" constructor_arg="True" name="ax" />
+ <inputPortSpec arg="array" name="array" />
+ <inputPortSpec arg="data" name="data">
+ <docstring>Set the grid for the pixel centers, and the pixel values.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="filterrad" name="filterrad" />
+ <inputPortSpec arg="interpolation" name="interpolation" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image.BboxImage" name="MplBboxImageProperties" superclass="Mpl_AxesImageBaseProperties">
+ <docstring>The Image class whose size is determined by the given bbox.</docstring>
+ <inputPortSpec arg="origin" arg_pos="4" constructor_arg="True" name="origin" />
+ <inputPortSpec arg="interp_at_native" arg_pos="8" constructor_arg="True" name="interp_at_native" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="resample" arg_pos="7" constructor_arg="True" name="resample" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="1" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="filternorm" arg_pos="5" constructor_arg="True" name="filternorm" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="2" constructor_arg="True" name="norm" />
+ <inputPortSpec arg="interpolation" arg_pos="3" constructor_arg="True" name="interpolation" />
+ <inputPortSpec arg="filterrad" arg_pos="6" constructor_arg="True" name="filterrad" port_type="basic:Float">
+ <defaults>['4.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox" arg_pos="0" constructor_arg="True" name="bbox" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image.PcolorImage" name="MplPcolorImageProperties" superclass="MplArtistProperties">
+ <docstring>
+ Make a pcolor-style plot with an irregular rectangular grid.
+
+ This uses a variation of the original irregular image code,
+ and it is used by pcolorfast for the corresponding grid type.
+ </docstring>
+ <inputPortSpec arg="A" arg_pos="3" constructor_arg="True" name="A" />
+ <inputPortSpec arg="ax" arg_pos="0" constructor_arg="True" name="ax" />
+ <inputPortSpec arg="cmap" arg_pos="4" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="x" arg_pos="1" constructor_arg="True" name="x" />
+ <inputPortSpec arg="y" arg_pos="2" constructor_arg="True" name="y" />
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>Set the alpha value used for blending - not supported on all backends</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="array" name="array" />
+ <inputPortSpec arg="data" name="data" />
+ <inputPortSpec arg="norm" arg_pos="5" constructor_arg="True" name="norm" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image.FigureImage" name="MplFigureImageProperties" superclass="MplArtistProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="origin" arg_pos="5" constructor_arg="True" name="origin" />
+ <inputPortSpec arg="offsetx" arg_pos="3" constructor_arg="True" name="offsetx" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="offsety" arg_pos="4" constructor_arg="True" name="offsety" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="1" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="fig" arg_pos="0" constructor_arg="True" name="fig" />
+ <inputPortSpec arg="array" name="array">
+ <docstring>Deprecated; use set_data for consistency with other image types.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="data" name="data">
+ <docstring>Set the image array.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="2" constructor_arg="True" name="norm" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.Collection" name="MplCollectionProperties" superclass="MplArtistProperties">
+ <docstring>
+ Base class for Collections. Must be subclassed to be usable.
+
+ All properties in a collection must be sequences or scalars;
+ if scalars, they will be converted to sequences. The
+ property of the ith element of the collection is::
+
+ prop[i % len(props)]
+
+ Keyword arguments and default values:
+
+ * *edgecolors*: None
+ * *facecolors*: None
+ * *linewidths*: None
+ * *antialiaseds*: None
+ * *offsets*: None
+ * *transOffset*: transforms.IdentityTransform()
+ * *offset_position*: 'screen' (default) or 'data'
+ * *norm*: None (optional for
+ :class:`matplotlib.cm.ScalarMappable`)
+ * *cmap*: None (optional for
+ :class:`matplotlib.cm.ScalarMappable`)
+ * *hatch*: None
+
+ *offsets* and *transOffset* are used to translate the patch after
+ rendering (default no offsets). If offset_position is 'screen'
+ (default) the offset is applied after the master transform has
+ been applied, that is, the offsets are in screen coordinates. If
+ offset_position is 'data', the offset is applied before the master
+ transform, i.e., the offsets are in data coordinates.
+
+ If any of *edgecolors*, *facecolors*, *linewidths*, *antialiaseds*
+ are None, they default to their :data:`matplotlib.rcParams` patch
+ setting, in sequence form.
+
+ The use of :class:`~matplotlib.cm.ScalarMappable` is optional. If
+ the :class:`~matplotlib.cm.ScalarMappable` matrix _A is not None
+ (ie a call to set_array has been made), at draw time a call to
+ scalar mappable will be made to set the face colors.
+ </docstring>
+ <inputPortSpec arg="transOffset" arg_pos="6" constructor_arg="True" name="transOffset" />
+ <inputPortSpec arg="edgecolor" name="edgecolor" port_type="basic:List">
+ <docstring>Set the edgecolor(s) of the collection. c can be a matplotlib color arg (all patches have same color), or a sequence of rgba tuples; if it is a sequence the patches will cycle through the sequence.
+
+If c is 'face', the edge color will always be the same as the face color. If it is 'none', the patch boundary will not be drawn.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="offset_position" name="offset_position">
+ <docstring>Set how offsets are applied. If offset_position is 'screen' (default) the offset is applied after the master transform has been applied, that is, the offsets are in screen coordinates. If offset_position is 'data', the offset is applied before the master transform, i.e., the offsets are in data coordinates.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="edgecolors" arg_pos="0" constructor_arg="True" name="edgecolors" />
+ <inputPortSpec arg="facecolor" name="facecolor" port_type="basic:List">
+ <docstring>Set the facecolor(s) of the collection. c can be a matplotlib color arg (all patches have same color), or a sequence of rgba tuples; if it is a sequence the patches will cycle through the sequence.
+
+If c is 'none', the patch will not be filled.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyles" arg_pos="3" constructor_arg="True" name="linestyles" port_type="basic:String">
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="offsets" name="offsetsSequence" port_type="basic:List">
+ <docstring>Set the offsets for the collection. offsets can be a scalar or a sequence.</docstring>
+ <alternateSpec arg="offsets" name="offsetsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:List">
+ <docstring>Set both the edgecolor and the facecolor. .. seealso:
+
+:meth:`set_facecolor`, :meth:`set_edgecolor` For setting the edge or face color individually.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="pickradius" name="pickradius" />
+ <inputPortSpec arg="antialiaseds" arg_pos="4" constructor_arg="True" name="antialiaseds" />
+ <inputPortSpec arg="linewidths" arg_pos="2" constructor_arg="True" name="linewidths" />
+ <inputPortSpec arg="cmap" arg_pos="8" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="antialiased" name="antialiasedSequence" port_type="basic:List">
+ <docstring>Set the antialiasing state for rendering.</docstring>
+ <alternateSpec arg="antialiased" name="antialiasedScalar" port_type="basic:Boolean" />
+ </inputPortSpec>
+ <inputPortSpec arg="urls" name="urls" />
+ <inputPortSpec arg="hatch" name="hatch" port_type="basic:String">
+ <docstring>Set the hatching pattern
+
+hatch can be one of:
+
+/ - diagonal hatching \ - back diagonal | - vertical - - horizontal + - crossed x - crossed diagonal o - small circle O - large circle . - dots * - stars
+
+Letters can be combined, in which case all the specified hatchings are done. If same letter repeats, it increases the density of hatching of that pattern.
+
+Hatching is supported in the PostScript, PDF, SVG and Agg backends only.
+
+Unlike other properties such as linewidth and colors, hatching can only be specified for the collection as a whole, not separately for each member.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['/', "'\\'", "'", "'", '-', '+', 'x', 'o', 'O', '.', '*']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>Set the alpha tranparencies of the collection. alpha must be a float or None.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="paths" name="paths" />
+ <inputPortSpec arg="linewidth" name="linewidthSequence" port_type="basic:List">
+ <docstring>Set the linewidth(s) for the collection. lw can be a scalar or a sequence; if it is a sequence the patches will cycle through the sequence</docstring>
+ <alternateSpec arg="linewidth" name="linewidthScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="linestyle" name="linestyle" port_type="basic:String">
+ <docstring>Set the linestyle(s) for the collection.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['solid', ('dashed', 'dashdot', 'dotted'), '(offset, on-off-dash-seq)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="facecolors" arg_pos="1" constructor_arg="True" name="facecolors" />
+ <inputPortSpec arg="norm" arg_pos="7" constructor_arg="True" name="norm" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.PathCollection" name="MplPathCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>
+ This is the most basic :class:`Collection` subclass.
+ </docstring>
+ <inputPortSpec arg="paths" name="paths" />
+ <inputPortSpec arg="sizes" arg_pos="1" constructor_arg="True" name="sizes" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.PolyCollection" name="MplPolyCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="paths" name="paths">
+ <docstring>This allows one to delay initialization of the vertices.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="verts" name="verts">
+ <docstring>This allows one to delay initialization of the vertices.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="closed" arg_pos="2" constructor_arg="True" name="closed" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="sizes" arg_pos="1" constructor_arg="True" name="sizes" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.BrokenBarHCollection" name="MplBrokenBarHCollectionProperties" superclass="MplPolyCollectionProperties">
+ <docstring>
+ A collection of horizontal bars spanning *yrange* with a sequence of
+ *xranges*.
+ </docstring>
+ <inputPortSpec arg="xranges" arg_pos="0" constructor_arg="True" name="xranges" />
+ <inputPortSpec arg="yrange" arg_pos="1" constructor_arg="True" name="yrange" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.RegularPolyCollection" name="MplRegularPolyCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>Draw a collection of regular polygons with *numsides*.</docstring>
+ <inputPortSpec arg="numsides" arg_pos="0" constructor_arg="True" name="numsides" />
+ <inputPortSpec arg="rotation" arg_pos="1" constructor_arg="True" name="rotation" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="sizes" arg_pos="2" constructor_arg="True" name="sizes">
+ <defaults>['(1,)']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.StarPolygonCollection" name="MplStarPolygonCollectionProperties" superclass="MplRegularPolyCollectionProperties">
+ <docstring>
+ Draw a collection of regular stars with *numsides* points.</docstring>
+ <inputPortSpec arg="numsides" arg_pos="0" constructor_arg="True" name="numsides" />
+ <inputPortSpec arg="rotation" arg_pos="1" constructor_arg="True" name="rotation" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="sizes" arg_pos="2" constructor_arg="True" name="sizes">
+ <defaults>['(1,)']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.AsteriskPolygonCollection" name="MplAsteriskPolygonCollectionProperties" superclass="MplRegularPolyCollectionProperties">
+ <docstring>
+ Draw a collection of regular asterisks with *numsides* points.</docstring>
+ <inputPortSpec arg="numsides" arg_pos="0" constructor_arg="True" name="numsides" />
+ <inputPortSpec arg="rotation" arg_pos="1" constructor_arg="True" name="rotation" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="sizes" arg_pos="2" constructor_arg="True" name="sizes">
+ <defaults>['(1,)']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.LineCollection" name="MplLineCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>
+ All parameters must be sequences or scalars; if scalars, they will
+ be converted to sequences. The property of the ith line
+ segment is::
+
+ prop[i % len(props)]
+
+ i.e., the properties cycle if the ``len`` of props is less than the
+ number of segments.
+ </docstring>
+ <inputPortSpec arg="paths" name="paths" />
+ <inputPortSpec arg="antialiaseds" arg_pos="3" constructor_arg="True" name="antialiaseds" />
+ <inputPortSpec arg="linestyles" arg_pos="4" constructor_arg="True" name="linestyles" port_type="basic:String">
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="offsets" arg_pos="5" constructor_arg="True" name="offsets" />
+ <inputPortSpec arg="color" name="color" port_type="basic:List">
+ <docstring>Set the color(s) of the line collection. c can be a matplotlib color arg (all patches have same color), or a sequence or rgba tuples; if it is a sequence the patches will cycle through the sequence.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="segments" name="segments" />
+ <inputPortSpec arg="linewidths" arg_pos="1" constructor_arg="True" name="linewidths" />
+ <inputPortSpec arg="colors" arg_pos="2" constructor_arg="True" name="colors" />
+ <inputPortSpec arg="cmap" arg_pos="8" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="transOffset" arg_pos="6" constructor_arg="True" name="transOffset" />
+ <inputPortSpec arg="verts" name="verts" />
+ <inputPortSpec arg="pickradius" arg_pos="9" constructor_arg="True" name="pickradius" port_type="basic:Integer">
+ <defaults>['5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="7" constructor_arg="True" name="norm" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.CircleCollection" name="MplCircleCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>
+ A collection of circles, drawn using splines.
+ </docstring>
+ <inputPortSpec arg="sizes" arg_pos="0" constructor_arg="True" name="sizes" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.EllipseCollection" name="MplEllipseCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>
+ A collection of ellipses, drawn using splines.
+ </docstring>
+ <inputPortSpec arg="units" arg_pos="3" constructor_arg="True" name="units" port_type="basic:String">
+ <defaults>['points']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="widths" arg_pos="0" constructor_arg="True" name="widths" />
+ <inputPortSpec arg="angles" arg_pos="2" constructor_arg="True" name="angles" />
+ <inputPortSpec arg="heights" arg_pos="1" constructor_arg="True" name="heights" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.PatchCollection" name="MplPatchCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>
+ A generic collection of patches.
+
+ This makes it easier to assign a color map to a heterogeneous
+ collection of patches.
+
+ This also may improve plotting speed, since PatchCollection will
+ draw faster than a large number of patches.
+ </docstring>
+ <inputPortSpec arg="paths" name="paths" />
+ <inputPortSpec arg="patches" arg_pos="0" constructor_arg="True" name="patches" />
+ <inputPortSpec arg="match_original" arg_pos="1" constructor_arg="True" name="match_original" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.TriMesh" name="MplTriMeshProperties" superclass="MplCollectionProperties">
+ <docstring>
+ Class for the efficient drawing of a triangular mesh using
+ Gouraud shading.
+
+ A triangular mesh is a :class:`~matplotlib.tri.Triangulation`
+ object.
+ </docstring>
+ <inputPortSpec arg="triangulation" arg_pos="0" constructor_arg="True" name="triangulation" />
+ <inputPortSpec arg="paths" name="paths" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.QuadMesh" name="MplQuadMeshProperties" superclass="MplCollectionProperties">
+ <docstring>
+ Class for the efficient drawing of a quadrilateral mesh.
+
+ A quadrilateral mesh consists of a grid of vertices. The
+ dimensions of this array are (*meshWidth* + 1, *meshHeight* +
+ 1). Each vertex in the mesh has a different set of "mesh
+ coordinates" representing its position in the topology of the
+ mesh. For any values (*m*, *n*) such that 0 <= *m* <= *meshWidth*
+ and 0 <= *n* <= *meshHeight*, the vertices at mesh coordinates
+ (*m*, *n*), (*m*, *n* + 1), (*m* + 1, *n* + 1), and (*m* + 1, *n*)
+ form one of the quadrilaterals in the mesh. There are thus
+ (*meshWidth* * *meshHeight*) quadrilaterals in the mesh. The mesh
+ need not be regular and the polygons need not be convex.
+
+ A quadrilateral mesh is represented by a (2 x ((*meshWidth* + 1) *
+ (*meshHeight* + 1))) numpy array *coordinates*, where each row is
+ the *x* and *y* coordinates of one of the vertices. To define the
+ function that maps from a data point to its corresponding color,
+ use the :meth:`set_cmap` method. Each of these arrays is indexed in
+ row-major order by the mesh coordinates of the vertex (or the mesh
+ coordinates of the lower left vertex, in the case of the
+ colors).
+
+ For example, the first entry in *coordinates* is the
+ coordinates of the vertex at mesh coordinates (0, 0), then the one
+ at (0, 1), then at (0, 2) .. (0, meshWidth), (1, 0), (1, 1), and
+ so on.
+
+ *shading* may be 'flat', or 'gouraud'
+ </docstring>
+ <inputPortSpec arg="paths" name="paths" />
+ <inputPortSpec arg="meshWidth" arg_pos="0" constructor_arg="True" name="meshWidth" />
+ <inputPortSpec arg="coordinates" arg_pos="2" constructor_arg="True" name="coordinates" />
+ <inputPortSpec arg="antialiased" arg_pos="3" constructor_arg="True" name="antialiased" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="shading" arg_pos="4" constructor_arg="True" name="shading" port_type="basic:String">
+ <defaults>['flat']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="meshHeight" arg_pos="1" constructor_arg="True" name="meshHeight" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Patch" name="MplPatchProperties" superclass="MplArtistProperties">
+ <docstring>
+ A patch is a 2D artist with a face color and an edge color.
+
+ If any of *edgecolor*, *facecolor*, *linewidth*, or *antialiased*
+ are *None*, they default to their rc params setting.
+ </docstring>
+ <inputPortSpec arg="edgecolor" name="edgecolor" port_type="basic:Color">
+ <docstring>Set the patch edge color</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="facecolor" name="facecolor" port_type="basic:Color">
+ <docstring>Set the patch face color</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="path_effects" name="path_effects">
+ <docstring>set path_effects, which should be a list of instances of matplotlib.patheffect._Base class or its derivatives.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>Set both the edgecolor and the facecolor. .. seealso:
+
+:meth:`set_facecolor`, :meth:`set_edgecolor` For setting the edge or face color individually.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="antialiased" name="antialiased" port_type="basic:Boolean">
+ <docstring>Set whether to use antialiased rendering</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="hatch" name="hatch" port_type="basic:String">
+ <docstring>Set the hatching pattern
+
+hatch can be one of:
+
+/ - diagonal hatching \ - back diagonal | - vertical - - horizontal + - crossed x - crossed diagonal o - small circle O - large circle . - dots * - stars
+
+Letters can be combined, in which case all the specified hatchings are done. If same letter repeats, it increases the density of hatching of that pattern.
+
+Hatching is supported in the PostScript, PDF, SVG and Agg backends only.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['/', "'\\'", "'", "'", '-', '+', 'x', 'o', 'O', '.', '*']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>Set the alpha tranparency of the patch.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidth" name="linewidth" port_type="basic:Float">
+ <docstring>Set the patch linewidth in points</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyle" name="linestyle" port_type="basic:String">
+ <docstring>Set the patch linestyle</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['solid', 'dashed', 'dashdot', 'dotted']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="fill" name="fill" port_type="basic:Boolean">
+ <docstring>Set whether to fill the patch</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Shadow" name="MplShadowProperties" superclass="MplPatchProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="patch" arg_pos="0" constructor_arg="True" name="patch" />
+ <inputPortSpec arg="props" arg_pos="3" constructor_arg="True" name="props" />
+ <inputPortSpec arg="oy" arg_pos="2" constructor_arg="True" name="oy" />
+ <inputPortSpec arg="ox" arg_pos="1" constructor_arg="True" name="ox" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Rectangle" name="MplRectangleProperties" superclass="MplPatchProperties">
+ <docstring>
+ Draw a rectangle with lower left at *xy* = (*x*, *y*) with
+ specified *width* and *height*.
+ </docstring>
+ <inputPortSpec arg="bounds" name="bounds">
+ <docstring>Set the bounds of the rectangle: l,b,w,h</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="height" name="height" port_type="basic:Float">
+ <docstring>Set the width rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="width" name="width" port_type="basic:Float">
+ <docstring>Set the width rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xy" name="xy" port_type="basic:List">
+ <docstring>Set the left and bottom coords of the rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" name="y" port_type="basic:Float">
+ <docstring>Set the bottom coord of the rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="x" name="x" port_type="basic:Float">
+ <docstring>Set the left coord of the rectangle</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.RegularPolygon" name="MplRegularPolygonProperties" superclass="MplPatchProperties">
+ <docstring>
+ A regular polygon patch.
+ </docstring>
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy">
+ <docstring>A length 2 tuple (x, y) of the center.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="radius" arg_pos="2" constructor_arg="True" name="radius" port_type="basic:Integer">
+ <docstring>The distance from the center to each of the vertices.</docstring>
+ <defaults>['5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="orientation" arg_pos="3" constructor_arg="True" name="orientation" port_type="basic:Integer">
+ <docstring>rotates the polygon (in radians).</docstring>
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="numVertices" arg_pos="1" constructor_arg="True" name="numVertices">
+ <docstring>the number of vertices.</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.CirclePolygon" name="MplCirclePolygonProperties" superclass="MplRegularPolygonProperties">
+ <docstring>
+ A polygon-approximation of a circle patch.
+ </docstring>
+ <inputPortSpec arg="radius" arg_pos="1" constructor_arg="True" name="radius" port_type="basic:Integer">
+ <defaults>['5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy" />
+ <inputPortSpec arg="resolution" arg_pos="2" constructor_arg="True" name="resolution" port_type="basic:Integer">
+ <defaults>['20']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.PathPatch" name="MplPathPatchProperties" superclass="MplPatchProperties">
+ <docstring>
+ A general polycurve path patch.
+ </docstring>
+ <inputPortSpec arg="path" arg_pos="0" constructor_arg="True" name="path" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Polygon" name="MplPolygonProperties" superclass="MplPatchProperties">
+ <docstring>
+ A general polygon patch.
+ </docstring>
+ <inputPortSpec arg="xy" name="xy" />
+ <inputPortSpec arg="closed" name="closed" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.FancyArrow" name="MplFancyArrowProperties" superclass="MplPolygonProperties">
+ <docstring>
+ Like Arrow, but lets you set head width and head height independently.
+ </docstring>
+ <inputPortSpec arg="length_includes_head" arg_pos="5" constructor_arg="True" name="length_includes_head" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="head_length" arg_pos="7" constructor_arg="True" name="head_length" />
+ <inputPortSpec arg="head_width" arg_pos="6" constructor_arg="True" name="head_width" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" port_type="basic:Float">
+ <defaults>['0.001']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="shape" arg_pos="8" constructor_arg="True" name="shape" port_type="basic:String">
+ <defaults>['full']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="dx" arg_pos="2" constructor_arg="True" name="dx" />
+ <inputPortSpec arg="dy" arg_pos="3" constructor_arg="True" name="dy" />
+ <inputPortSpec arg="y" arg_pos="1" constructor_arg="True" name="y" />
+ <inputPortSpec arg="x" arg_pos="0" constructor_arg="True" name="x" />
+ <inputPortSpec arg="head_starts_at_zero" arg_pos="10" constructor_arg="True" name="head_starts_at_zero" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="overhang" arg_pos="9" constructor_arg="True" name="overhang" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Wedge" name="MplWedgeProperties" superclass="MplPatchProperties">
+ <docstring>
+ Wedge shaped patch.
+ </docstring>
+ <inputPortSpec arg="theta2" arg_pos="3" constructor_arg="True" name="theta2" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" />
+ <inputPortSpec arg="r" arg_pos="1" constructor_arg="True" name="r" />
+ <inputPortSpec arg="theta1" arg_pos="2" constructor_arg="True" name="theta1" />
+ <inputPortSpec arg="center" arg_pos="0" constructor_arg="True" name="center" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Arrow" name="MplArrowProperties" superclass="MplPatchProperties">
+ <docstring>
+ An arrow patch.
+ </docstring>
+ <inputPortSpec arg="y" arg_pos="1" constructor_arg="True" name="y" />
+ <inputPortSpec arg="x" arg_pos="0" constructor_arg="True" name="x" />
+ <inputPortSpec arg="dy" arg_pos="3" constructor_arg="True" name="dy" />
+ <inputPortSpec arg="dx" arg_pos="2" constructor_arg="True" name="dx" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" port_type="basic:Float">
+ <defaults>['1.0']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.YAArrow" name="MplYAArrowProperties" superclass="MplPatchProperties">
+ <docstring>
+ Yet another arrow class.
+
+ This is an arrow that is defined in display space and has a tip at
+ *x1*, *y1* and a base at *x2*, *y2*.
+ </docstring>
+ <inputPortSpec arg="xytip" arg_pos="1" constructor_arg="True" name="xytip">
+ <docstring>(x, y) location of arrow tip</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="headwidth" arg_pos="5" constructor_arg="True" name="headwidth" port_type="basic:Integer">
+ <docstring>The width of the base of the arrow head in points</docstring>
+ <defaults>['12']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="frac" arg_pos="4" constructor_arg="True" name="frac" port_type="basic:Float">
+ <docstring>The fraction of the arrow length occupied by the head</docstring>
+ <defaults>['0.1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="figure" arg_pos="0" constructor_arg="True" name="figure">
+ <docstring>The :class:`~matplotlib.figure.Figure` instance (fig.dpi)</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xybase" arg_pos="2" constructor_arg="True" name="xybase">
+ <docstring>(x, y) location the arrow base mid point</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="width" arg_pos="3" constructor_arg="True" name="width" port_type="basic:Integer">
+ <docstring>The width of the arrow in points</docstring>
+ <defaults>['4']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Ellipse" name="MplEllipseProperties" superclass="MplPatchProperties">
+ <docstring>
+ A scale-free ellipse.
+ </docstring>
+ <inputPortSpec arg="width" arg_pos="1" constructor_arg="True" name="width" />
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy" />
+ <inputPortSpec arg="angle" arg_pos="3" constructor_arg="True" name="angle" port_type="basic:Float">
+ <defaults>['0.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="height" arg_pos="2" constructor_arg="True" name="height" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Circle" name="MplCircleProperties" superclass="MplEllipseProperties">
+ <docstring>
+ A circle patch.
+ </docstring>
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy" />
+ <inputPortSpec arg="radius" name="radius" port_type="basic:Float">
+ <docstring>Set the radius of the circle</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Arc" name="MplArcProperties" superclass="MplEllipseProperties">
+ <docstring>
+ An elliptical arc. Because it performs various optimizations, it
+ can not be filled.
+
+ The arc must be used in an :class:`~matplotlib.axes.Axes`
+ instance---it can not be added directly to a
+ :class:`~matplotlib.figure.Figure`---because it is optimized to
+ only render the segments that are inside the axes bounding box
+ with high resolution.
+ </docstring>
+ <inputPortSpec arg="theta2" arg_pos="5" constructor_arg="True" name="theta2" port_type="basic:Float">
+ <defaults>['360.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="theta1" arg_pos="4" constructor_arg="True" name="theta1" port_type="basic:Float">
+ <defaults>['0.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="angle" arg_pos="3" constructor_arg="True" name="angle" port_type="basic:Float">
+ <defaults>['0.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="height" arg_pos="2" constructor_arg="True" name="height" />
+ <inputPortSpec arg="width" arg_pos="1" constructor_arg="True" name="width" />
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.FancyBboxPatch" name="MplFancyBboxPatchProperties" superclass="MplPatchProperties">
+ <docstring>
+ Draw a fancy box around a rectangle with lower left at *xy*=(*x*,
+ *y*) with specified width and height.
+
+ :class:`FancyBboxPatch` class is similar to :class:`Rectangle`
+ class, but it draws a fancy box around the rectangle. The
+ transformation of the rectangle box to the fancy box is delegated
+ to the :class:`BoxTransmuterBase` and its derived classes.
+
+ </docstring>
+ <inputPortSpec arg="mutation_scale" name="mutation_scale" port_type="basic:Float">
+ <docstring>Set the mutation scale.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox_transmuter" arg_pos="4" constructor_arg="True" name="bbox_transmuter" />
+ <inputPortSpec arg="bounds" name="bounds">
+ <docstring>Set the bounds of the rectangle: l,b,w,h</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="height" name="height" port_type="basic:Float">
+ <docstring>Set the width rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="width" name="width" port_type="basic:Float">
+ <docstring>Set the width rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy" />
+ <inputPortSpec arg="boxstyle" name="boxstyle">
+ <docstring>Set the box style.
+
+boxstyle can be a string with boxstyle name with optional comma-separated attributes. Alternatively, the attrs can be provided as keywords:
+
+set_boxstyle("round,pad=0.2") set_boxstyle("round", pad=0.2)
+
+Old attrs simply are forgotten.
+
+Without argument (or with boxstyle = None), it returns available box styles.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="mutation_aspect" name="mutation_aspect" port_type="basic:Float">
+ <docstring>Set the aspect ratio of the bbox mutation.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" name="y" port_type="basic:Float">
+ <docstring>Set the bottom coord of the rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="x" name="x" port_type="basic:Float">
+ <docstring>Set the left coord of the rectangle</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.FancyArrowPatch" name="MplFancyArrowPatchProperties" superclass="MplPatchProperties">
+ <docstring>
+ A fancy arrow patch. It draws an arrow using the :class:ArrowStyle.
+ </docstring>
+ <inputPortSpec arg="connectionstyle" name="connectionstyle">
+ <docstring>Set the connection style.
+
+Old attrs simply are forgotten.
+
+Without argument (or with connectionstyle=None), return available styles as a list of strings.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="mutation_scale" name="mutation_scale" port_type="basic:Float">
+ <docstring>Set the mutation scale.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="arrowstyle" name="arrowstyle">
+ <docstring>Set the arrow style.
+
+Old attrs simply are forgotten.
+
+Without argument (or with arrowstyle=None), return available box styles as a list of strings.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="arrow_transmuter" arg_pos="4" constructor_arg="True" name="arrow_transmuter" />
+ <inputPortSpec arg="positions" name="positions" />
+ <inputPortSpec arg="shrinkA" arg_pos="9" constructor_arg="True" name="shrinkA" port_type="basic:Float">
+ <defaults>['2.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="posB" arg_pos="1" constructor_arg="True" name="posB" />
+ <inputPortSpec arg="dpi_cor" name="dpi_cor">
+ <docstring>dpi_cor is currently used for linewidth-related things and shink factor. Mutation scale is not affected by this.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="connector" arg_pos="6" constructor_arg="True" name="connector" />
+ <inputPortSpec arg="path" arg_pos="2" constructor_arg="True" name="path" />
+ <inputPortSpec arg="shrinkB" arg_pos="10" constructor_arg="True" name="shrinkB" port_type="basic:Float">
+ <defaults>['2.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="mutation_aspect" name="mutation_aspect" port_type="basic:Float">
+ <docstring>Set the aspect ratio of the bbox mutation.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="patchA" name="patchA">
+ <docstring>set the begin patch.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="patchB" name="patchB">
+ <docstring>set the begin patch</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="posA" arg_pos="0" constructor_arg="True" name="posA" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.ConnectionPatch" name="MplConnectionPatchProperties" superclass="MplFancyArrowPatchProperties">
+ <docstring>
+ A :class:`~matplotlib.patches.ConnectionPatch` class is to make
+ connecting lines between two points (possibly in different axes).
+ </docstring>
+ <inputPortSpec arg="connectionstyle" arg_pos="8" constructor_arg="True" name="connectionstyle" port_type="basic:String">
+ <docstring>the connection style</docstring>
+ <defaults>['arc3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="coordsA" arg_pos="2" constructor_arg="True" name="coordsA">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="arrowstyle" arg_pos="6" constructor_arg="True" name="arrowstyle" port_type="basic:String">
+ <docstring>the arrow style</docstring>
+ <defaults>['-']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="clip_on" arg_pos="16" constructor_arg="True" name="clip_on" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="arrow_transmuter" arg_pos="7" constructor_arg="True" name="arrow_transmuter" />
+ <inputPortSpec arg="axesA" arg_pos="4" constructor_arg="True" name="axesA" />
+ <inputPortSpec arg="axesB" arg_pos="5" constructor_arg="True" name="axesB" />
+ <inputPortSpec arg="annotation_clip" name="annotation_clip">
+ <docstring>set annotation_clip attribute.
+
+None: the self.xy will be checked only if xycoords is "data"</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dpi_cor" arg_pos="17" constructor_arg="True" name="dpi_cor" port_type="basic:Float">
+ <defaults>['1.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="connector" arg_pos="9" constructor_arg="True" name="connector" />
+ <inputPortSpec arg="xyA" arg_pos="0" constructor_arg="True" name="xyA" />
+ <inputPortSpec arg="xyB" arg_pos="1" constructor_arg="True" name="xyB" />
+ <inputPortSpec arg="relpos" constructor_arg="True" name="relpos" port_type="basic:String">
+ <docstring>default is (0.5, 0.5)</docstring>
+ <defaults>['(0.5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="shrinkB" arg_pos="13" constructor_arg="True" name="shrinkB" port_type="basic:Float">
+ <docstring>default is 2 points</docstring>
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="shrinkA" arg_pos="12" constructor_arg="True" name="shrinkA" port_type="basic:Float">
+ <docstring>default is 2 points</docstring>
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="mutation_aspect" arg_pos="15" constructor_arg="True" name="mutation_aspect" port_type="basic:Integer">
+ <docstring>default is 1.</docstring>
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="mutation_scale" arg_pos="14" constructor_arg="True" name="mutation_scale">
+ <docstring>default is text size (in points)</docstring>
+ <defaults>['text']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="patchA" arg_pos="10" constructor_arg="True" name="patchA" port_type="basic:String">
+ <docstring>default is bounding box of the text</docstring>
+ <defaults>['bounding']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="patchB" arg_pos="11" constructor_arg="True" name="patchB">
+ <docstring>default is None</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="coordsB" arg_pos="3" constructor_arg="True" name="coordsB">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="?" constructor_arg="True" name="?">
+ <docstring>any key for :class:`matplotlib.patches.PathPatch`</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.lines.Line2D" name="MplLine2DProperties" superclass="MplArtistProperties">
+ <docstring>
+ A line - the line can have both a solid linestyle connecting all
+ the vertices, and a marker at each vertex. Additionally, the
+ drawing of the solid line is influenced by the drawstyle, eg one
+ can create "stepped" lines in various styles.
+
+
+ </docstring>
+ <inputPortSpec arg="picker" name="picker" port_type="basic:Float">
+ <docstring>Sets the event picker details for the line.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dash_capstyle" name="dash_capstyle" port_type="basic:String">
+ <docstring>Set the cap style for dashed linestyles</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['butt', 'round', 'projecting']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>Set the color of the line</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="markevery" name="markevery">
+ <docstring>Set the markevery property to subsample the plot when using markers. Eg if markevery=5, every 5-th marker will be plotted. every can be</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['(startind, stride)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="markeredgecolor" name="markeredgecolor" port_type="basic:Color">
+ <docstring>Set the marker edge color</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="marker" name="marker" port_type="basic:String">
+ <docstring>Set the line marker
+
+The marker can also be a tuple (numsides, style, angle), which will create a custom, regular symbol.
+
+
+
+For backward compatibility, the form (verts, 0) is also accepted, but it is equivalent to just verts for giving a raw set of vertices that define the shape.</docstring>
+ <translations>{'caretright': 5, 'star': '*', 'point': '.', 'tickdown': 3, 'triangle_right': '>', 'tickup': 2, 'hexagon1': 'h', 'hline': '_', 'vline': '|', 'mathtext': '$...$', 'nothing': ' ', 'caretleft': 4, 'pentagon': 'p', 'tri_left': '3', 'caretdown': 7, 'tri_down': '1', 'tickright': 1, 'tri_right': '4', 'thin_diamond': 'd', 'diamond': 'D', 'octagon': '8', 'tickleft': 0, 'square': 's', 'tri_up': '2', 'plus': '+', 'x': 'x', 'triangle_down': 'v', 'triangle_up': '^', 'hexagon2': [...]
+ <entry_types>['enum']</entry_types>
+ <values>[['caretdown', 'caretleft', 'caretright', 'caretup', 'circle', 'diamond', 'hexagon1', 'hexagon2', 'hline', 'nothing', 'octagon', 'pentagon', 'pixel', 'plus', 'point', 'square', 'star', 'thin_diamond', 'tickdown', 'tickleft', 'tickright', 'tickup', 'tri_down', 'tri_left', 'tri_right', 'tri_up', 'triangle_down', 'triangle_left', 'triangle_right', 'triangle_up', 'vline', 'x', 'mathtext']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="markerfacecoloralt" name="markerfacecoloralt" port_type="basic:Color">
+ <docstring>Set the alternate marker face color.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidth" name="linewidth" port_type="basic:Float">
+ <docstring>Set the line width in points</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyle" name="linestyle" port_type="basic:String">
+ <docstring>Set the linestyle of the line (also accepts drawstyles)
+
+'steps' is equivalent to 'steps-pre' and is maintained for backward-compatibility.</docstring>
+ <translations>{'solid': '-', 'dashed': '--', 'dash_dot': '-.', 'dotted': ':', 'draw nothing': ''}</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['solid', 'dashed', 'dash_dot', 'dotted', 'draw nothing', 'draw nothing', 'draw nothing']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="solid_joinstyle" name="solid_joinstyle" port_type="basic:String">
+ <docstring>Set the join style for solid linestyles</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['miter', 'round', 'bevel']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="markerfacecolor" name="markerfacecolor" port_type="basic:Color">
+ <docstring>Set the marker face color.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="axes" name="axes">
+ <docstring>Set the :class:`~matplotlib.axes.Axes` instance in which the artist resides, if any.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="transform" name="transform">
+ <docstring>set the Transformation instance used by this artist</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="fillstyle" name="fillstyle" port_type="basic:String">
+ <docstring>Set the marker fill style; 'full' means fill the whole marker. 'none' means no filling; other options are for half-filled markers.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['full', 'left', 'right', 'bottom', 'top', 'none']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="markeredgewidth" name="markeredgewidth" port_type="basic:Float">
+ <docstring>Set the marker edge width in points</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="solid_capstyle" name="solid_capstyle" port_type="basic:String">
+ <docstring>Set the cap style for solid linestyles</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['butt', 'round', 'projecting']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="dashes" name="dashes" port_type="basic:List">
+ <docstring>Set the dash sequence, sequence of dashes with on off ink in points. If seq is empty or if seq = (None, None), the linestyle will be set to solid.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="markersize" name="markersize" port_type="basic:Float">
+ <docstring>Set the marker size in points</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="antialiased" name="antialiased" port_type="basic:Boolean">
+ <docstring>True if line should be drawin with antialiased rendering</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xdata" name="xdata">
+ <docstring>Set the data np.array for x</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="drawstyle" name="drawstyle" port_type="basic:String">
+ <docstring>Set the drawstyle of the plot
+
+'default' connects the points with lines. The steps variants produce step-plots. 'steps' is equivalent to 'steps-pre' and is maintained for backward-compatibility.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['default', 'steps', 'steps-pre', 'steps-mid', 'steps-post']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="data" name="data">
+ <docstring>Set the x and y data</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dash_joinstyle" name="dash_joinstyle" port_type="basic:String">
+ <docstring>Set the join style for dashed linestyles</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['miter', 'round', 'bevel']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="pickradius" name="pickradius" port_type="basic:Float">
+ <docstring>Sets the pick radius used for containment tests</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ydata" name="ydata">
+ <docstring>Set the data np.array for y</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.text.Text" name="MplTextProperties" superclass="MplArtistProperties">
+ <docstring>
+ Handle storing and drawing of text in window or data coordinates.
+ </docstring>
+ <inputPortSpec arg="rotation_mode" name="rotation_mode">
+ <docstring>set text rotation mode. If "anchor", the un-rotated text will first aligned according to their ha and va, and then will be rotated with the alignement reference point as a origin. If None (default), the text will be rotated first then will be aligned.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="style" name="style" port_type="basic:String">
+ <docstring>Set the font style.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['normal', 'italic', 'oblique']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="linespacing" name="linespacing" port_type="basic:Float">
+ <docstring>Set the line spacing as a multiple of the font size. Default is 1.2.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="family" name="family" port_type="basic:String">
+ <docstring>Set the font family. May be either a single string, or a list of strings in decreasing priority. Each string may be either a real font name or a generic font class name. If the latter, the specific font names will be looked up in the :file:`matplotlibrc` file.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['FONTNAME', 'serif', 'sans-serif', 'cursive', 'fantasy', 'monospace']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="x" name="x" port_type="basic:Float">
+ <docstring>Set the x position of the text</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>Set the foreground color of the text</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="text" name="text" port_type="basic:String">
+ <docstring>Set the text string s
+
+It may contain newlines (\n) or math in LaTeX syntax.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="verticalalignment" name="verticalalignment" port_type="basic:String">
+ <docstring>Set the vertical alignment</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['center', 'top', 'bottom', 'baseline']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="variant" name="variant" port_type="basic:String">
+ <docstring>Set the font variant, either 'normal' or 'small-caps'.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['normal', 'small-caps']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="path_effects" name="path_effects" />
+ <inputPortSpec arg="weight" name="weight" port_type="basic:String">
+ <docstring>Set the font weight.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['a numeric value in range 0-1000', 'ultralight', 'light', 'normal', 'regular', 'book', 'medium', 'roman', 'semibold', 'demibold', 'demi', 'bold', 'heavy', 'extra bold', 'black']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="stretch" name="stretch" port_type="basic:String">
+ <docstring>Set the font stretch (horizontal condensation or expansion).</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['a numeric value in range 0-1000', 'ultra-condensed', 'extra-condensed', 'condensed', 'semi-condensed', 'normal', 'semi-expanded', 'expanded', 'extra-expanded', 'ultra-expanded']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="fontproperties" name="fontproperties">
+ <docstring>Set the font properties that control the text. fp must be a :class:`matplotlib.font_manager.FontProperties` object.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="horizontalalignment" name="horizontalalignment" port_type="basic:String">
+ <docstring>Set the horizontal alignment to one of</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['center', 'right', 'left']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox" name="bbox">
+ <docstring>Draw a bounding box around self. rectprops are any settable properties for a rectangle, eg facecolor='red', alpha=0.5.
+
+t.set_bbox(dict(facecolor='red', alpha=0.5))
+
+If rectprops has "boxstyle" key. A FancyBboxPatch is initialized with rectprops and will be drawn. The mutation scale of the FancyBboxPath is set to the fontsize.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="backgroundcolor" name="backgroundcolor" port_type="basic:Color">
+ <docstring>Set the background color of the text by updating the bbox.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="position" name="position">
+ <docstring>Set the (x, y) position of the text</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" name="y" port_type="basic:Float">
+ <docstring>Set the y position of the text</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="multialignment" name="multialignment" port_type="basic:String">
+ <docstring>Set the alignment for multiple lines layout. The layout of the bounding box of all the lines is determined bu the horizontalalignment and verticalalignment properties, but the multiline text within that box can be</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['left', 'right', 'center']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="rotation" name="rotation" port_type="basic:String">
+ <docstring>Set the rotation of the text</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['angle in degrees', 'vertical', 'horizontal']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="size" name="size" port_type="basic:String">
+ <docstring>Set the font size. May be either a size string, relative to the default font size, or an absolute font size in points.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['size in points', 'xx-small', 'x-small', 'small', 'medium', 'large', 'x-large', 'xx-large']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.text.TextWithDash" name="MplTextWithDashProperties" superclass="MplTextProperties">
+ <docstring>
+ This is basically a :class:`~matplotlib.text.Text` with a dash
+ (drawn with a :class:`~matplotlib.lines.Line2D`) before/after
+ it. It is intended to be a drop-in replacement for
+ :class:`~matplotlib.text.Text`, and should behave identically to
+ it when *dashlength* = 0.0.
+
+ The dash always comes between the point specified by
+ :meth:`~matplotlib.text.Text.set_position` and the text. When a
+ dash exists, the text alignment arguments (*horizontalalignment*,
+ *verticalalignment*) are ignored.
+
+ *dashlength* is the length of the dash in canvas units.
+ (default = 0.0).
+
+ *dashdirection* is one of 0 or 1, where 0 draws the dash after the
+ text and 1 before. (default = 0).
+
+ *dashrotation* specifies the rotation of the dash, and should
+ generally stay *None*. In this case
+ :meth:`~matplotlib.text.TextWithDash.get_dashrotation` returns
+ :meth:`~matplotlib.text.Text.get_rotation`. (I.e., the dash takes
+ its rotation from the text's rotation). Because the text center is
+ projected onto the dash, major deviations in the rotation cause
+ what may be considered visually unappealing results.
+ (default = *None*)
+
+ *dashpad* is a padding length to add (or subtract) space
+ between the text and the dash, in canvas units.
+ (default = 3)
+
+ *dashpush* "pushes" the dash and text away from the point
+ specified by :meth:`~matplotlib.text.Text.set_position` by the
+ amount in canvas units. (default = 0)
+
+ .. note::
+
+ The alignment of the two objects is based on the bounding box
+ of the :class:`~matplotlib.text.Text`, as obtained by
+ :meth:`~matplotlib.artist.Artist.get_window_extent`. This, in
+ turn, appears to depend on the font metrics as given by the
+ rendering backend. Hence the quality of the "centering" of the
+ label text with respect to the dash varies depending on the
+ backend used.
+
+ .. note::
+
+ I'm not sure that I got the
+ :meth:`~matplotlib.text.TextWithDash.get_window_extent` right,
+ or whether that's sufficient for providing the object bounding
+ box.
+
+ </docstring>
+ <inputPortSpec arg="dashpush" name="dashpush" port_type="basic:Float">
+ <docstring>Set the "push" of the TextWithDash, which is the extra spacing between the beginning of the dash and the specified position.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dashdirection" name="dashdirection">
+ <docstring>Set the direction of the dash following the text. 1 is before the text and 0 is after. The default is 0, which is what you'd want for the typical case of ticks below and on the left of the figure.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="linespacing" arg_pos="9" constructor_arg="True" name="linespacing" />
+ <inputPortSpec arg="figure" name="figure">
+ <docstring>Set the figure instance the artist belong to.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="3" constructor_arg="True" name="color" />
+ <inputPortSpec arg="text" arg_pos="2" constructor_arg="True" name="text" port_type="basic:String">
+ <defaults>['']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="verticalalignment" arg_pos="4" constructor_arg="True" name="verticalalignment" port_type="basic:String">
+ <defaults>['center']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="dashpad" name="dashpad" port_type="basic:Float">
+ <docstring>Set the "pad" of the TextWithDash, which is the extra spacing between the dash and the text, in canvas units.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dashrotation" name="dashrotation" port_type="basic:Float">
+ <docstring>Set the rotation of the dash, in degrees</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="transform" name="transform">
+ <docstring>Set the :class:`matplotlib.transforms.Transform` instance used by this artist.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="fontproperties" arg_pos="7" constructor_arg="True" name="fontproperties" />
+ <inputPortSpec arg="multialignment" arg_pos="6" constructor_arg="True" name="multialignment" />
+ <inputPortSpec arg="x" name="x" port_type="basic:Float">
+ <docstring>Set the x position of the :class:`TextWithDash`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" name="y" port_type="basic:Float">
+ <docstring>Set the y position of the :class:`TextWithDash`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="position" name="position">
+ <docstring>Set the (x, y) position of the :class:`TextWithDash`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dashlength" name="dashlength" port_type="basic:Float">
+ <docstring>Set the length of the dash.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rotation" arg_pos="8" constructor_arg="True" name="rotation" />
+ <inputPortSpec arg="horizontalalignment" arg_pos="5" constructor_arg="True" name="horizontalalignment" port_type="basic:String">
+ <defaults>['center']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.Tick" name="MplTickProperties" superclass="MplArtistProperties">
+ <docstring>
+ Abstract base class for the axis ticks, grid lines and labels
+
+ 1 refers to the bottom of the plot for xticks and the left for yticks
+ 2 refers to the top of the plot for xticks and the right for yticks
+
+ Publicly accessible attributes:
+
+ :attr:`tick1line`
+ a Line2D instance
+
+ :attr:`tick2line`
+ a Line2D instance
+
+ :attr:`gridline`
+ a Line2D instance
+
+ :attr:`label1`
+ a Text instance
+
+ :attr:`label2`
+ a Text instance
+
+ :attr:`gridOn`
+ a boolean which determines whether to draw the tickline
+
+ :attr:`tick1On`
+ a boolean which determines whether to draw the 1st tickline
+
+ :attr:`tick2On`
+ a boolean which determines whether to draw the 2nd tickline
+
+ :attr:`label1On`
+ a boolean which determines whether to draw tick label
+
+ :attr:`label2On`
+ a boolean which determines whether to draw tick label
+
+ </docstring>
+ <inputPortSpec arg="label1On" arg_pos="14" constructor_arg="True" name="label1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="loc" arg_pos="1" constructor_arg="True" name="loc" />
+ <inputPortSpec arg="major" arg_pos="16" constructor_arg="True" name="major" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label2On" arg_pos="15" constructor_arg="True" name="label2On" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="5" constructor_arg="True" name="color" />
+ <inputPortSpec arg="label1" name="label1">
+ <docstring>Set the text of ticklabel</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="label2" name="label2">
+ <docstring>Set the text of ticklabel2</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="clip_path" name="clip_path" port_type="basic:String">
+ <docstring>Set the artist's clip path, which may be:
+
+a :class:`~matplotlib.patches.Patch` (or subclass) instance
+
+
+
+None, to remove the clipping path
+
+For efficiency, if the path happens to be an axis-aligned rectangle, this method will set the clipping box to the corresponding rectangle and set the clipping path to None.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['(:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`)', ':class:`~matplotlib.patches.Patch`']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="label" name="label">
+ <docstring>Set the text of ticklabel</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="labelcolor" arg_pos="9" constructor_arg="True" name="labelcolor" />
+ <inputPortSpec arg="tickdir" arg_pos="6" constructor_arg="True" name="tickdir" />
+ <inputPortSpec arg="pad" name="pad" port_type="basic:Float">
+ <docstring>Set the tick label pad in points</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="gridOn" arg_pos="11" constructor_arg="True" name="gridOn" />
+ <inputPortSpec arg="zorder" arg_pos="10" constructor_arg="True" name="zorder" />
+ <inputPortSpec arg="tick2On" arg_pos="13" constructor_arg="True" name="tick2On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="labelsize" arg_pos="8" constructor_arg="True" name="labelsize" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" />
+ <inputPortSpec arg="tick1On" arg_pos="12" constructor_arg="True" name="tick1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="size" arg_pos="3" constructor_arg="True" name="size" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.XTick" name="MplXTickProperties" superclass="MplTickProperties">
+ <docstring>
+ Contains all the Artists needed to make an x tick - the tick line,
+ the label text and the grid line
+ </docstring>
+ <inputPortSpec arg="label1On" arg_pos="14" constructor_arg="True" name="label1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="loc" arg_pos="1" constructor_arg="True" name="loc" />
+ <inputPortSpec arg="major" arg_pos="16" constructor_arg="True" name="major" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label2On" arg_pos="15" constructor_arg="True" name="label2On" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="5" constructor_arg="True" name="color" />
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="label" arg_pos="2" constructor_arg="True" name="label" />
+ <inputPortSpec arg="labelcolor" arg_pos="9" constructor_arg="True" name="labelcolor" />
+ <inputPortSpec arg="tickdir" arg_pos="6" constructor_arg="True" name="tickdir" />
+ <inputPortSpec arg="pad" arg_pos="7" constructor_arg="True" name="pad" />
+ <inputPortSpec arg="gridOn" arg_pos="11" constructor_arg="True" name="gridOn" />
+ <inputPortSpec arg="zorder" arg_pos="10" constructor_arg="True" name="zorder" />
+ <inputPortSpec arg="tick2On" arg_pos="13" constructor_arg="True" name="tick2On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="labelsize" arg_pos="8" constructor_arg="True" name="labelsize" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" />
+ <inputPortSpec arg="tick1On" arg_pos="12" constructor_arg="True" name="tick1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="size" arg_pos="3" constructor_arg="True" name="size" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.YTick" name="MplYTickProperties" superclass="MplTickProperties">
+ <docstring>
+ Contains all the Artists needed to make a Y tick - the tick line,
+ the label text and the grid line
+ </docstring>
+ <inputPortSpec arg="label1On" arg_pos="14" constructor_arg="True" name="label1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="loc" arg_pos="1" constructor_arg="True" name="loc" />
+ <inputPortSpec arg="major" arg_pos="16" constructor_arg="True" name="major" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label2On" arg_pos="15" constructor_arg="True" name="label2On" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="5" constructor_arg="True" name="color" />
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="label" arg_pos="2" constructor_arg="True" name="label" />
+ <inputPortSpec arg="labelcolor" arg_pos="9" constructor_arg="True" name="labelcolor" />
+ <inputPortSpec arg="tickdir" arg_pos="6" constructor_arg="True" name="tickdir" />
+ <inputPortSpec arg="pad" arg_pos="7" constructor_arg="True" name="pad" />
+ <inputPortSpec arg="gridOn" arg_pos="11" constructor_arg="True" name="gridOn" />
+ <inputPortSpec arg="zorder" arg_pos="10" constructor_arg="True" name="zorder" />
+ <inputPortSpec arg="tick2On" arg_pos="13" constructor_arg="True" name="tick2On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="labelsize" arg_pos="8" constructor_arg="True" name="labelsize" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" />
+ <inputPortSpec arg="tick1On" arg_pos="12" constructor_arg="True" name="tick1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="size" arg_pos="3" constructor_arg="True" name="size" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.Axis" name="MplAxisProperties" superclass="MplArtistProperties">
+ <docstring>
+ Public attributes
+
+ * :attr:`axes.transData` - transform data coords to display coords
+ * :attr:`axes.transAxes` - transform axis coords to display coords
+ * :attr:`labelpad` - number of points between the axis and its label
+ </docstring>
+ <inputPortSpec arg="pickradius" name="pickradius">
+ <docstring>Set the depth of the axis used by the picker</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="minor_formatter" name="minor_formatter">
+ <docstring>Set the formatter of the minor ticker</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="smart_bounds" name="smart_bounds">
+ <docstring>set the axis to have smart bounds</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ticks" name="ticksSequence" port_type="basic:List">
+ <docstring>Set the locations of the tick marks from sequence ticks</docstring>
+ <alternateSpec arg="ticks" name="ticksScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="view_interval" name="view_interval" />
+ <inputPortSpec arg="major_locator" name="major_locator">
+ <docstring>Set the locator of the major ticker</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="major_formatter" name="major_formatter">
+ <docstring>Set the formatter of the major ticker</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ticklabels" name="ticklabelsSequence" port_type="basic:List">
+ <docstring>Set the text values of the tick labels. Return a list of Text instances. Use kwarg minor=True to select minor ticks. All other kwargs are used to update the text object properties. As for get_ticklabels, label1 (left or bottom) is affected for a given tick only if its label1On attribute is True, and similarly for label2. The list of returned label text objects consists of all such label1 objects followed by all such label2 objects.
+
+The input ticklabels is assumed to match the set of tick locations, regardless of the state of label1On and label2On.</docstring>
+ <alternateSpec arg="ticklabels" name="ticklabelsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="clip_path" name="clip_path" />
+ <inputPortSpec arg="minor_locator" name="minor_locator">
+ <docstring>Set the locator of the minor ticker</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="default_intervals" name="default_intervals" />
+ <inputPortSpec arg="scale" name="scale" />
+ <inputPortSpec arg="data_interval" name="data_interval">
+ <docstring>set the axis data limits</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="label_text" name="label_text" port_type="basic:String">
+ <docstring>Sets the text value of the axis label</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="label_coords" name="label_coords">
+ <docstring>Set the coordinates of the label. By default, the x coordinate of the y label is determined by the tick label bounding boxes, but this can lead to poor alignment of multiple ylabels if there are multiple axes. Ditto for the y coodinate of the x label.
+
+You can also specify the coordinate system of the label with the transform. If None, the default coordinate system will be the axes coordinate system (0,0) is (left,bottom), (0.5, 0.5) is middle, etc</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="units" name="units">
+ <docstring>set the units for axis</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="tick_params" name="tick_params">
+ <docstring>Set appearance parameters for ticks and ticklabels.
+
+For documentation of keyword arguments, see :meth:`matplotlib.axes.Axes.tick_params`.</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.XAxis" name="MplXAxisProperties" superclass="MplAxisProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="view_interval" name="view_interval">
+ <docstring>If ignore is False, the order of vmin, vmax does not matter; the original axis orientation will be preserved. In addition, the view limits can be expanded, but will not be reduced. This method is for mpl internal use; for normal use, see :meth:`~matplotlib.axes.Axes.set_xlim`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ticks_position" name="ticks_position" port_type="basic:String">
+ <docstring>Set the ticks position (top, bottom, both, default or none) both sets the ticks to appear on both positions, but does not change the tick labels. 'default' resets the tick positions to the default: ticks on both positions, labels at bottom. 'none' can be used if you don't want any ticks. 'none' and 'both' affect only the ticks, not the labels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['top', 'bottom', 'both', 'default', 'none']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="label_position" name="label_position" port_type="basic:String">
+ <docstring>Set the label position (top or bottom)</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['top', 'bottom']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="default_intervals" name="default_intervals">
+ <docstring>set the default limits for the axis interval if they are not mutated</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="data_interval" name="data_interval">
+ <docstring>set the axis data limits</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="pickradius" arg_pos="1" constructor_arg="True" name="pickradius" port_type="basic:Integer">
+ <defaults>['15']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.YAxis" name="MplYAxisProperties" superclass="MplAxisProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="offset_position" name="offset_position" />
+ <inputPortSpec arg="view_interval" name="view_interval">
+ <docstring>If ignore is False, the order of vmin, vmax does not matter; the original axis orientation will be preserved. In addition, the view limits can be expanded, but will not be reduced. This method is for mpl internal use; for normal use, see :meth:`~matplotlib.axes.Axes.set_ylim`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ticks_position" name="ticks_position" port_type="basic:String">
+ <docstring>Set the ticks position (left, right, both, default or none) 'both' sets the ticks to appear on both positions, but does not change the tick labels. 'default' resets the tick positions to the default: ticks on both positions, labels at left. 'none' can be used if you don't want any ticks. 'none' and 'both' affect only the ticks, not the labels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['left', 'right', 'both', 'default', 'none']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="label_position" name="label_position" port_type="basic:String">
+ <docstring>Set the label position (left or right)</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['left', 'right']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="default_intervals" name="default_intervals">
+ <docstring>set the default limits for the axis interval if they are not mutated</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="data_interval" name="data_interval">
+ <docstring>set the axis data limits</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="pickradius" arg_pos="1" constructor_arg="True" name="pickradius" port_type="basic:Integer">
+ <defaults>['15']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.legend.Legend" name="MplLegendProperties" superclass="MplArtistProperties">
+ <docstring>
+ Place a legend on the axes at location loc. Labels are a
+ sequence of strings and loc can be a string or an integer
+ specifying the legend location
+
+ The location codes are::
+
+ 'best' : 0, (only implemented for axis legends)
+ 'upper right' : 1,
+ 'upper left' : 2,
+ 'lower left' : 3,
+ 'lower right' : 4,
+ 'right' : 5,
+ 'center left' : 6,
+ 'center right' : 7,
+ 'lower center' : 8,
+ 'upper center' : 9,
+ 'center' : 10,
+
+ loc can be a tuple of the noramilzed coordinate values with
+ respect its parent.
+
+ </docstring>
+ <inputPortSpec arg="fancybox" arg_pos="24" constructor_arg="True" name="fancybox" />
+ <inputPortSpec arg="handlelength" arg_pos="17" constructor_arg="True" name="handlelength" />
+ <inputPortSpec arg="labels" arg_pos="2" constructor_arg="True" name="labels" />
+ <inputPortSpec arg="labelspacing" arg_pos="16" constructor_arg="True" name="labelspacing" />
+ <inputPortSpec arg="columnspacing" arg_pos="21" constructor_arg="True" name="columnspacing" />
+ <inputPortSpec arg="handletextpad" arg_pos="19" constructor_arg="True" name="handletextpad" />
+ <inputPortSpec arg="ncol" arg_pos="22" constructor_arg="True" name="ncol" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="borderaxespad" arg_pos="20" constructor_arg="True" name="borderaxespad" />
+ <inputPortSpec arg="loc" arg_pos="3" constructor_arg="True" name="loc" />
+ <inputPortSpec arg="bbox_to_anchor" name="bbox_to_anchor">
+ <docstring>set the bbox that the legend will be anchored.
+
+bbox can be a BboxBase instance, a tuple of [left, bottom, width, height] in the given transform (normalized axes coordinate if None), or a tuple of [left, bottom] where the width and height will be assumed to be zero.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="title" name="title">
+ <docstring>set the legend title. Fontproperties can be optionally set with prop parameter.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="handletextsep" arg_pos="13" constructor_arg="True" name="handletextsep" />
+ <inputPortSpec arg="numpoints" arg_pos="4" constructor_arg="True" name="numpoints" />
+ <inputPortSpec arg="prop" arg_pos="8" constructor_arg="True" name="prop" />
+ <inputPortSpec arg="handles" arg_pos="1" constructor_arg="True" name="handles" />
+ <inputPortSpec arg="pad" arg_pos="10" constructor_arg="True" name="pad" />
+ <inputPortSpec arg="borderpad" arg_pos="15" constructor_arg="True" name="borderpad" />
+ <inputPortSpec arg="parent" arg_pos="0" constructor_arg="True" name="parent" />
+ <inputPortSpec arg="axespad" arg_pos="14" constructor_arg="True" name="axespad" />
+ <inputPortSpec arg="labelsep" arg_pos="11" constructor_arg="True" name="labelsep" />
+ <inputPortSpec arg="frame_on" name="frame_on" port_type="basic:Boolean">
+ <docstring>Set whether the legend box patch is drawn</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="scatterpoints" arg_pos="6" constructor_arg="True" name="scatterpoints" port_type="basic:Integer">
+ <defaults>['3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="fontsize" arg_pos="9" constructor_arg="True" name="fontsize" />
+ <inputPortSpec arg="shadow" arg_pos="25" constructor_arg="True" name="shadow" />
+ <inputPortSpec arg="handler_map" arg_pos="30" constructor_arg="True" name="handler_map" />
+ <inputPortSpec arg="handleheight" arg_pos="18" constructor_arg="True" name="handleheight" />
+ <inputPortSpec arg="scatteryoffsets" arg_pos="7" constructor_arg="True" name="scatteryoffsets" />
+ <inputPortSpec arg="markerscale" arg_pos="5" constructor_arg="True" name="markerscale" />
+ <inputPortSpec arg="frameon" arg_pos="29" constructor_arg="True" name="frameon" />
+ <inputPortSpec arg="mode" arg_pos="23" constructor_arg="True" name="mode" />
+ <inputPortSpec arg="handlelen" arg_pos="12" constructor_arg="True" name="handlelen" />
+ <inputPortSpec arg="default_handler_map" name="default_handler_map">
+ <docstring>A class method to set the default handler map.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox_transform" arg_pos="28" constructor_arg="True" name="bbox_transform" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axes.Axes" name="MplAxesProperties" superclass="MplArtistProperties">
+ <docstring>
+ The :class:`Axes` contains most of the figure elements:
+ :class:`~matplotlib.axis.Axis`, :class:`~matplotlib.axis.Tick`,
+ :class:`~matplotlib.lines.Line2D`, :class:`~matplotlib.text.Text`,
+ :class:`~matplotlib.patches.Polygon`, etc., and sets the
+ coordinate system.
+
+ The :class:`Axes` instance supports callbacks through a callbacks
+ attribute which is a :class:`~matplotlib.cbook.CallbackRegistry`
+ instance. The events you can connect to are 'xlim_changed' and
+ 'ylim_changed' and the callback will be called with func(*ax*)
+ where *ax* is the :class:`Axes` instance.
+ </docstring>
+ <inputPortSpec arg="adjustable" name="adjustable" port_type="basic:String">
+ <entry_types>['enum']</entry_types>
+ <values>[['box', 'datalim', 'box-forced']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cursor_props" name="cursor_props" port_type="basic:Float">
+ <docstring>Set the cursor property as:
+
+ax.set_cursor_props(linewidth, color)
+
+or:
+
+ax.set_cursor_props((linewidth, color))</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="figure" name="figure">
+ <docstring>Set the class:~matplotlib.axes.Axes figure
+
+accepts a class:~matplotlib.figure.Figure instance</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="yscale" name="yscale">
+ <docstring>Call signature:
+
+set_yscale(value)
+
+Set the scaling of the y-axis: 'linear' | 'log' | 'symlog' Different kwargs are accepted, depending on the scale: 'linear'
+
+'log'
+
+
+
+'symlog'</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="navigate" name="navigate" port_type="basic:Boolean">
+ <docstring>Set whether the axes responds to navigation toolbar commands</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="aspect" name="aspect">
+ <docstring>aspect
+
+
+
+adjustable
+
+
+
+'box' does not allow axes sharing, as this can cause unintended side effect. For cases when sharing axes is fine, use 'box-forced'.
+
+anchor</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['auto', 'normal', 'equal', 'num']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="axis_bgcolor" name="axis_bgcolor" port_type="basic:Color">
+ <docstring>set the axes background color</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="ylim" name="ylimSequence" port_type="basic:List">
+ <docstring>Call signature:
+
+set_ylim(self, *args, **kwargs):
+
+Set the data limits for the yaxis
+
+Examples:
+
+set_ylim((bottom, top)) set_ylim(bottom, top) set_ylim(bottom=1) # top unchanged set_ylim(top=1) # bottom unchanged
+
+Keyword arguments:
+
+
+
+Note, the bottom (formerly ymin) value may be greater than the top (formerly ymax). For example, suppose y is depth in the ocean. Then one might use:
+
+set_ylim(5000, 0)
+
+so 5000 m depth is at the bottom of the plot and the surface, 0 m, is at the top.
+
+Returns the current ylimits as a length 2 tuple</docstring>
+ <alternateSpec arg="ylim" name="ylimScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="sharey" arg_pos="5" constructor_arg="True" name="sharey" />
+ <inputPortSpec arg="xlim" name="xlimSequence" port_type="basic:List">
+ <docstring>Call signature:
+
+set_xlim(self, *args, **kwargs):
+
+Set the data limits for the xaxis
+
+Examples:
+
+set_xlim((left, right)) set_xlim(left, right) set_xlim(left=1) # right unchanged set_xlim(right=1) # left unchanged
+
+Keyword arguments:
+
+
+
+Note, the left (formerly xmin) value may be greater than the right (formerly xmax). For example, suppose x is years before present. Then one might use:
+
+set_ylim(5000, 0)
+
+so 5000 years ago is on the left of the plot and the present is on the right.
+
+Returns the current xlimits as a length 2 tuple</docstring>
+ <alternateSpec arg="xlim" name="xlimScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="axis_on" name="axis_on">
+ <docstring>turn on the axis</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="title" name="title">
+ <docstring>Call signature:
+
+set_title(label, fontdict=None, **kwargs):
+
+Set the title for the axes.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axisbg" arg_pos="2" constructor_arg="True" name="axisbg" />
+ <inputPortSpec arg="label" arg_pos="6" constructor_arg="True" name="label" port_type="basic:String">
+ <defaults>['']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xticks" name="xticks" port_type="basic:List">
+ <docstring>Set the x ticks with list of ticks</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="fig" arg_pos="0" constructor_arg="True" name="fig" />
+ <inputPortSpec arg="ylabel" name="ylabel">
+ <docstring>Call signature:
+
+set_ylabel(ylabel, fontdict=None, labelpad=None, **kwargs)
+
+Set the label for the yaxis
+
+labelpad is the spacing in points between the label and the y-axis</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="autoscalex_on" name="autoscalex_on" port_type="basic:Boolean">
+ <docstring>Set whether autoscaling for the x-axis is applied on plot commands</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rasterization_zorder" name="rasterization_zorder">
+ <docstring>Set zorder value below which artists will be rasterized. Set to None to disable rasterizing of artists below a particular zorder.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axes_locator" name="axes_locator">
+ <docstring>set axes_locator</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axisbelow" name="axisbelow" port_type="basic:Boolean">
+ <docstring>Set whether the axis ticks and gridlines are above or below most artists</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="frame_on" name="frame_on" port_type="basic:Boolean">
+ <docstring>Set whether the axes rectangle patch is drawn</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="navigate_mode" name="navigate_mode">
+ <docstring>Set the navigation toolbar button status;
+
+this is not a user-API function.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xscale" name="xscale">
+ <docstring>Call signature:
+
+set_xscale(value)
+
+Set the scaling of the x-axis: 'linear' | 'log' | 'symlog' Different kwargs are accepted, depending on the scale: 'linear'
+
+'log'
+
+
+
+'symlog'</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axis_off" name="axis_off">
+ <docstring>turn off the axis</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="autoscale_on" name="autoscale_on" port_type="basic:Boolean">
+ <docstring>Set whether autoscaling is applied on plot commands</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ybound" name="ybound">
+ <docstring>Set the lower and upper numerical bounds of the y-axis. This method will honor axes inversion regardless of parameter order. It will not change the _autoscaleYon attribute.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rect" arg_pos="1" constructor_arg="True" name="rect" />
+ <inputPortSpec arg="sharex" arg_pos="4" constructor_arg="True" name="sharex" />
+ <inputPortSpec arg="yticklabels" name="yticklabelsSequence" port_type="basic:List">
+ <docstring>Call signature:
+
+set_yticklabels(labels, fontdict=None, minor=False, **kwargs)
+
+Set the y tick labels with list of strings labels. Return a list of :class:`~matplotlib.text.Text` instances.
+
+kwargs set :class:`~matplotlib.text.Text` properties for the labels. Valid properties are
+
+agg_filter: unknown alpha: float (0.0 transparent through 1.0 opaque) animated: [True | False] axes: an :class:`~matplotlib.axes.Axes` instance backgroundcolor: any matplotlib color bbox: rectangle prop dict clip_box: a :class:`matplotlib.transforms.Bbox` instance clip_on: [True | False] clip_path: [ (:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`) | :class:`~matplotlib.patches.Patch` | None ] color: any matplotlib color contains: a callable fun [...]
+ <alternateSpec arg="yticklabels" name="yticklabelsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="autoscaley_on" name="autoscaley_on" port_type="basic:Boolean">
+ <docstring>Set whether autoscaling for the y-axis is applied on plot commands</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xmargin" name="xmargin" port_type="basic:Float">
+ <docstring>Set padding of X data limits prior to autoscaling.
+
+m times the data interval will be added to each end of that interval before it is used in autoscaling.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="color_cycle" name="color_cycle" port_type="basic:Color">
+ <docstring>Set the color cycle for any future plot commands on this Axes.
+
+clist is a list of mpl color specifiers.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="frameon" arg_pos="3" constructor_arg="True" name="frameon" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xlabel" name="xlabel">
+ <docstring>Call signature:
+
+set_xlabel(xlabel, fontdict=None, labelpad=None, **kwargs)
+
+Set the label for the xaxis.
+
+labelpad is the spacing in points between the label and the x-axis</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xbound" name="xbound">
+ <docstring>Set the lower and upper numerical bounds of the x-axis. This method will honor axes inversion regardless of parameter order. It will not change the _autoscaleXon attribute.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="yticks" name="yticks" port_type="basic:List">
+ <docstring>Set the y ticks with list of ticks Keyword arguments:</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ymargin" name="ymargin" port_type="basic:Float">
+ <docstring>Set padding of Y data limits prior to autoscaling.
+
+m times the data interval will be added to each end of that interval before it is used in autoscaling.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="position" name="position">
+ <docstring>Set the axes position with:
+
+pos = [left, bottom, width, height]
+
+in relative 0,1 coords, or pos can be a :class:`~matplotlib.transforms.Bbox`
+
+There are two position variables: one which is ultimately used, but which may be modified by :meth:`apply_aspect`, and a second which is the starting point for :meth:`apply_aspect`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="anchor" name="anchor" port_type="basic:String">
+ <docstring>anchor</docstring>
+ <translations>{'bottom right': 'SE', 'right': 'E', 'Center': 'C', 'bottom': 'S', 'top right': 'NE', 'bottom left': 'SW', 'top left': 'NW', 'top': 'N', 'left': 'W'}</translations>
+ <values>[['Center', 'bottom left', 'bottom', 'bottom right', 'right', 'top right', 'top', 'top left', 'left']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="xticklabels" name="xticklabelsSequence" port_type="basic:List">
+ <docstring>Call signature:
+
+set_xticklabels(labels, fontdict=None, minor=False, **kwargs)
+
+Set the xtick labels with list of strings labels. Return a list of axis text instances.
+
+kwargs set the :class:`~matplotlib.text.Text` properties. Valid properties are
+
+agg_filter: unknown alpha: float (0.0 transparent through 1.0 opaque) animated: [True | False] axes: an :class:`~matplotlib.axes.Axes` instance backgroundcolor: any matplotlib color bbox: rectangle prop dict clip_box: a :class:`matplotlib.transforms.Bbox` instance clip_on: [True | False] clip_path: [ (:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`) | :class:`~matplotlib.patches.Patch` | None ] color: any matplotlib color contains: a callable fun [...]
+ <alternateSpec arg="xticklabels" name="xticklabelsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <outputPortSpec arg="title" compute_name="title" compute_parent="title" name="titleProperties" port_type="__property__" property_key="__none__" property_type="matplotlib.text.Text" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axes.AxesSubplot" name="MplAxesSubplotProperties" superclass="MplAxesProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="fig" arg_pos="0" constructor_arg="True" name="fig" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.figure.Figure" name="MplFigureProperties" superclass="MplArtistProperties">
+ <docstring>
+ The Figure instance supports callbacks through a *callbacks*
+ attribute which is a :class:`matplotlib.cbook.CallbackRegistry`
+ instance. The events you can connect to are 'dpi_changed', and
+ the callback will be called with ``func(fig)`` where fig is the
+ :class:`Figure` instance.
+
+ *patch*
+ The figure patch is drawn by a
+ :class:`matplotlib.patches.Rectangle` instance
+
+ *suppressComposite*
+ For multiple figure images, the figure will make composite
+ images depending on the renderer option_image_nocomposite
+ function. If suppressComposite is True|False, this will
+ override the renderer.
+ </docstring>
+ <inputPortSpec arg="edgecolor" name="edgecolor" port_type="basic:Color">
+ <docstring>Set the edge color of the Figure rectangle</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="canvas" name="canvas">
+ <docstring>Set the canvas the contains the figure</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="facecolor" name="facecolor" port_type="basic:Color">
+ <docstring>Set the face color of the Figure rectangle</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="size_inches" name="size_inches">
+ <docstring>set_size_inches(w,h, forward=False)
+
+Set the figure size in inches
+
+Usage:
+
+fig.set_size_inches(w,h) # OR fig.set_size_inches((w,h) )
+
+optional kwarg forward=True will cause the canvas size to be automatically updated; eg you can resize the figure window from the shell</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="figwidth" name="figwidth" port_type="basic:Float">
+ <docstring>Set the width of the figure in inches</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="frameon" name="frameon" port_type="basic:Boolean">
+ <docstring>Set whether the figure frame (background) is displayed or invisible</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="subplotpars" arg_pos="6" constructor_arg="True" name="subplotpars" />
+ <inputPortSpec arg="figheight" name="figheight" port_type="basic:Float">
+ <docstring>Set the height of the figure in inches</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="figsize" arg_pos="0" constructor_arg="True" name="figsize" />
+ <inputPortSpec arg="linewidth" arg_pos="4" constructor_arg="True" name="linewidth" port_type="basic:Float">
+ <defaults>['0.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="tight_layout" name="tight_layout" port_type="basic:Boolean">
+ <docstring>Set whether :meth:`tight_layout` is used upon drawing. If None, the rcParams['figure.autolayout'] value will be set.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dpi" name="dpi" port_type="basic:Float">
+ <docstring>Set the dots-per-inch of the figure</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.text.Annotation" name="MplAnnotationProperties" superclass="MplTextProperties">
+ <docstring>
+ A :class:`~matplotlib.text.Text` class to make annotating things
+ in the figure, such as :class:`~matplotlib.figure.Figure`,
+ :class:`~matplotlib.axes.Axes`,
+ :class:`~matplotlib.patches.Rectangle`, etc., easier.
+ </docstring>
+ <inputPortSpec arg="xycoords" arg_pos="3" constructor_arg="True" name="xycoords" port_type="basic:String">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ <defaults>['data']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="figure" name="figure" />
+ <inputPortSpec arg="annotation_clip" arg_pos="6" constructor_arg="True" name="annotation_clip" />
+ <inputPortSpec arg="xytext" arg_pos="2" constructor_arg="True" name="xytext" />
+ <inputPortSpec arg="s" arg_pos="0" constructor_arg="True" name="s" />
+ <inputPortSpec arg="xy" arg_pos="1" constructor_arg="True" name="xy" />
+ <inputPortSpec arg="textcoords" arg_pos="4" constructor_arg="True" name="textcoords">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="arrowprops" arg_pos="5" constructor_arg="True" name="arrowprops" />
+ </moduleSpec>
+</specs>
diff --git a/vistrails/packages/matplotlib/mpl_artists_diff.xml b/vistrails/packages/matplotlib/mpl_artists_diff.xml
new file mode 100644
index 0000000..b160a37
--- /dev/null
+++ b/vistrails/packages/matplotlib/mpl_artists_diff.xml
@@ -0,0 +1,36 @@
+<diff>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.artist.Artist" port="picker" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.artist.Artist" port="picker" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.artist.Artist" port="clip_path" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.artist.Artist" port="clip_path" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="name" code_ref="matplotlib.axes.Axes" port="xticks" type="input">
+ <value>xticks</value>
+ </changePortSpec>
+ <deletePortSpec altName="xticksScalar" code_ref="matplotlib.axes.Axes" port="xticks" type="alternate" />
+ <changePortSpec attr="name" code_ref="matplotlib.axes.Axes" port="yticks" type="input">
+ <value>yticks</value>
+ </changePortSpec>
+ <deletePortSpec altName="yticksScalar" code_ref="matplotlib.axes.Axes" port="yticks" type="alternate" />
+ <addPortSpec code_ref="matplotlib.axes.Axes" port="title" type="output">
+ <value>
+ <outputPortSpec arg="title" compute_name="title" compute_parent="title" name="titleProperties" port_type="__property__" property_key="__none__" property_type="matplotlib.text.Text" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="translations" code_ref="matplotlib.lines.Line2D" port="marker" type="input">
+ <value>{'caretright': 5, 'star': '*', 'point': '.', 'mathtext': '$...$', 'triangle_right': '>', 'tickup': 2, 'hexagon1': 'h', 'plus': '+', 'hline': '_', 'vline': '|', 'tickdown': 3, 'nothing': ' ', 'caretup': 6, 'caretleft': 4, 'pentagon': 'p', 'tri_left': '3', 'tickleft': 0, 'tickright': 1, 'tri_down': '1', 'thin_diamond': 'd', 'diamond': 'D', 'caretdown': 7, 'hexagon2': 'H', 'tri_up': '2', 'square': 's', 'x': 'x', 'triangle_down': 'v', 'triangle_up': '^', 'octagon': '8', 'tri_ri [...]
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.lines.Line2D" port="marker" type="input">
+ <value>['enum']</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.lines.Line2D" port="marker" type="input">
+ <value>[['caretdown', 'caretleft', 'caretright', 'caretup', 'circle', 'diamond', 'hexagon1', 'hexagon2', 'hline', 'nothing', 'octagon', 'pentagon', 'pixel', 'plus', 'point', 'square', 'star', 'thin_diamond', 'tickdown', 'tickleft', 'tickright', 'tickup', 'tri_down', 'tri_left', 'tri_right', 'tri_up', 'triangle_down', 'triangle_left', 'triangle_right', 'triangle_up', 'vline', 'x', 'mathtext']]</value>
+ </changePortSpec>
+</diff>
diff --git a/vistrails/packages/matplotlib/mpl_artists_raw.xml b/vistrails/packages/matplotlib/mpl_artists_raw.xml
new file mode 100644
index 0000000..d3c6f67
--- /dev/null
+++ b/vistrails/packages/matplotlib/mpl_artists_raw.xml
@@ -0,0 +1,1935 @@
+<specs>
+ <customCode />
+ <moduleSpec code_ref="matplotlib.artist.Artist" name="MplArtistProperties" superclass="MplProperties">
+ <docstring>
+ Abstract base class for someone who renders into a
+ :class:`FigureCanvas`.
+ </docstring>
+ <inputPortSpec arg="picker" name="picker">
+ <docstring>Set the epsilon for picking used by this artist
+
+picker can be one of the following:
+
+None: picking is disabled for this artist (default)
+
+A boolean: if True then picking will be enabled and the artist will fire a pick event if the mouse event is over the artist
+
+A float: if picker is a number it is interpreted as an epsilon tolerance in points and the artist will fire off an event if it's data is within epsilon of the mouse event. For some artists like lines and patch collections, the artist may provide additional data to the pick event that is generated, e.g. the indices of the data within epsilon of the pick event
+
+A function: if picker is callable, it is a user supplied function which determines whether the artist is hit by the mouse event:
+
+hit, props = picker(artist, mouseevent)
+
+to determine the hit test. if the mouse event is over the artist, return hit=True and props is a dictionary of properties you want added to the PickEvent attributes.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[[<built-in function callable>]]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="contains" name="contains">
+ <docstring>Replace the contains test used by this artist. The new picker should be a callable function which determines whether the artist is hit by the mouse event:
+
+hit, props = picker(artist, mouseevent)
+
+If the mouse event is over the artist, return hit = True and props is a dictionary of properties you want returned with the contains test.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="clip_on" name="clip_on" port_type="basic:Boolean">
+ <docstring>Set whether artist uses clipping.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="agg_filter" name="agg_filter">
+ <docstring>set agg_filter fuction.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="visible" name="visible" port_type="basic:Boolean">
+ <docstring>Set the artist's visiblity.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="url" name="url" port_type="basic:String">
+ <docstring>Sets the url for the artist</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="transform" name="transform">
+ <docstring>Set the :class:`~matplotlib.transforms.Transform` instance used by this artist.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axes" name="axes">
+ <docstring>Set the :class:`~matplotlib.axes.Axes` instance in which the artist resides, if any.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="clip_box" name="clip_box">
+ <docstring>Set the artist's clip :class:`~matplotlib.transforms.Bbox`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="clip_path" name="clip_path" port_type="basic:String">
+ <docstring>Set the artist's clip path, which may be:
+
+a :class:`~matplotlib.patches.Patch` (or subclass) instance
+
+
+
+None, to remove the clipping path
+
+For efficiency, if the path happens to be an axis-aligned rectangle, this method will set the clipping box to the corresponding rectangle and set the clipping path to None.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['(:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`)', ':class:`~matplotlib.patches.Patch`']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="lod" name="lod" port_type="basic:Boolean">
+ <docstring>Set Level of Detail on or off. If on, the artists may examine things like the pixel width of the axes and draw a subset of their contents accordingly</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="label" name="label" port_type="basic:String">
+ <docstring>Set the label to s for auto legend.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rasterized" name="rasterized" port_type="basic:Boolean">
+ <docstring>Force rasterized (bitmap) drawing in vector backend output.
+
+Defaults to None, which implies the backend's default behavior</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="gid" name="gid" port_type="basic:String">
+ <docstring>Sets the (group) id for the artist</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="zorder" name="zorder">
+ <docstring>Set the zorder for the artist. Artists with lower zorder values are drawn first.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="snap" name="snap">
+ <docstring>Sets the snap setting which may be:
+
+True: snap vertices to the nearest pixel center
+
+False: leave vertices as-is
+
+None: (auto) If the path contains only rectilinear line segments, round to the nearest pixel center
+
+Only supported by the Agg and MacOSX backends.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>Set the alpha value used for blending - not supported on all backends.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="animated" name="animated" port_type="basic:Boolean">
+ <docstring>Set the artist's animation state.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="figure" name="figure">
+ <docstring>Set the :class:`~matplotlib.figure.Figure` instance the artist belongs to.</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image._AxesImageBase" name="Mpl_AxesImageBaseProperties" superclass="MplArtistProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="origin" arg_pos="4" constructor_arg="True" name="origin" />
+ <inputPortSpec arg="resample" name="resample" port_type="basic:Boolean">
+ <docstring>Set whether or not image resampling is used</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="2" constructor_arg="True" name="norm" />
+ <inputPortSpec arg="cmap" arg_pos="1" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="filternorm" name="filternorm">
+ <docstring>Set whether the resize filter norms the weights -- see help for imshow</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ax" arg_pos="0" constructor_arg="True" name="ax" />
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>Set the alpha value used for blending - not supported on all backends</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="array" name="array">
+ <docstring>Retained for backwards compatibility - use set_data instead</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="data" name="data">
+ <docstring>Set the image array</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="filterrad" name="filterrad" port_type="basic:Float">
+ <docstring>Set the resize filter radius only applicable to some interpolation schemes -- see help for imshow</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="interpolation" name="interpolation" port_type="basic:String">
+ <docstring>Set the interpolation method the image uses when resizing.
+
+if None, use a value from rc setting. If 'none', the image is shown as is without interpolating. 'none' is only supported in agg, ps and pdf backends and will fall back to 'nearest' mode for other backends.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['nearest', 'bilinear', 'bicubic', 'spline16', 'spline36', 'hanning', 'hamming', 'hermite', 'kaiser', 'quadric', 'catrom', 'gaussian', 'bessel', 'mitchell', 'sinc', 'lanczos', 'none', '']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image.AxesImage" name="MplAxesImageProperties" superclass="Mpl_AxesImageBaseProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="origin" arg_pos="4" constructor_arg="True" name="origin" />
+ <inputPortSpec arg="resample" arg_pos="8" constructor_arg="True" name="resample" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="2" constructor_arg="True" name="norm" />
+ <inputPortSpec arg="cmap" arg_pos="1" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="filterrad" arg_pos="7" constructor_arg="True" name="filterrad" port_type="basic:Float">
+ <defaults>['4.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="extent" name="extent">
+ <docstring>extent is data axes (left, right, bottom, top) for making image plots
+
+This updates ax.dataLim, and, if autoscaling, sets viewLim to tightly fit the image, regardless of dataLim. Autoscaling state is not changed, so following this with ax.autoscale_view will redo the autoscaling in accord with dataLim.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ax" arg_pos="0" constructor_arg="True" name="ax" />
+ <inputPortSpec arg="filternorm" arg_pos="6" constructor_arg="True" name="filternorm" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="interpolation" arg_pos="3" constructor_arg="True" name="interpolation" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image.NonUniformImage" name="MplNonUniformImageProperties" superclass="MplAxesImageProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="norm" name="norm" />
+ <inputPortSpec arg="cmap" name="cmap" />
+ <inputPortSpec arg="filternorm" name="filternorm" />
+ <inputPortSpec arg="ax" arg_pos="0" constructor_arg="True" name="ax" />
+ <inputPortSpec arg="array" name="array" />
+ <inputPortSpec arg="data" name="data">
+ <docstring>Set the grid for the pixel centers, and the pixel values.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="filterrad" name="filterrad" />
+ <inputPortSpec arg="interpolation" name="interpolation" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image.BboxImage" name="MplBboxImageProperties" superclass="Mpl_AxesImageBaseProperties">
+ <docstring>The Image class whose size is determined by the given bbox.</docstring>
+ <inputPortSpec arg="origin" arg_pos="4" constructor_arg="True" name="origin" />
+ <inputPortSpec arg="interp_at_native" arg_pos="8" constructor_arg="True" name="interp_at_native" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="resample" arg_pos="7" constructor_arg="True" name="resample" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="1" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="filternorm" arg_pos="5" constructor_arg="True" name="filternorm" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="2" constructor_arg="True" name="norm" />
+ <inputPortSpec arg="interpolation" arg_pos="3" constructor_arg="True" name="interpolation" />
+ <inputPortSpec arg="filterrad" arg_pos="6" constructor_arg="True" name="filterrad" port_type="basic:Float">
+ <defaults>['4.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox" arg_pos="0" constructor_arg="True" name="bbox" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image.PcolorImage" name="MplPcolorImageProperties" superclass="MplArtistProperties">
+ <docstring>
+ Make a pcolor-style plot with an irregular rectangular grid.
+
+ This uses a variation of the original irregular image code,
+ and it is used by pcolorfast for the corresponding grid type.
+ </docstring>
+ <inputPortSpec arg="A" arg_pos="3" constructor_arg="True" name="A" />
+ <inputPortSpec arg="ax" arg_pos="0" constructor_arg="True" name="ax" />
+ <inputPortSpec arg="cmap" arg_pos="4" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="x" arg_pos="1" constructor_arg="True" name="x" />
+ <inputPortSpec arg="y" arg_pos="2" constructor_arg="True" name="y" />
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>Set the alpha value used for blending - not supported on all backends</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="array" name="array" />
+ <inputPortSpec arg="data" name="data" />
+ <inputPortSpec arg="norm" arg_pos="5" constructor_arg="True" name="norm" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.image.FigureImage" name="MplFigureImageProperties" superclass="MplArtistProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="origin" arg_pos="5" constructor_arg="True" name="origin" />
+ <inputPortSpec arg="offsetx" arg_pos="3" constructor_arg="True" name="offsetx" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="offsety" arg_pos="4" constructor_arg="True" name="offsety" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="1" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="fig" arg_pos="0" constructor_arg="True" name="fig" />
+ <inputPortSpec arg="array" name="array">
+ <docstring>Deprecated; use set_data for consistency with other image types.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="data" name="data">
+ <docstring>Set the image array.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="2" constructor_arg="True" name="norm" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.Collection" name="MplCollectionProperties" superclass="MplArtistProperties">
+ <docstring>
+ Base class for Collections. Must be subclassed to be usable.
+
+ All properties in a collection must be sequences or scalars;
+ if scalars, they will be converted to sequences. The
+ property of the ith element of the collection is::
+
+ prop[i % len(props)]
+
+ Keyword arguments and default values:
+
+ * *edgecolors*: None
+ * *facecolors*: None
+ * *linewidths*: None
+ * *antialiaseds*: None
+ * *offsets*: None
+ * *transOffset*: transforms.IdentityTransform()
+ * *offset_position*: 'screen' (default) or 'data'
+ * *norm*: None (optional for
+ :class:`matplotlib.cm.ScalarMappable`)
+ * *cmap*: None (optional for
+ :class:`matplotlib.cm.ScalarMappable`)
+ * *hatch*: None
+
+ *offsets* and *transOffset* are used to translate the patch after
+ rendering (default no offsets). If offset_position is 'screen'
+ (default) the offset is applied after the master transform has
+ been applied, that is, the offsets are in screen coordinates. If
+ offset_position is 'data', the offset is applied before the master
+ transform, i.e., the offsets are in data coordinates.
+
+ If any of *edgecolors*, *facecolors*, *linewidths*, *antialiaseds*
+ are None, they default to their :data:`matplotlib.rcParams` patch
+ setting, in sequence form.
+
+ The use of :class:`~matplotlib.cm.ScalarMappable` is optional. If
+ the :class:`~matplotlib.cm.ScalarMappable` matrix _A is not None
+ (ie a call to set_array has been made), at draw time a call to
+ scalar mappable will be made to set the face colors.
+ </docstring>
+ <inputPortSpec arg="transOffset" arg_pos="6" constructor_arg="True" name="transOffset" />
+ <inputPortSpec arg="edgecolor" name="edgecolor" port_type="basic:List">
+ <docstring>Set the edgecolor(s) of the collection. c can be a matplotlib color arg (all patches have same color), or a sequence of rgba tuples; if it is a sequence the patches will cycle through the sequence.
+
+If c is 'face', the edge color will always be the same as the face color. If it is 'none', the patch boundary will not be drawn.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="offset_position" name="offset_position">
+ <docstring>Set how offsets are applied. If offset_position is 'screen' (default) the offset is applied after the master transform has been applied, that is, the offsets are in screen coordinates. If offset_position is 'data', the offset is applied before the master transform, i.e., the offsets are in data coordinates.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="edgecolors" arg_pos="0" constructor_arg="True" name="edgecolors" />
+ <inputPortSpec arg="facecolor" name="facecolor" port_type="basic:List">
+ <docstring>Set the facecolor(s) of the collection. c can be a matplotlib color arg (all patches have same color), or a sequence of rgba tuples; if it is a sequence the patches will cycle through the sequence.
+
+If c is 'none', the patch will not be filled.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyles" arg_pos="3" constructor_arg="True" name="linestyles" port_type="basic:String">
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="offsets" name="offsetsSequence" port_type="basic:List">
+ <docstring>Set the offsets for the collection. offsets can be a scalar or a sequence.</docstring>
+ <alternateSpec arg="" name="offsetsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:List">
+ <docstring>Set both the edgecolor and the facecolor. .. seealso:
+
+:meth:`set_facecolor`, :meth:`set_edgecolor` For setting the edge or face color individually.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="pickradius" name="pickradius" />
+ <inputPortSpec arg="antialiaseds" arg_pos="4" constructor_arg="True" name="antialiaseds" />
+ <inputPortSpec arg="linewidths" arg_pos="2" constructor_arg="True" name="linewidths" />
+ <inputPortSpec arg="cmap" arg_pos="8" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="antialiased" name="antialiasedSequence" port_type="basic:List">
+ <docstring>Set the antialiasing state for rendering.</docstring>
+ <alternateSpec arg="" name="antialiasedScalar" port_type="basic:Boolean" />
+ </inputPortSpec>
+ <inputPortSpec arg="urls" name="urls" />
+ <inputPortSpec arg="hatch" name="hatch" port_type="basic:String">
+ <docstring>Set the hatching pattern
+
+hatch can be one of:
+
+/ - diagonal hatching \ - back diagonal | - vertical - - horizontal + - crossed x - crossed diagonal o - small circle O - large circle . - dots * - stars
+
+Letters can be combined, in which case all the specified hatchings are done. If same letter repeats, it increases the density of hatching of that pattern.
+
+Hatching is supported in the PostScript, PDF, SVG and Agg backends only.
+
+Unlike other properties such as linewidth and colors, hatching can only be specified for the collection as a whole, not separately for each member.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['/', "'\\'", "'", "'", '-', '+', 'x', 'o', 'O', '.', '*']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>Set the alpha tranparencies of the collection. alpha must be a float or None.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="paths" name="paths" />
+ <inputPortSpec arg="linewidth" name="linewidthSequence" port_type="basic:List">
+ <docstring>Set the linewidth(s) for the collection. lw can be a scalar or a sequence; if it is a sequence the patches will cycle through the sequence</docstring>
+ <alternateSpec arg="" name="linewidthScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="linestyle" name="linestyle" port_type="basic:String">
+ <docstring>Set the linestyle(s) for the collection.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['solid', ('dashed', 'dashdot', 'dotted'), '(offset, on-off-dash-seq)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="facecolors" arg_pos="1" constructor_arg="True" name="facecolors" />
+ <inputPortSpec arg="norm" arg_pos="7" constructor_arg="True" name="norm" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.PathCollection" name="MplPathCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>
+ This is the most basic :class:`Collection` subclass.
+ </docstring>
+ <inputPortSpec arg="paths" name="paths" />
+ <inputPortSpec arg="sizes" arg_pos="1" constructor_arg="True" name="sizes" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.PolyCollection" name="MplPolyCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="paths" name="paths">
+ <docstring>This allows one to delay initialization of the vertices.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="verts" name="verts">
+ <docstring>This allows one to delay initialization of the vertices.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="closed" arg_pos="2" constructor_arg="True" name="closed" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="sizes" arg_pos="1" constructor_arg="True" name="sizes" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.BrokenBarHCollection" name="MplBrokenBarHCollectionProperties" superclass="MplPolyCollectionProperties">
+ <docstring>
+ A collection of horizontal bars spanning *yrange* with a sequence of
+ *xranges*.
+ </docstring>
+ <inputPortSpec arg="xranges" arg_pos="0" constructor_arg="True" name="xranges" />
+ <inputPortSpec arg="yrange" arg_pos="1" constructor_arg="True" name="yrange" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.RegularPolyCollection" name="MplRegularPolyCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>Draw a collection of regular polygons with *numsides*.</docstring>
+ <inputPortSpec arg="numsides" arg_pos="0" constructor_arg="True" name="numsides" />
+ <inputPortSpec arg="rotation" arg_pos="1" constructor_arg="True" name="rotation" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="sizes" arg_pos="2" constructor_arg="True" name="sizes">
+ <defaults>['(1,)']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.StarPolygonCollection" name="MplStarPolygonCollectionProperties" superclass="MplRegularPolyCollectionProperties">
+ <docstring>
+ Draw a collection of regular stars with *numsides* points.</docstring>
+ <inputPortSpec arg="numsides" arg_pos="0" constructor_arg="True" name="numsides" />
+ <inputPortSpec arg="rotation" arg_pos="1" constructor_arg="True" name="rotation" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="sizes" arg_pos="2" constructor_arg="True" name="sizes">
+ <defaults>['(1,)']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.AsteriskPolygonCollection" name="MplAsteriskPolygonCollectionProperties" superclass="MplRegularPolyCollectionProperties">
+ <docstring>
+ Draw a collection of regular asterisks with *numsides* points.</docstring>
+ <inputPortSpec arg="numsides" arg_pos="0" constructor_arg="True" name="numsides" />
+ <inputPortSpec arg="rotation" arg_pos="1" constructor_arg="True" name="rotation" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="sizes" arg_pos="2" constructor_arg="True" name="sizes">
+ <defaults>['(1,)']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.LineCollection" name="MplLineCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>
+ All parameters must be sequences or scalars; if scalars, they will
+ be converted to sequences. The property of the ith line
+ segment is::
+
+ prop[i % len(props)]
+
+ i.e., the properties cycle if the ``len`` of props is less than the
+ number of segments.
+ </docstring>
+ <inputPortSpec arg="paths" name="paths" />
+ <inputPortSpec arg="antialiaseds" arg_pos="3" constructor_arg="True" name="antialiaseds" />
+ <inputPortSpec arg="linestyles" arg_pos="4" constructor_arg="True" name="linestyles" port_type="basic:String">
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="offsets" arg_pos="5" constructor_arg="True" name="offsets" />
+ <inputPortSpec arg="color" name="color" port_type="basic:List">
+ <docstring>Set the color(s) of the line collection. c can be a matplotlib color arg (all patches have same color), or a sequence or rgba tuples; if it is a sequence the patches will cycle through the sequence.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="segments" name="segments" />
+ <inputPortSpec arg="linewidths" arg_pos="1" constructor_arg="True" name="linewidths" />
+ <inputPortSpec arg="colors" arg_pos="2" constructor_arg="True" name="colors" />
+ <inputPortSpec arg="cmap" arg_pos="8" constructor_arg="True" name="cmap" />
+ <inputPortSpec arg="transOffset" arg_pos="6" constructor_arg="True" name="transOffset" />
+ <inputPortSpec arg="verts" name="verts" />
+ <inputPortSpec arg="pickradius" arg_pos="9" constructor_arg="True" name="pickradius" port_type="basic:Integer">
+ <defaults>['5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="7" constructor_arg="True" name="norm" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.CircleCollection" name="MplCircleCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>
+ A collection of circles, drawn using splines.
+ </docstring>
+ <inputPortSpec arg="sizes" arg_pos="0" constructor_arg="True" name="sizes" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.EllipseCollection" name="MplEllipseCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>
+ A collection of ellipses, drawn using splines.
+ </docstring>
+ <inputPortSpec arg="units" arg_pos="3" constructor_arg="True" name="units" port_type="basic:String">
+ <defaults>['points']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="widths" arg_pos="0" constructor_arg="True" name="widths" />
+ <inputPortSpec arg="angles" arg_pos="2" constructor_arg="True" name="angles" />
+ <inputPortSpec arg="heights" arg_pos="1" constructor_arg="True" name="heights" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.PatchCollection" name="MplPatchCollectionProperties" superclass="MplCollectionProperties">
+ <docstring>
+ A generic collection of patches.
+
+ This makes it easier to assign a color map to a heterogeneous
+ collection of patches.
+
+ This also may improve plotting speed, since PatchCollection will
+ draw faster than a large number of patches.
+ </docstring>
+ <inputPortSpec arg="paths" name="paths" />
+ <inputPortSpec arg="patches" arg_pos="0" constructor_arg="True" name="patches" />
+ <inputPortSpec arg="match_original" arg_pos="1" constructor_arg="True" name="match_original" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.TriMesh" name="MplTriMeshProperties" superclass="MplCollectionProperties">
+ <docstring>
+ Class for the efficient drawing of a triangular mesh using
+ Gouraud shading.
+
+ A triangular mesh is a :class:`~matplotlib.tri.Triangulation`
+ object.
+ </docstring>
+ <inputPortSpec arg="triangulation" arg_pos="0" constructor_arg="True" name="triangulation" />
+ <inputPortSpec arg="paths" name="paths" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.collections.QuadMesh" name="MplQuadMeshProperties" superclass="MplCollectionProperties">
+ <docstring>
+ Class for the efficient drawing of a quadrilateral mesh.
+
+ A quadrilateral mesh consists of a grid of vertices. The
+ dimensions of this array are (*meshWidth* + 1, *meshHeight* +
+ 1). Each vertex in the mesh has a different set of "mesh
+ coordinates" representing its position in the topology of the
+ mesh. For any values (*m*, *n*) such that 0 <= *m* <= *meshWidth*
+ and 0 <= *n* <= *meshHeight*, the vertices at mesh coordinates
+ (*m*, *n*), (*m*, *n* + 1), (*m* + 1, *n* + 1), and (*m* + 1, *n*)
+ form one of the quadrilaterals in the mesh. There are thus
+ (*meshWidth* * *meshHeight*) quadrilaterals in the mesh. The mesh
+ need not be regular and the polygons need not be convex.
+
+ A quadrilateral mesh is represented by a (2 x ((*meshWidth* + 1) *
+ (*meshHeight* + 1))) numpy array *coordinates*, where each row is
+ the *x* and *y* coordinates of one of the vertices. To define the
+ function that maps from a data point to its corresponding color,
+ use the :meth:`set_cmap` method. Each of these arrays is indexed in
+ row-major order by the mesh coordinates of the vertex (or the mesh
+ coordinates of the lower left vertex, in the case of the
+ colors).
+
+ For example, the first entry in *coordinates* is the
+ coordinates of the vertex at mesh coordinates (0, 0), then the one
+ at (0, 1), then at (0, 2) .. (0, meshWidth), (1, 0), (1, 1), and
+ so on.
+
+ *shading* may be 'flat', or 'gouraud'
+ </docstring>
+ <inputPortSpec arg="paths" name="paths" />
+ <inputPortSpec arg="meshWidth" arg_pos="0" constructor_arg="True" name="meshWidth" />
+ <inputPortSpec arg="coordinates" arg_pos="2" constructor_arg="True" name="coordinates" />
+ <inputPortSpec arg="antialiased" arg_pos="3" constructor_arg="True" name="antialiased" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="shading" arg_pos="4" constructor_arg="True" name="shading" port_type="basic:String">
+ <defaults>['flat']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="meshHeight" arg_pos="1" constructor_arg="True" name="meshHeight" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Patch" name="MplPatchProperties" superclass="MplArtistProperties">
+ <docstring>
+ A patch is a 2D artist with a face color and an edge color.
+
+ If any of *edgecolor*, *facecolor*, *linewidth*, or *antialiased*
+ are *None*, they default to their rc params setting.
+ </docstring>
+ <inputPortSpec arg="edgecolor" name="edgecolor" port_type="basic:Color">
+ <docstring>Set the patch edge color</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="facecolor" name="facecolor" port_type="basic:Color">
+ <docstring>Set the patch face color</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="path_effects" name="path_effects">
+ <docstring>set path_effects, which should be a list of instances of matplotlib.patheffect._Base class or its derivatives.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>Set both the edgecolor and the facecolor. .. seealso:
+
+:meth:`set_facecolor`, :meth:`set_edgecolor` For setting the edge or face color individually.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="antialiased" name="antialiased" port_type="basic:Boolean">
+ <docstring>Set whether to use antialiased rendering</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="hatch" name="hatch" port_type="basic:String">
+ <docstring>Set the hatching pattern
+
+hatch can be one of:
+
+/ - diagonal hatching \ - back diagonal | - vertical - - horizontal + - crossed x - crossed diagonal o - small circle O - large circle . - dots * - stars
+
+Letters can be combined, in which case all the specified hatchings are done. If same letter repeats, it increases the density of hatching of that pattern.
+
+Hatching is supported in the PostScript, PDF, SVG and Agg backends only.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['/', "'\\'", "'", "'", '-', '+', 'x', 'o', 'O', '.', '*']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>Set the alpha tranparency of the patch.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidth" name="linewidth" port_type="basic:Float">
+ <docstring>Set the patch linewidth in points</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyle" name="linestyle" port_type="basic:String">
+ <docstring>Set the patch linestyle</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['solid', 'dashed', 'dashdot', 'dotted']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="fill" name="fill" port_type="basic:Boolean">
+ <docstring>Set whether to fill the patch</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Shadow" name="MplShadowProperties" superclass="MplPatchProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="patch" arg_pos="0" constructor_arg="True" name="patch" />
+ <inputPortSpec arg="props" arg_pos="3" constructor_arg="True" name="props" />
+ <inputPortSpec arg="oy" arg_pos="2" constructor_arg="True" name="oy" />
+ <inputPortSpec arg="ox" arg_pos="1" constructor_arg="True" name="ox" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Rectangle" name="MplRectangleProperties" superclass="MplPatchProperties">
+ <docstring>
+ Draw a rectangle with lower left at *xy* = (*x*, *y*) with
+ specified *width* and *height*.
+ </docstring>
+ <inputPortSpec arg="bounds" name="bounds">
+ <docstring>Set the bounds of the rectangle: l,b,w,h</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="height" name="height" port_type="basic:Float">
+ <docstring>Set the width rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="width" name="width" port_type="basic:Float">
+ <docstring>Set the width rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xy" name="xy" port_type="basic:List">
+ <docstring>Set the left and bottom coords of the rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" name="y" port_type="basic:Float">
+ <docstring>Set the bottom coord of the rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="x" name="x" port_type="basic:Float">
+ <docstring>Set the left coord of the rectangle</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.RegularPolygon" name="MplRegularPolygonProperties" superclass="MplPatchProperties">
+ <docstring>
+ A regular polygon patch.
+ </docstring>
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy">
+ <docstring>A length 2 tuple (x, y) of the center.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="radius" arg_pos="2" constructor_arg="True" name="radius" port_type="basic:Integer">
+ <docstring>The distance from the center to each of the vertices.</docstring>
+ <defaults>['5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="orientation" arg_pos="3" constructor_arg="True" name="orientation" port_type="basic:Integer">
+ <docstring>rotates the polygon (in radians).</docstring>
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="numVertices" arg_pos="1" constructor_arg="True" name="numVertices">
+ <docstring>the number of vertices.</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.CirclePolygon" name="MplCirclePolygonProperties" superclass="MplRegularPolygonProperties">
+ <docstring>
+ A polygon-approximation of a circle patch.
+ </docstring>
+ <inputPortSpec arg="radius" arg_pos="1" constructor_arg="True" name="radius" port_type="basic:Integer">
+ <defaults>['5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy" />
+ <inputPortSpec arg="resolution" arg_pos="2" constructor_arg="True" name="resolution" port_type="basic:Integer">
+ <defaults>['20']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.PathPatch" name="MplPathPatchProperties" superclass="MplPatchProperties">
+ <docstring>
+ A general polycurve path patch.
+ </docstring>
+ <inputPortSpec arg="path" arg_pos="0" constructor_arg="True" name="path" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Polygon" name="MplPolygonProperties" superclass="MplPatchProperties">
+ <docstring>
+ A general polygon patch.
+ </docstring>
+ <inputPortSpec arg="xy" name="xy" />
+ <inputPortSpec arg="closed" name="closed" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.FancyArrow" name="MplFancyArrowProperties" superclass="MplPolygonProperties">
+ <docstring>
+ Like Arrow, but lets you set head width and head height independently.
+ </docstring>
+ <inputPortSpec arg="length_includes_head" arg_pos="5" constructor_arg="True" name="length_includes_head" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="head_length" arg_pos="7" constructor_arg="True" name="head_length" />
+ <inputPortSpec arg="head_width" arg_pos="6" constructor_arg="True" name="head_width" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" port_type="basic:Float">
+ <defaults>['0.001']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="shape" arg_pos="8" constructor_arg="True" name="shape" port_type="basic:String">
+ <defaults>['full']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="dx" arg_pos="2" constructor_arg="True" name="dx" />
+ <inputPortSpec arg="dy" arg_pos="3" constructor_arg="True" name="dy" />
+ <inputPortSpec arg="y" arg_pos="1" constructor_arg="True" name="y" />
+ <inputPortSpec arg="x" arg_pos="0" constructor_arg="True" name="x" />
+ <inputPortSpec arg="head_starts_at_zero" arg_pos="10" constructor_arg="True" name="head_starts_at_zero" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="overhang" arg_pos="9" constructor_arg="True" name="overhang" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Wedge" name="MplWedgeProperties" superclass="MplPatchProperties">
+ <docstring>
+ Wedge shaped patch.
+ </docstring>
+ <inputPortSpec arg="theta2" arg_pos="3" constructor_arg="True" name="theta2" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" />
+ <inputPortSpec arg="r" arg_pos="1" constructor_arg="True" name="r" />
+ <inputPortSpec arg="theta1" arg_pos="2" constructor_arg="True" name="theta1" />
+ <inputPortSpec arg="center" arg_pos="0" constructor_arg="True" name="center" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Arrow" name="MplArrowProperties" superclass="MplPatchProperties">
+ <docstring>
+ An arrow patch.
+ </docstring>
+ <inputPortSpec arg="y" arg_pos="1" constructor_arg="True" name="y" />
+ <inputPortSpec arg="x" arg_pos="0" constructor_arg="True" name="x" />
+ <inputPortSpec arg="dy" arg_pos="3" constructor_arg="True" name="dy" />
+ <inputPortSpec arg="dx" arg_pos="2" constructor_arg="True" name="dx" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" port_type="basic:Float">
+ <defaults>['1.0']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.YAArrow" name="MplYAArrowProperties" superclass="MplPatchProperties">
+ <docstring>
+ Yet another arrow class.
+
+ This is an arrow that is defined in display space and has a tip at
+ *x1*, *y1* and a base at *x2*, *y2*.
+ </docstring>
+ <inputPortSpec arg="xytip" arg_pos="1" constructor_arg="True" name="xytip">
+ <docstring>(x, y) location of arrow tip</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="headwidth" arg_pos="5" constructor_arg="True" name="headwidth" port_type="basic:Integer">
+ <docstring>The width of the base of the arrow head in points</docstring>
+ <defaults>['12']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="frac" arg_pos="4" constructor_arg="True" name="frac" port_type="basic:Float">
+ <docstring>The fraction of the arrow length occupied by the head</docstring>
+ <defaults>['0.1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="figure" arg_pos="0" constructor_arg="True" name="figure">
+ <docstring>The :class:`~matplotlib.figure.Figure` instance (fig.dpi)</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xybase" arg_pos="2" constructor_arg="True" name="xybase">
+ <docstring>(x, y) location the arrow base mid point</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="width" arg_pos="3" constructor_arg="True" name="width" port_type="basic:Integer">
+ <docstring>The width of the arrow in points</docstring>
+ <defaults>['4']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Ellipse" name="MplEllipseProperties" superclass="MplPatchProperties">
+ <docstring>
+ A scale-free ellipse.
+ </docstring>
+ <inputPortSpec arg="width" arg_pos="1" constructor_arg="True" name="width" />
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy" />
+ <inputPortSpec arg="angle" arg_pos="3" constructor_arg="True" name="angle" port_type="basic:Float">
+ <defaults>['0.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="height" arg_pos="2" constructor_arg="True" name="height" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Circle" name="MplCircleProperties" superclass="MplEllipseProperties">
+ <docstring>
+ A circle patch.
+ </docstring>
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy" />
+ <inputPortSpec arg="radius" name="radius" port_type="basic:Float">
+ <docstring>Set the radius of the circle</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.Arc" name="MplArcProperties" superclass="MplEllipseProperties">
+ <docstring>
+ An elliptical arc. Because it performs various optimizations, it
+ can not be filled.
+
+ The arc must be used in an :class:`~matplotlib.axes.Axes`
+ instance---it can not be added directly to a
+ :class:`~matplotlib.figure.Figure`---because it is optimized to
+ only render the segments that are inside the axes bounding box
+ with high resolution.
+ </docstring>
+ <inputPortSpec arg="theta2" arg_pos="5" constructor_arg="True" name="theta2" port_type="basic:Float">
+ <defaults>['360.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="theta1" arg_pos="4" constructor_arg="True" name="theta1" port_type="basic:Float">
+ <defaults>['0.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="angle" arg_pos="3" constructor_arg="True" name="angle" port_type="basic:Float">
+ <defaults>['0.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="height" arg_pos="2" constructor_arg="True" name="height" />
+ <inputPortSpec arg="width" arg_pos="1" constructor_arg="True" name="width" />
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.FancyBboxPatch" name="MplFancyBboxPatchProperties" superclass="MplPatchProperties">
+ <docstring>
+ Draw a fancy box around a rectangle with lower left at *xy*=(*x*,
+ *y*) with specified width and height.
+
+ :class:`FancyBboxPatch` class is similar to :class:`Rectangle`
+ class, but it draws a fancy box around the rectangle. The
+ transformation of the rectangle box to the fancy box is delegated
+ to the :class:`BoxTransmuterBase` and its derived classes.
+
+ </docstring>
+ <inputPortSpec arg="mutation_scale" name="mutation_scale" port_type="basic:Float">
+ <docstring>Set the mutation scale.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox_transmuter" arg_pos="4" constructor_arg="True" name="bbox_transmuter" />
+ <inputPortSpec arg="bounds" name="bounds">
+ <docstring>Set the bounds of the rectangle: l,b,w,h</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="height" name="height" port_type="basic:Float">
+ <docstring>Set the width rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="width" name="width" port_type="basic:Float">
+ <docstring>Set the width rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xy" arg_pos="0" constructor_arg="True" name="xy" />
+ <inputPortSpec arg="boxstyle" name="boxstyle">
+ <docstring>Set the box style.
+
+boxstyle can be a string with boxstyle name with optional comma-separated attributes. Alternatively, the attrs can be provided as keywords:
+
+set_boxstyle("round,pad=0.2") set_boxstyle("round", pad=0.2)
+
+Old attrs simply are forgotten.
+
+Without argument (or with boxstyle = None), it returns available box styles.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="mutation_aspect" name="mutation_aspect" port_type="basic:Float">
+ <docstring>Set the aspect ratio of the bbox mutation.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" name="y" port_type="basic:Float">
+ <docstring>Set the bottom coord of the rectangle</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="x" name="x" port_type="basic:Float">
+ <docstring>Set the left coord of the rectangle</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.FancyArrowPatch" name="MplFancyArrowPatchProperties" superclass="MplPatchProperties">
+ <docstring>
+ A fancy arrow patch. It draws an arrow using the :class:ArrowStyle.
+ </docstring>
+ <inputPortSpec arg="connectionstyle" name="connectionstyle">
+ <docstring>Set the connection style.
+
+Old attrs simply are forgotten.
+
+Without argument (or with connectionstyle=None), return available styles as a list of strings.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="mutation_scale" name="mutation_scale" port_type="basic:Float">
+ <docstring>Set the mutation scale.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="arrowstyle" name="arrowstyle">
+ <docstring>Set the arrow style.
+
+Old attrs simply are forgotten.
+
+Without argument (or with arrowstyle=None), return available box styles as a list of strings.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="arrow_transmuter" arg_pos="4" constructor_arg="True" name="arrow_transmuter" />
+ <inputPortSpec arg="positions" name="positions" />
+ <inputPortSpec arg="shrinkA" arg_pos="9" constructor_arg="True" name="shrinkA" port_type="basic:Float">
+ <defaults>['2.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="posB" arg_pos="1" constructor_arg="True" name="posB" />
+ <inputPortSpec arg="dpi_cor" name="dpi_cor">
+ <docstring>dpi_cor is currently used for linewidth-related things and shink factor. Mutation scale is not affected by this.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="connector" arg_pos="6" constructor_arg="True" name="connector" />
+ <inputPortSpec arg="path" arg_pos="2" constructor_arg="True" name="path" />
+ <inputPortSpec arg="shrinkB" arg_pos="10" constructor_arg="True" name="shrinkB" port_type="basic:Float">
+ <defaults>['2.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="mutation_aspect" name="mutation_aspect" port_type="basic:Float">
+ <docstring>Set the aspect ratio of the bbox mutation.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="patchA" name="patchA">
+ <docstring>set the begin patch.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="patchB" name="patchB">
+ <docstring>set the begin patch</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="posA" arg_pos="0" constructor_arg="True" name="posA" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.patches.ConnectionPatch" name="MplConnectionPatchProperties" superclass="MplFancyArrowPatchProperties">
+ <docstring>
+ A :class:`~matplotlib.patches.ConnectionPatch` class is to make
+ connecting lines between two points (possibly in different axes).
+ </docstring>
+ <inputPortSpec arg="connectionstyle" arg_pos="8" constructor_arg="True" name="connectionstyle" port_type="basic:String">
+ <docstring>the connection style</docstring>
+ <defaults>['arc3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="coordsA" arg_pos="2" constructor_arg="True" name="coordsA">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="arrowstyle" arg_pos="6" constructor_arg="True" name="arrowstyle" port_type="basic:String">
+ <docstring>the arrow style</docstring>
+ <defaults>['-']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="clip_on" arg_pos="16" constructor_arg="True" name="clip_on" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="arrow_transmuter" arg_pos="7" constructor_arg="True" name="arrow_transmuter" />
+ <inputPortSpec arg="axesA" arg_pos="4" constructor_arg="True" name="axesA" />
+ <inputPortSpec arg="axesB" arg_pos="5" constructor_arg="True" name="axesB" />
+ <inputPortSpec arg="annotation_clip" name="annotation_clip">
+ <docstring>set annotation_clip attribute.
+
+None: the self.xy will be checked only if xycoords is "data"</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dpi_cor" arg_pos="17" constructor_arg="True" name="dpi_cor" port_type="basic:Float">
+ <defaults>['1.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="connector" arg_pos="9" constructor_arg="True" name="connector" />
+ <inputPortSpec arg="xyA" arg_pos="0" constructor_arg="True" name="xyA" />
+ <inputPortSpec arg="xyB" arg_pos="1" constructor_arg="True" name="xyB" />
+ <inputPortSpec arg="relpos" constructor_arg="True" name="relpos" port_type="basic:String">
+ <docstring>default is (0.5, 0.5)</docstring>
+ <defaults>['(0.5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="shrinkB" arg_pos="13" constructor_arg="True" name="shrinkB" port_type="basic:Float">
+ <docstring>default is 2 points</docstring>
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="shrinkA" arg_pos="12" constructor_arg="True" name="shrinkA" port_type="basic:Float">
+ <docstring>default is 2 points</docstring>
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="mutation_aspect" arg_pos="15" constructor_arg="True" name="mutation_aspect" port_type="basic:Integer">
+ <docstring>default is 1.</docstring>
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="mutation_scale" arg_pos="14" constructor_arg="True" name="mutation_scale">
+ <docstring>default is text size (in points)</docstring>
+ <defaults>['text']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="patchA" arg_pos="10" constructor_arg="True" name="patchA" port_type="basic:String">
+ <docstring>default is bounding box of the text</docstring>
+ <defaults>['bounding']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="patchB" arg_pos="11" constructor_arg="True" name="patchB">
+ <docstring>default is None</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="coordsB" arg_pos="3" constructor_arg="True" name="coordsB">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="?" constructor_arg="True" name="?">
+ <docstring>any key for :class:`matplotlib.patches.PathPatch`</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.lines.Line2D" name="MplLine2DProperties" superclass="MplArtistProperties">
+ <docstring>
+ A line - the line can have both a solid linestyle connecting all
+ the vertices, and a marker at each vertex. Additionally, the
+ drawing of the solid line is influenced by the drawstyle, eg one
+ can create "stepped" lines in various styles.
+
+
+ </docstring>
+ <inputPortSpec arg="picker" name="picker" port_type="basic:Float">
+ <docstring>Sets the event picker details for the line.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dash_capstyle" name="dash_capstyle" port_type="basic:String">
+ <docstring>Set the cap style for dashed linestyles</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['butt', 'round', 'projecting']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>Set the color of the line</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="markevery" name="markevery">
+ <docstring>Set the markevery property to subsample the plot when using markers. Eg if markevery=5, every 5-th marker will be plotted. every can be</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['(startind, stride)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="markeredgecolor" name="markeredgecolor" port_type="basic:Color">
+ <docstring>Set the marker edge color</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="marker" name="marker" port_type="basic:String">
+ <docstring>Set the line marker
+
+The marker can also be a tuple (numsides, style, angle), which will create a custom, regular symbol.
+
+
+
+For backward compatibility, the form (verts, 0) is also accepted, but it is equivalent to just verts for giving a raw set of vertices that define the shape.</docstring>
+ <translations>{'caretright': 5, 'point': '.', 'triangle_right': '>', 'tickup': 2, 'square': 's', 'vline': '|', 'caretleft': 4, 'pentagon': 'p', 'tri_left': '3', 'x': 'x', 'tickright': 1, 'tri_right': '4', 'see below': '(numsides, style, angle)', 'tickleft': 0, 'tri_up': '2', 'circle': 'o', 'pixel': ',', 'diamond': 'D', 'star': '*', 'hexagon1': 'h', 'hexagon2': 'H', 'octagon': '8', 'tickdown': 3, 'nothing': ' ', 'render the string using mathtext.': '$...$', 'thin_diamond': 'd', ' [...]
+ <values>[['caretdown', 'caretleft', 'caretright', 'caretup', 'circle', 'diamond', 'hexagon1', 'hexagon2', 'hline', 'nothing', 'nothing', 'nothing', 'nothing', 'octagon', 'pentagon', 'pixel', 'plus', 'point', 'square', 'star', 'thin_diamond', 'tickdown', 'tickleft', 'tickright', 'tickup', 'tri_down', 'tri_left', 'tri_right', 'tri_up', 'triangle_down', 'triangle_left', 'triangle_right', 'triangle_up', 'vline', 'x', 'render the string using mathtext.', 'a list of (x, y) pairs used for [...]
+ </inputPortSpec>
+ <inputPortSpec arg="markerfacecoloralt" name="markerfacecoloralt" port_type="basic:Color">
+ <docstring>Set the alternate marker face color.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidth" name="linewidth" port_type="basic:Float">
+ <docstring>Set the line width in points</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyle" name="linestyle" port_type="basic:String">
+ <docstring>Set the linestyle of the line (also accepts drawstyles)
+
+'steps' is equivalent to 'steps-pre' and is maintained for backward-compatibility.</docstring>
+ <translations>{'solid': '-', 'dashed': '--', 'dash_dot': '-.', 'dotted': ':', 'draw nothing': ''}</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['solid', 'dashed', 'dash_dot', 'dotted', 'draw nothing', 'draw nothing', 'draw nothing']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="solid_joinstyle" name="solid_joinstyle" port_type="basic:String">
+ <docstring>Set the join style for solid linestyles</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['miter', 'round', 'bevel']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="markerfacecolor" name="markerfacecolor" port_type="basic:Color">
+ <docstring>Set the marker face color.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="axes" name="axes">
+ <docstring>Set the :class:`~matplotlib.axes.Axes` instance in which the artist resides, if any.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="transform" name="transform">
+ <docstring>set the Transformation instance used by this artist</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="fillstyle" name="fillstyle" port_type="basic:String">
+ <docstring>Set the marker fill style; 'full' means fill the whole marker. 'none' means no filling; other options are for half-filled markers.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['full', 'left', 'right', 'bottom', 'top', 'none']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="markeredgewidth" name="markeredgewidth" port_type="basic:Float">
+ <docstring>Set the marker edge width in points</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="solid_capstyle" name="solid_capstyle" port_type="basic:String">
+ <docstring>Set the cap style for solid linestyles</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['butt', 'round', 'projecting']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="dashes" name="dashes" port_type="basic:List">
+ <docstring>Set the dash sequence, sequence of dashes with on off ink in points. If seq is empty or if seq = (None, None), the linestyle will be set to solid.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="markersize" name="markersize" port_type="basic:Float">
+ <docstring>Set the marker size in points</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="antialiased" name="antialiased" port_type="basic:Boolean">
+ <docstring>True if line should be drawin with antialiased rendering</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xdata" name="xdata">
+ <docstring>Set the data np.array for x</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="drawstyle" name="drawstyle" port_type="basic:String">
+ <docstring>Set the drawstyle of the plot
+
+'default' connects the points with lines. The steps variants produce step-plots. 'steps' is equivalent to 'steps-pre' and is maintained for backward-compatibility.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['default', 'steps', 'steps-pre', 'steps-mid', 'steps-post']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="data" name="data">
+ <docstring>Set the x and y data</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dash_joinstyle" name="dash_joinstyle" port_type="basic:String">
+ <docstring>Set the join style for dashed linestyles</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['miter', 'round', 'bevel']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="pickradius" name="pickradius" port_type="basic:Float">
+ <docstring>Sets the pick radius used for containment tests</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ydata" name="ydata">
+ <docstring>Set the data np.array for y</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.text.Text" name="MplTextProperties" superclass="MplArtistProperties">
+ <docstring>
+ Handle storing and drawing of text in window or data coordinates.
+ </docstring>
+ <inputPortSpec arg="rotation_mode" name="rotation_mode">
+ <docstring>set text rotation mode. If "anchor", the un-rotated text will first aligned according to their ha and va, and then will be rotated with the alignement reference point as a origin. If None (default), the text will be rotated first then will be aligned.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="style" name="style" port_type="basic:String">
+ <docstring>Set the font style.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['normal', 'italic', 'oblique']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="linespacing" name="linespacing" port_type="basic:Float">
+ <docstring>Set the line spacing as a multiple of the font size. Default is 1.2.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="family" name="family" port_type="basic:String">
+ <docstring>Set the font family. May be either a single string, or a list of strings in decreasing priority. Each string may be either a real font name or a generic font class name. If the latter, the specific font names will be looked up in the :file:`matplotlibrc` file.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['FONTNAME', 'serif', 'sans-serif', 'cursive', 'fantasy', 'monospace']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="x" name="x" port_type="basic:Float">
+ <docstring>Set the x position of the text</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>Set the foreground color of the text</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="text" name="text" port_type="basic:String">
+ <docstring>Set the text string s
+
+It may contain newlines (\n) or math in LaTeX syntax.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="verticalalignment" name="verticalalignment" port_type="basic:String">
+ <docstring>Set the vertical alignment</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['center', 'top', 'bottom', 'baseline']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="variant" name="variant" port_type="basic:String">
+ <docstring>Set the font variant, either 'normal' or 'small-caps'.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['normal', 'small-caps']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="path_effects" name="path_effects" />
+ <inputPortSpec arg="weight" name="weight" port_type="basic:String">
+ <docstring>Set the font weight.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['a numeric value in range 0-1000', 'ultralight', 'light', 'normal', 'regular', 'book', 'medium', 'roman', 'semibold', 'demibold', 'demi', 'bold', 'heavy', 'extra bold', 'black']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="stretch" name="stretch" port_type="basic:String">
+ <docstring>Set the font stretch (horizontal condensation or expansion).</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['a numeric value in range 0-1000', 'ultra-condensed', 'extra-condensed', 'condensed', 'semi-condensed', 'normal', 'semi-expanded', 'expanded', 'extra-expanded', 'ultra-expanded']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="fontproperties" name="fontproperties">
+ <docstring>Set the font properties that control the text. fp must be a :class:`matplotlib.font_manager.FontProperties` object.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="horizontalalignment" name="horizontalalignment" port_type="basic:String">
+ <docstring>Set the horizontal alignment to one of</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['center', 'right', 'left']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox" name="bbox">
+ <docstring>Draw a bounding box around self. rectprops are any settable properties for a rectangle, eg facecolor='red', alpha=0.5.
+
+t.set_bbox(dict(facecolor='red', alpha=0.5))
+
+If rectprops has "boxstyle" key. A FancyBboxPatch is initialized with rectprops and will be drawn. The mutation scale of the FancyBboxPath is set to the fontsize.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="backgroundcolor" name="backgroundcolor" port_type="basic:Color">
+ <docstring>Set the background color of the text by updating the bbox.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="position" name="position">
+ <docstring>Set the (x, y) position of the text</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" name="y" port_type="basic:Float">
+ <docstring>Set the y position of the text</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="multialignment" name="multialignment" port_type="basic:String">
+ <docstring>Set the alignment for multiple lines layout. The layout of the bounding box of all the lines is determined bu the horizontalalignment and verticalalignment properties, but the multiline text within that box can be</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['left', 'right', 'center']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="rotation" name="rotation" port_type="basic:String">
+ <docstring>Set the rotation of the text</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['angle in degrees', 'vertical', 'horizontal']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="size" name="size" port_type="basic:String">
+ <docstring>Set the font size. May be either a size string, relative to the default font size, or an absolute font size in points.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['size in points', 'xx-small', 'x-small', 'small', 'medium', 'large', 'x-large', 'xx-large']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.text.TextWithDash" name="MplTextWithDashProperties" superclass="MplTextProperties">
+ <docstring>
+ This is basically a :class:`~matplotlib.text.Text` with a dash
+ (drawn with a :class:`~matplotlib.lines.Line2D`) before/after
+ it. It is intended to be a drop-in replacement for
+ :class:`~matplotlib.text.Text`, and should behave identically to
+ it when *dashlength* = 0.0.
+
+ The dash always comes between the point specified by
+ :meth:`~matplotlib.text.Text.set_position` and the text. When a
+ dash exists, the text alignment arguments (*horizontalalignment*,
+ *verticalalignment*) are ignored.
+
+ *dashlength* is the length of the dash in canvas units.
+ (default = 0.0).
+
+ *dashdirection* is one of 0 or 1, where 0 draws the dash after the
+ text and 1 before. (default = 0).
+
+ *dashrotation* specifies the rotation of the dash, and should
+ generally stay *None*. In this case
+ :meth:`~matplotlib.text.TextWithDash.get_dashrotation` returns
+ :meth:`~matplotlib.text.Text.get_rotation`. (I.e., the dash takes
+ its rotation from the text's rotation). Because the text center is
+ projected onto the dash, major deviations in the rotation cause
+ what may be considered visually unappealing results.
+ (default = *None*)
+
+ *dashpad* is a padding length to add (or subtract) space
+ between the text and the dash, in canvas units.
+ (default = 3)
+
+ *dashpush* "pushes" the dash and text away from the point
+ specified by :meth:`~matplotlib.text.Text.set_position` by the
+ amount in canvas units. (default = 0)
+
+ .. note::
+
+ The alignment of the two objects is based on the bounding box
+ of the :class:`~matplotlib.text.Text`, as obtained by
+ :meth:`~matplotlib.artist.Artist.get_window_extent`. This, in
+ turn, appears to depend on the font metrics as given by the
+ rendering backend. Hence the quality of the "centering" of the
+ label text with respect to the dash varies depending on the
+ backend used.
+
+ .. note::
+
+ I'm not sure that I got the
+ :meth:`~matplotlib.text.TextWithDash.get_window_extent` right,
+ or whether that's sufficient for providing the object bounding
+ box.
+
+ </docstring>
+ <inputPortSpec arg="dashpush" name="dashpush" port_type="basic:Float">
+ <docstring>Set the "push" of the TextWithDash, which is the extra spacing between the beginning of the dash and the specified position.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dashdirection" name="dashdirection">
+ <docstring>Set the direction of the dash following the text. 1 is before the text and 0 is after. The default is 0, which is what you'd want for the typical case of ticks below and on the left of the figure.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="linespacing" arg_pos="9" constructor_arg="True" name="linespacing" />
+ <inputPortSpec arg="figure" name="figure">
+ <docstring>Set the figure instance the artist belong to.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="3" constructor_arg="True" name="color" />
+ <inputPortSpec arg="text" arg_pos="2" constructor_arg="True" name="text" port_type="basic:String">
+ <defaults>['']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="verticalalignment" arg_pos="4" constructor_arg="True" name="verticalalignment" port_type="basic:String">
+ <defaults>['center']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="dashpad" name="dashpad" port_type="basic:Float">
+ <docstring>Set the "pad" of the TextWithDash, which is the extra spacing between the dash and the text, in canvas units.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dashrotation" name="dashrotation" port_type="basic:Float">
+ <docstring>Set the rotation of the dash, in degrees</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="transform" name="transform">
+ <docstring>Set the :class:`matplotlib.transforms.Transform` instance used by this artist.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="fontproperties" arg_pos="7" constructor_arg="True" name="fontproperties" />
+ <inputPortSpec arg="multialignment" arg_pos="6" constructor_arg="True" name="multialignment" />
+ <inputPortSpec arg="x" name="x" port_type="basic:Float">
+ <docstring>Set the x position of the :class:`TextWithDash`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" name="y" port_type="basic:Float">
+ <docstring>Set the y position of the :class:`TextWithDash`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="position" name="position">
+ <docstring>Set the (x, y) position of the :class:`TextWithDash`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dashlength" name="dashlength" port_type="basic:Float">
+ <docstring>Set the length of the dash.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rotation" arg_pos="8" constructor_arg="True" name="rotation" />
+ <inputPortSpec arg="horizontalalignment" arg_pos="5" constructor_arg="True" name="horizontalalignment" port_type="basic:String">
+ <defaults>['center']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.Tick" name="MplTickProperties" superclass="MplArtistProperties">
+ <docstring>
+ Abstract base class for the axis ticks, grid lines and labels
+
+ 1 refers to the bottom of the plot for xticks and the left for yticks
+ 2 refers to the top of the plot for xticks and the right for yticks
+
+ Publicly accessible attributes:
+
+ :attr:`tick1line`
+ a Line2D instance
+
+ :attr:`tick2line`
+ a Line2D instance
+
+ :attr:`gridline`
+ a Line2D instance
+
+ :attr:`label1`
+ a Text instance
+
+ :attr:`label2`
+ a Text instance
+
+ :attr:`gridOn`
+ a boolean which determines whether to draw the tickline
+
+ :attr:`tick1On`
+ a boolean which determines whether to draw the 1st tickline
+
+ :attr:`tick2On`
+ a boolean which determines whether to draw the 2nd tickline
+
+ :attr:`label1On`
+ a boolean which determines whether to draw tick label
+
+ :attr:`label2On`
+ a boolean which determines whether to draw tick label
+
+ </docstring>
+ <inputPortSpec arg="label1On" arg_pos="14" constructor_arg="True" name="label1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="loc" arg_pos="1" constructor_arg="True" name="loc" />
+ <inputPortSpec arg="major" arg_pos="16" constructor_arg="True" name="major" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label2On" arg_pos="15" constructor_arg="True" name="label2On" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="5" constructor_arg="True" name="color" />
+ <inputPortSpec arg="label1" name="label1">
+ <docstring>Set the text of ticklabel</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="label2" name="label2">
+ <docstring>Set the text of ticklabel2</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="clip_path" name="clip_path" port_type="basic:String">
+ <docstring>Set the artist's clip path, which may be:
+
+a :class:`~matplotlib.patches.Patch` (or subclass) instance
+
+
+
+None, to remove the clipping path
+
+For efficiency, if the path happens to be an axis-aligned rectangle, this method will set the clipping box to the corresponding rectangle and set the clipping path to None.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['(:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`)', ':class:`~matplotlib.patches.Patch`']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="label" name="label">
+ <docstring>Set the text of ticklabel</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="labelcolor" arg_pos="9" constructor_arg="True" name="labelcolor" />
+ <inputPortSpec arg="tickdir" arg_pos="6" constructor_arg="True" name="tickdir" />
+ <inputPortSpec arg="pad" name="pad" port_type="basic:Float">
+ <docstring>Set the tick label pad in points</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="gridOn" arg_pos="11" constructor_arg="True" name="gridOn" />
+ <inputPortSpec arg="zorder" arg_pos="10" constructor_arg="True" name="zorder" />
+ <inputPortSpec arg="tick2On" arg_pos="13" constructor_arg="True" name="tick2On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="labelsize" arg_pos="8" constructor_arg="True" name="labelsize" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" />
+ <inputPortSpec arg="tick1On" arg_pos="12" constructor_arg="True" name="tick1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="size" arg_pos="3" constructor_arg="True" name="size" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.XTick" name="MplXTickProperties" superclass="MplTickProperties">
+ <docstring>
+ Contains all the Artists needed to make an x tick - the tick line,
+ the label text and the grid line
+ </docstring>
+ <inputPortSpec arg="label1On" arg_pos="14" constructor_arg="True" name="label1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="loc" arg_pos="1" constructor_arg="True" name="loc" />
+ <inputPortSpec arg="major" arg_pos="16" constructor_arg="True" name="major" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label2On" arg_pos="15" constructor_arg="True" name="label2On" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="5" constructor_arg="True" name="color" />
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="label" arg_pos="2" constructor_arg="True" name="label" />
+ <inputPortSpec arg="labelcolor" arg_pos="9" constructor_arg="True" name="labelcolor" />
+ <inputPortSpec arg="tickdir" arg_pos="6" constructor_arg="True" name="tickdir" />
+ <inputPortSpec arg="pad" arg_pos="7" constructor_arg="True" name="pad" />
+ <inputPortSpec arg="gridOn" arg_pos="11" constructor_arg="True" name="gridOn" />
+ <inputPortSpec arg="zorder" arg_pos="10" constructor_arg="True" name="zorder" />
+ <inputPortSpec arg="tick2On" arg_pos="13" constructor_arg="True" name="tick2On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="labelsize" arg_pos="8" constructor_arg="True" name="labelsize" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" />
+ <inputPortSpec arg="tick1On" arg_pos="12" constructor_arg="True" name="tick1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="size" arg_pos="3" constructor_arg="True" name="size" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.YTick" name="MplYTickProperties" superclass="MplTickProperties">
+ <docstring>
+ Contains all the Artists needed to make a Y tick - the tick line,
+ the label text and the grid line
+ </docstring>
+ <inputPortSpec arg="label1On" arg_pos="14" constructor_arg="True" name="label1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="loc" arg_pos="1" constructor_arg="True" name="loc" />
+ <inputPortSpec arg="major" arg_pos="16" constructor_arg="True" name="major" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label2On" arg_pos="15" constructor_arg="True" name="label2On" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="5" constructor_arg="True" name="color" />
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="label" arg_pos="2" constructor_arg="True" name="label" />
+ <inputPortSpec arg="labelcolor" arg_pos="9" constructor_arg="True" name="labelcolor" />
+ <inputPortSpec arg="tickdir" arg_pos="6" constructor_arg="True" name="tickdir" />
+ <inputPortSpec arg="pad" arg_pos="7" constructor_arg="True" name="pad" />
+ <inputPortSpec arg="gridOn" arg_pos="11" constructor_arg="True" name="gridOn" />
+ <inputPortSpec arg="zorder" arg_pos="10" constructor_arg="True" name="zorder" />
+ <inputPortSpec arg="tick2On" arg_pos="13" constructor_arg="True" name="tick2On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="labelsize" arg_pos="8" constructor_arg="True" name="labelsize" />
+ <inputPortSpec arg="width" arg_pos="4" constructor_arg="True" name="width" />
+ <inputPortSpec arg="tick1On" arg_pos="12" constructor_arg="True" name="tick1On" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="size" arg_pos="3" constructor_arg="True" name="size" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.Axis" name="MplAxisProperties" superclass="MplArtistProperties">
+ <docstring>
+ Public attributes
+
+ * :attr:`axes.transData` - transform data coords to display coords
+ * :attr:`axes.transAxes` - transform axis coords to display coords
+ * :attr:`labelpad` - number of points between the axis and its label
+ </docstring>
+ <inputPortSpec arg="pickradius" name="pickradius">
+ <docstring>Set the depth of the axis used by the picker</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="minor_formatter" name="minor_formatter">
+ <docstring>Set the formatter of the minor ticker</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="smart_bounds" name="smart_bounds">
+ <docstring>set the axis to have smart bounds</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ticks" name="ticksSequence" port_type="basic:List">
+ <docstring>Set the locations of the tick marks from sequence ticks</docstring>
+ <alternateSpec arg="" name="ticksScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="view_interval" name="view_interval" />
+ <inputPortSpec arg="major_locator" name="major_locator">
+ <docstring>Set the locator of the major ticker</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="major_formatter" name="major_formatter">
+ <docstring>Set the formatter of the major ticker</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ticklabels" name="ticklabelsSequence" port_type="basic:List">
+ <docstring>Set the text values of the tick labels. Return a list of Text instances. Use kwarg minor=True to select minor ticks. All other kwargs are used to update the text object properties. As for get_ticklabels, label1 (left or bottom) is affected for a given tick only if its label1On attribute is True, and similarly for label2. The list of returned label text objects consists of all such label1 objects followed by all such label2 objects.
+
+The input ticklabels is assumed to match the set of tick locations, regardless of the state of label1On and label2On.</docstring>
+ <alternateSpec arg="" name="ticklabelsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="clip_path" name="clip_path" />
+ <inputPortSpec arg="minor_locator" name="minor_locator">
+ <docstring>Set the locator of the minor ticker</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="default_intervals" name="default_intervals" />
+ <inputPortSpec arg="scale" name="scale" />
+ <inputPortSpec arg="data_interval" name="data_interval">
+ <docstring>set the axis data limits</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="label_text" name="label_text" port_type="basic:String">
+ <docstring>Sets the text value of the axis label</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="label_coords" name="label_coords">
+ <docstring>Set the coordinates of the label. By default, the x coordinate of the y label is determined by the tick label bounding boxes, but this can lead to poor alignment of multiple ylabels if there are multiple axes. Ditto for the y coodinate of the x label.
+
+You can also specify the coordinate system of the label with the transform. If None, the default coordinate system will be the axes coordinate system (0,0) is (left,bottom), (0.5, 0.5) is middle, etc</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="units" name="units">
+ <docstring>set the units for axis</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="tick_params" name="tick_params">
+ <docstring>Set appearance parameters for ticks and ticklabels.
+
+For documentation of keyword arguments, see :meth:`matplotlib.axes.Axes.tick_params`.</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.XAxis" name="MplXAxisProperties" superclass="MplAxisProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="view_interval" name="view_interval">
+ <docstring>If ignore is False, the order of vmin, vmax does not matter; the original axis orientation will be preserved. In addition, the view limits can be expanded, but will not be reduced. This method is for mpl internal use; for normal use, see :meth:`~matplotlib.axes.Axes.set_xlim`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ticks_position" name="ticks_position" port_type="basic:String">
+ <docstring>Set the ticks position (top, bottom, both, default or none) both sets the ticks to appear on both positions, but does not change the tick labels. 'default' resets the tick positions to the default: ticks on both positions, labels at bottom. 'none' can be used if you don't want any ticks. 'none' and 'both' affect only the ticks, not the labels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['top', 'bottom', 'both', 'default', 'none']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="label_position" name="label_position" port_type="basic:String">
+ <docstring>Set the label position (top or bottom)</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['top', 'bottom']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="default_intervals" name="default_intervals">
+ <docstring>set the default limits for the axis interval if they are not mutated</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="data_interval" name="data_interval">
+ <docstring>set the axis data limits</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="pickradius" arg_pos="1" constructor_arg="True" name="pickradius" port_type="basic:Integer">
+ <defaults>['15']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axis.YAxis" name="MplYAxisProperties" superclass="MplAxisProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="offset_position" name="offset_position" />
+ <inputPortSpec arg="view_interval" name="view_interval">
+ <docstring>If ignore is False, the order of vmin, vmax does not matter; the original axis orientation will be preserved. In addition, the view limits can be expanded, but will not be reduced. This method is for mpl internal use; for normal use, see :meth:`~matplotlib.axes.Axes.set_ylim`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ticks_position" name="ticks_position" port_type="basic:String">
+ <docstring>Set the ticks position (left, right, both, default or none) 'both' sets the ticks to appear on both positions, but does not change the tick labels. 'default' resets the tick positions to the default: ticks on both positions, labels at left. 'none' can be used if you don't want any ticks. 'none' and 'both' affect only the ticks, not the labels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['left', 'right', 'both', 'default', 'none']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="axes" arg_pos="0" constructor_arg="True" name="axes" />
+ <inputPortSpec arg="label_position" name="label_position" port_type="basic:String">
+ <docstring>Set the label position (left or right)</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['left', 'right']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="default_intervals" name="default_intervals">
+ <docstring>set the default limits for the axis interval if they are not mutated</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="data_interval" name="data_interval">
+ <docstring>set the axis data limits</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="pickradius" arg_pos="1" constructor_arg="True" name="pickradius" port_type="basic:Integer">
+ <defaults>['15']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.legend.Legend" name="MplLegendProperties" superclass="MplArtistProperties">
+ <docstring>
+ Place a legend on the axes at location loc. Labels are a
+ sequence of strings and loc can be a string or an integer
+ specifying the legend location
+
+ The location codes are::
+
+ 'best' : 0, (only implemented for axis legends)
+ 'upper right' : 1,
+ 'upper left' : 2,
+ 'lower left' : 3,
+ 'lower right' : 4,
+ 'right' : 5,
+ 'center left' : 6,
+ 'center right' : 7,
+ 'lower center' : 8,
+ 'upper center' : 9,
+ 'center' : 10,
+
+ loc can be a tuple of the noramilzed coordinate values with
+ respect its parent.
+
+ </docstring>
+ <inputPortSpec arg="fancybox" arg_pos="24" constructor_arg="True" name="fancybox" />
+ <inputPortSpec arg="handlelength" arg_pos="17" constructor_arg="True" name="handlelength" />
+ <inputPortSpec arg="labels" arg_pos="2" constructor_arg="True" name="labels" />
+ <inputPortSpec arg="labelspacing" arg_pos="16" constructor_arg="True" name="labelspacing" />
+ <inputPortSpec arg="columnspacing" arg_pos="21" constructor_arg="True" name="columnspacing" />
+ <inputPortSpec arg="handletextpad" arg_pos="19" constructor_arg="True" name="handletextpad" />
+ <inputPortSpec arg="ncol" arg_pos="22" constructor_arg="True" name="ncol" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="borderaxespad" arg_pos="20" constructor_arg="True" name="borderaxespad" />
+ <inputPortSpec arg="loc" arg_pos="3" constructor_arg="True" name="loc" />
+ <inputPortSpec arg="bbox_to_anchor" name="bbox_to_anchor">
+ <docstring>set the bbox that the legend will be anchored.
+
+bbox can be a BboxBase instance, a tuple of [left, bottom, width, height] in the given transform (normalized axes coordinate if None), or a tuple of [left, bottom] where the width and height will be assumed to be zero.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="title" name="title">
+ <docstring>set the legend title. Fontproperties can be optionally set with prop parameter.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="handletextsep" arg_pos="13" constructor_arg="True" name="handletextsep" />
+ <inputPortSpec arg="numpoints" arg_pos="4" constructor_arg="True" name="numpoints" />
+ <inputPortSpec arg="prop" arg_pos="8" constructor_arg="True" name="prop" />
+ <inputPortSpec arg="handles" arg_pos="1" constructor_arg="True" name="handles" />
+ <inputPortSpec arg="pad" arg_pos="10" constructor_arg="True" name="pad" />
+ <inputPortSpec arg="borderpad" arg_pos="15" constructor_arg="True" name="borderpad" />
+ <inputPortSpec arg="parent" arg_pos="0" constructor_arg="True" name="parent" />
+ <inputPortSpec arg="axespad" arg_pos="14" constructor_arg="True" name="axespad" />
+ <inputPortSpec arg="labelsep" arg_pos="11" constructor_arg="True" name="labelsep" />
+ <inputPortSpec arg="frame_on" name="frame_on" port_type="basic:Boolean">
+ <docstring>Set whether the legend box patch is drawn</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="scatterpoints" arg_pos="6" constructor_arg="True" name="scatterpoints" port_type="basic:Integer">
+ <defaults>['3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="fontsize" arg_pos="9" constructor_arg="True" name="fontsize" />
+ <inputPortSpec arg="shadow" arg_pos="25" constructor_arg="True" name="shadow" />
+ <inputPortSpec arg="handler_map" arg_pos="30" constructor_arg="True" name="handler_map" />
+ <inputPortSpec arg="handleheight" arg_pos="18" constructor_arg="True" name="handleheight" />
+ <inputPortSpec arg="scatteryoffsets" arg_pos="7" constructor_arg="True" name="scatteryoffsets" />
+ <inputPortSpec arg="markerscale" arg_pos="5" constructor_arg="True" name="markerscale" />
+ <inputPortSpec arg="frameon" arg_pos="29" constructor_arg="True" name="frameon" />
+ <inputPortSpec arg="mode" arg_pos="23" constructor_arg="True" name="mode" />
+ <inputPortSpec arg="handlelen" arg_pos="12" constructor_arg="True" name="handlelen" />
+ <inputPortSpec arg="default_handler_map" name="default_handler_map">
+ <docstring>A class method to set the default handler map.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox_transform" arg_pos="28" constructor_arg="True" name="bbox_transform" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axes.Axes" name="MplAxesProperties" superclass="MplArtistProperties">
+ <docstring>
+ The :class:`Axes` contains most of the figure elements:
+ :class:`~matplotlib.axis.Axis`, :class:`~matplotlib.axis.Tick`,
+ :class:`~matplotlib.lines.Line2D`, :class:`~matplotlib.text.Text`,
+ :class:`~matplotlib.patches.Polygon`, etc., and sets the
+ coordinate system.
+
+ The :class:`Axes` instance supports callbacks through a callbacks
+ attribute which is a :class:`~matplotlib.cbook.CallbackRegistry`
+ instance. The events you can connect to are 'xlim_changed' and
+ 'ylim_changed' and the callback will be called with func(*ax*)
+ where *ax* is the :class:`Axes` instance.
+ </docstring>
+ <inputPortSpec arg="adjustable" name="adjustable" port_type="basic:String">
+ <entry_types>['enum']</entry_types>
+ <values>[['box', 'datalim', 'box-forced']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cursor_props" name="cursor_props" port_type="basic:Float">
+ <docstring>Set the cursor property as:
+
+ax.set_cursor_props(linewidth, color)
+
+or:
+
+ax.set_cursor_props((linewidth, color))</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="figure" name="figure">
+ <docstring>Set the class:~matplotlib.axes.Axes figure
+
+accepts a class:~matplotlib.figure.Figure instance</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="yscale" name="yscale">
+ <docstring>Call signature:
+
+set_yscale(value)
+
+Set the scaling of the y-axis: 'linear' | 'log' | 'symlog' Different kwargs are accepted, depending on the scale: 'linear'
+
+'log'
+
+
+
+'symlog'</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="navigate" name="navigate" port_type="basic:Boolean">
+ <docstring>Set whether the axes responds to navigation toolbar commands</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="aspect" name="aspect">
+ <docstring>aspect
+
+
+
+adjustable
+
+
+
+'box' does not allow axes sharing, as this can cause unintended side effect. For cases when sharing axes is fine, use 'box-forced'.
+
+anchor</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['auto', 'normal', 'equal', 'num']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="axis_bgcolor" name="axis_bgcolor" port_type="basic:Color">
+ <docstring>set the axes background color</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="ylim" name="ylimSequence" port_type="basic:List">
+ <docstring>Call signature:
+
+set_ylim(self, *args, **kwargs):
+
+Set the data limits for the yaxis
+
+Examples:
+
+set_ylim((bottom, top)) set_ylim(bottom, top) set_ylim(bottom=1) # top unchanged set_ylim(top=1) # bottom unchanged
+
+Keyword arguments:
+
+
+
+Note, the bottom (formerly ymin) value may be greater than the top (formerly ymax). For example, suppose y is depth in the ocean. Then one might use:
+
+set_ylim(5000, 0)
+
+so 5000 m depth is at the bottom of the plot and the surface, 0 m, is at the top.
+
+Returns the current ylimits as a length 2 tuple</docstring>
+ <alternateSpec arg="" name="ylimScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="sharey" arg_pos="5" constructor_arg="True" name="sharey" />
+ <inputPortSpec arg="xlim" name="xlimSequence" port_type="basic:List">
+ <docstring>Call signature:
+
+set_xlim(self, *args, **kwargs):
+
+Set the data limits for the xaxis
+
+Examples:
+
+set_xlim((left, right)) set_xlim(left, right) set_xlim(left=1) # right unchanged set_xlim(right=1) # left unchanged
+
+Keyword arguments:
+
+
+
+Note, the left (formerly xmin) value may be greater than the right (formerly xmax). For example, suppose x is years before present. Then one might use:
+
+set_ylim(5000, 0)
+
+so 5000 years ago is on the left of the plot and the present is on the right.
+
+Returns the current xlimits as a length 2 tuple</docstring>
+ <alternateSpec arg="" name="xlimScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="axis_on" name="axis_on">
+ <docstring>turn on the axis</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="title" name="title">
+ <docstring>Call signature:
+
+set_title(label, fontdict=None, **kwargs):
+
+Set the title for the axes.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axisbg" arg_pos="2" constructor_arg="True" name="axisbg" />
+ <inputPortSpec arg="label" arg_pos="6" constructor_arg="True" name="label" port_type="basic:String">
+ <defaults>['']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xticks" name="xticksSequence" port_type="basic:List">
+ <docstring>Set the x ticks with list of ticks</docstring>
+ <alternateSpec arg="" name="xticksScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="fig" arg_pos="0" constructor_arg="True" name="fig" />
+ <inputPortSpec arg="ylabel" name="ylabel">
+ <docstring>Call signature:
+
+set_ylabel(ylabel, fontdict=None, labelpad=None, **kwargs)
+
+Set the label for the yaxis
+
+labelpad is the spacing in points between the label and the y-axis</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="autoscalex_on" name="autoscalex_on" port_type="basic:Boolean">
+ <docstring>Set whether autoscaling for the x-axis is applied on plot commands</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rasterization_zorder" name="rasterization_zorder">
+ <docstring>Set zorder value below which artists will be rasterized. Set to None to disable rasterizing of artists below a particular zorder.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axes_locator" name="axes_locator">
+ <docstring>set axes_locator</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axisbelow" name="axisbelow" port_type="basic:Boolean">
+ <docstring>Set whether the axis ticks and gridlines are above or below most artists</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="frame_on" name="frame_on" port_type="basic:Boolean">
+ <docstring>Set whether the axes rectangle patch is drawn</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="navigate_mode" name="navigate_mode">
+ <docstring>Set the navigation toolbar button status;
+
+this is not a user-API function.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xscale" name="xscale">
+ <docstring>Call signature:
+
+set_xscale(value)
+
+Set the scaling of the x-axis: 'linear' | 'log' | 'symlog' Different kwargs are accepted, depending on the scale: 'linear'
+
+'log'
+
+
+
+'symlog'</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="axis_off" name="axis_off">
+ <docstring>turn off the axis</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="autoscale_on" name="autoscale_on" port_type="basic:Boolean">
+ <docstring>Set whether autoscaling is applied on plot commands</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ybound" name="ybound">
+ <docstring>Set the lower and upper numerical bounds of the y-axis. This method will honor axes inversion regardless of parameter order. It will not change the _autoscaleYon attribute.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rect" arg_pos="1" constructor_arg="True" name="rect" />
+ <inputPortSpec arg="sharex" arg_pos="4" constructor_arg="True" name="sharex" />
+ <inputPortSpec arg="yticklabels" name="yticklabelsSequence" port_type="basic:List">
+ <docstring>Call signature:
+
+set_yticklabels(labels, fontdict=None, minor=False, **kwargs)
+
+Set the y tick labels with list of strings labels. Return a list of :class:`~matplotlib.text.Text` instances.
+
+kwargs set :class:`~matplotlib.text.Text` properties for the labels. Valid properties are
+
+agg_filter: unknown alpha: float (0.0 transparent through 1.0 opaque) animated: [True | False] axes: an :class:`~matplotlib.axes.Axes` instance backgroundcolor: any matplotlib color bbox: rectangle prop dict clip_box: a :class:`matplotlib.transforms.Bbox` instance clip_on: [True | False] clip_path: [ (:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`) | :class:`~matplotlib.patches.Patch` | None ] color: any matplotlib color contains: a callable fun [...]
+ <alternateSpec arg="" name="yticklabelsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="autoscaley_on" name="autoscaley_on" port_type="basic:Boolean">
+ <docstring>Set whether autoscaling for the y-axis is applied on plot commands</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xmargin" name="xmargin" port_type="basic:Float">
+ <docstring>Set padding of X data limits prior to autoscaling.
+
+m times the data interval will be added to each end of that interval before it is used in autoscaling.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="color_cycle" name="color_cycle" port_type="basic:Color">
+ <docstring>Set the color cycle for any future plot commands on this Axes.
+
+clist is a list of mpl color specifiers.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="frameon" arg_pos="3" constructor_arg="True" name="frameon" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xlabel" name="xlabel">
+ <docstring>Call signature:
+
+set_xlabel(xlabel, fontdict=None, labelpad=None, **kwargs)
+
+Set the label for the xaxis.
+
+labelpad is the spacing in points between the label and the x-axis</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xbound" name="xbound">
+ <docstring>Set the lower and upper numerical bounds of the x-axis. This method will honor axes inversion regardless of parameter order. It will not change the _autoscaleXon attribute.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="yticks" name="yticksSequence" port_type="basic:List">
+ <docstring>Set the y ticks with list of ticks Keyword arguments:</docstring>
+ <alternateSpec arg="" name="yticksScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="ymargin" name="ymargin" port_type="basic:Float">
+ <docstring>Set padding of Y data limits prior to autoscaling.
+
+m times the data interval will be added to each end of that interval before it is used in autoscaling.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="position" name="position">
+ <docstring>Set the axes position with:
+
+pos = [left, bottom, width, height]
+
+in relative 0,1 coords, or pos can be a :class:`~matplotlib.transforms.Bbox`
+
+There are two position variables: one which is ultimately used, but which may be modified by :meth:`apply_aspect`, and a second which is the starting point for :meth:`apply_aspect`.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="anchor" name="anchor" port_type="basic:String">
+ <docstring>anchor</docstring>
+ <translations>{'right': 'E', 'Center': 'C', 'bottom': 'S', 'top right': 'NE', 'bottom left': 'SW', 'top left': 'NW', 'bottom right': 'SE', 'top': 'N', 'left': 'W'}</translations>
+ <values>[['Center', 'bottom left', 'bottom', 'bottom right', 'right', 'top right', 'top', 'top left', 'left']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="xticklabels" name="xticklabelsSequence" port_type="basic:List">
+ <docstring>Call signature:
+
+set_xticklabels(labels, fontdict=None, minor=False, **kwargs)
+
+Set the xtick labels with list of strings labels. Return a list of axis text instances.
+
+kwargs set the :class:`~matplotlib.text.Text` properties. Valid properties are
+
+agg_filter: unknown alpha: float (0.0 transparent through 1.0 opaque) animated: [True | False] axes: an :class:`~matplotlib.axes.Axes` instance backgroundcolor: any matplotlib color bbox: rectangle prop dict clip_box: a :class:`matplotlib.transforms.Bbox` instance clip_on: [True | False] clip_path: [ (:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`) | :class:`~matplotlib.patches.Patch` | None ] color: any matplotlib color contains: a callable fun [...]
+ <alternateSpec arg="" name="xticklabelsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.axes.AxesSubplot" name="MplAxesSubplotProperties" superclass="MplAxesProperties">
+ <docstring>None</docstring>
+ <inputPortSpec arg="fig" arg_pos="0" constructor_arg="True" name="fig" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.figure.Figure" name="MplFigureProperties" superclass="MplArtistProperties">
+ <docstring>
+ The Figure instance supports callbacks through a *callbacks*
+ attribute which is a :class:`matplotlib.cbook.CallbackRegistry`
+ instance. The events you can connect to are 'dpi_changed', and
+ the callback will be called with ``func(fig)`` where fig is the
+ :class:`Figure` instance.
+
+ *patch*
+ The figure patch is drawn by a
+ :class:`matplotlib.patches.Rectangle` instance
+
+ *suppressComposite*
+ For multiple figure images, the figure will make composite
+ images depending on the renderer option_image_nocomposite
+ function. If suppressComposite is True|False, this will
+ override the renderer.
+ </docstring>
+ <inputPortSpec arg="edgecolor" name="edgecolor" port_type="basic:Color">
+ <docstring>Set the edge color of the Figure rectangle</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="canvas" name="canvas">
+ <docstring>Set the canvas the contains the figure</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="facecolor" name="facecolor" port_type="basic:Color">
+ <docstring>Set the face color of the Figure rectangle</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="size_inches" name="size_inches">
+ <docstring>set_size_inches(w,h, forward=False)
+
+Set the figure size in inches
+
+Usage:
+
+fig.set_size_inches(w,h) # OR fig.set_size_inches((w,h) )
+
+optional kwarg forward=True will cause the canvas size to be automatically updated; eg you can resize the figure window from the shell</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="figwidth" name="figwidth" port_type="basic:Float">
+ <docstring>Set the width of the figure in inches</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="frameon" name="frameon" port_type="basic:Boolean">
+ <docstring>Set whether the figure frame (background) is displayed or invisible</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="subplotpars" arg_pos="6" constructor_arg="True" name="subplotpars" />
+ <inputPortSpec arg="figheight" name="figheight" port_type="basic:Float">
+ <docstring>Set the height of the figure in inches</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="figsize" arg_pos="0" constructor_arg="True" name="figsize" />
+ <inputPortSpec arg="linewidth" arg_pos="4" constructor_arg="True" name="linewidth" port_type="basic:Float">
+ <defaults>['0.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="tight_layout" name="tight_layout" port_type="basic:Boolean">
+ <docstring>Set whether :meth:`tight_layout` is used upon drawing. If None, the rcParams['figure.autolayout'] value will be set.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="dpi" name="dpi" port_type="basic:Float">
+ <docstring>Set the dots-per-inch of the figure</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.text.Annotation" name="MplAnnotationProperties" superclass="MplTextProperties">
+ <docstring>
+ A :class:`~matplotlib.text.Text` class to make annotating things
+ in the figure, such as :class:`~matplotlib.figure.Figure`,
+ :class:`~matplotlib.axes.Axes`,
+ :class:`~matplotlib.patches.Rectangle`, etc., easier.
+ </docstring>
+ <inputPortSpec arg="xycoords" arg_pos="3" constructor_arg="True" name="xycoords" port_type="basic:String">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ <defaults>['data']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="figure" name="figure" />
+ <inputPortSpec arg="annotation_clip" arg_pos="6" constructor_arg="True" name="annotation_clip" />
+ <inputPortSpec arg="xytext" arg_pos="2" constructor_arg="True" name="xytext" />
+ <inputPortSpec arg="s" arg_pos="0" constructor_arg="True" name="s" />
+ <inputPortSpec arg="xy" arg_pos="1" constructor_arg="True" name="xy" />
+ <inputPortSpec arg="textcoords" arg_pos="4" constructor_arg="True" name="textcoords">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="arrowprops" arg_pos="5" constructor_arg="True" name="arrowprops" />
+ </moduleSpec>
+</specs>
diff --git a/vistrails/packages/matplotlib/mpl_plots.xml b/vistrails/packages/matplotlib/mpl_plots.xml
new file mode 100644
index 0000000..325ca51
--- /dev/null
+++ b/vistrails/packages/matplotlib/mpl_plots.xml
@@ -0,0 +1,3277 @@
+<specs>
+ <customCode />
+ <moduleSpec code_ref="matplotlib.pyplot.acorr" name="MplAcorr" output_type="tuple" superclass="MplPlot">
+ <docstring>Plot the autocorrelation of x.
+
+Call signature:
+
+acorr(x, normed=True, detrend=mlab.detrend_none, usevlines=True, maxlags=10, **kwargs)
+
+If normed = True, normalize the data by the autocorrelation at 0-th lag. x is detrended by the detrend callable (default no normalization).
+
+Data are plotted as plot(lags, c, **kwargs)
+
+Return value is a tuple (lags, c, line) where:
+
+lags are a length 2*maxlags+1 lag vector
+
+c is the 2*maxlags+1 auto correlation vector
+
+line is a :class:`~matplotlib.lines.Line2D` instance returned by :meth:`plot`
+
+The default linestyle is None and the default marker is 'o', though these can be overridden with keyword args. The cross correlation is performed with :func:`numpy.correlate` with mode = 2.
+
+If usevlines is True, :meth:`~matplotlib.axes.Axes.vlines` rather than :meth:`~matplotlib.axes.Axes.plot` is used to draw vertical lines from the origin to the acorr. Otherwise, the plot style is determined by the kwargs, which are :class:`~matplotlib.lines.Line2D` properties.
+
+maxlags is a positive integer detailing the number of lags to show. The default value of None will return all (2*len(x)-1) lags.
+
+The return value is a tuple (lags, c, linecol, b) where
+
+linecol is the :class:`~matplotlib.collections.LineCollection`
+
+b is the x-axis.
+
+Example:
+
+:func:`~matplotlib.pyplot.xcorr` is top graph, and :func:`~matplotlib.pyplot.acorr` is bottom graph.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="normed" arg_pos="1" name="normed" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="usevlines" arg_pos="3" name="usevlines" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="detrend" arg_pos="2" name="detrend" />
+ <inputPortSpec arg="maxlags" arg_pos="4" name="maxlags" port_type="basic:Integer">
+ <defaults>['10']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="1" name="hold" />
+ <outputPortSpec arg="lineCollection" compute_name="lineCollection" name="lineCollectionProperties" port_type="__property__" property_key="4" property_type="matplotlib.collections.LineCollection" />
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="2" property_type="matplotlib.lines.Line2D" />
+ <outputPortSpec arg="xaxis" compute_name="xaxis" name="xaxisProperties" port_type="__property__" property_key="3" property_type="matplotlib.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.arrow" name="MplArrow" superclass="MplPlot">
+ <docstring>Add an arrow to the axes.
+
+Call signature:
+
+arrow(x, y, dx, dy, **kwargs)
+
+Draws arrow on specified axis from (x, y) to (x + dx, y + dy). Uses FancyArrow patch to construct the arrow.
+
+Optional kwargs control the arrow construction and properties:
+
+%(FancyArrow)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:Float" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:Float" required="True" />
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="dx" arg_pos="2" name="dx" port_type="basic:Float" required="True" />
+ <inputPortSpec arg="dy" arg_pos="3" name="dy" port_type="basic:Float" required="True" />
+ <inputPortSpec arg="arrow" constructor_arg="True" name="arrowProperties" port_type="__property__" property_type="matplotlib.patches.FancyArrow" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.axhline" name="MplAxhline" output_type="object" superclass="MplPlot">
+ <docstring>Add a horizontal line across the axis.
+
+Call signature:
+
+axhline(y=0, xmin=0, xmax=1, **kwargs)
+
+Draw a horizontal line at y from xmin to xmax. With the default values of xmin = 0 and xmax = 1, this line will always span the horizontal extent of the axes, regardless of the xlim settings, even if you change them, eg. with the :meth:`set_xlim` command. That is, the horizontal extent is in axes coords: 0=left, 0.5=middle, 1.0=right but the y location is in data coordinates.
+
+Return value is the :class:`~matplotlib.lines.Line2D` instance. kwargs are the same as kwargs to plot, and can be used to control the line properties. Eg.,
+
+draw a thick red hline at y = 0 that spans the xrange:
+
+>>> axhline(linewidth=4, color='r')
+
+draw a default hline at y = 1 that spans the xrange:
+
+>>> axhline(y=1)
+
+draw a default hline at y = .5 that spans the the middle half of the xrange:
+
+>>> axhline(y=.5, xmin=0.25, xmax=0.75)
+
+Valid kwargs are :class:`~matplotlib.lines.Line2D` properties, with the exception of 'transform':
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="y" arg_pos="0" name="y" port_type="basic:Float">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xmin" arg_pos="1" name="xmin" port_type="basic:Float">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="3" name="hold" />
+ <inputPortSpec arg="xmax" arg_pos="2" name="xmax" port_type="basic:Float">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <outputPortSpec arg="line" compute_name="line" name="lineProperties" port_type="__property__" property_key="0" property_type="matplotlib.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.axhspan" name="MplAxhspan" output_type="object" superclass="MplPlot">
+ <docstring>Add a horizontal span (rectangle) across the axis.
+
+Call signature:
+
+axhspan(ymin, ymax, xmin=0, xmax=1, **kwargs)
+
+y coords are in data units and x coords are in axes (relative 0-1) units.
+
+Draw a horizontal span (rectangle) from ymin to ymax. With the default values of xmin = 0 and xmax = 1, this always spans the xrange, regardless of the xlim settings, even if you change them, eg. with the :meth:`set_xlim` command. That is, the horizontal extent is in axes coords: 0=left, 0.5=middle, 1.0=right but the y location is in data coordinates.
+
+Return value is a :class:`matplotlib.patches.Polygon` instance.
+
+Examples:
+
+draw a gray rectangle from y = 0.25-0.75 that spans the horizontal extent of the axes:
+
+>>> axhspan(0.25, 0.75, facecolor='0.5', alpha=0.5)
+
+Valid kwargs are :class:`~matplotlib.patches.Polygon` properties:
+
+%(Polygon)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="xmin" arg_pos="2" name="xmin" port_type="basic:Float">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="ymin" arg_pos="0" name="ymin" port_type="basic:Float" required="True" />
+ <inputPortSpec arg="ymax" arg_pos="1" name="ymax" port_type="basic:Float" required="True" />
+ <inputPortSpec arg="xmax" arg_pos="3" name="xmax" port_type="basic:Float">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <outputPortSpec arg="patch" compute_name="patch" name="patchProperties" port_type="__property__" property_key="-1" property_type="matplotlib.patches.Polygon" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.axvline" name="MplAxvline" output_type="object" superclass="MplPlot">
+ <docstring>Add a vertical line across the axes.
+
+Call signature:
+
+axvline(x=0, ymin=0, ymax=1, **kwargs)
+
+Draw a vertical line at x from ymin to ymax. With the default values of ymin = 0 and ymax = 1, this line will always span the vertical extent of the axes, regardless of the ylim settings, even if you change them, eg. with the :meth:`set_ylim` command. That is, the vertical extent is in axes coords: 0=bottom, 0.5=middle, 1.0=top but the x location is in data coordinates.
+
+Return value is the :class:`~matplotlib.lines.Line2D` instance. kwargs are the same as kwargs to plot, and can be used to control the line properties. Eg.,
+
+draw a thick red vline at x = 0 that spans the yrange:
+
+>>> axvline(linewidth=4, color='r')
+
+draw a default vline at x = 1 that spans the yrange:
+
+>>> axvline(x=1)
+
+draw a default vline at x = .5 that spans the the middle half of the yrange:
+
+>>> axvline(x=.5, ymin=0.25, ymax=0.75)
+
+Valid kwargs are :class:`~matplotlib.lines.Line2D` properties, with the exception of 'transform':
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:Float">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="3" name="hold" />
+ <inputPortSpec arg="ymin" arg_pos="1" name="ymin" port_type="basic:Float">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ymax" arg_pos="2" name="ymax" port_type="basic:Float">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <outputPortSpec arg="line" compute_name="line" name="lineProperties" port_type="__property__" property_key="0" property_type="matplotlib.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.axvspan" name="MplAxvspan" output_type="object" superclass="MplPlot">
+ <docstring>Add a vertical span (rectangle) across the axes.
+
+Call signature:
+
+axvspan(xmin, xmax, ymin=0, ymax=1, **kwargs)
+
+x coords are in data units and y coords are in axes (relative 0-1) units.
+
+Draw a vertical span (rectangle) from xmin to xmax. With the default values of ymin = 0 and ymax = 1, this always spans the yrange, regardless of the ylim settings, even if you change them, eg. with the :meth:`set_ylim` command. That is, the vertical extent is in axes coords: 0=bottom, 0.5=middle, 1.0=top but the y location is in data coordinates.
+
+Return value is the :class:`matplotlib.patches.Polygon` instance.
+
+Examples:
+
+draw a vertical green translucent rectangle from x=1.25 to 1.55 that spans the yrange of the axes:
+
+>>> axvspan(1.25, 1.55, facecolor='g', alpha=0.5)
+
+Valid kwargs are :class:`~matplotlib.patches.Polygon` properties:
+
+%(Polygon)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="xmin" arg_pos="0" name="xmin" port_type="basic:Float" required="True" />
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="ymin" arg_pos="2" name="ymin" port_type="basic:Float">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ymax" arg_pos="3" name="ymax" port_type="basic:Float">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xmax" arg_pos="1" name="xmax" port_type="basic:Float" required="True" />
+ <outputPortSpec arg="patch" compute_name="patch" name="patchProperties" port_type="__property__" property_key="-1" property_type="matplotlib.patches.Polygon" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.bar" name="MplBar" output_type="object" superclass="MplPlot">
+ <docstring>Make a bar plot.
+
+Call signature:
+
+bar(left, height, width=0.8, bottom=0, **kwargs)
+
+Make a bar plot with rectangles bounded by:
+
+
+
+left, height, width, and bottom can be either scalars or sequences
+
+Return value is a list of :class:`matplotlib.patches.Rectangle` instances.
+
+Required arguments:
+
+
+
+Optional keyword arguments:
+
+
+
+For vertical bars, align = 'edge' aligns bars by their left edges in left, while align = 'center' interprets these values as the x coordinates of the bar centers. For horizontal bars, align = 'edge' aligns bars by their bottom edges in bottom, while align = 'center' interprets these values as the y coordinates of the bar centers.
+
+The optional arguments color, edgecolor, linewidth, xerr, and yerr can be either scalars or sequences of length equal to the number of bars. This enables you to use bar as the basis for stacked bar charts, or candlestick plots. Detail: xerr and yerr are passed directly to :meth:`errorbar`, so they can also have shape 2xN for independent specification of lower and upper errors.
+
+Other optional kwargs:
+
+%(Rectangle)s
+
+Example: A stacked bar chart.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="edgecolor" name="edgecolor" port_type="basic:Color">
+ <docstring>the colors of the bar edges</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidth" name="linewidth">
+ <docstring>width of bar edges; None means use default linewidth; 0 means don't draw edges.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="capsize" name="capsize" port_type="basic:Integer">
+ <docstring>(default 3) determines the length in points of the error bar caps</docstring>
+ <defaults>['3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="orientation" name="orientation" port_type="basic:String">
+ <docstring>'vertical' | 'horizontal'</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['vertical', 'horizontal']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="bottom" arg_pos="3" name="bottom" port_type="basic:Float">
+ <docstring>the y coordinates of the bottom edges of the bars</docstring>
+ <defaults>['0']</defaults>
+ <alternateSpec arg="bottom" name="bottomSequence" port_type="basic:List" />
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>the colors of the bars</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="xerr" name="xerr">
+ <docstring>if not None, will be used to generate errorbars on the bar chart</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="align" name="align" port_type="basic:String">
+ <docstring>'edge' (default) | 'center'</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['edge', 'center']]</values>
+ <defaults>['edge']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ecolor" name="ecolor" port_type="basic:Color">
+ <docstring>specifies the color of any errorbar</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="height" arg_pos="1" name="height" port_type="basic:List" required="True">
+ <docstring>the heights of the bars</docstring>
+ <alternateSpec arg="height" name="heightScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="width" arg_pos="2" name="width" port_type="basic:Float">
+ <docstring>the widths of the bars</docstring>
+ <defaults>['0.8']</defaults>
+ <alternateSpec arg="width" name="widthSequence" port_type="basic:List" />
+ </inputPortSpec>
+ <inputPortSpec arg="error_kw" name="error_kw">
+ <docstring>dictionary of kwargs to be passed to errorbar method. ecolor and capsize may be specified here rather than as independent kwargs.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="log" name="log" port_type="basic:Boolean">
+ <docstring>[False|True] False (default) leaves the orientation axis as-is; True sets it to log scale</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="yerr" name="yerr">
+ <docstring>if not None, will be used to generate errorbars on the bar chart</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="left" arg_pos="0" name="left" port_type="basic:List" required="False">
+ <docstring>the x coordinates of the left sides of the bars</docstring>
+ <alternateSpec arg="left" name="leftScalar" port_type="basic:Float">
+ <docstring>the x coordinate of the left side of the bar</docstring>
+ </alternateSpec>
+ </inputPortSpec>
+ <outputPortSpec arg="rectangle" compute_name="rectangles" name="rectangleProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.Rectangle" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.barh" name="MplBarh" output_type="object" superclass="MplPlot">
+ <docstring>Make a horizontal bar plot.
+
+Call signature:
+
+barh(bottom, width, height=0.8, left=0, **kwargs)
+
+Make a horizontal bar plot with rectangles bounded by:
+
+
+
+bottom, width, height, and left can be either scalars or sequences
+
+Return value is a list of :class:`matplotlib.patches.Rectangle` instances.
+
+Required arguments:
+
+
+
+Optional keyword arguments:
+
+
+
+Setting align = 'edge' aligns bars by their bottom edges in bottom, while align = 'center' interprets these values as the y coordinates of the bar centers.
+
+The optional arguments color, edgecolor, linewidth, xerr, and yerr can be either scalars or sequences of length equal to the number of bars. This enables you to use barh as the basis for stacked bar charts, or candlestick plots.
+
+other optional kwargs:
+
+%(Rectangle)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="edgecolor" name="edgecolor" port_type="basic:Color">
+ <docstring>the colors of the bar edges</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidth" name="linewidth">
+ <docstring>width of bar edges; None means use default linewidth; 0 means don't draw edges.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="capsize" name="capsize" port_type="basic:Integer">
+ <docstring>(default 3) determines the length in points of the error bar caps</docstring>
+ <defaults>['3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="log" name="log" port_type="basic:Boolean">
+ <docstring>[False|True] False (default) leaves the horizontal axis as-is; True sets it to log scale</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="bottom" arg_pos="0" name="bottom" port_type="basic:List" required="True">
+ <docstring>the vertical positions of the bottom edges of the bars</docstring>
+ <alternateSpec arg="bottom" name="bottomScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>the colors of the bars</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="xerr" name="xerr">
+ <docstring>if not None, will be used to generate errorbars on the bar chart</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="align" name="align" port_type="basic:String">
+ <docstring>'edge' (default) | 'center'</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['edge', 'center']]</values>
+ <defaults>['edge']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ecolor" name="ecolor" port_type="basic:Color">
+ <docstring>specifies the color of any errorbar</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="height" arg_pos="2" name="height" port_type="basic:Float">
+ <docstring>the heights (thicknesses) of the bars</docstring>
+ <defaults>['0.8']</defaults>
+ <alternateSpec arg="height" name="heightSequence" port_type="basic:List" />
+ </inputPortSpec>
+ <inputPortSpec arg="width" arg_pos="1" name="width" port_type="basic:List" required="True">
+ <docstring>the lengths of the bars</docstring>
+ <alternateSpec arg="width" name="widthScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="yerr" name="yerr">
+ <docstring>if not None, will be used to generate errorbars on the bar chart</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="left" arg_pos="3" name="left" port_type="basic:Float">
+ <docstring>the x coordinates of the left edges of the bars</docstring>
+ <defaults>['0']</defaults>
+ <alternateSpec arg="left" name="leftSequence" port_type="basic:List" />
+ </inputPortSpec>
+ <outputPortSpec arg="rectangle" compute_name="rectangles" name="rectangleProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.Rectangle" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.broken_barh" name="MplBrokenBarh" superclass="MplPlot">
+ <docstring>Plot horizontal bars.
+
+Call signature:
+
+broken_barh(self, xranges, yrange, **kwargs)
+
+A collection of horizontal bars spanning yrange with a sequence of xranges.
+
+Required arguments:
+
+
+
+kwargs are :class:`matplotlib.collections.BrokenBarHCollection` properties:
+
+%(BrokenBarHCollection)s
+
+these can either be a single argument, ie:
+
+facecolors = 'black'
+
+or a sequence of arguments for the various bars, ie:
+
+facecolors = ('black', 'red', 'green')
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="xranges" arg_pos="0" name="xranges" port_type="basic:List" required="True">
+ <docstring>sequence of (xmin, xwidth)</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="2" name="hold" />
+ <inputPortSpec arg="yrange" arg_pos="1" name="yrange" port_type="basic:Float,basic:Float" required="True">
+ <docstring>(ymin, ywidth)</docstring>
+ </inputPortSpec>
+ <outputPortSpec arg="brokenBarHCollection" compute_name="brokenBarHCollection" name="brokenBarHCollectionProperties" port_type="__property__" property_key="__none__" property_type="matplotlib.collections.BrokenBarHCollection" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.boxplot" name="MplBoxplot" output_type="dict" superclass="MplPlot">
+ <docstring>Make a box and whisker plot.
+
+Call signature:
+
+boxplot(x, notch=False, sym='+', vert=True, whis=1.5, positions=None, widths=None, patch_artist=False, bootstrap=None, usermedians=None, conf_intervals=None)
+
+Make a box and whisker plot for each column of x or each vector in sequence x. The box extends from the lower to upper quartile values of the data, with a line at the median. The whiskers extend from the box to show the range of the data. Flier points are those past the end of the whiskers.
+
+Function Arguments:
+
+
+
+Returns a dictionary mapping each component of the boxplot to a list of the :class:`matplotlib.lines.Line2D` instances created. That dictionary has the following keys (assuming vertical boxplots):
+
+boxes: the main body of the boxplot showing the quartiles and the median's confidence intervals if enabled.
+
+medians: horizonal lines at the median of each box.
+
+whiskers: the vertical lines extending to the most extreme, n-outlier data points.
+
+caps: the horizontal lines at the ends of the whiskers.
+
+fliers: points representing data that extend beyone the whiskers (outliers).
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="hold" arg_pos="11" name="hold" />
+ <inputPortSpec arg="vert" arg_pos="3" name="vert" port_type="basic:Boolean">
+ <docstring>If True (default), makes the boxes vertical. If False, makes horizontal boxes.</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="positions" arg_pos="5" name="positions">
+ <docstring>Sets the horizontal positions of the boxes. The ticks and limits are automatically set to match the positions.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="bootstrap" arg_pos="8" name="bootstrap">
+ <docstring>Specifies whether to bootstrap the confidence intervals around the median for notched boxplots. If bootstrap==None, no bootstrapping is performed, and notches are calculated using a Gaussian-based asymptotic approximation (see McGill, R., Tukey, J.W., and Larsen, W.A., 1978, and Kendall and Stuart, 1967). Otherwise, bootstrap specifies the number of times to bootstrap the median to determine it's 95% confidence intervals. Values between 1000 and 10000 are recommended.</ [...]
+ </inputPortSpec>
+ <inputPortSpec arg="usermedians" arg_pos="9" name="usermedians" port_type="basic:List">
+ <docstring>An array or sequence whose first dimension (or length) is compatible with x. This overrides the medians computed by matplotlib for each element of usermedians that is not None. When an element of usermedians == None, the median will be computed directly as normal.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="sym" arg_pos="2" name="sym" port_type="basic:String">
+ <docstring>The default symbol for flier points. Enter an empty string ('') if you don't want to show fliers.</docstring>
+ <defaults>['b+']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="widths" arg_pos="6" name="widths" port_type="basic:Float">
+ <docstring>Either a scalar or a vector and sets the width of each box. The default is 0.5, or 0.15*(distance between extreme positions) if that is smaller.</docstring>
+ <defaults>['0.5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="patch_artist" arg_pos="7" name="patch_artist" port_type="basic:Boolean">
+ <docstring>If False produces boxes with the Line2D artist If True produces boxes with the Patch artist</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True">
+ <docstring>Array or a sequence of vectors.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="notch" arg_pos="1" name="notch" port_type="basic:Boolean">
+ <docstring>If False (default), produces a rectangular box plot. If True, will produce a notched box plot</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="whis" arg_pos="4" name="whis" port_type="basic:Float">
+ <docstring>Defines the length of the whiskers as a function of the inner quartile range. They extend to the most extreme data point within ( whis*(75%-25%) ) data range.</docstring>
+ <defaults>['1.5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="conf_intervals" arg_pos="10" name="conf_intervals" port_type="basic:List">
+ <docstring>Array or sequence whose first dimension (or length) is compatible with x and whose second dimension is 2. When the current element of conf_intervals is not None, the notch locations computed by matplotlib are overridden (assuming notch is True). When an element of conf_intervals is None, boxplot compute notches the method specified by the other kwargs (e.g. bootstrap).</docstring>
+ </inputPortSpec>
+ <outputPortSpec arg="box" compute_name="boxes" name="boxProperties" plural="True" port_type="__property__" property_key="boxes" property_type="matplotlib.artist.Line2D" />
+ <outputPortSpec arg="flier" compute_name="fliers" name="flierProperties" plural="True" port_type="__property__" property_key="fliers" property_type="matplotlib.artist.Line2D" />
+ <outputPortSpec arg="cap" compute_name="caps" name="capProperties" plural="True" port_type="__property__" property_key="caps" property_type="matplotlib.artist.Line2D" />
+ <outputPortSpec arg="median" compute_name="medians" name="medianProperties" plural="True" port_type="__property__" property_key="medians" property_type="matplotlib.artist.Line2D" />
+ <outputPortSpec arg="boxPatch" compute_name="boxPatches" name="boxPatchProperties" plural="True" port_type="__property__" property_key="boxPatches" property_type="matplotlib.artist.PathPatch" />
+ <outputPortSpec arg="whisker" compute_name="whiskers" name="whiskerProperties" plural="True" port_type="__property__" property_key="whiskers" property_type="matplotlib.artist.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.cohere" name="MplCohere" superclass="MplPlot">
+ <docstring>Plot the coherence between x and y.
+
+Call signature:
+
+cohere(x, y, NFFT=256, Fs=2, Fc=0, detrend = mlab.detrend_none, window = mlab.window_hanning, noverlap=0, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+Plot the coherence between x and y. Coherence is the normalized cross spectral density:
+
+C_{xy} = \frac{|P_{xy}|^2}{P_{xx}P_{yy}}
+
+%(PSD)s
+
+
+
+The return value is a tuple (Cxy, f), where f are the frequencies of the coherence vector.
+
+kwargs are applied to the lines.
+
+References:
+
+Bendat & Piersol -- Random Data: Analysis and Measurement Procedures, John Wiley & Sons (1986)
+
+kwargs control the :class:`~matplotlib.lines.Line2D` properties of the coherence plot:
+
+%(Line2D)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="Fs" arg_pos="3" name="Fs" port_type="basic:Integer">
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pad_to" arg_pos="8" name="pad_to" />
+ <inputPortSpec arg="scale_by_freq" arg_pos="10" name="scale_by_freq" />
+ <inputPortSpec arg="detrend" arg_pos="5" name="detrend">
+ <defaults>['<function detrend_none at 0x02F5A3F0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="window" arg_pos="6" name="window">
+ <defaults>['<function window_hanning at 0x02F5A2B0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="Fc" arg_pos="4" name="Fc" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="NFFT" arg_pos="2" name="NFFT" port_type="basic:Integer">
+ <defaults>['256']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="11" name="hold" />
+ <inputPortSpec arg="sides" arg_pos="9" name="sides" port_type="basic:String">
+ <defaults>['default']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="noverlap" arg_pos="7" name="noverlap" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="line" constructor_arg="True" name="lineProperties" port_type="__property__" property_type="matplotlib.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.clabel" name="MplClabel" output_type="object" superclass="MplPlot">
+ <docstring>Label a contour plot.
+
+Call signature:
+
+clabel(cs, **kwargs)
+
+Adds labels to line contours in cs, where cs is a :class:`~matplotlib.contour.ContourSet` object returned by contour.
+
+clabel(cs, v, **kwargs)
+
+only labels contours listed in v.
+
+Optional keyword arguments:
+
+
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="inline_spacing" name="inline_spacing">
+ <docstring>space in pixels to leave on each side of label when placing inline. Defaults to 5. This spacing will be exact for labels at locations where the contour is straight, less so for labels on curved contours.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="use_clabeltext" name="use_clabeltext" port_type="basic:String">
+ <docstring>if True (default is False), ClabelText class (instead of matplotlib.Text) is used to create labels. ClabelText recalculates rotation angles of texts during the drawing time, therefore this can be used if aspect of the axes changes.</docstring>
+ <defaults>['False)']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="fmt" name="fmt" port_type="basic:String">
+ <docstring>a format string for the label. Default is '%1.3f' Alternatively, this can be a dictionary matching contour levels with arbitrary strings to use for each contour level (i.e., fmt[level]=string), or it can be any callable, such as a :class:`~matplotlib.ticker.Formatter` instance, that returns a string when called with a numeric contour level.</docstring>
+ <defaults>['%1.3f']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="manual" name="manual">
+ <docstring>if True, contour labels will be placed manually using mouse clicks. Click the first button near a contour to add a label, click the second button (or potentially both mouse buttons at once) to finish adding labels. The third button can be used to remove the last label added, but only if labels are not inline. Alternatively, the keyboard can be used to select label locations (enter to end label placement, delete or backspace act like the third mouse button, and any oth [...]
+
+manual can be an iterable object of x,y tuples. Contour labels will be created as if mouse is clicked at each x,y positions.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="cs" arg_pos="0" in_args="True" name="cs" port_type="MplContourSet" required="True" />
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>if None, the color of each label matches the color of the corresponding contour
+
+if one string color, e.g. colors = 'r' or colors = 'red', all labels will be plotted in this color
+
+if a tuple of matplotlib color args (string, float, rgb, etc), different labels will be plotted in different colors in the order specified</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="fontsize" name="fontsize">
+ <docstring>size in points or relative size eg 'smaller', 'x-large'</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rightside_up" name="rightside_up" port_type="basic:Boolean">
+ <docstring>if True (default), label rotations will always be plus or minus 90 degrees from level.</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="inline" name="inline" port_type="basic:Boolean">
+ <docstring>controls whether the underlying contour is removed or not. Default is True.</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="v" arg_pos="1" in_args="True" name="v" port_type="basic:List" />
+ <outputPortSpec arg="text" compute_name="texts" name="textProperties" plural="True" port_type="__property__" property_key="__none__" property_type="matplotlib.text.Text" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.contour" name="MplContour" output_type="tuple" superclass="MplPlot">
+ <docstring>Plot contours.
+
+:func:`~matplotlib.pyplot.contour` and :func:`~matplotlib.pyplot.contourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+:func:`~matplotlib.pyplot.contourf` differs from the MATLAB version in that it does not draw the polygon edges. To draw edges, add line contours with calls to :func:`~matplotlib.pyplot.contour`.
+
+Call signatures:
+
+contour(Z)
+
+make a contour plot of an array Z. The level values are chosen automatically.
+
+contour(X,Y,Z)
+
+X, Y specify the (x, y) coordinates of the surface
+
+contour(Z,N) contour(X,Y,Z,N)
+
+contour N automatically-chosen levels.
+
+contour(Z,V) contour(X,Y,Z,V)
+
+draw contour lines at the values specified in sequence V
+
+contourf(..., V)
+
+fill the len(V)-1 regions between the values in V
+
+contour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+X and Y must both be 2-D with the same shape as Z, or they must both be 1-D such that len(X) is the number of columns in Z and len(Y) is the number of rows in Z.
+
+C = contour(...) returns a :class:`~matplotlib.contour.QuadContourSet` object.
+
+Optional keyword arguments:
+
+
+
+contour-only keyword arguments:
+
+
+
+contourf-only keyword arguments:
+
+
+
+Note: contourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="origin" name="origin" port_type="basic:String">
+ <docstring>If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.
+
+This keyword is not active if X and Y are specified in the call to contour.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'upper', 'lower', 'image']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="xunits" name="xunits" port_type="basic:String">
+ <docstring>Override axis units by specifying an instance of a :class:`matplotlib.units.ConversionInterface`.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'registered units']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="extend" name="extend" port_type="basic:String">
+ <docstring>Unless this is 'neither', contour levels are automatically added to one or both ends of the range so that all data are included. These added ranges are then mapped to the special colormap values which default to the ends of the colormap range, but can be set via :meth:`matplotlib.colors.Colormap.set_under` and :meth:`matplotlib.colors.Colormap.set_over` methods.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['neither', 'both', 'min', 'max']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" name="vmin">
+ <docstring>If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="nchunk" name="nchunk" port_type="basic:Integer">
+ <docstring>If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[[0]]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyles" name="linestyles" port_type="basic:String">
+ <docstring>If linestyles is None, the default is 'solid' unless the lines are monochrome. In that case, negative contours will take their linestyle from the matplotlibrc contour.negative_linestyle setting.
+
+linestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'solid', 'dashed', 'dashdot', 'dotted']]</values>
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hatches" name="hatches" port_type="basic:List">
+ <docstring>A list of cross hatch patterns to use on the filled areas. If None, no hatching will be added to the contour. Hatching is supported in the PostScript, PDF, SVG and Agg backends only.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="levels" name="levelsSequence" port_type="basic:List">
+ <docstring>A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]</docstring>
+ <alternateSpec arg="levels" name="levelsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" name="linewidths" port_type="basic:String">
+ <docstring>If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.
+
+If a number, all levels will be plotted with this linewidth.
+
+If a tuple, different levels will be plotted with different linewidths in the order specified</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'number', 'tuple of numbers']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="locator" name="locator" port_type="basic:String">
+ <docstring>If locator is None, the default :class:`~matplotlib.ticker.MaxNLocator` is used. The locator is used to determine the contour levels if they are not given explicitly via the V argument.</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ </inputPortSpec>
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>If None, the colormap specified by cmap will be used.
+
+If a string, like 'r' or 'red', all levels will be plotted in this color.
+
+If a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ </inputPortSpec>
+ <inputPortSpec arg="yunits" name="yunits" port_type="basic:String">
+ <docstring>Override axis units by specifying an instance of a :class:`matplotlib.units.ConversionInterface`.</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ </inputPortSpec>
+ <inputPortSpec arg="extent" name="extent" port_type="basic:String">
+ <docstring>If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].
+
+This keyword is not active if X and Y are specified in the call to contour.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', '(x0,x1,y0,y1)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="vmax" name="vmax">
+ <docstring>If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>The alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="Z" arg_pos="2" in_args="True" name="Z" port_type="basic:List" required="True" />
+ <inputPortSpec arg="antialiased" name="antialiased" port_type="basic:Boolean">
+ <docstring>enable antialiasing, overriding the defaults. For filled contours, the default is True. For line contours, it is taken from rcParams['lines.antialiased'].</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ </inputPortSpec>
+ <inputPortSpec arg="X" arg_pos="0" in_args="True" name="X" port_type="basic:List" />
+ <inputPortSpec arg="V" arg_pos="3" in_args="True" name="V" port_type="basic:List" />
+ <inputPortSpec arg="Y" arg_pos="1" in_args="True" name="Y" port_type="basic:List" />
+ <inputPortSpec arg="N" arg_pos="4" in_args="True" name="N" port_type="basic:Integer" />
+ <outputPortSpec arg="contourSet" compute_name="contourSet" name="contourSet" port_type="MplQuadContourSet" property_key="0" />
+ <outputPortSpec arg="lineCollection" compute_name="lineCollections" name="lineCollectionProperties" plural="True" port_type="__property__" property_key="1" property_type="matplotlib.collections.LineCollection" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.contourf" name="MplContourf" output_type="tuple" superclass="MplPlot">
+ <docstring>Plot contours.
+
+:func:`~matplotlib.pyplot.contour` and :func:`~matplotlib.pyplot.contourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+:func:`~matplotlib.pyplot.contourf` differs from the MATLAB version in that it does not draw the polygon edges. To draw edges, add line contours with calls to :func:`~matplotlib.pyplot.contour`.
+
+Call signatures:
+
+contour(Z)
+
+make a contour plot of an array Z. The level values are chosen automatically.
+
+contour(X,Y,Z)
+
+X, Y specify the (x, y) coordinates of the surface
+
+contour(Z,N) contour(X,Y,Z,N)
+
+contour N automatically-chosen levels.
+
+contour(Z,V) contour(X,Y,Z,V)
+
+draw contour lines at the values specified in sequence V
+
+contourf(..., V)
+
+fill the len(V)-1 regions between the values in V
+
+contour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+X and Y must both be 2-D with the same shape as Z, or they must both be 1-D such that len(X) is the number of columns in Z and len(Y) is the number of rows in Z.
+
+C = contour(...) returns a :class:`~matplotlib.contour.QuadContourSet` object.
+
+Optional keyword arguments:
+
+extent: [ None | (x0,x1,y0,y1) ]
+
+If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].
+
+This keyword is not active if X and Y are specified in the call to contour.
+
+contour-only keyword arguments:
+
+
+
+contourf-only keyword arguments:
+
+
+
+Note: contourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="origin" name="origin" port_type="basic:String">
+ <docstring>If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.
+
+This keyword is not active if X and Y are specified in the call to contour.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'upper', 'lower', 'image']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyles" name="linestyles" port_type="basic:String">
+ <docstring>If linestyles is None, the default is 'solid' unless the lines are monochrome. In that case, negative contours will take their linestyle from the matplotlibrc contour.negative_linestyle setting.
+
+linestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'solid', 'dashed', 'dashdot', 'dotted']]</values>
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" name="vmin">
+ <docstring>If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="nchunk" name="nchunk" port_type="basic:Integer">
+ <docstring>If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[[0]]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="hatches" name="hatches" port_type="basic:List">
+ <docstring>A list of cross hatch patterns to use on the filled areas. If None, no hatching will be added to the contour. Hatching is supported in the PostScript, PDF, SVG and Agg backends only.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="levels" name="levelsSequence" port_type="basic:List">
+ <docstring>A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]</docstring>
+ <alternateSpec arg="levels" name="levelsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" name="linewidths" port_type="basic:String">
+ <docstring>If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.
+
+If a number, all levels will be plotted with this linewidth.
+
+If a tuple, different levels will be plotted with different linewidths in the order specified</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'number', 'tuple of numbers']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>If None, the colormap specified by cmap will be used.
+
+If a string, like 'r' or 'red', all levels will be plotted in this color.
+
+If a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['', '(mpl_colors)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="vmax" name="vmax">
+ <docstring>If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>The alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="Z" arg_pos="2" in_args="True" name="Z" port_type="basic:List" required="True" />
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="N" arg_pos="4" in_args="True" name="N" port_type="basic:Integer" />
+ <inputPortSpec arg="V" arg_pos="3" in_args="True" name="V" port_type="basic:List" />
+ <inputPortSpec arg="Y" arg_pos="1" in_args="True" name="Y" port_type="basic:List" />
+ <inputPortSpec arg="X" arg_pos="0" in_args="True" name="X" port_type="basic:List" />
+ <outputPortSpec arg="contourSet" compute_name="contourSet" name="contourSet" port_type="MplQuadContourSet" property_key="0" />
+ <outputPortSpec arg="polyCollection" compute_name="polyCollections" name="polyCollectionProperties" plural="True" port_type="__property__" property_key="1" property_type="matplotlib.collections.PolyCollection" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.csd" name="MplCsd" superclass="MplPlot">
+ <docstring>Plot cross-spectral density.
+
+Call signature:
+
+csd(x, y, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none, window=mlab.window_hanning, noverlap=0, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+The cross spectral density P_{xy} by Welch's average periodogram method. The vectors x and y are divided into NFFT length segments. Each segment is detrended by function detrend and windowed by function window. The product of the direct FFTs of x and y are averaged over each segment to compute P_{xy}, with a scaling to correct for power loss due to windowing.
+
+Returns the tuple (Pxy, freqs). P is the cross spectrum (complex valued), and 10\log_{10}|P_{xy}| is plotted.
+
+%(PSD)s
+
+
+
+kwargs control the Line2D properties:
+
+%(Line2D)s
+
+Example:
+
+seealso: :meth:`psd` For a description of the optional parameters.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="Fs" arg_pos="3" name="Fs" port_type="basic:Integer">
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pad_to" arg_pos="8" name="pad_to" />
+ <inputPortSpec arg="scale_by_freq" arg_pos="10" name="scale_by_freq" />
+ <inputPortSpec arg="detrend" arg_pos="5" name="detrend">
+ <defaults>['<function detrend_none at 0x02F5A3F0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="window" arg_pos="6" name="window">
+ <defaults>['<function window_hanning at 0x02F5A2B0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="Fc" arg_pos="4" name="Fc" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="NFFT" arg_pos="2" name="NFFT" port_type="basic:Integer">
+ <defaults>['256']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="11" name="hold" />
+ <inputPortSpec arg="sides" arg_pos="9" name="sides" port_type="basic:String">
+ <defaults>['default']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="noverlap" arg_pos="7" name="noverlap" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="line" constructor_arg="True" name="lineProperties" port_type="__property__" property_type="matplotlib.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.errorbar" name="MplErrorbar" output_type="tuple" superclass="MplPlot">
+ <docstring>Plot an errorbar graph.
+
+Call signature:
+
+errorbar(x, y, yerr=None, xerr=None, fmt='-', ecolor=None, elinewidth=None, capsize=3, barsabove=False, lolims=False, uplims=False, xlolims=False, xuplims=False, errorevery=1, capthick=None)
+
+Plot x versus y with error deltas in yerr and xerr. Vertical errorbars are plotted if yerr is not None. Horizontal errorbars are plotted if xerr is not None.
+
+x, y, xerr, and yerr can all be scalars, which plots a single error bar at x, y.
+
+Optional keyword arguments:
+
+
+
+All other keyword arguments are passed on to the plot command for the markers. For example, this code makes big red squares with thick green edges:
+
+x,y,yerr = rand(3,10) errorbar(x, y, yerr, marker='s', mfc='red', mec='green', ms=20, mew=4)
+
+where mfc, mec, ms and mew are aliases for the longer property names, markerfacecolor, markeredgecolor, markersize and markeredgewith.
+
+valid kwargs for the marker properties are
+
+%(Line2D)s
+
+Returns (plotline, caplines, barlinecols):
+
+
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="lolims" arg_pos="9" name="lolims" port_type="basic:Boolean">
+ <docstring>These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="capsize" arg_pos="7" name="capsize" port_type="basic:Float">
+ <docstring>The length of the error bar caps in points</docstring>
+ <defaults>['3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="uplims" arg_pos="10" name="uplims" port_type="basic:Boolean">
+ <docstring>These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xlolims" arg_pos="11" name="xlolims" port_type="basic:Boolean">
+ <docstring>These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="barsabove" arg_pos="8" name="barsabove">
+ <docstring>if True, will plot the errorbars above the plot symbols. Default is below.</docstring>
+ <defaults>['below']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xerr" arg_pos="3" name="xerr" port_type="basic:List">
+ <docstring>If a scalar number, len(N) array-like object, or an Nx1 array-like object, errorbars are drawn +/- value.
+
+If a sequence of shape 2xN, errorbars are drawn at -row1 and +row2</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ <alternateSpec arg="xerr" name="xerrScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="fmt" arg_pos="4" name="fmt" port_type="basic:String">
+ <docstring>The plot format symbol. If fmt is None, only the errorbars are plotted. This is used for adding errorbars to a bar plot, for example.</docstring>
+ <defaults>['-']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ecolor" arg_pos="5" name="ecolor" port_type="basic:Color">
+ <docstring>A matplotlib color arg which gives the color the errorbar lines; if None, use the marker color.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'mpl color']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="errorevery" arg_pos="13" name="errorevery" port_type="basic:Integer">
+ <docstring>subsamples the errorbars. Eg if everyerror=5, errorbars for every 5-th datapoint will be plotted. The data plot itself still shows all data points.</docstring>
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="capthick" arg_pos="14" name="capthick" port_type="basic:Float">
+ <docstring>An alias kwarg to markeredgewidth (a.k.a. - mew). This setting is a more sensible name for the property that controls the thickness of the error bar cap in points. For backwards compatibility, if mew or markeredgewidth are given, then they will over-ride capthick. This may change in future releases.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xuplims" arg_pos="12" name="xuplims" port_type="basic:Boolean">
+ <docstring>These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="elinewidth" arg_pos="6" name="elinewidth" port_type="basic:Float">
+ <docstring>The linewidth of the errorbar lines. If None, use the linewidth.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="15" name="hold" />
+ <inputPortSpec arg="yerr" arg_pos="2" name="yerr" port_type="basic:List">
+ <docstring>If a scalar number, len(N) array-like object, or an Nx1 array-like object, errorbars are drawn +/- value.
+
+If a sequence of shape 2xN, errorbars are drawn at -row1 and +row2</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ <alternateSpec arg="yerr" name="yerrScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <outputPortSpec arg="capline" compute_name="caplines" name="caplineProperties" plural="True" port_type="__property__" property_key="1" property_type="matplotlib.lines.Line2D" />
+ <outputPortSpec arg="barline" compute_name="barlines" name="barlineProperties" plural="True" port_type="__property__" property_key="2" property_type="matplotlib.collections.LineCollection" />
+ <outputPortSpec arg="plotline" compute_name="plotline" name="plotlineProperties" port_type="__property__" property_key="0" property_type="matplotlib.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.fill" name="MplFill" output_type="object" superclass="MplPlot">
+ <docstring>Plot filled polygons.
+
+Call signature:
+
+fill(*args, **kwargs)
+
+args is a variable length argument, allowing for multiple x, y pairs with an optional color format string; see :func:`~matplotlib.pyplot.plot` for details on the argument parsing. For example, to plot a polygon with vertices at x, y in blue.:
+
+ax.fill(x,y, 'b' )
+
+An arbitrary number of x, y, color groups can be specified:
+
+ax.fill(x1, y1, 'g', x2, y2, 'r')
+
+Return value is a list of :class:`~matplotlib.patches.Patch` instances that were added.
+
+The same color strings that :func:`~matplotlib.pyplot.plot` supports are supported by the fill format string.
+
+If you would like to fill below a curve, eg. shade a region between 0 and y along x, use :meth:`fill_between`
+
+The closed kwarg will close the polygon when True (default).
+
+kwargs control the :class:`~matplotlib.patches.Polygon` properties:
+
+%(Polygon)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" required="True" />
+ <outputPortSpec arg="polygon" compute_name="polygons" name="polygonProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.patches.Polygon" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.fill_between" name="MplFillBetween" output_type="object" superclass="MplPlot">
+ <docstring>Make filled polygons between two curves.
+
+Call signature:
+
+fill_between(x, y1, y2=0, where=None, **kwargs)
+
+Create a :class:`~matplotlib.collections.PolyCollection` filling the regions between y1 and y2 where where==True
+
+
+
+kwargs control the :class:`~matplotlib.patches.Polygon` properties:
+
+%(PolyCollection)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="y2" arg_pos="2" name="y2" port_type="basic:Float">
+ <docstring>A scalar y-value</docstring>
+ <defaults>['0.0']</defaults>
+ <alternateSpec arg="y2" name="y2Sequence" port_type="basic:List">
+ <docstring>An N-length array of the y data</docstring>
+ </alternateSpec>
+ </inputPortSpec>
+ <inputPortSpec arg="interpolate" arg_pos="4" name="interpolate" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y1" arg_pos="1" in_args="True" name="y1" port_type="basic:List" required="True">
+ <docstring>An N-length array of the y data</docstring>
+ <alternateSpec arg="y1" name="y1Scalar" port_type="basic:Float">
+ <docstring>A scalar y-value</docstring>
+ </alternateSpec>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" required="True">
+ <docstring>An N-length array of the x data</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="5" name="hold" />
+ <inputPortSpec arg="where" arg_pos="3" name="where" port_type="basic:List">
+ <docstring>An N-length boolean array that specifies where the fill is effective</docstring>
+ </inputPortSpec>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="__none__" property_type="matplotlib.collections.PolyCollection" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.fill_betweenx" name="MplFillBetweenx" output_type="object" superclass="MplPlot">
+ <docstring>Make filled polygons between two horizontal curves.
+
+Call signature:
+
+fill_between(y, x1, x2=0, where=None, **kwargs)
+
+Create a :class:`~matplotlib.collections.PolyCollection` filling the regions between x1 and x2 where where==True
+
+
+
+kwargs control the :class:`~matplotlib.patches.Polygon` properties:
+
+%(PolyCollection)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="y" arg_pos="0" in_args="True" name="y" port_type="basic:List" required="True">
+ <docstring>An N-length array of the y data</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="x2" arg_pos="2" name="x2" port_type="basic:Float">
+ <docstring>A scalar x-value</docstring>
+ <defaults>['0']</defaults>
+ <alternateSpec arg="x2" name="x2Sequence" port_type="basic:List">
+ <docstring>An N-length array of the x data</docstring>
+ </alternateSpec>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="x1" arg_pos="1" in_args="True" name="x1" port_type="basic:List" required="True">
+ <docstring>An N-length array of the x data</docstring>
+ <alternateSpec arg="x1" name="x1Scalar" port_type="basic:Float">
+ <docstring>A scalar x-value</docstring>
+ </alternateSpec>
+ </inputPortSpec>
+ <inputPortSpec arg="where" arg_pos="3" name="where" port_type="basic:List">
+ <docstring>An N-length boolean array that specifies where the fill is effective</docstring>
+ </inputPortSpec>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="__none__" property_type="matplotlib.collections.PolyCollection" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.hexbin" name="MplHexbin" output_type="object" superclass="MplPlot">
+ <docstring>Make a hexagonal binning plot.
+
+Call signature:
+
+hexbin(x, y, C = None, gridsize = 100, bins = None, xscale = 'linear', yscale = 'linear', cmap=None, norm=None, vmin=None, vmax=None, alpha=None, linewidths=None, edgecolors='none' reduce_C_function = np.mean, mincnt=None, marginals=True **kwargs)
+
+Make a hexagonal binning plot of x versus y, where x, y are 1-D sequences of the same length, N. If C is None (the default), this is a histogram of the number of occurences of the observations at (x[i],y[i]).
+
+If C is specified, it specifies values at the coordinate (x[i],y[i]). These values are accumulated for each hexagonal bin and then reduced according to reduce_C_function, which defaults to numpy's mean function (np.mean). (If C is specified, it must also be a 1-D sequence of the same length as x and y.)
+
+x, y and/or C may be masked arrays, in which case only unmasked points will be plotted.
+
+Optional keyword arguments:
+
+Other keyword arguments controlling color mapping and normalization arguments:
+
+Other keyword arguments controlling the Collection properties:
+
+Here are the standard descriptions of all the :class:`~matplotlib.collections.Collection` kwargs:
+
+%(Collection)s
+
+The return value is a :class:`~matplotlib.collections.PolyCollection` instance; use :meth:`~matplotlib.collections.PolyCollection.get_array` on this :class:`~matplotlib.collections.PolyCollection` to get the counts in each hexagon. If marginals is True, horizontal bar and vertical bar (both PolyCollections) will be attached to the return collection as attributes hbar and vbar.
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="vmax" arg_pos="11" name="vmax" port_type="basic:Float">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="edgecolors" arg_pos="14" name="edgecolorsSequence" port_type="basic:List">
+ <docstring>If 'none', draws the edges in the same color as the fill color. This is the default, as it avoids unsightly unpainted pixels between the hexagons.
+
+If None, draws the outlines in the default color.
+
+If a matplotlib color arg or sequence of rgba tuples, draws the outlines in the specified color.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'none', 'mpl color']]</values>
+ <defaults>['none']</defaults>
+ <alternateSpec arg="edgecolors" name="edgecolorsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="C" arg_pos="2" name="C" port_type="basic:List" />
+ <inputPortSpec arg="gridsize" arg_pos="3" name="gridsize" port_type="basic:Integer">
+ <docstring>The number of hexagons in the x-direction, default is 100. The corresponding number of hexagons in the y-direction is chosen such that the hexagons are approximately regular. Alternatively, gridsize can be a tuple with two elements specifying the number of hexagons in the x-direction and the y-direction.</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ <defaults>['100']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" arg_pos="10" name="vmin" port_type="basic:Float">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="yscale" arg_pos="6" name="yscale" port_type="basic:String">
+ <defaults>['linear']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="reduce_C_function" arg_pos="15" name="reduce_C_function">
+ <defaults>['<function mean at 0x0277B3B0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" arg_pos="13" name="linewidths">
+ <docstring>If None, defaults to rc lines.linewidth. Note that this is a tuple, and if you set the linewidths argument you must set it as a sequence of floats, as required by :class:`~matplotlib.collections.RegularPolyCollection`.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="xscale" arg_pos="5" name="xscale" port_type="basic:String">
+ <docstring>Use a linear or log10 scale on the horizontal axis.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['linear', 'log']]</values>
+ <defaults>['linear']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="8" name="cmap" port_type="basic:String">
+ <docstring>a :class:`matplotlib.colors.Colormap` instance. If None, defaults to rc image.cmap.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="9" name="norm" port_type="basic:String">
+ <docstring>:class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0,1.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="extent" arg_pos="7" name="extent">
+ <docstring>The limits of the bins. The default assigns the limits based on gridsize, x, y, xscale and yscale.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" arg_pos="12" name="alpha" port_type="basic:Float">
+ <docstring>the alpha value for the patches</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="18" name="hold" />
+ <inputPortSpec arg="mincnt" arg_pos="16" name="mincnt">
+ <docstring>If not None, only display cells with more than mincnt number of points in the cell</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="marginals" arg_pos="17" name="marginals" port_type="basic:Boolean">
+ <docstring>if marginals is True, plot the marginal density as colormapped rectagles along the bottom of the x-axis and left of the y-axis</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="bins" arg_pos="4" name="bins" port_type="basic:Integer">
+ <docstring>If None, no binning is applied; the color of each hexagon directly corresponds to its count value.
+
+If 'log', use a logarithmic scale for the color map. Internally, log_{10}(i+1) is used to determine the hexagon color.
+
+If an integer, divide the counts in the specified number of bins, and color the hexagons accordingly.
+
+If a sequence of values, the values of the lower bound of the bins to be used.</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ </inputPortSpec>
+ <inputPortSpec arg="scale" name="scale" port_type="basic:String">
+ <docstring>Use a linear or log10 scale on the vertical axis.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['linear', 'log']]</values>
+ </inputPortSpec>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="-1" property_type="matplotlib.collections.PolyCollection" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.hist" name="MplHist" output_type="tuple" superclass="MplPlot">
+ <docstring>Plot a histogram.
+
+Call signature:
+
+hist(x, bins=10, range=None, normed=False, weights=None, cumulative=False, bottom=None, histtype='bar', align='mid', orientation='vertical', rwidth=None, log=False, color=None, label=None, stacked=False, **kwargs)
+
+Compute and draw the histogram of x. The return value is a tuple (n, bins, patches) or ([n0, n1, ...], bins, [patches0, patches1,...]) if the input contains multiple data.
+
+Multiple data can be provided via x as a list of datasets of potentially different length ([x0, x1, ...]), or as a 2-D ndarray in which each column is a dataset. Note that the ndarray form is transposed relative to the list form.
+
+Masked arrays are not supported at present.
+
+Keyword arguments:
+
+
+
+kwargs are used to update the properties of the :class:`~matplotlib.patches.Patch` instances returned by hist:
+
+%(Patch)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="rwidth" arg_pos="10" name="rwidth">
+ <docstring>The relative width of the bars as a fraction of the bin width. If None, automatically compute the width. Ignored if histtype = 'step' or 'stepfilled'.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="normed" arg_pos="3" name="normed" port_type="basic:Boolean">
+ <docstring>If True, the first element of the return tuple will be the counts normalized to form a probability density, i.e., n/(len(x)*dbin). In a probability density, the integral of the histogram should be 1; you can verify that with a trapezoidal integration of the probability density function:
+
+pdf, bins, patches = ax.hist(...) print np.sum(pdf * np.diff(bins))
+
+Until numpy release 1.5, the underlying numpy histogram function was incorrect with normed*=*True if bin sizes were unequal. MPL inherited that error. It is now corrected within MPL when using earlier numpy versions</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="stacked" arg_pos="14" name="stacked" port_type="basic:Boolean">
+ <docstring>If True, multiple data are stacked on top of each other If False multiple data are aranged side by side if histtype is 'bar' or on top of each other if histtype is 'step'
+
+.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="orientation" arg_pos="9" name="orientation" port_type="basic:String">
+ <docstring>If 'horizontal', :func:`~matplotlib.pyplot.barh` will be used for bar-type histograms and the bottom kwarg will be the left edges.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['horizontal', 'vertical']]</values>
+ <defaults>['vertical']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="bottom" arg_pos="6" name="bottom" />
+ <inputPortSpec arg="color" arg_pos="12" name="colorSequence" port_type="basic:List">
+ <docstring>Color spec or sequence of color specs, one per dataset. Default (None) uses the standard line color sequence.</docstring>
+ <alternateSpec arg="color" name="colorScalar" port_type="basic:Color">
+ <translations>translate_color</translations>
+ </alternateSpec>
+ </inputPortSpec>
+ <inputPortSpec arg="histtype" arg_pos="7" name="histtype" port_type="basic:String">
+ <docstring>The type of histogram to draw.
+
+'bar' is a traditional bar-type histogram. If multiple data are given the bars are aranged side by side.
+
+'barstacked' is a bar-type histogram where multiple data are stacked on top of each other.
+
+'step' generates a lineplot that is by default unfilled.
+
+'stepfilled' generates a lineplot that is by default filled.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['bar', 'barstacked', 'step', 'stepfilled']]</values>
+ <defaults>['bar']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="align" arg_pos="8" name="align" port_type="basic:String">
+ <docstring>Controls how the histogram is plotted.
+
+'left': bars are centered on the left bin edges.
+
+'mid': bars are centered between the bin edges.
+
+'right': bars are centered on the right bin edges.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['left', 'mid', 'right']]</values>
+ <defaults>['mid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cumulative" arg_pos="5" name="cumulative" port_type="basic:Boolean">
+ <docstring>If True, then a histogram is computed where each bin gives the counts in that bin plus all bins for smaller values. The last bin gives the total number of datapoints. If normed is also True then the histogram is normalized such that the last bin equals 1. If cumulative evaluates to less than 0 (e.g. -1), the direction of accumulation is reversed. In this case, if normed is also True, then the histogram is normalized such that the first bin equals 1.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label" arg_pos="13" name="labelSequence" port_type="basic:List">
+ <docstring>String, or sequence of strings to match multiple datasets. Bar charts yield multiple patches per dataset, but only the first gets the label, so that the legend command will work as expected:
+
+ax.hist(10+2*np.random.randn(1000), label='men') ax.hist(12+3*np.random.randn(1000), label='women', alpha=0.5) ax.legend()</docstring>
+ <alternateSpec arg="label" name="labelScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="range" arg_pos="2" name="range" port_type="basic:List">
+ <docstring>The lower and upper range of the bins. Lower and upper outliers are ignored. If not provided, range is (x.min(), x.max()). Range has no effect if bins is a sequence.
+
+If bins is a sequence or range is specified, autoscaling is based on the specified bin range instead of the range of x.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="weights" arg_pos="4" name="weights">
+ <docstring>An array of weights, of the same shape as x. Each value in x only contributes its associated weight towards the bin count (instead of 1). If normed is True, the weights are normalized, so that the integral of the density over the range remains 1.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="15" name="hold" />
+ <inputPortSpec arg="bins" arg_pos="1" name="bins" port_type="basic:Integer">
+ <docstring>Either an integer number of bins or a sequence giving the bins. If bins is an integer, bins + 1 bin edges will be returned, consistent with :func:`numpy.histogram` for numpy version >= 1.3, and with the new = True argument in earlier versions. Unequally spaced bins are supported if bins is a sequence.</docstring>
+ <defaults>['10']</defaults>
+ <alternateSpec arg="bins" name="binsSequence" port_type="basic:List" />
+ </inputPortSpec>
+ <inputPortSpec arg="log" arg_pos="11" name="log" port_type="basic:Boolean">
+ <docstring>If True, the histogram axis will be set to a log scale. If log is True and x is a 1D array, empty bins will be filtered out and only the non-empty (n, bins, patches) will be returned.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <outputPortSpec arg="rectangle" compute_name="rectangles" name="rectangleProperties" plural="True" port_type="__property__" property_key="2" property_type="matplotlib.patches.Rectangle" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.hist2d" name="MplHist2d" superclass="MplPlot">
+ <docstring>Make a 2D histogram plot.
+
+Call signature:
+
+hist2d(x, y, bins = None, range=None, weights=None, cmin=None, cmax=None **kwargs)
+
+Make a 2d histogram plot of x versus y, where x, y are 1-D sequences of the same length.
+
+The return value is (counts, xedges, yedges, Image).
+
+Optional keyword arguments: bins: [None | int | [int, int] | array_like | [array, array]]
+
+The bin specification:
+
+If int, the number of bins for the two dimensions (nx=ny=bins).
+
+If [int, int], the number of bins in each dimension (nx, ny = bins).
+
+If array_like, the bin edges for the two dimensions (x_edges=y_edges=bins).
+
+If [array, array], the bin edges in each dimension (x_edges, y_edges = bins).
+
+The default value is 10.
+
+Remaining keyword arguments are passed directly to :meth:`pcolorfast`.
+
+Rendering the histogram with a logarithmic color scale is accomplished by passing a :class:`colors.LogNorm` instance to the norm keyword argument.
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="normed" arg_pos="4" name="normed" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmin" arg_pos="6" name="cmin" />
+ <inputPortSpec arg="range" arg_pos="3" name="range" />
+ <inputPortSpec arg="weights" arg_pos="5" name="weights" />
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="8" name="hold" />
+ <inputPortSpec arg="cmax" arg_pos="7" name="cmax" />
+ <inputPortSpec arg="bins" arg_pos="2" name="bins" port_type="basic:Integer">
+ <defaults>['10']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.hlines" name="MplHlines" output_type="object" superclass="MplPlot">
+ <docstring>Plot horizontal lines.
+
+call signature:
+
+hlines(y, xmin, xmax, colors='k', linestyles='solid', **kwargs)
+
+Plot horizontal lines at each y from xmin to xmax.
+
+Returns the :class:`~matplotlib.collections.LineCollection` that was added.
+
+Required arguments:
+
+
+
+Optional keyword arguments:
+
+
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="linestyles" arg_pos="4" name="linestyles" port_type="basic:String">
+ <docstring>[ 'solid' | 'dashed' | 'dashdot' | 'dotted' ]</docstring>
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label" arg_pos="5" name="label" port_type="basic:String">
+ <defaults>['']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xmin" arg_pos="1" name="xminScalar" port_type="basic:Float" required="True">
+ <docstring>can be scalars or len(x) numpy arrays. If they are scalars, then the respective values are constant, else the widths of the lines are determined by xmin and xmax.</docstring>
+ <alternateSpec arg="xmin" name="xminSequence" port_type="basic:List" />
+ </inputPortSpec>
+ <inputPortSpec arg="colors" arg_pos="3" name="colorsSequence" port_type="basic:List">
+ <docstring>a line collections color argument, either a single color or a len(y) list of colors</docstring>
+ <defaults>['k']</defaults>
+ <alternateSpec arg="colors" name="colorsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="xmax" arg_pos="2" name="xmaxScalar" port_type="basic:Float" required="True">
+ <docstring>can be scalars or len(x) numpy arrays. If they are scalars, then the respective values are constant, else the widths of the lines are determined by xmin and xmax.</docstring>
+ <alternateSpec arg="xmax" name="xmaxSequence" port_type="basic:List" />
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="0" name="y" port_type="basic:List" required="True">
+ <docstring>a 1-D numpy array or iterable.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="6" name="hold" />
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.collections.LineCollection" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.imshow" name="MplImshow" superclass="MplPlot">
+ <docstring>Display an image on the axes.
+
+Call signature:
+
+imshow(X, cmap=None, norm=None, aspect=None, interpolation=None, alpha=None, vmin=None, vmax=None, origin=None, extent=None, **kwargs)
+
+Display the image in X to current axes. X may be a float array, a uint8 array or a PIL image. If X is an array, X can have the following shapes:
+
+MxN -- luminance (grayscale, float array only)
+
+MxNx3 -- RGB (float or uint8 array)
+
+MxNx4 -- RGBA (float or uint8 array)
+
+The value for each component of MxNx3 and MxNx4 float arrays should be in the range 0.0 to 1.0; MxN float arrays may be normalised.
+
+An :class:`matplotlib.image.AxesImage` instance is returned.
+
+Keyword arguments:
+
+interpolation:
+
+Acceptable values are None, 'none', 'nearest', 'bilinear', 'bicubic', 'spline16', 'spline36', 'hanning', 'hamming', 'hermite', 'kaiser', 'quadric', 'catrom', 'gaussian', 'bessel', 'mitchell', 'sinc', 'lanczos'
+
+If interpolation is None, default to rc image.interpolation. See also the filternorm and filterrad parameters
+
+If interpolation is 'none', then no interpolation is performed on the Agg, ps and pdf backends. Other backends will fall back to 'nearest'.
+
+Additional kwargs are :class:`~matplotlib.artist.Artist` properties:
+
+%(Artist)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="origin" arg_pos="8" name="origin" />
+ <inputPortSpec arg="imlim" arg_pos="13" name="imlim" />
+ <inputPortSpec arg="extent" arg_pos="9" name="extent" />
+ <inputPortSpec arg="vmin" arg_pos="6" name="vmin" />
+ <inputPortSpec arg="url" arg_pos="15" name="url" />
+ <inputPortSpec arg="resample" arg_pos="14" name="resample" />
+ <inputPortSpec arg="shape" arg_pos="10" name="shape" />
+ <inputPortSpec arg="cmap" arg_pos="1" name="cmap" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Colormap` instance, eg. cm.jet. If None, default to rc image.cmap value.
+
+cmap is ignored when X has RGB(A) information</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="filterrad" arg_pos="12" name="filterrad" port_type="basic:Float">
+ <defaults>['4.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="filternorm" arg_pos="11" name="filternorm" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="aspect" arg_pos="3" name="aspect">
+ <docstring>If 'auto', changes the image aspect ratio to match that of the axes
+
+If 'equal', and extent is None, changes the axes aspect ratio to match that of the image. If extent is not None, the axes aspect ratio is changed to match that of the extent.
+
+If None, default to rc image.aspect value.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'auto', 'equal']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" arg_pos="5" name="alpha" />
+ <inputPortSpec arg="vmax" arg_pos="7" name="vmax" />
+ <inputPortSpec arg="X" arg_pos="0" name="X" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="16" name="hold" />
+ <inputPortSpec arg="norm" arg_pos="2" name="norm" />
+ <inputPortSpec arg="interpolation" arg_pos="4" name="interpolation" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.loglog" name="MplLoglog" output_type="object" superclass="MplPlot">
+ <docstring>Make a plot with log scaling on both the x and y axis.
+
+Call signature:
+
+loglog(*args, **kwargs)
+
+:func:`~matplotlib.pyplot.loglog` supports all the keyword arguments of :func:`~matplotlib.pyplot.plot` and :meth:`matplotlib.axes.Axes.set_xscale` / :meth:`matplotlib.axes.Axes.set_yscale`.
+
+Notable keyword arguments:
+
+
+
+The remaining valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="nonposx" name="nonposx" port_type="basic:String">
+ <docstring>Non-positive values in x or y can be masked as invalid, or clipped to a very small positive number</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['mask', 'clip']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="nonposy" name="nonposy" port_type="basic:String">
+ <docstring>Non-positive values in x or y can be masked as invalid, or clipped to a very small positive number</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['mask', 'clip']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="basex" name="basex" port_type="basic:Float">
+ <docstring>Base of the x/y logarithm</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="basey" name="basey" port_type="basic:Float">
+ <docstring>Base of the x/y logarithm</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="subsx" name="subsxSequence" port_type="basic:List">
+ <docstring>The location of the minor x/y ticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`matplotlib.axes.Axes.set_xscale` / :meth:`matplotlib.axes.Axes.set_yscale` for details</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="subsx" name="subsxScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="subsy" name="subsySequence" port_type="basic:List">
+ <docstring>The location of the minor x/y ticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`matplotlib.axes.Axes.set_xscale` / :meth:`matplotlib.axes.Axes.set_yscale` for details</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="subsy" name="subsyScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" required="True" />
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.pcolor" name="MplPcolor" output_type="object" superclass="MplPlot">
+ <docstring>Create a pseudocolor plot of a 2-D array.
+
+Note: pcolor can be very slow for large arrays; consider using the similar but much faster :func:`~matplotlib.pyplot.pcolormesh` instead.
+
+Call signatures:
+
+pcolor(C, **kwargs) pcolor(X, Y, C, **kwargs)
+
+C is the array of color values.
+
+X and Y, if given, specify the (x, y) coordinates of the colored quadrilaterals; the quadrilateral for C[i,j] has corners at:
+
+(X[i, j], Y[i, j]), (X[i, j+1], Y[i, j+1]), (X[i+1, j], Y[i+1, j]), (X[i+1, j+1], Y[i+1, j+1]).
+
+Ideally the dimensions of X and Y should be one greater than those of C; if the dimensions are the same, then the last row and column of C will be ignored.
+
+Note that the the column index corresponds to the x-coordinate, and the row index corresponds to y; for details, see the :ref:`Grid Orientation <axes-pcolor-grid-orientation>` section below.
+
+If either or both of X and Y are 1-D arrays or column vectors, they will be expanded as needed into the appropriate 2-D arrays, making a rectangular grid.
+
+X, Y and C may be masked arrays. If either C[i, j], or one of the vertices surrounding C[i,j] (X or Y at [i, j], [i+1, j], [i, j+1],[i+1, j+1]) is masked, nothing is plotted.
+
+Keyword arguments:
+
+
+
+Return value is a :class:`matplotlib.collections.Collection` instance.
+
+The grid orientation follows the MATLAB convention: an array C with shape (nrows, ncolumns) is plotted with the column number as X and the row number as Y, increasing up; hence it is plotted the way the array would be printed, except that the Y axis is reversed. That is, C is taken as C*(*y, x).
+
+Similarly for :func:`meshgrid`:
+
+x = np.arange(5) y = np.arange(3) X, Y = meshgrid(x,y)
+
+is equivalent to:
+
+X = array([[0, 1, 2, 3, 4], [0, 1, 2, 3, 4], [0, 1, 2, 3, 4]]) Y = array([[0, 0, 0, 0, 0], [1, 1, 1, 1, 1], [2, 2, 2, 2, 2]])
+
+so if you have:
+
+C = rand( len(x), len(y))
+
+then you need:
+
+pcolor(X, Y, C.T)
+
+or:
+
+pcolor(C.T)
+
+MATLAB :func:`pcolor` always discards the last row and column of C, but matplotlib displays the last row and column if X and Y are not specified, or if X and Y have one more row and column than C.
+
+kwargs can be used to control the :class:`~matplotlib.collections.PolyCollection` properties:
+
+%(PolyCollection)s
+
+Note: the default antialiaseds is False if the default edgecolors*="none" is used. This eliminates artificial lines at patch boundaries, and works regardless of the value of alpha. If *edgecolors is not "none", then the default antialiaseds is taken from rcParams['patch.antialiased'], which defaults to True. Stroking the edges may be preferred if alpha is 1, but will cause artifacts otherwise.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="edgecolors" name="edgecolorsSequence" port_type="basic:List">
+ <docstring>If None, the rc setting is used by default.
+
+If 'none', edges will not be visible.
+
+An mpl color or sequence of colors will set the edge color</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'none', 'color']]</values>
+ <alternateSpec arg="edgecolors" name="edgecolorsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" name="vmin">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Colormap` instance. If None, use rc settings.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>the alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="vmax" name="vmax">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="shading" name="shading" port_type="basic:String">
+ <docstring>If 'faceted', a black grid is drawn around each rectangle; if 'flat', edges are not drawn. Default is 'flat', contrary to MATLAB.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['flat', 'faceted']]</values>
+ <defaults>['flat']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>An :class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0,1. If None, defaults to :func:`normalize`.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="Y" arg_pos="1" in_args="True" name="Y" port_type="basic:List" />
+ <inputPortSpec arg="X" arg_pos="0" in_args="True" name="X" port_type="basic:List" />
+ <inputPortSpec arg="Z" arg_pos="2" in_args="True" name="Z" port_type="basic:List" required="True" />
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="0" property_type="matplotlib.collections.PolyCollection" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.pcolormesh" name="MplPcolormesh" superclass="MplPlot">
+ <docstring>Plot a quadrilateral mesh.
+
+Call signatures:
+
+pcolormesh(C) pcolormesh(X, Y, C) pcolormesh(C, **kwargs)
+
+Create a pseudocolor plot of a 2-D array.
+
+pcolormesh is similar to :func:`~matplotlib.pyplot.pcolor`, but uses a different mechanism and returns a different object; pcolor returns a :class:`~matplotlib.collections.PolyCollection` but pcolormesh returns a :class:`~matplotlib.collections.QuadMesh`. It is much faster, so it is almost always preferred for large arrays.
+
+C may be a masked array, but X and Y may not. Masked array support is implemented via cmap and norm; in contrast, :func:`~matplotlib.pyplot.pcolor` simply does not draw quadrilaterals with masked colors or vertices.
+
+Keyword arguments:
+
+
+
+Return value is a :class:`matplotlib.collections.QuadMesh` object.
+
+kwargs can be used to control the :class:`matplotlib.collections.QuadMesh` properties:
+
+%(QuadMesh)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="edgecolors" name="edgecolorsSequence" port_type="basic:List">
+ <docstring>If None, the rc setting is used by default.
+
+If 'None', edges will not be visible.
+
+If 'face', edges will have the same color as the faces.
+
+An mpl color or sequence of colors will set the edge color</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'None', 'face', 'color']]</values>
+ <alternateSpec arg="edgecolors" name="edgecolorsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" name="vmin">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Colormap` instance. If None, use rc settings.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>the alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="vmax" name="vmax">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="shading" name="shading" port_type="basic:String">
+ <docstring>'flat' indicates a solid color for each quad. When 'gouraud', each quad will be Gouraud shaded. When gouraud shading, edgecolors is ignored.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['flat', 'gouraud']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0,1. If None, defaults to :func:`normalize`.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.pie" name="MplPie" output_type="tuple" superclass="MplPlot">
+ <docstring>Plot a pie chart.
+
+Call signature:
+
+pie(x, explode=None, labels=None, colors=('b', 'g', 'r', 'c', 'm', 'y', 'k', 'w'), autopct=None, pctdistance=0.6, shadow=False, labeldistance=1.1, startangle=None, radius=None)
+
+Make a pie chart of array x. The fractional area of each wedge is given by x/sum(x). If sum(x) <= 1, then the values of x give the fractional area directly and the array will not be normalized. The wedges are plotted counterclockwise, by default starting from the x-axis.
+
+Keyword arguments:
+
+radius: [ None | scalar ] The radius of the pie, if radius is None it will be set to 1.
+
+The pie chart will probably look best if the figure and axes are square. Eg.:
+
+figure(figsize=(8,8)) ax = axes([0.1, 0.1, 0.8, 0.8])
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="autopct" arg_pos="4" name="autopct" port_type="basic:String">
+ <docstring>If not None, is a string or function used to label the wedges with their numeric value. The label will be placed inside the wedge. If it is a format string, the label will be fmt%pct. If it is a function, it will be called.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'format function']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="pctdistance" arg_pos="5" name="pctdistance" port_type="basic:Float">
+ <docstring>The ratio between the center of each pie slice and the start of the text generated by autopct. Ignored if autopct is None; default is 0.6.</docstring>
+ <defaults>['0.6']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="labels" arg_pos="2" name="labelsSequence" port_type="basic:List">
+ <docstring>A sequence of strings providing the labels for each wedge</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="labels" name="labelsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="explode" arg_pos="1" name="explodeSequence" port_type="basic:List">
+ <docstring>If not None, is a len(x) array which specifies the fraction of the radius with which to offset each wedge.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="explode" name="explodeScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="colors" arg_pos="3" name="colors" port_type="basic:Color">
+ <docstring>A sequence of matplotlib color args through which the pie chart will cycle.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <defaults>None</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="radius" arg_pos="9" name="radius" />
+ <inputPortSpec arg="startangle" arg_pos="8" name="startangle" port_type="basic:String">
+ <docstring>If not None, rotates the start of the pie chart by angle degrees counterclockwise from the x-axis.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Offset angle']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="shadow" arg_pos="6" name="shadow" port_type="basic:Boolean">
+ <docstring>Draw a shadow beneath the pie.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="10" name="hold" />
+ <inputPortSpec arg="labeldistance" arg_pos="7" name="labeldistance" port_type="basic:Float">
+ <docstring>The radial distance at which the pie labels are drawn</docstring>
+ <defaults>['1.1']</defaults>
+ </inputPortSpec>
+ <outputPortSpec arg="autotext" compute_name="autotexts" name="autotextProperties" plural="True" port_type="__property__" property_key="2" property_type="matplotlib.text.Text" />
+ <outputPortSpec arg="wedge" compute_name="wedges" name="wedgeProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.patches.Wedge" />
+ <outputPortSpec arg="text" compute_name="texts" name="textProperties" plural="True" port_type="__property__" property_key="1" property_type="matplotlib.text.Text" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.plot_date" name="MplPlotDate" output_type="object" superclass="MplPlot">
+ <docstring>Plot with data with dates.
+
+Call signature:
+
+plot_date(x, y, fmt='bo', tz=None, xdate=True, ydate=False, **kwargs)
+
+Similar to the :func:`~matplotlib.pyplot.plot` command, except the x or y (or both) data is considered to be dates, and the axis is labeled accordingly.
+
+x and/or y can be a sequence of dates represented as float days since 0001-01-01 UTC.
+
+Keyword arguments:
+
+
+
+Note if you are using custom date tickers and formatters, it may be necessary to set the formatters/locators after the call to :meth:`plot_date` since :meth:`plot_date` will set the default tick locator to :class:`matplotlib.dates.AutoDateLocator` (if the tick locator is not already set to a :class:`matplotlib.dates.DateLocator` instance) and the default tick formatter to :class:`matplotlib.dates.AutoDateFormatter` (if the tick formatter is not already set to a :class:`matplotlib.dates.D [...]
+
+Valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="tz" arg_pos="3" name="tz" port_type="basic:String">
+ <docstring>The time zone to use in labeling dates. If None, defaults to rc value.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', ':class:`tzinfo` instance']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="fmt" arg_pos="2" name="fmt" port_type="basic:String">
+ <docstring>The plot format string.</docstring>
+ <defaults>['bo']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ydate" arg_pos="5" name="ydate" port_type="basic:Boolean">
+ <docstring>If True, the y-axis will be labeled with dates.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xdate" arg_pos="4" name="xdate" port_type="basic:Boolean">
+ <docstring>If True, the x-axis will be labeled with dates.</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="6" name="hold" />
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.psd" name="MplPsd" superclass="MplPlot">
+ <docstring>Plot the power spectral density.
+
+Call signature:
+
+psd(x, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none, window=mlab.window_hanning, noverlap=0, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+The power spectral density by Welch's average periodogram method. The vector x is divided into NFFT length segments. Each segment is detrended by function detrend and windowed by function window. noverlap gives the length of the overlap between segments. The |\mathrm{fft}(i)|^2 of each segment i are averaged to compute Pxx, with a scaling to correct for power loss due to windowing. Fs is the sampling frequency.
+
+%(PSD)s
+
+
+
+Returns the tuple (Pxx, freqs).
+
+For plotting, the power is plotted as 10\log_{10}(P_{xx}) for decibels, though Pxx itself is returned.
+
+kwargs control the :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="Fs" arg_pos="2" name="Fs" port_type="basic:Integer">
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pad_to" arg_pos="7" name="pad_to" />
+ <inputPortSpec arg="scale_by_freq" arg_pos="9" name="scale_by_freq" />
+ <inputPortSpec arg="detrend" arg_pos="4" name="detrend">
+ <defaults>['<function detrend_none at 0x02F5A3F0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="window" arg_pos="5" name="window">
+ <defaults>['<function window_hanning at 0x02F5A2B0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="Fc" arg_pos="3" name="Fc" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="NFFT" arg_pos="1" name="NFFT" port_type="basic:Integer">
+ <defaults>['256']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="10" name="hold" />
+ <inputPortSpec arg="sides" arg_pos="8" name="sides" port_type="basic:String">
+ <defaults>['default']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="noverlap" arg_pos="6" name="noverlap" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="line" constructor_arg="True" name="lineProperties" port_type="__property__" property_type="matplotlib.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.quiver" name="MplQuiver" output_type="object" superclass="MplPlot">
+ <docstring>Plot a 2-D field of arrows.
+
+call signatures:
+
+quiver(U, V, **kw) quiver(U, V, C, **kw) quiver(X, Y, U, V, **kw) quiver(X, Y, U, V, C, **kw)
+
+Arguments:
+
+
+
+All arguments may be 1-D or 2-D arrays or sequences. If X and Y are absent, they will be generated as a uniform grid. If U and V are 2-D arrays but X and Y are 1-D, and if len(X) and len(Y) match the column and row dimensions of U, then X and Y will be expanded with :func:`numpy.meshgrid`.
+
+U, V, C may be masked arrays, but masked X, Y are not supported at present.
+
+Keyword arguments:
+
+
+
+The defaults give a slightly swept-back arrow; to make the head a triangle, make headaxislength the same as headlength. To make the arrow more pointed, reduce headwidth or increase headlength and headaxislength. To make the head smaller relative to the shaft, scale down all the head parameters. You will probably do best to leave minshaft alone.
+
+linewidths and edgecolors can be used to customize the arrow outlines. Additional :class:`~matplotlib.collections.PolyCollection` keyword arguments:
+
+agg_filter: unknown alpha: float or None animated: [True | False] antialiased or antialiaseds: Boolean or sequence of booleans array: unknown axes: an :class:`~matplotlib.axes.Axes` instance clim: a length 2 sequence of floats clip_box: a :class:`matplotlib.transforms.Bbox` instance clip_on: [True | False] clip_path: [ (:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`) | :class:`~matplotlib.patches.Patch` | None ] cmap: a colormap or registered co [...]
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="headaxislength" name="headaxislength" port_type="basic:Float">
+ <docstring>Head length at shaft intersection, default is 4.5</docstring>
+ <defaults>['4.5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="C" arg_pos="4" in_args="True" name="C" port_type="basic:List">
+ <docstring>None</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="scale" name="scale">
+ <docstring>Data units per arrow length unit, e.g. m/s per plot width; a smaller scale parameter makes the arrow longer. If None, a simple autoscaling algorithm is used, based on the average vector length and the number of vectors. The arrow length unit is given by the scale_units parameter</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="width" name="width" port_type="basic:List">
+ <docstring>Shaft width in arrow units; default depends on choice of units, above, and number of vectors; a typical starting value is about 0.005 times the width of the plot.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="headlength" name="headlength" port_type="basic:Float">
+ <docstring>Head length as multiple of shaft width, default is 5</docstring>
+ <defaults>['5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="minlength" name="minlength" port_type="basic:Float">
+ <docstring>Minimum length as a multiple of shaft width; if an arrow length is less than this, plot a dot (hexagon) of this diameter instead. Default is 1.</docstring>
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="minshaft" name="minshaft" port_type="basic:Float">
+ <docstring>Length below which arrow scales, in units of head length. Do not set this to less than 1, or small arrows will look terrible! Default is 1</docstring>
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pivot" name="pivot" port_type="basic:String">
+ <docstring>The part of the arrow that is at the grid point; the arrow rotates about this point, hence the name pivot.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['tail', 'middle', 'tip']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="units" name="unitsSequence" port_type="basic:List">
+ <docstring>For example, if scale_units is 'inches', scale is 2.0, and (u,v) = (1,0), then the vector will be 0.5 inches long. If scale_units is 'width', then the vector will be half the width of the axes.
+
+If scale_units is 'x' then the vector will be 0.5 x-axis units. To plot vectors in the x-y plane, with u and v having the same units as x and y, use "angles='xy', scale_units='xy', scale=1".</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['width', 'height', 'dots', 'inches', 'x', 'y', 'xy']]</values>
+ <alternateSpec arg="units" name="unitsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="headwidth" name="headwidth" port_type="basic:Float">
+ <docstring>Head width as multiple of shaft width, default is 3</docstring>
+ <defaults>['3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="U" arg_pos="2" in_args="True" name="U" port_type="basic:List" required="True">
+ <docstring>None</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="angles" name="angles" port_type="basic:String">
+ <docstring>With the default 'uv', the arrow aspect ratio is 1, so that if U*==*V the angle of the arrow on the plot is 45 degrees CCW from the x-axis. With 'xy', the arrow points from (x,y) to (x+u, y+v). Alternatively, arbitrary angles may be specified as an array of values in degrees, CCW from the x-axis.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['uv', 'xy', 'array']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="V" arg_pos="3" in_args="True" name="V" port_type="basic:List" required="True">
+ <docstring>None</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="Y" arg_pos="1" in_args="True" name="Y" port_type="basic:List">
+ <docstring>None</docstring>
+ <defaults>None</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="X" arg_pos="0" in_args="True" name="X" port_type="basic:List">
+ <docstring>None</docstring>
+ <defaults>None</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="scale_units" name="scale_units" port_type="basic:List">
+ <docstring>For example, if scale_units is 'inches', scale is 2.0, and (u,v) = (1,0), then the vector will be 0.5 inches long. If scale_units is 'width', then the vector will be half the width of the axes.
+
+If scale_units is 'x' then the vector will be 0.5 x-axis units. To plot vectors in the x-y plane, with u and v having the same units as x and y, use "angles='xy', scale_units='xy', scale=1".</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="colorSequence" port_type="basic:List">
+ <docstring>This is a synonym for the :class:`~matplotlib.collections.PolyCollection` facecolor kwarg. If C has been set, color has no effect.</docstring>
+ <alternateSpec arg="color" name="colorScalar" port_type="basic:String">
+ <translations>translate_color</translations>
+ </alternateSpec>
+ </inputPortSpec>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="0" property_type="matplotlib.collections.PolyCollection" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.quiverkey" name="MplQuiverkey" superclass="MplPlot">
+ <docstring>Add a key to a quiver plot.
+
+Call signature:
+
+quiverkey(Q, X, Y, U, label, **kw)
+
+Arguments:
+
+
+
+Keyword arguments:
+
+
+
+Any additional keyword arguments are used to override vector properties taken from Q.
+
+The positioning of the key depends on X, Y, coordinates, and labelpos. If labelpos is 'N' or 'S', X, Y give the position of the middle of the key arrow. If labelpos is 'E', X, Y positions the head, and if labelpos is 'W', X, Y positions the tail; in either of these two cases, X, Y is somewhere in the middle of the arrow+label key object.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>overrides face and edge colors from Q.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="coordinates" name="coordinatesSequence" port_type="basic:List">
+ <docstring>Coordinate system and units for X, Y: 'axes' and 'figure' are normalized coordinate systems with 0,0 in the lower left and 1,1 in the upper right; 'data' are the axes data coordinates (used for the locations of the vectors in the quiver plot itself); 'inches' is position in the figure in inches, with 0,0 at the lower left corner.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['axes', 'figure', 'data', 'inches']]</values>
+ <alternateSpec arg="coordinates" name="coordinatesScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="label" arg_pos="4" name="label" port_type="basic:String" required="True">
+ <docstring>A string with the length and units of the key</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="Q" arg_pos="0" name="Q" required="True">
+ <docstring>The Quiver instance returned by a call to quiver.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="labelcolor" name="labelcolor" port_type="basic:Color">
+ <docstring>defaults to default :class:`~matplotlib.text.Text` color.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="fontproperties" name="fontproperties">
+ <docstring>A dictionary with keyword arguments accepted by the :class:`~matplotlib.font_manager.FontProperties` initializer: family, style, variant, size, weight</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="U" arg_pos="3" name="U" required="True">
+ <docstring>The length of the key</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="labelpos" name="labelpos" port_type="basic:String">
+ <docstring>Position the label above, below, to the right, to the left of the arrow, respectively.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['N', 'S', 'E', 'W']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="Y" arg_pos="2" name="Y" required="True">
+ <docstring>The location of the key; additional explanation follows.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="X" arg_pos="1" name="X" required="True">
+ <docstring>The location of the key; additional explanation follows.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="labelsep" name="labelsep" port_type="basic:Float">
+ <docstring>Distance in inches between the arrow and the label. Default is 0.1</docstring>
+ <defaults>['0.1']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.scatter" name="MplScatter" output_type="object" superclass="MplPlot">
+ <docstring>Make a scatter plot.
+
+Call signatures:
+
+scatter(x, y, s=20, c='b', marker='o', cmap=None, norm=None, vmin=None, vmax=None, alpha=None, linewidths=None, verts=None, **kwargs)
+
+Make a scatter plot of x versus y, where x, y are converted to 1-D sequences which must be of the same length, N.
+
+Keyword arguments:
+
+
+
+Any or all of x, y, s, and c may be masked arrays, in which case all masks will be combined and only unmasked points will be plotted.
+
+Other keyword arguments: the color mapping and normalization arguments will be used only if c is an array of floats.
+
+
+
+Optional kwargs control the :class:`~matplotlib.collections.Collection` properties; in particular:
+
+
+
+Here are the standard descriptions of all the :class:`~matplotlib.collections.Collection` kwargs:
+
+%(Collection)s
+
+A :class:`~matplotlib.collections.Collection` instance is returned.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="vmax" arg_pos="8" name="vmax">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="edgecolors" name="edgecolors" port_type="basic:String">
+ <docstring>The string 'none' to plot faces with no outlines</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="c" arg_pos="3" name="cSequence" port_type="basic:List">
+ <docstring>a color. c can be a single color format string, or a sequence of color specifications of length N, or a sequence of N numbers to be mapped to colors using the cmap and norm specified via kwargs (see below). Note that c should not be a single numeric RGB or RGBA sequence because that is indistinguishable from an array of values to be colormapped. c can be a 2-D array in which the rows are RGB or RGBA, however.</docstring>
+ <defaults>['b']</defaults>
+ <alternateSpec arg="c" name="cScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" arg_pos="7" name="vmin">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="faceted" arg_pos="11" name="faceted" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" arg_pos="10" name="linewidths">
+ <docstring>If None, defaults to (lines.linewidth,). Note that this is a tuple, and if you set the linewidths argument you must set it as a sequence of floats, as required by :class:`~matplotlib.collections.RegularPolyCollection`.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="marker" arg_pos="4" name="marker" port_type="basic:String">
+ <docstring>can be one of:
+
+%(MarkerTable)s</docstring>
+ <defaults>['o']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="s" arg_pos="2" name="s" port_type="basic:Float">
+ <docstring>size in points^2. It is a scalar or an array of the same length as x and y.</docstring>
+ <defaults>['20']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="5" name="cmap">
+ <docstring>A :class:`matplotlib.colors.Colormap` instance or registered name. If None, defaults to rc image.cmap. cmap is only used if c is an array of floats.</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ </inputPortSpec>
+ <inputPortSpec arg="verts" arg_pos="12" name="verts" />
+ <inputPortSpec arg="alpha" arg_pos="9" name="alpha" port_type="basic:Float">
+ <docstring>The alpha value for the patches</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="13" name="hold" />
+ <inputPortSpec arg="facecolors" name="facecolors" port_type="basic:String">
+ <docstring>The string 'none' to plot unfilled outlines</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="6" name="norm">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0, 1. If None, use the default :func:`normalize`. norm is only used if c is an array of floats.</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ </inputPortSpec>
+ <outputPortSpec arg="pathCollection" compute_name="pathCollection" name="pathCollectionProperties" port_type="__property__" property_key="0" property_type="matplotlib.collections.PathCollection" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.semilogx" name="MplSemilogx" output_type="object" superclass="MplPlot">
+ <docstring>Make a plot with log scaling on the x axis.
+
+Call signature:
+
+semilogx(*args, **kwargs)
+
+:func:`semilogx` supports all the keyword arguments of :func:`~matplotlib.pyplot.plot` and :meth:`matplotlib.axes.Axes.set_xscale`.
+
+Notable keyword arguments:
+
+
+
+The remaining valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="basex" name="basex" port_type="basic:Float">
+ <docstring>Base of the x logarithm</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="nonposx" name="nonposx" port_type="basic:String">
+ <docstring>Non-positive values in x can be masked as invalid, or clipped to a very small positive number</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['mask', 'clip']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="subsx" name="subsxSequence" port_type="basic:List">
+ <docstring>The location of the minor xticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`~matplotlib.axes.Axes.set_xscale` for details.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="subsx" name="subsxScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.semilogy" name="MplSemilogy" output_type="object" superclass="MplPlot">
+ <docstring>Make a plot with log scaling on the y axis.
+
+call signature:
+
+semilogy(*args, **kwargs)
+
+:func:`semilogy` supports all the keyword arguments of :func:`~matplotlib.pylab.plot` and :meth:`matplotlib.axes.Axes.set_yscale`.
+
+Notable keyword arguments:
+
+
+
+The remaining valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="basey" name="basey" port_type="basic:Float">
+ <docstring>Base of the y logarithm</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="nonposy" name="nonposy" port_type="basic:String">
+ <docstring>Non-positive values in y can be masked as invalid, or clipped to a very small positive number</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['mask', 'clip']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="subsy" name="subsySequence" port_type="basic:List">
+ <docstring>The location of the minor yticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`~matplotlib.axes.Axes.set_yscale` for details.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="subsy" name="subsyScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" required="True" />
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.specgram" name="MplSpecgram" superclass="MplPlot">
+ <docstring>Plot a spectrogram.
+
+Call signature:
+
+specgram(x, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none, window=mlab.window_hanning, noverlap=128, cmap=None, xextent=None, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+Compute a spectrogram of data in x. Data are split into NFFT length segments and the PSD of each section is computed. The windowing function window is applied to each segment, and the amount of overlap of each segment is specified with noverlap.
+
+%(PSD)s
+
+kwargs:
+
+Additional kwargs are passed on to imshow which makes the specgram image
+
+Return value is (Pxx, freqs, bins, im):
+
+bins are the time points the spectrogram is calculated over
+
+freqs is an array of frequencies
+
+Pxx is an array of shape (len(times), len(freqs)) of power
+
+im is a :class:`~matplotlib.image.AxesImage` instance
+
+Note: If x is real (i.e. non-complex), only the positive spectrum is shown. If x is complex, both positive and negative parts of the spectrum are shown. This can be overridden using the sides keyword argument.
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="Fs" arg_pos="2" name="Fs" port_type="basic:Integer">
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pad_to" arg_pos="9" name="pad_to" />
+ <inputPortSpec arg="scale_by_freq" arg_pos="11" name="scale_by_freq" />
+ <inputPortSpec arg="xextent" arg_pos="8" name="xextent" />
+ <inputPortSpec arg="detrend" arg_pos="4" name="detrend">
+ <defaults>['<function detrend_none at 0x02F5A3F0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="window" arg_pos="5" name="window">
+ <defaults>['<function window_hanning at 0x02F5A2B0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="Fc" arg_pos="3" name="Fc" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="NFFT" arg_pos="1" name="NFFT" port_type="basic:Integer">
+ <defaults>['256']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="7" name="cmap" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="12" name="hold" />
+ <inputPortSpec arg="sides" arg_pos="10" name="sides" port_type="basic:String">
+ <defaults>['default']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="noverlap" arg_pos="6" name="noverlap" port_type="basic:Integer">
+ <defaults>['128']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.stackplot" name="MplStackplot" superclass="MplPlot">
+ <docstring>Draws a stacked area plot.
+
+x : 1d array of dimension N
+
+Keyword arguments:
+
+Returns r : A list of :class:`~matplotlib.collections.PolyCollection`, one for each element in the stacked area plot.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="x" arg_pos="0" name="x" required="True" />
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>used to colour the stacked areas. All other keyword arguments are passed to :func:`~matplotlib.Axes.fill_between`</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.stem" name="MplStem" output_type="tuple" superclass="MplPlot">
+ <docstring>Create a stem plot.
+
+Call signature:
+
+stem(x, y, linefmt='b-', markerfmt='bo', basefmt='r-')
+
+A stem plot plots vertical lines (using linefmt) at each x location from the baseline to y, and places a marker there using markerfmt. A horizontal line at 0 is is plotted using basefmt.
+
+Return value is a tuple (markerline, stemlines, baseline).
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="bottom" arg_pos="5" name="bottom" />
+ <inputPortSpec arg="label" arg_pos="6" name="label" />
+ <inputPortSpec arg="linefmt" arg_pos="2" name="linefmt" port_type="basic:String">
+ <defaults>['b-']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="markerfmt" arg_pos="3" name="markerfmt" port_type="basic:String">
+ <defaults>['bo']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="7" name="hold" />
+ <inputPortSpec arg="basefmt" arg_pos="4" name="basefmt" port_type="basic:String">
+ <defaults>['r-']</defaults>
+ </inputPortSpec>
+ <outputPortSpec arg="stemline" compute_name="stemlines" name="stemlineProperties" plural="True" port_type="__property__" property_key="1" property_type="matplotlib.lines.Line2D" />
+ <outputPortSpec arg="markerline" compute_name="markerline" name="markerlineProperties" port_type="__property__" property_key="0" property_type="matplotlib.lines.Line2D" />
+ <outputPortSpec arg="baseline" compute_name="baseline" name="baselineProperties" port_type="__property__" property_key="2" property_type="matplotlib.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.step" name="MplStep" output_type="object" superclass="MplPlot">
+ <docstring>Make a step plot.
+
+Call signature:
+
+step(x, y, *args, **kwargs)
+
+Additional keyword args to :func:`step` are the same as those for :func:`~matplotlib.pyplot.plot`.
+
+x and y must be 1-D sequences, and it is assumed, but not checked, that x is uniformly increasing.
+
+Keyword arguments:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="where" name="where" port_type="basic:String">
+ <docstring>If 'pre', the interval from x[i] to x[i+1] has level y[i+1]
+
+If 'post', that interval has level y[i]
+
+If 'mid', the jumps in y occur half-way between the x-values.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['pre', 'post', 'mid']]</values>
+ </inputPortSpec>
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.streamplot" name="MplStreamplot" superclass="MplPlot">
+ <docstring>Draws streamlines of a vector flow.
+
+Returns:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="hold" arg_pos="13" name="hold" />
+ <inputPortSpec arg="arrowstyle" arg_pos="10" name="arrowstyle" port_type="basic:String">
+ <defaults>['-|>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="density" arg_pos="4" name="density" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="6" name="color" />
+ <inputPortSpec arg="minlength" arg_pos="11" name="minlength" port_type="basic:Float">
+ <defaults>['0.1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="transform" arg_pos="12" name="transform" />
+ <inputPortSpec arg="arrowsize" arg_pos="9" name="arrowsize" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="7" name="cmap" />
+ <inputPortSpec arg="u" arg_pos="2" name="u" required="True" />
+ <inputPortSpec arg="v" arg_pos="3" name="v" required="True" />
+ <inputPortSpec arg="y" arg_pos="1" name="y" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" required="True" />
+ <inputPortSpec arg="linewidth" arg_pos="5" name="linewidth" />
+ <inputPortSpec arg="norm" arg_pos="8" name="norm" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.tricontour" name="MplTricontour" superclass="MplPlot">
+ <docstring>Draw contours on an unstructured triangular grid. :func:`~matplotlib.pyplot.tricontour` and :func:`~matplotlib.pyplot.tricontourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+The triangulation can be specified in one of two ways; either:
+
+tricontour(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+tricontour(x, y, ...) tricontour(x, y, triangles, ...) tricontour(x, y, triangles=triangles, ...) tricontour(x, y, mask=mask, ...) tricontour(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The remaining arguments may be:
+
+tricontour(..., Z)
+
+where Z is the array of values to contour, one per point in the triangulation. The level values are chosen automatically.
+
+tricontour(..., Z, N)
+
+contour N automatically-chosen levels.
+
+tricontour(..., Z, V)
+
+draw contour lines at the values specified in sequence V
+
+tricontourf(..., Z, V)
+
+fill the (len(V)-1) regions between the values in V
+
+tricontour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+C = tricontour(...) returns a :class:`~matplotlib.contour.TriContourSet` object.
+
+Optional keyword arguments:
+
+extent: [ None | (x0,x1,y0,y1) ]
+
+If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].
+
+This keyword is not active if X and Y are specified in the call to contour.
+
+tricontour-only keyword arguments:
+
+
+
+tricontourf-only keyword arguments:
+
+
+
+Note: tricontourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="origin" name="origin" port_type="basic:String">
+ <docstring>If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.
+
+This keyword is not active if X and Y are specified in the call to contour.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'upper', 'lower', 'image']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyles" name="linestyles" port_type="basic:String">
+ <docstring>If linestyles is None, the 'solid' is used.
+
+linestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.
+
+If contour is using a monochrome colormap and the contour level is less than 0, then the linestyle specified in contour.negative_linestyle in matplotlibrc will be used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'solid', 'dashed', 'dashdot', 'dotted']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="levels" name="levelsSequence" port_type="basic:List">
+ <docstring>A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]</docstring>
+ <alternateSpec arg="levels" name="levelsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" name="linewidths" port_type="basic:String">
+ <docstring>If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.
+
+If a number, all levels will be plotted with this linewidth.
+
+If a tuple, different levels will be plotted with different linewidths in the order specified</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'number', 'tuple of numbers']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>If None, the colormap specified by cmap will be used.
+
+If a string, like 'r' or 'red', all levels will be plotted in this color.
+
+If a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['', '(mpl_colors)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="antialiased" name="antialiased" port_type="basic:Boolean">
+ <docstring>enable antialiasing</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="nchunk" name="nchunk" port_type="basic:Integer">
+ <docstring>If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[[0]]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>The alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.tricontourf" name="MplTricontourf" superclass="MplPlot">
+ <docstring>Draw contours on an unstructured triangular grid. :func:`~matplotlib.pyplot.tricontour` and :func:`~matplotlib.pyplot.tricontourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+The triangulation can be specified in one of two ways; either:
+
+tricontour(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+tricontour(x, y, ...) tricontour(x, y, triangles, ...) tricontour(x, y, triangles=triangles, ...) tricontour(x, y, mask=mask, ...) tricontour(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The remaining arguments may be:
+
+tricontour(..., Z)
+
+where Z is the array of values to contour, one per point in the triangulation. The level values are chosen automatically.
+
+tricontour(..., Z, N)
+
+contour N automatically-chosen levels.
+
+tricontour(..., Z, V)
+
+draw contour lines at the values specified in sequence V
+
+tricontourf(..., Z, V)
+
+fill the (len(V)-1) regions between the values in V
+
+tricontour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+C = tricontour(...) returns a :class:`~matplotlib.contour.TriContourSet` object.
+
+Optional keyword arguments:
+
+extent: [ None | (x0,x1,y0,y1) ]
+
+If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].
+
+This keyword is not active if X and Y are specified in the call to contour.
+
+tricontour-only keyword arguments:
+
+
+
+tricontourf-only keyword arguments:
+
+
+
+Note: tricontourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="origin" name="origin" port_type="basic:String">
+ <docstring>If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.
+
+This keyword is not active if X and Y are specified in the call to contour.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'upper', 'lower', 'image']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyles" name="linestyles" port_type="basic:String">
+ <docstring>If linestyles is None, the 'solid' is used.
+
+linestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.
+
+If contour is using a monochrome colormap and the contour level is less than 0, then the linestyle specified in contour.negative_linestyle in matplotlibrc will be used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'solid', 'dashed', 'dashdot', 'dotted']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="levels" name="levelsSequence" port_type="basic:List">
+ <docstring>A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]</docstring>
+ <alternateSpec arg="levels" name="levelsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" name="linewidths" port_type="basic:String">
+ <docstring>If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.
+
+If a number, all levels will be plotted with this linewidth.
+
+If a tuple, different levels will be plotted with different linewidths in the order specified</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'number', 'tuple of numbers']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>If None, the colormap specified by cmap will be used.
+
+If a string, like 'r' or 'red', all levels will be plotted in this color.
+
+If a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['', '(mpl_colors)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="antialiased" name="antialiased" port_type="basic:Boolean">
+ <docstring>enable antialiasing</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="nchunk" name="nchunk" port_type="basic:Integer">
+ <docstring>If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[[0]]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>The alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.tripcolor" name="MplTripcolor" superclass="MplPlot">
+ <docstring>Create a pseudocolor plot of an unstructured triangular grid.
+
+The triangulation can be specified in one of two ways; either:
+
+tripcolor(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+tripcolor(x, y, ...) tripcolor(x, y, triangles, ...) tripcolor(x, y, triangles=triangles, ...) tripcolor(x, y, mask=mask, ...) tripcolor(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The next argument must be C, the array of color values, either one per point in the triangulation if color values are defined at points, or one per triangle in the triangulation if color values are defined at triangles. If there are the same number of points and triangles in the triangulation it is assumed that color values are defined at points; to force the use of color values at triangles use the kwarg facecolors*=C instead of just *C.
+
+shading may be 'flat' (the default) or 'gouraud'. If shading is 'flat' and C values are defined at points, the color values used for each triangle are from the mean C of the triangle's three points. If shading is 'gouraud' then color values must be defined at points. shading of 'faceted' is deprecated; please use edgecolors instead.
+
+The remaining kwargs are the same as for :meth:`~matplotlib.axes.Axes.pcolor`.
+
+Example:
+
+
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.triplot" name="MplTriplot" superclass="MplPlot">
+ <docstring>Draw a unstructured triangular grid as lines and/or markers.
+
+The triangulation to plot can be specified in one of two ways; either:
+
+triplot(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+triplot(x, y, ...) triplot(x, y, triangles, ...) triplot(x, y, triangles=triangles, ...) triplot(x, y, mask=mask, ...) triplot(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The remaining args and kwargs are the same as for :meth:`~matplotlib.axes.Axes.plot`.
+
+Example:
+
+
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.vlines" name="MplVlines" superclass="MplPlot">
+ <docstring>Plot vertical lines.
+
+Call signature:
+
+vlines(x, ymin, ymax, color='k', linestyles='solid')
+
+Plot vertical lines at each x from ymin to ymax. ymin or ymax can be scalars or len(x) numpy arrays. If they are scalars, then the respective values are constant, else the heights of the lines are determined by ymin and ymax.
+
+linestyles : [ 'solid' | 'dashed' | 'dashdot' | 'dotted' ]
+
+Returns the :class:`matplotlib.collections.LineCollection` that was added.
+
+kwargs are :class:`~matplotlib.collections.LineCollection` properties:
+
+%(LineCollection)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="hold" arg_pos="6" name="hold" />
+ <inputPortSpec arg="ymax" arg_pos="2" name="ymax" required="True" />
+ <inputPortSpec arg="linestyles" arg_pos="4" name="linestyles" port_type="basic:String">
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="3" name="color" port_type="basic:String">
+ <defaults>['k']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label" arg_pos="5" name="label" port_type="basic:String">
+ <defaults>['']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="colors" arg_pos="3" name="colors" port_type="basic:String">
+ <defaults>['k']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="ymin" arg_pos="1" name="ymin" required="True" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.xcorr" name="MplXcorr" output_type="tuple" superclass="MplPlot">
+ <docstring>Plot the cross correlation between x and y.
+
+Call signature:
+
+xcorr(self, x, y, normed=True, detrend=mlab.detrend_none, usevlines=True, maxlags=10, **kwargs)
+
+If normed = True, normalize the data by the cross correlation at 0-th lag. x and y are detrended by the detrend callable (default no normalization). x and y must be equal length.
+
+Data are plotted as plot(lags, c, **kwargs)
+
+Return value is a tuple (lags, c, line) where:
+
+lags are a length 2*maxlags+1 lag vector
+
+c is the 2*maxlags+1 auto correlation vector
+
+The default linestyle is None and the default marker is 'o', though these can be overridden with keyword args. The cross correlation is performed with :func:`numpy.correlate` with mode = 2.
+
+If usevlines is True:
+
+:func:`~matplotlib.pyplot.vlines` rather than :func:`~matplotlib.pyplot.plot` is used to draw vertical lines from the origin to the xcorr. Otherwise the plotstyle is determined by the kwargs, which are :class:`~matplotlib.lines.Line2D` properties.
+
+The return value is a tuple (lags, c, linecol, b) where linecol is the :class:`matplotlib.collections.LineCollection` instance and b is the x-axis.
+
+maxlags is a positive integer detailing the number of lags to show. The default value of None will return all (2*len(x)-1) lags.
+
+Example:
+
+:func:`~matplotlib.pyplot.xcorr` is top graph, and :func:`~matplotlib.pyplot.acorr` is bottom graph.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="normed" arg_pos="2" name="normed" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="usevlines" arg_pos="4" name="usevlines" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="detrend" arg_pos="3" name="detrend">
+ <defaults>['<function detrend_none at 0x02F5A3F0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="maxlags" arg_pos="5" name="maxlags" port_type="basic:Integer">
+ <defaults>['10']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="6" name="hold" />
+ <outputPortSpec arg="lineCollection" compute_name="lineCollection" name="lineCollectionProperties" port_type="__property__" property_key="4" property_type="matplotlib.collections.LineCollection" />
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="2" property_type="matplotlib.lines.Line2D" />
+ <outputPortSpec arg="xaxis" compute_name="xaxis" name="xaxisProperties" port_type="__property__" property_key="3" property_type="matplotlib.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.barbs" name="MplBarbs" output_type="object" superclass="MplPlot">
+ <docstring>Plot a 2-D field of barbs.
+
+Call signatures:
+
+barb(U, V, **kw) barb(U, V, C, **kw) barb(X, Y, U, V, **kw) barb(X, Y, U, V, C, **kw)
+
+Arguments:
+
+
+
+All arguments may be 1-D or 2-D arrays or sequences. If X and Y are absent, they will be generated as a uniform grid. If U and V are 2-D arrays but X and Y are 1-D, and if len(X) and len(Y) match the column and row dimensions of U, then X and Y will be expanded with :func:`numpy.meshgrid`.
+
+U, V, C may be masked arrays, but masked X, Y are not supported at present.
+
+Keyword arguments:
+
+
+
+Barbs are traditionally used in meteorology as a way to plot the speed and direction of wind observations, but can technically be used to plot any two dimensional vector quantity. As opposed to arrows, which give vector magnitude by the length of the arrow, the barbs give more quantitative information about the vector magnitude by putting slanted lines or a triangle for various increments in magnitude, as show schematically below:
+
+: /\ \ : / \ \ : / \ \ \ : / \ \ \ : ------------------------------
+
+note the double \ at the end of each line to make the figure
+
+render correctly
+
+The largest increment is given by a triangle (or "flag"). After those come full lines (barbs). The smallest increment is a half line. There is only, of course, ever at most 1 half line. If the magnitude is small and only needs a single half-line and no full lines or triangles, the half-line is offset from the end of the barb so that it can be easily distinguished from barbs with a single full line. The magnitude for the barb shown above would nominally be 65, using the standard increm [...]
+
+linewidths and edgecolors can be used to customize the barb. Additional :class:`~matplotlib.collections.PolyCollection` keyword arguments:
+
+agg_filter: unknown alpha: float or None animated: [True | False] antialiased or antialiaseds: Boolean or sequence of booleans array: unknown axes: an :class:`~matplotlib.axes.Axes` instance clim: a length 2 sequence of floats clip_box: a :class:`matplotlib.transforms.Bbox` instance clip_on: [True | False] clip_path: [ (:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`) | :class:`~matplotlib.patches.Patch` | None ] cmap: a colormap or registered co [...]
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="barbcolor" name="barbcolor" port_type="basic:Color">
+ <docstring>Specifies the color all parts of the barb except any flags. This parameter is analagous to the edgecolor parameter for polygons, which can be used instead. However this parameter will override facecolor.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ <alternateSpec arg="barbcolor" name="barbcolorSequence" port_type="basic:List" />
+ </inputPortSpec>
+ <inputPortSpec arg="C" arg_pos="4" in_args="True" name="C" port_type="basic:List">
+ <docstring>An optional array used to map colors to the barbs</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="sizes" name="sizes" port_type="basic:Dictionary">
+ <docstring>A dictionary of coefficients specifying the ratio of a given feature to the length of the barb. Only those values one wishes to override need to be included. These features include:
+
+'spacing' - space between features (flags, full/half barbs)
+
+'height' - height (distance from shaft to top) of a flag or full barb
+
+'width' - width of a flag, twice the width of a full barb
+
+'emptybarb' - radius of the circle used for low magnitudes</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rounding" name="rounding" port_type="basic:Boolean">
+ <docstring>A flag to indicate whether the vector magnitude should be rounded when allocating barb components. If True, the magnitude is rounded to the nearest multiple of the half-barb increment. If False, the magnitude is simply truncated to the next lowest multiple. Default is True</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pivot" name="pivot" port_type="basic:String">
+ <docstring>The part of the arrow that is at the grid point; the arrow rotates about this point, hence the name pivot. Default is 'tip'</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['tip', 'middle']]</values>
+ <defaults>['tip']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="flip_barb" name="flip_barb" port_type="basic:Boolean">
+ <docstring>Either a single boolean flag or an array of booleans. Single boolean indicates whether the lines and flags should point opposite to normal for all barbs. An array (which should be the same size as the other data arrays) indicates whether to flip for each individual barb. Normal behavior is for the barbs and lines to point right (comes from wind barbs having these features point towards low pressure in the Northern Hemisphere.) Default is False</docstring>
+ <defaults>['False']</defaults>
+ <alternateSpec arg="flip_barb" name="flip_barbSequence" port_type="basic:List" />
+ </inputPortSpec>
+ <inputPortSpec arg="length" name="length" port_type="basic:Integer">
+ <docstring>Length of the barb in points; the other parts of the barb are scaled against this. Default is 9</docstring>
+ <defaults>['9']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="barb_increments" name="barb_increments" port_type="basic:Dictionary">
+ <docstring>A dictionary of increments specifying values to associate with different parts of the barb. Only those values one wishes to override need to be included.
+
+'half' - half barbs (Default is 5)
+
+'full' - full barbs (Default is 10)
+
+'flag' - flags (default is 50)</docstring>
+ <defaults>None</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="U" arg_pos="2" in_args="True" name="U" port_type="basic:List" required="True">
+ <docstring>Give the x and y components of the barb shaft</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="V" arg_pos="3" in_args="True" name="V" port_type="basic:List" required="True">
+ <docstring>Give the x and y components of the barb shaft</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="Y" arg_pos="1" in_args="True" name="Y" port_type="basic:List">
+ <docstring>The x and y coordinates of the barb locations (default is head of barb; see pivot kwarg)</docstring>
+ <defaults>None</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="X" arg_pos="0" in_args="True" name="X" port_type="basic:List">
+ <docstring>The x and y coordinates of the barb locations (default is head of barb; see pivot kwarg)</docstring>
+ <defaults>None</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="flagcolor" name="flagcolor" port_type="basic:Color">
+ <docstring>Specifies the color of any flags on the barb. This parameter is analagous to the facecolor parameter for polygons, which can be used instead. However this parameter will override facecolor. If this is not set (and C has not either) then flagcolor will be set to match barbcolor so that the barb has a uniform color. If C has been set, flagcolor has no effect.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ <alternateSpec arg="flagcolor" name="flagcolorSequence" port_type="basic:List" />
+ </inputPortSpec>
+ <inputPortSpec arg="fill_empty" name="fill_empty" port_type="basic:Boolean">
+ <docstring>A flag on whether the empty barbs (circles) that are drawn should be filled with the flag color. If they are not filled, they will be drawn such that no color is applied to the center. Default is False</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="__none__" property_type="matplotlib.collections.PolyCollection" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.spy" name="MplSpy" output_type="tuple" superclass="MplPlot">
+ <docstring>Plot the sparsity pattern on a 2-D array.
+
+Call signature:
+
+spy(Z, precision=0, marker=None, markersize=None, aspect='equal', **kwargs)
+
+spy(Z) plots the sparsity pattern of the 2-D array Z.
+
+If precision is 0, any non-zero value will be plotted; else, values of |Z| > precision will be plotted.
+
+For :class:`scipy.sparse.spmatrix` instances, there is a special case: if precision is 'present', any value present in the array will be plotted, even if it is identically zero.
+
+The array will be plotted as it would be printed, with the first index (row) increasing down and the second index (column) increasing to the right.
+
+By default aspect is 'equal', so that each array element occupies a square space; set the aspect kwarg to 'auto' to allow the plot to fill the plot box, or to any scalar number to specify the aspect ratio of an array element directly.
+
+Two plotting styles are available: image or marker. Both are available for full arrays, but only the marker style works for :class:`scipy.sparse.spmatrix` instances.
+
+If marker and markersize are None, an image will be returned and any remaining kwargs are passed to :func:`~matplotlib.pyplot.imshow`; else, a :class:`~matplotlib.lines.Line2D` object will be returned with the value of marker determining the marker type, and any remaining kwargs passed to the :meth:`~matplotlib.axes.Axes.plot` method.
+
+If marker and markersize are None, useful kwargs include:
+
+cmap
+
+alpha
+
+For controlling colors, e.g. cyan background and red marks, use:
+
+cmap = mcolors.ListedColormap(['c','r'])
+
+If marker or markersize is not None, useful kwargs include:
+
+marker
+
+markersize
+
+color
+
+Useful values for marker include:
+
+'s' square (default)
+
+'o' circle
+
+'.' point
+
+',' pixel
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="hold" arg_pos="5" name="hold" />
+ <inputPortSpec arg="markersize" arg_pos="3" name="markersize" />
+ <inputPortSpec arg="precision" arg_pos="1" name="precision" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="aspect" arg_pos="4" name="aspect" port_type="basic:String">
+ <defaults>['equal']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="marker" arg_pos="2" name="marker" />
+ <inputPortSpec arg="Z" arg_pos="0" name="Z" port_type="basic:List" required="True" />
+ <outputPortSpec arg="image" compute_name="image" name="imageProperties" port_type="__property__" property_key="0" property_type="matplotlib.image.AxesImage" />
+ <outputPortSpec arg="marks" compute_name="marks" name="marksProperties" port_type="__property__" property_key="1" property_type="matplotlib.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.polar" name="MplPolar" output_type="object" superclass="MplPlot">
+ <docstring>Make a polar plot.
+
+call signature:
+
+polar(theta, r, **kwargs)
+
+Multiple theta, r arguments are supported, with format strings, as in :func:`~matplotlib.pyplot.plot`.</docstring>
+ <inputPortSpec arg="theta" arg_pos="0" in_args="True" name="theta" port_type="basic:List" required="True" />
+ <inputPortSpec arg="r" arg_pos="1" in_args="True" name="r" port_type="basic:List" required="True" />
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.legend" name="MplLegend" superclass="MplPlot">
+ <docstring>Place a legend on the current axes.
+
+Call signature:
+
+legend(*args, **kwargs)
+
+Places legend at location loc. Labels are a sequence of strings and loc can be a string or an integer specifying the legend location.
+
+To make a legend with existing lines:
+
+legend()
+
+:meth:`legend` by itself will try and build a legend using the label property of the lines/patches/collections. You can set the label of a line by doing:
+
+plot(x, y, label='my data')
+
+or:
+
+line.set_label('my data').
+
+If label is set to '_nolegend_', the item will not be shown in legend.
+
+To automatically generate the legend from labels:
+
+legend( ('label1', 'label2', 'label3') )
+
+To make a legend for a list of lines and labels:
+
+legend( (line1, line2, line3), ('label1', 'label2', 'label3') )
+
+To make a legend at a given location, using a location argument:
+
+legend( ('label1', 'label2', 'label3'), loc='upper left')
+
+or:
+
+legend( (line1, line2, line3), ('label1', 'label2', 'label3'), loc=2)
+
+The location codes are
+
+
+
+Users can specify any arbitrary location for the legend using the bbox_to_anchor keyword argument. bbox_to_anchor can be an instance of BboxBase(or its derivatives) or a tuple of 2 or 4 floats. For example,
+
+loc = 'upper right', bbox_to_anchor = (0.5, 0.5)
+
+will place the legend so that the upper right corner of the legend at the center of the axes.
+
+The legend location can be specified in other coordinate, by using the bbox_transform keyword.
+
+The loc itslef can be a 2-tuple giving x,y of the lower-left corner of the legend in axes coords (bbox_to_anchor is ignored).
+
+Keyword arguments:
+
+fontsize: [ size in points | 'xx-small' | 'x-small' | 'small' | 'medium' | 'large' | 'x-large' | 'xx-large' ]
+
+Set the font size. May be either a size string, relative to the default font size, or an absolute font size in points. This argument is only used if prop is not specified.
+
+Padding and spacing between various elements use following keywords parameters. These values are measure in font-size units. E.g., a fontsize of 10 points and a handlelength=5 implies a handlelength of 50 points. Values from rcParams will be used if None.
+
+Not all kinds of artist are supported by the legend command. See LINK (FIXME) for details.
+
+Example:</docstring>
+ <inputPortSpec arg="loc" name="loc">
+ <translations>{'right': 5, 'center left': 6, 'upper right': 1, 'lower right': 4, 'best': 0, 'center': 10, 'lower left': 3, 'center right': 7, 'upper left': 2, 'upper center': 9, 'lower center': 8}</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['best', 'upper right', 'upper left', 'lower left', 'lower right', 'right', 'center left', 'center right', 'lower center', 'upper center', 'center']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="fancybox" name="fancybox">
+ <docstring>if True, draw a frame with a round fancybox. If None, use rc settings</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox_to_anchor" name="bbox_to_anchor">
+ <docstring>the bbox that the legend will be anchored.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="title" name="title">
+ <docstring>the legend title</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="handlelength" name="handlelength">
+ <docstring>the length of the legend handles</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="markerscale" name="markerscale">
+ <docstring>The relative size of legend markers vs. original. If None, use rc settings.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="numpoints" name="numpoints" port_type="basic:Integer">
+ <docstring>The number of points in the legend for line</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="labelspacing" name="labelspacing">
+ <docstring>the vertical space between the legend entries</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="scatterpoints" name="scatterpoints" port_type="basic:Integer">
+ <docstring>The number of points in the legend for scatter plot</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="frameon" name="frameon" port_type="basic:Boolean">
+ <docstring>if True, draw a frame around the legend. The default is set by the rcParam 'legend.frameon'</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="columnspacing" name="columnspacing">
+ <docstring>the spacing between columns</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="handletextpad" name="handletextpad">
+ <docstring>the pad between the legend handle and text</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="scatteroffsets" name="scatteroffsetsSequence" port_type="basic:List">
+ <docstring>a list of yoffsets for scatter symbols in legend</docstring>
+ <alternateSpec arg="scatteroffsets" name="scatteroffsetsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="mode" name="mode">
+ <docstring>if mode is "expand", the legend will be horizontally expanded to fill the axes area (or bbox_to_anchor)</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ncol" name="ncol" port_type="basic:Integer">
+ <docstring>number of columns. default is 1</docstring>
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="shadow" name="shadow">
+ <docstring>If True, draw a shadow behind legend. If None, use rc settings.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="prop" name="prop" port_type="basic:String">
+ <docstring>A :class:`matplotlib.font_manager.FontProperties` instance. If prop is a dictionary, a new instance will be created with prop. If None, use rc settings.</docstring>
+ <entry_types>None</entry_types>
+ <values>None</values>
+ </inputPortSpec>
+ <inputPortSpec arg="borderpad" name="borderpad">
+ <docstring>the fractional whitespace inside the legend border</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox_transform" name="bbox_transform">
+ <docstring>the transform for the bbox. transAxes if None.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="borderaxespad" name="borderaxespad">
+ <docstring>the pad between the axes and legend border</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.annotate" name="MplAnnotate" output_type="object" superclass="MplPlot">
+ <docstring>Create an annotation: a piece of text referring to a data point.
+
+Call signature:
+
+annotate(s, xy, xytext=None, xycoords='data', textcoords='data', arrowprops=None, **kwargs)
+
+Keyword arguments:
+
+Annotate the x, y point xy with text s at x, y location xytext. (If xytext = None, defaults to xy, and if textcoords = None, defaults to xycoords).
+
+arrowprops, if not None, is a dictionary of line properties (see :class:`matplotlib.lines.Line2D`) for the arrow that connects annotation to the point.
+
+If the dictionary has a key arrowstyle, a FancyArrowPatch instance is created with the given dictionary and is drawn. Otherwise, a YAArow patch instance is created and drawn. Valid keys for YAArow are
+
+Valid keys for FancyArrowPatch are
+
+xycoords and textcoords are strings that indicate the coordinates of xy and xytext.
+
+If a 'points' or 'pixels' option is specified, values will be added to the bottom-left and if negative, values will be subtracted from the top-right. Eg:
+
+# 10 points to the right of the left border of the axes and # 5 points below the top border xy=(10,-5), xycoords='axes points'
+
+You may use an instance of :class:`~matplotlib.transforms.Transform` or :class:`~matplotlib.artist.Artist`. See :ref:`plotting-guide-annotation` for more details.
+
+The annotation_clip attribute contols the visibility of the annotation when it goes outside the axes area. If True, the annotation will only be drawn when the xy is inside the axes. If False, the annotation will always be drawn regardless of its position. The default is None, which behave as True only if xycoords is"data".
+
+Additional kwargs are Text properties:
+
+%(Text)s</docstring>
+ <inputPortSpec arg="xycoords" arg_pos="3" name="xycoords" port_type="basic:String">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ <defaults>None</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xytext" arg_pos="2" name="xytext" port_type="basic:Float, basic:Float" />
+ <inputPortSpec arg="s" arg_pos="0" name="s" port_type="basic:String" required="True" />
+ <inputPortSpec arg="xy" arg_pos="1" name="xy" port_type="basic:Float, basic:Float" required="True" />
+ <inputPortSpec arg="textcoords" arg_pos="4" name="textcoords" port_type="basic:String">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ <defaults>None</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="arrow_patch" in_kwargs="False" name="fancyArrowProperties" port_type="MplFancyArrowPatchProperties" />
+ <inputPortSpec arg="arrow" in_kwargs="False" name="arrowProperties" port_type="MplYAArrowProperties" />
+ <outputPortSpec arg="annotation" compute_name="annotation" name="annotationProperties" port_type="__property__" property_key="0" property_type="matplotlib.text.Annotation" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.plot" name="MplLinePlot" output_type="object" superclass="MplPlot">
+ <docstring>Plot lines and/or markers to the :class:`~matplotlib.axes.Axes`. args is a variable length argument, allowing for multiple x, y pairs with an optional format string. For example, each of the following is legal:
+
+plot(x, y) # plot x and y using default line style and color plot(x, y, 'bo') # plot x and y using blue circle markers plot(y) # plot y using x as index array 0..N-1 plot(y, 'r+') # ditto, but with red plusses
+
+If x and/or y is 2-dimensional, then the corresponding columns will be plotted.
+
+An arbitrary number of x, y, fmt groups can be specified, as in:
+
+a.plot(x1, y1, 'g^', x2, y2, 'g-')
+
+Return value is a list of lines that were added.
+
+By default, each line is assigned a different color specified by a 'color cycle'. To change this behavior, you can edit the axes.color_cycle rcParam. Alternatively, you can use :meth:`~matplotlib.axes.Axes.set_default_color_cycle`.
+
+The following format string characters are accepted to control the line style or marker:
+
+The following color abbreviations are supported:
+
+In addition, you can specify colors in many weird and wonderful ways, including full names ('green'), hex strings ('#008000'), RGB or RGBA tuples ((0,1,0,1)) or grayscale intensities as a string ('0.8'). Of these, the string specifications can be used in place of a fmt group, but the tuple forms can be used only as kwargs.
+
+Line styles and colors are combined in a single format string, as in 'bo' for blue circles.
+
+The kwargs can be used to set line properties (any property that has a set_* method). You can use this to set a line label (for auto legends), linewidth, anitialising, marker face color, etc. Here is an example:
+
+plot([1,2,3], [1,2,3], 'go-', label='line 1', linewidth=2) plot([1,2,3], [1,4,9], 'rs', label='line 2') axis([0, 4, 0, 10]) legend()
+
+If you make multiple lines with one plot command, the kwargs apply to all those lines, e.g.:
+
+plot(x1, y1, x2, y2, antialised=False)
+
+Neither line will be antialiased.
+
+You do not need to use format strings, which are just abbreviations. All of the line properties can be controlled by keyword arguments. For example, you can set the color, marker, linestyle, and markercolor with:
+
+plot(x, y, color='green', linestyle='dashed', marker='o', markerfacecolor='blue', markersize=12).
+
+See :class:`~matplotlib.lines.Line2D` for details.
+
+The kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+kwargs scalex and scaley, if defined, are passed on to :meth:`~matplotlib.axes.Axes.autoscale_view` to determine whether the x and y axes are autoscaled; the default is True.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="marker" name="marker">
+ <translations>{'tri_down marker': '1', 'pentagon marker': 'p', 'hline marker': '_', 'pixel marker': ',', 'triangle_up marker': '^', 'point marker': '.', 'square marker': 's', 'hexagon2 marker': 'H', 'tri_right marker': '4', 'plus marker': '+', 'vline marker': '|', 'triangle_left marker': '<', 'triangle_down marker': 'v', 'triangle_right marker': '>', 'tri_left marker': '3', 'x marker': 'x', 'circle marker': 'o', 'dashed line style': '--', 'hexagon1 marker': 'h', 'dash-dot lin [...]
+ <entry_types>['enum']</entry_types>
+ <values>[['solid line style', 'dashed line style', 'dash-dot line style', 'dotted line style', 'point marker', 'pixel marker', 'circle marker', 'triangle_down marker', 'triangle_up marker', 'triangle_left marker', 'triangle_right marker', 'tri_down marker', 'tri_up marker', 'tri_left marker', 'tri_right marker', 'square marker', 'pentagon marker', 'star marker', 'hexagon1 marker', 'hexagon2 marker', 'plus marker', 'x marker', 'diamond marker', 'thin_diamond marker', 'vline marker', [...]
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" />
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </moduleSpec>
+</specs>
diff --git a/vistrails/packages/matplotlib/mpl_plots_diff.xml b/vistrails/packages/matplotlib/mpl_plots_diff.xml
new file mode 100644
index 0000000..feaef5e
--- /dev/null
+++ b/vistrails/packages/matplotlib/mpl_plots_diff.xml
@@ -0,0 +1,1113 @@
+<diff>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.hexbin">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.hexbin" port="C" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.hexbin" port="gridsize" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.hexbin" port="gridsize" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.hexbin" port="y" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.hexbin" port="bins" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.hexbin" port="bins" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.hexbin" port="bins" type="input">
+ <value>basic:Integer</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.hexbin" port="x" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.hexbin" port="polyCollection" type="output">
+ <value>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="-1" property_type="matplotlib.collections.PolyCollection" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.clabel">
+ <value>object</value>
+ </changeModule>
+ <deletePortSpec code_ref="matplotlib.pyplot.clabel" port="CS" type="input" />
+ <addPortSpec code_ref="matplotlib.pyplot.clabel" port="v" type="input">
+ <value>
+ <inputPortSpec arg="v" arg_pos="1" in_args="True" name="v" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.clabel" port="cs" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.clabel" port="cs" type="input">
+ <value>MplContourSet</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.clabel" port="text" type="output">
+ <value>
+ <outputPortSpec arg="text" compute_name="texts" name="textProperties" plural="True" port_type="__property__" property_key="__none__" property_type="matplotlib.text.Text" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.cohere" port="line" type="input">
+ <value>
+ <inputPortSpec arg="line" constructor_arg="True" name="lineProperties" port_type="__property__" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.fill_betweenx">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.fill_betweenx" port="y" type="input">
+ <value>An N-length array of the y data</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.fill_betweenx" port="y" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.fill_betweenx" port="x2" type="input">
+ <value>A scalar x-value</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.fill_betweenx" port="x2" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <addPortSpec altName="x2Sequence" code_ref="matplotlib.pyplot.fill_betweenx" port="x2" type="alternate">
+ <value>
+ <alternateSpec arg="x2" name="x2Sequence" port_type="basic:List">
+ <docstring>An N-length array of the x data</docstring>
+ </alternateSpec>
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.fill_betweenx" port="x1" type="input">
+ <value>An N-length array of the x data</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.fill_betweenx" port="x1" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.fill_betweenx" port="x1" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec altName="x1Scalar" code_ref="matplotlib.pyplot.fill_betweenx" port="x1" type="alternate">
+ <value>
+ <alternateSpec arg="x1" name="x1Scalar" port_type="basic:Float">
+ <docstring>A scalar x-value</docstring>
+ </alternateSpec>
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.fill_betweenx" port="where" type="input">
+ <value>An N-length boolean array that specifies where the fill is effective</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.fill_betweenx" port="where" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.fill_betweenx" port="polyCollection" type="output">
+ <value>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="__none__" property_type="matplotlib.collections.PolyCollection" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.axhspan">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axhspan" port="xmin" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axhspan" port="ymin" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axhspan" port="ymax" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axhspan" port="xmax" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.axhspan" port="patch" type="output">
+ <value>
+ <outputPortSpec arg="patch" compute_name="patch" name="patchProperties" port_type="__property__" property_key="-1" property_type="matplotlib.patches.Polygon" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.xcorr">
+ <value>tuple</value>
+ </changeModule>
+ <addPortSpec code_ref="matplotlib.pyplot.xcorr" port="lineCollection" type="output">
+ <value>
+ <outputPortSpec arg="lineCollection" compute_name="lineCollection" name="lineCollectionProperties" port_type="__property__" property_key="4" property_type="matplotlib.collections.LineCollection" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.xcorr" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="2" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.xcorr" port="xaxis" type="output">
+ <value>
+ <outputPortSpec arg="xaxis" compute_name="xaxis" name="xaxisProperties" port_type="__property__" property_key="3" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.axhline">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axhline" port="y" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axhline" port="xmin" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axhline" port="xmax" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.axhline" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="line" name="lineProperties" port_type="__property__" property_key="0" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.arrow" port="dx" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.arrow" port="arrow" type="input">
+ <value>
+ <inputPortSpec arg="arrow" constructor_arg="True" name="arrowProperties" port_type="__property__" property_type="matplotlib.patches.FancyArrow" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.arrow" port="dy" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.arrow" port="y" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.arrow" port="x" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.pcolor">
+ <value>object</value>
+ </changeModule>
+ <addPortSpec code_ref="matplotlib.pyplot.pcolor" port="Y" type="input">
+ <value>
+ <inputPortSpec arg="Y" arg_pos="1" in_args="True" name="Y" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.pcolor" port="X" type="input">
+ <value>
+ <inputPortSpec arg="X" arg_pos="0" in_args="True" name="X" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.pcolor" port="Z" type="input">
+ <value>
+ <inputPortSpec arg="Z" arg_pos="2" in_args="True" name="Z" port_type="basic:List" required="True" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.pcolor" port="polyCollection" type="output">
+ <value>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="0" property_type="matplotlib.collections.PolyCollection" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.annotate">
+ <value>object</value>
+ </changeModule>
+ <deletePortSpec code_ref="matplotlib.pyplot.annotate" port="arrowprops" type="input" />
+ <addPortSpec code_ref="matplotlib.pyplot.annotate" port="arrow_patch" type="input">
+ <value>
+ <inputPortSpec arg="arrow_patch" in_kwargs="False" name="fancyArrowProperties" port_type="MplFancyArrowPatchProperties" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.annotate" port="xytext" type="input">
+ <value>basic:Float, basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="defaults" code_ref="matplotlib.pyplot.annotate" port="xycoords" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.annotate" port="s" type="input">
+ <value>basic:String</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.annotate" port="xy" type="input">
+ <value>basic:Float, basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="defaults" code_ref="matplotlib.pyplot.annotate" port="textcoords" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.annotate" port="arrow" type="input">
+ <value>
+ <inputPortSpec arg="arrow" in_kwargs="False" name="arrowProperties" port_type="MplYAArrowProperties" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.annotate" port="annotation" type="output">
+ <value>
+ <outputPortSpec arg="annotation" compute_name="annotation" name="annotationProperties" port_type="__property__" property_key="0" property_type="matplotlib.text.Annotation" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.csd" port="line" type="input">
+ <value>
+ <inputPortSpec arg="line" constructor_arg="True" name="lineProperties" port_type="__property__" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.axvline">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axvline" port="ymin" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axvline" port="x" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axvline" port="ymax" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.axvline" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="line" name="lineProperties" port_type="__property__" property_key="0" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.contour">
+ <value>tuple</value>
+ </changeModule>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.contour" port="locator" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.contour" port="locator" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.contour" port="colors" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.contour" port="colors" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.contour" port="cmap" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.contour" port="cmap" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.contour" port="yunits" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.contour" port="yunits" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.contour" port="norm" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.contour" port="norm" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.contour" port="V" type="input">
+ <value>
+ <inputPortSpec arg="V" arg_pos="3" in_args="True" name="V" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.contour" port="Y" type="input">
+ <value>
+ <inputPortSpec arg="Y" arg_pos="1" in_args="True" name="Y" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.contour" port="X" type="input">
+ <value>
+ <inputPortSpec arg="X" arg_pos="0" in_args="True" name="X" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.contour" port="Z" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.contour" port="Z" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.contour" port="Z" type="input">
+ <value>2</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.contour" port="N" type="input">
+ <value>
+ <inputPortSpec arg="N" arg_pos="4" in_args="True" name="N" port_type="basic:Integer" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.contour" port="contourSet" type="output">
+ <value>
+ <outputPortSpec arg="contourSet" compute_name="contourSet" name="contourSet" port_type="MplQuadContourSet" property_key="0" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.contour" port="lineCollection" type="output">
+ <value>
+ <outputPortSpec arg="lineCollection" compute_name="lineCollections" name="lineCollectionProperties" plural="True" port_type="__property__" property_key="1" property_type="matplotlib.collections.LineCollection" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.barh">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barh" port="bottom" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec altName="bottomScalar" code_ref="matplotlib.pyplot.barh" port="bottom" type="alternate">
+ <value>
+ <alternateSpec arg="bottom" name="bottomScalar" port_type="basic:Float" />
+ </value>
+ </addPortSpec>
+ <addPortSpec altName="heightSequence" code_ref="matplotlib.pyplot.barh" port="height" type="alternate">
+ <value>
+ <alternateSpec arg="height" name="heightSequence" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barh" port="width" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec altName="widthScalar" code_ref="matplotlib.pyplot.barh" port="width" type="alternate">
+ <value>
+ <alternateSpec arg="width" name="widthScalar" port_type="basic:Float" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barh" port="left" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <addPortSpec altName="leftSequence" code_ref="matplotlib.pyplot.barh" port="left" type="alternate">
+ <value>
+ <alternateSpec arg="left" name="leftSequence" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.barh" port="rectangle" type="output">
+ <value>
+ <outputPortSpec arg="rectangle" compute_name="rectangles" name="rectangleProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.Rectangle" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.bar">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.bar" port="bottom" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <addPortSpec altName="bottomSequence" code_ref="matplotlib.pyplot.bar" port="bottom" type="alternate">
+ <value>
+ <alternateSpec arg="bottom" name="bottomSequence" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.bar" port="height" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec altName="heightScalar" code_ref="matplotlib.pyplot.bar" port="height" type="alternate">
+ <value>
+ <alternateSpec arg="height" name="heightScalar" port_type="basic:Float" />
+ </value>
+ </addPortSpec>
+ <addPortSpec altName="widthSequence" code_ref="matplotlib.pyplot.bar" port="width" type="alternate">
+ <value>
+ <alternateSpec arg="width" name="widthSequence" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="required" code_ref="matplotlib.pyplot.bar" port="left" type="input">
+ <value>False</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.bar" port="left" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec altName="leftScalar" code_ref="matplotlib.pyplot.bar" port="left" type="alternate">
+ <value>
+ <alternateSpec arg="left" name="leftScalar" port_type="basic:Float">
+ <docstring>the x coordinate of the left side of the bar</docstring>
+ </alternateSpec>
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.bar" port="rectangle" type="output">
+ <value>
+ <outputPortSpec arg="rectangle" compute_name="rectangles" name="rectangleProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.Rectangle" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.imshow" port="X" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.plot">
+ <value>object</value>
+ </changeModule>
+ <addPortSpec code_ref="matplotlib.pyplot.plot" port="y" type="input">
+ <value>
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.plot" port="x" type="input">
+ <value>
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.plot" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.stem">
+ <value>tuple</value>
+ </changeModule>
+ <addPortSpec code_ref="matplotlib.pyplot.stem" port="stemline" type="output">
+ <value>
+ <outputPortSpec arg="stemline" compute_name="stemlines" name="stemlineProperties" plural="True" port_type="__property__" property_key="1" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.stem" port="markerline" type="output">
+ <value>
+ <outputPortSpec arg="markerline" compute_name="markerline" name="markerlineProperties" port_type="__property__" property_key="0" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.stem" port="baseline" type="output">
+ <value>
+ <outputPortSpec arg="baseline" compute_name="baseline" name="baselineProperties" port_type="__property__" property_key="2" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.broken_barh" port="yrange" type="input">
+ <value>(ymin, ywidth)</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.broken_barh" port="yrange" type="input">
+ <value>basic:Float,basic:Float</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.broken_barh" port="brokenBarHCollection" type="output">
+ <value>
+ <outputPortSpec arg="brokenBarHCollection" compute_name="brokenBarHCollection" name="brokenBarHCollectionProperties" port_type="__property__" property_key="__none__" property_type="matplotlib.collections.BrokenBarHCollection" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.fill_between">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.fill_between" port="y2" type="input">
+ <value>A scalar y-value</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.fill_between" port="y2" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="defaults" code_ref="matplotlib.pyplot.fill_between" port="y2" type="input">
+ <value>['0.0']</value>
+ </changePortSpec>
+ <addPortSpec altName="y2Sequence" code_ref="matplotlib.pyplot.fill_between" port="y2" type="alternate">
+ <value>
+ <alternateSpec arg="y2" name="y2Sequence" port_type="basic:List">
+ <docstring>An N-length array of the y data</docstring>
+ </alternateSpec>
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.fill_between" port="y1" type="input">
+ <value>An N-length array of the y data</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.fill_between" port="y1" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.fill_between" port="y1" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec altName="y1Scalar" code_ref="matplotlib.pyplot.fill_between" port="y1" type="alternate">
+ <value>
+ <alternateSpec arg="y1" name="y1Scalar" port_type="basic:Float">
+ <docstring>A scalar y-value</docstring>
+ </alternateSpec>
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.fill_between" port="x" type="input">
+ <value>An N-length array of the x data</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.fill_between" port="x" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.fill_between" port="where" type="input">
+ <value>An N-length boolean array that specifies where the fill is effective</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.fill_between" port="where" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.fill_between" port="polyCollection" type="output">
+ <value>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="__none__" property_type="matplotlib.collections.PolyCollection" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.hlines">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="name" code_ref="matplotlib.pyplot.hlines" port="xmax" type="input">
+ <value>xmaxScalar</value>
+ </changePortSpec>
+ <addPortSpec altName="xmaxSequence" code_ref="matplotlib.pyplot.hlines" port="xmax" type="alternate">
+ <value>
+ <alternateSpec arg="xmax" name="xmaxSequence" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="name" code_ref="matplotlib.pyplot.hlines" port="xmin" type="input">
+ <value>xminScalar</value>
+ </changePortSpec>
+ <addPortSpec altName="xminSequence" code_ref="matplotlib.pyplot.hlines" port="xmin" type="alternate">
+ <value>
+ <alternateSpec arg="xmin" name="xminSequence" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.hlines" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.collections.LineCollection" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.quiver">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.quiver" port="C" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.quiver" port="C" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.quiver" port="C" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.quiver" port="C" type="input">
+ <value>4</value>
+ </changePortSpec>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.quiver" port="Y" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.quiver" port="Y" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.quiver" port="Y" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="defaults" code_ref="matplotlib.pyplot.quiver" port="Y" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.quiver" port="Y" type="input">
+ <value>1</value>
+ </changePortSpec>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.quiver" port="X" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.quiver" port="X" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.quiver" port="X" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="defaults" code_ref="matplotlib.pyplot.quiver" port="X" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.quiver" port="X" type="input">
+ <value>0</value>
+ </changePortSpec>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.quiver" port="U" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="required" code_ref="matplotlib.pyplot.quiver" port="U" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.quiver" port="U" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.quiver" port="U" type="input">
+ <value>2</value>
+ </changePortSpec>
+ <changePortSpec attr="docstring" code_ref="matplotlib.pyplot.quiver" port="V" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="required" code_ref="matplotlib.pyplot.quiver" port="V" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.quiver" port="V" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.quiver" port="V" type="input">
+ <value>3</value>
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.quiver" port="color" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.quiver" port="color" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec altName="colorScalar" attr="translations" code_ref="matplotlib.pyplot.quiver" port="color" type="alternate">
+ <value>translate_color</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.quiver" port="polyCollection" type="output">
+ <value>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="0" property_type="matplotlib.collections.PolyCollection" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.pie">
+ <value>tuple</value>
+ </changeModule>
+ <changePortSpec attr="defaults" code_ref="matplotlib.pyplot.pie" port="colors" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.pie" port="autotext" type="output">
+ <value>
+ <outputPortSpec arg="autotext" compute_name="autotexts" name="autotextProperties" plural="True" port_type="__property__" property_key="2" property_type="matplotlib.text.Text" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.pie" port="wedge" type="output">
+ <value>
+ <outputPortSpec arg="wedge" compute_name="wedges" name="wedgeProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.patches.Wedge" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.pie" port="text" type="output">
+ <value>
+ <outputPortSpec arg="text" compute_name="texts" name="textProperties" plural="True" port_type="__property__" property_key="1" property_type="matplotlib.text.Text" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.semilogx">
+ <value>object</value>
+ </changeModule>
+ <addPortSpec code_ref="matplotlib.pyplot.semilogx" port="x" type="input">
+ <value>
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" required="True" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.semilogx" port="y" type="input">
+ <value>
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.semilogx" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.errorbar">
+ <value>tuple</value>
+ </changeModule>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.errorbar" port="xerr" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.errorbar" port="xerr" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.errorbar" port="xerr" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec altName="xerrScalar" code_ref="matplotlib.pyplot.errorbar" port="xerr" type="alternate">
+ <value>
+ <alternateSpec arg="xerr" name="xerrScalar" port_type="basic:Float" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.errorbar" port="yerr" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.errorbar" port="yerr" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.errorbar" port="yerr" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec altName="yerrScalar" code_ref="matplotlib.pyplot.errorbar" port="yerr" type="alternate">
+ <value>
+ <alternateSpec arg="yerr" name="yerrScalar" port_type="basic:Float" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.errorbar" port="capline" type="output">
+ <value>
+ <outputPortSpec arg="capline" compute_name="caplines" name="caplineProperties" plural="True" port_type="__property__" property_key="1" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.errorbar" port="barline" type="output">
+ <value>
+ <outputPortSpec arg="barline" compute_name="barlines" name="barlineProperties" plural="True" port_type="__property__" property_key="2" property_type="matplotlib.collections.LineCollection" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.errorbar" port="plotline" type="output">
+ <value>
+ <outputPortSpec arg="plotline" compute_name="plotline" name="plotlineProperties" port_type="__property__" property_key="0" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.step">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.step" port="y" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.step" port="x" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.step" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.hist">
+ <value>tuple</value>
+ </changeModule>
+ <changePortSpec attr="translations" code_ref="matplotlib.pyplot.hist" port="color" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec altName="colorScalar" attr="translations" code_ref="matplotlib.pyplot.hist" port="color" type="alternate">
+ <value>translate_color</value>
+ </changePortSpec>
+ <changePortSpec attr="name" code_ref="matplotlib.pyplot.hist" port="bins" type="input">
+ <value>bins</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.hist" port="bins" type="input">
+ <value>basic:Integer</value>
+ </changePortSpec>
+ <deletePortSpec altName="binsScalar" code_ref="matplotlib.pyplot.hist" port="bins" type="alternate" />
+ <addPortSpec altName="binsSequence" code_ref="matplotlib.pyplot.hist" port="bins" type="alternate">
+ <value>
+ <alternateSpec arg="bins" name="binsSequence" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.hist" port="rectangle" type="output">
+ <value>
+ <outputPortSpec arg="rectangle" compute_name="rectangles" name="rectangleProperties" plural="True" port_type="__property__" property_key="2" property_type="matplotlib.patches.Rectangle" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.scatter">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.scatter" port="cmap" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.scatter" port="cmap" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.scatter" port="norm" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.scatter" port="norm" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.scatter" port="pathCollection" type="output">
+ <value>
+ <outputPortSpec arg="pathCollection" compute_name="pathCollection" name="pathCollectionProperties" port_type="__property__" property_key="0" property_type="matplotlib.collections.PathCollection" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.plot_date">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.plot_date" port="y" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.plot_date" port="x" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.plot_date" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.psd" port="line" type="input">
+ <value>
+ <inputPortSpec arg="line" constructor_arg="True" name="lineProperties" port_type="__property__" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.polar">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.polar" port="theta" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.polar" port="theta" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.polar" port="r" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.polar" port="r" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.polar" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.loglog">
+ <value>object</value>
+ </changeModule>
+ <addPortSpec code_ref="matplotlib.pyplot.loglog" port="y" type="input">
+ <value>
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.loglog" port="x" type="input">
+ <value>
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" required="True" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.loglog" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.contourf">
+ <value>tuple</value>
+ </changeModule>
+ <addPortSpec code_ref="matplotlib.pyplot.contourf" port="N" type="input">
+ <value>
+ <inputPortSpec arg="N" arg_pos="4" in_args="True" name="N" port_type="basic:Integer" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.contourf" port="V" type="input">
+ <value>
+ <inputPortSpec arg="V" arg_pos="3" in_args="True" name="V" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.contourf" port="Y" type="input">
+ <value>
+ <inputPortSpec arg="Y" arg_pos="1" in_args="True" name="Y" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.contourf" port="X" type="input">
+ <value>
+ <inputPortSpec arg="X" arg_pos="0" in_args="True" name="X" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.contourf" port="Z" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.contourf" port="Z" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.contourf" port="Z" type="input">
+ <value>2</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.contourf" port="contourSet" type="output">
+ <value>
+ <outputPortSpec arg="contourSet" compute_name="contourSet" name="contourSet" port_type="MplQuadContourSet" property_key="0" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.contourf" port="polyCollection" type="output">
+ <value>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollections" name="polyCollectionProperties" plural="True" port_type="__property__" property_key="1" property_type="matplotlib.collections.PolyCollection" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.legend" port="prop" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.legend" port="prop" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.semilogy">
+ <value>object</value>
+ </changeModule>
+ <addPortSpec code_ref="matplotlib.pyplot.semilogy" port="y" type="input">
+ <value>
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.semilogy" port="x" type="input">
+ <value>
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" required="True" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.semilogy" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.spy">
+ <value>tuple</value>
+ </changeModule>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.spy" port="Z" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.spy" port="image" type="output">
+ <value>
+ <outputPortSpec arg="image" compute_name="image" name="imageProperties" port_type="__property__" property_key="0" property_type="matplotlib.image.AxesImage" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.spy" port="marks" type="output">
+ <value>
+ <outputPortSpec arg="marks" compute_name="marks" name="marksProperties" port_type="__property__" property_key="1" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.acorr">
+ <value>tuple</value>
+ </changeModule>
+ <addPortSpec code_ref="matplotlib.pyplot.acorr" port="lineCollection" type="output">
+ <value>
+ <outputPortSpec arg="lineCollection" compute_name="lineCollection" name="lineCollectionProperties" port_type="__property__" property_key="4" property_type="matplotlib.collections.LineCollection" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.acorr" port="line" type="output">
+ <value>
+ <outputPortSpec arg="line" compute_name="lines" name="lineProperties" plural="True" port_type="__property__" property_key="2" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.acorr" port="xaxis" type="output">
+ <value>
+ <outputPortSpec arg="xaxis" compute_name="xaxis" name="xaxisProperties" port_type="__property__" property_key="3" property_type="matplotlib.lines.Line2D" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.fill">
+ <value>object</value>
+ </changeModule>
+ <addPortSpec code_ref="matplotlib.pyplot.fill" port="y" type="input">
+ <value>
+ <inputPortSpec arg="y" arg_pos="1" in_args="True" name="y" port_type="basic:List" required="True" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.fill" port="x" type="input">
+ <value>
+ <inputPortSpec arg="x" arg_pos="0" in_args="True" name="x" port_type="basic:List" required="True" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.fill" port="polygon" type="output">
+ <value>
+ <outputPortSpec arg="polygon" compute_name="polygons" name="polygonProperties" plural="True" port_type="__property__" property_key="0" property_type="matplotlib.artist.patches.Polygon" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.barbs">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="name" code_ref="matplotlib.pyplot.barbs" port="barbcolor" type="input">
+ <value>barbcolor</value>
+ </changePortSpec>
+ <changePortSpec attr="translations" code_ref="matplotlib.pyplot.barbs" port="barbcolor" type="input">
+ <value>translate_color</value>
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.barbs" port="barbcolor" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.barbs" port="barbcolor" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barbs" port="barbcolor" type="input">
+ <value>basic:Color</value>
+ </changePortSpec>
+ <deletePortSpec altName="barbcolorScalar" code_ref="matplotlib.pyplot.barbs" port="barbcolor" type="alternate" />
+ <addPortSpec altName="barbcolorSequence" code_ref="matplotlib.pyplot.barbs" port="barbcolor" type="alternate">
+ <value>
+ <alternateSpec arg="barbcolor" name="barbcolorSequence" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.barbs" port="C" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barbs" port="C" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.barbs" port="C" type="input">
+ <value>4</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barbs" port="sizes" type="input">
+ <value>basic:Dictionary</value>
+ </changePortSpec>
+ <addPortSpec altName="flip_barbSequence" code_ref="matplotlib.pyplot.barbs" port="flip_barb" type="alternate">
+ <value>
+ <alternateSpec arg="flip_barb" name="flip_barbSequence" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barbs" port="barb_increments" type="input">
+ <value>basic:Dictionary</value>
+ </changePortSpec>
+ <changePortSpec attr="defaults" code_ref="matplotlib.pyplot.barbs" port="barb_increments" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="required" code_ref="matplotlib.pyplot.barbs" port="U" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.barbs" port="U" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barbs" port="U" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.barbs" port="U" type="input">
+ <value>2</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.barbs" port="X" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barbs" port="X" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="defaults" code_ref="matplotlib.pyplot.barbs" port="X" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.barbs" port="X" type="input">
+ <value>0</value>
+ </changePortSpec>
+ <changePortSpec attr="required" code_ref="matplotlib.pyplot.barbs" port="V" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.barbs" port="V" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barbs" port="V" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.barbs" port="V" type="input">
+ <value>3</value>
+ </changePortSpec>
+ <changePortSpec attr="in_args" code_ref="matplotlib.pyplot.barbs" port="Y" type="input">
+ <value>True</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barbs" port="Y" type="input">
+ <value>basic:List</value>
+ </changePortSpec>
+ <changePortSpec attr="defaults" code_ref="matplotlib.pyplot.barbs" port="Y" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="arg_pos" code_ref="matplotlib.pyplot.barbs" port="Y" type="input">
+ <value>1</value>
+ </changePortSpec>
+ <changePortSpec attr="name" code_ref="matplotlib.pyplot.barbs" port="flagcolor" type="input">
+ <value>flagcolor</value>
+ </changePortSpec>
+ <changePortSpec attr="translations" code_ref="matplotlib.pyplot.barbs" port="flagcolor" type="input">
+ <value>translate_color</value>
+ </changePortSpec>
+ <changePortSpec attr="entry_types" code_ref="matplotlib.pyplot.barbs" port="flagcolor" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="values" code_ref="matplotlib.pyplot.barbs" port="flagcolor" type="input">
+ <value>None</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.barbs" port="flagcolor" type="input">
+ <value>basic:Color</value>
+ </changePortSpec>
+ <deletePortSpec altName="flagcolorScalar" code_ref="matplotlib.pyplot.barbs" port="flagcolor" type="alternate" />
+ <addPortSpec altName="flagcolorSequence" code_ref="matplotlib.pyplot.barbs" port="flagcolor" type="alternate">
+ <value>
+ <alternateSpec arg="flagcolor" name="flagcolorSequence" port_type="basic:List" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.barbs" port="polyCollection" type="output">
+ <value>
+ <outputPortSpec arg="polyCollection" compute_name="polyCollection" name="polyCollectionProperties" port_type="__property__" property_key="__none__" property_type="matplotlib.collections.PolyCollection" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.axvspan">
+ <value>object</value>
+ </changeModule>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axvspan" port="xmin" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axvspan" port="ymin" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axvspan" port="ymax" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <changePortSpec attr="port_type" code_ref="matplotlib.pyplot.axvspan" port="xmax" type="input">
+ <value>basic:Float</value>
+ </changePortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.axvspan" port="patch" type="output">
+ <value>
+ <outputPortSpec arg="patch" compute_name="patch" name="patchProperties" port_type="__property__" property_key="-1" property_type="matplotlib.patches.Polygon" />
+ </value>
+ </addPortSpec>
+ <changeModule attr="output_type" code_ref="matplotlib.pyplot.boxplot">
+ <value>dict</value>
+ </changeModule>
+ <addPortSpec code_ref="matplotlib.pyplot.boxplot" port="box" type="output">
+ <value>
+ <outputPortSpec arg="box" compute_name="boxes" name="boxProperties" plural="True" port_type="__property__" property_key="boxes" property_type="matplotlib.artist.Line2D" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.boxplot" port="flier" type="output">
+ <value>
+ <outputPortSpec arg="flier" compute_name="fliers" name="flierProperties" plural="True" port_type="__property__" property_key="fliers" property_type="matplotlib.artist.Line2D" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.boxplot" port="cap" type="output">
+ <value>
+ <outputPortSpec arg="cap" compute_name="caps" name="capProperties" plural="True" port_type="__property__" property_key="caps" property_type="matplotlib.artist.Line2D" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.boxplot" port="median" type="output">
+ <value>
+ <outputPortSpec arg="median" compute_name="medians" name="medianProperties" plural="True" port_type="__property__" property_key="medians" property_type="matplotlib.artist.Line2D" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.boxplot" port="boxPatch" type="output">
+ <value>
+ <outputPortSpec arg="boxPatch" compute_name="boxPatches" name="boxPatchProperties" plural="True" port_type="__property__" property_key="boxPatches" property_type="matplotlib.artist.PathPatch" />
+ </value>
+ </addPortSpec>
+ <addPortSpec code_ref="matplotlib.pyplot.boxplot" port="whisker" type="output">
+ <value>
+ <outputPortSpec arg="whisker" compute_name="whiskers" name="whiskerProperties" plural="True" port_type="__property__" property_key="whiskers" property_type="matplotlib.artist.Line2D" />
+ </value>
+ </addPortSpec>
+</diff>
diff --git a/vistrails/packages/matplotlib/mpl_plots_raw.xml b/vistrails/packages/matplotlib/mpl_plots_raw.xml
new file mode 100644
index 0000000..2d9dc75
--- /dev/null
+++ b/vistrails/packages/matplotlib/mpl_plots_raw.xml
@@ -0,0 +1,3154 @@
+<specs>
+ <customCode />
+ <moduleSpec code_ref="matplotlib.pyplot.acorr" name="MplAcorr" superclass="MplPlot">
+ <docstring>Plot the autocorrelation of x.
+
+Call signature:
+
+acorr(x, normed=True, detrend=mlab.detrend_none, usevlines=True, maxlags=10, **kwargs)
+
+If normed = True, normalize the data by the autocorrelation at 0-th lag. x is detrended by the detrend callable (default no normalization).
+
+Data are plotted as plot(lags, c, **kwargs)
+
+Return value is a tuple (lags, c, line) where:
+
+lags are a length 2*maxlags+1 lag vector
+
+c is the 2*maxlags+1 auto correlation vector
+
+line is a :class:`~matplotlib.lines.Line2D` instance returned by :meth:`plot`
+
+The default linestyle is None and the default marker is 'o', though these can be overridden with keyword args. The cross correlation is performed with :func:`numpy.correlate` with mode = 2.
+
+If usevlines is True, :meth:`~matplotlib.axes.Axes.vlines` rather than :meth:`~matplotlib.axes.Axes.plot` is used to draw vertical lines from the origin to the acorr. Otherwise, the plot style is determined by the kwargs, which are :class:`~matplotlib.lines.Line2D` properties.
+
+maxlags is a positive integer detailing the number of lags to show. The default value of None will return all (2*len(x)-1) lags.
+
+The return value is a tuple (lags, c, linecol, b) where
+
+linecol is the :class:`~matplotlib.collections.LineCollection`
+
+b is the x-axis.
+
+Example:
+
+:func:`~matplotlib.pyplot.xcorr` is top graph, and :func:`~matplotlib.pyplot.acorr` is bottom graph.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="normed" arg_pos="1" name="normed" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="usevlines" arg_pos="3" name="usevlines" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="detrend" arg_pos="2" name="detrend" />
+ <inputPortSpec arg="maxlags" arg_pos="4" name="maxlags" port_type="basic:Integer">
+ <defaults>['10']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="1" name="hold" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.arrow" name="MplArrow" superclass="MplPlot">
+ <docstring>Add an arrow to the axes.
+
+Call signature:
+
+arrow(x, y, dx, dy, **kwargs)
+
+Draws arrow on specified axis from (x, y) to (x + dx, y + dy). Uses FancyArrow patch to construct the arrow.
+
+Optional kwargs control the arrow construction and properties:
+
+%(FancyArrow)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="dx" arg_pos="2" name="dx" required="True" />
+ <inputPortSpec arg="dy" arg_pos="3" name="dy" required="True" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.axhline" name="MplAxhline" superclass="MplPlot">
+ <docstring>Add a horizontal line across the axis.
+
+Call signature:
+
+axhline(y=0, xmin=0, xmax=1, **kwargs)
+
+Draw a horizontal line at y from xmin to xmax. With the default values of xmin = 0 and xmax = 1, this line will always span the horizontal extent of the axes, regardless of the xlim settings, even if you change them, eg. with the :meth:`set_xlim` command. That is, the horizontal extent is in axes coords: 0=left, 0.5=middle, 1.0=right but the y location is in data coordinates.
+
+Return value is the :class:`~matplotlib.lines.Line2D` instance. kwargs are the same as kwargs to plot, and can be used to control the line properties. Eg.,
+
+draw a thick red hline at y = 0 that spans the xrange:
+
+>>> axhline(linewidth=4, color='r')
+
+draw a default hline at y = 1 that spans the xrange:
+
+>>> axhline(y=1)
+
+draw a default hline at y = .5 that spans the the middle half of the xrange:
+
+>>> axhline(y=.5, xmin=0.25, xmax=0.75)
+
+Valid kwargs are :class:`~matplotlib.lines.Line2D` properties, with the exception of 'transform':
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="y" arg_pos="0" name="y" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xmin" arg_pos="1" name="xmin" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="3" name="hold" />
+ <inputPortSpec arg="xmax" arg_pos="2" name="xmax" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.axhspan" name="MplAxhspan" superclass="MplPlot">
+ <docstring>Add a horizontal span (rectangle) across the axis.
+
+Call signature:
+
+axhspan(ymin, ymax, xmin=0, xmax=1, **kwargs)
+
+y coords are in data units and x coords are in axes (relative 0-1) units.
+
+Draw a horizontal span (rectangle) from ymin to ymax. With the default values of xmin = 0 and xmax = 1, this always spans the xrange, regardless of the xlim settings, even if you change them, eg. with the :meth:`set_xlim` command. That is, the horizontal extent is in axes coords: 0=left, 0.5=middle, 1.0=right but the y location is in data coordinates.
+
+Return value is a :class:`matplotlib.patches.Polygon` instance.
+
+Examples:
+
+draw a gray rectangle from y = 0.25-0.75 that spans the horizontal extent of the axes:
+
+>>> axhspan(0.25, 0.75, facecolor='0.5', alpha=0.5)
+
+Valid kwargs are :class:`~matplotlib.patches.Polygon` properties:
+
+%(Polygon)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="xmin" arg_pos="2" name="xmin" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="ymin" arg_pos="0" name="ymin" required="True" />
+ <inputPortSpec arg="ymax" arg_pos="1" name="ymax" required="True" />
+ <inputPortSpec arg="xmax" arg_pos="3" name="xmax" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.axvline" name="MplAxvline" superclass="MplPlot">
+ <docstring>Add a vertical line across the axes.
+
+Call signature:
+
+axvline(x=0, ymin=0, ymax=1, **kwargs)
+
+Draw a vertical line at x from ymin to ymax. With the default values of ymin = 0 and ymax = 1, this line will always span the vertical extent of the axes, regardless of the ylim settings, even if you change them, eg. with the :meth:`set_ylim` command. That is, the vertical extent is in axes coords: 0=bottom, 0.5=middle, 1.0=top but the x location is in data coordinates.
+
+Return value is the :class:`~matplotlib.lines.Line2D` instance. kwargs are the same as kwargs to plot, and can be used to control the line properties. Eg.,
+
+draw a thick red vline at x = 0 that spans the yrange:
+
+>>> axvline(linewidth=4, color='r')
+
+draw a default vline at x = 1 that spans the yrange:
+
+>>> axvline(x=1)
+
+draw a default vline at x = .5 that spans the the middle half of the yrange:
+
+>>> axvline(x=.5, ymin=0.25, ymax=0.75)
+
+Valid kwargs are :class:`~matplotlib.lines.Line2D` properties, with the exception of 'transform':
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="3" name="hold" />
+ <inputPortSpec arg="ymin" arg_pos="1" name="ymin" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ymax" arg_pos="2" name="ymax" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.axvspan" name="MplAxvspan" superclass="MplPlot">
+ <docstring>Add a vertical span (rectangle) across the axes.
+
+Call signature:
+
+axvspan(xmin, xmax, ymin=0, ymax=1, **kwargs)
+
+x coords are in data units and y coords are in axes (relative 0-1) units.
+
+Draw a vertical span (rectangle) from xmin to xmax. With the default values of ymin = 0 and ymax = 1, this always spans the yrange, regardless of the ylim settings, even if you change them, eg. with the :meth:`set_ylim` command. That is, the vertical extent is in axes coords: 0=bottom, 0.5=middle, 1.0=top but the y location is in data coordinates.
+
+Return value is the :class:`matplotlib.patches.Polygon` instance.
+
+Examples:
+
+draw a vertical green translucent rectangle from x=1.25 to 1.55 that spans the yrange of the axes:
+
+>>> axvspan(1.25, 1.55, facecolor='g', alpha=0.5)
+
+Valid kwargs are :class:`~matplotlib.patches.Polygon` properties:
+
+%(Polygon)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="xmin" arg_pos="0" name="xmin" required="True" />
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="ymin" arg_pos="2" name="ymin" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ymax" arg_pos="3" name="ymax" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xmax" arg_pos="1" name="xmax" required="True" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.bar" name="MplBar" superclass="MplPlot">
+ <docstring>Make a bar plot.
+
+Call signature:
+
+bar(left, height, width=0.8, bottom=0, **kwargs)
+
+Make a bar plot with rectangles bounded by:
+
+
+
+left, height, width, and bottom can be either scalars or sequences
+
+Return value is a list of :class:`matplotlib.patches.Rectangle` instances.
+
+Required arguments:
+
+
+
+Optional keyword arguments:
+
+
+
+For vertical bars, align = 'edge' aligns bars by their left edges in left, while align = 'center' interprets these values as the x coordinates of the bar centers. For horizontal bars, align = 'edge' aligns bars by their bottom edges in bottom, while align = 'center' interprets these values as the y coordinates of the bar centers.
+
+The optional arguments color, edgecolor, linewidth, xerr, and yerr can be either scalars or sequences of length equal to the number of bars. This enables you to use bar as the basis for stacked bar charts, or candlestick plots. Detail: xerr and yerr are passed directly to :meth:`errorbar`, so they can also have shape 2xN for independent specification of lower and upper errors.
+
+Other optional kwargs:
+
+%(Rectangle)s
+
+Example: A stacked bar chart.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="edgecolor" name="edgecolor" port_type="basic:Color">
+ <docstring>the colors of the bar edges</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidth" name="linewidth">
+ <docstring>width of bar edges; None means use default linewidth; 0 means don't draw edges.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="capsize" name="capsize" port_type="basic:Integer">
+ <docstring>(default 3) determines the length in points of the error bar caps</docstring>
+ <defaults>['3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="orientation" name="orientation" port_type="basic:String">
+ <docstring>'vertical' | 'horizontal'</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['vertical', 'horizontal']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="bottom" arg_pos="3" name="bottom" port_type="basic:Integer">
+ <docstring>the y coordinates of the bottom edges of the bars</docstring>
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>the colors of the bars</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="xerr" name="xerr">
+ <docstring>if not None, will be used to generate errorbars on the bar chart</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="align" name="align" port_type="basic:String">
+ <docstring>'edge' (default) | 'center'</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['edge', 'center']]</values>
+ <defaults>['edge']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ecolor" name="ecolor" port_type="basic:Color">
+ <docstring>specifies the color of any errorbar</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="height" arg_pos="1" name="height" required="True">
+ <docstring>the heights of the bars</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="width" arg_pos="2" name="width" port_type="basic:Float">
+ <docstring>the widths of the bars</docstring>
+ <defaults>['0.8']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="error_kw" name="error_kw">
+ <docstring>dictionary of kwargs to be passed to errorbar method. ecolor and capsize may be specified here rather than as independent kwargs.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="log" name="log" port_type="basic:Boolean">
+ <docstring>[False|True] False (default) leaves the orientation axis as-is; True sets it to log scale</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="yerr" name="yerr">
+ <docstring>if not None, will be used to generate errorbars on the bar chart</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="left" arg_pos="0" name="left" required="True">
+ <docstring>the x coordinates of the left sides of the bars</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.barh" name="MplBarh" superclass="MplPlot">
+ <docstring>Make a horizontal bar plot.
+
+Call signature:
+
+barh(bottom, width, height=0.8, left=0, **kwargs)
+
+Make a horizontal bar plot with rectangles bounded by:
+
+
+
+bottom, width, height, and left can be either scalars or sequences
+
+Return value is a list of :class:`matplotlib.patches.Rectangle` instances.
+
+Required arguments:
+
+
+
+Optional keyword arguments:
+
+
+
+Setting align = 'edge' aligns bars by their bottom edges in bottom, while align = 'center' interprets these values as the y coordinates of the bar centers.
+
+The optional arguments color, edgecolor, linewidth, xerr, and yerr can be either scalars or sequences of length equal to the number of bars. This enables you to use barh as the basis for stacked bar charts, or candlestick plots.
+
+other optional kwargs:
+
+%(Rectangle)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="edgecolor" name="edgecolor" port_type="basic:Color">
+ <docstring>the colors of the bar edges</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidth" name="linewidth">
+ <docstring>width of bar edges; None means use default linewidth; 0 means don't draw edges.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="capsize" name="capsize" port_type="basic:Integer">
+ <docstring>(default 3) determines the length in points of the error bar caps</docstring>
+ <defaults>['3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="log" name="log" port_type="basic:Boolean">
+ <docstring>[False|True] False (default) leaves the horizontal axis as-is; True sets it to log scale</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="bottom" arg_pos="0" name="bottom" required="True">
+ <docstring>the vertical positions of the bottom edges of the bars</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>the colors of the bars</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="xerr" name="xerr">
+ <docstring>if not None, will be used to generate errorbars on the bar chart</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="align" name="align" port_type="basic:String">
+ <docstring>'edge' (default) | 'center'</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['edge', 'center']]</values>
+ <defaults>['edge']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ecolor" name="ecolor" port_type="basic:Color">
+ <docstring>specifies the color of any errorbar</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="height" arg_pos="2" name="height" port_type="basic:Float">
+ <docstring>the heights (thicknesses) of the bars</docstring>
+ <defaults>['0.8']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="width" arg_pos="1" name="width" required="True">
+ <docstring>the lengths of the bars</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="yerr" name="yerr">
+ <docstring>if not None, will be used to generate errorbars on the bar chart</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="left" arg_pos="3" name="left" port_type="basic:Integer">
+ <docstring>the x coordinates of the left edges of the bars</docstring>
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.broken_barh" name="MplBrokenBarh" superclass="MplPlot">
+ <docstring>Plot horizontal bars.
+
+Call signature:
+
+broken_barh(self, xranges, yrange, **kwargs)
+
+A collection of horizontal bars spanning yrange with a sequence of xranges.
+
+Required arguments:
+
+
+
+kwargs are :class:`matplotlib.collections.BrokenBarHCollection` properties:
+
+%(BrokenBarHCollection)s
+
+these can either be a single argument, ie:
+
+facecolors = 'black'
+
+or a sequence of arguments for the various bars, ie:
+
+facecolors = ('black', 'red', 'green')
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="xranges" arg_pos="0" name="xranges" port_type="basic:List" required="True">
+ <docstring>sequence of (xmin, xwidth)</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="2" name="hold" />
+ <inputPortSpec arg="yrange" arg_pos="1" name="yrange" port_type="basic:List" required="True">
+ <docstring>sequence of (ymin, ywidth)</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.boxplot" name="MplBoxplot" superclass="MplPlot">
+ <docstring>Make a box and whisker plot.
+
+Call signature:
+
+boxplot(x, notch=False, sym='+', vert=True, whis=1.5, positions=None, widths=None, patch_artist=False, bootstrap=None, usermedians=None, conf_intervals=None)
+
+Make a box and whisker plot for each column of x or each vector in sequence x. The box extends from the lower to upper quartile values of the data, with a line at the median. The whiskers extend from the box to show the range of the data. Flier points are those past the end of the whiskers.
+
+Function Arguments:
+
+
+
+Returns a dictionary mapping each component of the boxplot to a list of the :class:`matplotlib.lines.Line2D` instances created. That dictionary has the following keys (assuming vertical boxplots):
+
+boxes: the main body of the boxplot showing the quartiles and the median's confidence intervals if enabled.
+
+medians: horizonal lines at the median of each box.
+
+whiskers: the vertical lines extending to the most extreme, n-outlier data points.
+
+caps: the horizontal lines at the ends of the whiskers.
+
+fliers: points representing data that extend beyone the whiskers (outliers).
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="hold" arg_pos="11" name="hold" />
+ <inputPortSpec arg="vert" arg_pos="3" name="vert" port_type="basic:Boolean">
+ <docstring>If True (default), makes the boxes vertical. If False, makes horizontal boxes.</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="positions" arg_pos="5" name="positions">
+ <docstring>Sets the horizontal positions of the boxes. The ticks and limits are automatically set to match the positions.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="bootstrap" arg_pos="8" name="bootstrap">
+ <docstring>Specifies whether to bootstrap the confidence intervals around the median for notched boxplots. If bootstrap==None, no bootstrapping is performed, and notches are calculated using a Gaussian-based asymptotic approximation (see McGill, R., Tukey, J.W., and Larsen, W.A., 1978, and Kendall and Stuart, 1967). Otherwise, bootstrap specifies the number of times to bootstrap the median to determine it's 95% confidence intervals. Values between 1000 and 10000 are recommended.</ [...]
+ </inputPortSpec>
+ <inputPortSpec arg="usermedians" arg_pos="9" name="usermedians" port_type="basic:List">
+ <docstring>An array or sequence whose first dimension (or length) is compatible with x. This overrides the medians computed by matplotlib for each element of usermedians that is not None. When an element of usermedians == None, the median will be computed directly as normal.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="sym" arg_pos="2" name="sym" port_type="basic:String">
+ <docstring>The default symbol for flier points. Enter an empty string ('') if you don't want to show fliers.</docstring>
+ <defaults>['b+']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="widths" arg_pos="6" name="widths" port_type="basic:Float">
+ <docstring>Either a scalar or a vector and sets the width of each box. The default is 0.5, or 0.15*(distance between extreme positions) if that is smaller.</docstring>
+ <defaults>['0.5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="patch_artist" arg_pos="7" name="patch_artist" port_type="basic:Boolean">
+ <docstring>If False produces boxes with the Line2D artist If True produces boxes with the Patch artist</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True">
+ <docstring>Array or a sequence of vectors.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="notch" arg_pos="1" name="notch" port_type="basic:Boolean">
+ <docstring>If False (default), produces a rectangular box plot. If True, will produce a notched box plot</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="whis" arg_pos="4" name="whis" port_type="basic:Float">
+ <docstring>Defines the length of the whiskers as a function of the inner quartile range. They extend to the most extreme data point within ( whis*(75%-25%) ) data range.</docstring>
+ <defaults>['1.5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="conf_intervals" arg_pos="10" name="conf_intervals" port_type="basic:List">
+ <docstring>Array or sequence whose first dimension (or length) is compatible with x and whose second dimension is 2. When the current element of conf_intervals is not None, the notch locations computed by matplotlib are overridden (assuming notch is True). When an element of conf_intervals is None, boxplot compute notches the method specified by the other kwargs (e.g. bootstrap).</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.cohere" name="MplCohere" superclass="MplPlot">
+ <docstring>Plot the coherence between x and y.
+
+Call signature:
+
+cohere(x, y, NFFT=256, Fs=2, Fc=0, detrend = mlab.detrend_none, window = mlab.window_hanning, noverlap=0, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+Plot the coherence between x and y. Coherence is the normalized cross spectral density:
+
+C_{xy} = \frac{|P_{xy}|^2}{P_{xx}P_{yy}}
+
+%(PSD)s
+
+
+
+The return value is a tuple (Cxy, f), where f are the frequencies of the coherence vector.
+
+kwargs are applied to the lines.
+
+References:
+
+Bendat & Piersol -- Random Data: Analysis and Measurement Procedures, John Wiley & Sons (1986)
+
+kwargs control the :class:`~matplotlib.lines.Line2D` properties of the coherence plot:
+
+%(Line2D)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="Fs" arg_pos="3" name="Fs" port_type="basic:Integer">
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pad_to" arg_pos="8" name="pad_to" />
+ <inputPortSpec arg="scale_by_freq" arg_pos="10" name="scale_by_freq" />
+ <inputPortSpec arg="detrend" arg_pos="5" name="detrend">
+ <defaults>['<function detrend_none at 0x02F5A3F0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="window" arg_pos="6" name="window">
+ <defaults>['<function window_hanning at 0x02F5A2B0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="Fc" arg_pos="4" name="Fc" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="NFFT" arg_pos="2" name="NFFT" port_type="basic:Integer">
+ <defaults>['256']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="11" name="hold" />
+ <inputPortSpec arg="sides" arg_pos="9" name="sides" port_type="basic:String">
+ <defaults>['default']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="noverlap" arg_pos="7" name="noverlap" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.clabel" name="MplClabel" superclass="MplPlot">
+ <docstring>Label a contour plot.
+
+Call signature:
+
+clabel(cs, **kwargs)
+
+Adds labels to line contours in cs, where cs is a :class:`~matplotlib.contour.ContourSet` object returned by contour.
+
+clabel(cs, v, **kwargs)
+
+only labels contours listed in v.
+
+Optional keyword arguments:
+
+
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="inline_spacing" name="inline_spacing">
+ <docstring>space in pixels to leave on each side of label when placing inline. Defaults to 5. This spacing will be exact for labels at locations where the contour is straight, less so for labels on curved contours.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="use_clabeltext" name="use_clabeltext" port_type="basic:String">
+ <docstring>if True (default is False), ClabelText class (instead of matplotlib.Text) is used to create labels. ClabelText recalculates rotation angles of texts during the drawing time, therefore this can be used if aspect of the axes changes.</docstring>
+ <defaults>['False)']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="fmt" name="fmt" port_type="basic:String">
+ <docstring>a format string for the label. Default is '%1.3f' Alternatively, this can be a dictionary matching contour levels with arbitrary strings to use for each contour level (i.e., fmt[level]=string), or it can be any callable, such as a :class:`~matplotlib.ticker.Formatter` instance, that returns a string when called with a numeric contour level.</docstring>
+ <defaults>['%1.3f']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="manual" name="manual">
+ <docstring>if True, contour labels will be placed manually using mouse clicks. Click the first button near a contour to add a label, click the second button (or potentially both mouse buttons at once) to finish adding labels. The third button can be used to remove the last label added, but only if labels are not inline. Alternatively, the keyboard can be used to select label locations (enter to end label placement, delete or backspace act like the third mouse button, and any oth [...]
+
+manual can be an iterable object of x,y tuples. Contour labels will be created as if mouse is clicked at each x,y positions.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="cs" arg_pos="0" name="cs" required="True" />
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>if None, the color of each label matches the color of the corresponding contour
+
+if one string color, e.g. colors = 'r' or colors = 'red', all labels will be plotted in this color
+
+if a tuple of matplotlib color args (string, float, rgb, etc), different labels will be plotted in different colors in the order specified</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="fontsize" name="fontsize">
+ <docstring>size in points or relative size eg 'smaller', 'x-large'</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rightside_up" name="rightside_up" port_type="basic:Boolean">
+ <docstring>if True (default), label rotations will always be plus or minus 90 degrees from level.</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="CS" arg_pos="0" name="CS" required="True" />
+ <inputPortSpec arg="inline" name="inline" port_type="basic:Boolean">
+ <docstring>controls whether the underlying contour is removed or not. Default is True.</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.contour" name="MplContour" superclass="MplPlot">
+ <docstring>Plot contours.
+
+:func:`~matplotlib.pyplot.contour` and :func:`~matplotlib.pyplot.contourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+:func:`~matplotlib.pyplot.contourf` differs from the MATLAB version in that it does not draw the polygon edges. To draw edges, add line contours with calls to :func:`~matplotlib.pyplot.contour`.
+
+Call signatures:
+
+contour(Z)
+
+make a contour plot of an array Z. The level values are chosen automatically.
+
+contour(X,Y,Z)
+
+X, Y specify the (x, y) coordinates of the surface
+
+contour(Z,N) contour(X,Y,Z,N)
+
+contour N automatically-chosen levels.
+
+contour(Z,V) contour(X,Y,Z,V)
+
+draw contour lines at the values specified in sequence V
+
+contourf(..., V)
+
+fill the len(V)-1 regions between the values in V
+
+contour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+X and Y must both be 2-D with the same shape as Z, or they must both be 1-D such that len(X) is the number of columns in Z and len(Y) is the number of rows in Z.
+
+C = contour(...) returns a :class:`~matplotlib.contour.QuadContourSet` object.
+
+Optional keyword arguments:
+
+
+
+contour-only keyword arguments:
+
+
+
+contourf-only keyword arguments:
+
+
+
+Note: contourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="origin" name="origin" port_type="basic:String">
+ <docstring>If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.
+
+This keyword is not active if X and Y are specified in the call to contour.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'upper', 'lower', 'image']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="xunits" name="xunits" port_type="basic:String">
+ <docstring>Override axis units by specifying an instance of a :class:`matplotlib.units.ConversionInterface`.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'registered units']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="extend" name="extend" port_type="basic:String">
+ <docstring>Unless this is 'neither', contour levels are automatically added to one or both ends of the range so that all data are included. These added ranges are then mapped to the special colormap values which default to the ends of the colormap range, but can be set via :meth:`matplotlib.colors.Colormap.set_under` and :meth:`matplotlib.colors.Colormap.set_over` methods.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['neither', 'both', 'min', 'max']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" name="vmin">
+ <docstring>If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="nchunk" name="nchunk" port_type="basic:Integer">
+ <docstring>If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[[0]]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyles" name="linestyles" port_type="basic:String">
+ <docstring>If linestyles is None, the default is 'solid' unless the lines are monochrome. In that case, negative contours will take their linestyle from the matplotlibrc contour.negative_linestyle setting.
+
+linestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'solid', 'dashed', 'dashdot', 'dotted']]</values>
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hatches" name="hatches" port_type="basic:List">
+ <docstring>A list of cross hatch patterns to use on the filled areas. If None, no hatching will be added to the contour. Hatching is supported in the PostScript, PDF, SVG and Agg backends only.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="levels" name="levelsSequence" port_type="basic:List">
+ <docstring>A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]</docstring>
+ <alternateSpec arg="" name="levelsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" name="linewidths" port_type="basic:String">
+ <docstring>If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.
+
+If a number, all levels will be plotted with this linewidth.
+
+If a tuple, different levels will be plotted with different linewidths in the order specified</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'number', 'tuple of numbers']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="locator" name="locator" port_type="basic:String">
+ <docstring>If locator is None, the default :class:`~matplotlib.ticker.MaxNLocator` is used. The locator is used to determine the contour levels if they are not given explicitly via the V argument.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'ticker.Locator subclass']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>If None, the colormap specified by cmap will be used.
+
+If a string, like 'r' or 'red', all levels will be plotted in this color.
+
+If a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['', '(mpl_colors)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="yunits" name="yunits" port_type="basic:String">
+ <docstring>Override axis units by specifying an instance of a :class:`matplotlib.units.ConversionInterface`.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'registered units']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="extent" name="extent" port_type="basic:String">
+ <docstring>If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].
+
+This keyword is not active if X and Y are specified in the call to contour.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', '(x0,x1,y0,y1)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="vmax" name="vmax">
+ <docstring>If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>The alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="Z" arg_pos="0" name="Z" required="True" />
+ <inputPortSpec arg="antialiased" name="antialiased" port_type="basic:Boolean">
+ <docstring>enable antialiasing, overriding the defaults. For filled contours, the default is True. For line contours, it is taken from rcParams['lines.antialiased'].</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.contourf" name="MplContourf" superclass="MplPlot">
+ <docstring>Plot contours.
+
+:func:`~matplotlib.pyplot.contour` and :func:`~matplotlib.pyplot.contourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+:func:`~matplotlib.pyplot.contourf` differs from the MATLAB version in that it does not draw the polygon edges. To draw edges, add line contours with calls to :func:`~matplotlib.pyplot.contour`.
+
+Call signatures:
+
+contour(Z)
+
+make a contour plot of an array Z. The level values are chosen automatically.
+
+contour(X,Y,Z)
+
+X, Y specify the (x, y) coordinates of the surface
+
+contour(Z,N) contour(X,Y,Z,N)
+
+contour N automatically-chosen levels.
+
+contour(Z,V) contour(X,Y,Z,V)
+
+draw contour lines at the values specified in sequence V
+
+contourf(..., V)
+
+fill the len(V)-1 regions between the values in V
+
+contour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+X and Y must both be 2-D with the same shape as Z, or they must both be 1-D such that len(X) is the number of columns in Z and len(Y) is the number of rows in Z.
+
+C = contour(...) returns a :class:`~matplotlib.contour.QuadContourSet` object.
+
+Optional keyword arguments:
+
+extent: [ None | (x0,x1,y0,y1) ]
+
+If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].
+
+This keyword is not active if X and Y are specified in the call to contour.
+
+contour-only keyword arguments:
+
+
+
+contourf-only keyword arguments:
+
+
+
+Note: contourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="origin" name="origin" port_type="basic:String">
+ <docstring>If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.
+
+This keyword is not active if X and Y are specified in the call to contour.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'upper', 'lower', 'image']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyles" name="linestyles" port_type="basic:String">
+ <docstring>If linestyles is None, the default is 'solid' unless the lines are monochrome. In that case, negative contours will take their linestyle from the matplotlibrc contour.negative_linestyle setting.
+
+linestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'solid', 'dashed', 'dashdot', 'dotted']]</values>
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" name="vmin">
+ <docstring>If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="nchunk" name="nchunk" port_type="basic:Integer">
+ <docstring>If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[[0]]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="hatches" name="hatches" port_type="basic:List">
+ <docstring>A list of cross hatch patterns to use on the filled areas. If None, no hatching will be added to the contour. Hatching is supported in the PostScript, PDF, SVG and Agg backends only.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="levels" name="levelsSequence" port_type="basic:List">
+ <docstring>A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]</docstring>
+ <alternateSpec arg="" name="levelsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" name="linewidths" port_type="basic:String">
+ <docstring>If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.
+
+If a number, all levels will be plotted with this linewidth.
+
+If a tuple, different levels will be plotted with different linewidths in the order specified</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'number', 'tuple of numbers']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>If None, the colormap specified by cmap will be used.
+
+If a string, like 'r' or 'red', all levels will be plotted in this color.
+
+If a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['', '(mpl_colors)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="vmax" name="vmax">
+ <docstring>If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>The alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="Z" arg_pos="0" name="Z" required="True" />
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.csd" name="MplCsd" superclass="MplPlot">
+ <docstring>Plot cross-spectral density.
+
+Call signature:
+
+csd(x, y, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none, window=mlab.window_hanning, noverlap=0, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+The cross spectral density P_{xy} by Welch's average periodogram method. The vectors x and y are divided into NFFT length segments. Each segment is detrended by function detrend and windowed by function window. The product of the direct FFTs of x and y are averaged over each segment to compute P_{xy}, with a scaling to correct for power loss due to windowing.
+
+Returns the tuple (Pxy, freqs). P is the cross spectrum (complex valued), and 10\log_{10}|P_{xy}| is plotted.
+
+%(PSD)s
+
+
+
+kwargs control the Line2D properties:
+
+%(Line2D)s
+
+Example:
+
+seealso: :meth:`psd` For a description of the optional parameters.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="Fs" arg_pos="3" name="Fs" port_type="basic:Integer">
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pad_to" arg_pos="8" name="pad_to" />
+ <inputPortSpec arg="scale_by_freq" arg_pos="10" name="scale_by_freq" />
+ <inputPortSpec arg="detrend" arg_pos="5" name="detrend">
+ <defaults>['<function detrend_none at 0x02F5A3F0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="window" arg_pos="6" name="window">
+ <defaults>['<function window_hanning at 0x02F5A2B0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="Fc" arg_pos="4" name="Fc" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="NFFT" arg_pos="2" name="NFFT" port_type="basic:Integer">
+ <defaults>['256']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="11" name="hold" />
+ <inputPortSpec arg="sides" arg_pos="9" name="sides" port_type="basic:String">
+ <defaults>['default']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="noverlap" arg_pos="7" name="noverlap" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.errorbar" name="MplErrorbar" superclass="MplPlot">
+ <docstring>Plot an errorbar graph.
+
+Call signature:
+
+errorbar(x, y, yerr=None, xerr=None, fmt='-', ecolor=None, elinewidth=None, capsize=3, barsabove=False, lolims=False, uplims=False, xlolims=False, xuplims=False, errorevery=1, capthick=None)
+
+Plot x versus y with error deltas in yerr and xerr. Vertical errorbars are plotted if yerr is not None. Horizontal errorbars are plotted if xerr is not None.
+
+x, y, xerr, and yerr can all be scalars, which plots a single error bar at x, y.
+
+Optional keyword arguments:
+
+
+
+All other keyword arguments are passed on to the plot command for the markers. For example, this code makes big red squares with thick green edges:
+
+x,y,yerr = rand(3,10) errorbar(x, y, yerr, marker='s', mfc='red', mec='green', ms=20, mew=4)
+
+where mfc, mec, ms and mew are aliases for the longer property names, markerfacecolor, markeredgecolor, markersize and markeredgewith.
+
+valid kwargs for the marker properties are
+
+%(Line2D)s
+
+Returns (plotline, caplines, barlinecols):
+
+
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="lolims" arg_pos="9" name="lolims" port_type="basic:Boolean">
+ <docstring>These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="capsize" arg_pos="7" name="capsize" port_type="basic:Float">
+ <docstring>The length of the error bar caps in points</docstring>
+ <defaults>['3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="uplims" arg_pos="10" name="uplims" port_type="basic:Boolean">
+ <docstring>These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xlolims" arg_pos="11" name="xlolims" port_type="basic:Boolean">
+ <docstring>These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="barsabove" arg_pos="8" name="barsabove">
+ <docstring>if True, will plot the errorbars above the plot symbols. Default is below.</docstring>
+ <defaults>['below']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xerr" arg_pos="3" name="xerr">
+ <docstring>If a scalar number, len(N) array-like object, or an Nx1 array-like object, errorbars are drawn +/- value.
+
+If a sequence of shape 2xN, errorbars are drawn at -row1 and +row2</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['N, Nx1, or 2xN array-like']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="fmt" arg_pos="4" name="fmt" port_type="basic:String">
+ <docstring>The plot format symbol. If fmt is None, only the errorbars are plotted. This is used for adding errorbars to a bar plot, for example.</docstring>
+ <defaults>['-']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ecolor" arg_pos="5" name="ecolor" port_type="basic:Color">
+ <docstring>A matplotlib color arg which gives the color the errorbar lines; if None, use the marker color.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'mpl color']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="errorevery" arg_pos="13" name="errorevery" port_type="basic:Integer">
+ <docstring>subsamples the errorbars. Eg if everyerror=5, errorbars for every 5-th datapoint will be plotted. The data plot itself still shows all data points.</docstring>
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="capthick" arg_pos="14" name="capthick" port_type="basic:Float">
+ <docstring>An alias kwarg to markeredgewidth (a.k.a. - mew). This setting is a more sensible name for the property that controls the thickness of the error bar cap in points. For backwards compatibility, if mew or markeredgewidth are given, then they will over-ride capthick. This may change in future releases.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="xuplims" arg_pos="12" name="xuplims" port_type="basic:Boolean">
+ <docstring>These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="elinewidth" arg_pos="6" name="elinewidth" port_type="basic:Float">
+ <docstring>The linewidth of the errorbar lines. If None, use the linewidth.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="15" name="hold" />
+ <inputPortSpec arg="yerr" arg_pos="2" name="yerr">
+ <docstring>If a scalar number, len(N) array-like object, or an Nx1 array-like object, errorbars are drawn +/- value.
+
+If a sequence of shape 2xN, errorbars are drawn at -row1 and +row2</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['N, Nx1, or 2xN array-like']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.fill" name="MplFill" superclass="MplPlot">
+ <docstring>Plot filled polygons.
+
+Call signature:
+
+fill(*args, **kwargs)
+
+args is a variable length argument, allowing for multiple x, y pairs with an optional color format string; see :func:`~matplotlib.pyplot.plot` for details on the argument parsing. For example, to plot a polygon with vertices at x, y in blue.:
+
+ax.fill(x,y, 'b' )
+
+An arbitrary number of x, y, color groups can be specified:
+
+ax.fill(x1, y1, 'g', x2, y2, 'r')
+
+Return value is a list of :class:`~matplotlib.patches.Patch` instances that were added.
+
+The same color strings that :func:`~matplotlib.pyplot.plot` supports are supported by the fill format string.
+
+If you would like to fill below a curve, eg. shade a region between 0 and y along x, use :meth:`fill_between`
+
+The closed kwarg will close the polygon when True (default).
+
+kwargs control the :class:`~matplotlib.patches.Polygon` properties:
+
+%(Polygon)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.fill_between" name="MplFillBetween" superclass="MplPlot">
+ <docstring>Make filled polygons between two curves.
+
+Call signature:
+
+fill_between(x, y1, y2=0, where=None, **kwargs)
+
+Create a :class:`~matplotlib.collections.PolyCollection` filling the regions between y1 and y2 where where==True
+
+
+
+kwargs control the :class:`~matplotlib.patches.Polygon` properties:
+
+%(PolyCollection)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="y2" arg_pos="2" name="y2" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="interpolate" arg_pos="4" name="interpolate" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y1" arg_pos="1" name="y1" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="5" name="hold" />
+ <inputPortSpec arg="where" arg_pos="3" name="where" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.fill_betweenx" name="MplFillBetweenx" superclass="MplPlot">
+ <docstring>Make filled polygons between two horizontal curves.
+
+Call signature:
+
+fill_between(y, x1, x2=0, where=None, **kwargs)
+
+Create a :class:`~matplotlib.collections.PolyCollection` filling the regions between x1 and x2 where where==True
+
+
+
+kwargs control the :class:`~matplotlib.patches.Polygon` properties:
+
+%(PolyCollection)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="y" arg_pos="0" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x2" arg_pos="2" name="x2" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="4" name="hold" />
+ <inputPortSpec arg="x1" arg_pos="1" name="x1" required="True" />
+ <inputPortSpec arg="where" arg_pos="3" name="where" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.hexbin" name="MplHexbin" superclass="MplPlot">
+ <docstring>Make a hexagonal binning plot.
+
+Call signature:
+
+hexbin(x, y, C = None, gridsize = 100, bins = None, xscale = 'linear', yscale = 'linear', cmap=None, norm=None, vmin=None, vmax=None, alpha=None, linewidths=None, edgecolors='none' reduce_C_function = np.mean, mincnt=None, marginals=True **kwargs)
+
+Make a hexagonal binning plot of x versus y, where x, y are 1-D sequences of the same length, N. If C is None (the default), this is a histogram of the number of occurences of the observations at (x[i],y[i]).
+
+If C is specified, it specifies values at the coordinate (x[i],y[i]). These values are accumulated for each hexagonal bin and then reduced according to reduce_C_function, which defaults to numpy's mean function (np.mean). (If C is specified, it must also be a 1-D sequence of the same length as x and y.)
+
+x, y and/or C may be masked arrays, in which case only unmasked points will be plotted.
+
+Optional keyword arguments:
+
+Other keyword arguments controlling color mapping and normalization arguments:
+
+Other keyword arguments controlling the Collection properties:
+
+Here are the standard descriptions of all the :class:`~matplotlib.collections.Collection` kwargs:
+
+%(Collection)s
+
+The return value is a :class:`~matplotlib.collections.PolyCollection` instance; use :meth:`~matplotlib.collections.PolyCollection.get_array` on this :class:`~matplotlib.collections.PolyCollection` to get the counts in each hexagon. If marginals is True, horizontal bar and vertical bar (both PolyCollections) will be attached to the return collection as attributes hbar and vbar.
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="vmax" arg_pos="11" name="vmax" port_type="basic:Float">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="edgecolors" arg_pos="14" name="edgecolorsSequence" port_type="basic:List">
+ <docstring>If 'none', draws the edges in the same color as the fill color. This is the default, as it avoids unsightly unpainted pixels between the hexagons.
+
+If None, draws the outlines in the default color.
+
+If a matplotlib color arg or sequence of rgba tuples, draws the outlines in the specified color.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'none', 'mpl color']]</values>
+ <defaults>['none']</defaults>
+ <alternateSpec arg="" name="edgecolorsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="C" arg_pos="2" name="C" />
+ <inputPortSpec arg="gridsize" arg_pos="3" name="gridsize" port_type="basic:Integer">
+ <docstring>The number of hexagons in the x-direction, default is 100. The corresponding number of hexagons in the y-direction is chosen such that the hexagons are approximately regular. Alternatively, gridsize can be a tuple with two elements specifying the number of hexagons in the x-direction and the y-direction.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[[100]]</values>
+ <defaults>['100']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" arg_pos="10" name="vmin" port_type="basic:Float">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="yscale" arg_pos="6" name="yscale" port_type="basic:String">
+ <defaults>['linear']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="reduce_C_function" arg_pos="15" name="reduce_C_function">
+ <defaults>['<function mean at 0x0277B3B0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" arg_pos="13" name="linewidths">
+ <docstring>If None, defaults to rc lines.linewidth. Note that this is a tuple, and if you set the linewidths argument you must set it as a sequence of floats, as required by :class:`~matplotlib.collections.RegularPolyCollection`.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="xscale" arg_pos="5" name="xscale" port_type="basic:String">
+ <docstring>Use a linear or log10 scale on the horizontal axis.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['linear', 'log']]</values>
+ <defaults>['linear']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="8" name="cmap" port_type="basic:String">
+ <docstring>a :class:`matplotlib.colors.Colormap` instance. If None, defaults to rc image.cmap.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="9" name="norm" port_type="basic:String">
+ <docstring>:class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0,1.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="extent" arg_pos="7" name="extent">
+ <docstring>The limits of the bins. The default assigns the limits based on gridsize, x, y, xscale and yscale.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" arg_pos="12" name="alpha" port_type="basic:Float">
+ <docstring>the alpha value for the patches</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" required="True" />
+ <inputPortSpec arg="hold" arg_pos="18" name="hold" />
+ <inputPortSpec arg="mincnt" arg_pos="16" name="mincnt">
+ <docstring>If not None, only display cells with more than mincnt number of points in the cell</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="marginals" arg_pos="17" name="marginals" port_type="basic:Boolean">
+ <docstring>if marginals is True, plot the marginal density as colormapped rectagles along the bottom of the x-axis and left of the y-axis</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="bins" arg_pos="4" name="bins">
+ <docstring>If None, no binning is applied; the color of each hexagon directly corresponds to its count value.
+
+If 'log', use a logarithmic scale for the color map. Internally, log_{10}(i+1) is used to determine the hexagon color.
+
+If an integer, divide the counts in the specified number of bins, and color the hexagons accordingly.
+
+If a sequence of values, the values of the lower bound of the bins to be used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'log']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="scale" name="scale" port_type="basic:String">
+ <docstring>Use a linear or log10 scale on the vertical axis.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['linear', 'log']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.hist" name="MplHist" superclass="MplPlot">
+ <docstring>Plot a histogram.
+
+Call signature:
+
+hist(x, bins=10, range=None, normed=False, weights=None, cumulative=False, bottom=None, histtype='bar', align='mid', orientation='vertical', rwidth=None, log=False, color=None, label=None, stacked=False, **kwargs)
+
+Compute and draw the histogram of x. The return value is a tuple (n, bins, patches) or ([n0, n1, ...], bins, [patches0, patches1,...]) if the input contains multiple data.
+
+Multiple data can be provided via x as a list of datasets of potentially different length ([x0, x1, ...]), or as a 2-D ndarray in which each column is a dataset. Note that the ndarray form is transposed relative to the list form.
+
+Masked arrays are not supported at present.
+
+Keyword arguments:
+
+
+
+kwargs are used to update the properties of the :class:`~matplotlib.patches.Patch` instances returned by hist:
+
+%(Patch)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="rwidth" arg_pos="10" name="rwidth">
+ <docstring>The relative width of the bars as a fraction of the bin width. If None, automatically compute the width. Ignored if histtype = 'step' or 'stepfilled'.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="normed" arg_pos="3" name="normed" port_type="basic:Boolean">
+ <docstring>If True, the first element of the return tuple will be the counts normalized to form a probability density, i.e., n/(len(x)*dbin). In a probability density, the integral of the histogram should be 1; you can verify that with a trapezoidal integration of the probability density function:
+
+pdf, bins, patches = ax.hist(...) print np.sum(pdf * np.diff(bins))
+
+Until numpy release 1.5, the underlying numpy histogram function was incorrect with normed*=*True if bin sizes were unequal. MPL inherited that error. It is now corrected within MPL when using earlier numpy versions</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="stacked" arg_pos="14" name="stacked" port_type="basic:Boolean">
+ <docstring>If True, multiple data are stacked on top of each other If False multiple data are aranged side by side if histtype is 'bar' or on top of each other if histtype is 'step'
+
+.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="orientation" arg_pos="9" name="orientation" port_type="basic:String">
+ <docstring>If 'horizontal', :func:`~matplotlib.pyplot.barh` will be used for bar-type histograms and the bottom kwarg will be the left edges.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['horizontal', 'vertical']]</values>
+ <defaults>['vertical']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="bottom" arg_pos="6" name="bottom" />
+ <inputPortSpec arg="color" arg_pos="12" name="colorSequence" port_type="basic:List">
+ <docstring>Color spec or sequence of color specs, one per dataset. Default (None) uses the standard line color sequence.</docstring>
+ <translations>translate_color</translations>
+ <alternateSpec arg="" name="colorScalar" port_type="basic:Color" />
+ </inputPortSpec>
+ <inputPortSpec arg="histtype" arg_pos="7" name="histtype" port_type="basic:String">
+ <docstring>The type of histogram to draw.
+
+'bar' is a traditional bar-type histogram. If multiple data are given the bars are aranged side by side.
+
+'barstacked' is a bar-type histogram where multiple data are stacked on top of each other.
+
+'step' generates a lineplot that is by default unfilled.
+
+'stepfilled' generates a lineplot that is by default filled.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['bar', 'barstacked', 'step', 'stepfilled']]</values>
+ <defaults>['bar']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="align" arg_pos="8" name="align" port_type="basic:String">
+ <docstring>Controls how the histogram is plotted.
+
+'left': bars are centered on the left bin edges.
+
+'mid': bars are centered between the bin edges.
+
+'right': bars are centered on the right bin edges.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['left', 'mid', 'right']]</values>
+ <defaults>['mid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cumulative" arg_pos="5" name="cumulative" port_type="basic:Boolean">
+ <docstring>If True, then a histogram is computed where each bin gives the counts in that bin plus all bins for smaller values. The last bin gives the total number of datapoints. If normed is also True then the histogram is normalized such that the last bin equals 1. If cumulative evaluates to less than 0 (e.g. -1), the direction of accumulation is reversed. In this case, if normed is also True, then the histogram is normalized such that the first bin equals 1.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label" arg_pos="13" name="labelSequence" port_type="basic:List">
+ <docstring>String, or sequence of strings to match multiple datasets. Bar charts yield multiple patches per dataset, but only the first gets the label, so that the legend command will work as expected:
+
+ax.hist(10+2*np.random.randn(1000), label='men') ax.hist(12+3*np.random.randn(1000), label='women', alpha=0.5) ax.legend()</docstring>
+ <alternateSpec arg="" name="labelScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="range" arg_pos="2" name="range" port_type="basic:List">
+ <docstring>The lower and upper range of the bins. Lower and upper outliers are ignored. If not provided, range is (x.min(), x.max()). Range has no effect if bins is a sequence.
+
+If bins is a sequence or range is specified, autoscaling is based on the specified bin range instead of the range of x.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="weights" arg_pos="4" name="weights">
+ <docstring>An array of weights, of the same shape as x. Each value in x only contributes its associated weight towards the bin count (instead of 1). If normed is True, the weights are normalized, so that the integral of the density over the range remains 1.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="15" name="hold" />
+ <inputPortSpec arg="bins" arg_pos="1" name="binsSequence" port_type="basic:List">
+ <docstring>Either an integer number of bins or a sequence giving the bins. If bins is an integer, bins + 1 bin edges will be returned, consistent with :func:`numpy.histogram` for numpy version >= 1.3, and with the new = True argument in earlier versions. Unequally spaced bins are supported if bins is a sequence.</docstring>
+ <defaults>['10']</defaults>
+ <alternateSpec arg="" name="binsScalar" port_type="basic:Integer" />
+ </inputPortSpec>
+ <inputPortSpec arg="log" arg_pos="11" name="log" port_type="basic:Boolean">
+ <docstring>If True, the histogram axis will be set to a log scale. If log is True and x is a 1D array, empty bins will be filtered out and only the non-empty (n, bins, patches) will be returned.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.hist2d" name="MplHist2d" superclass="MplPlot">
+ <docstring>Make a 2D histogram plot.
+
+Call signature:
+
+hist2d(x, y, bins = None, range=None, weights=None, cmin=None, cmax=None **kwargs)
+
+Make a 2d histogram plot of x versus y, where x, y are 1-D sequences of the same length.
+
+The return value is (counts, xedges, yedges, Image).
+
+Optional keyword arguments: bins: [None | int | [int, int] | array_like | [array, array]]
+
+The bin specification:
+
+If int, the number of bins for the two dimensions (nx=ny=bins).
+
+If [int, int], the number of bins in each dimension (nx, ny = bins).
+
+If array_like, the bin edges for the two dimensions (x_edges=y_edges=bins).
+
+If [array, array], the bin edges in each dimension (x_edges, y_edges = bins).
+
+The default value is 10.
+
+Remaining keyword arguments are passed directly to :meth:`pcolorfast`.
+
+Rendering the histogram with a logarithmic color scale is accomplished by passing a :class:`colors.LogNorm` instance to the norm keyword argument.
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="normed" arg_pos="4" name="normed" port_type="basic:Boolean">
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmin" arg_pos="6" name="cmin" />
+ <inputPortSpec arg="range" arg_pos="3" name="range" />
+ <inputPortSpec arg="weights" arg_pos="5" name="weights" />
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="8" name="hold" />
+ <inputPortSpec arg="cmax" arg_pos="7" name="cmax" />
+ <inputPortSpec arg="bins" arg_pos="2" name="bins" port_type="basic:Integer">
+ <defaults>['10']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.hlines" name="MplHlines" superclass="MplPlot">
+ <docstring>Plot horizontal lines.
+
+call signature:
+
+hlines(y, xmin, xmax, colors='k', linestyles='solid', **kwargs)
+
+Plot horizontal lines at each y from xmin to xmax.
+
+Returns the :class:`~matplotlib.collections.LineCollection` that was added.
+
+Required arguments:
+
+
+
+Optional keyword arguments:
+
+
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="linestyles" arg_pos="4" name="linestyles" port_type="basic:String">
+ <docstring>[ 'solid' | 'dashed' | 'dashdot' | 'dotted' ]</docstring>
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label" arg_pos="5" name="label" port_type="basic:String">
+ <defaults>['']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xmin" arg_pos="1" name="xmin" port_type="basic:Float" required="True">
+ <docstring>can be scalars or len(x) numpy arrays. If they are scalars, then the respective values are constant, else the widths of the lines are determined by xmin and xmax.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="colors" arg_pos="3" name="colorsSequence" port_type="basic:List">
+ <docstring>a line collections color argument, either a single color or a len(y) list of colors</docstring>
+ <defaults>['k']</defaults>
+ <alternateSpec arg="" name="colorsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="xmax" arg_pos="2" name="xmax" port_type="basic:Float" required="True">
+ <docstring>can be scalars or len(x) numpy arrays. If they are scalars, then the respective values are constant, else the widths of the lines are determined by xmin and xmax.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="0" name="y" port_type="basic:List" required="True">
+ <docstring>a 1-D numpy array or iterable.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="6" name="hold" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.imshow" name="MplImshow" superclass="MplPlot">
+ <docstring>Display an image on the axes.
+
+Call signature:
+
+imshow(X, cmap=None, norm=None, aspect=None, interpolation=None, alpha=None, vmin=None, vmax=None, origin=None, extent=None, **kwargs)
+
+Display the image in X to current axes. X may be a float array, a uint8 array or a PIL image. If X is an array, X can have the following shapes:
+
+MxN -- luminance (grayscale, float array only)
+
+MxNx3 -- RGB (float or uint8 array)
+
+MxNx4 -- RGBA (float or uint8 array)
+
+The value for each component of MxNx3 and MxNx4 float arrays should be in the range 0.0 to 1.0; MxN float arrays may be normalised.
+
+An :class:`matplotlib.image.AxesImage` instance is returned.
+
+Keyword arguments:
+
+interpolation:
+
+Acceptable values are None, 'none', 'nearest', 'bilinear', 'bicubic', 'spline16', 'spline36', 'hanning', 'hamming', 'hermite', 'kaiser', 'quadric', 'catrom', 'gaussian', 'bessel', 'mitchell', 'sinc', 'lanczos'
+
+If interpolation is None, default to rc image.interpolation. See also the filternorm and filterrad parameters
+
+If interpolation is 'none', then no interpolation is performed on the Agg, ps and pdf backends. Other backends will fall back to 'nearest'.
+
+Additional kwargs are :class:`~matplotlib.artist.Artist` properties:
+
+%(Artist)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="origin" arg_pos="8" name="origin" />
+ <inputPortSpec arg="imlim" arg_pos="13" name="imlim" />
+ <inputPortSpec arg="extent" arg_pos="9" name="extent" />
+ <inputPortSpec arg="vmin" arg_pos="6" name="vmin" />
+ <inputPortSpec arg="url" arg_pos="15" name="url" />
+ <inputPortSpec arg="resample" arg_pos="14" name="resample" />
+ <inputPortSpec arg="shape" arg_pos="10" name="shape" />
+ <inputPortSpec arg="cmap" arg_pos="1" name="cmap" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Colormap` instance, eg. cm.jet. If None, default to rc image.cmap value.
+
+cmap is ignored when X has RGB(A) information</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="filterrad" arg_pos="12" name="filterrad" port_type="basic:Float">
+ <defaults>['4.0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="filternorm" arg_pos="11" name="filternorm" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="aspect" arg_pos="3" name="aspect">
+ <docstring>If 'auto', changes the image aspect ratio to match that of the axes
+
+If 'equal', and extent is None, changes the axes aspect ratio to match that of the image. If extent is not None, the axes aspect ratio is changed to match that of the extent.
+
+If None, default to rc image.aspect value.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'auto', 'equal']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" arg_pos="5" name="alpha" />
+ <inputPortSpec arg="vmax" arg_pos="7" name="vmax" />
+ <inputPortSpec arg="X" arg_pos="0" name="X" required="True" />
+ <inputPortSpec arg="hold" arg_pos="16" name="hold" />
+ <inputPortSpec arg="norm" arg_pos="2" name="norm" />
+ <inputPortSpec arg="interpolation" arg_pos="4" name="interpolation" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.loglog" name="MplLoglog" superclass="MplPlot">
+ <docstring>Make a plot with log scaling on both the x and y axis.
+
+Call signature:
+
+loglog(*args, **kwargs)
+
+:func:`~matplotlib.pyplot.loglog` supports all the keyword arguments of :func:`~matplotlib.pyplot.plot` and :meth:`matplotlib.axes.Axes.set_xscale` / :meth:`matplotlib.axes.Axes.set_yscale`.
+
+Notable keyword arguments:
+
+
+
+The remaining valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="nonposx" name="nonposx" port_type="basic:String">
+ <docstring>Non-positive values in x or y can be masked as invalid, or clipped to a very small positive number</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['mask', 'clip']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="nonposy" name="nonposy" port_type="basic:String">
+ <docstring>Non-positive values in x or y can be masked as invalid, or clipped to a very small positive number</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['mask', 'clip']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="basex" name="basex" port_type="basic:Float">
+ <docstring>Base of the x/y logarithm</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="basey" name="basey" port_type="basic:Float">
+ <docstring>Base of the x/y logarithm</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="subsx" name="subsxSequence" port_type="basic:List">
+ <docstring>The location of the minor x/y ticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`matplotlib.axes.Axes.set_xscale` / :meth:`matplotlib.axes.Axes.set_yscale` for details</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="" name="subsxScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="subsy" name="subsySequence" port_type="basic:List">
+ <docstring>The location of the minor x/y ticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`matplotlib.axes.Axes.set_xscale` / :meth:`matplotlib.axes.Axes.set_yscale` for details</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="" name="subsyScalar" port_type="basic:String" />
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.pcolor" name="MplPcolor" superclass="MplPlot">
+ <docstring>Create a pseudocolor plot of a 2-D array.
+
+Note: pcolor can be very slow for large arrays; consider using the similar but much faster :func:`~matplotlib.pyplot.pcolormesh` instead.
+
+Call signatures:
+
+pcolor(C, **kwargs) pcolor(X, Y, C, **kwargs)
+
+C is the array of color values.
+
+X and Y, if given, specify the (x, y) coordinates of the colored quadrilaterals; the quadrilateral for C[i,j] has corners at:
+
+(X[i, j], Y[i, j]), (X[i, j+1], Y[i, j+1]), (X[i+1, j], Y[i+1, j]), (X[i+1, j+1], Y[i+1, j+1]).
+
+Ideally the dimensions of X and Y should be one greater than those of C; if the dimensions are the same, then the last row and column of C will be ignored.
+
+Note that the the column index corresponds to the x-coordinate, and the row index corresponds to y; for details, see the :ref:`Grid Orientation <axes-pcolor-grid-orientation>` section below.
+
+If either or both of X and Y are 1-D arrays or column vectors, they will be expanded as needed into the appropriate 2-D arrays, making a rectangular grid.
+
+X, Y and C may be masked arrays. If either C[i, j], or one of the vertices surrounding C[i,j] (X or Y at [i, j], [i+1, j], [i, j+1],[i+1, j+1]) is masked, nothing is plotted.
+
+Keyword arguments:
+
+
+
+Return value is a :class:`matplotlib.collections.Collection` instance.
+
+The grid orientation follows the MATLAB convention: an array C with shape (nrows, ncolumns) is plotted with the column number as X and the row number as Y, increasing up; hence it is plotted the way the array would be printed, except that the Y axis is reversed. That is, C is taken as C*(*y, x).
+
+Similarly for :func:`meshgrid`:
+
+x = np.arange(5) y = np.arange(3) X, Y = meshgrid(x,y)
+
+is equivalent to:
+
+X = array([[0, 1, 2, 3, 4], [0, 1, 2, 3, 4], [0, 1, 2, 3, 4]]) Y = array([[0, 0, 0, 0, 0], [1, 1, 1, 1, 1], [2, 2, 2, 2, 2]])
+
+so if you have:
+
+C = rand( len(x), len(y))
+
+then you need:
+
+pcolor(X, Y, C.T)
+
+or:
+
+pcolor(C.T)
+
+MATLAB :func:`pcolor` always discards the last row and column of C, but matplotlib displays the last row and column if X and Y are not specified, or if X and Y have one more row and column than C.
+
+kwargs can be used to control the :class:`~matplotlib.collections.PolyCollection` properties:
+
+%(PolyCollection)s
+
+Note: the default antialiaseds is False if the default edgecolors*="none" is used. This eliminates artificial lines at patch boundaries, and works regardless of the value of alpha. If *edgecolors is not "none", then the default antialiaseds is taken from rcParams['patch.antialiased'], which defaults to True. Stroking the edges may be preferred if alpha is 1, but will cause artifacts otherwise.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="edgecolors" name="edgecolorsSequence" port_type="basic:List">
+ <docstring>If None, the rc setting is used by default.
+
+If 'none', edges will not be visible.
+
+An mpl color or sequence of colors will set the edge color</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'none', 'color']]</values>
+ <alternateSpec arg="" name="edgecolorsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" name="vmin">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Colormap` instance. If None, use rc settings.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>the alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="vmax" name="vmax">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="shading" name="shading" port_type="basic:String">
+ <docstring>If 'faceted', a black grid is drawn around each rectangle; if 'flat', edges are not drawn. Default is 'flat', contrary to MATLAB.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['flat', 'faceted']]</values>
+ <defaults>['flat']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>An :class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0,1. If None, defaults to :func:`normalize`.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.pcolormesh" name="MplPcolormesh" superclass="MplPlot">
+ <docstring>Plot a quadrilateral mesh.
+
+Call signatures:
+
+pcolormesh(C) pcolormesh(X, Y, C) pcolormesh(C, **kwargs)
+
+Create a pseudocolor plot of a 2-D array.
+
+pcolormesh is similar to :func:`~matplotlib.pyplot.pcolor`, but uses a different mechanism and returns a different object; pcolor returns a :class:`~matplotlib.collections.PolyCollection` but pcolormesh returns a :class:`~matplotlib.collections.QuadMesh`. It is much faster, so it is almost always preferred for large arrays.
+
+C may be a masked array, but X and Y may not. Masked array support is implemented via cmap and norm; in contrast, :func:`~matplotlib.pyplot.pcolor` simply does not draw quadrilaterals with masked colors or vertices.
+
+Keyword arguments:
+
+
+
+Return value is a :class:`matplotlib.collections.QuadMesh` object.
+
+kwargs can be used to control the :class:`matplotlib.collections.QuadMesh` properties:
+
+%(QuadMesh)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="edgecolors" name="edgecolorsSequence" port_type="basic:List">
+ <docstring>If None, the rc setting is used by default.
+
+If 'None', edges will not be visible.
+
+If 'face', edges will have the same color as the faces.
+
+An mpl color or sequence of colors will set the edge color</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'None', 'face', 'color']]</values>
+ <alternateSpec arg="" name="edgecolorsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" name="vmin">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Colormap` instance. If None, use rc settings.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>the alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="vmax" name="vmax">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="shading" name="shading" port_type="basic:String">
+ <docstring>'flat' indicates a solid color for each quad. When 'gouraud', each quad will be Gouraud shaded. When gouraud shading, edgecolors is ignored.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['flat', 'gouraud']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0,1. If None, defaults to :func:`normalize`.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.pie" name="MplPie" superclass="MplPlot">
+ <docstring>Plot a pie chart.
+
+Call signature:
+
+pie(x, explode=None, labels=None, colors=('b', 'g', 'r', 'c', 'm', 'y', 'k', 'w'), autopct=None, pctdistance=0.6, shadow=False, labeldistance=1.1, startangle=None, radius=None)
+
+Make a pie chart of array x. The fractional area of each wedge is given by x/sum(x). If sum(x) <= 1, then the values of x give the fractional area directly and the array will not be normalized. The wedges are plotted counterclockwise, by default starting from the x-axis.
+
+Keyword arguments:
+
+radius: [ None | scalar ] The radius of the pie, if radius is None it will be set to 1.
+
+The pie chart will probably look best if the figure and axes are square. Eg.:
+
+figure(figsize=(8,8)) ax = axes([0.1, 0.1, 0.8, 0.8])
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="autopct" arg_pos="4" name="autopct" port_type="basic:String">
+ <docstring>If not None, is a string or function used to label the wedges with their numeric value. The label will be placed inside the wedge. If it is a format string, the label will be fmt%pct. If it is a function, it will be called.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'format function']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="pctdistance" arg_pos="5" name="pctdistance" port_type="basic:Float">
+ <docstring>The ratio between the center of each pie slice and the start of the text generated by autopct. Ignored if autopct is None; default is 0.6.</docstring>
+ <defaults>['0.6']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="labels" arg_pos="2" name="labelsSequence" port_type="basic:List">
+ <docstring>A sequence of strings providing the labels for each wedge</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="" name="labelsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="explode" arg_pos="1" name="explodeSequence" port_type="basic:List">
+ <docstring>If not None, is a len(x) array which specifies the fraction of the radius with which to offset each wedge.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="" name="explodeScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="colors" arg_pos="3" name="colors" port_type="basic:Color">
+ <docstring>A sequence of matplotlib color args through which the pie chart will cycle.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <defaults>["('b', 'g', 'r', 'c', 'm', 'y', 'k', 'w')"]</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="radius" arg_pos="9" name="radius" />
+ <inputPortSpec arg="startangle" arg_pos="8" name="startangle" port_type="basic:String">
+ <docstring>If not None, rotates the start of the pie chart by angle degrees counterclockwise from the x-axis.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Offset angle']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="shadow" arg_pos="6" name="shadow" port_type="basic:Boolean">
+ <docstring>Draw a shadow beneath the pie.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="hold" arg_pos="10" name="hold" />
+ <inputPortSpec arg="labeldistance" arg_pos="7" name="labeldistance" port_type="basic:Float">
+ <docstring>The radial distance at which the pie labels are drawn</docstring>
+ <defaults>['1.1']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.plot_date" name="MplPlotDate" superclass="MplPlot">
+ <docstring>Plot with data with dates.
+
+Call signature:
+
+plot_date(x, y, fmt='bo', tz=None, xdate=True, ydate=False, **kwargs)
+
+Similar to the :func:`~matplotlib.pyplot.plot` command, except the x or y (or both) data is considered to be dates, and the axis is labeled accordingly.
+
+x and/or y can be a sequence of dates represented as float days since 0001-01-01 UTC.
+
+Keyword arguments:
+
+
+
+Note if you are using custom date tickers and formatters, it may be necessary to set the formatters/locators after the call to :meth:`plot_date` since :meth:`plot_date` will set the default tick locator to :class:`matplotlib.dates.AutoDateLocator` (if the tick locator is not already set to a :class:`matplotlib.dates.DateLocator` instance) and the default tick formatter to :class:`matplotlib.dates.AutoDateFormatter` (if the tick formatter is not already set to a :class:`matplotlib.dates.D [...]
+
+Valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="tz" arg_pos="3" name="tz" port_type="basic:String">
+ <docstring>The time zone to use in labeling dates. If None, defaults to rc value.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', ':class:`tzinfo` instance']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="fmt" arg_pos="2" name="fmt" port_type="basic:String">
+ <docstring>The plot format string.</docstring>
+ <defaults>['bo']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="ydate" arg_pos="5" name="ydate" port_type="basic:Boolean">
+ <docstring>If True, the y-axis will be labeled with dates.</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xdate" arg_pos="4" name="xdate" port_type="basic:Boolean">
+ <docstring>If True, the x-axis will be labeled with dates.</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="6" name="hold" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.psd" name="MplPsd" superclass="MplPlot">
+ <docstring>Plot the power spectral density.
+
+Call signature:
+
+psd(x, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none, window=mlab.window_hanning, noverlap=0, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+The power spectral density by Welch's average periodogram method. The vector x is divided into NFFT length segments. Each segment is detrended by function detrend and windowed by function window. noverlap gives the length of the overlap between segments. The |\mathrm{fft}(i)|^2 of each segment i are averaged to compute Pxx, with a scaling to correct for power loss due to windowing. Fs is the sampling frequency.
+
+%(PSD)s
+
+
+
+Returns the tuple (Pxx, freqs).
+
+For plotting, the power is plotted as 10\log_{10}(P_{xx}) for decibels, though Pxx itself is returned.
+
+kwargs control the :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="Fs" arg_pos="2" name="Fs" port_type="basic:Integer">
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pad_to" arg_pos="7" name="pad_to" />
+ <inputPortSpec arg="scale_by_freq" arg_pos="9" name="scale_by_freq" />
+ <inputPortSpec arg="detrend" arg_pos="4" name="detrend">
+ <defaults>['<function detrend_none at 0x02F5A3F0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="window" arg_pos="5" name="window">
+ <defaults>['<function window_hanning at 0x02F5A2B0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="Fc" arg_pos="3" name="Fc" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="NFFT" arg_pos="1" name="NFFT" port_type="basic:Integer">
+ <defaults>['256']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="10" name="hold" />
+ <inputPortSpec arg="sides" arg_pos="8" name="sides" port_type="basic:String">
+ <defaults>['default']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="noverlap" arg_pos="6" name="noverlap" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.quiver" name="MplQuiver" superclass="MplPlot">
+ <docstring>Plot a 2-D field of arrows.
+
+call signatures:
+
+quiver(U, V, **kw) quiver(U, V, C, **kw) quiver(X, Y, U, V, **kw) quiver(X, Y, U, V, C, **kw)
+
+Arguments:
+
+
+
+All arguments may be 1-D or 2-D arrays or sequences. If X and Y are absent, they will be generated as a uniform grid. If U and V are 2-D arrays but X and Y are 1-D, and if len(X) and len(Y) match the column and row dimensions of U, then X and Y will be expanded with :func:`numpy.meshgrid`.
+
+U, V, C may be masked arrays, but masked X, Y are not supported at present.
+
+Keyword arguments:
+
+
+
+The defaults give a slightly swept-back arrow; to make the head a triangle, make headaxislength the same as headlength. To make the arrow more pointed, reduce headwidth or increase headlength and headaxislength. To make the head smaller relative to the shaft, scale down all the head parameters. You will probably do best to leave minshaft alone.
+
+linewidths and edgecolors can be used to customize the arrow outlines. Additional :class:`~matplotlib.collections.PolyCollection` keyword arguments:
+
+agg_filter: unknown alpha: float or None animated: [True | False] antialiased or antialiaseds: Boolean or sequence of booleans array: unknown axes: an :class:`~matplotlib.axes.Axes` instance clim: a length 2 sequence of floats clip_box: a :class:`matplotlib.transforms.Bbox` instance clip_on: [True | False] clip_path: [ (:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`) | :class:`~matplotlib.patches.Patch` | None ] cmap: a colormap or registered co [...]
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="headaxislength" name="headaxislength" port_type="basic:Float">
+ <docstring>Head length at shaft intersection, default is 4.5</docstring>
+ <defaults>['4.5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="C" name="C">
+ <docstring>An optional array used to map colors to the arrows</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="scale" name="scale">
+ <docstring>Data units per arrow length unit, e.g. m/s per plot width; a smaller scale parameter makes the arrow longer. If None, a simple autoscaling algorithm is used, based on the average vector length and the number of vectors. The arrow length unit is given by the scale_units parameter</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="width" name="width" port_type="basic:List">
+ <docstring>Shaft width in arrow units; default depends on choice of units, above, and number of vectors; a typical starting value is about 0.005 times the width of the plot.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="headlength" name="headlength" port_type="basic:Float">
+ <docstring>Head length as multiple of shaft width, default is 5</docstring>
+ <defaults>['5']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="minlength" name="minlength" port_type="basic:Float">
+ <docstring>Minimum length as a multiple of shaft width; if an arrow length is less than this, plot a dot (hexagon) of this diameter instead. Default is 1.</docstring>
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="minshaft" name="minshaft" port_type="basic:Float">
+ <docstring>Length below which arrow scales, in units of head length. Do not set this to less than 1, or small arrows will look terrible! Default is 1</docstring>
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pivot" name="pivot" port_type="basic:String">
+ <docstring>The part of the arrow that is at the grid point; the arrow rotates about this point, hence the name pivot.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['tail', 'middle', 'tip']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="units" name="unitsSequence" port_type="basic:List">
+ <docstring>For example, if scale_units is 'inches', scale is 2.0, and (u,v) = (1,0), then the vector will be 0.5 inches long. If scale_units is 'width', then the vector will be half the width of the axes.
+
+If scale_units is 'x' then the vector will be 0.5 x-axis units. To plot vectors in the x-y plane, with u and v having the same units as x and y, use "angles='xy', scale_units='xy', scale=1".</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['width', 'height', 'dots', 'inches', 'x', 'y', 'xy']]</values>
+ <alternateSpec arg="" name="unitsScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="headwidth" name="headwidth" port_type="basic:Float">
+ <docstring>Head width as multiple of shaft width, default is 3</docstring>
+ <defaults>['3']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="U" name="U" port_type="basic:List">
+ <docstring>Give the x and y components of the arrow vectors</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="angles" name="angles" port_type="basic:String">
+ <docstring>With the default 'uv', the arrow aspect ratio is 1, so that if U*==*V the angle of the arrow on the plot is 45 degrees CCW from the x-axis. With 'xy', the arrow points from (x,y) to (x+u, y+v). Alternatively, arbitrary angles may be specified as an array of values in degrees, CCW from the x-axis.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['uv', 'xy', 'array']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="V" name="V" port_type="basic:List">
+ <docstring>Give the x and y components of the arrow vectors</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="Y" name="Y" port_type="basic:String">
+ <docstring>The x and y coordinates of the arrow locations (default is tail of arrow; see pivot kwarg)</docstring>
+ <defaults>['tail']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="X" name="X" port_type="basic:String">
+ <docstring>The x and y coordinates of the arrow locations (default is tail of arrow; see pivot kwarg)</docstring>
+ <defaults>['tail']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="scale_units" name="scale_units" port_type="basic:List">
+ <docstring>For example, if scale_units is 'inches', scale is 2.0, and (u,v) = (1,0), then the vector will be 0.5 inches long. If scale_units is 'width', then the vector will be half the width of the axes.
+
+If scale_units is 'x' then the vector will be 0.5 x-axis units. To plot vectors in the x-y plane, with u and v having the same units as x and y, use "angles='xy', scale_units='xy', scale=1".</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="color" name="colorSequence" port_type="basic:List">
+ <docstring>This is a synonym for the :class:`~matplotlib.collections.PolyCollection` facecolor kwarg. If C has been set, color has no effect.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['color']]</values>
+ <alternateSpec arg="" name="colorScalar" port_type="basic:String" />
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.quiverkey" name="MplQuiverkey" superclass="MplPlot">
+ <docstring>Add a key to a quiver plot.
+
+Call signature:
+
+quiverkey(Q, X, Y, U, label, **kw)
+
+Arguments:
+
+
+
+Keyword arguments:
+
+
+
+Any additional keyword arguments are used to override vector properties taken from Q.
+
+The positioning of the key depends on X, Y, coordinates, and labelpos. If labelpos is 'N' or 'S', X, Y give the position of the middle of the key arrow. If labelpos is 'E', X, Y positions the head, and if labelpos is 'W', X, Y positions the tail; in either of these two cases, X, Y is somewhere in the middle of the arrow+label key object.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="color" name="color" port_type="basic:Color">
+ <docstring>overrides face and edge colors from Q.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="coordinates" name="coordinatesSequence" port_type="basic:List">
+ <docstring>Coordinate system and units for X, Y: 'axes' and 'figure' are normalized coordinate systems with 0,0 in the lower left and 1,1 in the upper right; 'data' are the axes data coordinates (used for the locations of the vectors in the quiver plot itself); 'inches' is position in the figure in inches, with 0,0 at the lower left corner.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['axes', 'figure', 'data', 'inches']]</values>
+ <alternateSpec arg="" name="coordinatesScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="label" arg_pos="4" name="label" port_type="basic:String" required="True">
+ <docstring>A string with the length and units of the key</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="Q" arg_pos="0" name="Q" required="True">
+ <docstring>The Quiver instance returned by a call to quiver.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="labelcolor" name="labelcolor" port_type="basic:Color">
+ <docstring>defaults to default :class:`~matplotlib.text.Text` color.</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ <inputPortSpec arg="fontproperties" name="fontproperties">
+ <docstring>A dictionary with keyword arguments accepted by the :class:`~matplotlib.font_manager.FontProperties` initializer: family, style, variant, size, weight</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="U" arg_pos="3" name="U" required="True">
+ <docstring>The length of the key</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="labelpos" name="labelpos" port_type="basic:String">
+ <docstring>Position the label above, below, to the right, to the left of the arrow, respectively.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['N', 'S', 'E', 'W']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="Y" arg_pos="2" name="Y" required="True">
+ <docstring>The location of the key; additional explanation follows.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="X" arg_pos="1" name="X" required="True">
+ <docstring>The location of the key; additional explanation follows.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="labelsep" name="labelsep" port_type="basic:Float">
+ <docstring>Distance in inches between the arrow and the label. Default is 0.1</docstring>
+ <defaults>['0.1']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.scatter" name="MplScatter" superclass="MplPlot">
+ <docstring>Make a scatter plot.
+
+Call signatures:
+
+scatter(x, y, s=20, c='b', marker='o', cmap=None, norm=None, vmin=None, vmax=None, alpha=None, linewidths=None, verts=None, **kwargs)
+
+Make a scatter plot of x versus y, where x, y are converted to 1-D sequences which must be of the same length, N.
+
+Keyword arguments:
+
+
+
+Any or all of x, y, s, and c may be masked arrays, in which case all masks will be combined and only unmasked points will be plotted.
+
+Other keyword arguments: the color mapping and normalization arguments will be used only if c is an array of floats.
+
+
+
+Optional kwargs control the :class:`~matplotlib.collections.Collection` properties; in particular:
+
+
+
+Here are the standard descriptions of all the :class:`~matplotlib.collections.Collection` kwargs:
+
+%(Collection)s
+
+A :class:`~matplotlib.collections.Collection` instance is returned.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="vmax" arg_pos="8" name="vmax">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="edgecolors" name="edgecolors" port_type="basic:String">
+ <docstring>The string 'none' to plot faces with no outlines</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="c" arg_pos="3" name="cSequence" port_type="basic:List">
+ <docstring>a color. c can be a single color format string, or a sequence of color specifications of length N, or a sequence of N numbers to be mapped to colors using the cmap and norm specified via kwargs (see below). Note that c should not be a single numeric RGB or RGBA sequence because that is indistinguishable from an array of values to be colormapped. c can be a 2-D array in which the rows are RGB or RGBA, however.</docstring>
+ <defaults>['b']</defaults>
+ <alternateSpec arg="" name="cScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="vmin" arg_pos="7" name="vmin">
+ <docstring>vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="faceted" arg_pos="11" name="faceted" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" arg_pos="10" name="linewidths">
+ <docstring>If None, defaults to (lines.linewidth,). Note that this is a tuple, and if you set the linewidths argument you must set it as a sequence of floats, as required by :class:`~matplotlib.collections.RegularPolyCollection`.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="marker" arg_pos="4" name="marker" port_type="basic:String">
+ <docstring>can be one of:
+
+%(MarkerTable)s</docstring>
+ <defaults>['o']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="s" arg_pos="2" name="s" port_type="basic:Float">
+ <docstring>size in points^2. It is a scalar or an array of the same length as x and y.</docstring>
+ <defaults>['20']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="5" name="cmap">
+ <docstring>A :class:`matplotlib.colors.Colormap` instance or registered name. If None, defaults to rc image.cmap. cmap is only used if c is an array of floats.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="verts" arg_pos="12" name="verts" />
+ <inputPortSpec arg="alpha" arg_pos="9" name="alpha" port_type="basic:Float">
+ <docstring>The alpha value for the patches</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="13" name="hold" />
+ <inputPortSpec arg="facecolors" name="facecolors" port_type="basic:String">
+ <docstring>The string 'none' to plot unfilled outlines</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" arg_pos="6" name="norm">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0, 1. If None, use the default :func:`normalize`. norm is only used if c is an array of floats.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.semilogx" name="MplSemilogx" superclass="MplPlot">
+ <docstring>Make a plot with log scaling on the x axis.
+
+Call signature:
+
+semilogx(*args, **kwargs)
+
+:func:`semilogx` supports all the keyword arguments of :func:`~matplotlib.pyplot.plot` and :meth:`matplotlib.axes.Axes.set_xscale`.
+
+Notable keyword arguments:
+
+
+
+The remaining valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="basex" name="basex" port_type="basic:Float">
+ <docstring>Base of the x logarithm</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="nonposx" name="nonposx" port_type="basic:String">
+ <docstring>Non-positive values in x can be masked as invalid, or clipped to a very small positive number</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['mask', 'clip']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="subsx" name="subsxSequence" port_type="basic:List">
+ <docstring>The location of the minor xticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`~matplotlib.axes.Axes.set_xscale` for details.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="" name="subsxScalar" port_type="basic:String" />
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.semilogy" name="MplSemilogy" superclass="MplPlot">
+ <docstring>Make a plot with log scaling on the y axis.
+
+call signature:
+
+semilogy(*args, **kwargs)
+
+:func:`semilogy` supports all the keyword arguments of :func:`~matplotlib.pylab.plot` and :meth:`matplotlib.axes.Axes.set_yscale`.
+
+Notable keyword arguments:
+
+
+
+The remaining valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="basey" name="basey" port_type="basic:Float">
+ <docstring>Base of the y logarithm</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="nonposy" name="nonposy" port_type="basic:String">
+ <docstring>Non-positive values in y can be masked as invalid, or clipped to a very small positive number</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['mask', 'clip']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="subsy" name="subsySequence" port_type="basic:List">
+ <docstring>The location of the minor yticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`~matplotlib.axes.Axes.set_yscale` for details.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ <alternateSpec arg="" name="subsyScalar" port_type="basic:String" />
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.specgram" name="MplSpecgram" superclass="MplPlot">
+ <docstring>Plot a spectrogram.
+
+Call signature:
+
+specgram(x, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none, window=mlab.window_hanning, noverlap=128, cmap=None, xextent=None, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+Compute a spectrogram of data in x. Data are split into NFFT length segments and the PSD of each section is computed. The windowing function window is applied to each segment, and the amount of overlap of each segment is specified with noverlap.
+
+%(PSD)s
+
+kwargs:
+
+Additional kwargs are passed on to imshow which makes the specgram image
+
+Return value is (Pxx, freqs, bins, im):
+
+bins are the time points the spectrogram is calculated over
+
+freqs is an array of frequencies
+
+Pxx is an array of shape (len(times), len(freqs)) of power
+
+im is a :class:`~matplotlib.image.AxesImage` instance
+
+Note: If x is real (i.e. non-complex), only the positive spectrum is shown. If x is complex, both positive and negative parts of the spectrum are shown. This can be overridden using the sides keyword argument.
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="Fs" arg_pos="2" name="Fs" port_type="basic:Integer">
+ <defaults>['2']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pad_to" arg_pos="9" name="pad_to" />
+ <inputPortSpec arg="scale_by_freq" arg_pos="11" name="scale_by_freq" />
+ <inputPortSpec arg="xextent" arg_pos="8" name="xextent" />
+ <inputPortSpec arg="detrend" arg_pos="4" name="detrend">
+ <defaults>['<function detrend_none at 0x02F5A3F0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="window" arg_pos="5" name="window">
+ <defaults>['<function window_hanning at 0x02F5A2B0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="Fc" arg_pos="3" name="Fc" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="NFFT" arg_pos="1" name="NFFT" port_type="basic:Integer">
+ <defaults>['256']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="7" name="cmap" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="12" name="hold" />
+ <inputPortSpec arg="sides" arg_pos="10" name="sides" port_type="basic:String">
+ <defaults>['default']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="noverlap" arg_pos="6" name="noverlap" port_type="basic:Integer">
+ <defaults>['128']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.stackplot" name="MplStackplot" superclass="MplPlot">
+ <docstring>Draws a stacked area plot.
+
+x : 1d array of dimension N
+
+Keyword arguments:
+
+Returns r : A list of :class:`~matplotlib.collections.PolyCollection`, one for each element in the stacked area plot.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="x" arg_pos="0" name="x" required="True" />
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>used to colour the stacked areas. All other keyword arguments are passed to :func:`~matplotlib.Axes.fill_between`</docstring>
+ <translations>translate_color</translations>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.stem" name="MplStem" superclass="MplPlot">
+ <docstring>Create a stem plot.
+
+Call signature:
+
+stem(x, y, linefmt='b-', markerfmt='bo', basefmt='r-')
+
+A stem plot plots vertical lines (using linefmt) at each x location from the baseline to y, and places a marker there using markerfmt. A horizontal line at 0 is is plotted using basefmt.
+
+Return value is a tuple (markerline, stemlines, baseline).
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="bottom" arg_pos="5" name="bottom" />
+ <inputPortSpec arg="label" arg_pos="6" name="label" />
+ <inputPortSpec arg="linefmt" arg_pos="2" name="linefmt" port_type="basic:String">
+ <defaults>['b-']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="markerfmt" arg_pos="3" name="markerfmt" port_type="basic:String">
+ <defaults>['bo']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="7" name="hold" />
+ <inputPortSpec arg="basefmt" arg_pos="4" name="basefmt" port_type="basic:String">
+ <defaults>['r-']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.step" name="MplStep" superclass="MplPlot">
+ <docstring>Make a step plot.
+
+Call signature:
+
+step(x, y, *args, **kwargs)
+
+Additional keyword args to :func:`step` are the same as those for :func:`~matplotlib.pyplot.plot`.
+
+x and y must be 1-D sequences, and it is assumed, but not checked, that x is uniformly increasing.
+
+Keyword arguments:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="where" name="where" port_type="basic:String">
+ <docstring>If 'pre', the interval from x[i] to x[i+1] has level y[i+1]
+
+If 'post', that interval has level y[i]
+
+If 'mid', the jumps in y occur half-way between the x-values.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['pre', 'post', 'mid']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.streamplot" name="MplStreamplot" superclass="MplPlot">
+ <docstring>Draws streamlines of a vector flow.
+
+Returns:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="hold" arg_pos="13" name="hold" />
+ <inputPortSpec arg="arrowstyle" arg_pos="10" name="arrowstyle" port_type="basic:String">
+ <defaults>['-|>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="density" arg_pos="4" name="density" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="6" name="color" />
+ <inputPortSpec arg="minlength" arg_pos="11" name="minlength" port_type="basic:Float">
+ <defaults>['0.1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="transform" arg_pos="12" name="transform" />
+ <inputPortSpec arg="arrowsize" arg_pos="9" name="arrowsize" port_type="basic:Integer">
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" arg_pos="7" name="cmap" />
+ <inputPortSpec arg="u" arg_pos="2" name="u" required="True" />
+ <inputPortSpec arg="v" arg_pos="3" name="v" required="True" />
+ <inputPortSpec arg="y" arg_pos="1" name="y" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" required="True" />
+ <inputPortSpec arg="linewidth" arg_pos="5" name="linewidth" />
+ <inputPortSpec arg="norm" arg_pos="8" name="norm" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.tricontour" name="MplTricontour" superclass="MplPlot">
+ <docstring>Draw contours on an unstructured triangular grid. :func:`~matplotlib.pyplot.tricontour` and :func:`~matplotlib.pyplot.tricontourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+The triangulation can be specified in one of two ways; either:
+
+tricontour(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+tricontour(x, y, ...) tricontour(x, y, triangles, ...) tricontour(x, y, triangles=triangles, ...) tricontour(x, y, mask=mask, ...) tricontour(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The remaining arguments may be:
+
+tricontour(..., Z)
+
+where Z is the array of values to contour, one per point in the triangulation. The level values are chosen automatically.
+
+tricontour(..., Z, N)
+
+contour N automatically-chosen levels.
+
+tricontour(..., Z, V)
+
+draw contour lines at the values specified in sequence V
+
+tricontourf(..., Z, V)
+
+fill the (len(V)-1) regions between the values in V
+
+tricontour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+C = tricontour(...) returns a :class:`~matplotlib.contour.TriContourSet` object.
+
+Optional keyword arguments:
+
+extent: [ None | (x0,x1,y0,y1) ]
+
+If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].
+
+This keyword is not active if X and Y are specified in the call to contour.
+
+tricontour-only keyword arguments:
+
+
+
+tricontourf-only keyword arguments:
+
+
+
+Note: tricontourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="origin" name="origin" port_type="basic:String">
+ <docstring>If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.
+
+This keyword is not active if X and Y are specified in the call to contour.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'upper', 'lower', 'image']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyles" name="linestyles" port_type="basic:String">
+ <docstring>If linestyles is None, the 'solid' is used.
+
+linestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.
+
+If contour is using a monochrome colormap and the contour level is less than 0, then the linestyle specified in contour.negative_linestyle in matplotlibrc will be used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'solid', 'dashed', 'dashdot', 'dotted']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="levels" name="levelsSequence" port_type="basic:List">
+ <docstring>A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]</docstring>
+ <alternateSpec arg="" name="levelsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" name="linewidths" port_type="basic:String">
+ <docstring>If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.
+
+If a number, all levels will be plotted with this linewidth.
+
+If a tuple, different levels will be plotted with different linewidths in the order specified</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'number', 'tuple of numbers']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>If None, the colormap specified by cmap will be used.
+
+If a string, like 'r' or 'red', all levels will be plotted in this color.
+
+If a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['', '(mpl_colors)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="antialiased" name="antialiased" port_type="basic:Boolean">
+ <docstring>enable antialiasing</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="nchunk" name="nchunk" port_type="basic:Integer">
+ <docstring>If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[[0]]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>The alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.tricontourf" name="MplTricontourf" superclass="MplPlot">
+ <docstring>Draw contours on an unstructured triangular grid. :func:`~matplotlib.pyplot.tricontour` and :func:`~matplotlib.pyplot.tricontourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+The triangulation can be specified in one of two ways; either:
+
+tricontour(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+tricontour(x, y, ...) tricontour(x, y, triangles, ...) tricontour(x, y, triangles=triangles, ...) tricontour(x, y, mask=mask, ...) tricontour(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The remaining arguments may be:
+
+tricontour(..., Z)
+
+where Z is the array of values to contour, one per point in the triangulation. The level values are chosen automatically.
+
+tricontour(..., Z, N)
+
+contour N automatically-chosen levels.
+
+tricontour(..., Z, V)
+
+draw contour lines at the values specified in sequence V
+
+tricontourf(..., Z, V)
+
+fill the (len(V)-1) regions between the values in V
+
+tricontour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+C = tricontour(...) returns a :class:`~matplotlib.contour.TriContourSet` object.
+
+Optional keyword arguments:
+
+extent: [ None | (x0,x1,y0,y1) ]
+
+If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].
+
+This keyword is not active if X and Y are specified in the call to contour.
+
+tricontour-only keyword arguments:
+
+
+
+tricontourf-only keyword arguments:
+
+
+
+Note: tricontourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="origin" name="origin" port_type="basic:String">
+ <docstring>If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.
+
+This keyword is not active if X and Y are specified in the call to contour.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'upper', 'lower', 'image']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="linestyles" name="linestyles" port_type="basic:String">
+ <docstring>If linestyles is None, the 'solid' is used.
+
+linestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.
+
+If contour is using a monochrome colormap and the contour level is less than 0, then the linestyle specified in contour.negative_linestyle in matplotlibrc will be used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'solid', 'dashed', 'dashdot', 'dotted']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="levels" name="levelsSequence" port_type="basic:List">
+ <docstring>A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]</docstring>
+ <alternateSpec arg="" name="levelsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="linewidths" name="linewidths" port_type="basic:String">
+ <docstring>If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.
+
+If a number, all levels will be plotted with this linewidth.
+
+If a tuple, different levels will be plotted with different linewidths in the order specified</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'number', 'tuple of numbers']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="colors" name="colors" port_type="basic:Color">
+ <docstring>If None, the colormap specified by cmap will be used.
+
+If a string, like 'r' or 'red', all levels will be plotted in this color.
+
+If a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified.</docstring>
+ <translations>translate_color</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['', '(mpl_colors)']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="cmap" name="cmap" port_type="basic:String">
+ <docstring>A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Colormap']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="antialiased" name="antialiased" port_type="basic:Boolean">
+ <docstring>enable antialiasing</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="nchunk" name="nchunk" port_type="basic:Integer">
+ <docstring>If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[[0]]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="alpha" name="alpha" port_type="basic:Float">
+ <docstring>The alpha blending value</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="norm" name="norm" port_type="basic:String">
+ <docstring>A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'Normalize']]</values>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.tripcolor" name="MplTripcolor" superclass="MplPlot">
+ <docstring>Create a pseudocolor plot of an unstructured triangular grid.
+
+The triangulation can be specified in one of two ways; either:
+
+tripcolor(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+tripcolor(x, y, ...) tripcolor(x, y, triangles, ...) tripcolor(x, y, triangles=triangles, ...) tripcolor(x, y, mask=mask, ...) tripcolor(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The next argument must be C, the array of color values, either one per point in the triangulation if color values are defined at points, or one per triangle in the triangulation if color values are defined at triangles. If there are the same number of points and triangles in the triangulation it is assumed that color values are defined at points; to force the use of color values at triangles use the kwarg facecolors*=C instead of just *C.
+
+shading may be 'flat' (the default) or 'gouraud'. If shading is 'flat' and C values are defined at points, the color values used for each triangle are from the mean C of the triangle's three points. If shading is 'gouraud' then color values must be defined at points. shading of 'faceted' is deprecated; please use edgecolors instead.
+
+The remaining kwargs are the same as for :meth:`~matplotlib.axes.Axes.pcolor`.
+
+Example:
+
+
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.triplot" name="MplTriplot" superclass="MplPlot">
+ <docstring>Draw a unstructured triangular grid as lines and/or markers.
+
+The triangulation to plot can be specified in one of two ways; either:
+
+triplot(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+triplot(x, y, ...) triplot(x, y, triangles, ...) triplot(x, y, triangles=triangles, ...) triplot(x, y, mask=mask, ...) triplot(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The remaining args and kwargs are the same as for :meth:`~matplotlib.axes.Axes.plot`.
+
+Example:
+
+
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.vlines" name="MplVlines" superclass="MplPlot">
+ <docstring>Plot vertical lines.
+
+Call signature:
+
+vlines(x, ymin, ymax, color='k', linestyles='solid')
+
+Plot vertical lines at each x from ymin to ymax. ymin or ymax can be scalars or len(x) numpy arrays. If they are scalars, then the respective values are constant, else the heights of the lines are determined by ymin and ymax.
+
+linestyles : [ 'solid' | 'dashed' | 'dashdot' | 'dotted' ]
+
+Returns the :class:`matplotlib.collections.LineCollection` that was added.
+
+kwargs are :class:`~matplotlib.collections.LineCollection` properties:
+
+%(LineCollection)s
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="hold" arg_pos="6" name="hold" />
+ <inputPortSpec arg="ymax" arg_pos="2" name="ymax" required="True" />
+ <inputPortSpec arg="linestyles" arg_pos="4" name="linestyles" port_type="basic:String">
+ <defaults>['solid']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="color" arg_pos="3" name="color" port_type="basic:String">
+ <defaults>['k']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="label" arg_pos="5" name="label" port_type="basic:String">
+ <defaults>['']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="colors" arg_pos="3" name="colors" port_type="basic:String">
+ <defaults>['k']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="ymin" arg_pos="1" name="ymin" required="True" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.xcorr" name="MplXcorr" superclass="MplPlot">
+ <docstring>Plot the cross correlation between x and y.
+
+Call signature:
+
+xcorr(self, x, y, normed=True, detrend=mlab.detrend_none, usevlines=True, maxlags=10, **kwargs)
+
+If normed = True, normalize the data by the cross correlation at 0-th lag. x and y are detrended by the detrend callable (default no normalization). x and y must be equal length.
+
+Data are plotted as plot(lags, c, **kwargs)
+
+Return value is a tuple (lags, c, line) where:
+
+lags are a length 2*maxlags+1 lag vector
+
+c is the 2*maxlags+1 auto correlation vector
+
+The default linestyle is None and the default marker is 'o', though these can be overridden with keyword args. The cross correlation is performed with :func:`numpy.correlate` with mode = 2.
+
+If usevlines is True:
+
+:func:`~matplotlib.pyplot.vlines` rather than :func:`~matplotlib.pyplot.plot` is used to draw vertical lines from the origin to the xcorr. Otherwise the plotstyle is determined by the kwargs, which are :class:`~matplotlib.lines.Line2D` properties.
+
+The return value is a tuple (lags, c, linecol, b) where linecol is the :class:`matplotlib.collections.LineCollection` instance and b is the x-axis.
+
+maxlags is a positive integer detailing the number of lags to show. The default value of None will return all (2*len(x)-1) lags.
+
+Example:
+
+:func:`~matplotlib.pyplot.xcorr` is top graph, and :func:`~matplotlib.pyplot.acorr` is bottom graph.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="normed" arg_pos="2" name="normed" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="usevlines" arg_pos="4" name="usevlines" port_type="basic:Boolean">
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="detrend" arg_pos="3" name="detrend">
+ <defaults>['<function detrend_none at 0x02F5A3F0>']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="maxlags" arg_pos="5" name="maxlags" port_type="basic:Integer">
+ <defaults>['10']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="y" arg_pos="1" name="y" port_type="basic:List" required="True" />
+ <inputPortSpec arg="x" arg_pos="0" name="x" port_type="basic:List" required="True" />
+ <inputPortSpec arg="hold" arg_pos="6" name="hold" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.barbs" name="MplBarbs" superclass="MplPlot">
+ <docstring>Plot a 2-D field of barbs.
+
+Call signatures:
+
+barb(U, V, **kw) barb(U, V, C, **kw) barb(X, Y, U, V, **kw) barb(X, Y, U, V, C, **kw)
+
+Arguments:
+
+
+
+All arguments may be 1-D or 2-D arrays or sequences. If X and Y are absent, they will be generated as a uniform grid. If U and V are 2-D arrays but X and Y are 1-D, and if len(X) and len(Y) match the column and row dimensions of U, then X and Y will be expanded with :func:`numpy.meshgrid`.
+
+U, V, C may be masked arrays, but masked X, Y are not supported at present.
+
+Keyword arguments:
+
+
+
+Barbs are traditionally used in meteorology as a way to plot the speed and direction of wind observations, but can technically be used to plot any two dimensional vector quantity. As opposed to arrows, which give vector magnitude by the length of the arrow, the barbs give more quantitative information about the vector magnitude by putting slanted lines or a triangle for various increments in magnitude, as show schematically below:
+
+: /\ \ : / \ \ : / \ \ \ : / \ \ \ : ------------------------------
+
+note the double \ at the end of each line to make the figure
+
+render correctly
+
+The largest increment is given by a triangle (or "flag"). After those come full lines (barbs). The smallest increment is a half line. There is only, of course, ever at most 1 half line. If the magnitude is small and only needs a single half-line and no full lines or triangles, the half-line is offset from the end of the barb so that it can be easily distinguished from barbs with a single full line. The magnitude for the barb shown above would nominally be 65, using the standard increm [...]
+
+linewidths and edgecolors can be used to customize the barb. Additional :class:`~matplotlib.collections.PolyCollection` keyword arguments:
+
+agg_filter: unknown alpha: float or None animated: [True | False] antialiased or antialiaseds: Boolean or sequence of booleans array: unknown axes: an :class:`~matplotlib.axes.Axes` instance clim: a length 2 sequence of floats clip_box: a :class:`matplotlib.transforms.Bbox` instance clip_on: [True | False] clip_path: [ (:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`) | :class:`~matplotlib.patches.Patch` | None ] cmap: a colormap or registered co [...]
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="barbcolor" name="barbcolorSequence" port_type="basic:List">
+ <docstring>Specifies the color all parts of the barb except any flags. This parameter is analagous to the edgecolor parameter for polygons, which can be used instead. However this parameter will override facecolor.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['color']]</values>
+ <alternateSpec arg="" name="barbcolorScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="C" name="C">
+ <docstring>An optional array used to map colors to the barbs</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="sizes" name="sizes">
+ <docstring>A dictionary of coefficients specifying the ratio of a given feature to the length of the barb. Only those values one wishes to override need to be included. These features include:
+
+'spacing' - space between features (flags, full/half barbs)
+
+'height' - height (distance from shaft to top) of a flag or full barb
+
+'width' - width of a flag, twice the width of a full barb
+
+'emptybarb' - radius of the circle used for low magnitudes</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="rounding" name="rounding" port_type="basic:Boolean">
+ <docstring>A flag to indicate whether the vector magnitude should be rounded when allocating barb components. If True, the magnitude is rounded to the nearest multiple of the half-barb increment. If False, the magnitude is simply truncated to the next lowest multiple. Default is True</docstring>
+ <defaults>['True']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="pivot" name="pivot" port_type="basic:String">
+ <docstring>The part of the arrow that is at the grid point; the arrow rotates about this point, hence the name pivot. Default is 'tip'</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['tip', 'middle']]</values>
+ <defaults>['tip']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="flip_barb" name="flip_barb" port_type="basic:Boolean">
+ <docstring>Either a single boolean flag or an array of booleans. Single boolean indicates whether the lines and flags should point opposite to normal for all barbs. An array (which should be the same size as the other data arrays) indicates whether to flip for each individual barb. Normal behavior is for the barbs and lines to point right (comes from wind barbs having these features point towards low pressure in the Northern Hemisphere.) Default is False</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="length" name="length" port_type="basic:Integer">
+ <docstring>Length of the barb in points; the other parts of the barb are scaled against this. Default is 9</docstring>
+ <defaults>['9']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="barb_increments" name="barb_increments" port_type="basic:String">
+ <docstring>A dictionary of increments specifying values to associate with different parts of the barb. Only those values one wishes to override need to be included.
+
+'half' - half barbs (Default is 5)
+
+'full' - full barbs (Default is 10)
+
+'flag' - flags (default is 50)</docstring>
+ <defaults>['5)']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="U" name="U">
+ <docstring>Give the x and y components of the barb shaft</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="V" name="V">
+ <docstring>Give the x and y components of the barb shaft</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="Y" name="Y" port_type="basic:String">
+ <docstring>The x and y coordinates of the barb locations (default is head of barb; see pivot kwarg)</docstring>
+ <defaults>['head']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="X" name="X" port_type="basic:String">
+ <docstring>The x and y coordinates of the barb locations (default is head of barb; see pivot kwarg)</docstring>
+ <defaults>['head']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="flagcolor" name="flagcolorSequence" port_type="basic:List">
+ <docstring>Specifies the color of any flags on the barb. This parameter is analagous to the facecolor parameter for polygons, which can be used instead. However this parameter will override facecolor. If this is not set (and C has not either) then flagcolor will be set to match barbcolor so that the barb has a uniform color. If C has been set, flagcolor has no effect.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['color']]</values>
+ <alternateSpec arg="" name="flagcolorScalar" port_type="basic:String" />
+ </inputPortSpec>
+ <inputPortSpec arg="fill_empty" name="fill_empty" port_type="basic:Boolean">
+ <docstring>A flag on whether the empty barbs (circles) that are drawn should be filled with the flag color. If they are not filled, they will be drawn such that no color is applied to the center. Default is False</docstring>
+ <defaults>['False']</defaults>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.spy" name="MplSpy" superclass="MplPlot">
+ <docstring>Plot the sparsity pattern on a 2-D array.
+
+Call signature:
+
+spy(Z, precision=0, marker=None, markersize=None, aspect='equal', **kwargs)
+
+spy(Z) plots the sparsity pattern of the 2-D array Z.
+
+If precision is 0, any non-zero value will be plotted; else, values of |Z| > precision will be plotted.
+
+For :class:`scipy.sparse.spmatrix` instances, there is a special case: if precision is 'present', any value present in the array will be plotted, even if it is identically zero.
+
+The array will be plotted as it would be printed, with the first index (row) increasing down and the second index (column) increasing to the right.
+
+By default aspect is 'equal', so that each array element occupies a square space; set the aspect kwarg to 'auto' to allow the plot to fill the plot box, or to any scalar number to specify the aspect ratio of an array element directly.
+
+Two plotting styles are available: image or marker. Both are available for full arrays, but only the marker style works for :class:`scipy.sparse.spmatrix` instances.
+
+If marker and markersize are None, an image will be returned and any remaining kwargs are passed to :func:`~matplotlib.pyplot.imshow`; else, a :class:`~matplotlib.lines.Line2D` object will be returned with the value of marker determining the marker type, and any remaining kwargs passed to the :meth:`~matplotlib.axes.Axes.plot` method.
+
+If marker and markersize are None, useful kwargs include:
+
+cmap
+
+alpha
+
+For controlling colors, e.g. cyan background and red marks, use:
+
+cmap = mcolors.ListedColormap(['c','r'])
+
+If marker or markersize is not None, useful kwargs include:
+
+marker
+
+markersize
+
+color
+
+Useful values for marker include:
+
+'s' square (default)
+
+'o' circle
+
+'.' point
+
+',' pixel
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="hold" arg_pos="5" name="hold" />
+ <inputPortSpec arg="markersize" arg_pos="3" name="markersize" />
+ <inputPortSpec arg="precision" arg_pos="1" name="precision" port_type="basic:Integer">
+ <defaults>['0']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="aspect" arg_pos="4" name="aspect" port_type="basic:String">
+ <defaults>['equal']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="marker" arg_pos="2" name="marker" />
+ <inputPortSpec arg="Z" arg_pos="0" name="Z" required="True" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.polar" name="MplPolar" superclass="MplPlot">
+ <docstring>Make a polar plot.
+
+call signature:
+
+polar(theta, r, **kwargs)
+
+Multiple theta, r arguments are supported, with format strings, as in :func:`~matplotlib.pyplot.plot`.</docstring>
+ <inputPortSpec arg="theta" arg_pos="0" name="theta" required="True" />
+ <inputPortSpec arg="r" arg_pos="1" name="r" required="True" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.legend" name="MplLegend" superclass="MplPlot">
+ <docstring>Place a legend on the current axes.
+
+Call signature:
+
+legend(*args, **kwargs)
+
+Places legend at location loc. Labels are a sequence of strings and loc can be a string or an integer specifying the legend location.
+
+To make a legend with existing lines:
+
+legend()
+
+:meth:`legend` by itself will try and build a legend using the label property of the lines/patches/collections. You can set the label of a line by doing:
+
+plot(x, y, label='my data')
+
+or:
+
+line.set_label('my data').
+
+If label is set to '_nolegend_', the item will not be shown in legend.
+
+To automatically generate the legend from labels:
+
+legend( ('label1', 'label2', 'label3') )
+
+To make a legend for a list of lines and labels:
+
+legend( (line1, line2, line3), ('label1', 'label2', 'label3') )
+
+To make a legend at a given location, using a location argument:
+
+legend( ('label1', 'label2', 'label3'), loc='upper left')
+
+or:
+
+legend( (line1, line2, line3), ('label1', 'label2', 'label3'), loc=2)
+
+The location codes are
+
+
+
+Users can specify any arbitrary location for the legend using the bbox_to_anchor keyword argument. bbox_to_anchor can be an instance of BboxBase(or its derivatives) or a tuple of 2 or 4 floats. For example,
+
+loc = 'upper right', bbox_to_anchor = (0.5, 0.5)
+
+will place the legend so that the upper right corner of the legend at the center of the axes.
+
+The legend location can be specified in other coordinate, by using the bbox_transform keyword.
+
+The loc itslef can be a 2-tuple giving x,y of the lower-left corner of the legend in axes coords (bbox_to_anchor is ignored).
+
+Keyword arguments:
+
+fontsize: [ size in points | 'xx-small' | 'x-small' | 'small' | 'medium' | 'large' | 'x-large' | 'xx-large' ]
+
+Set the font size. May be either a size string, relative to the default font size, or an absolute font size in points. This argument is only used if prop is not specified.
+
+Padding and spacing between various elements use following keywords parameters. These values are measure in font-size units. E.g., a fontsize of 10 points and a handlelength=5 implies a handlelength of 50 points. Values from rcParams will be used if None.
+
+Not all kinds of artist are supported by the legend command. See LINK (FIXME) for details.
+
+Example:</docstring>
+ <inputPortSpec arg="loc" name="loc">
+ <translations>{'right': 5, 'center': 10, 'lower left': 3, 'center right': 7, 'upper left': 2, 'center left': 6, 'upper right': 1, 'lower right': 4, 'upper center': 9, 'lower center': 8, 'best': 0}</translations>
+ <entry_types>['enum']</entry_types>
+ <values>[['best', 'upper right', 'upper left', 'lower left', 'lower right', 'right', 'center left', 'center right', 'lower center', 'upper center', 'center']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="fancybox" name="fancybox">
+ <docstring>if True, draw a frame with a round fancybox. If None, use rc settings</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox_to_anchor" name="bbox_to_anchor">
+ <docstring>the bbox that the legend will be anchored.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="title" name="title">
+ <docstring>the legend title</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="handlelength" name="handlelength">
+ <docstring>the length of the legend handles</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="markerscale" name="markerscale">
+ <docstring>The relative size of legend markers vs. original. If None, use rc settings.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="numpoints" name="numpoints" port_type="basic:Integer">
+ <docstring>The number of points in the legend for line</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="labelspacing" name="labelspacing">
+ <docstring>the vertical space between the legend entries</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="scatterpoints" name="scatterpoints" port_type="basic:Integer">
+ <docstring>The number of points in the legend for scatter plot</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="frameon" name="frameon" port_type="basic:Boolean">
+ <docstring>if True, draw a frame around the legend. The default is set by the rcParam 'legend.frameon'</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="columnspacing" name="columnspacing">
+ <docstring>the spacing between columns</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="handletextpad" name="handletextpad">
+ <docstring>the pad between the legend handle and text</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="scatteroffsets" name="scatteroffsetsSequence" port_type="basic:List">
+ <docstring>a list of yoffsets for scatter symbols in legend</docstring>
+ <alternateSpec arg="" name="scatteroffsetsScalar" port_type="basic:Float" />
+ </inputPortSpec>
+ <inputPortSpec arg="mode" name="mode">
+ <docstring>if mode is "expand", the legend will be horizontally expanded to fill the axes area (or bbox_to_anchor)</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="ncol" name="ncol" port_type="basic:Integer">
+ <docstring>number of columns. default is 1</docstring>
+ <defaults>['1']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="shadow" name="shadow">
+ <docstring>If True, draw a shadow behind legend. If None, use rc settings.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['']]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="prop" name="prop" port_type="basic:String">
+ <docstring>A :class:`matplotlib.font_manager.FontProperties` instance. If prop is a dictionary, a new instance will be created with prop. If None, use rc settings.</docstring>
+ <entry_types>['enum']</entry_types>
+ <values>[['', 'FontProperties', None]]</values>
+ </inputPortSpec>
+ <inputPortSpec arg="borderpad" name="borderpad">
+ <docstring>the fractional whitespace inside the legend border</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="bbox_transform" name="bbox_transform">
+ <docstring>the transform for the bbox. transAxes if None.</docstring>
+ </inputPortSpec>
+ <inputPortSpec arg="borderaxespad" name="borderaxespad">
+ <docstring>the pad between the axes and legend border</docstring>
+ </inputPortSpec>
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.annotate" name="MplAnnotate" superclass="MplPlot">
+ <docstring>Create an annotation: a piece of text referring to a data point.
+
+Call signature:
+
+annotate(s, xy, xytext=None, xycoords='data', textcoords='data', arrowprops=None, **kwargs)
+
+Keyword arguments:
+
+Annotate the x, y point xy with text s at x, y location xytext. (If xytext = None, defaults to xy, and if textcoords = None, defaults to xycoords).
+
+arrowprops, if not None, is a dictionary of line properties (see :class:`matplotlib.lines.Line2D`) for the arrow that connects annotation to the point.
+
+If the dictionary has a key arrowstyle, a FancyArrowPatch instance is created with the given dictionary and is drawn. Otherwise, a YAArow patch instance is created and drawn. Valid keys for YAArow are
+
+Valid keys for FancyArrowPatch are
+
+xycoords and textcoords are strings that indicate the coordinates of xy and xytext.
+
+If a 'points' or 'pixels' option is specified, values will be added to the bottom-left and if negative, values will be subtracted from the top-right. Eg:
+
+# 10 points to the right of the left border of the axes and # 5 points below the top border xy=(10,-5), xycoords='axes points'
+
+You may use an instance of :class:`~matplotlib.transforms.Transform` or :class:`~matplotlib.artist.Artist`. See :ref:`plotting-guide-annotation` for more details.
+
+The annotation_clip attribute contols the visibility of the annotation when it goes outside the axes area. If True, the annotation will only be drawn when the xy is inside the axes. If False, the annotation will always be drawn regardless of its position. The default is None, which behave as True only if xycoords is"data".
+
+Additional kwargs are Text properties:
+
+%(Text)s</docstring>
+ <inputPortSpec arg="xycoords" arg_pos="3" name="xycoords" port_type="basic:String">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ <defaults>['data']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="xytext" arg_pos="2" name="xytext" />
+ <inputPortSpec arg="s" arg_pos="0" name="s" required="True" />
+ <inputPortSpec arg="xy" arg_pos="1" name="xy" required="True" />
+ <inputPortSpec arg="textcoords" arg_pos="4" name="textcoords" port_type="basic:String">
+ <entry_types>['enum']</entry_types>
+ <values>[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]</values>
+ <defaults>['data']</defaults>
+ </inputPortSpec>
+ <inputPortSpec arg="arrowprops" arg_pos="5" name="arrowprops" />
+ </moduleSpec>
+ <moduleSpec code_ref="matplotlib.pyplot.plot" name="MplLinePlot" superclass="MplPlot">
+ <docstring>Plot lines and/or markers to the :class:`~matplotlib.axes.Axes`. args is a variable length argument, allowing for multiple x, y pairs with an optional format string. For example, each of the following is legal:
+
+plot(x, y) # plot x and y using default line style and color plot(x, y, 'bo') # plot x and y using blue circle markers plot(y) # plot y using x as index array 0..N-1 plot(y, 'r+') # ditto, but with red plusses
+
+If x and/or y is 2-dimensional, then the corresponding columns will be plotted.
+
+An arbitrary number of x, y, fmt groups can be specified, as in:
+
+a.plot(x1, y1, 'g^', x2, y2, 'g-')
+
+Return value is a list of lines that were added.
+
+By default, each line is assigned a different color specified by a 'color cycle'. To change this behavior, you can edit the axes.color_cycle rcParam. Alternatively, you can use :meth:`~matplotlib.axes.Axes.set_default_color_cycle`.
+
+The following format string characters are accepted to control the line style or marker:
+
+The following color abbreviations are supported:
+
+In addition, you can specify colors in many weird and wonderful ways, including full names ('green'), hex strings ('#008000'), RGB or RGBA tuples ((0,1,0,1)) or grayscale intensities as a string ('0.8'). Of these, the string specifications can be used in place of a fmt group, but the tuple forms can be used only as kwargs.
+
+Line styles and colors are combined in a single format string, as in 'bo' for blue circles.
+
+The kwargs can be used to set line properties (any property that has a set_* method). You can use this to set a line label (for auto legends), linewidth, anitialising, marker face color, etc. Here is an example:
+
+plot([1,2,3], [1,2,3], 'go-', label='line 1', linewidth=2) plot([1,2,3], [1,4,9], 'rs', label='line 2') axis([0, 4, 0, 10]) legend()
+
+If you make multiple lines with one plot command, the kwargs apply to all those lines, e.g.:
+
+plot(x1, y1, x2, y2, antialised=False)
+
+Neither line will be antialiased.
+
+You do not need to use format strings, which are just abbreviations. All of the line properties can be controlled by keyword arguments. For example, you can set the color, marker, linestyle, and markercolor with:
+
+plot(x, y, color='green', linestyle='dashed', marker='o', markerfacecolor='blue', markersize=12).
+
+See :class:`~matplotlib.lines.Line2D` for details.
+
+The kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+kwargs scalex and scaley, if defined, are passed on to :meth:`~matplotlib.axes.Axes.autoscale_view` to determine whether the x and y axes are autoscaled; the default is True.
+
+Additional kwargs: hold = [True|False] overrides default hold state</docstring>
+ <inputPortSpec arg="marker" name="marker">
+ <translations>{'tri_down marker': '1', 'pentagon marker': 'p', 'hline marker': '_', 'pixel marker': ',', 'triangle_up marker': '^', 'point marker': '.', 'square marker': 's', 'hexagon2 marker': 'H', 'tri_right marker': '4', 'plus marker': '+', 'vline marker': '|', 'triangle_left marker': '<', 'triangle_down marker': 'v', 'triangle_right marker': '>', 'tri_left marker': '3', 'x marker': 'x', 'circle marker': 'o', 'dashed line style': '--', 'hexagon1 marker': 'h', 'dash-dot lin [...]
+ <entry_types>['enum']</entry_types>
+ <values>[['solid line style', 'dashed line style', 'dash-dot line style', 'dotted line style', 'point marker', 'pixel marker', 'circle marker', 'triangle_down marker', 'triangle_up marker', 'triangle_left marker', 'triangle_right marker', 'tri_down marker', 'tri_up marker', 'tri_left marker', 'tri_right marker', 'square marker', 'pentagon marker', 'star marker', 'hexagon1 marker', 'hexagon2 marker', 'plus marker', 'x marker', 'diamond marker', 'thin_diamond marker', 'vline marker', [...]
+ </inputPortSpec>
+ </moduleSpec>
+</specs>
diff --git a/vistrails/packages/matplotlib/object.py b/vistrails/packages/matplotlib/object.py
new file mode 100644
index 0000000..ace8acc
--- /dev/null
+++ b/vistrails/packages/matplotlib/object.py
@@ -0,0 +1,20 @@
+from vistrails.core.modules.vistrails_module import Module
+
+class MplObject(Module):
+ _input_ports = [("subfigRow", "(org.vistrails.vistrails.spreadsheet:Integer)",
+ {"defaults": ["1"]}),
+ ("subfigCol", "(org.vistrails.vistrails.spreadsheet:Integer)",
+ {"defaults": ["1"]})]
+ _output_ports = [("self", "(org.vistrails.vistrails.matplotlib:MplObject)")]
+
+ def __init__(self):
+ Module.__init__(self)
+ self.figInstance = None
+
+ def set_fig(self, fig):
+ self.figInstance = fig
+
+ def get_fig(self):
+ if self.figInstance is None:
+ self.figInstance = pylab.figure()
+ return self.figInstance
diff --git a/vistrails/packages/matplotlib/parse.py b/vistrails/packages/matplotlib/parse.py
new file mode 100644
index 0000000..18ff809
--- /dev/null
+++ b/vistrails/packages/matplotlib/parse.py
@@ -0,0 +1,1001 @@
+import ast
+import re
+import sys
+from xml.etree import ElementTree as ET
+import docutils.core
+import docutils.nodes
+from itertools import izip
+import inspect
+import matplotlib
+matplotlib.use('Qt4Agg')
+import matplotlib.docstring
+def new_call(self, func):
+ # print "!!!CALLING NEW CALL!!!"
+ return func
+# print id(matplotlib.docstring.interpd.__call__)
+
+matplotlib.docstring.Substitution.__call__ = new_call
+
+# def test_func():
+# """this is something cool %(Line2D)s"""
+# pass
+# # matplotlib.docstring.interpd(test_func)
+# print "docstring:", test_func.__doc__
+# print id(matplotlib.docstring.interpd.__call__), id(new_call)
+
+
+import matplotlib.pyplot
+from matplotlib.artist import Artist, ArtistInspector
+import matplotlib.cbook
+# want to get lowercase accepts too
+ArtistInspector._get_valid_values_regex = re.compile(
+ r"\n\s*ACCEPTS:\s*((?:.|\n)*?)(?:$|(?:\n\n))", re.IGNORECASE)
+
+from specs import SpecList, ModuleSpec, InputPortSpec, OutputPortSpec, \
+ AlternatePortSpec
+
+sys.path.append('/vistrails/src/git')
+from vistrails.core.modules.utils import expand_port_spec_string
+
+##############################################################################
+# docutils parsing code
+##############################################################################
+
+def parse_docutils_thead(elt):
+ header = []
+ for child in elt.children:
+ if child.__class__ == docutils.nodes.row:
+ assert len(header) == 0, "More than one row in header"
+ for subchild in child.children:
+ if subchild.__class__ == docutils.nodes.entry:
+ header.append(parse_docutils_elt(subchild)[0].strip())
+ return header
+
+def parse_docutils_tbody(elt):
+ rows = []
+ for child in elt.children:
+ if child.__class__ == docutils.nodes.row:
+ row = []
+ for subchild in child.children:
+ if subchild.__class__ == docutils.nodes.entry:
+ row.append(parse_docutils_elt(subchild)[0].strip())
+ rows.append(row)
+ return rows
+
+def parse_docutils_table(elt):
+ header = []
+ rows = []
+ for child in elt.children:
+ if child.__class__ == docutils.nodes.tgroup:
+ for subchild in child.children:
+ if subchild.__class__ == docutils.nodes.thead:
+ header = parse_docutils_thead(subchild)
+ elif subchild.__class__ == docutils.nodes.tbody:
+ rows = parse_docutils_tbody(subchild)
+ print "== TABLE =="
+ print "HEADER:", header
+ print "ROWS:", '\n'.join(str(r) for r in rows)
+ return (header, rows)
+
+def parse_docutils_term(elt):
+ # term = ""
+ terms = []
+ accepts = ""
+ for child in elt.children:
+ if child.__class__ == docutils.nodes.emphasis:
+ term = parse_docutils_elt(child)[0].strip()
+ if term in ('True', 'False'):
+ accepts += term
+ elif term != "None":
+ terms.append(term)
+ elif child.__class__ == docutils.nodes.Text:
+ accepts += str(child)
+ else:
+ accepts += parse_docutils_elt(child)[0]
+ accepts = accepts.strip()
+ if accepts.startswith(':'):
+ accepts = accepts[1:].strip()
+ return terms, accepts
+
+def parse_docutils_deflist(elt):
+ print "GOT DEFLIST!"
+ args = []
+ term = None
+ definition = None
+ for child in elt.children:
+ assert child.__class__ == docutils.nodes.definition_list_item, "NO DEF LIST ITEM!"
+ for subchild in child.children:
+ if subchild.__class__ == docutils.nodes.term:
+ terms, accepts = parse_docutils_term(subchild)
+ print "TERMS:", terms
+ if accepts:
+ print "ACCEPTS:", accepts
+ elif subchild.__class__ == docutils.nodes.definition:
+ definition = parse_docutils_elt(subchild)[0].rstrip()
+ print "DEFINITION:", definition
+ for term in terms:
+ args.append((term, accepts, definition))
+ return args
+
+def parse_docutils_elt(elt, last_text=""):
+ def get_last_block(cur_text):
+ num_newlines = 1
+ end_idx = len(cur_text)
+ while cur_text.endswith("\n\n" * num_newlines):
+ num_newlines += 1
+ end_idx -= 2
+ idx = cur_text.rfind("\n\n",0,end_idx)
+ if idx < 0:
+ idx = 0
+ else:
+ idx += 2
+ return cur_text[idx:].strip()
+
+ text = ""
+ args = []
+ tables = []
+ call_signatures = []
+ for child in elt.children:
+ if child.__class__ == docutils.nodes.Text:
+ # cur_block.extend(s.strip() for s in str(child).split('\n'))
+ ntext = ' '.join(s for s in str(child).split('\n'))
+ text += ntext
+ elif child.__class__ == docutils.nodes.system_message:
+ pass
+ elif child.__class__ == docutils.nodes.definition_list:
+ # print "DEFLIST BLOCK:", text[-20:]
+ # print get_last_block(last_text + text)
+ args.append((get_last_block(last_text + text),
+ parse_docutils_deflist(child)))
+ elif child.__class__ == docutils.nodes.table:
+ # print "TABLE BLOCK:", text[-20:]
+ # print get_last_block(last_text + text)
+ tables.append((get_last_block(last_text + text),) + \
+ parse_docutils_table(child))
+ elif isinstance(child, docutils.nodes.Inline):
+ (ntext, nargs, ntables, ncall_sigs) = \
+ parse_docutils_elt(child, last_text + text)
+ text += ntext
+ args += nargs
+ tables += ntables
+ call_signatures += ncall_sigs
+ else:
+ (ntext, nargs, ntables, ncall_sigs) = \
+ parse_docutils_elt(child, last_text + text)
+ if child.__class__ == docutils.nodes.literal_block:
+ check_str = (last_text + text).lower().strip()
+ if check_str.endswith("\ncall signature:") or \
+ check_str.endswith("\ncall signatures:"):
+ call_signatures.append(ntext)
+ text += ntext.strip() + "\n\n"
+ args += nargs
+ tables += ntables
+ call_signatures += ncall_sigs
+ return (text.rstrip(), args, tables, call_signatures)
+
+def parse_docutils_str(docstring, should_print=False):
+ root = docutils.core.publish_doctree(docstring)
+ if should_print:
+ print root
+ # for child in root.children:
+ # print "CHILD:", child.__class__, child
+ # for subchild in child.children:
+ # print "SUBCHILD:", subchild.__class__, subchild
+ return parse_docutils_elt(root)
+
+##############################################################################
+# util methods
+##############################################################################
+
+def capfirst(s):
+ return s[0].upper() + s[1:]
+
+def pretty_name(s):
+ cap = True
+ new_s = ""
+ for i, c in enumerate(s):
+ if cap:
+ c = c.upper()
+ cap = False
+ if c != '_' or i == 0:
+ new_s += c
+ else:
+ cap = True
+ return new_s
+
+def get_value_and_type(s):
+ try:
+ val = eval(s)
+ if isinstance(val, type):
+ return (None, None)
+ except:
+ val = s
+ port_type = get_type_from_val(val)
+ return (val, port_type)
+
+def get_type_from_val(val):
+ if isinstance(val, float):
+ return "basic:Float"
+ elif isinstance(val, (int, long)):
+ return "basic:Integer"
+ elif isinstance(val, basestring):
+ return "basic:String"
+ elif isinstance(val, bool):
+ return "basic:Boolean"
+ elif isinstance(val, list):
+ return "basic:List"
+ return None
+
+def resolve_port_type(port_types, port_spec):
+ port_types_set = set(p for p in port_types if p is not None)
+ was_set = False
+ if port_spec.port_type is not None:
+ port_types_set.add(port_spec.port_type)
+ if len(port_types_set) == 1:
+ port_spec.port_type = next(iter(port_types_set))
+ was_set = True
+ elif len(port_types_set) == 2:
+ if 'basic:Float' in port_types_set and \
+ 'basic:Integer' in port_types_set:
+ port_spec.port_type = 'basic:Float'
+ was_set = True
+ elif 'basic:List' in port_types_set:
+ port_spec.port_type = 'basic:List'
+ base_name = port_spec.name
+ port_spec.name = base_name + "Sequence"
+ port_types_set.discard('basic:List')
+ alternate_spec = \
+ AlternatePortSpec(name=base_name + "Scalar",
+ port_type=next(iter(port_types_set)))
+ port_spec.alternate_specs.append(alternate_spec)
+ was_set = True
+ if not was_set:
+ if "color" in port_spec.name:
+ port_spec.port_type = "basic:Color"
+ port_spec.translations = "translate_color"
+ elif port_spec.name == "x":
+ port_spec.port_type = "basic:List"
+ elif port_spec.name == "y":
+ port_spec.port_type = "basic:List"
+ else:
+ port_spec.port_type = None
+
+ # # FIXME
+ # # what to do with scalar/sequence-type args
+ # elif len(port_types_set) == 2 and 'basic:List' in port_types_set:
+ # port_type = 'basic:List'
+ # else:
+ # port_type = None
+ # return port_type
+
+def parse_description(desc):
+ key_to_type = {'string': 'basic:String',
+ 'integer': 'basic:Integer',
+ 'sequence': 'basic:List',
+ 'float': 'basic:Float',
+ 'boolean': 'basic:Boolean',
+ 'scalar': 'basic:Float',
+ 'vector': 'basic:List',
+ 'list': 'basic:List'}
+ port_types = []
+ option_strs = []
+ default_val = None
+ allows_none = False
+ default_paren_re = re.compile(r"((\S*)\s+)?\(default:?(\s+(\S*))?\)",
+ re.IGNORECASE)
+ default_is_re = re.compile(r"default\s+is\s+(\S*)", re.IGNORECASE)
+
+ if '|' in desc:
+ m = re.search("\[([\s\S]*?)\]", desc)
+ if m:
+ opt_str = m.group(1)
+ else:
+ opt_str = desc
+ opts = opt_str.split('|')
+ for opt in opts:
+ opt = opt.strip()
+ m = default_paren_re.search(opt)
+ if m:
+ (_, before_res, _, after_res) = m.groups()
+ if after_res:
+ assert default_val is None, ('Multiple defaults: '
+ '"%s" "%s"' % (default_val, after_res))
+ default_val = after_res
+ opt = after_res
+ elif before_res:
+ assert default_val is None, ('Multiple defaults: '
+ '"%s" "%s"' % (default_val, after_res))
+ default_val = before_res
+ opt = before_res
+ found_type = False
+ opt_lower = opt.lower()
+ if opt_lower == "none":
+ found_type = True
+ allows_none = True
+ elif opt_lower == "true" or opt_lower == "false":
+ found_type = True
+ port_types.append("basic:Boolean")
+ else:
+ for key in key_to_type:
+ if key in opt_lower:
+ found_type = True
+ port_types.append(key_to_type[key])
+
+ if not found_type:
+ (val, port_type) = get_value_and_type(opt)
+ option_strs.append(val)
+ if port_type is not None:
+ port_types.append(port_type)
+ found_type = True
+ # option_strs.append(opt)
+ # if opt.startswith("'") or opt.startswith('"'):
+ # port_types.append("basic:String")
+ # found_type = True
+
+ if default_val is None:
+ m = default_paren_re.search(desc)
+ if m:
+ (_, before_res, _, after_res) = m.groups()
+ if after_res:
+ default_val = after_res
+ elif before_res:
+ default_val = before_res
+ else:
+ m = default_is_re.search(desc)
+ if m:
+ (default_val,) = m.groups()
+ if default_val.endswith('.') or default_val.endswith(','):
+ default_val = default_val[:-1]
+
+ if default_val:
+ (default_val, port_type) = get_value_and_type(default_val)
+ if port_type is not None:
+ port_types.append(port_type)
+
+ should_print = False
+ if len(port_types) == 0:
+ for key, port_type in key_to_type.iteritems():
+ if key in desc:
+ port_types.append(port_type)
+
+ # port_type = resolve_port_type(port_types)
+
+ return (port_types, option_strs, default_val, allows_none)
+
+def parse_translation(rows, should_reverse=True):
+ t = {}
+ port_types = []
+ values = []
+ for row in rows:
+ (val1, port_type1) = get_value_and_type(row[0])
+ (val2, port_type2) = get_value_and_type(row[1])
+ if should_reverse:
+ if val2 != None:
+ port_types.append(port_type2)
+ values.append(val2)
+ t[val2] = val1
+ else:
+ if val1 != None:
+ port_types.append(port_type1)
+ values.append(val1)
+ t[val1] = val2
+
+ # port_type = resolve_port_type(port_types)
+ return (t, port_types, values)
+
+def do_translation_override(port_specs, names, rows, opts):
+ if 'name' in opts:
+ names = opts['name']
+ if names is None:
+ raise ValueError("Must specify name of port to use translation for")
+ if isinstance(names, basestring) or not matplotlib.cbook.iterable(names):
+ names = [names]
+ should_reverse = opts.get('reverse', True)
+ values_only = opts.get('values_only', False)
+ (t, port_type, values) = \
+ parse_translation(rows, should_reverse)
+ for name in names:
+ print "TRANSLATING", name
+ if name not in port_specs:
+ port_specs[name] = InputPortSpec(name)
+ port_specs[name].entry_types = ['enum']
+ port_specs[name].values = [values]
+ if not values_only:
+ port_specs[name].translations = t
+
+def get_names(obj, default_module_base, default_super_base,
+ prefix="Mpl", suffix=""):
+ module_name = None
+ super_name = None
+ if isinstance(obj, tuple):
+ if len(obj) > 2:
+ super_name = obj[2]
+ if len(obj) < 2:
+ raise ValueError("Need to specify 2- or 3-tuple")
+ (obj, module_name) = obj[:2]
+ if module_name is None:
+ module_name = "%s%s%s" % (prefix,
+ pretty_name(default_module_base(obj)),
+ suffix)
+ if super_name is None:
+ super_name = "%s%s%s" % (prefix,
+ pretty_name(default_super_base(obj)),
+ suffix)
+
+ return (obj, module_name, super_name)
+
+##############################################################################
+# main methods
+##############################################################################
+
+def parse_argspec(obj_or_str):
+ if isinstance(obj_or_str, basestring):
+ obj_or_str = obj_or_str.strip()
+ if not obj_or_str.endswith(":"):
+ obj_or_str += ":"
+ if not obj_or_str.startswith("def "):
+ obj_or_str = "def " + obj_or_str
+ try:
+ tree = ast.parse(obj_or_str + "\n pass")
+ except SyntaxError:
+ # cannot parse the argspec
+ print "*** CANNOT PARSE", obj_or_str
+ return []
+ argspec_name = tree.body[0].name
+ argspec_args = [a.id for a in tree.body[0].args.args]
+ print tree.body[0].args.defaults
+ argspec_defaults = []
+ for i, d in enumerate(tree.body[0].args.defaults):
+ try:
+ d_val = ast.literal_eval(d)
+ except ValueError:
+ d_val = None
+ argspec_defaults.append(d_val)
+ # argspec_defaults = \
+ # [ast.literal_eval(d) for d in tree.body[0].args.defaults]
+ else:
+ argspec = inspect.getargspec(obj_or_str)
+ argspec_args = argspec.args
+ argspec_defaults = argspec.defaults
+
+ # print argspec
+ if not argspec_defaults:
+ start_defaults = len(argspec_args) + 1
+ else:
+ start_defaults = len(argspec_args) - len(argspec_defaults)
+ port_specs_list = []
+ has_self = False
+ for i, arg in enumerate(argspec_args):
+ if i == 0 and arg == "self":
+ has_self = True
+ continue
+ port_spec = InputPortSpec(arg)
+ port_spec.arg_pos = (i-1) if has_self else i
+ if i >= start_defaults:
+ port_spec.required = False
+ default_val = argspec_defaults[i-start_defaults]
+ if default_val is not None:
+ port_spec.defaults = [str(default_val)]
+ port_type = get_type_from_val(default_val)
+ if port_type is not None:
+ port_spec.port_type = port_type
+ else:
+ port_spec.required = True
+ # port_specs[arg].entry_types = [None,]
+ # port_specs[arg].values = [[]]
+ # port_specs[arg].translations = [None,]
+ port_specs_list.append(port_spec)
+ return port_specs_list
+
+def process_docstring(docstring, port_specs, parent, table_overrides):
+ (cleaned_docstring, args, tables, call_sigs) = \
+ parse_docutils_str(docstring)
+
+ if len(call_sigs) > 0:
+ for call_sig in call_sigs:
+ port_specs_list = parse_argspec(call_sig)
+ for port_spec in port_specs_list:
+ if port_spec.arg in port_specs:
+ # have to reconcile the two
+ old_port_spec = port_specs[port_spec.arg]
+ resolve_port_type([port_spec.port_type], old_port_spec)
+ if old_port_spec.defaults is None:
+ old_port_spec.defaults = port_spec.defaults
+ elif old_port_spec.defaults != port_spec.defaults:
+ # keep it as the old spec is
+ print "*** Different defaults!" + \
+ str(old_port_spec.defaults) + \
+ " : " + str(port_spec.defaults)
+ # raise RuntimeError("Different defaults! %s: %s" % (
+ # old_port_spec.defaults,
+ # port_spec.defaults))
+ else:
+ port_specs[port_spec.arg] = port_spec
+
+ output_port_specs = []
+ for (deflist_intro, deflist) in args:
+ print "PROCESSING DEFLIST", deflist_intro
+ if re.search("return value", deflist_intro, re.IGNORECASE):
+ print " -> RETURN VALUE"
+ for (name, accepts, port_doc) in deflist:
+ (port_types, option_strs, default_val, allows_none) = \
+ parse_description(accepts)
+ (pt2, _, dv2, _) = parse_description(port_doc)
+ port_types.extend(pt2)
+ if default_val is None:
+ default_val = dv2
+ oport = OutputPortSpec(name, docstring=port_doc)
+ resolve_port_type(port_types, oport)
+ output_port_specs.append(oport)
+ elif (re.search("argument", deflist_intro, re.IGNORECASE) or
+ re.search("kwarg", deflist_intro, re.IGNORECASE)):
+ print " -> ARGUMENTS"
+ for (name, accepts, port_doc) in deflist:
+ if name not in port_specs:
+ port_specs[name] = InputPortSpec(name, docstring=port_doc)
+ else:
+ port_specs[name].docstring = port_doc
+ (port_types, option_strs, default_val, allows_none) = \
+ parse_description(accepts)
+ (pt2, _, dv2, _) = parse_description(port_doc)
+ port_types.extend(pt2)
+ if default_val is None:
+ default_val = dv2
+ resolve_port_type(port_types, port_specs[name])
+ if len(option_strs) > 0:
+ port_specs[name].entry_types = ['enum']
+ port_specs[name].values = [option_strs]
+ if default_val is not None:
+ port_specs[name].defaults = [str(default_val)]
+
+ for (table_intro, header, rows) in tables:
+ print "GOT TABLE", table_intro, rows[0]
+ table_key = parent + (table_intro,)
+ if table_key in table_overrides:
+ (override_type, opts) = table_overrides[table_key]
+ if override_type == "translation":
+ do_translation_override(port_specs, None, rows, opts)
+ continue
+ elif override_type == "ports":
+ table_intro = "kwarg"
+ elif override_type == "skip":
+ continue
+
+ if re.search("return value", table_intro, re.IGNORECASE):
+ print " -> RETURN"
+ if len(rows[0]) != 2:
+ raise ValueError("row that has more/less than 2 columns!")
+ for (name, port_doc) in rows:
+ (port_types, option_strs, default_val, allows_none) = \
+ parse_description(port_doc)
+ # (port_types, option_strs) = parse_desc(port_doc)
+ # port_type_set = set(port_types)
+ # # print port_name, "PORT_TYPES:", port_type_set
+ # port_type = "UNKNOWN"
+ # if len(port_type_set) == 1:
+ # port_type = port_types[0]
+ oport = OutputPortSpec(name, docstring=port_doc)
+ resolve_port_type(oport, port_types)
+ output_port_specs.append(oport)
+ elif (re.search("argument", table_intro, re.IGNORECASE) or
+ re.search("kwarg", table_intro, re.IGNORECASE)):
+ print " -> ARGUMENT"
+ if len(rows[0]) != 2:
+ raise ValueError("row that has more/less than 2 columns!")
+ for (name, port_doc) in rows:
+ if name not in port_specs:
+ port_specs[name] = InputPortSpec(name, docstring=port_doc)
+ else:
+ port_specs[name].docstring = port_doc
+ (port_types, option_strs, default_val, allows_none) = \
+ parse_description(port_doc)
+ # (port_types, option_strs) = parse_desc(port_doc)
+ # port_type_set = set(port_types)
+ # # print port_name, "PORT_TYPES:", port_type_set
+ # port_type = "UNKNOWN"
+ # if len(port_type_set) == 1:
+ # port_specs[name].port_type = port_types[0]
+ resolve_port_type(port_types, port_specs[name])
+ if len(option_strs) > 0:
+ port_specs[name].entry_types = ['enum']
+ port_specs[name].values = [option_strs]
+ if default_val is not None:
+ port_specs[name].defaults = [str(default_val)]
+ else:
+ raise ValueError("Unknown table: %s\n %s %s" % (
+ parent, table_intro, header))
+ # print "HIT SPEC:", name
+ # if name not in port_specs:
+ # port_specs[name] = PortSpec(name, name, "UNKNOWN", "")
+ # port_specs[name].translations = dict(reversed(r) for r in rows)
+ return cleaned_docstring, output_port_specs
+
+def parse_plots(plot_types, table_overrides):
+ def get_module_base(n):
+ return n
+ def get_super_base(n):
+ return "plot"
+
+ module_specs = []
+ for plot in plot_types:
+ port_specs = {}
+ print "========================================"
+ print plot
+ print "========================================"
+
+ (plot, module_name, super_name) = \
+ get_names(plot, get_module_base, get_super_base, "Mpl", "")
+
+ try:
+ plot_obj = getattr(matplotlib.pyplot, plot)
+ except AttributeError:
+ print '*** CANNOT ADD PLOT "%s";' \
+ 'IT DOES NOT EXIST IN THIS MPL VERSION ***' % plot
+ continue
+ # argspec = inspect.getargspec(plot_obj)
+ # print argspec
+ # if argspec.defaults is None:
+ # start_defaults = len(argspec.args) + 1
+ # else:
+ # start_defaults = len(argspec.args) - len(argspec.defaults)
+ # for i, arg in enumerate(argspec.args):
+ # port_specs[arg] = PortSpec(arg, arg)
+ # if i >= start_defaults:
+ # port_specs[arg].required = False
+ # default_val = argspec.defaults[i-start_defaults]
+ # if default_val is not None:
+ # port_specs[arg].defaults = [str(default_val)]
+ # port_type = get_type_from_val(default_val)
+ # if port_type is not None:
+ # port_specs[arg].port_type = port_type
+ # else:
+ # port_specs[arg].required = True
+ # # port_specs[arg].entry_types = [None,]
+ # # port_specs[arg].values = [[]]
+ # # port_specs[arg].translations = [None,]
+
+ port_specs_list = parse_argspec(plot_obj)
+ for port_spec in port_specs_list:
+ port_specs[port_spec.arg] = port_spec
+
+ docstring = plot_obj.__doc__
+ if plot == 'contour':
+ # want to change the double newline to single newline...
+ print "&*&* FINDING:", \
+ docstring.find("*extent*: [ *None* | (x0,x1,y0,y1) ]\n\n")
+ docstring = docstring.replace("*extent*: [ *None* | (x0,x1,y0,y1) ]\n\n",
+ "*extent*: [ *None* | (x0,x1,y0,y1) ]\n")
+ if plot == 'annotate':
+ docstring = docstring % dict((k,v) for k, v in matplotlib.docstring.interpd.params.iteritems() if k == 'Annotation')
+ elif plot == 'barbs':
+ docstring = docstring % dict((k,v) for k,v in matplotlib.docstring.interpd.params.iteritems() if k == 'barbs_doc')
+
+ cleaned_docstring, output_port_specs = \
+ process_docstring(docstring, port_specs, ('pyplot', plot),
+ table_overrides)
+
+ module_specs.append(ModuleSpec(module_name, super_name,
+ "matplotlib.pyplot.%s" % plot,
+ cleaned_docstring, port_specs.values(),
+ output_port_specs))
+ my_specs = SpecList(module_specs)
+ return my_specs
+
+_get_accepts_regex = re.compile(
+ r"([\s\S]*)\n\s*ACCEPTS:\s*((?:.|\n)*?)(?:$|(?:\n\n))([\s\S]*)",
+ re.IGNORECASE)
+
+def parse_artists(artist_types, table_overrides={}):
+ def get_module_name(obj):
+ return obj.__name__
+ def get_super_name(obj):
+ for base in obj.__bases__:
+ if issubclass(base, Artist):
+ return base.__name__
+ return ""
+ # if obj.__bases__[0].__name__ != 'object':
+ # return obj.__bases__[0].__name__
+ # else:
+ # return ""
+
+ module_specs = []
+ for klass in artist_types:
+ (klass, module_name, super_name) = \
+ get_names(klass, get_module_name, get_super_name, "Mpl",
+ "Properties")
+
+ port_specs = {}
+ insp = ArtistInspector(klass)
+ klass_name = klass.__name__
+ klass_qualname = klass.__module__ + "." + klass_name
+ for (s, t) in insp._get_setters_and_targets():
+ print "** %s **" % s
+ if t.rsplit('.',1)[0] != klass_qualname:
+ # let inheritance work
+ continue
+
+ if s in port_specs:
+ raise ValueError('duplicate port "%s"' % s)
+ port_spec = InputPortSpec(s)
+ port_specs[s] = port_spec
+
+ accepts_raw = insp.get_valid_values(s)
+ (accepts, deflists, tables, call_sigs) = \
+ parse_docutils_str(accepts_raw)
+ if len(deflists) + len(tables) > 0:
+ raise ValueError("accepts has deflists and/or tables")
+ (port_types, option_strs, default_val, allows_none) = \
+ parse_description(accepts)
+ # port_spec.port_type = port_type
+ if default_val is not None:
+ port_spec.default_val = default_val
+ if len(option_strs) > 0:
+ port_spec.entry_types = ['enum']
+ port_spec.values = [option_strs]
+ port_spec.hide = False
+
+ docstring = getattr(insp.o, 'set_' + s).__doc__
+ if docstring is None:
+ docstring = ""
+ else:
+ docstring = docstring % matplotlib.docstring.interpd.params
+ match = _get_accepts_regex.search(docstring)
+ if match is not None:
+ print "STARTING DOCSTRING:", docstring
+ groups = match.groups()
+ if len(groups) > 2 and groups[2]:
+ docstring = groups[0] + groups[2]
+ else:
+ docstring = groups[0]
+ print "FIXED DOCSTRING:", docstring
+
+ (cleaned_docstring, args, tables, call_sigs) = \
+ parse_docutils_str(docstring)
+ port_spec.docstring = cleaned_docstring
+
+ translations = None
+ for (table_intro, header, rows) in tables:
+ print "TABLE:", table_intro
+ if (klass.__name__, s, table_intro) in table_overrides:
+ (override_type, opts) = \
+ table_overrides[(klass.__name__, s, table_intro)]
+ if override_type == "translation":
+ do_translation_override(port_specs, s, rows, opts)
+ continue
+ elif override_type == "ports":
+ table_intro = "kwarg"
+ elif override_type == "skip":
+ continue
+ if len(header) != 2:
+ raise ValueError("Table not two columns!")
+ if translations is not None:
+ raise ValueError("Two translations in one attr")
+ (translations, pt2, values) = parse_translation(rows)
+ port_spec.translations = translations
+ port_spec.values = [values]
+ port_types.extend(pt2)
+ resolve_port_type(port_types, port_spec)
+
+ constructor_port_specs = {}
+ port_specs_list = parse_argspec(klass.__init__)
+ for port_spec in port_specs_list:
+ constructor_port_specs[port_spec.arg] = port_spec
+ constructor_docstring = klass.__init__.__doc__
+ if constructor_docstring is not None:
+ _, output_port_specs = process_docstring(constructor_docstring,
+ constructor_port_specs,
+ (klass.__name__,
+ '__init__'),
+ table_overrides)
+ for arg, ps in constructor_port_specs.iteritems():
+ if arg not in port_specs:
+ ps.constructor_arg = True
+ ps.required = False
+ port_specs[arg] = ps
+
+ module_spec = ModuleSpec(module_name, super_name, klass_qualname,
+ klass.__doc__, port_specs.values())
+ module_specs.append(module_spec)
+
+ my_specs = SpecList(module_specs)
+ return my_specs
+
+def run_artists():
+ import matplotlib.axes
+ import matplotlib.axis
+ import matplotlib.collections
+ import matplotlib.figure
+ import matplotlib.image
+ import matplotlib.lines
+ import matplotlib.patches
+ import matplotlib.text
+
+ artist_py_modules = [matplotlib.axes,
+ matplotlib.axis,
+ matplotlib.collections,
+ matplotlib.figure,
+ matplotlib.image,
+ matplotlib.lines,
+ matplotlib.patches,
+ matplotlib.text,
+ ]
+
+ exclude = set([])
+
+ artist_types = set() # (Artist, None, "MplProperties")]
+ for py_module in artist_py_modules:
+ for cls_name, cls in inspect.getmembers(py_module, inspect.isclass):
+ if cls_name in exclude:
+ continue
+ if issubclass(cls, Artist) and cls != Artist:
+ artist_types.add(cls)
+
+ print "ARTIST TYPES:", artist_types
+ artist_types = [(Artist, None, "MplProperties")] + \
+ list(sorted(artist_types, key=lambda x: list(reversed(x.mro()))))
+ print "SORTED ARTIST TYPES:", artist_types
+
+ # from matplotlib.collections import Collection, PathCollection, \
+ # LineCollection
+ # from matplotlib.lines import Line2D
+ # from matplotlib.patches import Patch, Rectangle, PathPatch, Wedge, \
+ # FancyArrowPatch, YAArrow
+ # from matplotlib.text import Text, Annotation
+ # from matplotlib.axes import Axes
+ # from matplotlib.figure import Figure
+
+ # artist_types = [(Artist, None, "MplProperties"),
+ # Line2D, Patch, Rectangle, Axes, Figure, PathPatch, Wedge,
+ # Collection, PathCollection, LineCollection, Text,
+ # Annotation, FancyArrowPatch, YAArrow]
+
+ # FIXME want this to be indexed by artist name, too...
+ artist_overrides = {('Axes', 'aspect', 'aspect'):
+ ('translation', {'reverse': False,
+ 'values_only': True}),
+ # FIXME may want documentation from adjustable?
+ ('Axes', 'aspect', 'adjustable'):
+ ('skip', {}),
+ # FIXME may want documentation from anchor?
+ ('Axes', 'aspect', 'anchor'):
+ ('skip', {}),
+ ('ConnectionPatch', '__init__', "Valid keys are"):
+ ('ports', {}),
+ ('ConnectionPatch', '__init__', "coordsA and coordsB are strings that indicate the coordinates of xyA and xyB."):
+ ('translation', {'name': ['coordsA', 'coordsB'],
+ 'reverse': False,
+ 'values_only': True}),
+ ('Annotation', '__init__', "If the dictionary has a key arrowstyle, a FancyArrowPatch instance is created with the given dictionary and is drawn. Otherwise, a YAArow patch instance is created and drawn. Valid keys for YAArow are"):
+ ('skip', {}),
+ ('Annotation', '__init__', "Valid keys for FancyArrowPatch are"):
+ ('skip', {}),
+ ('Annotation', '__init__', "xycoords and textcoords are strings that indicate the coordinates of xy and xytext."):
+ ('translation', {'name': ['xycoords', 'textcoords'],
+ 'reverse': False,
+ 'values_only': True}),
+ }
+
+ # test_xml()
+ specs = parse_artists(artist_types, artist_overrides)
+ specs.write_to_xml("mpl_artists_raw.xml")
+
+
+def run_plots():
+ # from matplotlib's boilerplate.py
+ plot_types = ['acorr',
+ 'arrow',
+ 'axhline',
+ 'axhspan',
+ 'axvline',
+ 'axvspan',
+ 'bar',
+ 'barh',
+ 'broken_barh',
+ 'boxplot',
+ 'cohere',
+ 'clabel',
+ 'contour',
+ 'contourf',
+ 'csd',
+ 'errorbar',
+ 'fill',
+ 'fill_between',
+ 'fill_betweenx',
+ 'hexbin',
+ 'hist',
+ 'hist2d',
+ 'hlines',
+ 'imshow',
+ 'loglog',
+ 'pcolor',
+ 'pcolormesh',
+ 'pie',
+ # add plot later
+ # 'plot',
+ 'plot_date',
+ 'psd',
+ 'quiver',
+ 'quiverkey',
+ 'scatter',
+ 'semilogx',
+ 'semilogy',
+ 'specgram',
+ 'stackplot',
+ 'stem',
+ 'step',
+ 'streamplot',
+ 'tricontour',
+ 'tricontourf',
+ 'tripcolor',
+ 'triplot',
+ 'vlines',
+ 'xcorr',
+ 'barbs',
+ ]
+
+ plot_types += ['spy',
+ 'polar',
+ ]
+
+ # FIXME added to keep existing code happy for now
+ plot_types += ['legend',
+ 'annotate',
+ ('plot', 'MplLinePlot')]
+
+ # others = ['plotfile', 'legend', 'matshow',]
+
+ # plot_types = ['acorr', 'bar', 'barbs', 'barh', 'boxplot', 'broken_barh', 'cohere', 'contour', 'contourf', 'csd', 'errorbar', 'hexbin', 'hist', 'loglog', 'pcolor', 'pcolormesh', 'pie', 'plot', 'plot_date', 'pie', 'polar', 'psd', 'quiver', 'scatter', 'semilogx', 'semilogy', 'specgram', 'spy', 'stem', 'tricontour', 'tricontourf', 'tripcolor', 'triplot', 'xcorr']
+
+ # plot_types = ['bar', 'boxplot', 'contour', 'hist', ('plot', "MplLinePlot"),
+ # 'scatter', 'pie', 'legend', 'annotate', 'hlines',
+ # 'axvline', 'axhline', 'errorbar']
+
+ table_overrides = {('pyplot', 'plot', 'The following format string characters are accepted to control the line style or marker:'):
+ ('translation', {'name': 'marker'}),
+ ('pyplot', 'plot', 'The following color abbreviations are supported:'):
+ ('skip', {}),
+ ('pyplot', 'legend', 'The location codes are'):
+ ('translation', {'name': 'loc',
+ 'reverse': False}),
+ ('pyplot', 'legend', 'Padding and spacing between various elements use following keywords parameters. These values are measure in font-size units. E.g., a fontsize of 10 points and a handlelength=5 implies a handlelength of 50 points. Values from rcParams will be used if None.'):
+ ('ports', {}),
+ ('pyplot', 'annotate', "If the dictionary has a key arrowstyle, a FancyArrowPatch instance is created with the given dictionary and is drawn. Otherwise, a YAArow patch instance is created and drawn. Valid keys for YAArow are"):
+ ('skip', {}),
+ ('pyplot', 'annotate', "Valid keys for FancyArrowPatch are"):
+ ('skip', {}),
+ ('pyplot', 'annotate', "xycoords and textcoords are strings that indicate the coordinates of xy and xytext."):
+ ('translation', {'name': ['xycoords', 'textcoords'],
+ 'reverse': False,
+ 'values_only': True}),
+ }
+
+
+
+ specs = parse_plots(plot_types, table_overrides)
+ specs.write_to_xml("mpl_plots_raw.xml")
+
+
+def run(which="all"):
+ if which == "all" or which == "artists":
+ run_artists()
+ if which == "all" or which == "plots":
+ run_plots()
+
+ # write_specs("test.xml")
+ # write_specs("mpl.xml")
+ # test_table()
+
+def get_docutils(plot):
+ import matplotlib.pyplot
+ plot_obj = getattr(matplotlib.pyplot, plot)
+ (_, _, _, call_sigs) = parse_docutils_str(plot_obj.__doc__, True)
+ print call_sigs
+
+if __name__ == '__main__':
+ if len(sys.argv) <= 1:
+ run()
+ elif len(sys.argv) == 2:
+ run(sys.argv[1])
+ else:
+ raise TypeError("usage: python parse.py [all|artists|plots]")
+ # get_docutils("axhline")
diff --git a/vistrails/packages/matplotlib/plots.py b/vistrails/packages/matplotlib/plots.py
new file mode 100644
index 0000000..5d342ea
--- /dev/null
+++ b/vistrails/packages/matplotlib/plots.py
@@ -0,0 +1,5482 @@
+import matplotlib.pyplot
+from vistrails.core.modules.vistrails_module import Module, ModuleError
+from bases import MplPlot
+
+
+
+
+
+def translate_color(c):
+ return c.tuple
+
+def translate_MplLegend_loc(val):
+ translate_dict = {'right': 5, 'center left': 6, 'upper right': 1, 'lower right': 4, 'best': 0, 'center': 10, 'lower left': 3, 'center right': 7, 'upper left': 2, 'upper center': 9, 'lower center': 8}
+ return translate_dict[val]
+def translate_MplLinePlot_marker(val):
+ translate_dict = {'tri_down marker': '1', 'pentagon marker': 'p', 'hline marker': '_', 'pixel marker': ',', 'triangle_up marker': '^', 'point marker': '.', 'square marker': 's', 'hexagon2 marker': 'H', 'tri_right marker': '4', 'plus marker': '+', 'vline marker': '|', 'triangle_left marker': '<', 'triangle_down marker': 'v', 'triangle_right marker': '>', 'tri_left marker': '3', 'x marker': 'x', 'circle marker': 'o', 'dashed line style': '--', 'hexagon1 marker': 'h', 'dash-dot line sty [...]
+ return translate_dict[val]
+
+class MplAcorr(MplPlot):
+ """Plot the autocorrelation of x.
+
+Call signature:
+
+acorr(x, normed=True, detrend=mlab.detrend_none, usevlines=True, maxlags=10, **kwargs)
+
+If normed = True, normalize the data by the autocorrelation at 0-th lag. x is detrended by the detrend callable (default no normalization).
+
+Data are plotted as plot(lags, c, **kwargs)
+
+Return value is a tuple (lags, c, line) where:
+
+lags are a length 2*maxlags+1 lag vector
+
+c is the 2*maxlags+1 auto correlation vector
+
+line is a :class:`~matplotlib.lines.Line2D` instance returned by :meth:`plot`
+
+The default linestyle is None and the default marker is 'o', though these can be overridden with keyword args. The cross correlation is performed with :func:`numpy.correlate` with mode = 2.
+
+If usevlines is True, :meth:`~matplotlib.axes.Axes.vlines` rather than :meth:`~matplotlib.axes.Axes.plot` is used to draw vertical lines from the origin to the acorr. Otherwise, the plot style is determined by the kwargs, which are :class:`~matplotlib.lines.Line2D` properties.
+
+maxlags is a positive integer detailing the number of lags to show. The default value of None will return all (2*len(x)-1) lags.
+
+The return value is a tuple (lags, c, linecol, b) where
+
+linecol is the :class:`~matplotlib.collections.LineCollection`
+
+b is the x-axis.
+
+Example:
+
+:func:`~matplotlib.pyplot.xcorr` is top graph, and :func:`~matplotlib.pyplot.acorr` is bottom graph.
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("normed", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("usevlines", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("detrend", "basic:String",
+ {'optional': True}),
+ ("maxlags", "basic:Integer",
+ {'optional': True, 'defaults': "['10']"}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("lineCollectionProperties", "MplLineCollectionProperties",
+ {}),
+ ("lineProperties", "MplLine2DProperties",
+ {}),
+ ("xaxisProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplAcorr)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('normed'):
+ val = self.getInputFromPort('normed')
+ kwargs['normed'] = val
+ if self.hasInputFromPort('usevlines'):
+ val = self.getInputFromPort('usevlines')
+ kwargs['usevlines'] = val
+ if self.hasInputFromPort('detrend'):
+ val = self.getInputFromPort('detrend')
+ kwargs['detrend'] = val
+ if self.hasInputFromPort('maxlags'):
+ val = self.getInputFromPort('maxlags')
+ kwargs['maxlags'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+
+ output = matplotlib.pyplot.acorr(*args, **kwargs)
+ if 'usevlines' in kwargs and kwargs['usevlines']:
+ output = output + (output[2],)
+ else:
+ output = output + (None, None)
+ lines = output[2]
+ xaxis = output[3]
+ lineCollection = output[4]
+ if self.hasInputFromPort('lineCollectionProperties'):
+ properties = self.getInputFromPort('lineCollectionProperties')
+ if lineCollection is not None:
+ properties.update_props(lineCollection)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if lines is not None:
+ properties.update_props(lines)
+ if self.hasInputFromPort('xaxisProperties'):
+ properties = self.getInputFromPort('xaxisProperties')
+ if xaxis is not None:
+ properties.update_props(xaxis)
+
+class MplArrow(MplPlot):
+ """Add an arrow to the axes.
+
+Call signature:
+
+arrow(x, y, dx, dy, **kwargs)
+
+Draws arrow on specified axis from (x, y) to (x + dx, y + dy). Uses FancyArrow patch to construct the arrow.
+
+Optional kwargs control the arrow construction and properties:
+
+%(FancyArrow)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("y", "basic:Float",
+ {}),
+ ("x", "basic:Float",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("dx", "basic:Float",
+ {}),
+ ("dy", "basic:Float",
+ {}),
+ ("arrowProperties", "MplFancyArrowProperties",
+ {'optional': True}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplArrow)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ val = self.getInputFromPort('dx')
+ kwargs['dx'] = val
+ val = self.getInputFromPort('dy')
+ kwargs['dy'] = val
+ if self.hasInputFromPort('arrowProperties'):
+ properties = self.getInputFromPort('arrowProperties')
+ properties.update_kwargs(kwargs)
+
+ matplotlib.pyplot.arrow(*args, **kwargs)
+
+class MplAxhline(MplPlot):
+ """Add a horizontal line across the axis.
+
+Call signature:
+
+axhline(y=0, xmin=0, xmax=1, **kwargs)
+
+Draw a horizontal line at y from xmin to xmax. With the default values of xmin = 0 and xmax = 1, this line will always span the horizontal extent of the axes, regardless of the xlim settings, even if you change them, eg. with the :meth:`set_xlim` command. That is, the horizontal extent is in axes coords: 0=left, 0.5=middle, 1.0=right but the y location is in data coordinates.
+
+Return value is the :class:`~matplotlib.lines.Line2D` instance. kwargs are the same as kwargs to plot, and can be used to control the line properties. Eg.,
+
+draw a thick red hline at y = 0 that spans the xrange:
+
+>>> axhline(linewidth=4, color='r')
+
+draw a default hline at y = 1 that spans the xrange:
+
+>>> axhline(y=1)
+
+draw a default hline at y = .5 that spans the the middle half of the xrange:
+
+>>> axhline(y=.5, xmin=0.25, xmax=0.75)
+
+Valid kwargs are :class:`~matplotlib.lines.Line2D` properties, with the exception of 'transform':
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("y", "basic:Float",
+ {'optional': True, 'defaults': "['0']"}),
+ ("xmin", "basic:Float",
+ {'optional': True, 'defaults': "['0']"}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("xmax", "basic:Float",
+ {'optional': True, 'defaults': "['1']"}),
+ ("lineProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplAxhline)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('y'):
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ if self.hasInputFromPort('xmin'):
+ val = self.getInputFromPort('xmin')
+ kwargs['xmin'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('xmax'):
+ val = self.getInputFromPort('xmax')
+ kwargs['xmax'] = val
+
+ line = matplotlib.pyplot.axhline(*args, **kwargs)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if line is not None:
+ properties.update_props(line)
+
+class MplAxhspan(MplPlot):
+ """Add a horizontal span (rectangle) across the axis.
+
+Call signature:
+
+axhspan(ymin, ymax, xmin=0, xmax=1, **kwargs)
+
+y coords are in data units and x coords are in axes (relative 0-1) units.
+
+Draw a horizontal span (rectangle) from ymin to ymax. With the default values of xmin = 0 and xmax = 1, this always spans the xrange, regardless of the xlim settings, even if you change them, eg. with the :meth:`set_xlim` command. That is, the horizontal extent is in axes coords: 0=left, 0.5=middle, 1.0=right but the y location is in data coordinates.
+
+Return value is a :class:`matplotlib.patches.Polygon` instance.
+
+Examples:
+
+draw a gray rectangle from y = 0.25-0.75 that spans the horizontal extent of the axes:
+
+>>> axhspan(0.25, 0.75, facecolor='0.5', alpha=0.5)
+
+Valid kwargs are :class:`~matplotlib.patches.Polygon` properties:
+
+%(Polygon)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("xmin", "basic:Float",
+ {'optional': True, 'defaults': "['0']"}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("ymin", "basic:Float",
+ {}),
+ ("ymax", "basic:Float",
+ {}),
+ ("xmax", "basic:Float",
+ {'optional': True, 'defaults': "['1']"}),
+ ("patchProperties", "MplPolygonProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplAxhspan)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('xmin'):
+ val = self.getInputFromPort('xmin')
+ kwargs['xmin'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ val = self.getInputFromPort('ymin')
+ kwargs['ymin'] = val
+ val = self.getInputFromPort('ymax')
+ kwargs['ymax'] = val
+ if self.hasInputFromPort('xmax'):
+ val = self.getInputFromPort('xmax')
+ kwargs['xmax'] = val
+
+ patch = matplotlib.pyplot.axhspan(*args, **kwargs)
+ if self.hasInputFromPort('patchProperties'):
+ properties = self.getInputFromPort('patchProperties')
+ if patch is not None:
+ properties.update_props(patch)
+
+class MplAxvline(MplPlot):
+ """Add a vertical line across the axes.
+
+Call signature:
+
+axvline(x=0, ymin=0, ymax=1, **kwargs)
+
+Draw a vertical line at x from ymin to ymax. With the default values of ymin = 0 and ymax = 1, this line will always span the vertical extent of the axes, regardless of the ylim settings, even if you change them, eg. with the :meth:`set_ylim` command. That is, the vertical extent is in axes coords: 0=bottom, 0.5=middle, 1.0=top but the x location is in data coordinates.
+
+Return value is the :class:`~matplotlib.lines.Line2D` instance. kwargs are the same as kwargs to plot, and can be used to control the line properties. Eg.,
+
+draw a thick red vline at x = 0 that spans the yrange:
+
+>>> axvline(linewidth=4, color='r')
+
+draw a default vline at x = 1 that spans the yrange:
+
+>>> axvline(x=1)
+
+draw a default vline at x = .5 that spans the the middle half of the yrange:
+
+>>> axvline(x=.5, ymin=0.25, ymax=0.75)
+
+Valid kwargs are :class:`~matplotlib.lines.Line2D` properties, with the exception of 'transform':
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("x", "basic:Float",
+ {'optional': True, 'defaults': "['0']"}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("ymin", "basic:Float",
+ {'optional': True, 'defaults': "['0']"}),
+ ("ymax", "basic:Float",
+ {'optional': True, 'defaults': "['1']"}),
+ ("lineProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplAxvline)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('x'):
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('ymin'):
+ val = self.getInputFromPort('ymin')
+ kwargs['ymin'] = val
+ if self.hasInputFromPort('ymax'):
+ val = self.getInputFromPort('ymax')
+ kwargs['ymax'] = val
+
+ line = matplotlib.pyplot.axvline(*args, **kwargs)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if line is not None:
+ properties.update_props(line)
+
+class MplAxvspan(MplPlot):
+ """Add a vertical span (rectangle) across the axes.
+
+Call signature:
+
+axvspan(xmin, xmax, ymin=0, ymax=1, **kwargs)
+
+x coords are in data units and y coords are in axes (relative 0-1) units.
+
+Draw a vertical span (rectangle) from xmin to xmax. With the default values of ymin = 0 and ymax = 1, this always spans the yrange, regardless of the ylim settings, even if you change them, eg. with the :meth:`set_ylim` command. That is, the vertical extent is in axes coords: 0=bottom, 0.5=middle, 1.0=top but the y location is in data coordinates.
+
+Return value is the :class:`matplotlib.patches.Polygon` instance.
+
+Examples:
+
+draw a vertical green translucent rectangle from x=1.25 to 1.55 that spans the yrange of the axes:
+
+>>> axvspan(1.25, 1.55, facecolor='g', alpha=0.5)
+
+Valid kwargs are :class:`~matplotlib.patches.Polygon` properties:
+
+%(Polygon)s
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("xmin", "basic:Float",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("ymin", "basic:Float",
+ {'optional': True, 'defaults': "['0']"}),
+ ("ymax", "basic:Float",
+ {'optional': True, 'defaults': "['1']"}),
+ ("xmax", "basic:Float",
+ {}),
+ ("patchProperties", "MplPolygonProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplAxvspan)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ val = self.getInputFromPort('xmin')
+ kwargs['xmin'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('ymin'):
+ val = self.getInputFromPort('ymin')
+ kwargs['ymin'] = val
+ if self.hasInputFromPort('ymax'):
+ val = self.getInputFromPort('ymax')
+ kwargs['ymax'] = val
+ val = self.getInputFromPort('xmax')
+ kwargs['xmax'] = val
+
+ patch = matplotlib.pyplot.axvspan(*args, **kwargs)
+ if self.hasInputFromPort('patchProperties'):
+ properties = self.getInputFromPort('patchProperties')
+ if patch is not None:
+ properties.update_props(patch)
+
+class MplBar(MplPlot):
+ """Make a bar plot.
+
+Call signature:
+
+bar(left, height, width=0.8, bottom=0, **kwargs)
+
+Make a bar plot with rectangles bounded by:
+
+
+
+left, height, width, and bottom can be either scalars or sequences
+
+Return value is a list of :class:`matplotlib.patches.Rectangle` instances.
+
+Required arguments:
+
+
+
+Optional keyword arguments:
+
+
+
+For vertical bars, align = 'edge' aligns bars by their left edges in left, while align = 'center' interprets these values as the x coordinates of the bar centers. For horizontal bars, align = 'edge' aligns bars by their bottom edges in bottom, while align = 'center' interprets these values as the y coordinates of the bar centers.
+
+The optional arguments color, edgecolor, linewidth, xerr, and yerr can be either scalars or sequences of length equal to the number of bars. This enables you to use bar as the basis for stacked bar charts, or candlestick plots. Detail: xerr and yerr are passed directly to :meth:`errorbar`, so they can also have shape 2xN for independent specification of lower and upper errors.
+
+Other optional kwargs:
+
+%(Rectangle)s
+
+Example: A stacked bar chart.
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("edgecolor", "basic:Color",
+ {'optional': True, 'docstring': 'the colors of the bar edges'}),
+ ("linewidth", "basic:String",
+ {'optional': True, 'docstring': "width of bar edges; None means use default linewidth; 0 means don't draw edges."}),
+ ("capsize", "basic:Integer",
+ {'optional': True, 'docstring': '(default 3) determines the length in points of the error bar caps', 'defaults': "['3']"}),
+ ("orientation", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "'vertical' | 'horizontal'", 'values': "[['vertical', 'horizontal']]", 'optional': True}),
+ ("bottom", "basic:Float",
+ {'optional': True, 'docstring': 'the y coordinates of the bottom edges of the bars', 'defaults': "['0']"}),
+ ("bottomSequence", "basic:List",
+ {'docstring': 'the y coordinates of the bottom edges of the bars', 'optional': True}),
+ ("color", "basic:Color",
+ {'optional': True, 'docstring': 'the colors of the bars'}),
+ ("xerr", "basic:String",
+ {'optional': True, 'docstring': 'if not None, will be used to generate errorbars on the bar chart'}),
+ ("align", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "'edge' (default) | 'center'", 'values': "[['edge', 'center']]", 'optional': True, 'defaults': "['edge']"}),
+ ("ecolor", "basic:Color",
+ {'optional': True, 'docstring': 'specifies the color of any errorbar'}),
+ ("height", "basic:List",
+ {'docstring': 'the heights of the bars'}),
+ ("heightScalar", "basic:Float",
+ {'docstring': 'the heights of the bars', 'optional': True}),
+ ("width", "basic:Float",
+ {'optional': True, 'docstring': 'the widths of the bars', 'defaults': "['0.8']"}),
+ ("widthSequence", "basic:List",
+ {'docstring': 'the widths of the bars', 'optional': True}),
+ ("error_kw", "basic:String",
+ {'optional': True, 'docstring': 'dictionary of kwargs to be passed to errorbar method. ecolor and capsize may be specified here rather than as independent kwargs.'}),
+ ("log", "basic:Boolean",
+ {'optional': True, 'docstring': '[False|True] False (default) leaves the orientation axis as-is; True sets it to log scale', 'defaults': "['False']"}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("yerr", "basic:String",
+ {'optional': True, 'docstring': 'if not None, will be used to generate errorbars on the bar chart'}),
+ ("left", "basic:List",
+ {'optional': True, 'docstring': 'the x coordinates of the left sides of the bars'}),
+ ("leftScalar", "basic:Float",
+ {'optional': True, 'docstring': 'the x coordinate of the left side of the bar'}),
+ ("rectangleProperties", "MplRectangleProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplBar)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('edgecolor'):
+ val = self.getInputFromPort('edgecolor')
+ val = translate_color(val)
+ kwargs['edgecolor'] = val
+ if self.hasInputFromPort('linewidth'):
+ val = self.getInputFromPort('linewidth')
+ kwargs['linewidth'] = val
+ if self.hasInputFromPort('capsize'):
+ val = self.getInputFromPort('capsize')
+ kwargs['capsize'] = val
+ if self.hasInputFromPort('orientation'):
+ val = self.getInputFromPort('orientation')
+ kwargs['orientation'] = val
+ if self.hasInputFromPort('bottom'):
+ val = self.getInputFromPort('bottom')
+ kwargs['bottom'] = val
+ elif self.hasInputFromPort('bottomSequence'):
+ val = self.getInputFromPort('bottomSequence')
+ kwargs['bottom'] = val
+ if self.hasInputFromPort('color'):
+ val = self.getInputFromPort('color')
+ val = translate_color(val)
+ kwargs['color'] = val
+ if self.hasInputFromPort('xerr'):
+ val = self.getInputFromPort('xerr')
+ kwargs['xerr'] = val
+ if self.hasInputFromPort('align'):
+ val = self.getInputFromPort('align')
+ kwargs['align'] = val
+ if self.hasInputFromPort('ecolor'):
+ val = self.getInputFromPort('ecolor')
+ val = translate_color(val)
+ kwargs['ecolor'] = val
+ if self.hasInputFromPort('height'):
+ val = self.getInputFromPort('height')
+ kwargs['height'] = val
+ elif self.hasInputFromPort('heightScalar'):
+ val = self.getInputFromPort('heightScalar')
+ kwargs['height'] = val
+ else:
+ raise ModuleError(self, 'Must set one of "height", ' '"heightScalar"')
+ if self.hasInputFromPort('width'):
+ val = self.getInputFromPort('width')
+ kwargs['width'] = val
+ elif self.hasInputFromPort('widthSequence'):
+ val = self.getInputFromPort('widthSequence')
+ kwargs['width'] = val
+ if self.hasInputFromPort('error_kw'):
+ val = self.getInputFromPort('error_kw')
+ kwargs['error_kw'] = val
+ if self.hasInputFromPort('log'):
+ val = self.getInputFromPort('log')
+ kwargs['log'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('yerr'):
+ val = self.getInputFromPort('yerr')
+ kwargs['yerr'] = val
+ if self.hasInputFromPort('left'):
+ val = self.getInputFromPort('left')
+ kwargs['left'] = val
+ elif self.hasInputFromPort('leftScalar'):
+ val = self.getInputFromPort('leftScalar')
+ kwargs['left'] = val
+
+ if not kwargs.has_key('left'):
+ kwargs['left'] = range(len(kwargs['height']))
+ rectangles = matplotlib.pyplot.bar(*args, **kwargs)
+ if self.hasInputFromPort('rectangleProperties'):
+ properties = self.getInputFromPort('rectangleProperties')
+ if rectangles is not None:
+ properties.update_props(rectangles)
+
+class MplBarh(MplPlot):
+ """Make a horizontal bar plot.
+
+Call signature:
+
+barh(bottom, width, height=0.8, left=0, **kwargs)
+
+Make a horizontal bar plot with rectangles bounded by:
+
+
+
+bottom, width, height, and left can be either scalars or sequences
+
+Return value is a list of :class:`matplotlib.patches.Rectangle` instances.
+
+Required arguments:
+
+
+
+Optional keyword arguments:
+
+
+
+Setting align = 'edge' aligns bars by their bottom edges in bottom, while align = 'center' interprets these values as the y coordinates of the bar centers.
+
+The optional arguments color, edgecolor, linewidth, xerr, and yerr can be either scalars or sequences of length equal to the number of bars. This enables you to use barh as the basis for stacked bar charts, or candlestick plots.
+
+other optional kwargs:
+
+%(Rectangle)s
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("edgecolor", "basic:Color",
+ {'optional': True, 'docstring': 'the colors of the bar edges'}),
+ ("linewidth", "basic:String",
+ {'optional': True, 'docstring': "width of bar edges; None means use default linewidth; 0 means don't draw edges."}),
+ ("capsize", "basic:Integer",
+ {'optional': True, 'docstring': '(default 3) determines the length in points of the error bar caps', 'defaults': "['3']"}),
+ ("log", "basic:Boolean",
+ {'optional': True, 'docstring': '[False|True] False (default) leaves the horizontal axis as-is; True sets it to log scale', 'defaults': "['False']"}),
+ ("bottom", "basic:List",
+ {'docstring': 'the vertical positions of the bottom edges of the bars'}),
+ ("bottomScalar", "basic:Float",
+ {'docstring': 'the vertical positions of the bottom edges of the bars', 'optional': True}),
+ ("color", "basic:Color",
+ {'optional': True, 'docstring': 'the colors of the bars'}),
+ ("xerr", "basic:String",
+ {'optional': True, 'docstring': 'if not None, will be used to generate errorbars on the bar chart'}),
+ ("align", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "'edge' (default) | 'center'", 'values': "[['edge', 'center']]", 'optional': True, 'defaults': "['edge']"}),
+ ("ecolor", "basic:Color",
+ {'optional': True, 'docstring': 'specifies the color of any errorbar'}),
+ ("height", "basic:Float",
+ {'optional': True, 'docstring': 'the heights (thicknesses) of the bars', 'defaults': "['0.8']"}),
+ ("heightSequence", "basic:List",
+ {'docstring': 'the heights (thicknesses) of the bars', 'optional': True}),
+ ("width", "basic:List",
+ {'docstring': 'the lengths of the bars'}),
+ ("widthScalar", "basic:Float",
+ {'docstring': 'the lengths of the bars', 'optional': True}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("yerr", "basic:String",
+ {'optional': True, 'docstring': 'if not None, will be used to generate errorbars on the bar chart'}),
+ ("left", "basic:Float",
+ {'optional': True, 'docstring': 'the x coordinates of the left edges of the bars', 'defaults': "['0']"}),
+ ("leftSequence", "basic:List",
+ {'docstring': 'the x coordinates of the left edges of the bars', 'optional': True}),
+ ("rectangleProperties", "MplRectangleProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplBarh)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('edgecolor'):
+ val = self.getInputFromPort('edgecolor')
+ val = translate_color(val)
+ kwargs['edgecolor'] = val
+ if self.hasInputFromPort('linewidth'):
+ val = self.getInputFromPort('linewidth')
+ kwargs['linewidth'] = val
+ if self.hasInputFromPort('capsize'):
+ val = self.getInputFromPort('capsize')
+ kwargs['capsize'] = val
+ if self.hasInputFromPort('log'):
+ val = self.getInputFromPort('log')
+ kwargs['log'] = val
+ if self.hasInputFromPort('bottom'):
+ val = self.getInputFromPort('bottom')
+ kwargs['bottom'] = val
+ elif self.hasInputFromPort('bottomScalar'):
+ val = self.getInputFromPort('bottomScalar')
+ kwargs['bottom'] = val
+ else:
+ raise ModuleError(self, 'Must set one of "bottom", ' '"bottomScalar"')
+ if self.hasInputFromPort('color'):
+ val = self.getInputFromPort('color')
+ val = translate_color(val)
+ kwargs['color'] = val
+ if self.hasInputFromPort('xerr'):
+ val = self.getInputFromPort('xerr')
+ kwargs['xerr'] = val
+ if self.hasInputFromPort('align'):
+ val = self.getInputFromPort('align')
+ kwargs['align'] = val
+ if self.hasInputFromPort('ecolor'):
+ val = self.getInputFromPort('ecolor')
+ val = translate_color(val)
+ kwargs['ecolor'] = val
+ if self.hasInputFromPort('height'):
+ val = self.getInputFromPort('height')
+ kwargs['height'] = val
+ elif self.hasInputFromPort('heightSequence'):
+ val = self.getInputFromPort('heightSequence')
+ kwargs['height'] = val
+ if self.hasInputFromPort('width'):
+ val = self.getInputFromPort('width')
+ kwargs['width'] = val
+ elif self.hasInputFromPort('widthScalar'):
+ val = self.getInputFromPort('widthScalar')
+ kwargs['width'] = val
+ else:
+ raise ModuleError(self, 'Must set one of "width", ' '"widthScalar"')
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('yerr'):
+ val = self.getInputFromPort('yerr')
+ kwargs['yerr'] = val
+ if self.hasInputFromPort('left'):
+ val = self.getInputFromPort('left')
+ kwargs['left'] = val
+ elif self.hasInputFromPort('leftSequence'):
+ val = self.getInputFromPort('leftSequence')
+ kwargs['left'] = val
+
+ rectangles = matplotlib.pyplot.barh(*args, **kwargs)
+ if self.hasInputFromPort('rectangleProperties'):
+ properties = self.getInputFromPort('rectangleProperties')
+ if rectangles is not None:
+ properties.update_props(rectangles)
+
+class MplBrokenBarh(MplPlot):
+ """Plot horizontal bars.
+
+Call signature:
+
+broken_barh(self, xranges, yrange, **kwargs)
+
+A collection of horizontal bars spanning yrange with a sequence of xranges.
+
+Required arguments:
+
+
+
+kwargs are :class:`matplotlib.collections.BrokenBarHCollection` properties:
+
+%(BrokenBarHCollection)s
+
+these can either be a single argument, ie:
+
+facecolors = 'black'
+
+or a sequence of arguments for the various bars, ie:
+
+facecolors = ('black', 'red', 'green')
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("xranges", "basic:List",
+ {'docstring': 'sequence of (xmin, xwidth)'}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("yrange", "basic:Float,basic:Float",
+ {'docstring': '(ymin, ywidth)'}),
+ ("brokenBarHCollectionProperties", "MplBrokenBarHCollectionProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplBrokenBarh)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ val = self.getInputFromPort('xranges')
+ kwargs['xranges'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ val = self.getInputFromPort('yrange')
+ kwargs['yrange'] = val
+
+ matplotlib.pyplot.broken_barh(*args, **kwargs)
+ if self.hasInputFromPort('brokenBarHCollectionProperties'):
+ properties = self.getInputFromPort('brokenBarHCollectionProperties')
+ if brokenBarHCollection is not None:
+ properties.update_props(brokenBarHCollection)
+
+class MplBoxplot(MplPlot):
+ """Make a box and whisker plot.
+
+Call signature:
+
+boxplot(x, notch=False, sym='+', vert=True, whis=1.5, positions=None, widths=None, patch_artist=False, bootstrap=None, usermedians=None, conf_intervals=None)
+
+Make a box and whisker plot for each column of x or each vector in sequence x. The box extends from the lower to upper quartile values of the data, with a line at the median. The whiskers extend from the box to show the range of the data. Flier points are those past the end of the whiskers.
+
+Function Arguments:
+
+
+
+Returns a dictionary mapping each component of the boxplot to a list of the :class:`matplotlib.lines.Line2D` instances created. That dictionary has the following keys (assuming vertical boxplots):
+
+boxes: the main body of the boxplot showing the quartiles and the median's confidence intervals if enabled.
+
+medians: horizonal lines at the median of each box.
+
+whiskers: the vertical lines extending to the most extreme, n-outlier data points.
+
+caps: the horizontal lines at the ends of the whiskers.
+
+fliers: points representing data that extend beyone the whiskers (outliers).
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("vert", "basic:Boolean",
+ {'optional': True, 'docstring': 'If True (default), makes the boxes vertical. If False, makes horizontal boxes.', 'defaults': "['True']"}),
+ ("positions", "basic:String",
+ {'optional': True, 'docstring': 'Sets the horizontal positions of the boxes. The ticks and limits are automatically set to match the positions.'}),
+ ("bootstrap", "basic:String",
+ {'optional': True, 'docstring': "Specifies whether to bootstrap the confidence intervals around the median for notched boxplots. If bootstrap==None, no bootstrapping is performed, and notches are calculated using a Gaussian-based asymptotic approximation (see McGill, R., Tukey, J.W., and Larsen, W.A., 1978, and Kendall and Stuart, 1967). Otherwise, bootstrap specifies the number of times to bootstrap the median to determine it's 95% confidence intervals. Values between 10 [...]
+ ("usermedians", "basic:List",
+ {'optional': True, 'docstring': 'An array or sequence whose first dimension (or length) is compatible with x. This overrides the medians computed by matplotlib for each element of usermedians that is not None. When an element of usermedians == None, the median will be computed directly as normal.'}),
+ ("sym", "basic:String",
+ {'optional': True, 'docstring': "The default symbol for flier points. Enter an empty string ('') if you don't want to show fliers.", 'defaults': "['b+']"}),
+ ("widths", "basic:Float",
+ {'optional': True, 'docstring': 'Either a scalar or a vector and sets the width of each box. The default is 0.5, or 0.15*(distance between extreme positions) if that is smaller.', 'defaults': "['0.5']"}),
+ ("patch_artist", "basic:Boolean",
+ {'optional': True, 'docstring': 'If False produces boxes with the Line2D artist If True produces boxes with the Patch artist', 'defaults': "['False']"}),
+ ("x", "basic:List",
+ {'docstring': 'Array or a sequence of vectors.'}),
+ ("notch", "basic:Boolean",
+ {'optional': True, 'docstring': 'If False (default), produces a rectangular box plot. If True, will produce a notched box plot', 'defaults': "['False']"}),
+ ("whis", "basic:Float",
+ {'optional': True, 'docstring': 'Defines the length of the whiskers as a function of the inner quartile range. They extend to the most extreme data point within ( whis*(75%-25%) ) data range.', 'defaults': "['1.5']"}),
+ ("conf_intervals", "basic:List",
+ {'optional': True, 'docstring': 'Array or sequence whose first dimension (or length) is compatible with x and whose second dimension is 2. When the current element of conf_intervals is not None, the notch locations computed by matplotlib are overridden (assuming notch is True). When an element of conf_intervals is None, boxplot compute notches the method specified by the other kwargs (e.g. bootstrap).'}),
+ ("boxProperties", "MplLine2DProperties",
+ {}),
+ ("flierProperties", "MplLine2DProperties",
+ {}),
+ ("capProperties", "MplLine2DProperties",
+ {}),
+ ("medianProperties", "MplLine2DProperties",
+ {}),
+ ("boxPatchProperties", "MplPathPatchProperties",
+ {}),
+ ("whiskerProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplBoxplot)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('vert'):
+ val = self.getInputFromPort('vert')
+ kwargs['vert'] = val
+ if self.hasInputFromPort('positions'):
+ val = self.getInputFromPort('positions')
+ kwargs['positions'] = val
+ if self.hasInputFromPort('bootstrap'):
+ val = self.getInputFromPort('bootstrap')
+ kwargs['bootstrap'] = val
+ if self.hasInputFromPort('usermedians'):
+ val = self.getInputFromPort('usermedians')
+ kwargs['usermedians'] = val
+ if self.hasInputFromPort('sym'):
+ val = self.getInputFromPort('sym')
+ kwargs['sym'] = val
+ if self.hasInputFromPort('widths'):
+ val = self.getInputFromPort('widths')
+ kwargs['widths'] = val
+ if self.hasInputFromPort('patch_artist'):
+ val = self.getInputFromPort('patch_artist')
+ kwargs['patch_artist'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('notch'):
+ val = self.getInputFromPort('notch')
+ kwargs['notch'] = val
+ if self.hasInputFromPort('whis'):
+ val = self.getInputFromPort('whis')
+ kwargs['whis'] = val
+ if self.hasInputFromPort('conf_intervals'):
+ val = self.getInputFromPort('conf_intervals')
+ kwargs['conf_intervals'] = val
+
+ output = matplotlib.pyplot.boxplot(*args, **kwargs)
+ if 'patch_artist' in kwargs and kwargs['patch_artist']:
+ output['boxPatches'] = output['boxes']
+ output['boxes'] = []
+ else:
+ output['boxPatches'] = []
+ boxes = output['boxes']
+ fliers = output['fliers']
+ caps = output['caps']
+ medians = output['medians']
+ boxPatches = output['boxPatches']
+ whiskers = output['whiskers']
+ if self.hasInputFromPort('boxProperties'):
+ properties = self.getInputFromPort('boxProperties')
+ if boxes is not None:
+ properties.update_props(boxes)
+ if self.hasInputFromPort('flierProperties'):
+ properties = self.getInputFromPort('flierProperties')
+ if fliers is not None:
+ properties.update_props(fliers)
+ if self.hasInputFromPort('capProperties'):
+ properties = self.getInputFromPort('capProperties')
+ if caps is not None:
+ properties.update_props(caps)
+ if self.hasInputFromPort('medianProperties'):
+ properties = self.getInputFromPort('medianProperties')
+ if medians is not None:
+ properties.update_props(medians)
+ if self.hasInputFromPort('boxPatchProperties'):
+ properties = self.getInputFromPort('boxPatchProperties')
+ if boxPatches is not None:
+ properties.update_props(boxPatches)
+ if self.hasInputFromPort('whiskerProperties'):
+ properties = self.getInputFromPort('whiskerProperties')
+ if whiskers is not None:
+ properties.update_props(whiskers)
+
+class MplCohere(MplPlot):
+ """Plot the coherence between x and y.
+
+Call signature:
+
+cohere(x, y, NFFT=256, Fs=2, Fc=0, detrend = mlab.detrend_none, window = mlab.window_hanning, noverlap=0, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+Plot the coherence between x and y. Coherence is the normalized cross spectral density:
+
+C_{xy} = \frac{|P_{xy}|^2}{P_{xx}P_{yy}}
+
+%(PSD)s
+
+
+
+The return value is a tuple (Cxy, f), where f are the frequencies of the coherence vector.
+
+kwargs are applied to the lines.
+
+References:
+
+Bendat & Piersol -- Random Data: Analysis and Measurement Procedures, John Wiley & Sons (1986)
+
+kwargs control the :class:`~matplotlib.lines.Line2D` properties of the coherence plot:
+
+%(Line2D)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("Fs", "basic:Integer",
+ {'optional': True, 'defaults': "['2']"}),
+ ("pad_to", "basic:String",
+ {'optional': True}),
+ ("scale_by_freq", "basic:String",
+ {'optional': True}),
+ ("detrend", "basic:String",
+ {'optional': True, 'defaults': "['<function detrend_none at 0x02F5A3F0>']"}),
+ ("window", "basic:String",
+ {'optional': True, 'defaults': "['<function window_hanning at 0x02F5A2B0>']"}),
+ ("Fc", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("NFFT", "basic:Integer",
+ {'optional': True, 'defaults': "['256']"}),
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("sides", "basic:String",
+ {'optional': True, 'defaults': "['default']"}),
+ ("noverlap", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("lineProperties", "MplLine2DProperties",
+ {'optional': True}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplCohere)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('Fs'):
+ val = self.getInputFromPort('Fs')
+ kwargs['Fs'] = val
+ if self.hasInputFromPort('pad_to'):
+ val = self.getInputFromPort('pad_to')
+ kwargs['pad_to'] = val
+ if self.hasInputFromPort('scale_by_freq'):
+ val = self.getInputFromPort('scale_by_freq')
+ kwargs['scale_by_freq'] = val
+ if self.hasInputFromPort('detrend'):
+ val = self.getInputFromPort('detrend')
+ kwargs['detrend'] = val
+ if self.hasInputFromPort('window'):
+ val = self.getInputFromPort('window')
+ kwargs['window'] = val
+ if self.hasInputFromPort('Fc'):
+ val = self.getInputFromPort('Fc')
+ kwargs['Fc'] = val
+ if self.hasInputFromPort('NFFT'):
+ val = self.getInputFromPort('NFFT')
+ kwargs['NFFT'] = val
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('sides'):
+ val = self.getInputFromPort('sides')
+ kwargs['sides'] = val
+ if self.hasInputFromPort('noverlap'):
+ val = self.getInputFromPort('noverlap')
+ kwargs['noverlap'] = val
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ properties.update_kwargs(kwargs)
+
+ matplotlib.pyplot.cohere(*args, **kwargs)
+
+class MplClabel(MplPlot):
+ """Label a contour plot.
+
+Call signature:
+
+clabel(cs, **kwargs)
+
+Adds labels to line contours in cs, where cs is a :class:`~matplotlib.contour.ContourSet` object returned by contour.
+
+clabel(cs, v, **kwargs)
+
+only labels contours listed in v.
+
+Optional keyword arguments:
+
+
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("inline_spacing", "basic:String",
+ {'optional': True, 'docstring': 'space in pixels to leave on each side of label when placing inline. Defaults to 5. This spacing will be exact for labels at locations where the contour is straight, less so for labels on curved contours.'}),
+ ("use_clabeltext", "basic:String",
+ {'optional': True, 'docstring': 'if True (default is False), ClabelText class (instead of matplotlib.Text) is used to create labels. ClabelText recalculates rotation angles of texts during the drawing time, therefore this can be used if aspect of the axes changes.', 'defaults': "['False)']"}),
+ ("fmt", "basic:String",
+ {'optional': True, 'docstring': "a format string for the label. Default is '%1.3f' Alternatively, this can be a dictionary matching contour levels with arbitrary strings to use for each contour level (i.e., fmt[level]=string), or it can be any callable, such as a :class:`~matplotlib.ticker.Formatter` instance, that returns a string when called with a numeric contour level.", 'defaults': "['%1.3f']"}),
+ ("manual", "basic:String",
+ {'optional': True, 'docstring': 'if True, contour labels will be placed manually using mouse clicks. Click the first button near a contour to add a label, click the second button (or potentially both mouse buttons at once) to finish adding labels. The third button can be used to remove the last label added, but only if labels are not inline. Alternatively, the keyboard can be used to select label locations (enter to end label placement, delete or backspace act like the [...]
+ ("cs", "MplContourSet",
+ {}),
+ ("colors", "basic:Color",
+ {'optional': True, 'docstring': "if None, the color of each label matches the color of the corresponding contour\n\nif one string color, e.g. colors = 'r' or colors = 'red', all labels will be plotted in this color\n\nif a tuple of matplotlib color args (string, float, rgb, etc), different labels will be plotted in different colors in the order specified"}),
+ ("fontsize", "basic:String",
+ {'optional': True, 'docstring': "size in points or relative size eg 'smaller', 'x-large'"}),
+ ("rightside_up", "basic:Boolean",
+ {'optional': True, 'docstring': 'if True (default), label rotations will always be plus or minus 90 degrees from level.', 'defaults': "['True']"}),
+ ("inline", "basic:Boolean",
+ {'optional': True, 'docstring': 'controls whether the underlying contour is removed or not. Default is True.', 'defaults': "['True']"}),
+ ("v", "basic:List",
+ {'optional': True}),
+ ("textProperties", "MplTextProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplClabel)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ val = self.getInputFromPort('cs')
+ args.append(val)
+ if self.hasInputFromPort('v'):
+ val = self.getInputFromPort('v')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('inline_spacing'):
+ val = self.getInputFromPort('inline_spacing')
+ kwargs['inline_spacing'] = val
+ if self.hasInputFromPort('use_clabeltext'):
+ val = self.getInputFromPort('use_clabeltext')
+ kwargs['use_clabeltext'] = val
+ if self.hasInputFromPort('fmt'):
+ val = self.getInputFromPort('fmt')
+ kwargs['fmt'] = val
+ if self.hasInputFromPort('manual'):
+ val = self.getInputFromPort('manual')
+ kwargs['manual'] = val
+ if self.hasInputFromPort('colors'):
+ val = self.getInputFromPort('colors')
+ val = translate_color(val)
+ kwargs['colors'] = val
+ if self.hasInputFromPort('fontsize'):
+ val = self.getInputFromPort('fontsize')
+ kwargs['fontsize'] = val
+ if self.hasInputFromPort('rightside_up'):
+ val = self.getInputFromPort('rightside_up')
+ kwargs['rightside_up'] = val
+ if self.hasInputFromPort('inline'):
+ val = self.getInputFromPort('inline')
+ kwargs['inline'] = val
+
+ texts = matplotlib.pyplot.clabel(*args, **kwargs)
+ if self.hasInputFromPort('textProperties'):
+ properties = self.getInputFromPort('textProperties')
+ if texts is not None:
+ properties.update_props(texts)
+
+class MplContour(MplPlot):
+ """Plot contours.
+
+:func:`~matplotlib.pyplot.contour` and :func:`~matplotlib.pyplot.contourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+:func:`~matplotlib.pyplot.contourf` differs from the MATLAB version in that it does not draw the polygon edges. To draw edges, add line contours with calls to :func:`~matplotlib.pyplot.contour`.
+
+Call signatures:
+
+contour(Z)
+
+make a contour plot of an array Z. The level values are chosen automatically.
+
+contour(X,Y,Z)
+
+X, Y specify the (x, y) coordinates of the surface
+
+contour(Z,N) contour(X,Y,Z,N)
+
+contour N automatically-chosen levels.
+
+contour(Z,V) contour(X,Y,Z,V)
+
+draw contour lines at the values specified in sequence V
+
+contourf(..., V)
+
+fill the len(V)-1 regions between the values in V
+
+contour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+X and Y must both be 2-D with the same shape as Z, or they must both be 1-D such that len(X) is the number of columns in Z and len(Y) is the number of rows in Z.
+
+C = contour(...) returns a :class:`~matplotlib.contour.QuadContourSet` object.
+
+Optional keyword arguments:
+
+
+
+contour-only keyword arguments:
+
+
+
+contourf-only keyword arguments:
+
+
+
+Note: contourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("origin", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.\n\nThis keyword is not active if X and Y are specified in the call to contour.", 'values': "[['', 'upper', 'lower', 'image']]", 'optional': True}),
+ ("xunits", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Override axis units by specifying an instance of a :class:`matplotlib.units.ConversionInterface`.', 'values': "[['', 'registered units']]", 'optional': True}),
+ ("extend", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "Unless this is 'neither', contour levels are automatically added to one or both ends of the range so that all data are included. These added ranges are then mapped to the special colormap values which default to the ends of the colormap range, but can be set via :meth:`matplotlib.colors.Colormap.set_under` and :meth:`matplotlib.colors.Colormap.set_over` methods.", 'values': "[['neither', 'both', 'min', 'max']]", 'optional': True}),
+ ("vmin", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.', 'values': "[['']]", 'optional': True}),
+ ("nchunk", "basic:Integer",
+ {'entry_types': "['enum']", 'docstring': 'If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.', 'values': '[[0]]', 'optional': True}),
+ ("linestyles", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If linestyles is None, the default is 'solid' unless the lines are monochrome. In that case, negative contours will take their linestyle from the matplotlibrc contour.negative_linestyle setting.\n\nlinestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.", 'values': "[['', 'solid', 'dashed', 'da [...]
+ ("hatches", "basic:List",
+ {'optional': True, 'docstring': 'A list of cross hatch patterns to use on the filled areas. If None, no hatching will be added to the contour. Hatching is supported in the PostScript, PDF, SVG and Agg backends only.'}),
+ ("levelsSequence", "basic:List",
+ {'optional': True, 'docstring': 'A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]'}),
+ ("levelsScalar", "basic:Float",
+ {'docstring': 'A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]', 'optional': True}),
+ ("linewidths", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.\n\nIf a number, all levels will be plotted with this linewidth.\n\nIf a tuple, different levels will be plotted with different linewidths in the order specified', 'values': "[['', 'number', 'tuple of numbers']]", 'optional': True}),
+ ("locator", "basic:String",
+ {'optional': True, 'docstring': 'If locator is None, the default :class:`~matplotlib.ticker.MaxNLocator` is used. The locator is used to determine the contour levels if they are not given explicitly via the V argument.'}),
+ ("colors", "basic:Color",
+ {'optional': True, 'docstring': "If None, the colormap specified by cmap will be used.\n\nIf a string, like 'r' or 'red', all levels will be plotted in this color.\n\nIf a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified."}),
+ ("cmap", "basic:String",
+ {'optional': True, 'docstring': 'A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.'}),
+ ("yunits", "basic:String",
+ {'optional': True, 'docstring': 'Override axis units by specifying an instance of a :class:`matplotlib.units.ConversionInterface`.'}),
+ ("extent", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].\n\nThis keyword is not active if X and Y are specified in the call to contour.', 'values': "[['', '(x0,x1,y0,y1)']]", 'optional [...]
+ ("vmax", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.', 'values': "[['']]", 'optional': True}),
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'The alpha blending value'}),
+ ("Z", "basic:List",
+ {}),
+ ("antialiased", "basic:Boolean",
+ {'optional': True, 'docstring': "enable antialiasing, overriding the defaults. For filled contours, the default is True. For line contours, it is taken from rcParams['lines.antialiased'].", 'defaults': "['True']"}),
+ ("norm", "basic:String",
+ {'optional': True, 'docstring': 'A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.'}),
+ ("X", "basic:List",
+ {'optional': True}),
+ ("V", "basic:List",
+ {'optional': True}),
+ ("Y", "basic:List",
+ {'optional': True}),
+ ("N", "basic:Integer",
+ {'optional': True}),
+ ("lineCollectionProperties", "MplLineCollectionProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplContour)"),
+ ("contourSet", "MplQuadContourSet",
+ {}),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ if self.hasInputFromPort('X'):
+ val = self.getInputFromPort('X')
+ args.append(val)
+ if self.hasInputFromPort('Y'):
+ val = self.getInputFromPort('Y')
+ args.append(val)
+ val = self.getInputFromPort('Z')
+ args.append(val)
+ if self.hasInputFromPort('V'):
+ val = self.getInputFromPort('V')
+ args.append(val)
+ if self.hasInputFromPort('N'):
+ val = self.getInputFromPort('N')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('origin'):
+ val = self.getInputFromPort('origin')
+ kwargs['origin'] = val
+ if self.hasInputFromPort('xunits'):
+ val = self.getInputFromPort('xunits')
+ kwargs['xunits'] = val
+ if self.hasInputFromPort('extend'):
+ val = self.getInputFromPort('extend')
+ kwargs['extend'] = val
+ if self.hasInputFromPort('vmin'):
+ val = self.getInputFromPort('vmin')
+ kwargs['vmin'] = val
+ if self.hasInputFromPort('nchunk'):
+ val = self.getInputFromPort('nchunk')
+ kwargs['nchunk'] = val
+ if self.hasInputFromPort('linestyles'):
+ val = self.getInputFromPort('linestyles')
+ kwargs['linestyles'] = val
+ if self.hasInputFromPort('hatches'):
+ val = self.getInputFromPort('hatches')
+ kwargs['hatches'] = val
+ if self.hasInputFromPort('levelsSequence'):
+ val = self.getInputFromPort('levelsSequence')
+ kwargs['levels'] = val
+ elif self.hasInputFromPort('levelsScalar'):
+ val = self.getInputFromPort('levelsScalar')
+ kwargs['levels'] = val
+ if self.hasInputFromPort('linewidths'):
+ val = self.getInputFromPort('linewidths')
+ kwargs['linewidths'] = val
+ if self.hasInputFromPort('locator'):
+ val = self.getInputFromPort('locator')
+ kwargs['locator'] = val
+ if self.hasInputFromPort('colors'):
+ val = self.getInputFromPort('colors')
+ val = translate_color(val)
+ kwargs['colors'] = val
+ if self.hasInputFromPort('cmap'):
+ val = self.getInputFromPort('cmap')
+ kwargs['cmap'] = val
+ if self.hasInputFromPort('yunits'):
+ val = self.getInputFromPort('yunits')
+ kwargs['yunits'] = val
+ if self.hasInputFromPort('extent'):
+ val = self.getInputFromPort('extent')
+ kwargs['extent'] = val
+ if self.hasInputFromPort('vmax'):
+ val = self.getInputFromPort('vmax')
+ kwargs['vmax'] = val
+ if self.hasInputFromPort('alpha'):
+ val = self.getInputFromPort('alpha')
+ kwargs['alpha'] = val
+ if self.hasInputFromPort('antialiased'):
+ val = self.getInputFromPort('antialiased')
+ kwargs['antialiased'] = val
+ if self.hasInputFromPort('norm'):
+ val = self.getInputFromPort('norm')
+ kwargs['norm'] = val
+
+ if self.hasInputFromPort("N") and self.hasInputFromPort("V"):
+ del args[-1]
+ contour_set = matplotlib.pyplot.contour(*args, **kwargs)
+ output = (contour_set, contour_set.collections)
+ contourSet = output[0]
+ lineCollections = output[1]
+ self.setResult('contourSet', contourSet)
+ if self.hasInputFromPort('lineCollectionProperties'):
+ properties = self.getInputFromPort('lineCollectionProperties')
+ if lineCollections is not None:
+ properties.update_props(lineCollections)
+
+class MplContourf(MplPlot):
+ """Plot contours.
+
+:func:`~matplotlib.pyplot.contour` and :func:`~matplotlib.pyplot.contourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+:func:`~matplotlib.pyplot.contourf` differs from the MATLAB version in that it does not draw the polygon edges. To draw edges, add line contours with calls to :func:`~matplotlib.pyplot.contour`.
+
+Call signatures:
+
+contour(Z)
+
+make a contour plot of an array Z. The level values are chosen automatically.
+
+contour(X,Y,Z)
+
+X, Y specify the (x, y) coordinates of the surface
+
+contour(Z,N) contour(X,Y,Z,N)
+
+contour N automatically-chosen levels.
+
+contour(Z,V) contour(X,Y,Z,V)
+
+draw contour lines at the values specified in sequence V
+
+contourf(..., V)
+
+fill the len(V)-1 regions between the values in V
+
+contour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+X and Y must both be 2-D with the same shape as Z, or they must both be 1-D such that len(X) is the number of columns in Z and len(Y) is the number of rows in Z.
+
+C = contour(...) returns a :class:`~matplotlib.contour.QuadContourSet` object.
+
+Optional keyword arguments:
+
+extent: [ None | (x0,x1,y0,y1) ]
+
+If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].
+
+This keyword is not active if X and Y are specified in the call to contour.
+
+contour-only keyword arguments:
+
+
+
+contourf-only keyword arguments:
+
+
+
+Note: contourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("origin", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.\n\nThis keyword is not active if X and Y are specified in the call to contour.", 'values': "[['', 'upper', 'lower', 'image']]", 'optional': True}),
+ ("linestyles", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If linestyles is None, the default is 'solid' unless the lines are monochrome. In that case, negative contours will take their linestyle from the matplotlibrc contour.negative_linestyle setting.\n\nlinestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.", 'values': "[['', 'solid', 'dashed', 'da [...]
+ ("vmin", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.', 'values': "[['']]", 'optional': True}),
+ ("nchunk", "basic:Integer",
+ {'entry_types': "['enum']", 'docstring': 'If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.', 'values': '[[0]]', 'optional': True}),
+ ("hatches", "basic:List",
+ {'optional': True, 'docstring': 'A list of cross hatch patterns to use on the filled areas. If None, no hatching will be added to the contour. Hatching is supported in the PostScript, PDF, SVG and Agg backends only.'}),
+ ("levelsSequence", "basic:List",
+ {'optional': True, 'docstring': 'A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]'}),
+ ("levelsScalar", "basic:Float",
+ {'docstring': 'A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]', 'optional': True}),
+ ("linewidths", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.\n\nIf a number, all levels will be plotted with this linewidth.\n\nIf a tuple, different levels will be plotted with different linewidths in the order specified', 'values': "[['', 'number', 'tuple of numbers']]", 'optional': True}),
+ ("colors", "basic:Color",
+ {'entry_types': "['enum']", 'docstring': "If None, the colormap specified by cmap will be used.\n\nIf a string, like 'r' or 'red', all levels will be plotted in this color.\n\nIf a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified.", 'values': "[['', '(mpl_colors)']]", 'optional': True}),
+ ("cmap", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.', 'values': "[['', 'Colormap']]", 'optional': True}),
+ ("vmax", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If not None, either or both of these values will be supplied to the :class:`matplotlib.colors.Normalize` instance, overriding the default color scaling based on levels.', 'values': "[['']]", 'optional': True}),
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'The alpha blending value'}),
+ ("Z", "basic:List",
+ {}),
+ ("norm", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.', 'values': "[['', 'Normalize']]", 'optional': True}),
+ ("N", "basic:Integer",
+ {'optional': True}),
+ ("V", "basic:List",
+ {'optional': True}),
+ ("Y", "basic:List",
+ {'optional': True}),
+ ("X", "basic:List",
+ {'optional': True}),
+ ("polyCollectionProperties", "MplPolyCollectionProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplContourf)"),
+ ("contourSet", "MplQuadContourSet",
+ {}),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ if self.hasInputFromPort('X'):
+ val = self.getInputFromPort('X')
+ args.append(val)
+ if self.hasInputFromPort('Y'):
+ val = self.getInputFromPort('Y')
+ args.append(val)
+ val = self.getInputFromPort('Z')
+ args.append(val)
+ if self.hasInputFromPort('V'):
+ val = self.getInputFromPort('V')
+ args.append(val)
+ if self.hasInputFromPort('N'):
+ val = self.getInputFromPort('N')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('origin'):
+ val = self.getInputFromPort('origin')
+ kwargs['origin'] = val
+ if self.hasInputFromPort('linestyles'):
+ val = self.getInputFromPort('linestyles')
+ kwargs['linestyles'] = val
+ if self.hasInputFromPort('vmin'):
+ val = self.getInputFromPort('vmin')
+ kwargs['vmin'] = val
+ if self.hasInputFromPort('nchunk'):
+ val = self.getInputFromPort('nchunk')
+ kwargs['nchunk'] = val
+ if self.hasInputFromPort('hatches'):
+ val = self.getInputFromPort('hatches')
+ kwargs['hatches'] = val
+ if self.hasInputFromPort('levelsSequence'):
+ val = self.getInputFromPort('levelsSequence')
+ kwargs['levels'] = val
+ elif self.hasInputFromPort('levelsScalar'):
+ val = self.getInputFromPort('levelsScalar')
+ kwargs['levels'] = val
+ if self.hasInputFromPort('linewidths'):
+ val = self.getInputFromPort('linewidths')
+ kwargs['linewidths'] = val
+ if self.hasInputFromPort('colors'):
+ val = self.getInputFromPort('colors')
+ val = translate_color(val)
+ kwargs['colors'] = val
+ if self.hasInputFromPort('cmap'):
+ val = self.getInputFromPort('cmap')
+ kwargs['cmap'] = val
+ if self.hasInputFromPort('vmax'):
+ val = self.getInputFromPort('vmax')
+ kwargs['vmax'] = val
+ if self.hasInputFromPort('alpha'):
+ val = self.getInputFromPort('alpha')
+ kwargs['alpha'] = val
+ if self.hasInputFromPort('norm'):
+ val = self.getInputFromPort('norm')
+ kwargs['norm'] = val
+
+ if self.hasInputFromPort("N") and self.hasInputFromPort("V"):
+ del args[-1]
+ contour_set = matplotlib.pyplot.contourf(*args, **kwargs)
+ output = (contour_set, contour_set.collections)
+ contourSet = output[0]
+ polyCollections = output[1]
+ self.setResult('contourSet', contourSet)
+ if self.hasInputFromPort('polyCollectionProperties'):
+ properties = self.getInputFromPort('polyCollectionProperties')
+ if polyCollections is not None:
+ properties.update_props(polyCollections)
+
+class MplCsd(MplPlot):
+ """Plot cross-spectral density.
+
+Call signature:
+
+csd(x, y, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none, window=mlab.window_hanning, noverlap=0, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+The cross spectral density P_{xy} by Welch's average periodogram method. The vectors x and y are divided into NFFT length segments. Each segment is detrended by function detrend and windowed by function window. The product of the direct FFTs of x and y are averaged over each segment to compute P_{xy}, with a scaling to correct for power loss due to windowing.
+
+Returns the tuple (Pxy, freqs). P is the cross spectrum (complex valued), and 10\log_{10}|P_{xy}| is plotted.
+
+%(PSD)s
+
+
+
+kwargs control the Line2D properties:
+
+%(Line2D)s
+
+Example:
+
+seealso: :meth:`psd` For a description of the optional parameters.
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("Fs", "basic:Integer",
+ {'optional': True, 'defaults': "['2']"}),
+ ("pad_to", "basic:String",
+ {'optional': True}),
+ ("scale_by_freq", "basic:String",
+ {'optional': True}),
+ ("detrend", "basic:String",
+ {'optional': True, 'defaults': "['<function detrend_none at 0x02F5A3F0>']"}),
+ ("window", "basic:String",
+ {'optional': True, 'defaults': "['<function window_hanning at 0x02F5A2B0>']"}),
+ ("Fc", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("NFFT", "basic:Integer",
+ {'optional': True, 'defaults': "['256']"}),
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("sides", "basic:String",
+ {'optional': True, 'defaults': "['default']"}),
+ ("noverlap", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("lineProperties", "MplLine2DProperties",
+ {'optional': True}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplCsd)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('Fs'):
+ val = self.getInputFromPort('Fs')
+ kwargs['Fs'] = val
+ if self.hasInputFromPort('pad_to'):
+ val = self.getInputFromPort('pad_to')
+ kwargs['pad_to'] = val
+ if self.hasInputFromPort('scale_by_freq'):
+ val = self.getInputFromPort('scale_by_freq')
+ kwargs['scale_by_freq'] = val
+ if self.hasInputFromPort('detrend'):
+ val = self.getInputFromPort('detrend')
+ kwargs['detrend'] = val
+ if self.hasInputFromPort('window'):
+ val = self.getInputFromPort('window')
+ kwargs['window'] = val
+ if self.hasInputFromPort('Fc'):
+ val = self.getInputFromPort('Fc')
+ kwargs['Fc'] = val
+ if self.hasInputFromPort('NFFT'):
+ val = self.getInputFromPort('NFFT')
+ kwargs['NFFT'] = val
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('sides'):
+ val = self.getInputFromPort('sides')
+ kwargs['sides'] = val
+ if self.hasInputFromPort('noverlap'):
+ val = self.getInputFromPort('noverlap')
+ kwargs['noverlap'] = val
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ properties.update_kwargs(kwargs)
+
+ matplotlib.pyplot.csd(*args, **kwargs)
+
+class MplErrorbar(MplPlot):
+ """Plot an errorbar graph.
+
+Call signature:
+
+errorbar(x, y, yerr=None, xerr=None, fmt='-', ecolor=None, elinewidth=None, capsize=3, barsabove=False, lolims=False, uplims=False, xlolims=False, xuplims=False, errorevery=1, capthick=None)
+
+Plot x versus y with error deltas in yerr and xerr. Vertical errorbars are plotted if yerr is not None. Horizontal errorbars are plotted if xerr is not None.
+
+x, y, xerr, and yerr can all be scalars, which plots a single error bar at x, y.
+
+Optional keyword arguments:
+
+
+
+All other keyword arguments are passed on to the plot command for the markers. For example, this code makes big red squares with thick green edges:
+
+x,y,yerr = rand(3,10) errorbar(x, y, yerr, marker='s', mfc='red', mec='green', ms=20, mew=4)
+
+where mfc, mec, ms and mew are aliases for the longer property names, markerfacecolor, markeredgecolor, markersize and markeredgewith.
+
+valid kwargs for the marker properties are
+
+%(Line2D)s
+
+Returns (plotline, caplines, barlinecols):
+
+
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("lolims", "basic:Boolean",
+ {'optional': True, 'docstring': 'These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.', 'defaults': "['False']"}),
+ ("capsize", "basic:Float",
+ {'optional': True, 'docstring': 'The length of the error bar caps in points', 'defaults': "['3']"}),
+ ("uplims", "basic:Boolean",
+ {'optional': True, 'docstring': 'These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.', 'defaults': "['False']"}),
+ ("xlolims", "basic:Boolean",
+ {'optional': True, 'docstring': 'These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.', 'defaults': "['False']"}),
+ ("barsabove", "basic:String",
+ {'optional': True, 'docstring': 'if True, will plot the errorbars above the plot symbols. Default is below.', 'defaults': "['below']"}),
+ ("xerr", "basic:List",
+ {'optional': True, 'docstring': 'If a scalar number, len(N) array-like object, or an Nx1 array-like object, errorbars are drawn +/- value.\n\nIf a sequence of shape 2xN, errorbars are drawn at -row1 and +row2'}),
+ ("xerrScalar", "basic:Float",
+ {'docstring': 'If a scalar number, len(N) array-like object, or an Nx1 array-like object, errorbars are drawn +/- value.\n\nIf a sequence of shape 2xN, errorbars are drawn at -row1 and +row2', 'optional': True}),
+ ("fmt", "basic:String",
+ {'optional': True, 'docstring': 'The plot format symbol. If fmt is None, only the errorbars are plotted. This is used for adding errorbars to a bar plot, for example.', 'defaults': "['-']"}),
+ ("ecolor", "basic:Color",
+ {'entry_types': "['enum']", 'docstring': 'A matplotlib color arg which gives the color the errorbar lines; if None, use the marker color.', 'values': "[['', 'mpl color']]", 'optional': True}),
+ ("errorevery", "basic:Integer",
+ {'optional': True, 'docstring': 'subsamples the errorbars. Eg if everyerror=5, errorbars for every 5-th datapoint will be plotted. The data plot itself still shows all data points.', 'defaults': "['1']"}),
+ ("capthick", "basic:Float",
+ {'optional': True, 'docstring': 'An alias kwarg to markeredgewidth (a.k.a. - mew). This setting is a more sensible name for the property that controls the thickness of the error bar cap in points. For backwards compatibility, if mew or markeredgewidth are given, then they will over-ride capthick. This may change in future releases.'}),
+ ("xuplims", "basic:Boolean",
+ {'optional': True, 'docstring': 'These arguments can be used to indicate that a value gives only upper/lower limits. In that case a caret symbol is used to indicate this. lims-arguments may be of the same type as xerr and yerr.', 'defaults': "['False']"}),
+ ("elinewidth", "basic:Float",
+ {'optional': True, 'docstring': 'The linewidth of the errorbar lines. If None, use the linewidth.'}),
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("yerr", "basic:List",
+ {'optional': True, 'docstring': 'If a scalar number, len(N) array-like object, or an Nx1 array-like object, errorbars are drawn +/- value.\n\nIf a sequence of shape 2xN, errorbars are drawn at -row1 and +row2'}),
+ ("yerrScalar", "basic:Float",
+ {'docstring': 'If a scalar number, len(N) array-like object, or an Nx1 array-like object, errorbars are drawn +/- value.\n\nIf a sequence of shape 2xN, errorbars are drawn at -row1 and +row2', 'optional': True}),
+ ("caplineProperties", "MplLine2DProperties",
+ {}),
+ ("barlineProperties", "MplLineCollectionProperties",
+ {}),
+ ("plotlineProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplErrorbar)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('lolims'):
+ val = self.getInputFromPort('lolims')
+ kwargs['lolims'] = val
+ if self.hasInputFromPort('capsize'):
+ val = self.getInputFromPort('capsize')
+ kwargs['capsize'] = val
+ if self.hasInputFromPort('uplims'):
+ val = self.getInputFromPort('uplims')
+ kwargs['uplims'] = val
+ if self.hasInputFromPort('xlolims'):
+ val = self.getInputFromPort('xlolims')
+ kwargs['xlolims'] = val
+ if self.hasInputFromPort('barsabove'):
+ val = self.getInputFromPort('barsabove')
+ kwargs['barsabove'] = val
+ if self.hasInputFromPort('xerr'):
+ val = self.getInputFromPort('xerr')
+ kwargs['xerr'] = val
+ elif self.hasInputFromPort('xerrScalar'):
+ val = self.getInputFromPort('xerrScalar')
+ kwargs['xerr'] = val
+ if self.hasInputFromPort('fmt'):
+ val = self.getInputFromPort('fmt')
+ kwargs['fmt'] = val
+ if self.hasInputFromPort('ecolor'):
+ val = self.getInputFromPort('ecolor')
+ val = translate_color(val)
+ kwargs['ecolor'] = val
+ if self.hasInputFromPort('errorevery'):
+ val = self.getInputFromPort('errorevery')
+ kwargs['errorevery'] = val
+ if self.hasInputFromPort('capthick'):
+ val = self.getInputFromPort('capthick')
+ kwargs['capthick'] = val
+ if self.hasInputFromPort('xuplims'):
+ val = self.getInputFromPort('xuplims')
+ kwargs['xuplims'] = val
+ if self.hasInputFromPort('elinewidth'):
+ val = self.getInputFromPort('elinewidth')
+ kwargs['elinewidth'] = val
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('yerr'):
+ val = self.getInputFromPort('yerr')
+ kwargs['yerr'] = val
+ elif self.hasInputFromPort('yerrScalar'):
+ val = self.getInputFromPort('yerrScalar')
+ kwargs['yerr'] = val
+
+ output = matplotlib.pyplot.errorbar(*args, **kwargs)
+ plotline = output[0]
+ caplines = output[1]
+ barlines = output[2]
+ if self.hasInputFromPort('caplineProperties'):
+ properties = self.getInputFromPort('caplineProperties')
+ if caplines is not None:
+ properties.update_props(caplines)
+ if self.hasInputFromPort('barlineProperties'):
+ properties = self.getInputFromPort('barlineProperties')
+ if barlines is not None:
+ properties.update_props(barlines)
+ if self.hasInputFromPort('plotlineProperties'):
+ properties = self.getInputFromPort('plotlineProperties')
+ if plotline is not None:
+ properties.update_props(plotline)
+
+class MplFill(MplPlot):
+ """Plot filled polygons.
+
+Call signature:
+
+fill(*args, **kwargs)
+
+args is a variable length argument, allowing for multiple x, y pairs with an optional color format string; see :func:`~matplotlib.pyplot.plot` for details on the argument parsing. For example, to plot a polygon with vertices at x, y in blue.:
+
+ax.fill(x,y, 'b' )
+
+An arbitrary number of x, y, color groups can be specified:
+
+ax.fill(x1, y1, 'g', x2, y2, 'r')
+
+Return value is a list of :class:`~matplotlib.patches.Patch` instances that were added.
+
+The same color strings that :func:`~matplotlib.pyplot.plot` supports are supported by the fill format string.
+
+If you would like to fill below a curve, eg. shade a region between 0 and y along x, use :meth:`fill_between`
+
+The closed kwarg will close the polygon when True (default).
+
+kwargs control the :class:`~matplotlib.patches.Polygon` properties:
+
+%(Polygon)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("polygonProperties", "MplPolygonProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplFill)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ val = self.getInputFromPort('x')
+ args.append(val)
+ val = self.getInputFromPort('y')
+ args.append(val)
+
+ kwargs = {}
+
+ polygons = matplotlib.pyplot.fill(*args, **kwargs)
+ if self.hasInputFromPort('polygonProperties'):
+ properties = self.getInputFromPort('polygonProperties')
+ if polygons is not None:
+ properties.update_props(polygons)
+
+class MplFillBetween(MplPlot):
+ """Make filled polygons between two curves.
+
+Call signature:
+
+fill_between(x, y1, y2=0, where=None, **kwargs)
+
+Create a :class:`~matplotlib.collections.PolyCollection` filling the regions between y1 and y2 where where==True
+
+
+
+kwargs control the :class:`~matplotlib.patches.Polygon` properties:
+
+%(PolyCollection)s
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("y2", "basic:Float",
+ {'optional': True, 'docstring': 'A scalar y-value', 'defaults': "['0.0']"}),
+ ("y2Sequence", "basic:List",
+ {'optional': True, 'docstring': 'An N-length array of the y data'}),
+ ("interpolate", "basic:Boolean",
+ {'optional': True, 'defaults': "['False']"}),
+ ("y1", "basic:List",
+ {'docstring': 'An N-length array of the y data'}),
+ ("y1Scalar", "basic:Float",
+ {'optional': True, 'docstring': 'A scalar y-value'}),
+ ("x", "basic:List",
+ {'docstring': 'An N-length array of the x data'}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("where", "basic:List",
+ {'optional': True, 'docstring': 'An N-length boolean array that specifies where the fill is effective'}),
+ ("polyCollectionProperties", "MplPolyCollectionProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplFillBetween)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ val = self.getInputFromPort('x')
+ args.append(val)
+ if self.hasInputFromPort('y1'):
+ val = self.getInputFromPort('y1')
+ args.append(val)
+ elif self.hasInputFromPort('y1Scalar'):
+ val = self.getInputFromPort('y1Scalar')
+ args.append(val)
+ else:
+ raise ModuleError(self, 'Must set one of "y1", ' '"y1Scalar"')
+
+ kwargs = {}
+ if self.hasInputFromPort('y2'):
+ val = self.getInputFromPort('y2')
+ kwargs['y2'] = val
+ elif self.hasInputFromPort('y2Sequence'):
+ val = self.getInputFromPort('y2Sequence')
+ kwargs['y2'] = val
+ if self.hasInputFromPort('interpolate'):
+ val = self.getInputFromPort('interpolate')
+ kwargs['interpolate'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('where'):
+ val = self.getInputFromPort('where')
+ kwargs['where'] = val
+
+ polyCollection = matplotlib.pyplot.fill_between(*args, **kwargs)
+ if self.hasInputFromPort('polyCollectionProperties'):
+ properties = self.getInputFromPort('polyCollectionProperties')
+ if polyCollection is not None:
+ properties.update_props(polyCollection)
+
+class MplFillBetweenx(MplPlot):
+ """Make filled polygons between two horizontal curves.
+
+Call signature:
+
+fill_between(y, x1, x2=0, where=None, **kwargs)
+
+Create a :class:`~matplotlib.collections.PolyCollection` filling the regions between x1 and x2 where where==True
+
+
+
+kwargs control the :class:`~matplotlib.patches.Polygon` properties:
+
+%(PolyCollection)s
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("y", "basic:List",
+ {'docstring': 'An N-length array of the y data'}),
+ ("x2", "basic:Float",
+ {'optional': True, 'docstring': 'A scalar x-value', 'defaults': "['0']"}),
+ ("x2Sequence", "basic:List",
+ {'optional': True, 'docstring': 'An N-length array of the x data'}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("x1", "basic:List",
+ {'docstring': 'An N-length array of the x data'}),
+ ("x1Scalar", "basic:Float",
+ {'optional': True, 'docstring': 'A scalar x-value'}),
+ ("where", "basic:List",
+ {'optional': True, 'docstring': 'An N-length boolean array that specifies where the fill is effective'}),
+ ("polyCollectionProperties", "MplPolyCollectionProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplFillBetweenx)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ val = self.getInputFromPort('y')
+ args.append(val)
+ if self.hasInputFromPort('x1'):
+ val = self.getInputFromPort('x1')
+ args.append(val)
+ elif self.hasInputFromPort('x1Scalar'):
+ val = self.getInputFromPort('x1Scalar')
+ args.append(val)
+ else:
+ raise ModuleError(self, 'Must set one of "x1", ' '"x1Scalar"')
+
+ kwargs = {}
+ if self.hasInputFromPort('x2'):
+ val = self.getInputFromPort('x2')
+ kwargs['x2'] = val
+ elif self.hasInputFromPort('x2Sequence'):
+ val = self.getInputFromPort('x2Sequence')
+ kwargs['x2'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('where'):
+ val = self.getInputFromPort('where')
+ kwargs['where'] = val
+
+ polyCollection = matplotlib.pyplot.fill_betweenx(*args, **kwargs)
+ if self.hasInputFromPort('polyCollectionProperties'):
+ properties = self.getInputFromPort('polyCollectionProperties')
+ if polyCollection is not None:
+ properties.update_props(polyCollection)
+
+class MplHexbin(MplPlot):
+ """Make a hexagonal binning plot.
+
+Call signature:
+
+hexbin(x, y, C = None, gridsize = 100, bins = None, xscale = 'linear', yscale = 'linear', cmap=None, norm=None, vmin=None, vmax=None, alpha=None, linewidths=None, edgecolors='none' reduce_C_function = np.mean, mincnt=None, marginals=True **kwargs)
+
+Make a hexagonal binning plot of x versus y, where x, y are 1-D sequences of the same length, N. If C is None (the default), this is a histogram of the number of occurences of the observations at (x[i],y[i]).
+
+If C is specified, it specifies values at the coordinate (x[i],y[i]). These values are accumulated for each hexagonal bin and then reduced according to reduce_C_function, which defaults to numpy's mean function (np.mean). (If C is specified, it must also be a 1-D sequence of the same length as x and y.)
+
+x, y and/or C may be masked arrays, in which case only unmasked points will be plotted.
+
+Optional keyword arguments:
+
+Other keyword arguments controlling color mapping and normalization arguments:
+
+Other keyword arguments controlling the Collection properties:
+
+Here are the standard descriptions of all the :class:`~matplotlib.collections.Collection` kwargs:
+
+%(Collection)s
+
+The return value is a :class:`~matplotlib.collections.PolyCollection` instance; use :meth:`~matplotlib.collections.PolyCollection.get_array` on this :class:`~matplotlib.collections.PolyCollection` to get the counts in each hexagon. If marginals is True, horizontal bar and vertical bar (both PolyCollections) will be attached to the return collection as attributes hbar and vbar.
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("vmax", "basic:Float",
+ {'optional': True, 'docstring': 'vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.'}),
+ ("edgecolorsSequence", "basic:List",
+ {'entry_types': "['enum']", 'docstring': "If 'none', draws the edges in the same color as the fill color. This is the default, as it avoids unsightly unpainted pixels between the hexagons.\n\nIf None, draws the outlines in the default color.\n\nIf a matplotlib color arg or sequence of rgba tuples, draws the outlines in the specified color.", 'values': "[['', 'none', 'mpl color']]", 'optional': True, 'defaults': "['none']"}),
+ ("edgecolorsScalar", "basic:String",
+ {'docstring': "If 'none', draws the edges in the same color as the fill color. This is the default, as it avoids unsightly unpainted pixels between the hexagons.\n\nIf None, draws the outlines in the default color.\n\nIf a matplotlib color arg or sequence of rgba tuples, draws the outlines in the specified color.", 'optional': True}),
+ ("C", "basic:List",
+ {'optional': True}),
+ ("gridsize", "basic:Integer",
+ {'optional': True, 'docstring': 'The number of hexagons in the x-direction, default is 100. The corresponding number of hexagons in the y-direction is chosen such that the hexagons are approximately regular. Alternatively, gridsize can be a tuple with two elements specifying the number of hexagons in the x-direction and the y-direction.', 'defaults': "['100']"}),
+ ("vmin", "basic:Float",
+ {'optional': True, 'docstring': 'vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.'}),
+ ("yscale", "basic:String",
+ {'optional': True, 'defaults': "['linear']"}),
+ ("reduce_C_function", "basic:String",
+ {'optional': True, 'defaults': "['<function mean at 0x0277B3B0>']"}),
+ ("linewidths", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If None, defaults to rc lines.linewidth. Note that this is a tuple, and if you set the linewidths argument you must set it as a sequence of floats, as required by :class:`~matplotlib.collections.RegularPolyCollection`.', 'values': "[['']]", 'optional': True}),
+ ("xscale", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Use a linear or log10 scale on the horizontal axis.', 'values': "[['linear', 'log']]", 'optional': True, 'defaults': "['linear']"}),
+ ("cmap", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'a :class:`matplotlib.colors.Colormap` instance. If None, defaults to rc image.cmap.', 'values': "[['', 'Colormap']]", 'optional': True}),
+ ("norm", "basic:String",
+ {'entry_types': "['enum']", 'docstring': ':class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0,1.', 'values': "[['', 'Normalize']]", 'optional': True}),
+ ("extent", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'The limits of the bins. The default assigns the limits based on gridsize, x, y, xscale and yscale.', 'values': "[['']]", 'optional': True}),
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'the alpha value for the patches'}),
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("mincnt", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If not None, only display cells with more than mincnt number of points in the cell', 'values': "[['']]", 'optional': True}),
+ ("marginals", "basic:Boolean",
+ {'optional': True, 'docstring': 'if marginals is True, plot the marginal density as colormapped rectagles along the bottom of the x-axis and left of the y-axis', 'defaults': "['False']"}),
+ ("bins", "basic:Integer",
+ {'optional': True, 'docstring': "If None, no binning is applied; the color of each hexagon directly corresponds to its count value.\n\nIf 'log', use a logarithmic scale for the color map. Internally, log_{10}(i+1) is used to determine the hexagon color.\n\nIf an integer, divide the counts in the specified number of bins, and color the hexagons accordingly.\n\nIf a sequence of values, the values of the lower bound of the bins to be used."}),
+ ("scale", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Use a linear or log10 scale on the vertical axis.', 'values': "[['linear', 'log']]", 'optional': True}),
+ ("polyCollectionProperties", "MplPolyCollectionProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplHexbin)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('vmax'):
+ val = self.getInputFromPort('vmax')
+ kwargs['vmax'] = val
+ if self.hasInputFromPort('edgecolorsSequence'):
+ val = self.getInputFromPort('edgecolorsSequence')
+ kwargs['edgecolors'] = val
+ elif self.hasInputFromPort('edgecolorsScalar'):
+ val = self.getInputFromPort('edgecolorsScalar')
+ kwargs['edgecolors'] = val
+ if self.hasInputFromPort('C'):
+ val = self.getInputFromPort('C')
+ kwargs['C'] = val
+ if self.hasInputFromPort('gridsize'):
+ val = self.getInputFromPort('gridsize')
+ kwargs['gridsize'] = val
+ if self.hasInputFromPort('vmin'):
+ val = self.getInputFromPort('vmin')
+ kwargs['vmin'] = val
+ if self.hasInputFromPort('yscale'):
+ val = self.getInputFromPort('yscale')
+ kwargs['yscale'] = val
+ if self.hasInputFromPort('reduce_C_function'):
+ val = self.getInputFromPort('reduce_C_function')
+ kwargs['reduce_C_function'] = val
+ if self.hasInputFromPort('linewidths'):
+ val = self.getInputFromPort('linewidths')
+ kwargs['linewidths'] = val
+ if self.hasInputFromPort('xscale'):
+ val = self.getInputFromPort('xscale')
+ kwargs['xscale'] = val
+ if self.hasInputFromPort('cmap'):
+ val = self.getInputFromPort('cmap')
+ kwargs['cmap'] = val
+ if self.hasInputFromPort('norm'):
+ val = self.getInputFromPort('norm')
+ kwargs['norm'] = val
+ if self.hasInputFromPort('extent'):
+ val = self.getInputFromPort('extent')
+ kwargs['extent'] = val
+ if self.hasInputFromPort('alpha'):
+ val = self.getInputFromPort('alpha')
+ kwargs['alpha'] = val
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('mincnt'):
+ val = self.getInputFromPort('mincnt')
+ kwargs['mincnt'] = val
+ if self.hasInputFromPort('marginals'):
+ val = self.getInputFromPort('marginals')
+ kwargs['marginals'] = val
+ if self.hasInputFromPort('bins'):
+ val = self.getInputFromPort('bins')
+ kwargs['bins'] = val
+ if self.hasInputFromPort('scale'):
+ val = self.getInputFromPort('scale')
+ kwargs['scale'] = val
+
+ polyCollection = matplotlib.pyplot.hexbin(*args, **kwargs)
+ if self.hasInputFromPort('polyCollectionProperties'):
+ properties = self.getInputFromPort('polyCollectionProperties')
+ if polyCollection is not None:
+ properties.update_props(polyCollection)
+
+class MplHist(MplPlot):
+ """Plot a histogram.
+
+Call signature:
+
+hist(x, bins=10, range=None, normed=False, weights=None, cumulative=False, bottom=None, histtype='bar', align='mid', orientation='vertical', rwidth=None, log=False, color=None, label=None, stacked=False, **kwargs)
+
+Compute and draw the histogram of x. The return value is a tuple (n, bins, patches) or ([n0, n1, ...], bins, [patches0, patches1,...]) if the input contains multiple data.
+
+Multiple data can be provided via x as a list of datasets of potentially different length ([x0, x1, ...]), or as a 2-D ndarray in which each column is a dataset. Note that the ndarray form is transposed relative to the list form.
+
+Masked arrays are not supported at present.
+
+Keyword arguments:
+
+
+
+kwargs are used to update the properties of the :class:`~matplotlib.patches.Patch` instances returned by hist:
+
+%(Patch)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("rwidth", "basic:String",
+ {'optional': True, 'docstring': "The relative width of the bars as a fraction of the bin width. If None, automatically compute the width. Ignored if histtype = 'step' or 'stepfilled'."}),
+ ("normed", "basic:Boolean",
+ {'optional': True, 'docstring': 'If True, the first element of the return tuple will be the counts normalized to form a probability density, i.e., n/(len(x)*dbin). In a probability density, the integral of the histogram should be 1; you can verify that with a trapezoidal integration of the probability density function:\n\npdf, bins, patches = ax.hist(...) print np.sum(pdf * np.diff(bins))\n\nUntil numpy release 1.5, the underlying numpy histogram function was incorrect wi [...]
+ ("stacked", "basic:Boolean",
+ {'optional': True, 'docstring': "If True, multiple data are stacked on top of each other If False multiple data are aranged side by side if histtype is 'bar' or on top of each other if histtype is 'step'\n\n.", 'defaults': "['False']"}),
+ ("orientation", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If 'horizontal', :func:`~matplotlib.pyplot.barh` will be used for bar-type histograms and the bottom kwarg will be the left edges.", 'values': "[['horizontal', 'vertical']]", 'optional': True, 'defaults': "['vertical']"}),
+ ("bottom", "basic:String",
+ {'optional': True}),
+ ("colorSequence", "basic:List",
+ {'optional': True, 'docstring': 'Color spec or sequence of color specs, one per dataset. Default (None) uses the standard line color sequence.'}),
+ ("colorScalar", "basic:Color",
+ {'docstring': 'Color spec or sequence of color specs, one per dataset. Default (None) uses the standard line color sequence.', 'optional': True}),
+ ("histtype", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "The type of histogram to draw.\n\n'bar' is a traditional bar-type histogram. If multiple data are given the bars are aranged side by side.\n\n'barstacked' is a bar-type histogram where multiple data are stacked on top of each other.\n\n'step' generates a lineplot that is by default unfilled.\n\n'stepfilled' generates a lineplot that is by default filled.", 'values': "[['bar', 'barstacked', 'step', 'stepfilled']]", 'optional': True [...]
+ ("align", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "Controls how the histogram is plotted.\n\n'left': bars are centered on the left bin edges.\n\n'mid': bars are centered between the bin edges.\n\n'right': bars are centered on the right bin edges.", 'values': "[['left', 'mid', 'right']]", 'optional': True, 'defaults': "['mid']"}),
+ ("cumulative", "basic:Boolean",
+ {'optional': True, 'docstring': 'If True, then a histogram is computed where each bin gives the counts in that bin plus all bins for smaller values. The last bin gives the total number of datapoints. If normed is also True then the histogram is normalized such that the last bin equals 1. If cumulative evaluates to less than 0 (e.g. -1), the direction of accumulation is reversed. In this case, if normed is also True, then the histogram is normalized such that the first bi [...]
+ ("labelSequence", "basic:List",
+ {'optional': True, 'docstring': "String, or sequence of strings to match multiple datasets. Bar charts yield multiple patches per dataset, but only the first gets the label, so that the legend command will work as expected:\n\nax.hist(10+2*np.random.randn(1000), label='men') ax.hist(12+3*np.random.randn(1000), label='women', alpha=0.5) ax.legend()"}),
+ ("labelScalar", "basic:String",
+ {'docstring': "String, or sequence of strings to match multiple datasets. Bar charts yield multiple patches per dataset, but only the first gets the label, so that the legend command will work as expected:\n\nax.hist(10+2*np.random.randn(1000), label='men') ax.hist(12+3*np.random.randn(1000), label='women', alpha=0.5) ax.legend()", 'optional': True}),
+ ("range", "basic:List",
+ {'optional': True, 'docstring': 'The lower and upper range of the bins. Lower and upper outliers are ignored. If not provided, range is (x.min(), x.max()). Range has no effect if bins is a sequence.\n\nIf bins is a sequence or range is specified, autoscaling is based on the specified bin range instead of the range of x.'}),
+ ("weights", "basic:String",
+ {'optional': True, 'docstring': 'An array of weights, of the same shape as x. Each value in x only contributes its associated weight towards the bin count (instead of 1). If normed is True, the weights are normalized, so that the integral of the density over the range remains 1.'}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("bins", "basic:Integer",
+ {'optional': True, 'docstring': 'Either an integer number of bins or a sequence giving the bins. If bins is an integer, bins + 1 bin edges will be returned, consistent with :func:`numpy.histogram` for numpy version >= 1.3, and with the new = True argument in earlier versions. Unequally spaced bins are supported if bins is a sequence.', 'defaults': "['10']"}),
+ ("binsSequence", "basic:List",
+ {'docstring': 'Either an integer number of bins or a sequence giving the bins. If bins is an integer, bins + 1 bin edges will be returned, consistent with :func:`numpy.histogram` for numpy version >= 1.3, and with the new = True argument in earlier versions. Unequally spaced bins are supported if bins is a sequence.', 'optional': True}),
+ ("log", "basic:Boolean",
+ {'optional': True, 'docstring': 'If True, the histogram axis will be set to a log scale. If log is True and x is a 1D array, empty bins will be filtered out and only the non-empty (n, bins, patches) will be returned.', 'defaults': "['False']"}),
+ ("rectangleProperties", "MplRectangleProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplHist)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('rwidth'):
+ val = self.getInputFromPort('rwidth')
+ kwargs['rwidth'] = val
+ if self.hasInputFromPort('normed'):
+ val = self.getInputFromPort('normed')
+ kwargs['normed'] = val
+ if self.hasInputFromPort('stacked'):
+ val = self.getInputFromPort('stacked')
+ kwargs['stacked'] = val
+ if self.hasInputFromPort('orientation'):
+ val = self.getInputFromPort('orientation')
+ kwargs['orientation'] = val
+ if self.hasInputFromPort('bottom'):
+ val = self.getInputFromPort('bottom')
+ kwargs['bottom'] = val
+ if self.hasInputFromPort('colorSequence'):
+ val = self.getInputFromPort('colorSequence')
+ kwargs['color'] = val
+ elif self.hasInputFromPort('colorScalar'):
+ val = self.getInputFromPort('colorScalar')
+ val = translate_color(val)
+ kwargs['color'] = val
+ if self.hasInputFromPort('histtype'):
+ val = self.getInputFromPort('histtype')
+ kwargs['histtype'] = val
+ if self.hasInputFromPort('align'):
+ val = self.getInputFromPort('align')
+ kwargs['align'] = val
+ if self.hasInputFromPort('cumulative'):
+ val = self.getInputFromPort('cumulative')
+ kwargs['cumulative'] = val
+ if self.hasInputFromPort('labelSequence'):
+ val = self.getInputFromPort('labelSequence')
+ kwargs['label'] = val
+ elif self.hasInputFromPort('labelScalar'):
+ val = self.getInputFromPort('labelScalar')
+ kwargs['label'] = val
+ if self.hasInputFromPort('range'):
+ val = self.getInputFromPort('range')
+ kwargs['range'] = val
+ if self.hasInputFromPort('weights'):
+ val = self.getInputFromPort('weights')
+ kwargs['weights'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('bins'):
+ val = self.getInputFromPort('bins')
+ kwargs['bins'] = val
+ elif self.hasInputFromPort('binsSequence'):
+ val = self.getInputFromPort('binsSequence')
+ kwargs['bins'] = val
+ if self.hasInputFromPort('log'):
+ val = self.getInputFromPort('log')
+ kwargs['log'] = val
+
+ output = matplotlib.pyplot.hist(*args, **kwargs)
+ rectangles = output[2]
+ if self.hasInputFromPort('rectangleProperties'):
+ properties = self.getInputFromPort('rectangleProperties')
+ if rectangles is not None:
+ properties.update_props(rectangles)
+
+class MplHist2d(MplPlot):
+ """Make a 2D histogram plot.
+
+Call signature:
+
+hist2d(x, y, bins = None, range=None, weights=None, cmin=None, cmax=None **kwargs)
+
+Make a 2d histogram plot of x versus y, where x, y are 1-D sequences of the same length.
+
+The return value is (counts, xedges, yedges, Image).
+
+Optional keyword arguments: bins: [None | int | [int, int] | array_like | [array, array]]
+
+The bin specification:
+
+If int, the number of bins for the two dimensions (nx=ny=bins).
+
+If [int, int], the number of bins in each dimension (nx, ny = bins).
+
+If array_like, the bin edges for the two dimensions (x_edges=y_edges=bins).
+
+If [array, array], the bin edges in each dimension (x_edges, y_edges = bins).
+
+The default value is 10.
+
+Remaining keyword arguments are passed directly to :meth:`pcolorfast`.
+
+Rendering the histogram with a logarithmic color scale is accomplished by passing a :class:`colors.LogNorm` instance to the norm keyword argument.
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("normed", "basic:Boolean",
+ {'optional': True, 'defaults': "['False']"}),
+ ("cmin", "basic:String",
+ {'optional': True}),
+ ("range", "basic:String",
+ {'optional': True}),
+ ("weights", "basic:String",
+ {'optional': True}),
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("cmax", "basic:String",
+ {'optional': True}),
+ ("bins", "basic:Integer",
+ {'optional': True, 'defaults': "['10']"}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplHist2d)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('normed'):
+ val = self.getInputFromPort('normed')
+ kwargs['normed'] = val
+ if self.hasInputFromPort('cmin'):
+ val = self.getInputFromPort('cmin')
+ kwargs['cmin'] = val
+ if self.hasInputFromPort('range'):
+ val = self.getInputFromPort('range')
+ kwargs['range'] = val
+ if self.hasInputFromPort('weights'):
+ val = self.getInputFromPort('weights')
+ kwargs['weights'] = val
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('cmax'):
+ val = self.getInputFromPort('cmax')
+ kwargs['cmax'] = val
+ if self.hasInputFromPort('bins'):
+ val = self.getInputFromPort('bins')
+ kwargs['bins'] = val
+
+ matplotlib.pyplot.hist2d(*args, **kwargs)
+
+class MplHlines(MplPlot):
+ """Plot horizontal lines.
+
+call signature:
+
+hlines(y, xmin, xmax, colors='k', linestyles='solid', **kwargs)
+
+Plot horizontal lines at each y from xmin to xmax.
+
+Returns the :class:`~matplotlib.collections.LineCollection` that was added.
+
+Required arguments:
+
+
+
+Optional keyword arguments:
+
+
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("linestyles", "basic:String",
+ {'optional': True, 'docstring': "[ 'solid' | 'dashed' | 'dashdot' | 'dotted' ]", 'defaults': "['solid']"}),
+ ("label", "basic:String",
+ {'optional': True, 'defaults': "['']"}),
+ ("xminScalar", "basic:Float",
+ {'docstring': 'can be scalars or len(x) numpy arrays. If they are scalars, then the respective values are constant, else the widths of the lines are determined by xmin and xmax.'}),
+ ("xminSequence", "basic:List",
+ {'docstring': 'can be scalars or len(x) numpy arrays. If they are scalars, then the respective values are constant, else the widths of the lines are determined by xmin and xmax.', 'optional': True}),
+ ("colorsSequence", "basic:List",
+ {'optional': True, 'docstring': 'a line collections color argument, either a single color or a len(y) list of colors', 'defaults': "['k']"}),
+ ("colorsScalar", "basic:String",
+ {'docstring': 'a line collections color argument, either a single color or a len(y) list of colors', 'optional': True}),
+ ("xmaxScalar", "basic:Float",
+ {'docstring': 'can be scalars or len(x) numpy arrays. If they are scalars, then the respective values are constant, else the widths of the lines are determined by xmin and xmax.'}),
+ ("xmaxSequence", "basic:List",
+ {'docstring': 'can be scalars or len(x) numpy arrays. If they are scalars, then the respective values are constant, else the widths of the lines are determined by xmin and xmax.', 'optional': True}),
+ ("y", "basic:List",
+ {'docstring': 'a 1-D numpy array or iterable.'}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("lineProperties", "MplLineCollectionProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplHlines)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('linestyles'):
+ val = self.getInputFromPort('linestyles')
+ kwargs['linestyles'] = val
+ if self.hasInputFromPort('label'):
+ val = self.getInputFromPort('label')
+ kwargs['label'] = val
+ if self.hasInputFromPort('xminScalar'):
+ val = self.getInputFromPort('xminScalar')
+ kwargs['xmin'] = val
+ elif self.hasInputFromPort('xminSequence'):
+ val = self.getInputFromPort('xminSequence')
+ kwargs['xmin'] = val
+ else:
+ raise ModuleError(self, 'Must set one of "xminScalar", ' '"xminSequence"')
+ if self.hasInputFromPort('colorsSequence'):
+ val = self.getInputFromPort('colorsSequence')
+ kwargs['colors'] = val
+ elif self.hasInputFromPort('colorsScalar'):
+ val = self.getInputFromPort('colorsScalar')
+ kwargs['colors'] = val
+ if self.hasInputFromPort('xmaxScalar'):
+ val = self.getInputFromPort('xmaxScalar')
+ kwargs['xmax'] = val
+ elif self.hasInputFromPort('xmaxSequence'):
+ val = self.getInputFromPort('xmaxSequence')
+ kwargs['xmax'] = val
+ else:
+ raise ModuleError(self, 'Must set one of "xmaxScalar", ' '"xmaxSequence"')
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+
+ lines = matplotlib.pyplot.hlines(*args, **kwargs)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if lines is not None:
+ properties.update_props(lines)
+
+class MplImshow(MplPlot):
+ """Display an image on the axes.
+
+Call signature:
+
+imshow(X, cmap=None, norm=None, aspect=None, interpolation=None, alpha=None, vmin=None, vmax=None, origin=None, extent=None, **kwargs)
+
+Display the image in X to current axes. X may be a float array, a uint8 array or a PIL image. If X is an array, X can have the following shapes:
+
+MxN -- luminance (grayscale, float array only)
+
+MxNx3 -- RGB (float or uint8 array)
+
+MxNx4 -- RGBA (float or uint8 array)
+
+The value for each component of MxNx3 and MxNx4 float arrays should be in the range 0.0 to 1.0; MxN float arrays may be normalised.
+
+An :class:`matplotlib.image.AxesImage` instance is returned.
+
+Keyword arguments:
+
+interpolation:
+
+Acceptable values are None, 'none', 'nearest', 'bilinear', 'bicubic', 'spline16', 'spline36', 'hanning', 'hamming', 'hermite', 'kaiser', 'quadric', 'catrom', 'gaussian', 'bessel', 'mitchell', 'sinc', 'lanczos'
+
+If interpolation is None, default to rc image.interpolation. See also the filternorm and filterrad parameters
+
+If interpolation is 'none', then no interpolation is performed on the Agg, ps and pdf backends. Other backends will fall back to 'nearest'.
+
+Additional kwargs are :class:`~matplotlib.artist.Artist` properties:
+
+%(Artist)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("origin", "basic:String",
+ {'optional': True}),
+ ("imlim", "basic:String",
+ {'optional': True}),
+ ("extent", "basic:String",
+ {'optional': True}),
+ ("vmin", "basic:String",
+ {'optional': True}),
+ ("url", "basic:String",
+ {'optional': True}),
+ ("resample", "basic:String",
+ {'optional': True}),
+ ("shape", "basic:String",
+ {'optional': True}),
+ ("cmap", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'A :class:`matplotlib.colors.Colormap` instance, eg. cm.jet. If None, default to rc image.cmap value.\n\ncmap is ignored when X has RGB(A) information', 'values': "[['', 'Colormap']]", 'optional': True}),
+ ("filterrad", "basic:Float",
+ {'optional': True, 'defaults': "['4.0']"}),
+ ("filternorm", "basic:Integer",
+ {'optional': True, 'defaults': "['1']"}),
+ ("aspect", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If 'auto', changes the image aspect ratio to match that of the axes\n\nIf 'equal', and extent is None, changes the axes aspect ratio to match that of the image. If extent is not None, the axes aspect ratio is changed to match that of the extent.\n\nIf None, default to rc image.aspect value.", 'values': "[['', 'auto', 'equal']]", 'optional': True}),
+ ("alpha", "basic:String",
+ {'optional': True}),
+ ("vmax", "basic:String",
+ {'optional': True}),
+ ("X", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("norm", "basic:String",
+ {'optional': True}),
+ ("interpolation", "basic:String",
+ {'optional': True}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplImshow)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('origin'):
+ val = self.getInputFromPort('origin')
+ kwargs['origin'] = val
+ if self.hasInputFromPort('imlim'):
+ val = self.getInputFromPort('imlim')
+ kwargs['imlim'] = val
+ if self.hasInputFromPort('extent'):
+ val = self.getInputFromPort('extent')
+ kwargs['extent'] = val
+ if self.hasInputFromPort('vmin'):
+ val = self.getInputFromPort('vmin')
+ kwargs['vmin'] = val
+ if self.hasInputFromPort('url'):
+ val = self.getInputFromPort('url')
+ kwargs['url'] = val
+ if self.hasInputFromPort('resample'):
+ val = self.getInputFromPort('resample')
+ kwargs['resample'] = val
+ if self.hasInputFromPort('shape'):
+ val = self.getInputFromPort('shape')
+ kwargs['shape'] = val
+ if self.hasInputFromPort('cmap'):
+ val = self.getInputFromPort('cmap')
+ kwargs['cmap'] = val
+ if self.hasInputFromPort('filterrad'):
+ val = self.getInputFromPort('filterrad')
+ kwargs['filterrad'] = val
+ if self.hasInputFromPort('filternorm'):
+ val = self.getInputFromPort('filternorm')
+ kwargs['filternorm'] = val
+ if self.hasInputFromPort('aspect'):
+ val = self.getInputFromPort('aspect')
+ kwargs['aspect'] = val
+ if self.hasInputFromPort('alpha'):
+ val = self.getInputFromPort('alpha')
+ kwargs['alpha'] = val
+ if self.hasInputFromPort('vmax'):
+ val = self.getInputFromPort('vmax')
+ kwargs['vmax'] = val
+ val = self.getInputFromPort('X')
+ kwargs['X'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('norm'):
+ val = self.getInputFromPort('norm')
+ kwargs['norm'] = val
+ if self.hasInputFromPort('interpolation'):
+ val = self.getInputFromPort('interpolation')
+ kwargs['interpolation'] = val
+
+ matplotlib.pyplot.imshow(*args, **kwargs)
+
+class MplLoglog(MplPlot):
+ """Make a plot with log scaling on both the x and y axis.
+
+Call signature:
+
+loglog(*args, **kwargs)
+
+:func:`~matplotlib.pyplot.loglog` supports all the keyword arguments of :func:`~matplotlib.pyplot.plot` and :meth:`matplotlib.axes.Axes.set_xscale` / :meth:`matplotlib.axes.Axes.set_yscale`.
+
+Notable keyword arguments:
+
+
+
+The remaining valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("nonposx", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Non-positive values in x or y can be masked as invalid, or clipped to a very small positive number', 'values': "[['mask', 'clip']]", 'optional': True}),
+ ("nonposy", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Non-positive values in x or y can be masked as invalid, or clipped to a very small positive number', 'values': "[['mask', 'clip']]", 'optional': True}),
+ ("basex", "basic:Float",
+ {'optional': True, 'docstring': 'Base of the x/y logarithm'}),
+ ("basey", "basic:Float",
+ {'optional': True, 'docstring': 'Base of the x/y logarithm'}),
+ ("subsxSequence", "basic:List",
+ {'entry_types': "['enum']", 'docstring': 'The location of the minor x/y ticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`matplotlib.axes.Axes.set_xscale` / :meth:`matplotlib.axes.Axes.set_yscale` for details', 'values': "[['']]", 'optional': True}),
+ ("subsxScalar", "basic:String",
+ {'docstring': 'The location of the minor x/y ticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`matplotlib.axes.Axes.set_xscale` / :meth:`matplotlib.axes.Axes.set_yscale` for details', 'optional': True}),
+ ("subsySequence", "basic:List",
+ {'entry_types': "['enum']", 'docstring': 'The location of the minor x/y ticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`matplotlib.axes.Axes.set_xscale` / :meth:`matplotlib.axes.Axes.set_yscale` for details', 'values': "[['']]", 'optional': True}),
+ ("subsyScalar", "basic:String",
+ {'docstring': 'The location of the minor x/y ticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`matplotlib.axes.Axes.set_xscale` / :meth:`matplotlib.axes.Axes.set_yscale` for details', 'optional': True}),
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("lineProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplLoglog)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ val = self.getInputFromPort('x')
+ args.append(val)
+ val = self.getInputFromPort('y')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('nonposx'):
+ val = self.getInputFromPort('nonposx')
+ kwargs['nonposx'] = val
+ if self.hasInputFromPort('nonposy'):
+ val = self.getInputFromPort('nonposy')
+ kwargs['nonposy'] = val
+ if self.hasInputFromPort('basex'):
+ val = self.getInputFromPort('basex')
+ kwargs['basex'] = val
+ if self.hasInputFromPort('basey'):
+ val = self.getInputFromPort('basey')
+ kwargs['basey'] = val
+ if self.hasInputFromPort('subsxSequence'):
+ val = self.getInputFromPort('subsxSequence')
+ kwargs['subsx'] = val
+ elif self.hasInputFromPort('subsxScalar'):
+ val = self.getInputFromPort('subsxScalar')
+ kwargs['subsx'] = val
+ if self.hasInputFromPort('subsySequence'):
+ val = self.getInputFromPort('subsySequence')
+ kwargs['subsy'] = val
+ elif self.hasInputFromPort('subsyScalar'):
+ val = self.getInputFromPort('subsyScalar')
+ kwargs['subsy'] = val
+
+ lines = matplotlib.pyplot.loglog(*args, **kwargs)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if lines is not None:
+ properties.update_props(lines)
+
+class MplPcolor(MplPlot):
+ """Create a pseudocolor plot of a 2-D array.
+
+Note: pcolor can be very slow for large arrays; consider using the similar but much faster :func:`~matplotlib.pyplot.pcolormesh` instead.
+
+Call signatures:
+
+pcolor(C, **kwargs) pcolor(X, Y, C, **kwargs)
+
+C is the array of color values.
+
+X and Y, if given, specify the (x, y) coordinates of the colored quadrilaterals; the quadrilateral for C[i,j] has corners at:
+
+(X[i, j], Y[i, j]), (X[i, j+1], Y[i, j+1]), (X[i+1, j], Y[i+1, j]), (X[i+1, j+1], Y[i+1, j+1]).
+
+Ideally the dimensions of X and Y should be one greater than those of C; if the dimensions are the same, then the last row and column of C will be ignored.
+
+Note that the the column index corresponds to the x-coordinate, and the row index corresponds to y; for details, see the :ref:`Grid Orientation <axes-pcolor-grid-orientation>` section below.
+
+If either or both of X and Y are 1-D arrays or column vectors, they will be expanded as needed into the appropriate 2-D arrays, making a rectangular grid.
+
+X, Y and C may be masked arrays. If either C[i, j], or one of the vertices surrounding C[i,j] (X or Y at [i, j], [i+1, j], [i, j+1],[i+1, j+1]) is masked, nothing is plotted.
+
+Keyword arguments:
+
+
+
+Return value is a :class:`matplotlib.collections.Collection` instance.
+
+The grid orientation follows the MATLAB convention: an array C with shape (nrows, ncolumns) is plotted with the column number as X and the row number as Y, increasing up; hence it is plotted the way the array would be printed, except that the Y axis is reversed. That is, C is taken as C*(*y, x).
+
+Similarly for :func:`meshgrid`:
+
+x = np.arange(5) y = np.arange(3) X, Y = meshgrid(x,y)
+
+is equivalent to:
+
+X = array([[0, 1, 2, 3, 4], [0, 1, 2, 3, 4], [0, 1, 2, 3, 4]]) Y = array([[0, 0, 0, 0, 0], [1, 1, 1, 1, 1], [2, 2, 2, 2, 2]])
+
+so if you have:
+
+C = rand( len(x), len(y))
+
+then you need:
+
+pcolor(X, Y, C.T)
+
+or:
+
+pcolor(C.T)
+
+MATLAB :func:`pcolor` always discards the last row and column of C, but matplotlib displays the last row and column if X and Y are not specified, or if X and Y have one more row and column than C.
+
+kwargs can be used to control the :class:`~matplotlib.collections.PolyCollection` properties:
+
+%(PolyCollection)s
+
+Note: the default antialiaseds is False if the default edgecolors*="none" is used. This eliminates artificial lines at patch boundaries, and works regardless of the value of alpha. If *edgecolors is not "none", then the default antialiaseds is taken from rcParams['patch.antialiased'], which defaults to True. Stroking the edges may be preferred if alpha is 1, but will cause artifacts otherwise.
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("edgecolorsSequence", "basic:List",
+ {'entry_types': "['enum']", 'docstring': "If None, the rc setting is used by default.\n\nIf 'none', edges will not be visible.\n\nAn mpl color or sequence of colors will set the edge color", 'values': "[['', 'none', 'color']]", 'optional': True}),
+ ("edgecolorsScalar", "basic:String",
+ {'docstring': "If None, the rc setting is used by default.\n\nIf 'none', edges will not be visible.\n\nAn mpl color or sequence of colors will set the edge color", 'optional': True}),
+ ("vmin", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.', 'values': "[['']]", 'optional': True}),
+ ("cmap", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'A :class:`matplotlib.colors.Colormap` instance. If None, use rc settings.', 'values': "[['', 'Colormap']]", 'optional': True}),
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'the alpha blending value'}),
+ ("vmax", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.', 'values': "[['']]", 'optional': True}),
+ ("shading", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If 'faceted', a black grid is drawn around each rectangle; if 'flat', edges are not drawn. Default is 'flat', contrary to MATLAB.", 'values': "[['flat', 'faceted']]", 'optional': True, 'defaults': "['flat']"}),
+ ("norm", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'An :class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0,1. If None, defaults to :func:`normalize`.', 'values': "[['', 'Normalize']]", 'optional': True}),
+ ("Y", "basic:List",
+ {'optional': True}),
+ ("X", "basic:List",
+ {'optional': True}),
+ ("Z", "basic:List",
+ {}),
+ ("polyCollectionProperties", "MplPolyCollectionProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplPcolor)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ if self.hasInputFromPort('X'):
+ val = self.getInputFromPort('X')
+ args.append(val)
+ if self.hasInputFromPort('Y'):
+ val = self.getInputFromPort('Y')
+ args.append(val)
+ val = self.getInputFromPort('Z')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('edgecolorsSequence'):
+ val = self.getInputFromPort('edgecolorsSequence')
+ kwargs['edgecolors'] = val
+ elif self.hasInputFromPort('edgecolorsScalar'):
+ val = self.getInputFromPort('edgecolorsScalar')
+ kwargs['edgecolors'] = val
+ if self.hasInputFromPort('vmin'):
+ val = self.getInputFromPort('vmin')
+ kwargs['vmin'] = val
+ if self.hasInputFromPort('cmap'):
+ val = self.getInputFromPort('cmap')
+ kwargs['cmap'] = val
+ if self.hasInputFromPort('alpha'):
+ val = self.getInputFromPort('alpha')
+ kwargs['alpha'] = val
+ if self.hasInputFromPort('vmax'):
+ val = self.getInputFromPort('vmax')
+ kwargs['vmax'] = val
+ if self.hasInputFromPort('shading'):
+ val = self.getInputFromPort('shading')
+ kwargs['shading'] = val
+ if self.hasInputFromPort('norm'):
+ val = self.getInputFromPort('norm')
+ kwargs['norm'] = val
+
+ polyCollection = matplotlib.pyplot.pcolor(*args, **kwargs)
+ if self.hasInputFromPort('polyCollectionProperties'):
+ properties = self.getInputFromPort('polyCollectionProperties')
+ if polyCollection is not None:
+ properties.update_props(polyCollection)
+
+class MplPcolormesh(MplPlot):
+ """Plot a quadrilateral mesh.
+
+Call signatures:
+
+pcolormesh(C) pcolormesh(X, Y, C) pcolormesh(C, **kwargs)
+
+Create a pseudocolor plot of a 2-D array.
+
+pcolormesh is similar to :func:`~matplotlib.pyplot.pcolor`, but uses a different mechanism and returns a different object; pcolor returns a :class:`~matplotlib.collections.PolyCollection` but pcolormesh returns a :class:`~matplotlib.collections.QuadMesh`. It is much faster, so it is almost always preferred for large arrays.
+
+C may be a masked array, but X and Y may not. Masked array support is implemented via cmap and norm; in contrast, :func:`~matplotlib.pyplot.pcolor` simply does not draw quadrilaterals with masked colors or vertices.
+
+Keyword arguments:
+
+
+
+Return value is a :class:`matplotlib.collections.QuadMesh` object.
+
+kwargs can be used to control the :class:`matplotlib.collections.QuadMesh` properties:
+
+%(QuadMesh)s
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("edgecolorsSequence", "basic:List",
+ {'entry_types': "['enum']", 'docstring': "If None, the rc setting is used by default.\n\nIf 'None', edges will not be visible.\n\nIf 'face', edges will have the same color as the faces.\n\nAn mpl color or sequence of colors will set the edge color", 'values': "[['', 'None', 'face', 'color']]", 'optional': True}),
+ ("edgecolorsScalar", "basic:String",
+ {'docstring': "If None, the rc setting is used by default.\n\nIf 'None', edges will not be visible.\n\nIf 'face', edges will have the same color as the faces.\n\nAn mpl color or sequence of colors will set the edge color", 'optional': True}),
+ ("vmin", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.', 'values': "[['']]", 'optional': True}),
+ ("cmap", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'A :class:`matplotlib.colors.Colormap` instance. If None, use rc settings.', 'values': "[['', 'Colormap']]", 'optional': True}),
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'the alpha blending value'}),
+ ("vmax", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'vmin and vmax are used in conjunction with norm to normalize luminance data. If either is None, it is autoscaled to the respective min or max of the color array C. If not None, vmin or vmax passed in here override any pre-existing values supplied in the norm instance.', 'values': "[['']]", 'optional': True}),
+ ("shading", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "'flat' indicates a solid color for each quad. When 'gouraud', each quad will be Gouraud shaded. When gouraud shading, edgecolors is ignored.", 'values': "[['flat', 'gouraud']]", 'optional': True}),
+ ("norm", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'A :class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0,1. If None, defaults to :func:`normalize`.', 'values': "[['', 'Normalize']]", 'optional': True}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplPcolormesh)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('edgecolorsSequence'):
+ val = self.getInputFromPort('edgecolorsSequence')
+ kwargs['edgecolors'] = val
+ elif self.hasInputFromPort('edgecolorsScalar'):
+ val = self.getInputFromPort('edgecolorsScalar')
+ kwargs['edgecolors'] = val
+ if self.hasInputFromPort('vmin'):
+ val = self.getInputFromPort('vmin')
+ kwargs['vmin'] = val
+ if self.hasInputFromPort('cmap'):
+ val = self.getInputFromPort('cmap')
+ kwargs['cmap'] = val
+ if self.hasInputFromPort('alpha'):
+ val = self.getInputFromPort('alpha')
+ kwargs['alpha'] = val
+ if self.hasInputFromPort('vmax'):
+ val = self.getInputFromPort('vmax')
+ kwargs['vmax'] = val
+ if self.hasInputFromPort('shading'):
+ val = self.getInputFromPort('shading')
+ kwargs['shading'] = val
+ if self.hasInputFromPort('norm'):
+ val = self.getInputFromPort('norm')
+ kwargs['norm'] = val
+
+ matplotlib.pyplot.pcolormesh(*args, **kwargs)
+
+class MplPie(MplPlot):
+ """Plot a pie chart.
+
+Call signature:
+
+pie(x, explode=None, labels=None, colors=('b', 'g', 'r', 'c', 'm', 'y', 'k', 'w'), autopct=None, pctdistance=0.6, shadow=False, labeldistance=1.1, startangle=None, radius=None)
+
+Make a pie chart of array x. The fractional area of each wedge is given by x/sum(x). If sum(x) <= 1, then the values of x give the fractional area directly and the array will not be normalized. The wedges are plotted counterclockwise, by default starting from the x-axis.
+
+Keyword arguments:
+
+radius: [ None | scalar ] The radius of the pie, if radius is None it will be set to 1.
+
+The pie chart will probably look best if the figure and axes are square. Eg.:
+
+figure(figsize=(8,8)) ax = axes([0.1, 0.1, 0.8, 0.8])
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("autopct", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If not None, is a string or function used to label the wedges with their numeric value. The label will be placed inside the wedge. If it is a format string, the label will be fmt%pct. If it is a function, it will be called.', 'values': "[['', 'format function']]", 'optional': True}),
+ ("pctdistance", "basic:Float",
+ {'optional': True, 'docstring': 'The ratio between the center of each pie slice and the start of the text generated by autopct. Ignored if autopct is None; default is 0.6.', 'defaults': "['0.6']"}),
+ ("labelsSequence", "basic:List",
+ {'entry_types': "['enum']", 'docstring': 'A sequence of strings providing the labels for each wedge', 'values': "[['']]", 'optional': True}),
+ ("labelsScalar", "basic:String",
+ {'docstring': 'A sequence of strings providing the labels for each wedge', 'optional': True}),
+ ("explodeSequence", "basic:List",
+ {'entry_types': "['enum']", 'docstring': 'If not None, is a len(x) array which specifies the fraction of the radius with which to offset each wedge.', 'values': "[['']]", 'optional': True}),
+ ("explodeScalar", "basic:String",
+ {'docstring': 'If not None, is a len(x) array which specifies the fraction of the radius with which to offset each wedge.', 'optional': True}),
+ ("colors", "basic:Color",
+ {'entry_types': "['enum']", 'docstring': 'A sequence of matplotlib color args through which the pie chart will cycle.', 'values': "[['']]", 'optional': True}),
+ ("radius", "basic:String",
+ {'optional': True}),
+ ("startangle", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If not None, rotates the start of the pie chart by angle degrees counterclockwise from the x-axis.', 'values': "[['', 'Offset angle']]", 'optional': True}),
+ ("x", "basic:List",
+ {}),
+ ("shadow", "basic:Boolean",
+ {'optional': True, 'docstring': 'Draw a shadow beneath the pie.', 'defaults': "['False']"}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("labeldistance", "basic:Float",
+ {'optional': True, 'docstring': 'The radial distance at which the pie labels are drawn', 'defaults': "['1.1']"}),
+ ("autotextProperties", "MplTextProperties",
+ {}),
+ ("wedgeProperties", "MplWedgeProperties",
+ {}),
+ ("textProperties", "MplTextProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplPie)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('autopct'):
+ val = self.getInputFromPort('autopct')
+ kwargs['autopct'] = val
+ if self.hasInputFromPort('pctdistance'):
+ val = self.getInputFromPort('pctdistance')
+ kwargs['pctdistance'] = val
+ if self.hasInputFromPort('labelsSequence'):
+ val = self.getInputFromPort('labelsSequence')
+ kwargs['labels'] = val
+ elif self.hasInputFromPort('labelsScalar'):
+ val = self.getInputFromPort('labelsScalar')
+ kwargs['labels'] = val
+ if self.hasInputFromPort('explodeSequence'):
+ val = self.getInputFromPort('explodeSequence')
+ kwargs['explode'] = val
+ elif self.hasInputFromPort('explodeScalar'):
+ val = self.getInputFromPort('explodeScalar')
+ kwargs['explode'] = val
+ if self.hasInputFromPort('colors'):
+ val = self.getInputFromPort('colors')
+ val = translate_color(val)
+ kwargs['colors'] = val
+ if self.hasInputFromPort('radius'):
+ val = self.getInputFromPort('radius')
+ kwargs['radius'] = val
+ if self.hasInputFromPort('startangle'):
+ val = self.getInputFromPort('startangle')
+ kwargs['startangle'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('shadow'):
+ val = self.getInputFromPort('shadow')
+ kwargs['shadow'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('labeldistance'):
+ val = self.getInputFromPort('labeldistance')
+ kwargs['labeldistance'] = val
+
+ output = matplotlib.pyplot.pie(*args, **kwargs)
+ if len(output) < 3:
+ output = output + ([],)
+ wedges = output[0]
+ texts = output[1]
+ autotexts = output[2]
+ if self.hasInputFromPort('autotextProperties'):
+ properties = self.getInputFromPort('autotextProperties')
+ if autotexts is not None:
+ properties.update_props(autotexts)
+ if self.hasInputFromPort('wedgeProperties'):
+ properties = self.getInputFromPort('wedgeProperties')
+ if wedges is not None:
+ properties.update_props(wedges)
+ if self.hasInputFromPort('textProperties'):
+ properties = self.getInputFromPort('textProperties')
+ if texts is not None:
+ properties.update_props(texts)
+
+class MplPlotDate(MplPlot):
+ """Plot with data with dates.
+
+Call signature:
+
+plot_date(x, y, fmt='bo', tz=None, xdate=True, ydate=False, **kwargs)
+
+Similar to the :func:`~matplotlib.pyplot.plot` command, except the x or y (or both) data is considered to be dates, and the axis is labeled accordingly.
+
+x and/or y can be a sequence of dates represented as float days since 0001-01-01 UTC.
+
+Keyword arguments:
+
+
+
+Note if you are using custom date tickers and formatters, it may be necessary to set the formatters/locators after the call to :meth:`plot_date` since :meth:`plot_date` will set the default tick locator to :class:`matplotlib.dates.AutoDateLocator` (if the tick locator is not already set to a :class:`matplotlib.dates.DateLocator` instance) and the default tick formatter to :class:`matplotlib.dates.AutoDateFormatter` (if the tick formatter is not already set to a :class:`matplotlib.dates.D [...]
+
+Valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("tz", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'The time zone to use in labeling dates. If None, defaults to rc value.', 'values': "[['', ':class:`tzinfo` instance']]", 'optional': True}),
+ ("fmt", "basic:String",
+ {'optional': True, 'docstring': 'The plot format string.', 'defaults': "['bo']"}),
+ ("ydate", "basic:Boolean",
+ {'optional': True, 'docstring': 'If True, the y-axis will be labeled with dates.', 'defaults': "['False']"}),
+ ("xdate", "basic:Boolean",
+ {'optional': True, 'docstring': 'If True, the x-axis will be labeled with dates.', 'defaults': "['True']"}),
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("lineProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplPlotDate)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ val = self.getInputFromPort('x')
+ args.append(val)
+ val = self.getInputFromPort('y')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('tz'):
+ val = self.getInputFromPort('tz')
+ kwargs['tz'] = val
+ if self.hasInputFromPort('fmt'):
+ val = self.getInputFromPort('fmt')
+ kwargs['fmt'] = val
+ if self.hasInputFromPort('ydate'):
+ val = self.getInputFromPort('ydate')
+ kwargs['ydate'] = val
+ if self.hasInputFromPort('xdate'):
+ val = self.getInputFromPort('xdate')
+ kwargs['xdate'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+
+ lines = matplotlib.pyplot.plot_date(*args, **kwargs)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if lines is not None:
+ properties.update_props(lines)
+
+class MplPsd(MplPlot):
+ """Plot the power spectral density.
+
+Call signature:
+
+psd(x, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none, window=mlab.window_hanning, noverlap=0, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+The power spectral density by Welch's average periodogram method. The vector x is divided into NFFT length segments. Each segment is detrended by function detrend and windowed by function window. noverlap gives the length of the overlap between segments. The |\mathrm{fft}(i)|^2 of each segment i are averaged to compute Pxx, with a scaling to correct for power loss due to windowing. Fs is the sampling frequency.
+
+%(PSD)s
+
+
+
+Returns the tuple (Pxx, freqs).
+
+For plotting, the power is plotted as 10\log_{10}(P_{xx}) for decibels, though Pxx itself is returned.
+
+kwargs control the :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("Fs", "basic:Integer",
+ {'optional': True, 'defaults': "['2']"}),
+ ("pad_to", "basic:String",
+ {'optional': True}),
+ ("scale_by_freq", "basic:String",
+ {'optional': True}),
+ ("detrend", "basic:String",
+ {'optional': True, 'defaults': "['<function detrend_none at 0x02F5A3F0>']"}),
+ ("window", "basic:String",
+ {'optional': True, 'defaults': "['<function window_hanning at 0x02F5A2B0>']"}),
+ ("Fc", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("NFFT", "basic:Integer",
+ {'optional': True, 'defaults': "['256']"}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("sides", "basic:String",
+ {'optional': True, 'defaults': "['default']"}),
+ ("noverlap", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("lineProperties", "MplLine2DProperties",
+ {'optional': True}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplPsd)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('Fs'):
+ val = self.getInputFromPort('Fs')
+ kwargs['Fs'] = val
+ if self.hasInputFromPort('pad_to'):
+ val = self.getInputFromPort('pad_to')
+ kwargs['pad_to'] = val
+ if self.hasInputFromPort('scale_by_freq'):
+ val = self.getInputFromPort('scale_by_freq')
+ kwargs['scale_by_freq'] = val
+ if self.hasInputFromPort('detrend'):
+ val = self.getInputFromPort('detrend')
+ kwargs['detrend'] = val
+ if self.hasInputFromPort('window'):
+ val = self.getInputFromPort('window')
+ kwargs['window'] = val
+ if self.hasInputFromPort('Fc'):
+ val = self.getInputFromPort('Fc')
+ kwargs['Fc'] = val
+ if self.hasInputFromPort('NFFT'):
+ val = self.getInputFromPort('NFFT')
+ kwargs['NFFT'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('sides'):
+ val = self.getInputFromPort('sides')
+ kwargs['sides'] = val
+ if self.hasInputFromPort('noverlap'):
+ val = self.getInputFromPort('noverlap')
+ kwargs['noverlap'] = val
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ properties.update_kwargs(kwargs)
+
+ matplotlib.pyplot.psd(*args, **kwargs)
+
+class MplQuiver(MplPlot):
+ """Plot a 2-D field of arrows.
+
+call signatures:
+
+quiver(U, V, **kw) quiver(U, V, C, **kw) quiver(X, Y, U, V, **kw) quiver(X, Y, U, V, C, **kw)
+
+Arguments:
+
+
+
+All arguments may be 1-D or 2-D arrays or sequences. If X and Y are absent, they will be generated as a uniform grid. If U and V are 2-D arrays but X and Y are 1-D, and if len(X) and len(Y) match the column and row dimensions of U, then X and Y will be expanded with :func:`numpy.meshgrid`.
+
+U, V, C may be masked arrays, but masked X, Y are not supported at present.
+
+Keyword arguments:
+
+
+
+The defaults give a slightly swept-back arrow; to make the head a triangle, make headaxislength the same as headlength. To make the arrow more pointed, reduce headwidth or increase headlength and headaxislength. To make the head smaller relative to the shaft, scale down all the head parameters. You will probably do best to leave minshaft alone.
+
+linewidths and edgecolors can be used to customize the arrow outlines. Additional :class:`~matplotlib.collections.PolyCollection` keyword arguments:
+
+agg_filter: unknown alpha: float or None animated: [True | False] antialiased or antialiaseds: Boolean or sequence of booleans array: unknown axes: an :class:`~matplotlib.axes.Axes` instance clim: a length 2 sequence of floats clip_box: a :class:`matplotlib.transforms.Bbox` instance clip_on: [True | False] clip_path: [ (:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`) | :class:`~matplotlib.patches.Patch` | None ] cmap: a colormap or registered co [...]
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("headaxislength", "basic:Float",
+ {'optional': True, 'docstring': 'Head length at shaft intersection, default is 4.5', 'defaults': "['4.5']"}),
+ ("C", "basic:List",
+ {'optional': True, 'docstring': 'None'}),
+ ("scale", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Data units per arrow length unit, e.g. m/s per plot width; a smaller scale parameter makes the arrow longer. If None, a simple autoscaling algorithm is used, based on the average vector length and the number of vectors. The arrow length unit is given by the scale_units parameter', 'values': "[['']]", 'optional': True}),
+ ("width", "basic:List",
+ {'optional': True, 'docstring': 'Shaft width in arrow units; default depends on choice of units, above, and number of vectors; a typical starting value is about 0.005 times the width of the plot.'}),
+ ("headlength", "basic:Float",
+ {'optional': True, 'docstring': 'Head length as multiple of shaft width, default is 5', 'defaults': "['5']"}),
+ ("minlength", "basic:Float",
+ {'optional': True, 'docstring': 'Minimum length as a multiple of shaft width; if an arrow length is less than this, plot a dot (hexagon) of this diameter instead. Default is 1.', 'defaults': "['1']"}),
+ ("minshaft", "basic:Float",
+ {'optional': True, 'docstring': 'Length below which arrow scales, in units of head length. Do not set this to less than 1, or small arrows will look terrible! Default is 1', 'defaults': "['1']"}),
+ ("pivot", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'The part of the arrow that is at the grid point; the arrow rotates about this point, hence the name pivot.', 'values': "[['tail', 'middle', 'tip']]", 'optional': True}),
+ ("unitsSequence", "basic:List",
+ {'entry_types': "['enum']", 'docstring': 'For example, if scale_units is \'inches\', scale is 2.0, and (u,v) = (1,0), then the vector will be 0.5 inches long. If scale_units is \'width\', then the vector will be half the width of the axes.\n\nIf scale_units is \'x\' then the vector will be 0.5 x-axis units. To plot vectors in the x-y plane, with u and v having the same units as x and y, use "angles=\'xy\', scale_units=\'xy\', scale=1".', 'values': "[['width', 'height', 'd [...]
+ ("unitsScalar", "basic:String",
+ {'docstring': 'For example, if scale_units is \'inches\', scale is 2.0, and (u,v) = (1,0), then the vector will be 0.5 inches long. If scale_units is \'width\', then the vector will be half the width of the axes.\n\nIf scale_units is \'x\' then the vector will be 0.5 x-axis units. To plot vectors in the x-y plane, with u and v having the same units as x and y, use "angles=\'xy\', scale_units=\'xy\', scale=1".', 'optional': True}),
+ ("headwidth", "basic:Float",
+ {'optional': True, 'docstring': 'Head width as multiple of shaft width, default is 3', 'defaults': "['3']"}),
+ ("U", "basic:List",
+ {'docstring': 'None'}),
+ ("angles", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "With the default 'uv', the arrow aspect ratio is 1, so that if U*==*V the angle of the arrow on the plot is 45 degrees CCW from the x-axis. With 'xy', the arrow points from (x,y) to (x+u, y+v). Alternatively, arbitrary angles may be specified as an array of values in degrees, CCW from the x-axis.", 'values': "[['uv', 'xy', 'array']]", 'optional': True}),
+ ("V", "basic:List",
+ {'docstring': 'None'}),
+ ("Y", "basic:List",
+ {'optional': True, 'docstring': 'None'}),
+ ("X", "basic:List",
+ {'optional': True, 'docstring': 'None'}),
+ ("scale_units", "basic:List",
+ {'optional': True, 'docstring': 'For example, if scale_units is \'inches\', scale is 2.0, and (u,v) = (1,0), then the vector will be 0.5 inches long. If scale_units is \'width\', then the vector will be half the width of the axes.\n\nIf scale_units is \'x\' then the vector will be 0.5 x-axis units. To plot vectors in the x-y plane, with u and v having the same units as x and y, use "angles=\'xy\', scale_units=\'xy\', scale=1".'}),
+ ("colorSequence", "basic:List",
+ {'optional': True, 'docstring': 'This is a synonym for the :class:`~matplotlib.collections.PolyCollection` facecolor kwarg. If C has been set, color has no effect.'}),
+ ("colorScalar", "basic:String",
+ {'docstring': 'This is a synonym for the :class:`~matplotlib.collections.PolyCollection` facecolor kwarg. If C has been set, color has no effect.', 'optional': True}),
+ ("polyCollectionProperties", "MplPolyCollectionProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplQuiver)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ if self.hasInputFromPort('X'):
+ val = self.getInputFromPort('X')
+ args.append(val)
+ if self.hasInputFromPort('Y'):
+ val = self.getInputFromPort('Y')
+ args.append(val)
+ val = self.getInputFromPort('U')
+ args.append(val)
+ val = self.getInputFromPort('V')
+ args.append(val)
+ if self.hasInputFromPort('C'):
+ val = self.getInputFromPort('C')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('headaxislength'):
+ val = self.getInputFromPort('headaxislength')
+ kwargs['headaxislength'] = val
+ if self.hasInputFromPort('scale'):
+ val = self.getInputFromPort('scale')
+ kwargs['scale'] = val
+ if self.hasInputFromPort('width'):
+ val = self.getInputFromPort('width')
+ kwargs['width'] = val
+ if self.hasInputFromPort('headlength'):
+ val = self.getInputFromPort('headlength')
+ kwargs['headlength'] = val
+ if self.hasInputFromPort('minlength'):
+ val = self.getInputFromPort('minlength')
+ kwargs['minlength'] = val
+ if self.hasInputFromPort('minshaft'):
+ val = self.getInputFromPort('minshaft')
+ kwargs['minshaft'] = val
+ if self.hasInputFromPort('pivot'):
+ val = self.getInputFromPort('pivot')
+ kwargs['pivot'] = val
+ if self.hasInputFromPort('unitsSequence'):
+ val = self.getInputFromPort('unitsSequence')
+ kwargs['units'] = val
+ elif self.hasInputFromPort('unitsScalar'):
+ val = self.getInputFromPort('unitsScalar')
+ kwargs['units'] = val
+ if self.hasInputFromPort('headwidth'):
+ val = self.getInputFromPort('headwidth')
+ kwargs['headwidth'] = val
+ if self.hasInputFromPort('angles'):
+ val = self.getInputFromPort('angles')
+ kwargs['angles'] = val
+ if self.hasInputFromPort('scale_units'):
+ val = self.getInputFromPort('scale_units')
+ kwargs['scale_units'] = val
+ if self.hasInputFromPort('colorSequence'):
+ val = self.getInputFromPort('colorSequence')
+ kwargs['color'] = val
+ elif self.hasInputFromPort('colorScalar'):
+ val = self.getInputFromPort('colorScalar')
+ val = translate_color(val)
+ kwargs['color'] = val
+
+ polyCollection = matplotlib.pyplot.quiver(*args, **kwargs)
+ if self.hasInputFromPort('polyCollectionProperties'):
+ properties = self.getInputFromPort('polyCollectionProperties')
+ if polyCollection is not None:
+ properties.update_props(polyCollection)
+
+class MplQuiverkey(MplPlot):
+ """Add a key to a quiver plot.
+
+Call signature:
+
+quiverkey(Q, X, Y, U, label, **kw)
+
+Arguments:
+
+
+
+Keyword arguments:
+
+
+
+Any additional keyword arguments are used to override vector properties taken from Q.
+
+The positioning of the key depends on X, Y, coordinates, and labelpos. If labelpos is 'N' or 'S', X, Y give the position of the middle of the key arrow. If labelpos is 'E', X, Y positions the head, and if labelpos is 'W', X, Y positions the tail; in either of these two cases, X, Y is somewhere in the middle of the arrow+label key object.
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("color", "basic:Color",
+ {'optional': True, 'docstring': 'overrides face and edge colors from Q.'}),
+ ("coordinatesSequence", "basic:List",
+ {'entry_types': "['enum']", 'docstring': "Coordinate system and units for X, Y: 'axes' and 'figure' are normalized coordinate systems with 0,0 in the lower left and 1,1 in the upper right; 'data' are the axes data coordinates (used for the locations of the vectors in the quiver plot itself); 'inches' is position in the figure in inches, with 0,0 at the lower left corner.", 'values': "[['axes', 'figure', 'data', 'inches']]", 'optional': True}),
+ ("coordinatesScalar", "basic:String",
+ {'docstring': "Coordinate system and units for X, Y: 'axes' and 'figure' are normalized coordinate systems with 0,0 in the lower left and 1,1 in the upper right; 'data' are the axes data coordinates (used for the locations of the vectors in the quiver plot itself); 'inches' is position in the figure in inches, with 0,0 at the lower left corner.", 'optional': True}),
+ ("label", "basic:String",
+ {'docstring': 'A string with the length and units of the key'}),
+ ("Q", "basic:String",
+ {'docstring': 'The Quiver instance returned by a call to quiver.'}),
+ ("labelcolor", "basic:Color",
+ {'optional': True, 'docstring': 'defaults to default :class:`~matplotlib.text.Text` color.'}),
+ ("fontproperties", "basic:String",
+ {'optional': True, 'docstring': 'A dictionary with keyword arguments accepted by the :class:`~matplotlib.font_manager.FontProperties` initializer: family, style, variant, size, weight'}),
+ ("U", "basic:String",
+ {'docstring': 'The length of the key'}),
+ ("labelpos", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Position the label above, below, to the right, to the left of the arrow, respectively.', 'values': "[['N', 'S', 'E', 'W']]", 'optional': True}),
+ ("Y", "basic:String",
+ {'docstring': 'The location of the key; additional explanation follows.'}),
+ ("X", "basic:String",
+ {'docstring': 'The location of the key; additional explanation follows.'}),
+ ("labelsep", "basic:Float",
+ {'optional': True, 'docstring': 'Distance in inches between the arrow and the label. Default is 0.1', 'defaults': "['0.1']"}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplQuiverkey)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('color'):
+ val = self.getInputFromPort('color')
+ val = translate_color(val)
+ kwargs['color'] = val
+ if self.hasInputFromPort('coordinatesSequence'):
+ val = self.getInputFromPort('coordinatesSequence')
+ kwargs['coordinates'] = val
+ elif self.hasInputFromPort('coordinatesScalar'):
+ val = self.getInputFromPort('coordinatesScalar')
+ kwargs['coordinates'] = val
+ val = self.getInputFromPort('label')
+ kwargs['label'] = val
+ val = self.getInputFromPort('Q')
+ kwargs['Q'] = val
+ if self.hasInputFromPort('labelcolor'):
+ val = self.getInputFromPort('labelcolor')
+ val = translate_color(val)
+ kwargs['labelcolor'] = val
+ if self.hasInputFromPort('fontproperties'):
+ val = self.getInputFromPort('fontproperties')
+ kwargs['fontproperties'] = val
+ val = self.getInputFromPort('U')
+ kwargs['U'] = val
+ if self.hasInputFromPort('labelpos'):
+ val = self.getInputFromPort('labelpos')
+ kwargs['labelpos'] = val
+ val = self.getInputFromPort('Y')
+ kwargs['Y'] = val
+ val = self.getInputFromPort('X')
+ kwargs['X'] = val
+ if self.hasInputFromPort('labelsep'):
+ val = self.getInputFromPort('labelsep')
+ kwargs['labelsep'] = val
+
+ matplotlib.pyplot.quiverkey(*args, **kwargs)
+
+class MplScatter(MplPlot):
+ """Make a scatter plot.
+
+Call signatures:
+
+scatter(x, y, s=20, c='b', marker='o', cmap=None, norm=None, vmin=None, vmax=None, alpha=None, linewidths=None, verts=None, **kwargs)
+
+Make a scatter plot of x versus y, where x, y are converted to 1-D sequences which must be of the same length, N.
+
+Keyword arguments:
+
+
+
+Any or all of x, y, s, and c may be masked arrays, in which case all masks will be combined and only unmasked points will be plotted.
+
+Other keyword arguments: the color mapping and normalization arguments will be used only if c is an array of floats.
+
+
+
+Optional kwargs control the :class:`~matplotlib.collections.Collection` properties; in particular:
+
+
+
+Here are the standard descriptions of all the :class:`~matplotlib.collections.Collection` kwargs:
+
+%(Collection)s
+
+A :class:`~matplotlib.collections.Collection` instance is returned.
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("vmax", "basic:String",
+ {'optional': True, 'docstring': 'vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.'}),
+ ("edgecolors", "basic:String",
+ {'optional': True, 'docstring': "The string 'none' to plot faces with no outlines"}),
+ ("cSequence", "basic:List",
+ {'optional': True, 'docstring': 'a color. c can be a single color format string, or a sequence of color specifications of length N, or a sequence of N numbers to be mapped to colors using the cmap and norm specified via kwargs (see below). Note that c should not be a single numeric RGB or RGBA sequence because that is indistinguishable from an array of values to be colormapped. c can be a 2-D array in which the rows are RGB or RGBA, however.', 'defaults': "['b']"}),
+ ("cScalar", "basic:String",
+ {'docstring': 'a color. c can be a single color format string, or a sequence of color specifications of length N, or a sequence of N numbers to be mapped to colors using the cmap and norm specified via kwargs (see below). Note that c should not be a single numeric RGB or RGBA sequence because that is indistinguishable from an array of values to be colormapped. c can be a 2-D array in which the rows are RGB or RGBA, however.', 'optional': True}),
+ ("vmin", "basic:String",
+ {'optional': True, 'docstring': 'vmin and vmax are used in conjunction with norm to normalize luminance data. If either are None, the min and max of the color array C is used. Note if you pass a norm instance, your settings for vmin and vmax will be ignored.'}),
+ ("faceted", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("linewidths", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If None, defaults to (lines.linewidth,). Note that this is a tuple, and if you set the linewidths argument you must set it as a sequence of floats, as required by :class:`~matplotlib.collections.RegularPolyCollection`.', 'values': "[['']]", 'optional': True}),
+ ("marker", "basic:String",
+ {'optional': True, 'docstring': 'can be one of:\n\n%(MarkerTable)s', 'defaults': "['o']"}),
+ ("s", "basic:Float",
+ {'optional': True, 'docstring': 'size in points^2. It is a scalar or an array of the same length as x and y.', 'defaults': "['20']"}),
+ ("cmap", "basic:String",
+ {'optional': True, 'docstring': 'A :class:`matplotlib.colors.Colormap` instance or registered name. If None, defaults to rc image.cmap. cmap is only used if c is an array of floats.'}),
+ ("verts", "basic:String",
+ {'optional': True}),
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'The alpha value for the patches'}),
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("facecolors", "basic:String",
+ {'optional': True, 'docstring': "The string 'none' to plot unfilled outlines"}),
+ ("norm", "basic:String",
+ {'optional': True, 'docstring': 'A :class:`matplotlib.colors.Normalize` instance is used to scale luminance data to 0, 1. If None, use the default :func:`normalize`. norm is only used if c is an array of floats.'}),
+ ("pathCollectionProperties", "MplPathCollectionProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplScatter)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('vmax'):
+ val = self.getInputFromPort('vmax')
+ kwargs['vmax'] = val
+ if self.hasInputFromPort('edgecolors'):
+ val = self.getInputFromPort('edgecolors')
+ kwargs['edgecolors'] = val
+ if self.hasInputFromPort('cSequence'):
+ val = self.getInputFromPort('cSequence')
+ kwargs['c'] = val
+ elif self.hasInputFromPort('cScalar'):
+ val = self.getInputFromPort('cScalar')
+ kwargs['c'] = val
+ if self.hasInputFromPort('vmin'):
+ val = self.getInputFromPort('vmin')
+ kwargs['vmin'] = val
+ if self.hasInputFromPort('faceted'):
+ val = self.getInputFromPort('faceted')
+ kwargs['faceted'] = val
+ if self.hasInputFromPort('linewidths'):
+ val = self.getInputFromPort('linewidths')
+ kwargs['linewidths'] = val
+ if self.hasInputFromPort('marker'):
+ val = self.getInputFromPort('marker')
+ kwargs['marker'] = val
+ if self.hasInputFromPort('s'):
+ val = self.getInputFromPort('s')
+ kwargs['s'] = val
+ if self.hasInputFromPort('cmap'):
+ val = self.getInputFromPort('cmap')
+ kwargs['cmap'] = val
+ if self.hasInputFromPort('verts'):
+ val = self.getInputFromPort('verts')
+ kwargs['verts'] = val
+ if self.hasInputFromPort('alpha'):
+ val = self.getInputFromPort('alpha')
+ kwargs['alpha'] = val
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('facecolors'):
+ val = self.getInputFromPort('facecolors')
+ kwargs['facecolors'] = val
+ if self.hasInputFromPort('norm'):
+ val = self.getInputFromPort('norm')
+ kwargs['norm'] = val
+
+ pathCollection = matplotlib.pyplot.scatter(*args, **kwargs)
+ if self.hasInputFromPort('pathCollectionProperties'):
+ properties = self.getInputFromPort('pathCollectionProperties')
+ if pathCollection is not None:
+ properties.update_props(pathCollection)
+
+class MplSemilogx(MplPlot):
+ """Make a plot with log scaling on the x axis.
+
+Call signature:
+
+semilogx(*args, **kwargs)
+
+:func:`semilogx` supports all the keyword arguments of :func:`~matplotlib.pyplot.plot` and :meth:`matplotlib.axes.Axes.set_xscale`.
+
+Notable keyword arguments:
+
+
+
+The remaining valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("basex", "basic:Float",
+ {'optional': True, 'docstring': 'Base of the x logarithm'}),
+ ("nonposx", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Non-positive values in x can be masked as invalid, or clipped to a very small positive number', 'values': "[['mask', 'clip']]", 'optional': True}),
+ ("subsxSequence", "basic:List",
+ {'entry_types': "['enum']", 'docstring': 'The location of the minor xticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`~matplotlib.axes.Axes.set_xscale` for details.', 'values': "[['']]", 'optional': True}),
+ ("subsxScalar", "basic:String",
+ {'docstring': 'The location of the minor xticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`~matplotlib.axes.Axes.set_xscale` for details.', 'optional': True}),
+ ("x", "basic:List",
+ {}),
+ ("y", "basic:List",
+ {}),
+ ("lineProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplSemilogx)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ val = self.getInputFromPort('x')
+ args.append(val)
+ val = self.getInputFromPort('y')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('basex'):
+ val = self.getInputFromPort('basex')
+ kwargs['basex'] = val
+ if self.hasInputFromPort('nonposx'):
+ val = self.getInputFromPort('nonposx')
+ kwargs['nonposx'] = val
+ if self.hasInputFromPort('subsxSequence'):
+ val = self.getInputFromPort('subsxSequence')
+ kwargs['subsx'] = val
+ elif self.hasInputFromPort('subsxScalar'):
+ val = self.getInputFromPort('subsxScalar')
+ kwargs['subsx'] = val
+
+ lines = matplotlib.pyplot.semilogx(*args, **kwargs)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if lines is not None:
+ properties.update_props(lines)
+
+class MplSemilogy(MplPlot):
+ """Make a plot with log scaling on the y axis.
+
+call signature:
+
+semilogy(*args, **kwargs)
+
+:func:`semilogy` supports all the keyword arguments of :func:`~matplotlib.pylab.plot` and :meth:`matplotlib.axes.Axes.set_yscale`.
+
+Notable keyword arguments:
+
+
+
+The remaining valid kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("basey", "basic:Float",
+ {'optional': True, 'docstring': 'Base of the y logarithm'}),
+ ("nonposy", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'Non-positive values in y can be masked as invalid, or clipped to a very small positive number', 'values': "[['mask', 'clip']]", 'optional': True}),
+ ("subsySequence", "basic:List",
+ {'entry_types': "['enum']", 'docstring': 'The location of the minor yticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`~matplotlib.axes.Axes.set_yscale` for details.', 'values': "[['']]", 'optional': True}),
+ ("subsyScalar", "basic:String",
+ {'docstring': 'The location of the minor yticks; None defaults to autosubs, which depend on the number of decades in the plot; see :meth:`~matplotlib.axes.Axes.set_yscale` for details.', 'optional': True}),
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("lineProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplSemilogy)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ val = self.getInputFromPort('x')
+ args.append(val)
+ val = self.getInputFromPort('y')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('basey'):
+ val = self.getInputFromPort('basey')
+ kwargs['basey'] = val
+ if self.hasInputFromPort('nonposy'):
+ val = self.getInputFromPort('nonposy')
+ kwargs['nonposy'] = val
+ if self.hasInputFromPort('subsySequence'):
+ val = self.getInputFromPort('subsySequence')
+ kwargs['subsy'] = val
+ elif self.hasInputFromPort('subsyScalar'):
+ val = self.getInputFromPort('subsyScalar')
+ kwargs['subsy'] = val
+
+ lines = matplotlib.pyplot.semilogy(*args, **kwargs)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if lines is not None:
+ properties.update_props(lines)
+
+class MplSpecgram(MplPlot):
+ """Plot a spectrogram.
+
+Call signature:
+
+specgram(x, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none, window=mlab.window_hanning, noverlap=128, cmap=None, xextent=None, pad_to=None, sides='default', scale_by_freq=None, **kwargs)
+
+Compute a spectrogram of data in x. Data are split into NFFT length segments and the PSD of each section is computed. The windowing function window is applied to each segment, and the amount of overlap of each segment is specified with noverlap.
+
+%(PSD)s
+
+kwargs:
+
+Additional kwargs are passed on to imshow which makes the specgram image
+
+Return value is (Pxx, freqs, bins, im):
+
+bins are the time points the spectrogram is calculated over
+
+freqs is an array of frequencies
+
+Pxx is an array of shape (len(times), len(freqs)) of power
+
+im is a :class:`~matplotlib.image.AxesImage` instance
+
+Note: If x is real (i.e. non-complex), only the positive spectrum is shown. If x is complex, both positive and negative parts of the spectrum are shown. This can be overridden using the sides keyword argument.
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("Fs", "basic:Integer",
+ {'optional': True, 'defaults': "['2']"}),
+ ("pad_to", "basic:String",
+ {'optional': True}),
+ ("scale_by_freq", "basic:String",
+ {'optional': True}),
+ ("xextent", "basic:String",
+ {'optional': True}),
+ ("detrend", "basic:String",
+ {'optional': True, 'defaults': "['<function detrend_none at 0x02F5A3F0>']"}),
+ ("window", "basic:String",
+ {'optional': True, 'defaults': "['<function window_hanning at 0x02F5A2B0>']"}),
+ ("Fc", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("NFFT", "basic:Integer",
+ {'optional': True, 'defaults': "['256']"}),
+ ("cmap", "basic:String",
+ {'optional': True}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("sides", "basic:String",
+ {'optional': True, 'defaults': "['default']"}),
+ ("noverlap", "basic:Integer",
+ {'optional': True, 'defaults': "['128']"}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplSpecgram)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('Fs'):
+ val = self.getInputFromPort('Fs')
+ kwargs['Fs'] = val
+ if self.hasInputFromPort('pad_to'):
+ val = self.getInputFromPort('pad_to')
+ kwargs['pad_to'] = val
+ if self.hasInputFromPort('scale_by_freq'):
+ val = self.getInputFromPort('scale_by_freq')
+ kwargs['scale_by_freq'] = val
+ if self.hasInputFromPort('xextent'):
+ val = self.getInputFromPort('xextent')
+ kwargs['xextent'] = val
+ if self.hasInputFromPort('detrend'):
+ val = self.getInputFromPort('detrend')
+ kwargs['detrend'] = val
+ if self.hasInputFromPort('window'):
+ val = self.getInputFromPort('window')
+ kwargs['window'] = val
+ if self.hasInputFromPort('Fc'):
+ val = self.getInputFromPort('Fc')
+ kwargs['Fc'] = val
+ if self.hasInputFromPort('NFFT'):
+ val = self.getInputFromPort('NFFT')
+ kwargs['NFFT'] = val
+ if self.hasInputFromPort('cmap'):
+ val = self.getInputFromPort('cmap')
+ kwargs['cmap'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('sides'):
+ val = self.getInputFromPort('sides')
+ kwargs['sides'] = val
+ if self.hasInputFromPort('noverlap'):
+ val = self.getInputFromPort('noverlap')
+ kwargs['noverlap'] = val
+
+ matplotlib.pyplot.specgram(*args, **kwargs)
+
+class MplStackplot(MplPlot):
+ """Draws a stacked area plot.
+
+x : 1d array of dimension N
+
+Keyword arguments:
+
+Returns r : A list of :class:`~matplotlib.collections.PolyCollection`, one for each element in the stacked area plot.
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("x", "basic:String",
+ {}),
+ ("colors", "basic:Color",
+ {'optional': True, 'docstring': 'used to colour the stacked areas. All other keyword arguments are passed to :func:`~matplotlib.Axes.fill_between`'}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplStackplot)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('colors'):
+ val = self.getInputFromPort('colors')
+ val = translate_color(val)
+ kwargs['colors'] = val
+
+ matplotlib.pyplot.stackplot(*args, **kwargs)
+
+class MplStem(MplPlot):
+ """Create a stem plot.
+
+Call signature:
+
+stem(x, y, linefmt='b-', markerfmt='bo', basefmt='r-')
+
+A stem plot plots vertical lines (using linefmt) at each x location from the baseline to y, and places a marker there using markerfmt. A horizontal line at 0 is is plotted using basefmt.
+
+Return value is a tuple (markerline, stemlines, baseline).
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("bottom", "basic:String",
+ {'optional': True}),
+ ("label", "basic:String",
+ {'optional': True}),
+ ("linefmt", "basic:String",
+ {'optional': True, 'defaults': "['b-']"}),
+ ("markerfmt", "basic:String",
+ {'optional': True, 'defaults': "['bo']"}),
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("basefmt", "basic:String",
+ {'optional': True, 'defaults': "['r-']"}),
+ ("stemlineProperties", "MplLine2DProperties",
+ {}),
+ ("markerlineProperties", "MplLine2DProperties",
+ {}),
+ ("baselineProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplStem)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('bottom'):
+ val = self.getInputFromPort('bottom')
+ kwargs['bottom'] = val
+ if self.hasInputFromPort('label'):
+ val = self.getInputFromPort('label')
+ kwargs['label'] = val
+ if self.hasInputFromPort('linefmt'):
+ val = self.getInputFromPort('linefmt')
+ kwargs['linefmt'] = val
+ if self.hasInputFromPort('markerfmt'):
+ val = self.getInputFromPort('markerfmt')
+ kwargs['markerfmt'] = val
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('basefmt'):
+ val = self.getInputFromPort('basefmt')
+ kwargs['basefmt'] = val
+
+ output = matplotlib.pyplot.stem(*args, **kwargs)
+ markerline = output[0]
+ stemlines = output[1]
+ baseline = output[2]
+ if self.hasInputFromPort('stemlineProperties'):
+ properties = self.getInputFromPort('stemlineProperties')
+ if stemlines is not None:
+ properties.update_props(stemlines)
+ if self.hasInputFromPort('markerlineProperties'):
+ properties = self.getInputFromPort('markerlineProperties')
+ if markerline is not None:
+ properties.update_props(markerline)
+ if self.hasInputFromPort('baselineProperties'):
+ properties = self.getInputFromPort('baselineProperties')
+ if baseline is not None:
+ properties.update_props(baseline)
+
+class MplStep(MplPlot):
+ """Make a step plot.
+
+Call signature:
+
+step(x, y, *args, **kwargs)
+
+Additional keyword args to :func:`step` are the same as those for :func:`~matplotlib.pyplot.plot`.
+
+x and y must be 1-D sequences, and it is assumed, but not checked, that x is uniformly increasing.
+
+Keyword arguments:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("where", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If 'pre', the interval from x[i] to x[i+1] has level y[i+1]\n\nIf 'post', that interval has level y[i]\n\nIf 'mid', the jumps in y occur half-way between the x-values.", 'values': "[['pre', 'post', 'mid']]", 'optional': True}),
+ ("lineProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplStep)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ val = self.getInputFromPort('x')
+ args.append(val)
+ val = self.getInputFromPort('y')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('where'):
+ val = self.getInputFromPort('where')
+ kwargs['where'] = val
+
+ lines = matplotlib.pyplot.step(*args, **kwargs)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if lines is not None:
+ properties.update_props(lines)
+
+class MplStreamplot(MplPlot):
+ """Draws streamlines of a vector flow.
+
+Returns:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("arrowstyle", "basic:String",
+ {'optional': True, 'defaults': "['-|>']"}),
+ ("density", "basic:Integer",
+ {'optional': True, 'defaults': "['1']"}),
+ ("color", "basic:String",
+ {'optional': True}),
+ ("minlength", "basic:Float",
+ {'optional': True, 'defaults': "['0.1']"}),
+ ("transform", "basic:String",
+ {'optional': True}),
+ ("arrowsize", "basic:Integer",
+ {'optional': True, 'defaults': "['1']"}),
+ ("cmap", "basic:String",
+ {'optional': True}),
+ ("u", "basic:String",
+ {}),
+ ("v", "basic:String",
+ {}),
+ ("y", "basic:String",
+ {}),
+ ("x", "basic:String",
+ {}),
+ ("linewidth", "basic:String",
+ {'optional': True}),
+ ("norm", "basic:String",
+ {'optional': True}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplStreamplot)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('arrowstyle'):
+ val = self.getInputFromPort('arrowstyle')
+ kwargs['arrowstyle'] = val
+ if self.hasInputFromPort('density'):
+ val = self.getInputFromPort('density')
+ kwargs['density'] = val
+ if self.hasInputFromPort('color'):
+ val = self.getInputFromPort('color')
+ kwargs['color'] = val
+ if self.hasInputFromPort('minlength'):
+ val = self.getInputFromPort('minlength')
+ kwargs['minlength'] = val
+ if self.hasInputFromPort('transform'):
+ val = self.getInputFromPort('transform')
+ kwargs['transform'] = val
+ if self.hasInputFromPort('arrowsize'):
+ val = self.getInputFromPort('arrowsize')
+ kwargs['arrowsize'] = val
+ if self.hasInputFromPort('cmap'):
+ val = self.getInputFromPort('cmap')
+ kwargs['cmap'] = val
+ val = self.getInputFromPort('u')
+ kwargs['u'] = val
+ val = self.getInputFromPort('v')
+ kwargs['v'] = val
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('linewidth'):
+ val = self.getInputFromPort('linewidth')
+ kwargs['linewidth'] = val
+ if self.hasInputFromPort('norm'):
+ val = self.getInputFromPort('norm')
+ kwargs['norm'] = val
+
+ matplotlib.pyplot.streamplot(*args, **kwargs)
+
+class MplTricontour(MplPlot):
+ """Draw contours on an unstructured triangular grid. :func:`~matplotlib.pyplot.tricontour` and :func:`~matplotlib.pyplot.tricontourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+The triangulation can be specified in one of two ways; either:
+
+tricontour(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+tricontour(x, y, ...) tricontour(x, y, triangles, ...) tricontour(x, y, triangles=triangles, ...) tricontour(x, y, mask=mask, ...) tricontour(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The remaining arguments may be:
+
+tricontour(..., Z)
+
+where Z is the array of values to contour, one per point in the triangulation. The level values are chosen automatically.
+
+tricontour(..., Z, N)
+
+contour N automatically-chosen levels.
+
+tricontour(..., Z, V)
+
+draw contour lines at the values specified in sequence V
+
+tricontourf(..., Z, V)
+
+fill the (len(V)-1) regions between the values in V
+
+tricontour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+C = tricontour(...) returns a :class:`~matplotlib.contour.TriContourSet` object.
+
+Optional keyword arguments:
+
+extent: [ None | (x0,x1,y0,y1) ]
+
+If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].
+
+This keyword is not active if X and Y are specified in the call to contour.
+
+tricontour-only keyword arguments:
+
+
+
+tricontourf-only keyword arguments:
+
+
+
+Note: tricontourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("origin", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.\n\nThis keyword is not active if X and Y are specified in the call to contour.", 'values': "[['', 'upper', 'lower', 'image']]", 'optional': True}),
+ ("linestyles", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If linestyles is None, the 'solid' is used.\n\nlinestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.\n\nIf contour is using a monochrome colormap and the contour level is less than 0, then the linestyle specified in contour.negative_linestyle in matplotlibrc will be used.", 'values': "[['', 's [...]
+ ("levelsSequence", "basic:List",
+ {'optional': True, 'docstring': 'A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]'}),
+ ("levelsScalar", "basic:Float",
+ {'docstring': 'A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]', 'optional': True}),
+ ("linewidths", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.\n\nIf a number, all levels will be plotted with this linewidth.\n\nIf a tuple, different levels will be plotted with different linewidths in the order specified', 'values': "[['', 'number', 'tuple of numbers']]", 'optional': True}),
+ ("colors", "basic:Color",
+ {'entry_types': "['enum']", 'docstring': "If None, the colormap specified by cmap will be used.\n\nIf a string, like 'r' or 'red', all levels will be plotted in this color.\n\nIf a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified.", 'values': "[['', '(mpl_colors)']]", 'optional': True}),
+ ("cmap", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.', 'values': "[['', 'Colormap']]", 'optional': True}),
+ ("antialiased", "basic:Boolean",
+ {'optional': True, 'docstring': 'enable antialiasing'}),
+ ("nchunk", "basic:Integer",
+ {'entry_types': "['enum']", 'docstring': 'If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.', 'values': '[[0]]', 'optional': True}),
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'The alpha blending value'}),
+ ("norm", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.', 'values': "[['', 'Normalize']]", 'optional': True}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplTricontour)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('origin'):
+ val = self.getInputFromPort('origin')
+ kwargs['origin'] = val
+ if self.hasInputFromPort('linestyles'):
+ val = self.getInputFromPort('linestyles')
+ kwargs['linestyles'] = val
+ if self.hasInputFromPort('levelsSequence'):
+ val = self.getInputFromPort('levelsSequence')
+ kwargs['levels'] = val
+ elif self.hasInputFromPort('levelsScalar'):
+ val = self.getInputFromPort('levelsScalar')
+ kwargs['levels'] = val
+ if self.hasInputFromPort('linewidths'):
+ val = self.getInputFromPort('linewidths')
+ kwargs['linewidths'] = val
+ if self.hasInputFromPort('colors'):
+ val = self.getInputFromPort('colors')
+ val = translate_color(val)
+ kwargs['colors'] = val
+ if self.hasInputFromPort('cmap'):
+ val = self.getInputFromPort('cmap')
+ kwargs['cmap'] = val
+ if self.hasInputFromPort('antialiased'):
+ val = self.getInputFromPort('antialiased')
+ kwargs['antialiased'] = val
+ if self.hasInputFromPort('nchunk'):
+ val = self.getInputFromPort('nchunk')
+ kwargs['nchunk'] = val
+ if self.hasInputFromPort('alpha'):
+ val = self.getInputFromPort('alpha')
+ kwargs['alpha'] = val
+ if self.hasInputFromPort('norm'):
+ val = self.getInputFromPort('norm')
+ kwargs['norm'] = val
+
+ matplotlib.pyplot.tricontour(*args, **kwargs)
+
+class MplTricontourf(MplPlot):
+ """Draw contours on an unstructured triangular grid. :func:`~matplotlib.pyplot.tricontour` and :func:`~matplotlib.pyplot.tricontourf` draw contour lines and filled contours, respectively. Except as noted, function signatures and return values are the same for both versions.
+
+The triangulation can be specified in one of two ways; either:
+
+tricontour(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+tricontour(x, y, ...) tricontour(x, y, triangles, ...) tricontour(x, y, triangles=triangles, ...) tricontour(x, y, mask=mask, ...) tricontour(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The remaining arguments may be:
+
+tricontour(..., Z)
+
+where Z is the array of values to contour, one per point in the triangulation. The level values are chosen automatically.
+
+tricontour(..., Z, N)
+
+contour N automatically-chosen levels.
+
+tricontour(..., Z, V)
+
+draw contour lines at the values specified in sequence V
+
+tricontourf(..., Z, V)
+
+fill the (len(V)-1) regions between the values in V
+
+tricontour(Z, **kwargs)
+
+Use keyword args to control colors, linewidth, origin, cmap ... see below for more details.
+
+C = tricontour(...) returns a :class:`~matplotlib.contour.TriContourSet` object.
+
+Optional keyword arguments:
+
+extent: [ None | (x0,x1,y0,y1) ]
+
+If origin is not None, then extent is interpreted as in :func:`matplotlib.pyplot.imshow`: it gives the outer pixel boundaries. In this case, the position of Z[0,0] is the center of the pixel, not a corner. If origin is None, then (x0, y0) is the position of Z[0,0], and (x1, y1) is the position of Z[-1,-1].
+
+This keyword is not active if X and Y are specified in the call to contour.
+
+tricontour-only keyword arguments:
+
+
+
+tricontourf-only keyword arguments:
+
+
+
+Note: tricontourf fills intervals that are closed at the top; that is, for boundaries z1 and z2, the filled region is:
+
+z1 < z <= z2
+
+There is one exception: if the lowest boundary coincides with the minimum value of the z array, then that minimum value will be included in the lowest interval.
+
+Examples:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("origin", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If None, the first value of Z will correspond to the lower left corner, location (0,0). If 'image', the rc value for image.origin will be used.\n\nThis keyword is not active if X and Y are specified in the call to contour.", 'values': "[['', 'upper', 'lower', 'image']]", 'optional': True}),
+ ("linestyles", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "If linestyles is None, the 'solid' is used.\n\nlinestyles can also be an iterable of the above strings specifying a set of linestyles to be used. If this iterable is shorter than the number of contour levels it will be repeated as necessary.\n\nIf contour is using a monochrome colormap and the contour level is less than 0, then the linestyle specified in contour.negative_linestyle in matplotlibrc will be used.", 'values': "[['', 's [...]
+ ("levelsSequence", "basic:List",
+ {'optional': True, 'docstring': 'A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]'}),
+ ("levelsScalar", "basic:Float",
+ {'docstring': 'A list of floating point numbers indicating the level curves to draw; eg to draw just the zero contour pass levels=[0]', 'optional': True}),
+ ("linewidths", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If linewidths is None, the default width in lines.linewidth in matplotlibrc is used.\n\nIf a number, all levels will be plotted with this linewidth.\n\nIf a tuple, different levels will be plotted with different linewidths in the order specified', 'values': "[['', 'number', 'tuple of numbers']]", 'optional': True}),
+ ("colors", "basic:Color",
+ {'entry_types': "['enum']", 'docstring': "If None, the colormap specified by cmap will be used.\n\nIf a string, like 'r' or 'red', all levels will be plotted in this color.\n\nIf a tuple of matplotlib color args (string, float, rgb, etc), different levels will be plotted in different colors in the order specified.", 'values': "[['', '(mpl_colors)']]", 'optional': True}),
+ ("cmap", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'A cm :class:`~matplotlib.colors.Colormap` instance or None. If cmap is None and colors is None, a default Colormap is used.', 'values': "[['', 'Colormap']]", 'optional': True}),
+ ("antialiased", "basic:Boolean",
+ {'optional': True, 'docstring': 'enable antialiasing'}),
+ ("nchunk", "basic:Integer",
+ {'entry_types': "['enum']", 'docstring': 'If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of roughly nchunk by nchunk points. This may never actually be advantageous, so this option may be removed. Chunking introduces artifacts at the chunk boundaries unless antialiased is False.', 'values': '[[0]]', 'optional': True}),
+ ("alpha", "basic:Float",
+ {'optional': True, 'docstring': 'The alpha blending value'}),
+ ("norm", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'A :class:`matplotlib.colors.Normalize` instance for scaling data values to colors. If norm is None and colors is None, the default linear scaling is used.', 'values': "[['', 'Normalize']]", 'optional': True}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplTricontourf)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('origin'):
+ val = self.getInputFromPort('origin')
+ kwargs['origin'] = val
+ if self.hasInputFromPort('linestyles'):
+ val = self.getInputFromPort('linestyles')
+ kwargs['linestyles'] = val
+ if self.hasInputFromPort('levelsSequence'):
+ val = self.getInputFromPort('levelsSequence')
+ kwargs['levels'] = val
+ elif self.hasInputFromPort('levelsScalar'):
+ val = self.getInputFromPort('levelsScalar')
+ kwargs['levels'] = val
+ if self.hasInputFromPort('linewidths'):
+ val = self.getInputFromPort('linewidths')
+ kwargs['linewidths'] = val
+ if self.hasInputFromPort('colors'):
+ val = self.getInputFromPort('colors')
+ val = translate_color(val)
+ kwargs['colors'] = val
+ if self.hasInputFromPort('cmap'):
+ val = self.getInputFromPort('cmap')
+ kwargs['cmap'] = val
+ if self.hasInputFromPort('antialiased'):
+ val = self.getInputFromPort('antialiased')
+ kwargs['antialiased'] = val
+ if self.hasInputFromPort('nchunk'):
+ val = self.getInputFromPort('nchunk')
+ kwargs['nchunk'] = val
+ if self.hasInputFromPort('alpha'):
+ val = self.getInputFromPort('alpha')
+ kwargs['alpha'] = val
+ if self.hasInputFromPort('norm'):
+ val = self.getInputFromPort('norm')
+ kwargs['norm'] = val
+
+ matplotlib.pyplot.tricontourf(*args, **kwargs)
+
+class MplTripcolor(MplPlot):
+ """Create a pseudocolor plot of an unstructured triangular grid.
+
+The triangulation can be specified in one of two ways; either:
+
+tripcolor(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+tripcolor(x, y, ...) tripcolor(x, y, triangles, ...) tripcolor(x, y, triangles=triangles, ...) tripcolor(x, y, mask=mask, ...) tripcolor(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The next argument must be C, the array of color values, either one per point in the triangulation if color values are defined at points, or one per triangle in the triangulation if color values are defined at triangles. If there are the same number of points and triangles in the triangulation it is assumed that color values are defined at points; to force the use of color values at triangles use the kwarg facecolors*=C instead of just *C.
+
+shading may be 'flat' (the default) or 'gouraud'. If shading is 'flat' and C values are defined at points, the color values used for each triangle are from the mean C of the triangle's three points. If shading is 'gouraud' then color values must be defined at points. shading of 'faceted' is deprecated; please use edgecolors instead.
+
+The remaining kwargs are the same as for :meth:`~matplotlib.axes.Axes.pcolor`.
+
+Example:
+
+
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ]
+
+ _output_ports = [
+ ("self", "(MplTripcolor)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+
+ matplotlib.pyplot.tripcolor(*args, **kwargs)
+
+class MplTriplot(MplPlot):
+ """Draw a unstructured triangular grid as lines and/or markers.
+
+The triangulation to plot can be specified in one of two ways; either:
+
+triplot(triangulation, ...)
+
+where triangulation is a :class:`~matplotlib.tri.Triangulation` object, or
+
+triplot(x, y, ...) triplot(x, y, triangles, ...) triplot(x, y, triangles=triangles, ...) triplot(x, y, mask=mask, ...) triplot(x, y, triangles, mask=mask, ...)
+
+in which case a Triangulation object will be created. See :class:`~matplotlib.tri.Triangulation` for a explanation of these possibilities.
+
+The remaining args and kwargs are the same as for :meth:`~matplotlib.axes.Axes.plot`.
+
+Example:
+
+
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ]
+
+ _output_ports = [
+ ("self", "(MplTriplot)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+
+ matplotlib.pyplot.triplot(*args, **kwargs)
+
+class MplVlines(MplPlot):
+ """Plot vertical lines.
+
+Call signature:
+
+vlines(x, ymin, ymax, color='k', linestyles='solid')
+
+Plot vertical lines at each x from ymin to ymax. ymin or ymax can be scalars or len(x) numpy arrays. If they are scalars, then the respective values are constant, else the heights of the lines are determined by ymin and ymax.
+
+linestyles : [ 'solid' | 'dashed' | 'dashdot' | 'dotted' ]
+
+Returns the :class:`matplotlib.collections.LineCollection` that was added.
+
+kwargs are :class:`~matplotlib.collections.LineCollection` properties:
+
+%(LineCollection)s
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("ymax", "basic:String",
+ {}),
+ ("linestyles", "basic:String",
+ {'optional': True, 'defaults': "['solid']"}),
+ ("color", "basic:String",
+ {'optional': True, 'defaults': "['k']"}),
+ ("label", "basic:String",
+ {'optional': True, 'defaults': "['']"}),
+ ("colors", "basic:String",
+ {'optional': True, 'defaults': "['k']"}),
+ ("x", "basic:List",
+ {}),
+ ("ymin", "basic:String",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplVlines)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ val = self.getInputFromPort('ymax')
+ kwargs['ymax'] = val
+ if self.hasInputFromPort('linestyles'):
+ val = self.getInputFromPort('linestyles')
+ kwargs['linestyles'] = val
+ if self.hasInputFromPort('color'):
+ val = self.getInputFromPort('color')
+ kwargs['color'] = val
+ if self.hasInputFromPort('label'):
+ val = self.getInputFromPort('label')
+ kwargs['label'] = val
+ if self.hasInputFromPort('colors'):
+ val = self.getInputFromPort('colors')
+ kwargs['colors'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ val = self.getInputFromPort('ymin')
+ kwargs['ymin'] = val
+
+ matplotlib.pyplot.vlines(*args, **kwargs)
+
+class MplXcorr(MplPlot):
+ """Plot the cross correlation between x and y.
+
+Call signature:
+
+xcorr(self, x, y, normed=True, detrend=mlab.detrend_none, usevlines=True, maxlags=10, **kwargs)
+
+If normed = True, normalize the data by the cross correlation at 0-th lag. x and y are detrended by the detrend callable (default no normalization). x and y must be equal length.
+
+Data are plotted as plot(lags, c, **kwargs)
+
+Return value is a tuple (lags, c, line) where:
+
+lags are a length 2*maxlags+1 lag vector
+
+c is the 2*maxlags+1 auto correlation vector
+
+The default linestyle is None and the default marker is 'o', though these can be overridden with keyword args. The cross correlation is performed with :func:`numpy.correlate` with mode = 2.
+
+If usevlines is True:
+
+:func:`~matplotlib.pyplot.vlines` rather than :func:`~matplotlib.pyplot.plot` is used to draw vertical lines from the origin to the xcorr. Otherwise the plotstyle is determined by the kwargs, which are :class:`~matplotlib.lines.Line2D` properties.
+
+The return value is a tuple (lags, c, linecol, b) where linecol is the :class:`matplotlib.collections.LineCollection` instance and b is the x-axis.
+
+maxlags is a positive integer detailing the number of lags to show. The default value of None will return all (2*len(x)-1) lags.
+
+Example:
+
+:func:`~matplotlib.pyplot.xcorr` is top graph, and :func:`~matplotlib.pyplot.acorr` is bottom graph.
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("normed", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("usevlines", "basic:Boolean",
+ {'optional': True, 'defaults': "['True']"}),
+ ("detrend", "basic:String",
+ {'optional': True, 'defaults': "['<function detrend_none at 0x02F5A3F0>']"}),
+ ("maxlags", "basic:Integer",
+ {'optional': True, 'defaults': "['10']"}),
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {}),
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("lineCollectionProperties", "MplLineCollectionProperties",
+ {}),
+ ("lineProperties", "MplLine2DProperties",
+ {}),
+ ("xaxisProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplXcorr)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('normed'):
+ val = self.getInputFromPort('normed')
+ kwargs['normed'] = val
+ if self.hasInputFromPort('usevlines'):
+ val = self.getInputFromPort('usevlines')
+ kwargs['usevlines'] = val
+ if self.hasInputFromPort('detrend'):
+ val = self.getInputFromPort('detrend')
+ kwargs['detrend'] = val
+ if self.hasInputFromPort('maxlags'):
+ val = self.getInputFromPort('maxlags')
+ kwargs['maxlags'] = val
+ val = self.getInputFromPort('y')
+ kwargs['y'] = val
+ val = self.getInputFromPort('x')
+ kwargs['x'] = val
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+
+ output = matplotlib.pyplot.xcorr(*args, **kwargs)
+ if 'usevlines' in kwargs and kwargs['usevlines']:
+ output = output + (output[2],)
+ else:
+ output = output + (None, None)
+ lines = output[2]
+ xaxis = output[3]
+ lineCollection = output[4]
+ if self.hasInputFromPort('lineCollectionProperties'):
+ properties = self.getInputFromPort('lineCollectionProperties')
+ if lineCollection is not None:
+ properties.update_props(lineCollection)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if lines is not None:
+ properties.update_props(lines)
+ if self.hasInputFromPort('xaxisProperties'):
+ properties = self.getInputFromPort('xaxisProperties')
+ if xaxis is not None:
+ properties.update_props(xaxis)
+
+class MplBarbs(MplPlot):
+ """Plot a 2-D field of barbs.
+
+Call signatures:
+
+barb(U, V, **kw) barb(U, V, C, **kw) barb(X, Y, U, V, **kw) barb(X, Y, U, V, C, **kw)
+
+Arguments:
+
+
+
+All arguments may be 1-D or 2-D arrays or sequences. If X and Y are absent, they will be generated as a uniform grid. If U and V are 2-D arrays but X and Y are 1-D, and if len(X) and len(Y) match the column and row dimensions of U, then X and Y will be expanded with :func:`numpy.meshgrid`.
+
+U, V, C may be masked arrays, but masked X, Y are not supported at present.
+
+Keyword arguments:
+
+
+
+Barbs are traditionally used in meteorology as a way to plot the speed and direction of wind observations, but can technically be used to plot any two dimensional vector quantity. As opposed to arrows, which give vector magnitude by the length of the arrow, the barbs give more quantitative information about the vector magnitude by putting slanted lines or a triangle for various increments in magnitude, as show schematically below:
+
+: /\ \ : / \ \ : / \ \ \ : / \ \ \ : ------------------------------
+
+note the double \ at the end of each line to make the figure
+
+render correctly
+
+The largest increment is given by a triangle (or "flag"). After those come full lines (barbs). The smallest increment is a half line. There is only, of course, ever at most 1 half line. If the magnitude is small and only needs a single half-line and no full lines or triangles, the half-line is offset from the end of the barb so that it can be easily distinguished from barbs with a single full line. The magnitude for the barb shown above would nominally be 65, using the standard increm [...]
+
+linewidths and edgecolors can be used to customize the barb. Additional :class:`~matplotlib.collections.PolyCollection` keyword arguments:
+
+agg_filter: unknown alpha: float or None animated: [True | False] antialiased or antialiaseds: Boolean or sequence of booleans array: unknown axes: an :class:`~matplotlib.axes.Axes` instance clim: a length 2 sequence of floats clip_box: a :class:`matplotlib.transforms.Bbox` instance clip_on: [True | False] clip_path: [ (:class:`~matplotlib.path.Path`, :class:`~matplotlib.transforms.Transform`) | :class:`~matplotlib.patches.Patch` | None ] cmap: a colormap or registered co [...]
+
+Example:
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("barbcolor", "basic:Color",
+ {'optional': True, 'docstring': 'Specifies the color all parts of the barb except any flags. This parameter is analagous to the edgecolor parameter for polygons, which can be used instead. However this parameter will override facecolor.'}),
+ ("barbcolorSequence", "basic:List",
+ {'docstring': 'Specifies the color all parts of the barb except any flags. This parameter is analagous to the edgecolor parameter for polygons, which can be used instead. However this parameter will override facecolor.', 'optional': True}),
+ ("C", "basic:List",
+ {'optional': True, 'docstring': 'An optional array used to map colors to the barbs'}),
+ ("sizes", "basic:Dictionary",
+ {'optional': True, 'docstring': "A dictionary of coefficients specifying the ratio of a given feature to the length of the barb. Only those values one wishes to override need to be included. These features include:\n\n'spacing' - space between features (flags, full/half barbs)\n\n'height' - height (distance from shaft to top) of a flag or full barb\n\n'width' - width of a flag, twice the width of a full barb\n\n'emptybarb' - radius of the circle used for low magnitudes"}),
+ ("rounding", "basic:Boolean",
+ {'optional': True, 'docstring': 'A flag to indicate whether the vector magnitude should be rounded when allocating barb components. If True, the magnitude is rounded to the nearest multiple of the half-barb increment. If False, the magnitude is simply truncated to the next lowest multiple. Default is True', 'defaults': "['True']"}),
+ ("pivot", "basic:String",
+ {'entry_types': "['enum']", 'docstring': "The part of the arrow that is at the grid point; the arrow rotates about this point, hence the name pivot. Default is 'tip'", 'values': "[['tip', 'middle']]", 'optional': True, 'defaults': "['tip']"}),
+ ("flip_barb", "basic:Boolean",
+ {'optional': True, 'docstring': 'Either a single boolean flag or an array of booleans. Single boolean indicates whether the lines and flags should point opposite to normal for all barbs. An array (which should be the same size as the other data arrays) indicates whether to flip for each individual barb. Normal behavior is for the barbs and lines to point right (comes from wind barbs having these features point towards low pressure in the Northern Hemisphere.) Default i [...]
+ ("flip_barbSequence", "basic:List",
+ {'docstring': 'Either a single boolean flag or an array of booleans. Single boolean indicates whether the lines and flags should point opposite to normal for all barbs. An array (which should be the same size as the other data arrays) indicates whether to flip for each individual barb. Normal behavior is for the barbs and lines to point right (comes from wind barbs having these features point towards low pressure in the Northern Hemisphere.) Default is False', 'optiona [...]
+ ("length", "basic:Integer",
+ {'optional': True, 'docstring': 'Length of the barb in points; the other parts of the barb are scaled against this. Default is 9', 'defaults': "['9']"}),
+ ("barb_increments", "basic:Dictionary",
+ {'optional': True, 'docstring': "A dictionary of increments specifying values to associate with different parts of the barb. Only those values one wishes to override need to be included.\n\n'half' - half barbs (Default is 5)\n\n'full' - full barbs (Default is 10)\n\n'flag' - flags (default is 50)"}),
+ ("U", "basic:List",
+ {'docstring': 'Give the x and y components of the barb shaft'}),
+ ("V", "basic:List",
+ {'docstring': 'Give the x and y components of the barb shaft'}),
+ ("Y", "basic:List",
+ {'optional': True, 'docstring': 'The x and y coordinates of the barb locations (default is head of barb; see pivot kwarg)'}),
+ ("X", "basic:List",
+ {'optional': True, 'docstring': 'The x and y coordinates of the barb locations (default is head of barb; see pivot kwarg)'}),
+ ("flagcolor", "basic:Color",
+ {'optional': True, 'docstring': 'Specifies the color of any flags on the barb. This parameter is analagous to the facecolor parameter for polygons, which can be used instead. However this parameter will override facecolor. If this is not set (and C has not either) then flagcolor will be set to match barbcolor so that the barb has a uniform color. If C has been set, flagcolor has no effect.'}),
+ ("flagcolorSequence", "basic:List",
+ {'docstring': 'Specifies the color of any flags on the barb. This parameter is analagous to the facecolor parameter for polygons, which can be used instead. However this parameter will override facecolor. If this is not set (and C has not either) then flagcolor will be set to match barbcolor so that the barb has a uniform color. If C has been set, flagcolor has no effect.', 'optional': True}),
+ ("fill_empty", "basic:Boolean",
+ {'optional': True, 'docstring': 'A flag on whether the empty barbs (circles) that are drawn should be filled with the flag color. If they are not filled, they will be drawn such that no color is applied to the center. Default is False', 'defaults': "['False']"}),
+ ("polyCollectionProperties", "MplPolyCollectionProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplBarbs)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ if self.hasInputFromPort('X'):
+ val = self.getInputFromPort('X')
+ args.append(val)
+ if self.hasInputFromPort('Y'):
+ val = self.getInputFromPort('Y')
+ args.append(val)
+ val = self.getInputFromPort('U')
+ args.append(val)
+ val = self.getInputFromPort('V')
+ args.append(val)
+ if self.hasInputFromPort('C'):
+ val = self.getInputFromPort('C')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('barbcolor'):
+ val = self.getInputFromPort('barbcolor')
+ val = translate_color(val)
+ kwargs['barbcolor'] = val
+ elif self.hasInputFromPort('barbcolorSequence'):
+ val = self.getInputFromPort('barbcolorSequence')
+ kwargs['barbcolor'] = val
+ if self.hasInputFromPort('sizes'):
+ val = self.getInputFromPort('sizes')
+ kwargs['sizes'] = val
+ if self.hasInputFromPort('rounding'):
+ val = self.getInputFromPort('rounding')
+ kwargs['rounding'] = val
+ if self.hasInputFromPort('pivot'):
+ val = self.getInputFromPort('pivot')
+ kwargs['pivot'] = val
+ if self.hasInputFromPort('flip_barb'):
+ val = self.getInputFromPort('flip_barb')
+ kwargs['flip_barb'] = val
+ elif self.hasInputFromPort('flip_barbSequence'):
+ val = self.getInputFromPort('flip_barbSequence')
+ kwargs['flip_barb'] = val
+ if self.hasInputFromPort('length'):
+ val = self.getInputFromPort('length')
+ kwargs['length'] = val
+ if self.hasInputFromPort('barb_increments'):
+ val = self.getInputFromPort('barb_increments')
+ kwargs['barb_increments'] = val
+ if self.hasInputFromPort('flagcolor'):
+ val = self.getInputFromPort('flagcolor')
+ val = translate_color(val)
+ kwargs['flagcolor'] = val
+ elif self.hasInputFromPort('flagcolorSequence'):
+ val = self.getInputFromPort('flagcolorSequence')
+ kwargs['flagcolor'] = val
+ if self.hasInputFromPort('fill_empty'):
+ val = self.getInputFromPort('fill_empty')
+ kwargs['fill_empty'] = val
+
+ polyCollection = matplotlib.pyplot.barbs(*args, **kwargs)
+ if self.hasInputFromPort('polyCollectionProperties'):
+ properties = self.getInputFromPort('polyCollectionProperties')
+ if polyCollection is not None:
+ properties.update_props(polyCollection)
+
+class MplSpy(MplPlot):
+ """Plot the sparsity pattern on a 2-D array.
+
+Call signature:
+
+spy(Z, precision=0, marker=None, markersize=None, aspect='equal', **kwargs)
+
+spy(Z) plots the sparsity pattern of the 2-D array Z.
+
+If precision is 0, any non-zero value will be plotted; else, values of |Z| > precision will be plotted.
+
+For :class:`scipy.sparse.spmatrix` instances, there is a special case: if precision is 'present', any value present in the array will be plotted, even if it is identically zero.
+
+The array will be plotted as it would be printed, with the first index (row) increasing down and the second index (column) increasing to the right.
+
+By default aspect is 'equal', so that each array element occupies a square space; set the aspect kwarg to 'auto' to allow the plot to fill the plot box, or to any scalar number to specify the aspect ratio of an array element directly.
+
+Two plotting styles are available: image or marker. Both are available for full arrays, but only the marker style works for :class:`scipy.sparse.spmatrix` instances.
+
+If marker and markersize are None, an image will be returned and any remaining kwargs are passed to :func:`~matplotlib.pyplot.imshow`; else, a :class:`~matplotlib.lines.Line2D` object will be returned with the value of marker determining the marker type, and any remaining kwargs passed to the :meth:`~matplotlib.axes.Axes.plot` method.
+
+If marker and markersize are None, useful kwargs include:
+
+cmap
+
+alpha
+
+For controlling colors, e.g. cyan background and red marks, use:
+
+cmap = mcolors.ListedColormap(['c','r'])
+
+If marker or markersize is not None, useful kwargs include:
+
+marker
+
+markersize
+
+color
+
+Useful values for marker include:
+
+'s' square (default)
+
+'o' circle
+
+'.' point
+
+',' pixel
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("hold", "basic:String",
+ {'optional': True}),
+ ("markersize", "basic:String",
+ {'optional': True}),
+ ("precision", "basic:Integer",
+ {'optional': True, 'defaults': "['0']"}),
+ ("aspect", "basic:String",
+ {'optional': True, 'defaults': "['equal']"}),
+ ("marker", "basic:String",
+ {'optional': True}),
+ ("Z", "basic:List",
+ {}),
+ ("imageProperties", "MplAxesImageProperties",
+ {}),
+ ("marksProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplSpy)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('hold'):
+ val = self.getInputFromPort('hold')
+ kwargs['hold'] = val
+ if self.hasInputFromPort('markersize'):
+ val = self.getInputFromPort('markersize')
+ kwargs['markersize'] = val
+ if self.hasInputFromPort('precision'):
+ val = self.getInputFromPort('precision')
+ kwargs['precision'] = val
+ if self.hasInputFromPort('aspect'):
+ val = self.getInputFromPort('aspect')
+ kwargs['aspect'] = val
+ if self.hasInputFromPort('marker'):
+ val = self.getInputFromPort('marker')
+ kwargs['marker'] = val
+ val = self.getInputFromPort('Z')
+ kwargs['Z'] = val
+
+ output = matplotlib.pyplot.spy(*args, **kwargs)
+ if "marker" not in kwargs and "markersize" not in kwargs and \
+ not hasattr(kwargs["Z"], 'tocoo'):
+ output = (output, None)
+ else:
+ output = (None, output)
+ image = output[0]
+ marks = output[1]
+ if self.hasInputFromPort('imageProperties'):
+ properties = self.getInputFromPort('imageProperties')
+ if image is not None:
+ properties.update_props(image)
+ if self.hasInputFromPort('marksProperties'):
+ properties = self.getInputFromPort('marksProperties')
+ if marks is not None:
+ properties.update_props(marks)
+
+class MplPolar(MplPlot):
+ """Make a polar plot.
+
+call signature:
+
+polar(theta, r, **kwargs)
+
+Multiple theta, r arguments are supported, with format strings, as in :func:`~matplotlib.pyplot.plot`.
+ """
+ _input_ports = [
+ ("theta", "basic:List",
+ {}),
+ ("r", "basic:List",
+ {}),
+ ("lineProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplPolar)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ val = self.getInputFromPort('theta')
+ args.append(val)
+ val = self.getInputFromPort('r')
+ args.append(val)
+
+ kwargs = {}
+
+ lines = matplotlib.pyplot.polar(*args, **kwargs)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if lines is not None:
+ properties.update_props(lines)
+
+class MplLegend(MplPlot):
+ """Place a legend on the current axes.
+
+Call signature:
+
+legend(*args, **kwargs)
+
+Places legend at location loc. Labels are a sequence of strings and loc can be a string or an integer specifying the legend location.
+
+To make a legend with existing lines:
+
+legend()
+
+:meth:`legend` by itself will try and build a legend using the label property of the lines/patches/collections. You can set the label of a line by doing:
+
+plot(x, y, label='my data')
+
+or:
+
+line.set_label('my data').
+
+If label is set to '_nolegend_', the item will not be shown in legend.
+
+To automatically generate the legend from labels:
+
+legend( ('label1', 'label2', 'label3') )
+
+To make a legend for a list of lines and labels:
+
+legend( (line1, line2, line3), ('label1', 'label2', 'label3') )
+
+To make a legend at a given location, using a location argument:
+
+legend( ('label1', 'label2', 'label3'), loc='upper left')
+
+or:
+
+legend( (line1, line2, line3), ('label1', 'label2', 'label3'), loc=2)
+
+The location codes are
+
+
+
+Users can specify any arbitrary location for the legend using the bbox_to_anchor keyword argument. bbox_to_anchor can be an instance of BboxBase(or its derivatives) or a tuple of 2 or 4 floats. For example,
+
+loc = 'upper right', bbox_to_anchor = (0.5, 0.5)
+
+will place the legend so that the upper right corner of the legend at the center of the axes.
+
+The legend location can be specified in other coordinate, by using the bbox_transform keyword.
+
+The loc itslef can be a 2-tuple giving x,y of the lower-left corner of the legend in axes coords (bbox_to_anchor is ignored).
+
+Keyword arguments:
+
+fontsize: [ size in points | 'xx-small' | 'x-small' | 'small' | 'medium' | 'large' | 'x-large' | 'xx-large' ]
+
+Set the font size. May be either a size string, relative to the default font size, or an absolute font size in points. This argument is only used if prop is not specified.
+
+Padding and spacing between various elements use following keywords parameters. These values are measure in font-size units. E.g., a fontsize of 10 points and a handlelength=5 implies a handlelength of 50 points. Values from rcParams will be used if None.
+
+Not all kinds of artist are supported by the legend command. See LINK (FIXME) for details.
+
+Example:
+ """
+ _input_ports = [
+ ("loc", "basic:String",
+ {'entry_types': "['enum']", 'values': "[['best', 'upper right', 'upper left', 'lower left', 'lower right', 'right', 'center left', 'center right', 'lower center', 'upper center', 'center']]", 'optional': True}),
+ ("fancybox", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'if True, draw a frame with a round fancybox. If None, use rc settings', 'values': "[['']]", 'optional': True}),
+ ("bbox_to_anchor", "basic:String",
+ {'optional': True, 'docstring': 'the bbox that the legend will be anchored.'}),
+ ("title", "basic:String",
+ {'optional': True, 'docstring': 'the legend title'}),
+ ("handlelength", "basic:String",
+ {'optional': True, 'docstring': 'the length of the legend handles'}),
+ ("markerscale", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'The relative size of legend markers vs. original. If None, use rc settings.', 'values': "[['']]", 'optional': True}),
+ ("numpoints", "basic:Integer",
+ {'optional': True, 'docstring': 'The number of points in the legend for line'}),
+ ("labelspacing", "basic:String",
+ {'optional': True, 'docstring': 'the vertical space between the legend entries'}),
+ ("scatterpoints", "basic:Integer",
+ {'optional': True, 'docstring': 'The number of points in the legend for scatter plot'}),
+ ("frameon", "basic:Boolean",
+ {'optional': True, 'docstring': "if True, draw a frame around the legend. The default is set by the rcParam 'legend.frameon'"}),
+ ("columnspacing", "basic:String",
+ {'optional': True, 'docstring': 'the spacing between columns'}),
+ ("handletextpad", "basic:String",
+ {'optional': True, 'docstring': 'the pad between the legend handle and text'}),
+ ("scatteroffsetsSequence", "basic:List",
+ {'optional': True, 'docstring': 'a list of yoffsets for scatter symbols in legend'}),
+ ("scatteroffsetsScalar", "basic:Float",
+ {'docstring': 'a list of yoffsets for scatter symbols in legend', 'optional': True}),
+ ("mode", "basic:String",
+ {'optional': True, 'docstring': 'if mode is "expand", the legend will be horizontally expanded to fill the axes area (or bbox_to_anchor)'}),
+ ("ncol", "basic:Integer",
+ {'optional': True, 'docstring': 'number of columns. default is 1', 'defaults': "['1']"}),
+ ("shadow", "basic:String",
+ {'entry_types': "['enum']", 'docstring': 'If True, draw a shadow behind legend. If None, use rc settings.', 'values': "[['']]", 'optional': True}),
+ ("prop", "basic:String",
+ {'optional': True, 'docstring': 'A :class:`matplotlib.font_manager.FontProperties` instance. If prop is a dictionary, a new instance will be created with prop. If None, use rc settings.'}),
+ ("borderpad", "basic:String",
+ {'optional': True, 'docstring': 'the fractional whitespace inside the legend border'}),
+ ("bbox_transform", "basic:String",
+ {'optional': True, 'docstring': 'the transform for the bbox. transAxes if None.'}),
+ ("borderaxespad", "basic:String",
+ {'optional': True, 'docstring': 'the pad between the axes and legend border'}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplLegend)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('loc'):
+ val = self.getInputFromPort('loc')
+ val = translate_MplLegend_loc(val)
+ kwargs['loc'] = val
+ if self.hasInputFromPort('fancybox'):
+ val = self.getInputFromPort('fancybox')
+ kwargs['fancybox'] = val
+ if self.hasInputFromPort('bbox_to_anchor'):
+ val = self.getInputFromPort('bbox_to_anchor')
+ kwargs['bbox_to_anchor'] = val
+ if self.hasInputFromPort('title'):
+ val = self.getInputFromPort('title')
+ kwargs['title'] = val
+ if self.hasInputFromPort('handlelength'):
+ val = self.getInputFromPort('handlelength')
+ kwargs['handlelength'] = val
+ if self.hasInputFromPort('markerscale'):
+ val = self.getInputFromPort('markerscale')
+ kwargs['markerscale'] = val
+ if self.hasInputFromPort('numpoints'):
+ val = self.getInputFromPort('numpoints')
+ kwargs['numpoints'] = val
+ if self.hasInputFromPort('labelspacing'):
+ val = self.getInputFromPort('labelspacing')
+ kwargs['labelspacing'] = val
+ if self.hasInputFromPort('scatterpoints'):
+ val = self.getInputFromPort('scatterpoints')
+ kwargs['scatterpoints'] = val
+ if self.hasInputFromPort('frameon'):
+ val = self.getInputFromPort('frameon')
+ kwargs['frameon'] = val
+ if self.hasInputFromPort('columnspacing'):
+ val = self.getInputFromPort('columnspacing')
+ kwargs['columnspacing'] = val
+ if self.hasInputFromPort('handletextpad'):
+ val = self.getInputFromPort('handletextpad')
+ kwargs['handletextpad'] = val
+ if self.hasInputFromPort('scatteroffsetsSequence'):
+ val = self.getInputFromPort('scatteroffsetsSequence')
+ kwargs['scatteroffsets'] = val
+ elif self.hasInputFromPort('scatteroffsetsScalar'):
+ val = self.getInputFromPort('scatteroffsetsScalar')
+ kwargs['scatteroffsets'] = val
+ if self.hasInputFromPort('mode'):
+ val = self.getInputFromPort('mode')
+ kwargs['mode'] = val
+ if self.hasInputFromPort('ncol'):
+ val = self.getInputFromPort('ncol')
+ kwargs['ncol'] = val
+ if self.hasInputFromPort('shadow'):
+ val = self.getInputFromPort('shadow')
+ kwargs['shadow'] = val
+ if self.hasInputFromPort('prop'):
+ val = self.getInputFromPort('prop')
+ kwargs['prop'] = val
+ if self.hasInputFromPort('borderpad'):
+ val = self.getInputFromPort('borderpad')
+ kwargs['borderpad'] = val
+ if self.hasInputFromPort('bbox_transform'):
+ val = self.getInputFromPort('bbox_transform')
+ kwargs['bbox_transform'] = val
+ if self.hasInputFromPort('borderaxespad'):
+ val = self.getInputFromPort('borderaxespad')
+ kwargs['borderaxespad'] = val
+
+ matplotlib.pyplot.legend(*args, **kwargs)
+
+class MplAnnotate(MplPlot):
+ """Create an annotation: a piece of text referring to a data point.
+
+Call signature:
+
+annotate(s, xy, xytext=None, xycoords='data', textcoords='data', arrowprops=None, **kwargs)
+
+Keyword arguments:
+
+Annotate the x, y point xy with text s at x, y location xytext. (If xytext = None, defaults to xy, and if textcoords = None, defaults to xycoords).
+
+arrowprops, if not None, is a dictionary of line properties (see :class:`matplotlib.lines.Line2D`) for the arrow that connects annotation to the point.
+
+If the dictionary has a key arrowstyle, a FancyArrowPatch instance is created with the given dictionary and is drawn. Otherwise, a YAArow patch instance is created and drawn. Valid keys for YAArow are
+
+Valid keys for FancyArrowPatch are
+
+xycoords and textcoords are strings that indicate the coordinates of xy and xytext.
+
+If a 'points' or 'pixels' option is specified, values will be added to the bottom-left and if negative, values will be subtracted from the top-right. Eg:
+
+# 10 points to the right of the left border of the axes and # 5 points below the top border xy=(10,-5), xycoords='axes points'
+
+You may use an instance of :class:`~matplotlib.transforms.Transform` or :class:`~matplotlib.artist.Artist`. See :ref:`plotting-guide-annotation` for more details.
+
+The annotation_clip attribute contols the visibility of the annotation when it goes outside the axes area. If True, the annotation will only be drawn when the xy is inside the axes. If False, the annotation will always be drawn regardless of its position. The default is None, which behave as True only if xycoords is"data".
+
+Additional kwargs are Text properties:
+
+%(Text)s
+ """
+ _input_ports = [
+ ("xycoords", "basic:String",
+ {'entry_types': "['enum']", 'values': "[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]", 'optional': True}),
+ ("xytext", "basic:Float, basic:Float",
+ {'optional': True}),
+ ("s", "basic:String",
+ {}),
+ ("xy", "basic:Float, basic:Float",
+ {}),
+ ("textcoords", "basic:String",
+ {'entry_types': "['enum']", 'values': "[['figure points', 'figure pixels', 'figure fraction', 'axes points', 'axes pixels', 'axes fraction', 'data', 'offset points', 'polar']]", 'optional': True}),
+ ("fancyArrowProperties", "MplFancyArrowPatchProperties",
+ {'optional': True}),
+ ("arrowProperties", "MplYAArrowProperties",
+ {'optional': True}),
+ ("annotationProperties", "MplAnnotationProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplAnnotate)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+
+ kwargs = {}
+ if self.hasInputFromPort('xycoords'):
+ val = self.getInputFromPort('xycoords')
+ kwargs['xycoords'] = val
+ if self.hasInputFromPort('xytext'):
+ val = self.getInputFromPort('xytext')
+ kwargs['xytext'] = val
+ val = self.getInputFromPort('s')
+ kwargs['s'] = val
+ val = self.getInputFromPort('xy')
+ kwargs['xy'] = val
+ if self.hasInputFromPort('textcoords'):
+ val = self.getInputFromPort('textcoords')
+ kwargs['textcoords'] = val
+
+ if self.hasInputFromPort("fancyArrowProperties"):
+ kwargs['arrowprops'] = \
+ self.getInputFromPort("fancyArrowProperties").props
+ elif self.hasInputFromPort("arrowProperties"):
+ kwargs['arrowprops'] = \
+ self.getInputFromPort("arrowProperties").props
+ annotation = matplotlib.pyplot.annotate(*args, **kwargs)
+ if self.hasInputFromPort('annotationProperties'):
+ properties = self.getInputFromPort('annotationProperties')
+ if annotation is not None:
+ properties.update_props(annotation)
+
+class MplLinePlot(MplPlot):
+ """Plot lines and/or markers to the :class:`~matplotlib.axes.Axes`. args is a variable length argument, allowing for multiple x, y pairs with an optional format string. For example, each of the following is legal:
+
+plot(x, y) # plot x and y using default line style and color plot(x, y, 'bo') # plot x and y using blue circle markers plot(y) # plot y using x as index array 0..N-1 plot(y, 'r+') # ditto, but with red plusses
+
+If x and/or y is 2-dimensional, then the corresponding columns will be plotted.
+
+An arbitrary number of x, y, fmt groups can be specified, as in:
+
+a.plot(x1, y1, 'g^', x2, y2, 'g-')
+
+Return value is a list of lines that were added.
+
+By default, each line is assigned a different color specified by a 'color cycle'. To change this behavior, you can edit the axes.color_cycle rcParam. Alternatively, you can use :meth:`~matplotlib.axes.Axes.set_default_color_cycle`.
+
+The following format string characters are accepted to control the line style or marker:
+
+The following color abbreviations are supported:
+
+In addition, you can specify colors in many weird and wonderful ways, including full names ('green'), hex strings ('#008000'), RGB or RGBA tuples ((0,1,0,1)) or grayscale intensities as a string ('0.8'). Of these, the string specifications can be used in place of a fmt group, but the tuple forms can be used only as kwargs.
+
+Line styles and colors are combined in a single format string, as in 'bo' for blue circles.
+
+The kwargs can be used to set line properties (any property that has a set_* method). You can use this to set a line label (for auto legends), linewidth, anitialising, marker face color, etc. Here is an example:
+
+plot([1,2,3], [1,2,3], 'go-', label='line 1', linewidth=2) plot([1,2,3], [1,4,9], 'rs', label='line 2') axis([0, 4, 0, 10]) legend()
+
+If you make multiple lines with one plot command, the kwargs apply to all those lines, e.g.:
+
+plot(x1, y1, x2, y2, antialised=False)
+
+Neither line will be antialiased.
+
+You do not need to use format strings, which are just abbreviations. All of the line properties can be controlled by keyword arguments. For example, you can set the color, marker, linestyle, and markercolor with:
+
+plot(x, y, color='green', linestyle='dashed', marker='o', markerfacecolor='blue', markersize=12).
+
+See :class:`~matplotlib.lines.Line2D` for details.
+
+The kwargs are :class:`~matplotlib.lines.Line2D` properties:
+
+%(Line2D)s
+
+kwargs scalex and scaley, if defined, are passed on to :meth:`~matplotlib.axes.Axes.autoscale_view` to determine whether the x and y axes are autoscaled; the default is True.
+
+Additional kwargs: hold = [True|False] overrides default hold state
+ """
+ _input_ports = [
+ ("marker", "basic:String",
+ {'entry_types': "['enum']", 'values': "[['solid line style', 'dashed line style', 'dash-dot line style', 'dotted line style', 'point marker', 'pixel marker', 'circle marker', 'triangle_down marker', 'triangle_up marker', 'triangle_left marker', 'triangle_right marker', 'tri_down marker', 'tri_up marker', 'tri_left marker', 'tri_right marker', 'square marker', 'pentagon marker', 'star marker', 'hexagon1 marker', 'hexagon2 marker', 'plus marker', 'x marker', 'diamond marker' [...]
+ ("y", "basic:List",
+ {}),
+ ("x", "basic:List",
+ {'optional': True}),
+ ("lineProperties", "MplLine2DProperties",
+ {}),
+ ]
+
+ _output_ports = [
+ ("self", "(MplLinePlot)"),
+ ]
+
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ if self.hasInputFromPort('x'):
+ val = self.getInputFromPort('x')
+ args.append(val)
+ val = self.getInputFromPort('y')
+ args.append(val)
+
+ kwargs = {}
+ if self.hasInputFromPort('marker'):
+ val = self.getInputFromPort('marker')
+ val = translate_MplLinePlot_marker(val)
+ kwargs['marker'] = val
+
+ lines = matplotlib.pyplot.plot(*args, **kwargs)
+ if self.hasInputFromPort('lineProperties'):
+ properties = self.getInputFromPort('lineProperties')
+ if lines is not None:
+ properties.update_props(lines)
+
+
+_modules = [
+ MplAcorr,
+ MplArrow,
+ MplAxhline,
+ MplAxhspan,
+ MplAxvline,
+ MplAxvspan,
+ MplBar,
+ MplBarh,
+ MplBrokenBarh,
+ MplBoxplot,
+ MplCohere,
+ MplClabel,
+ MplContour,
+ MplContourf,
+ MplCsd,
+ MplErrorbar,
+ MplFill,
+ MplFillBetween,
+ MplFillBetweenx,
+ MplHexbin,
+ MplHist,
+ MplHist2d,
+ MplHlines,
+ MplImshow,
+ MplLoglog,
+ MplPcolor,
+ MplPcolormesh,
+ MplPie,
+ MplPlotDate,
+ MplPsd,
+ MplQuiver,
+ MplQuiverkey,
+ MplScatter,
+ MplSemilogx,
+ MplSemilogy,
+ MplSpecgram,
+ MplStackplot,
+ MplStem,
+ MplStep,
+ MplStreamplot,
+ MplTricontour,
+ MplTricontourf,
+ MplTripcolor,
+ MplTriplot,
+ MplVlines,
+ MplXcorr,
+ MplBarbs,
+ MplSpy,
+ MplPolar,
+ MplLegend,
+ MplAnnotate,
+ MplLinePlot,
+]
diff --git a/vistrails/packages/matplotlib/plots_template.py.mako b/vistrails/packages/matplotlib/plots_template.py.mako
new file mode 100644
index 0000000..0ca518e
--- /dev/null
+++ b/vistrails/packages/matplotlib/plots_template.py.mako
@@ -0,0 +1,210 @@
+import matplotlib.pyplot
+from vistrails.core.modules.vistrails_module import Module, ModuleError
+from bases import MplPlot
+
+<%def name="do_translate(t_spec, t_ps)">\
+% if type(t_ps.translations) == dict:
+val = translate_${t_spec.name}_${t_ps.name}(val)\
+% else:
+val = ${t_ps.translations}(val)\
+% endif
+</%def>
+
+<%def name="get_port_val(spec, t_ps)">\
+ % if t_ps.required:
+ % if t_ps.has_alternate_versions():
+ if self.hasInputFromPort('${t_ps.name}'):
+ val = self.getInputFromPort('${t_ps.name}')
+ % if t_ps.translations:
+ ${do_translate(spec, t_ps)}
+ % endif
+ % if t_ps.in_args:
+ args.append(val)
+ % elif t_ps.in_kwargs:
+ kwargs['${t_ps.arg}'] = val
+ % endif
+ % for alt_ps in t_ps.alternate_specs:
+ elif self.hasInputFromPort('${alt_ps.name}'):
+ val = self.getInputFromPort('${alt_ps.name}')
+ % if alt_ps.translations:
+ ${do_translate(spec, alt_ps)}
+ % endif
+ % if t_ps.in_args:
+ args.append(val)
+ % elif t_ps.in_kwargs:
+ kwargs['${t_ps.arg}'] = val
+ % endif
+ % endfor
+ else:
+ raise ModuleError(self, 'Must set one of "${t_ps.name}", ' \
+ '${', '.join('"%s"' % alt_ps.name for alt_ps in t_ps.alternate_specs)}')
+ % else:
+ val = self.getInputFromPort('${t_ps.name}')
+ % if t_ps.in_args:
+ args.append(val)
+ % elif t_ps.in_kwargs:
+ kwargs['${t_ps.arg}'] = val
+ % endif
+ % if t_ps.translations:
+ ${do_translate(spec, t_ps)}
+ % endif
+ % endif
+ % else:
+ if self.hasInputFromPort('${t_ps.name}'):
+ val = self.getInputFromPort('${t_ps.name}')
+ % if t_ps.translations:
+ ${do_translate(spec, t_ps)}
+ % endif
+ % if t_ps.in_args:
+ args.append(val)
+ % elif t_ps.in_kwargs:
+ kwargs['${t_ps.arg}'] = val
+ % endif
+ % for alt_ps in t_ps.alternate_specs:
+ elif self.hasInputFromPort('${alt_ps.name}'):
+ val = self.getInputFromPort('${alt_ps.name}')
+ % if alt_ps.translations:
+ ${do_translate(spec, alt_ps)}
+ % endif
+ % if t_ps.in_args:
+ args.append(val)
+ % elif t_ps.in_kwargs:
+ kwargs['${t_ps.arg}'] = val
+ % endif
+ % endfor
+ % endif
+</%def>
+
+def translate_color(c):
+ return c.tuple
+
+% for spec in specs.module_specs:
+% for ps in spec.port_specs:
+% if ps.translations and type(ps.translations) == dict:
+def translate_${spec.name}_${ps.name}(val):
+ translate_dict = ${ps.translations}
+ return translate_dict[val]
+% endif
+% endfor
+% endfor
+
+% for spec in specs.module_specs:
+class ${spec.name}(${spec.superklass}):
+ """${spec.docstring}
+ """
+ _input_ports = [
+ % for ps in spec.port_specs:
+ % if not ps.hide:
+ % if ps.is_property():
+ ("${ps.name}", "${ps.get_property_type()}",
+ ${ps.get_port_attrs()}),
+ % else:
+ ("${ps.name}", "${ps.get_port_type()}",
+ ${ps.get_port_attrs()}),
+ % endif
+ % for alt_ps in ps.alternate_specs:
+ ("${alt_ps.name}", "${alt_ps.get_port_type()}",
+ ${alt_ps.get_port_attrs()}),
+ % endfor
+ % endif
+ % endfor
+ % for ps in spec.output_port_specs:
+ % if ps.is_property():
+ ("${ps.name}", "${ps.get_property_type()}",
+ ${ps.get_port_attrs()}),
+ % endif
+ % endfor
+ ]
+
+ _output_ports = [
+ ("self", "(${spec.name})"),
+ % for ps in spec.output_port_specs:
+ % if not ps.is_property():
+ ("${ps.name}", "${ps.get_port_type()}",
+ ${ps.get_port_attrs()}),
+ % endif
+ % endfor
+ ]
+
+ % if spec.get_init():
+ ${spec.get_init()}
+ % endif
+
+ def compute(self):
+ # get args into args, kwargs
+ # write out translations
+ args = []
+ % for ps in spec.get_input_args():
+${get_port_val(spec, ps)}\
+ % endfor
+
+ kwargs = {}
+ % for ps in spec.port_specs:
+ % if ps.is_property():
+ if self.hasInputFromPort('${ps.name}'):
+ properties = self.getInputFromPort('${ps.name}')
+ properties.update_kwargs(kwargs)
+ % elif not ps.hide and not ps.in_args and ps.in_kwargs:
+${get_port_val(spec, ps)}\
+ % endif
+ % endfor
+
+ % if spec.get_compute_before():
+ ${spec.get_compute_before()}
+ % endif
+ % if spec.get_compute_inner():
+ ${spec.get_compute_inner()}
+ % elif spec.output_type is None:
+ ${spec.code_ref}(*args, **kwargs)
+ % elif spec.output_type == "object":
+ ${spec.get_returned_output_port_specs()[0].compute_name} = ${spec.code_ref}(*args, **kwargs)
+ % else:
+ output = ${spec.code_ref}(*args, **kwargs)
+ % endif
+ % if spec.get_compute_after():
+ ${spec.get_compute_after()}
+ % endif
+ % if spec.output_type == "dict":
+ % for ps in spec.get_returned_output_port_specs():
+ ${ps.compute_name} = output['${ps.property_key}']
+ % endfor
+ % elif spec.output_type == "tuple":
+ % for ps in sorted(spec.get_returned_output_port_specs(), \
+ key=lambda ps: ps.property_key):
+ ${ps.compute_name} = output[${ps.property_key}]
+ % endfor
+ % endif
+ % for ps in spec.output_port_specs:
+ % if ps.is_property():
+ if self.hasInputFromPort('${ps.name}'):
+ properties = self.getInputFromPort('${ps.name}')
+ % if ps.compute_parent:
+ % if spec.get_output_port_spec(ps.compute_parent).plural:
+ for obj in ${spec.get_output_port_spec(ps.compute_parent).compute_name}:
+ properties.update(obj.${ps.compute_name})
+ % else:
+ if ${spec.get_output_port_spec(ps.compute_parent).compute_name}.${ps.compute_name} is not None:
+ properties.update(${spec.get_output_port_spec(ps.compute_parent).compute_name}.${ps.compute_name})
+ % endif
+ ## % if ps.plural:
+ ## for obj in ${ps.compute_name}:
+ ## properties.update(obj)
+ ## % else:
+ ## properties.update(${ps.compute_name})
+ ## % endif
+ % else:
+ if ${ps.compute_name} is not None:
+ properties.update_props(${ps.compute_name})
+ % endif
+ % else:
+ self.setResult('${ps.name}', ${ps.compute_name})
+ % endif
+ % endfor
+
+% endfor
+
+_modules = [
+% for spec in specs.module_specs:
+ ${spec.name},
+% endfor
+]
diff --git a/vistrails/packages/matplotlib/specs.py b/vistrails/packages/matplotlib/specs.py
new file mode 100644
index 0000000..74c90fc
--- /dev/null
+++ b/vistrails/packages/matplotlib/specs.py
@@ -0,0 +1,753 @@
+import inspect
+import mixins
+from xml.etree import ElementTree as ET
+
+def capfirst(s):
+ return s[0].upper() + s[1:]
+
+_mixin_classes = None
+def load_mixin_classes():
+ return dict(inspect.getmembers(mixins, inspect.isclass))
+
+def get_mixin_classes():
+ global _mixin_classes
+ if _mixin_classes is None:
+ _mixin_classes = load_mixin_classes()
+ return _mixin_classes
+
+class SpecList(object):
+ def __init__(self, module_specs=[], custom_code=""):
+ self.module_specs = module_specs
+ self.custom_code = custom_code
+
+ def write_to_xml(self, fname):
+ root = ET.Element("specs")
+ subelt = ET.Element("customCode")
+ subelt.text = self.custom_code
+ root.append(subelt)
+ for spec in self.module_specs:
+ root.append(spec.to_xml())
+ tree = ET.ElementTree(root)
+
+ def indent(elem, level=0):
+ i = "\n" + level*" "
+ if len(elem):
+ if not elem.text or not elem.text.strip():
+ elem.text = i + " "
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ for elem in elem:
+ indent(elem, level+1)
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ else:
+ if level and (not elem.tail or not elem.tail.strip()):
+ elem.tail = i
+ indent(tree.getroot())
+
+ tree.write(fname)
+
+ @staticmethod
+ def read_from_xml(fname):
+ module_specs = []
+ custom_code = ""
+ tree = ET.parse(fname)
+ for elt in tree.getroot():
+ if elt.tag == "moduleSpec":
+ module_specs.append(ModuleSpec.from_xml(elt))
+ elif elt.tag == "customCode":
+ custom_code = elt.text
+ retval = SpecList(module_specs, custom_code)
+ # for spec in retval.module_specs:
+ # print "==", spec.name, "=="
+ # for ps in spec.port_specs:
+ # print " ", ps.arg, ps.name
+ # for alt_ps in ps.alternate_specs:
+ # print " !!!", ps.arg, ps.name, alt_ps.name
+ return retval
+
+class ModuleSpec(object):
+ attrs = ["name", "superklass", "docstring", "output_type"]
+ def __init__(self, name, superklass, code_ref, docstring="", port_specs=[],
+ output_port_specs=[], output_type=None):
+ self.name = name
+ self.superklass = superklass
+ self.code_ref = code_ref
+ self.docstring = docstring
+ self.port_specs = port_specs
+ self.output_port_specs = output_port_specs
+ self.output_type = output_type
+ self._mixin_class = None
+ self._mixin_functions = None
+
+ def to_xml(self, elt=None):
+ if elt is None:
+ elt = ET.Element("moduleSpec")
+ elt.set("name", self.name)
+ elt.set("superclass", self.superklass)
+ elt.set("code_ref", self.code_ref)
+ if self.output_type is not None:
+ elt.set("output_type", self.output_type)
+ subelt = ET.Element("docstring")
+ subelt.text = str(self.docstring)
+ elt.append(subelt)
+ for port_spec in self.port_specs:
+ subelt = port_spec.to_xml()
+ elt.append(subelt)
+ for port_spec in self.output_port_specs:
+ subelt = port_spec.to_xml()
+ elt.append(subelt)
+ return elt
+
+ @classmethod
+ def from_xml(cls, elt):
+ name = elt.get("name", "")
+ superklass = elt.get("superclass", "")
+ code_ref = elt.get("code_ref", "")
+ output_type = elt.get("output_type", None)
+ docstring = ""
+ port_specs = []
+ output_port_specs = []
+ for child in elt.getchildren():
+ if child.tag == "inputPortSpec":
+ port_specs.append(InputPortSpec.from_xml(child))
+ elif child.tag == "outputPortSpec":
+ output_port_specs.append(OutputPortSpec.from_xml(child))
+ elif child.tag == "docstring":
+ if child.text:
+ docstring = child.text
+ return cls(name, superklass, code_ref, docstring, port_specs,
+ output_port_specs, output_type)
+
+ def get_returned_output_port_specs(self):
+ return [ps for ps in self.output_port_specs
+ if ps.property_key is not None]
+
+ def get_input_args(self):
+ args = [ps for ps in self.port_specs if ps.in_args]
+ args.sort(key=lambda ps: ps.arg_pos)
+ if len(args) > 1 and len(args) != (args[-1].arg_pos + 1):
+ raise ValueError("Argument positions are numbered incorrectly")
+ return args
+
+ def get_output_port_spec(self, compute_name):
+ for ps in self.output_port_specs:
+ if ps.compute_name == compute_name:
+ return ps
+ return None
+
+ def get_mixin_name(self):
+ return self.name + "Mixin"
+
+ def has_mixin(self):
+ if self._mixin_class is None:
+ mixin_classes = get_mixin_classes()
+ if self.get_mixin_name() in mixin_classes:
+ self._mixin_class = mixin_classes[self.get_mixin_name()]
+ else:
+ self._mixin_class = False
+ return (self._mixin_class is not False)
+
+ def get_mixin_function(self, f_name):
+ if not self.has_mixin():
+ return None
+ if self._mixin_functions is None:
+ self._mixin_functions = \
+ dict(inspect.getmembers(self._mixin_class, inspect.ismethod))
+ if f_name in self._mixin_functions:
+ s = inspect.getsource(self._mixin_functions[f_name])
+ return s[s.find(':')+1:].strip()
+ return None
+
+ def get_compute_before(self):
+ return self.get_mixin_function("compute_before")
+
+ def get_compute_inner(self):
+ return self.get_mixin_function("compute_inner")
+
+ def get_compute_after(self):
+ return self.get_mixin_function("compute_after")
+
+ def get_init(self):
+ return self.get_mixin_function("__init__")
+
+class PortSpec(object):
+ xml_name = "portSpec"
+ attrs = {"name": "",
+ "port_type": None,
+ "docstring": ("", True),
+ "required": (False, False, True),
+ "show_port": (False, False, True),
+ "hide": (False, False, True),
+ "property_type": ""}
+
+ def __init__(self, arg, **kwargs):
+ self.arg = arg
+ self.set_defaults(**kwargs)
+
+ def set_defaults(self, **kwargs):
+ for attr, props in self.attrs.iteritems():
+ if isinstance(props, tuple):
+ default_val = props[0]
+ else:
+ default_val = props
+ if attr in kwargs:
+ setattr(self, attr, kwargs[attr])
+ else:
+ setattr(self, attr, default_val)
+
+ if not self.name:
+ if self.port_type == "__property__":
+ self.name = self.arg + "Properties"
+ else:
+ self.name = self.arg
+
+ def to_xml(self, elt=None):
+ if elt is None:
+ elt = ET.Element(self.xml_name)
+ elt.set("arg", self.arg)
+ for attr, props in self.attrs.iteritems():
+ attr_val = getattr(self, attr)
+ is_subelt = False
+ if isinstance(props, tuple):
+ default_val = props[0]
+ if len(props) > 1:
+ is_subelt = props[1]
+ else:
+ default_val = props
+
+ if default_val != attr_val:
+ if is_subelt:
+ subelt = ET.Element(attr)
+ subelt.text = str(getattr(self, attr))
+ elt.append(subelt)
+ else:
+ elt.set(attr, str(attr_val))
+ return elt
+
+ # if self.name != "":
+ # elt.set("name", self.name)
+ # if self.port_type is not None:
+ # elt.set("port_type", self.port_type)
+ # else:
+ # elt.set("port_type", "__unknown__")
+ # if self.port_type == "__property__":
+ # elt.set("property_type", self.property_type)
+ # if self.required != False:
+ # elt.set("required", str(self.required))
+ # if self.
+ # elt.set("hide", str(self.hide))
+ # elt.set("show_port", str(self.show_port))
+
+ @classmethod
+ def internal_from_xml(cls, elt, obj=None):
+ arg = elt.get("arg", "")
+ if obj is None:
+ obj = cls(arg)
+ else:
+ obj.arg = arg
+
+ child_elts = {}
+ for child in elt.getchildren():
+ # if child.tag not in obj.attrs:
+ # raise RuntimeError('Cannot deal with tag "%s"' % child.tag)
+ if child.tag not in child_elts:
+ child_elts[child.tag] = []
+ child_elts[child.tag].append(child)
+
+ kwargs = {}
+ for attr, props in obj.attrs.iteritems():
+ is_subelt = False
+ run_eval = False
+ if isinstance(props, tuple):
+ if len(props) > 1:
+ is_subelt = props[1]
+ if len(props) > 2:
+ run_eval = props[2]
+ attr_vals = []
+ if is_subelt:
+ if attr in child_elts:
+ attr_vals = [c.text for c in child_elts[attr]
+ if c.text is not None]
+ if attr == "docstring":
+ print "()() docstring attr_vals:", attr_vals
+ else:
+ attr_val = elt.get(attr)
+ if attr_val is not None:
+ attr_vals = [attr_val]
+
+ if len(attr_vals) > 1:
+ raise ValueError('Should have only one value for '
+ 'attribute "%s"' % attr)
+ if len(attr_vals) > 0:
+ attr_val = attr_vals[0]
+ if run_eval:
+ try:
+ kwargs[attr] = eval(attr_val)
+ except (NameError, SyntaxError):
+ kwargs[attr] = attr_val
+ else:
+ kwargs[attr] = attr_val
+ obj.set_defaults(**kwargs)
+ return obj, child_elts
+
+ @classmethod
+ def from_xml(cls, elt, obj=None):
+ obj, child_elts = cls.internal_from_xml(elt, obj)
+ return obj
+
+ @staticmethod
+ def create_from_xml(elt):
+ if elt.tag == "inputPortSpec":
+ return InputPortSpec.from_xml(elt)
+ elif elt.tag == "outputPortSpec":
+ return OutputPortSpec.from_xml(elt)
+ elif elt.tag == "alternateSpec":
+ return AlternatePortSpec.from_xml(elt)
+ raise TypeError('Cannot create spec from element of type "%s"' %
+ elt.tag)
+
+
+ # @staticmethod
+ # def from_xml(elt, obj=None):
+ # arg = elt.get("arg", "")
+ # if obj is None:
+ # obj = PortSpec(arg)
+ # else:
+ # obj.arg = arg
+ # obj.port_type = elt.get("port_type", "")
+ # if obj.port_type == "__unknown__":
+ # obj.port_type = None
+
+ # if obj.port_type is not None and \
+ # obj.port_type.lower() == "__property__":
+ # obj.name = elt.get("name", obj.arg + "Properties")
+ # else:
+ # obj.name = elt.get("name", obj.arg)
+ # obj.required = eval(elt.get("required", "False"))
+ # obj.hide = eval(elt.get("hide", "False"))
+ # obj.show_port = eval(elt.get("show_port", "False"))
+ # return obj
+
+ def is_property(self):
+ return self.port_type == "__property__"
+
+ def get_property_type(self):
+ return "Mpl%sProperties" % \
+ capfirst(self.property_type.rsplit('.', 1)[1])
+
+ def get_port_type(self):
+ if self.port_type is None:
+ return "basic:String"
+ return self.port_type
+
+class InputPortSpec(PortSpec):
+ xml_name = "inputPortSpec"
+ attrs = {"entry_types": (None, True, True),
+ "values": (None, True, True),
+ "defaults": (None, True, True),
+ "translations": (None, True, True),
+ "in_kwargs": (True, False, True),
+ "in_args": (False, False, True),
+ "constructor_arg": (False, False, True),
+ "arg_pos": (-1, False, True),
+ }
+ attrs.update(PortSpec.attrs)
+
+ def __init__(self, arg, **kwargs):
+ if "alternate_specs" in kwargs and kwargs["alternate_specs"]:
+ self.alternate_specs = kwargs.pop("alternate_specs")
+ else:
+ self.alternate_specs = []
+ PortSpec.__init__(self, arg, **kwargs)
+ for spec in self.alternate_specs:
+ spec.set_parent(self)
+
+ def to_xml(self, elt=None):
+ elt = PortSpec.to_xml(self, elt)
+ for spec in self.alternate_specs:
+ # write the spec
+ subelt = spec.to_xml()
+ elt.append(subelt)
+ return elt
+
+ @classmethod
+ def from_xml(cls, elt, obj=None):
+ obj, child_elts = cls.internal_from_xml(elt, obj)
+
+ if "alternateSpec" in child_elts:
+ for child_elt in child_elts["alternateSpec"]:
+ spec = AlternatePortSpec.from_xml(child_elt)
+ spec.set_parent(obj)
+ obj.alternate_specs.append(spec)
+
+ return obj
+
+ def get_port_attr_dict(self):
+ attrs = {}
+ if self.values:
+ attrs["values"] = str(self.values)
+ if self.entry_types:
+ attrs["entry_types"] = str(self.entry_types)
+ if self.defaults:
+ attrs["defaults"] = str(self.defaults)
+ if self.docstring:
+ attrs["docstring"] = self.docstring
+ if not self.required and not self.show_port:
+ attrs["optional"] = True
+ return attrs
+
+ def get_port_attrs(self):
+ return str(self.get_port_attr_dict())
+
+ def has_alternate_versions(self):
+ return len(self.alternate_specs) > 0
+
+ # def is_property_input(self):
+ # return self.get_port_type().lower() == "__property__"
+
+class AlternatePortSpec(InputPortSpec):
+ # attrs = ["name", "port_type", "docstring", "required", "hide",
+ # "entry_types", "values", "defaults", "translations",
+ # "property_type"]
+
+ xml_name = "alternateSpec"
+ def __init__(self, *args, **kwargs):
+ if len(args) < 1:
+ args = [""]
+ InputPortSpec.__init__(self, *args, **kwargs)
+ self._parent = None
+
+ def set_parent(self, parent):
+ self._parent = parent
+ if not self.name:
+ if self._parent.name.endswith("Sequence"):
+ base_name = self._parent.name[:-8]
+ elif self._parent.name.endswith("Scalar"):
+ base_name = self._parent.name[:-6]
+ else:
+ base_name = self._parent.name
+ if self.port_type == "basic:List":
+ self.name = base_name + "Sequence"
+ else:
+ self.name = base_name + "Scalar"
+ self.arg = self._parent.arg
+
+ # def to_xml(self, elt=None):
+ # if elt is None:
+ # elt = ET.Element("alternateSpec")
+ # return PortSpec.to_xml(self, elt)
+
+ def get_port_attr_dict(self):
+ print "CALLING AlternatePortSpec.get_port_attr_dict", self.arg
+ my_attrs = InputPortSpec.get_port_attr_dict(self)
+ print "=> my_attrs:", my_attrs
+ par_attrs = self._parent.get_port_attr_dict()
+ print "=> par_attrs:", par_attrs
+ for k, v in par_attrs.iteritems():
+ if k == 'defaults' or k == "values" or k == "entry_types" or \
+ k == "translations":
+ continue
+ if k not in my_attrs or my_attrs[k] is None:
+ my_attrs[k] = v
+ print my_attrs
+ return my_attrs
+
+class OutputPortSpec(PortSpec):
+ xml_name = "outputPortSpec"
+ attrs = {"compute_name": "",
+ "property_key": None,
+ "plural": (False, False, True),
+ "compute_parent": "",
+ }
+ attrs.update(PortSpec.attrs)
+
+ def set_defaults(self, **kwargs):
+ PortSpec.set_defaults(self, **kwargs)
+ if self.compute_name == "":
+ if self.plural and self.is_property():
+ self.compute_name = self.arg + 's'
+ else:
+ self.compute_name = self.arg
+
+ @classmethod
+ def from_xml(cls, elt, obj=None):
+ obj, child_elts = cls.internal_from_xml(elt, obj)
+
+ output_type = elt.get("output_type")
+ if output_type is not None:
+ obj.port_type = output_type
+ return obj
+
+ def get_port_attrs(self):
+ attrs = {}
+ if self.docstring:
+ attrs["docstring"] = self.docstring
+ return str(attrs)
+
+
+# class OutputPortSpec(object):
+# attrs = ["name", "compute_name", "output_type", "docstring",
+# "property_type", "property_key", "plural", "compute_parent"]
+# def __init__(self, arg, name, compute_name, output_type, docstring="",
+# property_type="", property_key=None, plural=False,
+# compute_parent=""):
+# self.arg = arg
+# self.name = name
+# self.compute_name = compute_name
+# self.output_type = output_type
+# self.docstring = docstring
+# self.property_type = property_type
+# self.property_key = property_key
+# self.plural = plural
+# self.compute_parent = compute_parent
+
+# self._property_name = None
+
+# def to_xml(self, elt=None):
+# if elt is None:
+# elt = ET.Element("outputPortSpec")
+# elt.set("arg", self.arg)
+# elt.set("name", self.name)
+# elt.set("compute_name", self.compute_name)
+# if self.output_type is not None:
+# elt.set("output_type", self.output_type)
+# else:
+# elt.set("output_type", "__unknown__")
+# elt.set("property_type", self.property_type)
+# if self.property_key is None:
+# elt.set("property_key", "__none__")
+# else:
+# elt.set("property_key", str(self.property_key))
+# elt.set("plural", str(self.plural))
+# elt.set("compute_parent", self.compute_parent)
+
+# subelt = ET.Element("docstring")
+# subelt.text = str(self.docstring)
+# elt.append(subelt)
+# return elt
+
+# @classmethod
+# def from_xml(cls, elt):
+# arg = elt.get("arg", "")
+# output_type = elt.get("output_type", "")
+# if output_type == "__unknown__":
+# output_type = None
+# plural = eval(elt.get("plural", "False"))
+
+# if output_type.lower() == "__property__":
+# name = elt.get("name", arg + "Properties")
+# compute_name = elt.get("compute_name", arg +
+# ("s" if plural else ""))
+# else:
+# name = elt.get("name", arg)
+# compute_name = elt.get("name", arg)
+# property_type = elt.get("property_type", "")
+# property_key = elt.get("property_key", None)
+# if property_key is not None:
+# if property_key == "__none__":
+# property_key = None
+# else:
+# try:
+# property_key = int(property_key)
+# except ValueError:
+# pass
+# compute_parent = elt.get("compute_parent", "")
+# docstring = ""
+# for child in elt.getchildren():
+# if child.tag == "docstring" and child.text:
+# docstring = child.text
+# return cls(arg, name, compute_name, output_type, docstring,
+# property_type, property_key, plural, compute_parent)
+
+# def is_property_output(self):
+# return self.output_type.lower() == "__property__"
+
+# def get_property_type(self):
+# return "Mpl%sProperties" % \
+# capfirst(self.property_type.rsplit('.', 1)[1])
+
+# def get_port_type(self):
+# if self.output_type is None:
+# return "basic:String"
+# return self.output_type
+
+# class InputPortSpec(PortSpec):
+# def __init__(self, arg="", name="", port_type=None, docstring="",
+# required=False, show_port=False, hide=False, property_type="",
+# entry_types=None, values=None, defaults=None,
+# translations=None, alternate_specs=None, in_kwargs=True,
+# in_args=False, constructor_arg=False):
+# PortSpec.__init__(self, arg, name, port_type, docstring, required,
+# show_port, hide, property_type)
+# self.entry_types = entry_types
+# self.values = values
+# self.defaults = defaults
+# self.translations = translations
+# self.in_kwargs = in_kwargs
+# self.in_args = in_args
+# self.constructor_arg = constructor_arg
+# if alternate_specs is None:
+# self.alternate_specs = []
+# else:
+# self.alternate_specs = alternate_specs
+# for spec in self.alternate_specs:
+# spec.set_parent(self)
+
+# def to_xml(self, elt=None):
+# if elt is None:
+# elt = ET.Element("inputPortSpec")
+# PortSpec.to_xml(self, elt)
+# elt.set("in_kwargs", str(self.in_kwargs))
+# elt.set("in_args", str(self.in_args))
+# elt.set("constructor_arg", str(self.constructor_arg))
+# if self.entry_types is not None:
+# subelt = ET.Element("entry_types")
+# subelt.text = str(self.entry_types)
+# elt.append(subelt)
+# if self.values is not None:
+# subelt = ET.Element("values")
+# subelt.text = str(self.values)
+# elt.append(subelt)
+# if self.translations is not None:
+# subelt = ET.Element("translations")
+# subelt.text = str(self.translations)
+# elt.append(subelt)
+# if self.defaults is not None:
+# subelt = ET.Element("defaults")
+# subelt.text = str(self.defaults)
+# elt.append(subelt)
+# for spec in self.alternate_specs:
+# # print "FOUND ALT:", spec.name, spec.alternate_specs, spec
+# subelt = ET.Element("alternateSpec")
+# spec.to_xml(subelt)
+# elt.append(subelt)
+# # if self.entry_types is not None and self.values is not None and \
+# # self.defaults is not None and self.translations is not None:
+# # for entry_type, value, default, translation in \
+# # izip(self.entry_types, self.values, self.defaults,
+# # self.translations):
+# # subelt = ET.Element("entry")
+# # subelt.set("type", str(entry_type))
+# # valueselt = ET.Element("values")
+# # valueselt.text = str(value)
+# # subelt.append(valueselt)
+# # transelt = ET.Element("translation")
+# # transelt.text = str(translation)
+# # subelt.append(transelt)
+# # defaultelt = ET.Element("default")
+# # if isinstance(default, basestring):
+# # defaultelt.text = "'%s'" % default
+# # else:
+# # defaultelt.text = str(default)
+# # subelt.append(defaultelt)
+# # elt.append(subelt)
+# docelt = ET.Element("docstring")
+# docelt.text = self.docstring
+# elt.append(docelt)
+# return elt
+
+# @classmethod
+# def from_xml(cls, elt):
+# arg = elt.get("arg", "")
+# port_type = elt.get("port_type", "")
+# if port_type == "__unknown__":
+# port_type = None
+# required = eval(elt.get("required", "False"))
+# hide = eval(elt.get("hide", "False"))
+# in_kwargs = eval(elt.get("in_kwargs", "True"))
+# property_type = elt.get("property_type", "")
+# constructor_arg = eval(elt.get("constructor_arg", "False"))
+# if port_type is not None and port_type.lower() == "__property__":
+# name = elt.get("name", arg + "Properties")
+# else:
+# name = elt.get("name", arg)
+# entry_types = None
+# values = None
+# defaults = None
+# translations = None
+# docstring = ""
+# alternate_specs = []
+# for child in elt.getchildren():
+# if child.tag == "entry_types":
+# entry_types = eval(child.text)
+# elif child.tag == "values":
+# try:
+# values = eval(child.text)
+# except SyntaxError:
+# values = [[child.text[2:-2]]]
+# elif child.tag == "translations":
+# try:
+# translations = eval(child.text)
+# except NameError:
+# translations = child.text
+# elif child.tag == "defaults":
+# if child.text:
+# defaults = eval(child.text)
+# elif child.tag == "docstring":
+# if child.text:
+# docstring = child.text
+# elif child.tag == "alternateSpec":
+# alternate_specs.append(AlternatePortSpec.from_xml(child))
+
+# # if child.tag == "entry":
+# # if entry_types is None:
+# # entry_types = []
+# # values = []
+# # defaults = []
+# # translations = []
+# # entry_types.append(child.get("type", None))
+# # for subchild in child.getchildren():
+# # if subchild.tag == "values":
+# # values.append(eval(subchild.text))
+# # elif subchild.tag == "translation":
+# # try:
+# # translation = eval(subchild.text)
+# # except NameError:
+# # translation = subchild.text
+# # translations.append(translation)
+# # elif subchild.tag == "default":
+# # defaults.append(eval(subchild.text))
+# # elif child.tag == "docstring":
+# # docstring = child.text
+
+# return cls(arg, name, port_type, docstring, required, hide,
+# entry_types, values, defaults, translations,
+# alternate_specs, in_kwargs, property_type, constructor_arg)
+
+
+# # def has_scalar_version(self):
+# # return self.scalar_type and self.scalar_type != self.port_type
+
+# # def get_scalar_name(self):
+# # return self.name + "Scalar"
+
+# # def has_sequence_version(self):
+# # return self.sequence_type and self.sequence_type != self.port_type
+
+# # def get_sequence_name(self):
+# # return self.name + "Sequence"
+
+# # def has_other_version(self):
+# # return self.has_scalar_version() or self.has_sequence_version()
+
+# # def get_other_name(self):
+# # if self.has_scalar_version():
+# # return self.get_scalar_name()
+# # elif self.has_sequence_version():
+# # return self.get_sequence_name()
+# # return None
+
+# # def get_other_type(self):
+# # if self.has_scalar_version():
+# # return self.scalar_type
+# # elif self.has_sequence_version():
+# # return self.sequence_type
+# # return None
+
+def run():
+ specs = SpecList.read_from_xml("mpl_plots_raw.xml")
+ specs.write_to_xml("mpl_plots_raw_out.xml")
+
+if __name__ == '__main__':
+ run()
diff --git a/vistrails/packages/matplotlib/update.py b/vistrails/packages/matplotlib/update.py
new file mode 100644
index 0000000..7d80c04
--- /dev/null
+++ b/vistrails/packages/matplotlib/update.py
@@ -0,0 +1,78 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import os
+import shutil
+
+from parse import run as run_parse
+from diff import compute_diff, apply_diff
+from generate import run as run_generate
+
+_bases = ["artists", "plots"]
+
+def backup():
+ if not os.path.exists("backup"):
+ os.mkdir("backup")
+ backup_files = ["mpl_%s_raw.xml", "mpl_%s.xml", "mpl_%s_diff.xml"]
+ for base in _bases:
+ for fname_base in backup_files:
+ fname = fname_base % base
+ shutil.copy(fname, "backup")
+
+def run(which="all"):
+ backup()
+ if which == "all":
+ bases = _bases
+ else:
+ bases = [which]
+ for base in bases:
+ compute_diff("mpl_%s_raw.xml" % base,
+ "mpl_%s.xml" % base,
+ "mpl_%s_diff.xml" % base)
+ run_parse(base)
+ apply_diff("mpl_%s_raw.xml" % base,
+ "mpl_%s_diff.xml" % base,
+ "mpl_%s.xml" % base)
+ run_generate(base)
+
+if __name__ == "__main__":
+ import sys
+ if len(sys.argv) > 1:
+ if sys.argv[1] == 'backup':
+ backup()
+ else:
+ run(sys.argv[1])
+ else:
+ run()
diff --git a/vistrails/packages/matplotlib/widgets.py b/vistrails/packages/matplotlib/widgets.py
new file mode 100644
index 0000000..c11560e
--- /dev/null
+++ b/vistrails/packages/matplotlib/widgets.py
@@ -0,0 +1,49 @@
+###############################################################################
+##
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from vistrails.gui.modules.python_source_configure import PythonEditor
+from vistrails.gui.modules.source_configure import SourceConfigurationWidget
+
+class MplSourceConfigurationWidget(SourceConfigurationWidget):
+ def __init__(self, module, controller, parent=None):
+ """ MplSourceConfigurationWidget(module: Module,
+ controller: VistrailController,
+ parent: QWidget)
+ -> MplSourceConfigurationWidget
+ Setup the dialog to similar to PythonSource but with a
+ different name
+
+ """
+ SourceConfigurationWidget.__init__(self, module, controller,
+ PythonEditor, True, False, parent)
diff --git a/vistrails/packages/parallelflow/__init__.py b/vistrails/packages/parallelflow/__init__.py
new file mode 100644
index 0000000..0f26f60
--- /dev/null
+++ b/vistrails/packages/parallelflow/__init__.py
@@ -0,0 +1,3 @@
+identifier="edu.poly.vistrails.parallel_flow"
+name="Parallel Flow"
+version="0.1.1"
diff --git a/vistrails/packages/parallelflow/api.py b/vistrails/packages/parallelflow/api.py
new file mode 100644
index 0000000..7ee4a5f
--- /dev/null
+++ b/vistrails/packages/parallelflow/api.py
@@ -0,0 +1,116 @@
+"""Provides access to IPython to packages.
+
+get_client() returns the Client object, from which you can construct a view.
+This may return None if no client is available, if the user cancels, etc, in
+which case you can raise an exception.
+
+direct_view() returns a DirectView of the whole cluster. It is equivalent to
+get_client()[:], with the difference that it will prompt the user to create new
+engines if none are started.
+
+load_balanced_view() returns a LoadBalancedView of the cluster. It is
+equivalent to get_client().load_balanced_view(), with the difference that it
+will prompt the user to create new engines if none are started.
+
+parallel_map() might use IPython's parallel map_sync(), or the standard map()
+function if IPython cannot be used.
+If the 'ipython' keyword argument is True, the function will return an
+additional boolean indicating whether this was computed through IPython (True)
+or with the default map() function (False).
+
+All of these functions have an 'ask' parameter, that indicates whether to
+prompt the user to start a cluster if none is available. It is True by default
+(except for parallel_map).
+"""
+
+
+__all__ = ['get_client', 'direct_view', 'load_balanced_view', 'parallel_map']
+
+
+def get_client(ask=True):
+ """Returns a Client object, from which you can construct a view.
+
+ This may return None if no client is available, if the user cancels, etc.
+ In this case, you might want to raise a ModuleError.
+ """
+ from engine_manager import EngineManager
+
+ c = EngineManager.ensure_controller(connect_only=not ask)
+ if c is not None and ask and not c.ids:
+ EngineManager.start_engines(
+ prompt="A module requested an IPython cluster, but no engines "
+ "are started. Do you want to start some?")
+ if c is not None and c.ids:
+ return c
+ else:
+ return None
+
+
+def direct_view(ask=True):
+ """Returns a DirectView of the whole cluster.
+
+ This is equivalent to get_client()[:], with the difference that it will
+ prompt the user to create new engines if none are started.
+ """
+ c = get_client()
+ if c is not None:
+ return c[:]
+ else:
+ return None
+
+
+def load_balanced_view(ask=True):
+ """Returns a LoadBalancedView of the cluster.
+
+ This is equivalent to get_client().load_balanced_view(), with the
+ difference that it will prompt the user to create new engines if none are
+ started.
+ """
+ c = get_client()
+ if c is not None:
+ return c.load_balanced_view()
+ else:
+ return None
+
+
+def parallel_map(function, *args, **kwargs):
+ """Wrapper around IPython's map_sync() that defaults to map().
+
+ This might use IPython's parallel map_sync(), or the standard map()
+ function if IPython cannot be used.
+
+ If the 'ask' keyword argument is true, the user will be prompted to start
+ IPython engines, but the function will still default to map() if the user
+ cancels.
+ If the 'ipython' keyword argument is True, the function will return an
+ additional boolean indicating whether this was computed through IPython
+ (True) or with the default map() function (False).
+ """
+ say_ipython = kwargs.pop('ipython', False)
+ ask = kwargs.pop('ask', False)
+ if kwargs:
+ raise TypeError("map() got unexpected keyword arguments")
+
+ try:
+ import IPython.parallel
+ except ImportError:
+ result, ipython = map(function, *args), False
+ else:
+ from engine_manager import EngineManager
+ c = EngineManager.ensure_controller(connect_only=not ask)
+ if c is not None and not c.ids:
+ EngineManager.start_engines(
+ prompt="A module is performing a parallelizable "
+ "operation, however no IPython engines are running. Do "
+ "you want to start some?")
+
+ if c is None or not c.ids:
+ result, ipython = map(function, *args), False
+ else:
+ ldview = c.load_balanced_view()
+ result, ipython = ldview.map_sync(function, *args), True
+
+ if say_ipython:
+ return result, ipython
+ else:
+ return result
diff --git a/vistrails/packages/parallelflow/engine_manager.py b/vistrails/packages/parallelflow/engine_manager.py
new file mode 100644
index 0000000..58763f6
--- /dev/null
+++ b/vistrails/packages/parallelflow/engine_manager.py
@@ -0,0 +1,491 @@
+import os
+import subprocess
+import sys
+import time
+
+from IPython.utils.path import get_ipython_dir, locate_profile
+from IPython.parallel import Client
+from IPython.parallel import error
+
+from vistrails.core.system import vistrails_root_directory
+
+
+try:
+ from PyQt4 import QtCore, QtGui
+ QtGui.QDialog
+except Exception:
+ qt_available = False
+else:
+ qt_available = True
+
+
+class ProfileItem(QtGui.QListWidgetItem):
+ def __init__(self, profile, text, italic=False):
+ QtGui.QListWidgetItem.__init__(self, text)
+ if italic:
+ font = self.font()
+ font.setItalic(True)
+ self.setFont(font)
+ self.profile = profile
+
+
+def choose_profile(profiles):
+ dialog = QtGui.QDialog()
+ dialog.setWindowTitle("IPython profile selection")
+
+ layout = QtGui.QVBoxLayout()
+ profile_list = QtGui.QListWidget()
+ profile_list.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
+ for profile in profiles:
+ profile_list.addItem(ProfileItem(profile, profile))
+
+ # If no profiles are available, still provide an option to use the
+ # 'default' profile
+ if not profiles:
+ profile_list.addItem(ProfileItem('default', "default (create)", True))
+
+ buttons = QtGui.QHBoxLayout()
+ ok = QtGui.QPushButton("Select")
+ QtCore.QObject.connect(ok, QtCore.SIGNAL('clicked()'),
+ dialog, QtCore.SLOT('accept()'))
+ buttons.addWidget(ok)
+ cancel = QtGui.QPushButton("Cancel")
+ QtCore.QObject.connect(cancel, QtCore.SIGNAL('clicked()'),
+ dialog, QtCore.SLOT('reject()'))
+ buttons.addWidget(cancel)
+
+ def check_selection():
+ selection = profile_list.selectedItems()
+ ok.setEnabled(len(selection) == 1)
+ QtCore.QObject.connect(
+ profile_list, QtCore.SIGNAL('itemSelectionChanged()'),
+ check_selection)
+ check_selection()
+
+ layout.addWidget(profile_list)
+ layout.addLayout(buttons)
+ dialog.setLayout(layout)
+
+ if dialog.exec_() == QtGui.QDialog.Accepted:
+ return profile_list.selectedItems()[0].profile
+ else:
+ return None
+
+
+class EngineManager(object):
+ def __init__(self):
+ self.profile = None
+ self.started_controller = None
+ self.started_engines = set()
+ self._client = None
+
+ def _select_profile(self):
+ # See IPython.core.profileapp:list_profile_in()
+ profiles = []
+ for filename in os.listdir(get_ipython_dir()):
+ if filename.startswith('profile_'):
+ profiles.append(filename[8:])
+
+ if profiles == ['default'] and not qt_available:
+ self.profile = 'default'
+ elif not qt_available:
+ raise ValueError("'default' IPython profile does not exist "
+ "and PyQt4 is not available")
+ else:
+ self.profile = choose_profile(profiles)
+
+ def ensure_controller(self, connect_only=False):
+ """Make sure a controller is available, else start a local one.
+ """
+ if self._client:
+ return self._client
+
+ if self.profile is None:
+ self._select_profile()
+ if self.profile is None:
+ return None
+ print "parallelflow: using IPython profile %r" % self.profile
+
+ try:
+ self._client = Client(profile=self.profile)
+ print "parallelflow: connected to controller"
+ return self._client
+ except error.TimeoutError:
+ print "parallelflow: timeout when connecting to controller"
+ if connect_only:
+ start_ctrl = False
+ elif qt_available:
+ res = QtGui.QMessageBox.question(
+ None,
+ "Start controller",
+ "Unable to connect to the configured IPython "
+ "controller. Do you want to start one?",
+ QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
+ start_ctrl = res == QtGui.QMessageBox.Yes
+ else:
+ start_ctrl = True
+ except IOError:
+ print "parallelflow: didn't find a controller to connect to"
+ if connect_only:
+ start_ctrl = False
+ elif qt_available:
+ res = QtGui.QMessageBox.question(
+ None,
+ "Start controller",
+ "No controller is configured in this IPython profile. "
+ "Do you want to start one?",
+ QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
+ start_ctrl = res == QtGui.QMessageBox.Yes
+ else:
+ start_ctrl = True
+
+ if start_ctrl:
+ ctrl_pid = os.path.join(
+ locate_profile(self.profile),
+ 'pid',
+ 'ipcontroller.pid')
+ if os.path.exists(ctrl_pid):
+ os.remove(ctrl_pid)
+ print "parallelflow: starting controller"
+ proc, code = self.start_process(
+ lambda: os.path.exists(ctrl_pid),
+ sys.executable,
+ '-m',
+ 'IPython.parallel.apps.ipcontrollerapp',
+ '--profile=%s' % self.profile)
+ if code is not None:
+ if qt_available:
+ QtGui.QMessageBox.critical(
+ None,
+ "Error",
+ "Controller exited with code %d" % code)
+ print ("parallelflow: controller process exited with "
+ "code %d" % code)
+ return None
+ else:
+ self.started_controller = proc
+ print "parallelflow: controller started, connecting"
+ self._client = Client(profile=self.profile)
+ return self._client
+
+ return None
+
+ @staticmethod
+ def start_process(condition, *args):
+ """Executes a file and waits for a condition.
+ """
+ prev_dir = os.getcwd()
+ os.chdir(os.path.join(vistrails_root_directory(), os.path.pardir))
+ try:
+ p = subprocess.Popen(args)
+ finally:
+ os.chdir(prev_dir)
+ if condition is None:
+ return p, None
+ else:
+ while True:
+ time.sleep(0.5)
+ if condition():
+ return p, None
+ res = p.poll()
+ if res is not None:
+ return None, res
+
+ def start_engines(self, nb=None, prompt="Number of engines to start"):
+ """Start some engines locally
+ """
+ c = self.ensure_controller()
+ if c is None:
+ if qt_available:
+ QtGui.QMessageBox.warning(
+ None,
+ "No controller",
+ "Can't start engines: couldn't connect to a "
+ "controller")
+ print "parallelflow: no controller, not starting engines"
+ else:
+ if not nb and qt_available:
+ nb, res = QtGui.QInputDialog.getInt(
+ None,
+ "Start engines",
+ prompt,
+ 1, # value
+ 1, # min
+ 16) # max
+ if not res:
+ return
+ elif nb is None:
+ nb = 1
+ print "parallelflow: about to start %d engines" % nb
+ if qt_available:
+ bar = QtGui.QProgressDialog(
+ "Starting engines...",
+ None,
+ 0, nb)
+ def progress(n):
+ bar.setValue(n)
+ bar.show()
+ else:
+ def progress(n): pass
+ progress(0)
+
+ init_engines = set(c.ids)
+ # Start the processes
+ starting = set()
+ for i in xrange(nb):
+ proc, res = self.start_process(
+ None,
+ sys.executable,
+ '-m',
+ 'IPython.parallel.apps.ipengineapp',
+ '--profile=%s' % self.profile)
+ starting.add(proc)
+ # Wait for each one to either fail or connect
+ failed = []
+ connected = 0
+ while connected < len(starting):
+ connected = len(set(c.ids) - init_engines)
+ progress(len(failed) + connected)
+ time.sleep(0.5)
+ for p in list(starting):
+ res = p.poll()
+ if res is not None:
+ failed.append(res)
+ starting.remove(p)
+ if failed:
+ nb_failed = len(failed)
+ if nb_failed > 3:
+ failed = "%s, ..." % (', '.join('%d' % f for f in failed))
+ else:
+ failed = ', '.join('%d' % f for f in failed)
+ if qt_available:
+ QtGui.QMessageBox.critical(
+ None,
+ "Error",
+ "%d engine(s) exited with codes: %s" % (
+ nb_failed, failed))
+ print "parallelflow: %d engine(s) exited with codes: %s" % (
+ nb_failed, failed)
+ self.started_engines.update(starting)
+
+ if qt_available:
+ bar.hide()
+ bar.deleteLater()
+ print "parallelflow: %d engines started" % (i + 1)
+
+ def info(self):
+ """Show some information on the cluster.
+ """
+ client = self.ensure_controller(connect_only=True)
+
+ print "----- IPython information -----"
+ print "profile: %s" % self.profile
+ connected = client is not None
+ print "connected to controller: %s" % (
+ "yes" if connected else "no")
+ st_ctrl = (self.started_controller is not None and
+ self.started_controller.poll() is None)
+ print "controller started from VisTrails: %s" % (
+ "running" if st_ctrl else "no")
+ st_engines = sum(1 for p in self.started_engines if p.poll() is None)
+ print "engines started from VisTrails: %d" % st_engines
+ if client is not None:
+ nb_engines = len(client.ids)
+ else:
+ nb_engines = None
+ print "total engines in cluster: %s" % (
+ nb_engines if nb_engines is not None else "(unknown)")
+ if connected and client.ids:
+ dview = client[:]
+ with dview.sync_imports():
+ import os
+ import platform
+ import socket
+ engines = dview.apply_async(
+ eval,
+ '(os.getpid(), platform.system(), socket.getfqdn())'
+ ).get_dict()
+ engines = sorted(
+ engines.items(),
+ key=lambda (ip_id, (pid, system, fqdn)): (fqdn, ip_id))
+ print "engines:"
+ print "\tid\tsystem\tPID\tnode FQDN"
+ print "\t--\t------\t---\t---------"
+ for ip_id, (pid, system, fqdn) in engines:
+ print "\t%d\t%s\t%d\t%s" % (ip_id, system, pid, fqdn)
+ print ""
+
+ if qt_available:
+ dialog = QtGui.QDialog()
+ layout = QtGui.QVBoxLayout()
+ form = QtGui.QFormLayout()
+ form.addRow(
+ "Profile:",
+ QtGui.QLabel(self.profile))
+ form.addRow(
+ "Connected:",
+ QtGui.QLabel("yes" if connected else "no"))
+ form.addRow(
+ "Controller started from VisTrails:",
+ QtGui.QLabel("running" if st_ctrl else "no"))
+ form.addRow(
+ "Engines started from VisTrails:",
+ QtGui.QLabel(str(st_engines)))
+ form.addRow(
+ "Total engines in cluster:",
+ QtGui.QLabel(str(nb_engines)
+ if nb_engines is not None
+ else "(unknown)"))
+ layout.addLayout(form)
+ if connected and client.ids:
+ tree = QtGui.QTreeWidget()
+ tree.setHeaderHidden(False)
+ tree.setHeaderLabels(["IPython id", "PID", "System type"])
+ engine_tree = dict()
+ for ip_id, (pid, system, fqdn) in engines:
+ engine_tree.setdefault(fqdn, []).append(
+ (ip_id, pid, system))
+ for fqdn, info in engine_tree.iteritems():
+ node = QtGui.QTreeWidgetItem([fqdn])
+ tree.addTopLevelItem(node)
+ tree.setFirstItemColumnSpanned(node, True)
+ for ip_id, pid, system in info:
+ node.addChild(QtGui.QTreeWidgetItem([
+ str(ip_id),
+ str(pid),
+ system]))
+ for i in xrange(tree.columnCount()):
+ tree.resizeColumnToContents(i)
+ tree.expandAll()
+ layout.addWidget(tree)
+
+ ok = QtGui.QPushButton("Ok")
+ QtCore.QObject.connect(ok, QtCore.SIGNAL('clicked()'),
+ dialog, QtCore.SLOT('accept()'))
+ layout.addWidget(ok, 1, QtCore.Qt.AlignHCenter)
+ dialog.setLayout(layout)
+ dialog.exec_()
+
+ def change_profile(self):
+ self.cleanup()
+
+ old_profile = self.profile
+ self._select_profile()
+ if not self.profile:
+ self.profile = old_profile
+
+ if self.profile != old_profile:
+ # Here, the processes that were started but the user didn't want to
+ # clean up are abandonned
+ # They will continue running but later cleanups won't ask for these
+ # ones
+ self.started_engines = set()
+ self.started_controller = None
+
+ def cleanup(self):
+ """Shut down the started processes (with user confirmation).
+ """
+ engines = sum(1 for p in self.started_engines if p.poll() is None)
+ ctrl = (self.started_controller is not None and
+ self.started_controller.poll() is None)
+ print ("parallelflow: cleanup: %s, %d engines running" % (
+ "controller running" if ctrl else "no controller",
+ engines))
+
+ hub_shutdown = False
+
+ if ctrl:
+ if qt_available:
+ res = QtGui.QMessageBox.question(
+ None,
+ "Shutdown controller",
+ "The controller is still running. Do you want to stop "
+ "it?",
+ QtGui.QMessageBox.Yes,
+ QtGui.QMessageBox.No)
+ res = res != QtGui.QMessageBox.No
+ else:
+ res = True
+ if res:
+ if self._client is not None:
+ self._client.shutdown(
+ targets='all',
+ restart=False,
+ hub=True,
+ block=False)
+ hub_shutdown = True
+ print "parallelflow: requested hub shutdown"
+ else:
+ if self.started_controller.poll() is not None:
+ self.started_controller.terminate()
+ self.started_controller.wait()
+ print "parallelflow: controller terminated"
+ self.started_controller = None
+
+ if engines > 0 and not hub_shutdown:
+ if qt_available:
+ if self._client is not None:
+ total = " (among %d total)" % len(self._client.ids)
+ else:
+ total = ''
+ res = QtGui.QMessageBox.question(
+ None,
+ "Shutdown engines",
+ "%d engines started here%s are still "
+ "running. Do you want to stop them?" % (
+ engines,
+ total),
+ QtGui.QMessageBox.Yes,
+ QtGui.QMessageBox.No)
+ res = res != QtGui.QMessageBox.No
+ else:
+ res = True
+ if res:
+ for engine in self.started_engines:
+ if engine.poll() is not None:
+ engine.terminate()
+ engine.wait()
+ print ("parallelflow: %d engines terminated" %
+ len(self.started_engines))
+ self.started_engines = set()
+
+ if self._client is not None:
+ print "parallelflow: closing client"
+ self._client.close()
+ self._client = None
+
+ def shutdown_cluster(self):
+ """Use the client to request a shutdown of the whole cluster.
+ """
+ client = self.ensure_controller(connect_only=True)
+ if client is None:
+ if qt_available:
+ QtGui.QMessageBox.information(
+ None,
+ "Couldn't connect",
+ "Couldn't connect to a controller. Is the cluster "
+ "down already?")
+ print ("parallelflow: shutdown_cluster requested, but could "
+ "not connect to a controller")
+ return
+
+ if qt_available:
+ res = QtGui.QMessageBox.question(
+ None,
+ "Shutdown cluster",
+ "This will use the client connection to request the hub "
+ "and every engine to shutdown. Continue?",
+ QtGui.QMessageBox.Ok,
+ QtGui.QMessageBox.Cancel)
+ if res != QtGui.QMessageBox.Ok:
+ return
+
+ self._client.shutdown(
+ targets='all',
+ restart=False,
+ hub=True,
+ block=False)
+ print "parallelflow: cluster shutdown requested"
+ self._client = None
+
+EngineManager = EngineManager()
diff --git a/vistrails/packages/parallelflow/init.py b/vistrails/packages/parallelflow/init.py
new file mode 100644
index 0000000..3d36dda
--- /dev/null
+++ b/vistrails/packages/parallelflow/init.py
@@ -0,0 +1,36 @@
+from vistrails.core.modules.vistrails_module import Module
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.modules.basic_modules import List, String
+
+from engine_manager import EngineManager
+from map import Map
+
+
+def initialize(*args,**keywords):
+ reg = get_module_registry()
+
+ reg.add_module(Map)
+ reg.add_input_port(Map, 'FunctionPort', (Module, ''))
+ reg.add_input_port(Map, 'InputList', (List, ''))
+ reg.add_input_port(Map, 'InputPort', (List, ''))
+ reg.add_input_port(Map, 'OutputPort', (String, ''))
+ reg.add_output_port(Map, 'Result', (List, ''))
+
+
+def finalize():
+ EngineManager.cleanup()
+
+
+def menu_items():
+ return (
+ ("Start new engine processes",
+ lambda: EngineManager.start_engines()),
+ ("Show information on the cluster",
+ lambda: EngineManager.info()),
+ ("Change profile",
+ lambda: EngineManager.change_profile()),
+ ("Cleanup started processes",
+ lambda: EngineManager.cleanup()),
+ ("Request cluster shutdown",
+ lambda: EngineManager.shutdown_cluster()),
+ )
diff --git a/vistrails/packages/parallelflow/map.py b/vistrails/packages/parallelflow/map.py
new file mode 100644
index 0000000..737f978
--- /dev/null
+++ b/vistrails/packages/parallelflow/map.py
@@ -0,0 +1,581 @@
+import vistrails.core.db.action
+import vistrails.db.versions
+import vistrails.core.modules.module_registry
+import vistrails.core.modules.utils
+from vistrails.core.modules.vistrails_module import Module, ModuleError, \
+ ModuleConnector, InvalidOutput
+from vistrails.core.modules.basic_modules import NotCacheable, Constant
+from vistrails.core.vistrail.pipeline import Pipeline
+from vistrails.core.vistrail.annotation import Annotation
+from vistrails.core.vistrail.group import Group
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.vistrail import Vistrail
+from vistrails.core.db.locator import XMLFileLocator
+from vistrails.core.vistrail.controller import VistrailController
+from vistrails.core.interpreter.default import get_default_interpreter
+from vistrails.core.db.io import serialize, unserialize
+from vistrails.core.log.module_exec import ModuleExec
+from vistrails.core.log.group_exec import GroupExec
+from vistrails.core.log.machine import Machine
+from vistrails.db.domain import IdScope
+
+import copy
+import inspect
+from itertools import izip
+import os
+import re
+import sys
+import tempfile
+
+from IPython.parallel.error import CompositeError
+
+from .api import get_client
+
+
+###############################################################################
+# This function is sent to the engines which execute it
+#
+# It receives the workflow, and the list of targeted output ports
+#
+# It returns the corresponding computed outputs and the execution log
+#
+def execute_wf(wf, output_port):
+ # Save the workflow in a temporary file
+ temp_wf_fd, temp_wf = tempfile.mkstemp()
+
+ try:
+ f = open(temp_wf, 'w')
+ f.write(wf)
+ f.close()
+ os.close(temp_wf_fd)
+
+ # Clean the cache
+ interpreter = get_default_interpreter()
+ interpreter.flush()
+
+ # Load the Pipeline from the temporary file
+ vistrail = Vistrail()
+ locator = XMLFileLocator(temp_wf)
+ workflow = locator.load(Pipeline)
+
+ # Build a Vistrail from this single Pipeline
+ action_list = []
+ for module in workflow.module_list:
+ action_list.append(('add', module))
+ for connection in workflow.connection_list:
+ action_list.append(('add', connection))
+ action = vistrails.core.db.action.create_action(action_list)
+
+ vistrail.add_action(action, 0L)
+ vistrail.update_id_scope()
+ tag = 'parallel flow'
+ vistrail.addTag(tag, action.id)
+
+ # Build a controller and execute
+ controller = VistrailController()
+ controller.set_vistrail(vistrail, None)
+ controller.change_selected_version(vistrail.get_version_number(tag))
+ execution = controller.execute_current_workflow(
+ custom_aliases=None,
+ custom_params=None,
+ extra_info=None,
+ reason='API Pipeline Execution')
+
+ # Build a list of errors
+ errors = []
+ pipeline = vistrail.getPipeline(tag)
+ execution_errors = execution[0][0].errors
+ if execution_errors:
+ for key in execution_errors:
+ module = pipeline.modules[key]
+ msg = '%s: %s' %(module.name, execution_errors[key])
+ errors.append(msg)
+
+ # Get the execution log from the controller
+ try:
+ module_log = controller.log.workflow_execs[0].item_execs[0]
+ except IndexError:
+ errors.append("Module log not found")
+ return dict(errors=errors)
+ else:
+ machine = controller.log.machine_list[0]
+ xml_log = serialize(module_log)
+ machine_log = serialize(machine)
+
+ # Get the output value
+ output = None
+ serializable = None
+ if not execution_errors:
+ executed_module, = execution[0][0].executed
+ executed_module = execution[0][0].objects[executed_module]
+ try:
+ output = executed_module.get_output(output_port)
+ except ModuleError:
+ errors.append("Output port not found: %s" % output_port)
+ return dict(errors=errors)
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ base_classes = inspect.getmro(type(output))
+ if Module in base_classes:
+ serializable = reg.get_descriptor(type(output)).sigstring
+ output = output.serialize()
+
+ # Return the dictionary, that will be sent back to the client
+ return dict(errors=errors,
+ output=output,
+ serializable=serializable,
+ xml_log=xml_log,
+ machine_log=machine_log)
+ finally:
+ os.unlink(temp_wf)
+
+###############################################################################
+
+_ansi_code = re.compile(r'%s(?:(?:\[[^A-Za-z]*[A-Za-z])|[^\[])' % '\x1B')
+
+def strip_ansi_codes(s):
+ return _ansi_code.sub('', s)
+
+###############################################################################
+# Map Operator
+#
+class Map(Module):
+ """The Map Module executes a map operator in parallel on IPython engines.
+
+ The FunctionPort should be connected to the 'self' output of the module you
+ want to execute.
+ The InputList is the list of values to be scattered on the engines.
+ """
+ def __init__(self):
+ Module.__init__(self)
+
+ def updateUpstream(self):
+ """A modified version of the updateUpstream method."""
+
+ # everything is the same except that we don't update anything
+ # upstream of FunctionPort
+ for port_name, connector_list in self.inputPorts.iteritems():
+ if port_name == 'FunctionPort':
+ for connector in connector_list:
+ connector.obj.updateUpstream()
+ else:
+ for connector in connector_list:
+ connector.obj.update()
+ for port_name, connectorList in copy.copy(self.inputPorts.items()):
+ if port_name != 'FunctionPort':
+ for connector in connectorList:
+ if connector.obj.get_output(connector.port) is \
+ InvalidOutput:
+ self.removeInputConnector(port_name, connector)
+
+ @staticmethod
+ def print_compositeerror(e):
+ sys.stderr.write("Got %d exceptions from IPython engines:\n" %
+ len(e.elist))
+ for e_type, e_msg, formatted_tb, infos in e.elist:
+ sys.stderr.write("Error from engine %d (%r):\n" % (
+ infos['engine_id'], infos['engine_uuid']))
+ sys.stderr.write("%s\n" % strip_ansi_codes(formatted_tb))
+
+ @staticmethod
+ def list_exceptions(e):
+ return '\n'.join(
+ "% 3d: %s: %s" % (infos['engine_id'],
+ e_type,
+ e_msg)
+ for e_type, e_msg, tb, infos in e.elist)
+
+ def updateFunctionPort(self):
+ """
+ Function to be used inside the updateUsptream method of the Map module. It
+ updates the module connected to the FunctionPort port, executing it in
+ parallel.
+ """
+ nameInput = self.getInputFromPort('InputPort')
+ nameOutput = self.getInputFromPort('OutputPort')
+ rawInputList = self.getInputFromPort('InputList')
+
+ # Create inputList to always have iterable elements
+ # to simplify code
+ if len(nameInput) == 1:
+ element_is_iter = False
+ inputList = [[element] for element in rawInputList]
+ else:
+ element_is_iter = True
+ inputList = rawInputList
+
+ workflows = []
+ module = None
+ vtType = None
+
+ # iterating through the connectors
+ for connector in self.inputPorts.get('FunctionPort'):
+ module = connector.obj
+
+ # pipeline
+ original_pipeline = connector.obj.moduleInfo['pipeline']
+
+ # module
+ module_id = connector.obj.moduleInfo['moduleId']
+ vtType = original_pipeline.modules[module_id].vtType
+
+ # serialize the module for each value in the list
+ for i, element in enumerate(inputList):
+ if element_is_iter:
+ self.element = element
+ else:
+ self.element = element[0]
+
+ # checking type and setting input in the module
+ self.typeChecking(connector.obj, nameInput, inputList)
+ self.setInputValues(connector.obj, nameInput, element)
+
+ pipeline_db_module = original_pipeline.modules[module_id].do_copy()
+
+ # transforming a subworkflow in a group
+ # TODO: should we also transform inner subworkflows?
+ if pipeline_db_module.is_abstraction():
+ group = Group(id=pipeline_db_module.id,
+ cache=pipeline_db_module.cache,
+ location=pipeline_db_module.location,
+ functions=pipeline_db_module.functions,
+ annotations=pipeline_db_module.annotations)
+
+ source_port_specs = pipeline_db_module.sourcePorts()
+ dest_port_specs = pipeline_db_module.destinationPorts()
+ for source_port_spec in source_port_specs:
+ group.add_port_spec(source_port_spec)
+ for dest_port_spec in dest_port_specs:
+ group.add_port_spec(dest_port_spec)
+
+ group.pipeline = pipeline_db_module.pipeline
+ pipeline_db_module = group
+
+ # getting highest id between functions to guarantee unique ids
+ # TODO: can get current IdScope here?
+ if pipeline_db_module.functions:
+ high_id = max(function.db_id
+ for function in pipeline_db_module.functions)
+ else:
+ high_id = 0
+
+ # adding function and parameter to module in pipeline
+ # TODO: 'pos' should not be always 0 here
+ id_scope = IdScope(beginId=long(high_id+1))
+ for elementValue, inputPort in izip(element, nameInput):
+
+ p_spec = pipeline_db_module.get_port_spec(inputPort, 'input')
+ descrs = p_spec.descriptors()
+ if len(descrs) != 1:
+ raise ModuleError(
+ self,
+ "Tuple input ports are not supported")
+ if not issubclass(descrs[0].module, Constant):
+ raise ModuleError(
+ self,
+ "Module inputs should be Constant types")
+ type = p_spec.sigstring[1:-1]
+
+ mod_function = ModuleFunction(id=id_scope.getNewId(ModuleFunction.vtType),
+ pos=0,
+ name=inputPort)
+ mod_param = ModuleParam(id=0L,
+ pos=0,
+ type=type,
+ val=elementValue)
+
+ mod_function.add_parameter(mod_param)
+ pipeline_db_module.add_function(mod_function)
+
+ # serializing module
+ wf = self.serialize_module(pipeline_db_module)
+ workflows.append(wf)
+
+ # getting first connector, ignoring the rest
+ break
+
+ # IPython stuff
+ try:
+ rc = get_client()
+ except Exception, error:
+ raise ModuleError(self, "Exception while loading IPython: "
+ "%s" % error)
+ if rc is None:
+ raise ModuleError(self, "Couldn't get an IPython connection")
+ engines = rc.ids
+ if not engines:
+ raise ModuleError(
+ self,
+ "Exception while loading IPython: No IPython engines "
+ "detected!")
+
+ # initializes each engine
+ # importing modules and initializing the VisTrails application
+ # in the engines *only* in the first execution on this engine
+ uninitialized = []
+ for eng in engines:
+ try:
+ rc[eng]['init']
+ except:
+ uninitialized.append(eng)
+ if uninitialized:
+ init_view = rc[uninitialized]
+ with init_view.sync_imports():
+ import tempfile
+ import inspect
+
+ # VisTrails API
+ import vistrails
+ import vistrails.core
+ import vistrails.core.db.action
+ import vistrails.core.application
+ import vistrails.core.modules.module_registry
+ from vistrails.core.db.io import serialize
+ from vistrails.core.vistrail.vistrail import Vistrail
+ from vistrails.core.vistrail.pipeline import Pipeline
+ from vistrails.core.db.locator import XMLFileLocator
+ from vistrails.core.vistrail.controller import VistrailController
+ from vistrails.core.interpreter.default import get_default_interpreter
+
+ # initializing a VisTrails application
+ try:
+ init_view.execute(
+ 'app = vistrails.core.application.init('
+ ' {"spawned": True},'
+ ' args=[])',
+ block=True)
+ except CompositeError, e:
+ self.print_compositeerror(e)
+ raise ModuleError(self, "Error initializing application on "
+ "IPython engines:\n"
+ "%s" % self.list_exceptions(e))
+
+ init_view['init'] = True
+
+ # setting computing color
+ module.logging.set_computing(module)
+
+ # executing function in engines
+ # each map returns a dictionary
+ try:
+ ldview = rc.load_balanced_view()
+ map_result = ldview.map_sync(execute_wf, workflows, [nameOutput]*len(workflows))
+ except CompositeError, e:
+ self.print_compositeerror(e)
+ raise ModuleError(self, "Error from IPython engines:\n"
+ "%s" % self.list_exceptions(e))
+
+ # verifying errors
+ errors = []
+ for engine in range(len(map_result)):
+ if map_result[engine]['errors']:
+ msg = "ModuleError in engine %d: '%s'" % (
+ engine,
+ ', '.join(map_result[engine]['errors']))
+ errors.append(msg)
+
+ if errors:
+ raise ModuleError(self, '\n'.join(errors))
+
+ # setting success color
+ module.logging.signalSuccess(module)
+
+ import vistrails.core.modules.module_registry
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ self.result = []
+ for map_execution in map_result:
+ serializable = map_execution['serializable']
+ output = None
+ if not serializable:
+ output = map_execution['output']
+ else:
+ d_tuple = vistrails.core.modules.utils.parse_descriptor_string(serializable)
+ d = reg.get_descriptor_by_name(*d_tuple)
+ module_klass = d.module
+ output = module_klass().deserialize(map_execution['output'])
+ self.result.append(output)
+
+ # including execution logs
+ for engine in range(len(map_result)):
+ log = map_result[engine]['xml_log']
+ exec_ = None
+ if (vtType == 'abstraction') or (vtType == 'group'):
+ exec_ = unserialize(log, GroupExec)
+ elif (vtType == 'module'):
+ exec_ = unserialize(log, ModuleExec)
+ else:
+ # something is wrong...
+ continue
+
+ # assigning new ids to existing annotations
+ exec_annotations = exec_.annotations
+ for i in range(len(exec_annotations)):
+ exec_annotations[i].id = self.logging.log.log.id_scope.getNewId(Annotation.vtType)
+
+ parallel_annotation = Annotation(key='parallel_execution', value=True)
+ parallel_annotation.id = self.logging.log.log.id_scope.getNewId(Annotation.vtType)
+ annotations = [parallel_annotation] + exec_annotations
+ exec_.annotations = annotations
+
+ # before adding the execution log, we need to get the machine information
+ machine = unserialize(map_result[engine]['machine_log'], Machine)
+ machine.id = self.logging.log.log.id_scope.getNewId(Machine.vtType) #assigning new id
+ self.logging.log.log.add_machine(machine)
+
+ # recursively add machine information to execution items
+ def add_machine_recursive(exec_):
+ for i in range(len(exec_.item_execs)):
+ if hasattr(exec_.item_execs[i], 'machine_id'):
+ exec_.item_execs[i].machine_id = machine.id
+ vt_type = exec_.item_execs[i].vtType
+ if (vt_type == 'abstraction') or (vt_type == 'group'):
+ add_machine_recursive(exec_.item_execs[i])
+
+ exec_.machine_id = machine.id
+ if (vtType == 'abstraction') or (vtType == 'group'):
+ add_machine_recursive(exec_)
+
+ self.logging.add_exec(exec_)
+
+
+ def serialize_module(self, module):
+ """
+ Serializes a module to be executed in parallel.
+ """
+
+ def process_group(group):
+ group.pipeline.id = None
+ for module in group.pipeline.module_list:
+ if module.is_group():
+ process_group(module)
+
+ pipeline = Pipeline(version=vistrails.db.versions.currentVersion)
+
+ if module.is_group():
+ process_group(module)
+
+ module = module.do_copy()
+ pipeline.add_module(module)
+
+ return serialize(pipeline)
+
+ def setInputValues(self, module, inputPorts, elementList):
+ """
+ Function used to set a value inside 'module', given the input port(s).
+ """
+ for element, inputPort in izip(elementList, inputPorts):
+ ## Cleaning the previous connector...
+ if inputPort in module.inputPorts:
+ del module.inputPorts[inputPort]
+ new_connector = ModuleConnector(create_constant(element), 'value')
+ module.set_input_port(inputPort, new_connector)
+
+ def typeChecking(self, module, inputPorts, inputList):
+ """
+ Function used to check if the types of the input list element and of the
+ inputPort of 'module' match.
+ """
+ for elementList in inputList:
+ if len(elementList) != len(inputPorts):
+ raise ModuleError(self,
+ 'The number of input values and input ports '
+ 'are not the same.')
+ for element, inputPort in izip(elementList, inputPorts):
+ p_modules = module.moduleInfo['pipeline'].modules
+ p_module = p_modules[module.moduleInfo['moduleId']]
+ port_spec = p_module.get_port_spec(inputPort, 'input')
+ v_module = get_module(element, port_spec.signature)
+ if v_module is not None:
+ if not self.compare(port_spec, v_module, inputPort):
+ raise ModuleError(self,
+ 'The type of a list element does '
+ 'not match with the type of the '
+ 'port %s.' % inputPort)
+
+ del v_module
+ else:
+ break
+
+ def createSignature(self, v_module):
+ """
+ ` Function used to create a signature, given v_module, for a port spec.
+ """
+ if isinstance(v_module, tuple):
+ v_module_class = []
+ for module_ in v_module:
+ v_module_class.append(self.createSignature(module_))
+ return v_module_class
+ else:
+ return v_module
+
+ def compare(self, port_spec, v_module, port):
+ """
+ Function used to compare two port specs.
+ """
+ port_spec1 = port_spec
+
+ from vistrails.core.modules.module_registry import get_module_registry
+ reg = get_module_registry()
+
+ from vistrails.core.vistrail.port_spec import PortSpec
+ v_module = self.createSignature(v_module)
+ port_spec2 = PortSpec(**{'signature': v_module})
+ matched = reg.are_specs_matched(port_spec2, port_spec1)
+
+ return matched
+
+ def compute(self):
+ """The compute method for Map."""
+
+ self.result = None
+ self.updateFunctionPort()
+
+ self.setResult('Result', self.result)
+
+###############################################################################
+
+class NewConstant(Constant):
+ """
+ A new Constant module to be used inside the Map module.
+ """
+ def setValue(self, v):
+ self.setResult("value", v)
+ self.upToDate = True
+
+def create_constant(value):
+ """
+ Creates a NewConstant module, to be used for the ModuleConnector.
+ """
+ constant = NewConstant()
+ constant.setValue(value)
+ return constant
+
+def get_module(value, signature):
+ """
+ Creates a module for value, in order to do the type checking.
+ """
+
+ from vistrails.core.modules.basic_modules import Boolean, String, Integer, Float, List
+
+ if isinstance(value, Constant):
+ return type(value)
+ elif isinstance(value, bool):
+ return Boolean
+ elif isinstance(value, str):
+ return String
+ elif isinstance(value, int):
+ return Integer
+ elif isinstance(value, float):
+ return Float
+ elif isinstance(value, list):
+ return List
+ elif isinstance(value, tuple):
+ v_modules = ()
+ for element in xrange(len(value)):
+ v_modules += (get_module(value[element], signature[element]))
+ return v_modules
+ else:
+ from vistrails.core import debug
+ debug.warning("Could not identify the type of the list element.")
+ debug.warning("Type checking is not going to be done inside Map module.")
+ return None
diff --git a/vistrails/packages/persistence/__init__.py b/vistrails/packages/persistence/__init__.py
new file mode 100644
index 0000000..3ac93c6
--- /dev/null
+++ b/vistrails/packages/persistence/__init__.py
@@ -0,0 +1,44 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.configuration import ConfigurationObject
+
+from identifiers import *
+
+configuration = ConfigurationObject(global_db=(None, str),
+ local_db=(None, str),
+ git_bin=(None, str),
+ search_dbs=(None, str),
+ compress_by_default=False,
+ debug=False)
diff --git a/vistrails/packages/persistence/compute_hash.py b/vistrails/packages/persistence/compute_hash.py
new file mode 100644
index 0000000..fe2c8b5
--- /dev/null
+++ b/vistrails/packages/persistence/compute_hash.py
@@ -0,0 +1,82 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import os
+try:
+ import hashlib
+ sha_hash = hashlib.sha1
+except ImportError:
+ import sha
+ sha_hash = sha.new
+
+def compute_hash(persistent_path, is_dir=None):
+ def hash_file(filename, hasher):
+ f = open(filename, 'rb')
+ while True:
+ block = f.read(8192)
+ if not block:
+ break
+ hasher.update(block)
+
+ sha_hasher = sha_hash()
+ if is_dir is None:
+ is_dir = os.path.isdir(persistent_path)
+ if is_dir:
+ # get all of the files we need to hash
+ fnames = []
+ base_dir = persistent_path
+ dir_stack = ['.']
+ while dir_stack:
+ dir = dir_stack.pop()
+ for base in sorted(os.listdir(os.path.join(base_dir, dir))):
+ name = os.path.join(dir, base)
+ if os.path.isdir(os.path.join(base_dir, name)):
+ dir_stack.append(name)
+ else:
+ fnames.append(name)
+
+ # hash filenames and files to ensure directory structure
+ # is accounted for
+ for fname in fnames:
+ # print fname
+ sha_hasher.update(fname)
+ hash_file(os.path.join(base_dir, fname), sha_hasher)
+ else:
+ hash_file(persistent_path, sha_hasher)
+ return sha_hasher.hexdigest()
+
+if __name__ == '__main__':
+ import sys
+ print compute_hash(sys.argv[1])
diff --git a/vistrails/packages/persistence/db_utils.py b/vistrails/packages/persistence/db_utils.py
new file mode 100644
index 0000000..c564394
--- /dev/null
+++ b/vistrails/packages/persistence/db_utils.py
@@ -0,0 +1,171 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import os
+import sqlite3
+
+class DatabaseAccessSingleton(object):
+ def __new__(cls, *args, **kw):
+ if DatabaseAccess._instance is None:
+ obj = DatabaseAccess(*args, **kw)
+ DatabaseAccess._instance = obj
+ return DatabaseAccess._instance
+
+class DatabaseAccess(object):
+ _instance = None
+ def __init__(self, db_file):
+ #print 'initing DatabaseAccess'
+ self.db_file = db_file
+ run_schema = False
+ if not os.path.exists(db_file):
+ run_schema = True
+ self.conn = sqlite3.connect(db_file)
+ if run_schema:
+ #print 'running schema'
+ #print 'schema file:', os.path.join(os.path.dirname(
+ # os.path.abspath(__file__)), 'schema.sql')
+ cur = self.conn.cursor()
+ self.run_sql_file(cur, os.path.join(os.path.dirname(
+ os.path.abspath(__file__)), 'schema.sql'))
+ self.ensure_deleted_column_exist()
+ self.model = None
+
+ def ensure_deleted_column_exist(self):
+ """ Add a "deleted" column if not already exist
+ This was added in version 0.2.2 without bumping the schema
+ """
+ cur = self.conn.cursor()
+ if 'deleted' not in [i[1] for i in cur.execute(
+ "PRAGMA table_info(file);").fetchall()]:
+ cur.execute("ALTER TABLE file ADD COLUMN "
+ "deleted bool NOT NULL DEFAULT False;")
+ self.conn.commit()
+
+ def set_model(self, model):
+ self.model = model
+
+ def run_sql_file(self, cur, sql_file):
+ cmd = ''
+ for line in open(sql_file):
+ cmd += line
+ if line.strip().endswith(';'):
+ cur.execute(cmd.strip())
+ cmd = ''
+
+ def finalize(self):
+ self.conn.close()
+
+ def write_database(self, value_dict):
+# db_file = '/vistrails/managed/files.db'
+# self.conn = sqlite3.connect(db_file)
+
+ cur = self.conn.cursor()
+ cols, vals = zip(*value_dict.iteritems())
+ col_str = ', '.join(cols)
+ # print "executing sql:", "INSERT INTO file(%s) VALUES (%s);" % \
+ # (col_str, ','.join(['?'] * len(vals)))
+ # print " ", vals
+ cur.execute("INSERT INTO file(%s) VALUES (%s);" % \
+ (col_str, ','.join(['?'] * len(vals))),
+ vals)
+ self.conn.commit()
+
+ if self.model:
+ self.model.add_data(value_dict)
+
+ # cur.execute("SELECT id, name, tags, user, date_created, "
+ # "date_modified, content_hash, version, signature "
+ # "FROM file;")
+
+ def read_database(self, cols=None, where_dict=None):
+ # self.conn = sqlite3.connect(db_file)
+ cur = self.conn.cursor()
+ if cols is None:
+ cols = ["id", "name", "tags", "user", "date_created",
+ "date_modified", "content_hash", "version", "signature"]
+ col_str = ', '.join(cols)
+ if where_dict is None or len(where_dict) <= 0:
+ cur.execute("SELECT " + ", ".join(cols) +
+ " FROM file WHERE deleted != 'True';")
+ else:
+ where_cols, where_vals = zip(*where_dict.iteritems())
+ where_str = '=? AND '.join(where_cols) + '=?'
+ cur.execute("SELECT " + ", ".join(cols) + " FROM file WHERE "
+ "%s AND deleted != 'True';" % where_str, where_vals)
+ return cur.fetchall()
+
+ def search_by_signature(self, signature):
+ cur = self.conn.cursor()
+ cur.execute("SELECT id, version, name FROM file WHERE signature=? "
+ "ORDER BY date_created DESC LIMIT 1;", (signature,))
+ res = cur.fetchone()
+ if res:
+ return res
+ return None
+
+ def get_signature(self, id, version=None):
+ cur = self.conn.cursor()
+ cur.execute("SELECT signature FROM file where id=? and version=?;",
+ (id, version))
+ res = cur.fetchone()
+ if res:
+ return res[0]
+ return None
+
+ def ref_exists(self, id, version=None):
+ cur = self.conn.cursor()
+ if version is None:
+ cur.execute("SELECT id, version, name, signature FROM file "
+ "WHERE id=?;", (id,))
+ else:
+ cur.execute("SELECT id, version, name, signature FROM file "
+ "WHERE id=? AND version=?;", (id, version))
+ res = cur.fetchone()
+ return res is not None
+
+ def delete_from_database(self, where_dict=None):
+ cur = self.conn.cursor()
+ if where_dict is None or len(where_dict) <= 0:
+ cur.execute("UPDATE file SET deleted='True';")
+ else:
+ where_cols, where_vals = zip(*where_dict.iteritems())
+ where_str = '=? AND '.join(where_cols) + '=?'
+ cur.execute("UPDATE file SET deleted='True' WHERE %s;" %
+ where_str, where_vals)
+ self.conn.commit()
+ if self.model:
+ self.model.remove_data(where_dict)
+ # return cur.fetchall()
+
diff --git a/vistrails/packages/persistence/find_files.py b/vistrails/packages/persistence/find_files.py
new file mode 100644
index 0000000..3acc6c8
--- /dev/null
+++ b/vistrails/packages/persistence/find_files.py
@@ -0,0 +1,113 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import os
+import shutil
+import sys
+
+vistrails_src = None
+if not vistrails_src:
+ vistrails_src = os.path.dirname(
+ os.path.dirname(os.path.dirname(sys.path[0])))
+if vistrails_src not in sys.path:
+ sys.path.append(vistrails_src)
+
+import vistrails.db.services.io
+
+from identifiers import identifier as persistence_pkg, \
+ old_identifiers as persistence_old_ids
+persistence_pkg_ids = set(persistence_old_ids)
+persistence_pkg_ids.add(persistence_pkg)
+
+def find_files(filename, version=None):
+ save_bundle, save_dir = \
+ vistrails.db.services.io.open_vistrail_bundle_from_zip_xml(filename)
+ vistrail = save_bundle.vistrail
+ # FIXME hack for now, should change in the future
+ log_fname = vistrail.db_log_filename
+ log = vistrails.db.services.io.open_log_from_xml(log_fname, True)
+
+ if version:
+ if isinstance(version, basestring):
+ # need to lookup version number
+ if version in vistrail.db_tags_name_index:
+ version = vistrail.db_tags_name_index[version].db_id
+
+ persistent_module_ids = set()
+ for action in vistrail.db_actions:
+ for op in action.db_operations:
+ if op.db_what == 'module' and (op.vtType == 'add' or
+ op.vtType == 'change'):
+ module = op.db_data
+ if module.db_package in persistence_pkg_ids:
+ persistent_module_ids.add(module.db_id)
+
+ filenames = {}
+ tags = {}
+ for workflow_exec in log.db_workflow_execs:
+ cur_version = workflow_exec.db_parent_version
+ if version is not None and cur_version != version:
+ continue
+ if cur_version in vistrail.db_tags_id_index:
+ tags[cur_version] = vistrail.db_tags_id_index[cur_version].db_name
+
+ for module_exec in workflow_exec.db_item_execs:
+ if module_exec.db_module_id in persistent_module_ids:
+ for annotation in module_exec.db_annotations:
+ if annotation.db_key == 'signature':
+ if cur_version not in filenames:
+ filenames[cur_version] = set()
+ val = annotation.db_value.upper()
+ filenames[cur_version].add(os.path.join(val[:2],
+ val[2:]))
+ shutil.rmtree(save_dir)
+ return filenames, tags
+
+if __name__ == '__main__':
+ fname = sys.argv[1]
+ version = sys.argv[2] if len(sys.argv) > 2 else None
+ if version:
+ try:
+ version = int(version)
+ except ValueError:
+ pass
+ all_files, tags = find_files(fname, version)
+ for version, filenames in all_files.iteritems():
+ if version in tags:
+ print str(version) + ' (' + tags[version] + '):'
+ else:
+ print str(version) + ':'
+ for fname in filenames:
+ print ' ', fname
+
diff --git a/vistrails/packages/persistence/find_workflows.py b/vistrails/packages/persistence/find_workflows.py
new file mode 100644
index 0000000..80140e9
--- /dev/null
+++ b/vistrails/packages/persistence/find_workflows.py
@@ -0,0 +1,132 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import os
+import shutil
+import sys
+
+from compute_hash import compute_hash
+from identifiers import identifier as persistence_pkg, \
+ old_identifiers as persistence_old_ids
+persistence_pkg_ids = set(persistence_old_ids)
+persistence_pkg_ids.add(persistence_pkg)
+
+vistrails_src = None
+if not vistrails_src:
+ vistrails_src = os.path.dirname(
+ os.path.dirname(os.path.dirname(sys.path[0])))
+if vistrails_src not in sys.path:
+ sys.path.append(vistrails_src)
+
+import vistrails.db.services.io
+
+def find_workflows(path_name, vistrail_dir):
+ file_hash = compute_hash(path_name)
+ vt_files = []
+ dir_stack = [vistrail_dir]
+ while dir_stack:
+ dir = dir_stack.pop()
+ for base in os.listdir(dir):
+ name = os.path.join(dir, base)
+ if os.path.isdir(name):
+ dir_stack.append(name)
+ elif name.endswith('.vt'):
+ vt_files.append(name)
+
+ vt_finds = {}
+ for filename in vt_files:
+ save_bundle, save_dir = \
+ vistrails.db.services.io.open_vistrail_bundle_from_zip_xml(filename)
+ vistrail = save_bundle.vistrail
+ log_fname = vistrail.db_log_filename
+ log = vistrails.db.services.io.open_log_from_xml(log_fname, True)
+
+ persistent_module_ids = set()
+ for action in vistrail.db_actions:
+ for op in action.db_operations:
+ if op.db_what == 'module' and (op.vtType == 'add' or
+ op.vtType == 'change'):
+ module = op.db_data
+ if module.db_package in persistence_pkg_ids:
+ persistent_module_ids.add(module.db_id)
+
+ execs = {}
+ tags = {}
+ for workflow_exec in log.db_workflow_execs:
+ cur_version = workflow_exec.db_parent_version
+ if cur_version in vistrail.db_tags_id_index:
+ tags[cur_version] = \
+ vistrail.db_tags_id_index[cur_version].db_name
+
+ for module_exec in workflow_exec.db_item_execs:
+ if module_exec.db_module_id in persistent_module_ids:
+ found = False
+ for annotation in module_exec.db_annotations:
+ if annotation.db_key == 'sha_hash':
+ if annotation.db_value == file_hash:
+ # found the file/dir
+ # do something
+ found = True
+ if annotation.db_key == 'signature':
+ val = annotation.db_value.upper()
+ cache_fname = os.path.join(val[:2], val[2:])
+ if found:
+ if cur_version not in execs:
+ execs[cur_version] = []
+ execs[cur_version].append((workflow_exec.db_ts_start,
+ cache_fname))
+
+ if len(execs) > 0:
+ vt_finds[filename] = (execs, tags)
+
+ shutil.rmtree(save_dir)
+
+ return vt_finds
+
+if __name__ == '__main__':
+ path_name = sys.argv[1]
+ vistrail_dir = sys.argv[2]
+ vt_finds = find_workflows(path_name, vistrail_dir)
+
+ for fname, (execs, tags) in vt_finds.iteritems():
+ print fname + ':'
+ for version, exec_list in execs.iteritems():
+ for (exec_time, cache_fname) in exec_list:
+ if version in tags:
+ print ' ', str(version) + ' (' + tags[version] + '):', \
+ exec_time
+ print ' ', cache_fname
+ else:
+ print ' ', str(version) + ':', exec_time
+ print ' ', cache_fname
diff --git a/vistrails/packages/persistence/identifiers.py b/vistrails/packages/persistence/identifiers.py
new file mode 100644
index 0000000..f108807
--- /dev/null
+++ b/vistrails/packages/persistence/identifiers.py
@@ -0,0 +1,40 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+identifier = 'org.vistrails.vistrails.persistence'
+version = '0.3.2'
+name = 'Persistence'
+old_identifiers = ['edu.utah.sci.vistrails.persistence',
+ 'edu.utah.sci.vistrails.persistence.exp']
diff --git a/vistrails/packages/persistence/init.py b/vistrails/packages/persistence/init.py
new file mode 100644
index 0000000..d02add9
--- /dev/null
+++ b/vistrails/packages/persistence/init.py
@@ -0,0 +1,682 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import copy
+import os
+import shutil
+import tempfile
+import uuid
+
+import vistrails.core.debug
+from vistrails.core.configuration import ConfigurationObject
+from vistrails.core.cache.hasher import Hasher
+from vistrails.core.modules.basic_modules import Path, File, Directory, Boolean, \
+ String, Constant
+from vistrails.core.modules.module_registry import get_module_registry, MissingModule, \
+ MissingPackageVersion, MissingModuleVersion
+from vistrails.core.modules.vistrails_module import Module, ModuleError, NotCacheable
+from vistrails.core.system import current_dot_vistrails, execute_cmdline2, \
+ execute_piped_cmdlines, systemType, \
+ current_user, current_time, get_executable_path
+from vistrails.core.upgradeworkflow import UpgradeWorkflowHandler, UpgradeWorkflowError
+from compute_hash import compute_hash
+from widgets import PersistentRefInlineWidget, \
+ PersistentInputFileConfiguration, PersistentOutputFileConfiguration, \
+ PersistentInputDirConfiguration, PersistentOutputDirConfiguration, \
+ PersistentRefModel, PersistentConfiguration
+from db_utils import DatabaseAccessSingleton
+import repo
+
+try:
+ import hashlib
+ sha_hash = hashlib.sha1
+except ImportError:
+ import sha
+ sha_hash = sha.new
+
+
+global_db = None
+local_db = None
+search_dbs = None
+db_access = None
+git_bin = "@executable_path/git"
+tar_bin = "@executable_path/tar"
+compress_by_default = False
+debug = False
+
+def debug_print(*args):
+ global debug
+ if debug:
+ for arg in args:
+ print arg,
+ print ''
+
+class PersistentRef(Constant):
+
+ # ref types
+ ALWAYS_NEW = 0
+ CREATE = 1
+ EXISTING = 2
+
+ def __init__(self):
+ Constant.__init__(self)
+ self.default_value = self
+
+ self.type = PersistentRef.CREATE
+ self.id = None
+ self.version = None
+ self.local_path = None
+ self.local_read = False
+ self.local_writeback = False
+ self.versioned = False
+ self.name = ''
+ self.tags = ''
+
+ # @staticmethod
+ # def get_widget_class():
+ # return PersistentRefInlineWidget
+
+ @staticmethod
+ def translate_to_python(x):
+ try:
+ res = PersistentRef()
+ s_tuple = eval(x)
+ (res.type, res.id, res.version, res.local_path, res.local_read,
+ res.local_writeback, res.versioned, res.name, res.tags) = s_tuple
+ except:
+ return None
+# result.settings = dict(zip(sorted(default_settings.iterkeys()),
+# s_tuple))
+# print 'from_string:', result.settings
+ return res
+
+ @staticmethod
+ def translate_to_string(x):
+ rep = str((x.type, x.id, x.version, x.local_path,
+ x.local_read, x.local_writeback, x.versioned,
+ x.name, x.tags))
+ # rep = str(tuple(y[1] for y in sorted(x.settings.iteritems())))
+ # print 'to_string:', rep
+ return rep
+
+ @staticmethod
+ def validate(x):
+ return isinstance(x, PersistentRef)
+
+ _input_ports = [('value', '(PersistentRef)')]
+ _output_ports = [('value', '(PersistentRef)')]
+
+class PersistentPath(Module):
+ def __init__(self):
+ Module.__init__(self)
+
+ # FIXME find a way to do this through dulwich and move to repo.py
+ @staticmethod
+ def git_remove_path(path):
+ global git_bin, local_db
+ # only recommended for intermediate files!
+ inner_cmd = [git_bin, "rm", "-r", "--cached", "--ignore-unmatch",path]
+ inner_cmd_str = ' '.join(inner_cmd)
+ cmd_line = PersistentPath.git_command() + \
+ ['filter-branch', '--index-filter', inner_cmd_str, 'HEAD']
+ debug_print('executing', cmd_line)
+ result, output, errs = execute_cmdline2(cmd_line)
+ debug_print('result:', result)
+ debug_print('stdout:', type(output), output)
+ debug_print('stderr:', type(errs), errs)
+ debug_print('***')
+ shutil.rmtree(os.path.join(local_db, ".git", "refs", "original"))
+ cmd_line = PersistentPath.git_command() + ["reflog", "expire","--all"]
+ debug_print('executing', cmd_line)
+ result, output, errs = execute_cmdline2(cmd_line)
+ debug_print('result:', result)
+ debug_print('stdout:', type(output), output)
+ debug_print('stderr:', type(errs), errs)
+ debug_print('***')
+ cmd_line = PersistentPath.git_command() + ["gc", "--aggressive",
+ "--prune"]
+ debug_print('executing', cmd_line)
+ result, output, errs = execute_cmdline2(cmd_line)
+ debug_print('result:', result)
+ debug_print('stdout:', type(output), output)
+ debug_print('stderr:', type(errs), errs)
+ debug_print('***')
+
+ @staticmethod
+ def git_command():
+ if systemType in ['Windows', 'Microsoft']:
+ return ['cd', '/D', local_db, '&&', git_bin]
+ else:
+ return ['cd', local_db, '&&', git_bin]
+
+ def get_path_type(self, path):
+ if os.path.isdir(path):
+ return 'tree'
+ elif os.path.isfile(path):
+ return 'blob'
+
+ def copypath(self, src, dst, path_type=None):
+ if path_type is None:
+ path_type = self.get_path_type(src)
+
+ if path_type == 'blob':
+ shutil.copyfile(src, dst)
+ elif path_type == 'tree':
+ if os.path.exists(dst):
+ shutil.rmtree(dst)
+ shutil.copytree(src, dst)
+ else:
+ raise ModuleError(self, "Unknown path type '%s'" % path_type)
+
+ def set_result(self, path):
+ persistent_path = Path()
+ persistent_path.name = path
+ persistent_path.setResult('value', self)
+ persistent_path.upToDate = True
+ self.setResult("value", persistent_path)
+
+ def updateUpstream(self, is_input=None, path_type=None):
+ global db_access
+
+ if is_input is None:
+ if not self.hasInputFromPort('value'):
+ is_input = True
+ else:
+ # FIXME: check if the signature is the signature of
+ # the value if so we know that it's an input...
+ is_input = False
+
+ self.persistent_ref = None
+ self.persistent_path = None
+ if is_input:
+ return super(PersistentPath, self).updateUpstream()
+
+ # can check updateUpstream
+ if not hasattr(self, 'signature'):
+ raise ModuleError(self, 'Module has no signature')
+
+ ref_exists = False
+ if not self.hasInputFromPort('ref'):
+ # create new reference with no name or tags
+ ref = PersistentRef()
+ ref.signature = self.signature
+ else:
+ # update single port
+ self.updateUpstreamPort('ref')
+ ref = self.getInputFromPort('ref')
+ if db_access.ref_exists(ref.id, ref.version):
+ ref_exists = True
+ if ref.version is None:
+ ref.version = \
+ repo.get_current_repo().get_latest_version(ref.id)
+ signature = db_access.get_signature(ref.id, ref.version)
+ if signature == self.signature:
+ # don't need to create a new version
+ self.persistent_ref = ref
+
+ # Note that ref_exists is True if the reference is a fixed
+ # reference; if it was assigned a new uuid, we can still
+ # reuse a reference with the same signature
+ if not ref_exists:
+ signature = self.signature
+ debug_print('searching for signature', signature)
+ sig_ref = db_access.search_by_signature(signature)
+ debug_print('sig_ref:', sig_ref)
+ if sig_ref:
+ debug_print('setting persistent_ref')
+ ref.id, ref.version, ref.name = sig_ref
+ self.persistent_ref = ref
+ # else:
+ # ref.id = uuid.uuid1()
+
+ # copy as normal
+ # don't copy if equal
+
+ # FIXME also need to check that the file actually exists here!
+ if self.persistent_ref is not None:
+ _, suffix = os.path.splitext(self.persistent_ref.name)
+ self.persistent_path = repo.get_current_repo().get_path(
+ self.persistent_ref.id,
+ self.persistent_ref.version,
+ out_suffix=suffix)
+ debug_print("FOUND persistent path")
+ debug_print(self.persistent_path)
+ debug_print(self.persistent_ref.local_path)
+
+ if self.persistent_ref is None or self.persistent_path is None:
+ debug_print("NOT FOUND persistent path")
+ super(PersistentPath, self).updateUpstream()
+
+ def compute(self, is_input=None, path_type=None):
+ global db_access
+ if not self.hasInputFromPort('value') and \
+ not self.hasInputFromPort('ref'):
+ raise ModuleError(self, "Need to specify path or reference")
+
+ if self.persistent_path is not None:
+ debug_print('using persistent path')
+ ref = self.persistent_ref
+ path = self.persistent_path
+ elif self.hasInputFromPort('ref'):
+ ref = self.getInputFromPort('ref')
+ if ref.id is None:
+ ref.id = str(uuid.uuid1())
+ else:
+ # create a new reference
+ ref = PersistentRef()
+ ref.id = str(uuid.uuid1())
+
+ if self.hasInputFromPort('localPath'):
+ ref.local_path = self.getInputFromPort('localPath').name
+ if self.hasInputFromPort('readLocal'):
+ ref.local_read = self.getInputFromPort('readLocal')
+ if self.hasInputFromPort('writeLocal'):
+ ref.local_writeback = self.getInputFromPort('writeLocal')
+
+ if is_input is None:
+ is_input = False
+ if not self.hasInputFromPort('value'):
+ is_input = True
+ else:
+ if ref.local_path and ref.local_read:
+ debug_print('found local path with local read')
+ is_input = True
+ # FIXME: check if the signature is the signature of
+ # the value if so we know that it's an input...
+
+ # if just reference, pull path from repository (get latest
+ # version unless specified as specific version)
+ if self.persistent_path is None and not self.hasInputFromPort('value') \
+ and is_input and not (ref.local_path and ref.local_read):
+ _, suffix = os.path.splitext(ref.name)
+ if not db_access.ref_exists(ref.id, ref.version):
+ raise ModuleError(self, "Persistent entity '%s' does not "
+ "exist in the local repository." % ref.id)
+ if ref.version is None:
+ ref.version = repo.get_current_repo().get_latest_version(ref.id)
+
+ # get specific ref.uuid, ref.version combo
+ path = repo.get_current_repo().get_path(ref.id, ref.version,
+ out_suffix=suffix)
+
+ elif self.persistent_path is None:
+ # copy path to persistent directory with uuid as name
+ if is_input and ref.local_path and ref.local_read:
+ debug_print('using local_path')
+ path = ref.local_path
+ else:
+ path = self.getInputFromPort('value').name
+ # this is a static method so we need to add module ourselves
+ try:
+ new_hash = repo.get_current_repo().compute_hash(path)
+ except ModuleError, e:
+ e.module = self
+ raise e
+ rep_path = os.path.join(local_db, ref.id)
+ do_update = True
+ if os.path.exists(rep_path):
+ if os.path.isdir(rep_path):
+ actual_type = 'tree'
+ elif os.path.isfile(rep_path):
+ actual_type = 'blob'
+ else:
+ raise ModuleError(self, "Path is something not a file or "
+ "a directory")
+ if path_type is None:
+ path_type = actual_type
+ else:
+ if path_type != actual_type:
+ def show_type(t):
+ if t == 'tree': return "directory"
+ elif t == 'blob': return "file"
+ else: return '"%s"' % t
+ raise ModuleError(self, "Path is not a %s but a %s" % (
+ show_type(path_type),
+ show_type(actual_type)))
+
+ old_hash = repo.get_current_repo().get_hash(ref.id,
+ path_type=path_type)
+ debug_print('old_hash:', old_hash)
+ debug_print('new_hash:', new_hash)
+ if old_hash == new_hash:
+ do_update = False
+
+ if do_update:
+ debug_print('doing update')
+
+ if path_type == 'tree':
+ if (not os.path.exists(path) or
+ not os.listdir(path)):
+ raise ModuleError(self, "This directory is empty")
+
+ self.copypath(path, os.path.join(local_db, ref.id))
+
+ # commit (and add to) repository
+ # get commit id as version id
+ # persist object-hash, commit-version to repository
+ version = repo.get_current_repo().add_commit(ref.id)
+ ref.version = version
+
+ # write object-hash, commit-version to provenance
+ if is_input:
+ signature = new_hash
+ else:
+ signature = self.signature
+ db_access.write_database({'id': ref.id,
+ 'name': ref.name,
+ 'tags': ref.tags,
+ 'user': current_user(),
+ 'date_created': current_time(),
+ 'date_modified': current_time(),
+ 'content_hash': new_hash,
+ 'version': version,
+ 'signature': signature,
+ 'type': path_type})
+
+ # if keep-local and path is different than the selected path, copy
+ # the path to the keep-local path
+ if ref.local_path and ref.local_writeback:
+ if path != ref.local_path:
+ self.copypath(path, ref.local_path)
+ if not str(ref.version):
+ vistrails.core.debug.critical("Persistent version annotation not set correctly "
+ "for persistent_id=%s" % ref.id)
+ # for all paths
+ self.annotate({'persistent_id': ref.id,
+ 'persistent_version': ref.version})
+ self.set_result(path)
+
+ _input_ports = [('value', '(basic:Path)'),
+ ('ref', '(PersistentRef)'),
+ ('localPath', '(basic:Path)'),
+ ('readLocal', '(basic:Boolean)', True),
+ ('writeLocal','(basic:Boolean)', True)]
+ _output_ports = [('value', '(basic:Path)')]
+
+class PersistentFile(PersistentPath):
+ _input_ports = [('value', '(basic:File)'),
+ ('localPath', '(basic:File)')]
+ _output_ports = [('value', '(basic:File)')]
+
+ def updateUpstream(self, is_input=None):
+ PersistentPath.updateUpstream(self, is_input, 'blob')
+
+ def compute(self, is_input=None):
+ PersistentPath.compute(self, is_input, 'blob')
+
+ def set_result(self, path):
+ persistent_path = File()
+ persistent_path.name = path
+ persistent_path.setResult('value', self)
+ persistent_path.upToDate = True
+ self.setResult("value", persistent_path)
+
+class PersistentDir(PersistentPath):
+ _input_ports = [('value', '(basic:Directory)'),
+ ('localPath', '(basic:Directory)')]
+ _output_ports = [('value', '(basic:Directory)')]
+
+ def updateUpstream(self, is_input=None):
+ PersistentPath.updateUpstream(self, is_input, 'tree')
+
+ def compute(self, is_input=None):
+ PersistentPath.compute(self, is_input, 'tree')
+
+ def set_result(self, path):
+ persistent_path = Directory()
+ persistent_path.name = path
+ persistent_path.setResult('value', self)
+ persistent_path.upToDate = True
+ self.setResult("value", persistent_path)
+
+class PersistentInputDir(PersistentDir):
+ _input_ports = [('value', '(basic:Directory)', True)]
+
+ def updateUpstream(self):
+ PersistentDir.updateUpstream(self, True)
+
+ def compute(self):
+ PersistentDir.compute(self, True)
+
+class PersistentIntermediateDir(PersistentDir):
+ def updateUpstream(self):
+ PersistentDir.updateUpstream(self, False)
+
+ def compute(self):
+ PersistentDir.compute(self, False)
+
+class PersistentOutputDir(PersistentDir):
+ _output_ports = [('value', '(basic:Directory)', True)]
+
+ def updateUpstream(self):
+ PersistentDir.updateUpstream(self, False)
+
+ def compute(self):
+ PersistentDir.compute(self, False)
+
+class PersistentInputFile(PersistentFile):
+ _input_ports = [('value', '(basic:File)', True)]
+
+ def updateUpstream(self):
+ PersistentFile.updateUpstream(self, True)
+
+ def compute(self):
+ PersistentFile.compute(self, True)
+
+class PersistentIntermediateFile(PersistentFile):
+ def updateUpstream(self):
+ PersistentFile.updateUpstream(self, False)
+
+ def compute(self):
+ PersistentFile.compute(self, False)
+
+class PersistentOutputFile(PersistentFile):
+ _output_ports = [('value', '(basic:File)', True)]
+
+ def updateUpstream(self):
+ PersistentFile.updateUpstream(self, False)
+
+ def compute(self):
+ PersistentFile.compute(self, False)
+
+#def persistent_ref_hasher(p):
+# return Hasher.parameter_signature(p)
+
+def persistent_module_hasher(pipeline, module, chm):
+ current_hash = Hasher.module_signature(module, chm)
+ ref = None
+ read_local = False
+ for function in module.functions:
+ if function.name == "ref":
+ ref = PersistentRef.translate_to_python(function.params[0].strValue)
+ if function.name == 'readLocal':
+ read_local = \
+ Boolean.translate_to_python(function.params[0].strValue)
+ if ref and not read_local and db_access.ref_exists(ref.id, ref.version):
+ if ref.version is None:
+ ref.version = repo.get_current_repo().get_latest_version(ref.id)
+ return Hasher.compound_signature([current_hash, str(ref.id),
+ str(ref.version)])
+ return current_hash
+
+_modules = [PersistentRef, PersistentPath, PersistentFile, PersistentDir,
+ (PersistentInputFile, {'configureWidgetType': \
+ PersistentInputFileConfiguration,
+ 'signatureCallable': \
+ persistent_module_hasher}),
+ (PersistentOutputFile, {'configureWidgetType': \
+ PersistentOutputFileConfiguration,
+ 'signatureCallable': \
+ persistent_module_hasher}),
+ (PersistentIntermediateFile, {'configureWidgetType': \
+ PersistentOutputFileConfiguration,
+ 'signatureCallable': \
+ persistent_module_hasher}),
+ (PersistentInputDir, {'configureWidgetType': \
+ PersistentInputDirConfiguration,
+ 'signatureCallable': \
+ persistent_module_hasher}),
+ (PersistentOutputDir, {'configureWidgetType': \
+ PersistentOutputDirConfiguration,
+ 'signatureCallable': \
+ persistent_module_hasher}),
+ (PersistentIntermediateDir, {'configureWidgetType': \
+ PersistentOutputDirConfiguration,
+ 'signatureCallable': \
+ persistent_module_hasher})]
+
+def initialize():
+ global global_db, local_db, search_dbs, compress_by_default, db_access, \
+ git_bin, debug
+
+ if configuration.check('git_bin'):
+ git_bin = configuration.git_bin
+ if git_bin.startswith("@executable_path/"):
+ non_expand_path = git_bin
+ git_bin = get_executable_path(git_bin[len("@executable_path/"):])
+ if git_bin is not None:
+ configuration.git_bin = non_expand_path
+ if git_bin is None:
+ git_bin = 'git'
+ configuration.git_bin = git_bin
+
+ if configuration.check('compress_by_default'):
+ compress_by_default = configuration.compress_by_default
+ if configuration.check('debug'):
+ debug = configuration.debug
+ if configuration.check('global_db'):
+ global_db = configuration.global_db
+ if configuration.check('local_db'):
+ local_db = configuration.local_db
+ if not os.path.exists(local_db):
+ raise RuntimeError('local_db "%s" does not exist' % local_db)
+ else:
+ local_db = os.path.join(current_dot_vistrails(), 'persistent_files')
+ if not os.path.exists(local_db):
+ try:
+ os.mkdir(local_db)
+ except:
+ raise RuntimeError('local_db "%s" does not exist' % local_db)
+
+ local_repo = repo.get_repo(local_db)
+ repo.set_current_repo(local_repo)
+
+ debug_print('creating DatabaseAccess')
+ db_path = os.path.join(local_db, '.files.db')
+ db_access = DatabaseAccessSingleton(db_path)
+ debug_print('done', db_access)
+
+ search_dbs = [local_db,]
+ if configuration.check('search_dbs'):
+ try:
+ check_paths = eval(configuration.search_dbs)
+ except:
+ print "*** persistence error: cannot parse search_dbs ***"
+ for path in check_paths:
+ if os.path.exists(path):
+ search_dbs.append(path)
+ else:
+ print '*** persistence warning: cannot find path "%s"' % path
+
+_configuration_widget = None
+
+def finalize():
+ # delete all temporary files/directories used by zip
+ global db_access, _configuration_widget
+
+ for fname in repo.get_current_repo().temp_persist_files:
+ if os.path.isfile(fname):
+ os.remove(fname)
+ elif os.path.isdir(fname):
+ shutil.rmtree(fname)
+ db_access.finalize()
+ if _configuration_widget is not None:
+ _configuration_widget.deleteLater()
+
+def menu_items():
+ def show_configure():
+ global _configuration_widget
+ if _configuration_widget is None:
+ _configuration_widget = PersistentConfiguration()
+ _configuration_widget.show()
+ menu_tuple = (("Manage Store...", show_configure),)
+ return menu_tuple
+
+def handle_module_upgrade_request(controller, module_id, pipeline):
+ module_remap = {
+ # Migrates from pre-0.1.0 to 0.2.0+
+ 'PersistentFile': [
+ (None, '0.1.0', 'PersistentIntermediateFile', {
+ 'dst_port_remap': {
+ 'compress': None}})],
+ 'PersistentDirectory': [
+ (None, '0.1.0', 'PersistentIntermediateDir', {
+ 'dst_port_remap': {
+ 'compress': None}})],
+ # Migrates from persistence_exp (0.1.0-0.2.0) to 0.2.0+
+ 'ManagedRef': [
+ ('0.1.0', None, 'persistence:PersistentRef', {})],
+ 'ManagedPath': [
+ ('0.1.0', None, 'persistence:PersistentPath', {})],
+ 'ManagedFile': [
+ ('0.1.0', None, 'persistence:PersistentFile', {})],
+ 'ManagedDir': [
+ ('0.1.0', None, 'persistence:PersistentDir', {})],
+ 'ManagedInputFile': [
+ ('0.1.0', None, 'persistence:PersistentInputFile', {})],
+ 'ManagedOutputFile': [
+ ('0.1.0', None, 'persistence:PersistentOutputFile', {})],
+ 'ManagedIntermediateFile': [
+ ('0.1.0', None, 'persistence:PersistentIntermediateFile', {})],
+ 'ManagedInputDir': [
+ ('0.1.0', None, 'persistence:PersistentInputDir', {})],
+ 'ManagedOutputDir': [
+ ('0.1.0', None, 'persistence:PersistentOutputDir', {})],
+ 'ManagedIntermediateDir': [
+ ('0.1.0', None, 'persistence:PersistentIntermediateDir', {})]
+ }
+ for module in ['PersistentPath', 'PersistentFile', 'PersistentDir',
+ 'PersistentInputFile', 'PersistentOutputFile',
+ 'PersistentIntermediateFile',
+ 'PersistentInputDir', 'PersistentOutputDir',
+ 'PersistentIntermediateDir']:
+ upgrade = ('0.2.0', '0.2.2', None,
+ {'dst_port_remap': {'ref': 'ref'}})
+ if module in module_remap:
+ module_remap[module].append(upgrade)
+ else:
+ module_remap[module] = [upgrade]
+
+ return UpgradeWorkflowHandler.remap_module(controller, module_id, pipeline,
+ module_remap)
diff --git a/vistrails/packages/persistence/repo.py b/vistrails/packages/persistence/repo.py
new file mode 100644
index 0000000..b43eec9
--- /dev/null
+++ b/vistrails/packages/persistence/repo.py
@@ -0,0 +1,272 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from vistrails.core.bundles import py_import
+py_import('dulwich', {
+ 'pip': 'dulwich',
+ 'linux-debian': 'python-dulwich',
+ 'linux-ubuntu': 'python-dulwich',
+ 'linux-fedora': 'python-dulwich'})
+from vistrails.core import debug
+
+from dulwich.errors import NotCommitError, NotGitRepository
+from dulwich.repo import Repo
+from dulwich.objects import Commit, Blob, Tree, object_header
+from dulwich.pack import iter_sha1
+from dulwich.walk import Walker
+from itertools import chain
+import os
+import shutil
+import stat
+import tempfile
+
+class GitRepo(object):
+ def __init__(self, path):
+ if os.path.exists(path):
+ if not os.path.isdir(path):
+ raise IOError('Git repository "%s" must be a directory.' %
+ path)
+ try:
+ self.repo = Repo(path)
+ except NotGitRepository:
+ # repo does not exist
+ self.repo = Repo.init(path, not os.path.exists(path))
+
+ self.temp_persist_files = []
+
+ def _get_commit(self, version="HEAD"):
+ commit = self.repo[version]
+ if not isinstance(commit, Commit):
+ raise NotCommitError(commit)
+ return commit
+
+ def get_type(self, name, version="HEAD"):
+ commit = self._get_commit(version)
+
+ tree = self.repo.tree(commit.tree)
+ if name not in tree:
+ raise KeyError('Cannot find object "%s"' % name)
+ if tree[name][0] & stat.S_IFDIR:
+ return "tree"
+ else:
+ return "blob"
+
+ def get_path(self, name, version="HEAD", path_type=None, out_name=None,
+ out_suffix=''):
+ if path_type is None:
+ path_type = self.get_type(name, version)
+ if path_type == 'tree':
+ return self.get_dir(name, version, out_name, out_suffix)
+ elif path_type == 'blob':
+ return self.get_file(name, version, out_name, out_suffix)
+
+ raise TypeError("Unknown path type '%s'" % path_type)
+
+ def _write_blob(self, blob_sha, out_fname=None, out_suffix=''):
+ if out_fname is None:
+ # create a temporary file
+ (fd, out_fname) = tempfile.mkstemp(suffix=out_suffix,
+ prefix='vt_persist')
+ os.close(fd)
+ self.temp_persist_files.append(out_fname)
+ else:
+ out_dirname = os.path.dirname(out_fname)
+ if out_dirname and not os.path.exists(out_dirname):
+ os.makedirs(out_dirname)
+
+ blob = self.repo.get_blob(blob_sha)
+ with open(out_fname, "wb") as f:
+ for b in blob.as_raw_chunks():
+ f.write(b)
+ return out_fname
+
+ def get_file(self, name, version="HEAD", out_fname=None,
+ out_suffix=''):
+ commit = self._get_commit(version)
+ tree = self.repo.tree(commit.tree)
+ if name not in tree:
+ raise KeyError('Cannot find blob "%s"' % name)
+ blob_sha = tree[name][1]
+ out_fname = self._write_blob(blob_sha, out_fname, out_suffix)
+ return out_fname
+
+ def get_dir(self, name, version="HEAD", out_dirname=None,
+ out_suffix=''):
+ if out_dirname is None:
+ # create a temporary directory
+ out_dirname = tempfile.mkdtemp(suffix=out_suffix,
+ prefix='vt_persist')
+ self.temp_persist_files.append(out_dirname)
+ elif not os.path.exists(out_dirname):
+ os.makedirs(out_dirname)
+
+ commit = self._get_commit(version)
+ tree = self.repo.tree(commit.tree)
+ if name not in tree:
+ raise KeyError('Cannot find tree "%s"' % name)
+ subtree_id = tree[name][1]
+ # subtree = self.repo.tree(subtree_id)
+ for entry in self.repo.object_store.iter_tree_contents(subtree_id):
+ out_fname = os.path.join(out_dirname, entry.path)
+ self._write_blob(entry.sha, out_fname)
+ return out_dirname
+
+ def get_hash(self, name, version="HEAD", path_type=None):
+ commit = self._get_commit(version)
+ tree = self.repo.tree(commit.tree)
+ if name not in tree:
+ raise KeyError('Cannot find object "%s"' % name)
+ return tree[name][1]
+
+ @staticmethod
+ def compute_blob_hash(fname, chunk_size=1<<16):
+ obj_len = os.path.getsize(fname)
+ head = object_header(Blob.type_num, obj_len)
+ with open(fname, "rb") as f:
+ def read_chunk():
+ return f.read(chunk_size)
+ my_iter = chain([head], iter(read_chunk,''))
+ return iter_sha1(my_iter)
+ return None
+
+ @staticmethod
+ def compute_tree_hash(dirname):
+ tree = Tree()
+ for entry in sorted(os.listdir(dirname)):
+ fname = os.path.join(dirname, entry)
+ if os.path.isdir(fname):
+ thash = GitRepo.compute_tree_hash(fname)
+ mode = stat.S_IFDIR # os.stat(fname)[stat.ST_MODE]
+ tree.add(entry, mode, thash)
+ elif os.path.isfile(fname):
+ bhash = GitRepo.compute_blob_hash(fname)
+ mode = os.stat(fname)[stat.ST_MODE]
+ tree.add(entry, mode, bhash)
+ return tree.id
+
+ @staticmethod
+ def compute_hash(path):
+ if os.path.isdir(path):
+ return GitRepo.compute_tree_hash(path)
+ elif os.path.isfile(path):
+ return GitRepo.compute_blob_hash(path)
+ raise TypeError("Do not support this type of path")
+
+ def get_latest_version(self, path):
+ head = self.repo.head()
+ walker = Walker(self.repo.object_store, [head], max_entries=1,
+ paths=[path])
+ return iter(walker).next().commit.id
+
+ def _stage(self, filename):
+ fullpath = os.path.join(self.repo.path, filename)
+ if os.path.islink(fullpath):
+ debug.warning("Warning: not staging symbolic link %s" % os.path.basename(filename))
+ elif os.path.isdir(fullpath):
+ for f in os.listdir(fullpath):
+ self._stage(os.path.join(filename, f))
+ else:
+ if os.path.sep != '/':
+ filename = filename.replace(os.path.sep, '/')
+ self.repo.stage(filename)
+
+ def add_commit(self, filename):
+ self.setup_git()
+ self._stage(filename)
+ commit_id = self.repo.do_commit('Updated %s' % filename)
+ return commit_id
+
+ def setup_git(self):
+ config_stack = self.repo.get_config_stack()
+
+ try:
+ config_stack.get(('user',), 'name')
+ config_stack.get(('user',), 'email')
+ except KeyError:
+ from vistrails.core.system import current_user
+ from dulwich.config import ConfigFile
+ user = current_user()
+ repo_conf = self.repo.get_config()
+ repo_conf.set(('user',), 'name', user)
+ repo_conf.set(('user',), 'email', '%s at localhost' % user)
+ repo_conf.write_to_path()
+
+current_repo = None
+
+def get_current_repo():
+ return current_repo
+def set_current_repo(repo):
+ global current_repo
+ current_repo = repo
+
+def get_repo(path):
+ return GitRepo(path)
+
+def run_get_file_test():
+ r = GitRepo("/vistrails/src/git")
+ r.get_file("README.md", "HEAD", "testREADMEout.md")
+
+def run_get_dir_test():
+ r = GitRepo("/vistrails/src/git")
+ r.get_dir("scripts", "HEAD", "testScriptsout")
+
+def run_get_type_test():
+ r = GitRepo("/vistrails/src/git")
+ print "README.md:", r.get_type("README.md")
+ print "scripts:", r.get_type("scripts")
+
+def run_compute_sha_test():
+ r = GitRepo("/vistrails/src/git")
+ print r.get_hash("README.md")
+ # print r.compute_blob_hash("/Users/dakoop/Downloads/xcode_2.4.1_8m1910_6936315.dmg")
+ print r.compute_blob_hash("/vistrails/src/git/README.md")
+
+def run_compute_sha_dir_test():
+ r = GitRepo("/vistrails/src/git")
+ print r.get_hash("scripts")
+ print r.compute_tree_hash("/vistrails/src/git/scripts")
+
+def run_get_latest_test():
+ r = GitRepo("/vistrails/src/git")
+ print r.get_latest_version("README.md")
+
+def run_init_add_test():
+ r = GitRepo("/Users/dakoop/.vistrails/git_test")
+ shutil.copy("/vistrails/src/git/README.md",
+ "/Users/dakoop/.vistrails/git_test")
+ print r.add_commit("README.md")
+
+if __name__ == '__main__':
+ run_init_add_test()
diff --git a/vistrails/packages/persistence/schema.sql b/vistrails/packages/persistence/schema.sql
new file mode 100644
index 0000000..068d5ea
--- /dev/null
+++ b/vistrails/packages/persistence/schema.sql
@@ -0,0 +1,37 @@
+--#############################################################################
+--
+-- Copyright (C) 2011-2014, NYU-Poly.
+-- Copyright (C) 2006-2011, University of Utah.
+-- All rights reserved.
+-- Contact: contact at vistrails.org
+--
+-- This file is part of VisTrails.
+--
+-- "Redistribution and use in source and binary forms, with or without
+-- modification, are permitted provided that the following conditions are met:
+--
+-- - Redistributions of source code must retain the above copyright notice,
+-- this list of conditions and the following disclaimer.
+-- - Redistributions in binary form must reproduce the above copyright
+-- notice, this list of conditions and the following disclaimer in the
+-- documentation and/or other materials provided with the distribution.
+-- - Neither the name of the University of Utah nor the names of its
+-- contributors may be used to endorse or promote products derived from
+-- this software without specific prior written permission.
+--
+-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+-- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+-- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+-- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+-- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+-- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+-- OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+-- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+-- OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+-- ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+--
+--#############################################################################
+
+create table file (id text, name text, tags text, user text, date_created text, date_modified text, content_hash text, version text, signature text, type text);
+create index signature_idx on file(signature);
\ No newline at end of file
diff --git a/vistrails/packages/persistence/widgets.py b/vistrails/packages/persistence/widgets.py
new file mode 100644
index 0000000..ec5b50e
--- /dev/null
+++ b/vistrails/packages/persistence/widgets.py
@@ -0,0 +1,1184 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+import os
+import re
+import uuid
+
+from vistrails.core.modules.basic_modules import Path
+from vistrails.gui.common_widgets import QSearchBox, QSearchEditBox
+from vistrails.gui.modules.constant_configuration import ConstantWidgetMixin
+from vistrails.gui.modules.module_configure import StandardModuleConfigurationWidget
+
+from db_utils import DatabaseAccessSingleton
+from identifiers import identifier as persistence_pkg
+import repo
+
+class IntegerWrapper(object):
+ def __init__(self, idx):
+ self.idx = idx
+
+class PersistentRefModelSingleton(object):
+ def __new__(self, *args, **kw):
+ if PersistentRefModel._instance is None:
+ obj = PersistentRefModel(*args, **kw)
+ PersistentRefModel._instance = obj
+ return PersistentRefModel._instance
+
+class PersistentRefModel(QtCore.QAbstractItemModel):
+
+ _instance = None
+
+ # 2013-09-03 18:57:53.133000
+ _DATE_FORMAT = re.compile(r'^(?P<y>[0-9]{4})-'
+ r'(?P<m>[0-9]{2})-'
+ r'(?P<d>[0-9]{2}) '
+ r'(?P<H>[0-9]{2}):'
+ r'(?P<M>[0-9]{2}):'
+ r'(?P<S>[0-9]{2}).'
+ r'(?P<ms>[0-9]+)$')
+
+ cols = {0: "name",
+ 1: "type",
+ 2: "tags",
+ 3: "user",
+ 4: "date_created",
+ 5: "date_modified",
+ 6: "id",
+ 7: "version",
+ 8: "content_hash",
+ 9: "signature"}
+ idxs = dict((v,k) for (k,v) in cols.iteritems())
+ headers = {"id": "ID",
+ "name": "Name",
+ "tags": "Tags",
+ "user": "User",
+ "date_created": "Date Created",
+ "date_modified": "Date Modified",
+ "content_hash": "Content Hash",
+ "version": "Version",
+ "signature": "Signature",
+ "type": "Type"}
+
+ def __init__(self, parent=None):
+ QtCore.QAbstractItemModel.__init__(self, parent)
+
+ self.db_access = DatabaseAccessSingleton()
+ self.db_access.set_model(self)
+ rows = self.db_access.read_database(
+ [c[1] for c in sorted(self.cols.iteritems())])
+ rows = map(self.fix_dates, rows)
+
+ self.id_lists = {}
+ for ref in rows:
+ if ref[self.idxs['id']] not in self.id_lists:
+ self.id_lists[ref[self.idxs['id']]] = []
+ self.id_lists[ref[self.idxs['id']]].append(ref)
+
+ self.id_lists_keys = self.id_lists.keys()
+
+ self.integer_wrappers = {}
+
+ @staticmethod
+ def fix_dates(row):
+ row = list(row)
+ for c in ('date_created', 'date_modified'):
+ c = PersistentRefModel.idxs[c]
+ m = PersistentRefModel._DATE_FORMAT.match(row[c])
+ if m is not None:
+ row[c] = '{y}-{m}-{d} {H}:{M}'.format(**m.groupdict())
+ return tuple(row)
+
+ def rowCount(self, parent=QtCore.QModelIndex()):
+ if not parent.isValid():
+ # print 'rowCount:', len(self.id_lists_keys)
+ return len(self.id_lists_keys)
+ # print 'parentValid rowCount:', \
+ # len(self.id_lists[self.id_lists_keys[parent.row()]])
+ return len(self.id_lists[self.id_lists_keys[parent.row()]])
+
+ def columnCount(self, parent=QtCore.QModelIndex()):
+ # print 'columnCount:', len(self.headers)
+ return len(self.headers)
+
+ def hasChildren(self, parent=QtCore.QModelIndex()):
+ # print 'hasChildren:'
+ if not parent.isValid():
+ # print ' True'
+ return True
+ else:
+ # print ' PARENT:', parent.row(), parent.column(), \
+ # parent.internalPointer()
+ if not parent.parent().isValid():
+ # print ' TRUE'
+ return True
+ # print ' False'
+ return False
+
+ def headerData(self, section, orientation, role=QtCore.Qt.DisplayRole):
+ if role != QtCore.Qt.DisplayRole:
+ return None
+ if section in self.cols:
+ return self.headers[self.cols[section]]
+ return None
+
+ def data(self, index, role):
+ if not index.isValid() or role != QtCore.Qt.DisplayRole:
+ return None
+ # if index.parent().isValid():
+ # print 'data', index.row(), index.column(), index.parent().row()
+ if index.parent().isValid():
+ # have a child node
+ # print 'got child node!', index.parent().row()
+ id_list = self.id_lists[self.id_lists_keys[index.parent().row()]]
+ data = id_list[index.row()]
+ else:
+ # have a parent node
+ id_list = self.id_lists[self.id_lists_keys[index.row()]]
+ data = id_list[0]
+ # want to have the earliest created date and latest modified date
+ if index.column() == self.idxs['date_created']:
+ dates = [l[index.column()] for l in id_list]
+ return min(dates)
+ if index.column() == self.idxs['date_modified']:
+ dates = [l[index.column()] for l in id_list]
+ return max(dates)
+ if index.column() == self.idxs['version'] or \
+ index.column() == self.idxs['signature'] or \
+ index.column() == self.idxs['content_hash'] or \
+ index.column() == self.idxs['user']:
+ return None
+
+ if index.column() < len(data):
+ return data[index.column()]
+ return None
+
+ def parent(self, index):
+ # print 'calling parent() method'
+ if index.isValid():
+ # print ' index is valid', index.row(), index.column()
+ if index.internalPointer():
+ parent_item = index.internalPointer().idx
+ # print ' parent_item:', parent_item
+ return self.createIndex(parent_item, 0, None)
+# else:
+# # print ' internalPointer is not valid'
+# else:
+# # print 'index not valid for parent call'
+ return QtCore.QModelIndex()
+
+ def index(self, row, column, parent):
+ # print 'index:', row, column
+ if not parent.isValid():
+ if len(self.id_lists_keys) > row:
+ # print ' no parent item'
+ return self.createIndex(row, column, None)
+ else:
+ # print ' **** parent_item', row, column, parent.row()
+ if len(self.id_lists[self.id_lists_keys[parent.row()]]) > row:
+ # print ' ++++ creating index'
+ # !!! internalPointer is a weakref in PyQt !!!
+ if parent.row() not in self.integer_wrappers:
+ integer_wrapper = IntegerWrapper(parent.row())
+ self.integer_wrappers[parent.row()] = integer_wrapper
+ else:
+ integer_wrapper = self.integer_wrappers[parent.row()]
+ # print ' ---- created parent wrapper'
+ return self.createIndex(row, column, integer_wrapper)
+ return QtCore.QModelIndex()
+
+ def sort(self, column, order=QtCore.Qt.AscendingOrder):
+ self.emit(QtCore.SIGNAL('layoutAboutToBeChanged()'))
+ if column == -1:
+ return
+ self.id_lists_keys.sort(key=lambda x: self.id_lists[x][0][column],
+ reverse=(order==QtCore.Qt.AscendingOrder))
+ self.emit(QtCore.SIGNAL('layoutChanged()'))
+
+ def find_row(self, id, version=None):
+ if id in self.id_lists:
+ i = self.id_lists_keys.index(id)
+ if version is not None:
+ for j, data in enumerate(self.id_lists[id]):
+ if data[self.idxs['version']] == version:
+ if i not in self.integer_wrappers:
+ integer_wrapper = IntegerWrapper(i)
+ self.integer_wrappers[i] = integer_wrapper
+ else:
+ integer_wrapper = self.integer_wrappers[i]
+ return self.createIndex(j, 0, integer_wrapper)
+ return self.createIndex(i, 0, 0)
+# for i, id in enumerate(self.id_lists_keys):
+
+# if version is not None:
+# for data in enumerate(self.id_lists[id]):
+# if
+# for i, data in enumerate(self.id_lists):
+# if data[self.idxs['id']] == id and \
+# (not version or data[self.idxs['version']] == version):
+# return self.createIndex(i, 0, 0)
+ return QtCore.QModelIndex()
+
+ def add_data(self, value_dict):
+ id = value_dict['id']
+ value_list = []
+ for _, c in sorted(self.cols.iteritems()):
+ if c in value_dict:
+ value_list.append(str(value_dict[c]))
+ else:
+ value_list.append(None)
+ if id not in self.id_lists:
+ self.id_lists[id] = []
+ self.id_lists_keys.append(id)
+ self.id_lists[id].append(self.fix_dates(value_list))
+ self.reset()
+
+ def remove_data(self, where_dict):
+ id = where_dict['id']
+ version = where_dict.get('version', None)
+ if version is not None:
+ found = False
+ for idx, value_tuple in enumerate(self.id_lists[id]):
+ if value_tuple[self.idxs['version']] == version:
+ found = True
+ break
+ if found:
+ del self.id_lists[id][idx]
+ else:
+ path_type = self.id_lists[id][0][self.idxs['type']]
+ found = False
+ for idx, key_id in enumerate(self.id_lists_keys):
+ if key_id == id:
+ found = True
+ break
+ if found:
+ del self.id_lists_keys[idx]
+ del self.id_lists[id]
+ self.reset()
+
+class PersistentRefView(QtGui.QTreeView):
+ def __init__(self, path_type=None, parent=None):
+ QtGui.QTreeView.__init__(self, parent)
+ self.my_model = PersistentRefModelSingleton()
+ print 'my_model:', id(self.my_model)
+ proxy_model = QtGui.QSortFilterProxyModel(self)
+ proxy_model.setSourceModel(self.my_model)
+ proxy_model.setFilterKeyColumn(-1)
+ self.setModel(proxy_model)
+ self.set_visibility(path_type)
+
+ self.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
+ self.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
+ self.setEditTriggers(QtGui.QAbstractItemView.NoEditTriggers)
+ self.setSortingEnabled(True)
+ self.current_id = None
+ self.current_version = None
+
+ for i in xrange(self.my_model.columnCount()):
+ self.resizeColumnToContents(i)
+
+ def set_visibility(self, path_type=None):
+ if path_type == "blob":
+ self.header().hideSection(self.my_model.idxs["type"])
+ for i, key in enumerate(self.my_model.id_lists_keys):
+ id_list = self.my_model.id_lists[key]
+ if id_list[0][self.my_model.idxs["type"]] != "blob":
+ # if i not in self.my_model.file_idxs:
+ print "setting index", i, "to hidden"
+ my_index = self.my_model.createIndex(i, 0, None)
+ index = self.model().mapFromSource(my_index)
+ self.setRowHidden(index.row(), QtCore.QModelIndex(), True)
+ elif path_type == "tree":
+ self.header().hideSection(self.my_model.idxs["type"])
+ for i, key in enumerate(self.my_model.id_lists_keys):
+ id_list = self.my_model.id_lists[key]
+ if id_list[0][self.my_model.idxs["type"]] != "tree":
+ # if i not in self.my_model.dir_idxs:
+ print "setting index", i, "to hidden"
+ my_index = self.my_model.createIndex(i, 0, None)
+ index = self.model().mapFromSource(my_index)
+ self.setRowHidden(index.row(), QtCore.QModelIndex(), True)
+
+ def set_selection(self):
+ if self.current_id:
+ my_index = self.my_model.find_row(self.current_id,
+ self.current_version)
+
+ index = self.model().mapFromSource(my_index)
+ if index.isValid():
+ print 'checking internalPointer', my_index.internalPointer()
+ if my_index.internalPointer():
+ my_expand_index = \
+ self.my_model.createIndex(
+ my_index.internalPointer().idx, 0, 0)
+ expand_index = self.model().mapFromSource(my_expand_index)
+ self.expand(expand_index)
+ self.selectionModel().select(
+ index, QtGui.QItemSelectionModel.ClearAndSelect | \
+ QtGui.QItemSelectionModel.Rows)
+ return True
+ return False
+
+ def set_id(self, id):
+ self.current_id = id
+ return self.set_selection()
+
+ def set_version(self, version):
+ self.current_version = version
+ return self.set_selection()
+
+ def get_id(self):
+ sf_index = self.selectionModel().selectedRows()[0]
+ index = self.model().mapToSource(sf_index)
+ if index.internalPointer():
+ paridx = index.internalPointer().idx
+ id_list = \
+ self.my_model.id_lists[self.my_model.id_lists_keys[paridx]]
+ id = id_list[index.row()][self.my_model.idxs['id']]
+ else:
+ id_list = \
+ self.my_model.id_lists[self.my_model.id_lists_keys[index.row()]]
+ id = id_list[0][self.my_model.idxs['id']]
+ return str(id)
+
+ def get_version(self):
+ sf_index = self.selectionModel().selectedRows()[0]
+ index = self.model().mapToSource(sf_index)
+ if index.internalPointer():
+ paridx = index.internalPointer().idx
+ id_list = \
+ self.my_model.id_lists[self.my_model.id_lists_keys[paridx]]
+ version = id_list[index.row()][self.my_model.idxs['version']]
+ return str(version)
+ return None
+
+ def get_info(self):
+ return self.get_info_list()[0]
+
+ def get_info_list(self):
+ s_indexes = self.selectionModel().selectedRows()
+ info_list = []
+ for s_idx in s_indexes:
+ index = self.model().mapToSource(s_idx)
+ if index.internalPointer():
+ paridx = index.internalPointer().idx
+ id_list = \
+ self.my_model.id_lists[self.my_model.id_lists_keys[paridx]]
+ info = id_list[index.row()]
+ version = str(info[self.my_model.idxs['version']])
+ else:
+ id_list = self.my_model.id_lists[ \
+ self.my_model.id_lists_keys[index.row()]]
+ info = id_list[0]
+ version = None
+ info_list.append((str(info[self.my_model.idxs['id']]),
+ version,
+ str(info[self.my_model.idxs['name']]),
+ str(info[self.my_model.idxs['tags']])))
+ return info_list
+
+class PersistentRefDialog(QtGui.QDialog):
+ def __init__(self, param, parent=None):
+ QtGui.QDialog.__init__(self, parent)
+ # two tabs, one for starting from managed, one for local file
+ # options are set accordingly
+ # uuid assigned when options are set, either new or existing
+ # don't compute uuid for local file that hasn't been run
+ # need PersistentReference parameter
+ # allow user to pass contents in to PersistentRef
+ self.setWindowTitle("Configure Persistent Reference...")
+
+ self.settings = {'ref_id': None,
+ 'ref_version': None,
+ 'local_path': None,
+ 'versioning': False,
+ 'local_read_priority': True,
+ 'write_back': True}
+
+ self.current_file = ""
+ db_file = "/vistrails/managed/files.db"
+
+ layout = QtGui.QVBoxLayout()
+ managed_group = QtGui.QGroupBox("Persistent Data")
+ managed_layout = QtGui.QVBoxLayout()
+ search = QSearchBox(False, False)
+
+ def keyPressEvent(obj, e):
+ print "got to key press event", e.key()
+ if e.key() in (QtCore.Qt.Key_Return,QtCore.Qt.Key_Enter):
+ if obj.currentText():
+ obj.emit(QtCore.SIGNAL('executeSearch(QString)'),
+ obj.searchEdit.currentText())
+ else:
+ obj.emit(QtCore.SIGNAL('resetSearch()'))
+ QtGui.QComboBox.keyPressEvent(obj, e)
+
+ print 'keyPressEvent:', search.searchEdit.keyPressEvent
+ search.searchEdit.keyPressEvent = keyPressEvent
+ print 'keyPressEvent:', search.searchEdit.keyPressEvent
+ self.connect(search, QtCore.SIGNAL('executeSearch(QString)'),
+ self.search_string)
+ self.connect(search, QtCore.SIGNAL('resetSearch()'),
+ self.reset_search)
+ managed_layout.addWidget(search)
+ self.table = PersistentRefView(db_file, self)
+ managed_layout.addWidget(self.table)
+ managed_group.setLayout(managed_layout)
+ layout.addWidget(managed_group)
+
+ local_group = QtGui.QGroupBox("Local Data")
+ local_layout = QtGui.QHBoxLayout()
+ self.filename_edit = QtGui.QLineEdit()
+ local_layout.addWidget(self.filename_edit)
+
+ filename_button = QtGui.QToolButton()
+ filename_button.setIcon(
+ QtGui.QIcon(filename_button.style().standardPixmap(
+ QtGui.QStyle.SP_DirOpenIcon)))
+ filename_button.setIconSize(QtCore.QSize(12,12))
+ filename_button.connect(filename_button,
+ QtCore.SIGNAL('clicked()'),
+ self.choose_file)
+ local_layout.addWidget(filename_button)
+ local_group.setLayout(local_layout)
+ layout.addWidget(local_group)
+
+ pref_layout = QtGui.QHBoxLayout()
+ version_group = QtGui.QGroupBox("Versioning")
+ version_layout = QtGui.QVBoxLayout()
+ version_off = QtGui.QRadioButton("Create New ID")
+ version_layout.addWidget(version_off)
+ version_on = QtGui.QRadioButton("Create New Version")
+ version_layout.addWidget(version_on)
+ version_group.setLayout(version_layout)
+ pref_layout.addWidget(version_group)
+
+ r_priority_group = QtGui.QGroupBox("Read Priority")
+ r_priority_layout = QtGui.QVBoxLayout()
+ r_priority_off = QtGui.QRadioButton("Local")
+ r_priority_layout.addWidget(r_priority_off)
+ r_priority_on = QtGui.QRadioButton("Persistent Store")
+ r_priority_layout.addWidget(r_priority_on)
+ r_priority_group.setLayout(r_priority_layout)
+ pref_layout.addWidget(r_priority_group)
+
+ w_priority_group = QtGui.QGroupBox("Write Priority")
+ w_priority_layout = QtGui.QVBoxLayout()
+ w_priority_off = QtGui.QRadioButton("Local")
+ w_priority_layout.addWidget(w_priority_off)
+ w_priority_on = QtGui.QRadioButton("Persistent Store")
+ w_priority_layout.addWidget(w_priority_on)
+ w_priority_group.setLayout(w_priority_layout)
+ pref_layout.addWidget(w_priority_group)
+ layout.addLayout(pref_layout)
+
+ button_layout = QtGui.QHBoxLayout()
+ button_layout.setDirection(QtGui.QBoxLayout.RightToLeft)
+ button_layout.setAlignment(QtCore.Qt.AlignRight)
+ ok_button = QtGui.QPushButton("OK")
+ ok_button.setFixedWidth(100)
+ self.connect(ok_button, QtCore.SIGNAL('clicked()'), self.close)
+ button_layout.addWidget(ok_button)
+ cancel_button = QtGui.QPushButton("Cancel")
+ cancel_button.setFixedWidth(100)
+ self.connect(cancel_button, QtCore.SIGNAL('clicked()'), self.cancel)
+ button_layout.addWidget(cancel_button)
+ layout.addLayout(button_layout)
+ self.setLayout(layout)
+
+ def close(self):
+ self.done(QtGui.QDialog.Accepted)
+
+ def cancel(self):
+ self.done(QtGui.QDialog.Rejected)
+
+ def choose_file(self):
+ chosen_file = \
+ QtGui.QFileDialog.getOpenFileName(self,
+ 'Use File...',
+ self.current_file,
+ 'All files (*.*)')
+ if chosen_file:
+ self.current_file = chosen_file
+ self.filename_edit.setText(self.current_file)
+
+ def build_table(self):
+ # read sql table from sqlite3
+ # display table
+ pass
+
+ def select_file(self):
+ # present file dialog and allow user to choose file
+ # compute file hash
+ # if content exists in persistent store, ask to reuse
+ # (or set reuse checkbox)
+ # set use_local checkbox to True
+ # don't transfer until execution?
+ # create uuid for file
+ pass
+
+ def select_remote(self):
+ # present table of data with search box
+ # each data has name, id, user, date, tags, etc.
+ # if user selects, check use_local checkbox to False
+ # store local is False, too?
+ # don't transfer file until execution?
+ # populate uuid
+ pass
+
+
+ # starting choice: local file or find existing managed file?
+ # allow branch off of existing managed file -- ie no longer a
+ # version of the initial file?
+
+ # === options ===
+ # overwrite managed on change
+ # overwrite local on change
+ # local is authoritative
+ # keep local copy -- need to allow where to store
+
+class PathChooserLayout(QtGui.QHBoxLayout):
+ def __init__(self, is_dir=False, par_widget=None, parent=None):
+ # QtGui.QWidget.__init__(self, parent)
+ QtGui.QHBoxLayout.__init__(self, parent)
+ self.par_widget = par_widget
+ # layout = QtGui.QHBoxLayout()
+ self.pathname_edit = QtGui.QLineEdit()
+ self.addWidget(self.pathname_edit)
+
+ pathname_button = QtGui.QToolButton()
+ pathname_button.setIcon(
+ QtGui.QIcon(pathname_button.style().standardPixmap(
+ QtGui.QStyle.SP_DirOpenIcon)))
+ pathname_button.setIconSize(QtCore.QSize(12,12))
+ pathname_button.connect(pathname_button,
+ QtCore.SIGNAL('clicked()'),
+ self.choose_path)
+ self.addWidget(pathname_button)
+ # layout.setContentsMargins(1,1,1,1)
+ # self.setLayout(layout)
+ self.is_dir = is_dir
+
+ def choose_path(self):
+ if self.is_dir:
+ chosen_path = \
+ QtGui.QFileDialog.getExistingDirectory(self.par_widget,
+ 'Use Directory...',
+ self.pathname_edit.text())
+ else:
+ chosen_path = \
+ QtGui.QFileDialog.getOpenFileName(self.par_widget,
+ 'Use File...',
+ self.pathname_edit.text(),
+ 'All files (*.*)')
+
+ if chosen_path and chosen_path:
+ self.pathname_edit.setText(chosen_path)
+ self.emit(QtCore.SIGNAL('pathnameChanged()'))
+
+ def get_path(self):
+ return str(self.pathname_edit.text())
+
+ def set_path(self, pathname):
+ if pathname:
+ self.pathname_edit.setText(pathname)
+ else:
+ self.pathname_edit.clear()
+
+class PersistentRefViewSearch(QtGui.QGroupBox):
+ def __init__(self, path_type=None, parent=None):
+ QtGui.QGroupBox.__init__(self, parent)
+ self.build_gui(path_type)
+
+ def build_gui(self, path_type):
+ layout = QtGui.QVBoxLayout()
+ self.search_ref = QSearchBox(False, False)
+
+ self.connect(self.search_ref,
+ QtCore.SIGNAL('executeSearch(QString)'),
+ self.search_string)
+ self.connect(self.search_ref,
+ QtCore.SIGNAL('resetSearch()'),
+ self.reset_search)
+
+ layout.addWidget(self.search_ref)
+ self.ref_widget = PersistentRefView(path_type, self)
+ layout.addWidget(self.ref_widget)
+ layout.setMargin(0)
+ self.setLayout(layout)
+
+ def search_string(self, str):
+ self.ref_widget.model().setFilterWildcard(str)
+
+ def reset_search(self):
+ self.ref_widget.model().setFilterWildcard('')
+ self.ref_widget.model().invalidate()
+
+
+class PersistentPathConfiguration(StandardModuleConfigurationWidget):
+ def __init__(self, module, controller, parent=None,
+ is_input=None, path_type=None):
+ StandardModuleConfigurationWidget.__init__(self, module, controller,
+ parent)
+
+ # set title
+ if module.has_annotation_with_key('__desc__'):
+ label = module.get_annotation_by_key('__desc__').value.strip()
+ title = '%s (%s) Module Configuration' % (label, module.name)
+ else:
+ title = '%s Module Configuration' % module.name
+ self.setWindowTitle(title)
+
+ self.build_gui(is_input, path_type)
+ self.set_values()
+
+ def sizeHint(self):
+ return QtCore.QSize(800, 600)
+
+ def build_gui(self, is_input, path_type):
+ self.current_path = ""
+
+ layout = QtGui.QVBoxLayout()
+# layout.setMargin(0)
+# layout.setSpacing(0)
+
+ if not is_input:
+ self.managed_change = \
+ QtGui.QRadioButton("Always Create New Reference")
+ layout.addWidget(self.managed_change)
+ self.connect(self.managed_change, QtCore.SIGNAL("toggled(bool)"),
+ self.managed_toggle)
+
+ else:
+ self.managed_change = None
+
+ self.managed_new = QtGui.QRadioButton("Create New Reference")
+ self.connect(self.managed_new, QtCore.SIGNAL("toggled(bool)"),
+ self.new_toggle)
+ layout.addWidget(self.managed_new)
+ self.new_group = QtGui.QGroupBox()
+ new_layout = QtGui.QGridLayout()
+ self.new_file = None
+ if is_input:
+ new_layout.addWidget(QtGui.QLabel("Path:"), 0, 0)
+ self.new_file = self.get_chooser_layout()
+ if hasattr(self.new_file, 'pathname_edit'):
+ self.connect(self.new_file.pathname_edit,
+ QtCore.SIGNAL("textChanged(QString)"),
+ self.stateChange)
+ new_layout.addLayout(self.new_file, 0, 1)
+ self.connect(self.new_file, QtCore.SIGNAL("pathnameChanged()"),
+ self.new_file_changed)
+ new_layout.addWidget(QtGui.QLabel("Name:"), 1, 0)
+ self.name_edit = QtGui.QLineEdit()
+ self.connect(self.name_edit, QtCore.SIGNAL("textChanged(QString)"),
+ self.stateChange)
+ new_layout.addWidget(self.name_edit, 1, 1)
+ new_layout.addWidget(QtGui.QLabel("Tags:"), 2, 0)
+ self.tags_edit = QtGui.QLineEdit()
+ self.connect(self.tags_edit, QtCore.SIGNAL("textChanged(QString)"),
+ self.stateChange)
+ new_layout.addWidget(self.tags_edit, 2, 1)
+ self.new_group.setLayout(new_layout)
+ layout.addWidget(self.new_group)
+
+ self.managed_existing = QtGui.QRadioButton("Use Existing Reference")
+ self.connect(self.managed_existing, QtCore.SIGNAL("toggled(bool)"),
+ self.existing_toggle)
+ layout.addWidget(self.managed_existing)
+
+ # self.existing_group = QtGui.QGroupBox()
+ # existing_layout = QtGui.QVBoxLayout()
+ # self.search_ref = QSearchBox(False, False)
+
+ # self.connect(self.search_ref,
+ # QtCore.SIGNAL('executeSearch(QString)'),
+ # self.search_string)
+ # self.connect(self.search_ref,
+ # QtCore.SIGNAL('resetSearch()'),
+ # self.reset_search)
+
+ # existing_layout.addWidget(self.search_ref)
+ # self.ref_widget = PersistentRefView(path_type, self)
+ # existing_layout.addWidget(self.ref_widget)
+ # self.existing_group.setLayout(existing_layout)
+ self.existing_group = PersistentRefViewSearch(path_type)
+ self.ref_widget = self.existing_group.ref_widget
+ self.connect(self.ref_widget,
+ QtCore.SIGNAL("clicked(QModelIndex)"),
+ self.ref_changed)
+ layout.addWidget(self.existing_group)
+
+ self.keep_local = QtGui.QCheckBox("Keep Local Version")
+ layout.addWidget(self.keep_local)
+ self.connect(self.keep_local, QtCore.SIGNAL("toggled(bool)"),
+ self.local_toggle)
+ self.local_group = QtGui.QGroupBox()
+ local_layout = QtGui.QGridLayout()
+ self.local_path = self.get_chooser_layout()
+ if hasattr(self.local_path, 'pathname_edit'):
+ self.connect(self.local_path.pathname_edit,
+ QtCore.SIGNAL("textChanged(QString)"),
+ self.stateChange)
+ local_layout.addLayout(self.local_path,0,0,1,2)
+
+ self.r_priority_local = QtGui.QCheckBox("Read From Local Path")
+ local_layout.addWidget(self.r_priority_local,1,0)
+ self.write_managed_checkbox = QtGui.QCheckBox("Write To Local Path")
+ self.connect(self.write_managed_checkbox, QtCore.SIGNAL("toggled(bool)"),
+ self.stateChange)
+ local_layout.addWidget(self.write_managed_checkbox,1,1)
+ self.local_group.setLayout(local_layout)
+ layout.addWidget(self.local_group)
+
+ if is_input:
+ self.r_priority_local.setEnabled(True)
+ self.write_managed_checkbox.setEnabled(False)
+ else:
+ self.r_priority_local.setEnabled(False)
+ self.write_managed_checkbox.setEnabled(True)
+
+ button_layout = QtGui.QHBoxLayout()
+ button_layout.setDirection(QtGui.QBoxLayout.RightToLeft)
+ button_layout.setAlignment(QtCore.Qt.AlignRight)
+ self.saveButton = QtGui.QPushButton("Save")
+ self.saveButton.setFixedWidth(100)
+ self.connect(self.saveButton, QtCore.SIGNAL('clicked(bool)'),
+ self.saveTriggered)
+ button_layout.addWidget(self.saveButton)
+ self.resetButton = QtGui.QPushButton("Reset")
+ self.resetButton.setFixedWidth(100)
+ self.connect(self.resetButton, QtCore.SIGNAL('clicked()'),
+ self.resetTriggered)
+ button_layout.addWidget(self.resetButton)
+ layout.addLayout(button_layout)
+ self.setLayout(layout)
+
+ def saveTriggered(self, checked = False):
+ self.get_values()
+ self.saveButton.setEnabled(False)
+ self.resetButton.setEnabled(False)
+ self.state_changed = False
+ self.emit(QtCore.SIGNAL('doneConfigure'), self.module.id)
+
+ def closeEvent(self, event):
+ self.askToSaveChanges()
+ event.accept()
+
+ def resetTriggered(self):
+ self.set_values()
+ self.setUpdatesEnabled(True)
+ self.state_changed = False
+ self.saveButton.setEnabled(False)
+ self.resetButton.setEnabled(False)
+
+ def stateChange(self, checked = False, old = None):
+ if not self.state_changed:
+ self.state_changed = True
+ self.saveButton.setEnabled(True)
+ self.resetButton.setEnabled(True)
+
+ def managed_toggle(self, checked):
+ self.stateChange()
+ self.new_group.setEnabled(not checked)
+ self.existing_group.setEnabled(not checked)
+
+ def new_toggle(self, checked):
+ self.stateChange()
+ self.new_group.setEnabled(checked)
+ self.existing_group.setEnabled(not checked)
+ if not checked and self.keep_local.isChecked():
+ self.keep_local.setChecked(False)
+
+ def existing_toggle(self, checked):
+ self.stateChange()
+ self.existing_group.setEnabled(checked)
+ self.new_group.setEnabled(not checked)
+
+ def local_toggle(self, checked):
+ self.stateChange()
+ self.local_group.setEnabled(checked)
+
+ def new_file_changed(self):
+ self.stateChange()
+ new_file = str(self.new_file.get_path())
+ if new_file:
+ base_name = os.path.basename(new_file)
+ self.name_edit.setText(base_name)
+ self.keep_local.setChecked(True)
+ self.local_path.set_path(new_file)
+ self.r_priority_local.setChecked(True)
+ self.write_managed_checkbox.setChecked(False)
+
+ def ref_changed(self, index):
+ self.stateChange()
+ if self.keep_local.isChecked():
+ self.keep_local.setChecked(False)
+
+ def set_values(self):
+ from vistrails.core.modules.module_registry import get_module_registry
+ reg = get_module_registry()
+ PersistentRef = \
+ reg.get_descriptor_by_name(persistence_pkg, 'PersistentRef').module
+
+ def func_to_bool(function):
+ try:
+ value = function.parameters[0].strValue
+ if value and value == 'True':
+ return True
+ except:
+ pass
+ return False
+
+ ref_exists = False
+ self.existing_ref = None
+ local_path = None
+ local_read = None
+ local_write = None
+ for function in self.module.functions:
+ if function.name == 'ref':
+ self.existing_ref = PersistentRef.translate_to_python(
+ function.parameters[0].strValue)
+ self.ref_widget.set_id(self.existing_ref.id)
+ ref_exists = \
+ self.ref_widget.set_version(self.existing_ref.version)
+ self.existing_ref._exists = ref_exists
+ print 'ref_exists:', ref_exists, self.existing_ref.id, \
+ self.existing_ref.version
+ elif function.name == 'value':
+ if self.new_file:
+ self.new_file.set_path(function.parameters[0].strValue)
+ elif function.name == 'localPath':
+ local_path = Path.translate_to_python(
+ function.parameters[0].strValue).name
+ elif function.name == 'readLocal':
+ local_read = func_to_bool(function)
+ elif function.name == 'writeLocal':
+ local_write = func_to_bool(function)
+
+ if ref_exists:
+ self.managed_existing.setChecked(True)
+ self.existing_toggle(True)
+ elif self.managed_change and (not self.existing_ref or \
+ not self.existing_ref.id):
+ self.managed_change.setChecked(True)
+ self.managed_toggle(True)
+ else:
+ self.managed_new.setChecked(True)
+ self.new_toggle(True)
+ if self.existing_ref:
+ self.name_edit.setText(self.existing_ref.name)
+ self.tags_edit.setText(self.existing_ref.tags)
+
+ if self.existing_ref:
+ if self.existing_ref.local_path:
+ self.keep_local.setChecked(True)
+ self.local_toggle(True)
+ else:
+ self.keep_local.setChecked(False)
+ self.local_toggle(False)
+ self.local_path.set_path(self.existing_ref.local_path)
+ self.r_priority_local.setChecked(self.existing_ref.local_read)
+ self.write_managed_checkbox.setChecked(
+ self.existing_ref.local_writeback)
+ else:
+ self.keep_local.setChecked(False)
+ self.local_toggle(False)
+
+ if local_path is not None:
+ if local_path:
+ self.keep_local.setChecked(True)
+ self.local_toggle(True)
+ else:
+ self.keep_local.setChecked(False)
+ self.local_toggle(False)
+ self.local_path.set_path(local_path)
+ if local_read is not None:
+ self.r_priority_local.setChecked(local_read)
+ if local_write is not None:
+ self.write_managed_checkbox.setChecked(local_write)
+ self.saveButton.setEnabled(False)
+ self.resetButton.setEnabled(False)
+ self.state_changed = False
+
+ def get_values(self):
+ from vistrails.core.modules.module_registry import get_module_registry
+ reg = get_module_registry()
+ PersistentRef = \
+ reg.get_descriptor_by_name(persistence_pkg, 'PersistentRef').module
+
+ functions = []
+ if self.new_file and self.new_file.get_path() and \
+ self.managed_new.isChecked():
+ # if self.new_file and self.new_file.get_path():
+ functions.append(('value', [self.new_file.get_path()]))
+ else:
+ functions.append(('value', None))
+ pass
+ ref = PersistentRef()
+ if self.managed_new.isChecked():
+ if self.existing_ref and not self.existing_ref._exists:
+ ref.id = self.existing_ref.id
+ ref.version = self.existing_ref.version
+ else:
+ ref.id = str(uuid.uuid1())
+ ref.version = None
+ # endif
+ ref.name = str(self.name_edit.text())
+ ref.tags = str(self.tags_edit.text())
+ elif self.managed_existing.isChecked():
+ (ref.id, ref.version, ref.name, ref.tags) = \
+ self.ref_widget.get_info()
+ if self.keep_local.isChecked():
+ functions.append(('localPath', [self.local_path.get_path()]))
+ functions.append(('readLocal',
+ [str(self.r_priority_local.isChecked())]))
+ functions.append(('writeLocal',
+ [str(self.write_managed_checkbox.isChecked())]))
+# ref.local_path = self.local_path.get_path()
+# ref.local_read = self.r_priority_local.isChecked()
+# ref.local_writeback = self.write_managed_checkbox.isChecked()
+ else:
+ ref.local_path = None
+ # functions.append(('localPath', None))
+ functions.append(('readLocal', None))
+ functions.append(('writeLocal', None))
+ pass
+ functions.append(('ref', [PersistentRef.translate_to_string(ref)]))
+ self.controller.update_functions(self.module, functions)
+
+class PersistentInputPathConfiguration(PersistentPathConfiguration):
+ def __init__(self, module, controller, parent=None, path_type=None):
+ PersistentPathConfiguration.__init__(self, module, controller, parent,
+ True, path_type)
+
+class PersistentOutputPathConfiguration(PersistentPathConfiguration):
+ def __init__(self, module, controller, parent=None, path_type=None):
+ PersistentPathConfiguration.__init__(self, module, controller, parent,
+ False, path_type)
+
+class PersistentRefInlineWidget(QtGui.QWidget, ConstantWidgetMixin):
+ def __init__(self, param, parent=None):
+ self.param = param
+ self.strValue = param.strValue
+ contentsType = param.type
+ QtGui.QWidget.__init__(self, parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ layout = QtGui.QHBoxLayout()
+ # FIXME Use a greyed QLineEdit?
+ # layout.addWidget(QtGui.QLabel("File Info:"))
+ button = QtGui.QPushButton("Configure")
+ button.setMaximumWidth(100)
+ self.connect(button, QtCore.SIGNAL('clicked()'), self.run_dialog)
+ layout.addWidget(button)
+ layout.setMargin(5)
+ layout.setSpacing(5)
+ self.setLayout(layout)
+
+ def run_dialog(self):
+ dialog = PersistentRefDialog(self.param)
+ if dialog.exec_() == QtGui.QDialog.Accepted:
+ self.setContents("test")
+ #use same translate call?, False)
+
+ def contents(self):
+ return self.strValue
+
+ def setContents(self, strValue, silent=True):
+ self.strValue = strValue
+ if not silent:
+ self.update_parent()
+
+class PersistentInputFileConfiguration(PersistentInputPathConfiguration):
+ def __init__(self, module, controller, parent=None):
+ PersistentInputPathConfiguration.__init__(self, module, controller,
+ parent, "blob")
+ def get_chooser_layout(self):
+ return PathChooserLayout(False, self)
+
+class PersistentInputDirConfiguration(PersistentInputPathConfiguration):
+ def __init__(self, module, controller, parent=None):
+ PersistentInputPathConfiguration.__init__(self, module, controller,
+ parent, "tree")
+
+ def get_chooser_layout(self):
+ return PathChooserLayout(True, self)
+
+class PersistentOutputFileConfiguration(PersistentOutputPathConfiguration):
+ def __init__(self, module, controller, parent=None):
+ PersistentOutputPathConfiguration.__init__(self, module, controller,
+ parent, "blob")
+
+ def get_chooser_layout(self):
+ return PathChooserLayout(False, self)
+
+class PersistentOutputDirConfiguration(PersistentOutputPathConfiguration):
+ def __init__(self, module, controller, parent=None):
+ PersistentOutputPathConfiguration.__init__(self, module, controller,
+ parent, "tree")
+
+ def get_chooser_layout(self):
+ return PathChooserLayout(True, self)
+
+class PersistentConfiguration(QtGui.QDialog):
+ def __init__(self, parent=None):
+ QtGui.QDialog.__init__(self, parent)
+ self.setModal(False)
+ self.build_gui()
+ self.db_access = DatabaseAccessSingleton()
+
+ def build_gui(self):
+ layout = QtGui.QVBoxLayout()
+ self.ref_search = PersistentRefViewSearch(None)
+ self.ref_search.ref_widget.setSelectionMode(
+ QtGui.QAbstractItemView.ExtendedSelection)
+ layout.addWidget(self.ref_search)
+
+ button_layout = QtGui.QHBoxLayout()
+ button_layout.setAlignment(QtCore.Qt.AlignRight)
+ write_button = QtGui.QPushButton("Write...")
+ write_button.setAutoDefault(False)
+ self.connect(write_button, QtCore.SIGNAL("clicked()"), self.write)
+ button_layout.addWidget(write_button)
+ delete_button = QtGui.QPushButton("Delete...")
+ delete_button.setAutoDefault(False)
+ self.connect(delete_button, QtCore.SIGNAL("clicked()"), self.delete)
+ button_layout.addWidget(delete_button)
+ layout.addLayout(button_layout)
+ self.setLayout(layout)
+
+ def sizeHint(self):
+ return QtCore.QSize(800,320)
+
+ def write(self):
+ info_list = self.ref_search.ref_widget.get_info_list()
+ if len(info_list) < 1:
+ return
+ elif len(info_list) == 1:
+ # save single file/dir
+ info = info_list[0]
+ name = info[2]
+ chosen_path = QtGui.QFileDialog.getSaveFileName(
+ self,
+ 'Save...',
+ name)
+ if not chosen_path:
+ return
+
+ # FIXME really should move this calls to a higher level so
+ # we don't need to instantiate a module
+ if info[1] is None:
+ version = "HEAD"
+ else:
+ version = info[1]
+ repo.get_current_repo().get_path(info[0], version, None,
+ chosen_path)
+ else:
+ # have multiple files/dirs
+ chosen_path = QtGui.QFileDialog.getExistingDirectory(
+ self,
+ 'Save All to Directory...')
+ has_overwrite = False
+ # if untitled (no name, use the uuid)
+ for info in info_list:
+ if info[2]:
+ name = info[2]
+ else:
+ name = info[0]
+ full_path = os.path.join(chosen_path, name)
+ if os.path.exists(full_path):
+ has_overwrite = True
+ if has_overwrite:
+ question_str = "One or more of the paths already exist. " + \
+ "Overwrite?"
+ ret_val = \
+ QtGui.QMessageBox.question(self, "Overwrite", \
+ question_str, \
+ QtGui.QMessageBox.Cancel | \
+ QtGui.QMessageBox.No | \
+ QtGui.QMessageBox.Yes)
+ if ret_val != QtGui.QMessageBox.Yes:
+ return
+
+ for info in info_list:
+ if info[1] is None:
+ version = "HEAD"
+ else:
+ version = info[1]
+ if info[2]:
+ name = info[2]
+ else:
+ name = info[0]
+ full_path = os.path.join(chosen_path, name)
+ repo.get_current_repo().git_get_path(info[0], version, None,
+ full_path)
+
+ def delete(self):
+ QtGui.QMessageBox.critical(self, "Delete",
+ "This feature is not functional in the "
+ "current version of VisTrails and has been "
+ "disabled for this release.")
+ return
+
+ from init import PersistentPath
+ info_list = self.ref_search.ref_widget.get_info_list()
+ if len(info_list) < 1:
+ return
+
+ delete_str = "This will permanently delete the selected data " + \
+ "from the peristent store. This cannot be undone. Proceed?"
+ question_f = QtGui.QMessageBox.question
+ ret_val = question_f(self, "Delete", delete_str, \
+ QtGui.QMessageBox.Cancel | \
+ QtGui.QMessageBox.Ok)
+ if ret_val != QtGui.QMessageBox.Ok:
+ return
+
+ git_util = PersistentPath()
+ db_access = DatabaseAccessSingleton()
+ # FIXME keep entry in database with flag for deleted?
+ # NEED TO update the model...
+ for info in info_list:
+ delete_where = {'id': info[0]}
+ if info[1] is None:
+ git_util.git_remove_path(info[0])
+ db_access.delete_from_database(delete_where)
+ else:
+ # FIXME implement delete for versions...
+ delete_where['version'] = info[1]
+ print "NOT IMPLEMENTED FOR VERSIONS!!"
+
+
+
diff --git a/vistrails/packages/pipelineEdit/__init__.py b/vistrails/packages/pipelineEdit/__init__.py
new file mode 100644
index 0000000..ce8f86c
--- /dev/null
+++ b/vistrails/packages/pipelineEdit/__init__.py
@@ -0,0 +1,42 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""This package implements a very simple Qt GUI that can load a
+pipeline, change its parameters based on aliases, and execute them on
+the spreadsheet."""
+
+identifier = 'org.vistrails.vistrails.pipelineedit'
+name = 'Pipeline Editor'
+version = '0.0.2'
+old_identifiers = ['edu.utah.sci.vistrails.pipelineedit']
diff --git a/vistrails/packages/pipelineEdit/init.py b/vistrails/packages/pipelineEdit/init.py
new file mode 100644
index 0000000..61b4397
--- /dev/null
+++ b/vistrails/packages/pipelineEdit/init.py
@@ -0,0 +1,153 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+import vistrails.api
+from vistrails.core.utils import DummyView
+from vistrails.core.vistrail.controller import VistrailController
+
+class QPipelineEditor(QtGui.QWidget):
+ """QPipelineEditor is a simple widget that can load a vistrail,
+ select a pipeline and dipslay aliases of that pipeline."""
+
+ def __init__(self, parent=None):
+ """ init(parent: QWidget) -> None
+ Construct and layout GUI elements
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self.setWindowTitle('Pipeline Editor')
+
+ self.vistrail = None
+ self.versions = []
+
+ vbox = QtGui.QVBoxLayout()
+ self.setLayout(vbox)
+
+ hbox = QtGui.QHBoxLayout()
+ vbox.addLayout(hbox)
+
+ self.filenameLabel = QtGui.QLabel('Vistrail: N/A')
+ hbox.addWidget(self.filenameLabel)
+ self.browseButton = QtGui.QPushButton('Browse...')
+ hbox.addWidget(self.browseButton)
+ self.connect(self.browseButton, QtCore.SIGNAL('clicked()'),
+ self.selectFile)
+
+ vbox.addWidget(QtGui.QLabel('Pipelines'))
+ self.pipelineList = QtGui.QListWidget()
+ vbox.addWidget(self.pipelineList)
+ self.connect(self.pipelineList, QtCore.SIGNAL('currentRowChanged(int)'),
+ self.currentPipelineChanged)
+
+ vbox.addWidget(QtGui.QLabel('Aliases'))
+ self.aliasTable = QtGui.QTableWidget(0, 2)
+ self.aliasTable.horizontalHeader().setStretchLastSection(True)
+ vbox.addWidget(self.aliasTable)
+
+ hbox = QtGui.QHBoxLayout()
+ vbox.addLayout(hbox)
+ self.executeButton = QtGui.QPushButton('Execute')
+ hbox.addWidget(self.executeButton)
+ self.connect(self.executeButton, QtCore.SIGNAL('clicked()'),
+ self.execute)
+
+ def selectFile(self):
+ """ selectFile() -> None
+ Open a file dialog and select a vistrail file. Then display a
+ list of tagged version on the pipeline list.
+
+ """
+ fn = QtGui.QFileDialog.getOpenFileName(self,
+ 'Load Vistrail',
+ '.',
+ 'Vistrail (*.vt)')
+ if not fn.isNull():
+ self.filenameLabel.setText('Vistrail: %s' % fn)
+ self.vistrail = vistrails.api.get_vistrail_from_file(str(fn))
+ for item in self.vistrail.get_tagMap().items():
+ self.versions.append(item)
+ self.pipelineList.clear()
+ self.pipelineList.addItems([version for (name, version) in self.versions])
+
+ def currentPipelineChanged(self, row):
+ """ currentPipelineChanged(row: int) -> None
+ When the current pipeline is changed in the pipeline list,
+ update the alias table with aliases in that pipeline.
+
+ """
+ if row<0:
+ self.aliasTable.setRowCount(0)
+ else:
+ versionName = self.pipelineList.currentItem().text()
+ pipeline = self.vistrail.getPipelineVersionName(str(versionName))
+ aliases = pipeline.aliases.keys()
+ self.aliasTable.setRowCount(len(aliases))
+ row = 0
+ for name in aliases:
+ self.aliasTable.setItem(row, 0, QtGui.QTableWidgetItem(name))
+ value = pipeline.get_alias_str_value(name)
+ self.aliasTable.setItem(row, 1, QtGui.QTableWidgetItem(value))
+ row += 1
+
+ def execute(self):
+ """ execute() -> None
+ Execute the selected pipeline with the edited aliases
+
+ """
+ aliases = {}
+ for r in xrange(self.aliasTable.rowCount()):
+ name = str(self.aliasTable.item(r, 0).text())
+ value = str(self.aliasTable.item(r, 1).text())
+ aliases[name] = value
+
+ versionNumber = self.versions[self.pipelineList.currentIndex().row()][0]
+ pipeline = self.vistrail.getPipelineVersionNumber(versionNumber)
+ controller = VistrailController(self.vistrail)
+ controller.execute_workflow_list([(self.vistrail.locator,
+ versionNumber,
+ pipeline,
+ DummyView(),
+ aliases,
+ None)])
+
+def initialize(*args, **keywords):
+ """ initialize() -> None
+ Package-entry to initialize the package. We just create and show
+ the main window, a QPipelineEditor widget, here.
+
+ """
+ global mainWindow
+ mainWindow = QPipelineEditor()
+ mainWindow.show()
diff --git a/vistrails/packages/pythonCalc/__init__.py b/vistrails/packages/pythonCalc/__init__.py
new file mode 100644
index 0000000..e2f845f
--- /dev/null
+++ b/vistrails/packages/pythonCalc/__init__.py
@@ -0,0 +1,47 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""This package implements a very simple VisTrails module called
+PythonCalc. This is intended as a simple example that can be referred
+to by users to create their own packages and modules later.
+
+If you're interested in developing new modules for VisTrails, you
+should also consult the documentation in the User's Guide and in
+core/modules/vistrails_module.py.
+"""
+
+identifier = 'org.vistrails.vistrails.pythoncalc'
+name = 'PythonCalc'
+version = '0.9.1'
+old_identifiers = ['edu.utah.sci.vistrails.pythoncalc']
diff --git a/vistrails/packages/pythonCalc/init.py b/vistrails/packages/pythonCalc/init.py
new file mode 100644
index 0000000..32b73b6
--- /dev/null
+++ b/vistrails/packages/pythonCalc/init.py
@@ -0,0 +1,127 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import vistrails.core.modules.module_registry
+from vistrails.core.modules.vistrails_module import Module, ModuleError
+
+###############################################################################
+# PythonCalc
+#
+# A VisTrails package is simply a Python class that subclasses from
+# Module. For this class to be executable, it must define a method
+# compute(self) that will perform the appropriate computations and set
+# the results.
+#
+# Extra helper methods can be defined, as usual. In this case, we're
+# using a helper method op(self, v1, v2) that performs the right
+# operations.
+
+class PythonCalc(Module):
+ """PythonCalc is a module that performs simple arithmetic operations
+on its inputs."""
+
+ # This constructor is strictly unnecessary. However, some modules
+ # might want to initialize per-object data. When implementing your
+ # own constructor, remember that it must not take any extra
+ # parameters.
+ def __init__(self):
+ Module.__init__(self)
+
+ # This is the method you should implement in every module that
+ # will be executed directly. VisTrails does not use the return
+ # value of this method.
+ def compute(self):
+ # getInputFromPort is a method defined in Module that returns
+ # the value stored at an input port. If there's no value
+ # stored on the port, the method will return None.
+ v1 = self.getInputFromPort("value1")
+ v2 = self.getInputFromPort("value2")
+
+ # You should call setResult to store the appropriate results
+ # on the ports. In this case, we are only storing a
+ # floating-point result, so we can use the number types
+ # directly. For more complicated data, you should
+ # return an instance of a VisTrails Module. This will be made
+ # clear in further examples that use these more complicated data.
+ self.setResult("value", self.op(v1, v2))
+
+ def op(self, v1, v2):
+ op = self.getInputFromPort("op")
+ if op == '+':
+ return v1 + v2
+ elif op == '-':
+ return v1 - v2
+ elif op == '*':
+ return v1 * v2
+ elif op == '/':
+ return v1 / v2
+ # If a module wants to report an error to VisTrails, it should raise
+ # ModuleError with a descriptive error. This allows the interpreter
+ # to capture the error and report it to the caller of the evaluation
+ # function.
+ raise ModuleError(self, "unrecognized operation: '%s'" % op)
+
+###############################################################################
+# the function initialize is called for each package, after all
+# packages have been loaded. It is used to register the module with
+# the VisTrails runtime.
+
+def initialize(*args, **keywords):
+
+ # We'll first create a local alias for the module_registry so that
+ # we can refer to it in a shorter way.
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+
+ # VisTrails cannot currently automatically detect your derived
+ # classes, and the ports that they support as input and
+ # output. Because of this, you as a module developer need to let
+ # VisTrails know that you created a new module. This is done by calling
+ # function addModule:
+ reg.add_module(PythonCalc)
+
+ # In a similar way, you need to report the ports the module wants
+ # to make available. This is done by calling addInputPort and
+ # addOutputPort appropriately. These calls only show how to set up
+ # one-parameter ports. We'll see in later tutorials how to set up
+ # multiple-parameter plots.
+ reg.add_input_port(PythonCalc, "value1",
+ (vistrails.core.modules.basic_modules.Float, 'the first argument'))
+ reg.add_input_port(PythonCalc, "value2",
+ (vistrails.core.modules.basic_modules.Float, 'the second argument'))
+ reg.add_input_port(PythonCalc, "op",
+ (vistrails.core.modules.basic_modules.String, 'the operation'),
+ entry_types=['enum'], values=["['+', '-', '*', '/']"])
+ reg.add_output_port(PythonCalc, "value",
+ (vistrails.core.modules.basic_modules.Float, 'the result'))
+
diff --git a/vistrails/packages/pythonCalcQt/__init__.py b/vistrails/packages/pythonCalcQt/__init__.py
new file mode 100644
index 0000000..de5584b
--- /dev/null
+++ b/vistrails/packages/pythonCalcQt/__init__.py
@@ -0,0 +1,51 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""This package implements a very simple Qt GUI over the PythonCalc
+package to provide an example of how a package may add GUI elements
+including independent windows, menu items as well as dependency
+requirements.
+
+If you're interested in developing new modules for VisTrails, you
+should also consult the documentation in the User's Guide and in
+core/modules/vistrails_module.py.
+"""
+
+identifier = 'org.vistrails.vistrails.pythoncalcqt'
+name = 'PythonCalcQt'
+version = '0.0.2'
+old_identifiers = ['edu.utah.sci.vistrails.pythoncalcqt']
+
+def package_dependencies():
+ return ['org.vistrails.vistrails.pythoncalc']
diff --git a/vistrails/packages/pythonCalcQt/init.py b/vistrails/packages/pythonCalcQt/init.py
new file mode 100644
index 0000000..8d885b7
--- /dev/null
+++ b/vistrails/packages/pythonCalcQt/init.py
@@ -0,0 +1,139 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import vistrails.core.modules.module_registry
+from vistrails.core.modules.vistrails_module import Module, ModuleError
+from PyQt4 import QtCore, QtGui
+import vistrails.api
+
+class QPythonCalc(QtGui.QWidget):
+ """QPythonCalc is a widget used for specifying PythonCalc
+ parameters and providing two buttons for compute and add that
+ module to the pipeline. """
+
+ def __init__(self, parent=None):
+ """ init(parent: QWidget) -> None
+ We construct a simple GUI with edit boxes for 2 operands and a
+ combo box for the operator. There are also 2 buttons: (1)
+ perform the calculation and display the result, (2) create a
+ PythonCalc module with the specified parameters and add to the
+ current pipeline.
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ self.setWindowTitle('PythonCalc GUI')
+ gridLayout = QtGui.QGridLayout()
+ self.setLayout(gridLayout)
+ gridLayout.addWidget(QtGui.QLabel('value1'), 0, 0)
+ gridLayout.addWidget(QtGui.QLabel('value2'), 1, 0)
+ gridLayout.addWidget(QtGui.QLabel('op'), 2, 0)
+ gridLayout.addWidget(QtGui.QLabel('result'), 3, 0)
+
+ numberValidator = QtGui.QIntValidator(self)
+ self.value1Edit = QtGui.QLineEdit('0')
+ self.value2Edit = QtGui.QLineEdit('0')
+ self.value1Edit.setValidator(numberValidator)
+ self.value2Edit.setValidator(numberValidator)
+ gridLayout.addWidget(self.value1Edit, 0, 1)
+ gridLayout.addWidget(self.value2Edit, 1, 1)
+
+ self.opCombo = QtGui.QComboBox()
+ self.opCombo.addItems(['+', '-', '*', '/'])
+ gridLayout.addWidget(self.opCombo, 2, 1)
+
+ self.resultLabel = QtGui.QLabel()
+ gridLayout.addWidget(self.resultLabel, 3, 1)
+
+ self.calculateButton = QtGui.QPushButton('Calculate')
+ gridLayout.addWidget(self.calculateButton, 4, 0)
+ self.connect(self.calculateButton, QtCore.SIGNAL('clicked()'),
+ self.calculate)
+
+ self.createModuleButton = QtGui.QPushButton('Create Module')
+ gridLayout.addWidget(self.createModuleButton, 4, 1)
+ self.connect(self.createModuleButton, QtCore.SIGNAL('clicked()'),
+ self.createModule)
+
+ def calculate(self):
+ """ calculate() -> None
+ Perform the calculation based on value1, value2 and op,
+ similar to the PythonCalc module, but through the GUI.
+
+ """
+ result = eval(str(self.value1Edit.text() +
+ self.opCombo.currentText() +
+ self.value2Edit.text()))
+ self.resultLabel.setText(str(result))
+
+ def createModule(self):
+ """ createModule() -> None
+ Collect parameters, values and operator, and create a
+ PythonCalc module to the current pipeline using the API
+ provided in vistrails.api.
+
+ """
+ pythoncalc = "org.vistrails.vistrails.pythoncalc"
+ module = vistrails.api.add_module(0, 0, pythoncalc, 'PythonCalc', '')
+ vistrails.api.get_current_controller().update_function(module, 'value1',
+ [str(self.value1Edit.text())])
+ vistrails.api.get_current_controller().update_function(module, 'value2',
+ [str(self.value2Edit.text())])
+ vistrails.api.get_current_controller().update_function(module, 'op',
+ [str(self.opCombo.currentText())])
+ vistrails.api.switch_to_pipeline_view()
+
+def initialize(*args, **keywords):
+ """ initialize() -> None
+ Package-entry to initialize the package. We just create and show
+ the main window, a QPythonCalc widget, here.
+
+ """
+ global mainWindow
+ mainWindow = QPythonCalc()
+ mainWindow.show()
+
+def menu_items():
+ """menu_items() -> tuple of (str,function)
+ It returns a list of pairs containing text for the menu and a
+ callback function that will be executed when that menu item is
+ selected. This will add a 'Create Module' menu item under the
+ Packages>PythonCalcQt menu. It has the same functionality as the
+ 'Create Module' button, which adds a PythonCalc with specified
+ parameters module to the current pipeline.
+
+ """
+ lst = []
+ global mainWindow
+ lst.append(("Create Module", mainWindow.createModule))
+ return tuple(lst)
diff --git a/vistrails/packages/qgis/__init__.py b/vistrails/packages/qgis/__init__.py
new file mode 100644
index 0000000..fd91230
--- /dev/null
+++ b/vistrails/packages/qgis/__init__.py
@@ -0,0 +1,48 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import vistrails.core
+identifier = 'org.vistrails.vistrails.qgis'
+version = '0.0.2'
+name = "QGIS"
+old_identifiers = ['edu.utah.sci.vistrails.qgis']
+
+def package_dependencies():
+ import vistrails.core.packagemanager
+ manager = vistrails.core.packagemanager.get_package_manager()
+ if manager.has_package('org.vistrails.vistrails.spreadsheet'):
+ return ['org.vistrails.vistrails.spreadsheet']
+ else:
+ return []
+
diff --git a/vistrails/packages/qgis/init.py b/vistrails/packages/qgis/init.py
new file mode 100644
index 0000000..636bb01
--- /dev/null
+++ b/vistrails/packages/qgis/init.py
@@ -0,0 +1,172 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from PyQt4 import QtCore, QtGui
+from vistrails.core.modules.vistrails_module import Module
+from vistrails.packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+
+import qgis.core
+import qgis.gui
+
+import itertools
+import os
+
+class RasterLayer(Module):
+ _input_ports = [('file', '(basic:File)'),
+ ('name', '(basic:String)')]
+ _output_ports = [('self', '(RasterLayer)')]
+
+ def __init__(self):
+ Module.__init__(self)
+ self.qgis_obj = None
+
+ def compute(self):
+ fname = self.getInputFromPort('file').name
+ if self.hasInputFromPort('name'):
+ name = self.getInputFromPort('name')
+ else:
+ name = os.path.splitext(os.path.basename(fname))[0]
+ self.qgis_obj = qgis.core.QgsRasterLayer(fname, name)
+ self.setResult('self', self)
+
+class VectorLayer(Module):
+ _input_ports = [('file', '(basic:File)'),
+ ('name', '(basic:String)')]
+ _output_ports = [('self', '(VectorLayer)')]
+
+ def __init__(self):
+ Module.__init__(self)
+ self.qgis_obj = None
+
+ def compute(self):
+ fname = self.getInputFromPort('file').name
+ if self.hasInputFromPort('name'):
+ name = self.getInputFromPort('name')
+ else:
+ name = os.path.splitext(os.path.basename(fname))[0]
+ self.qgis_obj = qgis.core.QgsVectorLayer(fname, name, "ogr")
+ self.setResult('self', self)
+
+class QGISCell(SpreadsheetCell):
+ """
+ QGISCell is a VisTrails Module that can display QGIS inside a cell
+
+ """
+ _input_ports = [('rasterLayers', '(RasterLayer)'),
+ ('vectorLayers', '(VectorLayer)')]
+
+ def __init__(self):
+ SpreadsheetCell.__init__(self)
+
+ def compute(self):
+ rasterLayers = self.forceGetInputListFromPort('rasterLayers')
+ vectorLayers = self.forceGetInputListFromPort('vectorLayers')
+ self.displayAndWait(QGISCellWidget, (rasterLayers, vectorLayers))
+
+class QGISCellWidget(QCellWidget):
+ """
+ QGISCellWidget is the actual QWidget taking the FigureManager
+ as a child for displaying figures
+
+ """
+ def __init__(self, parent=None):
+ """ QGISCellWidget(parent: QWidget) -> QGISCellWidget
+ Initialize the widget with its central layout
+
+ """
+ QCellWidget.__init__(self, parent)
+ centralLayout = QtGui.QVBoxLayout()
+ self.setLayout(centralLayout)
+ centralLayout.setMargin(0)
+ centralLayout.setSpacing(0)
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple) -> None
+ Update the widget contents based on the input data
+
+ """
+ (rasterLayers, vectorLayers) = inputPorts
+
+ canvas = qgis.gui.QgsMapCanvas()
+ canvas.show()
+
+ canvas.setCanvasColor(QtCore.Qt.white)
+ canvas.enableAntiAliasing(True)
+
+ for layer in itertools.chain(rasterLayers, vectorLayers):
+ print 'adding layer', layer.qgis_obj
+ qgis.core.QgsMapLayerRegistry.instance().addMapLayer(layer.qgis_obj)
+
+ canvas.setExtent(rasterLayers[0].qgis_obj.extent())
+ canvas.setLayerSet([qgis.gui.QgsMapCanvasLayer(layer.qgis_obj)
+ for layer in itertools.chain(vectorLayers,
+ rasterLayers)])
+
+ # raster_fname = "/vistrails/local_packages/qgis/qgis_sample_data/raster/landcover.img"
+ # raster = qgis.core.QgsRasterLayer(raster_fname, os.path.splitext(os.path.basename(raster_fname))[0])
+ # qgis.core.QgsMapLayerRegistry.instance().addMapLayer(raster)
+
+ # layer = qgis.core.QgsVectorLayer("/vistrails/local_packages/qgis/qgis_sample_data/vmap0_shapefiles/majrivers.shp", "Rivers", "ogr")
+ # print layer.isValid()
+ # qgis.core.QgsMapLayerRegistry.instance().addMapLayer(layer)
+ # canvas.setLayerSet([qgis.gui.QgsMapCanvasLayer(layer),
+ # qgis.gui.QgsMapCanvasLayer(raster)])
+
+ self.layout().addWidget(canvas)
+
+ # Update the new figure canvas
+ self.update()
+
+ def grabWindowPixmap(self):
+ """ grabWindowPixmap() -> QPixmap
+ Widget special grabbing function
+
+ """
+ # return QtGui.QPixmap.grabWidget(self.figManager.canvas)
+ return None
+
+ def dumpToFile(self, filename):
+ pass
+
+ def saveToPDF(self, filename):
+ pass
+
+_modules = [RasterLayer, VectorLayer, QGISCell,]
+
+def initialize():
+ qgis.core.QgsApplication.setPrefixPath(
+ "/vistrails/local_packages/qgis/QGIS.app/Contents/MacOS", True)
+ qgis.core.QgsApplication.initQgis()
+
diff --git a/vistrails/packages/rpy/README b/vistrails/packages/rpy/README
new file mode 100644
index 0000000..49b996b
--- /dev/null
+++ b/vistrails/packages/rpy/README
@@ -0,0 +1,11 @@
+On the Mac, I needed to patch rpy2 2.0.8:
+
+rinterface/__init__.py:
+- R_HOME = os.popen("R RHOME").readlines()
++ p = os.popen("R RHOME")
++ time.sleep(1)
++ R_HOME = p.readlines()
+
+robjects/__init__.py:
+- import rpy2.robjects.conversion
++ import conversion
\ No newline at end of file
diff --git a/vistrails/packages/rpy/__init__.py b/vistrails/packages/rpy/__init__.py
new file mode 100644
index 0000000..b115553
--- /dev/null
+++ b/vistrails/packages/rpy/__init__.py
@@ -0,0 +1,39 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+name = "R"
+identifier = "org.vistrails.vistrails.rpy"
+version = "0.1.2"
+old_identifiers = ["edu.utah.sci.vistrails.rpy"]
+
diff --git a/vistrails/packages/rpy/init.py b/vistrails/packages/rpy/init.py
new file mode 100644
index 0000000..c0920ee
--- /dev/null
+++ b/vistrails/packages/rpy/init.py
@@ -0,0 +1,482 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import os
+import sys
+import tempfile
+import urllib
+import rpy2.robjects as robjects
+
+from vistrails.core.modules.basic_modules import File, Constant, \
+ new_constant
+
+from vistrails.core.modules.vistrails_module import Module, ModuleError, \
+ ModuleConnector, NotCacheable
+from vistrails.core.modules.basic_modules import new_constant
+import vistrails.core.modules.module_registry
+from widgets import RSourceConfigurationWidget, RFigureConfigurationWidget
+
+# FIXME when rpy2 is installed on the path, we won't need this
+old_sys_path = sys.path
+sys.path.append(os.path.dirname(__file__))
+sys.path = old_sys_path
+
+r_temp_files = []
+
+class TypeException(Exception):
+ pass
+
+def create_vector(v_list, desired_type=None):
+ is_bool = True
+ is_int = True
+ is_float = True
+ is_str = True
+ for elt in v_list:
+ if isinstance(elt, basestring):
+ is_bool = False
+ is_int = False
+ is_float = False
+ elif isinstance(elt, float):
+ is_bool = False
+ is_int = False
+ elif isinstance(elt, (int, long)):
+ is_bool = False
+ else:
+ is_bool = False
+ is_int = False
+ is_float = False
+ is_str = False
+ break
+
+ if is_bool and (desired_type is None or desired_type == bool):
+ return robjects.BoolVector(v_list)
+ elif is_int and (desired_type is None or desired_type == int):
+ res = [int(elt) for elt in v_list]
+ return robjects.IntVector(res)
+ elif is_float and (desired_type is None or desired_type == float):
+ res = [float(elt) for elt in v_list]
+ return robjects.FloatVector(res)
+ elif is_str and (desired_type is None or desired_type == str):
+ res = [str(elt) for elt in v_list]
+ return robjects.StrVector(res)
+
+ if desired_type is not None:
+ raise TypeException("Cannot coerce vector to type '%s'" % desired_type)
+ return robjects.RVector(v_list)
+
+def vector_conv(v, desired_type=None):
+ v_list = eval(v)
+ return create_vector(v_list, desired_type)
+
+RVector = new_constant('RVector', staticmethod(vector_conv),
+ robjects.Vector([]),
+ staticmethod(lambda x: isinstance(x, robjects.Vector)))
+
+def bool_vector_conv(v):
+ return vector_conv(v, bool)
+
+RBoolVector = new_constant('RBoolVector' , staticmethod(bool_vector_conv),
+ robjects.BoolVector([]),
+ staticmethod(lambda x: isinstance(x, robjects.Vector)),
+ base_class=RVector)
+
+def int_vector_conv(v):
+ return vector_conv(v, int)
+
+RIntVector = new_constant('RIntVector' , staticmethod(int_vector_conv),
+ robjects.IntVector([]),
+ staticmethod(lambda x: isinstance(x, robjects.Vector)),
+ base_class=RVector)
+
+def float_vector_conv(v):
+ return vector_conv(v, float)
+
+RFloatVector = new_constant('RFloatVector' , staticmethod(float_vector_conv),
+ robjects.FloatVector([]),
+ staticmethod(lambda x: isinstance(x, robjects.Vector)),
+ base_class=RVector)
+
+def str_vector_conv(v):
+ return vector_conv(v, str)
+
+RStrVector = new_constant('RStrVector' , staticmethod(str_vector_conv),
+ robjects.StrVector([]),
+ staticmethod(lambda x: isinstance(x, robjects.Vector)),
+ base_class=RVector)
+
+def array_conv(v):
+ return robjects.r.array(vector_conv(v))
+
+RArray = new_constant('RArray', staticmethod(array_conv),
+ robjects.r.array(),
+ staticmethod(lambda x: isinstance(x, robjects.RArray)),
+ base_class=RVector)
+
+def create_matrix(v_list):
+ vec_list = []
+ nrow = 0
+ ncol = -1
+ for v_sublist in v_list:
+ if ncol == -1:
+ ncol = len(v_sublist)
+ elif ncol != len(v_sublist):
+ raise TypeException("Matrix must be rectangular")
+ nrow += 1
+ vec_list.extend(v_sublist)
+ vec = create_vector(vec_list)
+ return robjects.r.matrix(vec, nrow=nrow)
+
+def matrix_conv(v):
+ # should be a double list
+ v_list = eval(v)
+ create_matrix(v_list)
+
+def matrix_compute(self):
+ if self.hasInputFromPort('rvector'):
+ rvector = self.getInputFromPort('rvector')
+ nrows = self.getInputFromPort('nrows')
+ self.setResult('value', robjects.r.matrix(rvector, nrow=nrows))
+ else:
+ RArray.compute(self)
+
+RMatrix = new_constant('RMatrix', staticmethod(matrix_conv),
+ robjects.r.matrix(),
+ staticmethod(lambda x: isinstance(x, robjects.RArray)),
+ base_class=RArray,
+ compute=matrix_compute)
+RMatrix._input_ports.extend([('rvector', '(Types|RVector)'),
+ ('nrows', '(basic:Integer)')])
+
+def create_list(v_dict):
+ data_dict = {}
+ for k,v in v_dict.iteritems():
+ if isinstance(v, list):
+ data_dict[k] = create_vector(v)
+ elif isinstance(v, dict):
+ data_dict[k] = create_list(v)
+ else:
+ data_dict[k] = v
+ return robjects.r['list'](**data_dict)
+
+def list_conv(v):
+ v_dict = eval(v)
+ return create_list(v_dict)
+
+RList = new_constant('RList', staticmethod(list_conv),
+ robjects.r.list(),
+ staticmethod(lambda x: isinstance(x, robjects.Vector)),
+ base_class=RVector)
+# compute=list_compute)
+
+def create_data_frame(v_dict):
+ data_dict = {}
+ for k,v in v_dict.iteritems():
+ if isinstance(v, list):
+ data_dict[k] = create_vector(v)
+ elif isinstance(v, dict):
+ data_dict[k] = create_data_frame(v)
+ else:
+ data_dict[k] = v
+ return robjects.r['data.frame'](**data_dict)
+
+def data_frame_conv(v):
+ v_dict = eval(v)
+ return create_data_frame(v_dict)
+
+RDataFrame = new_constant('RDataFrame', staticmethod(data_frame_conv),
+ robjects.r['data.frame'](),
+ staticmethod(lambda x: \
+ isinstance(x, robjects.RDataFrame)))
+
+class RVectorFromList(Module):
+ _input_ports = [('list', '(basic:List)')]
+ _output_ports = [('rvector', '(Types|RVector)')]
+
+ def compute(self):
+ ilist = self.getInputFromPort('list')
+ rvector = create_vector(ilist)
+ self.setResult('rvector', rvector)
+
+class ListFromRVector(Module):
+ _input_ports = [('rvector', '(Types|RVector)')]
+ _output_ports = [('list', '(basic:List)')]
+
+ def compute(self):
+ rvector = self.getInputFromPort('rvector')
+ olist = list(rvector)
+ self.setResult('list', olist)
+
+class RMatrixFromNestedList(Module):
+ _input_ports = [('list', '(basic:List)')]
+ _output_ports = [('rmatrix', '(Types|RMatrix)')]
+
+ def compute(self):
+ ilist = self.getInputFromPort('list')
+ rmatrix = create_matrix(ilist)
+ self.setResult('rmatrix', rmatrix)
+
+class NestedListFromRMatrix(Module):
+ _input_ports = [('rmatrix', '(Types|RMatrix)')]
+ _output_ports = [('list', '(basic:List)')]
+
+ def compute(self):
+ rmatrix = self.getInputFromPort('rmatrix')
+ mlist = list(rmatrix)
+ nrows = rmatrix.nrow
+ ncols = len(mlist) / nrows
+ olist = []
+ for row in xrange(nrows):
+ olist.append(mlist[row*ncols:(row+1)*ncols])
+ self.setResult('list', olist)
+
+class RDataFrameFromDict(Module):
+ _input_ports = [('dict', '(basic:Dictionary)')]
+ _output_ports = [('rdataframe', '(Types|RDataFrame)')]
+
+ def compute(self):
+ idict = self.getInputFromPort('dict')
+ rdataframe = create_data_frame(idict)
+ self.setResult('rdataframe', rdataframe)
+
+class DictFromRDataFrame(Module):
+ _input_ports = [('rdataframe','(Types|RDataFrame)')]
+ _output_ports = [('dict', '(basic:Dictionary)')]
+
+ def compute(self):
+ rdataframe = self.getInputFromPort('rdataframe')
+ colnames = list(rdataframe.colnames())
+ odict = {}
+ for i in xrange(len(rdataframe)):
+ # FIXME !!! just assume that each row can be converted to a list!!!
+ odict[colnames[i]] = list(rdataframe[i])
+ self.setResult('dict', odict)
+
+class RListFromDict(Module):
+ # _input_ports = [('dict', '(basic:Dictionary)')]
+ _input_ports = [('dict', '(basic:Module)')]
+ _output_ports = [('rlist', '(Types|RList)')]
+
+ def compute(self):
+ idict = self.getInputFromPort('dict')
+ rlist = create_list(idict)
+ self.setResult('rlist', rlist)
+
+class DictFromRList(Module):
+ _input_ports = [('rlist', '(Types|RList)')]
+ # _output_ports = [('dict', '(basic:Dictionary)')]
+ _output_ports = [('dict', '(basic:Module)')]
+
+ def compute(self):
+ rlist = self.getInputFromPort('rlist')
+ colnames = list(rlist.names)
+ odict = {}
+ for i in xrange(len(rlist)):
+ # FIXME !!! just assume that each row can be converted to a list!!!
+ # FIXME this may need to be a list of lists
+ odict[colnames[i]] = list(rlist[i])
+ self.setResult('dict', odict)
+
+class RRead(Module):
+ _input_ports = [('file', '(basic:File)'),
+ ('header', '(basic:Boolean)', True),
+ ('sep', '(basic:String)', True),
+ ('commentChar', '(basic:String)', True),
+ ('quote', '(basic:String)', True),
+ ('dec', '(basic:String)', True),
+ ('fill', '(basic:Boolean)', True)]
+ _output_ports = [('rdataframe', '(Types|RDataFrame)')]
+
+ def do_read(self, read_cmd):
+ fname = self.getInputFromPort('file').name
+ options_dict = {}
+ for port in RRead._input_ports:
+ if port[0] != 'file' and self.hasInputFromPort(port):
+ options_dict[port] = self.getInputFromPort(port)
+ rdataframe = robjects.r[read_cmd](fname, **options_dict)
+ self.setResult('rdataframe', rdataframe)
+
+class RReadTable(RRead):
+ def compute(self):
+ self.do_read('read.table')
+
+class RReadCSV(RRead):
+ def compute(self):
+ self.do_read('read.csv')
+
+class RReadCSV2(RRead):
+ def compute(self):
+ self.do_read('read.csv2')
+
+class RReadDelim(RRead):
+ def compute(self):
+ self.do_read('read.delim')
+
+class RReadDelim2(RRead):
+ def compute(self):
+ self.do_read('read.delim2')
+
+# class RSource(NotCacheable, Module):
+class RSource(Module):
+ _input_ports = [('source', '(basic:String)', True)]
+ def run_code(self, code_str,
+ use_input=False,
+ use_output=False,
+ excluded_inputs=set(),
+ excluded_outputs=set()):
+ """run_code runs a piece of code as a VisTrails module.
+ use_input and use_output control whether to use the inputport
+ and output port dictionary as local variables inside the
+ execution."""
+ import vistrails.core.packagemanager
+ def fail(msg):
+ raise ModuleError(self, msg)
+ def cache_this():
+ self.is_cacheable = lambda *args, **kwargs: True
+ if use_input:
+ inputDict = dict([(k, self.getInputFromPort(k))
+ for k in self.inputPorts
+ if k not in excluded_inputs])
+ for k,v in inputDict.iteritems():
+ robjects.globalEnv[k] = v
+ robjects.r(code_str)
+ if use_output:
+ for k in self.outputPorts:
+ if k not in excluded_outputs and k in robjects.globalEnv:
+ self.setResult(k, robjects.globalEnv[k])
+
+ def run_file(self, fname, excluded_inputs=set(['source']),
+ excluded_outputs=set()):
+ f = open(fname, 'rU')
+ code_str = f.readlines()
+ f.close()
+ self.run_code(code_str, use_input=True, use_output=True,
+ excluded_inputs=excluded_inputs,
+ excluded_outputs=excluded_outputs)
+
+ def set_variable(self, name, value):
+ robjects.globalEnv[name] = value
+
+ def get_variable(self, name):
+ # return robjects.globalEnv[name]
+ return robjects.r(name)
+
+ def chdir(self, dir):
+ robjects.r('setwd("%s")' % dir)
+
+ def compute(self):
+ code_str = urllib.unquote(str(self.forceGetInputFromPort('source', '')))
+ self.run_code(code_str, use_input=True, use_output=True,
+ excluded_inputs=set(['source']))
+
+class RFigure(RSource):
+ _output_ports = [('imageFile', '(basic:File)')]
+ def run_figure(self, code_str, graphics_dev, width, height,
+ excluded_inputs=set(['source'])):
+ fname = self.interpreter.filePool.create_file(prefix='vtr', suffix='.' + graphics_dev)
+ r_temp_files.append(fname)
+ robjects.r[graphics_dev](file=fname, width=width, height=height)
+ self.run_code(code_str, use_input=True,
+ excluded_inputs=excluded_inputs)
+ robjects.r['dev.off']()
+ image_file = File()
+ image_file.name = fname
+ image_file.upToDate = True
+ self.setResult('imageFile', image_file)
+
+ def run_figure_file(self, fname, graphics_dev, width, height,
+ excluded_inputs=set(['source'])):
+ f = open(fname)
+ code_str = f.readlines()
+ f.close()
+ self.run_figure(code_str, graphics_dev, width, height, excluded_inputs)
+
+class RSVGFigure(RFigure):
+ def compute(self):
+ code_str = \
+ urllib.unquote(str(self.forceGetInputFromPort('source', '')))
+ RFigure.run_figure(self, code_str, 'svg', 4, 3)
+
+class RPNGFigure(RFigure):
+ def compute(self):
+ code_str = \
+ urllib.unquote(str(self.forceGetInputFromPort('source', '')))
+ RFigure.run_figure(self, code_str, 'png', 640, 480)
+
+class RPDFFigure(RFigure):
+ def compute(self):
+ code_str = \
+ urllib.unquote(str(self.forceGetInputFromPort('source', '')))
+ RFigure.run_figure(self, code_str, 'pdf', 4, 3)
+
+class RFactor(Module):
+ pass
+
+_modules = {None: [(RSource,
+ {'configureWidgetType': RSourceConfigurationWidget})],
+ 'Types': [RVector,
+ RBoolVector,
+ RIntVector,
+ RFloatVector,
+ RStrVector,
+ RArray,
+ RMatrix,
+ RDataFrame,
+ RList,
+ RFactor],
+ 'Readers': [(RRead, {'abstract': True}),
+ RReadTable,
+ RReadCSV,
+ RReadCSV2,
+ RReadDelim,
+ RReadDelim2],
+ 'Converters': [RVectorFromList,
+ ListFromRVector,
+ RMatrixFromNestedList,
+ NestedListFromRMatrix,
+ RDataFrameFromDict,
+ DictFromRDataFrame,
+ RListFromDict,
+ DictFromRList],
+ 'Figures': [(RFigure, {'abstract': True}),
+ (RSVGFigure, {'configureWidgetType': \
+ RFigureConfigurationWidget}),
+ (RPNGFigure, {'configureWidgetType': \
+ RFigureConfigurationWidget}),
+ (RPDFFigure, {'configureWidgetType': \
+ RFigureConfigurationWidget})]
+ }
+
+def finalize():
+ for file in r_temp_files:
+ os.remove(file)
diff --git a/vistrails/packages/rpy/widgets.py b/vistrails/packages/rpy/widgets.py
new file mode 100644
index 0000000..dc599b4
--- /dev/null
+++ b/vistrails/packages/rpy/widgets.py
@@ -0,0 +1,46 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.gui.modules.source_configure import SourceConfigurationWidget
+
+class RSourceConfigurationWidget(SourceConfigurationWidget):
+
+ def __init__(self, module, controller, parent=None):
+ SourceConfigurationWidget.__init__(self, module, controller, None,
+ True, True, parent)
+
+class RFigureConfigurationWidget(SourceConfigurationWidget):
+ def __init__(self, module, controller, parent=None):
+ SourceConfigurationWidget.__init__(self, module, controller, None,
+ True, False, parent)
diff --git a/vistrails/packages/spreadsheet/__init__.py b/vistrails/packages/spreadsheet/__init__.py
new file mode 100644
index 0000000..280fd6d
--- /dev/null
+++ b/vistrails/packages/spreadsheet/__init__.py
@@ -0,0 +1,39 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+from identifiers import *
+
+# This must be here because of VisTrails protocol
+from spreadsheet_config import configuration
diff --git a/vistrails/packages/spreadsheet/analogy_api.py b/vistrails/packages/spreadsheet/analogy_api.py
new file mode 100644
index 0000000..0562f3d
--- /dev/null
+++ b/vistrails/packages/spreadsheet/analogy_api.py
@@ -0,0 +1,133 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file describes the analogy structure the spreadsheet holding
+# and it should be reimplemented to integrate between the spreadsheet
+# and the analogy
+################################################################################
+import os
+import vistrails.core.analogy
+import vistrails.gui
+
+class SpreadsheetAnalogyObject(object):
+ """
+ SpreadsheetAnalogyObject provides a API functions to integrate
+ between the spreadsheet and the analogy. There will be only one
+ instance of the analogy object
+
+ """
+ def __init__(self):
+ """ SpreadsheetAnalogyObject() -> SpreadsheetAnalogyObject
+ Initialize object properties
+
+ """
+ pass
+
+ def isValid(self):
+ """ isValid() -> bool
+ Is the current analogy object is valid and can be applied to
+ other pipeline
+
+ """
+ return True
+
+ def createAnalogy(self, p1Info, p2Info):
+ """ createAnalogy(p1Info: tuple, p2Info) -> bool
+ p1Info, p2Info: (vistrailName, versionNumber, actions, pipeline)
+
+ Setup an analogy object from p1 to p2 given their info in
+ p1Info and p2Info. CAUTION: sometimes the actual 'pipeline' on
+ the spreadsheet is different than the one created from the
+ vistrailName:versionNumber. For example, the parameter
+ exploration. If that is the case, actions is a list of all
+ actions has performed on the original pipeline to get to the
+ pipeline.
+
+ This function should return a boolean saying if the analogy
+ has been successfully created or not.
+
+ """
+# (p1_vistrail, p1_number, p1_actions, p1_pipeline) = p1Info
+# (p2_vistrail, p2_number, p2_actions, p2_pipeline) = p2Info
+ self._p1Info = p1Info
+ self._p2Info = p2Info
+ return True
+
+ def applyAnalogy(self, pInfo):
+ """ createAnalogy(pInfo: tuple) -> pInfo
+ pInfo: (vistrailName, versionNumber, actions, pipeline)
+
+ Given the analogy, apply on the pipeline in pInfo and return
+ the modified pipeline as a result. Along with the pipeline is
+ the list of actions that has been applied. If no actions
+ given (i.e. []), this can not be put back to the builder. If
+ analogy is not applicable, this should return None
+
+ """
+
+ (p1_locator, p1_number, p1_actions, p1_pipeline, p1_controller) = self._p1Info
+ (p2_locator, p2_number, p2_actions, p2_pipeline, p2_controller) = self._p2Info
+ (p3_locator, p3_number, p3_actions, p3_pipeline, p3_controller) = pInfo
+
+ if (p1_controller != p2_controller or
+ p1_controller != p3_controller or
+ p1_actions or
+ p2_actions or
+ p3_actions):
+ return None
+
+ perform = vistrails.core.analogy.perform_analogy_on_vistrail
+
+ controller = p1_controller
+ vt = controller.vistrail
+ if controller.current_version != p3_number:
+ controller.change_selected_version(p3_number)
+ action = perform( vt, p1_number, p2_number, p3_number)
+
+ controller.add_new_action(action)
+ controller.perform_action(action)
+
+ new_version = controller.current_version
+ new_pipeline = vt.getPipeline(new_version)
+ return (controller.locator, new_version, [], new_pipeline, controller)
+
+ def __call__(self):
+ """ __call__() -> SpreadsheetAnalogy
+ Return self for calling method
+
+ """
+ return self
+
+SpreadsheetAnalogy = SpreadsheetAnalogyObject()
diff --git a/vistrails/packages/spreadsheet/basic_widgets.py b/vistrails/packages/spreadsheet/basic_widgets.py
new file mode 100644
index 0000000..1228529
--- /dev/null
+++ b/vistrails/packages/spreadsheet/basic_widgets.py
@@ -0,0 +1,267 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file describes basic VisTrails Modules of the Spreadsheet package:
+# CellLocation
+# SheetReference
+# SingleCellSheetReference
+# SpreadsheetCell
+################################################################################
+from vistrails.core.modules.vistrails_module import Module, NotCacheable, ModuleError
+from spreadsheet_base import (StandardSheetReference,
+ StandardSingleCellSheetReference)
+from spreadsheet_controller import spreadsheetController
+from spreadsheet_event import DisplayCellEvent
+from PyQt4 import QtCore
+
+################################################################################
+
+def widgetName():
+ """ widgetName() -> str
+ Identify the name of the package
+
+ """
+ return 'Basic Widgets'
+
+def registerWidget(reg, basicModules, basicWidgets):
+ """ registerWidget(reg: module_registry, basicModules: package,
+ basicWidgets:package) -> None
+ Register widgets with VisTrails registry
+
+ """
+ reg.add_module(SheetReference)
+ reg.add_input_port(SheetReference, "MinRowCount", basicModules.Integer, True)
+ reg.add_input_port(SheetReference, "MinColumnCount",
+ basicModules.Integer, True)
+ reg.add_input_port(SheetReference, "SheetName", basicModules.String, True)
+ reg.add_output_port(SheetReference, "self", SheetReference)
+
+ reg.add_module(CellLocation)
+ reg.add_input_port(CellLocation, "ColumnRowAddress",
+ basicModules.String, True)
+ reg.add_input_port(CellLocation, "Row", basicModules.Integer, True)
+ reg.add_input_port(CellLocation, "Column", basicModules.Integer, True)
+ reg.add_input_port(CellLocation, "RowSpan", basicModules.Integer, True)
+ reg.add_input_port(CellLocation, "ColumnSpan", basicModules.Integer, True)
+ reg.add_input_port(CellLocation, "SheetReference", SheetReference)
+ reg.add_output_port(CellLocation, "self", CellLocation)
+
+ reg.add_module(SpreadsheetCell)
+ reg.add_input_port(SpreadsheetCell, "Location", CellLocation)
+
+ reg.add_module(SingleCellSheetReference)
+ reg.add_input_port(SingleCellSheetReference, "SheetName",
+ basicModules.String, True)
+ reg.add_output_port(SingleCellSheetReference, "self",
+ SingleCellSheetReference)
+
+class SheetReference(Module):
+ """
+ SheetReference is a VisTrail Module that allows users to specify
+ which sheet (page) to put the visualiation on. This is as
+ well a wrapper to simply contain real sheet reference classes
+
+ """
+ def __init__(self):
+ """ SheetReference() -> SheetReference
+ Instantiate an empty SheetReference
+
+ """
+ Module.__init__(self)
+ self.sheetReference = None
+
+ def compute(self):
+ """ compute() -> None
+ Store information on input ports and ready to be passed on to whoever
+ needs it
+
+ """
+ if self.sheetReference==None:
+ self.sheetReference = StandardSheetReference()
+ ref = self.sheetReference
+ ref.minimumRowCount = self.forceGetInputFromPort("MinRowCount", 1)
+ ref.minimumColumnCount = self.forceGetInputFromPort("MinColumnCount", 1)
+ ref.sheetName = self.forceGetInputFromPort("SheetName")
+
+ def getSheetReference(self):
+ """ getSheetReference() -> subclass of StandardSheetReference
+ Return the actual information stored in the SheetReference
+
+ """
+ return self.sheetReference
+
+class CellLocation(Module):
+ """
+ CellLocation is a Vistrail Module that allow users to specify
+ where to put a visualization on a sheet, i.e. row, column
+ location
+
+ """
+ def __init__(self):
+ """ CellLocation() -> CellLocation
+ Instantiate an empty cell location, i.e. any available cell
+
+ """
+ Module.__init__(self)
+ self.row = -1
+ self.col = -1
+ self.rowSpan = -1
+ self.colSpan = -1
+ self.sheetReference = None
+
+ def compute(self):
+ """ compute() -> None
+ Translate input ports into (row, column) location
+
+ """
+ def set_row_col(row, col):
+ try:
+ self.col = ord(col)-ord('A')
+ self.row = int(row)-1
+ except:
+ raise ModuleError(self, 'ColumnRowAddress format error')
+
+ ref = self.forceGetInputFromPort("SheetReference")
+ if ref:
+ self.sheetReference = ref.getSheetReference()
+
+ self.rowSpan = self.forceGetInputFromPort("RowSpan", -1)
+ self.colSpan = self.forceGetInputFromPort("ColumnSpan", -1)
+ if self.hasInputFromPort("Row") and self.hasInputFromPort("Column"):
+ self.row = self.getInputFromPort("Row")-1
+ self.col = self.getInputFromPort("Column")-1
+ elif self.hasInputFromPort("ColumnRowAddress"):
+ address = self.getInputFromPort("ColumnRowAddress")
+ address = address.replace(' ', '').upper()
+ if len(address)>1:
+ if address[0] >= 'A' and address[0] <= 'Z':
+ set_row_col(address[1:], address[0])
+ else:
+ set_row_col(address[:-1], address[-1])
+
+class SpreadsheetCell(NotCacheable, Module):
+ """
+ SpreadsheetCell is a base class to other widget types. It provides
+ a simple protocol to dispatch information to the spreadsheet
+ cells. But it doesn't know how to display the information
+ itself. That should be done by the specific widget type.
+
+ """
+ def __init__(self):
+ """ SpreadsheetCell() -> SpreadsheetCell
+ Initialize attributes
+
+ """
+ Module.__init__(self)
+ self.location = None
+
+ def overrideLocation(self, location):
+ """ overrideLocation(location: CellLocation) -> None
+ Make the cell always use this location instead of reading from
+ the port
+
+ """
+ self.location = location
+
+ def createDisplayEvent(self, cellType, inputPorts):
+ """ display(cellType: python type, iputPorts: tuple) -> None
+ Create a DisplayEvent with all the parameters from the cell
+ locations and inputs
+
+ """
+ e = DisplayCellEvent()
+ e.vistrail = self.moduleInfo
+ if self.location:
+ location = self.location
+ else:
+ location = self.forceGetInputFromPort("Location")
+ if location:
+ e.row = location.row
+ e.col = location.col
+ e.rowSpan = location.rowSpan
+ e.colSpan = location.colSpan
+ e.sheetReference = location.sheetReference
+ e.cellType = cellType
+ e.inputPorts = inputPorts
+ return e
+
+ def display(self, cellType, inputPorts):
+ """ display(cellType: python type, iputPorts: tuple) -> None
+ Dispatch the cellType to the spreadsheet with appropriate input data
+ to display it
+
+ Keyword arguments:
+ cellType --- widget type, this is truely a python type
+ inputPorts --- a tuple of input data that cellType() will understand
+
+ """
+ if spreadsheetController.echoMode():
+ return self.displayAndWait(cellType, inputPorts)
+ e = self.createDisplayEvent(cellType, inputPorts)
+ spreadsheetController.postEventToSpreadsheet(e)
+
+ def displayAndWait(self, cellType, inputPorts):
+ """ displayAndWait(cellType: python type, iputPorts: tuple)
+ Send the message and wait for the cell to complete its movement
+ constructed to return it
+
+ Keyword arguments:
+ cellType --- widget type, this is truely a python type
+ inputPorts --- a tuple of input data that cellType() will understand
+
+ """
+ e = self.createDisplayEvent(cellType, inputPorts)
+ QtCore.QCoreApplication.processEvents()
+ spreadsheetWindow = spreadsheetController.findSpreadsheetWindow()
+ if spreadsheetWindow.echoMode == False:
+ spreadsheetWindow.configShow(show=True)
+ return spreadsheetWindow.displayCellEvent(e)
+
+class SingleCellSheetReference(SheetReference):
+ """
+ SingleCellSheetReference is a wrapper of StandardSingleCellSheetReference
+ that will allow users to dedicate a whole sheet to view a single
+ visualization by pass all other sheet control widgets.
+
+ """
+ def compute(self):
+ """ compute() -> None
+ Store information from input ports into internal structure
+
+ """
+ if self.sheetReference==None:
+ self.sheetReference = StandardSingleCellSheetReference()
+ self.sheetReference.sheetName = self.forceGetInputFromPort("SheetName")
+
diff --git a/vistrails/packages/spreadsheet/cell_rc.py b/vistrails/packages/spreadsheet/cell_rc.py
new file mode 100644
index 0000000..134c0aa
--- /dev/null
+++ b/vistrails/packages/spreadsheet/cell_rc.py
@@ -0,0 +1,3259 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# -*- coding: utf-8 -*-
+
+# Resource object code
+#
+# Created: Fri Nov 30 16:53:17 2007
+# by: The Resource Compiler for PyQt (Qt v4.2.2)
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore
+
+qt_resource_data = b"\
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+
+qt_resource_name = b"\
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+"
+
+qt_resource_struct = b"\
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+\x00\x00\x00\x76\x00\x00\x00\x00\x00\x01\x00\x00\x59\x53\
+"
+
+def qInitResources():
+ QtCore.qRegisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+def qCleanupResources():
+ QtCore.qUnregisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+qInitResources()
diff --git a/vistrails/packages/spreadsheet/celltoolbar_rc.py b/vistrails/packages/spreadsheet/celltoolbar_rc.py
new file mode 100644
index 0000000..7bc26d6
--- /dev/null
+++ b/vistrails/packages/spreadsheet/celltoolbar_rc.py
@@ -0,0 +1,677 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# -*- coding: utf-8 -*-
+
+# Resource object code
+#
+# Created: Mon Jul 19 16:02:46 2010
+# by: The Resource Compiler for PyQt (Qt v4.6.3)
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore
+
+qt_resource_data = b"\
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+
+qt_resource_name = b"\
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+
+qt_resource_struct = b"\
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+"
+
+def qInitResources():
+ QtCore.qRegisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+def qCleanupResources():
+ QtCore.qUnregisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+qInitResources()
diff --git a/vistrails/packages/spreadsheet/identifiers.py b/vistrails/packages/spreadsheet/identifiers.py
new file mode 100644
index 0000000..1823bee
--- /dev/null
+++ b/vistrails/packages/spreadsheet/identifiers.py
@@ -0,0 +1,39 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+identifier = 'org.vistrails.vistrails.spreadsheet'
+name = 'VisTrails Spreadsheet'
+version = '0.9.2'
+old_identifiers = ['edu.utah.sci.vistrails.spreadsheet']
diff --git a/vistrails/packages/spreadsheet/init.py b/vistrails/packages/spreadsheet/init.py
new file mode 100644
index 0000000..1273905
--- /dev/null
+++ b/vistrails/packages/spreadsheet/init.py
@@ -0,0 +1,153 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# Spreadsheet Package for VisTrails
+################################################################################
+from PyQt4 import QtCore, QtGui
+from vistrails.core import debug
+from vistrails.core.modules import basic_modules
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.modules.vistrails_module import Module
+from vistrails.core.system import vistrails_root_directory
+from spreadsheet_controller import spreadsheetController
+from spreadsheet_registry import spreadsheetRegistry
+from spreadsheet_window import SpreadsheetWindow
+import os
+import string
+import sys
+from spreadsheet_config import configuration
+import vistrails.core
+
+# This must be here because of VisTrails protocol
+
+################################################################################
+
+basicWidgets = None
+
+def importReturnLast(name):
+ """ importReturnLast(name: str) -> package
+ Import a package whose name is specified in name and return right-most
+ package on the package name
+
+ """
+ mod = __import__(name)
+ components = name.split('.')
+ for comp in components[1:]:
+ mod = getattr(mod, comp)
+ return mod
+
+def addWidget(packagePath):
+ """ addWidget(packagePath: str) -> package
+ Add a new widget type to the spreadsheet registry supplying a
+ basic set of spreadsheet widgets
+
+ """
+ try:
+ registry = get_module_registry()
+ widget = importReturnLast(packagePath)
+ if hasattr(widget, 'widgetName'):
+ widgetName = widget.widgetName()
+ else:
+ widgetName = packagePath
+ widget.registerWidget(registry, basic_modules, basicWidgets)
+ spreadsheetRegistry.registerPackage(widget, packagePath)
+ debug.log(' ==> Successfully import <%s>' % widgetName)
+ except:
+ debug.log(' ==> Ignored package <%s>' % packagePath)
+ widget = None
+ return widget
+
+def importWidgetModules(basicWidgets):
+ """ importWidgetModules(basicWidgets: widget) -> None
+ Find all widget package under ./widgets/* to add to the spreadsheet registry
+
+ """
+ packageName = __name__.lower().endswith('.init') and \
+ __name__[:-5] or __name__
+ widgetDir = os.path.join(
+ os.path.join(os.path.dirname(vistrails_root_directory()),
+ *packageName.split('.')),
+ 'widgets')
+ candidates = os.listdir(widgetDir)
+ for folder in candidates:
+ if os.path.isdir(os.path.join(widgetDir, folder)) and folder != '.svn':
+ addWidget('.'.join([packageName, 'widgets', folder]))
+
+def initialize(*args, **keywords):
+ """ initialize() -> None
+ Package-entry to initialize the package
+
+ """
+ import vistrails.core.application
+ if not vistrails.core.application.is_running_gui():
+ raise RuntimeError, "GUI is not running. The Spreadsheet package requires the GUI"
+
+ # initialize widgets
+ debug.log('Loading Spreadsheet widgets...')
+ global basicWidgets
+ if basicWidgets==None:
+ basicWidgets = addWidget('vistrails.packages.spreadsheet.basic_widgets')
+ importWidgetModules(basicWidgets)
+
+ # Create application if there is no one available
+ global app
+ app = QtCore.QCoreApplication.instance()
+ if app==None:
+ app = QtGui.QApplication(sys.argv)
+ if hasattr(app, 'builderWindow'):
+ global spreadsheetWindow
+ spreadsheetWindow = spreadsheetController.findSpreadsheetWindow(show=False)
+
+def menu_items():
+ """menu_items() -> tuple of (str,function)
+ It returns a list of pairs containing text for the menu and a
+ callback function that will be executed when that menu item is selected.
+
+ """
+ def show_spreadsheet():
+ spreadsheetWindow.show()
+ spreadsheetWindow.activateWindow()
+ spreadsheetWindow.raise_()
+ lst = []
+ lst.append(("Show Spreadsheet", show_spreadsheet))
+ return tuple(lst)
+
+def finalize():
+ spreadsheetWindow = spreadsheetController.findSpreadsheetWindow()
+ ### DO NOT ADD BACK spreadsheetWindow.destroy()
+ ### That will crash VisTrails on Mac.
+ ### It is not supposed to be called directly
+ spreadsheetWindow.cleanup()
+ spreadsheetWindow.deleteLater()
diff --git a/vistrails/packages/spreadsheet/spreadsheet_base.py b/vistrails/packages/spreadsheet/spreadsheet_base.py
new file mode 100644
index 0000000..983b705
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_base.py
@@ -0,0 +1,316 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file contains a set of internal Spreadsheet basic classes used
+# by others:
+# StandardSheetReference
+# StandardSingleCellSheetReference
+# StandardSingleCellSheetTab
+################################################################################
+from PyQt4 import QtCore, QtGui
+from spreadsheet_helpers import CellHelpers
+from spreadsheet_registry import spreadsheetRegistry
+from spreadsheet_tab import (StandardWidgetSheetTab,
+ StandardWidgetSheetTabInterface)
+
+################################################################################
+
+class StandardSheetReference(object):
+ """
+ StandardSheetReference is used to specify which sheet a cell want
+ to be on. It also knows how to decide if a sheet on the
+ spreadsheet is appropriate for itself.
+ """
+
+ def __init__(self):
+ """ StandardSheetReference() -> StandardSheetReference
+ Initialize to the current sheet with no minimum size
+
+ """
+ self.sheetName = None
+ self.minimumRowCount = 1
+ self.minimumColumnCount = 1
+ self.candidate = None
+
+ def isTabValid(self, tabWidget):
+ """ isTabValid(tabWidget: QWidget) -> boolean
+ Check to see if the tab is an acceptable type
+
+ """
+ return issubclass(tabWidget.__class__, StandardWidgetSheetTab)
+
+ def clearCandidate(self):
+ """ clearCandidate() -> None
+ Begin the candidate searching process by clearing the previous
+ candidate sheet. The searching process is done by looping
+ through all available sheets and let the SheetReference decides
+ and keep track of which one is the best appropriate
+
+ """
+ self.candidate = None
+
+ def checkCandidate(self, tabWidget, tabLabel, tabIndex, curIndex):
+ """ checkCandidate(tabWidget: QWidget,
+ tabLabel: str,
+ tabIndex: int,
+ curIndex: int) -> None
+ Check to see if this new candidate is better than the one we
+ have right now. If it is then use this one instead. The
+ condition is very simple, sheet type comes first, then name
+ and dimensions.
+
+ Keyword arguments:
+ tabWidget --- QWidget controlling actual sheet widget
+ tabLabel --- the display label of the sheet
+ tabIndex --- its index inside the tab controller
+ curIndex --- the current active index of the tab controller
+
+ """
+ if self.isTabValid(tabWidget):
+ if (self.sheetName!=None and
+ str(tabLabel)!=str(self.sheetName)):
+ return
+ if self.candidate!=None:
+ if (self.sheetName==None or
+ (str(tabLabel)==str(self.sheetName))==
+ (str(self.candidate[1])==str(self.sheetName))):
+ storedSheet = self.candidate[0].sheet
+ newSheet = tabWidget.sheet
+ if (newSheet.rowCount()<self.minimumRowCount and
+ storedSheet.rowCount()>=self.minimumRowCount):
+ return
+ if (newSheet.columnCount()<self.minimumColumnCount and
+ storedSheet.columnCount()>=self.minimumColumnCount):
+ return
+ if (((newSheet.rowCount()<self.minimumRowCount)==
+ (storedSheet.rowCount()<self.minimumRowCount)) and
+ ((newSheet.columnCount()<self.minimumColumnCount)==
+ (storedSheet.columnCount()<self.minimumColumnCount))):
+ if tabIndex!=curIndex:
+ return
+ self.candidate = (tabWidget, tabLabel, tabIndex, curIndex)
+
+ def setupCandidate(self, tabController):
+ """ setupCandidate(tabController: SpreadsheetTabController) -> None
+ Setup the candidate we have to completely satisfy the reference,
+ making ready to be displayed on, e.g. extend the number of row and
+ column
+
+ """
+ if self.candidate==None:
+ candidate = StandardWidgetSheetTab(tabController,
+ self.minimumRowCount,
+ self.minimumColumnCount)
+ idx = tabController.addTabWidget(candidate, self.sheetName)
+ tabController.setCurrentIndex(idx)
+ candidate.sheet.stretchCells()
+ return candidate
+ else:
+ if self.candidate[0].sheet.rowCount()<self.minimumRowCount:
+ self.candidate[0].sheet.setRowCount(self.minimumRowCount)
+ if self.candidate[0].sheet.columnCount()<self.minimumColumnCount:
+ self.candidate[0].sheet.setColumnCount(self.minimumColumnCount)
+ tabController.setCurrentWidget(self.candidate[0])
+ return self.candidate[0]
+
+class StandardSingleCellSheetTab(QtGui.QWidget,
+ StandardWidgetSheetTabInterface):
+ """
+ StandardSingleCellSheetTab is a container of StandardWidgetSheet
+ with only a single cell. This will be added directly to a
+ QTabWidget on the spreadsheet as a sheet for displaying
+
+ """
+ def __init__(self, tabWidget, row=1, col=1):
+ """ StandardSingleCellSheetTab(row: int,
+ col: int) -> StandardSingleCellSheetTab
+ Initialize with the vertical layout containing only a single widget
+
+ """
+ QtGui.QWidget.__init__(self, None)
+ StandardWidgetSheetTabInterface.__init__(self)
+ self.type = 'StandardSingleCellSheetTab'
+ self.tabWidget = tabWidget
+ self.vLayout = QtGui.QVBoxLayout()
+ self.vLayout.setSpacing(0)
+ self.vLayout.setMargin(0)
+ self.setLayout(self.vLayout)
+ self.cell = QtGui.QWidget()
+ self.layout().addWidget(self.cell)
+ self.helpers = CellHelpers(self)
+ self.toolBars = {}
+ self.blankCellToolBar = None
+ self.pipelineInfo = {}
+
+ ### Belows are API Wrappers to connect to self.sheet
+
+ def getDimension(self):
+ """ getDimension() -> tuple
+ Get the sheet dimensions
+
+ """
+ return (1,1)
+
+ def getCell(self, row, col):
+ """ getCell(row: int, col: int) -> QWidget
+ Get cell at a specific row and column.
+
+ """
+ return self.cell
+
+ def getCellToolBar(self, row, col):
+ """ getCellToolBar(row: int, col: int) -> QWidget
+ Return the toolbar widget at cell location (row, col)
+
+ """
+ cell = self.getCell(row, col)
+ if cell and hasattr(cell, 'toolBarType'):
+ if not self.toolBars.has_key(cell.toolBarType):
+ self.toolBars[cell.toolBarType] = cell.toolBarType(self)
+ return self.toolBars[cell.toolBarType]
+ else:
+ return self.blankCellToolBar
+ return self.sheet.getCellToolBar(row, col)
+
+ def getCellRect(self, row, col):
+ """ getCellRect(row: int, col: int) -> QRect
+ Return the rectangle surrounding the cell at location (row, col)
+ in parent coordinates
+
+ """
+ return self.contentsRect()
+
+ def getCellGlobalRect(self, row, col):
+ """ getCellGlobalRect(row: int, col: int) -> QRect
+ Return the rectangle surrounding the cell at location (row, col)
+ in global coordinates
+
+ """
+ rect = self.getCellRect(row, col)
+ rect.moveTo(self.mapToGlobal(rect.topLeft()))
+ return rect
+
+ def setCellByType(self, row, col, cellType, inputPorts):
+ """ setCellByType(row: int,
+ col: int,
+ cellType: a type inherits from QWidget,
+ inpurPorts: tuple) -> None
+ Replace the current location (row, col) with a cell of
+ cellType. If the current type of that cell is the same as
+ cellType, only the contents is updated with inputPorts.
+
+ """
+ oldCell = self.getCell(row, col)
+ if type(oldCell)!=cellType:
+ oldCell.hide()
+ self.layout().removeWidget(oldCell)
+ if cellType:
+ self.cell = cellType(self)
+# self.cell.setGeometry(self.getCellRect(row, col))
+ self.layout().addWidget(self.cell)
+ self.cell.show()
+ self.cell.updateContents(inputPorts)
+ if hasattr(oldCell, 'deleteLater'):
+ oldCell.deleteLater()
+ del oldCell
+ else:
+ oldCell.updateContents(inputPorts)
+
+ def showHelpers(self, show, globalPos):
+ """ showHelpers(show: boolean, globalPos: QPoint) -> None
+ Show the helpers (toolbar, resizer) when show==True
+
+ """
+ if show:
+ self.helpers.snapTo(0,0)
+ self.helpers.adjustPosition()
+ self.helpers.show()
+ else:
+ self.helpers.hide()
+
+ def getSelectedLocations(self):
+ """ getSelectedLocations() -> tuple
+ Return the selected locations (row, col) of the current sheet
+
+ """
+ return [(0,0)]
+
+class StandardSingleCellSheetReference(StandardSheetReference):
+ """
+ StandardSingleCellSheetReference is a sheet reference that only
+ accepts a single cell. This overrides the StandardSheetReference
+
+ """
+ def isTabValid(self, tabWidget):
+ """ isTabValid(tabWidget: QWidget) -> boolean
+ Only accepts StandardSingleCellSheetTab
+
+ """
+ return issubclass(tabWidget.__class__, StandardSingleCellSheetTab)
+
+ def checkCandidate(self, tabWidget, tabLabel, tabIndex, curIndex):
+ """ checkCandidate(tabWidget: QWidget,
+ tabLabel: str,
+ tabIndex: int,
+ curIndex: int) -> None
+ Better candidate is decided merely if it is the current index
+
+ """
+ if self.isTabValid(tabWidget):
+ better = False
+ if (self.sheetName!=None and
+ str(tabLabel)!=str(self.sheetName)):
+ return
+ if self.candidate!=None:
+ if self.candidate[2]==curIndex or tabIndex!=curIndex:
+ return
+ self.candidate = (tabWidget, tabLabel, tabIndex, curIndex)
+
+ def setupCandidate(self, tabController):
+ """ setupCandidate(tabController: SpreadsheetTabController) -> None
+ Set up the sheet to be single-cell sheet
+
+ """
+ if self.candidate==None:
+ candidate = StandardSingleCellSheetTab(tabController)
+ index = tabController.addTabWidget(candidate, self.sheetName)
+ tabController.setCurrentIndex(index)
+ return candidate
+ else:
+ return self.candidate[0]
+
+spreadsheetRegistry.registerSheet('StandardSingleCellSheetTab',
+ StandardSingleCellSheetTab)
+
diff --git a/vistrails/packages/spreadsheet/spreadsheet_cell.py b/vistrails/packages/spreadsheet/spreadsheet_cell.py
new file mode 100644
index 0000000..31f39ad
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_cell.py
@@ -0,0 +1,1179 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file contains classes working with cell helper widgets, i.e. toolbar,
+# resizer, etc.:
+# QCellWidget
+# QCellToolBar
+################################################################################
+from PyQt4 import QtCore, QtGui
+import datetime
+import os
+import tempfile
+from vistrails.core import debug
+import cell_rc
+import celltoolbar_rc
+import spreadsheet_controller
+import analogy_api
+from vistrails.core.configuration import get_vistrails_configuration
+
+################################################################################
+
+class QCellWidget(QtGui.QWidget):
+ """
+ QCellWidget is the base cell class. All types of spreadsheet cells
+ should inherit from this.
+
+ """
+
+ def __init__(self, parent=None, flags=QtCore.Qt.WindowFlags()):
+ """ QCellWidget(parent: QWidget) -> QCellWidget
+ Instantiate the cell and helper properties
+
+ """
+ QtGui.QWidget.__init__(self, parent, flags)
+ self._historyImages = []
+ self._player = QtGui.QLabel(self.parent())
+ self._player.setAutoFillBackground(True)
+ self._player.setFocusPolicy(QtCore.Qt.NoFocus)
+ self._player.setScaledContents(True)
+ self._playerTimer = QtCore.QTimer()
+ self._playerTimer.setSingleShot(True)
+ self._currentFrame = 0
+ self._playing = False
+ # cell can be captured if it re-implements saveToPNG
+ self._capturingEnabled = (not isinstance(self, QCellWidget) and
+ hasattr(self, 'saveToPNG'))
+ self.connect(self._playerTimer,
+ QtCore.SIGNAL('timeout()'),
+ self.playNextFrame)
+ if getattr(get_vistrails_configuration(),'fixedSpreadsheetCells',False):
+ self.setSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
+ self.setFixedSize(200, 180)
+
+ def setAnimationEnabled(self, enabled):
+ """ setAnimationEnabled(enabled: bool) -> None
+
+ """
+ self._capturingEnabled = enabled
+ if not enabled:
+ self.clearHistory()
+
+ def saveToPNG(self, filename):
+ """ saveToPNG(filename: str) -> Bool
+ Abtract function for saving the current widget contents to an
+ image file
+ Returns True when succesful
+
+ """
+ debug.critical('saveToPNG() is unimplemented by the inherited cell')
+
+ def saveToHistory(self):
+ """ saveToHistory() -> None
+ Save the current contents to the history
+
+ """
+ # Generate filename
+ current = datetime.datetime.now()
+ tmpDir = tempfile.gettempdir()
+ fn = ( "hist_" + current.strftime("%Y_%m_%d__%H_%M_%S") +
+ "_" + str(current.microsecond)+".png")
+ fn = os.path.join(tmpDir, fn)
+ if self.saveToPNG(fn):
+ self._historyImages.append(fn)
+
+ def clearHistory(self):
+ """ clearHistory() -> None
+ Clear all history files
+
+ """
+ for fn in self._historyImages:
+ os.remove(fn)
+ self._historyImages = []
+
+ def deleteLater(self):
+ """ deleteLater() -> None
+ Make sure to clear history and delete the widget
+
+ """
+ self.clearHistory()
+ QtGui.QWidget.deleteLater(self)
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple)
+ Make sure to capture to history
+
+ """
+ # Capture window into history for playback
+ if self._capturingEnabled:
+ self.saveToHistory()
+
+ def resizeEvent(self, e):
+ """ resizeEvent(e: QEvent) -> None
+ Re-adjust the player widget
+
+ """
+ QtGui.QWidget.resizeEvent(self, e)
+
+ if self._player.isVisible():
+ self._player.setGeometry(self.geometry())
+
+ def setPlayerFrame(self, frame):
+ """ setPlayerFrame(frame: int) -> None
+ Set the player to display a particular frame number
+
+ """
+ if (len(self._historyImages)==0):
+ return
+ if frame>=len(self._historyImages):
+ frame = frame % len(self._historyImages)
+ if frame>=len(self._historyImages):
+ return
+ self._player.setPixmap(QtGui.QPixmap(self._historyImages[frame]))
+
+ def startPlayer(self):
+ """ startPlayer() -> None
+ Adjust the size of the player to the cell and show it
+
+ """
+ if not self._capturingEnabled:
+ return
+ self._player.setParent(self.parent())
+ self._player.setGeometry(self.geometry())
+ self._player.raise_()
+ self._currentFrame = -1
+ self.playNextFrame()
+ self._player.show()
+ self.hide()
+ self._playing = True
+
+ def stopPlayer(self):
+ """ startPlayer() -> None
+ Adjust the size of the player to the cell and show it
+
+ """
+ if not self._capturingEnabled:
+ return
+ self._playerTimer.stop()
+ self._player.hide()
+ self.show()
+ self._playing = False
+
+ def showNextFrame(self):
+ """ showNextFrame() -> None
+ Display the next frame in the history
+
+ """
+ self._currentFrame += 1
+ if self._currentFrame>=len(self._historyImages):
+ self._currentFrame = 0
+ self.setPlayerFrame(self._currentFrame)
+
+ def playNextFrame(self):
+ """ playNextFrame() -> None
+ Display the next frame in the history and start the timer for
+ the frame after
+
+ """
+ self.showNextFrame()
+ self._playerTimer.start(100)
+
+ def grabWindowPixmap(self):
+ """ grabWindowPixmap() -> QPixmap
+ Widget special grabbing function
+
+ """
+ return QtGui.QPixmap.grabWidget(self)
+
+ def dumpToFile(self, filename):
+ """ dumpToFile(filename: str, dump_as_pdf: bool) -> None
+ Dumps itself as an image to a file, calling grabWindowPixmap """
+ pixmap = self.grabWindowPixmap()
+ pixmap.save(filename,"PNG")
+
+ def saveToPDF(self, filename):
+ printer = QtGui.QPrinter()
+
+ printer.setOutputFormat(QtGui.QPrinter.PdfFormat)
+ printer.setOutputFileName(filename)
+ pixmap = self.grabWindowPixmap()
+ size = pixmap.size()
+ printer.setPaperSize(QtCore.QSizeF(size.width(), size.height()),
+ QtGui.QPrinter.Point)
+ painter = QtGui.QPainter()
+ painter.begin(printer)
+ rect = painter.viewport()
+ size.scale(rect.size(), QtCore.Qt.KeepAspectRatio)
+ painter.setViewport(rect.x(), rect.y(), size.width(), size.height())
+ painter.setWindow(pixmap.rect())
+ painter.drawPixmap(0, 0, pixmap)
+ painter.end()
+
+
+################################################################################
+
+class QCellToolBar(QtGui.QToolBar):
+ """
+ CellToolBar is inherited from QToolBar with some functionalities
+ for interacting with CellHelpers
+
+ """
+ def __init__(self, sheet):
+ """ CellToolBar(sheet: SpreadsheetSheet) -> CellToolBar
+ Initialize the cell toolbar by calling the user-defined
+ toolbar construction function
+
+ """
+ QtGui.QToolBar.__init__(self,sheet)
+ self.setOrientation(QtCore.Qt.Horizontal)
+ self.sheet = sheet
+ self.row = -1
+ self.col = -1
+ self.layout().setMargin(0)
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Preferred)
+ pixmap = self.style().standardPixmap(QtGui.QStyle.SP_DialogCloseButton)
+ self.appendAction(QCellToolBarRemoveCell(QtGui.QIcon(pixmap), self))
+ self.appendAction(QCellToolBarMergeCells(QtGui.QIcon(':celltoolbar/mergecells.png'), self))
+ self.createToolBar()
+
+ def addAnimationButtons(self):
+ """ addAnimationButtons() -> None
+
+ """
+ self.appendAction(QCellToolBarCaptureToHistory(self))
+ self.appendAction(QCellToolBarPlayHistory(self))
+ self.appendAction(QCellToolBarClearHistory(self))
+
+ def createToolBar(self):
+ """ createToolBar() -> None
+ A user-defined method for customizing the toolbar. This is
+ going to be an empty method here for inherited classes to
+ override.
+
+ """
+ self.addAnimationButtons()
+
+ def snapTo(self, row, col):
+ """ snapTo(row, col) -> None
+ Assign which row and column the toolbar should be snapped to
+
+ """
+ self.row = row
+ self.col = col
+ self.updateToolBar()
+
+ def updateToolBar(self):
+ """ updateToolBar() -> None
+ This will get called when the toolbar widgets need to have
+ their status updated. It sends out needUpdateStatus signal
+ to let the widget have a change to update their own status
+
+ """
+ cellWidget = self.sheet.getCell(self.row, self.col)
+ for action in self.actions():
+ action.emit(QtCore.SIGNAL('needUpdateStatus'),
+ (self.sheet, self.row, self.col, cellWidget))
+
+ def connectAction(self, action, widget):
+ """ connectAction(action: QAction, widget: QWidget) -> None
+ Connect actions to special slots of a widget
+
+ """
+ if hasattr(widget, 'updateStatus'):
+ self.connect(action, QtCore.SIGNAL('needUpdateStatus'),
+ widget.updateStatus)
+ if hasattr(widget, 'triggeredSlot'):
+ self.connect(action, QtCore.SIGNAL('triggered()'),
+ widget.triggeredSlot)
+ if hasattr(widget, 'toggledSlot'):
+ self.connect(action, QtCore.SIGNAL('toggled(bool)'),
+ widget.toggledSlot)
+
+ def appendAction(self, action):
+ """ appendAction(action: QAction) -> QAction
+ Setup and add action to the tool bar
+
+ """
+ action.toolBar = self
+ self.addAction(action)
+ self.connectAction(action, action)
+ return action
+
+ def appendWidget(self, widget):
+ """ appendWidget(widget: QWidget) -> QAction
+ Setup the widget as an action and add it to the tool bar
+
+ """
+ action = self.addWidget(widget)
+ widget.toolBar = self
+ action.toolBar = self
+ self.connectAction(action, widget)
+ return action
+
+ def getSnappedWidget(self):
+ """ getSnappedWidget() -> QWidget
+ Return the widget being snapped by the toolbar
+
+ """
+ if self.row>=0 and self.col>=0:
+ return self.sheet.getCell(self.row, self.col)
+ else:
+ return None
+
+class QCellToolBarRemoveCell(QtGui.QAction):
+ """
+ QCellToolBarRemoveCell is the action to clear the current cell
+
+ """
+ def __init__(self, icon, parent=None):
+ """ QCellToolBarRemoveCell(icon: QIcon, parent: QWidget)
+ -> QCellToolBarRemoveCell
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ icon,
+ "&Clear the current cell",
+ parent)
+ self.setStatusTip("Clear the current cell")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ r = QtGui.QMessageBox.question(cellWidget, 'Clear cell',
+ 'Are you sure to clear the cell?',
+ QtGui.QMessageBox.Yes |
+ QtGui.QMessageBox.No,
+ QtGui.QMessageBox.No)
+ if (r==QtGui.QMessageBox.Yes):
+ self.toolBar.sheet.deleteCell(self.toolBar.row, self.toolBar.col)
+
+ def updateStatus(self, info):
+ """ updateStatus(info: tuple) -> None
+ Updates the status of the button based on the input info
+
+ """
+ (sheet, row, col, cellWidget) = info
+ self.setVisible(cellWidget!=None)
+
+class QCellToolBarMergeCells(QtGui.QAction):
+ """
+ QCellToolBarMergeCells is the action to merge selected cells to a
+ single cell if they are in consecutive poisitions
+
+ """
+ def __init__(self, icon, parent=None):
+ """ QCellToolBarMergeCells(icon: QIcon, parent: QWidget)
+ -> QCellToolBarMergeCells
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ icon,
+ "&Merge cells",
+ parent)
+ self.setStatusTip("Merge selected cells to a single cell if "
+ "they are in consecutive poisitions")
+ self.setCheckable(True)
+
+ def triggeredSlot(self):
+ """ toggledSlot() -> None
+ Execute the action when the button is clicked
+
+ """
+ # Merge
+ if self.isChecked():
+ sheet = self.toolBar.sheet
+ selectedCells = sorted(sheet.getSelectedLocations())
+ topLeft = selectedCells[0]
+ bottomRight = selectedCells[-1]
+ sheet.setSpan(topLeft[0], topLeft[1],
+ bottomRight[0]-topLeft[0]+1,
+ bottomRight[1]-topLeft[1]+1)
+ else:
+ sheet = self.toolBar.sheet
+ selectedCells = sorted(sheet.getSelectedLocations())
+ for (row, col) in selectedCells:
+ sheet.setSpan(row, col, 1, 1)
+ sheet.clearSelection()
+ self.toolBar.updateToolBar()
+
+ def updateStatus(self, info):
+ """ updateStatus(info: tuple) -> None
+ Updates the status of the button based on the input info
+
+ """
+ (sheet, row, col, cellWidget) = info
+ selectedCells = sorted(sheet.getSelectedLocations())
+
+ # Will not show up if there is no cell selected
+ if len(selectedCells)==0:
+ self.setVisible(False)
+
+ # If there is a single cell selected, only show up if it has
+ # been merged before so that user can un-merge cells
+ elif len(selectedCells)==1:
+ showUp = False
+ if selectedCells[0]==(row, col):
+ span = sheet.getSpan(row, col)
+ if span[0]>1 or span[1]>1:
+ showUp = True
+ if showUp:
+ self.setChecked(True)
+ self.setVisible(True)
+ else:
+ self.setVisible(False)
+
+ # If there are multiple cells selected, only show up if they
+ # can be merged, i.e. cells are in consecutive position and
+ # none of them is already merged
+ else:
+ showUp = False
+ validRange = False
+ topLeft = selectedCells[0]
+ bottomRight = selectedCells[-1]
+ fullCount = (bottomRight[0]-topLeft[0]+1)*(bottomRight[1]-topLeft[1]+1)
+ validRange = len(selectedCells)==fullCount
+ if validRange:
+ showUp = True
+ for (r, c) in selectedCells:
+ span = sheet.getSpan(r, c)
+ if span[0]>1 or span[1]>1:
+ showUp = False
+ break
+ if showUp:
+ self.setChecked(False)
+ self.setVisible(True)
+ else:
+ self.setVisible(False)
+
+class QCellToolBarCaptureToHistory(QtGui.QAction):
+ """
+ QCellToolBarCaptureToHistory is the action to capture the
+ underlying widget to history for play back. The cell type must
+ support function saveToPNG(filename)
+
+ """
+ def __init__(self, parent=None):
+ """ QCellToolBarCaptureToHistory(parent: QWidget)
+ -> QCellToolBarCaptureToHistory
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/camera_mount.png"),
+ "&Capture image to history",
+ parent)
+ self.setStatusTip("Capture the cell contents to the history for "
+ "playback later")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ self.toolBar.hide()
+ cellWidget.saveToHistory()
+ self.toolBar.updateToolBar()
+ self.toolBar.show()
+
+ def updateStatus(self, info):
+ """ updateStatus(info: tuple) -> None
+ Updates the status of the button based on the input info
+
+ """
+ (sheet, row, col, cellWidget) = info
+ if cellWidget:
+ self.setVisible(cellWidget._capturingEnabled)
+ else:
+ self.setVisible(False)
+
+################################################################################
+
+class QCellToolBarPlayHistory(QtGui.QAction):
+ """
+ QCellToolBarPlayHistory is the action to play the history as an
+ animation
+
+ """
+ def __init__(self, parent=None):
+ """ QCellToolBarPlayHistory(parent: QWidget)
+ -> QCellToolBarPlayHistory
+ Setup the image, status tip, etc. of the action
+
+ """
+ self.icons = [QtGui.QIcon(":/images/player_play.png"),
+ QtGui.QIcon(":/images/player_pause.png")]
+ self.toolTips = ["&Play the history",
+ "Pa&use the history playback"]
+ self.statusTips = ["Playback all image files kept in the history",
+ "Pause the playback"]
+ QtGui.QAction.__init__(self, self.icons[0], self.toolTips[0], parent)
+ self.setStatusTip(self.statusTips[0])
+ self.status = 0
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ if self.status==0:
+ cellWidget.startPlayer()
+ else:
+ cellWidget.stopPlayer()
+ self.toolBar.updateToolBar()
+
+ def updateStatus(self, info):
+ """ updateStatus(info: tuple) -> None
+ Updates the status of the button based on the input info
+
+ """
+ (sheet, row, col, cellWidget) = info
+ if cellWidget:
+ self.setVisible(cellWidget._capturingEnabled)
+ newStatus = int(cellWidget._playing)
+ if newStatus!=self.status:
+ self.status = newStatus
+ self.setIcon(self.icons[self.status])
+ self.setToolTip(self.toolTips[self.status])
+ self.setStatusTip(self.statusTips[self.status])
+ self.setEnabled(len(cellWidget._historyImages)>0)
+ else:
+ self.setVisible(False)
+
+################################################################################
+
+class QCellToolBarClearHistory(QtGui.QAction):
+ """
+ QCellToolBarClearHistory is the action to reset cell history
+
+ """
+ def __init__(self, parent=None):
+ """ QCellToolBarClearHistory(parent: QWidget)
+ -> QCellToolBarClearHistory
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/noatunloopsong.png"),
+ "&Clear this cell history",
+ parent)
+ self.setStatusTip("Clear the cell history and its temporary "
+ "image files on disk")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ cellWidget.clearHistory()
+ self.toolBar.updateToolBar()
+
+ def updateStatus(self, info):
+ """ updateStatus(info: tuple) -> None
+ Updates the status of the button based on the input info
+
+ """
+ (sheet, row, col, cellWidget) = info
+ if cellWidget:
+ self.setVisible(cellWidget._capturingEnabled)
+ self.setEnabled((len(cellWidget._historyImages)>0
+ and cellWidget._playing==False))
+ else:
+ self.setVisible(False)
+
+################################################################################
+
+class QCellContainer(QtGui.QWidget):
+ """ QCellContainer is a simple QWidget containing the actual cell
+ widget as a child. This also acts as a sentinel protecting the
+ actual cell widget from being destroyed by sheet widgets
+ (e.g. QTableWidget) where they take control of the cell widget.
+
+ """
+ def __init__(self, widget=None, parent=None):
+ """ QCellContainer(parent: QWidget) -> QCellContainer
+ Create an empty container
+
+ """
+ QtGui.QWidget.__init__(self, parent)
+ layout = QtGui.QVBoxLayout()
+ layout.setSpacing(0)
+ layout.setMargin(0)
+ self.setLayout(layout)
+ self.containedWidget = None
+ self.setWidget(widget)
+ self.toolBar = None
+
+ def setWidget(self, widget):
+ """ setWidget(widget: QWidget) -> None
+ Set the contained widget of this container
+
+ """
+ if widget!=self.containedWidget:
+ if self.containedWidget:
+ self.layout().removeWidget(self.containedWidget)
+ self.containedWidget.deleteLater()
+ self.toolBar = None
+ if widget:
+ widget.setParent(self)
+ self.layout().addWidget(widget)
+ widget.show()
+ self.containedWidget = widget
+
+ def widget(self):
+ """ widget() -> QWidget
+ Return the contained widget
+
+ """
+ return self.containedWidget
+
+ def takeWidget(self):
+ """ widget() -> QWidget
+ Take the contained widget out without deleting
+
+ """
+ widget = self.containedWidget
+ if self.containedWidget:
+ self.layout().removeWidget(self.containedWidget)
+ self.containedWidget.setParent(None)
+ self.containedWidget = None
+ self.toolBar = None
+ return widget
+
+################################################################################
+
+class QCellPresenter(QtGui.QLabel):
+ """
+ QCellPresenter represents a cell in the Editing Mode. It has an
+ info bar on top and control dragable icons on the bottom
+
+ """
+ def __init__(self, parent=None):
+ """ QCellPresenter(parent: QWidget) -> QCellPresenter
+ Create the layout of the widget
+
+ """
+ QtGui.QLabel.__init__(self, parent)
+ self.setAutoFillBackground(True)
+ self.setScaledContents(True)
+ self.setMargin(0)
+ self.setFocusPolicy(QtCore.Qt.ClickFocus)
+ self.cellWidget = None
+
+ layout = QtGui.QGridLayout(self)
+ layout.setSpacing(2)
+ layout.setMargin(self.margin())
+ layout.setRowStretch(1, 1)
+ self.setLayout(layout)
+
+ self.info = QPipelineInfo()
+ layout.addWidget(self.info, 0, 0, 1, 2)
+
+ self.manipulator = QCellManipulator()
+ layout.addWidget(self.manipulator, 1, 0, 1, 2)
+
+ def assignCellWidget(self, cellWidget):
+ """ updateFromCellWidget(cellWidget: QWidget) -> None
+ Assign a cell widget to this presenter
+
+ """
+ self.cellWidget = cellWidget
+ if cellWidget:
+ if hasattr(cellWidget, 'grabWindowPixmap'):
+ bgPixmap = cellWidget.grabWindowPixmap()
+ else:
+ bgPixmap = QtGui.QPixmap.grabWidget(cellWidget)
+ self.info.show()
+ else:
+ self.info.hide()
+ bgPixmap = QtGui.QPixmap.grabWidget(self)
+ self.thumbnail = QtGui.QPixmap(bgPixmap)
+ painter = QtGui.QPainter(bgPixmap)
+ painter.fillRect(bgPixmap.rect(),
+ QtGui.QBrush(QtGui.QColor(175, 198, 229, 196)))
+ painter.end()
+ self.setPixmap(bgPixmap)
+
+ def assignCell(self, sheet, row, col):
+ """ assignCell(sheet: Sheet, row: int, col: int) -> None
+ Assign a sheet cell to the presenter
+
+ """
+ self.manipulator.assignCell(sheet, row, col)
+ self.assignCellWidget(sheet.getCell(row, col))
+ info = sheet.getCellPipelineInfo(row, col)
+ self.info.updateInfo(info)
+
+ def releaseCellWidget(self):
+ """ releaseCellWidget() -> QWidget
+ Return the ownership of self.cellWidget to the caller
+
+ """
+ cellWidget = self.cellWidget
+ self.assignCellWidget(None)
+ self.manipulator.assignCell(None, -1, -1)
+ if cellWidget:
+ cellWidget.setParent(None)
+ return cellWidget
+
+ def deleteLater(self):
+ """ deleteLater() -> None
+ Make sure to delete the cell widget if it exists
+
+ """
+ if (self.cellWidget):
+ self.cellWidget.deleteLater()
+ QtGui.QLabel.deleteLater(self)
+
+################################################################################
+
+class QInfoLineEdit(QtGui.QLineEdit):
+ """
+ QInfoLineEdit is wrapper for a transparent, un-frame, read-only
+ line edit
+
+ """
+ def __init__(self, parent=None):
+ """ QInfoLineEdit(parent: QWidget) -> QInfoLineEdit
+ Initialize the line edit
+
+ """
+ QtGui.QLineEdit.__init__(self, parent)
+ self.setReadOnly(True)
+ self.setFrame(False)
+ pal = QtGui.QPalette(self.palette())
+ pal.setBrush(QtGui.QPalette.Base,
+ QtGui.QBrush(QtCore.Qt.NoBrush))
+ self.setPalette(pal)
+
+
+class QInfoLabel(QtGui.QLabel):
+ """
+ QInfoLabel is wrapper for a transparent, bolded label
+
+ """
+ def __init__(self, text='', parent=None):
+ """ QInfoLabel(text: str, parent: QWidget) -> QInfoLabel
+ Initialize the line edit
+
+ """
+ QtGui.QLabel.__init__(self, text, parent)
+ font = QtGui.QFont(self.font())
+ font.setBold(True)
+ self.setFont(font)
+
+################################################################################
+
+class QPipelineInfo(QtGui.QFrame):
+ """
+ QPipelineInfo displays information about the executed pipeline of
+ a cell. It has 3 static lines: Vistrail name, (pipeline name,
+ pipeline id) and the cell type
+
+ """
+ def __init__(self, parent=None):
+ """ QPipelineInfo(parent: QWidget) -> None
+ Create the 3 information lines
+
+ """
+ QtGui.QFrame.__init__(self, parent)
+ self.setAutoFillBackground(True)
+ self.setFrameStyle(QtGui.QFrame.NoFrame)
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Maximum)
+
+ pal = QtGui.QPalette(self.palette())
+ color = QtGui.QColor(pal.brush(QtGui.QPalette.Base).color())
+ color.setAlpha(196)
+ pal.setBrush(QtGui.QPalette.Base, QtGui.QBrush(color))
+ self.setPalette(pal)
+
+ topLayout = QtGui.QVBoxLayout(self)
+ topLayout.setSpacing(0)
+ topLayout.setMargin(0)
+ self.setLayout(topLayout)
+
+ hLine = QtGui.QFrame()
+ hLine.setFrameStyle(QtGui.QFrame.HLine | QtGui.QFrame.Plain)
+ hLine.setFixedHeight(1)
+ topLayout.addWidget(hLine)
+
+ layout = QtGui.QGridLayout()
+ layout.setSpacing(2)
+ layout.setMargin(2)
+ topLayout.addLayout(layout)
+
+ self.edits = []
+ texts = ['Vistrail', 'Index', 'Created by']
+ for i in xrange(len(texts)):
+ label = QInfoLabel(texts[i])
+ layout.addWidget(label, i, 0, 1, 1)
+ edit = QInfoLineEdit()
+ self.edits.append(edit)
+ layout.addWidget(edit, i, 1, 1, 1)
+
+ topLayout.addStretch()
+ hLine = QtGui.QFrame()
+ hLine.setFrameStyle(QtGui.QFrame.HLine | QtGui.QFrame.Plain)
+ hLine.setFixedHeight(1)
+ topLayout.addWidget(hLine)
+
+ def updateInfo(self, info):
+ """ updateInfo(info: (dict, pid)) -> None
+ Update the information of a pipeline info
+
+ """
+ if info!=None and info[0]['locator']!=None:
+ self.edits[0].setText(str(info[0]['locator'].name))
+ self.edits[1].setText('(Pipeline: %d, Module: %d)'
+ % (info[0]['version'], info[0]['moduleId']))
+ self.edits[2].setText(str(info[0]['reason']))
+ else:
+ for edit in self.edits:
+ edit.setText('N/A')
+
+################################################################################
+
+class QCellManipulator(QtGui.QFrame):
+ """
+ QCellManipulator contains several dragable icons that allow users
+ to move/copy or perform some operation from one cell to
+ another. It also inclues a button for update the pipeline under
+ the cell to be a new version on the pipeline. It is useful for the
+ parameter exploration talks back to the builder
+
+ """
+ def __init__(self, parent=None):
+ """ QPipelineInfo(parent: QWidget) -> None
+ Create the 3 information lines
+
+ """
+ QtGui.QFrame.__init__(self, parent)
+ self.setAcceptDrops(True)
+ self.setFrameStyle(QtGui.QFrame.NoFrame)
+ self.setSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
+
+ layout = QtGui.QVBoxLayout(self)
+ layout.setSpacing(0)
+ layout.setMargin(0)
+ self.setLayout(layout)
+
+ layout.addStretch()
+
+ bLayout = QtGui.QHBoxLayout()
+ layout.addLayout(bLayout)
+
+ bInfo = [(':/images/copy_cell.png',
+ 'Drag to copy this cell to another place',
+ 'copy', 'Copy'),
+ (':/images/move_cell.png',
+ 'Drag to move this cell to another place',
+ 'move', 'Move'),
+ (':/images/create_analogy.png',
+ 'Drag to create an analogy between this cell and another one',
+ 'create_analogy', 'Create\nAnalogy'),
+ (':/images/apply_analogy.png',
+ 'Drag to apply the current analogy to this cell and put it '
+ 'at another place', 'apply_analogy', 'Apply\nAnalogy')]
+
+ self.buttons = []
+
+ bLayout.addStretch()
+ for b in bInfo:
+ button = QCellDragLabel(QtGui.QPixmap(b[0]))
+ button.setToolTip(b[1])
+ button.setStatusTip(b[1])
+ button.action = b[2]
+ vLayout = QtGui.QVBoxLayout()
+ vLayout.addWidget(button)
+ label = QtGui.QLabel(b[3])
+ label.setAlignment(QtCore.Qt.AlignCenter)
+ vLayout.addWidget(label)
+ bLayout.addLayout(vLayout)
+ self.buttons.append(button)
+ self.buttons.append(label)
+
+ self.updateButton = QtGui.QToolButton()
+ self.updateButton.setIconSize(QtCore.QSize(64, 64))
+ self.updateButton.setIcon(QtGui.QIcon(QtGui.QPixmap(
+ ':/images/update.png')))
+ self.updateButton.setAutoRaise(True)
+ self.updateButton.setToolTip('Add this cell as a new version')
+ self.updateButton.setStatusTip(self.updateButton.toolTip())
+ self.updateButton.setText('Create Version')
+ self.updateButton.setToolButtonStyle(QtCore.Qt.ToolButtonTextUnderIcon)
+ self.connect(self.updateButton, QtCore.SIGNAL('clicked(bool)'),
+ self.updateVersion)
+ self.buttons.append(self.updateButton)
+
+ self.locateButton = QtGui.QToolButton()
+ self.locateButton.setIconSize(QtCore.QSize(64, 64))
+ self.locateButton.setIcon(QtGui.QIcon(QtGui.QPixmap(
+ ':/images/locate.png')))
+ self.locateButton.setAutoRaise(True)
+ self.locateButton.setToolTip('Select this pipeline in the version tree ')
+ self.locateButton.setStatusTip(self.locateButton.toolTip())
+ self.locateButton.setText('Locate Version')
+ self.locateButton.setToolButtonStyle(QtCore.Qt.ToolButtonTextUnderIcon)
+ self.connect(self.locateButton, QtCore.SIGNAL('clicked(bool)'),
+ self.locateVersion)
+ self.buttons.append(self.locateButton)
+
+
+ uLayout = QtGui.QHBoxLayout()
+ uLayout.addStretch()
+ uLayout.addWidget(self.locateButton)
+ uLayout.addWidget(self.updateButton)
+ uLayout.addStretch()
+ layout.addLayout(uLayout)
+
+ bLayout.addStretch()
+
+ layout.addStretch()
+
+ self.innerRubberBand = QtGui.QRubberBand(QtGui.QRubberBand.Rectangle,
+ self)
+
+ def assignCell(self, sheet, row, col):
+ """ assignCell(sheet: Sheet, row: int, col: int) -> None
+ Assign a cell to the manipulator, so it knows where to drag
+ and drop
+
+ """
+ self.cellInfo = (sheet, row, col)
+ for b in self.buttons:
+ if hasattr(b, 'updateCellInfo'):
+ b.updateCellInfo(self.cellInfo)
+ if sheet and sheet.getCell(row, col)!=None:
+ widget = sheet.getCell(row, col)
+ b.setVisible(not isinstance(widget, QCellPresenter) or
+ widget.cellWidget is not None)
+ else:
+ b.setVisible(False)
+ self.updateButton.setVisible(False)
+ if sheet:
+ info = sheet.getCellPipelineInfo(row, col)
+ if info:
+ self.updateButton.setVisible(len(info[0]['actions'])>0)
+
+ def dragEnterEvent(self, event):
+ """ dragEnterEvent(event: QDragEnterEvent) -> None
+ Set to accept drops from the other cell info
+
+ """
+ mimeData = event.mimeData()
+ if hasattr(mimeData, 'cellInfo'):
+ if (mimeData.cellInfo==self.cellInfo or
+ mimeData.cellInfo[0]==None or
+ self.cellInfo[0]==None):
+ event.ignore()
+ else:
+ event.setDropAction(QtCore.Qt.MoveAction)
+ event.accept()
+ self.highlight()
+ else:
+ event.ignore()
+
+ def dragLeaveEvent(self, event):
+ """ dragLeaveEvent(event: QDragLeaveEvent) -> None
+ Unhighlight when the cursor leaves
+
+ """
+ self.highlight(False)
+
+ def dropEvent(self, event):
+ """ dragLeaveEvent(event: QDragLeaveEvent) -> None
+ Unhighlight when the cursor leaves
+
+ """
+ self.highlight(False)
+ mimeData = event.mimeData()
+ action = mimeData.action
+ cellInfo = mimeData.cellInfo
+ manipulator = mimeData.manipulator
+ if action in ['move', 'copy', 'create_analogy', 'apply_analogy']:
+ event.setDropAction(QtCore.Qt.MoveAction)
+ event.accept()
+
+ if action=='move':
+ self.cellInfo[0].swapCell(self.cellInfo[1], self.cellInfo[2],
+ cellInfo[0], cellInfo[1], cellInfo[2])
+ manipulator.assignCell(*self.cellInfo)
+ self.assignCell(*cellInfo)
+
+ if action=='copy':
+ cellInfo[0].copyCell(cellInfo[1], cellInfo[2],
+ self.cellInfo[0], self.cellInfo[1],
+ self.cellInfo[2])
+
+ if action=='create_analogy':
+ p1Info = cellInfo[0].getPipelineInfo(cellInfo[1], cellInfo[2])
+ p2Info = self.cellInfo[0].getPipelineInfo(self.cellInfo[1],
+ self.cellInfo[2])
+ if p1Info!=None and p2Info!=None:
+ analogy = analogy_api.SpreadsheetAnalogy()
+ analogy.createAnalogy(p1Info, p2Info)
+
+ if action=='apply_analogy':
+ p1Info = cellInfo[0].getPipelineInfo(cellInfo[1], cellInfo[2])
+ analogy = analogy_api.SpreadsheetAnalogy()
+ newPipeline = analogy.applyAnalogy(p1Info)
+ if newPipeline:
+ self.cellInfo[0].executePipelineToCell(newPipeline,
+ self.cellInfo[1],
+ self.cellInfo[2],
+ 'Apply Analogy')
+
+ else:
+ event.ignore()
+
+
+ def highlight(self, on=True):
+ """ highlight(on: bool) -> None
+ Highlight the cell as if being selected
+
+ """
+ if on:
+ self.innerRubberBand.setGeometry(self.rect())
+ self.innerRubberBand.show()
+ else:
+ self.innerRubberBand.hide()
+
+ def updateVersion(self):
+ """ updateVersion() -> None
+ Use the performed action of this cell to add back a new
+ version to the version tree
+
+ """
+ spreadsheetController = spreadsheet_controller.spreadsheetController
+ builderWindow = spreadsheetController.getBuilderWindow()
+ if builderWindow:
+ info = self.cellInfo[0].getCellPipelineInfo(self.cellInfo[1],
+ self.cellInfo[2])
+ if info:
+ info = info[0]
+ view = builderWindow.ensureController(info['controller'])
+ if view:
+ controller = view.controller
+ controller.change_selected_version(info['version'])
+ controller.perform_param_changes(info['actions'])
+ # controller.performBulkActions(info['actions'])
+
+ def locateVersion(self):
+ """ locateVersion() -> None
+ Select the version node on the version that has generated this cell
+
+ """
+ spreadsheetController = spreadsheet_controller.spreadsheetController
+ builderWindow = spreadsheetController.getBuilderWindow()
+ if builderWindow:
+ info = self.cellInfo[0].getCellPipelineInfo(self.cellInfo[1],
+ self.cellInfo[2])
+ if info:
+ info = info[0]
+ view = builderWindow.ensureController(info['controller'])
+ if view:
+ view.version_selected(info['version'], True)
+ view.version_view.select_current_version()
+ builderWindow.view_changed(view)
+ w = view.window()
+ # this has no effect
+ w.qactions['history'].trigger()
+ # so we need to use this one
+ view.history_selected()
+ view.activateWindow()
+
+################################################################################
+
+class QCellDragLabel(QtGui.QLabel):
+ """
+ QCellDragLabel is a pixmap label allowing users to drag it to
+ another cell manipulator
+
+ """
+ def __init__(self, pixmap, parent=None):
+ """ QCellDragLabel(pixmap: QPixmap, parent: QWidget) -> QCellDragLabel
+ Construct the pixmap label
+
+ """
+ QtGui.QLabel.__init__(self, parent)
+ self.setMargin(0)
+ self.setSizePolicy(QtGui.QSizePolicy.Maximum, QtGui.QSizePolicy.Maximum)
+ self.setPixmap(pixmap)
+ self.setScaledContents(True)
+ self.setFixedSize(64, 64)
+ self.cursorPixmap = pixmap.scaled(self.size())
+
+ self.startPos = None
+ self.cellInfo = (None, -1, -1)
+ self.action = None
+
+ def updateCellInfo(self, cellInfo):
+ """ updateCellInfo(cellInfo: tuple) -> None
+ Update cellInfo for mime data while dragging
+
+ """
+ self.cellInfo = cellInfo
+
+ def mousePressEvent(self, event):
+ """ mousePressEvent(event: QMouseEvent) -> None
+ Store the start position for drag event
+
+ """
+ self.startPos = QtCore.QPoint(event.pos())
+ QtGui.QLabel.mousePressEvent(self, event)
+
+ def mouseMoveEvent(self, event):
+ """ mouseMoveEvent(event: QMouseEvent) -> None
+ Prepare to drag
+
+ """
+ p = event.pos() - self.startPos
+ if p.manhattanLength()>=QtGui.QApplication.startDragDistance():
+ drag = QtGui.QDrag(self)
+ data = QtCore.QMimeData()
+ data.cellInfo = self.cellInfo
+ data.action = self.action
+ data.manipulator = self.parent()
+ drag.setMimeData(data)
+ drag.setHotSpot(self.cursorPixmap.rect().center())
+ drag.setPixmap(self.cursorPixmap)
+ drag.start(QtCore.Qt.MoveAction)
diff --git a/vistrails/packages/spreadsheet/spreadsheet_config.py b/vistrails/packages/spreadsheet/spreadsheet_config.py
new file mode 100644
index 0000000..c75ccb2
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_config.py
@@ -0,0 +1,39 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.configuration import ConfigurationObject
+configuration = ConfigurationObject(rowCount=2,
+ columnCount=3,
+ dumpfileType='PNG')
+# other possible value for dumpfileType is PDF
diff --git a/vistrails/packages/spreadsheet/spreadsheet_controller.py b/vistrails/packages/spreadsheet/spreadsheet_controller.py
new file mode 100644
index 0000000..0d16f73
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_controller.py
@@ -0,0 +1,129 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file contains the spreadsheet controller to take care of
+# interactions to the spreadsheet:
+# SpreadsheetController
+################################################################################
+from PyQt4 import QtCore, QtGui
+from spreadsheet_window import SpreadsheetWindow
+
+################################################################################
+
+class SpreadsheetController(object):
+ """
+ SpreadsheetController will act like an event dispatcher to
+ interact and control the spreadsheet in a thread-safe manner
+ (postEvent).
+
+ """
+ def __init__(self):
+ """ SpreadsheetController() -> SpreadsheetController
+ This class is more like an interface where there is no data inside
+
+ """
+ pass
+
+ def findSpreadsheetWindow(self, show=True):
+ """ findSpreadsheetWindow() -> QWidget
+ Looking for the spreadsheet window
+
+ """
+ wList = QtGui.QApplication.topLevelWidgets()
+ for w in wList:
+ if isinstance(w, SpreadsheetWindow):
+ return w
+ global spreadsheetWindow
+ spreadsheetWindow = SpreadsheetWindow()
+ if show:
+ spreadsheetWindow.configShow()
+ return spreadsheetWindow
+
+ def postEventToSpreadsheet(self, event):
+ """ postEventToSpreadsheet(event: QEvent) -> None
+ Post an event to the spreadsheet to make thread-safe connection
+ """
+ spreadsheetWindow = self.findSpreadsheetWindow()
+ if spreadsheetWindow:
+ QtCore.QCoreApplication.postEvent(spreadsheetWindow, QtGui.QShowEvent())
+ QtCore.QCoreApplication.postEvent(spreadsheetWindow, event)
+
+ def getBuilderWindow(self):
+ """ getBuilderWindow() -> QWidget
+ Return the builder window of the application, or None if
+ couldn't fine one
+
+ """
+ spreadsheetWindow = self.findSpreadsheetWindow()
+ if hasattr(spreadsheetWindow.visApp, 'builderWindow'):
+ return spreadsheetWindow.visApp.builderWindow
+ else:
+ return None
+
+ def setEchoMode(self, echo):
+ """ setEchoMode(echo: bool)
+ Instruct the spreadsheet to dispatch (echo) all cell widgets
+ instead of managing them on the spreadsheet
+
+ """
+ spreadsheetWindow = self.findSpreadsheetWindow(show=False)
+ if spreadsheetWindow:
+ spreadsheetWindow.setEchoMode(echo)
+
+ def echoMode(self):
+ """ echoMode() -> bool
+ Return true if the spreadsheet is in echo mode
+
+ """
+ spreadsheetWindow = self.findSpreadsheetWindow(show=False)
+ if spreadsheetWindow:
+ return spreadsheetWindow.echoMode
+ return None
+
+ def getEchoCellEvents(self):
+ """ getEchoCellEvents() -> [DisplayCellEvent]
+ Echo back the list of all cell events that have been captured
+ earlier
+
+ """
+ spreadsheetWindow = self.findSpreadsheetWindow(show=False)
+ if spreadsheetWindow:
+ events = spreadsheetWindow.getEchoCellEvents()
+ spreadsheetWindow.clearEchoCellEvents()
+ return events
+ return None
+
+spreadsheetController = SpreadsheetController()
+registeredWidgets = {}
diff --git a/vistrails/packages/spreadsheet/spreadsheet_event.py b/vistrails/packages/spreadsheet/spreadsheet_event.py
new file mode 100644
index 0000000..a86f697
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_event.py
@@ -0,0 +1,97 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file contains all Spreadsheet special Qt event classes
+################################################################################
+from PyQt4 import QtCore, QtGui
+
+################################################################################
+
+# A list of newly added events starting from QtCore.QEvent.User
+DisplayCellEventType = QtCore.QEvent.Type(QtCore.QEvent.User)
+BatchDisplayCellEventType = QtCore.QEvent.Type(QtCore.QEvent.User+1)
+RepaintCurrentSheetEventType = QtCore.QEvent.Type(QtCore.QEvent.User+2)
+
+class DisplayCellEvent(QtCore.QEvent):
+ """
+ DisplayCellEvent is an event to notify the spreadsheet that we want to
+ display input data on a specific type of widget. This is more of a data
+ container class
+
+ """
+ def __init__(self):
+ """ DisplayCellEvent() -> DisplayCellEvent
+ Instantiate a display event with no location, cell type, input data nor
+ an associated vistrail
+
+ """
+ QtCore.QEvent.__init__(self, DisplayCellEventType)
+ self.sheetReference = None
+ self.row = -1
+ self.col = -1
+ self.rowSpan = -1
+ self.colSpan = -1
+ self.cellType = None
+ self.inputPorts = None
+ self.vistrail = None
+
+class BatchDisplayCellEvent(QtCore.QEvent):
+ """
+ BatchDisplayCellEvent is similar to DisplayCellEvent but it is holding a
+ serie of DisplayCellEvent. This is very helpful since DisplayCellEvent
+ requires a thread-safe procedure, thus, very slow/un-safe when displaying
+ more than one cell with multiple events.
+
+ """
+ def __init__(self):
+ """ BatchDisplayCellEvent()
+ Instantiate an empty BatchDisplayCellEvent
+ """
+ QtCore.QEvent.__init__(self, BatchDisplayCellEventType)
+ self.displayEvents = []
+ self.vistrail = None
+
+class RepaintCurrentSheetEvent(QtCore.QEvent):
+ """
+ RepaintCurrentSheetEvent signal the spreadsheet to call repaint
+ for all cells in the current sheet
+
+ """
+ def __init__(self):
+ """ RepaintCurrentSheetEvent() -> RepaintCurrentSheetEvent
+ Initialize the event type
+
+ """
+ QtCore.QEvent.__init__(self, RepaintCurrentSheetEventType)
diff --git a/vistrails/packages/spreadsheet/spreadsheet_execute.py b/vistrails/packages/spreadsheet/spreadsheet_execute.py
new file mode 100644
index 0000000..89b566e
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_execute.py
@@ -0,0 +1,207 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file contains useful functions for executing pipelines on the spreadsheet
+# assignPipelineCellLocations
+# executePipelineWithProgress
+################################################################################
+from PyQt4 import QtCore, QtGui
+from vistrails.core.vistrail.controller import VistrailController
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.inspector import PipelineInspector
+from vistrails.core.interpreter.default import get_default_interpreter
+from vistrails.core.utils import DummyView
+from vistrails.core.vistrail.action import Action
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.port import Port
+from vistrails.core.vistrail import module
+from vistrails.core.vistrail import connection
+import vistrails.db.services.action
+import copy
+
+from identifiers import identifier as spreadsheet_pkg
+
+# FIXME broke this as Actions have been changed around
+#
+# from core.vistrail.action import AddModuleAction, AddConnectionAction, \
+# DeleteConnectionAction, ChangeParameterAction
+
+################################################################################
+
+def assignPipelineCellLocations(pipeline, sheetName,
+ row, col, cellIds=None,
+ minRowCount=None, minColCount=None):
+
+ reg = get_module_registry()
+ spreadsheet_cell_desc = \
+ reg.get_descriptor_by_name(spreadsheet_pkg, 'SpreadsheetCell')
+
+ create_module = VistrailController.create_module_static
+ create_function = VistrailController.create_function_static
+ create_connection = VistrailController.create_connection_static
+
+ pipeline = copy.copy(pipeline)
+ root_pipeline = pipeline
+ if cellIds is None:
+ inspector = PipelineInspector()
+ inspector.inspect_spreadsheet_cells(pipeline)
+ inspector.inspect_ambiguous_modules(pipeline)
+ cellIds = inspector.spreadsheet_cells
+
+ for id_list in cellIds:
+ # find at which depth we need to be working
+ try:
+ id_iter = iter(id_list)
+ m = pipeline.modules[id_iter.next()]
+ for mId in id_iter:
+ pipeline = m.pipeline
+ m = pipeline.modules[mId]
+ except TypeError:
+ mId = id_list
+
+ m = pipeline.modules[mId]
+ if not reg.is_descriptor_subclass(m.module_descriptor,
+ spreadsheet_cell_desc):
+ continue
+
+ # Walk through all connections and remove all CellLocation
+ # modules connected to this spreadsheet cell
+ conns_to_delete = []
+ for (cId,c) in pipeline.connections.iteritems():
+ if (c.destinationId==mId and
+ pipeline.modules[c.sourceId].name=="CellLocation"):
+ conns_to_delete.append(c.id)
+ for c_id in conns_to_delete:
+ pipeline.delete_connection(c_id)
+
+ # a hack to first get the id_scope to the local pipeline scope
+ # then make them negative by hacking the getNewId method
+ # all of this is reset at the end of this block
+ id_scope = pipeline.tmp_id
+ orig_getNewId = pipeline.tmp_id.__class__.getNewId
+ def getNewId(self, objType):
+ return -orig_getNewId(self, objType)
+ pipeline.tmp_id.__class__.getNewId = getNewId
+
+ # Add a sheet reference with a specific name
+ sheetReference = create_module(id_scope, spreadsheet_pkg,
+ "SheetReference")
+ sheetNameFunction = create_function(id_scope, sheetReference,
+ "SheetName", [str(sheetName)])
+ # ["%s %d" % (sheetPrefix, sheet)])
+
+ sheetReference.add_function(sheetNameFunction)
+
+ if minRowCount is not None:
+ minRowFunction = create_function(id_scope, sheetReference,
+ "MinRowCount", [str(minRowCount)])
+ # [str(rowCount*vRCount)])
+ sheetReference.add_function(minRowFunction)
+ if minColCount is not None:
+ minColFunction = create_function(id_scope, sheetReference,
+ "MinColumnCount",
+ [str(minColCount)])
+ # [str(colCount*vCCount)])
+ sheetReference.add_function(minColFunction)
+
+ # Add a cell location module with a specific row and column
+ cellLocation = create_module(id_scope, spreadsheet_pkg,
+ "CellLocation")
+ rowFunction = create_function(id_scope, cellLocation, "Row", [str(row)])
+ # [str(row*vRCount+vRow+1)])
+ colFunction = create_function(id_scope, cellLocation, "Column",
+ [str(col)])
+ # [str(col*vCCount+vCol+1)])
+
+ cellLocation.add_function(rowFunction)
+ cellLocation.add_function(colFunction)
+
+ # Then connect the SheetReference to the CellLocation
+ sheet_conn = create_connection(id_scope, sheetReference, "self",
+ cellLocation, "SheetReference")
+
+ # Then connect the CellLocation to the spreadsheet cell
+ cell_module = pipeline.get_module_by_id(mId)
+ cell_conn = create_connection(id_scope, cellLocation, "self",
+ cell_module, "Location")
+
+ pipeline.add_module(sheetReference)
+ pipeline.add_module(cellLocation)
+ pipeline.add_connection(sheet_conn)
+ pipeline.add_connection(cell_conn)
+ # replace the getNewId method
+ pipeline.tmp_id.__class__.getNewId = orig_getNewId
+
+ return root_pipeline
+
+def executePipelineWithProgress(pipeline,
+ pTitle='Pipeline Execution',
+ pCaption='Executing...',
+ pCancel='&Cancel',
+ **kwargs):
+ """ executePipelineWithProgress(pipeline: Pipeline,
+ pTitle: str, pCaption: str, pCancel: str,
+ kwargs: keyword arguments) -> bool
+ Execute the pipeline while showing a progress dialog with title
+ pTitle, caption pCaption and the cancel button text
+ pCancel. kwargs is the keyword arguments that will be passed to
+ the interpreter. A bool will be returned indicating if the
+ execution was performed without cancel or not.
+
+ """
+ withoutCancel = True
+ totalProgress = len(pipeline.modules)
+ progress = QtGui.QProgressDialog(pCaption,
+ pCancel,
+ 0, totalProgress)
+ progress.setWindowTitle(pTitle)
+ progress.setWindowModality(QtCore.Qt.WindowModal)
+ progress.show()
+ def moduleExecuted(objId):
+ if not progress.wasCanceled():
+ progress.setValue(progress.value()+1)
+ QtCore.QCoreApplication.processEvents()
+ else:
+ withoutCancel = False
+ interpreter = get_default_interpreter()
+ if kwargs.has_key('module_executed_hook'):
+ kwargs['module_executed_hook'].append(moduleExecuted)
+ else:
+ kwargs['module_executed_hook'] = [moduleExecuted]
+ kwargs['view'] = DummyView()
+ interpreter.execute(pipeline, **kwargs)
+ progress.setValue(totalProgress)
+ return withoutCancel
diff --git a/vistrails/packages/spreadsheet/spreadsheet_helpers.py b/vistrails/packages/spreadsheet/spreadsheet_helpers.py
new file mode 100644
index 0000000..4521fef
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_helpers.py
@@ -0,0 +1,294 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file contains classes working with cell helper widgets, i.e. toolbar,
+# resizer, etc.:
+# CellHelpers
+# CellResizer
+# CellResizerConfig
+################################################################################
+from PyQt4 import QtCore, QtGui
+
+################################################################################
+
+class CellResizerConfig(object):
+ """
+ CellResizerConfig can be used to config different parameters of
+ the CellResizer widget such as shape, mask, pixmap, color, size,
+ and cursor. By default, it has a black, triangular shape of size
+ 25x25. In order to change the shape, we have to override this
+ class
+
+ """
+ def __init__(self, size=25, color=QtGui.QColor(0,0,0)):
+ """ CellResizerConfig(size: int, color: QColor) -> CellResizerConfig
+ Create mask and pixmap of a triangular shape with the specifc size
+ and color
+
+ """
+ self.size = size
+ self.transparentColor = QtGui.QColor(QtCore.Qt.blue)
+ self.image = QtGui.QImage(size,size,QtGui.QImage.Format_RGB32)
+ for i in xrange(size):
+ for j in xrange(size):
+ if i+j<size-1:
+ self.image.setPixel(i, j, self.transparentColor.rgb())
+ else:
+ if i+j==size-1 or i==size-1 or j==size-1:
+ self.image.setPixel(i, j,
+ QtGui.QColor(QtCore.Qt.white).rgb())
+ else:
+ self.image.setPixel(i, j, color.rgb())
+ self.pixmapVar = self.maskVar = self.cursorVar = None
+
+ def pixmap(self):
+ """ pixmap() -> QPixmap
+ Return the pixmap of the resizer shape
+
+ """
+ if not self.pixmapVar:
+ self.pixmapVar = QtGui.QPixmap.fromImage(self.image)
+ return self.pixmapVar
+
+ def mask(self):
+ """ mask() -> QRegion
+ Return only the region of the resizer that will be shown on screen
+
+ """
+ if not self.maskVar:
+ mask = self.pixmap().createMaskFromColor(self.transparentColor)
+ self.maskVar = QtGui.QRegion(mask)
+ return self.maskVar
+
+ def cursor(self):
+ """ cursor() -> QCursor
+ Return the cursor that will be shown inside the resizer
+
+ """
+ return QtGui.QCursor(QtCore.Qt.SizeFDiagCursor)
+
+class CellResizer(QtGui.QLabel):
+ """
+ CellResizer is a customized shape SizeGrip that stays on top of
+ the widget, moving this size grip will end up resizing the
+ corresponding cell in the table. This is different from QSizeGrip
+ because it allows overlapping on top of the widget
+
+ """
+ def __init__(self, sheet, config=CellResizerConfig(), parent=None):
+ """ CellResizer(sheet: SpreadsheetSheet,
+ config: subclass of CellResizerConfig,
+ parent: QWidget) -> CellResizer
+ Initialize the size grip with the default triangular shape
+
+ """
+ QtGui.QLabel.__init__(self,sheet)
+ self.setFixedSize(config.size, config.size)
+ self.setPixmap(config.pixmap())
+ self.setMask(config.mask())
+ self.setCursor(config.cursor())
+ self.setStatusTip("Left/Right-click drag to resize the underlying"
+ "cell or the whole spreadsheet ")
+ self.setFocusPolicy(QtCore.Qt.NoFocus)
+ self.sheet = sheet
+ self.config = config
+ self.resizeAll = False
+ self.dragging = False
+ self.lastPos = None
+ self.row = -1
+ self.col = -1
+ self.hide()
+
+ def setDragging(self,b):
+ """ setDragging(b: boolean) -> None
+ Set the resizer state to busy dragging
+
+ """
+ self.dragging = b
+
+ def snapTo(self,row,col):
+ """ snapTo(row, col) -> None
+ Assign which row and column the resizer should be controlling
+
+ """
+ self.row = row
+ self.col = col
+
+ def adjustPosition(self, rect):
+ """ adjustPosition(rect: QRect) -> None
+ Adjust resizer position to be on the bottom-right corner of the cell
+
+ """
+ p = self.parent().mapFromGlobal(rect.topLeft())
+ self.move(p.x()+rect.width()-self.width(),
+ p.y()+rect.height()-self.height())
+
+ def mousePressEvent(self,e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Handle Qt mouse press event to track if we need to resize
+ either left or right mouse button is clicked
+
+ """
+ if self.col>=0:
+ if e.button()==QtCore.Qt.LeftButton:
+ self.resizeAll = False
+ self.dragging = True
+ if e.button()==QtCore.Qt.RightButton and not self.sheet.fitToWindow:
+ self.resizeAll = True
+ self.dragging = True
+ self.lastPos = (e.globalX()-self.sheet.columnWidth(self.col),
+ e.globalY()-self.sheet.rowHeight(self.row))
+
+ def mouseReleaseEvent(self,e):
+ """ mouseReleaseEvent(e: QMouseEvent) -> None
+ Handle Qt mouse release event to clean up all state
+
+ """
+ if (e.button()==QtCore.Qt.LeftButton or
+ e.button()==QtCore.Qt.RightButton):
+ self.dragging = False
+
+ def mouseMoveEvent(self,e):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Interactively resize the corresponding column and row when the
+ mouse moves
+
+ """
+ if self.dragging:
+ hSize = self.sheet.columnWidth(self.col)
+ vSize = self.sheet.rowHeight(self.row)
+ hd = e.globalX() - self.lastPos[0] - hSize
+ vd = e.globalY() - self.lastPos[1] - vSize
+
+ # All sections should have the same size (Right-Click)
+ if self.resizeAll:
+ # Resize the columns first
+ dS = int(hd / (self.col+1))
+ mS = hd % (self.col+1)
+ for i in xrange(self.sheet.columnCount()):
+ if i>self.col:
+ newValue = hSize+dS
+ else:
+ newValue = self.sheet.columnWidth(i)+dS+(i<mS)
+ self.sheet.setColumnWidth(i, newValue)
+ # Then resize the rows
+ dS = int(vd / (self.row+1))
+ mS = vd % (self.row+1)
+ for i in xrange(self.sheet.rowCount()):
+ if i>self.row:
+ newValue = vSize+dS
+ else:
+ newValue = self.sheet.rowHeight(i)+dS+(i<mS)
+ self.sheet.setRowHeight(i, newValue)
+
+ # Only resize the corresponding column and row (Left-Click)
+ else:
+ self.sheet.setColumnWidth(self.col, hSize+hd)
+ self.sheet.setRowHeight(self.row, vSize+vd)
+ rect = self.sheet.getCellRect(self.row, self.col)
+ rect.moveTo(self.sheet.viewport().mapToGlobal(rect.topLeft()))
+ self.adjustPosition(rect)
+
+class CellHelpers(object):
+ """
+ CellHelpers is a container include CellResizer that will shows up
+ whenever the Ctrl key is hold down and the mouse hovers the cell.
+
+ """
+ def __init__(self, sheet, resizerInstance=None):
+ """ CellHelpers(sheet: SpreadsheetSheet,
+ resizerInstance: CellResizer) -> CellHelpers
+ Initialize with a cell resizer
+
+ """
+ self.sheet = sheet
+ self.resizer = resizerInstance
+ self.row = -1
+ self.col = -1
+
+ def snapTo(self, row, col):
+ """ snapTo(row: int, col: int) -> None
+ Assign the resizer to the correct cell
+
+ """
+ if row>=0 and ((row!=self.row) or (col!=self.col)):
+ self.hide()
+ self.row = row
+ self.col = col
+ if self.resizer:
+ self.resizer.snapTo(row,col)
+ self.adjustPosition()
+
+ def adjustPosition(self):
+ """ adjustPosition() -> None
+ Adjust the resizer
+
+ """
+ rect = self.sheet.getCellGlobalRect(self.row, self.col)
+ if self.resizer:
+ self.resizer.adjustPosition(rect)
+
+ def show(self):
+ """ show() -> None
+ An helper function derived from setVisible
+
+ """
+ self.setVisible(True)
+
+ def hide(self):
+ """ hide() -> None
+ An helper function derived from setVisible
+
+ """
+ self.setVisible(False)
+
+ def setVisible(self,b):
+ """ setVisible(b: boolean) -> None
+ Show/hide the cell helpers
+ """
+ if self.resizer:
+ self.resizer.setVisible(b)
+ if not b and self.resizer:
+ self.resizer.setDragging(False)
+
+ def isInteracting(self):
+ """ isInteracting() -> boolean
+ Check to see if the helper is in action with the resizer
+
+ """
+ if self.resizer:
+ return self.resizer.dragging
+ else:
+ return False
diff --git a/vistrails/packages/spreadsheet/spreadsheet_rc.py b/vistrails/packages/spreadsheet/spreadsheet_rc.py
new file mode 100644
index 0000000..ca1f8d4
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_rc.py
@@ -0,0 +1,1872 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# Resource object code
+#
+# Created: Fri Oct 6 13:32:35 2006
+# by: The Resource Compiler for PyQt (Qt v4.1.3)
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore
+
+qt_resource_data = b"\
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+\x00\x6f\x00\x72\x00\x77\x00\x61\x00\x72\x00\x64\x00\x2e\x00\x70\x00\x6e\x00\x67\
+\x00\x08\
+\x08\xc8\x58\x67\
+\x00\x73\
+\x00\x61\x00\x76\x00\x65\x00\x2e\x00\x70\x00\x6e\x00\x67\
+\x00\x0c\
+\x05\x5e\x84\x87\
+\x00\x6e\
+\x00\x65\x00\x77\x00\x73\x00\x68\x00\x65\x00\x65\x00\x74\x00\x2e\x00\x70\x00\x6e\x00\x67\
+\x00\x0a\
+\x0b\x8d\x66\xc7\
+\x00\x73\
+\x00\x61\x00\x76\x00\x65\x00\x61\x00\x73\x00\x2e\x00\x70\x00\x6e\x00\x67\
+\x00\x08\
+\x06\xc1\x59\x87\
+\x00\x6f\
+\x00\x70\x00\x65\x00\x6e\x00\x2e\x00\x70\x00\x6e\x00\x67\
+"
+
+qt_resource_struct = b"\
+\x00\x00\x00\x00\x00\x02\x00\x00\x00\x01\x00\x00\x00\x01\
+\x00\x00\x00\x00\x00\x02\x00\x00\x00\x0a\x00\x00\x00\x02\
+\x00\x00\x00\xce\x00\x00\x00\x00\x00\x01\x00\x00\x4c\xb9\
+\x00\x00\x01\x06\x00\x00\x00\x00\x00\x01\x00\x00\x5d\xd7\
+\x00\x00\x00\x8a\x00\x00\x00\x00\x00\x01\x00\x00\x2d\x1f\
+\x00\x00\x00\x36\x00\x00\x00\x00\x00\x01\x00\x00\x07\x7b\
+\x00\x00\x00\x9c\x00\x00\x00\x00\x00\x01\x00\x00\x35\x1b\
+\x00\x00\x00\xb8\x00\x00\x00\x00\x00\x01\x00\x00\x42\x61\
+\x00\x00\x00\xec\x00\x00\x00\x00\x00\x01\x00\x00\x54\x4a\
+\x00\x00\x00\x12\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\
+\x00\x00\x00\x4c\x00\x00\x00\x00\x00\x01\x00\x00\x15\x01\
+\x00\x00\x00\x66\x00\x00\x00\x00\x00\x01\x00\x00\x23\x26\
+"
+
+def qInitResources():
+ QtCore.qRegisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+def qCleanupResources():
+ QtCore.qUnregisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+qInitResources()
diff --git a/vistrails/packages/spreadsheet/spreadsheet_registry.py b/vistrails/packages/spreadsheet/spreadsheet_registry.py
new file mode 100644
index 0000000..03b9f80
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_registry.py
@@ -0,0 +1,104 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file contains the spreadsheet registry:
+# SpreadsheetRegistry
+################################################################################
+
+class SpreadsheetRegistry(object):
+ """
+ SpreadsheetRegistry is the class holding information about cell and sheet
+ types. Each sheet name will only have one sheet type associated with it
+
+ """
+ def __init__(self):
+ """ SpreadsheetRegistry() -> SpreadsheetRegistry
+ Initialize the registry with no member
+
+ """
+ self.packages = {}
+ self.sheets = {}
+
+ def registerPackage(self, package, name):
+ """ registerPackage(package: python package, name: str) -> None
+ Register a package containing spreadsheet widgets to the spreadsheet
+
+ """
+ self.packages[package] = name
+
+ def unregisterPackage(self, package):
+ """ unregisterPackage(package: python package) -> None
+ Unregister a package out of the spreadsheet
+
+ """
+ if self.packages.has_key(package):
+ del self.packages[package]
+
+ def registerSheet(self, name, sheetType):
+ """ registerSheet(name: str, sheetType: type) -> None
+ Register a name for a sheet type
+
+ """
+ self.sheets[name] = sheetType
+
+ def unregisterSheet(self, name):
+ """ unregisterSheet(name: str) -> None
+ Unregister a named sheet type
+
+ """
+ if self.sheets.has_key(name):
+ del self.sheets[name]
+
+ def getSheet(self, name):
+ """ getSheet(name: str) -> type
+ Return the type of sheet with the corresponding name
+
+ """
+ if self.sheets.has_key(name):
+ return self.sheets[name]
+ else:
+ return None
+
+ def getSheetByType(self, type):
+ """ getSheetByType(type) -> name
+ Return the name of sheet with the corresponding type
+
+ """
+ for (n,t) in self.sheets.items():
+ if t==type:
+ return n
+ return None
+
+spreadsheetRegistry = SpreadsheetRegistry()
diff --git a/vistrails/packages/spreadsheet/spreadsheet_sheet.py b/vistrails/packages/spreadsheet/spreadsheet_sheet.py
new file mode 100644
index 0000000..4c2e9d2
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_sheet.py
@@ -0,0 +1,531 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file contains a set of internal Spreadsheet basic classes used
+# by others:
+# StandardWidgetHeaderView
+# StandardWidgetItemDelegate
+# StandardWidgetSheet
+################################################################################
+from PyQt4 import QtCore, QtGui
+from spreadsheet_helpers import CellHelpers, CellResizer
+
+################################################################################
+
+class StandardWidgetHeaderView(QtGui.QHeaderView):
+ """
+ StandardWidgetHeaderView is the standard header view (containing
+ column/row labels) inheriting from QHeaderView. The main
+ difference between this class and the original one is that it
+ allows resizing and stretching at the same time
+
+ """
+ minimumSize = 50
+
+ def __init__(self, orientation, parent=None):
+ """ StandardWidgetHeaderView(orientation: QtCore.Qt.Align...,
+ parent: QWidget)
+ -> StandardWidgetHeaderView
+ Initialize the header view to be like the one in the spreadsheet table
+
+ """
+ QtGui.QHeaderView.__init__(self, orientation, parent)
+ self.setMovable(True)
+ self.setFont(QtGui.QFont("Helvetica",12,QtGui.QFont.Bold))
+ self.resizeSections(QtGui.QHeaderView.Stretch)
+ self.setClickable(True)
+ self.setHighlightSections(True)
+ self.fitToViewport = False
+ if orientation==QtCore.Qt.Vertical:
+ self.setDefaultAlignment(QtCore.Qt.AlignHCenter |
+ QtCore.Qt.AlignVCenter)
+
+ def setFitToViewport(self, fit=True):
+ """ setFitToViewport(fit: boolean) -> None
+ Set fit to viewport for have all the sections always stretch
+ to the whole viewport
+
+ """
+ self.fitToViewport = fit
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+ Set a default thickness of the bar to 30
+
+ """
+ size = QtGui.QHeaderView.sizeHint(self)
+ if self.orientation()==QtCore.Qt.Vertical:
+ size.setWidth(30)
+ else:
+ size.setHeight(30)
+ return size
+
+class StandardWidgetItemDelegate(QtGui.QItemDelegate):
+ """
+ StandardWidgetItemDelegate will replace the QTableWidget default
+ display to have a padding around every cell widget
+
+ """
+ def __init__(self, table):
+ """ StandardWidgetItemDelegate(table: QTableWidget)
+ -> StandardWidgetItemDelegate
+ Initialize to store a table and padding
+
+ """
+ self.table = table
+ self.padding = 4
+ QtGui.QItemDelegate.__init__(self, None)
+
+ def setPadding(self, padding):
+ """ setPadding(padding: int) -> None
+ Re-set padding to a different value
+
+ """
+ if self.padding!=padding:
+ self.padding = padding
+
+ def updateEditorGeometry(self, editor, option, index):
+ """ updateEditorGeometry(editor: QWidget,
+ option: QStyleOptionViewItem,
+ index: QModelIndex) -> None
+ Make sure the widget only occupied inside the padded area
+
+ """
+ rect = self.table.visualRect(index)
+ rect.adjust(self.padding,self.padding,-self.padding,-self.padding)
+ editor.setGeometry(rect)
+ editor.setFixedSize(rect.width(), rect.height())
+
+ def paint(self, painter, option, index):
+ """ paint(painter: QPainter, option: QStyleOptionViewItem,
+ index: QModelIndex) -> None
+ Paint the current cell with a ring outside
+
+ """
+ QtGui.QItemDelegate.paint(self, painter, option, index)
+ if ((index.row(), index.column())==self.table.activeCell):
+ painter.save()
+ painter.setPen(QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(0.8549*255, 0.6971*255, 0.2255*255)), self.padding))
+ r = self.table.visualRect(index)
+ painter.setClipRegion(QtGui.QRegion(r))
+ r.adjust(self.padding/2,self.padding/2,-self.padding/2,-self.padding/2)
+ painter.drawRoundedRect(r, self.padding, self.padding)
+ painter.restore()
+
+
+class StandardWidgetSheet(QtGui.QTableWidget):
+ """
+ StandardWidgetSheet is a standard sheet that can contain any type
+ of cell widget. Each of them will be put into a separate cell. In
+ the case of vtkRenderWindow, where creating each sheet separately
+ can end up with a large number of GL contexts, a special type of
+ VTK sheet need to be derived from this one
+
+ """
+ def __init__(self, rows=0, cols=0, parent=None):
+ """ StandardWidgetSheet(rows: int, cols: int, parent: QWidget)
+ -> StandardWidgetSheet
+ Construct a sheet with rows x cols cells
+
+ """
+ QtGui.QTableWidget.__init__(self, 0, 0, parent)
+ self.setSelectionMode(QtGui.QAbstractItemView.NoSelection)
+ self.fitToWindow = False
+ self.setEditTriggers(QtGui.QAbstractItemView.NoEditTriggers)
+ self.setHorizontalHeader(StandardWidgetHeaderView(QtCore.Qt.Horizontal,
+ self))
+ self.horizontalHeader().setSelectionModel(self.selectionModel())
+ self.connect(self.horizontalHeader(),
+ QtCore.SIGNAL('sectionCountChanged(int, int)'),
+ self.updateColumnLabels)
+ self.connect(self.horizontalHeader(),
+ QtCore.SIGNAL('sectionMoved(int,int,int)'),
+ self.columnMoved)
+ self.connect(self.horizontalHeader(),
+ QtCore.SIGNAL('sectionPressed(int)'),
+ self.forceColumnMultiSelect)
+ self.setVerticalHeader(StandardWidgetHeaderView(QtCore.Qt.Vertical,
+ self))
+ self.verticalHeader().setSelectionModel(self.selectionModel())
+ self.connect(self.verticalHeader(),
+ QtCore.SIGNAL('sectionCountChanged(int, int)'),
+ self.updateRowLabels)
+ self.connect(self.verticalHeader(),
+ QtCore.SIGNAL('sectionMoved(int,int,int)'),
+ self.rowMoved)
+ self.connect(self.verticalHeader(),
+ QtCore.SIGNAL('sectionPressed(int)'),
+ self.forceRowMultiSelect)
+
+ # A hack to force the select all button in single click mode
+ cornerButton = self.findChild(QtGui.QAbstractButton)
+ if cornerButton:
+ self.connect(cornerButton,
+ QtCore.SIGNAL('clicked()'),
+ self.forceSheetSelect)
+
+ self.delegate = StandardWidgetItemDelegate(self)
+ self.setItemDelegate(self.delegate)
+ self.helpers = CellHelpers(parent, CellResizer(self))
+ self.setRowCount(rows)
+ self.setColumnCount(cols)
+ self.setFitToWindow(True)
+ self.connect(self,
+ QtCore.SIGNAL('cellActivated(int, int, bool)'),
+ self.selectCell)
+ self.activeCell = (-1,-1)
+
+ def forceColumnMultiSelect(self, logicalIndex):
+ """ forceColumnMultiSelect(logicalIndex: int) -> None
+ Make sure we always toggle the headerview in the right way
+ NOTE: the MultiSelection type of SelectionMode does not work
+ correctly for overlapping columns and rows selection
+
+ """
+ if (self.selectionModel().isColumnSelected(logicalIndex, QtCore.QModelIndex())):
+ self.selectionModel().select(self.model().index(0, logicalIndex),
+ QtGui.QItemSelectionModel.Deselect |
+ QtGui.QItemSelectionModel.Columns)
+ else:
+ self.selectionModel().select(self.model().index(0, logicalIndex),
+ QtGui.QItemSelectionModel.Select |
+ QtGui.QItemSelectionModel.Columns)
+
+ def forceRowMultiSelect(self, logicalIndex):
+ """ forceRowMultiSelect(logicalIndex: int) -> None
+ Make sure we always toggle the headerview in the right way
+ NOTE: the MultiSelection type of SelectionMode does not work
+ correctly for overlapping columns and rows selection
+
+ """
+ if (self.selectionModel().isRowSelected(logicalIndex, QtCore.QModelIndex())):
+ self.selectionModel().select(self.model().index(logicalIndex, 0),
+ QtGui.QItemSelectionModel.Deselect |
+ QtGui.QItemSelectionModel.Rows)
+ else:
+ self.selectionModel().select(self.model().index(logicalIndex, 0),
+ QtGui.QItemSelectionModel.Select |
+ QtGui.QItemSelectionModel.Rows)
+
+ def forceSheetSelect(self):
+ """ forceSheetSelect() -> None
+ Make sure we can toggle the whole sheet selection
+
+ """
+ totalCells = self.rowCount()*self.columnCount()
+ if (len(self.selectionModel().selectedIndexes())<totalCells):
+ self.selectionModel().select(
+ QtGui.QItemSelection(self.model().index(0,0),
+ self.model().index(self.rowCount()-1,
+ self.columnCount()-1)),
+ QtGui.QItemSelectionModel.Select)
+ else:
+ self.selectionModel().clearSelection()
+
+ def updateHeaderStatus(self):
+ """ updateHeaderStatus() -> None
+ Update the visibility of the row and column header
+
+ """
+ return
+ self.horizontalHeader().setVisible(self.columnCount() > 1 or
+ self.rowCount() > 1)
+ self.verticalHeader().setVisible(self.columnCount() > 1 or
+ self.rowCount() > 1)
+
+ def updateRowLabels(self, oldCount, newCount):
+ """ updateRowLabels(oldCount: int, newCount: int) -> None
+ Update vertical labels when the number of row changed
+
+ """
+ vLabels = []
+ vIdx = self.verticalHeader().visualIndex
+ for i in xrange(newCount):
+ vLabels.append(str(vIdx(i)+1))
+ self.setVerticalHeaderLabels(vLabels)
+ self.updateHeaderStatus()
+
+ def rowMoved(self, row, old, new):
+ """ rowMove(row: int, old: int, new: int) -> None
+ Renumber the vertical header labels when rows moved
+
+ """
+ self.updateRowLabels(self.rowCount(), self.rowCount())
+
+ def updateColumnLabels(self, oldCount, newCount):
+ """ updateColumnLabels(oldCount: int, newCount: int) -> None
+ Update horizontal labels when the number of column changed
+
+ """
+ hLabels = []
+ vIdx = self.horizontalHeader().visualIndex
+ for i in xrange(newCount):
+ hLabels.append(chr(vIdx(i)+ord('A')))
+ self.setHorizontalHeaderLabels(hLabels)
+ self.updateHeaderStatus()
+
+ def columnMoved(self, row, old, new):
+ """ columnMoved(row: int, old: int, new: int) -> None
+ Renumber the horizontal header labels when columns moved
+
+ """
+ self.updateColumnLabels(self.columnCount(), self.columnCount())
+
+ def setFitToWindow(self, fit=True):
+ """ setFitToWindow(fit: boolean) -> None
+ Force to fit all cells into the visible area. Set fit=False
+ for the scroll mode where hidden cell can be viewed by scrolling
+ the scrollbars.
+
+ """
+ if fit!=self.fitToWindow:
+ self.fitToWindow = fit
+ self.horizontalHeader().setFitToViewport(fit)
+ self.verticalHeader().setFitToViewport(fit)
+ if not fit:
+ width = self.columnWidth(self.columnCount()-1)
+ height = self.rowHeight(self.rowCount()-1)
+
+ self.setColumnWidth(self.columnCount()-1, width)
+ self.setRowHeight(self.rowCount()-1, height)
+ self.horizontalHeader().setStretchLastSection(fit)
+ self.verticalHeader().setStretchLastSection(fit)
+ self.stretchCells()
+
+ def showEvent(self, event):
+ """ showEvent(event: QShowEvent) -> None
+ Make sure to stretch the sheet on the first appearance
+
+ """
+ self.stretchCells()
+
+ def stretchCells(self):
+ """ stretchCells() -> None
+ Stretch all the cells with equally spaces to fit in the viewport
+
+ """
+ if self.fitToWindow:
+ self.horizontalHeader().setFitToViewport(False)
+ self.horizontalHeader().resizeSections(QtGui.QHeaderView.Stretch)
+ self.horizontalHeader().setFitToViewport(True)
+ self.verticalHeader().setFitToViewport(False)
+ self.verticalHeader().resizeSections(QtGui.QHeaderView.Stretch)
+ self.verticalHeader().setFitToViewport(True)
+
+ def resizeEvent(self, e):
+ """ resizeEvent(e: QResizeEvent) -> None
+ Resizes each row/column keeping the size ratios between them
+
+ """
+ if self.fitToWindow:
+ for min_size, getter, setter, count, final_size in [
+ (self.horizontalHeader().minimumSize,
+ self.columnWidth, self.setColumnWidth, self.columnCount(),
+ e.size().width()),
+ (self.verticalHeader().minimumSize,
+ self.rowHeight, self.setRowHeight, self.rowCount(),
+ e.size().height())]:
+ # Computes the total size of the columns
+ initial_size = 0
+ for i in xrange(count):
+ size = getter(i)
+ if size < min_size:
+ initial_size += min_size
+ else:
+ initial_size += size
+
+ if initial_size == 0:
+ continue
+
+ # Computes the resize ratio
+ ratio = float(final_size)/initial_size
+
+ i_total = 0
+ f_total = 0
+ for i in xrange(count - 1):
+ initial = getter(i)
+ if initial < min_size:
+ initial = min_size
+ final = int((initial + i_total) * ratio - f_total)
+ if final < min_size:
+ final = min_size
+ setter(i, final)
+ i_total += initial
+ f_total += final
+ final = final_size - f_total
+ if final < min_size:
+ final = min_size
+ setter(count - 1, final)
+
+ QtGui.QTableWidget.resizeEvent(self, e)
+
+ def showHelpers(self, show, row, col):
+ """ showHelpers(show: boolean, row: int, col: int) -> None
+ Show/hide the helpers (resizer, toolbar) on the current cell
+ depending on the value of show
+
+ """
+ if self.helpers.isInteracting():
+ return
+ if show:
+ if row>=0 and col>=0:
+ self.helpers.snapTo(row, col)
+ self.helpers.adjustPosition()
+ self.helpers.show()
+ else:
+ self.helpers.hide()
+ else:
+ self.helpers.hide()
+
+ def getRealLocation(self, vRow, vCol, visual=False):
+ """ getRealLocation(vRow: int, vCol: int, visual: bool) -> (int, int)
+ Return the actual location even if there is spanning at (vRow, vCol)
+
+ """
+ # Qt doesn't provide a mechanism to map from a cell to its
+ # span region, so we have to scan the whole spreadsheet N^2
+ # for now, but our spreadsheet is usuallly small enough.
+ if visual:
+ (row, col) = (vRow, vCol)
+ else:
+ row = self.verticalHeader().logicalIndex(vRow)
+ col = self.horizontalHeader().logicalIndex(vCol)
+ cellSet = set()
+ for r in xrange(self.rowCount()):
+ for c in xrange(self.columnCount()):
+ cellSet.add((r, c))
+ for r in xrange(self.rowCount()):
+ for c in xrange(self.columnCount()):
+ if (r, c) not in cellSet:
+ continue
+ rect = self.visualRect(self.model().index(r, c))
+ rSpan = self.rowSpan(r, c)
+ cSpan = self.columnSpan(r, c)
+ for rs in xrange(rSpan):
+ for cs in xrange(cSpan):
+ if (row==r+rs) and (col==c+cs):
+ return (r, c)
+ if (r+rs, c+cs) in cellSet:
+ cellSet.remove((r+rs, c+cs))
+ return (-1, -1)
+
+ def getCell(self, row, col):
+ """ getCell(row: int, col: int) -> QWidget
+ Get cell at a specific row and column
+
+ """
+ return self.cellWidget(*self.getRealLocation(row, col))
+
+ def getCellRect(self, row, col):
+ """ getCellRect(row: int, col: int) -> QRect
+ Return the rectangle surrounding the cell at location (row, col)
+ in parent coordinates
+
+ """
+ idx = self.model().index(*self.getRealLocation(row, col))
+ return self.visualRect(idx)
+
+ def getCellGlobalRect(self, row, col):
+ """ getCellGlobalRect(row: int, col: int) -> QRect
+ Return the rectangle surrounding the cell at location (row, col)
+ in global coordinates
+
+ """
+ rect = self.getCellRect(row, col)
+ rect.moveTo(self.viewport().mapToGlobal(rect.topLeft()))
+ return rect
+
+ def setCellByWidget(self, row, col, cellWidget):
+ """ setCellByWidget(row: int,
+ col: int,
+ cellWidget: QWidget) -> None
+ Replace the current location (row, col) with a cell widget
+
+ """
+ if cellWidget:
+ # Relax the size constraint of the widget
+ cellWidget.setMinimumSize(QtCore.QSize(0, 0))
+ cellWidget.setMaximumSize(QtCore.QSize(16777215, 16777215))
+ cellWidget.setParent(self)
+ (row, col) = self.getRealLocation(row, col)
+ index = self.model().index(row, col)
+ self.setCellWidget(row, col, cellWidget)
+ if cellWidget:
+ self.delegate.updateEditorGeometry(cellWidget, None, index)
+
+ def selectCell(self, row, col, toggling):
+ """ selectCell(row: int, col: int, toggling: bool) -> None
+ Select a cell based on its current selection
+
+ """
+ (row, col) = self.getRealLocation(row, col, visual=True)
+ if toggling:
+ self.selectionModel().setCurrentIndex(self.model().index(row, col),
+ QtGui.QItemSelectionModel.Toggle)
+ if (self.selectionModel().isSelected(self.model().index(row, col))):
+ self.setActiveCell(row, col)
+ else:
+ self.setActiveCell(-1, -1)
+ else:
+ if len(self.selectionModel().selectedIndexes())<=1:
+ self.selectionModel().setCurrentIndex(
+ self.model().index(row, col),
+ QtGui.QItemSelectionModel.ClearAndSelect)
+ self.setActiveCell(row, col)
+ self.viewport().repaint()
+
+ def setActiveCell(self, row, col):
+ """ setActiveCell(row: int, col: int) -> None
+ Set the location of an active cell also bring up the
+ corresponding toolbar
+
+ """
+ self.activeCell = (row, col)
+ toolBar = self.parent().getCellToolBar(row, col)
+ if toolBar:
+ toolBar.snapTo(row, col)
+ self.parent().toolBar.setCellToolBar(toolBar)
+
+ def adjustWidgetGeometry(self, row, col):
+ """ setActiveCell(row: int, col: int) -> None
+ Adjust the widget at cell (row, col) to fit inside the cell
+
+ """
+ cellWidget = self.getCell(row, col)
+ if cellWidget:
+ index = self.model().index(*self.getRealLocation(row, col))
+ self.delegate.updateEditorGeometry(cellWidget, None, index)
+
diff --git a/vistrails/packages/spreadsheet/spreadsheet_tab.py b/vistrails/packages/spreadsheet/spreadsheet_tab.py
new file mode 100644
index 0000000..c1d2096
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_tab.py
@@ -0,0 +1,1203 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file contains classes controlling tabs in the spreadsheets. A tab is
+# a container of a sheet:
+# SizeSpinBox
+# StandardTabDockWidget
+# StandardWidgetSheetTab
+# StandardWidgetTabBar
+# StandardWidgetTabBarEditor
+# StandardWidgetToolBar
+################################################################################
+from PyQt4 import QtCore, QtGui
+import os.path
+from spreadsheet_registry import spreadsheetRegistry
+from spreadsheet_sheet import StandardWidgetSheet
+from spreadsheet_cell import QCellPresenter, QCellContainer, QCellToolBar
+from spreadsheet_execute import assignPipelineCellLocations, \
+ executePipelineWithProgress
+from spreadsheet_config import configuration
+from vistrails.core.inspector import PipelineInspector
+import spreadsheet_rc
+
+################################################################################
+
+class SizeSpinBox(QtGui.QSpinBox):
+ """
+ SizeSpinBox is just an overrided spin box that will also emit
+ 'editingFinished()' signal when the user interact with mouse
+
+ """
+ def __init__(self, initValue=0, parent=None):
+ """ SizeSpinBox(initValue: int, parent: QWidget) -> SizeSpinBox
+ Initialize with a default width of 50 and a value of 0
+
+ """
+ QtGui.QSpinBox.__init__(self, parent)
+ self.setMinimum(1)
+ self.setMinimumWidth(50)
+ self.setMaximumWidth(50)
+ self.setValue(initValue)
+
+ def mouseReleaseEvent(self, event):
+ """ mouseReleaseEvent(event: QMouseEvent) -> None
+ Emit 'editingFinished()' signal when the user release a mouse button
+
+ """
+ QtGui.QSpinBox.mouseReleaseEvent(self, event)
+ self.emit(QtCore.SIGNAL("editingFinished()"))
+
+class StandardWidgetToolBar(QtGui.QToolBar):
+ """
+ StandardWidgetToolBar: The default toolbar for each sheet
+ container. By default, only FitToWindow and Table resizing are
+ included
+
+ """
+ def __init__(self, parent=None):
+ """ StandardWidgetToolBar(parent: QWidget) -> StandardWidgetToolBar
+ Init the toolbar with default actions
+
+ """
+ QtGui.QToolBar.__init__(self, parent)
+ self.sheetTab = parent
+ self.addAction(self.sheetTab.tabWidget.newSheetAction())
+ self.addAction(self.sheetTab.tabWidget.openAction())
+ self.addAction(self.sheetTab.tabWidget.saveAction())
+ self.addWidget(self.rowCountSpinBox())
+ self.addWidget(self.colCountSpinBox())
+ self.addAction(self.sheetTab.tabWidget.exportSheetToImageAction())
+ self.addSeparator()
+ self.layout().setSpacing(2)
+ self.currentToolBarAction = None
+
+ def rowCountSpinBox(self):
+ """ rowCountSpinBox() -> SizeSpinBox
+ Return the row spin box widget:
+
+ """
+ if not hasattr(self, 'rowSpinBox'):
+ self.rowSpinBox = SizeSpinBox(self.sheetTab.sheet.rowCount())
+ self.rowSpinBox.setToolTip('The number of rows')
+ self.rowSpinBox.setStatusTip('Change the number of rows '
+ 'of the current sheet')
+ self.connect(self.rowSpinBox,
+ QtCore.SIGNAL('editingFinished()'),
+ self.sheetTab.rowSpinBoxChanged)
+ return self.rowSpinBox
+
+ def colCountSpinBox(self):
+ """ colCountSpinBox() -> SizeSpinBox
+ Return the column spin box widget:
+
+ """
+ if not hasattr(self, 'colSpinBox'):
+ self.colSpinBox = SizeSpinBox(self.sheetTab.sheet.columnCount())
+ self.colSpinBox.setToolTip('The number of columns')
+ self.colSpinBox.setStatusTip('Change the number of columns '
+ 'of the current sheet')
+ self.connect(self.colSpinBox,
+ QtCore.SIGNAL('editingFinished()'),
+ self.sheetTab.colSpinBoxChanged)
+ return self.colSpinBox
+
+ def setCellToolBar(self, cellToolBar):
+ """ setCellToolBar(cellToolBar: QToolBar) -> None
+ Set the current cell toolbar on this toolbar. Use None to
+ remove the cell toolbar
+
+ """
+ if (not self.currentToolBarAction or
+ self.widgetForAction(self.currentToolBarAction)!=cellToolBar):
+ if self.currentToolBarAction:
+ self.removeAction(self.currentToolBarAction)
+ if cellToolBar:
+ self.currentToolBarAction = self.addWidget(cellToolBar)
+ self.currentToolBarAction.setVisible(True)
+ self.currentToolBarAction.setEnabled(True)
+ else:
+ self.currentToolBarAction = None
+
+class StandardWidgetSheetTabInterface(object):
+ """
+ StandardWidgetSheetTabInterface is the interface for tab
+ controller to call for manipulating a tab
+
+ """
+ ### Belows are API Wrappers to connect to self.sheet
+
+ def __init__(self):
+ self.lastCellLocation = (0, 0)
+ self.emptyCellToolBar = None
+
+ def isSheetTabWidget(self):
+ """ isSheetTabWidget() -> boolean
+ Return True if this is a sheet tab widget
+
+ """
+ return True
+
+ def getDimension(self):
+ """ getDimension() -> tuple
+ Get the sheet dimensions
+
+ """
+ return (0,0)
+
+ def setDimension(self, rc, cc):
+ """ setDimension(rc: int, cc: int) -> None
+ Set the sheet dimensions
+
+ """
+ pass
+
+ def getCell(self, row, col):
+ """ getCell(row: int, col: int) -> QWidget
+ Get cell at a specific row and column. In reality, this cell
+ widget is inside a QCellContainer and the cell container is
+ the actual widget under the cell
+
+ """
+ cellWidget = self.getCellWidget(row, col)
+ if isinstance(cellWidget, QCellContainer):
+ return cellWidget.widget()
+ return cellWidget
+
+ def getCellWidget(self, row, col):
+ """ getCellWidget(row: int, col: int) -> QWidget
+ Get actual cell at a specific row and column. This will in
+ fact return the container widget of a cell
+
+ """
+ return None
+
+ def setCellWidget(self, row, col, cellWidget):
+ """ setCellWidget(row: int,
+ col: int,
+ cellWidget: QWidget) -> None
+ Replace the current location (row, col) with a
+ widget. The widget will be put into a container to be
+ protected from being destroyed when taken out.
+
+ """
+ pass
+
+ def setCellByWidget(self, row, col, cellWidget):
+ """ setCellByWidget(row: int,
+ col: int,
+ cellWidget: QWidget) -> None
+ Put the cellWidget inside a container and place it on the sheet
+
+ """
+ if not isinstance(cellWidget, QCellContainer):
+ container = QCellContainer(cellWidget)
+ else:
+ container = cellWidget
+ self.setCellWidget(row, col, container)
+ self.lastCellLocation = (row, col)
+
+ def getCellToolBar(self, row, col):
+ """ getCellToolBar(row: int, col: int) -> QWidget
+ Return the toolbar widget at cell location (row, col)
+
+ """
+ cell = self.getCell(row, col)
+ if cell:
+ if hasattr(cell, 'toolBarType'):
+ toolBarType = cell.toolBarType
+ else:
+ toolBarType = QCellToolBar
+ container = self.getCellWidget(row, col)
+ if isinstance(container, QCellContainer):
+ if container.toolBar==None:
+ container.toolBar = toolBarType(self)
+ return container.toolBar
+ else:
+ if self.emptyCellToolBar==None:
+ self.emptyCellToolBar = QCellToolBar(self)
+ return self.emptyCellToolBar
+
+ def getCellRect(self, row, col):
+ """ getCellRect(row: int, col: int) -> QRect
+ Return the rectangle surrounding the cell at location (row, col)
+ in parent coordinates
+
+ """
+ return QtCore.QRect()
+
+ def getCellGlobalRect(self, row, col):
+ """ getCellGlobalRect(row: int, col: int) -> QRect
+ Return the rectangle surrounding the cell at location (row, col)
+ in global coordinates
+
+ """
+ return QtCore.QRect()
+
+ def getFreeCell(self):
+ """ getFreeCell() -> tuple
+ Get a free cell location (row, col) on the spreadsheet
+
+ """
+ (rowCount, colCount) = self.getDimension()
+ for r in xrange(rowCount):
+ for c in xrange(colCount):
+ w = self.getCell(r, c)
+ if w==None or (isinstance(w, QCellPresenter) and w.cellWidget==None):
+ return (r,c)
+ (r, c) = self.lastCellLocation
+ (rs, cs) = self.getSpan(r, c)
+ index = (colCount * r + c + cs) % (rowCount*colCount)
+ return (index/colCount, index%colCount)
+
+ def setCellByType(self, row, col, cellType, inputPorts):
+ """ setCellByType(row: int,
+ col: int,
+ cellType: a type inherits from QWidget,
+ inpurPorts: tuple) -> None
+ Replace the current location (row, col) with a cell of
+ cellType. If the current type of that cell is the same as
+ cellType, only the contents is updated with inputPorts.
+
+ """
+ oldCell = self.getCell(row, col)
+ if cellType is None or not isinstance(oldCell, cellType):
+ if cellType:
+ newCell = cellType(self)
+ self.setCellByWidget(row, col, newCell)
+ newCell.show()
+ newCell.updateContents(inputPorts)
+ else:
+ self.setCellByWidget(row, col, None)
+ if hasattr(oldCell, 'deleteLater'):
+ oldCell.deleteLater()
+ else:
+ oldCell.updateContents(inputPorts)
+ self.lastCellLocation = (row, col)
+
+ def showHelpers(self, show, globalPos):
+ """ showHelpers(show: boolean, globalPos: QPoint) -> None
+ Show/hide the helpers (toolbar, resizer when the mouse is at
+ globalPos
+
+ """
+ pass
+
+ def setCellPipelineInfo(self, row, col, info):
+ """ setCellPipelineInfo(row: int, col: int, info: any type) -> None
+ Provide a way for the spreadsheet to store vistrail
+ information, info, for the cell (row, col)
+
+ """
+ if not (row,col) in self.pipelineInfo:
+ self.pipelineInfo[(row,col)] = {}
+ self.pipelineInfo[(row,col)] = info
+
+ def getCellPipelineInfo(self, row, col):
+ """ getCellPipelineInfo(row: int, col: int) -> any type
+ Provide a way for the spreadsheet to extract vistrail
+ information, info, for the cell (row, col)
+
+ """
+ if not (row,col) in self.pipelineInfo:
+ return None
+ return self.pipelineInfo[(row,col)]
+
+ def getSelectedLocations(self):
+ """ getSelectedLocations() -> list
+ Return the selected locations (row, col) of the current sheet
+
+ """
+ return []
+
+ def clearSelection(self):
+ """ clearSelection() -> None
+ Clear all the selection in the current sheet
+
+ """
+ pass
+
+ def deleteCell(self, row, col):
+ """ deleteCell(row, col: int) -> None
+ Delete a cell in the sheet
+
+ """
+ self.setCellByType(row, col, None, None)
+ self.setCellPipelineInfo(row, col, None)
+
+ def deleteAllCells(self):
+ """ deleteAllCells() -> None
+ Delete all cells in the sheet
+
+ """
+ (rowCount, columnCount) = self.getDimension()
+ for r in xrange(rowCount):
+ for c in xrange(columnCount):
+ self.deleteCell(r, c)
+
+ def takeCell(self, row, col):
+ """ takeCell(row, col) -> QWidget
+ Free the cell widget at (row, col) from the tab and return as
+ the result of the function. If there is no widget at (row,
+ col). This returns None. The ownership of the widget is passed
+ to the caller.
+
+ """
+ cell = self.getCellWidget(row, col)
+ if isinstance(cell, QCellContainer):
+ widget = cell.takeWidget()
+ self.setCellWidget(row, col, None)
+ return widget
+ else:
+ return cell
+
+ def setCellEditingMode(self, r, c, editing=True):
+ """ setCellEditingMode(r: int, c: int, editing: bool) -> None
+ Turn on/off the editing mode of a single cell
+
+ """
+ if editing:
+ cellWidget = self.getCell(r, c)
+ if isinstance(cellWidget, QCellPresenter):
+ return
+ presenter = QCellPresenter()
+ presenter.assignCell(self, r, c)
+ cellWidget = self.takeCell(r, c)
+ self.setCellByWidget(r, c, presenter)
+ if cellWidget:
+ cellWidget.hide()
+ else:
+ presenter = self.getCell(r, c)
+ if not isinstance(presenter, QCellPresenter):
+ return
+ presenter = self.takeCell(r, c)
+ if presenter:
+ cellWidget = presenter.releaseCellWidget()
+ self.setCellByWidget(r, c, cellWidget)
+ presenter.hide()
+
+ def setEditingMode(self, editing=True):
+ """ setEditingMode(editing: bool) -> None
+ Turn on/off the editing mode of the tab
+
+ """
+ # Turn off active cell selection
+ self.sheet.clearSelection()
+ self.sheet.setActiveCell(-1, -1)
+ # Go over all the cells and set the editing widget up
+ (rowCount, colCount) = self.getDimension()
+ for r in xrange(rowCount):
+ for c in xrange(colCount):
+ self.setCellEditingMode(r, c, editing)
+ QtCore.QCoreApplication.processEvents()
+
+ def swapCell(self, row, col, newSheet, newRow, newCol):
+ """ swapCell(row, col: int, newSheet: Sheet,
+ newRow, newCol: int) -> None
+ Swap the (row, col) of this sheet to (newRow, newCol) of newSheet
+
+ """
+ myWidget = self.takeCell(row, col)
+ theirWidget = newSheet.takeCell(newRow, newCol)
+ self.setCellByWidget(row, col, theirWidget)
+ newSheet.setCellByWidget(newRow, newCol, myWidget)
+ info = self.getCellPipelineInfo(row, col)
+ self.setCellPipelineInfo(row, col,
+ newSheet.getCellPipelineInfo(newRow, newCol))
+ newSheet.setCellPipelineInfo(newRow, newCol, info)
+
+ def copyCell(self, row, col, newSheet, newRow, newCol):
+ """ copyCell(row, col: int, newSheet: Sheet,
+ newRow, newCol: int) -> None
+ Copy the (row, col) of this sheet to (newRow, newCol) of newSheet
+
+ """
+ info = self.getCellPipelineInfo(row, col)
+ if info:
+ info = info[0]
+ mId = info['moduleId']
+ pipeline = newSheet.setPipelineToLocateAt(newRow, newCol,
+ info['pipeline'], [mId])
+ executePipelineWithProgress(pipeline, 'Copy Cell',
+ current_version=info['version'],
+ actions=info['actions'],
+ reason=info['reason'],
+ locator=info['locator'],
+ controller=info['controller'],
+ sinks=[mId])
+
+ def executePipelineToCell(self, pInfo, row, col, reason=''):
+ """ executePipelineToCell(p: tuple, row: int, col: int) -> None
+ p: (locator, version, actions, pipeline)
+
+ Execute a pipeline and put all of its cell to (row, col). This
+ need to be fixed to layout all cells inside the pipeline
+
+ """
+ pipeline = self.setPipelineToLocateAt(row, col, pInfo[3])
+ executePipelineWithProgress(pipeline, 'Execute Cell',
+ locator=pInfo[0],
+ controller=pInfo[4],
+ current_version=pInfo[1],
+ actions=pInfo[2],
+ reason=reason)
+
+ def setPipelineToLocateAt(self, row, col, inPipeline, cellIds=[]):
+ """ setPipelineToLocateAt(row: int, col: int, inPipeline: Pipeline,
+ cellIds: [ids]) -> Pipeline
+ Modify the pipeline to have its cells (provided by cellIds) to
+ be located at (row, col) of this sheet
+
+ """
+ sheetName = str(self.tabWidget.tabText(self.tabWidget.indexOf(self)))
+ # Note that we must increment row/col by 1 to match how the
+ # CellReference module expects them
+ return assignPipelineCellLocations(inPipeline, sheetName,
+ row + 1, col + 1, cellIds)
+
+ def getPipelineInfo(self, row, col):
+ """ getPipelineInfo(row: int, col: int) -> tuple
+ Return (locator, versionNumber, actions, pipeline, controller) for a cell
+
+ """
+ info = self.getCellPipelineInfo(row, col)
+ if info:
+ return (info[0]['locator'],
+ info[0]['version'],
+ info[0]['actions'],
+ info[0]['pipeline'],
+ info[0]['controller'])
+ return None
+
+ def exportSheetToImage(self, fileName):
+ """ exportSheetToImage() -> None
+ Montage all the cell images and export to a file
+
+ """
+ (rCount, cCount) = self.getDimension()
+ if rCount<1 or cCount<1: return
+ cellHeights = [self.getCellRect(r, 0).height()
+ for r in xrange(rCount)]
+ cellWidths = [self.getCellRect(0, c).width()
+ for c in xrange(cCount)]
+ finalImage = QtGui.QImage(sum(cellWidths), sum(cellHeights), QtGui.QImage.Format_ARGB32)
+ finalImage.fill(0xFFFFFFFF)
+ painter = QtGui.QPainter(finalImage)
+ y = 0
+ for r in xrange(rCount):
+ x = 0
+ for c in xrange(cCount):
+ widget = self.getCell(r, c)
+ if widget:
+ pix = widget.grabWindowPixmap()
+ cx = (cellWidths[c]-pix.width())/2
+ cy = (cellHeights[r]-pix.height())/2
+ painter.drawPixmap(x+cx, y+cy, widget.grabWindowPixmap())
+ x += cellWidths[c]
+ y += cellHeights[r]
+ painter.end()
+
+ #forcing png format if no extension was provided
+ (_,ext) = os.path.splitext(fileName)
+ if ext == '':
+ finalImage.save(fileName, 'png')
+ else:
+ #try to guess based on the extension
+ finalImage.save(fileName)
+
+ def exportSheetToImages(self, dirPath, format='png'):
+ """ exportSheetToImage() -> None
+ Montage all the cell images and export to a file
+
+ """
+ (rCount, cCount) = self.getDimension()
+ for r in xrange(rCount):
+ for c in xrange(cCount):
+ widget = self.getCell(r, c)
+ if widget:
+ widget.grabWindowPixmap().save(dirPath+'/'+
+ chr(c+ord('a'))+
+ str(r+1)+
+ '.'+format)
+
+ def setSpan(self, row, col, rowSpan, colSpan):
+ """ setSpan(row, col, rowSpan, colSpan: int) -> None
+ Set the spanning at location (row, col). This is only a place
+ holder. Subclasses should implement this and getSpan for a
+ fully functioning spanning feature.
+
+ """
+ pass
+
+ def getSpan(self, row, col):
+ """ setSpan(row, col: int) -> (rowSpan, colSpan: int)
+ Return the spanning at location (row, col). This is only a
+ place holder. Subclasses should implement this and setSpan for
+ a fully functioning spanning feature.
+
+ """
+ return (1, 1)
+
+class StandardWidgetSheetTab(QtGui.QWidget, StandardWidgetSheetTabInterface):
+ """
+ StandardWidgetSheetTab is a container of StandardWidgetSheet with
+ a toolbar on top. This will be added directly to a QTabWidget for
+ displaying the spreadsheet.
+
+ """
+ def __init__(self, tabWidget,row=None , col=None):
+ """ StandardWidgetSheet(tabWidget: QTabWidget,
+ row: int,
+ col: int) -> StandardWidgetSheet
+ Initialize with a toolbar and a sheet widget
+
+ """
+ QtGui.QWidget.__init__(self, None)
+ StandardWidgetSheetTabInterface.__init__(self)
+ if not row:
+ row = configuration.rowCount
+ if not col:
+ col = configuration.columnCount
+ self.type = 'StandardWidgetSheetTab'
+ self.tabWidget = tabWidget
+ self.sheet = StandardWidgetSheet(row, col, self)
+ self.sheet.setFitToWindow(True)
+ self.toolBar = StandardWidgetToolBar(self)
+ self.vLayout = QtGui.QVBoxLayout()
+ self.vLayout.setSpacing(0)
+ self.vLayout.setMargin(0)
+ self.vLayout.addWidget(self.toolBar, 0)
+ self.vLayout.addWidget(self.sheet, 1)
+ self.setLayout(self.vLayout)
+ self.pipelineInfo = {}
+ self.setAcceptDrops(True)
+
+ def rowSpinBoxChanged(self):
+ """ rowSpinBoxChanged() -> None
+ Handle the number of row changed
+
+ """
+ if self.toolBar.rowSpinBox.value()!=self.sheet.rowCount():
+ self.sheet.setRowCount(self.toolBar.rowSpinBox.value())
+ self.sheet.stretchCells()
+ self.setEditingMode(self.tabWidget.editingMode)
+
+ def colSpinBoxChanged(self):
+ """ colSpinBoxChanged() -> None
+ Handle the number of row changed
+
+ """
+ if self.toolBar.colSpinBox.value()!=self.sheet.columnCount():
+ self.sheet.setColumnCount(self.toolBar.colSpinBox.value())
+ self.sheet.stretchCells()
+ self.setEditingMode(self.tabWidget.editingMode)
+
+ ### Belows are API Wrappers to connect to self.sheet
+
+ def getDimension(self):
+ """ getDimension() -> tuple
+ Get the sheet dimensions
+
+ """
+ return (self.sheet.rowCount(), self.sheet.columnCount())
+
+ def setDimension(self, rc, cc):
+ """ setDimension(rc: int, cc: int) -> None
+ Set the sheet dimensions
+
+ """
+ self.toolBar.rowCountSpinBox().setValue(rc)
+ self.toolBar.colCountSpinBox().setValue(cc)
+
+ def getCellWidget(self, row, col):
+ """ getCellWidget(row: int, col: int) -> QWidget
+ Get cell at a specific row and column.
+
+ """
+ return self.sheet.getCell(row, col)
+
+ def getCellRect(self, row, col):
+ """ getCellRect(row: int, col: int) -> QRect
+ Return the rectangle surrounding the cell at location (row, col)
+ in parent coordinates
+
+ """
+ return self.sheet.getCellRect(row, col)
+
+ def getCellGlobalRect(self, row, col):
+ """ getCellGlobalRect(row: int, col: int) -> QRect
+ Return the rectangle surrounding the cell at location (row, col)
+ in global coordinates
+
+ """
+ return self.sheet.getCellGlobalRect(row, col)
+
+ def showHelpers(self, show, globalPos):
+ """ showHelpers(show: boolean, globalPos: QPoint) -> None
+ Show/hide the helpers (toolbar, resizer) depending on the
+ status of show and the global position of the cursor
+
+ """
+ localPos = self.sheet.viewport().mapFromGlobal(QtGui.QCursor.pos())
+ row = self.sheet.rowAt(localPos.y())
+ col = self.sheet.columnAt(localPos.x())
+ rect = self.sheet.getCellRect(row, col)
+ show = show and (rect.x()+rect.width()-localPos.x()<100 and
+ rect.y()+rect.height()-localPos.y()<100)
+ self.sheet.showHelpers(show, row, col)
+
+ def getSelectedLocations(self):
+ """ getSelectedLocations() -> list
+ Return the selected locations (row, col) of the current sheet
+
+ """
+ indexes = self.sheet.selectedIndexes()
+ return [(idx.row(), idx.column()) for idx in indexes]
+
+ def clearSelection(self):
+ """ clearSelection() -> None
+ Clear all the selection in the current sheet
+
+ """
+ self.sheet.clearSelection()
+
+ def setCellWidget(self, row, col, cellWidget):
+ """ setCellWidget(row: int,
+ col: int,
+ cellWidget: QWidget) -> None
+ Replace the current location (row, col) with a cell widget
+
+ """
+ self.sheet.setCellByWidget(row, col, cellWidget)
+
+ def dragEnterEvent(self, event):
+ """ dragEnterEvent(event: QDragEnterEvent) -> None
+ Set to accept drops from the version tree
+
+ """
+ mimeData = event.mimeData()
+ if hasattr(mimeData, 'versionId'):
+ event.accept()
+ else:
+ event.ignore()
+
+ def dragMoveEvent(self, event):
+ """ dragEnterEvent(event: QDragEnterEvent) -> None
+ Set to accept drops while moving from the version tree
+
+ """
+ mimeData = event.mimeData()
+ if (hasattr(mimeData, 'versionId') and
+ hasattr(mimeData, 'controller')):
+ event.accept()
+ else:
+ event.ignore()
+
+ def dropEvent(self, event):
+ """ Execute the pipeline at the particular location """
+ mimeData = event.mimeData()
+ if (hasattr(mimeData, 'versionId') and
+ hasattr(mimeData, 'controller')):
+ event.accept()
+ versionId = mimeData.versionId
+ controller = mimeData.controller
+ pipeline = controller.vistrail.getPipeline(versionId)
+
+ inspector = PipelineInspector()
+ inspector.inspect_spreadsheet_cells(pipeline)
+ inspector.inspect_ambiguous_modules(pipeline)
+ if len(inspector.spreadsheet_cells)==1:
+ localPos = self.sheet.viewport().mapFromGlobal(QtGui.QCursor.pos())
+ row = self.sheet.rowAt(localPos.y())
+ col = self.sheet.columnAt(localPos.x())
+ if (row!=-1 and col!=-1):
+ pipeline = self.setPipelineToLocateAt(row, col, pipeline)
+ executePipelineWithProgress(pipeline, 'Execute Cell',
+ controller=controller,
+ locator=controller.locator,
+ current_version=versionId,
+ reason='Drop Version')
+ else:
+ event.ignore()
+
+ def setSpan(self, row, col, rowSpan, colSpan):
+ """ setSpan(row, col, rowSpan, colSpan: int) -> None
+ Set the spanning at location (row, col).
+
+ """
+ colSpan = max(colSpan, 1)
+ rowSpan = max(rowSpan, 1)
+ (curRowSpan, curColSpan) = self.getSpan(row, col)
+ if rowSpan!=curRowSpan or colSpan!=curColSpan:
+ # Need to remove all cell except the top-left
+ for r in xrange(rowSpan):
+ for c in xrange(colSpan):
+ if r!=0 or c!=0:
+ self.deleteCell(row+r, col+c)
+
+ # Take the current widget out
+ curWidget = self.takeCell(row, col)
+
+ # ... before setting the span
+ self.sheet.setSpan(row, col, rowSpan, colSpan)
+
+ # Then put it back in
+ if curWidget:
+ self.setCellByWidget(row, col, curWidget)
+
+ def getSpan(self, row, col):
+ """ setSpan(row, col: int) -> (rowSpan, colSpan: int)
+ Return the spanning at location (row, col). This is only a
+ place holder. Subclasses should implement this and setSpan for
+ a fully functioning spanning feature.
+
+ """
+ return (self.sheet.rowSpan(row, col), self.sheet.columnSpan(row, col))
+
+
+class StandardWidgetTabBarEditor(QtGui.QLineEdit):
+ """
+ StandardWidgetTabBarEditor overrides QLineEdit to enable canceling
+ edit when Esc is pressed
+
+ """
+ def __init__(self, text='', parent=None):
+ """ StandardWidgetTabBarEditor(text: str, parent: QWidget)
+ -> StandardWidgetTabBarEditor
+ Store the original text at during initialization
+
+ """
+ QtGui.QLineEdit.__init__(self, text, parent)
+ self.originalText = text
+
+ def keyPressEvent(self, e):
+ """ keyPressEvent(e: QKeyEvent) -> None
+ Override keyPressEvent to handle Esc key
+
+ """
+ if e.key()==QtCore.Qt.Key_Escape:
+ e.ignore()
+ self.setText(self.originalText)
+ self.clearFocus()
+ else:
+ QtGui.QLineEdit.keyPressEvent(self, e)
+
+class StandardWidgetTabBar(QtGui.QTabBar):
+ """
+ StandardWidgetTabBar: a customized QTabBar to allow double-click
+ to change tab name
+
+ """
+ def __init__(self, parent=None):
+ """ StandardWidgetTabBar(parent: QWidget) -> StandardWidgetTabBar
+ Initialize like the original QTabWidget TabBar
+
+ """
+ QtGui.QTabBar.__init__(self, parent)
+ self.setAcceptDrops(True)
+ self.setStatusTip('Move the sheet in, out and around'
+ 'by dragging the tabs')
+ self.setDrawBase(False)
+ self.editingIndex = -1
+ self.editor = None
+ self.setFocusPolicy(QtCore.Qt.NoFocus)
+ self.connect(self, QtCore.SIGNAL('currentChanged(int)'),
+ self.updateTabText)
+ self.startDragPos = None
+ self.dragging = False
+ self.targetTab = -1
+ self.innerRubberBand = QtGui.QRubberBand(QtGui.QRubberBand.Rectangle,
+ self)
+ self.outerRubberBand = QtGui.QRubberBand(QtGui.QRubberBand.Rectangle,
+ None)
+
+ def mouseDoubleClickEvent(self, e):
+ """ mouseDoubleClickEvent(e: QMouseEvent) -> None
+ Handle Double-Click event to start the editor
+
+ """
+ if e.buttons()!=QtCore.Qt.LeftButton or self.editor: return
+
+ # Update the current editing tab widget
+ self.editingIndex = self.currentIndex()
+
+ # A hack to capture the rect of the triangular tab from commonstyle.cpp
+ rect = self.tabRect(self.editingIndex)
+ h = rect.height()-2
+ dx = h/3 + 3
+ rect.adjust(dx+1,1,-dx,-1)
+
+ # Display the editor inplace of the tab text
+ text = self.tabText(self.editingIndex)
+ self.editor = StandardWidgetTabBarEditor(text, self)
+ self.editor.setFont(self.font())
+ self.editor.setFrame(False)
+ self.editor.setGeometry(rect)
+ self.editor.setAlignment(QtCore.Qt.AlignHCenter)
+ self.editor.selectAll()
+ self.connect(self.editor, QtCore.SIGNAL('editingFinished()'),
+ self.updateTabText)
+ self.editor.show()
+ self.editor.setFocus(QtCore.Qt.MouseFocusReason)
+
+ def updateTabText(self, idx=0):
+ """ updateTabText(idx: int) -> None
+ Update the tab text after editing has been finished
+
+ """
+ if self.editingIndex>=0 and self.editor:
+ self.setTabText(self.editingIndex, self.editor.text())
+ self.emit(QtCore.SIGNAL('tabTextChanged(int,QString)'),
+ self.editingIndex,self.editor.text())
+ self.editor.deleteLater()
+ self.editingIndex = -1
+ self.editor = None
+
+ def indexAtPos(self, p):
+ """ indexAtPos(p: QPoint) -> int Reimplement of the private
+ indexAtPos to find the tab index under a point
+
+ """
+ if self.tabRect(self.currentIndex()).contains(p):
+ return self.currentIndex()
+ for i in xrange(self.count()):
+ if self.isTabEnabled(i) and self.tabRect(i).contains(p):
+ return i
+ return -1;
+
+ def mousePressEvent(self, e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Handle mouse press event to see if we should start to drag tabs or not
+
+ """
+ QtGui.QTabBar.mousePressEvent(self, e)
+ if e.buttons()==QtCore.Qt.LeftButton and self.editor==None:
+ self.startDragPos = QtCore.QPoint(e.x(), e.y())
+
+ def getGlobalRect(self, index):
+ """ getGlobalRect(self, index: int)
+ Get the rectangle of a tab in global coordinates
+
+ """
+ if index<0: return None
+ rect = self.tabRect(index)
+ rect.moveTo(self.mapToGlobal(rect.topLeft()))
+ return rect
+
+ def highlightTab(self, index):
+ """ highlightTab(index: int)
+ Highlight the rubber band of a tab
+
+ """
+ if index==-1:
+ self.innerRubberBand.hide()
+ else:
+ self.innerRubberBand.setGeometry(self.tabRect(index))
+ self.innerRubberBand.show()
+
+ def mouseMoveEvent(self, e):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Handle dragging tabs in and out or around
+
+ """
+ QtGui.QTabBar.mouseMoveEvent(self, e)
+ if self.startDragPos:
+ # We already move more than 4 pixels
+ if (self.startDragPos-e.pos()).manhattanLength()>=4:
+ self.startDragPos = None
+ self.dragging = True
+ if self.dragging:
+ t = self.indexAtPos(e.pos())
+ if t!=-1:
+ if t!=self.targetTab:
+ self.targetTab = t
+ self.outerRubberBand.hide()
+ self.highlightTab(t)
+ else:
+ self.highlightTab(-1)
+ if t!=self.targetTab:
+ self.targetTab = t
+ if self.count()>0:
+ if not self.outerRubberBand.isVisible():
+ index = self.getGlobalRect(self.currentIndex())
+ self.outerRubberBand.setGeometry(index)
+ self.outerRubberBand.move(e.globalPos())
+ self.outerRubberBand.show()
+ else:
+ self.outerRubberBand.move(e.globalPos())
+
+ def mouseReleaseEvent(self, e):
+ """ mouseReleaseEvent(e: QMouseEvent) -> None
+ Make sure the tab moved at the end
+
+ """
+ QtGui.QTabBar.mouseReleaseEvent(self, e)
+ if self.dragging:
+ if self.targetTab!=-1 and self.targetTab!=self.currentIndex():
+ self.emit(QtCore.SIGNAL('tabMoveRequest(int,int)'),
+ self.currentIndex(),
+ self.targetTab)
+ elif self.targetTab==-1:
+ self.emit(QtCore.SIGNAL('tabSplitRequest(int,QPoint)'),
+ self.currentIndex(),
+ e.globalPos())
+ self.dragging = False
+ self.targetTab = -1
+ self.highlightTab(-1)
+ self.outerRubberBand.hide()
+
+ def slotIndex(self, pos):
+ """ slotIndex(pos: QPoint) -> int
+ Return the slot index between the slots at the cursor pos
+
+ """
+ p = self.mapFromGlobal(pos)
+ for i in xrange(self.count()):
+ r = self.tabRect(i)
+ if self.isTabEnabled(i) and r.contains(p):
+ if p.x()<(r.x()+r.width()/2):
+ return i
+ else:
+ return i+1
+ return -1
+
+ def slotGeometry(self, idx):
+ """ slotGeometry(idx: int) -> QRect
+ Return the geometry between the slots at cursor pos
+
+ """
+ if idx<0 or self.count()==0: return None
+ if idx<self.count():
+ rect = self.getGlobalRect(idx)
+ rect = QtCore.QRect(rect.x()-5, rect.y(), 5*2, rect.height())
+ return rect
+ else:
+ rect = self.getGlobalRect(self.count()-1)
+ rect = QtCore.QRect(rect.x()+rect.width()-5, rect.y(),
+ 5*2, rect.height())
+ return rect
+
+ def dragEnterEvent(self, event):
+ """ dragEnterEvent(event: QDragEnterEvent) -> None
+ Set to accept drops from the other cell info
+
+ """
+ mimeData = event.mimeData()
+ if hasattr(mimeData, 'cellInfo'):
+ event.setDropAction(QtCore.Qt.MoveAction)
+ event.accept()
+ idx = self.indexAtPos(event.pos())
+ if idx>=0:
+ self.setCurrentIndex(idx)
+ else:
+ event.ignore()
+
+ def dragMoveEvent(self, event):
+ """ dragMoveEvent(event: QDragMoveEvent) -> None
+ Set to accept drops from the other cell info
+
+ """
+ idx = self.indexAtPos(event.pos())
+ if idx>=0:
+ self.setCurrentIndex(idx)
+
+
+class StandardTabDockWidget(QtGui.QDockWidget):
+ """
+ StandardTabDockWidget inherits from QDockWidget to contain a sheet
+ widget floating around that can be merge back to tab controller
+
+ """
+ def __init__(self, title, tabWidget, tabBar, tabController):
+ """ StandardTabDockWidget(title: str,
+ tabWidget: QTabWidget,
+ tabBar: QTabBar,
+ tabController: StandardWidgetTabController)
+ -> StandardTabDockWidget
+ Initialize the dock widget to override the floating button
+
+ """
+ QtGui.QDockWidget.__init__(self, title, None,
+ QtCore.Qt.FramelessWindowHint)
+ self.tabBar = tabBar
+ self.tabController = tabController
+ self.setFeatures(QtGui.QDockWidget.DockWidgetClosable |
+ QtGui.QDockWidget.DockWidgetMovable |
+ QtGui.QDockWidget.DockWidgetFloatable)
+ self.setFloating(True)
+ self.floatingButton = self.findFloatingButton()
+ if self.floatingButton:
+ self.floatingButton.blockSignals(True)
+ self.floatingButton.installEventFilter(self)
+ self.startDragPos = None
+ self.startDragging = False
+ self.windowRubberBand = QtGui.QRubberBand(QtGui.QRubberBand.Rectangle,
+ None)
+ tabWidget.setParent(self)
+ self.setWidget(tabWidget)
+ tabWidget.show()
+ self.resize(tabWidget.size())
+
+ def findFloatingButton(self):
+ """ findFloatingButton() -> QAbstractButton
+ Hack to find the private Floating Button. Since there is only
+ one button exists, we just need to find QAbstractButton
+
+ """
+ for c in self.children():
+ if isinstance(c, QtGui.QAbstractButton):
+ return c
+ return None
+
+ def eventFilter(self, q, e):
+ """ eventFilter(q: QObject, e: QEvent) -> depends on event type
+ Event filter the floating button to makes it merge to the tab controller
+
+ """
+ if q and q==self.floatingButton:
+ if (e.type()==QtCore.QEvent.MouseButtonRelease and
+ e.button()&QtCore.Qt.LeftButton):
+ if self.isMaximized():
+ self.showNormal()
+ else:
+ self.showMaximized()
+ return False
+ return QtGui.QDockWidget.eventFilter(self, q, e)
+
+ def isTabControllerUnderMouse(self, tb):
+ """ Check if any of common parent of the tab controller and tb
+ is under the mouse """
+ tbp = []
+ while tb!=None:
+ tbp.append(tb)
+ tb = tb.parent()
+ tc = self.tabController
+ while tc!=None:
+ if tc in tbp:
+ return True
+ tc = tc.parent()
+ return False
+
+ def event(self, e):
+ """ event(e: QEvent) -> depends on event type
+ Handle movement of the dock widget to snap to the tab controller
+
+ """
+ # MOUSE PRESS (QtCore.QEvent.NonClientAreaMouseButtonPress=174)
+ if e.type() in [QtCore.QEvent.MouseButtonPress,174]:
+ if e.type()==174:
+ gp = QtGui.QCursor.pos()
+ ontitle = True
+ else:
+ gp = e.globalPos()
+ ontitle = e.y()<self.widget().y() and e.buttons()&QtCore.Qt.LeftButton
+ if ontitle:
+ self.startDragPos = QtCore.QPoint(gp)
+ self.grabMouse()
+ return True
+
+ elif e.type()==QtCore.QEvent.MouseMove:
+ if not (e.buttons() & QtCore.Qt.LeftButton):
+ self.windowRubberBand.hide()
+ self.setMouseTracking(False)
+ return QtGui.QDockWidget.event(self, e)
+ gp = e.globalPos()
+ if (not self.startDragging and
+ self.startDragPos and
+ (self.startDragPos-gp).manhattanLength()>=4):
+ self.startDragging = True
+ self.windowRubberBand.setGeometry(self.geometry())
+ self.startDragPos = self.pos()-gp
+ self.windowRubberBand.show()
+ self.setMouseTracking(True)
+ if self.startDragging:
+ tb = QtGui.QApplication.widgetAt(gp)
+ if tb==self.tabBar:
+ idx = tb.slotIndex(gp)
+ if idx>=0:
+ self.windowRubberBand.setGeometry(tb.slotGeometry(idx))
+ elif (tb!=None and self.tabController.count()==0 and
+ self.isTabControllerUnderMouse(tb)):
+ r = self.tabController.frameGeometry()
+ r.moveTo(self.tabController.mapToGlobal(r.topLeft()))
+ self.windowRubberBand.setGeometry(r)
+ else:
+ rect = QtCore.QRect(self.startDragPos+gp, self.size())
+ self.windowRubberBand.setGeometry(rect)
+ return True
+
+ # MOUSE RELEASE (QtCore.QEvent.NonClientAreaMouseRelease=175)
+ elif e.type()==QtCore.QEvent.MouseButtonRelease:
+ if self.startDragging:
+ if e.type()==173:
+ gp = QtGui.QCursor.pos()
+ else:
+ gp = e.globalPos()
+ self.setMouseTracking(False)
+ self.windowRubberBand.hide()
+ self.startDragPos = None
+ self.startDragging = False
+ tb = QtGui.QApplication.widgetAt(gp)
+ if tb==self.tabBar:
+ idx = tb.slotIndex(gp)
+ if idx>=0:
+ self.hide()
+ self.tabController.mergeTab(self, idx)
+ elif (tb!=None and self.tabController.count()==0 and
+ self.isTabControllerUnderMouse(tb)):
+ self.hide()
+ self.tabController.mergeTab(self, 0)
+ else:
+ self.move(self.windowRubberBand.pos())
+ self.releaseMouse()
+ self.setFocus(QtCore.Qt.MouseFocusReason)
+ return True
+
+ # MOUSE DOUBLE CLICK (QtCore.QEvent.NonClientAreaMouseButtonDblClick=176)
+ elif e.type() in [QtCore.QEvent.MouseButtonDblClick, 176]:
+ if (e.type()==176) or (e.buttons()&QtCore.Qt.LeftButton):
+ self.hide()
+ self.tabController.mergeTab(self, self.tabController.count())
+ return True
+
+ return QtGui.QDockWidget.event(self, e)
+
+ def closeEvent(self, event):
+ """ On close event dock the sheet back to the spreadsheet window """
+ self.tabController.mergeTab(self, self.tabController.count())
+ event.accept()
+
+spreadsheetRegistry.registerSheet('StandardWidgetSheetTab',
+ StandardWidgetSheetTab)
diff --git a/vistrails/packages/spreadsheet/spreadsheet_tabcontroller.py b/vistrails/packages/spreadsheet/spreadsheet_tabcontroller.py
new file mode 100644
index 0000000..17725ab
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_tabcontroller.py
@@ -0,0 +1,822 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file implements the Spreadsheet Tab Controller, to manages tabs
+# StandardWidgetTabController
+################################################################################
+import os.path
+from PyQt4 import QtCore, QtGui
+from vistrails.core.db.locator import FileLocator, _DBLocator as DBLocator
+from vistrails.core.interpreter.default import get_default_interpreter
+from vistrails.db.services.io import SaveBundle
+from spreadsheet_registry import spreadsheetRegistry
+from spreadsheet_tab import (StandardWidgetTabBar,
+ StandardWidgetSheetTab, StandardTabDockWidget)
+from spreadsheet_registry import spreadsheetRegistry
+from vistrails.core.utils import DummyView
+from vistrails.core.utils.uxml import XMLWrapper, named_elements
+import copy
+import gc
+from vistrails.gui.theme import CurrentTheme
+from vistrails.gui.utils import show_warning
+
+################################################################################
+
+class StandardWidgetTabController(QtGui.QTabWidget):
+ """
+ StandardWidgetTabController inherits from QTabWidget to contain a
+ list of StandardWidgetSheetTab. This is the major component that
+ will handle most of the spreadsheet actions
+
+ """
+ def __init__(self, parent=None):
+ """ StandardWidgetTabController(parent: QWidget)
+ -> StandardWidgetTabController
+ Initialize signals/slots and widgets for the tab bar
+
+ """
+
+ QtGui.QTabWidget.__init__(self, parent)
+ self.operatingWidget = self
+ self.setTabBar(StandardWidgetTabBar(self))
+ self.setTabShape(QtGui.QTabWidget.Triangular)
+ self.setTabPosition(QtGui.QTabWidget.South)
+ self.tabWidgets = []
+ self.floatingTabWidgets = []
+ self.addTabWidget(StandardWidgetSheetTab(self), 'Sheet 1')
+ self.connect(self.tabBar(),
+ QtCore.SIGNAL('tabMoveRequest(int,int)'),
+ self.moveTab)
+ self.connect(self.tabBar(),
+ QtCore.SIGNAL('tabSplitRequest(int,QPoint)'),
+ self.splitTab)
+ self.connect(self.tabBar(),
+ QtCore.SIGNAL('tabTextChanged(int,QString)'),
+ self.changeTabText)
+ self.addAction(self.showNextTabAction())
+ self.addAction(self.showPrevTabAction())
+ self.executedPipelines = [[],{},{}]
+ self.monitoredPipelines = {}
+ self.spreadsheetFileName = None
+ self.loadingMode = False
+ self.editingMode = False
+ self.closeButton = QtGui.QToolButton(self)
+ self.closeButton.setIcon(CurrentTheme.VIEW_MANAGER_CLOSE_ICON)
+ self.closeButton.setAutoRaise(True)
+ self.setCornerWidget(self.closeButton)
+ self.connect(self.closeButton, QtCore.SIGNAL('clicked()'),
+ self.deleteSheetAction().trigger)
+
+ def isLoadingMode(self):
+ """ isLoadingMode() -> boolean
+ Checking if the controller is in loading mode
+
+ """
+ return self.loadingMode
+
+ def getMonitoredLocations(self, spec):
+ """ getMonitoredLocations(spec: tuple) -> location
+ Return the monitored location associated with spec
+
+ """
+ key = ((spec[0]['locator'], spec[0]['version']), spec[1], spec[2])
+ if key in self.monitoredPipelines:
+ return self.monitoredPipelines[key]
+ else:
+ return []
+
+ def appendMonitoredLocations(self, spec, value):
+ """ getMonitoredLocations(spec: tuple, value: location) -> None
+ Return the monitored location associated with spec
+
+ """
+ key = ((spec[0]['locator'], spec[0]['version']), spec[1], spec[2])
+ if key in self.monitoredPipelines:
+ self.monitoredPipelines[key].append(value)
+ else:
+ self.monitoredPipelines[key] = [value]
+
+ def newSheetAction(self):
+ """ newSheetAction() -> QAction
+ Return the 'New Sheet' action
+
+ """
+ if not hasattr(self, 'newSheetActionVar'):
+ icon = QtGui.QIcon(':/images/newsheet.png')
+ self.newSheetActionVar = QtGui.QAction(icon, '&New sheet', self)
+ self.newSheetActionVar.setToolTip('Create a new sheet')
+ self.newSheetActionVar.setStatusTip('Create and show a new sheet')
+ self.newSheetActionVar.setShortcut(QtGui.QKeySequence('Ctrl+N'))
+ self.connect(self.newSheetActionVar,
+ QtCore.SIGNAL('triggered()'),
+ self.newSheetActionTriggered)
+ return self.newSheetActionVar
+
+ def deleteSheetAction(self):
+ """ deleteSheetAction() -> QAction
+ Return the 'Delete Sheet' action:
+
+ """
+ if not hasattr(self, 'deleteSheetActionVar'):
+ icon = QtGui.QIcon(':/images/deletesheet.png')
+ self.deleteSheetActionVar = QtGui.QAction(icon, '&Delete sheet',
+ self)
+ self.deleteSheetActionVar.setToolTip('Delete the current sheet')
+ self.deleteSheetActionVar.setStatusTip('Delete the current sheet '
+ 'if there are more than one')
+ key = QtGui.QKeySequence('Ctrl+Backspace')
+ self.deleteSheetActionVar.setShortcut(key)
+ self.connect(self.deleteSheetActionVar,
+ QtCore.SIGNAL('triggered()'),
+ self.deleteSheetActionTriggered)
+ return self.deleteSheetActionVar
+
+ def showNextTabAction(self):
+ """ showNextTabAction() -> QAction
+ Return the 'Next Sheet' action
+
+ """
+ if not hasattr(self, 'showNextTabActionVar'):
+ icon = QtGui.QIcon(':/images/forward.png')
+ self.showNextTabActionVar = QtGui.QAction(icon, '&Next sheet', self)
+ self.showNextTabActionVar.setToolTip('Show the next sheet')
+ self.showNextTabActionVar.setStatusTip('Show the next sheet if it '
+ 'is available')
+ self.showNextTabActionShortcut = QtGui.QShortcut(self)
+ self.showNextTabActionVar.setShortcut('Ctrl+PgDown')
+ self.connect(self.showNextTabActionVar,
+ QtCore.SIGNAL('triggered()'),
+ self.showNextTab)
+ return self.showNextTabActionVar
+
+ def showPrevTabAction(self):
+ """ showPrevTabAction() -> QAction
+ Return the 'Prev Sheet' action
+
+ """
+ if not hasattr(self, 'showPrevTabActionVar'):
+ icon = QtGui.QIcon(':/images/back.png')
+ self.showPrevTabActionVar = QtGui.QAction(icon, '&Prev sheet', self)
+ self.showPrevTabActionVar.setToolTip('Show the previous sheet')
+ self.showPrevTabActionVar.setStatusTip('Show the previous sheet if '
+ 'it is available')
+ self.showPrevTabActionVar.setShortcut('Ctrl+PgUp')
+ self.connect(self.showPrevTabActionVar,
+ QtCore.SIGNAL('triggered()'),
+ self.showPrevTab)
+ return self.showPrevTabActionVar
+
+ def saveAction(self):
+ """ saveAction() -> QAction
+ Return the 'Save' action
+
+ """
+ if not hasattr(self, 'saveActionVar'):
+ self.saveActionVar = QtGui.QAction(QtGui.QIcon(':/images/save.png'),
+ '&Save', self)
+ self.saveActionVar.setStatusTip('Save the current spreadsheet')
+ self.saveActionVar.setShortcut('Ctrl+S')
+ self.connect(self.saveActionVar,
+ QtCore.SIGNAL('triggered()'),
+ self.saveSpreadsheet)
+ return self.saveActionVar
+
+ def saveAsAction(self):
+ """ saveAsAction() -> QAction
+ Return the 'Save As...' action
+
+ """
+ if not hasattr(self, 'saveAsActionVar'):
+ icon = QtGui.QIcon(':/images/saveas.png')
+ self.saveAsActionVar = QtGui.QAction(icon, 'Save &As...', self)
+ self.saveAsActionVar.setStatusTip('Save the current spreadsheet '
+ 'at a new location')
+ self.connect(self.saveAsActionVar,
+ QtCore.SIGNAL('triggered()'),
+ self.saveSpreadsheetAs)
+ return self.saveAsActionVar
+
+ def openAction(self):
+ """ openAction() -> QAction
+ Return the 'Open...' action
+
+ """
+ if not hasattr(self, 'openActionVar'):
+ self.openActionVar = QtGui.QAction(QtGui.QIcon(':/images/open.png'),
+ '&Open...', self)
+ self.openActionVar.setStatusTip('Open a saved spreadsheet')
+ self.openActionVar.setShortcut('Ctrl+O')
+ self.connect(self.openActionVar,
+ QtCore.SIGNAL('triggered()'),
+ self.openSpreadsheetAs)
+ return self.openActionVar
+
+ def exportSheetToImageAction(self):
+ """ exportSheetToImageAction() -> QAction
+ Export the current sheet to an image
+
+ """
+ if not hasattr(self, 'exportSheetToImageVar'):
+ self.exportSheetToImageVar = QtGui.QAction('Export', self)
+ self.exportSheetToImageVar.setStatusTip(
+ 'Export all cells in the spreadsheet to a montaged image')
+
+ exportMenu = QtGui.QMenu(self)
+ singleAction = exportMenu.addAction('As a Single Image')
+ multiAction = exportMenu.addAction('Separately')
+ self.exportSheetToImageVar.setMenu(exportMenu)
+
+ self.connect(self.exportSheetToImageVar,
+ QtCore.SIGNAL('triggered(bool)'),
+ self.exportSheetToImageActionTriggered)
+
+ self.connect(exportMenu,
+ QtCore.SIGNAL('triggered(QAction*)'),
+ self.exportSheetToImageActionTriggered)
+ return self.exportSheetToImageVar
+
+ def exportSheetToImageActionTriggered(self, action=None):
+ """ exportSheetToImageActionTriggered(checked: boolean) -> None
+ Actual code to create export an image
+
+ """
+ if not isinstance(action, bool) and action.text() == 'Separately':
+ dir = QtGui.QFileDialog.getExistingDirectory(
+ self, 'Select a Directory to Export Images', ".",
+ QtGui.QFileDialog.ShowDirsOnly)
+ if dir:
+ self.currentWidget().exportSheetToImages(dir)
+ else:
+ file = QtGui.QFileDialog.getSaveFileName(
+ self, "Select a File to Export the Sheet",
+ ".", "Images (*.png *.xpm *.jpg)")
+ if file:
+ self.currentWidget().exportSheetToImage(str(file))
+
+ def newSheetActionTriggered(self, checked=False):
+ """ newSheetActionTriggered(checked: boolean) -> None
+ Actual code to create a new sheet
+
+ """
+ self.setCurrentIndex(self.addTabWidget(StandardWidgetSheetTab(self),
+ 'Sheet %d' % (self.count()+1)))
+ self.currentWidget().sheet.stretchCells()
+
+ def tabInserted(self, index):
+ """tabInserted(index: int) -> None
+ event handler to get when sheets are inserted """
+ self.deleteSheetAction().setEnabled(True)
+ self.saveAction().setEnabled(True)
+ self.saveAsAction().setEnabled(True)
+
+ def tabRemoved(self, index):
+ """tabInserted(index: int) -> None
+ event handler to get when sheets are removed """
+ if self.count() == 0:
+ self.deleteSheetAction().setEnabled(False)
+ self.saveAction().setEnabled(False)
+ self.saveAsAction().setEnabled(False)
+
+ def removeSheetReference(self, sheet):
+ """ removeSheetReference(sheet: StandardWidgetSheetTab) -> None
+ Remove references of a sheet from the spreadsheet
+ """
+ for (code, locations) in self.monitoredPipelines.iteritems():
+ for lid in reversed(xrange(len(locations))):
+ if sheet==locations[lid][0]:
+ del locations[lid]
+
+ def deleteSheetActionTriggered(self, checked=False):
+ """ deleteSheetActionTriggered(checked: boolean) -> None
+ Actual code to delete the current sheet
+
+ """
+ if self.count()>0:
+ widget = self.currentWidget()
+ self.tabWidgets.remove(widget)
+ self.removeTab(self.currentIndex())
+ self.removeSheetReference(widget)
+ widget.deleteAllCells()
+ widget.deleteLater()
+ QtCore.QCoreApplication.processEvents()
+ gc.collect()
+
+ def clearTabs(self):
+ """ clearTabs() -> None
+ Clear and reset the controller
+
+ """
+ self.executedPipelines = [[], {}, {}]
+ while self.count()>0:
+ self.deleteSheetActionTriggered()
+ for i in reversed(range(len(self.tabWidgets))):
+ t = self.tabWidgets[i]
+ del self.tabWidgets[i]
+ self.removeSheetReference(t)
+ t.deleteAllCells()
+ t.deleteLater()
+
+ def insertTab(self, idx, tabWidget, tabText):
+ """ insertTab(idx: int, tabWidget: QWidget, tabText: str)
+ -> QTabWidget
+ Redirect insertTab command to operatingWidget, this can either be a
+ QTabWidget or a QStackedWidget
+
+ """
+ if self.operatingWidget!=self:
+ ret = self.operatingWidget.insertWidget(idx, tabWidget)
+ self.operatingWidget.setCurrentIndex(ret)
+ return ret
+ else:
+ return QtGui.QTabWidget.insertTab(self, idx, tabWidget, tabText)
+
+ def findSheet(self, sheetReference):
+ """ findSheet(sheetReference: subclass(SheetReference)) -> Sheet widget
+ Find/Create a sheet that meets a certen sheet reference
+
+ """
+ if not sheetReference:
+ return None
+ sheetReference.clearCandidate()
+ for idx in xrange(len(self.tabWidgets)):
+ tabWidget = self.tabWidgets[idx]
+ tabLabel = tabWidget.windowTitle()
+ sheetReference.checkCandidate(tabWidget, tabLabel, idx,
+ self.operatingWidget.currentIndex())
+ return sheetReference.setupCandidate(self)
+
+ def changeTabText(self, tabIdx, newTabText):
+ """ changeTabText(tabIdx: int, newTabText: str) -> None
+ Update window title on the operating widget when the tab text
+ has changed
+
+ """
+ self.operatingWidget.widget(tabIdx).setWindowTitle(newTabText)
+
+ def moveTab(self, tabIdx, destination):
+ """ moveTab(tabIdx: int, destination: int) -> None
+ Move a tab at tabIdx to a different position at destination
+
+ """
+ if (tabIdx<0 or tabIdx>self.count() or
+ destination<0 or destination>self.count()):
+ return
+ tabText = self.tabText(tabIdx)
+ tabWidget = self.widget(tabIdx)
+ self.removeTab(tabIdx)
+ self.insertTab(destination, tabWidget, tabText)
+ if tabIdx==self.currentIndex():
+ self.setCurrentIndex(destination)
+
+ def splitTab(self, tabIdx, pos=None):
+ """ splitTab(tabIdx: int, pos: QPoint) -> None
+ Split a tab to be a stand alone window and move to position pos
+
+ """
+ if tabIdx<0 or tabIdx>self.count() or self.count()==0:
+ return
+ tabWidget = self.widget(tabIdx)
+ self.removeTab(tabIdx)
+
+ frame = StandardTabDockWidget(tabWidget.windowTitle(), tabWidget,
+ self.tabBar(), self)
+ if pos:
+ frame.move(pos)
+ frame.show()
+ self.floatingTabWidgets.append(frame)
+
+ def mergeTab(self, frame, tabIdx):
+ """ mergeTab(frame: StandardTabDockWidget, tabIdx: int) -> None
+ Merge a tab dock widget back to the controller at position tabIdx
+
+ """
+ if tabIdx<0 or tabIdx>self.count():
+ return
+ if tabIdx==self.count(): tabIdx = -1
+ tabWidget = frame.widget()
+ frame.setWidget(None)
+ while frame in self.floatingTabWidgets:
+ self.floatingTabWidgets.remove(frame)
+ frame.deleteLater()
+ tabWidget.setParent(None)
+ newIdx = self.insertTab(tabIdx, tabWidget, tabWidget.windowTitle())
+ self.setCurrentIndex(newIdx)
+
+ def addTabWidget(self, tabWidget, sheetLabel):
+ """ addTabWidget(tabWidget: QWidget, sheetLabel: str) -> int
+ Add a new tab widget to the controller
+
+ """
+ return self.insertTabWidget(-1, tabWidget, sheetLabel)
+
+ def insertTabWidget(self, index, tabWidget, sheetLabel):
+ """ insertTabWidget(index: int, tabWidget: QWidget, sheetLabel: str)
+ -> int
+ Insert a tab widget to the controller at some location
+
+ """
+ if sheetLabel==None:
+ sheetLabel = 'Sheet %d' % (len(self.tabWidgets)+1)
+ if not tabWidget in self.tabWidgets:
+ self.tabWidgets.append(tabWidget)
+ tabWidget.setWindowTitle(sheetLabel)
+ return self.insertTab(index, tabWidget, sheetLabel)
+
+ def tabWidgetUnderMouse(self):
+ """ tabWidgetUnderMouse() -> QWidget
+ Return the tab widget that is under mouse, hide helpers for the rest
+
+ """
+ result = None
+ for t in self.tabWidgets:
+ if t.underMouse():
+ result = t
+ else:
+ t.showHelpers(False, QtCore.QPoint(-1,-1))
+ return result
+
+ def setupFullScreenWidget(self, fs, stackedWidget):
+ """ setupFullScreenWidget(fs: boolean, stackedWidget: QStackedWidget)
+ -> None
+ Prepare(fs=True)/Clean(fs=False) up full screen mode
+
+ """
+ if fs:
+ idx = self.currentIndex()
+ for i in xrange(self.count()):
+ widget = self.widget(0)
+ self.removeTab(0)
+ self.tabTrueParent = widget.parent()
+ widget.setParent(stackedWidget)
+ stackedWidget.addWidget(widget)
+ stackedWidget.setCurrentIndex(idx)
+ self.operatingWidget = stackedWidget
+ else:
+ idx = stackedWidget.currentIndex()
+ for i in xrange(stackedWidget.count()):
+ widget = stackedWidget.widget(0)
+ stackedWidget.removeWidget(widget)
+ widget.setParent(self.tabTrueParent)
+ self.addTab(widget, widget.windowTitle())
+ self.setCurrentIndex(idx)
+ self.operatingWidget = self
+
+ def showNextTab(self):
+ """ showNextTab() -> None
+ Bring the next tab up
+
+ """
+ if self.operatingWidget.currentIndex()<self.operatingWidget.count()-1:
+ index = self.operatingWidget.currentIndex()+1
+ self.operatingWidget.setCurrentIndex(index)
+
+ def showPrevTab(self):
+ """ showPrevTab() -> None
+ Bring the previous tab up
+
+ """
+ if self.operatingWidget.currentIndex()>0:
+ index = self.operatingWidget.currentIndex()-1
+ self.operatingWidget.setCurrentIndex(index)
+
+ def tabPopupMenu(self):
+ """ tabPopupMenu() -> QMenu
+ Return a menu containing a list of all tabs
+
+ """
+ menu = QtGui.QMenu(self)
+ en = self.operatingWidget.currentIndex()<self.operatingWidget.count()-1
+ self.showNextTabAction().setEnabled(en)
+ menu.addAction(self.showNextTabAction())
+ en = self.operatingWidget.currentIndex()>0
+ self.showPrevTabAction().setEnabled(en)
+ menu.addAction(self.showPrevTabAction())
+ menu.addSeparator()
+ for idx in xrange(self.operatingWidget.count()):
+ t = self.operatingWidget.widget(idx)
+ action = menu.addAction(t.windowTitle())
+ action.setData(idx)
+ if t==self.operatingWidget.currentWidget():
+ action.setIcon(QtGui.QIcon(':/images/ok.png'))
+ menu.addAction(self.parent().parent().fullScreenAction())
+ return menu
+
+ def showPopupMenu(self):
+ """ showPopupMenu() -> None
+ Activate the tab list and show the popup menu
+
+ """
+ menu = self.tabPopupMenu()
+ action = menu.exec_(QtGui.QCursor.pos())
+ self.showNextTabAction().setEnabled(True)
+ self.showPrevTabAction().setEnabled(True)
+ if not action: return
+ if not action in self.actions():
+ self.operatingWidget.setCurrentIndex(action.data()[0])
+ menu.deleteLater()
+
+ def changeSpreadsheetFileName(self, fileName):
+ """ changeSpreadsheetFileName(fileName: str) -> None
+ Change the current spreadsheet filename and reflect it on the
+ window title
+
+ """
+ self.spreadsheetFileName = fileName
+ if self.spreadsheetFileName:
+ displayName = self.spreadsheetFileName
+ else:
+ displayName = 'Untitled'
+ self.emit(QtCore.SIGNAL('needChangeTitle'),
+ '%s - VisTrails Spreadsheet' % displayName)
+
+ def pipelineId(self, pipelineInfo):
+ return (pipelineInfo['controller'], pipelineInfo['version'])
+
+ def addPipeline(self, pipelineInfo):
+ """ addPipeline(pipelineInfo: dict) -> None
+ Add vistrail pipeline executions to history
+
+ """
+ vistrail = self.pipelineId(pipelineInfo)
+ self.executedPipelines[0].append(vistrail)
+ if not vistrail in self.executedPipelines[1]:
+ self.executedPipelines[1][vistrail] = 0
+ else:
+ self.executedPipelines[1][vistrail] += 1
+ self.executedPipelines[2][vistrail] = 0
+
+ def getCurrentPipelineId(self, pipelineInfo):
+ """ getCurrentPipelineId(pipelineInfo: dict) -> Int
+ Get the current pipeline id
+
+ """
+ vistrail = self.pipelineId(pipelineInfo)
+ return self.executedPipelines[1][vistrail]
+
+ def increasePipelineCellId(self, pipelineInfo):
+ """ increasePipelineCellId(pipelineInfo: dict) -> int
+ Increase the current cell pipeline id
+
+ """
+ vistrail = self.pipelineId(pipelineInfo)
+ cid = self.executedPipelines[2][vistrail]
+ self.executedPipelines[2][vistrail] += 1
+ return cid
+
+ def getCurrentPipelineCellId(self, pipelineInfo):
+ """ getCurrentPipelineCellId(pipelineInfo: dict) -> int
+ Get current pipeline cell id
+
+ """
+ vistrail = self.pipelineId(pipelineInfo)
+ return self.executedPipelines[2][vistrail]
+
+ def addPipelineCell(self, pipelineInfo):
+ """ addPipelineCell(pipelineInfo: dict) -> None
+ Add vistrail pipeline executions to history
+
+ """
+ vistrail = self.pipelineId(pipelineInfo)
+ self.executedPipelines[0].append(vistrail)
+ if not vistrail in self.executedPipelines[1]:
+ self.executedPipelines[1][vistrail] = 0
+ else:
+ self.executedPipelines[1][vistrail] += 1
+
+
+ def saveSpreadsheet(self, fileName=None):
+ """ saveSpreadsheet(fileName: str) -> None
+ Save the current spreadsheet to a file if fileName is not
+ None. Else, pop up a dialog to ask for a file name.
+
+ """
+ def serialize_locator(locator):
+ wrapper = XMLWrapper()
+ dom = wrapper.create_document('spreadsheet_locator')
+ root = dom.documentElement
+ root.setAttribute("version", "1.0")
+ locator.serialize(dom,root)
+ return dom.toxml()
+
+ def need_save():
+ from vistrails.gui.vistrails_window import _app
+ need_save_vt = False
+ for t in self.tabWidgets:
+ dim = t.getDimension()
+ for r in xrange(dim[0]):
+ for c in xrange(dim[1]):
+ info = t.getCellPipelineInfo(r,c)
+ if info:
+ controller = info[0]['controller']
+ view = _app.ensureController(controller)
+ if view:
+ controller = view.get_controller()
+ if controller.changed:
+ need_save_vt = True
+ return need_save_vt
+
+ if need_save():
+ show_warning('Save Spreadsheet', 'Please save your vistrails and try again.')
+ return
+
+ if fileName==None:
+ fileName = self.spreadsheetFileName
+ if fileName:
+ indexFile = open(fileName, 'w')
+ indexFile.write(str(len(self.tabWidgets))+'\n')
+ for t in self.tabWidgets:
+ dim = t.getDimension()
+ sheet = spreadsheetRegistry.getSheetByType(type(t))
+ indexFile.write('%s\n'%str((str(t.windowTitle()),
+ sheet,
+ dim[0], dim[1])))
+ for r in xrange(dim[0]):
+ for c in xrange(dim[1]):
+ info = t.getCellPipelineInfo(r,c)
+ if info:
+ newinfo0 = copy.copy(info[0])
+ newinfo0['pipeline'] = None
+ newinfo0['actions'] = []
+ newinfo0['locator'] = \
+ serialize_locator(newinfo0['controller'].locator)
+ newinfo0['controller'] = None
+ indexFile.write('%s\n'
+ %str((r, c,
+ newinfo0,
+ info[1], info[2])))
+ indexFile.write('---\n')
+ indexFile.write(str(len(self.executedPipelines[0]))+'\n')
+ for vistrail in self.executedPipelines[0]:
+ indexFile.write('%s\n'%str((serialize_locator(vistrail[0].locator),
+ vistrail[1])))
+ self.changeSpreadsheetFileName(fileName)
+ indexFile.close()
+ else:
+ self.saveSpreadsheetAs()
+
+ def saveSpreadsheetAs(self):
+ """ saveSpreadsheetAs() -> None
+ Asking a file name before saving the spreadsheet
+
+ """
+ fileName = QtGui.QFileDialog.getSaveFileName(self,
+ 'Choose a spreadsheet '
+ 'name',
+ '',
+ 'VisTrails Spreadsheet '
+ '(*.vss)')
+ if fileName:
+ (root, ext) = os.path.splitext(fileName)
+ if ext=='':
+ fileName += '.vss'
+ self.saveSpreadsheet(fileName)
+
+ def openSpreadsheet(self, fileName):
+ """ openSpreadsheet(fileName: str) -> None
+ Open a saved spreadsheet assuming that all VTK files must exist and have
+ all the version using the saved spreadsheet
+
+ """
+ def parse_locator(text):
+ locator = None
+ wrapper = XMLWrapper()
+ dom = wrapper.create_document_from_string(text)
+ root = dom.documentElement
+ version = None
+ version = root.getAttribute('version')
+ if version == '1.0':
+ for element in named_elements(root, 'locator'):
+ if str(element.getAttribute('type')) == 'file':
+ locator = FileLocator.parse(element)
+ elif str(element.getAttribute('type')) == 'db':
+ locator = DBLocator.parse(element)
+ return locator
+ locators = {}
+ indexFile = open(fileName, 'r')
+ contents = indexFile.read()
+ self.clearTabs()
+ lidx = 0
+ lines = contents.split('\n')
+ tabCount = int(lines[lidx])
+ lidx += 1
+ for tabIdx in xrange(tabCount):
+ # FIXME: eval should pretty much never be used
+ tabInfo = eval(lines[lidx])
+ lidx += 1
+ sheet = spreadsheetRegistry.getSheet(tabInfo[1])(self)
+ sheet.setDimension(tabInfo[2], tabInfo[3])
+ self.addTabWidget(sheet, tabInfo[0])
+ while lines[lidx]!='---':
+ (r, c, vistrail, pid, cid) = eval(lines[lidx])
+ locator = vistrail['locator']
+ if locators.has_key(locator):
+ vistrail['locator'] = locators[locator]
+ else:
+ locators[locator] = parse_locator(vistrail['locator'])
+ vistrail['locator'] = locators[locator]
+ self.appendMonitoredLocations((vistrail, pid, cid),
+ (sheet, r, c))
+ lidx += 1
+ lidx += 1
+ pipelineCount = int(lines[lidx])
+ lidx += 1
+ self.loadingMode = True
+ progress = QtGui.QProgressDialog("Loading spreadsheet...",
+ "&Cancel", 0, pipelineCount,
+ self,
+ QtCore.Qt.WindowStaysOnTopHint
+ );
+ progress.show()
+ for pipelineIdx in xrange(pipelineCount):
+ # FIXME: eval should pretty much never be used
+ (serializedLocator, version) = eval(lines[lidx])
+ try:
+ locator = locators[serializedLocator]
+ except KeyError:
+ locator = parse_locator(serializedLocator)
+ if locator:
+ bundle = locator.load()
+ if isinstance(bundle, SaveBundle):
+ pipeline = bundle.vistrail.getPipeline(version)
+ else:
+ pipeline = bundle.getPipeline(version)
+ execution = get_default_interpreter()
+ progress.setValue(pipelineIdx)
+ QtCore.QCoreApplication.processEvents()
+ if progress.wasCanceled():
+ break
+ kwargs = {'locator': locator,
+ 'current_version': version,
+ 'view': DummyView(),
+ }
+ execution.execute(pipeline, **kwargs)
+ else:
+ raise RuntimeError("Couldn't load spreadsheet")
+ lidx += 1
+ progress.setValue(pipelineCount)
+ QtCore.QCoreApplication.processEvents()
+ self.changeSpreadsheetFileName(fileName)
+ self.loadingMode = False
+ indexFile.close()
+
+ def openSpreadsheetAs(self):
+ """ openSpreadsheetAs() -> None
+ Open a saved spreadsheet and set its filename in the dialog box
+
+ """
+ fileName = QtGui.QFileDialog.getOpenFileName(self,
+ 'Choose a spreadsheet',
+ '',
+ 'VisTrails Spreadsheet '
+ '(*.vss)',
+ )
+ if fileName:
+ self.openSpreadsheet(fileName)
+
+ def cleanup(self):
+ """ cleanup() -> None
+ Clear reference of non-collectable objects/temp files for gc
+
+ """
+ self.clearTabs()
+
+ def setEditingMode(self, editing=True):
+ """ setEditingMode(editing: bool) -> None
+ Turn on/off the editing mode of the whole spreadsheet
+
+ """
+ self.editingMode = editing
+ for w in self.tabWidgets:
+ w.setEditingMode(editing)
diff --git a/vistrails/packages/spreadsheet/spreadsheet_window.py b/vistrails/packages/spreadsheet/spreadsheet_window.py
new file mode 100644
index 0000000..51cc4c4
--- /dev/null
+++ b/vistrails/packages/spreadsheet/spreadsheet_window.py
@@ -0,0 +1,668 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This file implements the main spreadsheet window:
+# SpreadsheetWindow
+################################################################################
+from PyQt4 import QtCore, QtGui
+from spreadsheet_base import StandardSheetReference
+from spreadsheet_event import BatchDisplayCellEventType, DisplayCellEventType, \
+ RepaintCurrentSheetEventType
+from spreadsheet_tabcontroller import StandardWidgetTabController
+from spreadsheet_sheet import StandardWidgetSheet
+from spreadsheet_cell import QCellContainer
+from spreadsheet_config import configuration
+from vistrails.core.modules import module_utils
+from vistrails.core.utils import trace_method
+import ctypes
+import os.path
+import sys
+import tempfile
+
+################################################################################
+class SpreadsheetWindow(QtGui.QMainWindow):
+ """
+ SpreadsheetWindow is the top-level main window containing a
+ stacked widget of QTabWidget and its stacked widget for slideshow
+ mode
+
+ """
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ """ SpreadsheetWindow(parent: QWidget, f: WindowFlags)
+ -> SpreadsheetWindow
+ Layout menu, status bar and tab widget
+
+ """
+ QtGui.QMainWindow.__init__(self, parent, f)
+ self.createEventMap()
+ self.setWindowTitle('Untitled - VisTrails Spreadsheet')
+ self.shownConfig = False #flag to control the window setup code is done only once
+ self.stackedCentralWidget = QtGui.QStackedWidget(self)
+ self.tabController = StandardWidgetTabController(
+ self.stackedCentralWidget)
+ self.stackedCentralWidget.addWidget(self.tabController)
+ self.fullScreenStackedWidget = QtGui.QStackedWidget(
+ self.stackedCentralWidget)
+ self.stackedCentralWidget.addWidget(self.fullScreenStackedWidget)
+ self.setCentralWidget(self.stackedCentralWidget)
+ self.setStatusBar(QtGui.QStatusBar(self))
+ self.modeActionGroup = QtGui.QActionGroup(self)
+
+ self.visApp = QtCore.QCoreApplication.instance()
+ self.visApp.installEventFilter(self)
+
+ self.setupMenu()
+
+ self.connect(self.tabController,
+ QtCore.SIGNAL('needChangeTitle'),
+ self.setWindowTitle)
+ self.file_pool = module_utils.FilePool()
+ self.echoMode = False
+ self.echoCellEvents = []
+
+ if hasattr(self.visApp, 'builderWindow'):
+ self.quitAction = QtGui.QAction('&Quit VisTrails', self)
+ self.addAction(self.quitAction)
+ self.quitAction.setShortcut('Ctrl+Q')
+ self.connect(self.quitAction,
+ QtCore.SIGNAL('triggered()'),
+ self.quitActionTriggered)
+
+ # if the spreadsheet has one row and 2 columns
+ # this will cause the spreadsheet to have each cell
+ # 550 x 450 size in the server
+ #self.resize(1156, 599)
+
+ def quitActionTriggered(self):
+ if self.visApp and hasattr(self.visApp, 'builderWindow') and \
+ self.visApp.builderWindow.isVisible():
+ self.visApp.builderWindow.quit()
+
+
+ def cleanup(self):
+ if self.visApp!=None:
+ self.visApp.removeEventFilter(self)
+ self.file_pool.cleanup()
+ self.tabController.cleanup()
+
+ def destroy(self):
+ self.tabController.cleanup()
+ self.file_pool.cleanup()
+
+ def setupMenu(self):
+ """ setupMenu() -> None
+ Add all available actions to the menu bar
+
+ """
+ self.setMenuBar(QtGui.QMenuBar(self))
+ self.mainMenu = QtGui.QMenu('&Main', self.menuBar())
+ self.menuBar().addAction(self.mainMenu.menuAction())
+ self.mainMenu.addAction(self.tabController.saveAction())
+ self.mainMenu.addAction(self.tabController.saveAsAction())
+ self.mainMenu.addAction(self.tabController.openAction())
+ self.mainMenu.addSeparator()
+ self.mainMenu.addAction(self.tabController.newSheetAction())
+ self.mainMenu.addAction(self.tabController.deleteSheetAction())
+ self.viewMenu = QtGui.QMenu('&View', self.menuBar())
+ self.menuBar().addAction(self.viewMenu.menuAction())
+ self.viewMenu.addAction(self.interactiveModeAction())
+ self.viewMenu.addAction(self.editingModeAction())
+ self.viewMenu.addSeparator()
+ self.viewMenu.addAction(self.fitToWindowAction())
+ self.viewMenu.addAction(self.fullScreenAction())
+ self.windowMenu = QtGui.QMenu('&Window', self.menuBar())
+ self.menuBar().addAction(self.windowMenu.menuAction())
+ self.windowMenu.addAction(self.showBuilderWindowAction())
+
+ self.connect(self.modeActionGroup,
+ QtCore.SIGNAL('triggered(QAction*)'),
+ self.modeChanged)
+
+ def fitToWindowAction(self):
+ """ fitToWindowAction() -> QAction
+ Return the fit to window action
+
+ """
+ if not hasattr(self, 'fitAction'):
+ self.fitAction = QtGui.QAction('Fit to window', self)
+ self.fitAction.setStatusTip('Stretch spreadsheet cells '
+ 'to fit the window size')
+ self.fitAction.setCheckable(True)
+ checked = self.tabController.currentWidget().sheet.fitToWindow
+ self.fitAction.setChecked(checked)
+ self.connect(self.fitAction,
+ QtCore.SIGNAL('toggled(bool)'),
+ self.fitActionToggled)
+ return self.fitAction
+
+ def fitActionToggled(self, checked):
+ """ fitActionToggled(checked: boolean) -> None
+ Handle fitToWindow Action toggled
+
+ """
+ self.tabController.currentWidget().sheet.setFitToWindow(checked)
+
+ def fullScreenAction(self):
+ """ fullScreenAction() -> QAction
+ Return the fullscreen action
+
+ """
+ if not hasattr(self, 'fullScreenActionVar'):
+ self.fullScreenActionVar = QtGui.QAction('&Full Screen', self)
+ self.fullScreenActionVar.setShortcut('Ctrl+F')
+ self.fullScreenActionVar.setCheckable(True)
+ self.fullScreenActionVar.setChecked(False)
+ self.fullScreenActionVar.setStatusTip('Show sheets without any '
+ 'menubar or statusbar')
+ self.connect(self.fullScreenActionVar,
+ QtCore.SIGNAL('triggered(bool)'),
+ self.fullScreenActivated)
+ self.fullScreenAlternativeShortcuts = [QtGui.QShortcut('F11', self),
+ QtGui.QShortcut('Alt+Return',
+ self),
+ QtGui.QShortcut('Alt+Enter',
+ self)]
+ for sc in self.fullScreenAlternativeShortcuts:
+ self.connect(sc, QtCore.SIGNAL('activated()'),
+ self.fullScreenActionVar.trigger)
+ return self.fullScreenActionVar
+
+ def fullScreenActivated(self, full=None):
+ """ fullScreenActivated(full: bool) -> None
+ if fullScreen has been requested has pressed, then go to fullscreen now
+
+ """
+ if full==None:
+ fs = self.isFullScreen()
+ fs = not fs
+ else:
+ fs = full
+ if fs:
+ self.setWindowState(QtCore.Qt.WindowFullScreen)
+ else:
+ self.setWindowState(QtCore.Qt.WindowNoState)
+ fs = self.isFullScreen()
+ self.menuBar().setVisible(not fs)
+ self.statusBar().setVisible(not fs)
+ self.tabController.setupFullScreenWidget(fs,
+ self.fullScreenStackedWidget)
+ self.stackedCentralWidget.setCurrentIndex(int(fs))
+
+ def interactiveModeAction(self):
+ """ interactiveModeAction() -> QAction
+ Return the interactive mode action, this is the mode where users can
+ interact with the content of the cells
+
+ """
+ if not hasattr(self, 'interactiveModeActionVar'):
+ self.interactiveModeActionVar = QtGui.QAction('&Interactive Mode',
+ self.modeActionGroup)
+ self.interactiveModeActionVar.setCheckable(True)
+ self.interactiveModeActionVar.setChecked(True)
+ self.interactiveModeActionVar.setShortcut('Ctrl+Shift+I')
+ self.interactiveModeActionVar.setStatusTip('Use this mode to '
+ 'interact with '
+ 'the cell contents')
+ return self.interactiveModeActionVar
+
+ def editingModeAction(self):
+ """ editingModeAction() -> QAction
+ Return the editing mode action, this is the mode where users can
+ interact with the content of the cells
+
+ """
+ if not hasattr(self, 'editingModeActionVar'):
+ self.editingModeActionVar = QtGui.QAction('&Editing Mode',
+ self.modeActionGroup)
+ self.editingModeActionVar.setCheckable(True)
+ self.editingModeActionVar.setShortcut('Ctrl+Shift+E')
+ self.editingModeActionVar.setStatusTip('Use this mode to '
+ 'layout cells and '
+ 'interact cells with '
+ 'the builder')
+ return self.editingModeActionVar
+
+ def showBuilderWindowAction(self):
+ """ showBuilderWindowAction() -> QAction
+ Return the show builder action, this is used to show the builder window
+ when only the spreadsheet window is visible.
+
+ """
+ if not hasattr(self, 'showBuilderWindowActionVar'):
+ self.showBuilderWindowActionVar = \
+ QtGui.QAction('&Show Builder Window',
+ self)
+ self.showBuilderWindowActionVar.setShortcut('Ctrl+Shift+B')
+ self.showBuilderWindowActionVar.setStatusTip('Show the '
+ 'Builder Window')
+ if hasattr(self.visApp, 'builderWindow'):
+ self.showBuilderWindowActionVar.setEnabled(True)
+ else:
+ self.showBuilderWindowActionVar.setEnabled(False)
+
+ self.connect(self.showBuilderWindowActionVar,
+ QtCore.SIGNAL('triggered()'),
+ self.showBuilderWindowActionTriggered)
+
+ return self.showBuilderWindowActionVar
+
+ def modeChanged(self, action):
+ """ modeChanged(action: QAction) -> None
+ Handle the new mode (interactive or editing) based on the
+ triggered action
+
+ """
+ editing = self.editingModeAction().isChecked()
+ self.tabController.setEditingMode(editing)
+
+ def configShow(self, show=False):
+ """ configShow() -> None
+ Read VisTrails setting and show the spreadsheet window accordingly
+
+ """
+ if hasattr(self.visApp, 'configuration'):
+ if self.shownConfig:
+ self.show()
+ ### Multiheads
+ desktop = QtGui.QApplication.desktop()
+ if self.visApp.temp_configuration.multiHeads and desktop.numScreens()>1:
+ builderScreen = desktop.screenNumber(self.visApp.builderWindow)
+ r = desktop.availableGeometry(builderScreen)
+ self.visApp.builderWindow.ensurePolished()
+ self.visApp.builderWindow.updateGeometry()
+ frame = self.visApp.builderWindow.frameGeometry()
+ rect = self.visApp.builderWindow.rect()
+ frameDiff = QtCore.QPoint((frame.width()-rect.width())/2,
+ (frame.height()-rect.height())/2)
+ self.visApp.builderWindow.move(
+ frame.topLeft()+r.center()-frame.center())
+ for i in xrange(desktop.numScreens()):
+ if i!=builderScreen:
+ r = desktop.availableGeometry(i)
+ self.adjustSize()
+ self.move(r.center()-self.rect().center()-frameDiff)
+ break
+ if not self.visApp.temp_configuration.interactiveMode:
+ self.shownConfig = True
+ if show:
+ self.show()
+ return
+ ### Maximize
+ if self.visApp.temp_configuration.maximizeWindows:
+ self.showMaximized()
+ ### When the builder is hidden, the spreadsheet window does
+ ### not have focus. We have to force it
+ if self.visApp.temp_configuration.showSpreadsheetOnly:
+ self.raise_()
+ else:
+ self.show()
+ ### When the builder is hidden, the spreadsheet window does
+ ### not have focus. We have to force it to have the focus
+ if self.visApp.temp_configuration.showSpreadsheetOnly:
+ self.raise_()
+ else:
+ self.show()
+
+ self.shownConfig = True
+
+ def showEvent(self, e):
+ """ showEvent(e: QShowEvent) -> None
+ Make sure we show ourself for show event
+
+ """
+ self.show()
+ # Without this Ubuntu Unity will not show the menu bar
+ self.raise_()
+
+ def closeEvent(self, e):
+ """ closeEvent(e: QCloseEvent) -> None
+ When close, just hide instead
+
+ """
+ if hasattr(self.visApp, 'builderWindow'):
+ if self.visApp.builderWindow.isVisible():
+ e.ignore()
+ self.hide()
+ else:
+ #if the window is not visible, we need to quit the application
+ QtCore.QCoreApplication.quit()
+ else:
+ QtGui.QMainWindow.closeEvent(self, e)
+
+ def sizeHint(self):
+ """ sizeHint() -> QSize
+ Return a default size of the window
+
+ """
+ return QtCore.QSize(1024, 768)
+
+ def eventFilter(self,q,e):
+ """ eventFilter(q: QObject, e: QEvent) -> depends on event type
+ An application-wide eventfilter to capture mouse/keyboard events
+
+ """
+ eType = e.type()
+ # Handle Show/Hide cell resizer on MouseMove
+ if eType==QtCore.QEvent.MouseMove:
+ sheetWidget = self.tabController.tabWidgetUnderMouse()
+ if sheetWidget:
+ sheetWidget.showHelpers(True, QtGui.QCursor.pos())
+
+ # Slideshow mode
+ if (eType==QtCore.QEvent.MouseButtonPress and
+ self.isFullScreen() and
+ e.buttons()&QtCore.Qt.RightButton):
+ self.tabController.showPopupMenu()
+ return True
+
+ # Handle slideshow shortcuts
+ if (eType==QtCore.QEvent.KeyPress and
+ self.isFullScreen()):
+ if (e.key() in [QtCore.Qt.Key_Space,
+ QtCore.Qt.Key_PageDown,QtCore.Qt.Key_Right]):
+ self.tabController.showNextTab()
+ return True
+ if (e.key() in [QtCore.Qt.Key_PageUp,QtCore.Qt.Key_Left]):
+ self.tabController.showPrevTab()
+ return True
+ if (e.key()==QtCore.Qt.Key_Escape or
+ (e.key()==QtCore.Qt.Key_F and e.modifiers()&QtCore.Qt.ControlModifier)):
+ self.fullScreenAction().trigger()
+ return True
+
+ # Perform single-click event on the spread sheet
+ if (not self.tabController.editingMode and
+ eType==QtCore.QEvent.MouseButtonPress):
+ if isinstance(q, QCellContainer):
+ return q.containedWidget!=None
+ p = q
+ while (p and (not p.isModal()) and not isinstance(p, StandardWidgetSheet) and p.parent):
+ p = p.parent()
+ if p and isinstance(p, StandardWidgetSheet) and not p.isModal():
+ pos = p.viewport().mapFromGlobal(e.globalPos())
+ p.emit(QtCore.SIGNAL('cellActivated(int, int, bool)'),
+ p.rowAt(pos.y()), p.columnAt(pos.x()),
+ e.modifiers()==QtCore.Qt.ControlModifier)
+ return False
+ #return QtGui.QMainWindow.eventFilter(self,q,e)
+
+ def event(self, e):
+ """ event(e: QEvent) -> depends on event type
+ Handle all special events from spreadsheet controller
+
+ """
+ if self.eventMap.has_key(e.type()):
+ self.eventMap[e.type()](e)
+ return False
+ return QtGui.QMainWindow.event(self, e)
+
+ def createEventMap(self):
+ """ createEventMap() -> None
+ Create the event map to call inside the event(). This must be
+ called before anything else
+
+ """
+ self.eventMap = {
+ DisplayCellEventType : self.displayCellEvent,
+ BatchDisplayCellEventType : self.batchDisplayCellEvent,
+ RepaintCurrentSheetEventType: self.repaintCurrentSheetEvent
+ }
+
+ def displayCellEvent(self, e):
+ """ displayCellEvent(e: DisplayCellEvent) -> None
+ Display a cell when receive this event
+
+ """
+ if self.echoMode:
+ self.echoCellEvents.append(e)
+ return None
+ self.tabController.addPipeline(e.vistrail)
+ cid = self.tabController.increasePipelineCellId(e.vistrail)
+ pid = self.tabController.getCurrentPipelineId(e.vistrail)
+ if self.tabController.isLoadingMode():
+ locations = self.tabController.getMonitoredLocations((
+ (e.vistrail), pid, cid))
+ for (sheet, row, col) in locations:
+ sheet.tabWidget.setCurrentWidget(sheet)
+ sheet.setCellPipelineInfo(row, col, (e.vistrail, pid, cid))
+ sheet.setCellByType(row, col, e.cellType, e.inputPorts)
+ return None
+ else:
+ reference = e.sheetReference
+ if reference==None:
+ reference = StandardSheetReference()
+ sheet = self.tabController.findSheet(reference)
+ row = e.row
+ col = e.col
+ if row<0 or col<0:
+ (row, col) = sheet.getFreeCell()
+ sheet.tabWidget.setCurrentWidget(sheet)
+ sheet.setCellPipelineInfo(row, col,
+ (e.vistrail, pid, cid))
+ if e.rowSpan>=1 or e.colSpan>=1:
+ sheet.setSpan(row, col, e.rowSpan, e.colSpan)
+ if e.inputPorts!=None:
+ sheet.setCellByType(row, col, e.cellType, e.inputPorts)
+ else:
+ sheet.setCellByWidget(row, col, e.cellType)
+ QtCore.QCoreApplication.processEvents()
+ cell = sheet.getCell(row, col)
+ if self.editingModeAction().isChecked():
+ sheet.setCellEditingMode(row, col, True)
+ #If a cell has to dump its contents to a file, it will be in the
+ #extra_info dictionary
+ if cell and e.vistrail.has_key('extra_info'):
+ dump_as_pdf = False
+ extra_info = e.vistrail['extra_info']
+ if extra_info.has_key('pathDumpCells'):
+ dumppath = extra_info['pathDumpCells']
+ if extra_info.has_key('nameDumpCells'):
+ name = extra_info['nameDumpCells']
+ base_fname = os.path.join(dumppath,
+ name)
+ else:
+ locator = e.vistrail['locator']
+ if locator is not None:
+ name = e.vistrail['locator'].short_name
+ else:
+ name = 'untitled'
+ version = e.vistrail['version']
+ if version is None:
+ version = 0L
+ base_fname = os.path.join(dumppath,"%s_%s" % \
+ (name, e.vistrail['version']))
+
+ if configuration.dumpfileType == 'PNG':
+ dump_as_pdf = False
+ elif configuration.dumpfileType == 'PDF':
+ dump_as_pdf = True
+
+ #extra_info configuration overwrites global configuration
+ if extra_info.has_key('pdf'):
+ dump_as_pdf = extra_info['pdf']
+
+ file_extension = '.png'
+ if dump_as_pdf == True:
+ file_extension = '.pdf'
+
+ # add cell location by default
+ if not extra_info.has_key('nameDumpCells'):
+ base_fname = base_fname + "_%d_%d" % (row, col)
+ # make a unique filename
+ filename = base_fname + file_extension
+ counter = 2
+ while os.path.exists(filename):
+ filename = base_fname + "_%d%s" % (counter,
+ file_extension)
+ counter += 1
+ if not dump_as_pdf:
+ cell.dumpToFile(filename)
+ else:
+ cell.saveToPDF(filename)
+ #if the cell was already selected, then we need to update
+ #the toolbar with this new cell
+ if hasattr(sheet, 'sheet'):
+ if sheet.sheet.activeCell == (row,col):
+ sheet.sheet.setActiveCell(row,col)
+ return cell
+
+ def batchDisplayCellEvent(self, batchEvent):
+ """ batchDisplayCellEvent(batchEvent: BatchDisplayCellEvent) -> None
+ Handle event where a series of cells are arrived
+
+ """
+ self.tabController.addPipeline(batchEvent.vistrail)
+ for e in batchEvent.displayEvents:
+ e.vistrail = batchEvent.vistrail
+ self.displayCellEvent(e)
+
+ def repaintCurrentSheetEvent(self, e):
+ """ repaintCurrentSheetEvent(e: RepaintCurrentSheetEvent) -> None
+ Repaint the current sheet
+
+ """
+ currentTab = self.tabController.currentWidget()
+ if currentTab:
+ (rCount, cCount) = currentTab.getDimension()
+ for r in xrange(rCount):
+ for c in xrange(cCount):
+ widget = currentTab.getCell(r, c)
+ if widget:
+ widget.repaint()
+
+ def showBuilderWindowActionTriggered(self):
+ """showBuilderWindowActionTriggered() -> None
+ This will show the builder window """
+ self.visApp.builderWindow.show()
+
+ def prepareReviewingMode(self, vCol):
+ """ Trim down most of the spreadsheet window """
+ self.menuBar().hide()
+ self.statusBar().hide()
+ self.tabController.tabBar().hide()
+ self.tabController.clearTabs()
+ self.setWindowFlags(QtCore.Qt.Tool | QtCore.Qt.WindowStaysOnTopHint)
+ self.setWindowTitle('Pipeline Review - VisTrails Spreadsheet')
+ self.resize(560*vCol, 512)
+ self.show()
+
+ def startReviewingMode(self):
+ """ startReviewingMode()
+ Reorganize the spreadsheet to contain only cells executed from locator:version
+
+ """
+ currentTab = self.tabController.currentWidget()
+ if currentTab:
+ currentTab.toolBar.hide()
+ buttonLayout = QtGui.QHBoxLayout()
+ buttons = [QtGui.QPushButton('&Accept'),
+ QtGui.QPushButton('&Discard')]
+ buttonLayout.addStretch()
+ buttonLayout.addWidget(buttons[0])
+ buttonLayout.addWidget(buttons[1])
+ buttonLayout.addStretch()
+ currentTab.layout().addLayout(buttonLayout)
+ self.connect(buttons[0], QtCore.SIGNAL('clicked()'),
+ self.acceptReview)
+ self.connect(buttons[1], QtCore.SIGNAL('clicked()'),
+ self.discardReview)
+
+ def discardReview(self):
+ """ Just quit the program """
+ QtCore.QCoreApplication.quit()
+
+ def acceptReview(self):
+ """ Copy image of all cells to the clipboard and then exit """
+ currentTab = self.tabController.currentWidget()
+ height = 0
+ width = 0
+ pixmaps = []
+ version = -1
+ if currentTab:
+ (rCount, cCount) = currentTab.getDimension()
+ for r in xrange(rCount):
+ for c in xrange(cCount):
+ widget = currentTab.getCell(r, c)
+ if widget:
+ version = currentTab.getCellPipelineInfo(r, c)[0]['version']
+ pix = widget.grabWindowPixmap()
+ pixmaps.append(pix)
+ width += pix.width()
+ height = max(height, pix.height())
+ finalImage = QtGui.QImage(width, height, QtGui.QImage.Format_ARGB32)
+ painter = QtGui.QPainter(finalImage)
+ x = 0
+ for pix in pixmaps:
+ painter.drawPixmap(x, 0, pix)
+ x += pix.width()
+ painter.end()
+ filename = tempfile.gettempdir() + '/' + 'vtexport.png'
+ finalImage.save(filename, 'PNG')
+ sm = QtCore.QSharedMemory('VisTrailsPipelineImage')
+ sm.create(32768)
+ sm.attach()
+ sm.lock()
+ pfn = ctypes.c_char_p(filename)
+ ctypes.memmove(int(sm.data()), pfn, len(filename))
+ pfn = ctypes.c_char_p(str(version))
+ ctypes.memmove(int(sm.data())+256, pfn, len(str(version)))
+ sm.unlock()
+ sm.detach()
+ QtCore.QCoreApplication.quit()
+
+ def setEchoMode(self, echo):
+ """ setEchoMode(echo: bool)
+ Instruct the spreadsheet to dispatch (echo) all cell widgets
+ instead of managing them on the spreadsheet
+
+ """
+ self.echoMode = echo
+
+ def getEchoCellEvents(self):
+ """ getEchoCellEvents() -> [DisplayCellEvent]
+ Echo back the list of all cell events that have been captured
+ earlier
+
+ """
+ return self.echoCellEvents
+
+ def clearEchoCellEvents(self):
+ """ clearEchoCellEvents()
+ Erase the list of echoed events
+
+ """
+ self.echoCellEvents = []
+
+
diff --git a/vistrails/packages/spreadsheet/widgets/__init__.py b/vistrails/packages/spreadsheet/widgets/__init__.py
new file mode 100644
index 0000000..cdc9214
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# Nothing here on purpose
+pass
diff --git a/vistrails/packages/spreadsheet/widgets/iebrowser/__init__.py b/vistrails/packages/spreadsheet/widgets/iebrowser/__init__.py
new file mode 100644
index 0000000..dc0cdd5
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/iebrowser/__init__.py
@@ -0,0 +1,59 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# Internet Explorer plugin for VisTrails Spreadsheet
+################################################################################
+from iecell import IECell
+
+################################################################################
+
+def widgetName():
+ """ widgetName() -> str
+ Return the name of this widget plugin
+
+ """
+ return 'Internet Explorer Control'
+
+def registerWidget(reg, basicModules, basicWidgets):
+ """ registerWidget(reg: module_registry,
+ basicModules: python package,
+ basicWidgets: python package) -> None
+ Register all widgets in this package to VisTrails module_registry
+
+ """
+ reg.add_module(IECell)
+ reg.add_input_port(IECell, "Location", basicWidgets.CellLocation)
+ reg.add_input_port(IECell, "url", basicModules.String)
+ reg.add_input_port(IECell, "file", basicModules.File)
diff --git a/vistrails/packages/spreadsheet/widgets/iebrowser/iecell.py b/vistrails/packages/spreadsheet/widgets/iebrowser/iecell.py
new file mode 100644
index 0000000..28feaa5
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/iebrowser/iecell.py
@@ -0,0 +1,110 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+############################################################################
+# web browser view implementation
+############################################################################
+from vistrails.core.modules.vistrails_module import Module
+from PyQt4 import QtCore, QtGui, QAxContainer
+from vistrails.packages.spreadsheet.basic_widgets import SpreadsheetCell
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellWidget
+import shutil
+############################################################################
+
+class IECell(SpreadsheetCell):
+ """
+ IECell is a custom Module to view URLs using the IE ActiveX Control
+
+ """
+ def compute(self):
+ """ compute() -> None
+ Dispatch the URL to the spreadsheet
+ """
+ if self.hasInputFromPort("url"):
+ urlValue = self.getInputFromPort("url")
+ fileValue = None
+ elif self.hasInputFromPort("file"):
+ fileValue = self.getInputFromPort("file")
+ urlValue = None
+ else:
+ fileValue = None
+ urlValue = None
+ self.display(IECellWidget, (urlValue, fileValue))
+
+class IECellWidget(QCellWidget):
+ """
+ IECellWidget has a QAxContainer to display supported documents
+
+ """
+ def __init__(self, parent=None):
+ """ IECellWidget(parent: QWidget) -> IECellWidget
+ Create a ActiveX Container pointing to the IE Cell
+
+ """
+ QCellWidget.__init__(self, parent)
+ vbox = QtGui.QVBoxLayout(self)
+ vbox.setMargin(0)
+ self.setLayout(vbox)
+ self.browser = QAxContainer.QAxWidget(self)
+ self.browser.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.browser.setControl("{8856F961-340A-11D0-A96B-00C04FD705A2}")
+ vbox.addWidget(self.browser)
+ self.urlSrc = None
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple) -> None
+ Updates the contents with a new changed in filename
+
+ """
+ self.urlSrc = None
+ (urlValue, fileValue) = inputPorts
+ if urlValue:
+ self.urlSrc = QtCore.QUrl(urlValue)
+ elif fileValue:
+ self.urlSrc = QtCore.QUrl.fromLocalFile(fileValue.name)
+ if self.urlSrc!=None:
+ self.browser.dynamicCall('Navigate(const QString&)', self.urlSrc)
+ else:
+ self.browser.dynamicCall('Navigate(const QString&)', 'about:blank')
+
+ def dumpToFile(self, filename):
+ if self.urlSrc is not None:
+ shutil.copyfile(str(self.urlSrc.toLocalFile()), filename)
+
+ def saveToPDF(self, filename):
+ printer = QtGui.QPrinter()
+ printer.setOutputFormat(QtGui.QPrinter.PdfFormat)
+ printer.setOutputFileName(filename)
+ self.browser.print_(printer)
diff --git a/vistrails/packages/spreadsheet/widgets/imageviewer/__init__.py b/vistrails/packages/spreadsheet/widgets/imageviewer/__init__.py
new file mode 100644
index 0000000..38432e2
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/imageviewer/__init__.py
@@ -0,0 +1,58 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# ImageViewer plugin for VisTrails Spreadsheet
+################################################################################
+from imageviewer import ImageViewerCell
+
+################################################################################
+
+def widgetName():
+ """ widgetName() -> str
+ Return the name of this widget plugin
+
+ """
+ return 'Image Viewer'
+
+def registerWidget(reg, basicModules, basicWidgets):
+ """ registerWidget(reg: module_registry,
+ basicModules: python package,
+ basicWidgets: python package) -> None
+ Register all widgets in this package to VisTrails module_registry
+
+ """
+ reg.add_module(ImageViewerCell)
+ reg.add_input_port(ImageViewerCell, "Location", basicWidgets.CellLocation)
+ reg.add_input_port(ImageViewerCell, "File", basicModules.File)
diff --git a/vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer.py b/vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer.py
new file mode 100644
index 0000000..53e7e3a
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer.py
@@ -0,0 +1,371 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# ImageViewer widgets/toolbar implementation
+################################################################################
+from PyQt4 import QtCore, QtGui
+from vistrails.core.modules.vistrails_module import Module
+from vistrails.packages.spreadsheet.basic_widgets import SpreadsheetCell
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+from vistrails.packages.spreadsheet.spreadsheet_controller import spreadsheetController
+import imageviewer_rc
+
+################################################################################
+
+class ImageViewerCell(SpreadsheetCell):
+ """
+ ImageViewerCell is a custom Module to display labels, images, etc.
+
+ """
+ def compute(self):
+ """ compute() -> None
+ Dispatch the display event to the spreadsheet with images and labels
+
+ """
+ if self.hasInputFromPort("File"):
+ window = spreadsheetController.findSpreadsheetWindow()
+ file_to_display = self.getInputFromPort("File")
+ fileValue = window.file_pool.make_local_copy(file_to_display.name)
+ else:
+ fileValue = None
+ self.cellWidget = self.displayAndWait(ImageViewerCellWidget, (fileValue, ))
+
+class ImageViewerCellWidget(QCellWidget):
+ """
+ ImageViewerCellWidget is the actual QLabel that will draw
+ labels/images on the spreadsheet
+
+ """
+ def __init__(self, parent=None):
+ """ ImageViewerCellWidget(parent: QWidget) -> ImageViewerCellWidget
+ Initialize the widget with its toolbar type and aligment
+
+ """
+ QCellWidget.__init__(self, parent)
+ self.setLayout(QtGui.QVBoxLayout(self))
+ self.setAnimationEnabled(True)
+
+ self.label = QtGui.QLabel()
+ self.layout().addWidget(self.label)
+
+ self.label.setAutoFillBackground(True)
+ self.label.palette().setColor(QtGui.QPalette.Window, QtCore.Qt.white)
+ self.label.setMouseTracking(False)
+ self.label.setAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
+ self.label.setScaledContents(False)
+ self.toolBarType = ImageViewerToolBar
+ self.originalPix = None
+ self.setMinimumSize(1, 1)
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple) -> None
+ Update the widget contents based on the input data
+
+ """
+ (fileValue, ) = inputPorts
+ if fileValue:
+ img = QtGui.QImage()
+ if img.load(fileValue.name):
+ self.originalPix = QtGui.QPixmap.fromImage(img)
+ self.label.setPixmap(self.originalPix.scaled(len(self.label),
+ QtCore.Qt.KeepAspectRatio,
+ QtCore.Qt.SmoothTransformation))
+ else:
+ self.label.setText("Invalid image file!")
+
+ QCellWidget.updateContents(self, inputPorts)
+
+ def saveToPNG(self, filename):
+ """ saveToPNG(filename: str) -> bool
+ Save the current widget contents to an image file
+
+ """
+ pixmap = self.label.pixmap()
+ if pixmap and (not pixmap.isNull()):
+ return pixmap.save(filename)
+ return False
+
+ def saveToPDF(self, filename):
+ """ saveToPDF(filename: str) -> bool
+ Save the current widget contents to a pdf file
+
+ """
+ printer = QtGui.QPrinter()
+
+ printer.setOutputFormat(QtGui.QPrinter.PdfFormat)
+ printer.setOutputFileName(filename)
+ painter = QtGui.QPainter()
+ painter.begin(printer)
+ rect = painter.viewport()
+ pixmap = self.label.pixmap()
+ size = pixmap.size()
+ size.scale(rect.size(), QtCore.Qt.KeepAspectRatio)
+ painter.setViewport(rect.x(), rect.y(), size.width(), size.height())
+ painter.setWindow(pixmap.rect())
+ painter.drawPixmap(0, 0, pixmap)
+ painter.end()
+
+ def resizeEvent(self, e):
+ if self.originalPix!=None:
+ self.label.setPixmap(self.originalPix.scaled(self.label.size(),
+ QtCore.Qt.KeepAspectRatio,
+ QtCore.Qt.SmoothTransformation))
+
+class ImageViewerFitToCellAction(QtGui.QAction):
+ """
+ ImageViewerFitToCellAction is the action to stretch the image to
+ fit inside a cell
+
+ """
+ def __init__(self, parent=None):
+ """ ImageViewerFitToCellAction(parent: QWidget)
+ -> ImageViewerFitToCellAction
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/fittocell.png"),
+ "&Fit To Cell",
+ parent)
+ self.setStatusTip("Scale image content to fit cell frame")
+ self.setCheckable(True)
+ self.setChecked(True)
+
+ def toggledSlot(self, checked):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is toggled
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ cellWidget.label.setScaledContents(checked)
+ self.toolBar.slider.updateStatus((self.toolBar.sheet,
+ self.toolBar.row,
+ self.toolBar.col,
+ cellWidget))
+
+ def updateStatus(self, info):
+ """ updateStatus(info: tuple) -> None
+ Updates the status of the button based on the input info
+
+ """
+ (sheet, row, col, cellWidget) = info
+ self.setChecked(cellWidget.label.hasScaledContents())
+
+class ImageViewerSaveAction(QtGui.QAction):
+ """
+ ImageViewerSaveAction is the action to save the image to file
+
+ """
+ def __init__(self, parent=None):
+ """ ImageViewerSaveAction(parent: QWidget) -> ImageViewerSaveAction
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/save.png"),
+ "&Save image as...",
+ parent)
+ self.setStatusTip("Save image to file")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ if not cellWidget.label.pixmap() or cellWidget.label.pixmap().isNull():
+ return
+ fn = QtGui.QFileDialog.getSaveFileName(None, "Save image as...",
+ "screenshot.png",
+ "Images (*.png);;PDF files (*.pdf)")
+ if fn:
+ if fn.lower().endswith("png"):
+ cellWidget.label.pixmap().toImage().save(fn, "png")
+ elif fn.lower().endswith("pdf"):
+ cellWidget.saveToPDF(fn)
+
+
+class ImageViewerZoomSlider(QtGui.QSlider):
+ """
+ ImageViewerZoomSlider is a slider that allows user to zoom in and
+ out by dragging it
+
+ """
+ def __init__(self, parent=None):
+ """ ImageViewerZoomSlider(parent: QWidget) -> ImageViewerZoomSlider
+ Setup the ranges, status tip, etc. of the slider
+
+ """
+ QtGui.QSlider.__init__(self, QtCore.Qt.Horizontal, parent)
+ self.setRange(100, 300)
+ self.setValue(100)
+ self.setTracking(True)
+ self.setStatusTip("Zoom in the image")
+ self.connect(self, QtCore.SIGNAL("valueChanged(int)"), self.updateZoom)
+ self.connect(self, QtCore.SIGNAL("needUpdateStatus"), self.updateStatus)
+ self.setSizePolicy(QtGui.QSizePolicy.Preferred,
+ QtGui.QSizePolicy.Expanding)
+
+ def updateZoom(self, value):
+ """ updateZoom(value: int) -> None
+ Update the image when the slider value changed
+
+ """
+ if self.toolBar:
+ cellWidget = self.toolBar.getSnappedWidget()
+ if not cellWidget.label.hasScaledContents():
+ newWidth = cellWidget.originalPix.width()*value/100
+ pixmap = cellWidget.originalPix.scaledToWidth(newWidth)
+ cellWidget.label.setPixmap(pixmap)
+
+ def updateStatus(self, info):
+ """ updateStatus(info: tuple) -> None
+ Updates the status of the button based on the input info
+
+ """
+ (sheet, row, col, cellWidget) = info
+ if cellWidget:
+ if (not cellWidget.label.hasScaledContents() and
+ not cellWidget._playing):
+ self.setEnabled(True)
+ originalWidth = cellWidget.originalPix.width()
+ self.setValue(cellWidget.label.pixmap().width()*100/originalWidth)
+ else:
+ self.setEnabled(False)
+ self.setValue(100)
+
+class ImageViewerZoomLabel(QtGui.QLabel):
+ """
+ ImageViewerZoomLabel is the label sitting next to the ImageViewerZoomSlider
+
+ """
+ def __init__(self, parent=None):
+ """ ImageViewerZoomSlider(parent: QWidget) -> None
+ Setup the label with a status tip
+
+ """
+ QtGui.QLabel.__init__(self, "100%", parent)
+ self.setStatusTip("Zoom in the image")
+
+ def updateValue(self, value):
+ """ updateValue(value: int)
+ Updates the label with the new percentage value
+ """
+ self.setText(str(value)+"%")
+
+class ImageViewerRotateAction(QtGui.QAction):
+ """
+ ImageViewerRotateAction is the action to rotate the image
+
+ """
+ def __init__(self, parent=None):
+ """ ImageViewerRotateAction(parent: QWidget)
+ -> ImageViewerRotateAction
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/rotate.png"),
+ "&Rotate CW...",
+ parent)
+ self.setStatusTip("Rotate 90 degrees CW")
+ self.rotationMatrix = QtGui.QMatrix(0,1,-1,0,0,0)
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ if not cellWidget.label.pixmap() or cellWidget.label.pixmap().isNull():
+ return
+ cellWidget.originalPix = cellWidget.originalPix.transformed(
+ self.rotationMatrix)
+ cellWidget.label.setPixmap(cellWidget.label.pixmap().transformed(
+ self.rotationMatrix))
+
+class ImageViewerFlipAction(QtGui.QAction):
+ """
+ ImageViewerFlipAction is the action to flip the image
+
+ """
+ def __init__(self, parent=None):
+ """ ImageViewerFlipAction(parent: QWidget) -> ImageViewerFlipAction
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/flip.png"),
+ "&Flip Horizontal...",
+ parent)
+ self.setStatusTip("Flip the image horizontally")
+ self.flipMatrix = QtGui.QMatrix(-1,0,0,1,0,0)
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ label = cellWidget.label
+ if not label.pixmap() or label.pixmap().isNull():
+ return
+ cellWidget.originalPix = cellWidget.originalPix.transformed(
+ self.flipMatrix)
+ label.setPixmap(label.pixmap().transformed(self.flipMatrix))
+
+class ImageViewerToolBar(QCellToolBar):
+ """
+ ImageViewerToolBar derives from CellToolBar to give the ImageViewerCellWidget
+ a customizable toolbar
+
+ """
+ def createToolBar(self):
+ """ createToolBar() -> None
+ This will get call initiallly to add customizable widgets
+
+ """
+ self.appendAction(ImageViewerFitToCellAction(self))
+ self.appendAction(ImageViewerSaveAction(self))
+ self.appendAction(ImageViewerRotateAction(self))
+ self.appendAction(ImageViewerFlipAction(self))
+ self.slider = ImageViewerZoomSlider(self)
+ label = ImageViewerZoomLabel(self)
+ self.connect(self.slider,
+ QtCore.SIGNAL("valueChanged(int)"),
+ label.updateValue)
+ self.appendWidget(self.slider)
+ self.appendWidget(label)
+ self.addAnimationButtons()
diff --git a/vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer_rc.py b/vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer_rc.py
new file mode 100644
index 0000000..9412c41
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer_rc.py
@@ -0,0 +1,557 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# Resource object code
+#
+# Created: Thu Sep 21 00:22:30 2006
+# by: The Resource Compiler for PyQt (Qt v4.1.3)
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore
+
+qt_resource_data = b"\
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+\x7c\x33\x7f\x4b\x7b\xe1\x09\xd6\x76\x9c\x78\xd9\xc0\x72\xcb\x6f\
+\x3e\xfe\x07\x44\x59\x76\x36\x1e\xee\x54\x0f\x00\x00\x00\x00\x49\
+\x45\x4e\x44\xae\x42\x60\x82\
+"
+
+qt_resource_name = b"\
+\x00\x06\
+\x07\x03\x7d\xc3\
+\x00\x69\
+\x00\x6d\x00\x61\x00\x67\x00\x65\x00\x73\
+\x00\x0a\
+\x08\xab\x7a\x07\
+\x00\x72\
+\x00\x6f\x00\x74\x00\x61\x00\x74\x00\x65\x00\x2e\x00\x70\x00\x6e\x00\x67\
+\x00\x08\
+\x03\x03\x5a\xe7\
+\x00\x66\
+\x00\x6c\x00\x69\x00\x70\x00\x2e\x00\x70\x00\x6e\x00\x67\
+\x00\x08\
+\x08\xc8\x58\x67\
+\x00\x73\
+\x00\x61\x00\x76\x00\x65\x00\x2e\x00\x70\x00\x6e\x00\x67\
+\x00\x0d\
+\x02\x38\x3d\xc7\
+\x00\x66\
+\x00\x69\x00\x74\x00\x74\x00\x6f\x00\x63\x00\x65\x00\x6c\x00\x6c\x00\x2e\x00\x70\x00\x6e\x00\x67\
+"
+
+qt_resource_struct = b"\
+\x00\x00\x00\x00\x00\x02\x00\x00\x00\x01\x00\x00\x00\x01\
+\x00\x00\x00\x00\x00\x02\x00\x00\x00\x04\x00\x00\x00\x02\
+\x00\x00\x00\x58\x00\x00\x00\x00\x00\x01\x00\x00\x17\x30\
+\x00\x00\x00\x2c\x00\x00\x00\x00\x00\x01\x00\x00\x07\xc6\
+\x00\x00\x00\x12\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\
+\x00\x00\x00\x42\x00\x00\x00\x00\x00\x01\x00\x00\x0d\xa3\
+"
+
+def qInitResources():
+ QtCore.qRegisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+def qCleanupResources():
+ QtCore.qUnregisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+qInitResources()
diff --git a/vistrails/packages/spreadsheet/widgets/richtext/__init__.py b/vistrails/packages/spreadsheet/widgets/richtext/__init__.py
new file mode 100644
index 0000000..564257c
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/richtext/__init__.py
@@ -0,0 +1,66 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# RichText plugin for VisTrails Spreadsheet
+################################################################################
+from richtext import RichTextCell, XSLCell
+
+################################################################################
+
+def widgetName():
+ """ widgetName() -> str
+ Return the name of this widget plugin
+
+ """
+ return 'HTML Viewer'
+
+def registerWidget(reg, basicModules, basicWidgets):
+ """ registerWidget(reg: module_registry,
+ basicModules: python package,
+ basicWidgets: python package) -> None
+ Register all widgets in this package to VisTrails module_registry
+
+ """
+ reg.add_module(RichTextCell)
+ reg.add_input_port(RichTextCell, "Location", basicWidgets.CellLocation)
+ reg.add_input_port(RichTextCell, "File", basicModules.File)
+ reg.add_input_port(RichTextCell, "Format", basicModules.String,
+ entry_types=['enum'], values=["['html', 'rtf']"],
+ optional=True, defaults="['html']")
+
+ reg.add_module(XSLCell)
+ reg.add_input_port(XSLCell, "Location", basicWidgets.CellLocation)
+ reg.add_input_port(XSLCell, "XML", basicModules.File)
+ reg.add_input_port(XSLCell, "XSL", basicModules.File)
diff --git a/vistrails/packages/spreadsheet/widgets/richtext/richtext.py b/vistrails/packages/spreadsheet/widgets/richtext/richtext.py
new file mode 100644
index 0000000..11849ce
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/richtext/richtext.py
@@ -0,0 +1,143 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# Richtext widgets implementation
+################################################################################
+import os
+from PyQt4 import QtGui
+from PyQt4.QtCore import QUrl
+from PyQt4.QtXmlPatterns import QXmlQuery
+
+from vistrails.core.bundles.pyimport import py_import
+from vistrails.core.modules.vistrails_module import ModuleError
+from vistrails.packages.spreadsheet.basic_widgets import SpreadsheetCell
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellWidget
+################################################################################
+
+class RichTextCell(SpreadsheetCell):
+ """
+ RichTextCell is a custom Module to view HTML files
+
+ """
+ def compute(self):
+ """ compute() -> None
+ Dispatch the HTML contents to the spreadsheet
+ """
+ filename = self.getInputFromPort("File").name
+
+ text_format = self.getInputFromPort("Format")
+ with open(filename, 'rb') as fp:
+ if text_format == 'html':
+ html = fp.read()
+ elif text_format == 'rtf':
+ try:
+ py_import('pyth', {'pip': 'pyth'})
+ except ImportError:
+ raise ModuleError(self, "'rtf' format requires the pyth "
+ "Python library")
+ else:
+ from pyth.plugins.rtf15.reader import Rtf15Reader
+ from pyth.plugins.xhtml.writer import XHTMLWriter
+ doc = Rtf15Reader.read(fp)
+ html = XHTMLWriter.write(doc).read().decode('utf-8')
+ else:
+ raise ModuleError(self, "'%s' format is unknown" % text_format)
+
+ self.cellWidget = self.displayAndWait(RichTextCellWidget, (html,))
+
+
+class XSLCell(SpreadsheetCell):
+ """
+ XSLCell is a custom Module to render an XML file via an XSL stylesheet
+
+ """
+ def compute(self):
+ """ compute() -> None
+ Render the XML tree and display it on the spreadsheet
+ """
+ xml = self.getInputFromPort('XML').name
+ xsl = self.getInputFromPort('XSL').name
+
+ query = QXmlQuery(QXmlQuery.XSLT20)
+ query.setFocus(QUrl.fromLocalFile(os.path.join(os.getcwd(), xml)))
+ query.setQuery(QUrl.fromLocalFile(os.path.join(os.getcwd(), xsl)))
+ html = query.evaluateToString()
+
+ self.cellWidget = self.displayAndWait(RichTextCellWidget, (html,))
+
+
+class RichTextCellWidget(QCellWidget):
+ """
+ RichTextCellWidget has a QTextBrowser to display HTML files
+
+ """
+ def __init__(self, parent=None):
+ """ RichTextCellWidget(parent: QWidget) -> RichTextCellWidget
+ Create a rich text cell without a toolbar
+
+ """
+ QCellWidget.__init__(self, parent)
+ self.setLayout(QtGui.QVBoxLayout(self))
+ self.browser = QtGui.QTextBrowser()
+ self.layout().addWidget(self.browser)
+ self.browser.setMouseTracking(True)
+ self.browser.controlBarType = None
+ self.html = None
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple) -> None
+ Updates the contents with a new HTML document
+
+ """
+ (self.html,) = inputPorts
+ self.browser.setHtml(self.html)
+
+ def dumpToFile(self, filename):
+ """ dumpToFile(filename) -> None
+ It will generate a screenshot of the cell contents and dump to filename.
+ It will also create a copy of the original text file used with
+ filename's basename and the original extension.
+ """
+ if self.html is not None:
+ basename, ext = os.path.splitext(filename)
+ with open(basename + '.html', 'wb') as fp:
+ fp.write(self.html.encode('utf-8'))
+ QCellWidget.dumpToFile(self,filename)
+
+ def saveToPDF(self, filename):
+ printer = QtGui.QPrinter()
+ printer.setOutputFormat(QtGui.QPrinter.PdfFormat)
+ printer.setOutputFileName(filename)
+ self.browser.print_(printer)
diff --git a/vistrails/packages/spreadsheet/widgets/svg/__init__.py b/vistrails/packages/spreadsheet/widgets/svg/__init__.py
new file mode 100644
index 0000000..203aebf
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/svg/__init__.py
@@ -0,0 +1,61 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# SVG plugin for VisTrails Spreadsheet
+################################################################################
+from svg import SVGCell, SVGSplitter
+
+################################################################################
+
+def widgetName():
+ """ widgetName() -> str
+ Return the name of this widget plugin
+
+ """
+ return 'SVG Widgets'
+
+def registerWidget(reg, basicModules, basicWidgets):
+ """ registerWidget(reg: module_registry,
+ basicModules: python package,
+ basicWidgets: python package) -> None
+ Register all widgets in this package to VisTrails module_registry
+
+ """
+ reg.add_module(SVGCell)
+ reg.add_input_port(SVGCell, "Location", basicWidgets.CellLocation)
+ reg.add_input_port(SVGCell, "File", basicModules.File)
+
+ reg.add_module(SVGSplitter)
+ reg.add_input_port(SVGSplitter, "File", basicModules.File)
diff --git a/vistrails/packages/spreadsheet/widgets/svg/svg.py b/vistrails/packages/spreadsheet/widgets/svg/svg.py
new file mode 100644
index 0000000..f431983
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/svg/svg.py
@@ -0,0 +1,194 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# SVG widgets implementation
+################################################################################
+from vistrails.core.modules.basic_modules import File
+from vistrails.core.modules.vistrails_module import Module
+from PyQt4 import QtCore, QtGui, QtSvg
+from vistrails.packages.spreadsheet.basic_widgets import SpreadsheetCell
+from vistrails.packages.spreadsheet.spreadsheet_base import StandardSingleCellSheetReference
+from vistrails.packages.spreadsheet.spreadsheet_controller import spreadsheetController
+from vistrails.packages.spreadsheet.spreadsheet_event import (DisplayCellEvent,
+ BatchDisplayCellEvent)
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+import shutil
+################################################################################
+
+class SVGCell(SpreadsheetCell):
+ """
+ SVGCell is a VisTrails Module that can display SVG files
+
+ """
+ def compute(self):
+ """ compute() -> None
+ Dispatch SVG file into the spreadshet for display
+ """
+ if self.hasInputFromPort("File"):
+ window = spreadsheetController.findSpreadsheetWindow()
+ file_to_display = self.getInputFromPort("File")
+ fileValue = window.file_pool.make_local_copy(file_to_display.name)
+ else:
+ fileValue = None
+ self.display(SVGCellWidget, (fileValue,))
+
+### SVG Cell widget type
+class SVGCellWidget(QCellWidget):
+ """
+ SVGCellWidget derives from QSvgWidget to dispay SVG contents and
+ received SVG file from the SVGCell
+
+ """
+ def __init__(self, parent=None):
+ """ SVGCellWidget(parent: QWidget) -> SVGCellWidget
+ Create a SVGCellWidget without any toolbar
+ """
+ QCellWidget.__init__(self, parent)
+ self.setLayout(QtGui.QVBoxLayout(self))
+
+ self.svgWidget = QtSvg.QSvgWidget()
+ self.layout().addWidget(self.svgWidget)
+
+ self.controlBarType = None
+ self.fileSrc = None
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple) -> None
+ Updates the contents of the SVG widget with a new file name
+
+ """
+ (fileValue,) = inputPorts
+ self.svgWidget.load(fileValue.name)
+ self.fileSrc = fileValue.name
+
+ def dumpToFile(self, filename):
+ if self.fileSrc is not None:
+ shutil.copyfile(self.fileSrc, filename)
+
+ def saveToPDF(self, filename):
+ printer = QtGui.QPrinter()
+ printer.setOutputFormat(QtGui.QPrinter.PdfFormat)
+ printer.setOutputFileName(filename)
+ b_rect = self.svgWidget.contentsRect()
+ printer.setPaperSize(QtCore.QSizeF(b_rect.width(), b_rect.height()),
+ QtGui.QPrinter.Point)
+ painter = QtGui.QPainter(printer)
+ self.svgWidget.render(painter, QtCore.QRectF(), b_rect)
+ painter.end()
+
+# A custom widget to displays SVG slide show
+class SVGSplitter(Module):
+ """
+ SVGSplitter is a special Module that can dispatch multiple SVG
+ files to the spreadsheet for displaying a slideshow
+
+ """
+ def compute(self):
+ """ compute() -> None
+ Use BatchDisplayCellEvent to display a serie of SVG files
+
+ """
+ if self.hasInputFromPort("File"):
+ fileValue = self.getInputFromPort("File")
+ else:
+ fileValue = None
+ if fileValue:
+ batchDisplayEvent = BatchDisplayCellEvent()
+ # FIXME: Will this work? there should be no
+ # self.currentVersion in the module (there is a
+ # self.version)
+ batchDisplayEvent.vistrail = (self.vistrailName,
+ self.currentVersion)
+ f = open(fileValue.name, 'r')
+ for line in f.read().split('\n'):
+ comps = line.split('|')
+ if len(comps)==2:
+ e = DisplayCellEvent()
+ e.sheetReference = StandardSingleCellSheetReference()
+ e.sheetReference.sheetName = comps[1]
+ e.cellType = SVGCellWidget
+ F = File()
+ from os.path import abspath, basename, dirname
+ F.name = (dirname(abspath(fileValue.name))+
+ '/'+basename(comps[0]))
+ e.inputPorts = (F,)
+ batchDisplayEvent.displayEvents.append(e)
+ f.close()
+ spreadsheetController.postEventToSpreadsheet(batchDisplayEvent)
+
+class SVGSaveAction(QtGui.QAction):
+ """
+ ImageViewerSaveAction is the action to save the image to file
+
+ """
+ def __init__(self, parent=None):
+ """ ImageViewerSaveAction(parent: QWidget) -> ImageViewerSaveAction
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/save.png"),
+ "&Save svg as...",
+ parent)
+ self.setStatusTip("Save svg to file")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+
+ fn = QtGui.QFileDialog.getSaveFileName(None, "Save svg as...",
+ "screenshot.png",
+ "SVG (*.svg);;PDF files (*.pdf)")
+ if fn:
+ if fn.lower().endswith("svg"):
+ cellWidget.dumpToFile(fn)
+ elif fn.lower().endswith("pdf"):
+ cellWidget.saveToPDF(fn)
+
+class SVGToolBar(QCellToolBar):
+ """
+ ImageViewerToolBar derives from CellToolBar to give the ImageViewerCellWidget
+ a customizable toolbar
+
+ """
+ def createToolBar(self):
+ """ createToolBar() -> None
+ This will get call initiallly to add customizable widgets
+
+ """
+ self.appendAction(SVGSaveAction(self))
diff --git a/vistrails/packages/spreadsheet/widgets/webview/__init__.py b/vistrails/packages/spreadsheet/widgets/webview/__init__.py
new file mode 100644
index 0000000..58d4880
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/webview/__init__.py
@@ -0,0 +1,59 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# WebView plugin for VisTrails Spreadsheet
+################################################################################
+from webview import WebViewCell
+
+################################################################################
+
+def widgetName():
+ """ widgetName() -> str
+ Return the name of this widget plugin
+
+ """
+ return 'WebKit Viewer'
+
+def registerWidget(reg, basicModules, basicWidgets):
+ """ registerWidget(reg: module_registry,
+ basicModules: python package,
+ basicWidgets: python package) -> None
+ Register all widgets in this package to VisTrails module_registry
+
+ """
+ reg.add_module(WebViewCell)
+ reg.add_input_port(WebViewCell, "Location", basicWidgets.CellLocation)
+ reg.add_input_port(WebViewCell, "url", basicModules.String)
+ reg.add_input_port(WebViewCell, "file", basicModules.File)
diff --git a/vistrails/packages/spreadsheet/widgets/webview/webview.py b/vistrails/packages/spreadsheet/widgets/webview/webview.py
new file mode 100644
index 0000000..58418ff
--- /dev/null
+++ b/vistrails/packages/spreadsheet/widgets/webview/webview.py
@@ -0,0 +1,110 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+############################################################################
+# web browser view implementation
+############################################################################
+from vistrails.core.modules.vistrails_module import Module
+from PyQt4 import QtCore, QtGui, QtWebKit
+from vistrails.packages.spreadsheet.basic_widgets import SpreadsheetCell
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellWidget
+import shutil
+############################################################################
+
+class WebViewCell(SpreadsheetCell):
+ """
+ WebViewCell is a custom Module to view URLs using WebKit
+
+ """
+ def compute(self):
+ """ compute() -> None
+ Dispatch the URL to the spreadsheet
+ """
+ if self.hasInputFromPort("url"):
+ urlValue = self.getInputFromPort("url")
+ fileValue = None
+ elif self.hasInputFromPort("file"):
+ fileValue = self.getInputFromPort("file")
+ urlValue = None
+ else:
+ fileValue = None
+ urlValue = None
+ self.display(WebViewCellWidget, (urlValue, fileValue))
+
+class WebViewCellWidget(QCellWidget):
+ """
+ WebViewCellWidget has a QTextBrowser to display HTML files
+
+ """
+ def __init__(self, parent=None):
+ """ WebViewCellWidget(parent: QWidget) -> WebViewCellWidget
+ Create a rich text cell without a toolbar
+
+ """
+ QCellWidget.__init__(self, parent)
+ self.setLayout(QtGui.QVBoxLayout(self))
+ self.browser = QtWebKit.QWebView()
+ self.layout().addWidget(self.browser)
+ self.browser.setMouseTracking(True)
+ self.urlSrc = None
+ # self.browser.controlBarType = None
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple) -> None
+ Updates the contents with a new changed in filename
+
+ """
+ self.urlSrc = None
+ (urlValue, fileValue) = inputPorts
+ if urlValue:
+ url = QtCore.QUrl(urlValue)
+ self.browser.load(url)
+ self.urlSrc = url
+ elif fileValue:
+ url = QtCore.QUrl.fromLocalFile(fileValue.name)
+ self.browser.load(url)
+ self.urlSrc = url
+ else:
+ self.browser.setHtml("No HTML file is specified!")
+
+ def dumpToFile(self, filename):
+ if self.urlSrc is not None:
+ shutil.copyfile(str(self.urlSrc.toLocalFile()), filename)
+
+ def saveToPDF(self, filename):
+ printer = QtGui.QPrinter()
+ printer.setOutputFormat(QtGui.QPrinter.PdfFormat)
+ printer.setOutputFileName(filename)
+ self.browser.print_(printer)
\ No newline at end of file
diff --git a/vistrails/packages/sql/__init__.py b/vistrails/packages/sql/__init__.py
new file mode 100644
index 0000000..ae81603
--- /dev/null
+++ b/vistrails/packages/sql/__init__.py
@@ -0,0 +1,47 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""
+SQL Scripting package. It supports MySQL and PostgreSQL.
+
+Preliminary work at adding DBConnection and SQLSource modules.
+Interfaces may change so don't write any critical code using this
+package!
+
+"""
+
+identifier = 'org.vistrails.vistrails.sql'
+name = 'SQL'
+version = '0.0.4'
+old_identifiers = ['edu.utah.sci.vistrails.sql']
diff --git a/vistrails/packages/sql/init.py b/vistrails/packages/sql/init.py
new file mode 100644
index 0000000..e6420bc
--- /dev/null
+++ b/vistrails/packages/sql/init.py
@@ -0,0 +1,225 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+from vistrails.core.bundles import py_import
+from PyQt4 import QtCore, QtGui
+import urllib
+
+from vistrails.core import debug
+from vistrails.core.modules.vistrails_module import Module, ModuleError, NotCacheable
+from vistrails.gui.modules.source_configure import SourceConfigurationWidget
+from vistrails.core.upgradeworkflow import UpgradeWorkflowHandler
+from vistrails.core.utils import PortAlreadyExists
+from vistrails.gui.theme import CurrentTheme
+
+MySQLdb = py_import('MySQLdb', {
+ 'pip': 'mysql-python',
+ 'linux-debian': 'python-mysqldb',
+ 'linux-ubuntu': 'python-mysqldb',
+ 'linux-fedora': 'MySQL-python'})
+
+psycopg2 = py_import('psycopg2', {
+ 'pip': 'psycopg2',
+ 'linux-debian':'python-psycopg2',
+ 'linux-ubuntu':'python-psycopg2',
+ 'linux-fedora':'python-psycopg2'})
+
+
+class QPasswordEntry(QtGui.QDialog):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ self.setModal(True)
+ self.setWindowTitle("Enter Password:")
+ self.setLayout(QtGui.QVBoxLayout())
+ hbox = QtGui.QHBoxLayout()
+ hbox.addWidget(QtGui.QLabel("Password:"))
+ self.line_edit = QtGui.QLineEdit()
+ self.line_edit.setEchoMode(QtGui.QLineEdit.Password)
+ hbox.addWidget(self.line_edit)
+ self.layout().addLayout(hbox)
+
+ bbox = QtGui.QHBoxLayout()
+ cancel = QtGui.QPushButton("Cancel")
+ ok = QtGui.QPushButton("OK")
+ ok.setDefault(True)
+ bbox.addWidget(cancel, 1, QtCore.Qt.AlignRight)
+ bbox.addWidget(ok, 0, QtCore.Qt.AlignRight)
+ self.layout().addLayout(bbox)
+ self.connect(ok, QtCore.SIGNAL("clicked(bool)"), self.accept)
+ self.connect(cancel, QtCore.SIGNAL("clicked(bool)"), self.reject)
+
+ def get_password(self):
+ return str(self.line_edit.text())
+
+class DBConnection(Module):
+ def __init__(self):
+ Module.__init__(self)
+ self.conn = None
+ self.protocol = 'mysql'
+
+ def get_db_lib(self):
+ if self.protocol == 'mysql':
+ return MySQLdb
+ elif self.protocol == 'postgresql':
+ return psycopg2
+ else:
+ raise ModuleError(self, "Currently no support for '%s'" % protocol)
+
+ def ping(self):
+ """ping() -> boolean
+ It will ping the database to check if the connection is alive.
+ It returns True if it is, False otherwise.
+ This can be used for preventing the "MySQL Server has gone away" error.
+ """
+ result = False
+ if self.conn:
+ try:
+ self.conn.ping()
+ result = True
+ except self.get_db_lib().OperationalError, e:
+ result = False
+ except AttributeError, e:
+ #psycopg2 connections don't have a ping method
+ try:
+ if self.conn.status == 1:
+ result = True
+ except Exception, e:
+ result = False
+ return result
+
+ def open(self):
+ retry = True
+ while retry:
+ config = {'host': self.host,
+ 'port': self.port,
+ 'user': self.user}
+
+ # unfortunately keywords are not standard across libraries
+ if self.protocol == 'mysql':
+ config['db'] = self.db_name
+ if self.password is not None:
+ config['passwd'] = self.password
+ elif self.protocol == 'postgresql':
+ config['database'] = self.db_name
+ if self.password is not None:
+ config['password'] = self.password
+ try:
+ self.conn = self.get_db_lib().connect(**config)
+ break
+ except self.get_db_lib().Error, e:
+ debug.warning(str(e))
+ if (e[0] == 1045 or self.get_db_lib().OperationalError
+ and self.password is None):
+ passwd_dlg = QPasswordEntry()
+ if passwd_dlg.exec_():
+ self.password = passwd_dlg.get_password()
+ else:
+ retry = False
+ else:
+ raise ModuleError(self, str(e))
+
+ def compute(self):
+ self.checkInputPort('db_name')
+ self.host = self.forceGetInputFromPort('host', 'localhost')
+ self.port = self.forceGetInputFromPort('port', 3306)
+ self.user = self.forceGetInputFromPort('user', None)
+ self.db_name = self.getInputFromPort('db_name')
+ self.protocol = self.forceGetInputFromPort('protocol', 'mysql')
+ if self.hasInputFromPort('password'):
+ self.password = self.getInputFromPort('password')
+ else:
+ self.password = None
+
+ self.open()
+
+ # nice to have enumeration constant type
+ _input_ports = [('host', '(basic:String)'),
+ ('port', '(basic:Integer)'),
+ ('user', '(basic:String)'),
+ ('db_name', '(basic:String)'),
+ ('protocol', '(basic:String)')]
+ _output_ports = [('self', '(DBConnection)')]
+
+class SQLSource(Module):
+ def __init__(self):
+ Module.__init__(self)
+ self.is_cacheable = self.cachedOff
+
+ def compute(self):
+ cached = False
+ if self.hasInputFromPort('cacheResults'):
+ cached = self.getInputFromPort('cacheResults')
+ self.checkInputPort('connection')
+ connection = self.getInputFromPort('connection')
+ inputs = [self.getInputFromPort(k) for k in self.inputPorts
+ if k != 'source' and k != 'connection' and k!= 'cacheResults']
+ #print 'inputs:', inputs
+ s = urllib.unquote(str(self.forceGetInputFromPort('source', '')))
+ if not connection.ping():
+ connection.open()
+ cur = connection.conn.cursor()
+ cur.execute(s, inputs)
+
+ if cached:
+ self.is_cacheable = self.cachedOn
+ else:
+ self.is_cacheable = self.cachedOff
+
+ self.setResult('resultSet', cur.fetchall())
+
+ def cachedOn(self):
+ return True
+
+ def cachedOff(self):
+ return False
+
+ _input_ports = [('connection', '(DBConnection)'),
+ ('cacheResults', '(basic:Boolean)'),
+ ('source', '(basic:String)')]
+ _output_ports = \
+ [('resultSet', '(basic:List)')]
+
+class SQLSourceConfigurationWidget(SourceConfigurationWidget):
+ def __init__(self, module, controller, parent=None):
+ SourceConfigurationWidget.__init__(self, module, controller, None,
+ True, False, parent)
+
+_modules = [DBConnection,
+ (SQLSource, {'configureWidgetType': SQLSourceConfigurationWidget})]
+
+def handle_module_upgrade_request(controller, module_id, pipeline):
+ module_remap = {'SQLSource': [(None, '0.0.3', None, {})]}
+
+ return UpgradeWorkflowHandler.remap_module(controller, module_id, pipeline,
+ module_remap)
diff --git a/vistrails/packages/tabledata/__init__.py b/vistrails/packages/tabledata/__init__.py
new file mode 100644
index 0000000..6b7d29f
--- /dev/null
+++ b/vistrails/packages/tabledata/__init__.py
@@ -0,0 +1,29 @@
+"""Table data package for VisTrails.
+
+This package contains data extraction and manipulation facilities. It wraps
+numpy and csv and allows the use of several file types from VisTrails, with
+extraction and conversion routines.
+
+"""
+
+from vistrails.core.packagemanager import get_package_manager
+
+from identifiers import *
+
+
+def package_dependencies():
+ pm = get_package_manager()
+ if pm.has_package('org.vistrails.vistrails.spreadsheet'):
+ return ['org.vistrails.vistrails.spreadsheet']
+ else:
+ return []
+
+
+def package_requirements():
+ from vistrails.core.requirements import require_python_module
+ require_python_module('numpy', {
+ 'pip': 'numpy',
+ 'linux-debian': 'python-numpy',
+ 'linux-ubuntu': 'python-numpy',
+ 'linux-fedora': 'numpy'})
+ require_python_module('csv')
diff --git a/vistrails/packages/tabledata/common.py b/vistrails/packages/tabledata/common.py
new file mode 100644
index 0000000..0f5be29
--- /dev/null
+++ b/vistrails/packages/tabledata/common.py
@@ -0,0 +1,64 @@
+from vistrails.core.modules.vistrails_module import Module, ModuleError
+
+
+class Table(Module):
+ columns = None
+ rows = None
+
+ names = None
+
+ def get_column(self, i):
+ raise NotImplementedError
+
+
+class ExtractColumn(Module):
+ _input_ports = [
+ ('table', Table),
+ ('column_name', '(org.vistrails.vistrails.basic:String)',
+ {'optional': True}),
+ ('column_index', '(org.vistrails.vistrails.basic:Integer)',
+ {'optional': True}),
+ ('numeric', '(org.vistrails.vistrails.basic:Boolean)',
+ {'optional': True, 'defaults': "['False']"})]
+ _output_ports = [
+ ('value', '(org.vistrails.vistrails.basic:List)')]
+
+ def compute(self):
+ table = self.getInputFromPort('table')
+ if self.hasInputFromPort('column_index'):
+ column_index = self.getInputFromPort('column_index')
+ if self.hasInputFromPort('column_name'):
+ name = self.getInputFromPort('column_name')
+ if isinstance(name, unicode):
+ name = name.encode('utf-8')
+ if table.names is None:
+ raise ModuleError("Unable to get column by names: table "
+ "doesn't have column names")
+ try:
+ index = table.names.index(name)
+ except ValueError:
+ try:
+ name = name.strip()
+ index = table.column_names.index(name)
+ except:
+ raise ModuleError(self, "Column name was not found")
+ if self.hasInputFromPort('column_index'):
+ if column_index != index:
+ raise ModuleError(self,
+ "Both column_name and column_index were "
+ "specified, and they don't agree")
+ elif self.hasInputFromPort('column_index'):
+ index = column_index
+ else:
+ raise ModuleError(self,
+ "You must set one of column_name or "
+ "column_index")
+
+ result = table.get_column(
+ index,
+ numeric=self.getInputFromPort('numeric', allowDefault=True))
+
+ self.setResult('value', result)
+
+
+_modules = [(Table, {'abstract': True}), ExtractColumn]
diff --git a/vistrails/packages/tabledata/convert/__init__.py b/vistrails/packages/tabledata/convert/__init__.py
new file mode 100644
index 0000000..d369879
--- /dev/null
+++ b/vistrails/packages/tabledata/convert/__init__.py
@@ -0,0 +1,6 @@
+from vistrails.core.modules.utils import make_modules_dict
+
+from convert_dates import _modules as dates_modules
+
+
+_modules = make_modules_dict(dates_modules, namespace='convert')
diff --git a/vistrails/packages/tabledata/convert/convert_dates.py b/vistrails/packages/tabledata/convert/convert_dates.py
new file mode 100644
index 0000000..6e4e6af
--- /dev/null
+++ b/vistrails/packages/tabledata/convert/convert_dates.py
@@ -0,0 +1,580 @@
+import datetime
+from distutils.version import LooseVersion
+import re
+import time
+import warnings
+
+from vistrails.core.modules.vistrails_module import Module, ModuleError
+from vistrails.core.bundles import py_import
+
+
+class UTC(datetime.tzinfo):
+ def utcoffset(self, dt):
+ return datetime.timedelta(0)
+
+ def tzname(self, dt):
+ return "UTC"
+
+ def dst(self, dt):
+ return datetime.timedelta(0)
+
+utc = UTC()
+
+
+class FixedOffset(datetime.tzinfo):
+ def __init__(self, offset, name):
+ self.offset = offset
+ self.name = name
+
+ def utcoffset(self, dt):
+ return self.offset
+
+ def tzname(self, dt):
+ return self.name
+
+ def dst(self, dt):
+ return datetime.timedelta(0)
+
+
+class LocalTimezone(datetime.tzinfo):
+ STDOFFSET = datetime.timedelta(seconds=time.timezone)
+ if time.daylight:
+ DSTOFFSET = datetime.timedelta(seconds=-time.altzone)
+ else:
+ DSTOFFSET = STDOFFSET
+
+ DSTDIFF = DSTOFFSET - STDOFFSET
+
+ def utcoffset(self, dt):
+ if self._isdst(dt):
+ return self.DSTOFFSET
+ else:
+ return self.STDOFFSET
+
+ def dst(self, dt):
+ if self._isdst(dt):
+ return self.DSTDIFF
+ else:
+ return datetime.timedelta(0)
+
+ def tzname(self, dt):
+ return time.tzname[self._isdst(dt)]
+
+ def _isdst(self, dt):
+ tt = (dt.year, dt.month, dt.day,
+ dt.hour, dt.minute, dt.second,
+ dt.weekday(), 0, 0)
+ timestamp = time.mktime(tt)
+ tt = time.localtime(timestamp)
+ return tt.tm_isdst > 0
+
+
+_decimal_fmt = re.compile(
+ r'^'
+ '([-+]?)' # + means we are advancing compared to UTC
+ '([0-9]?[0-9])' # hours
+ '([0-9][0-9])?$') # minutes
+
+def make_timezone(s):
+ if s == 'local':
+ return LocalTimezone()
+
+ match = _decimal_fmt.match(s)
+ if match is not None:
+ sign, hours, minutes = match.groups('')
+ sign = -1 if sign == '-' else 1
+ hours = int(hours)
+ minutes = int(minutes) if minutes else 0
+ offset = datetime.timedelta(
+ minutes=sign * (hours*60 + minutes))
+ name = '%s%02d%02d' % (
+ '-' if sign == -1 else '+',
+ hours,
+ minutes)
+ return FixedOffset(offset, name)
+
+ try:
+ pytz = py_import('pytz', {
+ 'pip': 'pytz',
+ 'linux-debian': 'python-tz',
+ 'linux-ubuntu': 'python-tz',
+ 'linux-fedora': 'pytz'})
+ except ImportError:
+ raise ValueError("can't understand timezone %r (maybe you should "
+ "install pytz?)" % s)
+ else:
+ ver = LooseVersion(pytz.__version__)
+ if ver < LooseVersion('2012'):
+ warnings.warn(
+ "You are using an old version of pytz (%s). You might "
+ "run into some issues with daylight saving handling." %
+ pytz.__version__,
+ category=UserWarning)
+ try:
+ return pytz.timezone(s)
+ except KeyError:
+ raise ValueError("can't understand timezone %r (defaulted to "
+ "pytz, which gave no answer)" % s)
+
+
+class TimestampsToDates(Module):
+ """
+ Converts a List or numpy array of timestamps into datetime objects.
+
+ A UNIX timestamp represents the number of seconds since Jan 1 1970 0:00,
+ UTC. It represents a specific point in time that is not dependent on a
+ timezone.
+ The returned datetime objects are in the UTC timezone.
+ """
+ _input_ports = [
+ ('timestamps', '(org.vistrails.vistrails.basic:List)')]
+ _output_ports = [
+ ('dates', '(org.vistrails.vistrails.basic:List)')]
+
+ @staticmethod
+ def convert(timestamps):
+ return [datetime.datetime.fromtimestamp(t, utc) for t in timestamps]
+
+ def compute(self):
+ timestamps = self.getInputFromPort('timestamps')
+
+ result = self.convert(timestamps)
+ self.setResult('dates', result)
+
+
+class StringsToDates(Module):
+ """
+ Converts a List of dates (as strings) into datetime objects.
+
+ If no format is given, the dateutil.parser module will be used to guess
+ what each string refers to; else, it is passed to strptime() to read each
+ date. For example: '%Y-%m-%d %H:%M:%S'.
+ The 'timezone' parameter indicates which timezone these dates are expressed
+ in. It can be either:
+ * 'local', in which case each date is interpreted as being in whatever
+ timezone the system is set to use;
+ * an offset in hours/minutes from UTC, for instance '-0400' for DST
+ (eastern America time, when daylight saving is in effect). Note that in
+ this case, the same offset is used for every date, without regard for
+ daylight saving (if a date falls in winter, '-0500' will not be used
+ instead).
+ * if pytz is available, anything else will be passed to pytz.timezone(),
+ so you would be able to use strings such as 'US/Eastern' or
+ 'Europe/Amsterdam'.
+ """
+ _input_ports = [
+ ('strings', '(org.vistrails.vistrails.basic:List)'),
+ ('format', '(org.vistrails.vistrails.basic:String)',
+ {'optional': True, 'defaults': "['']"}),
+ ('timezone', '(org.vistrails.vistrails.basic:String)',
+ {'optional': True, 'defaults': "['']"})]
+ _output_ports = [
+ ('dates', '(org.vistrails.vistrails.basic:List)')]
+
+ @staticmethod
+ def convert(strings, fmt, tz):
+ if tz:
+ tz = make_timezone(tz) # Might raise ValueError
+ else:
+ tz = None
+
+ if not fmt:
+ try:
+ py_import('dateutil', {
+ 'pip': 'python-dateutil',
+ 'linux-debian': 'python-dateutil',
+ 'linux-ubuntu': 'python-dateutil',
+ 'linux-fedora': 'python-dateutil'})
+ except ImportError:
+ raise ValueError("can't read dates without a format without "
+ "the dateutil package")
+ from dateutil import parser
+ result = [parser.parse(s, ignoretz=tz is not None)
+ for s in strings]
+ else:
+ result = [datetime.datetime.strptime(s, fmt) for s in strings]
+
+ if tz:
+ # Compute the time without daylight saving
+ result = [dt.replace(tzinfo=tz) for dt in result]
+
+ # Check if it is in fact during daylight saving
+ if hasattr(tz, 'normalize'):
+ for i in xrange(len(result)):
+ dt = result[i]
+ dst = tz.dst(dt.replace(tzinfo=None))
+ if dst:
+ result[i] = tz.normalize(dt) - dst
+ # This is close enough but the way this work is by
+ # essence ambiguous
+ # If the given datetime falls right during the time
+ # change period (one hour, two times a year):
+ # For standard -> dst (spring): the time will be in
+ # dst, although it doesn't actually exist (we stepped
+ # over it by changing the clock)
+ # For dst -> standard (fall): the time will be in dst,
+ # although it could also have been standard (there is
+ # noway to know which one was meant)
+ else:
+ result = [dt.replace(tzinfo=None) for dt in result]
+
+ return result
+
+ def compute(self):
+ tz = self.getInputFromPort('timezone')
+
+ strings = self.getInputFromPort('strings')
+ fmt = self.getInputFromPort('format')
+
+ try:
+ result = self.convert(strings, fmt, tz)
+ except ValueError, e:
+ raise ModuleError(self, e.message)
+ self.setResult('dates', result)
+
+
+class DatesToMatplotlib(Module):
+ """
+ Converts a List of Python's datetime objects to an array for matplotlib.
+ """
+ _input_ports = [('datetimes', '(org.vistrails.vistrails.basic:List)')]
+ _output_ports = [('dates', '(org.vistrails.vistrails.basic:List)')]
+
+ @staticmethod
+ def convert(datetimes):
+ from matplotlib.dates import date2num
+ return date2num(datetimes)
+
+ def compute(self):
+ try:
+ py_import('matplotlib', {
+ 'pip': 'matplotlib',
+ 'linux-debian': 'python-matplotlib',
+ 'linux-ubuntu': 'python-matplotlib',
+ 'linux-fedora': 'python-matplotlib'})
+ except ImportError:
+ raise ModuleError(self, "matplotlib is not available")
+
+ datetimes = self.getInputFromPort('datetimes')
+ result = self.convert(datetimes)
+ self.setResult('dates', result)
+
+
+class TimestampsToMatplotlib(Module):
+ """
+ Converts a List or numpy array of timestamps into an array for matplotlib.
+ """
+ _input_ports = [
+ ('timestamps', '(org.vistrails.vistrails.basic:List)')]
+ _output_ports = [
+ ('dates', '(org.vistrails.vistrails.basic:List)')]
+
+ @staticmethod
+ def convert(timestamps):
+ from matplotlib.dates import date2num
+ result = TimestampsToDates.convert(timestamps)
+ return date2num(result)
+
+ def compute(self):
+ try:
+ py_import('matplotlib', {
+ 'pip': 'matplotlib',
+ 'linux-debian': 'python-matplotlib',
+ 'linux-ubuntu': 'python-matplotlib',
+ 'linux-fedora': 'python-matplotlib'})
+ except ImportError:
+ raise ModuleError(self, "matplotlib is not available")
+
+ timestamps = self.getInputFromPort('timestamps')
+ result = self.convert(timestamps)
+ self.setResult('dates', result)
+
+
+class StringsToMatplotlib(Module):
+ """
+ Converts a List of dates (as strings) to an array accepted by matplotlib.
+ """
+ _input_ports = [
+ ('strings', '(org.vistrails.vistrails.basic:List)'),
+ ('format', '(org.vistrails.vistrails.basic:String)',
+ {'optional': True, 'defaults': "['']"}),
+ ('timezone', '(org.vistrails.vistrails.basic:String)',
+ {'optional': True, 'defaults': "['']"})]
+ _output_ports = [
+ ('dates', '(org.vistrails.vistrails.basic:List)')]
+
+ @staticmethod
+ def convert(strings, fmt, tz):
+ from matplotlib.dates import date2num
+ datetimes = StringsToDates.convert(strings, fmt, tz)
+ return date2num(datetimes)
+
+ def compute(self):
+ try:
+ py_import('matplotlib', {
+ 'pip': 'matplotlib',
+ 'linux-debian': 'python-matplotlib',
+ 'linux-ubuntu': 'python-matplotlib',
+ 'linux-fedora': 'python-matplotlib'})
+ except ImportError:
+ raise ModuleError(self, "matplotlib is not available")
+
+ tz = self.getInputFromPort('timezone')
+
+ strings = self.getInputFromPort('strings')
+ fmt = self.getInputFromPort('format')
+
+ try:
+ result = self.convert(strings, fmt, tz)
+ except ValueError, e:
+ raise ModuleError(self, e.message)
+ self.setResult('dates', result)
+
+
+_modules = {'dates': [
+ TimestampsToDates, StringsToDates,
+ DatesToMatplotlib, TimestampsToMatplotlib, StringsToMatplotlib]}
+
+
+###############################################################################
+
+import unittest
+from vistrails.tests.utils import execute, intercept_result
+from ..identifiers import identifier
+
+
+class TestTimestampToDates(unittest.TestCase):
+ def test_timestamps(self):
+ """Test conversion to datetime objects.
+ """
+ timestamps = [1369041900, 1369042260, 1357153500]
+ with intercept_result(TimestampsToDates, 'dates') as results:
+ self.assertFalse(execute([
+ ('convert|dates|TimestampsToDates', identifier, [
+ ('timestamps', [('List', repr(timestamps))]),
+ ]),
+ ]))
+ self.assertEqual(len(results), 1)
+ results = results[0]
+ self.assertTrue(all(d.tzinfo is utc for d in results))
+ fmt = '%Y-%m-%d %H:%M:%S %Z %z'
+ self.assertEqual(
+ [d.strftime(fmt) for d in results],
+ ['2013-05-20 09:25:00 UTC +0000',
+ '2013-05-20 09:31:00 UTC +0000',
+ '2013-01-02 19:05:00 UTC +0000'])
+ try:
+ import pytz
+ except ImportError:
+ pass
+ else:
+ self.assertEqual(
+ [d.astimezone(pytz.timezone('US/Eastern')).strftime(fmt)
+ for d in results],
+ ['2013-05-20 05:25:00 EDT -0400',
+ '2013-05-20 05:31:00 EDT -0400',
+ '2013-01-02 14:05:00 EST -0500'])
+
+
+class TestStringsToDates(unittest.TestCase):
+ def test_naive(self):
+ """Test reading non-timezone-aware dates.
+ """
+ dates = ['2013-05-20 9:25', '2013-05-20 09:31', '2013-01-02 19:05']
+ in_fmt = '%Y-%m-%d %H:%M'
+ with intercept_result(StringsToDates, 'dates') as results:
+ self.assertFalse(execute([
+ ('convert|dates|StringsToDates', identifier, [
+ ('strings', [('List', repr(dates))]),
+ ('format', [('String', in_fmt)]),
+ ]),
+ ]))
+ self.assertEqual(len(results), 1)
+ results = results[0]
+ self.assertTrue(all(d.tzinfo is None for d in results))
+ fmt = '%Y-%m-%d %H:%M:%S %Z %z'
+ self.assertEqual(
+ [d.strftime(fmt) for d in results],
+ ['2013-05-20 09:25:00 ',
+ '2013-05-20 09:31:00 ',
+ '2013-01-02 19:05:00 '])
+
+ def test_dateutil(self):
+ """Test reading non-timezone-aware dates without providing the format.
+
+ dateutil is required for this one.
+ """
+ try:
+ import dateutil
+ except ImportError:
+ self.skipTest("dateutil is not available")
+
+ dates = ['2013-05-20 9:25',
+ 'Thu Sep 25 10:36:26 2003',
+ '2003 10:36:28 CET 25 Sep Thu'] # Timezone will be ignored
+ with intercept_result(StringsToDates, 'dates') as results:
+ self.assertFalse(execute([
+ ('convert|dates|StringsToDates', identifier, [
+ ('strings', [('List', repr(dates))]),
+ ]),
+ ]))
+ self.assertEqual(len(results), 1)
+ results = results[0]
+ fmt = '%Y-%m-%d %H:%M:%S %Z %z'
+ self.assertEqual(
+ [d.strftime(fmt) for d in results],
+ ['2013-05-20 09:25:00 ',
+ '2003-09-25 10:36:26 ',
+ '2003-09-25 10:36:28 '])
+
+ def test_timezone(self):
+ """Test reading timezone-aware dates by supplying an offset.
+ """
+ dates = ['2013-05-20 9:25', '2013-05-20 09:31', '2013-01-02 19:05']
+ in_fmt = '%Y-%m-%d %H:%M'
+ with intercept_result(StringsToDates, 'dates') as results:
+ self.assertFalse(execute([
+ ('convert|dates|StringsToDates', identifier, [
+ ('strings', [('List', repr(dates))]),
+ ('format', [('String', in_fmt)]),
+ ('timezone', [('String', '-0500')])
+ ]),
+ ]))
+ self.assertEqual(len(results), 1)
+ results = results[0]
+ self.assertTrue(all(d.tzinfo is not None for d in results))
+ fmt = '%Y-%m-%d %H:%M:%S %z'
+ self.assertEqual(
+ [d.strftime(fmt) for d in results],
+ ['2013-05-20 09:25:00 -0500',
+ '2013-05-20 09:31:00 -0500',
+ '2013-01-02 19:05:00 -0500'])
+
+ def test_timezone_pytz(self):
+ """Test reading timezone-aware dates through pytz.
+ """
+ try:
+ import pytz
+ except ImportError:
+ self.skipTest("pytz is not available")
+ if LooseVersion(pytz.__version__) < LooseVersion('2012'):
+ self.skipTest("pytz version is known to cause issues (%s)" %
+ pytz.__version__)
+
+ dates = ['2013-01-20 9:25', '2013-01-20 09:31', '2013-06-02 19:05']
+ in_fmt = '%Y-%m-%d %H:%M'
+ with intercept_result(StringsToDates, 'dates') as results:
+ self.assertFalse(execute([
+ ('convert|dates|StringsToDates', identifier, [
+ ('strings', [('List', repr(dates))]),
+ ('format', [('String', in_fmt)]),
+ ('timezone', [('String', 'America/New_York')])
+ ]),
+ ]))
+ self.assertEqual(len(results), 1)
+ results = results[0]
+ self.assertTrue(all(d.tzinfo is not None for d in results))
+ fmt = '%Y-%m-%d %H:%M:%S %Z %z'
+ self.assertEqual(
+ [d.strftime(fmt) for d in results],
+ ['2013-01-20 09:25:00 EST -0500',
+ '2013-01-20 09:31:00 EST -0500',
+ '2013-06-02 19:05:00 EDT -0400'])
+
+
+class TestDatesToMatplotlib(unittest.TestCase):
+ def test_simple(self):
+ """Test converting datetime objects into matplotlib's format.
+
+ This uses a PythonSource module to emit the datetime objects.
+ """
+ try:
+ import matplotlib
+ except ImportError:
+ self.skipTest("matplotlib is not available")
+
+ from matplotlib.dates import date2num
+
+ import urllib2
+ source = (""
+ "import datetime\n"
+ "from vistrails.packages.tabledata.convert.convert_dates import \\\n"
+ " make_timezone\n"
+ "datetimes = [\n"
+ " datetime.datetime(2013, 5, 29, 11, 18, 33),\n"
+ " datetime.datetime(2013, 5, 29, 8, 11, 47,\n"
+ " tzinfo=make_timezone('-0700'))]\n")
+ source = urllib2.quote(source)
+
+ with intercept_result(DatesToMatplotlib, 'dates') as results:
+ self.assertFalse(execute([
+ ('PythonSource', 'org.vistrails.vistrails.basic', [
+ ('source', [('String', source)]),
+ ]),
+ ('convert|dates|DatesToMatplotlib', identifier, []),
+ ],
+ [
+ (0, 'datetimes', 1, 'datetimes')
+ ],
+ add_port_specs=[
+ (0, 'output', 'datetimes',
+ 'org.vistrails.vistrails.basic:List'),
+ ]))
+ self.assertEqual(len(results), 1)
+ results = results[0]
+ self.assertEqual(list(results), list(date2num([
+ datetime.datetime(2013, 5, 29, 11, 18, 33),
+ datetime.datetime(2013, 5, 29, 15, 11, 47)])))
+
+
+class TestTimestampsToMatplotlib(unittest.TestCase):
+ def test_simple(self):
+ """Test converting timestamps into matplotlib's format.
+ """
+ try:
+ import matplotlib
+ except ImportError:
+ self.skipTest("matplotlib is not available")
+
+ from matplotlib.dates import date2num
+
+ with intercept_result(TimestampsToMatplotlib, 'dates') as results:
+ self.assertFalse(execute([
+ ('convert|dates|TimestampsToMatplotlib', identifier, [
+ ('timestamps', [('List', '[1324842375, 1369842877]')]),
+ ]),
+ ]))
+ self.assertEqual(len(results), 1)
+ results = results[0]
+ self.assertEqual(list(results), list(date2num([
+ datetime.datetime.utcfromtimestamp(1324842375),
+ datetime.datetime.utcfromtimestamp(1369842877)])))
+
+
+class TestStringsToMatplotlib(unittest.TestCase):
+ def test_timezone(self):
+ """Test reading timezone-aware dates by supplying an offset.
+ """
+ try:
+ import matplotlib
+ except ImportError:
+ self.skipTest("matplotlib is not available")
+
+ from matplotlib.dates import date2num
+
+ dates = ['2013-05-20 9:25', '2013-05-20 09:31', '2013-01-02 18:05']
+ in_fmt = '%Y-%m-%d %H:%M'
+ with intercept_result(StringsToMatplotlib, 'dates') as results:
+ self.assertFalse(execute([
+ ('convert|dates|StringsToMatplotlib', identifier, [
+ ('strings', [('List', repr(dates))]),
+ ('format', [('String', in_fmt)]),
+ ('timezone', [('String', '-0500')])
+ ]),
+ ]))
+ self.assertEqual(len(results), 1)
+ results = results[0]
+ self.assertEqual(list(results), list(date2num([
+ datetime.datetime(2013, 5, 20, 14, 25, 0),
+ datetime.datetime(2013, 5, 20, 14, 31, 0),
+ datetime.datetime(2013, 1, 2, 23, 5, 0)])))
diff --git a/vistrails/packages/tabledata/identifiers.py b/vistrails/packages/tabledata/identifiers.py
new file mode 100644
index 0000000..81fb4b9
--- /dev/null
+++ b/vistrails/packages/tabledata/identifiers.py
@@ -0,0 +1,3 @@
+identifier = 'org.vistrails.vistrails.tabledata'
+name = 'tabledata'
+version = '0.1.0'
diff --git a/vistrails/packages/tabledata/init.py b/vistrails/packages/tabledata/init.py
new file mode 100644
index 0000000..cf1df2d
--- /dev/null
+++ b/vistrails/packages/tabledata/init.py
@@ -0,0 +1,17 @@
+from vistrails.core.modules.utils import make_modules_dict
+from vistrails.core.packagemanager import get_package_manager
+
+from .common import _modules as common_modules
+from .convert import _modules as convert_modules
+from .read import _modules as read_modules
+
+
+_modules = [common_modules,
+ convert_modules,
+ read_modules]
+
+if get_package_manager().has_package('org.vistrails.vistrails.spreadsheet'):
+ from .viewer import _modules as viewer_modules
+ _modules.append(viewer_modules)
+
+_modules = make_modules_dict(*_modules)
diff --git a/vistrails/packages/tabledata/read/__init__.py b/vistrails/packages/tabledata/read/__init__.py
new file mode 100644
index 0000000..ae083df
--- /dev/null
+++ b/vistrails/packages/tabledata/read/__init__.py
@@ -0,0 +1,7 @@
+from vistrails.core.modules.utils import make_modules_dict
+
+from read_numpy import _modules as numpy_modules
+from read_csv import _modules as csv_modules
+
+
+_modules = make_modules_dict(numpy_modules, csv_modules, namespace='read')
diff --git a/vistrails/packages/tabledata/read/read_csv.py b/vistrails/packages/tabledata/read/read_csv.py
new file mode 100644
index 0000000..65f8ddc
--- /dev/null
+++ b/vistrails/packages/tabledata/read/read_csv.py
@@ -0,0 +1,241 @@
+import csv
+from itertools import izip
+import numpy
+
+from vistrails.core.modules.vistrails_module import ModuleError
+from ..common import Table
+
+
+def count_lines(fp):
+ lines = 0
+ for line in fp:
+ lines += 1
+ return lines
+
+
+class CSVFile(Table):
+ _input_ports = [
+ ('file', '(org.vistrails.vistrails.basic:File)'),
+ ('delimiter', '(org.vistrails.vistrails.basic:String)',
+ {'optional': True}),
+ ('header_present', '(org.vistrails.vistrails.basic:Boolean)',
+ {'optional': True, 'defaults': "['True']"})]
+ _output_ports = [
+ ('column_count', '(org.vistrails.vistrails.basic:Integer)'),
+ ('column_names', '(org.vistrails.vistrails.basic:List)'),
+ ('self', '(org.vistrails.vistrails.tabledata:read|csv|CSVFile)')]
+
+ _STANDARD_DELIMITERS = [';', ',', '\t', '|']
+
+ def __init__(self):
+ Table.__init__(self)
+ self._rows = None
+
+ @staticmethod
+ def read_file(filename, delimiter=None, header_present=True):
+ try:
+ with open(filename, 'rb') as fp:
+ first_line = fp.readline()
+ if delimiter is None:
+ counts = [first_line.count(d)
+ for d in CSVFile._STANDARD_DELIMITERS]
+ read_delimiter, count = max(
+ izip(CSVFile._STANDARD_DELIMITERS, counts),
+ key=lambda (delim, count): count)
+ if count == 0:
+ raise ModuleError(self,
+ "Couldn't guess the field delimiter")
+ else:
+ delimiter = read_delimiter
+ else:
+ count = first_line.count(delimiter)
+
+ column_count = count + 1
+
+ if header_present:
+ column_names = [
+ name.strip()
+ for name in first_line.split(delimiter)]
+ else:
+ column_names = None
+ except IOError:
+ raise ModuleError(self, "File does not exist")
+
+ return column_count, column_names, delimiter
+
+ def compute(self):
+ csv_file = self.getInputFromPort('file').name
+ self.header_present = self.getInputFromPort('header_present',
+ allowDefault=True)
+ if self.hasInputFromPort('delimiter'):
+ self.delimiter = self.getInputFromPort('delimiter')
+ else:
+ self.delimiter = None
+
+ self.filename = csv_file
+
+ self.columns, self.names, self.delimiter = \
+ self.read_file(csv_file, self.delimiter, self.header_present)
+
+ self.column_cache = {}
+
+ self.setResult('column_count', self.columns)
+ self.setResult('column_names', self.names)
+
+ def get_column(self, index, numeric=False):
+ if index in self.column_cache:
+ return self.column_cache[index]
+
+ if numeric:
+ result = numpy.loadtxt(
+ self.filename,
+ dtype=numpy.float32,
+ delimiter=self.delimiter,
+ skiprows=1 if self.header_present else 0,
+ usecols=[index])
+ else:
+ with open(self.filename, 'rb') as fp:
+ if self.header_present:
+ fp.readline()
+ reader = csv.reader(
+ fp,
+ delimiter=self.delimiter)
+ result = [row[index] for row in reader]
+
+ self.column_cache[index] = result
+ return result
+
+ @property
+ def rows(self):
+ if self._rows is not None:
+ return self._rows
+ with open(self.filename, 'rb') as fp:
+ self._rows = count_lines(fp)
+ if self.header_present:
+ self._rows -= 1
+ return self._rows
+
+
+_modules = {'csv': [CSVFile]}
+
+
+###############################################################################
+
+from StringIO import StringIO
+import unittest
+from vistrails.tests.utils import execute, intercept_result
+from ..identifiers import identifier
+from ..common import ExtractColumn
+
+
+class CSVTestCase(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ import os
+ cls._test_dir = os.path.join(
+ os.path.dirname(__file__),
+ os.pardir,
+ 'test_files')
+
+ def test_csv_numeric(self):
+ """Uses CSVFile and ExtractColumn to load a numeric array.
+ """
+ with intercept_result(ExtractColumn, 'value') as results:
+ with intercept_result(CSVFile, 'column_count') as columns:
+ self.assertFalse(execute([
+ ('read|csv|CSVFile', identifier, [
+ ('file', [('File', self._test_dir + '/test.csv')]),
+ ]),
+ ('ExtractColumn', identifier, [
+ ('column_index', [('Integer', '1')]),
+ ('column_name', [('String', 'col 2')]),
+ ('numeric', [('Boolean', 'True')]),
+ ]),
+ ('PythonSource', 'org.vistrails.vistrails.basic', [
+ ('source', [('String', '')]),
+ ]),
+ ],
+ [
+ (0, 'self', 1, 'table'),
+ (1, 'value', 2, 'l'),
+ ],
+ add_port_specs=[
+ (2, 'input', 'l',
+ 'org.vistrails.vistrails.basic:List'),
+ ]))
+ # Here we use a PythonSource just to check that a numpy array
+ # can be passed on a List port
+ self.assertEqual(columns, [3])
+ self.assertEqual(len(results), 1)
+ self.assertEqual(list(results[0]), [2.0, 3.0, 14.5])
+
+ def test_csv_mismatch(self):
+ """Uses CSVFile and ExtractColumn with mismatching columns.
+ """
+ self.assertTrue(execute([
+ ('read|csv|CSVFile', identifier, [
+ ('file', [('File', self._test_dir + '/test.csv')]),
+ ]),
+ ('ExtractColumn', identifier, [
+ ('column_index', [('Integer', '0')]), # index is wrong
+ ('column_name', [('String', 'col 2')]),
+ ]),
+ ],
+ [
+ (0, 'self', 1, 'table'),
+ ]))
+
+ def test_csv_missing(self):
+ """Uses CSVFile and ExtractColumn with a nonexisting column.
+ """
+ self.assertTrue(execute([
+ ('read|csv|CSVFile', identifier, [
+ ('file', [('File', self._test_dir + '/test.csv')]),
+ ]),
+ ('ExtractColumn', identifier, [
+ ('column_name', [('String', 'col not here')]),
+ ]),
+ ],
+ [
+ (0, 'self', 1, 'table'),
+ ]))
+
+ def test_csv_nonnumeric(self):
+ """Uses CSVFile and ExtractColumn to load strings.
+ """
+ with intercept_result(ExtractColumn, 'value') as results:
+ self.assertFalse(execute([
+ ('read|csv|CSVFile', identifier, [
+ ('file', [('File', self._test_dir + '/test.csv')]),
+ ('header_present', [('Boolean', 'False')]),
+ ]),
+ ('ExtractColumn', identifier, [
+ ('column_index', [('Integer', '2')]),
+ ('numeric', [('Boolean', 'False')]),
+ ]),
+ ],
+ [
+ (0, 'self', 1, 'table'),
+ ]))
+ self.assertEqual(len(results), 1)
+ self.assertEqual(results[0],
+ ['col moutarde', '4', 'not a number', '7'])
+
+
+class TestCountlines(unittest.TestCase):
+ def test_countlines(self):
+ # Simple
+ fp = StringIO("first\nsecond")
+ self.assertEqual(count_lines(fp), 2)
+
+ # With newline at EOF
+ fp = StringIO("first\nsecond\n")
+ self.assertEqual(count_lines(fp), 2)
+
+ # Empty
+ fp = StringIO("")
+ self.assertEqual(count_lines(fp), 0)
+
+ # Single newline
+ fp = StringIO("\n")
+ self.assertEqual(count_lines(fp), 1)
diff --git a/vistrails/packages/tabledata/read/read_numpy.py b/vistrails/packages/tabledata/read/read_numpy.py
new file mode 100644
index 0000000..8f251f4
--- /dev/null
+++ b/vistrails/packages/tabledata/read/read_numpy.py
@@ -0,0 +1,136 @@
+import numpy
+
+from vistrails.core.modules.vistrails_module import Module
+
+
+class NumPyArray(Module):
+ """
+ A Numpy Array, that can be loaded from a file.
+
+ Declared as returning a List, but returns a Numpy array instead!
+ """
+ _input_ports = [
+ ('file', '(org.vistrails.vistrails.basic:File)'),
+ ('datatype', '(org.vistrails.vistrails.basic:String)'),
+ ('shape', '(org.vistrails.vistrails.basic:List)')]
+ _output_ports = [
+ ('value', '(org.vistrails.vistrails.basic:List)')]
+
+ NPY_FMT = object()
+
+ FORMAT_MAP = dict(
+ npy = NPY_FMT,
+
+ int8 = numpy.int8,
+ uint8 = numpy.uint8,
+ int16 = numpy.int16,
+ uint16 = numpy.uint16,
+ int32 = numpy.int32,
+ uint32 = numpy.uint32,
+ int64 = numpy.int64,
+ uint64 = numpy.uint64,
+
+ float32 = numpy.float32,
+ float64 = numpy.float64,
+
+ complex64 = numpy.complex64,
+ complex128 = numpy.complex128,
+ )
+
+ def compute(self):
+ filename = self.getInputFromPort('file').name
+ if self.hasInputFromPort('datatype'):
+ dtype = NumPyArray.FORMAT_MAP[self.getInputFromPort('datatype')]
+ else:
+ if filename[-4:].lower() == '.npy':
+ dtype = self.NPY_FMT
+ else:
+ dtype = numpy.float32
+ if dtype is self.NPY_FMT:
+ # Numpy's ".NPY" format
+ # Written with: numpy.save('xxx.npy', array)
+ array = numpy.load(filename)
+ else:
+ # Numpy's plain binary format
+ # Written with: array.tofile('xxx.dat')
+ array = numpy.fromfile(filename, dtype)
+ if self.hasInputFromPort('shape'):
+ array.shape = tuple(self.getInputFromPort('shape'))
+ self.setResult('value', array)
+
+
+_modules = {'numpy': [NumPyArray]}
+
+
+###############################################################################
+
+import unittest
+
+
+class NumpyTestCase(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ import os
+ cls._test_dir = os.path.join(
+ os.path.dirname(__file__),
+ os.pardir,
+ 'test_files')
+
+ def test_raw_numpy(self):
+ """Uses NumPyArray to load an array in raw format.
+ """
+ from ..identifiers import identifier
+ from vistrails.tests.utils import execute, intercept_result
+
+ with intercept_result(NumPyArray, 'value') as results:
+ self.assertFalse(execute([
+ ('read|numpy|NumPyArray', identifier, [
+ ('datatype', [('String', 'float32')]),
+ ('shape', [('List', '[2, 3]')]),
+ ('file', [('File', self._test_dir + '/random.dat')]),
+ ]),
+ ]))
+ self.assertEqual(len(results), 1)
+ self.assertTrue(
+ (results[0] == [[1.0, 7.0, 5.0], [3.0, 6.0, 1.0]]).all())
+
+ def test_npy_numpy(self):
+ """Uses NumPyArray to load an array in .NPY format.
+ """
+ from ..identifiers import identifier
+ from vistrails.tests.utils import execute, intercept_result
+
+ with intercept_result(NumPyArray, 'value') as results:
+ self.assertFalse(execute([
+ ('read|numpy|NumPyArray', identifier, [
+ ('datatype', [('String', 'npy')]),
+ ('file', [('File', self._test_dir + '/random.npy')]),
+ ]),
+ ('PythonSource', 'org.vistrails.vistrails.basic', [
+ ('source', [('String', '')]),
+ ]),
+ ],
+ [
+ (0, 'value', 1, 'l'),
+ ],
+ add_port_specs=[
+ (1, 'input', 'l',
+ 'org.vistrails.vistrails.basic:List'),
+ ]))
+ self.assertEqual(len(results), 1)
+ self.assertEqual(list(results[0]), [1.0, 7.0, 5.0, 3.0, 6.0, 1.0])
+
+ def test_npy_auto_numpy(self):
+ """Uses NumPyArray to load an array in (autodetected) .NPY format.
+ """
+ from ..identifiers import identifier
+ from vistrails.tests.utils import execute, intercept_result
+
+ with intercept_result(NumPyArray, 'value') as results:
+ self.assertFalse(execute([
+ ('read|numpy|NumPyArray', identifier, [
+ ('file', [('File', self._test_dir + '/random.npy')]),
+ ]),
+ ]))
+ self.assertEqual(len(results), 1)
+ self.assertEqual(list(results[0]), [1.0, 7.0, 5.0, 3.0, 6.0, 1.0])
diff --git a/vistrails/packages/tabledata/test_files/random.dat b/vistrails/packages/tabledata/test_files/random.dat
new file mode 100644
index 0000000..a97c0c5
Binary files /dev/null and b/vistrails/packages/tabledata/test_files/random.dat differ
diff --git a/vistrails/packages/tabledata/test_files/random.npy b/vistrails/packages/tabledata/test_files/random.npy
new file mode 100644
index 0000000..6f4f696
Binary files /dev/null and b/vistrails/packages/tabledata/test_files/random.npy differ
diff --git a/vistrails/packages/tabledata/test_files/test.csv b/vistrails/packages/tabledata/test_files/test.csv
new file mode 100644
index 0000000..6d1d62e
--- /dev/null
+++ b/vistrails/packages/tabledata/test_files/test.csv
@@ -0,0 +1,4 @@
+col 1;col 2;col moutarde
+-1;2;4
+2;3;not a number
+6;14.5;7
diff --git a/vistrails/packages/tabledata/viewer.py b/vistrails/packages/tabledata/viewer.py
new file mode 100644
index 0000000..7b39b09
--- /dev/null
+++ b/vistrails/packages/tabledata/viewer.py
@@ -0,0 +1,55 @@
+from PyQt4 import QtCore, QtGui
+
+from vistrails.packages.spreadsheet.basic_widgets import SpreadsheetCell
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellWidget
+
+
+class TableCell(SpreadsheetCell):
+ """Shows a table in a spreadsheet cell.
+ """
+ _input_ports = [('table', '(org.vistrails.vistrails.tabledata:Table)')]
+
+ def compute(self):
+ table = self.getInputFromPort('table')
+ self.cellWidget = self.displayAndWait(TableCellWidget, (table,))
+
+
+class TableCellWidget(QCellWidget):
+ def __init__(self, parent=None):
+ QCellWidget.__init__(self, parent)
+
+ layout = QtGui.QVBoxLayout()
+
+ self.table = QtGui.QTableWidget()
+
+ scrollarea = QtGui.QScrollArea(self)
+ scrollarea.setWidgetResizable(True)
+ scrollarea.setWidget(self.table)
+ layout.addWidget(scrollarea)
+
+ self.setLayout(layout)
+
+ def updateContents(self, inputPorts):
+ table, = inputPorts
+
+ self.table.setColumnCount(table.columns)
+ self.table.setRowCount(table.rows)
+
+ for col in xrange(table.columns):
+ column = table.get_column(col)
+ for row in xrange(table.rows):
+ elem = column[row]
+ if isinstance(elem, bytes):
+ elem = elem.decode('utf-8', 'replace')
+ elif not isinstance(elem, unicode):
+ elem = unicode(elem)
+ item = QtGui.QTableWidgetItem(elem)
+ item.setFlags(QtCore.Qt.ItemIsEnabled |
+ QtCore.Qt.ItemIsSelectable)
+ self.table.setItem(row, col, item)
+
+ if table.names is not None:
+ self.table.setHorizontalHeaderLabels(table.names)
+
+
+_modules = [TableCell]
diff --git a/vistrails/packages/vtk/__init__.py b/vistrails/packages/vtk/__init__.py
new file mode 100644
index 0000000..a5d56cc
--- /dev/null
+++ b/vistrails/packages/vtk/__init__.py
@@ -0,0 +1,61 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""The Visualization ToolKit (VTK) is an open source, freely available
+software system for 3D computer graphics, image processing, and
+visualization used by thousands of researchers and developers around
+the world. http://www.vtk.org"""
+
+from identifiers import *
+import vistrails.core
+
+def package_dependencies():
+ import vistrails.core.packagemanager
+ manager = vistrails.core.packagemanager.get_package_manager()
+ if manager.has_package('org.vistrails.vistrails.spreadsheet'):
+ return ['org.vistrails.vistrails.spreadsheet']
+ else:
+ return []
+
+def package_requirements():
+ from vistrails.core.requirements import require_python_module, \
+ python_module_exists
+ require_python_module('vtk', {
+ 'linux-debian': 'python-vtk',
+ 'linux-ubuntu': 'python-vtk',
+ 'linux-fedora': 'vtk-python'})
+ if not python_module_exists('PyQt4'):
+ from vistrails.core import debug
+ debug.warning('PyQt4 is not available. There will be no interaction '
+ 'between VTK and the spreadsheet.')
diff --git a/vistrails/packages/vtk/base_module.py b/vistrails/packages/vtk/base_module.py
new file mode 100644
index 0000000..5f64fce
--- /dev/null
+++ b/vistrails/packages/vtk/base_module.py
@@ -0,0 +1,272 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# This describes basic modules used by other VTK module
+################################################################################
+from itertools import izip
+import vtk
+
+from vistrails.core.interpreter.base import AbortExecution
+from vistrails.core.modules.module_registry import registry
+from vistrails.core.modules.vistrails_module import Module, ModuleError
+from identifiers import identifier as vtk_pkg_identifier
+
+################################################################################
+
+class vtkBaseModule(Module):
+ """
+ vtkBaseModule is the base class for all VTK modules in VisTrails, it acts
+ as a wrapper to direct all input/output ports to appropriate VTK function
+ calls
+
+ """
+
+ def __init__(self):
+ """ vtkBaseModule() -> vtkBaseModule
+ Instantiate an emptt VTK Module with real VTK instance
+
+ """
+ Module.__init__(self)
+ self.vtkInstance = None
+
+ def is_cacheable(self):
+ # VTK objects are by default cacheable only if they're subclasses
+ # of vtkAlgorithm
+ return (issubclass(self.vtkClass, vtk.vtkAlgorithm)
+ and (not issubclass(self.vtkClass, vtk.vtkAbstractMapper)))
+
+ def call_input_function(self, function, params):
+ """self.call_input_function(function, params) -> None
+ Calls the input function on the vtkInstance, or a special
+ input function if one exists in the class."""
+ if hasattr(self, '_special_input_function_' + function):
+ attr = getattr(self, '_special_input_function_' + function)
+ else:
+ try:
+ attr = getattr(self.vtkInstance, function)
+ except AttributeError:
+ # Compensates for overload by exploiting the fact that
+ # no VTK method has underscores.
+ f = function.find('_')
+ if f != -1:
+ function = function[:f]
+ attr = getattr(self.vtkInstance, function)
+
+ from init import get_method_signature, prune_signatures
+
+ doc = ''
+ try:
+ # doc = self.provide_output_port_documentation(function)
+ doc = self.get_doc(function)
+ except:
+ doc = ''
+
+ setterSig = []
+ if doc != '': setterSig = get_method_signature(None, doc, function)
+
+ if len(setterSig) > 1:
+ prune_signatures(self, function, setterSig)
+
+ pp = []
+ for j in xrange(len(setterSig)):
+ setter = list(setterSig[j][1]) if setterSig[j][1] != None else None
+ aux = []
+ if setter != None and len(setter) == len(params) and pp == []:
+ for i in xrange(len(setter)):
+ if setter[i].find('[') != -1:
+ del aux[:]
+ aux.append(params[i])
+ elif setter[i].find(']') != -1:
+ aux.append(params[i])
+ pp.append(aux)
+ else:
+ if len(aux) > 0:
+ aux.append(params[i])
+ else:
+ pp.append(params[i])
+ if pp != []:
+ params = pp
+ attr(*params)
+ else:
+ attr(*params)
+ # print "Called ",attr,function,params
+
+ @classmethod
+ def get_doc(cls, port_name):
+ f = port_name.find('_')
+ if f != -1:
+ name = port_name[:f]
+ else:
+ name = port_name
+ return getattr(cls.vtkClass, name).__doc__
+
+ # @classmethod
+ # def provide_input_port_documentation(cls, port_name):
+ # return cls.get_doc(port_name)
+
+ # @classmethod
+ # def provide_output_port_documentation(cls, port_name):
+ # return cls.get_doc(port_name)
+
+ def compute(self):
+ """ compute() -> None
+ Actually perform real VTK task by directing all input/output ports
+ to VTK function calls
+
+ """
+
+ def call_it(function, p):
+ # Translate between VisTrails objects and VTK objects
+ if p is None:
+ # None indicates a call with no parameters
+ params = []
+ elif isinstance(p, tuple):
+ # A tuple indicates a call with many parameters
+ params = list(p)
+ else:
+ # Otherwise, it's a single parameter
+ params = [p]
+
+ # Unwraps VTK objects
+ for i in xrange(len(params)):
+ if hasattr(params[i], 'vtkInstance'):
+ params[i] = params[i].vtkInstance
+ try:
+ self.call_input_function(function, params)
+ except Exception, e:
+ msg = 'VTK Exception: '
+ raise ModuleError(self, msg + str(type(e)) + ': ' + str(e))
+
+ # Always re-create vtkInstance module, no caching here
+ if self.vtkInstance:
+ del self.vtkInstance
+ self.vtkInstance = self.vtkClass()
+
+ # We need to call method ports before anything else, and in
+ # the right order.
+
+ # FIXME: This does not belong here, it belongs in the main class
+ # No time for that now
+ methods = self.is_method.values()
+ methods.sort()
+ for value in methods:
+ (_, port) = value
+ conn = self.is_method.inverse[value]
+ p = conn()
+ call_it(port, p)
+
+ # Make sure all input ports are called correctly
+ for (function, connector_list) in self.inputPorts.iteritems():
+ paramList = self.forceGetInputListFromPort(function)
+ if function[:18]=='SetInputConnection':
+ paramList = zip([int(function[18:])]*len(paramList),
+ paramList)
+ function = 'SetInputConnection'
+ if function=='AddInputConnection':
+ desc = registry.get_descriptor_by_name(
+ vtk_pkg_identifier,
+ 'vtkAlgorithmOutput')
+ for i in xrange(len(paramList)):
+ if isinstance(paramList[i], desc.module):
+ paramList[i] = (0, paramList[i])
+ for p,connector in izip(paramList, connector_list):
+ # Don't call method
+ if connector in self.is_method:
+ continue
+ call_it(function, p)
+
+ #In the case of a vtkRenderer,
+ # we need to call the methods after the
+ #input ports are set.
+ if isinstance(self.vtkInstance, vtk.vtkRenderer):
+ for value in methods:
+ (_, port) = value
+ conn = self.is_method.inverse[value]
+ p = conn()
+ call_it(port, p)
+
+ # Call update if appropriate
+ if hasattr(self.vtkInstance, 'Update'):
+ is_aborted = False
+ isAlgorithm = issubclass(self.vtkClass, vtk.vtkAlgorithm)
+ cbId = None
+ if isAlgorithm:
+ def ProgressEvent(obj, event):
+ try:
+ self.logging.update_progress(self, obj.GetProgress())
+ except AbortExecution:
+ obj.SetAbortExecute(True)
+ self.vtkInstance.RemoveObserver(cbId)
+ is_aborted = True
+ cbId = self.vtkInstance.AddObserver('ProgressEvent', ProgressEvent)
+ self.vtkInstance.Update()
+ if isAlgorithm and not is_aborted:
+ self.vtkInstance.RemoveObserver(cbId)
+
+ # Then update the output ports also with appropriate function calls
+ for function in self.outputPorts.keys():
+ if function[:13]=='GetOutputPort':
+ i = int(function[13:])
+ vtkOutput = self.vtkInstance.GetOutputPort(i)
+ output = vtkBaseModule.wrapperModule('vtkAlgorithmOutput',
+ vtkOutput)
+ self.setResult(function, output)
+ elif hasattr(self.vtkInstance, function):
+ retValues = getattr(self.vtkInstance, function)()
+ if issubclass(retValues.__class__, vtk.vtkObject):
+ className = retValues.GetClassName()
+ output = vtkBaseModule.wrapperModule(className, retValues)
+ self.setResult(function, output)
+ elif isinstance(retValues, (tuple, list)):
+ result = list(retValues)
+ for i in xrange(len(result)):
+ if issubclass(result[i].__class__, vtk.vtkObject):
+ className = result[i].GetClassName()
+ result[i] = vtkBaseModule.wrapperModule(className,
+ result[i])
+ self.setResult(function, type(retValues)(result))
+ else:
+ self.setResult(function, retValues)
+
+ @staticmethod
+ def wrapperModule(classname, instance):
+ """ wrapperModule(classname: str, instance: vtk class) -> Module
+ Create a wrapper module in VisTrails with a vtk instance
+
+ """
+ result = registry.get_descriptor_by_name(vtk_pkg_identifier,
+ classname).module()
+ result.vtkInstance = instance
+ return result
diff --git a/vistrails/packages/vtk/class_tree.py b/vistrails/packages/vtk/class_tree.py
new file mode 100644
index 0000000..9451e0e
--- /dev/null
+++ b/vistrails/packages/vtk/class_tree.py
@@ -0,0 +1,303 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# Author: Prabhu Ramachandran
+# Copyright (c) 2004, Enthought, Inc.
+# License: BSD Style.
+
+"""This module generates the class hierarchy for any given Python
+modules. This can be used (among other things) to generate the
+traitified VTK classes in the correct order.
+
+"""
+
+import __builtin__
+
+
+class TreeNode(object):
+ """Represents a node in the class tree.
+
+ Stores information on the sub and super classes of a particular
+ class. It also stores the inheritance level of the class inside
+ the inheritance tree (essentially how many levels of inheritance
+ are there below this class). This inheritance level is computed
+ when the `get_level` method is called. The `get_level` method
+ works only when the parent information is complete.
+
+ """
+
+ def __init__(self, klass):
+ """Given a class, create a node in the tree.
+
+ Parameters
+ ----------
+ - klass : `class`
+
+ The class which is represented as a node in the tree.
+
+ """
+ self.klass = klass
+ self.name = klass.__name__
+ self.children = []
+ self.parents = []
+ # Uninitialized level is set to None
+ self.level = None
+
+ def add_parent(self, parent):
+ """Add a parent node."""
+ assert isinstance(parent, TreeNode)
+ if parent not in self.parents:
+ self.parents.append(parent)
+
+ def add_child(self, child):
+ """Add a child node. """
+ assert isinstance(child, TreeNode)
+ if child not in self.children:
+ self.children.append(child)
+
+ def get_level(self):
+ """Returns the inheritance level of the node (an int). If the
+ level has not been set, the method computes it. Note however,
+ that this computation will fail if the parent information is
+ incorrect.
+
+ """
+ if not self.level:
+ if self.parents:
+ self.level = max([x.get_level() for x in self.parents]) + 1
+ else:
+ self.level = 0
+ return self.level
+
+ def get_ancestors(self):
+ """Returns a list of ancestor nodes from which this class has
+ descended.
+
+ """
+ def _get_ancestors(node, ancestors):
+ ancestors.extend(node.parents)
+ for p in node.parents:
+ _get_ancestors(p, ancestors)
+ ancestors = []
+ _get_ancestors(self, ancestors)
+ return ancestors
+
+
+class ClassTree(object):
+ """Contains and generates all the class tree information.
+
+ On initialization of the instance, nothing is done. The classes
+ are obtained using the list of modules (or a single module) that
+ is used to initialize the instance. One must then call the
+ `create` method to generate the tree structure. The instance of
+ the class also can be treated as an iterator which iterates over
+ the nodes of the tree.
+
+ There are two ways in which the tree hierarchy is stored. A
+ dictionary mapping class names to the tree node and a tree
+ represented as a list of lists containing the nodes. The tree is
+ organized based on a concept of an inheritance level. A class
+ that has no parent classes (no base classes) is said to be at
+ level zero. If a class inherits successively from 7 classes, it
+ is at level 6. An example of inheritance for a vtkFoo class is
+ given below:
+
+ vtkFoo -> vtkBar -> vtkObject -> vtkObjectBase
+
+ Here, vtkObjectBase has an inheritance level of 0 and vtkFoo a
+ level of 3. One can traverse the tree by using the level as an
+ index and find all the classes at a particular level.
+
+ Here is some example usage of this class::
+
+ >>> import vtk
+ >>> t = ClassTree(vtk)
+ >>> t.create()
+ >>> print t.get_node('vtkObject').name
+ vtkObject
+ >>> print t.get_node('vtkObject').parents[0].name
+ vtkObjectBase
+ >>> print len(t.tree[0])
+ 1
+ >>> t.tree[0][0].name
+ vtkObjectBase
+
+ """
+
+ def __init__(self, modules):
+ """Initialize the instance with the given modules.
+
+ Parameters
+ ----------
+
+ - modules : `sequence` of modules or a module
+
+ This is either a single module or a sequence of modules.
+ The instance uses these list of modules to generate the
+ class tree.
+
+ """
+ self.nodes = {}
+ self.tree = [[]]
+ if not hasattr(modules, '__iter__'):
+ self.modules = [modules]
+ else:
+ self.modules = modules
+
+ def __iter__(self):
+ return iter(self.nodes.values())
+
+ def _generate_hierarchy(self, klass):
+ """Does the hard work of generating the class hierarchy."""
+ node = self.get_node(klass.__name__, create=1)
+ for base in klass.__bases__:
+ base_node = self.get_node_from_class(base, create=1)
+ node.add_parent(base_node)
+ base_node.add_child(node)
+ self._generate_hierarchy(base)
+
+ def get_class(self, name):
+ """Given a class name in the given modules returns the class."""
+ klass = None
+ for m in self.modules:
+ if hasattr(m, name):
+ return getattr(m, name)
+ if hasattr(__builtin__, name):
+ klass = getattr(__builtin__, name)
+ if not klass:
+ try:
+ klass = self.nodes[name].klass
+ except KeyError:
+ raise KeyError, "Cannot find class of name %s"%name
+ return klass
+
+ def add_node(self, klass):
+ """Create a node for the given class."""
+ name = klass.__name__
+ if not self.nodes.has_key(name):
+ node = TreeNode(klass)
+ self.nodes[name] = node
+ return node
+
+ def get_node(self, name, create=0):
+ """Get a node of the given name.
+
+ Parameters
+ ----------
+
+ - name : `str`
+
+ Name of the node to get.
+
+ - create : `boolean`
+
+ If True, a new node will be added if no node of the given
+ name is available. Defaults to False.
+
+ Returns
+ -------
+
+ - `TreeNode`
+
+ """
+ if self.nodes.has_key(name):
+ return self.nodes[name]
+ elif create:
+ return self.add_node(self.get_class(name))
+
+ def get_node_from_class(self, cls, create=0):
+ """Get a node of the given class.
+
+ Parameters
+ ----------
+
+ - cls : `class`
+
+ Class of the node to get.
+
+ - create : `boolean`
+
+ If True, a new node will be added if no node of the given
+ name is available. Defaults to False.
+
+ Returns
+ -------
+
+ - `TreeNode`
+
+ """
+ name = cls.__name__
+ if self.nodes.has_key(name):
+ return self.nodes[name]
+ elif create:
+ return self.add_node(cls)
+
+ def create(self, class_names=None):
+ """This method generates the class tree given an optional list
+ of class names.
+
+ Parameters
+ ----------
+
+ - class_names - `list` of `str`
+
+ An optional list of names of the classes to generate the
+ tree for. Defaults to None where the class list is computed
+ from the modules.
+
+ """
+ if class_names is None:
+ class_names = []
+ for m in self.modules:
+ class_names.extend(dir(m))
+
+ # Generate the nodes.
+ for name in class_names:
+ klass = self.get_class(name)
+ if klass and hasattr(klass, '__bases__'):
+ self._generate_hierarchy(klass)
+
+ # Compute the inheritance level and store the nodes in the tree.
+ for node in self:
+ d = node.get_level()
+ while len(self.tree) <= d:
+ self.tree.append([])
+ self.tree[d].append(node)
+
+ # Sort the nodes alphabetically.
+ def _comp(x, y):
+ return cmp(x.name, y.name)
+ for nodes in self.tree:
+ nodes.sort(_comp)
diff --git a/vistrails/packages/vtk/fix_classes.py b/vistrails/packages/vtk/fix_classes.py
new file mode 100644
index 0000000..084ea5f
--- /dev/null
+++ b/vistrails/packages/vtk/fix_classes.py
@@ -0,0 +1,67 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import vtk
+
+################################################################################
+# Some fixed classes that solve a few VTK API issues
+
+# This dictionary stores the patched class to vtk class mapping.
+# This would be naturally better stored as an attribute directly on the
+# patched class. VTK, however, doesn't like class attributes.
+description = {}
+
+# http://www.vtk.org/doc/nightly/html/classvtkImagePlaneWidget.html
+# SetUserControlledLookupTable needs to be set before calling
+# SetLookupTable. VTK should do it automatically, so let's fix it
+
+
+# This fix seems to break on VTK versions larger than 5.0.3. It might also
+# be because of an interaction with python 2.6, but I haven't checked that.
+class vtkImagePlaneWidget_fixed(vtk.vtkImagePlaneWidget):
+ def SetLookupTable(self, lookup_table):
+ self.UserControlledLookupTableOn()
+ vtk.vtkImagePlaneWidget.SetLookupTable(self, lookup_table)
+v = vtk.vtkVersion()
+version = [v.GetVTKMajorVersion(),
+ v.GetVTKMinorVersion(),
+ v.GetVTKBuildVersion()]
+if version < [5, 0, 4]:
+ description[vtkImagePlaneWidget_fixed] = vtk.vtkImagePlaneWidget
+else:
+ description[id(vtkImagePlaneWidget_fixed)] = vtk.vtkImagePlaneWidget
+
+# Set docstring to wrap it correctly
+vtkImagePlaneWidget_fixed.SetLookupTable.__doc__ = vtk.vtkImagePlaneWidget.SetLookupTable.__doc__
diff --git a/vistrails/packages/vtk/hasher.py b/vistrails/packages/vtk/hasher.py
new file mode 100644
index 0000000..a238541
--- /dev/null
+++ b/vistrails/packages/vtk/hasher.py
@@ -0,0 +1,49 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# This is the user-defined hasher for VTK, that takes into account
+# incoming and outgoing connections
+from vistrails.core.cache.hasher import Hasher
+
+def vtk_hasher(pipeline, module, chm):
+ outgoing_connections = pipeline.graph.edges_from(module.id)
+ incoming_connections = pipeline.graph.edges_to(module.id)
+ current_hash = Hasher.module_signature(module, chm)
+ chashes = [Hasher.connection_signature(pipeline.connections[c_id])
+ for (_, c_id) in outgoing_connections]
+ chashes += [Hasher.connection_signature(pipeline.connections[c_id])
+ for (_, c_id) in incoming_connections]
+ compound_hash = Hasher.compound_signature(chashes)
+ return Hasher.compound_signature([current_hash, compound_hash])
diff --git a/vistrails/packages/vtk/identifiers.py b/vistrails/packages/vtk/identifiers.py
new file mode 100644
index 0000000..3402231
--- /dev/null
+++ b/vistrails/packages/vtk/identifiers.py
@@ -0,0 +1,38 @@
+###############################################################################
+##
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+identifier = 'org.vistrails.vistrails.vtk'
+old_identifiers = ['edu.utah.sci.vistrails.vtk']
+name = 'VTK'
+version = '0.9.4'
diff --git a/vistrails/packages/vtk/init.py b/vistrails/packages/vtk/init.py
new file mode 100644
index 0000000..75961de
--- /dev/null
+++ b/vistrails/packages/vtk/init.py
@@ -0,0 +1,1383 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# VTK Package for VisTrails
+################################################################################
+
+from vistrails.core.debug import debug
+from vistrails.core.modules.basic_modules import Integer, Float, String, File, \
+ Color, identifier as basic_pkg
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.modules.vistrails_module import new_module, ModuleError
+from vistrails.core.system import get_vistrails_default_pkg_prefix
+from identifiers import identifier as vtk_pkg_identifier
+from vistrails.core.upgradeworkflow import UpgradeWorkflowHandler
+from vistrails.core.utils import all, any, InstanceObject
+from vistrails.core.vistrail.connection import Connection
+
+from hasher import vtk_hasher
+from itertools import izip
+import os.path
+import re
+import warnings
+
+import vtk
+
+from base_module import vtkBaseModule
+from class_tree import ClassTree
+import fix_classes
+import inspectors
+import offscreen
+import tf_widget
+from vtk_parser import VTKMethodParser
+
+
+#TODO: Change the Core > Module > Registry > Add Input : To support vector as type.
+
+################################################################################
+
+# filter some deprecation warnings coming from the fact that vtk calls
+# range() with float parameters
+
+warnings.filterwarnings("ignore",
+ message="integer argument expected, got float")
+
+################################################################################
+v = vtk.vtkVersion()
+version = [v.GetVTKMajorVersion(),
+ v.GetVTKMinorVersion(),
+ v.GetVTKBuildVersion()]
+if version < [5, 0, 4]:
+ def get_description_class(klass):
+ """Because sometimes we need to patch VTK classes, the klass that
+ has the methods is different than the klass we want to
+ instantiate. get_description_class makes sure that for patched
+ classes we get the correct one."""
+ try:
+ return fix_classes.description[klass]
+ except KeyError:
+ return klass
+else:
+ # On VTK 5.0.4, we use the id of the class to hash, because it
+ # seems that VTK hasn't implemented hash() correctly for their
+ # classes.
+ def get_description_class(klass):
+ """Because sometimes we need to patch VTK classes, the klass that
+ has the methods is different than the klass we want to
+ instantiate. get_description_class makes sure that for patched
+ classes we get the correct one."""
+ try:
+ return fix_classes.description[id(klass)]
+ except KeyError:
+ return klass
+
+parser = VTKMethodParser()
+
+typeMapDict = {'int': Integer,
+ 'long': Integer,
+ 'float': Float,
+ 'char*': String,
+ 'char *': String,
+ 'string': String,
+ 'char': String,
+ 'const char*': String,
+ 'const char *': String,
+ '[float': Float,
+ 'float]': Float,
+ '[int': Integer,
+ 'int]': Integer}
+typeMapDictValues = [Integer, Float, String]
+
+file_name_pattern = re.compile('.*FileName$')
+set_file_name_pattern = re.compile('Set.*FileName$')
+
+def resolve_overloaded_name(name, ix, signatures):
+ # VTK supports static overloading, VisTrails does not. The
+ # solution is to check whether the current function has
+ # overloads and change the names appropriately.
+ if len(signatures) == 1:
+ return name
+ else:
+ return name + '_' + str(ix+1)
+
+def typeMap(name, package=None):
+ """ typeMap(name: str) -> Module
+ Convert from C/C++ types into VisTrails Module type
+
+ """
+ if package is None:
+ package = identifier
+ if isinstance(name, tuple):
+ return [typeMap(x, package) for x in name]
+ if name in typeMapDict:
+ return typeMapDict[name]
+ else:
+ registry = get_module_registry()
+ if not registry.has_descriptor_with_name(package, name):
+ return None
+ else:
+ return registry.get_descriptor_by_name(package,
+ name).module
+
+def get_method_signature(method, docum='', name=''):
+ """ get_method_signature(method: vtkmethod) -> [ret, arg]
+ Re-wrap Prabu's method to increase performance
+
+ """
+ doc = method.__doc__ if docum=='' else docum
+ tmptmp = doc.split('\n')
+ tmp = []
+ for l in tmptmp:
+ l = l.strip('\n \t')
+ if l.startswith('V.') or l.startswith('C++:'):
+ tmp.append(l)
+ else:
+ if (len(tmp) != 0):
+ tmp[-1] = tmp[-1] + ' ' + l
+ tmp.append('')
+ sig = []
+ pat = re.compile(r'\b')
+
+ # Remove all the C++ function signatures and V.<method_name> field
+ name = method.__name__ if name == '' else name
+ offset = 2+len(name)
+ for i in xrange(len(tmp)):
+ s = tmp[i]
+ if s=='': break
+ if i%2==0:
+ x = s.split('->')
+ arg = x[0].strip()[offset:]
+ if len(x) == 1: # No return value
+ ret = None
+ else:
+ ret = x[1].strip()
+
+ # Remove leading and trailing parens for arguments.
+ arg = arg[1:-1]
+ if not arg:
+ arg = None
+ if arg and arg[-1] == ')':
+ arg = arg + ','
+
+ # Now quote the args and eval them. Easy!
+ if ret and ret[:3]!='vtk':
+ try:
+ ret = eval(pat.sub('\"', ret))
+ except:
+ continue
+ if arg:
+ if arg.find('(')!=-1:
+ try:
+ arg = eval(pat.sub('\"', arg))
+ except:
+ continue
+ else:
+ arg = arg.split(', ')
+ if len(arg)>1:
+ arg = tuple(arg)
+ else:
+ arg = arg[0]
+ if isinstance(arg, str):
+ arg = [arg]
+
+ sig.append(([ret], arg))
+ return sig
+
+def prune_signatures(module, name, signatures, output=False):
+ """prune_signatures tries to remove redundant signatures to reduce
+ overloading. It _mutates_ the given parameter.
+
+ It does this by performing several operations:
+
+ 1) It compares a 'flattened' version of the types
+ against the other 'flattened' signatures. If any of them match, we
+ keep only the 'flatter' ones.
+
+ A 'flattened' signature is one where parameters are not inside a
+ tuple.
+
+ 2) We explicitly forbid a few signatures based on modules and names
+
+ """
+ # yeah, this is Omega(n^2) on the number of overloads. Who cares?
+
+ def flatten(type_):
+ if type_ is None:
+ return []
+ def convert(entry):
+ if isinstance(entry, tuple):
+ return list(entry)
+ elif isinstance(entry, str):
+ return [entry]
+ else:
+ result = []
+ first = True
+ lastList = True
+ for e in entry:
+ if (isinstance(e, list)):
+ if lastList == False: result[len(result)] = result[len(result)] + ']'
+ aux = e
+ aux.reverse()
+ aux[0] = '[' + aux[0]
+ aux[-1] = aux[-1] + ']'
+ result.extend(aux)
+ lastList = True
+ else:
+ if first: e = '[' + e
+ result.append(e)
+ lastList = False
+ first = False
+ return result
+ result = []
+ for entry in type_:
+ result.extend(convert(entry))
+ return result
+ flattened_entries = [flatten(sig[1]) for
+ sig in signatures]
+ def hit_count(entry):
+ result = 0
+ for entry in flattened_entries:
+ if entry in flattened_entries:
+ result += 1
+ return result
+ hits = [hit_count(entry) for entry in flattened_entries]
+
+ def forbidden(flattened, hit_count, original):
+ if (issubclass(get_description_class(module.vtkClass), vtk.vtk3DWidget) and
+ name == 'PlaceWidget' and
+ flattened == []):
+ return True
+ # We forbid this because addPorts hardcodes this but
+ # SetInputArrayToProcess is an exception for the InfoVis
+ # package
+ if (get_description_class(module.vtkClass) == vtk.vtkAlgorithm and
+ name!='SetInputArrayToProcess'):
+ return True
+ return False
+
+ # This is messy: a signature is only allowed if there's no
+ # explicit disallowing of it. Then, if it's not overloaded,
+ # it is also allowed. If it is overloaded and not the flattened
+ # version, it is pruned. If these are output ports, there can be
+ # no parameters.
+
+ def passes(flattened, hit_count, original):
+ if forbidden(flattened, hit_count, original):
+ return False
+ if hit_count == 1:
+ return True
+ if original[1] is None:
+ return True
+ if output and len(original[1]) > 0:
+ return False
+ if hit_count > 1 and len(original[1]) == len(flattened):
+ return True
+ return False
+
+ signatures[:] = [original for (flattened, hit_count, original)
+ in izip(flattened_entries,
+ hits,
+ signatures)
+ if passes(flattened, hit_count, original)]
+
+ #then we remove the duplicates, if necessary
+ unique_signatures = []
+
+ #Remove the arrays and tuples inside the signature
+ # in order to transform it in a single array
+ #Also remove the '[]' from the Strings
+ def removeBracts(signatures):
+ result = []
+ stack = list(signatures)
+ while (len(stack) != 0):
+ curr = stack.pop(0)
+ if (isinstance(curr, (String, str))):
+ c = curr.replace('[', '')
+ c = c.replace(']', '')
+ result.append(c)
+ elif (curr == None):
+ result.append(curr)
+ elif (isinstance(curr, list)):
+ curr.reverse()
+ for c in curr: stack.insert(0, c)
+ elif (isinstance(curr, tuple)):
+ cc = list(curr)
+ cc.reverse()
+ for c in cc: stack.insert(0, c)
+ else:
+ result.append(curr)
+ return result
+
+ unique2 = []
+ for s in signatures:
+ aux = removeBracts(s)
+ if not unique2.count(aux):
+ unique_signatures.append(s)
+ unique2.append(aux)
+ signatures[:] = unique_signatures
+
+disallowed_classes = set(
+ [
+ 'simplewrapper', # ticket 464: VTK 5.10 on OpenSuSE needs this
+ 'vtkCriticalSection',
+ 'vtkDataArraySelection',
+ 'vtkDebugLeaks',
+ 'vtkDirectory',
+ 'vtkDynamicLoader',
+ 'vtkFunctionParser',
+ 'vtkGarbageCollector',
+ 'vtkHeap',
+ 'vtkInformationKey',
+ 'vtkInstantiator',
+ 'vtkLogLookupTable', # VTK: use vtkLookupTable.SetScaleToLog10() instead
+ 'vtkMath',
+ 'vtkModelMetadata',
+ 'vtkMultiProcessController',
+ 'vtkMutexLock',
+ 'vtkOutputWindow',
+ 'vtkPriorityQueue',
+ 'vtkQtInitialization',
+ 'vtkReferenceCount',
+ 'vtkRenderWindowCollection',
+ 'vtkRenderWindowInteractor',
+ 'vtkTesting',
+ 'vtkWindow',
+ 'vtkContext2D', #Not working for VTK 5.7.0
+ 'vtkPLYWriter', #Not working for VTK 5.7.0.
+ 'vtkBooleanTexture', #Not working for VTK 5.7.0
+ 'vtkImageMaskBits', #Not working for VTK 5.7.0
+ 'vtkHardwareSelector',#Not working for VTK 5.7.0
+ ])
+
+def is_class_allowed(module):
+ if module is None:
+ return False
+ try:
+ name = module.__name__
+ return not (name in disallowed_classes)
+ except AttributeError:
+ return True
+
+def addAlgorithmPorts(module):
+ """ addAlgorithmPorts(module: Module) -> None
+ If module is a subclass of vtkAlgorithm, this function will add all
+ SetInputConnection([id],[port]) and GetOutputPort([id]) as
+ SetInputConnection{id}([port]) and GetOutputPort{id}.
+
+ """
+ if issubclass(get_description_class(module.vtkClass), vtk.vtkAlgorithm):
+ if get_description_class(module.vtkClass)!=vtk.vtkStructuredPointsGeometryFilter:
+ # We try to instantiate the class here to get the number of
+ # ports and to avoid abstract classes
+ try:
+ instance = module.vtkClass()
+ except TypeError:
+ pass
+ else:
+ reg = get_module_registry()
+ des = reg.get_descriptor_by_name(vtk_pkg_identifier,
+ 'vtkAlgorithmOutput')
+ for i in xrange(0,instance.GetNumberOfInputPorts()):
+ reg.add_input_port(module, 'SetInputConnection%d'%i,
+ des.module,
+ docstring=\
+ module.get_doc('SetInputConnection'))
+ for i in xrange(0,instance.GetNumberOfOutputPorts()):
+ reg.add_output_port(module, 'GetOutputPort%d'%i,
+ des.module,
+ docstring=\
+ module.get_doc('GetOutputPort'))
+
+disallowed_set_get_ports = set(['ReferenceCount',
+ 'InputConnection',
+ 'OutputPort',
+ 'Progress',
+ 'ProgressText',
+ 'InputArrayToProcess',
+ ])
+def addSetGetPorts(module, get_set_dict, delayed):
+ """ addSetGetPorts(module: Module, get_set_dict: dict) -> None
+ Convert all Setxxx methods of module into input ports and all Getxxx
+ methods of module into output ports
+
+ Keyword arguments:
+ module --- Module
+ get_set_dict --- the Set/Get method signatures returned by vtk_parser
+
+ """
+
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in get_set_dict.iterkeys():
+ if name in disallowed_set_get_ports: continue
+ getterMethod = getattr(klass, 'Get%s'%name)
+ setterMethod = getattr(klass, 'Set%s'%name)
+ getterSig = get_method_signature(getterMethod)
+ setterSig = get_method_signature(setterMethod)
+ if len(getterSig) > 1:
+ prune_signatures(module, 'Get%s'%name, getterSig, output=True)
+ for order, getter in enumerate(getterSig):
+ if getter[1]:
+ debug("Can't handle getter %s (%s) of class %s: Needs input to "
+ "get output" % (order+1, name, klass))
+ continue
+ if len(getter[0]) != 1:
+ debug("Can't handle getter %s (%s) of class %s: More than a "
+ "single output" % (order+1, name, str(klass)))
+ continue
+ class_ = typeMap(getter[0][0])
+ if is_class_allowed(class_):
+ port_name = 'Get'+name
+ registry.add_output_port(module, port_name, class_, True,
+ docstring=module.get_doc(port_name))
+ if len(setterSig) > 1:
+ prune_signatures(module, 'Set%s'%name, setterSig)
+ for ix, setter in enumerate(setterSig):
+ if setter[1]==None: continue
+ n = resolve_overloaded_name('Set' + name, ix, setterSig)
+ if len(setter[1]) == 1 and is_class_allowed(typeMap(setter[1][0])):
+ registry.add_input_port(module, n,
+ typeMap(setter[1][0]),
+ setter[1][0] in typeMapDict,
+ docstring=module.get_doc(n))
+ else:
+ classes = [typeMap(i) for i in setter[1]]
+
+ if all(is_class_allowed(x) for x in classes):
+ registry.add_input_port(module, n, classes, True,
+ docstring=module.get_doc(n))
+
+
+ # Wrap SetFileNames for VisTrails file access
+ if file_name_pattern.match(name):
+ # FIXME add documentation...
+ registry.add_input_port(module, 'Set' + name[:-4],
+ (File, 'input file'), False)
+ # Wrap SetRenderWindow for exporters
+ elif name == 'RenderWindow':
+ # cscheid 2008-07-11 This is messy: VTKCell isn't
+ # registered yet, so we can't use it as a port
+ # However, we can't register VTKCell before these either,
+ # because VTKCell requires vtkRenderer. The "right" way would
+ # be to add all modules first, then all ports. However, that would
+ # be too slow.
+ # Workaround: delay the addition of the port by storing
+ # the information in a list
+ if registry.has_module('%s.spreadsheet' % \
+ get_vistrails_default_pkg_prefix(),
+ 'SpreadsheetCell'):
+ from vtkcell import VTKCell
+ # FIXME add documentation
+ delayed.add_input_port.append((module, 'SetVTKCell', VTKCell, False))
+ # Wrap color methods for VisTrails GUI facilities
+ # FIXME add documentation for all of these!
+ elif name == 'DiffuseColor':
+ registry.add_input_port(module, 'SetDiffuseColorWidget',
+ (Color, 'color'), True)
+ elif name == 'Color':
+ registry.add_input_port(module, 'SetColorWidget',
+ (Color, 'color'), True)
+ elif name == 'AmbientColor':
+ registry.add_input_port(module, 'SetAmbientColorWidget',
+ (Color, 'color'), True)
+ elif name == 'SpecularColor':
+ registry.add_input_port(module, 'SetSpecularColorWidget',
+ (Color, 'color'), True)
+ elif name == 'EdgeColor':
+ registry.add_input_port(module, 'SetEdgeColorWidget',
+ (Color, 'color'), True)
+ elif name == 'Background' :
+ registry.add_input_port(module, 'SetBackgroundWidget',
+ (Color, 'color'), True)
+ elif name == 'Background2' :
+ registry.add_input_port(module, 'SetBackground2Widget',
+ (Color, 'color'), True)
+
+disallowed_toggle_ports = set(['GlobalWarningDisplay',
+ 'Debug',
+ ])
+def addTogglePorts(module, toggle_dict):
+ """ addTogglePorts(module: Module, toggle_dict: dict) -> None
+ Convert all xxxOn/Off methods of module into input ports
+
+ Keyword arguments:
+ module --- Module
+ toggle_dict --- the Toggle method signatures returned by vtk_parser
+
+ """
+ registry = get_module_registry()
+ for name in toggle_dict.iterkeys():
+ if name in disallowed_toggle_ports:
+ continue
+ port_name = name+'On'
+ registry.add_input_port(module, port_name, [], True,
+ docstring=module.get_doc(port_name))
+ port_name = name+'Off'
+ registry.add_input_port(module, port_name, [], True,
+ docstring=module.get_doc(port_name))
+
+disallowed_state_ports = set(['SetInputArrayToProcess'])
+def addStatePorts(module, state_dict):
+ """ addStatePorts(module: Module, state_dict: dict) -> None
+ Convert all SetxxxToyyy methods of module into input ports
+
+ Keyword arguments:
+ module --- Module
+ state_dict --- the State method signatures returned by vtk_parser
+
+ """
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in state_dict.iterkeys():
+ for mode in state_dict[name]:
+ # Creates the port Set foo to bar
+ field = 'Set'+name+'To'+mode[0]
+ if field in disallowed_state_ports:
+ continue
+ if not registry.has_input_port(module, field):
+ registry.add_input_port(module, field, [], True,
+ docstring=module.get_doc(field))
+
+ # Now create the port Set foo with parameter
+ if hasattr(klass, 'Set%s'%name):
+ setterMethod = getattr(klass, 'Set%s'%name)
+ setterSig = get_method_signature(setterMethod)
+ # if the signature looks like an enum, we'll skip it, it shouldn't
+ # be necessary
+ if len(setterSig) > 1:
+ prune_signatures(module, 'Set%s'%name, setterSig)
+ for ix, setter in enumerate(setterSig):
+ n = resolve_overloaded_name('Set' + name, ix, setterSig)
+ tm = typeMap(setter[1][0])
+ if len(setter[1]) == 1 and is_class_allowed(tm):
+ registry.add_input_port(module, n, tm,
+ setter[1][0] in typeMapDict,
+ docstring=module.get_doc(n))
+ else:
+ classes = [typeMap(i) for i in setter[1]]
+ if all(is_class_allowed(x) for x in classes):
+ registry.add_input_port(module, n, classes, True,
+ docstring=module.get_doc(n))
+
+disallowed_other_ports = set(
+ [
+ 'BreakOnError',
+ 'DeepCopy',
+ 'FastDelete',
+ 'HasObserver',
+ 'HasExecutive',
+ 'InvokeEvent',
+ 'IsA',
+ 'Modified',
+ 'NewInstance',
+ 'PrintRevisions',
+ 'RemoveAllInputs',
+ 'RemoveObserver',
+ 'RemoveObservers',
+ 'SafeDownCast',
+# 'SetInputArrayToProcess',
+ 'ShallowCopy',
+ 'Update',
+ 'UpdateInformation',
+ 'UpdateProgress',
+ 'UpdateWholeExtent',
+ # DAK: These are taken care of by s.upper() == s test
+ # 'GUI_HIDE',
+ # 'INPUT_ARRAYS_TO_PROCESS',
+ # 'INPUT_CONNECTION',
+ # 'INPUT_IS_OPTIONAL',
+ # 'INPUT_IS_REPEATABLE',
+ # 'INPUT_PORT',
+ # 'INPUT_REQUIRED_DATA_TYPE',
+ # 'INPUT_REQUIRED_FIELDS',
+ # 'IS_INTERNAL_VOLUME',
+ # 'IS_EXTERNAL_SURFACE',
+ # 'MANAGES_METAINFORMATION',
+ # 'POINT_DATA',
+ # 'POINTS',
+ # 'PRESERVES_ATTRIBUTES',
+ # 'PRESERVES_BOUNDS',
+ # 'PRESERVES_DATASET',
+ # 'PRESERVES_GEOMETRY',
+ # 'PRESERVES_RANGES',
+ # 'PRESERVES_TOPOLOGY',
+ ])
+
+
+
+force_not_optional_port = set(
+ ['ApplyViewTheme',
+ ])
+
+
+def addOtherPorts(module, other_list):
+ """ addOtherPorts(module: Module, other_list: list) -> None
+ Convert all other ports such as Insert/Add.... into input/output
+
+ Keyword arguments:
+ module --- Module
+ other_dict --- any other method signatures that is not
+ Algorithm/SetGet/Toggle/State type
+
+ """
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in other_list:
+ if name=='CopyImportVoidPointer':
+ # FIXME add documentation
+ registry.add_input_port(module, 'CopyImportVoidString', (String, 'value'), False)
+ if name[:3] in ['Add','Set'] or name[:6]=='Insert':
+ if name in disallowed_other_ports:
+ continue
+ method = getattr(klass, name)
+ signatures = ""
+ if not isinstance(method, int):
+ signatures = get_method_signature(method)
+
+ if len(signatures) > 1:
+ prune_signatures(module, name, signatures)
+ for (ix, sig) in enumerate(signatures):
+ ([result], params) = sig
+ types = []
+ if params:
+ for p in params:
+ t = typeMap(p)
+ if not t:
+ types = None
+ break
+ else: types.append(t)
+ else:
+ types = [[]]
+ if types:
+ if not all(is_class_allowed(x) for x in types):
+ continue
+ n = resolve_overloaded_name(name, ix, signatures)
+ if len(types)<=1:
+ registry.add_input_port(module, n, types[0],
+ types[0] in typeMapDictValues,
+ docstring=module.get_doc(n))
+ else:
+ registry.add_input_port(module, n, types, True,
+ docstring=module.get_doc(n))
+ else:
+ # DAK: check for static methods as name.upper() == name
+ if name in disallowed_other_ports or name.upper() == name:
+ continue
+ method = getattr(klass, name)
+ signatures = ""
+ if not isinstance(method, int):
+ signatures = get_method_signature(method)
+
+ if len(signatures) > 1:
+ prune_signatures(module, name, signatures)
+ for (ix, sig) in enumerate(signatures):
+ ([result], params) = sig
+ types = []
+ if params:
+ paramsList = list(params)
+ while (len(paramsList) != 0):
+ p = paramsList.pop(0)
+ if isinstance(p, list):
+ for aux in p: paramsList.insert(0, aux)
+ else:
+ types.append(typeMap(p))
+ else:
+ types = []
+ if not all(is_class_allowed(x) for x in types):
+ continue
+ if types==[] or (result==None):
+ n = resolve_overloaded_name(name, ix, signatures)
+ # print module.vtkClass.__name__, n
+ try:
+ doc = module.get_doc(n)
+ registry.add_input_port(module, n, types,
+ not (n in force_not_optional_port),
+ docstring=module.get_doc(n))
+ except:
+ print "&*& ERROR WITH ", module.vtkClass.__name__, n
+
+disallowed_get_ports = set([
+ 'GetClassName',
+ 'GetErrorCode',
+ 'GetNumberOfInputPorts',
+ 'GetNumberOfOutputPorts',
+ 'GetOutputPortInformation',
+ 'GetTotalNumberOfInputConnections',
+ ])
+
+def addGetPorts(module, get_list):
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ for name in get_list:
+ if name in disallowed_get_ports:
+ continue
+ method = getattr(klass, name)
+ signatures = get_method_signature(method)
+ if len(signatures) > 1:
+ prune_signatures(module, name, signatures, output=True)
+ for ix, getter in enumerate(signatures):
+ if getter[1] or len(getter[0]) > 1:
+ continue
+ class_ = typeMap(getter[0][0])
+ if is_class_allowed(class_):
+ if len(signatures) > 1:
+ n = name + "_" + str(ix+1)
+ else:
+ n = name
+ registry.add_output_port(module, n, class_, True,
+ docstring=module.get_doc(n))
+
+def addPorts(module, delayed):
+ """ addPorts(module: VTK module inherited from Module,
+ delayed: object with add_input_port slot
+ ) -> None
+
+ Search all metamethods of module and add appropriate ports
+
+ ports that cannot be added immediately should be appended to
+ the delayed object that is passed. see the SetRenderWindow cases.
+
+ """
+ klass = get_description_class(module.vtkClass)
+ registry = get_module_registry()
+ registry.add_output_port(module, 'self', module)
+ parser.parse(klass)
+ addAlgorithmPorts(module)
+ addGetPorts(module, parser.get_get_methods())
+ addSetGetPorts(module, parser.get_get_set_methods(), delayed)
+ addTogglePorts(module, parser.get_toggle_methods())
+ addStatePorts(module, parser.get_state_methods())
+ addOtherPorts(module, parser.get_other_methods())
+ # CVS version of VTK doesn't support AddInputConnect(vtkAlgorithmOutput)
+ # FIXME Add documentation
+ basic_pkg = '%s.basic' % get_vistrails_default_pkg_prefix()
+ if klass==vtk.vtkAlgorithm:
+ registry.add_input_port(module, 'AddInputConnection',
+ typeMap('vtkAlgorithmOutput'))
+ # vtkWriters have a custom File port
+ elif klass==vtk.vtkWriter:
+ registry.add_output_port(module, 'file', typeMap('File', basic_pkg))
+ elif klass==vtk.vtkImageWriter:
+ registry.add_output_port(module, 'file', typeMap('File', basic_pkg))
+ elif klass==vtk.vtkVolumeProperty:
+ registry.add_input_port(module, 'SetTransferFunction',
+ typeMap('TransferFunction'))
+ elif klass==vtk.vtkDataSet:
+ registry.add_input_port(module, 'SetPointData', typeMap('vtkPointData'))
+ registry.add_input_port(module, 'SetCellData', typeMap('vtkCellData'))
+ elif klass==vtk.vtkCell:
+ registry.add_input_port(module, 'SetPointIds', typeMap('vtkIdList'))
+
+def setAllPorts(descriptor, delayed):
+ """ setAllPorts(descriptor: ModuleDescriptor) -> None
+ Traverse descriptor and all of its children/grand-children to add all ports
+
+ """
+ addPorts(descriptor.module, delayed)
+ for child in descriptor.children:
+ setAllPorts(child, delayed)
+
+def class_dict(base_module, node):
+ """class_dict(base_module, node) -> dict
+ Returns the class dictionary for the module represented by node and
+ with base class base_module"""
+
+ class_dict_ = {}
+ def update_dict(name, callable_):
+ if class_dict_.has_key(name):
+ class_dict_[name] = callable_(class_dict_[name])
+ elif hasattr(base_module, name):
+ class_dict_[name] = callable_(getattr(base_module, name))
+ else:
+ class_dict_[name] = callable_(None)
+
+ def guarded_SimpleScalarTree_wrap_compute(old_compute):
+ # This builds the scalar tree and makes it cacheable
+
+ def compute(self):
+ self.is_cacheable = lambda *args, **kwargs: True
+ old_compute(self)
+ self.vtkInstance.BuildTree()
+ return compute
+
+ def guarded_SetFileName_wrap_compute(old_compute):
+ # This checks for the presence of file in VTK readers
+ def compute(self):
+
+ # Skips the check if it's a vtkImageReader or vtkPLOT3DReader, because
+ # it has other ways of specifying files, like SetFilePrefix for
+ # multiple files
+ skip = [vtk.vtkBYUReader,
+ vtk.vtkImageReader,
+ vtk.vtkDICOMImageReader,
+ vtk.vtkTIFFReader]
+
+ # vtkPLOT3DReader does not exist from version 6.0.0
+ v = vtk.vtkVersion()
+ version = [v.GetVTKMajorVersion(),
+ v.GetVTKMinorVersion(),
+ v.GetVTKBuildVersion()]
+ if version < [6, 0, 0]:
+ skip.append(vtk.vtkPLOT3DReader)
+ if any(issubclass(self.vtkClass, x) for x in skip):
+ old_compute(self)
+ return
+ if self.hasInputFromPort('SetFileName'):
+ name = self.getInputFromPort('SetFileName')
+ elif self.hasInputFromPort('SetFile'):
+ name = self.getInputFromPort('SetFile').name
+ else:
+ raise ModuleError(self, 'Missing filename')
+ if not os.path.isfile(name):
+ raise ModuleError(self, 'File does not exist')
+ old_compute(self)
+ return compute
+
+ def compute_SetDiffuseColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetDiffuseColorWidget(self, color):
+ self.vtkInstance.SetDiffuseColor(color.tuple)
+ return call_SetDiffuseColorWidget
+
+ def compute_SetAmbientColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetAmbientColorWidget(self, color):
+ self.vtkInstance.SetAmbientColor(color.tuple)
+ return call_SetAmbientColorWidget
+
+ def compute_SetSpecularColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetSpecularColorWidget(self, color):
+ self.vtkInstance.SetSpecularColor(color.tuple)
+ return call_SetSpecularColorWidget
+
+ def compute_SetColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetColorWidget(self, color):
+ self.vtkInstance.SetColor(color.tuple)
+ return call_SetColorWidget
+
+ def compute_SetEdgeColorWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetEdgeColorWidget(self, color):
+ self.vtkInstance.SetEdgeColor(color.tuple)
+ return call_SetEdgeColorWidget
+
+ def compute_SetBackgroundWidget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetBackgroundWidget(self, color):
+ self.vtkInstance.SetBackground(color.tuple)
+ return call_SetBackgroundWidget
+
+ def compute_SetBackground2Widget(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetBackground2Widget(self, color):
+ self.vtkInstance.SetBackground2(color.tuple)
+ return call_SetBackground2Widget
+
+ def compute_SetVTKCell(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetRenderWindow(self, cellObj):
+ if cellObj.cellWidget:
+ self.vtkInstance.SetRenderWindow(cellObj.cellWidget.mRenWin)
+ return call_SetRenderWindow
+
+ def compute_SetTransferFunction(old_compute):
+ # This sets the transfer function
+ if old_compute != None:
+ return old_compute
+ def call_SetTransferFunction(self, tf):
+ tf.set_on_vtk_volume_property(self.vtkInstance)
+ return call_SetTransferFunction
+
+ def compute_SetPointData(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetPointData(self, pd):
+ self.vtkInstance.GetPointData().ShallowCopy(pd)
+ return call_SetPointData
+
+ def compute_SetCellData(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetCellData(self, cd):
+ self.vtkInstance.GetCellData().ShallowCopy(cd)
+ return call_SetCellData
+
+ def compute_SetPointIds(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetPointIds(self, point_ids):
+ self.vtkInstance.GetPointIds().SetNumberOfIds(point_ids.GetNumberOfIds())
+ for i in xrange(point_ids.GetNumberOfIds()):
+ self.vtkInstance.GetPointIds().SetId(i, point_ids.GetId(i))
+ return call_SetPointIds
+
+ def compute_CopyImportString(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_CopyImportVoidPointer(self, pointer):
+ self.vtkInstance.CopyImportVoidPointer(pointer, len(pointer))
+ return call_CopyImportVoidPointer
+
+ def guarded_Writer_wrap_compute(old_compute):
+ # The behavior for vtkWriter subclasses is to call Write()
+ # If the user sets a name, we will create a file with that name
+ # If not, we will create a temporary file from the file pool
+ def compute(self):
+ old_compute(self)
+ fn = self.vtkInstance.GetFileName()
+ if not fn:
+ o = self.interpreter.filePool.create_file(suffix='.vtk')
+ self.vtkInstance.SetFileName(o.name)
+ else:
+ o = File()
+ o.name = fn
+ self.vtkInstance.Write()
+ self.setResult('file', o)
+ return compute
+
+ for var in dir(node.klass):
+ # Everyone that has a Set.*FileName should have a Set.*File port too
+ if set_file_name_pattern.match(var):
+ def get_compute_SetFile(method_name):
+ def compute_SetFile(old_compute):
+ if old_compute != None:
+ return old_compute
+ def call_SetFile(self, file_obj):
+ getattr(self.vtkInstance, method_name)(file_obj.name)
+ return call_SetFile
+ return compute_SetFile
+ update_dict('_special_input_function_' + var[:-4],
+ get_compute_SetFile(var))
+
+ if hasattr(node.klass, 'SetFileName'):
+ # ... BUT we only want to check existence of filenames on
+ # readers. VTK is nice enough to be consistent with names, but
+ # this is brittle..
+ if node.klass.__name__.endswith('Reader'):
+ if not node.klass.__name__.endswith('TiffReader'):
+ update_dict('compute', guarded_SetFileName_wrap_compute)
+ if hasattr(node.klass, 'SetRenderWindow'):
+ update_dict('_special_input_function_SetVTKCell',
+ compute_SetVTKCell)
+ #color gui wrapping
+ if hasattr(node.klass, 'SetDiffuseColor'):
+ update_dict('_special_input_function_SetDiffuseColorWidget',
+ compute_SetDiffuseColorWidget)
+ if hasattr(node.klass, 'SetAmbientColor'):
+ update_dict('_special_input_function_SetAmbientColorWidget',
+ compute_SetAmbientColorWidget)
+ if hasattr(node.klass, 'SetSpecularColor'):
+ update_dict('_special_input_function_SetSpecularColorWidget',
+ compute_SetSpecularColorWidget)
+ if hasattr(node.klass, 'SetEdgeColor'):
+ update_dict('_special_input_function_SetEdgeColorWidget',
+ compute_SetEdgeColorWidget)
+ if hasattr(node.klass, 'SetColor'):
+ update_dict('_special_input_function_SetColorWidget',
+ compute_SetColorWidget)
+ if (issubclass(node.klass, vtk.vtkRenderer) and
+ hasattr(node.klass, 'SetBackground')):
+ update_dict('_special_input_function_SetBackgroundWidget',
+ compute_SetBackgroundWidget)
+ if (issubclass(node.klass, vtk.vtkRenderer) and
+ hasattr(node.klass, 'SetBackground2')):
+ update_dict('_special_input_function_SetBackground2Widget',
+ compute_SetBackground2Widget)
+ if issubclass(node.klass, vtk.vtkWriter):
+ update_dict('compute', guarded_Writer_wrap_compute)
+
+ if issubclass(node.klass, vtk.vtkScalarTree):
+ update_dict('compute', guarded_SimpleScalarTree_wrap_compute)
+
+ if issubclass(node.klass, vtk.vtkVolumeProperty):
+ update_dict('_special_input_function_SetTransferFunction',
+ compute_SetTransferFunction)
+ if issubclass(node.klass, vtk.vtkDataSet):
+ update_dict('_special_input_function_SetPointData',
+ compute_SetPointData)
+ update_dict('_special_input_function_SetCellData',
+ compute_SetCellData)
+ if issubclass(node.klass, vtk.vtkCell):
+ update_dict('_special_input_function_SetPointIds',
+ compute_SetPointIds)
+ if issubclass(node.klass, vtk.vtkImageImport):
+ update_dict('_special_input_function_CopyImportString',
+ compute_CopyImportString)
+ return class_dict_
+
+disallowed_modules = set([
+ 'vtkGeoAlignedImageCache',
+ 'vtkGeoTerrainCache',
+ 'vtkMPIGroup'
+ ])
+def createModule(baseModule, node):
+ """ createModule(baseModule: a Module subclass, node: TreeNode) -> None
+ Construct a module inherits baseModule with specification from node
+
+ """
+ if node.name in disallowed_modules: return
+ def obsolete_class_list():
+ lst = []
+ items = ['vtkInteractorStyleTrackball',
+ 'vtkStructuredPointsGeometryFilter',
+ 'vtkConstrainedPointHandleRepresentation']
+ def try_to_add_item(item):
+ try:
+ lst.append(getattr(vtk, item))
+ except AttributeError:
+ pass
+ for item in items:
+ try_to_add_item(item)
+ return lst
+
+ obsolete_list = obsolete_class_list()
+
+ def is_abstract():
+ """is_abstract tries to instantiate the class. If it's
+ abstract, this will raise."""
+ # Consider obsolete classes abstract
+ if node.klass in obsolete_list:
+ return True
+ try:
+ getattr(vtk, node.name)()
+ except (TypeError, NotImplementedError): # VTK raises type error on abstract classes
+ return True
+ return False
+ module = new_module(baseModule, node.name,
+ class_dict(baseModule, node),
+ docstring=getattr(vtk, node.name).__doc__
+ )
+
+ # This is sitting on the class
+ if hasattr(fix_classes, node.klass.__name__ + '_fixed'):
+ module.vtkClass = getattr(fix_classes, node.klass.__name__ + '_fixed')
+ else:
+ module.vtkClass = node.klass
+ registry = get_module_registry()
+ registry.add_module(module, abstract=is_abstract(),
+ signatureCallable=vtk_hasher)
+ for child in node.children:
+ if child.name in disallowed_classes:
+ continue
+ createModule(module, child)
+
+def createAllModules(g):
+ """ createAllModules(g: ClassTree) -> None
+ Traverse the VTK class tree and add all modules into the module registry
+
+ """
+ v = vtk.vtkVersion()
+ version = [v.GetVTKMajorVersion(),
+ v.GetVTKMinorVersion(),
+ v.GetVTKBuildVersion()]
+ if version < [5, 7, 0]:
+ assert len(g.tree[0]) == 1
+ base = g.tree[0][0]
+ assert base.name == 'vtkObjectBase'
+
+ vtkObjectBase = new_module(vtkBaseModule, 'vtkObjectBase')
+ vtkObjectBase.vtkClass = vtk.vtkObjectBase
+ registry = get_module_registry()
+ registry.add_module(vtkObjectBase)
+ if version < [5, 7, 0]:
+ for child in base.children:
+ if child.name in disallowed_classes:
+ continue
+ createModule(vtkObjectBase, child)
+ else:
+ for base in g.tree[0]:
+ for child in base.children:
+ if child.name in disallowed_classes:
+ continue
+ createModule(vtkObjectBase, child)
+
+
+################################################################################
+
+def initialize():
+ """ initialize() -> None
+ Package-entry to initialize the package
+
+ """
+ # Check VTK version
+ v = vtk.vtkVersion()
+ version = [v.GetVTKMajorVersion(),
+ v.GetVTKMinorVersion(),
+ v.GetVTKBuildVersion()]
+ if version < [5, 0, 0]:
+ raise RuntimeError("You need to upgrade your VTK install to version "
+ ">= 5.0.0")
+ inheritanceGraph = ClassTree(vtk)
+ inheritanceGraph.create()
+
+ # Transfer Function constant
+ tf_widget.initialize()
+
+ delayed = InstanceObject(add_input_port=[])
+ # Add VTK modules
+ registry = get_module_registry()
+ registry.add_module(vtkBaseModule)
+ createAllModules(inheritanceGraph)
+ setAllPorts(registry.get_descriptor_by_name(identifier,
+ 'vtkObjectBase'),
+ delayed)
+
+ # Register the VTKCell and VTKHandler type if the spreadsheet is up
+ if registry.has_module('%s.spreadsheet' % \
+ get_vistrails_default_pkg_prefix(),
+ 'SpreadsheetCell'):
+ import vtkhandler
+ import vtkcell
+ import vtkviewcell
+ vtkhandler.registerSelf()
+ vtkcell.registerSelf()
+ vtkviewcell.registerSelf()
+
+ # register offscreen rendering module
+ offscreen.register_self()
+
+ # Now add all "delayed" ports - see comment on addSetGetPorts
+ for args in delayed.add_input_port:
+
+ registry.add_input_port(*args)
+
+ # register Transfer Function adjustment
+ # This can't be reordered -- TransferFunction needs to go before
+ # vtkVolumeProperty, but vtkScaledTransferFunction needs
+ # to go after vtkAlgorithmOutput
+ getter = registry.get_descriptor_by_name
+ registry.add_module(tf_widget.vtkScaledTransferFunction)
+ # FIXME Add documentation
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'Input', getter(vtk_pkg_identifier,
+ 'vtkAlgorithmOutput').module)
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'Dataset', getter (vtk_pkg_identifier,
+ 'vtkDataObject').module)
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'Range', [Float, Float])
+ registry.add_input_port(tf_widget.vtkScaledTransferFunction,
+ 'TransferFunction',
+ tf_widget.TransferFunctionConstant)
+ registry.add_output_port(tf_widget.vtkScaledTransferFunction,
+ 'TransferFunction',
+ tf_widget.TransferFunctionConstant)
+ registry.add_output_port(tf_widget.vtkScaledTransferFunction,
+ 'vtkPiecewiseFunction',
+ getter(vtk_pkg_identifier,
+ 'vtkPiecewiseFunction').module)
+ registry.add_output_port(tf_widget.vtkScaledTransferFunction,
+ 'vtkColorTransferFunction',
+ getter(vtk_pkg_identifier,
+ 'vtkColorTransferFunction').module)
+
+ inspectors.initialize()
+
+################################################################################
+
+_remap = None
+_controller = None
+_pipeline = None
+
+def _get_controller():
+ global _controller
+ return _controller
+
+def _get_pipeline():
+ global _pipeline
+ return _pipeline
+
+def build_remap(module_name=None):
+ global _remap, _controller
+
+ reg = get_module_registry()
+ uscore_num = re.compile(r"(.+)_(\d+)$")
+
+ def get_port_specs(descriptor, port_type):
+ ports = {}
+ for desc in reversed(reg.get_module_hierarchy(descriptor)):
+ ports.update(reg.module_ports(port_type, desc))
+ return ports
+
+ def build_remap_method(desc, port_prefix, port_num, port_type):
+ # for connection, need to differentiate between src and dst
+ if port_type == 'input':
+ conn_lookup = Connection._get_destination
+ get_port_spec = reg.get_input_port_spec
+ idx = 1
+ else:
+ conn_lookup = Connection._get_source
+ get_port_spec = reg.get_output_port_spec
+ idx = 0
+
+ def remap(old_conn, new_module):
+ create_new_connection = UpgradeWorkflowHandler.create_new_connection
+ port = conn_lookup(old_conn)
+ pipeline = _get_pipeline()
+ modules = [pipeline.modules[old_conn.source.moduleId],
+ pipeline.modules[old_conn.destination.moduleId]]
+ modules[idx] = new_module
+ ports = [old_conn.source, old_conn.destination]
+ for i in xrange(1, port_num):
+ port_name = "%s_%d" % (port_prefix, i)
+ port_spec = get_port_spec(modules[idx], port_name)
+ if port_spec.sigstring == port.signature:
+ ports[idx] = port_name
+ new_conn = create_new_connection(_get_controller(),
+ modules[0],
+ ports[0],
+ modules[1],
+ ports[1])
+ return [('add', new_conn)]
+
+ # if get here, just try to use _1 version?
+ ports[idx] = "%s_%d" % (port_prefix, 1)
+ new_conn = create_new_connection(_get_controller(),
+ modules[0],
+ ports[0],
+ modules[1],
+ ports[1])
+ return [('add', new_conn)]
+ return remap
+
+ def build_function_remap_method(desc, port_prefix, port_num):
+ f_map = {"vtkCellArray": {"InsertNextCell": 3}}
+ def build_function(old_function, new_function_name, new_module):
+ controller = _get_controller()
+ if len(old_function.parameters) > 0:
+ new_param_vals, aliases = \
+ zip(*[(p.strValue, p.alias)
+ for p in old_function.parameters])
+ else:
+ new_param_vals = []
+ aliases = []
+ new_function = controller.create_function(new_module,
+ new_function_name,
+ new_param_vals,
+ aliases)
+ return new_function
+
+ def remap(old_function, new_module):
+ for i in xrange(1, port_num):
+ port_name = "%s_%d" % (port_prefix, i)
+ port_spec = reg.get_input_port_spec(new_module, port_name)
+ old_sigstring = \
+ reg.expand_port_spec_string(old_function.sigstring,
+ basic_pkg)
+ if port_spec.sigstring == old_sigstring:
+ new_function = build_function(old_function, port_name,
+ new_module)
+ new_module.add_function(new_function)
+ return []
+ port_idx = 1
+ if desc.name in f_map:
+ if port_prefix in f_map[desc.name]:
+ port_idx = f_map[desc.name][port_prefix]
+ port_name = "%s_%d" % (port_prefix, port_idx)
+ new_function = build_function(old_function, port_name, new_module)
+ new_module.add_function(new_function)
+ return []
+
+ return remap
+
+ def process_ports(desc, port_type):
+ if port_type == 'input':
+ remap_dict_key = 'dst_port_remap'
+ else:
+ remap_dict_key = 'src_port_remap'
+ ports = get_port_specs(desc, port_type)
+ port_nums = {}
+ for port_name, port_spec in ports.iteritems():
+ # FIXME just start at 1 and go until don't find port (no
+ # need to track max)?
+ search_res = uscore_num.search(port_name)
+ if search_res:
+ port_prefix = search_res.group(1)
+ port_num = int(search_res.group(2))
+ if port_prefix not in port_nums:
+ port_nums[port_prefix] = port_num
+ elif port_num > port_nums[port_prefix]:
+ port_nums[port_prefix] = port_num
+ if desc.name not in _remap:
+ _remap[desc.name] = [(None, '0.9.3', None, dict())]
+ for port_prefix, port_num in port_nums.iteritems():
+ my_remap_dict = _remap[desc.name][0][3]
+ if remap_dict_key not in my_remap_dict:
+ my_remap_dict[remap_dict_key] = dict()
+ remap = build_remap_method(desc, port_prefix, port_num, port_type)
+ my_remap_dict[remap_dict_key][port_prefix] = remap
+ if port_type == 'input':
+ remap = build_function_remap_method(desc, port_prefix, port_num)
+ if 'function_remap' not in my_remap_dict:
+ my_remap_dict['function_remap'] = {}
+ my_remap_dict['function_remap'][port_prefix] = remap
+
+ pkg = reg.get_package_by_name(identifier)
+ if module_name is not None:
+ # print 'building remap for', module_name
+ desc = reg.get_descriptor_by_name(identifier, module_name)
+ process_ports(desc, 'input')
+ process_ports(desc, 'output')
+ else:
+ # print 'building entire remap'
+ # FIXME do this by descriptor first, then build the hierarchies for each
+ # module after that...
+ for desc in pkg.descriptor_list:
+ process_ports(desc, 'input')
+ process_ports(desc, 'output')
+
+def handle_module_upgrade_request(controller, module_id, pipeline):
+ global _remap, _controller, _pipeline
+ reg = get_module_registry()
+ if _remap is None:
+ _remap = {}
+
+ _controller = controller
+ _pipeline = pipeline
+ module_name = pipeline.modules[module_id].name
+ if module_name not in _remap:
+ build_remap(module_name)
+ return UpgradeWorkflowHandler.remap_module(controller, module_id, pipeline,
+ _remap)
diff --git a/vistrails/packages/vtk/inspectors.py b/vistrails/packages/vtk/inspectors.py
new file mode 100644
index 0000000..2cd770b
--- /dev/null
+++ b/vistrails/packages/vtk/inspectors.py
@@ -0,0 +1,244 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+##############################################################################
+# Data inspectors for VTK
+from vistrails.core.modules.vistrails_module import ModuleError
+from vistrails.core.utils import VistrailsInternalError
+from vistrails.core.modules.basic_modules import Module, Float, Integer
+from vistrails.core.modules.module_registry import get_module_registry
+import vtk
+from base_module import vtkBaseModule
+from hasher import vtk_hasher
+from identifiers import identifier as vtk_pkg_identifier
+
+class vtkBaseInspector(Module):
+
+ @classmethod
+ def register_self(cls, **kwargs):
+ registry = get_module_registry()
+ def resolve_type(t):
+ if isinstance(t, tuple):
+ return registry.get_descriptor_by_name(*t).module
+ elif isinstance(t, type):
+ return t
+ else:
+ assert False, ("Unknown type " + str(type(t)))
+
+ registry.add_module(cls, **kwargs)
+ try:
+ ips = cls.input_ports
+ except AttributeError:
+ pass
+ else:
+ for (port_name, types) in ips:
+ registry.add_input_port(cls,
+ port_name,
+ list(resolve_type(t) for t in types))
+
+ try:
+ ops = cls.output_ports
+ except AttributeError:
+ pass
+ else:
+ for (port_name, types) in ops:
+ registry.add_output_port(cls,
+ port_name,
+ list(resolve_type(t) for t in types))
+
+ def auto_set_results(self, vtk_object):
+ for function in self.outputPorts.keys():
+ if hasattr(vtk_object, function):
+ retValues = getattr(vtk_object, function)()
+ if issubclass(retValues.__class__, vtk.vtkObject):
+ className = retValues.GetClassName()
+ output = vtkBaseModule.wrapperModule(className, retValues)
+ self.setResult(function, output)
+ elif isinstance(retValues, (tuple, list)):
+ result = list(retValues)
+ for i in xrange(len(result)):
+ if issubclass(result[i].__class__, vtk.vtkObject):
+ className = result[i].GetClassName()
+ result[i] = vtkBaseModule.wrapperModule(className,
+ result[i])
+ self.setResult(function, type(retValues)(result))
+ else:
+ self.setResult(function, retValues)
+
+class vtkDataSetInspector(vtkBaseInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInputConnection0"):
+ ic = self.getInputFromPort("SetInputConnection0")
+ port_object = ic.vtkInstance
+ ix = port_object.GetIndex()
+ producer = port_object.GetProducer()
+ try:
+ vtk_object = producer.GetOutput()
+ except AttributeError:
+ raise ModuleError(self,
+ "expected a module that supports GetOutput")
+ elif self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+ input_ports = [('SetInputConnection0',
+ [(vtk_pkg_identifier, 'vtkAlgorithmOutput')]),
+ ('SetInput',
+ [(vtk_pkg_identifier, 'vtkDataSet')]),
+ ]
+ output_ports = [('GetBounds', [Float] * 6),
+ ('GetScalarRange', [Float] * 2),
+ ('GetLength', [Float]),
+ ('GetCenter', [Float] * 3),
+ ('GetNumberOfPoints', [Integer]),
+ ('GetNumberOfCells', [Integer]),
+ ('GetPointData',
+ [(vtk_pkg_identifier, 'vtkPointData')]),
+ ('GetCellData',
+ [(vtk_pkg_identifier, 'vtkCellData')]),
+ ]
+
+class vtkDataSetAttributesInspector(vtkBaseInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+ input_ports = [('SetInput',
+ [(vtk_pkg_identifier, 'vtkDataSetAttributes')]),
+ ]
+ output_ports = [('GetScalars',
+ [(vtk_pkg_identifier, 'vtkDataArray')]),
+ ('GetVectors',
+ [(vtk_pkg_identifier, 'vtkDataArray')]),
+ ('GetNormals',
+ [(vtk_pkg_identifier, 'vtkDataArray')]),
+ ('GetTCoords',
+ [(vtk_pkg_identifier, 'vtkDataArray')]),
+ ('GetTensors',
+ [(vtk_pkg_identifier, 'vtkDataArray')]),
+ ('GetGlobalIds',
+ [(vtk_pkg_identifier, 'vtkDataArray')]),
+ ('GetPedigreeIds',
+ [(vtk_pkg_identifier, 'vtkAbstractArray')]),
+ ]
+
+class vtkDataArrayInspector(vtkBaseInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+ input_ports = [('SetInput',
+ [(vtk_pkg_identifier, 'vtkDataArray')])]
+ output_ports = [('GetMaxNorm', [Float]),
+ ('GetRange', [Float] * 2)]
+
+class vtkPolyDataInspector(vtkDataSetInspector):
+
+ def compute(self):
+ vtk_object = None
+ if self.hasInputFromPort("SetInputConnection0"):
+ ic = self.getInputFromPort("SetInputConnection0")
+ port_object = ic.vtkInstance
+ ix = port_object.GetIndex()
+ producer = port_object.GetProducer()
+ try:
+ vtk_object = producer.GetOutput()
+ except AttributeError:
+ raise ModuleError(self,
+ "expected a module that supports GetOutput")
+ elif self.hasInputFromPort("SetInput"):
+ port_object = self.getInputFromPort("SetInput")
+ if hasattr(port_object, "vtkInstance"):
+ vtk_object = port_object.vtkInstance
+ else:
+ raise ModuleError(self, "expected a vtk module")
+ if vtk_object:
+ self.auto_set_results(vtk_object)
+
+ input_ports = [('SetInputConnection0',
+ [(vtk_pkg_identifier, 'vtkAlgorithmOutput')]),
+ ('SetInput',
+ [(vtk_pkg_identifier, 'vtkDataSet')]),
+ ]
+ output_ports = [('GetVerts',
+ [(vtk_pkg_identifier, 'vtkCellArray')]),
+ ('GetLines',
+ [(vtk_pkg_identifier, 'vtkCellArray')]),
+ ('GetPolys',
+ [(vtk_pkg_identifier, 'vtkCellArray')]),
+ ('GetStrips',
+ [(vtk_pkg_identifier, 'vtkCellArray')]),
+ ('GetPoints',
+ [(vtk_pkg_identifier, 'vtkPoints')]),
+ ('GetNumberOfVerts', [Integer]),
+ ('GetNumberOfLines', [Integer]),
+ ('GetNumberOfPolys', [Integer]),
+ ('GetNumberOfStrips', [Integer]),
+ ]
+
+def initialize():
+ vtkBaseInspector.register_self(abstract=True, signatureCallable=vtk_hasher)
+ vtkDataSetInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+ vtkDataSetAttributesInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+ vtkDataArrayInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+ vtkPolyDataInspector.register_self(abstract=False,
+ signatureCallable=vtk_hasher)
+
diff --git a/vistrails/packages/vtk/offscreen.py b/vistrails/packages/vtk/offscreen.py
new file mode 100644
index 0000000..f8b2d15
--- /dev/null
+++ b/vistrails/packages/vtk/offscreen.py
@@ -0,0 +1,87 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import vtk
+from identifiers import identifier as vtk_pkg_identifier
+
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.modules.vistrails_module import Module
+from vistrails.core.modules.basic_modules import File, Integer
+from vistrails.core import system
+
+class VTKRenderOffscreen(Module):
+
+ def compute(self):
+ r = self.getInputFromPort("renderer").vtkInstance
+ window = vtk.vtkRenderWindow()
+ w = self.forceGetInputFromPort("width", 512)
+ h = self.forceGetInputFromPort("height", 512)
+ window.OffScreenRenderingOn()
+ window.SetSize(w, h)
+ # r.ResetCamera()
+
+ widget = None
+ if system.systemType=='Darwin':
+ from PyQt4 import QtCore, QtGui
+ widget = QtGui.QWidget(None, QtCore.Qt.FramelessWindowHint)
+ widget.resize(w, h)
+ widget.show()
+ window.SetWindowInfo(str(int(widget.winId())))
+
+ window.AddRenderer(r)
+# window.Start()
+ window.Render()
+ win2image = vtk.vtkWindowToImageFilter()
+ win2image.SetInput(window)
+ win2image.Update()
+ writer = vtk.vtkPNGWriter()
+ writer.SetInput(win2image.GetOutput())
+ output = self.interpreter.filePool.create_file(suffix='.png')
+ writer.SetFileName(output.name)
+ writer.Write()
+ window.Finalize()
+ if widget!=None:
+ widget.close()
+ self.setResult("image", output)
+
+def register_self():
+ registry = get_module_registry()
+ r = registry.get_descriptor_by_name(vtk_pkg_identifier,
+ 'vtkRenderer').module
+ registry.add_module(VTKRenderOffscreen)
+ registry.add_input_port(VTKRenderOffscreen, 'renderer', r)
+ registry.add_input_port(VTKRenderOffscreen, 'width', Integer)
+ registry.add_input_port(VTKRenderOffscreen, 'height', Integer)
+ registry.add_output_port(VTKRenderOffscreen, 'image', File)
+
diff --git a/vistrails/packages/vtk/tf_widget.py b/vistrails/packages/vtk/tf_widget.py
new file mode 100644
index 0000000..b5ebc7e
--- /dev/null
+++ b/vistrails/packages/vtk/tf_widget.py
@@ -0,0 +1,736 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+##############################################################################
+# Transfer Function Widget for VTK
+from PyQt4 import QtCore, QtGui
+from vistrails.gui.modules.constant_configuration import ConstantWidgetMixin
+from vistrails.core.modules.basic_modules import new_constant, init_constant, Module
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.system import get_elementtree_library
+from vistrails.core.utils.color import ColorByName
+import vtk
+import math
+import pickle
+import copy
+import StringIO
+import unittest
+ElementTree = get_elementtree_library()
+
+from identifiers import identifier as vtk_pkg_identifier
+
+################################################################################
+# etc
+
+def clamp(v, mn, mx, eps=0.0):
+ mne = mn + eps
+ mxe = mx - eps
+ if v < mne: return mn
+ if v > mxe: return mx
+ return v
+# Because of a Qt bug see
+# http://bugreports.qt.nokia.com/browse/QTBUG-17985
+# We cannot set the scene from 0 to 1. In this case we will set it
+# 4000 x 4000 with GLOBAL_SCALE. When the bug is fixed, just set it to 1.0
+
+GLOBAL_SCALE = 4000.0
+##############################################################################
+# Transfer Function object
+
+class TransferFunction(object):
+
+ def __init__(self):
+ self._min_range = 0.0
+ self._max_range = 1.0
+ self._pts = []
+
+ def set_range(self, mn, mx):
+ self._min_range = mn
+ self._max_range = mx
+
+ def set_on_vtk_volume_property(self, vtk_volume_property):
+ # Builds the opacity and color functions
+ of = vtk.vtkPiecewiseFunction()
+ cf = vtk.vtkColorTransferFunction()
+ vp = vtk_volume_property
+ for pt in self._pts:
+ (scalar, opacity, color) = pt
+ # Map scalar to tf range
+ s = self._min_range + (self._max_range - self._min_range) * scalar
+ of.AddPoint(s, opacity)
+ cf.AddRGBPoint(s, color[0], color[1], color[2])
+ vp.SetScalarOpacity(of)
+ vp.SetColor(cf)
+
+ def get_vtk_transfer_functions(self):
+ of = vtk.vtkPiecewiseFunction()
+ cf = vtk.vtkColorTransferFunction()
+ for pt in self._pts:
+ (scalar, opacity, color) = pt
+ # Map scalar to tf range
+ s = self._min_range + (self._max_range - self._min_range) * scalar
+ of.AddPoint(s, opacity)
+ cf.AddRGBPoint(s, color[0], color[1], color[2])
+ return (of,cf)
+
+ def add_point(self, scalar, opacity, color):
+ self._pts.append((scalar, opacity, color))
+ self._pts.sort()
+
+ def get_value(self, scalar):
+ """get_value(scalar): returns the opacity and color
+ linearly interpolated at the value. Useful for
+ adding knots."""
+ ix = 0
+ while ix < len(self._pts) and self._pts[ix][0] > scalar:
+ ix += 1
+ if ix == 0:
+ return (self._pts[0][1], self._pts[0][2])
+ elif ix == len(self._pts):
+ return (self._pts[-1][1], self._pts[-1][2])
+ else:
+ u = ((self._pts[ix][0] - scalar) /
+ (self._pts[ix][0] - self._pts[ix-1][0]))
+ do = self._pts[ix][1] - self._pts[ix-1][1]
+ dr = self._pts[ix][2][0] - self._pts[ix-1][2][0]
+ dg = self._pts[ix][2][1] - self._pts[ix-1][2][1]
+ db = self._pts[ix][2][2] - self._pts[ix-1][2][2]
+ return (self._pts[ix-1][1] + u * do,
+ (self._pts[ix-1][2][0] + u * dr,
+ self._pts[ix-1][2][1] + u * dg,
+ self._pts[ix-1][2][2] + u * db))
+
+ def __copy__(self):
+ result = TransferFunction()
+ result._min_range = self._min_range
+ result._max_range = self._max_range
+ result._pts = copy.copy(self._pts)
+ return result
+
+ def __eq__(self, other):
+ if type(other) != type(self):
+ return False
+ if self._min_range != other._min_range:
+ return False
+ if self._max_range != other._max_range:
+ return False
+ for my_pt, other_pt in zip(self._pts, other._pts):
+ if my_pt != other_pt:
+ return False
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+ def serialize(self, node=None):
+ """serialize(node: ElementTree.Element) -> str
+ Convert this object to an XML representation in string format.
+ """
+ if node is None:
+ node = ElementTree.Element('transfer_function')
+
+ node.set('min_range', str(self._min_range))
+ node.set('max_range', str(self._max_range))
+ for pt in self._pts:
+ ptNode = ElementTree.SubElement(node, 'point')
+ ptNode.set('scalar', str(pt[0]))
+ ptNode.set('opacity', str(pt[1]))
+ color = pt[2]
+ colorNode = ElementTree.SubElement(ptNode, 'color')
+ colorNode.set('R', str(color[0]))
+ colorNode.set('G', str(color[1]))
+ colorNode.set('B', str(color[2]))
+
+ return ElementTree.tostring(node)
+
+ @staticmethod
+ def parse(strNode):
+ """parse(strNode: str) -> TransferFunction
+ Parses a string representing a TransferFunction and returns a
+ TransferFunction object
+ """
+ try:
+ node = ElementTree.fromstring(strNode)
+ except SyntaxError:
+ #it was serialized using pickle
+ class FixUnpickler(pickle.Unpickler):
+ def find_class(self, module, name):
+ if module == 'packages.vtk.tf_widget':
+ module = 'vistrails.packages.vtk.tf_widget'
+ return pickle.Unpickler.find_class(self, module, name)
+ tf = FixUnpickler(StringIO.StringIO(strNode.decode('hex'))).load()
+ tf._pts.sort()
+ return tf
+
+ if node.tag != 'transfer_function':
+ return None
+ #read attributes
+ tf = TransferFunction()
+ tf._min_range = float(node.get('min_range', "0.0"))
+ tf._max_range = float(node.get('max_range', "1.0"))
+ for ptNode in node.getchildren():
+ if ptNode.tag == 'point':
+ scalar = float(ptNode.get('scalar','-1.0'))
+ opacity = float(ptNode.get('opacity', '1.0'))
+ for colorNode in ptNode.getchildren():
+ if colorNode.tag == 'color':
+ color = (float(colorNode.get('R','0.0')),
+ float(colorNode.get('G','0.0')),
+ float(colorNode.get('B','0.0')))
+ break
+ tf._pts.append((scalar,opacity,color))
+ tf._pts.sort()
+ return tf
+
+##############################################################################
+# Graphics Items
+
+class TransferFunctionPoint(QtGui.QGraphicsEllipseItem):
+
+ selection_pens = { True: QtGui.QPen(QtGui.QBrush(
+ QtGui.QColor(*(ColorByName.get_int('goldenrod_medium')))),GLOBAL_SCALE * 0.012),
+ False: QtGui.QPen() }
+
+ def __init__(self, scalar, opacity, color, parent=None):
+ QtGui.QGraphicsEllipseItem.__init__(self, parent)
+ self._scalar = scalar
+ self._opacity = opacity
+ self._color = QtGui.QColor(color[0]*255,
+ color[1]*255,
+ color[2]*255)
+ self.setPen(QtGui.QPen(QtGui.QColor(0,0,0)))
+ self.setFlag(QtGui.QGraphicsItem.ItemIsMovable)
+ self.setFlag(QtGui.QGraphicsItem.ItemIsSelectable)
+ self.setFlag(QtGui.QGraphicsItem.ItemIsFocusable)
+ if QtCore.QT_VERSION >= 0x40600:
+ self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges)
+ self.setZValue(2.0)
+
+ self._sx = 1.0
+ self._sy = 1.0
+ # fixed scale
+ self._fsx = GLOBAL_SCALE
+ self._fsy = GLOBAL_SCALE
+ self._left_line = None
+ self._right_line = None
+ self._point = QtCore.QPointF(scalar * self._fsx, opacity * self._fsy)
+ self.refresh()
+
+ self.setToolTip("Double-click to change color\n"
+ "Right-click to remove point\n"
+ "Scalar: %.5f, Opacity: %.5f" % (self._scalar,
+ self._opacity))
+ # This sets up the linked list of Lines
+
+ def keyPressEvent(self, event):
+ if event.key() == QtCore.Qt.Key_Backspace or \
+ event.key() == QtCore.Qt.Key_Delete:
+ self.remove_self()
+
+ def refresh(self):
+ dx = self._fsx * 0.025 / self._sx
+ dy = self._fsy * 0.025/ self._sy
+ # this is the setup
+ self.setBrush(QtGui.QBrush(self._color))
+ self.setRect(-dx,
+ -dy,
+ 2 * dx, 2 * dy)
+ self.setPos(self._fsx * self._scalar,
+ self._fsy * self._opacity)
+ self.update()
+
+ def update_scale(self, sx, sy):
+ self._sx = sx
+ self._sy = sy
+ self.refresh()
+
+ def itemChange(self, change, value):
+ if change == QtGui.QGraphicsItem.ItemSelectedChange:
+ self.setPen(self.selection_pens[value])
+ if change == QtGui.QGraphicsItem.ItemPositionChange:
+ # moves point
+ # value is now a QPointF, not a QPoint so no conversion needed
+ pt = value
+ pt.setY(clamp(pt.y(), 0.0, 1.0 * self._fsy) )
+ self._opacity = pt.y() / self._fsy
+ self._point.setY(pt.y())
+ if not self._left_line:
+ pt.setX(0.0)
+ elif not self._right_line:
+ pt.setX(1.0 * self._fsx)
+ else:
+ assert self._left_line._point_right == self
+ assert self._right_line._point_left == self
+ pt.setX(clamp(pt.x(),
+ self._left_line._point_left._point.x(),
+ self._right_line._point_right._point.x(),
+ 1e-6))
+ self._point.setX(pt.x())
+ self._scalar = pt.x() / self._fsx
+ if self._left_line:
+ self._left_line.refresh()
+ if self._right_line:
+ self._right_line.refresh()
+ if self.scene():
+ self.scene()._tf_poly.setup()
+ self.setToolTip("Double-click to change color\n"
+ "Right-click to remove point\n"
+ "Scalar: %.5f, Opacity: %.5f" % (self._scalar,
+ self._opacity))
+ return QtGui.QGraphicsItem.itemChange(self, change, pt)
+ return QtGui.QGraphicsItem.itemChange(self, change, value)
+
+ def remove_self(self):
+ if not self._left_line or not self._right_line:
+ # Ignore, self is a corner node that can't be removed
+ return
+
+ # Removes the right line and self, re-ties data structure
+ self._left_line._point_right = self._right_line._point_right
+ self._left_line._point_right._left_line = self._left_line
+
+ # be friends with garbage collector
+ self._right_line._point_left = None
+ self._right_line._point_right = None
+ self.scene()._tf_poly.setup()
+ self.scene().removeItem(self._right_line)
+ self.scene().removeItem(self)
+ self._left_line.refresh()
+
+ def mouseDoubleClickEvent(self, event):
+ new_color = QtGui.QColorDialog.getColor(self._color)
+ if not new_color.isValid():
+ return
+ self._color = new_color
+ if self._left_line:
+ self._left_line.refresh()
+ if self._right_line:
+ self._right_line.refresh()
+ self.refresh()
+ self.scene()._tf_poly.setup()
+ QtGui.QGraphicsEllipseItem.mouseDoubleClickEvent(self, event)
+
+ def mousePressEvent(self, event):
+ if event.button() == QtCore.Qt.RightButton:
+ event.accept()
+ self.remove_self()
+ else:
+ QtGui.QGraphicsEllipseItem.mousePressEvent(self, event)
+
+ def paint(self, painter, option, widget=None):
+ """ paint(painter: QPainter, option: QStyleOptionGraphicsItem,
+ widget: QWidget) -> None
+ Peform painting of the point without the ugly default dashed-line black
+ square
+
+ """
+ painter.setBrush(self.brush())
+ painter.setPen(self.pen())
+ painter.drawEllipse(self.rect())
+
+ def add_self_to_transfer_function(self, tf):
+ tf.add_point(self._scalar,
+ self._opacity,
+ (self._color.redF(),
+ self._color.greenF(),
+ self._color.blueF()))
+
+class TransferFunctionPolygon(QtGui.QGraphicsPolygonItem):
+
+ def __init__(self):
+ QtGui.QGraphicsPolygonItem.__init__(self)
+
+ def setup(self):
+ # This inspects the scene, finds the left-most point, and
+ # then builds the polygon traversing the linked list structure
+ if not self.scene():
+ return
+ pt = self.scene().get_leftmost_point()
+ first_pt = pt
+ self.setZValue(1.25)
+ g = QtGui.QLinearGradient()
+ g.setStart(0.0, 0.5)
+ g.setFinalStop(1.0, 0.5)
+ g.setCoordinateMode(QtGui.QGradient.ObjectBoundingMode)
+ p = QtGui.QPen()
+ p.setStyle(QtCore.Qt.NoPen)
+ pts = [QtCore.QPointF(pt.x(), 0)]
+ self.setPen(p)
+ while 1:
+ c = QtGui.QColor(pt._color)
+ c.setAlphaF(pt._opacity)
+ g.setColorAt(pt._scalar, c)
+ pts.append(pt._point)
+ # move cursor fwd
+ if pt._right_line:
+ pt = pt._right_line._point_right
+ else:
+ break
+ self.setBrush(QtGui.QBrush(g))
+ pts.append(QtCore.QPointF(pt._point.x(), 0))
+ polygon = QtGui.QPolygonF(pts)
+ self.setPolygon(polygon)
+
+class TransferFunctionLine(QtGui.QGraphicsPolygonItem):
+
+ def __init__(self, point_left, point_right, parent=None):
+ assert point_right._scalar >= point_left._scalar
+ QtGui.QGraphicsPolygonItem.__init__(self, parent)
+ self._point_left = point_left
+ self._point_right = point_right
+ self._point_left._right_line = self
+ self._point_right._left_line = self
+ self.setup(1.0, 1.0)
+ self._sx = 1.0
+ self._sy = 1.0
+ # fixed scale
+ self._fsx = GLOBAL_SCALE
+ self._fsy = GLOBAL_SCALE
+ self.setToolTip('')
+
+ def setup(self, sx, sy):
+ d = self._point_right._point - self._point_left._point
+ d_normal = QtCore.QPointF(d.y(), -d.x())
+ l = math.sqrt(d.x() * d.x() + d.y() * d.y())
+ if l != 0.0:
+ d_normal /= l
+ d_normal *= GLOBAL_SCALE * 0.010
+ d_normal.setX(d_normal.x() / sx)
+ d_normal.setY(d_normal.y() / sy)
+ ps = [self._point_left._point + d_normal,
+ self._point_right._point + d_normal,
+ self._point_right._point - d_normal,
+ self._point_left._point - d_normal]
+ self.setPolygon(QtGui.QPolygonF(ps))
+ self.setZValue(1.5)
+ # Gradient for filling
+ g = QtGui.QLinearGradient()
+ g.setCoordinateMode(QtGui.QGradient.ObjectBoundingMode)
+ g.setStart(self._point_left._scalar, self._point_left._opacity)
+ g.setFinalStop(self._point_right._scalar, self._point_right._opacity)
+ g.setColorAt(0.0, self._point_left._color)
+ g.setColorAt(1.0, self._point_right._color)
+ self.setBrush(QtGui.QBrush(g))
+ # Gradient for outlining
+ g = QtGui.QLinearGradient()
+ g.setStart(self._point_left._point)
+ g.setFinalStop(self._point_right._point)
+ dark_pl = QtGui.QColor(self._point_left._color.red() * 0.5,
+ self._point_left._color.green() * 0.5,
+ self._point_left._color.blue() * 0.5)
+ dark_pr = QtGui.QColor(self._point_right._color.red() * 0.5,
+ self._point_right._color.green() * 0.5,
+ self._point_right._color.blue() * 0.5)
+ g.setColorAt(0.0, dark_pl)
+ g.setColorAt(1.0, dark_pr)
+ p = QtGui.QPen()
+ p.setBrush(QtGui.QBrush(g))
+ self.setPen(p)
+
+ def update_scale(self, sx, sy):
+ self._sx = sx
+ self._sy = sy
+ self.refresh()
+
+ def refresh(self):
+ self.setup(self._sx, self._sy)
+
+ def mouseDoubleClickEvent(self, event):
+ p = event.scenePos()
+ c_left = self._point_left._color
+ c_right = self._point_right._color
+ u = ((p.x() - self._point_left._point.x()) /
+ (self._point_right._point.x() - self._point_left._point.x()))
+ new_c = (u * c_right.redF() + (1-u) * c_left.redF(),
+ u * c_right.greenF() + (1-u) * c_left.greenF(),
+ u * c_right.blueF() + (1-u) * c_left.blueF())
+ new_point = TransferFunctionPoint(p.x()/ self._fsx, p.y()/self._fsy, new_c)
+ new_line = TransferFunctionLine(new_point, self._point_right)
+ new_point._left_line = self
+ self._point_right = new_point
+ self.scene().addItem(new_line)
+ self.scene().addItem(new_point)
+ new_line.update_scale(self._point_left._sx,
+ self._point_left._sy)
+ new_point.update_scale(self._point_left._sx,
+ self._point_left._sy)
+ new_point.refresh()
+ self.refresh()
+
+ def mousePressEvent(self, event):
+ # This needs to be here, otherwise mouseDoubleClickEvent does
+ # not get called.
+ event.accept()
+
+
+##############################################################################
+# Scene, view, widget
+
+class TransferFunctionScene(QtGui.QGraphicsScene):
+
+ def __init__(self, tf, parent=None):
+ QtGui.QGraphicsScene.__init__(self, parent)
+ self._tf_items = []
+ poly = TransferFunctionPolygon()
+ poly.setup()
+ self._tf_poly = poly
+ self.addItem(poly)
+ self.create_tf_items(tf)
+ self._tf_poly.setup()
+ #current scale
+ self._sx = 1.0
+ self._sy = 1.0
+ # Add outlines
+ line_color = QtGui.QColor(200, 200, 200)
+ pen = QtGui.QPen(line_color)
+ ps = [QtCore.QPointF(0.0, 0.0),
+ QtCore.QPointF(GLOBAL_SCALE, 0.0),
+ QtCore.QPointF(GLOBAL_SCALE, GLOBAL_SCALE),
+ QtCore.QPointF(0.0, GLOBAL_SCALE)]
+ outline = QtGui.QPolygonF(ps)
+ self.addPolygon(outline, pen)
+
+ for i in xrange(51):
+ u = GLOBAL_SCALE * float(i) / 50.0
+ self.addLine(QtCore.QLineF(u, 0.0, u, GLOBAL_SCALE), pen)
+ self.addLine(QtCore.QLineF(0.0, u, GLOBAL_SCALE, u), pen)
+
+ def reset_transfer_function(self, tf):
+ self.create_tf_items(tf)
+ self.update_scale(self._sx, self._sy)
+ self._tf_poly.setup()
+
+ def removeItem(self, item):
+ if item in self._tf_items:
+ self._tf_items.remove(item)
+ QtGui.QGraphicsScene.removeItem(self, item)
+
+ def addItem(self, item):
+ # Ugly, but hey
+ if isinstance(item, TransferFunctionLine) or \
+ isinstance(item, TransferFunctionPoint):
+ self._tf_items.append(item)
+ QtGui.QGraphicsScene.addItem(self, item)
+
+ def create_tf_items(self, tf):
+ items = copy.copy(self._tf_items)
+ for item in items:
+ self.removeItem(item)
+ self._tf_items = []
+ if len(tf._pts) == 0:
+ pt_left = TransferFunctionPoint(0.0, 0.0, (0.0, 0.0, 0.0))
+ pt_right = TransferFunctionPoint(1.0, 0.0, (0.0, 0.0, 0.0))
+ line = TransferFunctionLine(pt_left, pt_right)
+
+ self.addItem(pt_left)
+ self.addItem(pt_right)
+ self.addItem(line)
+
+ else:
+ pts = [TransferFunctionPoint(*pt)
+ for pt in tf._pts]
+ lines = [TransferFunctionLine(pt_l, pt_r)
+ for (pt_l, pt_r) in zip(pts[:-1], pts[1:])]
+ for pt in pts:
+ self.addItem(pt)
+ for line in lines:
+ self.addItem(line)
+
+ def add_knot(self, scalar, opacity):
+ pass
+
+ def update_scale(self, sx, sy):
+ for item in self._tf_items:
+ item.update_scale(sx, sy)
+ self._sx = sx
+ self._sy = sy
+
+ def get_leftmost_point(self):
+ pt = None
+
+ for item in self._tf_items:
+ if hasattr(item, '_left_line') and not item._left_line:
+ pt = item
+ break
+ assert pt
+ return pt
+
+ def get_transfer_function(self):
+ result = TransferFunction()
+ pt = self.get_leftmost_point()
+ while 1:
+ pt.add_self_to_transfer_function(result)
+ if pt._right_line:
+ pt = pt._right_line._point_right
+ else:
+ break
+ return result
+
+class TransferFunctionView(QtGui.QGraphicsView):
+ def __init__(self, parent=None):
+ QtGui.QGraphicsView.__init__(self, parent)
+ self.setRenderHint(QtGui.QPainter.Antialiasing)
+ self.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ self.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+
+ def resizeEvent(self, event):
+ self.resetMatrix()
+ self.setMatrix(QtGui.QMatrix(event.size().width() / (GLOBAL_SCALE *10.0/9) , 0,
+ 0, -event.size().height() / (GLOBAL_SCALE*10.0/9), 0, 0))
+ self.scene().update_scale(event.size().width()/(2000.0/9), event.size().height()/(2000.0/9))
+
+ def focusOutEvent(self, event):
+ self.parent().update_parent()
+ QtGui.QGraphicsView.focusOutEvent(self, event)
+
+default_tf = TransferFunction()
+default_tf.add_point(0.0, 0.0, (0.0, 0.0, 0.0))
+default_tf.add_point(1.0, 0.0, (0.0, 0.0, 0.0))
+
+class TransferFunctionWidget(QtGui.QWidget, ConstantWidgetMixin):
+
+ def __init__(self, param, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ if not param.strValue:
+ self._tf = copy.copy(default_tf)
+ else:
+ self._tf = TransferFunction.parse(param.strValue)
+ self._scene = TransferFunctionScene(self._tf, self)
+ layout = QtGui.QVBoxLayout()
+ self.setLayout(layout)
+ self._view = TransferFunctionView(self)
+ self._view.setScene(self._scene)
+ self._view.setMinimumSize(200,200)
+ self._view.setMaximumHeight(280)
+ self._view.show()
+ self._view.setSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding)
+ self._view.setMatrix(QtGui.QMatrix(1, 0, 0, -1, 0, 0))
+ self.setMinimumSize(260,240)
+ caption = QtGui.QLabel("Double-click on the line to add a point")
+ font = QtGui.QFont('Arial', 11)
+ font.setItalic(True)
+ caption.setFont(font)
+ layout.addWidget(self._view)
+ layout.addWidget(caption)
+
+ def contents(self):
+ return self._scene.get_transfer_function().serialize()
+
+ def setContents(self, strValue, silent=True):
+ if not strValue:
+ self._tf = copy.copy(default_tf)
+ else:
+ self._tf = TransferFunction.parse(strValue)
+ self._scene.reset_transfer_function(self._tf)
+ if not silent:
+ self.update_parent()
+
+##############################################################################
+# Helper module to adjust range
+
+class vtkScaledTransferFunction(Module):
+
+ def compute(self):
+ reg = get_module_registry()
+ tf = self.getInputFromPort('TransferFunction')
+ new_tf = copy.copy(tf)
+ if self.hasInputFromPort('Input'):
+ port = self.getInputFromPort('Input')
+ algo = port.vtkInstance.GetProducer()
+ output = algo.GetOutput(port.vtkInstance.GetIndex())
+ (new_tf._min_range, new_tf._max_range) = output.GetScalarRange()
+ elif self.hasInputFromPort('Dataset'):
+ algo = self.getInputFromPort('Dataset').vtkInstance
+ output = algo
+ (new_tf._min_range, new_tf._max_range) = output.GetScalarRange()
+ else:
+ (new_tf._min_range, new_tf._max_range) = self.getInputFromPort('Range')
+
+ self.setResult('TransferFunction', new_tf)
+ (of,cf) = new_tf.get_vtk_transfer_functions()
+
+ of_module = reg.get_descriptor_by_name(vtk_pkg_identifier,
+ 'vtkPiecewiseFunction').module()
+ of_module.vtkInstance = of
+
+ cf_module = reg.get_descriptor_by_name(vtk_pkg_identifier,
+ 'vtkColorTransferFunction').module()
+ cf_module.vtkInstance = cf
+
+ self.setResult('vtkPicewiseFunction', of_module)
+ self.setResult('vtkColorTransferFunction', cf_module)
+
+string_conversion = staticmethod(lambda x: x.serialize())
+conversion = staticmethod(lambda x: TransferFunction.parse(x))
+validation = staticmethod(lambda x: isinstance(x, TransferFunction))
+TransferFunctionConstant = new_constant('TransferFunction',
+ conversion,
+ default_tf,
+ validation,
+ TransferFunctionWidget)
+TransferFunctionConstant.translate_to_string = string_conversion
+
+##############################################################################
+
+def initialize():
+ init_constant(TransferFunctionConstant)
+
+##############################################################################
+class TestTransferFunction(unittest.TestCase):
+ def test_serialization(self):
+ tf = TransferFunction()
+ tf._min_range = 0.1
+ tf._max_range = 2.0
+ tf._pts.append((0.3,0.5,(1.0,1.0,1.0)))
+ tf._pts.append((0.6,0.7,(1.0,0.5,1.0)))
+ tf._pts.append((0.2,0.8,(1.0,0.0,1.0)))
+ tf._pts.sort()
+
+ #simulate old serialization method
+ ser1 = pickle.dumps(tf).encode('hex')
+
+ ser2 = tf.serialize()
+
+ tf1 = TransferFunction.parse(ser1)
+ tf2 = TransferFunction.parse(ser2)
+
+ assert tf == tf1
+ assert tf == tf2
+ assert tf1 == tf2
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/vistrails/packages/vtk/vtk_parser.py b/vistrails/packages/vtk/vtk_parser.py
new file mode 100644
index 0000000..2306ad9
--- /dev/null
+++ b/vistrails/packages/vtk/vtk_parser.py
@@ -0,0 +1,548 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+# Author: Prabhu Ramachandran
+# Copyright (c) 2004, Enthought, Inc.
+# License: BSD Style.
+
+# Modified for VisTrails by the VisTrails team.
+
+"""This module parses the VTK methods, obtains the argument and return
+type information, and organizes them.
+
+"""
+import re
+import vtk
+import class_tree
+import vistrails.core.debug
+
+log = vistrails.core.debug.log
+warning = vistrails.core.debug.warning
+critical = vistrails.core.debug.critical
+debug = vistrails.core.debug.debug
+
+class VTKMethodParser(object):
+ """This class provides useful methods for parsing methods of a VTK
+ class or instance.
+
+ The class allows one to categorize the methods of the VTK class
+ and also obtain the method signatures in a form that is easy to
+ use. When the `parse` method is called, it in turn calls the
+ `_organize_methods` method. This method organizes the VTK methods
+ into different instance variables described in the following.
+ `self.toggle_meths` contains a dictionary of all the boolean
+ methods of the form <Value>On/Off. The dictionary keys are
+ strings with the <Value>'s and the value of each item is the
+ default value (0/1) of the item (the example below will clarify
+ this). `self.state_meths` contains a dictionary which collects
+ the Set<Prop>To<Value> type of methods. The key is the <Prop> and
+ the value is a list containing the different string <Value>'s and
+ their corresponding mapped value. The first value in these is the
+ default value of the <Prop>. `self.get_set_meths` will contain a
+ dictionary which collects all the methods of the form
+ Set/Get<Prop> that are not already specified in
+ `self.toggle_meths` or `self.state_meths`. The default value of
+ the Get<Prop> is stored. If the value accepted by the method has
+ a range (via the methods `Get<Prop>MinValue` and
+ `Get<Prop>MaxValue`), then that range is computed and stored.
+ `self.get_meths` stores the methods that are of the form
+ `Get<Prop>`. `self.other_meths` stores the remaining methods.
+ The parsing is quite fast. Parsing every class in the VTK API
+ takes a couple of seconds (on a Pentium III @ 450Mhz).
+
+ Here is an example::
+
+ >>> import vtk
+ >>> p = VTKMethodParser()
+ >>> p.parse(vtk.vtkProperty)
+ >>> print p.get_toggle_methods()
+ {'EdgeVisibility': 0, 'BackfaceCulling': 0, 'FrontfaceCulling': 0}
+ >>> print p.get_state_methods()['Representation']
+ [['Surface', 2], ['Points', 0], ['Surface', 2], ['Wireframe', 1]]
+ >>> print p.get_get_set_methods()['Opacity']
+ (1.0, (0.0, 1.0))
+ >>> print p.get_get_methods()
+ ['GetClassName']
+ >>> print p.get_other_methods()[:3]
+ ['BackfaceRender', 'DeepCopy', 'IsA']
+
+
+ The class also provides a method called `get_method_signature`
+ that obtains the Python method signature given the VTK method
+ object. Here is an example::
+
+ >>> import vtk
+ >>> p = VTKMethodParser()
+ >>> o = vtk.vtkProperty
+ >>> print p.get_method_signature(o.GetClassName)
+ [(['string'], None)]
+ >>> print p.get_method_signature(o.GetColor)[0]
+ ([('float', 'float', 'float')], None)
+ >>> print p.get_method_signature(o.GetColor)[1]
+ ([None], (('float', 'float', 'float'),))
+
+ The `get_method_signature` is fairly efficient and obtaining the
+ signature for every method in every class in the VTK API takes
+ around 6 seconds (on a Pentium III @ 450Mhz).
+
+ """
+
+ def __init__(self, use_tree=True):
+ """Initializes the object.
+
+ Parameters
+ ----------
+
+ - use_tree : `bool`
+
+ If True (default), use a ClassTree instance to obtain a
+ concrete subclass for an abstract base class. This is used
+ only to find the range and default values for some of the
+ methods. If False, no ClassTree instance is created.
+
+ This is optional because, creating a ClassTree is expensive.
+ The parser functionality can be very useful even without the
+ use of a ClassTree. For example, if one wants to save the
+ state of a VTK object one only needs to know the names of
+ the methods and not their default values, ranges etc. In
+ that case using a parser should be cheap.
+
+ """
+ # The ClassTree is needed to find an instantiable child class
+ # for an abstract VTK parent class. This instance is used to
+ # obtain the state values and the ranges of the arguments
+ # accepted by the Get/Set methods that have a
+ # Get<Prop>{MaxValue,MinValue} method.
+ if use_tree:
+ self._tree = class_tree.ClassTree(vtk)
+ self._tree.create()
+ else:
+ self._tree = None
+ self._state_patn = re.compile('To[A-Z0-9]')
+ self._initialize()
+
+ #################################################################
+ # 'VTKMethodParser' interface.
+ #################################################################
+
+ def parse(self, obj, no_warn=True):
+ """Parse the methods for a given VTK object/class.
+
+ Given a VTK class or object, this method parses the methods
+ and orgaizes them into useful categories. The categories and
+ their usage is documented in the documentation for the class.
+
+ Parameters
+ ----------
+
+ - obj : VTK class or instance
+
+ - no_warn : `bool` (default: True)
+
+ If True (default), it suppresses any warnings generated by
+ the VTK object when parsing the methods. This is safe to
+ use.
+
+ """
+ if not hasattr(obj, '__bases__'):
+ klass = obj.__class__
+ else:
+ klass = obj
+
+ methods = self.get_methods(klass)
+
+ if no_warn:
+ # Save warning setting and shut it off before parsing.
+ warn = vtk.vtkObject.GetGlobalWarningDisplay()
+ if klass.__name__ <> 'vtkObject':
+ vtk.vtkObject.GlobalWarningDisplayOff()
+
+ self._organize_methods(klass, methods)
+
+ if no_warn:
+ # Reset warning status.
+ vtk.vtkObject.SetGlobalWarningDisplay(warn)
+
+ def get_methods(self, klass):
+ """Returns all the relevant methods of the given VTK class."""
+ methods = dir(klass)[:]
+ if hasattr(klass, '__members__'):
+ # Only VTK versions < 4.5 have these.
+ for m in klass.__members__:
+ methods.remove(m)
+
+ return methods
+
+ def get_toggle_methods(self):
+ """Returns a dictionary of the parsed <Value>On/Off methods
+ along with the default value.
+
+ """
+ return self.toggle_meths
+
+ def get_state_methods(self):
+ """Returns a dict of the parsed Set<Prop>To<Value>.
+
+ The keys are the <Prop> string with a list of the different
+ <Value> strings along with their corresponding value (if
+ obtainable). The first value is the default value of the
+ state.
+
+ """
+ return self.state_meths
+
+ def get_get_set_methods(self):
+ """Returns a dict of the parsed Get/Set<Value> methods.
+
+ The keys of the dict are the <Value> strings and contain a
+ two-tuple containing the default value (or None if it is not
+ obtainable for some reason) and a pair of numbers specifying
+ an acceptable range of values (or None if not obtainable).
+
+ """
+ return self.get_set_meths
+
+ def get_get_methods(self):
+ """Return a list of parsed Get<Value> methods.
+
+ All of these methods do NOT have a corresponding Set<Value>.
+
+ """
+ return self.get_meths
+
+ def get_other_methods(self):
+ """Return list of all other methods, that are not
+ categorizable.
+
+ """
+ return self.other_meths
+
+ def get_method_signature(self, method):
+ """Returns information on the Python method signature given
+ the VTK method.
+
+ The doc string of the given method object to get the method
+ signature. The method returns a list of tuples, each of which
+ contains 2 items, the first is a list representing the return
+ value the second represents the arguments to be passed to the
+ function. If the method supports different return values and
+ arguments, this function returns all of their signatures.
+
+ Parameters
+ ----------
+
+ - method : `method`
+
+ A VTK method object.
+
+ """
+ doc = method.__doc__
+ doc = doc[:doc.find('\n\n')]
+ sig = doc.split('\n')
+ sig = [x.strip() for x in sig]
+
+ # Remove all the C++ function signatures.
+ for i in sig[:]:
+ if i[:4] == 'C++:':
+ sig.remove(i)
+
+ # Remove the V.<method_name>
+ sig = [x.replace('V.' + method.__name__, '') for x in sig]
+
+ pat = re.compile(r'\b')
+
+ # Split into [return_value, arguments] after processing them.
+ tmp = list(sig)
+ sig = []
+ for i in tmp:
+ # Split to get return values.
+ x = i.split('->')
+ # Strip each part.
+ x = [y.strip() for y in x]
+
+ if len(x) == 1: # No return value
+ x = [None, x[0]]
+ else:
+ x.reverse()
+
+ ret, arg = x
+
+ # Remove leading and trailing parens for arguments.
+ arg = arg[1:-1]
+ if not arg:
+ arg = None
+ if arg and arg[-1] == ')':
+ arg = arg + ','
+
+ # Now quote the args and eval them. Easy!
+ if ret:
+ ret = eval(pat.sub('\"', ret))
+ if arg:
+ arg = eval(pat.sub('\"', arg))
+ if isinstance(arg, basestring):
+ arg = [arg]
+
+ sig.append(([ret], arg))
+
+ return sig
+
+ def get_tree(self):
+ """Return the ClassTree instance used by this class."""
+ return self._tree
+
+ #################################################################
+ # Non-public interface.
+ #################################################################
+
+ def _initialize(self):
+ """Initializes the method categories."""
+ # Collects the <Value>On/Off methods.
+ self.toggle_meths = {}
+ # Collects the Set<Prop>To<Value> methods.
+ self.state_meths = {}
+ # Collects the Set/Get<Value> pairs.
+ self.get_set_meths = {}
+ # Collects the Get<Value> methods.
+ self.get_meths = []
+ # Collects all the remaining methods.
+ self.other_meths = []
+
+ def _organize_methods(self, klass, methods):
+ """Organizes the given methods of a VTK class into different
+ categories.
+
+ Parameters
+ ----------
+
+ - klass : A VTK class
+
+ - methods : `list` of `str`
+
+ A list of the methods to be categorized.
+
+ """
+ self._initialize()
+ meths = methods[:]
+ meths = self._find_toggle_methods(klass, meths)
+ meths = self._find_state_methods(klass, meths)
+ meths = self._find_get_set_methods(klass, meths)
+ meths = self._find_get_methods(klass, meths)
+ self.other_meths = [x for x in meths if '__' not in x]
+
+ def _remove_method(self, meths, method):
+ try:
+ meths.remove(method)
+ except ValueError:
+ pass
+
+ def _find_toggle_methods(self, klass, methods):
+ """Find/store methods of the form <Value>{On,Off} in the given
+ `methods`. Returns the remaining list of methods.
+
+ """
+ meths = methods[:]
+ tm = self.toggle_meths
+ for method in meths[:]:
+ if method[-2:] == 'On':
+ key = method[:-2]
+ if (key + 'Off') in meths and ('Get' + key) in meths:
+ tm[key] = None
+ meths.remove(method)
+ meths.remove(key + 'Off')
+ self._remove_method(meths, 'Set' + key)
+ self._remove_method(meths, 'Get' + key)
+ # get defaults
+ if tm:
+ obj = self._get_instance(klass)
+ if obj:
+ for key in tm:
+ try:
+ tm[key] = getattr(obj, 'Get%s'%key)()
+ except TypeError, e:
+ log("Type error during parsing: class %s will not expose method %s " % (klass.__name__, key))
+ except AttributeError, e:
+ log("Attribute error during parsing: class %s will not expose method %s " % (klass.__name__, key))
+ return meths
+
+ def _find_state_methods(self, klass, methods):
+ """Find/store methods of the form Set<Prop>To<Value> in the
+ given `methods`. Returns the remaining list of methods. The
+ method also computes the mapped value of the different
+ <Values>.
+
+ """
+ # These ignored ones are really not state methods.
+ ignore = ['SetUpdateExtentToWholeExtent']
+ meths = methods[:]
+ sm = self.state_meths
+ for method in meths[:]:
+ if method not in ignore and method[:3] == 'Set':
+ # Methods of form Set<Prop>To<Value>
+ match = self._state_patn.search(method)
+ # Second cond. ensures that this is not an accident.
+ if match and (('Get'+method[3:]) not in meths):
+ key = method[3:match.start()] # The <Prop> part.
+ if (('Get' + key) in methods):
+ val = method[match.start()+2:] # <Value> part.
+ meths.remove(method)
+ if sm.has_key(key):
+ sm[key].append([val, None])
+ else:
+ sm[key] = [[val, None]]
+ meths.remove('Get'+ key)
+ self._remove_method(meths, 'Set'+ key)
+ if ('Get' + key + 'MaxValue') in meths:
+ meths.remove('Get' + key + 'MaxValue')
+ meths.remove('Get' + key + 'MinValue')
+ try:
+ meths.remove('Get' + key + 'AsString')
+ except ValueError:
+ pass
+
+ # Find the values for each of the states, i.e. find that
+ # vtkProperty.SetRepresentationToWireframe() corresponds to
+ # vtkProperty.SetRepresentation(1).
+ if sm:
+ obj = self._get_instance(klass)
+ if obj:
+ for key, values in sm.items():
+ default = getattr(obj, 'Get%s'%key)()
+ for x in values[:]:
+ try:
+ getattr(obj, 'Set%sTo%s'%(key, x[0]))()
+ except:
+ continue
+ val = getattr(obj, 'Get%s'%key)()
+ x[1] = val
+ if val == default:
+ values.insert(0, [x[0], val])
+ return meths
+
+ def _find_get_set_methods(self, klass, methods):
+ """Find/store methods of the form {Get,Set}Prop in the given
+ `methods` and returns the remaining list of methods.
+
+ Note that it makes sense to call this *after*
+ `_find_state_methods` is called in order to avoid incorrect
+ duplication. This method also computes the default value and
+ the ranges of the arguments (when possible) by using the
+ Get<Prop>{MaxValue,MinValue} methods.
+
+ """
+ meths = methods[:]
+ gsm = self.get_set_meths
+
+ for method in meths[:]:
+ # Methods of the Set/Get form.
+ if method in ['Get', 'Set']:
+ # This occurs with the vtkInformation class.
+ continue
+ elif (method[:3] == 'Set') and ('Get' + method[3:]) in methods:
+ key = method[3:]
+ meths.remove('Set' + key)
+ meths.remove('Get' + key)
+ if ('Get' + key + 'MaxValue') in meths:
+ meths.remove('Get' + key + 'MaxValue')
+ meths.remove('Get' + key + 'MinValue')
+ gsm[key] = 1
+ else:
+ gsm[key] = None
+
+ # Find the default and range of the values.
+ if gsm:
+ obj = self._get_instance(klass)
+ if obj:
+ klass_name = klass.__name__
+ for key, value in gsm.items():
+ if klass_name == 'vtkPolyData':
+ # Evil hack, this class segfaults!
+ default = None
+ else:
+ try:
+ default = getattr(obj, 'Get%s'%key)()
+ except TypeError:
+ default = None
+ if value:
+ low = getattr(obj, 'Get%sMinValue'%key)()
+ high = getattr(obj, 'Get%sMaxValue'%key)()
+ gsm[key] = (default, (low, high))
+ else:
+ gsm[key] = (default, None)
+ else:
+ # We still might have methods that have a default range.
+ for key, value in gsm.items():
+ if value == 1:
+ gsm[key] = None
+
+ return meths
+
+ def _find_get_methods(self, klass, methods):
+ """Find/store methods of the form Get<Value> in the given
+ `methods` and returns the remaining list of methods.
+
+ """
+ meths = methods[:]
+ gm = self.get_meths
+ for method in meths[:]:
+ if method == 'Get':
+ # Occurs with vtkInformation
+ continue
+ elif method[:3] == 'Get':
+ gm.append(method)
+ meths.remove(method)
+ return meths
+
+ def _get_instance(self, klass):
+ """Given a VTK class, `klass`, returns an instance of the
+ class.
+
+ If the class is abstract, it uses the class tree to return an
+ instantiable subclass. This is necessary to get the values of
+ the 'state' methods and the ranges for the Get/Set methods.
+
+ """
+ obj = None
+ try:
+ obj = klass()
+ except (TypeError, NotImplementedError):
+ if self._tree:
+ t = self._tree
+ n = t.get_node(klass.__name__)
+ for c in n.children:
+ obj = self._get_instance(t.get_class(c.name))
+ if obj:
+ break
+ return obj
+
diff --git a/vistrails/packages/vtk/vtkcell.py b/vistrails/packages/vtk/vtkcell.py
new file mode 100644
index 0000000..0b87922
--- /dev/null
+++ b/vistrails/packages/vtk/vtkcell.py
@@ -0,0 +1,1146 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# File QVTKWidget.py
+# File for displaying a vtkRenderWindow in a Qt's QWidget ported from
+# VTK/GUISupport/QVTK. Combine altogether to a single class: QVTKWidget
+################################################################################
+import vtk
+from PyQt4 import QtCore, QtGui
+import sip
+from vistrails.core import system
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+from vtk.qt4.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
+import vtkcell_rc
+import gc
+from vistrails.gui.qt import qt_super
+import vistrails.core.db.action
+from vistrails.core.vistrail.action import Action
+from vistrails.core.vistrail.port import Port
+from vistrails.core.vistrail import module
+from vistrails.core.vistrail import connection
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.location import Location
+from vistrails.core.modules.vistrails_module import ModuleError
+import copy
+
+from identifiers import identifier as vtk_pkg_identifier
+
+################################################################################
+
+class VTKCell(SpreadsheetCell):
+ """
+ VTKCell is a VisTrails Module that can display vtkRenderWindow inside a cell
+
+ """
+
+ def __init__(self):
+ SpreadsheetCell.__init__(self)
+ self.cellWidget = None
+
+ def compute(self):
+ """ compute() -> None
+ Dispatch the vtkRenderer to the actual rendering widget
+ """
+ renderers = self.forceGetInputListFromPort('AddRenderer')
+ renderViews = self.forceGetInputListFromPort('SetRenderView')
+ if len(renderViews)>1:
+ raise ModuleError(self, 'There can only be one vtkRenderView '
+ 'per cell')
+ if len(renderViews)==1 and len(renderers)>0:
+ raise ModuleError(self, 'Cannot set both vtkRenderView '
+ 'and vtkRenderer to a cell')
+ renderView = self.forceGetInputFromPort('SetRenderView')
+ iHandlers = self.forceGetInputListFromPort('InteractionHandler')
+ iStyle = self.forceGetInputFromPort('InteractorStyle')
+ picker = self.forceGetInputFromPort('AddPicker')
+ self.cellWidget = self.displayAndWait(QVTKWidget, (renderers, renderView, iHandlers, iStyle, picker))
+
+AsciiToKeySymTable = ( None, None, None, None, None, None, None,
+ None, None,
+ "Tab", None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None,
+ "space", "exclam", "quotedbl", "numbersign",
+ "dollar", "percent", "ampersand", "quoteright",
+ "parenleft", "parenright", "asterisk", "plus",
+ "comma", "minus", "period", "slash",
+ "0", "1", "2", "3", "4", "5", "6", "7",
+ "8", "9", "colon", "semicolon", "less", "equal",
+ "greater", "question",
+ "at", "A", "B", "C", "D", "E", "F", "G",
+ "H", "I", "J", "K", "L", "M", "N", "O",
+ "P", "Q", "R", "S", "T", "U", "V", "W",
+ "X", "Y", "Z", "bracketleft",
+ "backslash", "bracketright", "asciicircum",
+ "underscore",
+ "quoteleft", "a", "b", "c", "d", "e", "f", "g",
+ "h", "i", "j", "k", "l", "m", "n", "o",
+ "p", "q", "r", "s", "t", "u", "v", "w",
+ "x", "y", "z", "braceleft", "bar", "braceright",
+ "asciitilde", "Delete",
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None)
+
+class QVTKWidget(QCellWidget):
+ """
+ QVTKWidget is the actual rendering widget that can display
+ vtkRenderer inside a Qt QWidget
+
+ """
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QVTKWidget(parent: QWidget, f: WindowFlags) -> QVTKWidget
+ Initialize QVTKWidget with a toolbar with its own device
+ context
+
+ """
+ QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
+
+ self.interacting = None
+ self.mRenWin = None
+ self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
+ self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
+ self.setMouseTracking(True)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding))
+ self.toolBarType = QVTKWidgetToolBar
+ self.iHandlers = []
+ self.setAnimationEnabled(True)
+ self.renderer_maps = {}
+
+ def removeObserversFromInteractorStyle(self):
+ """ removeObserversFromInteractorStyle() -> None
+ Remove all python binding from interactor style observers for
+ safely freeing the cell
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.RemoveObservers("InteractionEvent")
+ style.RemoveObservers("EndPickEvent")
+ style.RemoveObservers("CharEvent")
+ style.RemoveObservers("MouseWheelForwardEvent")
+ style.RemoveObservers("MouseWheelBackwardEvent")
+
+ def addObserversToInteractorStyle(self):
+ """ addObserversToInteractorStyle() -> None
+ Assign observer to the current interactor style
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.AddObserver("InteractionEvent", self.interactionEvent)
+ style.AddObserver("EndPickEvent", self.interactionEvent)
+ style.AddObserver("CharEvent", self.charEvent)
+ style.AddObserver("MouseWheelForwardEvent", self.interactionEvent)
+ style.AddObserver("MouseWheelBackwardEvent", self.interactionEvent)
+
+ def deleteLater(self):
+ """ deleteLater() -> None
+ Make sure to free render window resource when
+ deallocating. Overriding PyQt deleteLater to free up
+ resources
+
+ """
+ self.renderer_maps = {}
+ for ren in self.getRendererList():
+ self.mRenWin.RemoveRenderer(ren)
+
+ self.removeObserversFromInteractorStyle()
+
+ self.updateContents(([], None, [], None, None))
+
+ self.SetRenderWindow(None)
+
+ QCellWidget.deleteLater(self)
+
+ def updateContents(self, inputPorts, cameralist = None):
+ """ updateContents(inputPorts: tuple)
+ Updates the cell contents with new vtkRenderer
+
+ """
+ renWin = self.GetRenderWindow()
+ for iHandler in self.iHandlers:
+ if iHandler.observer:
+ iHandler.observer.vtkInstance.SetInteractor(None)
+ iHandler.clear()
+
+ # Remove old renderers first
+ oldRenderers = self.getRendererList()
+ for renderer in oldRenderers:
+ renWin.RemoveRenderer(renderer)
+ renderer.SetRenderWindow(None)
+ del oldRenderers
+
+ (renderers, renderView, self.iHandlers, iStyle, picker) = inputPorts
+ if renderView:
+ renderView.vtkInstance.SetupRenderWindow(renWin)
+ renderers = [renderView.vtkInstance.GetRenderer()]
+ self.renderer_maps = {}
+ self.usecameras = False
+ if cameralist != None and len(cameralist) == len(renderers):
+ self.usecameras = True
+ j = 0
+ for renderer in renderers:
+ if renderView==None:
+ vtkInstance = renderer.vtkInstance
+ renWin.AddRenderer(vtkInstance)
+ self.renderer_maps[vtkInstance] = renderer.moduleInfo['moduleId']
+ else:
+ vtkInstance = renderer
+ if hasattr(vtkInstance, 'IsActiveCameraCreated'):
+ if self.usecameras:
+ vtkInstance.SetActiveCamera(cameralist[j])
+ j = j + 1
+ if not vtkInstance.IsActiveCameraCreated():
+ vtkInstance.ResetCamera()
+ else:
+ vtkInstance.ResetCameraClippingRange()
+
+ iren = renWin.GetInteractor()
+ if picker:
+ iren.SetPicker(picker.vtkInstance)
+
+ # Update interactor style
+ self.removeObserversFromInteractorStyle()
+ if renderView==None:
+ if iStyle==None:
+ iStyleInstance = vtk.vtkInteractorStyleTrackballCamera()
+ else:
+ iStyleInstance = iStyle.vtkInstance
+ iren.SetInteractorStyle(iStyleInstance)
+ self.addObserversToInteractorStyle()
+
+ for iHandler in self.iHandlers:
+ if iHandler.observer:
+ iHandler.observer.vtkInstance.SetInteractor(iren)
+ renWin.Render()
+
+ # Capture window into history for playback
+ # Call this at the end to capture the image after rendering
+ QCellWidget.updateContents(self, inputPorts)
+
+ def GetRenderWindow(self):
+ """ GetRenderWindow() -> vtkRenderWindow
+ Return the associated vtkRenderWindow
+
+ """
+ if not self.mRenWin:
+ win = vtk.vtkRenderWindow()
+ win.DoubleBufferOn()
+ self.SetRenderWindow(win)
+ del win
+
+ return self.mRenWin
+
+ def SetRenderWindow(self,w):
+ """ SetRenderWindow(w: vtkRenderWindow)
+ Set a new render window to QVTKWidget and initialize the
+ interactor as well
+
+ """
+ if w == self.mRenWin:
+ return
+
+ if self.mRenWin:
+ if system.systemType!='Linux':
+ self.mRenWin.SetInteractor(None)
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+
+ self.mRenWin = w
+
+ if self.mRenWin:
+ self.mRenWin.Register(None)
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+ if system.systemType=='Linux':
+ try:
+ vp = '_%s_void_p' % (hex(int(QtGui.QX11Info.display()))[2:])
+ except TypeError:
+ #This was change for PyQt4.2
+ if isinstance(QtGui.QX11Info.display(),QtGui.Display):
+ display = sip.unwrapinstance(QtGui.QX11Info.display())
+ vp = '_%s_void_p' % (hex(display)[2:])
+ v = vtk.vtkVersion()
+ version = [v.GetVTKMajorVersion(),
+ v.GetVTKMinorVersion(),
+ v.GetVTKBuildVersion()]
+ if version < [5, 7, 0]:
+ vp = vp + '\0x00'
+ self.mRenWin.SetDisplayId(vp)
+ self.resizeWindow(1,1)
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ if not self.mRenWin.GetInteractor():
+ #iren = vtk.vtkRenderWindowInteractor()
+ iren = QVTKRenderWindowInteractor()
+# if system.systemType=='Darwin':
+# iren.InstallMessageProcOff()
+ iren.SetRenderWindow(self.mRenWin)
+ iren.Initialize()
+# if system.systemType=='Linux':
+# system.XDestroyWindow(self.mRenWin.GetGenericDisplayId(),
+# self.mRenWin.GetGenericWindowId())
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ self.resizeWindow(self.width(), self.height())
+ self.mRenWin.SetPosition(self.x(), self.y())
+
+ def GetInteractor(self):
+ """ GetInteractor() -> vtkInteractor
+ Return the vtkInteractor control this QVTKWidget
+ """
+ return self.GetRenderWindow().GetInteractor()
+
+ def event(self, e):
+ """ event(e: QEvent) -> depends on event type
+ Process window and interaction events
+
+ """
+ if e.type()==QtCore.QEvent.ParentAboutToChange:
+ if self.mRenWin:
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+ else:
+ if e.type()==QtCore.QEvent.ParentChange:
+ if self.mRenWin:
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ if QtCore.QObject.event(self,e):
+ return 1
+
+ if e.type() == QtCore.QEvent.KeyPress:
+ self.keyPressEvent(e)
+ if e.isAccepted():
+ return e.isAccepted()
+
+ return qt_super(QVTKWidget, self).event(e)
+
+ # return QtGui.QWidget.event(self,e)
+ # Was this right? Wasn't this supposed to be QCellWidget.event()?
+
+ def resizeWindow(self, width, height):
+ """ resizeWindow(width: int, height: int) -> None
+ Work around vtk bugs for resizing window
+
+ """
+ ########################################################
+ # VTK - BUGGGGGGGGG - GRRRRRRRRR
+ # This is a 'bug' in vtkWin32OpenGLRenderWindow(.cxx)
+ # If a render window is mapped to screen, the actual
+ # window size is the client area of the window in Win32.
+ # However, this real window size is only updated through
+ # vtkWin32OpenGLRenderWindow::GetSize(). So this has to
+ # be called here to get the cell size correctly. This
+ # invalidates the condition in the next SetSize().
+ # We can use self.mRenWin.SetSize(0,0) here but it will
+ # cause flickering and decrease performance!
+ # SetPosition(curX,curY) also works here but slower.
+ self.mRenWin.GetSize()
+
+ self.mRenWin.SetSize(width, height)
+ if self.mRenWin.GetInteractor():
+ self.mRenWin.GetInteractor().SetSize(width, height)
+
+ def resizeEvent(self, e):
+ """ resizeEvent(e: QEvent) -> None
+ Re-adjust the vtkRenderWindow size then QVTKWidget resized
+
+ """
+ qt_super(QVTKWidget, self).resizeEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.resizeWindow(self.width(), self.height())
+ if self.mRenWin.GetInteractor():
+ self.mRenWin.GetInteractor().Render()
+ else:
+ self.mRenWin.Render()
+
+ def moveEvent(self,e):
+ """ moveEvent(e: QEvent) -> None
+ Echo the move event into vtkRenderWindow
+
+ """
+ qt_super(QVTKWidget, self).moveEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.mRenWin.SetPosition(self.x(),self.y())
+
+ def paintEngine(self):
+ """ paintEngine() -> QPaintEngine
+ On Windows, this has to return None to fully disable
+ double-buffer (we let vtkRenderWindow handle this instead).
+
+ """
+ if system.systemType in ['Windows', 'Microsoft']:
+ return None
+ else:
+ return QCellWidget.paintEngine(self)
+
+ def paintEvent(self, e):
+ """ paintEvent(e: QPaintEvent) -> None
+ Paint the QVTKWidget with vtkRenderWindow
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ if hasattr(self.mRenWin, 'UpdateGLRegion'):
+ self.mRenWin.UpdateGLRegion()
+ if self.mRenWin.GetInteractor():
+ self.mRenWin.GetInteractor().Render()
+ else:
+ self.mRenWin.Render()
+
+ def SelectActiveRenderer(self,iren):
+ """ SelectActiveRenderer(iren: vtkRenderWindowIteractor) -> None
+ Only make the vtkRenderer below the mouse cursor active
+
+ """
+ epos = iren.GetEventPosition()
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ ren.SetInteractive(ren.IsInViewport(epos[0], epos[1]))
+
+ def mousePressEvent(self,e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ isDoubleClick = e.type()==QtCore.QEvent.MouseButtonDblClick
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ ctrl,
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),
+ isDoubleClick,
+ None)
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonPressEvent",
+ QtCore.Qt.MidButton:"MiddleButtonPressEvent",
+ QtCore.Qt.RightButton:"RightButtonPressEvent"}
+
+ self.SelectActiveRenderer(iren)
+
+ if ctrl:
+ e.ignore()
+ return
+
+ self.interacting = self.getActiveRenderer(iren)
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def mouseMoveEvent(self,e):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0), 0, None)
+
+ iren.InvokeEvent("MouseMoveEvent")
+
+ def enterEvent(self,e):
+ """ enterEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("EnterEvent")
+
+ def leaveEvent(self,e):
+ """ leaveEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("LeaveEvent")
+
+ def mouseReleaseEvent(self,e):
+ """ mouseReleaseEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonReleaseEvent",
+ QtCore.Qt.MidButton:"MiddleButtonReleaseEvent",
+ QtCore.Qt.RightButton:"RightButtonReleaseEvent"}
+
+ self.interacting = None
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def keyPressEvent(self,e):
+ """ keyPressEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if len(e.text())>0:
+ ascii_key = e.text()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q', 'e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl,shift,ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyPressEvent")
+
+ if ascii_key:
+ iren.InvokeEvent("CharEvent")
+
+
+ def keyReleaseEvent(self,e):
+ """ keyReleaseEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if len(e.text())>0:
+ ascii_key = e.text()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q','e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl, shift, ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyReleaseEvent")
+
+ def wheelEvent(self,e):
+ """ wheelEvent(e: QWheelEvent) -> None
+ Zoom in/out while scrolling the mouse
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ self.SelectActiveRenderer(iren)
+
+ if e.delta()>0:
+ iren.InvokeEvent("MouseWheelForwardEvent")
+ else:
+ iren.InvokeEvent("MouseWheelBackwardEvent")
+
+ def focusInEvent(self,e):
+ """ focusInEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def focusOutEvent(self,e):
+ """ focusOutEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def contextMenuEvent(self,e):
+ """ contextMenuEvent(e: QContextMenuEvent) -> None
+ Make sure to get the right mouse position for the context menu
+ event, i.e. also the right click
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = int(e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = int(e.modifiers()&QtCore.Qt.ShiftModifier)
+ iren.SetEventInformationFlipY(e.x(),e.y(),ctrl,shift,chr(0),0,None)
+ iren.InvokeEvent("ContextMenuEvent")
+
+ def ascii_to_key_sym(self,i):
+ """ ascii_to_key_sym(i: int) -> str
+ Convert ASCII code into key name
+
+ """
+ global AsciiToKeySymTable
+ return AsciiToKeySymTable[i]
+
+ def qt_key_to_key_sym(self,i):
+ """ qt_key_to_key_sym(i: QtCore.Qt.Keycode) -> str
+ Convert Qt key code into key name
+
+ """
+ handler = {QtCore.Qt.Key_Backspace:"BackSpace",
+ QtCore.Qt.Key_Tab:"Tab",
+ QtCore.Qt.Key_Backtab:"Tab",
+ QtCore.Qt.Key_Return:"Return",
+ QtCore.Qt.Key_Enter:"Return",
+ QtCore.Qt.Key_Shift:"Shift_L",
+ QtCore.Qt.Key_Control:"Control_L",
+ QtCore.Qt.Key_Alt:"Alt_L",
+ QtCore.Qt.Key_Pause:"Pause",
+ QtCore.Qt.Key_CapsLock:"Caps_Lock",
+ QtCore.Qt.Key_Escape:"Escape",
+ QtCore.Qt.Key_Space:"space",
+ QtCore.Qt.Key_End:"End",
+ QtCore.Qt.Key_Home:"Home",
+ QtCore.Qt.Key_Left:"Left",
+ QtCore.Qt.Key_Up:"Up",
+ QtCore.Qt.Key_Right:"Right",
+ QtCore.Qt.Key_Down:"Down",
+ QtCore.Qt.Key_SysReq:"Snapshot",
+ QtCore.Qt.Key_Insert:"Insert",
+ QtCore.Qt.Key_Delete:"Delete",
+ QtCore.Qt.Key_Help:"Help",
+ QtCore.Qt.Key_0:"0",
+ QtCore.Qt.Key_1:"1",
+ QtCore.Qt.Key_2:"2",
+ QtCore.Qt.Key_3:"3",
+ QtCore.Qt.Key_4:"4",
+ QtCore.Qt.Key_5:"5",
+ QtCore.Qt.Key_6:"6",
+ QtCore.Qt.Key_7:"7",
+ QtCore.Qt.Key_8:"8",
+ QtCore.Qt.Key_9:"9",
+ QtCore.Qt.Key_A:"a",
+ QtCore.Qt.Key_B:"b",
+ QtCore.Qt.Key_C:"c",
+ QtCore.Qt.Key_D:"d",
+ QtCore.Qt.Key_E:"e",
+ QtCore.Qt.Key_F:"f",
+ QtCore.Qt.Key_G:"g",
+ QtCore.Qt.Key_H:"h",
+ QtCore.Qt.Key_I:"i",
+ QtCore.Qt.Key_J:"h",
+ QtCore.Qt.Key_K:"k",
+ QtCore.Qt.Key_L:"l",
+ QtCore.Qt.Key_M:"m",
+ QtCore.Qt.Key_N:"n",
+ QtCore.Qt.Key_O:"o",
+ QtCore.Qt.Key_P:"p",
+ QtCore.Qt.Key_Q:"q",
+ QtCore.Qt.Key_R:"r",
+ QtCore.Qt.Key_S:"s",
+ QtCore.Qt.Key_T:"t",
+ QtCore.Qt.Key_U:"u",
+ QtCore.Qt.Key_V:"v",
+ QtCore.Qt.Key_W:"w",
+ QtCore.Qt.Key_X:"x",
+ QtCore.Qt.Key_Y:"y",
+ QtCore.Qt.Key_Z:"z",
+ QtCore.Qt.Key_Asterisk:"asterisk",
+ QtCore.Qt.Key_Plus:"plus",
+ QtCore.Qt.Key_Minus:"minus",
+ QtCore.Qt.Key_Period:"period",
+ QtCore.Qt.Key_Slash:"slash",
+ QtCore.Qt.Key_F1:"F1",
+ QtCore.Qt.Key_F2:"F2",
+ QtCore.Qt.Key_F3:"F3",
+ QtCore.Qt.Key_F4:"F4",
+ QtCore.Qt.Key_F5:"F5",
+ QtCore.Qt.Key_F6:"F6",
+ QtCore.Qt.Key_F7:"F7",
+ QtCore.Qt.Key_F8:"F8",
+ QtCore.Qt.Key_F9:"F9",
+ QtCore.Qt.Key_F10:"F10",
+ QtCore.Qt.Key_F11:"F11",
+ QtCore.Qt.Key_F12:"F12",
+ QtCore.Qt.Key_F13:"F13",
+ QtCore.Qt.Key_F14:"F14",
+ QtCore.Qt.Key_F15:"F15",
+ QtCore.Qt.Key_F16:"F16",
+ QtCore.Qt.Key_F17:"F17",
+ QtCore.Qt.Key_F18:"F18",
+ QtCore.Qt.Key_F19:"F19",
+ QtCore.Qt.Key_F20:"F20",
+ QtCore.Qt.Key_F21:"F21",
+ QtCore.Qt.Key_F22:"F22",
+ QtCore.Qt.Key_F23:"F23",
+ QtCore.Qt.Key_F24:"F24",
+ QtCore.Qt.Key_NumLock:"Num_Lock",
+ QtCore.Qt.Key_ScrollLock:"Scroll_Lock"}
+ if i in handler:
+ return handler[i]
+ else:
+ return "None"
+
+ def getRendererList(self):
+ """ getRendererList() -> list
+ Return a list of vtkRenderer running in this QVTKWidget
+ """
+ result = []
+ renWin = self.GetRenderWindow()
+ renderers = renWin.GetRenderers()
+ renderers.InitTraversal()
+ for i in xrange(renderers.GetNumberOfItems()):
+ result.append(renderers.GetNextItem())
+ return result
+
+ def getActiveRenderer(self, iren):
+ """ getActiveRenderer(iren: vtkRenderWindowwInteractor) -> vtkRenderer
+ Return the active vtkRenderer under mouse
+
+ """
+ epos = list(iren.GetEventPosition())
+ if epos[1]<0:
+ epos[1] = -epos[1]
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ if ren.IsInViewport(epos[0], epos[1]):
+ return ren
+ return None
+
+ def findSheetTabWidget(self):
+ """ findSheetTabWidget() -> QTabWidget
+ Find and return the sheet tab widget
+
+ """
+ p = self.parent()
+ while p:
+ if hasattr(p, 'isSheetTabWidget'):
+ if p.isSheetTabWidget()==True:
+ return p
+ p = p.parent()
+ return None
+
+ def getRenderersInCellList(self, sheet, cells):
+ """ isRendererIn(sheet: spreadsheet.StandardWidgetSheet,
+ cells: [(int,int)]) -> bool
+ Get the list of renderers in side a list of (row, column)
+ cells.
+
+ """
+ rens = []
+ for (row, col) in cells:
+ cell = sheet.getCell(row, col)
+ if hasattr(cell, 'getRendererList'):
+ rens += cell.getRendererList()
+ return rens
+
+ def getSelectedCellWidgets(self):
+ sheet = self.findSheetTabWidget()
+ if sheet:
+ iren = self.mRenWin.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ cells = sheet.getSelectedLocations()
+ if (ren in self.getRenderersInCellList(sheet, cells)):
+ return [sheet.getCell(row, col)
+ for (row, col) in cells
+ if hasattr(sheet.getCell(row, col),
+ 'getRendererList')]
+ return []
+
+ def interactionEvent(self, istyle, name):
+ """ interactionEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure interactions sync across selected renderers
+
+ """
+ if name=='MouseWheelForwardEvent':
+ istyle.OnMouseWheelForward()
+ if name=='MouseWheelBackwardEvent':
+ istyle.OnMouseWheelBackward()
+ ren = self.interacting
+ if not ren:
+ ren = self.getActiveRenderer(istyle.GetInteractor())
+ if ren:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ for cell in self.getSelectedCellWidgets():
+ if cell!=self and hasattr(cell, 'getRendererList'):
+ rens = cell.getRendererList()
+ for r in rens:
+ if r!=ren:
+ dcam = r.GetActiveCamera()
+ dcam.SetPosition(cpos)
+ dcam.SetFocalPoint(cfol)
+ dcam.SetViewUp(cup)
+ r.ResetCameraClippingRange()
+ cell.update()
+
+ def charEvent(self, istyle, name):
+ """ charEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure key presses also sync across selected renderers
+
+ """
+ iren = istyle.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ keyCode = iren.GetKeyCode()
+ if keyCode in ['w','W','s','S','r','R','p','P']:
+ for cell in self.getSelectedCellWidgets():
+ if hasattr(cell, 'GetInteractor'):
+ selectedIren = cell.GetInteractor()
+ selectedIren.SetKeyCode(keyCode)
+ selectedIren.GetInteractorStyle().OnChar()
+ selectedIren.Render()
+ istyle.OnChar()
+
+ def saveToPNG(self, filename):
+ """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
+
+ Save the current widget contents to an image file. If
+ str==None, then it returns the vtkUnsignedCharArray containing
+ the PNG image. Otherwise, the filename is returned.
+
+ """
+ w2i = vtk.vtkWindowToImageFilter()
+ w2i.ReadFrontBufferOff()
+ w2i.SetInput(self.mRenWin)
+ # Render twice to get a clean image on the back buffer
+ if self.mRenWin.GetInteractor():
+ self.mRenWin.GetInteractor().Render()
+ self.mRenWin.GetInteractor().Render()
+ else:
+ self.mRenWin.Render()
+ self.mRenWin.Render()
+ w2i.Update()
+ writer = vtk.vtkPNGWriter()
+ writer.SetInputConnection(w2i.GetOutputPort())
+ if filename!=None:
+ writer.SetFileName(filename)
+ else:
+ writer.WriteToMemoryOn()
+ writer.Write()
+ if filename:
+ return filename
+ else:
+ return writer.GetResult()
+
+ def captureWindow(self):
+ """ captureWindow() -> None
+ Capture the window contents to file
+
+ """
+ fn = QtGui.QFileDialog.getSaveFileName(None,
+ "Save file as...",
+ "screenshot.png",
+ "Images (*.png);;PDF files (*.pdf)")
+ if fn:
+ if fn.lower().endswith("png"):
+ self.saveToPNG(fn)
+ elif fn.lower().endswith("pdf"):
+ self.saveToPDF(fn)
+
+ def grabWindowPixmap(self):
+ """ grabWindowImage() -> QPixmap
+ Widget special grabbing function
+
+ """
+ uchar = self.saveToPNG(None)
+
+ ba = QtCore.QByteArray()
+ buf = QtCore.QBuffer(ba)
+ buf.open(QtCore.QIODevice.WriteOnly)
+ for i in xrange(uchar.GetNumberOfTuples()):
+ c = uchar.GetValue(i)
+ buf.putChar(chr(c))
+ buf.close()
+
+ pixmap = QtGui.QPixmap()
+ pixmap.loadFromData(ba, 'PNG')
+ return pixmap
+
+ def dumpToFile(self, filename):
+ """dumpToFile() -> None
+ Dumps itself as an image to a file, calling saveToPNG
+ """
+ self.saveToPNG(filename)
+
+class QVTKWidgetCapture(QtGui.QAction):
+ """
+ QVTKWidgetCapture is the action to capture the vtk rendering
+ window to an image
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKWidgetCapture(parent: QWidget) -> QVTKWidgetCapture
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/camera.png"),
+ "&Capture image to file",
+ parent)
+ self.setStatusTip("Capture the rendered image to a file")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ cellWidget.captureWindow()
+
+class QVTKWidgetSaveCamera(QtGui.QAction):
+ """
+ QVTKWidgetSaveCamera is the action to capture the current camera
+ of the vtk renderers and save it back to the pipeline
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKWidgetSaveCamera(parent: QWidget) -> QVTKWidgetSaveCamera
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ "Save &Camera",
+ parent)
+ self.setStatusTip("Save current camera views to the pipeline")
+
+ def setCamera(self, controller):
+ ops = []
+ pipeline = controller.current_pipeline
+ cellWidget = self.toolBar.getSnappedWidget()
+ renderers = cellWidget.getRendererList()
+ for ren in renderers:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ rendererId = cellWidget.renderer_maps[ren]
+ # Looking for SetActiveCamera()
+ camera = None
+ renderer = pipeline.modules[rendererId]
+ for c in pipeline.connections.values():
+ if c.destination.moduleId==rendererId:
+ if c.destination.name=='SetActiveCamera':
+ camera = pipeline.modules[c.source.moduleId]
+ break
+
+ if not camera:
+ # Create camera
+ vtk_package = vtk_pkg_identifier
+ camera = controller.create_module(vtk_package, 'vtkCamera', '',
+ 0.0, 0.0)
+ ops.append(('add', camera))
+
+ # Connect camera to renderer
+ camera_conn = controller.create_connection(camera, 'self',
+ renderer,
+ 'SetActiveCamera')
+ ops.append(('add', camera_conn))
+ # update functions
+ def convert_to_str(arglist):
+ new_arglist = []
+ for arg in arglist:
+ new_arglist.append(str(arg))
+ return new_arglist
+ functions = [('SetPosition', convert_to_str(cpos)),
+ ('SetFocalPoint', convert_to_str(cfol)),
+ ('SetViewUp', convert_to_str(cup))]
+ ops.extend(controller.update_functions_ops(camera, functions))
+
+ action = vistrails.core.db.action.create_action(ops)
+ controller.add_new_action(action)
+ controller.perform_action(action)
+ controller.select_latest_version()
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ visApp = QtCore.QCoreApplication.instance()
+ if hasattr(visApp, 'builderWindow'):
+ builderWindow = visApp.builderWindow
+ if builderWindow:
+ info = self.toolBar.sheet.getCellPipelineInfo(
+ self.toolBar.row, self.toolBar.col)
+ if info:
+ info = info[0]
+ view = builderWindow.ensureController(info['controller'])
+ if view:
+ controller = view.controller
+ controller.change_selected_version(info['version'])
+ self.setCamera(controller)
+
+
+class QVTKWidgetToolBar(QCellToolBar):
+ """
+ QVTKWidgetToolBar derives from QCellToolBar to give the VTKCell
+ a customizable toolbar
+
+ """
+ def createToolBar(self):
+ """ createToolBar() -> None
+ This will get call initiallly to add customizable widgets
+
+ """
+ self.appendAction(QVTKWidgetCapture(self))
+ self.addAnimationButtons()
+ self.appendAction(QVTKWidgetSaveCamera(self))
+
+def registerSelf():
+ """ registerSelf() -> None
+ Registry module with the registry
+ """
+ registry = get_module_registry()
+ registry.add_module(VTKCell)
+ registry.add_input_port(VTKCell, "Location", CellLocation)
+ import vistrails.core.debug
+ for (port,module) in [("AddRenderer",'vtkRenderer'),
+ ("SetRenderView",'vtkRenderView'),
+ ("InteractionHandler",'vtkInteractionHandler'),
+ ("InteractorStyle", 'vtkInteractorStyle'),
+ ("AddPicker",'vtkAbstractPicker')]:
+ try:
+ registry.add_input_port(VTKCell, port,'(%s:%s)' % \
+ (vtk_pkg_identifier,module))
+
+ except Exception, e:
+ vistrails.core.debug.warning(str(e))
+
+ registry.add_output_port(VTKCell, "self", VTKCell)
diff --git a/vistrails/packages/vtk/vtkcell_rc.py b/vistrails/packages/vtk/vtkcell_rc.py
new file mode 100644
index 0000000..ae51b30
--- /dev/null
+++ b/vistrails/packages/vtk/vtkcell_rc.py
@@ -0,0 +1,198 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+# -*- coding: utf-8 -*-
+
+# Resource object code
+#
+# Created: Mon Jul 19 16:02:11 2010
+# by: The Resource Compiler for PyQt (Qt v4.6.3)
+#
+# WARNING! All changes made in this file will be lost!
+
+from PyQt4 import QtCore
+
+qt_resource_data = b"\
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+\x44\xae\x42\x60\x82\
+"
+
+qt_resource_name = b"\
+\x00\x06\
+\x07\x03\x7d\xc3\
+\x00\x69\
+\x00\x6d\x00\x61\x00\x67\x00\x65\x00\x73\
+\x00\x0a\
+\x0c\x91\x67\x27\
+\x00\x63\
+\x00\x61\x00\x6d\x00\x65\x00\x72\x00\x61\x00\x2e\x00\x70\x00\x6e\x00\x67\
+"
+
+qt_resource_struct = b"\
+\x00\x00\x00\x00\x00\x02\x00\x00\x00\x01\x00\x00\x00\x01\
+\x00\x00\x00\x00\x00\x02\x00\x00\x00\x01\x00\x00\x00\x02\
+\x00\x00\x00\x12\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\
+"
+
+def qInitResources():
+ QtCore.qRegisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+def qCleanupResources():
+ QtCore.qUnregisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
+
+qInitResources()
diff --git a/vistrails/packages/vtk/vtkhandler.py b/vistrails/packages/vtk/vtkhandler.py
new file mode 100644
index 0000000..337c36e
--- /dev/null
+++ b/vistrails/packages/vtk/vtkhandler.py
@@ -0,0 +1,220 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Modules for handling vtkRenderWindowInteractor events"""
+from PyQt4 import QtCore, QtGui
+from vistrails.core.modules.basic_modules import String
+from vistrails.core.modules.vistrails_module import Module, NotCacheable
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.core.vistrail.module_function import ModuleFunction, ModuleParam
+from vistrails.gui.modules.source_configure import SourceConfigurationWidget
+from vistrails.gui.modules.python_source_configure import PythonEditor
+import urllib
+
+from identifiers import identifier as vtk_pkg_identifier
+
+################################################################################
+class vtkInteractionHandler(NotCacheable, Module):
+ """
+ vtkInteractionHandler allow users to insert callback code for interacting
+ with the vtkRenderWindowInteractor InteractionEvent
+
+ """
+
+ # Since vtkCommand is not wrapped in Python, we need to hardcoded all events
+ # string from vtkCommand.h
+ vtkEvents = [
+ 'AnyEvent',
+ 'DeleteEvent',
+ 'StartEvent',
+ 'EndEvent',
+ 'RenderEvent',
+ 'ProgressEvent',
+ 'PickEvent',
+ 'StartPickEvent',
+ 'EndPickEvent',
+ 'AbortCheckEvent',
+ 'ExitEvent',
+ 'LeftButtonPressEvent',
+ 'LeftButtonReleaseEvent',
+ 'MiddleButtonPressEvent',
+ 'MiddleButtonReleaseEvent',
+ 'RightButtonPressEvent',
+ 'RightButtonReleaseEvent',
+ 'EnterEvent',
+ 'LeaveEvent',
+ 'KeyPressEvent',
+ 'KeyReleaseEvent',
+ 'CharEvent',
+ 'ExposeEvent',
+ 'ConfigureEvent',
+ 'TimerEvent',
+ 'MouseMoveEvent',
+ 'MouseWheelForwardEvent',
+ 'MouseWheelBackwardEvent',
+ 'ResetCameraEvent',
+ 'ResetCameraClippingRangeEvent',
+ 'ModifiedEvent',
+ 'WindowLevelEvent',
+ 'StartWindowLevelEvent',
+ 'EndWindowLevelEvent',
+ 'ResetWindowLevelEvent',
+ 'SetOutputEvent',
+ 'ErrorEvent',
+ 'WarningEvent',
+ 'StartInteractionEvent',
+ 'InteractionEvent',
+ 'EndInteractionEvent',
+ 'EnableEvent',
+ 'DisableEvent',
+ 'CreateTimerEvent',
+ 'DestroyTimerEvent',
+ 'PlacePointEvent',
+ 'PlaceWidgetEvent',
+ 'CursorChangedEvent',
+ 'ExecuteInformationEvent',
+ 'RenderWindowMessageEvent',
+ 'WrongTagEvent',
+ 'StartAnimationCueEvent',
+ 'AnimationCueTickEvent',
+ 'EndAnimationCueEvent',
+ 'VolumeMapperRenderEndEvent',
+ 'VolumeMapperRenderProgressEvent',
+ 'VolumeMapperRenderStartEvent',
+ 'VolumeMapperComputeGradientsEndEvent',
+ 'VolumeMapperComputeGradientsProgressEvent',
+ 'VolumeMapperComputeGradientsStartEvent',
+ 'WidgetModifiedEvent',
+ 'WidgetValueChangedEvent',
+ 'WidgetActivateEvent',
+ 'ConnectionCreatedEvent',
+ 'ConnectionClosedEvent',
+ 'DomainModifiedEvent',
+ 'PropertyModifiedEvent',
+ 'UpdateEvent',
+ 'RegisterEvent',
+ 'UnRegisterEvent',
+ 'UpdateInformationEvent']
+
+ def __init__(self):
+ Module.__init__(self)
+ self.observer = None
+ self.handler = None
+ self.shareddata = None
+
+ def compute(self):
+ """ compute() -> None
+ Actually compute nothing
+ """
+ self.observer = self.forceGetInputFromPort('Observer')
+ self.handler = self.forceGetInputFromPort('Handler', '')
+ self.shareddata = self.forceGetInputListFromPort('SharedData')
+ if len(self.shareddata)==1:
+ self.shareddata = self.shareddata[0]
+ if self.observer:
+ source = urllib.unquote(self.handler)
+ observer = self.observer.vtkInstance
+ for e in vtkInteractionHandler.vtkEvents:
+ f = e[0].lower() + e[1:]
+ f = f.replace('Event', 'Handler')
+ source += ('\nif locals().has_key("%s"):\n' % f +
+ '\tobserver.AddObserver("%s", ' % e +
+ 'self.eventHandler)\n')
+ exec(source)
+ if hasattr(self.observer.vtkInstance, 'PlaceWidget'):
+ self.observer.vtkInstance.PlaceWidget()
+
+ def eventHandler(self, obj, event):
+ """ eventHandler(obj: vtkObject, event: str) -> None
+ A proxy for all vtk events to direct to the correct calls
+
+ """
+ if self.handler!='':
+ source = urllib.unquote(self.handler)
+ f = event[0].lower() + event[1:]
+ f = f.replace('Event', 'Handler')
+ myGlobals = globals()
+ myGlobals.update({'self':self})
+ exec(source + ('\nif locals().has_key("%s"):\n' % f)+
+ ('\t%s(obj, self.shareddata)' % f)) in myGlobals, locals()
+
+ def clear(self):
+ """ clear() -> None
+ Remove event handler so the object can be freed correctly
+
+ """
+ # Remove all observers
+ if self.observer:
+ for e in vtkInteractionHandler.vtkEvents:
+ self.observer.vtkInstance.RemoveObservers(e)
+ Module.clear(self)
+
+ def repaintCells(self):
+ """ repaintCells() -> None
+ Redraw all cells on the current sheet
+
+ """
+ from vistrails.packages.spreadsheet.spreadsheet_controller \
+ import spreadsheetController
+ from vistrails.packages.spreadsheet.spreadsheet_event \
+ import RepaintCurrentSheetEvent
+ spreadsheetController.postEventToSpreadsheet(RepaintCurrentSheetEvent())
+
+class HandlerConfigurationWidget(SourceConfigurationWidget):
+ def __init__(self, module, controller, parent=None):
+ """ HandlerConfigurationWidget(module: Module,
+ controller: VistrailController,
+ parent: QWidget)
+ -> HandlerConfigurationWidget
+ Setup the dialog to similar to PythonSource but with a
+ different name
+
+ """
+ SourceConfigurationWidget.__init__(self, module, controller,
+ PythonEditor, False, False, parent,
+ portName='Handler')
+
+def registerSelf():
+ """ registerSelf() -> None
+ Registry module with the registry
+ """
+ registry = get_module_registry()
+ vIO = registry.get_descriptor_by_name(vtk_pkg_identifier,
+ 'vtkInteractorObserver').module
+ registry.add_module(vtkInteractionHandler, configureWidgetType=HandlerConfigurationWidget)
+ registry.add_input_port(vtkInteractionHandler, 'Observer', vIO)
+ registry.add_input_port(vtkInteractionHandler, 'Handler', String, True)
+ registry.add_input_port(vtkInteractionHandler, 'SharedData', Module)
+ registry.add_output_port(vtkInteractionHandler, 'self',
+ vtkInteractionHandler)
diff --git a/vistrails/packages/vtk/vtkviewcell.py b/vistrails/packages/vtk/vtkviewcell.py
new file mode 100644
index 0000000..b06eacc
--- /dev/null
+++ b/vistrails/packages/vtk/vtkviewcell.py
@@ -0,0 +1,1045 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+################################################################################
+# File QVTKViewWidget.py
+# File for displaying a vtkRenderWindow in a Qt's QWidget ported from
+# VTK/GUISupport/QVTK. Combine altogether to a single class: QVTKViewWidget
+################################################################################
+import vtk
+from PyQt4 import QtCore, QtGui
+import sip
+from vistrails.core import system
+from vistrails.core.modules.module_registry import get_module_registry
+from vistrails.packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
+import vtkcell_rc
+import gc
+from vistrails.gui.qt import qt_super
+import vistrails.core.db.action
+from vistrails.core.vistrail.action import Action
+from vistrails.core.vistrail.port import Port
+from vistrails.core.vistrail import module
+from vistrails.core.vistrail import connection
+from vistrails.core.vistrail.module_function import ModuleFunction
+from vistrails.core.vistrail.module_param import ModuleParam
+from vistrails.core.vistrail.location import Location
+from vistrails.core.modules.vistrails_module import ModuleError
+import copy
+
+from identifiers import identifier as vtk_pkg_identifier
+
+################################################################################
+
+class VTKViewCell(SpreadsheetCell):
+ """
+ VTKViewCell is a VisTrails Module that can display vtkRenderWindow inside a cell
+
+ """
+
+ def __init__(self):
+ SpreadsheetCell.__init__(self)
+ self.cellWidget = None
+
+ def compute(self):
+ """ compute() -> None
+ Dispatch the vtkRenderer to the actual rendering widget
+ """
+ renderView = self.forceGetInputFromPort('SetRenderView')
+ if renderView==None:
+ raise ModuleError(self, 'A vtkRenderView input is required.')
+ self.cellWidget = self.displayAndWait(QVTKViewWidget, (renderView,))
+
+AsciiToKeySymTable = ( None, None, None, None, None, None, None,
+ None, None,
+ "Tab", None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None, None, None,
+ None, None, None, None,
+ "space", "exclam", "quotedbl", "numbersign",
+ "dollar", "percent", "ampersand", "quoteright",
+ "parenleft", "parenright", "asterisk", "plus",
+ "comma", "minus", "period", "slash",
+ "0", "1", "2", "3", "4", "5", "6", "7",
+ "8", "9", "colon", "semicolon", "less", "equal",
+ "greater", "question",
+ "at", "A", "B", "C", "D", "E", "F", "G",
+ "H", "I", "J", "K", "L", "M", "N", "O",
+ "P", "Q", "R", "S", "T", "U", "V", "W",
+ "X", "Y", "Z", "bracketleft",
+ "backslash", "bracketright", "asciicircum",
+ "underscore",
+ "quoteleft", "a", "b", "c", "d", "e", "f", "g",
+ "h", "i", "j", "k", "l", "m", "n", "o",
+ "p", "q", "r", "s", "t", "u", "v", "w",
+ "x", "y", "z", "braceleft", "bar", "braceright",
+ "asciitilde", "Delete",
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None,
+ None, None, None, None, None, None, None, None)
+
+class QVTKViewWidget(QCellWidget):
+ """
+ QVTKViewWidget is the actual rendering widget that can display
+ vtkRenderer inside a Qt QWidget
+
+ """
+ def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
+ """ QVTKViewWidget(parent: QWidget, f: WindowFlags) -> QVTKViewWidget
+ Initialize QVTKViewWidget with a toolbar with its own device
+ context
+
+ """
+ QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
+
+ self.interacting = None
+ self.mRenWin = None
+ self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
+ self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
+ self.setMouseTracking(True)
+ self.setFocusPolicy(QtCore.Qt.StrongFocus)
+ self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
+ QtGui.QSizePolicy.Expanding))
+ self.toolBarType = QVTKViewWidgetToolBar
+ self.setAnimationEnabled(True)
+
+ def removeObserversFromInteractorStyle(self):
+ """ removeObserversFromInteractorStyle() -> None
+ Remove all python binding from interactor style observers for
+ safely freeing the cell
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.RemoveObservers("InteractionEvent")
+ style.RemoveObservers("EndPickEvent")
+ style.RemoveObservers("CharEvent")
+ style.RemoveObservers("MouseWheelForwardEvent")
+ style.RemoveObservers("MouseWheelBackwardEvent")
+
+ def addObserversToInteractorStyle(self):
+ """ addObserversToInteractorStyle() -> None
+ Assign observer to the current interactor style
+
+ """
+ iren = self.mRenWin.GetInteractor()
+ if iren:
+ style = iren.GetInteractorStyle()
+ style.AddObserver("InteractionEvent", self.interactionEvent)
+ style.AddObserver("EndPickEvent", self.interactionEvent)
+ style.AddObserver("CharEvent", self.charEvent)
+ style.AddObserver("MouseWheelForwardEvent", self.interactionEvent)
+ style.AddObserver("MouseWheelBackwardEvent", self.interactionEvent)
+
+ def deleteLater(self):
+ """ deleteLater() -> None
+ Make sure to free render window resource when
+ deallocating. Overriding PyQt deleteLater to free up
+ resources
+
+ """
+ self.renderer_maps = {}
+ for ren in self.getRendererList():
+ self.mRenWin.RemoveRenderer(ren)
+ self.removeObserversFromInteractorStyle()
+ self.SetRenderWindow(None)
+ QCellWidget.deleteLater(self)
+
+ def updateContents(self, inputPorts):
+ """ updateContents(inputPorts: tuple)
+ Updates the cell contents with new vtkRenderer
+
+ """
+ (renderView, ) = inputPorts
+ renWin = renderView.vtkInstance.GetRenderWindow()
+ renWin.DoubleBufferOn()
+ self.SetRenderWindow(renWin)
+ renderView.vtkInstance.ResetCamera()
+ self.addObserversToInteractorStyle()
+
+# renWin = self.GetRenderWindow()
+# renderers = [renderView.vtkInstance.GetRenderer()]
+# iren = renWin.GetInteractor()
+ # Update interactor style
+# self.removeObserversFromInteractorStyle()
+# if renderView==None:
+# if iStyle==None:
+# iStyleInstance = vtk.vtkInteractorStyleTrackballCamera()
+# else:
+# iStyleInstance = iStyle.vtkInstance
+# iren.SetInteractorStyle(iStyleInstance)
+# self.addObserversToInteractorStyle()
+ # Capture window into history for playback
+ # Call this at the end to capture the image after rendering
+ QCellWidget.updateContents(self, inputPorts)
+
+ def GetRenderWindow(self):
+ """ GetRenderWindow() -> vtkRenderWindow
+ Return the associated vtkRenderWindow
+
+ """
+ if not self.mRenWin:
+ win = vtk.vtkRenderWindow()
+ win.DoubleBufferOn()
+ self.SetRenderWindow(win)
+ del win
+
+ return self.mRenWin
+
+ def SetRenderWindow(self,w):
+ """ SetRenderWindow(w: vtkRenderWindow)
+ Set a new render window to QVTKViewWidget and initialize the
+ interactor as well
+
+ """
+ if w == self.mRenWin:
+ return
+
+ if self.mRenWin:
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+
+ self.mRenWin = w
+
+ if self.mRenWin:
+ self.mRenWin.Register(None)
+ if system.systemType=='Linux':
+ try:
+ vp = '_%s_void_p' % (hex(int(QtGui.QX11Info.display()))[2:])
+ except TypeError:
+ #This was change for PyQt4.2
+ if isinstance(QtGui.QX11Info.display(),QtGui.Display):
+ display = sip.unwrapinstance(QtGui.QX11Info.display())
+ vp = '_%s_void_p' % (hex(display)[2:])
+ self.mRenWin.SetDisplayId(vp)
+ if not self.mRenWin.GetMapped():
+ self.mRenWin.GetInteractor().Initialize()
+ system.XDestroyWindow(self.mRenWin.GetGenericDisplayId(),
+ self.mRenWin.GetGenericWindowId())
+ self.mRenWin.Finalize()
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ else:
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ def GetInteractor(self):
+ """ GetInteractor() -> vtkInteractor
+ Return the vtkInteractor control this QVTKViewWidget
+ """
+ return self.GetRenderWindow().GetInteractor()
+
+ def event(self, e):
+ """ event(e: QEvent) -> depends on event type
+ Process window and interaction events
+
+ """
+ if e.type()==QtCore.QEvent.ParentAboutToChange:
+ if self.mRenWin:
+ if self.mRenWin.GetMapped():
+ self.mRenWin.Finalize()
+ else:
+ if e.type()==QtCore.QEvent.ParentChange:
+ if self.mRenWin:
+ self.mRenWin.SetWindowInfo(str(int(self.winId())))
+ if self.isVisible():
+ self.mRenWin.Start()
+
+ if QtCore.QObject.event(self,e):
+ return 1
+
+ if e.type() == QtCore.QEvent.KeyPress:
+ self.keyPressEvent(e)
+ if e.isAccepted():
+ return e.isAccepted()
+
+ return qt_super(QVTKViewWidget, self).event(e)
+
+ # return QtGui.QWidget.event(self,e)
+ # Was this right? Wasn't this supposed to be QCellWidget.event()?
+
+ def resizeWindow(self, width, height):
+ """ resizeWindow(width: int, height: int) -> None
+ Work around vtk bugs for resizing window
+
+ """
+ ########################################################
+ # VTK - BUGGGGGGGGG - GRRRRRRRRR
+ # This is a 'bug' in vtkWin32OpenGLRenderWindow(.cxx)
+ # If a render window is mapped to screen, the actual
+ # window size is the client area of the window in Win32.
+ # However, this real window size is only updated through
+ # vtkWin32OpenGLRenderWindow::GetSize(). So this has to
+ # be called here to get the cell size correctly. This
+ # invalidates the condition in the next SetSize().
+ # We can use self.mRenWin.SetSize(0,0) here but it will
+ # cause flickering and decrease performance!
+ # SetPosition(curX,curY) also works here but slower.
+ self.mRenWin.GetSize()
+
+ self.mRenWin.SetSize(width, height)
+ if self.mRenWin.GetInteractor():
+ self.mRenWin.GetInteractor().SetSize(width, height)
+
+ def resizeEvent(self, e):
+ """ resizeEvent(e: QEvent) -> None
+ Re-adjust the vtkRenderWindow size then QVTKViewWidget resized
+
+ """
+ qt_super(QVTKViewWidget, self).resizeEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.resizeWindow(self.width(), self.height())
+ self.mRenWin.Render()
+
+ def moveEvent(self,e):
+ """ moveEvent(e: QEvent) -> None
+ Echo the move event into vtkRenderWindow
+
+ """
+ qt_super(QVTKViewWidget, self).moveEvent(e)
+ if not self.mRenWin:
+ return
+
+ self.mRenWin.SetPosition(self.x(),self.y())
+
+ def paintEvent(self, e):
+ """ paintEvent(e: QPaintEvent) -> None
+ Paint the QVTKViewWidget with vtkRenderWindow
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ if hasattr(self.mRenWin, 'UpdateGLRegion'):
+ self.mRenWin.UpdateGLRegion()
+ self.mRenWin.Render()
+
+ def SelectActiveRenderer(self,iren):
+ """ SelectActiveRenderer(iren: vtkRenderWindowIteractor) -> None
+ Only make the vtkRenderer below the mouse cursor active
+
+ """
+ epos = iren.GetEventPosition()
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ ren.SetInteractive(ren.IsInViewport(epos[0], epos[1]))
+
+ def mousePressEvent(self,e):
+ """ mousePressEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ isDoubleClick = e.type()==QtCore.QEvent.MouseButtonDblClick
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ ctrl,
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),
+ isDoubleClick,
+ None)
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonPressEvent",
+ QtCore.Qt.MidButton:"MiddleButtonPressEvent",
+ QtCore.Qt.RightButton:"RightButtonPressEvent"}
+
+ self.SelectActiveRenderer(iren)
+
+ if ctrl:
+ e.ignore()
+ return
+
+ self.interacting = self.getActiveRenderer(iren)
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def mouseMoveEvent(self,e):
+ """ mouseMoveEvent(e: QMouseEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0), 0, None)
+
+ iren.InvokeEvent("MouseMoveEvent")
+
+ def enterEvent(self,e):
+ """ enterEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("EnterEvent")
+
+ def leaveEvent(self,e):
+ """ leaveEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.InvokeEvent("LeaveEvent")
+
+ def mouseReleaseEvent(self,e):
+ """ mouseReleaseEvent(e: QEvent) -> None
+ Echo mouse event to vtkRenderWindowwInteractor
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ invoke = {QtCore.Qt.LeftButton:"LeftButtonReleaseEvent",
+ QtCore.Qt.MidButton:"MiddleButtonReleaseEvent",
+ QtCore.Qt.RightButton:"RightButtonReleaseEvent"}
+
+ self.interacting = None
+
+ if e.button() in invoke:
+ iren.InvokeEvent(invoke[e.button()])
+
+ def keyPressEvent(self,e):
+ """ keyPressEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if len(e.text())>0:
+ ascii_key = e.text()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q', 'e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl,shift,ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyPressEvent")
+
+ if ascii_key:
+ iren.InvokeEvent("CharEvent")
+
+
+ def keyReleaseEvent(self,e):
+ """ keyReleaseEvent(e: QKeyEvent) -> None
+ Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ascii_key = None
+ if len(e.text())>0:
+ ascii_key = e.text()[0]
+ else:
+ ascii_key = chr(0)
+
+ keysym = self.ascii_to_key_sym(ord(ascii_key))
+
+ if not keysym:
+ keysym = self.qt_key_to_key_sym(e.key())
+
+ # Ignore 'q' or 'e' or Ctrl-anykey
+ ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
+ if (keysym in ['q','e'] or ctrl):
+ e.ignore()
+ return
+
+ iren.SetKeyEventInformation(ctrl, shift, ascii_key, e.count(), keysym)
+
+ iren.InvokeEvent("KeyReleaseEvent")
+
+ def wheelEvent(self,e):
+ """ wheelEvent(e: QWheelEvent) -> None
+ Zoom in/out while scrolling the mouse
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ iren.SetEventInformationFlipY(e.x(),e.y(),
+ (e.modifiers()&QtCore.Qt.ControlModifier),
+ (e.modifiers()&QtCore.Qt.ShiftModifier),
+ chr(0),0,None)
+
+ self.SelectActiveRenderer(iren)
+
+ if e.delta()>0:
+ iren.InvokeEvent("MouseWheelForwardEvent")
+ else:
+ iren.InvokeEvent("MouseWheelBackwardEvent")
+
+ def focusInEvent(self,e):
+ """ focusInEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def focusOutEvent(self,e):
+ """ focusOutEvent(e: QFocusEvent) -> None
+ Ignore focus event
+
+ """
+ pass
+
+ def contextMenuEvent(self,e):
+ """ contextMenuEvent(e: QContextMenuEvent) -> None
+ Make sure to get the right mouse position for the context menu
+ event, i.e. also the right click
+
+ """
+ iren = None
+ if self.mRenWin:
+ iren = self.mRenWin.GetInteractor()
+
+ if (not iren) or (not iren.GetEnabled()):
+ return
+
+ ctrl = int(e.modifiers()&QtCore.Qt.ControlModifier)
+ shift = int(e.modifiers()&QtCore.Qt.ShiftModifier)
+ iren.SetEventInformationFlipY(e.x(),e.y(),ctrl,shift,chr(0),0,None)
+ iren.InvokeEvent("ContextMenuEvent")
+
+ def ascii_to_key_sym(self,i):
+ """ ascii_to_key_sym(i: int) -> str
+ Convert ASCII code into key name
+
+ """
+ global AsciiToKeySymTable
+ return AsciiToKeySymTable[i]
+
+ def qt_key_to_key_sym(self,i):
+ """ qt_key_to_key_sym(i: QtCore.Qt.Keycode) -> str
+ Convert Qt key code into key name
+
+ """
+ handler = {QtCore.Qt.Key_Backspace:"BackSpace",
+ QtCore.Qt.Key_Tab:"Tab",
+ QtCore.Qt.Key_Backtab:"Tab",
+ QtCore.Qt.Key_Return:"Return",
+ QtCore.Qt.Key_Enter:"Return",
+ QtCore.Qt.Key_Shift:"Shift_L",
+ QtCore.Qt.Key_Control:"Control_L",
+ QtCore.Qt.Key_Alt:"Alt_L",
+ QtCore.Qt.Key_Pause:"Pause",
+ QtCore.Qt.Key_CapsLock:"Caps_Lock",
+ QtCore.Qt.Key_Escape:"Escape",
+ QtCore.Qt.Key_Space:"space",
+ QtCore.Qt.Key_End:"End",
+ QtCore.Qt.Key_Home:"Home",
+ QtCore.Qt.Key_Left:"Left",
+ QtCore.Qt.Key_Up:"Up",
+ QtCore.Qt.Key_Right:"Right",
+ QtCore.Qt.Key_Down:"Down",
+ QtCore.Qt.Key_SysReq:"Snapshot",
+ QtCore.Qt.Key_Insert:"Insert",
+ QtCore.Qt.Key_Delete:"Delete",
+ QtCore.Qt.Key_Help:"Help",
+ QtCore.Qt.Key_0:"0",
+ QtCore.Qt.Key_1:"1",
+ QtCore.Qt.Key_2:"2",
+ QtCore.Qt.Key_3:"3",
+ QtCore.Qt.Key_4:"4",
+ QtCore.Qt.Key_5:"5",
+ QtCore.Qt.Key_6:"6",
+ QtCore.Qt.Key_7:"7",
+ QtCore.Qt.Key_8:"8",
+ QtCore.Qt.Key_9:"9",
+ QtCore.Qt.Key_A:"a",
+ QtCore.Qt.Key_B:"b",
+ QtCore.Qt.Key_C:"c",
+ QtCore.Qt.Key_D:"d",
+ QtCore.Qt.Key_E:"e",
+ QtCore.Qt.Key_F:"f",
+ QtCore.Qt.Key_G:"g",
+ QtCore.Qt.Key_H:"h",
+ QtCore.Qt.Key_I:"i",
+ QtCore.Qt.Key_J:"h",
+ QtCore.Qt.Key_K:"k",
+ QtCore.Qt.Key_L:"l",
+ QtCore.Qt.Key_M:"m",
+ QtCore.Qt.Key_N:"n",
+ QtCore.Qt.Key_O:"o",
+ QtCore.Qt.Key_P:"p",
+ QtCore.Qt.Key_Q:"q",
+ QtCore.Qt.Key_R:"r",
+ QtCore.Qt.Key_S:"s",
+ QtCore.Qt.Key_T:"t",
+ QtCore.Qt.Key_U:"u",
+ QtCore.Qt.Key_V:"v",
+ QtCore.Qt.Key_W:"w",
+ QtCore.Qt.Key_X:"x",
+ QtCore.Qt.Key_Y:"y",
+ QtCore.Qt.Key_Z:"z",
+ QtCore.Qt.Key_Asterisk:"asterisk",
+ QtCore.Qt.Key_Plus:"plus",
+ QtCore.Qt.Key_Minus:"minus",
+ QtCore.Qt.Key_Period:"period",
+ QtCore.Qt.Key_Slash:"slash",
+ QtCore.Qt.Key_F1:"F1",
+ QtCore.Qt.Key_F2:"F2",
+ QtCore.Qt.Key_F3:"F3",
+ QtCore.Qt.Key_F4:"F4",
+ QtCore.Qt.Key_F5:"F5",
+ QtCore.Qt.Key_F6:"F6",
+ QtCore.Qt.Key_F7:"F7",
+ QtCore.Qt.Key_F8:"F8",
+ QtCore.Qt.Key_F9:"F9",
+ QtCore.Qt.Key_F10:"F10",
+ QtCore.Qt.Key_F11:"F11",
+ QtCore.Qt.Key_F12:"F12",
+ QtCore.Qt.Key_F13:"F13",
+ QtCore.Qt.Key_F14:"F14",
+ QtCore.Qt.Key_F15:"F15",
+ QtCore.Qt.Key_F16:"F16",
+ QtCore.Qt.Key_F17:"F17",
+ QtCore.Qt.Key_F18:"F18",
+ QtCore.Qt.Key_F19:"F19",
+ QtCore.Qt.Key_F20:"F20",
+ QtCore.Qt.Key_F21:"F21",
+ QtCore.Qt.Key_F22:"F22",
+ QtCore.Qt.Key_F23:"F23",
+ QtCore.Qt.Key_F24:"F24",
+ QtCore.Qt.Key_NumLock:"Num_Lock",
+ QtCore.Qt.Key_ScrollLock:"Scroll_Lock"}
+ if i in handler:
+ return handler[i]
+ else:
+ return "None"
+
+ def getRendererList(self):
+ """ getRendererList() -> list
+ Return a list of vtkRenderer running in this QVTKViewWidget
+ """
+ result = []
+ renWin = self.GetRenderWindow()
+ renderers = renWin.GetRenderers()
+ renderers.InitTraversal()
+ for i in xrange(renderers.GetNumberOfItems()):
+ result.append(renderers.GetNextItem())
+ return result
+
+ def getActiveRenderer(self, iren):
+ """ getActiveRenderer(iren: vtkRenderWindowwInteractor) -> vtkRenderer
+ Return the active vtkRenderer under mouse
+
+ """
+ epos = list(iren.GetEventPosition())
+ if epos[1]<0:
+ epos[1] = -epos[1]
+ rens = iren.GetRenderWindow().GetRenderers()
+ rens.InitTraversal()
+ for i in xrange(rens.GetNumberOfItems()):
+ ren = rens.GetNextItem()
+ if ren.IsInViewport(epos[0], epos[1]):
+ return ren
+ return None
+
+ def findSheetTabWidget(self):
+ """ findSheetTabWidget() -> QTabWidget
+ Find and return the sheet tab widget
+
+ """
+ p = self.parent()
+ while p:
+ if hasattr(p, 'isSheetTabWidget'):
+ if p.isSheetTabWidget()==True:
+ return p
+ p = p.parent()
+ return None
+
+ def getRenderersInCellList(self, sheet, cells):
+ """ isRendererIn(sheet: spreadsheet.StandardWidgetSheet,
+ cells: [(int,int)]) -> bool
+ Get the list of renderers in side a list of (row, column)
+ cells.
+
+ """
+ rens = []
+ for (row, col) in cells:
+ cell = sheet.getCell(row, col)
+ if hasattr(cell, 'getRendererList'):
+ rens += cell.getRendererList()
+ return rens
+
+ def getSelectedCellWidgets(self):
+ sheet = self.findSheetTabWidget()
+ if sheet:
+ iren = self.mRenWin.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ cells = sheet.getSelectedLocations()
+ if (ren in self.getRenderersInCellList(sheet, cells)):
+ return [sheet.getCell(row, col)
+ for (row, col) in cells
+ if hasattr(sheet.getCell(row, col),
+ 'getRendererList')]
+ return []
+
+ def interactionEvent(self, istyle, name):
+ """ interactionEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure interactions sync across selected renderers
+
+ """
+ if name=='MouseWheelForwardEvent':
+ istyle.OnMouseWheelForward()
+ if name=='MouseWheelBackwardEvent':
+ istyle.OnMouseWheelBackward()
+ ren = self.interacting
+ if not ren:
+ ren = self.getActiveRenderer(istyle.GetInteractor())
+ if ren:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ for cell in self.getSelectedCellWidgets():
+ if cell!=self and hasattr(cell, 'getRendererList'):
+ rens = cell.getRendererList()
+ for r in rens:
+ if r!=ren:
+ dcam = r.GetActiveCamera()
+ dcam.SetPosition(cpos)
+ dcam.SetFocalPoint(cfol)
+ dcam.SetViewUp(cup)
+ r.ResetCameraClippingRange()
+ cell.update()
+
+ def charEvent(self, istyle, name):
+ """ charEvent(istyle: vtkInteractorStyle, name: str) -> None
+ Make sure key presses also sync across selected renderers
+
+ """
+ iren = istyle.GetInteractor()
+ ren = self.interacting
+ if not ren: ren = self.getActiveRenderer(iren)
+ if ren:
+ keyCode = iren.GetKeyCode()
+ if keyCode in ['w','W','s','S','r','R','p','P']:
+ for cell in self.getSelectedCellWidgets():
+ if hasattr(cell, 'GetInteractor'):
+ selectedIren = cell.GetInteractor()
+ selectedIren.SetKeyCode(keyCode)
+ selectedIren.GetInteractorStyle().OnChar()
+ selectedIren.Render()
+ istyle.OnChar()
+
+ def saveToPNG(self, filename):
+ """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
+
+ Save the current widget contents to an image file. If
+ str==None, then it returns the vtkUnsignedCharArray containing
+ the PNG image. Otherwise, the filename is returned.
+
+ """
+ w2i = vtk.vtkWindowToImageFilter()
+ w2i.ReadFrontBufferOff()
+ w2i.SetInput(self.mRenWin)
+ # Render twice to get a clean image on the back buffer
+ self.mRenWin.Render()
+ self.mRenWin.Render()
+ w2i.Update()
+ writer = vtk.vtkPNGWriter()
+ writer.SetInputConnection(w2i.GetOutputPort())
+ if filename!=None:
+ writer.SetFileName(filename)
+ else:
+ writer.WriteToMemoryOn()
+ writer.Write()
+ if filename:
+ return filename
+ else:
+ return writer.GetResult()
+
+ def captureWindow(self):
+ """ captureWindow() -> None
+ Capture the window contents to file
+
+ """
+ fn = QtGui.QFileDialog.getSaveFileName(None,
+ "Save file as...",
+ "screenshot.png",
+ "Images (*.png)")
+ if fn:
+ self.saveToPNG(fn)
+
+ def grabWindowPixmap(self):
+ """ grabWindowImage() -> QPixmap
+ Widget special grabbing function
+
+ """
+ uchar = self.saveToPNG(None)
+
+ ba = QtCore.QByteArray()
+ buf = QtCore.QBuffer(ba)
+ buf.open(QtCore.QIODevice.WriteOnly)
+ for i in xrange(uchar.GetNumberOfTuples()):
+ c = uchar.GetValue(i)
+ buf.putChar(chr(c))
+ buf.close()
+
+ pixmap = QtGui.QPixmap()
+ pixmap.loadFromData(ba, 'PNG')
+ return pixmap
+
+ def dumpToFile(self, filename):
+ """dumpToFile() -> None
+ Dumps itself as an image to a file, calling saveToPNG
+ """
+ self.saveToPNG(filename)
+
+class QVTKViewWidgetCapture(QtGui.QAction):
+ """
+ QVTKViewWidgetCapture is the action to capture the vtk rendering
+ window to an image
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKViewWidgetCapture(parent: QWidget) -> QVTKViewWidgetCapture
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ QtGui.QIcon(":/images/camera.png"),
+ "&Capture image to file",
+ parent)
+ self.setStatusTip("Capture the rendered image to a file")
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ cellWidget = self.toolBar.getSnappedWidget()
+ cellWidget.captureWindow()
+
+class QVTKViewWidgetSaveCamera(QtGui.QAction):
+ """
+ QVTKViewWidgetSaveCamera is the action to capture the current camera
+ of the vtk renderers and save it back to the pipeline
+
+ """
+ def __init__(self, parent=None):
+ """ QVTKViewWidgetSaveCamera(parent: QWidget) -> QVTKViewWidgetSaveCamera
+ Setup the image, status tip, etc. of the action
+
+ """
+ QtGui.QAction.__init__(self,
+ "Save &Camera",
+ parent)
+ self.setStatusTip("Save current camera views to the pipeline")
+
+ def setCamera(self, controller):
+ ops = []
+ pipeline = controller.current_pipeline
+ cellWidget = self.toolBar.getSnappedWidget()
+ renderers = cellWidget.getRendererList()
+ for ren in renderers:
+ cam = ren.GetActiveCamera()
+ cpos = cam.GetPosition()
+ cfol = cam.GetFocalPoint()
+ cup = cam.GetViewUp()
+ rendererId = cellWidget.renderer_maps[ren]
+ # Looking for SetActiveCamera()
+ camera = None
+ renderer = pipeline.modules[rendererId]
+ for c in pipeline.connections.values():
+ if c.destination.moduleId==rendererId:
+ if c.destination.name=='SetActiveCamera':
+ camera = pipeline.modules[c.source.moduleId]
+ break
+
+ if not camera:
+ # Create camera
+ vtk_package = vtk_pkg_identifier
+ camera = controller.create_module(vtk_package, 'vtkCamera', '',
+ 0.0, 0.0)
+ ops.append(('add', camera))
+
+ # Connect camera to renderer
+ camera_conn = controller.create_connection(camera, 'self',
+ renderer,
+ 'SetActiveCamera')
+ ops.append(('add', camera_conn))
+ # update functions
+ def convert_to_str(arglist):
+ new_arglist = []
+ for arg in arglist:
+ new_arglist.append(str(arg))
+ return new_arglist
+ functions = [('SetPosition', convert_to_str(cpos)),
+ ('SetFocalPoint', convert_to_str(cfol)),
+ ('SetViewUp', convert_to_str(cup))]
+ ops.extend(controller.update_functions_ops(camera, functions))
+
+ action = vistrails.core.db.action.create_action(ops)
+ controller.add_new_action(action)
+ controller.perform_action(action)
+ controller.select_latest_version()
+
+ def triggeredSlot(self, checked=False):
+ """ toggledSlot(checked: boolean) -> None
+ Execute the action when the button is clicked
+
+ """
+ visApp = QtCore.QCoreApplication.instance()
+ if hasattr(visApp, 'builderWindow'):
+ builderWindow = visApp.builderWindow
+ if builderWindow:
+ info = self.toolBar.sheet.getCellPipelineInfo(
+ self.toolBar.row, self.toolBar.col)
+ if info:
+ info = info[0]
+ viewManager = builderWindow.viewManager
+ view = viewManager.ensureController(info['controller'])
+ if view:
+ controller = view.controller
+ controller.change_selected_version(info['version'])
+ self.setCamera(controller)
+
+class QVTKViewWidgetToolBar(QCellToolBar):
+ """
+ QVTKViewWidgetToolBar derives from QCellToolBar to give the VTKViewCell
+ a customizable toolbar
+
+ """
+ def createToolBar(self):
+ """ createToolBar() -> None
+ This will get call initiallly to add customizable widgets
+
+ """
+ self.appendAction(QVTKViewWidgetCapture(self))
+ self.addAnimationButtons()
+ self.appendAction(QVTKViewWidgetSaveCamera(self))
+
+def registerSelf():
+ """ registerSelf() -> None
+ Registry module with the registry
+ """
+ registry = get_module_registry()
+ registry.add_module(VTKViewCell)
+ registry.add_input_port(VTKViewCell, "Location", CellLocation)
+ import vistrails.core.debug
+ for (port,module) in [("SetRenderView",'vtkRenderView')]:
+ try:
+ registry.add_input_port(VTKViewCell, port,'(%s:%s)'% \
+ (vtk_pkg_identifier, module))
+
+ except Exception, e:
+ vistrails.core.debug.warning(str(e))
+
+ registry.add_output_port(VTKViewCell, "self", VTKViewCell)
diff --git a/vistrails/packages/vtlcreator/__init__.py b/vistrails/packages/vtlcreator/__init__.py
new file mode 100644
index 0000000..a3b950f
--- /dev/null
+++ b/vistrails/packages/vtlcreator/__init__.py
@@ -0,0 +1,41 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""This package contains a module that generates a .vtl file for the
+workflow it is contained into."""
+
+identifier = 'org.vistrails.vistrails.vtlcreator'
+name = 'vtlCreator'
+version = '0.0.4'
+old_identifiers = ['edu.utah.sci.vistrails.vtlcreator']
diff --git a/vistrails/packages/vtlcreator/init.py b/vistrails/packages/vtlcreator/init.py
new file mode 100644
index 0000000..9a1ae0f
--- /dev/null
+++ b/vistrails/packages/vtlcreator/init.py
@@ -0,0 +1,176 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+import base64
+import os
+import vistrails.core.db.action
+from vistrails.core.modules.basic_modules import File, Boolean, String, Directory
+from vistrails.core.modules.vistrails_module import Module, ModuleError, NotCacheable
+from vistrails.core.vistrail.vistrail import Vistrail
+from vistrails.db.services.locator import DBLocator
+from vistrails.core.system import get_elementtree_library
+from vistrails.db.services import io
+from vistrails.db.versions import currentVersion
+
+ElementTree = get_elementtree_library()
+
+class VtlFileCreator(NotCacheable, Module):
+ """This Module creates a vtl file for the workflow where it is
+ present.
+ By default it generates a string with an <vtlink> </vtlink> XML
+ element or it can write the vtl file to disk if filename is
+ provided. If directory is provided, the final filename will be
+ the concatenation of directory and filename.
+
+ Other input ports:
+
+ execute: Boolean
+ tells VisTrails to execute the workflow when the vtl is open
+
+ showSpreadsheetOnly: Boolean
+ tells VisTrails to hide the builder window and show only the
+ spreadsheet when the vtl is open
+
+ embedWorkflow: Boolean
+ it will embed a vistrail encoded as base64 containing only
+ the workflow where the module is. It can be loaded by
+ VisTrails.
+
+ """
+ def __init__(self):
+ Module.__init__(self)
+ self.locator = None
+ self.version = -1
+ self.pipeline = None
+ self.execute = False
+ self.embedWorkflow = False
+ self.showSpreadsheetOnly = False
+ self.forceDB = False
+
+ def get_locator_and_version(self):
+ self.locator = self.moduleInfo['locator']
+ self.version = self.moduleInfo['version']
+ self.pipeline = self.moduleInfo['pipeline']
+
+ if self.locator is None:
+ raise ModuleError(self, 'could not get the locator for this pipeline')
+ if self.version is None:
+ raise ModuleError(self, 'could not get the version number of this peline')
+
+ @staticmethod
+ def generate_vtl(locator,version,pipeline,execute=False,forceDB=False,
+ showSpreadsheetOnly=False,embedWorkflow=False):
+ """generate_vtl(locator:DBLocator or XMLLocator,
+ version: str, pipeline:Pipeline, execute:boolean,
+ forceDB:boolean, showspreadsheetOnly:boolean,
+ embedWorkflow: boolean) -> str
+ It generates the contents of a .vtl file with the information
+ given.
+ """
+ node = ElementTree.Element('vtlink')
+
+ if isinstance(locator, DBLocator):
+ node.set('host', str(locator.host))
+ node.set('port', str(locator.port))
+ node.set('database', str(locator.db))
+ node.set('vtid', str(locator.obj_id))
+ elif locator is not None:
+ node.set('filename', str(locator.name))
+
+ node.set('version', str(version))
+ node.set('execute', str(execute))
+ node.set('forceDB', str(forceDB))
+ node.set('showSpreadsheetOnly', str(showSpreadsheetOnly))
+
+ if embedWorkflow == True:
+ vistrail = Vistrail()
+ action_list = []
+ for module in pipeline.module_list:
+ action_list.append(('add', module))
+ for connection in pipeline.connection_list:
+ action_list.append(('add', connection))
+ action = vistrails.core.db.action.create_action(action_list)
+ vistrail.add_action(action, 0L)
+ vistrail.addTag("Imported workflow", action.id)
+ if not forceDB:
+ node.set('version', str(action.id))
+ if not vistrail.db_version:
+ vistrail.db_version = currentVersion
+ pipxmlstr = io.serialize(vistrail)
+ vtcontent = base64.b64encode(pipxmlstr)
+ node.set('vtcontent',vtcontent)
+
+ return ElementTree.tostring(node)
+
+
+ def compute(self):
+ self.get_locator_and_version()
+
+ if self.hasInputFromPort('execute'):
+ self.execute = self.getInputFromPort('execute')
+
+ if self.hasInputFromPort('forceDB'):
+ self.forceDB = self.getInputFromPort('forceDB')
+
+ if self.hasInputFromPort('showSpreadsheetOnly'):
+ self.showSpreadsheetOnly = self.getInputFromPort('showSpreadsheetOnly')
+
+ if self.hasInputFromPort('embedWorkflow'):
+ self.embedWorkflow = self.getInputFromPort('embedWorkflow')
+
+ xmlstring = self.generate_vtl(self.locator,self.version,self.pipeline,
+ self.execute,self.forceDB,
+ self.showSpreadsheetOnly,self.embedWorkflow)
+
+ if self.hasInputFromPort('filename'):
+ filename = self.getInputFromPort('filename')
+ if self.hasInputFromPort('directory'):
+ directory = self.getInputFromPort('directory').name
+ filename = os.path.join(directory,filename)
+ file_ = open(filename,'w')
+ file_.write(xmlstring)
+ file_.close()
+
+ self.setResult("xmlstring", xmlstring)
+
+ _input_ports = [('execute', Boolean, True),
+ ('showspreadsheetOnly', Boolean, True),
+ ('embedWorkflow', Boolean, True),
+ ('forceDB', Boolean, True),
+ ('filename', String),
+ ('directory', Directory)]
+
+ _output_ports = [('xmlstring', String)]
+
+_modules = [VtlFileCreator]
diff --git a/vistrails/packages/webServices/__init__.py b/vistrails/packages/webServices/__init__.py
new file mode 100644
index 0000000..9049569
--- /dev/null
+++ b/vistrails/packages/webServices/__init__.py
@@ -0,0 +1,79 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This package defines a set of methods to deal with web services.
+It requires ZSI library to be installed (please use the trunk version as it has
+important fixes. Click on configure to add wsdl urls to the package
+(use a ; to separate the urls).
+
+ChangeLog
+2013-04-26 (by VisTrails Team)
+ * Updated package to version 0.9.4
+ * Updated to new org.vistrails identifiers
+2010-02-25 (by VisTrails Team)
+ * Updated package to version 0.9.3
+ * Fixed bug with new package reloading
+ * If you see the error ('Error loading configuration file: ',
+ '~/.vistrails/webServices/modules.conf')
+ Just remove your ~/.vistrails/webServices and enable the package again
+ * Adding http package to package dependencies
+2010-01-27 (by VisTrails Team)
+ * Updated package to version 0.9.2
+ * Supporting hierarchy of types (not fully tested yet)
+ * Changing the default port names of modules to 'self', keeping the old
+ names (as optional ports) for backwards compatibility
+2010-01-25 (by VisTrails Team)
+ * Updated package to version 0.9.1
+ * Expanded map of simple types
+"""
+from vistrails.core.configuration import ConfigurationObject
+import vistrails.core
+
+identifier = 'org.vistrails.vistrails.webservices'
+name = 'Web Services'
+version = '0.9.4'
+old_identifiers = ['edu.utah.sci.vistrails.webservices']
+configuration = ConfigurationObject(wsdlList=(None, str),
+ showWarning=True)
+
+def package_dependencies():
+ return ['org.vistrails.vistrails.http']
+
+def package_requirements():
+ from vistrails.core.requirements import require_python_module
+ require_python_module('ZSI', {
+ 'pip': 'zsi',
+ 'linux-debian': 'python-zsi',
+ 'linux-ubuntu': 'python-zsi',
+ 'linux-fedora': 'python-ZSI'})
diff --git a/vistrails/packages/webServices/enumeration_widget.py b/vistrails/packages/webServices/enumeration_widget.py
new file mode 100644
index 0000000..4712bd2
--- /dev/null
+++ b/vistrails/packages/webServices/enumeration_widget.py
@@ -0,0 +1,115 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+##############################################################################
+# Enumeration Widget for Web Services
+from PyQt4 import QtCore, QtGui
+import vistrails.core.modules
+from vistrails.gui.modules.constant_configuration import ConstantWidgetMixin, \
+ StandardConstantWidget
+from vistrails.core.modules.basic_modules import Constant, Module
+import vistrails.core.modules.module_registry
+from vistrails.core.modules.vistrails_module import new_module
+import vistrails.packages.webServices
+
+class EnumerationWidget(QtGui.QComboBox, ConstantWidgetMixin):
+ enumerationlist = []
+ def __init__(self, param, parent=None):
+ """__init__(param: core.vistrail.module_param.ModuleParam,
+ parent: QWidget)
+ Initializes the line edit with contents
+ """
+ dictkey = param._namespace
+ typedict = vistrails.packages.webServices.webServicesmodulesDict[dictkey]
+ w = param._namespace.replace('|Types','')
+ dictkey = w + "." + param._type
+ obj = typedict[dictkey]
+ self.enumerationlist = obj.ports[0][0]
+ QtGui.QComboBox.__init__(self, parent)
+ ConstantWidgetMixin.__init__(self, param.strValue)
+ QtGui.QComboBox.clear(self)
+ listqt = []
+ for element in self.enumerationlist:
+ listqt.append(element)
+
+ QtGui.QComboBox.addItems(self, listqt)
+ foundindex = self.findText(param.strValue)
+ if not foundindex == -1:
+ self.setCurrentIndex(foundindex)
+ else:
+ self.setCurrentIndex(0)
+ param.strValue = self.enumerationlist[self.currentIndex()]
+ self.connect(self, QtCore.SIGNAL('activated(int)'), self.change_state)
+
+ def contents(self):
+ return self.enumerationlist[self.currentIndex()]
+
+ def change_state(self, state):
+ self.update_parent()
+
+def initialize(namemodule,namespace,identifier, version):
+ enumerationConstant = new_constant(namemodule,
+ namespace,
+ identifier,
+ version,
+ EnumerationWidget)
+ return enumerationConstant
+
+def new_constant(name, namespace, identifier,
+ version, widget_type=StandardConstantWidget):
+ """new_constant(name: str, namespace: str,widget_type: QWidget type) -> Module
+
+ new_constant dynamically creates a new Module derived from Constant
+ with a widget type."""
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+
+ def __init__(self):
+ Constant.__init__(self)
+
+ @staticmethod
+ def get_widget_class():
+ return widget_type
+
+ @staticmethod
+ def conversion(self): return self
+
+ m = new_module(Constant, name, {'__init__': __init__,
+ 'get_widget_class': get_widget_class,
+ 'translate_to_python': conversion})
+ m.name = name
+ m.isEnumeration = True
+ reg.add_module(m,namespace=namespace,package=identifier,
+ package_version=version)
+ return m
diff --git a/vistrails/packages/webServices/init.py b/vistrails/packages/webServices/init.py
new file mode 100644
index 0000000..f9165bc
--- /dev/null
+++ b/vistrails/packages/webServices/init.py
@@ -0,0 +1,1527 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+import sys
+import os.path
+import httplib
+import urllib
+
+import vistrails.core.modules.module_registry
+import vistrails.core.modules.basic_modules
+from vistrails.core.modules import vistrails_module
+from vistrails.core.modules.vistrails_module import Module, ModuleError, new_module
+import vistrails.core.system
+import enumeration_widget
+
+import cPickle
+
+from ZSI.ServiceProxy import ServiceProxy
+from ZSI.generate.wsdl2python import WriteServiceModule
+from ZSI.wstools import WSDLTools
+
+
+package_directory = None
+#Dictionary that contains the methods and complex types of all the web services
+webServicesmodulesDict = {}
+complexsdict ={}
+
+pm = vistrails.core.packagemanager.get_package_manager()
+###############################################################################
+
+class WebService(Module):
+ """ WebService is the base Module.
+ We will create a WebService Module for each method published by
+ the web service.
+
+ """
+ def __init__(self):
+ Module.__init__(self)
+
+ def compute(self):
+ raise vistrails_module.IncompleteImplementation
+
+ def runMethod(self, methodName, *args):
+ return getattr(self.server,methodName)(*args)
+
+#Class for complex types
+class WBModule:
+ def __init__(self,name):
+ self.name = name
+ self.namespace = ''
+ self.webservice = ''
+ self.typeobj = '' #Enumeration, ComplexType or Method.
+ self.ports = [] #Have the elements of a complex type and the elements of an enumeration.
+ self.attributes = [] #Have the attributes of a complex type
+ self.hasAttributes = False
+ self.isRequestType = False
+ self.isEmptySequence = False
+ self.isExtension = False
+ self.ExtensionBase = ''
+ self.superClass = ''
+
+def webServiceNameClassifier():
+ """ """
+ def compute(self):
+ raise vistrails_module.IncompleteImplementation
+
+ return { 'compute': compute}
+
+def webServiceNameMethodDict():
+ """ This returns the method dictionary for the web service address base
+ class. """
+ def compute(self):
+ raise vistrails_module.IncompleteImplementation
+
+ return { 'compute': compute}
+
+def webServiceTypesDict(WBobj):
+ """ This will create a correct compute method according to the complex type
+ or enumeration name. """
+
+ def unwrapRequestobj(self,libobj,visobj):
+
+ #Find the children for the vistrail type and set the attributes
+ #Check to see if the name of the port is repeated
+ portname = visobj.name
+ dictkey = WBobj.webservice + "." + portname
+ complexsdict = webServicesmodulesDict[WBobj.namespace]
+ obj = complexsdict[dictkey]
+ for child in obj.ports:
+ namechild = child[0]
+ typechild = child[1]
+ nameattrib = str(namechild)
+ nameattrib = nameattrib[0].upper() + nameattrib[1:]
+ sentence = "visobj" + "." + nameattrib
+ visdata = eval(sentence)
+ if visdata != None:
+ try:
+ Type = wsdlTypesDict[str(typechild)]
+ setattr(libobj,nameattrib,visdata)
+ except KeyError:
+ #Check if the port is an Enumeration Constant
+ keyvalue = WBobj.namespace.replace('|Types','') + "." + str(child[1])
+ childType = complexsdict[keyvalue]
+ if childType.typeobj == 'Enumeration':
+ visobjchild = getattr(visobj,nameattrib)
+ setattr(libobj, nameattrib, visobjchild)
+ else:
+ namemethod = "new_" + namechild
+ libobjchild = getattr(libobj,namemethod)()
+ visobjchild = getattr(visobj,nameattrib)
+ setattr(libobj,nameattrib,libobjchild)
+ unwrapRequestobj(self,libobjchild,visobjchild)
+ if obj.hasAttributes:
+ for attributes in obj.attributes:
+ nameattrib = str(attributes[0])
+ nameattribute = nameattrib[0].upper() + nameattrib[1:]
+ sentence = "visobj" + "." + nameattribute
+ visdata = eval(sentence)
+ if visdata != None:
+ nameattrib = "attribute_typecode_dict[" + nameattrib + "].pname"
+ setattr(libobj,nameattrib,visdata)
+
+ def compute(self):
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ #Check if it is an enumeration
+ if WBobj.typeobj == 'Enumeration':
+ nameport = str(WBobj.ports[0][0])
+ if self.hasInputFromPort(nameport):
+ inputport = self.getInputFromPort(nameport)
+ self.holder = inputport
+ self.setResult(WBobj.name,self)
+ self.setResult('self',self)
+ else:
+ #Check if it is a request type
+ modbyname = reg.get_module_by_name(identifier = identifier, name = WBobj.name, namespace = WBobj.namespace)
+ porttype = str(modbyname.server._wsdl.portTypes.keys()[0][0][1])
+ listoperations = modbyname.server._wsdl.portTypes[porttype].operations.values()
+ isrequest = False
+ requestname = ''
+ modname = WBobj.name
+ for element in listoperations:
+ parts = modbyname.server._wsdl.messages[element.input.getMessage().name].parts.values()
+ for part in parts:
+ if str(part.element[1]).strip() == modname.strip():
+ requestname = element.input.getMessage().name
+ isrequest = True
+ break
+ if (isrequest == True):
+ WBobj.isRequestType = True
+ #Create the request object
+ try:
+ req = getattr(self.modclient,requestname)()
+ except:
+ print "sys.exc_value: ", sys.exc_value
+ #Set the values of the input ports in the resquest object
+ for types in WBobj.ports:
+ nameport = str(types[0])
+ if self.hasInputFromPort(nameport):
+ #We need to distinguish between simple and complex types.
+ inputport = self.getInputFromPort(nameport)
+ try:
+ Type = str(types[1])
+ if isArray(Type):
+ Type = 'Array'
+ Type = wsdlTypesDict[Type]
+ namemethod = "set_element_" + nameport
+ try:
+ getattr(req, namemethod)(inputport)
+ except:
+ namemethod = nameport
+ setattr(req, namemethod,inputport)
+ except KeyError:
+ keyvalue = WBobj.namespace.replace('|Types','') + "." + str(types[1])
+ #Check if the port is an Enumeration Constant
+ complexsdict = webServicesmodulesDict[WBobj.namespace]
+ childType = complexsdict[keyvalue]
+ if childType.typeobj == 'Enumeration':
+ namemethod = "set_element_" + nameport
+ getattr(req, namemethod)(inputport)
+ else:
+ namemethod = "new_" + nameport
+ libobj = getattr(req,namemethod)()
+ unwrapRequestobj(self,libobj,inputport)
+ namemethod = "set_element_" + nameport
+ getattr(req, namemethod)(libobj)
+ if WBobj.hasAttributes:
+ for types in WBobj.attributes:
+ nameport = str(types[0])
+ if self.hasInputFromPort(nameport):
+ inputport = self.getInputFromPort(nameport)
+ Type = wsdlTypesDict[str(types[1])]
+ nameattrib = "attribute_typecode_dict[" + nameport + "].pname"
+ setattr(req, nameattrib,inputport)
+
+ #Set the value in the response output port
+ nameport = str(WBobj.name)
+ #This step is to warranty that the name are not going to repeat
+ for ports in WBobj.ports:
+ if str(WBobj.name.strip()) == str(ports[0].strip()):
+ nameport = WBobj.vistrailsname
+ break
+ if WBobj.hasAttributes:
+ for attributes in WBobj.attributes:
+ if str(WBobj.name.strip()) == str(attributes[0].strip()):
+ nameport = WBobj.vistrailsname
+ break
+ self.setResult(nameport,req)
+ self.setResult('self',req)
+ else:
+ nameport = str(WBobj.name)
+ for ports in WBobj.ports:
+ if str(WBobj.name.strip()) == str(ports[0].strip()):
+ nameport = WBobj.vistrailsname
+ break
+ if WBobj.hasAttributes:
+ for attributes in WBobj.attributes:
+ if str(WBobj.name.strip()) == str(attributes[0].strip()):
+ nameport = WBobj.vistrailsname
+ break
+ if self.hasInputFromPort(nameport):
+ #Output modules
+ inputport = self.getInputFromPort(nameport)
+ for nameport in WBobj.ports:
+ nameattrib = nameport[0][0].upper() + nameport[0][1:]
+ sentence = "inputport" + "." + nameattrib
+ outputport = eval(sentence)
+ self.setResult(nameport[0],outputport)
+ if WBobj.hasAttributes:
+ for attributes in WBobj.attributes:
+ nameattrib = attributes[0][0].upper() + attributes[0][1:]
+ sentence = "inputport" + "." + nameattrib
+ outputport = eval(sentence)
+ self.setResult(attributes[0],outputport)
+ elif self.hasInputFromPort('self'):
+ #Now we use the 'self' input port name
+ #we keep the old for backwards compatibility
+ #Output modules
+ inputport = self.getInputFromPort('self')
+ for nameport in WBobj.ports:
+ nameattrib = nameport[0][0].upper() + nameport[0][1:]
+ sentence = "inputport" + "." + nameattrib
+ outputport = eval(sentence)
+ self.setResult(nameport[0],outputport)
+ if WBobj.hasAttributes:
+ for attributes in WBobj.attributes:
+ nameattrib = attributes[0][0].upper() + attributes[0][1:]
+ sentence = "inputport" + "." + nameattrib
+ outputport = eval(sentence)
+ self.setResult(attributes[0],outputport)
+ else:
+ #Set the values in the input ports
+ #Input modules
+ for types in WBobj.ports:
+ nameport = str(types[0])
+ nameattrib = str(nameport)
+ nameattrib = nameattrib[0].upper() + nameattrib[1:]
+ if self.hasInputFromPort(nameport):
+ inputport = self.getInputFromPort(nameport)
+ setattr(self,nameattrib,inputport)
+ else:
+ setattr(self,nameattrib,None)
+ if WBobj.hasAttributes:
+ for types in WBobj.attributes:
+ nameport = str(types[0])
+ nameattrib = str(nameport)
+ nameattrib = nameattrib[0].upper() + nameattrib[1:]
+ if self.hasInputFromPort(nameport):
+ inputport = self.getInputFromPort(nameport)
+ setattr(self,nameattrib,inputport)
+ else:
+ setattr(self,nameattrib,None)
+ #Set the value in the response output port
+ nameport = str(WBobj.name)
+ #This step is to warranty that the name are not going to repeat
+ for ports in WBobj.ports:
+ if str(WBobj.name.strip()) == str(ports[0].strip()):
+ nameport = WBobj.vistrailsname
+ break
+ if WBobj.hasAttributes:
+ for attributes in WBobj.attributes:
+ if str(WBobj.name.strip()) == str(attributes[0].strip()):
+ nameport = WBobj.vistrailsname
+ break
+ self.setResult(nameport,self)
+ self.setResult('self',self)
+
+ return {'compute':compute}
+
+
+def webServiceParamsMethodDict(name, server, inparams, outparams):
+ """ This will create a correct compute method according to the
+ inparams and outparams. Right now, only the first outparam is used
+ for setting the result. """
+
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+
+ def wrapResponseobj(self,resp,visobj):
+ if isinstance(resp, list):
+ ptype = resp[0].typecode.type[1]
+ else:
+ if resp.typecode.type[1] == None:
+ ptype = resp.typecode.pname
+ else:
+ ptype = resp.typecode.type[1]
+
+ #Find the children for the vistrail type and set the attributes
+ dictkey = self.webservice + "|Types"
+ complexsdict = webServicesmodulesDict[dictkey]
+ dictkey = self.webservice + "." + str(ptype)
+ obj = complexsdict[dictkey]
+ for child in obj.ports:
+ namechild = child[0]
+ typechild = child[1]
+ try:
+ Type = wsdlTypesDict[str(typechild)]
+ namemethod = "get_element_" + str(namechild)
+ try:
+ ans = getattr(resp, namemethod)()
+ except:
+ #Some times when there is no complex type in the wsdl
+ #the get and set methods are not generated
+ namemethod = str(namechild)
+ sentence = "resp" + "." + namemethod
+ ans = eval(sentence)
+ nameattrib = str(namechild)
+ nameattrib = nameattrib[0].upper() + nameattrib[1:]
+ setattr(visobj,nameattrib,ans)
+
+ except KeyError:
+ if not isinstance(resp, list):
+ namemethod = "get_element_" + namechild
+ try:
+ resp = getattr(resp, namemethod)()
+ except:
+ namemethod = str(namechild)
+ sentence = "resp" + "." + namemethod
+ resp = eval(sentence)
+
+ if isinstance(resp, list):
+ objlist = []
+ for element in resp:
+ ptype = element.typecode.type[1]
+ dictkey = self.webservice + "|Types"
+ complexsdict = webServicesmodulesDict[dictkey]
+ dictkey = self.webservice + "." + str(ptype)
+ obj = complexsdict[dictkey]
+ visclass = reg.get_module_by_name(identifier=identifier,
+ name=obj.name,
+ namespace=obj.namespace)
+ vischildobj = visclass()
+ wrapResponseobj(self,element,vischildobj)
+ objlist.append(vischildobj)
+ nameattrib = str(namechild)
+ nameattrib = nameattrib[0].upper() + nameattrib[1:]
+ setattr(visobj,nameattrib,objlist)
+ else:
+ ptype = str(typechild)
+ dictkey = self.webservice + "|Types"
+ complexsdict = webServicesmodulesDict[dictkey]
+ dictkey = self.webservice + "." + ptype
+ obj = complexsdict[dictkey]
+ vischildclass = reg.get_module_by_name(identifier=identifier,
+ name=obj.name,
+ namespace = obj.namespace)
+ vischildobj = vischildclass()
+ nameattrib = str(namechild)
+ nameattrib = nameattrib[0].upper() + nameattrib[1:]
+ #Set the attribute in the vistrail object (Same as in
+ # schema but with the first letter uppercase)
+ setattr(visobj,nameattrib,vischildobj)
+ visobjchild = getattr(visobj,nameattrib)
+ wrapResponseobj(self,resp,visobjchild)
+
+ def compute(self):
+ dirmodule = dir(self.modclient)
+ #Get the locator name
+ for elemlist in dirmodule:
+ if elemlist.find('Locator') != -1:
+ namelocator = elemlist
+ break
+ #Get the port name
+ loc = getattr(self.modclient, namelocator)()
+ dirloc = dir(loc)
+ for elemlist in dirloc:
+ if ((elemlist.find('Address') == -1) and
+ ((elemlist.find('Port') != -1 and
+ elemlist.find('get') != -1) or
+ (elemlist.find('get') != -1 and
+ elemlist.find('Soap') != -1) or
+ (elemlist.find('get') != -1))):
+ portname = elemlist
+ port = getattr(loc, portname)()
+ try:
+ #This part is for the primitive or simple types methods parameters
+ Type = str(inparams[0].type[1])
+ if isArray(Type):
+ Type = 'Array'
+ Type = wsdlTypesDict[Type]
+ porttype = server._wsdl.portTypes.keys()[0][0][1]
+ listoperations = server._wsdl.portTypes[porttype].operations.values()
+ for element in listoperations: #list of operations instances
+ if str(element.name) == str(name):
+ #get the request method name
+ reqname = element.input.getMessage().name
+ try:
+ req = getattr(self.modclient,reqname)()
+ except:
+ print "sys.exc_value: ", sys.exc_value
+ for inparam in inparams:
+ #Now set all attributes for the request object
+ if self.hasInputFromPort(inparam.name):
+ inputport = self.getInputFromPort(inparam.name)
+ namemethod = "set_element_" + inparam.name
+ try:
+ getattr(req, namemethod)(inputport)
+ except:
+ namemethod = inparam.name
+ setattr(req, namemethod,inputport)
+ try:
+ resp = getattr(port,name)(req)
+ except:
+ print "sys.exc_value: ", sys.exc_value
+ raise ModuleError(self, str(sys.exc_value))
+ namemethod = "get_element_" + outparams[0].name
+
+ try:
+ result = getattr(resp,namemethod)()
+ except:
+ namemethod = outparams[0].name
+ sentence = "resp" + "." + namemethod
+ result = eval(sentence)
+ self.setResult(outparams[0].name,result)
+ except KeyError:
+ #This part is for the complex types methods parameters
+ inparam = str(inparams[0].name)
+ if self.hasInputFromPort(inparam):
+ request = self.getInputFromPort(inparam)
+ try:
+ resp = getattr(port,name)(request)
+ except:
+ print "sys.exc_value: ", sys.exc_value
+ raise ModuleError(self, str(sys.exc_value))
+ #Wrap the ZSI attributes into the vistrails module attributes
+ nameclass = str(outparams[0].type[1])
+ dictkey = self.webservice + "|Types"
+ complexsdict = webServicesmodulesDict[dictkey]
+ dictkey = self.webservice + "." + nameclass
+ obj = complexsdict[dictkey]
+ visclass = reg.get_module_by_name(identifier=identifier,
+ name=obj.name,
+ namespace=obj.namespace)
+ visobj = visclass()
+ wrapResponseobj(self,resp, visobj)
+ self.setResult(outparams[0].name,visobj)
+
+ return {'compute':compute}
+
+def processEnumeration(complexschema):
+ listenum = []
+ Type = complexschema.content.attributes['base'][1]
+ for facets in complexschema.content.facets:
+ listenum.append(facets.getAttributeDictionary()['value'])
+ return (listenum,Type)
+
+def processArray(complexschema,w):
+ # the problem here is that sometimes we are told that complexschema is an
+ # array but it is not. So if we get an AttributeError we will consider that
+ # complexschema is a regular complex type.
+ try:
+ contentschema = complexschema.content.content.attr_content
+ except AttributeError:
+ print "warning: type is not an array..."
+ processType(complexschema,w)
+ return
+
+ for child in contentschema:
+ nametype = str(child.attributes['http://schemas.xmlsoap.org/wsdl/']['arrayType'])
+ index = nametype.find(':')
+ nametype = nametype[index+1:]
+ #verify if is an array of complex types
+ index = nametype.find('[')
+ if index != -1:
+ Type = nametype[0:index]
+ try:
+ Type = wsdlTypesDict[str(Type)]
+ except KeyError:
+ try:
+ complex1 = schema.types[str(Type)]
+ processType(complex1,w)
+ except KeyError:
+ pass
+
+def isArray(Type):
+ #FIXME: this function not always work!!
+ #Just because there's the word Array doesn't mean it will be an array (Emanuele)
+ if len(Type) > 5:
+ if Type[0:5] == 'Array':
+ return True
+ else:
+ return False
+
+def generatename(name):
+ name = name + "_1"
+ return name
+
+def processType(complexschema,w):
+
+ contentschema = ''
+ modulename = str(complexschema.attributes['name'])
+ #print "processType: %s,%s"%(modulename,w)
+ try:
+ moduletype = str(complexschema.attributes['type'][1])
+ except KeyError:
+ moduletype = ''
+ modulekey = w + "." + modulename
+ objModule = WBModule(modulename)
+ objModule.superClass = moduletype
+ if complexschema.isSimple():
+ objModule.typeobj = 'Enumeration'
+ objModule.ports.append(processEnumeration(complexschema))
+
+ if complexschema.isElement():
+ try:
+ if complexschema.content.content == None:
+ contentschema = []
+ else:
+ contentschema = complexschema.content.content.content
+ objModule.typeobj = 'ComplexType'
+ if (complexschema.content.content == None or
+ complexschema.content.content.content == ()):
+ objModule.isEmptySequence = True
+ except AttributeError:
+ pass
+
+ if complexschema.isComplex():
+ try:
+ #Extensions in a complex type
+ if complexschema.content.content.isExtension():
+ objModule = WBModule(modulename)
+ objModule.typeobj = 'ComplexType'
+ objModule.isExtension = True
+ objModule.ExtensionBase = str(complexschema.content.content.attributes['base'][1])
+ contentschema = complexschema.content.content.content.content
+ except AttributeError:
+ contentschema = complexschema.content.content
+ try:
+ #Get all the attributes of the complex type
+ if complexschema.attr_content != None:
+ for attribute in complexschema.attr_content:
+ nametype = attribute.getAttributeName()
+ Type = 'string'
+ objModule.hasAttributes = True
+ objModule.attributes.append((nametype,Type))
+ except AttributeError:
+ pass
+
+ #Get all the child elements of the complex type
+ for child in contentschema:
+ try:
+ nametype = child.attributes['name']
+ Type = child.attributes['type'][1]
+ if isArray(Type):
+ Type = 'Array'
+ objModule.ports.append((nametype,Type))
+ processArray(child,w)
+ objModule.ports.append((nametype,Type))
+ try:
+ Type = wsdlTypesDict[str(Type)]
+ except KeyError:
+ try:
+ complex1 = schema.types[str(Type)]
+ processType(complex1,w)
+ except KeyError:
+ pass
+ except AttributeError:
+ pass
+
+ objModule.webservice = str(w)
+ complexsdict [modulekey] = objModule
+
+def addExtensionsModules(w, server, extensionbase):
+ """ Add complex types specified in the extension base if they are not in
+ the complex types dictionary. """
+ try:
+ dictkey = w + "|Types"
+ complexsdict = webServicesmodulesDict[dictkey]
+ dictkey = w + "." + extensionbase
+ extensionobj = complexsdict[dictkey]
+ except KeyError:
+ for schematypes in server._wsdl.types.keys():
+ schema = server._wsdl.types[str(schematypes)]
+ if len(schema.types.keys()) != 0:
+ try:
+ extensionbasestr = str(extensionbase)
+ complex1 = schema.types[extensionbasestr]
+ processType(complex1,w)
+ except KeyError:
+ pass
+ if len(schema.elements.keys()) != 0:
+ try:
+ extensionbasestr = str(extensionbase)
+ complex1 = schema.elements[str(extensionbasestr)]
+ processType(complex1,w)
+ except KeyError:
+ pass
+
+def processExtension(w, server):
+ dictkey = w + "|Types"
+ complexsdict = webServicesmodulesDict[dictkey]
+ keys = complexsdict.keys()
+ keys.sort()
+ for types in keys:
+ obj = complexsdict[types]
+ if obj.isExtension:
+ #Add extensions to modulesDict dictionary
+ extensionbase = obj.ExtensionBase
+ addExtensionsModules(w, server, extensionbase)
+ keys2 = complexsdict.keys()
+ keys2.sort()
+ for types2 in keys2:
+ obj2 = complexsdict[types2]
+ if obj2.name == extensionbase:
+ for port in obj2.ports:
+ obj.ports.append(port)
+ break
+
+def addTypesModules(w,modclient,server):
+ """ Create a VisTrails module for each complex type specified in
+ webservicesmodulesDict dictionary. """
+ def addObj(obj, namespace):
+ if hasattr(obj,"superClass"):
+ SuperType = str(obj.superClass)
+ else:
+ SuperType = ''
+ #print "Adding obj ", obj.name, " ", SuperType
+ if SuperType != '':
+ try:
+ if isArray(SuperType):
+ SuperType = 'Array'
+ SuperType = wsdlTypesDict[SuperType]
+ mt = new_module(SuperType,str(obj.name), webServiceTypesDict(obj))
+ mt.name = obj.name
+ mt.webservice = w
+ mt.modclient = modclient
+ mt.server = server
+ mt.isEnumeration = False
+ mt.namespace = namespace
+ #print " add to reg: ", mt.name, namespace, identifier
+ reg.add_module(mt, namespace=namespace,
+ package=identifier, package_version=version)
+ except KeyError:
+ try:
+ modname = SuperType
+ dictkey = w + "|Types"
+ typedict = webServicesmodulesDict[dictkey]
+ dictkey = w + "." + modname
+ typeObj = typedict[dictkey]
+ try:
+ SuperType = reg.get_module_by_name(identifier =identifier,
+ name=typeObj.name,
+ namespace = typeObj.namespace)
+ mt = new_module(SuperType,str(obj.name), webServiceTypesDict(obj))
+ mt.name = obj.name
+ mt.webservice = w
+ mt.modclient = modclient
+ mt.server = server
+ mt.isEnumeration = False
+ mt.namespace = namespace
+ #print " add to reg: ", mt.name, namespace, identifier
+ reg.add_module(mt, namespace=namespace,
+ package=identifier, package_version=version)
+ except:
+ addObj(typeObj,namespace)
+
+ except KeyError:
+ pass
+ else:
+ mt = new_module(WebService,str(obj.name), webServiceTypesDict(obj))
+ mt.name = obj.name
+ mt.webservice = w
+ mt.modclient = modclient
+ mt.server = server
+ mt.isEnumeration = False
+ mt.namespace = namespace
+ #print " add to reg: ", mt.name, namespace, identifier
+ reg.add_module(mt, namespace=namespace,
+ package=identifier, package_version=version)
+
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ namespace = w + "|Types"
+ complexsdict = webServicesmodulesDict[namespace]
+ keys = complexsdict.keys()
+ keys.sort()
+ for dictkey in keys:
+ obj = complexsdict[dictkey]
+ #print "key: ", dictkey, " obj: ", obj.name
+ obj.namespace = namespace
+ if obj.typeobj == 'Enumeration':
+ mt = enumeration_widget.initialize(obj.name, namespace,identifier,
+ version)
+ else:
+
+ addObj(obj,namespace)
+ #mt = new_module(WebService,str(obj.name), webServiceTypesDict(obj))
+ #mt.name = obj.name
+ #mt.webservice = w
+ #mt.modclient = modclient
+ #mt.server = server
+ #mt.isEnumeration = False
+ #mt.namespace = namespace
+ #reg.add_module(mt, namespace=namespace,
+ # package=identifier, package_version=version)
+
+def addMethodsModules(w,modclient,server):
+ """ Create a VisTrails module for each complex type specified in
+ webservicesmodulesDict dictionary. """
+
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ namespace = w + "|Methods"
+ complexsdict = webServicesmodulesDict[namespace]
+ keys = complexsdict.keys()
+ keys.sort()
+ for dictkey in keys:
+ obj = complexsdict[dictkey]
+ obj.namespace = namespace
+ mt = new_module(WebService,str(obj.name),
+ webServiceParamsMethodDict(str(obj.name), server,
+ obj.ports[0], obj.ports[1]))
+ mt.name = obj.name
+ mt.webservice = w
+ mt.modclient = modclient
+ mt.server = server
+ mt.namespace = namespace
+ reg.add_module(mt, namespace= namespace, package=identifier,
+ package_version=version)
+
+def addPortsToTypes(w):
+ """ Add input and output ports to the VisTrails complex type modules. """
+
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ dictkey = w + "|Types"
+ complexsdict = webServicesmodulesDict[dictkey]
+ keys = complexsdict.keys()
+ for dictkey in keys:
+ #Add the Ports that are of the module type
+ obj = complexsdict[dictkey]
+ if obj.webservice == w:
+ objtype = reg.get_module_by_name(identifier=identifier,
+ name=obj.name,
+ namespace=obj.namespace)
+ #print "Adding ports to ", obj.name
+ portname = 'self'
+ if obj.typeobj != 'Enumeration':
+ for ports in obj.ports:
+ #This step is to warranty that the name are not going
+ #to repeat
+ #print " > ", ports
+ if str(portname.strip()) == str(ports[0].strip()):
+ obj.vistrailsname = generatename(portname)
+ portname = obj.vistrailsname
+ break
+ if obj.hasAttributes:
+ for attributes in obj.attributes:
+ #This step is to warranty that the name are not
+ #going to repeat
+ if str(portname.strip()) == str(attributes[0].strip()):
+ obj.vistrailsname = generatename(portname)
+ portname = obj.vistrailsname
+ break
+ reg.add_input_port(objtype,portname,(objtype, ''))
+ reg.add_output_port(objtype,portname,(objtype, ''))
+
+ # this is to keep compatibility with previous versions
+ # we will add as optional ports.
+ reg.add_input_port(objtype,obj.name,(objtype, ''), optional=True)
+ reg.add_output_port(objtype,obj.name,(objtype, ''), optional=True)
+
+ if obj.typeobj != 'Enumeration':
+ #Add ports according to the input and output parameters
+ for ports in obj.ports:
+ try:
+ Type = wsdlTypesDict[str(ports[1])]
+ except KeyError:
+ portname = str(ports[1])
+ namespace = w + '|Types'
+ Type = reg.get_module_by_name(identifier = identifier, name =portname, namespace = namespace)
+ reg.add_input_port(objtype,str(ports[0]),(Type, ''))
+ reg.add_output_port(objtype,str(ports[0]),(Type, ''))
+ if obj.hasAttributes == True:
+ for attributes in obj.attributes:
+ Type = wsdlTypesDict[str(attributes[1])]
+ reg.add_input_port(objtype,str(attributes[0]),(Type, ''))
+ reg.add_output_port(objtype,str(attributes[0]),(Type, ''))
+
+def addPortsToMethods(w):
+ """ Add input and output ports to the VisTrails complex type modules. """
+
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ dictkey = w + "|Methods"
+ complexsdict = webServicesmodulesDict[dictkey]
+ keys = complexsdict.keys()
+ for dictkey in keys:
+ obj = complexsdict[dictkey]
+ objtype = reg.get_module_by_name(identifier = identifier, name = obj.name, namespace = obj.namespace)
+ #Add input ports
+ for port in obj.ports[0]:
+ try:
+ nameport = str(port.name)
+ Type = str(port.type[1])
+ if isArray(Type):
+ Type = 'Array'
+ Type = wsdlTypesDict[Type]
+ reg.add_input_port(objtype,nameport,(Type, ''))
+ except KeyError:
+ try:
+ modname = str(port.type[1])
+ dictkey = w + "|Types"
+ typedict = webServicesmodulesDict[dictkey]
+ dictkey = w + "." + modname
+ typeObj = typedict[dictkey]
+ Type = reg.get_module_by_name(identifier=identifier,
+ name=typeObj.name,
+ namespace=typeObj.namespace)
+ reg.add_input_port(objtype,str(port.name),(Type, ''))
+ except KeyError:
+ pass
+ #Add output ports
+ for port in obj.ports[1]:
+ try:
+ nameport = str(port.name)
+ Type = str(port.type[1])
+ if isArray(Type):
+ Type = 'Array'
+ Type = wsdlTypesDict[Type]
+ reg.add_output_port(objtype,nameport,(Type, ''))
+ except KeyError:
+ try:
+ modname = str(port.type[1])
+ dictkey = w + "|Types"
+ typedict = webServicesmodulesDict[dictkey]
+ dictkey = w + "." + modname
+ typeObj = typedict[dictkey]
+ Type = reg.get_module_by_name(identifier=identifier,
+ name=typeObj.name,
+ namespace=typeObj.namespace)
+ reg.add_output_port(objtype,str(port.name),(Type, ''))
+ except KeyError:
+ pass
+
+#Dictionary of primitive types
+#list extracted from http://www.w3.org/2001/XMLSchema
+wsdlTypesDict = { 'string' : vistrails.core.modules.basic_modules.String,
+ 'float': vistrails.core.modules.basic_modules.Float,
+ 'decimal': vistrails.core.modules.basic_modules.Float,
+ 'double': vistrails.core.modules.basic_modules.Float,
+ 'boolean': vistrails.core.modules.basic_modules.Boolean,
+ 'anyType': vistrails.core.modules.basic_modules.Variant,
+ 'anyURI': vistrails.core.modules.basic_modules.String,
+ 'DataHandler':vistrails.core.modules.basic_modules.String,
+ 'dateTime': vistrails.core.modules.basic_modules.String,
+ 'duration': vistrails.core.modules.basic_modules.String,
+ 'time': vistrails.core.modules.basic_modules.String,
+ 'date': vistrails.core.modules.basic_modules.String,
+ 'gYearMonth': vistrails.core.modules.basic_modules.String,
+ 'gYear': vistrails.core.modules.basic_modules.String,
+ 'gMonthDay': vistrails.core.modules.basic_modules.String,
+ 'gDay': vistrails.core.modules.basic_modules.String,
+ 'gMonth': vistrails.core.modules.basic_modules.String,
+ 'hexBinary': vistrails.core.modules.basic_modules.String,
+ 'base64Binary': vistrails.core.modules.basic_modules.String,
+ 'QName': vistrails.core.modules.basic_modules.String,
+ 'normalizedString': vistrails.core.modules.basic_modules.String,
+ 'token': vistrails.core.modules.basic_modules.String,
+ 'language': vistrails.core.modules.basic_modules.String,
+ 'IDREFS': vistrails.core.modules.basic_modules.String,
+ 'ENTITIES': vistrails.core.modules.basic_modules.String,
+ 'NMTOKEN': vistrails.core.modules.basic_modules.String,
+ 'NMTOKENS': vistrails.core.modules.basic_modules.String,
+ 'Name': vistrails.core.modules.basic_modules.String,
+ 'NCName': vistrails.core.modules.basic_modules.String,
+ 'ID': vistrails.core.modules.basic_modules.String,
+ 'IDREF': vistrails.core.modules.basic_modules.String,
+ 'ENTITY': vistrails.core.modules.basic_modules.String,
+ 'integer' : vistrails.core.modules.basic_modules.Integer,
+ 'nonPositiveInteger' : vistrails.core.modules.basic_modules.Integer,
+ 'negativeInteger' : vistrails.core.modules.basic_modules.Integer,
+ 'long' : vistrails.core.modules.basic_modules.Integer,
+ 'int' : vistrails.core.modules.basic_modules.Integer,
+ 'short' : vistrails.core.modules.basic_modules.Integer,
+ 'byte' : vistrails.core.modules.basic_modules.Integer,
+ 'nonNegativeInteger' : vistrails.core.modules.basic_modules.Integer,
+ 'unsignedLong' : vistrails.core.modules.basic_modules.Integer,
+ 'unsignedInt' : vistrails.core.modules.basic_modules.Integer,
+ 'unsignedShort' : vistrails.core.modules.basic_modules.Integer,
+ 'unsignedByte' : vistrails.core.modules.basic_modules.Integer,
+ 'positiveInteger' : vistrails.core.modules.basic_modules.Integer,
+ 'Array': vistrails.core.modules.basic_modules.List}
+
+################################################################################
+def load_wsdl_no_config(wsdlList):
+ """load_wsdl_no_config(wsdlList: list of urls) -> (bool, errors)
+ This loads the wsdl list without creating config files.
+ Returns a tuple with two values. The first is a boolean that is True
+ in case of success. The second is a list with problematic urls.
+
+ """
+ global complexsdict
+ result = True
+ not_loaded = []
+ for w in wsdlList:
+ # Validation if the user introduces a blank space in the list of web
+ # services
+ if w == '':
+ continue
+ complexsdict = {} #Dictionary that contains the methods or the
+ #types of a web service
+ w = w.strip()
+ numtimes = 0
+ for element in wsdlList:
+ if w == element.strip():
+ numtimes = numtimes + 1
+ if numtimes > 1:
+ # as this is not a big problem, let's just print on the console
+ print "Warning: Web service '%s' is repeated in the list and won't \
+be loaded again." % w
+ # this is not a problem, we will just ignore it
+ continue
+ try:
+ s = w.split('/')
+ host = s[2]
+ except:
+ msg = "Malformed URL."
+ not_loaded.append((w,msg))
+ result = False
+ continue
+ location = w
+ try:
+ reader = WSDLTools.WSDLReader()
+ wsdl = reader.loadFromURL(location)
+
+ except Exception, e:
+ # we will not show this every time. Just in the end
+ # so we can show a single message for everybody
+ not_loaded.append((w,str(e)))
+ result = False
+ continue
+
+ #create a directory for each webservice if it does not exist
+ package_directory = os.path.join(vistrails.core.system.current_dot_vistrails(),
+ "webServices")
+ sys.path.append(package_directory)
+ directoryname = urllib.quote_plus(w)
+ directoryname = directoryname.replace(".","_")
+ directoryname = directoryname.replace("%","_")
+ directoryname = directoryname.replace("+","_")
+ package_subdirectory = os.path.join(package_directory, directoryname)
+ wsm = WriteServiceModule(wsdl)
+ client_mod = wsm.getClientModuleName()
+ types_mod = wsm.getTypesModuleName()
+
+ #import the stub generated files
+ try:
+ importpackage = __import__(directoryname)
+ modclient = getattr(importpackage,client_mod)
+ server = ServiceProxy(w, pyclass=True, tracefile=sys.stdout)
+ except Exception, e:
+ msg = "Couldn't load generated stub file: %s"%str(e)
+ not_loaded.append((w,msg))
+ result = False
+ continue
+
+ addTypesModules(w,modclient,server)
+ addPortsToTypes(w)
+ addMethodsModules(w,modclient,server)
+ addPortsToMethods(w)
+ return (result, not_loaded)
+
+def load_wsdl_with_config(wsdlList):
+ """load_wsdl_with_config(wsdlList: list of urls) -> (bool,list)
+ This loads the wsdl list creating config files.
+ Returns a tuple with two values. The first is a boolean that is True
+ in case of success. The second is a list with problematic urls"""
+
+ global schema
+ global webServicesmodulesDict
+ global complexsdict
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ basic = vistrails.core.modules.basic_modules
+ not_loaded = []
+ result = True
+ for w in wsdlList:
+ #Validation if the user introduces a blank space in the list of
+ #web services
+ if w == '':
+ continue
+ complexsdict = {} #This dictionary stores the complex types for
+ #a webservice w
+ w = w.strip()
+ #Check to see if the element is not repeated in the web services list
+ numtimes = 0
+ for element in wsdlList:
+ if w == element.strip():
+ numtimes = numtimes + 1
+ if numtimes > 1:
+ print "The following web service is repeated in the list and won't \
+be loaded again: %s"% w
+ continue
+
+ #Create the stub files for the webservices that have been
+ # modified since the last time they where loaded in VisTrails
+ try:
+ s = w.split('/')
+ host = s[2]
+ except:
+ msg = "Malformed URL."
+ not_loaded.append((w,msg))
+ result = False
+ continue
+ location = w
+ ok = 0 # Trying to load a few times
+ # a couple of times, because sometimes we have timeout
+ msg = ''
+ while ok < 3:
+ try:
+ reader = WSDLTools.WSDLReader()
+ wsdl = reader.loadFromURL(location)
+ ok = 4
+ failed = False
+ except Exception, e:
+ ok += 1
+ failed = True
+ msg = str(e)
+
+ if failed:
+ not_loaded.append((w,msg))
+ result = False
+ continue
+ #create a directory for each webservice if it does not exist
+ directoryname = urllib.quote_plus(w)
+ directoryname = directoryname.replace(".","_")
+ directoryname = directoryname.replace("%","_")
+ directoryname = directoryname.replace("+","_")
+
+ package_directory = os.path.join(vistrails.core.system.current_dot_vistrails(),
+ "webServices")
+ sys.path.append(package_directory)
+ package_subdirectory = os.path.join(package_directory,
+ directoryname)
+
+ wsm = WriteServiceModule(wsdl)
+ client_mod = wsm.getClientModuleName()
+ types_mod = wsm.getTypesModuleName()
+ client_file = os.path.join(package_subdirectory, '%s.py' %client_mod)
+ types_file = os.path.join(package_subdirectory, '%s.py' %types_mod)
+ filename = '__init__'
+ init_file = os.path.join(package_subdirectory, '%s.py' %filename)
+ conn = httplib.HTTPConnection(host)
+ filename = '/' + '/'.join(s[3:])
+ request = conn.request("GET", filename)
+ response = conn.getresponse()
+ if not os.path.isdir(package_subdirectory):
+ try:
+ print "Creating package subdirectory...",
+ os.mkdir(package_subdirectory)
+ print "done."
+ except:
+ msg = "\nCould not create package subdirectory. Make sure \
+'%s' does not exist and parent directory is writable." % package_subdirectory
+ print "Skipping '%s'" % w
+ # We don't need to exit here. Continuing try to load
+ # the other files
+ not_loaded.append((w,msg))
+ result = False
+ continue
+
+ #generate the stub files
+ try:
+ from ZSI.generate.containers import ServiceHeaderContainer,\
+ TypecodeContainerBase, TypesHeaderContainer
+ kwargs = {'module':'ZSI.generate.pyclass',
+ 'metaclass':'pyclass_type'}
+ TypecodeContainerBase.metaclass = kwargs['metaclass']
+ TypesHeaderContainer.imports.append(\
+ 'from %(module)s import %(metaclass)s' %kwargs
+ )
+ ServiceHeaderContainer.imports.append (\
+ 'from %(module)s import %(metaclass)s' %kwargs
+ )
+
+ fd = open(client_file, 'w+')
+ wsm.writeClient(fd)
+ fd.close()
+
+ fd = open(types_file, 'w+' )
+ wsm.writeTypes(fd)
+ fd.close()
+
+ fd = open(init_file, 'w')
+ content = 'import ' + client_mod
+ fd.write(content)
+ fd.close()
+ except Exception, e:
+ msg = "Couldn't generate stub file: %s"% str(e)
+ not_loaded.append((w,msg))
+ result = False
+ continue
+ #import the stub generated files
+ try:
+ importpackage = __import__(directoryname)
+ modclient = getattr(importpackage,client_mod)
+ server = ServiceProxy(w, pyclass=True, tracefile=sys.stdout)
+ except Exception, e:
+ msg = "Problem importing the generated stub files: %s", str(e)
+ not_loaded.append((w,msg))
+ result = False
+ continue
+
+ #Set up the dictionary with all the complex types modules and their ports.
+ for schematypes in server._wsdl.types.keys():
+ schema = server._wsdl.types[str(schematypes)]
+ if len(schema.types.keys()) != 0:
+ for schematype in schema.types.keys():
+ try:
+ complex1 = schema.types[str(schematype)]
+ modulename = str(complex1.attributes['name'])
+ try:
+ dictkey = w + "." + modulename
+ typeObj = complexsdict[dictkey]
+ except KeyError:
+ #Check if it is an array. Arrays are python
+ #lists, not complex types though they can
+ #contain complex types elements.
+ Type = str(schematype)
+ if isArray(Type):
+ processArray(complex1,w)
+ else:
+ processType(complex1,w)
+ except KeyError:
+ pass
+ if len(schema.elements.keys()) != 0:
+ for schematype in schema.elements.keys():
+ try:
+ complex1 = schema.elements[str(schematype)]
+ modulename = str(complex1.attributes['name'])
+ try:
+ dictkey = w + "." + modulename
+ typeObj = complexsdict[dictkey]
+ except KeyError:
+ #Check if it is an array. Arrays are python
+ #lists, not complex types, though they can
+ #contain complex types elements.
+ Type = str(schematype)
+ if isArray(Type):
+ processArray(complex1,w)
+ else:
+ processType(complex1,w)
+ except KeyError:
+ pass
+ dictkey = w + "|Types"
+ webServicesmodulesDict[dictkey] = complexsdict
+ complexsdict = {}
+ #get all the service's methods and for each method create a
+ #module also create
+ # a module for the complex types classes and enumerations.
+
+ # Add the Extensions if there is any in the complex types
+ processExtension(w,server)
+
+ #Create the VisTrails modules with their ports
+ addTypesModules(w,modclient,server)
+
+ addPortsToTypes(w)
+
+ #Open the file with methods
+ #Add the Methods
+ keys = server._methods.keys()
+ keys.sort()
+
+ for kw in keys:
+ methods = server._methods[kw]
+ callInfo = methods[0].callinfo
+ inparams = callInfo.inparams
+ outparams = callInfo.outparams
+ mt = new_module(WebService,str(kw),
+ webServiceParamsMethodDict(str(kw),server,
+ inparams,
+ outparams))
+ mt.webservice = w
+ mt.modclient = modclient
+ namespace = w + '|Methods'
+ mt.namespace = namespace
+
+ reg.add_module(mt, namespace= namespace, package=identifier,
+ package_version=version)
+
+ objModule = WBModule(kw)
+ objModule.namespace = namespace
+ objModule.webservice = w
+ objModule.typeobj = 'Method'
+ objModule.ports.append(inparams)
+ objModule.ports.append(outparams)
+ #Add the input (ports) parameters to the methods
+ for p in inparams:
+ try:
+ nameport = str(p.name)
+ Type = str(p.type[1])
+ if isArray(Type):
+ Type = 'Array'
+ Type = wsdlTypesDict[Type]
+ reg.add_input_port(mt,nameport,(Type, ''))
+ except KeyError:
+ try:
+ modname = str(p.type[1])
+ dictkey = w + "|Types"
+ typedict = webServicesmodulesDict[dictkey]
+ dictkey = w + "." + modname
+ typeObj = typedict[dictkey]
+ Type = reg.get_module_by_name(identifier =identifier,
+ name=typeObj.name,
+ namespace = typeObj.namespace)
+ reg.add_input_port(mt,str(p.name),(Type, ''))
+ except KeyError:
+ pass
+ #Add the output (ports) parameters to the methods
+ for p in outparams:
+ try:
+ nameport = str(p.name)
+ Type = str(p.type[1])
+ if isArray(Type):
+ Type = 'Array'
+ Type = wsdlTypesDict[Type]
+ reg.add_output_port(mt,nameport,(Type, ''))
+ except KeyError:
+ try:
+ modname = str(p.type[1])
+ dictkey = w + "|Types"
+ typedict = webServicesmodulesDict[dictkey]
+ dictkey = w + "." + modname
+ typeObj = typedict[dictkey]
+ Type = reg.get_module_by_name(identifier=identifier,
+ name=typeObj.name,
+ namespace = typeObj.namespace)
+ reg.add_output_port(mt,str(p.name),(Type, ''))
+ except KeyError:
+ pass
+ modulekey = w + "." + str(kw)
+ complexsdict[modulekey] = objModule
+ dictkey = w + "|Methods"
+ webServicesmodulesDict[dictkey] = complexsdict
+ #Write modules.conf file that will contain the types and methods
+ #dictionary of the web services.
+ namefile = os.path.join(vistrails.core.system.current_dot_vistrails(),
+ 'webServices',
+ 'modules.conf')
+ try:
+ ouf = open(namefile, 'w')
+ cPickle.dump(webServicesmodulesDict,ouf)
+ ouf.close()
+ except Exception, e:
+ msg = "Error generating web services configuration file %s"%str(e)
+ raise RuntimeError(msg)
+
+ return(result,not_loaded)
+
+def verify_wsdl(wsdlList):
+ """verify_wsdl(wsdlList: list of urls) -> (list,list,list)
+
+ This checks for the wsdls that need to be updated or the files need to be
+ generated and splits them in 3 lists: files that are outdated, updated and
+ ones that an error was generated.
+
+ """
+ outdated_list = []
+ updated_list = []
+ error_list = []
+ for w in wsdlList:
+ if w == '':
+ continue
+ try:
+ s = w.split('/')
+ host = s[2]
+ except:
+ msg = "Malformed URL."
+ error_list.append((w,msg))
+ continue
+ location = w
+ reader = WSDLTools.WSDLReader()
+ load = reader.loadFromURL
+ try:
+ wsdl = load(location)
+ except Exception, e:
+ msg = "Couldn't load wsdl from the web: %s."%str(e)
+ error_list.append((w,msg))
+ continue
+ directoryname = urllib.quote_plus(w)
+ directoryname = directoryname.replace(".","_")
+ directoryname = directoryname.replace("%","_")
+ directoryname = directoryname.replace("+","_")
+ package_subdirectory = os.path.join(vistrails.core.system.current_dot_vistrails(),
+ "webServices",
+ directoryname)
+ wsm = WriteServiceModule(wsdl)
+ client_mod = wsm.getClientModuleName()
+ client_file = os.path.join(package_subdirectory, '%s.py' %client_mod)
+ conn = httplib.HTTPConnection(host)
+ filename = '/' + '/'.join(s[3:])
+ request = conn.request("GET", filename)
+ response = conn.getresponse()
+ remoteHeader = response.msg.getheader('last-modified')
+ isoutdated = False
+ if remoteHeader != None:
+ localFile = client_file
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ httpfile = reg.get_descriptor_by_name(
+ 'org.vistrails.vistrails.http', 'HTTPFile').module()
+ try:
+ isoutdated = httpfile._is_outdated(remoteHeader, localFile)
+ except OSError:
+ print "File doesn't exist"
+ isoutdated = True
+ if isoutdated or remoteHeader == None:
+ outdated_list.append(w)
+ else:
+ updated_list.append(w)
+ return (outdated_list,updated_list, error_list)
+
+def initialize(*args, **keywords):
+ import vistrails.core.packagemanager
+ global schema
+ global webServicesmodulesDict
+ global complexsdict
+ wsdlList = []
+ if configuration.showWarning == True:
+ msg = "The Web Services package is deprecated and will be removed from \
+next VisTrails release. Please consider using the new SUDS Web Services package. \
+This message will not be shown again."
+ pm.show_error_message(pm.get_package(identifier),msg)
+ try:
+ from vistrails.gui.application import get_vistrails_application
+ if get_vistrails_application() is not None:
+ configuration.showWarning = False
+ VisTrailsApplication.save_configuration()
+ except:
+ pass
+ if configuration.check('wsdlList'):
+ wsdlList = configuration.wsdlList.split(";")
+
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ basic = vistrails.core.modules.basic_modules
+ reg.add_module(WebService)
+
+ #Create a directory for the webServices package
+ global package_directory
+ package_directory = os.path.join(vistrails.core.system.current_dot_vistrails(),
+ "webServices")
+ if not os.path.isdir(package_directory):
+ try:
+ print "Creating package directory..."
+ os.mkdir(package_directory)
+ except:
+ print "Could not create package directory. Make sure"
+ print "'%s' does not exist and parent directory is writable"
+ sys.exit(1)
+
+ pathfile = os.path.join(vistrails.core.system.current_dot_vistrails(),
+ "webServices",
+ "modules.conf")
+ outdated_list = []
+ updated_list = []
+ error_list = []
+ if os.path.isfile(pathfile):
+ #Verify if there is a need to update the modules configuration
+ #file (modules.conf)
+ (outdated_list, updated_list, error_list) = verify_wsdl(wsdlList)
+
+ else:
+ #If the modules configuration file doesn't exist, create it
+ outdated_list = wsdlList
+
+ #If the stub files are not updated or there is not information in
+ # the header about the modification date of the web service, the
+ # stubs files and a modules configuration file will be created
+ # otherwise the information of the modules will be obtained from
+ # the modules.conf files that contains serialized data of the methods
+ # and the complex types of the web services
+ if os.path.isfile(pathfile):
+ try:
+ inf = open(pathfile)
+ webServicesmodulesDict = cPickle.load(inf)
+ inf.close()
+ except Exception, e:
+ msg = "Error loading configuration file: ", pathfile
+ raise IOError(msg)
+
+ #print wsdlList, outdated_list, updated_list
+ (res, not_loaded) = load_wsdl_no_config(updated_list)
+ if not res:
+ #there was a problem when trying to load the stubs
+ # let's try creating them again
+ for (w,e) in not_loaded:
+ outdated_list.append(w)
+ print "There were problems loading the webservices %s" % not_loaded
+ print "We will try to load them again..."
+ (res, not_loaded) = load_wsdl_with_config(outdated_list)
+ if not res or len(error_list) > 0:
+ msg = """ There were problems loading the webservices.
+The following could not be loaded:\n"""
+ error_list.extend(not_loaded)
+ for (w,e) in error_list:
+ msg += "Url: '%s', error: '%s'\n"%(w,e)
+ pm.show_error_message(pm.get_package(identifier),msg)
+
+def handle_missing_module(*args, **kwargs):
+ global webServicesmodulesDict
+
+ #this is the order the arguments are passed to the function
+ controller = args[0]
+ m_id = args[1]
+ pipeline = args[2]
+
+ def get_wsdl_from_namespace(m_namespace):
+ try:
+ wsdl = m_namespace.split("|")
+ return wsdl[0]
+ except:
+ print "invalid namespace"
+ return None
+ m = pipeline.modules[m_id]
+ m_namespace = m.namespace
+
+ wsdl = get_wsdl_from_namespace(m_namespace)
+ if wsdl:
+ outdated_list = []
+ updated_list = []
+ error_list = []
+ print "Downloading %s and adding to the Module list..."%wsdl
+ pathfile = os.path.join(vistrails.core.system.current_dot_vistrails(),
+ "webServices",
+ "modules.conf")
+ if os.path.isfile(pathfile):
+ #Verify if there is a need to update the modules configuration
+ #file (modules.conf)
+ (outdated_list, updated_list, error_list) = verify_wsdl([wsdl])
+ #print "verified: createconfig file is %s"%createconfigfile
+ else:
+ #If the modules configuration file doesn't exist, create it
+ outdated_list = [wsdl]
+
+ #If the stub files are not updated or there is not information in
+ # the header about the modification date of the web service, the
+ # stubs files and a modules configuration file will be created
+ # otherwise the information of the modules will be obtained from
+ # the modules.conf files that contains serialized data of the methods
+ # and the complex types of the web services
+ # print outdated_list, updated_list, error_list
+ if os.path.isfile(pathfile):
+ try:
+ inf = open(pathfile)
+ webServicesmodulesDict = cPickle.load(inf)
+ inf.close()
+ except:
+ print "Error loading configuration file"
+ return False
+ try:
+ (res,not_loaded) = load_wsdl_no_config(updated_list)
+ #print "done loading_no_config"
+ if not res:
+ outdated_list.extend([wsdl])
+
+ (res, not_loaded) = load_wsdl_with_config(outdated_list)
+ #print "done loading_with_config"
+ if res:
+ #add new url to package config file
+ wsdlList = []
+ if configuration.check('wsdlList'):
+ wsdlList = configuration.wsdlList.split(";")
+ if wsdl not in wsdlList:
+ wsdlList.append(wsdl)
+ swsdlList = ";".join(wsdlList)
+ configuration.wsdlList = swsdlList
+ print "done."
+ return True
+ else:
+ msg = """ There were problems loading the webservice.
+The following could not be loaded:\n"""
+ error_list.extend(not_loaded)
+ for (w,e) in error_list:
+ msg += "Url: '%s', error: '%s'\n"%(w,e)
+ pm.show_error_message(pm.get_package(identifier),msg)
+ except Exception, e:
+ print e
+ import traceback
+ traceback.print_stack()
+ print "An error occurred. Could not add missing wsdl."
+ return False
diff --git a/vistrails/run.py b/vistrails/run.py
new file mode 100644
index 0000000..681d63a
--- /dev/null
+++ b/vistrails/run.py
@@ -0,0 +1,147 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Main file for the VisTrails distribution."""
+
+import os
+import sys
+
+# Allows the userpackages directory to be overridden through an environment
+# variable
+# As this variable is set by the package manager, this also allows
+# multiprocessing to work correctly on Windows, where fork is not used and thus
+# 'userpackages' needs to be available in processes spawned from a
+# userpackage's code
+try:
+ userpackages_dir = os.environ['VISTRAILS_USERPACKAGES_DIR']
+except KeyError:
+ pass
+else:
+ old_sys_path = list(sys.path)
+ sys.path.insert(0, os.path.join(userpackages_dir, os.path.pardir))
+ try:
+ import userpackages
+ except ImportError:
+ sys.stderr.write("Couldn't import VISTRAILS_USERPACKAGES_DIR (%s), "
+ "continuing\n" % userpackages_dir)
+
+def disable_lion_restore():
+ """ Prevent Mac OS 10.7 to restore windows state since it would
+ make Qt 4.7.3 unstable due to its lack of handling Cocoa's Main
+ Window. """
+ import platform
+ if platform.system()!='Darwin': return
+ release = platform.mac_ver()[0].split('.')
+ if len(release)<2: return
+ major = int(release[0])
+ minor = int(release[1])
+ if major*100+minor<107: return
+ ssPath = os.path.expanduser('~/Library/Saved Application State/org.vistrails.savedState')
+ if os.path.exists(ssPath):
+ os.system('rm -rf "%s"' % ssPath)
+ os.system('defaults write org.vistrails NSQuitAlwaysKeepsWindows -bool false')
+
+
+def fix_site():
+ # py2app ships a stripped version of site.py
+ # USER_BASE and USER_SITE is not set,
+ # this is needed by at least scipy.weave
+ import platform
+ if platform.system()!='Darwin': return
+ import site
+ if hasattr(site, "USER_BASE"): return
+ from vistrails.core.system import mac_site
+ site.USER_BASE = mac_site.getuserbase()
+ site.USER_SITE = mac_site.getusersitepackages()
+ site._Helper = mac_site._Helper
+
+def fix_paths():
+ import site
+ if not hasattr(site, "USER_BASE"): return # We are running py2app
+
+ # Fix import path: add parent directory(so that we can
+ # import vistrails.[gui|...] and remove other paths below it (we might have
+ # been started from a subdir)
+ # A better solution is probably to move run.py up a
+ # directory in the repo
+ old_dir = os.path.realpath(os.path.dirname(__file__))
+ vistrails_dir = os.path.realpath(os.path.join(os.path.dirname(__file__), '..'))
+ i = 0
+ while i < len(sys.path):
+ rpath = os.path.realpath(sys.path[i])
+ if rpath.startswith(old_dir):
+ del sys.path[i]
+ else:
+ i += 1
+ if vistrails_dir not in sys.path:
+ sys.path.insert(0, vistrails_dir)
+
+if __name__ == '__main__':
+ fix_paths()
+ disable_lion_restore()
+ fix_site()
+
+ from vistrails.gui.requirements import require_pyqt4_api2
+ require_pyqt4_api2()
+
+ from PyQt4 import QtGui
+ import vistrails.gui.application
+ from vistrails.core.application import APP_SUCCESS, APP_FAIL, APP_DONE
+ try:
+ v = vistrails.gui.application.start_application()
+ if v != APP_SUCCESS:
+ app = vistrails.gui.application.get_vistrails_application()
+ if app:
+ app.finishSession()
+ sys.exit(APP_SUCCESS if v == APP_DONE else APP_FAIL)
+ app = vistrails.gui.application.get_vistrails_application()()
+ except SystemExit, e:
+ app = vistrails.gui.application.get_vistrails_application()
+ if app:
+ app.finishSession()
+ sys.exit(e)
+ except Exception, e:
+ app = vistrails.gui.application.get_vistrails_application()
+ if app:
+ app.finishSession()
+ print "Uncaught exception on initialization: %s" % e
+ import traceback
+ traceback.print_exc()
+ sys.exit(255)
+ if (app.temp_configuration.interactiveMode and
+ not app.temp_configuration.check('spreadsheetDumpCells')):
+ v = app.exec_()
+
+ vistrails.gui.application.stop_application()
+ sys.exit(v)
diff --git a/vistrails/stop_vistrails_server.py b/vistrails/stop_vistrails_server.py
new file mode 100644
index 0000000..2eb817e
--- /dev/null
+++ b/vistrails/stop_vistrails_server.py
@@ -0,0 +1,57 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+""" This script stops VisTrails server. It can only stop with an XML Request """
+
+import xmlrpclib
+import sys
+import socket
+
+def usage():
+ return "%s server_url"%sys.argv[0]
+
+if __name__ == '__main__':
+ try:
+ uri = sys.argv[1]
+ except Exception, e:
+ print usage()
+ sys.exit(1)
+
+ try:
+ proxy = xmlrpclib.ServerProxy(uri)
+ print proxy.quit()
+ except socket.error, e:
+ print "Vistrails was not running on ", uri
+
+ #print proxy.run_from_db('vistrails.sci.utah.edu', 3306,'vt_test',1,'/tmp/spreadsheet',598)
diff --git a/vistrails/tests/__init__.py b/vistrails/tests/__init__.py
new file mode 100644
index 0000000..4808ee9
--- /dev/null
+++ b/vistrails/tests/__init__.py
@@ -0,0 +1,50 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+class NotModule(Exception):
+ """This is a special exception that is caught by the testing
+ infrastructure. If a particular python file is not meant to be
+ imported as a module, that file should have the following lines:
+
+ if __name__ != '__main__':
+ from vistrails.tests import NotModule
+ raise NotModule('This should not be imported as a module')
+
+ This way, the testing infrastructure will know not to report failure
+ to import that file as an error.
+ """
+
+ pass
+
diff --git a/vistrails/tests/resources/__init__.py b/vistrails/tests/resources/__init__.py
new file mode 100644
index 0000000..86c4a06
--- /dev/null
+++ b/vistrails/tests/resources/__init__.py
@@ -0,0 +1,36 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+pass
diff --git a/vistrails/tests/resources/console_mode_test.py b/vistrails/tests/resources/console_mode_test.py
new file mode 100644
index 0000000..6e7c899
--- /dev/null
+++ b/vistrails/tests/resources/console_mode_test.py
@@ -0,0 +1,101 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Testing package for console_mode"""
+
+##############################################################################
+import vistrails.core.modules
+import vistrails.core.modules.module_registry
+from vistrails.core.modules.vistrails_module import Module, ModuleError, NotCacheable
+from vistrails.core.modules.basic_modules import Float, Integer
+
+identifier = 'org.vistrails.vistrails.console_mode_test'
+version = '0.9.1'
+name = 'Console Mode Tests'
+old_identifiers = ['edu.utah.sci.vistrails.console_mode_test']
+
+class TestTupleExecution(Module):
+
+ def compute(self):
+ v1, v2 = self.getInputFromPort('input')
+ self.setResult('output', v1 + v2)
+
+
+class TestDynamicModuleError(Module):
+
+ def compute(self):
+ c = TestDynamicModuleError()
+ c.die()
+
+ def die(self):
+ raise ModuleError(self, "I died!")
+
+class TestChangeVistrail(NotCacheable, Module):
+
+ def compute(self):
+ if self.hasInputFromPort('foo'):
+ v1 = self.getInputFromPort('foo')
+ else:
+ v1 = 0
+ if v1 != 12:
+ self.change_parameter('foo', v1 + 1)
+
+class TestCustomNamed(Module):
+
+ pass
+
+
+class TestOptionalPorts(Module):
+
+ pass
+
+##############################################################################
+
+def initialize():
+ reg = vistrails.core.modules.module_registry.get_module_registry()
+ reg.add_module(TestTupleExecution)
+ reg.add_input_port(TestTupleExecution, 'input', [Float, Float])
+ reg.add_output_port(TestTupleExecution, 'output', (Float, 'output'))
+ reg.add_module(TestDynamicModuleError)
+ reg.add_module(TestChangeVistrail)
+ reg.add_input_port(TestChangeVistrail, 'foo', Integer)
+
+ reg.add_module(TestCustomNamed, name='different name')
+ reg.add_input_port(TestCustomNamed, 'input', Float)
+
+ reg.add_module(TestOptionalPorts)
+ reg.add_input_port(TestOptionalPorts, 'foo', Float, optional=True)
+ reg.add_output_port(TestOptionalPorts, 'foo', Float, optional=True)
+
diff --git a/vistrails/tests/resources/dummy.xml b/vistrails/tests/resources/dummy.xml
new file mode 100644
index 0000000..bb546b4
--- /dev/null
+++ b/vistrails/tests/resources/dummy.xml
@@ -0,0 +1,164 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+ <visTrail version="0.3.0">
+ <action date="09 Nov 2006 11:11:45" parent="0" time="2" user="cscheid" what="addModule">
+ <object cache="0" id="0" name="File" x="-0.405904047613" y="0.590405904059"/>
+ </action>
+ <action date="09 Nov 2006 11:11:49" parent="2" time="3" user="cscheid" what="addModule">
+ <object cache="0" id="1" name="String" x="-79.7416969521" y="113.505537534"/>
+ </action>
+ <action date="09 Nov 2006 11:11:52" parent="3" time="4" user="cscheid" what="addConnection">
+ <connect destinationId="0" destinationModule="File" destinationPort="name(String)" id="0" sourceId="1" sourceModule="String" sourcePort="value(String)"/>
+ </action>
+ <action date="09 Nov 2006 11:12:01" parent="4" time="5" user="cscheid" what="addModule">
+ <object cache="0" id="2" name="FileSink" x="-25.1291511435" y="-88.7084891257"/>
+ </action>
+ <action date="09 Nov 2006 11:12:04" parent="5" time="6" user="cscheid" what="addConnection">
+ <connect destinationId="2" destinationModule="FileSink" destinationPort="file(File)" id="1" sourceId="0" sourceModule="File" sourcePort="self(File)"/>
+ </action>
+ <action date="09 Nov 2006 11:12:06" parent="6" time="7" user="cscheid" what="moveModule">
+ <move dx="88.5608850951" dy="-27.3062736731" id="2"/>
+ </action>
+ <action date="09 Nov 2006 11:12:06" parent="7" time="8" user="cscheid" what="addModule">
+ <object cache="0" id="3" name="String" x="135.756456779" y="-26.7158678139"/>
+ </action>
+ <action date="09 Nov 2006 11:12:09" parent="8" time="9" user="cscheid" what="addConnection">
+ <connect destinationId="2" destinationModule="FileSink" destinationPort="outputName(String)" id="2" sourceId="3" sourceModule="String" sourcePort="value(String)"/>
+ </action>
+ <action date="09 Nov 2006 11:12:12" parent="9" time="10" user="cscheid" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="String" value=""/>
+ </action>
+ <action date="09 Nov 2006 11:12:23" parent="10" time="11" user="cscheid" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="String" value="/tmp/unimportant.tmp"/>
+ </action>
+ <action date="21 Nov 2006 22:10:52" parent="0" time="12" user="emanuele" what="addModule">
+ <object cache="0" id="0" name="Float" x="-11.8561695459" y="98.7737701549"/>
+ </action>
+ <action date="21 Nov 2006 22:11:01" parent="12" time="13" user="emanuele" what="moveModule">
+ <move dx="6.72586935127" dy="37.8330149522" id="0"/>
+ </action>
+ <action date="21 Nov 2006 22:11:02" parent="13" time="14" user="emanuele" what="addModule">
+ <object cache="0" id="1" name="Float" x="100.802142088" y="40.7631472281"/>
+ </action>
+ <action date="21 Nov 2006 22:11:06" parent="14" time="15" user="emanuele" what="moveModule">
+ <move dx="-24.3812763984" dy="-26.0627436337" id="1"/>
+ </action>
+ <action date="21 Nov 2006 22:11:06" parent="15" time="16" user="emanuele" what="addConnection">
+ <connect destinationId="1" destinationModule="Float" destinationPort="value(Float)" id="0" sourceId="0" sourceModule="Float" sourcePort="value(Float)"/>
+ </action>
+ <action date="21 Nov 2006 22:11:16" parent="16" time="17" user="emanuele" what="moveModule">
+ <move dx="5.88513568236" dy="-5.88513565923" id="1"/>
+ <move dx="-54.6476884791" dy="5.88513565923" id="0"/>
+ <move dx="-15.9739397093" dy="54.6476882643" id="1"/>
+ </action>
+ <action date="21 Nov 2006 22:11:16" parent="17" time="18" user="emanuele" what="addModule">
+ <object cache="0" id="2" name="Float" x="156.290564236" y="-60.1248926444"/>
+ </action>
+ <action date="21 Nov 2006 22:11:18" parent="18" time="19" user="emanuele" what="addConnection">
+ <connect destinationId="2" destinationModule="Float" destinationPort="value(Float)" id="1" sourceId="1" sourceModule="Float" sourcePort="value(Float)"/>
+ </action>
+ <action date="21 Nov 2006 22:12:06" parent="19" time="20" user="emanuele" what="addModule">
+ <object cache="0" id="3" name="Integer" x="-74.0704610451" y="2.93013227592"/>
+ </action>
+ <action date="21 Nov 2006 22:12:10" parent="20" time="21" user="emanuele" what="moveModule">
+ <move dx="-15.9739397093" dy="16.8146733121" id="3"/>
+ </action>
+ <action date="21 Nov 2006 22:12:10" parent="21" time="22" user="emanuele" what="addModule">
+ <object cache="0" id="4" name="Integer" x="24.2953782172" y="-86.1876362782"/>
+ </action>
+ <action date="21 Nov 2006 22:12:14" parent="22" time="23" user="emanuele" what="addConnection">
+ <connect destinationId="4" destinationModule="Integer" destinationPort="value(Integer)" id="2" sourceId="3" sourceModule="Integer" sourcePort="value(Integer)"/>
+ </action>
+ <action date="21 Nov 2006 22:12:20" parent="23" time="24" user="emanuele" what="moveModule">
+ <move dx="-39.5144824387" dy="-8.40733665605" id="4"/>
+ <move dx="4.20366834454" dy="11.7702713185" id="3"/>
+ </action>
+ <action date="21 Nov 2006 22:12:21" parent="24" time="25" user="emanuele" what="deleteConnection">
+ <connection connectionId="0"/>
+ </action>
+ <action date="21 Nov 2006 22:12:21" parent="25" time="26" user="emanuele" what="deleteModule">
+ <module moduleId="0"/>
+ </action>
+ <action date="21 Nov 2006 22:12:23" parent="26" time="27" user="emanuele" what="deleteConnection">
+ <connection connectionId="1"/>
+ </action>
+ <action date="21 Nov 2006 22:12:23" parent="27" time="28" user="emanuele" what="deleteModule">
+ <module moduleId="1"/>
+ </action>
+ <action date="21 Nov 2006 22:12:26" parent="28" time="29" user="emanuele" what="deleteConnection"/>
+ <action date="21 Nov 2006 22:12:26" parent="29" time="30" user="emanuele" what="deleteModule">
+ <module moduleId="2"/>
+ </action>
+ <action date="21 Nov 2006 22:12:41" parent="30" time="31" user="emanuele" what="moveModule">
+ <move dx="85.7548342287" dy="41.1959496146" id="4"/>
+ <move dx="63.8957588371" dy="52.1254872675" id="3"/>
+ <move dx="10.9295376958" dy="41.1959496146" id="4"/>
+ </action>
+ <action date="21 Nov 2006 22:12:41" parent="31" time="32" user="emanuele" what="addModule">
+ <object cache="0" id="0" name="StandardOutput" x="112.572413453" y="-161.853666183"/>
+ </action>
+ <action date="21 Nov 2006 22:12:44" parent="32" time="33" user="emanuele" what="addConnection">
+ <connect destinationId="0" destinationModule="StandardOutput" destinationPort="value(Module)" id="0" sourceId="4" sourceModule="Integer" sourcePort="value(Integer)"/>
+ </action>
+ <action date="21 Nov 2006 22:12:49" parent="33" time="34" user="emanuele" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="Integer" value="0"/>
+ </action>
+ <action date="21 Nov 2006 22:12:53" parent="34" time="35" user="emanuele" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="Integer" value="2"/>
+ </action>
+ <action date="21 Nov 2006 22:13:08" parent="35" time="36" user="emanuele" what="moveModule">
+ <move dx="-54.6476884791" dy="49.6032862707" id="0"/>
+ <move dx="-25.2220100673" dy="5.88513565923" id="4"/>
+ </action>
+ <action date="21 Nov 2006 22:13:23" parent="19" time="37" user="emanuele" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="0" parameter="<no description>" parameterId="0" type="Float" value="0.0"/>
+ </action>
+ <action date="21 Nov 2006 22:13:27" parent="37" time="38" user="emanuele" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="0" parameter="<no description>" parameterId="0" type="Float" value="1.2"/>
+ </action>
+ <action date="21 Nov 2006 22:13:33" parent="38" time="39" user="emanuele" what="addModule">
+ <object cache="0" id="3" name="StandardOutput" x="73.8986646828" y="-196.323746472"/>
+ </action>
+ <action date="21 Nov 2006 22:13:36" parent="39" time="40" user="emanuele" what="addConnection">
+ <connect destinationId="3" destinationModule="StandardOutput" destinationPort="value(Module)" id="2" sourceId="2" sourceModule="Float" sourcePort="value(Float)"/>
+ </action>
+ <action date="21 Nov 2006 22:13:42" parent="40" time="41" user="emanuele" what="moveModule">
+ <move dx="-11.7702713647" dy="31.1071456274" id="3"/>
+ </action>
+ <tag name="int chain" time="36"/>
+ <tag name="float chain" time="41"/>
+ <tag name="final" time="11"/>
+ </visTrail>
diff --git a/vistrails/tests/resources/dummy_broken.xml b/vistrails/tests/resources/dummy_broken.xml
new file mode 100644
index 0000000..0d17a63
--- /dev/null
+++ b/vistrails/tests/resources/dummy_broken.xml
@@ -0,0 +1,165 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+THIS FILE IS BROKEN ON PURPOSE
+ <visTrail version="0.3.0">
+ <action date="09 Nov 2006 11:11:45" parent="0" time="2" user="cscheid" what="addModule">
+ <object cache="0" id="0" name="File" x="-0.405904047613" y="0.590405904059"/>
+ </action>
+ <action date="09 Nov 2006 11:11:49" parent="2" time="3" user="cscheid" what="addModule">
+ <object cache="0" id="1" name="String" x="-79.7416969521" y="113.505537534"/>
+ </action>
+ <action date="09 Nov 2006 11:11:52" parent="3" time="4" user="cscheid" what="addConnection">
+ <connect destinationId="0" destinationModule="File" destinationPort="name(String)" id="0" sourceId="1" sourceModule="String" sourcePort="value(String)"/>
+ </action>
+ <action date="09 Nov 2006 11:12:01" parent="4" time="5" user="cscheid" what="addModule">
+ <object cache="0" id="2" name="FileSink" x="-25.1291511435" y="-88.7084891257"/>
+ </action>
+ <action date="09 Nov 2006 11:12:04" parent="5" time="6" user="cscheid" what="addConnection">
+ <connect destinationId="2" destinationModule="FileSink" destinationPort="file(File)" id="1" sourceId="0" sourceModule="File" sourcePort="self(File)"/>
+ </action>
+ <action date="09 Nov 2006 11:12:06" parent="6" time="7" user="cscheid" what="moveModule">
+ <move dx="88.5608850951" dy="-27.3062736731" id="2"/>
+ </action>
+ <action date="09 Nov 2006 11:12:06" parent="7" time="8" user="cscheid" what="addModule">
+ <object cache="0" id="3" name="String" x="135.756456779" y="-26.7158678139"/>
+ </action>
+ <action date="09 Nov 2006 11:12:09" parent="8" time="9" user="cscheid" what="addConnection">
+ <connect destinationId="2" destinationModule="FileSink" destinationPort="outputName(String)" id="2" sourceId="3" sourceModule="String" sourcePort="value(String)"/>
+ </action>
+ <action date="09 Nov 2006 11:12:12" parent="9" time="10" user="cscheid" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="String" value=""/>
+ </action>
+ <action date="09 Nov 2006 11:12:23" parent="10" time="11" user="cscheid" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="String" value="/tmp/unimportant.tmp"/>
+ </action>
+ <action date="21 Nov 2006 22:10:52" parent="0" time="12" user="emanuele" what="addModule">
+ <object cache="0" id="0" name="Float" x="-11.8561695459" y="98.7737701549"/>
+ </action>
+ <action date="21 Nov 2006 22:11:01" parent="12" time="13" user="emanuele" what="moveModule">
+ <move dx="6.72586935127" dy="37.8330149522" id="0"/>
+ </action>
+ <action date="21 Nov 2006 22:11:02" parent="13" time="14" user="emanuele" what="addModule">
+ <object cache="0" id="1" name="Float" x="100.802142088" y="40.7631472281"/>
+ </action>
+ <action date="21 Nov 2006 22:11:06" parent="14" time="15" user="emanuele" what="moveModule">
+ <move dx="-24.3812763984" dy="-26.0627436337" id="1"/>
+ </action>
+ <action date="21 Nov 2006 22:11:06" parent="15" time="16" user="emanuele" what="addConnection">
+ <connect destinationId="1" destinationModule="Float" destinationPort="value(Float)" id="0" sourceId="0" sourceModule="Float" sourcePort="value(Float)"/>
+ </action>
+ <action date="21 Nov 2006 22:11:16" parent="16" time="17" user="emanuele" what="moveModule">
+ <move dx="5.88513568236" dy="-5.88513565923" id="1"/>
+ <move dx="-54.6476884791" dy="5.88513565923" id="0"/>
+ <move dx="-15.9739397093" dy="54.6476882643" id="1"/>
+ </action>
+ <action date="21 Nov 2006 22:11:16" parent="17" time="18" user="emanuele" what="addModule">
+ <object cache="0" id="2" name="Float" x="156.290564236" y="-60.1248926444"/>
+ </action>
+ <action date="21 Nov 2006 22:11:18" parent="18" time="19" user="emanuele" what="addConnection">
+ <connect destinationId="2" destinationModule="Float" destinationPort="value(Float)" id="1" sourceId="1" sourceModule="Float" sourcePort="value(Float)"/>
+ </action>
+ <action date="21 Nov 2006 22:12:06" parent="19" time="20" user="emanuele" what="addModule">
+ <object cache="0" id="3" name="Integer" x="-74.0704610451" y="2.93013227592"/>
+ </action>
+ <action date="21 Nov 2006 22:12:10" parent="20" time="21" user="emanuele" what="moveModule">
+ <move dx="-15.9739397093" dy="16.8146733121" id="3"/>
+ </action>
+ <action date="21 Nov 2006 22:12:10" parent="21" time="22" user="emanuele" what="addModule">
+ <object cache="0" id="4" name="Integer" x="24.2953782172" y="-86.1876362782"/>
+ </action>
+ <action date="21 Nov 2006 22:12:14" parent="22" time="23" user="emanuele" what="addConnection">
+ <connect destinationId="4" destinationModule="Integer" destinationPort="value(Integer)" id="2" sourceId="3" sourceModule="Integer" sourcePort="value(Integer)"/>
+ </action>
+ <action date="21 Nov 2006 22:12:20" parent="23" time="24" user="emanuele" what="moveModule">
+ <move dx="-39.5144824387" dy="-8.40733665605" id="4"/>
+ <move dx="4.20366834454" dy="11.7702713185" id="3"/>
+ </action>
+ <action date="21 Nov 2006 22:12:21" parent="24" time="25" user="emanuele" what="deleteConnection">
+ <connection connectionId="0"/>
+ </action>
+ <action date="21 Nov 2006 22:12:21" parent="25" time="26" user="emanuele" what="deleteModule">
+ <module moduleId="0"/>
+ </action>
+ <action date="21 Nov 2006 22:12:23" parent="26" time="27" user="emanuele" what="deleteConnection">
+ <connection connectionId="1"/>
+ </action>
+ <action date="21 Nov 2006 22:12:23" parent="27" time="28" user="emanuele" what="deleteModule">
+ <module moduleId="1"/>
+ </action>
+ <action date="21 Nov 2006 22:12:26" parent="28" time="29" user="emanuele" what="deleteConnection"/>
+ <action date="21 Nov 2006 22:12:26" parent="29" time="30" user="emanuele" what="deleteModule">
+ <module moduleId="2"/>
+ </action>
+ <action date="21 Nov 2006 22:12:41" parent="30" time="31" user="emanuele" what="moveModule">
+ <move dx="85.7548342287" dy="41.1959496146" id="4"/>
+ <move dx="63.8957588371" dy="52.1254872675" id="3"/>
+ <move dx="10.9295376958" dy="41.1959496146" id="4"/>
+ </action>
+ <action date="21 Nov 2006 22:12:41" parent="31" time="32" user="emanuele" what="addModule">
+ <object cache="0" id="0" name="StandardOutput" x="112.572413453" y="-161.853666183"/>
+ </action>
+ <action date="21 Nov 2006 22:12:44" parent="32" time="33" user="emanuele" what="addConnection">
+ <connect destinationId="0" destinationModule="StandardOutput" destinationPort="value(Module)" id="0" sourceId="4" sourceModule="Integer" sourcePort="value(Integer)"/>
+ </action>
+ <action date="21 Nov 2006 22:12:49" parent="33" time="34" user="emanuele" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="Integer" value="0"/>
+ </action>
+ <action date="21 Nov 2006 22:12:53" parent="34" time="35" user="emanuele" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="3" parameter="<no description>" parameterId="0" type="Integer" value="2"/>
+ </action>
+ <action date="21 Nov 2006 22:13:08" parent="35" time="36" user="emanuele" what="moveModule">
+ <move dx="-54.6476884791" dy="49.6032862707" id="0"/>
+ <move dx="-25.2220100673" dy="5.88513565923" id="4"/>
+ </action>
+ <action date="21 Nov 2006 22:13:23" parent="19" time="37" user="emanuele" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="0" parameter="<no description>" parameterId="0" type="Float" value="0.0"/>
+ </action>
+ <action date="21 Nov 2006 22:13:27" parent="37" time="38" user="emanuele" what="changeParameter">
+ <set alias="" function="value" functionId="0" moduleId="0" parameter="<no description>" parameterId="0" type="Float" value="1.2"/>
+ </action>
+ <action date="21 Nov 2006 22:13:33" parent="38" time="39" user="emanuele" what="addModule">
+ <object cache="0" id="3" name="StandardOutput" x="73.8986646828" y="-196.323746472"/>
+ </action>
+ <action date="21 Nov 2006 22:13:36" parent="39" time="40" user="emanuele" what="addConnection">
+ <connect destinationId="3" destinationModule="StandardOutput" destinationPort="value(Module)" id="2" sourceId="2" sourceModule="Float" sourcePort="value(Float)"/>
+ </action>
+ <action date="21 Nov 2006 22:13:42" parent="40" time="41" user="emanuele" what="moveModule">
+ <move dx="-11.7702713647" dy="31.1071456274" id="3"/>
+ </action>
+ <tag name="int chain" time="36"/>
+ <tag name="float chain" time="41"/>
+ <tag name="final" time="11"/>
+ </visTrail>
diff --git a/vistrails/tests/resources/dummy_new.vt b/vistrails/tests/resources/dummy_new.vt
new file mode 100644
index 0000000..9ae5e63
Binary files /dev/null and b/vistrails/tests/resources/dummy_new.vt differ
diff --git a/vistrails/tests/resources/dummy_new.xml b/vistrails/tests/resources/dummy_new.xml
new file mode 100644
index 0000000..b342d08
--- /dev/null
+++ b/vistrails/tests/resources/dummy_new.xml
@@ -0,0 +1,342 @@
+<?xml version="1.0" ?>
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<vistrail dbHost="" dbName="" dbPort="" id="" name="" version="0.5.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/vistrail.xsd">
+ <action date="2006-11-09 11:11:45" id="2" prevId="0" user="cscheid">
+ <add id="0" objectId="0" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="0" name="File"/>
+ </add>
+ <add id="1" objectId="0" parentObjId="0" parentObjType="module" what="location">
+ <location id="0" x="-0.405904047613" y="0.590405904059"/>
+ </add>
+ </action>
+ <action date="2006-11-09 11:11:49" id="3" prevId="2" user="cscheid">
+ <add id="2" objectId="1" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="1" name="String"/>
+ </add>
+ <add id="3" objectId="1" parentObjId="1" parentObjType="module" what="location">
+ <location id="1" x="-79.7416969521" y="113.505537534"/>
+ </add>
+ </action>
+ <action date="2006-11-09 11:11:52" id="4" prevId="3" user="cscheid">
+ <add id="4" objectId="0" parentObjId="" parentObjType="" what="connection">
+ <connection id="0"/>
+ </add>
+ <add id="5" objectId="0" parentObjId="0" parentObjType="connection" what="port">
+ <port id="0" moduleId="1" moduleName="String" sig="value(String)" type="source"/>
+ </add>
+ <add id="6" objectId="1" parentObjId="0" parentObjType="connection" what="port">
+ <port id="1" moduleId="0" moduleName="File" sig="name(String)" type="destination"/>
+ </add>
+ </action>
+ <action date="2006-11-09 11:12:01" id="5" prevId="4" user="cscheid">
+ <add id="7" objectId="2" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="2" name="FileSink"/>
+ </add>
+ <add id="8" objectId="2" parentObjId="2" parentObjType="module" what="location">
+ <location id="2" x="-25.1291511435" y="-88.7084891257"/>
+ </add>
+ </action>
+ <action date="2006-11-09 11:12:04" id="6" prevId="5" user="cscheid">
+ <add id="9" objectId="1" parentObjId="" parentObjType="" what="connection">
+ <connection id="1"/>
+ </add>
+ <add id="10" objectId="2" parentObjId="1" parentObjType="connection" what="port">
+ <port id="2" moduleId="0" moduleName="File" sig="self(File)" type="source"/>
+ </add>
+ <add id="11" objectId="3" parentObjId="1" parentObjType="connection" what="port">
+ <port id="3" moduleId="2" moduleName="FileSink" sig="file(File)" type="destination"/>
+ </add>
+ </action>
+ <action date="2006-11-09 11:12:06" id="7" prevId="6" user="cscheid">
+ <change id="12" newObjId="3" oldObjId="2" parentObjId="2" parentObjType="module" what="location">
+ <location id="3" x="63.4317339516" y="-116.014762799"/>
+ </change>
+ </action>
+ <action date="2006-11-09 11:12:06" id="8" prevId="7" user="cscheid">
+ <add id="13" objectId="3" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="3" name="String"/>
+ </add>
+ <add id="14" objectId="4" parentObjId="3" parentObjType="module" what="location">
+ <location id="4" x="135.756456779" y="-26.7158678139"/>
+ </add>
+ </action>
+ <action date="2006-11-09 11:12:09" id="9" prevId="8" user="cscheid">
+ <add id="15" objectId="2" parentObjId="" parentObjType="" what="connection">
+ <connection id="2"/>
+ </add>
+ <add id="16" objectId="4" parentObjId="2" parentObjType="connection" what="port">
+ <port id="4" moduleId="3" moduleName="String" sig="value(String)" type="source"/>
+ </add>
+ <add id="17" objectId="5" parentObjId="2" parentObjType="connection" what="port">
+ <port id="5" moduleId="2" moduleName="FileSink" sig="outputName(String)" type="destination"/>
+ </add>
+ </action>
+ <action date="2006-11-09 11:12:12" id="10" prevId="9" user="cscheid">
+ <add id="18" objectId="0" parentObjId="3" parentObjType="module" what="function">
+ <function id="0" name="value" pos="0"/>
+ </add>
+ <add id="19" objectId="0" parentObjId="0" parentObjType="function" what="parameter">
+ <parameter alias="" id="0" name="<no description>" pos="0" type="String" val=""/>
+ </add>
+ </action>
+ <action date="2006-11-09 11:12:23" id="11" prevId="10" user="cscheid">
+ <change id="20" newObjId="1" oldObjId="0" parentObjId="0" parentObjType="function" what="parameter">
+ <parameter alias="" id="1" name="<no description>" pos="0" type="String" val="/tmp/unimportant.tmp"/>
+ </change>
+ </action>
+ <action date="2006-11-21 22:10:52" id="12" prevId="0" user="emanuele">
+ <add id="21" objectId="4" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="4" name="Float"/>
+ </add>
+ <add id="22" objectId="5" parentObjId="4" parentObjType="module" what="location">
+ <location id="5" x="-11.8561695459" y="98.7737701549"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:11:01" id="13" prevId="12" user="emanuele">
+ <change id="23" newObjId="6" oldObjId="5" parentObjId="4" parentObjType="module" what="location">
+ <location id="6" x="-5.13030019463" y="136.606785107"/>
+ </change>
+ </action>
+ <action date="2006-11-21 22:11:02" id="14" prevId="13" user="emanuele">
+ <add id="24" objectId="5" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="5" name="Float"/>
+ </add>
+ <add id="25" objectId="7" parentObjId="5" parentObjType="module" what="location">
+ <location id="7" x="100.802142088" y="40.7631472281"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:11:06" id="15" prevId="14" user="emanuele">
+ <change id="26" newObjId="8" oldObjId="7" parentObjId="5" parentObjType="module" what="location">
+ <location id="8" x="76.4208656896" y="14.7004035944"/>
+ </change>
+ </action>
+ <action date="2006-11-21 22:11:06" id="16" prevId="15" user="emanuele">
+ <add id="27" objectId="3" parentObjId="" parentObjType="" what="connection">
+ <connection id="3"/>
+ </add>
+ <add id="28" objectId="6" parentObjId="3" parentObjType="connection" what="port">
+ <port id="6" moduleId="4" moduleName="Float" sig="value(Float)" type="source"/>
+ </add>
+ <add id="29" objectId="7" parentObjId="3" parentObjType="connection" what="port">
+ <port id="7" moduleId="5" moduleName="Float" sig="value(Float)" type="destination"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:11:16" id="17" prevId="16" user="emanuele">
+ <change id="30" newObjId="9" oldObjId="8" parentObjId="5" parentObjType="module" what="location">
+ <location id="9" x="82.306001372" y="8.81526793517"/>
+ </change>
+ <change id="31" newObjId="10" oldObjId="6" parentObjId="4" parentObjType="module" what="location">
+ <location id="10" x="-59.7779886737" y="142.491920766"/>
+ </change>
+ <change id="32" newObjId="11" oldObjId="9" parentObjId="5" parentObjType="module" what="location">
+ <location id="11" x="66.3320616627" y="63.4629561995"/>
+ </change>
+ </action>
+ <action date="2006-11-21 22:11:16" id="18" prevId="17" user="emanuele">
+ <add id="33" objectId="6" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="6" name="Float"/>
+ </add>
+ <add id="34" objectId="12" parentObjId="6" parentObjType="module" what="location">
+ <location id="12" x="156.290564236" y="-60.1248926444"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:11:18" id="19" prevId="18" user="emanuele">
+ <add id="35" objectId="4" parentObjId="" parentObjType="" what="connection">
+ <connection id="4"/>
+ </add>
+ <add id="36" objectId="8" parentObjId="4" parentObjType="connection" what="port">
+ <port id="8" moduleId="5" moduleName="Float" sig="value(Float)" type="source"/>
+ </add>
+ <add id="37" objectId="9" parentObjId="4" parentObjType="connection" what="port">
+ <port id="9" moduleId="6" moduleName="Float" sig="value(Float)" type="destination"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:12:06" id="20" prevId="19" user="emanuele">
+ <add id="38" objectId="7" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="7" name="Integer"/>
+ </add>
+ <add id="39" objectId="13" parentObjId="7" parentObjType="module" what="location">
+ <location id="13" x="-74.0704610451" y="2.93013227592"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:12:10" id="21" prevId="20" user="emanuele">
+ <change id="40" newObjId="14" oldObjId="13" parentObjId="7" parentObjType="module" what="location">
+ <location id="14" x="-90.0444007544" y="19.744805588"/>
+ </change>
+ </action>
+ <action date="2006-11-21 22:12:10" id="22" prevId="21" user="emanuele">
+ <add id="41" objectId="8" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="8" name="Integer"/>
+ </add>
+ <add id="42" objectId="15" parentObjId="8" parentObjType="module" what="location">
+ <location id="15" x="24.2953782172" y="-86.1876362782"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:12:14" id="23" prevId="22" user="emanuele">
+ <add id="43" objectId="5" parentObjId="" parentObjType="" what="connection">
+ <connection id="5"/>
+ </add>
+ <add id="44" objectId="10" parentObjId="5" parentObjType="connection" what="port">
+ <port id="10" moduleId="7" moduleName="Integer" sig="value(Integer)" type="source"/>
+ </add>
+ <add id="45" objectId="11" parentObjId="5" parentObjType="connection" what="port">
+ <port id="11" moduleId="8" moduleName="Integer" sig="value(Integer)" type="destination"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:12:20" id="24" prevId="23" user="emanuele">
+ <change id="46" newObjId="16" oldObjId="15" parentObjId="8" parentObjType="module" what="location">
+ <location id="16" x="-15.2191042215" y="-94.5949729342"/>
+ </change>
+ <change id="47" newObjId="17" oldObjId="14" parentObjId="7" parentObjType="module" what="location">
+ <location id="17" x="-85.8407324099" y="31.5150769065"/>
+ </change>
+ </action>
+ <action date="2006-11-21 22:12:21" id="25" prevId="24" user="emanuele">
+ <delete id="48" objectId="6" parentObjId="3" parentObjType="connection" what="port"/>
+ <delete id="49" objectId="7" parentObjId="3" parentObjType="connection" what="port"/>
+ <delete id="50" objectId="3" parentObjId="" parentObjType="" what="connection"/>
+ </action>
+ <action date="2006-11-21 22:12:21" id="26" prevId="25" user="emanuele">
+ <delete id="51" objectId="10" parentObjId="4" parentObjType="module" what="location"/>
+ <delete id="52" objectId="4" parentObjId="" parentObjType="" what="module"/>
+ </action>
+ <action date="2006-11-21 22:12:23" id="27" prevId="26" user="emanuele">
+ <delete id="53" objectId="8" parentObjId="4" parentObjType="connection" what="port"/>
+ <delete id="54" objectId="9" parentObjId="4" parentObjType="connection" what="port"/>
+ <delete id="55" objectId="4" parentObjId="" parentObjType="" what="connection"/>
+ </action>
+ <action date="2006-11-21 22:12:23" id="28" prevId="27" user="emanuele">
+ <delete id="56" objectId="11" parentObjId="5" parentObjType="module" what="location"/>
+ <delete id="57" objectId="5" parentObjId="" parentObjType="" what="module"/>
+ </action>
+ <action date="2006-11-21 22:12:26" id="29" prevId="28" user="emanuele"/>
+ <action date="2006-11-21 22:12:26" id="30" prevId="29" user="emanuele">
+ <delete id="58" objectId="12" parentObjId="6" parentObjType="module" what="location"/>
+ <delete id="59" objectId="6" parentObjId="" parentObjType="" what="module"/>
+ </action>
+ <action date="2006-11-21 22:12:41" id="31" prevId="30" user="emanuele">
+ <change id="60" newObjId="18" oldObjId="16" parentObjId="8" parentObjType="module" what="location">
+ <location id="18" x="70.5357300072" y="-53.3990233196"/>
+ </change>
+ <change id="61" newObjId="19" oldObjId="17" parentObjId="7" parentObjType="module" what="location">
+ <location id="19" x="-21.9449735728" y="83.640564174"/>
+ </change>
+ <change id="62" newObjId="20" oldObjId="18" parentObjId="8" parentObjType="module" what="location">
+ <location id="20" x="81.465267703" y="-12.203073705"/>
+ </change>
+ </action>
+ <action date="2006-11-21 22:12:41" id="32" prevId="31" user="emanuele">
+ <add id="63" objectId="9" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="9" name="StandardOutput"/>
+ </add>
+ <add id="64" objectId="21" parentObjId="9" parentObjType="module" what="location">
+ <location id="21" x="112.572413453" y="-161.853666183"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:12:44" id="33" prevId="32" user="emanuele">
+ <add id="65" objectId="6" parentObjId="" parentObjType="" what="connection">
+ <connection id="6"/>
+ </add>
+ <add id="66" objectId="12" parentObjId="6" parentObjType="connection" what="port">
+ <port id="12" moduleId="8" moduleName="Integer" sig="value(Integer)" type="source"/>
+ </add>
+ <add id="67" objectId="13" parentObjId="6" parentObjType="connection" what="port">
+ <port id="13" moduleId="9" moduleName="StandardOutput" sig="value(Module)" type="destination"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:12:49" id="34" prevId="33" user="emanuele">
+ <add id="68" objectId="1" parentObjId="7" parentObjType="module" what="function">
+ <function id="1" name="value" pos="0"/>
+ </add>
+ <add id="69" objectId="2" parentObjId="1" parentObjType="function" what="parameter">
+ <parameter alias="" id="2" name="<no description>" pos="0" type="Integer" val="0"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:12:53" id="35" prevId="34" user="emanuele">
+ <change id="70" newObjId="3" oldObjId="2" parentObjId="1" parentObjType="function" what="parameter">
+ <parameter alias="" id="3" name="<no description>" pos="0" type="Integer" val="2"/>
+ </change>
+ </action>
+ <action date="2006-11-21 22:13:08" id="36" prevId="35" user="emanuele">
+ <change id="71" newObjId="22" oldObjId="21" parentObjId="9" parentObjType="module" what="location">
+ <location id="22" x="57.9247249739" y="-112.250379912"/>
+ </change>
+ <change id="72" newObjId="23" oldObjId="20" parentObjId="8" parentObjType="module" what="location">
+ <location id="23" x="56.2432576357" y="-6.31793804582"/>
+ </change>
+ </action>
+ <action date="2006-11-21 22:13:23" id="37" prevId="19" user="emanuele">
+ <add id="73" objectId="2" parentObjId="4" parentObjType="module" what="function">
+ <function id="2" name="value" pos="0"/>
+ </add>
+ <add id="74" objectId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="4" name="<no description>" pos="0" type="Float" val="0.0"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:13:27" id="38" prevId="37" user="emanuele">
+ <change id="75" newObjId="5" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="5" name="<no description>" pos="0" type="Float" val="1.2"/>
+ </change>
+ </action>
+ <action date="2006-11-21 22:13:33" id="39" prevId="38" user="emanuele">
+ <add id="76" objectId="10" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="10" name="StandardOutput"/>
+ </add>
+ <add id="77" objectId="24" parentObjId="10" parentObjType="module" what="location">
+ <location id="24" x="73.8986646828" y="-196.323746472"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:13:36" id="40" prevId="39" user="emanuele">
+ <add id="78" objectId="7" parentObjId="" parentObjType="" what="connection">
+ <connection id="7"/>
+ </add>
+ <add id="79" objectId="14" parentObjId="7" parentObjType="connection" what="port">
+ <port id="14" moduleId="6" moduleName="Float" sig="value(Float)" type="source"/>
+ </add>
+ <add id="80" objectId="15" parentObjId="7" parentObjType="connection" what="port">
+ <port id="15" moduleId="10" moduleName="StandardOutput" sig="value(Module)" type="destination"/>
+ </add>
+ </action>
+ <action date="2006-11-21 22:13:42" id="41" prevId="40" user="emanuele">
+ <change id="81" newObjId="25" oldObjId="24" parentObjId="10" parentObjType="module" what="location">
+ <location id="25" x="62.1283933181" y="-165.216600845"/>
+ </change>
+ </action>
+ <tag name="int chain" time="36"/>
+ <tag name="float chain" time="41"/>
+ <tag name="final" time="11"/>
+</vistrail>
diff --git a/vistrails/tests/resources/dynamic_module_error.xml b/vistrails/tests/resources/dynamic_module_error.xml
new file mode 100644
index 0000000..1215d17
--- /dev/null
+++ b/vistrails/tests/resources/dynamic_module_error.xml
@@ -0,0 +1,42 @@
+<?xml version="1.0" ?>
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+ <visTrail version="0.3.1">
+ <action date="15 Mar 2007 16:53:42" parent="0" time="1" user="cscheid" what="addModule">
+ <object cache="0" id="0" name="TestDynamicModuleError" x="-7.0" y="18.0"/>
+ </action>
+ <tag name="test" time="1"/>
+ </visTrail>
diff --git a/vistrails/tests/resources/empty_bookmarks.xml b/vistrails/tests/resources/empty_bookmarks.xml
new file mode 100644
index 0000000..45ff5f3
--- /dev/null
+++ b/vistrails/tests/resources/empty_bookmarks.xml
@@ -0,0 +1,36 @@
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+ <bookmarks/>
diff --git a/vistrails/tests/resources/import_pkg/__init__.py b/vistrails/tests/resources/import_pkg/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/vistrails/tests/resources/import_pkg/test_import_pkg/__init__.py b/vistrails/tests/resources/import_pkg/test_import_pkg/__init__.py
new file mode 100644
index 0000000..ae172b9
--- /dev/null
+++ b/vistrails/tests/resources/import_pkg/test_import_pkg/__init__.py
@@ -0,0 +1,8 @@
+name = 'test_import_pkg'
+identifier = 'org.vistrails.tests.test_import_pkg'
+version = '0.42'
+
+import vistrails.tests.resources.import_targets.test1
+import tests.resources.import_targets.test2
+
+import module1
diff --git a/vistrails/tests/resources/import_pkg/test_import_pkg/init.py b/vistrails/tests/resources/import_pkg/test_import_pkg/init.py
new file mode 100644
index 0000000..1d4ff55
--- /dev/null
+++ b/vistrails/tests/resources/import_pkg/test_import_pkg/init.py
@@ -0,0 +1 @@
+import module2
diff --git a/vistrails/tests/resources/import_pkg/test_import_pkg/module1.py b/vistrails/tests/resources/import_pkg/test_import_pkg/module1.py
new file mode 100644
index 0000000..f3f9c43
--- /dev/null
+++ b/vistrails/tests/resources/import_pkg/test_import_pkg/module1.py
@@ -0,0 +1,2 @@
+import vistrails.tests.resources.import_targets.test3
+import tests.resources.import_targets.test4
diff --git a/vistrails/tests/resources/import_pkg/test_import_pkg/module2.py b/vistrails/tests/resources/import_pkg/test_import_pkg/module2.py
new file mode 100644
index 0000000..0f295a5
--- /dev/null
+++ b/vistrails/tests/resources/import_pkg/test_import_pkg/module2.py
@@ -0,0 +1,2 @@
+import vistrails.tests.resources.import_targets.test5
+import tests.resources.import_targets.test6
diff --git a/vistrails/tests/resources/import_targets/__init__.py b/vistrails/tests/resources/import_targets/__init__.py
new file mode 100644
index 0000000..65a1ff1
--- /dev/null
+++ b/vistrails/tests/resources/import_targets/__init__.py
@@ -0,0 +1,5 @@
+"""This is a target for importing a non-package module.
+
+It is used in the PackageManager's tests to check that the dependency-tracking
+name-fixing import override works correctly.
+"""
diff --git a/vistrails/tests/resources/import_targets/test1.py b/vistrails/tests/resources/import_targets/test1.py
new file mode 100644
index 0000000..3a2255a
--- /dev/null
+++ b/vistrails/tests/resources/import_targets/test1.py
@@ -0,0 +1,7 @@
+try:
+ import core.packagemanager
+except ImportError:
+ pass
+else:
+ raise AssertionError("Importing without prefix from outside the package "
+ "didn't raise ImportError")
diff --git a/vistrails/tests/resources/import_targets/test2.py b/vistrails/tests/resources/import_targets/test2.py
new file mode 100644
index 0000000..e69de29
diff --git a/vistrails/tests/resources/import_targets/test3.py b/vistrails/tests/resources/import_targets/test3.py
new file mode 100644
index 0000000..e69de29
diff --git a/vistrails/tests/resources/import_targets/test4.py b/vistrails/tests/resources/import_targets/test4.py
new file mode 100644
index 0000000..e69de29
diff --git a/vistrails/tests/resources/import_targets/test5.py b/vistrails/tests/resources/import_targets/test5.py
new file mode 100644
index 0000000..e69de29
diff --git a/vistrails/tests/resources/import_targets/test6.py b/vistrails/tests/resources/import_targets/test6.py
new file mode 100644
index 0000000..e69de29
diff --git a/vistrails/tests/resources/paramexp-1.0.2.vt b/vistrails/tests/resources/paramexp-1.0.2.vt
new file mode 100644
index 0000000..74fa2f1
Binary files /dev/null and b/vistrails/tests/resources/paramexp-1.0.2.vt differ
diff --git a/vistrails/tests/resources/paramexp-1.0.3.vt b/vistrails/tests/resources/paramexp-1.0.3.vt
new file mode 100644
index 0000000..a059689
Binary files /dev/null and b/vistrails/tests/resources/paramexp-1.0.3.vt differ
diff --git a/vistrails/tests/resources/pythonsource.xml b/vistrails/tests/resources/pythonsource.xml
new file mode 100644
index 0000000..cb95484
--- /dev/null
+++ b/vistrails/tests/resources/pythonsource.xml
@@ -0,0 +1,288 @@
+<?xml version="1.0" ?>
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<vistrail dbHost="" dbName="" dbPort="" id="" name="" version="0.5.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/vistrail.xsd">
+ <action date="2007-03-02 14:30:19" id="1" prevId="0" user="cscheid">
+ <add id="0" objectId="0" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="0" name="PythonSource"/>
+ </add>
+ <add id="1" objectId="0" parentObjId="0" parentObjType="module" what="location">
+ <location id="0" x="-2.0" y="-19.0"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:30:47" id="2" prevId="1" user="cscheid">
+ <add id="2" objectId="0" parentObjId="0" parentObjType="module" what="portSpec">
+ <portSpec id="0" name="v1" spec="(Float)" type="input"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:30:47" id="3" prevId="2" user="cscheid">
+ <add id="3" objectId="1" parentObjId="0" parentObjType="module" what="portSpec">
+ <portSpec id="1" name="v2" spec="(Float)" type="input"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:30:47" id="4" prevId="3" user="cscheid">
+ <add id="4" objectId="2" parentObjId="0" parentObjType="module" what="portSpec">
+ <portSpec id="2" name="o" spec="(Float)" type="output"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:30:48" id="5" prevId="4" user="cscheid">
+ <add id="5" objectId="0" parentObjId="0" parentObjType="module" what="function">
+ <function id="0" name="source" pos="0"/>
+ </add>
+ <add id="6" objectId="0" parentObjId="0" parentObjType="function" what="parameter">
+ <parameter alias="" id="0" name="<no description>" pos="0" type="String" val="o%20%3D%20v1%20%2B%20v2"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:30:50" id="6" prevId="5" user="cscheid">
+ <add id="7" objectId="1" parentObjId="0" parentObjType="module" what="function">
+ <function id="1" name="v1" pos="1"/>
+ </add>
+ <add id="8" objectId="1" parentObjId="1" parentObjType="function" what="parameter">
+ <parameter alias="" id="1" name="<no description>" pos="0" type="Float" val="0.0"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:30:51" id="7" prevId="6" user="cscheid">
+ <change id="9" newObjId="2" oldObjId="1" parentObjId="1" parentObjType="function" what="parameter">
+ <parameter alias="" id="2" name="<no description>" pos="0" type="Float" val="1"/>
+ </change>
+ </action>
+ <action date="2007-03-02 14:30:53" id="8" prevId="7" user="cscheid">
+ <add id="10" objectId="2" parentObjId="0" parentObjType="module" what="function">
+ <function id="2" name="v2" pos="2"/>
+ </add>
+ <add id="11" objectId="3" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="3" name="<no description>" pos="0" type="Float" val="0.0"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:30:54" id="9" prevId="8" user="cscheid">
+ <change id="12" newObjId="4" oldObjId="3" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="4" name="<no description>" pos="0" type="Float" val="2"/>
+ </change>
+ </action>
+ <action date="2007-03-02 14:31:00" id="10" prevId="9" user="cscheid">
+ <add id="13" objectId="1" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="1" name="StandardOutput"/>
+ </add>
+ <add id="14" objectId="1" parentObjId="1" parentObjType="module" what="location">
+ <location id="1" x="11.0" y="-158.0"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:31:02" id="11" prevId="10" user="cscheid">
+ <add id="15" objectId="0" parentObjId="" parentObjType="" what="connection">
+ <connection id="0"/>
+ </add>
+ <add id="16" objectId="0" parentObjId="0" parentObjType="connection" what="port">
+ <port id="0" moduleId="0" moduleName="PythonSource" sig="o(Float)" type="source"/>
+ </add>
+ <add id="17" objectId="1" parentObjId="0" parentObjType="connection" what="port">
+ <port id="1" moduleId="1" moduleName="StandardOutput" sig="value(Module)" type="destination"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:35:38" id="12" prevId="11" user="cscheid">
+ <delete id="18" objectId="0" parentObjId="0" parentObjType="connection" what="port"/>
+ <delete id="19" objectId="1" parentObjId="0" parentObjType="connection" what="port"/>
+ <delete id="20" objectId="0" parentObjId="" parentObjType="" what="connection"/>
+ </action>
+ <action date="2007-03-02 14:35:38" id="13" prevId="12" user="cscheid">
+ <delete id="21" objectId="1" parentObjId="1" parentObjType="module" what="location"/>
+ <delete id="22" objectId="1" parentObjId="" parentObjType="" what="module"/>
+ </action>
+ <action date="2007-03-02 14:36:05" id="14" prevId="13" user="cscheid">
+ <add id="23" objectId="2" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="2" name="PythonSource"/>
+ </add>
+ <add id="24" objectId="2" parentObjId="2" parentObjType="module" what="location">
+ <location id="2" x="-1.1116424772" y="-107.829320288"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:36:30" id="15" prevId="14" user="cscheid">
+ <add id="25" objectId="3" parentObjId="2" parentObjType="module" what="portSpec">
+ <portSpec id="3" name="v" spec="(Float)" type="input"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:36:30" id="16" prevId="15" user="cscheid">
+ <add id="26" objectId="3" parentObjId="2" parentObjType="module" what="function">
+ <function id="3" name="source" pos="0"/>
+ </add>
+ <add id="27" objectId="5" parentObjId="3" parentObjType="function" what="parameter">
+ <parameter alias="" id="5" name="<no description>" pos="0" type="String" val="if%20v%20%21%3D%202.0%3A%0A%20%20%20raise%20ModuleError%28self%2C%20%22assert%20failed%22%29"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:36:32" id="17" prevId="16" user="cscheid">
+ <add id="28" objectId="1" parentObjId="" parentObjType="" what="connection">
+ <connection id="1"/>
+ </add>
+ <add id="29" objectId="2" parentObjId="1" parentObjType="connection" what="port">
+ <port id="2" moduleId="0" moduleName="PythonSource" sig="o(Float)" type="source"/>
+ </add>
+ <add id="30" objectId="3" parentObjId="1" parentObjType="connection" what="port">
+ <port id="3" moduleId="2" moduleName="PythonSource" sig="v(Float)" type="destination"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:37:44" id="18" prevId="17" user="cscheid">
+ <add id="31" objectId="3" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="3" name="StandardOutput"/>
+ </add>
+ <add id="32" objectId="3" parentObjId="3" parentObjType="module" what="location">
+ <location id="3" x="43.9797583425" y="-186.913972956"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:37:45" id="19" prevId="18" user="cscheid">
+ <add id="33" objectId="2" parentObjId="" parentObjType="" what="connection">
+ <connection id="2"/>
+ </add>
+ <add id="34" objectId="4" parentObjId="2" parentObjType="connection" what="port">
+ <port id="4" moduleId="0" moduleName="PythonSource" sig="o(Float)" type="source"/>
+ </add>
+ <add id="35" objectId="5" parentObjId="2" parentObjType="connection" what="port">
+ <port id="5" moduleId="3" moduleName="StandardOutput" sig="value(Module)" type="destination"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:37:52" id="20" prevId="19" user="cscheid">
+ <change id="36" newObjId="4" oldObjId="2" parentObjId="2" parentObjType="module" what="location">
+ <location id="4" x="201.195245898" y="-103.431344454"/>
+ </change>
+ </action>
+ <action date="2007-03-02 14:37:52" id="21" prevId="20" user="cscheid">
+ <delete id="37" objectId="2" parentObjId="1" parentObjType="connection" what="port"/>
+ <delete id="38" objectId="3" parentObjId="1" parentObjType="connection" what="port"/>
+ <delete id="39" objectId="1" parentObjId="" parentObjType="" what="connection"/>
+ </action>
+ <action date="2007-03-02 14:38:06" id="22" prevId="21" user="cscheid">
+ <change id="40" newObjId="6" oldObjId="5" parentObjId="3" parentObjType="function" what="parameter">
+ <parameter alias="" id="6" name="<no description>" pos="0" type="String" val="return%0Aif%20v%20%21%3D%202.0%3A%0A%20%20%20raise%20ModuleError%28self%2C%20%22assert%20failed%22%29"/>
+ </change>
+ </action>
+ <action date="2007-03-02 14:38:23" id="23" prevId="22" user="cscheid">
+ <change id="41" newObjId="7" oldObjId="6" parentObjId="3" parentObjType="function" what="parameter">
+ <parameter alias="" id="7" name="<no description>" pos="0" type="String" val="%23if%20v%20%21%3D%202.0%3A%0A%23%20%20%20raise%20ModuleError%28self%2C%20%22assert%20failed%22%29%0Apass"/>
+ </change>
+ </action>
+ <action date="2007-03-02 14:38:29" id="24" prevId="23" user="cscheid">
+ <add id="42" objectId="3" parentObjId="" parentObjType="" what="connection">
+ <connection id="3"/>
+ </add>
+ <add id="43" objectId="6" parentObjId="3" parentObjType="connection" what="port">
+ <port id="6" moduleId="0" moduleName="PythonSource" sig="o(Float)" type="source"/>
+ </add>
+ <add id="44" objectId="7" parentObjId="3" parentObjType="connection" what="port">
+ <port id="7" moduleId="2" moduleName="PythonSource" sig="v(Float)" type="destination"/>
+ </add>
+ </action>
+ <action date="2007-03-02 14:38:34" id="25" prevId="24" user="cscheid">
+ <change id="45" newObjId="8" oldObjId="7" parentObjId="3" parentObjType="function" what="parameter">
+ <parameter alias="" id="8" name="<no description>" pos="0" type="String" val="%23if%20v%20%21%3D%202.0%3A%0A%23%20%20%20raise%20ModuleError%28self%2C%20%22assert%20failed%22%29%0Aprint%20v"/>
+ </change>
+ </action>
+ <action date="2007-03-02 14:39:39" id="26" prevId="25" user="cscheid">
+ <change id="46" newObjId="9" oldObjId="8" parentObjId="3" parentObjType="function" what="parameter">
+ <parameter alias="" id="9" name="<no description>" pos="0" type="String" val="if%20v%20%21%3D%202.0%3A%0A%20%20%20raise%20ModuleError%28self%2C%20%22assert%20failed%22%29%0A"/>
+ </change>
+ </action>
+ <action date="2007-03-02 14:42:03" id="27" prevId="26" user="cscheid">
+ <delete id="47" objectId="4" parentObjId="2" parentObjType="connection" what="port"/>
+ <delete id="48" objectId="5" parentObjId="2" parentObjType="connection" what="port"/>
+ <delete id="49" objectId="2" parentObjId="" parentObjType="" what="connection"/>
+ </action>
+ <action date="2007-03-02 14:42:03" id="28" prevId="27" user="cscheid">
+ <delete id="50" objectId="3" parentObjId="3" parentObjType="module" what="location"/>
+ <delete id="51" objectId="3" parentObjId="" parentObjType="" what="module"/>
+ </action>
+ <action date="2007-03-02 14:42:09" id="29" prevId="28" user="cscheid">
+ <change id="52" newObjId="10" oldObjId="9" parentObjId="3" parentObjType="function" what="parameter">
+ <parameter alias="" id="10" name="<no description>" pos="0" type="String" val="if%20v%20%21%3D%203.0%3A%0A%20%20%20raise%20ModuleError%28self%2C%20%22assert%20failed%22%29%0A"/>
+ </change>
+ </action>
+ <action date="2007-03-02 14:43:30" id="30" prevId="29" user="cscheid">
+ <change id="53" newObjId="11" oldObjId="10" parentObjId="3" parentObjType="function" what="parameter">
+ <parameter alias="" id="11" name="<no description>" pos="0" type="String" val="if%20v%20%21%3D%202.0%3A%0A%20%20%20raise%20ModuleError%28self%2C%20%22assert%20failed%22%29%0A"/>
+ </change>
+ </action>
+ <action date="2007-03-02 14:43:43" id="31" prevId="30" user="cscheid">
+ <change id="54" newObjId="12" oldObjId="11" parentObjId="3" parentObjType="function" what="parameter">
+ <parameter alias="" id="12" name="<no description>" pos="0" type="String" val="if%20v%20%21%3D%202.0%3A%0A%20%20%20fail%28%22assert%20failed%22%29%0A"/>
+ </change>
+ </action>
+ <action date="2007-03-15 17:09:27" id="32" prevId="31" user="cscheid">
+ <change id="55" newObjId="13" oldObjId="12" parentObjId="3" parentObjType="function" what="parameter">
+ <parameter alias="" id="13" name="<no description>" pos="0" type="String" val="if%20v%20%21%3D%203.0%3A%0A%20%20%20fail%28%22assert%20failed%22%29%0A"/>
+ </change>
+ </action>
+ <action date="2007-07-13 14:20:10" id="33" prevId="32" user="cscheid">
+ <add id="56" objectId="4" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="4" name="PythonSource"/>
+ </add>
+ <add id="57" objectId="5" parentObjId="4" parentObjType="module" what="location">
+ <location id="5" x="106.04612809" y="-290.823472489"/>
+ </add>
+ </action>
+ <action date="2007-07-13 14:20:12" id="34" prevId="33" user="cscheid">
+ <delete id="58" objectId="6" parentObjId="3" parentObjType="connection" what="port"/>
+ <delete id="59" objectId="7" parentObjId="3" parentObjType="connection" what="port"/>
+ <delete id="60" objectId="3" parentObjId="" parentObjType="" what="connection"/>
+ <delete id="61" objectId="0" parentObjId="0" parentObjType="module" what="location"/>
+ <delete id="62" objectId="0" parentObjId="0" parentObjType="function" what="parameter"/>
+ <delete id="63" objectId="0" parentObjId="0" parentObjType="module" what="function"/>
+ <delete id="64" objectId="2" parentObjId="1" parentObjType="function" what="parameter"/>
+ <delete id="65" objectId="1" parentObjId="0" parentObjType="module" what="function"/>
+ <delete id="66" objectId="4" parentObjId="2" parentObjType="function" what="parameter"/>
+ <delete id="67" objectId="2" parentObjId="0" parentObjType="module" what="function"/>
+ <delete id="68" objectId="0" parentObjId="0" parentObjType="module" what="portSpec"/>
+ <delete id="69" objectId="1" parentObjId="0" parentObjType="module" what="portSpec"/>
+ <delete id="70" objectId="2" parentObjId="0" parentObjType="module" what="portSpec"/>
+ <delete id="71" objectId="0" parentObjId="" parentObjType="" what="module"/>
+ <delete id="72" objectId="4" parentObjId="2" parentObjType="module" what="location"/>
+ <delete id="73" objectId="13" parentObjId="3" parentObjType="function" what="parameter"/>
+ <delete id="74" objectId="3" parentObjId="2" parentObjType="module" what="function"/>
+ <delete id="75" objectId="3" parentObjId="2" parentObjType="module" what="portSpec"/>
+ <delete id="76" objectId="2" parentObjId="" parentObjType="" what="module"/>
+ </action>
+ <action date="2007-07-13 14:20:27" id="35" prevId="34" user="cscheid">
+ <add id="77" objectId="4" parentObjId="4" parentObjType="module" what="portSpec">
+ <portSpec id="4" name="foo" spec="(String)" type="output"/>
+ </add>
+ </action>
+ <action date="2007-07-13 14:20:27" id="36" prevId="35" user="cscheid">
+ <add id="78" objectId="4" parentObjId="4" parentObjType="module" what="function">
+ <function id="4" name="source" pos="0"/>
+ </add>
+ <add id="79" objectId="14" parentObjId="4" parentObjType="function" what="parameter">
+ <parameter alias="" id="14" name="<no description>" pos="0" type="String" val="foo%20%3D%20%22foo%22"/>
+ </add>
+ </action>
+ <tag name="test_simple_success" time="36"/>
+ <tag name="testPortsAndFail" time="32"/>
+</vistrail>
diff --git a/vistrails/tests/resources/spx_loop.vt b/vistrails/tests/resources/spx_loop.vt
new file mode 100644
index 0000000..d1680bd
Binary files /dev/null and b/vistrails/tests/resources/spx_loop.vt differ
diff --git a/vistrails/tests/resources/terminator.vt b/vistrails/tests/resources/terminator.vt
new file mode 100644
index 0000000..022889b
Binary files /dev/null and b/vistrails/tests/resources/terminator.vt differ
diff --git a/vistrails/tests/resources/test_abstraction.xml b/vistrails/tests/resources/test_abstraction.xml
new file mode 100644
index 0000000..9532b60
--- /dev/null
+++ b/vistrails/tests/resources/test_abstraction.xml
@@ -0,0 +1,227 @@
+<vistrail id="" name="" version="1.0.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/vistrail.xsd">
+ <action date="2007-08-27 17:13:44" id="1" prevId="0" session="" user="dakoop">
+ <add id="0" objectId="0" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="0" name="Float" namespace="" package="edu.utah.sci.vistrails.basic" version="" />
+ </add>
+ <add id="1" objectId="0" parentObjId="0" parentObjType="module" what="location">
+ <location id="0" x="62.0" y="180.0" />
+ </add>
+ </action>
+ <action date="2007-08-27 17:13:46" id="2" prevId="1" session="" user="dakoop">
+ <add id="2" objectId="1" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="1" name="Float" namespace="" package="edu.utah.sci.vistrails.basic" version="" />
+ </add>
+ <add id="3" objectId="1" parentObjId="1" parentObjType="module" what="location">
+ <location id="1" x="-109.0" y="146.0" />
+ </add>
+ </action>
+ <action date="2007-08-27 17:13:51" id="3" prevId="2" session="" user="dakoop">
+ <add id="4" objectId="2" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="2" name="List" namespace="" package="edu.utah.sci.vistrails.basic" version="" />
+ </add>
+ <add id="5" objectId="2" parentObjId="2" parentObjType="module" what="location">
+ <location id="2" x="18.0" y="85.0" />
+ </add>
+ </action>
+ <action date="2007-08-27 17:13:53" id="4" prevId="3" session="" user="dakoop">
+ <add id="6" objectId="3" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="3" name="List" namespace="" package="edu.utah.sci.vistrails.basic" version="" />
+ </add>
+ <add id="7" objectId="3" parentObjId="3" parentObjType="module" what="location">
+ <location id="3" x="17.0" y="-31.0" />
+ </add>
+ </action>
+ <action date="2007-08-27 17:13:57" id="5" prevId="4" session="" user="dakoop">
+ <add id="8" objectId="0" parentObjId="" parentObjType="" what="connection">
+ <connection id="0" />
+ </add>
+ <add id="9" objectId="1" parentObjId="0" parentObjType="connection" what="port">
+ <port id="1" moduleId="2" moduleName="List" name="head" signature="(edu.utah.sci.vistrails.basic:Module)" type="destination" />
+ </add>
+ <add id="10" objectId="0" parentObjId="0" parentObjType="connection" what="port">
+ <port id="0" moduleId="1" moduleName="Float" name="value" signature="(edu.utah.sci.vistrails.basic:Float)" type="source" />
+ </add>
+ </action>
+ <action date="2007-08-27 17:14:03" id="6" prevId="5" session="" user="dakoop">
+ <delete id="11" objectId="1" parentObjId="0" parentObjType="connection" what="port" />
+ <delete id="12" objectId="0" parentObjId="0" parentObjType="connection" what="port" />
+ <delete id="13" objectId="0" parentObjId="" parentObjType="" what="connection" />
+ </action>
+ <action date="2007-08-27 17:14:06" id="7" prevId="6" session="" user="dakoop">
+ <add id="14" objectId="1" parentObjId="" parentObjType="" what="connection">
+ <connection id="1" />
+ </add>
+ <add id="15" objectId="3" parentObjId="1" parentObjType="connection" what="port">
+ <port id="3" moduleId="3" moduleName="List" name="head" signature="(edu.utah.sci.vistrails.basic:Module)" type="destination" />
+ </add>
+ <add id="16" objectId="2" parentObjId="1" parentObjType="connection" what="port">
+ <port id="2" moduleId="1" moduleName="Float" name="value" signature="(edu.utah.sci.vistrails.basic:Float)" type="source" />
+ </add>
+ </action>
+ <action date="2007-08-27 17:14:09" id="8" prevId="7" session="" user="dakoop">
+ <add id="17" objectId="2" parentObjId="" parentObjType="" what="connection">
+ <connection id="2" />
+ </add>
+ <add id="18" objectId="5" parentObjId="2" parentObjType="connection" what="port">
+ <port id="5" moduleId="2" moduleName="List" name="head" signature="(edu.utah.sci.vistrails.basic:Module)" type="destination" />
+ </add>
+ <add id="19" objectId="4" parentObjId="2" parentObjType="connection" what="port">
+ <port id="4" moduleId="0" moduleName="Float" name="value" signature="(edu.utah.sci.vistrails.basic:Float)" type="source" />
+ </add>
+ </action>
+ <action date="2007-08-27 17:14:11" id="9" prevId="8" session="" user="dakoop">
+ <add id="20" objectId="3" parentObjId="" parentObjType="" what="connection">
+ <connection id="3" />
+ </add>
+ <add id="21" objectId="7" parentObjId="3" parentObjType="connection" what="port">
+ <port id="7" moduleId="3" moduleName="List" name="tail" signature="(edu.utah.sci.vistrails.basic:List)" type="destination" />
+ </add>
+ <add id="22" objectId="6" parentObjId="3" parentObjType="connection" what="port">
+ <port id="6" moduleId="2" moduleName="List" name="value" signature="(edu.utah.sci.vistrails.basic:List)" type="source" />
+ </add>
+ </action>
+ <action date="2012-08-02 17:59:40" id="10" prevId="9" session="2" user="tommy">
+ <annotation id="0" key="__description__" value="Upgrade" />
+ <delete id="23" objectId="3" parentObjId="1" parentObjType="connection" what="port" />
+ <delete id="24" objectId="2" parentObjId="1" parentObjType="connection" what="port" />
+ <delete id="25" objectId="1" parentObjId="" parentObjType="" what="connection" />
+ <delete id="26" objectId="7" parentObjId="3" parentObjType="connection" what="port" />
+ <delete id="27" objectId="6" parentObjId="3" parentObjType="connection" what="port" />
+ <delete id="28" objectId="3" parentObjId="" parentObjType="" what="connection" />
+ <delete id="29" objectId="3" parentObjId="3" parentObjType="module" what="location" />
+ <delete id="30" objectId="3" parentObjId="" parentObjType="" what="module" />
+ <delete id="31" objectId="1" parentObjId="1" parentObjType="module" what="location" />
+ <delete id="32" objectId="1" parentObjId="" parentObjType="" what="module" />
+ <delete id="33" objectId="5" parentObjId="2" parentObjType="connection" what="port" />
+ <delete id="34" objectId="4" parentObjId="2" parentObjType="connection" what="port" />
+ <delete id="35" objectId="2" parentObjId="" parentObjType="" what="connection" />
+ <delete id="36" objectId="2" parentObjId="2" parentObjType="module" what="location" />
+ <delete id="37" objectId="2" parentObjId="" parentObjType="" what="module" />
+ <delete id="38" objectId="0" parentObjId="0" parentObjType="module" what="location" />
+ <delete id="39" objectId="0" parentObjId="" parentObjType="" what="module" />
+ <add id="40" objectId="4" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="4" name="List" namespace="" package="edu.utah.sci.vistrails.basic" version="1.6" />
+ </add>
+ <add id="41" objectId="4" parentObjId="4" parentObjType="module" what="location">
+ <location id="4" x="17.0" y="-31.0" />
+ </add>
+ <add id="42" objectId="5" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="5" name="Float" namespace="" package="edu.utah.sci.vistrails.basic" version="1.6" />
+ </add>
+ <add id="43" objectId="5" parentObjId="5" parentObjType="module" what="location">
+ <location id="5" x="-109.0" y="146.0" />
+ </add>
+ <add id="44" objectId="6" parentObjId="" parentObjType="" what="connection">
+ <connection id="6" />
+ </add>
+ <add id="45" objectId="12" parentObjId="6" parentObjType="connection" what="port">
+ <port id="12" moduleId="5" moduleName="Float" name="value" signature="(edu.utah.sci.vistrails.basic:Float)" type="source" />
+ </add>
+ <add id="46" objectId="13" parentObjId="6" parentObjType="connection" what="port">
+ <port id="13" moduleId="4" moduleName="List" name="head" signature="(edu.utah.sci.vistrails.basic:Module)" type="destination" />
+ </add>
+ <add id="47" objectId="6" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="6" name="List" namespace="" package="edu.utah.sci.vistrails.basic" version="1.6" />
+ </add>
+ <add id="48" objectId="6" parentObjId="6" parentObjType="module" what="location">
+ <location id="6" x="18.0" y="85.0" />
+ </add>
+ <add id="49" objectId="7" parentObjId="" parentObjType="" what="connection">
+ <connection id="7" />
+ </add>
+ <add id="50" objectId="14" parentObjId="7" parentObjType="connection" what="port">
+ <port id="14" moduleId="6" moduleName="List" name="value" signature="(edu.utah.sci.vistrails.basic:List)" type="source" />
+ </add>
+ <add id="51" objectId="15" parentObjId="7" parentObjType="connection" what="port">
+ <port id="15" moduleId="4" moduleName="List" name="tail" signature="(edu.utah.sci.vistrails.basic:List)" type="destination" />
+ </add>
+ <add id="52" objectId="7" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="7" name="Float" namespace="" package="edu.utah.sci.vistrails.basic" version="1.6" />
+ </add>
+ <add id="53" objectId="7" parentObjId="7" parentObjType="module" what="location">
+ <location id="7" x="62.0" y="180.0" />
+ </add>
+ <add id="54" objectId="9" parentObjId="" parentObjType="" what="connection">
+ <connection id="9" />
+ </add>
+ <add id="55" objectId="18" parentObjId="9" parentObjType="connection" what="port">
+ <port id="18" moduleId="7" moduleName="Float" name="value" signature="(edu.utah.sci.vistrails.basic:Float)" type="source" />
+ </add>
+ <add id="56" objectId="19" parentObjId="9" parentObjType="connection" what="port">
+ <port id="19" moduleId="6" moduleName="List" name="head" signature="(edu.utah.sci.vistrails.basic:Module)" type="destination" />
+ </add>
+ </action>
+ <action date="2013-05-08 17:48:29" id="11" prevId="10" session="3" user="dakoop">
+ <annotation id="3" key="__description__" value="Upgrade" />
+ <delete id="57" objectId="12" parentObjId="6" parentObjType="connection" what="port" />
+ <delete id="58" objectId="13" parentObjId="6" parentObjType="connection" what="port" />
+ <delete id="59" objectId="6" parentObjId="" parentObjType="" what="connection" />
+ <delete id="60" objectId="14" parentObjId="7" parentObjType="connection" what="port" />
+ <delete id="61" objectId="15" parentObjId="7" parentObjType="connection" what="port" />
+ <delete id="62" objectId="7" parentObjId="" parentObjType="" what="connection" />
+ <delete id="63" objectId="4" parentObjId="4" parentObjType="module" what="location" />
+ <delete id="64" objectId="4" parentObjId="" parentObjType="" what="module" />
+ <delete id="65" objectId="18" parentObjId="9" parentObjType="connection" what="port" />
+ <delete id="66" objectId="19" parentObjId="9" parentObjType="connection" what="port" />
+ <delete id="67" objectId="9" parentObjId="" parentObjType="" what="connection" />
+ <delete id="68" objectId="7" parentObjId="7" parentObjType="module" what="location" />
+ <delete id="69" objectId="7" parentObjId="" parentObjType="" what="module" />
+ <delete id="70" objectId="5" parentObjId="5" parentObjType="module" what="location" />
+ <delete id="71" objectId="5" parentObjId="" parentObjType="" what="module" />
+ <delete id="72" objectId="6" parentObjId="6" parentObjType="module" what="location" />
+ <delete id="73" objectId="6" parentObjId="" parentObjType="" what="module" />
+ <add id="74" objectId="8" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="8" name="List" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="75" objectId="8" parentObjId="8" parentObjType="module" what="location">
+ <location id="8" x="17.0" y="-31.0" />
+ </add>
+ <add id="76" objectId="9" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="9" name="Float" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="77" objectId="9" parentObjId="9" parentObjType="module" what="location">
+ <location id="9" x="62.0" y="180.0" />
+ </add>
+ <add id="78" objectId="10" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="10" name="Float" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="79" objectId="10" parentObjId="10" parentObjType="module" what="location">
+ <location id="10" x="-109.0" y="146.0" />
+ </add>
+ <add id="80" objectId="13" parentObjId="" parentObjType="" what="connection">
+ <connection id="13" />
+ </add>
+ <add id="81" objectId="26" parentObjId="13" parentObjType="connection" what="port">
+ <port id="26" moduleId="10" moduleName="Float" name="value" signature="(org.vistrails.vistrails.basic:Float)" type="source" />
+ </add>
+ <add id="82" objectId="27" parentObjId="13" parentObjType="connection" what="port">
+ <port id="27" moduleId="8" moduleName="List" name="head" signature="(org.vistrails.vistrails.basic:Module)" type="destination" />
+ </add>
+ <add id="83" objectId="11" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="11" name="List" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
+ </add>
+ <add id="84" objectId="11" parentObjId="11" parentObjType="module" what="location">
+ <location id="11" x="18.0" y="85.0" />
+ </add>
+ <add id="85" objectId="14" parentObjId="" parentObjType="" what="connection">
+ <connection id="14" />
+ </add>
+ <add id="86" objectId="28" parentObjId="14" parentObjType="connection" what="port">
+ <port id="28" moduleId="11" moduleName="List" name="value" signature="(org.vistrails.vistrails.basic:List)" type="source" />
+ </add>
+ <add id="87" objectId="29" parentObjId="14" parentObjType="connection" what="port">
+ <port id="29" moduleId="8" moduleName="List" name="tail" signature="(org.vistrails.vistrails.basic:List)" type="destination" />
+ </add>
+ <add id="88" objectId="15" parentObjId="" parentObjType="" what="connection">
+ <connection id="15" />
+ </add>
+ <add id="89" objectId="30" parentObjId="15" parentObjType="connection" what="port">
+ <port id="30" moduleId="9" moduleName="Float" name="value" signature="(org.vistrails.vistrails.basic:Float)" type="source" />
+ </add>
+ <add id="90" objectId="31" parentObjId="15" parentObjType="connection" what="port">
+ <port id="31" moduleId="11" moduleName="List" name="head" signature="(org.vistrails.vistrails.basic:Module)" type="destination" />
+ </add>
+ </action>
+ <actionAnnotation actionId="9" date="2012-08-02 17:59:40" id="2" key="__upgrade__" user="tommy" value="10" />
+ <actionAnnotation actionId="10" date="2013-05-08 17:48:29" id="6" key="__upgrade__" user="dakoop" value="11" />
+</vistrail>
diff --git a/vistrails/tests/resources/test_alias.xml b/vistrails/tests/resources/test_alias.xml
new file mode 100644
index 0000000..e2c76af
--- /dev/null
+++ b/vistrails/tests/resources/test_alias.xml
@@ -0,0 +1,178 @@
+<?xml version="1.0" ?>
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+ <visTrail version="0.3.0">
+ <action date="22 Feb 2007 16:47:32" parent="0" time="1" user="manu" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="0" name="Float" x="-119.0" y="150.0"/>
+ </action>
+ <action date="22 Feb 2007 16:47:50" parent="1" time="2" user="manu" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="1" name="PythonSource" x="-98.0" y="11.0"/>
+ </action>
+ <action date="22 Feb 2007 16:47:55" parent="2" time="3" user="manu" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="6.0" dy="41.0" id="1"/>
+ </action>
+ <action date="22 Feb 2007 16:47:55" parent="3" time="4" user="manu" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="value" functionId="0" moduleId="0" parameter="<no description>" parameterId="0" type="Float" value="0.0"/>
+ </action>
+ <action date="22 Feb 2007 16:48:02" parent="4" time="5" user="manu" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="value" functionId="0" moduleId="0" parameter="<no description>" parameterId="0" type="Float" value="2.0"/>
+ </action>
+ <action date="22 Feb 2007 16:48:03" parent="5" time="6" user="manu" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="value" functionId="0" moduleId="0" parameter="<no description>" parameterId="0" type="Float" value="2.0"/>
+ </action>
+ <action date="22 Feb 2007 16:48:11" parent="6" time="7" user="manu" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="v1" function="value" functionId="0" moduleId="0" parameter="<no description>" parameterId="0" type="Float" value="2.0"/>
+ </action>
+ <action date="22 Feb 2007 16:51:14" parent="7" time="8" user="manu" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="-21.0" dy="37.0" id="0"/>
+ </action>
+ <action date="22 Feb 2007 16:51:14" parent="8" time="9" user="manu" what="addModulePort">
+ <notes>
+ None
+ </notes>
+ <addPort moduleId="1" portName="v1" portSpec="(Float)" portType="input"/>
+ </action>
+ <action date="22 Feb 2007 16:51:14" parent="9" time="10" user="manu" what="addModulePort">
+ <notes>
+ None
+ </notes>
+ <addPort moduleId="1" portName="v2" portSpec="(Float)" portType="input"/>
+ </action>
+ <action date="22 Feb 2007 16:51:15" parent="10" time="11" user="manu" what="addModulePort">
+ <notes>
+ None
+ </notes>
+ <addPort moduleId="1" portName="res" portSpec="(Float)" portType="output"/>
+ </action>
+ <action date="22 Feb 2007 16:51:15" parent="11" time="12" user="manu" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="source" functionId="0" moduleId="1" parameter="<no description>" parameterId="0" type="String" value="v1%20%3D%20self.getInputFromPort%28%22v1%22%29%0Av2%20%3D%20self.getInputFromPort%28%22v2%22%29%0A%0Aself.setResult%28%22res%22%2C%20v1%2Bv2%29"/>
+ </action>
+ <action date="22 Feb 2007 16:51:21" parent="12" time="13" user="manu" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="1" destinationModule="PythonSource" destinationPort="v1(Float)" id="0" sourceId="0" sourceModule="Float" sourcePort="value(Float)"/>
+ </action>
+ <action date="22 Feb 2007 16:51:32" parent="13" time="14" user="manu" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="-17.0" dy="-20.0" id="0"/>
+ </action>
+ <action date="22 Feb 2007 16:51:32" parent="14" time="15" user="manu" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="2" name="Float" x="-130.0" y="197.0"/>
+ </action>
+ <action date="22 Feb 2007 16:51:32" parent="15" time="16" user="manu" what="changeParameter">
+ <notes>
+ None
+ </notes>
+ <set alias="" function="value" functionId="0" moduleId="2" parameter="<no description>" parameterId="0" type="Float" value="2.0"/>
+ </action>
+ <action date="22 Feb 2007 16:51:32" parent="16" time="17" user="manu" what="changeAnnotation">
+ <notes>
+ None
+ </notes>
+ <set key="" moduleId="2" value=""/>
+ </action>
+ <action date="22 Feb 2007 16:52:21" parent="17" time="18" user="manu" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="67.0" dy="-28.0" id="2"/>
+ </action>
+ <action date="22 Feb 2007 16:52:21" parent="18" time="19" user="manu" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="1" destinationModule="PythonSource" destinationPort="v2(Float)" id="1" sourceId="2" sourceModule="Float" sourcePort="value(Float)"/>
+ </action>
+ <action date="22 Feb 2007 16:52:41" parent="19" time="20" user="manu" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="0.0" dy="-1.0" id="0"/>
+ <move dx="0.0" dy="-2.0" id="2"/>
+ </action>
+ <action date="22 Feb 2007 16:52:41" parent="20" time="21" user="manu" what="addModule">
+ <notes>
+ None
+ </notes>
+ <object cache="0" id="3" name="Float" x="-93.0" y="-85.0"/>
+ </action>
+ <action date="22 Feb 2007 16:52:45" parent="21" time="22" user="manu" what="moveModule">
+ <notes>
+ None
+ </notes>
+ <move dx="47.0" dy="52.0" id="3"/>
+ </action>
+ <action date="22 Feb 2007 16:52:45" parent="22" time="23" user="manu" what="addConnection">
+ <notes>
+ None
+ </notes>
+ <connect destinationId="3" destinationModule="Float" destinationPort="value(Float)" id="2" sourceId="1" sourceModule="PythonSource" sourcePort="res(Float)"/>
+ </action>
+ <tag name="alias" time="23"/>
+ </visTrail>
diff --git a/vistrails/tests/resources/test_archive.zip b/vistrails/tests/resources/test_archive.zip
new file mode 100644
index 0000000..80e524e
Binary files /dev/null and b/vistrails/tests/resources/test_archive.zip differ
diff --git a/vistrails/tests/resources/test_change_vistrail.xml b/vistrails/tests/resources/test_change_vistrail.xml
new file mode 100644
index 0000000..fc99e20
--- /dev/null
+++ b/vistrails/tests/resources/test_change_vistrail.xml
@@ -0,0 +1,386 @@
+<vistrail id="" name="" version="1.0.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/vistrail.xsd">
+ <action date="2007-07-16 15:56:55" id="1" prevId="0" session="" user="cscheid">
+ <add id="0" objectId="0" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="0" name="TestChangeVistrail" namespace="" package="edu.utah.sci.vistrails.console_mode_test" version="" />
+ </add>
+ <add id="1" objectId="0" parentObjId="0" parentObjType="module" what="location">
+ <location id="0" x="-12.0" y="36.0" />
+ </add>
+ </action>
+ <action date="2007-07-16 15:57:04" id="2" prevId="1" session="" user="cscheid">
+ <add id="2" objectId="0" parentObjId="0" parentObjType="module" what="function">
+ <function id="0" name="foo" pos="0" />
+ </add>
+ <add id="3" objectId="0" parentObjId="0" parentObjType="function" what="parameter">
+ <parameter alias="" id="0" name="<no description>" pos="0" type="Integer" val="" />
+ </add>
+ </action>
+ <action date="2007-07-16 15:57:05" id="3" prevId="2" session="" user="cscheid">
+ <change id="4" newObjId="1" oldObjId="0" parentObjId="0" parentObjType="function" what="parameter">
+ <parameter alias="" id="1" name="<no description>" pos="0" type="Integer" val="10" />
+ </change>
+ </action>
+ <action date="2007-07-19 16:38:29" id="4" prevId="3" session="" user="cscheid">
+ <delete id="5" objectId="1" parentObjId="0" parentObjType="function" what="parameter" />
+ <delete id="6" objectId="0" parentObjId="0" parentObjType="module" what="function" />
+ </action>
+ <action date="2011-06-30 15:14:47" id="5" prevId="3" session="0" user="emanuele">
+ <change id="7" newObjId="2" oldObjId="1" parentObjId="0" parentObjType="function" what="parameter">
+ <parameter alias="" id="2" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 15:14:47" id="6" prevId="4" session="1" user="emanuele">
+ <annotation id="2" key="__description__" value="Upgrade" />
+ <delete id="8" objectId="0" parentObjId="0" parentObjType="module" what="location" />
+ <delete id="9" objectId="0" parentObjId="" parentObjType="" what="module" />
+ <add id="10" objectId="1" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="1" name="TestChangeVistrail" namespace="" package="edu.utah.sci.vistrails.console_mode_test" version="0.9.0" />
+ </add>
+ <add id="11" objectId="1" parentObjId="1" parentObjType="module" what="location">
+ <location id="1" x="-12.0" y="36.0" />
+ </add>
+ </action>
+ <action date="2011-06-30 15:14:47" id="7" prevId="6" session="1" user="emanuele">
+ <add id="12" objectId="1" parentObjId="1" parentObjType="module" what="function">
+ <function id="1" name="foo" pos="0" />
+ </add>
+ <add id="13" objectId="3" parentObjId="1" parentObjType="function" what="parameter">
+ <parameter alias="" id="3" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 15:30:25" id="8" prevId="3" session="2" user="emanuele">
+ <annotation id="4" key="__description__" value="Upgrade" />
+ <delete id="14" objectId="0" parentObjId="0" parentObjType="module" what="location" />
+ <delete id="15" objectId="1" parentObjId="0" parentObjType="function" what="parameter" />
+ <delete id="16" objectId="0" parentObjId="0" parentObjType="module" what="function" />
+ <delete id="17" objectId="0" parentObjId="" parentObjType="" what="module" />
+ <add id="18" objectId="2" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="2" name="TestChangeVistrail" namespace="" package="edu.utah.sci.vistrails.console_mode_test" version="0.9.0" />
+ </add>
+ <add id="19" objectId="2" parentObjId="2" parentObjType="module" what="function">
+ <function id="2" name="foo" pos="0" />
+ </add>
+ <add id="20" objectId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="4" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="10" />
+ </add>
+ <add id="21" objectId="2" parentObjId="2" parentObjType="module" what="location">
+ <location id="2" x="-12.0" y="36.0" />
+ </add>
+ </action>
+ <action date="2011-06-30 15:30:25" id="9" prevId="8" session="2" user="emanuele">
+ <change id="22" newObjId="5" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="5" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 15:30:25" id="10" prevId="6" session="3" user="emanuele">
+ <add id="23" objectId="3" parentObjId="1" parentObjType="module" what="function">
+ <function id="3" name="foo" pos="0" />
+ </add>
+ <add id="24" objectId="6" parentObjId="3" parentObjType="function" what="parameter">
+ <parameter alias="" id="6" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 15:30:47" id="11" prevId="8" session="4" user="emanuele">
+ <change id="25" newObjId="7" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="7" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 15:30:47" id="12" prevId="6" session="5" user="emanuele">
+ <add id="26" objectId="4" parentObjId="1" parentObjType="module" what="function">
+ <function id="4" name="foo" pos="0" />
+ </add>
+ <add id="27" objectId="8" parentObjId="4" parentObjType="function" what="parameter">
+ <parameter alias="" id="8" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 15:32:51" id="13" prevId="8" session="6" user="emanuele">
+ <change id="28" newObjId="9" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="9" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 15:32:51" id="14" prevId="6" session="7" user="emanuele">
+ <add id="29" objectId="5" parentObjId="1" parentObjType="module" what="function">
+ <function id="5" name="foo" pos="0" />
+ </add>
+ <add id="30" objectId="10" parentObjId="5" parentObjType="function" what="parameter">
+ <parameter alias="" id="10" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 15:35:57" id="15" prevId="8" session="8" user="emanuele">
+ <change id="31" newObjId="11" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="11" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 15:35:57" id="16" prevId="6" session="9" user="emanuele">
+ <add id="32" objectId="6" parentObjId="1" parentObjType="module" what="function">
+ <function id="6" name="foo" pos="0" />
+ </add>
+ <add id="33" objectId="12" parentObjId="6" parentObjType="function" what="parameter">
+ <parameter alias="" id="12" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 15:41:37" id="17" prevId="8" session="10" user="emanuele">
+ <change id="34" newObjId="13" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="13" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 15:41:37" id="18" prevId="6" session="11" user="emanuele">
+ <add id="35" objectId="7" parentObjId="1" parentObjType="module" what="function">
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+ <action date="2011-06-30 16:01:31" id="26" prevId="6" session="19" user="emanuele">
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+ </action>
+ <action date="2011-06-30 16:02:57" id="27" prevId="8" session="20" user="emanuele">
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+ </action>
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+ </add>
+ </action>
+ <action date="2011-06-30 16:23:24" id="31" prevId="8" session="24" user="emanuele">
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+ </change>
+ </action>
+ <action date="2011-06-30 16:23:24" id="32" prevId="6" session="25" user="emanuele">
+ <add id="56" objectId="14" parentObjId="1" parentObjType="module" what="function">
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+ <parameter alias="" id="28" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 16:29:05" id="33" prevId="8" session="26" user="emanuele">
+ <change id="58" newObjId="29" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
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+ </change>
+ </action>
+ <action date="2011-06-30 16:29:05" id="34" prevId="6" session="27" user="emanuele">
+ <add id="59" objectId="15" parentObjId="1" parentObjType="module" what="function">
+ <function id="15" name="foo" pos="0" />
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+ <parameter alias="" id="30" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 16:46:53" id="35" prevId="8" session="28" user="emanuele">
+ <change id="61" newObjId="31" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="31" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 16:46:53" id="36" prevId="6" session="29" user="emanuele">
+ <add id="62" objectId="16" parentObjId="1" parentObjType="module" what="function">
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+ </action>
+ <action date="2011-06-30 16:57:25" id="37" prevId="8" session="30" user="emanuele">
+ <change id="64" newObjId="33" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
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+ </change>
+ </action>
+ <action date="2011-06-30 16:57:25" id="38" prevId="6" session="31" user="emanuele">
+ <add id="65" objectId="17" parentObjId="1" parentObjType="module" what="function">
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+ <parameter alias="" id="34" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 17:07:47" id="39" prevId="8" session="32" user="emanuele">
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+ </change>
+ </action>
+ <action date="2011-06-30 17:07:47" id="40" prevId="6" session="33" user="emanuele">
+ <add id="68" objectId="18" parentObjId="1" parentObjType="module" what="function">
+ <function id="18" name="foo" pos="0" />
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+ <add id="69" objectId="36" parentObjId="18" parentObjType="function" what="parameter">
+ <parameter alias="" id="36" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 17:09:48" id="41" prevId="8" session="34" user="emanuele">
+ <change id="70" newObjId="37" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="37" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 17:09:48" id="42" prevId="6" session="35" user="emanuele">
+ <add id="71" objectId="19" parentObjId="1" parentObjType="module" what="function">
+ <function id="19" name="foo" pos="0" />
+ </add>
+ <add id="72" objectId="38" parentObjId="19" parentObjType="function" what="parameter">
+ <parameter alias="" id="38" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 17:13:14" id="43" prevId="8" session="36" user="emanuele">
+ <change id="73" newObjId="39" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="39" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 17:13:15" id="44" prevId="6" session="37" user="emanuele">
+ <add id="74" objectId="20" parentObjId="1" parentObjType="module" what="function">
+ <function id="20" name="foo" pos="0" />
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+ <parameter alias="" id="40" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 17:21:57" id="45" prevId="8" session="38" user="emanuele">
+ <change id="76" newObjId="41" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="41" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 17:21:57" id="46" prevId="6" session="39" user="emanuele">
+ <add id="77" objectId="21" parentObjId="1" parentObjType="module" what="function">
+ <function id="21" name="foo" pos="0" />
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+ <parameter alias="" id="42" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 17:23:07" id="47" prevId="8" session="40" user="emanuele">
+ <change id="79" newObjId="43" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
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+ </change>
+ </action>
+ <action date="2011-06-30 17:23:08" id="48" prevId="6" session="41" user="emanuele">
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+ <parameter alias="" id="44" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 17:25:56" id="49" prevId="8" session="42" user="emanuele">
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+ </change>
+ </action>
+ <action date="2011-06-30 17:25:57" id="50" prevId="6" session="43" user="emanuele">
+ <add id="83" objectId="23" parentObjId="1" parentObjType="module" what="function">
+ <function id="23" name="foo" pos="0" />
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+ <parameter alias="" id="46" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 17:29:30" id="51" prevId="8" session="44" user="emanuele">
+ <change id="85" newObjId="47" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="47" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 17:29:30" id="52" prevId="6" session="45" user="emanuele">
+ <add id="86" objectId="24" parentObjId="1" parentObjType="module" what="function">
+ <function id="24" name="foo" pos="0" />
+ </add>
+ <add id="87" objectId="48" parentObjId="24" parentObjType="function" what="parameter">
+ <parameter alias="" id="48" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 17:30:46" id="53" prevId="8" session="46" user="emanuele">
+ <change id="88" newObjId="49" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="49" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 17:30:46" id="54" prevId="6" session="47" user="emanuele">
+ <add id="89" objectId="25" parentObjId="1" parentObjType="module" what="function">
+ <function id="25" name="foo" pos="0" />
+ </add>
+ <add id="90" objectId="50" parentObjId="25" parentObjType="function" what="parameter">
+ <parameter alias="" id="50" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <action date="2011-06-30 17:31:14" id="55" prevId="8" session="48" user="emanuele">
+ <change id="91" newObjId="51" oldObjId="4" parentObjId="2" parentObjType="function" what="parameter">
+ <parameter alias="" id="51" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="11" />
+ </change>
+ </action>
+ <action date="2011-06-30 17:31:14" id="56" prevId="6" session="49" user="emanuele">
+ <add id="92" objectId="26" parentObjId="1" parentObjType="module" what="function">
+ <function id="26" name="foo" pos="0" />
+ </add>
+ <add id="93" objectId="52" parentObjId="26" parentObjType="function" what="parameter">
+ <parameter alias="" id="52" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Integer" val="1" />
+ </add>
+ </action>
+ <actionAnnotation actionId="3" date="" id="0" key="__tag__" user="" value="v1" />
+ <actionAnnotation actionId="4" date="" id="1" key="__tag__" user="" value="v2" />
+ <actionAnnotation actionId="4" date="2011-06-30 15:14:47" id="3" key="__upgrade__" user="emanuele" value="6" />
+ <actionAnnotation actionId="3" date="2011-06-30 15:30:25" id="5" key="__upgrade__" user="emanuele" value="8" />
+</vistrail>
diff --git a/vistrails/tests/resources/test_ticket_73.xml b/vistrails/tests/resources/test_ticket_73.xml
new file mode 100644
index 0000000..a26ea43
--- /dev/null
+++ b/vistrails/tests/resources/test_ticket_73.xml
@@ -0,0 +1,46 @@
+<?xml version="1.0" ?>
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<vistrail dbHost="" dbName="" dbPort="" id="" name="" version="0.5.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/vistrail.xsd">
+ <action date="2007-07-23 15:57:26" id="1" prevId="0" user="cscheid">
+ <add id="0" objectId="0" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="0" name="different name"/>
+ </add>
+ <add id="1" objectId="0" parentObjId="0" parentObjType="module" what="location">
+ <location id="0" x="-30.0" y="-12.0"/>
+ </add>
+ </action>
+</vistrail>
diff --git a/vistrails/tests/resources/triangle_count.vt b/vistrails/tests/resources/triangle_count.vt
new file mode 100644
index 0000000..33950e5
Binary files /dev/null and b/vistrails/tests/resources/triangle_count.vt differ
diff --git a/vistrails/tests/resources/visvar-1.0.2.vt b/vistrails/tests/resources/visvar-1.0.2.vt
new file mode 100644
index 0000000..0d1e08c
Binary files /dev/null and b/vistrails/tests/resources/visvar-1.0.2.vt differ
diff --git a/vistrails/tests/resources/visvar-1.0.3.vt b/vistrails/tests/resources/visvar-1.0.3.vt
new file mode 100644
index 0000000..72171c0
Binary files /dev/null and b/vistrails/tests/resources/visvar-1.0.3.vt differ
diff --git a/vistrails/tests/resources/vtk.xml b/vistrails/tests/resources/vtk.xml
new file mode 100644
index 0000000..3f11dbc
--- /dev/null
+++ b/vistrails/tests/resources/vtk.xml
@@ -0,0 +1,3840 @@
+<?xml version="1.0" ?>
+<!--###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+-->
+<vistrail dbHost="" dbName="" dbPort="" id="" name="" version="0.5.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/vistrail.xsd">
+ <action date="2006-09-21 14:07:44" id="2" prevId="0" user="hvo">
+ <add id="0" objectId="0" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="0" name="vtkDataSetReader"/>
+ </add>
+ <add id="1" objectId="0" parentObjId="0" parentObjType="module" what="location">
+ <location id="0" x="-2.94277920552" y="1.77656675749"/>
+ </add>
+ </action>
+ <action date="2006-09-21 14:07:49" id="3" prevId="2" user="hvo">
+ <change id="2" newObjId="1" oldObjId="0" parentObjId="0" parentObjType="module" what="location">
+ <location id="1" x="3.23342404537" y="82.0672161716"/>
+ </change>
+ </action>
+ <action date="2006-09-22 03:52:04" id="4" prevId="3" user="hvo">
+ <add id="3" objectId="1" parentObjId="" parentObjType="" what="module">
+ <module cache="1" id="1" name="vtkDataSetMapper"/>
+ </add>
+ <add id="4" objectId="2" parentObjId="1" parentObjType="module" what="location">
+ <location id="2" x="-14.284824029" y="-23.0422741235"/>
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+ </change>
+ </action>
+ <action date="2007-07-23 11:01:03" id="407" prevId="406" user="cscheid">
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+ <delete id="1040" objectId="67" parentObjId="" parentObjType="" what="connection"/>
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+ <delete id="1042" objectId="138" parentObjId="69" parentObjType="connection" what="port"/>
+ <delete id="1043" objectId="69" parentObjId="" parentObjType="" what="connection"/>
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+ <delete id="1045" objectId="371" parentObjId="44" parentObjType="function" what="parameter"/>
+ <delete id="1046" objectId="44" parentObjId="65" parentObjType="module" what="function"/>
+ <delete id="1047" objectId="65" parentObjId="" parentObjType="" what="module"/>
+ </action>
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+ <module cache="1" id="67" name="FileSink"/>
+ </add>
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+ <location id="254" x="-22.5524013263" y="-205.790662102"/>
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+ </action>
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+ </add>
+ <add id="1054" objectId="140" parentObjId="70" parentObjType="connection" what="port">
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+ </add>
+ </action>
+ <action date="2007-07-23 11:01:15" id="412" prevId="411" user="cscheid">
+ <add id="1055" objectId="71" parentObjId="" parentObjType="" what="connection">
+ <connection id="71"/>
+ </add>
+ <add id="1056" objectId="143" parentObjId="71" parentObjType="connection" what="port">
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+ </add>
+ <add id="1057" objectId="142" parentObjId="71" parentObjType="connection" what="port">
+ <port id="142" moduleId="66" moduleName="PythonSource" sig="filename(String)" type="source"/>
+ </add>
+ </action>
+ <tag name="Four Cells" time="368"/>
+ <tag name="Implicit Plane Clipper" time="322"/>
+ <tag name="Hidden Port" time="182"/>
+ <tag name="Double Renderer" time="85"/>
+ <tag name="vtk_book_3rd_p189" time="215"/>
+ <tag name="writer_test_filesink" time="412"/>
+ <tag name="Single Renderer" time="43"/>
+ <tag name="writer_test" time="406"/>
+</vistrail>
diff --git a/vistrails/tests/resources/vtkfiles/vtk_quadric_writer_test.vtk b/vistrails/tests/resources/vtkfiles/vtk_quadric_writer_test.vtk
new file mode 100644
index 0000000..6da8f6f
--- /dev/null
+++ b/vistrails/tests/resources/vtkfiles/vtk_quadric_writer_test.vtk
@@ -0,0 +1,9001 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
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+
diff --git a/vistrails/tests/run_on_mac.sh b/vistrails/tests/run_on_mac.sh
new file mode 100755
index 0000000..de4deda
--- /dev/null
+++ b/vistrails/tests/run_on_mac.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+if [ -z "$1" ]
+then
+ echo "usage: $0 <app_path>"
+ exit 65
+fi
+
+THIS_DIR=`dirname $0`
+PYTHON_EXEC_PATH="Contents/MacOS/python"
+RESOURCES_PATH="Contents/Resources"
+
+if [ ! -e "$1/$RESOURCES_PATH" ]
+then
+ echo "$1/$RESOURCES_PATH does not exist"
+ exit 66
+fi
+
+if [ ! -e "$1/$PYTHON_EXEC_PATH" ]
+then
+ echo "$1/$PYTHON_EXEC_PATH does not exist"
+ exit 67
+fi
+
+PYTHONHOME="$1/$RESOURCES_PATH" ${1}/${PYTHON_EXEC_PATH} ${THIS_DIR}/runtestsuite.py
diff --git a/vistrails/tests/runtestsuite.py b/vistrails/tests/runtestsuite.py
new file mode 100755
index 0000000..8c9f055
--- /dev/null
+++ b/vistrails/tests/runtestsuite.py
@@ -0,0 +1,484 @@
+#!/usr/bin/env python
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+
+"""Runs all tests available in VisTrails modules by importing all of
+them, stealing the classes that look like unit tests, and running
+all of them.
+
+runtestsuite.py also reports all VisTrails modules that don't export
+any unit tests, as a crude measure of code coverage.
+
+"""
+
+# First, import unittest, replacing it with unittest2 if necessary
+import sys
+try:
+ import unittest2
+except ImportError:
+ pass
+else:
+ sys.modules['unittest'] = unittest2
+import unittest
+
+import atexit
+from distutils.version import LooseVersion
+#import doctest
+import os
+import traceback
+import os.path
+import optparse
+from optparse import OptionParser
+import platform
+import shutil
+import tempfile
+
+# Makes sure we can import modules as if we were running VisTrails
+# from the root directory
+_this_dir = os.path.dirname(os.path.realpath(__file__))
+root_directory = os.path.realpath(os.path.join(_this_dir, '..'))
+sys.path.insert(0, os.path.realpath(os.path.join(root_directory, '..')))
+
+# Use a different temporary directory
+test_temp_dir = tempfile.mkdtemp(prefix='vt_testsuite_')
+tempfile.tempdir = test_temp_dir
+ at atexit.register
+def clean_tempdir():
+ nb_dirs = 0
+ nb_files = 0
+ for f in os.listdir(test_temp_dir):
+ if os.path.isdir(f):
+ nb_dirs += 1
+ else:
+ nb_files += 1
+ if nb_dirs > 0 or nb_files > 0:
+ sys.stdout.write("Warning: %d dirs and %d files were left behind in "
+ "tempdir, cleaning up\n" % (nb_dirs, nb_files))
+ shutil.rmtree(test_temp_dir, ignore_errors=True)
+
+def setNewPyQtAPI():
+ try:
+ import sip
+ # We now use the new PyQt API - IPython needs it
+ sip.setapi('QString', 2)
+ sip.setapi('QVariant', 2)
+ except:
+ print "Could not set PyQt API, is PyQt4 installed?"
+setNewPyQtAPI()
+
+import vistrails.tests
+import vistrails.core
+import vistrails.core.db.io
+import vistrails.core.db.locator
+import vistrails.gui.application
+from vistrails.core.system import vistrails_root_directory, \
+ vistrails_examples_directory
+
+###############################################################################
+# Testing Examples
+
+EXAMPLES_PATH = vistrails_examples_directory()
+#dictionary of examples that will be run with the workflows that will be ignored
+VT_EXAMPLES = { 'EMBOSS_webservices.vt': ["ProphetOutput"],
+ 'KEGGPathway.vt': [],
+ 'KEGG_SearchEntities_webservice.vt': [],
+ 'KEGG_webservices.vt': [],
+ 'brain_vistrail.vt': [],
+ 'chebi_webservice.vt': [],
+ 'head.vt': [],
+ 'infovis.vt': [],
+ 'noaa_webservices.vt': [],
+ 'offscreen.vt': [],
+ 'plot.vt': [],
+ 'spx.vt': [],
+ 'structure_or_id_webservice.vt': [],
+ 'terminator.vt': ["Isosurface Script"],
+ 'triangle_area.vt': [],
+ 'vtk.vt': [],
+ 'vtk_book_3rd_p189.vt': ["quadric", "SmapleFunction",
+ "Almost there"],
+ 'vtk_book_3rd_p193.vt': ["modules", "connections",
+ "lookup table"],
+ 'vtk_http.vt': [],
+ }
+
+
+###############################################################################
+# Utility
+
+def sub_print(s, overline=False):
+ """Prints line with underline (and optionally overline) ASCII dashes."""
+ if overline:
+ print "-" * len(s)
+ print s
+ print "-" * len(s)
+
+###############################################################################
+
+usage = "Usage: %prog [options] [module1 module2 ...]"
+parser = OptionParser(usage=usage)
+parser.add_option("-V", "--verbose", action="store", type="int",
+ default=0, dest="verbose",
+ help="set verboseness level(0--2, default=0, "
+ "higher means more verbose)")
+parser.add_option("-e", "--examples", action="store_true",
+ default=False,
+ help="run vistrails examples")
+parser.add_option("-i", "--images", action="store_true",
+ default=False,
+ help="perform image comparisons")
+parser.add_option("--installbundles", action='store_true',
+ default=False,
+ help=("Attempt to install missing Python packages "
+ "automatically"))
+parser.add_option("-S", "--startup", action="store", type="str", default=None,
+ dest="dotVistrails",
+ help="Set startup file (default is temporary directory)")
+
+(options, args) = parser.parse_args()
+# remove empty strings
+args = filter(len, args)
+verbose = options.verbose
+test_examples = options.examples
+test_images = options.images
+installbundles = options.installbundles
+dotVistrails = options.dotVistrails
+test_modules = None
+if len(args) > 0:
+ test_modules = args
+else:
+ test_images = True
+
+def module_filter(name):
+ if test_modules is None:
+ return True
+ for mod in test_modules:
+ if name.startswith(mod):
+ return True
+ return False
+
+###############################################################################
+# reinitializing arguments and options so VisTrails does not try parsing them
+sys.argv = sys.argv[:1]
+
+# creates the app so that testing can happen
+
+# We need the windows so we can test events, etc.
+optionsDict = {
+ 'interactiveMode': True,
+ 'nologger': True,
+ 'singleInstance': False,
+ 'fixedSpreadsheetCells': True,
+ 'installBundles': installbundles,
+ 'enablePackagesSilently': True,
+ 'handlerDontAsk': True,
+ }
+if dotVistrails:
+ optionsDict['dotVistrails'] = dotVistrails
+else:
+ optionsDict['spawned'] = True
+v = vistrails.gui.application.start_application(optionsDict)
+if v != 0:
+ app = vistrails.gui.application.get_vistrails_application()
+ if app:
+ app.finishSession()
+ sys.exit(v)
+
+# disable first vistrail
+app = vistrails.gui.application.get_vistrails_application()
+app.builderWindow.auto_view = False
+app.builderWindow.close_all_vistrails(True)
+
+print "Test Suite for VisTrails"
+print "Running on %s" % ', '.join(platform.uname())
+print "Python is %s" % sys.version
+try:
+ from PyQt4 import QtCore
+ print "Using PyQt4 %s with Qt %s" % (QtCore.PYQT_VERSION_STR, QtCore.qVersion())
+except ImportError:
+ print "PyQt4 not available"
+for pkg in ('numpy', 'scipy', 'matplotlib'):
+ try:
+ ipkg = __import__(pkg, globals(), locals(), [], -1)
+ print "Using %s %s" % (pkg, ipkg.__version__)
+ except ImportError:
+ print "%s not available" % pkg
+try:
+ import vtk
+ print "Using vtk %s" % vtk.vtkVersion().GetVTKVersion()
+except ImportError:
+ print "vtk not available"
+
+
+print ""
+
+tests_passed = True
+
+main_test_suite = unittest.TestSuite()
+test_loader = unittest.TestLoader()
+
+if test_modules:
+ sub_print("Trying to import some of the modules")
+else:
+ sub_print("Trying to import all modules")
+
+for (p, subdirs, files) in os.walk(root_directory):
+ # skip subversion subdirectories
+ if p.find('.svn') != -1 or p.find('.git') != -1 :
+ continue
+ for filename in files:
+ # skip files that don't look like VisTrails python modules
+ if not filename.endswith('.py'):
+ continue
+ module = os.path.join("vistrails", p[len(root_directory)+1:],
+ filename[:-3])
+ if (module.startswith(os.sep) or
+ ('#' in module)):
+ continue
+
+ # use qualified import names with periods instead of
+ # slashes to avoid duplicates in sys.modules
+ module = module.replace('/','.')
+ module = module.replace('\\','.')
+ if module.endswith('__init__'):
+ module = module[:-9]
+
+ if not module_filter(module):
+ continue
+ if module.startswith('vistrails.tests.run'):
+ continue
+ if module.startswith('vistrails.tests.resources'):
+ continue
+ if ('.system.' in module and not
+ module.endswith('__init__')):
+ continue
+
+ msg = ("%s %s |" % (" " * (40 - len(module)), module))
+
+ m = None
+ try:
+ if '.' in module:
+ m = __import__(module, globals(), locals(), ['foo'])
+ else:
+ m = __import__(module)
+ except vistrails.tests.NotModule:
+ if verbose >= 1:
+ print "Skipping %s, not an importable module" % filename
+ continue
+ except:
+ print msg, "ERROR: Could not import module!"
+ if verbose >= 1:
+ traceback.print_exc(file=sys.stdout)
+ continue
+
+ # Load the unittest TestCases
+ suite = test_loader.loadTestsFromModule(m)
+
+ # Load the doctests
+ #try:
+ # suite.addTests(doctest.DocTestSuite(m))
+ #except ValueError:
+ # pass # No doctest is fine, we check that some tests exist later
+ # The doctests are currently opt-in; a load_tests method can be
+ # defined to build a DocTestSuite
+ # This is because some modules have interpreter-formatted examples that
+ # are NOT doctests, and because mining the codebase for doctests is
+ # painfully slow
+
+ main_test_suite.addTests(suite)
+
+ if suite.countTestCases() == 0 and verbose >= 1:
+ print msg, "WARNING: %s has no tests!" % filename
+ elif verbose >= 2:
+ print msg, "Ok: %d test cases." % suite.countTestCases()
+
+sub_print("Imported modules. Running %d tests%s..." % (
+ main_test_suite.countTestCases(),
+ ", and thumbnails comparison" if test_images else ''),
+ overline=True)
+
+############## TEST VISTRAIL IMAGES ####################
+# Compares thumbnails with the generated images to detect broken visualizations
+
+image_tests = [("terminator.vt", [("terminator_isosurface", "Isosurface"),
+ ("terminator_VRSW", "Volume Rendering SW"),
+ ("terminator_CPSW", "Clipping Plane SW"),
+ ("terminator_CRSW", "Combined Rendering SW"),
+ ("terminator_ISSW", "Image Slices SW")])
+ ]
+compare_use_vtk = False
+try:
+ import vtk
+ if LooseVersion(vtk.vtkVersion().GetVTKVersion()) >= LooseVersion('5.8.0'):
+ compare_use_vtk = True
+except ImportError:
+ pass
+if compare_use_vtk:
+ def compare_thumbnails(prev, next):
+ #vtkImageDifference assumes RGB, so strip alpha
+ def removeAlpha(file):
+ freader = vtk.vtkPNGReader()
+ freader.SetFileName(file)
+ removealpha = vtk.vtkImageExtractComponents()
+ removealpha.SetComponents(0,1,2)
+ removealpha.SetInputConnection(freader.GetOutputPort())
+ removealpha.Update()
+ return removealpha.GetOutput()
+ #do the image comparison
+ a = removeAlpha(prev)
+ b = removeAlpha(next)
+ idiff = vtk.vtkImageDifference()
+ idiff.SetInput(a)
+ idiff.SetImage(b)
+ idiff.Update()
+ return idiff.GetThresholdedError()
+else:
+ try:
+ from scipy.misc import imread
+ except ImportError:
+ imread = None
+ if test_images:
+ print "Warning: old VTK version detected, NOT comparing thumbnails"
+ if imread is not None:
+ def compare_thumbnails(prev, next):
+ prev_img = imread(prev)
+ next_img = imread(next)
+ assert len(prev_img.shape) == 3
+ assert len(next_img.shape) == 3
+ if prev_img.shape[:2] == next_img.shape[:2]:
+ return 0
+ else:
+ return float('Inf')
+ else:
+ def compare_thumbnails(prev, next):
+ if os.path.isfile(prev) and os.path.isfile(next):
+ return 0
+ else:
+ return float('Inf')
+
+def image_test_generator(vtfile, version):
+ from vistrails.core.db.locator import FileLocator
+ from vistrails.core.db.io import load_vistrail
+ import vistrails.core.console_mode
+ def test(self):
+ try:
+ errs = []
+ filename = os.path.join(EXAMPLES_PATH, vtfile)
+ locator = FileLocator(os.path.abspath(filename))
+ (v, abstractions, thumbnails, mashups) = load_vistrail(locator)
+ errs = vistrails.core.console_mode.run(
+ [(locator, version)],
+ update_vistrail=False,
+ extra_info={'compare_thumbnails': compare_thumbnails})
+ if len(errs) > 0:
+ for err in errs:
+ print(" *** Error in %s:%s:%s -- %s" % err)
+ self.fail(str(err))
+ except Exception, e:
+ self.fail(str(e))
+ return test
+
+class TestVistrailImages(unittest.TestCase):
+ pass
+
+if test_images:
+ for vt, t in image_tests:
+ for name, version in t:
+ test_name = 'test_%s' % name
+ test = image_test_generator(vt, version)
+ setattr(TestVistrailImages, test_name, test)
+ main_test_suite.addTest(TestVistrailImages(test_name))
+
+############## RUN TEST SUITE ####################
+
+result = unittest.TextTestRunner(verbosity=max(verbose, 1)).run(main_test_suite)
+
+if not result.wasSuccessful():
+ tests_passed = False
+
+sub_print("Tests finished.", overline=True)
+
+if test_examples:
+ import vistrails.core.console_mode
+ sub_print("Testing examples:")
+ summary = {}
+ nworkflows = 0
+ nvtfiles = 0
+ for vtfile in VT_EXAMPLES.keys():
+ try:
+ errs = []
+ filename = os.path.join(EXAMPLES_PATH,
+ vtfile)
+ print filename
+ locator = vistrails.core.db.locator.FileLocator(os.path.abspath(filename))
+ (v, abstractions, thumbnails, mashups) = vistrails.core.db.io.load_vistrail(locator)
+ w_list = []
+ for version,tag in v.get_tagMap().iteritems():
+ if tag not in VT_EXAMPLES[vtfile]:
+ w_list.append((locator,version))
+ nworkflows += 1
+ if len(w_list) > 0:
+ errs = vistrails.core.console_mode.run(w_list, update_vistrail=False)
+ summary[vtfile] = errs
+ except Exception, e:
+ errs.append((vtfile,"None", "None", str(e)))
+ summary[vtfile] = errs
+ nvtfiles += 1
+
+ print "-" * 79
+ print "Summary of Examples: %s workflows in %s vistrail files" % (
+ nworkflows, nvtfiles)
+ print ""
+ errors = False
+ for vtfile, errs in summary.iteritems():
+ print vtfile
+ if len(errs) > 0:
+ for err in errs:
+ print(" *** Error in %s:%s:%s -- %s" % err)
+ errors = True
+ else:
+ print " Ok."
+ print "-" * 79
+ if errors:
+ tests_passed = False
+ sub_print("There were errors. See summary for more information")
+ else:
+ sub_print("Examples ran successfully.")
+
+vistrails.gui.application.get_vistrails_application().finishSession()
+vistrails.gui.application.stop_application()
+
+# Test Runners can use the return value to know if the tests passed
+sys.exit(0 if tests_passed else 1)
diff --git a/vistrails/tests/utils.py b/vistrails/tests/utils.py
new file mode 100644
index 0000000..dfbaa55
--- /dev/null
+++ b/vistrails/tests/utils.py
@@ -0,0 +1,212 @@
+import contextlib
+
+from vistrails.core.modules.vistrails_module import Module
+
+
+def execute(modules, connections=[], add_port_specs=[], enable_pkg=True):
+ """Build a pipeline and execute it.
+
+ This is useful to simply build a pipeline in a test case, and run it. When
+ doing that, intercept_result() can be used to check the results of each
+ module.
+
+ modules is a list of module tuples describing the modules to be created,
+ with the following format:
+ [('ModuleName', 'package.identifier', [
+ # Functions
+ ('port_name', [
+ # Function parameters
+ ('Signature', 'value-as-string'),
+ ]),
+ ])]
+
+ connections is a list of tuples describing the connections to make, with
+ the following format:
+ [
+ (source_module_index, 'source_port_name',
+ dest_module_index, 'dest_module_name'),
+ ]
+
+ add_port_specs is a list of specs to add to modules, with the following
+ format:
+ [
+ (mod_id, 'input'/'output', 'portname',
+ '(port_sig)'),
+ ]
+ It is useful to test modules that can have custom ports through a
+ configuration widget.
+
+ The function returns the 'errors' dict it gets from the interpreter, so you
+ should use a construct like self.assertFalse(execute(...)) if the execution
+ is not supposed to fail.
+
+
+ For example, this creates (and runs) an Integer module with its value set
+ to 44, connected to a PythonCalc module, connected to a StandardOutput:
+
+ self.assertFalse(execute([
+ ('Float', 'org.vistrails.vistrails.basic', [
+ ('value', [('Float', '44.0')]),
+ ]),
+ ('PythonCalc', 'org.vistrails.vistrails.pythoncalc', [
+ ('value2', [('Float', '2.0')]),
+ ('op', [('String', '-')]),
+ ]),
+ ('StandardOutput', 'org.vistrails.vistrails.basic', []),
+ ],
+ [
+ (0, 'value', 1, 'value1'),
+ (1, 'value', 2, 'value'),
+ ]))
+ """
+ from vistrails.core.db.locator import XMLFileLocator
+ from vistrails.core.modules.module_registry import MissingPackage
+ from vistrails.core.packagemanager import get_package_manager
+ from vistrails.core.utils import DummyView
+ from vistrails.core.vistrail.connection import Connection
+ from vistrails.core.vistrail.module import Module
+ from vistrails.core.vistrail.module_function import ModuleFunction
+ from vistrails.core.vistrail.module_param import ModuleParam
+ from vistrails.core.vistrail.pipeline import Pipeline
+ from vistrails.core.vistrail.port import Port
+ from vistrails.core.vistrail.port_spec import PortSpec
+ from vistrails.core.interpreter.noncached import Interpreter
+
+ pm = get_package_manager()
+
+ port_spec_per_module = {} # mod_id -> [portspec: PortSpec]
+ j = 0
+ for i, (mod_id, inout, name, sig) in enumerate(add_port_specs):
+ mod_specs = port_spec_per_module.setdefault(mod_id, [])
+ ps = PortSpec(id=i,
+ name=name,
+ type=inout,
+ sigstring=sig,
+ sort_key=-1)
+ for psi in ps.port_spec_items:
+ psi.id = j
+ j += 1
+ mod_specs.append(ps)
+
+ pipeline = Pipeline()
+ module_list = []
+ for i, (name, identifier, functions) in enumerate(modules):
+ function_list = []
+ try:
+ pkg = pm.get_package(identifier)
+ except MissingPackage:
+ if not enable_pkg:
+ raise
+ pkg = pm.identifier_is_available(identifier)
+ if pkg:
+ pm.late_enable_package(pkg.codepath)
+ pkg = pm.get_package(identifier)
+
+ for func_name, params in functions:
+ param_list = []
+ for param_type, param_val in params:
+ param_list.append(ModuleParam(type=param_type,
+ val=param_val))
+ function_list.append(ModuleFunction(name=func_name,
+ parameters=param_list))
+ name = name.rsplit('|', 1)
+ if len(name) == 2:
+ namespace, name = name
+ else:
+ namespace = None
+ name, = name
+ module = Module(name=name,
+ namespace=namespace,
+ package=identifier,
+ version=pkg.version,
+ id=i,
+ functions=function_list)
+ for port_spec in port_spec_per_module.get(i, []):
+ module.add_port_spec(port_spec)
+ pipeline.add_module(module)
+ module_list.append(module)
+
+ for i, (sid, sport, did, dport) in enumerate(connections):
+ s_sig = module_list[sid].get_port_spec(sport, 'output').sigstring
+ d_sig = module_list[did].get_port_spec(dport, 'input').sigstring
+ pipeline.add_connection(Connection(
+ id=i,
+ ports=[
+ Port(id=i*2,
+ type='source',
+ moduleId=sid,
+ name=sport,
+ signature=s_sig),
+ Port(id=i*2+1,
+ type='destination',
+ moduleId=did,
+ name=dport,
+ signature=d_sig),
+ ]))
+
+ interpreter = Interpreter.get()
+ result = interpreter.execute(
+ pipeline,
+ locator=XMLFileLocator('foo.xml'),
+ current_version=1,
+ view=DummyView())
+ return result.errors
+
+
+ at contextlib.contextmanager
+def intercept_result(module, output_name):
+ """This temporarily hooks a module to intercept its results.
+
+ It is used as a context manager, for instance:
+ class MyModule(Module):
+ def compute(self):
+ self.setResult('res', 42)
+ ...
+ with intercept_result(MyModule, 'res') as results:
+ self.assertFalse(execute(...))
+ self.assertEqual(results, [42])
+ """
+ actual_setResult = module.setResult
+ old_setResult = module.__dict__.get('setResult', None)
+ results = []
+ modules_index = {} # Maps a Module to an index in the list, so a module
+ # can change its result
+ def new_setResult(self, name, value):
+ if name == output_name:
+ if self in modules_index:
+ results[modules_index[self]] = value
+ else:
+ modules_index[self] = len(results)
+ results.append(value)
+ actual_setResult(self, name, value)
+ module.setResult = new_setResult
+ try:
+ yield results
+ finally:
+ if old_setResult is not None:
+ module.setResult = old_setResult
+ else:
+ del module.setResult
+
+
+def intercept_results(*args):
+ """This calls intercept_result() several times.
+
+ You can pass it multiple modules and port names and it will nest the
+ managers, for instance:
+ with intercept_results(ModOne, 'one1', 'one2', ModTwo, 'two1', 'two2') as (
+ one1, one2, two1, two2):
+ self.assertFalse(execute(...))
+ """
+ ctx = []
+ current_module = None
+ for arg in args:
+ if isinstance(arg, type) and issubclass(arg, Module):
+ current_module = arg
+ elif isinstance(arg, basestring):
+ if current_module is None:
+ raise ValueError
+ ctx.append(intercept_result(current_module, arg))
+ else:
+ raise TypeError
+ return contextlib.nested(*ctx)
diff --git a/vistrails/vistrails_server.py b/vistrails/vistrails_server.py
new file mode 100644
index 0000000..b285641
--- /dev/null
+++ b/vistrails/vistrails_server.py
@@ -0,0 +1,77 @@
+###############################################################################
+##
+## Copyright (C) 2011-2014, NYU-Poly.
+## Copyright (C) 2006-2011, University of Utah.
+## All rights reserved.
+## Contact: contact at vistrails.org
+##
+## This file is part of VisTrails.
+##
+## "Redistribution and use in source and binary forms, with or without
+## modification, are permitted provided that the following conditions are met:
+##
+## - Redistributions of source code must retain the above copyright notice,
+## this list of conditions and the following disclaimer.
+## - Redistributions in binary form must reproduce the above copyright
+## notice, this list of conditions and the following disclaimer in the
+## documentation and/or other materials provided with the distribution.
+## - Neither the name of the University of Utah nor the names of its
+## contributors may be used to endorse or promote products derived from
+## this software without specific prior written permission.
+##
+## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
+##
+###############################################################################
+"""Main file for running VisTrails in server mode"""
+import os
+import sys
+if __name__ == '__main__':
+ # Fix import path: add parent directory(so that we can
+ # import vistrails.[gui|...] and remove other paths below it (we might have
+ # been started from a subdir)
+
+ # DAK: the deletes screw things up in the binary (definitely for
+ # Mac) and since subdir is unlikely, I'm commenting them out. A
+ # better solution is probably to move run.py up a
+ # directory in the repo
+ vistrails_dir = os.path.realpath(os.path.join(os.path.dirname(__file__), '..'))
+ # i = 0
+ # print "vistrails_dir:", vistrails_dir
+ # while i < len(sys.path):
+ # rpath = os.path.realpath(sys.path[i])
+ # if rpath.startswith(vistrails_dir):
+ # print " deleting", rpath, sys.path[i]
+ # del sys.path[i]
+ # else:
+ # i += 1
+ sys.path.insert(0, vistrails_dir)
+
+ import vistrails.gui.requirements
+ vistrails.gui.requirements.require_pyqt4_api2()
+
+ import vistrails.gui.application_server
+ try:
+ v = vistrails.gui.application_server.start_server()
+ app = vistrails.gui.application_server.VistrailsServer()
+ except SystemExit, e:
+ print str(e)
+ sys.exit(e)
+ except Exception, e:
+ print "Uncaught exception on initialization: %s" % e
+ import traceback
+ traceback.print_exc()
+ sys.exit(255)
+
+ v = app.run_server()
+ vistrails.gui.application_server.stop_server()
+ sys.exit(v)
--
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